Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019308.1 Corchorus olitorius cultivar O-4 contig19341, 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: 6034
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:1890 original size:96 final size:96
Alignment explanation
Indices: 1725--1919 Score: 340
Period size: 96 Copynumber: 2.0 Consensus size: 96
1715 CGGGAAATTA
1725 ATGATGCGCCAAGGACTCATCATTGGCTTGAAGAGCACAATGGAGATCATGGCAAGGATGTGCAC
1 ATGATGCGCCAAGGACTCATCATTGGCTTGAAGAGCACAATGGAGATCATGGCAAGGATGTGCAC
1790 ATGCGGCAAGGAGGCTTGGAGAAGCTTGAAG
66 ATGCGGCAAGGAGGCTTGGAGAAGCTTGAAG
*
1821 ATGATGCGCCAAGGACTCATCA-TGGTCTTGAAGGGCACAATGGAGATCATGG-AGAGGATGTGC
1 ATGATGCGCCAAGGACTCATCATTGG-CTTGAAGAGCACAATGGAGATCATGGCA-AGGATGTGC
*
1884 ATATGCGGCAAGGAGGCTTGGAGAAGCTTGAAG
64 ACATGCGGCAAGGAGGCTTGGAGAAGCTTGAAG
1917 ATG
1 ATG
1920 CTAAGGAAGA
Statistics
Matches: 95, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
95 4 0.04
96 91 0.96
ACGTcount: A:0.30, C:0.16, G:0.34, T:0.19
Consensus pattern (96 bp):
ATGATGCGCCAAGGACTCATCATTGGCTTGAAGAGCACAATGGAGATCATGGCAAGGATGTGCAC
ATGCGGCAAGGAGGCTTGGAGAAGCTTGAAG
Found at i:2911 original size:15 final size:15
Alignment explanation
Indices: 2891--2926 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
2881 TTTCCTTTTC
2891 CTAGTTGGGTTTGGG
1 CTAGTTGGGTTTGGG
2906 CTAGTTGGGTTTGGG
1 CTAGTTGGGTTTGGG
2921 CTAGTT
1 CTAGTT
2927 TTACCCTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.08, G:0.42, T:0.42
Consensus pattern (15 bp):
CTAGTTGGGTTTGGG
Found at i:3322 original size:599 final size:584
Alignment explanation
Indices: 2165--3348 Score: 1810
Period size: 599 Copynumber: 2.0 Consensus size: 584
2155 CGATGAGCAT
*
2165 TAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTTTAATTAGCTTATTTTTA
1 TAGGTAATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTTTAATTAGCTTATTTTTA
2230 AGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGTCTTT
66 AGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGTCTTT
2295 ATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGGCCATATATTTGGACGAAAATTAG
131 ATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGGCCATATATTTGGACGAAAATTAG
2360 GTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCACCAAACCCCTCTTGTAAA
196 GTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCACCAAACCCCTCTTGTAAA
2425 CATAAGTTGAGTTGATTAATAAAATTGAGGTTTTACACCCAAATTGATTATCTTAGCTTCTTTGT
261 CATAAGTTGAGTTGATTAATAAAATTGAGGTTTTACACCCAAATTGATTATCTTAGCTTCTTTGT
* *
2490 TCTAGTTTGAGCAAAACTTAGGGTTCTTCTATCTTGTAGAGTCCTAGCAAACAATTAAGTTGTGT
326 TCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGTGA
* * * * **
2555 TGCTTGTTTGTTTGTGAATCTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTTGG
391 TACTTGATTGCTTGTGAATCTTGTGATCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTAAG
* * *
2620 GCCGACGAAAGAAGAGGATTCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAG
456 GCCGACGAAAGAAGAAGATT-ACCTTGTGAAGATCATCGACATACACATCTAGAAGTTGAAGAAG
*
2685 TTCAAGTCGACTTTGATAGATATTCAAGGCTAGATTTGAATC-TAACACAACTAGATTCGTATCA
520 TTCAAGTCGACTTTGACAGATA-TCAAGGCTAGATTTGAATCTTAACACAACTAGATTCGTATCA
2749 C
584 C
2750 TAGGTAATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTTTAATTAGCTTATTTTTA
1 TAGGTAATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTTTAATTAGCTTATTTTTA
*
2815 AGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGATTAAGTCCAATCCTTGTTTAATTATGTCTTT
66 AGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGTCTTT
2880 ATTTCCTTTTCCTAGTTGGGTTTGGGCTAGTTGGGTTTGGGCTAGTTTTACCCTAGGCCATATAT
131 ATTTCCTTTTCCTAGTTGGGTTT-GG--A------------CTAGTTTTACCCTAGGCCATATAT
2945 TTGGACGAAAATTAGGTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCACCA
181 TTGGACGAAAATTAGGTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCACCA
*
3010 AACCCCTCTTGTAAACATAAGTTGAGTTGATTAATAAAATTGAGGTTTT-TACCCAAATTGATTA
246 AACCCCTCTTGTAAACATAAGTTGAGTTGATTAATAAAATTGAGGTTTTACACCCAAATTGATTA
3074 TCTTAGCTTCTTTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAA
311 TCTTAGCTTCTTTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAA
*
3139 ACAATTAAGTTGTGATACTTGATTGCTTGTGAATCTTGTGATCTTAG-GTGT-TCAATTGCAGGT
376 ACAATTAAGTTGTGATACTTGATTGCTTGTGAATCTTGTGATC-TAGAGT-TAACAATTGCAGGT
** * **
3202 CTAATTGG-GGGTCTAAGGCCGACGAAAGAAGAAGATT-GCTTGGGTG-AGATTGTCGACATACA
439 CTAATTGGAGACT-TAAGGCCGACGAAAGAAGAAGATTACCTT--GTGAAGATCATCGACATACA
** * * * * *
3264 CATCTAGAAGTTGAAAGTTGTTCAAGTTGATTCTTGGCAGGTCA-CAATGG-TGGATTTGAATCT
501 CATCTAGAAGTTG-AAGAAGTTCAAGTCGACT-TTGACAGAT-ATCAA-GGCTAGATTTGAATCT
*
3327 TAATACAACTAGATTCGTATCA
562 TAACACAACTAGATTCGTATCA
3349 ATTAAGATCA
Statistics
Matches: 545, Mismatches: 29, Indels: 35
0.89 0.05 0.06
Matches are distributed among these distances:
585 151 0.28
586 2 0.00
588 1 0.00
597 3 0.01
598 28 0.05
599 188 0.34
600 171 0.31
601 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (584 bp):
TAGGTAATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTTTAATTAGCTTATTTTTA
AGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGTCTTT
ATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGGCCATATATTTGGACGAAAATTAG
GTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCACCAAACCCCTCTTGTAAA
CATAAGTTGAGTTGATTAATAAAATTGAGGTTTTACACCCAAATTGATTATCTTAGCTTCTTTGT
TCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGTGA
TACTTGATTGCTTGTGAATCTTGTGATCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTAAG
GCCGACGAAAGAAGAAGATTACCTTGTGAAGATCATCGACATACACATCTAGAAGTTGAAGAAGT
TCAAGTCGACTTTGACAGATATCAAGGCTAGATTTGAATCTTAACACAACTAGATTCGTATCAC
Done.