Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011061.1 Corchorus olitorius cultivar O-4 contig11094, 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, 633
Length: 1055
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:757 original size:331 final size:326
Alignment explanation
Indices: 1--1051 Score: 1284
Period size: 329 Copynumber: 3.2 Consensus size: 326
* *
1 AGATAAATATATATGTTTCGAGGATTTTGGGAGACC-AAAATCAAGCAAAACTGAGC-TAGGGCC
1 AGATAAATATATATGTTTC-AGGAGTTTGGGCG-CCAAAAATCAAGCAAAACTGAGCAT-GGGCC
* * *
64 CCGGAACGCGTTTTTAGCTAAAAACC--------GT-CACGATTTTGGCTAAAATTTTGCAAAAA
63 CCGGAACGCATTTTTAGCTAAAAACCGTGATGGAGTACATGATTTCGGCTAAAATTTTGCAAAAA
* *
120 ATGACCCGAAAATTTTTCCTC-AATATTTGACCCCAATTCTC--AAAAATATATATAATTCAACG
128 ATCACCCGAAAATTTTTCCTCAAAT-TTTGACCACAATTCTCATAAAAATATATATAATTCAACG
*
182 TCAAAAAGATTGAAGGGCTTTTTTCGAGC-TGCTAATATCGTTTTTCCATTTTTTCCTGAATTAA
192 CCAAAAAGATTGAAGGGC--TTTTCGAGCAT-CTAATATCGTTTTTCCATTTTTTCCTGAATTAA
* * * *
246 TTTCTAATTAAAACGAACCAAGATTCAAATACTCGTGAAAACAAATCCTTAAGTCCAACATGGCT
254 TTTCTAATTAAAACGAAACAAGATTCAAATGCT--TGAAAAAAAATCC-TAAGTCCAACGTGGCT
*
311 GAGATTTTGTT
316 GAGATTTGGTT
* * *
322 AGATAAATATATATGTTTCAAGGATTTTGGGCGCCAATAATCAAGCAAAACTGAGCTTGGGCCCC
1 AGATAAATATATATGTTTC-AGGAGTTTGGGCGCCAAAAATCAAGCAAAACTGAGCATGGGCCCC
*
387 GGAACGCATTTTTAGCTAAAAACCGTGATGGAGTACATGATTTCGGCTAAAAGTTTGCAAAAAAT
65 GGAACGCATTTTTAGCTAAAAACCGTGATGGAGTACATGATTTCGGCTAAAATTTTGCAAAAAAT
* * * *
452 TACCCGAAAATTTTTTCCTCAAATTTTGACAAAAATTCTCATAAAAATATATATAATTCAACACC
130 CACCCGAAAA-TTTTTCCTCAAATTTTGACCACAATTCTCATAAAAATATATATAATTCAACGCC
* **
517 ATAAAA-ATTGAAGGGCTTTTCGAGCATCTAAAATTATTTTTTCCA-TTTTTCCTGAATTAATTT
194 A-AAAAGATTGAAGGGCTTTTCGAGCATCTAATA-TCGTTTTTCCATTTTTTCCTGAATTAATTT
* * *
580 CTAATTAAAACGAAACAAGATTCAAATGCTTGAAAAGAAAATCCTAAATACAACGTGACTGAGAT
257 CTAATTAAAACGAAACAAGATTCAAATGCTTGAAAA-AAAATCCTAAGTCCAACGTGGCTGAGAT
645 TTGGTT
321 TTGGTT
* * * *
651 AAATGAATATATATGTTTCGAGGAGTTTGGGCACCAAAAATCAAGCAAAACTGAG-ATGGAGTCC
1 AGATAAATATATATGTTTC-AGGAGTTTGGGCGCCAAAAATCAAGCAAAACTGAGCATGG-GCCC
* * * *
715 CGGAACGCGTTTTTAGAC-AAAATCTGTGATGGTTATTACATGATTTCGGCTAAAATTTTGCAAA
64 CGGAACGCATTTTTAG-CTAAAAACCGTGATGG--AGTACATGATTTCGGCTAAAATTTTGCAAA
* * *
779 AAAACATCCGAAAAATTTTTCCTCAATTTTTGACCACAATTCTCAT--AAATATATATAATTCAA
126 AAATCACCCG-AAAATTTTTCCTCAAATTTTGACCACAATTCTCATAAAAATATATATAATTCAA
* * * **
842 CGCCAAAAAGATAGAAGGGCTTTTCGAGAATCTAATATCGTTTTCCCATTTTTTCCACAATTAAT
190 CGCCAAAAAGATTGAAGGGCTTTTCGAGCATCTAATATCGTTTTTCCATTTTTTCCTGAATTAAT
*
907 TTCTAATTAAAACG-AACAAGATTCAAATGCTCGTAAAAACAAATCACTAAGTCCAACGTGGCTG
255 TTCTAATTAAAACGAAACAAGATTCAAATGCTTG-AAAAA-AAATC-CTAAGTCCAACGTGGCTG
971 AGATTTGGTT
317 AGATTTGGTT
* * *
981 AGATTAATATATACGTTTCATGGAGTTTGGGCGCCAAAAATCAAGCAAAACTGAGC-TGGGGCCC
1 AGATAAATATATATGTTTCA-GGAGTTTGGGCGCCAAAAATCAAGCAAAACTGAGCATGGGCCCC
*
1045 GTAACGC
65 GGAACGC
1052 CGTG
Statistics
Matches: 637, Mismatches: 62, Indels: 54
0.85 0.08 0.07
Matches are distributed among these distances:
320 2 0.00
321 80 0.13
322 1 0.00
328 34 0.05
329 202 0.32
330 120 0.19
331 145 0.23
332 17 0.03
333 32 0.05
334 4 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (326 bp):
AGATAAATATATATGTTTCAGGAGTTTGGGCGCCAAAAATCAAGCAAAACTGAGCATGGGCCCCG
GAACGCATTTTTAGCTAAAAACCGTGATGGAGTACATGATTTCGGCTAAAATTTTGCAAAAAATC
ACCCGAAAATTTTTCCTCAAATTTTGACCACAATTCTCATAAAAATATATATAATTCAACGCCAA
AAAGATTGAAGGGCTTTTCGAGCATCTAATATCGTTTTTCCATTTTTTCCTGAATTAATTTCTAA
TTAAAACGAAACAAGATTCAAATGCTTGAAAAAAAATCCTAAGTCCAACGTGGCTGAGATTTGGT
T
Done.