Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015010.1 Corchorus capsularis cultivar CVL-1 contig15031, 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: 29705
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1073 original size:333 final size:325
Alignment explanation
Indices: 473--1415 Score: 886
Period size: 332 Copynumber: 2.8 Consensus size: 325
463 GTTAATATAC
* * * * * * *
473 GATTTCGGCTAAAATTTTGCAAAAATTAACTCGAAAGTTTTTTTTCCTCCATTTCTAGCAAAAAT
1 GATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA--TATTTTT-CTCAATTTTTAGCCACAAT
* * *
538 ACTCAT-AAAAA-ATATAATTCAATGCCAAAAAAATTGAAA-ACCTTTTTCAGGCTTCTAATATC
63 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGA-C-TTTTCACGCTTCTAATATC
* *
600 GTTTTTTCTATTTTATTTCCAAATTAATTTATGATTAAATC--AACATTACAAA-CTCGTAAAAA
126 --ATTTTCT-TTTT-TTT-CAAATTAATTTATAATTAAATCGAAACATT-CAAAGCTCGTAAAAA
* * * *
662 CAAACCCTTAAATACAATGTGACTGAGATTTGGTTAGATAAATATAAATATACTTTAAGGAATGT
185 CAAATCCTTAAATACAATGTGACTAAGATTTGATTAGATAAATATAGATAT--TTTAAGG-ATGT
*** * * * *
727 TGGTGTCAAAAATCATGCAAAATTGACACAAG-GCCCCGGAACGCGTTTTTAGGCAAAAAAAAAA
247 TGGCCACAAAAATCATGCAAAACTGAC-C-AGTGCCCCGAAACACGTTTTTA-ACAAAAAAAAAA
791 ACCAAGA-TGGT-CAAA
309 ACCAAGATTGGTACAAA
*
806 GATTTCGGGTAAAAATTTTGCAAAAATTGACCCGAAATATTTTTCTCAATTTTTAGCCACAATAC
1 GATTTCGGCT-AAAATTTTGCAAAAATTGACCCGAAATATTTTTCTCAATTTTTAGCCACAATAC
* * * * *
871 TCTTAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCATTT
65 TCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGACTTTTCACGCTTCTAATATCATTT
* * * *
936 TCCCTTTTTTTTCAAATAAATTTTTAATTATATCGAAACGTGATTCAAACGCTCGTAACAACAAA
130 T--CTTTTTTTTCAAATTAATTTATAATTAAATCGAAAC---ATTCAAA-GCTCGTAAAAACAAA
* * * *
1001 TCCTTAAATCCAAAGTGACTAAGATTTGATTAGATAAATATAGATATTTTAAGGATTTTTGCCAC
189 TCCTTAAATACAATGTGACTAAGATTTGATTAGATAAATATAGATATTTTAAGGATGTTGGCCAC
* * *
1066 AAAAAATCATGCAAAACTGACCCGTGCCCCGAAACACGTTTTTAACAAAAAAAAAAACTATGATT
254 -AAAAATCATGCAAAACTGACCAGTGCCCCGAAACACGTTTTTAACAAAAAAAAAAACCAAGATT
*
1131 GGTACACA
318 GGTACAAA
** * * * *
1139 -ATTTCTACTAAAATTTTGTATAAATTGACCTGAAATATTTTTTCTCAATTTTTAGCCACAATAA
1 GATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATA-TTTTTCTCAATTTTTAGCCACAATAC
* * * * * *
1203 TCATAAAATATATATAATTCAACGCCAAAAAGATTGGACGACTTTTCACACTTTTAATATTATTC
65 TCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGACTTTTCACGCTTCTAATATCATT-
* * * * * *
1268 TTCATATTTTTCTGAATTAATTTCTAGA-TAAATCGAAACAAAATCCAGATGCTCGTAAAAACAA
129 TTCTTTTTTTTC-AAATTAATTTATA-ATTAAATCGAAAC---ATTCA-AAGCTCGTAAAAACAA
* * * * *
1332 ATCCTTAAATTCAATGTGTCTAATATTTGATTAGATGAATATAGATATTTCAAGGA-GTCTCGGC
188 ATCCTTAAATACAATGTGACTAAGATTTGATTAGATAAATATAGATATTTTAAGGATGT-T-GGC
*
1396 TC-CAAAAATCATGCAGAACT
251 -CACAAAAATCATGCAAAACT
1416 AAGACAGGGC
Statistics
Matches: 506, Mismatches: 79, Indels: 51
0.80 0.12 0.08
Matches are distributed among these distances:
329 18 0.04
330 7 0.01
331 78 0.15
332 247 0.49
333 74 0.15
334 28 0.06
335 54 0.11
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33
Consensus pattern (325 bp):
GATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCTCAATTTTTAGCCACAATACT
CATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGACTTTTCACGCTTCTAATATCATTTT
CTTTTTTTTCAAATTAATTTATAATTAAATCGAAACATTCAAAGCTCGTAAAAACAAATCCTTAA
ATACAATGTGACTAAGATTTGATTAGATAAATATAGATATTTTAAGGATGTTGGCCACAAAAATC
ATGCAAAACTGACCAGTGCCCCGAAACACGTTTTTAACAAAAAAAAAAACCAAGATTGGTACAAA
Found at i:5083 original size:2 final size:2
Alignment explanation
Indices: 5076--5100 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5066 TACTCATGAA
5076 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5101 AAATTTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29214 original size:28 final size:28
Alignment explanation
Indices: 29152--29222 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
29142 CCTGAGAGGC
*
29152 CAAAACGTCCCAAAATTGAAGTTCAAGGTG
1 CAAAACGT-CC-AAATTGAAGTTCAAGGGG
* *
29182 TAAAATGTCCAAATTGAAGTTC-AGTGGG
1 CAAAACGTCCAAATTGAAGTTCAAG-GGG
29210 CAAAACGTCCAAA
1 CAAAACGTCCAAA
29223 CGCTACAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.06
28 25 0.71
29 2 0.06
30 6 0.17
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (28 bp):
CAAAACGTCCAAATTGAAGTTCAAGGGG
Done.