Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001064.1 Corchorus capsularis cultivar CVL-1 contig01064, 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: 11856
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Found at i:345 original size:13 final size:12
Alignment explanation
Indices: 319--353 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
309 ATGGGTCCAA
319 GAAAAAAAAA-G
1 GAAAAAAAAATG
330 GAAAAACAAAATG
1 GAAAAA-AAAATG
343 GAAAAAAAAAT
1 GAAAAAAAAAT
354 TTGCTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 9 0.41
13 7 0.32
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.06
Consensus pattern (12 bp):
GAAAAAAAAATG
Found at i:3117 original size:322 final size:321
Alignment explanation
Indices: 2157--3117 Score: 1258
Period size: 324 Copynumber: 3.0 Consensus size: 321
2147 TTCAGTAGTG
* * * * *
2157 CTATATCAATACATACAAATTTCCAGTTCCATCTATTCATACATTTAATCTCTAAATT-TCTACA
1 CTATATCTATACATACAAATCTCCAGTCCCATCCATTCATACATTTAATCTCTAAATTCT-TAAA
* * *
2221 CGTACATACATATTTCTGTGTGC-GCGCAATAAATAAAGAACTAAAAAGTGGTAGATGAAAGAAG
65 CGTACATACA-ATATCTATGTGCAGCGCAATAAATAAAGAACTAAAAAGTGGTGGATGAAAGAAG
* * * *
2285 GTAAATAAAAAAACTTTTAATCAC-ACTAACTTATTTATCATACAAATTTGTCATAGTTCAACAA
129 GTAAATAATAAAACTTTTAATC-CTACTCATTTATTTATCATACAAATTTGTCACAGTTCAACAA
* ** **
2349 GAAATTAAGGAAGTTAGCATACAATGAACTTAAACTTTAATATTATTGTATATTTGGTGTCTTTA
193 GAAATTAAGCAAGGCATAATACAATGAACTTAAACTTTAATATTATTGTATATTTGGTGTCTTTA
* * * *
2414 CCAAAAAGAGATAATGCAGACAATATACTAAGGAAAAGATATCAAATTTTC-CTTTTTTTCGTGT
258 CCAAAAA-AGATAATCCAGACAATATACTAAGGAAAATATATCAAATTTCCTCTTTTTTTCATGT
* *
2478 CTATATCTATACATACAAATCTCCAGTCCCATCCATTCATACATTTTTTATCTCTAAATTCCTAA
1 CTATATCTATACATACAAATCTCCAGTCCCATCCATTCATACA--TTTAATCTCTAAATTCTTAA
* * * *
2543 ACATACATACAATATCTATGTGCAAGCGCAATAAATAAAGAACTAAAAACTGGAGGAGGAAAGAA
64 ACGTACATACAATATCTATGTGC-AGCGCAATAAATAAAGAACTAAAAAGTGGTGGATGAAAGAA
* *
2608 GGTAAACAATAAAACTTTTAATCCTACTCATTTATTTATCATACAAATCTGTCACAGTTCAACAA
128 GGTAAATAATAAAACTTTTAATCCTACTCATTTATTTATCATACAAATTTGTCACAGTTCAACAA
***
2673 GAAATTAAGCAA-GC-TAGCATACAATGAACTTAAACTTTAATATTATTGTATATTTGGTGTGAA
193 GAAATTAAGCAAGGCATA--ATACAATGAACTTAAACTTTAATATTATTGTATATTTGGTGTCTT
* ** *
2736 AAGGAAAAAAAGATAATCCAGACAATATACTAAGGAAAATATATTAAATTTCC-CTTTTTTTCAT
256 TA-CCAAAAAAGATAATCCAGACAATATACTAAGGAAAATATATCAAATTTCCTCTTTTTTTCAT
2800 GT
320 GT
* * * * *
2802 CTATATCTGTACAAACAAATCTCGAGTCCCATCCATTCATACATTTGATTTCTAAATTCTTAAAC
1 CTATATCTATACATACAAATCTCCAGTCCCATCCATTCATACATTTAATCTCTAAATTCTTAAAC
* * *
2867 GTGCATACAATATCTATGTACATGCGCAATAAATAAAGAACTAAAAAGTGGTGGTTGAAAGAAGG
66 GTACATACAATATCTATGTGCA-GCGCAATAAATAAAGAACTAAAAAGTGGTGGATGAAAGAAGG
* *
2932 TAAATAATAAAACGTTTAATCCTACTCATTTATTTATCATACAAGATTTGTTACAGTTCAACAAG
130 TAAATAATAAAACTTTTAATCCTACTCATTTATTTATCATACAA-ATTTGTCACAGTTCAACAAG
* * *
2997 AAATTAAGCAAGGCATAATACAAATGAACTTAAACTTTAGTATCATTGTATACTTGGTGTCTTTA
194 AAATTAAGCAAGGCATAATAC-AATGAACTTAAACTTTAATATTATTGTATATTTGGTGTCTTTA
* **
3062 CCAAAAAA-A-AAT-TAGACAATATACTTTGGAAAATATATCAAATTTCCTTCTTTTTT
258 CCAAAAAAGATAATCCAGACAATATACTAAGGAAAATATATCAAATTTCC-TCTTTTTT
3118 AATCAACTTT
Statistics
Matches: 558, Mismatches: 66, Indels: 31
0.85 0.10 0.05
Matches are distributed among these distances:
320 31 0.06
321 43 0.08
322 135 0.24
323 66 0.12
324 276 0.49
325 7 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (321 bp):
CTATATCTATACATACAAATCTCCAGTCCCATCCATTCATACATTTAATCTCTAAATTCTTAAAC
GTACATACAATATCTATGTGCAGCGCAATAAATAAAGAACTAAAAAGTGGTGGATGAAAGAAGGT
AAATAATAAAACTTTTAATCCTACTCATTTATTTATCATACAAATTTGTCACAGTTCAACAAGAA
ATTAAGCAAGGCATAATACAATGAACTTAAACTTTAATATTATTGTATATTTGGTGTCTTTACCA
AAAAAGATAATCCAGACAATATACTAAGGAAAATATATCAAATTTCCTCTTTTTTTCATGT
Found at i:4826 original size:311 final size:306
Alignment explanation
Indices: 4138--5065 Score: 1011
Period size: 311 Copynumber: 3.0 Consensus size: 306
4128 TGTATATGTG
** * * *
4138 GGTGTCTTTACCAAAAAAAAAAAGCAGACAGTATACTTGGGAAAATATATCAAATTTCCTTCTTT
1 GGTGTCTTTACC---AAAAAAAATTAGACAATATACTTAGGAAAATATATCAAATTTCCTTTTTT
*
4203 TTCATGTCTATATCTATACATACAAATCTCCAATTCCATCCATTCATACATTTGATCTCTAAATT
63 TTCATGTCTATATCTGTACATACAAATCTCCAATTCCATCCATTCATACATTTGATCTCTAAATT
* * * * *
4268 CCTACATGTACATATATATTCCTGTGCGCGGACAATAAATAAAGAACT----A--A-AAAGTA-G
128 CCTACACGTACATACATATT-ATGTGCGCGCACAATAAATAAAGAACTAAAAAGGAGAAAGAAGG
*
4325 TAAACAATAAAACTTTTAATCCTACTCATTTATTTATCATACAAATCTGTCATAGTTCAACAAGA
192 TAAACAATAAAACTTTTAATCCTACTCATTTATTTATCATACAAATCTGTCACAGTTCAACAAGA
* * *
4390 AATTAAGCAAGCTAACATACAATGAACTTAAACTTTAATATTATTATATATTT
257 AATTAAGCAAG---GCATACAATGAACTTAAACTTTAATATCATTATATACTT
*
4443 GGTGTCTTTACCAAAAACAAAAAGATAATTCAGACAATATACTAAGGAAAATATATCAAATTTCC
1 GGTGTCTTTA-C-----CAAAAA-A-AATT-AGACAATATACTTAGGAAAATATATCAAATTTCC
* * * * *
4508 CTTTTTTTCTTGTCTATATCTGTACATACAAATCTCCAGTCCCATCCATTCATACATTTAATCTC
57 TTTTTTTTCATGTCTATATCTGTACATACAAATCTCCAATTCCATCCATTCATACATTTGATCTC
* *
4573 TAAATTCCTACACGTACATACAATATCTATGTACACGCACAATAAATAAAGAACTAAAAACGGAG
122 TAAATTCCTACACGTACATAC-ATAT-TATGTGCGCGCACAATAAATAAAGAACTAAAAA-GGA-
* * * * * * *
4638 GAAAGAAGGTAAATAATAAAACTTGTAGTCATACTCAATTATTTATCATACAAATTTGTTACAGT
183 GAAAGAAGGTAAACAATAAAACTTTTAATCCTACTCATTTATTTATCATACAAATCTGTCACAGT
* * *
4703 TCAACAAGAATTTAAGCAAGGCATA-AGATGAACTTAAACTTTAGTATCATTGTATACTT
248 TCAACAAGAAATTAAGCAAGGCATACA-ATGAACTTAAACTTTAATATCATTATATACTT
*
4762 GGTGTCTTTACCAAAAAAAATTAGACAATATACTTTGGAAAATATATCAAATTTCCTTTTTTTTT
1 GGTGTCTTTACCAAAAAAAATTAGACAATATACTTAGGAAAATATATCAAATTTCC---TTTTTT
* * * * *
4827 TTCATGTCTATAACTG----TACAAATCTCCATTTCCATCCGTTTATACATTTGATTTCTAAATT
63 TTCATGTCTATATCTGTACATACAAATCTCCAATTCCATCCATTCATACATTTGATCTCTAAATT
* * *
4888 CTTAAATGTACGTACATACATATTTGTGTGCGCGCACAATAAATAAAGAACTAAAAAGTGGGGGA
128 CCT--A--CACGTACATACATA-TTATGTGCGCGCACAATAAATAAAGAACTAAAAA-----GGA
*
4953 TGAAAGAAGGTAAACAATAAAACTTTTAATCCTACTCATTTATTTATCATACAAATCTGTCCCAA
183 -GAAAGAAGGTAAACAATAAAACTTTTAATCCTACTCATTTATTTATCATACAAATCTGTCAC-A
*
5018 G-TCAACAAGAAATTAAGCAAACTAGCATACAATGAACTTAAACTTTAA
246 GTTCAACAAGAAATTAAGC-AA--GGCATACAATGAACTTAAACTTTAA
5066 ACACATAAAT
Statistics
Matches: 522, Mismatches: 62, Indels: 64
0.81 0.10 0.10
Matches are distributed among these distances:
305 10 0.02
306 1 0.00
308 5 0.01
309 42 0.08
310 34 0.07
311 114 0.22
312 61 0.12
313 37 0.07
316 74 0.14
317 4 0.01
318 2 0.00
319 64 0.12
320 1 0.00
321 5 0.01
322 68 0.13
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (306 bp):
GGTGTCTTTACCAAAAAAAATTAGACAATATACTTAGGAAAATATATCAAATTTCCTTTTTTTTC
ATGTCTATATCTGTACATACAAATCTCCAATTCCATCCATTCATACATTTGATCTCTAAATTCCT
ACACGTACATACATATTATGTGCGCGCACAATAAATAAAGAACTAAAAAGGAGAAAGAAGGTAAA
CAATAAAACTTTTAATCCTACTCATTTATTTATCATACAAATCTGTCACAGTTCAACAAGAAATT
AAGCAAGGCATACAATGAACTTAAACTTTAATATCATTATATACTT
Done.