Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009557.1 Corchorus olitorius cultivar O-4 contig09589, 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: 6009
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Found at i:2382 original size:22 final size:24
Alignment explanation
Indices: 2346--2392 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
2336 CTTTTCAGTC
*
2346 ATTTAACTTTATTTTTTTAAAATG
1 ATTTAACTTTATTTTATTAAAATG
*
2370 ATTTAAC-TT-TTTTATTAATATG
1 ATTTAACTTTATTTTATTAAAATG
2392 A
1 A
2393 AAAAGATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 2 0.10
24 7 0.33
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTTAACTTTATTTTATTAAAATG
Found at i:3833 original size:53 final size:53
Alignment explanation
Indices: 3775--3881 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
3765 AGCCCTTCAA
3775 TCTTTTTGGCGTTGAATTATACTATATTTTTTATGAGTATTGTGGCTAAAAAT
1 TCTTTTTGGCGTTGAATTATACTATATTTTTTATGAGTATTGTGGCTAAAAAT
*
3828 TCTTTTTGGCGTTGAATTATATTATATTTTTTATGAGTATTGTGGCTAAAAAT
1 TCTTTTTGGCGTTGAATTATACTATATTTTTTATGAGTATTGTGGCTAAAAAT
3881 T
1 T
3882 GAGAAAAAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (53 bp):
TCTTTTTGGCGTTGAATTATACTATATTTTTTATGAGTATTGTGGCTAAAAAT
Found at i:5541 original size:325 final size:321
Alignment explanation
Indices: 4598--6009 Score: 1199
Period size: 313 Copynumber: 4.4 Consensus size: 321
4588 CGAAATCGTG
* * * *
4598 TTGTTTTGATTTAATTAGAAATTAATTCAGATAAAAAAT-GAAAAAATGATATTAGACGCATGAA
1 TTGTTTTGATTTAATTAGAAATAAATTC-GAGAAAAAATGGAAAAAATGATATTAGAAGCGTG-A
* * * * *
4662 AAAACCCTTCAATCTTTTTAGCATTGAATTATATAT-TTTTTCTAAGTGTTGCGGCAAAAAATTG
64 AAAACTCTTCAATCTTTTTGGCATTGAATTATATATATTTTTTTAA-TATTGTGGCAAAAAATT-
* * * *
4726 AGAAAAAAAATTTCCGTGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCATCGTTTTTGGCTA
127 AGAGAAAAAATTTTCGTGTCAGTTTTTA-CCGAAATCATGTACTAACCATCATGGTTTTTGGCTA
* * * * * * *
4791 AAAACGCATTTCGGGATCTCGACTCACTTTTGCATGGTTTTTGGCATATAGACTCCTTGAAATAT
191 AAAACGCGTTTCGGG-TCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATAT
* * * *
4856 CTATATTCATGTACCCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAA
255 CTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
4921 TC
320 TC
* * * *
4923 TTGTTTTGATGTAATTAAAAATAAATTCGAAAAAAAATGG-AAAAACGATATTAGAAGCGTGAAA
1 TTGTTTTGATTTAATTAGAAATAAATTCGAGAAAAAATGGAAAAAATGATATTAGAAGCGTGAAA
* *
4987 AACTCTTCAATTTTTTTGGCATTGAATTATATATATTTTTATTGAGTATTGTGGCAAAAAATT-G
66 AACTCTTCAATCTTTTTGGCATTGAATTATATATATTTTT-TT-AATATTGTGGCAAAAAATTAG
* * * * *
5051 AGGAAAAACTTTTCGTGTCAGTTTTT-GC-AAA--AT-T--T---CGT-GTCGATTTTTGGCTAA
129 A-GAAAAAATTTTCGTGTCAGTTTTTACCGAAATCATGTACTAACCATCAT-GGTTTTTGGCTAA
* * * *
5105 AAACGCGTTCCGGAATCCCGGCTCAATTTTGCATGATTTTTGGC-GCAAAGTCTCCATGAAATAT
192 AAACGCGTTTCGG-GTCCCGGCTCAATTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATAT
* * * * * *
5169 CTATATTCATCGAACCAAATTTCAACCGCATTGGATATAAAGATTTGTTTTTATGAGCATCTGAA
255 CTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
5234 TC
320 TC
* * * *
5236 TTGTTTTGATTTAGTTAGAAATTAATTCG-GGAAAAATGGAAAAAATGATATTAGAAACGTGAAA
1 TTGTTTTGATTTAATTAGAAATAAATTCGAGAAAAAATGGAAAAAATGATATTAGAAGCGTGAAA
** * **
5300 AACTCGACAATCTTTTTGGCGTTGAATTATATATATTTTTTTAATATTGTGGTGAAAAATTCAGA
66 AACTCTTCAATCTTTTTGGCATTGAATTATATATATTTTTTTAATATTGTGGCAAAAAATT-AGA
** *
5365 TGAAAATTTTTTCG-GATAAGTTTTTAACCGAAATCATGTACTAACCATCATGGTTTTTGGGCTA
130 -GAAAAAATTTTCGTG-TCAGTTTTT-ACCGAAATCATGTACTAACCATCATGGTTTTT-GGCTA
* * *
5429 AAAACGCGTTTCGTGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGAGTCCTTGAAATAT
191 AAAACGCGTTTCG-GGTCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATAT
* * *
5494 CTATATTCATCTAACCAAATCTCACCCACATTGGATTTAAGGATTTGTTTTTACAAGCACCTGAA
255 CTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
5559 TC
320 TC
* * * * * * *
5561 TTGTTTCGATTTAATTGGAAACAAATTCAGGAAAAAAAATTG-AAAAACGATATTGGAAGCGTG-
1 TTGTTTTGATTTAATTAGAAATAAATTC--GAGAAAAAATGGAAAAAATGATATTAGAAGCGTGA
* * * * * *
5624 AAAACTCTTCAATTTTTTTTG-TTTAAATTATATAT-TTTTTCTGAGTA-T-TGG-AAAAGAATT
64 AAAACTCTTCAATCTTTTTGGCATTGAATTATATATATTTTT-TTAATATTGTGGCAAAA-AATT
* * * * **
5684 -GAGGAAAAATTTTTCGGGTCAATTTTTACAAAATTTAGCTGAAATCGTGTACTAACCATCACAG
127 AGA-GAAAAAATTTTCGTGTCAGTTTTTAC---------C-GAAATCATGTACTAACCATCATGG
* * * * * *
5748 TTTTTTGCTAAAAATGTG-TTCTGGAGCCCCAGG-TCAGTTTTGCAT-ATTTTTGG-TGTAAAGA
181 TTTTTGGCTAAAAACGCGTTTC-GG-GTCCC-GGCTCAATTTTGCATGATTTTTGGCAG-AAAGA
* ** * ** * * *
5809 TTTTTTAAAATATCTATATTCAT-TGAACCAAATCTCAGTCATATTGAATTTAAGGATTTGCTTT
242 CTCCTTGAAATATCTATATTCATCT-AACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTT
*
5873 TACGAGCATCTTAA--
306 TACGAGCATCTGAATC
* * * ** *
5887 TTGTTTCGATTTAATTAGAAATTAATT-TAGAAAAAAGTAAAAAAAAAATGATATTAGAAGCATG
1 TTGTTTTGATTTAATTAGAAATAAATTCGAGAAAAAA-T--GGAAAAAATGATATTAGAAGCGTG
* * * * *
5951 AAAAGC-CTGTCAATCTTTTTGGCGTT-AAAT-TATAT-TTTTTTTAGTATTATGGCAAAAAA
63 AAAAACTCT-TCAATCTTTTTGGCATTGAATTATATATATTTTTTTAATATTGTGGCAAAAAA
Statistics
Matches: 887, Mismatches: 142, Indels: 113
0.78 0.12 0.10
Matches are distributed among these distances:
311 16 0.02
312 12 0.01
313 225 0.25
315 1 0.00
316 4 0.00
318 3 0.00
319 2 0.00
320 2 0.00
321 25 0.03
322 5 0.01
323 50 0.06
324 68 0.08
325 199 0.22
326 49 0.06
327 52 0.06
328 111 0.13
329 35 0.04
330 28 0.03
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (321 bp):
TTGTTTTGATTTAATTAGAAATAAATTCGAGAAAAAATGGAAAAAATGATATTAGAAGCGTGAAA
AACTCTTCAATCTTTTTGGCATTGAATTATATATATTTTTTTAATATTGTGGCAAAAAATTAGAG
AAAAAATTTTCGTGTCAGTTTTTACCGAAATCATGTACTAACCATCATGGTTTTTGGCTAAAAAC
GCGTTTCGGGTCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATAT
TCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
Done.