Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022467.1 Corchorus olitorius cultivar O-4 contig22500, 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: 6461
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:678 original size:13 final size:13
Alignment explanation
Indices: 660--685 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
650 TGCCTTTATT
660 ATTAGTATAGATA
1 ATTAGTATAGATA
673 ATTAGTATAGATA
1 ATTAGTATAGATA
686 GTAGTGCAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
ATTAGTATAGATA
Found at i:768 original size:4 final size:4
Alignment explanation
Indices: 761--791 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
751 TGTGTGTGTG
761 AAGA AAGA AAGA AAGAA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAG-A AAGA AAGA AAGA AA
792 AGAATAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:782 original size:13 final size:13
Alignment explanation
Indices: 764--795 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
754 GTGTGTGAAG
764 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
777 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
790 AAAGAA
1 AAAGAA
796 TAGTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:3420 original size:332 final size:327
Alignment explanation
Indices: 2776--3767 Score: 1161
Period size: 332 Copynumber: 3.0 Consensus size: 327
2766 GTGTACTAAC
* ** *
2776 TAACCATCACGATTTTTTGGCTAAAAACACGTTCCGGGGACCCAGCTCAATTTTGCATGATTTTT
1 TAACCATCAC-AGTTTTTGGCTAAAAACGTGTTCC-GGGACCCAGCTCAATTTTGCATGACTTTT
* *
2841 GGC-TCAGAGACTAATGGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAG
64 GGCGCCA-AGACTAATTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAG
*
2905 GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGGTTTAATTAAAAATTAATTCAGAAAAAAATA
128 GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTC--AAAAAAATA
* * *
2970 TGAAAAATGATATTAGAAGCGTGAAAAGCCCTTCAAT-ATGTTTGGCGTTGAATTATATATTTTT
191 TGAAAAATGATATTAAAAGCGTGAAAAACCCTTCAATCTTG-TTGGCGTTGAATTATATA-TTTT
* ** * * *
3034 TATGAGCATTGTGGCCAAATATTGAGGAAATATCTTTTGGGTCAATTTTTACAAAATTTTAGCCG
254 TATGAGTATTGTTACAAAAT-TTGAGAAAATATC-TTTGGGTCAATTTTTACAAAATTTTAGCCA
3099 AAATCGTGTAA
317 AAATCGTGTAA
* * * *
3110 TAACCATCACAGTTTTTGGCTAAAAAGGTGTTCCGCGGTCCCGGTTCAATTTTGCATGA-TTTTG
1 TAACCATCACAGTTTTTGGCTAAAAACGTGTTCCG-GGACCCAGCTCAATTTTGCATGACTTTTG
* * * * * *
3174 GCGCCAAGACTAATTGAGATATCCATATTCATCTATTCAAATCTCAGTCACATTGGATTTAAGAA
65 GCGCCAAGACTAATTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGA
* * * * *
3239 TTTTTTTTTAAGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTAAAAAAATATGAA
130 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAAAAAAATATGAA
** * ** * *
3304 AAACAATATTAAAATTAGCGTGAAAAATCCACCAATCTTGTTGTCGTTAAATTATATATATTTTA
195 AAATGATATT-AAA--AGCGTGAAAAACCCTTCAATCTTGTTGGCGTTGAATTATATAT-TTTTA
* * *
3369 TGAGTATTTTATACAAAATTTGAGAAAAAAT-TTTCGGGTC-ATTTCTTACAAAATTTTAGCAAA
256 TGAGTATTGT-TACAAAATTTGAGAAAATATCTTT-GGGTCAATTT-TTACAAAATTTTAGCCAA
* *
3432 AATCATGTAC
318 AATCGTGTAA
** * * *
3442 TAACCATCATGGTTTTTGGCTAAAAATGTGTTTCGGGACCCCAGCTCAGTTTTGCATGACTTTTG
1 TAACCATCACAGTTTTTGGCTAAAAACGTGTTCCGGGA-CCCAGCTCAATTTTGCATGACTTTTG
* ** * * *
3507 GCGCCGAGACTCCTTGAAATATCTATACTCATCTAAT-AAAGTCTTAGCCACATTACA-TTAAGG
65 GCGCCAAGACTAATTGAAATATCTATATTCATCTAATCAAA-TCTCAGCCACATTGCATTTAAGG
* **
3570 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCCGAAAAATATGA
129 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAAAAAAATATGA
* * *
3635 AAAATGATATTAAAAGCATGAAAAACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTATGA
194 AAAATGATATTAAAAGCGTGAAAAACCCTTCAATCTTGTTGGCGTTGAATTATATATTTTTATGA
* ** * * *
3700 GTATCGTGGCTAAAAATTGAGAAAATATCTTTGGGTCAATTTTTGCAAAATTTTAGACAAAATCG
259 GTATTGTTAC-AAAATTTGAGAAAATATCTTTGGGTCAATTTTTACAAAATTTTAGCCAAAATCG
3765 TGT
323 TGT
3768 TTGGCGCCGA
Statistics
Matches: 552, Mismatches: 90, Indels: 38
0.81 0.13 0.06
Matches are distributed among these distances:
327 1 0.00
328 55 0.10
329 42 0.08
330 21 0.04
331 14 0.03
332 258 0.47
333 144 0.26
334 17 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (327 bp):
TAACCATCACAGTTTTTGGCTAAAAACGTGTTCCGGGACCCAGCTCAATTTTGCATGACTTTTGG
CGCCAAGACTAATTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGAT
TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAAAAAAATATGAAA
AATGATATTAAAAGCGTGAAAAACCCTTCAATCTTGTTGGCGTTGAATTATATATTTTTATGAGT
ATTGTTACAAAATTTGAGAAAATATCTTTGGGTCAATTTTTACAAAATTTTAGCCAAAATCGTGT
AA
Found at i:4452 original size:330 final size:331
Alignment explanation
Indices: 3832--4574 Score: 878
Period size: 330 Copynumber: 2.2 Consensus size: 331
3822 TGTTTTTAGA
* *
3832 AGCATCTGAATCATGTTTCGATTTAATTAAAAATTAATTCGGCAATAATAGG-AAAACGATATTA
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAA-TAATTCGG-AA-AATAGGAAAAACGATATTA
* * * *
3896 AAATCGTGAAAAGCCCTTCAACCTTTTTTGGCGTTGAATTATATATATTTTTTTATGAGTATTGT
63 AAAGCGTAAAAAACCCTTCAA-CTTTTTTGACGTTGAA-TATATATATTTTTTTATGAGTATTGT
** * * *
3961 AATTAAAAATTGAGGAAAATATTCCCGGTCAATTTTTGCAAAATATTAGGCGAAATCGTGTATCA
126 AACCAAAAAATGAGGAAAATATTCCCGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTATAA
*** * * ** *
4026 TCACGATTTTTTTGTTGTTGCTAATAACGCGTTCCGCGGCCCCGGGTCAGTTTTGCATGATTTTT
191 TCACGATGGCTTTGTCGCT-CTAATAACGCGTTCCAAGGCCCCAGGTCAGTTTTGCATGATTTTT
* * * * *
4091 GGCTGCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCTACCACATTGGATTTAGGG
255 GGCTGCAAGACTCCTTGAAATATCCATATTCATCTAATCAAATCTCAACCACATTGCATTGAAGG
4156 ATTTGATTTTACG
320 ATTTG-TTTTACG
*
4169 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATGAATTCGGATAAAGTAGGAAAAACGATATTA
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAAT-AATTCGGA-AAA-TAGGAAAAACGATATTA
* *
4234 GAAGCGTAAAAAACCCTTCAA-TGTTTTTGACGTTG-A-A-ATATA-TTTTTTATGAGTATTTTA
63 AAAGCGTAAAAAACCCTTCAACT-TTTTTGACGTTGAATATATATATTTTTTTATGAGTATTGTA
* * * * *
4294 GCCAAAAAATGAGGAAATATCTTCCGGGTCCATTTTTGCAAAATTTTAGCCGAAATCGTGTAATA
127 ACCAAAAAATGAGGAAA-ATATTCCCGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGT-ATA
4359 ATCATC-ATGGCTTT-TCGCT-TAA-AACGCGTTCCAAGGCCCCAGGTCAGTTTTGCATGATTTT
190 ATCA-CGATGGCTTTGTCGCTCTAATAACGCGTTCCAAGGCCCCAGGTCAGTTTTGCATGATTTT
* * * *
4420 TGGC-GTTAAGACTCCTTGAGATATCCATATTCATCTCATCAAATCTCAACCACATTTCATTGAA
254 TGGCTG-CAAGACTCCTTGAAATATCCATATTCATCTAATCAAATCTCAACCACATTGCATTGAA
4484 GGATTTGTTTTACG
318 GGATTTGTTTTACG
* ** * *
4498 AGCATCTGAATCTTGTTTCGATTAAATTAGAAACTAATTCACAAAAATTATGAAAAACGATATGA
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAA-TAATTC-GGAAAA-TAGGAAAAACGATATTA
4563 AAAGCGTAAAAA
63 AAAGCGTAAAAA
4575 GTCCTCCAAG
Statistics
Matches: 351, Mismatches: 44, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
329 73 0.21
330 98 0.28
331 3 0.01
332 30 0.09
333 46 0.13
334 12 0.03
335 1 0.00
336 6 0.02
337 53 0.15
338 29 0.08
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (331 bp):
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAATTCGGAAAATAGGAAAAACGATATTAAAA
GCGTAAAAAACCCTTCAACTTTTTTGACGTTGAATATATATATTTTTTTATGAGTATTGTAACCA
AAAAATGAGGAAAATATTCCCGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTATAATCACG
ATGGCTTTGTCGCTCTAATAACGCGTTCCAAGGCCCCAGGTCAGTTTTGCATGATTTTTGGCTGC
AAGACTCCTTGAAATATCCATATTCATCTAATCAAATCTCAACCACATTGCATTGAAGGATTTGT
TTTACG
Done.