Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024570.1 Corchorus olitorius cultivar O-4 contig24603, 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: 7888
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:2319 original size:33 final size:33
Alignment explanation
Indices: 2214--2399 Score: 167
Period size: 33 Copynumber: 5.6 Consensus size: 33
2204 TATTTATTGG
** * * *
2214 TGCCGCCCAAGGAGGGCGGCGTAACCATGGCTA
1 TGCCGCCCACCGAGGGCGGCATAGCCATGGCCA
** * * *
2247 TGCCGCCCAAGGAGGGCGGCATGGCTATGGTCA
1 TGCCGCCCACCGAGGGCGGCATAGCCATGGCCA
* **
2280 TACCGCCCACCGAGGGCGGCATAGCCATGGTTA
1 TGCCGCCCACCGAGGGCGGCATAGCCATGGCCA
* * **
2313 GGCCGCCCTCCTTGGGCGGCAT-GACCATGGCCA
1 TGCCGCCCACCGAGGGCGGCATAG-CCATGGCCA
* * **
2346 CGCCGCCCACTGAGGGCGGCATCCCCATGGCCA
1 TGCCGCCCACCGAGGGCGGCATAGCCATGGCCA
2379 TGCCGCCCACCGAGGGCGGCA
1 TGCCGCCCACCGAGGGCGGCA
2400 CCGACCATTT
Statistics
Matches: 124, Mismatches: 27, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
32 1 0.01
33 123 0.99
ACGTcount: A:0.17, C:0.36, G:0.34, T:0.12
Consensus pattern (33 bp):
TGCCGCCCACCGAGGGCGGCATAGCCATGGCCA
Found at i:2396 original size:66 final size:66
Alignment explanation
Indices: 2215--2399 Score: 190
Period size: 66 Copynumber: 2.8 Consensus size: 66
2205 ATTTATTGGT
** * ** * * *
2215 GCCGCCCAAGGAGGGCGGCGTAACCATGGCTATGCCGCCCAAGGAGGGCGGCATGGCTATGGTCA
1 GCCGCCCACCGAGGGCGGCATAACCATGGCTATGCCGCCCACCGAGGGCGGCATGACCATGGCCA
*
2280 T
66 C
* * * * * **
2281 ACCGCCCACCGAGGGCGGCATAGCCATGGTTAGGCCGCCCTCCTTGGGCGGCATGACCATGGCCA
1 GCCGCCCACCGAGGGCGGCATAACCATGGCTATGCCGCCCACCGAGGGCGGCATGACCATGGCCA
2346 C
66 C
* ** *
2347 GCCGCCCACTGAGGGCGGCATCCCCATGGCCATGCCGCCCACCGAGGGCGGCA
1 GCCGCCCACCGAGGGCGGCATAACCATGGCTATGCCGCCCACCGAGGGCGGCA
2400 CCGACCATTT
Statistics
Matches: 93, Mismatches: 26, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
66 93 1.00
ACGTcount: A:0.17, C:0.36, G:0.35, T:0.12
Consensus pattern (66 bp):
GCCGCCCACCGAGGGCGGCATAACCATGGCTATGCCGCCCACCGAGGGCGGCATGACCATGGCCA
C
Found at i:7486 original size:334 final size:334
Alignment explanation
Indices: 6765--7821 Score: 988
Period size: 334 Copynumber: 3.2 Consensus size: 334
6755 CCACTGTAGC
* * * * ***
6765 GAAATATCTATATTCATCTAACCAAATCTCAGCGACATTGGATTTAAGGATTTG-TAAAAC-AAG
1 GAAATATCTATATTCATCTAATCAAATATCAGCAACATTGAATTTAAGGATTTGTTTTGACGAA-
* * * * * *
6828 CATTTGAATCAT-GTTTCGATTTAATTAGAATTTAATTCTGAAAATAATAGGAAAAA-CAATATT
65 CATCTAAATC-TGGTTTCAATTTAATTAGAAATTAATTCAGAAAAT-AT--GAAAAATCGATATT
** * *** * * * * * * *
6891 GGAAGCATGAAAAGCCCTTCAATC--TTTTTGGCATTCAATTATATATTTTTTATGAGTATTGT-
126 AAAAGCGTGAAAAATACTCCAATCTTTTTTTGACGTTAAATTATATATATATTATGAGTATTTTA
* * * *
6953 GCCTAAAAATTGTA--TATATATCTTTCGAGTCAATTT-TTGCAAAATTCTA-ACCGAAATCGTG
191 GCC-AAAAATTG-ACGAAAATATTTTTCGAGTC-ATTTCTTGCAAAATTTTAGA-CGAAATCGTG
* * * ** * * * * * *
7014 TAATAATCATCACGGTTTTGGGCTAAAATCGTGTTCCGGGGCCCCAGA-TAAGTTTTGCATGATT
252 TACTAACCATCACAGTTTTTAGCAAAAAACGCGTTTCGGAGCCCC-GACTTAGTTTTGCATGATT
* * * **
7078 T-TTGACGCCATA-TCTCTTT
316 TGTGGA-ACCA-ACACTCCAT
** * * * * * *
7097 GGGATGT-TCATATTCATCTAATCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAA
1 GAAATATCT-ATATTCATCTAATCAAATATCAGCAACATTGAATTTAAGGATTTGTTTTGACGAA
*
7161 CATCTGAATCTGGTTTCAATTTAATTAGAAATTAATTCAGAAAAATATGAAAAA-CGATATTAAA
65 CATCTAAATCTGGTTTCAATTTAATTAGAAATTAATTCAG-AAAATATGAAAAATCGATATTAAA
*
7225 AGCGTGAAAAATA-TCCCAATC-TTTTTT-ACGTTAACTTATATATATATTATGAGTATTTTAGC
129 AGCGTGAAAAATACT-CCAATCTTTTTTTGACGTTAAATTATATATATATTATGAGTATTTTAGC
* * *
7287 CAAAAATTGACGGAAATATTTTTCGGGTCATTTTTTGCAAAATTTTAGACGAAATCGTGTACTAA
193 CAAAAATTGACGAAAATATTTTTCGAGTCATTTCTTGCAAAATTTTAGACGAAATCGTGTACTAA
*
7352 CCATCACAGTTTTT-GACAAAAAAAACGTGTTTCGG-GTCCCCGACTTAGTTTTGCATGATTTGT
258 CCATCACAGTTTTTAG-C--AAAAAACGCGTTTCGGAG-CCCCGACTTAGTTTTGCATGATTTGT
** **
7415 GGCGCTGACACTCCAT
319 GGAACCAACACTCCAT
* * * * * *
7431 GAAATTTCTATATTCATCTAATCAATTTTCAATC-GCATTGAATTTAAGGATTTGTTTTGACGAG
1 GAAATATCTATATTCATCTAATCAAATATC-AGCAACATTGAATTTAAGGATTTGTTTTGACGAA
* * *
7495 CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAATTATGAAAAATCGATATTAAAA
65 CATCTAAATCTGGTTTCAATTTAATTAGAAATTAATTCAGAAAATATGAAAAATCGATATTAAAA
* * * *
7560 GCGTGGAAAGTACTCCAATCTTTTTTTGATGTTAAATTATATATATTTTATGAGTATTTTAGCCA
130 GCGTGAAAAATACTCCAATCTTTTTTTGACGTTAAATTATATATATATTATGAGTATTTTAGCCA
* * * *
7625 AAAATTGACTAAAATTTTTTTTGAGTCATTTCTTGCAAAATTTTAGCCGAAATCGTGTACTAACC
195 AAAATTGACGAAAATATTTTTCGAGTCATTTCTTGCAAAATTTTAGACGAAATCGTGTACTAACC
* * * * *
7690 ATCACGGTTTTTAGCTAAAAAGGCGTTTCGGAGCCCCGGCTTAGTTTTGCATGATTTTTGGAACC
260 ATCACAGTTTTTAGCAAAAAACGCGTTTCGGAGCCCCGACTTAGTTTTGCATGATTTGTGGAACC
*
7755 AAGACTCCAT
325 AACACTCCAT
*
7765 GAAATATCTATATTCATCTAATCAAATATCAGCAACATTGAATATAAGGATTTGTTT
1 GAAATATCTATATTCATCTAATCAAATATCAGCAACATTGAATTTAAGGATTTGTTT
7822 GGCCAAAAAA
Statistics
Matches: 605, Mismatches: 92, Indels: 54
0.81 0.12 0.07
Matches are distributed among these distances:
330 2 0.00
331 66 0.11
332 107 0.18
333 58 0.10
334 254 0.42
335 13 0.02
336 104 0.17
337 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (334 bp):
GAAATATCTATATTCATCTAATCAAATATCAGCAACATTGAATTTAAGGATTTGTTTTGACGAAC
ATCTAAATCTGGTTTCAATTTAATTAGAAATTAATTCAGAAAATATGAAAAATCGATATTAAAAG
CGTGAAAAATACTCCAATCTTTTTTTGACGTTAAATTATATATATATTATGAGTATTTTAGCCAA
AAATTGACGAAAATATTTTTCGAGTCATTTCTTGCAAAATTTTAGACGAAATCGTGTACTAACCA
TCACAGTTTTTAGCAAAAAACGCGTTTCGGAGCCCCGACTTAGTTTTGCATGATTTGTGGAACCA
ACACTCCAT
Done.