Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006456.1 Corchorus capsularis cultivar CVL-1 contig06477, 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, 928
Length: 1548
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Found at i:1239 original size:49 final size:48
Alignment explanation
Indices: 1059--1548 Score: 344
Period size: 49 Copynumber: 10.1 Consensus size: 48
1049 ATTTTAAAAA
* * * * *
1059 AAAAAGCAAGTGAAACTAATGCCTTTCATCCGGGAAGGGCGTTTTAGG
1 AAAAAGCAAGTAAAATTAGTGCCTTCCATCCGGGAAGGGCATTTTAGG
* * * ** ** * *
1107 AAAAAACAAATAAAAATTAGAGCCTTTCTGTTGGGGAAGGGCACTTTGGG
1 AAAAAGCAAGT-AAAATTAGTGCC-TTCCATCCGGGAAGGGCATTTTAGG
* *** * * ** * *
1157 GAAAAGTGGGTAAAAGTGAGCGTTTTCCATCCGGGAAGGGCGTTTTCGG
1 AAAAAGCAAGTAAAA-TTAGTGCCTTCCATCCGGGAAGGGCATTTTAGG
* * * *
1206 AAAATAGCAAGTAAAATAAGTGCCTTTCGTCCGGGAAGAGCATTTT-GAG
1 AAAA-AGCAAGTAAAATTAGTGCCTTCCATCCGGGAAGGGCATTTTAG-G
* * * * **
1255 AAAAA-CAGGTAGAGATTAGTGCCTTCCATCGGGGAATGGCGCTTTAGG
1 AAAAAGCAAGTA-AAATTAGTGCCTTCCATCCGGGAAGGGCATTTTAGG
* * *
1303 ACAAAGCAAGTAAAAGTCAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG
1 AAAAAGCAAGTAAAA-TTAGTGCCTTCCATCCGGGAAGGGCATTTTAGG
* * * *
1352 AAAAA-CAGGTAAAAATAAATGCC-TGCAGTCCGGGAAGGGCATTTT-GAG
1 AAAAAGCAAGT-AAAATTAGTGCCTTCCA-TCCGGGAAGGGCATTTTAG-G
* * * **
1400 AAAAA-CAGGTAGAGATTAGTGCCTTCCATCCGGGAATGGCGCTTTAGG
1 AAAAAGCAAGTA-AAATTAGTGCCTTCCATCCGGGAAGGGCATTTTAGG
* * * * *
1448 ACAAAGCAAGTAAAAATCAGTGCCTTCCATCCGGGACGGGCACTTTGGG
1 AAAAAGCAAGT-AAAATTAGTGCCTTCCATCCGGGAAGGGCATTTTAGG
* *
1497 AAAATGCAAGTAAGGATTAGTGCCTTCCATCCGGGAAGGGCATTTTAGG
1 AAAAAGCAAGTAA-AATTAGTGCCTTCCATCCGGGAAGGGCATTTTAGG
1546 AAA
1 AAA
Statistics
Matches: 336, Mismatches: 88, Indels: 35
0.73 0.19 0.08
Matches are distributed among these distances:
47 10 0.03
48 108 0.32
49 183 0.54
50 35 0.10
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (48 bp):
AAAAAGCAAGTAAAATTAGTGCCTTCCATCCGGGAAGGGCATTTTAGG
Found at i:1325 original size:97 final size:97
Alignment explanation
Indices: 1181--1548 Score: 311
Period size: 97 Copynumber: 3.8 Consensus size: 97
1171 AGTGAGCGTT
* * * *
1181 TTCCATCCGGGAAGGGCGTTTTCGGAAAATAGCAAGTAAAATAAGTGCCTTTCGTCCGGGAAGAG
1 TTCCATCCGGGAAGGGCGCTTTAGGAAAATAGCAAGTAAAATAAGTGCCTTCCATCCGGGAAGAG
1246 CATTTT-GAGAAAAACAGGTAGAGATTAGTGCC
66 CATTTTAG-GAAAAACAGGTAGAGATTAGTGCC
* * * * *
1278 TTCCATCGGGGAATGGCGCTTTAGGACAA-AGCAAGTAAAAGTCAGTGCCTTCCATCCGGGAAGG
1 TTCCATCCGGGAAGGGCGCTTTAGGAAAATAGCAAGTAAAA-TAAGTGCCTTCCATCCGGGAAGA
* * * * *
1342 GCGTTTTAGGAAAAACAGGTAAAAATAAATGCC
65 GCATTTTAGGAAAAACAGGTAGAGATTAGTGCC
* * * * * *
1375 -TGCAGTCCGGGAAGGGC-ATTTTGAGAAAA-A-CAGGTAGAGATTAGTGCCTTCCATCCGGGAA
1 TTCCA-TCCGGGAAGGGCGCTTTAG-GAAAATAGCAAGTA-AAATAAGTGCCTTCCATCCGGGAA
** * * * * *
1436 TG-GCGCTTTAGGACAAAGCAAGTAAAAATCAGTGCC
63 -GAGCATTTTAGGA-AAAACAGGTAGAGATTAGTGCC
* * * * * *
1472 TTCCATCCGGGACGGGCACTTTGGGAAAAT-GCAAGTAAGGATTAGTGCCTTCCATCCGGGAAGG
1 TTCCATCCGGGAAGGGCGCTTTAGGAAAATAGCAAGTAA-AATAAGTGCCTTCCATCCGGGAAGA
1536 GCATTTTAGGAAA
65 GCATTTTAGGAAA
Statistics
Matches: 223, Mismatches: 35, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
96 53 0.24
97 125 0.56
98 45 0.20
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (97 bp):
TTCCATCCGGGAAGGGCGCTTTAGGAAAATAGCAAGTAAAATAAGTGCCTTCCATCCGGGAAGAG
CATTTTAGGAAAAACAGGTAGAGATTAGTGCC
Found at i:1409 original size:145 final size:146
Alignment explanation
Indices: 1181--1542 Score: 516
Period size: 145 Copynumber: 2.5 Consensus size: 146
1171 AGTGAGCGTT
* * *
1181 TTCCATCCGGGAAGGGCGTTTTCGGAAAATAGCAAGTAAAATAAGTGCCTTTCGTCCGGGAAGAG
1 TTCCATCCGGGAAGGGCGTTTTAGGAAAATAGCAAGTAAAATAAATGCCTTGCGTCCGGGAAGAG
*
1246 CATTTTGAGAAAAACAGGTAGAGATTAGTGCCTTCCATCGGGGAATGGCGCTTTAGGACAAAGCA
66 CATTTTGAGAAAAACAGGTAGAGATTAGTGCCTTCCATCCGGGAATGGCGCTTTAGGACAAAGCA
*
1311 AGTAAAAGTCAGTGCC
131 AGTAAAAATCAGTGCC
*
1327 TTCCATCCGGGAAGGGCGTTTTAGGAAAA-A-CAGGTAAAAATAAATGCC-TGCAGTCCGGGAAG
1 TTCCATCCGGGAAGGGCGTTTTAGGAAAATAGCAAGT-AAAATAAATGCCTTGC-GTCCGGGAAG
*
1389 GGCATTTTGAGAAAAACAGGTAGAGATTAGTGCCTTCCATCCGGGAATGGCGCTTTAGGACAAAG
64 AGCATTTTGAGAAAAACAGGTAGAGATTAGTGCCTTCCATCCGGGAATGGCGCTTTAGGACAAAG
1454 CAAGTAAAAATCAGTGCC
129 CAAGTAAAAATCAGTGCC
* ** * * * * * * *
1472 TTCCATCCGGGACGGGCACTTTGGGAAAAT-GCAAGTAAGGATTAGTGCCTTCCATCCGGGAAGG
1 TTCCATCCGGGAAGGGCGTTTTAGGAAAATAGCAAGTAA-AATAAATGCCTTGCGTCCGGGAAGA
1536 GCATTTT
65 GCATTTT
1543 AGGAAA
Statistics
Matches: 193, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
144 6 0.03
145 129 0.67
146 56 0.29
147 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (146 bp):
TTCCATCCGGGAAGGGCGTTTTAGGAAAATAGCAAGTAAAATAAATGCCTTGCGTCCGGGAAGAG
CATTTTGAGAAAAACAGGTAGAGATTAGTGCCTTCCATCCGGGAATGGCGCTTTAGGACAAAGCA
AGTAAAAATCAGTGCC
Done.