Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009674.1 Corchorus olitorius cultivar O-4 contig09706, 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: 1925
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Found at i:905 original size:19 final size:18
Alignment explanation
Indices: 876--911 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
866 TTGAAATAAA
876 TCTTCAATGGTCTTCAAG
1 TCTTCAATGGTCTTCAAG
894 TCTTCAAATGGTCTTCAA
1 TCTTC-AATGGTCTTCAA
912 ACACGAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAG
Found at i:1221 original size:55 final size:55
Alignment explanation
Indices: 1146--1252 Score: 162
Period size: 55 Copynumber: 1.9 Consensus size: 55
1136 TCAAGAACAC
* *
1146 CGGAAGACGGTTTGCTAGAAAGGATTTTCA-AATGTTGATTGGAAGACAATCTCAT
1 CGGAAGACGGTTTGCTAGAAAGAATTTTCAGAA-GTTGATCGGAAGACAATCTCAT
* *
1201 CGGAAGACGGTTTGCTAGAAAGAATTTTCAGGAGTTGATCGGAAGACGATCT
1 CGGAAGACGGTTTGCTAGAAAGAATTTTCAGAAGTTGATCGGAAGACAATCT
1253 TGTCAAGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
55 46 0.98
56 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (55 bp):
CGGAAGACGGTTTGCTAGAAAGAATTTTCAGAAGTTGATCGGAAGACAATCTCAT
Found at i:1307 original size:64 final size:64
Alignment explanation
Indices: 1233--1708 Score: 580
Period size: 64 Copynumber: 7.4 Consensus size: 64
1223 AATTTTCAGG
1233 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCCTA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCCTA
*
1297 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAAATTTCCTA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCCTA
* * * * * **
1361 AGCTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGTTGTTTTCTCAACAGTTTTCAGA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCCTA
* * * * * *
1425 AGTGGATCGGAAGATGATCTTGTCAAAAAGTACATCAGAAGATGGTTTCTC-AACAGTTTCC-A
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCCTA
1487 GGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCCT
1 --AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCCT
1552 A
64 A
* * * * **
1553 AGTTGATCGGAAGACGATCTTGCCAAGAACTACGCCAGAAGATGGATTCTC-AAAATTTTCAAA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCCTA
* * * * * * * * * ** **
1616 AGTCGGTCGGAAGATGCTCTTGTTAAAAAGCACATCAGAAGATAGTTTCTCGAAAAGGTTTCAGA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAAAATTTTCCTA
* * *
1681 AGTGGGTCGGAAGACGATCTTGTTAAGA
1 AGTTGATCGGAAGACGATCTTGTCAAGA
1709 GATGCACCGG
Statistics
Matches: 353, Mismatches: 53, Indels: 11
0.85 0.13 0.03
Matches are distributed among these distances:
62 1 0.00
63 53 0.15
64 257 0.73
65 41 0.12
66 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (64 bp):
AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCCTA
Found at i:1466 original size:192 final size:190
Alignment explanation
Indices: 1223--1708 Score: 661
Period size: 192 Copynumber: 2.5 Consensus size: 190
1213 TGCTAGAAAG
* * * * *
1223 AATTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAA
1 AATTTTCAGAAGTGGATCGGAAGATGATCTTGTCAAAAAGTACATCAGAAGATGGTTTCTCAAAA
*
1288 ATTTTCCTAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAA
66 AGTTTCC-AAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAA
* * * **
1353 ATTTCCTAAGCTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGTTGTTTTCTCAA
130 ATTTCCTAAGCTGATCGGAAGACGATCTTGCCAAGAACTACACCAGAAGATGGATTCTCAA
*
1414 CAGTTTTCAGAAGTGGATCGGAAGATGATCTTGTCAAAAAGTACATCAGAAGATGGTTTCTC-AA
1 -AATTTTCAGAAGTGGATCGGAAGATGATCTTGTCAAAAAGTACATCAGAAGATGGTTTCTCAAA
*
1478 CAGTTTCCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
65 AAGTTTCCA--AGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * *
1543 AATTTTCCTAAGTTGATCGGAAGACGATCTTGCCAAGAACTACGCCAGAAGATGGATTCTCAA
128 AAATTTCCTAAGCTGATCGGAAGACGATCTTGCCAAGAACTACACCAGAAGATGGATTCTCAA
* * * * *
1606 AATTTTCAAAAGTCGG-TCGGAAGATGCTCTTGTTAAAAAGCACATCAGAAGATAGTTTCTCGAA
1 AATTTTCAGAAGT-GGATCGGAAGATGATCTTGTCAAAAAGTACATCAGAAGATGGTTTCTC-AA
* * * * *
1670 AAGGTTTCAGAAGTGGGTCGGAAGACGATCTTGTTAAGA
64 AAAGTTTC-CAAGTTGATCGGAAGACGATCTTGTCAAGA
1709 GATGCACCGG
Statistics
Matches: 260, Mismatches: 28, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
190 1 0.00
191 60 0.23
192 191 0.73
193 7 0.03
194 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (190 bp):
AATTTTCAGAAGTGGATCGGAAGATGATCTTGTCAAAAAGTACATCAGAAGATGGTTTCTCAAAA
AGTTTCCAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAAA
TTTCCTAAGCTGATCGGAAGACGATCTTGCCAAGAACTACACCAGAAGATGGATTCTCAA
Done.