Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001533.1 Corchorus olitorius cultivar O-4 contig01533, 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, 975
Length: 1625
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:684 original size:31 final size:33
Alignment explanation
Indices: 649--731 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 33
639 TTGTGAAATG
* *
649 GACCAGTCCGTGGTCGATTTTG-AATTGAGA-A
1 GACCAGTCCGTGGTCGATTTTGAAACTAAGAGA
** * *
680 GACCAGTCTATGGTTGATATTGAAACTAAGAGA
1 GACCAGTCCGTGGTCGATTTTGAAACTAAGAGA
*
713 GACCAATCCGTGGTC-ATTT
1 GACCAGTCCGTGGTCGATTT
732 GCTGATGTTG
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
31 18 0.46
32 9 0.23
33 12 0.31
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (33 bp):
GACCAGTCCGTGGTCGATTTTGAAACTAAGAGA
Found at i:944 original size:38 final size:39
Alignment explanation
Indices: 885--1335 Score: 413
Period size: 38 Copynumber: 11.9 Consensus size: 39
875 TCAAATAGAA
* *
885 GAAA-ATGACTTGTTTCTAGTCAA-TTCTGATAATTGCT
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGATAATTGCT
**
922 GAAAGATGACCTGTTTTGAGTCAACTTC-GATAAACTT-CT
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGAT-AA-TTGCT
* * ***
961 GAAAAATGACATGTTTCCAGTCAACTTC-GATAACAACT
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGATAATTGCT
* * * * *
999 GAAAGGTGACCTGTTTCCAGTCGA-TTTTGGT-ATCTTCT
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGATAAT-TGCT
* * *
1037 GAAAGATGACCTGTTTCCAGTCGA-TTTTGATAACTGCT
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGATAATTGCT
* *
1075 TAAAGATGACCTGTTTCCAGTCAACTTC-GATAACTGCT
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGATAATTGCT
*
1113 GAAAGATGACCTGTTTCCAGTCAACTTC-GATAACTGCT
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGATAATTGCT
* *
1151 GAAAGATGACCTGTTTCCAGTCGA-TGT-TGGTAACTT-CT
1 GAAAGATGACCTGTTTCCAGTCAACT-TCTGATAA-TTGCT
* * * *
1189 GAAAAATGACTTGTTTCCAGTCGA-TT-TTAGTAACTT-CT
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGA-TAA-TTGCT
* * *
1227 GAAAAATGACCTGTTTCCAGTCGA-TTTTGATAACTT-CT
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGATAA-TTGCT
1265 GAAAGATGACCTGTTTCCAGTCAACTTC-GAT-ATCTGCT
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGATAAT-TGCT
1303 GAAAGATGACCTGTTTCCAGTCAACTT-TGATAA
1 GAAAGATGACCTGTTTCCAGTCAACTTCTGATAA
1336 CTTCTTTGAG
Statistics
Matches: 357, Mismatches: 38, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
36 1 0.00
37 12 0.03
38 299 0.84
39 43 0.12
40 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (39 bp):
GAAAGATGACCTGTTTCCAGTCAACTTCTGATAATTGCT
Found at i:1069 original size:76 final size:76
Alignment explanation
Indices: 885--1340 Score: 549
Period size: 76 Copynumber: 6.0 Consensus size: 76
875 TCAAATAGAA
* * * ** * *
885 GAAA-ATGACTTGTTTCTAGTCAA-TTCTGATAATTGCTGAAAGATGACCTGTTTTGAGTCAACT
1 GAAAGATGACCTGTTTCCAGTCAACTTC-GATAACTGCTGAAAGATGACCTGTTTCCAGTCGATT
*
948 TCGATAAACTTCT
65 TTGAT-AACTTCT
* * ** *
961 GAAAAATGACATGTTTCCAGTCAACTTCGATAACAACTGAAAGGTGACCTGTTTCCAGTCGATTT
1 GAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCGATTT
* *
1026 TGGTATCTTCT
66 TGATAACTTCT
* * * * * *
1037 GAAAGATGACCTGTTTCCAGTCGATTTTGATAACTGCTTAAAGATGACCTGTTTCCAGTCAACTT
1 GAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCGATTT
* *
1102 CGATAACTGCT
66 TGATAACTTCT
*
1113 GAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCGATGT
1 GAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCGATTT
*
1178 TGGTAACTTCT
66 TGATAACTTCT
* * * ** * *
1189 GAAAAATGACTTGTTTCCAGTCGA-TTTTAGTAACTTCTGAAAAATGACCTGTTTCCAGTCGATT
1 GAAAGATGACCTGTTTCCAGTCAACTTCGA-TAACTGCTGAAAGATGACCTGTTTCCAGTCGATT
1253 TTGATAACTTCT
65 TTGATAACTTCT
* * *
1265 GAAAGATGACCTGTTTCCAGTCAACTTCGATATCTGCTGAAAGATGACCTGTTTCCAGTCAACTT
1 GAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCGATTT
1330 TGATAACTTCT
66 TGATAACTTCT
1341 TTGAGTTTGA
Statistics
Matches: 319, Mismatches: 57, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
75 3 0.01
76 262 0.82
77 51 0.16
78 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (76 bp):
GAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCGATTT
TGATAACTTCT
Found at i:1338 original size:114 final size:114
Alignment explanation
Indices: 886--1340 Score: 529
Period size: 114 Copynumber: 4.0 Consensus size: 114
876 CAAATAGAAG
* * * **
886 AAAATGACTTGTTTCTAGTCAATTCTGATAA-TTGCTGAAAGATGACCTGTTTTGAGTCAACTTC
1 AAAATGACCTGTTTCCAGTCAATTTTGATAACTT-CTGAAAGATGACCTGTTTCCAGTCAACTTC
* * **
950 GATAAACTTCTGAAAAATGACATGTTTCCAGTCAACTTCGATAACAACTGA
65 GAT-AACTGCTGAAAAATGACCTGTTTCCAGTCAACTTCGATAACTTCTGA
** * * * * * *
1001 AAGGTGACCTGTTTCCAGTCGATTTTGGTATCTTCTGAAAGATGACCTGTTTCCAGTCGATTTTG
1 AAAATGACCTGTTTCCAGTCAATTTTGATAACTTCTGAAAGATGACCTGTTTCCAGTCAACTTCG
* * *
1066 ATAACTGCTTAAAGATGACCTGTTTCCAGTCAACTTCGATAACTGCTGA
66 ATAACTGCTGAAAAATGACCTGTTTCCAGTCAACTTCGATAACTTCTGA
* * * * * *
1115 AAGATGACCTGTTTCCAGTCAACTTCGATAACTGCTGAAAGATGACCTGTTTCCAGTCGA-TGTT
1 AAAATGACCTGTTTCCAGTCAATTTTGATAACTTCTGAAAGATGACCTGTTTCCAGTCAACT-TC
* * * * **
1179 GGTAACTTCTGAAAAATGACTTGTTTCCAGTCGA-TTTTAGTAACTTCTGA
65 GATAACTGCTGAAAAATGACCTGTTTCCAGTCAACTTCGA-TAACTTCTGA
*
1229 AAAATGACCTGTTTCCAGTCGATTTTGATAACTTCTGAAAGATGACCTGTTTCCAGTCAACTTCG
1 AAAATGACCTGTTTCCAGTCAATTTTGATAACTTCTGAAAGATGACCTGTTTCCAGTCAACTTCG
* * *
1294 ATATCTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCT
66 ATAACTGCTGAAAAATGACCTGTTTCCAGTCAACTTCGATAACTTCT
1341 TTGAGTTTGA
Statistics
Matches: 286, Mismatches: 49, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
113 4 0.01
114 224 0.78
115 56 0.20
116 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (114 bp):
AAAATGACCTGTTTCCAGTCAATTTTGATAACTTCTGAAAGATGACCTGTTTCCAGTCAACTTCG
ATAACTGCTGAAAAATGACCTGTTTCCAGTCAACTTCGATAACTTCTGA
Done.