Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011310.1 Corchorus olitorius cultivar O-4 contig11343, 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: 3299
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Found at i:952 original size:36 final size:35
Alignment explanation
Indices: 875--1313 Score: 434
Period size: 36 Copynumber: 12.3 Consensus size: 35
865 GCTTAAATTC
* * * *
875 ATTTCAGTTGACCCAGGATGGTCCTAT-TTCAGTTT
1 ATTTCAGTTGATCCAGGGTGAT-CTTTCTTCAGTTT
* *
910 ATTTCAGTTTGATCCAGGGTGATCTTTCTTCAATTC
1 ATTTCAG-TTGATCCAGGGTGATCTTTCTTCAGTTT
* * * * * *
946 ACTTCAGTTGATCCAGGGCGATCCTTATTCAATTC
1 ATTTCAGTTGATCCAGGGTGATCTTTCTTCAGTTT
* *
981 ATTTCAGTTGA-CCTAGGGTGGTCCTAT-TTCAGTTT
1 ATTTCAGTTGATCC-AGGGTGAT-CTTTCTTCAGTTT
* *
1016 ATTTCAGTTTGATCTAGGGTGATCTTTTCTTCATTTT
1 ATTTCAG-TTGATCCAGGGTGATC-TTTCTTCAGTTT
*
1053 ACTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTT
1 ATTTCAGTTGATCCAGGGTGAT-CTTTCTTCAGTTT
** * *
1089 ATTTTTGTTGACCCAGGGTGGTCTTTCTTCAGTTT
1 ATTTCAGTTGATCCAGGGTGATCTTTCTTCAGTTT
* *
1124 ATTTCAGTTGATCCAGGGCGATCTTTTCTTCAATTT
1 ATTTCAGTTGATCCAGGGTGATC-TTTCTTCAGTTT
* *
1160 ATTTCAATTGATCCAGGGCGATCTTTTCTTCAGTTT
1 ATTTCAGTTGATCCAGGGTGATC-TTTCTTCAGTTT
*
1196 ATTTCACTTGATCCAGGGTGATCTTTTCTTCAGTTT
1 ATTTCAGTTGATCCAGGGTGATC-TTTCTTCAGTTT
* ** * *
1232 ATTTCAATTGATCCAGGACGATCTTTCCTCAATTT
1 ATTTCAGTTGATCCAGGGTGATCTTTCTTCAGTTT
* * * *
1267 ACTTCAGTAGATCCAGGGCGATCTTCTCTGCAGTTT
1 ATTTCAGTTGATCCAGGGTGATCTT-TCTTCAGTTT
*
1303 ATTTCAATTGA
1 ATTTCAGTTGA
1314 CTGCAAAATG
Statistics
Matches: 339, Mismatches: 54, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
34 2 0.01
35 127 0.37
36 195 0.58
37 15 0.04
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (35 bp):
ATTTCAGTTGATCCAGGGTGATCTTTCTTCAGTTT
Found at i:1071 original size:72 final size:71
Alignment explanation
Indices: 902--1313 Score: 427
Period size: 71 Copynumber: 5.8 Consensus size: 71
892 ATGGTCCTAT
* * * * *
902 TTCAGTTTATTTCAGTTTGATCCAGGGTGAT-CTTTCTTCAATTCACTTCAGTTGATCCAGGGCG
1 TTCAGTTTACTTCAG-TTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAATTGATCCAGGGCG
* *
966 ATCCTTA
65 ATCTTTC
* * * * * * * *
973 TTCAATTCATTTCAGTTGA-CCTAGGGTGGTCCTAT-TTCAGTTTATTTCAGTTTGATCTAGGGT
1 TTCAGTTTACTTCAGTTGATCC-AGGGTGATCCTTTCTTCAGTTTATTTCA-ATTGATCCAGGGC
1036 GATCTTTTC
64 GATC-TTTC
* *** * * *
1045 TTCATTTTACTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTTTGTTGACCCAGGGTGG
1 TTCAGTTTACTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAATTGATCCAGGGCGA
1110 TCTTTC
66 TCTTTC
* * * *
1116 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAATTTATTTCAATTGATCCAGGGCGA
1 TTCAGTTTACTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAATTGATCCAGGGCGA
1181 TCTTTTC
66 TC-TTTC
* * * *
1188 TTCAGTTTATTTCACTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGACGA
1 TTCAGTTTACTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAATTGATCCAGGGCGA
1253 TCTTTC
66 TCTTTC
* * * * *
1259 CTCAATTTACTTCAGTAGATCCAGGGCGAT-CTTCTCTGCAGTTTATTTCAATTGA
1 TTCAGTTTACTTCAGTTGATCCAGGGTGATCCTT-TCTTCAGTTTATTTCAATTGA
1314 CTGCAAAATG
Statistics
Matches: 287, Mismatches: 46, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
69 2 0.01
70 24 0.08
71 138 0.48
72 109 0.38
73 14 0.05
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.44
Consensus pattern (71 bp):
TTCAGTTTACTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAATTGATCCAGGGCGA
TCTTTC
Found at i:1135 original size:107 final size:107
Alignment explanation
Indices: 875--1314 Score: 548
Period size: 107 Copynumber: 4.1 Consensus size: 107
865 GCTTAAATTC
* *
875 ATTTCAGTTGACCCAGGATGGTCCTATTTCAGTTTATTTCAGTTTGATCCAGGGTGATCTTTCTT
1 ATTTCAGTTGACCCAGGGTGGTCCTATTTCAGTTTATTTCAGTTTGATCCAGGGCGATCTTTCTT
* * * *
940 CAATTCACTTCAGTTGATCCAGGGCGATCC-TTATTCAATTC
66 CAATTTACTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTT
* * *
981 ATTTCAGTTGACCTAGGGTGGTCCTATTTCAGTTTATTTCAGTTTGATCTAGGGTGATCTTTTCT
1 ATTTCAGTTGACCCAGGGTGGTCCTATTTCAGTTTATTTCAGTTTGATCCAGGGCGATC-TTTCT
* *
1046 TCATTTTACTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTT
65 TCAATTTACTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTT
** *
1089 ATTTTTGTTGACCCAGGGTGGT-CTTTCTTCAGTTTATTTCAG-TTGATCCAGGGCGATCTTTTC
1 ATTTCAGTTGACCCAGGGTGGTCCTAT-TTCAGTTTATTTCAGTTTGATCCAGGGCGATC-TTTC
* * *
1152 TTCAATTTATTTCAATTGATCCAGGGCGATCTTTTCTTCAGTTT
64 TTCAATTTACTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTT
* * * * * * * *
1196 ATTTCACTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCA-ATTGATCCAGGACGATCTTTCC
1 ATTTCAGTTGACCCAGGGTGGTCCTAT-TTCAGTTTATTTCAGTTTGATCCAGGGCGATCTTTCT
* *
1260 TCAATTTACTTCAGTAGATCCAGGGCGAT-CTTCTCTGCAGTTT
65 TCAATTTACTTCAGTTGATCCAGGGCGATCCTT-TCTTCAGTTT
*
1303 ATTTCAATTGAC
1 ATTTCAGTTGAC
1315 TGCAAAATGG
Statistics
Matches: 293, Mismatches: 35, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
106 58 0.20
107 160 0.55
108 75 0.26
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (107 bp):
ATTTCAGTTGACCCAGGGTGGTCCTATTTCAGTTTATTTCAGTTTGATCCAGGGCGATCTTTCTT
CAATTTACTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTT
Found at i:1171 original size:143 final size:143
Alignment explanation
Indices: 902--1313 Score: 497
Period size: 143 Copynumber: 2.9 Consensus size: 143
892 ATGGTCCTAT
* * *
902 TTCAGTTTATTTCAGTTTGATCCAGGGTGAT-CTTTCTTCAATTCACTTCAGTTGATCCAGGGCG
1 TTCAGTTTATTTCAG-TTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
* * * * * * *
966 ATCCTTATTCAATTCATTTCAGTTGA-CCTAGGGTGGTCCTAT-TTCAGTTTATTTCAGTTTGAT
65 ATCTTTCTTCAATTTATTTCAGTTGATCC-AGGGCGATCTTATCTTCAGTTTATTTCA-ATTGAT
* *
1029 CTAGGGTGATCTTTTC
128 CCAGGGCGATCTTTTC
* * ** * * *
1045 TTCATTTTACTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTTTGTTGACCCAGGGTGG
1 TTCAGTTTATTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGA
* * *
1110 TCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAATTTATTTCAATTGATCCA
66 TCTTTCTTCAATTTATTTCAGTTGATCCAGGGCGATCTTATCTTCAGTTTATTTCAATTGATCCA
1175 GGGCGATCTTTTC
131 GGGCGATCTTTTC
* * * *
1188 TTCAGTTTATTTCACTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGACGA
1 TTCAGTTTATTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGA
* * * * *
1253 TCTTTCCTCAATTTACTTCAGTAGATCCAGGGCGATCTTCTCTGCAGTTTATTTCAATTGA
66 TCTTTCTTCAATTTATTTCAGTTGATCCAGGGCGATCTTATCTTCAGTTTATTTCAATTGA
1314 CTGCAAAATG
Statistics
Matches: 226, Mismatches: 40, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
142 15 0.07
143 196 0.87
144 15 0.07
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.44
Consensus pattern (143 bp):
TTCAGTTTATTTCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGA
TCTTTCTTCAATTTATTTCAGTTGATCCAGGGCGATCTTATCTTCAGTTTATTTCAATTGATCCA
GGGCGATCTTTTC
Found at i:1612 original size:30 final size:30
Alignment explanation
Indices: 1576--2063 Score: 523
Period size: 30 Copynumber: 16.2 Consensus size: 30
1566 TGCTTTATCA
*
1576 GCTTTATTTGAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
1606 ACTTTATGATTAATCCTGTTTGAGGATCATT
1 GCTTTAT-TTTAATCCTGTTTGAGGATCATT
* * *
1637 ACTTCATTTTTAATCCTGTTTGAGGATCGTT
1 GCTTTA-TTTTAATCCTGTTTGAGGATCATT
* * *
1668 ACTTTATTTTTATCCTGGTTGAGGAT-ATCT
1 GCTTTATTTTAATCCTGTTTGAGGATCAT-T
* * ** *
1698 GCTCTATGTTAATCCTGTTCAAGGATCTTT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
1728 GCTTTATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
1758 GCTTTATGTTTAATCCTGGTTAAGGATCATT
1 GCTTTAT-TTTAATCCTGTTTGAGGATCATT
* *
1789 GCTTTATTTTAATCCTGGTTAAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
1819 GCTTTATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* * *
1849 GC-TTATGTTTAATCATGGTTGAGGATCATA
1 GCTTTAT-TTTAATCCTGTTTGAGGATCATT
* * *
1879 GCGTCATTTTAATCCTGTTTGAGAATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
*
1909 GCTTTATTTTAATCCCGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* * * **
1939 GCTTCATTTTAATCCTGGTTAAGGATTGTT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* * * *
1969 GCTTTATTTTAATCATGGTTGAAGACCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* * * *
1999 GCTTTACTTTAATCTTGGTTGAGGATCATC
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* * *
2029 GCTATATTTTTATCCTGATTT-AGGATTATT
1 GCTTTATTTTAATCCTG-TTTGAGGATCATT
*
2059 ACTTT
1 GCTTT
2064 GGTTTATTTG
Statistics
Matches: 384, Mismatches: 66, Indels: 16
0.82 0.14 0.03
Matches are distributed among these distances:
29 5 0.01
30 292 0.76
31 86 0.22
32 1 0.00
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (30 bp):
GCTTTATTTTAATCCTGTTTGAGGATCATT
Found at i:2529 original size:29 final size:29
Alignment explanation
Indices: 2490--2574 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
2480 TTGCATATTC
*
2490 GCACATCCAGGGGCATTTTGGTCATTTTT
1 GCACATTCAGGGGCATTTTGGTCATTTTT
* *
2519 GCATATTCAGGGGCATTATGGTCATTTTT
1 GCACATTCAGGGGCATTTTGGTCATTTTT
* *
2548 GCACATTTAGGGGTATTTTGGTCATTT
1 GCACATTCAGGGGCATTTTGGTCATTT
2575 GTACTCCAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (29 bp):
GCACATTCAGGGGCATTTTGGTCATTTTT
Found at i:2832 original size:30 final size:30
Alignment explanation
Indices: 2796--2859 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
2786 TGTCAATTAT
2796 TTGGATTAATTCACATTGTTAAGTATAGAG
1 TTGGATTAATTCACATTGTTAAGTATAGAG
*
2826 TTGGATTAATTCACATTGTTAAGTATGGAG
1 TTGGATTAATTCACATTGTTAAGTATAGAG
2856 TTGG
1 TTGG
2860 CATTTTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.41
Consensus pattern (30 bp):
TTGGATTAATTCACATTGTTAAGTATAGAG
Done.