Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017479.1 Corchorus olitorius cultivar O-4 contig17512, 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: 9253
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:353 original size:16 final size:16
Alignment explanation
Indices: 332--362 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
322 TCTACAAATT
332 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
348 ATAAAGATTTAGTAA
1 ATAAAGATTTAGTAA
363 TATTTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:6975 original size:18 final size:19
Alignment explanation
Indices: 6952--6992 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
6942 GAAATGATTC
6952 TTATCT-AAAAAAAATTTA
1 TTATCTAAAAAAAAATTTA
6970 TTATCTCAAAAAAAAATTTA
1 TTATCT-AAAAAAAAATTTA
6990 TTA
1 TTA
6993 AATGAACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
TTATCTAAAAAAAAATTTA
Found at i:8945 original size:43 final size:43
Alignment explanation
Indices: 8811--9088 Score: 370
Period size: 43 Copynumber: 6.5 Consensus size: 43
8801 CCAATAACCA
* *
8811 AAAGTCCCCAAACACATATATAACACAGGGGCATCC-CTATTCC
1 AAAGTCCTCAAACACATATATAACACAGGGGCA-CCTCTATTAC
* ** *
8854 AAAAGTCCTCAAACACATATACAACACAGATGCACCTATATT-C
1 -AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
*
8897 -AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
* *
8939 AAAGTCCTCAAACACGTATATAACACAGAGGCA--TCTA-TATC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTA-C
* *
8980 AAAGTCCCCAAACACATATATAACATAGGGGCACCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
* *
9023 AAAGTCCTCAAACACATATATAACACATGGGCATCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
9066 AAAGTCCTCAAACACATATATAA
1 AAAGTCCTCAAACACATATATAA
9089 TACAAAGGCA
Statistics
Matches: 206, Mismatches: 21, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
40 2 0.01
41 69 0.33
42 1 0.00
43 99 0.48
44 35 0.17
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (43 bp):
AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
Found at i:8988 original size:84 final size:85
Alignment explanation
Indices: 8811--9088 Score: 420
Period size: 84 Copynumber: 3.3 Consensus size: 85
8801 CCAATAACCA
*
8811 AAAGTCCCCAAACACATATATAACACAGGGGCATCC-CTATTCCAAAAGTCCTCAAACACATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCA-CCTCTATTAC-AAAGTCCTCAAACACATATA
* * *
8875 CAACACAGATGCACCTATATTC
64 TAACACAGAGGCATCTATATTC
*
8897 -AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACGTATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
8961 ACACAGAGGCATCTATA-TC
66 ACACAGAGGCATCTATATTC
*
8980 AAAGTCCCCAAACACATATATAACATAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
*
9045 ACACATG-GGCATCTCTATTAC
66 ACACA-GAGGCATCTATATT-C
*
9066 AAAGTCCTCAAACACATATATAA
1 AAAGTCCCCAAACACATATATAA
9089 TACAAAGGCA
Statistics
Matches: 178, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
83 2 0.01
84 113 0.63
85 40 0.22
86 23 0.13
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (85 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATTC
Found at i:9128 original size:127 final size:125
Alignment explanation
Indices: 8811--9099 Score: 355
Period size: 127 Copynumber: 2.3 Consensus size: 125
8801 CCAATAACCA
* ** **
8811 AAAGTCCCCAAACACATATATAACACAGGGGCATCCCTAT-TCCAAAAGTCCTCAAACACATATA
1 AAAGTCCTCAAACACATATATAACACAAAGGCAT--CTATAT-C-AAAGTCCAAAAACACATATA
* * **
8875 CAACACAGATGCACCTATATTCAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
62 TAACATAGGGGCACCTATATTCAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
* * **
8939 AAAGTCCTCAAACACGTATATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAAC
1 AAAGTCCTCAAACACATATATAACACAAAGGCATCTATATCAAAGTCCAAAAACACATATATAAC
* * * *
9004 ATAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATAACACATGGGCATCTCTATTAC
66 ATAGGGGCACCTATATT-C-AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
*
9066 AAAGTCCTCAAACACATATATAATACAAAGGCAT
1 AAAGTCCTCAAACACATATATAACACAAAGGCAT
9100 TTCTCCTTAT
Statistics
Matches: 143, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
125 35 0.24
126 6 0.04
127 71 0.50
128 31 0.22
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.21
Consensus pattern (125 bp):
AAAGTCCTCAAACACATATATAACACAAAGGCATCTATATCAAAGTCCAAAAACACATATATAAC
ATAGGGGCACCTATATTCAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
Found at i:9220 original size:2 final size:2
Alignment explanation
Indices: 9208--9253 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
9198 ACCAAATTCC
9208 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9249 TA TA T
1 TA TA T
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.