Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018119.1 Corchorus olitorius cultivar O-4 contig18152, 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: 2977
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Found at i:1221 original size:4 final size:4
Alignment explanation
Indices: 1212--1359 Score: 50
Period size: 4 Copynumber: 38.8 Consensus size: 4
1202 GGATAATAAT
* ** *
1212 AATA AATA AATA GAT- AATA GCTA AATT AATA AATA AA-A AA-A ATATTA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-A-TA
* * *
1259 AATA AATA GAT- AAT- AATT AA-A AATA AATA AA-A AGATA AAT- AGTA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA AATA
* * * * *
1303 AATA AGTA GATA ATAGTT AA-A AA-A AATA GATA AAT- AGTA AATA AAT-
1 AATA AATA AATA A-A-TA AATA AATA AATA AATA AATA AATA AATA AATA
*
1349 AATA AAAA AAT
1 AATA AATA AAT
1360 CTTTTTGGTC
Statistics
Matches: 105, Mismatches: 25, Indels: 28
0.66 0.16 0.18
Matches are distributed among these distances:
3 28 0.27
4 68 0.65
5 5 0.05
6 4 0.04
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1304 original size:25 final size:25
Alignment explanation
Indices: 1257--1304 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1247 AAAAAAATAT
* *
1257 TAAATAAATAGATAATAATTAAAAA
1 TAAATAAAAAGATAATAAGTAAAAA
1282 TAAATAAAAAGATAA-ATAGTAAA
1 TAAATAAAAAGATAATA-AGTAAA
1305 TAAGTAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (25 bp):
TAAATAAAAAGATAATAAGTAAAAA
Found at i:1355 original size:31 final size:31
Alignment explanation
Indices: 1279--1358 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
1269 TAATAATTAA
*
1279 AAATAAATAA-AAAGATAAATAGTAAATAAGT
1 AAATAAATAATAAA-AAAAATAGTAAATAAGT
* *
1310 AGAT-AATAGTTAAAAAAAATAGATAAAT-AGT
1 AAATAAATA-ATAAAAAAAATAG-TAAATAAGT
1341 AAATAAATAATAAAAAAA
1 AAATAAATAATAAAAAAA
1359 TCTTTTTGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
30 4 0.10
31 24 0.60
32 12 0.30
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (31 bp):
AAATAAATAATAAAAAAAATAGTAAATAAGT
Found at i:2890 original size:37 final size:37
Alignment explanation
Indices: 2821--2977 Score: 207
Period size: 35 Copynumber: 4.3 Consensus size: 37
2811 ATCAATGTGA
**
2821 AGATCAACTCTGATCAT--CGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAATG
*
2856 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAATG
*
2893 AGATCAACTCTGACCATATAAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATA-AAAAAAACTTCTTGAAATG
**
2931 AGATCAACTCTGATC--AACGAAAAC-TCTTTGAAATG
1 AGATCAACTCTGATCATAAAAAAAACTTC-TTGAAATG
2966 AGATCAACTCTG
1 AGATCAACTCTG
Statistics
Matches: 110, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
34 2 0.02
35 43 0.39
36 1 0.01
37 32 0.29
38 32 0.29
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (37 bp):
AGATCAACTCTGATCATAAAAAAAACTTCTTGAAATG
Found at i:2925 original size:38 final size:37
Alignment explanation
Indices: 2840--2977 Score: 192
Period size: 37 Copynumber: 3.8 Consensus size: 37
2830 CTGATCATCG
*
2840 AAAACTTCTTGAAATGAGATCAACTCTGATCATAAAA
1 AAAACTTCTTGAAATGAGATCAACTCTGACCATAAAA
*
2877 AAAACTTCTTGAAAGGAGATCAACTCTGACCATATAAA
1 AAAACTTCTTGAAATGAGATCAACTCTGACCATA-AAA
* **
2915 AAAACTTCTTGAAATGAGATCAACTCTGATC--AACG
1 AAAACTTCTTGAAATGAGATCAACTCTGACCATAAAA
2950 AAAAC-TCTTTGAAATGAGATCAACTCTG
1 AAAACTTC-TTGAAATGAGATCAACTCTG
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
34 2 0.02
35 26 0.28
36 1 0.01
37 32 0.34
38 32 0.34
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (37 bp):
AAAACTTCTTGAAATGAGATCAACTCTGACCATAAAA
Found at i:2941 original size:75 final size:73
Alignment explanation
Indices: 2840--2977 Score: 215
Period size: 75 Copynumber: 1.9 Consensus size: 73
2830 CTGATCATCG
2840 AAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAAAACT-TCTTGAAAGGAGATCAACTCT
1 AAAACTTCTTGAAATGAGATCAACTCTGATC--AAAAAAAACTCT-TTGAAAGGAGATCAACTCT
2904 GACCATATAAA
63 GACCATATAAA
** *
2915 AAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACTCTTTGAAATGAGATCAACTCTG
1 AAAACTTCTTGAAATGAGATCAACTCTGATCAAAAAAAACTCTTTGAAAGGAGATCAACTCTG
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
73 27 0.46
74 1 0.02
75 31 0.53
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (73 bp):
AAAACTTCTTGAAATGAGATCAACTCTGATCAAAAAAAACTCTTTGAAAGGAGATCAACTCTGAC
CATATAAA
Done.