Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024128.1 Corchorus olitorius cultivar O-4 contig24161, 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: 11539
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:801 original size:11 final size:11
Alignment explanation
Indices: 785--819 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
775 TTTTTCTGTT
785 TTTTGTTTTTG
1 TTTTGTTTTTG
*
796 TTTTGTTTTCG
1 TTTTGTTTTTG
807 TTTTGTTTTTG
1 TTTTGTTTTTG
818 TT
1 TT
820 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:3314 original size:20 final size:20
Alignment explanation
Indices: 3289--3329 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3279 TTCATACATA
3289 TATAAAATAAGATCTTGTCG
1 TATAAAATAAGATCTTGTCG
3309 TATAAAATAAGATCTTGTCG
1 TATAAAATAAGATCTTGTCG
3329 T
1 T
3330 GTCGTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (20 bp):
TATAAAATAAGATCTTGTCG
Found at i:4118 original size:18 final size:19
Alignment explanation
Indices: 4079--4118 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
4069 GTGCTCCCGT
4079 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
4100 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
4118 T
1 T
4119 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:6466 original size:12 final size:12
Alignment explanation
Indices: 6441--6492 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
6431 TAGTTACTAA
*
6441 AAAACGAAGCAG
1 AAAACGAAGAAG
*
6453 AAAACGGAGAAG
1 AAAACGAAGAAG
* *
6465 AAGA-GAATAAAG
1 AAAACGAA-GAAG
6477 AAAACGAAGAAG
1 AAAACGAAGAAG
6489 AAAA
1 AAAA
6493 GAATAAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
11 2 0.06
12 26 0.84
13 3 0.10
ACGTcount: A:0.65, C:0.08, G:0.25, T:0.02
Consensus pattern (12 bp):
AAAACGAAGAAG
Found at i:6487 original size:24 final size:24
Alignment explanation
Indices: 6451--6499 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
6441 AAAACGAAGC
* *
6451 AGAAAACGGAGAAGAAGAGAATAA
1 AGAAAACGAAGAAGAAAAGAATAA
6475 AGAAAACGAAGAAGAAAAGAATAA
1 AGAAAACGAAGAAGAAAAGAATAA
6499 A
1 A
6500 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.67, C:0.04, G:0.24, T:0.04
Consensus pattern (24 bp):
AGAAAACGAAGAAGAAAAGAATAA
Found at i:7423 original size:15 final size:16
Alignment explanation
Indices: 7395--7427 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
7385 GAAACAAATC
7395 AAAAAAAAAGGAAAAG
1 AAAAAAAAAGGAAAAG
*
7411 AAAAGAAAA-GAAAAG
1 AAAAAAAAAGGAAAAG
7426 AA
1 AA
7428 TGAAGAGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGGAAAAG
Found at i:7946 original size:41 final size:41
Alignment explanation
Indices: 7845--8088 Score: 269
Period size: 43 Copynumber: 5.8 Consensus size: 41
7835 AATAACCAAA
*
7845 AAGTCCCCAAACACATATATAACACAG-GAGCAATTCTAT-TCC
1 AAGTCCCCAAACACATATATAACACAGAG-GC-A-CCTATATCC
*
7887 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATATCC
1 --AAGTCCCCAAACACATATATAACACAGAGGCACCTATATCC
* * *
7930 AAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTACA
1 AAGTCCCCAAACACATATATAACACAGAGGCACCTATA-T-CC
* * *
7973 AAGTCCTCAAACACATATATAACACAGAGACACCTATATTC
1 AAGTCCCCAAACACATATATAACACAGAGGCACCTATATCC
* * *
8014 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTAT-TACA
1 AAGTCCCCAAACACATATATAACACAGAGGC-A-CCTATAT-CC
*
8057 AAGTCCTCAAACACATATATAACACAGAGGCA
1 AAGTCCCCAAACACATATATAACACAGAGGCA
8089 TTTCTCCTTA
Statistics
Matches: 173, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
41 63 0.36
42 9 0.05
43 72 0.42
44 28 0.16
45 1 0.01
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (41 bp):
AAGTCCCCAAACACATATATAACACAGAGGCACCTATATCC
Found at i:7978 original size:43 final size:42
Alignment explanation
Indices: 7844--8088 Score: 293
Period size: 41 Copynumber: 5.8 Consensus size: 42
7834 CAATAACCAA
*
7844 AAAGTCCCCAAACACATATATAACACAG-GAGCA-ATTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAG-GCACCTT-TATT-C
* *
7887 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATA-TC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCACCTTTATTC
* *
7929 CAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTTTATT-C
* * *
7972 AAAGTCCTCAAACACATATATAACACAGAGACACCTATATTC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTTTATTC
* *
8014 -AAGTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTT-TATT-C
*
8056 AAAGTCCTCAAACACATATATAACACAGAGGCA
1 AAAGTCCCCAAACACATATATAACACAGAGGCA
8089 TTTCTCCTTA
Statistics
Matches: 175, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.01
41 68 0.39
42 4 0.02
43 68 0.39
44 32 0.18
45 2 0.01
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCACCTTTATTC
Found at i:7999 original size:84 final size:84
Alignment explanation
Indices: 7845--8088 Score: 418
Period size: 84 Copynumber: 2.9 Consensus size: 84
7835 AATAACCAAA
* *
7845 AAGTCCCCAAACACATATATAACACAGGAGCAATTCTATTCCAAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC-AAAGTCCTCAAACACATATATA
7910 ACACAGAGGCACCTATATCC
65 ACACAGAGGCACCTATATCC
*
7930 AAGTCCCCAAACACATATATAACACAGGGGCACCTT-TATTACAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTACAAAGTCCTCAAACACATATATA
* *
7994 ACACAGAGACACCTATATTC
65 ACACAGAGGCACCTATATCC
8014 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
8079 CACAGAGGCA
66 CACAGAGGCA
8089 TTTCTCCTTA
Statistics
Matches: 150, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
83 2 0.01
84 110 0.73
85 36 0.24
86 2 0.01
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (84 bp):
AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
CACAGAGGCACCTATATCC
Found at i:8210 original size:2 final size:2
Alignment explanation
Indices: 8198--8235 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
8188 ACCAAATTCC
*
8198 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8236 GACAAAGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.