Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015995.1 Corchorus olitorius cultivar O-4 contig16028, 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: 27550
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2596 original size:18 final size:18
Alignment explanation
Indices: 2573--2609 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2563 AAAGGGTAAT
2573 TAAAAA-AAATTGTTTTCA
1 TAAAAAGAAA-TGTTTTCA
2591 TAAAAAGAAATGTTTTCA
1 TAAAAAGAAATGTTTTCA
2609 T
1 T
2610 GATAGAGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
TAAAAAGAAATGTTTTCA
Found at i:3472 original size:22 final size:21
Alignment explanation
Indices: 3447--3500 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
3437 GAAGTTCGTG
3447 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
3469 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
3488 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
3501 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:24295 original size:32 final size:32
Alignment explanation
Indices: 24251--24314 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
24241 TTTTTGCAAA
*
24251 TAGTGGCGTTTATTCAGTAAAACGCCACTAAT
1 TAGTGGCATTTATTCAGTAAAACGCCACTAAT
*
24283 TAGTGGCATTTATTGAGTAAAACGCCACTAAT
1 TAGTGGCATTTATTCAGTAAAACGCCACTAAT
24315 CCACTAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (32 bp):
TAGTGGCATTTATTCAGTAAAACGCCACTAAT
Found at i:24345 original size:40 final size:40
Alignment explanation
Indices: 24275--24354 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
24265 CAGTAAAACG
24275 CCACTAATTAGTGGCATTTATTGAGTAAAACGCCACTAAT
1 CCACTAATTAGTGGCATTTATTGAGTAAAACGCCACTAAT
* *
24315 CCACTAATTAGTGGCGTTT-TATGAAG-AAAACGCCCCTAAT
1 CCACTAATTAGTGGCATTTAT-TG-AGTAAAACGCCACTAAT
24355 TTGCAATCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
39 1 0.03
40 33 0.92
41 2 0.06
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (40 bp):
CCACTAATTAGTGGCATTTATTGAGTAAAACGCCACTAAT
Found at i:25107 original size:15 final size:15
Alignment explanation
Indices: 25087--25153 Score: 77
Period size: 15 Copynumber: 4.7 Consensus size: 15
25077 TGAAGTTGGT
25087 GATGATGCAAATGTA
1 GATGATGCAAATGTA
25102 GATGATGCAAATGTA
1 GATGATGCAAATGTA
* **
25117 GGTGAT---TTTGTA
1 GATGATGCAAATGTA
25129 GATGATGCAAATGTA
1 GATGATGCAAATGTA
*
25144 GGTGATGCAA
1 GATGATGCAA
25154 GGGACGAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
12 9 0.21
15 33 0.79
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (15 bp):
GATGATGCAAATGTA
Found at i:25136 original size:27 final size:27
Alignment explanation
Indices: 25098--25149 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
25088 ATGATGCAAA
25098 TGTAGATGATGCAAATGTAGGTGATTT
1 TGTAGATGATGCAAATGTAGGTGATTT
25125 TGTAGATGATGCAAATGTAGGTGAT
1 TGTAGATGATGCAAATGTAGGTGAT
25150 GCAAGGGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (27 bp):
TGTAGATGATGCAAATGTAGGTGATTT
Found at i:26314 original size:33 final size:33
Alignment explanation
Indices: 26197--26319 Score: 142
Period size: 33 Copynumber: 3.7 Consensus size: 33
26187 GCTTGCAAGA
*
26197 ATTGAAGAAGAAAGAAGACAA-GAGCTGGCTCGC
1 ATTGAAGAAGAAAGAAGA-AATGAGCTAGCTCGC
* * * *
26230 ATTGAAGAAGATAGACGACAGGAGCTAGCTCG-
1 ATTGAAGAAGAAAGAAGAAATGAGCTAGCTCGC
*
26262 AGTTGAAGAAGAGAGAAGAAATGAGCTAGCTCGC
1 A-TTGAAGAAGAAAGAAGAAATGAGCTAGCTCGC
* *
26296 CTTGAAGAAGACAGAAGAAATGAG
1 ATTGAAGAAGAAAGAAGAAATGAG
26320 ATTGATCGTT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.03
33 75 0.97
ACGTcount: A:0.42, C:0.13, G:0.31, T:0.14
Consensus pattern (33 bp):
ATTGAAGAAGAAAGAAGAAATGAGCTAGCTCGC
Found at i:27047 original size:32 final size:32
Alignment explanation
Indices: 27011--27162 Score: 198
Period size: 32 Copynumber: 4.8 Consensus size: 32
27001 TTTATTGAAT
* **
27011 AAAACGCCACAAATCAGTGGCGTTCTCTAAAG
1 AAAACGCCACTAATTTGTGGCGTTCTCTAAAG
*
27043 AAAACGCCACTAATTTGTGGCGTTCTTTAAAG
1 AAAACGCCACTAATTTGTGGCGTTCTCTAAAG
*
27075 AAAACGCCACTAATTTGTGGCGTTC-CTGGAAG
1 AAAACGCCACTAATTTGTGGCGTTCTCT-AAAG
* * * *
27107 AAAATGCCACTAATTTGTGGCGTACTTTCAAG
1 AAAACGCCACTAATTTGTGGCGTTCTCTAAAG
*
27139 AAAACGCCACTAATCTGTGGCGTT
1 AAAACGCCACTAATTTGTGGCGTT
27163 TTTCTTTAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
31 1 0.01
32 103 0.98
33 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (32 bp):
AAAACGCCACTAATTTGTGGCGTTCTCTAAAG
Found at i:27095 original size:64 final size:64
Alignment explanation
Indices: 27011--27162 Score: 225
Period size: 64 Copynumber: 2.4 Consensus size: 64
27001 TTTATTGAAT
* * *
27011 AAAACGCCACAAATCAGTGGCGTTCTCT-AAAGAAAACGCCACTAATTTGTGGCGTTCTTTAAAG
1 AAAACGCCACTAATCTGTGGCGTTC-CTGAAAGAAAACGCCACTAATTTGTGGCGTACTTTAAAG
* * * *
27075 AAAACGCCACTAATTTGTGGCGTTCCTGGAAGAAAATGCCACTAATTTGTGGCGTACTTTCAAG
1 AAAACGCCACTAATCTGTGGCGTTCCTGAAAGAAAACGCCACTAATTTGTGGCGTACTTTAAAG
27139 AAAACGCCACTAATCTGTGGCGTT
1 AAAACGCCACTAATCTGTGGCGTT
27163 TTTCTTTAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
63 2 0.03
64 77 0.97
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (64 bp):
AAAACGCCACTAATCTGTGGCGTTCCTGAAAGAAAACGCCACTAATTTGTGGCGTACTTTAAAG
Done.