Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015703.1 Corchorus olitorius cultivar O-4 contig15736, 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: 6302
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:943 original size:15 final size:15
Alignment explanation
Indices: 923--959 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
913 TTATTGTTCA
923 CACCATTGTTATTCG
1 CACCATTGTTATTCG
* *
938 CACCATTGTTGTTTG
1 CACCATTGTTATTCG
953 CACCATT
1 CACCATT
960 CACCCTAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41
Consensus pattern (15 bp):
CACCATTGTTATTCG
Found at i:1883 original size:48 final size:47
Alignment explanation
Indices: 1783--1917 Score: 159
Period size: 48 Copynumber: 2.9 Consensus size: 47
1773 GAGCGTGCCA
* * *
1783 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAACTAAAAG
*
1830 ATCAATTTTGTCTTAAAAATTGAGATAAAGATGCAAGTAAAACT-AAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAACTAAAAG
* *
1878 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGTAAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAA
1918 AGTAAAGGAT
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
46 7 0.09
47 15 0.19
48 44 0.57
49 10 0.13
50 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.29
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAACTAAAAG
Found at i:3222 original size:9 final size:9
Alignment explanation
Indices: 3202--3239 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
3192 TTAATTCATT
3202 TAATTTCC-
1 TAATTTCCA
3210 TAATTTCCA
1 TAATTTCCA
*
3219 TAATTTCCC
1 TAATTTCCA
3228 TAATTTCCA
1 TAATTTCCA
3237 TAA
1 TAA
3240 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:3231 original size:18 final size:17
Alignment explanation
Indices: 3202--3239 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
3192 TTAATTCATT
3202 TAATTTCCTAATTTCCA
1 TAATTTCCTAATTTCCA
3219 TAATTTCCCTAATTTCCA
1 TAATTT-CCTAATTTCCA
3237 TAA
1 TAA
3240 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTTCCTAATTTCCA
Found at i:3993 original size:32 final size:32
Alignment explanation
Indices: 3951--4034 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
3941 CAAATACCTG
* *
3951 AACCCAAAAAAACCCGAACAC-GAAAAAGCTCA
1 AACCCGAAAAAACCCGAAC-CTGAAAAAGCTAA
* * *
3983 AACCCGAAAAAACCAGAACCTGAAAGATCTAA
1 AACCCGAAAAAACCCGAACCTGAAAAAGCTAA
*
4015 AACCCGATAAAACCCGAACC
1 AACCCGAAAAAACCCGAACC
4035 CCAACCAGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 1 0.02
32 43 0.98
ACGTcount: A:0.52, C:0.31, G:0.11, T:0.06
Consensus pattern (32 bp):
AACCCGAAAAAACCCGAACCTGAAAAAGCTAA
Found at i:4002 original size:16 final size:16
Alignment explanation
Indices: 3950--4035 Score: 57
Period size: 16 Copynumber: 5.4 Consensus size: 16
3940 TCAAATACCT
* *
3950 GAACCCAAAAAAACCC
1 GAACCCGAAAAAACCA
* *
3966 GAACACGAAAAAGCTCA
1 GAACCCGAAAAAAC-CA
3983 -AACCCGAAAAAACCA
1 GAACCCGAAAAAACCA
* * * *
3998 GAACCTGAAAGATCTA
1 GAACCCGAAAAAACCA
* * *
4014 AAACCCGATAAAACCC
1 GAACCCGAAAAAACCA
4030 GAACCC
1 GAACCC
4036 CAACCAGAAA
Statistics
Matches: 50, Mismatches: 18, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
15 2 0.04
16 47 0.94
17 1 0.02
ACGTcount: A:0.51, C:0.31, G:0.12, T:0.06
Consensus pattern (16 bp):
GAACCCGAAAAAACCA
Found at i:4269 original size:16 final size:16
Alignment explanation
Indices: 4250--4342 Score: 53
Period size: 16 Copynumber: 5.8 Consensus size: 16
4240 CCCGAATCCG
*
4250 AATTAACCTGACCCAA
1 AATTAACCCGACCCAA
* * **
4266 AATTGACCCGAACCTG
1 AATTAACCCGACCCAA
* *
4282 AATCAACCTGACCCAA
1 AATTAACCCGACCCAA
* *
4298 ATTTAACCCGAACCC-G
1 AATTAACCCG-ACCCAA
* * *
4314 AATCAAGCTGACCCAA
1 AATTAACCCGACCCAA
*
4330 ATTTAACCCGACC
1 AATTAACCCGACC
4343 TTACTCAAAT
Statistics
Matches: 51, Mismatches: 24, Indels: 4
0.65 0.30 0.05
Matches are distributed among these distances:
15 4 0.08
16 43 0.84
17 4 0.08
ACGTcount: A:0.38, C:0.34, G:0.11, T:0.17
Consensus pattern (16 bp):
AATTAACCCGACCCAA
Found at i:4290 original size:32 final size:31
Alignment explanation
Indices: 4238--4340 Score: 143
Period size: 32 Copynumber: 3.2 Consensus size: 31
4228 CCCAGCCTAA
* *
4238 AACCCGAATCCGAATTAACCTGACCCAAAATT
1 AACCCGAA-CCGAATCAACCTGACCCAAATTT
*
4270 GACCCGAACCTGAATCAACCTGACCCAAATTT
1 AACCCGAACC-GAATCAACCTGACCCAAATTT
*
4302 AACCCGAACCCGAATCAAGCTGACCCAAATTT
1 AACCCGAA-CCGAATCAACCTGACCCAAATTT
4334 AACCCGA
1 AACCCGA
4341 CCTTACTCAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
31 2 0.03
32 60 0.94
33 2 0.03
ACGTcount: A:0.38, C:0.34, G:0.12, T:0.17
Consensus pattern (31 bp):
AACCCGAACCGAATCAACCTGACCCAAATTT
Done.