Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017530.1 Corchorus olitorius cultivar O-4 contig17563, 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: 36363
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:6592 original size:5 final size:5
Alignment explanation
Indices: 6582--6642 Score: 122
Period size: 5 Copynumber: 12.2 Consensus size: 5
6572 TCTTGAAGAA
6582 ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG
1 ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG
6632 ATGGG ATGGG A
1 ATGGG ATGGG A
6643 CGAGAATGTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.21, C:0.00, G:0.59, T:0.20
Consensus pattern (5 bp):
ATGGG
Found at i:7913 original size:3 final size:3
Alignment explanation
Indices: 7900--7933 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
7890 CGAAGGTTGT
*
7900 TGA TGA AGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
7934 TGTGTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:8979 original size:58 final size:58
Alignment explanation
Indices: 8889--9004 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
8879 TTCTGTCGTG
*
8889 TGGTATTAGGGGCATTAACTTGCTGATTGTATGCTAGTTAGTATATTATGTTTAACCT
1 TGGTATTAGGGGCATTAACTTGCTGATTGTATGCTAGTTAATATATTATGTTTAACCT
* *
8947 TGGTATTAGGGGCATTCACTTGCTGATTGTATGCTTGTTAATATATTATGTTTAACCT
1 TGGTATTAGGGGCATTAACTTGCTGATTGTATGCTAGTTAATATATTATGTTTAACCT
9005 CTGTCTCCGT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.44
Consensus pattern (58 bp):
TGGTATTAGGGGCATTAACTTGCTGATTGTATGCTAGTTAATATATTATGTTTAACCT
Found at i:15307 original size:30 final size:30
Alignment explanation
Indices: 15271--15327 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
15261 TTAGTAAGAT
15271 ATTAAAATTTGAGGGTATAAGAGGAAAATC
1 ATTAAAATTTGAGGGTATAAGAGGAAAATC
*
15301 ATTAAAATTTGATGGTATAAGAGGAAA
1 ATTAAAATTTGAGGGTATAAGAGGAAA
15328 GTCAAGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.23, T:0.28
Consensus pattern (30 bp):
ATTAAAATTTGAGGGTATAAGAGGAAAATC
Found at i:17232 original size:22 final size:22
Alignment explanation
Indices: 17202--17247 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
17192 TTTTAGTTTA
*
17202 TAATATTCTTGGATCATCCGGGT
1 TAATATTCTCGG-TCATCCGGGT
*
17225 TAAT-TTCTCGGTTATCCGGGT
1 TAATATTCTCGGTCATCCGGGT
17246 TA
1 TA
17248 CGAGATTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 6 0.29
23 4 0.19
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (22 bp):
TAATATTCTCGGTCATCCGGGT
Found at i:20226 original size:15 final size:15
Alignment explanation
Indices: 20204--20241 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
20194 TGCTAGGGTG
20204 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
*
20219 ATTGGTGCAAACAAC
1 AATGGTGCAAACAAC
20234 AATGGTGC
1 AATGGTGC
20242 GGATGACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:34192 original size:49 final size:48
Alignment explanation
Indices: 34093--34224 Score: 142
Period size: 49 Copynumber: 2.7 Consensus size: 48
34083 CATTTTTACT
* *
34093 GCACTCTTATTCTCAATTTTTACAACAAAAATTGAACTTTTAATTTTCCTC
1 GCAC-CTTTTTCTCAATTTTTGC-AC-AAAATTGAACTTTTAATTTTCCTC
*
34144 GCACCTTTTTCTCAATTTTTGCATCAAAATTGAA-TATTTACTTTTCCTC
1 GCACCTTTTTCTCAATTTTTGCA-CAAAATTGAACT-TTTAATTTTCCTC
* * *
34193 GCATCC-TTTTATCAATTTCTGGACAAAATTGA
1 GCA-CCTTTTTCTCAATTTTTGCACAAAATTGA
34225 TTGGCACGCT
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
48 10 0.14
49 39 0.54
50 19 0.26
51 4 0.06
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (48 bp):
GCACCTTTTTCTCAATTTTTGCACAAAATTGAACTTTTAATTTTCCTC
Found at i:35567 original size:42 final size:43
Alignment explanation
Indices: 35516--35609 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
35506 AGTGCATTAC
*
35516 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCACTAGGTAATTCATCAAAATAAAG
35557 CTAATATTCTACTCCTCCATCACTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCACTAGGTAATTCATCAAAATAAAG
35602 CTAATATT
1 CTAATATT
35610 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.33
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCACTAGGTAATTCATCAAAATAAAG
Done.