Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007373.1 Corchorus capsularis cultivar CVL-1 contig07394, 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: 36513
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3890 original size:33 final size:34
Alignment explanation
Indices: 3843--3929 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 34
3833 AGTTTTTGCA
* * **
3843 ATGACACTAAATCTGTTTTAGG-TGTTGTTTGTG
1 ATGAAACTAAATCTGTTTTAGGATGCTAATTGTG
*
3876 ATGAAACTAAATCTGTTTT-GGATGCTAATTGTT
1 ATGAAACTAAATCTGTTTTAGGATGCTAATTGTG
3909 ATGAAAAC-AAATCTGTTTTAG
1 ATG-AAACTAAATCTGTTTTAG
3930 TTAATCATAG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
32 2 0.04
33 39 0.85
34 5 0.11
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (34 bp):
ATGAAACTAAATCTGTTTTAGGATGCTAATTGTG
Found at i:3994 original size:33 final size:33
Alignment explanation
Indices: 3920--4025 Score: 148
Period size: 33 Copynumber: 3.3 Consensus size: 33
3910 TGAAAACAAA
* *
3920 TCTGTTTTAGTTAATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
3953 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
*
3986 TCTGTTTTGGTTG---ATGGCATTG-AAAGTAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAA-TAAT
4016 TCTGTTTTGG
1 TCTGTTTTGG
4026 GTGAAAAGAA
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
29 3 0.04
30 22 0.32
33 44 0.64
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.44
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:4423 original size:30 final size:31
Alignment explanation
Indices: 4383--4446 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
4373 TTCTTCAAGG
4383 GGAAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAAGGGAATGATGCG-CCAAGGACTTATCAT
*
4414 GGAA-GGAATGATGCGCCAAGGACTTATTAT
1 GGAAGGGAATGATGCGCCAAGGACTTATCAT
4444 GGA
1 GGA
4447 CTTGAAGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 6 0.19
30 21 0.68
31 4 0.13
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (31 bp):
GGAAGGGAATGATGCGCCAAGGACTTATCAT
Found at i:7053 original size:29 final size:29
Alignment explanation
Indices: 7021--7080 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
7011 CTGATCTGAG
*
7021 TGTTGTTTGCAATGACACTAAATCTGTTT
1 TGTTGTTTGCAATGAAACTAAATCTGTTT
**
7050 TGTTGTTTGTGATGAAACTAAATCTGTTT
1 TGTTGTTTGCAATGAAACTAAATCTGTTT
7079 TG
1 TG
7081 GATGCTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (29 bp):
TGTTGTTTGCAATGAAACTAAATCTGTTT
Found at i:7142 original size:33 final size:33
Alignment explanation
Indices: 7105--7244 Score: 214
Period size: 33 Copynumber: 4.3 Consensus size: 33
7095 TGAAAACAAA
*
7105 TCTGTTTTGGTTGATCATAGTATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
7138 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
7171 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
* * *
7204 TCTGTTTTTCGTTG---ATGGCATTGAAAATAAT
1 TCTG-TTTTGGTTGATCATAGCATTGCAAATAAT
7235 TCTGTTTTGG
1 TCTGTTTTGG
7245 GTGAAAAGAA
Statistics
Matches: 101, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
30 5 0.05
31 19 0.19
33 69 0.68
34 8 0.08
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:7144 original size:66 final size:66
Alignment explanation
Indices: 7072--7211 Score: 183
Period size: 66 Copynumber: 2.1 Consensus size: 66
7062 TGAAACTAAA
* * * *
7072 TCTGTTTTGGATGCTAATTG-TTATGAAAACAAATCTGTTTTGGTTGATCATAGTATTGCAAATA
1 TCTGTTTTGGATGATAATAGCAT-TGAAAACAAATCTGTTTTGGTTGATCATAGCATTGCAAATA
7136 AT
65 AT
* * * * *
7138 TCTGTTTTGGTTGATCATAGCATTGCAAATAATTCTGTTTTGGTTGATCATAGCATTGCAAATAA
1 TCTGTTTTGGATGATAATAGCATTGAAAACAAATCTGTTTTGGTTGATCATAGCATTGCAAATAA
7203 T
66 T
7204 TCTGTTTT
1 TCTGTTTT
7212 TCGTTGATGG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 63 0.98
67 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (66 bp):
TCTGTTTTGGATGATAATAGCATTGAAAACAAATCTGTTTTGGTTGATCATAGCATTGCAAATAA
T
Found at i:7660 original size:30 final size:30
Alignment explanation
Indices: 7624--7681 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
7614 AAGGGGGAGG
7624 GAATGATGCGCCAAAGG-CTTATCATGGAAT
1 GAATGATGCGCC-AAGGACTTATCATGGAAT
*
7654 GAATGATGCGCCAAGGACTTATTATGGA
1 GAATGATGCGCCAAGGACTTATCATGGA
7682 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.24
Consensus pattern (30 bp):
GAATGATGCGCCAAGGACTTATCATGGAAT
Found at i:8831 original size:273 final size:272
Alignment explanation
Indices: 8340--8877 Score: 925
Period size: 273 Copynumber: 2.0 Consensus size: 272
8330 ATTATCTTAG
* *
8340 CTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTTATAGCAAGCAATTA
1 CTTCATTGTTCTAGTCTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCATAGCAAGCAATTA
*
8405 GGTTGTGATTGCTTAATTGTTTGTGAACCTTGTGACATAGGTGTTCAATTGCAAGTCGAATTGAG
66 GGTTGTGATTGCTTAATTGTTTGTGAACCTTGTGACATAGGTGTTCAACTGCAAGTCGAATTGAG
8470 GGTCTAAGGCCGACGAACGAAGGAGGATTTATCAAGGGAAGATTGTAGACTTACTCATCTAGAAG
131 GGTCTAAGGCCGACGAACGAAGGAGGATTTATCAAGGGAAGATTGTAGACTTACTCATCTAGAAG
* * *
8535 TTTGGTGATTCAAATTTATCTTAGGTGGGTCTCTGAGGTGGATTTGGACCGATATACAACTAGAT
196 TTTGGTGATTCAAATTGATCTTAGGCGGGTCTCTAAGGTGGATTTGGACCGATATACAACTAGAT
8600 TCGTATCAATAA
261 TCGTATCAATAA
*
8612 CTTCATTGTTCTAGTCTGAGCAAACTTAGGGTTCTTCAATCTTGTATG-GTCCTAGCAAGCAATT
1 CTTCATTGTTCTAGTCTGAGCAAACTTAGGGTTCTTCAATCTTGTA-GAGTCATAGCAAGCAATT
* * *
8676 AGGTTGTGATTGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTGTTCAACTGCAGGTCGAATTG
65 AGGTTGTGATTGCTTAATTGTTTGTGAACCTTGTGA-CATAGGTGTTCAACTGCAAGTCGAATTG
* *
8741 AGGGTCTAAGGCCGACGAACGAAGGAGGATTTATCAAGTGAAGATTGTCGACTTACTCATCTAGA
129 AGGGTCTAAGGCCGACGAACGAAGGAGGATTTATCAAGGGAAGATTGTAGACTTACTCATCTAGA
* *
8806 AGTTTGGTGATTCAAGTTGATCTTAGGCGGGTCTCTAAGGTGGATTTGGACTGATATACAACTAG
194 AGTTTGGTGATTCAAATTGATCTTAGGCGGGTCTCTAAGGTGGATTTGGACCGATATACAACTAG
8871 ATTCGTA
259 ATTCGTA
8878 CCAGTTGTAC
Statistics
Matches: 250, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
272 94 0.38
273 156 0.62
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (272 bp):
CTTCATTGTTCTAGTCTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCATAGCAAGCAATTA
GGTTGTGATTGCTTAATTGTTTGTGAACCTTGTGACATAGGTGTTCAACTGCAAGTCGAATTGAG
GGTCTAAGGCCGACGAACGAAGGAGGATTTATCAAGGGAAGATTGTAGACTTACTCATCTAGAAG
TTTGGTGATTCAAATTGATCTTAGGCGGGTCTCTAAGGTGGATTTGGACCGATATACAACTAGAT
TCGTATCAATAA
Found at i:11800 original size:30 final size:30
Alignment explanation
Indices: 11764--11828 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
11754 CATCGGATGC
11764 GCCATCGCATGAGG-CAACCGGCCACAACCG
1 GCCATCGCATG-GGCCAACCGGCCACAACCG
* *
11794 GCCATCGCATGGGCCATCCGGGCACAACCG
1 GCCATCGCATGGGCCAACCGGCCACAACCG
11824 GCCAT
1 GCCAT
11829 TTGACCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.09
Consensus pattern (30 bp):
GCCATCGCATGGGCCAACCGGCCACAACCG
Found at i:21370 original size:15 final size:16
Alignment explanation
Indices: 21344--21374 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
21334 TGGAATCCTA
21344 AAAACAAAAGAAAAAT
1 AAAACAAAAGAAAAAT
21360 AAAAC-AAAGAAAAAT
1 AAAACAAAAGAAAAAT
21375 TAAGGTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAACAAAAGAAAAAT
Found at i:30099 original size:6 final size:6
Alignment explanation
Indices: 30084--30117 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
30074 TGTATTACCG
* *
30084 TCATCA TCATCC TCATCC TCATCG TCATCC TCAT
1 TCATCC TCATCC TCATCC TCATCC TCATCC TCAT
30118 GCGCAAATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.41, G:0.03, T:0.35
Consensus pattern (6 bp):
TCATCC
Found at i:33923 original size:21 final size:21
Alignment explanation
Indices: 33897--33949 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
33887 GCACTGGAGT
33897 ACATGGGTCG-CAAGGAAAACC
1 ACATGGGTCGCCAA-GAAAACC
* *
33918 ACATGGGTCGCCAAGCATACC
1 ACATGGGTCGCCAAGAAAACC
33939 ACATGGG-CGCC
1 ACATGGGTCGCC
33950 CAGCGCTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 22 0.76
22 3 0.10
ACGTcount: A:0.30, C:0.30, G:0.28, T:0.11
Consensus pattern (21 bp):
ACATGGGTCGCCAAGAAAACC
Done.