Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007695.1 Corchorus capsularis cultivar CVL-1 contig07716, 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: 28564
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Found at i:3038 original size:27 final size:27
Alignment explanation
Indices: 2998--3067 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
2988 CTGAATGTGC
* *
2998 AAAATGACCAAAATGCCCCTTAGTCTA
1 AAAATGACCAAAATGCCCCTAAATCTA
* * *
3025 AGAATGACCAAAATACCCCTAAATGTA
1 AAAATGACCAAAATGCCCCTAAATCTA
*
3052 AAAAAGACCAAAATGC
1 AAAATGACCAAAATGC
3068 TAATTCGACC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.49, C:0.23, G:0.11, T:0.17
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAATCTA
Found at i:6816 original size:64 final size:63
Alignment explanation
Indices: 6673--6829 Score: 206
Period size: 64 Copynumber: 2.5 Consensus size: 63
6663 GATAAAACTG
* * * **
6673 ACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAAACTTAAATGCAGGAATGTGACGAAACTG
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAAACCTAAATGCAAGAATGTGACAAAACCA
* * * **
6736 GCCCTTTGTTCAAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGAATGTGACAAAACCA
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTA-AACCTAAATGCAAGAATGTGACAAAACCA
*
6800 ACCCTTGGTCCGAAAGGGTATTTTGGGAAA
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAA
6830 TAGCAAGTAA
Statistics
Matches: 77, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
63 29 0.38
64 48 0.62
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (63 bp):
ACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAAACCTAAATGCAAGAATGTGACAAAACCA
Found at i:6939 original size:49 final size:49
Alignment explanation
Indices: 6813--7170 Score: 519
Period size: 49 Copynumber: 7.4 Consensus size: 49
6803 CTTGGTCCGA
* * ** * *
6813 AAGGGTATTTTGGGAAATAGCA-AGT-AAAATAAGTATCTTTCGTCCAGG
1 AAGGGCATTTTGGGAAATAGCAGA-TAAAAACAAGTGCCTTCCGTCCGGG
*
6861 AAGGGAATTTT-GGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
6909 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
**
6958 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGTTTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
* *
7007 AAGGGCATTTTGGGAAATAACAGATAAAAACAAGTACCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
*
7056 AAGGGCATTTTGGGAAATAGCAGATAAAAACAGGTGCCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
* *
7105 AAGGGCATTTTGGGAAATAACAGATGAAAAA-AA-TGCCTTCCATCCGGG
1 AAGGGCATTTTGGGAAATAGCAGAT-AAAAACAAGTGCCTTCCGTCCGGG
* *
7153 AAGGGTATTTTGGAAAAT
1 AAGGGCATTTTGGGAAAT
7171 GTAAAGTTTG
Statistics
Matches: 285, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
47 11 0.04
48 69 0.24
49 200 0.70
50 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (49 bp):
AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
Found at i:12649 original size:13 final size:13
Alignment explanation
Indices: 12631--12665 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
12621 ATAATTATTG
12631 TTTGCTTTATTAA
1 TTTGCTTTATTAA
12644 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
12657 TCTGCTTTA
1 TTTGCTTTA
12666 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:12673 original size:6 final size:6
Alignment explanation
Indices: 12662--12688 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12652 ATTAATCTGC
12662 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
12689 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:13023 original size:33 final size:35
Alignment explanation
Indices: 12977--13049 Score: 114
Period size: 33 Copynumber: 2.1 Consensus size: 35
12967 TAGTTTTTGT
*
12977 TTTTTCCGTTTTTTCTATAAAAAAA-AGTTTTCC-
1 TTTTTCCGATTTTTCTATAAAAAAATAGTTTTCCG
*
13010 TTTTTCCGATTTTTCTATAAAAAAATATTTTTCCG
1 TTTTTCCGATTTTTCTATAAAAAAATAGTTTTCCG
13045 TTTTT
1 TTTTT
13050 AATTTTAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 24 0.67
34 7 0.19
35 5 0.14
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.55
Consensus pattern (35 bp):
TTTTTCCGATTTTTCTATAAAAAAATAGTTTTCCG
Found at i:18183 original size:11 final size:11
Alignment explanation
Indices: 18167--18191 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18157 GATTGAAGCC
18167 AAGTCCAGAAG
1 AAGTCCAGAAG
18178 AAGTCCAGAAG
1 AAGTCCAGAAG
18189 AAG
1 AAG
18192 CCCGAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.28, T:0.08
Consensus pattern (11 bp):
AAGTCCAGAAG
Found at i:18234 original size:10 final size:10
Alignment explanation
Indices: 18219--18244 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
18209 AGTTGCTGCC
18219 AAATTCCAGA
1 AAATTCCAGA
18229 AAATTCCAGA
1 AAATTCCAGA
18239 AAATTC
1 AAATTC
18245 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:19175 original size:13 final size:13
Alignment explanation
Indices: 19157--19191 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
19147 ATAATTATTG
19157 TTTGCTTTATTAA
1 TTTGCTTTATTAA
19170 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
19183 TCTGCTTTA
1 TTTGCTTTA
19192 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:19199 original size:6 final size:6
Alignment explanation
Indices: 19188--19214 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19178 ATTAATCTGC
19188 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
19215 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:27925 original size:20 final size:20
Alignment explanation
Indices: 27886--27925 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27876 CATCATTCGA
*
27886 ATTACATCATTCAAATTTTG
1 ATTACATCATCCAAATTTTG
27906 ATTACATCA-CCAAATATTTG
1 ATTACATCATCCAAAT-TTTG
27926 TCTGTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (20 bp):
ATTACATCATCCAAATTTTG
Done.