Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011485.1 Corchorus capsularis cultivar CVL-1 contig11506, 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: 36128
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:13015 original size:139 final size:139
Alignment explanation
Indices: 12792--13072 Score: 562
Period size: 139 Copynumber: 2.0 Consensus size: 139
12782 CAACACATGT
12792 ATGCTTGCTAAAATCACAAGGAAATCCTTTCCTAAGGTACAAAGAAATTCTAAATTGCTTGAATT
1 ATGCTTGCTAAAATCACAAGGAAATCCTTTCCTAAGGTACAAAGAAATTCTAAATTGCTTGAATT
12857 GATACATAGTGATTTATGTGACATGCATTCAACACCTACCATGTCTGGAAAGAAATATTTTGTCA
66 GATACATAGTGATTTATGTGACATGCATTCAACACCTACCATGTCTGGAAAGAAATATTTTGTCA
12922 CATTTATTG
131 CATTTATTG
12931 ATGCTTGCTAAAATCACAAGGAAATCCTTTCCTAAGGTACAAAGAAATTCTAAATTGCTTGAATT
1 ATGCTTGCTAAAATCACAAGGAAATCCTTTCCTAAGGTACAAAGAAATTCTAAATTGCTTGAATT
12996 GATACATAGTGATTTATGTGACATGCATTCAACACCTACCATGTCTGGAAAGAAATATTTTGTCA
66 GATACATAGTGATTTATGTGACATGCATTCAACACCTACCATGTCTGGAAAGAAATATTTTGTCA
13061 CATTTATTG
131 CATTTATTG
13070 ATG
1 ATG
13073 ATGCAACAAA
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 142 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (139 bp):
ATGCTTGCTAAAATCACAAGGAAATCCTTTCCTAAGGTACAAAGAAATTCTAAATTGCTTGAATT
GATACATAGTGATTTATGTGACATGCATTCAACACCTACCATGTCTGGAAAGAAATATTTTGTCA
CATTTATTG
Found at i:13876 original size:33 final size:33
Alignment explanation
Indices: 13834--13915 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
13824 AATTTGGTCT
13834 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
*
13867 AGCCGCCCCAGTGGGGCGGCCTGCTCATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
13900 AGCCGCCCCAGTGGGG
1 AGCCGCCCCAGTGGGG
13916 AGGCTCCGCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.12, C:0.35, G:0.40, T:0.12
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
Found at i:13937 original size:33 final size:33
Alignment explanation
Indices: 13834--13987 Score: 145
Period size: 33 Copynumber: 4.7 Consensus size: 33
13824 AATTTGGTCT
* *
13834 AGCCGCCCCAGTGGGGCGGC-CTGCCCATGGTGA
1 AGCCGCCCCAGTGGGGAGGCTCCG-CCATGGTGA
* *
13867 AGCCGCCCCAGTGGGGCGGC-CTGCTCATGGTGA
1 AGCCGCCCCAGTGGGGAGGCTCCGC-CATGGTGA
*
13900 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGGTTG-
1 AGCCGCCCCAGTGGGGAGGCTCCGCCATGG-TGA
* * * *
13933 AGCCGTCCTAGTGGGGAAGCTCCGCCGTGGCTG-
1 AGCCGCCCCAGTGGGGAGGCTCCGCCATGG-TGA
* *
13966 AGCCGTCCTAGTGGGGAGGCTC
1 AGCCGCCCCAGTGGGGAGGCTC
13988 AGTGTAAAAG
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
32 1 0.01
33 104 0.95
34 5 0.05
ACGTcount: A:0.12, C:0.32, G:0.40, T:0.16
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGAGGCTCCGCCATGGTGA
Found at i:18185 original size:2 final size:2
Alignment explanation
Indices: 18178--18205 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18168 TAAAACAATA
18178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18206 TGGAAGCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19137 original size:2 final size:2
Alignment explanation
Indices: 19130--19157 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19120 AGATGCAAAC
19130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19158 GTCCTAGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22714 original size:3 final size:3
Alignment explanation
Indices: 22708--22756 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
22698 GATGATGATC
* *
22708 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
22756 A
1 A
22757 AAGATGGGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:23684 original size:22 final size:22
Alignment explanation
Indices: 23656--23702 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
23646 ATTTATTCAT
23656 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
23678 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
23700 TAT
1 TAT
23703 AGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:23698 original size:11 final size:11
Alignment explanation
Indices: 23656--23698 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
23646 ATTTATTCAT
*
23656 TATTAATTAAC
1 TATTAATTAGC
*
23667 TATTAATTAGA
1 TATTAATTAGC
23678 TATTAATTAGC
1 TATTAATTAGC
23689 TATTAATTAG
1 TATTAATTAG
23699 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:29587 original size:49 final size:46
Alignment explanation
Indices: 29534--29792 Score: 171
Period size: 49 Copynumber: 5.3 Consensus size: 46
29524 CTTTGTCCGA
* * *
29534 AAGGGCATTTCGGGAACAACAAGTAAGAGAATGGTGCCTTCCGTCCGGG
1 AAGGGCATTTTGGGAA-AACAGGTAA-A-AATAGTGCCTTCCGTCCGGG
* * * *
29583 AAGGGCGTTTTAGGAAAAACAGGTAAAAATTAGTGCCTTCGGTCTGGG
1 AAGGGCATTTT-GGGAAAACAGGTAAAAA-TAGTGCCTTCCGTCCGGG
* * *
29631 GAGGGCATTTTGGGAGAAACAGGTAATAATCAGTGCCTTTCGTCCGGG
1 AAGGGCATTTTGGGA-AAACAGGTAAAAAT-AGTGCCTTCCGTCCGGG
* * * **
29679 AAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAACG-GCC-TCCGTCTAGG
1 AAGGGCATTTTGGGAAA-A-CAGGTAAA-A-ATA-GTGCCTTCCGTCCGGG
* * * * * * *
29728 AAGGGCGTTTTGGGAAATAGCAAGCAAAAACAAATGGCTTCCGTCTGGG
1 AAGGGCATTTTGGGAAA-A-CAGGTAAAAA-TAGTGCCTTCCGTCCGGG
29777 AAGGGCATTTTGGGAA
1 AAGGGCATTTTGGGAA
29793 GTAACAAGTG
Statistics
Matches: 171, Mismatches: 27, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
47 9 0.05
48 70 0.41
49 81 0.47
50 9 0.05
51 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (46 bp):
AAGGGCATTTTGGGAAAACAGGTAAAAATAGTGCCTTCCGTCCGGG
Found at i:29619 original size:48 final size:48
Alignment explanation
Indices: 29567--29792 Score: 188
Period size: 48 Copynumber: 4.7 Consensus size: 48
29557 TAAGAGAATG
* *
29567 GTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTAAAAATTA
1 GTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTAAAAATCA
* * * * * *
29615 GTGCCTTCGGTCTGGGGAGGGCATTTTGGGAGAAACAGGTAATAATCA
1 GTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTAAAAATCA
* * * * *
29663 GTGCCTTTCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAA
1 GTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAA-AACAGGTAAAAAT-CA
** * * *
29713 CG-GCC-TCCGTCTAGGAAGGGCGTTTTGGGAAATAGCAAGCAAAAA-CAA
1 -GTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAA-AACAGGTAAAAATC-A
* * * *
29761 ATGGCTTCCGTCTGGGAAGGGCATTTTGGGAA
1 GTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAA
29793 GTAACAAGTG
Statistics
Matches: 143, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
48 70 0.49
49 68 0.48
50 4 0.03
51 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.23
Consensus pattern (48 bp):
GTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTAAAAATCA
Found at i:32591 original size:23 final size:23
Alignment explanation
Indices: 32561--32609 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
32551 AAAGGAACGG
*
32561 ATTTACTTAAAAATAAACTATGA
1 ATTTACTTAAAAATAAACTACGA
*
32584 ATTTACTTAAAAATGAACTACGA
1 ATTTACTTAAAAATAAACTACGA
32607 ATT
1 ATT
32610 GACCAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (23 bp):
ATTTACTTAAAAATAAACTACGA
Found at i:34925 original size:5 final size:5
Alignment explanation
Indices: 34912--34964 Score: 79
Period size: 5 Copynumber: 10.6 Consensus size: 5
34902 TCGTCTGTAC
* * *
34912 CATAT CATAA CATAA CATAA CTTAA CATAA CATAA CATAA CATAA CGTAA
1 CATAA CATAA CATAA CATAA CATAA CATAA CATAA CATAA CATAA CATAA
34962 CAT
1 CAT
34965 CATATTAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.53, C:0.21, G:0.02, T:0.25
Consensus pattern (5 bp):
CATAA
Done.