Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017667.1 Corchorus olitorius cultivar O-4 contig17700, 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: 35302
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1407 original size:16 final size:17
Alignment explanation
Indices: 1388--1420 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1378 CACAAAAAAT
1388 AAAAACAAGAA-AAGAA
1 AAAAACAAGAAGAAGAA
*
1404 AAAAAGAAGAAGAAGAA
1 AAAAACAAGAAGAAGAA
1421 GGGGCTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAACAAGAAGAAGAA
Found at i:7624 original size:66 final size:66
Alignment explanation
Indices: 7540--7917 Score: 461
Period size: 66 Copynumber: 5.7 Consensus size: 66
7530 CAGAGATGGT
** * * *
7540 GATGGCGGAGAAAGACACAATGCATTTGCCGGTTTTGAGAAAAGCCCAGATTTGAAGGAGTCACG
1 GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCAAG
7605 G
66 G
* * * * *
7606 GATGGTGCAGAAAGACACAATGCATTTGGGAGTTTTGAGAAAAACCCAGATTTCAAGGAGTCAAT
1 GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCAAG
7671 G
66 G
*
7672 GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCAAT
1 GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCAAG
7737 G
66 G
* * *
7738 GATGGCGGAGAAAGACATAATGCATTTGGGGGTTTTGAGAAAACCCCATATTTCAAGGAGTCACG
1 GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCAAG
7803 G
66 G
** * * * * * *** * * *
7804 GATCCCGGGGAAAGATAAAATGCATCTGGGGGTTTTGATAAAAGGACAGAATTCAAGGGGTCAAA
1 GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCAAG
*
7869 T
66 G
* * *
7870 GAT-GCTGGAGAAAGACACAATGCATTTGGGAGTTTTCACAAAACCCCA
1 GATGGC-GGAGAAAGACACAATGCATTTGGGGGTTTTGAGAAAACCCCA
7918 ATGAAGCAGG
Statistics
Matches: 267, Mismatches: 44, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
65 1 0.00
66 266 1.00
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.21
Consensus pattern (66 bp):
GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCAAG
G
Found at i:7882 original size:198 final size:198
Alignment explanation
Indices: 7540--7917 Score: 508
Period size: 198 Copynumber: 1.9 Consensus size: 198
7530 CAGAGATGGT
* *
7540 GATGGCGGAGAAAGACACAATGCATTTGCCGGTTTTGAGAAAAGCCCAGATTTGAAGGAGTCACG
1 GATGGCGGAGAAAGACACAATGCATTTGCCGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCACG
*** * * * *
7605 GGATGGTGCAGAAAGACACAATGCATTTGGGAGTTTTGAGAAAAACCCAGATTTCAAGGAGTCAA
66 GGATCCCGCAGAAAGACAAAATGCATCTGGGAGTTTTGAGAAAAACACAGAATTCAAGGAGTCAA
* * *
7670 TGGATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCA
131 TGGATGGCGGAGAAAGACACAATGCATTTGGGAGTTTTCACAAAACCCCAGATTTCAAGGAGTCA
7735 ATG
196 ATG
* ** *
7738 GATGGCGGAGAAAGACATAATGCATTTGGGGGTTTTGAGAAAACCCCATATTTCAAGGAGTCACG
1 GATGGCGGAGAAAGACACAATGCATTTGCCGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCACG
** * * * ** *
7803 GGATCCCGGGGAAAGATAAAATGCATCTGGGGGTTTTGATAAAAGGACAGAATTCAAGGGGTCAA
66 GGATCCCGCAGAAAGACAAAATGCATCTGGGAGTTTTGAGAAAAACACAGAATTCAAGGAGTC-A
7868 AT-GAT-GCTGGAGAAAGACACAATGCATTTGGGAGTTTTCACAAAACCCCA
130 ATGGATGGC-GGAGAAAGACACAATGCATTTGGGAGTTTTCACAAAACCCCA
7918 ATGAAGCAGG
Statistics
Matches: 154, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
197 2 0.01
198 149 0.97
199 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.21
Consensus pattern (198 bp):
GATGGCGGAGAAAGACACAATGCATTTGCCGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCACG
GGATCCCGCAGAAAGACAAAATGCATCTGGGAGTTTTGAGAAAAACACAGAATTCAAGGAGTCAA
TGGATGGCGGAGAAAGACACAATGCATTTGGGAGTTTTCACAAAACCCCAGATTTCAAGGAGTCA
ATG
Found at i:11908 original size:16 final size:16
Alignment explanation
Indices: 11887--11922 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
11877 TCATTGCTGT
11887 CTCCCTTTTCCCTTTG
1 CTCCCTTTTCCCTTTG
11903 CTCCCTTTTCCCTTTG
1 CTCCCTTTTCCCTTTG
11919 CTCC
1 CTCC
11923 ACATGTAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.06, T:0.47
Consensus pattern (16 bp):
CTCCCTTTTCCCTTTG
Found at i:12860 original size:36 final size:36
Alignment explanation
Indices: 12788--12860 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
12778 CAATATCGAA
*
12788 GGAAATACTTGTACTTGCCTAATTTATACTGGTTCT
1 GGAAATACTTGTACTTGCCTAATTTATACTGATTCT
* *
12824 GGAAATACTTGTAGTTGCCTAATTTATACTTATTCT
1 GGAAATACTTGTACTTGCCTAATTTATACTGATTCT
12860 G
1 G
12861 CCATGGTGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.42
Consensus pattern (36 bp):
GGAAATACTTGTACTTGCCTAATTTATACTGATTCT
Found at i:14205 original size:16 final size:16
Alignment explanation
Indices: 14180--14213 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14170 GGTTCATCAC
*
14180 CTCACTAGCTCGGCCT
1 CTCACAAGCTCGGCCT
*
14196 CTCACAAGCTGGGCCT
1 CTCACAAGCTCGGCCT
14212 CT
1 CT
14214 ACTAGGTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.41, G:0.21, T:0.24
Consensus pattern (16 bp):
CTCACAAGCTCGGCCT
Found at i:16952 original size:2 final size:2
Alignment explanation
Indices: 16945--16975 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16935 TGAAAACTAT
16945 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16976 GGTGTCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17529 original size:21 final size:21
Alignment explanation
Indices: 17503--17548 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
17493 TGTATAATTG
17503 CCATCATATTAGTGTTTGGAC
1 CCATCATATTAGTGTTTGGAC
17524 CCATCATATTAGTGTTTGGAC
1 CCATCATATTAGTGTTTGGAC
17545 CCAT
1 CCAT
17549 TGATGACGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (21 bp):
CCATCATATTAGTGTTTGGAC
Found at i:17784 original size:16 final size:15
Alignment explanation
Indices: 17765--17794 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17755 TATAAATTAT
17765 ATAAATATAAATAAAA
1 ATAAATAT-AATAAAA
17781 ATAAATATAATAAA
1 ATAAATATAATAAA
17795 TCCAACATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAATATAATAAAA
Found at i:17788 original size:22 final size:22
Alignment explanation
Indices: 17741--17790 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
17731 TCAACATGCT
* * *
17741 ATATAAATATATATTATAAATT
1 ATATAAATATATAATAAAAATA
17763 ATATAAATATA-AATAAAAATAA
1 ATATAAATATATAATAAAAAT-A
17785 ATATAA
1 ATATAA
17791 TAAATCCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATAAATATATAATAAAAATA
Found at i:26170 original size:19 final size:19
Alignment explanation
Indices: 26146--26182 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
26136 TTGGTTAAAA
26146 AAAGGCAAGTCATAATATT
1 AAAGGCAAGTCATAATATT
26165 AAAGGCAAGTCATAATAT
1 AAAGGCAAGTCATAATAT
26183 AAGCTGACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (19 bp):
AAAGGCAAGTCATAATATT
Found at i:29192 original size:16 final size:16
Alignment explanation
Indices: 29171--29202 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29161 CAATATCTGA
29171 AAATATGTAGATATAT
1 AAATATGTAGATATAT
*
29187 AAATATGTAGTTATAT
1 AAATATGTAGATATAT
29203 TTTGTGAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (16 bp):
AAATATGTAGATATAT
Found at i:30922 original size:29 final size:29
Alignment explanation
Indices: 30888--30945 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
30878 AAGGACCTGA
30888 TTAGTTTAATAATCATATATTCTTTTTTT
1 TTAGTTTAATAATCATATATTCTTTTTTT
30917 TTAGTTTAATAATCATATATTCTTTTTTT
1 TTAGTTTAATAATCATATATTCTTTTTTT
30946 AGTTTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (29 bp):
TTAGTTTAATAATCATATATTCTTTTTTT
Found at i:35264 original size:2 final size:2
Alignment explanation
Indices: 35259--35301 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
35249 AATGTGTGTG
35259 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
35301 T
1 T
35302 G
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.