Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013059.1 Corchorus olitorius cultivar O-4 contig13092, 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: 37923
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2301 original size:18 final size:19
Alignment explanation
Indices: 2268--2303 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2258 TGCCTATATG
*
2268 ATAAAAAGAAATTGTTTTC
1 ATAAAAAGAAAGTGTTTTC
2287 ATAAAAAG-AAGTGTTTT
1 ATAAAAAGAAAGTGTTTT
2304 TCATGATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (19 bp):
ATAAAAAGAAAGTGTTTTC
Found at i:2773 original size:21 final size:21
Alignment explanation
Indices: 2747--2797 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
2737 TTGGGTTGGG
2747 CCTTGTTTGACTAAGTCCAAT
1 CCTTGTTTGACTAAGTCCAAT
2768 CCTTGTTTGACTAAGTCCAAT
1 CCTTGTTTGACTAAGTCCAAT
2789 CCTTGTTTG
1 CCTTGTTTG
2798 TTATTTTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.41
Consensus pattern (21 bp):
CCTTGTTTGACTAAGTCCAAT
Found at i:6158 original size:21 final size:21
Alignment explanation
Indices: 6132--6180 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
6122 TTGGGTTGGA
6132 CCTTGTTTGACTAAGTCCAAT
1 CCTTGTTTGACTAAGTCCAAT
6153 CCTTGTTTGACTAAGTCCAAT
1 CCTTGTTTGACTAAGTCCAAT
6174 CCTTGTT
1 CCTTGTT
6181 CGTTATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (21 bp):
CCTTGTTTGACTAAGTCCAAT
Found at i:8837 original size:22 final size:22
Alignment explanation
Indices: 8795--8837 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
8785 TTTCTAATTA
**
8795 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
8817 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
8838 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:13935 original size:114 final size:114
Alignment explanation
Indices: 13735--13963 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
13725 CTGGACAAAT
13735 CCTTCTCCCTGCTCCGAAAGGCATCATTTTAATCTCCCTCCTCCCCATTATATCAAACACTTCCA
1 CCTTCTCCCTGCTCCGAAAGGCATCATTTTAATCTCCCTCCTCCCCATTATATCAAACACTTCCA
13800 TCATCATGCTTCCGTCATCATTAATGTTACTTTTCAAGAATCTCTCAGG
66 TCATCATGCTTCCGTCATCATTAATGTTACTTTTCAAGAATCTCTCAGG
13849 CCTTCTCCCTGCTCCGAAAGGCATCATTTTAATCTCCCTCCTCCCCATTATATCAAACACTTCCA
1 CCTTCTCCCTGCTCCGAAAGGCATCATTTTAATCTCCCTCCTCCCCATTATATCAAACACTTCCA
13914 TCATCATGCTTCCGTCATCATTAATGTTACTTTTCAAGAATCTCTCAGG
66 TCATCATGCTTCCGTCATCATTAATGTTACTTTTCAAGAATCTCTCAGG
13963 C
1 C
13964 TTAAATGCCA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.24, C:0.34, G:0.09, T:0.34
Consensus pattern (114 bp):
CCTTCTCCCTGCTCCGAAAGGCATCATTTTAATCTCCCTCCTCCCCATTATATCAAACACTTCCA
TCATCATGCTTCCGTCATCATTAATGTTACTTTTCAAGAATCTCTCAGG
Found at i:27875 original size:16 final size:16
Alignment explanation
Indices: 27851--27885 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27841 GTATTAACGA
*
27851 AAAGCTTAGTATCTTC
1 AAAGCTTAGTATCTGC
*
27867 AAAGTTTAGTATCTGC
1 AAAGCTTAGTATCTGC
27883 AAA
1 AAA
27886 TTAAGTGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (16 bp):
AAAGCTTAGTATCTGC
Found at i:33308 original size:2 final size:2
Alignment explanation
Indices: 33303--33335 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33293 AATTTTTTAT
33303 TA 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 TA T
33336 GAAGGATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35301 original size:21 final size:21
Alignment explanation
Indices: 35199--35301 Score: 66
Period size: 22 Copynumber: 4.6 Consensus size: 21
35189 AGTTAATTAG
**
35199 GTTATCAAAGTTTCTTATGG-A
1 GTTATCAAA-TTTAATATGGTA
*
35220 GTTTATCATAATTTTATATGTACGTA
1 G-TTATCA-AATTTAATATG---GTA
* *
35246 GTTATCAAGATTTCATATGGTG
1 GTTATCAA-ATTTAATATGGTA
35268 GTTATCAAAATTTAATA-GGATA
1 GTTATC-AAATTTAATATGG-TA
35290 GTTATCAAATTT
1 GTTATCAAATTT
35302 TCATAAAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
21 9 0.13
22 35 0.52
23 4 0.06
24 1 0.01
25 16 0.24
26 2 0.03
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.44
Consensus pattern (21 bp):
GTTATCAAATTTAATATGGTA
Found at i:37302 original size:35 final size:35
Alignment explanation
Indices: 37237--37303 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
37227 GATCCTCTTT
* *
37237 GATATTGGAGTTAGTAGGATATTAATGTGTTTGGA
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA
* * *
37272 GATATTGAAGTTAGTGGGGTTTTAAGGTGTTT
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTT
37304 AAACAGTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (35 bp):
GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA
Done.