Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009082.1 Corchorus capsularis cultivar CVL-1 contig09103, 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: 32750
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6361 original size:49 final size:49
Alignment explanation
Indices: 5781--6366 Score: 669
Period size: 49 Copynumber: 11.9 Consensus size: 49
5771 AAAGTGAACT
* * ** * * *
5781 TGCCTTTCGTCCGGAAAGGGCATTTTAAGAAAAAAC-GAGTAAAACT-AA
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAG-GTAAAAATAAA
* * * * * * * *
5829 CGCCTTCCATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAATAAA
* * * * * *
5878 TGCCTTCCGTCCGGGAAGGGCACTCTGGGAAAAAGTAAGTAAAAATAAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAATAAA
* * * * *
5927 CGTCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAAGT-AAAATAAG
1 TGCCTTCCGTCCGGGAAGGGCA-TTTTGGGAAATAGCAGGTAAAAATAAA
* * * * * *
5976 TGCCTTCAGTCCGAGAAGGGCATTTTGGGAAAAAAACAAGT-AAAATAAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGG-AAATAGCAGGTAAAAATAAA
*
6025 TGCCTTCCGTCTGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAATAAA
6074 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAATAAA
* * * * *
6123 TGCCTTCTGTCCGAGAAGGGCATTTTGGGAAATAGTAAGTGAAAAATAAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGT-AAAAATAAA
*
6173 TGCCTTCTGTCCGGGAAAGGGCATTTTGGGAAATAGCAGGTAAAAAATAAA
1 TGCCTTCCGTCCGGG-AAGGGCATTTTGGGAAATAGCAGGT-AAAAATAAA
* *
6224 TGCCTTCCGTCCAGGAAGGGAATTTTGGGAAATAGCAGGTAAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAATAAA
* * *
6273 TGCCTTCTGTCCGGGAAGGACATTTTGGAAAATAGCAGGTAAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAATAAA
*
6322 TGCCTTCCGTCTGGGAAGGGCATTTTGGGAAAT-GACAGGTAAAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAG-CAGGTAAAAA
6367 CTGAAAATTG
Statistics
Matches: 468, Mismatches: 62, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
48 51 0.11
49 314 0.67
50 59 0.13
51 44 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (49 bp):
TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAATAAA
Found at i:8837 original size:21 final size:21
Alignment explanation
Indices: 8811--8853 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
8801 CTAATGTATA
*
8811 TTGGTGACAGGTTCAATTTTG
1 TTGGTGACAAGTTCAATTTTG
8832 TTGGTGACAAGTTCAATTTTG
1 TTGGTGACAAGTTCAATTTTG
8853 T
1 T
8854 AAGAACTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (21 bp):
TTGGTGACAAGTTCAATTTTG
Found at i:15741 original size:150 final size:151
Alignment explanation
Indices: 15544--15850 Score: 499
Period size: 150 Copynumber: 2.0 Consensus size: 151
15534 GGTCAATCAT
* * * *
15544 AATAACCTTTTAACTTAAAATGGTAAAAATAAAATGATTATAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
* * *
15609 AAAATAGAGTTTTTAGTAGAATCAGACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAAT
66 AAAATAGAGCTTTTAGTAGAATCAAACTATATATTAAAAAAAATTAATATATCCAAGTTTTTAAT
*
15674 GTAAAATAGTAAAATGATAAA
131 GAAAAATAGTAAAATGATAAA
* *
15695 AATAAACTTTTAAATTAAAATGAT-ACAATAAAATAATTATAAAAATATTGAATTTAATTGAATG
1 AATAAACTTTTAAATTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
15759 AAAATAGAGCTTTTAGTAGAATCAAACTATATATTAAAAAAAATTAATATATCCAAGTTTTTAAT
66 AAAATAGAGCTTTTAGTAGAATCAAACTATATATTAAAAAAAATTAATATATCCAAGTTTTTAAT
* *
15824 GAAAAATTGTAAAATGGTAAA
131 GAAAAATAGTAAAATGATAAA
15845 AATAAA
1 AATAAA
15851 GTAATTATAA
Statistics
Matches: 144, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
150 123 0.85
151 21 0.15
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (151 bp):
AATAAACTTTTAAATTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
AAAATAGAGCTTTTAGTAGAATCAAACTATATATTAAAAAAAATTAATATATCCAAGTTTTTAAT
GAAAAATAGTAAAATGATAAA
Found at i:17096 original size:151 final size:151
Alignment explanation
Indices: 16928--17221 Score: 489
Period size: 151 Copynumber: 1.9 Consensus size: 151
16918 ATAACCTAAC
* *
16928 TTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTT
1 TTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGCTTTT
* *
16993 AGTAGAATCAGACTATATATTAAAAAATTTTAATATATCAAAGTTTTTAATGAAAAATAGTAAAA
66 AGTAGAATCAAACTATATATTAAAAAAATTTAATATATCAAAGTTTTTAATGAAAAATAGTAAAA
*
17058 TGATGAAAATAAACTTTTAAA
131 TGATAAAAATAAACTTTTAAA
* * *
17079 TTAAAATGATAACAATAAAATAATTATAAAAATGTTGAATTTAATTGAATGAAAATAGAGCTTTT
1 TTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGCTTTT
* *
17144 AGTAGAATTAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAATGAAAAATAGTAAAA
66 AGTAGAATCAAACTATATATTAAAAAAATTTAATATATCAAAGTTTTTAATGAAAAATAGTAAAA
*
17209 TGGTAAAAATAAA
131 TGATAAAAATAAA
17222 GTAATTATAA
Statistics
Matches: 132, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
151 132 1.00
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.34
Consensus pattern (151 bp):
TTAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGCTTTT
AGTAGAATCAAACTATATATTAAAAAAATTTAATATATCAAAGTTTTTAATGAAAAATAGTAAAA
TGATAAAAATAAACTTTTAAA
Found at i:26091 original size:2 final size:2
Alignment explanation
Indices: 26084--26111 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26074 GTTTTGTTTG
26084 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
26112 CCTGTTTTTT
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:28626 original size:22 final size:22
Alignment explanation
Indices: 28601--28649 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28591 GCGCTTTAAA
*
28601 TACATAATTGCAGCACATTTAT
1 TACATAATTGCAACACATTTAT
* *
28623 TACATGATTGCAACATATTTAT
1 TACATAATTGCAACACATTTAT
28645 TACAT
1 TACAT
28650 TTTATTTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (22 bp):
TACATAATTGCAACACATTTAT
Found at i:28936 original size:24 final size:24
Alignment explanation
Indices: 28908--28958 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
28898 AGCAGCAGCA
*
28908 TTGTCAAATATTCTCCCTGGTATG
1 TTGTCAAATATTCTCACTGGTATG
*
28932 TTGTCAAATATTCTTACTGGTATG
1 TTGTCAAATATTCTCACTGGTATG
28956 TTG
1 TTG
28959 GCTTCTATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.45
Consensus pattern (24 bp):
TTGTCAAATATTCTCACTGGTATG
Done.