Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015433.1 Corchorus capsularis cultivar CVL-1 contig15454, 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: 5399
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4595 original size:49 final size:49
Alignment explanation
Indices: 4482--4869 Score: 343
Period size: 49 Copynumber: 7.7 Consensus size: 49
4472 AAAATGCAAC
* * **
4482 GCCTTCCGTCCGGGAAGGGGCGTTTTAGGAAA-A-CAAATAAAAATC-GGT
1 GCCTTCCGTCCGGGAA-GGGCGTTTTGGGAAATAGCAGATAAAAA-CAAAT
* *
4530 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAGATGAAAACAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAGATAAAAACAAAT
* * *
4579 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCATATGAAAACAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAGATAAAAACAAAT
* * *
4628 GCCTTCCGTCCGGGAAGGGCATTTT-GGAATATAGCAGGTAAAAACAAAAAAAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAA-ATAGCAGATAAAAAC----AAAT
* * * * * * *
4681 ACCTTCCGTCCGGGAAGAGCATTTTTGGAAAAAAACACAGGTAAAAACAAAT
1 GCCTTCCGTCCGGGAAGGGC-GTTTTGG-GAAATA-GCAGATAAAAACAAAT
* * * * **
4733 GCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATGGCAGGTAAAAGTAAAT
1 GCCTTCCGTCCGGGAAGGGC-GTTTTGGGAAATAGCAGATAAAAACAAAT
* * * **
4783 GCCTTCCGTCCGGGAAGGGCGTTTTTGGAAAACAGCAGGTAAAAGTAAAT
1 GCCTTCCGTCCGGGAAGGGCG-TTTTGGGAAATAGCAGATAAAAACAAAT
* *
4833 GCCTTCCGTCCGGGAAGGGCATTTTTGGAACATAGCA
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAA-ATAGCA
4870 AGTGAAAACT
Statistics
Matches: 294, Mismatches: 32, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
47 14 0.05
48 22 0.07
49 101 0.34
50 84 0.29
51 4 0.01
52 29 0.10
53 20 0.07
54 4 0.01
55 3 0.01
56 13 0.04
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (49 bp):
GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAGATAAAAACAAAT
Found at i:4793 original size:50 final size:50
Alignment explanation
Indices: 4529--4878 Score: 382
Period size: 50 Copynumber: 6.9 Consensus size: 50
4519 TAAAAATCGG
* * * * *
4529 TGCCTTCCGTCCGGGAAGGGC-GTTTTGGGAAATAGCAGATGAAAACAAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAACAAA
* * ** * *
4578 TGCCTTCCGTCCGGGAAGGGC-GTTTTGGGAAATAGCATATGAAAACAAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAACAAA
*
4627 TGCCTTCCGTCCGGGAAGGGCA-TTTTGGAATATAGCAGGTAAAAACAAAAAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAAC----AAA
** * * *
4680 AACCTTCCGTCCGGGAAGAGCATTTTTGGAAAAAAACACAGGTAAAAACAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGG-AAAATA-GCAGGTAAAAACAAA
* **
4732 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATGGCAGGTAAAAGTAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAACAAA
* * **
4782 TGCCTTCCGTCCGGGAAGGGCGTTTTTGGAAAACAGCAGGTAAAAGTAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAACAAA
* * *
4832 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAACATAGCAAGTGAAAAC
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAAC
4879 TGAAAAATGA
Statistics
Matches: 262, Mismatches: 31, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
49 88 0.34
50 99 0.38
51 4 0.02
52 29 0.11
53 21 0.08
54 6 0.02
55 4 0.02
56 11 0.04
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (50 bp):
TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAACAAA
Found at i:4795 original size:102 final size:100
Alignment explanation
Indices: 4529--4869 Score: 361
Period size: 102 Copynumber: 3.4 Consensus size: 100
4519 TAAAAATCGG
* * * * * *
4529 TGCCTTCCGTCCGGGAAGGGC-GTTTTGGGAAATAGCAGATGAAAACAAGTGCCTTCCGTCCGGG
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAAAAAATGCCTTCCGTCCGGG
* * * * * *
4593 AAGGGCGTTTTGGGAAATAGCATA--TGAAAACAAG
66 AAGGGC-TTTTTGGAAAAAACACAGGTAAAAACAAA
* **
4627 TGCCTTCCGTCCGGGAAGGGCA-TTTTGGAATATAGCAGGTAAAAACAAAAAAAAACCTTCCGTC
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGT---AA-AAAAAAATGCCTTCCGTC
*
4691 CGGGAAGAGCATTTTTGGAAAAAAACACAGGTAAAAACAAA
62 CGGGAAGGGC-TTTTTGG-AAAAAACACAGGTAAAAACAAA
* **
4732 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATGGCAGGTAAAAGTAAATGCCTTCCGTCCGGG
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAAAAAATGCCTTCCGTCCGGG
**
4797 AAGGGCGTTTTTGG--AAAACAGCAGGTAAAAGTAAA
66 AAGGGC-TTTTTGGAAAAAACA-CAGGTAAAAACAAA
*
4832 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAACATAGCA
1 TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCA
4870 AGTGAAAACT
Statistics
Matches: 205, Mismatches: 28, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
98 36 0.18
99 6 0.03
100 48 0.23
101 1 0.00
102 59 0.29
103 9 0.04
105 30 0.15
106 16 0.08
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (100 bp):
TGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAAAAAATGCCTTCCGTCCGGG
AAGGGCTTTTTGGAAAAAACACAGGTAAAAACAAA
Done.