Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013577.1 Corchorus capsularis cultivar CVL-1 contig13598, 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: 22815
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3421 original size:29 final size:30
Alignment explanation
Indices: 3366--3426 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
3356 ATATTTATCT
* *
3366 TATAATAGGTAGTTTTTTTTCTAAAATTGG
1 TATAATAGGTAGTTTTTTATCTAAAATGGG
3396 TATAAT-GAGTAG-TTTTTATCTAAAATGGG
1 TATAATAG-GTAGTTTTTTATCTAAAATGGG
3425 TA
1 TA
3427 GTTTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (30 bp):
TATAATAGGTAGTTTTTTATCTAAAATGGG
Found at i:4208 original size:23 final size:23
Alignment explanation
Indices: 4181--4226 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4171 TATCTATAGT
* *
4181 AATAAGAATAACTATATAGATTA
1 AATAAGAATAACTACAAAGATTA
*
4204 AATAATAATAACTACAAAGATTA
1 AATAAGAATAACTACAAAGATTA
4227 TGATATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (23 bp):
AATAAGAATAACTACAAAGATTA
Found at i:10075 original size:14 final size:14
Alignment explanation
Indices: 10053--10083 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10043 TTAATAAGTG
*
10053 AATTTAACTAAATT
1 AATTAAACTAAATT
10067 AATTAAACTAAATT
1 AATTAAACTAAATT
10081 AAT
1 AAT
10084 AAATGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTAAACTAAATT
Found at i:10303 original size:27 final size:27
Alignment explanation
Indices: 10265--10326 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
10255 GTATAATCCT
*
10265 CAGCCCCATCATAATAACCCGGTTGAG
1 CAGCCCCATCATAATAACCCGGCTGAG
*
10292 CAGCCCCATCATAGTAACCCGGCTGAG
1 CAGCCCCATCATAATAACCCGGCTGAG
*
10319 CAACCCCA
1 CAGCCCCA
10327 GCCCCAACCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.29, C:0.39, G:0.18, T:0.15
Consensus pattern (27 bp):
CAGCCCCATCATAATAACCCGGCTGAG
Found at i:10804 original size:15 final size:18
Alignment explanation
Indices: 10784--10820 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10774 CCTAAAACTA
10784 AATTAAT-TT-AA-TAAT
1 AATTAATATTAAATTAAT
10799 AATTAATATTAAATTAAT
1 AATTAATATTAAATTAAT
10817 AATT
1 AATT
10821 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 2 0.11
17 2 0.11
18 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTAATATTAAATTAAT
Found at i:10990 original size:32 final size:32
Alignment explanation
Indices: 10848--10995 Score: 106
Period size: 32 Copynumber: 4.6 Consensus size: 32
10838 GGACGGCACA
* * *
10848 GCCGTGGCCAAGCCG-CCCTAGTGGGGCGGCAT
1 GCCGTGGCGAAGCCGCCCCAAG-AGGGCGGCAT
* * * * *
10880 GCCATGGC-AAGGCCACCCC-AGGGGTGCGACTT
1 GCCGTGGCGAA-GCCGCCCCAAGAGG-GCGGCAT
*
10912 GCCGTGGCAAAGCCGCCCCAAGAGGGCGGCAT
1 GCCGTGGCGAAGCCGCCCCAAGAGGGCGGCAT
* * *
10944 GCCGTGTCGAAGCCGCGCCAGGAGGGCGGCAT
1 GCCGTGGCGAAGCCGCCCCAAGAGGGCGGCAT
*
10976 GCTC-TGGCGCAGCCGTCCCC
1 GC-CGTGGCGAAGCCG-CCCC
10996 TTTGGGCGGC
Statistics
Matches: 93, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
31 5 0.05
32 75 0.81
33 13 0.14
ACGTcount: A:0.16, C:0.36, G:0.38, T:0.11
Consensus pattern (32 bp):
GCCGTGGCGAAGCCGCCCCAAGAGGGCGGCAT
Found at i:11111 original size:14 final size:14
Alignment explanation
Indices: 11092--11124 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
11082 AAAGCCCTAG
11092 ATCTATTTCTCTAC
1 ATCTATTTCTCTAC
*
11106 ATCTATTTCTCTAG
1 ATCTATTTCTCTAC
11120 ATCTA
1 ATCTA
11125 GATCTGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.03, T:0.48
Consensus pattern (14 bp):
ATCTATTTCTCTAC
Found at i:14579 original size:13 final size:12
Alignment explanation
Indices: 14549--14591 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
14539 CATCGATACC
*
14549 TCGATATATCCA
1 TCGATATATCCG
14561 TCGATATATCCG
1 TCGATATATCCG
14573 TTCGATATATCCG
1 -TCGATATATCCG
14586 TCGATA
1 TCGATA
14592 CCTGTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:17125 original size:17 final size:17
Alignment explanation
Indices: 17112--17144 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17102 GCAACCTATC
17112 ACCTCATGCTACCTAGT
1 ACCTCATGCTACCTAGT
*
17129 ACCTCATACTACCTAG
1 ACCTCATGCTACCTAG
17145 GTATCATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.36, G:0.09, T:0.27
Consensus pattern (17 bp):
ACCTCATGCTACCTAGT
Found at i:18378 original size:2 final size:2
Alignment explanation
Indices: 18373--18420 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
18363 ATATATCCAC
** *
18373 AT AT AT AT AT AT AT AT AT AT AT AT CC AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18415 AT AT AT
1 AT AT AT
18421 GTTTAAGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:18382 original size:14 final size:14
Alignment explanation
Indices: 18363--18410 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
18353 TCATCTTATC
18363 ATATATCCACATAT
1 ATATATCCACATAT
** *
18377 ATATATATATATAT
1 ATATATCCACATAT
18391 ATATATCCACATAT
1 ATATATCCACATAT
18405 ATATAT
1 ATATAT
18411 ATATATATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATCCACATAT
Found at i:18401 original size:28 final size:28
Alignment explanation
Indices: 18363--18420 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
18353 TCATCTTATC
18363 ATATATCCACATATATATATATATATAT
1 ATATATCCACATATATATATATATATAT
18391 ATATATCCACATATATATATATATATAT
1 ATATATCCACATATATATATATATATAT
18419 AT
1 AT
18421 GTTTAAGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (28 bp):
ATATATCCACATATATATATATATATAT
Done.