Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008475.1 Corchorus capsularis cultivar CVL-1 contig08496, 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: 17705
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:2472 original size:15 final size:15
Alignment explanation
Indices: 2452--2483 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2442 ATAACTTAAT
*
2452 AATCATCATCATTTG
1 AATCATCATCATCTG
2467 AATCATCATCATCTG
1 AATCATCATCATCTG
2482 AA
1 AA
2484 CTACTTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (15 bp):
AATCATCATCATCTG
Found at i:5877 original size:27 final size:29
Alignment explanation
Indices: 5847--5912 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 29
5837 TTTTTGGGTA
*
5847 AAATTACCATGT-T-AACCTCGATTAATG
1 AAATTACCATGTATGAACCACGATTAATG
**
5874 AAATTACCAT-TATGCCCCACGATTAATG
1 AAATTACCATGTATGAACCACGATTAATG
5902 AAATTACCATG
1 AAATTACCATG
5913 AGAGAATTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 11 0.33
28 21 0.64
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (29 bp):
AAATTACCATGTATGAACCACGATTAATG
Found at i:6301 original size:13 final size:13
Alignment explanation
Indices: 6283--6328 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
6273 ATCTGATTGT
6283 TTTGGTTTATTA-
1 TTTGGTTTATTAC
6295 TTCTGGTTTATTAC
1 TT-TGGTTTATTAC
*
6309 TTTGGTTTATGAC
1 TTTGGTTTATTAC
6322 TTTGGTT
1 TTTGGTT
6329 ATGATACTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
12 2 0.06
13 27 0.87
14 2 0.06
ACGTcount: A:0.13, C:0.07, G:0.20, T:0.61
Consensus pattern (13 bp):
TTTGGTTTATTAC
Found at i:7850 original size:2 final size:2
Alignment explanation
Indices: 7843--7878 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7833 GTTTTGCATG
7843 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
7879 CTAGATCCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8501 original size:12 final size:12
Alignment explanation
Indices: 8469--8502 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
8459 TATTTTTTTT
8469 AATGTTTTCACC
1 AATGTTTTCACC
8481 AAT-TCTTTCACC
1 AATGT-TTTCACC
8493 AATGTTTTCA
1 AATGTTTTCA
8503 AACCAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (12 bp):
AATGTTTTCACC
Found at i:10379 original size:30 final size:32
Alignment explanation
Indices: 10351--10413 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
10341 CAATATCCTT
*
10351 AACAACACCTTTGACTACCTTCAGATCCTCCTC
1 AACAACACCTTTAACTACCTTCAGATCCT-CTC
* * *
10384 AAGAACACCTTTAATTAGCTTCAGATCCTC
1 AACAACACCTTTAACTACCTTCAGATCCTC
10414 CACAGCTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.30, C:0.33, G:0.08, T:0.29
Consensus pattern (32 bp):
AACAACACCTTTAACTACCTTCAGATCCTCTC
Found at i:10659 original size:20 final size:19
Alignment explanation
Indices: 10600--10659 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
10590 GAGGTGCTTT
10600 TAATAAGGCAAGTTCAATG
1 TAATAAGGCAAGTTCAATG
** * **
10619 TCAATTGGGAAAGTTGGATG
1 T-AATAAGGCAAGTTCAATG
10639 TAATCAAGGCAAGTTCAATG
1 TAAT-AAGGCAAGTTCAATG
10659 T
1 T
10660 TGATTGGGAA
Statistics
Matches: 29, Mismatches: 10, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (19 bp):
TAATAAGGCAAGTTCAATG
Found at i:11696 original size:41 final size:40
Alignment explanation
Indices: 11582--11778 Score: 263
Period size: 41 Copynumber: 4.9 Consensus size: 40
11572 AAAATGTCAT
* * * * *
11582 TTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATATCAT
1 TTGGAAAATTTGGATGTGAATAAGGCAAGTTCAATGTTAA
* *
11622 TTGGGAAAA-CTGGATGTGAATAAGGCAAGTTCAATGTTGA
1 TT-GGAAAATTTGGATGTGAATAAGGCAAGTTCAATGTTAA
*
11662 TTGGAAAATTTGGATGTGAATCAAGGCTAGTTCAATGTTAA
1 TTGGAAAATTTGGATGTGAAT-AAGGCAAGTTCAATGTTAA
*
11703 TTGGAAAATTTAGATGTGAATAA-GCAAGTTCAATGTTAA
1 TTGGAAAATTTGGATGTGAATAAGGCAAGTTCAATGTTAA
*
11742 TTGGAAAATTTGAATGTGAATTAAGGCAAGTTCAATG
1 TTGGAAAATTTGGATGTGAA-TAAGGCAAGTTCAATG
11779 CCAATTGGTT
Statistics
Matches: 139, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
39 39 0.28
40 46 0.33
41 54 0.39
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (40 bp):
TTGGAAAATTTGGATGTGAATAAGGCAAGTTCAATGTTAA
Found at i:11709 original size:80 final size:80
Alignment explanation
Indices: 11582--11786 Score: 270
Period size: 80 Copynumber: 2.5 Consensus size: 80
11572 AAAATGTCAT
* * * * *
11582 TTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATATCATTTGGGAAAA-CTGGATGTGAATAAG
1 TTGGAAAATTTGGATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAATCTAGATGTGAATAA-
*
11646 GCAAGTTCAATGTTGA
65 GCAAGTTCAATGTTAA
* * *
11662 TTGGAAAATTTGGATGTGAATCAAGGCTAGTTCAATGTTAATT-GGAAAATTTAGATGTGAATAA
1 TTGGAAAATTTGGATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAATCTAGATGTGAATAA
11726 GCAAGTTCAATGTTAA
65 GCAAGTTCAATGTTAA
* *
11742 TTGGAAAATTTGAATGTGAATTAAGGCAAGTTCAATGCCAATTGG
1 TTGGAAAATTTGGATGTGAA-TAAGGCAAGTTCAATGTCAATTGG
11787 TTTAGGTTGG
Statistics
Matches: 108, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
80 77 0.71
81 31 0.29
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.31
Consensus pattern (80 bp):
TTGGAAAATTTGGATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAATCTAGATGTGAATAAG
CAAGTTCAATGTTAA
Found at i:11763 original size:20 final size:19
Alignment explanation
Indices: 11695--11763 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
11685 AGGCTAGTTC
*
11695 AATGTTAATTGGAAAATTT
1 AATGTGAATTGGAAAATTT
** * * *
11714 AGATGTGAATAAGCAAGTTC
1 A-ATGTGAATTGGAAAATTT
*
11734 AATGTTAATTGGAAAATTT
1 AATGTGAATTGGAAAATTT
11753 GAATGTGAATT
1 -AATGTGAATT
11764 AAGGCAAGTT
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (19 bp):
AATGTGAATTGGAAAATTT
Found at i:12744 original size:17 final size:17
Alignment explanation
Indices: 12722--12754 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12712 TCATTAGGTC
12722 AATTAA-AATTATAAATT
1 AATTAATAA-TATAAATT
12739 AATTAATAATATAAAT
1 AATTAATAATATAAAT
12755 ATCCTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAATAATATAAATT
Found at i:12984 original size:15 final size:16
Alignment explanation
Indices: 12958--12988 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
12948 ACTGATTTAG
12958 TATTTATTCATATAAT
1 TATTTATTCATATAAT
12974 TATTT-TTCATATAAT
1 TATTTATTCATATAAT
12989 GAAGTTTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTATTCATATAAT
Found at i:16934 original size:16 final size:16
Alignment explanation
Indices: 16898--16949 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
16888 ATCAAATGTC
16898 GGGTC-ATT-TGGGTT
1 GGGTCAATTCTGGGTT
16912 CGGGTCAATTCTGGGTT
1 -GGGTCAATTCTGGGTT
16929 GGGTCAATTCTGGGTT
1 GGGTCAATTCTGGGTT
16945 GGGTC
1 GGGTC
16950 GTTTTCGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 5 0.14
16 24 0.69
17 6 0.17
ACGTcount: A:0.10, C:0.13, G:0.40, T:0.37
Consensus pattern (16 bp):
GGGTCAATTCTGGGTT
Found at i:17275 original size:2 final size:2
Alignment explanation
Indices: 17268--17298 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
17258 ATCAGTACAA
17268 AT AT AT AT AGT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
17299 TTAGGCCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Done.