Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011762.1 Corchorus capsularis cultivar CVL-1 contig11783, 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: 78733
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:17583 original size:95 final size:94
Alignment explanation
Indices: 17397--17588 Score: 305
Period size: 95 Copynumber: 2.0 Consensus size: 94
17387 AAAATTGTAA
17397 TTAGGAGAATATATAGAGGAAAATGAAAAGGAAAGCTAGAAATAACCATGGCCAGTAGATCGATG
1 TTAGGAGAATATATAGAGGAAAATGAAAAGGAAAGCTAGAAATAACCATGGCCAGTAGATCGATG
*
17462 TACTAAAATCTGATCCAACGGTCTAGATT
66 TACCAAAATCTGATCCAACGGTCTAGATT
* * * *
17491 TTAGGAGAATATATAGAGGAAAATGAAAAGGAAAGCTATTAAGTAACCATGGCCAGTGGATCGGT
1 TTAGGAGAATATATAGAGGAAAATGAAAAGGAAAGCTA-GAAATAACCATGGCCAGTAGATCGAT
*
17556 GTACCAATATCTTG-TCCAACGGTCTAGATT
65 GTACCAAAATC-TGATCCAACGGTCTAGATT
17586 TTA
1 TTA
17589 TGAGGTTGAT
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
94 38 0.42
95 50 0.56
96 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (94 bp):
TTAGGAGAATATATAGAGGAAAATGAAAAGGAAAGCTAGAAATAACCATGGCCAGTAGATCGATG
TACCAAAATCTGATCCAACGGTCTAGATT
Found at i:18955 original size:20 final size:20
Alignment explanation
Indices: 18920--18957 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18910 TAGTCCAAGG
*
18920 GGAGGCGGTGTCTAGTAAAA
1 GGAGGCGGTATCTAGTAAAA
*
18940 GGAGGCGGTATTTAGTAA
1 GGAGGCGGTATCTAGTAA
18958 TTCCCTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.39, T:0.24
Consensus pattern (20 bp):
GGAGGCGGTATCTAGTAAAA
Found at i:20625 original size:21 final size:20
Alignment explanation
Indices: 20582--20627 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
20572 TCAAAATAAA
* *
20582 ATAAAAACTACCCTTTTTAG
1 ATAAAAACTACCCATTATAG
*
20602 ATAAAAACTATCCATTATAGG
1 ATAAAAACTACCCATTATA-G
20623 ATAAA
1 ATAAA
20628 TATAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (20 bp):
ATAAAAACTACCCATTATAG
Found at i:20962 original size:29 final size:29
Alignment explanation
Indices: 20905--20969 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
20895 GAACTTAATT
* *
20905 AGAAAAGACACATGTTTTTACCAAGAAAA
1 AGAAAAGACACATGTTCTTACCAACAAAA
**
20934 AGAAAAGACACATGTTCTTACCTTCAAAA
1 AGAAAAGACACATGTTCTTACCAACAAAA
20963 AGTAAAA
1 AG-AAAA
20970 ACATCTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (29 bp):
AGAAAAGACACATGTTCTTACCAACAAAA
Found at i:26066 original size:27 final size:27
Alignment explanation
Indices: 26016--26068 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
26006 ACTAAAAAAA
***
26016 AACATACCATGTAAATTTTTTTTGAAG
1 AACATACCATGTAAATTAACTTTGAAG
26043 AACATACCATGTAAATTAACTTTGAA
1 AACATACCATGTAAATTAACTTTGAA
26069 TCAAAACAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (27 bp):
AACATACCATGTAAATTAACTTTGAAG
Found at i:41007 original size:29 final size:29
Alignment explanation
Indices: 40961--41016 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
40951 AATGTGGAAA
* *
40961 AAAATAAAATATTAGAGTTCAAAGTGATC
1 AAAATAAAAAATTAGAGTGCAAAGTGATC
40990 AAAATAAAAAAGTT-GAGTGCAAAGTGA
1 AAAATAAAAAA-TTAGAGTGCAAAGTGA
41017 CGGTACGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.54, C:0.05, G:0.18, T:0.23
Consensus pattern (29 bp):
AAAATAAAAAATTAGAGTGCAAAGTGATC
Found at i:43915 original size:2 final size:2
Alignment explanation
Indices: 43908--43958 Score: 66
Period size: 2 Copynumber: 25.0 Consensus size: 2
43898 TAGCTATTGC
* * *
43908 TA TA TA TA TA CA CTG TA TA TT 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 TA TA TA
43951 TA TA TA TA
1 TA TA TA TA
43959 GTTTAACAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:49899 original size:3 final size:3
Alignment explanation
Indices: 49891--49917 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
49881 TTAATTAAAC
49891 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
49918 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:49922 original size:3 final size:3
Alignment explanation
Indices: 49916--49947 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
49906 AATAATAATA
49916 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
49948 AATTGGAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:65235 original size:14 final size:14
Alignment explanation
Indices: 65216--65242 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65206 AAAGATTAAG
65216 AAAAATCCTTTTAC
1 AAAAATCCTTTTAC
65230 AAAAATCCTTTTA
1 AAAAATCCTTTTA
65243 GGGAAACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATCCTTTTAC
Found at i:67819 original size:2 final size:2
Alignment explanation
Indices: 67812--67863 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
67802 TCTTAAAGTG
* *
67812 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TG TA TGG TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
67853 T- TA TA TA TA TA
1 TA TA TA TA TA TA
67864 CAACATTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
1 3 0.07
2 38 0.90
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:67976 original size:20 final size:21
Alignment explanation
Indices: 67951--67992 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
67941 TCTTGGGTTC
*
67951 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGAAATTGTGAGT
67971 TACTCTCACGAAATTGTGAGT
1 TACTCTCACGAAATTGTGAGT
67992 T
1 T
67993 TTCTTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
TACTCTCACGAAATTGTGAGT
Found at i:68251 original size:2 final size:2
Alignment explanation
Indices: 68244--68279 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
68234 CACATTTGGC
68244 AT AT AT AT AT AT AT AT AT AT AT 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
68280 GTGTGGTGTT
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):
AT
Found at i:78385 original size:14 final size:14
Alignment explanation
Indices: 78368--78402 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
78358 ACGAGAACTA
78368 GAGAGGGAGAAGGG
1 GAGAGGGAGAAGGG
*
78382 GAGAAGGAGAAGGG
1 GAGAGGGAGAAGGG
78396 GAGAGGG
1 GAGAGGG
78403 GAGCGGCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (14 bp):
GAGAGGGAGAAGGG
Found at i:78528 original size:62 final size:61
Alignment explanation
Indices: 78424--78543 Score: 213
Period size: 62 Copynumber: 2.0 Consensus size: 61
78414 GTTCCCCTCC
*
78424 ATTTCTTATTAAATATTTTATTTAAAAGTAATATCATCCTTACCTTTCATAAAGCCAACTT
1 ATTTCTTATTAAATATTTTATTTAAAAGTAATATAATCCTTACCTTTCATAAAGCCAACTT
*
78485 ATTTCTTATTAAATGTTTTATTTTAAAAGTAATATAATCCTTACCTTTCATAAAGCCAA
1 ATTTCTTATTAAATATTTTA-TTTAAAAGTAATATAATCCTTACCTTTCATAAAGCCAA
78544 GTCCCCAGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 19 0.34
62 37 0.66
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (61 bp):
ATTTCTTATTAAATATTTTATTTAAAAGTAATATAATCCTTACCTTTCATAAAGCCAACTT
Done.