Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014829.1 Corchorus olitorius cultivar O-4 contig14862, 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: 46102
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:909 original size:22 final size:22
Alignment explanation
Indices: 881--927 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
871 CTTAACAATA
881 TATATACACGTATACACATATG
1 TATATACACGTATACACATATG
903 TATATACACGTATACACATATG
1 TATATACACGTATACACATATG
925 TAT
1 TAT
928 TTGTGTCGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (22 bp):
TATATACACGTATACACATATG
Found at i:17233 original size:1 final size:1
Alignment explanation
Indices: 17227--17252 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
17217 ATAAGAACTC
17227 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
17253 AAAAAAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24820 original size:6 final size:5
Alignment explanation
Indices: 24790--24819 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
24780 CGCTCATTCT
24790 TTTTG TTTTG TTTTG TTTTG TTTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG -TTTTG TTTT
24820 TTTGGGCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:30170 original size:2 final size:2
Alignment explanation
Indices: 30165--30211 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
30155 TTCTTATTCT
*
30165 TA TA TA -A TA TA TA -A TA TA AA TA -A 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
30204 T- TA TA TA T
1 TA TA TA TA T
30212 GTCTTTTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:30208 original size:9 final size:9
Alignment explanation
Indices: 30171--30211 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
30161 TTCTTATATA
30171 ATATATAAT
1 ATATATAAT
*
30180 ATAAATAAT
1 ATATATAAT
30189 ATATAT-AT
1 ATATATAAT
*
30197 ATATATATT
1 ATATATAAT
30206 ATATAT
1 ATATAT
30212 GTCTTTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATATATAAT
Found at i:30991 original size:3 final size:3
Alignment explanation
Indices: 30983--31024 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
30973 TACCTAAAGT
30983 TAA TAA TAA TATA TAA TAA T-A TAA T-A TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31025 TAAGAAGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.17
3 26 0.74
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:31006 original size:8 final size:8
Alignment explanation
Indices: 30985--31027 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
30975 CCTAAAGTTA
30985 ATAATAAT
1 ATAATAAT
30993 AT-ATAAT
1 ATAATAAT
31000 A-ATATAAT
1 ATA-ATAAT
31008 ATAATAAT
1 ATAATAAT
31016 ATAATAAT
1 ATAATAAT
31024 ATAA
1 ATAA
31028 GAAGAAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.19
8 25 0.78
9 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATAATAAT
Found at i:31027 original size:13 final size:13
Alignment explanation
Indices: 30983--31021 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
30973 TACCTAAAGT
30983 TAATAATA-ATATA
1 TAATAATATA-ATA
30996 TAATAATATAATA
1 TAATAATATAATA
31009 TAATAATATAATA
1 TAATAATATAATA
31022 ATATAAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 24 0.96
14 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:33004 original size:3 final size:3
Alignment explanation
Indices: 32998--33040 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
32988 CAAATTAATA
* *
32998 ATT ATT AGT GTT A-T ATT ATT ATT ATT ATT ATT ATTT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT A
33041 GTAGTTAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:33018 original size:37 final size:35
Alignment explanation
Indices: 32950--33015 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
32940 ATAATTAAAA
32950 TTACAAACATAATAATTATTAGTATTATATTAGTG
1 TTACAAACATAATAATTATTAGTATTATATTAGTG
* *
32985 TTACAAA-TTAATAATTATTAGTGTTATATTA
1 TTACAAACATAATAATTATTAGTATTATATTA
33016 TTATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 22 0.76
35 7 0.24
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (35 bp):
TTACAAACATAATAATTATTAGTATTATATTAGTG
Found at i:33024 original size:23 final size:23
Alignment explanation
Indices: 32966--33040 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
32956 ACATAATAAT
*
32966 TATTAGTATTA-TATTAGTGTTA
1 TATTATTATTATTATTAGTGTTA
* * *
32988 CA-AATTAATAATTATTAGTGTTA
1 TATTATT-ATTATTATTAGTGTTA
* *
33011 TATTATTATTATTATTATTATT-
1 TATTATTATTATTATTAGTGTTA
33033 TATTATTA
1 TATTATTA
33041 GTAGTTAGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
21 2 0.05
22 12 0.29
23 24 0.59
24 3 0.07
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (23 bp):
TATTATTATTATTATTAGTGTTA
Found at i:33339 original size:31 final size:31
Alignment explanation
Indices: 33301--33408 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 31
33291 TTAGACTAAT
33301 TGCTCAAATAAGGGCCTAACGTTTGCAAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCAAAAA
* * * **
33332 TGCTCAAATAAGGACCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCAAAAA
*
33361 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCAAAAA
*
33392 TACTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
33409 GGCGTCGAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
28 2 0.03
29 18 0.30
30 3 0.05
31 35 0.58
32 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCAAAAA
Found at i:33549 original size:31 final size:29
Alignment explanation
Indices: 33450--33613 Score: 86
Period size: 31 Copynumber: 5.5 Consensus size: 29
33440 TGACGCCAGA
*
33450 CCCTTATTTGAGCATTTTTTTATAACGTTAGG
1 CCCTTATTTGAGCA--TTTTGA-AACGTTAGG
* ** * * *
33482 CTCTTATTTG-GCCAAATT-AAAAGATCGG
1 CCCTTATTTGAG-CATTTTGAAACGTTAGG
33510 ACCCTTATTTGAGCATTTTCGATAACGTTAGG
1 -CCCTTATTTGAGCATTTT-GA-AACGTTAGG
** * * *
33542 CCCTTATTTG-GCCAAATT-AAAAGAT-CG
1 CCCTTATTTGAG-CATTTTGAAACGTTAGG
*
33569 CCCTTAGTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-G-AAACGTTAGG
33600 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
33614 ATTAGCCTTA
Statistics
Matches: 96, Mismatches: 24, Indels: 25
0.66 0.17 0.17
Matches are distributed among these distances:
27 14 0.15
28 11 0.11
29 15 0.16
30 9 0.09
31 30 0.31
32 17 0.18
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGAAACGTTAGG
Found at i:33601 original size:58 final size:60
Alignment explanation
Indices: 33448--33609 Score: 240
Period size: 60 Copynumber: 2.7 Consensus size: 60
33438 ATTGACGCCA
** *
33448 GACCCTTATTTGAGCATTTTTTTATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCA-TTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
33509 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC-
1 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* *
33568 G-CCCTTAGTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 GACCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
33610 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
58 37 0.39
59 2 0.02
60 40 0.42
61 16 0.17
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (60 bp):
GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:37879 original size:29 final size:28
Alignment explanation
Indices: 37833--37887 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
37823 AACTCGTATG
* *
37833 ATTTTGACGTTTTCCCCCTTAAACTTTA
1 ATTTTGACATTTTACCCCTTAAACTTTA
*
37861 ATTTTGAACATTTTACCCCTTGAACTT
1 ATTTTG-ACATTTTACCCCTTAAACTT
37888 GCAATTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (28 bp):
ATTTTGACATTTTACCCCTTAAACTTTA
Found at i:39923 original size:29 final size:28
Alignment explanation
Indices: 39878--39932 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
39868 ACGCATCATT
39878 GGTTGGGCTGAGATTTAGATTTTCTAATG
1 GGTTGGGCTGAGATTTAG-TTTTCTAATG
* *
39907 GGTTGGGTTGAGTTTTAGTTTTCTAA
1 GGTTGGGCTGAGATTTAGTTTTCTAA
39933 AAAGTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.18, C:0.05, G:0.31, T:0.45
Consensus pattern (28 bp):
GGTTGGGCTGAGATTTAGTTTTCTAATG
Found at i:42864 original size:47 final size:47
Alignment explanation
Indices: 42764--42909 Score: 265
Period size: 47 Copynumber: 3.1 Consensus size: 47
42754 AGTTTGATGG
42764 AAAATAAAGTAGAGGGCAAAATAGTCCAAAGGGGGGGCGGTGACTAGT
1 AAAATAAAGTAGAGGGCAAAATAGTCCAAA-GGGGGGCGGTGACTAGT
42812 AAAATAAAGTAGAGGGCAAAATAGTCCAAAGGGGGGCGGTGACTAGT
1 AAAATAAAGTAGAGGGCAAAATAGTCCAAAGGGGGGCGGTGACTAGT
* *
42859 AAAATAAAGTAGAGGGCAAAATAGTCCAAAGAGGGGCAGTGACTAGT
1 AAAATAAAGTAGAGGGCAAAATAGTCCAAAGGGGGGCGGTGACTAGT
42906 AAAA
1 AAAA
42910 GGGGCGGTAT
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
47 66 0.69
48 30 0.31
ACGTcount: A:0.43, C:0.10, G:0.32, T:0.14
Consensus pattern (47 bp):
AAAATAAAGTAGAGGGCAAAATAGTCCAAAGGGGGGCGGTGACTAGT
Done.