Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021128.1 Corchorus olitorius cultivar O-4 contig21161, 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: 56169
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:538 original size:32 final size:32
Alignment explanation
Indices: 502--572 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
492 AAATTGATAG
* * *
502 ACAAAATAGCCCTCGAATTTTAACATAGAAGA
1 ACAAAATAACCCTCAAATTTTAACAAAGAAGA
* * *
534 ACAAAATAACCCTCAAATTTTGACAAAGTAGG
1 ACAAAATAACCCTCAAATTTTAACAAAGAAGA
566 ACAAAAT
1 ACAAAAT
573 GTTCTTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.21
Consensus pattern (32 bp):
ACAAAATAACCCTCAAATTTTAACAAAGAAGA
Found at i:946 original size:18 final size:18
Alignment explanation
Indices: 919--953 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
909 GGAATTTACA
919 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
937 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
954 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:6047 original size:4 final size:4
Alignment explanation
Indices: 6038--6070 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
6028 ATATTCTCAA
*
6038 ATCT ATCT ATCA ATCT ATCT ATCT ATCT ATCT A
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT A
6071 CCAATCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.45
Consensus pattern (4 bp):
ATCT
Found at i:6054 original size:12 final size:12
Alignment explanation
Indices: 6037--6083 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
6027 AATATTCTCA
6037 AATCTATCTATC
1 AATCTATCTATC
6049 AATCTATCTATC
1 AATCTATCTATC
* *
6061 TATCTATCTACC
1 AATCTATCTATC
6073 AATCATATCTA
1 AATC-TATCTA
6084 CTATAAATCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
12 25 0.81
13 6 0.19
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (12 bp):
AATCTATCTATC
Found at i:6911 original size:2 final size:2
Alignment explanation
Indices: 6904--6930 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6894 ACTCAACTTC
6904 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6931 TAGTACTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13979 original size:19 final size:20
Alignment explanation
Indices: 13949--14012 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
13939 TTGACACTGT
13949 TTAGCAACTGTACAGATAAGA
1 TTAGC-ACTGTACAGATAAGA
*
13970 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATAAGA
* *
13989 TTAGGTACTGTACAGATGAGA
1 TTA-GCACTGTACAGATAAGA
14010 TTA
1 TTA
14013 TTAGAACAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 17 0.45
20 1 0.03
21 20 0.53
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
TTAGCACTGTACAGATAAGA
Found at i:16915 original size:29 final size:29
Alignment explanation
Indices: 16881--16939 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
16871 TAGAAATAAG
16881 TTCTAACCAAGACCATCACACATAACTAC
1 TTCTAACCAAGACCATCACACATAACTAC
16910 TTCTAACCAAGACCATCACACATAACTAC
1 TTCTAACCAAGACCATCACACATAACTAC
16939 T
1 T
16940 ATTTTCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.34, G:0.03, T:0.22
Consensus pattern (29 bp):
TTCTAACCAAGACCATCACACATAACTAC
Found at i:25869 original size:38 final size:38
Alignment explanation
Indices: 25809--25978 Score: 225
Period size: 38 Copynumber: 4.5 Consensus size: 38
25799 TAGCCTTGGC
* * *
25809 CCTTGGGCACCTCGGCCACCATCACCCGTGATGGTTAG
1 CCTTGGGCACCTCGGCCGCCATCGCACGTGATGGTTAG
* *
25847 CCTTGGGCACCT-TGCCTGCCATCGCATGTGATGGTTAG
1 CCTTGGGCACCTCGGCC-GCCATCGCACGTGATGGTTAG
25885 CCTTGGGCACCTCGGCCGCCATCGCACGTGATGGTTAG
1 CCTTGGGCACCTCGGCCGCCATCGCACGTGATGGTTAG
* * * *
25923 CCTTGGGCACCTCGGCCACCATCGCGCGTGATGCTCAG
1 CCTTGGGCACCTCGGCCGCCATCGCACGTGATGGTTAG
* *
25961 TCTCGGGCACCTCGGCCG
1 CCTTGGGCACCTCGGCCG
25979 ATGGAAAGAC
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
37 3 0.03
38 110 0.95
39 3 0.03
ACGTcount: A:0.13, C:0.36, G:0.29, T:0.22
Consensus pattern (38 bp):
CCTTGGGCACCTCGGCCGCCATCGCACGTGATGGTTAG
Found at i:28121 original size:32 final size:33
Alignment explanation
Indices: 28058--28124 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
28048 CGGATGTTTG
28058 ATTTTTTGAGTTTAAATCTTGTAATCGAAACTT
1 ATTTTTTGAGTTTAAATCTTGTAATCGAAACTT
28091 ATTTTTTGAGTTTAAATCTTGTAATC-AAACTT
1 ATTTTTTGAGTTTAAATCTTGTAATCGAAACTT
28123 AT
1 AT
28125 AAGAATCGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.49
Consensus pattern (33 bp):
ATTTTTTGAGTTTAAATCTTGTAATCGAAACTT
Found at i:30637 original size:20 final size:20
Alignment explanation
Indices: 30595--30637 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
30585 ATCCCTGGTT
* *
30595 TCAATAATGTTATCGATCGA
1 TCAATAATGTGATCGATCAA
30615 TCAATAATG-GATCGATCTAA
1 TCAATAATGTGATCGATC-AA
30635 TCA
1 TCA
30638 TTCAACCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (20 bp):
TCAATAATGTGATCGATCAA
Found at i:39485 original size:19 final size:20
Alignment explanation
Indices: 39461--39511 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
39451 CTGTTTAGCA
39461 ACTGTACATATGAGATTA-T
1 ACTGTACATATGAGATTAGT
* *
39480 ACTGTACAAATTAGATTAGGT
1 ACTGTACATATGAGATTA-GT
39501 ACTGTACATAT
1 ACTGTACATAT
39512 ATATGAGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
21 11 0.41
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (20 bp):
ACTGTACATATGAGATTAGT
Found at i:45601 original size:14 final size:13
Alignment explanation
Indices: 45570--45614 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
45560 GTCGGGTTTT
45570 AGTCAGTTTGTTG
1 AGTCAGTTTGTTG
*
45583 AGTCAGTTTTTTCG
1 AGTCAGTTTGTT-G
45597 AGTCAGTTAGTGTTG
1 AGTCAGTT--TGTTG
45612 AGT
1 AGT
45615 GTGAGTCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.41
14 9 0.33
15 4 0.15
16 3 0.11
ACGTcount: A:0.18, C:0.09, G:0.29, T:0.44
Consensus pattern (13 bp):
AGTCAGTTTGTTG
Found at i:50792 original size:15 final size:16
Alignment explanation
Indices: 50768--50800 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
50758 TGACTATTGA
50768 TTTTTCTCCTCT-TTT
1 TTTTTCTCCTCTCTTT
*
50783 TTTTTTTCCTCTCTTT
1 TTTTTCTCCTCTCTTT
50799 TT
1 TT
50801 CTTGCTATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTCCTCTCTTT
Done.