Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016526.1 Corchorus olitorius cultivar O-4 contig16559, 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: 49865
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:1010 original size:11 final size:11
Alignment explanation
Indices: 989--1033 Score: 58
Period size: 10 Copynumber: 4.3 Consensus size: 11
979 TTTTACTTAA
989 ATTTTCA-TAT
1 ATTTTCATTAT
999 ATTTTCATTAT
1 ATTTTCATTAT
* *
1010 A-TATCAATAT
1 ATTTTCATTAT
1020 ATTTTCATTAT
1 ATTTTCATTAT
1031 ATT
1 ATT
1034 AATTAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 15 0.52
11 14 0.48
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTTCATTAT
Found at i:7746 original size:22 final size:22
Alignment explanation
Indices: 7718--7766 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
7708 AGAAGAAAGG
7718 GAAACTCTCACGAA-AGGAGAGA
1 GAAACTCTCAC-AAGAGGAGAGA
*
7740 GAAACTCTCACAAGAGGAGAGG
1 GAAACTCTCACAAGAGGAGAGA
7762 GAAAC
1 GAAAC
7767 CTTTCATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.45, C:0.18, G:0.29, T:0.08
Consensus pattern (22 bp):
GAAACTCTCACAAGAGGAGAGA
Found at i:10040 original size:14 final size:14
Alignment explanation
Indices: 10008--10050 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
9998 TATATACTCC
*
10008 TATAGATATAGATATA
1 TATAGAT-TA-ATAGA
10024 TATAGATTAATAGA
1 TATAGATTAATAGA
10038 TATAGATT-ATAGA
1 TATAGATTAATAGA
10051 CTAGTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 12 0.46
15 2 0.08
16 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (14 bp):
TATAGATTAATAGA
Found at i:21014 original size:70 final size:72
Alignment explanation
Indices: 20936--21070 Score: 229
Period size: 73 Copynumber: 1.9 Consensus size: 72
20926 ACAAGTGGAA
*
20936 AATGACAAC-AA-AATAATGGAGAAAAGATCCCAAAATTTTCCTTCAATAATGTAATAATCAAAA
1 AATGACAACAAATAATAATGGAGAAAAGATCCCAAAATTTTCCTTCAATAATATAATAATCAAAA
20999 ATTAATT
66 ATTAATT
*
21006 AATGACAACAAAATAATAATGGAGAAAAGATCCCAAAATTTTCCTTTAATAATATAATAATCAAA
1 AATGACAAC-AAATAATAATGGAGAAAAGATCCCAAAATTTTCCTTCAATAATATAATAATCAAA
21071 TTAATTTACA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
70 9 0.15
72 2 0.03
73 49 0.82
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.27
Consensus pattern (72 bp):
AATGACAACAAATAATAATGGAGAAAAGATCCCAAAATTTTCCTTCAATAATATAATAATCAAAA
ATTAATT
Found at i:21860 original size:12 final size:12
Alignment explanation
Indices: 21843--21874 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
21833 TGGTAGGAAG
21843 GATGGAAAATTA
1 GATGGAAAATTA
21855 GATGGAAAATTA
1 GATGGAAAATTA
*
21867 GAAGGAAA
1 GATGGAAA
21875 TAAATTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.19
Consensus pattern (12 bp):
GATGGAAAATTA
Found at i:22246 original size:23 final size:24
Alignment explanation
Indices: 22200--22246 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
22190 AACTTTTGTA
* **
22200 AATTGCACTATTTTTTTTTTGGTG
1 AATTGCACTATTTATTTTGAGGTG
22224 AATTGCACTA-TTATTTTGAGGTG
1 AATTGCACTATTTATTTTGAGGTG
22247 CTATATACGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (24 bp):
AATTGCACTATTTATTTTGAGGTG
Found at i:23620 original size:22 final size:24
Alignment explanation
Indices: 23595--23647 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
23585 AATTTGAGGT
23595 ATTAA-CATA-TATGATTTTTGAC
1 ATTAATCATAGTATGATTTTTGAC
*
23617 ATTAATTTATAGTATGATTTTTGAC
1 ATTAA-TCATAGTATGATTTTTGAC
23642 ATTAAT
1 ATTAAT
23648 TTATGGTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 5 0.19
24 4 0.15
25 18 0.67
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTAATCATAGTATGATTTTTGAC
Found at i:23637 original size:25 final size:25
Alignment explanation
Indices: 23604--23656 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
23594 TATTAACATA
23604 TATGATTTTTGACATTAATTTATAG
1 TATGATTTTTGACATTAATTTATAG
*
23629 TATGATTTTTGACATTAATTTATGG
1 TATGATTTTTGACATTAATTTATAG
23654 TAT
1 TAT
23657 CTAATTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (25 bp):
TATGATTTTTGACATTAATTTATAG
Found at i:29135 original size:51 final size:51
Alignment explanation
Indices: 29059--29160 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
29049 TGTCAAAATG
*
29059 GTATGCACCCTAAAAACAAGTTGCATTATCAATTAGAACTTTATGGAGTGA
1 GTATGCACCCTAAAAACAAGTTGCATTATCAATTAGAACTTCATGGAGTGA
29110 GTATGCACCCTAAAAACAAGTTGCATTATCAATTAGAACTTCATGGAGTGA
1 GTATGCACCCTAAAAACAAGTTGCATTATCAATTAGAACTTCATGGAGTGA
29161 TAAACACTCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (51 bp):
GTATGCACCCTAAAAACAAGTTGCATTATCAATTAGAACTTCATGGAGTGA
Found at i:29454 original size:52 final size:51
Alignment explanation
Indices: 29373--29477 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 51
29363 CTTCAACTTA
* *
29373 AATACAAAACCATAAGCTCTGTATGATCATTTGCTTTTTGACTAAACAACCT
1 AATACAAAACCATAAGCTCTGTATCATCATTTGCTTTTTAACTAAA-AACCT
*
29425 AATACAAAACCATAAGCTCTGTATCATCATTTTCTTTTTAACTAAAAACCT
1 AATACAAAACCATAAGCTCTGTATCATCATTTGCTTTTTAACTAAAAACCT
29476 AA
1 AA
29478 ATTAGTTCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
51 7 0.14
52 43 0.86
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (51 bp):
AATACAAAACCATAAGCTCTGTATCATCATTTGCTTTTTAACTAAAAACCT
Found at i:40522 original size:15 final size:15
Alignment explanation
Indices: 40502--40531 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40492 GTAGTCAAAG
*
40502 CCAATCATGGTGTAT
1 CCAATCATGGCGTAT
40517 CCAATCATGGCGTAT
1 CCAATCATGGCGTAT
40532 AGAATCTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (15 bp):
CCAATCATGGCGTAT
Found at i:49033 original size:62 final size:61
Alignment explanation
Indices: 48954--49071 Score: 209
Period size: 62 Copynumber: 1.9 Consensus size: 61
48944 CCCTTCCATG
* *
48954 GTCTCTCATTCATAGGGGCTGAAATTACGAAGCTTTAAATTTCACACTTATTCAACAGTACC
1 GTCTCTCATTCAAAGGGGCTGAAATTACGAAG-GTTAAATTTCACACTTATTCAACAGTACC
49016 GTCTCTCATTCAAAGGGGCTGAAATTACGAAGGTTAAATTTCACACTTATTCAACA
1 GTCTCTCATTCAAAGGGGCTGAAATTACGAAGGTTAAATTTCACACTTATTCAACA
49072 CTATCTATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
61 23 0.43
62 31 0.57
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (61 bp):
GTCTCTCATTCAAAGGGGCTGAAATTACGAAGGTTAAATTTCACACTTATTCAACAGTACC
Found at i:49152 original size:28 final size:28
Alignment explanation
Indices: 49120--49181 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
49110 ACTAGCTTGC
49120 TCGACCTAATTTTATTGTCTGATATTCA
1 TCGACCTAATTTTATTGTCTGATATTCA
49148 TCGACCTAATTTTATTGTCTGATATTCA
1 TCGACCTAATTTTATTGTCTGATATTCA
49176 T-GACCT
1 TCGACCT
49182 GACACTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.45
Consensus pattern (28 bp):
TCGACCTAATTTTATTGTCTGATATTCA
Done.