Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020624.1 Corchorus olitorius cultivar O-4 contig20657, 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: 13070
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Found at i:1966 original size:3 final size:3
Alignment explanation
Indices: 1958--2004 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
1948 CTAGAGAATG
*
1958 AGA AGA AGA AGA AGA AGA AGA AGA ATA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
2005 GGCAAGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:2383 original size:50 final size:49
Alignment explanation
Indices: 2305--2520 Score: 218
Period size: 50 Copynumber: 4.3 Consensus size: 49
2295 ACATTTAGCC
* * * * *
2305 AGAAATTTGTAAGTGAAGGTTGAACTTTTAATTAAAAGATGGAACCTTTA
1 AGAAATTTGTAAATAAAAG-TGGACTTTTAATTAAAAGATTGAACCTTTA
* *
2355 AGCAATTTGTAAATAAAAGTGGAACTTTTAATTAAAAGATTGAACTTTTA
1 AGAAATTTGTAAATAAAAGTGG-ACTTTTAATTAAAAGATTGAACCTTTA
* * *
2405 AGAAATTGGTGAATAAAAGTTGGACTTTTAATTAAAAGATTGAAGCTTGTA
1 AGAAATTTGTAAATAAAAG-TGGACTTTTAATTAAAAGATTGAACCTT-TA
* * * * ** *
2456 AGTAGTTTGTAAATAATGATTGGAC-TTTAGATTAAAAGATCAAACTTTTA
1 AGAAATTTGTAAATAA-AAGTGGACTTTTA-ATTAAAAGATTGAACCTTTA
2506 AGAAATTTGTAAATA
1 AGAAATTTGTAAATA
2521 TAAACAAACA
Statistics
Matches: 137, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
49 2 0.01
50 98 0.72
51 36 0.26
52 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (49 bp):
AGAAATTTGTAAATAAAAGTGGACTTTTAATTAAAAGATTGAACCTTTA
Found at i:2392 original size:19 final size:20
Alignment explanation
Indices: 2368--2405 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2358 AATTTGTAAA
2368 TAAAAG-TGGAACTTTTAAT
1 TAAAAGATGGAACTTTTAAT
*
2387 TAAAAGATTGAACTTTTAA
1 TAAAAGATGGAACTTTTAA
2406 GAAATTGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAAAGATGGAACTTTTAAT
Found at i:2493 original size:101 final size:100
Alignment explanation
Indices: 2323--2512 Score: 258
Period size: 101 Copynumber: 1.9 Consensus size: 100
2313 GTAAGTGAAG
2323 GTTGAACTTTTAATTAAAAGATGGAACCTTTAAGCAATTTGTAAATAAAAGTGGAACTTTTAATT
1 GTTGAACTTTTAATTAAAAGATGGAACCTTTAAGCAATTTGTAAATAAAAGTGGAACTTTTAATT
**
2388 AAAAGATTGAACTTTTAAGAAATTGGTGAATAAAA
66 AAAAGATCAAACTTTTAAGAAATTGGTGAATAAAA
* * * * * * *
2423 GTTGGACTTTTAATTAAAAGATTGAAGCTTGTAAGTAGTTTGTAAATAATGATTGG-AC-TTTAG
1 GTTGAACTTTTAATTAAAAGATGGAACCTT-TAAGCAATTTGTAAATAA-AAGTGGAACTTTTA-
2486 ATTAAAAGATCAAACTTTTAAGAAATT
63 ATTAAAAGATCAAACTTTTAAGAAATT
2513 TGTAAATATA
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
100 31 0.40
101 43 0.55
102 4 0.05
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (100 bp):
GTTGAACTTTTAATTAAAAGATGGAACCTTTAAGCAATTTGTAAATAAAAGTGGAACTTTTAATT
AAAAGATCAAACTTTTAAGAAATTGGTGAATAAAA
Found at i:2857 original size:25 final size:25
Alignment explanation
Indices: 2829--2878 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2819 TATGTTGTGT
*
2829 GTTAGGGTTT-GCCTTTCATGTCATG
1 GTTAGGGTTTAG-CTTTCATGACATG
2854 GTTAGGGTTTAGCTTTCATGACATG
1 GTTAGGGTTTAGCTTTCATGACATG
2879 TCATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.16, C:0.14, G:0.28, T:0.42
Consensus pattern (25 bp):
GTTAGGGTTTAGCTTTCATGACATG
Found at i:2912 original size:97 final size:97
Alignment explanation
Indices: 2811--3013 Score: 300
Period size: 97 Copynumber: 2.1 Consensus size: 97
2801 TCTATCTCAC
*
2811 TTAGGGTTTATGTTGTGTGTTAGGGT-TTGCCTTTCATGTCATGGTTAGGGTTTAGCTTTCATGA
1 TTAGGGTTCAT-TTGTGTGTTAGGGTCTTGCCTTTCATGTCATGGTTAGGGTTTAGCTTTCATGA
2875 CATGTCATTTTTTTGTCTCCCTTAGCCATTTTT
65 CATGTCATTTTTTTGTCTCCCTTAGCCATTTTT
* * * * *** *
2908 TTAGGGTTCCTTTTTTTTTTTTTGTCTTGGCTTTCATGTCATGGTTAGGGTTTAGCTTTCATGAC
1 TTAGGGTTCATTTGTGTGTTAGGGTCTTGCCTTTCATGTCATGGTTAGGGTTTAGCTTTCATGAC
*
2973 ATGTCATTTTTTTGTTTCCCTTAGCCATTTTT
66 ATGTCATTTTTTTGTCTCCCTTAGCCATTTTT
3005 TTAGGGTTC
1 TTAGGGTTC
3014 CTTTTTTTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 8 0.08
97 87 0.92
ACGTcount: A:0.12, C:0.15, G:0.21, T:0.52
Consensus pattern (97 bp):
TTAGGGTTCATTTGTGTGTTAGGGTCTTGCCTTTCATGTCATGGTTAGGGTTTAGCTTTCATGAC
ATGTCATTTTTTTGTCTCCCTTAGCCATTTTT
Found at i:3014 original size:97 final size:97
Alignment explanation
Indices: 2841--3025 Score: 361
Period size: 97 Copynumber: 1.9 Consensus size: 97
2831 TAGGGTTTGC
2841 CTTTCATGTCATGGTTAGGGTTTAGCTTTCATGACATGTCATTTTTTTGTCTCCCTTAGCCATTT
1 CTTTCATGTCATGGTTAGGGTTTAGCTTTCATGACATGTCATTTTTTTGTCTCCCTTAGCCATTT
2906 TTTTAGGGTTCCTTTTTTTTTTTTTGTCTTGG
66 TTTTAGGGTTCCTTTTTTTTTTTTTGTCTTGG
*
2938 CTTTCATGTCATGGTTAGGGTTTAGCTTTCATGACATGTCATTTTTTTGTTTCCCTTAGCCATTT
1 CTTTCATGTCATGGTTAGGGTTTAGCTTTCATGACATGTCATTTTTTTGTCTCCCTTAGCCATTT
3003 TTTTAGGGTTCCTTTTTTTTTTT
66 TTTTAGGGTTCCTTTTTTTTTTT
3026 GTCTTCCCAC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 87 1.00
ACGTcount: A:0.12, C:0.16, G:0.17, T:0.55
Consensus pattern (97 bp):
CTTTCATGTCATGGTTAGGGTTTAGCTTTCATGACATGTCATTTTTTTGTCTCCCTTAGCCATTT
TTTTAGGGTTCCTTTTTTTTTTTTTGTCTTGG
Found at i:7341 original size:83 final size:82
Alignment explanation
Indices: 7176--7340 Score: 287
Period size: 83 Copynumber: 2.0 Consensus size: 82
7166 ACTTCTTAAG
7176 TTAAAACTTTAAATTTCAACTGCTTTTAACATTTCACATTAACCTAAAAAAAAAATTCCCTAATC
1 TTAAAACTTTAAATTTCAACTGCTTTTAACATTTCACATTAACCT-AAAAAAAAATTCCCTAATC
7241 ATAGGTCATGAAAAAAAA
65 ATAGGTCATGAAAAAAAA
* *
7259 TTAAAACTTTAAATTTCAACTGCTTTTACCATTTCACATTAACCT-AAAAAAAATGTCCCTGATC
1 TTAAAACTTTAAATTTCAACTGCTTTTAACATTTCACATTAACCTAAAAAAAAAT-TCCCTAATC
7323 ATAGGTCATGAAAAAAAA
65 ATAGGTCATGAAAAAAAA
7341 AACTAAACTC
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
81 9 0.11
82 26 0.33
83 44 0.56
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.32
Consensus pattern (82 bp):
TTAAAACTTTAAATTTCAACTGCTTTTAACATTTCACATTAACCTAAAAAAAAATTCCCTAATCA
TAGGTCATGAAAAAAAA
Found at i:7481 original size:50 final size:50
Alignment explanation
Indices: 7412--7718 Score: 307
Period size: 50 Copynumber: 6.1 Consensus size: 50
7402 CCAAACCTAG
* * *
7412 TAAAGGTTGAAATTTTAATTAAAAAATTGAACTTTTAAGAAA-TTGTTGAA
1 TAAAGGTTGAACTTTTAATTAAAAGATTGAACTTTTAAGAAATTTG-TAAA
* * * * *
7462 TAAAAGTTGGACTTTTAATTAAAAGATTGAAGCTTGTAAGTAGTTTGTAAA
1 TAAAGGTTGAACTTTTAATTAAAAGATTGAA-CTTTTAAGAAATTTGTAAA
* * * **
7513 TAATGATTGGAC-TTTAGATTAAAAGATCAAACTTTTAAGAAATTTGTAAA
1 TAAAGGTTGAACTTTTA-ATTAAAAGATTGAACTTTTAAGAAATTTGTAAA
* *
7563 TAAAGGTTGAAATTTTAATTAAAAGGTTGAACTTTTAAGAAATTTGTAAA
1 TAAAGGTTGAACTTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAA
* * *
7613 TGAAGGTTGAACTTTTAATTGAAAG-TTGAAACCTTTTAAGCAATTTGTAAA
1 TAAAGGTTGAACTTTTAATTAAAAGATTG-AA-CTTTTAAGAAATTTGTAAA
* * * * **
7664 TAAA-GATGAAATCTTTAAATTAAAATATTGAACTTTAAATTAATTTGTAAA
1 TAAAGGTTG-AA-CTTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAA
7715 TAAA
1 TAAA
7719 AATGAAATTT
Statistics
Matches: 213, Mismatches: 35, Indels: 17
0.80 0.13 0.06
Matches are distributed among these distances:
49 3 0.01
50 112 0.53
51 79 0.37
52 16 0.08
53 3 0.01
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.37
Consensus pattern (50 bp):
TAAAGGTTGAACTTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAA
Found at i:7576 original size:20 final size:20
Alignment explanation
Indices: 7551--7600 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
7541 AAACTTTTAA
7551 GAAATTTGTAAAT-AAAGGTT
1 GAAATTT-TAAATAAAAGGTT
*
7571 GAAATTTTAATTAAAAGGTT
1 GAAATTTTAAATAAAAGGTT
*
7591 GAACTTTTAA
1 GAAATTTTAA
7601 GAAATTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.38
Consensus pattern (20 bp):
GAAATTTTAAATAAAAGGTT
Found at i:7579 original size:30 final size:30
Alignment explanation
Indices: 7542--7630 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
7532 TAAAAGATCA
7542 AACTTTTAAGAAATTTGTAAATAAAGGTTG
1 AACTTTTAAGAAATTTGTAAATAAAGGTTG
*
7572 AAATTTT----AA--T-T--A-AAAGGTTG
1 AACTTTTAAGAAATTTGTAAATAAAGGTTG
*
7592 AACTTTTAAGAAATTTGTAAATGAAGGTTG
1 AACTTTTAAGAAATTTGTAAATAAAGGTTG
7622 AACTTTTAA
1 AACTTTTAA
7631 TTGAAAGTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 20
0.67 0.04 0.29
Matches are distributed among these distances:
20 14 0.30
21 1 0.02
23 1 0.02
24 3 0.07
26 3 0.07
27 1 0.02
29 1 0.02
30 22 0.48
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (30 bp):
AACTTTTAAGAAATTTGTAAATAAAGGTTG
Found at i:7649 original size:101 final size:98
Alignment explanation
Indices: 7414--7717 Score: 317
Period size: 101 Copynumber: 3.0 Consensus size: 98
7404 AAACCTAGTA
* * * * *
7414 AAGGTTGAAATTTTAATTAAAAAATTG-AACTTTTAAGAAA-TTGTTGAATAAAAGTTGGACTTT
1 AAGGTTGAACTTTTAATT-AAAAGTTGAAACTTTTAAGAAATTTG-TAAAT-AAAGTTGAAATTT
* *
7477 TAATTAAAAGATTGAAGCTTGTAAGTAGTTTGTAAAT
63 TAATTAAAAGATTGAA-CTTTTAAGTAATTTGTAAAT
* * * *
7514 AATGATTGGAC-TTTAGATTAAAAGATCAAACTTTTAAGAAATTTGTAAATAAAGGTTGAAATTT
1 AA-GGTTGAACTTTTA-ATTAAAAGTTGAAACTTTTAAGAAATTTGTAAATAAA-GTTGAAATTT
* *
7578 TAATTAAAAGGTTGAACTTTTAAGAAATTTGTAAAT
63 TAATTAAAAGATTGAACTTTTAAGTAATTTGTAAAT
* * *
7614 GAAGGTTGAACTTTTAATTGAAAGTTGAAACCTTTTAAGCAATTTGTAAATAAAGATGAAATCTT
1 -AAGGTTGAACTTTTAATTAAAAGTTGAAA-CTTTTAAGAAATTTGTAAATAAAGTTGAAAT-TT
* * *
7679 TAAATTAAAATATTGAACTTTAAATTAATTTGTAAAT
63 T-AATTAAAAGATTGAACTTTTAAGTAATTTGTAAAT
7716 AA
1 AA
7718 AAATGAAATT
Statistics
Matches: 169, Mismatches: 25, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
100 55 0.33
101 81 0.48
102 33 0.20
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (98 bp):
AAGGTTGAACTTTTAATTAAAAGTTGAAACTTTTAAGAAATTTGTAAATAAAGTTGAAATTTTAA
TTAAAAGATTGAACTTTTAAGTAATTTGTAAAT
Found at i:10182 original size:42 final size:42
Alignment explanation
Indices: 10130--10209 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
10120 TCTAAAATCT
* *
10130 GTTTGGGCCTTGCATGTTTATTATTTGGGCTTCAGTTGATCC
1 GTTTGAGCCTTGCATGTTTATTATCTGGGCTTCAGTTGATCC
**
10172 GTTTGAGCCTTGTGTGTTTATTATCTGGGCTTCAGTTG
1 GTTTGAGCCTTGCATGTTTATTATCTGGGCTTCAGTTG
10210 TTATTCATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.11, C:0.15, G:0.28, T:0.46
Consensus pattern (42 bp):
GTTTGAGCCTTGCATGTTTATTATCTGGGCTTCAGTTGATCC
Done.