Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024545.1 Corchorus olitorius cultivar O-4 contig24578, 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: 18388
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:911 original size:107 final size:108
Alignment explanation
Indices: 774--979 Score: 258
Period size: 107 Copynumber: 1.9 Consensus size: 108
764 CAAATTGAAA
* *
774 ATCAACTCTGATCATCAAAAACGTCTTGGAATGACTGCACTGTAGCAAT-TGAAGATCAACTCT-
1 ATCAACTCTGATCATCAAAAACGTCTTGGAATGACCGCACTGGAGC-ATCTG-AGATCAACTCTG
*
837 GATCATTG-AAAATTTCTTGGAAAGACCGCACTAGATCATCTGGG
64 GATCATTGAAAAACTTCTTGGAAAGACCGCACTAGATCATCTGGG
* * * *
881 ATCAACTCTGATC-TCTAAGAACTTCTTGGAATGACCGCACTGGATCATCTGGGATCAACTCTGA
1 ATCAACTCTGATCATC-AAAAACGTCTTGGAATGACCGCACTGGAGCATCTGAGATCAACTCT--
*
945 GGATCATTGAAAAAACTTCTTGGAATGACCGCACT
63 GGATCATTG-AAAAACTTCTTGGAAAGACCGCACT
980 GGTTCTTGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
106 14 0.17
107 40 0.48
109 8 0.10
111 22 0.26
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (108 bp):
ATCAACTCTGATCATCAAAAACGTCTTGGAATGACCGCACTGGAGCATCTGAGATCAACTCTGGA
TCATTGAAAAACTTCTTGGAAAGACCGCACTAGATCATCTGGG
Found at i:979 original size:58 final size:54
Alignment explanation
Indices: 741--981 Score: 233
Period size: 53 Copynumber: 4.4 Consensus size: 54
731 ACGGAAACCT
* ** *
741 TTCTTGGAATGATCGCACTGGATCAAAT-TGAAAATCAACTCTGATCA-TCAAAAAC
1 TTCTTGGAATGACCGCACTGGATC--ATCTG-GGATCAACTCTGATCATTGAAAAAC
* * * * * *
796 GTCTTGGAATGACTGCACTGTAGCAAT-TGAAGATCAACTCTGATCATTG-AAAAT
1 TTCTTGGAATGACCGCACTGGATC-ATCTG-GGATCAACTCTGATCATTGAAAAAC
* * *
850 TTCTTGGAAAGACCGCACTAGATCATCTGGGATCAACTCTGATC-TCT-AAGAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGGGATCAACTCTGATCAT-TGAAAAAC
903 TTCTTGGAATGACCGCACTGGATCATCTGGGATCAACTCTGAGGATCATTGAAAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGGGATCAACTCT---GATCATTG-AAAAAC
961 TTCTTGGAATGACCGCACTGG
1 TTCTTGGAATGACCGCACTGG
982 TTCTTGAAAC
Statistics
Matches: 156, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
52 1 0.01
53 58 0.37
54 45 0.29
55 20 0.13
56 5 0.03
57 1 0.01
58 26 0.17
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (54 bp):
TTCTTGGAATGACCGCACTGGATCATCTGGGATCAACTCTGATCATTGAAAAAC
Found at i:1022 original size:35 final size:35
Alignment explanation
Indices: 982--1586 Score: 951
Period size: 35 Copynumber: 17.3 Consensus size: 35
972 ACCGCACTGG
* *
982 TTCTTGAAACGAGATCAACTCTGATAATCGAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
*
1017 TTCTTGAAACGAGATCAACTCTGATCATCGAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
1052 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
*
1087 TTCTTGAAACGAGATCAACTCTGATCATCGAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
* *
1122 TTCTTGAAATGAGATCAACTCTGATCATAAAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
*
1157 TTCTTGAAACTAGATCAACTCTGATCATCAAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
1192 TTCTTGAAACGAGATCAACTCTGATCATC-AAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
* *
1226 TTCTTGAAACGAGATGAACTCTGATCATCGAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
* * *
1261 TTCTAGAAATGAGATCAACTCTGATCATAAAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
* *
1296 TTCTTGAAACGAGATCAACTCTGATTATCGAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
* *
1331 TTCTTGAAAGGAGATCAACTCTGATCATAAAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
* *
1366 TTCTTGAAACGAGATCAACTCTGATCATAAAAAAAT
1 TTCTTGAAACGAGATCAACTCTGATCAT-CAAAAAC
* *
1402 TTCTTGAAATGAGATCAACTCTGATCTTCAAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
* *
1437 TTCTTGAAATGAGATCAACTCTGATCTTCAAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
* *
1472 TTCTTGAAAGGAGATCAACTCTGATCATCGAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
*
1507 TTCTTGAAACGAGATCAACTCTGATCATCGAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
*
1542 TTCTTGAAACGAGATCAACTCTGATCATCGAAAAC
1 TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
1577 TTCTATGAAA
1 TTCT-TGAAA
1587 GGCCACACAG
Statistics
Matches: 532, Mismatches: 35, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
34 33 0.06
35 462 0.87
36 37 0.07
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (35 bp):
TTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
Found at i:2823 original size:39 final size:39
Alignment explanation
Indices: 2745--2825 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
2735 ATCTTTTTGA
* *
2745 AAAACATTTTTTCTCTTTTAAAAAGATTCCACTTTGAGG
1 AAAACATTTTTTCTCTTTTAAAAAGATTCCACCTAGAGG
*
2784 AAAACATTTTTT-TCTTTTGAAAAAGA-TCACGCCTAGAGG
1 AAAACATTTTTTCTCTTTT-AAAAAGATTC-CACCTAGAGG
2823 AAA
1 AAA
2826 GTTTCATTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 8 0.22
39 29 0.78
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTTAAAAAGATTCCACCTAGAGG
Found at i:3039 original size:20 final size:22
Alignment explanation
Indices: 3004--3049 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
2994 ATTTCCTCCG
3004 TCTTTTGCTCTTTCAACT-TTT
1 TCTTTTGCTCTTTCAACTCTTT
* *
3025 TCTTTT-CTTTTTCAATTCTTT
1 TCTTTTGCTCTTTCAACTCTTT
3046 TCTT
1 TCTT
3050 CATTTTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.09, C:0.22, G:0.02, T:0.67
Consensus pattern (22 bp):
TCTTTTGCTCTTTCAACTCTTT
Found at i:3445 original size:14 final size:13
Alignment explanation
Indices: 3410--3456 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
3400 AAAACCGATT
*
3410 TTTTTGAAAACCC
1 TTTTTGAAAACAC
3423 TTTTCTGAAAACAC
1 TTTT-TGAAAACAC
3437 TTTCTTGAAAAGCA-
1 TTT-TTGAAAA-CAC
3451 TTTTTG
1 TTTTTG
3457 GCTTTTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 7 0.23
14 20 0.67
15 3 0.10
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (13 bp):
TTTTTGAAAACAC
Found at i:12470 original size:29 final size:30
Alignment explanation
Indices: 12423--12482 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
12413 GAAGTTCGTG
* *
12423 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
12454 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
12483 GGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:13866 original size:16 final size:15
Alignment explanation
Indices: 13845--13883 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
13835 TTACTTTGCT
13845 TTGTTTCCTAGTTTAA
1 TTGTTTCCT-GTTTAA
*
13861 TTGTTTTCTGTTTAA
1 TTGTTTCCTGTTTAA
13876 TTGCTTTC
1 TTG-TTTC
13884 TTTCAACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.62
Consensus pattern (15 bp):
TTGTTTCCTGTTTAA
Found at i:13875 original size:15 final size:16
Alignment explanation
Indices: 13845--13884 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
13835 TTACTTTGCT
*
13845 TTGTTTCCTAGTTTAA
1 TTGTTTTCTAGTTTAA
13861 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
13876 TTGCTTTCT
1 TTGTTTTCT
13885 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:15607 original size:27 final size:25
Alignment explanation
Indices: 15577--15626 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
15567 TTTTGTAGTA
15577 TTGAAATTTCGGTTTTGAAACCAAAGC
1 TTGAAATTTC--TTTTGAAACCAAAGC
* *
15604 TTGAATTTTCTTTTGAACCCAAA
1 TTGAAATTTCTTTTGAAACCAAA
15627 TTATTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
27 9 0.43
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (25 bp):
TTGAAATTTCTTTTGAAACCAAAGC
Done.