Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017312.1 Corchorus olitorius cultivar O-4 contig17345, 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: 8685
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:907 original size:52 final size:52
Alignment explanation
Indices: 871--1079 Score: 345
Period size: 52 Copynumber: 4.1 Consensus size: 52
861 TCTAATATAT
* **
871 TAAAAGGATCGTCTTCCATTTATCCTTTGAACTGTCTACCAATTCAA-TCT-
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
*
921 CAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
973 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
*
1025 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAAATCAA-TCT-
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
1075 TAAAA
1 TAAAA
1080 AAAGGTAATG
Statistics
Matches: 151, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
50 48 0.32
51 6 0.04
52 97 0.64
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (52 bp):
TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
Found at i:1072 original size:104 final size:100
Alignment explanation
Indices: 870--1079 Score: 339
Period size: 102 Copynumber: 2.1 Consensus size: 100
860 TTCTAATATA
* *
870 TTAAAAGGATCGTCTTCCATTTATCCTTTGAACTGTCTACCAATTCAATCTCAAAAGGACCGTCT
1 TTAAAAGGACCGTCTTCCACTTATCCTTTGAACTGTCTACCAATTCAATCTCAAAAGGACCGTCT
*
935 TCCGCTTATCCTTTGAACTGTCTACCAATTCAATTC
66 TCCGCTTATCCTTTGAACTGTCTACCAAATCAA-TC
* *
971 TATAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTATAAAAGGACCG
1 T-TAAAAGGACCGTCTTCCACTTATCCTTTGAACTGTCTACCAATTCAA-TCT-CAAAAGGACCG
1036 TCTTCCGCTTATCCTTTGAACTGTCTACCAAATCAATC
63 TCTTCCGCTTATCCTTTGAACTGTCTACCAAATCAATC
1074 TTAAAA
1 TTAAAA
1080 AAAGGTAATG
Statistics
Matches: 101, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
101 1 0.01
102 49 0.49
103 6 0.06
104 45 0.45
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (100 bp):
TTAAAAGGACCGTCTTCCACTTATCCTTTGAACTGTCTACCAATTCAATCTCAAAAGGACCGTCT
TCCGCTTATCCTTTGAACTGTCTACCAAATCAATC
Found at i:1940 original size:50 final size:50
Alignment explanation
Indices: 1881--2024 Score: 211
Period size: 50 Copynumber: 2.9 Consensus size: 50
1871 CTTCAATGTC
* *
1881 CTTTGAAAAGCGAATTTTGATCTTGGACTCATAAATGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATCTTA
* * ** *
1931 CTTTGAAAAGCAAATTTTGATATTGAACTCACGAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATCTTA
1981 --TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAAT
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAAT
2025 TTTATTGTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
48 40 0.48
50 43 0.52
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATCTTA
Found at i:2005 original size:48 final size:48
Alignment explanation
Indices: 1883--2036 Score: 218
Period size: 48 Copynumber: 3.1 Consensus size: 48
1873 TCAATGTCCT
* * *
1883 TTGAAAAGCGAATTTTGATCTTGGACTCATAAATGGAATGCAATCTTA
1 TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
* * **
1931 CTTTGAAAAGCAAATTTTGATATTGAACTCACGAATGGAAAGCAATTTTA
1 --TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1981 TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1 TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
2029 TTGTAAAA
1 TTG-AAAA
2037 CTTCTTGTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
48 47 0.51
49 4 0.04
50 41 0.45
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (48 bp):
TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
Found at i:2657 original size:5 final size:5
Alignment explanation
Indices: 2642--2722 Score: 60
Period size: 5 Copynumber: 15.6 Consensus size: 5
2632 TCAATTCTCT
*
2642 TTTGAA TTTGA TTTGA TTTGA TTTGA TTTTTGA -TTGA CTTGA TTTTTGA
1 TTTG-A TTTGA TTTGA TTTGA TTTGA --TTTGA TTTGA TTTGA --TTTGA
* *
2691 -TTGA CTTTGA TTTGA TTT-T TTTGA ATTGA TTT
1 TTTGA -TTTGA TTTGA TTTGA TTTGA TTTGA TTT
2723 TTTTGAATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
4 11 0.18
5 34 0.55
6 8 0.13
7 9 0.15
ACGTcount: A:0.20, C:0.02, G:0.17, T:0.60
Consensus pattern (5 bp):
TTTGA
Found at i:2678 original size:16 final size:16
Alignment explanation
Indices: 2653--2703 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
2643 TTGAATTTGA
2653 TTTGATTTGATTTGATT
1 TTTGA-TTGATTTGATT
*
2670 TTTGATTGACTTGATT
1 TTTGATTGATTTGATT
2686 TTTGATTGACTTTGATT
1 TTTGATTGA-TTTGATT
2703 T
1 T
2704 GATTTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTGATTGATTTGATT
Found at i:2719 original size:14 final size:14
Alignment explanation
Indices: 2696--2740 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
2686 TTTGATTGAC
*
2696 TTTGATTTGATTTT
1 TTTGAATTGATTTT
2710 TTTGAATTGATTTT
1 TTTGAATTGATTTT
2724 TTTGAATT--TTTT
1 TTTGAATTGATTTT
2736 TTTGA
1 TTTGA
2741 GTTTCTTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 9 0.30
14 21 0.70
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (14 bp):
TTTGAATTGATTTT
Found at i:2728 original size:38 final size:37
Alignment explanation
Indices: 2648--2724 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 37
2638 CTCTTTTGAA
*
2648 TTTGATTTGATTTGATTTGATTTTTGATTGACTTGATT
1 TTTGATTTGATTTGATTTGATTTTT-ATTGAATTGATT
2686 TTTGA-TTGACTTTGATTTGATTTTT-TTGAATTGATT
1 TTTGATTTGA-TTTGATTTGATTTTTATTGAATTGATT
2722 TTT
1 TTT
2725 TTGAATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
36 13 0.35
37 4 0.11
38 20 0.54
ACGTcount: A:0.18, C:0.03, G:0.17, T:0.62
Consensus pattern (37 bp):
TTTGATTTGATTTGATTTGATTTTTATTGAATTGATT
Found at i:2732 original size:24 final size:24
Alignment explanation
Indices: 2643--2736 Score: 65
Period size: 24 Copynumber: 3.9 Consensus size: 24
2633 CAATTCTCTT
* *
2643 TTGAATTTGATTTGATTTGATTTGA
1 TTGACTTTGATTTGATTT-TTTTGA
2668 TT---TTTGA-TTGACTTGATTTTTGA
1 TTGACTTTGATTTGA-TT--TTTTTGA
2691 TTGACTTTGATTTGATTTTTTTGAA
1 TTGACTTTGATTTGATTTTTTTG-A
*
2716 TTGA-TTT-TTTTGAATTTTTTT
1 TTGACTTTGATTTG-ATTTTTTT
2737 TTGAGTTTCT
Statistics
Matches: 58, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
21 4 0.07
22 7 0.12
23 11 0.19
24 18 0.31
25 7 0.12
26 7 0.12
27 4 0.07
ACGTcount: A:0.19, C:0.02, G:0.16, T:0.63
Consensus pattern (24 bp):
TTGACTTTGATTTGATTTTTTTGA
Found at i:3134 original size:12 final size:11
Alignment explanation
Indices: 3114--3161 Score: 64
Period size: 10 Copynumber: 4.5 Consensus size: 11
3104 TCCAAGTTGC
3114 TTTTTTTTCAT
1 TTTTTTTTCAT
3125 TTTCTTTTTCAT
1 TTT-TTTTTCAT
3137 TTTTTTTTC-T
1 TTTTTTTTCAT
*
3147 TCTTTTTT-AT
1 TTTTTTTTCAT
3157 TTTTT
1 TTTTT
3162 ATTATTGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 13 0.39
11 9 0.27
12 11 0.33
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCAT
Found at i:3671 original size:76 final size:76
Alignment explanation
Indices: 3531--3679 Score: 183
Period size: 76 Copynumber: 2.0 Consensus size: 76
3521 CACTCACCTT
* * * * *
3531 GAAATCATCGCTTTGACCAAAATTGATTTTGAAACATCTTTTGATTAAAACACCGTCATTCCTTT
1 GAAATCATAGCTTTGACCAAAACTGATTTTGAAAAATCTTTTGATTAAAACACCATCATCCCTTT
*
3596 GCTTACAGCTC
66 GCTCACAGCTC
* * * * *
3607 GAAATCATAGTTTTGACTAAAACTGATTTTGAAAAATCTTTTTGTTTGAAAC-TCATCATCCCTT
1 GAAATCATAGCTTTGACCAAAACTGATTTTGAAAAATC-TTTTGATTAAAACACCATCATCCCTT
3671 TGCTCACAG
65 TGCTCACAG
3680 TCCAGATAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
76 50 0.82
77 11 0.18
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (76 bp):
GAAATCATAGCTTTGACCAAAACTGATTTTGAAAAATCTTTTGATTAAAACACCATCATCCCTTT
GCTCACAGCTC
Done.