Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013734.1 Corchorus olitorius cultivar O-4 contig13767, 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: 4194
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Found at i:2603 original size:39 final size:39
Alignment explanation
Indices: 2552--2689 Score: 204
Period size: 39 Copynumber: 3.5 Consensus size: 39
2542 AGGATTTTTT
2552 TGAAATTGACTGATAAAGCAAGGATCCTAAATGGGATTC
1 TGAAATTGACTGATAAAGCAAGGATCCTAAATGGGATTC
2591 TGAAATTGACTGATAAAGCAAGGATCCTAAATGGGATTC
1 TGAAATTGACTGATAAAGCAAGGATCCTAAATGGGATTC
* * * * *
2630 TGAAATTGACTGATAAAGAAATGATCCTGAGTAGGATTC
1 TGAAATTGACTGATAAAGCAAGGATCCTAAATGGGATTC
* *
2669 TGAAATTAATTTGATAAAGCA
1 TGAAATTGA-CTGATAAAGCA
2690 TTGATCCTGA
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 81 0.90
40 9 0.10
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.28
Consensus pattern (39 bp):
TGAAATTGACTGATAAAGCAAGGATCCTAAATGGGATTC
Found at i:2695 original size:40 final size:40
Alignment explanation
Indices: 2640--2984 Score: 500
Period size: 40 Copynumber: 8.7 Consensus size: 40
2630 TGAAATTGAC
* * *
2640 TGATAAAGAAATGATCCTGAGTAGGATTCTGAAATTAATT
1 TGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
* * *
2680 TGATAAAGCATTGATCCTGAGCGGGGTTTTGAAATTAATT
1 TGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
*
2720 TG-TAAAGCAATGATCCTGAGTAGGATTTTGAAATTAATT
1 TGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
2759 TGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATT
1 TGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
* * *
2799 TGATAAAGCAATGATCTTGAGCAGGGTTTTGAAATTAACT
1 TGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
* *
2839 TGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATT
1 TGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
2879 TGATAAAG-AGATGATCCTGAGCAGGATTTTGAAATTAATT
1 TGATAAAGCA-ATGATCCTGAGCAGGATTTTGAAATTAATT
* *
2919 TG-TAAAGCAATGATCCTGAGCGGGGTTTTGAAATTAATT
1 TGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
*
2958 TG-TAAAGCAATGATCCTGAGTAGGATT
1 TGATAAAGCAATGATCCTGAGCAGGATT
2985 GTGATTGACT
Statistics
Matches: 276, Mismatches: 26, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
39 93 0.34
40 183 0.66
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (40 bp):
TGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATT
Found at i:2726 original size:79 final size:80
Alignment explanation
Indices: 2640--2984 Score: 545
Period size: 79 Copynumber: 4.3 Consensus size: 80
2630 TGAAATTGAC
* * * * *
2640 TGATAAAGAAATGATCCTGAGTAGGATTCTGAAATTAATTTGATAAAGCATTGATCCTGAGCGGG
1 TGATAAAGCAATGATCCTGAGTAGGATTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAGG
2705 GTTTTGAAATTAATT
66 GTTTTGAAATTAATT
2720 TG-TAAAGCAATGATCCTGAGTAGGATTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAGG
1 TGATAAAGCAATGATCCTGAGTAGGATTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAGG
2784 GTTTTGAAATTAATT
66 GTTTTGAAATTAATT
* * * *
2799 TGATAAAGCAATGATCTTGAGCAGGGTTTTGAAATTAACTTGATAAAACAATGATCCTGAGCAGG
1 TGATAAAGCAATGATCCTGAGTAGGATTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAGG
2864 GTTTTGAAATTAATT
66 GTTTTGAAATTAATT
* * *
2879 TGATAAAG-AGATGATCCTGAGCAGGATTTTGAAATTAATTTG-TAAAGCAATGATCCTGAGCGG
1 TGATAAAGCA-ATGATCCTGAGTAGGATTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAG
2942 GGTTTTGAAATTAATT
65 GGTTTTGAAATTAATT
2958 TG-TAAAGCAATGATCCTGAGTAGGATT
1 TGATAAAGCAATGATCCTGAGTAGGATT
2985 GTGATTGACT
Statistics
Matches: 247, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
78 22 0.09
79 113 0.46
80 112 0.45
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (80 bp):
TGATAAAGCAATGATCCTGAGTAGGATTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAGG
GTTTTGAAATTAATT
Found at i:3058 original size:39 final size:37
Alignment explanation
Indices: 2960--3060 Score: 121
Period size: 39 Copynumber: 2.7 Consensus size: 37
2950 AATTAATTTG
* * **
2960 TAAAGCAATGATCCTGAGTAGGATTGTGATTGACTGG
1 TAAAGCAATGATCCTGAGTAGGATTCTGATCGACTAA
*
2997 TAAAGAAATGATCCTGAGTAGGATTCTGGAATCGACTAA
1 TAAAGCAATGATCCTGAGTAGGATTCT-G-ATCGACTAA
* *
3036 TAAAGCAATGATCATGAATAGGATT
1 TAAAGCAATGATCCTGAGTAGGATT
3061 AAAACACATA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
37 25 0.46
38 1 0.02
39 28 0.52
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28
Consensus pattern (37 bp):
TAAAGCAATGATCCTGAGTAGGATTCTGATCGACTAA
Found at i:3359 original size:47 final size:47
Alignment explanation
Indices: 3290--3415 Score: 216
Period size: 47 Copynumber: 2.7 Consensus size: 47
3280 GAGGTTTCTG
* *
3290 AAATTGAAGACTCGCATGGAAGCGAGAAAAGACCATCTTTGGTCACT
1 AAATTGCAGACTCGCATGGAAGCGAGAAAAGACCAACTTTGGTCACT
*
3337 AAATTGCAGACTCGCGTGGAAGCGAGAAAAGACCAACTTTGGTCACT
1 AAATTGCAGACTCGCATGGAAGCGAGAAAAGACCAACTTTGGTCACT
*
3384 AAATTGCAAACTCGCATGGAAGCGAGAAAAGA
1 AAATTGCAGACTCGCATGGAAGCGAGAAAAGA
3416 TTACCTGGAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 74 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (47 bp):
AAATTGCAGACTCGCATGGAAGCGAGAAAAGACCAACTTTGGTCACT
Found at i:3827 original size:137 final size:135
Alignment explanation
Indices: 3526--3935 Score: 491
Period size: 137 Copynumber: 3.0 Consensus size: 135
3516 CTCATGGGAC
* * * * *
3526 TTGGCTTATGGAAAAGCCCTTGTTGCTTGGATGGAACCAATGTTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGT-GAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTG-CTCGTATGGAAAC
* * * * * * * *
3591 GAGTTTGGCTTGTG-GAAAAGCCCTTACCGCATGTATGGAACCGAGGCTTGAACTTATTCGTATG
63 GAGTTTGGCTTGTGAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTGACTCGTATG
* *
3655 GAAATGAGT
127 GAAACGAAT
* * *
3664 TTGGCTTGTAAGAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTAGCTCGTGTGGGAACG
1 TTGGCTTGTGA-AAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACT-GCTCGTATGGAAACG
* * * *
3729 AGTTTGGCTTGGGAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTGTGGG
64 AGTTTGGCTTGTGAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGACTCGTATGGA
3794 AACGAAT
129 AACGAAT
*
3801 TTGGTTTGTTGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
1 TTGGCTTG-TGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACT-GCTCGTATGGAAACG
* *
3866 AGTTTGGCTTGTAAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAAACT-ACCCCGTATG
64 AGTTTGGCTTGTGAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTGA-CTCGTATG
3930 GAAACG
127 GAAACG
3936 GGTCTGACTT
Statistics
Matches: 233, Mismatches: 33, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
137 149 0.64
138 84 0.36
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (135 bp):
TTGGCTTGTGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGCTCGTATGGAAACGAG
TTTGGCTTGTGAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGACTCGTATGGAAA
CGAAT
Found at i:3850 original size:68 final size:68
Alignment explanation
Indices: 3526--3935 Score: 489
Period size: 69 Copynumber: 6.0 Consensus size: 68
3516 CTCATGGGAC
* * * * * * *
3526 TTGGCTTATGGAAAAGCCCTTGTTGCTTGGATGGAACCAATGTTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTGGCTCGTATGGAAAC
3591 GAGT
65 GAGT
* * * * * * * *** *
3595 TTGGCTTGTGGAAAAGCCCTTACCGCATGTATGGAACCGAGGCTTGAACTTATTCGTATGGAAAT
1 TTGGCTTGTAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTGGCTCGTATGGAAAC
3660 GAGT
65 GAGT
* * *
3664 TTGGCTTGTA-AGAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTAGCTCGTGTGGGAAC
1 TTGGCTTGTAGA-AAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
3728 GAGT
65 GAGT
* * *
3732 TTGGCTTGGGAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTGTGGGAAC
1 TTGGCTT-GTAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
*
3797 GAAT
65 GAGT
* *
3801 TTGGTTTGTTGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
1 TTGGCTTGTAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
3866 AGT
66 AGT
** *
3869 TTGGCTTGTAAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAAACTACCCCGTATGGAAA
1 TTGGCTTGT-AGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTGGCTCGTATGGAAA
3934 CG
64 CG
3936 GGTCTGACTT
Statistics
Matches: 297, Mismatches: 39, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
68 89 0.30
69 190 0.64
70 18 0.06
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (68 bp):
TTGGCTTGTAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
AGT
Found at i:3970 original size:137 final size:136
Alignment explanation
Indices: 3692--3975 Score: 336
Period size: 137 Copynumber: 2.1 Consensus size: 136
3682 CCTGCTGCTT
* * *
3692 GGATGGAACCAAGGCTTAACTAGCTCGTGTGGGAACGAGTTTGGCTTGGGAGAAAAGCCCCTGCT
1 GGATGGAACCAAGGCTTAACTAGCTCGTATGGAAACGAGTTTGGCTTGGAAGAAAAGCCCCTGCT
** * * * * ** * * ***
3757 GCTTGGATGGAACCAAGGCTTAACTGGCTCGTGTGGGAACGAATTTGGTTTGTTGAAAAGCCCCT
66 GCTTGGATGGAACCAAGGCTTAACTACCCCGTATGGAAACGAATCTGACTTATGGAAAAGCCAAA
*
3822 GCTGCTT
131 GCT-CTC
* *
3829 GGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACGAGTTTGGCTTGTAAGAAAAGCCCCTGCT
1 GGATGGAACCAAGGCTTAACTAGCTCGTATGGAAACGAGTTTGGCTTGGAAGAAAAGCCCCTGCT
** *
3894 GCTTGGATGGAACCAAGGCTTAAACTACCCCGTATGGAAACGGGTCTGACTTATGGAAAAGTCAA
66 GCTTGGATGGAACCAAGGCTT-AACTACCCCGTATGGAAACGAATCTGACTTATGGAAAAGCCAA
3959 AGCAT-TC
130 AGC-TCTC
3966 GGATGGAACC
1 GGATGGAACC
3976 GAAGAAAAAT
Statistics
Matches: 123, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
137 92 0.75
138 30 0.24
139 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (136 bp):
GGATGGAACCAAGGCTTAACTAGCTCGTATGGAAACGAGTTTGGCTTGGAAGAAAAGCCCCTGCT
GCTTGGATGGAACCAAGGCTTAACTACCCCGTATGGAAACGAATCTGACTTATGGAAAAGCCAAA
GCTCTC
Done.