Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023965.1 Corchorus olitorius cultivar O-4 contig23998, 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: 6705
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:2803 original size:4 final size:5
Alignment explanation
Indices: 2782--2877 Score: 58
Period size: 6 Copynumber: 18.8 Consensus size: 5
2772 GAAATTCAAA
*
2782 AAAAT AATAAT AAAAT -AAAT AAAAT AAAAT AAAATT AAAA- AAAA- AAACAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAA-AT
* * *
2832 AAAAT -CAAT AAAAA AAAAG AAGAA- AAAAT CAAAAT CAAAAT CAAAA
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT -AAAAT -AAAAT -AAAA
2878 GAGAATTGAT
Statistics
Matches: 77, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
4 16 0.21
5 30 0.39
6 31 0.40
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:2807 original size:14 final size:15
Alignment explanation
Indices: 2779--2814 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2769 TAAGAAATTC
2779 AAAA-AAATAATAAT
1 AAAATAAATAATAAT
2793 AAAATAAATAA-AAT
1 AAAATAAATAATAAT
2807 AAAATAAA
1 AAAATAAA
2815 ATTAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAAATAATAAT
Found at i:2807 original size:20 final size:19
Alignment explanation
Indices: 2782--2877 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 19
2772 GAAATTCAAA
2782 AAAATAATAATAAAATAAAT
1 AAAATAA-AATAAAATAAAT
2802 AAAATAAAATAAAATTAAA-
1 AAAATAAAATAAAA-TAAAT
* * *
2821 AAAAAAAACAAAAAATCAAT
1 AAAATAAA-ATAAAATAAAT
* * *
2841 AAAAAAAAAGAAGAAAAAAT
1 AAAATAAAATAA-AATAAAT
2861 CAAAATCAAAATCAAAA
1 -AAAAT-AAAAT-AAAA
2878 GAGAATTGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
19 20 0.33
20 29 0.48
21 4 0.07
22 6 0.10
23 2 0.03
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (19 bp):
AAAATAAAATAAAATAAAT
Found at i:2826 original size:11 final size:10
Alignment explanation
Indices: 2779--2865 Score: 59
Period size: 11 Copynumber: 8.2 Consensus size: 10
2769 TAAGAAATTC
2779 AAAAAAATAA
1 AAAAAAATAA
*
2789 TAATAAAAT-A
1 -AAAAAAATAA
*
2799 AATAAAATAA
1 AAAAAAATAA
*
2809 AATAAAATTAA
1 AA-AAAAATAA
*
2820 AAAAAAAAACA
1 AAAAAAATA-A
2831 AAAAATCAATAA
1 AAAAA--AATAA
*
2843 AAAAAAAGAA
1 AAAAAAATAA
*
2853 GAAAAAATCAA
1 AAAAAAAT-AA
2864 AA
1 AA
2866 TCAAAATCAA
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
9 8 0.13
10 19 0.32
11 24 0.40
12 6 0.10
13 3 0.05
ACGTcount: A:0.80, C:0.03, G:0.02, T:0.14
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:2836 original size:39 final size:40
Alignment explanation
Indices: 2773--2849 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
2763 CTCAATTAAG
* * * *
2773 AAATTCAAAAAAATAATAATAAAATAAATAAAATAAAATA
1 AAATTAAAAAAAAAAACAATAAAATAAATAAAAAAAAATA
*
2813 AAATTAAAAAAAAAAACAA-AAAATCAATAAAAAAAAA
1 AAATTAAAAAAAAAAACAATAAAATAAATAAAAAAAAA
2850 GAAGAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 16 0.50
40 16 0.50
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (40 bp):
AAATTAAAAAAAAAAACAATAAAATAAATAAAAAAAAATA
Found at i:2857 original size:23 final size:24
Alignment explanation
Indices: 2778--2863 Score: 63
Period size: 25 Copynumber: 3.5 Consensus size: 24
2768 TTAAGAAATT
2778 CAAAAAAAT-AATAATAAAATAAATAA
1 CAAAAAAATCAATAA-AAAA-AAA-AA
* *
2804 -AATAAAATAAAATTAAAAAAAAAAA
1 CAAAAAAAT-CAA-TAAAAAAAAAAA
2829 C-AAAAAATCAATAAAAAAAAAGAA
1 CAAAAAAATCAATAAAAAAAAA-AA
*
2853 -GAAAAAATCAA
1 CAAAAAAATCAA
2864 AATCAAAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
23 10 0.20
24 14 0.27
25 15 0.29
26 3 0.06
27 6 0.12
28 3 0.06
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (24 bp):
CAAAAAAATCAATAAAAAAAAAAA
Found at i:2871 original size:24 final size:24
Alignment explanation
Indices: 2818--2863 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2808 AAATAAAATT
2818 AAAAAAAAAAACAAAAAATCAATA
1 AAAAAAAAAAACAAAAAATCAATA
* *
2842 AAAAAAAAGAAGAAAAAATCAA
1 AAAAAAAAAAACAAAAAATCAA
2864 AATCAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.83, C:0.07, G:0.04, T:0.07
Consensus pattern (24 bp):
AAAAAAAAAAACAAAAAATCAATA
Found at i:3549 original size:50 final size:50
Alignment explanation
Indices: 3474--3623 Score: 228
Period size: 50 Copynumber: 3.0 Consensus size: 50
3464 AGTTTTACAA
* *
3474 TAAAATTGCTTTCCATTTATGAGTTCAAGACCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
*
3524 TAAAATTGCTTTCCATTTGTTAGTTCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
** * **
3574 TAGGATTGCATTCCATTTGTGAGACCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
3624 GGCATTTAAG
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
Found at i:4372 original size:50 final size:50
Alignment explanation
Indices: 4297--4638 Score: 488
Period size: 50 Copynumber: 6.8 Consensus size: 50
4287 GAATGTTTTG
* * *
4297 GGCTTTTTCACAAGCCGAACTCGTTTCCATATGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
4347 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATTAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
4397 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * * *
4447 GGCTTTTCCACAAGTCAAACTTGTTTCCATACGAGT-AAATATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
4496 GGCTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * *
4546 GGCTTTTCCACAAGCCAAACTCGTTTCCGTACGAGTCGACTATCCAAGCCACGTA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAT-CAA--CA--TA
* *
4601 GGCTTTTCCACAAGTCTAACTCGTTTCCATACGAGTCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
4639 GTTCAAACAT
Statistics
Matches: 266, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
49 46 0.17
50 179 0.67
51 3 0.01
53 2 0.01
55 36 0.14
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
Found at i:4539 original size:99 final size:100
Alignment explanation
Indices: 4297--4638 Score: 497
Period size: 99 Copynumber: 3.4 Consensus size: 100
4287 GAATGTTTTG
* *
4297 GGCTTTTTCACAAGCCGAACTCGTTTCCATATGAGTCAATTATCAACATAGGCTTTTCCACAAGC
1 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGC
* * *
4362 CGAACTCGTTTCCATACGAGTCAATTATTAACATA
66 CAAACTCGTTTCCATACGAGTCAAATATCAACATA
*
4397 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGT
1 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGC
* *
4462 CAAACTTGTTTCCATACGAGT-AAATATCAACATG
66 CAAACTCGTTTCCATACGAGTCAAATATCAACATA
* *
4496 GGCTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGC
1 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGC
* * *
4561 CAAACTCGTTTCCGTACGAGTCGACTATCCAAGCCACGTA
66 CAAACTCGTTTCCATACGAGTCAAATAT-CAA--CA--TA
* *
4601 GGCTTTTCCACAAGTCTAACTCGTTTCCATACGAGTCA
1 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCA
4639 GTTCAAACAT
Statistics
Matches: 219, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
99 91 0.42
100 85 0.39
101 3 0.01
103 2 0.01
105 38 0.17
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (100 bp):
GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGC
CAAACTCGTTTCCATACGAGTCAAATATCAACATA
Found at i:4568 original size:149 final size:153
Alignment explanation
Indices: 4297--4638 Score: 503
Period size: 149 Copynumber: 2.2 Consensus size: 153
4287 GAATGTTTTG
* * * * *
4297 GGCTTTTTCACAAGCCGAACTCGTTTCCATATGAGTCAATTATCAACATAGGCTTTTCCACAAGC
1 GGCTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAAATATCAACATAGGCTTTTCCACAAGC
* * *
4362 CGAACTCGTTTCCATACGAGTCAATTATTAACATAGGCTTTTCCACAAGCCGAACTCGTTTCCAT
66 CAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCAT
*
4427 ACGAGTCAATTAT-CAA-CA-TA
131 ACGAGTCAACTATCCAACCACTA
* * *
4447 GGCTTTTCCACAAGTCAAACTTGTTTCCATACGAGT-AAATATCAACATGGGCTTTTCCACAAGT
1 GGCTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAAATATCAACATAGGCTTTTCCACAAGC
*
4511 CAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCGT
66 CAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCAT
*
4576 ACGAGTCGACTATCCAAGCCACGTA
131 ACGAGTCAACTATCCAA-CCAC-TA
*
4601 GGCTTTTCCACAAGTCTAACTCGTTTCCATACGAGTCA
1 GGCTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCA
4639 GTTCAAACAT
Statistics
Matches: 170, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
149 97 0.57
150 34 0.20
152 2 0.01
154 36 0.21
155 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (153 bp):
GGCTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAAATATCAACATAGGCTTTTCCACAAGC
CAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCAT
ACGAGTCAACTATCCAACCACTA
Found at i:5171 original size:19 final size:19
Alignment explanation
Indices: 5147--5184 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5137 GGGTCACATA
5147 AGGGGCACTTCGGTCATTT
1 AGGGGCACTTCGGTCATTT
* *
5166 AGGGGCATTTTGGTCATTT
1 AGGGGCACTTCGGTCATTT
5185 TTACATTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.37
Consensus pattern (19 bp):
AGGGGCACTTCGGTCATTT
Found at i:5486 original size:10 final size:10
Alignment explanation
Indices: 5471--5497 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5461 GATTAGGTTC
5471 AAAAAATCCA
1 AAAAAATCCA
5481 AAAAAATCCA
1 AAAAAATCCA
5491 AAAAAAT
1 AAAAAAT
5498 GTGATTGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAATCCA
Done.