Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022024.1 Corchorus olitorius cultivar O-4 contig22057, 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: 30175
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:168 original size:39 final size:39
Alignment explanation
Indices: 125--201 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
115 TTAAAAGCAC
*
125 TTTTTTACAAAT-CAAGTTTTTCCCAACTGCAACCTCAAG
1 TTTTTCACAAATGC-AGTTTTTCCCAACTGCAACCTCAAG
* * *
164 TTTTTCCCAATTGCAGTTTTTCCCAACTGCAATCTCAA
1 TTTTTCACAAATGCAGTTTTTCCCAACTGCAACCTCAA
202 TGTCAAAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (39 bp):
TTTTTCACAAATGCAGTTTTTCCCAACTGCAACCTCAAG
Found at i:183 original size:16 final size:16
Alignment explanation
Indices: 162--194 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
152 TGCAACCTCA
*
162 AGTTTTTCCCAATTGC
1 AGTTTTTCCCAACTGC
178 AGTTTTTCCCAACTGC
1 AGTTTTTCCCAACTGC
194 A
1 A
195 ATCTCAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.39
Consensus pattern (16 bp):
AGTTTTTCCCAACTGC
Found at i:250 original size:47 final size:47
Alignment explanation
Indices: 181--277 Score: 158
Period size: 47 Copynumber: 2.1 Consensus size: 47
171 CAATTGCAGT
* *
181 TTTTCCCAACTGCAATCTCAATGTCAAAGTAAACCGAACTCCCAAGC
1 TTTTCCCAACTGCAACCTCAATGTCAAAGTAAACCAAACTCCCAAGC
* *
228 TTTTCCCAACTGCAACCTCAATGTCAAATTAAGCCAAACTCCCAAGC
1 TTTTCCCAACTGCAACCTCAATGTCAAAGTAAACCAAACTCCCAAGC
275 TTT
1 TTT
278 ACATTTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.33, C:0.32, G:0.09, T:0.26
Consensus pattern (47 bp):
TTTTCCCAACTGCAACCTCAATGTCAAAGTAAACCAAACTCCCAAGC
Found at i:393 original size:47 final size:47
Alignment explanation
Indices: 324--420 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
314 CAAAAGTAAG
324 ATGAAAATTCAATAATAAATATTGATCATAAACATCCTCCAACATAT
1 ATGAAAATTCAATAATAAATATTGATCATAAACATCCTCCAACATAT
371 ATGAAAATTCAATAATAAATATTGATCATAAACATCCTCCAACATAT
1 ATGAAAATTCAATAATAAATATTGATCATAAACATCCTCCAACATAT
418 ATG
1 ATG
421 GCCAAAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.30
Consensus pattern (47 bp):
ATGAAAATTCAATAATAAATATTGATCATAAACATCCTCCAACATAT
Found at i:2695 original size:39 final size:37
Alignment explanation
Indices: 2652--3035 Score: 247
Period size: 36 Copynumber: 10.8 Consensus size: 37
2642 ACCACCAGTT
*
2652 TACAAGTACAAGTCCCCTCCTCCTCCTCCTAAGGAGGCA
1 TACAAGTACAAGT--CCTCCTCCTCCTCCCAAGGAGGCA
*
2691 TACAAGTACAAGTCC-CCTCCTCCTCCTAAGGAGGCA
1 TACAAGTACAAGTCCTCCTCCTCCTCCCAAGGAGGCA
*
2727 TACAAGTACAAGT-CTCCTCCTCCTCCCAAGGAGTCA
1 TACAAGTACAAGTCCTCCTCCTCCTCCCAAGGAGGCA
* *
2763 TACAAGTACAAGT-CTCCTCCACCT-CC----AGTC-
1 TACAAGTACAAGTCCTCCTCCTCCTCCCAAGGAGGCA
*
2793 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
1 TACAAGTACAAGT--CCTCCTCCTCCTCCCAAGGAGGCA
* * **** **
2832 TACAAGTACAAGT-CTCCTCCACCACCACCCCCA-GTT
1 TACAAGTACAAGTCCTCCTCCTCCTCC-CAAGGAGGCA
* * *
2868 TACAAATACAAGT-CTCCTCCACCT-CC---G-GTC-
1 TACAAGTACAAGTCCTCCTCCTCCTCCCAAGGAGGCA
*
2898 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
1 TACAAGTACAAGT--CCTCCTCCTCCTCCCAAGGAGGCA
* * * **** *
2937 TACAAGTACAAGT-CTCCCCCACCACCACCTCCAGTC-
1 TACAAGTACAAGTCCTCCTCCTCCTCC-CAAGGAGGCA
* *
2973 TATAAGTACAAGT-CTCCTCCTCCTCCTAAGGA-GCA
1 TACAAGTACAAGTCCTCCTCCTCCTCCCAAGGAGGCA
* * *
3008 TTACAAGTATAAGT-CTCCCCCACCTCCC
1 -TACAAGTACAAGTCCTCCTCCTCCTCCC
3036 CCTCCAGTCT
Statistics
Matches: 276, Mismatches: 45, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
30 25 0.09
31 4 0.01
33 20 0.07
34 6 0.02
35 5 0.02
36 163 0.59
37 9 0.03
38 5 0.02
39 39 0.14
ACGTcount: A:0.27, C:0.40, G:0.12, T:0.21
Consensus pattern (37 bp):
TACAAGTACAAGTCCTCCTCCTCCTCCCAAGGAGGCA
Found at i:2748 original size:69 final size:69
Alignment explanation
Indices: 2652--2953 Score: 210
Period size: 69 Copynumber: 4.2 Consensus size: 69
2642 ACCACCAGTT
* *
2652 TACAAGTACAAGTCCCCTCCTCCTCCTCCTAAGGAGGCATACAAGTACAAGTCCCCTCCTCCTCC
1 TACAAGTACAAGT---CTCCTCCTCCT-C-AAGGAGTCATACAAGTACAAGTCCCCTCCACCTCC
2717 TAAGGAGGCA
61 -AAGGAGGCA
*
2727 TACAAGTACAAGTCTCCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCTCCTCCACCTCC---
1 TACAAGTACAAGTCTCCTCCTCCT--CAAGGAGTCATACAAGTACAAGTCCCCTCCACCTCCAAG
*
2789 -AGTC-
64 GAGGCA
* * *
2793 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCTCCACCACC
1 TACAAGTACAAGT---CTCCTCCTCCT--CAAGGAGTCATACAAGTACAAGTCCCCTCCACCTCC
*** **
2858 ACCCCCA-GTT
61 A--AGGAGGCA
* * * *
2868 TACAAATACAAGTCTCCTCCACCTC--CG-GTC-TACAAGTACAAGTCCCCTCCTCCTCCTCCCA
1 TACAAGTACAAGTCTCCTCCTCCTCAAGGAGTCATACAAGTACAAGT--CC-CCTCCACCT-CCA
*
2929 AGGAGCCA
62 AGGAGGCA
2937 TACAAGTACAAGTCTCC
1 TACAAGTACAAGTCTCC
2954 CCCACCACCA
Statistics
Matches: 189, Mismatches: 22, Indels: 38
0.76 0.09 0.15
Matches are distributed among these distances:
66 26 0.14
67 5 0.03
68 3 0.02
69 70 0.37
70 4 0.02
72 53 0.28
73 2 0.01
75 26 0.14
ACGTcount: A:0.27, C:0.40, G:0.13, T:0.21
Consensus pattern (69 bp):
TACAAGTACAAGTCTCCTCCTCCTCAAGGAGTCATACAAGTACAAGTCCCCTCCACCTCCAAGGA
GGCA
Found at i:2797 original size:30 final size:30
Alignment explanation
Indices: 2727--2923 Score: 124
Period size: 30 Copynumber: 5.9 Consensus size: 30
2717 TAAGGAGGCA
*
2727 TACAAGTACAAGTCTCCTCCTCCTCCCAAGGAGTC
1 TACAAGTACAAGTCTCCTCCACCT-CC----AGTC
2762 ATACAAGTACAAGTCTCCTCCACCTCCAGTC
1 -TACAAGTACAAGTCTCCTCCACCTCCAGTC
* *
2793 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCC
1 TACAAGTACAAGT---CTCCTCCACCT-CC----AGTC
* *
2831 ATACAAGTACAAGTCTCCTCCACCACCACCCCCAGTT
1 -TACAAGTACAAGTCTCCT------CCACCTCCAGTC
* *
2868 TACAAATACAAGTCTCCTCCACCTCCGGTC
1 TACAAGTACAAGTCTCCTCCACCTCCAGTC
* *
2898 TACAAGTACAAGTCCCCTCCTCCTCC
1 TACAAGTACAAGTCTCCTCCACCTCC
2924 TCCCAAGGAG
Statistics
Matches: 132, Mismatches: 14, Indels: 36
0.73 0.08 0.20
Matches are distributed among these distances:
30 45 0.34
31 4 0.03
33 10 0.08
34 2 0.02
35 2 0.02
36 45 0.34
37 2 0.02
38 3 0.02
39 13 0.10
41 2 0.02
42 4 0.03
ACGTcount: A:0.26, C:0.42, G:0.11, T:0.21
Consensus pattern (30 bp):
TACAAGTACAAGTCTCCTCCACCTCCAGTC
Found at i:2834 original size:105 final size:105
Alignment explanation
Indices: 2616--2998 Score: 432
Period size: 105 Copynumber: 3.6 Consensus size: 105
2606 CCACCCACCT
* * * * * *
2616 TACAAATACAAGTCTCCTCCTCCACCACCACCAGTTTACAAGTACAAGTCCCCTCCTCCTCCTCC
1 TACAAGTACAAGTCTCCTCCACCACCACAACCAGTATACAAATACAAGT---CTCCTCCACCTCC
* *
2681 TAAGGAGGCATACAAGTACAAGTCCCCTCCTCCTCCT---AAGGAGGCA
63 -----AGTC-TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
* * ** *
2727 TACAAGTACAAGTCTCCTCCTCCTCC-CAAGGAGTCATACAAGTACAAGTCTCCTCCACCTCCAG
1 TACAAGTACAAGTCTCCTCCACCACCACAACCAGT-ATACAAATACAAGTCTCCTCCACCTCCAG
2791 TCTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
65 TCTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
** * *
2832 TACAAGTACAAGTCTCCTCCACCACCACCCCCAGTTTACAAATACAAGTCTCCTCCACCTCCGGT
1 TACAAGTACAAGTCTCCTCCACCACCACAACCAGTATACAAATACAAGTCTCCTCCACCTCCAGT
2897 CTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
66 CTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
* ** * * * *
2937 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTATAAGTACAAGTCTCCTCCTCCTCC
1 TACAAGTACAAGTCTCCTCCACCACCACAACCAGTATACAAATACAAGTCTCCTCCACCTCC
2999 TAAGGAGCAT
Statistics
Matches: 243, Mismatches: 24, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
102 27 0.11
103 3 0.01
105 155 0.64
106 4 0.02
108 12 0.05
110 5 0.02
111 37 0.15
ACGTcount: A:0.27, C:0.41, G:0.11, T:0.21
Consensus pattern (105 bp):
TACAAGTACAAGTCTCCTCCACCACCACAACCAGTATACAAATACAAGTCTCCTCCACCTCCAGT
CTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
Found at i:2872 original size:36 final size:36
Alignment explanation
Indices: 2781--3073 Score: 154
Period size: 36 Copynumber: 8.1 Consensus size: 36
2771 CAAGTCTCCT
* * * *
2781 CCACCTCCAGTCTACAAGTACAAGTCCCCTCCTCCT
1 CCACCCCCAGTCTACAAGTACAAGTCTCCTCCACCA
* ** *
2817 CCTCCCAAGGAGCCATACAAGTACAAGTCTCCTCCACCA
1 CCACCC--CCAGTC-TACAAGTACAAGTCTCCTCCACCA
* *
2856 CCACCCCCAGTTTACAAATACAAGTCTCCT------
1 CCACCCCCAGTCTACAAGTACAAGTCTCCTCCACCA
* * * * *
2886 CCACCTCCGGTCTACAAGTACAAGTCCCCTCCTCCT
1 CCACCCCCAGTCTACAAGTACAAGTCTCCTCCACCA
* ** * *
2922 CCTCCCAAGGAGCCATACAAGTACAAGTCTCCCCCACCA
1 CCACCC--CCAGTC-TACAAGTACAAGTCTCCTCCACCA
* * * *
2961 CCACCTCCAGTCTATAAGTACAAGTCTCCTCCTCCT
1 CCACCCCCAGTCTACAAGTACAAGTCTCCTCCACCA
**** * * *
2997 CCTAAGGAGCA-T-TACAAGTATAAGTCTCCCCCACCT
1 CC--ACCCCCAGTCTACAAGTACAAGTCTCCTCCACCA
*
3033 CC-CCCTCCAGTCTACAAGTACAAGTTTCCTCCACCA
1 CCACCC-CCAGTCTACAAGTACAAGTCTCCTCCACCA
3069 CCACC
1 CCACC
3074 ACCCCATTAT
Statistics
Matches: 185, Mismatches: 54, Indels: 35
0.68 0.20 0.13
Matches are distributed among these distances:
30 25 0.14
34 2 0.01
35 1 0.01
36 91 0.49
37 8 0.04
38 8 0.04
39 50 0.27
ACGTcount: A:0.26, C:0.43, G:0.10, T:0.20
Consensus pattern (36 bp):
CCACCCCCAGTCTACAAGTACAAGTCTCCTCCACCA
Found at i:2872 original size:141 final size:135
Alignment explanation
Indices: 2635--2923 Score: 339
Period size: 141 Copynumber: 2.1 Consensus size: 135
2625 AAGTCTCCTC
* * * * *
2635 CTCCACCACCACCAGTTTACAAGTACAAGTCCCCTCCTCCTCCTCCTAAGGAGGCATACAAGTAC
1 CTCCTCCACCTCCAGTCTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTAC
* * ** * *
2700 AAGTCCCCTCCTCCTCCTAAGGAGGCATACAAGTACAAGTCTCCTCCTCCTCCCAAGGAGTCATA
66 AAGTCCCCTCCACCACCTAACCAGGCATACAAATACAAGTCTCCTCCACCT-CC---G-GTC-TA
2765 CAAGTACAAGT
125 CAAGTACAAGT
2776 CTCCTCCACCTCCAGTCTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTAC
1 CTCCTCCACCTCCAGTCTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTAC
* * **
2841 AAGTCTCCTCCACCACC-ACCCCCA-GTTTACAAATACAAGTCTCCTCCACCTCCGGTCTACAAG
66 AAGTCCCCTCCACCACCTA--ACCAGGCATACAAATACAAGTCTCCTCCACCTCCGGTCTACAAG
2904 TACAAGT
129 TACAAGT
* *
2911 CCCCTCCTCCTCC
1 CTCCTCCACCTCC
2924 TCCCAAGGAG
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
135 24 0.19
136 3 0.02
137 1 0.01
140 3 0.02
141 97 0.75
142 1 0.01
ACGTcount: A:0.26, C:0.41, G:0.12, T:0.21
Consensus pattern (135 bp):
CTCCTCCACCTCCAGTCTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTAC
AAGTCCCCTCCACCACCTAACCAGGCATACAAATACAAGTCTCCTCCACCTCCGGTCTACAAGTA
CAAGT
Found at i:3040 original size:72 final size:72
Alignment explanation
Indices: 2883--3064 Score: 258
Period size: 72 Copynumber: 2.5 Consensus size: 72
2873 ATACAAGTCT
*
2883 CCTCCACCTCCGGTCTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAA
1 CCTCCACCTCCAGTCTACAAGTACAAGT---CTCCTCCTCCTCCCAAGGAGCCATACAAGTACAA
2948 GTCTCCCCCA
63 GTCTCCCCCA
* * * *
2958 CCACCACCTCCAGTCTATAAGTACAAGTCTCCTCCTCCTCCTAAGGAG-CATTACAAGTATAAGT
1 CCTCCACCTCCAGTCTACAAGTACAAGTCTCCTCCTCCTCCCAAGGAGCCA-TACAAGTACAAGT
3022 CTCCCCCA
65 CTCCCCCA
* *
3030 CCTCCCCCTCCAGTCTACAAGTACAAGTTTCCTCC
1 CCTCCACCTCCAGTCTACAAGTACAAGTCTCCTCC
3065 ACCACCACCA
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
71 2 0.02
72 70 0.72
75 25 0.26
ACGTcount: A:0.25, C:0.42, G:0.11, T:0.22
Consensus pattern (72 bp):
CCTCCACCTCCAGTCTACAAGTACAAGTCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTC
TCCCCCA
Found at i:8448 original size:20 final size:20
Alignment explanation
Indices: 8420--8512 Score: 57
Period size: 20 Copynumber: 4.5 Consensus size: 20
8410 ATGAAAAGTG
*
8420 TAATTTAAATATTCAAAATA
1 TAATCTAAATATTCAAAATA
* *
8440 TAATCTAAATAAACTCTAAATA
1 TAATCTAAAT--ATTCAAAATA
* **
8462 -ATAT-AAAATATT-ACACTTA
1 TA-ATCTAAATATTCA-AAATA
*
8481 TTAATTTAAATATTCAAAATA
1 -TAATCTAAATATTCAAAATA
8502 TAATCTAAATA
1 TAATCTAAATA
8513 AACTCTAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
19 5 0.09
20 21 0.40
21 16 0.30
22 11 0.21
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATCTAAATATTCAAAATA
Found at i:8488 original size:62 final size:62
Alignment explanation
Indices: 8420--8543 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
8410 ATGAAAAGTG
8420 TAATTTAAATATTCAAAATATAATCTAAATAAACTCTAAATAATATAAAATATTACACTTAT
1 TAATTTAAATATTCAAAATATAATCTAAATAAACTCTAAATAATATAAAATATTACACTTAT
8482 TAATTTAAATATTCAAAATATAATCTAAATAAACTCTAAATAATATAAAATATTACACTTAT
1 TAATTTAAATATTCAAAATATAATCTAAATAAACTCTAAATAATATAAAATATTACACTTAT
8544 CAGTCATATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (62 bp):
TAATTTAAATATTCAAAATATAATCTAAATAAACTCTAAATAATATAAAATATTACACTTAT
Found at i:8701 original size:2 final size:2
Alignment explanation
Indices: 8694--8726 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8684 CACCTAAAAC
8694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8727 ACATTTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9819 original size:31 final size:31
Alignment explanation
Indices: 9784--9845 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
9774 CACAAGAGAA
*
9784 CTCTTGATTCATGAATAATAACAATATTCAT
1 CTCTTCATTCATGAATAATAACAATATTCAT
* *
9815 CTCTTCATTTATGAATAATCACAATATTCAT
1 CTCTTCATTCATGAATAATAACAATATTCAT
9846 TAATGACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (31 bp):
CTCTTCATTCATGAATAATAACAATATTCAT
Found at i:27618 original size:31 final size:31
Alignment explanation
Indices: 27583--27644 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
27573 CACAAGAGAA
* *
27583 CTCTTGATTCATGAATATTTACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
27614 CTCTTGATTCATGAATAATCACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
27645 TAATAACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (31 bp):
CTCTTGATTCATGAATAATCACAATATTCAT
Done.