Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020300.1 Corchorus olitorius cultivar O-4 contig20333, 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: 3628
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Found at i:1086 original size:21 final size:21
Alignment explanation
Indices: 1053--1092 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1043 CTAAAAACAG
* *
1053 GACAAGTCTTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
1074 GACAACTCCTGCCCAGGAC
1 GACAACTCCTGCCCAGGAC
1093 CTGGTCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.23, T:0.17
Consensus pattern (21 bp):
GACAACTCCTGCCCAGGACTT
Found at i:1151 original size:21 final size:21
Alignment explanation
Indices: 1125--1187 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
1115 AAAAATCAGA
1125 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
1146 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
*
1167 ACAACTCCTGCCTAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
1188 GTCTGTTGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
ACAACTCCTGCCCAGGACTTG
Found at i:1210 original size:92 final size:93
Alignment explanation
Indices: 1052--1259 Score: 301
Period size: 92 Copynumber: 2.2 Consensus size: 93
1042 CCTAAAAACA
* * *
1052 GGACAAGTCTTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAGACGGAAGAA
1 GGACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAACGGAAGAA
* *
1117 AAATCAGAACAACTCCTGCCCAGGACTT
66 AAATCAGAACAACTCATGCCCAAGACTT
* *
1145 -GACAACTCCTGCCCAGGACTTGACAACTCCTGCCTAGGACTTGGTCTGTTGAAAAACGGAAGAA
1 GGACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAACGGAAGAA
* * * *
1209 AATTCAGAACAAGTCATGTCCAAGATTT
66 AAATCAGAACAACTCATGCCCAAGACTT
*
1237 GGAGAACTCCTGCCCAGGACTTG
1 GGACAACTCCTGCCCAGGACTTG
1260 TTGCGGAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
92 81 0.79
93 21 0.21
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.20
Consensus pattern (93 bp):
GGACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAACGGAAGAA
AAATCAGAACAACTCATGCCCAAGACTT
Found at i:2438 original size:57 final size:56
Alignment explanation
Indices: 2361--2645 Score: 239
Period size: 57 Copynumber: 5.1 Consensus size: 56
2351 ACCTATTATC
* *
2361 TTACTATTGATTACC-CTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAA
1 TTACTATTGATT-CCTTTTTTACTTCTT-ATTAACTTAATTACTCTGAATTAAGCCAA
* * * *
2418 TTACTATTGATTCCTTTTTTACTTCTTGATTAACTTAATTGCTCTAAATGAAGCTAA
1 TTACTATTGATTCCTTTTTTACTTCTT-ATTAACTTAATTACTCTGAATTAAGCCAA
* * * *
2475 TT-CTATTGATTACTTTTTTTACTTCTT-TTAAACTT-ATAATTCTGAATTAAGCCCA
1 TTACTATTGATT-CCTTTTTTACTTCTTATT-AACTTAATTACTCTGAATTAAGCCAA
* * *
2530 -T--TATTGATCACCATTTTTTAC-TCTTTTTAACTTAATTACTCTGAATTAAACCAA
1 TTACTATTGAT-TCC-TTTTTTACTTCTTATTAACTTAATTACTCTGAATTAAGCCAA
* * * * * *
2584 TTACTGATTACCATT-TTTTTTTAC-TCTTTTTAACTTAATTACTTTGAATTGAGCCCA
1 TTACT-ATT--GATTCCTTTTTTACTTCTTATTAACTTAATTACTCTGAATTAAGCCAA
2641 TTACT
1 TTACT
2646 GATTACCATT
Statistics
Matches: 190, Mismatches: 25, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
53 17 0.09
54 27 0.14
55 16 0.08
56 16 0.08
57 109 0.57
58 3 0.02
60 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.48
Consensus pattern (56 bp):
TTACTATTGATTCCTTTTTTACTTCTTATTAACTTAATTACTCTGAATTAAGCCAA
Found at i:2755 original size:62 final size:62
Alignment explanation
Indices: 2705--3223 Score: 186
Period size: 65 Copynumber: 8.3 Consensus size: 62
2695 TACTATTTTT
* *
2705 AACTTACTTACTGATTACCAGT-TTTTTGAATTAAATTACTGATTTCCA-TTTTCCTTATAG
1 AACTTAATTACTGATTACCAGTATTTTTGAATTAAATTACTGATTTCCATTTTTACTTATAG
* * * * *
2765 AACTTAATTACTGATTATCATTACTTTTTGAATTTACTTACTGATTTCCA-TTTTACTCT-TTG
1 AACTTAATTACTGATTACCAGTA-TTTTTGAATTAAATTACTGATTTCCATTTTTACT-TATAG
* * * * * *
2827 AATTTAATTACTGATTCCCA-TTTTACTCTTCG-A--AAATTACTGATTACCA---TTACTTTTT
1 AACTTAATTACTGATTACCAGTATT--T-TT-GAATTAAATTACTGATTTCCATTTTTACTTATA
2885 G
62 G
** * * * * * *
2886 AA-TTGAATTACTGATTTTCATTTTCCTTATTGAATTTAATTATTGAGTACCA-TTTTACTCT-T
1 AACTT-AATTACTGATTACCAGTAT--TT-TTGAATTAAATTACTGATTTCCATTTTTACT-TAT
*
2948 TG
61 AG
* * * * * * *
2950 AATTTAATTACTGAATACCATTTTACTTTTTGAACTTGAATTACTGATTACCA-TTTTACTTTTT
1 AACTTAATTACTGATTACCA--GTA-TTTTTGAA-TTAAATTACTGATTTCCATTTTTACTTATA
3014 G
62 G
* ** * * * *
3015 AA-TTGAATTACTGATTTCCA-CCTTATTGAATTTAATTACTGATTACCA-TTTTACTCT-TTG
1 AACTT-AATTACTGATTACCAGTATTTTTGAATTAAATTACTGATTTCCATTTTTACT-TATAG
* * * * * *
3075 AATTTAATTACTGATTACCATTTTACTTTTTGAACTTGAATTATTGATTACCA-TTTTACTCTCT
1 AACTTAATTACTGATTACCA--GTA-TTTTTGAA-TTAAATTACTGATTTCCATTTTTACT-TAT
3139 -G
61 AG
* * * *
3140 AA-TAAAATTACTGATTACCATTTTACTCTTTGAATTGAATTACTGATTTCCA-TTTTACTCT-T
1 AACT-TAATTACTGATTACCA--GTA-TTTTTGAATTAAATTACTGATTTCCATTTTTACT-TAT
*
3202 AT
61 AG
* *
3204 AATTTAATTACTAATTACCA
1 AACTTAATTACTGATTACCA
3224 TTCTACTCAT
Statistics
Matches: 377, Mismatches: 46, Indels: 68
0.77 0.09 0.14
Matches are distributed among these distances:
58 3 0.01
59 24 0.06
60 71 0.19
61 24 0.06
62 64 0.17
63 5 0.01
64 80 0.21
65 102 0.27
66 3 0.01
67 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.48
Consensus pattern (62 bp):
AACTTAATTACTGATTACCAGTATTTTTGAATTAAATTACTGATTTCCATTTTTACTTATAG
Found at i:2774 original size:32 final size:31
Alignment explanation
Indices: 2712--3253 Score: 435
Period size: 32 Copynumber: 17.4 Consensus size: 31
2702 TTTAACTTAC
* *
2712 TTACTGATTACCA-GTT--TTTTGAATTAAA
1 TTACTGATTACCATTTTCCTTTTGAATTTAA
* * *
2740 TTACTGATTTCCATTTTCCTTATAGAACTTAA
1 TTACTGATTACCATTTTCCTT-TTGAATTTAA
* * * *
2772 TTACTGATTATCA-TTACTTTTTGAATTTAC
1 TTACTGATTACCATTTTCCTTTTGAATTTAA
* *
2802 TTACTGATTTCCATTTTACTCTTTGAATTTAA
1 TTACTGATTACCATTTTCCT-TTTGAATTTAA
* * *
2834 TTACTGATTCCCATTTTACTCTTCGAA---AA
1 TTACTGATTACCATTTTCCT-TTTGAATTTAA
* * *
2863 TTACTGATTACCA-TTACTTTTTGAATTGAA
1 TTACTGATTACCATTTTCCTTTTGAATTTAA
**
2893 TTACTGATTTTCATTTTCCTTATTGAATTTAA
1 TTACTGATTACCATTTTCCTT-TTGAATTTAA
* * *
2925 TTATTGAGTACCATTTTACTCTTTGAATTTAA
1 TTACTGATTACCATTTTCCT-TTTGAATTTAA
* * *
2957 TTACTGAATACCATTTTACTTTTTGAACTTGAA
1 TTACTGATTACCATTTT-CCTTTTGAA-TTTAA
* *
2990 TTACTGATTACCATTTTACTTTTTGAATTGAA
1 TTACTGATTACCATTTT-CCTTTTGAATTTAA
*
3022 TTACTGATTTCCA----CCTTATTGAATTTAA
1 TTACTGATTACCATTTTCCTT-TTGAATTTAA
*
3050 TTACTGATTACCATTTTACTCTTTGAATTTAA
1 TTACTGATTACCATTTTCCT-TTTGAATTTAA
* *
3082 TTACTGATTACCATTTTACTTTTTGAACTTGAA
1 TTACTGATTACCATTTT-CCTTTTGAA-TTTAA
* * * **
3115 TTATTGATTACCATTTTACTCTCTGAATAAAA
1 TTACTGATTACCATTTTCCT-TTTGAATTTAA
* *
3147 TTACTGATTACCATTTTACTCTTTGAATTGAA
1 TTACTGATTACCATTTTCCT-TTTGAATTTAA
* *
3179 TTACTGATTTCCATTTTACTCTTAT-AATTTAA
1 TTACTGATTACCATTTT-C-CTTTTGAATTTAA
* * * * *
3211 TTACTAATTACCATTCTACTCATTGAATTTGA
1 TTACTGATTACCATTTTCCT-TTTGAATTTAA
3243 TTACTGATTAC
1 TTACTGATTAC
3254 AATTACTTTT
Statistics
Matches: 416, Mismatches: 71, Indels: 50
0.77 0.13 0.09
Matches are distributed among these distances:
27 8 0.02
28 36 0.09
29 16 0.04
30 33 0.08
31 16 0.04
32 244 0.59
33 61 0.15
34 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (31 bp):
TTACTGATTACCATTTTCCTTTTGAATTTAA
Found at i:3094 original size:157 final size:155
Alignment explanation
Indices: 2712--3324 Score: 607
Period size: 157 Copynumber: 3.9 Consensus size: 155
2702 TTTAACTTAC
** * * * *
2712 TTACTGATTACCAGTTTTTTGAATTAAATTACTGATTTCCATTTT-C-CTTATAGAACTTAATTA
1 TTACTGATTACCAACTTATTGAATTTAATTACTGATTACCATTTTACTCTT-T-GAATTTAATTA
* * * *
2775 CTGATTATCA-TTACTTTTTGAATTTACTTACTGATTTCCATTTTACTCTTTGAATTTAATTACT
64 CTGATTACCATTTACTTTTTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTGAATTACT
* *
2839 GATTCCCATTTTACTCTTCGAA---AA
129 GATTACCATTTTACTCTTTGAATTGAA
* * ** *
2863 TTACTGATTACCATTACTTTTTGAATTGAATTACTGATTTTCATTTTCCT-TATTGAATTTAATT
1 TTACTGATTACCA--ACTTATTGAATTTAATTACTGATTACCATTTTACTCT-TTGAATTTAATT
* * * * *
2927 ATTGAGTACCATTTTACTCTTTGAATTTAATTACTGAATACCATTTTACTTTTTGAACTTGAATT
63 ACTGATTACCA-TTTACTTTTTGAATTTAATTACTGATTACCATTTTACTCTTTGAA-TTGAATT
*
2992 ACTGATTACCATTTTACTTTTTGAATTGAA
126 ACTGATTACCATTTTACTCTTTGAATTGAA
* *
3022 TTACTGATTTCCACCTTATTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTTAATTACT
1 TTACTGATTACCAACTTATTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTTAATTACT
* * * **
3087 GATTACCATTTTACTTTTTGAACTTGAATTATTGATTACCATTTTACTCTCTGAATAAAATTACT
66 GATTACCA-TTTACTTTTTGAA-TTTAATTACTGATTACCATTTTACTCTTTGAATTGAATTACT
3152 GATTACCATTTTACTCTTTGAATTGAA
129 GATTACCATTTTACTCTTTGAATTGAA
* ** * * * * *
3179 TTACTGATTTCCATTTTACTCTTATAATTTAATTACTAATTACCATTCTACTCATTGAATTTGAT
1 TTACTGATTACCAACTTA---TT-GAATTTAATTACTGATTACCATTTTACTCTTTGAATTTAAT
* * *
3244 TACTGATTA-CAATTACTTTTT-ACTGATTTCCATTTTACTGATTATCATTTTACTCTTTGAACT
62 TACTGATTACCATTTACTTTTTGA---ATTT--A-ATTACTGATTACCATTTTACTCTTTGAA-T
3307 TG-ATTACTGATTACCATT
120 TGAATTACTGATTACCATT
3325 ACTTTTTACT
Statistics
Matches: 388, Mismatches: 50, Indels: 36
0.82 0.11 0.08
Matches are distributed among these distances:
151 13 0.03
153 45 0.12
154 3 0.01
155 40 0.10
156 28 0.07
157 113 0.29
158 29 0.07
159 23 0.06
160 6 0.02
161 46 0.12
162 1 0.00
163 40 0.10
164 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.49
Consensus pattern (155 bp):
TTACTGATTACCAACTTATTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTTAATTACT
GATTACCATTTACTTTTTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTGAATTACTGA
TTACCATTTTACTCTTTGAATTGAA
Found at i:3221 original size:64 final size:64
Alignment explanation
Indices: 2729--3324 Score: 511
Period size: 64 Copynumber: 9.4 Consensus size: 64
2719 TTACCAGTTT
* * * *
2729 TTTGAA-TTAAATTACTGATTTCCATTTT-C-CTTATAGAACTTAATTACTGATTATCA--TTAC
1 TTTGAACTTGAATTACTGATTACCATTTTACTCTT-T--AATTTAATTACTGATTACCATTTTAC
*
2789 TT
63 TC
* * * *
2791 TTTGAA-TTTACTTACTGATTTCCATTTTACTCTTTGAATTTAATTACTGATTCCCATTTTACTC
1 TTTGAACTTGAATTACTGATTACCATTTTACTCTTT-AATTTAATTACTGATTACCATTTTACTC
* * * ** *
2855 TTCGAA----AATTACTGATTACCA--TTACTTTTTGAATTGAATTACTGATTTTCATTTTCCT-
1 TTTGAACTTGAATTACTGATTACCATTTTACTCTTT-AATTTAATTACTGATTACCATTTTACTC
* * * *
2913 TATTGAA-TTTAATTATTGAGTACCATTTTACTCTTTGAATTTAATTACTGAATACCATTTTACT
1 T-TTGAACTTGAATTACTGATTACCATTTTACTCTTT-AATTTAATTACTGATTACCATTTTACT
*
2977 T
64 C
* * * **
2978 TTTGAACTTGAATTACTGATTACCATTTTACTTTTTGAATTGAATTACTGATTTCCACCTTA---
1 TTTGAACTTGAATTACTGATTACCATTTTACTCTTT-AATTTAATTACTGATTACCATTTTACTC
* *
3040 -TTGAA-TTTAATTACTGATTACCATTTTACTCTTTGAATTTAATTACTGATTACCATTTTACTT
1 TTTGAACTTGAATTACTGATTACCATTTTACTCTTT-AATTTAATTACTGATTACCATTTTACTC
* * **
3103 TTTGAACTTGAATTATTGATTACCATTTTACTCTCTGAATAAAATTACTGATTACCATTTTACTC
1 TTTGAACTTGAATTACTGATTACCATTTTACTCT-TTAATTTAATTACTGATTACCATTTTACTC
* * *
3168 TTTGAA-TTGAATTACTGATTTCCATTTTACTCTTATAATTTAATTACTAATTACCATTCTACTC
1 TTTGAACTTGAATTACTGATTACCATTTTACTCTT-TAATTTAATTACTGATTACCATTTTACTC
* * * * * *
3232 ATTGAATTTG-ATTACTGATTA-CA-ATTACTTTTTACTGATTTCCATTTTACTGATTATCATTT
1 TTTGAACTTGAATTACTGATTACCATTTTACTCTTTA---ATTT--A-ATTACTGATTACCATTT
3294 TACTC
60 TACTC
3299 TTTGAACTTG-ATTACTGATTACCATT
1 TTTGAACTTGAATTACTGATTACCATT
3325 ACTTTTTACT
Statistics
Matches: 444, Mismatches: 62, Indels: 49
0.80 0.11 0.09
Matches are distributed among these distances:
58 1 0.00
59 36 0.08
60 49 0.11
61 20 0.05
62 64 0.14
63 5 0.01
64 122 0.27
65 106 0.24
66 2 0.00
67 37 0.08
68 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (64 bp):
TTTGAACTTGAATTACTGATTACCATTTTACTCTTTAATTTAATTACTGATTACCATTTTACTC
Found at i:3281 original size:15 final size:15
Alignment explanation
Indices: 3261--3297 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3251 TACAATTACT
3261 TTTTACTGATT-TCCA
1 TTTTACTGATTAT-CA
3276 TTTTACTGATTATCA
1 TTTTACTGATTATCA
3291 TTTTACT
1 TTTTACT
3298 CTTTGAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 20 0.95
16 1 0.05
ACGTcount: A:0.22, C:0.16, G:0.05, T:0.57
Consensus pattern (15 bp):
TTTTACTGATTATCA
Found at i:3304 original size:67 final size:66
Alignment explanation
Indices: 3147--3346 Score: 214
Period size: 67 Copynumber: 3.0 Consensus size: 66
3137 CTGAATAAAA
* * * *
3147 TTACTGATTACCATTTTACTCTTTGAATTGAATTACTGATTTCCATTTTAC-TCTTA-TAATTT-
1 TTACTGATTACCATTTTACTCTTTGAATTG-ATTACTGA-TTACA-ATTACTTTTTACTGATTTC
*
3209 -A-A
63 CATT
* * *
3211 TTACTAATTACCATTCTACTCATTGAATTTGATTACTGATTACAATTACTTTTTACTGATTTCCA
1 TTACTGATTACCATTTTACTCTTTGAA-TTGATTACTGATTACAATTACTTTTTACTGATTTCCA
3276 TT
65 TT
* *
3278 TTACTGATTATCATTTTACTCTTTGAACTTGATTACTGATTACCATTACTTTTTACTGATTATCC
1 TTACTGATTACCATTTTACTCTTTGAA-TTGATTACTGATTACAATTACTTTTTACTGATT-TCC
3343 -TT
64 ATT
3345 TT
1 TT
3347 CTTCTTGACC
Statistics
Matches: 115, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
62 4 0.03
63 8 0.07
64 37 0.32
65 3 0.03
66 1 0.01
67 59 0.51
68 3 0.03
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (66 bp):
TTACTGATTACCATTTTACTCTTTGAATTGATTACTGATTACAATTACTTTTTACTGATTTCCAT
T
Done.