Multiple sequence alignment - TraesCS3B01G534400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G534400 chr3B 100.000 3169 0 0 1 3169 773899726 773902894 0.000000e+00 5853.0
1 TraesCS3B01G534400 chr3B 88.000 1875 177 21 363 2216 773759554 773757707 0.000000e+00 2172.0
2 TraesCS3B01G534400 chr3B 82.882 1145 117 39 1507 2596 773743745 773742625 0.000000e+00 955.0
3 TraesCS3B01G534400 chr3B 91.765 170 14 0 1981 2150 773877938 773878107 1.470000e-58 237.0
4 TraesCS3B01G534400 chr3B 95.385 130 6 0 1 130 773759993 773759864 1.150000e-49 207.0
5 TraesCS3B01G534400 chr3B 100.000 32 0 0 2564 2595 773751913 773751882 3.410000e-05 60.2
6 TraesCS3B01G534400 chr3D 92.434 1771 103 13 457 2216 579587107 579588857 0.000000e+00 2499.0
7 TraesCS3B01G534400 chr3D 89.211 1826 155 20 363 2173 579422325 579420527 0.000000e+00 2242.0
8 TraesCS3B01G534400 chr3D 89.023 1075 85 14 363 1430 579394662 579393614 0.000000e+00 1301.0
9 TraesCS3B01G534400 chr3D 91.803 793 51 6 1426 2216 579383798 579383018 0.000000e+00 1092.0
10 TraesCS3B01G534400 chr3D 87.150 428 18 8 2214 2606 579588888 579589313 4.820000e-123 451.0
11 TraesCS3B01G534400 chr3D 93.561 264 14 1 2598 2861 579589347 579589607 1.070000e-104 390.0
12 TraesCS3B01G534400 chr3D 83.832 334 25 16 2859 3169 579590457 579590784 1.110000e-74 291.0
13 TraesCS3B01G534400 chr3D 91.803 183 15 0 148 330 579422651 579422469 4.060000e-64 255.0
14 TraesCS3B01G534400 chr3D 95.395 152 7 0 157 308 579586527 579586678 3.160000e-60 243.0
15 TraesCS3B01G534400 chr3D 96.154 130 5 0 1 130 579395071 579394942 2.480000e-51 213.0
16 TraesCS3B01G534400 chr3D 96.154 130 5 0 1 130 579422764 579422635 2.480000e-51 213.0
17 TraesCS3B01G534400 chr3D 93.077 130 9 0 1 130 579586405 579586534 1.160000e-44 191.0
18 TraesCS3B01G534400 chr3D 92.523 107 7 1 148 254 579394958 579394853 5.470000e-33 152.0
19 TraesCS3B01G534400 chr3D 100.000 31 0 0 343 373 579586698 579586728 1.230000e-04 58.4
20 TraesCS3B01G534400 chr3A 91.361 1771 115 18 457 2216 714645540 714647283 0.000000e+00 2388.0
21 TraesCS3B01G534400 chr3A 91.165 1777 128 17 452 2216 714590057 714588298 0.000000e+00 2385.0
22 TraesCS3B01G534400 chr3A 88.540 637 60 6 1538 2173 714602902 714602278 0.000000e+00 760.0
23 TraesCS3B01G534400 chr3A 92.992 371 21 3 3 372 714644788 714645154 1.290000e-148 536.0
24 TraesCS3B01G534400 chr3A 87.209 430 18 8 2214 2608 714647314 714647741 3.730000e-124 455.0
25 TraesCS3B01G534400 chr3A 91.513 271 19 2 2598 2868 714647772 714648038 1.390000e-98 370.0
26 TraesCS3B01G534400 chr3A 89.674 184 16 2 148 330 714628209 714628390 6.840000e-57 231.0
27 TraesCS3B01G534400 chr3A 90.341 176 15 2 157 330 714590446 714590271 2.460000e-56 230.0
28 TraesCS3B01G534400 chr3A 92.308 130 10 0 1 130 714590568 714590439 5.400000e-43 185.0
29 TraesCS3B01G534400 chr3A 92.308 130 10 0 1 130 714628096 714628225 5.400000e-43 185.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G534400 chr3B 773899726 773902894 3168 False 5853.000000 5853 100.000000 1 3169 1 chr3B.!!$F2 3168
1 TraesCS3B01G534400 chr3B 773757707 773759993 2286 True 1189.500000 2172 91.692500 1 2216 2 chr3B.!!$R3 2215
2 TraesCS3B01G534400 chr3B 773742625 773743745 1120 True 955.000000 955 82.882000 1507 2596 1 chr3B.!!$R1 1089
3 TraesCS3B01G534400 chr3D 579383018 579383798 780 True 1092.000000 1092 91.803000 1426 2216 1 chr3D.!!$R1 790
4 TraesCS3B01G534400 chr3D 579420527 579422764 2237 True 903.333333 2242 92.389333 1 2173 3 chr3D.!!$R3 2172
5 TraesCS3B01G534400 chr3D 579586405 579590784 4379 False 589.057143 2499 92.207000 1 3169 7 chr3D.!!$F1 3168
6 TraesCS3B01G534400 chr3D 579393614 579395071 1457 True 555.333333 1301 92.566667 1 1430 3 chr3D.!!$R2 1429
7 TraesCS3B01G534400 chr3A 714644788 714648038 3250 False 937.250000 2388 90.768750 3 2868 4 chr3A.!!$F2 2865
8 TraesCS3B01G534400 chr3A 714588298 714590568 2270 True 933.333333 2385 91.271333 1 2216 3 chr3A.!!$R2 2215
9 TraesCS3B01G534400 chr3A 714602278 714602902 624 True 760.000000 760 88.540000 1538 2173 1 chr3A.!!$R1 635

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
519 1004 0.251165 TTCAGGGAAAGGGCGAAAGG 60.251 55.0 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2987 0.606604 TACTTCAGCGGGTTCAGGAC 59.393 55.0 0.0 0.0 0.0 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 1.813513 GCTTGCTGCCTTCTCAAGTA 58.186 50.000 0.00 0.00 39.36 2.24
119 120 2.363683 GCTTGCTGCCTTCTCAAGTAT 58.636 47.619 0.00 0.00 39.36 2.12
120 121 2.097142 GCTTGCTGCCTTCTCAAGTATG 59.903 50.000 0.00 0.00 39.36 2.39
121 122 3.341823 CTTGCTGCCTTCTCAAGTATGT 58.658 45.455 0.00 0.00 34.20 2.29
122 123 3.423539 TGCTGCCTTCTCAAGTATGTT 57.576 42.857 0.00 0.00 0.00 2.71
123 124 3.338249 TGCTGCCTTCTCAAGTATGTTC 58.662 45.455 0.00 0.00 0.00 3.18
124 125 2.680339 GCTGCCTTCTCAAGTATGTTCC 59.320 50.000 0.00 0.00 0.00 3.62
125 126 3.620966 GCTGCCTTCTCAAGTATGTTCCT 60.621 47.826 0.00 0.00 0.00 3.36
126 127 4.187694 CTGCCTTCTCAAGTATGTTCCTC 58.812 47.826 0.00 0.00 0.00 3.71
127 128 3.840666 TGCCTTCTCAAGTATGTTCCTCT 59.159 43.478 0.00 0.00 0.00 3.69
128 129 4.287067 TGCCTTCTCAAGTATGTTCCTCTT 59.713 41.667 0.00 0.00 0.00 2.85
129 130 5.221925 TGCCTTCTCAAGTATGTTCCTCTTT 60.222 40.000 0.00 0.00 0.00 2.52
130 131 5.707764 GCCTTCTCAAGTATGTTCCTCTTTT 59.292 40.000 0.00 0.00 0.00 2.27
131 132 6.128145 GCCTTCTCAAGTATGTTCCTCTTTTC 60.128 42.308 0.00 0.00 0.00 2.29
132 133 7.164803 CCTTCTCAAGTATGTTCCTCTTTTCT 58.835 38.462 0.00 0.00 0.00 2.52
133 134 7.663493 CCTTCTCAAGTATGTTCCTCTTTTCTT 59.337 37.037 0.00 0.00 0.00 2.52
134 135 8.980481 TTCTCAAGTATGTTCCTCTTTTCTTT 57.020 30.769 0.00 0.00 0.00 2.52
135 136 8.608844 TCTCAAGTATGTTCCTCTTTTCTTTC 57.391 34.615 0.00 0.00 0.00 2.62
136 137 8.432805 TCTCAAGTATGTTCCTCTTTTCTTTCT 58.567 33.333 0.00 0.00 0.00 2.52
137 138 8.980481 TCAAGTATGTTCCTCTTTTCTTTCTT 57.020 30.769 0.00 0.00 0.00 2.52
138 139 9.408648 TCAAGTATGTTCCTCTTTTCTTTCTTT 57.591 29.630 0.00 0.00 0.00 2.52
256 321 2.943033 ACAACTTGCTGCTTTAACTCGT 59.057 40.909 0.00 0.00 0.00 4.18
284 349 6.449635 AAATTGTGAGTTGCTGACACTTTA 57.550 33.333 3.25 0.00 31.53 1.85
287 352 2.224314 GTGAGTTGCTGACACTTTAGCC 59.776 50.000 0.00 0.00 39.15 3.93
294 359 1.004745 CTGACACTTTAGCCCCACCAT 59.995 52.381 0.00 0.00 0.00 3.55
299 364 3.011257 ACACTTTAGCCCCACCATTACAT 59.989 43.478 0.00 0.00 0.00 2.29
339 479 6.013293 AGAGGGTATTAGTTCTATTCCCATGC 60.013 42.308 0.00 0.00 35.62 4.06
391 593 1.236616 TTGAGCCCAAGTGCACATCG 61.237 55.000 21.04 6.40 31.92 3.84
409 611 4.400251 ACATCGAAAACATTCCTGATGCAT 59.600 37.500 0.00 0.00 39.47 3.96
414 616 7.374272 TCGAAAACATTCCTGATGCATTTAAA 58.626 30.769 0.00 0.00 39.47 1.52
415 617 8.034215 TCGAAAACATTCCTGATGCATTTAAAT 58.966 29.630 0.00 0.00 39.47 1.40
416 618 9.299963 CGAAAACATTCCTGATGCATTTAAATA 57.700 29.630 0.00 0.00 39.47 1.40
440 642 5.604010 ACTATAGGTTACGCGTGATACTC 57.396 43.478 24.59 10.80 0.00 2.59
444 646 2.097142 AGGTTACGCGTGATACTCAGAC 59.903 50.000 24.59 6.07 0.00 3.51
451 653 2.663602 GCGTGATACTCAGACAACACTG 59.336 50.000 0.00 0.00 39.02 3.66
460 945 8.813643 ATACTCAGACAACACTGTTAAAGTAC 57.186 34.615 0.00 0.00 36.83 2.73
519 1004 0.251165 TTCAGGGAAAGGGCGAAAGG 60.251 55.000 0.00 0.00 0.00 3.11
558 1043 8.122472 AGTTATACCAGCAATTTTAGCAAGTT 57.878 30.769 0.00 0.00 0.00 2.66
596 1081 2.816777 TGGCATGCCTTGTATGGTTA 57.183 45.000 35.53 10.21 36.94 2.85
646 1136 3.691049 TTTGAAGCAGTTTGGAAGACG 57.309 42.857 0.00 0.00 0.00 4.18
654 1144 3.429085 CAGTTTGGAAGACGCATATTGC 58.571 45.455 0.00 0.00 40.69 3.56
710 1200 7.750229 TCTCTTAAGCAAACATGACAAGAAT 57.250 32.000 0.00 0.00 0.00 2.40
852 1346 8.772250 TCTCTATGTCCAATTTGTTAGGAGAAT 58.228 33.333 0.00 0.00 30.78 2.40
924 1418 8.416329 GTCCCTAATTGCACTGAAATATGAAAT 58.584 33.333 0.00 0.00 0.00 2.17
960 1454 3.951306 TGCTGTGATTCAAAACTGAACG 58.049 40.909 0.00 0.00 0.00 3.95
977 1471 7.925703 ACTGAACGATACTATTTTGTATCCG 57.074 36.000 8.49 6.89 43.36 4.18
1176 1673 8.342634 GGCGATGAAAAGCTACTTATTTATGAA 58.657 33.333 0.00 0.00 0.00 2.57
1223 1724 5.998363 ACACCTTCCTTTTCAGTATGTTCTC 59.002 40.000 0.00 0.00 37.40 2.87
1233 1734 9.338291 CTTTTCAGTATGTTCTCATCACAAATG 57.662 33.333 0.00 0.00 37.40 2.32
1237 1738 9.234827 TCAGTATGTTCTCATCACAAATGAATT 57.765 29.630 0.00 0.00 36.27 2.17
1358 1866 9.793259 TTCAATATAATAAAAGGAGTGGCTAGG 57.207 33.333 0.00 0.00 0.00 3.02
1628 2144 8.380867 TCTTGCTGATGATATGATTTATCCAGT 58.619 33.333 0.00 0.00 0.00 4.00
1807 2325 7.086376 AGATTACGATTTATCATTGCCAATGC 58.914 34.615 12.62 0.00 38.77 3.56
1838 2359 7.595819 TTCCTTTGACCACATGACTTAATTT 57.404 32.000 0.00 0.00 0.00 1.82
1839 2360 7.595819 TCCTTTGACCACATGACTTAATTTT 57.404 32.000 0.00 0.00 0.00 1.82
1840 2361 8.017418 TCCTTTGACCACATGACTTAATTTTT 57.983 30.769 0.00 0.00 0.00 1.94
1934 2455 2.369860 TCCATGTGTTTCAGAGAGCTGT 59.630 45.455 0.00 0.00 42.84 4.40
1937 2458 2.838736 TGTGTTTCAGAGAGCTGTTCC 58.161 47.619 0.00 0.00 42.84 3.62
1939 2460 2.805099 GTGTTTCAGAGAGCTGTTCCAG 59.195 50.000 0.00 0.00 42.84 3.86
1955 2476 0.595095 CCAGTGAAGAGGCTTTGTGC 59.405 55.000 0.00 0.00 41.94 4.57
2048 2569 1.546476 ACCTTGGAGAGTAGAAGCACG 59.454 52.381 0.00 0.00 0.00 5.34
2064 2585 3.964875 CGCCACTTGCAACGCCTT 61.965 61.111 0.00 0.00 41.33 4.35
2113 2636 0.174617 AAGGTAGCGAAGAGAGCAGC 59.825 55.000 0.00 0.00 37.01 5.25
2115 2638 0.804156 GGTAGCGAAGAGAGCAGCAC 60.804 60.000 0.00 0.00 37.01 4.40
2153 2678 2.711547 GGATATGGAGGCCCTTACAGTT 59.288 50.000 0.00 0.00 0.00 3.16
2173 2698 0.784495 ATAGAGGGGCGATAGGGTCA 59.216 55.000 0.00 0.00 0.00 4.02
2182 2707 1.278238 CGATAGGGTCACGCAGTTTC 58.722 55.000 0.00 0.00 41.61 2.78
2202 2727 0.676466 CAAGTTCCGCCCATGCACTA 60.676 55.000 0.00 0.00 37.32 2.74
2274 2831 4.639310 CCCTCTCAGTTCAAAGATGGAATG 59.361 45.833 0.00 0.00 31.13 2.67
2281 2838 5.181245 CAGTTCAAAGATGGAATGTACCGTT 59.819 40.000 0.00 0.00 0.00 4.44
2295 2852 0.549469 ACCGTTGGAGGACAAGGTTT 59.451 50.000 0.00 0.00 42.01 3.27
2298 2859 1.269051 CGTTGGAGGACAAGGTTTTGC 60.269 52.381 0.00 0.00 40.38 3.68
2376 2937 2.494059 ACTTTTGTGTCCCGTGATCAG 58.506 47.619 0.00 0.00 0.00 2.90
2390 2981 4.447054 CCGTGATCAGTTCTATGAGAATGC 59.553 45.833 0.00 0.00 36.50 3.56
2396 2987 3.002042 CAGTTCTATGAGAATGCTTGCGG 59.998 47.826 0.00 0.00 36.50 5.69
2452 3049 5.470098 TGTGCTTTTATCCTGTTCTCTTGTC 59.530 40.000 0.00 0.00 0.00 3.18
2462 3059 5.046591 TCCTGTTCTCTTGTCGATGGTATTT 60.047 40.000 0.00 0.00 0.00 1.40
2463 3060 5.063944 CCTGTTCTCTTGTCGATGGTATTTG 59.936 44.000 0.00 0.00 0.00 2.32
2497 3094 7.164122 TCTTAGCTTGTGATTGTTCATCTCTT 58.836 34.615 0.00 0.00 33.56 2.85
2520 3130 1.663135 GCCTCTGAAGCTGAACGATTC 59.337 52.381 0.00 0.00 38.49 2.52
2598 3209 9.129209 GTTTCAGTTTCCTTTATTCATGTTAGC 57.871 33.333 0.00 0.00 0.00 3.09
2621 3274 0.721718 GCATGTTGTCGTAGGTGCTC 59.278 55.000 0.00 0.00 0.00 4.26
2626 3279 0.523072 TTGTCGTAGGTGCTCGGTAC 59.477 55.000 0.00 0.00 0.00 3.34
2707 3360 3.738429 GAAATGCCGCCCATTGCCC 62.738 63.158 1.06 0.00 43.22 5.36
2795 3448 9.684448 TTACAAATATTGATTTCAGTTTTGCGA 57.316 25.926 0.00 0.00 32.73 5.10
2861 3514 6.321181 GGAGCATACCAATTTGTGATTCCTTA 59.679 38.462 0.00 0.00 0.00 2.69
2863 3516 7.719483 AGCATACCAATTTGTGATTCCTTATG 58.281 34.615 0.00 0.00 0.00 1.90
2870 3523 8.026607 CCAATTTGTGATTCCTTATGTAAACGT 58.973 33.333 0.00 0.00 0.00 3.99
2876 3529 9.881529 TGTGATTCCTTATGTAAACGTAAAAAC 57.118 29.630 0.00 0.00 0.00 2.43
2894 4395 9.943163 CGTAAAAACAAAATTTGAAATTCCCAT 57.057 25.926 13.19 0.00 0.00 4.00
2916 4417 6.306356 CCATTCATTTTCTAAAGTGCGAACAG 59.694 38.462 0.00 0.00 0.00 3.16
2923 4424 7.485418 TTTCTAAAGTGCGAACAGTTTATGA 57.515 32.000 0.00 4.81 45.90 2.15
2928 4429 9.820229 CTAAAGTGCGAACAGTTTATGAAATTA 57.180 29.630 0.00 0.00 45.90 1.40
3003 4507 8.502161 AAAAGCGAACACTTTTTGATACATAC 57.498 30.769 0.00 0.00 45.29 2.39
3005 4509 7.197071 AGCGAACACTTTTTGATACATACAA 57.803 32.000 0.00 0.00 0.00 2.41
3007 4511 8.296713 AGCGAACACTTTTTGATACATACAAAT 58.703 29.630 0.00 0.00 37.15 2.32
3026 4530 7.722795 ACAAATTTTTATGAAAAGGGGAACG 57.277 32.000 1.69 0.00 38.09 3.95
3037 4541 6.508777 TGAAAAGGGGAACGACTTTTTAATG 58.491 36.000 0.00 0.00 42.92 1.90
3042 4550 7.114866 AGGGGAACGACTTTTTAATGAAAAA 57.885 32.000 0.72 0.72 41.24 1.94
3065 4573 6.660887 AAATTGCACAAACTTTCAAACGAT 57.339 29.167 0.00 0.00 0.00 3.73
3132 4655 6.086871 TGTTCGCGCATTTCATAATTTGTTA 58.913 32.000 8.75 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 8.614469 AGAAAGAAAAGAGGAACATACTTGAG 57.386 34.615 0.00 0.00 0.00 3.02
150 151 5.137551 AGAGCTATAGAAAGAGGAGTGTCC 58.862 45.833 3.21 0.00 36.58 4.02
151 152 6.096282 ACAAGAGCTATAGAAAGAGGAGTGTC 59.904 42.308 3.21 0.00 0.00 3.67
168 203 5.470098 ACGTTGATGAACATAAACAAGAGCT 59.530 36.000 13.38 0.00 32.74 4.09
256 321 8.165239 AGTGTCAGCAACTCACAATTTATTAA 57.835 30.769 0.00 0.00 34.94 1.40
284 349 0.396139 CTGCATGTAATGGTGGGGCT 60.396 55.000 0.00 0.00 46.86 5.19
287 352 1.184431 TTGCTGCATGTAATGGTGGG 58.816 50.000 1.84 0.00 46.86 4.61
294 359 5.355071 CCTCTAGTGATTTTGCTGCATGTAA 59.645 40.000 1.84 0.00 0.00 2.41
299 364 2.040278 ACCCTCTAGTGATTTTGCTGCA 59.960 45.455 0.00 0.00 0.00 4.41
330 395 4.870069 TGGCAACAGCATGGGAAT 57.130 50.000 0.00 0.00 46.17 3.01
409 611 9.579768 TCACGCGTAACCTATAGTTTATTTAAA 57.420 29.630 13.44 0.00 40.05 1.52
414 616 8.103948 AGTATCACGCGTAACCTATAGTTTAT 57.896 34.615 13.44 0.00 40.05 1.40
415 617 7.226523 TGAGTATCACGCGTAACCTATAGTTTA 59.773 37.037 13.44 0.00 42.56 2.01
416 618 6.038603 TGAGTATCACGCGTAACCTATAGTTT 59.961 38.462 13.44 0.00 42.56 2.66
417 619 5.528690 TGAGTATCACGCGTAACCTATAGTT 59.471 40.000 13.44 0.00 42.56 2.24
418 620 5.059161 TGAGTATCACGCGTAACCTATAGT 58.941 41.667 13.44 7.99 42.56 2.12
419 621 5.407691 TCTGAGTATCACGCGTAACCTATAG 59.592 44.000 13.44 6.62 42.56 1.31
420 622 5.178252 GTCTGAGTATCACGCGTAACCTATA 59.822 44.000 13.44 2.36 42.56 1.31
421 623 4.024218 GTCTGAGTATCACGCGTAACCTAT 60.024 45.833 13.44 3.40 42.56 2.57
430 632 2.663602 CAGTGTTGTCTGAGTATCACGC 59.336 50.000 0.00 0.00 42.56 5.34
440 642 7.534085 TCTTGTACTTTAACAGTGTTGTCTG 57.466 36.000 18.90 8.36 36.23 3.51
519 1004 7.041644 TGCTGGTATAACTTTTATTACGATGCC 60.042 37.037 0.00 0.00 0.00 4.40
558 1043 5.252547 TGCCAATAGAAGTATCAGCAACAA 58.747 37.500 0.00 0.00 0.00 2.83
596 1081 7.448748 AATCAATCTACCTTTAAACTTGCGT 57.551 32.000 0.00 0.00 0.00 5.24
693 1183 4.828939 TCTTCCATTCTTGTCATGTTTGCT 59.171 37.500 0.00 0.00 0.00 3.91
710 1200 6.434028 CCATTAACATTCTCTTTGGTCTTCCA 59.566 38.462 0.00 0.00 42.66 3.53
726 1216 1.412343 GCGCAAATCCCCCATTAACAT 59.588 47.619 0.30 0.00 0.00 2.71
729 1219 1.786937 ATGCGCAAATCCCCCATTAA 58.213 45.000 17.11 0.00 0.00 1.40
852 1346 2.950309 TGTAAACTTTACCAAAGCCGCA 59.050 40.909 8.85 0.00 42.27 5.69
929 1423 6.662865 TTTGAATCACAGCAAAAAGGGATA 57.337 33.333 0.00 0.00 31.64 2.59
930 1424 5.549742 TTTGAATCACAGCAAAAAGGGAT 57.450 34.783 0.00 0.00 31.64 3.85
977 1471 8.068380 GCATTATACCAACGAGGAGAAAATTAC 58.932 37.037 5.70 0.00 41.22 1.89
1176 1673 4.721776 TCCAGGCTTCTGTTTGGTAGATAT 59.278 41.667 0.00 0.00 36.81 1.63
1223 1724 7.546316 TGATTGTTGGCTAATTCATTTGTGATG 59.454 33.333 0.00 0.00 0.00 3.07
1233 1734 6.311200 GGTGTCAAATGATTGTTGGCTAATTC 59.689 38.462 0.00 0.00 37.79 2.17
1237 1738 4.022416 GTGGTGTCAAATGATTGTTGGCTA 60.022 41.667 0.00 0.00 37.79 3.93
1358 1866 3.176924 TGATGGAGATAGAGTAGCCCC 57.823 52.381 0.00 0.00 0.00 5.80
1402 1910 5.630121 TGTTGCTTCTTTTCAGATCCCTAA 58.370 37.500 0.00 0.00 0.00 2.69
1628 2144 5.247337 TGCATATTCCGGAGACATATAACCA 59.753 40.000 3.34 1.71 0.00 3.67
1807 2325 2.875296 TGTGGTCAAAGGAATTCCAGG 58.125 47.619 26.22 14.44 38.89 4.45
1845 2366 9.784531 TGCCTGAATAAACCAAATCAAAAATAA 57.215 25.926 0.00 0.00 0.00 1.40
1846 2367 9.956640 ATGCCTGAATAAACCAAATCAAAAATA 57.043 25.926 0.00 0.00 0.00 1.40
1847 2368 8.732531 CATGCCTGAATAAACCAAATCAAAAAT 58.267 29.630 0.00 0.00 0.00 1.82
1859 2380 5.471456 CCATAGACTCCATGCCTGAATAAAC 59.529 44.000 0.00 0.00 0.00 2.01
1918 2439 2.838736 TGGAACAGCTCTCTGAAACAC 58.161 47.619 0.00 0.00 42.95 3.32
1934 2455 2.575532 CACAAAGCCTCTTCACTGGAA 58.424 47.619 0.00 0.00 0.00 3.53
1955 2476 1.471119 AGAGCCCAACATGAATGCAG 58.529 50.000 0.00 0.00 0.00 4.41
2048 2569 1.091537 TATAAGGCGTTGCAAGTGGC 58.908 50.000 15.12 15.12 45.13 5.01
2064 2585 7.987458 CCTCTGAGAAAAATACAGTGGCTTATA 59.013 37.037 6.17 0.00 38.07 0.98
2113 2636 1.338484 CCACAGAGTCCTGACCATGTG 60.338 57.143 18.49 18.49 43.02 3.21
2115 2638 1.269958 TCCACAGAGTCCTGACCATG 58.730 55.000 0.00 0.00 43.02 3.66
2153 2678 1.997791 TGACCCTATCGCCCCTCTATA 59.002 52.381 0.00 0.00 0.00 1.31
2173 2698 1.782028 GCGGAACTTGGAAACTGCGT 61.782 55.000 0.00 0.00 0.00 5.24
2176 2701 0.821711 TGGGCGGAACTTGGAAACTG 60.822 55.000 0.00 0.00 0.00 3.16
2182 2707 2.676121 TGCATGGGCGGAACTTGG 60.676 61.111 0.00 0.00 45.35 3.61
2202 2727 4.281941 GGCTTTGAAAGAGAACTGGGAAAT 59.718 41.667 9.48 0.00 0.00 2.17
2254 2811 6.173339 GGTACATTCCATCTTTGAACTGAGA 58.827 40.000 0.00 0.00 0.00 3.27
2274 2831 0.683412 ACCTTGTCCTCCAACGGTAC 59.317 55.000 0.00 0.00 34.69 3.34
2281 2838 1.214175 TGAGCAAAACCTTGTCCTCCA 59.786 47.619 0.00 0.00 34.79 3.86
2295 2852 2.224744 TGGCAGTATCAAGGTTGAGCAA 60.225 45.455 0.00 0.00 41.08 3.91
2298 2859 4.148128 AGATGGCAGTATCAAGGTTGAG 57.852 45.455 0.00 0.00 41.08 3.02
2339 2900 2.656947 AGTACAACACCAGCACCAAT 57.343 45.000 0.00 0.00 0.00 3.16
2340 2901 2.428544 AAGTACAACACCAGCACCAA 57.571 45.000 0.00 0.00 0.00 3.67
2376 2937 2.939103 ACCGCAAGCATTCTCATAGAAC 59.061 45.455 0.00 0.00 37.00 3.01
2396 2987 0.606604 TACTTCAGCGGGTTCAGGAC 59.393 55.000 0.00 0.00 0.00 3.85
2452 3049 7.278868 GCTAAGATAATCCTCCAAATACCATCG 59.721 40.741 0.00 0.00 0.00 3.84
2462 3059 6.753913 ATCACAAGCTAAGATAATCCTCCA 57.246 37.500 0.00 0.00 0.00 3.86
2463 3060 6.995091 ACAATCACAAGCTAAGATAATCCTCC 59.005 38.462 0.00 0.00 0.00 4.30
2497 3094 1.824852 TCGTTCAGCTTCAGAGGCATA 59.175 47.619 7.36 0.00 0.00 3.14
2520 3130 1.801913 GACGACAGCACCAGTAGCG 60.802 63.158 0.00 0.00 37.01 4.26
2598 3209 1.995484 CACCTACGACAACATGCTCAG 59.005 52.381 0.00 0.00 0.00 3.35
2621 3274 4.842091 CGGGGCTTCGACGTACCG 62.842 72.222 10.80 10.80 35.01 4.02
2626 3279 2.125269 AAATCCGGGGCTTCGACG 60.125 61.111 0.00 0.00 0.00 5.12
2635 3288 1.956170 CGCTCCGATGAAATCCGGG 60.956 63.158 0.00 0.00 41.39 5.73
2729 3382 0.807496 GATTCCAGTGGCAGCTCAAC 59.193 55.000 3.51 0.00 0.00 3.18
2795 3448 3.904339 CCCCAGAGGTATTAGTAGCATGT 59.096 47.826 0.00 0.00 0.00 3.21
2868 3521 9.943163 ATGGGAATTTCAAATTTTGTTTTTACG 57.057 25.926 8.89 0.00 0.00 3.18
2889 4390 5.007034 TCGCACTTTAGAAAATGAATGGGA 58.993 37.500 0.00 0.00 0.00 4.37
2894 4395 6.371809 ACTGTTCGCACTTTAGAAAATGAA 57.628 33.333 0.00 0.00 0.00 2.57
2895 4396 6.371809 AACTGTTCGCACTTTAGAAAATGA 57.628 33.333 0.00 0.00 0.00 2.57
2975 4478 8.555166 TGTATCAAAAAGTGTTCGCTTTTAAG 57.445 30.769 19.61 15.94 44.88 1.85
3003 4507 7.655732 AGTCGTTCCCCTTTTCATAAAAATTTG 59.344 33.333 0.00 0.00 34.00 2.32
3005 4509 7.297936 AGTCGTTCCCCTTTTCATAAAAATT 57.702 32.000 0.00 0.00 34.00 1.82
3007 4511 6.718522 AAGTCGTTCCCCTTTTCATAAAAA 57.281 33.333 0.00 0.00 33.42 1.94
3042 4550 6.660887 ATCGTTTGAAAGTTTGTGCAATTT 57.339 29.167 0.00 0.00 0.00 1.82
3044 4552 6.660887 AAATCGTTTGAAAGTTTGTGCAAT 57.339 29.167 0.00 0.00 0.00 3.56


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.