Multiple sequence alignment - TraesCS2A01G291800

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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 TraesCS2A01G291800 chr2A 100.000 2392 0 0 1 2392 502628785 502626394 0.000000e+00 4418
1 TraesCS2A01G291800 chr2A 100.000 297 0 0 2713 3009 502626073 502625777 1.580000e-152 549
2 TraesCS2A01G291800 chr2D 94.472 1212 56 8 470 1676 371926250 371925045 0.000000e+00 1857
3 TraesCS2A01G291800 chr2D 95.483 642 19 3 1725 2366 371924971 371924340 0.000000e+00 1016
4 TraesCS2A01G291800 chr2D 94.602 352 16 2 1 351 371928639 371928290 2.640000e-150 542
5 TraesCS2A01G291800 chr2D 92.683 82 4 1 388 469 371926402 371926323 1.900000e-22 117
6 TraesCS2A01G291800 chr2B 93.523 1158 54 8 473 1624 441081519 441080377 0.000000e+00 1703
7 TraesCS2A01G291800 chr2B 93.324 734 34 10 1646 2376 441080382 441079661 0.000000e+00 1070
8 TraesCS2A01G291800 chr2B 90.341 352 31 3 1 351 441082238 441081889 2.730000e-125 459
9 TraesCS2A01G291800 chr2B 95.690 116 5 0 354 469 441081710 441081595 1.420000e-43 187
10 TraesCS2A01G291800 chr2B 78.277 267 31 17 2722 2980 441079633 441079386 2.420000e-31 147


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 TraesCS2A01G291800 chr2A 502625777 502628785 3008 True 2483.5 4418 100.000 1 3009 2 chr2A.!!$R1 3008
1 TraesCS2A01G291800 chr2D 371924340 371928639 4299 True 883.0 1857 94.310 1 2366 4 chr2D.!!$R1 2365
2 TraesCS2A01G291800 chr2B 441079386 441082238 2852 True 713.2 1703 90.231 1 2980 5 chr2B.!!$R1 2979

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
400 2253 0.108138 CCGCCTACTCCAAGTCCAAG 60.108 60.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 4045 1.265635 CGTGCCAAACCAATTCGAGAA 59.734 47.619 0.0 0.0 0.0 2.87 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
42 43 0.317160 CGTAGAGGACACTGGCACAA 59.683 55.000 0.00 0.00 38.70 3.33
52 53 1.047801 ACTGGCACAATTTGGTTCCC 58.952 50.000 0.78 0.00 38.70 3.97
107 108 1.418637 TGTGTCCCCAGTTCCTACAAC 59.581 52.381 0.00 0.00 0.00 3.32
109 110 0.971386 GTCCCCAGTTCCTACAACGA 59.029 55.000 0.00 0.00 0.00 3.85
124 125 0.255890 AACGATAGCATTGTGGCCCT 59.744 50.000 0.00 0.00 42.67 5.19
125 126 0.255890 ACGATAGCATTGTGGCCCTT 59.744 50.000 0.00 0.00 42.67 3.95
153 154 6.683537 TCTCTTTCTTCCTCACCATATCCTA 58.316 40.000 0.00 0.00 0.00 2.94
166 167 3.973973 CCATATCCTACTTCCCACCTTGA 59.026 47.826 0.00 0.00 0.00 3.02
167 168 4.599241 CCATATCCTACTTCCCACCTTGAT 59.401 45.833 0.00 0.00 0.00 2.57
308 309 6.456181 GCGTGATTTTGGAGTTTGATCTCTAG 60.456 42.308 0.00 0.00 35.11 2.43
351 353 4.883585 TCACCATTCATACTTGATCCTTGC 59.116 41.667 0.00 0.00 0.00 4.01
352 354 3.879295 ACCATTCATACTTGATCCTTGCG 59.121 43.478 0.00 0.00 0.00 4.85
366 544 0.664166 CTTGCGCATGTGTTCAACCC 60.664 55.000 12.75 0.00 0.00 4.11
400 2253 0.108138 CCGCCTACTCCAAGTCCAAG 60.108 60.000 0.00 0.00 0.00 3.61
488 2415 3.732219 CGCGCAAATTCAATGCAATAGAT 59.268 39.130 8.75 0.00 44.01 1.98
509 2436 5.895534 AGATATCAAATGGGCATGACTTTGT 59.104 36.000 11.78 4.26 31.98 2.83
513 2440 5.964758 TCAAATGGGCATGACTTTGTAATC 58.035 37.500 11.78 0.00 31.98 1.75
523 2450 7.816995 GGCATGACTTTGTAATCACCAAATTTA 59.183 33.333 0.00 0.00 31.85 1.40
646 2579 5.999205 AATTGACAAGCCAATCACCAATA 57.001 34.783 0.00 0.00 35.86 1.90
666 2599 7.615365 ACCAATAGTTACAATGATTCCATGTGT 59.385 33.333 0.00 0.00 32.36 3.72
667 2600 9.119418 CCAATAGTTACAATGATTCCATGTGTA 57.881 33.333 0.00 0.00 32.36 2.90
699 2632 1.066858 TGCCGTTCTCATCTCACCTTC 60.067 52.381 0.00 0.00 0.00 3.46
741 2674 2.094854 CCAGTTGCTTCTGGCTTTGATC 60.095 50.000 13.09 0.00 46.53 2.92
951 2885 3.458163 TCTGATCGCCCGGGTGTC 61.458 66.667 32.48 26.57 0.00 3.67
1368 3302 2.457778 CGCCGTGGGGATTTACGTG 61.458 63.158 0.00 0.00 38.56 4.49
1469 3403 3.999663 AGTAAGTCTGTTGCATCTGAAGC 59.000 43.478 5.99 0.00 0.00 3.86
1474 3408 1.236616 TGTTGCATCTGAAGCCCACG 61.237 55.000 2.09 0.00 0.00 4.94
1480 3414 0.907704 ATCTGAAGCCCACGGTACCA 60.908 55.000 13.54 0.00 0.00 3.25
1507 3441 3.574284 TTTCATTCCAGAATTGCACCG 57.426 42.857 0.00 0.00 0.00 4.94
1538 3472 5.913137 TCAAAGTGGAAAGTCAACACAAT 57.087 34.783 0.00 0.00 37.58 2.71
1539 3473 6.279513 TCAAAGTGGAAAGTCAACACAATT 57.720 33.333 0.00 0.00 37.58 2.32
1540 3474 7.397892 TCAAAGTGGAAAGTCAACACAATTA 57.602 32.000 0.00 0.00 37.58 1.40
1543 3477 6.131544 AGTGGAAAGTCAACACAATTACAC 57.868 37.500 0.00 0.00 36.42 2.90
1544 3478 5.650266 AGTGGAAAGTCAACACAATTACACA 59.350 36.000 0.00 0.00 37.66 3.72
1620 3554 0.320247 GCCGGCGAGATGAATCAGAT 60.320 55.000 12.58 0.00 0.00 2.90
1635 3569 7.149569 TGAATCAGATCATTTGTTTCCTCAC 57.850 36.000 0.00 0.00 0.00 3.51
1708 3686 1.149987 GTCGGTCGCAACAACCATTA 58.850 50.000 0.00 0.00 36.53 1.90
1870 3849 3.721706 CTGTGCCCCAGGTCCTCC 61.722 72.222 0.00 0.00 37.54 4.30
1909 3888 1.077068 CTCGTCCTCCTGCTCCTCT 60.077 63.158 0.00 0.00 0.00 3.69
2047 4026 4.347360 TCATCCATGATGATCACTGGAC 57.653 45.455 20.91 3.15 43.11 4.02
2066 4045 3.728373 GCCCACCCTCGGTCCATT 61.728 66.667 0.00 0.00 31.02 3.16
2128 4107 3.589654 TAGCGTGCTGGTGCCTGAC 62.590 63.158 4.25 0.00 38.71 3.51
2191 4170 3.490890 GCCACGCCAGATTCAGAC 58.509 61.111 0.00 0.00 0.00 3.51
2205 4184 6.865726 CCAGATTCAGACAGTAGGAAATATCG 59.134 42.308 0.00 0.00 0.00 2.92
2207 4186 6.778069 AGATTCAGACAGTAGGAAATATCGGA 59.222 38.462 0.00 0.00 0.00 4.55
2257 4236 1.480545 GCCCGGGCAATTAAGATTGTT 59.519 47.619 40.73 0.00 43.67 2.83
2258 4237 2.691011 GCCCGGGCAATTAAGATTGTTA 59.309 45.455 40.73 0.00 43.67 2.41
2341 4322 1.063567 AGTAGAGGAGATTGACCGGCT 60.064 52.381 0.00 0.00 0.00 5.52
2366 4347 5.878627 TGTATGGATGGATCACATATGCAA 58.121 37.500 1.58 0.00 40.72 4.08
2367 4348 5.941647 TGTATGGATGGATCACATATGCAAG 59.058 40.000 1.58 0.00 40.72 4.01
2368 4349 4.442401 TGGATGGATCACATATGCAAGT 57.558 40.909 1.58 0.00 40.72 3.16
2369 4350 4.795469 TGGATGGATCACATATGCAAGTT 58.205 39.130 1.58 0.00 40.72 2.66
2370 4351 4.581409 TGGATGGATCACATATGCAAGTTG 59.419 41.667 1.58 0.00 40.72 3.16
2371 4352 4.823442 GGATGGATCACATATGCAAGTTGA 59.177 41.667 7.16 0.00 40.72 3.18
2380 4361 2.363306 ATGCAAGTTGACAAGTGGGA 57.637 45.000 7.16 0.00 0.00 4.37
2382 4363 2.023673 TGCAAGTTGACAAGTGGGAAG 58.976 47.619 7.16 0.00 0.00 3.46
2755 4743 1.234615 CGTCGGCACTGGACCAAAAT 61.235 55.000 0.00 0.00 0.00 1.82
2757 4745 0.953471 TCGGCACTGGACCAAAATCG 60.953 55.000 0.00 0.00 0.00 3.34
2773 4761 8.259049 ACCAAAATCGACGAATACTCAATTTA 57.741 30.769 0.00 0.00 0.00 1.40
2786 4774 5.907197 ACTCAATTTACTCAACTGACACG 57.093 39.130 0.00 0.00 0.00 4.49
2793 4781 1.206132 ACTCAACTGACACGACACCAA 59.794 47.619 0.00 0.00 0.00 3.67
2840 4846 7.664731 AGAACATCTGAAATGACAAATCTCAGT 59.335 33.333 0.00 0.00 35.93 3.41
2845 4851 6.592994 TCTGAAATGACAAATCTCAGTAGCAG 59.407 38.462 0.00 0.00 35.93 4.24
2849 4855 3.244181 TGACAAATCTCAGTAGCAGCACA 60.244 43.478 0.00 0.00 0.00 4.57
2850 4856 3.070018 ACAAATCTCAGTAGCAGCACAC 58.930 45.455 0.00 0.00 0.00 3.82
2851 4857 3.244353 ACAAATCTCAGTAGCAGCACACT 60.244 43.478 0.00 0.00 0.00 3.55
2879 4885 2.027377 CAGGAGTTCAGAATGCCAGACT 60.027 50.000 6.93 0.00 34.76 3.24
2880 4886 2.027377 AGGAGTTCAGAATGCCAGACTG 60.027 50.000 0.00 0.00 34.76 3.51
2881 4887 2.354259 GAGTTCAGAATGCCAGACTGG 58.646 52.381 17.83 17.83 41.55 4.00
2882 4888 1.004044 AGTTCAGAATGCCAGACTGGG 59.996 52.381 23.09 5.26 38.19 4.45
2883 4889 1.003580 GTTCAGAATGCCAGACTGGGA 59.996 52.381 23.09 21.14 43.78 4.37
2884 4890 0.615331 TCAGAATGCCAGACTGGGAC 59.385 55.000 23.09 9.46 41.95 4.46
2885 4891 0.617413 CAGAATGCCAGACTGGGACT 59.383 55.000 23.09 10.63 41.95 3.85
2886 4892 1.833630 CAGAATGCCAGACTGGGACTA 59.166 52.381 23.09 0.00 41.95 2.59
2887 4893 1.834263 AGAATGCCAGACTGGGACTAC 59.166 52.381 23.09 14.22 41.95 2.73
2888 4894 1.555075 GAATGCCAGACTGGGACTACA 59.445 52.381 23.09 12.01 41.95 2.74
2889 4895 1.885049 ATGCCAGACTGGGACTACAT 58.115 50.000 23.09 13.73 41.95 2.29
2890 4896 0.904649 TGCCAGACTGGGACTACATG 59.095 55.000 23.09 0.00 38.19 3.21
2891 4897 0.462759 GCCAGACTGGGACTACATGC 60.463 60.000 23.09 1.23 38.19 4.06
2892 4898 0.179000 CCAGACTGGGACTACATGCC 59.821 60.000 14.26 0.00 39.94 4.40
2900 4906 2.851195 GGGACTACATGCCAACCTATG 58.149 52.381 0.00 0.00 39.10 2.23
2901 4907 2.222027 GGACTACATGCCAACCTATGC 58.778 52.381 0.00 0.00 0.00 3.14
2902 4908 2.421388 GGACTACATGCCAACCTATGCA 60.421 50.000 0.00 0.00 42.52 3.96
2903 4909 3.278574 GACTACATGCCAACCTATGCAA 58.721 45.455 0.00 0.00 41.50 4.08
2904 4910 3.885297 GACTACATGCCAACCTATGCAAT 59.115 43.478 0.00 0.00 41.50 3.56
2905 4911 3.633525 ACTACATGCCAACCTATGCAATG 59.366 43.478 0.00 0.00 41.50 2.82
2906 4912 2.737544 ACATGCCAACCTATGCAATGA 58.262 42.857 0.00 0.00 41.50 2.57
2907 4913 3.098377 ACATGCCAACCTATGCAATGAA 58.902 40.909 0.00 0.00 41.50 2.57
2908 4914 3.119029 ACATGCCAACCTATGCAATGAAC 60.119 43.478 0.00 0.00 41.50 3.18
2909 4915 1.824230 TGCCAACCTATGCAATGAACC 59.176 47.619 0.00 0.00 33.87 3.62
2910 4916 1.824230 GCCAACCTATGCAATGAACCA 59.176 47.619 0.00 0.00 0.00 3.67
2911 4917 2.417243 GCCAACCTATGCAATGAACCAC 60.417 50.000 0.00 0.00 0.00 4.16
2912 4918 2.166254 CCAACCTATGCAATGAACCACC 59.834 50.000 0.00 0.00 0.00 4.61
2913 4919 3.091545 CAACCTATGCAATGAACCACCT 58.908 45.455 0.00 0.00 0.00 4.00
2914 4920 2.726821 ACCTATGCAATGAACCACCTG 58.273 47.619 0.00 0.00 0.00 4.00
2941 4947 0.593128 AGCAAAGCTAACAGGTTGCG 59.407 50.000 11.73 0.00 36.99 4.85
2980 4986 5.873179 TGGTCAAACAATATTCGGTTCTC 57.127 39.130 0.00 0.00 0.00 2.87
2981 4987 5.556915 TGGTCAAACAATATTCGGTTCTCT 58.443 37.500 0.00 0.00 0.00 3.10
2982 4988 6.703319 TGGTCAAACAATATTCGGTTCTCTA 58.297 36.000 0.00 0.00 0.00 2.43
2983 4989 6.816640 TGGTCAAACAATATTCGGTTCTCTAG 59.183 38.462 0.00 0.00 0.00 2.43
2984 4990 6.238130 GGTCAAACAATATTCGGTTCTCTAGC 60.238 42.308 0.00 0.00 0.00 3.42
2985 4991 6.535508 GTCAAACAATATTCGGTTCTCTAGCT 59.464 38.462 0.00 0.00 0.00 3.32
2986 4992 6.535150 TCAAACAATATTCGGTTCTCTAGCTG 59.465 38.462 0.00 0.00 0.00 4.24
2987 4993 4.950050 ACAATATTCGGTTCTCTAGCTGG 58.050 43.478 0.00 0.00 0.00 4.85
2988 4994 4.406003 ACAATATTCGGTTCTCTAGCTGGT 59.594 41.667 0.00 0.00 0.00 4.00
2989 4995 5.597182 ACAATATTCGGTTCTCTAGCTGGTA 59.403 40.000 0.00 0.00 0.00 3.25
2990 4996 6.097839 ACAATATTCGGTTCTCTAGCTGGTAA 59.902 38.462 0.00 0.00 0.00 2.85
2991 4997 6.919775 ATATTCGGTTCTCTAGCTGGTAAT 57.080 37.500 0.00 0.00 0.00 1.89
2992 4998 4.386867 TTCGGTTCTCTAGCTGGTAATG 57.613 45.455 0.00 0.00 0.00 1.90
2993 4999 3.362706 TCGGTTCTCTAGCTGGTAATGT 58.637 45.455 0.00 0.00 0.00 2.71
2994 5000 3.767673 TCGGTTCTCTAGCTGGTAATGTT 59.232 43.478 0.00 0.00 0.00 2.71
2995 5001 4.222145 TCGGTTCTCTAGCTGGTAATGTTT 59.778 41.667 0.00 0.00 0.00 2.83
2996 5002 4.330074 CGGTTCTCTAGCTGGTAATGTTTG 59.670 45.833 0.00 0.00 0.00 2.93
2997 5003 5.488341 GGTTCTCTAGCTGGTAATGTTTGA 58.512 41.667 0.00 0.00 0.00 2.69
2998 5004 6.116126 GGTTCTCTAGCTGGTAATGTTTGAT 58.884 40.000 0.00 0.00 0.00 2.57
2999 5005 6.037610 GGTTCTCTAGCTGGTAATGTTTGATG 59.962 42.308 0.00 0.00 0.00 3.07
3000 5006 6.299805 TCTCTAGCTGGTAATGTTTGATGT 57.700 37.500 0.00 0.00 0.00 3.06
3001 5007 6.108687 TCTCTAGCTGGTAATGTTTGATGTG 58.891 40.000 0.00 0.00 0.00 3.21
3002 5008 6.048732 TCTAGCTGGTAATGTTTGATGTGA 57.951 37.500 0.00 0.00 0.00 3.58
3003 5009 6.472016 TCTAGCTGGTAATGTTTGATGTGAA 58.528 36.000 0.00 0.00 0.00 3.18
3004 5010 6.939730 TCTAGCTGGTAATGTTTGATGTGAAA 59.060 34.615 0.00 0.00 0.00 2.69
3005 5011 6.403866 AGCTGGTAATGTTTGATGTGAAAA 57.596 33.333 0.00 0.00 0.00 2.29
3006 5012 6.815089 AGCTGGTAATGTTTGATGTGAAAAA 58.185 32.000 0.00 0.00 0.00 1.94
3007 5013 6.925165 AGCTGGTAATGTTTGATGTGAAAAAG 59.075 34.615 0.00 0.00 0.00 2.27
3008 5014 6.922957 GCTGGTAATGTTTGATGTGAAAAAGA 59.077 34.615 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.820787 CCAGTGTCCTCTACGAGAAGTT 59.179 50.000 0.00 0.00 0.00 2.66
52 53 4.230657 GTCGAACATGGAGGAATATCGAG 58.769 47.826 0.00 0.00 38.35 4.04
107 108 1.392589 AAAGGGCCACAATGCTATCG 58.607 50.000 6.18 0.00 0.00 2.92
125 126 7.611855 GGATATGGTGAGGAAGAAAGAGAAAAA 59.388 37.037 0.00 0.00 0.00 1.94
153 154 5.047235 GCGATACTATATCAAGGTGGGAAGT 60.047 44.000 0.00 0.00 0.00 3.01
166 167 7.011576 CCAGAGATAGTCGTTGCGATACTATAT 59.988 40.741 10.42 8.39 38.42 0.86
167 168 6.313164 CCAGAGATAGTCGTTGCGATACTATA 59.687 42.308 10.42 0.00 38.42 1.31
224 225 2.750141 TCTACTATTCGGAGCCACCT 57.250 50.000 0.00 0.00 36.31 4.00
351 353 1.285641 GTGGGGTTGAACACATGCG 59.714 57.895 0.00 0.00 37.54 4.73
352 354 1.112315 TGGTGGGGTTGAACACATGC 61.112 55.000 0.00 0.00 39.31 4.06
366 544 2.347490 CGGAGGGTCAAGTGGTGG 59.653 66.667 0.00 0.00 0.00 4.61
400 2253 5.337169 GGAGCATATGGATAGAGGACTTCAC 60.337 48.000 4.56 0.00 0.00 3.18
488 2415 7.341512 TGATTACAAAGTCATGCCCATTTGATA 59.658 33.333 14.53 6.17 36.41 2.15
535 2462 6.679327 CCACTAAGGGCAAAATACTCTTAC 57.321 41.667 0.00 0.00 0.00 2.34
583 2516 7.419172 GCCTCTCCTCCACAAATTAAGTACTAT 60.419 40.741 0.00 0.00 0.00 2.12
646 2579 9.851686 ACATATACACATGGAATCATTGTAACT 57.148 29.630 0.00 0.00 34.21 2.24
699 2632 2.094649 GGAAGTGACTTGTACCGGAGAG 60.095 54.545 9.46 2.22 0.00 3.20
951 2885 2.684843 GCCGCAGAAACAGCTCCAG 61.685 63.158 0.00 0.00 0.00 3.86
1053 2987 4.664267 TGCCCTCCTGCCTCCTGT 62.664 66.667 0.00 0.00 0.00 4.00
1255 3189 2.908073 CGTTCACCAGCACCTTGCC 61.908 63.158 0.00 0.00 46.52 4.52
1362 3296 1.980052 CCTGCCCTCCTTCACGTAA 59.020 57.895 0.00 0.00 0.00 3.18
1469 3403 2.194201 AAAACAGATGGTACCGTGGG 57.806 50.000 12.53 5.69 0.00 4.61
1474 3408 5.710099 TCTGGAATGAAAAACAGATGGTACC 59.290 40.000 4.43 4.43 35.24 3.34
1480 3414 6.647895 GTGCAATTCTGGAATGAAAAACAGAT 59.352 34.615 0.00 0.00 39.46 2.90
1507 3441 5.008613 TGACTTTCCACTTTGATAGTTGTGC 59.991 40.000 0.00 0.00 33.85 4.57
1539 3473 9.321562 GCTTGGCTAATACTAGTATTTTGTGTA 57.678 33.333 28.42 12.09 37.07 2.90
1540 3474 8.047310 AGCTTGGCTAATACTAGTATTTTGTGT 58.953 33.333 28.42 10.01 36.99 3.72
1543 3477 7.865707 CCAGCTTGGCTAATACTAGTATTTTG 58.134 38.462 28.42 21.97 36.40 2.44
1582 3516 4.681942 CCGGCTATTCTCAAATAGAGTTCG 59.318 45.833 8.91 6.55 44.87 3.95
1590 3524 1.412710 TCTCGCCGGCTATTCTCAAAT 59.587 47.619 26.68 0.00 0.00 2.32
1620 3554 4.141824 GGGGTTTTGTGAGGAAACAAATGA 60.142 41.667 3.57 0.00 46.44 2.57
1662 3596 1.826921 CTCAGTGGGCCCATGCATC 60.827 63.158 31.45 15.35 40.13 3.91
1708 3686 5.401531 TCACTAACTGTCGCCTAAAGATT 57.598 39.130 0.00 0.00 0.00 2.40
2045 4024 4.083862 GACCGAGGGTGGGCAGTC 62.084 72.222 0.00 0.00 36.84 3.51
2066 4045 1.265635 CGTGCCAAACCAATTCGAGAA 59.734 47.619 0.00 0.00 0.00 2.87
2128 4107 2.858344 CCGCCTAAACAACGAGATACTG 59.142 50.000 0.00 0.00 0.00 2.74
2191 4170 3.675225 CACGCATCCGATATTTCCTACTG 59.325 47.826 0.00 0.00 38.29 2.74
2205 4184 2.604046 ACTGTCCTAATCACGCATCC 57.396 50.000 0.00 0.00 0.00 3.51
2207 4186 2.420129 GGGAACTGTCCTAATCACGCAT 60.420 50.000 0.00 0.00 44.28 4.73
2257 4236 8.743714 CACATCATGCTTCCTGTAGTCTATATA 58.256 37.037 0.00 0.00 0.00 0.86
2258 4237 7.234371 ACACATCATGCTTCCTGTAGTCTATAT 59.766 37.037 0.00 0.00 0.00 0.86
2300 4279 6.239217 ACTTGCATCCACAATCAGATAGTA 57.761 37.500 0.00 0.00 0.00 1.82
2301 4280 5.108187 ACTTGCATCCACAATCAGATAGT 57.892 39.130 0.00 0.00 0.00 2.12
2302 4281 6.519382 TCTACTTGCATCCACAATCAGATAG 58.481 40.000 0.00 0.00 0.00 2.08
2312 4291 4.125703 CAATCTCCTCTACTTGCATCCAC 58.874 47.826 0.00 0.00 0.00 4.02
2341 4322 7.197901 TGCATATGTGATCCATCCATACATA 57.802 36.000 4.29 0.00 38.25 2.29
2366 4347 3.053619 AGTTTCCTTCCCACTTGTCAACT 60.054 43.478 0.00 0.00 0.00 3.16
2367 4348 3.288092 AGTTTCCTTCCCACTTGTCAAC 58.712 45.455 0.00 0.00 0.00 3.18
2368 4349 3.662759 AGTTTCCTTCCCACTTGTCAA 57.337 42.857 0.00 0.00 0.00 3.18
2369 4350 3.493699 CGTAGTTTCCTTCCCACTTGTCA 60.494 47.826 0.00 0.00 0.00 3.58
2370 4351 3.064931 CGTAGTTTCCTTCCCACTTGTC 58.935 50.000 0.00 0.00 0.00 3.18
2371 4352 3.121738 CGTAGTTTCCTTCCCACTTGT 57.878 47.619 0.00 0.00 0.00 3.16
2712 4693 0.454600 CATCTGCAACTGATGTGGGC 59.545 55.000 6.32 0.00 35.86 5.36
2713 4694 0.454600 GCATCTGCAACTGATGTGGG 59.545 55.000 13.98 0.00 40.38 4.61
2714 4695 0.454600 GGCATCTGCAACTGATGTGG 59.545 55.000 13.98 0.00 44.36 4.17
2715 4696 1.135489 GTGGCATCTGCAACTGATGTG 60.135 52.381 13.98 0.00 41.68 3.21
2716 4697 1.171308 GTGGCATCTGCAACTGATGT 58.829 50.000 13.98 0.00 41.68 3.06
2717 4698 0.454600 GGTGGCATCTGCAACTGATG 59.545 55.000 9.45 9.48 44.30 3.07
2718 4699 2.877975 GGTGGCATCTGCAACTGAT 58.122 52.632 9.45 0.00 44.30 2.90
2719 4700 4.402851 GGTGGCATCTGCAACTGA 57.597 55.556 9.45 0.00 44.30 3.41
2720 4701 2.872557 CGGTGGCATCTGCAACTG 59.127 61.111 9.45 6.88 44.30 3.16
2745 4726 4.178540 GAGTATTCGTCGATTTTGGTCCA 58.821 43.478 0.00 0.00 0.00 4.02
2746 4727 4.178540 TGAGTATTCGTCGATTTTGGTCC 58.821 43.478 0.00 0.00 0.00 4.46
2747 4728 5.773239 TTGAGTATTCGTCGATTTTGGTC 57.227 39.130 0.00 0.00 0.00 4.02
2755 4743 7.272731 CAGTTGAGTAAATTGAGTATTCGTCGA 59.727 37.037 0.00 0.00 0.00 4.20
2757 4745 8.373992 GTCAGTTGAGTAAATTGAGTATTCGTC 58.626 37.037 0.00 0.00 35.40 4.20
2773 4761 0.821517 TGGTGTCGTGTCAGTTGAGT 59.178 50.000 0.00 0.00 0.00 3.41
2786 4774 5.243426 TCTTTTGTTAGCTGTTTGGTGTC 57.757 39.130 0.00 0.00 0.00 3.67
2840 4846 2.028112 CCTGAACCTTAGTGTGCTGCTA 60.028 50.000 0.00 0.00 0.00 3.49
2845 4851 2.841442 ACTCCTGAACCTTAGTGTGC 57.159 50.000 0.00 0.00 0.00 4.57
2849 4855 5.799213 CATTCTGAACTCCTGAACCTTAGT 58.201 41.667 0.00 0.00 35.90 2.24
2850 4856 4.633565 GCATTCTGAACTCCTGAACCTTAG 59.366 45.833 0.00 0.00 35.90 2.18
2851 4857 4.565652 GGCATTCTGAACTCCTGAACCTTA 60.566 45.833 0.00 0.00 35.90 2.69
2879 4885 1.959710 TAGGTTGGCATGTAGTCCCA 58.040 50.000 0.00 0.00 0.00 4.37
2880 4886 2.851195 CATAGGTTGGCATGTAGTCCC 58.149 52.381 0.00 0.00 0.00 4.46
2881 4887 2.222027 GCATAGGTTGGCATGTAGTCC 58.778 52.381 0.00 0.00 0.00 3.85
2882 4888 2.917933 TGCATAGGTTGGCATGTAGTC 58.082 47.619 0.00 0.00 34.58 2.59
2883 4889 3.364460 TTGCATAGGTTGGCATGTAGT 57.636 42.857 0.00 0.00 40.17 2.73
2884 4890 3.884693 TCATTGCATAGGTTGGCATGTAG 59.115 43.478 0.00 0.00 40.17 2.74
2885 4891 3.895998 TCATTGCATAGGTTGGCATGTA 58.104 40.909 0.00 0.00 40.17 2.29
2886 4892 2.737544 TCATTGCATAGGTTGGCATGT 58.262 42.857 0.00 0.00 40.17 3.21
2887 4893 3.450578 GTTCATTGCATAGGTTGGCATG 58.549 45.455 0.00 0.00 40.17 4.06
2888 4894 2.431782 GGTTCATTGCATAGGTTGGCAT 59.568 45.455 0.00 0.00 40.17 4.40
2889 4895 1.824230 GGTTCATTGCATAGGTTGGCA 59.176 47.619 0.00 0.00 38.46 4.92
2890 4896 1.824230 TGGTTCATTGCATAGGTTGGC 59.176 47.619 0.00 0.00 0.00 4.52
2891 4897 2.166254 GGTGGTTCATTGCATAGGTTGG 59.834 50.000 0.00 0.00 0.00 3.77
2892 4898 3.091545 AGGTGGTTCATTGCATAGGTTG 58.908 45.455 0.00 0.00 0.00 3.77
2893 4899 3.091545 CAGGTGGTTCATTGCATAGGTT 58.908 45.455 0.00 0.00 0.00 3.50
2894 4900 2.726821 CAGGTGGTTCATTGCATAGGT 58.273 47.619 0.00 0.00 0.00 3.08
2895 4901 1.406539 GCAGGTGGTTCATTGCATAGG 59.593 52.381 0.00 0.00 36.59 2.57
2896 4902 1.064505 CGCAGGTGGTTCATTGCATAG 59.935 52.381 0.00 0.00 36.37 2.23
2897 4903 1.093972 CGCAGGTGGTTCATTGCATA 58.906 50.000 0.00 0.00 36.37 3.14
2898 4904 1.885157 CGCAGGTGGTTCATTGCAT 59.115 52.632 0.00 0.00 36.37 3.96
2899 4905 3.353600 CGCAGGTGGTTCATTGCA 58.646 55.556 0.00 0.00 36.37 4.08
2912 4918 4.712425 GCTTTGCTGTGGCCGCAG 62.712 66.667 36.88 36.88 38.80 5.18
2913 4919 3.841137 TAGCTTTGCTGTGGCCGCA 62.841 57.895 19.93 19.93 40.10 5.69
2914 4920 2.625823 TTAGCTTTGCTGTGGCCGC 61.626 57.895 10.11 10.11 40.10 6.53
2924 4930 2.032799 TGAACGCAACCTGTTAGCTTTG 59.967 45.455 0.00 0.00 0.00 2.77
2941 4947 2.479275 GACCAAGAACGCCTTACTGAAC 59.521 50.000 0.00 0.00 32.86 3.18
2980 4986 6.741992 TTCACATCAAACATTACCAGCTAG 57.258 37.500 0.00 0.00 0.00 3.42
2981 4987 7.517614 TTTTCACATCAAACATTACCAGCTA 57.482 32.000 0.00 0.00 0.00 3.32
2982 4988 6.403866 TTTTCACATCAAACATTACCAGCT 57.596 33.333 0.00 0.00 0.00 4.24
2983 4989 6.922957 TCTTTTTCACATCAAACATTACCAGC 59.077 34.615 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.