Multiple sequence alignment - TraesCS2B01G299100

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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 TraesCS2B01G299100 chr2B 100.000 3015 0 0 1 3015 419323691 419320677 0.000000e+00 5568
1 TraesCS2B01G299100 chr2A 88.573 2783 147 68 263 2950 471006700 471003994 0.000000e+00 3219
2 TraesCS2B01G299100 chr2A 83.165 297 7 17 4 265 471007120 471006832 6.500000e-57 231
3 TraesCS2B01G299100 chr2D 89.461 2097 93 51 4 2046 352906601 352904579 0.000000e+00 2531
4 TraesCS2B01G299100 chr2D 92.031 916 50 8 2108 3015 352904563 352903663 0.000000e+00 1266
5 TraesCS2B01G299100 chr7A 85.185 135 20 0 1583 1717 680542156 680542290 4.050000e-29 139
6 TraesCS2B01G299100 chr7D 86.555 119 16 0 1599 1717 589054716 589054598 6.780000e-27 132


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 TraesCS2B01G299100 chr2B 419320677 419323691 3014 True 5568.0 5568 100.000 1 3015 1 chr2B.!!$R1 3014
1 TraesCS2B01G299100 chr2A 471003994 471007120 3126 True 1725.0 3219 85.869 4 2950 2 chr2A.!!$R1 2946
2 TraesCS2B01G299100 chr2D 352903663 352906601 2938 True 1898.5 2531 90.746 4 3015 2 chr2D.!!$R1 3011

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
864 1081 0.313672 CACACACCCATTGTTTCCCG 59.686 55.0 0.0 0.0 35.67 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 2670 0.534203 GCCAAGGACGTCAAGTTGGA 60.534 55.0 31.98 0.0 41.82 3.53 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
37 42 3.461773 CCTGTGCCGAGATCCCGT 61.462 66.667 0.00 0.00 0.00 5.28
127 138 3.317795 GTACGCGGGCGATTCGAC 61.318 66.667 20.98 6.85 42.83 4.20
218 253 2.429571 CCACATGCAAGCACGCAC 60.430 61.111 1.79 0.00 46.56 5.34
233 268 3.857854 CACGCAGCATCGACCAGC 61.858 66.667 4.64 0.00 0.00 4.85
234 269 4.074526 ACGCAGCATCGACCAGCT 62.075 61.111 4.64 3.26 42.94 4.24
253 294 2.192175 CGCCCAATCACCCTACCC 59.808 66.667 0.00 0.00 0.00 3.69
254 295 2.375345 CGCCCAATCACCCTACCCT 61.375 63.158 0.00 0.00 0.00 4.34
255 296 1.227383 GCCCAATCACCCTACCCTG 59.773 63.158 0.00 0.00 0.00 4.45
256 297 1.571773 GCCCAATCACCCTACCCTGT 61.572 60.000 0.00 0.00 0.00 4.00
257 298 0.546598 CCCAATCACCCTACCCTGTC 59.453 60.000 0.00 0.00 0.00 3.51
258 299 1.584724 CCAATCACCCTACCCTGTCT 58.415 55.000 0.00 0.00 0.00 3.41
259 300 2.628559 CCCAATCACCCTACCCTGTCTA 60.629 54.545 0.00 0.00 0.00 2.59
299 471 5.924786 TGCTTAATCTATAGTCGTACTCGC 58.075 41.667 0.00 0.00 36.96 5.03
317 489 1.404986 CGCGGTTCCCAGAATACTCAA 60.405 52.381 0.00 0.00 0.00 3.02
318 490 2.706890 GCGGTTCCCAGAATACTCAAA 58.293 47.619 0.00 0.00 0.00 2.69
322 494 5.336451 GCGGTTCCCAGAATACTCAAATTTT 60.336 40.000 0.00 0.00 0.00 1.82
323 495 6.687604 CGGTTCCCAGAATACTCAAATTTTT 58.312 36.000 0.00 0.00 0.00 1.94
324 496 7.576098 GCGGTTCCCAGAATACTCAAATTTTTA 60.576 37.037 0.00 0.00 0.00 1.52
326 498 8.033038 GGTTCCCAGAATACTCAAATTTTTACC 58.967 37.037 0.00 0.00 0.00 2.85
327 499 8.803235 GTTCCCAGAATACTCAAATTTTTACCT 58.197 33.333 0.00 0.00 0.00 3.08
333 505 8.177456 AGAATACTCAAATTTTTACCTCCCCTT 58.823 33.333 0.00 0.00 0.00 3.95
334 506 8.736097 AATACTCAAATTTTTACCTCCCCTTT 57.264 30.769 0.00 0.00 0.00 3.11
367 539 2.357517 CACCGTCCCAGCTGACAC 60.358 66.667 17.39 10.11 34.88 3.67
377 549 1.880027 CCAGCTGACACTTACCAAACC 59.120 52.381 17.39 0.00 0.00 3.27
378 550 1.531149 CAGCTGACACTTACCAAACCG 59.469 52.381 8.42 0.00 0.00 4.44
382 554 3.790789 GCTGACACTTACCAAACCGTTTG 60.791 47.826 15.83 15.83 40.32 2.93
390 578 3.857638 CAAACCGTTTGGCCAGTAC 57.142 52.632 15.11 7.82 39.70 2.73
395 583 3.446507 CGTTTGGCCAGTACGGTAT 57.553 52.632 26.14 0.00 36.97 2.73
399 587 3.396560 GTTTGGCCAGTACGGTATATCC 58.603 50.000 5.11 0.00 36.97 2.59
462 655 5.047802 GGAAATCTCATGTGTTGTTGATGGT 60.048 40.000 0.00 0.00 0.00 3.55
463 656 5.633830 AATCTCATGTGTTGTTGATGGTC 57.366 39.130 0.00 0.00 0.00 4.02
464 657 3.411446 TCTCATGTGTTGTTGATGGTCC 58.589 45.455 0.00 0.00 0.00 4.46
481 675 2.351350 GGTCCCACAATTTACAACAGCG 60.351 50.000 0.00 0.00 0.00 5.18
487 681 2.556189 ACAATTTACAACAGCGCCATCA 59.444 40.909 2.29 0.00 0.00 3.07
500 694 2.670479 CGCCATCACTCACTAGCTATG 58.330 52.381 0.00 0.00 0.00 2.23
541 735 5.614324 AGCTGCCTACAATAATGTGAGTA 57.386 39.130 0.00 0.00 40.84 2.59
542 736 5.989477 AGCTGCCTACAATAATGTGAGTAA 58.011 37.500 0.00 0.00 40.84 2.24
543 737 5.817816 AGCTGCCTACAATAATGTGAGTAAC 59.182 40.000 0.00 0.00 40.84 2.50
544 738 5.817816 GCTGCCTACAATAATGTGAGTAACT 59.182 40.000 0.00 0.00 40.84 2.24
545 739 6.238211 GCTGCCTACAATAATGTGAGTAACTG 60.238 42.308 0.00 0.00 40.84 3.16
546 740 6.941857 TGCCTACAATAATGTGAGTAACTGA 58.058 36.000 0.00 0.00 40.84 3.41
559 757 4.955811 AGTAACTGACTCACAATGACCA 57.044 40.909 0.00 0.00 29.95 4.02
566 764 5.221722 ACTGACTCACAATGACCACAATACT 60.222 40.000 0.00 0.00 0.00 2.12
592 790 6.342111 CCAAAGTTAAAAGGCCACAAACTTA 58.658 36.000 19.48 1.50 38.95 2.24
593 791 6.989759 CCAAAGTTAAAAGGCCACAAACTTAT 59.010 34.615 19.48 11.10 38.95 1.73
600 798 6.510879 AAAGGCCACAAACTTATTAGTAGC 57.489 37.500 5.01 0.00 33.17 3.58
644 851 5.464057 TCACCATGAACTTTGTTACTACACG 59.536 40.000 0.00 0.00 32.98 4.49
709 916 4.159244 TCTTTGAAAGGAAAGAACCCGA 57.841 40.909 4.94 0.00 38.69 5.14
803 1015 9.971922 ATCATCTTTTTGACTACTTTTCCTTTG 57.028 29.630 0.00 0.00 0.00 2.77
864 1081 0.313672 CACACACCCATTGTTTCCCG 59.686 55.000 0.00 0.00 35.67 5.14
949 1168 1.984026 CAATTGCTCACCCCCACCC 60.984 63.158 0.00 0.00 0.00 4.61
950 1169 2.477893 AATTGCTCACCCCCACCCA 61.478 57.895 0.00 0.00 0.00 4.51
955 1174 4.995058 TCACCCCCACCCACCCTC 62.995 72.222 0.00 0.00 0.00 4.30
990 1217 4.127744 CCCATGGCATCCCACGGT 62.128 66.667 6.09 0.00 43.01 4.83
1042 1269 1.459592 CACCTTGCGCTACTGTACAAC 59.540 52.381 9.73 0.00 0.00 3.32
1046 1284 1.504359 TGCGCTACTGTACAACCAAC 58.496 50.000 9.73 0.00 0.00 3.77
1047 1285 1.202545 TGCGCTACTGTACAACCAACA 60.203 47.619 9.73 0.00 0.00 3.33
1061 1299 1.008194 CAACACACGCAGCAAGCAT 60.008 52.632 0.00 0.00 46.13 3.79
1062 1300 1.000233 CAACACACGCAGCAAGCATC 61.000 55.000 0.00 0.00 46.13 3.91
1063 1301 1.168407 AACACACGCAGCAAGCATCT 61.168 50.000 0.00 0.00 46.13 2.90
1064 1302 1.154282 CACACGCAGCAAGCATCTG 60.154 57.895 0.00 0.00 46.13 2.90
1065 1303 1.301953 ACACGCAGCAAGCATCTGA 60.302 52.632 0.00 0.00 46.13 3.27
1066 1304 0.675837 ACACGCAGCAAGCATCTGAT 60.676 50.000 0.00 0.00 46.13 2.90
1067 1305 0.027716 CACGCAGCAAGCATCTGATC 59.972 55.000 0.00 0.00 46.13 2.92
1068 1306 0.392060 ACGCAGCAAGCATCTGATCA 60.392 50.000 0.00 0.00 46.13 2.92
1069 1307 0.945099 CGCAGCAAGCATCTGATCAT 59.055 50.000 0.00 0.00 46.13 2.45
1070 1308 2.140717 CGCAGCAAGCATCTGATCATA 58.859 47.619 0.00 0.00 46.13 2.15
1071 1309 2.546789 CGCAGCAAGCATCTGATCATAA 59.453 45.455 0.00 0.00 46.13 1.90
1072 1310 3.188667 CGCAGCAAGCATCTGATCATAAT 59.811 43.478 0.00 0.00 46.13 1.28
1073 1311 4.390909 CGCAGCAAGCATCTGATCATAATA 59.609 41.667 0.00 0.00 46.13 0.98
1074 1312 5.106830 CGCAGCAAGCATCTGATCATAATAA 60.107 40.000 0.00 0.00 46.13 1.40
1075 1313 6.403309 CGCAGCAAGCATCTGATCATAATAAT 60.403 38.462 0.00 0.00 46.13 1.28
1076 1314 6.967767 GCAGCAAGCATCTGATCATAATAATC 59.032 38.462 0.00 0.00 44.79 1.75
1077 1315 7.148222 GCAGCAAGCATCTGATCATAATAATCT 60.148 37.037 0.00 0.00 44.79 2.40
1078 1316 8.391859 CAGCAAGCATCTGATCATAATAATCTC 58.608 37.037 0.00 0.00 33.54 2.75
1102 1340 3.279116 CCGGCACCACACACACAG 61.279 66.667 0.00 0.00 0.00 3.66
1106 1344 1.356624 GCACCACACACACAGCTTC 59.643 57.895 0.00 0.00 0.00 3.86
1107 1345 2.024918 CACCACACACACAGCTTCC 58.975 57.895 0.00 0.00 0.00 3.46
1108 1346 0.464373 CACCACACACACAGCTTCCT 60.464 55.000 0.00 0.00 0.00 3.36
1109 1347 0.179045 ACCACACACACAGCTTCCTC 60.179 55.000 0.00 0.00 0.00 3.71
1110 1348 0.107456 CCACACACACAGCTTCCTCT 59.893 55.000 0.00 0.00 0.00 3.69
1111 1349 1.475751 CCACACACACAGCTTCCTCTT 60.476 52.381 0.00 0.00 0.00 2.85
1112 1350 2.224281 CCACACACACAGCTTCCTCTTA 60.224 50.000 0.00 0.00 0.00 2.10
1113 1351 3.557898 CCACACACACAGCTTCCTCTTAT 60.558 47.826 0.00 0.00 0.00 1.73
1127 1365 5.567138 TCCTCTTATTTTTGCAAGCTAGC 57.433 39.130 6.62 6.62 0.00 3.42
1133 1371 4.629251 ATTTTTGCAAGCTAGCTAGAGC 57.371 40.909 25.15 21.57 43.19 4.09
1226 1464 1.070786 GTCAAGGCCAAGTCCACGA 59.929 57.895 5.01 0.00 0.00 4.35
1468 1721 2.766229 GCCCAGGAGGAGGAGGAC 60.766 72.222 0.00 0.00 38.24 3.85
1737 2010 2.109126 GCGCTTGATCCACCTCCAC 61.109 63.158 0.00 0.00 0.00 4.02
1797 2071 2.356125 GCTCCATCACTCCTTAAGCCAA 60.356 50.000 0.00 0.00 0.00 4.52
1842 2116 2.291741 GCCCATGCATGTAAGTAGAAGC 59.708 50.000 24.58 9.39 37.47 3.86
1913 2187 1.416772 GGGGATGCCAAGGTCTACTAC 59.583 57.143 5.30 0.00 0.00 2.73
2230 2510 3.126514 CAGAATCAAGCTGATGACCACAC 59.873 47.826 0.00 0.00 37.15 3.82
2246 2526 1.399089 CACACGACAACGAAAAAGGGT 59.601 47.619 0.00 0.00 42.66 4.34
2254 2534 3.969795 CGAAAAAGGGTTCGCTAGC 57.030 52.632 4.06 4.06 43.38 3.42
2376 2665 3.237741 CATCCCCTCGGCCTCCTC 61.238 72.222 0.00 0.00 0.00 3.71
2377 2666 4.565850 ATCCCCTCGGCCTCCTCC 62.566 72.222 0.00 0.00 0.00 4.30
2380 2669 3.787001 CCCTCGGCCTCCTCCAAC 61.787 72.222 0.00 0.00 0.00 3.77
2381 2670 2.685380 CCTCGGCCTCCTCCAACT 60.685 66.667 0.00 0.00 0.00 3.16
2438 2727 2.515523 CCTCCATTGCCTCCTGCG 60.516 66.667 0.00 0.00 45.60 5.18
2459 2748 0.827368 GGAGAGACGCAGGGAGAATT 59.173 55.000 0.00 0.00 0.00 2.17
2555 2844 1.546476 GATACCTGGCGATCTCGGATT 59.454 52.381 1.34 0.00 40.23 3.01
2561 2850 3.393800 CTGGCGATCTCGGATTGTAATT 58.606 45.455 1.34 0.00 40.23 1.40
2565 2854 4.058817 GCGATCTCGGATTGTAATTCCTT 58.941 43.478 1.34 0.00 40.23 3.36
2649 2938 2.757077 GGAGGTGGAGGTGGTTGG 59.243 66.667 0.00 0.00 0.00 3.77
2692 2981 1.376424 CGGATTGTCCTGCAGTGCT 60.376 57.895 17.60 0.00 33.30 4.40
2700 2989 2.031516 CCTGCAGTGCTGACGAAGG 61.032 63.158 22.25 12.58 0.00 3.46
2785 3074 3.752339 CCGCTTGCCCCTGCTTTC 61.752 66.667 0.00 0.00 38.71 2.62
2789 3078 1.252904 GCTTGCCCCTGCTTTCATGA 61.253 55.000 0.00 0.00 38.71 3.07
2792 3081 2.054453 GCCCCTGCTTTCATGACCC 61.054 63.158 0.00 0.00 33.53 4.46
2896 3185 7.119387 CAGTTAAAACCCTGATATCTTTCCCT 58.881 38.462 3.98 0.00 0.00 4.20
2901 3190 1.517242 CTGATATCTTTCCCTGCGGC 58.483 55.000 3.98 0.00 0.00 6.53
2902 3191 0.249868 TGATATCTTTCCCTGCGGCG 60.250 55.000 0.51 0.51 0.00 6.46
2903 3192 0.951040 GATATCTTTCCCTGCGGCGG 60.951 60.000 9.78 0.65 0.00 6.13
2904 3193 2.397413 ATATCTTTCCCTGCGGCGGG 62.397 60.000 21.22 21.22 46.13 6.13
2947 3236 1.134877 CGAGCATCCTTTCTCTCAGCA 60.135 52.381 0.00 0.00 0.00 4.41
2971 3260 1.594331 GAGCTTGTTCTCCACGGTTT 58.406 50.000 0.00 0.00 0.00 3.27
2984 3273 2.034999 GGTTTGCCCCATCACCGA 59.965 61.111 0.00 0.00 0.00 4.69
2985 3274 2.340328 GGTTTGCCCCATCACCGAC 61.340 63.158 0.00 0.00 0.00 4.79
2986 3275 2.034999 TTTGCCCCATCACCGACC 59.965 61.111 0.00 0.00 0.00 4.79
2987 3276 3.910914 TTTGCCCCATCACCGACCG 62.911 63.158 0.00 0.00 0.00 4.79
2989 3278 4.832608 GCCCCATCACCGACCGTC 62.833 72.222 0.00 0.00 0.00 4.79
2990 3279 3.387091 CCCCATCACCGACCGTCA 61.387 66.667 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 84 1.740296 GCAAGCAGGCAATGGCAAG 60.740 57.895 10.05 2.01 43.71 4.01
218 253 3.260483 GAGCTGGTCGATGCTGCG 61.260 66.667 13.74 0.00 39.91 5.18
233 268 1.146263 GTAGGGTGATTGGGCGGAG 59.854 63.158 0.00 0.00 0.00 4.63
234 269 2.372074 GGTAGGGTGATTGGGCGGA 61.372 63.158 0.00 0.00 0.00 5.54
253 294 7.013274 AGCAGCTCTTCTTCTTACTATAGACAG 59.987 40.741 6.78 1.75 0.00 3.51
254 295 6.831353 AGCAGCTCTTCTTCTTACTATAGACA 59.169 38.462 6.78 0.00 0.00 3.41
255 296 7.272037 AGCAGCTCTTCTTCTTACTATAGAC 57.728 40.000 6.78 0.00 0.00 2.59
256 297 7.889873 AAGCAGCTCTTCTTCTTACTATAGA 57.110 36.000 6.78 0.00 0.00 1.98
259 300 8.923270 AGATTAAGCAGCTCTTCTTCTTACTAT 58.077 33.333 0.00 0.00 31.76 2.12
317 489 3.754850 CGTCGAAAGGGGAGGTAAAAATT 59.245 43.478 0.00 0.00 0.00 1.82
318 490 3.244665 ACGTCGAAAGGGGAGGTAAAAAT 60.245 43.478 0.00 0.00 31.37 1.82
322 494 1.001181 CAACGTCGAAAGGGGAGGTAA 59.999 52.381 0.00 0.00 32.70 2.85
323 495 0.604578 CAACGTCGAAAGGGGAGGTA 59.395 55.000 0.00 0.00 32.70 3.08
324 496 1.117142 TCAACGTCGAAAGGGGAGGT 61.117 55.000 0.00 0.00 34.28 3.85
326 498 0.317479 ACTCAACGTCGAAAGGGGAG 59.683 55.000 0.00 0.00 0.00 4.30
327 499 0.032952 CACTCAACGTCGAAAGGGGA 59.967 55.000 0.00 0.00 0.00 4.81
333 505 1.142097 TGCCACACTCAACGTCGAA 59.858 52.632 0.00 0.00 0.00 3.71
334 506 1.590525 GTGCCACACTCAACGTCGA 60.591 57.895 0.00 0.00 0.00 4.20
377 549 2.582728 TATACCGTACTGGCCAAACG 57.417 50.000 25.93 25.93 43.94 3.60
378 550 3.396560 GGATATACCGTACTGGCCAAAC 58.603 50.000 7.01 7.42 43.94 2.93
382 554 1.636148 TGGGATATACCGTACTGGCC 58.364 55.000 0.00 0.00 43.94 5.36
383 555 2.565834 ACATGGGATATACCGTACTGGC 59.434 50.000 0.00 0.00 43.94 4.85
384 556 3.576982 ACACATGGGATATACCGTACTGG 59.423 47.826 0.00 2.71 46.41 4.00
385 557 4.866508 ACACATGGGATATACCGTACTG 57.133 45.455 0.00 0.04 40.11 2.74
386 558 5.145564 AGAACACATGGGATATACCGTACT 58.854 41.667 0.00 0.00 40.11 2.73
390 578 6.693315 AAAAAGAACACATGGGATATACCG 57.307 37.500 0.00 0.00 40.11 4.02
462 655 1.268352 GCGCTGTTGTAAATTGTGGGA 59.732 47.619 0.00 0.00 0.00 4.37
463 656 1.668628 GGCGCTGTTGTAAATTGTGGG 60.669 52.381 7.64 0.00 0.00 4.61
464 657 1.000827 TGGCGCTGTTGTAAATTGTGG 60.001 47.619 7.64 0.00 0.00 4.17
481 675 2.869636 GCCATAGCTAGTGAGTGATGGC 60.870 54.545 15.18 15.18 46.63 4.40
504 698 0.031178 CAGCTTGTTTCCGCTTGCTT 59.969 50.000 0.00 0.00 33.45 3.91
541 735 3.558931 TGTGGTCATTGTGAGTCAGTT 57.441 42.857 0.00 0.00 0.00 3.16
542 736 3.558931 TTGTGGTCATTGTGAGTCAGT 57.441 42.857 0.00 0.00 0.00 3.41
543 737 5.121298 CAGTATTGTGGTCATTGTGAGTCAG 59.879 44.000 0.00 0.00 0.00 3.51
544 738 4.996758 CAGTATTGTGGTCATTGTGAGTCA 59.003 41.667 0.00 0.00 0.00 3.41
545 739 4.142816 GCAGTATTGTGGTCATTGTGAGTC 60.143 45.833 0.00 0.00 0.00 3.36
546 740 3.753272 GCAGTATTGTGGTCATTGTGAGT 59.247 43.478 0.00 0.00 0.00 3.41
559 757 5.510690 GGCCTTTTAACTTTGGCAGTATTGT 60.511 40.000 0.00 0.00 46.53 2.71
566 764 2.111384 TGTGGCCTTTTAACTTTGGCA 58.889 42.857 3.32 0.00 46.53 4.92
668 875 8.576442 TCAAAGAAAAAGCTTTAGGTTATCCTG 58.424 33.333 13.10 2.97 44.81 3.86
949 1168 6.039941 GGTATATATAGCAGTAGCAGAGGGTG 59.960 46.154 15.49 0.00 45.49 4.61
950 1169 6.130569 GGTATATATAGCAGTAGCAGAGGGT 58.869 44.000 15.49 0.00 45.49 4.34
952 1171 6.129874 TGGGTATATATAGCAGTAGCAGAGG 58.870 44.000 20.52 0.00 45.49 3.69
953 1172 7.255766 CCATGGGTATATATAGCAGTAGCAGAG 60.256 44.444 20.52 8.12 45.49 3.35
954 1173 6.551227 CCATGGGTATATATAGCAGTAGCAGA 59.449 42.308 20.52 0.00 45.49 4.26
955 1174 6.739843 GCCATGGGTATATATAGCAGTAGCAG 60.740 46.154 20.52 6.32 45.49 4.24
956 1175 5.070446 GCCATGGGTATATATAGCAGTAGCA 59.930 44.000 20.52 10.96 45.49 3.49
957 1176 5.070446 TGCCATGGGTATATATAGCAGTAGC 59.930 44.000 20.52 17.06 42.56 3.58
958 1177 6.731292 TGCCATGGGTATATATAGCAGTAG 57.269 41.667 20.52 9.56 32.63 2.57
990 1217 2.942804 TGCTTGGACATGGAGTTTTGA 58.057 42.857 0.00 0.00 0.00 2.69
1042 1269 2.353839 GCTTGCTGCGTGTGTTGG 60.354 61.111 0.00 0.00 0.00 3.77
1046 1284 1.154282 CAGATGCTTGCTGCGTGTG 60.154 57.895 7.09 7.09 46.63 3.82
1047 1285 0.675837 ATCAGATGCTTGCTGCGTGT 60.676 50.000 1.93 0.00 46.63 4.49
1061 1299 6.900186 GGAGGGGAGAGATTATTATGATCAGA 59.100 42.308 0.09 0.00 0.00 3.27
1062 1300 6.183360 CGGAGGGGAGAGATTATTATGATCAG 60.183 46.154 0.09 0.00 0.00 2.90
1063 1301 5.658634 CGGAGGGGAGAGATTATTATGATCA 59.341 44.000 0.00 0.00 0.00 2.92
1064 1302 6.155475 CGGAGGGGAGAGATTATTATGATC 57.845 45.833 0.00 0.00 0.00 2.92
1096 1334 4.919754 GCAAAAATAAGAGGAAGCTGTGTG 59.080 41.667 0.00 0.00 0.00 3.82
1106 1344 5.573337 AGCTAGCTTGCAAAAATAAGAGG 57.427 39.130 22.05 0.00 34.99 3.69
1107 1345 7.545362 TCTAGCTAGCTTGCAAAAATAAGAG 57.455 36.000 24.88 9.25 34.99 2.85
1108 1346 6.037610 GCTCTAGCTAGCTTGCAAAAATAAGA 59.962 38.462 24.88 13.88 39.50 2.10
1109 1347 6.197981 GCTCTAGCTAGCTTGCAAAAATAAG 58.802 40.000 24.88 12.09 39.50 1.73
1110 1348 5.220662 CGCTCTAGCTAGCTTGCAAAAATAA 60.221 40.000 24.88 0.00 40.49 1.40
1111 1349 4.271049 CGCTCTAGCTAGCTTGCAAAAATA 59.729 41.667 24.88 0.00 40.49 1.40
1112 1350 3.064545 CGCTCTAGCTAGCTTGCAAAAAT 59.935 43.478 24.88 3.56 40.49 1.82
1113 1351 2.416547 CGCTCTAGCTAGCTTGCAAAAA 59.583 45.455 24.88 1.10 40.49 1.94
1140 1378 9.920946 AAGCCTTGGTCTTCATCTTAATAATTA 57.079 29.630 0.00 0.00 0.00 1.40
1141 1379 8.829373 AAGCCTTGGTCTTCATCTTAATAATT 57.171 30.769 0.00 0.00 0.00 1.40
1144 1382 6.069673 TGGAAGCCTTGGTCTTCATCTTAATA 60.070 38.462 18.31 0.00 41.16 0.98
1147 1385 3.587061 TGGAAGCCTTGGTCTTCATCTTA 59.413 43.478 18.31 4.49 41.16 2.10
1243 1481 3.114616 CGCGTCTTGAGGGTGCTG 61.115 66.667 0.00 0.00 0.00 4.41
1454 1692 2.422231 CGCTGTCCTCCTCCTCCTG 61.422 68.421 0.00 0.00 0.00 3.86
1468 1721 0.165295 TCAAGTACTCGTCGTCGCTG 59.835 55.000 0.00 0.00 36.96 5.18
1543 1796 1.292223 CACGTCAATCACCGACCCT 59.708 57.895 0.00 0.00 0.00 4.34
1630 1883 2.490217 CGGATGAAGACGTCGGCT 59.510 61.111 10.46 0.00 33.26 5.52
1797 2071 8.403236 GGCGTCCAATTAAGTTAAACATAATCT 58.597 33.333 0.00 0.00 0.00 2.40
1820 2094 2.238942 TCTACTTACATGCATGGGCG 57.761 50.000 29.41 18.32 45.35 6.13
1842 2116 2.559668 TCTTGCCTGGCTTCATCTTTTG 59.440 45.455 21.03 0.00 0.00 2.44
1880 2154 2.651455 GCATCCCCACTAAAACCCTAC 58.349 52.381 0.00 0.00 0.00 3.18
1913 2187 7.377928 CGTAATGATTAAAGTACCACGTAGGAG 59.622 40.741 10.46 0.00 41.22 3.69
2046 2320 3.120477 CGTGTTACATTTCGGCTTGCTAA 60.120 43.478 0.00 0.00 0.00 3.09
2146 2420 2.038164 AGTTCAACTCTCGGGGGTTAAC 59.962 50.000 0.00 6.26 0.00 2.01
2147 2421 2.301009 GAGTTCAACTCTCGGGGGTTAA 59.699 50.000 10.55 0.00 41.88 2.01
2151 2425 0.685097 TTGAGTTCAACTCTCGGGGG 59.315 55.000 18.49 0.00 45.27 5.40
2177 2451 7.759886 TCTTATGACTGCTTGAACTGTATGTAC 59.240 37.037 0.00 0.00 0.00 2.90
2230 2510 2.013286 CGAACCCTTTTTCGTTGTCG 57.987 50.000 0.00 0.00 42.78 4.35
2246 2526 1.752498 TCCGTCCATAAAGCTAGCGAA 59.248 47.619 9.55 0.00 0.00 4.70
2254 2534 2.487934 CAGAGGCATCCGTCCATAAAG 58.512 52.381 0.00 0.00 0.00 1.85
2376 2665 1.202651 AGGACGTCAAGTTGGAGTTGG 60.203 52.381 18.91 0.00 0.00 3.77
2377 2666 2.240493 AGGACGTCAAGTTGGAGTTG 57.760 50.000 18.91 0.00 0.00 3.16
2378 2667 2.561569 CAAGGACGTCAAGTTGGAGTT 58.438 47.619 18.91 0.00 0.00 3.01
2379 2668 1.202651 CCAAGGACGTCAAGTTGGAGT 60.203 52.381 27.31 3.46 41.82 3.85
2380 2669 1.512926 CCAAGGACGTCAAGTTGGAG 58.487 55.000 27.31 10.39 41.82 3.86
2381 2670 0.534203 GCCAAGGACGTCAAGTTGGA 60.534 55.000 31.98 0.00 41.82 3.53
2532 2821 1.239347 CGAGATCGCCAGGTATCTCA 58.761 55.000 23.45 0.00 45.56 3.27
2555 2844 3.605634 CGATGGACACCAAGGAATTACA 58.394 45.455 0.00 0.00 36.95 2.41
2561 2850 1.773856 TTGGCGATGGACACCAAGGA 61.774 55.000 0.00 0.00 38.52 3.36
2565 2854 2.358125 CGTTGGCGATGGACACCA 60.358 61.111 0.00 0.00 41.33 4.17
2584 2873 1.883084 CGACATAGGAGTTGCGGCC 60.883 63.158 0.00 0.00 0.00 6.13
2646 2935 2.180769 CGACGTCCTCATCGCCAA 59.819 61.111 10.58 0.00 0.00 4.52
2649 2938 2.024871 CCTCGACGTCCTCATCGC 59.975 66.667 10.58 0.00 38.24 4.58
2692 2981 3.927555 GGAACACATCCCTTCGTCA 57.072 52.632 0.00 0.00 43.00 4.35
2785 3074 1.446099 CACGGTCAGTCGGGTCATG 60.446 63.158 0.00 0.00 0.00 3.07
2792 3081 0.852777 CAAGACAACACGGTCAGTCG 59.147 55.000 0.00 0.00 40.29 4.18
2901 3190 1.739562 GTTGCTGAGTCTGCTCCCG 60.740 63.158 20.92 0.00 40.95 5.14
2902 3191 1.739562 CGTTGCTGAGTCTGCTCCC 60.740 63.158 20.92 9.11 40.95 4.30
2903 3192 2.386660 GCGTTGCTGAGTCTGCTCC 61.387 63.158 20.92 11.24 40.95 4.70
2904 3193 2.386660 GGCGTTGCTGAGTCTGCTC 61.387 63.158 20.92 13.42 41.97 4.26
2910 3199 2.591715 GTGTGGGCGTTGCTGAGT 60.592 61.111 0.00 0.00 0.00 3.41
2917 3206 2.742372 GATGCTCGTGTGGGCGTT 60.742 61.111 0.00 0.00 0.00 4.84
2956 3245 1.104577 GGGCAAACCGTGGAGAACAA 61.105 55.000 0.00 0.00 36.48 2.83


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

AutoCloner maintained by Alex Coulton.