Multiple sequence alignment - TraesCS3D01G489800

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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 TraesCS3D01G489800 chr3D 100.000 3001 0 0 1 3001 584128808 584131808 0.000000e+00 5542.0
1 TraesCS3D01G489800 chr3D 86.173 1338 129 31 853 2174 584048576 584049873 0.000000e+00 1395.0
2 TraesCS3D01G489800 chr3D 84.927 1234 123 23 793 1996 584457149 584455949 0.000000e+00 1190.0
3 TraesCS3D01G489800 chr3D 93.869 734 44 1 2267 2999 79110834 79111567 0.000000e+00 1105.0
4 TraesCS3D01G489800 chr3D 94.118 102 4 2 99 200 584047116 584047215 1.440000e-33 154.0
5 TraesCS3D01G489800 chr3D 94.845 97 4 1 409 504 584129165 584129261 1.860000e-32 150.0
6 TraesCS3D01G489800 chr3D 94.845 97 4 1 358 454 584129216 584129311 1.860000e-32 150.0
7 TraesCS3D01G489800 chr3B 93.464 1331 53 6 595 1902 781355756 781357075 0.000000e+00 1945.0
8 TraesCS3D01G489800 chr3B 87.102 1225 118 26 996 2214 781210465 781211655 0.000000e+00 1351.0
9 TraesCS3D01G489800 chr3B 84.556 1295 139 30 917 2171 781344441 781345714 0.000000e+00 1227.0
10 TraesCS3D01G489800 chr3B 86.972 1090 97 25 921 1996 781494952 781493894 0.000000e+00 1184.0
11 TraesCS3D01G489800 chr3B 90.652 460 29 5 1 455 781355182 781355632 1.540000e-167 599.0
12 TraesCS3D01G489800 chr3B 93.931 379 15 5 1898 2268 781362341 781362719 1.560000e-157 566.0
13 TraesCS3D01G489800 chr3B 88.021 192 20 3 409 598 781355535 781355725 1.080000e-54 224.0
14 TraesCS3D01G489800 chr3B 87.634 186 19 4 17 200 781341154 781341337 2.340000e-51 213.0
15 TraesCS3D01G489800 chr3B 90.909 121 7 4 82 200 781208468 781208586 3.100000e-35 159.0
16 TraesCS3D01G489800 chr3B 93.750 48 3 0 147 194 781533353 781533306 4.150000e-09 73.1
17 TraesCS3D01G489800 chr7D 85.211 1589 132 47 598 2119 588419337 588420889 0.000000e+00 1537.0
18 TraesCS3D01G489800 chr7D 94.521 730 38 2 2271 2999 29932139 29931411 0.000000e+00 1125.0
19 TraesCS3D01G489800 chr7D 85.535 477 44 11 1 460 588418749 588419217 2.710000e-130 475.0
20 TraesCS3D01G489800 chr7D 91.810 232 17 2 2038 2268 588420914 588421144 3.730000e-84 322.0
21 TraesCS3D01G489800 chr7D 95.745 47 1 1 459 504 588419115 588419161 1.150000e-09 75.0
22 TraesCS3D01G489800 chr3A 85.618 1481 120 34 598 1994 21360814 21359343 0.000000e+00 1469.0
23 TraesCS3D01G489800 chr3A 92.169 166 13 0 2106 2271 21359281 21359116 5.000000e-58 235.0
24 TraesCS3D01G489800 chr3A 95.745 47 1 1 459 504 21361038 21360992 1.150000e-09 75.0
25 TraesCS3D01G489800 chrUn 85.117 1243 125 32 996 2211 45483307 45482098 0.000000e+00 1216.0
26 TraesCS3D01G489800 chrUn 89.583 48 5 0 146 193 419501568 419501615 8.980000e-06 62.1
27 TraesCS3D01G489800 chr1D 95.205 730 33 2 2271 2999 414306701 414307429 0.000000e+00 1153.0
28 TraesCS3D01G489800 chr1D 93.405 743 47 2 2258 2999 113040513 113041254 0.000000e+00 1099.0
29 TraesCS3D01G489800 chr2D 94.384 730 37 3 2271 2999 53782835 53783561 0.000000e+00 1118.0
30 TraesCS3D01G489800 chr5D 94.110 730 43 0 2270 2999 388765592 388764863 0.000000e+00 1110.0
31 TraesCS3D01G489800 chr5D 93.997 733 43 1 2267 2999 35818573 35817842 0.000000e+00 1109.0
32 TraesCS3D01G489800 chr5D 94.110 730 41 2 2271 2999 434974994 434975722 0.000000e+00 1109.0
33 TraesCS3D01G489800 chr6D 94.102 729 43 0 2271 2999 131058201 131058929 0.000000e+00 1109.0
34 TraesCS3D01G489800 chr1B 90.411 73 6 1 409 480 16801209 16801137 8.860000e-16 95.3
35 TraesCS3D01G489800 chr7B 85.366 82 9 3 529 608 228919470 228919550 6.900000e-12 82.4


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 TraesCS3D01G489800 chr3D 584128808 584131808 3000 False 1947.333333 5542 96.563333 1 3001 3 chr3D.!!$F3 3000
1 TraesCS3D01G489800 chr3D 584455949 584457149 1200 True 1190.000000 1190 84.927000 793 1996 1 chr3D.!!$R1 1203
2 TraesCS3D01G489800 chr3D 79110834 79111567 733 False 1105.000000 1105 93.869000 2267 2999 1 chr3D.!!$F1 732
3 TraesCS3D01G489800 chr3D 584047116 584049873 2757 False 774.500000 1395 90.145500 99 2174 2 chr3D.!!$F2 2075
4 TraesCS3D01G489800 chr3B 781493894 781494952 1058 True 1184.000000 1184 86.972000 921 1996 1 chr3B.!!$R1 1075
5 TraesCS3D01G489800 chr3B 781355182 781357075 1893 False 922.666667 1945 90.712333 1 1902 3 chr3B.!!$F4 1901
6 TraesCS3D01G489800 chr3B 781208468 781211655 3187 False 755.000000 1351 89.005500 82 2214 2 chr3B.!!$F2 2132
7 TraesCS3D01G489800 chr3B 781341154 781345714 4560 False 720.000000 1227 86.095000 17 2171 2 chr3B.!!$F3 2154
8 TraesCS3D01G489800 chr7D 29931411 29932139 728 True 1125.000000 1125 94.521000 2271 2999 1 chr7D.!!$R1 728
9 TraesCS3D01G489800 chr7D 588418749 588421144 2395 False 602.250000 1537 89.575250 1 2268 4 chr7D.!!$F1 2267
10 TraesCS3D01G489800 chr3A 21359116 21361038 1922 True 593.000000 1469 91.177333 459 2271 3 chr3A.!!$R1 1812
11 TraesCS3D01G489800 chrUn 45482098 45483307 1209 True 1216.000000 1216 85.117000 996 2211 1 chrUn.!!$R1 1215
12 TraesCS3D01G489800 chr1D 414306701 414307429 728 False 1153.000000 1153 95.205000 2271 2999 1 chr1D.!!$F2 728
13 TraesCS3D01G489800 chr1D 113040513 113041254 741 False 1099.000000 1099 93.405000 2258 2999 1 chr1D.!!$F1 741
14 TraesCS3D01G489800 chr2D 53782835 53783561 726 False 1118.000000 1118 94.384000 2271 2999 1 chr2D.!!$F1 728
15 TraesCS3D01G489800 chr5D 388764863 388765592 729 True 1110.000000 1110 94.110000 2270 2999 1 chr5D.!!$R2 729
16 TraesCS3D01G489800 chr5D 35817842 35818573 731 True 1109.000000 1109 93.997000 2267 2999 1 chr5D.!!$R1 732
17 TraesCS3D01G489800 chr5D 434974994 434975722 728 False 1109.000000 1109 94.110000 2271 2999 1 chr5D.!!$F1 728
18 TraesCS3D01G489800 chr6D 131058201 131058929 728 False 1109.000000 1109 94.102000 2271 2999 1 chr6D.!!$F1 728

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
652 3074 0.031449 GGCGATCGAGAGGAAGAAGG 59.969 60.0 21.57 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 6543 0.108615 CGTGCCTAGAACCAGGACAG 60.109 60.0 0.0 0.0 38.0 3.51 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
21 25 1.670406 AAGCAAGCTGGCGAGAGTG 60.670 57.895 7.63 0.00 39.27 3.51
67 72 1.802365 GTTTCGTTACTCAATGCCCGT 59.198 47.619 0.00 0.00 0.00 5.28
68 73 2.172851 TTCGTTACTCAATGCCCGTT 57.827 45.000 0.00 0.00 0.00 4.44
99 105 3.196469 CACCAGCTAGTTTCCAGATCTCA 59.804 47.826 0.00 0.00 0.00 3.27
256 2640 7.993821 TTCAAATAGCTAAAGATCAGTCGAG 57.006 36.000 0.00 0.00 0.00 4.04
279 2663 6.345298 AGTGAATTTTGTTTTTGGATCGGTT 58.655 32.000 0.00 0.00 0.00 4.44
282 2666 6.989169 TGAATTTTGTTTTTGGATCGGTTGAT 59.011 30.769 0.00 0.00 37.60 2.57
283 2667 7.497249 TGAATTTTGTTTTTGGATCGGTTGATT 59.503 29.630 0.00 0.00 34.09 2.57
284 2668 7.800155 ATTTTGTTTTTGGATCGGTTGATTT 57.200 28.000 0.00 0.00 34.09 2.17
285 2669 7.617041 TTTTGTTTTTGGATCGGTTGATTTT 57.383 28.000 0.00 0.00 34.09 1.82
286 2670 7.617041 TTTGTTTTTGGATCGGTTGATTTTT 57.383 28.000 0.00 0.00 34.09 1.94
316 2700 4.437682 TTTGAGAAGGAAGAAGGAAGCA 57.562 40.909 0.00 0.00 0.00 3.91
345 2732 1.002011 GGAAGGAGACACCAAGGCC 60.002 63.158 0.00 0.00 42.04 5.19
369 2756 2.034221 GCCGGGGAAGAAGCAACT 59.966 61.111 2.18 0.00 0.00 3.16
389 2776 4.080687 ACTCCACTATCTATCGTTAGGGC 58.919 47.826 0.80 0.00 0.00 5.19
390 2777 4.079970 CTCCACTATCTATCGTTAGGGCA 58.920 47.826 0.80 0.00 0.00 5.36
392 2779 3.367498 CCACTATCTATCGTTAGGGCAGC 60.367 52.174 0.80 0.00 0.00 5.25
413 2800 1.104577 GGTGCAGGTTCACCGGAAAA 61.105 55.000 9.46 0.00 45.95 2.29
414 2801 0.310854 GTGCAGGTTCACCGGAAAAG 59.689 55.000 9.46 0.00 42.08 2.27
415 2802 1.285950 GCAGGTTCACCGGAAAAGC 59.714 57.895 9.46 11.63 42.08 3.51
416 2803 1.452145 GCAGGTTCACCGGAAAAGCA 61.452 55.000 9.46 0.00 42.08 3.91
417 2804 1.028905 CAGGTTCACCGGAAAAGCAA 58.971 50.000 9.46 0.00 42.08 3.91
418 2805 1.029681 AGGTTCACCGGAAAAGCAAC 58.970 50.000 9.46 0.83 42.08 4.17
419 2806 0.031585 GGTTCACCGGAAAAGCAACC 59.968 55.000 9.46 6.83 34.13 3.77
420 2807 0.031585 GTTCACCGGAAAAGCAACCC 59.968 55.000 9.46 0.00 34.13 4.11
421 2808 1.110518 TTCACCGGAAAAGCAACCCC 61.111 55.000 9.46 0.00 0.00 4.95
422 2809 1.830408 CACCGGAAAAGCAACCCCA 60.830 57.895 9.46 0.00 0.00 4.96
423 2810 1.830847 ACCGGAAAAGCAACCCCAC 60.831 57.895 9.46 0.00 0.00 4.61
424 2811 1.530655 CCGGAAAAGCAACCCCACT 60.531 57.895 0.00 0.00 0.00 4.00
425 2812 0.250989 CCGGAAAAGCAACCCCACTA 60.251 55.000 0.00 0.00 0.00 2.74
426 2813 1.615919 CCGGAAAAGCAACCCCACTAT 60.616 52.381 0.00 0.00 0.00 2.12
427 2814 1.743394 CGGAAAAGCAACCCCACTATC 59.257 52.381 0.00 0.00 0.00 2.08
428 2815 2.618045 CGGAAAAGCAACCCCACTATCT 60.618 50.000 0.00 0.00 0.00 1.98
429 2816 3.370103 CGGAAAAGCAACCCCACTATCTA 60.370 47.826 0.00 0.00 0.00 1.98
430 2817 4.686122 CGGAAAAGCAACCCCACTATCTAT 60.686 45.833 0.00 0.00 0.00 1.98
431 2818 4.822350 GGAAAAGCAACCCCACTATCTATC 59.178 45.833 0.00 0.00 0.00 2.08
432 2819 3.753294 AAGCAACCCCACTATCTATCG 57.247 47.619 0.00 0.00 0.00 2.92
433 2820 2.679082 AGCAACCCCACTATCTATCGT 58.321 47.619 0.00 0.00 0.00 3.73
434 2821 3.039011 AGCAACCCCACTATCTATCGTT 58.961 45.455 0.00 0.00 0.00 3.85
435 2822 4.220724 AGCAACCCCACTATCTATCGTTA 58.779 43.478 0.00 0.00 0.00 3.18
436 2823 4.281182 AGCAACCCCACTATCTATCGTTAG 59.719 45.833 0.00 0.00 0.00 2.34
437 2824 4.560919 GCAACCCCACTATCTATCGTTAGG 60.561 50.000 0.80 0.00 0.00 2.69
438 2825 3.775910 ACCCCACTATCTATCGTTAGGG 58.224 50.000 0.80 0.00 38.04 3.53
439 2826 2.496470 CCCCACTATCTATCGTTAGGGC 59.504 54.545 0.80 0.00 33.68 5.19
440 2827 3.162666 CCCACTATCTATCGTTAGGGCA 58.837 50.000 0.80 0.00 0.00 5.36
441 2828 3.193691 CCCACTATCTATCGTTAGGGCAG 59.806 52.174 0.80 0.00 0.00 4.85
442 2829 3.367498 CCACTATCTATCGTTAGGGCAGC 60.367 52.174 0.80 0.00 0.00 5.25
443 2830 2.488545 ACTATCTATCGTTAGGGCAGCG 59.511 50.000 0.80 0.00 0.00 5.18
444 2831 0.603569 ATCTATCGTTAGGGCAGCGG 59.396 55.000 0.80 0.00 0.00 5.52
445 2832 1.006102 CTATCGTTAGGGCAGCGGG 60.006 63.158 0.00 0.00 0.00 6.13
446 2833 1.745320 CTATCGTTAGGGCAGCGGGT 61.745 60.000 0.00 0.00 0.00 5.28
447 2834 2.023414 TATCGTTAGGGCAGCGGGTG 62.023 60.000 2.14 2.14 0.00 4.61
456 2843 3.357079 CAGCGGGTGCAGGTTCAC 61.357 66.667 0.00 0.00 46.23 3.18
461 2848 2.112297 GGTGCAGGTTCACCGGAA 59.888 61.111 9.46 0.00 45.95 4.30
462 2849 1.527380 GGTGCAGGTTCACCGGAAA 60.527 57.895 9.46 0.00 45.95 3.13
504 2891 2.123468 GGTGGTGGGTGCAGGTTT 60.123 61.111 0.00 0.00 0.00 3.27
516 2903 1.890174 CAGGTTTGCCGGGGATTTC 59.110 57.895 2.18 0.00 40.50 2.17
523 2910 2.978946 GCCGGGGATTTCTGGGTGA 61.979 63.158 2.18 0.00 33.82 4.02
546 2933 1.632018 CCGGGTTTAGAGGGATGGCA 61.632 60.000 0.00 0.00 0.00 4.92
551 2939 1.141858 GTTTAGAGGGATGGCAGGGAG 59.858 57.143 0.00 0.00 0.00 4.30
627 3049 2.033602 GCGGTTAGGGCAGTGGTT 59.966 61.111 0.00 0.00 0.00 3.67
637 3059 2.350895 CAGTGGTTCATGGGGCGA 59.649 61.111 0.00 0.00 0.00 5.54
652 3074 0.031449 GGCGATCGAGAGGAAGAAGG 59.969 60.000 21.57 0.00 0.00 3.46
663 3085 2.900546 GAGGAAGAAGGTGAACAGGAGA 59.099 50.000 0.00 0.00 0.00 3.71
763 3191 2.802816 GGCGATTGTCATCTAGCGAAAT 59.197 45.455 0.00 0.00 30.88 2.17
840 3296 1.535896 TCTCTGACTACACGAGTGCAC 59.464 52.381 9.40 9.40 39.06 4.57
881 3341 6.808704 GTGCTTGACAATATGAGATCGCTATA 59.191 38.462 0.00 0.00 0.00 1.31
1038 4937 1.065102 CATGCTTTGCCTTCTCATCCG 59.935 52.381 0.00 0.00 0.00 4.18
1077 4985 1.821136 ACCACGGTGCTAACTACCTAC 59.179 52.381 1.68 0.00 36.03 3.18
1305 5235 5.885230 TTCTCTCGTTCGGACAAGTATAA 57.115 39.130 0.00 0.00 0.00 0.98
1316 5255 6.061441 TCGGACAAGTATAAATCATGCCAAT 58.939 36.000 0.00 0.00 0.00 3.16
1589 5575 0.244994 GCGCCACCGAGATCATCTAT 59.755 55.000 0.00 0.00 36.29 1.98
1717 5703 2.696707 ACTACCAGAAGAACAACGGTGA 59.303 45.455 7.88 0.00 0.00 4.02
1821 5807 4.697756 CGGTGCCCACGGATGTGT 62.698 66.667 0.20 0.00 44.92 3.72
1848 5834 4.193334 CGCTCCAGATCGACGGCA 62.193 66.667 0.00 0.00 0.00 5.69
1871 5857 0.842030 TGGTGGAGGCCATCAAGTCT 60.842 55.000 5.01 0.00 42.23 3.24
1885 5871 2.304761 TCAAGTCTAAGTTCCCGCCAAT 59.695 45.455 0.00 0.00 0.00 3.16
1953 5953 4.986034 TGCGTACGTGCTGCTAATAATAAT 59.014 37.500 17.90 0.00 35.36 1.28
1990 5990 6.544038 AAGTGCAGTTTTAATTCATTTGCC 57.456 33.333 0.00 0.00 0.00 4.52
1996 5996 6.369615 GCAGTTTTAATTCATTTGCCTGACAT 59.630 34.615 0.00 0.00 0.00 3.06
1997 5997 7.412237 GCAGTTTTAATTCATTTGCCTGACATC 60.412 37.037 0.00 0.00 0.00 3.06
1998 5998 7.063780 CAGTTTTAATTCATTTGCCTGACATCC 59.936 37.037 0.00 0.00 0.00 3.51
2001 6001 7.953005 TTAATTCATTTGCCTGACATCCTAA 57.047 32.000 0.00 0.00 0.00 2.69
2002 6002 6.855763 AATTCATTTGCCTGACATCCTAAA 57.144 33.333 0.00 0.00 0.00 1.85
2003 6003 6.855763 ATTCATTTGCCTGACATCCTAAAA 57.144 33.333 0.00 0.00 0.00 1.52
2004 6004 6.662865 TTCATTTGCCTGACATCCTAAAAA 57.337 33.333 0.00 0.00 0.00 1.94
2034 6036 5.902613 TTGCCTGAGAATATCTTTTGTGG 57.097 39.130 0.00 0.00 0.00 4.17
2053 6156 1.472480 GGCGGTGCATGTTTAGTGAAT 59.528 47.619 0.00 0.00 0.00 2.57
2067 6170 1.375396 TGAATGGCCTCGTCGGTTG 60.375 57.895 3.32 0.00 34.25 3.77
2144 6255 6.826231 ACGTGTCCATTATTGGTGAATGAATA 59.174 34.615 3.65 0.00 44.06 1.75
2148 6259 8.998377 TGTCCATTATTGGTGAATGAATATACG 58.002 33.333 3.65 0.00 44.06 3.06
2164 6275 6.912051 TGAATATACGTGATTGCTTGAATTGC 59.088 34.615 0.00 0.00 0.00 3.56
2218 6332 3.957497 TCTATCTCCCTCTCTTTGCAGAC 59.043 47.826 0.00 0.00 0.00 3.51
2220 6334 0.108424 CTCCCTCTCTTTGCAGACCG 60.108 60.000 0.00 0.00 0.00 4.79
2231 6345 1.271856 TGCAGACCGATACCCAAGAA 58.728 50.000 0.00 0.00 0.00 2.52
2368 6484 1.153784 GCATTCGACCCGGTTCGTA 60.154 57.895 21.40 12.60 40.07 3.43
2414 6531 2.034999 GGCATTGGTCCCGGTTCA 59.965 61.111 0.00 0.00 0.00 3.18
2426 6543 1.271379 CCCGGTTCATATGGACCCATC 60.271 57.143 24.98 3.07 37.82 3.51
2501 6618 2.522367 ATTGGTCCCGGTTCGTGGT 61.522 57.895 0.00 0.00 0.00 4.16
2524 6641 0.840722 AACCGGGACAGAAGGTGGAT 60.841 55.000 6.32 0.00 38.44 3.41
2566 6683 1.404986 CGAACCGGGACAAATGAGCTA 60.405 52.381 6.32 0.00 0.00 3.32
2573 6690 4.557205 CGGGACAAATGAGCTACCTATAC 58.443 47.826 0.00 0.00 0.00 1.47
2645 6762 2.983879 CGAGGGGAGGGCATTTGGT 61.984 63.158 0.00 0.00 0.00 3.67
2720 6837 6.574465 GCCACACTAGTTAATCTTTCTCCTCA 60.574 42.308 0.00 0.00 0.00 3.86
2999 7120 2.891580 GCCCTCGTCCTGTCTATGATTA 59.108 50.000 0.00 0.00 0.00 1.75
3000 7121 3.057174 GCCCTCGTCCTGTCTATGATTAG 60.057 52.174 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 57 4.251268 AGTAGAAACGGGCATTGAGTAAC 58.749 43.478 0.00 0.00 0.00 2.50
67 72 5.995897 GGAAACTAGCTGGTGAAAGTAGAAA 59.004 40.000 2.40 0.00 0.00 2.52
68 73 5.071250 TGGAAACTAGCTGGTGAAAGTAGAA 59.929 40.000 2.40 0.00 0.00 2.10
99 105 1.075536 AGGAGGAAAAGAATTGGGCGT 59.924 47.619 0.00 0.00 0.00 5.68
256 2640 6.256757 TCAACCGATCCAAAAACAAAATTCAC 59.743 34.615 0.00 0.00 0.00 3.18
293 2677 5.067805 GTGCTTCCTTCTTCCTTCTCAAAAA 59.932 40.000 0.00 0.00 0.00 1.94
316 2700 1.215679 TCTCCTTCCTCTCCCTCGGT 61.216 60.000 0.00 0.00 0.00 4.69
369 2756 4.079970 CTGCCCTAACGATAGATAGTGGA 58.920 47.826 0.56 0.00 39.58 4.02
389 2776 3.357079 GTGAACCTGCACCCGCTG 61.357 66.667 0.00 0.00 39.64 5.18
413 2800 2.679082 ACGATAGATAGTGGGGTTGCT 58.321 47.619 0.00 0.00 41.38 3.91
414 2801 3.470645 AACGATAGATAGTGGGGTTGC 57.529 47.619 0.00 0.00 41.38 4.17
415 2802 4.021368 CCCTAACGATAGATAGTGGGGTTG 60.021 50.000 0.56 0.00 39.58 3.77
416 2803 4.158015 CCCTAACGATAGATAGTGGGGTT 58.842 47.826 0.56 0.00 39.58 4.11
417 2804 3.775910 CCCTAACGATAGATAGTGGGGT 58.224 50.000 0.56 0.00 39.58 4.95
418 2805 2.496470 GCCCTAACGATAGATAGTGGGG 59.504 54.545 0.56 8.63 39.58 4.96
419 2806 3.162666 TGCCCTAACGATAGATAGTGGG 58.837 50.000 0.56 0.00 39.58 4.61
420 2807 3.367498 GCTGCCCTAACGATAGATAGTGG 60.367 52.174 0.56 0.00 39.58 4.00
421 2808 3.670895 CGCTGCCCTAACGATAGATAGTG 60.671 52.174 0.56 0.23 39.58 2.74
422 2809 2.488545 CGCTGCCCTAACGATAGATAGT 59.511 50.000 0.56 0.00 39.58 2.12
423 2810 2.159366 CCGCTGCCCTAACGATAGATAG 60.159 54.545 0.56 0.00 40.75 2.08
424 2811 1.816835 CCGCTGCCCTAACGATAGATA 59.183 52.381 0.56 0.00 41.38 1.98
425 2812 0.603569 CCGCTGCCCTAACGATAGAT 59.396 55.000 0.56 0.00 41.38 1.98
426 2813 1.461091 CCCGCTGCCCTAACGATAGA 61.461 60.000 0.56 0.00 41.38 1.98
427 2814 1.006102 CCCGCTGCCCTAACGATAG 60.006 63.158 0.00 0.00 46.19 2.08
428 2815 1.759299 ACCCGCTGCCCTAACGATA 60.759 57.895 0.00 0.00 0.00 2.92
429 2816 3.081409 ACCCGCTGCCCTAACGAT 61.081 61.111 0.00 0.00 0.00 3.73
430 2817 4.077184 CACCCGCTGCCCTAACGA 62.077 66.667 0.00 0.00 0.00 3.85
432 2819 4.715523 TGCACCCGCTGCCCTAAC 62.716 66.667 0.00 0.00 46.51 2.34
433 2820 4.408821 CTGCACCCGCTGCCCTAA 62.409 66.667 0.00 0.00 46.51 2.69
439 2826 3.357079 GTGAACCTGCACCCGCTG 61.357 66.667 0.00 0.00 39.64 5.18
445 2832 0.310854 CTTTTCCGGTGAACCTGCAC 59.689 55.000 0.00 0.00 38.05 4.57
446 2833 1.452145 GCTTTTCCGGTGAACCTGCA 61.452 55.000 0.00 0.00 0.00 4.41
447 2834 1.285950 GCTTTTCCGGTGAACCTGC 59.714 57.895 0.00 0.00 0.00 4.85
448 2835 1.028905 TTGCTTTTCCGGTGAACCTG 58.971 50.000 0.00 0.00 0.00 4.00
449 2836 1.029681 GTTGCTTTTCCGGTGAACCT 58.970 50.000 0.00 0.00 0.00 3.50
450 2837 0.031585 GGTTGCTTTTCCGGTGAACC 59.968 55.000 0.00 2.47 0.00 3.62
451 2838 0.031585 GGGTTGCTTTTCCGGTGAAC 59.968 55.000 0.00 0.00 0.00 3.18
452 2839 1.110518 GGGGTTGCTTTTCCGGTGAA 61.111 55.000 0.00 0.00 0.00 3.18
453 2840 1.529713 GGGGTTGCTTTTCCGGTGA 60.530 57.895 0.00 0.00 0.00 4.02
454 2841 1.830408 TGGGGTTGCTTTTCCGGTG 60.830 57.895 0.00 0.00 0.00 4.94
455 2842 1.830847 GTGGGGTTGCTTTTCCGGT 60.831 57.895 0.00 0.00 0.00 5.28
456 2843 0.250989 TAGTGGGGTTGCTTTTCCGG 60.251 55.000 0.00 0.00 0.00 5.14
457 2844 1.743394 GATAGTGGGGTTGCTTTTCCG 59.257 52.381 0.00 0.00 0.00 4.30
458 2845 3.087370 AGATAGTGGGGTTGCTTTTCC 57.913 47.619 0.00 0.00 0.00 3.13
459 2846 4.511826 CGATAGATAGTGGGGTTGCTTTTC 59.488 45.833 0.00 0.00 39.76 2.29
460 2847 4.080526 ACGATAGATAGTGGGGTTGCTTTT 60.081 41.667 0.00 0.00 41.38 2.27
461 2848 3.454812 ACGATAGATAGTGGGGTTGCTTT 59.545 43.478 0.00 0.00 41.38 3.51
462 2849 3.039011 ACGATAGATAGTGGGGTTGCTT 58.961 45.455 0.00 0.00 41.38 3.91
504 2891 2.938798 ACCCAGAAATCCCCGGCA 60.939 61.111 0.00 0.00 0.00 5.69
516 2903 2.246761 TAAACCCGGCGATCACCCAG 62.247 60.000 9.30 0.00 0.00 4.45
523 2910 0.763223 ATCCCTCTAAACCCGGCGAT 60.763 55.000 9.30 0.00 0.00 4.58
546 2933 3.009714 GGTCTTTCCGCCCTCCCT 61.010 66.667 0.00 0.00 0.00 4.20
627 3049 2.203082 CCTCTCGATCGCCCCATGA 61.203 63.158 11.09 0.93 0.00 3.07
637 3059 3.165875 TGTTCACCTTCTTCCTCTCGAT 58.834 45.455 0.00 0.00 0.00 3.59
652 3074 3.685139 TCAGTCCAATCTCCTGTTCAC 57.315 47.619 0.00 0.00 0.00 3.18
663 3085 3.823304 GCTTCTTCAACCTTCAGTCCAAT 59.177 43.478 0.00 0.00 0.00 3.16
699 3121 1.950828 TGTTTTAAGCCGTTGGACGA 58.049 45.000 1.51 0.00 46.05 4.20
700 3122 2.759538 TTGTTTTAAGCCGTTGGACG 57.240 45.000 0.00 0.00 42.11 4.79
701 3123 4.023536 TCAGATTGTTTTAAGCCGTTGGAC 60.024 41.667 0.00 0.00 0.00 4.02
784 3215 3.521531 GAGGAGGGAGGAAAGATCAAAGT 59.478 47.826 0.00 0.00 0.00 2.66
840 3296 2.193306 GCACCATAGAATTTGTGCCG 57.807 50.000 2.19 0.00 46.33 5.69
881 3341 3.788227 TCAGCTTGAAGGTATGGTTGT 57.212 42.857 0.00 0.00 0.00 3.32
1038 4937 2.159028 GGTGAAGTAGCTGAGGATGACC 60.159 54.545 0.00 0.00 0.00 4.02
1077 4985 3.977244 GGTTGGTTGGTGCAGCGG 61.977 66.667 11.91 0.00 0.00 5.52
1305 5235 6.324512 TGCATTACCTCTTTATTGGCATGATT 59.675 34.615 0.00 0.00 0.00 2.57
1589 5575 2.530151 AGGGAGCCCTCAAGCACA 60.530 61.111 1.14 0.00 44.43 4.57
1692 5678 4.099881 ACCGTTGTTCTTCTGGTAGTGTAA 59.900 41.667 0.00 0.00 0.00 2.41
1694 5680 2.433239 ACCGTTGTTCTTCTGGTAGTGT 59.567 45.455 0.00 0.00 0.00 3.55
1871 5857 3.706600 AGTTACATTGGCGGGAACTTA 57.293 42.857 0.00 0.00 0.00 2.24
1885 5871 2.416680 TGCATGCATGGCTAGTTACA 57.583 45.000 27.34 11.60 0.00 2.41
1912 5908 1.904865 ACGTAGAGCCGACCCAACA 60.905 57.895 0.00 0.00 0.00 3.33
1953 5953 1.139256 TGCACTTTTACGTGGTCCTCA 59.861 47.619 0.00 0.00 35.47 3.86
2001 6001 9.198475 AGATATTCTCAGGCAAATGATCTTTTT 57.802 29.630 3.93 0.00 0.00 1.94
2002 6002 8.763984 AGATATTCTCAGGCAAATGATCTTTT 57.236 30.769 0.88 0.88 0.00 2.27
2003 6003 8.763984 AAGATATTCTCAGGCAAATGATCTTT 57.236 30.769 0.00 0.00 0.00 2.52
2004 6004 8.763984 AAAGATATTCTCAGGCAAATGATCTT 57.236 30.769 0.00 0.00 29.20 2.40
2005 6005 8.630917 CAAAAGATATTCTCAGGCAAATGATCT 58.369 33.333 0.00 0.00 0.00 2.75
2006 6006 8.411683 ACAAAAGATATTCTCAGGCAAATGATC 58.588 33.333 0.00 0.00 0.00 2.92
2008 6008 7.363181 CCACAAAAGATATTCTCAGGCAAATGA 60.363 37.037 0.00 0.00 0.00 2.57
2011 6011 5.336690 GCCACAAAAGATATTCTCAGGCAAA 60.337 40.000 0.00 0.00 38.27 3.68
2013 6013 3.696051 GCCACAAAAGATATTCTCAGGCA 59.304 43.478 0.00 0.00 38.27 4.75
2014 6014 3.242870 CGCCACAAAAGATATTCTCAGGC 60.243 47.826 0.00 0.00 35.19 4.85
2015 6015 3.313526 CCGCCACAAAAGATATTCTCAGG 59.686 47.826 0.00 0.00 0.00 3.86
2018 6018 3.487544 GCACCGCCACAAAAGATATTCTC 60.488 47.826 0.00 0.00 0.00 2.87
2019 6019 2.423538 GCACCGCCACAAAAGATATTCT 59.576 45.455 0.00 0.00 0.00 2.40
2022 6022 1.832883 TGCACCGCCACAAAAGATAT 58.167 45.000 0.00 0.00 0.00 1.63
2023 6023 1.472082 CATGCACCGCCACAAAAGATA 59.528 47.619 0.00 0.00 0.00 1.98
2024 6024 0.244450 CATGCACCGCCACAAAAGAT 59.756 50.000 0.00 0.00 0.00 2.40
2034 6036 2.518949 CATTCACTAAACATGCACCGC 58.481 47.619 0.00 0.00 0.00 5.68
2053 6156 1.904865 AGTACAACCGACGAGGCCA 60.905 57.895 5.01 0.00 46.52 5.36
2144 6255 3.487376 CGGCAATTCAAGCAATCACGTAT 60.487 43.478 0.00 0.00 0.00 3.06
2148 6259 1.987770 CACGGCAATTCAAGCAATCAC 59.012 47.619 0.00 0.00 0.00 3.06
2164 6275 4.506288 TGTTCATCGCTAACAATATCACGG 59.494 41.667 0.00 0.00 34.04 4.94
2194 6306 3.703556 CTGCAAAGAGAGGGAGATAGACA 59.296 47.826 0.00 0.00 0.00 3.41
2218 6332 6.041751 AGTCTACCTAAATTCTTGGGTATCGG 59.958 42.308 1.18 0.00 44.89 4.18
2220 6334 8.265764 ACAAGTCTACCTAAATTCTTGGGTATC 58.734 37.037 0.00 0.00 44.89 2.24
2264 6378 7.862675 AGCCCTGTTTTCTACTAGTGATAATT 58.137 34.615 5.39 0.00 0.00 1.40
2268 6382 5.763876 AAGCCCTGTTTTCTACTAGTGAT 57.236 39.130 5.39 0.00 0.00 3.06
2316 6430 3.234630 TTCGTGGCTGAACCGGGAG 62.235 63.158 6.32 0.00 43.94 4.30
2349 6463 1.875420 TACGAACCGGGTCGAATGCA 61.875 55.000 45.93 22.38 43.86 3.96
2426 6543 0.108615 CGTGCCTAGAACCAGGACAG 60.109 60.000 0.00 0.00 38.00 3.51
2501 6618 1.621814 CACCTTCTGTCCCGGTTCTAA 59.378 52.381 0.00 0.00 0.00 2.10
2524 6641 1.002773 GGCTGAAACCGGGACTAAAGA 59.997 52.381 6.32 0.00 0.00 2.52
2566 6683 2.185387 GGCGATGGGGTATGTATAGGT 58.815 52.381 0.00 0.00 0.00 3.08
2573 6690 1.893808 GCTGTGGCGATGGGGTATG 60.894 63.158 0.00 0.00 0.00 2.39
2645 6762 2.828661 TAGGAGGTGAGCTAGAGCAA 57.171 50.000 4.01 0.00 45.16 3.91
2720 6837 4.069869 TCGGAGGTCGAGTTTCGT 57.930 55.556 0.00 0.00 43.74 3.85


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

AutoCloner maintained by Alex Coulton.