Multiple sequence alignment - TraesCS3A01G355300

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 TraesCS3A01G355300 chr3A 100.000 2627 0 0 1 2627 602922216 602919590 0.000000e+00 4852.0
1 TraesCS3A01G355300 chr3D 93.832 1751 91 5 878 2627 460501041 460499307 0.000000e+00 2619.0
2 TraesCS3A01G355300 chr3D 92.507 347 10 5 1 343 460503333 460502999 1.410000e-132 483.0
3 TraesCS3A01G355300 chr3D 84.099 283 30 8 554 832 460501768 460501497 2.590000e-65 259.0
4 TraesCS3A01G355300 chr3D 92.398 171 13 0 391 561 460503003 460502833 7.260000e-61 244.0
5 TraesCS3A01G355300 chr3B 93.672 1754 84 14 875 2627 610753007 610751280 0.000000e+00 2599.0
6 TraesCS3A01G355300 chr3B 89.704 709 38 10 1 706 610754280 610753604 0.000000e+00 872.0
7 TraesCS3A01G355300 chr3B 97.500 40 1 0 849 888 610753004 610752965 4.690000e-08 69.4


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 TraesCS3A01G355300 chr3A 602919590 602922216 2626 True 4852.000000 4852 100.000000 1 2627 1 chr3A.!!$R1 2626
1 TraesCS3A01G355300 chr3D 460499307 460503333 4026 True 901.250000 2619 90.709000 1 2627 4 chr3D.!!$R1 2626
2 TraesCS3A01G355300 chr3B 610751280 610754280 3000 True 1180.133333 2599 93.625333 1 2627 3 chr3B.!!$R1 2626

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
486 491 0.03213 GCTCGGTCAGTTGTCTGTGA 59.968 55.0 0.0 0.0 41.91 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 3208 0.183492 TTCACAGCCTTCACAGCCTT 59.817 50.0 0.0 0.0 0.0 4.35 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
173 174 1.066257 CAAGTGCAAAAGCGTGGCT 59.934 52.632 0.00 0.00 42.56 4.75
222 224 2.144730 ACCGTGTATAAACGCTTTGCA 58.855 42.857 10.09 0.00 42.23 4.08
232 234 3.575965 AACGCTTTGCATAAAAGGAGG 57.424 42.857 0.00 0.00 44.73 4.30
233 235 1.818674 ACGCTTTGCATAAAAGGAGGG 59.181 47.619 0.00 0.00 44.73 4.30
234 236 1.818674 CGCTTTGCATAAAAGGAGGGT 59.181 47.619 0.00 0.00 44.73 4.34
235 237 2.415893 CGCTTTGCATAAAAGGAGGGTG 60.416 50.000 0.00 0.00 44.73 4.61
236 238 2.825532 GCTTTGCATAAAAGGAGGGTGA 59.174 45.455 0.00 0.00 44.73 4.02
237 239 3.258123 GCTTTGCATAAAAGGAGGGTGAA 59.742 43.478 0.00 0.00 44.73 3.18
238 240 4.262420 GCTTTGCATAAAAGGAGGGTGAAA 60.262 41.667 0.00 0.00 44.73 2.69
239 241 5.741673 GCTTTGCATAAAAGGAGGGTGAAAA 60.742 40.000 0.00 0.00 44.73 2.29
240 242 5.467035 TTGCATAAAAGGAGGGTGAAAAG 57.533 39.130 0.00 0.00 0.00 2.27
241 243 3.831911 TGCATAAAAGGAGGGTGAAAAGG 59.168 43.478 0.00 0.00 0.00 3.11
242 244 4.086457 GCATAAAAGGAGGGTGAAAAGGA 58.914 43.478 0.00 0.00 0.00 3.36
243 245 4.158579 GCATAAAAGGAGGGTGAAAAGGAG 59.841 45.833 0.00 0.00 0.00 3.69
431 436 3.557054 CGAAGGAAGGATGTTGGACAAGA 60.557 47.826 0.00 0.00 0.00 3.02
459 464 0.179040 TTTGGTGACTCCGGTTGGAC 60.179 55.000 0.00 0.00 40.17 4.02
481 486 1.444553 CTCCGCTCGGTCAGTTGTC 60.445 63.158 8.28 0.00 36.47 3.18
486 491 0.032130 GCTCGGTCAGTTGTCTGTGA 59.968 55.000 0.00 0.00 41.91 3.58
494 499 2.094442 TCAGTTGTCTGTGAACACGTCA 60.094 45.455 0.00 0.00 41.91 4.35
495 500 2.670905 CAGTTGTCTGTGAACACGTCAA 59.329 45.455 0.00 3.62 38.23 3.18
524 529 4.749598 TCCGTGGATATTTGATGATGTTCG 59.250 41.667 0.00 0.00 0.00 3.95
535 540 3.960755 TGATGATGTTCGATAGGTGACCT 59.039 43.478 10.00 10.00 37.71 3.85
565 1643 4.546674 AGTTGCCCTTATAGATTTTGGGG 58.453 43.478 0.00 0.00 38.34 4.96
572 1650 2.775490 ATAGATTTTGGGGGAAGGGC 57.225 50.000 0.00 0.00 0.00 5.19
573 1651 1.388174 TAGATTTTGGGGGAAGGGCA 58.612 50.000 0.00 0.00 0.00 5.36
630 1708 5.013183 AGTGAGTTATAAGCCTTGTTGGAGT 59.987 40.000 0.00 0.00 38.35 3.85
633 1711 4.288626 AGTTATAAGCCTTGTTGGAGTGGA 59.711 41.667 0.00 0.00 38.35 4.02
655 1733 6.100279 TGGACAGAAATGCTCTAATCCTACAT 59.900 38.462 5.85 0.00 38.58 2.29
811 1929 1.966451 CGTCAAAGTGGGGGACAGC 60.966 63.158 0.00 0.00 0.00 4.40
832 1950 3.059325 GCGTCTGGTCATGAATTAGCATC 60.059 47.826 0.00 0.00 0.00 3.91
833 1951 3.496130 CGTCTGGTCATGAATTAGCATCC 59.504 47.826 0.00 0.00 0.00 3.51
834 1952 4.454678 GTCTGGTCATGAATTAGCATCCA 58.545 43.478 0.00 0.00 0.00 3.41
835 1953 5.068636 GTCTGGTCATGAATTAGCATCCAT 58.931 41.667 0.00 0.00 0.00 3.41
836 1954 5.048921 GTCTGGTCATGAATTAGCATCCATG 60.049 44.000 0.00 0.00 38.12 3.66
838 1956 4.147321 GGTCATGAATTAGCATCCATGGT 58.853 43.478 12.58 0.00 41.93 3.55
839 1957 4.217118 GGTCATGAATTAGCATCCATGGTC 59.783 45.833 12.58 0.00 39.52 4.02
840 1958 5.068636 GTCATGAATTAGCATCCATGGTCT 58.931 41.667 12.58 10.07 39.52 3.85
842 1960 6.040166 GTCATGAATTAGCATCCATGGTCTTT 59.960 38.462 12.58 0.45 39.52 2.52
856 2437 2.697751 TGGTCTTTGTGAACCAAATGGG 59.302 45.455 4.17 0.00 42.02 4.00
883 2464 1.666888 GGTTCGTTGCAGAGCCAAATG 60.667 52.381 4.24 0.00 40.64 2.32
884 2465 0.597568 TTCGTTGCAGAGCCAAATGG 59.402 50.000 0.00 0.00 38.53 3.16
885 2466 0.250684 TCGTTGCAGAGCCAAATGGA 60.251 50.000 2.98 0.00 37.39 3.41
886 2467 0.169672 CGTTGCAGAGCCAAATGGAG 59.830 55.000 2.98 0.00 37.39 3.86
887 2468 0.108945 GTTGCAGAGCCAAATGGAGC 60.109 55.000 2.98 1.97 37.39 4.70
888 2469 0.251474 TTGCAGAGCCAAATGGAGCT 60.251 50.000 2.98 0.00 43.55 4.09
889 2470 0.963856 TGCAGAGCCAAATGGAGCTG 60.964 55.000 2.98 10.13 40.11 4.24
890 2471 1.807886 CAGAGCCAAATGGAGCTGC 59.192 57.895 2.98 0.00 40.11 5.25
891 2472 0.680280 CAGAGCCAAATGGAGCTGCT 60.680 55.000 6.82 0.00 40.11 4.24
892 2473 0.680280 AGAGCCAAATGGAGCTGCTG 60.680 55.000 7.01 0.00 40.11 4.41
893 2474 1.664321 GAGCCAAATGGAGCTGCTGG 61.664 60.000 7.01 7.23 40.11 4.85
894 2475 1.980772 GCCAAATGGAGCTGCTGGT 60.981 57.895 7.01 0.00 37.39 4.00
895 2476 1.538687 GCCAAATGGAGCTGCTGGTT 61.539 55.000 7.01 0.00 37.39 3.67
896 2477 0.529378 CCAAATGGAGCTGCTGGTTC 59.471 55.000 7.01 0.00 37.39 3.62
897 2478 0.169672 CAAATGGAGCTGCTGGTTCG 59.830 55.000 7.01 0.00 0.00 3.95
898 2479 0.250901 AAATGGAGCTGCTGGTTCGT 60.251 50.000 7.01 0.00 0.00 3.85
899 2480 0.250901 AATGGAGCTGCTGGTTCGTT 60.251 50.000 7.01 2.90 0.00 3.85
900 2481 0.957395 ATGGAGCTGCTGGTTCGTTG 60.957 55.000 7.01 0.00 0.00 4.10
901 2482 2.558313 GAGCTGCTGGTTCGTTGC 59.442 61.111 7.01 0.00 0.00 4.17
902 2483 2.203195 AGCTGCTGGTTCGTTGCA 60.203 55.556 0.00 0.00 35.30 4.08
905 2486 4.047834 TGCTGGTTCGTTGCAGAG 57.952 55.556 0.00 0.00 32.55 3.35
906 2487 2.253758 TGCTGGTTCGTTGCAGAGC 61.254 57.895 0.00 0.00 32.55 4.09
907 2488 2.970974 GCTGGTTCGTTGCAGAGCC 61.971 63.158 2.30 2.30 41.21 4.70
908 2489 1.597854 CTGGTTCGTTGCAGAGCCA 60.598 57.895 10.48 10.48 46.85 4.75
909 2490 1.153066 TGGTTCGTTGCAGAGCCAA 60.153 52.632 8.79 0.00 46.21 4.52
910 2491 0.749818 TGGTTCGTTGCAGAGCCAAA 60.750 50.000 8.79 0.00 46.21 3.28
911 2492 0.598065 GGTTCGTTGCAGAGCCAAAT 59.402 50.000 4.24 0.00 40.64 2.32
923 2504 0.319405 AGCCAAATGGAGCAGTTTGC 59.681 50.000 2.98 0.00 38.66 3.68
941 2522 0.310854 GCCTTTGTGAACCAACTCCG 59.689 55.000 0.00 0.00 31.20 4.63
943 2524 1.021202 CTTTGTGAACCAACTCCGCA 58.979 50.000 0.00 0.00 31.20 5.69
972 2553 6.741992 CTACATAAGCAAATCACACAGGAA 57.258 37.500 0.00 0.00 0.00 3.36
974 2555 5.772521 ACATAAGCAAATCACACAGGAAAC 58.227 37.500 0.00 0.00 0.00 2.78
992 2573 2.968206 GCCCGTAACCTCACGACT 59.032 61.111 0.00 0.00 44.69 4.18
1033 2615 2.436646 GTGCCCACATCCTCACCG 60.437 66.667 0.00 0.00 0.00 4.94
1064 2646 2.017782 TGCTCTCACGCTCCTACTAAG 58.982 52.381 0.00 0.00 0.00 2.18
1068 2650 1.746220 CTCACGCTCCTACTAAGCACT 59.254 52.381 0.00 0.00 39.81 4.40
1077 2659 4.801891 TCCTACTAAGCACTGTAAACACG 58.198 43.478 0.00 0.00 0.00 4.49
1083 2665 1.857364 CACTGTAAACACGGCGTCC 59.143 57.895 10.85 0.00 0.00 4.79
1084 2666 0.876777 CACTGTAAACACGGCGTCCA 60.877 55.000 10.85 0.93 0.00 4.02
1158 2740 3.451178 AGACCATAACGCTCTACACCAAT 59.549 43.478 0.00 0.00 0.00 3.16
1164 2746 0.176680 CGCTCTACACCAATGGAGCT 59.823 55.000 6.16 0.00 46.04 4.09
1176 2758 1.181098 ATGGAGCTGCACCACCAAAC 61.181 55.000 21.00 0.00 40.36 2.93
1206 2788 1.375523 CCCTTCCTCGAAACACCCG 60.376 63.158 0.00 0.00 0.00 5.28
1317 2899 1.154016 CGTCGACGAGCAGTTCCAT 60.154 57.895 33.35 0.00 43.02 3.41
1320 2902 1.215382 CGACGAGCAGTTCCATGGA 59.785 57.895 11.44 11.44 0.00 3.41
1394 2976 3.018856 CCAGCTTGGATGATAACAGCAA 58.981 45.455 0.00 0.00 40.96 3.91
1397 2979 2.754552 GCTTGGATGATAACAGCAACCA 59.245 45.455 0.00 0.00 33.73 3.67
1401 2983 6.430925 GCTTGGATGATAACAGCAACCATATA 59.569 38.462 0.00 0.00 33.73 0.86
1404 2986 7.517320 TGGATGATAACAGCAACCATATAGTT 58.483 34.615 0.00 0.00 33.73 2.24
1462 3044 1.347707 ACAGCATCAGGTTCTTCGGAA 59.652 47.619 0.00 0.00 0.00 4.30
1469 3051 2.837591 TCAGGTTCTTCGGAATCCATCA 59.162 45.455 0.00 0.00 35.78 3.07
1470 3052 2.939103 CAGGTTCTTCGGAATCCATCAC 59.061 50.000 0.00 0.00 35.78 3.06
1471 3053 2.571653 AGGTTCTTCGGAATCCATCACA 59.428 45.455 0.00 0.00 35.78 3.58
1473 3055 3.127030 GGTTCTTCGGAATCCATCACAAC 59.873 47.826 0.00 0.00 36.27 3.32
1476 3058 0.611200 TCGGAATCCATCACAACGGT 59.389 50.000 0.00 0.00 0.00 4.83
1488 3070 1.186267 ACAACGGTCAGGAGGAGTCC 61.186 60.000 0.00 0.00 44.33 3.85
1521 3103 2.613421 GGAGGGACGGGGAGGTAT 59.387 66.667 0.00 0.00 0.00 2.73
1525 3107 1.382146 GGGACGGGGAGGTATGACA 60.382 63.158 0.00 0.00 0.00 3.58
1528 3110 2.351336 GACGGGGAGGTATGACAGCG 62.351 65.000 0.00 0.00 0.00 5.18
1548 3130 1.161843 CCACCGGTTTCGCTGTTATT 58.838 50.000 2.97 0.00 34.56 1.40
1575 3157 3.438087 CAGCAGATGTACCTGAAACAAGG 59.562 47.826 3.57 0.00 43.57 3.61
1583 3165 3.611025 ACCTGAAACAAGGGGAAATGA 57.389 42.857 0.00 0.00 42.11 2.57
1598 3180 2.574006 AATGACAGCTTCAGCAGGAA 57.426 45.000 0.75 0.00 45.16 3.36
1602 3184 2.278854 GACAGCTTCAGCAGGAATCTC 58.721 52.381 0.75 0.00 45.16 2.75
1616 3198 3.072184 AGGAATCTCAGTTTCAGTGTGCT 59.928 43.478 0.00 0.00 0.00 4.40
1623 3205 2.547211 CAGTTTCAGTGTGCTCCTCAAG 59.453 50.000 0.00 0.00 0.00 3.02
1624 3206 2.171448 AGTTTCAGTGTGCTCCTCAAGT 59.829 45.455 0.00 0.00 0.00 3.16
1625 3207 2.245159 TTCAGTGTGCTCCTCAAGTG 57.755 50.000 0.00 0.00 0.00 3.16
1626 3208 1.413118 TCAGTGTGCTCCTCAAGTGA 58.587 50.000 0.00 0.00 0.00 3.41
1627 3209 1.762370 TCAGTGTGCTCCTCAAGTGAA 59.238 47.619 0.00 0.00 0.00 3.18
1628 3210 2.141517 CAGTGTGCTCCTCAAGTGAAG 58.858 52.381 0.00 0.00 0.00 3.02
1629 3211 1.071385 AGTGTGCTCCTCAAGTGAAGG 59.929 52.381 0.00 0.00 0.00 3.46
1630 3212 0.250467 TGTGCTCCTCAAGTGAAGGC 60.250 55.000 0.00 0.00 0.00 4.35
1631 3213 0.036022 GTGCTCCTCAAGTGAAGGCT 59.964 55.000 0.00 0.00 0.00 4.58
1667 3250 4.910195 AGTCTCACATACCATTCTGCAAA 58.090 39.130 0.00 0.00 0.00 3.68
1678 3261 4.219288 ACCATTCTGCAAATCAACTTCTCC 59.781 41.667 0.00 0.00 0.00 3.71
1799 3382 7.646314 CAATCTCATCCCATTACATTTCACTC 58.354 38.462 0.00 0.00 0.00 3.51
1874 3457 6.018433 ACCCAATAGCTCCTGAAATACAAT 57.982 37.500 0.00 0.00 0.00 2.71
1895 3478 7.102346 ACAATCTCTTCACCTATCTTTCACTG 58.898 38.462 0.00 0.00 0.00 3.66
2036 3619 1.361668 CGGATCCAGTTGGTGAAGCG 61.362 60.000 13.41 0.00 36.34 4.68
2083 3666 8.498054 TTCAGAACCAAATAGATTCATCTCAC 57.502 34.615 0.00 0.00 38.32 3.51
2227 3810 3.937706 GCTTTCTCATATGGGGATCATCG 59.062 47.826 1.90 0.00 37.30 3.84
2493 4076 9.473007 TGGATGGAAATATCATGACAAACTTAA 57.527 29.630 0.00 0.00 0.00 1.85
2576 4159 5.938710 AGATAAGCAAGCAGGTGATATGATG 59.061 40.000 0.00 0.00 0.00 3.07
2612 4195 7.911651 TGATATTTGTATGCAAAGGGGAAAAA 58.088 30.769 14.39 0.00 46.30 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 174 3.384348 GGTCCGCACCTTCACCTA 58.616 61.111 0.00 0.00 40.00 3.08
205 207 7.024768 TCCTTTTATGCAAAGCGTTTATACAC 58.975 34.615 0.00 0.00 40.75 2.90
210 212 4.082463 CCCTCCTTTTATGCAAAGCGTTTA 60.082 41.667 0.00 0.00 40.75 2.01
222 224 4.814521 GCCTCCTTTTCACCCTCCTTTTAT 60.815 45.833 0.00 0.00 0.00 1.40
232 234 6.096673 TCAATTTTTAGCCTCCTTTTCACC 57.903 37.500 0.00 0.00 0.00 4.02
233 235 6.749139 ACTCAATTTTTAGCCTCCTTTTCAC 58.251 36.000 0.00 0.00 0.00 3.18
234 236 6.976934 ACTCAATTTTTAGCCTCCTTTTCA 57.023 33.333 0.00 0.00 0.00 2.69
235 237 9.929180 AATAACTCAATTTTTAGCCTCCTTTTC 57.071 29.630 0.00 0.00 0.00 2.29
237 239 9.710900 CAAATAACTCAATTTTTAGCCTCCTTT 57.289 29.630 0.00 0.00 0.00 3.11
238 240 8.314021 CCAAATAACTCAATTTTTAGCCTCCTT 58.686 33.333 0.00 0.00 0.00 3.36
239 241 7.579531 GCCAAATAACTCAATTTTTAGCCTCCT 60.580 37.037 0.00 0.00 0.00 3.69
240 242 6.535150 GCCAAATAACTCAATTTTTAGCCTCC 59.465 38.462 0.00 0.00 0.00 4.30
241 243 7.063426 GTGCCAAATAACTCAATTTTTAGCCTC 59.937 37.037 0.00 0.00 0.00 4.70
242 244 6.873605 GTGCCAAATAACTCAATTTTTAGCCT 59.126 34.615 0.00 0.00 0.00 4.58
243 245 6.183360 CGTGCCAAATAACTCAATTTTTAGCC 60.183 38.462 0.00 0.00 0.00 3.93
279 281 2.038863 TCGATACCATAAGCCCCCAT 57.961 50.000 0.00 0.00 0.00 4.00
293 295 5.743636 TTCACATCCATGATCCATCGATA 57.256 39.130 0.00 0.00 0.00 2.92
410 415 4.006319 CTCTTGTCCAACATCCTTCCTTC 58.994 47.826 0.00 0.00 0.00 3.46
431 436 1.523758 GAGTCACCAAATGTTCGCCT 58.476 50.000 0.00 0.00 0.00 5.52
475 480 2.665649 TGACGTGTTCACAGACAACT 57.334 45.000 0.00 0.00 0.00 3.16
481 486 4.434198 CGGATACATTTGACGTGTTCACAG 60.434 45.833 0.00 0.00 32.26 3.66
494 499 8.733458 CATCATCAAATATCCACGGATACATTT 58.267 33.333 7.96 4.73 39.56 2.32
495 500 7.884877 ACATCATCAAATATCCACGGATACATT 59.115 33.333 7.96 4.40 39.56 2.71
524 529 0.535335 TCCAACGCAGGTCACCTATC 59.465 55.000 0.00 0.00 29.64 2.08
535 540 0.037590 ATAAGGGCAACTCCAACGCA 59.962 50.000 0.00 0.00 36.21 5.24
565 1643 2.498644 AAGCTACTTCTTGCCCTTCC 57.501 50.000 0.00 0.00 0.00 3.46
572 1650 6.931840 AGTTTGAGGAGTTAAGCTACTTCTTG 59.068 38.462 0.00 0.00 38.86 3.02
573 1651 6.931840 CAGTTTGAGGAGTTAAGCTACTTCTT 59.068 38.462 0.00 0.00 38.86 2.52
608 1686 5.245531 CACTCCAACAAGGCTTATAACTCA 58.754 41.667 0.00 0.00 37.29 3.41
630 1708 5.425217 TGTAGGATTAGAGCATTTCTGTCCA 59.575 40.000 10.84 0.00 41.17 4.02
633 1711 8.709308 AGTAATGTAGGATTAGAGCATTTCTGT 58.291 33.333 0.00 0.00 36.61 3.41
655 1733 4.393680 AGCGTATTGGCGATTGAAAAGTAA 59.606 37.500 0.00 0.00 38.18 2.24
811 1929 3.496130 GGATGCTAATTCATGACCAGACG 59.504 47.826 0.00 0.00 0.00 4.18
842 1960 1.470996 GCAGCCCCATTTGGTTCACA 61.471 55.000 0.00 0.00 0.00 3.58
856 2437 3.286751 TGCAACGAACCAGCAGCC 61.287 61.111 0.00 0.00 33.75 4.85
883 2464 2.970974 GCAACGAACCAGCAGCTCC 61.971 63.158 0.00 0.00 0.00 4.70
884 2465 2.253758 TGCAACGAACCAGCAGCTC 61.254 57.895 0.00 0.00 33.75 4.09
885 2466 2.203195 TGCAACGAACCAGCAGCT 60.203 55.556 0.00 0.00 33.75 4.24
888 2469 2.253758 GCTCTGCAACGAACCAGCA 61.254 57.895 0.00 0.00 36.72 4.41
889 2470 2.558313 GCTCTGCAACGAACCAGC 59.442 61.111 0.00 0.00 0.00 4.85
890 2471 1.165907 TTGGCTCTGCAACGAACCAG 61.166 55.000 0.00 0.00 31.35 4.00
891 2472 0.749818 TTTGGCTCTGCAACGAACCA 60.750 50.000 0.00 0.00 0.00 3.67
892 2473 0.598065 ATTTGGCTCTGCAACGAACC 59.402 50.000 0.00 0.00 0.00 3.62
893 2474 1.666888 CCATTTGGCTCTGCAACGAAC 60.667 52.381 0.00 0.00 0.00 3.95
894 2475 0.597568 CCATTTGGCTCTGCAACGAA 59.402 50.000 0.00 0.00 0.00 3.85
895 2476 0.250684 TCCATTTGGCTCTGCAACGA 60.251 50.000 0.00 0.00 34.44 3.85
896 2477 0.169672 CTCCATTTGGCTCTGCAACG 59.830 55.000 0.00 0.00 34.44 4.10
897 2478 0.108945 GCTCCATTTGGCTCTGCAAC 60.109 55.000 0.00 0.00 34.44 4.17
898 2479 0.540133 TGCTCCATTTGGCTCTGCAA 60.540 50.000 0.00 0.00 34.44 4.08
899 2480 0.963856 CTGCTCCATTTGGCTCTGCA 60.964 55.000 0.00 0.00 34.44 4.41
900 2481 0.964358 ACTGCTCCATTTGGCTCTGC 60.964 55.000 0.00 0.00 34.44 4.26
901 2482 1.542492 AACTGCTCCATTTGGCTCTG 58.458 50.000 0.00 0.00 34.44 3.35
902 2483 1.891150 CAAACTGCTCCATTTGGCTCT 59.109 47.619 0.00 0.00 33.11 4.09
903 2484 1.670967 GCAAACTGCTCCATTTGGCTC 60.671 52.381 0.00 0.00 40.96 4.70
904 2485 0.319405 GCAAACTGCTCCATTTGGCT 59.681 50.000 0.00 0.00 40.96 4.75
905 2486 2.831597 GCAAACTGCTCCATTTGGC 58.168 52.632 0.00 0.00 40.96 4.52
906 2487 0.971386 AGGCAAACTGCTCCATTTGG 59.029 50.000 0.00 0.00 44.28 3.28
907 2488 2.803956 CAAAGGCAAACTGCTCCATTTG 59.196 45.455 0.00 2.70 44.28 2.32
908 2489 2.435437 ACAAAGGCAAACTGCTCCATTT 59.565 40.909 0.00 0.00 44.28 2.32
909 2490 2.041701 ACAAAGGCAAACTGCTCCATT 58.958 42.857 0.00 0.00 44.28 3.16
910 2491 1.342174 CACAAAGGCAAACTGCTCCAT 59.658 47.619 0.00 0.00 44.28 3.41
911 2492 0.746063 CACAAAGGCAAACTGCTCCA 59.254 50.000 0.00 0.00 44.28 3.86
923 2504 0.310854 GCGGAGTTGGTTCACAAAGG 59.689 55.000 0.00 0.00 41.58 3.11
953 2534 4.615912 GCGTTTCCTGTGTGATTTGCTTAT 60.616 41.667 0.00 0.00 0.00 1.73
968 2549 1.294459 GAGGTTACGGGCGTTTCCT 59.706 57.895 0.00 0.00 34.54 3.36
970 2551 1.620413 CGTGAGGTTACGGGCGTTTC 61.620 60.000 0.00 0.00 40.22 2.78
972 2553 2.048877 CGTGAGGTTACGGGCGTT 60.049 61.111 0.00 0.00 40.22 4.84
974 2555 2.505557 GTCGTGAGGTTACGGGCG 60.506 66.667 0.00 0.00 43.85 6.13
992 2573 1.610038 CTTGTGGTTGCATCTTGCTCA 59.390 47.619 0.75 0.00 45.31 4.26
1013 2595 1.221840 GTGAGGATGTGGGCACGAT 59.778 57.895 0.00 0.00 0.00 3.73
1064 2646 1.203313 GACGCCGTGTTTACAGTGC 59.797 57.895 0.00 0.00 0.00 4.40
1068 2650 1.957186 GCTGGACGCCGTGTTTACA 60.957 57.895 0.00 0.00 0.00 2.41
1158 2740 1.827789 GTTTGGTGGTGCAGCTCCA 60.828 57.895 30.25 30.25 32.61 3.86
1317 2899 2.057922 AGCCCAAACTCTCTCTTTCCA 58.942 47.619 0.00 0.00 0.00 3.53
1320 2902 1.546548 GGCAGCCCAAACTCTCTCTTT 60.547 52.381 0.00 0.00 0.00 2.52
1394 2976 3.545703 GCCTTCACTGCAACTATATGGT 58.454 45.455 0.00 0.00 0.00 3.55
1397 2979 2.780010 AGGGCCTTCACTGCAACTATAT 59.220 45.455 0.00 0.00 0.00 0.86
1401 2983 1.228367 CAGGGCCTTCACTGCAACT 60.228 57.895 1.32 0.00 0.00 3.16
1404 2986 1.228245 GAACAGGGCCTTCACTGCA 60.228 57.895 1.32 0.00 38.25 4.41
1430 3012 3.687321 ATGCTGTCTTCCGCGCCAT 62.687 57.895 0.00 0.00 0.00 4.40
1462 3044 1.208052 CTCCTGACCGTTGTGATGGAT 59.792 52.381 0.00 0.00 35.77 3.41
1469 3051 1.186267 GGACTCCTCCTGACCGTTGT 61.186 60.000 0.00 0.00 33.07 3.32
1470 3052 1.592223 GGACTCCTCCTGACCGTTG 59.408 63.158 0.00 0.00 33.07 4.10
1471 3053 1.609794 GGGACTCCTCCTGACCGTT 60.610 63.158 0.00 0.00 36.68 4.44
1473 3055 1.381872 ATGGGACTCCTCCTGACCG 60.382 63.158 0.00 0.00 36.68 4.79
1476 3058 0.684479 CGACATGGGACTCCTCCTGA 60.684 60.000 0.00 0.00 36.68 3.86
1515 3097 1.521681 GGTGGCGCTGTCATACCTC 60.522 63.158 7.64 0.00 0.00 3.85
1521 3103 4.555709 AAACCGGTGGCGCTGTCA 62.556 61.111 8.52 0.00 0.00 3.58
1548 3130 3.018423 TCAGGTACATCTGCTGCTCTA 57.982 47.619 0.00 0.00 34.91 2.43
1557 3139 3.256704 TCCCCTTGTTTCAGGTACATCT 58.743 45.455 0.00 0.00 30.96 2.90
1575 3157 1.471684 CTGCTGAAGCTGTCATTTCCC 59.528 52.381 3.61 0.00 42.66 3.97
1598 3180 2.636893 AGGAGCACACTGAAACTGAGAT 59.363 45.455 0.00 0.00 0.00 2.75
1602 3184 2.245159 TGAGGAGCACACTGAAACTG 57.755 50.000 0.00 0.00 0.00 3.16
1616 3198 1.423584 TCACAGCCTTCACTTGAGGA 58.576 50.000 0.00 0.00 0.00 3.71
1623 3205 0.536006 ACAGCCTTCACAGCCTTCAC 60.536 55.000 0.00 0.00 0.00 3.18
1624 3206 0.535780 CACAGCCTTCACAGCCTTCA 60.536 55.000 0.00 0.00 0.00 3.02
1625 3207 0.250467 TCACAGCCTTCACAGCCTTC 60.250 55.000 0.00 0.00 0.00 3.46
1626 3208 0.183492 TTCACAGCCTTCACAGCCTT 59.817 50.000 0.00 0.00 0.00 4.35
1627 3209 0.250640 CTTCACAGCCTTCACAGCCT 60.251 55.000 0.00 0.00 0.00 4.58
1628 3210 0.536006 ACTTCACAGCCTTCACAGCC 60.536 55.000 0.00 0.00 0.00 4.85
1629 3211 0.871057 GACTTCACAGCCTTCACAGC 59.129 55.000 0.00 0.00 0.00 4.40
1630 3212 2.224137 TGAGACTTCACAGCCTTCACAG 60.224 50.000 0.00 0.00 0.00 3.66
1631 3213 1.762370 TGAGACTTCACAGCCTTCACA 59.238 47.619 0.00 0.00 0.00 3.58
1874 3457 4.528206 TGCAGTGAAAGATAGGTGAAGAGA 59.472 41.667 0.00 0.00 0.00 3.10
1895 3478 5.725110 CACATGTGGAACTATAGAAGTGC 57.275 43.478 18.51 0.00 38.88 4.40
2017 3600 1.361668 CGCTTCACCAACTGGATCCG 61.362 60.000 7.39 4.62 38.94 4.18
2036 3619 1.660333 GCTGCGAATATAGGCAAACGC 60.660 52.381 0.00 0.00 44.95 4.84
2083 3666 4.264253 TGGATGAGTAATCAAGGCAACAG 58.736 43.478 0.00 0.00 36.98 3.16
2227 3810 0.681175 AATTCAAGCCCAACACAGCC 59.319 50.000 0.00 0.00 0.00 4.85
2273 3856 2.365293 CCTTTTTCCAGGTTGTGAAGGG 59.635 50.000 0.00 0.00 0.00 3.95
2493 4076 9.225436 GACCTTTTGATTTCTCTTATCAAGTCT 57.775 33.333 0.00 0.00 41.53 3.24


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

AutoCloner maintained by Alex Coulton.