Multiple sequence alignment - TraesCS6A01G320800

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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 TraesCS6A01G320800 chr6A 100.000 3999 0 0 1 3999 555440209 555444207 0.000000e+00 7385
1 TraesCS6A01G320800 chr6A 92.422 1821 120 13 312 2126 74148499 74150307 0.000000e+00 2582
2 TraesCS6A01G320800 chr6A 95.988 1022 41 0 2124 3145 74150276 74151297 0.000000e+00 1661
3 TraesCS6A01G320800 chr6A 94.912 1022 51 1 2124 3145 74143604 74144624 0.000000e+00 1598
4 TraesCS6A01G320800 chr6A 88.608 316 25 9 5 311 52185854 52185541 1.360000e-99 374
5 TraesCS6A01G320800 chr6A 88.535 314 28 6 5 311 52290291 52289979 1.360000e-99 374
6 TraesCS6A01G320800 chr6A 87.500 320 30 4 2 311 74148222 74148541 1.060000e-95 361
7 TraesCS6A01G320800 chr7D 94.402 1822 83 10 312 2126 562196833 562198642 0.000000e+00 2782
8 TraesCS6A01G320800 chr7D 92.688 1819 120 11 312 2126 524311654 524313463 0.000000e+00 2610
9 TraesCS6A01G320800 chr7D 92.354 1818 126 11 312 2126 524304002 524305809 0.000000e+00 2575
10 TraesCS6A01G320800 chr7D 92.240 1817 127 12 312 2126 524249276 524251080 0.000000e+00 2562
11 TraesCS6A01G320800 chr7D 92.024 1818 132 10 312 2126 524257113 524258920 0.000000e+00 2542
12 TraesCS6A01G320800 chr7D 96.872 1023 31 1 2124 3145 562198611 562199633 0.000000e+00 1711
13 TraesCS6A01G320800 chr7D 96.086 1022 40 0 2124 3145 524251049 524252070 0.000000e+00 1666
14 TraesCS6A01G320800 chr7D 95.992 1023 40 1 2124 3145 524313432 524314454 0.000000e+00 1661
15 TraesCS6A01G320800 chr7D 95.894 1023 39 3 2124 3145 524305778 524306798 0.000000e+00 1653
16 TraesCS6A01G320800 chr7D 92.949 312 16 4 5 311 562196565 562196875 2.190000e-122 449
17 TraesCS6A01G320800 chr7D 88.710 310 29 4 6 311 524256848 524257155 1.360000e-99 374
18 TraesCS6A01G320800 chr7D 88.291 316 31 4 2 311 524311381 524311696 1.360000e-99 374
19 TraesCS6A01G320800 chr7D 87.859 313 30 6 2 311 524303736 524304043 1.060000e-95 361
20 TraesCS6A01G320800 chr7A 91.914 1818 135 9 312 2125 604260920 604262729 0.000000e+00 2532
21 TraesCS6A01G320800 chr7A 91.694 1818 139 9 312 2125 604250139 604251948 0.000000e+00 2510
22 TraesCS6A01G320800 chr7A 91.309 1818 138 13 312 2125 604221864 604223665 0.000000e+00 2464
23 TraesCS6A01G320800 chr7A 90.542 1438 122 11 312 1744 604290138 604291566 0.000000e+00 1890
24 TraesCS6A01G320800 chr7A 95.201 1021 47 2 2124 3143 604251918 604252937 0.000000e+00 1613
25 TraesCS6A01G320800 chr7A 94.819 1023 52 1 2124 3146 604257319 604258340 0.000000e+00 1594
26 TraesCS6A01G320800 chr7A 94.330 1023 55 3 2124 3145 604304168 604305188 0.000000e+00 1565
27 TraesCS6A01G320800 chr7A 97.445 861 22 0 3139 3999 127718001 127718861 0.000000e+00 1469
28 TraesCS6A01G320800 chr7A 97.329 861 23 0 3139 3999 669015446 669014586 0.000000e+00 1463
29 TraesCS6A01G320800 chr7A 97.213 861 20 4 3139 3999 145436942 145436086 0.000000e+00 1454
30 TraesCS6A01G320800 chr7A 88.854 314 31 3 2 311 604260649 604260962 2.250000e-102 383
31 TraesCS6A01G320800 chr7A 87.859 313 34 3 2 311 604249870 604250181 8.170000e-97 364
32 TraesCS6A01G320800 chr5A 97.892 854 18 0 3146 3999 229419911 229420764 0.000000e+00 1478
33 TraesCS6A01G320800 chr3A 97.451 863 21 1 3137 3999 654249779 654250640 0.000000e+00 1471
34 TraesCS6A01G320800 chr3A 97.658 854 19 1 3147 3999 72166537 72165684 0.000000e+00 1465
35 TraesCS6A01G320800 chr1A 97.770 852 17 2 3148 3999 397361030 397360181 0.000000e+00 1467
36 TraesCS6A01G320800 chr2A 97.329 861 23 0 3139 3999 179945477 179944617 0.000000e+00 1463
37 TraesCS6A01G320800 chr2A 97.213 861 24 0 3139 3999 749930946 749931806 0.000000e+00 1458
38 TraesCS6A01G320800 chr6B 90.023 441 35 5 321 754 95553544 95553982 2.700000e-156 562


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 TraesCS6A01G320800 chr6A 555440209 555444207 3998 False 7385.000000 7385 100.000000 1 3999 1 chr6A.!!$F1 3998
1 TraesCS6A01G320800 chr6A 74143604 74151297 7693 False 1550.500000 2582 92.705500 2 3145 4 chr6A.!!$F2 3143
2 TraesCS6A01G320800 chr7D 524249276 524252070 2794 False 2114.000000 2562 94.163000 312 3145 2 chr7D.!!$F1 2833
3 TraesCS6A01G320800 chr7D 562196565 562199633 3068 False 1647.333333 2782 94.741000 5 3145 3 chr7D.!!$F5 3140
4 TraesCS6A01G320800 chr7D 524311381 524314454 3073 False 1548.333333 2610 92.323667 2 3145 3 chr7D.!!$F4 3143
5 TraesCS6A01G320800 chr7D 524303736 524306798 3062 False 1529.666667 2575 92.035667 2 3145 3 chr7D.!!$F3 3143
6 TraesCS6A01G320800 chr7D 524256848 524258920 2072 False 1458.000000 2542 90.367000 6 2126 2 chr7D.!!$F2 2120
7 TraesCS6A01G320800 chr7A 604221864 604223665 1801 False 2464.000000 2464 91.309000 312 2125 1 chr7A.!!$F2 1813
8 TraesCS6A01G320800 chr7A 604290138 604291566 1428 False 1890.000000 1890 90.542000 312 1744 1 chr7A.!!$F3 1432
9 TraesCS6A01G320800 chr7A 604304168 604305188 1020 False 1565.000000 1565 94.330000 2124 3145 1 chr7A.!!$F4 1021
10 TraesCS6A01G320800 chr7A 604257319 604262729 5410 False 1503.000000 2532 91.862333 2 3146 3 chr7A.!!$F6 3144
11 TraesCS6A01G320800 chr7A 604249870 604252937 3067 False 1495.666667 2510 91.584667 2 3143 3 chr7A.!!$F5 3141
12 TraesCS6A01G320800 chr7A 127718001 127718861 860 False 1469.000000 1469 97.445000 3139 3999 1 chr7A.!!$F1 860
13 TraesCS6A01G320800 chr7A 669014586 669015446 860 True 1463.000000 1463 97.329000 3139 3999 1 chr7A.!!$R2 860
14 TraesCS6A01G320800 chr7A 145436086 145436942 856 True 1454.000000 1454 97.213000 3139 3999 1 chr7A.!!$R1 860
15 TraesCS6A01G320800 chr5A 229419911 229420764 853 False 1478.000000 1478 97.892000 3146 3999 1 chr5A.!!$F1 853
16 TraesCS6A01G320800 chr3A 654249779 654250640 861 False 1471.000000 1471 97.451000 3137 3999 1 chr3A.!!$F1 862
17 TraesCS6A01G320800 chr3A 72165684 72166537 853 True 1465.000000 1465 97.658000 3147 3999 1 chr3A.!!$R1 852
18 TraesCS6A01G320800 chr1A 397360181 397361030 849 True 1467.000000 1467 97.770000 3148 3999 1 chr1A.!!$R1 851
19 TraesCS6A01G320800 chr2A 179944617 179945477 860 True 1463.000000 1463 97.329000 3139 3999 1 chr2A.!!$R1 860
20 TraesCS6A01G320800 chr2A 749930946 749931806 860 False 1458.000000 1458 97.213000 3139 3999 1 chr2A.!!$F1 860

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
268 5910 0.111061 GCTGCCCATATGGTCCATCA 59.889 55.0 20.46 8.85 36.04 3.07 F
282 5924 0.178767 CCATCATCCTGGCGTCTGAA 59.821 55.0 0.00 0.00 0.00 3.02 F
1704 7371 0.250901 AGCACATGGACGCTTCCTTT 60.251 50.0 11.01 0.00 43.31 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 7497 0.317160 AACGCTCTTCGATGACCACA 59.683 50.000 0.00 0.0 41.67 4.17 R
1959 7626 3.181449 TGCTTACCTTGGACTGTGCTTTA 60.181 43.478 0.00 0.0 0.00 1.85 R
3420 9093 0.252881 TGCTGGATGGAGTCTTCCCT 60.253 55.000 9.34 0.0 43.33 4.20 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
100 5738 2.416680 AGATGCTTCTGCTTTCCCTC 57.583 50.000 0.48 0.00 40.48 4.30
105 5743 1.818642 CTTCTGCTTTCCCTCCACAG 58.181 55.000 0.00 0.00 0.00 3.66
112 5750 1.352352 CTTTCCCTCCACAGACATGGT 59.648 52.381 0.00 0.00 40.95 3.55
150 5789 3.075005 GGGAGCAGGGAGTACGCA 61.075 66.667 0.00 0.00 0.00 5.24
152 5791 2.184579 GAGCAGGGAGTACGCACC 59.815 66.667 0.00 0.00 0.00 5.01
216 5858 4.619160 CGATAGCATCTCATTGAATCCCGA 60.619 45.833 0.00 0.00 0.00 5.14
246 5888 1.812571 CCAACCATCTCTTCAAACCGG 59.187 52.381 0.00 0.00 0.00 5.28
268 5910 0.111061 GCTGCCCATATGGTCCATCA 59.889 55.000 20.46 8.85 36.04 3.07
269 5911 1.272313 GCTGCCCATATGGTCCATCAT 60.272 52.381 20.46 0.00 36.04 2.45
270 5912 2.719739 CTGCCCATATGGTCCATCATC 58.280 52.381 20.46 0.00 36.04 2.92
271 5913 1.355381 TGCCCATATGGTCCATCATCC 59.645 52.381 20.46 0.00 36.04 3.51
272 5914 1.637553 GCCCATATGGTCCATCATCCT 59.362 52.381 20.46 0.00 36.04 3.24
273 5915 2.619849 GCCCATATGGTCCATCATCCTG 60.620 54.545 20.46 1.69 36.04 3.86
274 5916 2.025605 CCCATATGGTCCATCATCCTGG 60.026 54.545 20.46 8.65 37.66 4.45
275 5917 2.619849 CCATATGGTCCATCATCCTGGC 60.620 54.545 14.09 0.00 36.16 4.85
276 5918 0.686789 TATGGTCCATCATCCTGGCG 59.313 55.000 7.92 0.00 36.16 5.69
277 5919 1.348008 ATGGTCCATCATCCTGGCGT 61.348 55.000 0.00 0.00 36.16 5.68
278 5920 1.227674 GGTCCATCATCCTGGCGTC 60.228 63.158 0.00 0.00 36.16 5.19
279 5921 1.690219 GGTCCATCATCCTGGCGTCT 61.690 60.000 0.00 0.00 36.16 4.18
280 5922 0.531532 GTCCATCATCCTGGCGTCTG 60.532 60.000 0.00 0.00 36.16 3.51
281 5923 0.687427 TCCATCATCCTGGCGTCTGA 60.687 55.000 0.00 0.00 36.16 3.27
282 5924 0.178767 CCATCATCCTGGCGTCTGAA 59.821 55.000 0.00 0.00 0.00 3.02
283 5925 1.407299 CCATCATCCTGGCGTCTGAAA 60.407 52.381 0.00 0.00 0.00 2.69
284 5926 2.569059 CATCATCCTGGCGTCTGAAAT 58.431 47.619 0.00 0.00 0.00 2.17
285 5927 3.494924 CCATCATCCTGGCGTCTGAAATA 60.495 47.826 0.00 0.00 0.00 1.40
286 5928 3.179443 TCATCCTGGCGTCTGAAATAC 57.821 47.619 0.00 0.00 0.00 1.89
287 5929 2.766263 TCATCCTGGCGTCTGAAATACT 59.234 45.455 0.00 0.00 0.00 2.12
288 5930 3.197766 TCATCCTGGCGTCTGAAATACTT 59.802 43.478 0.00 0.00 0.00 2.24
289 5931 3.695830 TCCTGGCGTCTGAAATACTTT 57.304 42.857 0.00 0.00 0.00 2.66
290 5932 4.015872 TCCTGGCGTCTGAAATACTTTT 57.984 40.909 0.00 0.00 0.00 2.27
291 5933 3.751175 TCCTGGCGTCTGAAATACTTTTG 59.249 43.478 0.00 0.00 0.00 2.44
292 5934 3.119849 CCTGGCGTCTGAAATACTTTTGG 60.120 47.826 0.00 0.00 0.00 3.28
293 5935 3.745799 TGGCGTCTGAAATACTTTTGGA 58.254 40.909 0.00 0.00 0.00 3.53
294 5936 4.138290 TGGCGTCTGAAATACTTTTGGAA 58.862 39.130 0.00 0.00 0.00 3.53
295 5937 4.580995 TGGCGTCTGAAATACTTTTGGAAA 59.419 37.500 0.00 0.00 0.00 3.13
296 5938 5.154222 GGCGTCTGAAATACTTTTGGAAAG 58.846 41.667 0.00 0.00 0.00 2.62
297 5939 5.048991 GGCGTCTGAAATACTTTTGGAAAGA 60.049 40.000 7.37 0.00 0.00 2.52
298 5940 5.851703 GCGTCTGAAATACTTTTGGAAAGAC 59.148 40.000 7.37 0.00 0.00 3.01
299 5941 6.512741 GCGTCTGAAATACTTTTGGAAAGACA 60.513 38.462 7.37 0.00 0.00 3.41
300 5942 7.414436 CGTCTGAAATACTTTTGGAAAGACAA 58.586 34.615 7.37 0.00 0.00 3.18
301 5943 8.076178 CGTCTGAAATACTTTTGGAAAGACAAT 58.924 33.333 7.37 0.00 0.00 2.71
302 5944 9.750125 GTCTGAAATACTTTTGGAAAGACAATT 57.250 29.630 7.37 2.37 0.00 2.32
764 6431 6.207221 GCCATGTGATAAATGATCCACACATA 59.793 38.462 0.00 0.00 43.74 2.29
766 6433 8.294577 CCATGTGATAAATGATCCACACATAAG 58.705 37.037 0.00 0.00 43.74 1.73
767 6434 7.806409 TGTGATAAATGATCCACACATAAGG 57.194 36.000 0.00 0.00 34.19 2.69
768 6435 7.572814 TGTGATAAATGATCCACACATAAGGA 58.427 34.615 0.00 0.00 38.50 3.36
769 6436 8.052141 TGTGATAAATGATCCACACATAAGGAA 58.948 33.333 0.00 0.00 37.48 3.36
770 6437 9.071276 GTGATAAATGATCCACACATAAGGAAT 57.929 33.333 0.00 0.00 37.48 3.01
771 6438 9.070179 TGATAAATGATCCACACATAAGGAATG 57.930 33.333 0.00 0.00 37.48 2.67
772 6439 9.288576 GATAAATGATCCACACATAAGGAATGA 57.711 33.333 0.00 0.00 39.07 2.57
773 6440 7.959658 AAATGATCCACACATAAGGAATGAA 57.040 32.000 0.00 0.00 39.07 2.57
774 6441 8.543293 AAATGATCCACACATAAGGAATGAAT 57.457 30.769 0.00 0.00 39.07 2.57
775 6442 9.645128 AAATGATCCACACATAAGGAATGAATA 57.355 29.630 0.00 0.00 39.07 1.75
776 6443 9.818270 AATGATCCACACATAAGGAATGAATAT 57.182 29.630 0.00 0.00 39.07 1.28
777 6444 9.818270 ATGATCCACACATAAGGAATGAATATT 57.182 29.630 0.00 0.00 39.07 1.28
778 6445 9.645128 TGATCCACACATAAGGAATGAATATTT 57.355 29.630 0.00 0.00 39.07 1.40
936 6603 1.144913 AGCAAAGTTGGCTTCCCTACA 59.855 47.619 0.00 0.00 38.81 2.74
951 6618 2.498481 CCCTACACACCGATAACAAGGA 59.502 50.000 0.00 0.00 0.00 3.36
1011 6678 0.609957 TCTCCACAATGCTGGCTTGG 60.610 55.000 8.65 0.00 0.00 3.61
1087 6754 0.951040 GACCAAGAGCAAGGTCCACG 60.951 60.000 0.00 0.00 46.79 4.94
1106 6773 1.374631 GTGGCACGTGCTCATCAGA 60.375 57.895 36.84 10.62 41.70 3.27
1272 6939 2.994995 AGCGTCCACGTCATCCCA 60.995 61.111 0.36 0.00 42.22 4.37
1332 6999 4.192317 AGCAAGACAAAAACTTCTCGTCT 58.808 39.130 0.00 0.00 38.55 4.18
1335 7002 4.043037 AGACAAAAACTTCTCGTCTCGT 57.957 40.909 0.00 0.00 31.39 4.18
1551 7218 0.323629 GGGGGTCGTCATCTTCAACA 59.676 55.000 0.00 0.00 0.00 3.33
1704 7371 0.250901 AGCACATGGACGCTTCCTTT 60.251 50.000 11.01 0.00 43.31 3.11
1830 7497 5.356190 CACAAAAGTGGATAGACTGCATGAT 59.644 40.000 0.00 0.00 0.00 2.45
1959 7626 2.744202 GTTGCTCAACATCGATGAGGTT 59.256 45.455 31.33 12.92 43.60 3.50
2060 7727 4.473196 TGACCAATTGCCTCATAGTCCTAA 59.527 41.667 0.00 0.00 0.00 2.69
2062 7729 6.018433 ACCAATTGCCTCATAGTCCTAAAT 57.982 37.500 0.00 0.00 0.00 1.40
2471 8139 0.980231 GGCAGTGGAGGAGATGGACT 60.980 60.000 0.00 0.00 0.00 3.85
2556 8224 1.737236 GTGCATACGTGAGGCATTTCA 59.263 47.619 12.60 0.00 40.05 2.69
2584 8252 1.209504 CCAATCGCTCCCTTCAACCTA 59.790 52.381 0.00 0.00 0.00 3.08
2993 8661 2.045524 ACCTCTACCCTCTCATGCATG 58.954 52.381 21.07 21.07 0.00 4.06
2994 8662 2.045524 CCTCTACCCTCTCATGCATGT 58.954 52.381 25.43 8.46 0.00 3.21
3000 8668 2.306805 ACCCTCTCATGCATGTTTGAGA 59.693 45.455 29.75 23.74 44.55 3.27
3031 8699 3.261643 AGCTATGAATCACCGATATGGCA 59.738 43.478 0.00 0.00 43.94 4.92
3187 8859 9.643693 AGAAATTCAAAATTTTCTACGCATCAT 57.356 25.926 0.00 0.00 39.70 2.45
3202 8874 8.960591 TCTACGCATCATCAAGATCAATCTATA 58.039 33.333 0.00 0.00 35.76 1.31
3317 8990 3.526931 ACTCGTCGTGATCCAAATCAT 57.473 42.857 0.56 0.00 43.62 2.45
3420 9093 2.834113 CAAGGGGAGAAGGAGAGGTTA 58.166 52.381 0.00 0.00 0.00 2.85
3494 9167 1.609501 TACTCCAGCAGGGCTTCGT 60.610 57.895 0.00 0.00 36.40 3.85
3582 9255 1.228552 GCAGCCCCAAGTCCTCAAA 60.229 57.895 0.00 0.00 0.00 2.69
3700 9373 3.706373 GAGAGGGAGGCGCACCAA 61.706 66.667 21.05 0.00 39.06 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 5645 9.504708 TTCGGGATTTCAATAAAGTTACAACTA 57.495 29.630 0.00 0.00 38.57 2.24
100 5738 1.377725 GGCTGGACCATGTCTGTGG 60.378 63.158 0.00 0.00 45.04 4.17
130 5768 2.363925 GTACTCCCTGCTCCCCGT 60.364 66.667 0.00 0.00 0.00 5.28
139 5778 4.691359 ACGGGGTGCGTACTCCCT 62.691 66.667 17.66 2.05 45.27 4.20
268 5910 3.914426 AAGTATTTCAGACGCCAGGAT 57.086 42.857 0.00 0.00 0.00 3.24
269 5911 3.695830 AAAGTATTTCAGACGCCAGGA 57.304 42.857 0.00 0.00 27.08 3.86
270 5912 3.119849 CCAAAAGTATTTCAGACGCCAGG 60.120 47.826 0.00 0.00 37.28 4.45
271 5913 3.751175 TCCAAAAGTATTTCAGACGCCAG 59.249 43.478 0.00 0.00 37.28 4.85
272 5914 3.745799 TCCAAAAGTATTTCAGACGCCA 58.254 40.909 0.00 0.00 37.28 5.69
273 5915 4.759516 TTCCAAAAGTATTTCAGACGCC 57.240 40.909 0.00 0.00 37.28 5.68
274 5916 5.851703 GTCTTTCCAAAAGTATTTCAGACGC 59.148 40.000 0.00 0.00 37.28 5.19
275 5917 6.954944 TGTCTTTCCAAAAGTATTTCAGACG 58.045 36.000 0.00 0.00 37.28 4.18
276 5918 9.750125 AATTGTCTTTCCAAAAGTATTTCAGAC 57.250 29.630 0.00 0.00 37.28 3.51
290 5932 9.565090 CAGGATCTAATCATAATTGTCTTTCCA 57.435 33.333 0.00 0.00 0.00 3.53
291 5933 9.007901 CCAGGATCTAATCATAATTGTCTTTCC 57.992 37.037 0.00 0.00 0.00 3.13
292 5934 8.510505 GCCAGGATCTAATCATAATTGTCTTTC 58.489 37.037 0.00 0.00 0.00 2.62
293 5935 7.173907 CGCCAGGATCTAATCATAATTGTCTTT 59.826 37.037 0.00 0.00 0.00 2.52
294 5936 6.652481 CGCCAGGATCTAATCATAATTGTCTT 59.348 38.462 0.00 0.00 0.00 3.01
295 5937 6.169094 CGCCAGGATCTAATCATAATTGTCT 58.831 40.000 0.00 0.00 0.00 3.41
296 5938 5.934625 ACGCCAGGATCTAATCATAATTGTC 59.065 40.000 0.00 0.00 0.00 3.18
297 5939 5.869579 ACGCCAGGATCTAATCATAATTGT 58.130 37.500 0.00 0.00 0.00 2.71
298 5940 6.091849 CAGACGCCAGGATCTAATCATAATTG 59.908 42.308 0.00 0.00 0.00 2.32
299 5941 6.014242 TCAGACGCCAGGATCTAATCATAATT 60.014 38.462 0.00 0.00 0.00 1.40
300 5942 5.481824 TCAGACGCCAGGATCTAATCATAAT 59.518 40.000 0.00 0.00 0.00 1.28
301 5943 4.832823 TCAGACGCCAGGATCTAATCATAA 59.167 41.667 0.00 0.00 0.00 1.90
302 5944 4.407365 TCAGACGCCAGGATCTAATCATA 58.593 43.478 0.00 0.00 0.00 2.15
303 5945 3.234353 TCAGACGCCAGGATCTAATCAT 58.766 45.455 0.00 0.00 0.00 2.45
304 5946 2.666317 TCAGACGCCAGGATCTAATCA 58.334 47.619 0.00 0.00 0.00 2.57
305 5947 3.735237 TTCAGACGCCAGGATCTAATC 57.265 47.619 0.00 0.00 0.00 1.75
306 5948 4.696479 ATTTCAGACGCCAGGATCTAAT 57.304 40.909 0.00 0.00 0.00 1.73
307 5949 4.649674 AGTATTTCAGACGCCAGGATCTAA 59.350 41.667 0.00 0.00 0.00 2.10
308 5950 4.215908 AGTATTTCAGACGCCAGGATCTA 58.784 43.478 0.00 0.00 0.00 1.98
309 5951 3.034635 AGTATTTCAGACGCCAGGATCT 58.965 45.455 0.00 0.00 0.00 2.75
310 5952 3.460857 AGTATTTCAGACGCCAGGATC 57.539 47.619 0.00 0.00 0.00 3.36
495 6139 6.928979 TCCAAACGTAATCAAAACAGAAGA 57.071 33.333 0.00 0.00 0.00 2.87
496 6140 8.717821 TCTATCCAAACGTAATCAAAACAGAAG 58.282 33.333 0.00 0.00 0.00 2.85
580 6224 6.378710 AGTCCAAACAGAAAAAGCTTCTAC 57.621 37.500 0.00 0.00 0.00 2.59
722 6376 8.700722 TCACATGGCATTTCAAATGTATTTAC 57.299 30.769 11.80 0.00 32.15 2.01
893 6560 2.113433 GTGCTGCTCTGCCCATGAG 61.113 63.158 0.00 0.00 34.87 2.90
936 6603 3.418684 AGCTTTCCTTGTTATCGGTGT 57.581 42.857 0.00 0.00 0.00 4.16
951 6618 0.674895 CAGGCTTGCGAGGTAGCTTT 60.675 55.000 2.37 0.00 37.54 3.51
1011 6678 0.249031 GGGACACAACAAAGCAGCAC 60.249 55.000 0.00 0.00 0.00 4.40
1087 6754 2.358615 TGATGAGCACGTGCCACC 60.359 61.111 35.51 23.98 43.38 4.61
1106 6773 2.045926 GTGGAAGCGGCACCATCT 60.046 61.111 18.62 0.00 38.48 2.90
1255 6922 1.899437 ATTGGGATGACGTGGACGCT 61.899 55.000 0.00 0.00 44.43 5.07
1267 6934 2.582172 TCTTGGGACATGTGATTGGGAT 59.418 45.455 1.15 0.00 39.30 3.85
1272 6939 2.292267 GCGATCTTGGGACATGTGATT 58.708 47.619 1.15 0.00 39.30 2.57
1314 6981 4.043037 ACGAGACGAGAAGTTTTTGTCT 57.957 40.909 14.61 14.61 42.25 3.41
1332 6999 2.649034 GCGAAGGTGAGTGGACGA 59.351 61.111 0.00 0.00 0.00 4.20
1335 7002 2.283529 GGAGGCGAAGGTGAGTGGA 61.284 63.158 0.00 0.00 0.00 4.02
1551 7218 0.968901 TGACGTTGGCTAGTCCCGAT 60.969 55.000 10.08 0.00 36.61 4.18
1616 7283 1.961277 CGTTGGCCGAAGACAAGCT 60.961 57.895 0.00 0.00 39.56 3.74
1635 7302 1.403687 GCTGAGGCTCCCCGAAGTAT 61.404 60.000 12.86 0.00 35.76 2.12
1740 7407 1.632409 AGTAGACACGGGAGGTAGTCA 59.368 52.381 0.00 0.00 32.52 3.41
1830 7497 0.317160 AACGCTCTTCGATGACCACA 59.683 50.000 0.00 0.00 41.67 4.17
1959 7626 3.181449 TGCTTACCTTGGACTGTGCTTTA 60.181 43.478 0.00 0.00 0.00 1.85
2060 7727 7.232737 TCTCATGGATGACGTATTAGTACCATT 59.767 37.037 0.00 0.00 33.65 3.16
2062 7729 6.066032 TCTCATGGATGACGTATTAGTACCA 58.934 40.000 0.00 0.00 32.50 3.25
2158 7825 4.475944 CCTTTTCTAACACCTGCGAAATG 58.524 43.478 0.00 0.00 0.00 2.32
2330 7998 7.864379 GCATTCCATGGAGATAAATGTAAGTTG 59.136 37.037 15.53 0.00 31.52 3.16
2471 8139 4.308458 CTCGCGACCAACCACCCA 62.308 66.667 3.71 0.00 0.00 4.51
2497 8165 1.293924 GCATGATGTCCGACTCTTGG 58.706 55.000 0.00 0.00 0.00 3.61
2556 8224 2.670148 GGAGCGATTGGGTGGAGGT 61.670 63.158 0.00 0.00 0.00 3.85
2880 8548 2.148723 ATTGATGGCCGACACCCCAA 62.149 55.000 0.00 0.00 34.25 4.12
2993 8661 9.427127 GATTCATAGCTCGTTATTTTCTCAAAC 57.573 33.333 0.00 0.00 0.00 2.93
2994 8662 9.161629 TGATTCATAGCTCGTTATTTTCTCAAA 57.838 29.630 0.00 0.00 0.00 2.69
3000 8668 6.046593 TCGGTGATTCATAGCTCGTTATTTT 58.953 36.000 0.00 0.00 0.00 1.82
3103 8774 5.576447 ATCAAAGTGGAACGAAACAAAGT 57.424 34.783 0.00 0.00 45.86 2.66
3202 8874 2.041350 TCCCTCGTTGGTAGACTTCTCT 59.959 50.000 0.00 0.00 0.00 3.10
3317 8990 2.481276 CGTTTGGCACTAGGATCATCGA 60.481 50.000 0.00 0.00 0.00 3.59
3420 9093 0.252881 TGCTGGATGGAGTCTTCCCT 60.253 55.000 9.34 0.00 43.33 4.20
3494 9167 1.664649 CGTCTCTTGCGGTGCTTGA 60.665 57.895 0.00 0.00 0.00 3.02
3582 9255 4.935840 CCCCTCCCTCTCCCCTATATATAT 59.064 50.000 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.