Multiple sequence alignment - TraesCS6A01G001200

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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 TraesCS6A01G001200 chr6A 100.000 1608 0 0 1 1608 736473 734866 0.000000e+00 2970.0
1 TraesCS6A01G001200 chr6A 100.000 1291 0 0 1970 3260 734504 733214 0.000000e+00 2385.0
2 TraesCS6A01G001200 chr6A 83.387 1541 148 55 91 1577 690067 688581 0.000000e+00 1328.0
3 TraesCS6A01G001200 chr6A 88.921 686 66 2 1970 2655 688291 687616 0.000000e+00 837.0
4 TraesCS6A01G001200 chr6A 92.446 278 21 0 1331 1608 688570 688293 6.550000e-107 398.0
5 TraesCS6A01G001200 chr6A 94.737 190 10 0 1419 1608 734503 734314 2.460000e-76 296.0
6 TraesCS6A01G001200 chr6A 94.737 190 10 0 1971 2160 735055 734866 2.460000e-76 296.0
7 TraesCS6A01G001200 chr6A 88.073 218 26 0 1391 1608 688414 688197 3.230000e-65 259.0
8 TraesCS6A01G001200 chr6A 78.624 407 69 11 1205 1608 688492 688101 1.500000e-63 254.0
9 TraesCS6A01G001200 chr6A 85.075 134 17 3 2778 2910 687490 687359 2.040000e-27 134.0
10 TraesCS6A01G001200 chr6B 90.653 888 62 14 1 879 3869259 3870134 0.000000e+00 1160.0
11 TraesCS6A01G001200 chr6B 87.333 750 84 5 622 1369 4175488 4174748 0.000000e+00 848.0
12 TraesCS6A01G001200 chr6B 87.808 689 78 4 1970 2655 4163634 4162949 0.000000e+00 802.0
13 TraesCS6A01G001200 chr6B 91.552 580 46 1 972 1551 3870135 3870711 0.000000e+00 797.0
14 TraesCS6A01G001200 chr6B 90.097 616 39 7 2045 2655 4174154 4173556 0.000000e+00 780.0
15 TraesCS6A01G001200 chr6B 87.970 532 54 5 838 1367 4164356 4163833 1.280000e-173 619.0
16 TraesCS6A01G001200 chr6B 87.925 530 54 6 2734 3260 4173504 4172982 1.660000e-172 616.0
17 TraesCS6A01G001200 chr6B 88.539 349 35 4 2304 2652 3871507 3871850 5.030000e-113 418.0
18 TraesCS6A01G001200 chr6B 80.692 549 55 26 56 580 4176181 4175660 2.370000e-101 379.0
19 TraesCS6A01G001200 chr6B 83.523 352 58 0 1196 1547 4174850 4174499 2.420000e-86 329.0
20 TraesCS6A01G001200 chr6B 93.194 191 13 0 1415 1605 3871139 3871329 6.890000e-72 281.0
21 TraesCS6A01G001200 chr6B 92.308 195 15 0 1971 2165 3871143 3871337 8.910000e-71 278.0
22 TraesCS6A01G001200 chr6B 90.341 176 17 0 1971 2146 4163729 4163554 7.030000e-57 231.0
23 TraesCS6A01G001200 chr6B 85.496 131 17 2 2781 2910 4162819 4162690 5.670000e-28 135.0
24 TraesCS6A01G001200 chr6B 97.368 38 1 0 1 38 4165955 4165918 7.550000e-07 65.8
25 TraesCS6A01G001200 chr6D 88.875 818 77 8 796 1608 4202754 4203562 0.000000e+00 994.0
26 TraesCS6A01G001200 chr6D 89.557 699 45 15 1979 2655 4203897 4204589 0.000000e+00 861.0
27 TraesCS6A01G001200 chr6D 89.112 698 50 13 1979 2655 2167641 2168333 0.000000e+00 845.0
28 TraesCS6A01G001200 chr6D 80.526 1217 111 56 209 1369 2166218 2167364 0.000000e+00 819.0
29 TraesCS6A01G001200 chr6D 89.434 530 46 5 2734 3260 4204641 4205163 0.000000e+00 660.0
30 TraesCS6A01G001200 chr6D 89.908 327 25 3 2734 3059 2168385 2168704 6.510000e-112 414.0
31 TraesCS6A01G001200 chr6D 93.564 202 7 3 1 200 4201575 4201772 2.460000e-76 296.0
32 TraesCS6A01G001200 chr6D 92.079 202 12 4 1 200 2165636 2165835 6.890000e-72 281.0
33 TraesCS6A01G001200 chr6D 88.542 192 20 1 1971 2160 4203371 4203562 7.030000e-57 231.0
34 TraesCS6A01G001200 chr6D 100.000 36 0 0 1970 2005 2167668 2167703 2.100000e-07 67.6
35 TraesCS6A01G001200 chr6D 100.000 36 0 0 1970 2005 4203924 4203959 2.100000e-07 67.6


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 TraesCS6A01G001200 chr6A 733214 736473 3259 True 1486.750000 2970 97.368500 1 3260 4 chr6A.!!$R2 3259
1 TraesCS6A01G001200 chr6A 687359 690067 2708 True 535.000000 1328 86.087667 91 2910 6 chr6A.!!$R1 2819
2 TraesCS6A01G001200 chr6B 4172982 4176181 3199 True 590.400000 848 85.914000 56 3260 5 chr6B.!!$R2 3204
3 TraesCS6A01G001200 chr6B 3869259 3871850 2591 False 586.800000 1160 91.249200 1 2652 5 chr6B.!!$F1 2651
4 TraesCS6A01G001200 chr6B 4162690 4165955 3265 True 370.560000 802 89.796600 1 2910 5 chr6B.!!$R1 2909
5 TraesCS6A01G001200 chr6D 4201575 4205163 3588 False 518.266667 994 91.662000 1 3260 6 chr6D.!!$F2 3259
6 TraesCS6A01G001200 chr6D 2165636 2168704 3068 False 485.320000 845 90.325000 1 3059 5 chr6D.!!$F1 3058

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
848 2421 0.401738 TATAAGGGGAGGCATGCAGC 59.598 55.0 21.36 10.33 44.65 5.25 F
966 2541 0.829990 TATGAAGATGGAGGCGCACA 59.170 50.0 10.83 5.27 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 4045 0.038166 GTGGGTTTGGATCAGGCTGA 59.962 55.0 21.19 21.19 0.00 4.26 R
2659 5498 0.247894 GCGTTGAATCGCGCCATAAA 60.248 50.0 0.00 0.00 46.93 1.40 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
184 199 7.956420 ATGTGTTGTTTGAGTCGTAGAATAA 57.044 32.000 0.00 0.00 39.69 1.40
236 632 8.642432 CATAGGACTCATTTACACTAGATTCCA 58.358 37.037 0.00 0.00 33.65 3.53
239 639 8.865090 AGGACTCATTTACACTAGATTCCATAG 58.135 37.037 0.00 0.00 33.65 2.23
391 806 6.139048 AGGTGTGGTGTGTTAATACAAAAC 57.861 37.500 6.62 8.76 35.69 2.43
636 1894 6.878389 GGACAATTTAAAATTCCCATGCTCAA 59.122 34.615 0.00 0.00 0.00 3.02
650 1909 3.165058 TGCTCAAAGCCATCTACTACG 57.835 47.619 0.00 0.00 41.51 3.51
658 1917 3.687125 AGCCATCTACTACGCTGCTATA 58.313 45.455 0.00 0.00 0.00 1.31
745 2004 1.847328 TGCTCTCCCACGATCAACTA 58.153 50.000 0.00 0.00 0.00 2.24
769 2028 0.687354 ATGCCACATCTATCCGGACC 59.313 55.000 6.12 0.00 0.00 4.46
775 2034 1.485066 ACATCTATCCGGACCAACACC 59.515 52.381 6.12 0.00 0.00 4.16
842 2415 1.424638 GAGCACTATAAGGGGAGGCA 58.575 55.000 0.00 0.00 0.00 4.75
848 2421 0.401738 TATAAGGGGAGGCATGCAGC 59.598 55.000 21.36 10.33 44.65 5.25
966 2541 0.829990 TATGAAGATGGAGGCGCACA 59.170 50.000 10.83 5.27 0.00 4.57
994 2579 1.792006 AGTACGTAGCAACACAAGCC 58.208 50.000 0.00 0.00 0.00 4.35
1097 2682 4.648626 TGCTGCAGGGAGGCACAC 62.649 66.667 17.12 0.00 39.25 3.82
1118 2703 3.270960 ACCTTGATCACTAGAGACCCTCT 59.729 47.826 0.00 1.86 43.83 3.69
1179 2764 5.104151 ACCAGGAAAACAACCAAATCCAAAT 60.104 36.000 0.00 0.00 32.47 2.32
1191 2776 5.180271 CCAAATCCAAATCCTCAACCATTG 58.820 41.667 0.00 0.00 0.00 2.82
1251 2836 2.582436 CCGCAACCACTACCCGAT 59.418 61.111 0.00 0.00 0.00 4.18
1261 2846 3.052642 ACCACTACCCGATCCTAAACCTA 60.053 47.826 0.00 0.00 0.00 3.08
1264 2849 5.279356 CCACTACCCGATCCTAAACCTAATC 60.279 48.000 0.00 0.00 0.00 1.75
1284 2869 1.042559 CAAACCCACAACCACTGCCT 61.043 55.000 0.00 0.00 0.00 4.75
1305 2890 2.225091 TGAGCCACAACCTGATCCAAAT 60.225 45.455 0.00 0.00 0.00 2.32
1409 2994 2.123468 AAACCCAAACCCGCAGCT 60.123 55.556 0.00 0.00 0.00 4.24
1498 3094 3.226777 CAACCATTACCAGACCCAAACA 58.773 45.455 0.00 0.00 0.00 2.83
1521 3119 2.282816 CCATTGCCGGACCCACAA 60.283 61.111 5.05 0.00 0.00 3.33
1581 3551 3.312890 TGATCCAAACCCACAACCATTT 58.687 40.909 0.00 0.00 0.00 2.32
1596 3571 0.887933 CATTTCCAGACCCAAACCCG 59.112 55.000 0.00 0.00 0.00 5.28
2010 4045 1.916181 CCTCAACCATTACCAGGACCT 59.084 52.381 0.00 0.00 0.00 3.85
2073 4795 2.282816 CCATTGCCGGACCCACAA 60.283 61.111 5.05 0.00 0.00 3.33
2233 5018 4.058124 GGAAAAGGAAAATGTGGAAGCAC 58.942 43.478 0.00 0.00 0.00 4.40
2268 5056 0.103026 CGCTGGGATGAGATGTTCGA 59.897 55.000 0.00 0.00 0.00 3.71
2281 5069 1.705256 TGTTCGAGTACATCAACCGC 58.295 50.000 0.00 0.00 0.00 5.68
2297 5085 4.103357 CAACCGCGCCAGATATAGTATAC 58.897 47.826 0.00 0.00 0.00 1.47
2300 5088 3.303197 CCGCGCCAGATATAGTATACTCG 60.303 52.174 9.12 5.36 0.00 4.18
2315 5137 7.762588 AGTATACTCGTGACTTATATTGCCT 57.237 36.000 0.00 0.00 0.00 4.75
2365 5188 2.291153 CCCACCACCATCAAGTCATTCT 60.291 50.000 0.00 0.00 0.00 2.40
2366 5189 2.751259 CCACCACCATCAAGTCATTCTG 59.249 50.000 0.00 0.00 0.00 3.02
2454 5277 6.769512 TCTGACTTACTTTTCTGGCTTGTAT 58.230 36.000 0.00 0.00 0.00 2.29
2458 5281 6.485171 ACTTACTTTTCTGGCTTGTATGGAT 58.515 36.000 0.00 0.00 0.00 3.41
2459 5282 6.375455 ACTTACTTTTCTGGCTTGTATGGATG 59.625 38.462 0.00 0.00 0.00 3.51
2462 5285 6.662755 ACTTTTCTGGCTTGTATGGATGATA 58.337 36.000 0.00 0.00 0.00 2.15
2605 5444 9.678941 AAGCTTTAAATTTGTGCTAGTAAGAAC 57.321 29.630 12.48 0.00 33.28 3.01
2624 5463 7.571080 AAGAACGGTGGAAACTTATTTACAA 57.429 32.000 0.00 0.00 40.45 2.41
2655 5494 7.619964 TCCTAGCGGAAATTTAAACTTAAGG 57.380 36.000 7.53 0.00 36.03 2.69
2656 5495 7.396418 TCCTAGCGGAAATTTAAACTTAAGGA 58.604 34.615 7.53 0.00 36.03 3.36
2657 5496 7.884354 TCCTAGCGGAAATTTAAACTTAAGGAA 59.116 33.333 7.53 0.00 36.03 3.36
2658 5497 8.517056 CCTAGCGGAAATTTAAACTTAAGGAAA 58.483 33.333 7.53 4.84 0.00 3.13
2668 5507 8.468720 TTTAAACTTAAGGAAATTTATGGCGC 57.531 30.769 7.53 0.00 0.00 6.53
2669 5508 4.287238 ACTTAAGGAAATTTATGGCGCG 57.713 40.909 0.00 0.00 0.00 6.86
2670 5509 3.942748 ACTTAAGGAAATTTATGGCGCGA 59.057 39.130 12.10 0.00 0.00 5.87
2671 5510 4.578928 ACTTAAGGAAATTTATGGCGCGAT 59.421 37.500 12.10 10.52 0.00 4.58
2672 5511 5.067283 ACTTAAGGAAATTTATGGCGCGATT 59.933 36.000 12.10 0.00 0.00 3.34
2673 5512 3.626028 AGGAAATTTATGGCGCGATTC 57.374 42.857 12.10 1.91 0.00 2.52
2674 5513 2.948979 AGGAAATTTATGGCGCGATTCA 59.051 40.909 12.10 4.76 0.00 2.57
2675 5514 3.380004 AGGAAATTTATGGCGCGATTCAA 59.620 39.130 12.10 4.69 0.00 2.69
2676 5515 3.485743 GGAAATTTATGGCGCGATTCAAC 59.514 43.478 12.10 0.00 0.00 3.18
2677 5516 2.383298 ATTTATGGCGCGATTCAACG 57.617 45.000 12.10 0.00 0.00 4.10
2715 5554 3.903876 GCATGGTGCACTCAATACG 57.096 52.632 17.98 5.22 44.26 3.06
2716 5555 1.086696 GCATGGTGCACTCAATACGT 58.913 50.000 17.98 0.00 44.26 3.57
2718 5557 2.675844 GCATGGTGCACTCAATACGTAA 59.324 45.455 17.98 0.00 44.26 3.18
2919 5795 3.914435 AGTATTTTGTCTAGTGGGGGTGT 59.086 43.478 0.00 0.00 0.00 4.16
2920 5796 5.046159 CAGTATTTTGTCTAGTGGGGGTGTA 60.046 44.000 0.00 0.00 0.00 2.90
2921 5797 5.729718 AGTATTTTGTCTAGTGGGGGTGTAT 59.270 40.000 0.00 0.00 0.00 2.29
2922 5798 3.992943 TTTGTCTAGTGGGGGTGTATG 57.007 47.619 0.00 0.00 0.00 2.39
2929 5805 2.349755 GGGGGTGTATGTGCACGT 59.650 61.111 17.19 17.19 40.08 4.49
2935 5811 2.603652 GGGTGTATGTGCACGTTTGTTC 60.604 50.000 18.34 3.95 40.08 3.18
2938 5814 2.546368 TGTATGTGCACGTTTGTTCCTC 59.454 45.455 18.34 0.00 0.00 3.71
2972 5848 3.247948 TGCCTGGATTATGCCATCAAT 57.752 42.857 0.00 0.00 37.30 2.57
3019 5895 3.388841 TCCTTCTTGGAGGGTCGC 58.611 61.111 0.00 0.00 40.56 5.19
3033 5909 4.742201 TCGCCGTGCAGCTCTTCC 62.742 66.667 0.00 0.00 0.00 3.46
3040 5916 1.093159 GTGCAGCTCTTCCATCTTGG 58.907 55.000 0.00 0.00 39.43 3.61
3041 5917 0.694771 TGCAGCTCTTCCATCTTGGT 59.305 50.000 0.00 0.00 39.03 3.67
3048 5924 2.307098 CTCTTCCATCTTGGTCACCCTT 59.693 50.000 0.00 0.00 39.03 3.95
3059 5935 1.340114 GGTCACCCTTGGGATGTCTTC 60.340 57.143 13.39 0.00 0.00 2.87
3060 5936 1.351017 GTCACCCTTGGGATGTCTTCA 59.649 52.381 13.39 0.00 0.00 3.02
3061 5937 1.630369 TCACCCTTGGGATGTCTTCAG 59.370 52.381 13.39 0.00 0.00 3.02
3062 5938 1.352352 CACCCTTGGGATGTCTTCAGT 59.648 52.381 13.39 0.00 0.00 3.41
3063 5939 2.571653 CACCCTTGGGATGTCTTCAGTA 59.428 50.000 13.39 0.00 0.00 2.74
3075 5952 5.562298 TGTCTTCAGTAAAAGCCTAAGGT 57.438 39.130 0.00 0.00 0.00 3.50
3084 5961 0.038310 AAGCCTAAGGTCCCTGTTGC 59.962 55.000 0.00 0.00 0.00 4.17
3085 5962 1.133809 AGCCTAAGGTCCCTGTTGCA 61.134 55.000 0.00 0.00 0.00 4.08
3103 5980 1.604604 CAGGGTCGGACAACATTGTT 58.395 50.000 10.76 0.00 42.43 2.83
3104 5981 2.773487 CAGGGTCGGACAACATTGTTA 58.227 47.619 10.76 0.00 42.43 2.41
3147 6024 0.179189 GGCGCCGTCTTGAAGATTTG 60.179 55.000 12.58 0.00 0.00 2.32
3157 6034 3.397618 TCTTGAAGATTTGTTCCCCTCCA 59.602 43.478 0.00 0.00 0.00 3.86
3177 6054 3.499563 CCACACTTTTCCTGGGTTGGATA 60.500 47.826 0.00 0.00 35.83 2.59
3182 6059 2.435372 TTCCTGGGTTGGATATGCAC 57.565 50.000 0.00 0.00 35.83 4.57
3186 6063 2.624838 CCTGGGTTGGATATGCACATTC 59.375 50.000 0.00 0.00 0.00 2.67
3204 6081 1.302431 CTCACGGTTGGATGGTGCA 60.302 57.895 0.00 0.00 0.00 4.57
3209 6086 1.604593 GGTTGGATGGTGCACAGCT 60.605 57.895 20.43 1.44 35.35 4.24
3222 6099 1.803998 GCACAGCTGATGATGCGAGTA 60.804 52.381 23.35 0.00 31.91 2.59
3234 6111 0.882927 TGCGAGTAGTTGGTGTTGGC 60.883 55.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
236 632 9.816354 GTTTGCATGTATGGGTTTATTTTCTAT 57.184 29.630 0.00 0.00 0.00 1.98
239 639 7.102993 AGGTTTGCATGTATGGGTTTATTTTC 58.897 34.615 0.00 0.00 0.00 2.29
248 648 3.091545 ACTTGAGGTTTGCATGTATGGG 58.908 45.455 0.00 0.00 0.00 4.00
253 653 6.294731 GGATTCTAAACTTGAGGTTTGCATGT 60.295 38.462 2.71 0.00 46.30 3.21
273 674 9.221775 GTTTTATTGTACACAATCATCGGATTC 57.778 33.333 10.74 0.00 44.67 2.52
294 700 6.121776 TGAAGAAGCCTGTAGGATGTTTTA 57.878 37.500 1.17 0.00 37.39 1.52
357 770 3.023832 ACACCACACCTTTTTCTTGAGG 58.976 45.455 0.00 0.00 39.02 3.86
464 1588 3.196254 CCAGCCCAAATGCAGTAGAAATT 59.804 43.478 0.00 0.00 0.00 1.82
612 1743 7.903995 TTGAGCATGGGAATTTTAAATTGTC 57.096 32.000 7.72 0.92 0.00 3.18
624 1882 1.006281 AGATGGCTTTGAGCATGGGAA 59.994 47.619 2.04 0.00 44.75 3.97
626 1884 1.952296 GTAGATGGCTTTGAGCATGGG 59.048 52.381 2.04 0.00 44.75 4.00
636 1894 1.115467 AGCAGCGTAGTAGATGGCTT 58.885 50.000 0.00 0.00 32.46 4.35
650 1909 9.390795 CAATAATTCTGTTGAACATATAGCAGC 57.609 33.333 0.00 0.00 34.71 5.25
769 2028 1.133792 AGGGAAGTTGGAGTGGTGTTG 60.134 52.381 0.00 0.00 0.00 3.33
775 2034 5.941555 AGTTATCTAGGGAAGTTGGAGTG 57.058 43.478 0.00 0.00 0.00 3.51
848 2421 0.612732 TGCCTTTTGGAGATGCAGGG 60.613 55.000 0.00 0.00 44.07 4.45
851 2424 1.001181 GCTTTGCCTTTTGGAGATGCA 59.999 47.619 0.00 0.00 44.07 3.96
940 2515 6.036517 GTGCGCCTCCATCTTCATATTTATAG 59.963 42.308 4.18 0.00 0.00 1.31
949 2524 1.375908 GTGTGCGCCTCCATCTTCA 60.376 57.895 4.18 0.00 0.00 3.02
956 2531 4.030452 GCAAGTGTGTGCGCCTCC 62.030 66.667 4.18 0.00 34.21 4.30
966 2541 2.519377 TGCTACGTACTTGCAAGTGT 57.481 45.000 36.50 28.65 40.07 3.55
994 2579 2.865670 GCTTCCTCATCGTCATGGCTAG 60.866 54.545 0.00 0.00 0.00 3.42
1097 2682 3.909732 AGAGGGTCTCTAGTGATCAAGG 58.090 50.000 7.34 0.00 39.28 3.61
1179 2764 0.038166 GGTCTGGCAATGGTTGAGGA 59.962 55.000 0.00 0.00 0.00 3.71
1191 2776 1.898574 CAGTGGTTGTGGGTCTGGC 60.899 63.158 0.00 0.00 0.00 4.85
1251 2836 4.354387 TGTGGGTTTGGATTAGGTTTAGGA 59.646 41.667 0.00 0.00 0.00 2.94
1261 2846 2.038659 CAGTGGTTGTGGGTTTGGATT 58.961 47.619 0.00 0.00 0.00 3.01
1264 2849 1.441311 GCAGTGGTTGTGGGTTTGG 59.559 57.895 0.00 0.00 0.00 3.28
1284 2869 0.770499 TTGGATCAGGTTGTGGCTCA 59.230 50.000 0.00 0.00 0.00 4.26
1305 2890 1.004277 GGTCCTGGTAATGGTTGAGCA 59.996 52.381 0.00 0.00 0.00 4.26
1387 2972 2.840102 CGGGTTTGGGTTTGGCCA 60.840 61.111 0.00 0.00 39.65 5.36
1388 2973 4.308458 GCGGGTTTGGGTTTGGCC 62.308 66.667 0.00 0.00 0.00 5.36
1409 2994 1.683365 GGCCGTGGGTCTGGTAGTA 60.683 63.158 0.00 0.00 0.00 1.82
1498 3094 1.468506 GGGTCCGGCAATGGTTTTGT 61.469 55.000 0.00 0.00 0.00 2.83
1521 3119 0.759060 GCTGAGGGTTTGGGTTTGGT 60.759 55.000 0.00 0.00 0.00 3.67
1581 3551 0.179012 GTTTCGGGTTTGGGTCTGGA 60.179 55.000 0.00 0.00 0.00 3.86
2010 4045 0.038166 GTGGGTTTGGATCAGGCTGA 59.962 55.000 21.19 21.19 0.00 4.26
2073 4795 0.759060 GCTGAGGGTTTGGGTTTGGT 60.759 55.000 0.00 0.00 0.00 3.67
2211 4996 4.058124 GTGCTTCCACATTTTCCTTTTCC 58.942 43.478 0.00 0.00 41.67 3.13
2233 5018 1.817099 GCGGCTCCTCTTGGATGTG 60.817 63.158 0.00 0.00 42.29 3.21
2268 5056 1.447838 CTGGCGCGGTTGATGTACT 60.448 57.895 8.83 0.00 0.00 2.73
2281 5069 5.581479 AGTCACGAGTATACTATATCTGGCG 59.419 44.000 5.09 5.14 0.00 5.69
2297 5085 3.492383 CAGCAGGCAATATAAGTCACGAG 59.508 47.826 0.00 0.00 0.00 4.18
2300 5088 3.808728 TCCAGCAGGCAATATAAGTCAC 58.191 45.455 0.00 0.00 33.74 3.67
2315 5137 5.321102 ACACACCACTTATTTAATCCAGCA 58.679 37.500 0.00 0.00 0.00 4.41
2454 5277 6.038492 CAGCACACACATACAATTATCATCCA 59.962 38.462 0.00 0.00 0.00 3.41
2458 5281 5.252547 ACCAGCACACACATACAATTATCA 58.747 37.500 0.00 0.00 0.00 2.15
2459 5282 5.818136 ACCAGCACACACATACAATTATC 57.182 39.130 0.00 0.00 0.00 1.75
2462 5285 3.636300 ACAACCAGCACACACATACAATT 59.364 39.130 0.00 0.00 0.00 2.32
2562 5401 4.404185 AGCTTTGGGGTAAATCCTTTCT 57.596 40.909 0.00 0.00 36.25 2.52
2605 5444 5.952526 ACCTTGTAAATAAGTTTCCACCG 57.047 39.130 0.00 0.00 0.00 4.94
2655 5494 3.177643 CGTTGAATCGCGCCATAAATTTC 59.822 43.478 0.00 0.00 0.00 2.17
2656 5495 3.105203 CGTTGAATCGCGCCATAAATTT 58.895 40.909 0.00 0.00 0.00 1.82
2657 5496 2.715268 CGTTGAATCGCGCCATAAATT 58.285 42.857 0.00 0.00 0.00 1.82
2658 5497 1.596954 GCGTTGAATCGCGCCATAAAT 60.597 47.619 0.00 0.00 46.93 1.40
2659 5498 0.247894 GCGTTGAATCGCGCCATAAA 60.248 50.000 0.00 0.00 46.93 1.40
2660 5499 1.350319 GCGTTGAATCGCGCCATAA 59.650 52.632 0.00 0.00 46.93 1.90
2686 5525 1.153647 CACCATGCATGCTGCCAAG 60.154 57.895 21.69 8.18 44.23 3.61
2687 5526 2.974717 CACCATGCATGCTGCCAA 59.025 55.556 21.69 0.00 44.23 4.52
2688 5527 3.765578 GCACCATGCATGCTGCCA 61.766 61.111 29.02 0.00 44.23 4.92
2707 5546 8.912787 AAATGTGTCTAGACTTACGTATTGAG 57.087 34.615 23.01 0.00 0.00 3.02
2713 5552 9.701098 TTTCATTAAATGTGTCTAGACTTACGT 57.299 29.630 23.01 12.54 0.00 3.57
2718 5557 8.926710 CGAACTTTCATTAAATGTGTCTAGACT 58.073 33.333 23.01 5.66 0.00 3.24
2720 5559 9.140286 CTCGAACTTTCATTAAATGTGTCTAGA 57.860 33.333 0.00 0.00 0.00 2.43
2721 5560 8.383619 CCTCGAACTTTCATTAAATGTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
2722 5561 7.876068 ACCTCGAACTTTCATTAAATGTGTCTA 59.124 33.333 0.00 0.00 0.00 2.59
2723 5562 6.710744 ACCTCGAACTTTCATTAAATGTGTCT 59.289 34.615 0.00 0.00 0.00 3.41
2743 5589 5.244178 AGAATCCTAGCCACTTTATACCTCG 59.756 44.000 0.00 0.00 0.00 4.63
2882 5758 8.422566 AGACAAAATACTGCCTTACCTATAGAC 58.577 37.037 0.00 0.00 0.00 2.59
2904 5780 2.184533 CACATACACCCCCACTAGACA 58.815 52.381 0.00 0.00 0.00 3.41
2919 5795 2.147958 GGAGGAACAAACGTGCACATA 58.852 47.619 18.64 0.00 0.00 2.29
2920 5796 0.951558 GGAGGAACAAACGTGCACAT 59.048 50.000 18.64 0.00 0.00 3.21
2921 5797 1.433053 CGGAGGAACAAACGTGCACA 61.433 55.000 18.64 0.00 0.00 4.57
2922 5798 1.278637 CGGAGGAACAAACGTGCAC 59.721 57.895 6.82 6.82 0.00 4.57
2935 5811 4.366684 AAGCCTTTGCCCCGGAGG 62.367 66.667 0.73 1.32 41.65 4.30
2972 5848 0.251634 TAGCAACCGCCACATCATCA 59.748 50.000 0.00 0.00 39.83 3.07
3015 5891 3.482783 GAAGAGCTGCACGGCGAC 61.483 66.667 16.62 5.70 37.29 5.19
3019 5895 0.392193 AAGATGGAAGAGCTGCACGG 60.392 55.000 1.02 0.00 0.00 4.94
3040 5916 1.351017 TGAAGACATCCCAAGGGTGAC 59.649 52.381 4.80 3.95 36.47 3.67
3041 5917 1.630369 CTGAAGACATCCCAAGGGTGA 59.370 52.381 4.80 0.00 36.47 4.02
3048 5924 3.330701 AGGCTTTTACTGAAGACATCCCA 59.669 43.478 0.00 0.00 37.11 4.37
3059 5935 3.009143 ACAGGGACCTTAGGCTTTTACTG 59.991 47.826 0.00 1.55 0.00 2.74
3060 5936 3.257578 ACAGGGACCTTAGGCTTTTACT 58.742 45.455 0.00 0.00 0.00 2.24
3061 5937 3.715638 ACAGGGACCTTAGGCTTTTAC 57.284 47.619 0.00 0.00 0.00 2.01
3062 5938 3.812882 GCAACAGGGACCTTAGGCTTTTA 60.813 47.826 0.00 0.00 0.00 1.52
3063 5939 2.876581 CAACAGGGACCTTAGGCTTTT 58.123 47.619 0.00 0.00 0.00 2.27
3084 5961 1.604604 AACAATGTTGTCCGACCCTG 58.395 50.000 0.00 0.00 41.31 4.45
3085 5962 3.713826 ATAACAATGTTGTCCGACCCT 57.286 42.857 9.15 0.00 41.31 4.34
3093 5970 4.858692 GCGATGCAGAAATAACAATGTTGT 59.141 37.500 9.15 0.00 44.72 3.32
3103 5980 0.836606 TGGGGAGCGATGCAGAAATA 59.163 50.000 0.00 0.00 0.00 1.40
3104 5981 0.749454 GTGGGGAGCGATGCAGAAAT 60.749 55.000 0.00 0.00 0.00 2.17
3147 6024 1.145119 AGGAAAAGTGTGGAGGGGAAC 59.855 52.381 0.00 0.00 0.00 3.62
3157 6034 4.344104 CATATCCAACCCAGGAAAAGTGT 58.656 43.478 0.00 0.00 41.92 3.55
3177 6054 1.167851 CCAACCGTGAGAATGTGCAT 58.832 50.000 0.00 0.00 0.00 3.96
3182 6059 1.739466 CACCATCCAACCGTGAGAATG 59.261 52.381 0.00 0.00 0.00 2.67
3186 6063 1.302431 TGCACCATCCAACCGTGAG 60.302 57.895 0.00 0.00 0.00 3.51
3204 6081 1.753649 ACTACTCGCATCATCAGCTGT 59.246 47.619 14.67 0.00 0.00 4.40
3209 6086 2.233676 ACACCAACTACTCGCATCATCA 59.766 45.455 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.