Multiple sequence alignment - TraesCS7B01G287900

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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 TraesCS7B01G287900 chr7B 100.000 2675 0 0 1 2675 524037961 524035287 0.000000e+00 4940.0
1 TraesCS7B01G287900 chr7B 94.771 153 8 0 2238 2390 353327267 353327115 3.440000e-59 239.0
2 TraesCS7B01G287900 chr7B 86.567 201 18 4 1992 2186 353327468 353327271 2.090000e-51 213.0
3 TraesCS7B01G287900 chr7B 97.619 42 1 0 1088 1129 636630296 636630255 3.690000e-09 73.1
4 TraesCS7B01G287900 chr7B 79.121 91 15 4 1178 1266 600965070 600964982 2.880000e-05 60.2
5 TraesCS7B01G287900 chr7D 94.959 972 38 7 1711 2675 495697171 495696204 0.000000e+00 1513.0
6 TraesCS7B01G287900 chr7D 94.022 987 36 15 724 1696 495704834 495703857 0.000000e+00 1474.0
7 TraesCS7B01G287900 chr7D 88.191 398 15 13 202 577 495705318 495704931 1.890000e-121 446.0
8 TraesCS7B01G287900 chr7D 96.269 134 4 1 11 144 495705448 495705316 4.480000e-53 219.0
9 TraesCS7B01G287900 chr7D 78.505 107 19 3 1025 1129 412184393 412184497 1.720000e-07 67.6
10 TraesCS7B01G287900 chr7A 89.850 1064 44 20 805 1845 561584148 561583126 0.000000e+00 1308.0
11 TraesCS7B01G287900 chr7A 93.782 788 38 6 1899 2675 561583113 561582326 0.000000e+00 1173.0
12 TraesCS7B01G287900 chr7A 83.958 667 47 20 5 655 561584865 561584243 3.840000e-163 584.0
13 TraesCS7B01G287900 chr7A 78.022 91 16 4 1178 1266 640550634 640550546 1.000000e-03 54.7
14 TraesCS7B01G287900 chr5B 83.281 317 43 5 1195 1510 498882503 498882810 1.570000e-72 283.0
15 TraesCS7B01G287900 chr5B 87.500 192 18 5 1010 1198 498879053 498879241 1.610000e-52 217.0
16 TraesCS7B01G287900 chr5B 97.619 42 1 0 1088 1129 112256867 112256826 3.690000e-09 73.1
17 TraesCS7B01G287900 chr5A 82.965 317 44 4 1195 1510 526396179 526396486 7.290000e-71 278.0
18 TraesCS7B01G287900 chr5A 86.070 201 18 5 1992 2186 85293338 85293534 9.710000e-50 207.0
19 TraesCS7B01G287900 chr5A 94.175 103 6 0 2238 2340 85293538 85293640 9.910000e-35 158.0
20 TraesCS7B01G287900 chr5D 82.334 317 46 5 1195 1510 413700643 413700950 1.580000e-67 267.0
21 TraesCS7B01G287900 chr5D 87.500 192 18 5 1010 1198 413698368 413698556 1.610000e-52 217.0
22 TraesCS7B01G287900 chr3A 94.805 154 8 0 2237 2390 455229229 455229382 9.570000e-60 241.0
23 TraesCS7B01G287900 chr3A 83.085 201 17 7 1992 2186 455229037 455229226 1.650000e-37 167.0
24 TraesCS7B01G287900 chr3B 94.118 153 9 0 2238 2390 449167980 449168132 1.600000e-57 233.0
25 TraesCS7B01G287900 chr3B 87.065 201 17 4 1992 2186 449167779 449167976 4.480000e-53 219.0
26 TraesCS7B01G287900 chr3D 91.558 154 13 0 2238 2391 9423724 9423571 2.090000e-51 213.0
27 TraesCS7B01G287900 chr2B 97.619 42 1 0 1088 1129 39749183 39749142 3.690000e-09 73.1
28 TraesCS7B01G287900 chr1B 97.619 42 1 0 1088 1129 322471449 322471408 3.690000e-09 73.1


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 TraesCS7B01G287900 chr7B 524035287 524037961 2674 True 4940.000000 4940 100.000000 1 2675 1 chr7B.!!$R1 2674
1 TraesCS7B01G287900 chr7D 495696204 495697171 967 True 1513.000000 1513 94.959000 1711 2675 1 chr7D.!!$R1 964
2 TraesCS7B01G287900 chr7D 495703857 495705448 1591 True 713.000000 1474 92.827333 11 1696 3 chr7D.!!$R2 1685
3 TraesCS7B01G287900 chr7A 561582326 561584865 2539 True 1021.666667 1308 89.196667 5 2675 3 chr7A.!!$R2 2670
4 TraesCS7B01G287900 chr5B 498879053 498882810 3757 False 250.000000 283 85.390500 1010 1510 2 chr5B.!!$F1 500
5 TraesCS7B01G287900 chr5D 413698368 413700950 2582 False 242.000000 267 84.917000 1010 1510 2 chr5D.!!$F1 500

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
680 715 0.321564 CATCCTTGCTCCACCACGAA 60.322 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 5238 0.610232 GCTTGGTGTCTTCCAGCCAT 60.61 55.0 0.0 0.0 40.95 4.4 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
154 155 2.427080 GGCGACGTCGATCGATCC 60.427 66.667 39.74 25.66 45.13 3.36
155 156 2.326897 GCGACGTCGATCGATCCA 59.673 61.111 39.74 3.89 45.13 3.41
156 157 2.004489 GCGACGTCGATCGATCCAC 61.004 63.158 39.74 15.95 45.13 4.02
157 158 1.718066 CGACGTCGATCGATCCACG 60.718 63.158 34.00 34.00 45.13 4.94
158 159 1.368969 GACGTCGATCGATCCACGG 60.369 63.158 36.67 23.90 43.96 4.94
159 160 1.769098 GACGTCGATCGATCCACGGA 61.769 60.000 36.67 19.91 43.96 4.69
160 161 1.368969 CGTCGATCGATCCACGGAC 60.369 63.158 30.22 23.11 42.86 4.79
161 162 1.008767 GTCGATCGATCCACGGACC 60.009 63.158 22.50 0.53 42.82 4.46
162 163 2.191513 TCGATCGATCCACGGACCC 61.192 63.158 19.51 0.00 42.82 4.46
163 164 2.735237 GATCGATCCACGGACCCC 59.265 66.667 14.76 0.00 42.82 4.95
164 165 2.042333 ATCGATCCACGGACCCCA 60.042 61.111 0.00 0.00 42.82 4.96
165 166 2.088674 GATCGATCCACGGACCCCAG 62.089 65.000 14.76 0.00 42.82 4.45
166 167 4.530857 CGATCCACGGACCCCAGC 62.531 72.222 0.00 0.00 38.46 4.85
167 168 3.083997 GATCCACGGACCCCAGCT 61.084 66.667 0.00 0.00 0.00 4.24
168 169 2.610859 ATCCACGGACCCCAGCTT 60.611 61.111 0.00 0.00 0.00 3.74
169 170 2.198304 GATCCACGGACCCCAGCTTT 62.198 60.000 0.00 0.00 0.00 3.51
170 171 2.198304 ATCCACGGACCCCAGCTTTC 62.198 60.000 0.00 0.00 0.00 2.62
171 172 2.742372 CACGGACCCCAGCTTTCG 60.742 66.667 0.00 0.00 0.00 3.46
172 173 3.239253 ACGGACCCCAGCTTTCGT 61.239 61.111 0.00 0.00 0.00 3.85
173 174 2.742372 CGGACCCCAGCTTTCGTG 60.742 66.667 0.00 0.00 0.00 4.35
174 175 3.056328 GGACCCCAGCTTTCGTGC 61.056 66.667 0.00 0.00 0.00 5.34
175 176 2.281484 GACCCCAGCTTTCGTGCA 60.281 61.111 0.00 0.00 34.99 4.57
176 177 2.281761 ACCCCAGCTTTCGTGCAG 60.282 61.111 0.00 0.00 34.99 4.41
177 178 3.741476 CCCCAGCTTTCGTGCAGC 61.741 66.667 0.00 0.00 37.56 5.25
178 179 3.741476 CCCAGCTTTCGTGCAGCC 61.741 66.667 0.00 0.00 38.09 4.85
179 180 3.741476 CCAGCTTTCGTGCAGCCC 61.741 66.667 0.00 0.00 38.09 5.19
180 181 3.741476 CAGCTTTCGTGCAGCCCC 61.741 66.667 0.00 0.00 38.09 5.80
188 189 3.443045 GTGCAGCCCCGGTGATTG 61.443 66.667 0.00 0.00 32.22 2.67
216 217 1.398390 CTTGCACGCTAATCCTCAACC 59.602 52.381 0.00 0.00 0.00 3.77
254 255 9.743057 GATCTATATATTCTGTAGCCACATGTC 57.257 37.037 0.00 0.00 33.14 3.06
256 257 2.315925 ATTCTGTAGCCACATGTCGG 57.684 50.000 0.00 2.40 33.14 4.79
320 327 3.498018 TGTGTCAAAGGATGATGAACACG 59.502 43.478 0.00 0.00 40.97 4.49
329 336 4.039245 AGGATGATGAACACGTACATAGGG 59.961 45.833 0.00 0.00 0.00 3.53
330 337 3.173668 TGATGAACACGTACATAGGGC 57.826 47.619 0.00 0.00 0.00 5.19
380 393 6.126409 GGACTTATGTGGGTTTGGAATATGA 58.874 40.000 0.00 0.00 0.00 2.15
535 556 1.270839 TGAGTGCCGAAAGAGAAAGGG 60.271 52.381 0.00 0.00 0.00 3.95
577 606 0.748005 GTACCCGGCTACCTGTACGA 60.748 60.000 0.00 0.00 0.00 3.43
578 607 0.464373 TACCCGGCTACCTGTACGAG 60.464 60.000 0.00 0.00 0.00 4.18
579 608 1.452651 CCCGGCTACCTGTACGAGA 60.453 63.158 0.00 0.00 0.00 4.04
580 609 1.722636 CCCGGCTACCTGTACGAGAC 61.723 65.000 0.00 0.00 0.00 3.36
581 610 1.351012 CGGCTACCTGTACGAGACG 59.649 63.158 0.00 0.00 34.98 4.18
582 611 1.086067 CGGCTACCTGTACGAGACGA 61.086 60.000 6.34 0.00 44.73 4.20
583 612 1.089920 GGCTACCTGTACGAGACGAA 58.910 55.000 0.00 0.00 0.00 3.85
584 613 1.470098 GGCTACCTGTACGAGACGAAA 59.530 52.381 0.00 0.00 0.00 3.46
585 614 2.098770 GGCTACCTGTACGAGACGAAAT 59.901 50.000 0.00 0.00 0.00 2.17
586 615 3.361414 GCTACCTGTACGAGACGAAATC 58.639 50.000 0.00 0.00 0.00 2.17
587 616 3.065095 GCTACCTGTACGAGACGAAATCT 59.935 47.826 0.00 0.00 41.91 2.40
588 617 4.272018 GCTACCTGTACGAGACGAAATCTA 59.728 45.833 0.00 0.00 38.00 1.98
589 618 4.612932 ACCTGTACGAGACGAAATCTAC 57.387 45.455 0.00 0.00 38.00 2.59
590 619 4.005650 ACCTGTACGAGACGAAATCTACA 58.994 43.478 0.00 0.00 38.00 2.74
591 620 4.094590 ACCTGTACGAGACGAAATCTACAG 59.905 45.833 0.00 0.00 38.00 2.74
592 621 4.012319 TGTACGAGACGAAATCTACAGC 57.988 45.455 0.00 0.00 38.00 4.40
597 626 2.263077 AGACGAAATCTACAGCAAGCG 58.737 47.619 0.00 0.00 35.15 4.68
600 629 2.094390 ACGAAATCTACAGCAAGCGGTA 60.094 45.455 5.04 5.04 0.00 4.02
620 649 4.021894 GGTAGGACATCACTACTGGCTATG 60.022 50.000 0.00 0.00 40.43 2.23
635 664 4.009675 TGGCTATGATGAACCAAGAACAC 58.990 43.478 0.00 0.00 0.00 3.32
636 665 3.063997 GGCTATGATGAACCAAGAACACG 59.936 47.826 0.00 0.00 0.00 4.49
637 666 3.063997 GCTATGATGAACCAAGAACACGG 59.936 47.826 0.00 0.00 0.00 4.94
638 667 2.920724 TGATGAACCAAGAACACGGA 57.079 45.000 0.00 0.00 0.00 4.69
639 668 3.201353 TGATGAACCAAGAACACGGAA 57.799 42.857 0.00 0.00 0.00 4.30
640 669 2.875933 TGATGAACCAAGAACACGGAAC 59.124 45.455 0.00 0.00 0.00 3.62
641 670 2.702592 TGAACCAAGAACACGGAACT 57.297 45.000 0.00 0.00 0.00 3.01
652 687 5.123227 AGAACACGGAACTTTTGATCTTGA 58.877 37.500 0.00 0.00 0.00 3.02
663 698 7.001099 ACTTTTGATCTTGAAGAATTGGCAT 57.999 32.000 0.00 0.00 0.00 4.40
664 699 7.095270 ACTTTTGATCTTGAAGAATTGGCATC 58.905 34.615 0.00 0.00 0.00 3.91
665 700 5.587388 TTGATCTTGAAGAATTGGCATCC 57.413 39.130 0.00 0.00 0.00 3.51
667 702 5.266788 TGATCTTGAAGAATTGGCATCCTT 58.733 37.500 0.00 0.00 0.00 3.36
677 712 3.595819 GCATCCTTGCTCCACCAC 58.404 61.111 0.00 0.00 45.77 4.16
678 713 2.401766 GCATCCTTGCTCCACCACG 61.402 63.158 0.00 0.00 45.77 4.94
680 715 0.321564 CATCCTTGCTCCACCACGAA 60.322 55.000 0.00 0.00 0.00 3.85
682 717 0.400213 TCCTTGCTCCACCACGAAAT 59.600 50.000 0.00 0.00 0.00 2.17
684 719 1.611673 CCTTGCTCCACCACGAAATCT 60.612 52.381 0.00 0.00 0.00 2.40
686 721 0.684535 TGCTCCACCACGAAATCTGA 59.315 50.000 0.00 0.00 0.00 3.27
687 722 1.278985 TGCTCCACCACGAAATCTGAT 59.721 47.619 0.00 0.00 0.00 2.90
688 723 1.936547 GCTCCACCACGAAATCTGATC 59.063 52.381 0.00 0.00 0.00 2.92
689 724 2.419297 GCTCCACCACGAAATCTGATCT 60.419 50.000 0.00 0.00 0.00 2.75
690 725 3.866651 CTCCACCACGAAATCTGATCTT 58.133 45.455 0.00 0.00 0.00 2.40
691 726 4.256920 CTCCACCACGAAATCTGATCTTT 58.743 43.478 0.00 0.00 0.00 2.52
692 727 5.414789 TCCACCACGAAATCTGATCTTTA 57.585 39.130 0.00 0.00 0.00 1.85
694 729 5.046591 TCCACCACGAAATCTGATCTTTAGT 60.047 40.000 0.00 0.00 0.00 2.24
696 731 6.986817 CCACCACGAAATCTGATCTTTAGTAT 59.013 38.462 0.00 0.00 0.00 2.12
697 732 7.495934 CCACCACGAAATCTGATCTTTAGTATT 59.504 37.037 0.00 0.00 0.00 1.89
698 733 8.883731 CACCACGAAATCTGATCTTTAGTATTT 58.116 33.333 0.00 0.00 0.00 1.40
699 734 9.449719 ACCACGAAATCTGATCTTTAGTATTTT 57.550 29.630 0.00 0.00 0.00 1.82
762 797 5.815581 TCAAATACTAGCAACACCTCCATT 58.184 37.500 0.00 0.00 0.00 3.16
775 810 7.201884 GCAACACCTCCATTACTACTATAGTGA 60.202 40.741 15.90 1.41 39.81 3.41
827 868 4.260784 CCTTTCAAGTTTCAACCACTCTCG 60.261 45.833 0.00 0.00 0.00 4.04
955 1004 4.933563 TGCAGCTTCACGCCAGCA 62.934 61.111 4.12 0.00 44.60 4.41
956 1005 4.099170 GCAGCTTCACGCCAGCAG 62.099 66.667 4.12 0.00 39.99 4.24
957 1006 4.099170 CAGCTTCACGCCAGCAGC 62.099 66.667 4.12 0.00 39.99 5.25
1521 5035 2.418910 CGAGGAGATCCACGCCACT 61.419 63.158 5.78 0.00 42.60 4.00
1728 5248 6.583806 GCGATTAATTAATTCATGGCTGGAAG 59.416 38.462 17.27 0.00 0.00 3.46
1729 5249 7.522073 GCGATTAATTAATTCATGGCTGGAAGA 60.522 37.037 17.27 0.00 34.07 2.87
1774 5294 1.577328 AAACCAGCGCCATGAAGACG 61.577 55.000 2.29 0.00 0.00 4.18
1784 5304 0.957395 CATGAAGACGCCAAGCAGGT 60.957 55.000 0.00 0.00 40.61 4.00
1816 5336 5.512753 CTGATAGACTCAGCAGCTCTTAA 57.487 43.478 0.00 0.00 44.73 1.85
1821 5343 7.923344 TGATAGACTCAGCAGCTCTTAATAAAC 59.077 37.037 0.00 0.00 0.00 2.01
1831 5353 4.091509 AGCTCTTAATAAACACAAGCGTCG 59.908 41.667 0.00 0.00 33.62 5.12
1891 5413 2.951475 AAAACACGGCGCTTCTCCCA 62.951 55.000 6.90 0.00 0.00 4.37
1934 5458 3.577805 ATGGATAGGGGTGCAAGTAAC 57.422 47.619 0.00 0.00 0.00 2.50
1958 5482 7.923888 ACATTCAGATGATATGAAAAGAACGG 58.076 34.615 6.58 0.00 39.92 4.44
2038 5565 7.052873 TGTATAGAGTCTGTCTACCCTACAAC 58.947 42.308 1.86 0.00 40.76 3.32
2119 5652 4.874970 AGAATTCTGCATTTTCCACACAC 58.125 39.130 7.30 0.00 0.00 3.82
2412 5945 2.480416 GCTCTGTACCTGGTCATCTTCG 60.480 54.545 0.63 0.00 0.00 3.79
2439 5972 3.717294 GGCCGGATCCACACAGGT 61.717 66.667 13.41 0.00 39.02 4.00
2454 5987 1.388531 AGGTGACTGGAGACCCGAT 59.611 57.895 0.00 0.00 41.13 4.18
2456 5989 1.258445 GGTGACTGGAGACCCGATGT 61.258 60.000 0.00 0.00 34.29 3.06
2572 6105 5.652452 AGTTACAAGCAAAAAGGTCAGAACT 59.348 36.000 0.00 0.00 0.00 3.01
2599 6132 6.420008 ACGAATACATAATGAGGAACTTACGC 59.580 38.462 0.00 0.00 41.55 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.009815 GCATGGTGTGATTGATTAATTCAACTG 59.990 37.037 0.00 4.30 46.80 3.16
2 3 6.812656 TGCATGGTGTGATTGATTAATTCAAC 59.187 34.615 0.00 0.00 46.80 3.18
4 5 6.527057 TGCATGGTGTGATTGATTAATTCA 57.473 33.333 0.00 0.00 0.00 2.57
5 6 7.042321 CCATTGCATGGTGTGATTGATTAATTC 60.042 37.037 0.00 0.00 45.54 2.17
6 7 6.764085 CCATTGCATGGTGTGATTGATTAATT 59.236 34.615 0.00 0.00 45.54 1.40
7 8 6.285224 CCATTGCATGGTGTGATTGATTAAT 58.715 36.000 0.00 0.00 45.54 1.40
8 9 5.662456 CCATTGCATGGTGTGATTGATTAA 58.338 37.500 0.00 0.00 45.54 1.40
9 10 5.265350 CCATTGCATGGTGTGATTGATTA 57.735 39.130 0.00 0.00 45.54 1.75
10 11 4.131649 CCATTGCATGGTGTGATTGATT 57.868 40.909 0.00 0.00 45.54 2.57
11 12 3.812156 CCATTGCATGGTGTGATTGAT 57.188 42.857 0.00 0.00 45.54 2.57
32 33 3.393800 GGAGATGGATGGATTACGTGTG 58.606 50.000 0.00 0.00 0.00 3.82
34 35 2.035961 ACGGAGATGGATGGATTACGTG 59.964 50.000 0.00 0.00 0.00 4.49
150 151 2.198304 AAAGCTGGGGTCCGTGGATC 62.198 60.000 0.00 0.00 0.00 3.36
151 152 2.198304 GAAAGCTGGGGTCCGTGGAT 62.198 60.000 0.00 0.00 0.00 3.41
152 153 2.852075 AAAGCTGGGGTCCGTGGA 60.852 61.111 0.00 0.00 0.00 4.02
153 154 2.359975 GAAAGCTGGGGTCCGTGG 60.360 66.667 0.00 0.00 0.00 4.94
154 155 2.742372 CGAAAGCTGGGGTCCGTG 60.742 66.667 0.00 0.00 0.00 4.94
155 156 3.239253 ACGAAAGCTGGGGTCCGT 61.239 61.111 0.00 0.00 0.00 4.69
156 157 2.742372 CACGAAAGCTGGGGTCCG 60.742 66.667 0.00 0.00 0.00 4.79
157 158 3.056328 GCACGAAAGCTGGGGTCC 61.056 66.667 0.00 0.00 0.00 4.46
158 159 2.281484 TGCACGAAAGCTGGGGTC 60.281 61.111 0.00 0.00 34.99 4.46
159 160 2.281761 CTGCACGAAAGCTGGGGT 60.282 61.111 0.00 0.00 34.99 4.95
160 161 3.741476 GCTGCACGAAAGCTGGGG 61.741 66.667 0.00 0.00 37.69 4.96
161 162 3.741476 GGCTGCACGAAAGCTGGG 61.741 66.667 0.50 0.00 40.64 4.45
162 163 3.741476 GGGCTGCACGAAAGCTGG 61.741 66.667 0.50 0.00 40.64 4.85
163 164 3.741476 GGGGCTGCACGAAAGCTG 61.741 66.667 0.50 5.55 40.64 4.24
171 172 2.813226 TACAATCACCGGGGCTGCAC 62.813 60.000 6.32 0.00 0.00 4.57
172 173 1.920734 ATACAATCACCGGGGCTGCA 61.921 55.000 6.32 0.00 0.00 4.41
173 174 0.107831 TATACAATCACCGGGGCTGC 59.892 55.000 6.32 0.00 0.00 5.25
174 175 2.038426 TCATATACAATCACCGGGGCTG 59.962 50.000 6.32 5.06 0.00 4.85
175 176 2.038557 GTCATATACAATCACCGGGGCT 59.961 50.000 6.32 0.00 0.00 5.19
176 177 2.038557 AGTCATATACAATCACCGGGGC 59.961 50.000 6.32 0.00 0.00 5.80
177 178 4.065088 CAAGTCATATACAATCACCGGGG 58.935 47.826 6.32 0.00 0.00 5.73
178 179 3.498397 GCAAGTCATATACAATCACCGGG 59.502 47.826 6.32 0.00 0.00 5.73
179 180 4.024893 GTGCAAGTCATATACAATCACCGG 60.025 45.833 0.00 0.00 0.00 5.28
180 181 4.318050 CGTGCAAGTCATATACAATCACCG 60.318 45.833 0.00 0.00 0.00 4.94
181 182 4.552767 GCGTGCAAGTCATATACAATCACC 60.553 45.833 0.59 0.00 0.00 4.02
182 183 4.271049 AGCGTGCAAGTCATATACAATCAC 59.729 41.667 0.59 0.00 0.00 3.06
183 184 4.441792 AGCGTGCAAGTCATATACAATCA 58.558 39.130 0.59 0.00 0.00 2.57
184 185 6.525121 TTAGCGTGCAAGTCATATACAATC 57.475 37.500 0.59 0.00 0.00 2.67
185 186 6.147821 GGATTAGCGTGCAAGTCATATACAAT 59.852 38.462 0.59 0.00 0.00 2.71
186 187 5.465390 GGATTAGCGTGCAAGTCATATACAA 59.535 40.000 0.59 0.00 0.00 2.41
187 188 4.988540 GGATTAGCGTGCAAGTCATATACA 59.011 41.667 0.59 0.00 0.00 2.29
188 189 5.230942 AGGATTAGCGTGCAAGTCATATAC 58.769 41.667 0.59 0.00 0.00 1.47
254 255 1.737838 AACAGTACCATCACATGCCG 58.262 50.000 0.00 0.00 0.00 5.69
256 257 4.870363 ACAAAAACAGTACCATCACATGC 58.130 39.130 0.00 0.00 0.00 4.06
320 327 2.706190 ACTCCATTCCTGCCCTATGTAC 59.294 50.000 0.00 0.00 0.00 2.90
329 336 1.021390 CGTGTCCACTCCATTCCTGC 61.021 60.000 0.00 0.00 0.00 4.85
330 337 1.021390 GCGTGTCCACTCCATTCCTG 61.021 60.000 0.00 0.00 0.00 3.86
380 393 6.664428 TGCATGATCATTCATCCATTCATT 57.336 33.333 5.16 0.00 40.70 2.57
577 606 2.263077 CGCTTGCTGTAGATTTCGTCT 58.737 47.619 0.00 0.00 41.11 4.18
578 607 1.324736 CCGCTTGCTGTAGATTTCGTC 59.675 52.381 0.00 0.00 0.00 4.20
579 608 1.337823 ACCGCTTGCTGTAGATTTCGT 60.338 47.619 0.00 0.00 0.00 3.85
580 609 1.359848 ACCGCTTGCTGTAGATTTCG 58.640 50.000 0.00 0.00 0.00 3.46
581 610 2.866762 CCTACCGCTTGCTGTAGATTTC 59.133 50.000 20.44 0.00 37.26 2.17
582 611 2.500098 TCCTACCGCTTGCTGTAGATTT 59.500 45.455 20.44 0.00 37.26 2.17
583 612 2.108168 TCCTACCGCTTGCTGTAGATT 58.892 47.619 20.44 0.00 37.26 2.40
584 613 1.409427 GTCCTACCGCTTGCTGTAGAT 59.591 52.381 20.44 0.00 37.26 1.98
585 614 0.815734 GTCCTACCGCTTGCTGTAGA 59.184 55.000 20.44 8.28 37.26 2.59
586 615 0.530744 TGTCCTACCGCTTGCTGTAG 59.469 55.000 14.46 14.46 35.33 2.74
587 616 1.136305 GATGTCCTACCGCTTGCTGTA 59.864 52.381 0.00 0.00 0.00 2.74
588 617 0.108138 GATGTCCTACCGCTTGCTGT 60.108 55.000 0.00 0.00 0.00 4.40
589 618 0.108186 TGATGTCCTACCGCTTGCTG 60.108 55.000 0.00 0.00 0.00 4.41
590 619 0.108138 GTGATGTCCTACCGCTTGCT 60.108 55.000 0.00 0.00 0.00 3.91
591 620 0.108138 AGTGATGTCCTACCGCTTGC 60.108 55.000 0.00 0.00 0.00 4.01
592 621 2.427453 AGTAGTGATGTCCTACCGCTTG 59.573 50.000 0.00 0.00 36.30 4.01
597 626 2.389715 AGCCAGTAGTGATGTCCTACC 58.610 52.381 0.00 0.00 36.30 3.18
600 629 3.916035 TCATAGCCAGTAGTGATGTCCT 58.084 45.455 0.00 0.00 0.00 3.85
620 649 3.139077 AGTTCCGTGTTCTTGGTTCATC 58.861 45.455 0.00 0.00 0.00 2.92
635 664 6.583806 CCAATTCTTCAAGATCAAAAGTTCCG 59.416 38.462 0.00 0.00 0.00 4.30
636 665 6.367149 GCCAATTCTTCAAGATCAAAAGTTCC 59.633 38.462 0.00 0.00 0.00 3.62
637 666 6.925165 TGCCAATTCTTCAAGATCAAAAGTTC 59.075 34.615 0.00 0.00 0.00 3.01
638 667 6.819284 TGCCAATTCTTCAAGATCAAAAGTT 58.181 32.000 0.00 0.00 0.00 2.66
639 668 6.409524 TGCCAATTCTTCAAGATCAAAAGT 57.590 33.333 0.00 0.00 0.00 2.66
640 669 6.534079 GGATGCCAATTCTTCAAGATCAAAAG 59.466 38.462 0.00 0.00 0.00 2.27
641 670 6.211986 AGGATGCCAATTCTTCAAGATCAAAA 59.788 34.615 0.00 0.00 0.00 2.44
663 698 0.400213 ATTTCGTGGTGGAGCAAGGA 59.600 50.000 0.00 0.00 0.00 3.36
664 699 0.804989 GATTTCGTGGTGGAGCAAGG 59.195 55.000 0.00 0.00 0.00 3.61
665 700 1.466167 CAGATTTCGTGGTGGAGCAAG 59.534 52.381 0.00 0.00 0.00 4.01
667 702 0.684535 TCAGATTTCGTGGTGGAGCA 59.315 50.000 0.00 0.00 0.00 4.26
671 706 5.178797 ACTAAAGATCAGATTTCGTGGTGG 58.821 41.667 0.00 0.00 0.00 4.61
672 707 8.425577 AATACTAAAGATCAGATTTCGTGGTG 57.574 34.615 0.00 0.00 0.00 4.17
673 708 9.449719 AAAATACTAAAGATCAGATTTCGTGGT 57.550 29.630 0.00 0.00 0.00 4.16
734 769 6.543831 GGAGGTGTTGCTAGTATTTGATTGAT 59.456 38.462 0.00 0.00 0.00 2.57
752 787 7.813331 TCTCACTATAGTAGTAATGGAGGTGT 58.187 38.462 4.74 0.00 37.23 4.16
762 797 5.211174 TCGCTGCTCTCACTATAGTAGTA 57.789 43.478 4.74 0.00 37.23 1.82
827 868 2.592308 GGTGACATGGGGGAGAGC 59.408 66.667 0.00 0.00 0.00 4.09
963 1012 0.319900 TGAACTCTGAAGGCAGACGC 60.320 55.000 0.00 0.00 45.88 5.19
964 1013 1.270826 TCTGAACTCTGAAGGCAGACG 59.729 52.381 0.00 0.00 45.88 4.18
965 1014 2.611722 GGTCTGAACTCTGAAGGCAGAC 60.612 54.545 17.87 17.87 45.88 3.51
967 1016 1.671261 CGGTCTGAACTCTGAAGGCAG 60.671 57.143 0.00 0.00 43.67 4.85
968 1017 0.318441 CGGTCTGAACTCTGAAGGCA 59.682 55.000 0.00 0.00 0.00 4.75
969 1018 0.603569 TCGGTCTGAACTCTGAAGGC 59.396 55.000 0.00 0.00 0.00 4.35
970 1019 2.478709 CGATCGGTCTGAACTCTGAAGG 60.479 54.545 7.38 0.00 0.00 3.46
974 1023 0.526524 GGCGATCGGTCTGAACTCTG 60.527 60.000 18.30 0.00 0.00 3.35
975 1024 1.810532 GGCGATCGGTCTGAACTCT 59.189 57.895 18.30 0.00 0.00 3.24
996 1045 1.749334 CGTAGTCCTCCTCCATGGCC 61.749 65.000 6.96 0.00 35.26 5.36
1519 5033 2.743718 CGGCTTCCTGGACACAGT 59.256 61.111 0.00 0.00 43.36 3.55
1521 5035 3.241530 AGCGGCTTCCTGGACACA 61.242 61.111 0.00 0.00 0.00 3.72
1718 5238 0.610232 GCTTGGTGTCTTCCAGCCAT 60.610 55.000 0.00 0.00 40.95 4.40
1728 5248 1.126846 CGATTTGAGACGCTTGGTGTC 59.873 52.381 3.39 3.39 42.60 3.67
1729 5249 1.148310 CGATTTGAGACGCTTGGTGT 58.852 50.000 0.00 0.00 0.00 4.16
1730 5250 1.148310 ACGATTTGAGACGCTTGGTG 58.852 50.000 0.00 0.00 0.00 4.17
1731 5251 1.798813 GAACGATTTGAGACGCTTGGT 59.201 47.619 0.00 0.00 0.00 3.67
1732 5252 1.798223 TGAACGATTTGAGACGCTTGG 59.202 47.619 0.00 0.00 0.00 3.61
1798 5318 7.036220 GTGTTTATTAAGAGCTGCTGAGTCTA 58.964 38.462 7.01 0.00 0.00 2.59
1802 5322 6.486253 TTGTGTTTATTAAGAGCTGCTGAG 57.514 37.500 7.01 0.00 0.00 3.35
1815 5335 2.139917 TCAGCGACGCTTGTGTTTATT 58.860 42.857 21.97 0.00 36.40 1.40
1816 5336 1.790755 TCAGCGACGCTTGTGTTTAT 58.209 45.000 21.97 0.00 36.40 1.40
1821 5343 1.617755 AACGATCAGCGACGCTTGTG 61.618 55.000 21.97 10.66 44.57 3.33
1831 5353 5.180117 AGCATCAATACCATAAACGATCAGC 59.820 40.000 0.00 0.00 0.00 4.26
1906 5428 3.205056 TGCACCCCTATCCATTGAGATTT 59.795 43.478 0.00 0.00 0.00 2.17
1916 5438 3.577805 ATGTTACTTGCACCCCTATCC 57.422 47.619 0.00 0.00 0.00 2.59
1919 5441 3.585289 TCTGAATGTTACTTGCACCCCTA 59.415 43.478 0.00 0.00 0.00 3.53
1934 5458 8.066595 GTCCGTTCTTTTCATATCATCTGAATG 58.933 37.037 0.00 0.00 32.94 2.67
1958 5482 5.379732 TTCCATGGTTCAAAAATACCGTC 57.620 39.130 12.58 0.00 37.23 4.79
2038 5565 9.291664 TGTAATTTTCGTTTTGGAACTTAACTG 57.708 29.630 0.00 0.00 33.51 3.16
2106 5639 3.961477 TCGTTCTGTGTGTGGAAAATG 57.039 42.857 0.00 0.00 0.00 2.32
2119 5652 4.811555 TGTTTTGAGTTCCATCGTTCTG 57.188 40.909 0.00 0.00 0.00 3.02
2421 5954 3.716195 CCTGTGTGGATCCGGCCA 61.716 66.667 7.39 0.00 38.35 5.36
2434 5967 1.908793 CGGGTCTCCAGTCACCTGT 60.909 63.158 0.00 0.00 36.95 4.00
2439 5972 1.313091 CGACATCGGGTCTCCAGTCA 61.313 60.000 6.58 0.00 44.68 3.41
2451 5984 4.505217 GCAAGCGGTGCGACATCG 62.505 66.667 7.93 7.93 45.10 3.84
2462 5995 2.176792 GAAAGAAGGCCGCAAGCG 59.823 61.111 7.60 7.60 45.17 4.68
2572 6105 9.454585 CGTAAGTTCCTCATTATGTATTCGTTA 57.545 33.333 0.00 0.00 0.00 3.18
2625 6161 6.033341 TGCATTTATGTTTGGATAGCGAAAC 58.967 36.000 11.16 11.16 41.39 2.78


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

AutoCloner maintained by Alex Coulton.