Multiple sequence alignment - TraesCS3D01G369400

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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 TraesCS3D01G369400 chr3D 100.000 3685 0 0 1 3685 482264327 482260643 0.000000e+00 6806.0
1 TraesCS3D01G369400 chr3D 92.111 1483 96 9 1157 2638 482490612 482489150 0.000000e+00 2071.0
2 TraesCS3D01G369400 chr3D 93.086 1215 72 5 1408 2621 482345745 482344542 0.000000e+00 1768.0
3 TraesCS3D01G369400 chr3D 92.494 826 50 6 807 1630 482348886 482348071 0.000000e+00 1171.0
4 TraesCS3D01G369400 chr3D 86.423 847 69 26 1 812 482350870 482350035 0.000000e+00 885.0
5 TraesCS3D01G369400 chr3D 86.838 699 56 19 1 676 482346515 482345830 0.000000e+00 749.0
6 TraesCS3D01G369400 chr3D 92.473 93 6 1 742 834 482345833 482345742 8.300000e-27 132.0
7 TraesCS3D01G369400 chr3B 91.370 2897 180 36 219 3096 644544474 644541629 0.000000e+00 3901.0
8 TraesCS3D01G369400 chr3B 91.052 1531 100 13 1103 2622 644814249 644812745 0.000000e+00 2034.0
9 TraesCS3D01G369400 chr3B 88.525 488 55 1 3198 3685 644538023 644537537 1.140000e-164 590.0
10 TraesCS3D01G369400 chr3B 87.786 131 8 6 3096 3226 644541305 644541183 2.970000e-31 147.0
11 TraesCS3D01G369400 chr3A 92.422 1676 92 15 1103 2766 625335090 625333438 0.000000e+00 2359.0
12 TraesCS3D01G369400 chr3A 93.707 731 37 7 2960 3685 625333420 625332694 0.000000e+00 1086.0
13 TraesCS3D01G369400 chr7B 97.059 34 1 0 574 607 382218721 382218754 1.430000e-04 58.4
14 TraesCS3D01G369400 chr7A 100.000 28 0 0 2247 2274 19959327 19959300 7.000000e-03 52.8
15 TraesCS3D01G369400 chr1B 100.000 28 0 0 573 600 289118489 289118516 7.000000e-03 52.8


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 TraesCS3D01G369400 chr3D 482260643 482264327 3684 True 6806.0 6806 100.0000 1 3685 1 chr3D.!!$R1 3684
1 TraesCS3D01G369400 chr3D 482489150 482490612 1462 True 2071.0 2071 92.1110 1157 2638 1 chr3D.!!$R2 1481
2 TraesCS3D01G369400 chr3D 482344542 482350870 6328 True 941.0 1768 90.2628 1 2621 5 chr3D.!!$R3 2620
3 TraesCS3D01G369400 chr3B 644812745 644814249 1504 True 2034.0 2034 91.0520 1103 2622 1 chr3B.!!$R1 1519
4 TraesCS3D01G369400 chr3B 644537537 644544474 6937 True 1546.0 3901 89.2270 219 3685 3 chr3B.!!$R2 3466
5 TraesCS3D01G369400 chr3A 625332694 625335090 2396 True 1722.5 2359 93.0645 1103 3685 2 chr3A.!!$R1 2582

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
647 672 0.178879 AGGGGATAGGGCTGGAGATG 60.179 60.0 0.0 0.0 0.00 2.9 F
1037 2231 0.234884 CCACGTTCAGAAAACGGAGC 59.765 55.0 14.0 0.0 46.86 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2467 6221 1.228429 CTTCACCTTGGCCCCGAAA 60.228 57.895 0.0 0.0 0.0 3.46 R
3036 6791 0.659427 ATTCGACAGCAATGCCGATG 59.341 50.000 0.0 0.0 0.0 3.84 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
29 30 3.627041 AGGATCCTTGAGCATCCTCTA 57.373 47.619 9.02 0.00 45.00 2.43
35 36 3.196469 TCCTTGAGCATCCTCTACAACTG 59.804 47.826 0.00 0.00 38.93 3.16
36 37 2.680312 TGAGCATCCTCTACAACTGC 57.320 50.000 0.00 0.00 38.93 4.40
57 58 2.582978 GGGTTGTAGCCTCCCGTC 59.417 66.667 0.00 0.00 31.81 4.79
94 95 1.443872 CGGTCGTGAGCACTACCAC 60.444 63.158 20.04 3.65 44.65 4.16
98 99 1.443872 CGTGAGCACTACCACCGAC 60.444 63.158 0.00 0.00 0.00 4.79
103 104 2.718073 GCACTACCACCGACGGGAT 61.718 63.158 20.00 5.41 36.97 3.85
131 132 2.657237 GCAGCGTGGTGGTAGAGT 59.343 61.111 0.82 0.00 0.00 3.24
135 136 0.826256 AGCGTGGTGGTAGAGTGTCA 60.826 55.000 0.00 0.00 0.00 3.58
145 146 1.067142 GTAGAGTGTCAACGCCCATCA 60.067 52.381 0.00 0.00 0.00 3.07
150 151 1.139520 GTCAACGCCCATCAATGGC 59.860 57.895 3.33 0.00 46.70 4.40
172 173 0.322008 CAAAGGGTGGTGAGAGAGGC 60.322 60.000 0.00 0.00 0.00 4.70
191 193 1.671166 GTGTGAATGGGGTTTGGGC 59.329 57.895 0.00 0.00 0.00 5.36
214 216 1.886730 TAGGGGAGTGGAGTGGGGAG 61.887 65.000 0.00 0.00 0.00 4.30
221 223 1.203440 AGTGGAGTGGGGAGTAATGGT 60.203 52.381 0.00 0.00 0.00 3.55
233 235 5.398581 GGGGAGTAATGGTCAATACATTCCA 60.399 44.000 0.00 0.00 39.18 3.53
234 236 5.531287 GGGAGTAATGGTCAATACATTCCAC 59.469 44.000 0.00 0.00 39.18 4.02
259 261 0.896940 ATGCTTCCCAAGGTGTGCAG 60.897 55.000 0.00 0.00 33.87 4.41
280 282 4.154737 CAGACGAAAAGGCAGATTCAATCA 59.845 41.667 0.00 0.00 0.00 2.57
294 296 1.139654 TCAATCATTCCTCCTCAGCCG 59.860 52.381 0.00 0.00 0.00 5.52
329 331 3.632643 TTGAGCTTCATGCAGACCATA 57.367 42.857 0.00 0.00 45.94 2.74
345 347 5.178252 CAGACCATAAATTCGATGTAGCCTG 59.822 44.000 0.00 0.00 0.00 4.85
389 392 5.336213 CCATAGGATTTGTAATGGCTGCATC 60.336 44.000 0.50 0.00 33.02 3.91
455 462 4.692475 ACACCCGTGCGCCCTAAC 62.692 66.667 4.18 0.00 0.00 2.34
467 474 3.614399 CCCTAACGGCATCTCCATC 57.386 57.895 0.00 0.00 34.01 3.51
469 476 0.389391 CCTAACGGCATCTCCATCGT 59.611 55.000 0.00 0.00 37.45 3.73
471 478 1.067060 CTAACGGCATCTCCATCGTGA 59.933 52.381 0.00 0.00 35.93 4.35
484 491 2.225491 CCATCGTGAACCGTCAAACAAT 59.775 45.455 0.00 0.00 34.87 2.71
486 493 2.828877 TCGTGAACCGTCAAACAATCT 58.171 42.857 0.00 0.00 34.87 2.40
491 498 3.317711 TGAACCGTCAAACAATCTGCAAT 59.682 39.130 0.00 0.00 0.00 3.56
495 502 4.277174 ACCGTCAAACAATCTGCAATTGTA 59.723 37.500 20.25 0.89 40.94 2.41
528 552 9.929722 CATCCAATTTGCATGAAAATTTATCTG 57.070 29.630 19.96 10.47 37.59 2.90
565 590 8.879342 TTTCATTTGAAATATGTCCAAACGTT 57.121 26.923 0.00 0.00 38.94 3.99
566 591 8.879342 TTCATTTGAAATATGTCCAAACGTTT 57.121 26.923 7.96 7.96 33.33 3.60
567 592 8.291888 TCATTTGAAATATGTCCAAACGTTTG 57.708 30.769 29.80 29.80 37.90 2.93
601 626 3.857038 GGCCGGCTCCCGTATCAA 61.857 66.667 28.56 0.00 46.80 2.57
613 638 1.526887 CCGTATCAATGTCATGTCCGC 59.473 52.381 0.00 0.00 0.00 5.54
637 662 2.631545 ACGGATCGTTTTAGGGGATAGG 59.368 50.000 0.00 0.00 36.35 2.57
639 664 2.290134 GGATCGTTTTAGGGGATAGGGC 60.290 54.545 0.00 0.00 0.00 5.19
640 665 2.185663 TCGTTTTAGGGGATAGGGCT 57.814 50.000 0.00 0.00 0.00 5.19
641 666 1.766496 TCGTTTTAGGGGATAGGGCTG 59.234 52.381 0.00 0.00 0.00 4.85
642 667 1.202770 CGTTTTAGGGGATAGGGCTGG 60.203 57.143 0.00 0.00 0.00 4.85
644 669 2.106684 GTTTTAGGGGATAGGGCTGGAG 59.893 54.545 0.00 0.00 0.00 3.86
645 670 1.251136 TTAGGGGATAGGGCTGGAGA 58.749 55.000 0.00 0.00 0.00 3.71
646 671 1.483692 TAGGGGATAGGGCTGGAGAT 58.516 55.000 0.00 0.00 0.00 2.75
647 672 0.178879 AGGGGATAGGGCTGGAGATG 60.179 60.000 0.00 0.00 0.00 2.90
648 673 1.204113 GGGGATAGGGCTGGAGATGG 61.204 65.000 0.00 0.00 0.00 3.51
649 674 1.682257 GGATAGGGCTGGAGATGGC 59.318 63.158 0.00 0.00 0.00 4.40
654 679 1.149401 GGGCTGGAGATGGCCTAAC 59.851 63.158 3.32 0.00 46.80 2.34
655 680 1.149401 GGCTGGAGATGGCCTAACC 59.851 63.158 3.32 2.95 44.48 2.85
656 681 1.348775 GGCTGGAGATGGCCTAACCT 61.349 60.000 3.32 0.00 44.48 3.50
657 682 0.548510 GCTGGAGATGGCCTAACCTT 59.451 55.000 3.32 0.00 40.22 3.50
678 713 6.599244 ACCTTCTTTCGATTTTGATCTGCATA 59.401 34.615 0.00 0.00 0.00 3.14
757 792 4.024809 GTCGTTCCTGCTAAATAATGGAGC 60.025 45.833 0.00 0.00 36.72 4.70
772 807 0.827368 GGAGCCCACTCACTCTAAGG 59.173 60.000 0.00 0.00 45.42 2.69
778 813 3.491104 GCCCACTCACTCTAAGGATAACG 60.491 52.174 0.00 0.00 0.00 3.18
955 2144 2.031919 ATCCGTGACGCAGCCAAA 59.968 55.556 0.00 0.00 0.00 3.28
1018 2212 3.021451 CCATATTTGGCCCTCCGAC 57.979 57.895 0.00 0.00 35.85 4.79
1019 2213 0.537371 CCATATTTGGCCCTCCGACC 60.537 60.000 0.00 0.00 35.85 4.79
1028 2222 2.273179 CCCTCCGACCACGTTCAGA 61.273 63.158 0.00 0.00 37.88 3.27
1037 2231 0.234884 CCACGTTCAGAAAACGGAGC 59.765 55.000 14.00 0.00 46.86 4.70
1523 5277 2.833582 GATCGAGGCCGGACTGGA 60.834 66.667 25.53 25.53 42.00 3.86
2068 5822 4.214383 CAGCTGCAACGGATCGCG 62.214 66.667 0.00 0.00 0.00 5.87
2134 5888 3.812019 CCGACGGACTCCACCTCG 61.812 72.222 8.64 0.00 33.68 4.63
2167 5921 4.882396 GGCTTCGAGGAGCGGCTC 62.882 72.222 21.57 21.57 43.62 4.70
2239 5993 2.782222 GCTGGCCCATGCATCAGTG 61.782 63.158 13.02 0.00 40.13 3.66
2467 6221 2.647158 GGAAGACGAAGGCGAGGGT 61.647 63.158 0.00 0.00 41.64 4.34
2552 6306 0.741221 GCGAGATTTTCTCCGGCACT 60.741 55.000 0.00 0.00 40.34 4.40
2565 6319 2.607892 GGCACTTGTCGGAGCACAC 61.608 63.158 0.00 0.00 0.00 3.82
2580 6334 3.096092 AGCACACCAAAAAGAACCAAGA 58.904 40.909 0.00 0.00 0.00 3.02
2581 6335 3.706086 AGCACACCAAAAAGAACCAAGAT 59.294 39.130 0.00 0.00 0.00 2.40
2582 6336 4.051237 GCACACCAAAAAGAACCAAGATC 58.949 43.478 0.00 0.00 0.00 2.75
2593 6347 5.310409 AGAACCAAGATCAGGACTGAAAA 57.690 39.130 6.06 0.00 43.58 2.29
2608 6362 9.229784 CAGGACTGAAAATTTCAAATATCATCG 57.770 33.333 9.85 0.00 39.58 3.84
2651 6405 4.212716 AGCATGCTACATGTGATTTCCAT 58.787 39.130 21.21 0.00 0.00 3.41
2654 6408 6.492429 AGCATGCTACATGTGATTTCCATAAT 59.508 34.615 21.21 0.00 0.00 1.28
2658 6412 8.978874 TGCTACATGTGATTTCCATAATAAGT 57.021 30.769 9.11 0.00 0.00 2.24
2660 6414 8.292448 GCTACATGTGATTTCCATAATAAGTGG 58.708 37.037 9.11 0.00 38.11 4.00
2666 6420 2.519377 TCCATAATAAGTGGTCGCCG 57.481 50.000 0.00 0.00 37.96 6.46
2792 6546 1.000896 CGGTCCCTTCCAGCCAAAT 60.001 57.895 0.00 0.00 0.00 2.32
2799 6553 2.028748 CCCTTCCAGCCAAATTTGTCTG 60.029 50.000 19.80 19.80 0.00 3.51
2815 6569 1.742831 GTCTGTCACACTGCACCAAAA 59.257 47.619 0.00 0.00 0.00 2.44
2831 6585 3.282021 CCAAAATCCACCAGATCATCGT 58.718 45.455 0.00 0.00 32.47 3.73
2845 6599 2.622962 ATCGTCACTCGCCGTCACA 61.623 57.895 0.00 0.00 39.67 3.58
2897 6651 5.470047 ACATAGTAAGGGCGAGGATAAAG 57.530 43.478 0.00 0.00 0.00 1.85
2911 6665 5.063060 CGAGGATAAAGTTTACCTTTCACCG 59.937 44.000 14.24 10.53 42.44 4.94
3004 6759 1.591863 GACCGTGGCGAAGGATAGC 60.592 63.158 7.84 0.00 0.00 2.97
3007 6762 2.240500 CGTGGCGAAGGATAGCTGC 61.241 63.158 0.00 0.00 0.00 5.25
3024 6779 2.499205 CGCCACGGCATCCTTCTA 59.501 61.111 9.11 0.00 42.06 2.10
3031 6786 3.669354 GGCATCCTTCTACCGAGTG 57.331 57.895 0.00 0.00 0.00 3.51
3032 6787 1.112113 GGCATCCTTCTACCGAGTGA 58.888 55.000 0.00 0.00 0.00 3.41
3036 6791 2.125773 TCCTTCTACCGAGTGAGACC 57.874 55.000 0.00 0.00 0.00 3.85
3047 6802 0.745845 AGTGAGACCATCGGCATTGC 60.746 55.000 0.00 0.00 0.00 3.56
3132 7211 4.508551 TTTGGAGACTATCATGGCATGT 57.491 40.909 25.62 15.77 0.00 3.21
3136 7215 3.924144 GAGACTATCATGGCATGTCTCC 58.076 50.000 24.56 14.30 44.41 3.71
3164 7243 2.658807 TATCCTTGCTCGAGCTCCTA 57.341 50.000 35.27 19.91 42.66 2.94
3220 10486 5.940192 TTCTAAAACCACATGTGCAGTAG 57.060 39.130 20.81 16.34 0.00 2.57
3241 10507 7.861372 CAGTAGTATATCGACCAAAAGGTACTG 59.139 40.741 0.00 0.00 40.86 2.74
3244 10510 8.474710 AGTATATCGACCAAAAGGTACTGTAT 57.525 34.615 0.00 0.00 40.86 2.29
3245 10514 9.578576 AGTATATCGACCAAAAGGTACTGTATA 57.421 33.333 0.00 0.00 40.86 1.47
3256 10525 7.991084 AAAGGTACTGTATAAACCAACCTTC 57.009 36.000 7.58 0.00 40.86 3.46
3261 10530 8.096414 GGTACTGTATAAACCAACCTTCTGTTA 58.904 37.037 0.00 0.00 34.69 2.41
3262 10531 9.148104 GTACTGTATAAACCAACCTTCTGTTAG 57.852 37.037 0.00 0.00 34.69 2.34
3298 10567 6.724263 TGGTAAATGATATGAACGCATCAAC 58.276 36.000 0.00 0.00 42.54 3.18
3337 10606 6.371548 GCAGAAATGGAAGTACAGTATGAACA 59.628 38.462 0.00 0.00 39.69 3.18
3379 10648 9.185192 GATATCACCAGCAGCAAAAATATTAAC 57.815 33.333 0.00 0.00 0.00 2.01
3442 10711 4.400251 TCCATCATTGTCCAAGCAATCTTC 59.600 41.667 0.00 0.00 37.00 2.87
3467 10736 4.718774 AGCTCAGAACCTCTAATCCATGAA 59.281 41.667 0.00 0.00 0.00 2.57
3545 10814 0.251354 ACGACGTCCTGTAGAGCCTA 59.749 55.000 10.58 0.00 0.00 3.93
3561 10830 2.178764 AGCCTATCTCCCTCTGACATGA 59.821 50.000 0.00 0.00 0.00 3.07
3605 10874 7.867403 TGCTCCAAATAAACTTCAACATTCTTC 59.133 33.333 0.00 0.00 0.00 2.87
3645 10914 2.562738 GCCTTACCACCAGCTTTTTGAT 59.437 45.455 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.064824 ATGCTCAAGGATCCTCCCCC 61.065 60.000 16.52 5.14 37.19 5.40
13 14 3.196469 CAGTTGTAGAGGATGCTCAAGGA 59.804 47.826 17.24 0.00 0.00 3.36
19 20 0.543749 GGGCAGTTGTAGAGGATGCT 59.456 55.000 0.00 0.00 37.08 3.79
20 21 0.811616 CGGGCAGTTGTAGAGGATGC 60.812 60.000 0.00 0.00 36.16 3.91
35 36 4.484872 GAGGCTACAACCCCGGGC 62.485 72.222 17.73 0.37 0.00 6.13
36 37 3.793888 GGAGGCTACAACCCCGGG 61.794 72.222 15.80 15.80 0.00 5.73
87 88 1.396653 CTTATCCCGTCGGTGGTAGT 58.603 55.000 11.06 0.00 0.00 2.73
94 95 0.038526 CCGATTCCTTATCCCGTCGG 60.039 60.000 3.60 3.60 41.98 4.79
98 99 0.320771 CTGCCCGATTCCTTATCCCG 60.321 60.000 0.00 0.00 0.00 5.14
103 104 1.153449 CACGCTGCCCGATTCCTTA 60.153 57.895 0.61 0.00 41.02 2.69
127 128 0.396435 TTGATGGGCGTTGACACTCT 59.604 50.000 0.00 0.00 0.00 3.24
131 132 2.565647 CCATTGATGGGCGTTGACA 58.434 52.632 1.92 0.00 44.31 3.58
145 146 0.758123 CACCACCCTTTGTTGCCATT 59.242 50.000 0.00 0.00 0.00 3.16
150 151 2.498167 CTCTCTCACCACCCTTTGTTG 58.502 52.381 0.00 0.00 0.00 3.33
152 153 1.059913 CCTCTCTCACCACCCTTTGT 58.940 55.000 0.00 0.00 0.00 2.83
161 162 0.247736 ATTCACACGCCTCTCTCACC 59.752 55.000 0.00 0.00 0.00 4.02
172 173 1.963679 CCCAAACCCCATTCACACG 59.036 57.895 0.00 0.00 0.00 4.49
191 193 0.753262 CCACTCCACTCCCCTAATCG 59.247 60.000 0.00 0.00 0.00 3.34
214 216 6.038271 GTGAGGTGGAATGTATTGACCATTAC 59.962 42.308 0.00 0.00 34.35 1.89
221 223 3.947196 GCATGTGAGGTGGAATGTATTGA 59.053 43.478 0.00 0.00 0.00 2.57
233 235 0.038744 CCTTGGGAAGCATGTGAGGT 59.961 55.000 0.00 0.00 0.00 3.85
234 236 0.038744 ACCTTGGGAAGCATGTGAGG 59.961 55.000 0.00 0.00 0.00 3.86
259 261 4.685169 TGATTGAATCTGCCTTTTCGTC 57.315 40.909 6.73 0.00 0.00 4.20
280 282 2.066999 GGTCCGGCTGAGGAGGAAT 61.067 63.158 0.00 0.00 41.68 3.01
294 296 1.269778 GCTCAAAGCAGTTTTGGGTCC 60.270 52.381 10.96 0.00 46.88 4.46
329 331 3.914426 AGTCCAGGCTACATCGAATTT 57.086 42.857 0.00 0.00 0.00 1.82
345 347 2.872858 GGATGCAAATTCGGTCTAGTCC 59.127 50.000 0.00 0.00 0.00 3.85
389 392 2.729882 GCACACGTGTTTAGTAGGTCAG 59.270 50.000 20.79 4.05 0.00 3.51
455 462 1.154205 GGTTCACGATGGAGATGCCG 61.154 60.000 0.00 0.00 40.66 5.69
469 476 2.293170 TGCAGATTGTTTGACGGTTCA 58.707 42.857 0.00 0.00 0.00 3.18
471 478 4.050553 CAATTGCAGATTGTTTGACGGTT 58.949 39.130 11.27 0.00 0.00 4.44
540 564 8.879342 AACGTTTGGACATATTTCAAATGAAA 57.121 26.923 10.71 10.71 46.60 2.69
542 566 8.138074 TCAAACGTTTGGACATATTTCAAATGA 58.862 29.630 33.97 11.48 38.79 2.57
548 573 6.539324 TCGATCAAACGTTTGGACATATTTC 58.461 36.000 33.97 18.54 38.66 2.17
553 578 4.570772 CCTATCGATCAAACGTTTGGACAT 59.429 41.667 33.97 23.12 38.66 3.06
562 587 3.173668 TCCAACCCTATCGATCAAACG 57.826 47.619 0.00 0.00 0.00 3.60
563 588 3.815401 CCATCCAACCCTATCGATCAAAC 59.185 47.826 0.00 0.00 0.00 2.93
564 589 3.747388 GCCATCCAACCCTATCGATCAAA 60.747 47.826 0.00 0.00 0.00 2.69
565 590 2.224523 GCCATCCAACCCTATCGATCAA 60.225 50.000 0.00 0.00 0.00 2.57
566 591 1.347707 GCCATCCAACCCTATCGATCA 59.652 52.381 0.00 0.00 0.00 2.92
567 592 1.339151 GGCCATCCAACCCTATCGATC 60.339 57.143 0.00 0.00 0.00 3.69
595 620 2.469826 TCGCGGACATGACATTGATAC 58.530 47.619 6.13 0.00 0.00 2.24
601 626 3.780693 CGTTCGCGGACATGACAT 58.219 55.556 19.39 0.00 36.88 3.06
639 664 2.122768 AGAAGGTTAGGCCATCTCCAG 58.877 52.381 5.01 0.00 41.05 3.86
640 665 2.270434 AGAAGGTTAGGCCATCTCCA 57.730 50.000 5.01 0.00 41.05 3.86
641 666 3.546724 GAAAGAAGGTTAGGCCATCTCC 58.453 50.000 5.01 1.34 43.86 3.71
642 667 3.118738 TCGAAAGAAGGTTAGGCCATCTC 60.119 47.826 5.01 0.00 43.86 2.75
644 669 3.261981 TCGAAAGAAGGTTAGGCCATC 57.738 47.619 5.01 0.00 37.03 3.51
660 695 6.988580 AGATGAGTATGCAGATCAAAATCGAA 59.011 34.615 0.00 0.00 36.97 3.71
678 713 3.838903 AGAGTTTCCCCGTTAAGATGAGT 59.161 43.478 0.00 0.00 0.00 3.41
757 792 3.068307 CCGTTATCCTTAGAGTGAGTGGG 59.932 52.174 0.00 0.00 0.00 4.61
772 807 2.547826 GTACAGTGGCCTTCCGTTATC 58.452 52.381 3.32 0.00 34.14 1.75
778 813 3.735181 CTACGTACAGTGGCCTTCC 57.265 57.895 3.32 0.00 0.00 3.46
841 2030 1.854743 CGTAACATGACAGCGAGATGG 59.145 52.381 0.00 0.00 0.00 3.51
955 2144 3.496870 GGGACCAGATCAACAAGTCAGTT 60.497 47.826 0.00 0.00 0.00 3.16
1017 2211 1.578583 CTCCGTTTTCTGAACGTGGT 58.421 50.000 9.97 0.00 41.64 4.16
1018 2212 0.234884 GCTCCGTTTTCTGAACGTGG 59.765 55.000 9.97 4.17 41.64 4.94
1019 2213 0.111266 CGCTCCGTTTTCTGAACGTG 60.111 55.000 9.97 4.47 41.64 4.49
1028 2222 1.002087 ACTTGGATCTCGCTCCGTTTT 59.998 47.619 0.00 0.00 38.21 2.43
1037 2231 1.201812 CGCGTTTGAACTTGGATCTCG 60.202 52.381 0.00 0.00 0.00 4.04
1067 2261 3.485463 TCCGTGGAGTTCACAGATTTT 57.515 42.857 1.66 0.00 46.36 1.82
1769 5523 2.993264 GGAGTCGTCCGGGACCAA 60.993 66.667 21.06 7.19 37.66 3.67
2221 5975 2.441532 ACTGATGCATGGGCCAGC 60.442 61.111 13.78 16.16 40.13 4.85
2467 6221 1.228429 CTTCACCTTGGCCCCGAAA 60.228 57.895 0.00 0.00 0.00 3.46
2552 6306 1.403679 CTTTTTGGTGTGCTCCGACAA 59.596 47.619 0.00 0.00 0.00 3.18
2565 6319 4.829492 AGTCCTGATCTTGGTTCTTTTTGG 59.171 41.667 0.00 0.00 0.00 3.28
2582 6336 9.229784 CGATGATATTTGAAATTTTCAGTCCTG 57.770 33.333 11.41 0.00 41.38 3.86
2608 6362 5.928839 TGCTTCACTTCACTGAAAGATAGTC 59.071 40.000 0.00 0.00 37.43 2.59
2651 6405 3.865011 TGTAACGGCGACCACTTATTA 57.135 42.857 16.62 0.00 0.00 0.98
2654 6408 2.522836 TTTGTAACGGCGACCACTTA 57.477 45.000 16.62 0.00 0.00 2.24
2658 6412 3.136763 TGTAAATTTGTAACGGCGACCA 58.863 40.909 16.62 3.54 0.00 4.02
2660 6414 3.907788 GGTTGTAAATTTGTAACGGCGAC 59.092 43.478 16.62 1.95 0.00 5.19
2666 6420 7.328982 CGGTTTATGGGGTTGTAAATTTGTAAC 59.671 37.037 0.00 5.96 0.00 2.50
2792 6546 1.339535 TGGTGCAGTGTGACAGACAAA 60.340 47.619 5.43 0.00 35.91 2.83
2799 6553 1.680735 TGGATTTTGGTGCAGTGTGAC 59.319 47.619 0.00 0.00 0.00 3.67
2815 6569 2.363680 GAGTGACGATGATCTGGTGGAT 59.636 50.000 0.00 0.00 37.37 3.41
2831 6585 2.910479 ACCTGTGACGGCGAGTGA 60.910 61.111 16.62 0.00 0.00 3.41
2879 6633 4.838904 AAACTTTATCCTCGCCCTTACT 57.161 40.909 0.00 0.00 0.00 2.24
2897 6651 2.031420 GCTTCCACGGTGAAAGGTAAAC 60.031 50.000 10.28 0.00 0.00 2.01
2911 6665 2.045536 CTCTGCTGGGGCTTCCAC 60.046 66.667 0.00 0.00 41.46 4.02
3007 6762 1.883084 GTAGAAGGATGCCGTGGCG 60.883 63.158 6.37 0.00 45.51 5.69
3024 6779 3.604629 CCGATGGTCTCACTCGGT 58.395 61.111 2.18 0.00 45.30 4.69
3027 6782 1.293924 CAATGCCGATGGTCTCACTC 58.706 55.000 0.00 0.00 0.00 3.51
3029 6784 0.745845 AGCAATGCCGATGGTCTCAC 60.746 55.000 0.00 0.00 0.00 3.51
3030 6785 0.745486 CAGCAATGCCGATGGTCTCA 60.745 55.000 0.00 0.00 0.00 3.27
3031 6786 0.745845 ACAGCAATGCCGATGGTCTC 60.746 55.000 0.00 0.00 0.00 3.36
3032 6787 0.745845 GACAGCAATGCCGATGGTCT 60.746 55.000 0.00 0.00 0.00 3.85
3036 6791 0.659427 ATTCGACAGCAATGCCGATG 59.341 50.000 0.00 0.00 0.00 3.84
3078 6833 2.824689 TGATGCATGGGGCTAAAGAA 57.175 45.000 2.46 0.00 45.15 2.52
3132 7211 2.821546 CAAGGATATTTCGTGCGGAGA 58.178 47.619 0.00 0.00 0.00 3.71
3136 7215 1.071239 CGAGCAAGGATATTTCGTGCG 60.071 52.381 10.42 0.00 38.15 5.34
3244 10510 8.607713 TCCATTATCTAACAGAAGGTTGGTTTA 58.392 33.333 0.00 0.00 40.73 2.01
3245 10514 7.466804 TCCATTATCTAACAGAAGGTTGGTTT 58.533 34.615 0.00 0.00 40.73 3.27
3283 10552 4.517285 AGTTCCAGTTGATGCGTTCATAT 58.483 39.130 0.00 0.00 33.34 1.78
3298 10567 4.543692 CATTTCTGCTGTTGAAGTTCCAG 58.456 43.478 0.00 2.71 0.00 3.86
3337 10606 6.173339 GGTGATATCATTGACATTCCGGTAT 58.827 40.000 9.02 0.00 0.00 2.73
3379 10648 3.922171 ATCTAAGAGTGAAAGGCCAGG 57.078 47.619 5.01 0.00 0.00 4.45
3442 10711 2.768527 TGGATTAGAGGTTCTGAGCTGG 59.231 50.000 0.00 0.00 32.79 4.85
3467 10736 1.883275 CTCGACAGACCACTGAGTTCT 59.117 52.381 0.00 0.00 46.03 3.01
3545 10814 3.992999 AGAGTTCATGTCAGAGGGAGAT 58.007 45.455 0.00 0.00 0.00 2.75
3561 10830 4.037446 GGAGCAGTTGATCGATCTAGAGTT 59.963 45.833 25.02 11.33 0.00 3.01
3605 10874 0.725686 CACTGCTTTGGCTGAGATCG 59.274 55.000 2.18 0.00 40.03 3.69
3645 10914 5.139727 ACCAAGATTGTTGGAATCTGTTGA 58.860 37.500 18.72 0.00 42.06 3.18


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

AutoCloner maintained by Alex Coulton.