Multiple sequence alignment - TraesCS5D01G516400

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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 TraesCS5D01G516400 chr5D 100.000 3669 0 0 1 3669 539021507 539025175 0.000000e+00 6776
1 TraesCS5D01G516400 chr4A 92.333 2726 112 41 1 2678 629479996 629477320 0.000000e+00 3786
2 TraesCS5D01G516400 chr4A 93.538 944 35 7 2750 3669 629477293 629476352 0.000000e+00 1382
3 TraesCS5D01G516400 chr5B 91.748 2242 94 37 495 2721 680600959 680603124 0.000000e+00 3031
4 TraesCS5D01G516400 chr5B 92.316 937 52 9 2750 3669 680603130 680604063 0.000000e+00 1314
5 TraesCS5D01G516400 chr2D 92.476 1648 79 23 1040 2674 68584080 68582465 0.000000e+00 2314
6 TraesCS5D01G516400 chr2D 92.457 1644 79 22 1044 2674 68621227 68619616 0.000000e+00 2307
7 TraesCS5D01G516400 chr2D 92.383 1641 89 20 1044 2674 68561918 68560304 0.000000e+00 2305
8 TraesCS5D01G516400 chr2A 92.105 76 6 0 2126 2201 440069815 440069740 1.390000e-19 108
9 TraesCS5D01G516400 chr2B 90.789 76 7 0 2126 2201 400351689 400351614 6.480000e-18 102


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 TraesCS5D01G516400 chr5D 539021507 539025175 3668 False 6776.0 6776 100.0000 1 3669 1 chr5D.!!$F1 3668
1 TraesCS5D01G516400 chr4A 629476352 629479996 3644 True 2584.0 3786 92.9355 1 3669 2 chr4A.!!$R1 3668
2 TraesCS5D01G516400 chr5B 680600959 680604063 3104 False 2172.5 3031 92.0320 495 3669 2 chr5B.!!$F1 3174
3 TraesCS5D01G516400 chr2D 68582465 68584080 1615 True 2314.0 2314 92.4760 1040 2674 1 chr2D.!!$R2 1634
4 TraesCS5D01G516400 chr2D 68619616 68621227 1611 True 2307.0 2307 92.4570 1044 2674 1 chr2D.!!$R3 1630
5 TraesCS5D01G516400 chr2D 68560304 68561918 1614 True 2305.0 2305 92.3830 1044 2674 1 chr2D.!!$R1 1630

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
117 118 0.102481 GCCCGTATCGCTTGAGAGAA 59.898 55.0 0.00 0.0 0.00 2.87 F
239 242 0.169672 CCGTCGACGTTGACATAGGT 59.830 55.0 33.49 0.0 38.84 3.08 F
989 1023 0.980423 AGCTCTGTCAACCTTCCTCC 59.020 55.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1588 0.249868 TGACCTTGAGCGTGAACTGG 60.250 55.000 0.0 0.0 0.0 4.00 R
2138 2196 2.283529 ACCTGGAAGCCGTCGATGT 61.284 57.895 0.0 0.0 0.0 3.06 R
2742 2817 0.179174 CGCCACCTCGCCAATTAAAC 60.179 55.000 0.0 0.0 0.0 2.01 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
20 21 2.664185 CGATCCTGCCCAGCATCG 60.664 66.667 7.16 7.16 38.13 3.84
22 23 3.472943 GATCCTGCCCAGCATCGCT 62.473 63.158 0.00 0.00 38.13 4.93
41 42 2.360726 TCGGAGCCTCACGCACTA 60.361 61.111 0.00 0.00 41.38 2.74
53 54 1.002624 CGCACTACCACCCCATGTT 60.003 57.895 0.00 0.00 0.00 2.71
56 57 1.271926 GCACTACCACCCCATGTTTCT 60.272 52.381 0.00 0.00 0.00 2.52
57 58 2.436417 CACTACCACCCCATGTTTCTG 58.564 52.381 0.00 0.00 0.00 3.02
76 77 3.017581 CTACCCAGGCAAGCCCCT 61.018 66.667 7.62 0.00 36.58 4.79
109 110 2.491022 GGAGTCTGCCCGTATCGCT 61.491 63.158 0.00 0.00 0.00 4.93
117 118 0.102481 GCCCGTATCGCTTGAGAGAA 59.898 55.000 0.00 0.00 0.00 2.87
121 122 3.305676 CCCGTATCGCTTGAGAGAATCAT 60.306 47.826 0.00 0.00 37.89 2.45
128 129 2.802256 CTTGAGAGAATCATCGACGCA 58.198 47.619 0.00 0.00 37.89 5.24
135 138 2.159184 AGAATCATCGACGCATCACAGT 60.159 45.455 0.00 0.00 0.00 3.55
143 146 2.500442 CGCATCACAGTCGTCTCGC 61.500 63.158 0.00 0.00 0.00 5.03
167 170 4.320456 CCTCCGCCACACAGCTGT 62.320 66.667 15.25 15.25 0.00 4.40
168 171 2.740055 CTCCGCCACACAGCTGTC 60.740 66.667 18.64 4.61 0.00 3.51
169 172 3.519973 CTCCGCCACACAGCTGTCA 62.520 63.158 18.64 0.00 0.00 3.58
200 203 0.323302 TAGCATCGCAACCCTGACAA 59.677 50.000 0.00 0.00 0.00 3.18
201 204 1.210155 GCATCGCAACCCTGACAAC 59.790 57.895 0.00 0.00 0.00 3.32
206 209 2.258726 GCAACCCTGACAACCGACC 61.259 63.158 0.00 0.00 0.00 4.79
213 216 2.818274 GACAACCGACCGCATCCC 60.818 66.667 0.00 0.00 0.00 3.85
239 242 0.169672 CCGTCGACGTTGACATAGGT 59.830 55.000 33.49 0.00 38.84 3.08
269 272 2.317609 CGACAACACCTTCTGGCGG 61.318 63.158 0.00 0.00 40.47 6.13
271 274 2.594303 CAACACCTTCTGGCGGCA 60.594 61.111 12.58 12.58 36.63 5.69
272 275 2.192861 CAACACCTTCTGGCGGCAA 61.193 57.895 14.48 0.00 36.63 4.52
273 276 2.193536 AACACCTTCTGGCGGCAAC 61.194 57.895 14.48 0.00 36.63 4.17
290 307 3.077556 CGAGGTGGAGGAGGTGGG 61.078 72.222 0.00 0.00 0.00 4.61
300 317 2.590092 GAGGTGGGGGATTGTCCG 59.410 66.667 0.00 0.00 37.43 4.79
308 325 3.195698 GGATTGTCCGGCTGTCGC 61.196 66.667 0.00 0.00 37.59 5.19
339 356 2.158449 GCGAACAAGATGAAGGTGTCAG 59.842 50.000 0.00 0.00 40.43 3.51
340 357 2.738846 CGAACAAGATGAAGGTGTCAGG 59.261 50.000 0.00 0.00 40.43 3.86
353 370 1.137086 GTGTCAGGTCGTCAGCCATAT 59.863 52.381 0.00 0.00 0.00 1.78
358 375 1.337071 AGGTCGTCAGCCATATACACG 59.663 52.381 0.00 0.00 0.00 4.49
378 395 2.480224 CATTCATGCAACGGCTAAGG 57.520 50.000 0.00 0.00 41.91 2.69
389 406 1.208776 ACGGCTAAGGTACAACCATCC 59.791 52.381 0.00 0.00 41.95 3.51
390 407 1.485066 CGGCTAAGGTACAACCATCCT 59.515 52.381 0.00 0.00 41.95 3.24
409 426 6.379703 CCATCCTGTTAACCATTCAACCATAA 59.620 38.462 2.48 0.00 0.00 1.90
411 428 6.548321 TCCTGTTAACCATTCAACCATAAGT 58.452 36.000 2.48 0.00 0.00 2.24
455 472 9.398170 CAACTTTTGTAAATGAACATAGACCTG 57.602 33.333 0.00 0.00 0.00 4.00
487 504 5.244626 GGTAGGTACCTGTGAGTAGAAAACA 59.755 44.000 25.33 0.00 43.10 2.83
628 657 2.125512 GGCCGGCACACTCTACAG 60.126 66.667 30.85 0.00 0.00 2.74
643 672 6.492429 ACACTCTACAGGTCACACAAATACTA 59.508 38.462 0.00 0.00 0.00 1.82
644 673 7.030165 CACTCTACAGGTCACACAAATACTAG 58.970 42.308 0.00 0.00 0.00 2.57
646 675 7.886970 ACTCTACAGGTCACACAAATACTAGTA 59.113 37.037 4.77 4.77 0.00 1.82
647 676 8.048534 TCTACAGGTCACACAAATACTAGTAC 57.951 38.462 4.31 0.00 0.00 2.73
648 677 6.912951 ACAGGTCACACAAATACTAGTACT 57.087 37.500 4.31 0.00 0.00 2.73
649 678 7.299246 ACAGGTCACACAAATACTAGTACTT 57.701 36.000 4.31 0.00 0.00 2.24
650 679 7.376615 ACAGGTCACACAAATACTAGTACTTC 58.623 38.462 4.31 0.00 0.00 3.01
659 689 7.819900 CACAAATACTAGTACTTCTTTGGAGCT 59.180 37.037 21.91 0.00 0.00 4.09
666 696 8.688151 ACTAGTACTTCTTTGGAGCTGTTATAG 58.312 37.037 0.00 0.00 0.00 1.31
758 788 4.745125 GCTAAAGCAGAGCACGTAATCATA 59.255 41.667 0.00 0.00 39.84 2.15
780 810 9.822185 TCATAGATGTATGCATGGTGTATAATC 57.178 33.333 10.16 1.21 36.68 1.75
825 857 1.541588 GGCACCAAAGACAAAGGCTAG 59.458 52.381 0.00 0.00 0.00 3.42
864 896 2.368875 ACAATGGAACTCGAGTGAACCT 59.631 45.455 20.85 1.81 0.00 3.50
914 946 4.539152 GTAACGACGACGAGGCAA 57.461 55.556 15.32 0.00 42.66 4.52
981 1013 3.852536 GTGATACGTACAGCTCTGTCAAC 59.147 47.826 5.72 0.00 43.74 3.18
985 1017 2.288273 ACGTACAGCTCTGTCAACCTTC 60.288 50.000 5.72 0.00 43.74 3.46
989 1023 0.980423 AGCTCTGTCAACCTTCCTCC 59.020 55.000 0.00 0.00 0.00 4.30
1953 2011 3.755628 TTCCTCGGCGAGAACCCG 61.756 66.667 36.47 19.91 46.88 5.28
1988 2046 1.980784 CTCAGGGAGGAGCACATGGG 61.981 65.000 0.00 0.00 0.00 4.00
2263 2321 2.809601 GATTCGACGTGCGTGCCT 60.810 61.111 0.67 0.00 41.80 4.75
2264 2322 1.515519 GATTCGACGTGCGTGCCTA 60.516 57.895 0.67 0.00 41.80 3.93
2269 2331 3.060020 GACGTGCGTGCCTAGCCTA 62.060 63.158 0.67 0.00 0.00 3.93
2312 2374 2.547394 CGAGCAGCCGAGCTAGCTA 61.547 63.158 19.38 0.00 46.75 3.32
2453 2517 2.022129 CGTCTTCGCACACCACCTC 61.022 63.158 0.00 0.00 0.00 3.85
2484 2548 2.997897 AGTGAGTCGCTGTCCCCC 60.998 66.667 5.14 0.00 0.00 5.40
2522 2597 3.936203 GGCCACCGTGTCCAGTCA 61.936 66.667 0.00 0.00 0.00 3.41
2533 2608 2.558795 GTGTCCAGTCACTAGCTCTGAA 59.441 50.000 0.00 0.00 35.68 3.02
2534 2609 3.005897 GTGTCCAGTCACTAGCTCTGAAA 59.994 47.826 0.00 0.00 35.68 2.69
2535 2610 3.005897 TGTCCAGTCACTAGCTCTGAAAC 59.994 47.826 0.00 8.44 0.00 2.78
2536 2611 2.229062 TCCAGTCACTAGCTCTGAAACG 59.771 50.000 0.00 0.00 0.00 3.60
2537 2612 2.600731 CAGTCACTAGCTCTGAAACGG 58.399 52.381 0.00 0.00 0.00 4.44
2538 2613 1.067495 AGTCACTAGCTCTGAAACGGC 60.067 52.381 0.00 0.00 0.00 5.68
2539 2614 0.246635 TCACTAGCTCTGAAACGGCC 59.753 55.000 0.00 0.00 0.00 6.13
2540 2615 1.078759 CACTAGCTCTGAAACGGCCG 61.079 60.000 26.86 26.86 0.00 6.13
2541 2616 1.519455 CTAGCTCTGAAACGGCCGG 60.519 63.158 31.76 11.50 0.00 6.13
2542 2617 3.659089 TAGCTCTGAAACGGCCGGC 62.659 63.158 31.76 21.18 0.00 6.13
2544 2619 2.577059 CTCTGAAACGGCCGGCTA 59.423 61.111 31.76 11.78 0.00 3.93
2545 2620 1.079405 CTCTGAAACGGCCGGCTAA 60.079 57.895 31.76 11.48 0.00 3.09
2546 2621 1.359459 CTCTGAAACGGCCGGCTAAC 61.359 60.000 31.76 15.77 0.00 2.34
2547 2622 2.736682 CTGAAACGGCCGGCTAACG 61.737 63.158 31.76 23.74 43.80 3.18
2560 2635 3.460103 CGGCTAACGGTAATAATGGTGT 58.540 45.455 0.00 0.00 39.42 4.16
2561 2636 3.872771 CGGCTAACGGTAATAATGGTGTT 59.127 43.478 0.00 0.00 39.42 3.32
2562 2637 4.333372 CGGCTAACGGTAATAATGGTGTTT 59.667 41.667 0.00 0.00 39.42 2.83
2563 2638 5.575019 GGCTAACGGTAATAATGGTGTTTG 58.425 41.667 0.00 0.00 0.00 2.93
2675 2750 3.036429 GCGCTCCCCTGAACTCCAT 62.036 63.158 0.00 0.00 0.00 3.41
2689 2764 1.502163 CTCCATCTCCGGCGATTTGC 61.502 60.000 9.30 0.00 45.38 3.68
2700 2775 2.025156 GATTTGCGCCGATGCTGG 59.975 61.111 4.18 0.00 35.36 4.85
2721 2796 2.686835 GCTCTGACCCCAGCTCCT 60.687 66.667 0.00 0.00 40.20 3.69
2723 2798 1.305633 CTCTGACCCCAGCTCCTGA 60.306 63.158 0.00 0.00 40.20 3.86
2724 2799 0.906756 CTCTGACCCCAGCTCCTGAA 60.907 60.000 0.00 0.00 40.20 3.02
2725 2800 0.252881 TCTGACCCCAGCTCCTGAAT 60.253 55.000 0.00 0.00 40.20 2.57
2726 2801 0.622665 CTGACCCCAGCTCCTGAATT 59.377 55.000 0.00 0.00 32.44 2.17
2727 2802 1.839994 CTGACCCCAGCTCCTGAATTA 59.160 52.381 0.00 0.00 32.44 1.40
2728 2803 2.441001 CTGACCCCAGCTCCTGAATTAT 59.559 50.000 0.00 0.00 32.44 1.28
2729 2804 2.852449 TGACCCCAGCTCCTGAATTATT 59.148 45.455 0.00 0.00 32.44 1.40
2730 2805 3.269381 TGACCCCAGCTCCTGAATTATTT 59.731 43.478 0.00 0.00 32.44 1.40
2731 2806 4.476846 TGACCCCAGCTCCTGAATTATTTA 59.523 41.667 0.00 0.00 32.44 1.40
2732 2807 4.793201 ACCCCAGCTCCTGAATTATTTAC 58.207 43.478 0.00 0.00 32.44 2.01
2733 2808 4.478686 ACCCCAGCTCCTGAATTATTTACT 59.521 41.667 0.00 0.00 32.44 2.24
2734 2809 5.044105 ACCCCAGCTCCTGAATTATTTACTT 60.044 40.000 0.00 0.00 32.44 2.24
2735 2810 5.300286 CCCCAGCTCCTGAATTATTTACTTG 59.700 44.000 0.00 0.00 32.44 3.16
2736 2811 5.888161 CCCAGCTCCTGAATTATTTACTTGT 59.112 40.000 0.00 0.00 32.44 3.16
2737 2812 6.378280 CCCAGCTCCTGAATTATTTACTTGTT 59.622 38.462 0.00 0.00 32.44 2.83
2738 2813 7.556275 CCCAGCTCCTGAATTATTTACTTGTTA 59.444 37.037 0.00 0.00 32.44 2.41
2739 2814 9.125026 CCAGCTCCTGAATTATTTACTTGTTAT 57.875 33.333 0.00 0.00 32.44 1.89
2774 2849 1.281566 GGTGGCGGCATTTGTTTTCG 61.282 55.000 17.19 0.00 0.00 3.46
2803 2878 0.887836 AGACCGACACGCACTCTACA 60.888 55.000 0.00 0.00 0.00 2.74
2837 2914 4.041567 TCGGCATGGTCAGATTATGGTATT 59.958 41.667 0.00 0.00 0.00 1.89
2848 2925 7.715249 GTCAGATTATGGTATTTTGAGGCTACA 59.285 37.037 0.00 0.00 0.00 2.74
2881 2958 6.266168 TGGACCAACTATATGCAAACTTTG 57.734 37.500 0.00 0.00 0.00 2.77
3009 3088 8.154649 AGTGAACAAAACATTCTTTAGACGAT 57.845 30.769 0.00 0.00 0.00 3.73
3010 3089 8.621286 AGTGAACAAAACATTCTTTAGACGATT 58.379 29.630 0.00 0.00 0.00 3.34
3011 3090 9.872757 GTGAACAAAACATTCTTTAGACGATTA 57.127 29.630 0.00 0.00 0.00 1.75
3105 3184 2.028294 TGGCCATGTAAACTTGCAATGG 60.028 45.455 0.00 3.87 0.00 3.16
3195 3276 4.314121 CCAGGTAGCTCAGCATTATTCTC 58.686 47.826 0.00 0.00 0.00 2.87
3273 3354 3.013921 ACAGCTCAACGAAACAAGGAAA 58.986 40.909 0.00 0.00 0.00 3.13
3344 3425 2.104281 ACAAACTCCAGTGACCAGGTAC 59.896 50.000 0.00 0.00 0.00 3.34
3439 3520 1.343142 TGGCTATGGTATACTGGCACG 59.657 52.381 2.25 0.00 0.00 5.34
3451 3532 1.019673 CTGGCACGGATTGGAATCAG 58.980 55.000 1.94 0.31 37.15 2.90
3634 3732 3.812156 TTACGGACCGATGATTGTCAT 57.188 42.857 23.38 0.00 40.34 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.357947 GTGCGTGAGGCTCCGACA 62.358 66.667 23.46 18.07 44.05 4.35
24 25 2.360726 TAGTGCGTGAGGCTCCGA 60.361 61.111 23.46 10.08 44.05 4.55
26 27 2.184579 GGTAGTGCGTGAGGCTCC 59.815 66.667 12.86 2.37 44.05 4.70
36 37 1.173913 GAAACATGGGGTGGTAGTGC 58.826 55.000 0.00 0.00 0.00 4.40
41 42 1.228862 GGCAGAAACATGGGGTGGT 60.229 57.895 0.00 0.00 0.00 4.16
76 77 2.041430 TCCCCGTTCCATAGGGCA 59.959 61.111 0.00 0.00 46.24 5.36
77 78 2.041206 GACTCCCCGTTCCATAGGGC 62.041 65.000 0.00 0.00 46.24 5.19
79 80 0.753262 CAGACTCCCCGTTCCATAGG 59.247 60.000 0.00 0.00 0.00 2.57
80 81 0.105039 GCAGACTCCCCGTTCCATAG 59.895 60.000 0.00 0.00 0.00 2.23
109 110 2.939460 TGCGTCGATGATTCTCTCAA 57.061 45.000 9.31 0.00 37.44 3.02
117 118 1.845266 GACTGTGATGCGTCGATGAT 58.155 50.000 9.31 0.00 0.00 2.45
128 129 4.870305 GTGCGAGACGACTGTGAT 57.130 55.556 0.00 0.00 0.00 3.06
154 157 3.705638 CGTGACAGCTGTGTGGCG 61.706 66.667 27.27 17.94 36.88 5.69
155 158 2.588877 ACGTGACAGCTGTGTGGC 60.589 61.111 27.27 10.48 36.88 5.01
156 159 1.956170 GGACGTGACAGCTGTGTGG 60.956 63.158 27.27 14.75 36.88 4.17
157 160 1.956170 GGGACGTGACAGCTGTGTG 60.956 63.158 27.27 15.72 36.88 3.82
158 161 2.421739 GGGACGTGACAGCTGTGT 59.578 61.111 27.27 16.61 40.71 3.72
226 229 1.174783 AGCTCGACCTATGTCAACGT 58.825 50.000 0.00 0.00 41.85 3.99
269 272 2.266055 CCTCCTCCACCTCGTTGC 59.734 66.667 0.00 0.00 0.00 4.17
271 274 1.913762 CCACCTCCTCCACCTCGTT 60.914 63.158 0.00 0.00 0.00 3.85
272 275 2.283966 CCACCTCCTCCACCTCGT 60.284 66.667 0.00 0.00 0.00 4.18
273 276 3.077556 CCCACCTCCTCCACCTCG 61.078 72.222 0.00 0.00 0.00 4.63
275 278 4.354943 CCCCCACCTCCTCCACCT 62.355 72.222 0.00 0.00 0.00 4.00
280 297 1.636769 GGACAATCCCCCACCTCCTC 61.637 65.000 0.00 0.00 0.00 3.71
290 307 2.511600 CGACAGCCGGACAATCCC 60.512 66.667 5.05 0.00 31.13 3.85
316 333 0.179215 CACCTTCATCTTGTTCGCGC 60.179 55.000 0.00 0.00 0.00 6.86
318 335 2.143122 TGACACCTTCATCTTGTTCGC 58.857 47.619 0.00 0.00 0.00 4.70
339 356 1.767289 CGTGTATATGGCTGACGACC 58.233 55.000 0.00 0.00 31.71 4.79
340 357 1.129326 GCGTGTATATGGCTGACGAC 58.871 55.000 0.00 0.00 31.71 4.34
378 395 5.708230 TGAATGGTTAACAGGATGGTTGTAC 59.292 40.000 8.10 0.00 43.62 2.90
409 426 2.224281 TGATGAAGCGTGAGAACCAACT 60.224 45.455 0.00 0.00 0.00 3.16
411 428 2.542020 TGATGAAGCGTGAGAACCAA 57.458 45.000 0.00 0.00 0.00 3.67
628 657 8.709646 CAAAGAAGTACTAGTATTTGTGTGACC 58.290 37.037 16.27 2.36 0.00 4.02
692 722 8.029642 AGTTTCCTTGTAAACTGAACATATCG 57.970 34.615 1.41 0.00 45.60 2.92
792 824 0.179004 TGGTGCCGATTTGGTTGTCT 60.179 50.000 0.00 0.00 41.21 3.41
864 896 1.259142 CCATTTGGTGCCATGCCAGA 61.259 55.000 0.00 0.00 37.31 3.86
914 946 2.307768 TCGTTGTCTCTTGTCCTCTGT 58.692 47.619 0.00 0.00 0.00 3.41
981 1013 0.613260 TTGATGGTGTCGGAGGAAGG 59.387 55.000 0.00 0.00 0.00 3.46
985 1017 3.085208 CCATTGATGGTGTCGGAGG 57.915 57.895 1.73 0.00 43.05 4.30
1461 1498 2.098233 GCCGTCGATGAAGGCGAAA 61.098 57.895 6.11 0.00 45.79 3.46
1545 1588 0.249868 TGACCTTGAGCGTGAACTGG 60.250 55.000 0.00 0.00 0.00 4.00
1599 1642 3.378399 GAACTCCTCCTGCTCCGGC 62.378 68.421 0.00 0.00 39.26 6.13
1602 1645 2.726351 CCGGAACTCCTCCTGCTCC 61.726 68.421 0.00 0.00 42.85 4.70
2138 2196 2.283529 ACCTGGAAGCCGTCGATGT 61.284 57.895 0.00 0.00 0.00 3.06
2241 2299 1.443872 ACGCACGTCGAATCTGTCC 60.444 57.895 13.06 0.00 41.67 4.02
2263 2321 3.707102 GAGGAAGAAAGGAAGCTAGGCTA 59.293 47.826 0.00 0.00 38.25 3.93
2264 2322 2.503765 GAGGAAGAAAGGAAGCTAGGCT 59.496 50.000 0.00 0.00 42.56 4.58
2269 2331 2.232696 GAGACGAGGAAGAAAGGAAGCT 59.767 50.000 0.00 0.00 0.00 3.74
2303 2365 1.935199 AGTCGAGTCGTTAGCTAGCTC 59.065 52.381 23.26 6.97 0.00 4.09
2312 2374 2.460918 CACAAAGTCAGTCGAGTCGTT 58.539 47.619 13.12 0.00 0.00 3.85
2405 2469 3.764160 CTTGGCGAGGCTCATCCCC 62.764 68.421 15.95 9.18 34.51 4.81
2444 2508 1.758440 ATGTGCAGACGAGGTGGTGT 61.758 55.000 0.00 0.00 0.00 4.16
2453 2517 1.135660 ACTCACTCGTATGTGCAGACG 60.136 52.381 12.40 12.40 46.19 4.18
2519 2594 1.351153 GCCGTTTCAGAGCTAGTGAC 58.649 55.000 0.00 0.00 0.00 3.67
2521 2596 1.078759 CGGCCGTTTCAGAGCTAGTG 61.079 60.000 19.50 0.00 0.00 2.74
2522 2597 1.215647 CGGCCGTTTCAGAGCTAGT 59.784 57.895 19.50 0.00 0.00 2.57
2539 2614 3.460103 ACACCATTATTACCGTTAGCCG 58.540 45.455 0.00 0.00 0.00 5.52
2540 2615 5.124297 ACAAACACCATTATTACCGTTAGCC 59.876 40.000 0.00 0.00 0.00 3.93
2541 2616 6.185852 ACAAACACCATTATTACCGTTAGC 57.814 37.500 0.00 0.00 0.00 3.09
2542 2617 8.508875 AGAAACAAACACCATTATTACCGTTAG 58.491 33.333 0.00 0.00 0.00 2.34
2543 2618 8.291032 CAGAAACAAACACCATTATTACCGTTA 58.709 33.333 0.00 0.00 0.00 3.18
2544 2619 7.142680 CAGAAACAAACACCATTATTACCGTT 58.857 34.615 0.00 0.00 0.00 4.44
2545 2620 6.263617 ACAGAAACAAACACCATTATTACCGT 59.736 34.615 0.00 0.00 0.00 4.83
2546 2621 6.580791 CACAGAAACAAACACCATTATTACCG 59.419 38.462 0.00 0.00 0.00 4.02
2547 2622 6.364976 GCACAGAAACAAACACCATTATTACC 59.635 38.462 0.00 0.00 0.00 2.85
2548 2623 6.920758 TGCACAGAAACAAACACCATTATTAC 59.079 34.615 0.00 0.00 0.00 1.89
2549 2624 7.043961 TGCACAGAAACAAACACCATTATTA 57.956 32.000 0.00 0.00 0.00 0.98
2550 2625 5.911752 TGCACAGAAACAAACACCATTATT 58.088 33.333 0.00 0.00 0.00 1.40
2551 2626 5.528043 TGCACAGAAACAAACACCATTAT 57.472 34.783 0.00 0.00 0.00 1.28
2552 2627 4.736168 GCTGCACAGAAACAAACACCATTA 60.736 41.667 0.81 0.00 0.00 1.90
2553 2628 3.784338 CTGCACAGAAACAAACACCATT 58.216 40.909 0.00 0.00 0.00 3.16
2554 2629 2.481795 GCTGCACAGAAACAAACACCAT 60.482 45.455 0.81 0.00 0.00 3.55
2555 2630 1.135141 GCTGCACAGAAACAAACACCA 60.135 47.619 0.81 0.00 0.00 4.17
2556 2631 1.134946 AGCTGCACAGAAACAAACACC 59.865 47.619 1.02 0.00 0.00 4.16
2557 2632 2.187707 CAGCTGCACAGAAACAAACAC 58.812 47.619 0.00 0.00 0.00 3.32
2558 2633 1.134753 CCAGCTGCACAGAAACAAACA 59.865 47.619 8.66 0.00 0.00 2.83
2559 2634 1.405105 TCCAGCTGCACAGAAACAAAC 59.595 47.619 8.66 0.00 0.00 2.93
2560 2635 1.761449 TCCAGCTGCACAGAAACAAA 58.239 45.000 8.66 0.00 0.00 2.83
2561 2636 1.677576 CTTCCAGCTGCACAGAAACAA 59.322 47.619 8.66 0.00 0.00 2.83
2562 2637 1.311859 CTTCCAGCTGCACAGAAACA 58.688 50.000 8.66 0.00 0.00 2.83
2563 2638 0.595095 CCTTCCAGCTGCACAGAAAC 59.405 55.000 8.66 0.00 0.00 2.78
2695 2770 4.074526 GGTCAGAGCGAGCCAGCA 62.075 66.667 3.80 0.00 40.15 4.41
2700 2775 4.828925 GCTGGGGTCAGAGCGAGC 62.829 72.222 6.52 6.52 43.49 5.03
2730 2805 8.885722 CCTCGCCAATTAAACTAATAACAAGTA 58.114 33.333 0.00 0.00 0.00 2.24
2731 2806 7.392393 ACCTCGCCAATTAAACTAATAACAAGT 59.608 33.333 0.00 0.00 0.00 3.16
2732 2807 7.696453 CACCTCGCCAATTAAACTAATAACAAG 59.304 37.037 0.00 0.00 0.00 3.16
2733 2808 7.362229 CCACCTCGCCAATTAAACTAATAACAA 60.362 37.037 0.00 0.00 0.00 2.83
2734 2809 6.094325 CCACCTCGCCAATTAAACTAATAACA 59.906 38.462 0.00 0.00 0.00 2.41
2735 2810 6.492254 CCACCTCGCCAATTAAACTAATAAC 58.508 40.000 0.00 0.00 0.00 1.89
2736 2811 5.066764 GCCACCTCGCCAATTAAACTAATAA 59.933 40.000 0.00 0.00 0.00 1.40
2737 2812 4.577283 GCCACCTCGCCAATTAAACTAATA 59.423 41.667 0.00 0.00 0.00 0.98
2738 2813 3.380320 GCCACCTCGCCAATTAAACTAAT 59.620 43.478 0.00 0.00 0.00 1.73
2739 2814 2.750712 GCCACCTCGCCAATTAAACTAA 59.249 45.455 0.00 0.00 0.00 2.24
2740 2815 2.361789 GCCACCTCGCCAATTAAACTA 58.638 47.619 0.00 0.00 0.00 2.24
2741 2816 1.173913 GCCACCTCGCCAATTAAACT 58.826 50.000 0.00 0.00 0.00 2.66
2742 2817 0.179174 CGCCACCTCGCCAATTAAAC 60.179 55.000 0.00 0.00 0.00 2.01
2743 2818 1.309499 CCGCCACCTCGCCAATTAAA 61.309 55.000 0.00 0.00 0.00 1.52
2744 2819 1.747367 CCGCCACCTCGCCAATTAA 60.747 57.895 0.00 0.00 0.00 1.40
2745 2820 2.124901 CCGCCACCTCGCCAATTA 60.125 61.111 0.00 0.00 0.00 1.40
2762 2837 2.155539 GTCACATGCCGAAAACAAATGC 59.844 45.455 0.00 0.00 0.00 3.56
2774 2849 1.005037 TGTCGGTCTGTCACATGCC 60.005 57.895 0.00 0.00 0.00 4.40
2803 2878 0.534427 CCATGCCGATGACAGCATCT 60.534 55.000 0.00 0.00 46.58 2.90
2848 2925 8.382405 TGCATATAGTTGGTCCATACAATACAT 58.618 33.333 0.00 0.00 0.00 2.29
2881 2958 5.371115 TGGTTTCAGTTGCTAATACAAGC 57.629 39.130 0.00 0.00 43.08 4.01
2895 2972 5.192327 AGAAAAGTGATTGCTGGTTTCAG 57.808 39.130 0.00 0.00 43.64 3.02
3009 3088 7.280876 TGGCATTGCAAGTTTTACATGTTTTAA 59.719 29.630 11.39 0.00 0.00 1.52
3010 3089 6.763135 TGGCATTGCAAGTTTTACATGTTTTA 59.237 30.769 11.39 0.00 0.00 1.52
3011 3090 5.587844 TGGCATTGCAAGTTTTACATGTTTT 59.412 32.000 11.39 0.00 0.00 2.43
3226 3307 1.002359 TCGTCGCTAGAGATGCATCAC 60.002 52.381 27.81 21.68 0.00 3.06
3273 3354 2.498167 CTGGAGTTTGCTAGCTGTTGT 58.502 47.619 17.23 0.00 0.00 3.32
3344 3425 2.644992 GCTGTTGGTCGGCTTTGG 59.355 61.111 0.00 0.00 44.39 3.28
3411 3492 4.532126 CAGTATACCATAGCCATTGGAGGA 59.468 45.833 6.95 0.00 37.69 3.71
3439 3520 3.025978 TCATGTTGGCTGATTCCAATCC 58.974 45.455 0.00 0.00 46.64 3.01
3451 3532 3.631453 TGACTGAGGTCATGTTGGC 57.369 52.632 0.00 0.00 46.19 4.52
3558 3656 5.911838 GCTCTGTTTTTGAGATTGAGTTGAC 59.088 40.000 0.00 0.00 33.68 3.18
3560 3658 5.824429 TGCTCTGTTTTTGAGATTGAGTTG 58.176 37.500 0.00 0.00 33.68 3.16


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

AutoCloner maintained by Alex Coulton.