Multiple sequence alignment - TraesCS5A01G126300

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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 TraesCS5A01G126300 chr5A 100.000 3017 0 0 1 3017 278301384 278298368 0.000000e+00 5572.0
1 TraesCS5A01G126300 chr5A 84.000 100 12 3 2839 2936 105089262 105089165 3.200000e-15 93.5
2 TraesCS5A01G126300 chrUn 94.613 2042 55 23 543 2552 67923625 67925643 0.000000e+00 3110.0
3 TraesCS5A01G126300 chrUn 88.268 358 40 2 2649 3004 67925645 67926002 7.730000e-116 427.0
4 TraesCS5A01G126300 chrUn 91.124 169 8 6 328 490 67923373 67923540 3.910000e-54 222.0
5 TraesCS5A01G126300 chrUn 90.741 54 5 0 504 557 67923526 67923579 4.170000e-09 73.1
6 TraesCS5A01G126300 chr5B 93.497 1138 35 12 1446 2555 228271327 228270201 0.000000e+00 1655.0
7 TraesCS5A01G126300 chr5B 90.255 903 45 22 621 1507 228272195 228271320 0.000000e+00 1140.0
8 TraesCS5A01G126300 chr5B 88.108 370 40 4 2647 3013 228270196 228269828 1.280000e-118 436.0
9 TraesCS5A01G126300 chr5B 90.171 234 19 4 3 234 228272763 228272532 4.890000e-78 302.0
10 TraesCS5A01G126300 chr5B 93.939 165 8 1 328 490 228272495 228272331 6.460000e-62 248.0
11 TraesCS5A01G126300 chr5B 82.653 98 17 0 2826 2923 406604630 406604533 1.490000e-13 87.9
12 TraesCS5A01G126300 chr4D 87.379 206 26 0 1551 1756 95289864 95289659 1.400000e-58 237.0
13 TraesCS5A01G126300 chr4D 82.143 112 16 4 209 319 3612482 3612374 3.200000e-15 93.5
14 TraesCS5A01G126300 chr4B 87.624 202 25 0 1551 1752 134825140 134824939 5.030000e-58 235.0
15 TraesCS5A01G126300 chr4A 86.667 210 21 4 1551 1753 484672666 484672875 3.030000e-55 226.0
16 TraesCS5A01G126300 chr7B 88.793 116 9 3 2554 2667 328714842 328714729 4.060000e-29 139.0
17 TraesCS5A01G126300 chr7B 92.405 79 5 1 233 311 632911985 632911908 8.840000e-21 111.0
18 TraesCS5A01G126300 chr5D 93.478 92 6 0 2559 2650 1790753 1790844 1.460000e-28 137.0
19 TraesCS5A01G126300 chr5D 82.524 103 14 3 2839 2939 98247818 98247918 1.490000e-13 87.9
20 TraesCS5A01G126300 chr3D 91.000 100 9 0 2551 2650 64693609 64693708 5.250000e-28 135.0
21 TraesCS5A01G126300 chr2D 91.753 97 8 0 2554 2650 522707221 522707125 5.250000e-28 135.0
22 TraesCS5A01G126300 chr2D 82.301 113 20 0 2825 2937 539450475 539450587 6.880000e-17 99.0
23 TraesCS5A01G126300 chr7A 91.667 96 8 0 2559 2654 476947157 476947062 1.890000e-27 134.0
24 TraesCS5A01G126300 chr7A 87.500 88 11 0 232 319 437074372 437074459 5.320000e-18 102.0
25 TraesCS5A01G126300 chr2B 90.196 102 9 1 2554 2655 770103097 770102997 6.790000e-27 132.0
26 TraesCS5A01G126300 chr2B 90.099 101 9 1 2550 2650 462945867 462945966 2.440000e-26 130.0
27 TraesCS5A01G126300 chr2B 79.275 193 31 8 1567 1753 785271244 785271433 3.160000e-25 126.0
28 TraesCS5A01G126300 chr2B 88.636 88 10 0 232 319 798620656 798620569 1.140000e-19 108.0
29 TraesCS5A01G126300 chr2B 79.167 120 23 2 2819 2937 77200772 77200890 6.930000e-12 82.4
30 TraesCS5A01G126300 chr3B 90.722 97 9 0 2554 2650 177503872 177503776 2.440000e-26 130.0
31 TraesCS5A01G126300 chr3B 78.070 114 20 5 2824 2935 475469005 475468895 1.940000e-07 67.6
32 TraesCS5A01G126300 chr2A 90.722 97 9 0 2554 2650 419654385 419654481 2.440000e-26 130.0
33 TraesCS5A01G126300 chr2A 87.500 88 11 0 232 319 98897413 98897500 5.320000e-18 102.0
34 TraesCS5A01G126300 chr7D 88.636 88 10 0 232 319 531825269 531825356 1.140000e-19 108.0
35 TraesCS5A01G126300 chr6D 88.506 87 8 2 233 319 446736201 446736285 1.480000e-18 104.0
36 TraesCS5A01G126300 chr1A 87.640 89 11 0 231 319 355718014 355717926 1.480000e-18 104.0
37 TraesCS5A01G126300 chr1D 81.967 122 15 5 202 319 101458235 101458117 2.480000e-16 97.1
38 TraesCS5A01G126300 chr1D 76.974 152 31 3 2770 2919 467315382 467315233 1.930000e-12 84.2


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 TraesCS5A01G126300 chr5A 278298368 278301384 3016 True 5572.000 5572 100.0000 1 3017 1 chr5A.!!$R2 3016
1 TraesCS5A01G126300 chrUn 67923373 67926002 2629 False 958.025 3110 91.1865 328 3004 4 chrUn.!!$F1 2676
2 TraesCS5A01G126300 chr5B 228269828 228272763 2935 True 756.200 1655 91.1940 3 3013 5 chr5B.!!$R2 3010

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
493 500 0.027586 AAAGTGCTGAAACGTGCGTC 59.972 50.0 0.00 0.0 0.0 5.19 F
498 505 0.303493 GCTGAAACGTGCGTCTCAAA 59.697 50.0 2.39 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1500 0.243907 CCTGGTCGAAGAAGAAGCGA 59.756 55.0 0.00 0.0 39.69 4.93 R
2482 2671 0.742505 ACGCATGCATTGATGAAGGG 59.257 50.0 19.57 0.0 0.00 3.95 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
146 148 1.600023 GACAACATGGGGTTTCGTCA 58.400 50.000 0.00 0.00 37.72 4.35
152 154 2.556622 ACATGGGGTTTCGTCATGTTTC 59.443 45.455 0.00 0.00 46.20 2.78
188 190 6.978343 TTACACATTTGGACGGATAGAAAG 57.022 37.500 0.00 0.00 0.00 2.62
215 217 4.520492 CACATTTTCACTGGAGCCTAAGTT 59.480 41.667 0.00 0.00 0.00 2.66
216 218 5.705441 CACATTTTCACTGGAGCCTAAGTTA 59.295 40.000 0.00 0.00 0.00 2.24
217 219 5.940470 ACATTTTCACTGGAGCCTAAGTTAG 59.060 40.000 2.65 2.65 0.00 2.34
218 220 3.611766 TTCACTGGAGCCTAAGTTAGC 57.388 47.619 4.22 0.78 0.00 3.09
219 221 2.536066 TCACTGGAGCCTAAGTTAGCA 58.464 47.619 4.22 0.00 0.00 3.49
220 222 2.233922 TCACTGGAGCCTAAGTTAGCAC 59.766 50.000 4.22 0.00 0.00 4.40
221 223 1.555533 ACTGGAGCCTAAGTTAGCACC 59.444 52.381 4.22 8.62 39.85 5.01
222 224 1.834263 CTGGAGCCTAAGTTAGCACCT 59.166 52.381 15.94 8.24 40.07 4.00
223 225 3.031736 CTGGAGCCTAAGTTAGCACCTA 58.968 50.000 15.94 7.15 40.07 3.08
224 226 3.643792 CTGGAGCCTAAGTTAGCACCTAT 59.356 47.826 15.94 0.00 40.07 2.57
225 227 4.811498 TGGAGCCTAAGTTAGCACCTATA 58.189 43.478 15.94 1.57 40.07 1.31
256 258 3.724508 TTTTGCTGGAAATGCTTTCGA 57.275 38.095 0.00 0.00 40.57 3.71
257 259 3.940209 TTTGCTGGAAATGCTTTCGAT 57.060 38.095 0.00 0.00 40.57 3.59
260 262 5.384063 TTGCTGGAAATGCTTTCGATTTA 57.616 34.783 0.00 0.00 40.57 1.40
261 263 5.581126 TGCTGGAAATGCTTTCGATTTAT 57.419 34.783 0.00 0.00 40.57 1.40
263 265 6.397272 TGCTGGAAATGCTTTCGATTTATTT 58.603 32.000 0.00 0.00 40.57 1.40
264 266 7.542890 TGCTGGAAATGCTTTCGATTTATTTA 58.457 30.769 0.00 0.00 40.57 1.40
265 267 8.196771 TGCTGGAAATGCTTTCGATTTATTTAT 58.803 29.630 0.00 0.00 40.57 1.40
266 268 9.677567 GCTGGAAATGCTTTCGATTTATTTATA 57.322 29.630 0.00 0.00 40.57 0.98
293 295 9.647797 TTTAATCATGATAGTACAACGAACACT 57.352 29.630 9.04 0.00 0.00 3.55
295 297 8.858003 AATCATGATAGTACAACGAACACTAG 57.142 34.615 9.04 0.00 0.00 2.57
296 298 7.619964 TCATGATAGTACAACGAACACTAGA 57.380 36.000 0.00 0.00 0.00 2.43
297 299 8.047413 TCATGATAGTACAACGAACACTAGAA 57.953 34.615 0.00 0.00 0.00 2.10
298 300 8.517056 TCATGATAGTACAACGAACACTAGAAA 58.483 33.333 0.00 0.00 0.00 2.52
299 301 9.302345 CATGATAGTACAACGAACACTAGAAAT 57.698 33.333 0.00 0.00 0.00 2.17
334 336 3.695830 TCAGAATTAGCCTCCGTTGTT 57.304 42.857 0.00 0.00 0.00 2.83
336 338 2.084546 AGAATTAGCCTCCGTTGTTGC 58.915 47.619 0.00 0.00 0.00 4.17
436 443 4.829388 TGGTCCCCCACTCCTATG 57.171 61.111 0.00 0.00 35.17 2.23
459 466 0.234884 CAGGAACTCGTTTTCACCGC 59.765 55.000 2.06 0.00 34.60 5.68
490 497 1.208642 GCCAAAGTGCTGAAACGTGC 61.209 55.000 0.00 0.00 0.00 5.34
491 498 0.929824 CCAAAGTGCTGAAACGTGCG 60.930 55.000 0.00 0.00 0.00 5.34
492 499 0.248054 CAAAGTGCTGAAACGTGCGT 60.248 50.000 0.00 0.00 0.00 5.24
493 500 0.027586 AAAGTGCTGAAACGTGCGTC 59.972 50.000 0.00 0.00 0.00 5.19
494 501 0.810031 AAGTGCTGAAACGTGCGTCT 60.810 50.000 0.00 0.00 0.00 4.18
495 502 1.201825 GTGCTGAAACGTGCGTCTC 59.798 57.895 0.00 0.00 0.00 3.36
496 503 1.227118 TGCTGAAACGTGCGTCTCA 60.227 52.632 0.78 0.78 0.00 3.27
497 504 0.808060 TGCTGAAACGTGCGTCTCAA 60.808 50.000 2.39 0.00 0.00 3.02
498 505 0.303493 GCTGAAACGTGCGTCTCAAA 59.697 50.000 2.39 0.00 0.00 2.69
499 506 1.267832 GCTGAAACGTGCGTCTCAAAA 60.268 47.619 2.39 0.00 0.00 2.44
500 507 2.789779 GCTGAAACGTGCGTCTCAAAAA 60.790 45.455 2.39 0.00 0.00 1.94
534 541 2.360483 ACGTGTGATATCTGAGCCAGAG 59.640 50.000 3.98 0.00 44.08 3.35
537 544 2.620585 TGTGATATCTGAGCCAGAGACG 59.379 50.000 3.98 0.00 44.08 4.18
544 551 2.946329 TCTGAGCCAGAGACGTCTAATC 59.054 50.000 20.09 12.26 35.39 1.75
566 633 6.206395 TCTTCTCTCAGATTAGTTGCTCTG 57.794 41.667 0.00 0.00 40.20 3.35
634 701 4.647564 AGCTCTGAAGGATTTGGAAAGA 57.352 40.909 0.00 0.00 0.00 2.52
639 706 6.131972 TCTGAAGGATTTGGAAAGACATCT 57.868 37.500 0.00 0.00 0.00 2.90
666 733 3.430214 TGCATCGCACTCAGGTACTGG 62.430 57.143 0.00 0.00 45.89 4.00
702 769 1.000955 GTCACTGACATGACGGTCCTT 59.999 52.381 6.68 0.00 39.69 3.36
710 777 4.273969 TGACATGACGGTCCTTTAACAAAC 59.726 41.667 5.55 0.00 36.97 2.93
728 795 1.990424 CTGGCCCACATACCAGTGA 59.010 57.895 0.00 0.00 46.95 3.41
780 847 3.968649 CAGTAATCTGCTCTGCTCTCTC 58.031 50.000 0.00 0.00 34.79 3.20
781 848 3.380954 CAGTAATCTGCTCTGCTCTCTCA 59.619 47.826 0.00 0.00 34.79 3.27
782 849 3.633525 AGTAATCTGCTCTGCTCTCTCAG 59.366 47.826 0.00 0.00 35.46 3.35
783 850 2.440517 ATCTGCTCTGCTCTCTCAGA 57.559 50.000 0.00 0.00 40.50 3.27
784 851 1.462616 TCTGCTCTGCTCTCTCAGAC 58.537 55.000 0.00 0.00 38.11 3.51
859 927 3.257393 CATGTGTTCTTCCCTCTCTTCG 58.743 50.000 0.00 0.00 0.00 3.79
1062 1155 3.578272 AGCCTCGCTAGCGACTCG 61.578 66.667 34.66 24.38 44.01 4.18
1284 1377 1.731720 GCGAGTCATTCTCTTGCCTT 58.268 50.000 0.00 0.00 40.75 4.35
1311 1407 0.396811 AGGAGGAGGAAACGGTTGTG 59.603 55.000 0.00 0.00 0.00 3.33
1331 1427 2.341101 TGGAGGACGACGGCTTCTC 61.341 63.158 13.00 5.60 0.00 2.87
1443 1545 0.108138 CGACCAACTCCATCCTGTCC 60.108 60.000 0.00 0.00 0.00 4.02
1520 1676 3.423154 GGCGCTGTCCAAGAACGG 61.423 66.667 7.64 0.00 0.00 4.44
1790 1946 1.443872 GCACCTCGACGACGACAAT 60.444 57.895 5.75 0.00 43.81 2.71
2289 2463 1.421485 CGACATGAGCTGGTTTCGC 59.579 57.895 0.00 0.00 0.00 4.70
2455 2644 0.608035 GGTTCAATGCGACCAGGGAA 60.608 55.000 0.00 0.00 35.95 3.97
2464 2653 1.675552 CGACCAGGGAACAGTGTTTT 58.324 50.000 10.45 0.00 0.00 2.43
2538 2727 2.032681 GCCGCAGAACTGGACCTT 59.967 61.111 3.99 0.00 0.00 3.50
2552 2741 4.965532 ACTGGACCTTCAGAGCAAGTATAT 59.034 41.667 0.00 0.00 38.11 0.86
2555 2744 6.817184 TGGACCTTCAGAGCAAGTATATTAC 58.183 40.000 0.00 0.00 0.00 1.89
2559 2748 7.501844 ACCTTCAGAGCAAGTATATTACTTCC 58.498 38.462 0.00 0.00 45.38 3.46
2560 2749 7.345914 ACCTTCAGAGCAAGTATATTACTTCCT 59.654 37.037 0.00 0.00 45.38 3.36
2564 2753 6.086785 GAGCAAGTATATTACTTCCTCCGT 57.913 41.667 6.98 0.00 44.22 4.69
2565 2754 6.481434 AGCAAGTATATTACTTCCTCCGTT 57.519 37.500 0.00 0.00 45.38 4.44
2566 2755 7.592885 AGCAAGTATATTACTTCCTCCGTTA 57.407 36.000 0.00 0.00 45.38 3.18
2567 2756 8.191534 AGCAAGTATATTACTTCCTCCGTTAT 57.808 34.615 0.00 0.00 45.38 1.89
2568 2757 9.305555 AGCAAGTATATTACTTCCTCCGTTATA 57.694 33.333 0.00 0.00 45.38 0.98
2569 2758 9.918630 GCAAGTATATTACTTCCTCCGTTATAA 57.081 33.333 0.00 0.00 45.38 0.98
2580 2769 8.148999 ACTTCCTCCGTTATAAAATAGATGACC 58.851 37.037 0.00 0.00 0.00 4.02
2581 2770 7.001099 TCCTCCGTTATAAAATAGATGACCC 57.999 40.000 0.00 0.00 0.00 4.46
2582 2771 6.555738 TCCTCCGTTATAAAATAGATGACCCA 59.444 38.462 0.00 0.00 0.00 4.51
2583 2772 7.071447 TCCTCCGTTATAAAATAGATGACCCAA 59.929 37.037 0.00 0.00 0.00 4.12
2584 2773 7.717875 CCTCCGTTATAAAATAGATGACCCAAA 59.282 37.037 0.00 0.00 0.00 3.28
2585 2774 9.284968 CTCCGTTATAAAATAGATGACCCAAAT 57.715 33.333 0.00 0.00 0.00 2.32
2586 2775 9.635404 TCCGTTATAAAATAGATGACCCAAATT 57.365 29.630 0.00 0.00 0.00 1.82
2641 2830 9.667107 AAAATTGAGTCATCTATTTAGGAACGA 57.333 29.630 0.00 0.00 39.11 3.85
2642 2831 9.667107 AAATTGAGTCATCTATTTAGGAACGAA 57.333 29.630 0.00 0.00 38.54 3.85
2643 2832 8.879342 ATTGAGTCATCTATTTAGGAACGAAG 57.121 34.615 0.00 0.00 0.00 3.79
2644 2833 6.806751 TGAGTCATCTATTTAGGAACGAAGG 58.193 40.000 0.00 0.00 0.00 3.46
2645 2834 6.163135 AGTCATCTATTTAGGAACGAAGGG 57.837 41.667 0.00 0.00 0.00 3.95
2655 2844 8.773033 ATTTAGGAACGAAGGGAGTAATAGTA 57.227 34.615 0.00 0.00 0.00 1.82
2660 2849 6.406737 GGAACGAAGGGAGTAATAGTAAGCTT 60.407 42.308 3.48 3.48 0.00 3.74
2670 2859 8.417884 GGAGTAATAGTAAGCTTCATGAAGACT 58.582 37.037 34.43 28.45 40.79 3.24
2758 2950 1.153353 CGGACGCCTACAACAAACAT 58.847 50.000 0.00 0.00 0.00 2.71
2760 2952 2.737783 CGGACGCCTACAACAAACATTA 59.262 45.455 0.00 0.00 0.00 1.90
2763 2955 5.063691 CGGACGCCTACAACAAACATTATAA 59.936 40.000 0.00 0.00 0.00 0.98
2797 2989 3.252944 TGTGTTTACGGACAGTGATACGA 59.747 43.478 0.00 0.00 0.00 3.43
2805 2997 0.892755 ACAGTGATACGAAAGCCGGA 59.107 50.000 5.05 0.00 43.93 5.14
2806 2998 1.274167 ACAGTGATACGAAAGCCGGAA 59.726 47.619 5.05 0.00 43.93 4.30
2807 2999 2.093658 ACAGTGATACGAAAGCCGGAAT 60.094 45.455 5.05 0.00 43.93 3.01
2813 3005 1.165270 ACGAAAGCCGGAATTCCAAG 58.835 50.000 24.09 15.28 43.93 3.61
2816 3008 1.257750 AAAGCCGGAATTCCAAGCCC 61.258 55.000 25.50 9.84 36.03 5.19
2831 3023 5.376625 TCCAAGCCCATCTGTATACATTTC 58.623 41.667 5.91 0.00 0.00 2.17
2855 3047 6.811170 TCAAGTGGAATTTGAACAAACTGAAC 59.189 34.615 2.03 0.89 39.75 3.18
2893 3085 7.181569 ACCGGATGATTTTCATTTAAACCAT 57.818 32.000 9.46 0.00 37.20 3.55
2896 3088 6.291743 CGGATGATTTTCATTTAAACCATGCG 60.292 38.462 3.56 3.56 41.26 4.73
2953 3145 2.496899 AGCAGTTGGACCCTAACATG 57.503 50.000 0.00 0.00 0.00 3.21
2972 3164 5.670485 ACATGGTCTAAATATTCGTCAGCA 58.330 37.500 0.00 0.00 0.00 4.41
2981 3173 0.620556 ATTCGTCAGCACCCATCCTT 59.379 50.000 0.00 0.00 0.00 3.36
3013 3205 4.156922 TGTTGTTTTCTTCCGTGTTCATGT 59.843 37.500 0.00 0.00 0.00 3.21
3014 3206 4.545823 TGTTTTCTTCCGTGTTCATGTC 57.454 40.909 0.00 0.00 0.00 3.06
3015 3207 4.196193 TGTTTTCTTCCGTGTTCATGTCT 58.804 39.130 0.00 0.00 0.00 3.41
3016 3208 4.035091 TGTTTTCTTCCGTGTTCATGTCTG 59.965 41.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 51 2.816689 TCACTATAAACATGTCCGCGG 58.183 47.619 22.12 22.12 0.00 6.46
50 52 5.403897 AAATCACTATAAACATGTCCGCG 57.596 39.130 0.00 0.00 0.00 6.46
80 82 2.241160 GAACCACCCACCGGTTTTATT 58.759 47.619 2.97 0.00 46.80 1.40
81 83 1.145325 TGAACCACCCACCGGTTTTAT 59.855 47.619 2.97 0.00 46.80 1.40
93 95 3.733077 CGTATCCTTCTACGTGAACCACC 60.733 52.174 0.00 0.00 39.63 4.61
146 148 4.454161 TGTAAAGCACATACAGCGAAACAT 59.546 37.500 0.00 0.00 37.01 2.71
178 180 4.155826 TGAAAATGTGGCACTTTCTATCCG 59.844 41.667 24.12 0.00 31.67 4.18
188 190 1.336240 GCTCCAGTGAAAATGTGGCAC 60.336 52.381 11.55 11.55 30.35 5.01
267 269 9.647797 AGTGTTCGTTGTACTATCATGATTAAA 57.352 29.630 14.65 0.00 0.00 1.52
269 271 9.946165 CTAGTGTTCGTTGTACTATCATGATTA 57.054 33.333 14.65 0.00 0.00 1.75
270 272 8.683615 TCTAGTGTTCGTTGTACTATCATGATT 58.316 33.333 14.65 0.00 0.00 2.57
271 273 8.221965 TCTAGTGTTCGTTGTACTATCATGAT 57.778 34.615 13.81 13.81 0.00 2.45
272 274 7.619964 TCTAGTGTTCGTTGTACTATCATGA 57.380 36.000 0.00 0.00 0.00 3.07
273 275 8.683550 TTTCTAGTGTTCGTTGTACTATCATG 57.316 34.615 0.00 0.00 0.00 3.07
303 305 9.586435 CGGAGGCTAATTCTGAATTTAATTTTT 57.414 29.630 19.68 0.00 32.38 1.94
304 306 8.749354 ACGGAGGCTAATTCTGAATTTAATTTT 58.251 29.630 19.68 3.31 32.38 1.82
305 307 8.293699 ACGGAGGCTAATTCTGAATTTAATTT 57.706 30.769 19.68 4.24 32.38 1.82
306 308 7.881775 ACGGAGGCTAATTCTGAATTTAATT 57.118 32.000 19.68 5.50 32.38 1.40
307 309 7.339466 ACAACGGAGGCTAATTCTGAATTTAAT 59.661 33.333 19.68 5.46 32.38 1.40
308 310 6.657541 ACAACGGAGGCTAATTCTGAATTTAA 59.342 34.615 19.68 3.48 32.38 1.52
309 311 6.177610 ACAACGGAGGCTAATTCTGAATTTA 58.822 36.000 19.68 6.55 32.38 1.40
310 312 5.010282 ACAACGGAGGCTAATTCTGAATTT 58.990 37.500 19.68 3.03 32.38 1.82
311 313 4.589908 ACAACGGAGGCTAATTCTGAATT 58.410 39.130 18.64 18.64 34.90 2.17
312 314 4.222124 ACAACGGAGGCTAATTCTGAAT 57.778 40.909 0.00 0.00 0.00 2.57
313 315 3.695830 ACAACGGAGGCTAATTCTGAA 57.304 42.857 0.00 0.00 0.00 3.02
314 316 3.334691 CAACAACGGAGGCTAATTCTGA 58.665 45.455 0.00 0.00 0.00 3.27
315 317 2.159517 GCAACAACGGAGGCTAATTCTG 60.160 50.000 0.00 0.00 0.00 3.02
316 318 2.084546 GCAACAACGGAGGCTAATTCT 58.915 47.619 0.00 0.00 0.00 2.40
317 319 2.084546 AGCAACAACGGAGGCTAATTC 58.915 47.619 0.00 0.00 34.25 2.17
318 320 2.200373 AGCAACAACGGAGGCTAATT 57.800 45.000 0.00 0.00 34.25 1.40
319 321 2.200373 AAGCAACAACGGAGGCTAAT 57.800 45.000 0.00 0.00 35.11 1.73
320 322 1.606668 CAAAGCAACAACGGAGGCTAA 59.393 47.619 0.00 0.00 35.11 3.09
321 323 1.234821 CAAAGCAACAACGGAGGCTA 58.765 50.000 0.00 0.00 35.11 3.93
322 324 0.751643 ACAAAGCAACAACGGAGGCT 60.752 50.000 0.00 0.00 38.45 4.58
323 325 0.948678 TACAAAGCAACAACGGAGGC 59.051 50.000 0.00 0.00 0.00 4.70
324 326 1.944024 TGTACAAAGCAACAACGGAGG 59.056 47.619 0.00 0.00 0.00 4.30
325 327 3.896648 ATGTACAAAGCAACAACGGAG 57.103 42.857 0.00 0.00 0.00 4.63
326 328 3.187637 GCTATGTACAAAGCAACAACGGA 59.812 43.478 0.00 0.00 38.63 4.69
334 336 5.110814 AGGTAATGGCTATGTACAAAGCA 57.889 39.130 0.00 0.00 40.61 3.91
336 338 8.500753 TGTAAAGGTAATGGCTATGTACAAAG 57.499 34.615 0.00 0.00 0.00 2.77
436 443 3.545426 CGGTGAAAACGAGTTCCTGTTTC 60.545 47.826 0.00 0.00 37.31 2.78
459 466 2.607771 GCACTTTGGCACCACTTGTATG 60.608 50.000 0.00 0.00 0.00 2.39
497 504 4.083003 TCACACGTTTCAGCACTTCTTTTT 60.083 37.500 0.00 0.00 0.00 1.94
498 505 3.438781 TCACACGTTTCAGCACTTCTTTT 59.561 39.130 0.00 0.00 0.00 2.27
499 506 3.006940 TCACACGTTTCAGCACTTCTTT 58.993 40.909 0.00 0.00 0.00 2.52
500 507 2.627945 TCACACGTTTCAGCACTTCTT 58.372 42.857 0.00 0.00 0.00 2.52
501 508 2.309528 TCACACGTTTCAGCACTTCT 57.690 45.000 0.00 0.00 0.00 2.85
502 509 4.627467 AGATATCACACGTTTCAGCACTTC 59.373 41.667 5.32 0.00 0.00 3.01
503 510 4.389992 CAGATATCACACGTTTCAGCACTT 59.610 41.667 5.32 0.00 0.00 3.16
504 511 3.928992 CAGATATCACACGTTTCAGCACT 59.071 43.478 5.32 0.00 0.00 4.40
505 512 3.926527 TCAGATATCACACGTTTCAGCAC 59.073 43.478 5.32 0.00 0.00 4.40
506 513 4.176271 CTCAGATATCACACGTTTCAGCA 58.824 43.478 5.32 0.00 0.00 4.41
507 514 3.000724 GCTCAGATATCACACGTTTCAGC 59.999 47.826 5.32 0.00 0.00 4.26
508 515 3.553511 GGCTCAGATATCACACGTTTCAG 59.446 47.826 5.32 0.00 0.00 3.02
509 516 3.056179 TGGCTCAGATATCACACGTTTCA 60.056 43.478 5.32 0.00 0.00 2.69
510 517 3.521560 TGGCTCAGATATCACACGTTTC 58.478 45.455 5.32 0.00 0.00 2.78
511 518 3.195610 TCTGGCTCAGATATCACACGTTT 59.804 43.478 5.32 0.00 35.39 3.60
512 519 2.760650 TCTGGCTCAGATATCACACGTT 59.239 45.455 5.32 0.00 35.39 3.99
513 520 2.360483 CTCTGGCTCAGATATCACACGT 59.640 50.000 5.32 0.00 39.92 4.49
514 521 2.620585 TCTCTGGCTCAGATATCACACG 59.379 50.000 5.32 0.00 39.92 4.49
515 522 3.549827 CGTCTCTGGCTCAGATATCACAC 60.550 52.174 5.32 0.00 39.92 3.82
516 523 2.620585 CGTCTCTGGCTCAGATATCACA 59.379 50.000 5.32 0.00 39.92 3.58
544 551 5.964758 ACAGAGCAACTAATCTGAGAGAAG 58.035 41.667 9.06 0.00 44.68 2.85
561 628 6.100004 TCAGCACTAAACATACTTACAGAGC 58.900 40.000 0.00 0.00 0.00 4.09
605 672 5.180868 CCAAATCCTTCAGAGCTATACATGC 59.819 44.000 0.00 0.00 0.00 4.06
617 684 6.830873 AAGATGTCTTTCCAAATCCTTCAG 57.169 37.500 0.00 0.00 30.82 3.02
634 701 3.681705 CGATGCAACGCAAAGATGT 57.318 47.368 2.61 0.00 43.62 3.06
659 726 5.898397 ACCTAAGTTAGAGAATCCCAGTACC 59.102 44.000 11.66 0.00 33.66 3.34
666 733 6.153000 TGTCAGTGACCTAAGTTAGAGAATCC 59.847 42.308 20.43 0.00 33.66 3.01
702 769 3.158676 GGTATGTGGGCCAGTTTGTTAA 58.841 45.455 6.40 0.00 0.00 2.01
728 795 0.319297 GCAGTCACGTAACTTCGGGT 60.319 55.000 0.00 0.00 35.58 5.28
763 830 2.428171 GTCTGAGAGAGCAGAGCAGATT 59.572 50.000 0.00 0.00 44.92 2.40
764 831 2.026641 GTCTGAGAGAGCAGAGCAGAT 58.973 52.381 0.00 0.00 44.92 2.90
782 849 6.757010 CAGAGTAAGTAGAGAGACTGAGAGTC 59.243 46.154 0.00 0.00 45.38 3.36
783 850 6.640518 CAGAGTAAGTAGAGAGACTGAGAGT 58.359 44.000 0.00 0.00 0.00 3.24
784 851 5.523916 GCAGAGTAAGTAGAGAGACTGAGAG 59.476 48.000 0.00 0.00 0.00 3.20
825 892 6.152323 GGAAGAACACATGGACAGTACTACTA 59.848 42.308 0.00 0.00 0.00 1.82
826 893 5.047235 GGAAGAACACATGGACAGTACTACT 60.047 44.000 0.00 0.00 0.00 2.57
827 894 5.169295 GGAAGAACACATGGACAGTACTAC 58.831 45.833 0.00 0.00 0.00 2.73
859 927 5.241662 AGAAGAGAGAGGTGTGCAATTAAC 58.758 41.667 0.00 0.00 0.00 2.01
1211 1304 2.644555 CTTGTACATCTCGGCGGGGG 62.645 65.000 7.05 1.68 0.00 5.40
1284 1377 2.849096 TTTCCTCCTCCTCCGCGCTA 62.849 60.000 5.56 0.00 0.00 4.26
1311 1407 3.644399 GAAGCCGTCGTCCTCCACC 62.644 68.421 0.00 0.00 0.00 4.61
1331 1427 3.518998 ACTCATCCTCGGGCGTCG 61.519 66.667 0.00 0.00 40.90 5.12
1339 1435 2.022240 GCCTCCGACCACTCATCCTC 62.022 65.000 0.00 0.00 0.00 3.71
1340 1436 2.060980 GCCTCCGACCACTCATCCT 61.061 63.158 0.00 0.00 0.00 3.24
1341 1437 2.060980 AGCCTCCGACCACTCATCC 61.061 63.158 0.00 0.00 0.00 3.51
1344 1446 2.203640 ACAGCCTCCGACCACTCA 60.204 61.111 0.00 0.00 0.00 3.41
1398 1500 0.243907 CCTGGTCGAAGAAGAAGCGA 59.756 55.000 0.00 0.00 39.69 4.93
1772 1928 1.443872 ATTGTCGTCGTCGAGGTGC 60.444 57.895 14.08 9.35 46.96 5.01
1831 1987 3.626680 TACTCGTGCTGCTCGTGCC 62.627 63.158 21.39 0.00 38.71 5.01
2054 2211 5.233476 CCAAAATCACATGCATGCAGATTAC 59.767 40.000 31.62 0.00 35.88 1.89
2275 2449 0.811616 GATCGGCGAAACCAGCTCAT 60.812 55.000 15.93 0.00 39.03 2.90
2279 2453 2.517450 CGAGATCGGCGAAACCAGC 61.517 63.158 15.93 0.00 39.03 4.85
2289 2463 1.135139 AGTTGGTGTCATCGAGATCGG 59.865 52.381 1.91 0.00 40.29 4.18
2478 2667 1.483004 CATGCATTGATGAAGGGGCAA 59.517 47.619 0.00 0.00 34.64 4.52
2482 2671 0.742505 ACGCATGCATTGATGAAGGG 59.257 50.000 19.57 0.00 0.00 3.95
2555 2744 7.603024 GGGTCATCTATTTTATAACGGAGGAAG 59.397 40.741 0.00 0.00 0.00 3.46
2557 2746 6.555738 TGGGTCATCTATTTTATAACGGAGGA 59.444 38.462 0.00 0.00 0.00 3.71
2559 2748 8.671384 TTTGGGTCATCTATTTTATAACGGAG 57.329 34.615 0.00 0.00 0.00 4.63
2560 2749 9.635404 AATTTGGGTCATCTATTTTATAACGGA 57.365 29.630 0.00 0.00 0.00 4.69
2615 2804 9.667107 TCGTTCCTAAATAGATGACTCAATTTT 57.333 29.630 0.00 0.00 0.00 1.82
2616 2805 9.667107 TTCGTTCCTAAATAGATGACTCAATTT 57.333 29.630 0.00 0.00 0.00 1.82
2617 2806 9.319143 CTTCGTTCCTAAATAGATGACTCAATT 57.681 33.333 0.00 0.00 0.00 2.32
2618 2807 7.928706 CCTTCGTTCCTAAATAGATGACTCAAT 59.071 37.037 0.00 0.00 0.00 2.57
2619 2808 7.265673 CCTTCGTTCCTAAATAGATGACTCAA 58.734 38.462 0.00 0.00 0.00 3.02
2620 2809 6.183360 CCCTTCGTTCCTAAATAGATGACTCA 60.183 42.308 0.00 0.00 0.00 3.41
2621 2810 6.040616 TCCCTTCGTTCCTAAATAGATGACTC 59.959 42.308 0.00 0.00 0.00 3.36
2622 2811 5.897824 TCCCTTCGTTCCTAAATAGATGACT 59.102 40.000 0.00 0.00 0.00 3.41
2623 2812 6.158023 TCCCTTCGTTCCTAAATAGATGAC 57.842 41.667 0.00 0.00 0.00 3.06
2624 2813 5.897824 ACTCCCTTCGTTCCTAAATAGATGA 59.102 40.000 0.00 0.00 0.00 2.92
2625 2814 6.163135 ACTCCCTTCGTTCCTAAATAGATG 57.837 41.667 0.00 0.00 0.00 2.90
2626 2815 7.909485 TTACTCCCTTCGTTCCTAAATAGAT 57.091 36.000 0.00 0.00 0.00 1.98
2627 2816 7.909485 ATTACTCCCTTCGTTCCTAAATAGA 57.091 36.000 0.00 0.00 0.00 1.98
2628 2817 8.858094 ACTATTACTCCCTTCGTTCCTAAATAG 58.142 37.037 0.00 0.00 32.24 1.73
2629 2818 8.773033 ACTATTACTCCCTTCGTTCCTAAATA 57.227 34.615 0.00 0.00 0.00 1.40
2630 2819 7.672122 ACTATTACTCCCTTCGTTCCTAAAT 57.328 36.000 0.00 0.00 0.00 1.40
2631 2820 8.593945 TTACTATTACTCCCTTCGTTCCTAAA 57.406 34.615 0.00 0.00 0.00 1.85
2632 2821 7.201857 GCTTACTATTACTCCCTTCGTTCCTAA 60.202 40.741 0.00 0.00 0.00 2.69
2633 2822 6.264067 GCTTACTATTACTCCCTTCGTTCCTA 59.736 42.308 0.00 0.00 0.00 2.94
2634 2823 5.068855 GCTTACTATTACTCCCTTCGTTCCT 59.931 44.000 0.00 0.00 0.00 3.36
2635 2824 5.068855 AGCTTACTATTACTCCCTTCGTTCC 59.931 44.000 0.00 0.00 0.00 3.62
2636 2825 6.146601 AGCTTACTATTACTCCCTTCGTTC 57.853 41.667 0.00 0.00 0.00 3.95
2637 2826 6.154021 TGAAGCTTACTATTACTCCCTTCGTT 59.846 38.462 0.00 0.00 32.35 3.85
2638 2827 5.655532 TGAAGCTTACTATTACTCCCTTCGT 59.344 40.000 0.00 0.00 32.35 3.85
2639 2828 6.145338 TGAAGCTTACTATTACTCCCTTCG 57.855 41.667 0.00 0.00 32.35 3.79
2640 2829 7.727181 TCATGAAGCTTACTATTACTCCCTTC 58.273 38.462 0.00 0.00 0.00 3.46
2641 2830 7.676683 TCATGAAGCTTACTATTACTCCCTT 57.323 36.000 0.00 0.00 0.00 3.95
2642 2831 7.565398 TCTTCATGAAGCTTACTATTACTCCCT 59.435 37.037 27.45 0.00 38.28 4.20
2643 2832 7.654116 GTCTTCATGAAGCTTACTATTACTCCC 59.346 40.741 27.45 0.00 38.28 4.30
2644 2833 8.417884 AGTCTTCATGAAGCTTACTATTACTCC 58.582 37.037 27.45 0.19 38.28 3.85
2645 2834 9.810545 AAGTCTTCATGAAGCTTACTATTACTC 57.189 33.333 28.44 6.32 38.28 2.59
2721 2913 1.283736 CGCCTTACCCGTGTATGTTC 58.716 55.000 0.00 0.00 0.00 3.18
2797 2989 1.257750 GGGCTTGGAATTCCGGCTTT 61.258 55.000 28.92 0.00 39.43 3.51
2805 2997 5.387113 TGTATACAGATGGGCTTGGAATT 57.613 39.130 0.08 0.00 0.00 2.17
2806 2998 5.589367 ATGTATACAGATGGGCTTGGAAT 57.411 39.130 11.91 0.00 0.00 3.01
2807 2999 5.387113 AATGTATACAGATGGGCTTGGAA 57.613 39.130 11.91 0.00 0.00 3.53
2813 3005 5.009010 CCACTTGAAATGTATACAGATGGGC 59.991 44.000 11.91 0.00 0.00 5.36
2831 3023 6.237542 CGTTCAGTTTGTTCAAATTCCACTTG 60.238 38.462 1.33 0.00 0.00 3.16
2893 3085 6.914259 TGTCAAAAATGTAATGAATACCGCA 58.086 32.000 0.00 0.00 33.27 5.69
2953 3145 3.808174 GGGTGCTGACGAATATTTAGACC 59.192 47.826 0.00 0.00 0.00 3.85
2957 3149 4.102524 AGGATGGGTGCTGACGAATATTTA 59.897 41.667 0.00 0.00 0.00 1.40
2972 3164 2.065799 ACAAGGACTTGAAGGATGGGT 58.934 47.619 18.15 0.00 42.93 4.51
2981 3173 4.095782 CGGAAGAAAACAACAAGGACTTGA 59.904 41.667 18.15 0.00 42.93 3.02


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

AutoCloner maintained by Alex Coulton.