Multiple sequence alignment - TraesCS5D01G484300

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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 TraesCS5D01G484300 chr5D 100.000 4479 0 0 1 4479 520581547 520577069 0.000000e+00 8272.0
1 TraesCS5D01G484300 chr5D 84.790 1190 149 20 943 2109 509651677 509650497 0.000000e+00 1166.0
2 TraesCS5D01G484300 chr5D 86.401 978 115 16 2157 3120 509650476 509649503 0.000000e+00 1053.0
3 TraesCS5D01G484300 chr5D 83.416 1007 124 22 3118 4092 509648966 509647971 0.000000e+00 894.0
4 TraesCS5D01G484300 chr5D 86.250 400 42 3 4089 4478 509647942 509647546 5.360000e-114 422.0
5 TraesCS5D01G484300 chr5D 82.588 425 57 14 291 712 564989332 564988922 4.260000e-95 359.0
6 TraesCS5D01G484300 chr5D 80.563 355 63 5 995 1345 520510299 520509947 7.390000e-68 268.0
7 TraesCS5D01G484300 chr5D 80.726 358 41 14 249 603 26824892 26825224 2.070000e-63 254.0
8 TraesCS5D01G484300 chr5D 87.671 73 8 1 642 714 26825231 26825302 2.870000e-12 84.2
9 TraesCS5D01G484300 chr5D 83.333 84 11 3 441 524 351947527 351947607 1.730000e-09 75.0
10 TraesCS5D01G484300 chr5B 92.298 3778 244 27 715 4478 655901469 655897725 0.000000e+00 5321.0
11 TraesCS5D01G484300 chr5B 83.318 2224 288 55 882 3067 640491870 640489692 0.000000e+00 1975.0
12 TraesCS5D01G484300 chr5B 84.655 580 74 11 3118 3690 640489257 640488686 8.410000e-157 564.0
13 TraesCS5D01G484300 chr5B 84.466 412 58 4 3685 4092 640476719 640476310 6.980000e-108 401.0
14 TraesCS5D01G484300 chr5B 83.951 162 15 3 718 868 640492017 640491856 1.300000e-30 145.0
15 TraesCS5D01G484300 chr5B 78.355 231 36 10 127 349 367081144 367081368 2.170000e-28 137.0
16 TraesCS5D01G484300 chr5B 92.857 42 3 0 4051 4092 262129626 262129667 1.350000e-05 62.1
17 TraesCS5D01G484300 chr5A 91.442 3038 206 24 715 3736 648771248 648768249 0.000000e+00 4120.0
18 TraesCS5D01G484300 chr5A 91.722 749 62 0 3730 4478 648746537 648745789 0.000000e+00 1040.0
19 TraesCS5D01G484300 chr7A 90.204 1031 54 21 1 1017 28210084 28209087 0.000000e+00 1301.0
20 TraesCS5D01G484300 chr7A 75.786 318 48 25 1 311 691446178 691445883 2.810000e-27 134.0
21 TraesCS5D01G484300 chr1D 83.248 979 139 17 2151 3116 440581953 440582919 0.000000e+00 876.0
22 TraesCS5D01G484300 chr1D 82.234 985 149 20 2151 3120 440576278 440577251 0.000000e+00 826.0
23 TraesCS5D01G484300 chr1D 80.144 695 98 24 1467 2135 440581285 440581965 2.420000e-132 483.0
24 TraesCS5D01G484300 chr1D 81.754 422 66 8 2701 3119 440567054 440567467 4.290000e-90 342.0
25 TraesCS5D01G484300 chr1D 78.970 233 35 12 121 349 244622508 244622286 3.610000e-31 147.0
26 TraesCS5D01G484300 chr1D 100.000 28 0 0 685 712 340551269 340551242 8.000000e-03 52.8
27 TraesCS5D01G484300 chr1B 76.960 1684 291 64 1475 3120 597953501 597955125 0.000000e+00 870.0
28 TraesCS5D01G484300 chr1B 79.534 987 170 27 2151 3120 597961721 597962692 0.000000e+00 675.0
29 TraesCS5D01G484300 chr1B 77.489 693 111 31 1468 2135 597961061 597961733 1.520000e-99 374.0
30 TraesCS5D01G484300 chr1B 97.297 37 1 0 4049 4085 391829405 391829369 3.740000e-06 63.9
31 TraesCS5D01G484300 chr1A 82.132 985 148 21 2151 3120 537440799 537439828 0.000000e+00 819.0
32 TraesCS5D01G484300 chr1A 81.301 984 157 19 2151 3120 537367241 537366271 0.000000e+00 773.0
33 TraesCS5D01G484300 chr1A 81.034 696 92 23 1467 2135 537441469 537440787 6.640000e-143 518.0
34 TraesCS5D01G484300 chr1A 80.808 693 98 23 1467 2135 537367910 537367229 1.110000e-140 510.0
35 TraesCS5D01G484300 chr7B 78.198 766 84 33 1 714 468721283 468722017 3.220000e-111 412.0
36 TraesCS5D01G484300 chr7B 76.299 616 84 33 1 598 468190004 468189433 5.710000e-69 272.0
37 TraesCS5D01G484300 chr7B 80.851 94 11 3 277 368 691914580 691914492 2.890000e-07 67.6
38 TraesCS5D01G484300 chr7B 82.895 76 11 1 295 368 691963060 691962985 2.890000e-07 67.6
39 TraesCS5D01G484300 chr4D 78.758 612 60 23 1 583 421111747 421111177 3.320000e-91 346.0
40 TraesCS5D01G484300 chr4D 77.072 362 53 26 125 476 498412351 498412692 9.900000e-42 182.0
41 TraesCS5D01G484300 chr4D 73.304 457 89 22 121 572 488706374 488706802 2.170000e-28 137.0
42 TraesCS5D01G484300 chr2D 87.649 251 15 12 1 243 243114525 243114283 1.230000e-70 278.0
43 TraesCS5D01G484300 chr2D 86.667 210 20 7 1 205 424169207 424169413 4.510000e-55 226.0
44 TraesCS5D01G484300 chr2D 100.000 31 0 0 685 715 192733207 192733237 1.740000e-04 58.4
45 TraesCS5D01G484300 chr2D 100.000 29 0 0 685 713 61239377 61239405 2.000000e-03 54.7
46 TraesCS5D01G484300 chr3D 78.744 414 63 18 255 665 312705246 312704855 2.070000e-63 254.0
47 TraesCS5D01G484300 chr3D 84.409 186 18 6 1 177 23683752 23683935 5.960000e-39 172.0
48 TraesCS5D01G484300 chr3D 79.227 207 34 9 121 323 9998856 9999057 7.820000e-28 135.0
49 TraesCS5D01G484300 chr4A 77.955 440 61 17 276 712 606506406 606506000 4.480000e-60 243.0
50 TraesCS5D01G484300 chr7D 76.268 493 77 21 158 647 557072513 557072058 4.510000e-55 226.0
51 TraesCS5D01G484300 chr3A 86.935 199 19 6 1 197 668425334 668425527 2.710000e-52 217.0
52 TraesCS5D01G484300 chr3A 86.869 198 21 5 1 197 668599529 668599722 2.710000e-52 217.0
53 TraesCS5D01G484300 chr3A 89.247 93 6 3 1458 1548 244002342 244002252 3.660000e-21 113.0
54 TraesCS5D01G484300 chr6B 87.166 187 19 3 1 182 34318810 34318624 1.630000e-49 207.0
55 TraesCS5D01G484300 chr6B 74.000 250 50 10 121 368 591280470 591280234 2.220000e-13 87.9
56 TraesCS5D01G484300 chr6D 84.343 198 25 6 1 195 453752000 453751806 5.910000e-44 189.0
57 TraesCS5D01G484300 chr6A 77.778 234 38 13 121 348 30529200 30529425 1.010000e-26 132.0
58 TraesCS5D01G484300 chrUn 93.182 44 3 0 4049 4092 239341478 239341521 1.040000e-06 65.8
59 TraesCS5D01G484300 chr4B 97.297 37 1 0 4049 4085 584725142 584725106 3.740000e-06 63.9
60 TraesCS5D01G484300 chr3B 95.000 40 2 0 4043 4082 102941722 102941761 3.740000e-06 63.9
61 TraesCS5D01G484300 chr3B 97.297 37 1 0 4049 4085 491609196 491609160 3.740000e-06 63.9
62 TraesCS5D01G484300 chr2A 97.143 35 1 0 681 715 91143128 91143094 4.840000e-05 60.2
63 TraesCS5D01G484300 chr2B 100.000 30 0 0 684 713 104256570 104256541 6.260000e-04 56.5


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 TraesCS5D01G484300 chr5D 520577069 520581547 4478 True 8272.000000 8272 100.000000 1 4479 1 chr5D.!!$R2 4478
1 TraesCS5D01G484300 chr5D 509647546 509651677 4131 True 883.750000 1166 85.214250 943 4478 4 chr5D.!!$R4 3535
2 TraesCS5D01G484300 chr5B 655897725 655901469 3744 True 5321.000000 5321 92.298000 715 4478 1 chr5B.!!$R2 3763
3 TraesCS5D01G484300 chr5B 640488686 640492017 3331 True 894.666667 1975 83.974667 718 3690 3 chr5B.!!$R3 2972
4 TraesCS5D01G484300 chr5A 648768249 648771248 2999 True 4120.000000 4120 91.442000 715 3736 1 chr5A.!!$R2 3021
5 TraesCS5D01G484300 chr5A 648745789 648746537 748 True 1040.000000 1040 91.722000 3730 4478 1 chr5A.!!$R1 748
6 TraesCS5D01G484300 chr7A 28209087 28210084 997 True 1301.000000 1301 90.204000 1 1017 1 chr7A.!!$R1 1016
7 TraesCS5D01G484300 chr1D 440576278 440577251 973 False 826.000000 826 82.234000 2151 3120 1 chr1D.!!$F2 969
8 TraesCS5D01G484300 chr1D 440581285 440582919 1634 False 679.500000 876 81.696000 1467 3116 2 chr1D.!!$F3 1649
9 TraesCS5D01G484300 chr1B 597953501 597955125 1624 False 870.000000 870 76.960000 1475 3120 1 chr1B.!!$F1 1645
10 TraesCS5D01G484300 chr1B 597961061 597962692 1631 False 524.500000 675 78.511500 1468 3120 2 chr1B.!!$F2 1652
11 TraesCS5D01G484300 chr1A 537439828 537441469 1641 True 668.500000 819 81.583000 1467 3120 2 chr1A.!!$R2 1653
12 TraesCS5D01G484300 chr1A 537366271 537367910 1639 True 641.500000 773 81.054500 1467 3120 2 chr1A.!!$R1 1653
13 TraesCS5D01G484300 chr7B 468721283 468722017 734 False 412.000000 412 78.198000 1 714 1 chr7B.!!$F1 713
14 TraesCS5D01G484300 chr7B 468189433 468190004 571 True 272.000000 272 76.299000 1 598 1 chr7B.!!$R1 597
15 TraesCS5D01G484300 chr4D 421111177 421111747 570 True 346.000000 346 78.758000 1 583 1 chr4D.!!$R1 582

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
568 680 0.798771 TGCGGTTTGTTTGTTCGTGC 60.799 50.000 0.0 0.0 0.00 5.34 F
1267 1400 1.066430 GCGGACAACTCAGGGTATTCA 60.066 52.381 0.0 0.0 0.00 2.57 F
1713 1874 0.539438 TCCCGTGCTTCCAAATGCTT 60.539 50.000 0.0 0.0 0.00 3.91 F
3278 4070 0.114168 AGAGTCACCTCTGCTGGAGT 59.886 55.000 0.0 0.0 46.45 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1874 1.683943 GCCTCATTGCTGGCTATTGA 58.316 50.000 11.57 0.0 45.26 2.57 R
2894 3093 2.507471 CCTTTCACCTATCTTGGGCTCT 59.493 50.000 0.00 0.0 0.00 4.09 R
3328 4120 1.003003 GGGCATCTCTCAAGGATAGCC 59.997 57.143 0.00 0.0 37.02 3.93 R
4109 4962 1.270947 TGCCACTAAAGTACAACGGGG 60.271 52.381 0.00 0.0 0.00 5.73 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
108 111 9.524106 TGACATATACGAAAATGTAGAACGAAT 57.476 29.630 0.00 0.00 36.48 3.34
197 247 9.515020 TGAACAAGTATTTGAAGAAATGTTGAC 57.485 29.630 4.81 0.00 37.73 3.18
350 429 6.756542 GGAACAAGTATTTGAAAAGTGTTGCT 59.243 34.615 4.81 0.00 37.73 3.91
520 625 2.902343 GCGCCCTTGCTGGTATCC 60.902 66.667 0.00 0.00 34.43 2.59
568 680 0.798771 TGCGGTTTGTTTGTTCGTGC 60.799 50.000 0.00 0.00 0.00 5.34
569 681 1.793480 GCGGTTTGTTTGTTCGTGCG 61.793 55.000 0.00 0.00 0.00 5.34
612 724 7.532199 TGTTACCTCCTTTTTCCCTTCTATTT 58.468 34.615 0.00 0.00 0.00 1.40
647 759 2.614829 GGCTAGCCCAGAAAACGATA 57.385 50.000 24.19 0.00 0.00 2.92
651 763 2.240493 AGCCCAGAAAACGATATCCG 57.760 50.000 0.00 0.00 45.44 4.18
669 781 1.896660 GCAGGAAACCTTGGACGCA 60.897 57.895 0.00 0.00 0.00 5.24
683 795 4.530710 TGGACGCAAGAGTAGTTTGTAT 57.469 40.909 0.00 0.00 43.62 2.29
777 900 1.908483 GAGGTTAGGCCCAGGACAG 59.092 63.158 0.00 0.00 38.26 3.51
830 955 2.621556 AAAAGCAGGCCCCTTGATAA 57.378 45.000 0.00 0.00 0.00 1.75
912 1045 1.079336 GCTCGCGTTCCCCTACTTT 60.079 57.895 5.77 0.00 0.00 2.66
1263 1396 2.642254 CGGCGGACAACTCAGGGTA 61.642 63.158 0.00 0.00 0.00 3.69
1267 1400 1.066430 GCGGACAACTCAGGGTATTCA 60.066 52.381 0.00 0.00 0.00 2.57
1383 1517 8.407832 AGTTTGTTAACTATTTAAAGCCGTGTT 58.592 29.630 7.22 0.00 42.73 3.32
1713 1874 0.539438 TCCCGTGCTTCCAAATGCTT 60.539 50.000 0.00 0.00 0.00 3.91
1804 1967 8.902540 TCACTACAATTTCATAGTCAGTGTTT 57.097 30.769 0.00 0.00 34.99 2.83
1805 1968 9.337396 TCACTACAATTTCATAGTCAGTGTTTT 57.663 29.630 0.00 0.00 34.99 2.43
1806 1969 9.385902 CACTACAATTTCATAGTCAGTGTTTTG 57.614 33.333 0.00 0.00 28.91 2.44
1847 2011 4.038402 CCAAAAACTCTGGCTGAAATCACT 59.962 41.667 0.00 0.00 0.00 3.41
1855 2019 6.888632 ACTCTGGCTGAAATCACTAATTGAAT 59.111 34.615 0.00 0.00 37.92 2.57
1856 2020 7.395489 ACTCTGGCTGAAATCACTAATTGAATT 59.605 33.333 0.00 0.00 37.92 2.17
1907 2072 7.061441 GCTCATCATCACACAAAACACAATTAG 59.939 37.037 0.00 0.00 0.00 1.73
2057 2231 3.384789 TGGACGATCAGGTGGATTTCTAG 59.615 47.826 0.00 0.00 36.00 2.43
2118 2293 5.953548 TGTTATGCCAGTAGACTACCAACTA 59.046 40.000 9.06 0.00 0.00 2.24
2124 2299 5.661458 CCAGTAGACTACCAACTACCATTG 58.339 45.833 9.06 0.00 39.53 2.82
2179 2357 4.252073 TGTTGCCAATCATGCCATTTAAC 58.748 39.130 0.00 0.00 0.00 2.01
2276 2455 5.509498 AGGAACATAGTTGTATGCAATGGT 58.491 37.500 0.00 0.00 39.94 3.55
2361 2541 9.935241 TCTTATCATTCCACTTATCAAGATAGC 57.065 33.333 0.00 0.00 0.00 2.97
2384 2564 5.721510 GCGTTTGACTATGTTTCTAGAAGCG 60.722 44.000 13.77 3.51 0.00 4.68
2523 2708 6.139679 TCCCTCAATTCAACTCAAGGTATT 57.860 37.500 0.00 0.00 0.00 1.89
2665 2858 7.338800 ACCAGACAATTTCCATGCTTATTAG 57.661 36.000 0.00 0.00 0.00 1.73
2693 2886 6.318900 CCTTTACCATACCAAAGATGACTTCC 59.681 42.308 0.00 0.00 34.35 3.46
2783 2981 4.007659 GGGAAGAAATCACCGCTTTAGAA 58.992 43.478 0.00 0.00 0.00 2.10
2825 3023 6.778834 ATGACATCATTGAAGCAATACCAA 57.221 33.333 0.00 0.00 32.35 3.67
2838 3036 8.637986 TGAAGCAATACCAAATAGTCTTTTGTT 58.362 29.630 0.00 0.00 35.30 2.83
2894 3093 6.372659 CACTTTAGGTCTAGTAGAACCGTACA 59.627 42.308 11.75 0.00 30.45 2.90
2935 3135 8.407064 TGAAAGGCGTATCTTCTTTTTAACAAA 58.593 29.630 0.00 0.00 31.72 2.83
2973 3174 5.826737 CACCCAATAGCTCTTTCATCAGATT 59.173 40.000 0.00 0.00 0.00 2.40
3154 3941 3.033184 ACCATCATTCCCGCATTCATTT 58.967 40.909 0.00 0.00 0.00 2.32
3226 4018 2.425668 TCGACTTGTATCATGCTTCGGA 59.574 45.455 0.00 0.00 0.00 4.55
3245 4037 3.206150 GGAGTCTTCAGCAAACAACTCA 58.794 45.455 9.72 0.00 35.87 3.41
3278 4070 0.114168 AGAGTCACCTCTGCTGGAGT 59.886 55.000 0.00 0.00 46.45 3.85
3343 4135 2.302260 CTGACGGCTATCCTTGAGAGA 58.698 52.381 0.00 0.00 0.00 3.10
3365 4157 3.731431 TGCCCTATCTTGGAGGTTCTTA 58.269 45.455 0.00 0.00 31.52 2.10
3406 4198 1.372582 TCAACTCCAATGATGAGCGC 58.627 50.000 0.00 0.00 32.98 5.92
3471 4263 2.029290 AGTGGGATGACGAGTGTTGTAC 60.029 50.000 0.00 0.00 0.00 2.90
3628 4428 5.607119 AGTTCTTCGCGAATTTATGTTGT 57.393 34.783 23.67 0.00 33.45 3.32
3700 4501 6.657836 TTTTAATACCTTTGTCTCTAGCGC 57.342 37.500 0.00 0.00 0.00 5.92
3715 4516 2.770164 AGCGCTGTATCAAAGGACTT 57.230 45.000 10.39 0.00 0.00 3.01
3785 4592 3.614092 ACGGGAGAAACACTCGTATCTA 58.386 45.455 0.00 0.00 45.76 1.98
3825 4632 9.770097 CTCTCTTTATGAAATCTTGGTATGCTA 57.230 33.333 0.00 0.00 0.00 3.49
3845 4665 3.423539 ACATCTTCTTGGCTGCTACAA 57.576 42.857 0.00 0.00 0.00 2.41
3855 4675 7.466746 TCTTGGCTGCTACAAAATTATCTTT 57.533 32.000 0.00 0.00 0.00 2.52
3881 4701 9.772973 TCTAACAAAATCTTTAACAGAGTAGCA 57.227 29.630 0.00 0.00 33.87 3.49
3891 4711 1.002544 ACAGAGTAGCAGAAGGTTGGC 59.997 52.381 0.00 0.00 0.00 4.52
3990 4810 3.363787 AGGCTTCCCTGCGAAATTT 57.636 47.368 0.00 0.00 40.94 1.82
4008 4829 7.030165 CGAAATTTGCTAGAGTGAGAGTCTAA 58.970 38.462 0.00 0.00 30.36 2.10
4019 4840 7.874252 AGAGTGAGAGTCTAAGGACCTATTTA 58.126 38.462 0.00 0.00 43.05 1.40
4109 4962 4.708726 AGTGTATTTTCCTGAAGCATGC 57.291 40.909 10.51 10.51 0.00 4.06
4200 5053 2.171003 GCTGAAACAAATAGGGCCTGT 58.829 47.619 18.53 6.65 0.00 4.00
4239 5102 8.038351 TGGACTTTGATATTACGACTCATTTCA 58.962 33.333 0.00 0.00 0.00 2.69
4288 5151 2.368221 CCAACTTTCCTGGCCATTTGAA 59.632 45.455 5.51 7.18 0.00 2.69
4319 5182 9.146984 CCATGAGTCGTGAGTTTTAATTAGTTA 57.853 33.333 14.16 0.00 0.00 2.24
4424 5287 5.481105 CATTTCCATTGTTGTAGCCAATGT 58.519 37.500 11.02 0.00 44.87 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 82 9.567917 CGTTCTACATTTTCGTATATGTCAATG 57.432 33.333 1.65 13.14 36.46 2.82
398 478 6.939730 TCCTTTTCTTTGCTTTTGTTTTTCCT 59.060 30.769 0.00 0.00 0.00 3.36
400 480 9.457110 TTTTCCTTTTCTTTGCTTTTGTTTTTC 57.543 25.926 0.00 0.00 0.00 2.29
470 564 5.239306 TGAAGCATGAAGTGTCGATTTTCTT 59.761 36.000 0.00 0.00 0.00 2.52
477 571 2.802247 CACTTGAAGCATGAAGTGTCGA 59.198 45.455 12.33 0.00 42.71 4.20
520 625 1.517257 CTCTACGCCAGCAGTTCGG 60.517 63.158 0.00 0.00 0.00 4.30
612 724 2.642129 CCCATGTTCGCGCACAAA 59.358 55.556 16.88 0.00 0.00 2.83
631 743 2.547218 GCGGATATCGTTTTCTGGGCTA 60.547 50.000 0.00 0.00 41.72 3.93
647 759 0.322546 GTCCAAGGTTTCCTGCGGAT 60.323 55.000 0.00 0.00 38.02 4.18
651 763 1.452145 TTGCGTCCAAGGTTTCCTGC 61.452 55.000 0.00 0.00 32.13 4.85
662 774 2.902705 ACAAACTACTCTTGCGTCCA 57.097 45.000 0.00 0.00 0.00 4.02
663 775 4.491676 TCATACAAACTACTCTTGCGTCC 58.508 43.478 0.00 0.00 0.00 4.79
664 776 5.052304 CGATCATACAAACTACTCTTGCGTC 60.052 44.000 0.00 0.00 0.00 5.19
665 777 4.798907 CGATCATACAAACTACTCTTGCGT 59.201 41.667 0.00 0.00 0.00 5.24
669 781 9.035607 CATTAAGCGATCATACAAACTACTCTT 57.964 33.333 0.00 0.00 0.00 2.85
830 955 4.205587 GGCTGTTGATTGATGAGGAAGAT 58.794 43.478 0.00 0.00 0.00 2.40
912 1045 6.753913 ATTGAGAGACCAATTATAGAGGCA 57.246 37.500 0.00 0.00 33.29 4.75
1137 1270 0.386731 GCCACACGTCCGGAAAATTG 60.387 55.000 5.23 3.25 0.00 2.32
1247 1380 1.066430 TGAATACCCTGAGTTGTCCGC 60.066 52.381 0.00 0.00 0.00 5.54
1267 1400 1.065418 GGTGACAAACATCCTCCCGAT 60.065 52.381 0.00 0.00 0.00 4.18
1393 1527 9.685828 GCACAACAAATTATTACCTAAGTTGAA 57.314 29.630 10.91 0.00 44.34 2.69
1425 1561 9.597170 TCAGAAATCAAATCAATTTGTTGTTCA 57.403 25.926 13.57 0.00 45.49 3.18
1470 1606 5.228665 GGATTCCCTACTATTGTCGCTAAC 58.771 45.833 0.00 0.00 0.00 2.34
1576 1714 9.847224 CAAGCTTAAAGGAAGGGATACTATTTA 57.153 33.333 0.00 0.00 35.49 1.40
1687 1848 5.762045 CATTTGGAAGCACGGGAATATTAG 58.238 41.667 0.00 0.00 0.00 1.73
1690 1851 2.362077 GCATTTGGAAGCACGGGAATAT 59.638 45.455 0.00 0.00 0.00 1.28
1713 1874 1.683943 GCCTCATTGCTGGCTATTGA 58.316 50.000 11.57 0.00 45.26 2.57
1738 1899 6.983906 GGGGGATACTCAATTCAATTTCAT 57.016 37.500 0.00 0.00 41.13 2.57
1804 1967 2.884639 GGCTTGCTCTAGGTTTGAACAA 59.115 45.455 0.00 0.00 0.00 2.83
1805 1968 2.158682 TGGCTTGCTCTAGGTTTGAACA 60.159 45.455 0.00 0.00 0.00 3.18
1806 1969 2.504367 TGGCTTGCTCTAGGTTTGAAC 58.496 47.619 0.00 0.00 0.00 3.18
1907 2072 2.362077 AGCACTTCCACATTGAAACCAC 59.638 45.455 0.00 0.00 0.00 4.16
1958 2123 7.569639 TGTTTTGGCTACTATTACAACACAA 57.430 32.000 0.00 0.00 32.54 3.33
2039 2207 6.150396 ACTTACTAGAAATCCACCTGATCG 57.850 41.667 0.00 0.00 31.61 3.69
2096 2270 5.361857 GGTAGTTGGTAGTCTACTGGCATAA 59.638 44.000 9.85 0.00 37.33 1.90
2338 2518 7.896811 ACGCTATCTTGATAAGTGGAATGATA 58.103 34.615 0.00 0.00 0.00 2.15
2357 2537 7.222999 GCTTCTAGAAACATAGTCAAACGCTAT 59.777 37.037 6.63 0.00 0.00 2.97
2361 2541 5.220228 CCGCTTCTAGAAACATAGTCAAACG 60.220 44.000 6.63 0.00 0.00 3.60
2503 2685 7.487189 GCATGAAATACCTTGAGTTGAATTGAG 59.513 37.037 0.00 0.00 0.00 3.02
2523 2708 4.973168 ACAAGTTCTTCTACCAGCATGAA 58.027 39.130 0.00 0.00 39.69 2.57
2665 2858 6.884836 AGTCATCTTTGGTATGGTAAAGGAAC 59.115 38.462 0.00 0.00 35.24 3.62
2673 2866 3.873910 CGGAAGTCATCTTTGGTATGGT 58.126 45.455 0.00 0.00 33.64 3.55
2693 2886 3.004734 AGACCACTTTCAAAAATCTGGCG 59.995 43.478 0.00 0.00 0.00 5.69
2783 2981 4.954826 GTCATACTCTGGTAGGTTGGTACT 59.045 45.833 0.00 0.00 32.34 2.73
2838 3036 6.715264 TCTGATGCCTATCGTGTCTAGATTTA 59.285 38.462 0.00 0.00 36.04 1.40
2841 3039 4.657013 TCTGATGCCTATCGTGTCTAGAT 58.343 43.478 0.00 0.00 36.04 1.98
2894 3093 2.507471 CCTTTCACCTATCTTGGGCTCT 59.493 50.000 0.00 0.00 0.00 4.09
2935 3135 2.969821 TGGGTGGCTAACATTCTTGT 57.030 45.000 0.00 0.00 37.82 3.16
2973 3174 5.550403 AGTCCTCTTTGGTCCCAATTAGTAA 59.450 40.000 0.00 0.00 35.70 2.24
3226 4018 3.878778 AGTGAGTTGTTTGCTGAAGACT 58.121 40.909 0.00 0.00 0.00 3.24
3328 4120 1.003003 GGGCATCTCTCAAGGATAGCC 59.997 57.143 0.00 0.00 37.02 3.93
3343 4135 2.781667 AGAACCTCCAAGATAGGGCAT 58.218 47.619 0.00 0.00 38.54 4.40
3365 4157 5.769662 TGATCAAGAAACAATAGTGCAACCT 59.230 36.000 0.00 0.00 37.80 3.50
3471 4263 6.430451 GTCATTGTTGGAGCTTATTAATCGG 58.570 40.000 0.00 0.00 0.00 4.18
3628 4428 7.282585 AGCTAGAATTGGTACAGAATTATGCA 58.717 34.615 0.00 0.00 42.39 3.96
3785 4592 8.540507 TCATAAAGAGAGTTACTATGGAAGCT 57.459 34.615 0.00 0.00 0.00 3.74
3825 4632 3.423539 TTGTAGCAGCCAAGAAGATGT 57.576 42.857 0.00 0.00 0.00 3.06
3855 4675 9.772973 TGCTACTCTGTTAAAGATTTTGTTAGA 57.227 29.630 0.00 0.00 33.29 2.10
3881 4701 1.416401 TCAAAGAGTCGCCAACCTTCT 59.584 47.619 0.00 0.00 0.00 2.85
3891 4711 5.683859 CAAGAATTGGAGTTCAAAGAGTCG 58.316 41.667 0.00 0.00 43.94 4.18
3987 4807 6.096282 GTCCTTAGACTCTCACTCTAGCAAAT 59.904 42.308 0.00 0.00 40.10 2.32
3990 4810 4.519213 GTCCTTAGACTCTCACTCTAGCA 58.481 47.826 0.00 0.00 40.10 3.49
4008 4829 6.360618 CCTGAAGCTGAAATAAATAGGTCCT 58.639 40.000 0.00 0.00 0.00 3.85
4019 4840 1.005215 CCTGGTCCCTGAAGCTGAAAT 59.995 52.381 0.00 0.00 0.00 2.17
4109 4962 1.270947 TGCCACTAAAGTACAACGGGG 60.271 52.381 0.00 0.00 0.00 5.73
4239 5102 4.070716 CCTCAGAGTTGAAGAACTTGCAT 58.929 43.478 0.00 0.00 42.80 3.96
4288 5151 7.972832 TTAAAACTCACGACTCATGGTTAAT 57.027 32.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.