Multiple sequence alignment - TraesCS3D01G176000

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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 TraesCS3D01G176000 chr3D 100.000 2893 0 0 1 2893 157541830 157538938 0.000000e+00 5343.0
1 TraesCS3D01G176000 chr3D 79.180 610 114 11 1270 1874 157443366 157442765 7.460000e-111 411.0
2 TraesCS3D01G176000 chr3D 77.724 624 126 11 1256 1874 427294810 427294195 1.270000e-98 370.0
3 TraesCS3D01G176000 chr3D 89.583 48 5 0 1091 1138 451709916 451709963 8.660000e-06 62.1
4 TraesCS3D01G176000 chr3D 89.583 48 5 0 1091 1138 451885415 451885462 8.660000e-06 62.1
5 TraesCS3D01G176000 chr3B 88.782 2603 176 49 309 2850 228751714 228749167 0.000000e+00 3083.0
6 TraesCS3D01G176000 chr3B 78.431 612 115 15 1270 1874 228690773 228690172 1.630000e-102 383.0
7 TraesCS3D01G176000 chr3B 77.157 626 126 14 1256 1874 556960062 556959447 5.930000e-92 348.0
8 TraesCS3D01G176000 chr3B 91.667 48 4 0 1091 1138 593163661 593163708 1.860000e-07 67.6
9 TraesCS3D01G176000 chr3B 91.667 48 4 0 1091 1138 593541139 593541186 1.860000e-07 67.6
10 TraesCS3D01G176000 chr3A 93.889 1931 80 17 905 2831 170658526 170660422 0.000000e+00 2878.0
11 TraesCS3D01G176000 chr3A 90.578 467 23 8 1 465 170655798 170656245 1.480000e-167 599.0
12 TraesCS3D01G176000 chr3A 88.235 442 22 8 463 882 170658042 170658475 4.300000e-138 501.0
13 TraesCS3D01G176000 chr3A 79.412 612 112 11 1270 1874 170811701 170812305 1.240000e-113 420.0
14 TraesCS3D01G176000 chr3A 77.368 623 128 11 1254 1871 559334333 559334947 9.860000e-95 357.0
15 TraesCS3D01G176000 chr3A 91.667 48 4 0 1091 1138 594492286 594492333 1.860000e-07 67.6
16 TraesCS3D01G176000 chr4A 83.442 308 39 10 1268 1569 26413804 26413503 2.840000e-70 276.0


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 TraesCS3D01G176000 chr3D 157538938 157541830 2892 True 5343 5343 100.000000 1 2893 1 chr3D.!!$R2 2892
1 TraesCS3D01G176000 chr3D 157442765 157443366 601 True 411 411 79.180000 1270 1874 1 chr3D.!!$R1 604
2 TraesCS3D01G176000 chr3D 427294195 427294810 615 True 370 370 77.724000 1256 1874 1 chr3D.!!$R3 618
3 TraesCS3D01G176000 chr3B 228749167 228751714 2547 True 3083 3083 88.782000 309 2850 1 chr3B.!!$R2 2541
4 TraesCS3D01G176000 chr3B 228690172 228690773 601 True 383 383 78.431000 1270 1874 1 chr3B.!!$R1 604
5 TraesCS3D01G176000 chr3B 556959447 556960062 615 True 348 348 77.157000 1256 1874 1 chr3B.!!$R3 618
6 TraesCS3D01G176000 chr3A 170655798 170660422 4624 False 1326 2878 90.900667 1 2831 3 chr3A.!!$F4 2830
7 TraesCS3D01G176000 chr3A 170811701 170812305 604 False 420 420 79.412000 1270 1874 1 chr3A.!!$F1 604
8 TraesCS3D01G176000 chr3A 559334333 559334947 614 False 357 357 77.368000 1254 1871 1 chr3A.!!$F2 617

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
946 2810 0.320421 GGAACACACGCTAGGCTTCA 60.32 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2717 4624 0.248843 GCAGAGACCTCAGTTCCTGG 59.751 60.0 0.0 0.0 31.51 4.45 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
40 41 5.191522 TGTTCAGGGATCATACAAGAATCCA 59.808 40.000 0.00 0.00 33.24 3.41
81 82 1.375013 TAAACGTCTTCCAGCCCGC 60.375 57.895 0.00 0.00 0.00 6.13
96 97 1.893808 CCGCTTGCTGGTCACTTGT 60.894 57.895 0.00 0.00 0.00 3.16
108 109 0.682852 TCACTTGTGAGGTTACGGGG 59.317 55.000 0.00 0.00 0.00 5.73
109 110 0.953960 CACTTGTGAGGTTACGGGGC 60.954 60.000 0.00 0.00 0.00 5.80
128 130 4.380550 GGGGCAAAACTCCGAAGAAATTAG 60.381 45.833 0.00 0.00 0.00 1.73
138 140 6.814146 ACTCCGAAGAAATTAGTGAGTGAATC 59.186 38.462 0.00 0.00 0.00 2.52
141 143 5.805486 CGAAGAAATTAGTGAGTGAATCGGA 59.195 40.000 0.00 0.00 0.00 4.55
168 170 2.958137 TTCGTTTGCACTTGCGTCGC 62.958 55.000 11.10 11.10 45.83 5.19
178 180 2.850786 CTTGCGTCGCGTCTGAGCTA 62.851 60.000 13.38 2.27 34.40 3.32
216 218 3.499918 AGCGAACATAAGAGCATATTGCC 59.500 43.478 0.00 0.00 46.52 4.52
252 254 2.182030 GACGCGGCAGACTTAGCT 59.818 61.111 7.34 0.00 0.00 3.32
277 279 1.002033 CATTGCTTGCCGAGAATAGCC 60.002 52.381 0.00 0.00 32.73 3.93
280 282 0.601311 GCTTGCCGAGAATAGCCGAT 60.601 55.000 0.00 0.00 0.00 4.18
281 283 1.423395 CTTGCCGAGAATAGCCGATC 58.577 55.000 0.00 0.00 0.00 3.69
282 284 1.000283 CTTGCCGAGAATAGCCGATCT 60.000 52.381 0.00 0.00 0.00 2.75
283 285 0.598562 TGCCGAGAATAGCCGATCTC 59.401 55.000 0.00 1.24 38.94 2.75
288 290 3.106508 GAGAATAGCCGATCTCGTACG 57.893 52.381 9.53 9.53 37.74 3.67
289 291 2.735663 GAGAATAGCCGATCTCGTACGA 59.264 50.000 18.41 18.41 37.74 3.43
290 292 3.136763 AGAATAGCCGATCTCGTACGAA 58.863 45.455 20.00 10.69 37.74 3.85
291 293 3.752222 AGAATAGCCGATCTCGTACGAAT 59.248 43.478 20.00 14.85 37.74 3.34
292 294 4.934001 AGAATAGCCGATCTCGTACGAATA 59.066 41.667 20.00 10.83 37.74 1.75
293 295 5.585445 AGAATAGCCGATCTCGTACGAATAT 59.415 40.000 20.00 15.20 37.74 1.28
294 296 6.760298 AGAATAGCCGATCTCGTACGAATATA 59.240 38.462 20.00 5.62 37.74 0.86
295 297 4.596801 AGCCGATCTCGTACGAATATAC 57.403 45.455 20.00 7.50 37.74 1.47
478 2281 2.484889 GATGTAACTCCGGAATCTGCC 58.515 52.381 5.23 0.00 0.00 4.85
520 2323 3.271014 GACAGGCGTCACGGACTA 58.729 61.111 0.00 0.00 42.13 2.59
550 2356 4.577834 TTACGATATGGAGAATGCACGA 57.422 40.909 0.00 0.00 41.42 4.35
556 2362 2.103042 GGAGAATGCACGAGCGCTT 61.103 57.895 13.26 0.00 46.23 4.68
571 2377 1.333702 GCGCTTTCGTGATCACAAACA 60.334 47.619 24.93 5.41 38.14 2.83
572 2378 2.665519 GCGCTTTCGTGATCACAAACAT 60.666 45.455 24.93 0.00 38.14 2.71
583 2389 7.334171 TCGTGATCACAAACATATCACAAGAAT 59.666 33.333 24.93 0.00 46.34 2.40
612 2418 3.074412 CGCTTCCAAGGAACAACTACAT 58.926 45.455 0.00 0.00 0.00 2.29
759 2585 2.948979 GCATGACCCACGATTAATCCAA 59.051 45.455 9.87 0.00 0.00 3.53
768 2594 7.543756 ACCCACGATTAATCCAATAAACAAAG 58.456 34.615 9.87 0.00 0.00 2.77
769 2595 7.394923 ACCCACGATTAATCCAATAAACAAAGA 59.605 33.333 9.87 0.00 0.00 2.52
770 2596 7.915397 CCCACGATTAATCCAATAAACAAAGAG 59.085 37.037 9.87 0.00 0.00 2.85
771 2597 8.673711 CCACGATTAATCCAATAAACAAAGAGA 58.326 33.333 9.87 0.00 0.00 3.10
793 2619 0.321671 AAGCCACATGCACTCTACGT 59.678 50.000 0.00 0.00 44.83 3.57
794 2620 1.182667 AGCCACATGCACTCTACGTA 58.817 50.000 0.00 0.00 44.83 3.57
795 2621 1.135083 AGCCACATGCACTCTACGTAC 60.135 52.381 0.00 0.00 44.83 3.67
886 2721 1.446272 GCGAGGGACGGAAACAGAG 60.446 63.158 0.00 0.00 42.83 3.35
923 2787 0.673644 GCCGTCGCCCATATAAGCAT 60.674 55.000 0.00 0.00 0.00 3.79
946 2810 0.320421 GGAACACACGCTAGGCTTCA 60.320 55.000 0.00 0.00 0.00 3.02
993 2872 2.038295 CAGAGAAGCAGAGTTGGTCCTT 59.962 50.000 0.00 0.00 32.95 3.36
1032 2911 2.785258 GCGATCCTGGCGTTGTTC 59.215 61.111 0.00 0.00 0.00 3.18
1039 2918 3.850098 CTGGCGTTGTTCCTGGGCT 62.850 63.158 0.00 0.00 0.00 5.19
1065 2944 3.691342 TCACAGCTCGGGGGTTCG 61.691 66.667 0.00 0.00 0.00 3.95
1160 3057 3.103738 CGTAACCGTTTCCTGATACTCG 58.896 50.000 0.00 0.00 0.00 4.18
1175 3072 4.455533 TGATACTCGAGTTTTGCTGCAAAT 59.544 37.500 26.48 14.24 33.19 2.32
1177 3074 4.829064 ACTCGAGTTTTGCTGCAAATTA 57.171 36.364 26.48 11.69 33.19 1.40
1192 3091 8.026607 TGCTGCAAATTAAGTAAAGGTTATCAC 58.973 33.333 0.00 0.00 0.00 3.06
1193 3092 8.244113 GCTGCAAATTAAGTAAAGGTTATCACT 58.756 33.333 0.00 0.00 0.00 3.41
1225 3124 2.513897 GAGGATTTGCGTCGGGGG 60.514 66.667 0.00 0.00 0.00 5.40
2083 3990 7.757941 TCACATCAACCAAATTCTTATGTGA 57.242 32.000 10.31 10.31 45.55 3.58
2088 3995 9.903682 CATCAACCAAATTCTTATGTGATATCC 57.096 33.333 0.00 0.00 0.00 2.59
2090 3997 6.560253 ACCAAATTCTTATGTGATATCCGC 57.440 37.500 0.00 0.00 0.00 5.54
2127 4034 1.680735 TGATGTGGCCTTGAAACACAC 59.319 47.619 3.32 0.00 46.51 3.82
2223 4130 2.444706 CTCCCCTCGCTCATCCCA 60.445 66.667 0.00 0.00 0.00 4.37
2228 4135 1.475169 CCCTCGCTCATCCCAGCATA 61.475 60.000 0.00 0.00 39.62 3.14
2264 4171 3.490348 ACAGATGGTGGAGGAAACAAAG 58.510 45.455 0.00 0.00 0.00 2.77
2276 4183 3.960102 AGGAAACAAAGTTGAATCTGGCA 59.040 39.130 0.00 0.00 0.00 4.92
2307 4214 1.580658 ACAGATGATAGGGGTCCTCCA 59.419 52.381 0.00 0.00 37.22 3.86
2404 4311 2.434884 CGCTGACGGGAAGTGCAT 60.435 61.111 0.00 0.00 34.97 3.96
2488 4395 2.508526 CTTGTTTGCTGCTACCCTCTT 58.491 47.619 0.00 0.00 0.00 2.85
2526 4433 0.321653 ACAACGAGGGAAGTGGATGC 60.322 55.000 0.00 0.00 0.00 3.91
2531 4438 1.068588 CGAGGGAAGTGGATGCGATTA 59.931 52.381 0.00 0.00 0.00 1.75
2562 4469 2.291540 GGAAATGGGTCTGAATGGGTCA 60.292 50.000 0.00 0.00 34.17 4.02
2565 4472 0.834261 TGGGTCTGAATGGGTCACGA 60.834 55.000 0.00 0.00 31.13 4.35
2575 4482 0.684535 TGGGTCACGAAGCAGATCAA 59.315 50.000 0.00 0.00 0.00 2.57
2600 4507 5.339008 TGTAGAACTCAGTGTTGACTTGT 57.661 39.130 0.00 0.00 39.30 3.16
2659 4566 2.803492 GCAGTTCACGAGAGGTTCTGTT 60.803 50.000 0.00 0.00 0.00 3.16
2684 4591 0.979665 CAGGTGGCCGAGATATGGAT 59.020 55.000 0.00 0.00 0.00 3.41
2686 4593 2.167281 CAGGTGGCCGAGATATGGATAG 59.833 54.545 0.00 0.00 0.00 2.08
2690 4597 4.270834 GTGGCCGAGATATGGATAGACTA 58.729 47.826 0.00 0.00 0.00 2.59
2761 4668 1.176527 CCGCCACCTTCACAAATCAT 58.823 50.000 0.00 0.00 0.00 2.45
2792 4699 2.351276 GTCGTGGGGTTGCTGGAT 59.649 61.111 0.00 0.00 0.00 3.41
2793 4700 1.303317 GTCGTGGGGTTGCTGGATT 60.303 57.895 0.00 0.00 0.00 3.01
2794 4701 1.002624 TCGTGGGGTTGCTGGATTC 60.003 57.895 0.00 0.00 0.00 2.52
2795 4702 1.002134 CGTGGGGTTGCTGGATTCT 60.002 57.895 0.00 0.00 0.00 2.40
2796 4703 1.308069 CGTGGGGTTGCTGGATTCTG 61.308 60.000 0.00 0.00 0.00 3.02
2797 4704 0.967380 GTGGGGTTGCTGGATTCTGG 60.967 60.000 0.00 0.00 0.00 3.86
2798 4705 1.139498 TGGGGTTGCTGGATTCTGGA 61.139 55.000 0.00 0.00 0.00 3.86
2799 4706 0.394899 GGGGTTGCTGGATTCTGGAG 60.395 60.000 0.00 0.00 0.00 3.86
2800 4707 0.620556 GGGTTGCTGGATTCTGGAGA 59.379 55.000 0.00 0.00 0.00 3.71
2801 4708 1.004745 GGGTTGCTGGATTCTGGAGAA 59.995 52.381 0.00 0.00 38.56 2.87
2802 4709 2.363683 GGTTGCTGGATTCTGGAGAAG 58.636 52.381 0.00 0.00 37.48 2.85
2803 4710 1.742268 GTTGCTGGATTCTGGAGAAGC 59.258 52.381 0.00 0.00 39.52 3.86
2804 4711 1.283347 TGCTGGATTCTGGAGAAGCT 58.717 50.000 4.74 0.00 40.08 3.74
2805 4712 2.470990 TGCTGGATTCTGGAGAAGCTA 58.529 47.619 4.74 0.00 40.08 3.32
2806 4713 2.169352 TGCTGGATTCTGGAGAAGCTAC 59.831 50.000 4.74 0.00 40.08 3.58
2839 4746 1.262640 GGTGGGAAGCCGAGGAACTA 61.263 60.000 0.00 0.00 41.55 2.24
2852 4759 2.841442 GGAACTACCTCACAAGCTGT 57.159 50.000 0.00 0.00 35.41 4.40
2853 4760 3.127425 GGAACTACCTCACAAGCTGTT 57.873 47.619 0.00 0.00 35.41 3.16
2854 4761 2.808543 GGAACTACCTCACAAGCTGTTG 59.191 50.000 0.00 0.00 36.30 3.33
2855 4762 1.884235 ACTACCTCACAAGCTGTTGC 58.116 50.000 0.00 0.00 37.14 4.17
2856 4763 0.792640 CTACCTCACAAGCTGTTGCG 59.207 55.000 0.00 0.00 45.42 4.85
2857 4764 0.391228 TACCTCACAAGCTGTTGCGA 59.609 50.000 0.00 0.00 45.42 5.10
2858 4765 1.160329 ACCTCACAAGCTGTTGCGAC 61.160 55.000 0.00 0.00 45.42 5.19
2859 4766 1.202568 CTCACAAGCTGTTGCGACG 59.797 57.895 0.00 0.00 45.42 5.12
2860 4767 2.425773 CACAAGCTGTTGCGACGC 60.426 61.111 14.19 14.19 45.42 5.19
2861 4768 3.649986 ACAAGCTGTTGCGACGCC 61.650 61.111 18.69 2.90 45.42 5.68
2862 4769 4.389576 CAAGCTGTTGCGACGCCC 62.390 66.667 18.69 8.56 45.42 6.13
2877 4784 4.235762 CCCCGACCGCCGATGAAT 62.236 66.667 0.00 0.00 41.76 2.57
2878 4785 2.967076 CCCGACCGCCGATGAATG 60.967 66.667 0.00 0.00 41.76 2.67
2879 4786 2.967076 CCGACCGCCGATGAATGG 60.967 66.667 0.00 0.00 41.76 3.16
2880 4787 2.202878 CGACCGCCGATGAATGGT 60.203 61.111 0.00 0.00 41.76 3.55
2881 4788 2.525248 CGACCGCCGATGAATGGTG 61.525 63.158 0.00 0.00 41.76 4.17
2882 4789 1.449601 GACCGCCGATGAATGGTGT 60.450 57.895 0.00 0.00 34.12 4.16
2883 4790 1.429148 GACCGCCGATGAATGGTGTC 61.429 60.000 0.00 0.00 34.12 3.67
2884 4791 1.153369 CCGCCGATGAATGGTGTCT 60.153 57.895 0.00 0.00 35.17 3.41
2885 4792 0.744414 CCGCCGATGAATGGTGTCTT 60.744 55.000 0.00 0.00 35.17 3.01
2886 4793 1.086696 CGCCGATGAATGGTGTCTTT 58.913 50.000 0.00 0.00 32.27 2.52
2887 4794 1.202065 CGCCGATGAATGGTGTCTTTG 60.202 52.381 0.00 0.00 32.27 2.77
2888 4795 2.083774 GCCGATGAATGGTGTCTTTGA 58.916 47.619 0.00 0.00 0.00 2.69
2889 4796 2.159517 GCCGATGAATGGTGTCTTTGAC 60.160 50.000 0.00 0.00 0.00 3.18
2890 4797 2.420022 CCGATGAATGGTGTCTTTGACC 59.580 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 1.233019 CCTCACAAGTGACCAGCAAG 58.767 55.000 0.00 0.00 35.46 4.01
91 92 1.373812 GCCCCGTAACCTCACAAGT 59.626 57.895 0.00 0.00 0.00 3.16
96 97 0.475044 AGTTTTGCCCCGTAACCTCA 59.525 50.000 0.00 0.00 0.00 3.86
108 109 5.997385 TCACTAATTTCTTCGGAGTTTTGC 58.003 37.500 0.00 0.00 0.00 3.68
109 110 7.042051 TCACTCACTAATTTCTTCGGAGTTTTG 60.042 37.037 0.00 0.00 32.25 2.44
128 130 3.320673 AAGTTCCTCCGATTCACTCAC 57.679 47.619 0.00 0.00 0.00 3.51
138 140 1.332375 TGCAAACGAAAAGTTCCTCCG 59.668 47.619 0.00 0.00 43.37 4.63
141 143 3.769536 CAAGTGCAAACGAAAAGTTCCT 58.230 40.909 0.00 0.00 43.37 3.36
168 170 5.274718 ACAATTAATCGAGTAGCTCAGACG 58.725 41.667 0.00 0.00 0.00 4.18
178 180 6.715344 TGTTCGCTTAACAATTAATCGAGT 57.285 33.333 7.17 0.00 45.11 4.18
211 213 3.270877 GTCTGAACTTACGATGGGCAAT 58.729 45.455 0.00 0.00 0.00 3.56
212 214 2.037902 TGTCTGAACTTACGATGGGCAA 59.962 45.455 0.00 0.00 0.00 4.52
216 218 2.915463 GTCGTGTCTGAACTTACGATGG 59.085 50.000 0.00 0.00 45.66 3.51
252 254 0.324614 TCTCGGCAAGCAATGAGGAA 59.675 50.000 7.88 0.00 0.00 3.36
283 285 7.797587 ACAGAAAGATCTTCGTATATTCGTACG 59.202 37.037 9.53 9.53 40.33 3.67
294 296 7.804129 GCGTTCTATATACAGAAAGATCTTCGT 59.196 37.037 8.78 9.13 36.49 3.85
295 297 8.018520 AGCGTTCTATATACAGAAAGATCTTCG 58.981 37.037 8.78 3.89 36.49 3.79
315 317 5.379757 CATTGCAAAAATGGATAGCGTTC 57.620 39.130 1.71 0.00 0.00 3.95
478 2281 3.469008 TTATGTAGCCGATTGGTCCTG 57.531 47.619 0.00 0.00 37.67 3.86
520 2323 5.209818 TCTCCATATCGTAAAATTCGGCT 57.790 39.130 0.00 0.00 0.00 5.52
550 2356 1.069906 GTTTGTGATCACGAAAGCGCT 60.070 47.619 26.58 2.64 42.48 5.92
571 2377 6.992063 AGCGAGTTTCAATTCTTGTGATAT 57.008 33.333 0.00 0.00 0.00 1.63
572 2378 6.128282 GGAAGCGAGTTTCAATTCTTGTGATA 60.128 38.462 2.36 0.00 0.00 2.15
583 2389 2.616842 GTTCCTTGGAAGCGAGTTTCAA 59.383 45.455 1.83 0.00 0.00 2.69
612 2418 3.404081 TGGGATGGGGCATTATTAATCCA 59.596 43.478 0.00 0.00 36.17 3.41
665 2491 7.343357 ACTAATAATCCAAGATGGTTTCCGAA 58.657 34.615 0.00 0.00 39.03 4.30
720 2546 1.388837 GCATGGCATGGCAGATCACA 61.389 55.000 27.48 1.49 0.00 3.58
759 2585 6.626623 GCATGTGGCTTCATCTCTTTGTTTAT 60.627 38.462 0.00 0.00 40.25 1.40
768 2594 1.669779 GAGTGCATGTGGCTTCATCTC 59.330 52.381 0.00 0.00 45.15 2.75
769 2595 1.281287 AGAGTGCATGTGGCTTCATCT 59.719 47.619 0.00 0.00 45.15 2.90
770 2596 1.747709 AGAGTGCATGTGGCTTCATC 58.252 50.000 0.00 0.00 45.15 2.92
771 2597 2.636830 GTAGAGTGCATGTGGCTTCAT 58.363 47.619 0.00 0.00 45.15 2.57
775 2601 1.135083 GTACGTAGAGTGCATGTGGCT 60.135 52.381 0.00 0.00 45.15 4.75
793 2619 7.398332 AGGATCACTGATCATGCATATGTAGTA 59.602 37.037 18.77 0.00 40.50 1.82
794 2620 6.212993 AGGATCACTGATCATGCATATGTAGT 59.787 38.462 18.77 0.00 40.50 2.73
795 2621 6.641474 AGGATCACTGATCATGCATATGTAG 58.359 40.000 18.77 0.00 40.50 2.74
869 2704 1.446272 GCTCTGTTTCCGTCCCTCG 60.446 63.158 0.00 0.00 39.52 4.63
913 2777 5.682869 CGTGTGTTCCATGATGCTTATATG 58.317 41.667 0.00 0.00 31.20 1.78
923 2787 0.391130 GCCTAGCGTGTGTTCCATGA 60.391 55.000 0.00 0.00 31.20 3.07
936 2800 2.611292 CTGTTGCATACTGAAGCCTAGC 59.389 50.000 0.00 0.00 0.00 3.42
946 2810 3.692257 ACTTCAGCTCTGTTGCATACT 57.308 42.857 0.00 0.00 34.99 2.12
993 2872 3.461061 GAGATGATTCTCCATGTTCGCA 58.539 45.455 0.00 0.00 42.26 5.10
1032 2911 1.604308 TGACATGCACAAGCCCAGG 60.604 57.895 0.00 0.00 41.13 4.45
1156 3035 3.715628 AATTTGCAGCAAAACTCGAGT 57.284 38.095 24.15 13.58 36.90 4.18
1160 3057 7.438160 ACCTTTACTTAATTTGCAGCAAAACTC 59.562 33.333 24.15 0.00 36.90 3.01
1192 3091 4.543590 ATCCTCGGCATAGGTTGATAAG 57.456 45.455 3.71 0.00 37.91 1.73
1193 3092 4.974645 AATCCTCGGCATAGGTTGATAA 57.025 40.909 3.71 0.00 37.91 1.75
1194 3093 4.641396 CAAATCCTCGGCATAGGTTGATA 58.359 43.478 3.71 0.00 37.91 2.15
1195 3094 3.480470 CAAATCCTCGGCATAGGTTGAT 58.520 45.455 3.71 0.00 37.91 2.57
1196 3095 2.917933 CAAATCCTCGGCATAGGTTGA 58.082 47.619 3.71 0.00 37.91 3.18
1204 3103 2.813474 CGACGCAAATCCTCGGCA 60.813 61.111 0.00 0.00 32.26 5.69
1225 3124 8.698854 CAAGAAGCAGATATCTAAGAAATCGTC 58.301 37.037 4.54 0.00 0.00 4.20
1543 3448 3.771160 CGAAGCCGGCCTGGTAGT 61.771 66.667 26.15 0.00 41.21 2.73
2027 3934 9.743057 AGAGAAAGAATAAGAGATGTATTGACG 57.257 33.333 0.00 0.00 0.00 4.35
2083 3990 6.369890 CAGCTATTTGTAAGTGATGCGGATAT 59.630 38.462 0.00 0.00 0.00 1.63
2088 3995 5.007039 ACATCAGCTATTTGTAAGTGATGCG 59.993 40.000 9.47 0.00 43.28 4.73
2090 3997 6.722301 CCACATCAGCTATTTGTAAGTGATG 58.278 40.000 8.26 8.26 44.44 3.07
2127 4034 1.070445 GGATGAGACATCGCCCTGG 59.930 63.158 0.00 0.00 0.00 4.45
2228 4135 4.472833 ACCATCTGTTTCCTCTTAGCATCT 59.527 41.667 0.00 0.00 0.00 2.90
2238 4145 2.044793 TCCTCCACCATCTGTTTCCT 57.955 50.000 0.00 0.00 0.00 3.36
2239 4146 2.820197 GTTTCCTCCACCATCTGTTTCC 59.180 50.000 0.00 0.00 0.00 3.13
2247 4154 3.909732 TCAACTTTGTTTCCTCCACCAT 58.090 40.909 0.00 0.00 0.00 3.55
2264 4171 6.767902 TGTAGATATCCTTTGCCAGATTCAAC 59.232 38.462 0.00 0.00 0.00 3.18
2276 4183 7.491681 ACCCCTATCATCTGTAGATATCCTTT 58.508 38.462 0.00 0.00 32.63 3.11
2307 4214 2.437895 TCGTCGCACCCTCGATCT 60.438 61.111 0.00 0.00 40.84 2.75
2446 4353 1.659794 GGGTTGCAGCGTGAATTGT 59.340 52.632 0.00 0.00 0.00 2.71
2448 4355 1.577328 CTCGGGTTGCAGCGTGAATT 61.577 55.000 0.00 0.00 0.00 2.17
2526 4433 0.657312 TTTCCGCAGCTGCATAATCG 59.343 50.000 36.03 19.47 42.21 3.34
2531 4438 2.420568 CCCATTTCCGCAGCTGCAT 61.421 57.895 36.03 20.43 42.21 3.96
2540 4447 1.340991 ACCCATTCAGACCCATTTCCG 60.341 52.381 0.00 0.00 0.00 4.30
2562 4469 4.456280 TCTACATGTTGATCTGCTTCGT 57.544 40.909 2.30 0.00 0.00 3.85
2565 4472 5.798132 TGAGTTCTACATGTTGATCTGCTT 58.202 37.500 20.75 2.59 0.00 3.91
2575 4482 5.537300 AGTCAACACTGAGTTCTACATGT 57.463 39.130 2.69 2.69 38.74 3.21
2600 4507 3.706594 CCTCTCCTACATTTCTAGCCACA 59.293 47.826 0.00 0.00 0.00 4.17
2684 4591 7.808381 CACTTCGTCTTCAAAGAATGTAGTCTA 59.192 37.037 0.00 0.00 36.68 2.59
2686 4593 6.616682 GCACTTCGTCTTCAAAGAATGTAGTC 60.617 42.308 0.00 0.00 36.68 2.59
2690 4597 3.876914 TGCACTTCGTCTTCAAAGAATGT 59.123 39.130 0.00 0.00 36.68 2.71
2717 4624 0.248843 GCAGAGACCTCAGTTCCTGG 59.751 60.000 0.00 0.00 31.51 4.45
2761 4668 0.392863 CACGACCCCAATCATCTGCA 60.393 55.000 0.00 0.00 0.00 4.41
2770 4677 4.589675 GCAACCCCACGACCCCAA 62.590 66.667 0.00 0.00 0.00 4.12
2792 4699 1.257743 ACGCAGTAGCTTCTCCAGAA 58.742 50.000 0.00 0.00 41.94 3.02
2793 4700 2.124277 TACGCAGTAGCTTCTCCAGA 57.876 50.000 0.00 0.00 45.11 3.86
2806 4713 1.813753 CCACCACCCGAATACGCAG 60.814 63.158 0.00 0.00 38.29 5.18
2839 4746 1.146041 TCGCAACAGCTTGTGAGGT 59.854 52.632 0.00 0.00 41.12 3.85
2842 4749 2.881266 GCGTCGCAACAGCTTGTGA 61.881 57.895 13.44 0.00 43.25 3.58
2860 4767 4.235762 ATTCATCGGCGGTCGGGG 62.236 66.667 7.21 0.00 39.77 5.73
2861 4768 2.967076 CATTCATCGGCGGTCGGG 60.967 66.667 7.21 0.00 39.77 5.14
2862 4769 2.967076 CCATTCATCGGCGGTCGG 60.967 66.667 7.21 0.00 39.77 4.79
2863 4770 2.202878 ACCATTCATCGGCGGTCG 60.203 61.111 7.21 0.00 40.90 4.79
2864 4771 1.429148 GACACCATTCATCGGCGGTC 61.429 60.000 7.21 0.00 0.00 4.79
2865 4772 1.449601 GACACCATTCATCGGCGGT 60.450 57.895 7.21 0.00 0.00 5.68
2866 4773 0.744414 AAGACACCATTCATCGGCGG 60.744 55.000 7.21 0.00 0.00 6.13
2867 4774 1.086696 AAAGACACCATTCATCGGCG 58.913 50.000 0.00 0.00 0.00 6.46
2868 4775 2.083774 TCAAAGACACCATTCATCGGC 58.916 47.619 0.00 0.00 0.00 5.54
2869 4776 2.420022 GGTCAAAGACACCATTCATCGG 59.580 50.000 0.00 0.00 33.68 4.18
2870 4777 3.073678 TGGTCAAAGACACCATTCATCG 58.926 45.455 0.00 0.00 39.11 3.84


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

AutoCloner maintained by Alex Coulton.