Multiple sequence alignment - TraesCS5A01G093200

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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 TraesCS5A01G093200 chr5A 100.000 6759 0 0 1 6759 129605415 129598657 0.000000e+00 12482
1 TraesCS5A01G093200 chr5A 92.414 145 8 1 2798 2939 129602540 129602396 3.200000e-48 204
2 TraesCS5A01G093200 chr5A 92.414 145 8 1 2876 3020 129602618 129602477 3.200000e-48 204
3 TraesCS5A01G093200 chr5D 94.667 5982 224 50 818 6746 119489710 119483771 0.000000e+00 9191
4 TraesCS5A01G093200 chr5D 88.650 326 32 3 472 796 119490018 119489697 6.350000e-105 392
5 TraesCS5A01G093200 chr5D 90.698 215 18 2 31 243 119490302 119490088 1.110000e-72 285
6 TraesCS5A01G093200 chr5D 91.724 145 9 1 2876 3020 119487739 119487598 1.490000e-46 198
7 TraesCS5A01G093200 chr5B 96.920 5000 127 13 818 5797 132291083 132286091 0.000000e+00 8355
8 TraesCS5A01G093200 chr5B 95.665 1015 38 3 5745 6759 132286088 132285080 0.000000e+00 1626
9 TraesCS5A01G093200 chr5B 80.616 552 80 13 166 693 132292945 132292397 1.060000e-107 401
10 TraesCS5A01G093200 chr5B 90.148 203 12 5 11 207 132293144 132292944 2.420000e-64 257
11 TraesCS5A01G093200 chr5B 91.216 148 7 2 2876 3020 132289096 132288952 5.350000e-46 196
12 TraesCS5A01G093200 chr5B 90.244 123 11 1 216 337 57958187 57958065 7.020000e-35 159
13 TraesCS5A01G093200 chr2D 86.449 214 25 3 6546 6759 500811759 500811968 1.470000e-56 231
14 TraesCS5A01G093200 chr3A 85.000 220 24 5 6546 6759 25032143 25031927 1.480000e-51 215
15 TraesCS5A01G093200 chr2B 85.311 177 26 0 160 336 796178775 796178951 4.160000e-42 183
16 TraesCS5A01G093200 chr7A 85.897 156 21 1 181 336 228170085 228169931 1.510000e-36 165
17 TraesCS5A01G093200 chr7A 81.622 185 30 4 162 343 646840087 646840270 4.220000e-32 150
18 TraesCS5A01G093200 chr7A 86.923 130 15 2 208 336 721589702 721589830 1.960000e-30 145
19 TraesCS5A01G093200 chrUn 81.915 188 25 5 162 343 389438310 389438494 4.220000e-32 150
20 TraesCS5A01G093200 chrUn 81.915 188 25 5 162 343 415837373 415837557 4.220000e-32 150
21 TraesCS5A01G093200 chr7B 81.915 188 25 5 162 343 611262567 611262751 4.220000e-32 150
22 TraesCS5A01G093200 chr3D 81.921 177 28 4 162 336 606613616 606613790 5.460000e-31 147


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 TraesCS5A01G093200 chr5A 129598657 129605415 6758 True 4296.666667 12482 94.942667 1 6759 3 chr5A.!!$R1 6758
1 TraesCS5A01G093200 chr5D 119483771 119490302 6531 True 2516.500000 9191 91.434750 31 6746 4 chr5D.!!$R1 6715
2 TraesCS5A01G093200 chr5B 132285080 132293144 8064 True 2167.000000 8355 90.913000 11 6759 5 chr5B.!!$R2 6748

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
418 465 0.037590 TGGGACAAAAGCTATGCGGT 59.962 50.000 0.00 0.0 31.92 5.68 F
794 872 0.249322 CACAACTGACCGACGGAACT 60.249 55.000 23.38 0.0 0.00 3.01 F
1879 3192 0.108138 CGGCAGGAGAAACTTCCGAT 60.108 55.000 0.00 0.0 42.29 4.18 F
1957 3270 0.253207 CCTCCCCTCCCAAGTTAGGT 60.253 60.000 0.00 0.0 0.00 3.08 F
2849 4165 0.882042 AACAGAAGCTGTCACTGGCG 60.882 55.000 0.00 0.0 44.62 5.69 F
2850 4166 1.301244 CAGAAGCTGTCACTGGCGT 60.301 57.895 0.00 0.0 0.00 5.68 F
4464 5832 1.886777 GAAGCCTGAGCAGATCCGC 60.887 63.158 0.00 0.0 43.56 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 2880 0.034767 TGCTGAATTCAGGGGAGCTG 60.035 55.000 31.41 9.72 43.94 4.24 R
2065 3378 0.374758 CGGTGAATGCTCCAATGTCG 59.625 55.000 0.00 0.00 0.00 4.35 R
2849 4165 0.889306 ACTGTAGGAGGCTCAACGAC 59.111 55.000 17.69 6.94 0.00 4.34 R
3095 4411 0.976641 TCCTCAGTTACCACAGCAGG 59.023 55.000 0.00 0.00 0.00 4.85 R
4464 5832 0.876342 GGCCCTCGACAATCTTAGCG 60.876 60.000 0.00 0.00 0.00 4.26 R
4907 6275 7.993183 CCTGGAAACATAGGTATGTCAAGTTAT 59.007 37.037 3.12 0.00 45.55 1.89 R
6185 7607 1.004745 TCTCTTGGTGGGCAATCTTCC 59.995 52.381 0.00 0.00 0.00 3.46 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
30 31 2.224378 CGGAATCCTATGATGCAGGTGT 60.224 50.000 0.00 0.00 34.56 4.16
102 108 2.094390 GCTTAGACCATACGACACCACA 60.094 50.000 0.00 0.00 0.00 4.17
126 132 4.708576 TGTTGTCCTGGTTATTGTGGTA 57.291 40.909 0.00 0.00 0.00 3.25
214 260 7.979444 TTAAAGATGTAAAACAGGAGAGGTG 57.021 36.000 0.00 0.00 0.00 4.00
226 272 8.934023 AAACAGGAGAGGTGAAAATTTACATA 57.066 30.769 0.00 0.00 0.00 2.29
273 319 2.234300 AAAAGAGGCGACTTCAACGA 57.766 45.000 0.00 0.00 44.43 3.85
358 404 0.610174 AGAATTGAGACGGCTGAGCA 59.390 50.000 6.82 0.00 0.00 4.26
359 405 1.002430 AGAATTGAGACGGCTGAGCAA 59.998 47.619 6.82 0.00 0.00 3.91
374 420 1.298339 GCAACGGCGGTCATAATGC 60.298 57.895 13.24 0.00 0.00 3.56
381 427 1.719117 CGGTCATAATGCGGCGTTT 59.281 52.632 13.33 5.57 0.00 3.60
382 428 0.588730 CGGTCATAATGCGGCGTTTG 60.589 55.000 13.33 10.91 0.00 2.93
385 431 2.173964 GTCATAATGCGGCGTTTGAAC 58.826 47.619 13.33 5.30 0.00 3.18
412 459 1.302993 GGCCGTGGGACAAAAGCTA 60.303 57.895 0.00 0.00 44.16 3.32
418 465 0.037590 TGGGACAAAAGCTATGCGGT 59.962 50.000 0.00 0.00 31.92 5.68
456 523 4.007940 GCGGCAGCGACAACGAAA 62.008 61.111 0.00 0.00 42.66 3.46
457 524 2.629210 CGGCAGCGACAACGAAAA 59.371 55.556 0.00 0.00 42.66 2.29
458 525 1.721133 CGGCAGCGACAACGAAAAC 60.721 57.895 0.00 0.00 42.66 2.43
459 526 1.721133 GGCAGCGACAACGAAAACG 60.721 57.895 0.00 0.00 42.66 3.60
464 531 2.426261 GACAACGAAAACGGCGGC 60.426 61.111 13.24 0.00 0.00 6.53
465 532 3.170810 GACAACGAAAACGGCGGCA 62.171 57.895 13.24 0.00 0.00 5.69
467 534 2.589442 AACGAAAACGGCGGCAGA 60.589 55.556 13.24 0.00 0.00 4.26
468 535 2.181521 AACGAAAACGGCGGCAGAA 61.182 52.632 13.24 0.00 0.00 3.02
476 543 2.975799 GGCGGCAGAAACGAACCA 60.976 61.111 3.07 0.00 0.00 3.67
514 581 2.159626 CGGCACAAAATACGGTCGATTT 60.160 45.455 0.00 0.00 0.00 2.17
546 621 2.272146 GTGCGGTGATGGATGGGT 59.728 61.111 0.00 0.00 0.00 4.51
576 651 4.947147 GTTGGGTGGTGGCTGCGA 62.947 66.667 0.00 0.00 0.00 5.10
677 753 4.098960 TGTCCTATCAGATAACCACGGTTC 59.901 45.833 4.34 0.00 39.31 3.62
742 818 2.534019 CCTGCACACGCACGACTTT 61.534 57.895 0.00 0.00 45.36 2.66
766 844 1.473258 AAACCTGCACACACACACAT 58.527 45.000 0.00 0.00 0.00 3.21
784 862 1.522806 TGGGACACGCACAACTGAC 60.523 57.895 0.00 0.00 0.00 3.51
785 863 2.251642 GGGACACGCACAACTGACC 61.252 63.158 0.00 0.00 0.00 4.02
786 864 2.594962 GGACACGCACAACTGACCG 61.595 63.158 0.00 0.00 0.00 4.79
787 865 1.590525 GACACGCACAACTGACCGA 60.591 57.895 0.00 0.00 0.00 4.69
788 866 1.818221 GACACGCACAACTGACCGAC 61.818 60.000 0.00 0.00 0.00 4.79
789 867 2.657296 ACGCACAACTGACCGACG 60.657 61.111 0.00 0.00 0.00 5.12
790 868 3.403057 CGCACAACTGACCGACGG 61.403 66.667 13.61 13.61 0.00 4.79
791 869 2.028484 GCACAACTGACCGACGGA 59.972 61.111 23.38 0.00 0.00 4.69
792 870 1.593209 GCACAACTGACCGACGGAA 60.593 57.895 23.38 7.41 0.00 4.30
794 872 0.249322 CACAACTGACCGACGGAACT 60.249 55.000 23.38 0.00 0.00 3.01
796 874 0.314302 CAACTGACCGACGGAACTCT 59.686 55.000 23.38 0.00 0.00 3.24
797 875 0.597072 AACTGACCGACGGAACTCTC 59.403 55.000 23.38 7.77 0.00 3.20
799 877 1.935327 CTGACCGACGGAACTCTCCC 61.935 65.000 23.38 0.00 38.71 4.30
801 879 2.362632 CCGACGGAACTCTCCCCT 60.363 66.667 8.64 0.00 38.71 4.79
802 880 2.416432 CCGACGGAACTCTCCCCTC 61.416 68.421 8.64 0.00 38.71 4.30
803 881 1.677966 CGACGGAACTCTCCCCTCA 60.678 63.158 0.00 0.00 38.71 3.86
804 882 1.248785 CGACGGAACTCTCCCCTCAA 61.249 60.000 0.00 0.00 38.71 3.02
805 883 0.974383 GACGGAACTCTCCCCTCAAA 59.026 55.000 0.00 0.00 38.71 2.69
806 884 1.346722 GACGGAACTCTCCCCTCAAAA 59.653 52.381 0.00 0.00 38.71 2.44
842 2137 1.852067 CGGAACTCAAAGGCAACCCG 61.852 60.000 0.00 0.00 35.76 5.28
919 2219 1.147824 CCCAGCCATCCACTGCTAG 59.852 63.158 0.00 0.00 35.69 3.42
1010 2313 2.445654 CCTCCTCAGCCTCCCTCC 60.446 72.222 0.00 0.00 0.00 4.30
1116 2422 4.908877 GCTAGCTCGTCGGCGACC 62.909 72.222 31.86 19.19 42.81 4.79
1172 2478 2.764128 CCTCCCGCCCTTGCTCTA 60.764 66.667 0.00 0.00 34.43 2.43
1179 2485 1.617947 CGCCCTTGCTCTACCCTCTT 61.618 60.000 0.00 0.00 34.43 2.85
1267 2573 1.610038 TCGTCTTGTTTCGGAGCACTA 59.390 47.619 0.00 0.00 0.00 2.74
1275 2581 3.760035 CGGAGCACTACAGCCCGT 61.760 66.667 0.00 0.00 40.82 5.28
1277 2583 1.448013 GGAGCACTACAGCCCGTTC 60.448 63.158 0.00 0.00 34.23 3.95
1323 2633 0.251474 AGGGTGGTACTCGCTGTGTA 60.251 55.000 7.19 0.00 43.27 2.90
1325 2635 0.455633 GGTGGTACTCGCTGTGTACG 60.456 60.000 11.76 0.00 40.63 3.67
1402 2712 2.926778 CCCAAAATTTTGCTGGGTCA 57.073 45.000 22.90 0.00 44.24 4.02
1451 2764 4.965814 ACTTCTCAAGTGATGCTCTTTCA 58.034 39.130 0.00 0.00 41.01 2.69
1493 2806 6.801539 TTGCTCTTTGTTCGTCAGATTATT 57.198 33.333 0.00 0.00 0.00 1.40
1508 2821 5.412594 TCAGATTATTTTGCTCTTCTTGCGT 59.587 36.000 0.00 0.00 0.00 5.24
1533 2846 2.669950 GCTGAAACGAGTCTCTGTCCTC 60.670 54.545 0.00 0.68 0.00 3.71
1567 2880 8.825745 GTTCTCAAGGAATCAAGATTCTGATAC 58.174 37.037 19.04 13.20 44.90 2.24
1682 2995 5.437191 AATCCAGATAAGAAGGTTCCGTT 57.563 39.130 0.00 0.00 0.00 4.44
1754 3067 0.250901 GCCACAGACACCATTCCACT 60.251 55.000 0.00 0.00 0.00 4.00
1765 3078 3.021695 ACCATTCCACTTGATCAGCATG 58.978 45.455 0.00 0.00 37.54 4.06
1774 3087 5.396484 CACTTGATCAGCATGTACAAAAGG 58.604 41.667 0.00 0.00 37.40 3.11
1879 3192 0.108138 CGGCAGGAGAAACTTCCGAT 60.108 55.000 0.00 0.00 42.29 4.18
1957 3270 0.253207 CCTCCCCTCCCAAGTTAGGT 60.253 60.000 0.00 0.00 0.00 3.08
2065 3378 3.569701 TCAAGCCATTTGGAGTCTTTGTC 59.430 43.478 0.00 0.00 37.39 3.18
2083 3396 1.398390 GTCGACATTGGAGCATTCACC 59.602 52.381 11.55 0.00 0.00 4.02
2105 3418 3.432186 CGAAGGCCTTGTTCATATCTCCA 60.432 47.826 26.25 0.00 0.00 3.86
2125 3438 3.493503 CCAGAGTAAGTGACGGTTTTGTC 59.506 47.826 0.00 0.00 39.37 3.18
2275 3588 4.785453 CCAAGCGGTGGGAGGAGC 62.785 72.222 0.16 0.00 44.64 4.70
2384 3697 3.953612 TCTGACTGGCACTGTGAAAAATT 59.046 39.130 12.86 0.00 41.64 1.82
2521 3834 3.493503 GTCAAGAGGTAACGGTGAAAGTG 59.506 47.826 0.00 0.00 46.39 3.16
2581 3894 1.069358 GGGGGAGAAGATGATGACGAC 59.931 57.143 0.00 0.00 0.00 4.34
2770 4083 0.961753 CTTCTGGGGTTGAAAGCACC 59.038 55.000 0.00 0.00 0.00 5.01
2804 4117 2.231478 CTCGTTGAGCCTCCTACTGAAA 59.769 50.000 0.00 0.00 0.00 2.69
2849 4165 0.882042 AACAGAAGCTGTCACTGGCG 60.882 55.000 0.00 0.00 44.62 5.69
2850 4166 1.301244 CAGAAGCTGTCACTGGCGT 60.301 57.895 0.00 0.00 0.00 5.68
2983 4299 3.481453 AGTTGAAAGCAAAGAGGAGGAC 58.519 45.455 0.00 0.00 35.42 3.85
3042 4358 5.728741 AGGAAATCACTCCTCTTGATAAGGT 59.271 40.000 0.00 0.00 42.53 3.50
3207 4523 3.496884 GGTCAGCAGTAATTTTGTCGACA 59.503 43.478 15.76 15.76 0.00 4.35
3403 4724 6.548441 TGTTCCTTACTTTGGTAAATGACG 57.452 37.500 0.00 0.00 37.45 4.35
3438 4778 4.382754 GCACTTAATTTTGTTTCCTCGCTG 59.617 41.667 0.00 0.00 0.00 5.18
3619 4972 3.623060 TCTTCATTTGCATAGCTTCGGTC 59.377 43.478 0.00 0.00 0.00 4.79
3775 5134 4.454728 TGCATTTAGAAAGTGATTGCCC 57.545 40.909 0.00 0.00 0.00 5.36
4413 5781 2.368875 GGAGGTTGTGAAGAAGGAGACA 59.631 50.000 0.00 0.00 0.00 3.41
4464 5832 1.886777 GAAGCCTGAGCAGATCCGC 60.887 63.158 0.00 0.00 43.56 5.54
4907 6275 6.442541 TTCCCCTAAAGTCAACACTCAATA 57.557 37.500 0.00 0.00 29.93 1.90
5083 6451 0.325272 GGAAAAAGGGCCTCTCGTCT 59.675 55.000 6.46 0.00 0.00 4.18
5561 6929 0.247736 AATGAGACAGTGACCTCCGC 59.752 55.000 0.00 0.00 0.00 5.54
5583 6951 0.959553 CAATCCATGGCATCAGGAGC 59.040 55.000 6.96 0.00 34.40 4.70
5772 7194 6.941857 AGGATTACGGCAAATTAAATTGGTT 58.058 32.000 5.45 0.00 0.00 3.67
5776 7198 7.644986 TTACGGCAAATTAAATTGGTTTCTG 57.355 32.000 5.45 0.00 0.00 3.02
5820 7242 6.820335 AGTTTTTGCTTTAGCCAGAAGAATT 58.180 32.000 0.00 0.00 41.18 2.17
5856 7278 8.570038 TTTTTATCCCTGGTGGTACTATATGA 57.430 34.615 0.00 0.00 34.77 2.15
6049 7471 7.439655 GCTCAACAGTATCCCTAAGATTTACAG 59.560 40.741 0.00 0.00 36.33 2.74
6171 7593 8.667463 GTTAAAATCCAAACCATCAATCCAATG 58.333 33.333 0.00 0.00 0.00 2.82
6185 7607 1.524621 CAATGTAGCAGCTCGGGGG 60.525 63.158 0.00 0.00 0.00 5.40
6320 7742 1.792301 CACACATTCGAGCAGCTGG 59.208 57.895 17.12 0.00 0.00 4.85
6411 7833 4.574828 CGAAGAACTTTGGGAAGAAGAACA 59.425 41.667 0.00 0.00 36.69 3.18
6422 7844 6.653989 TGGGAAGAAGAACAAGAATATCCTC 58.346 40.000 0.00 0.00 0.00 3.71
6489 7911 1.728971 CTGATTCGCTGACTGAACCAC 59.271 52.381 0.00 0.00 0.00 4.16
6501 7923 1.532868 CTGAACCACTCCAAAGCTTCG 59.467 52.381 0.00 0.00 0.00 3.79
6532 7954 1.001706 GCTTCTTTCGGTTGTGTTCCC 60.002 52.381 0.00 0.00 0.00 3.97
6610 8032 6.474140 TGTTAAGACAGAACAAGAGTACCA 57.526 37.500 0.00 0.00 33.93 3.25
6662 8084 7.730067 TTAGTAACATTATCGAAGTGTGACG 57.270 36.000 8.97 0.00 33.37 4.35
6671 8093 1.321743 CGAAGTGTGACGAGCTAATGC 59.678 52.381 0.00 0.00 40.05 3.56
6702 8124 9.632807 GCAGTATCTAATCTAACAATCTACTGG 57.367 37.037 0.00 0.00 35.98 4.00
6750 8178 9.467258 GCAATTACATCTGTGCATATTTAACAT 57.533 29.630 0.00 0.00 36.97 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.544697 ATAGGATTCCGGCGGTTTGT 59.455 50.000 27.32 10.31 0.00 2.83
1 2 0.944386 CATAGGATTCCGGCGGTTTG 59.056 55.000 27.32 7.68 0.00 2.93
4 5 0.321671 CATCATAGGATTCCGGCGGT 59.678 55.000 27.32 7.44 0.00 5.68
5 6 1.021390 GCATCATAGGATTCCGGCGG 61.021 60.000 22.51 22.51 0.00 6.13
6 7 0.320683 TGCATCATAGGATTCCGGCG 60.321 55.000 0.00 0.00 0.00 6.46
7 8 1.446907 CTGCATCATAGGATTCCGGC 58.553 55.000 0.00 0.00 0.00 6.13
8 9 1.349026 ACCTGCATCATAGGATTCCGG 59.651 52.381 0.00 0.00 38.71 5.14
9 10 2.224378 ACACCTGCATCATAGGATTCCG 60.224 50.000 0.00 0.00 38.71 4.30
10 11 3.498774 ACACCTGCATCATAGGATTCC 57.501 47.619 0.00 0.00 38.71 3.01
11 12 5.841957 AAAACACCTGCATCATAGGATTC 57.158 39.130 0.00 0.00 38.71 2.52
102 108 4.898861 ACCACAATAACCAGGACAACAAAT 59.101 37.500 0.00 0.00 0.00 2.32
126 132 2.202932 CAGCGCGGCCTCAGTAAT 60.203 61.111 8.83 0.00 0.00 1.89
192 238 6.187727 TCACCTCTCCTGTTTTACATCTTT 57.812 37.500 0.00 0.00 0.00 2.52
193 239 5.825593 TCACCTCTCCTGTTTTACATCTT 57.174 39.130 0.00 0.00 0.00 2.40
261 307 4.577687 TTACATCATTCGTTGAAGTCGC 57.422 40.909 3.08 0.00 37.46 5.19
263 309 9.003112 CATCAATTTACATCATTCGTTGAAGTC 57.997 33.333 3.08 0.00 37.46 3.01
267 313 8.676401 ACATCATCAATTTACATCATTCGTTGA 58.324 29.630 0.00 0.00 39.12 3.18
325 371 8.936864 CCGTCTCAATTCTAGTTTTTACATCTT 58.063 33.333 0.00 0.00 0.00 2.40
337 383 2.159184 TGCTCAGCCGTCTCAATTCTAG 60.159 50.000 0.00 0.00 0.00 2.43
358 404 2.177580 CCGCATTATGACCGCCGTT 61.178 57.895 0.00 0.00 0.00 4.44
359 405 2.587753 CCGCATTATGACCGCCGT 60.588 61.111 0.00 0.00 0.00 5.68
365 411 2.173964 GTTCAAACGCCGCATTATGAC 58.826 47.619 0.00 0.00 0.00 3.06
366 412 1.131504 GGTTCAAACGCCGCATTATGA 59.868 47.619 0.00 0.00 0.00 2.15
399 446 0.037590 ACCGCATAGCTTTTGTCCCA 59.962 50.000 0.00 0.00 0.00 4.37
403 450 0.965363 CCCCACCGCATAGCTTTTGT 60.965 55.000 0.00 0.00 0.00 2.83
427 474 1.822613 CTGCCGCTCATCAGCCATT 60.823 57.895 0.00 0.00 43.56 3.16
428 475 2.203167 CTGCCGCTCATCAGCCAT 60.203 61.111 0.00 0.00 43.56 4.40
434 501 2.815211 TTGTCGCTGCCGCTCATC 60.815 61.111 0.00 0.00 0.00 2.92
435 502 3.121030 GTTGTCGCTGCCGCTCAT 61.121 61.111 0.00 0.00 0.00 2.90
448 515 3.175976 CTGCCGCCGTTTTCGTTGT 62.176 57.895 0.00 0.00 42.35 3.32
454 521 1.716826 TTCGTTTCTGCCGCCGTTTT 61.717 50.000 0.00 0.00 0.00 2.43
455 522 2.181521 TTCGTTTCTGCCGCCGTTT 61.182 52.632 0.00 0.00 0.00 3.60
456 523 2.589442 TTCGTTTCTGCCGCCGTT 60.589 55.556 0.00 0.00 0.00 4.44
457 524 3.343421 GTTCGTTTCTGCCGCCGT 61.343 61.111 0.00 0.00 0.00 5.68
458 525 4.084888 GGTTCGTTTCTGCCGCCG 62.085 66.667 0.00 0.00 0.00 6.46
459 526 2.966309 CTGGTTCGTTTCTGCCGCC 61.966 63.158 0.00 0.00 0.00 6.13
464 531 2.556287 GCGCCTGGTTCGTTTCTG 59.444 61.111 0.00 0.00 0.00 3.02
465 532 2.668550 GGCGCCTGGTTCGTTTCT 60.669 61.111 22.15 0.00 0.00 2.52
486 553 1.165270 GTATTTTGTGCCGCTCCACT 58.835 50.000 5.41 0.00 36.68 4.00
493 560 1.003851 ATCGACCGTATTTTGTGCCG 58.996 50.000 0.00 0.00 0.00 5.69
497 564 3.669557 GCTGCAAATCGACCGTATTTTGT 60.670 43.478 8.30 0.00 32.88 2.83
498 565 2.845967 GCTGCAAATCGACCGTATTTTG 59.154 45.455 0.00 3.16 33.32 2.44
541 616 2.440796 CGCCAAGCATCCACCCAT 60.441 61.111 0.00 0.00 0.00 4.00
546 621 2.676121 CCAACCGCCAAGCATCCA 60.676 61.111 0.00 0.00 0.00 3.41
576 651 3.036084 CGCTGTTTCTGCCGTCGT 61.036 61.111 0.00 0.00 0.00 4.34
584 659 4.699522 GTCCCCGCCGCTGTTTCT 62.700 66.667 0.00 0.00 0.00 2.52
609 684 3.599285 TTTTCTCCATCGCCGCCGT 62.599 57.895 0.00 0.00 35.54 5.68
618 693 4.610945 CTGTTTTTGAGCGTTTTCTCCAT 58.389 39.130 0.00 0.00 32.22 3.41
751 827 0.818852 TCCCATGTGTGTGTGTGCAG 60.819 55.000 0.00 0.00 0.00 4.41
766 844 1.522806 GTCAGTTGTGCGTGTCCCA 60.523 57.895 0.00 0.00 0.00 4.37
774 852 1.593209 TTCCGTCGGTCAGTTGTGC 60.593 57.895 11.88 0.00 0.00 4.57
784 862 2.362632 AGGGGAGAGTTCCGTCGG 60.363 66.667 4.39 4.39 45.04 4.79
785 863 1.248785 TTGAGGGGAGAGTTCCGTCG 61.249 60.000 0.00 0.00 45.04 5.12
786 864 0.974383 TTTGAGGGGAGAGTTCCGTC 59.026 55.000 0.00 0.00 45.04 4.79
787 865 1.430992 TTTTGAGGGGAGAGTTCCGT 58.569 50.000 0.00 0.00 45.04 4.69
788 866 2.561478 TTTTTGAGGGGAGAGTTCCG 57.439 50.000 0.00 0.00 45.04 4.30
810 888 2.101917 TGAGTTCCGTCGGTCTTTTCTT 59.898 45.455 11.88 0.00 0.00 2.52
811 889 1.684983 TGAGTTCCGTCGGTCTTTTCT 59.315 47.619 11.88 2.18 0.00 2.52
814 892 2.480845 CTTTGAGTTCCGTCGGTCTTT 58.519 47.619 11.88 0.00 0.00 2.52
816 894 0.317479 CCTTTGAGTTCCGTCGGTCT 59.683 55.000 11.88 11.03 0.00 3.85
904 2204 0.108207 GATGCTAGCAGTGGATGGCT 59.892 55.000 23.89 2.02 43.94 4.75
919 2219 2.364970 AGCAGAGGTGATAGACTGATGC 59.635 50.000 0.00 0.00 32.90 3.91
1010 2313 3.827898 GGCCGTCGTGAGGAGAGG 61.828 72.222 0.00 0.00 0.00 3.69
1144 2450 2.517402 CGGGAGGGAGACGAGAGG 60.517 72.222 0.00 0.00 0.00 3.69
1171 2477 4.384208 GCAAAGGAGATGCTTAAGAGGGTA 60.384 45.833 6.67 0.00 40.64 3.69
1172 2478 3.623453 GCAAAGGAGATGCTTAAGAGGGT 60.623 47.826 6.67 0.00 40.64 4.34
1179 2485 2.564771 CGATGGCAAAGGAGATGCTTA 58.435 47.619 0.00 0.00 43.34 3.09
1267 2573 3.637273 GGTGGGAGAACGGGCTGT 61.637 66.667 0.00 0.00 0.00 4.40
1275 2581 0.323629 CGCTTTACAGGGTGGGAGAA 59.676 55.000 0.00 0.00 0.00 2.87
1277 2583 0.541863 ATCGCTTTACAGGGTGGGAG 59.458 55.000 0.00 0.00 34.50 4.30
1323 2633 0.391661 CAGCATTCCAGTGCCTACGT 60.392 55.000 0.00 0.00 46.19 3.57
1325 2635 0.253044 TCCAGCATTCCAGTGCCTAC 59.747 55.000 0.00 0.00 46.19 3.18
1451 2764 6.014413 AGAGCAATACATGATAGAGATGCTGT 60.014 38.462 0.00 1.30 42.45 4.40
1493 2806 0.662619 CACCACGCAAGAAGAGCAAA 59.337 50.000 0.00 0.00 43.62 3.68
1508 2821 1.040646 AGAGACTCGTTTCAGCACCA 58.959 50.000 0.00 0.00 0.00 4.17
1533 2846 0.250295 TTCCTTGAGAACCCTGCACG 60.250 55.000 0.00 0.00 0.00 5.34
1567 2880 0.034767 TGCTGAATTCAGGGGAGCTG 60.035 55.000 31.41 9.72 43.94 4.24
1682 2995 5.775195 TGACTCTTGAATACCTCTCTGAACA 59.225 40.000 0.00 0.00 0.00 3.18
1754 3067 4.156556 GCTCCTTTTGTACATGCTGATCAA 59.843 41.667 0.00 0.00 0.00 2.57
1774 3087 0.898320 TGTTAGCAGAGGACCAGCTC 59.102 55.000 9.08 0.00 39.68 4.09
1789 3102 3.393278 ACAAGGTCCTTAGCCTGTTGTTA 59.607 43.478 3.08 0.00 36.30 2.41
1957 3270 1.373748 GCTCTTACGTGGGTTGCGA 60.374 57.895 0.00 0.00 0.00 5.10
2065 3378 0.374758 CGGTGAATGCTCCAATGTCG 59.625 55.000 0.00 0.00 0.00 4.35
2083 3396 3.134458 GGAGATATGAACAAGGCCTTCG 58.866 50.000 17.29 13.93 0.00 3.79
2105 3418 3.067180 TCGACAAAACCGTCACTTACTCT 59.933 43.478 0.00 0.00 35.54 3.24
2125 3438 7.392113 ACAGTGAAGAGGGTAGATATATCTTCG 59.608 40.741 20.13 2.17 45.65 3.79
2384 3697 3.138304 CAAATGACCCTGTTCTTGTCGA 58.862 45.455 0.00 0.00 0.00 4.20
2494 3807 1.071228 ACCGTTACCTCTTGACCAACC 59.929 52.381 0.00 0.00 0.00 3.77
2521 3834 0.727398 GGCCTCGTGCTACATTCAAC 59.273 55.000 0.00 0.00 40.92 3.18
2581 3894 2.097733 GGTGTTTAACGACGACAACTCG 60.098 50.000 0.00 0.00 46.06 4.18
2804 4117 8.414629 AAAGAACTATCCTCTTTGCTTTCAAT 57.585 30.769 0.00 0.00 40.72 2.57
2849 4165 0.889306 ACTGTAGGAGGCTCAACGAC 59.111 55.000 17.69 6.94 0.00 4.34
2850 4166 1.629043 AACTGTAGGAGGCTCAACGA 58.371 50.000 17.69 4.46 0.00 3.85
2874 4190 6.119536 TCCTCTTTGCTTTCAACTTCAGTAA 58.880 36.000 0.00 0.00 30.75 2.24
2983 4299 3.703316 GACAGCTTCTGTTGAAGGGCTG 61.703 54.545 14.30 14.30 45.44 4.85
3042 4358 2.909006 ACTGATTCTTCTGGCTCCTCAA 59.091 45.455 0.00 0.00 0.00 3.02
3095 4411 0.976641 TCCTCAGTTACCACAGCAGG 59.023 55.000 0.00 0.00 0.00 4.85
3207 4523 3.956848 GGGCCTTTTGCAGATAAGATCTT 59.043 43.478 13.56 13.56 43.89 2.40
3403 4724 7.799784 ACAAAATTAAGTGCATTGATTCTTGC 58.200 30.769 1.18 5.53 39.33 4.01
3619 4972 6.687958 GCCACATGAAACAAAACAAAAATCAG 59.312 34.615 0.00 0.00 0.00 2.90
3927 5294 2.969821 TGCAGGGACAGGTATGTTTT 57.030 45.000 0.00 0.00 40.68 2.43
4413 5781 1.202330 CCCTCTGCATCTCCAACTCT 58.798 55.000 0.00 0.00 0.00 3.24
4464 5832 0.876342 GGCCCTCGACAATCTTAGCG 60.876 60.000 0.00 0.00 0.00 4.26
4907 6275 7.993183 CCTGGAAACATAGGTATGTCAAGTTAT 59.007 37.037 3.12 0.00 45.55 1.89
5098 6466 2.492449 CTTCAGCGGTCAGGCGAGAA 62.492 60.000 0.00 0.00 38.18 2.87
5149 6517 7.062322 AGTTGATTTCAATCATGCACCCTATA 58.938 34.615 3.06 0.00 44.27 1.31
5561 6929 3.409570 CTCCTGATGCCATGGATTGTAG 58.590 50.000 18.40 6.21 0.00 2.74
5583 6951 2.795681 CGATGAATCAAAATGTGCCCGG 60.796 50.000 0.00 0.00 0.00 5.73
5772 7194 6.361433 TCTGAAGTAAAACATGGAACCAGAA 58.639 36.000 0.00 0.00 0.00 3.02
5776 7198 6.635030 AACTCTGAAGTAAAACATGGAACC 57.365 37.500 0.00 0.00 33.48 3.62
5820 7242 7.039363 CCACCAGGGATAAAAAGTGTAAAATCA 60.039 37.037 0.00 0.00 40.01 2.57
5856 7278 7.228706 AGTGAAAGACATTTCGACCTATGTTTT 59.771 33.333 8.03 6.49 46.55 2.43
6140 7562 4.755629 TGATGGTTTGGATTTTAACGTCGA 59.244 37.500 0.00 0.00 0.00 4.20
6185 7607 1.004745 TCTCTTGGTGGGCAATCTTCC 59.995 52.381 0.00 0.00 0.00 3.46
6320 7742 1.546029 GGAGTCCTTGCCAAATTGACC 59.454 52.381 0.41 0.00 0.00 4.02
6350 7772 1.152756 GGCCCAATACTTCCGGCAT 60.153 57.895 0.00 0.00 43.50 4.40
6411 7833 7.723172 CCTCTTTATTTGCCTGAGGATATTCTT 59.277 37.037 0.65 0.00 45.07 2.52
6422 7844 3.949754 TCAGCATCCTCTTTATTTGCCTG 59.050 43.478 0.00 0.00 33.85 4.85
6501 7923 2.159653 CCGAAAGAAGCACACAGTATGC 60.160 50.000 0.00 0.00 42.53 3.14
6532 7954 2.838736 CATATCTTGGTCCACGGAAGG 58.161 52.381 0.00 0.00 0.00 3.46
6600 8022 4.223032 AGGAAGTATGTGGTGGTACTCTTG 59.777 45.833 0.00 0.00 31.10 3.02
6720 8148 6.659745 ATATGCACAGATGTAATTGCCATT 57.340 33.333 0.00 0.00 33.86 3.16


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

AutoCloner maintained by Alex Coulton.