Multiple sequence alignment - TraesCS2A01G322600

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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 TraesCS2A01G322600 chr2A 100.000 5667 0 0 1 5667 551821321 551815655 0.000000e+00 10466
1 TraesCS2A01G322600 chr2B 94.739 4999 163 37 702 5644 513466125 513471079 0.000000e+00 7683
2 TraesCS2A01G322600 chr2B 90.000 570 35 8 1 559 513465572 513466130 0.000000e+00 717
3 TraesCS2A01G322600 chr2D 96.090 2711 85 10 614 3309 435040159 435042863 0.000000e+00 4399
4 TraesCS2A01G322600 chr2D 96.159 1380 48 3 3391 4769 435042862 435044237 0.000000e+00 2250
5 TraesCS2A01G322600 chr2D 88.652 846 60 23 4808 5634 435044606 435045434 0.000000e+00 998
6 TraesCS2A01G322600 chr2D 92.208 616 35 7 1 605 435039502 435040115 0.000000e+00 859
7 TraesCS2A01G322600 chr1A 90.722 97 7 2 3299 3393 568391297 568391201 1.660000e-25 128
8 TraesCS2A01G322600 chr1A 91.860 86 6 1 3308 3392 568391202 568391287 9.970000e-23 119
9 TraesCS2A01G322600 chr4D 90.426 94 8 1 3300 3392 107696516 107696609 7.710000e-24 122
10 TraesCS2A01G322600 chr3A 89.796 98 7 3 3298 3392 510299767 510299864 7.710000e-24 122
11 TraesCS2A01G322600 chr5B 91.011 89 7 1 3305 3392 391148406 391148494 9.970000e-23 119
12 TraesCS2A01G322600 chr7D 86.667 105 8 4 3308 3407 568370088 568369985 1.670000e-20 111
13 TraesCS2A01G322600 chr1B 84.821 112 14 3 3308 3417 133188941 133188831 6.000000e-20 110
14 TraesCS2A01G322600 chr3D 85.185 108 12 4 3305 3409 133538647 133538541 2.160000e-19 108


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 TraesCS2A01G322600 chr2A 551815655 551821321 5666 True 10466.0 10466 100.00000 1 5667 1 chr2A.!!$R1 5666
1 TraesCS2A01G322600 chr2B 513465572 513471079 5507 False 4200.0 7683 92.36950 1 5644 2 chr2B.!!$F1 5643
2 TraesCS2A01G322600 chr2D 435039502 435045434 5932 False 2126.5 4399 93.27725 1 5634 4 chr2D.!!$F1 5633

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
738 797 0.450583 GGCGTCGTACATGTCTCTCA 59.549 55.000 0.0 0.0 0.00 3.27 F
1497 1568 1.412710 TCCTATGAACGGGCACATCTC 59.587 52.381 0.0 0.0 0.00 2.75 F
2529 2600 1.376037 GCTTGGGAAGAGGGTCACG 60.376 63.158 0.0 0.0 0.00 4.35 F
3505 3601 0.096976 GCGATGCGTGTAACAGCAAT 59.903 50.000 0.0 0.0 45.91 3.56 F
3848 3945 0.613260 TCTCGGGTTCAATGTGGAGG 59.387 55.000 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2210 0.669318 TGAGAAGTGCCTTTACGCGG 60.669 55.0 12.47 0.00 0.00 6.46 R
2803 2874 0.391228 TGCTGACTTCTGTTACCGCA 59.609 50.0 0.00 0.00 0.00 5.69 R
3520 3616 0.097325 GCCGTCTACAGTGTCTCTCG 59.903 60.0 0.00 1.09 0.00 4.04 R
4588 4687 0.615331 TCTTGATGGACCTGCAGGAC 59.385 55.0 39.19 31.70 38.94 3.85 R
4745 4844 1.327303 GGTCAAGAAACCACATGGCA 58.673 50.0 0.00 0.00 39.27 4.92 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
41 42 4.467084 GCGGTCGATGGCCAAGGA 62.467 66.667 10.96 7.37 0.00 3.36
79 80 1.163554 CTGTTCTTGGCTTCAGCTCC 58.836 55.000 0.00 0.00 41.70 4.70
100 101 2.349817 CGCTTCTTCGCATCTTGTGTTT 60.350 45.455 0.00 0.00 0.00 2.83
102 103 3.665871 GCTTCTTCGCATCTTGTGTTTTC 59.334 43.478 0.00 0.00 0.00 2.29
105 106 5.095691 TCTTCGCATCTTGTGTTTTCTTC 57.904 39.130 0.00 0.00 0.00 2.87
107 108 4.732285 TCGCATCTTGTGTTTTCTTCTC 57.268 40.909 0.00 0.00 0.00 2.87
110 111 5.405571 TCGCATCTTGTGTTTTCTTCTCTAC 59.594 40.000 0.00 0.00 0.00 2.59
127 131 8.421784 TCTTCTCTACTTTACATCTTGTGTGTT 58.578 33.333 0.00 0.00 42.24 3.32
130 134 9.472361 TCTCTACTTTACATCTTGTGTGTTTAC 57.528 33.333 0.00 0.00 42.24 2.01
146 150 4.157289 GTGTTTACGACAGGAGGACTATGA 59.843 45.833 0.00 0.00 39.39 2.15
156 160 2.360801 GGAGGACTATGAGCTCTGTGAC 59.639 54.545 16.19 5.00 0.00 3.67
162 166 5.157940 ACTATGAGCTCTGTGACATTTGT 57.842 39.130 16.19 0.11 0.00 2.83
186 190 4.378046 GCGATACAAAACTAACCAGGTGTG 60.378 45.833 0.00 0.00 0.00 3.82
187 191 4.992319 CGATACAAAACTAACCAGGTGTGA 59.008 41.667 0.00 0.00 0.00 3.58
202 206 6.158598 CCAGGTGTGAGTTGGATTTTATTTG 58.841 40.000 0.00 0.00 33.76 2.32
203 207 6.239289 CCAGGTGTGAGTTGGATTTTATTTGT 60.239 38.462 0.00 0.00 33.76 2.83
221 225 3.467374 TGTTTTTGGAAATGGAGGTGC 57.533 42.857 0.00 0.00 0.00 5.01
224 228 4.058124 GTTTTTGGAAATGGAGGTGCTTC 58.942 43.478 0.00 0.00 0.00 3.86
225 229 1.923356 TTGGAAATGGAGGTGCTTCC 58.077 50.000 0.00 0.00 38.26 3.46
553 574 4.144297 TGGTAGCTGAACAGAGCATTTTT 58.856 39.130 5.97 0.00 41.83 1.94
575 596 2.039418 GGTTGCCACCTTCTTTCCTTT 58.961 47.619 0.00 0.00 40.44 3.11
609 630 7.684937 AGAAATGCTCATAATAAGATGGAGC 57.315 36.000 0.00 0.00 33.87 4.70
610 631 6.370994 AGAAATGCTCATAATAAGATGGAGCG 59.629 38.462 0.00 0.00 34.98 5.03
611 632 4.607293 TGCTCATAATAAGATGGAGCGT 57.393 40.909 0.00 0.00 34.98 5.07
612 633 4.960938 TGCTCATAATAAGATGGAGCGTT 58.039 39.130 0.00 0.00 34.98 4.84
635 691 0.978151 GGGCCCGGGTTTAATTTTGT 59.022 50.000 24.63 0.00 0.00 2.83
637 693 2.566279 GGGCCCGGGTTTAATTTTGTAA 59.434 45.455 24.63 0.00 0.00 2.41
673 732 6.653740 GTGTATATAAATGCTCCAGGGTTACC 59.346 42.308 0.00 0.00 0.00 2.85
674 733 2.702592 TAAATGCTCCAGGGTTACCG 57.297 50.000 0.00 0.00 43.47 4.02
722 781 2.350498 CGGATTTAACTGTTGTAGGGCG 59.650 50.000 2.69 0.00 0.00 6.13
738 797 0.450583 GGCGTCGTACATGTCTCTCA 59.549 55.000 0.00 0.00 0.00 3.27
751 810 9.383519 GTACATGTCTCTCAATTTATCTTTGGA 57.616 33.333 0.00 0.00 0.00 3.53
819 878 2.754552 TGCAATGTAGGGTTGAGCAATC 59.245 45.455 0.00 0.00 0.00 2.67
839 898 6.759827 GCAATCATTAAGGCATCTCATTGTTT 59.240 34.615 0.00 0.00 0.00 2.83
848 907 3.676646 GCATCTCATTGTTTCCTTTGCAC 59.323 43.478 0.00 0.00 0.00 4.57
907 978 8.464404 GTTTTTACTGTTTTACTTCAGGTTCCT 58.536 33.333 0.00 0.00 36.17 3.36
915 986 2.771763 CTTCAGGTTCCTGCGACGCT 62.772 60.000 22.08 0.00 34.33 5.07
945 1016 1.888512 GAAGCAGCCACATTCAAGGAA 59.111 47.619 0.00 0.00 0.00 3.36
947 1018 1.615392 AGCAGCCACATTCAAGGAAAC 59.385 47.619 0.00 0.00 0.00 2.78
985 1056 9.618890 AACTATAATCAGATATTGTTGCTGTGT 57.381 29.630 0.00 0.00 32.52 3.72
1023 1094 2.512515 GACATGAGGCGCCACTCC 60.513 66.667 31.54 14.98 36.66 3.85
1308 1379 7.308830 GCATCTTACAGGAAATCTTCAGTTGTT 60.309 37.037 0.00 0.00 0.00 2.83
1323 1394 4.081420 TCAGTTGTTAGGATCAGAGGCTTC 60.081 45.833 0.00 0.00 0.00 3.86
1362 1433 3.186047 GTTCATCGTGTCCGCGGG 61.186 66.667 27.83 9.38 0.00 6.13
1410 1481 6.902771 TCTAACCACTCTAATCATAGCTCC 57.097 41.667 0.00 0.00 0.00 4.70
1497 1568 1.412710 TCCTATGAACGGGCACATCTC 59.587 52.381 0.00 0.00 0.00 2.75
1500 1571 2.125512 GAACGGGCACATCTCGCT 60.126 61.111 0.00 0.00 0.00 4.93
1833 1904 6.617879 GTTCCAAGAAAATGTACCATACACC 58.382 40.000 0.00 0.00 42.23 4.16
1875 1946 2.163412 CCAAAAATTTCGCCCTCGATCA 59.837 45.455 0.00 0.00 45.04 2.92
1917 1988 1.656587 ATGTGGTTGCTCAGTCCCTA 58.343 50.000 0.00 0.00 0.00 3.53
2013 2084 2.670210 GGCACGCATTTTTGCTGCC 61.670 57.895 18.61 18.61 44.80 4.85
2133 2204 4.746535 TGATGCAGCAAAAATGGATCAT 57.253 36.364 0.00 0.00 46.49 2.45
2139 2210 3.375922 CAGCAAAAATGGATCATTTGGGC 59.624 43.478 15.47 15.47 42.32 5.36
2440 2511 4.498009 GGTTAGAATTTGACCATGATGCGG 60.498 45.833 0.00 0.00 33.61 5.69
2529 2600 1.376037 GCTTGGGAAGAGGGTCACG 60.376 63.158 0.00 0.00 0.00 4.35
2567 2638 7.148120 GCATGAACTTGTGAGTAGTACTACCTA 60.148 40.741 25.97 14.52 36.75 3.08
2590 2661 9.640963 CCTATAGTAATGACTATTGCCAGTTAC 57.359 37.037 8.09 0.00 44.98 2.50
2638 2709 5.329399 TGTTATTTGCAGGTAGGATTGGTT 58.671 37.500 0.00 0.00 0.00 3.67
2698 2769 3.331150 GTCATCGGACACAACCAATACA 58.669 45.455 0.00 0.00 43.73 2.29
2740 2811 1.810030 GGCGTCGTCAGTTGATCCC 60.810 63.158 0.00 0.00 0.00 3.85
2797 2868 2.468831 GACATTCTCTCAGGACGATGC 58.531 52.381 0.00 0.00 0.00 3.91
2803 2874 1.411977 CTCTCAGGACGATGCCAATCT 59.588 52.381 0.00 0.00 0.00 2.40
2809 2880 0.529773 GACGATGCCAATCTGCGGTA 60.530 55.000 0.00 0.00 0.00 4.02
2812 2883 1.378531 GATGCCAATCTGCGGTAACA 58.621 50.000 0.00 0.00 0.00 2.41
3056 3127 1.913419 TCCACATACCCTTCTGTTCCC 59.087 52.381 0.00 0.00 0.00 3.97
3135 3206 7.650104 GGTATAGAGAAACTAAGACATGCACTC 59.350 40.741 0.00 0.00 34.56 3.51
3222 3293 2.298411 CACTTTTGCAGTTTGGCAGT 57.702 45.000 0.00 0.00 45.88 4.40
3334 3405 5.546110 TCCCTCCGATCCATATTAATTGTCA 59.454 40.000 0.00 0.00 0.00 3.58
3382 3478 6.949352 AATCAGTGACAATTATGTGGATCC 57.051 37.500 4.20 4.20 40.74 3.36
3422 3518 5.420725 TGTGCCTGTACAGAATGATAGTT 57.579 39.130 24.68 0.00 39.69 2.24
3505 3601 0.096976 GCGATGCGTGTAACAGCAAT 59.903 50.000 0.00 0.00 45.91 3.56
3520 3616 3.821033 ACAGCAATAAGTCCAACTGTTCC 59.179 43.478 0.00 0.00 34.89 3.62
3671 3768 4.420522 AATTCAGGTGTGCCATGTTTTT 57.579 36.364 0.00 0.00 37.19 1.94
3672 3769 3.451141 TTCAGGTGTGCCATGTTTTTC 57.549 42.857 0.00 0.00 37.19 2.29
3676 3773 2.102925 AGGTGTGCCATGTTTTTCTTGG 59.897 45.455 0.00 0.00 42.22 3.61
3705 3802 3.686726 CCTTCTCATAGGTTTGTGCTGAC 59.313 47.826 0.00 0.00 0.00 3.51
3848 3945 0.613260 TCTCGGGTTCAATGTGGAGG 59.387 55.000 0.00 0.00 0.00 4.30
3850 3947 0.768622 TCGGGTTCAATGTGGAGGTT 59.231 50.000 0.00 0.00 0.00 3.50
3895 3992 1.945819 GCGAGGAAAGATGCAAGGTCA 60.946 52.381 0.00 0.00 0.00 4.02
4008 4105 1.768275 TGGAGCAAGAGAAACACCTCA 59.232 47.619 0.00 0.00 35.68 3.86
4009 4106 2.147150 GGAGCAAGAGAAACACCTCAC 58.853 52.381 0.00 0.00 35.68 3.51
4279 4376 3.131396 GCAAAAGAGGTTCTTCTCGTCA 58.869 45.455 0.00 0.00 35.27 4.35
4378 4475 1.321474 ATTTCTGCACATATGGGCCG 58.679 50.000 26.74 20.68 45.73 6.13
4423 4520 3.482722 TCAAGAGCTACTTACGGTTCG 57.517 47.619 0.00 0.00 37.03 3.95
4520 4619 4.692228 TGTTCGGTAGGAAACGTTTAGTT 58.308 39.130 14.65 5.14 46.76 2.24
4530 4629 7.047460 AGGAAACGTTTAGTTAGAGAACTGA 57.953 36.000 14.65 0.00 45.74 3.41
4554 4653 8.753133 TGAATACTCAATCACATTACTGTCTCT 58.247 33.333 0.00 0.00 31.62 3.10
4588 4687 4.681025 GTGCAACACCATACTCATTGTTTG 59.319 41.667 0.00 0.00 36.32 2.93
4716 4815 2.797837 GCATCAGTAGGCCATGCAA 58.202 52.632 17.64 0.00 42.18 4.08
4734 4833 3.055167 TGCAATTAGAGGTCTTGCTGCTA 60.055 43.478 0.00 0.00 44.29 3.49
4745 4844 5.187967 AGGTCTTGCTGCTATGTTACTAGTT 59.812 40.000 0.00 0.00 0.00 2.24
4793 4892 2.163010 AGCATGTACATGTTTGAGCAGC 59.837 45.455 31.10 16.90 40.80 5.25
4890 5319 5.390387 AGCCTTTTGTGTCCTGGTAAAATA 58.610 37.500 0.00 0.00 0.00 1.40
4905 5340 8.421002 CCTGGTAAAATAATTCGAATTCCCATT 58.579 33.333 25.89 17.10 0.00 3.16
4952 5387 6.272318 TGCACCAAACTAGTTTTCTTTCATG 58.728 36.000 18.25 5.48 0.00 3.07
5107 5553 3.760580 TTTTATGTTGTGGCCTTTGGG 57.239 42.857 3.32 0.00 0.00 4.12
5128 5574 4.022242 GGGATGCAGAAATGGATGATCAAG 60.022 45.833 0.00 0.00 0.00 3.02
5129 5575 4.022242 GGATGCAGAAATGGATGATCAAGG 60.022 45.833 0.00 0.00 0.00 3.61
5131 5577 4.800023 TGCAGAAATGGATGATCAAGGAT 58.200 39.130 0.00 0.00 0.00 3.24
5188 5634 2.363306 TTTTGCCTGAAGCTGGAGAA 57.637 45.000 0.00 0.00 44.23 2.87
5195 5641 1.471684 CTGAAGCTGGAGAATTGGCAC 59.528 52.381 0.00 0.00 0.00 5.01
5485 5933 2.997485 GCAGAAGCGGAAAATGAAGT 57.003 45.000 0.00 0.00 0.00 3.01
5504 5952 1.153958 GAGCGCATCAAACAAGCCC 60.154 57.895 11.47 0.00 0.00 5.19
5527 5975 5.163258 CCCTCTATACCTGAAATGTCTTGCT 60.163 44.000 0.00 0.00 0.00 3.91
5533 5981 7.944729 ATACCTGAAATGTCTTGCTAATTGT 57.055 32.000 0.00 0.00 0.00 2.71
5534 5982 6.655078 ACCTGAAATGTCTTGCTAATTGTT 57.345 33.333 0.00 0.00 0.00 2.83
5558 6006 7.608308 TTTTTCAAATTCAGTGGTTTTCTGG 57.392 32.000 0.00 0.00 34.15 3.86
5563 6011 6.953520 TCAAATTCAGTGGTTTTCTGGGATAT 59.046 34.615 0.00 0.00 34.15 1.63
5565 6013 6.780457 ATTCAGTGGTTTTCTGGGATATTG 57.220 37.500 0.00 0.00 34.15 1.90
5567 6015 6.381498 TCAGTGGTTTTCTGGGATATTGTA 57.619 37.500 0.00 0.00 34.15 2.41
5568 6016 6.177610 TCAGTGGTTTTCTGGGATATTGTAC 58.822 40.000 0.00 0.00 34.15 2.90
5572 6020 7.037873 AGTGGTTTTCTGGGATATTGTACTACA 60.038 37.037 0.00 0.00 0.00 2.74
5573 6021 7.065443 GTGGTTTTCTGGGATATTGTACTACAC 59.935 40.741 0.00 0.00 0.00 2.90
5574 6022 7.037873 TGGTTTTCTGGGATATTGTACTACACT 60.038 37.037 0.00 0.00 0.00 3.55
5575 6023 7.827729 GGTTTTCTGGGATATTGTACTACACTT 59.172 37.037 0.00 0.00 0.00 3.16
5576 6024 9.227777 GTTTTCTGGGATATTGTACTACACTTT 57.772 33.333 0.00 0.00 0.00 2.66
5580 6028 9.656323 TCTGGGATATTGTACTACACTTTATCT 57.344 33.333 0.00 0.00 0.00 1.98
5626 6076 4.470334 AACAAACATTTCAAGCACCACT 57.530 36.364 0.00 0.00 0.00 4.00
5639 6089 4.470334 AGCACCACTTGTCAAACATTTT 57.530 36.364 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 0.394565 GACCCTCGGCTGCATTATCT 59.605 55.000 0.50 0.00 0.00 1.98
79 80 0.792640 ACACAAGATGCGAAGAAGCG 59.207 50.000 0.00 0.00 40.67 4.68
100 101 8.421784 ACACACAAGATGTAAAGTAGAGAAGAA 58.578 33.333 0.00 0.00 40.64 2.52
102 103 8.594881 AACACACAAGATGTAAAGTAGAGAAG 57.405 34.615 0.00 0.00 40.64 2.85
105 106 8.425491 CGTAAACACACAAGATGTAAAGTAGAG 58.575 37.037 0.00 0.00 40.64 2.43
107 108 8.212495 GTCGTAAACACACAAGATGTAAAGTAG 58.788 37.037 0.00 0.00 40.64 2.57
110 111 6.939627 TGTCGTAAACACACAAGATGTAAAG 58.060 36.000 0.00 0.00 40.64 1.85
127 131 2.950309 GCTCATAGTCCTCCTGTCGTAA 59.050 50.000 0.00 0.00 0.00 3.18
130 134 1.606668 GAGCTCATAGTCCTCCTGTCG 59.393 57.143 9.40 0.00 0.00 4.35
146 150 0.870393 CGCACAAATGTCACAGAGCT 59.130 50.000 0.00 0.00 0.00 4.09
162 166 3.749088 CACCTGGTTAGTTTTGTATCGCA 59.251 43.478 0.00 0.00 0.00 5.10
202 206 3.751479 AGCACCTCCATTTCCAAAAAC 57.249 42.857 0.00 0.00 0.00 2.43
203 207 3.070878 GGAAGCACCTCCATTTCCAAAAA 59.929 43.478 0.00 0.00 39.09 1.94
221 225 0.186873 CCCATTCCCCATCCAGGAAG 59.813 60.000 0.00 0.00 46.29 3.46
224 228 1.538666 GACCCATTCCCCATCCAGG 59.461 63.158 0.00 0.00 37.03 4.45
225 229 1.538666 GGACCCATTCCCCATCCAG 59.461 63.158 0.00 0.00 38.70 3.86
293 297 4.748277 AAATCAAATCCAGAGCAATGGG 57.252 40.909 7.31 0.00 41.01 4.00
477 490 6.591834 CCGTCACTTCTTCTATTCACTGAAAT 59.408 38.462 0.00 0.00 0.00 2.17
610 631 1.120184 TTAAACCCGGGCCCCAAAAC 61.120 55.000 24.08 0.00 0.00 2.43
611 632 0.178900 ATTAAACCCGGGCCCCAAAA 60.179 50.000 24.08 7.10 0.00 2.44
612 633 0.178900 AATTAAACCCGGGCCCCAAA 60.179 50.000 24.08 8.71 0.00 3.28
673 732 5.470098 CCCCAAAGATAGGATGATTGTAACG 59.530 44.000 0.00 0.00 0.00 3.18
674 733 6.365520 ACCCCAAAGATAGGATGATTGTAAC 58.634 40.000 0.00 0.00 0.00 2.50
722 781 8.635877 AAGATAAATTGAGAGACATGTACGAC 57.364 34.615 0.00 0.00 0.00 4.34
738 797 9.541143 ACATTTTCGTGTTTCCAAAGATAAATT 57.459 25.926 0.00 0.00 0.00 1.82
819 878 6.461110 AGGAAACAATGAGATGCCTTAATG 57.539 37.500 0.00 0.00 0.00 1.90
839 898 2.559698 TGATTTCTCCGTGCAAAGGA 57.440 45.000 11.21 11.21 44.16 3.36
877 936 6.631636 CCTGAAGTAAAACAGTAAAAACGCTC 59.368 38.462 0.00 0.00 32.93 5.03
889 948 2.875933 CGCAGGAACCTGAAGTAAAACA 59.124 45.455 22.96 0.00 46.30 2.83
907 978 2.588027 TCCATTATAACAGCGTCGCA 57.412 45.000 21.09 0.00 0.00 5.10
915 986 3.961849 TGTGGCTGCTTCCATTATAACA 58.038 40.909 0.00 0.00 38.57 2.41
945 1016 6.711277 TGATTATAGTTCAGTTCTGGCTGTT 58.289 36.000 0.00 0.00 37.70 3.16
947 1018 6.577103 TCTGATTATAGTTCAGTTCTGGCTG 58.423 40.000 12.12 0.00 41.13 4.85
988 1059 7.335171 CCTCATGTCAGTCATTTTGAATCTGTA 59.665 37.037 0.00 0.00 34.09 2.74
992 1063 5.338365 GCCTCATGTCAGTCATTTTGAATC 58.662 41.667 0.00 0.00 34.09 2.52
994 1065 3.189080 CGCCTCATGTCAGTCATTTTGAA 59.811 43.478 0.00 0.00 34.09 2.69
1308 1379 2.119495 GGGTTGAAGCCTCTGATCCTA 58.881 52.381 6.10 0.00 31.81 2.94
1323 1394 1.480137 TGCTTGTTTCTTGGTGGGTTG 59.520 47.619 0.00 0.00 0.00 3.77
1362 1433 1.065418 ACCGATTTCCTGTGACCATCC 60.065 52.381 0.00 0.00 0.00 3.51
1410 1481 1.733402 TGTTTGCCAACTGCCGAAGG 61.733 55.000 2.01 0.00 42.14 3.46
1497 1568 1.792941 GCTCTTCTCTGGCAAAGCG 59.207 57.895 0.00 0.00 0.00 4.68
1500 1571 0.036952 CCTCGCTCTTCTCTGGCAAA 60.037 55.000 0.00 0.00 0.00 3.68
1833 1904 2.223377 GCTTAAACACCTTGGTGTCTCG 59.777 50.000 23.58 14.00 36.42 4.04
2013 2084 3.380142 GAGAGAGAGGCAATTTAGAGCG 58.620 50.000 0.00 0.00 0.00 5.03
2132 2203 2.706834 GCCTTTACGCGGCCCAAAT 61.707 57.895 12.47 0.00 41.73 2.32
2133 2204 3.366915 GCCTTTACGCGGCCCAAA 61.367 61.111 12.47 4.17 41.73 3.28
2139 2210 0.669318 TGAGAAGTGCCTTTACGCGG 60.669 55.000 12.47 0.00 0.00 6.46
2440 2511 1.790623 CTTTGCAGCAATGAAGTGCAC 59.209 47.619 14.52 9.40 46.57 4.57
2529 2600 5.628193 CACAAGTTCATGCACAAGAGAAATC 59.372 40.000 0.00 0.00 0.00 2.17
2567 2638 8.482943 TGTGTAACTGGCAATAGTCATTACTAT 58.517 33.333 0.00 0.00 43.60 2.12
2575 2646 8.888579 ATTATACTGTGTAACTGGCAATAGTC 57.111 34.615 0.00 0.00 40.44 2.59
2638 2709 6.128090 GCAACTCAATCAACTCATCATCAGAA 60.128 38.462 0.00 0.00 0.00 3.02
2695 2766 1.065926 TCCCGAGCTCGTCTAACTGTA 60.066 52.381 32.41 1.27 37.74 2.74
2698 2769 0.810016 GTTCCCGAGCTCGTCTAACT 59.190 55.000 32.41 0.00 37.74 2.24
2740 2811 1.218585 CTGAGAGACCAGCTGCAGG 59.781 63.158 17.12 9.78 0.00 4.85
2797 2868 2.673368 GACTTCTGTTACCGCAGATTGG 59.327 50.000 0.00 0.00 43.99 3.16
2803 2874 0.391228 TGCTGACTTCTGTTACCGCA 59.609 50.000 0.00 0.00 0.00 5.69
2809 2880 5.904362 AGAAACTTTTGCTGACTTCTGTT 57.096 34.783 0.00 0.00 0.00 3.16
2812 2883 4.098501 CCCAAGAAACTTTTGCTGACTTCT 59.901 41.667 0.00 0.00 0.00 2.85
2923 2994 8.862325 AGAACACAAAACACTCCATATTATCA 57.138 30.769 0.00 0.00 0.00 2.15
3135 3206 9.352784 TGTTTTTCAGTTTCTGACAGTATTTTG 57.647 29.630 1.59 0.00 40.46 2.44
3222 3293 7.410120 TTCTGCTACTATGTCAGATTCAGAA 57.590 36.000 0.00 0.00 36.81 3.02
3382 3478 3.770666 CACAAGTACACATACTCCCTCG 58.229 50.000 0.00 0.00 41.00 4.63
3505 3601 3.255149 GTCTCTCGGAACAGTTGGACTTA 59.745 47.826 0.00 0.00 0.00 2.24
3520 3616 0.097325 GCCGTCTACAGTGTCTCTCG 59.903 60.000 0.00 1.09 0.00 4.04
3671 3768 2.746279 TGAGAAGGCCAAAACCAAGA 57.254 45.000 5.01 0.00 0.00 3.02
3672 3769 3.445096 CCTATGAGAAGGCCAAAACCAAG 59.555 47.826 5.01 0.00 0.00 3.61
3676 3773 4.280929 ACAAACCTATGAGAAGGCCAAAAC 59.719 41.667 5.01 0.00 40.62 2.43
3848 3945 4.514066 ACACGGGACAAGTTTGAATCTAAC 59.486 41.667 0.00 0.00 0.00 2.34
3850 3947 4.062293 CACACGGGACAAGTTTGAATCTA 58.938 43.478 0.00 0.00 0.00 1.98
3895 3992 3.817647 GCAGGTTGAATGAGTGTCTCTTT 59.182 43.478 0.00 0.00 31.92 2.52
3987 4084 2.172505 TGAGGTGTTTCTCTTGCTCCAA 59.827 45.455 0.00 0.00 34.98 3.53
4279 4376 1.810755 CAGATTGTGTGTGCTGCATCT 59.189 47.619 5.27 0.00 0.00 2.90
4378 4475 3.119291 CGATCTTGGACACTGCTCATAC 58.881 50.000 0.00 0.00 0.00 2.39
4423 4520 8.134895 CAGATAACTTACAAGTCCTCATCTCTC 58.865 40.741 0.00 0.00 38.57 3.20
4505 4604 8.169977 TCAGTTCTCTAACTAAACGTTTCCTA 57.830 34.615 18.42 6.64 44.28 2.94
4554 4653 7.165485 AGTATGGTGTTGCACTGTAAAATCTA 58.835 34.615 0.00 0.00 34.40 1.98
4588 4687 0.615331 TCTTGATGGACCTGCAGGAC 59.385 55.000 39.19 31.70 38.94 3.85
4716 4815 5.365021 AACATAGCAGCAAGACCTCTAAT 57.635 39.130 0.00 0.00 0.00 1.73
4734 4833 4.301072 ACCACATGGCAACTAGTAACAT 57.699 40.909 0.00 0.00 39.32 2.71
4745 4844 1.327303 GGTCAAGAAACCACATGGCA 58.673 50.000 0.00 0.00 39.27 4.92
4805 4904 7.815549 TCAAAACACTATATGCGTAAGTCAGAA 59.184 33.333 0.00 0.00 41.68 3.02
4923 5358 7.582667 AAGAAAACTAGTTTGGTGCATAACT 57.417 32.000 21.22 13.86 38.16 2.24
4939 5374 2.365293 GTGTGCCCCATGAAAGAAAACT 59.635 45.455 0.00 0.00 0.00 2.66
4952 5387 2.040544 CCGATCAGTTGTGTGCCCC 61.041 63.158 0.00 0.00 0.00 5.80
5107 5553 4.825634 TCCTTGATCATCCATTTCTGCATC 59.174 41.667 0.00 0.00 0.00 3.91
5128 5574 6.698008 TTATGTGATTGTGGTTCATCATCC 57.302 37.500 0.00 0.00 0.00 3.51
5129 5575 9.241317 GAATTTATGTGATTGTGGTTCATCATC 57.759 33.333 0.00 0.00 0.00 2.92
5131 5577 8.245491 CAGAATTTATGTGATTGTGGTTCATCA 58.755 33.333 0.00 0.00 0.00 3.07
5176 5622 1.538047 GTGCCAATTCTCCAGCTTCA 58.462 50.000 0.00 0.00 0.00 3.02
5188 5634 2.586293 GCTGCCAAAGGGTGCCAAT 61.586 57.895 0.00 0.00 36.17 3.16
5293 5740 2.417719 CAGCCTACAGACAACAGGTTC 58.582 52.381 0.00 0.00 0.00 3.62
5297 5744 2.105006 ATGCAGCCTACAGACAACAG 57.895 50.000 0.00 0.00 0.00 3.16
5455 5903 2.300723 TCCGCTTCTGCTACAAAAGGTA 59.699 45.455 0.00 0.00 36.97 3.08
5485 5933 1.580942 GGCTTGTTTGATGCGCTCA 59.419 52.632 9.73 7.24 0.00 4.26
5504 5952 5.923204 AGCAAGACATTTCAGGTATAGAGG 58.077 41.667 0.00 0.00 0.00 3.69
5534 5982 6.597280 CCCAGAAAACCACTGAATTTGAAAAA 59.403 34.615 0.00 0.00 37.54 1.94


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

AutoCloner maintained by Alex Coulton.