Multiple sequence alignment - TraesCS4D01G217100

Loading Multiple Alignment...

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 TraesCS4D01G217100 chr4D 100.000 5116 0 0 1 5116 371799631 371794516 0.000000e+00 9448.0
1 TraesCS4D01G217100 chr4B 94.451 4019 153 27 784 4760 456609439 456605449 0.000000e+00 6122.0
2 TraesCS4D01G217100 chr4B 85.452 653 75 3 7 656 456610371 456609736 0.000000e+00 662.0
3 TraesCS4D01G217100 chr4B 89.222 167 10 1 4782 4948 456599487 456599329 8.690000e-48 202.0
4 TraesCS4D01G217100 chr4A 94.852 3807 128 29 860 4634 92211858 92215628 0.000000e+00 5882.0
5 TraesCS4D01G217100 chr4A 86.986 876 93 14 1 861 92206678 92207547 0.000000e+00 966.0
6 TraesCS4D01G217100 chr4A 83.214 280 15 14 4639 4915 92215660 92215910 1.430000e-55 228.0
7 TraesCS4D01G217100 chr4A 97.826 46 1 0 5041 5086 92216329 92216374 4.250000e-11 80.5


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 TraesCS4D01G217100 chr4D 371794516 371799631 5115 True 9448.0 9448 100.0000 1 5116 1 chr4D.!!$R1 5115
1 TraesCS4D01G217100 chr4B 456605449 456610371 4922 True 3392.0 6122 89.9515 7 4760 2 chr4B.!!$R2 4753
2 TraesCS4D01G217100 chr4A 92211858 92216374 4516 False 2063.5 5882 91.9640 860 5086 3 chr4A.!!$F2 4226
3 TraesCS4D01G217100 chr4A 92206678 92207547 869 False 966.0 966 86.9860 1 861 1 chr4A.!!$F1 860

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
416 425 0.179029 TTTATAAGGCGAGGCTGGGC 60.179 55.000 15.31 15.31 0.0 5.36 F
930 1117 1.145377 CTAAACCCATCCCGTCCCG 59.855 63.158 0.00 0.00 0.0 5.14 F
2191 2400 0.729116 ACATTGCTCGCCTTGATTCG 59.271 50.000 0.00 0.00 0.0 3.34 F
2963 3195 0.684479 TGGCAGCATCTCGTCTACCT 60.684 55.000 0.00 0.00 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1409 0.395173 AGCAACGGAACAGGTTTGGT 60.395 50.000 0.0 0.0 0.00 3.67 R
2891 3104 1.935933 ACGTGTTTGTCAGGTCTGTC 58.064 50.000 0.0 0.0 40.51 3.51 R
3174 3406 1.202879 CCCATGCCCCGCTTAATTCTA 60.203 52.381 0.0 0.0 0.00 2.10 R
4779 5048 0.318955 AAGAAGCATTGTGTTGCCGC 60.319 50.000 0.0 0.0 43.83 6.53 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
26 27 1.345741 CATGGTCGGCATCTGGATACT 59.654 52.381 0.00 0.00 37.61 2.12
31 32 4.102524 TGGTCGGCATCTGGATACTTTATT 59.897 41.667 0.00 0.00 37.61 1.40
40 41 6.499106 TCTGGATACTTTATTGGCAGATGA 57.501 37.500 0.00 0.00 37.61 2.92
47 48 2.526304 TATTGGCAGATGACGCTACC 57.474 50.000 0.00 0.00 0.00 3.18
58 59 2.728817 CGCTACCCGTCATCCTCC 59.271 66.667 0.00 0.00 0.00 4.30
64 65 3.083349 CCGTCATCCTCCAGGGCA 61.083 66.667 0.00 0.00 35.41 5.36
66 67 1.299648 CGTCATCCTCCAGGGCAAA 59.700 57.895 0.00 0.00 35.41 3.68
113 122 6.078664 AGTCATCGGGAATAGATAAGACCTT 58.921 40.000 0.00 0.00 0.00 3.50
196 205 2.355818 GGACCACTTTAAGGGCTACTGG 60.356 54.545 0.00 0.00 33.44 4.00
197 206 1.004394 ACCACTTTAAGGGCTACTGGC 59.996 52.381 0.00 0.00 40.90 4.85
199 208 1.066430 CACTTTAAGGGCTACTGGCGA 60.066 52.381 0.00 0.00 42.94 5.54
220 229 2.203252 CATGGACCCAGGGCATCG 60.203 66.667 4.91 0.00 0.00 3.84
223 232 2.764128 GGACCCAGGGCATCGAGA 60.764 66.667 4.91 0.00 0.00 4.04
224 233 2.367202 GGACCCAGGGCATCGAGAA 61.367 63.158 4.91 0.00 0.00 2.87
283 292 2.158445 GGGCTGACTACCCTATCTCAGA 60.158 54.545 0.00 0.00 44.68 3.27
329 338 2.908073 CGTCCAAGGCAAGCACACC 61.908 63.158 0.00 0.00 0.00 4.16
348 357 3.019590 CCGATGATCGTGGAGGACTCC 62.020 61.905 14.27 11.44 42.63 3.85
359 368 2.107953 GGACTCCTCATCGCCTGC 59.892 66.667 0.00 0.00 0.00 4.85
362 371 4.218578 CTCCTCATCGCCTGCGCT 62.219 66.667 9.73 0.00 39.59 5.92
385 394 6.075949 TGACTAGGACTCTGTAACCATAGT 57.924 41.667 0.00 0.00 31.28 2.12
416 425 0.179029 TTTATAAGGCGAGGCTGGGC 60.179 55.000 15.31 15.31 0.00 5.36
437 446 3.242804 GCTAGTCGATATGCCCTCGATAC 60.243 52.174 5.78 0.00 45.81 2.24
473 482 1.757699 TGTACTATGTGCACCGCCATA 59.242 47.619 15.69 4.47 0.00 2.74
509 518 4.367039 AGCAAGAAGTAGGGTTTTAGCA 57.633 40.909 0.00 0.00 0.00 3.49
511 520 3.818773 GCAAGAAGTAGGGTTTTAGCACA 59.181 43.478 0.00 0.00 0.00 4.57
522 531 4.287720 GGTTTTAGCACAAGCACTGTTAC 58.712 43.478 0.00 0.00 45.49 2.50
526 535 1.942657 AGCACAAGCACTGTTACACAG 59.057 47.619 2.23 2.23 44.67 3.66
570 579 4.976116 CACACACGACATGTCATATCGTAT 59.024 41.667 24.93 5.13 46.76 3.06
575 584 6.072452 ACACGACATGTCATATCGTATCATCT 60.072 38.462 24.93 0.00 46.76 2.90
634 643 2.788176 ATCGTGCGCATGTCGTTCG 61.788 57.895 27.72 17.81 41.07 3.95
635 644 4.483683 CGTGCGCATGTCGTTCGG 62.484 66.667 21.57 0.00 41.07 4.30
644 653 2.660490 CATGTCGTTCGGCAAAATGTT 58.340 42.857 3.18 0.00 0.00 2.71
649 658 1.778334 GTTCGGCAAAATGTTGTCCC 58.222 50.000 0.00 0.00 35.86 4.46
658 667 4.220602 GCAAAATGTTGTCCCTGATACCTT 59.779 41.667 0.00 0.00 37.06 3.50
662 809 5.615925 ATGTTGTCCCTGATACCTTAGAC 57.384 43.478 0.00 0.00 0.00 2.59
671 818 4.323257 CCTGATACCTTAGACGGGTTTGTT 60.323 45.833 0.00 0.00 38.19 2.83
682 829 2.962421 ACGGGTTTGTTGGATTTCACAT 59.038 40.909 0.00 0.00 0.00 3.21
683 830 3.386402 ACGGGTTTGTTGGATTTCACATT 59.614 39.130 0.00 0.00 0.00 2.71
812 997 5.520376 AGAGTTGTTCATTCCCTTTTGTG 57.480 39.130 0.00 0.00 0.00 3.33
854 1041 1.741401 CTCCAACGCCGCAATCTCA 60.741 57.895 0.00 0.00 0.00 3.27
855 1042 1.970917 CTCCAACGCCGCAATCTCAC 61.971 60.000 0.00 0.00 0.00 3.51
856 1043 2.480555 CAACGCCGCAATCTCACC 59.519 61.111 0.00 0.00 0.00 4.02
857 1044 2.746277 AACGCCGCAATCTCACCC 60.746 61.111 0.00 0.00 0.00 4.61
930 1117 1.145377 CTAAACCCATCCCGTCCCG 59.855 63.158 0.00 0.00 0.00 5.14
979 1169 2.041405 CCCCTCTCCCCTCCAGAC 60.041 72.222 0.00 0.00 0.00 3.51
1568 1761 3.623060 TGCGCTAAAGATTAGCCTTGAAG 59.377 43.478 9.73 3.22 37.26 3.02
1572 1776 6.223852 CGCTAAAGATTAGCCTTGAAGGATA 58.776 40.000 16.93 10.87 37.67 2.59
1721 1925 6.564328 CCTAACCATAAGACTTCATTTTGCC 58.436 40.000 0.00 0.00 0.00 4.52
1831 2037 3.419915 GAGCTTGCACAATGTTGTATCG 58.580 45.455 0.00 0.00 39.91 2.92
1875 2083 3.788227 TCCCTGAACACTATGCAAGTT 57.212 42.857 0.00 0.00 35.76 2.66
1926 2134 1.026584 CGATTGCAGGCATTCCATCA 58.973 50.000 9.74 0.00 33.74 3.07
2022 2231 3.689649 GGTAGACAGATCGCATGGTTTTT 59.310 43.478 0.00 0.00 0.00 1.94
2087 2296 6.094603 GTGATCCATTACTCAAGTTTCAGCAT 59.905 38.462 0.00 0.00 0.00 3.79
2184 2393 5.835113 ATTTTGTTATACATTGCTCGCCT 57.165 34.783 0.00 0.00 0.00 5.52
2191 2400 0.729116 ACATTGCTCGCCTTGATTCG 59.271 50.000 0.00 0.00 0.00 3.34
2194 2403 1.351430 TTGCTCGCCTTGATTCGTCG 61.351 55.000 0.00 0.00 0.00 5.12
2275 2487 1.176527 TGCAGTATGGAGCTTTTGCC 58.823 50.000 0.00 0.00 41.63 4.52
2320 2532 1.217882 CCAGACAAGGTGACAACGTC 58.782 55.000 0.00 0.00 0.00 4.34
2476 2688 4.401837 ACTCGATTACCCCTCAGTTCTTAC 59.598 45.833 0.00 0.00 0.00 2.34
2484 2696 3.264450 CCCCTCAGTTCTTACAAGGATGT 59.736 47.826 0.00 0.00 43.74 3.06
2744 2957 2.485426 CTGAGCAACCGACATGAATTGT 59.515 45.455 0.00 0.00 42.79 2.71
2775 2988 3.829026 AGTAGTCACAGATCAGTGCTTCA 59.171 43.478 13.08 0.00 39.35 3.02
2787 3000 2.743664 CAGTGCTTCATCATCGTCCAAA 59.256 45.455 0.00 0.00 0.00 3.28
2865 3078 4.938832 CCCATAATCGTGACCAGTTAAACA 59.061 41.667 0.00 0.00 0.00 2.83
2894 3107 3.533105 ACGACTGTGGCCACGACA 61.533 61.111 30.07 12.90 0.00 4.35
2963 3195 0.684479 TGGCAGCATCTCGTCTACCT 60.684 55.000 0.00 0.00 0.00 3.08
3000 3232 1.308216 CCCAGATCCCCACTCCCTT 60.308 63.158 0.00 0.00 0.00 3.95
3005 3237 1.229529 ATCCCCACTCCCTTGTCGT 60.230 57.895 0.00 0.00 0.00 4.34
3031 3263 3.795280 TACTATCGTCACCGCGCGC 62.795 63.158 27.36 23.91 0.00 6.86
3157 3389 3.521531 TGGTTTACTCATCCCTACATGCA 59.478 43.478 0.00 0.00 0.00 3.96
3174 3406 4.587262 ACATGCATGCAACATTAGATCCAT 59.413 37.500 26.68 0.00 0.00 3.41
3255 3487 1.599797 CGCCTCCTGTTTTCCGGTT 60.600 57.895 0.00 0.00 0.00 4.44
3307 3541 6.452757 TTAATATGGAATGGAGGAGCATCA 57.547 37.500 0.00 0.00 36.25 3.07
3310 3544 2.726821 TGGAATGGAGGAGCATCAAAC 58.273 47.619 0.00 0.00 36.25 2.93
3528 3762 7.816945 ATGTTTTCTTGTATGCTTGTATTGC 57.183 32.000 0.00 0.00 0.00 3.56
3916 4153 1.077915 CATCTGTGCATGCGTGTGTA 58.922 50.000 14.09 0.00 0.00 2.90
3917 4154 1.667212 CATCTGTGCATGCGTGTGTAT 59.333 47.619 14.09 0.00 0.00 2.29
3918 4155 1.077915 TCTGTGCATGCGTGTGTATG 58.922 50.000 14.09 0.00 40.73 2.39
3919 4156 0.798159 CTGTGCATGCGTGTGTATGT 59.202 50.000 14.09 0.00 40.01 2.29
3951 4188 5.031578 TGTGTCAGCGTGTTTATTTTGTTC 58.968 37.500 0.00 0.00 0.00 3.18
4273 4510 1.358759 CGTGGGGTTTGCACAGAAC 59.641 57.895 0.00 0.00 0.00 3.01
4539 4780 7.382218 GTGGAGGAATAACAAAACAAAGTGATG 59.618 37.037 0.00 0.00 0.00 3.07
4561 4802 5.188434 TGGAATAAGCAGAGGAATTGACTG 58.812 41.667 0.00 0.00 35.14 3.51
4622 4863 5.323371 TGTATGCCTTACAGGAATTTTGC 57.677 39.130 0.00 0.00 37.67 3.68
4624 4865 2.509569 TGCCTTACAGGAATTTTGCGA 58.490 42.857 0.00 0.00 37.67 5.10
4635 4876 6.155827 CAGGAATTTTGCGAGAAATTGGTTA 58.844 36.000 12.12 0.00 38.85 2.85
4641 4882 8.600449 ATTTTGCGAGAAATTGGTTATTTTGA 57.400 26.923 0.00 0.00 36.59 2.69
4643 4884 5.465935 TGCGAGAAATTGGTTATTTTGACC 58.534 37.500 0.00 0.00 36.59 4.02
4770 5039 4.511527 TCTGAGAAGCCAGATTTAAGCAG 58.488 43.478 0.00 0.00 38.18 4.24
4774 5043 3.265479 AGAAGCCAGATTTAAGCAGGACT 59.735 43.478 0.00 0.00 0.00 3.85
4775 5044 2.996631 AGCCAGATTTAAGCAGGACTG 58.003 47.619 0.00 0.00 0.00 3.51
4794 5063 3.683937 GGGCGGCAACACAATGCT 61.684 61.111 12.47 0.00 45.68 3.79
4795 5064 2.339712 GGCGGCAACACAATGCTT 59.660 55.556 3.07 0.00 45.68 3.91
4796 5065 1.734117 GGCGGCAACACAATGCTTC 60.734 57.895 3.07 0.00 45.68 3.86
4797 5066 1.286880 GCGGCAACACAATGCTTCT 59.713 52.632 0.00 0.00 45.68 2.85
4798 5067 0.318955 GCGGCAACACAATGCTTCTT 60.319 50.000 0.00 0.00 45.68 2.52
4799 5068 1.869342 GCGGCAACACAATGCTTCTTT 60.869 47.619 0.00 0.00 45.68 2.52
4800 5069 1.788308 CGGCAACACAATGCTTCTTTG 59.212 47.619 0.00 0.00 45.68 2.77
4801 5070 1.528161 GGCAACACAATGCTTCTTTGC 59.472 47.619 0.00 0.00 45.68 3.68
4802 5071 2.476821 GCAACACAATGCTTCTTTGCT 58.523 42.857 0.00 0.00 43.06 3.91
4809 5078 6.381801 ACACAATGCTTCTTTGCTATACAAC 58.618 36.000 0.00 0.00 38.23 3.32
4810 5079 6.016360 ACACAATGCTTCTTTGCTATACAACA 60.016 34.615 0.00 0.00 38.23 3.33
4815 5084 4.156739 GCTTCTTTGCTATACAACAAGGCT 59.843 41.667 0.00 0.00 38.23 4.58
4817 5086 5.165961 TCTTTGCTATACAACAAGGCTCT 57.834 39.130 0.00 0.00 38.23 4.09
4835 5104 7.056844 AGGCTCTAGAATGTAGGAATAACAC 57.943 40.000 0.00 0.00 0.00 3.32
4841 5110 9.656323 TCTAGAATGTAGGAATAACACCATAGT 57.344 33.333 0.00 0.00 0.00 2.12
4844 5113 9.396022 AGAATGTAGGAATAACACCATAGTTTG 57.604 33.333 0.00 0.00 33.07 2.93
4845 5114 9.391006 GAATGTAGGAATAACACCATAGTTTGA 57.609 33.333 0.00 0.00 33.07 2.69
4846 5115 8.964476 ATGTAGGAATAACACCATAGTTTGAG 57.036 34.615 0.00 0.00 33.07 3.02
4847 5116 7.335627 TGTAGGAATAACACCATAGTTTGAGG 58.664 38.462 0.00 0.00 33.07 3.86
4848 5117 5.193679 AGGAATAACACCATAGTTTGAGGC 58.806 41.667 0.00 0.00 33.07 4.70
4856 5125 2.096496 CCATAGTTTGAGGCTTTGAGCG 59.904 50.000 0.00 0.00 43.62 5.03
4872 5141 0.322816 AGCGCCATGTCTTGTGGATT 60.323 50.000 2.29 0.00 39.12 3.01
4891 5162 4.410555 GGATTCCTAGGATTTCACACCTCT 59.589 45.833 13.57 0.00 37.68 3.69
4892 5163 5.104318 GGATTCCTAGGATTTCACACCTCTT 60.104 44.000 13.57 0.00 37.68 2.85
4894 5165 4.168101 TCCTAGGATTTCACACCTCTTGT 58.832 43.478 7.62 0.00 39.97 3.16
4915 5186 7.822334 TCTTGTGTCAGAGTAAGAAAACAAAGA 59.178 33.333 0.00 0.00 0.00 2.52
4923 5369 7.802251 CAGAGTAAGAAAACAAAGAAGCTCATG 59.198 37.037 0.00 0.00 0.00 3.07
4927 5373 7.529880 AAGAAAACAAAGAAGCTCATGTTTG 57.470 32.000 15.42 11.43 43.16 2.93
4950 5420 6.925934 TGGAATCCTCCCTATGAAAATTCAT 58.074 36.000 12.82 12.82 44.50 2.57
4952 5422 7.944554 TGGAATCCTCCCTATGAAAATTCATAC 59.055 37.037 10.95 0.66 42.46 2.39
4953 5423 8.166726 GGAATCCTCCCTATGAAAATTCATACT 58.833 37.037 10.95 0.00 40.89 2.12
4954 5424 9.225436 GAATCCTCCCTATGAAAATTCATACTC 57.775 37.037 10.95 0.00 45.54 2.59
4955 5425 7.079451 TCCTCCCTATGAAAATTCATACTCC 57.921 40.000 10.95 0.00 45.54 3.85
4963 5443 4.324254 TGAAAATTCATACTCCGAAGGGCT 60.324 41.667 0.00 0.00 39.68 5.19
5027 5508 4.875544 TTTGTTCCAAAGAAGTCACGAG 57.124 40.909 0.00 0.00 30.91 4.18
5032 5513 3.926616 TCCAAAGAAGTCACGAGAATCC 58.073 45.455 0.00 0.00 0.00 3.01
5055 5619 6.892456 TCCAAGCATATACTATTCTCTCCGAT 59.108 38.462 0.00 0.00 0.00 4.18
5086 5650 3.610040 TGTGAGCTCAAACGGATGTAT 57.390 42.857 20.19 0.00 0.00 2.29
5087 5651 3.937814 TGTGAGCTCAAACGGATGTATT 58.062 40.909 20.19 0.00 0.00 1.89
5088 5652 4.323417 TGTGAGCTCAAACGGATGTATTT 58.677 39.130 20.19 0.00 0.00 1.40
5089 5653 5.483811 TGTGAGCTCAAACGGATGTATTTA 58.516 37.500 20.19 0.00 0.00 1.40
5090 5654 5.580691 TGTGAGCTCAAACGGATGTATTTAG 59.419 40.000 20.19 0.00 0.00 1.85
5091 5655 5.810587 GTGAGCTCAAACGGATGTATTTAGA 59.189 40.000 20.19 0.00 0.00 2.10
5092 5656 6.019479 GTGAGCTCAAACGGATGTATTTAGAG 60.019 42.308 20.19 0.00 0.00 2.43
5093 5657 5.978814 AGCTCAAACGGATGTATTTAGAGT 58.021 37.500 0.00 0.00 0.00 3.24
5094 5658 5.812642 AGCTCAAACGGATGTATTTAGAGTG 59.187 40.000 0.00 0.00 0.00 3.51
5095 5659 5.006746 GCTCAAACGGATGTATTTAGAGTGG 59.993 44.000 0.00 0.00 0.00 4.00
5096 5660 6.045072 TCAAACGGATGTATTTAGAGTGGT 57.955 37.500 0.00 0.00 0.00 4.16
5097 5661 7.172868 TCAAACGGATGTATTTAGAGTGGTA 57.827 36.000 0.00 0.00 0.00 3.25
5098 5662 7.788026 TCAAACGGATGTATTTAGAGTGGTAT 58.212 34.615 0.00 0.00 0.00 2.73
5099 5663 8.262227 TCAAACGGATGTATTTAGAGTGGTATT 58.738 33.333 0.00 0.00 0.00 1.89
5100 5664 8.335356 CAAACGGATGTATTTAGAGTGGTATTG 58.665 37.037 0.00 0.00 0.00 1.90
5101 5665 7.120923 ACGGATGTATTTAGAGTGGTATTGT 57.879 36.000 0.00 0.00 0.00 2.71
5102 5666 8.241497 ACGGATGTATTTAGAGTGGTATTGTA 57.759 34.615 0.00 0.00 0.00 2.41
5103 5667 8.867097 ACGGATGTATTTAGAGTGGTATTGTAT 58.133 33.333 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.178252 CGTCATCTGCCAATAAAGTATCCAG 59.822 44.000 0.00 0.00 0.00 3.86
26 27 3.202906 GGTAGCGTCATCTGCCAATAAA 58.797 45.455 0.00 0.00 38.51 1.40
31 32 2.900273 GGGTAGCGTCATCTGCCA 59.100 61.111 0.70 0.00 40.13 4.92
40 41 2.125961 GGAGGATGACGGGTAGCGT 61.126 63.158 0.00 0.00 0.00 5.07
47 48 2.196997 TTTGCCCTGGAGGATGACGG 62.197 60.000 0.00 0.00 38.24 4.79
52 53 1.000396 GCACTTTGCCCTGGAGGAT 60.000 57.895 0.00 0.00 37.42 3.24
88 96 6.078664 AGGTCTTATCTATTCCCGATGACTT 58.921 40.000 0.00 0.00 0.00 3.01
113 122 2.439409 CCATCTTCAGAATGTGTGGCA 58.561 47.619 0.00 0.00 37.40 4.92
142 151 0.246635 CTTCCGGACTGTGGTCGAAT 59.753 55.000 1.83 0.00 42.97 3.34
196 205 2.903855 CTGGGTCCATGGCATCGC 60.904 66.667 6.96 8.97 0.00 4.58
197 206 2.203252 CCTGGGTCCATGGCATCG 60.203 66.667 6.96 0.00 0.00 3.84
212 221 2.990479 GGTGGTTCTCGATGCCCT 59.010 61.111 0.00 0.00 0.00 5.19
218 227 1.859427 CGACTTCCGGTGGTTCTCGA 61.859 60.000 0.00 0.00 33.91 4.04
220 229 4.573162 CGACTTCCGGTGGTTCTC 57.427 61.111 0.00 0.00 33.91 2.87
277 286 1.911057 TCGTCTTGAAGGCTCTGAGA 58.089 50.000 9.28 0.00 0.00 3.27
329 338 3.855630 GAGTCCTCCACGATCATCG 57.144 57.895 5.22 5.22 46.93 3.84
359 368 2.097791 GGTTACAGAGTCCTAGTCAGCG 59.902 54.545 0.00 0.00 0.00 5.18
362 371 6.075949 ACTATGGTTACAGAGTCCTAGTCA 57.924 41.667 0.00 0.00 45.48 3.41
522 531 0.172578 TCCGGCAACTATCGTCTGTG 59.827 55.000 0.00 0.00 0.00 3.66
526 535 1.717194 TTTGTCCGGCAACTATCGTC 58.283 50.000 10.30 0.00 36.72 4.20
539 548 2.096819 ACATGTCGTGTGTGTTTTGTCC 59.903 45.455 0.00 0.00 40.28 4.02
543 552 5.389411 CGATATGACATGTCGTGTGTGTTTT 60.389 40.000 27.30 4.97 42.36 2.43
570 579 6.061022 TGTTTAGACTTTGCCCATAGATGA 57.939 37.500 0.00 0.00 0.00 2.92
575 584 5.594725 TGTTGTTGTTTAGACTTTGCCCATA 59.405 36.000 0.00 0.00 0.00 2.74
613 622 3.928769 CGACATGCGCACGATGGG 61.929 66.667 14.90 0.00 0.00 4.00
634 643 3.119137 GGTATCAGGGACAACATTTTGCC 60.119 47.826 0.00 0.00 36.00 4.52
635 644 3.763897 AGGTATCAGGGACAACATTTTGC 59.236 43.478 0.00 0.00 36.00 3.68
644 653 2.662866 CCGTCTAAGGTATCAGGGACA 58.337 52.381 0.00 0.00 0.00 4.02
649 658 4.467198 ACAAACCCGTCTAAGGTATCAG 57.533 45.455 0.00 0.00 36.27 2.90
658 667 3.816523 GTGAAATCCAACAAACCCGTCTA 59.183 43.478 0.00 0.00 0.00 2.59
662 809 3.658757 ATGTGAAATCCAACAAACCCG 57.341 42.857 0.00 0.00 0.00 5.28
671 818 7.053316 AGTCAAATTGTCAATGTGAAATCCA 57.947 32.000 18.21 0.00 36.90 3.41
812 997 6.978659 AGTCGAATTGTTCCTTTTTCTTTTCC 59.021 34.615 0.00 0.00 0.00 3.13
823 1008 2.413837 CGTTGGAGTCGAATTGTTCCT 58.586 47.619 0.00 0.00 0.00 3.36
825 1010 1.136057 GGCGTTGGAGTCGAATTGTTC 60.136 52.381 0.00 0.00 0.00 3.18
856 1043 4.078516 GAGGTTGGGTCGGGTCGG 62.079 72.222 0.00 0.00 0.00 4.79
857 1044 2.995574 AGAGGTTGGGTCGGGTCG 60.996 66.667 0.00 0.00 0.00 4.79
858 1045 2.663196 CAGAGGTTGGGTCGGGTC 59.337 66.667 0.00 0.00 0.00 4.46
1219 1409 0.395173 AGCAACGGAACAGGTTTGGT 60.395 50.000 0.00 0.00 0.00 3.67
1223 1413 1.528309 CCCAGCAACGGAACAGGTT 60.528 57.895 0.00 0.00 0.00 3.50
1568 1761 4.645535 TCATCTTAGCAATGGCAGTATCC 58.354 43.478 0.00 0.00 44.61 2.59
1572 1776 4.951715 TCAAATCATCTTAGCAATGGCAGT 59.048 37.500 0.00 0.00 44.61 4.40
1576 1780 7.223971 CACCAAATCAAATCATCTTAGCAATGG 59.776 37.037 0.00 0.00 0.00 3.16
1831 2037 4.233789 TGCAGAACATTTAAATTGTCCGC 58.766 39.130 0.00 3.92 0.00 5.54
1875 2083 5.949354 AGCATAACTAAAACCAGTGCCATTA 59.051 36.000 0.00 0.00 0.00 1.90
2022 2231 4.332543 GTGTCATGGCGTGATTAAGATGAA 59.667 41.667 13.34 0.00 39.48 2.57
2087 2296 6.080969 AGACTGGACCAGATTACTAGAGAA 57.919 41.667 28.56 0.00 35.18 2.87
2184 2393 8.082242 ACTATAATGATGATGACGACGAATCAA 58.918 33.333 17.46 6.96 36.44 2.57
2191 2400 7.148641 ACCAGAACTATAATGATGATGACGAC 58.851 38.462 0.00 0.00 0.00 4.34
2194 2403 8.893219 TTGACCAGAACTATAATGATGATGAC 57.107 34.615 0.00 0.00 0.00 3.06
2240 2452 3.424703 ACTGCATACTTTTGCTGACCAT 58.575 40.909 9.78 0.00 42.27 3.55
2275 2487 9.722056 GGTCAGTTCACAGCAATATATTTTTAG 57.278 33.333 0.00 0.00 0.00 1.85
2320 2532 6.594284 TTCGCTCATTCATGAAGAATAGTG 57.406 37.500 14.54 13.43 45.06 2.74
2476 2688 7.641020 GCAAAAGAAAATTTCACAACATCCTTG 59.359 33.333 8.55 0.20 0.00 3.61
2484 2696 7.173907 TGGTCTTTGCAAAAGAAAATTTCACAA 59.826 29.630 13.84 2.09 0.00 3.33
2744 2957 2.167662 TCTGTGACTACTCGCCATCAA 58.832 47.619 0.00 0.00 0.00 2.57
2787 3000 4.650754 ATCCTCTAACAATTACGCGTCT 57.349 40.909 18.63 0.37 0.00 4.18
2846 3059 6.460781 AGTCATGTTTAACTGGTCACGATTA 58.539 36.000 0.00 0.00 0.00 1.75
2865 3078 2.964740 CACAGTCGTGGATGAAGTCAT 58.035 47.619 0.00 0.00 39.64 3.06
2891 3104 1.935933 ACGTGTTTGTCAGGTCTGTC 58.064 50.000 0.00 0.00 40.51 3.51
2963 3195 4.659172 CAAGGTTGCCAGGGCCGA 62.659 66.667 8.02 0.00 41.09 5.54
3000 3232 1.469703 CGATAGTACCCACACACGACA 59.530 52.381 0.00 0.00 0.00 4.35
3063 3295 2.030185 AGTGTGCCGTTGTAGTAGACAG 60.030 50.000 0.00 0.00 39.88 3.51
3074 3306 1.536943 GGGAGAGAGAGTGTGCCGTT 61.537 60.000 0.00 0.00 0.00 4.44
3174 3406 1.202879 CCCATGCCCCGCTTAATTCTA 60.203 52.381 0.00 0.00 0.00 2.10
3310 3544 9.177304 CACATTTAAGAATTGTATGCAGCTATG 57.823 33.333 0.00 0.00 0.00 2.23
3454 3688 8.188799 CGACAGAGAGTTATGAATGGTTAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
3560 3794 5.431420 TCGCACAAATCACATAGTTGTTT 57.569 34.783 0.00 0.00 43.55 2.83
3916 4153 4.503734 CACGCTGACACATTTTTCAAACAT 59.496 37.500 0.00 0.00 0.00 2.71
3917 4154 3.856521 CACGCTGACACATTTTTCAAACA 59.143 39.130 0.00 0.00 0.00 2.83
3918 4155 3.857093 ACACGCTGACACATTTTTCAAAC 59.143 39.130 0.00 0.00 0.00 2.93
3919 4156 4.103365 ACACGCTGACACATTTTTCAAA 57.897 36.364 0.00 0.00 0.00 2.69
4249 4486 2.203294 GCAAACCCCACGTCCACT 60.203 61.111 0.00 0.00 0.00 4.00
4273 4510 5.288804 ACAAATGTGGTGAAAAATCTTCCG 58.711 37.500 0.00 0.00 0.00 4.30
4539 4780 5.189180 ACAGTCAATTCCTCTGCTTATTCC 58.811 41.667 0.00 0.00 33.12 3.01
4561 4802 9.846248 AAATTCTAAGATTGCACAAGACATTAC 57.154 29.630 0.00 0.00 0.00 1.89
4610 4851 4.039124 ACCAATTTCTCGCAAAATTCCTGT 59.961 37.500 5.04 2.20 36.86 4.00
4622 4863 6.019779 TGGGTCAAAATAACCAATTTCTCG 57.980 37.500 0.00 0.00 36.76 4.04
4624 4865 7.801104 AGTTTGGGTCAAAATAACCAATTTCT 58.199 30.769 0.00 0.00 42.09 2.52
4635 4876 6.716284 TCCTTTGAAAAGTTTGGGTCAAAAT 58.284 32.000 12.62 0.00 38.97 1.82
4641 4882 6.716284 TGAAATTCCTTTGAAAAGTTTGGGT 58.284 32.000 2.33 0.00 33.32 4.51
4643 4884 7.962373 GTGTTGAAATTCCTTTGAAAAGTTTGG 59.038 33.333 2.33 0.00 33.32 3.28
4778 5047 1.734117 GAAGCATTGTGTTGCCGCC 60.734 57.895 0.00 0.00 43.83 6.13
4779 5048 0.318955 AAGAAGCATTGTGTTGCCGC 60.319 50.000 0.00 0.00 43.83 6.53
4782 5051 2.476821 AGCAAAGAAGCATTGTGTTGC 58.523 42.857 0.00 0.00 43.09 4.17
4783 5052 6.380995 TGTATAGCAAAGAAGCATTGTGTTG 58.619 36.000 0.00 0.00 36.85 3.33
4784 5053 6.573664 TGTATAGCAAAGAAGCATTGTGTT 57.426 33.333 0.00 0.00 36.85 3.32
4785 5054 6.016360 TGTTGTATAGCAAAGAAGCATTGTGT 60.016 34.615 0.00 0.00 39.03 3.72
4786 5055 6.380995 TGTTGTATAGCAAAGAAGCATTGTG 58.619 36.000 0.00 0.00 39.03 3.33
4787 5056 6.573664 TGTTGTATAGCAAAGAAGCATTGT 57.426 33.333 0.00 0.00 39.03 2.71
4788 5057 6.529125 CCTTGTTGTATAGCAAAGAAGCATTG 59.471 38.462 0.00 0.00 39.03 2.82
4789 5058 6.624423 CCTTGTTGTATAGCAAAGAAGCATT 58.376 36.000 0.00 0.00 39.03 3.56
4790 5059 5.393461 GCCTTGTTGTATAGCAAAGAAGCAT 60.393 40.000 0.00 0.00 39.03 3.79
4791 5060 4.082787 GCCTTGTTGTATAGCAAAGAAGCA 60.083 41.667 0.00 0.00 39.03 3.91
4792 5061 4.156739 AGCCTTGTTGTATAGCAAAGAAGC 59.843 41.667 0.00 0.00 39.03 3.86
4793 5062 5.645497 AGAGCCTTGTTGTATAGCAAAGAAG 59.355 40.000 0.00 0.00 39.03 2.85
4794 5063 5.560724 AGAGCCTTGTTGTATAGCAAAGAA 58.439 37.500 0.00 0.00 39.03 2.52
4795 5064 5.165961 AGAGCCTTGTTGTATAGCAAAGA 57.834 39.130 0.00 0.00 39.03 2.52
4796 5065 6.341316 TCTAGAGCCTTGTTGTATAGCAAAG 58.659 40.000 0.00 0.00 39.03 2.77
4797 5066 6.294361 TCTAGAGCCTTGTTGTATAGCAAA 57.706 37.500 0.00 0.00 39.03 3.68
4798 5067 5.932619 TCTAGAGCCTTGTTGTATAGCAA 57.067 39.130 0.00 0.00 34.16 3.91
4799 5068 5.932619 TTCTAGAGCCTTGTTGTATAGCA 57.067 39.130 0.00 0.00 0.00 3.49
4800 5069 6.284459 ACATTCTAGAGCCTTGTTGTATAGC 58.716 40.000 0.00 0.00 0.00 2.97
4801 5070 8.085296 CCTACATTCTAGAGCCTTGTTGTATAG 58.915 40.741 0.00 0.00 0.00 1.31
4802 5071 7.783119 TCCTACATTCTAGAGCCTTGTTGTATA 59.217 37.037 0.00 0.00 0.00 1.47
4809 5078 7.439655 GTGTTATTCCTACATTCTAGAGCCTTG 59.560 40.741 0.00 0.00 0.00 3.61
4810 5079 7.419172 GGTGTTATTCCTACATTCTAGAGCCTT 60.419 40.741 0.00 0.00 0.00 4.35
4815 5084 9.656323 ACTATGGTGTTATTCCTACATTCTAGA 57.344 33.333 0.00 0.00 0.00 2.43
4835 5104 2.096496 CGCTCAAAGCCTCAAACTATGG 59.904 50.000 0.00 0.00 38.18 2.74
4847 5116 0.455633 CAAGACATGGCGCTCAAAGC 60.456 55.000 7.64 0.00 38.02 3.51
4848 5117 0.877071 ACAAGACATGGCGCTCAAAG 59.123 50.000 7.64 3.91 0.00 2.77
4856 5125 2.134789 AGGAATCCACAAGACATGGC 57.865 50.000 0.61 0.00 37.13 4.40
4872 5141 4.168101 ACAAGAGGTGTGAAATCCTAGGA 58.832 43.478 15.46 15.46 39.72 2.94
4891 5162 7.915293 TCTTTGTTTTCTTACTCTGACACAA 57.085 32.000 0.00 0.00 0.00 3.33
4892 5163 7.414098 GCTTCTTTGTTTTCTTACTCTGACACA 60.414 37.037 0.00 0.00 0.00 3.72
4894 5165 6.823689 AGCTTCTTTGTTTTCTTACTCTGACA 59.176 34.615 0.00 0.00 0.00 3.58
4898 5169 7.500559 ACATGAGCTTCTTTGTTTTCTTACTCT 59.499 33.333 0.00 0.00 0.00 3.24
4915 5186 3.359950 GGAGGATTCCAAACATGAGCTT 58.640 45.455 5.29 0.00 43.45 3.74
4923 5369 7.124147 TGAATTTTCATAGGGAGGATTCCAAAC 59.876 37.037 5.29 0.00 37.47 2.93
4950 5420 3.396946 TCTCCTATAAGCCCTTCGGAGTA 59.603 47.826 14.90 5.63 39.19 2.59
4952 5422 2.877866 TCTCCTATAAGCCCTTCGGAG 58.122 52.381 11.59 11.59 39.44 4.63
4953 5423 2.963782 GTTCTCCTATAAGCCCTTCGGA 59.036 50.000 0.00 0.00 0.00 4.55
4954 5424 2.966516 AGTTCTCCTATAAGCCCTTCGG 59.033 50.000 0.00 0.00 0.00 4.30
4955 5425 3.892588 AGAGTTCTCCTATAAGCCCTTCG 59.107 47.826 0.00 0.00 0.00 3.79
5027 5508 7.704472 CGGAGAGAATAGTATATGCTTGGATTC 59.296 40.741 0.00 2.96 0.00 2.52
5032 5513 7.199766 GGATCGGAGAGAATAGTATATGCTTG 58.800 42.308 0.00 0.00 43.63 4.01
5055 5619 4.794278 TTGAGCTCACAAGTAATACGGA 57.206 40.909 18.03 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.