Multiple sequence alignment - TraesCS5D01G177000

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 TraesCS5D01G177000 chr5D 100.000 2675 0 0 1 2675 276932812 276930138 0.000000e+00 4940.0
1 TraesCS5D01G177000 chr5D 98.679 757 10 0 1 757 352452250 352451494 0.000000e+00 1343.0
2 TraesCS5D01G177000 chr5A 92.835 1270 43 16 793 2031 365657022 365655770 0.000000e+00 1797.0
3 TraesCS5D01G177000 chr5A 87.647 340 32 10 2339 2675 365652646 365652314 1.160000e-103 387.0
4 TraesCS5D01G177000 chr5A 87.568 185 10 5 1852 2031 365654523 365654347 4.520000e-48 202.0
5 TraesCS5D01G177000 chr5B 92.259 1253 52 18 806 2031 314294741 314293507 0.000000e+00 1735.0
6 TraesCS5D01G177000 chr5B 86.207 348 37 6 2332 2675 314287418 314287078 1.510000e-97 366.0
7 TraesCS5D01G177000 chr7D 97.628 759 18 0 1 759 335478303 335479061 0.000000e+00 1303.0
8 TraesCS5D01G177000 chr7D 97.365 759 18 2 1 759 118342270 118341514 0.000000e+00 1290.0
9 TraesCS5D01G177000 chr3D 97.976 741 15 0 17 757 609616068 609616808 0.000000e+00 1286.0
10 TraesCS5D01G177000 chr7B 94.570 755 29 2 1 755 749318043 749318785 0.000000e+00 1157.0
11 TraesCS5D01G177000 chr1B 94.218 761 34 3 1 761 305299219 305298469 0.000000e+00 1153.0
12 TraesCS5D01G177000 chr2A 94.188 757 35 2 1 756 651276363 651275615 0.000000e+00 1146.0
13 TraesCS5D01G177000 chr4A 94.055 757 37 1 1 757 492534974 492535722 0.000000e+00 1142.0
14 TraesCS5D01G177000 chr4A 84.761 689 72 16 867 1545 522973482 522972817 0.000000e+00 660.0
15 TraesCS5D01G177000 chr3B 93.783 756 38 2 1 756 719915346 719914600 0.000000e+00 1127.0
16 TraesCS5D01G177000 chr4B 93.733 734 38 1 1 734 545150896 545150171 0.000000e+00 1094.0
17 TraesCS5D01G177000 chr4B 85.486 689 77 13 867 1545 104341798 104342473 0.000000e+00 697.0
18 TraesCS5D01G177000 chr4B 87.900 562 60 6 991 1545 103891086 103890526 0.000000e+00 654.0
19 TraesCS5D01G177000 chr4B 87.900 562 60 6 991 1545 104131548 104130988 0.000000e+00 654.0
20 TraesCS5D01G177000 chr4B 87.567 563 61 7 991 1545 104005641 104005080 0.000000e+00 643.0
21 TraesCS5D01G177000 chr4D 84.783 690 70 20 867 1545 70343489 70342824 0.000000e+00 660.0
22 TraesCS5D01G177000 chr4D 84.638 690 71 18 867 1545 70337780 70337115 0.000000e+00 654.0
23 TraesCS5D01G177000 chr2D 86.667 75 10 0 2481 2555 43948675 43948601 1.710000e-12 84.2


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 TraesCS5D01G177000 chr5D 276930138 276932812 2674 True 4940.000000 4940 100.000 1 2675 1 chr5D.!!$R1 2674
1 TraesCS5D01G177000 chr5D 352451494 352452250 756 True 1343.000000 1343 98.679 1 757 1 chr5D.!!$R2 756
2 TraesCS5D01G177000 chr5A 365652314 365657022 4708 True 795.333333 1797 89.350 793 2675 3 chr5A.!!$R1 1882
3 TraesCS5D01G177000 chr5B 314293507 314294741 1234 True 1735.000000 1735 92.259 806 2031 1 chr5B.!!$R2 1225
4 TraesCS5D01G177000 chr7D 335478303 335479061 758 False 1303.000000 1303 97.628 1 759 1 chr7D.!!$F1 758
5 TraesCS5D01G177000 chr7D 118341514 118342270 756 True 1290.000000 1290 97.365 1 759 1 chr7D.!!$R1 758
6 TraesCS5D01G177000 chr3D 609616068 609616808 740 False 1286.000000 1286 97.976 17 757 1 chr3D.!!$F1 740
7 TraesCS5D01G177000 chr7B 749318043 749318785 742 False 1157.000000 1157 94.570 1 755 1 chr7B.!!$F1 754
8 TraesCS5D01G177000 chr1B 305298469 305299219 750 True 1153.000000 1153 94.218 1 761 1 chr1B.!!$R1 760
9 TraesCS5D01G177000 chr2A 651275615 651276363 748 True 1146.000000 1146 94.188 1 756 1 chr2A.!!$R1 755
10 TraesCS5D01G177000 chr4A 492534974 492535722 748 False 1142.000000 1142 94.055 1 757 1 chr4A.!!$F1 756
11 TraesCS5D01G177000 chr4A 522972817 522973482 665 True 660.000000 660 84.761 867 1545 1 chr4A.!!$R1 678
12 TraesCS5D01G177000 chr3B 719914600 719915346 746 True 1127.000000 1127 93.783 1 756 1 chr3B.!!$R1 755
13 TraesCS5D01G177000 chr4B 545150171 545150896 725 True 1094.000000 1094 93.733 1 734 1 chr4B.!!$R4 733
14 TraesCS5D01G177000 chr4B 104341798 104342473 675 False 697.000000 697 85.486 867 1545 1 chr4B.!!$F1 678
15 TraesCS5D01G177000 chr4B 103890526 103891086 560 True 654.000000 654 87.900 991 1545 1 chr4B.!!$R1 554
16 TraesCS5D01G177000 chr4B 104130988 104131548 560 True 654.000000 654 87.900 991 1545 1 chr4B.!!$R3 554
17 TraesCS5D01G177000 chr4B 104005080 104005641 561 True 643.000000 643 87.567 991 1545 1 chr4B.!!$R2 554
18 TraesCS5D01G177000 chr4D 70342824 70343489 665 True 660.000000 660 84.783 867 1545 1 chr4D.!!$R2 678
19 TraesCS5D01G177000 chr4D 70337115 70337780 665 True 654.000000 654 84.638 867 1545 1 chr4D.!!$R1 678

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
192 201 0.65784 GCAGCTAACATACGGCAAGG 59.342 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 4210 1.003233 GAGGAAATGGTGAACTCGGGT 59.997 52.381 0.0 0.0 0.0 5.28 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
192 201 0.657840 GCAGCTAACATACGGCAAGG 59.342 55.000 0.00 0.00 0.00 3.61
472 481 4.166888 GCTGCCTGGCCGAGATCA 62.167 66.667 17.53 0.00 0.00 2.92
473 482 2.586245 CTGCCTGGCCGAGATCAA 59.414 61.111 17.53 0.00 0.00 2.57
484 494 1.664874 CCGAGATCAACAACGACGTCA 60.665 52.381 17.16 0.00 0.00 4.35
724 734 6.239204 CCAGAAATCGGGTTTAAGGAAAACTT 60.239 38.462 0.00 0.00 45.70 2.66
759 769 1.426215 AGGTATCCAAACAACCCCGTT 59.574 47.619 0.00 0.00 33.53 4.44
760 770 2.643801 AGGTATCCAAACAACCCCGTTA 59.356 45.455 0.00 0.00 33.53 3.18
761 771 3.267551 AGGTATCCAAACAACCCCGTTAT 59.732 43.478 0.00 0.00 33.53 1.89
762 772 3.379057 GGTATCCAAACAACCCCGTTATG 59.621 47.826 0.00 0.00 0.00 1.90
763 773 2.660670 TCCAAACAACCCCGTTATGT 57.339 45.000 0.00 0.00 0.00 2.29
764 774 2.231529 TCCAAACAACCCCGTTATGTG 58.768 47.619 0.00 0.00 0.00 3.21
765 775 1.271102 CCAAACAACCCCGTTATGTGG 59.729 52.381 0.00 0.00 0.00 4.17
766 776 2.231529 CAAACAACCCCGTTATGTGGA 58.768 47.619 0.00 0.00 0.00 4.02
767 777 2.623889 CAAACAACCCCGTTATGTGGAA 59.376 45.455 0.00 0.00 0.00 3.53
768 778 2.891191 ACAACCCCGTTATGTGGAAT 57.109 45.000 0.00 0.00 0.00 3.01
769 779 2.442413 ACAACCCCGTTATGTGGAATG 58.558 47.619 0.00 0.00 0.00 2.67
770 780 2.040545 ACAACCCCGTTATGTGGAATGA 59.959 45.455 0.00 0.00 0.00 2.57
771 781 3.287222 CAACCCCGTTATGTGGAATGAT 58.713 45.455 0.00 0.00 0.00 2.45
772 782 4.080243 ACAACCCCGTTATGTGGAATGATA 60.080 41.667 0.00 0.00 0.00 2.15
773 783 4.351874 ACCCCGTTATGTGGAATGATAG 57.648 45.455 0.00 0.00 0.00 2.08
774 784 3.074412 CCCCGTTATGTGGAATGATAGC 58.926 50.000 0.00 0.00 0.00 2.97
775 785 3.495983 CCCCGTTATGTGGAATGATAGCA 60.496 47.826 0.00 0.00 0.00 3.49
776 786 3.498397 CCCGTTATGTGGAATGATAGCAC 59.502 47.826 0.00 0.00 0.00 4.40
777 787 3.184379 CCGTTATGTGGAATGATAGCACG 59.816 47.826 0.00 0.00 0.00 5.34
778 788 4.048504 CGTTATGTGGAATGATAGCACGA 58.951 43.478 0.00 0.00 0.00 4.35
779 789 4.148871 CGTTATGTGGAATGATAGCACGAG 59.851 45.833 0.00 0.00 0.00 4.18
780 790 2.602257 TGTGGAATGATAGCACGAGG 57.398 50.000 0.00 0.00 0.00 4.63
781 791 1.831106 TGTGGAATGATAGCACGAGGT 59.169 47.619 0.00 0.00 0.00 3.85
782 792 3.028130 TGTGGAATGATAGCACGAGGTA 58.972 45.455 0.00 0.00 0.00 3.08
783 793 3.641436 TGTGGAATGATAGCACGAGGTAT 59.359 43.478 4.17 4.17 40.93 2.73
784 794 4.100963 TGTGGAATGATAGCACGAGGTATT 59.899 41.667 6.03 0.00 38.49 1.89
785 795 5.303333 TGTGGAATGATAGCACGAGGTATTA 59.697 40.000 6.03 2.71 38.49 0.98
786 796 5.864474 GTGGAATGATAGCACGAGGTATTAG 59.136 44.000 6.03 0.00 38.49 1.73
787 797 4.865365 GGAATGATAGCACGAGGTATTAGC 59.135 45.833 6.03 0.00 38.49 3.09
788 798 5.468540 AATGATAGCACGAGGTATTAGCA 57.531 39.130 6.03 0.96 38.49 3.49
789 799 5.667539 ATGATAGCACGAGGTATTAGCAT 57.332 39.130 6.03 3.13 38.49 3.79
790 800 4.809673 TGATAGCACGAGGTATTAGCATG 58.190 43.478 6.03 0.00 38.49 4.06
791 801 2.533266 AGCACGAGGTATTAGCATGG 57.467 50.000 0.00 0.00 0.00 3.66
923 937 1.120530 GAACTCAGGGCCCTAATCGA 58.879 55.000 28.13 17.19 0.00 3.59
1235 1254 2.049627 ATCGCCATGGAGAAGGAGGC 62.050 60.000 22.69 0.00 41.86 4.70
1690 1718 1.070975 CGTGATCGATTGCTGCTTAGC 60.071 52.381 0.00 0.00 39.71 3.09
1717 1745 5.120519 CCGAGTAGACCAGATTAGATCGTAC 59.879 48.000 0.00 0.00 0.00 3.67
1718 1746 5.927689 CGAGTAGACCAGATTAGATCGTACT 59.072 44.000 0.00 0.00 0.00 2.73
1719 1747 7.089538 CGAGTAGACCAGATTAGATCGTACTA 58.910 42.308 0.00 0.00 0.00 1.82
1720 1748 7.062138 CGAGTAGACCAGATTAGATCGTACTAC 59.938 44.444 0.00 0.00 32.59 2.73
1721 1749 7.733969 AGTAGACCAGATTAGATCGTACTACA 58.266 38.462 0.00 0.00 33.61 2.74
1954 2006 9.166173 CAACTGAGATGTGATTTGTAAATCCTA 57.834 33.333 13.19 4.59 43.19 2.94
1956 2008 9.911788 ACTGAGATGTGATTTGTAAATCCTATT 57.088 29.630 13.19 0.00 43.19 1.73
1963 2015 9.739276 TGTGATTTGTAAATCCTATTCTTCTGT 57.261 29.630 13.19 0.00 43.19 3.41
1964 2016 9.994432 GTGATTTGTAAATCCTATTCTTCTGTG 57.006 33.333 13.19 0.00 43.19 3.66
1965 2017 9.177608 TGATTTGTAAATCCTATTCTTCTGTGG 57.822 33.333 13.19 0.00 43.19 4.17
1966 2018 7.938140 TTTGTAAATCCTATTCTTCTGTGGG 57.062 36.000 0.00 0.00 0.00 4.61
1967 2019 6.636454 TGTAAATCCTATTCTTCTGTGGGT 57.364 37.500 0.00 0.00 0.00 4.51
1968 2020 7.743116 TGTAAATCCTATTCTTCTGTGGGTA 57.257 36.000 0.00 0.00 0.00 3.69
1974 2026 6.472887 TCCTATTCTTCTGTGGGTACTTTTG 58.527 40.000 0.00 0.00 0.00 2.44
1975 2027 6.043938 TCCTATTCTTCTGTGGGTACTTTTGT 59.956 38.462 0.00 0.00 0.00 2.83
1977 2029 7.230712 CCTATTCTTCTGTGGGTACTTTTGTTT 59.769 37.037 0.00 0.00 0.00 2.83
1978 2030 6.844097 TTCTTCTGTGGGTACTTTTGTTTT 57.156 33.333 0.00 0.00 0.00 2.43
1979 2031 7.941431 TTCTTCTGTGGGTACTTTTGTTTTA 57.059 32.000 0.00 0.00 0.00 1.52
1980 2032 8.528044 TTCTTCTGTGGGTACTTTTGTTTTAT 57.472 30.769 0.00 0.00 0.00 1.40
1981 2033 9.629878 TTCTTCTGTGGGTACTTTTGTTTTATA 57.370 29.630 0.00 0.00 0.00 0.98
1982 2034 9.629878 TCTTCTGTGGGTACTTTTGTTTTATAA 57.370 29.630 0.00 0.00 0.00 0.98
2047 2237 2.366533 TCTCTACTCATTTCTCCGCGT 58.633 47.619 4.92 0.00 0.00 6.01
2076 2266 1.839424 CCCTCCTCACATCCAAAACC 58.161 55.000 0.00 0.00 0.00 3.27
2085 2275 1.899142 ACATCCAAAACCCCAAATCCG 59.101 47.619 0.00 0.00 0.00 4.18
2111 2786 4.446385 CACAAAATGTGGCAAGTTCATCAG 59.554 41.667 2.56 0.00 44.27 2.90
2124 4162 3.372206 AGTTCATCAGCTGCATACGAAAC 59.628 43.478 9.47 6.37 0.00 2.78
2147 4185 4.395542 CGCCTAACGGTAGCTAGATAGATT 59.604 45.833 0.59 0.00 38.44 2.40
2171 4209 0.466124 GATATATGCGGAGGGAGGGC 59.534 60.000 0.00 0.00 0.00 5.19
2172 4210 0.252696 ATATATGCGGAGGGAGGGCA 60.253 55.000 0.00 0.00 41.48 5.36
2193 4231 1.003118 CCCGAGTTCACCATTTCCTCA 59.997 52.381 0.00 0.00 0.00 3.86
2195 4233 2.289694 CCGAGTTCACCATTTCCTCACT 60.290 50.000 0.00 0.00 0.00 3.41
2201 4239 0.541863 ACCATTTCCTCACTAGGCGG 59.458 55.000 0.00 0.00 43.31 6.13
2208 4246 1.677637 CCTCACTAGGCGGTTCCTCC 61.678 65.000 0.00 0.00 43.20 4.30
2218 4256 4.097361 GTTCCTCCCGGGCTCACC 62.097 72.222 18.49 0.00 34.39 4.02
2227 4265 2.668632 GGGCTCACCGGAATGACA 59.331 61.111 9.46 0.00 36.48 3.58
2230 4268 0.741221 GGCTCACCGGAATGACAGTC 60.741 60.000 9.46 0.00 0.00 3.51
2231 4269 0.037326 GCTCACCGGAATGACAGTCA 60.037 55.000 9.46 5.50 0.00 3.41
2235 4273 3.096852 TCACCGGAATGACAGTCATAGT 58.903 45.455 16.71 9.12 35.76 2.12
2241 4279 4.033358 CGGAATGACAGTCATAGTCTTTGC 59.967 45.833 16.71 5.23 35.76 3.68
2242 4280 4.937620 GGAATGACAGTCATAGTCTTTGCA 59.062 41.667 16.71 0.00 39.54 4.08
2253 4292 0.107654 GTCTTTGCATAGGCCTCGGT 60.108 55.000 9.68 0.00 40.13 4.69
2255 4294 1.077787 TTTGCATAGGCCTCGGTGG 60.078 57.895 9.68 0.00 40.13 4.61
2272 4311 1.613630 GGCCAGAGGGGAGTCTTCA 60.614 63.158 0.00 0.00 40.01 3.02
2278 4317 1.286553 AGAGGGGAGTCTTCATCGTCT 59.713 52.381 0.00 0.00 0.00 4.18
2280 4319 1.187087 GGGGAGTCTTCATCGTCTGT 58.813 55.000 0.00 0.00 0.00 3.41
2308 4361 2.835895 GGAGGAGGAGGAGCGGAC 60.836 72.222 0.00 0.00 0.00 4.79
2321 4374 2.838225 CGGACCCCGGCTAGACAT 60.838 66.667 0.00 0.00 44.15 3.06
2322 4375 2.432300 CGGACCCCGGCTAGACATT 61.432 63.158 0.00 0.00 44.15 2.71
2330 4383 2.124736 GCTAGACATTGGGCGGCA 60.125 61.111 12.47 0.00 0.00 5.69
2332 4385 1.221840 CTAGACATTGGGCGGCACT 59.778 57.895 12.47 2.51 0.00 4.40
2333 4386 0.392998 CTAGACATTGGGCGGCACTT 60.393 55.000 12.47 0.00 0.00 3.16
2334 4387 0.037590 TAGACATTGGGCGGCACTTT 59.962 50.000 12.47 0.00 0.00 2.66
2335 4388 0.037590 AGACATTGGGCGGCACTTTA 59.962 50.000 12.47 0.00 0.00 1.85
2336 4389 1.102978 GACATTGGGCGGCACTTTAT 58.897 50.000 12.47 0.00 0.00 1.40
2337 4390 0.817013 ACATTGGGCGGCACTTTATG 59.183 50.000 12.47 7.35 0.00 1.90
2396 5268 1.094785 CACTCAATGTAAAGGGCGGG 58.905 55.000 0.00 0.00 0.00 6.13
2421 5293 7.973601 GGTTTTACCCATTTGCATAAAATCTG 58.026 34.615 4.48 0.00 36.28 2.90
2422 5294 7.821846 GGTTTTACCCATTTGCATAAAATCTGA 59.178 33.333 4.48 0.00 36.28 3.27
2425 5297 4.467082 ACCCATTTGCATAAAATCTGAGCA 59.533 37.500 0.00 0.00 36.28 4.26
2440 5312 3.056891 TCTGAGCATGTTGACGTGTATCA 60.057 43.478 0.00 8.52 35.38 2.15
2441 5313 2.993220 TGAGCATGTTGACGTGTATCAC 59.007 45.455 0.00 0.00 35.38 3.06
2451 5323 1.636340 GTGTATCACATCGCCGCAC 59.364 57.895 0.00 0.00 34.08 5.34
2463 5335 2.954753 GCCGCACACTTTCTCACCG 61.955 63.158 0.00 0.00 0.00 4.94
2480 5352 5.069119 TCTCACCGACACATGAATTAGCTAT 59.931 40.000 0.00 0.00 0.00 2.97
2505 5377 4.853924 TTTTGGAATGAAGGCTTGAGAC 57.146 40.909 3.46 0.00 0.00 3.36
2506 5378 2.099141 TGGAATGAAGGCTTGAGACG 57.901 50.000 3.46 0.00 0.00 4.18
2509 5381 0.678048 AATGAAGGCTTGAGACGGGC 60.678 55.000 3.46 0.00 0.00 6.13
2530 5402 3.810386 GCCCGGCTTTGAATTAACAAAAA 59.190 39.130 0.71 0.00 38.90 1.94
2536 5408 7.254590 CCGGCTTTGAATTAACAAAAACATCAA 60.255 33.333 0.00 0.00 38.90 2.57
2579 5451 8.786898 CGGTCAATGACTTATAATGAATGGAAT 58.213 33.333 13.53 0.00 32.47 3.01
2608 5481 0.824109 GAGGCCATTAAACCCCAAGC 59.176 55.000 5.01 0.00 0.00 4.01
2646 5519 4.671508 GCAAGCAAAACATCGCATACACTA 60.672 41.667 0.00 0.00 0.00 2.74
2670 5543 7.426929 AAAGACATCACAAGCAACTACTAAG 57.573 36.000 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 201 1.640915 CTTTACGTCGTGTACTCGTGC 59.359 52.381 16.12 9.98 38.27 5.34
472 481 1.305201 AGCCAAATGACGTCGTTGTT 58.695 45.000 23.05 6.33 0.00 2.83
473 482 1.305201 AAGCCAAATGACGTCGTTGT 58.695 45.000 23.05 10.85 0.00 3.32
484 494 3.118665 ACAGCAACTTGACAAAGCCAAAT 60.119 39.130 0.00 0.00 36.84 2.32
759 769 3.641436 ACCTCGTGCTATCATTCCACATA 59.359 43.478 0.00 0.00 0.00 2.29
760 770 2.435805 ACCTCGTGCTATCATTCCACAT 59.564 45.455 0.00 0.00 0.00 3.21
761 771 1.831106 ACCTCGTGCTATCATTCCACA 59.169 47.619 0.00 0.00 0.00 4.17
762 772 2.604046 ACCTCGTGCTATCATTCCAC 57.396 50.000 0.00 0.00 0.00 4.02
763 773 4.955811 AATACCTCGTGCTATCATTCCA 57.044 40.909 0.00 0.00 0.00 3.53
764 774 4.865365 GCTAATACCTCGTGCTATCATTCC 59.135 45.833 0.00 0.00 0.00 3.01
765 775 5.470368 TGCTAATACCTCGTGCTATCATTC 58.530 41.667 0.00 0.00 0.00 2.67
766 776 5.468540 TGCTAATACCTCGTGCTATCATT 57.531 39.130 0.00 0.00 0.00 2.57
767 777 5.414360 CATGCTAATACCTCGTGCTATCAT 58.586 41.667 0.00 0.00 0.00 2.45
768 778 4.321974 CCATGCTAATACCTCGTGCTATCA 60.322 45.833 0.00 0.00 0.00 2.15
769 779 4.177026 CCATGCTAATACCTCGTGCTATC 58.823 47.826 0.00 0.00 0.00 2.08
770 780 3.578716 ACCATGCTAATACCTCGTGCTAT 59.421 43.478 0.00 0.00 0.00 2.97
771 781 2.963101 ACCATGCTAATACCTCGTGCTA 59.037 45.455 0.00 0.00 0.00 3.49
772 782 1.762957 ACCATGCTAATACCTCGTGCT 59.237 47.619 0.00 0.00 0.00 4.40
773 783 2.135933 GACCATGCTAATACCTCGTGC 58.864 52.381 0.00 0.00 0.00 5.34
774 784 3.319405 AGAGACCATGCTAATACCTCGTG 59.681 47.826 0.00 0.00 0.00 4.35
775 785 3.567397 AGAGACCATGCTAATACCTCGT 58.433 45.455 0.00 0.00 0.00 4.18
776 786 3.823873 AGAGAGACCATGCTAATACCTCG 59.176 47.826 0.00 0.00 0.00 4.63
777 787 5.076873 AGAGAGAGACCATGCTAATACCTC 58.923 45.833 0.00 0.00 0.00 3.85
778 788 5.073437 AGAGAGAGACCATGCTAATACCT 57.927 43.478 0.00 0.00 0.00 3.08
779 789 5.076873 AGAGAGAGAGACCATGCTAATACC 58.923 45.833 0.00 0.00 0.00 2.73
780 790 6.003950 AGAGAGAGAGAGACCATGCTAATAC 58.996 44.000 0.00 0.00 0.00 1.89
781 791 6.199557 AGAGAGAGAGAGACCATGCTAATA 57.800 41.667 0.00 0.00 0.00 0.98
782 792 5.065613 AGAGAGAGAGAGACCATGCTAAT 57.934 43.478 0.00 0.00 0.00 1.73
783 793 4.460263 GAGAGAGAGAGAGACCATGCTAA 58.540 47.826 0.00 0.00 0.00 3.09
784 794 3.181445 GGAGAGAGAGAGAGACCATGCTA 60.181 52.174 0.00 0.00 0.00 3.49
785 795 2.423373 GGAGAGAGAGAGAGACCATGCT 60.423 54.545 0.00 0.00 0.00 3.79
786 796 1.956477 GGAGAGAGAGAGAGACCATGC 59.044 57.143 0.00 0.00 0.00 4.06
787 797 2.158827 TCGGAGAGAGAGAGAGACCATG 60.159 54.545 0.00 0.00 0.00 3.66
788 798 2.123589 TCGGAGAGAGAGAGAGACCAT 58.876 52.381 0.00 0.00 0.00 3.55
789 799 1.574263 TCGGAGAGAGAGAGAGACCA 58.426 55.000 0.00 0.00 0.00 4.02
816 826 2.893637 CGGTTGGTTATCTGACTCCAG 58.106 52.381 0.00 0.00 41.74 3.86
864 875 1.138671 CGGCAATTTGTAAGGGGCG 59.861 57.895 0.00 0.00 41.00 6.13
912 926 3.090037 TGTCTAGCTATCGATTAGGGCC 58.910 50.000 1.71 0.00 0.00 5.80
923 937 3.323403 GCTCCTGGTCAATGTCTAGCTAT 59.677 47.826 0.00 0.00 0.00 2.97
983 998 2.113433 ATCTCGTGGACGGACGGAG 61.113 63.158 0.00 0.00 39.88 4.63
1690 1718 1.267261 CTAATCTGGTCTACTCGGCCG 59.733 57.143 22.12 22.12 0.00 6.13
1694 1722 5.927689 AGTACGATCTAATCTGGTCTACTCG 59.072 44.000 0.00 0.00 0.00 4.18
1954 2006 7.418337 AAAACAAAAGTACCCACAGAAGAAT 57.582 32.000 0.00 0.00 0.00 2.40
1956 2008 9.629878 TTATAAAACAAAAGTACCCACAGAAGA 57.370 29.630 0.00 0.00 0.00 2.87
2009 2061 4.044426 AGAGAAAAACGATTGCTTGTTGC 58.956 39.130 0.00 0.00 43.25 4.17
2012 2064 5.758296 TGAGTAGAGAAAAACGATTGCTTGT 59.242 36.000 0.00 0.00 0.00 3.16
2013 2065 6.228273 TGAGTAGAGAAAAACGATTGCTTG 57.772 37.500 0.00 0.00 0.00 4.01
2066 2256 1.899142 ACGGATTTGGGGTTTTGGATG 59.101 47.619 0.00 0.00 0.00 3.51
2067 2257 2.319025 ACGGATTTGGGGTTTTGGAT 57.681 45.000 0.00 0.00 0.00 3.41
2076 2266 4.233789 CACATTTTGTGTACGGATTTGGG 58.766 43.478 0.00 0.00 43.08 4.12
2085 2275 4.677584 TGAACTTGCCACATTTTGTGTAC 58.322 39.130 6.86 0.00 46.45 2.90
2108 2783 1.358725 GGCGTTTCGTATGCAGCTGA 61.359 55.000 20.43 2.70 40.72 4.26
2111 2786 1.003851 TTAGGCGTTTCGTATGCAGC 58.996 50.000 0.00 0.00 40.72 5.25
2124 4162 3.332919 TCTATCTAGCTACCGTTAGGCG 58.667 50.000 0.00 0.00 42.76 5.52
2147 4185 4.474394 CCTCCCTCCGCATATATCTATCA 58.526 47.826 0.00 0.00 0.00 2.15
2155 4193 2.122413 TGCCCTCCCTCCGCATAT 60.122 61.111 0.00 0.00 0.00 1.78
2156 4194 3.161450 GTGCCCTCCCTCCGCATA 61.161 66.667 0.00 0.00 34.51 3.14
2171 4209 1.165270 GGAAATGGTGAACTCGGGTG 58.835 55.000 0.00 0.00 0.00 4.61
2172 4210 1.003233 GAGGAAATGGTGAACTCGGGT 59.997 52.381 0.00 0.00 0.00 5.28
2175 4213 3.045601 AGTGAGGAAATGGTGAACTCG 57.954 47.619 0.00 0.00 0.00 4.18
2210 4248 1.450312 CTGTCATTCCGGTGAGCCC 60.450 63.158 0.00 0.00 0.00 5.19
2218 4256 4.033358 GCAAAGACTATGACTGTCATTCCG 59.967 45.833 26.56 17.43 38.26 4.30
2225 4263 4.446371 GCCTATGCAAAGACTATGACTGT 58.554 43.478 0.00 0.00 37.47 3.55
2227 4265 3.713764 AGGCCTATGCAAAGACTATGACT 59.286 43.478 1.29 0.00 40.13 3.41
2230 4268 3.062763 CGAGGCCTATGCAAAGACTATG 58.937 50.000 4.42 0.00 40.13 2.23
2231 4269 2.037772 CCGAGGCCTATGCAAAGACTAT 59.962 50.000 4.42 0.00 40.13 2.12
2235 4273 0.107703 CACCGAGGCCTATGCAAAGA 60.108 55.000 4.42 0.00 40.13 2.52
2253 4292 1.613630 GAAGACTCCCCTCTGGCCA 60.614 63.158 4.71 4.71 0.00 5.36
2255 4294 0.467804 GATGAAGACTCCCCTCTGGC 59.532 60.000 0.00 0.00 0.00 4.85
2262 4301 1.134965 CCACAGACGATGAAGACTCCC 60.135 57.143 0.00 0.00 0.00 4.30
2272 4311 2.048222 CGCACCACCACAGACGAT 60.048 61.111 0.00 0.00 0.00 3.73
2278 4317 3.625897 CCTCCTCGCACCACCACA 61.626 66.667 0.00 0.00 0.00 4.17
2280 4319 2.997315 CTCCTCCTCGCACCACCA 60.997 66.667 0.00 0.00 0.00 4.17
2308 4361 2.510906 CCCAATGTCTAGCCGGGG 59.489 66.667 2.18 0.00 32.88 5.73
2313 4366 2.124736 TGCCGCCCAATGTCTAGC 60.125 61.111 0.00 0.00 0.00 3.42
2315 4368 0.037590 AAAGTGCCGCCCAATGTCTA 59.962 50.000 0.00 0.00 0.00 2.59
2317 4370 1.102978 ATAAAGTGCCGCCCAATGTC 58.897 50.000 0.00 0.00 0.00 3.06
2321 4374 2.262183 CACATAAAGTGCCGCCCAA 58.738 52.632 0.00 0.00 42.15 4.12
2322 4375 3.995074 CACATAAAGTGCCGCCCA 58.005 55.556 0.00 0.00 42.15 5.36
2330 4383 8.181904 ACAATGTTTCAATCCTCACATAAAGT 57.818 30.769 0.00 0.00 0.00 2.66
2364 5236 9.950680 CTTTACATTGAGTGTTGTAATCAAGTT 57.049 29.630 0.00 0.00 45.36 2.66
2368 5240 6.072175 GCCCTTTACATTGAGTGTTGTAATCA 60.072 38.462 0.00 0.00 42.29 2.57
2369 5241 6.322491 GCCCTTTACATTGAGTGTTGTAATC 58.678 40.000 0.00 0.00 42.29 1.75
2370 5242 5.106317 CGCCCTTTACATTGAGTGTTGTAAT 60.106 40.000 0.00 0.00 42.29 1.89
2372 5244 3.749088 CGCCCTTTACATTGAGTGTTGTA 59.251 43.478 0.00 0.00 42.29 2.41
2373 5245 2.552315 CGCCCTTTACATTGAGTGTTGT 59.448 45.455 0.00 0.00 42.29 3.32
2379 5251 0.034477 ACCCCGCCCTTTACATTGAG 60.034 55.000 0.00 0.00 0.00 3.02
2396 5268 7.821846 TCAGATTTTATGCAAATGGGTAAAACC 59.178 33.333 0.00 0.00 35.02 3.27
2405 5277 7.276878 TCAACATGCTCAGATTTTATGCAAATG 59.723 33.333 0.00 0.00 35.02 2.32
2406 5278 7.277098 GTCAACATGCTCAGATTTTATGCAAAT 59.723 33.333 0.00 0.00 37.84 2.32
2409 5281 5.643664 GTCAACATGCTCAGATTTTATGCA 58.356 37.500 0.00 0.00 38.05 3.96
2410 5282 4.731961 CGTCAACATGCTCAGATTTTATGC 59.268 41.667 0.00 0.00 0.00 3.14
2411 5283 5.735892 CACGTCAACATGCTCAGATTTTATG 59.264 40.000 0.00 0.00 0.00 1.90
2412 5284 5.412594 ACACGTCAACATGCTCAGATTTTAT 59.587 36.000 0.00 0.00 0.00 1.40
2413 5285 4.754618 ACACGTCAACATGCTCAGATTTTA 59.245 37.500 0.00 0.00 0.00 1.52
2419 5291 3.061295 GTGATACACGTCAACATGCTCAG 59.939 47.826 0.00 0.00 0.00 3.35
2421 5293 2.993220 TGTGATACACGTCAACATGCTC 59.007 45.455 0.00 0.00 37.14 4.26
2422 5294 3.038788 TGTGATACACGTCAACATGCT 57.961 42.857 0.00 0.00 37.14 3.79
2425 5297 2.603110 GCGATGTGATACACGTCAACAT 59.397 45.455 19.37 0.00 46.98 2.71
2440 5312 1.291877 GAGAAAGTGTGCGGCGATGT 61.292 55.000 12.98 0.00 0.00 3.06
2441 5313 1.291184 TGAGAAAGTGTGCGGCGATG 61.291 55.000 12.98 0.00 0.00 3.84
2451 5323 2.754472 TCATGTGTCGGTGAGAAAGTG 58.246 47.619 0.00 0.00 0.00 3.16
2487 5359 1.339055 CCGTCTCAAGCCTTCATTCCA 60.339 52.381 0.00 0.00 0.00 3.53
2489 5361 1.373570 CCCGTCTCAAGCCTTCATTC 58.626 55.000 0.00 0.00 0.00 2.67
2491 5363 1.078143 GCCCGTCTCAAGCCTTCAT 60.078 57.895 0.00 0.00 0.00 2.57
2492 5364 2.347490 GCCCGTCTCAAGCCTTCA 59.653 61.111 0.00 0.00 0.00 3.02
2493 5365 2.436824 GGCCCGTCTCAAGCCTTC 60.437 66.667 0.00 0.00 43.62 3.46
2494 5366 4.035102 GGGCCCGTCTCAAGCCTT 62.035 66.667 5.69 0.00 46.31 4.35
2504 5376 2.487274 TAATTCAAAGCCGGGCCCGT 62.487 55.000 40.52 23.10 37.81 5.28
2505 5377 1.316706 TTAATTCAAAGCCGGGCCCG 61.317 55.000 37.99 37.99 39.44 6.13
2506 5378 0.174845 GTTAATTCAAAGCCGGGCCC 59.825 55.000 17.02 13.57 0.00 5.80
2509 5381 4.811557 TGTTTTTGTTAATTCAAAGCCGGG 59.188 37.500 2.18 0.00 38.32 5.73
2513 5385 7.582319 CGGTTGATGTTTTTGTTAATTCAAAGC 59.418 33.333 0.00 0.00 38.32 3.51
2530 5402 2.166870 TGTATTCGTAGCCGGTTGATGT 59.833 45.455 1.90 0.00 33.95 3.06
2536 5408 0.313043 CCGATGTATTCGTAGCCGGT 59.687 55.000 1.90 0.00 46.65 5.28
2583 5455 2.910319 GGGGTTTAATGGCCTCCTTTTT 59.090 45.455 3.32 0.00 0.00 1.94
2588 5460 1.485124 CTTGGGGTTTAATGGCCTCC 58.515 55.000 3.32 0.00 0.00 4.30
2589 5461 0.824109 GCTTGGGGTTTAATGGCCTC 59.176 55.000 3.32 0.00 0.00 4.70
2590 5462 0.116143 TGCTTGGGGTTTAATGGCCT 59.884 50.000 3.32 0.00 0.00 5.19
2601 5474 2.632512 ACCTTGTATTTGTTGCTTGGGG 59.367 45.455 0.00 0.00 0.00 4.96
2608 5481 3.715495 TGCTTGCACCTTGTATTTGTTG 58.285 40.909 0.00 0.00 0.00 3.33
2646 5519 7.217200 TCTTAGTAGTTGCTTGTGATGTCTTT 58.783 34.615 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.