Multiple sequence alignment - TraesCS5B01G196300

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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 TraesCS5B01G196300 chr5B 100.000 2799 0 0 1 2799 353988668 353985870 0.000000e+00 5169.0
1 TraesCS5B01G196300 chr5B 95.238 42 1 1 697 738 271956695 271956655 6.470000e-07 65.8
2 TraesCS5B01G196300 chr5D 90.590 1764 94 40 337 2071 308651077 308649357 0.000000e+00 2272.0
3 TraesCS5B01G196300 chr5D 85.794 718 64 17 2109 2799 308649362 308648656 0.000000e+00 726.0
4 TraesCS5B01G196300 chr5D 89.362 235 20 3 1 231 308651307 308651074 9.810000e-75 291.0
5 TraesCS5B01G196300 chr5D 95.122 41 0 2 697 737 389033716 389033678 2.330000e-06 63.9
6 TraesCS5B01G196300 chr5A 90.354 1327 75 27 765 2076 389153301 389154589 0.000000e+00 1692.0
7 TraesCS5B01G196300 chr5A 87.379 618 64 5 1 607 389147246 389147860 0.000000e+00 697.0
8 TraesCS5B01G196300 chr7D 95.122 41 1 1 692 732 5659955 5659994 2.330000e-06 63.9
9 TraesCS5B01G196300 chr7D 91.304 46 3 1 688 732 38011339 38011384 8.370000e-06 62.1
10 TraesCS5B01G196300 chr1B 97.297 37 1 0 697 733 136627090 136627054 2.330000e-06 63.9
11 TraesCS5B01G196300 chr3B 97.297 37 0 1 698 734 806504479 806504444 8.370000e-06 62.1
12 TraesCS5B01G196300 chr4A 92.683 41 3 0 692 732 250959793 250959753 3.010000e-05 60.2
13 TraesCS5B01G196300 chr4A 92.857 42 1 2 697 738 743443510 743443471 3.010000e-05 60.2
14 TraesCS5B01G196300 chr2D 97.143 35 1 0 697 731 613817967 613818001 3.010000e-05 60.2


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 TraesCS5B01G196300 chr5B 353985870 353988668 2798 True 5169.000000 5169 100.000 1 2799 1 chr5B.!!$R2 2798
1 TraesCS5B01G196300 chr5D 308648656 308651307 2651 True 1096.333333 2272 88.582 1 2799 3 chr5D.!!$R2 2798
2 TraesCS5B01G196300 chr5A 389153301 389154589 1288 False 1692.000000 1692 90.354 765 2076 1 chr5A.!!$F2 1311
3 TraesCS5B01G196300 chr5A 389147246 389147860 614 False 697.000000 697 87.379 1 607 1 chr5A.!!$F1 606

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
48 49 0.110644 GCAAGACCGCGAACTTCTTG 60.111 55.0 23.75 23.75 46.06 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2080 0.620556 TCATTTGTCCTGAGAGGGGC 59.379 55.0 0.0 0.0 35.59 5.8 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
48 49 0.110644 GCAAGACCGCGAACTTCTTG 60.111 55.000 23.75 23.75 46.06 3.02
55 56 1.067199 CGCGAACTTCTTGCCATTGC 61.067 55.000 0.00 0.00 38.26 3.56
65 66 3.689347 TCTTGCCATTGCTACATTGTCT 58.311 40.909 0.00 0.00 38.71 3.41
66 67 4.081406 TCTTGCCATTGCTACATTGTCTT 58.919 39.130 0.00 0.00 38.71 3.01
73 74 3.334583 TGCTACATTGTCTTGAGGACC 57.665 47.619 0.00 0.00 43.89 4.46
75 76 2.027192 GCTACATTGTCTTGAGGACCCA 60.027 50.000 0.00 0.00 43.89 4.51
105 106 2.760374 GCCAATATCCTCCTCAACTCG 58.240 52.381 0.00 0.00 0.00 4.18
134 135 1.139058 CTAAGCAATAGTGGACCGCCT 59.861 52.381 0.08 0.00 34.31 5.52
145 146 2.096980 GTGGACCGCCTGCTAAAAATAC 59.903 50.000 0.00 0.00 34.31 1.89
146 147 2.290387 TGGACCGCCTGCTAAAAATACA 60.290 45.455 0.00 0.00 34.31 2.29
147 148 2.096980 GGACCGCCTGCTAAAAATACAC 59.903 50.000 0.00 0.00 0.00 2.90
161 162 1.308998 ATACACGGCTAATGCTTGGC 58.691 50.000 0.00 0.00 39.59 4.52
229 232 3.061429 GCTTCGTGAATAAGCACTGAGAC 59.939 47.826 3.07 0.00 46.85 3.36
230 233 3.232213 TCGTGAATAAGCACTGAGACC 57.768 47.619 0.00 0.00 36.65 3.85
232 235 2.093973 CGTGAATAAGCACTGAGACCCT 60.094 50.000 0.00 0.00 36.65 4.34
234 237 2.501723 TGAATAAGCACTGAGACCCTCC 59.498 50.000 0.00 0.00 0.00 4.30
235 238 1.115467 ATAAGCACTGAGACCCTCCG 58.885 55.000 0.00 0.00 0.00 4.63
236 239 1.605058 TAAGCACTGAGACCCTCCGC 61.605 60.000 0.00 0.00 0.00 5.54
237 240 3.695606 GCACTGAGACCCTCCGCA 61.696 66.667 0.00 0.00 0.00 5.69
245 250 0.689080 AGACCCTCCGCACAGATGAT 60.689 55.000 0.00 0.00 0.00 2.45
246 251 0.179000 GACCCTCCGCACAGATGATT 59.821 55.000 0.00 0.00 0.00 2.57
274 279 0.396417 TGGCTAGAGCAGGTCTCCTC 60.396 60.000 5.10 0.00 42.90 3.71
275 280 0.396417 GGCTAGAGCAGGTCTCCTCA 60.396 60.000 5.10 0.00 42.90 3.86
287 292 2.229792 GTCTCCTCAATGCAAACCACA 58.770 47.619 0.00 0.00 0.00 4.17
288 293 2.821969 GTCTCCTCAATGCAAACCACAT 59.178 45.455 0.00 0.00 0.00 3.21
302 307 7.946207 TGCAAACCACATAAAAGACTAATTCA 58.054 30.769 0.00 0.00 0.00 2.57
308 313 8.462016 ACCACATAAAAGACTAATTCATTCAGC 58.538 33.333 0.00 0.00 0.00 4.26
309 314 8.461222 CCACATAAAAGACTAATTCATTCAGCA 58.539 33.333 0.00 0.00 0.00 4.41
327 332 1.810412 GCATAGCCTCCACTAAACCCG 60.810 57.143 0.00 0.00 0.00 5.28
334 339 3.626217 GCCTCCACTAAACCCGATTTTAG 59.374 47.826 11.90 11.90 42.50 1.85
356 361 2.158957 TGACACACTTCAACTCAGACCC 60.159 50.000 0.00 0.00 0.00 4.46
358 363 0.393077 ACACTTCAACTCAGACCCGG 59.607 55.000 0.00 0.00 0.00 5.73
468 479 3.432890 GCCCCTCCTCTTCTTGTATTCAG 60.433 52.174 0.00 0.00 0.00 3.02
469 480 3.777522 CCCCTCCTCTTCTTGTATTCAGT 59.222 47.826 0.00 0.00 0.00 3.41
485 496 6.592607 TGTATTCAGTAGGAAATTTGACGTCC 59.407 38.462 14.12 0.00 39.39 4.79
519 533 4.000988 ACATTGGTAGTGATGAAACGTCC 58.999 43.478 0.00 0.00 0.00 4.79
535 555 1.074775 TCCCGGCATGAAAGCACTT 59.925 52.632 0.00 0.00 35.83 3.16
536 556 0.539438 TCCCGGCATGAAAGCACTTT 60.539 50.000 0.00 0.00 35.83 2.66
537 557 0.388907 CCCGGCATGAAAGCACTTTG 60.389 55.000 0.00 0.00 35.83 2.77
538 558 0.388907 CCGGCATGAAAGCACTTTGG 60.389 55.000 0.00 0.00 35.83 3.28
539 559 0.314935 CGGCATGAAAGCACTTTGGT 59.685 50.000 0.00 0.00 35.83 3.67
540 560 1.269726 CGGCATGAAAGCACTTTGGTT 60.270 47.619 0.00 0.00 40.14 3.67
558 578 6.945938 TTGGTTCTTTGAAATAACCTTCGA 57.054 33.333 21.04 3.61 42.60 3.71
595 615 0.662619 TGTTCGCAAGCACCTTTGAG 59.337 50.000 0.00 0.00 30.22 3.02
608 628 9.817809 CAAGCACCTTTGAGACTAACTTATATA 57.182 33.333 0.00 0.00 0.00 0.86
609 629 9.819267 AAGCACCTTTGAGACTAACTTATATAC 57.181 33.333 0.00 0.00 0.00 1.47
610 630 8.978472 AGCACCTTTGAGACTAACTTATATACA 58.022 33.333 0.00 0.00 0.00 2.29
634 659 4.796038 ATTGCATATGCTAATTGGCCTC 57.204 40.909 27.13 0.00 42.66 4.70
657 711 7.663493 CCTCATATCCTTTATTCTCTTGGGTTC 59.337 40.741 0.00 0.00 0.00 3.62
676 730 4.089361 GTTCTTTGACCTTGGGGATCAAT 58.911 43.478 0.00 0.00 34.84 2.57
686 740 4.080356 CCTTGGGGATCAATACAACAGAGA 60.080 45.833 0.00 0.00 34.45 3.10
692 746 7.567250 TGGGGATCAATACAACAGAGATACTTA 59.433 37.037 0.00 0.00 0.00 2.24
693 747 8.429641 GGGGATCAATACAACAGAGATACTTAA 58.570 37.037 0.00 0.00 0.00 1.85
721 775 7.964604 AAAGAACGCTCTTATATTATGGGAC 57.035 36.000 0.67 0.00 41.23 4.46
722 776 5.710984 AGAACGCTCTTATATTATGGGACG 58.289 41.667 0.00 0.00 0.00 4.79
723 777 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
724 778 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
725 779 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
726 780 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
727 781 4.466726 GCTCTTATATTATGGGACGGAGGT 59.533 45.833 0.00 0.00 0.00 3.85
728 782 5.655532 GCTCTTATATTATGGGACGGAGGTA 59.344 44.000 0.00 0.00 0.00 3.08
729 783 6.183360 GCTCTTATATTATGGGACGGAGGTAG 60.183 46.154 0.00 0.00 0.00 3.18
730 784 6.797707 TCTTATATTATGGGACGGAGGTAGT 58.202 40.000 0.00 0.00 0.00 2.73
731 785 7.932134 TCTTATATTATGGGACGGAGGTAGTA 58.068 38.462 0.00 0.00 0.00 1.82
732 786 7.831193 TCTTATATTATGGGACGGAGGTAGTAC 59.169 40.741 0.00 0.00 0.00 2.73
733 787 3.959495 TTATGGGACGGAGGTAGTACT 57.041 47.619 0.00 0.00 0.00 2.73
734 788 2.361643 ATGGGACGGAGGTAGTACTC 57.638 55.000 0.00 0.00 36.76 2.59
735 789 1.293062 TGGGACGGAGGTAGTACTCT 58.707 55.000 0.00 0.00 37.63 3.24
739 793 3.513119 GGGACGGAGGTAGTACTCTTTTT 59.487 47.826 0.00 0.00 37.63 1.94
784 838 2.034179 CACCCGAGGAAAGAACAAAACC 59.966 50.000 0.00 0.00 0.00 3.27
893 947 1.506718 GCCGAAAAGCCCTACAAGC 59.493 57.895 0.00 0.00 0.00 4.01
986 1040 6.101296 TCCTCTATATATCCCAGTCTCGCATA 59.899 42.308 0.00 0.00 0.00 3.14
1066 1120 0.601311 GAAAGATCCCCGCATCCTCG 60.601 60.000 0.00 0.00 0.00 4.63
1104 1158 6.849588 ACAGATTTTGGCAAGTTGAATTTC 57.150 33.333 7.16 0.00 0.00 2.17
1119 1173 7.147976 AGTTGAATTTCAGTTTTAGCATGGAC 58.852 34.615 0.00 0.00 0.00 4.02
1359 1416 3.739922 TCCACCGCCATGGAGAAT 58.260 55.556 18.40 0.37 44.14 2.40
1567 1625 3.105937 CGAAGATCGCGTTGATGAACTA 58.894 45.455 5.77 0.00 37.47 2.24
1568 1626 3.546271 CGAAGATCGCGTTGATGAACTAA 59.454 43.478 5.77 0.00 37.47 2.24
1572 1630 4.929808 AGATCGCGTTGATGAACTAAAGTT 59.070 37.500 5.77 0.00 38.06 2.66
1835 1903 8.821686 ATCGGTGATAGAATCATAGAGAGATT 57.178 34.615 0.00 0.00 42.04 2.40
1879 1947 1.472728 CCTTGCGATGTACCTACCACC 60.473 57.143 0.00 0.00 0.00 4.61
1881 1949 0.615261 TGCGATGTACCTACCACCCA 60.615 55.000 0.00 0.00 0.00 4.51
1882 1950 0.756903 GCGATGTACCTACCACCCAT 59.243 55.000 0.00 0.00 0.00 4.00
1883 1951 1.540363 GCGATGTACCTACCACCCATG 60.540 57.143 0.00 0.00 0.00 3.66
1894 1971 2.676748 ACCACCCATGTGTCATGTTTT 58.323 42.857 8.57 0.00 41.09 2.43
1895 1972 2.627699 ACCACCCATGTGTCATGTTTTC 59.372 45.455 8.57 0.00 41.09 2.29
1905 1982 8.667463 CCATGTGTCATGTTTTCTTTTCTTTTT 58.333 29.630 8.57 0.00 0.00 1.94
1927 2004 1.002274 AGAGCTTCGACCCCTCCAT 59.998 57.895 0.00 0.00 0.00 3.41
1979 2056 2.063266 TGTGTTGTTATCGCGTCCTTC 58.937 47.619 5.77 0.00 0.00 3.46
2004 2081 3.847621 GCCAATTCTAGGGCCTGC 58.152 61.111 18.53 4.95 44.53 4.85
2117 2194 8.474006 AAAAATGTAGCCGAAAATTAATCCAC 57.526 30.769 0.00 0.00 0.00 4.02
2118 2195 6.767524 AATGTAGCCGAAAATTAATCCACA 57.232 33.333 0.00 0.00 0.00 4.17
2121 2198 5.650266 TGTAGCCGAAAATTAATCCACATGT 59.350 36.000 0.00 0.00 0.00 3.21
2122 2199 4.997565 AGCCGAAAATTAATCCACATGTG 58.002 39.130 19.31 19.31 0.00 3.21
2125 2202 5.036737 CCGAAAATTAATCCACATGTGCTC 58.963 41.667 20.81 4.22 0.00 4.26
2127 2204 6.324819 CGAAAATTAATCCACATGTGCTCTT 58.675 36.000 20.81 14.17 0.00 2.85
2132 2209 4.510038 AATCCACATGTGCTCTTGTTTC 57.490 40.909 20.81 0.00 31.09 2.78
2172 2250 0.531532 CACGGGCATCATCTCACCTC 60.532 60.000 0.00 0.00 0.00 3.85
2177 2255 1.211457 GGCATCATCTCACCTCAGGTT 59.789 52.381 0.00 0.00 31.02 3.50
2179 2257 2.093288 GCATCATCTCACCTCAGGTTGA 60.093 50.000 0.00 0.00 31.02 3.18
2180 2258 3.433314 GCATCATCTCACCTCAGGTTGAT 60.433 47.826 3.21 3.21 31.02 2.57
2181 2259 4.778579 CATCATCTCACCTCAGGTTGATT 58.221 43.478 6.06 0.00 31.02 2.57
2182 2260 4.478206 TCATCTCACCTCAGGTTGATTC 57.522 45.455 0.00 0.00 31.02 2.52
2183 2261 4.099633 TCATCTCACCTCAGGTTGATTCT 58.900 43.478 0.00 0.00 31.02 2.40
2184 2262 4.533707 TCATCTCACCTCAGGTTGATTCTT 59.466 41.667 0.00 0.00 31.02 2.52
2185 2263 4.982241 TCTCACCTCAGGTTGATTCTTT 57.018 40.909 0.00 0.00 31.02 2.52
2186 2264 5.310409 TCTCACCTCAGGTTGATTCTTTT 57.690 39.130 0.00 0.00 31.02 2.27
2187 2265 5.694995 TCTCACCTCAGGTTGATTCTTTTT 58.305 37.500 0.00 0.00 31.02 1.94
2244 2323 6.812160 CAGTATGGAGGTAGTACTTCACAAAC 59.188 42.308 13.79 6.55 0.00 2.93
2269 2348 1.192980 GTGCAAATTTTTGAGCTGCCG 59.807 47.619 7.21 0.00 40.55 5.69
2271 2350 1.866601 GCAAATTTTTGAGCTGCCGTT 59.133 42.857 7.21 0.00 40.55 4.44
2278 2357 1.803334 TTGAGCTGCCGTTATTTCGT 58.197 45.000 0.00 0.00 0.00 3.85
2285 2364 3.064271 GCTGCCGTTATTTCGTTATCCAA 59.936 43.478 0.00 0.00 0.00 3.53
2286 2365 4.785341 GCTGCCGTTATTTCGTTATCCAAG 60.785 45.833 0.00 0.00 0.00 3.61
2299 2378 6.696411 TCGTTATCCAAGGCAAATTTCAATT 58.304 32.000 0.00 0.00 0.00 2.32
2304 2383 7.910441 ATCCAAGGCAAATTTCAATTTACAG 57.090 32.000 0.00 0.00 36.52 2.74
2313 2392 8.011673 GCAAATTTCAATTTACAGCCTTCTTTC 58.988 33.333 0.00 0.00 36.52 2.62
2324 2403 1.199327 GCCTTCTTTCGGTACTTTGCC 59.801 52.381 0.00 0.00 0.00 4.52
2337 2416 1.340114 ACTTTGCCGAAGAGGGGAATC 60.340 52.381 0.00 0.00 37.25 2.52
2369 2448 7.559486 TGTTCATCTACATTTGCTCTATGAGT 58.441 34.615 0.00 0.00 31.39 3.41
2383 2462 5.459536 TCTATGAGTAGTCCATCACATGC 57.540 43.478 0.00 0.00 0.00 4.06
2391 2470 7.669722 TGAGTAGTCCATCACATGCACTATATA 59.330 37.037 0.00 0.00 0.00 0.86
2485 2566 7.304735 CAGGAAGATGATGTAGTTAGAGATCG 58.695 42.308 0.00 0.00 0.00 3.69
2500 2581 8.132362 AGTTAGAGATCGCAACTTCAAGTATAG 58.868 37.037 0.00 0.00 0.00 1.31
2508 2589 5.980116 CGCAACTTCAAGTATAGCACTAGAT 59.020 40.000 0.00 0.00 36.04 1.98
2510 2591 6.758886 GCAACTTCAAGTATAGCACTAGATGT 59.241 38.462 0.00 0.00 36.04 3.06
2522 2603 2.414481 CACTAGATGTGCAGTCTTGTGC 59.586 50.000 21.62 0.00 40.56 4.57
2531 2612 0.504384 CAGTCTTGTGCGTCGAAGTG 59.496 55.000 0.00 0.00 0.00 3.16
2544 2625 0.600255 CGAAGTGGAGTTGGCGAAGT 60.600 55.000 0.00 0.00 0.00 3.01
2553 2634 1.145803 GTTGGCGAAGTGTGTCTACC 58.854 55.000 0.00 0.00 0.00 3.18
2554 2635 0.319211 TTGGCGAAGTGTGTCTACCG 60.319 55.000 0.00 0.00 0.00 4.02
2560 2654 2.349580 CGAAGTGTGTCTACCGTCGATA 59.650 50.000 0.00 0.00 34.03 2.92
2563 2657 3.538591 AGTGTGTCTACCGTCGATATCA 58.461 45.455 3.12 0.00 0.00 2.15
2573 2667 4.755411 ACCGTCGATATCATGAACAGTTT 58.245 39.130 0.00 0.00 0.00 2.66
2574 2668 4.566759 ACCGTCGATATCATGAACAGTTTG 59.433 41.667 0.00 0.00 0.00 2.93
2620 2722 6.142818 TGTACAAAATTGAAGTGAGTTGGG 57.857 37.500 0.00 0.00 0.00 4.12
2621 2723 4.058721 ACAAAATTGAAGTGAGTTGGGC 57.941 40.909 0.00 0.00 0.00 5.36
2625 2727 2.032681 GAAGTGAGTTGGGCGGCT 59.967 61.111 9.56 0.00 0.00 5.52
2650 2752 2.032799 CGCTAGCAACTCCAAACAACAA 59.967 45.455 16.45 0.00 0.00 2.83
2651 2753 3.372060 GCTAGCAACTCCAAACAACAAC 58.628 45.455 10.63 0.00 0.00 3.32
2656 2758 3.734902 GCAACTCCAAACAACAACTCAGG 60.735 47.826 0.00 0.00 0.00 3.86
2678 2780 2.692741 GGAGGCACCCTAGGGCTT 60.693 66.667 28.88 11.28 41.74 4.35
2681 2783 1.977293 GAGGCACCCTAGGGCTTCTG 61.977 65.000 28.88 19.11 41.74 3.02
2687 2789 0.256177 CCCTAGGGCTTCTGAAACCC 59.744 60.000 16.90 19.09 44.62 4.11
2691 2793 3.571748 GGGCTTCTGAAACCCTACC 57.428 57.895 19.37 2.08 40.75 3.18
2746 2848 2.520968 GTTTGGTGCACCCCCTCT 59.479 61.111 32.62 0.00 34.29 3.69
2754 2856 2.241430 GGTGCACCCCCTCTACTATTTT 59.759 50.000 26.31 0.00 0.00 1.82
2760 2862 4.973211 CACCCCCTCTACTATTTTCCCTAA 59.027 45.833 0.00 0.00 0.00 2.69
2791 2893 1.406898 GCCAAATTAGCCTGCTCCTTC 59.593 52.381 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.668151 GGCAAGAAGTTCGCGGTCT 60.668 57.895 6.13 1.64 0.00 3.85
48 49 3.181493 CCTCAAGACAATGTAGCAATGGC 60.181 47.826 0.00 0.00 41.61 4.40
65 66 2.093869 GCGTTGTACTATGGGTCCTCAA 60.094 50.000 0.00 0.00 0.00 3.02
66 67 1.479323 GCGTTGTACTATGGGTCCTCA 59.521 52.381 0.00 0.00 0.00 3.86
73 74 4.894784 AGGATATTGGCGTTGTACTATGG 58.105 43.478 0.00 0.00 0.00 2.74
75 76 4.838986 AGGAGGATATTGGCGTTGTACTAT 59.161 41.667 0.00 0.00 0.00 2.12
105 106 2.808543 CACTATTGCTTAGGCGGAATCC 59.191 50.000 0.00 0.00 42.25 3.01
112 113 1.583054 CGGTCCACTATTGCTTAGGC 58.417 55.000 0.00 0.00 39.26 3.93
134 135 4.638421 AGCATTAGCCGTGTATTTTTAGCA 59.362 37.500 0.00 0.00 43.56 3.49
145 146 1.137404 GTGCCAAGCATTAGCCGTG 59.863 57.895 0.00 0.00 41.91 4.94
146 147 2.046285 GGTGCCAAGCATTAGCCGT 61.046 57.895 0.00 0.00 41.91 5.68
147 148 1.718757 GAGGTGCCAAGCATTAGCCG 61.719 60.000 0.00 0.00 41.91 5.52
161 162 3.136808 GCTAAAATTTGCGAGGAGGTG 57.863 47.619 0.00 0.00 0.00 4.00
229 232 1.541233 GGTAATCATCTGTGCGGAGGG 60.541 57.143 0.00 0.00 0.00 4.30
230 233 1.138859 TGGTAATCATCTGTGCGGAGG 59.861 52.381 0.00 0.00 0.00 4.30
232 235 3.342377 TTTGGTAATCATCTGTGCGGA 57.658 42.857 0.00 0.00 0.00 5.54
234 237 5.692814 CCATATTTGGTAATCATCTGTGCG 58.307 41.667 0.00 0.00 38.30 5.34
235 238 5.242393 AGCCATATTTGGTAATCATCTGTGC 59.758 40.000 4.00 0.00 45.57 4.57
236 239 6.889301 AGCCATATTTGGTAATCATCTGTG 57.111 37.500 4.00 0.00 45.57 3.66
237 240 7.977818 TCTAGCCATATTTGGTAATCATCTGT 58.022 34.615 4.00 0.00 45.57 3.41
245 250 4.412199 ACCTGCTCTAGCCATATTTGGTAA 59.588 41.667 4.00 0.00 45.57 2.85
246 251 3.973973 ACCTGCTCTAGCCATATTTGGTA 59.026 43.478 4.00 0.00 45.57 3.25
274 279 8.761575 ATTAGTCTTTTATGTGGTTTGCATTG 57.238 30.769 0.00 0.00 0.00 2.82
275 280 9.423061 GAATTAGTCTTTTATGTGGTTTGCATT 57.577 29.630 0.00 0.00 0.00 3.56
288 293 8.840321 GGCTATGCTGAATGAATTAGTCTTTTA 58.160 33.333 0.00 0.00 0.00 1.52
302 307 4.455606 GTTTAGTGGAGGCTATGCTGAAT 58.544 43.478 0.00 0.00 0.00 2.57
308 313 1.760613 TCGGGTTTAGTGGAGGCTATG 59.239 52.381 0.00 0.00 0.00 2.23
309 314 2.170012 TCGGGTTTAGTGGAGGCTAT 57.830 50.000 0.00 0.00 0.00 2.97
310 315 2.170012 ATCGGGTTTAGTGGAGGCTA 57.830 50.000 0.00 0.00 0.00 3.93
327 332 7.224753 TCTGAGTTGAAGTGTGTCACTAAAATC 59.775 37.037 4.27 9.66 44.62 2.17
334 339 2.866762 GGTCTGAGTTGAAGTGTGTCAC 59.133 50.000 0.00 0.00 34.10 3.67
356 361 2.297597 TGAGTAAAATGGGGTTTTGCCG 59.702 45.455 0.00 0.00 41.57 5.69
358 363 4.600692 AGTGAGTAAAATGGGGTTTTGC 57.399 40.909 0.00 0.00 40.17 3.68
407 412 2.076863 AGCAAACATTGGCTACGACTC 58.923 47.619 0.00 0.00 38.90 3.36
468 479 4.814771 CCTATGGGACGTCAAATTTCCTAC 59.185 45.833 18.91 0.00 33.58 3.18
469 480 4.685030 GCCTATGGGACGTCAAATTTCCTA 60.685 45.833 18.91 0.00 33.58 2.94
519 533 0.388907 CCAAAGTGCTTTCATGCCGG 60.389 55.000 0.00 0.00 0.00 6.13
535 555 6.945938 TCGAAGGTTATTTCAAAGAACCAA 57.054 33.333 25.09 7.90 44.29 3.67
536 556 6.945938 TTCGAAGGTTATTTCAAAGAACCA 57.054 33.333 25.09 5.06 44.29 3.67
537 557 7.423199 ACTTTCGAAGGTTATTTCAAAGAACC 58.577 34.615 17.52 17.52 42.54 3.62
538 558 9.378597 GTACTTTCGAAGGTTATTTCAAAGAAC 57.621 33.333 18.63 0.00 33.87 3.01
539 559 8.562052 GGTACTTTCGAAGGTTATTTCAAAGAA 58.438 33.333 18.63 0.00 33.87 2.52
540 560 7.716123 TGGTACTTTCGAAGGTTATTTCAAAGA 59.284 33.333 18.63 0.00 33.87 2.52
558 578 4.929808 CGAACATAGTGAAGCTGGTACTTT 59.070 41.667 3.50 0.00 0.00 2.66
608 628 6.211986 AGGCCAATTAGCATATGCAATATTGT 59.788 34.615 28.62 14.70 45.16 2.71
609 629 6.636705 AGGCCAATTAGCATATGCAATATTG 58.363 36.000 28.62 27.13 45.16 1.90
610 630 6.438108 TGAGGCCAATTAGCATATGCAATATT 59.562 34.615 28.62 19.72 45.16 1.28
612 632 5.323581 TGAGGCCAATTAGCATATGCAATA 58.676 37.500 28.62 13.81 45.16 1.90
631 656 7.084268 ACCCAAGAGAATAAAGGATATGAGG 57.916 40.000 0.00 0.00 0.00 3.86
634 659 8.986929 AAGAACCCAAGAGAATAAAGGATATG 57.013 34.615 0.00 0.00 0.00 1.78
657 711 4.599041 TGTATTGATCCCCAAGGTCAAAG 58.401 43.478 0.00 0.00 38.31 2.77
695 749 9.654663 GTCCCATAATATAAGAGCGTTCTTTAT 57.345 33.333 19.95 13.42 40.79 1.40
696 750 7.811236 CGTCCCATAATATAAGAGCGTTCTTTA 59.189 37.037 19.95 11.90 40.79 1.85
697 751 6.645415 CGTCCCATAATATAAGAGCGTTCTTT 59.355 38.462 19.95 10.21 40.79 2.52
698 752 6.157211 CGTCCCATAATATAAGAGCGTTCTT 58.843 40.000 18.78 18.78 45.45 2.52
699 753 5.336531 CCGTCCCATAATATAAGAGCGTTCT 60.337 44.000 0.00 0.00 34.29 3.01
700 754 4.863131 CCGTCCCATAATATAAGAGCGTTC 59.137 45.833 0.00 0.00 0.00 3.95
701 755 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
702 756 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
703 757 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
704 758 4.466726 ACCTCCGTCCCATAATATAAGAGC 59.533 45.833 0.00 0.00 0.00 4.09
705 759 6.890814 ACTACCTCCGTCCCATAATATAAGAG 59.109 42.308 0.00 0.00 0.00 2.85
706 760 6.797707 ACTACCTCCGTCCCATAATATAAGA 58.202 40.000 0.00 0.00 0.00 2.10
707 761 7.833183 AGTACTACCTCCGTCCCATAATATAAG 59.167 40.741 0.00 0.00 0.00 1.73
708 762 7.702785 AGTACTACCTCCGTCCCATAATATAA 58.297 38.462 0.00 0.00 0.00 0.98
709 763 7.183475 AGAGTACTACCTCCGTCCCATAATATA 59.817 40.741 0.00 0.00 31.53 0.86
710 764 6.011805 AGAGTACTACCTCCGTCCCATAATAT 60.012 42.308 0.00 0.00 31.53 1.28
711 765 5.311649 AGAGTACTACCTCCGTCCCATAATA 59.688 44.000 0.00 0.00 31.53 0.98
712 766 4.106019 AGAGTACTACCTCCGTCCCATAAT 59.894 45.833 0.00 0.00 31.53 1.28
713 767 3.461085 AGAGTACTACCTCCGTCCCATAA 59.539 47.826 0.00 0.00 31.53 1.90
714 768 3.051581 AGAGTACTACCTCCGTCCCATA 58.948 50.000 0.00 0.00 31.53 2.74
715 769 1.851653 AGAGTACTACCTCCGTCCCAT 59.148 52.381 0.00 0.00 31.53 4.00
716 770 1.293062 AGAGTACTACCTCCGTCCCA 58.707 55.000 0.00 0.00 31.53 4.37
717 771 2.433662 AAGAGTACTACCTCCGTCCC 57.566 55.000 0.00 0.00 31.53 4.46
718 772 4.797800 AAAAAGAGTACTACCTCCGTCC 57.202 45.455 0.00 0.00 31.53 4.79
739 793 4.819105 ATGACACCTCTGTTCGGATAAA 57.181 40.909 0.00 0.00 0.00 1.40
756 810 1.278127 TCTTTCCTCGGGTGGAATGAC 59.722 52.381 11.72 0.00 44.55 3.06
758 812 2.084546 GTTCTTTCCTCGGGTGGAATG 58.915 52.381 3.30 6.16 44.55 2.67
770 824 4.327898 GTGTTTTCCGGTTTTGTTCTTTCC 59.672 41.667 0.00 0.00 0.00 3.13
784 838 4.887763 TCGTTTTGTTTTGTGTTTTCCG 57.112 36.364 0.00 0.00 0.00 4.30
842 896 2.202756 GACCCGGCAACTCTAGCG 60.203 66.667 0.00 0.00 0.00 4.26
853 907 0.249573 ACGGCAATAATACGACCCGG 60.250 55.000 0.00 0.00 39.96 5.73
893 947 2.995450 GCACGCAGTAACACGACGG 61.995 63.158 0.00 0.00 41.61 4.79
1066 1120 6.480981 CCAAAATCTGTATGCCAATGGAATTC 59.519 38.462 2.05 0.00 31.22 2.17
1104 1158 3.120199 CGAACCTGTCCATGCTAAAACTG 60.120 47.826 0.00 0.00 0.00 3.16
1119 1173 1.883084 GACCATAGCGGCGAACCTG 60.883 63.158 12.98 1.22 39.03 4.00
1438 1495 4.388499 GAAGCCAACGCCCCTCGA 62.388 66.667 0.00 0.00 41.67 4.04
1835 1903 6.320164 GGTTGTGGCAATATATGGTGAAACTA 59.680 38.462 0.00 0.00 36.74 2.24
1879 1947 7.775397 AAAGAAAAGAAAACATGACACATGG 57.225 32.000 14.70 0.00 0.00 3.66
1894 1971 7.095187 GGTCGAAGCTCTCATAAAAAGAAAAGA 60.095 37.037 0.00 0.00 0.00 2.52
1895 1972 7.018235 GGTCGAAGCTCTCATAAAAAGAAAAG 58.982 38.462 0.00 0.00 0.00 2.27
1905 1982 1.693627 GAGGGGTCGAAGCTCTCATA 58.306 55.000 8.47 0.00 0.00 2.15
1927 2004 3.452755 ACACAATGCTACGCTATGCTA 57.547 42.857 0.00 0.00 0.00 3.49
1979 2056 1.571919 CCTAGAATTGGCGGTCGAAG 58.428 55.000 0.00 0.00 0.00 3.79
2003 2080 0.620556 TCATTTGTCCTGAGAGGGGC 59.379 55.000 0.00 0.00 35.59 5.80
2004 2081 3.439857 TTTCATTTGTCCTGAGAGGGG 57.560 47.619 0.00 0.00 35.59 4.79
2007 2084 5.334724 GCTGACTTTTCATTTGTCCTGAGAG 60.335 44.000 0.00 0.00 0.00 3.20
2008 2085 4.516698 GCTGACTTTTCATTTGTCCTGAGA 59.483 41.667 0.00 0.00 0.00 3.27
2009 2086 4.276678 TGCTGACTTTTCATTTGTCCTGAG 59.723 41.667 0.00 0.00 0.00 3.35
2010 2087 4.036734 GTGCTGACTTTTCATTTGTCCTGA 59.963 41.667 0.00 0.00 0.00 3.86
2012 2089 3.953612 TGTGCTGACTTTTCATTTGTCCT 59.046 39.130 0.00 0.00 0.00 3.85
2015 2092 5.266733 ACATGTGCTGACTTTTCATTTGT 57.733 34.783 0.00 0.00 0.00 2.83
2092 2169 8.091449 TGTGGATTAATTTTCGGCTACATTTTT 58.909 29.630 0.00 0.00 0.00 1.94
2093 2170 7.607250 TGTGGATTAATTTTCGGCTACATTTT 58.393 30.769 0.00 0.00 0.00 1.82
2094 2171 7.164230 TGTGGATTAATTTTCGGCTACATTT 57.836 32.000 0.00 0.00 0.00 2.32
2095 2172 6.767524 TGTGGATTAATTTTCGGCTACATT 57.232 33.333 0.00 0.00 0.00 2.71
2096 2173 6.321181 ACATGTGGATTAATTTTCGGCTACAT 59.679 34.615 0.00 0.00 0.00 2.29
2097 2174 5.650266 ACATGTGGATTAATTTTCGGCTACA 59.350 36.000 0.00 0.00 0.00 2.74
2098 2175 5.971202 CACATGTGGATTAATTTTCGGCTAC 59.029 40.000 18.51 0.00 0.00 3.58
2099 2176 5.449862 GCACATGTGGATTAATTTTCGGCTA 60.450 40.000 26.55 0.00 0.00 3.93
2100 2177 4.677779 GCACATGTGGATTAATTTTCGGCT 60.678 41.667 26.55 0.00 0.00 5.52
2101 2178 3.551485 GCACATGTGGATTAATTTTCGGC 59.449 43.478 26.55 3.65 0.00 5.54
2102 2179 4.997565 AGCACATGTGGATTAATTTTCGG 58.002 39.130 26.55 0.00 0.00 4.30
2103 2180 5.883661 AGAGCACATGTGGATTAATTTTCG 58.116 37.500 26.55 0.00 0.00 3.46
2104 2181 7.092716 ACAAGAGCACATGTGGATTAATTTTC 58.907 34.615 26.55 6.34 0.00 2.29
2105 2182 6.996509 ACAAGAGCACATGTGGATTAATTTT 58.003 32.000 26.55 0.00 0.00 1.82
2106 2183 6.594788 ACAAGAGCACATGTGGATTAATTT 57.405 33.333 26.55 0.00 0.00 1.82
2107 2184 6.594788 AACAAGAGCACATGTGGATTAATT 57.405 33.333 26.55 0.00 0.00 1.40
2108 2185 6.594788 AAACAAGAGCACATGTGGATTAAT 57.405 33.333 26.55 0.00 0.00 1.40
2109 2186 5.334802 CGAAACAAGAGCACATGTGGATTAA 60.335 40.000 26.55 0.00 0.00 1.40
2110 2187 4.154015 CGAAACAAGAGCACATGTGGATTA 59.846 41.667 26.55 0.00 0.00 1.75
2111 2188 3.058016 CGAAACAAGAGCACATGTGGATT 60.058 43.478 26.55 10.62 0.00 3.01
2112 2189 2.485426 CGAAACAAGAGCACATGTGGAT 59.515 45.455 26.55 6.86 0.00 3.41
2113 2190 1.872952 CGAAACAAGAGCACATGTGGA 59.127 47.619 26.55 0.00 0.00 4.02
2114 2191 1.069022 CCGAAACAAGAGCACATGTGG 60.069 52.381 26.55 12.25 0.00 4.17
2115 2192 1.069022 CCCGAAACAAGAGCACATGTG 60.069 52.381 21.83 21.83 0.00 3.21
2116 2193 1.202758 TCCCGAAACAAGAGCACATGT 60.203 47.619 0.00 0.00 0.00 3.21
2117 2194 1.197721 GTCCCGAAACAAGAGCACATG 59.802 52.381 0.00 0.00 0.00 3.21
2118 2195 1.523758 GTCCCGAAACAAGAGCACAT 58.476 50.000 0.00 0.00 0.00 3.21
2121 2198 1.301401 CGGTCCCGAAACAAGAGCA 60.301 57.895 0.00 0.00 42.83 4.26
2122 2199 2.033194 CCGGTCCCGAAACAAGAGC 61.033 63.158 7.42 0.00 42.83 4.09
2125 2202 1.964373 CACCCGGTCCCGAAACAAG 60.964 63.158 7.42 0.00 42.83 3.16
2127 2204 4.629523 GCACCCGGTCCCGAAACA 62.630 66.667 7.42 0.00 42.83 2.83
2164 2242 4.982241 AAAGAATCAACCTGAGGTGAGA 57.018 40.909 4.15 7.25 35.34 3.27
2201 2279 6.968904 CCATACTGAATACAAGACATGTTTGC 59.031 38.462 15.98 0.00 43.63 3.68
2206 2284 6.586344 ACCTCCATACTGAATACAAGACATG 58.414 40.000 0.00 0.00 0.00 3.21
2208 2286 6.895756 ACTACCTCCATACTGAATACAAGACA 59.104 38.462 0.00 0.00 0.00 3.41
2209 2287 7.349412 ACTACCTCCATACTGAATACAAGAC 57.651 40.000 0.00 0.00 0.00 3.01
2214 2292 8.351461 GTGAAGTACTACCTCCATACTGAATAC 58.649 40.741 0.00 0.00 0.00 1.89
2216 2294 6.895756 TGTGAAGTACTACCTCCATACTGAAT 59.104 38.462 0.00 0.00 0.00 2.57
2219 2297 6.525578 TTGTGAAGTACTACCTCCATACTG 57.474 41.667 0.00 0.00 0.00 2.74
2244 2323 5.390145 GGCAGCTCAAAAATTTGCACAATAG 60.390 40.000 0.98 0.00 38.05 1.73
2255 2334 4.165779 CGAAATAACGGCAGCTCAAAAAT 58.834 39.130 0.00 0.00 0.00 1.82
2261 2340 3.059800 GGATAACGAAATAACGGCAGCTC 60.060 47.826 0.00 0.00 37.61 4.09
2269 2348 8.474006 AAATTTGCCTTGGATAACGAAATAAC 57.526 30.769 0.00 0.00 0.00 1.89
2271 2350 7.831753 TGAAATTTGCCTTGGATAACGAAATA 58.168 30.769 0.00 0.00 0.00 1.40
2278 2357 9.434420 CTGTAAATTGAAATTTGCCTTGGATAA 57.566 29.630 10.56 0.00 39.34 1.75
2285 2364 5.488262 AGGCTGTAAATTGAAATTTGCCT 57.512 34.783 18.26 18.26 44.14 4.75
2286 2365 5.934043 AGAAGGCTGTAAATTGAAATTTGCC 59.066 36.000 15.45 15.45 41.56 4.52
2299 2378 4.612264 AAGTACCGAAAGAAGGCTGTAA 57.388 40.909 0.00 0.00 0.00 2.41
2304 2383 1.199327 GGCAAAGTACCGAAAGAAGGC 59.801 52.381 0.00 0.00 0.00 4.35
2324 2403 1.765314 AGGTGATGATTCCCCTCTTCG 59.235 52.381 0.00 0.00 0.00 3.79
2325 2404 2.507471 ACAGGTGATGATTCCCCTCTTC 59.493 50.000 0.00 0.00 0.00 2.87
2337 2416 5.356190 AGCAAATGTAGATGAACAGGTGATG 59.644 40.000 0.00 0.00 31.70 3.07
2345 2424 9.190858 CTACTCATAGAGCAAATGTAGATGAAC 57.809 37.037 0.00 0.00 32.04 3.18
2391 2470 5.072600 TGGTTCCCTACATCTACTTGTGTTT 59.927 40.000 0.00 0.00 0.00 2.83
2485 2566 6.758886 ACATCTAGTGCTATACTTGAAGTTGC 59.241 38.462 1.97 6.91 42.83 4.17
2508 2589 2.237066 CGACGCACAAGACTGCACA 61.237 57.895 0.00 0.00 36.94 4.57
2510 2591 1.215014 CTTCGACGCACAAGACTGCA 61.215 55.000 0.00 0.00 36.94 4.41
2516 2597 0.597637 ACTCCACTTCGACGCACAAG 60.598 55.000 0.00 0.00 0.00 3.16
2521 2602 2.668280 GCCAACTCCACTTCGACGC 61.668 63.158 0.00 0.00 0.00 5.19
2522 2603 2.372690 CGCCAACTCCACTTCGACG 61.373 63.158 0.00 0.00 0.00 5.12
2523 2604 0.599204 TTCGCCAACTCCACTTCGAC 60.599 55.000 0.00 0.00 0.00 4.20
2531 2612 0.249911 AGACACACTTCGCCAACTCC 60.250 55.000 0.00 0.00 0.00 3.85
2544 2625 4.131596 TCATGATATCGACGGTAGACACA 58.868 43.478 0.00 0.00 0.00 3.72
2553 2634 5.288472 TGACAAACTGTTCATGATATCGACG 59.712 40.000 0.00 0.00 0.00 5.12
2554 2635 6.647212 TGACAAACTGTTCATGATATCGAC 57.353 37.500 0.00 0.00 0.00 4.20
2560 2654 4.275689 TCGCTTTGACAAACTGTTCATGAT 59.724 37.500 0.00 0.00 0.00 2.45
2642 2744 2.241176 TCCACCTCCTGAGTTGTTGTTT 59.759 45.455 0.00 0.00 0.00 2.83
2650 2752 1.915769 GTGCCTCCACCTCCTGAGT 60.916 63.158 0.00 0.00 35.92 3.41
2651 2753 2.985456 GTGCCTCCACCTCCTGAG 59.015 66.667 0.00 0.00 35.92 3.35
2678 2780 1.205460 GCAGGGGGTAGGGTTTCAGA 61.205 60.000 0.00 0.00 0.00 3.27
2681 2783 2.681591 GGCAGGGGGTAGGGTTTC 59.318 66.667 0.00 0.00 0.00 2.78
2687 2789 1.289244 AAAGGATGGGCAGGGGGTAG 61.289 60.000 0.00 0.00 0.00 3.18
2688 2790 0.853586 AAAAGGATGGGCAGGGGGTA 60.854 55.000 0.00 0.00 0.00 3.69
2689 2791 0.853586 TAAAAGGATGGGCAGGGGGT 60.854 55.000 0.00 0.00 0.00 4.95
2690 2792 0.562674 ATAAAAGGATGGGCAGGGGG 59.437 55.000 0.00 0.00 0.00 5.40
2691 2793 3.140144 TCTTATAAAAGGATGGGCAGGGG 59.860 47.826 0.00 0.00 33.22 4.79
2732 2834 0.341961 ATAGTAGAGGGGGTGCACCA 59.658 55.000 35.78 12.98 42.91 4.17
2760 2862 2.967887 GCTAATTTGGCCTTGATCCCAT 59.032 45.455 3.32 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.