Multiple sequence alignment - TraesCS3D01G182300

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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 TraesCS3D01G182300 chr3D 100.000 3092 0 0 2762 5853 166483507 166486598 0.000000e+00 5710.0
1 TraesCS3D01G182300 chr3D 100.000 2511 0 0 1 2511 166480746 166483256 0.000000e+00 4638.0
2 TraesCS3D01G182300 chr3B 95.400 2500 77 13 2762 5253 242164165 242166634 0.000000e+00 3945.0
3 TraesCS3D01G182300 chr3B 97.005 868 22 3 1641 2508 242163279 242164142 0.000000e+00 1456.0
4 TraesCS3D01G182300 chr3B 90.727 949 44 18 736 1655 242162034 242162967 0.000000e+00 1225.0
5 TraesCS3D01G182300 chr3B 91.915 470 22 5 5310 5778 242167879 242168333 1.370000e-180 643.0
6 TraesCS3D01G182300 chr3B 83.140 688 66 26 53 711 242161301 242161967 3.040000e-162 582.0
7 TraesCS3D01G182300 chr3B 86.559 372 40 4 53 422 242149918 242150281 9.140000e-108 401.0
8 TraesCS3D01G182300 chr3B 100.000 34 0 0 3827 3860 242165283 242165316 4.900000e-06 63.9
9 TraesCS3D01G182300 chr3A 94.787 1899 76 16 627 2511 204825952 204827841 0.000000e+00 2937.0
10 TraesCS3D01G182300 chr3A 95.577 1266 42 5 4011 5270 204836058 204837315 0.000000e+00 2015.0
11 TraesCS3D01G182300 chr3A 95.444 1273 27 9 2762 4025 204827880 204829130 0.000000e+00 2001.0
12 TraesCS3D01G182300 chr3A 92.650 517 29 6 5280 5795 204837406 204837914 0.000000e+00 736.0
13 TraesCS3D01G182300 chr3A 87.324 284 27 7 5 284 204824136 204824414 3.400000e-82 316.0
14 TraesCS3D01G182300 chr2D 91.822 856 16 9 3342 4197 463882502 463883303 0.000000e+00 1144.0
15 TraesCS3D01G182300 chr2D 91.743 763 23 7 4540 5294 463923205 463923935 0.000000e+00 1024.0
16 TraesCS3D01G182300 chr2D 93.393 560 15 8 2781 3339 463881889 463882427 0.000000e+00 809.0
17 TraesCS3D01G182300 chr2D 89.615 260 12 4 5497 5755 463924013 463924258 3.400000e-82 316.0
18 TraesCS3D01G182300 chr2D 96.154 52 2 0 2460 2511 463881335 463881386 1.050000e-12 86.1
19 TraesCS3D01G182300 chr2D 94.000 50 3 0 5804 5853 463924257 463924306 6.290000e-10 76.8


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 TraesCS3D01G182300 chr3D 166480746 166486598 5852 False 5174.000000 5710 100.000000 1 5853 2 chr3D.!!$F1 5852
1 TraesCS3D01G182300 chr3B 242161301 242168333 7032 False 1319.150000 3945 93.031167 53 5778 6 chr3B.!!$F2 5725
2 TraesCS3D01G182300 chr3A 204824136 204829130 4994 False 1751.333333 2937 92.518333 5 4025 3 chr3A.!!$F1 4020
3 TraesCS3D01G182300 chr3A 204836058 204837914 1856 False 1375.500000 2015 94.113500 4011 5795 2 chr3A.!!$F2 1784
4 TraesCS3D01G182300 chr2D 463881335 463883303 1968 False 679.700000 1144 93.789667 2460 4197 3 chr2D.!!$F1 1737
5 TraesCS3D01G182300 chr2D 463923205 463924306 1101 False 472.266667 1024 91.786000 4540 5853 3 chr2D.!!$F2 1313

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
444 448 0.030908 CGGCCATCTCGTCTAGAACC 59.969 60.000 2.24 0.0 37.89 3.62 F
473 533 0.035439 TCGTCCCTGGCTCAATTTCC 60.035 55.000 0.00 0.0 0.00 3.13 F
947 2332 0.040204 CTGGGAGTTGGGGATTTGCT 59.960 55.000 0.00 0.0 0.00 3.91 F
1783 3513 1.134128 TGGCACACATAATGAGGCGAT 60.134 47.619 0.00 0.0 45.83 4.58 F
1819 3549 2.417933 GTGAGCTTGTTGATGCTACCAG 59.582 50.000 0.00 0.0 39.91 4.00 F
3125 5097 3.632145 ACATGTCACTGACCTTGAAAACC 59.368 43.478 13.45 0.0 0.00 3.27 F
3861 5910 4.324402 GCATGCGTTTGATACTGGAAAAAG 59.676 41.667 0.00 0.0 0.00 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 3447 2.303022 GTGGATTCAGTCTTCAGTGGGA 59.697 50.000 0.00 0.00 0.00 4.37 R
1879 3609 4.074970 ACAAACCTGACCATCATTCAGAC 58.925 43.478 0.83 0.00 42.81 3.51 R
2901 4865 6.099125 TCGATGGATTCTGTTTAGGGTAATCA 59.901 38.462 0.00 0.00 0.00 2.57 R
3066 5032 4.091424 GTTCTTCACTTATTGACGCATGC 58.909 43.478 7.91 7.91 32.26 4.06 R
3244 5216 5.009610 GTGGAAGGTCTGTTTAAAGCATCAA 59.990 40.000 0.00 0.00 0.00 2.57 R
4327 6378 0.462789 GAGCCTGCAAATGGATTGGG 59.537 55.000 0.00 0.00 39.54 4.12 R
5140 7227 1.542492 AAACTCTGGCTGCATCCAAG 58.458 50.000 11.06 12.69 35.36 3.61 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
151 153 7.269316 TGCACATATACGACATTCTTAAAGGA 58.731 34.615 0.00 0.00 0.00 3.36
152 154 7.438160 TGCACATATACGACATTCTTAAAGGAG 59.562 37.037 0.00 0.00 0.00 3.69
156 158 8.704234 CATATACGACATTCTTAAAGGAGCTTC 58.296 37.037 0.00 0.00 0.00 3.86
157 159 4.254492 ACGACATTCTTAAAGGAGCTTCC 58.746 43.478 0.00 0.00 36.58 3.46
253 257 2.935201 GTCTTCTTCCTCGCTACTCGTA 59.065 50.000 0.00 0.00 39.67 3.43
281 285 1.321074 CCTACCACCCTCTGACGTCC 61.321 65.000 14.12 0.00 0.00 4.79
359 363 1.299976 CTACCCACTCCAAGCCACC 59.700 63.158 0.00 0.00 0.00 4.61
368 372 0.034574 TCCAAGCCACCGCATATGTT 60.035 50.000 4.29 0.00 37.52 2.71
377 381 1.752498 ACCGCATATGTTCGTCTACCA 59.248 47.619 4.29 0.00 0.00 3.25
381 385 2.408704 GCATATGTTCGTCTACCATCGC 59.591 50.000 4.29 0.00 0.00 4.58
382 386 2.787601 TATGTTCGTCTACCATCGCC 57.212 50.000 0.00 0.00 0.00 5.54
383 387 0.821517 ATGTTCGTCTACCATCGCCA 59.178 50.000 0.00 0.00 0.00 5.69
384 388 0.108992 TGTTCGTCTACCATCGCCAC 60.109 55.000 0.00 0.00 0.00 5.01
386 390 1.402968 GTTCGTCTACCATCGCCACTA 59.597 52.381 0.00 0.00 0.00 2.74
387 391 1.306148 TCGTCTACCATCGCCACTAG 58.694 55.000 0.00 0.00 0.00 2.57
391 395 0.681733 CTACCATCGCCACTAGCCAT 59.318 55.000 0.00 0.00 38.78 4.40
406 410 1.378762 CCATCCCCTCAAACCACGT 59.621 57.895 0.00 0.00 0.00 4.49
410 414 1.646912 TCCCCTCAAACCACGTCATA 58.353 50.000 0.00 0.00 0.00 2.15
422 426 4.694339 ACCACGTCATATTTTCTAGCTCC 58.306 43.478 0.00 0.00 0.00 4.70
427 431 3.982058 GTCATATTTTCTAGCTCCGACGG 59.018 47.826 7.84 7.84 0.00 4.79
428 432 2.503920 TATTTTCTAGCTCCGACGGC 57.496 50.000 9.66 0.00 0.00 5.68
432 436 1.735376 TTCTAGCTCCGACGGCCATC 61.735 60.000 9.66 0.00 0.00 3.51
441 445 4.979657 ACGGCCATCTCGTCTAGA 57.020 55.556 2.24 0.00 35.87 2.43
442 446 3.186345 ACGGCCATCTCGTCTAGAA 57.814 52.632 2.24 0.00 37.89 2.10
444 448 0.030908 CGGCCATCTCGTCTAGAACC 59.969 60.000 2.24 0.00 37.89 3.62
445 449 1.112113 GGCCATCTCGTCTAGAACCA 58.888 55.000 0.00 0.00 37.89 3.67
446 450 1.202428 GGCCATCTCGTCTAGAACCAC 60.202 57.143 0.00 0.00 37.89 4.16
447 451 1.751924 GCCATCTCGTCTAGAACCACT 59.248 52.381 0.00 0.00 37.89 4.00
448 452 2.950309 GCCATCTCGTCTAGAACCACTA 59.050 50.000 0.00 0.00 37.89 2.74
449 453 3.570550 GCCATCTCGTCTAGAACCACTAT 59.429 47.826 0.00 0.00 37.89 2.12
452 512 4.634184 TCTCGTCTAGAACCACTATTGC 57.366 45.455 0.00 0.00 0.00 3.56
468 528 4.373116 GCGTCGTCCCTGGCTCAA 62.373 66.667 0.00 0.00 0.00 3.02
473 533 0.035439 TCGTCCCTGGCTCAATTTCC 60.035 55.000 0.00 0.00 0.00 3.13
479 539 2.362375 GGCTCAATTTCCCCGCCA 60.362 61.111 0.00 0.00 40.41 5.69
525 585 0.318441 TCAGGGTTGTGCTCTTCGAG 59.682 55.000 0.00 0.00 0.00 4.04
558 1830 1.001487 CGAGTTGCAAATTCAGGCACA 60.001 47.619 0.00 0.00 40.23 4.57
592 1916 6.036083 GCAAACACGACATCTTAGACACATAT 59.964 38.462 0.00 0.00 0.00 1.78
593 1917 7.222031 GCAAACACGACATCTTAGACACATATA 59.778 37.037 0.00 0.00 0.00 0.86
594 1918 8.532341 CAAACACGACATCTTAGACACATATAC 58.468 37.037 0.00 0.00 0.00 1.47
595 1919 7.569639 ACACGACATCTTAGACACATATACT 57.430 36.000 0.00 0.00 0.00 2.12
596 1920 8.672823 ACACGACATCTTAGACACATATACTA 57.327 34.615 0.00 0.00 0.00 1.82
597 1921 8.775527 ACACGACATCTTAGACACATATACTAG 58.224 37.037 0.00 0.00 0.00 2.57
598 1922 8.775527 CACGACATCTTAGACACATATACTAGT 58.224 37.037 0.00 0.00 0.00 2.57
599 1923 8.775527 ACGACATCTTAGACACATATACTAGTG 58.224 37.037 5.39 0.00 41.40 2.74
600 1924 8.231161 CGACATCTTAGACACATATACTAGTGG 58.769 40.741 5.39 0.00 39.99 4.00
601 1925 8.410673 ACATCTTAGACACATATACTAGTGGG 57.589 38.462 5.39 0.00 39.99 4.61
602 1926 7.451877 ACATCTTAGACACATATACTAGTGGGG 59.548 40.741 5.39 0.00 39.99 4.96
603 1927 5.773680 TCTTAGACACATATACTAGTGGGGC 59.226 44.000 5.39 0.00 39.99 5.80
604 1928 3.923648 AGACACATATACTAGTGGGGCA 58.076 45.455 5.39 0.00 39.99 5.36
605 1929 4.295201 AGACACATATACTAGTGGGGCAA 58.705 43.478 5.39 0.00 39.99 4.52
606 1930 4.719773 AGACACATATACTAGTGGGGCAAA 59.280 41.667 5.39 0.00 39.99 3.68
607 1931 5.190925 AGACACATATACTAGTGGGGCAAAA 59.809 40.000 5.39 0.00 39.99 2.44
608 1932 5.437060 ACACATATACTAGTGGGGCAAAAG 58.563 41.667 5.39 0.00 39.99 2.27
609 1933 5.190925 ACACATATACTAGTGGGGCAAAAGA 59.809 40.000 5.39 0.00 39.99 2.52
610 1934 6.119536 CACATATACTAGTGGGGCAAAAGAA 58.880 40.000 5.39 0.00 32.24 2.52
611 1935 6.038271 CACATATACTAGTGGGGCAAAAGAAC 59.962 42.308 5.39 0.00 32.24 3.01
612 1936 2.287977 ACTAGTGGGGCAAAAGAACC 57.712 50.000 0.00 0.00 0.00 3.62
613 1937 1.203013 ACTAGTGGGGCAAAAGAACCC 60.203 52.381 0.00 0.00 46.24 4.11
617 1941 4.943373 GGGCAAAAGAACCCCTCA 57.057 55.556 0.00 0.00 40.56 3.86
618 1942 3.141409 GGGCAAAAGAACCCCTCAA 57.859 52.632 0.00 0.00 40.56 3.02
619 1943 1.419381 GGGCAAAAGAACCCCTCAAA 58.581 50.000 0.00 0.00 40.56 2.69
620 1944 1.765904 GGGCAAAAGAACCCCTCAAAA 59.234 47.619 0.00 0.00 40.56 2.44
621 1945 2.171659 GGGCAAAAGAACCCCTCAAAAA 59.828 45.455 0.00 0.00 40.56 1.94
622 1946 3.202906 GGCAAAAGAACCCCTCAAAAAC 58.797 45.455 0.00 0.00 0.00 2.43
623 1947 3.369997 GGCAAAAGAACCCCTCAAAAACA 60.370 43.478 0.00 0.00 0.00 2.83
624 1948 4.257731 GCAAAAGAACCCCTCAAAAACAA 58.742 39.130 0.00 0.00 0.00 2.83
625 1949 4.697828 GCAAAAGAACCCCTCAAAAACAAA 59.302 37.500 0.00 0.00 0.00 2.83
626 1950 5.182190 GCAAAAGAACCCCTCAAAAACAAAA 59.818 36.000 0.00 0.00 0.00 2.44
648 1972 4.082125 ACTAGTGGGGCAAAAGAGAAATG 58.918 43.478 0.00 0.00 0.00 2.32
660 1984 1.978580 AGAGAAATGGACTGTTCCCGT 59.021 47.619 0.00 0.00 42.01 5.28
711 2035 9.525409 CAAATTAAATCCTTGGATTGATGACTC 57.475 33.333 14.81 0.00 0.00 3.36
712 2036 7.830099 ATTAAATCCTTGGATTGATGACTCC 57.170 36.000 14.81 0.00 0.00 3.85
720 2075 2.289320 GGATTGATGACTCCTCCATCGG 60.289 54.545 0.00 0.00 42.37 4.18
722 2077 1.369321 GATGACTCCTCCATCGGCC 59.631 63.158 0.00 0.00 32.23 6.13
761 2127 5.511729 CGCCTTCAATTTTCTATTCGTTTCC 59.488 40.000 0.00 0.00 0.00 3.13
772 2138 2.721425 TTCGTTTCCTTTGTGGGAGT 57.279 45.000 0.00 0.00 36.66 3.85
793 2159 0.179189 GACTTTTGCGCCTTCATCCG 60.179 55.000 4.18 0.00 0.00 4.18
815 2182 4.620184 CGTTTATCCGTTCTCTCGTTTTCT 59.380 41.667 0.00 0.00 0.00 2.52
922 2307 1.521141 GACCTAAAGTCTCCCCCGC 59.479 63.158 0.00 0.00 42.69 6.13
947 2332 0.040204 CTGGGAGTTGGGGATTTGCT 59.960 55.000 0.00 0.00 0.00 3.91
1136 2527 1.141185 GCCTGCCCTAGTAATCCCTT 58.859 55.000 0.00 0.00 0.00 3.95
1172 2563 6.222038 ACTAATCAGGCTAGAAATGTTCGA 57.778 37.500 0.00 0.00 34.02 3.71
1364 2755 3.684103 TTACTTTCTTGTGGTGTTGCG 57.316 42.857 0.00 0.00 0.00 4.85
1438 2832 4.136796 AGTTTGTTCATGAGTAGCTGCAA 58.863 39.130 4.12 0.00 0.00 4.08
1441 2835 3.743521 TGTTCATGAGTAGCTGCAAAGT 58.256 40.909 4.12 0.00 0.00 2.66
1457 2851 6.292328 GCTGCAAAGTTTTATCAAGGAAACAC 60.292 38.462 0.00 0.00 38.03 3.32
1493 2887 7.377662 CACGATTAGTAAAGTGGAAACCAAAAC 59.622 37.037 11.77 0.00 34.18 2.43
1717 3447 5.798125 TCTTCAGAGTCATCAGAAAGTGT 57.202 39.130 0.00 0.00 31.39 3.55
1737 3467 2.303022 GTCCCACTGAAGACTGAATCCA 59.697 50.000 0.00 0.00 0.00 3.41
1783 3513 1.134128 TGGCACACATAATGAGGCGAT 60.134 47.619 0.00 0.00 45.83 4.58
1819 3549 2.417933 GTGAGCTTGTTGATGCTACCAG 59.582 50.000 0.00 0.00 39.91 4.00
1879 3609 6.531240 GGATTTGGTTGTGTGTATAAAGCATG 59.469 38.462 0.00 0.00 31.96 4.06
3123 5095 4.522114 TGACATGTCACTGACCTTGAAAA 58.478 39.130 24.56 0.00 34.14 2.29
3125 5097 3.632145 ACATGTCACTGACCTTGAAAACC 59.368 43.478 13.45 0.00 0.00 3.27
3244 5216 8.738592 TGGATACCCCCATTAATAAATTACTGT 58.261 33.333 0.00 0.00 0.00 3.55
3775 5824 5.419760 GCTATAAAGCCTACCGAAAAAGG 57.580 43.478 0.00 0.00 43.40 3.11
3861 5910 4.324402 GCATGCGTTTGATACTGGAAAAAG 59.676 41.667 0.00 0.00 0.00 2.27
3872 5923 6.592607 TGATACTGGAAAAAGACGGTTATGTC 59.407 38.462 0.00 0.00 39.21 3.06
3915 5966 8.393671 TGATGAATATAATAACAGTGCATGCA 57.606 30.769 18.46 18.46 0.00 3.96
4327 6378 4.795278 GCGGATGTTGAATTGAATGTTCTC 59.205 41.667 0.00 0.00 0.00 2.87
4556 6607 0.537143 TGGGAATGACGCTGCTGTTT 60.537 50.000 0.00 0.00 0.00 2.83
4651 6702 3.503363 GTCAACATGGAGCTCAAACATCA 59.497 43.478 17.19 3.06 0.00 3.07
4708 6759 2.664402 AAGAACATTGCAGGAGTGGT 57.336 45.000 0.00 0.00 0.00 4.16
5005 7066 3.916392 GAGCCTGTCACGTCCACCG 62.916 68.421 0.00 0.00 44.03 4.94
5018 7079 4.409588 CACCGTCGTTTCGCTGCG 62.410 66.667 17.25 17.25 0.00 5.18
5022 7083 2.385361 GTCGTTTCGCTGCGTACG 59.615 61.111 30.66 30.66 37.34 3.67
5140 7227 4.320608 TTTTTCAGTCCATTGTTGGCTC 57.679 40.909 0.00 0.00 43.29 4.70
5203 7290 4.749598 TGGTAACATCTTGCAGCATATACG 59.250 41.667 0.00 0.00 46.17 3.06
5250 7337 0.879765 CTTTCTGCCAGTGCCTTCAG 59.120 55.000 0.00 0.00 36.33 3.02
5435 8730 4.172073 GAGGTTTCTCTGGCAACTAGCAG 61.172 52.174 0.00 0.00 40.00 4.24
5656 8983 2.806434 TGTATGCAGGCAGGTGAAAAT 58.194 42.857 0.00 0.00 0.00 1.82
5755 9082 3.378427 GCAATCACTCTTTCCATACCCAC 59.622 47.826 0.00 0.00 0.00 4.61
5756 9083 3.933861 ATCACTCTTTCCATACCCACC 57.066 47.619 0.00 0.00 0.00 4.61
5768 9095 2.259266 TACCCACCGAAAAGGAACAC 57.741 50.000 0.00 0.00 45.00 3.32
5772 9099 1.578583 CACCGAAAAGGAACACGAGT 58.421 50.000 0.00 0.00 45.00 4.18
5795 9122 0.685097 GGTACCCTCAGTCAGCACAA 59.315 55.000 0.00 0.00 0.00 3.33
5796 9123 1.279271 GGTACCCTCAGTCAGCACAAT 59.721 52.381 0.00 0.00 0.00 2.71
5797 9124 2.500098 GGTACCCTCAGTCAGCACAATA 59.500 50.000 0.00 0.00 0.00 1.90
5798 9125 3.134804 GGTACCCTCAGTCAGCACAATAT 59.865 47.826 0.00 0.00 0.00 1.28
5799 9126 4.384208 GGTACCCTCAGTCAGCACAATATT 60.384 45.833 0.00 0.00 0.00 1.28
5800 9127 4.307032 ACCCTCAGTCAGCACAATATTT 57.693 40.909 0.00 0.00 0.00 1.40
5801 9128 4.265073 ACCCTCAGTCAGCACAATATTTC 58.735 43.478 0.00 0.00 0.00 2.17
5802 9129 4.263462 ACCCTCAGTCAGCACAATATTTCA 60.263 41.667 0.00 0.00 0.00 2.69
5803 9130 4.095483 CCCTCAGTCAGCACAATATTTCAC 59.905 45.833 0.00 0.00 0.00 3.18
5804 9131 4.696877 CCTCAGTCAGCACAATATTTCACA 59.303 41.667 0.00 0.00 0.00 3.58
5805 9132 5.163784 CCTCAGTCAGCACAATATTTCACAG 60.164 44.000 0.00 0.00 0.00 3.66
5806 9133 4.696877 TCAGTCAGCACAATATTTCACAGG 59.303 41.667 0.00 0.00 0.00 4.00
5807 9134 4.012374 AGTCAGCACAATATTTCACAGGG 58.988 43.478 0.00 0.00 0.00 4.45
5808 9135 2.754552 TCAGCACAATATTTCACAGGGC 59.245 45.455 0.00 0.00 0.00 5.19
5809 9136 2.492881 CAGCACAATATTTCACAGGGCA 59.507 45.455 0.44 0.00 0.00 5.36
5810 9137 3.056678 CAGCACAATATTTCACAGGGCAA 60.057 43.478 0.44 0.00 0.00 4.52
5811 9138 3.770933 AGCACAATATTTCACAGGGCAAT 59.229 39.130 0.44 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.313292 AGCCATTTGTGTGTTGTCAATATATTT 58.687 29.630 0.00 0.00 0.00 1.40
28 29 4.405116 AAGCCATTTGTGTGTTGTCAAT 57.595 36.364 0.00 0.00 0.00 2.57
43 44 2.025887 AGGTGCAGTTTAGCTAAGCCAT 60.026 45.455 15.82 0.00 34.99 4.40
253 257 1.082392 GGGTGGTAGGAGGAAGGGT 59.918 63.158 0.00 0.00 0.00 4.34
330 334 3.712907 TGGGTAGGGCAACGAGGC 61.713 66.667 0.00 0.00 43.27 4.70
359 363 2.656897 CGATGGTAGACGAACATATGCG 59.343 50.000 1.58 1.67 0.00 4.73
368 372 1.306148 CTAGTGGCGATGGTAGACGA 58.694 55.000 0.00 0.00 0.00 4.20
377 381 2.520536 GGGGATGGCTAGTGGCGAT 61.521 63.158 0.00 0.00 41.98 4.58
381 385 0.918983 TTTGAGGGGATGGCTAGTGG 59.081 55.000 0.00 0.00 0.00 4.00
382 386 1.408822 GGTTTGAGGGGATGGCTAGTG 60.409 57.143 0.00 0.00 0.00 2.74
383 387 0.919710 GGTTTGAGGGGATGGCTAGT 59.080 55.000 0.00 0.00 0.00 2.57
384 388 0.918983 TGGTTTGAGGGGATGGCTAG 59.081 55.000 0.00 0.00 0.00 3.42
386 390 1.384191 GTGGTTTGAGGGGATGGCT 59.616 57.895 0.00 0.00 0.00 4.75
387 391 2.046285 CGTGGTTTGAGGGGATGGC 61.046 63.158 0.00 0.00 0.00 4.40
391 395 1.646912 TATGACGTGGTTTGAGGGGA 58.353 50.000 0.00 0.00 0.00 4.81
406 410 3.552273 GCCGTCGGAGCTAGAAAATATGA 60.552 47.826 17.49 0.00 0.00 2.15
410 414 0.179081 GGCCGTCGGAGCTAGAAAAT 60.179 55.000 17.49 0.00 0.00 1.82
427 431 1.751924 AGTGGTTCTAGACGAGATGGC 59.248 52.381 0.00 0.00 32.88 4.40
428 432 5.524284 CAATAGTGGTTCTAGACGAGATGG 58.476 45.833 0.00 0.00 32.88 3.51
432 436 3.181499 ACGCAATAGTGGTTCTAGACGAG 60.181 47.826 0.00 0.00 31.67 4.18
438 442 2.159338 GGACGACGCAATAGTGGTTCTA 60.159 50.000 0.00 0.00 33.27 2.10
439 443 1.403780 GGACGACGCAATAGTGGTTCT 60.404 52.381 0.00 0.00 33.27 3.01
440 444 0.997196 GGACGACGCAATAGTGGTTC 59.003 55.000 0.00 0.00 33.27 3.62
441 445 0.390735 GGGACGACGCAATAGTGGTT 60.391 55.000 0.00 0.00 33.27 3.67
442 446 1.217244 GGGACGACGCAATAGTGGT 59.783 57.895 0.00 0.00 35.79 4.16
444 448 0.806102 CCAGGGACGACGCAATAGTG 60.806 60.000 4.64 0.00 0.00 2.74
445 449 1.515954 CCAGGGACGACGCAATAGT 59.484 57.895 4.64 0.00 0.00 2.12
446 450 1.883084 GCCAGGGACGACGCAATAG 60.883 63.158 4.64 0.00 0.00 1.73
447 451 2.185867 GCCAGGGACGACGCAATA 59.814 61.111 4.64 0.00 0.00 1.90
448 452 3.665675 GAGCCAGGGACGACGCAAT 62.666 63.158 4.64 0.00 0.00 3.56
449 453 4.373116 GAGCCAGGGACGACGCAA 62.373 66.667 4.64 0.00 0.00 4.85
452 512 0.673644 AAATTGAGCCAGGGACGACG 60.674 55.000 0.00 0.00 0.00 5.12
467 527 1.304134 GGTGAGTGGCGGGGAAATT 60.304 57.895 0.00 0.00 0.00 1.82
468 528 2.355115 GGTGAGTGGCGGGGAAAT 59.645 61.111 0.00 0.00 0.00 2.17
504 564 0.318441 CGAAGAGCACAACCCTGAGA 59.682 55.000 0.00 0.00 0.00 3.27
525 585 5.530519 TTGCAACTCGTGTCAATCTATTC 57.469 39.130 0.00 0.00 0.00 1.75
558 1830 5.428253 AGATGTCGTGTTTGCTATTGGTAT 58.572 37.500 0.00 0.00 0.00 2.73
592 1916 2.040679 GGGTTCTTTTGCCCCACTAGTA 59.959 50.000 0.00 0.00 38.99 1.82
593 1917 1.203013 GGGTTCTTTTGCCCCACTAGT 60.203 52.381 0.00 0.00 38.99 2.57
594 1918 1.545841 GGGTTCTTTTGCCCCACTAG 58.454 55.000 0.00 0.00 38.99 2.57
595 1919 3.757836 GGGTTCTTTTGCCCCACTA 57.242 52.632 0.00 0.00 38.99 2.74
596 1920 4.619233 GGGTTCTTTTGCCCCACT 57.381 55.556 0.00 0.00 38.99 4.00
600 1924 1.419381 TTTGAGGGGTTCTTTTGCCC 58.581 50.000 0.00 0.00 44.09 5.36
601 1925 3.202906 GTTTTTGAGGGGTTCTTTTGCC 58.797 45.455 0.00 0.00 0.00 4.52
602 1926 3.867857 TGTTTTTGAGGGGTTCTTTTGC 58.132 40.909 0.00 0.00 0.00 3.68
603 1927 6.429692 AGTTTTGTTTTTGAGGGGTTCTTTTG 59.570 34.615 0.00 0.00 0.00 2.44
604 1928 6.539173 AGTTTTGTTTTTGAGGGGTTCTTTT 58.461 32.000 0.00 0.00 0.00 2.27
605 1929 6.121776 AGTTTTGTTTTTGAGGGGTTCTTT 57.878 33.333 0.00 0.00 0.00 2.52
606 1930 5.755409 AGTTTTGTTTTTGAGGGGTTCTT 57.245 34.783 0.00 0.00 0.00 2.52
607 1931 5.955959 ACTAGTTTTGTTTTTGAGGGGTTCT 59.044 36.000 0.00 0.00 0.00 3.01
608 1932 6.040247 CACTAGTTTTGTTTTTGAGGGGTTC 58.960 40.000 0.00 0.00 0.00 3.62
609 1933 5.105106 CCACTAGTTTTGTTTTTGAGGGGTT 60.105 40.000 0.00 0.00 0.00 4.11
610 1934 4.404394 CCACTAGTTTTGTTTTTGAGGGGT 59.596 41.667 0.00 0.00 0.00 4.95
611 1935 4.202212 CCCACTAGTTTTGTTTTTGAGGGG 60.202 45.833 0.00 0.00 0.00 4.79
612 1936 4.202212 CCCCACTAGTTTTGTTTTTGAGGG 60.202 45.833 0.00 0.00 0.00 4.30
613 1937 4.739436 GCCCCACTAGTTTTGTTTTTGAGG 60.739 45.833 0.00 0.00 0.00 3.86
614 1938 4.142049 TGCCCCACTAGTTTTGTTTTTGAG 60.142 41.667 0.00 0.00 0.00 3.02
615 1939 3.769844 TGCCCCACTAGTTTTGTTTTTGA 59.230 39.130 0.00 0.00 0.00 2.69
616 1940 4.130286 TGCCCCACTAGTTTTGTTTTTG 57.870 40.909 0.00 0.00 0.00 2.44
617 1941 4.828072 TTGCCCCACTAGTTTTGTTTTT 57.172 36.364 0.00 0.00 0.00 1.94
618 1942 4.828072 TTTGCCCCACTAGTTTTGTTTT 57.172 36.364 0.00 0.00 0.00 2.43
619 1943 4.468153 TCTTTTGCCCCACTAGTTTTGTTT 59.532 37.500 0.00 0.00 0.00 2.83
620 1944 4.027437 TCTTTTGCCCCACTAGTTTTGTT 58.973 39.130 0.00 0.00 0.00 2.83
621 1945 3.636764 CTCTTTTGCCCCACTAGTTTTGT 59.363 43.478 0.00 0.00 0.00 2.83
622 1946 3.888930 TCTCTTTTGCCCCACTAGTTTTG 59.111 43.478 0.00 0.00 0.00 2.44
623 1947 4.178956 TCTCTTTTGCCCCACTAGTTTT 57.821 40.909 0.00 0.00 0.00 2.43
624 1948 3.876309 TCTCTTTTGCCCCACTAGTTT 57.124 42.857 0.00 0.00 0.00 2.66
625 1949 3.876309 TTCTCTTTTGCCCCACTAGTT 57.124 42.857 0.00 0.00 0.00 2.24
626 1950 3.876309 TTTCTCTTTTGCCCCACTAGT 57.124 42.857 0.00 0.00 0.00 2.57
660 1984 2.813226 AAGTTGCATTCGCGCCCCTA 62.813 55.000 0.00 0.00 42.97 3.53
711 2035 4.899239 GACGCTGGCCGATGGAGG 62.899 72.222 0.00 0.00 41.02 4.30
712 2036 4.147449 TGACGCTGGCCGATGGAG 62.147 66.667 0.00 0.00 41.02 3.86
761 2127 3.058914 CGCAAAAGTCTACTCCCACAAAG 60.059 47.826 0.00 0.00 0.00 2.77
772 2138 2.356135 GGATGAAGGCGCAAAAGTCTA 58.644 47.619 10.83 0.00 0.00 2.59
793 2159 6.463483 AAGAAAACGAGAGAACGGATAAAC 57.537 37.500 0.00 0.00 37.61 2.01
815 2182 2.289694 CGGGCAGAAGAGGAGAAAGAAA 60.290 50.000 0.00 0.00 0.00 2.52
933 2318 6.269769 TCAAGAAATTTAGCAAATCCCCAACT 59.730 34.615 0.00 0.00 0.00 3.16
947 2332 7.233348 ACAAGAGGGCTGAAATCAAGAAATTTA 59.767 33.333 0.00 0.00 0.00 1.40
1136 2527 4.441079 GCCTGATTAGTAGGTAAAGCACGA 60.441 45.833 0.00 0.00 37.64 4.35
1172 2563 1.420138 AGACCGACCAACACCAAGAAT 59.580 47.619 0.00 0.00 0.00 2.40
1307 2698 2.756760 TGGAAATTTCTGATGGCTGAGC 59.243 45.455 17.42 0.00 0.00 4.26
1364 2755 3.496331 ACTGCTAGAGCCTAGAGGAATC 58.504 50.000 11.96 0.00 41.18 2.52
1438 2832 9.883142 TCAATTTGTGTTTCCTTGATAAAACTT 57.117 25.926 0.00 0.00 36.54 2.66
1457 2851 8.901748 CCACTTTACTAATCGTGTTTCAATTTG 58.098 33.333 0.00 0.00 0.00 2.32
1493 2887 9.944663 GTCTACTACTGTTCATCTTCTTCATAG 57.055 37.037 0.00 0.00 0.00 2.23
1717 3447 2.303022 GTGGATTCAGTCTTCAGTGGGA 59.697 50.000 0.00 0.00 0.00 4.37
1819 3549 5.836347 ACTGAAAATCCTTGCTGAAGTTTC 58.164 37.500 0.00 0.00 0.00 2.78
1879 3609 4.074970 ACAAACCTGACCATCATTCAGAC 58.925 43.478 0.83 0.00 42.81 3.51
2892 4856 8.141298 TCTGTTTAGGGTAATCACATCACTAA 57.859 34.615 0.00 0.00 0.00 2.24
2901 4865 6.099125 TCGATGGATTCTGTTTAGGGTAATCA 59.901 38.462 0.00 0.00 0.00 2.57
3066 5032 4.091424 GTTCTTCACTTATTGACGCATGC 58.909 43.478 7.91 7.91 32.26 4.06
3244 5216 5.009610 GTGGAAGGTCTGTTTAAAGCATCAA 59.990 40.000 0.00 0.00 0.00 2.57
3721 5767 9.853555 CATACTTCTCTAGACATGTATCCATTC 57.146 37.037 0.00 0.00 0.00 2.67
3762 5811 5.419760 GCTTTATAGCCTTTTTCGGTAGG 57.580 43.478 0.00 0.00 41.74 3.18
3776 5825 8.517878 ACAATGCATGCCTATTAAGCTTTATAG 58.482 33.333 20.64 20.64 0.00 1.31
3777 5826 8.408043 ACAATGCATGCCTATTAAGCTTTATA 57.592 30.769 16.68 4.41 0.00 0.98
3778 5827 7.294017 ACAATGCATGCCTATTAAGCTTTAT 57.706 32.000 16.68 3.16 0.00 1.40
3861 5910 1.326548 GCCACATTCGACATAACCGTC 59.673 52.381 0.00 0.00 0.00 4.79
3872 5923 0.110238 CAGTTCAACCGCCACATTCG 60.110 55.000 0.00 0.00 0.00 3.34
3915 5966 8.691661 AGTTGTACAGTTTTCCAGTATCAAAT 57.308 30.769 0.00 0.00 0.00 2.32
4306 6357 5.185635 TGGGAGAACATTCAATTCAACATCC 59.814 40.000 0.00 0.00 0.00 3.51
4327 6378 0.462789 GAGCCTGCAAATGGATTGGG 59.537 55.000 0.00 0.00 39.54 4.12
4534 6585 0.745486 CAGCAGCGTCATTCCCATCA 60.745 55.000 0.00 0.00 0.00 3.07
4556 6607 1.377987 GGCCATCAAGGTAACGGCA 60.378 57.895 0.00 0.00 44.82 5.69
4651 6702 3.565482 GGTCATTCATACGGTCATGCATT 59.435 43.478 0.00 0.00 0.00 3.56
5005 7066 1.869242 AACGTACGCAGCGAAACGAC 61.869 55.000 36.16 19.99 40.09 4.34
5022 7083 5.049680 ACATGTGAAATTCAGACCGTGTAAC 60.050 40.000 0.00 0.00 0.00 2.50
5140 7227 1.542492 AAACTCTGGCTGCATCCAAG 58.458 50.000 11.06 12.69 35.36 3.61
5203 7290 3.055312 AGGAATAGGAGACGAACCCAAAC 60.055 47.826 0.00 0.00 0.00 2.93
5435 8730 8.937634 ATTTTTAATCATGAGAATCCAAGTGC 57.062 30.769 0.09 0.00 0.00 4.40
5468 8763 7.124599 TGAGATCATCATTTTTGGGCTATTGTT 59.875 33.333 0.00 0.00 31.12 2.83
5469 8764 6.608405 TGAGATCATCATTTTTGGGCTATTGT 59.392 34.615 0.00 0.00 31.12 2.71
5634 8961 3.643199 TTTCACCTGCCTGCATACATA 57.357 42.857 0.00 0.00 0.00 2.29
5635 8962 2.512692 TTTCACCTGCCTGCATACAT 57.487 45.000 0.00 0.00 0.00 2.29
5636 8963 2.284754 TTTTCACCTGCCTGCATACA 57.715 45.000 0.00 0.00 0.00 2.29
5637 8964 3.947834 AGTATTTTCACCTGCCTGCATAC 59.052 43.478 0.00 0.00 0.00 2.39
5755 9082 2.735134 CCTTACTCGTGTTCCTTTTCGG 59.265 50.000 0.00 0.00 0.00 4.30
5756 9083 2.735134 CCCTTACTCGTGTTCCTTTTCG 59.265 50.000 0.00 0.00 0.00 3.46
5786 9113 3.428045 GCCCTGTGAAATATTGTGCTGAC 60.428 47.826 0.00 0.00 0.00 3.51
5797 9124 7.814107 CGCATATAAATTATTGCCCTGTGAAAT 59.186 33.333 11.58 0.00 0.00 2.17
5798 9125 7.013750 TCGCATATAAATTATTGCCCTGTGAAA 59.986 33.333 11.58 0.00 0.00 2.69
5799 9126 6.488344 TCGCATATAAATTATTGCCCTGTGAA 59.512 34.615 11.58 0.00 0.00 3.18
5800 9127 6.000840 TCGCATATAAATTATTGCCCTGTGA 58.999 36.000 11.58 0.00 0.00 3.58
5801 9128 6.149308 TCTCGCATATAAATTATTGCCCTGTG 59.851 38.462 11.58 0.00 0.00 3.66
5802 9129 6.237901 TCTCGCATATAAATTATTGCCCTGT 58.762 36.000 11.58 0.00 0.00 4.00
5803 9130 6.741992 TCTCGCATATAAATTATTGCCCTG 57.258 37.500 11.58 5.65 0.00 4.45
5804 9131 7.448469 ACTTTCTCGCATATAAATTATTGCCCT 59.552 33.333 11.58 0.00 0.00 5.19
5805 9132 7.593825 ACTTTCTCGCATATAAATTATTGCCC 58.406 34.615 11.58 0.00 0.00 5.36
5806 9133 9.463443 AAACTTTCTCGCATATAAATTATTGCC 57.537 29.630 11.58 0.73 0.00 4.52


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

AutoCloner maintained by Alex Coulton.