Multiple sequence alignment - TraesCS3B01G266400

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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 TraesCS3B01G266400 chr3B 100.000 3017 0 0 1 3017 427008221 427005205 0.000000e+00 5572
1 TraesCS3B01G266400 chr3A 91.321 1590 82 20 661 2223 444547027 444545467 0.000000e+00 2121
2 TraesCS3B01G266400 chr3A 88.609 676 60 10 2353 3017 444545379 444544710 0.000000e+00 806
3 TraesCS3B01G266400 chr3D 93.327 1019 48 8 725 1735 329520027 329519021 0.000000e+00 1487
4 TraesCS3B01G266400 chr3D 83.377 764 71 33 1816 2556 329519021 329518291 0.000000e+00 656
5 TraesCS3B01G266400 chr3D 88.281 384 28 8 2645 3017 329518224 329517847 7.670000e-121 444
6 TraesCS3B01G266400 chr2D 91.030 602 36 8 40 631 612335935 612335342 0.000000e+00 797
7 TraesCS3B01G266400 chr5D 93.165 278 19 0 1 278 50879266 50878989 2.800000e-110 409
8 TraesCS3B01G266400 chr5D 89.474 304 23 3 331 634 50878984 50878690 2.840000e-100 375
9 TraesCS3B01G266400 chr2A 92.580 283 21 0 1 283 656956190 656955908 1.010000e-109 407


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 TraesCS3B01G266400 chr3B 427005205 427008221 3016 True 5572.000000 5572 100.000000 1 3017 1 chr3B.!!$R1 3016
1 TraesCS3B01G266400 chr3A 444544710 444547027 2317 True 1463.500000 2121 89.965000 661 3017 2 chr3A.!!$R1 2356
2 TraesCS3B01G266400 chr3D 329517847 329520027 2180 True 862.333333 1487 88.328333 725 3017 3 chr3D.!!$R1 2292
3 TraesCS3B01G266400 chr2D 612335342 612335935 593 True 797.000000 797 91.030000 40 631 1 chr2D.!!$R1 591
4 TraesCS3B01G266400 chr5D 50878690 50879266 576 True 392.000000 409 91.319500 1 634 2 chr5D.!!$R1 633

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
690 701 0.168128 ATTGCTTTAACCACGCTCGC 59.832 50.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2144 0.035056 CCTCGCCCCTTCAATCAGTT 60.035 55.0 0.0 0.0 0.0 3.16 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
28 29 4.662961 CTCACCAGCCGCACACGA 62.663 66.667 0.00 0.00 43.93 4.35
110 111 4.169696 CGGGCCATAGGAACGCCA 62.170 66.667 4.39 0.00 44.90 5.69
144 145 4.514577 ACAGATCGAAGCGCCCCG 62.515 66.667 2.29 8.46 0.00 5.73
207 208 3.551496 CTCCAACAGCCAGGCGGAA 62.551 63.158 19.66 0.00 0.00 4.30
283 284 3.697439 ATGGCAACCCGCGCATAGT 62.697 57.895 8.75 0.00 43.84 2.12
286 287 2.244651 GCAACCCGCGCATAGTAGG 61.245 63.158 8.75 0.00 0.00 3.18
287 288 2.108362 AACCCGCGCATAGTAGGC 59.892 61.111 8.75 0.00 0.00 3.93
288 289 3.456105 AACCCGCGCATAGTAGGCC 62.456 63.158 8.75 0.00 0.00 5.19
290 291 4.681978 CCGCGCATAGTAGGCCCC 62.682 72.222 8.75 0.00 0.00 5.80
483 484 1.604278 GAAGCGGCTGTAATTGGATCC 59.396 52.381 1.81 4.20 0.00 3.36
635 646 4.570663 CGACACGGGAGCGGGATC 62.571 72.222 0.00 0.00 0.00 3.36
636 647 4.222847 GACACGGGAGCGGGATCC 62.223 72.222 1.92 1.92 38.76 3.36
637 648 4.779733 ACACGGGAGCGGGATCCT 62.780 66.667 12.58 0.00 39.50 3.24
638 649 3.917760 CACGGGAGCGGGATCCTC 61.918 72.222 12.58 0.76 39.50 3.71
642 653 3.568578 GGAGCGGGATCCTCCAAT 58.431 61.111 12.58 0.00 46.51 3.16
643 654 1.839894 GGAGCGGGATCCTCCAATT 59.160 57.895 12.58 0.00 46.51 2.32
644 655 0.250510 GGAGCGGGATCCTCCAATTC 60.251 60.000 12.58 1.62 46.51 2.17
645 656 0.761802 GAGCGGGATCCTCCAATTCT 59.238 55.000 12.58 0.00 38.64 2.40
646 657 0.471617 AGCGGGATCCTCCAATTCTG 59.528 55.000 12.58 0.00 38.64 3.02
647 658 0.536006 GCGGGATCCTCCAATTCTGG 60.536 60.000 12.58 0.00 45.08 3.86
690 701 0.168128 ATTGCTTTAACCACGCTCGC 59.832 50.000 0.00 0.00 0.00 5.03
708 719 1.070615 CCGTGTGGTGTGTGGATCA 59.929 57.895 0.00 0.00 0.00 2.92
781 792 7.709182 CCATAGTATCGTTGGAATTACTTCACA 59.291 37.037 0.00 0.00 32.70 3.58
884 895 1.599542 GCCCTGCGAGTTCATACATTC 59.400 52.381 0.00 0.00 0.00 2.67
946 969 0.178992 CCACTCACCCTCTTGCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
949 972 1.251251 CTCACCCTCTTGCCAAAAGG 58.749 55.000 0.00 0.00 0.00 3.11
1060 1083 2.684104 CCTCCCTCTCCGGTGAGA 59.316 66.667 30.40 13.47 45.39 3.27
1155 1178 3.854669 CGGAGGATCGCCAAGGCT 61.855 66.667 9.73 0.00 39.32 4.58
1180 1203 3.893763 CGCTCTCCGCCATCGACT 61.894 66.667 0.00 0.00 38.10 4.18
1182 1205 2.485795 GCTCTCCGCCATCGACTCT 61.486 63.158 0.00 0.00 38.10 3.24
1198 1221 2.488545 GACTCTCTGCGGAAGAAGTACA 59.511 50.000 10.51 0.00 38.22 2.90
1260 1283 2.825836 GAGATGGCGCCCCTGTTG 60.826 66.667 26.77 0.00 0.00 3.33
1331 1360 2.434185 GGACGATGTGCCGCTGAA 60.434 61.111 0.00 0.00 0.00 3.02
1368 1397 2.925170 AGGCAAGGCGAGACCAGT 60.925 61.111 0.00 0.00 43.14 4.00
1430 1459 1.892862 CGGTCGCTACTCCGGAGAT 60.893 63.158 37.69 22.80 42.61 2.75
1445 1474 1.077429 AGATTTCGAAGCAGGGGCC 60.077 57.895 0.00 0.00 42.56 5.80
1495 1524 2.124695 GAGGAATGCCCCGGACAC 60.125 66.667 0.73 0.00 34.66 3.67
1496 1525 2.933287 AGGAATGCCCCGGACACA 60.933 61.111 0.73 0.00 34.66 3.72
1497 1526 2.438434 GGAATGCCCCGGACACAG 60.438 66.667 0.73 0.00 0.00 3.66
1498 1527 2.668632 GAATGCCCCGGACACAGA 59.331 61.111 0.73 0.00 0.00 3.41
1499 1528 1.745489 GAATGCCCCGGACACAGAC 60.745 63.158 0.73 0.00 0.00 3.51
1500 1529 2.463589 GAATGCCCCGGACACAGACA 62.464 60.000 0.73 0.00 0.00 3.41
1501 1530 2.748058 AATGCCCCGGACACAGACAC 62.748 60.000 0.73 0.00 0.00 3.67
1542 1571 3.006967 GGCTTCTTCACAGGAGTGTTCTA 59.993 47.826 0.00 0.00 46.01 2.10
1543 1572 3.991121 GCTTCTTCACAGGAGTGTTCTAC 59.009 47.826 0.00 0.00 46.01 2.59
1544 1573 4.262249 GCTTCTTCACAGGAGTGTTCTACT 60.262 45.833 0.00 0.00 46.01 2.57
1558 1587 4.060205 TGTTCTACTACCAAAGGTTTCGC 58.940 43.478 0.00 0.00 37.09 4.70
1566 1595 0.750249 CAAAGGTTTCGCCCCAAAGT 59.250 50.000 0.00 0.00 38.26 2.66
1639 1668 4.223032 TCCTAGCAAGGGAAGTTAGTGAAG 59.777 45.833 0.00 0.00 43.84 3.02
1679 1708 6.761242 GGTAAAATTATCCAAACATCAAGGGC 59.239 38.462 0.00 0.00 0.00 5.19
1701 1730 3.220110 GGAATCATCATCCACATGTGCT 58.780 45.455 20.81 6.82 36.92 4.40
1724 1759 2.615912 GCAAGATATCTGGGACTGCAAC 59.384 50.000 17.57 0.00 0.00 4.17
1736 1771 1.205064 CTGCAACGAAAGAGTGCCG 59.795 57.895 0.00 0.00 42.28 5.69
1738 1773 0.602638 TGCAACGAAAGAGTGCCGAT 60.603 50.000 0.00 0.00 42.28 4.18
1740 1775 0.721718 CAACGAAAGAGTGCCGATCC 59.278 55.000 0.00 0.00 0.00 3.36
1752 1787 1.207089 TGCCGATCCCTTTGTAGACAG 59.793 52.381 0.00 0.00 0.00 3.51
1764 1799 5.335583 CCTTTGTAGACAGAGACAGACTGAG 60.336 48.000 10.08 0.00 38.55 3.35
1774 1809 2.183679 GACAGACTGAGGAATGGAGGT 58.816 52.381 10.08 0.00 0.00 3.85
1823 1858 0.035152 ACAAGAATGGCCGCATCTCA 60.035 50.000 0.00 0.00 0.00 3.27
1824 1859 1.315690 CAAGAATGGCCGCATCTCAT 58.684 50.000 0.00 0.00 0.00 2.90
1825 1860 1.266175 CAAGAATGGCCGCATCTCATC 59.734 52.381 0.00 0.00 0.00 2.92
1867 1902 2.125350 CTGGGGCAGAGCTTCGAC 60.125 66.667 0.00 0.00 32.44 4.20
1868 1903 3.997064 CTGGGGCAGAGCTTCGACG 62.997 68.421 0.00 0.00 32.44 5.12
1944 1982 4.312097 GCAAAATTTCTGCGATTTGACC 57.688 40.909 8.79 0.00 35.34 4.02
1949 1987 4.691860 ATTTCTGCGATTTGACCAAGAG 57.308 40.909 0.00 0.00 0.00 2.85
1974 2012 6.071320 AGGAAATGGCTTGTCTAAGAAACTT 58.929 36.000 0.00 0.00 35.92 2.66
2030 2068 3.438434 GGAGACTGAAGAGCATCCAAAAC 59.562 47.826 0.00 0.00 33.66 2.43
2031 2069 3.070018 AGACTGAAGAGCATCCAAAACG 58.930 45.455 0.00 0.00 33.66 3.60
2032 2070 1.537202 ACTGAAGAGCATCCAAAACGC 59.463 47.619 0.00 0.00 33.66 4.84
2033 2071 1.536766 CTGAAGAGCATCCAAAACGCA 59.463 47.619 0.00 0.00 33.66 5.24
2034 2072 1.952990 TGAAGAGCATCCAAAACGCAA 59.047 42.857 0.00 0.00 33.66 4.85
2035 2073 2.360483 TGAAGAGCATCCAAAACGCAAA 59.640 40.909 0.00 0.00 33.66 3.68
2036 2074 3.181482 TGAAGAGCATCCAAAACGCAAAA 60.181 39.130 0.00 0.00 33.66 2.44
2056 2094 7.742963 CGCAAAACGTACAGAAAATACTAATGT 59.257 33.333 0.00 0.00 36.87 2.71
2062 2100 9.745880 ACGTACAGAAAATACTAATGTAGATGG 57.254 33.333 0.00 0.00 31.51 3.51
2063 2101 9.193133 CGTACAGAAAATACTAATGTAGATGGG 57.807 37.037 0.00 0.00 31.51 4.00
2081 2119 6.407202 AGATGGGTCTACACAAATGTTAGTC 58.593 40.000 0.00 0.00 40.48 2.59
2100 2144 4.362677 AGTCCAGAGTAAAGCCTATCCAA 58.637 43.478 0.00 0.00 0.00 3.53
2138 2182 5.049680 GCGAGGTTCATTCTTTGTAGTTGAA 60.050 40.000 0.00 0.00 0.00 2.69
2182 2228 7.931407 TGCTTATGTAGATGGGTTTACTATGTG 59.069 37.037 0.00 0.00 0.00 3.21
2196 2242 3.550820 ACTATGTGTGTTTTGCTCCACA 58.449 40.909 0.00 0.00 41.58 4.17
2225 2278 4.095334 TGCTTGAATCAATCTGGTGAATCG 59.905 41.667 0.00 0.00 31.21 3.34
2235 2288 0.106918 TGGTGAATCGGTATTGGGCC 60.107 55.000 0.00 0.00 0.00 5.80
2253 2306 2.866762 GGCCGAGTAATTTGCACTCTAG 59.133 50.000 5.54 0.00 40.26 2.43
2254 2307 2.866762 GCCGAGTAATTTGCACTCTAGG 59.133 50.000 5.54 2.21 40.26 3.02
2255 2308 2.866762 CCGAGTAATTTGCACTCTAGGC 59.133 50.000 5.54 0.00 40.26 3.93
2264 2317 0.762461 GCACTCTAGGCCCTCTGGAT 60.762 60.000 0.00 0.00 32.40 3.41
2269 2322 1.203237 TCTAGGCCCTCTGGATCCATC 60.203 57.143 16.63 2.39 0.00 3.51
2273 2326 1.547223 GGCCCTCTGGATCCATCATTG 60.547 57.143 16.63 2.86 0.00 2.82
2284 2346 7.603784 TCTGGATCCATCATTGAACATATAACG 59.396 37.037 16.63 0.00 0.00 3.18
2286 2348 7.387673 TGGATCCATCATTGAACATATAACGAC 59.612 37.037 11.44 0.00 0.00 4.34
2305 2367 4.894798 GACGATTCGAAGCATAGGATTC 57.105 45.455 14.56 0.00 36.10 2.52
2306 2368 4.299155 GACGATTCGAAGCATAGGATTCA 58.701 43.478 14.56 0.00 39.36 2.57
2307 2369 4.051922 ACGATTCGAAGCATAGGATTCAC 58.948 43.478 14.56 0.00 39.36 3.18
2308 2370 4.051237 CGATTCGAAGCATAGGATTCACA 58.949 43.478 14.56 0.00 39.36 3.58
2309 2371 4.507756 CGATTCGAAGCATAGGATTCACAA 59.492 41.667 14.56 0.00 39.36 3.33
2310 2372 5.557136 CGATTCGAAGCATAGGATTCACAAC 60.557 44.000 14.56 0.00 39.36 3.32
2311 2373 4.200838 TCGAAGCATAGGATTCACAACA 57.799 40.909 6.18 0.00 39.36 3.33
2312 2374 4.574892 TCGAAGCATAGGATTCACAACAA 58.425 39.130 6.18 0.00 39.36 2.83
2313 2375 5.185454 TCGAAGCATAGGATTCACAACAAT 58.815 37.500 6.18 0.00 39.36 2.71
2314 2376 6.345298 TCGAAGCATAGGATTCACAACAATA 58.655 36.000 6.18 0.00 39.36 1.90
2315 2377 6.992123 TCGAAGCATAGGATTCACAACAATAT 59.008 34.615 6.18 0.00 39.36 1.28
2316 2378 8.147704 TCGAAGCATAGGATTCACAACAATATA 58.852 33.333 6.18 0.00 39.36 0.86
2317 2379 8.773645 CGAAGCATAGGATTCACAACAATATAA 58.226 33.333 6.18 0.00 39.36 0.98
2318 2380 9.884465 GAAGCATAGGATTCACAACAATATAAC 57.116 33.333 0.00 0.00 39.22 1.89
2319 2381 8.978874 AGCATAGGATTCACAACAATATAACA 57.021 30.769 0.00 0.00 0.00 2.41
2320 2382 9.407380 AGCATAGGATTCACAACAATATAACAA 57.593 29.630 0.00 0.00 0.00 2.83
2321 2383 9.450807 GCATAGGATTCACAACAATATAACAAC 57.549 33.333 0.00 0.00 0.00 3.32
2325 2387 9.295825 AGGATTCACAACAATATAACAACTTGA 57.704 29.630 0.00 0.00 0.00 3.02
2326 2388 9.559958 GGATTCACAACAATATAACAACTTGAG 57.440 33.333 0.00 0.00 0.00 3.02
2327 2389 9.559958 GATTCACAACAATATAACAACTTGAGG 57.440 33.333 0.00 0.00 0.00 3.86
2328 2390 7.447374 TCACAACAATATAACAACTTGAGGG 57.553 36.000 0.00 0.00 0.00 4.30
2329 2391 6.432783 TCACAACAATATAACAACTTGAGGGG 59.567 38.462 0.00 0.00 0.00 4.79
2330 2392 6.208599 CACAACAATATAACAACTTGAGGGGT 59.791 38.462 0.00 0.00 0.00 4.95
2331 2393 6.780522 ACAACAATATAACAACTTGAGGGGTT 59.219 34.615 0.00 0.00 0.00 4.11
2332 2394 7.945664 ACAACAATATAACAACTTGAGGGGTTA 59.054 33.333 0.00 0.00 0.00 2.85
2333 2395 7.933215 ACAATATAACAACTTGAGGGGTTAC 57.067 36.000 0.00 0.00 0.00 2.50
2334 2396 7.696017 ACAATATAACAACTTGAGGGGTTACT 58.304 34.615 0.00 0.00 0.00 2.24
2370 2445 7.490079 TCGTACATCACTATAATGTTTGTGTCC 59.510 37.037 0.00 0.00 38.31 4.02
2373 2448 7.857456 ACATCACTATAATGTTTGTGTCCCTA 58.143 34.615 0.00 0.00 33.62 3.53
2395 2470 8.567948 CCCTAAGTACCATTATGCAAAATACAG 58.432 37.037 0.00 0.00 0.00 2.74
2399 2474 8.752005 AGTACCATTATGCAAAATACAGTGAT 57.248 30.769 0.00 0.00 0.00 3.06
2475 2550 6.985188 TCTAGGAATGCACATTTTAGTGTC 57.015 37.500 0.00 0.00 41.52 3.67
2549 2624 5.560724 TCCTGAAGCTACTGCACTTTTTAT 58.439 37.500 0.00 0.00 42.74 1.40
2577 2652 7.893124 ATACTACTCCTCTGTCCGAAATTAA 57.107 36.000 0.00 0.00 0.00 1.40
2581 2656 4.636206 ACTCCTCTGTCCGAAATTAATTGC 59.364 41.667 0.39 0.00 0.00 3.56
2583 2658 3.694072 CCTCTGTCCGAAATTAATTGCCA 59.306 43.478 0.39 0.00 0.00 4.92
2586 2661 4.394920 TCTGTCCGAAATTAATTGCCACTC 59.605 41.667 0.39 0.00 0.00 3.51
2602 2677 5.109210 TGCCACTCAAACGAATGTATCTAG 58.891 41.667 0.00 0.00 0.00 2.43
2609 2684 5.662208 TCAAACGAATGTATCTAGGGGGTAA 59.338 40.000 0.00 0.00 0.00 2.85
2612 2687 4.587684 ACGAATGTATCTAGGGGGTAACTG 59.412 45.833 0.00 0.00 0.00 3.16
2634 2709 0.392998 AGCGCCACCTCAAATCGATT 60.393 50.000 4.39 4.39 0.00 3.34
2659 2762 3.439857 TGGTGCTCTTTTGGCTCTATT 57.560 42.857 0.00 0.00 0.00 1.73
2732 2835 6.587273 AGTTGGGACTTATCTTCTTAGATGC 58.413 40.000 0.00 0.00 41.25 3.91
2753 2856 3.496160 GCCTCCCTTTTGAACACTACTCA 60.496 47.826 0.00 0.00 0.00 3.41
2757 2861 6.463897 CCTCCCTTTTGAACACTACTCAGTAA 60.464 42.308 0.00 0.00 32.21 2.24
2769 2873 9.787435 AACACTACTCAGTAATTTGGTTGATTA 57.213 29.630 0.00 0.00 32.21 1.75
2784 2888 5.943416 TGGTTGATTATTCCATGTTCTCGTT 59.057 36.000 0.00 0.00 0.00 3.85
2812 2916 6.500684 ACCACAAAGCTTATATGTGAGTTG 57.499 37.500 24.71 13.79 45.61 3.16
2814 2918 6.886459 ACCACAAAGCTTATATGTGAGTTGAT 59.114 34.615 24.71 6.22 45.61 2.57
2818 2922 9.846248 ACAAAGCTTATATGTGAGTTGATTTTC 57.154 29.630 0.00 0.00 0.00 2.29
2819 2923 9.844790 CAAAGCTTATATGTGAGTTGATTTTCA 57.155 29.630 0.00 0.00 0.00 2.69
2935 3049 5.813672 TGGTTAGTAAAGATGCGATTGTACC 59.186 40.000 0.00 0.00 0.00 3.34
2973 3087 4.662278 CTTAACTTGGTCTTTGATGGGGA 58.338 43.478 0.00 0.00 0.00 4.81
2994 3108 4.024893 GGACGCACATGTTCAGGTATAATG 60.025 45.833 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.626081 GTGTGCGGCTGGTGAGGT 62.626 66.667 0.00 0.00 0.00 3.85
110 111 2.527624 TCTCTGGGCAGGTGCTGT 60.528 61.111 1.26 0.00 41.70 4.40
123 124 1.435515 GGCGCTTCGATCTGTCTCT 59.564 57.895 7.64 0.00 0.00 3.10
144 145 2.750237 CCGTTTAGGTGCTGGCCC 60.750 66.667 0.00 0.00 34.51 5.80
207 208 0.689080 AGATGCGGGTGGATGTCTCT 60.689 55.000 0.00 0.00 0.00 3.10
232 233 3.622514 GAGATGGCTCGGTCCTGT 58.377 61.111 0.00 0.00 0.00 4.00
306 307 3.716539 TTTCTCCAGATCCGCGCGG 62.717 63.158 42.13 42.13 0.00 6.46
307 308 2.202743 TTTCTCCAGATCCGCGCG 60.203 61.111 25.67 25.67 0.00 6.86
308 309 1.884926 CCTTTCTCCAGATCCGCGC 60.885 63.158 0.00 0.00 0.00 6.86
387 388 2.705821 CGCGGTCTCTGCCTTCTCT 61.706 63.158 0.00 0.00 0.00 3.10
391 392 4.379243 CCACGCGGTCTCTGCCTT 62.379 66.667 12.47 0.00 0.00 4.35
416 417 1.974875 TCGTCTTGCTCTACGGGCA 60.975 57.895 5.66 0.00 39.52 5.36
418 419 1.226323 CGTCGTCTTGCTCTACGGG 60.226 63.158 5.66 0.00 39.52 5.28
429 430 2.976350 TGTCCTGCGTCGTCGTCT 60.976 61.111 3.66 0.00 39.49 4.18
473 474 2.609747 CTCTCCCTCCGGATCCAATTA 58.390 52.381 13.41 0.00 37.60 1.40
483 484 4.504916 CACGCAGCTCTCCCTCCG 62.505 72.222 0.00 0.00 0.00 4.63
638 649 5.749462 ACCTATCAGAAAGTCCAGAATTGG 58.251 41.667 0.00 0.00 46.49 3.16
639 650 6.648192 AGACCTATCAGAAAGTCCAGAATTG 58.352 40.000 0.00 0.00 0.00 2.32
640 651 6.882768 AGACCTATCAGAAAGTCCAGAATT 57.117 37.500 0.00 0.00 0.00 2.17
641 652 8.560124 AATAGACCTATCAGAAAGTCCAGAAT 57.440 34.615 0.00 0.00 0.00 2.40
642 653 7.979786 AATAGACCTATCAGAAAGTCCAGAA 57.020 36.000 0.00 0.00 0.00 3.02
643 654 7.619698 TCAAATAGACCTATCAGAAAGTCCAGA 59.380 37.037 0.00 0.00 0.00 3.86
644 655 7.786030 TCAAATAGACCTATCAGAAAGTCCAG 58.214 38.462 0.00 0.00 0.00 3.86
645 656 7.619698 TCTCAAATAGACCTATCAGAAAGTCCA 59.380 37.037 0.00 0.00 0.00 4.02
646 657 8.012957 TCTCAAATAGACCTATCAGAAAGTCC 57.987 38.462 0.00 0.00 0.00 3.85
648 659 9.829507 CAATCTCAAATAGACCTATCAGAAAGT 57.170 33.333 0.00 0.00 36.93 2.66
649 660 8.772705 GCAATCTCAAATAGACCTATCAGAAAG 58.227 37.037 0.00 0.00 36.93 2.62
650 661 8.489489 AGCAATCTCAAATAGACCTATCAGAAA 58.511 33.333 0.00 0.00 36.93 2.52
651 662 8.027524 AGCAATCTCAAATAGACCTATCAGAA 57.972 34.615 0.00 0.00 36.93 3.02
652 663 7.609097 AGCAATCTCAAATAGACCTATCAGA 57.391 36.000 0.00 0.00 36.93 3.27
653 664 8.674263 AAAGCAATCTCAAATAGACCTATCAG 57.326 34.615 0.00 0.00 36.93 2.90
656 667 9.343539 GGTTAAAGCAATCTCAAATAGACCTAT 57.656 33.333 0.00 0.00 36.93 2.57
657 668 8.325787 TGGTTAAAGCAATCTCAAATAGACCTA 58.674 33.333 0.00 0.00 36.93 3.08
658 669 7.121315 GTGGTTAAAGCAATCTCAAATAGACCT 59.879 37.037 0.00 0.00 36.93 3.85
659 670 7.251281 GTGGTTAAAGCAATCTCAAATAGACC 58.749 38.462 0.00 0.00 36.93 3.85
673 684 2.322081 GGCGAGCGTGGTTAAAGCA 61.322 57.895 0.00 0.00 0.00 3.91
690 701 0.533978 TTGATCCACACACCACACGG 60.534 55.000 0.00 0.00 38.77 4.94
693 704 7.953005 ATTTATATTTGATCCACACACCACA 57.047 32.000 0.00 0.00 0.00 4.17
781 792 6.890814 AGGCAATCTGAAGATTCAAAAGATCT 59.109 34.615 2.50 0.00 42.41 2.75
910 928 4.097286 TGAGTGGGTGCTTTAAAAGTGTTC 59.903 41.667 0.00 0.00 0.00 3.18
946 969 1.303643 GGTAACTGCAGGCTGCCTT 60.304 57.895 34.58 26.24 44.23 4.35
949 972 1.603455 TTGGGTAACTGCAGGCTGC 60.603 57.895 31.91 31.91 45.29 5.25
1035 1058 3.591835 GAGAGGGAGGCGAGCTCG 61.592 72.222 31.37 31.37 43.27 5.03
1060 1083 1.985116 GGAGGAGGTCCACGAGCTT 60.985 63.158 0.00 0.00 46.10 3.74
1180 1203 3.849911 CATTGTACTTCTTCCGCAGAGA 58.150 45.455 0.00 0.00 31.12 3.10
1182 1205 2.346803 GCATTGTACTTCTTCCGCAGA 58.653 47.619 0.00 0.00 0.00 4.26
1198 1221 2.185350 CTCGTCCAGGAGCGCATT 59.815 61.111 11.47 0.00 0.00 3.56
1331 1360 3.799755 GCCGCTTCAAACGCCGAT 61.800 61.111 0.00 0.00 0.00 4.18
1368 1397 2.549992 CCTCTTCACCGATTCCACAACA 60.550 50.000 0.00 0.00 0.00 3.33
1430 1459 4.715523 CCGGCCCCTGCTTCGAAA 62.716 66.667 0.00 0.00 37.74 3.46
1445 1474 3.439540 CCGGTGCCACAATTCCCG 61.440 66.667 0.00 0.00 38.39 5.14
1495 1524 2.421619 GGAAAGAAGAGGCAGTGTCTG 58.578 52.381 0.00 0.00 34.12 3.51
1496 1525 1.349357 GGGAAAGAAGAGGCAGTGTCT 59.651 52.381 0.00 0.00 0.00 3.41
1497 1526 1.611936 GGGGAAAGAAGAGGCAGTGTC 60.612 57.143 0.00 0.00 0.00 3.67
1498 1527 0.402121 GGGGAAAGAAGAGGCAGTGT 59.598 55.000 0.00 0.00 0.00 3.55
1499 1528 0.674895 CGGGGAAAGAAGAGGCAGTG 60.675 60.000 0.00 0.00 0.00 3.66
1500 1529 1.679898 CGGGGAAAGAAGAGGCAGT 59.320 57.895 0.00 0.00 0.00 4.40
1501 1530 1.078143 CCGGGGAAAGAAGAGGCAG 60.078 63.158 0.00 0.00 0.00 4.85
1542 1571 0.251033 GGGGCGAAACCTTTGGTAGT 60.251 55.000 0.00 0.00 39.10 2.73
1543 1572 0.250989 TGGGGCGAAACCTTTGGTAG 60.251 55.000 0.00 0.00 39.10 3.18
1544 1573 0.185416 TTGGGGCGAAACCTTTGGTA 59.815 50.000 0.00 0.00 39.10 3.25
1558 1587 3.393106 GCCATGGCCACTTTGGGG 61.393 66.667 27.24 12.24 38.19 4.96
1639 1668 2.406596 TTACCATTTCCCCTGCGTAC 57.593 50.000 0.00 0.00 0.00 3.67
1679 1708 2.031420 GCACATGTGGATGATGATTCCG 60.031 50.000 26.55 0.00 35.94 4.30
1701 1730 3.308401 TGCAGTCCCAGATATCTTGCTA 58.692 45.455 21.19 9.71 0.00 3.49
1724 1759 0.108138 AAGGGATCGGCACTCTTTCG 60.108 55.000 0.00 0.00 0.00 3.46
1736 1771 4.707448 TCTGTCTCTGTCTACAAAGGGATC 59.293 45.833 0.00 0.00 0.00 3.36
1738 1773 3.827302 GTCTGTCTCTGTCTACAAAGGGA 59.173 47.826 0.00 0.00 0.00 4.20
1740 1775 4.520874 TCAGTCTGTCTCTGTCTACAAAGG 59.479 45.833 0.00 0.00 34.86 3.11
1752 1787 2.430332 CCTCCATTCCTCAGTCTGTCTC 59.570 54.545 0.00 0.00 0.00 3.36
1764 1799 2.025321 TCCCTTTGCTAACCTCCATTCC 60.025 50.000 0.00 0.00 0.00 3.01
1774 1809 2.344592 TGGAAGTCCTCCCTTTGCTAA 58.655 47.619 0.00 0.00 44.69 3.09
1823 1858 0.179034 GCGAATGCCCAGAGAAGGAT 60.179 55.000 0.00 0.00 33.98 3.24
1824 1859 1.221840 GCGAATGCCCAGAGAAGGA 59.778 57.895 0.00 0.00 33.98 3.36
1825 1860 1.078214 TGCGAATGCCCAGAGAAGG 60.078 57.895 0.00 0.00 41.78 3.46
1867 1902 4.566759 TCGTTCTGGCTTGAGAAAATATCG 59.433 41.667 0.00 0.00 33.73 2.92
1868 1903 6.092807 AGTTCGTTCTGGCTTGAGAAAATATC 59.907 38.462 0.00 0.00 33.73 1.63
1929 1967 3.738982 TCTCTTGGTCAAATCGCAGAAA 58.261 40.909 0.00 0.00 43.58 2.52
1943 1981 2.751806 GACAAGCCATTTCCTCTCTTGG 59.248 50.000 0.00 0.00 38.64 3.61
1944 1982 3.683802 AGACAAGCCATTTCCTCTCTTG 58.316 45.455 0.00 0.00 39.79 3.02
1949 1987 5.707764 AGTTTCTTAGACAAGCCATTTCCTC 59.292 40.000 0.00 0.00 0.00 3.71
1974 2012 1.124780 TTTTCGAGGACACACCCTGA 58.875 50.000 0.00 0.00 40.05 3.86
2031 2069 8.944212 ACATTAGTATTTTCTGTACGTTTTGC 57.056 30.769 0.00 0.00 0.00 3.68
2036 2074 9.745880 CCATCTACATTAGTATTTTCTGTACGT 57.254 33.333 0.00 0.00 0.00 3.57
2056 2094 7.364408 GGACTAACATTTGTGTAGACCCATCTA 60.364 40.741 0.00 0.00 36.29 1.98
2057 2095 6.374417 ACTAACATTTGTGTAGACCCATCT 57.626 37.500 0.00 0.00 39.15 2.90
2058 2096 5.585047 GGACTAACATTTGTGTAGACCCATC 59.415 44.000 0.00 0.00 0.00 3.51
2059 2097 5.013704 TGGACTAACATTTGTGTAGACCCAT 59.986 40.000 13.19 0.00 0.00 4.00
2060 2098 4.348461 TGGACTAACATTTGTGTAGACCCA 59.652 41.667 13.19 11.79 0.00 4.51
2061 2099 4.901868 TGGACTAACATTTGTGTAGACCC 58.098 43.478 13.19 10.40 0.00 4.46
2062 2100 5.790593 TCTGGACTAACATTTGTGTAGACC 58.209 41.667 10.94 10.94 0.00 3.85
2063 2101 6.456501 ACTCTGGACTAACATTTGTGTAGAC 58.543 40.000 6.81 0.00 0.00 2.59
2064 2102 6.665992 ACTCTGGACTAACATTTGTGTAGA 57.334 37.500 6.81 0.00 0.00 2.59
2065 2103 8.827177 TTTACTCTGGACTAACATTTGTGTAG 57.173 34.615 0.00 0.00 0.00 2.74
2081 2119 4.878397 CAGTTTGGATAGGCTTTACTCTGG 59.122 45.833 0.00 0.00 0.00 3.86
2100 2144 0.035056 CCTCGCCCCTTCAATCAGTT 60.035 55.000 0.00 0.00 0.00 3.16
2157 2201 7.931948 ACACATAGTAAACCCATCTACATAAGC 59.068 37.037 0.00 0.00 0.00 3.09
2168 2212 4.890581 AGCAAAACACACATAGTAAACCCA 59.109 37.500 0.00 0.00 0.00 4.51
2173 2219 5.126779 TGTGGAGCAAAACACACATAGTAA 58.873 37.500 0.00 0.00 42.20 2.24
2204 2250 4.637534 ACCGATTCACCAGATTGATTCAAG 59.362 41.667 5.21 0.00 0.00 3.02
2206 2252 4.220693 ACCGATTCACCAGATTGATTCA 57.779 40.909 0.00 0.00 0.00 2.57
2210 2256 4.450976 CCAATACCGATTCACCAGATTGA 58.549 43.478 0.00 0.00 0.00 2.57
2211 2257 3.565482 CCCAATACCGATTCACCAGATTG 59.435 47.826 0.00 0.00 0.00 2.67
2225 2278 2.034179 GCAAATTACTCGGCCCAATACC 59.966 50.000 0.00 0.00 0.00 2.73
2253 2306 0.776176 AATGATGGATCCAGAGGGCC 59.224 55.000 21.33 0.00 0.00 5.80
2254 2307 1.422781 TCAATGATGGATCCAGAGGGC 59.577 52.381 21.33 7.41 0.00 5.19
2255 2308 3.117776 TGTTCAATGATGGATCCAGAGGG 60.118 47.826 21.33 8.58 0.00 4.30
2264 2317 6.508777 TCGTCGTTATATGTTCAATGATGGA 58.491 36.000 0.00 0.00 30.79 3.41
2284 2346 4.149046 GTGAATCCTATGCTTCGAATCGTC 59.851 45.833 1.52 0.00 0.00 4.20
2286 2348 4.051237 TGTGAATCCTATGCTTCGAATCG 58.949 43.478 0.00 0.00 0.00 3.34
2301 2363 9.559958 CCTCAAGTTGTTATATTGTTGTGAATC 57.440 33.333 2.11 0.00 0.00 2.52
2302 2364 8.522830 CCCTCAAGTTGTTATATTGTTGTGAAT 58.477 33.333 2.11 0.00 0.00 2.57
2304 2366 6.432783 CCCCTCAAGTTGTTATATTGTTGTGA 59.567 38.462 2.11 0.00 0.00 3.58
2305 2367 6.208599 ACCCCTCAAGTTGTTATATTGTTGTG 59.791 38.462 2.11 0.00 0.00 3.33
2306 2368 6.311735 ACCCCTCAAGTTGTTATATTGTTGT 58.688 36.000 2.11 0.00 0.00 3.32
2307 2369 6.834168 ACCCCTCAAGTTGTTATATTGTTG 57.166 37.500 2.11 0.00 0.00 3.33
2308 2370 8.168058 AGTAACCCCTCAAGTTGTTATATTGTT 58.832 33.333 2.11 2.33 0.00 2.83
2309 2371 7.696017 AGTAACCCCTCAAGTTGTTATATTGT 58.304 34.615 2.11 0.00 0.00 2.71
2310 2372 9.847224 ATAGTAACCCCTCAAGTTGTTATATTG 57.153 33.333 2.11 0.00 0.00 1.90
2346 2408 7.769044 AGGGACACAAACATTATAGTGATGTAC 59.231 37.037 1.74 2.26 36.76 2.90
2365 2440 5.031066 TGCATAATGGTACTTAGGGACAC 57.969 43.478 0.00 0.00 0.00 3.67
2370 2445 9.120538 ACTGTATTTTGCATAATGGTACTTAGG 57.879 33.333 12.07 0.00 0.00 2.69
2373 2448 8.574251 TCACTGTATTTTGCATAATGGTACTT 57.426 30.769 12.07 0.00 0.00 2.24
2402 2477 9.651718 GGAGCGTAATAATGTTCAAATCTAAAG 57.348 33.333 0.00 0.00 0.00 1.85
2407 2482 6.038271 ACCTGGAGCGTAATAATGTTCAAATC 59.962 38.462 0.00 0.00 0.00 2.17
2475 2550 3.128242 CAGGAGCACAAGGAATAGCTTTG 59.872 47.826 0.00 0.00 39.31 2.77
2549 2624 7.707624 TTTCGGACAGAGGAGTAGTATTTAA 57.292 36.000 0.00 0.00 0.00 1.52
2566 2641 4.695217 TGAGTGGCAATTAATTTCGGAC 57.305 40.909 0.00 0.00 0.00 4.79
2570 2645 7.116233 ACATTCGTTTGAGTGGCAATTAATTTC 59.884 33.333 0.00 0.00 36.24 2.17
2577 2652 4.943705 AGATACATTCGTTTGAGTGGCAAT 59.056 37.500 0.00 0.00 36.24 3.56
2581 2656 5.050490 CCCTAGATACATTCGTTTGAGTGG 58.950 45.833 0.00 0.00 36.24 4.00
2583 2658 4.101119 CCCCCTAGATACATTCGTTTGAGT 59.899 45.833 0.00 0.00 0.00 3.41
2586 2661 4.417426 ACCCCCTAGATACATTCGTTTG 57.583 45.455 0.00 0.00 0.00 2.93
2602 2677 1.070957 GGCGCTATCAGTTACCCCC 59.929 63.158 7.64 0.00 0.00 5.40
2609 2684 0.613260 TTTGAGGTGGCGCTATCAGT 59.387 50.000 6.84 0.00 0.00 3.41
2612 2687 0.861837 CGATTTGAGGTGGCGCTATC 59.138 55.000 7.64 0.00 0.00 2.08
2634 2709 3.009473 AGAGCCAAAAGAGCACCATCTTA 59.991 43.478 0.00 0.00 38.59 2.10
2659 2762 5.192927 ACTTGAACTCATCTTCAAACCACA 58.807 37.500 0.00 0.00 39.19 4.17
2732 2835 4.202367 ACTGAGTAGTGTTCAAAAGGGAGG 60.202 45.833 0.00 0.00 35.34 4.30
2757 2861 7.122650 ACGAGAACATGGAATAATCAACCAAAT 59.877 33.333 0.00 0.00 37.24 2.32
2769 2873 6.882140 TGTGGTATAAAACGAGAACATGGAAT 59.118 34.615 0.00 0.00 0.00 3.01
2784 2888 9.899661 ACTCACATATAAGCTTTGTGGTATAAA 57.100 29.630 23.11 7.74 40.82 1.40
2818 2922 7.496591 CACCTTGATTTGGGGATGAAAAATATG 59.503 37.037 0.00 0.00 0.00 1.78
2819 2923 7.365831 CCACCTTGATTTGGGGATGAAAAATAT 60.366 37.037 0.00 0.00 0.00 1.28
2825 2929 2.111613 ACCACCTTGATTTGGGGATGAA 59.888 45.455 0.00 0.00 37.18 2.57
2826 2930 1.715931 ACCACCTTGATTTGGGGATGA 59.284 47.619 0.00 0.00 37.18 2.92
2827 2931 2.236489 ACCACCTTGATTTGGGGATG 57.764 50.000 0.00 0.00 37.18 3.51
2828 2932 3.336694 AGTTACCACCTTGATTTGGGGAT 59.663 43.478 0.00 0.00 37.18 3.85
2829 2933 2.719705 AGTTACCACCTTGATTTGGGGA 59.280 45.455 0.00 0.00 37.18 4.81
2831 2935 4.034285 AGAGTTACCACCTTGATTTGGG 57.966 45.455 0.00 0.00 37.18 4.12
2908 3022 5.163893 ACAATCGCATCTTTACTAACCAACG 60.164 40.000 0.00 0.00 0.00 4.10
2935 3049 4.517285 AGTTAAGCACCATACCACATGAG 58.483 43.478 0.00 0.00 0.00 2.90
2973 3087 4.570772 GTCATTATACCTGAACATGTGCGT 59.429 41.667 0.00 0.00 0.00 5.24


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

AutoCloner maintained by Alex Coulton.