Multiple sequence alignment - TraesCS1B01G273000

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 TraesCS1B01G273000 chr1B 100.000 1440 0 0 1 1440 479792213 479793652 0.000000e+00 2660.0
1 TraesCS1B01G273000 chr1B 100.000 1207 0 0 1789 2995 479794001 479795207 0.000000e+00 2230.0
2 TraesCS1B01G273000 chr1B 86.556 543 59 5 879 1407 480326619 480327161 1.200000e-163 586.0
3 TraesCS1B01G273000 chr1B 83.083 532 54 22 1795 2296 480327166 480327691 4.550000e-123 451.0
4 TraesCS1B01G273000 chr1B 80.392 153 18 5 2677 2818 480359718 480359869 4.080000e-19 106.0
5 TraesCS1B01G273000 chr1D 92.754 1380 77 8 79 1440 356362063 356360689 0.000000e+00 1973.0
6 TraesCS1B01G273000 chr1D 89.991 1069 46 34 1804 2866 356360621 356359608 0.000000e+00 1325.0
7 TraesCS1B01G273000 chr1D 88.535 471 48 2 943 1407 356859291 356859761 1.560000e-157 566.0
8 TraesCS1B01G273000 chr1D 83.466 502 43 19 1825 2291 356860261 356860757 5.930000e-117 431.0
9 TraesCS1B01G273000 chr1D 97.403 77 2 0 1 77 356362199 356362123 6.740000e-27 132.0
10 TraesCS1B01G273000 chr1D 93.333 60 4 0 2936 2995 356359577 356359518 4.110000e-14 89.8
11 TraesCS1B01G273000 chr1A 87.396 1325 113 25 79 1381 457371268 457372560 0.000000e+00 1472.0
12 TraesCS1B01G273000 chr1A 87.719 1140 61 36 1795 2891 457372963 457374066 0.000000e+00 1256.0
13 TraesCS1B01G273000 chr1A 86.939 490 55 3 927 1407 457945248 457945737 2.630000e-150 542.0
14 TraesCS1B01G273000 chr1A 90.504 337 27 3 1795 2128 457945742 457946076 9.850000e-120 440.0
15 TraesCS1B01G273000 chr1A 81.879 149 27 0 1832 1980 457372886 457373034 3.130000e-25 126.0
16 TraesCS1B01G273000 chr1A 95.000 80 3 1 3 81 457371134 457371213 1.130000e-24 124.0
17 TraesCS1B01G273000 chr1A 100.000 30 0 0 2677 2706 457954923 457954952 4.170000e-04 56.5
18 TraesCS1B01G273000 chr6A 86.905 84 8 2 663 745 583829642 583829561 1.140000e-14 91.6
19 TraesCS1B01G273000 chr4A 84.932 73 9 2 683 755 38906054 38905984 4.140000e-09 73.1
20 TraesCS1B01G273000 chr7B 100.000 28 0 0 663 690 560501457 560501430 5.000000e-03 52.8


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 TraesCS1B01G273000 chr1B 479792213 479795207 2994 False 2445.00 2660 100.00000 1 2995 2 chr1B.!!$F2 2994
1 TraesCS1B01G273000 chr1B 480326619 480327691 1072 False 518.50 586 84.81950 879 2296 2 chr1B.!!$F3 1417
2 TraesCS1B01G273000 chr1D 356359518 356362199 2681 True 879.95 1973 93.37025 1 2995 4 chr1D.!!$R1 2994
3 TraesCS1B01G273000 chr1D 356859291 356860757 1466 False 498.50 566 86.00050 943 2291 2 chr1D.!!$F1 1348
4 TraesCS1B01G273000 chr1A 457371134 457374066 2932 False 744.50 1472 87.99850 3 2891 4 chr1A.!!$F2 2888
5 TraesCS1B01G273000 chr1A 457945248 457946076 828 False 491.00 542 88.72150 927 2128 2 chr1A.!!$F3 1201

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
199 271 0.339859 TAGGCACTCCTCCTCACCAT 59.66 55.000 0.0 0.0 43.06 3.55 F
610 683 1.070134 TCAGCTACGTGCCAAGTTCTT 59.93 47.619 0.0 0.0 44.23 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1105 1195 0.681887 TAGCCGTCGGACTTGATGGA 60.682 55.0 17.49 0.00 46.14 3.41 R
2500 3413 0.035458 AGGTCTACAGTGGCACAAGC 59.965 55.0 21.41 8.94 44.16 4.01 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
94 153 2.965831 AGCAGTAGAATAATCCGAGGCA 59.034 45.455 0.00 0.00 0.00 4.75
105 164 1.753930 TCCGAGGCACGTAGTTGATA 58.246 50.000 3.22 0.00 41.61 2.15
119 178 5.221106 CGTAGTTGATATACCGAGGACCAAA 60.221 44.000 0.00 0.00 0.00 3.28
166 238 6.516360 CGAGATTCACCATCATGACTACATCT 60.516 42.308 0.00 0.60 34.15 2.90
168 240 5.937975 TTCACCATCATGACTACATCTCA 57.062 39.130 0.00 0.00 34.15 3.27
183 255 3.900601 ACATCTCAGGGCTTGACTATAGG 59.099 47.826 4.43 0.00 0.00 2.57
197 269 2.243810 CTATAGGCACTCCTCCTCACC 58.756 57.143 0.00 0.00 43.06 4.02
199 271 0.339859 TAGGCACTCCTCCTCACCAT 59.660 55.000 0.00 0.00 43.06 3.55
225 297 3.706373 AACATCGCACCTCGCCCT 61.706 61.111 0.00 0.00 37.30 5.19
326 398 6.245408 AGAATACAAATGGCTTGTTAGGACA 58.755 36.000 0.00 0.00 46.49 4.02
327 399 6.891908 AGAATACAAATGGCTTGTTAGGACAT 59.108 34.615 0.00 0.00 46.49 3.06
328 400 4.789012 ACAAATGGCTTGTTAGGACATG 57.211 40.909 0.00 0.00 46.49 3.21
336 408 4.507710 GCTTGTTAGGACATGATGACTCA 58.492 43.478 0.00 0.00 35.29 3.41
381 453 5.869888 ACGACTCAGAGTTCAATTGTAATCC 59.130 40.000 4.05 0.00 0.00 3.01
408 480 3.811722 ATACACAACATGCGACACAAG 57.188 42.857 0.00 0.00 0.00 3.16
444 516 4.789629 CGCATCAACATGACATTGTAACAG 59.210 41.667 0.00 0.00 30.57 3.16
481 553 1.128507 TGATCAATGAAGCAACGTCGC 59.871 47.619 0.00 0.00 0.00 5.19
494 567 3.057736 GCAACGTCGCTCCCTAATAGATA 60.058 47.826 0.00 0.00 0.00 1.98
610 683 1.070134 TCAGCTACGTGCCAAGTTCTT 59.930 47.619 0.00 0.00 44.23 2.52
634 707 4.221924 TGAGCAAGTGTACTGCTATTACCA 59.778 41.667 7.98 0.07 39.21 3.25
635 708 5.104941 TGAGCAAGTGTACTGCTATTACCAT 60.105 40.000 7.98 0.00 39.21 3.55
644 717 5.036117 ACTGCTATTACCATCGTCCAAAT 57.964 39.130 0.00 0.00 0.00 2.32
710 783 9.427821 AGATATTATCCGTATCTAGGCAAATCT 57.572 33.333 0.00 0.00 37.19 2.40
733 806 8.801882 TCTAAAACAAATAATTCAGGACGGAT 57.198 30.769 0.00 0.00 0.00 4.18
747 820 5.710567 TCAGGACGGATGGAGTATTATACAG 59.289 44.000 5.11 0.00 0.00 2.74
771 844 4.082026 GCAAAGCCACTATGGTGATCTTTT 60.082 41.667 19.13 9.21 45.61 2.27
772 845 5.125417 GCAAAGCCACTATGGTGATCTTTTA 59.875 40.000 19.13 0.00 45.61 1.52
982 1069 2.490902 CCTGCTAGGGTTTTGGTCCTTT 60.491 50.000 0.00 0.00 34.75 3.11
1105 1195 0.396811 CCTTTTCGTCCACCAGTCCT 59.603 55.000 0.00 0.00 0.00 3.85
1422 1521 1.070786 CCGTGGGTGCTACAAGTGT 59.929 57.895 0.00 0.00 0.00 3.55
2031 2907 1.201429 ATCTGAGTGCCCCGTTTCCT 61.201 55.000 0.00 0.00 0.00 3.36
2052 2928 2.822707 TCGCTCCTTTACCTACCTCT 57.177 50.000 0.00 0.00 0.00 3.69
2142 3035 2.460330 CTCGATGCGAGCTTGGTTT 58.540 52.632 2.37 0.00 46.75 3.27
2392 3301 3.333381 TGGAATCCTGTTCTCCCATTTCA 59.667 43.478 0.00 0.00 0.00 2.69
2396 3305 4.387026 TCCTGTTCTCCCATTTCAATGT 57.613 40.909 0.00 0.00 34.60 2.71
2422 3331 2.159254 CCATTGGCGTTTTGATAGTGGG 60.159 50.000 0.00 0.00 0.00 4.61
2423 3332 2.279935 TTGGCGTTTTGATAGTGGGT 57.720 45.000 0.00 0.00 0.00 4.51
2424 3333 3.420300 TTGGCGTTTTGATAGTGGGTA 57.580 42.857 0.00 0.00 0.00 3.69
2425 3334 2.702261 TGGCGTTTTGATAGTGGGTAC 58.298 47.619 0.00 0.00 0.00 3.34
2454 3367 4.567959 GCAAGTTTGATGCTTTTCAACAGT 59.432 37.500 0.00 0.00 40.64 3.55
2465 3378 5.108517 GCTTTTCAACAGTTTCATGGTTCA 58.891 37.500 0.00 0.00 0.00 3.18
2473 3386 8.040132 TCAACAGTTTCATGGTTCAAAATCTTT 58.960 29.630 0.00 0.00 0.00 2.52
2474 3387 8.330302 CAACAGTTTCATGGTTCAAAATCTTTC 58.670 33.333 0.00 0.00 0.00 2.62
2475 3388 7.785033 ACAGTTTCATGGTTCAAAATCTTTCT 58.215 30.769 0.00 0.00 0.00 2.52
2476 3389 8.260114 ACAGTTTCATGGTTCAAAATCTTTCTT 58.740 29.630 0.00 0.00 0.00 2.52
2477 3390 9.748708 CAGTTTCATGGTTCAAAATCTTTCTTA 57.251 29.630 0.00 0.00 0.00 2.10
2514 3427 2.849294 TATGTGCTTGTGCCACTGTA 57.151 45.000 0.00 0.00 38.71 2.74
2515 3428 1.527034 ATGTGCTTGTGCCACTGTAG 58.473 50.000 0.00 0.00 38.71 2.74
2516 3429 0.467804 TGTGCTTGTGCCACTGTAGA 59.532 50.000 0.00 0.00 38.71 2.59
2518 3431 0.250295 TGCTTGTGCCACTGTAGACC 60.250 55.000 0.00 0.00 38.71 3.85
2519 3432 0.035458 GCTTGTGCCACTGTAGACCT 59.965 55.000 0.00 0.00 0.00 3.85
2520 3433 1.800805 CTTGTGCCACTGTAGACCTG 58.199 55.000 0.00 0.00 0.00 4.00
2521 3434 0.250295 TTGTGCCACTGTAGACCTGC 60.250 55.000 0.00 0.00 0.00 4.85
2522 3435 1.371183 GTGCCACTGTAGACCTGCA 59.629 57.895 0.00 0.00 0.00 4.41
2523 3436 0.951040 GTGCCACTGTAGACCTGCAC 60.951 60.000 0.00 0.00 41.75 4.57
2524 3437 1.121407 TGCCACTGTAGACCTGCACT 61.121 55.000 0.00 0.00 0.00 4.40
2525 3438 0.671781 GCCACTGTAGACCTGCACTG 60.672 60.000 0.00 0.00 0.00 3.66
2526 3439 0.671781 CCACTGTAGACCTGCACTGC 60.672 60.000 0.00 0.00 0.00 4.40
2527 3440 0.319728 CACTGTAGACCTGCACTGCT 59.680 55.000 1.98 0.00 0.00 4.24
2528 3441 1.051812 ACTGTAGACCTGCACTGCTT 58.948 50.000 1.98 0.00 0.00 3.91
2529 3442 1.270518 ACTGTAGACCTGCACTGCTTG 60.271 52.381 1.98 0.00 0.00 4.01
2530 3443 0.758734 TGTAGACCTGCACTGCTTGT 59.241 50.000 1.98 0.00 0.00 3.16
2531 3444 1.270305 TGTAGACCTGCACTGCTTGTC 60.270 52.381 12.81 12.81 32.81 3.18
2532 3445 1.001406 GTAGACCTGCACTGCTTGTCT 59.999 52.381 21.76 21.76 40.77 3.41
2533 3446 0.250209 AGACCTGCACTGCTTGTCTG 60.250 55.000 19.12 0.00 38.15 3.51
2534 3447 0.250038 GACCTGCACTGCTTGTCTGA 60.250 55.000 13.22 0.00 31.07 3.27
2535 3448 0.533755 ACCTGCACTGCTTGTCTGAC 60.534 55.000 1.98 0.00 0.00 3.51
2536 3449 0.250209 CCTGCACTGCTTGTCTGACT 60.250 55.000 9.51 0.00 0.00 3.41
2537 3450 0.866427 CTGCACTGCTTGTCTGACTG 59.134 55.000 9.51 3.43 0.00 3.51
2538 3451 1.162181 TGCACTGCTTGTCTGACTGC 61.162 55.000 9.51 13.18 0.00 4.40
2539 3452 0.883814 GCACTGCTTGTCTGACTGCT 60.884 55.000 20.38 5.54 0.00 4.24
2540 3453 1.606480 GCACTGCTTGTCTGACTGCTA 60.606 52.381 20.38 10.67 0.00 3.49
2541 3454 2.064762 CACTGCTTGTCTGACTGCTAC 58.935 52.381 20.38 4.64 0.00 3.58
2544 3457 3.057174 ACTGCTTGTCTGACTGCTACTAC 60.057 47.826 20.38 1.48 0.00 2.73
2548 3461 4.396790 GCTTGTCTGACTGCTACTACTAGT 59.603 45.833 9.51 0.00 0.00 2.57
2557 3470 6.092396 TGACTGCTACTACTAGTTTCTTCTCG 59.908 42.308 0.00 0.00 0.00 4.04
2592 3505 8.188139 GCTTGCAAAATGTAACCTAGCTTAATA 58.812 33.333 0.00 0.00 0.00 0.98
2607 3520 6.207691 AGCTTAATATTTTTGCATCCGTGT 57.792 33.333 0.00 0.00 0.00 4.49
2617 3530 2.710377 TGCATCCGTGTTAAGCAAGAT 58.290 42.857 0.00 0.00 31.42 2.40
2618 3531 3.081061 TGCATCCGTGTTAAGCAAGATT 58.919 40.909 0.00 0.00 31.42 2.40
2621 3534 3.306917 TCCGTGTTAAGCAAGATTCGA 57.693 42.857 0.00 0.00 0.00 3.71
2633 3546 3.549625 GCAAGATTCGATGATTCCTTGCC 60.550 47.826 12.32 0.00 39.70 4.52
2639 3552 3.143728 TCGATGATTCCTTGCCATGATG 58.856 45.455 0.00 0.00 0.00 3.07
2644 3557 2.148446 TTCCTTGCCATGATGGAAGG 57.852 50.000 24.67 24.67 40.96 3.46
2658 3571 4.773674 TGATGGAAGGCAAATTCAATCAGT 59.226 37.500 10.12 0.00 42.24 3.41
2670 3583 6.395426 AATTCAATCAGTTCTGCTGTCAAA 57.605 33.333 0.00 0.00 45.23 2.69
2767 3704 0.037326 CCGTTGCAGCTTAGTGGAGA 60.037 55.000 0.00 0.00 0.00 3.71
2768 3705 1.354040 CGTTGCAGCTTAGTGGAGAG 58.646 55.000 0.00 0.00 0.00 3.20
2820 3757 5.810587 TGGAATCATGTCGCTTTAGACTTAC 59.189 40.000 0.00 0.00 41.47 2.34
2822 3759 4.430137 TCATGTCGCTTTAGACTTACGT 57.570 40.909 0.00 0.00 41.47 3.57
2848 3786 7.119992 TGTGCGAAGAATAACAGCCTAAATTTA 59.880 33.333 0.00 0.00 0.00 1.40
2861 3799 9.397280 ACAGCCTAAATTTAGATCTCCTTAAAC 57.603 33.333 23.95 2.03 32.47 2.01
2862 3800 9.396022 CAGCCTAAATTTAGATCTCCTTAAACA 57.604 33.333 23.95 0.00 32.47 2.83
2879 3819 7.990886 TCCTTAAACATATATGACTGAACCCAC 59.009 37.037 19.63 0.00 0.00 4.61
2891 3831 5.186215 TGACTGAACCCACGAACTATGATTA 59.814 40.000 0.00 0.00 0.00 1.75
2893 3833 4.426416 TGAACCCACGAACTATGATTACG 58.574 43.478 0.00 0.00 0.00 3.18
2894 3834 4.158209 TGAACCCACGAACTATGATTACGA 59.842 41.667 0.00 0.00 0.00 3.43
2895 3835 4.931661 ACCCACGAACTATGATTACGAT 57.068 40.909 0.00 0.00 0.00 3.73
2896 3836 4.617959 ACCCACGAACTATGATTACGATG 58.382 43.478 0.00 0.00 0.00 3.84
2897 3837 4.340097 ACCCACGAACTATGATTACGATGA 59.660 41.667 0.00 0.00 0.00 2.92
2898 3838 4.680110 CCCACGAACTATGATTACGATGAC 59.320 45.833 0.00 0.00 0.00 3.06
2899 3839 5.507482 CCCACGAACTATGATTACGATGACT 60.507 44.000 0.00 0.00 0.00 3.41
2900 3840 5.977725 CCACGAACTATGATTACGATGACTT 59.022 40.000 0.00 0.00 0.00 3.01
2901 3841 7.136772 CCACGAACTATGATTACGATGACTTA 58.863 38.462 0.00 0.00 0.00 2.24
2902 3842 7.808381 CCACGAACTATGATTACGATGACTTAT 59.192 37.037 0.00 0.00 0.00 1.73
2903 3843 9.181805 CACGAACTATGATTACGATGACTTATT 57.818 33.333 0.00 0.00 0.00 1.40
2910 3850 7.796958 TGATTACGATGACTTATTATCTGCG 57.203 36.000 0.00 0.00 0.00 5.18
2911 3851 6.806739 TGATTACGATGACTTATTATCTGCGG 59.193 38.462 0.00 0.00 0.00 5.69
2912 3852 3.318017 ACGATGACTTATTATCTGCGGC 58.682 45.455 0.00 0.00 0.00 6.53
2913 3853 3.005897 ACGATGACTTATTATCTGCGGCT 59.994 43.478 0.00 0.00 0.00 5.52
2914 3854 3.990469 CGATGACTTATTATCTGCGGCTT 59.010 43.478 0.00 0.00 0.00 4.35
2915 3855 4.449068 CGATGACTTATTATCTGCGGCTTT 59.551 41.667 0.00 0.00 0.00 3.51
2916 3856 5.050091 CGATGACTTATTATCTGCGGCTTTT 60.050 40.000 0.00 0.00 0.00 2.27
2917 3857 6.511767 CGATGACTTATTATCTGCGGCTTTTT 60.512 38.462 0.00 0.00 0.00 1.94
2918 3858 7.307160 CGATGACTTATTATCTGCGGCTTTTTA 60.307 37.037 0.00 0.00 0.00 1.52
2919 3859 7.246674 TGACTTATTATCTGCGGCTTTTTAG 57.753 36.000 0.00 0.00 0.00 1.85
2920 3860 6.061231 ACTTATTATCTGCGGCTTTTTAGC 57.939 37.500 0.00 0.00 0.00 3.09
2921 3861 5.588648 ACTTATTATCTGCGGCTTTTTAGCA 59.411 36.000 0.00 0.00 39.25 3.49
2922 3862 6.263168 ACTTATTATCTGCGGCTTTTTAGCAT 59.737 34.615 0.00 0.00 40.35 3.79
2923 3863 7.444183 ACTTATTATCTGCGGCTTTTTAGCATA 59.556 33.333 0.00 0.00 40.35 3.14
2924 3864 6.633500 ATTATCTGCGGCTTTTTAGCATAA 57.367 33.333 0.00 0.00 40.35 1.90
2925 3865 4.981806 ATCTGCGGCTTTTTAGCATAAA 57.018 36.364 0.00 0.00 40.35 1.40
2926 3866 4.981806 TCTGCGGCTTTTTAGCATAAAT 57.018 36.364 0.00 0.00 40.35 1.40
2927 3867 5.323371 TCTGCGGCTTTTTAGCATAAATT 57.677 34.783 0.00 0.00 40.35 1.82
2928 3868 5.719173 TCTGCGGCTTTTTAGCATAAATTT 58.281 33.333 0.00 0.00 40.35 1.82
2929 3869 6.857956 TCTGCGGCTTTTTAGCATAAATTTA 58.142 32.000 0.00 0.00 40.35 1.40
2930 3870 7.316640 TCTGCGGCTTTTTAGCATAAATTTAA 58.683 30.769 1.21 0.00 40.35 1.52
2931 3871 7.978975 TCTGCGGCTTTTTAGCATAAATTTAAT 59.021 29.630 1.21 0.00 40.35 1.40
2932 3872 9.243637 CTGCGGCTTTTTAGCATAAATTTAATA 57.756 29.630 1.21 0.00 40.35 0.98
2933 3873 9.243637 TGCGGCTTTTTAGCATAAATTTAATAG 57.756 29.630 1.21 0.00 35.81 1.73
2934 3874 8.214472 GCGGCTTTTTAGCATAAATTTAATAGC 58.786 33.333 1.21 7.19 36.33 2.97
2954 3894 2.346847 GCTGTGAGCTTACGATGACTTG 59.653 50.000 3.97 0.00 38.45 3.16
2956 3896 3.990092 TGTGAGCTTACGATGACTTGTT 58.010 40.909 3.97 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 153 3.817647 GGTCCTCGGTATATCAACTACGT 59.182 47.826 0.00 0.00 0.00 3.57
105 164 3.992943 TGATTGTTTGGTCCTCGGTAT 57.007 42.857 0.00 0.00 0.00 2.73
119 178 4.433615 GGTGTCATGTCTCGTATGATTGT 58.566 43.478 0.00 0.00 36.96 2.71
166 238 1.762957 GTGCCTATAGTCAAGCCCTGA 59.237 52.381 0.00 0.00 0.00 3.86
168 240 2.043227 GAGTGCCTATAGTCAAGCCCT 58.957 52.381 0.00 0.00 0.00 5.19
183 255 0.466124 GGTATGGTGAGGAGGAGTGC 59.534 60.000 0.00 0.00 0.00 4.40
197 269 1.257936 GTGCGATGTTGTAGCGGTATG 59.742 52.381 0.00 0.00 38.92 2.39
199 271 0.458889 GGTGCGATGTTGTAGCGGTA 60.459 55.000 0.00 0.00 38.92 4.02
342 414 8.322828 ACTCTGAGTCGTATGGTATGTAGATAT 58.677 37.037 4.06 0.00 0.00 1.63
381 453 5.959527 GTGTCGCATGTTGTGTATAAAGATG 59.040 40.000 0.00 0.00 32.85 2.90
408 480 5.090652 TGTTGATGCGAAAGTTGTTAGAC 57.909 39.130 0.00 0.00 0.00 2.59
444 516 4.755411 TGATCAACGAGGTCCATAAGAAC 58.245 43.478 0.00 0.00 0.00 3.01
536 609 0.684153 CCGGGTGCTCCATTTTCCAT 60.684 55.000 7.20 0.00 34.36 3.41
540 613 0.039618 ATGTCCGGGTGCTCCATTTT 59.960 50.000 0.00 0.00 34.36 1.82
610 683 5.175859 GGTAATAGCAGTACACTTGCTCAA 58.824 41.667 11.03 0.00 39.79 3.02
634 707 7.424227 TTTAAGACACGTAAATTTGGACGAT 57.576 32.000 17.89 7.39 41.60 3.73
635 708 6.841443 TTTAAGACACGTAAATTTGGACGA 57.159 33.333 17.89 0.00 41.60 4.20
710 783 7.612244 TCCATCCGTCCTGAATTATTTGTTTTA 59.388 33.333 0.00 0.00 0.00 1.52
733 806 4.714632 GGCTTTGCCTGTATAATACTCCA 58.285 43.478 0.73 0.00 46.69 3.86
982 1069 4.320928 CTTGCGCCGCCGAAAACA 62.321 61.111 6.63 0.00 36.29 2.83
1105 1195 0.681887 TAGCCGTCGGACTTGATGGA 60.682 55.000 17.49 0.00 46.14 3.41
1152 1242 1.405463 CCGGTGATGATCTCGAACTCA 59.595 52.381 9.52 0.00 0.00 3.41
1247 1337 3.998672 GGTCACCACCGCCTTCGA 61.999 66.667 0.00 0.00 38.10 3.71
2031 2907 3.438183 AGAGGTAGGTAAAGGAGCGAAA 58.562 45.455 0.00 0.00 0.00 3.46
2052 2928 3.691118 GGTATGACTTGCTGCAGAATCAA 59.309 43.478 20.43 11.45 0.00 2.57
2142 3035 2.158623 ACACCACCAGCAATTCTTCTGA 60.159 45.455 0.00 0.00 32.26 3.27
2392 3301 3.959535 AAACGCCAATGGAATCACATT 57.040 38.095 2.05 0.00 41.51 2.71
2396 3305 4.704540 ACTATCAAAACGCCAATGGAATCA 59.295 37.500 2.05 0.00 0.00 2.57
2422 3331 3.091417 GCATCAAACTTGCGAATCGTAC 58.909 45.455 4.07 0.00 0.00 3.67
2423 3332 3.000041 AGCATCAAACTTGCGAATCGTA 59.000 40.909 4.07 0.00 44.82 3.43
2424 3333 1.806542 AGCATCAAACTTGCGAATCGT 59.193 42.857 4.07 0.00 44.82 3.73
2425 3334 2.532531 AGCATCAAACTTGCGAATCG 57.467 45.000 0.00 0.00 44.82 3.34
2477 3390 9.646522 AAGCACATATAAGAATGGACCTTATTT 57.353 29.630 0.00 0.00 37.78 1.40
2478 3391 9.071276 CAAGCACATATAAGAATGGACCTTATT 57.929 33.333 0.00 0.00 37.78 1.40
2479 3392 8.220559 ACAAGCACATATAAGAATGGACCTTAT 58.779 33.333 0.00 0.00 39.41 1.73
2480 3393 7.498900 CACAAGCACATATAAGAATGGACCTTA 59.501 37.037 0.00 0.00 0.00 2.69
2481 3394 6.319658 CACAAGCACATATAAGAATGGACCTT 59.680 38.462 0.00 0.00 0.00 3.50
2500 3413 0.035458 AGGTCTACAGTGGCACAAGC 59.965 55.000 21.41 8.94 44.16 4.01
2514 3427 0.250209 CAGACAAGCAGTGCAGGTCT 60.250 55.000 26.63 26.63 42.03 3.85
2515 3428 0.250038 TCAGACAAGCAGTGCAGGTC 60.250 55.000 23.82 23.82 35.28 3.85
2516 3429 0.533755 GTCAGACAAGCAGTGCAGGT 60.534 55.000 19.20 14.66 0.00 4.00
2518 3431 0.866427 CAGTCAGACAAGCAGTGCAG 59.134 55.000 19.20 11.98 0.00 4.41
2519 3432 1.162181 GCAGTCAGACAAGCAGTGCA 61.162 55.000 19.20 0.00 36.62 4.57
2520 3433 0.883814 AGCAGTCAGACAAGCAGTGC 60.884 55.000 7.13 7.13 36.83 4.40
2521 3434 2.064762 GTAGCAGTCAGACAAGCAGTG 58.935 52.381 17.31 1.55 0.00 3.66
2522 3435 1.967066 AGTAGCAGTCAGACAAGCAGT 59.033 47.619 17.31 6.44 0.00 4.40
2523 3436 2.739885 AGTAGCAGTCAGACAAGCAG 57.260 50.000 17.31 0.00 0.00 4.24
2524 3437 3.157881 AGTAGTAGCAGTCAGACAAGCA 58.842 45.455 17.31 4.22 0.00 3.91
2525 3438 3.859411 AGTAGTAGCAGTCAGACAAGC 57.141 47.619 2.66 6.62 0.00 4.01
2526 3439 6.503589 AACTAGTAGTAGCAGTCAGACAAG 57.496 41.667 2.50 0.00 0.00 3.16
2527 3440 6.715718 AGAAACTAGTAGTAGCAGTCAGACAA 59.284 38.462 2.50 0.00 0.00 3.18
2528 3441 6.239396 AGAAACTAGTAGTAGCAGTCAGACA 58.761 40.000 2.50 0.00 0.00 3.41
2529 3442 6.746745 AGAAACTAGTAGTAGCAGTCAGAC 57.253 41.667 2.50 0.00 0.00 3.51
2530 3443 7.169591 AGAAGAAACTAGTAGTAGCAGTCAGA 58.830 38.462 2.50 0.00 0.00 3.27
2531 3444 7.385778 AGAAGAAACTAGTAGTAGCAGTCAG 57.614 40.000 2.50 0.00 0.00 3.51
2532 3445 6.092396 CGAGAAGAAACTAGTAGTAGCAGTCA 59.908 42.308 2.50 0.00 0.00 3.41
2533 3446 6.092533 ACGAGAAGAAACTAGTAGTAGCAGTC 59.907 42.308 2.50 0.39 0.00 3.51
2534 3447 5.939296 ACGAGAAGAAACTAGTAGTAGCAGT 59.061 40.000 2.50 0.00 0.00 4.40
2535 3448 6.252281 CACGAGAAGAAACTAGTAGTAGCAG 58.748 44.000 2.50 0.00 0.00 4.24
2536 3449 5.391736 GCACGAGAAGAAACTAGTAGTAGCA 60.392 44.000 2.50 0.00 0.00 3.49
2537 3450 5.029654 GCACGAGAAGAAACTAGTAGTAGC 58.970 45.833 2.50 0.00 0.00 3.58
2538 3451 5.123502 TGGCACGAGAAGAAACTAGTAGTAG 59.876 44.000 2.50 2.87 0.00 2.57
2539 3452 5.005740 TGGCACGAGAAGAAACTAGTAGTA 58.994 41.667 2.50 0.00 0.00 1.82
2540 3453 3.825014 TGGCACGAGAAGAAACTAGTAGT 59.175 43.478 0.00 0.00 0.00 2.73
2541 3454 4.082679 AGTGGCACGAGAAGAAACTAGTAG 60.083 45.833 12.71 0.00 0.00 2.57
2544 3457 3.305398 AGTGGCACGAGAAGAAACTAG 57.695 47.619 12.71 0.00 0.00 2.57
2548 3461 0.944386 GCAAGTGGCACGAGAAGAAA 59.056 50.000 12.71 0.00 43.97 2.52
2592 3505 4.250116 TGCTTAACACGGATGCAAAAAT 57.750 36.364 0.00 0.00 0.00 1.82
2607 3520 7.019774 CAAGGAATCATCGAATCTTGCTTAA 57.980 36.000 9.49 0.00 29.66 1.85
2617 3530 3.280197 TCATGGCAAGGAATCATCGAA 57.720 42.857 0.00 0.00 0.00 3.71
2618 3531 3.143728 CATCATGGCAAGGAATCATCGA 58.856 45.455 0.00 0.00 0.00 3.59
2621 3534 3.605726 TCCATCATGGCAAGGAATCAT 57.394 42.857 0.00 0.00 37.47 2.45
2633 3546 5.666462 TGATTGAATTTGCCTTCCATCATG 58.334 37.500 4.44 0.00 34.28 3.07
2639 3552 5.166398 CAGAACTGATTGAATTTGCCTTCC 58.834 41.667 0.00 0.00 0.00 3.46
2658 3571 8.284945 AGCTTATAATGAATTTGACAGCAGAA 57.715 30.769 0.00 0.00 0.00 3.02
2744 3681 1.738099 ACTAAGCTGCAACGGAGCG 60.738 57.895 1.02 0.00 41.61 5.03
2767 3704 3.144506 CATCCAAGACAAAGCACACTCT 58.855 45.455 0.00 0.00 0.00 3.24
2768 3705 3.141398 TCATCCAAGACAAAGCACACTC 58.859 45.455 0.00 0.00 0.00 3.51
2820 3757 1.201921 GGCTGTTATTCTTCGCACACG 60.202 52.381 0.00 0.00 42.01 4.49
2822 3759 2.472695 AGGCTGTTATTCTTCGCACA 57.527 45.000 0.00 0.00 0.00 4.57
2858 3796 5.984725 TCGTGGGTTCAGTCATATATGTTT 58.015 37.500 12.42 0.00 0.00 2.83
2859 3797 5.607939 TCGTGGGTTCAGTCATATATGTT 57.392 39.130 12.42 0.15 0.00 2.71
2861 3799 5.601662 AGTTCGTGGGTTCAGTCATATATG 58.398 41.667 6.36 6.36 0.00 1.78
2862 3800 5.871396 AGTTCGTGGGTTCAGTCATATAT 57.129 39.130 0.00 0.00 0.00 0.86
2863 3801 6.548251 TCATAGTTCGTGGGTTCAGTCATATA 59.452 38.462 0.00 0.00 0.00 0.86
2865 3803 4.707934 TCATAGTTCGTGGGTTCAGTCATA 59.292 41.667 0.00 0.00 0.00 2.15
2866 3804 3.513912 TCATAGTTCGTGGGTTCAGTCAT 59.486 43.478 0.00 0.00 0.00 3.06
2867 3805 2.894765 TCATAGTTCGTGGGTTCAGTCA 59.105 45.455 0.00 0.00 0.00 3.41
2868 3806 3.587797 TCATAGTTCGTGGGTTCAGTC 57.412 47.619 0.00 0.00 0.00 3.51
2869 3807 4.553330 AATCATAGTTCGTGGGTTCAGT 57.447 40.909 0.00 0.00 0.00 3.41
2870 3808 4.503007 CGTAATCATAGTTCGTGGGTTCAG 59.497 45.833 0.00 0.00 0.00 3.02
2871 3809 4.158209 TCGTAATCATAGTTCGTGGGTTCA 59.842 41.667 0.00 0.00 0.00 3.18
2876 3816 5.520632 AGTCATCGTAATCATAGTTCGTGG 58.479 41.667 0.00 0.00 0.00 4.94
2891 3831 3.005897 AGCCGCAGATAATAAGTCATCGT 59.994 43.478 0.00 0.00 0.00 3.73
2893 3833 5.931441 AAAGCCGCAGATAATAAGTCATC 57.069 39.130 0.00 0.00 0.00 2.92
2894 3834 6.699575 AAAAAGCCGCAGATAATAAGTCAT 57.300 33.333 0.00 0.00 0.00 3.06
2895 3835 6.238374 GCTAAAAAGCCGCAGATAATAAGTCA 60.238 38.462 0.00 0.00 0.00 3.41
2896 3836 6.136743 GCTAAAAAGCCGCAGATAATAAGTC 58.863 40.000 0.00 0.00 0.00 3.01
2897 3837 5.588648 TGCTAAAAAGCCGCAGATAATAAGT 59.411 36.000 0.00 0.00 0.00 2.24
2898 3838 6.060028 TGCTAAAAAGCCGCAGATAATAAG 57.940 37.500 0.00 0.00 0.00 1.73
2899 3839 6.633500 ATGCTAAAAAGCCGCAGATAATAA 57.367 33.333 0.00 0.00 0.00 1.40
2900 3840 7.737972 TTATGCTAAAAAGCCGCAGATAATA 57.262 32.000 0.00 0.00 0.00 0.98
2901 3841 6.633500 TTATGCTAAAAAGCCGCAGATAAT 57.367 33.333 0.00 0.00 0.00 1.28
2902 3842 6.443934 TTTATGCTAAAAAGCCGCAGATAA 57.556 33.333 0.00 0.00 0.00 1.75
2903 3843 6.633500 ATTTATGCTAAAAAGCCGCAGATA 57.367 33.333 0.00 0.00 0.00 1.98
2904 3844 4.981806 TTTATGCTAAAAAGCCGCAGAT 57.018 36.364 0.00 0.00 0.00 2.90
2905 3845 4.981806 ATTTATGCTAAAAAGCCGCAGA 57.018 36.364 0.00 0.00 0.00 4.26
2906 3846 7.518731 TTAAATTTATGCTAAAAAGCCGCAG 57.481 32.000 0.00 0.00 0.00 5.18
2907 3847 9.243637 CTATTAAATTTATGCTAAAAAGCCGCA 57.756 29.630 0.00 0.00 0.00 5.69
2908 3848 8.214472 GCTATTAAATTTATGCTAAAAAGCCGC 58.786 33.333 0.00 0.00 0.00 6.53
2909 3849 9.463443 AGCTATTAAATTTATGCTAAAAAGCCG 57.537 29.630 14.91 0.00 0.00 5.52
2915 3855 9.950680 GCTCACAGCTATTAAATTTATGCTAAA 57.049 29.630 15.63 0.00 38.45 1.85
2933 3873 2.285827 AGTCATCGTAAGCTCACAGC 57.714 50.000 0.00 0.00 42.84 4.40
2934 3874 3.579709 ACAAGTCATCGTAAGCTCACAG 58.420 45.455 0.00 0.00 37.18 3.66
2948 3888 2.472695 AAGCCGCAGATAACAAGTCA 57.527 45.000 0.00 0.00 0.00 3.41
2954 3894 3.757745 TGCTAAAAAGCCGCAGATAAC 57.242 42.857 0.00 0.00 0.00 1.89
2956 3896 4.981806 AAATGCTAAAAAGCCGCAGATA 57.018 36.364 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.