Multiple sequence alignment - TraesCS5D01G337600

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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 TraesCS5D01G337600 chr5D 100.000 3392 0 0 1 3392 426287135 426290526 0.000000e+00 6264.0
1 TraesCS5D01G337600 chr5A 95.441 1711 61 10 962 2668 540385158 540386855 0.000000e+00 2712.0
2 TraesCS5D01G337600 chr5A 93.051 662 44 2 301 961 588296235 588295575 0.000000e+00 966.0
3 TraesCS5D01G337600 chr5A 94.624 93 4 1 1 92 540384990 540385082 3.530000e-30 143.0
4 TraesCS5D01G337600 chr5A 98.684 76 0 1 148 222 540385080 540385155 2.120000e-27 134.0
5 TraesCS5D01G337600 chr5A 75.573 262 57 6 2903 3159 38786125 38785866 4.600000e-24 122.0
6 TraesCS5D01G337600 chr5A 93.056 72 3 2 214 284 197708646 197708576 1.660000e-18 104.0
7 TraesCS5D01G337600 chr5B 95.458 1431 43 3 963 2393 516066351 516067759 0.000000e+00 2263.0
8 TraesCS5D01G337600 chr5B 88.972 535 58 1 2842 3376 516081926 516082459 0.000000e+00 660.0
9 TraesCS5D01G337600 chr5B 91.525 236 10 6 1 229 516066125 516066357 1.960000e-82 316.0
10 TraesCS5D01G337600 chr5B 75.494 253 57 4 2903 3151 101350419 101350168 5.950000e-23 119.0
11 TraesCS5D01G337600 chr5B 81.890 127 23 0 3194 3320 50541718 50541844 1.290000e-19 108.0
12 TraesCS5D01G337600 chr6A 93.124 669 43 3 295 961 46945478 46946145 0.000000e+00 977.0
13 TraesCS5D01G337600 chr6A 100.000 62 0 0 223 284 537788032 537787971 7.690000e-22 115.0
14 TraesCS5D01G337600 chr2D 92.192 666 51 1 296 961 584673262 584672598 0.000000e+00 941.0
15 TraesCS5D01G337600 chr2B 91.566 664 52 3 304 964 475543144 475542482 0.000000e+00 913.0
16 TraesCS5D01G337600 chr2B 95.588 68 2 1 218 284 669489746 669489679 1.290000e-19 108.0
17 TraesCS5D01G337600 chr1D 91.541 662 54 2 301 961 297822054 297821394 0.000000e+00 911.0
18 TraesCS5D01G337600 chr1D 90.269 668 60 5 295 961 127098490 127099153 0.000000e+00 869.0
19 TraesCS5D01G337600 chr1D 100.000 58 0 0 228 285 297822097 297822040 1.290000e-19 108.0
20 TraesCS5D01G337600 chr1B 91.390 662 54 3 301 961 199932419 199931760 0.000000e+00 904.0
21 TraesCS5D01G337600 chr1B 73.980 711 137 32 2623 3331 639089987 639089323 9.400000e-61 244.0
22 TraesCS5D01G337600 chr1B 100.000 59 0 0 226 284 113798362 113798304 3.580000e-20 110.0
23 TraesCS5D01G337600 chr7D 90.361 664 59 5 301 961 133189333 133188672 0.000000e+00 867.0
24 TraesCS5D01G337600 chr7D 76.296 810 168 17 2584 3387 192516702 192515911 8.760000e-111 411.0
25 TraesCS5D01G337600 chr1A 90.030 662 64 2 301 962 571117909 571117250 0.000000e+00 856.0
26 TraesCS5D01G337600 chr1A 94.030 67 4 0 217 283 137813694 137813628 5.990000e-18 102.0
27 TraesCS5D01G337600 chr7B 75.907 689 142 19 2705 3385 218386971 218386299 7.020000e-87 331.0
28 TraesCS5D01G337600 chr7B 73.541 737 162 21 2619 3348 556742955 556743665 2.020000e-62 250.0
29 TraesCS5D01G337600 chr7B 74.762 420 71 20 2623 3040 708518020 708517634 4.530000e-34 156.0
30 TraesCS5D01G337600 chr2A 75.536 699 148 16 2584 3275 7968131 7968813 4.220000e-84 322.0
31 TraesCS5D01G337600 chr2A 75.107 699 151 16 2584 3275 8345013 8344331 4.250000e-79 305.0
32 TraesCS5D01G337600 chr4D 77.897 466 79 15 2622 3082 121465466 121465912 5.580000e-68 268.0
33 TraesCS5D01G337600 chr4D 75.292 514 98 21 2834 3339 481113679 481113187 5.700000e-53 219.0
34 TraesCS5D01G337600 chr4D 72.879 660 140 28 2584 3230 459553196 459552563 1.240000e-44 191.0
35 TraesCS5D01G337600 chr4D 88.235 68 6 2 1345 1411 320028722 320028788 2.810000e-11 80.5
36 TraesCS5D01G337600 chr4B 96.923 65 1 1 221 284 484766270 484766334 1.290000e-19 108.0
37 TraesCS5D01G337600 chr4B 93.103 58 3 1 1355 1411 400699091 400699034 2.170000e-12 84.2
38 TraesCS5D01G337600 chr4A 98.361 61 1 0 225 285 518432029 518432089 1.290000e-19 108.0
39 TraesCS5D01G337600 chr4A 93.103 58 3 1 1355 1411 153255924 153255867 2.170000e-12 84.2
40 TraesCS5D01G337600 chr7A 94.030 67 3 1 218 284 224819783 224819718 2.150000e-17 100.0


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 TraesCS5D01G337600 chr5D 426287135 426290526 3391 False 6264.000000 6264 100.000000 1 3392 1 chr5D.!!$F1 3391
1 TraesCS5D01G337600 chr5A 540384990 540386855 1865 False 996.333333 2712 96.249667 1 2668 3 chr5A.!!$F1 2667
2 TraesCS5D01G337600 chr5A 588295575 588296235 660 True 966.000000 966 93.051000 301 961 1 chr5A.!!$R3 660
3 TraesCS5D01G337600 chr5B 516066125 516067759 1634 False 1289.500000 2263 93.491500 1 2393 2 chr5B.!!$F3 2392
4 TraesCS5D01G337600 chr5B 516081926 516082459 533 False 660.000000 660 88.972000 2842 3376 1 chr5B.!!$F2 534
5 TraesCS5D01G337600 chr6A 46945478 46946145 667 False 977.000000 977 93.124000 295 961 1 chr6A.!!$F1 666
6 TraesCS5D01G337600 chr2D 584672598 584673262 664 True 941.000000 941 92.192000 296 961 1 chr2D.!!$R1 665
7 TraesCS5D01G337600 chr2B 475542482 475543144 662 True 913.000000 913 91.566000 304 964 1 chr2B.!!$R1 660
8 TraesCS5D01G337600 chr1D 127098490 127099153 663 False 869.000000 869 90.269000 295 961 1 chr1D.!!$F1 666
9 TraesCS5D01G337600 chr1D 297821394 297822097 703 True 509.500000 911 95.770500 228 961 2 chr1D.!!$R1 733
10 TraesCS5D01G337600 chr1B 199931760 199932419 659 True 904.000000 904 91.390000 301 961 1 chr1B.!!$R2 660
11 TraesCS5D01G337600 chr1B 639089323 639089987 664 True 244.000000 244 73.980000 2623 3331 1 chr1B.!!$R3 708
12 TraesCS5D01G337600 chr7D 133188672 133189333 661 True 867.000000 867 90.361000 301 961 1 chr7D.!!$R1 660
13 TraesCS5D01G337600 chr7D 192515911 192516702 791 True 411.000000 411 76.296000 2584 3387 1 chr7D.!!$R2 803
14 TraesCS5D01G337600 chr1A 571117250 571117909 659 True 856.000000 856 90.030000 301 962 1 chr1A.!!$R2 661
15 TraesCS5D01G337600 chr7B 218386299 218386971 672 True 331.000000 331 75.907000 2705 3385 1 chr7B.!!$R1 680
16 TraesCS5D01G337600 chr7B 556742955 556743665 710 False 250.000000 250 73.541000 2619 3348 1 chr7B.!!$F1 729
17 TraesCS5D01G337600 chr2A 7968131 7968813 682 False 322.000000 322 75.536000 2584 3275 1 chr2A.!!$F1 691
18 TraesCS5D01G337600 chr2A 8344331 8345013 682 True 305.000000 305 75.107000 2584 3275 1 chr2A.!!$R1 691

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
354 367 0.322098 TGTCCGCCCATGAACGAATT 60.322 50.0 8.66 0.0 0.00 2.17 F
1507 1528 1.204146 GGAGAACCAGATGCCCTACA 58.796 55.0 0.00 0.0 35.97 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2061 1.550065 CGTTCATCAGCACGAGGTAG 58.450 55.0 0.0 0.0 36.47 3.18 R
3268 3309 0.035630 CAGCTCCAGAGGAAACCCTG 60.036 60.0 0.0 0.0 33.25 4.45 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
57 60 3.989817 GCCGCACAAAGAAAAGAAATGAT 59.010 39.130 0.00 0.00 0.00 2.45
84 88 5.107375 GGCAATACAAAATCAAGTGCACAAG 60.107 40.000 21.04 11.01 32.18 3.16
124 128 6.206498 GCGAAGGAAGTCAATTTAAAACTGT 58.794 36.000 0.00 0.00 0.00 3.55
267 279 1.611519 GGTTTGGATCGGGTTGAACA 58.388 50.000 0.00 0.00 0.00 3.18
268 280 1.957877 GGTTTGGATCGGGTTGAACAA 59.042 47.619 0.00 0.00 0.00 2.83
269 281 2.560981 GGTTTGGATCGGGTTGAACAAT 59.439 45.455 0.00 0.00 30.67 2.71
270 282 3.759618 GGTTTGGATCGGGTTGAACAATA 59.240 43.478 0.00 0.00 30.67 1.90
271 283 4.401202 GGTTTGGATCGGGTTGAACAATAT 59.599 41.667 0.00 0.00 30.67 1.28
272 284 5.449999 GGTTTGGATCGGGTTGAACAATATC 60.450 44.000 0.00 0.00 30.67 1.63
273 285 4.495690 TGGATCGGGTTGAACAATATCA 57.504 40.909 0.00 0.00 0.00 2.15
274 286 4.849518 TGGATCGGGTTGAACAATATCAA 58.150 39.130 0.00 0.00 36.99 2.57
275 287 5.257262 TGGATCGGGTTGAACAATATCAAA 58.743 37.500 0.00 0.00 40.76 2.69
276 288 5.890985 TGGATCGGGTTGAACAATATCAAAT 59.109 36.000 0.00 0.00 40.76 2.32
277 289 6.039270 TGGATCGGGTTGAACAATATCAAATC 59.961 38.462 0.00 0.00 40.76 2.17
278 290 5.828299 TCGGGTTGAACAATATCAAATCC 57.172 39.130 0.00 0.00 40.76 3.01
279 291 5.257262 TCGGGTTGAACAATATCAAATCCA 58.743 37.500 0.00 0.00 40.76 3.41
280 292 5.890985 TCGGGTTGAACAATATCAAATCCAT 59.109 36.000 0.00 0.00 40.76 3.41
281 293 7.057264 TCGGGTTGAACAATATCAAATCCATA 58.943 34.615 0.00 0.00 40.76 2.74
282 294 7.723616 TCGGGTTGAACAATATCAAATCCATAT 59.276 33.333 0.00 0.00 40.76 1.78
283 295 8.023128 CGGGTTGAACAATATCAAATCCATATC 58.977 37.037 0.00 0.00 40.76 1.63
284 296 9.082313 GGGTTGAACAATATCAAATCCATATCT 57.918 33.333 0.00 0.00 40.76 1.98
337 349 6.070021 TCCATATCCATGAAGACAGTCTTTGT 60.070 38.462 17.19 6.43 36.73 2.83
349 362 0.521735 GTCTTTGTCCGCCCATGAAC 59.478 55.000 0.00 0.00 0.00 3.18
354 367 0.322098 TGTCCGCCCATGAACGAATT 60.322 50.000 8.66 0.00 0.00 2.17
368 381 5.285651 TGAACGAATTCATGGGTGAAAAAC 58.714 37.500 6.22 0.00 46.67 2.43
414 428 7.829224 TGGATATCCATACCCACTGAATATT 57.171 36.000 20.98 0.00 42.01 1.28
634 655 5.346181 AAAATAAGAGAAGGAGCGCTAGT 57.654 39.130 11.50 0.00 0.00 2.57
695 716 2.166050 CGATGGGGATTGTGCAATTTCA 59.834 45.455 0.00 0.01 0.00 2.69
771 792 4.479056 TGGGGTAGGGATAGCACATTTTTA 59.521 41.667 0.00 0.00 0.00 1.52
802 823 2.297033 GCATACTATCGGGTCGGGTTTA 59.703 50.000 0.00 0.00 0.00 2.01
822 843 6.407979 GGTTTAGGTATATCCACGGGTACAAA 60.408 42.308 0.00 0.00 39.02 2.83
904 925 6.630188 GCACAAAAGCATATCCAAACCCTATT 60.630 38.462 0.00 0.00 0.00 1.73
910 931 6.856757 AGCATATCCAAACCCTATTCATTCT 58.143 36.000 0.00 0.00 0.00 2.40
1419 1440 1.376553 GCTCCAGTTCCTGCTCCAC 60.377 63.158 0.00 0.00 0.00 4.02
1507 1528 1.204146 GGAGAACCAGATGCCCTACA 58.796 55.000 0.00 0.00 35.97 2.74
2315 2336 0.465705 TCCATCATCAACCTCCTCGC 59.534 55.000 0.00 0.00 0.00 5.03
2402 2423 4.264253 TCCTGCACCTGATCAAATAAGTG 58.736 43.478 0.00 1.34 0.00 3.16
2421 2442 6.585695 AAGTGTACTGTATTTCTTCGGAGA 57.414 37.500 0.00 0.00 0.00 3.71
2422 2443 6.197364 AGTGTACTGTATTTCTTCGGAGAG 57.803 41.667 0.00 0.00 38.43 3.20
2423 2444 5.125739 AGTGTACTGTATTTCTTCGGAGAGG 59.874 44.000 0.00 0.00 38.43 3.69
2424 2445 5.125097 GTGTACTGTATTTCTTCGGAGAGGA 59.875 44.000 0.00 0.00 42.21 3.71
2430 2451 1.893786 TCTTCGGAGAGGAAGCAGC 59.106 57.895 0.00 0.00 40.53 5.25
2453 2474 2.706190 ACTCAATATGGACCTGGTAGCC 59.294 50.000 0.00 0.00 0.00 3.93
2454 2475 1.691976 TCAATATGGACCTGGTAGCCG 59.308 52.381 0.00 0.00 0.00 5.52
2468 2493 2.352225 GGTAGCCGAGATACTCATGCAG 60.352 54.545 0.00 0.00 32.59 4.41
2497 2522 7.491696 GTCTCTGTAAATAACCTGTGACATACC 59.508 40.741 0.00 0.00 30.85 2.73
2501 2526 5.466127 AAATAACCTGTGACATACCCCAT 57.534 39.130 0.00 0.00 0.00 4.00
2503 2528 2.806945 ACCTGTGACATACCCCATTG 57.193 50.000 0.00 0.00 0.00 2.82
2506 2531 2.026356 CCTGTGACATACCCCATTGACA 60.026 50.000 0.00 0.00 0.00 3.58
2507 2532 3.273434 CTGTGACATACCCCATTGACAG 58.727 50.000 0.00 0.00 0.00 3.51
2508 2533 2.909662 TGTGACATACCCCATTGACAGA 59.090 45.455 0.00 0.00 0.00 3.41
2509 2534 3.329225 TGTGACATACCCCATTGACAGAA 59.671 43.478 0.00 0.00 0.00 3.02
2510 2535 4.018506 TGTGACATACCCCATTGACAGAAT 60.019 41.667 0.00 0.00 0.00 2.40
2511 2536 4.576463 GTGACATACCCCATTGACAGAATC 59.424 45.833 0.00 0.00 0.00 2.52
2512 2537 4.227073 TGACATACCCCATTGACAGAATCA 59.773 41.667 0.00 0.00 34.65 2.57
2528 2553 9.398538 TGACAGAATCAATCATCAATCATGTTA 57.601 29.630 0.00 0.00 33.02 2.41
2535 2560 8.692110 TCAATCATCAATCATGTTAAAGTTGC 57.308 30.769 0.00 0.00 33.66 4.17
2605 2630 6.039382 GGATTTGCCTCGTCCATTAATTAAGT 59.961 38.462 3.94 0.00 32.23 2.24
2643 2668 7.685884 GCCAAGTTAATTAGTGAAAAACCAGGT 60.686 37.037 0.00 0.00 0.00 4.00
2671 2696 1.532523 TCAACATCATTGAGCGGCAA 58.467 45.000 1.45 0.00 41.53 4.52
2677 2702 3.633525 ACATCATTGAGCGGCAAACATAT 59.366 39.130 1.45 0.00 40.48 1.78
2695 2720 7.642094 AACATATAATACCCCACACATACCT 57.358 36.000 0.00 0.00 0.00 3.08
2697 2722 7.023120 ACATATAATACCCCACACATACCTCT 58.977 38.462 0.00 0.00 0.00 3.69
2698 2723 7.180408 ACATATAATACCCCACACATACCTCTC 59.820 40.741 0.00 0.00 0.00 3.20
2699 2724 2.170012 TACCCCACACATACCTCTCC 57.830 55.000 0.00 0.00 0.00 3.71
2700 2725 0.118346 ACCCCACACATACCTCTCCA 59.882 55.000 0.00 0.00 0.00 3.86
2701 2726 1.285280 CCCCACACATACCTCTCCAA 58.715 55.000 0.00 0.00 0.00 3.53
2702 2727 1.633432 CCCCACACATACCTCTCCAAA 59.367 52.381 0.00 0.00 0.00 3.28
2703 2728 2.356125 CCCCACACATACCTCTCCAAAG 60.356 54.545 0.00 0.00 0.00 2.77
2761 2786 2.630889 TCTTGTCATCACTCCTCCCT 57.369 50.000 0.00 0.00 0.00 4.20
2763 2788 2.568956 TCTTGTCATCACTCCTCCCTTG 59.431 50.000 0.00 0.00 0.00 3.61
2764 2789 0.615331 TGTCATCACTCCTCCCTTGC 59.385 55.000 0.00 0.00 0.00 4.01
2765 2790 0.460987 GTCATCACTCCTCCCTTGCG 60.461 60.000 0.00 0.00 0.00 4.85
2766 2791 1.153289 CATCACTCCTCCCTTGCGG 60.153 63.158 0.00 0.00 0.00 5.69
2789 2814 2.201732 CGTCATCACCATCCCTAAACG 58.798 52.381 0.00 0.00 0.00 3.60
2863 2889 2.364324 TGTAGAGGCACTTGTCGAGTTT 59.636 45.455 0.00 0.00 41.55 2.66
2956 2987 1.272769 AGGACAAGTTAGGCACGACTC 59.727 52.381 0.00 0.00 0.00 3.36
2959 2990 0.666274 CAAGTTAGGCACGACTCGCA 60.666 55.000 0.00 0.00 0.00 5.10
2963 2994 1.884075 TTAGGCACGACTCGCACCAT 61.884 55.000 11.72 1.98 0.00 3.55
2986 3018 3.334691 GAGGATCATTGAACGAACCACA 58.665 45.455 0.00 0.00 33.17 4.17
3008 3040 0.455464 TTGACTGTCATCGTACGCCG 60.455 55.000 11.86 3.73 38.13 6.46
3011 3044 4.840288 TGTCATCGTACGCCGCCG 62.840 66.667 11.24 0.00 41.14 6.46
3083 3124 3.423154 CAGGCACGCCGGAGAAAC 61.423 66.667 13.83 0.52 41.95 2.78
3268 3309 1.134367 TCGTCCGATCACACAAGATCC 59.866 52.381 0.00 0.00 41.03 3.36
3278 3319 2.065799 ACACAAGATCCAGGGTTTCCT 58.934 47.619 0.00 0.00 46.26 3.36
3348 3389 1.308069 GCAGCGATGCCTCCAAGAAA 61.308 55.000 16.30 0.00 0.00 2.52
3390 3431 3.700577 CCATTGTTGGTCATGACGC 57.299 52.632 19.33 12.69 38.30 5.19
3391 3432 0.880441 CCATTGTTGGTCATGACGCA 59.120 50.000 19.33 15.03 38.30 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 60 6.098679 GTGCACTTGATTTTGTATTGCCATA 58.901 36.000 10.32 0.00 0.00 2.74
73 77 0.925267 CGTTCGCACTTGTGCACTTG 60.925 55.000 22.97 13.22 34.41 3.16
110 114 7.987649 ACGTTCCTGTTACAGTTTTAAATTGA 58.012 30.769 11.68 0.00 0.00 2.57
138 142 3.729966 TGTGTTTGCGGTTGAGTGTATA 58.270 40.909 0.00 0.00 0.00 1.47
139 143 2.566913 TGTGTTTGCGGTTGAGTGTAT 58.433 42.857 0.00 0.00 0.00 2.29
337 349 0.035915 TGAATTCGTTCATGGGCGGA 60.036 50.000 0.04 2.29 0.00 5.54
349 362 4.681025 CACAGTTTTTCACCCATGAATTCG 59.319 41.667 0.04 0.00 44.36 3.34
354 367 2.955660 GGACACAGTTTTTCACCCATGA 59.044 45.455 0.00 0.00 0.00 3.07
368 381 1.247567 GGGTTTGGACATGGACACAG 58.752 55.000 0.00 0.00 0.00 3.66
409 423 7.872138 TGTCTTTAGAGGACCCAATGAATATT 58.128 34.615 0.00 0.00 33.22 1.28
414 428 8.561536 TTATATGTCTTTAGAGGACCCAATGA 57.438 34.615 0.00 0.00 33.22 2.57
620 641 0.244994 CACACACTAGCGCTCCTTCT 59.755 55.000 16.34 0.00 0.00 2.85
634 655 3.866703 TTCAATCCCCACTAACACACA 57.133 42.857 0.00 0.00 0.00 3.72
695 716 9.195411 CACTTTGTTATGTAGAACATGCAAAAT 57.805 29.630 17.18 10.40 40.52 1.82
771 792 4.288626 ACCCGATAGTATGCATTAATGGGT 59.711 41.667 17.02 16.68 41.20 4.51
802 823 5.899631 ATTTTGTACCCGTGGATATACCT 57.100 39.130 0.00 0.00 39.86 3.08
822 843 7.043300 TCATGGGTAGGGCATGAATATAATT 57.957 36.000 0.00 0.00 33.05 1.40
830 851 2.487746 TACTCATGGGTAGGGCATGA 57.512 50.000 0.00 0.00 34.60 3.07
904 925 3.261643 CCATGGATATCCGACCAGAATGA 59.738 47.826 17.04 0.00 39.62 2.57
910 931 2.706112 TACCCATGGATATCCGACCA 57.294 50.000 15.22 0.00 40.57 4.02
951 972 5.014755 TGTGTGGGTTAAGGTTAAGGATGAT 59.985 40.000 0.00 0.00 0.00 2.45
952 973 4.351407 TGTGTGGGTTAAGGTTAAGGATGA 59.649 41.667 0.00 0.00 0.00 2.92
964 985 3.494398 GCTCTCAGTTCTGTGTGGGTTAA 60.494 47.826 0.00 0.00 0.00 2.01
965 986 2.037251 GCTCTCAGTTCTGTGTGGGTTA 59.963 50.000 0.00 0.00 0.00 2.85
966 987 1.202698 GCTCTCAGTTCTGTGTGGGTT 60.203 52.381 0.00 0.00 0.00 4.11
967 988 0.394565 GCTCTCAGTTCTGTGTGGGT 59.605 55.000 0.00 0.00 0.00 4.51
968 989 0.668706 CGCTCTCAGTTCTGTGTGGG 60.669 60.000 0.00 3.82 0.00 4.61
1110 1131 0.252057 TCCTGTTCATCTCCCGGACA 60.252 55.000 0.73 0.00 0.00 4.02
1373 1394 2.182791 CGTCGAGCACCAGCATCT 59.817 61.111 0.00 0.00 45.49 2.90
1507 1528 1.608717 AAGAGCTTGGCGAGGACGAT 61.609 55.000 3.44 0.00 42.66 3.73
2040 2061 1.550065 CGTTCATCAGCACGAGGTAG 58.450 55.000 0.00 0.00 36.47 3.18
2402 2423 5.831702 TCCTCTCCGAAGAAATACAGTAC 57.168 43.478 0.00 0.00 0.00 2.73
2421 2442 3.054139 TCCATATTGAGTTGCTGCTTCCT 60.054 43.478 0.00 0.00 0.00 3.36
2422 2443 3.065925 GTCCATATTGAGTTGCTGCTTCC 59.934 47.826 0.00 0.00 0.00 3.46
2423 2444 3.065925 GGTCCATATTGAGTTGCTGCTTC 59.934 47.826 0.00 0.00 0.00 3.86
2424 2445 3.019564 GGTCCATATTGAGTTGCTGCTT 58.980 45.455 0.00 0.00 0.00 3.91
2425 2446 2.240667 AGGTCCATATTGAGTTGCTGCT 59.759 45.455 0.00 0.00 0.00 4.24
2426 2447 2.357009 CAGGTCCATATTGAGTTGCTGC 59.643 50.000 0.00 0.00 0.00 5.25
2427 2448 2.947652 CCAGGTCCATATTGAGTTGCTG 59.052 50.000 0.00 0.00 0.00 4.41
2428 2449 2.578021 ACCAGGTCCATATTGAGTTGCT 59.422 45.455 0.00 0.00 0.00 3.91
2429 2450 3.004752 ACCAGGTCCATATTGAGTTGC 57.995 47.619 0.00 0.00 0.00 4.17
2430 2451 4.130118 GCTACCAGGTCCATATTGAGTTG 58.870 47.826 0.00 0.00 0.00 3.16
2453 2474 2.034432 AGACAGCTGCATGAGTATCTCG 59.966 50.000 15.27 0.00 34.92 4.04
2454 2475 3.318839 AGAGACAGCTGCATGAGTATCTC 59.681 47.826 15.27 15.31 34.92 2.75
2468 2493 5.348997 GTCACAGGTTATTTACAGAGACAGC 59.651 44.000 0.00 0.00 30.25 4.40
2501 2526 8.288689 ACATGATTGATGATTGATTCTGTCAA 57.711 30.769 0.00 0.00 41.95 3.18
2509 2534 9.309516 GCAACTTTAACATGATTGATGATTGAT 57.690 29.630 0.00 0.00 35.80 2.57
2510 2535 8.305317 TGCAACTTTAACATGATTGATGATTGA 58.695 29.630 0.00 0.00 35.80 2.57
2511 2536 8.468720 TGCAACTTTAACATGATTGATGATTG 57.531 30.769 0.00 0.00 35.80 2.67
2512 2537 8.928733 GTTGCAACTTTAACATGATTGATGATT 58.071 29.630 22.36 0.00 35.80 2.57
2515 2540 7.878477 AGTTGCAACTTTAACATGATTGATG 57.122 32.000 26.36 0.00 35.21 3.07
2575 2600 0.879090 GGACGAGGCAAATCCGTTTT 59.121 50.000 0.00 0.00 40.77 2.43
2581 2606 7.027778 ACTTAATTAATGGACGAGGCAAATC 57.972 36.000 0.00 0.00 0.00 2.17
2605 2630 7.829211 ACTAATTAACTTGGCAATTCTCTGCTA 59.171 33.333 0.00 0.00 42.25 3.49
2643 2668 5.472148 GCTCAATGATGTTGATGGTTTTCA 58.528 37.500 0.00 0.00 0.00 2.69
2671 2696 7.516209 AGAGGTATGTGTGGGGTATTATATGTT 59.484 37.037 0.00 0.00 0.00 2.71
2677 2702 4.228824 GGAGAGGTATGTGTGGGGTATTA 58.771 47.826 0.00 0.00 0.00 0.98
2695 2720 2.372172 GACCCTCTTTGGACTTTGGAGA 59.628 50.000 0.00 0.00 38.35 3.71
2697 2722 2.372172 GAGACCCTCTTTGGACTTTGGA 59.628 50.000 0.00 0.00 38.35 3.53
2698 2723 2.106511 TGAGACCCTCTTTGGACTTTGG 59.893 50.000 0.00 0.00 38.35 3.28
2699 2724 3.492102 TGAGACCCTCTTTGGACTTTG 57.508 47.619 0.00 0.00 38.35 2.77
2700 2725 3.307059 CGATGAGACCCTCTTTGGACTTT 60.307 47.826 0.00 0.00 38.35 2.66
2701 2726 2.234908 CGATGAGACCCTCTTTGGACTT 59.765 50.000 0.00 0.00 38.35 3.01
2702 2727 1.827969 CGATGAGACCCTCTTTGGACT 59.172 52.381 0.00 0.00 38.35 3.85
2703 2728 1.825474 TCGATGAGACCCTCTTTGGAC 59.175 52.381 0.00 0.00 38.35 4.02
2730 2755 0.798159 TGACAAGATGACGCATGTGC 59.202 50.000 6.08 0.00 37.78 4.57
2744 2769 1.003580 GCAAGGGAGGAGTGATGACAA 59.996 52.381 0.00 0.00 0.00 3.18
2745 2770 0.615331 GCAAGGGAGGAGTGATGACA 59.385 55.000 0.00 0.00 0.00 3.58
2763 2788 4.856801 ATGGTGATGACGCCCCGC 62.857 66.667 0.00 0.00 45.20 6.13
2764 2789 2.588877 GATGGTGATGACGCCCCG 60.589 66.667 0.00 0.00 45.20 5.73
2765 2790 2.203209 GGATGGTGATGACGCCCC 60.203 66.667 0.00 0.00 45.20 5.80
2766 2791 1.407656 TAGGGATGGTGATGACGCCC 61.408 60.000 0.00 0.00 45.20 6.13
2789 2814 0.235926 GTTGGAGTCGTTTGCTCAGC 59.764 55.000 0.00 0.00 34.83 4.26
2863 2889 0.616395 TCTGGCACGGGTCTCCATAA 60.616 55.000 0.00 0.00 33.92 1.90
2956 2987 0.863799 CAATGATCCTCGATGGTGCG 59.136 55.000 0.00 0.00 37.07 5.34
2959 2990 2.430694 TCGTTCAATGATCCTCGATGGT 59.569 45.455 0.00 0.00 37.07 3.55
2963 2994 2.232696 TGGTTCGTTCAATGATCCTCGA 59.767 45.455 8.00 0.00 0.00 4.04
2967 2998 3.440173 ACATGTGGTTCGTTCAATGATCC 59.560 43.478 0.00 0.17 0.00 3.36
2986 3018 2.259618 GCGTACGATGACAGTCAACAT 58.740 47.619 21.65 0.00 0.00 2.71
3011 3044 3.866582 CTGAGATGGCGGGGTCCC 61.867 72.222 0.00 0.00 0.00 4.46
3025 3058 2.330440 TGCTGTGAAGTTGAAGCTGA 57.670 45.000 0.00 0.00 36.60 4.26
3069 3110 3.723348 GGTGTTTCTCCGGCGTGC 61.723 66.667 6.01 0.00 0.00 5.34
3082 3123 3.244770 ACAATGGTTGAGGTAATCGGTGT 60.245 43.478 0.00 0.00 0.00 4.16
3083 3124 3.343617 ACAATGGTTGAGGTAATCGGTG 58.656 45.455 0.00 0.00 0.00 4.94
3089 3130 3.395639 GACACGACAATGGTTGAGGTAA 58.604 45.455 0.00 0.00 32.40 2.85
3231 3272 2.672996 ATGGTGGCGTCTTGGTGC 60.673 61.111 0.00 0.00 0.00 5.01
3268 3309 0.035630 CAGCTCCAGAGGAAACCCTG 60.036 60.000 0.00 0.00 33.25 4.45
3278 3319 1.893062 CCATCACGACAGCTCCAGA 59.107 57.895 0.00 0.00 0.00 3.86
3319 3360 2.396700 CATCGCTGCATTGCTACCA 58.603 52.632 10.49 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.