Multiple sequence alignment - TraesCS5A01G051300

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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 TraesCS5A01G051300 chr5A 100.000 3110 0 0 1 3110 46569143 46572252 0.000000e+00 5744.0
1 TraesCS5A01G051300 chr5A 80.851 282 29 9 2513 2769 534662996 534663277 6.800000e-47 198.0
2 TraesCS5A01G051300 chr5B 90.527 2333 160 29 1 2286 63358702 63361020 0.000000e+00 3027.0
3 TraesCS5A01G051300 chr5B 83.420 579 51 24 2268 2827 63361031 63361583 2.150000e-136 496.0
4 TraesCS5A01G051300 chr5B 92.606 284 16 5 2828 3110 63361676 63361955 1.340000e-108 403.0
5 TraesCS5A01G051300 chr5B 75.908 743 123 32 1072 1789 672441599 672440888 2.310000e-86 329.0
6 TraesCS5A01G051300 chr5B 78.327 526 94 14 1032 1547 671721268 671720753 3.870000e-84 322.0
7 TraesCS5A01G051300 chr5B 75.370 743 127 33 1072 1789 672474631 672473920 1.080000e-79 307.0
8 TraesCS5A01G051300 chr5B 77.154 499 97 9 1065 1553 676100566 676100075 1.100000e-69 274.0
9 TraesCS5A01G051300 chr5D 91.527 1015 59 9 1583 2570 58247934 58248948 0.000000e+00 1373.0
10 TraesCS5A01G051300 chr5D 95.486 576 23 1 1015 1587 58234425 58235000 0.000000e+00 917.0
11 TraesCS5A01G051300 chr5D 90.795 478 24 6 2640 3110 58255269 58255733 3.410000e-174 621.0
12 TraesCS5A01G051300 chr5D 78.445 733 125 21 1052 1769 534605590 534606304 6.120000e-122 448.0
13 TraesCS5A01G051300 chr5D 76.932 854 154 29 1065 1898 532248782 532247952 2.200000e-121 446.0
14 TraesCS5A01G051300 chr5D 88.158 304 22 8 681 983 58232945 58233235 1.770000e-92 350.0
15 TraesCS5A01G051300 chr7D 79.158 998 156 32 1048 2021 636779020 636778051 0.000000e+00 643.0
16 TraesCS5A01G051300 chr7D 82.935 586 77 16 1685 2259 636795619 636795046 9.950000e-140 507.0
17 TraesCS5A01G051300 chr7D 84.047 514 75 4 1025 1531 636796134 636795621 3.600000e-134 488.0
18 TraesCS5A01G051300 chr7D 80.044 456 70 14 1592 2029 636820201 636819749 5.000000e-83 318.0
19 TraesCS5A01G051300 chr7B 77.862 1057 177 33 1048 2072 739411823 739412854 1.230000e-168 603.0
20 TraesCS5A01G051300 chr7B 77.982 654 113 15 1048 1693 739420201 739420831 6.290000e-102 381.0
21 TraesCS5A01G051300 chr7B 78.588 425 62 18 1675 2072 739420843 739421265 1.430000e-63 254.0
22 TraesCS5A01G051300 chr6B 78.531 708 118 22 1053 1746 114334522 114335209 4.760000e-118 435.0
23 TraesCS5A01G051300 chr4A 75.501 698 130 21 1065 1746 639993530 639994202 1.400000e-78 303.0
24 TraesCS5A01G051300 chr4A 79.609 358 58 9 240 584 80218317 80218672 3.100000e-60 243.0
25 TraesCS5A01G051300 chr4A 77.926 299 50 10 1466 1762 637234745 637234461 4.120000e-39 172.0
26 TraesCS5A01G051300 chr4A 77.419 217 25 12 2513 2705 49202847 49203063 1.180000e-19 108.0
27 TraesCS5A01G051300 chr3A 83.624 287 23 17 2513 2776 615102809 615103094 6.660000e-62 248.0
28 TraesCS5A01G051300 chr2A 83.513 279 22 16 2513 2768 566474147 566474424 4.010000e-59 239.0
29 TraesCS5A01G051300 chr2A 82.143 280 26 10 2513 2769 423212798 423212520 5.220000e-53 219.0
30 TraesCS5A01G051300 chr2A 82.625 259 20 17 2513 2747 208579397 208579140 4.070000e-49 206.0
31 TraesCS5A01G051300 chr2A 93.893 131 7 1 2513 2643 492486363 492486234 2.450000e-46 196.0
32 TraesCS5A01G051300 chr1B 80.573 314 52 7 239 546 422375928 422376238 1.860000e-57 233.0
33 TraesCS5A01G051300 chr7A 82.624 282 24 11 2512 2770 115854601 115854322 3.120000e-55 226.0
34 TraesCS5A01G051300 chr1A 90.604 149 10 4 2513 2660 568394327 568394182 8.800000e-46 195.0
35 TraesCS5A01G051300 chr1A 88.636 88 10 0 2640 2727 512857778 512857865 1.180000e-19 108.0
36 TraesCS5A01G051300 chr2B 80.351 285 26 3 2513 2772 353782647 353782926 4.090000e-44 189.0
37 TraesCS5A01G051300 chr1D 76.282 312 52 17 258 556 25138596 25138294 2.500000e-31 147.0
38 TraesCS5A01G051300 chr2D 83.212 137 20 3 334 468 644394510 644394375 4.210000e-24 122.0
39 TraesCS5A01G051300 chr2D 100.000 30 0 0 2678 2707 522510050 522510079 4.330000e-04 56.5


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 TraesCS5A01G051300 chr5A 46569143 46572252 3109 False 5744.000000 5744 100.000 1 3110 1 chr5A.!!$F1 3109
1 TraesCS5A01G051300 chr5B 63358702 63361955 3253 False 1308.666667 3027 88.851 1 3110 3 chr5B.!!$F1 3109
2 TraesCS5A01G051300 chr5B 672440888 672441599 711 True 329.000000 329 75.908 1072 1789 1 chr5B.!!$R2 717
3 TraesCS5A01G051300 chr5B 671720753 671721268 515 True 322.000000 322 78.327 1032 1547 1 chr5B.!!$R1 515
4 TraesCS5A01G051300 chr5B 672473920 672474631 711 True 307.000000 307 75.370 1072 1789 1 chr5B.!!$R3 717
5 TraesCS5A01G051300 chr5D 58247934 58248948 1014 False 1373.000000 1373 91.527 1583 2570 1 chr5D.!!$F1 987
6 TraesCS5A01G051300 chr5D 58232945 58235000 2055 False 633.500000 917 91.822 681 1587 2 chr5D.!!$F4 906
7 TraesCS5A01G051300 chr5D 534605590 534606304 714 False 448.000000 448 78.445 1052 1769 1 chr5D.!!$F3 717
8 TraesCS5A01G051300 chr5D 532247952 532248782 830 True 446.000000 446 76.932 1065 1898 1 chr5D.!!$R1 833
9 TraesCS5A01G051300 chr7D 636778051 636779020 969 True 643.000000 643 79.158 1048 2021 1 chr7D.!!$R1 973
10 TraesCS5A01G051300 chr7D 636795046 636796134 1088 True 497.500000 507 83.491 1025 2259 2 chr7D.!!$R3 1234
11 TraesCS5A01G051300 chr7B 739411823 739412854 1031 False 603.000000 603 77.862 1048 2072 1 chr7B.!!$F1 1024
12 TraesCS5A01G051300 chr7B 739420201 739421265 1064 False 317.500000 381 78.285 1048 2072 2 chr7B.!!$F2 1024
13 TraesCS5A01G051300 chr6B 114334522 114335209 687 False 435.000000 435 78.531 1053 1746 1 chr6B.!!$F1 693
14 TraesCS5A01G051300 chr4A 639993530 639994202 672 False 303.000000 303 75.501 1065 1746 1 chr4A.!!$F3 681

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
287 289 0.243365 TTGCATCCGCGCTCAAAAAT 59.757 45.0 5.56 0.0 42.97 1.82 F
1267 2457 0.178981 CATGCCCGATTTCATCCCCT 60.179 55.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 3211 1.446272 GACTTCTTCCACCGGAGCG 60.446 63.158 9.46 0.0 31.21 5.03 R
2894 4340 0.464036 TGCTGGGATATGGACGACAC 59.536 55.000 0.00 0.0 0.00 3.67 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
76 77 9.855021 ACTATGGCATTTTTAGTTACAAACATC 57.145 29.630 4.78 0.00 0.00 3.06
126 127 5.487433 TCTGATTCGTTTGTACATGATGGT 58.513 37.500 0.00 0.00 0.00 3.55
127 128 5.351189 TCTGATTCGTTTGTACATGATGGTG 59.649 40.000 0.00 0.00 0.00 4.17
129 130 3.410631 TCGTTTGTACATGATGGTGGT 57.589 42.857 0.00 0.00 0.00 4.16
133 134 5.763698 TCGTTTGTACATGATGGTGGTTTTA 59.236 36.000 0.00 0.00 0.00 1.52
134 135 6.431543 TCGTTTGTACATGATGGTGGTTTTAT 59.568 34.615 0.00 0.00 0.00 1.40
169 170 6.325919 TGGAAATTCGCTTAATTGTGTCTT 57.674 33.333 0.00 0.00 37.85 3.01
170 171 6.744112 TGGAAATTCGCTTAATTGTGTCTTT 58.256 32.000 0.00 0.00 37.85 2.52
246 248 4.900635 ACCACAGGAAATTGCGATAATC 57.099 40.909 0.00 0.00 0.00 1.75
256 258 6.183360 GGAAATTGCGATAATCCACTTCTGAA 60.183 38.462 11.99 0.00 0.00 3.02
262 264 2.887151 AATCCACTTCTGAACCCAGG 57.113 50.000 0.00 0.00 40.76 4.45
268 270 1.707427 ACTTCTGAACCCAGGCTCATT 59.293 47.619 0.00 0.00 40.76 2.57
287 289 0.243365 TTGCATCCGCGCTCAAAAAT 59.757 45.000 5.56 0.00 42.97 1.82
295 297 4.992688 TCCGCGCTCAAAAATATCAAAAT 58.007 34.783 5.56 0.00 0.00 1.82
362 364 6.982141 TGGTACATAATTTGATACGTGAGGTC 59.018 38.462 0.00 0.00 0.00 3.85
367 369 0.892755 TTGATACGTGAGGTCCGCTT 59.107 50.000 0.00 0.00 0.00 4.68
374 376 1.128692 CGTGAGGTCCGCTTCAATTTC 59.871 52.381 0.00 0.00 32.39 2.17
380 382 3.193479 AGGTCCGCTTCAATTTCCAAATC 59.807 43.478 0.00 0.00 0.00 2.17
395 397 9.760077 AATTTCCAAATCATTTGATATCTGAGC 57.240 29.630 11.98 0.00 43.26 4.26
401 403 5.548181 TCATTTGATATCTGAGCAGCTCT 57.452 39.130 23.15 5.93 0.00 4.09
402 404 5.926663 TCATTTGATATCTGAGCAGCTCTT 58.073 37.500 23.15 10.58 0.00 2.85
403 405 7.059202 TCATTTGATATCTGAGCAGCTCTTA 57.941 36.000 23.15 11.46 0.00 2.10
462 465 3.146066 TGTTCATGCACTGTTCTTACCC 58.854 45.455 0.00 0.00 0.00 3.69
470 473 4.873827 TGCACTGTTCTTACCCGATTTATC 59.126 41.667 0.00 0.00 0.00 1.75
472 475 5.585047 GCACTGTTCTTACCCGATTTATCTT 59.415 40.000 0.00 0.00 0.00 2.40
506 510 5.954335 AGCTACTCAAATGTGCAAATAACC 58.046 37.500 0.00 0.00 0.00 2.85
523 527 5.638596 ATAACCTGAAAATTGGAACGGAC 57.361 39.130 0.00 0.00 0.00 4.79
599 611 0.881118 TTTTTCCGGTGCTGATGAGC 59.119 50.000 0.00 0.00 46.44 4.26
607 619 2.044650 GCTGATGAGCCTGGGCAA 60.045 61.111 14.39 1.98 44.88 4.52
624 636 1.581934 CAACGAAACTCTGCACTCCA 58.418 50.000 0.00 0.00 0.00 3.86
640 652 3.507622 CACTCCAGGAAATTGGTCCTTTC 59.492 47.826 0.00 0.00 46.42 2.62
644 656 2.749621 CAGGAAATTGGTCCTTTCTCGG 59.250 50.000 0.00 0.00 46.42 4.63
645 657 1.472878 GGAAATTGGTCCTTTCTCGGC 59.527 52.381 4.17 0.00 34.56 5.54
646 658 1.472878 GAAATTGGTCCTTTCTCGGCC 59.527 52.381 0.00 0.00 31.38 6.13
669 681 4.229096 CAATTGGGTCACGTTTTCAGATG 58.771 43.478 0.00 0.00 0.00 2.90
690 702 1.663643 GTGAGAGTTTGTGTGTTCGCA 59.336 47.619 0.00 0.00 0.00 5.10
746 760 3.583086 GAATAACGCGCTGGGGGC 61.583 66.667 5.73 0.00 38.15 5.80
830 849 5.578727 AGTCGGTAACTTACTACTGTAGTCG 59.421 44.000 22.79 17.43 40.14 4.18
846 865 8.200024 ACTGTAGTCGTCTATTCCTAGGTATA 57.800 38.462 9.08 8.33 0.00 1.47
847 866 8.824783 ACTGTAGTCGTCTATTCCTAGGTATAT 58.175 37.037 9.08 4.01 0.00 0.86
904 923 6.534436 GCAGCTATCATCACAGAATATCGATT 59.466 38.462 1.71 0.00 0.00 3.34
908 927 5.806654 TCATCACAGAATATCGATTGGGA 57.193 39.130 1.71 2.12 0.00 4.37
920 939 1.957177 CGATTGGGAGCAGACTAGCTA 59.043 52.381 0.00 0.00 46.75 3.32
930 949 3.053544 AGCAGACTAGCTAGGGTTAGACA 60.054 47.826 24.35 0.00 44.50 3.41
967 986 2.033049 CGACGGTGGATCGATAAGAAGT 59.967 50.000 0.00 0.00 42.25 3.01
983 1002 2.479412 AAGTCAGCCTCTGCGTCGTC 62.479 60.000 0.00 0.00 44.33 4.20
985 1004 4.056125 CAGCCTCTGCGTCGTCCA 62.056 66.667 0.00 0.00 44.33 4.02
986 1005 3.303135 AGCCTCTGCGTCGTCCAA 61.303 61.111 0.00 0.00 44.33 3.53
1010 1069 2.439156 GCTCACCATGGCACCTCC 60.439 66.667 13.04 0.00 0.00 4.30
1024 1083 4.142038 GGCACCTCCAGAAAAGAAAAGTA 58.858 43.478 0.00 0.00 34.01 2.24
1026 1085 5.068591 GGCACCTCCAGAAAAGAAAAGTAAA 59.931 40.000 0.00 0.00 34.01 2.01
1027 1086 5.977725 GCACCTCCAGAAAAGAAAAGTAAAC 59.022 40.000 0.00 0.00 0.00 2.01
1028 1087 6.183360 GCACCTCCAGAAAAGAAAAGTAAACT 60.183 38.462 0.00 0.00 0.00 2.66
1036 2214 2.344025 AGAAAAGTAAACTAGCGGCCG 58.656 47.619 24.05 24.05 0.00 6.13
1201 2385 4.162690 GCCGCCTCCTCCACGATT 62.163 66.667 0.00 0.00 0.00 3.34
1243 2433 1.210234 TCGGGTATCTCCACGACTACA 59.790 52.381 0.00 0.00 35.27 2.74
1257 2447 1.139058 GACTACAAGGACATGCCCGAT 59.861 52.381 0.00 0.00 37.37 4.18
1267 2457 0.178981 CATGCCCGATTTCATCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
1374 2567 1.969589 CAACCCCAAGTGCCCGTAC 60.970 63.158 0.00 0.00 0.00 3.67
1899 3148 1.815003 CAATTGTGGTCAAGAGAGGCC 59.185 52.381 0.00 0.00 36.97 5.19
1956 3211 1.538512 GGAAGTTTGTCCCTAAACGGC 59.461 52.381 0.00 0.00 43.51 5.68
2016 3280 4.406456 AGGGAGCAAACATCATTGTTGTA 58.594 39.130 0.94 0.00 45.30 2.41
2080 3354 1.609208 GTGTGTGATGAGGCCAAAGT 58.391 50.000 5.01 0.00 0.00 2.66
2088 3362 2.363306 TGAGGCCAAAGTGTGTGATT 57.637 45.000 5.01 0.00 0.00 2.57
2158 3435 1.171308 CCCAAGTTGAGCACATGAGG 58.829 55.000 3.87 0.00 0.00 3.86
2217 3496 1.812571 CAGCTTAACCGCCTGAATGTT 59.187 47.619 0.00 0.00 0.00 2.71
2231 3510 5.562890 GCCTGAATGTTCTGTTTACCAACTC 60.563 44.000 0.00 0.00 33.58 3.01
2256 3535 9.393249 TCGTGAAATAATAAAGCTTTTGAACTG 57.607 29.630 18.47 0.00 0.00 3.16
2441 3762 4.522789 GGTGTCACCTTGTATCCAAAACAT 59.477 41.667 15.22 0.00 34.73 2.71
2473 3794 2.337359 ACTACCAGGTGTACCCACAT 57.663 50.000 0.76 0.00 43.71 3.21
2518 3839 0.744771 CTCTCGTTGCCTTTAGCCCC 60.745 60.000 0.00 0.00 42.71 5.80
2520 3841 3.131478 CGTTGCCTTTAGCCCCCG 61.131 66.667 0.00 0.00 42.71 5.73
2534 3855 2.152016 GCCCCCGCTAACATATTTCTC 58.848 52.381 0.00 0.00 0.00 2.87
2536 3857 3.747708 GCCCCCGCTAACATATTTCTCTT 60.748 47.826 0.00 0.00 0.00 2.85
2575 3896 5.278315 CCACCTCATCATTCAACATGCATAG 60.278 44.000 0.00 0.00 0.00 2.23
2578 3899 6.262496 ACCTCATCATTCAACATGCATAGAAG 59.738 38.462 0.00 0.00 0.00 2.85
2583 3904 6.182627 TCATTCAACATGCATAGAAGAAGGT 58.817 36.000 0.00 0.00 0.00 3.50
2604 3927 5.190925 AGGTCCACCTTAACATGCAACTATA 59.809 40.000 0.00 0.00 46.09 1.31
2730 4085 8.687824 AACTAAAACCTCATTGAAATATTGCG 57.312 30.769 0.00 0.00 0.00 4.85
2764 4119 0.806868 CAACGTGCAAGGCATCATCT 59.193 50.000 4.26 0.00 41.91 2.90
2766 4121 1.945387 ACGTGCAAGGCATCATCTAG 58.055 50.000 4.26 0.00 41.91 2.43
2793 4148 6.992664 ATATAGTCAGCACATCCTTCTCTT 57.007 37.500 0.00 0.00 0.00 2.85
2814 4169 9.354673 TCTCTTGGATACTTCAAAATTTTCTGT 57.645 29.630 0.00 3.22 37.61 3.41
2815 4170 9.617975 CTCTTGGATACTTCAAAATTTTCTGTC 57.382 33.333 0.00 0.00 37.61 3.51
2816 4171 9.354673 TCTTGGATACTTCAAAATTTTCTGTCT 57.645 29.630 0.00 0.00 37.61 3.41
2833 4188 8.738199 TTTCTGTCTAGTACAAACTGAATACG 57.262 34.615 12.16 0.00 37.74 3.06
2834 4189 7.444629 TCTGTCTAGTACAAACTGAATACGT 57.555 36.000 0.00 0.00 37.74 3.57
2835 4190 7.879070 TCTGTCTAGTACAAACTGAATACGTT 58.121 34.615 0.00 0.00 37.74 3.99
2836 4191 7.806487 TCTGTCTAGTACAAACTGAATACGTTG 59.194 37.037 0.00 0.00 37.74 4.10
2837 4192 7.650890 TGTCTAGTACAAACTGAATACGTTGA 58.349 34.615 0.00 0.00 36.36 3.18
2858 4304 4.276678 TGACAAATCTTCAGAACCAGCAAG 59.723 41.667 0.00 0.00 0.00 4.01
2862 4308 1.417517 TCTTCAGAACCAGCAAGCTGA 59.582 47.619 22.76 0.00 46.30 4.26
2864 4310 2.105006 TCAGAACCAGCAAGCTGATC 57.895 50.000 22.76 18.51 46.30 2.92
2872 4318 1.129998 CAGCAAGCTGATCGAACTTGG 59.870 52.381 16.75 4.93 46.30 3.61
2873 4319 1.002430 AGCAAGCTGATCGAACTTGGA 59.998 47.619 18.34 0.00 40.87 3.53
2884 4330 7.035840 TGATCGAACTTGGAGTAGGTATAAC 57.964 40.000 0.00 0.00 0.00 1.89
2894 4340 4.023878 GGAGTAGGTATAACTGCTGTCTCG 60.024 50.000 13.63 0.00 33.40 4.04
2899 4345 2.264109 ATAACTGCTGTCTCGTGTCG 57.736 50.000 0.00 0.00 0.00 4.35
2903 4349 2.130073 CTGCTGTCTCGTGTCGTCCA 62.130 60.000 0.00 0.00 0.00 4.02
2928 4374 1.403780 CCAGCAAATCAGCCAAGCTTC 60.404 52.381 0.00 0.00 36.40 3.86
2930 4376 1.544691 AGCAAATCAGCCAAGCTTCTG 59.455 47.619 8.52 8.52 36.40 3.02
2951 4397 8.868522 TTCTGATTCTTGGTTATGATCAAACT 57.131 30.769 0.00 0.00 0.00 2.66
2960 4406 7.202016 TGGTTATGATCAAACTGACTGTTTC 57.798 36.000 0.00 0.00 46.11 2.78
2976 4422 3.073678 TGTTTCATTAGCACGCAGACAT 58.926 40.909 0.00 0.00 0.00 3.06
2994 4440 5.239306 CAGACATACAAGTCACACACCATTT 59.761 40.000 0.00 0.00 40.98 2.32
2995 4441 5.239306 AGACATACAAGTCACACACCATTTG 59.761 40.000 0.00 0.00 40.98 2.32
2996 4442 5.129634 ACATACAAGTCACACACCATTTGA 58.870 37.500 0.00 0.00 0.00 2.69
2997 4443 5.008613 ACATACAAGTCACACACCATTTGAC 59.991 40.000 0.00 0.00 40.04 3.18
3001 4447 3.884895 AGTCACACACCATTTGACTCAA 58.115 40.909 0.00 0.00 45.49 3.02
3002 4448 3.879295 AGTCACACACCATTTGACTCAAG 59.121 43.478 0.00 0.00 45.49 3.02
3085 4531 1.065358 GCACACAAATCTGCACATGC 58.935 50.000 0.00 0.00 42.50 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.081204 TGCCATAGTGATAATTTTATGCAAGAT 57.919 29.630 0.00 0.00 0.00 2.40
50 51 9.855021 GATGTTTGTAACTAAAAATGCCATAGT 57.145 29.630 0.00 0.00 0.00 2.12
142 143 7.120579 AGACACAATTAAGCGAATTTCCATGTA 59.879 33.333 0.00 0.00 35.45 2.29
226 228 3.631686 TGGATTATCGCAATTTCCTGTGG 59.368 43.478 0.00 0.00 0.00 4.17
246 248 0.322008 GAGCCTGGGTTCAGAAGTGG 60.322 60.000 0.00 0.00 43.49 4.00
256 258 0.685458 GGATGCAAATGAGCCTGGGT 60.685 55.000 0.00 0.00 0.00 4.51
262 264 2.653130 GCGCGGATGCAAATGAGC 60.653 61.111 8.83 0.00 42.97 4.26
268 270 0.243365 ATTTTTGAGCGCGGATGCAA 59.757 45.000 8.83 0.00 42.97 4.08
353 355 0.034896 AATTGAAGCGGACCTCACGT 59.965 50.000 0.00 0.00 0.00 4.49
355 357 1.468914 GGAAATTGAAGCGGACCTCAC 59.531 52.381 0.00 0.00 0.00 3.51
362 364 5.638657 TCAAATGATTTGGAAATTGAAGCGG 59.361 36.000 17.01 0.00 40.98 5.52
374 376 6.016192 AGCTGCTCAGATATCAAATGATTTGG 60.016 38.462 17.01 1.22 40.98 3.28
380 382 7.153315 TCTAAGAGCTGCTCAGATATCAAATG 58.847 38.462 29.49 8.39 32.06 2.32
432 434 7.491682 AGAACAGTGCATGAACAATAACTTTT 58.508 30.769 6.60 0.00 0.00 2.27
440 443 3.568007 GGGTAAGAACAGTGCATGAACAA 59.432 43.478 6.60 0.00 0.00 2.83
443 446 2.037902 TCGGGTAAGAACAGTGCATGAA 59.962 45.455 0.00 0.00 0.00 2.57
446 449 3.350219 AATCGGGTAAGAACAGTGCAT 57.650 42.857 0.00 0.00 0.00 3.96
492 496 7.222872 TCCAATTTTCAGGTTATTTGCACATT 58.777 30.769 0.00 0.00 0.00 2.71
506 510 3.146066 TGAGGTCCGTTCCAATTTTCAG 58.854 45.455 0.00 0.00 0.00 3.02
523 527 7.223387 GCATGGTAGAAAATTTATTGCTTGAGG 59.777 37.037 0.00 0.00 0.00 3.86
599 611 1.856265 GCAGAGTTTCGTTGCCCAGG 61.856 60.000 0.00 0.00 31.79 4.45
607 619 0.034059 CCTGGAGTGCAGAGTTTCGT 59.966 55.000 14.03 0.00 0.00 3.85
646 658 2.621055 TCTGAAAACGTGACCCAATTGG 59.379 45.455 18.21 18.21 41.37 3.16
664 676 3.470709 ACACACAAACTCTCACCATCTG 58.529 45.455 0.00 0.00 0.00 2.90
669 681 1.003866 GCGAACACACAAACTCTCACC 60.004 52.381 0.00 0.00 0.00 4.02
746 760 2.918571 TTCTGTTCGCTGCCAGAAG 58.081 52.632 13.48 0.00 41.47 2.85
778 792 0.404040 ACTTTCGCCTGGGGAATTCA 59.596 50.000 24.49 10.93 34.62 2.57
863 882 0.747644 CTGCCGCCAATACACATGGA 60.748 55.000 0.00 0.00 40.56 3.41
904 923 0.105964 CCCTAGCTAGTCTGCTCCCA 60.106 60.000 19.31 0.00 42.97 4.37
908 927 3.053544 TGTCTAACCCTAGCTAGTCTGCT 60.054 47.826 19.31 2.22 46.11 4.24
920 939 2.552367 AGCTAAGCCTTGTCTAACCCT 58.448 47.619 0.00 0.00 0.00 4.34
930 949 0.875059 GTCGTGCAAAGCTAAGCCTT 59.125 50.000 7.73 0.00 0.00 4.35
967 986 3.749064 GGACGACGCAGAGGCTGA 61.749 66.667 0.00 0.00 38.10 4.26
986 1005 1.412079 TGCCATGGTGAGCACTTTTT 58.588 45.000 14.67 0.00 33.08 1.94
1010 1069 5.851703 GCCGCTAGTTTACTTTTCTTTTCTG 59.148 40.000 0.00 0.00 0.00 3.02
1024 1083 2.824041 CATGGCGGCCGCTAGTTT 60.824 61.111 45.23 25.84 41.60 2.66
1063 2241 0.609957 TCTACAAGCTCGTCCGGGAA 60.610 55.000 0.00 0.00 0.00 3.97
1243 2433 2.301346 GATGAAATCGGGCATGTCCTT 58.699 47.619 15.80 1.17 31.13 3.36
1257 2447 1.570857 ATGCGGTGGAGGGGATGAAA 61.571 55.000 0.00 0.00 0.00 2.69
1267 2457 2.513666 GAATGGCGATGCGGTGGA 60.514 61.111 0.00 0.00 0.00 4.02
1956 3211 1.446272 GACTTCTTCCACCGGAGCG 60.446 63.158 9.46 0.00 31.21 5.03
2016 3280 2.885135 TGGATTGAGCAGATGTGGTT 57.115 45.000 0.00 0.00 33.41 3.67
2080 3354 7.946381 TTACCATAGCCAAAATAATCACACA 57.054 32.000 0.00 0.00 0.00 3.72
2158 3435 7.881751 GGTACCACCTATATCATAACCCTTTTC 59.118 40.741 7.15 0.00 34.73 2.29
2217 3496 7.972832 ATTATTTCACGAGTTGGTAAACAGA 57.027 32.000 0.00 0.00 38.88 3.41
2231 3510 9.393249 TCAGTTCAAAAGCTTTATTATTTCACG 57.607 29.630 13.10 0.00 0.00 4.35
2256 3535 7.541437 ACTTAGAAAGCAGTGTTAACTATCGTC 59.459 37.037 7.22 0.00 33.79 4.20
2331 3640 9.214957 CTACATTAAGAACTAACACATTCCACA 57.785 33.333 0.00 0.00 0.00 4.17
2332 3641 9.431887 TCTACATTAAGAACTAACACATTCCAC 57.568 33.333 0.00 0.00 0.00 4.02
2362 3674 4.452455 CCTGAATACGGTCTTATCCAATGC 59.548 45.833 0.00 0.00 0.00 3.56
2432 3753 1.686052 GCCACACCTTCATGTTTTGGA 59.314 47.619 0.00 0.00 0.00 3.53
2441 3762 1.899814 CTGGTAGTAGCCACACCTTCA 59.100 52.381 0.00 0.00 34.36 3.02
2473 3794 4.827692 AGTGCTAATTGTGGTCGTATCAA 58.172 39.130 0.00 0.00 0.00 2.57
2518 3839 7.072030 GCATGTTAAGAGAAATATGTTAGCGG 58.928 38.462 0.00 0.00 32.36 5.52
2520 3841 9.443283 CTTGCATGTTAAGAGAAATATGTTAGC 57.557 33.333 6.11 0.00 32.36 3.09
2552 3873 4.649088 ATGCATGTTGAATGATGAGGTG 57.351 40.909 0.00 0.00 0.00 4.00
2583 3904 6.056090 TGTATAGTTGCATGTTAAGGTGGA 57.944 37.500 0.00 0.00 0.00 4.02
2707 4062 8.909708 TTCGCAATATTTCAATGAGGTTTTAG 57.090 30.769 0.00 0.00 0.00 1.85
2708 4063 9.868277 ATTTCGCAATATTTCAATGAGGTTTTA 57.132 25.926 0.00 0.00 0.00 1.52
2716 4071 8.430063 GCAGGAATATTTCGCAATATTTCAATG 58.570 33.333 17.57 10.84 43.07 2.82
2730 4085 3.608073 GCACGTTGTTGCAGGAATATTTC 59.392 43.478 0.00 0.00 42.49 2.17
2754 4109 8.474025 GCTGACTATATAAACTAGATGATGCCT 58.526 37.037 0.00 0.00 0.00 4.75
2764 4119 9.368416 AGAAGGATGTGCTGACTATATAAACTA 57.632 33.333 0.00 0.00 0.00 2.24
2766 4121 8.364142 AGAGAAGGATGTGCTGACTATATAAAC 58.636 37.037 0.00 0.00 0.00 2.01
2793 4148 9.793259 ACTAGACAGAAAATTTTGAAGTATCCA 57.207 29.630 8.47 0.00 0.00 3.41
2813 4168 7.592533 TGTCAACGTATTCAGTTTGTACTAGAC 59.407 37.037 0.00 0.00 31.96 2.59
2814 4169 7.650890 TGTCAACGTATTCAGTTTGTACTAGA 58.349 34.615 0.00 0.00 31.96 2.43
2815 4170 7.862741 TGTCAACGTATTCAGTTTGTACTAG 57.137 36.000 0.00 0.00 31.96 2.57
2816 4171 8.645730 TTTGTCAACGTATTCAGTTTGTACTA 57.354 30.769 0.00 0.00 31.96 1.82
2817 4172 7.542534 TTTGTCAACGTATTCAGTTTGTACT 57.457 32.000 0.00 0.00 34.00 2.73
2827 4182 7.015877 GGTTCTGAAGATTTGTCAACGTATTC 58.984 38.462 0.00 0.00 0.00 1.75
2828 4183 6.485313 TGGTTCTGAAGATTTGTCAACGTATT 59.515 34.615 0.00 0.00 0.00 1.89
2833 4188 4.036734 TGCTGGTTCTGAAGATTTGTCAAC 59.963 41.667 0.00 0.00 0.00 3.18
2834 4189 4.206375 TGCTGGTTCTGAAGATTTGTCAA 58.794 39.130 0.00 0.00 0.00 3.18
2835 4190 3.819368 TGCTGGTTCTGAAGATTTGTCA 58.181 40.909 0.00 0.00 0.00 3.58
2836 4191 4.791974 CTTGCTGGTTCTGAAGATTTGTC 58.208 43.478 0.00 0.00 0.00 3.18
2837 4192 3.005155 GCTTGCTGGTTCTGAAGATTTGT 59.995 43.478 0.00 0.00 0.00 2.83
2858 4304 2.166664 ACCTACTCCAAGTTCGATCAGC 59.833 50.000 0.00 0.00 0.00 4.26
2862 4308 6.461231 GCAGTTATACCTACTCCAAGTTCGAT 60.461 42.308 0.00 0.00 0.00 3.59
2864 4310 5.041940 GCAGTTATACCTACTCCAAGTTCG 58.958 45.833 0.00 0.00 0.00 3.95
2872 4318 4.575645 ACGAGACAGCAGTTATACCTACTC 59.424 45.833 0.00 0.00 0.00 2.59
2873 4319 4.335874 CACGAGACAGCAGTTATACCTACT 59.664 45.833 0.00 0.00 0.00 2.57
2884 4330 1.442857 GGACGACACGAGACAGCAG 60.443 63.158 0.00 0.00 0.00 4.24
2894 4340 0.464036 TGCTGGGATATGGACGACAC 59.536 55.000 0.00 0.00 0.00 3.67
2899 4345 2.555757 GCTGATTTGCTGGGATATGGAC 59.444 50.000 0.00 0.00 0.00 4.02
2903 4349 3.228453 CTTGGCTGATTTGCTGGGATAT 58.772 45.455 0.00 0.00 0.00 1.63
2928 4374 8.180267 GTCAGTTTGATCATAACCAAGAATCAG 58.820 37.037 13.64 0.00 0.00 2.90
2930 4376 8.180267 CAGTCAGTTTGATCATAACCAAGAATC 58.820 37.037 13.64 0.00 0.00 2.52
2951 4397 2.480037 CTGCGTGCTAATGAAACAGTCA 59.520 45.455 0.00 0.00 41.67 3.41
2959 4405 3.518634 TGTATGTCTGCGTGCTAATGA 57.481 42.857 0.00 0.00 0.00 2.57
2960 4406 3.618594 ACTTGTATGTCTGCGTGCTAATG 59.381 43.478 0.00 0.00 0.00 1.90
2994 4440 6.538742 CAGTTTGAGTTAGGTTTCTTGAGTCA 59.461 38.462 0.00 0.00 0.00 3.41
2995 4441 6.761714 TCAGTTTGAGTTAGGTTTCTTGAGTC 59.238 38.462 0.00 0.00 0.00 3.36
2996 4442 6.650120 TCAGTTTGAGTTAGGTTTCTTGAGT 58.350 36.000 0.00 0.00 0.00 3.41
2997 4443 7.659390 AGATCAGTTTGAGTTAGGTTTCTTGAG 59.341 37.037 0.00 0.00 0.00 3.02
2998 4444 7.442364 CAGATCAGTTTGAGTTAGGTTTCTTGA 59.558 37.037 0.00 0.00 0.00 3.02
2999 4445 7.442364 TCAGATCAGTTTGAGTTAGGTTTCTTG 59.558 37.037 0.00 0.00 0.00 3.02
3001 4447 6.931840 GTCAGATCAGTTTGAGTTAGGTTTCT 59.068 38.462 0.00 0.00 0.00 2.52
3002 4448 6.706270 TGTCAGATCAGTTTGAGTTAGGTTTC 59.294 38.462 0.00 0.00 0.00 2.78
3085 4531 3.609373 CGTTATGCTGCTTCAAACAATGG 59.391 43.478 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.