Multiple sequence alignment - TraesCS1A01G105200

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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 TraesCS1A01G105200 chr1A 100.000 2414 0 0 1 2414 100545611 100548024 0.000000e+00 4458
1 TraesCS1A01G105200 chr3D 92.695 2341 151 8 1 2325 349444795 349442459 0.000000e+00 3358
2 TraesCS1A01G105200 chr3D 93.412 1791 109 5 548 2332 415199312 415197525 0.000000e+00 2645
3 TraesCS1A01G105200 chr3D 89.562 1667 127 24 1 1660 356669826 356671452 0.000000e+00 2071
4 TraesCS1A01G105200 chr3D 93.548 93 5 1 2323 2414 172948234 172948142 1.160000e-28 137
5 TraesCS1A01G105200 chr5D 92.659 2343 147 14 1 2324 192526200 192523864 0.000000e+00 3350
6 TraesCS1A01G105200 chr5D 89.194 1712 130 26 1 1697 434733265 434734936 0.000000e+00 2085
7 TraesCS1A01G105200 chr1D 92.624 2332 144 11 1 2318 194854479 194852162 0.000000e+00 3328
8 TraesCS1A01G105200 chr6B 91.966 2029 140 15 1 2022 144742065 144744077 0.000000e+00 2822
9 TraesCS1A01G105200 chr6B 88.403 1716 140 27 1 1700 436047352 436049024 0.000000e+00 2012
10 TraesCS1A01G105200 chr4D 94.244 1772 96 4 548 2319 65498831 65497066 0.000000e+00 2702
11 TraesCS1A01G105200 chr4D 89.556 1666 126 25 1 1660 63531850 63533473 0.000000e+00 2069
12 TraesCS1A01G105200 chr4D 89.309 1665 126 21 1 1660 14237822 14239439 0.000000e+00 2041
13 TraesCS1A01G105200 chr2D 94.055 1783 97 6 548 2330 260387532 260385759 0.000000e+00 2697
14 TraesCS1A01G105200 chr2D 93.427 1780 111 5 548 2323 471597008 471595231 0.000000e+00 2634
15 TraesCS1A01G105200 chr2D 89.676 1666 124 26 1 1660 409562429 409560806 0.000000e+00 2080
16 TraesCS1A01G105200 chr6D 93.525 1776 107 3 548 2323 273131113 273132880 0.000000e+00 2636
17 TraesCS1A01G105200 chr7B 88.533 1718 137 30 1 1700 534551243 534549568 0.000000e+00 2026
18 TraesCS1A01G105200 chr7B 93.617 94 4 2 2323 2414 387037398 387037305 3.240000e-29 139
19 TraesCS1A01G105200 chr5B 88.435 1712 140 24 1 1700 348893772 348892107 0.000000e+00 2012
20 TraesCS1A01G105200 chr4B 94.565 92 5 0 2323 2414 425986643 425986552 2.500000e-30 143
21 TraesCS1A01G105200 chr4B 93.548 93 5 1 2323 2414 206897719 206897811 1.160000e-28 137
22 TraesCS1A01G105200 chr7A 93.548 93 5 1 2323 2414 200499601 200499693 1.160000e-28 137
23 TraesCS1A01G105200 chr7A 93.548 93 5 1 2323 2414 423573075 423573167 1.160000e-28 137
24 TraesCS1A01G105200 chr2B 93.548 93 5 1 2323 2414 387227089 387227181 1.160000e-28 137
25 TraesCS1A01G105200 chr2A 93.478 92 6 0 2323 2414 525636602 525636693 1.160000e-28 137
26 TraesCS1A01G105200 chr1B 93.548 93 4 2 2323 2414 334952264 334952173 1.160000e-28 137


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 TraesCS1A01G105200 chr1A 100545611 100548024 2413 False 4458 4458 100.000 1 2414 1 chr1A.!!$F1 2413
1 TraesCS1A01G105200 chr3D 349442459 349444795 2336 True 3358 3358 92.695 1 2325 1 chr3D.!!$R2 2324
2 TraesCS1A01G105200 chr3D 415197525 415199312 1787 True 2645 2645 93.412 548 2332 1 chr3D.!!$R3 1784
3 TraesCS1A01G105200 chr3D 356669826 356671452 1626 False 2071 2071 89.562 1 1660 1 chr3D.!!$F1 1659
4 TraesCS1A01G105200 chr5D 192523864 192526200 2336 True 3350 3350 92.659 1 2324 1 chr5D.!!$R1 2323
5 TraesCS1A01G105200 chr5D 434733265 434734936 1671 False 2085 2085 89.194 1 1697 1 chr5D.!!$F1 1696
6 TraesCS1A01G105200 chr1D 194852162 194854479 2317 True 3328 3328 92.624 1 2318 1 chr1D.!!$R1 2317
7 TraesCS1A01G105200 chr6B 144742065 144744077 2012 False 2822 2822 91.966 1 2022 1 chr6B.!!$F1 2021
8 TraesCS1A01G105200 chr6B 436047352 436049024 1672 False 2012 2012 88.403 1 1700 1 chr6B.!!$F2 1699
9 TraesCS1A01G105200 chr4D 65497066 65498831 1765 True 2702 2702 94.244 548 2319 1 chr4D.!!$R1 1771
10 TraesCS1A01G105200 chr4D 63531850 63533473 1623 False 2069 2069 89.556 1 1660 1 chr4D.!!$F2 1659
11 TraesCS1A01G105200 chr4D 14237822 14239439 1617 False 2041 2041 89.309 1 1660 1 chr4D.!!$F1 1659
12 TraesCS1A01G105200 chr2D 260385759 260387532 1773 True 2697 2697 94.055 548 2330 1 chr2D.!!$R1 1782
13 TraesCS1A01G105200 chr2D 471595231 471597008 1777 True 2634 2634 93.427 548 2323 1 chr2D.!!$R3 1775
14 TraesCS1A01G105200 chr2D 409560806 409562429 1623 True 2080 2080 89.676 1 1660 1 chr2D.!!$R2 1659
15 TraesCS1A01G105200 chr6D 273131113 273132880 1767 False 2636 2636 93.525 548 2323 1 chr6D.!!$F1 1775
16 TraesCS1A01G105200 chr7B 534549568 534551243 1675 True 2026 2026 88.533 1 1700 1 chr7B.!!$R2 1699
17 TraesCS1A01G105200 chr5B 348892107 348893772 1665 True 2012 2012 88.435 1 1700 1 chr5B.!!$R1 1699

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
545 563 0.107897 TGTGAACGTGTTGGCTCTGT 60.108 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1838 0.465705 GCATGCACTAGCTAGGTGGA 59.534 55.0 24.35 19.44 42.74 4.02 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
21 22 2.885135 TGGTGCTCATTTGACCTCAT 57.115 45.000 0.00 0.00 0.00 2.90
30 31 1.234821 TTTGACCTCATTCGTGCCAC 58.765 50.000 0.00 0.00 0.00 5.01
130 138 5.242838 ACAGCGAAGGTTTCATATTTTTCCA 59.757 36.000 0.00 0.00 33.74 3.53
222 233 1.004200 CGCGGGGTTTCACCTAACT 60.004 57.895 0.00 0.00 38.64 2.24
230 241 3.514309 GGGTTTCACCTAACTCTAGCTCA 59.486 47.826 0.00 0.00 38.64 4.26
236 247 3.868077 CACCTAACTCTAGCTCACAATGC 59.132 47.826 0.00 0.00 0.00 3.56
242 253 0.393402 CTAGCTCACAATGCCAGCCA 60.393 55.000 0.00 0.00 33.28 4.75
283 294 3.068732 CCAAGCGACAATCCTCAGATCTA 59.931 47.826 0.00 0.00 0.00 1.98
353 364 0.904865 TGGATCACAAGGACGGCTCT 60.905 55.000 0.00 0.00 0.00 4.09
362 373 1.741770 GGACGGCTCTGCATCGTTT 60.742 57.895 0.00 0.00 37.25 3.60
373 384 1.024579 GCATCGTTTGATCGTGGGGT 61.025 55.000 0.00 0.00 30.49 4.95
433 444 2.438434 CCCACCATTGACTCCGCC 60.438 66.667 0.00 0.00 0.00 6.13
434 445 2.350895 CCACCATTGACTCCGCCA 59.649 61.111 0.00 0.00 0.00 5.69
441 454 2.351738 CCATTGACTCCGCCAGAAAAAC 60.352 50.000 0.00 0.00 0.00 2.43
542 560 2.553079 TTTTGTGAACGTGTTGGCTC 57.447 45.000 0.00 0.00 0.00 4.70
544 562 1.013596 TTGTGAACGTGTTGGCTCTG 58.986 50.000 0.00 0.00 0.00 3.35
545 563 0.107897 TGTGAACGTGTTGGCTCTGT 60.108 50.000 0.00 0.00 0.00 3.41
546 564 1.137282 TGTGAACGTGTTGGCTCTGTA 59.863 47.619 0.00 0.00 0.00 2.74
547 565 2.224185 TGTGAACGTGTTGGCTCTGTAT 60.224 45.455 0.00 0.00 0.00 2.29
556 587 4.990426 GTGTTGGCTCTGTATTTTTGCATT 59.010 37.500 0.00 0.00 0.00 3.56
595 626 3.064545 GTGAATGTGCTGGCTCTGTATTC 59.935 47.826 0.00 0.00 0.00 1.75
606 637 3.001736 GGCTCTGTATTCTTGCATCGTTC 59.998 47.826 0.00 0.00 0.00 3.95
607 638 3.868077 GCTCTGTATTCTTGCATCGTTCT 59.132 43.478 0.00 0.00 0.00 3.01
613 644 7.224753 TCTGTATTCTTGCATCGTTCTAAATCC 59.775 37.037 0.00 0.00 0.00 3.01
617 648 6.363577 TCTTGCATCGTTCTAAATCCATTC 57.636 37.500 0.00 0.00 0.00 2.67
629 660 6.345298 TCTAAATCCATTCACATTGCGTAGA 58.655 36.000 0.00 0.00 0.00 2.59
691 723 4.314121 TGCAAAATGGCCACAAACTATTC 58.686 39.130 8.16 0.00 0.00 1.75
780 813 9.964253 GCTTCTTTTTCTTCTTCTTTTTCAAAG 57.036 29.630 0.00 0.00 0.00 2.77
793 826 1.698506 TTCAAAGCACCGTTTCCCAT 58.301 45.000 0.00 0.00 0.00 4.00
805 838 1.877443 GTTTCCCATGCGTGTACACTT 59.123 47.619 23.01 5.85 0.00 3.16
853 886 3.499745 GGGTTACTTCACATTTGACCCCT 60.500 47.826 0.00 0.00 30.02 4.79
956 1009 0.255318 CTCTCTGCCATCTGCCCTTT 59.745 55.000 0.00 0.00 40.16 3.11
977 1030 0.241213 TGCTCTTCGACCACTTCTCG 59.759 55.000 0.00 0.00 0.00 4.04
1081 1136 2.399611 GCATGTACGTTGAGCGCC 59.600 61.111 2.29 0.00 46.11 6.53
1083 1138 2.508439 ATGTACGTTGAGCGCCCG 60.508 61.111 2.29 4.05 46.11 6.13
1098 1155 4.373116 CCGCTACGTGTGTGGGCT 62.373 66.667 13.11 0.00 0.00 5.19
1392 1449 1.329256 CTCTTCCGTACCCCATCGAT 58.671 55.000 0.00 0.00 0.00 3.59
1399 1456 1.409790 CGTACCCCATCGATAACACCA 59.590 52.381 0.00 0.00 0.00 4.17
1563 1633 2.385013 GGCTTGTTGGCCCTTTTATG 57.615 50.000 0.00 0.00 45.92 1.90
1649 1719 2.045708 TGCTATGGGCTTGTTGGCG 61.046 57.895 0.00 0.00 42.84 5.69
1672 1749 6.366061 GCGCTATCTACATGTATGTTGATTGA 59.634 38.462 23.17 10.92 46.07 2.57
1761 1838 8.574251 TTCTTACACAAGCCACAAATATGTAT 57.426 30.769 0.00 0.00 37.82 2.29
1784 1861 1.278985 ACCTAGCTAGTGCATGCAACA 59.721 47.619 24.58 12.21 42.74 3.33
1917 1995 0.892063 GCGAGAAGAGAGGAACCAGT 59.108 55.000 0.00 0.00 0.00 4.00
1943 2021 4.794439 CCGTCGCTGCATCCGTGA 62.794 66.667 0.00 0.00 0.00 4.35
1985 2068 0.107993 CTCGGTCAGTGCATCATGGT 60.108 55.000 0.00 0.00 0.00 3.55
1989 2072 1.378911 TCAGTGCATCATGGTGGCC 60.379 57.895 8.33 0.00 0.00 5.36
2039 2125 3.367743 CAACGCATGCAGGCAGGT 61.368 61.111 24.53 11.25 0.00 4.00
2058 2144 2.093553 GGTTTGTTGGGTGCATGCATAT 60.094 45.455 25.64 0.00 0.00 1.78
2073 2159 2.131183 GCATATCAGGCTTCTGTCGTC 58.869 52.381 0.00 0.00 39.45 4.20
2106 2193 0.800012 GCGTTTAATGCAAGGGACGA 59.200 50.000 16.69 0.00 32.73 4.20
2128 2215 1.560611 CCAATGAAACCATGGCCCAAT 59.439 47.619 13.04 0.00 0.00 3.16
2143 2230 1.468520 CCCAATGGTTGAACAGCTACG 59.531 52.381 0.00 0.00 0.00 3.51
2201 2288 4.129737 CACTGACCCGACGGCGAT 62.130 66.667 15.16 0.00 40.82 4.58
2250 2337 0.252239 GGCAAGGGAGTGGGGAAAAT 60.252 55.000 0.00 0.00 0.00 1.82
2355 2442 9.490379 AATTGTAATAGTAGGTTCCGATTCATC 57.510 33.333 0.00 0.00 0.00 2.92
2356 2443 7.591421 TGTAATAGTAGGTTCCGATTCATCA 57.409 36.000 0.00 0.00 0.00 3.07
2357 2444 8.190326 TGTAATAGTAGGTTCCGATTCATCAT 57.810 34.615 0.00 0.00 0.00 2.45
2358 2445 9.304335 TGTAATAGTAGGTTCCGATTCATCATA 57.696 33.333 0.00 0.00 0.00 2.15
2361 2448 9.712305 AATAGTAGGTTCCGATTCATCATAAAG 57.288 33.333 0.00 0.00 0.00 1.85
2362 2449 5.992217 AGTAGGTTCCGATTCATCATAAAGC 59.008 40.000 0.00 0.00 0.00 3.51
2363 2450 5.041191 AGGTTCCGATTCATCATAAAGCT 57.959 39.130 0.00 0.00 0.00 3.74
2364 2451 5.440610 AGGTTCCGATTCATCATAAAGCTT 58.559 37.500 0.00 0.00 0.00 3.74
2365 2452 5.888161 AGGTTCCGATTCATCATAAAGCTTT 59.112 36.000 17.30 17.30 0.00 3.51
2366 2453 6.038714 AGGTTCCGATTCATCATAAAGCTTTC 59.961 38.462 16.57 0.00 0.00 2.62
2367 2454 6.038714 GGTTCCGATTCATCATAAAGCTTTCT 59.961 38.462 16.57 2.47 0.00 2.52
2368 2455 7.226720 GGTTCCGATTCATCATAAAGCTTTCTA 59.773 37.037 16.57 0.00 0.00 2.10
2369 2456 7.953158 TCCGATTCATCATAAAGCTTTCTAG 57.047 36.000 16.57 7.03 0.00 2.43
2370 2457 6.931281 TCCGATTCATCATAAAGCTTTCTAGG 59.069 38.462 16.57 0.52 0.00 3.02
2371 2458 6.148480 CCGATTCATCATAAAGCTTTCTAGGG 59.852 42.308 16.57 4.43 0.00 3.53
2372 2459 6.931281 CGATTCATCATAAAGCTTTCTAGGGA 59.069 38.462 16.57 6.82 0.00 4.20
2373 2460 7.605691 CGATTCATCATAAAGCTTTCTAGGGAT 59.394 37.037 16.57 9.61 0.00 3.85
2374 2461 9.294614 GATTCATCATAAAGCTTTCTAGGGATT 57.705 33.333 16.57 6.15 0.00 3.01
2375 2462 8.455903 TTCATCATAAAGCTTTCTAGGGATTG 57.544 34.615 16.57 4.54 0.00 2.67
2376 2463 7.805163 TCATCATAAAGCTTTCTAGGGATTGA 58.195 34.615 16.57 6.71 0.00 2.57
2377 2464 8.274322 TCATCATAAAGCTTTCTAGGGATTGAA 58.726 33.333 16.57 0.00 0.00 2.69
2378 2465 8.906867 CATCATAAAGCTTTCTAGGGATTGAAA 58.093 33.333 16.57 0.00 0.00 2.69
2379 2466 8.281212 TCATAAAGCTTTCTAGGGATTGAAAC 57.719 34.615 16.57 0.00 0.00 2.78
2380 2467 8.109634 TCATAAAGCTTTCTAGGGATTGAAACT 58.890 33.333 16.57 0.00 0.00 2.66
2381 2468 8.743714 CATAAAGCTTTCTAGGGATTGAAACTT 58.256 33.333 16.57 0.00 31.59 2.66
2382 2469 6.825944 AAGCTTTCTAGGGATTGAAACTTC 57.174 37.500 0.00 0.00 0.00 3.01
2383 2470 5.257262 AGCTTTCTAGGGATTGAAACTTCC 58.743 41.667 0.00 0.00 0.00 3.46
2384 2471 5.010282 GCTTTCTAGGGATTGAAACTTCCA 58.990 41.667 0.00 0.00 33.43 3.53
2385 2472 5.476945 GCTTTCTAGGGATTGAAACTTCCAA 59.523 40.000 0.00 0.00 33.43 3.53
2386 2473 6.570571 GCTTTCTAGGGATTGAAACTTCCAAC 60.571 42.308 0.00 0.00 33.43 3.77
2387 2474 5.843019 TCTAGGGATTGAAACTTCCAACT 57.157 39.130 0.00 0.00 33.43 3.16
2388 2475 5.805728 TCTAGGGATTGAAACTTCCAACTC 58.194 41.667 0.00 0.00 33.43 3.01
2389 2476 3.767711 AGGGATTGAAACTTCCAACTCC 58.232 45.455 0.00 0.00 33.43 3.85
2390 2477 3.140144 AGGGATTGAAACTTCCAACTCCA 59.860 43.478 0.00 0.00 33.43 3.86
2391 2478 3.507622 GGGATTGAAACTTCCAACTCCAG 59.492 47.826 0.00 0.00 33.43 3.86
2392 2479 4.145052 GGATTGAAACTTCCAACTCCAGT 58.855 43.478 0.00 0.00 31.99 4.00
2393 2480 4.584743 GGATTGAAACTTCCAACTCCAGTT 59.415 41.667 0.00 0.00 39.12 3.16
2394 2481 5.069119 GGATTGAAACTTCCAACTCCAGTTT 59.931 40.000 0.00 0.00 42.23 2.66
2395 2482 5.993748 TTGAAACTTCCAACTCCAGTTTT 57.006 34.783 0.00 0.00 40.15 2.43
2396 2483 5.576447 TGAAACTTCCAACTCCAGTTTTC 57.424 39.130 0.00 0.00 40.15 2.29
2397 2484 5.261216 TGAAACTTCCAACTCCAGTTTTCT 58.739 37.500 0.00 0.00 40.15 2.52
2398 2485 5.714806 TGAAACTTCCAACTCCAGTTTTCTT 59.285 36.000 0.00 0.00 40.15 2.52
2399 2486 5.836821 AACTTCCAACTCCAGTTTTCTTC 57.163 39.130 0.00 0.00 35.83 2.87
2400 2487 4.855340 ACTTCCAACTCCAGTTTTCTTCA 58.145 39.130 0.00 0.00 35.83 3.02
2401 2488 5.261216 ACTTCCAACTCCAGTTTTCTTCAA 58.739 37.500 0.00 0.00 35.83 2.69
2402 2489 5.714806 ACTTCCAACTCCAGTTTTCTTCAAA 59.285 36.000 0.00 0.00 35.83 2.69
2403 2490 6.381133 ACTTCCAACTCCAGTTTTCTTCAAAT 59.619 34.615 0.00 0.00 35.83 2.32
2404 2491 6.147864 TCCAACTCCAGTTTTCTTCAAATG 57.852 37.500 0.00 0.00 35.83 2.32
2405 2492 5.890985 TCCAACTCCAGTTTTCTTCAAATGA 59.109 36.000 0.00 0.00 35.83 2.57
2406 2493 6.550854 TCCAACTCCAGTTTTCTTCAAATGAT 59.449 34.615 0.00 0.00 35.83 2.45
2407 2494 7.069826 TCCAACTCCAGTTTTCTTCAAATGATT 59.930 33.333 0.00 0.00 35.83 2.57
2408 2495 7.712205 CCAACTCCAGTTTTCTTCAAATGATTT 59.288 33.333 0.00 0.00 35.83 2.17
2409 2496 8.758715 CAACTCCAGTTTTCTTCAAATGATTTC 58.241 33.333 0.00 0.00 35.83 2.17
2410 2497 8.010733 ACTCCAGTTTTCTTCAAATGATTTCA 57.989 30.769 0.00 0.00 0.00 2.69
2411 2498 8.645110 ACTCCAGTTTTCTTCAAATGATTTCAT 58.355 29.630 0.00 0.00 38.41 2.57
2412 2499 9.136952 CTCCAGTTTTCTTCAAATGATTTCATC 57.863 33.333 0.00 0.00 35.10 2.92
2413 2500 8.640651 TCCAGTTTTCTTCAAATGATTTCATCA 58.359 29.630 0.00 0.00 44.55 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.475044 AAAACCCTAGGTGGCACGAA 59.525 50.000 12.17 0.61 35.34 3.85
30 31 6.014669 TGGTCATTTTCATGAAAAACCCTAGG 60.015 38.462 32.63 17.80 41.30 3.02
139 149 6.969473 GGCTTTGACTGAGCATAACTAATTTC 59.031 38.462 0.00 0.00 41.89 2.17
215 226 3.118592 GGCATTGTGAGCTAGAGTTAGGT 60.119 47.826 0.00 0.00 40.20 3.08
222 233 0.107508 GGCTGGCATTGTGAGCTAGA 60.108 55.000 2.64 0.00 42.44 2.43
230 241 0.820891 GATCGGATGGCTGGCATTGT 60.821 55.000 18.29 4.90 0.00 2.71
236 247 0.390340 CGGTATGATCGGATGGCTGG 60.390 60.000 0.00 0.00 0.00 4.85
242 253 1.209383 CGCGACGGTATGATCGGAT 59.791 57.895 0.00 0.00 38.78 4.18
283 294 5.663556 CCCACCTAATTCCTTCTAGAAGACT 59.336 44.000 30.17 14.96 40.79 3.24
331 342 0.605319 GCCGTCCTTGTGATCCAACA 60.605 55.000 0.00 0.00 0.00 3.33
353 364 1.024046 CCCCACGATCAAACGATGCA 61.024 55.000 0.00 0.00 37.03 3.96
362 373 1.904771 GTGGATCACCCCACGATCA 59.095 57.895 0.00 0.00 46.00 2.92
373 384 1.063642 AGGATCACCTCTCGTGGATCA 60.064 52.381 0.00 0.00 44.13 2.92
433 444 4.694982 GGGCCCAATAACAATGTTTTTCTG 59.305 41.667 19.95 0.00 0.00 3.02
434 445 4.349342 TGGGCCCAATAACAATGTTTTTCT 59.651 37.500 26.33 0.00 0.00 2.52
441 454 3.262915 TCCTTTTGGGCCCAATAACAATG 59.737 43.478 37.41 23.44 40.87 2.82
523 541 2.088423 AGAGCCAACACGTTCACAAAA 58.912 42.857 0.00 0.00 0.00 2.44
527 545 1.860676 TACAGAGCCAACACGTTCAC 58.139 50.000 0.00 0.00 0.00 3.18
528 546 2.831685 ATACAGAGCCAACACGTTCA 57.168 45.000 0.00 0.00 0.00 3.18
529 547 4.483476 AAAATACAGAGCCAACACGTTC 57.517 40.909 0.00 0.00 0.00 3.95
532 550 2.979813 GCAAAAATACAGAGCCAACACG 59.020 45.455 0.00 0.00 0.00 4.49
533 551 3.976169 TGCAAAAATACAGAGCCAACAC 58.024 40.909 0.00 0.00 0.00 3.32
534 552 4.870123 ATGCAAAAATACAGAGCCAACA 57.130 36.364 0.00 0.00 0.00 3.33
535 553 4.990426 ACAATGCAAAAATACAGAGCCAAC 59.010 37.500 0.00 0.00 0.00 3.77
536 554 5.212532 ACAATGCAAAAATACAGAGCCAA 57.787 34.783 0.00 0.00 0.00 4.52
538 556 5.919196 CAAACAATGCAAAAATACAGAGCC 58.081 37.500 0.00 0.00 0.00 4.70
556 587 4.527509 TTCACAAAAACCAGAGCAAACA 57.472 36.364 0.00 0.00 0.00 2.83
595 626 5.967674 GTGAATGGATTTAGAACGATGCAAG 59.032 40.000 0.00 0.00 0.00 4.01
606 637 6.603237 TCTACGCAATGTGAATGGATTTAG 57.397 37.500 0.00 0.00 0.00 1.85
607 638 6.993786 TTCTACGCAATGTGAATGGATTTA 57.006 33.333 0.00 0.00 0.00 1.40
613 644 5.512788 GGTCATTTTCTACGCAATGTGAATG 59.487 40.000 0.00 0.00 32.96 2.67
617 648 4.418013 TGGTCATTTTCTACGCAATGTG 57.582 40.909 0.00 0.00 32.96 3.21
629 660 6.368805 TGGCCCTTAAAAATTTGGTCATTTT 58.631 32.000 0.00 0.00 37.86 1.82
663 695 3.804786 TGTGGCCATTTTGCATGATAG 57.195 42.857 9.72 0.00 0.00 2.08
780 813 3.361977 ACGCATGGGAAACGGTGC 61.362 61.111 17.76 0.00 37.83 5.01
793 826 0.315886 ACATCGGAAGTGTACACGCA 59.684 50.000 19.93 4.33 36.20 5.24
853 886 3.258372 TGTTATTTGGCCGTGGCAATAAA 59.742 39.130 13.76 10.80 46.84 1.40
977 1030 3.194062 GCTGAGGATGTGCTAGAAGAAC 58.806 50.000 0.00 0.00 0.00 3.01
1081 1136 2.292794 ATAGCCCACACACGTAGCGG 62.293 60.000 0.00 0.00 0.00 5.52
1083 1138 2.035449 TGATATAGCCCACACACGTAGC 59.965 50.000 0.00 0.00 0.00 3.58
1098 1155 1.968493 GCGGTCCTCCACCTTGATATA 59.032 52.381 0.00 0.00 44.21 0.86
1392 1449 0.830444 ACTGCTCCTCCGTGGTGTTA 60.830 55.000 0.00 0.00 37.07 2.41
1399 1456 2.286523 CCCTTCACTGCTCCTCCGT 61.287 63.158 0.00 0.00 0.00 4.69
1672 1749 6.890979 AACAAAGCAAGCTCTCTAAGAAAT 57.109 33.333 0.00 0.00 0.00 2.17
1761 1838 0.465705 GCATGCACTAGCTAGGTGGA 59.534 55.000 24.35 19.44 42.74 4.02
1812 1889 5.182487 TCGCATCTGCACCTATTTTTCTAA 58.818 37.500 2.72 0.00 42.21 2.10
1875 1953 4.988540 CACACTTGTGTCCTCGATTTAGAA 59.011 41.667 3.13 0.00 40.96 2.10
1917 1995 4.662961 CAGCGACGGTCACTGCCA 62.663 66.667 12.69 0.00 0.00 4.92
1957 2035 2.048222 CTGACCGAGCCGCTTTCA 60.048 61.111 0.00 0.00 0.00 2.69
2039 2125 2.830321 TGATATGCATGCACCCAACAAA 59.170 40.909 25.37 0.00 0.00 2.83
2058 2144 2.258591 GCGACGACAGAAGCCTGA 59.741 61.111 0.00 0.00 43.02 3.86
2106 2193 0.909133 GGGCCATGGTTTCATTGGGT 60.909 55.000 14.67 0.00 0.00 4.51
2112 2199 2.681348 CCATTGGGCCATGGTTTCA 58.319 52.632 20.49 6.66 33.39 2.69
2201 2288 1.068588 CAGAAGAGGTCACAACGGACA 59.931 52.381 0.00 0.00 39.59 4.02
2250 2337 4.338118 CCCACACTCTTAACTTTTGCTCAA 59.662 41.667 0.00 0.00 0.00 3.02
2331 2418 8.014070 TGATGAATCGGAACCTACTATTACAA 57.986 34.615 0.00 0.00 0.00 2.41
2335 2422 9.712305 CTTTATGATGAATCGGAACCTACTATT 57.288 33.333 0.00 0.00 0.00 1.73
2336 2423 7.819900 GCTTTATGATGAATCGGAACCTACTAT 59.180 37.037 0.00 0.00 0.00 2.12
2337 2424 7.015292 AGCTTTATGATGAATCGGAACCTACTA 59.985 37.037 0.00 0.00 0.00 1.82
2338 2425 5.992217 GCTTTATGATGAATCGGAACCTACT 59.008 40.000 0.00 0.00 0.00 2.57
2339 2426 5.992217 AGCTTTATGATGAATCGGAACCTAC 59.008 40.000 0.00 0.00 0.00 3.18
2340 2427 6.174720 AGCTTTATGATGAATCGGAACCTA 57.825 37.500 0.00 0.00 0.00 3.08
2341 2428 5.041191 AGCTTTATGATGAATCGGAACCT 57.959 39.130 0.00 0.00 0.00 3.50
2342 2429 5.757850 AAGCTTTATGATGAATCGGAACC 57.242 39.130 0.00 0.00 0.00 3.62
2343 2430 7.020914 AGAAAGCTTTATGATGAATCGGAAC 57.979 36.000 12.68 0.00 0.00 3.62
2344 2431 7.442364 CCTAGAAAGCTTTATGATGAATCGGAA 59.558 37.037 16.44 0.00 0.00 4.30
2345 2432 6.931281 CCTAGAAAGCTTTATGATGAATCGGA 59.069 38.462 16.44 0.00 0.00 4.55
2346 2433 6.148480 CCCTAGAAAGCTTTATGATGAATCGG 59.852 42.308 16.44 4.11 0.00 4.18
2347 2434 6.931281 TCCCTAGAAAGCTTTATGATGAATCG 59.069 38.462 16.44 0.00 0.00 3.34
2348 2435 8.860780 ATCCCTAGAAAGCTTTATGATGAATC 57.139 34.615 16.44 0.00 0.00 2.52
2349 2436 9.075678 CAATCCCTAGAAAGCTTTATGATGAAT 57.924 33.333 16.44 0.66 0.00 2.57
2350 2437 8.274322 TCAATCCCTAGAAAGCTTTATGATGAA 58.726 33.333 16.44 0.00 0.00 2.57
2351 2438 7.805163 TCAATCCCTAGAAAGCTTTATGATGA 58.195 34.615 16.44 9.49 0.00 2.92
2352 2439 8.455903 TTCAATCCCTAGAAAGCTTTATGATG 57.544 34.615 16.44 6.48 0.00 3.07
2353 2440 8.907885 GTTTCAATCCCTAGAAAGCTTTATGAT 58.092 33.333 16.44 7.81 34.69 2.45
2354 2441 8.109634 AGTTTCAATCCCTAGAAAGCTTTATGA 58.890 33.333 16.44 5.74 34.69 2.15
2355 2442 8.286191 AGTTTCAATCCCTAGAAAGCTTTATG 57.714 34.615 16.44 7.46 34.69 1.90
2356 2443 8.885693 AAGTTTCAATCCCTAGAAAGCTTTAT 57.114 30.769 12.68 12.12 34.69 1.40
2357 2444 7.393515 GGAAGTTTCAATCCCTAGAAAGCTTTA 59.606 37.037 12.68 0.00 34.69 1.85
2358 2445 6.209589 GGAAGTTTCAATCCCTAGAAAGCTTT 59.790 38.462 12.53 12.53 34.69 3.51
2359 2446 5.712446 GGAAGTTTCAATCCCTAGAAAGCTT 59.288 40.000 0.00 0.00 34.69 3.74
2360 2447 5.222130 TGGAAGTTTCAATCCCTAGAAAGCT 60.222 40.000 0.00 0.00 34.69 3.74
2361 2448 5.010282 TGGAAGTTTCAATCCCTAGAAAGC 58.990 41.667 0.00 0.00 34.69 3.51
2362 2449 6.717084 AGTTGGAAGTTTCAATCCCTAGAAAG 59.283 38.462 0.00 0.00 34.69 2.62
2363 2450 6.610830 AGTTGGAAGTTTCAATCCCTAGAAA 58.389 36.000 0.00 0.00 34.68 2.52
2364 2451 6.200878 AGTTGGAAGTTTCAATCCCTAGAA 57.799 37.500 0.00 0.00 34.68 2.10
2365 2452 5.280521 GGAGTTGGAAGTTTCAATCCCTAGA 60.281 44.000 0.00 0.00 34.68 2.43
2366 2453 4.944317 GGAGTTGGAAGTTTCAATCCCTAG 59.056 45.833 0.00 0.00 34.68 3.02
2367 2454 4.352595 TGGAGTTGGAAGTTTCAATCCCTA 59.647 41.667 16.52 3.68 34.68 3.53
2368 2455 3.140144 TGGAGTTGGAAGTTTCAATCCCT 59.860 43.478 16.52 4.66 34.68 4.20
2369 2456 3.496331 TGGAGTTGGAAGTTTCAATCCC 58.504 45.455 16.52 13.26 34.68 3.85
2370 2457 4.145052 ACTGGAGTTGGAAGTTTCAATCC 58.855 43.478 14.07 14.07 36.21 3.01
2371 2458 5.774498 AACTGGAGTTGGAAGTTTCAATC 57.226 39.130 0.00 0.00 36.80 2.67
2372 2459 6.381133 AGAAAACTGGAGTTGGAAGTTTCAAT 59.619 34.615 0.00 0.00 41.93 2.57
2373 2460 5.714806 AGAAAACTGGAGTTGGAAGTTTCAA 59.285 36.000 0.00 0.00 41.93 2.69
2374 2461 5.261216 AGAAAACTGGAGTTGGAAGTTTCA 58.739 37.500 0.92 0.00 41.93 2.69
2375 2462 5.836821 AGAAAACTGGAGTTGGAAGTTTC 57.163 39.130 0.92 0.00 41.93 2.78
2376 2463 5.714806 TGAAGAAAACTGGAGTTGGAAGTTT 59.285 36.000 0.00 0.00 44.01 2.66
2377 2464 5.261216 TGAAGAAAACTGGAGTTGGAAGTT 58.739 37.500 0.00 0.00 38.44 2.66
2378 2465 4.855340 TGAAGAAAACTGGAGTTGGAAGT 58.145 39.130 0.00 0.00 38.44 3.01
2379 2466 5.835113 TTGAAGAAAACTGGAGTTGGAAG 57.165 39.130 0.00 0.00 38.44 3.46
2380 2467 6.379703 TCATTTGAAGAAAACTGGAGTTGGAA 59.620 34.615 0.00 0.00 38.44 3.53
2381 2468 5.890985 TCATTTGAAGAAAACTGGAGTTGGA 59.109 36.000 0.00 0.00 38.44 3.53
2382 2469 6.147864 TCATTTGAAGAAAACTGGAGTTGG 57.852 37.500 0.00 0.00 38.44 3.77
2383 2470 8.652810 AAATCATTTGAAGAAAACTGGAGTTG 57.347 30.769 0.00 0.00 38.44 3.16
2384 2471 8.477256 TGAAATCATTTGAAGAAAACTGGAGTT 58.523 29.630 0.00 0.00 40.50 3.01
2385 2472 8.010733 TGAAATCATTTGAAGAAAACTGGAGT 57.989 30.769 0.00 0.00 0.00 3.85
2386 2473 9.136952 GATGAAATCATTTGAAGAAAACTGGAG 57.863 33.333 0.00 0.00 44.70 3.86


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

AutoCloner maintained by Alex Coulton.