Multiple sequence alignment - TraesCS6A01G022700

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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 TraesCS6A01G022700 chr6A 100.000 2818 0 0 1 2818 11281861 11279044 0.000000e+00 5204
1 TraesCS6A01G022700 chr6A 79.500 1361 249 25 669 2010 9519609 9520958 0.000000e+00 941
2 TraesCS6A01G022700 chr6A 77.945 1061 189 28 659 1691 9946680 9947723 3.080000e-174 621
3 TraesCS6A01G022700 chr6A 77.389 1057 202 21 659 1691 9855971 9857014 6.720000e-166 593
4 TraesCS6A01G022700 chr6A 80.269 446 69 14 22 452 1512540 1512981 4.530000e-83 318
5 TraesCS6A01G022700 chr6B 92.976 2349 129 20 1 2341 17204534 17206854 0.000000e+00 3391
6 TraesCS6A01G022700 chr6B 92.073 492 28 5 2335 2818 17217120 17217608 0.000000e+00 682
7 TraesCS6A01G022700 chr6B 78.544 1044 189 22 659 1678 16995927 16996959 0.000000e+00 654
8 TraesCS6A01G022700 chr6B 91.057 492 32 6 2335 2818 17220797 17221284 0.000000e+00 654
9 TraesCS6A01G022700 chr6B 90.710 366 32 2 2454 2818 445867407 445867043 1.170000e-133 486
10 TraesCS6A01G022700 chr6B 76.446 951 176 28 657 1586 16628284 16629207 3.290000e-129 472
11 TraesCS6A01G022700 chr6B 76.571 939 173 27 657 1575 16683462 16684373 3.290000e-129 472
12 TraesCS6A01G022700 chr6D 92.898 2267 140 11 567 2818 9215751 9218011 0.000000e+00 3275
13 TraesCS6A01G022700 chr6D 76.890 939 173 25 657 1575 9114149 9115063 2.520000e-135 492
14 TraesCS6A01G022700 chr6D 79.271 439 71 16 29 452 315671371 315671804 3.550000e-74 289
15 TraesCS6A01G022700 chr6D 79.271 439 71 16 29 452 315678806 315679239 3.550000e-74 289
16 TraesCS6A01G022700 chr7B 91.914 371 24 4 2449 2818 409729896 409729531 5.380000e-142 514
17 TraesCS6A01G022700 chr5D 91.257 366 29 3 2453 2816 527384327 527384691 1.950000e-136 496
18 TraesCS6A01G022700 chr5A 90.761 368 29 5 2453 2818 172307975 172308339 1.170000e-133 486
19 TraesCS6A01G022700 chr2B 90.736 367 29 4 2453 2818 389479304 389478942 4.220000e-133 484
20 TraesCS6A01G022700 chr2B 79.022 491 75 18 5 470 667080802 667081289 7.580000e-81 311
21 TraesCS6A01G022700 chr7D 90.515 369 28 7 2453 2818 230371332 230370968 5.460000e-132 481
22 TraesCS6A01G022700 chr7D 81.070 486 64 14 5 466 585654211 585653730 2.060000e-96 363
23 TraesCS6A01G022700 chr7D 78.497 479 87 12 1 466 504261094 504260619 1.640000e-77 300
24 TraesCS6A01G022700 chr7D 76.520 477 75 23 1 446 282880775 282880305 2.820000e-55 226
25 TraesCS6A01G022700 chr2A 79.175 485 72 16 1 458 117728098 117728580 2.730000e-80 309
26 TraesCS6A01G022700 chr4A 79.398 432 71 14 36 452 395288881 395288453 3.550000e-74 289
27 TraesCS6A01G022700 chr3A 79.118 431 73 13 36 452 641625178 641625605 5.940000e-72 281
28 TraesCS6A01G022700 chr3A 76.734 447 84 17 22 452 567319233 567318791 6.070000e-57 231
29 TraesCS6A01G022700 chr4D 78.251 446 77 16 22 452 101551154 101550714 4.630000e-68 268
30 TraesCS6A01G022700 chr7A 77.101 476 89 17 6 466 572067617 572067147 1.000000e-64 257
31 TraesCS6A01G022700 chr2D 77.629 447 79 18 22 452 412809565 412810006 4.660000e-63 252
32 TraesCS6A01G022700 chr3D 77.405 447 80 19 22 452 158777423 158776982 2.170000e-61 246
33 TraesCS6A01G022700 chr3D 76.734 447 83 18 22 452 517022584 517023025 2.180000e-56 230


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 TraesCS6A01G022700 chr6A 11279044 11281861 2817 True 5204 5204 100.000 1 2818 1 chr6A.!!$R1 2817
1 TraesCS6A01G022700 chr6A 9519609 9520958 1349 False 941 941 79.500 669 2010 1 chr6A.!!$F2 1341
2 TraesCS6A01G022700 chr6A 9946680 9947723 1043 False 621 621 77.945 659 1691 1 chr6A.!!$F4 1032
3 TraesCS6A01G022700 chr6A 9855971 9857014 1043 False 593 593 77.389 659 1691 1 chr6A.!!$F3 1032
4 TraesCS6A01G022700 chr6B 17204534 17206854 2320 False 3391 3391 92.976 1 2341 1 chr6B.!!$F4 2340
5 TraesCS6A01G022700 chr6B 17217120 17221284 4164 False 668 682 91.565 2335 2818 2 chr6B.!!$F5 483
6 TraesCS6A01G022700 chr6B 16995927 16996959 1032 False 654 654 78.544 659 1678 1 chr6B.!!$F3 1019
7 TraesCS6A01G022700 chr6B 16628284 16629207 923 False 472 472 76.446 657 1586 1 chr6B.!!$F1 929
8 TraesCS6A01G022700 chr6B 16683462 16684373 911 False 472 472 76.571 657 1575 1 chr6B.!!$F2 918
9 TraesCS6A01G022700 chr6D 9215751 9218011 2260 False 3275 3275 92.898 567 2818 1 chr6D.!!$F2 2251
10 TraesCS6A01G022700 chr6D 9114149 9115063 914 False 492 492 76.890 657 1575 1 chr6D.!!$F1 918

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
568 571 0.109723 TAAGTTCCGGGCTGCAGTTT 59.890 50.0 16.64 0.65 0.00 2.66 F
1364 1388 0.041833 AGCAGGTCCAGAAGGCTAGA 59.958 55.0 0.00 0.00 32.09 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 1724 0.532573 GGCCACGAGAGAAGACATCA 59.467 55.0 0.0 0.0 0.00 3.07 R
2751 2799 1.459450 TGCTTTAGGGACAATTCCGC 58.541 50.0 0.0 0.0 43.94 5.54 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
46 47 6.309737 CACCCTATTACAGTTGACGTTAGAAC 59.690 42.308 0.00 0.00 0.00 3.01
62 63 3.733443 AGAACAACCCAAAAGTGCATC 57.267 42.857 0.00 0.00 0.00 3.91
109 110 7.921041 ACTCTCATGGTCTAAGGAATTATGA 57.079 36.000 0.00 0.00 0.00 2.15
144 145 9.656323 ACTTCCCATGTTATGACTATAGACTTA 57.344 33.333 6.78 0.18 0.00 2.24
180 181 7.074653 TCTCCTAGTACAAAATCCAACTTGT 57.925 36.000 0.00 0.00 39.13 3.16
223 224 4.832823 TCTTCTATCATCGTGCCCTCAATA 59.167 41.667 0.00 0.00 0.00 1.90
228 229 2.158769 TCATCGTGCCCTCAATATTGCT 60.159 45.455 10.76 0.00 0.00 3.91
233 234 0.386838 GCCCTCAATATTGCTGGCAC 59.613 55.000 28.73 16.61 41.34 5.01
241 242 1.286501 TATTGCTGGCACGATCGTTC 58.713 50.000 20.14 14.55 0.00 3.95
242 243 0.673333 ATTGCTGGCACGATCGTTCA 60.673 50.000 20.14 18.12 0.00 3.18
243 244 1.291184 TTGCTGGCACGATCGTTCAG 61.291 55.000 29.43 29.43 33.12 3.02
244 245 2.456119 GCTGGCACGATCGTTCAGG 61.456 63.158 31.93 19.65 31.68 3.86
245 246 1.215382 CTGGCACGATCGTTCAGGA 59.785 57.895 27.58 10.47 0.00 3.86
246 247 0.389817 CTGGCACGATCGTTCAGGAA 60.390 55.000 27.58 9.81 0.00 3.36
249 250 1.737793 GGCACGATCGTTCAGGAAAAT 59.262 47.619 20.14 0.00 0.00 1.82
250 251 2.933906 GGCACGATCGTTCAGGAAAATA 59.066 45.455 20.14 0.00 0.00 1.40
251 252 3.001330 GGCACGATCGTTCAGGAAAATAG 59.999 47.826 20.14 3.61 0.00 1.73
253 254 4.328983 GCACGATCGTTCAGGAAAATAGAA 59.671 41.667 20.14 0.00 0.00 2.10
254 255 5.724223 GCACGATCGTTCAGGAAAATAGAAC 60.724 44.000 20.14 0.00 38.54 3.01
256 257 4.868171 CGATCGTTCAGGAAAATAGAACCA 59.132 41.667 7.03 0.00 38.67 3.67
259 260 5.800296 TCGTTCAGGAAAATAGAACCATCA 58.200 37.500 0.00 0.00 38.67 3.07
260 261 6.414732 TCGTTCAGGAAAATAGAACCATCAT 58.585 36.000 0.00 0.00 38.67 2.45
261 262 6.316140 TCGTTCAGGAAAATAGAACCATCATG 59.684 38.462 0.00 0.00 38.67 3.07
262 263 6.268566 GTTCAGGAAAATAGAACCATCATGC 58.731 40.000 0.00 0.00 36.52 4.06
263 264 5.508567 TCAGGAAAATAGAACCATCATGCA 58.491 37.500 0.00 0.00 0.00 3.96
264 265 5.951148 TCAGGAAAATAGAACCATCATGCAA 59.049 36.000 0.00 0.00 0.00 4.08
265 266 6.038356 CAGGAAAATAGAACCATCATGCAAC 58.962 40.000 0.00 0.00 0.00 4.17
266 267 5.716228 AGGAAAATAGAACCATCATGCAACA 59.284 36.000 0.00 0.00 0.00 3.33
267 268 5.807011 GGAAAATAGAACCATCATGCAACAC 59.193 40.000 0.00 0.00 0.00 3.32
268 269 6.350445 GGAAAATAGAACCATCATGCAACACT 60.350 38.462 0.00 0.00 0.00 3.55
269 270 6.594788 AAATAGAACCATCATGCAACACTT 57.405 33.333 0.00 0.00 0.00 3.16
270 271 3.928727 AGAACCATCATGCAACACTTG 57.071 42.857 0.00 0.00 0.00 3.16
271 272 3.489355 AGAACCATCATGCAACACTTGA 58.511 40.909 0.00 0.00 36.91 3.02
272 273 3.504906 AGAACCATCATGCAACACTTGAG 59.495 43.478 0.00 0.00 36.04 3.02
273 274 1.542915 ACCATCATGCAACACTTGAGC 59.457 47.619 0.00 0.00 36.04 4.26
274 275 1.816835 CCATCATGCAACACTTGAGCT 59.183 47.619 0.00 0.00 36.04 4.09
275 276 3.011818 CCATCATGCAACACTTGAGCTA 58.988 45.455 0.00 0.00 36.04 3.32
276 277 3.064958 CCATCATGCAACACTTGAGCTAG 59.935 47.826 0.00 0.00 36.04 3.42
277 278 3.407424 TCATGCAACACTTGAGCTAGT 57.593 42.857 0.00 0.00 0.00 2.57
278 279 3.329386 TCATGCAACACTTGAGCTAGTC 58.671 45.455 0.00 0.00 0.00 2.59
279 280 2.169832 TGCAACACTTGAGCTAGTCC 57.830 50.000 0.00 0.00 0.00 3.85
354 357 6.875972 ATGAGTTTTCCTCTTAGCCTCTTA 57.124 37.500 0.00 0.00 41.11 2.10
360 363 8.827758 AGTTTTCCTCTTAGCCTCTTAGTTATT 58.172 33.333 0.00 0.00 0.00 1.40
392 395 5.630661 AGAGCCATAGTAGTTATAGCACG 57.369 43.478 0.00 0.00 29.90 5.34
491 494 7.529158 TCATTATCAAGGCAAATACATATGCG 58.471 34.615 1.58 0.00 43.47 4.73
496 499 5.994668 TCAAGGCAAATACATATGCGATACA 59.005 36.000 1.58 0.00 43.47 2.29
528 531 2.045561 TGCAGACGGTCAAGGAAAAA 57.954 45.000 11.27 0.00 0.00 1.94
530 533 2.293122 TGCAGACGGTCAAGGAAAAATG 59.707 45.455 11.27 0.00 0.00 2.32
560 563 2.398252 AGTTAGCTTAAGTTCCGGGC 57.602 50.000 0.00 0.00 0.00 6.13
568 571 0.109723 TAAGTTCCGGGCTGCAGTTT 59.890 50.000 16.64 0.65 0.00 2.66
585 588 1.106351 TTTGTCTGTGCGCCAATGGT 61.106 50.000 4.18 0.00 0.00 3.55
609 612 4.440802 GCAACAGGTCATCTAGTAGGAGTG 60.441 50.000 0.00 0.00 0.00 3.51
612 615 6.517013 ACAGGTCATCTAGTAGGAGTGATA 57.483 41.667 0.00 0.00 0.00 2.15
776 795 9.817809 CTAGTAAAGATGCATGTAGAAACCTTA 57.182 33.333 2.46 0.00 0.00 2.69
976 998 5.730296 AGATCCTCCACTATAAATCCACG 57.270 43.478 0.00 0.00 0.00 4.94
985 1007 5.297547 CACTATAAATCCACGCCACATACT 58.702 41.667 0.00 0.00 0.00 2.12
1145 1169 2.906691 AGATCCTGATGAAGAAGGCG 57.093 50.000 0.00 0.00 33.25 5.52
1279 1303 1.135460 GTTCAAGAGCATGCAAGAGGC 60.135 52.381 21.98 1.57 45.13 4.70
1364 1388 0.041833 AGCAGGTCCAGAAGGCTAGA 59.958 55.000 0.00 0.00 32.09 2.43
1371 1395 1.064946 CAGAAGGCTAGACGCGAGG 59.935 63.158 15.93 0.00 40.44 4.63
1475 1499 1.985116 GGGCTCGAAGGTGGACTCT 60.985 63.158 0.00 0.00 0.00 3.24
1591 1615 3.335748 TGGGGCCTCCAATTATGTATCT 58.664 45.455 10.25 0.00 43.84 1.98
1629 1653 4.228824 ACAGGAGGGTTGTCTTAACACTA 58.771 43.478 0.00 0.00 33.33 2.74
1700 1724 1.094785 GTGGCTATGACGGCAACAAT 58.905 50.000 0.00 0.00 41.38 2.71
1718 1742 2.593346 ATGATGTCTTCTCTCGTGGC 57.407 50.000 0.00 0.00 0.00 5.01
2065 2094 2.801063 CATCAAACGATCCAACCATGC 58.199 47.619 0.00 0.00 0.00 4.06
2066 2095 1.902938 TCAAACGATCCAACCATGCA 58.097 45.000 0.00 0.00 0.00 3.96
2067 2096 2.445427 TCAAACGATCCAACCATGCAT 58.555 42.857 0.00 0.00 0.00 3.96
2068 2097 2.164017 TCAAACGATCCAACCATGCATG 59.836 45.455 20.19 20.19 0.00 4.06
2128 2157 7.077605 CACATCGCCTATACAAAACCATAATG 58.922 38.462 0.00 0.00 0.00 1.90
2171 2200 8.071368 AGCACATTAATTGTTTGATGCAAAAAG 58.929 29.630 0.00 0.00 36.00 2.27
2246 2282 0.829990 TGACATTGAGCGCCAGGATA 59.170 50.000 2.29 0.00 0.00 2.59
2247 2283 1.209261 TGACATTGAGCGCCAGGATAA 59.791 47.619 2.29 0.00 0.00 1.75
2248 2284 2.158769 TGACATTGAGCGCCAGGATAAT 60.159 45.455 2.29 0.00 0.00 1.28
2249 2285 2.224606 ACATTGAGCGCCAGGATAATG 58.775 47.619 2.29 8.84 0.00 1.90
2250 2286 1.538512 CATTGAGCGCCAGGATAATGG 59.461 52.381 2.29 0.00 43.72 3.16
2303 2340 3.625853 TCAAAACCAGGTGATTGTGTCA 58.374 40.909 14.96 0.00 0.00 3.58
2323 2360 5.106594 TGTCAACCAGTTTCATCATCAATCG 60.107 40.000 0.00 0.00 0.00 3.34
2328 2365 4.194640 CAGTTTCATCATCAATCGGGTCT 58.805 43.478 0.00 0.00 0.00 3.85
2360 2397 3.087031 CTGAGAGGGCATTGTGTTTGAT 58.913 45.455 0.00 0.00 0.00 2.57
2388 2428 2.693591 TCAAGCTACTATGAGAACCCCG 59.306 50.000 0.00 0.00 0.00 5.73
2413 2453 2.170397 TCTATCGGGTGCATGTTGTGAT 59.830 45.455 0.00 0.00 0.00 3.06
2423 2463 4.093408 GTGCATGTTGTGATAGAACATCGT 59.907 41.667 1.85 0.00 41.16 3.73
2516 2563 7.333423 TCGATAAATAAGAGTGTCAAACCCAAG 59.667 37.037 0.00 0.00 0.00 3.61
2524 2571 0.609406 GTCAAACCCAAGGAGGAGCC 60.609 60.000 0.00 0.00 41.22 4.70
2531 2578 0.991920 CCAAGGAGGAGCCAAAGGTA 59.008 55.000 0.00 0.00 41.22 3.08
2547 2594 7.945109 AGCCAAAGGTAGAATTTATATTCCCTC 59.055 37.037 2.66 0.00 40.91 4.30
2589 2636 6.864685 CCGATACAACTCTACACACACTTAAA 59.135 38.462 0.00 0.00 0.00 1.52
2601 2648 7.743520 ACACACACTTAAAATTTGGTTTACG 57.256 32.000 0.00 0.00 0.00 3.18
2613 2660 9.857957 AAAATTTGGTTTACGTAGAACAAGAAA 57.142 25.926 15.25 3.36 0.00 2.52
2652 2700 8.883302 ACTTTGTAGTGTAAAGGGATAGGTTTA 58.117 33.333 0.00 0.00 38.99 2.01
2751 2799 4.022329 GTGGAAAAGTGGTGGTAGGATTTG 60.022 45.833 0.00 0.00 0.00 2.32
2767 2815 3.445805 GGATTTGCGGAATTGTCCCTAAA 59.554 43.478 0.00 0.00 41.44 1.85
2768 2816 4.440112 GGATTTGCGGAATTGTCCCTAAAG 60.440 45.833 0.00 0.00 41.44 1.85
2769 2817 1.459450 TGCGGAATTGTCCCTAAAGC 58.541 50.000 0.00 0.00 41.44 3.51
2771 2819 1.816224 GCGGAATTGTCCCTAAAGCAA 59.184 47.619 0.00 0.00 41.44 3.91
2773 2821 3.119137 GCGGAATTGTCCCTAAAGCAATT 60.119 43.478 0.00 0.00 43.06 2.32
2775 2823 4.183865 GGAATTGTCCCTAAAGCAATTGC 58.816 43.478 23.05 23.05 41.24 3.56
2790 2838 6.301169 AGCAATTGCCTAAGTTACTAGACT 57.699 37.500 26.45 0.00 43.38 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.920946 AATAGGGTGATCATAACAACAACTTAT 57.079 29.630 0.00 0.00 0.00 1.73
11 12 8.544622 TCAACTGTAATAGGGTGATCATAACAA 58.455 33.333 0.00 0.00 0.00 2.83
27 28 5.467735 GGGTTGTTCTAACGTCAACTGTAAT 59.532 40.000 14.41 0.00 40.52 1.89
46 47 1.335872 GGTCGATGCACTTTTGGGTTG 60.336 52.381 0.00 0.00 0.00 3.77
62 63 2.092323 TGAGTCACTCCATACTGGTCG 58.908 52.381 1.24 0.00 39.03 4.79
109 110 9.920946 AGTCATAACATGGGAAGTTAATGTATT 57.079 29.630 0.00 0.00 35.33 1.89
180 181 5.895636 AGAACACTTGTGTTGAATTGACA 57.104 34.783 21.74 0.00 31.35 3.58
207 208 2.158769 AGCAATATTGAGGGCACGATGA 60.159 45.455 19.73 0.00 0.00 2.92
211 212 0.664761 CCAGCAATATTGAGGGCACG 59.335 55.000 19.73 0.00 0.00 5.34
223 224 0.673333 TGAACGATCGTGCCAGCAAT 60.673 50.000 23.51 2.45 0.00 3.56
228 229 0.034198 TTTCCTGAACGATCGTGCCA 59.966 50.000 23.51 20.46 0.00 4.92
233 234 4.868171 TGGTTCTATTTTCCTGAACGATCG 59.132 41.667 14.88 14.88 40.44 3.69
241 242 5.840243 TGCATGATGGTTCTATTTTCCTG 57.160 39.130 0.00 0.00 0.00 3.86
242 243 5.716228 TGTTGCATGATGGTTCTATTTTCCT 59.284 36.000 0.00 0.00 0.00 3.36
243 244 5.807011 GTGTTGCATGATGGTTCTATTTTCC 59.193 40.000 0.00 0.00 0.00 3.13
244 245 6.624423 AGTGTTGCATGATGGTTCTATTTTC 58.376 36.000 0.00 0.00 0.00 2.29
245 246 6.594788 AGTGTTGCATGATGGTTCTATTTT 57.405 33.333 0.00 0.00 0.00 1.82
246 247 6.209192 TCAAGTGTTGCATGATGGTTCTATTT 59.791 34.615 0.00 0.00 0.00 1.40
249 250 4.650734 TCAAGTGTTGCATGATGGTTCTA 58.349 39.130 0.00 0.00 0.00 2.10
250 251 3.489355 TCAAGTGTTGCATGATGGTTCT 58.511 40.909 0.00 0.00 0.00 3.01
251 252 3.829948 CTCAAGTGTTGCATGATGGTTC 58.170 45.455 0.00 0.00 0.00 3.62
253 254 1.542915 GCTCAAGTGTTGCATGATGGT 59.457 47.619 0.00 0.00 0.00 3.55
254 255 1.816835 AGCTCAAGTGTTGCATGATGG 59.183 47.619 0.00 0.00 0.00 3.51
256 257 3.937706 GACTAGCTCAAGTGTTGCATGAT 59.062 43.478 0.00 0.00 0.00 2.45
259 260 2.304180 AGGACTAGCTCAAGTGTTGCAT 59.696 45.455 0.00 0.00 0.00 3.96
260 261 1.694150 AGGACTAGCTCAAGTGTTGCA 59.306 47.619 0.00 0.00 0.00 4.08
261 262 2.464157 AGGACTAGCTCAAGTGTTGC 57.536 50.000 0.00 0.00 0.00 4.17
262 263 4.142271 CCTCTAGGACTAGCTCAAGTGTTG 60.142 50.000 0.00 0.00 37.39 3.33
263 264 4.020543 CCTCTAGGACTAGCTCAAGTGTT 58.979 47.826 0.00 0.00 37.39 3.32
264 265 3.626930 CCTCTAGGACTAGCTCAAGTGT 58.373 50.000 0.00 0.00 37.39 3.55
265 266 2.360801 GCCTCTAGGACTAGCTCAAGTG 59.639 54.545 0.00 0.00 37.39 3.16
266 267 2.024846 TGCCTCTAGGACTAGCTCAAGT 60.025 50.000 0.00 0.00 37.39 3.16
267 268 2.660572 TGCCTCTAGGACTAGCTCAAG 58.339 52.381 0.00 0.00 37.39 3.02
268 269 2.828661 TGCCTCTAGGACTAGCTCAA 57.171 50.000 0.00 0.00 37.39 3.02
269 270 2.242452 TCTTGCCTCTAGGACTAGCTCA 59.758 50.000 0.00 0.00 37.39 4.26
270 271 2.621526 GTCTTGCCTCTAGGACTAGCTC 59.378 54.545 0.00 0.00 37.39 4.09
271 272 2.024846 TGTCTTGCCTCTAGGACTAGCT 60.025 50.000 0.00 0.00 37.39 3.32
272 273 2.379972 TGTCTTGCCTCTAGGACTAGC 58.620 52.381 0.00 0.00 37.39 3.42
273 274 3.383185 CCTTGTCTTGCCTCTAGGACTAG 59.617 52.174 0.00 0.00 37.39 2.57
274 275 3.011369 TCCTTGTCTTGCCTCTAGGACTA 59.989 47.826 0.00 0.00 37.39 2.59
275 276 2.183679 CCTTGTCTTGCCTCTAGGACT 58.816 52.381 0.00 0.00 37.39 3.85
276 277 2.180276 TCCTTGTCTTGCCTCTAGGAC 58.820 52.381 0.00 0.00 37.39 3.85
277 278 2.623418 TCCTTGTCTTGCCTCTAGGA 57.377 50.000 0.00 0.00 37.39 2.94
278 279 3.454082 AGATTCCTTGTCTTGCCTCTAGG 59.546 47.826 0.00 0.00 38.53 3.02
279 280 4.751767 AGATTCCTTGTCTTGCCTCTAG 57.248 45.455 0.00 0.00 0.00 2.43
354 357 4.270834 TGGCTCTCGAGTCTACAATAACT 58.729 43.478 13.13 0.00 33.37 2.24
360 363 3.562343 ACTATGGCTCTCGAGTCTACA 57.438 47.619 13.13 8.19 33.37 2.74
392 395 8.687301 CAAGTTTATGACAAATGTTTACGTTCC 58.313 33.333 0.00 0.00 0.00 3.62
453 456 8.039538 TGCCTTGATAATGATGTTGCAAAAATA 58.960 29.630 0.00 0.00 0.00 1.40
487 490 7.201835 TGCAAATGATTATGTTTGTATCGCAT 58.798 30.769 0.00 0.00 37.57 4.73
491 494 7.376866 CCGTCTGCAAATGATTATGTTTGTATC 59.623 37.037 0.00 0.00 37.57 2.24
496 499 5.182950 TGACCGTCTGCAAATGATTATGTTT 59.817 36.000 0.00 0.00 0.00 2.83
528 531 9.740710 AACTTAAGCTAACTATTTGAAGGACAT 57.259 29.630 1.29 0.00 0.00 3.06
530 533 8.666573 GGAACTTAAGCTAACTATTTGAAGGAC 58.333 37.037 1.29 0.00 0.00 3.85
568 571 2.112928 ACCATTGGCGCACAGACA 59.887 55.556 10.83 0.00 34.88 3.41
585 588 3.701542 CTCCTACTAGATGACCTGTTGCA 59.298 47.826 0.00 0.00 0.00 4.08
637 640 4.456535 TCGAGTGTCCATTCCTTTTTGAA 58.543 39.130 0.00 0.00 0.00 2.69
753 763 8.263940 TGTAAGGTTTCTACATGCATCTTTAC 57.736 34.615 0.00 1.98 0.00 2.01
776 795 8.637196 TGTAGATCGAAGGAGAACATATATGT 57.363 34.615 12.75 12.75 44.20 2.29
935 956 2.038689 TCTACGAGGATGAGGACGCTAT 59.961 50.000 0.00 0.00 0.00 2.97
1234 1258 2.280457 GGATAGCCACTGCCTCGC 60.280 66.667 0.00 0.00 38.69 5.03
1279 1303 1.683790 CGTCTTCTTTAGCCGTGCCG 61.684 60.000 0.00 0.00 0.00 5.69
1371 1395 2.433318 GGTGTGCTCGTCCTGCTC 60.433 66.667 0.00 0.00 0.00 4.26
1380 1404 2.354259 CAGGAGAATCTTGGTGTGCTC 58.646 52.381 0.00 0.00 38.73 4.26
1424 1448 2.169352 CTCCTCGATGTTGTCTGGGAAT 59.831 50.000 0.00 0.00 0.00 3.01
1591 1615 2.832661 GTTGCTGTGGTGGTGCCA 60.833 61.111 0.00 0.00 46.95 4.92
1629 1653 1.303282 GGGCCCTTTCGAACCTCAT 59.697 57.895 17.04 0.00 0.00 2.90
1700 1724 0.532573 GGCCACGAGAGAAGACATCA 59.467 55.000 0.00 0.00 0.00 3.07
1718 1742 6.524734 TCTACCAGCTTACATATTCATGTGG 58.475 40.000 0.58 0.00 45.17 4.17
1907 1934 6.451340 AGAGCATGGGGGATATCCATAATAAA 59.549 38.462 23.27 1.94 42.63 1.40
1923 1950 7.338800 ACTGATAAAACAAATAGAGCATGGG 57.661 36.000 0.00 0.00 0.00 4.00
2065 2094 1.556911 ACTGGGAGGTAGCACTTCATG 59.443 52.381 0.00 0.00 0.00 3.07
2066 2095 1.958288 ACTGGGAGGTAGCACTTCAT 58.042 50.000 0.00 0.00 0.00 2.57
2067 2096 1.729586 AACTGGGAGGTAGCACTTCA 58.270 50.000 0.00 0.00 0.00 3.02
2068 2097 2.814336 CAAAACTGGGAGGTAGCACTTC 59.186 50.000 0.00 0.00 0.00 3.01
2142 2171 7.155655 TGCATCAAACAATTAATGTGCTCTA 57.844 32.000 0.00 0.00 42.99 2.43
2246 2282 8.773033 AAAATATTGAGGATGTAGAAGCCATT 57.227 30.769 0.00 0.00 0.00 3.16
2247 2283 8.773033 AAAAATATTGAGGATGTAGAAGCCAT 57.227 30.769 0.00 0.00 0.00 4.40
2288 2325 1.881973 CTGGTTGACACAATCACCTGG 59.118 52.381 0.00 0.00 36.92 4.45
2303 2340 3.696051 CCCGATTGATGATGAAACTGGTT 59.304 43.478 0.00 0.00 0.00 3.67
2360 2397 7.666388 GGGTTCTCATAGTAGCTTGAGTATAGA 59.334 40.741 11.87 0.00 40.22 1.98
2388 2428 2.604046 ACATGCACCCGATAGAGTTC 57.396 50.000 0.00 0.00 39.76 3.01
2413 2453 8.178313 AGTGGATTCATATGTACGATGTTCTA 57.822 34.615 1.90 2.96 0.00 2.10
2423 2463 2.301870 GCCCGGAGTGGATTCATATGTA 59.698 50.000 0.73 0.00 42.00 2.29
2516 2563 3.653835 AATTCTACCTTTGGCTCCTCC 57.346 47.619 0.00 0.00 0.00 4.30
2524 2571 9.640952 TTGGAGGGAATATAAATTCTACCTTTG 57.359 33.333 0.00 0.00 41.18 2.77
2589 2636 9.857957 TTTTTCTTGTTCTACGTAAACCAAATT 57.142 25.926 14.08 0.00 0.00 1.82
2751 2799 1.459450 TGCTTTAGGGACAATTCCGC 58.541 50.000 0.00 0.00 43.94 5.54
2767 2815 6.070767 TCAGTCTAGTAACTTAGGCAATTGCT 60.071 38.462 28.42 17.09 41.70 3.91
2768 2816 6.106673 TCAGTCTAGTAACTTAGGCAATTGC 58.893 40.000 22.47 22.47 41.14 3.56
2769 2817 9.469807 CTATCAGTCTAGTAACTTAGGCAATTG 57.530 37.037 0.00 0.00 0.00 2.32
2771 2819 7.287927 TGCTATCAGTCTAGTAACTTAGGCAAT 59.712 37.037 0.00 0.00 0.00 3.56
2773 2821 6.127101 TGCTATCAGTCTAGTAACTTAGGCA 58.873 40.000 0.00 0.00 0.00 4.75
2775 2823 8.228035 ACTTGCTATCAGTCTAGTAACTTAGG 57.772 38.462 0.00 0.00 0.00 2.69
2790 2838 6.480763 TCTCCCACATAAAAACTTGCTATCA 58.519 36.000 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.