Multiple sequence alignment - TraesCS2D01G165400

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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 TraesCS2D01G165400 chr2D 100.000 2447 0 0 1 2447 109726370 109723924 0.000000e+00 4519
1 TraesCS2D01G165400 chr2B 87.992 2057 117 69 453 2447 159256877 159254889 0.000000e+00 2311
2 TraesCS2D01G165400 chr2B 85.464 399 44 6 1 386 159257629 159257232 1.050000e-108 403
3 TraesCS2D01G165400 chr2A 84.809 2067 145 73 458 2446 105499440 105497465 0.000000e+00 1921
4 TraesCS2D01G165400 chr2A 86.006 343 34 6 1 329 105508603 105508261 2.990000e-94 355


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 TraesCS2D01G165400 chr2D 109723924 109726370 2446 True 4519 4519 100.000 1 2447 1 chr2D.!!$R1 2446
1 TraesCS2D01G165400 chr2B 159254889 159257629 2740 True 1357 2311 86.728 1 2447 2 chr2B.!!$R1 2446
2 TraesCS2D01G165400 chr2A 105497465 105499440 1975 True 1921 1921 84.809 458 2446 1 chr2A.!!$R1 1988

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
396 410 0.10412 TATTGACCAGATCGGCACCG 59.896 55.0 1.73 1.73 39.03 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 2521 0.109319 CCCGGGAGCAACAATTTTCG 60.109 55.0 18.48 0.0 0.0 3.46 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
25 26 4.473196 TGTCTTATAGTCTCAAATGGGCCA 59.527 41.667 9.61 9.61 0.00 5.36
28 29 7.147391 TGTCTTATAGTCTCAAATGGGCCAATA 60.147 37.037 11.89 0.00 0.00 1.90
34 35 0.817013 CAAATGGGCCAATAGCGTGT 59.183 50.000 11.89 0.00 45.17 4.49
62 63 0.391661 TGCCTCTTCGTCATTGGAGC 60.392 55.000 0.00 0.00 0.00 4.70
64 65 0.462759 CCTCTTCGTCATTGGAGCCC 60.463 60.000 0.00 0.00 0.00 5.19
82 83 1.955778 CCCGCCAATCATTGCTAATCA 59.044 47.619 0.00 0.00 0.00 2.57
94 95 7.933215 TCATTGCTAATCATGGATAAGATGG 57.067 36.000 0.00 0.00 0.00 3.51
103 104 4.521639 TCATGGATAAGATGGCATCAAAGC 59.478 41.667 27.93 17.52 0.00 3.51
117 118 3.342377 TCAAAGCCATGGTCATAACGA 57.658 42.857 14.67 0.00 0.00 3.85
119 120 3.438781 TCAAAGCCATGGTCATAACGAAC 59.561 43.478 14.67 0.00 0.00 3.95
122 123 2.092429 AGCCATGGTCATAACGAACCAT 60.092 45.455 14.67 1.22 43.09 3.55
141 142 1.933021 TCGCCCTAGAGAAGAAACCA 58.067 50.000 0.00 0.00 0.00 3.67
152 153 3.988517 GAGAAGAAACCATCGAAGACGTT 59.011 43.478 0.00 0.00 42.51 3.99
153 154 5.048224 AGAGAAGAAACCATCGAAGACGTTA 60.048 40.000 0.00 0.00 42.51 3.18
156 157 3.006110 AGAAACCATCGAAGACGTTACCA 59.994 43.478 0.00 0.00 42.51 3.25
160 161 1.135603 CATCGAAGACGTTACCACCGA 60.136 52.381 0.00 0.00 42.51 4.69
163 164 1.717645 CGAAGACGTTACCACCGAAAG 59.282 52.381 0.00 0.00 34.56 2.62
165 166 3.582780 GAAGACGTTACCACCGAAAGAT 58.417 45.455 0.00 0.00 0.00 2.40
186 187 2.171003 CCAAGATCCCAACCTCCAAAC 58.829 52.381 0.00 0.00 0.00 2.93
206 207 4.292784 GCTGACAAGCCTCACTCC 57.707 61.111 0.00 0.00 44.22 3.85
207 208 1.739562 GCTGACAAGCCTCACTCCG 60.740 63.158 0.00 0.00 44.22 4.63
236 250 0.324943 TCACACCTAGGAGGCAAAGC 59.675 55.000 17.98 0.00 39.63 3.51
269 283 1.703411 CCACCATGTTGACAAACCCT 58.297 50.000 0.00 0.00 35.25 4.34
271 285 2.031120 CACCATGTTGACAAACCCTGT 58.969 47.619 0.00 0.00 42.61 4.00
287 301 3.244318 ACCCTGTAAACCCTAACTCAACG 60.244 47.826 0.00 0.00 0.00 4.10
288 302 3.007182 CCCTGTAAACCCTAACTCAACGA 59.993 47.826 0.00 0.00 0.00 3.85
290 304 3.992427 CTGTAAACCCTAACTCAACGACC 59.008 47.826 0.00 0.00 0.00 4.79
291 305 3.387374 TGTAAACCCTAACTCAACGACCA 59.613 43.478 0.00 0.00 0.00 4.02
301 315 3.752665 ACTCAACGACCAGAGAGACTAA 58.247 45.455 0.00 0.00 35.83 2.24
332 346 1.331756 CGCCAATTGAGCCATCTACAC 59.668 52.381 7.12 0.00 0.00 2.90
337 351 0.172578 TTGAGCCATCTACACGACCG 59.827 55.000 0.00 0.00 0.00 4.79
347 361 3.698463 CACGACCGCAACCGACAC 61.698 66.667 0.00 0.00 36.29 3.67
386 400 8.103948 AGACTCAAGAAAACATTATTGACCAG 57.896 34.615 0.00 0.00 0.00 4.00
387 401 7.939039 AGACTCAAGAAAACATTATTGACCAGA 59.061 33.333 0.00 0.00 0.00 3.86
388 402 8.641498 ACTCAAGAAAACATTATTGACCAGAT 57.359 30.769 0.00 0.00 0.00 2.90
389 403 8.734386 ACTCAAGAAAACATTATTGACCAGATC 58.266 33.333 0.00 0.00 0.00 2.75
390 404 7.751732 TCAAGAAAACATTATTGACCAGATCG 58.248 34.615 0.00 0.00 0.00 3.69
391 405 6.683974 AGAAAACATTATTGACCAGATCGG 57.316 37.500 2.55 2.55 42.50 4.18
392 406 4.900635 AAACATTATTGACCAGATCGGC 57.099 40.909 3.85 0.00 39.03 5.54
393 407 3.558931 ACATTATTGACCAGATCGGCA 57.441 42.857 3.85 1.51 39.03 5.69
394 408 3.206150 ACATTATTGACCAGATCGGCAC 58.794 45.455 3.85 0.67 39.03 5.01
395 409 2.325583 TTATTGACCAGATCGGCACC 57.674 50.000 3.85 0.00 39.03 5.01
396 410 0.104120 TATTGACCAGATCGGCACCG 59.896 55.000 1.73 1.73 39.03 4.94
397 411 1.899437 ATTGACCAGATCGGCACCGT 61.899 55.000 9.23 0.00 39.03 4.83
398 412 2.202756 GACCAGATCGGCACCGTC 60.203 66.667 9.23 6.29 39.03 4.79
399 413 4.129737 ACCAGATCGGCACCGTCG 62.130 66.667 9.23 0.00 39.03 5.12
409 423 4.619227 CACCGTCGCCACCAACCT 62.619 66.667 0.00 0.00 0.00 3.50
410 424 2.918802 ACCGTCGCCACCAACCTA 60.919 61.111 0.00 0.00 0.00 3.08
411 425 2.433664 CCGTCGCCACCAACCTAC 60.434 66.667 0.00 0.00 0.00 3.18
412 426 2.654877 CGTCGCCACCAACCTACT 59.345 61.111 0.00 0.00 0.00 2.57
413 427 1.597797 CCGTCGCCACCAACCTACTA 61.598 60.000 0.00 0.00 0.00 1.82
414 428 0.244450 CGTCGCCACCAACCTACTAA 59.756 55.000 0.00 0.00 0.00 2.24
415 429 1.337074 CGTCGCCACCAACCTACTAAA 60.337 52.381 0.00 0.00 0.00 1.85
416 430 2.769893 GTCGCCACCAACCTACTAAAA 58.230 47.619 0.00 0.00 0.00 1.52
417 431 3.140623 GTCGCCACCAACCTACTAAAAA 58.859 45.455 0.00 0.00 0.00 1.94
418 432 3.058708 GTCGCCACCAACCTACTAAAAAC 60.059 47.826 0.00 0.00 0.00 2.43
419 433 3.143728 CGCCACCAACCTACTAAAAACT 58.856 45.455 0.00 0.00 0.00 2.66
420 434 3.187842 CGCCACCAACCTACTAAAAACTC 59.812 47.826 0.00 0.00 0.00 3.01
421 435 3.504906 GCCACCAACCTACTAAAAACTCC 59.495 47.826 0.00 0.00 0.00 3.85
422 436 4.721132 CCACCAACCTACTAAAAACTCCA 58.279 43.478 0.00 0.00 0.00 3.86
423 437 5.134661 CCACCAACCTACTAAAAACTCCAA 58.865 41.667 0.00 0.00 0.00 3.53
424 438 5.595133 CCACCAACCTACTAAAAACTCCAAA 59.405 40.000 0.00 0.00 0.00 3.28
425 439 6.238925 CCACCAACCTACTAAAAACTCCAAAG 60.239 42.308 0.00 0.00 0.00 2.77
426 440 5.301045 ACCAACCTACTAAAAACTCCAAAGC 59.699 40.000 0.00 0.00 0.00 3.51
427 441 5.449304 CAACCTACTAAAAACTCCAAAGCG 58.551 41.667 0.00 0.00 0.00 4.68
428 442 4.964593 ACCTACTAAAAACTCCAAAGCGA 58.035 39.130 0.00 0.00 0.00 4.93
429 443 5.370679 ACCTACTAAAAACTCCAAAGCGAA 58.629 37.500 0.00 0.00 0.00 4.70
430 444 5.469084 ACCTACTAAAAACTCCAAAGCGAAG 59.531 40.000 0.00 0.00 0.00 3.79
431 445 4.830826 ACTAAAAACTCCAAAGCGAAGG 57.169 40.909 0.00 0.00 0.00 3.46
432 446 3.568430 ACTAAAAACTCCAAAGCGAAGGG 59.432 43.478 0.00 0.00 0.00 3.95
433 447 2.358322 AAAACTCCAAAGCGAAGGGA 57.642 45.000 0.00 0.00 0.00 4.20
435 449 4.625800 CTCCAAAGCGAAGGGAGG 57.374 61.111 8.37 0.00 43.59 4.30
436 450 1.078143 CTCCAAAGCGAAGGGAGGG 60.078 63.158 8.37 0.00 43.59 4.30
437 451 2.044946 CCAAAGCGAAGGGAGGGG 60.045 66.667 0.00 0.00 0.00 4.79
438 452 2.044946 CAAAGCGAAGGGAGGGGG 60.045 66.667 0.00 0.00 0.00 5.40
439 453 2.204090 AAAGCGAAGGGAGGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
440 454 2.301738 AAAGCGAAGGGAGGGGGAG 61.302 63.158 0.00 0.00 0.00 4.30
441 455 2.765705 AAAGCGAAGGGAGGGGGAGA 62.766 60.000 0.00 0.00 0.00 3.71
442 456 2.687566 GCGAAGGGAGGGGGAGAA 60.688 66.667 0.00 0.00 0.00 2.87
443 457 3.032667 GCGAAGGGAGGGGGAGAAC 62.033 68.421 0.00 0.00 0.00 3.01
444 458 1.306226 CGAAGGGAGGGGGAGAACT 60.306 63.158 0.00 0.00 0.00 3.01
445 459 1.331399 CGAAGGGAGGGGGAGAACTC 61.331 65.000 0.00 0.00 0.00 3.01
490 792 3.753815 TGCACTCCATTCAAGTCAATGA 58.246 40.909 0.00 0.00 36.03 2.57
499 806 4.934797 TTCAAGTCAATGAAGGAGGGAT 57.065 40.909 0.00 0.00 34.50 3.85
555 865 2.094597 TGCCCAGAAAAATCTCAATGCG 60.095 45.455 0.00 0.00 0.00 4.73
633 943 7.411486 AAGGCAGTAGAGCGTATATATGAAT 57.589 36.000 6.12 0.00 34.64 2.57
702 1012 2.869897 TGAGCAACAAAAACAACGACC 58.130 42.857 0.00 0.00 0.00 4.79
766 1077 1.744320 AACGCAAAAGCCACCTTCCC 61.744 55.000 0.00 0.00 0.00 3.97
787 1099 0.951040 GATCCGATCCATTCCGGCAC 60.951 60.000 0.00 0.00 44.96 5.01
889 1201 3.905678 CCCCGATCGCTTCGCTCT 61.906 66.667 10.32 0.00 46.71 4.09
945 1257 2.584608 CACCAGCTTACCTCCGGG 59.415 66.667 0.00 0.00 38.88 5.73
949 1261 1.745489 CAGCTTACCTCCGGGTTGC 60.745 63.158 0.00 1.08 44.73 4.17
958 1270 4.278513 CCGGGTTGCCCAGTTCCA 62.279 66.667 4.96 0.00 45.83 3.53
959 1271 2.672996 CGGGTTGCCCAGTTCCAG 60.673 66.667 4.96 0.00 45.83 3.86
960 1272 2.520968 GGGTTGCCCAGTTCCAGT 59.479 61.111 0.00 0.00 44.65 4.00
961 1273 1.152546 GGGTTGCCCAGTTCCAGTT 60.153 57.895 0.00 0.00 44.65 3.16
962 1274 1.179174 GGGTTGCCCAGTTCCAGTTC 61.179 60.000 0.00 0.00 44.65 3.01
963 1275 1.179174 GGTTGCCCAGTTCCAGTTCC 61.179 60.000 0.00 0.00 0.00 3.62
964 1276 0.467290 GTTGCCCAGTTCCAGTTCCA 60.467 55.000 0.00 0.00 0.00 3.53
965 1277 0.178992 TTGCCCAGTTCCAGTTCCAG 60.179 55.000 0.00 0.00 0.00 3.86
966 1278 1.352622 TGCCCAGTTCCAGTTCCAGT 61.353 55.000 0.00 0.00 0.00 4.00
967 1279 0.178990 GCCCAGTTCCAGTTCCAGTT 60.179 55.000 0.00 0.00 0.00 3.16
968 1280 1.754201 GCCCAGTTCCAGTTCCAGTTT 60.754 52.381 0.00 0.00 0.00 2.66
969 1281 2.230660 CCCAGTTCCAGTTCCAGTTTC 58.769 52.381 0.00 0.00 0.00 2.78
970 1282 2.422803 CCCAGTTCCAGTTCCAGTTTCA 60.423 50.000 0.00 0.00 0.00 2.69
993 1305 1.581447 GCCAAGAGCAAGAAACCCG 59.419 57.895 0.00 0.00 42.97 5.28
1170 1482 2.971452 GTCGTGAGGGTGGAGGTC 59.029 66.667 0.00 0.00 0.00 3.85
1469 1786 9.771534 CTAGTTAAGCCTCTTCAAGCTATAAAT 57.228 33.333 0.00 0.00 38.74 1.40
1477 1794 7.041780 GCCTCTTCAAGCTATAAATTCGATTCA 60.042 37.037 0.00 0.00 0.00 2.57
1544 1864 2.358267 AGCATGTACTACTACTCCGTGC 59.642 50.000 0.00 0.00 0.00 5.34
1551 1871 4.897025 ACTACTACTCCGTGCAGTAATC 57.103 45.455 0.00 0.00 0.00 1.75
1561 1881 2.288457 CGTGCAGTAATCCGATCATCCT 60.288 50.000 0.00 0.00 0.00 3.24
1596 1929 3.976793 AATTAAGCTGCATGATCCACG 57.023 42.857 1.02 0.00 0.00 4.94
1605 1952 0.659427 CATGATCCACGCATGTGTCC 59.341 55.000 9.44 0.05 44.92 4.02
1662 2012 0.535102 AAGAGCGTGGAACCTGGTTG 60.535 55.000 18.42 3.36 0.00 3.77
1676 2029 7.608761 TGGAACCTGGTTGATTACTTTATGTAC 59.391 37.037 18.42 0.00 0.00 2.90
1752 2111 4.206375 ACAAACACATGATGGACACTTGA 58.794 39.130 0.00 0.00 0.00 3.02
1753 2112 4.828939 ACAAACACATGATGGACACTTGAT 59.171 37.500 0.00 0.00 0.00 2.57
1754 2113 5.158494 CAAACACATGATGGACACTTGATG 58.842 41.667 0.00 0.00 0.00 3.07
1791 2155 0.743701 ATTCTCTTGCGAGCCTGCTG 60.744 55.000 0.00 0.00 37.19 4.41
1859 2223 3.384927 GGATTTCCGAGCACGACG 58.615 61.111 4.70 0.00 42.66 5.12
1860 2224 1.153901 GGATTTCCGAGCACGACGA 60.154 57.895 4.70 0.00 42.66 4.20
1861 2225 1.411493 GGATTTCCGAGCACGACGAC 61.411 60.000 4.70 0.00 42.66 4.34
1864 2228 1.512996 TTTCCGAGCACGACGACTCT 61.513 55.000 4.70 4.96 42.66 3.24
1867 2231 1.797933 CGAGCACGACGACTCTTGG 60.798 63.158 16.55 2.83 42.66 3.61
1868 2232 1.286260 GAGCACGACGACTCTTGGT 59.714 57.895 0.00 0.00 0.00 3.67
1869 2233 1.004277 GAGCACGACGACTCTTGGTG 61.004 60.000 0.00 0.00 0.00 4.17
1909 2273 1.741770 CGTGGCAACTACCCTGAGC 60.742 63.158 0.00 0.00 37.61 4.26
1910 2274 1.741770 GTGGCAACTACCCTGAGCG 60.742 63.158 0.00 0.00 37.61 5.03
1922 2311 4.451150 TGAGCGGTCGTGGATGGC 62.451 66.667 10.46 0.00 0.00 4.40
1947 2336 5.473039 TCAGTGTCAATGATCAGTAGTGTG 58.527 41.667 0.09 0.00 0.00 3.82
1948 2337 4.628766 CAGTGTCAATGATCAGTAGTGTGG 59.371 45.833 0.09 0.00 0.00 4.17
1949 2338 3.372206 GTGTCAATGATCAGTAGTGTGGC 59.628 47.826 0.09 0.00 0.00 5.01
1950 2339 3.007831 TGTCAATGATCAGTAGTGTGGCA 59.992 43.478 0.09 0.00 0.00 4.92
1951 2340 3.620374 GTCAATGATCAGTAGTGTGGCAG 59.380 47.826 0.09 0.00 0.00 4.85
1952 2341 2.941064 CAATGATCAGTAGTGTGGCAGG 59.059 50.000 0.09 0.00 0.00 4.85
1987 2376 0.179037 ACATGGATGATGGGCAGACG 60.179 55.000 0.00 0.00 36.23 4.18
2029 2418 0.540365 ATCCCAAGTGCCAAGGTGTG 60.540 55.000 0.00 0.00 0.00 3.82
2035 2424 3.497115 TGCCAAGGTGTGCCTCCA 61.497 61.111 0.00 0.00 46.33 3.86
2122 2513 4.253257 GCGCTAGCTAGCCGACGT 62.253 66.667 34.27 0.00 46.34 4.34
2142 2533 1.736282 CGGGGGCGAAAATTGTTGC 60.736 57.895 0.00 0.00 0.00 4.17
2144 2535 0.389817 GGGGGCGAAAATTGTTGCTC 60.390 55.000 7.80 3.27 0.00 4.26
2145 2536 0.389817 GGGGCGAAAATTGTTGCTCC 60.390 55.000 11.26 11.26 41.49 4.70
2146 2537 0.389817 GGGCGAAAATTGTTGCTCCC 60.390 55.000 7.80 0.00 0.00 4.30
2147 2538 0.732538 GGCGAAAATTGTTGCTCCCG 60.733 55.000 7.80 0.00 0.00 5.14
2148 2539 0.732538 GCGAAAATTGTTGCTCCCGG 60.733 55.000 0.02 0.00 0.00 5.73
2150 2541 0.966179 GAAAATTGTTGCTCCCGGGT 59.034 50.000 22.86 0.00 0.00 5.28
2151 2542 0.966179 AAAATTGTTGCTCCCGGGTC 59.034 50.000 22.86 14.46 0.00 4.46
2153 2544 2.119484 AATTGTTGCTCCCGGGTCGA 62.119 55.000 22.86 10.91 0.00 4.20
2154 2545 1.910580 ATTGTTGCTCCCGGGTCGAT 61.911 55.000 22.86 9.44 0.00 3.59
2187 2578 3.922850 CGTATCTGTGATGGATTGGATCG 59.077 47.826 0.00 0.00 0.00 3.69
2189 2580 2.118679 TCTGTGATGGATTGGATCGGT 58.881 47.619 0.00 0.00 0.00 4.69
2232 2628 1.656652 ACAGAATGCAGGCGATGTAC 58.343 50.000 0.00 0.00 42.53 2.90
2233 2629 1.208052 ACAGAATGCAGGCGATGTACT 59.792 47.619 0.00 0.00 42.53 2.73
2234 2630 2.283298 CAGAATGCAGGCGATGTACTT 58.717 47.619 0.00 0.00 0.00 2.24
2235 2631 3.118775 ACAGAATGCAGGCGATGTACTTA 60.119 43.478 0.00 0.00 42.53 2.24
2236 2632 3.871006 CAGAATGCAGGCGATGTACTTAA 59.129 43.478 0.00 0.00 0.00 1.85
2237 2633 4.025396 CAGAATGCAGGCGATGTACTTAAG 60.025 45.833 0.00 0.00 0.00 1.85
2238 2634 2.309528 TGCAGGCGATGTACTTAAGG 57.690 50.000 7.53 0.00 0.00 2.69
2394 2806 2.709170 CGTCTCTACGGGATCAGCT 58.291 57.895 0.00 0.00 45.50 4.24
2443 2855 1.745115 GCACCTACCTTGCGATGCA 60.745 57.895 0.00 0.00 36.47 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.401925 GCTATTGGCCCATTTGAGACTAT 58.598 43.478 0.00 0.00 34.27 2.12
9 10 3.744214 CGCTATTGGCCCATTTGAGACTA 60.744 47.826 0.00 0.00 37.74 2.59
10 11 2.659428 GCTATTGGCCCATTTGAGACT 58.341 47.619 0.00 0.00 34.27 3.24
14 15 1.102154 CACGCTATTGGCCCATTTGA 58.898 50.000 0.00 0.00 37.74 2.69
38 39 0.034896 AATGACGAAGAGGCAACCGT 59.965 50.000 0.00 0.00 44.01 4.83
40 41 0.804989 CCAATGACGAAGAGGCAACC 59.195 55.000 0.00 0.00 44.01 3.77
52 53 2.361104 TTGGCGGGCTCCAATGAC 60.361 61.111 2.38 0.00 40.92 3.06
62 63 1.955778 TGATTAGCAATGATTGGCGGG 59.044 47.619 7.35 0.00 34.54 6.13
64 65 3.253921 TCCATGATTAGCAATGATTGGCG 59.746 43.478 7.35 0.00 34.54 5.69
94 95 3.709987 GTTATGACCATGGCTTTGATGC 58.290 45.455 13.04 0.00 0.00 3.91
103 104 2.543848 CGATGGTTCGTTATGACCATGG 59.456 50.000 11.19 11.19 38.09 3.66
117 118 2.160721 TCTTCTCTAGGGCGATGGTT 57.839 50.000 0.00 0.00 0.00 3.67
119 120 2.483889 GGTTTCTTCTCTAGGGCGATGG 60.484 54.545 0.00 0.00 0.00 3.51
122 123 1.933021 TGGTTTCTTCTCTAGGGCGA 58.067 50.000 0.00 0.00 0.00 5.54
141 142 1.167851 TCGGTGGTAACGTCTTCGAT 58.832 50.000 0.00 0.00 40.62 3.59
152 153 3.134081 GGATCTTGGATCTTTCGGTGGTA 59.866 47.826 7.35 0.00 0.00 3.25
153 154 2.092914 GGATCTTGGATCTTTCGGTGGT 60.093 50.000 7.35 0.00 0.00 4.16
156 157 2.196595 TGGGATCTTGGATCTTTCGGT 58.803 47.619 7.35 0.00 0.00 4.69
160 161 3.053320 GGAGGTTGGGATCTTGGATCTTT 60.053 47.826 7.35 0.00 0.00 2.52
163 164 1.846439 TGGAGGTTGGGATCTTGGATC 59.154 52.381 0.00 0.00 0.00 3.36
165 166 1.753903 TTGGAGGTTGGGATCTTGGA 58.246 50.000 0.00 0.00 0.00 3.53
186 187 1.155042 GAGTGAGGCTTGTCAGCTTG 58.845 55.000 0.00 0.00 46.44 4.01
217 219 0.324943 GCTTTGCCTCCTAGGTGTGA 59.675 55.000 9.08 0.00 37.80 3.58
219 221 1.192146 TCGCTTTGCCTCCTAGGTGT 61.192 55.000 9.08 0.00 37.80 4.16
241 255 3.925630 AACATGGTGGCGAGGGCAG 62.926 63.158 0.00 0.00 42.47 4.85
269 283 3.387374 TGGTCGTTGAGTTAGGGTTTACA 59.613 43.478 0.00 0.00 0.00 2.41
271 285 3.896888 TCTGGTCGTTGAGTTAGGGTTTA 59.103 43.478 0.00 0.00 0.00 2.01
287 301 6.463995 AGATTCATGTTAGTCTCTCTGGTC 57.536 41.667 0.00 0.00 0.00 4.02
288 302 6.038825 CGTAGATTCATGTTAGTCTCTCTGGT 59.961 42.308 0.00 0.00 0.00 4.00
290 304 5.912396 GCGTAGATTCATGTTAGTCTCTCTG 59.088 44.000 0.00 0.00 0.00 3.35
291 305 5.009210 GGCGTAGATTCATGTTAGTCTCTCT 59.991 44.000 0.00 0.00 0.00 3.10
301 315 3.313526 GCTCAATTGGCGTAGATTCATGT 59.686 43.478 5.42 0.00 0.00 3.21
332 346 3.403057 CAGTGTCGGTTGCGGTCG 61.403 66.667 0.00 0.00 0.00 4.79
337 351 1.195448 CATCTCAACAGTGTCGGTTGC 59.805 52.381 0.00 0.00 44.02 4.17
347 361 4.462132 TCTTGAGTCTCCTCATCTCAACAG 59.538 45.833 0.00 0.00 46.80 3.16
367 381 6.404734 GCCGATCTGGTCAATAATGTTTTCTT 60.405 38.462 5.66 0.00 41.21 2.52
375 389 2.806745 CGGTGCCGATCTGGTCAATAAT 60.807 50.000 4.35 0.00 42.83 1.28
392 406 3.229156 TAGGTTGGTGGCGACGGTG 62.229 63.158 0.00 0.00 0.00 4.94
393 407 2.918802 TAGGTTGGTGGCGACGGT 60.919 61.111 0.00 0.00 0.00 4.83
394 408 1.597797 TAGTAGGTTGGTGGCGACGG 61.598 60.000 0.00 0.00 0.00 4.79
395 409 0.244450 TTAGTAGGTTGGTGGCGACG 59.756 55.000 0.00 0.00 0.00 5.12
396 410 2.460757 TTTAGTAGGTTGGTGGCGAC 57.539 50.000 0.00 0.00 0.00 5.19
397 411 3.140623 GTTTTTAGTAGGTTGGTGGCGA 58.859 45.455 0.00 0.00 0.00 5.54
398 412 3.143728 AGTTTTTAGTAGGTTGGTGGCG 58.856 45.455 0.00 0.00 0.00 5.69
399 413 3.504906 GGAGTTTTTAGTAGGTTGGTGGC 59.495 47.826 0.00 0.00 0.00 5.01
400 414 4.721132 TGGAGTTTTTAGTAGGTTGGTGG 58.279 43.478 0.00 0.00 0.00 4.61
401 415 6.702716 TTTGGAGTTTTTAGTAGGTTGGTG 57.297 37.500 0.00 0.00 0.00 4.17
402 416 5.301045 GCTTTGGAGTTTTTAGTAGGTTGGT 59.699 40.000 0.00 0.00 0.00 3.67
403 417 5.562113 CGCTTTGGAGTTTTTAGTAGGTTGG 60.562 44.000 0.00 0.00 0.00 3.77
404 418 5.237779 TCGCTTTGGAGTTTTTAGTAGGTTG 59.762 40.000 0.00 0.00 0.00 3.77
405 419 5.370679 TCGCTTTGGAGTTTTTAGTAGGTT 58.629 37.500 0.00 0.00 0.00 3.50
406 420 4.964593 TCGCTTTGGAGTTTTTAGTAGGT 58.035 39.130 0.00 0.00 0.00 3.08
407 421 5.106673 CCTTCGCTTTGGAGTTTTTAGTAGG 60.107 44.000 0.00 0.00 0.00 3.18
408 422 5.106673 CCCTTCGCTTTGGAGTTTTTAGTAG 60.107 44.000 0.00 0.00 0.00 2.57
409 423 4.758165 CCCTTCGCTTTGGAGTTTTTAGTA 59.242 41.667 0.00 0.00 0.00 1.82
410 424 3.568430 CCCTTCGCTTTGGAGTTTTTAGT 59.432 43.478 0.00 0.00 0.00 2.24
411 425 3.818773 TCCCTTCGCTTTGGAGTTTTTAG 59.181 43.478 0.00 0.00 0.00 1.85
412 426 3.818773 CTCCCTTCGCTTTGGAGTTTTTA 59.181 43.478 0.00 0.00 40.66 1.52
413 427 2.623416 CTCCCTTCGCTTTGGAGTTTTT 59.377 45.455 0.00 0.00 40.66 1.94
414 428 2.230660 CTCCCTTCGCTTTGGAGTTTT 58.769 47.619 0.00 0.00 40.66 2.43
415 429 1.545651 CCTCCCTTCGCTTTGGAGTTT 60.546 52.381 0.00 0.00 43.42 2.66
416 430 0.036875 CCTCCCTTCGCTTTGGAGTT 59.963 55.000 0.00 0.00 43.42 3.01
417 431 1.679898 CCTCCCTTCGCTTTGGAGT 59.320 57.895 0.00 0.00 43.42 3.85
418 432 1.078143 CCCTCCCTTCGCTTTGGAG 60.078 63.158 0.00 0.00 44.34 3.86
419 433 2.602676 CCCCTCCCTTCGCTTTGGA 61.603 63.158 0.00 0.00 0.00 3.53
420 434 2.044946 CCCCTCCCTTCGCTTTGG 60.045 66.667 0.00 0.00 0.00 3.28
421 435 2.044946 CCCCCTCCCTTCGCTTTG 60.045 66.667 0.00 0.00 0.00 2.77
422 436 2.204090 TCCCCCTCCCTTCGCTTT 60.204 61.111 0.00 0.00 0.00 3.51
423 437 2.689034 CTCCCCCTCCCTTCGCTT 60.689 66.667 0.00 0.00 0.00 4.68
424 438 3.254035 TTCTCCCCCTCCCTTCGCT 62.254 63.158 0.00 0.00 0.00 4.93
425 439 2.687566 TTCTCCCCCTCCCTTCGC 60.688 66.667 0.00 0.00 0.00 4.70
426 440 1.306226 AGTTCTCCCCCTCCCTTCG 60.306 63.158 0.00 0.00 0.00 3.79
427 441 0.983905 GGAGTTCTCCCCCTCCCTTC 60.984 65.000 7.57 0.00 41.22 3.46
428 442 1.083141 GGAGTTCTCCCCCTCCCTT 59.917 63.158 7.57 0.00 41.22 3.95
429 443 1.541168 ATGGAGTTCTCCCCCTCCCT 61.541 60.000 15.20 0.00 45.56 4.20
430 444 0.624795 AATGGAGTTCTCCCCCTCCC 60.625 60.000 15.20 0.00 45.56 4.30
431 445 0.840617 GAATGGAGTTCTCCCCCTCC 59.159 60.000 15.20 0.00 46.20 4.30
432 446 1.488393 CTGAATGGAGTTCTCCCCCTC 59.512 57.143 15.20 9.71 37.72 4.30
433 447 1.203492 ACTGAATGGAGTTCTCCCCCT 60.203 52.381 15.20 1.05 37.72 4.79
434 448 1.290134 ACTGAATGGAGTTCTCCCCC 58.710 55.000 15.20 6.00 37.72 5.40
435 449 2.436173 CCTACTGAATGGAGTTCTCCCC 59.564 54.545 15.20 6.31 37.72 4.81
436 450 3.108376 ACCTACTGAATGGAGTTCTCCC 58.892 50.000 15.20 2.20 37.72 4.30
437 451 3.181485 CGACCTACTGAATGGAGTTCTCC 60.181 52.174 11.53 11.53 37.72 3.71
438 452 3.181485 CCGACCTACTGAATGGAGTTCTC 60.181 52.174 0.00 0.00 37.72 2.87
439 453 2.761208 CCGACCTACTGAATGGAGTTCT 59.239 50.000 0.00 0.00 37.72 3.01
440 454 2.159085 CCCGACCTACTGAATGGAGTTC 60.159 54.545 0.00 0.00 37.35 3.01
441 455 1.831736 CCCGACCTACTGAATGGAGTT 59.168 52.381 0.00 0.00 0.00 3.01
442 456 1.486211 CCCGACCTACTGAATGGAGT 58.514 55.000 0.00 0.00 0.00 3.85
443 457 0.753262 CCCCGACCTACTGAATGGAG 59.247 60.000 0.00 0.00 0.00 3.86
444 458 1.335132 GCCCCGACCTACTGAATGGA 61.335 60.000 0.00 0.00 0.00 3.41
445 459 1.146263 GCCCCGACCTACTGAATGG 59.854 63.158 0.00 0.00 0.00 3.16
446 460 1.146263 GGCCCCGACCTACTGAATG 59.854 63.158 0.00 0.00 0.00 2.67
447 461 1.003051 AGGCCCCGACCTACTGAAT 59.997 57.895 0.00 0.00 38.67 2.57
448 462 1.684734 GAGGCCCCGACCTACTGAA 60.685 63.158 0.00 0.00 41.32 3.02
449 463 2.043248 GAGGCCCCGACCTACTGA 60.043 66.667 0.00 0.00 41.32 3.41
450 464 3.155167 GGAGGCCCCGACCTACTG 61.155 72.222 0.00 0.00 41.32 2.74
451 465 4.477119 GGGAGGCCCCGACCTACT 62.477 72.222 0.00 0.00 44.02 2.57
490 792 2.236395 CGTTTGTAGGTCATCCCTCCTT 59.764 50.000 0.00 0.00 44.81 3.36
499 806 2.028476 CACCTCATCCGTTTGTAGGTCA 60.028 50.000 0.00 0.00 38.51 4.02
633 943 4.508551 ACCTGCTTGATGTCATAATCCA 57.491 40.909 0.00 0.00 0.00 3.41
645 955 1.271379 GCCACCTAGAAACCTGCTTGA 60.271 52.381 0.00 0.00 0.00 3.02
702 1012 0.595588 CCTCTCTCGATCGACATGGG 59.404 60.000 15.15 10.50 0.00 4.00
889 1201 0.756294 TTTGGCTTCCGTGAGTGAGA 59.244 50.000 0.00 0.00 0.00 3.27
945 1257 0.467290 TGGAACTGGAACTGGGCAAC 60.467 55.000 0.00 0.00 0.00 4.17
949 1261 2.230660 GAAACTGGAACTGGAACTGGG 58.769 52.381 0.00 0.00 0.00 4.45
958 1270 0.538287 GGCCTGCTGAAACTGGAACT 60.538 55.000 0.00 0.00 0.00 3.01
959 1271 0.823356 TGGCCTGCTGAAACTGGAAC 60.823 55.000 3.32 0.00 0.00 3.62
960 1272 0.106268 TTGGCCTGCTGAAACTGGAA 60.106 50.000 3.32 0.00 0.00 3.53
961 1273 0.538057 CTTGGCCTGCTGAAACTGGA 60.538 55.000 3.32 0.00 0.00 3.86
962 1274 0.538057 TCTTGGCCTGCTGAAACTGG 60.538 55.000 3.32 0.00 0.00 4.00
963 1275 0.879765 CTCTTGGCCTGCTGAAACTG 59.120 55.000 3.32 0.00 0.00 3.16
964 1276 0.892814 GCTCTTGGCCTGCTGAAACT 60.893 55.000 3.32 0.00 34.27 2.66
965 1277 1.174712 TGCTCTTGGCCTGCTGAAAC 61.175 55.000 3.32 0.00 40.92 2.78
966 1278 0.467844 TTGCTCTTGGCCTGCTGAAA 60.468 50.000 3.32 0.00 40.92 2.69
967 1279 0.892358 CTTGCTCTTGGCCTGCTGAA 60.892 55.000 3.32 0.00 40.92 3.02
968 1280 1.303074 CTTGCTCTTGGCCTGCTGA 60.303 57.895 3.32 0.00 40.92 4.26
969 1281 0.892358 TTCTTGCTCTTGGCCTGCTG 60.892 55.000 3.32 1.75 40.92 4.41
970 1282 0.178981 TTTCTTGCTCTTGGCCTGCT 60.179 50.000 3.32 0.00 40.92 4.24
1059 1371 4.410400 AAGGTGTAGCAGCCGGCC 62.410 66.667 26.15 9.10 46.50 6.13
1181 1493 3.591254 AACACGCTCCTCGCCTTCC 62.591 63.158 0.00 0.00 43.23 3.46
1544 1864 6.183360 CGTACTAGAGGATGATCGGATTACTG 60.183 46.154 0.00 0.00 0.00 2.74
1551 1871 4.152045 GTGTACGTACTAGAGGATGATCGG 59.848 50.000 25.12 0.00 0.00 4.18
1561 1881 7.066163 TGCAGCTTAATTAGTGTACGTACTAGA 59.934 37.037 25.12 10.07 34.84 2.43
1596 1929 0.530650 ATCGATCCACGGACACATGC 60.531 55.000 0.00 0.00 42.82 4.06
1605 1952 2.293677 TCCAGTTGAATCGATCCACG 57.706 50.000 0.00 0.00 44.09 4.94
1727 2081 3.052036 GTGTCCATCATGTGTTTGTTGC 58.948 45.455 0.00 0.00 0.00 4.17
1806 2170 1.993370 GTTGCAGTTCTACGCACCTAG 59.007 52.381 0.00 0.00 38.00 3.02
1810 2174 0.234884 GGTGTTGCAGTTCTACGCAC 59.765 55.000 1.82 0.00 38.00 5.34
1811 2175 0.882927 GGGTGTTGCAGTTCTACGCA 60.883 55.000 1.82 0.00 33.58 5.24
1812 2176 1.866925 GGGTGTTGCAGTTCTACGC 59.133 57.895 0.00 0.00 0.00 4.42
1813 2177 1.897398 GCGGGTGTTGCAGTTCTACG 61.897 60.000 0.00 0.00 0.00 3.51
1864 2228 3.813166 GTCCATCGACTCTTTTTCACCAA 59.187 43.478 0.00 0.00 35.99 3.67
1867 2231 2.412089 CGGTCCATCGACTCTTTTTCAC 59.588 50.000 0.00 0.00 39.15 3.18
1868 2232 2.611971 CCGGTCCATCGACTCTTTTTCA 60.612 50.000 0.00 0.00 39.15 2.69
1869 2233 2.000447 CCGGTCCATCGACTCTTTTTC 59.000 52.381 0.00 0.00 39.15 2.29
1909 2273 3.723235 CTGAGGCCATCCACGACCG 62.723 68.421 5.01 0.00 33.74 4.79
1910 2274 2.187946 CTGAGGCCATCCACGACC 59.812 66.667 5.01 0.00 33.74 4.79
1922 2311 5.107824 CACTACTGATCATTGACACTGAGG 58.892 45.833 0.00 0.00 0.00 3.86
2011 2400 1.152777 CACACCTTGGCACTTGGGA 60.153 57.895 0.00 0.00 0.00 4.37
2029 2418 3.050275 GTCGTGCTGGTTGGAGGC 61.050 66.667 0.00 0.00 0.00 4.70
2108 2499 2.352457 CGCACGTCGGCTAGCTAG 60.352 66.667 16.84 16.84 33.78 3.42
2122 2513 2.203771 AACAATTTTCGCCCCCGCA 61.204 52.632 0.00 0.00 34.03 5.69
2126 2517 0.389817 GGAGCAACAATTTTCGCCCC 60.390 55.000 0.00 0.00 0.00 5.80
2130 2521 0.109319 CCCGGGAGCAACAATTTTCG 60.109 55.000 18.48 0.00 0.00 3.46
2132 2523 0.966179 GACCCGGGAGCAACAATTTT 59.034 50.000 32.02 0.00 0.00 1.82
2135 2526 1.910580 ATCGACCCGGGAGCAACAAT 61.911 55.000 32.02 0.00 0.00 2.71
2142 2533 3.122250 GACGACATCGACCCGGGAG 62.122 68.421 32.02 21.08 43.02 4.30
2153 2544 0.308068 CAGATACGCCTCGACGACAT 59.692 55.000 2.12 0.00 36.70 3.06
2154 2545 1.022982 ACAGATACGCCTCGACGACA 61.023 55.000 2.12 0.00 36.70 4.35
2187 2578 1.455773 GATTGGGGCCTAGGCAACC 60.456 63.158 34.09 31.83 44.11 3.77
2189 2580 0.411452 TTTGATTGGGGCCTAGGCAA 59.589 50.000 34.09 20.75 44.11 4.52
2232 2628 2.991190 TCGTGTCGCTTTAAGCCTTAAG 59.009 45.455 11.64 0.00 38.18 1.85
2233 2629 2.991190 CTCGTGTCGCTTTAAGCCTTAA 59.009 45.455 11.64 0.00 38.18 1.85
2234 2630 2.229543 TCTCGTGTCGCTTTAAGCCTTA 59.770 45.455 11.64 0.00 38.18 2.69
2235 2631 1.000506 TCTCGTGTCGCTTTAAGCCTT 59.999 47.619 11.64 0.00 38.18 4.35
2236 2632 0.601558 TCTCGTGTCGCTTTAAGCCT 59.398 50.000 11.64 0.00 38.18 4.58
2237 2633 0.714439 GTCTCGTGTCGCTTTAAGCC 59.286 55.000 11.64 0.00 38.18 4.35
2238 2634 0.362512 CGTCTCGTGTCGCTTTAAGC 59.637 55.000 6.92 6.92 38.02 3.09
2262 2658 3.044305 GCATATCCGGCGGCTGTC 61.044 66.667 23.83 10.61 0.00 3.51
2394 2806 8.627208 AAGTAAGTAAGCTGTATATAGCCGTA 57.373 34.615 16.96 7.90 44.76 4.02


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

AutoCloner maintained by Alex Coulton.