Multiple sequence alignment - TraesCS1B01G362400

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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 TraesCS1B01G362400 chr1B 100.000 2661 0 0 1 2661 591229511 591226851 0.000000e+00 4915.0
1 TraesCS1B01G362400 chr1D 91.345 1294 74 18 661 1931 436211214 436209936 0.000000e+00 1735.0
2 TraesCS1B01G362400 chr1D 82.850 379 45 10 1 367 436211737 436211367 3.300000e-84 322.0
3 TraesCS1B01G362400 chr1D 87.681 276 13 11 1968 2226 436209832 436209561 4.300000e-78 302.0
4 TraesCS1B01G362400 chr1D 88.235 119 11 3 2309 2424 436209410 436209292 3.570000e-29 139.0
5 TraesCS1B01G362400 chr1D 94.505 91 2 1 2563 2650 436209207 436209117 1.280000e-28 137.0
6 TraesCS1B01G362400 chr1D 84.884 86 8 1 2236 2316 436209523 436209438 6.110000e-12 82.4
7 TraesCS1B01G362400 chr1A 83.681 1967 118 91 370 2226 533462902 533461029 0.000000e+00 1666.0
8 TraesCS1B01G362400 chr1A 87.676 284 28 4 2359 2636 533460297 533460015 9.190000e-85 324.0
9 TraesCS1B01G362400 chr1A 80.670 388 38 23 1 372 533463312 533462946 1.570000e-67 267.0
10 TraesCS1B01G362400 chr1A 86.207 87 6 2 2219 2299 533461005 533460919 3.650000e-14 89.8
11 TraesCS1B01G362400 chr3B 80.952 399 36 15 3 373 565435141 565435527 2.020000e-71 279.0
12 TraesCS1B01G362400 chr3B 78.270 497 55 26 397 866 565565428 565565898 1.210000e-68 270.0
13 TraesCS1B01G362400 chr3B 86.842 190 14 4 3 185 565564968 565565153 4.490000e-48 202.0
14 TraesCS1B01G362400 chr3A 80.260 385 54 9 3 373 571399418 571399794 1.210000e-68 270.0
15 TraesCS1B01G362400 chr3D 78.772 391 39 26 3 373 433193396 433193762 3.450000e-54 222.0
16 TraesCS1B01G362400 chr3D 77.136 433 58 22 449 866 433194080 433194486 2.070000e-51 213.0
17 TraesCS1B01G362400 chr5B 81.026 195 21 7 2322 2515 461444625 461444446 9.930000e-30 141.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G362400 chr1B 591226851 591229511 2660 True 4915.0 4915 100.0000 1 2661 1 chr1B.!!$R1 2660
1 TraesCS1B01G362400 chr1D 436209117 436211737 2620 True 452.9 1735 88.2500 1 2650 6 chr1D.!!$R1 2649
2 TraesCS1B01G362400 chr1A 533460015 533463312 3297 True 586.7 1666 84.5585 1 2636 4 chr1A.!!$R1 2635
3 TraesCS1B01G362400 chr3B 565564968 565565898 930 False 236.0 270 82.5560 3 866 2 chr3B.!!$F2 863
4 TraesCS1B01G362400 chr3D 433193396 433194486 1090 False 217.5 222 77.9540 3 866 2 chr3D.!!$F1 863


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
657 965 0.033011 ATAGGCTCTCTGGTCGTGGT 60.033 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2552 3621 0.251033 GCTTCGGGTTAAGGGTTGGT 60.251 55.0 0.0 0.0 0.0 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
115 125 4.446371 CAAGTGGGACAGATCACTATTCC 58.554 47.826 0.00 0.00 42.67 3.01
122 133 3.456277 GACAGATCACTATTCCCAACCCT 59.544 47.826 0.00 0.00 0.00 4.34
123 134 3.200825 ACAGATCACTATTCCCAACCCTG 59.799 47.826 0.00 0.00 0.00 4.45
124 135 2.173569 AGATCACTATTCCCAACCCTGC 59.826 50.000 0.00 0.00 0.00 4.85
125 136 1.367346 TCACTATTCCCAACCCTGCA 58.633 50.000 0.00 0.00 0.00 4.41
130 141 0.974010 ATTCCCAACCCTGCATGCAG 60.974 55.000 35.88 35.88 43.26 4.41
145 156 2.512485 TGCAGGAACAATTTGCACTG 57.488 45.000 0.00 9.80 42.41 3.66
150 161 1.202510 GGAACAATTTGCACTGTGCCA 60.203 47.619 28.17 16.39 44.23 4.92
175 186 4.405680 TGAGAGAAAGTCCAACTCACTCAA 59.594 41.667 0.00 2.84 34.84 3.02
186 197 5.186797 TCCAACTCACTCAACAAATTTGGTT 59.813 36.000 21.74 10.50 34.94 3.67
188 199 6.371271 CCAACTCACTCAACAAATTTGGTTTT 59.629 34.615 21.74 5.00 0.00 2.43
190 201 6.106003 ACTCACTCAACAAATTTGGTTTTCC 58.894 36.000 21.74 0.00 41.14 3.13
212 223 7.379059 TCCATATTCTCATGTGGAGTAACAT 57.621 36.000 0.00 0.00 43.83 2.71
227 238 4.756502 AGTAACATTCTAAGGCTCCGTTC 58.243 43.478 0.00 0.00 0.00 3.95
232 249 1.481871 TCTAAGGCTCCGTTCGGATT 58.518 50.000 14.34 8.78 33.34 3.01
245 271 6.781138 TCCGTTCGGATTTTGATATTGAAAG 58.219 36.000 10.00 0.00 0.00 2.62
287 313 8.827832 TCAAATCTCCCAGACATTGATAATTT 57.172 30.769 0.00 0.00 32.08 1.82
288 314 8.689061 TCAAATCTCCCAGACATTGATAATTTG 58.311 33.333 0.00 0.00 32.08 2.32
289 315 8.689061 CAAATCTCCCAGACATTGATAATTTGA 58.311 33.333 0.00 0.00 34.11 2.69
290 316 9.430399 AAATCTCCCAGACATTGATAATTTGAT 57.570 29.630 0.00 0.00 0.00 2.57
311 337 9.950680 TTTGATATTGAAACTGAAACTGAACTC 57.049 29.630 0.00 0.00 0.00 3.01
314 340 5.818136 TTGAAACTGAAACTGAACTCTGG 57.182 39.130 0.00 0.00 0.00 3.86
333 361 4.338118 TCTGGTGTTTGGATGTTCAAGAAC 59.662 41.667 6.01 6.01 41.50 3.01
363 391 5.082251 TGGAATTCACATGAGAGACTCAG 57.918 43.478 7.93 3.13 44.08 3.35
367 395 3.839051 TCACATGAGAGACTCAGTTCG 57.161 47.619 5.02 0.00 44.08 3.95
395 505 9.685276 AATAGGATGAACATTGTACTTTGATGA 57.315 29.630 0.00 0.00 0.00 2.92
431 549 8.340618 ACTAACTTCTATGCAACATGTGAATT 57.659 30.769 0.00 0.00 0.00 2.17
468 750 9.508642 TGGTTATATACATCAAGAACACAACAA 57.491 29.630 0.00 0.00 0.00 2.83
477 759 4.697828 TCAAGAACACAACAACAGCACTTA 59.302 37.500 0.00 0.00 0.00 2.24
484 766 6.262601 ACACAACAACAGCACTTATACAAAC 58.737 36.000 0.00 0.00 0.00 2.93
486 768 6.414694 CACAACAACAGCACTTATACAAACAG 59.585 38.462 0.00 0.00 0.00 3.16
487 769 5.108385 ACAACAGCACTTATACAAACAGC 57.892 39.130 0.00 0.00 0.00 4.40
488 770 4.151070 CAACAGCACTTATACAAACAGCG 58.849 43.478 0.00 0.00 0.00 5.18
505 788 4.006989 ACAGCGGCACATATACAAAGAAA 58.993 39.130 1.45 0.00 0.00 2.52
592 900 4.308458 CGGCCGTGGTTGGTGAGA 62.308 66.667 19.50 0.00 0.00 3.27
650 958 2.739784 CCGGCATAGGCTCTCTGG 59.260 66.667 0.00 0.00 40.87 3.86
651 959 2.136878 CCGGCATAGGCTCTCTGGT 61.137 63.158 0.00 0.00 40.87 4.00
652 960 1.365633 CGGCATAGGCTCTCTGGTC 59.634 63.158 0.00 0.00 40.87 4.02
653 961 1.365633 GGCATAGGCTCTCTGGTCG 59.634 63.158 0.00 0.00 40.87 4.79
654 962 1.395826 GGCATAGGCTCTCTGGTCGT 61.396 60.000 0.00 0.00 40.87 4.34
655 963 0.249238 GCATAGGCTCTCTGGTCGTG 60.249 60.000 0.00 0.00 36.96 4.35
656 964 0.387202 CATAGGCTCTCTGGTCGTGG 59.613 60.000 0.00 0.00 0.00 4.94
657 965 0.033011 ATAGGCTCTCTGGTCGTGGT 60.033 55.000 0.00 0.00 0.00 4.16
658 966 0.251653 TAGGCTCTCTGGTCGTGGTT 60.252 55.000 0.00 0.00 0.00 3.67
762 1083 3.771160 GCGGGCGGAGAGAAGGAA 61.771 66.667 0.00 0.00 0.00 3.36
900 1232 9.050601 CAAATATGTGGAGGATCTTCTAGAAAC 57.949 37.037 6.63 0.00 33.73 2.78
901 1233 7.921041 ATATGTGGAGGATCTTCTAGAAACA 57.079 36.000 6.63 5.78 33.73 2.83
902 1234 6.627087 ATGTGGAGGATCTTCTAGAAACAA 57.373 37.500 6.63 0.00 33.73 2.83
903 1235 6.433847 TGTGGAGGATCTTCTAGAAACAAA 57.566 37.500 6.63 0.00 33.73 2.83
904 1236 6.837312 TGTGGAGGATCTTCTAGAAACAAAA 58.163 36.000 6.63 0.00 33.73 2.44
905 1237 7.287061 TGTGGAGGATCTTCTAGAAACAAAAA 58.713 34.615 6.63 0.00 33.73 1.94
1014 1346 1.066918 CGACCCGTATTCTTCCCCG 59.933 63.158 0.00 0.00 0.00 5.73
1308 1664 0.317269 ACGACGAAGAAAGCGACGAA 60.317 50.000 13.67 0.00 46.35 3.85
1318 1674 0.033504 AAGCGACGAAGAAGAAGGCA 59.966 50.000 0.00 0.00 0.00 4.75
1543 1904 1.821753 AGATGAGTTCTCGACCCACAG 59.178 52.381 0.00 0.00 0.00 3.66
1567 1928 2.799412 CACTGTGAGTTGTGAGAGCTTC 59.201 50.000 0.32 0.00 36.38 3.86
1573 1934 3.056250 TGAGTTGTGAGAGCTTCTGATCC 60.056 47.826 0.00 0.00 0.00 3.36
1584 1945 2.678190 GCTTCTGATCCGCCTTTGTACT 60.678 50.000 0.00 0.00 0.00 2.73
1620 1981 4.918588 TGTATCGCCATAGATCCAGTAGA 58.081 43.478 0.00 0.00 32.39 2.59
1648 2010 0.796312 TCGCTGCTTCGGAATGAAAC 59.204 50.000 0.00 0.00 35.79 2.78
1684 2048 1.000938 CGCCGATGAGATCAGTGATCA 60.001 52.381 30.05 16.12 41.12 2.92
1778 2146 1.064654 GTGGAGAAATCCGAATGCTGC 59.935 52.381 0.00 0.00 0.00 5.25
1803 2171 0.811616 CTGCTCTCCGTGGGCATAAC 60.812 60.000 0.65 0.00 35.37 1.89
1804 2172 1.264749 TGCTCTCCGTGGGCATAACT 61.265 55.000 0.00 0.00 0.00 2.24
1819 2187 4.083217 GGCATAACTCTCGACGATATCTGT 60.083 45.833 0.00 0.56 0.00 3.41
1820 2188 4.848841 GCATAACTCTCGACGATATCTGTG 59.151 45.833 0.00 0.00 0.00 3.66
1871 2239 8.726650 TGTGAAATTTTCAGTTGTATGAATCG 57.273 30.769 12.02 0.00 41.01 3.34
1879 2247 3.071479 AGTTGTATGAATCGGCAAACGT 58.929 40.909 0.00 0.00 44.69 3.99
1889 2257 5.399892 TGAATCGGCAAACGTTTAATTTGTC 59.600 36.000 14.20 2.00 44.69 3.18
1905 2273 1.363807 GTCTGTGCCCTTGTTTGCC 59.636 57.895 0.00 0.00 0.00 4.52
1963 2358 8.806429 AAGTGATCATGTAATTGGTATTCACA 57.194 30.769 0.00 0.00 0.00 3.58
1966 2361 5.733226 TCATGTAATTGGTATTCACAGCG 57.267 39.130 0.00 0.00 0.00 5.18
2020 2468 3.494626 ACAAGTACAGATTCAAGCACACG 59.505 43.478 0.00 0.00 0.00 4.49
2032 2480 2.100031 GCACACGTCCGCATCATCA 61.100 57.895 0.89 0.00 0.00 3.07
2033 2481 2.001357 CACACGTCCGCATCATCAG 58.999 57.895 0.00 0.00 0.00 2.90
2073 2521 3.272574 ACACACTCAATGATAGGCAGG 57.727 47.619 0.00 0.00 0.00 4.85
2128 2580 4.175516 ACGCCATGAACATTGCAAATAAG 58.824 39.130 1.71 0.00 30.63 1.73
2167 2619 4.262249 GCTCTGTACTATCCCAGAACCATC 60.262 50.000 0.00 0.00 37.27 3.51
2168 2620 5.144100 CTCTGTACTATCCCAGAACCATCT 58.856 45.833 0.00 0.00 37.27 2.90
2209 2674 8.213679 TGAATGGAATAGCTCTACTGCTAATTT 58.786 33.333 0.00 0.00 46.81 1.82
2213 2678 9.494271 TGGAATAGCTCTACTGCTAATTTATTG 57.506 33.333 0.00 0.00 46.81 1.90
2226 2691 6.127925 TGCTAATTTATTGAGACAGGCAAGTG 60.128 38.462 0.00 0.00 0.00 3.16
2228 2693 6.506500 AATTTATTGAGACAGGCAAGTGAG 57.493 37.500 0.00 0.00 0.00 3.51
2234 2731 7.603180 ATTGAGACAGGCAAGTGAGTATATA 57.397 36.000 0.00 0.00 0.00 0.86
2260 2757 2.100584 GCTGGAACACAACATCACCAAA 59.899 45.455 0.00 0.00 0.00 3.28
2269 2771 4.566360 CACAACATCACCAAACAAAACCTC 59.434 41.667 0.00 0.00 0.00 3.85
2302 2840 2.857592 AATTCAGACAATCATGCCGC 57.142 45.000 0.00 0.00 0.00 6.53
2307 2845 1.004610 CAGACAATCATGCCGCGTAAG 60.005 52.381 4.92 0.00 43.44 2.34
2404 3468 8.944212 AAAGAACATAAATTCGTTTTCTACCG 57.056 30.769 0.00 0.00 33.57 4.02
2423 3489 8.624701 TCTACCGATAAAAGAAACTGTAATCG 57.375 34.615 0.00 0.00 35.68 3.34
2429 3495 8.388103 CGATAAAAGAAACTGTAATCGGACAAT 58.612 33.333 0.00 0.00 33.10 2.71
2433 3499 8.786826 AAAGAAACTGTAATCGGACAATATGA 57.213 30.769 0.00 0.00 0.00 2.15
2459 3526 5.901552 TCGATGAATCAGCTATACACACAA 58.098 37.500 0.00 0.00 0.00 3.33
2480 3547 5.583854 ACAATGAGTTCATCCTTTCGATCTG 59.416 40.000 0.00 0.00 35.10 2.90
2484 3551 4.753233 AGTTCATCCTTTCGATCTGTCAG 58.247 43.478 0.00 0.00 0.00 3.51
2488 3555 5.354767 TCATCCTTTCGATCTGTCAGATTG 58.645 41.667 20.34 20.34 34.53 2.67
2494 3561 3.451526 TCGATCTGTCAGATTGTGCATC 58.548 45.455 23.81 8.25 37.39 3.91
2495 3562 3.119029 TCGATCTGTCAGATTGTGCATCA 60.119 43.478 23.81 6.43 37.39 3.07
2539 3608 7.473027 AATTGAACAATGCATAGCTAATTGC 57.527 32.000 14.01 12.91 43.29 3.56
2551 3620 3.892918 GCTAATTGCGCATGATCTTCT 57.107 42.857 12.75 0.00 0.00 2.85
2552 3621 4.997905 GCTAATTGCGCATGATCTTCTA 57.002 40.909 12.75 0.00 0.00 2.10
2561 3634 3.682718 CGCATGATCTTCTACCAACCCTT 60.683 47.826 0.00 0.00 0.00 3.95
2610 3683 1.522580 GGCAGAGGGCGTCATCTTC 60.523 63.158 0.00 0.00 46.16 2.87
2641 3717 2.173356 TGCTTTATCCATCACCTGGGAG 59.827 50.000 0.00 0.00 45.98 4.30
2650 3726 0.616111 TCACCTGGGAGGAAGCTCTC 60.616 60.000 0.00 0.00 37.67 3.20
2651 3727 0.617249 CACCTGGGAGGAAGCTCTCT 60.617 60.000 0.00 0.00 37.67 3.10
2652 3728 0.118144 ACCTGGGAGGAAGCTCTCTT 59.882 55.000 0.00 0.00 37.67 2.85
2653 3729 1.284313 CCTGGGAGGAAGCTCTCTTT 58.716 55.000 2.74 0.00 37.67 2.52
2654 3730 1.209261 CCTGGGAGGAAGCTCTCTTTC 59.791 57.143 2.74 0.00 37.67 2.62
2655 3731 2.187100 CTGGGAGGAAGCTCTCTTTCT 58.813 52.381 2.74 0.00 40.84 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 133 1.070289 TGCAAATTGTTCCTGCATGCA 59.930 42.857 21.29 21.29 41.01 3.96
123 134 1.461897 GTGCAAATTGTTCCTGCATGC 59.538 47.619 11.82 11.82 46.90 4.06
124 135 2.734606 CAGTGCAAATTGTTCCTGCATG 59.265 45.455 5.13 0.00 46.90 4.06
125 136 2.366266 ACAGTGCAAATTGTTCCTGCAT 59.634 40.909 5.13 0.00 46.90 3.96
130 141 4.051313 ATTGGCACAGTGCAAATTGTTCC 61.051 43.478 26.78 6.77 44.15 3.62
145 156 2.783135 TGGACTTTCTCTCATTGGCAC 58.217 47.619 0.00 0.00 0.00 5.01
150 161 5.070981 TGAGTGAGTTGGACTTTCTCTCATT 59.929 40.000 0.00 0.00 36.87 2.57
175 186 9.439500 CATGAGAATATGGAAAACCAAATTTGT 57.561 29.630 16.73 2.76 0.00 2.83
186 197 7.629157 TGTTACTCCACATGAGAATATGGAAA 58.371 34.615 0.00 0.00 44.42 3.13
188 199 6.806668 TGTTACTCCACATGAGAATATGGA 57.193 37.500 0.00 0.00 44.42 3.41
190 201 8.899427 AGAATGTTACTCCACATGAGAATATG 57.101 34.615 0.00 0.00 44.42 1.78
197 208 5.189736 AGCCTTAGAATGTTACTCCACATGA 59.810 40.000 0.00 0.00 37.46 3.07
198 209 5.431765 AGCCTTAGAATGTTACTCCACATG 58.568 41.667 0.00 0.00 37.46 3.21
201 212 4.443621 GGAGCCTTAGAATGTTACTCCAC 58.556 47.826 0.00 0.00 41.50 4.02
202 213 3.132289 CGGAGCCTTAGAATGTTACTCCA 59.868 47.826 0.00 0.00 41.87 3.86
210 221 1.136305 TCCGAACGGAGCCTTAGAATG 59.864 52.381 12.04 0.00 39.76 2.67
212 223 2.965805 TCCGAACGGAGCCTTAGAA 58.034 52.632 12.04 0.00 39.76 2.10
232 249 8.646004 TGGGACAAATTCACTTTCAATATCAAA 58.354 29.630 0.00 0.00 31.92 2.69
252 278 4.726317 TCTGGGAGATTTGATATTGGGACA 59.274 41.667 0.00 0.00 0.00 4.02
285 311 9.950680 GAGTTCAGTTTCAGTTTCAATATCAAA 57.049 29.630 0.00 0.00 0.00 2.69
286 312 9.342308 AGAGTTCAGTTTCAGTTTCAATATCAA 57.658 29.630 0.00 0.00 0.00 2.57
287 313 8.777413 CAGAGTTCAGTTTCAGTTTCAATATCA 58.223 33.333 0.00 0.00 0.00 2.15
288 314 8.233190 CCAGAGTTCAGTTTCAGTTTCAATATC 58.767 37.037 0.00 0.00 0.00 1.63
289 315 7.721399 ACCAGAGTTCAGTTTCAGTTTCAATAT 59.279 33.333 0.00 0.00 0.00 1.28
290 316 7.012327 CACCAGAGTTCAGTTTCAGTTTCAATA 59.988 37.037 0.00 0.00 0.00 1.90
291 317 5.888161 ACCAGAGTTCAGTTTCAGTTTCAAT 59.112 36.000 0.00 0.00 0.00 2.57
298 324 4.201950 CCAAACACCAGAGTTCAGTTTCAG 60.202 45.833 0.00 0.00 30.68 3.02
303 329 3.117888 ACATCCAAACACCAGAGTTCAGT 60.118 43.478 0.00 0.00 0.00 3.41
309 335 4.136796 TCTTGAACATCCAAACACCAGAG 58.863 43.478 0.00 0.00 0.00 3.35
311 337 4.339247 AGTTCTTGAACATCCAAACACCAG 59.661 41.667 14.80 0.00 0.00 4.00
314 340 5.163663 TGTCAGTTCTTGAACATCCAAACAC 60.164 40.000 14.80 1.96 37.61 3.32
333 361 4.999311 TCTCATGTGAATTCCAAGTGTCAG 59.001 41.667 2.27 0.00 0.00 3.51
363 391 6.761714 AGTACAATGTTCATCCTATTCCGAAC 59.238 38.462 0.00 0.00 38.55 3.95
367 395 8.506168 TCAAAGTACAATGTTCATCCTATTCC 57.494 34.615 0.00 0.00 0.00 3.01
442 560 9.508642 TTGTTGTGTTCTTGATGTATATAACCA 57.491 29.630 0.00 0.00 0.00 3.67
446 564 8.664798 GCTGTTGTTGTGTTCTTGATGTATATA 58.335 33.333 0.00 0.00 0.00 0.86
447 565 7.174772 TGCTGTTGTTGTGTTCTTGATGTATAT 59.825 33.333 0.00 0.00 0.00 0.86
452 734 3.792956 GTGCTGTTGTTGTGTTCTTGATG 59.207 43.478 0.00 0.00 0.00 3.07
468 750 2.742053 CCGCTGTTTGTATAAGTGCTGT 59.258 45.455 0.00 0.00 0.00 4.40
477 759 4.447290 TGTATATGTGCCGCTGTTTGTAT 58.553 39.130 0.00 0.00 0.00 2.29
484 766 4.614555 TTTCTTTGTATATGTGCCGCTG 57.385 40.909 0.00 0.00 0.00 5.18
486 768 5.157781 TGTTTTTCTTTGTATATGTGCCGC 58.842 37.500 0.00 0.00 0.00 6.53
487 769 5.286082 GCTGTTTTTCTTTGTATATGTGCCG 59.714 40.000 0.00 0.00 0.00 5.69
488 770 5.286082 CGCTGTTTTTCTTTGTATATGTGCC 59.714 40.000 0.00 0.00 0.00 5.01
505 788 2.811431 TGCTATTGTACAAGCGCTGTTT 59.189 40.909 23.84 0.00 41.77 2.83
640 948 1.534235 AACCACGACCAGAGAGCCT 60.534 57.895 0.00 0.00 0.00 4.58
645 953 2.738521 CGGCAACCACGACCAGAG 60.739 66.667 0.00 0.00 0.00 3.35
646 954 3.220999 CTCGGCAACCACGACCAGA 62.221 63.158 0.00 0.00 36.25 3.86
647 955 2.738521 CTCGGCAACCACGACCAG 60.739 66.667 0.00 0.00 36.25 4.00
648 956 4.980805 GCTCGGCAACCACGACCA 62.981 66.667 0.00 0.00 36.25 4.02
724 1041 2.736826 CCCGCCTTTCTCCCTCTCC 61.737 68.421 0.00 0.00 0.00 3.71
762 1083 1.692042 CAGGTCAGCCTCCCCATCT 60.692 63.158 0.00 0.00 44.97 2.90
833 1164 1.871039 TCCCGAAAAACAGAAGCGAAG 59.129 47.619 0.00 0.00 0.00 3.79
873 1205 7.921041 TCTAGAAGATCCTCCACATATTTGT 57.079 36.000 0.00 0.00 36.15 2.83
989 1321 1.153509 GAATACGGGTCGGTGGTGG 60.154 63.158 0.00 0.00 0.00 4.61
990 1322 0.248289 AAGAATACGGGTCGGTGGTG 59.752 55.000 0.00 0.00 0.00 4.17
991 1323 0.533951 GAAGAATACGGGTCGGTGGT 59.466 55.000 0.00 0.00 0.00 4.16
997 1329 0.388294 CTCGGGGAAGAATACGGGTC 59.612 60.000 0.00 0.00 0.00 4.46
1140 1472 2.750637 TCGGCCTCGGAGTCTGAC 60.751 66.667 0.00 0.00 36.95 3.51
1543 1904 2.992543 GCTCTCACAACTCACAGTGATC 59.007 50.000 2.97 0.00 43.18 2.92
1567 1928 2.672961 TCAGTACAAAGGCGGATCAG 57.327 50.000 0.00 0.00 0.00 2.90
1573 1934 2.489971 TGTTCCTTCAGTACAAAGGCG 58.510 47.619 17.87 1.68 42.57 5.52
1599 1960 5.899120 TTCTACTGGATCTATGGCGATAC 57.101 43.478 0.00 0.00 0.00 2.24
1601 1962 5.728471 CAATTCTACTGGATCTATGGCGAT 58.272 41.667 0.00 0.00 0.00 4.58
1648 2010 3.219117 CGATGATCTGCGCACGAG 58.781 61.111 5.66 0.00 0.00 4.18
1684 2048 1.299541 CAAGAACAGCGTCCAGTGTT 58.700 50.000 0.00 0.00 39.62 3.32
1693 2057 4.685169 AAATCCATACACAAGAACAGCG 57.315 40.909 0.00 0.00 0.00 5.18
1745 2110 6.180472 GGATTTCTCCACAATCAAGGTAAGA 58.820 40.000 0.00 0.00 41.64 2.10
1749 2114 3.009033 TCGGATTTCTCCACAATCAAGGT 59.991 43.478 0.00 0.00 42.19 3.50
1750 2115 3.609853 TCGGATTTCTCCACAATCAAGG 58.390 45.455 0.00 0.00 42.19 3.61
1778 2146 2.814341 CACGGAGAGCAGCAGCAG 60.814 66.667 3.17 0.00 45.49 4.24
1803 2171 1.399087 CCGCACAGATATCGTCGAGAG 60.399 57.143 0.00 0.00 0.00 3.20
1804 2172 0.586802 CCGCACAGATATCGTCGAGA 59.413 55.000 0.00 0.00 0.00 4.04
1819 2187 0.390998 TGATCGCATTTCTGACCGCA 60.391 50.000 0.00 0.00 0.00 5.69
1820 2188 0.726827 TTGATCGCATTTCTGACCGC 59.273 50.000 0.00 0.00 0.00 5.68
1871 2239 4.317769 GCACAGACAAATTAAACGTTTGCC 60.318 41.667 23.46 0.00 39.55 4.52
1879 2247 5.606348 AACAAGGGCACAGACAAATTAAA 57.394 34.783 0.00 0.00 0.00 1.52
1889 2257 1.108727 TCTGGCAAACAAGGGCACAG 61.109 55.000 0.00 0.00 36.73 3.66
1905 2273 7.439157 TGTTCAGAGTTTGTTCCATATTCTG 57.561 36.000 0.00 0.00 33.26 3.02
1963 2358 5.882557 ACCAATTAGATGATCACTTTTCGCT 59.117 36.000 0.00 0.00 0.00 4.93
2020 2468 3.751621 CTGTTTTTCTGATGATGCGGAC 58.248 45.455 0.00 0.00 0.00 4.79
2032 2480 4.394920 TGTTCGAAAGAGTGCTGTTTTTCT 59.605 37.500 0.00 0.00 43.69 2.52
2033 2481 4.495828 GTGTTCGAAAGAGTGCTGTTTTTC 59.504 41.667 0.00 0.00 43.69 2.29
2073 2521 2.262915 CTGTGGAGGAGTGGCGAC 59.737 66.667 0.00 0.00 0.00 5.19
2136 2588 7.500992 TCTGGGATAGTACAGAGCTAAATTTG 58.499 38.462 0.00 0.00 38.71 2.32
2175 2640 2.238646 AGCTATTCCATTCACCCGTCAA 59.761 45.455 0.00 0.00 0.00 3.18
2209 2674 5.939764 ATACTCACTTGCCTGTCTCAATA 57.060 39.130 0.00 0.00 0.00 1.90
2213 2678 6.642707 ACTATATACTCACTTGCCTGTCTC 57.357 41.667 0.00 0.00 0.00 3.36
2226 2691 7.333423 TGTTGTGTTCCAGCAAACTATATACTC 59.667 37.037 0.00 0.00 30.61 2.59
2228 2693 7.372451 TGTTGTGTTCCAGCAAACTATATAC 57.628 36.000 0.00 0.00 30.61 1.47
2234 2731 3.023119 TGATGTTGTGTTCCAGCAAACT 58.977 40.909 0.00 0.00 37.84 2.66
2260 2757 2.435372 TGCAGGTCTTGAGGTTTTGT 57.565 45.000 0.00 0.00 0.00 2.83
2269 2771 6.258230 TGTCTGAATTTTATGCAGGTCTTG 57.742 37.500 0.00 0.00 0.00 3.02
2302 2840 2.866762 GCCTCAACTTCCTATGCTTACG 59.133 50.000 0.00 0.00 0.00 3.18
2307 2845 2.128771 TTGGCCTCAACTTCCTATGC 57.871 50.000 3.32 0.00 0.00 3.14
2393 3457 7.570161 ACAGTTTCTTTTATCGGTAGAAAACG 58.430 34.615 0.00 0.00 39.01 3.60
2399 3463 7.838498 CCGATTACAGTTTCTTTTATCGGTAG 58.162 38.462 11.34 0.00 44.74 3.18
2400 3464 7.760131 CCGATTACAGTTTCTTTTATCGGTA 57.240 36.000 11.34 0.00 44.74 4.02
2401 3465 6.657836 CCGATTACAGTTTCTTTTATCGGT 57.342 37.500 11.34 0.00 44.74 4.69
2403 3467 7.285783 TGTCCGATTACAGTTTCTTTTATCG 57.714 36.000 0.00 0.00 34.74 2.92
2420 3486 7.603784 TGATTCATCGAATTCATATTGTCCGAT 59.396 33.333 6.22 0.00 35.95 4.18
2423 3489 7.020010 GCTGATTCATCGAATTCATATTGTCC 58.980 38.462 6.22 0.00 31.89 4.02
2429 3495 9.358872 GTGTATAGCTGATTCATCGAATTCATA 57.641 33.333 6.22 0.00 31.89 2.15
2433 3499 6.986231 TGTGTGTATAGCTGATTCATCGAATT 59.014 34.615 0.00 0.00 31.89 2.17
2459 3526 5.105187 TGACAGATCGAAAGGATGAACTCAT 60.105 40.000 0.00 0.00 39.70 2.90
2480 3547 4.959596 ACAAGATGATGCACAATCTGAC 57.040 40.909 12.48 0.00 36.15 3.51
2484 3551 4.707030 TGGAACAAGATGATGCACAATC 57.293 40.909 0.00 0.00 31.92 2.67
2517 3584 5.036090 CGCAATTAGCTATGCATTGTTCAA 58.964 37.500 17.24 0.00 42.68 2.69
2522 3589 3.002708 TGCGCAATTAGCTATGCATTG 57.997 42.857 8.16 14.02 42.68 2.82
2539 3608 2.158900 AGGGTTGGTAGAAGATCATGCG 60.159 50.000 0.00 0.00 0.00 4.73
2551 3620 1.003464 GCTTCGGGTTAAGGGTTGGTA 59.997 52.381 0.00 0.00 0.00 3.25
2552 3621 0.251033 GCTTCGGGTTAAGGGTTGGT 60.251 55.000 0.00 0.00 0.00 3.67
2561 3634 4.546829 AAGATGTTAGTGCTTCGGGTTA 57.453 40.909 0.00 0.00 0.00 2.85



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

AutoCloner maintained by Alex Coulton.