Multiple sequence alignment - TraesCS6B01G187400

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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 TraesCS6B01G187400 chr6B 100.000 2990 0 0 1 2990 213489328 213486339 0.000000e+00 5522.0
1 TraesCS6B01G187400 chr6B 94.516 1477 59 11 747 2203 212159940 212158466 0.000000e+00 2259.0
2 TraesCS6B01G187400 chr6B 82.759 116 15 3 566 680 212160056 212159945 6.820000e-17 99.0
3 TraesCS6B01G187400 chr6D 93.796 1644 64 15 585 2194 121580881 121579242 0.000000e+00 2436.0
4 TraesCS6B01G187400 chr6D 92.412 1700 76 22 540 2202 121064026 121065709 0.000000e+00 2375.0
5 TraesCS6B01G187400 chr6D 95.552 1349 48 4 748 2089 121225298 121226641 0.000000e+00 2148.0
6 TraesCS6B01G187400 chr6D 90.286 525 26 6 2489 2989 121261333 121261856 0.000000e+00 664.0
7 TraesCS6B01G187400 chr6D 92.584 445 21 5 44 484 121585273 121584837 1.960000e-176 628.0
8 TraesCS6B01G187400 chr6D 88.095 294 22 4 2342 2632 121066132 121066415 1.330000e-88 337.0
9 TraesCS6B01G187400 chr6D 94.783 115 5 1 2333 2446 121261220 121261334 8.520000e-41 178.0
10 TraesCS6B01G187400 chr6D 91.406 128 4 4 589 715 121220502 121220623 5.130000e-38 169.0
11 TraesCS6B01G187400 chr6D 97.059 68 2 0 2139 2206 121261056 121261123 6.770000e-22 115.0
12 TraesCS6B01G187400 chr6D 94.872 39 2 0 2087 2125 121226661 121226699 8.950000e-06 62.1
13 TraesCS6B01G187400 chr6A 91.908 1693 73 24 758 2397 158318094 158316413 0.000000e+00 2309.0
14 TraesCS6B01G187400 chr6A 95.827 1270 52 1 747 2016 162891716 162890448 0.000000e+00 2050.0
15 TraesCS6B01G187400 chr6A 94.800 827 43 0 737 1563 158455196 158454370 0.000000e+00 1290.0
16 TraesCS6B01G187400 chr6A 85.526 836 111 8 997 1827 60973177 60972347 0.000000e+00 865.0
17 TraesCS6B01G187400 chr6A 90.881 658 36 13 1558 2206 158449078 158448436 0.000000e+00 861.0
18 TraesCS6B01G187400 chr6A 83.973 730 78 22 2267 2989 162851264 162850567 0.000000e+00 664.0
19 TraesCS6B01G187400 chr6A 92.466 438 26 4 1 434 162907963 162907529 1.180000e-173 619.0
20 TraesCS6B01G187400 chr6A 84.691 307 21 10 2338 2632 158435162 158434870 1.750000e-72 283.0
21 TraesCS6B01G187400 chr6A 81.707 246 13 10 1991 2207 162890443 162890201 3.060000e-40 176.0
22 TraesCS6B01G187400 chr6A 82.524 206 23 8 540 744 162892022 162891829 5.130000e-38 169.0
23 TraesCS6B01G187400 chr6A 86.813 91 8 3 2266 2352 158448437 158448347 6.820000e-17 99.0
24 TraesCS6B01G187400 chr6A 81.197 117 18 2 2271 2383 535426011 535426127 1.140000e-14 91.6
25 TraesCS6B01G187400 chr4D 82.755 1009 149 18 997 1991 323097953 323096956 0.000000e+00 876.0
26 TraesCS6B01G187400 chr4D 96.000 50 2 0 2508 2557 394139611 394139562 6.870000e-12 82.4
27 TraesCS6B01G187400 chr1D 89.462 465 40 7 1 457 323577 324040 2.000000e-161 579.0
28 TraesCS6B01G187400 chr1D 90.533 169 15 1 286 453 212282149 212281981 3.880000e-54 222.0
29 TraesCS6B01G187400 chr1D 84.286 70 2 4 478 538 175771072 175771141 3.220000e-05 60.2
30 TraesCS6B01G187400 chr7A 87.169 491 53 8 1 484 455612775 455613262 1.570000e-152 549.0
31 TraesCS6B01G187400 chr3A 83.090 343 52 5 1 338 320610310 320610651 1.040000e-79 307.0
32 TraesCS6B01G187400 chr3A 82.286 350 55 6 1 345 320602313 320602660 2.250000e-76 296.0
33 TraesCS6B01G187400 chr3A 80.720 389 63 11 1 380 137514236 137513851 2.920000e-75 292.0
34 TraesCS6B01G187400 chr2B 80.585 376 63 9 1 367 335536883 335536509 6.310000e-72 281.0
35 TraesCS6B01G187400 chr2B 76.923 169 18 13 2439 2592 361574105 361573943 3.200000e-10 76.8
36 TraesCS6B01G187400 chr4A 79.434 389 69 10 1 380 435713205 435712819 6.360000e-67 265.0
37 TraesCS6B01G187400 chr4A 85.714 203 22 6 286 484 256366598 256366399 1.090000e-49 207.0
38 TraesCS6B01G187400 chr5D 90.533 169 15 1 286 453 86822073 86821905 3.880000e-54 222.0
39 TraesCS6B01G187400 chr5D 96.000 50 2 0 2508 2557 82322101 82322150 6.870000e-12 82.4
40 TraesCS6B01G187400 chr5D 94.000 50 3 0 2508 2557 346639855 346639806 3.200000e-10 76.8
41 TraesCS6B01G187400 chr1A 85.222 203 23 6 286 484 441049542 441049343 5.050000e-48 202.0
42 TraesCS6B01G187400 chr1A 82.653 98 13 2 2262 2355 507973418 507973515 1.910000e-12 84.2
43 TraesCS6B01G187400 chr1B 83.673 98 12 3 2262 2355 554512352 554512449 4.110000e-14 89.8
44 TraesCS6B01G187400 chr2D 83.333 102 6 4 2467 2557 14772020 14772121 1.910000e-12 84.2
45 TraesCS6B01G187400 chr3B 97.778 45 1 0 2205 2249 581090092 581090048 8.890000e-11 78.7
46 TraesCS6B01G187400 chr5A 94.000 50 3 0 2508 2557 51689062 51689013 3.200000e-10 76.8


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 TraesCS6B01G187400 chr6B 213486339 213489328 2989 True 5522.000000 5522 100.000000 1 2990 1 chr6B.!!$R1 2989
1 TraesCS6B01G187400 chr6B 212158466 212160056 1590 True 1179.000000 2259 88.637500 566 2203 2 chr6B.!!$R2 1637
2 TraesCS6B01G187400 chr6D 121579242 121585273 6031 True 1532.000000 2436 93.190000 44 2194 2 chr6D.!!$R1 2150
3 TraesCS6B01G187400 chr6D 121064026 121066415 2389 False 1356.000000 2375 90.253500 540 2632 2 chr6D.!!$F2 2092
4 TraesCS6B01G187400 chr6D 121225298 121226699 1401 False 1105.050000 2148 95.212000 748 2125 2 chr6D.!!$F3 1377
5 TraesCS6B01G187400 chr6D 121261056 121261856 800 False 319.000000 664 94.042667 2139 2989 3 chr6D.!!$F4 850
6 TraesCS6B01G187400 chr6A 158316413 158318094 1681 True 2309.000000 2309 91.908000 758 2397 1 chr6A.!!$R2 1639
7 TraesCS6B01G187400 chr6A 158454370 158455196 826 True 1290.000000 1290 94.800000 737 1563 1 chr6A.!!$R4 826
8 TraesCS6B01G187400 chr6A 60972347 60973177 830 True 865.000000 865 85.526000 997 1827 1 chr6A.!!$R1 830
9 TraesCS6B01G187400 chr6A 162890201 162892022 1821 True 798.333333 2050 86.686000 540 2207 3 chr6A.!!$R8 1667
10 TraesCS6B01G187400 chr6A 162850567 162851264 697 True 664.000000 664 83.973000 2267 2989 1 chr6A.!!$R5 722
11 TraesCS6B01G187400 chr6A 158448347 158449078 731 True 480.000000 861 88.847000 1558 2352 2 chr6A.!!$R7 794
12 TraesCS6B01G187400 chr4D 323096956 323097953 997 True 876.000000 876 82.755000 997 1991 1 chr4D.!!$R1 994

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
467 472 0.250513 GGCCTGCTAAGCTACAGTGT 59.749 55.0 0.0 0.0 31.76 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 6314 0.530744 TCCGTCTCGCAATGTTAGCT 59.469 50.0 0.0 0.0 0.0 3.32 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
22 23 4.635223 TCATGCTACAGTAATCTCATGCC 58.365 43.478 0.00 0.00 33.39 4.40
23 24 4.346127 TCATGCTACAGTAATCTCATGCCT 59.654 41.667 0.00 0.00 33.39 4.75
24 25 5.539955 TCATGCTACAGTAATCTCATGCCTA 59.460 40.000 0.00 0.00 33.39 3.93
25 26 5.869649 TGCTACAGTAATCTCATGCCTAA 57.130 39.130 0.00 0.00 0.00 2.69
26 27 6.425210 TGCTACAGTAATCTCATGCCTAAT 57.575 37.500 0.00 0.00 0.00 1.73
27 28 6.226052 TGCTACAGTAATCTCATGCCTAATG 58.774 40.000 0.00 0.00 37.66 1.90
28 29 6.041979 TGCTACAGTAATCTCATGCCTAATGA 59.958 38.462 0.00 0.00 43.24 2.57
29 30 7.102346 GCTACAGTAATCTCATGCCTAATGAT 58.898 38.462 0.00 0.00 44.40 2.45
30 31 7.064371 GCTACAGTAATCTCATGCCTAATGATG 59.936 40.741 0.00 0.00 44.40 3.07
31 32 7.071069 ACAGTAATCTCATGCCTAATGATGA 57.929 36.000 0.00 0.00 44.40 2.92
32 33 7.687388 ACAGTAATCTCATGCCTAATGATGAT 58.313 34.615 0.00 0.00 44.40 2.45
33 34 8.819845 ACAGTAATCTCATGCCTAATGATGATA 58.180 33.333 0.00 0.00 44.40 2.15
34 35 9.833917 CAGTAATCTCATGCCTAATGATGATAT 57.166 33.333 0.00 0.00 44.40 1.63
35 36 9.833917 AGTAATCTCATGCCTAATGATGATATG 57.166 33.333 0.00 0.00 44.40 1.78
36 37 9.610705 GTAATCTCATGCCTAATGATGATATGT 57.389 33.333 0.00 0.00 44.40 2.29
37 38 8.734218 AATCTCATGCCTAATGATGATATGTC 57.266 34.615 0.00 0.00 44.40 3.06
38 39 7.248743 TCTCATGCCTAATGATGATATGTCA 57.751 36.000 0.00 0.00 44.40 3.58
106 107 8.238481 TCAAATTTAAATTCGAATGCCAAGTC 57.762 30.769 12.25 0.00 0.00 3.01
166 167 8.792633 TGTTCCTTAGGTTGAAAATATTCACTG 58.207 33.333 0.00 0.00 45.01 3.66
232 237 7.630082 TGCCTATGGATATTAAATAGTGGACC 58.370 38.462 0.00 0.00 0.00 4.46
294 299 3.650281 AATGATTTCAATTTGGCCCCC 57.350 42.857 0.00 0.00 0.00 5.40
307 312 1.594021 GCCCCCAACTTTTTGTGCG 60.594 57.895 0.00 0.00 0.00 5.34
316 321 1.550976 ACTTTTTGTGCGACCCCAAAA 59.449 42.857 0.00 0.00 38.42 2.44
327 332 3.800604 GCGACCCCAAAATTTTGTGCTTA 60.801 43.478 25.25 0.00 36.45 3.09
362 367 7.598493 GCCAAGTTTCAGTTATAGCAAAAATCA 59.402 33.333 0.00 0.00 0.00 2.57
389 394 6.632909 TGCTGCATAATCTAATTGCAAAAGT 58.367 32.000 1.71 0.00 44.99 2.66
390 395 6.532302 TGCTGCATAATCTAATTGCAAAAGTG 59.468 34.615 1.71 0.08 44.99 3.16
429 434 8.909423 ACAGGAAATAAAAGGGAAAATATGGA 57.091 30.769 0.00 0.00 0.00 3.41
467 472 0.250513 GGCCTGCTAAGCTACAGTGT 59.749 55.000 0.00 0.00 31.76 3.55
475 480 1.127567 AAGCTACAGTGTGGCCCAGA 61.128 55.000 26.02 0.00 40.93 3.86
491 557 3.814316 GCCCAGACCACCTTGATAAGTTT 60.814 47.826 0.00 0.00 0.00 2.66
494 560 6.007703 CCCAGACCACCTTGATAAGTTTAAA 58.992 40.000 0.00 0.00 0.00 1.52
500 566 9.626045 GACCACCTTGATAAGTTTAAAATGAAG 57.374 33.333 0.00 0.00 0.00 3.02
513 579 2.149973 AATGAAGGATGGTGAAGGCC 57.850 50.000 0.00 0.00 0.00 5.19
541 607 2.283145 AGGCTTGCACTCATCAGTTT 57.717 45.000 0.00 0.00 0.00 2.66
614 4474 9.059260 TCTAATATCGGTATTTTAAAGTTGCCC 57.941 33.333 6.19 0.00 32.84 5.36
827 4797 1.334059 CGTGCACAATCAAAAGCGTCT 60.334 47.619 18.64 0.00 0.00 4.18
835 4806 5.519927 CACAATCAAAAGCGTCTTTTTCCTT 59.480 36.000 12.78 6.38 0.00 3.36
868 4839 4.505972 CGAAATCGCGCACAACAA 57.494 50.000 8.75 0.00 0.00 2.83
879 4858 2.223249 GCGCACAACAAAAGAAGTCTCA 60.223 45.455 0.30 0.00 0.00 3.27
931 4921 2.071540 TCAAAACTCATCGAGCAGCTG 58.928 47.619 10.11 10.11 32.04 4.24
986 4984 1.070289 AGAGTTCTTCCGGTCACCAAC 59.930 52.381 0.00 0.00 0.00 3.77
1275 5273 2.671963 GCCACCTTCGACAACCCC 60.672 66.667 0.00 0.00 0.00 4.95
1332 5330 1.185618 ACGTCAACCTCAGCAGGCTA 61.186 55.000 0.00 0.00 45.05 3.93
1740 5741 1.117150 GCTTCCTGTACCCCATCGTA 58.883 55.000 0.00 0.00 0.00 3.43
2117 6179 6.038936 GTGGAGTTGTGGTGTTAATTTACACT 59.961 38.462 22.82 6.22 45.98 3.55
2120 6183 4.735662 TGTGGTGTTAATTTACACTCGC 57.264 40.909 22.82 19.08 45.98 5.03
2125 6188 5.406175 TGGTGTTAATTTACACTCGCTACAC 59.594 40.000 22.82 8.09 45.98 2.90
2131 6200 3.837213 TTACACTCGCTACACAGTACC 57.163 47.619 0.00 0.00 0.00 3.34
2154 6223 6.106673 CCACTTGTATTTGTACCTGGAGTAG 58.893 44.000 0.00 0.00 0.00 2.57
2159 6228 5.544948 TGTATTTGTACCTGGAGTAGTGGTT 59.455 40.000 0.00 0.00 35.48 3.67
2212 6286 7.229506 AGTGCAATTGCTAAATAATACTCCCTC 59.770 37.037 29.37 0.00 42.66 4.30
2213 6287 6.490040 TGCAATTGCTAAATAATACTCCCTCC 59.510 38.462 29.37 0.00 42.66 4.30
2220 6294 2.077687 TAATACTCCCTCCGTCCCAC 57.922 55.000 0.00 0.00 0.00 4.61
2223 6297 0.901580 TACTCCCTCCGTCCCACAAC 60.902 60.000 0.00 0.00 0.00 3.32
2238 6312 5.684184 GTCCCACAACATAAGAACGTTTTTC 59.316 40.000 7.42 0.00 0.00 2.29
2240 6314 6.037098 CCCACAACATAAGAACGTTTTTCAA 58.963 36.000 7.42 0.00 0.00 2.69
2241 6315 6.198216 CCCACAACATAAGAACGTTTTTCAAG 59.802 38.462 7.42 2.32 0.00 3.02
2245 6319 8.185505 ACAACATAAGAACGTTTTTCAAGCTAA 58.814 29.630 7.42 0.00 0.00 3.09
2246 6320 8.469125 CAACATAAGAACGTTTTTCAAGCTAAC 58.531 33.333 7.42 0.00 0.00 2.34
2249 6323 9.180678 CATAAGAACGTTTTTCAAGCTAACATT 57.819 29.630 7.42 0.00 0.00 2.71
2250 6324 7.449934 AAGAACGTTTTTCAAGCTAACATTG 57.550 32.000 0.46 0.00 0.00 2.82
2251 6325 5.458779 AGAACGTTTTTCAAGCTAACATTGC 59.541 36.000 0.46 0.00 0.00 3.56
2252 6326 3.728718 ACGTTTTTCAAGCTAACATTGCG 59.271 39.130 0.00 0.00 35.28 4.85
2273 6367 2.427812 GAGACGGAGGGAGTAAGAAAGG 59.572 54.545 0.00 0.00 0.00 3.11
2280 6374 1.351350 GGGAGTAAGAAAGGGCAGTGT 59.649 52.381 0.00 0.00 0.00 3.55
2285 6379 5.242795 AGTAAGAAAGGGCAGTGTTATGT 57.757 39.130 0.00 0.00 0.00 2.29
2301 6395 5.745294 GTGTTATGTAGCCGACGATTCTTTA 59.255 40.000 0.00 0.00 0.00 1.85
2347 6716 8.438676 AATCACCGTTAGATTAAATTCCTCTG 57.561 34.615 0.00 0.00 34.14 3.35
2427 6796 4.931661 CGAAGCTACCATTAACTCCCTA 57.068 45.455 0.00 0.00 0.00 3.53
2592 7007 5.271598 TCCAAGCATCCTACAATTTGGAAT 58.728 37.500 0.78 0.00 40.61 3.01
2619 7034 6.636705 AGTTGATAATTAGTAAGCCGACACA 58.363 36.000 0.00 0.00 0.00 3.72
2652 7091 5.393243 GCAAGTATATAGTAAGAGGCCTCCG 60.393 48.000 29.54 0.00 0.00 4.63
2671 7110 2.738480 GTGCGTACACCCCAGACA 59.262 61.111 0.00 0.00 41.21 3.41
2672 7111 1.295423 GTGCGTACACCCCAGACAT 59.705 57.895 0.00 0.00 41.21 3.06
2692 7131 0.904649 TGAGCCATTCACACCTCGAT 59.095 50.000 0.00 0.00 0.00 3.59
2730 7169 2.044946 GCCACTCCCGCCTCAAAT 60.045 61.111 0.00 0.00 0.00 2.32
2791 7230 4.862902 GCACTAGGCATCTCTGATTCTA 57.137 45.455 0.00 0.00 43.97 2.10
2874 7314 0.465824 AGCAGCATCTGAGGCCATTC 60.466 55.000 11.08 0.00 32.44 2.67
2876 7316 1.147824 AGCATCTGAGGCCATTCCG 59.852 57.895 11.08 0.00 40.77 4.30
2924 7364 0.549950 ATCTTGGGAGGGCTGTGATG 59.450 55.000 0.00 0.00 0.00 3.07
2937 7377 1.880340 GTGATGAGCGGAAGAGCGG 60.880 63.158 0.00 0.00 43.00 5.52
2989 7429 8.921670 GTGTTGGTGTGGATTTATTTTATGAAC 58.078 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.639334 AGGCATGAGATTACTGTAGCATG 58.361 43.478 0.00 13.14 36.95 4.06
2 3 4.970860 AGGCATGAGATTACTGTAGCAT 57.029 40.909 0.00 0.00 0.00 3.79
3 4 5.869649 TTAGGCATGAGATTACTGTAGCA 57.130 39.130 0.00 0.00 0.00 3.49
4 5 6.459066 TCATTAGGCATGAGATTACTGTAGC 58.541 40.000 0.00 0.00 36.94 3.58
5 6 8.309656 TCATCATTAGGCATGAGATTACTGTAG 58.690 37.037 0.00 0.00 45.52 2.74
6 7 8.193953 TCATCATTAGGCATGAGATTACTGTA 57.806 34.615 0.00 0.00 45.52 2.74
7 8 7.071069 TCATCATTAGGCATGAGATTACTGT 57.929 36.000 0.00 0.00 45.52 3.55
8 9 9.833917 ATATCATCATTAGGCATGAGATTACTG 57.166 33.333 0.00 0.00 45.52 2.74
9 10 9.833917 CATATCATCATTAGGCATGAGATTACT 57.166 33.333 0.00 0.00 45.52 2.24
10 11 9.610705 ACATATCATCATTAGGCATGAGATTAC 57.389 33.333 0.00 0.00 45.52 1.89
11 12 9.828039 GACATATCATCATTAGGCATGAGATTA 57.172 33.333 0.00 0.00 45.52 1.75
12 13 8.326529 TGACATATCATCATTAGGCATGAGATT 58.673 33.333 0.00 0.00 45.52 2.40
13 14 7.858498 TGACATATCATCATTAGGCATGAGAT 58.142 34.615 0.00 0.00 45.52 2.75
14 15 7.248743 TGACATATCATCATTAGGCATGAGA 57.751 36.000 0.00 0.00 45.52 3.27
88 89 4.250464 ACTCGACTTGGCATTCGAATTTA 58.750 39.130 18.73 0.00 43.35 1.40
90 91 2.699954 ACTCGACTTGGCATTCGAATT 58.300 42.857 18.73 9.12 43.35 2.17
91 92 2.386661 ACTCGACTTGGCATTCGAAT 57.613 45.000 18.73 4.39 43.35 3.34
92 93 2.163818 AACTCGACTTGGCATTCGAA 57.836 45.000 18.73 0.00 43.35 3.71
93 94 3.520290 ATAACTCGACTTGGCATTCGA 57.480 42.857 17.61 17.61 41.83 3.71
94 95 5.907197 ATTATAACTCGACTTGGCATTCG 57.093 39.130 11.65 11.65 36.55 3.34
209 214 9.046846 TCTGGTCCACTATTTAATATCCATAGG 57.953 37.037 0.00 0.00 0.00 2.57
215 220 6.651225 GTGCCTCTGGTCCACTATTTAATATC 59.349 42.308 0.00 0.00 0.00 1.63
232 237 1.745489 GGCTAAACGGGTGCCTCTG 60.745 63.158 0.00 0.00 43.05 3.35
294 299 0.457851 TGGGGTCGCACAAAAAGTTG 59.542 50.000 0.00 0.00 40.84 3.16
316 321 7.661027 ACTTGGCACATAAATTAAGCACAAAAT 59.339 29.630 0.00 0.00 39.30 1.82
380 385 3.902881 ATTTCCACCACACTTTTGCAA 57.097 38.095 0.00 0.00 0.00 4.08
389 394 9.535170 TTTATTTCCTGTAATATTTCCACCACA 57.465 29.630 0.00 0.00 0.00 4.17
429 434 2.028020 GCCTAAGTGCACAGTAGGTCTT 60.028 50.000 31.54 15.52 0.00 3.01
467 472 0.548926 TATCAAGGTGGTCTGGGCCA 60.549 55.000 5.85 5.85 35.93 5.36
475 480 8.585018 CCTTCATTTTAAACTTATCAAGGTGGT 58.415 33.333 0.00 0.00 0.00 4.16
479 545 9.807649 CCATCCTTCATTTTAAACTTATCAAGG 57.192 33.333 0.00 0.00 0.00 3.61
491 557 4.023291 GGCCTTCACCATCCTTCATTTTA 58.977 43.478 0.00 0.00 0.00 1.52
494 560 1.642762 AGGCCTTCACCATCCTTCATT 59.357 47.619 0.00 0.00 0.00 2.57
500 566 2.239907 AGAGTAAAGGCCTTCACCATCC 59.760 50.000 20.79 4.24 0.00 3.51
513 579 4.193826 TGAGTGCAAGCCTAGAGTAAAG 57.806 45.455 0.00 0.00 0.00 1.85
608 4467 0.257039 ACATGGATGAGGAGGGCAAC 59.743 55.000 0.00 0.00 0.00 4.17
614 4474 3.539604 GTCTCCAAACATGGATGAGGAG 58.460 50.000 15.32 15.32 41.51 3.69
645 4505 1.346479 TTCGTCCAGTTTGGGTCCCA 61.346 55.000 6.47 6.47 38.32 4.37
692 4552 6.129009 GCTATGCTGAAGTTGACAACATTTTG 60.129 38.462 20.08 7.38 38.83 2.44
693 4553 5.922544 GCTATGCTGAAGTTGACAACATTTT 59.077 36.000 20.08 6.08 0.00 1.82
694 4554 5.464168 GCTATGCTGAAGTTGACAACATTT 58.536 37.500 20.08 6.80 0.00 2.32
695 4555 4.378770 CGCTATGCTGAAGTTGACAACATT 60.379 41.667 20.08 11.09 0.00 2.71
801 4770 3.311106 CTTTTGATTGTGCACGCTTCAT 58.689 40.909 13.13 0.00 0.00 2.57
827 4797 1.256812 GGCCTGCAGCTAAGGAAAAA 58.743 50.000 16.98 0.00 43.05 1.94
851 4822 1.116436 TTTTGTTGTGCGCGATTTCG 58.884 45.000 12.10 0.00 43.27 3.46
868 4839 4.899352 ATAGCAGTGGTGAGACTTCTTT 57.101 40.909 4.76 0.00 0.00 2.52
879 4858 3.437213 TGGGCGTATATATAGCAGTGGT 58.563 45.455 12.99 0.00 0.00 4.16
931 4921 1.298157 TGTGTGCCGCTGAATGCTAC 61.298 55.000 0.00 0.00 40.11 3.58
986 4984 5.221481 TGGGCATCCATGTTATAATTGCTTG 60.221 40.000 0.00 0.00 38.32 4.01
1332 5330 2.115911 CGCCAGGAGCTCGTACTCT 61.116 63.158 8.91 0.00 40.39 3.24
1740 5741 1.381872 CCTGATGTCCTCCGGGTCT 60.382 63.158 0.00 0.00 0.00 3.85
1794 5795 3.260380 CAGAGTTGATCACCTCACCTTCT 59.740 47.826 20.90 2.75 32.17 2.85
1906 5913 2.124983 GGAGAAGCTGCATGGCGA 60.125 61.111 1.02 0.00 37.29 5.54
2117 6179 1.958579 ACAAGTGGTACTGTGTAGCGA 59.041 47.619 0.00 0.00 0.00 4.93
2120 6183 7.330208 GGTACAAATACAAGTGGTACTGTGTAG 59.670 40.741 0.00 0.00 34.71 2.74
2125 6188 5.642063 CCAGGTACAAATACAAGTGGTACTG 59.358 44.000 0.00 0.00 35.75 2.74
2131 6200 6.590292 CACTACTCCAGGTACAAATACAAGTG 59.410 42.308 0.00 0.00 32.40 3.16
2154 6223 8.564574 TCACACATTATTTCTCTTACAAACCAC 58.435 33.333 0.00 0.00 0.00 4.16
2212 6286 1.730064 CGTTCTTATGTTGTGGGACGG 59.270 52.381 0.00 0.00 0.00 4.79
2213 6287 2.409975 ACGTTCTTATGTTGTGGGACG 58.590 47.619 0.00 0.00 0.00 4.79
2220 6294 8.469125 GTTAGCTTGAAAAACGTTCTTATGTTG 58.531 33.333 0.00 0.00 33.82 3.33
2223 6297 8.728088 ATGTTAGCTTGAAAAACGTTCTTATG 57.272 30.769 0.00 0.00 0.00 1.90
2238 6312 1.061131 CCGTCTCGCAATGTTAGCTTG 59.939 52.381 0.00 0.00 0.00 4.01
2240 6314 0.530744 TCCGTCTCGCAATGTTAGCT 59.469 50.000 0.00 0.00 0.00 3.32
2241 6315 0.924090 CTCCGTCTCGCAATGTTAGC 59.076 55.000 0.00 0.00 0.00 3.09
2245 6319 1.949847 CTCCCTCCGTCTCGCAATGT 61.950 60.000 0.00 0.00 0.00 2.71
2246 6320 1.227089 CTCCCTCCGTCTCGCAATG 60.227 63.158 0.00 0.00 0.00 2.82
2249 6323 1.001764 TTACTCCCTCCGTCTCGCA 60.002 57.895 0.00 0.00 0.00 5.10
2250 6324 0.747283 TCTTACTCCCTCCGTCTCGC 60.747 60.000 0.00 0.00 0.00 5.03
2251 6325 1.747709 TTCTTACTCCCTCCGTCTCG 58.252 55.000 0.00 0.00 0.00 4.04
2252 6326 2.427812 CCTTTCTTACTCCCTCCGTCTC 59.572 54.545 0.00 0.00 0.00 3.36
2273 6367 1.287425 GTCGGCTACATAACACTGCC 58.713 55.000 0.00 0.00 40.14 4.85
2280 6374 4.980434 GCTAAAGAATCGTCGGCTACATAA 59.020 41.667 0.00 0.00 0.00 1.90
2285 6379 1.268896 CGGCTAAAGAATCGTCGGCTA 60.269 52.381 0.00 0.00 0.00 3.93
2301 6395 1.139734 CTAGTGTCGTGCATCGGCT 59.860 57.895 13.00 9.35 45.15 5.52
2347 6716 7.977853 TGGTAGGATCTCACGTTCTTTATTTAC 59.022 37.037 0.00 0.00 0.00 2.01
2355 6724 2.619177 CGATGGTAGGATCTCACGTTCT 59.381 50.000 0.00 0.00 0.00 3.01
2427 6796 5.385198 TGGAGATAGCAAACTGGAGTTTTT 58.615 37.500 1.90 0.00 45.07 1.94
2559 6974 7.243604 TGTAGGATGCTTGGAAATTGAAATT 57.756 32.000 0.00 0.00 0.00 1.82
2564 6979 6.314400 CCAAATTGTAGGATGCTTGGAAATTG 59.686 38.462 0.00 0.00 36.26 2.32
2592 7007 9.090692 GTGTCGGCTTACTAATTATCAACTTTA 57.909 33.333 0.00 0.00 0.00 1.85
2643 7082 3.138798 TACGCACTCGGAGGCCTC 61.139 66.667 25.59 25.59 40.69 4.70
2652 7091 1.080025 GTCTGGGGTGTACGCACTC 60.080 63.158 8.87 0.00 45.15 3.51
2666 7105 2.163010 GGTGTGAATGGCTCAATGTCTG 59.837 50.000 0.00 0.00 35.22 3.51
2667 7106 2.040813 AGGTGTGAATGGCTCAATGTCT 59.959 45.455 0.00 0.00 35.22 3.41
2668 7107 2.421424 GAGGTGTGAATGGCTCAATGTC 59.579 50.000 0.00 0.00 35.22 3.06
2669 7108 2.440409 GAGGTGTGAATGGCTCAATGT 58.560 47.619 0.00 0.00 35.22 2.71
2670 7109 1.399440 CGAGGTGTGAATGGCTCAATG 59.601 52.381 0.00 0.00 35.22 2.82
2671 7110 1.278985 TCGAGGTGTGAATGGCTCAAT 59.721 47.619 0.00 0.00 35.22 2.57
2672 7111 0.684535 TCGAGGTGTGAATGGCTCAA 59.315 50.000 0.00 0.00 35.22 3.02
2692 7131 2.096980 CGATGGTTCTGCGAGTAGTGTA 59.903 50.000 0.00 0.00 0.00 2.90
2730 7169 1.579964 CTGCAGACGCCTTGCAATGA 61.580 55.000 8.42 0.00 38.15 2.57
2791 7230 4.104261 TGCATCCTCATTGATCTCCAGATT 59.896 41.667 0.00 0.00 34.37 2.40
2852 7291 2.186384 GCCTCAGATGCTGCTCGT 59.814 61.111 0.00 0.00 0.00 4.18
2859 7298 1.895707 CCGGAATGGCCTCAGATGC 60.896 63.158 3.32 0.00 0.00 3.91
2874 7314 3.752796 TCTTACGAAAGATGGCCGG 57.247 52.632 0.00 0.00 36.80 6.13
2924 7364 4.516195 GGGACCGCTCTTCCGCTC 62.516 72.222 0.00 0.00 33.43 5.03
2937 7377 0.030908 CGAAGAGCCTATGACGGGAC 59.969 60.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.