Multiple sequence alignment - TraesCS5B01G233000

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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 TraesCS5B01G233000 chr5B 100.000 3470 0 0 1 3470 411019836 411023305 0.000000e+00 6408.0
1 TraesCS5B01G233000 chr5B 93.220 118 8 0 1355 1472 411021070 411021187 1.280000e-39 174.0
2 TraesCS5B01G233000 chr5D 93.490 3441 126 37 59 3470 350321363 350324734 0.000000e+00 5024.0
3 TraesCS5B01G233000 chr5D 91.525 118 10 0 1355 1472 350322534 350322651 2.770000e-36 163.0
4 TraesCS5B01G233000 chr5D 100.000 37 0 0 1 37 350321329 350321365 6.210000e-08 69.4
5 TraesCS5B01G233000 chr5A 93.899 2426 63 27 668 3078 450735729 450738084 0.000000e+00 3581.0
6 TraesCS5B01G233000 chr5A 90.534 412 19 8 3033 3441 450738077 450738471 8.530000e-146 527.0
7 TraesCS5B01G233000 chr5A 91.525 118 10 0 1355 1472 450736278 450736395 2.770000e-36 163.0
8 TraesCS5B01G233000 chr4A 90.821 621 44 5 2851 3470 592453617 592454225 0.000000e+00 819.0
9 TraesCS5B01G233000 chr4A 90.660 621 45 5 2851 3470 593020473 593021081 0.000000e+00 813.0
10 TraesCS5B01G233000 chr4A 90.499 621 46 5 2851 3470 592731930 592732538 0.000000e+00 808.0
11 TraesCS5B01G233000 chr4A 90.064 624 43 7 2851 3470 591589137 591588529 0.000000e+00 791.0
12 TraesCS5B01G233000 chr4A 90.333 300 21 4 3169 3468 206732704 206732413 1.510000e-103 387.0
13 TraesCS5B01G233000 chr4A 90.099 303 22 3 3166 3468 254436058 254436352 1.510000e-103 387.0
14 TraesCS5B01G233000 chr1A 91.749 303 17 4 3166 3468 591009429 591009135 6.930000e-112 414.0


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 TraesCS5B01G233000 chr5B 411019836 411023305 3469 False 3291.000000 6408 96.610 1 3470 2 chr5B.!!$F1 3469
1 TraesCS5B01G233000 chr5D 350321329 350324734 3405 False 1752.133333 5024 95.005 1 3470 3 chr5D.!!$F1 3469
2 TraesCS5B01G233000 chr5A 450735729 450738471 2742 False 1423.666667 3581 91.986 668 3441 3 chr5A.!!$F1 2773
3 TraesCS5B01G233000 chr4A 592453617 592454225 608 False 819.000000 819 90.821 2851 3470 1 chr4A.!!$F2 619
4 TraesCS5B01G233000 chr4A 593020473 593021081 608 False 813.000000 813 90.660 2851 3470 1 chr4A.!!$F4 619
5 TraesCS5B01G233000 chr4A 592731930 592732538 608 False 808.000000 808 90.499 2851 3470 1 chr4A.!!$F3 619
6 TraesCS5B01G233000 chr4A 591588529 591589137 608 True 791.000000 791 90.064 2851 3470 1 chr4A.!!$R2 619

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
57 58 0.323725 ATTGGTCATCTGGTGCCACC 60.324 55.0 7.01 7.01 39.22 4.61 F
209 213 0.389817 CGCACATCTCAACGGAGGAA 60.390 55.0 0.00 0.00 41.69 3.36 F
300 304 0.535553 TTAAACCGGCCACCACACTC 60.536 55.0 0.00 0.00 0.00 3.51 F
308 312 0.605319 GCCACCACACTCCAATCGAA 60.605 55.0 0.00 0.00 0.00 3.71 F
566 578 0.765510 AGTCAAAAGAGAACGGGCCT 59.234 50.0 0.84 0.00 0.00 5.19 F
570 582 1.061546 AAAAGAGAACGGGCCTGGTA 58.938 50.0 18.00 0.00 0.00 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 1621 2.505405 CTGATGGGCTTGATGATGGAG 58.495 52.381 0.00 0.0 0.00 3.86 R
2157 2200 0.455410 TGCCATTTGCCGCTGTAATC 59.545 50.000 0.00 0.0 40.16 1.75 R
2181 2224 0.482446 TGACAGCCCCAAGTCCAATT 59.518 50.000 0.00 0.0 33.89 2.32 R
2271 2314 1.515020 CTCCTTGGACAGCTCCTCG 59.485 63.158 0.00 0.0 37.48 4.63 R
2384 2427 0.535797 CAGCTGCTGTCTGATCTCCA 59.464 55.000 21.21 0.0 33.54 3.86 R
2756 2799 0.398381 AAAAGGCCCAGCACAAAGGA 60.398 50.000 0.00 0.0 0.00 3.36 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
42 43 1.553706 AGGCAAAGGCTTGAGATTGG 58.446 50.000 0.00 0.00 40.87 3.16
43 44 1.203100 AGGCAAAGGCTTGAGATTGGT 60.203 47.619 0.00 0.00 40.87 3.67
44 45 1.203287 GGCAAAGGCTTGAGATTGGTC 59.797 52.381 0.00 0.00 40.87 4.02
45 46 1.888512 GCAAAGGCTTGAGATTGGTCA 59.111 47.619 0.00 0.00 34.14 4.02
46 47 2.494870 GCAAAGGCTTGAGATTGGTCAT 59.505 45.455 0.00 0.00 34.14 3.06
47 48 3.428589 GCAAAGGCTTGAGATTGGTCATC 60.429 47.826 0.00 0.00 34.14 2.92
48 49 4.015084 CAAAGGCTTGAGATTGGTCATCT 58.985 43.478 0.00 0.00 45.86 2.90
49 50 3.278668 AGGCTTGAGATTGGTCATCTG 57.721 47.619 0.00 0.00 42.92 2.90
50 51 2.092538 AGGCTTGAGATTGGTCATCTGG 60.093 50.000 0.00 0.00 42.92 3.86
51 52 2.356535 GGCTTGAGATTGGTCATCTGGT 60.357 50.000 0.00 0.00 42.92 4.00
52 53 2.681848 GCTTGAGATTGGTCATCTGGTG 59.318 50.000 0.00 0.00 42.92 4.17
53 54 2.408271 TGAGATTGGTCATCTGGTGC 57.592 50.000 0.00 0.00 42.92 5.01
54 55 1.065199 TGAGATTGGTCATCTGGTGCC 60.065 52.381 0.00 0.00 42.92 5.01
55 56 0.994247 AGATTGGTCATCTGGTGCCA 59.006 50.000 0.77 0.77 41.13 4.92
56 57 1.098050 GATTGGTCATCTGGTGCCAC 58.902 55.000 3.97 0.00 34.95 5.01
57 58 0.323725 ATTGGTCATCTGGTGCCACC 60.324 55.000 7.01 7.01 39.22 4.61
58 59 1.426251 TTGGTCATCTGGTGCCACCT 61.426 55.000 16.23 0.00 39.58 4.00
59 60 1.377725 GGTCATCTGGTGCCACCTG 60.378 63.158 16.23 15.12 39.58 4.00
70 71 2.565841 GTGCCACCTGACAATATCCTC 58.434 52.381 0.00 0.00 0.00 3.71
139 143 1.471119 TCTCGCTAACCCGACTTCAT 58.529 50.000 0.00 0.00 33.12 2.57
149 153 2.101582 ACCCGACTTCATATGAGAGCAC 59.898 50.000 5.39 4.71 0.00 4.40
152 156 3.430790 CCGACTTCATATGAGAGCACCAA 60.431 47.826 5.39 0.00 0.00 3.67
154 158 4.440663 CGACTTCATATGAGAGCACCAAGA 60.441 45.833 5.39 0.00 0.00 3.02
202 206 0.523072 ACCAATGCGCACATCTCAAC 59.477 50.000 14.90 0.00 34.62 3.18
209 213 0.389817 CGCACATCTCAACGGAGGAA 60.390 55.000 0.00 0.00 41.69 3.36
213 217 1.002087 ACATCTCAACGGAGGAACACC 59.998 52.381 0.00 0.00 41.69 4.16
214 218 0.613777 ATCTCAACGGAGGAACACCC 59.386 55.000 0.00 0.00 41.69 4.61
217 221 1.189524 TCAACGGAGGAACACCCGAT 61.190 55.000 7.86 0.00 46.68 4.18
224 228 3.680475 CGGAGGAACACCCGATGATAAAA 60.680 47.826 0.00 0.00 46.68 1.52
248 252 6.715347 AAGAAAACTAGAAGCAAACACCAT 57.285 33.333 0.00 0.00 0.00 3.55
251 255 5.438761 AAACTAGAAGCAAACACCATCAC 57.561 39.130 0.00 0.00 0.00 3.06
255 259 0.831711 AAGCAAACACCATCACCCCC 60.832 55.000 0.00 0.00 0.00 5.40
260 264 4.343323 CACCATCACCCCCGCACA 62.343 66.667 0.00 0.00 0.00 4.57
262 266 4.033776 CCATCACCCCCGCACAGT 62.034 66.667 0.00 0.00 0.00 3.55
273 277 0.664166 CCGCACAGTCAAATGCAACC 60.664 55.000 0.00 0.00 42.17 3.77
276 280 2.063266 GCACAGTCAAATGCAACCATG 58.937 47.619 0.00 0.00 41.65 3.66
300 304 0.535553 TTAAACCGGCCACCACACTC 60.536 55.000 0.00 0.00 0.00 3.51
308 312 0.605319 GCCACCACACTCCAATCGAA 60.605 55.000 0.00 0.00 0.00 3.71
346 350 3.870419 GACATGATCAGAGGCTTCAAGAC 59.130 47.826 0.00 0.00 0.00 3.01
372 376 1.804326 CAAGGAGGTTACGACGCCG 60.804 63.158 0.00 0.00 42.50 6.46
414 418 3.488778 CAGAAGCTGGATATGAGGCTT 57.511 47.619 0.00 0.00 45.91 4.35
415 419 3.818180 CAGAAGCTGGATATGAGGCTTT 58.182 45.455 0.00 0.00 43.74 3.51
416 420 3.814283 CAGAAGCTGGATATGAGGCTTTC 59.186 47.826 0.00 0.00 43.74 2.62
417 421 3.457380 AGAAGCTGGATATGAGGCTTTCA 59.543 43.478 0.00 0.00 43.74 2.69
432 436 3.510388 CTTTCACCTCGAGAGCACATA 57.490 47.619 15.71 0.00 0.00 2.29
454 458 3.073678 TGGTCAATGTGTGAAAGATCCG 58.926 45.455 0.00 0.00 38.23 4.18
493 497 1.804748 GGAAAGTGACGCCCTAAACTG 59.195 52.381 0.00 0.00 0.00 3.16
496 501 2.165319 AGTGACGCCCTAAACTGAAC 57.835 50.000 0.00 0.00 0.00 3.18
544 555 2.618709 CCAAACTTGAACCAGTCTGACC 59.381 50.000 3.76 0.00 0.00 4.02
565 577 1.157585 GAGTCAAAAGAGAACGGGCC 58.842 55.000 0.00 0.00 0.00 5.80
566 578 0.765510 AGTCAAAAGAGAACGGGCCT 59.234 50.000 0.84 0.00 0.00 5.19
570 582 1.061546 AAAAGAGAACGGGCCTGGTA 58.938 50.000 18.00 0.00 0.00 3.25
578 590 3.408853 GGGCCTGGTAGACACCCC 61.409 72.222 0.84 0.00 45.11 4.95
636 648 1.153823 CACGAGACGGCGAATCCTT 60.154 57.895 16.62 0.00 34.83 3.36
637 649 1.139095 ACGAGACGGCGAATCCTTC 59.861 57.895 16.62 0.00 33.54 3.46
653 665 3.256704 TCCTTCTGGGTCAGTAATTGGT 58.743 45.455 0.00 0.00 36.25 3.67
913 942 1.524621 AGAGCACAGCACACCACAC 60.525 57.895 0.00 0.00 0.00 3.82
915 944 2.828095 GCACAGCACACCACACCA 60.828 61.111 0.00 0.00 0.00 4.17
1188 1228 4.715130 TCCTCCACCCCCTCCGTG 62.715 72.222 0.00 0.00 0.00 4.94
1686 1729 3.933722 AGCGCCGCCATATCAGCT 61.934 61.111 4.98 0.00 0.00 4.24
2085 2128 7.012704 GGTGATAGTGATGAATTGCAATACAGT 59.987 37.037 13.39 14.63 0.00 3.55
2116 2159 6.313324 AGTGATGATGATATGGAGAGTCAGA 58.687 40.000 0.00 0.00 0.00 3.27
2238 2281 1.779061 AAAGCGGGCTTGAGAAGGGA 61.779 55.000 6.69 0.00 36.26 4.20
2271 2314 1.187087 CCTACCTGTGGGAGACTGTC 58.813 60.000 0.00 0.00 36.25 3.51
2345 2388 2.039084 AGGTGCTCGAAGGATCAAAAGT 59.961 45.455 0.00 0.00 0.00 2.66
2349 2392 2.337583 CTCGAAGGATCAAAAGTGCGA 58.662 47.619 0.00 0.00 0.00 5.10
2384 2427 3.185455 AGCTGAGGAGGTTTAGGTTGAT 58.815 45.455 0.00 0.00 0.00 2.57
2519 2562 2.171003 CTGTTGGAAGGGGGAAATCAC 58.829 52.381 0.00 0.00 0.00 3.06
2756 2799 3.939740 ATGCTGTGTTCACATATCCCT 57.060 42.857 6.09 0.00 0.00 4.20
2797 2841 2.257691 ATCACATCATCTGCAGGCTC 57.742 50.000 15.13 0.00 0.00 4.70
2815 2859 2.159517 GCTCGTCAAAATTGGGTGCTAG 60.160 50.000 0.00 0.00 0.00 3.42
2884 2928 2.038952 TGCTAGGTCAAGTCATTGTGCT 59.961 45.455 0.00 0.00 37.68 4.40
2885 2929 3.077359 GCTAGGTCAAGTCATTGTGCTT 58.923 45.455 0.00 0.00 37.68 3.91
2886 2930 4.253685 GCTAGGTCAAGTCATTGTGCTTA 58.746 43.478 0.00 0.00 37.68 3.09
2887 2931 4.695455 GCTAGGTCAAGTCATTGTGCTTAA 59.305 41.667 0.00 0.00 37.68 1.85
2940 2984 5.352293 GGTTTCTTGATTGATTGGCATTTCC 59.648 40.000 0.00 0.00 0.00 3.13
2992 3037 7.936847 TGTAATTGTAGTTGAGGAACAATCTGT 59.063 33.333 0.84 0.00 41.67 3.41
3049 3132 3.966218 CGGCGTGTTATATTTAAGCAAGC 59.034 43.478 0.00 0.00 34.70 4.01
3092 3177 9.796120 TTGTTTATATATGCTGTAAAGTTTGCC 57.204 29.630 0.00 0.00 0.00 4.52
3153 3242 7.104939 CCAATTTGGCTTGAATTGAATAGGAA 58.895 34.615 17.17 0.00 43.71 3.36
3154 3243 7.771826 CCAATTTGGCTTGAATTGAATAGGAAT 59.228 33.333 17.17 0.00 43.71 3.01
3156 3245 7.479352 TTTGGCTTGAATTGAATAGGAATGA 57.521 32.000 0.00 0.00 0.00 2.57
3157 3246 7.664552 TTGGCTTGAATTGAATAGGAATGAT 57.335 32.000 0.00 0.00 0.00 2.45
3158 3247 7.046292 TGGCTTGAATTGAATAGGAATGATG 57.954 36.000 0.00 0.00 0.00 3.07
3159 3248 6.608405 TGGCTTGAATTGAATAGGAATGATGT 59.392 34.615 0.00 0.00 0.00 3.06
3163 3252 9.512435 CTTGAATTGAATAGGAATGATGTTGTC 57.488 33.333 0.00 0.00 0.00 3.18
3182 3271 5.298989 TGTCCTGTGGTTGTTATAGTTGT 57.701 39.130 0.00 0.00 0.00 3.32
3200 3289 1.854280 TGTGGGTCAAAAGTAGGGGTT 59.146 47.619 0.00 0.00 0.00 4.11
3283 3372 2.229062 TCTGAAGTCGATGCTTTCTCGT 59.771 45.455 0.00 0.00 37.40 4.18
3284 3373 2.989840 CTGAAGTCGATGCTTTCTCGTT 59.010 45.455 0.00 0.00 37.40 3.85
3285 3374 2.987149 TGAAGTCGATGCTTTCTCGTTC 59.013 45.455 0.00 0.00 37.40 3.95
3287 3376 2.869897 AGTCGATGCTTTCTCGTTCTC 58.130 47.619 0.00 0.00 37.40 2.87
3290 3379 1.281899 GATGCTTTCTCGTTCTCGGG 58.718 55.000 0.00 0.00 39.14 5.14
3293 3382 1.281899 GCTTTCTCGTTCTCGGGATG 58.718 55.000 0.00 0.00 46.30 3.51
3294 3383 1.927895 CTTTCTCGTTCTCGGGATGG 58.072 55.000 0.00 0.00 46.30 3.51
3295 3384 0.535335 TTTCTCGTTCTCGGGATGGG 59.465 55.000 0.00 0.00 46.30 4.00
3344 3433 7.174946 GGAAACCTTTGTTGATTGTGATCTCTA 59.825 37.037 0.00 0.00 34.13 2.43
3353 3442 7.118245 TGTTGATTGTGATCTCTACACATGTTC 59.882 37.037 0.00 0.00 45.52 3.18
3360 3449 6.815641 GTGATCTCTACACATGTTCAATGTCT 59.184 38.462 0.00 0.00 38.05 3.41
3361 3450 7.976175 GTGATCTCTACACATGTTCAATGTCTA 59.024 37.037 0.00 0.00 38.05 2.59
3362 3451 8.699130 TGATCTCTACACATGTTCAATGTCTAT 58.301 33.333 0.00 0.00 0.00 1.98
3379 3468 4.038642 TGTCTATATATGCTGTTGTGCGGA 59.961 41.667 0.00 0.00 35.36 5.54
3390 3479 1.135803 GTTGTGCGGATGTTATGCGTT 60.136 47.619 4.73 0.00 46.32 4.84
3398 3487 4.260620 GCGGATGTTATGCGTTTCTATGTT 60.261 41.667 4.73 0.00 46.32 2.71
3413 3502 4.065088 TCTATGTTGGTGAGCTTGTGTTC 58.935 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.098050 GTGGCACCAGATGACCAATC 58.902 55.000 6.29 0.00 36.60 2.67
38 39 0.323725 GGTGGCACCAGATGACCAAT 60.324 55.000 31.26 0.00 38.42 3.16
39 40 1.074775 GGTGGCACCAGATGACCAA 59.925 57.895 31.26 0.00 38.42 3.67
40 41 1.847506 AGGTGGCACCAGATGACCA 60.848 57.895 36.28 0.00 41.95 4.02
41 42 1.377725 CAGGTGGCACCAGATGACC 60.378 63.158 36.28 9.00 41.95 4.02
42 43 0.674895 GTCAGGTGGCACCAGATGAC 60.675 60.000 36.28 32.69 41.95 3.06
43 44 1.126948 TGTCAGGTGGCACCAGATGA 61.127 55.000 36.28 27.52 41.95 2.92
44 45 0.250858 TTGTCAGGTGGCACCAGATG 60.251 55.000 36.28 25.78 41.95 2.90
45 46 0.700564 ATTGTCAGGTGGCACCAGAT 59.299 50.000 36.28 17.68 41.95 2.90
46 47 1.357137 TATTGTCAGGTGGCACCAGA 58.643 50.000 36.28 31.10 41.95 3.86
47 48 2.292267 GATATTGTCAGGTGGCACCAG 58.708 52.381 36.28 29.30 41.95 4.00
48 49 1.064758 GGATATTGTCAGGTGGCACCA 60.065 52.381 36.28 17.60 41.95 4.17
49 50 1.212935 AGGATATTGTCAGGTGGCACC 59.787 52.381 29.32 29.32 38.99 5.01
50 51 2.092968 TGAGGATATTGTCAGGTGGCAC 60.093 50.000 9.70 9.70 0.00 5.01
51 52 2.195727 TGAGGATATTGTCAGGTGGCA 58.804 47.619 0.00 0.00 0.00 4.92
52 53 3.209410 CTTGAGGATATTGTCAGGTGGC 58.791 50.000 0.00 0.00 0.00 5.01
53 54 3.455910 TCCTTGAGGATATTGTCAGGTGG 59.544 47.826 0.00 0.00 39.78 4.61
54 55 4.701765 CTCCTTGAGGATATTGTCAGGTG 58.298 47.826 0.00 0.00 44.46 4.00
70 71 4.444022 CCATATGAACACTCCTCCTCCTTG 60.444 50.000 3.65 0.00 0.00 3.61
118 122 1.822990 TGAAGTCGGGTTAGCGAGATT 59.177 47.619 0.00 0.00 0.00 2.40
139 143 4.686972 CGAAAGATCTTGGTGCTCTCATA 58.313 43.478 9.17 0.00 0.00 2.15
149 153 2.736721 TCGAGTTTGCGAAAGATCTTGG 59.263 45.455 9.17 5.58 37.35 3.61
152 156 2.854777 CGATCGAGTTTGCGAAAGATCT 59.145 45.455 10.26 0.00 44.22 2.75
154 158 2.876091 TCGATCGAGTTTGCGAAAGAT 58.124 42.857 15.15 0.00 44.22 2.40
202 206 1.037493 TATCATCGGGTGTTCCTCCG 58.963 55.000 0.00 0.00 46.89 4.63
224 228 6.524101 TGGTGTTTGCTTCTAGTTTTCTTT 57.476 33.333 0.00 0.00 0.00 2.52
226 230 5.827797 TGATGGTGTTTGCTTCTAGTTTTCT 59.172 36.000 0.00 0.00 0.00 2.52
227 231 5.915196 GTGATGGTGTTTGCTTCTAGTTTTC 59.085 40.000 0.00 0.00 0.00 2.29
237 241 1.228862 GGGGGTGATGGTGTTTGCT 60.229 57.895 0.00 0.00 0.00 3.91
248 252 2.063015 ATTTGACTGTGCGGGGGTGA 62.063 55.000 0.00 0.00 0.00 4.02
251 255 2.993471 GCATTTGACTGTGCGGGGG 61.993 63.158 0.00 0.00 0.00 5.40
255 259 0.030504 TGGTTGCATTTGACTGTGCG 59.969 50.000 0.00 0.00 44.11 5.34
260 264 1.895131 GGTCCATGGTTGCATTTGACT 59.105 47.619 12.58 0.00 0.00 3.41
262 266 2.307496 AGGTCCATGGTTGCATTTGA 57.693 45.000 12.58 0.00 0.00 2.69
273 277 0.322997 TGGCCGGTTTAAGGTCCATG 60.323 55.000 1.90 0.00 32.65 3.66
276 280 1.676635 GGTGGCCGGTTTAAGGTCC 60.677 63.158 1.90 0.00 30.98 4.46
300 304 2.719046 GCTTGTTTGACGTTTCGATTGG 59.281 45.455 0.00 0.00 0.00 3.16
308 312 3.376859 TCATGTCTTGCTTGTTTGACGTT 59.623 39.130 0.00 0.00 32.64 3.99
411 415 0.319900 TGTGCTCTCGAGGTGAAAGC 60.320 55.000 13.56 14.04 0.00 3.51
412 416 2.376808 ATGTGCTCTCGAGGTGAAAG 57.623 50.000 13.56 2.92 0.00 2.62
413 417 3.430790 CCATATGTGCTCTCGAGGTGAAA 60.431 47.826 13.56 0.00 0.00 2.69
414 418 2.101415 CCATATGTGCTCTCGAGGTGAA 59.899 50.000 13.56 0.00 0.00 3.18
415 419 1.683385 CCATATGTGCTCTCGAGGTGA 59.317 52.381 13.56 0.00 0.00 4.02
416 420 1.410517 ACCATATGTGCTCTCGAGGTG 59.589 52.381 13.56 7.28 0.00 4.00
417 421 1.683917 GACCATATGTGCTCTCGAGGT 59.316 52.381 13.56 0.00 0.00 3.85
432 436 3.691118 CGGATCTTTCACACATTGACCAT 59.309 43.478 0.00 0.00 32.26 3.55
454 458 0.371645 CTTCTCGAAGGCATTGTCGC 59.628 55.000 0.00 0.00 37.19 5.19
478 482 2.067013 GAGTTCAGTTTAGGGCGTCAC 58.933 52.381 0.00 0.00 0.00 3.67
479 483 1.689813 TGAGTTCAGTTTAGGGCGTCA 59.310 47.619 0.00 0.00 0.00 4.35
481 485 1.414919 TGTGAGTTCAGTTTAGGGCGT 59.585 47.619 0.00 0.00 0.00 5.68
483 487 3.674997 TGATGTGAGTTCAGTTTAGGGC 58.325 45.455 0.00 0.00 0.00 5.19
493 497 2.227149 TGCAACAGCATGATGTGAGTTC 59.773 45.455 18.80 5.94 41.42 3.01
515 520 4.141344 ACTGGTTCAAGTTTGGCTAGGTTA 60.141 41.667 0.00 0.00 0.00 2.85
544 555 1.429463 CCCGTTCTCTTTTGACTCGG 58.571 55.000 0.00 0.00 35.24 4.63
557 568 1.079336 GTGTCTACCAGGCCCGTTC 60.079 63.158 0.00 0.00 0.00 3.95
618 630 1.140407 GAAGGATTCGCCGTCTCGTG 61.140 60.000 0.00 0.00 41.37 4.35
620 632 3.999051 GAAGGATTCGCCGTCTCG 58.001 61.111 0.00 0.00 41.37 4.04
632 644 3.009033 CACCAATTACTGACCCAGAAGGA 59.991 47.826 0.45 0.00 39.89 3.36
636 648 2.552155 GCACACCAATTACTGACCCAGA 60.552 50.000 0.45 0.00 35.18 3.86
637 649 1.812571 GCACACCAATTACTGACCCAG 59.187 52.381 0.00 0.00 37.52 4.45
820 837 3.969250 TTTAAGAGGCAGGGCGCGG 62.969 63.158 8.83 0.00 43.84 6.46
821 838 1.376609 ATTTTAAGAGGCAGGGCGCG 61.377 55.000 0.00 0.00 43.84 6.86
822 839 1.675552 TATTTTAAGAGGCAGGGCGC 58.324 50.000 0.00 0.00 41.28 6.53
823 840 2.480419 CGATATTTTAAGAGGCAGGGCG 59.520 50.000 0.00 0.00 0.00 6.13
824 841 2.814336 CCGATATTTTAAGAGGCAGGGC 59.186 50.000 0.00 0.00 0.00 5.19
825 842 2.814336 GCCGATATTTTAAGAGGCAGGG 59.186 50.000 0.00 0.00 43.65 4.45
829 846 2.223377 CGGTGCCGATATTTTAAGAGGC 59.777 50.000 4.35 0.00 44.38 4.70
830 847 3.724374 TCGGTGCCGATATTTTAAGAGG 58.276 45.455 9.48 0.00 44.01 3.69
1578 1621 2.505405 CTGATGGGCTTGATGATGGAG 58.495 52.381 0.00 0.00 0.00 3.86
2085 2128 7.416731 TCTCCATATCATCATCACTATCTCCA 58.583 38.462 0.00 0.00 0.00 3.86
2116 2159 1.485066 GATGTGGTAACGGTCATCCCT 59.515 52.381 0.00 0.00 42.51 4.20
2127 2170 3.558321 CCTTCCGGTTCTTGATGTGGTAA 60.558 47.826 0.00 0.00 0.00 2.85
2157 2200 0.455410 TGCCATTTGCCGCTGTAATC 59.545 50.000 0.00 0.00 40.16 1.75
2169 2212 4.566070 CCAAGTCCAATTCCATTGCCATTT 60.566 41.667 0.00 0.00 38.92 2.32
2181 2224 0.482446 TGACAGCCCCAAGTCCAATT 59.518 50.000 0.00 0.00 33.89 2.32
2187 2230 1.607467 GGCATTGACAGCCCCAAGT 60.607 57.895 0.00 0.00 46.50 3.16
2271 2314 1.515020 CTCCTTGGACAGCTCCTCG 59.485 63.158 0.00 0.00 37.48 4.63
2345 2388 1.167851 CTTTTCCTCAATGGCTCGCA 58.832 50.000 0.00 0.00 35.26 5.10
2349 2392 2.444421 CTCAGCTTTTCCTCAATGGCT 58.556 47.619 0.00 0.00 35.26 4.75
2384 2427 0.535797 CAGCTGCTGTCTGATCTCCA 59.464 55.000 21.21 0.00 33.54 3.86
2756 2799 0.398381 AAAAGGCCCAGCACAAAGGA 60.398 50.000 0.00 0.00 0.00 3.36
2797 2841 1.465689 CGCTAGCACCCAATTTTGACG 60.466 52.381 16.45 0.00 0.00 4.35
2826 2870 3.256383 TGCAACTCTATGCTGCAAACAAT 59.744 39.130 6.36 0.00 43.76 2.71
2827 2871 2.622470 TGCAACTCTATGCTGCAAACAA 59.378 40.909 6.36 0.00 43.76 2.83
2829 2873 2.995466 TGCAACTCTATGCTGCAAAC 57.005 45.000 6.36 0.00 43.76 2.93
2833 2877 6.020121 CACAAAATTATGCAACTCTATGCTGC 60.020 38.462 0.00 0.00 46.54 5.25
2834 2878 7.219535 GTCACAAAATTATGCAACTCTATGCTG 59.780 37.037 0.00 0.00 46.54 4.41
2835 2879 7.253422 GTCACAAAATTATGCAACTCTATGCT 58.747 34.615 0.00 0.00 46.54 3.79
2885 2929 9.944376 AGAAGACACTGCAACTCTAATTAATTA 57.056 29.630 7.66 7.66 0.00 1.40
2886 2930 8.854614 AGAAGACACTGCAACTCTAATTAATT 57.145 30.769 5.89 5.89 0.00 1.40
2887 2931 8.854614 AAGAAGACACTGCAACTCTAATTAAT 57.145 30.769 0.00 0.00 0.00 1.40
2992 3037 1.825090 CCCTGAAGCATGCACAGTAA 58.175 50.000 29.25 8.95 0.00 2.24
3078 3163 3.923017 ACATCTGGCAAACTTTACAGC 57.077 42.857 0.00 0.00 0.00 4.40
3079 3164 3.983344 GCAACATCTGGCAAACTTTACAG 59.017 43.478 0.00 0.00 0.00 2.74
3092 3177 2.171237 TGGATGGTAGGAGCAACATCTG 59.829 50.000 0.00 0.00 39.61 2.90
3153 3242 3.228188 ACAACCACAGGACAACATCAT 57.772 42.857 0.00 0.00 0.00 2.45
3154 3243 2.727123 ACAACCACAGGACAACATCA 57.273 45.000 0.00 0.00 0.00 3.07
3156 3245 5.876357 ACTATAACAACCACAGGACAACAT 58.124 37.500 0.00 0.00 0.00 2.71
3157 3246 5.298989 ACTATAACAACCACAGGACAACA 57.701 39.130 0.00 0.00 0.00 3.33
3158 3247 5.529800 ACAACTATAACAACCACAGGACAAC 59.470 40.000 0.00 0.00 0.00 3.32
3159 3248 5.529430 CACAACTATAACAACCACAGGACAA 59.471 40.000 0.00 0.00 0.00 3.18
3163 3252 3.756434 CCCACAACTATAACAACCACAGG 59.244 47.826 0.00 0.00 0.00 4.00
3182 3271 3.499021 GCTAAACCCCTACTTTTGACCCA 60.499 47.826 0.00 0.00 0.00 4.51
3200 3289 6.238103 GCACTAGCGAATCATGTTAAAGCTAA 60.238 38.462 11.41 0.00 35.65 3.09
3283 3372 2.965831 CAGACTATTCCCATCCCGAGAA 59.034 50.000 0.00 0.00 0.00 2.87
3284 3373 2.177016 TCAGACTATTCCCATCCCGAGA 59.823 50.000 0.00 0.00 0.00 4.04
3285 3374 2.598565 TCAGACTATTCCCATCCCGAG 58.401 52.381 0.00 0.00 0.00 4.63
3287 3376 3.838244 TTTCAGACTATTCCCATCCCG 57.162 47.619 0.00 0.00 0.00 5.14
3290 3379 6.708054 CAGGTGTATTTCAGACTATTCCCATC 59.292 42.308 0.00 0.00 0.00 3.51
3293 3382 6.235231 TCAGGTGTATTTCAGACTATTCCC 57.765 41.667 0.00 0.00 0.00 3.97
3294 3383 6.708054 CCATCAGGTGTATTTCAGACTATTCC 59.292 42.308 0.00 0.00 0.00 3.01
3295 3384 7.500992 TCCATCAGGTGTATTTCAGACTATTC 58.499 38.462 0.00 0.00 35.89 1.75
3344 3433 8.996271 CAGCATATATAGACATTGAACATGTGT 58.004 33.333 0.00 0.00 31.52 3.72
3353 3442 6.301861 CGCACAACAGCATATATAGACATTG 58.698 40.000 0.00 0.00 0.00 2.82
3360 3449 4.893608 ACATCCGCACAACAGCATATATA 58.106 39.130 0.00 0.00 0.00 0.86
3361 3450 3.743521 ACATCCGCACAACAGCATATAT 58.256 40.909 0.00 0.00 0.00 0.86
3362 3451 3.192541 ACATCCGCACAACAGCATATA 57.807 42.857 0.00 0.00 0.00 0.86
3363 3452 2.042686 ACATCCGCACAACAGCATAT 57.957 45.000 0.00 0.00 0.00 1.78
3379 3468 5.645929 TCACCAACATAGAAACGCATAACAT 59.354 36.000 0.00 0.00 0.00 2.71
3390 3479 4.085357 ACACAAGCTCACCAACATAGAA 57.915 40.909 0.00 0.00 0.00 2.10
3398 3487 0.107263 TGCAGAACACAAGCTCACCA 60.107 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.