Multiple sequence alignment - TraesCS3D01G223400

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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 TraesCS3D01G223400 chr3D 100.000 2735 0 0 1 2735 304911252 304908518 0.000000e+00 5051
1 TraesCS3D01G223400 chr3A 94.501 1764 67 14 448 2185 429673239 429674998 0.000000e+00 2693
2 TraesCS3D01G223400 chr3A 90.343 466 36 6 2232 2696 429675020 429675477 1.080000e-168 603
3 TraesCS3D01G223400 chr3A 89.202 426 30 11 27 444 429672259 429672676 4.040000e-143 518
4 TraesCS3D01G223400 chr3B 92.294 1713 100 15 708 2402 416918983 416920681 0.000000e+00 2403
5 TraesCS3D01G223400 chr3B 93.585 265 13 2 448 712 416918343 416918603 2.550000e-105 392
6 TraesCS3D01G223400 chr3B 94.500 200 10 1 36 234 416857899 416858098 9.510000e-80 307


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 TraesCS3D01G223400 chr3D 304908518 304911252 2734 True 5051.000000 5051 100.000000 1 2735 1 chr3D.!!$R1 2734
1 TraesCS3D01G223400 chr3A 429672259 429675477 3218 False 1271.333333 2693 91.348667 27 2696 3 chr3A.!!$F1 2669
2 TraesCS3D01G223400 chr3B 416918343 416920681 2338 False 1397.500000 2403 92.939500 448 2402 2 chr3B.!!$F2 1954

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
84 85 0.040425 GCAACGTGTGGGACATTGTC 60.04 55.0 8.34 8.34 44.52 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2935 0.191064 TTGGAGAGCCCGATATCCCT 59.809 55.0 0.0 0.0 37.93 4.2 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 2.151881 TGCATGTTCCATTGCAACAC 57.848 45.000 0.00 0.00 45.30 3.32
23 24 1.687660 TGCATGTTCCATTGCAACACT 59.312 42.857 0.00 0.00 45.30 3.55
24 25 2.288334 TGCATGTTCCATTGCAACACTC 60.288 45.455 0.00 0.00 45.30 3.51
25 26 2.288334 GCATGTTCCATTGCAACACTCA 60.288 45.455 0.00 0.00 36.59 3.41
26 27 3.615592 GCATGTTCCATTGCAACACTCAT 60.616 43.478 0.00 0.72 36.59 2.90
27 28 4.562082 CATGTTCCATTGCAACACTCATT 58.438 39.130 0.00 0.00 36.59 2.57
28 29 4.669206 TGTTCCATTGCAACACTCATTT 57.331 36.364 0.00 0.00 0.00 2.32
29 30 5.781210 TGTTCCATTGCAACACTCATTTA 57.219 34.783 0.00 0.00 0.00 1.40
30 31 6.343716 TGTTCCATTGCAACACTCATTTAT 57.656 33.333 0.00 0.00 0.00 1.40
31 32 7.459795 TGTTCCATTGCAACACTCATTTATA 57.540 32.000 0.00 0.00 0.00 0.98
32 33 8.065473 TGTTCCATTGCAACACTCATTTATAT 57.935 30.769 0.00 0.00 0.00 0.86
33 34 9.183368 TGTTCCATTGCAACACTCATTTATATA 57.817 29.630 0.00 0.00 0.00 0.86
34 35 9.450807 GTTCCATTGCAACACTCATTTATATAC 57.549 33.333 0.00 0.00 0.00 1.47
42 43 8.903820 GCAACACTCATTTATATACCTCCTTTT 58.096 33.333 0.00 0.00 0.00 2.27
58 59 8.388656 ACCTCCTTTTGATGTAGGACTATAAA 57.611 34.615 0.00 0.00 35.66 1.40
69 70 5.883673 TGTAGGACTATAAACCAATGGCAAC 59.116 40.000 0.00 0.00 0.00 4.17
81 82 0.539438 ATGGCAACGTGTGGGACATT 60.539 50.000 0.00 0.00 40.56 2.71
84 85 0.040425 GCAACGTGTGGGACATTGTC 60.040 55.000 8.34 8.34 44.52 3.18
88 89 4.500127 CAACGTGTGGGACATTGTCTATA 58.500 43.478 16.02 2.50 44.52 1.31
184 186 4.522114 TGTGAAAGTTGGATGAGTGAACA 58.478 39.130 0.00 0.00 0.00 3.18
189 191 7.173218 GTGAAAGTTGGATGAGTGAACAAGATA 59.827 37.037 0.00 0.00 0.00 1.98
222 227 1.552792 TCGAATGCTCCATGGTGTACA 59.447 47.619 12.58 6.43 0.00 2.90
223 228 2.027653 TCGAATGCTCCATGGTGTACAA 60.028 45.455 12.58 0.00 0.00 2.41
275 283 3.734231 TGTCGTCGAAAGCAACTAAGAAG 59.266 43.478 0.00 0.00 0.00 2.85
279 287 4.444720 CGTCGAAAGCAACTAAGAAGAAGT 59.555 41.667 0.00 0.00 0.00 3.01
284 292 6.128956 CGAAAGCAACTAAGAAGAAGTGAGAG 60.129 42.308 0.00 0.00 0.00 3.20
309 317 6.315642 GCACTTTTGTTACCCTAGATAGGAAC 59.684 42.308 7.51 5.65 46.63 3.62
310 318 7.391620 CACTTTTGTTACCCTAGATAGGAACA 58.608 38.462 7.51 8.03 46.63 3.18
322 330 5.028549 AGATAGGAACAAATGTCGAGCAT 57.971 39.130 0.00 0.00 40.03 3.79
326 334 3.189287 AGGAACAAATGTCGAGCATTGTC 59.811 43.478 12.06 10.20 46.29 3.18
337 345 3.066203 TCGAGCATTGTCGAGCTATGTAA 59.934 43.478 0.00 0.00 43.91 2.41
342 350 4.330074 GCATTGTCGAGCTATGTAAACAGT 59.670 41.667 0.00 0.00 33.78 3.55
352 360 7.307396 CGAGCTATGTAAACAGTTATTCATGGG 60.307 40.741 0.00 3.72 0.00 4.00
363 371 0.935942 ATTCATGGGGATCTTGGCCA 59.064 50.000 0.00 0.00 0.00 5.36
366 374 0.754217 CATGGGGATCTTGGCCACTG 60.754 60.000 3.88 0.62 0.00 3.66
382 390 5.170748 GGCCACTGAACAATTAAATGAAGG 58.829 41.667 0.00 0.00 0.00 3.46
415 423 6.729187 ACAAGCTAAGCACTTGAGTAAAAAG 58.271 36.000 10.26 0.00 45.99 2.27
416 424 6.318900 ACAAGCTAAGCACTTGAGTAAAAAGT 59.681 34.615 10.26 0.00 45.99 2.66
417 425 6.944234 AGCTAAGCACTTGAGTAAAAAGTT 57.056 33.333 0.00 0.00 35.70 2.66
418 426 6.729187 AGCTAAGCACTTGAGTAAAAAGTTG 58.271 36.000 0.00 0.00 35.70 3.16
441 449 8.850452 GTTGTAGTTGCTAAGTATTTTTCATGC 58.150 33.333 0.00 0.00 0.00 4.06
442 450 8.105097 TGTAGTTGCTAAGTATTTTTCATGCA 57.895 30.769 0.00 0.00 0.00 3.96
443 451 8.020819 TGTAGTTGCTAAGTATTTTTCATGCAC 58.979 33.333 0.00 0.00 0.00 4.57
444 452 6.389906 AGTTGCTAAGTATTTTTCATGCACC 58.610 36.000 0.00 0.00 0.00 5.01
445 453 6.209391 AGTTGCTAAGTATTTTTCATGCACCT 59.791 34.615 0.00 0.00 0.00 4.00
453 1019 2.064434 TTTCATGCACCTGTCACCAA 57.936 45.000 0.00 0.00 0.00 3.67
454 1020 2.291209 TTCATGCACCTGTCACCAAT 57.709 45.000 0.00 0.00 0.00 3.16
456 1022 3.431673 TCATGCACCTGTCACCAATTA 57.568 42.857 0.00 0.00 0.00 1.40
476 1042 5.530519 TTATAAGCACTTTCGCACTGAAG 57.469 39.130 0.00 0.00 37.99 3.02
479 1045 0.944386 GCACTTTCGCACTGAAGGAA 59.056 50.000 0.00 0.00 37.99 3.36
491 1057 4.276926 GCACTGAAGGAAGCCTAATATTGG 59.723 45.833 0.00 0.00 31.13 3.16
492 1058 5.440610 CACTGAAGGAAGCCTAATATTGGT 58.559 41.667 0.00 0.00 31.13 3.67
493 1059 6.591935 CACTGAAGGAAGCCTAATATTGGTA 58.408 40.000 0.00 0.00 31.13 3.25
679 1251 1.080298 GCGCAGGTGTTACGTAGGT 60.080 57.895 0.30 0.00 0.00 3.08
692 1264 1.069258 GTAGGTAGCCGCCATGGTC 59.931 63.158 14.67 4.79 41.21 4.02
706 1662 3.553922 GCCATGGTCCTTCTAGAGAATCG 60.554 52.174 14.67 0.00 42.67 3.34
725 1681 7.858583 AGAATCGTAAGGAAACAAGTGTAAAC 58.141 34.615 0.00 0.00 38.47 2.01
726 1682 7.496591 AGAATCGTAAGGAAACAAGTGTAAACA 59.503 33.333 0.00 0.00 38.47 2.83
951 1915 0.539438 AAAGCCTCGCACCCAAATCA 60.539 50.000 0.00 0.00 0.00 2.57
989 1957 1.580256 GCCAAACAAACGACGTTTCAC 59.420 47.619 22.45 5.73 34.40 3.18
994 1962 2.018515 ACAAACGACGTTTCACCCAAT 58.981 42.857 22.45 0.00 33.10 3.16
1299 2270 3.756727 GTCGGGTCCACGTCCTCC 61.757 72.222 0.00 0.00 34.94 4.30
1596 2567 2.910479 ACCACCGAGCTCGACACA 60.910 61.111 36.59 0.00 43.02 3.72
1854 2834 1.802365 ACTTCGTGTTCGTAATTGGCC 59.198 47.619 0.00 0.00 38.33 5.36
1875 2855 4.887071 GCCATGGTATAACTGGATTGTTGA 59.113 41.667 14.67 0.00 31.38 3.18
1887 2867 2.423538 GGATTGTTGAACGGGATTGAGG 59.576 50.000 0.00 0.00 0.00 3.86
1889 2869 2.178912 TGTTGAACGGGATTGAGGTC 57.821 50.000 0.00 0.00 0.00 3.85
1943 2923 5.921962 AGGGAAATGTGAGGCTTAAATTC 57.078 39.130 0.00 0.00 0.00 2.17
1955 2935 5.819991 AGGCTTAAATTCTGGATTCAGTCA 58.180 37.500 0.00 0.00 41.59 3.41
1962 2942 6.776887 AATTCTGGATTCAGTCAGGGATAT 57.223 37.500 0.00 0.00 41.59 1.63
2207 3192 2.126914 TTTTTGCGCACATACACCAC 57.873 45.000 11.12 0.00 0.00 4.16
2218 3203 4.331443 GCACATACACCACGAACATGAATA 59.669 41.667 0.00 0.00 0.00 1.75
2224 3209 6.325919 ACACCACGAACATGAATATTTTGT 57.674 33.333 0.00 0.00 0.00 2.83
2267 3257 4.921515 TCACTTTCGAACCGTTAGATCTTG 59.078 41.667 0.00 0.00 0.00 3.02
2355 3348 8.385111 CCAAAAATAGATTGTGCATTGTTCATC 58.615 33.333 0.00 0.00 0.00 2.92
2356 3349 9.146984 CAAAAATAGATTGTGCATTGTTCATCT 57.853 29.630 0.00 0.00 0.00 2.90
2357 3350 9.715121 AAAAATAGATTGTGCATTGTTCATCTT 57.285 25.926 0.00 0.00 0.00 2.40
2369 3362 7.176165 TGCATTGTTCATCTTCTTCTTTCTCAT 59.824 33.333 0.00 0.00 0.00 2.90
2376 3369 4.717877 TCTTCTTCTTTCTCATGCAACCA 58.282 39.130 0.00 0.00 0.00 3.67
2402 3395 1.682684 ACCCAGCCCTAGTCGTCTG 60.683 63.158 0.00 0.00 0.00 3.51
2408 3401 1.360551 CCCTAGTCGTCTGCATCCG 59.639 63.158 0.00 0.00 0.00 4.18
2458 3451 2.652113 CCCTCCTCCTTCCCTCCCT 61.652 68.421 0.00 0.00 0.00 4.20
2486 3480 2.426023 GTGCTGGTTGTCGTCCCT 59.574 61.111 0.00 0.00 0.00 4.20
2487 3481 1.961277 GTGCTGGTTGTCGTCCCTG 60.961 63.158 0.00 0.00 0.00 4.45
2489 3483 2.743718 CTGGTTGTCGTCCCTGCT 59.256 61.111 0.00 0.00 0.00 4.24
2493 3487 1.367840 GTTGTCGTCCCTGCTGACT 59.632 57.895 0.00 0.00 33.81 3.41
2511 3505 2.894765 GACTATCTCTCTAAGCCCCACC 59.105 54.545 0.00 0.00 0.00 4.61
2525 3519 1.074072 CCACCCGATGAACAACCCA 59.926 57.895 0.00 0.00 0.00 4.51
2527 3521 0.810648 CACCCGATGAACAACCCATG 59.189 55.000 0.00 0.00 0.00 3.66
2532 3526 2.014128 CGATGAACAACCCATGTACCC 58.986 52.381 0.00 0.00 42.99 3.69
2541 3535 2.808206 CCATGTACCCCCTCGGCTC 61.808 68.421 0.00 0.00 33.26 4.70
2552 3546 3.358076 CTCGGCTCCGACAAGGTCC 62.358 68.421 6.95 0.00 44.01 4.46
2608 3602 2.578021 ACTATGTGGGACAAGGCATCTT 59.422 45.455 0.00 0.00 44.16 2.40
2620 3614 7.724061 GGGACAAGGCATCTTAGGATTAATAAA 59.276 37.037 0.00 0.00 0.00 1.40
2625 3619 7.287810 AGGCATCTTAGGATTAATAAAACCGT 58.712 34.615 0.00 0.00 32.91 4.83
2626 3620 8.434392 AGGCATCTTAGGATTAATAAAACCGTA 58.566 33.333 0.00 0.00 32.91 4.02
2627 3621 9.227777 GGCATCTTAGGATTAATAAAACCGTAT 57.772 33.333 0.00 0.00 32.91 3.06
2651 3645 2.432206 TTTCATCTGAGAACGTGCGA 57.568 45.000 0.00 0.00 0.00 5.10
2665 3659 0.170561 GTGCGACGATGACTACAGGT 59.829 55.000 0.00 0.00 0.00 4.00
2671 3665 3.427098 CGACGATGACTACAGGTAAAGCA 60.427 47.826 0.00 0.00 0.00 3.91
2679 3673 3.583086 ACTACAGGTAAAGCACACTCCAT 59.417 43.478 0.00 0.00 0.00 3.41
2684 3678 2.290323 GGTAAAGCACACTCCATGAGGT 60.290 50.000 0.00 0.00 33.35 3.85
2690 3684 2.292267 CACACTCCATGAGGTAATGCC 58.708 52.381 0.00 0.00 33.35 4.40
2696 3690 2.311542 TCCATGAGGTAATGCCCAAACT 59.688 45.455 0.00 0.00 38.26 2.66
2697 3691 3.099141 CCATGAGGTAATGCCCAAACTT 58.901 45.455 0.00 0.00 38.26 2.66
2698 3692 3.119029 CCATGAGGTAATGCCCAAACTTG 60.119 47.826 0.00 0.00 38.26 3.16
2699 3693 3.237268 TGAGGTAATGCCCAAACTTGT 57.763 42.857 0.00 0.00 38.26 3.16
2700 3694 3.571590 TGAGGTAATGCCCAAACTTGTT 58.428 40.909 0.00 0.00 38.26 2.83
2701 3695 4.730966 TGAGGTAATGCCCAAACTTGTTA 58.269 39.130 0.00 0.00 38.26 2.41
2702 3696 4.521256 TGAGGTAATGCCCAAACTTGTTAC 59.479 41.667 0.00 0.00 38.26 2.50
2703 3697 4.475345 AGGTAATGCCCAAACTTGTTACA 58.525 39.130 0.00 0.00 38.26 2.41
2704 3698 4.279922 AGGTAATGCCCAAACTTGTTACAC 59.720 41.667 0.00 0.00 38.26 2.90
2705 3699 4.038162 GGTAATGCCCAAACTTGTTACACA 59.962 41.667 0.00 0.00 0.00 3.72
2706 3700 4.320608 AATGCCCAAACTTGTTACACAG 57.679 40.909 0.00 0.00 0.00 3.66
2707 3701 2.729194 TGCCCAAACTTGTTACACAGT 58.271 42.857 0.00 0.00 0.00 3.55
2708 3702 3.887352 TGCCCAAACTTGTTACACAGTA 58.113 40.909 0.00 0.00 0.00 2.74
2709 3703 3.628487 TGCCCAAACTTGTTACACAGTAC 59.372 43.478 0.00 0.00 0.00 2.73
2710 3704 3.628487 GCCCAAACTTGTTACACAGTACA 59.372 43.478 0.00 0.00 0.00 2.90
2711 3705 4.261031 GCCCAAACTTGTTACACAGTACAG 60.261 45.833 0.00 0.00 0.00 2.74
2712 3706 5.120399 CCCAAACTTGTTACACAGTACAGA 58.880 41.667 0.00 0.00 0.00 3.41
2713 3707 5.007332 CCCAAACTTGTTACACAGTACAGAC 59.993 44.000 0.00 0.00 0.00 3.51
2714 3708 5.276678 CCAAACTTGTTACACAGTACAGACG 60.277 44.000 0.00 0.00 0.00 4.18
2715 3709 4.644103 ACTTGTTACACAGTACAGACGT 57.356 40.909 0.00 0.00 0.00 4.34
2716 3710 5.756195 ACTTGTTACACAGTACAGACGTA 57.244 39.130 0.00 0.00 0.00 3.57
2717 3711 5.755813 ACTTGTTACACAGTACAGACGTAG 58.244 41.667 0.00 0.00 0.00 3.51
2718 3712 5.528690 ACTTGTTACACAGTACAGACGTAGA 59.471 40.000 0.00 0.00 0.00 2.59
2719 3713 5.602458 TGTTACACAGTACAGACGTAGAG 57.398 43.478 0.00 0.00 0.00 2.43
2720 3714 4.453478 TGTTACACAGTACAGACGTAGAGG 59.547 45.833 0.00 0.00 0.00 3.69
2721 3715 1.811359 ACACAGTACAGACGTAGAGGC 59.189 52.381 0.00 0.00 0.00 4.70
2722 3716 1.810755 CACAGTACAGACGTAGAGGCA 59.189 52.381 0.00 0.00 0.00 4.75
2723 3717 1.811359 ACAGTACAGACGTAGAGGCAC 59.189 52.381 0.00 0.00 0.00 5.01
2724 3718 1.810755 CAGTACAGACGTAGAGGCACA 59.189 52.381 0.00 0.00 0.00 4.57
2725 3719 2.423892 CAGTACAGACGTAGAGGCACAT 59.576 50.000 0.00 0.00 0.00 3.21
2726 3720 3.626217 CAGTACAGACGTAGAGGCACATA 59.374 47.826 0.00 0.00 0.00 2.29
2727 3721 3.626670 AGTACAGACGTAGAGGCACATAC 59.373 47.826 0.00 0.00 0.00 2.39
2728 3722 2.443416 ACAGACGTAGAGGCACATACA 58.557 47.619 0.00 0.00 0.00 2.29
2729 3723 3.024547 ACAGACGTAGAGGCACATACAT 58.975 45.455 0.00 0.00 0.00 2.29
2730 3724 4.204799 ACAGACGTAGAGGCACATACATA 58.795 43.478 0.00 0.00 0.00 2.29
2731 3725 4.827835 ACAGACGTAGAGGCACATACATAT 59.172 41.667 0.00 0.00 0.00 1.78
2732 3726 6.002082 ACAGACGTAGAGGCACATACATATA 58.998 40.000 0.00 0.00 0.00 0.86
2733 3727 6.072618 ACAGACGTAGAGGCACATACATATAC 60.073 42.308 0.00 0.00 0.00 1.47
2734 3728 6.002082 AGACGTAGAGGCACATACATATACA 58.998 40.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.395608 GTTGCAATGGAACATGCATGC 59.604 47.619 26.53 11.82 46.14 4.06
1 2 2.413796 GTGTTGCAATGGAACATGCATG 59.586 45.455 25.09 25.09 46.14 4.06
2 3 2.300723 AGTGTTGCAATGGAACATGCAT 59.699 40.909 22.32 7.53 46.14 3.96
8 9 9.450807 GTATATAAATGAGTGTTGCAATGGAAC 57.549 33.333 10.77 10.77 0.00 3.62
9 10 8.629158 GGTATATAAATGAGTGTTGCAATGGAA 58.371 33.333 0.59 0.00 0.00 3.53
10 11 7.998383 AGGTATATAAATGAGTGTTGCAATGGA 59.002 33.333 0.59 0.00 0.00 3.41
11 12 8.169977 AGGTATATAAATGAGTGTTGCAATGG 57.830 34.615 0.59 0.00 0.00 3.16
12 13 8.292448 GGAGGTATATAAATGAGTGTTGCAATG 58.708 37.037 0.59 0.00 0.00 2.82
13 14 8.220559 AGGAGGTATATAAATGAGTGTTGCAAT 58.779 33.333 0.59 0.00 0.00 3.56
14 15 7.573710 AGGAGGTATATAAATGAGTGTTGCAA 58.426 34.615 0.00 0.00 0.00 4.08
15 16 7.136822 AGGAGGTATATAAATGAGTGTTGCA 57.863 36.000 0.00 0.00 0.00 4.08
16 17 8.451908 AAAGGAGGTATATAAATGAGTGTTGC 57.548 34.615 0.00 0.00 0.00 4.17
27 28 9.670442 AGTCCTACATCAAAAGGAGGTATATAA 57.330 33.333 0.00 0.00 41.50 0.98
29 30 9.845214 ATAGTCCTACATCAAAAGGAGGTATAT 57.155 33.333 0.00 0.00 41.50 0.86
31 32 9.670442 TTATAGTCCTACATCAAAAGGAGGTAT 57.330 33.333 0.00 0.00 41.50 2.73
32 33 9.496710 TTTATAGTCCTACATCAAAAGGAGGTA 57.503 33.333 0.00 0.00 42.55 3.08
33 34 7.989947 TTATAGTCCTACATCAAAAGGAGGT 57.010 36.000 0.00 0.00 42.55 3.85
34 35 7.715686 GGTTTATAGTCCTACATCAAAAGGAGG 59.284 40.741 0.00 0.00 42.55 4.30
42 43 6.126623 TGCCATTGGTTTATAGTCCTACATCA 60.127 38.462 4.26 0.00 0.00 3.07
58 59 2.199652 CCCACACGTTGCCATTGGT 61.200 57.895 4.26 0.00 0.00 3.67
69 70 7.962964 AATATTATAGACAATGTCCCACACG 57.037 36.000 10.12 0.00 32.18 4.49
170 172 6.665248 TCTCTCTATCTTGTTCACTCATCCAA 59.335 38.462 0.00 0.00 0.00 3.53
184 186 5.843673 TTCGAACATGCTCTCTCTATCTT 57.156 39.130 0.00 0.00 0.00 2.40
189 191 2.548875 GCATTCGAACATGCTCTCTCT 58.451 47.619 14.92 0.00 45.35 3.10
214 217 4.638421 GGCATATTTAGCACTTGTACACCA 59.362 41.667 0.00 0.00 0.00 4.17
222 227 5.329035 CCTTTGTGGCATATTTAGCACTT 57.671 39.130 0.00 0.00 0.00 3.16
223 228 4.989279 CCTTTGTGGCATATTTAGCACT 57.011 40.909 0.00 0.00 0.00 4.40
246 254 3.313274 TGCTTTCGACGACAGTTTTTC 57.687 42.857 12.29 0.00 0.00 2.29
252 260 3.305964 TCTTAGTTGCTTTCGACGACAG 58.694 45.455 6.65 6.65 0.00 3.51
279 287 3.857157 AGGGTAACAAAAGTGCTCTCA 57.143 42.857 0.00 0.00 39.74 3.27
284 292 5.985911 TCCTATCTAGGGTAACAAAAGTGC 58.014 41.667 3.47 0.00 43.79 4.40
322 330 7.815549 TGAATAACTGTTTACATAGCTCGACAA 59.184 33.333 0.00 0.00 0.00 3.18
326 334 7.307396 CCCATGAATAACTGTTTACATAGCTCG 60.307 40.741 0.00 0.00 0.00 5.03
329 337 6.770785 TCCCCATGAATAACTGTTTACATAGC 59.229 38.462 0.00 0.00 0.00 2.97
337 345 5.203528 CCAAGATCCCCATGAATAACTGTT 58.796 41.667 0.00 0.00 0.00 3.16
342 350 2.517553 TGGCCAAGATCCCCATGAATAA 59.482 45.455 0.61 0.00 0.00 1.40
352 360 1.909700 TTGTTCAGTGGCCAAGATCC 58.090 50.000 7.24 3.43 0.00 3.36
363 371 8.409358 AGCTAACCTTCATTTAATTGTTCAGT 57.591 30.769 0.00 0.00 0.00 3.41
392 400 6.729187 ACTTTTTACTCAAGTGCTTAGCTTG 58.271 36.000 5.60 2.68 43.26 4.01
415 423 8.850452 GCATGAAAAATACTTAGCAACTACAAC 58.150 33.333 0.00 0.00 0.00 3.32
416 424 8.572185 TGCATGAAAAATACTTAGCAACTACAA 58.428 29.630 0.00 0.00 0.00 2.41
417 425 8.020819 GTGCATGAAAAATACTTAGCAACTACA 58.979 33.333 0.00 0.00 32.03 2.74
418 426 7.484959 GGTGCATGAAAAATACTTAGCAACTAC 59.515 37.037 0.00 0.00 35.69 2.73
436 444 2.291209 AATTGGTGACAGGTGCATGA 57.709 45.000 0.00 0.00 44.54 3.07
437 445 5.734220 GCTTATAATTGGTGACAGGTGCATG 60.734 44.000 0.00 0.00 44.54 4.06
438 446 4.339247 GCTTATAATTGGTGACAGGTGCAT 59.661 41.667 0.00 0.00 44.54 3.96
439 447 3.694072 GCTTATAATTGGTGACAGGTGCA 59.306 43.478 0.00 0.00 44.54 4.57
440 448 3.694072 TGCTTATAATTGGTGACAGGTGC 59.306 43.478 0.00 0.00 44.54 5.01
441 449 4.943705 AGTGCTTATAATTGGTGACAGGTG 59.056 41.667 0.00 0.00 44.54 4.00
442 450 5.179452 AGTGCTTATAATTGGTGACAGGT 57.821 39.130 0.00 0.00 44.54 4.00
443 451 6.515272 AAAGTGCTTATAATTGGTGACAGG 57.485 37.500 0.00 0.00 44.54 4.00
444 452 6.250819 CGAAAGTGCTTATAATTGGTGACAG 58.749 40.000 0.00 0.00 44.54 3.51
445 453 5.391523 GCGAAAGTGCTTATAATTGGTGACA 60.392 40.000 0.00 0.00 39.83 3.58
453 1019 5.065218 CCTTCAGTGCGAAAGTGCTTATAAT 59.935 40.000 0.00 0.00 31.71 1.28
454 1020 4.391830 CCTTCAGTGCGAAAGTGCTTATAA 59.608 41.667 0.00 0.00 31.71 0.98
456 1022 2.744202 CCTTCAGTGCGAAAGTGCTTAT 59.256 45.455 0.00 0.00 31.71 1.73
476 1042 6.110411 TGCTACTACCAATATTAGGCTTCC 57.890 41.667 0.00 0.00 0.00 3.46
479 1045 6.996180 TCTTGCTACTACCAATATTAGGCT 57.004 37.500 0.00 0.00 0.00 4.58
509 1075 2.190841 GGGACACGTGTGTTTGGGG 61.191 63.158 28.82 0.00 45.05 4.96
656 1228 2.317609 CGTAACACCTGCGCTTGCT 61.318 57.895 9.73 0.00 40.12 3.91
679 1251 0.397957 TAGAAGGACCATGGCGGCTA 60.398 55.000 13.04 4.04 39.03 3.93
692 1264 6.864342 TGTTTCCTTACGATTCTCTAGAAGG 58.136 40.000 0.00 0.00 37.48 3.46
706 1662 8.205131 TCTCTTGTTTACACTTGTTTCCTTAC 57.795 34.615 0.00 0.00 0.00 2.34
739 1697 1.366366 CTTCCGTTCCGTGTGACCT 59.634 57.895 0.00 0.00 0.00 3.85
951 1915 1.539712 GGCTTGCTTGCTTTCTTTGCT 60.540 47.619 1.96 0.00 0.00 3.91
989 1957 2.808202 CGCTCCTCCATGTCTTATTGGG 60.808 54.545 0.00 0.00 33.62 4.12
994 1962 1.823295 GCCGCTCCTCCATGTCTTA 59.177 57.895 0.00 0.00 0.00 2.10
1138 2109 4.117661 GAAGAGCTCGTCGGCCGT 62.118 66.667 27.15 3.60 37.94 5.68
1558 2529 3.249189 TTTGCTGTCCCGGCCTCT 61.249 61.111 0.00 0.00 34.37 3.69
1579 2550 2.910479 TGTGTCGAGCTCGGTGGT 60.910 61.111 33.98 0.00 40.29 4.16
1854 2834 6.458206 CCGTTCAACAATCCAGTTATACCATG 60.458 42.308 0.00 0.00 0.00 3.66
1875 2855 1.189524 TGGACGACCTCAATCCCGTT 61.190 55.000 5.33 0.00 35.22 4.44
1943 2923 3.056250 CCGATATCCCTGACTGAATCCAG 60.056 52.174 0.00 0.00 45.76 3.86
1955 2935 0.191064 TTGGAGAGCCCGATATCCCT 59.809 55.000 0.00 0.00 37.93 4.20
1962 2942 0.250234 CATTGACTTGGAGAGCCCGA 59.750 55.000 0.00 0.00 37.93 5.14
2198 3183 7.967854 ACAAAATATTCATGTTCGTGGTGTATG 59.032 33.333 0.00 0.00 0.00 2.39
2207 3192 7.951287 TGATGCAAACAAAATATTCATGTTCG 58.049 30.769 15.83 9.25 36.33 3.95
2218 3203 5.301551 TGGTAGTGACTGATGCAAACAAAAT 59.698 36.000 0.00 0.00 0.00 1.82
2224 3209 3.070878 TGACTGGTAGTGACTGATGCAAA 59.929 43.478 0.00 0.00 0.00 3.68
2355 3348 4.320788 GGTGGTTGCATGAGAAAGAAGAAG 60.321 45.833 0.00 0.00 0.00 2.85
2356 3349 3.569701 GGTGGTTGCATGAGAAAGAAGAA 59.430 43.478 0.00 0.00 0.00 2.52
2357 3350 3.149196 GGTGGTTGCATGAGAAAGAAGA 58.851 45.455 0.00 0.00 0.00 2.87
2369 3362 2.443016 GGTGGGTTGGTGGTTGCA 60.443 61.111 0.00 0.00 0.00 4.08
2376 3369 3.821830 TAGGGCTGGGTGGGTTGGT 62.822 63.158 0.00 0.00 0.00 3.67
2466 3460 3.712881 GACGACAACCAGCACGGC 61.713 66.667 0.00 0.00 39.03 5.68
2476 3470 1.476891 GATAGTCAGCAGGGACGACAA 59.523 52.381 0.00 0.00 42.62 3.18
2478 3472 1.335496 GAGATAGTCAGCAGGGACGAC 59.665 57.143 0.00 0.00 42.62 4.34
2486 3480 3.226777 GGGCTTAGAGAGATAGTCAGCA 58.773 50.000 0.00 0.00 0.00 4.41
2487 3481 2.560981 GGGGCTTAGAGAGATAGTCAGC 59.439 54.545 0.00 0.00 0.00 4.26
2489 3483 3.567397 GTGGGGCTTAGAGAGATAGTCA 58.433 50.000 0.00 0.00 0.00 3.41
2493 3487 1.480683 CGGGTGGGGCTTAGAGAGATA 60.481 57.143 0.00 0.00 0.00 1.98
2511 3505 2.014128 GGTACATGGGTTGTTCATCGG 58.986 52.381 0.00 0.00 39.87 4.18
2525 3519 2.446036 GGAGCCGAGGGGGTACAT 60.446 66.667 0.00 0.00 46.15 2.29
2527 3521 4.828296 TCGGAGCCGAGGGGGTAC 62.828 72.222 7.66 0.00 46.15 3.34
2581 3575 3.877508 GCCTTGTCCCACATAGTAATGAC 59.122 47.826 0.00 0.00 36.54 3.06
2635 3629 0.454452 TCGTCGCACGTTCTCAGATG 60.454 55.000 8.22 0.00 43.14 2.90
2639 3633 0.728129 GTCATCGTCGCACGTTCTCA 60.728 55.000 8.22 0.00 43.14 3.27
2645 3639 0.861866 CCTGTAGTCATCGTCGCACG 60.862 60.000 2.79 2.79 44.19 5.34
2651 3645 3.257375 TGTGCTTTACCTGTAGTCATCGT 59.743 43.478 0.00 0.00 0.00 3.73
2665 3659 4.901197 TTACCTCATGGAGTGTGCTTTA 57.099 40.909 0.00 0.00 37.04 1.85
2671 3665 1.212935 GGGCATTACCTCATGGAGTGT 59.787 52.381 0.00 0.00 39.10 3.55
2679 3673 3.237268 ACAAGTTTGGGCATTACCTCA 57.763 42.857 0.00 0.00 39.10 3.86
2698 3692 4.671250 GCCTCTACGTCTGTACTGTGTAAC 60.671 50.000 0.00 0.00 37.35 2.50
2699 3693 3.438087 GCCTCTACGTCTGTACTGTGTAA 59.562 47.826 0.00 0.00 0.00 2.41
2700 3694 3.005554 GCCTCTACGTCTGTACTGTGTA 58.994 50.000 0.00 1.54 0.00 2.90
2701 3695 1.811359 GCCTCTACGTCTGTACTGTGT 59.189 52.381 0.00 0.38 0.00 3.72
2702 3696 1.810755 TGCCTCTACGTCTGTACTGTG 59.189 52.381 0.00 0.00 0.00 3.66
2703 3697 1.811359 GTGCCTCTACGTCTGTACTGT 59.189 52.381 0.00 0.00 0.00 3.55
2704 3698 1.810755 TGTGCCTCTACGTCTGTACTG 59.189 52.381 0.00 0.00 0.00 2.74
2705 3699 2.195741 TGTGCCTCTACGTCTGTACT 57.804 50.000 0.00 0.00 0.00 2.73
2706 3700 3.376234 TGTATGTGCCTCTACGTCTGTAC 59.624 47.826 0.00 0.00 0.00 2.90
2707 3701 3.613030 TGTATGTGCCTCTACGTCTGTA 58.387 45.455 0.00 0.00 0.00 2.74
2708 3702 2.443416 TGTATGTGCCTCTACGTCTGT 58.557 47.619 0.00 0.00 0.00 3.41
2709 3703 3.717400 ATGTATGTGCCTCTACGTCTG 57.283 47.619 0.00 0.00 0.00 3.51
2710 3704 6.002082 TGTATATGTATGTGCCTCTACGTCT 58.998 40.000 0.00 0.00 0.00 4.18
2711 3705 6.250344 TGTATATGTATGTGCCTCTACGTC 57.750 41.667 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.