Multiple sequence alignment - TraesCS3B01G428400

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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 TraesCS3B01G428400 chr3B 100.000 2504 0 0 1 2504 667172703 667175206 0.000000e+00 4625.0
1 TraesCS3B01G428400 chr3D 93.628 1491 48 18 740 2210 505404400 505405863 0.000000e+00 2183.0
2 TraesCS3B01G428400 chr3D 93.645 535 18 8 1 534 505403573 505404092 0.000000e+00 785.0
3 TraesCS3B01G428400 chr3D 92.568 296 22 0 2209 2504 505405944 505406239 2.300000e-115 425.0
4 TraesCS3B01G428400 chr3D 92.857 56 4 0 624 679 505404289 505404344 5.740000e-12 82.4
5 TraesCS3B01G428400 chr3D 96.970 33 0 1 579 610 505404277 505404309 1.000000e-03 54.7
6 TraesCS3B01G428400 chr3A 94.355 992 31 12 740 1712 643545520 643546505 0.000000e+00 1498.0
7 TraesCS3B01G428400 chr3A 88.000 625 42 9 1704 2321 643546843 643547441 0.000000e+00 708.0
8 TraesCS3B01G428400 chr3A 95.152 330 12 3 1 330 643544825 643545150 3.690000e-143 518.0
9 TraesCS3B01G428400 chr3A 99.057 106 1 0 455 560 643545198 643545303 9.140000e-45 191.0
10 TraesCS3B01G428400 chr3A 98.529 68 1 0 374 441 643545147 643545214 1.220000e-23 121.0
11 TraesCS3B01G428400 chr3A 92.593 81 4 2 2425 2504 643547534 643547613 5.660000e-22 115.0


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 TraesCS3B01G428400 chr3B 667172703 667175206 2503 False 4625.000000 4625 100.000000 1 2504 1 chr3B.!!$F1 2503
1 TraesCS3B01G428400 chr3D 505403573 505406239 2666 False 706.020000 2183 93.933600 1 2504 5 chr3D.!!$F1 2503
2 TraesCS3B01G428400 chr3A 643544825 643547613 2788 False 525.166667 1498 94.614333 1 2504 6 chr3A.!!$F1 2503

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
609 678 0.249741 AGTGGTTGTCTAGCGCGTTT 60.25 50.0 8.43 0.0 39.67 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2864 0.0293 TTTTGAGCAGCTGAACGTGC 59.971 50.0 20.43 0.47 40.17 5.34 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
96 97 3.589288 AGGGAGATGTCCTAAGTGCTTTT 59.411 43.478 9.08 0.00 43.36 2.27
97 98 4.043435 AGGGAGATGTCCTAAGTGCTTTTT 59.957 41.667 9.08 0.00 43.36 1.94
129 130 7.097192 TCATCATCTTGTATAATTAGTCCGGC 58.903 38.462 0.00 0.00 0.00 6.13
163 164 7.999450 TTATCGGTGTTAATGTTAAAACCCT 57.001 32.000 15.80 8.64 44.65 4.34
223 224 3.281727 TGTGTCTGGCTCCATAAATCC 57.718 47.619 0.00 0.00 0.00 3.01
245 246 3.400505 GGTGTAATTTAAGCACCGAGC 57.599 47.619 0.00 0.00 42.43 5.03
289 290 4.997395 TCACATTGTTCTGAAACTAGCTCC 59.003 41.667 0.00 0.00 36.30 4.70
300 301 3.589495 AACTAGCTCCGTACCTGTTTC 57.411 47.619 0.00 0.00 0.00 2.78
355 357 8.902806 TGTGATACTGAAACTCTTGTGATTTTT 58.097 29.630 0.00 0.00 0.00 1.94
578 647 3.359950 GAAGGATTCTCTTGGCAACCAT 58.640 45.455 0.00 0.00 43.23 3.55
579 648 3.463048 AGGATTCTCTTGGCAACCATT 57.537 42.857 0.00 0.00 31.53 3.16
580 649 3.359950 AGGATTCTCTTGGCAACCATTC 58.640 45.455 0.00 0.00 31.53 2.67
593 662 6.638610 TGGCAACCATTCCATTTTTATAGTG 58.361 36.000 0.00 0.00 0.00 2.74
595 664 6.351796 GGCAACCATTCCATTTTTATAGTGGT 60.352 38.462 0.00 0.00 40.21 4.16
596 665 7.102993 GCAACCATTCCATTTTTATAGTGGTT 58.897 34.615 0.00 0.00 46.39 3.67
598 667 7.790782 ACCATTCCATTTTTATAGTGGTTGT 57.209 32.000 0.00 0.00 35.31 3.32
599 668 7.836842 ACCATTCCATTTTTATAGTGGTTGTC 58.163 34.615 0.00 0.00 35.31 3.18
600 669 7.673926 ACCATTCCATTTTTATAGTGGTTGTCT 59.326 33.333 0.00 0.00 35.31 3.41
603 672 7.859325 TCCATTTTTATAGTGGTTGTCTAGC 57.141 36.000 0.00 0.00 34.61 3.42
605 674 5.789710 TTTTTATAGTGGTTGTCTAGCGC 57.210 39.130 0.00 0.00 35.00 5.92
606 675 2.768833 TATAGTGGTTGTCTAGCGCG 57.231 50.000 0.00 0.00 39.67 6.86
607 676 0.815734 ATAGTGGTTGTCTAGCGCGT 59.184 50.000 8.43 0.00 39.67 6.01
608 677 0.599558 TAGTGGTTGTCTAGCGCGTT 59.400 50.000 8.43 3.54 39.67 4.84
609 678 0.249741 AGTGGTTGTCTAGCGCGTTT 60.250 50.000 8.43 0.00 39.67 3.60
610 679 1.000060 AGTGGTTGTCTAGCGCGTTTA 60.000 47.619 8.43 0.00 39.67 2.01
612 681 2.028883 GTGGTTGTCTAGCGCGTTTATC 59.971 50.000 8.43 0.00 0.00 1.75
614 683 2.669434 GGTTGTCTAGCGCGTTTATCAA 59.331 45.455 8.43 6.04 0.00 2.57
615 684 3.123959 GGTTGTCTAGCGCGTTTATCAAA 59.876 43.478 8.43 0.00 0.00 2.69
616 685 4.377635 GGTTGTCTAGCGCGTTTATCAAAA 60.378 41.667 8.43 0.00 0.00 2.44
617 686 4.994220 TGTCTAGCGCGTTTATCAAAAA 57.006 36.364 8.43 0.00 0.00 1.94
646 758 3.058501 GTGGTTGTATAGCGCAGTTTGTT 60.059 43.478 11.47 0.00 34.91 2.83
678 790 1.401539 GCCAAGATCGTGGAAACTTGC 60.402 52.381 29.13 9.60 41.65 4.01
679 791 1.200020 CCAAGATCGTGGAAACTTGCC 59.800 52.381 21.80 0.00 41.65 4.52
680 792 1.200020 CAAGATCGTGGAAACTTGCCC 59.800 52.381 0.02 0.00 34.46 5.36
681 793 0.322546 AGATCGTGGAAACTTGCCCC 60.323 55.000 0.00 0.00 0.00 5.80
682 794 1.644786 GATCGTGGAAACTTGCCCCG 61.645 60.000 0.00 0.00 0.00 5.73
683 795 2.406002 ATCGTGGAAACTTGCCCCGT 62.406 55.000 0.00 0.00 0.00 5.28
684 796 2.190841 CGTGGAAACTTGCCCCGTT 61.191 57.895 0.00 0.00 0.00 4.44
685 797 0.885596 CGTGGAAACTTGCCCCGTTA 60.886 55.000 0.00 0.00 0.00 3.18
686 798 1.320507 GTGGAAACTTGCCCCGTTAA 58.679 50.000 0.00 0.00 0.00 2.01
687 799 1.682323 GTGGAAACTTGCCCCGTTAAA 59.318 47.619 0.00 0.00 0.00 1.52
688 800 1.957877 TGGAAACTTGCCCCGTTAAAG 59.042 47.619 0.00 0.00 0.00 1.85
689 801 2.232399 GGAAACTTGCCCCGTTAAAGA 58.768 47.619 0.00 0.00 0.00 2.52
690 802 2.624364 GGAAACTTGCCCCGTTAAAGAA 59.376 45.455 0.00 0.00 0.00 2.52
691 803 3.068448 GGAAACTTGCCCCGTTAAAGAAA 59.932 43.478 0.00 0.00 0.00 2.52
692 804 4.441773 GGAAACTTGCCCCGTTAAAGAAAA 60.442 41.667 0.00 0.00 0.00 2.29
693 805 4.739587 AACTTGCCCCGTTAAAGAAAAA 57.260 36.364 0.00 0.00 0.00 1.94
694 806 4.316205 ACTTGCCCCGTTAAAGAAAAAG 57.684 40.909 0.00 0.00 0.00 2.27
695 807 3.955551 ACTTGCCCCGTTAAAGAAAAAGA 59.044 39.130 0.00 0.00 0.00 2.52
696 808 4.587262 ACTTGCCCCGTTAAAGAAAAAGAT 59.413 37.500 0.00 0.00 0.00 2.40
697 809 4.776795 TGCCCCGTTAAAGAAAAAGATC 57.223 40.909 0.00 0.00 0.00 2.75
698 810 3.189702 TGCCCCGTTAAAGAAAAAGATCG 59.810 43.478 0.00 0.00 0.00 3.69
699 811 3.189910 GCCCCGTTAAAGAAAAAGATCGT 59.810 43.478 0.00 0.00 0.00 3.73
700 812 4.719040 CCCCGTTAAAGAAAAAGATCGTG 58.281 43.478 0.00 0.00 0.00 4.35
701 813 4.379082 CCCCGTTAAAGAAAAAGATCGTGG 60.379 45.833 0.00 0.00 0.00 4.94
702 814 4.453136 CCCGTTAAAGAAAAAGATCGTGGA 59.547 41.667 0.00 0.00 0.00 4.02
703 815 5.049267 CCCGTTAAAGAAAAAGATCGTGGAA 60.049 40.000 0.00 0.00 0.00 3.53
704 816 6.432107 CCGTTAAAGAAAAAGATCGTGGAAA 58.568 36.000 0.00 0.00 0.00 3.13
705 817 6.358822 CCGTTAAAGAAAAAGATCGTGGAAAC 59.641 38.462 0.00 0.00 0.00 2.78
706 818 7.130269 CGTTAAAGAAAAAGATCGTGGAAACT 58.870 34.615 0.00 0.00 0.00 2.66
707 819 7.642586 CGTTAAAGAAAAAGATCGTGGAAACTT 59.357 33.333 0.00 0.00 0.00 2.66
708 820 8.743099 GTTAAAGAAAAAGATCGTGGAAACTTG 58.257 33.333 0.00 0.00 0.00 3.16
719 831 3.751175 CGTGGAAACTTGCAGAGGATTTA 59.249 43.478 0.00 0.00 0.00 1.40
723 835 5.003804 GGAAACTTGCAGAGGATTTAGTCA 58.996 41.667 0.00 0.00 0.00 3.41
736 848 9.739276 AGAGGATTTAGTCATATACTGAGAGAG 57.261 37.037 0.00 0.00 39.39 3.20
737 849 9.733556 GAGGATTTAGTCATATACTGAGAGAGA 57.266 37.037 0.00 0.00 39.39 3.10
893 1033 1.522580 GCGAGTCTGCCCTCCATTC 60.523 63.158 0.00 0.00 0.00 2.67
921 1061 1.746220 CTCTGGTTCGATCGACTCCTT 59.254 52.381 27.48 0.00 0.00 3.36
932 1072 3.315749 GATCGACTCCTTCGGTACAGAAT 59.684 47.826 8.94 0.00 42.81 2.40
1513 1664 0.233590 CGAGGAGTAGATCAGCGACG 59.766 60.000 0.00 0.00 0.00 5.12
1514 1665 0.589223 GAGGAGTAGATCAGCGACGG 59.411 60.000 0.00 0.00 0.00 4.79
1515 1666 0.180642 AGGAGTAGATCAGCGACGGA 59.819 55.000 0.00 0.00 0.00 4.69
1516 1667 0.308376 GGAGTAGATCAGCGACGGAC 59.692 60.000 0.00 0.00 0.00 4.79
1517 1668 0.042013 GAGTAGATCAGCGACGGACG 60.042 60.000 0.00 0.00 45.66 4.79
1518 1669 1.009900 GTAGATCAGCGACGGACGG 60.010 63.158 1.66 0.00 42.83 4.79
1571 1725 1.005630 GGATCGGAGCGGGAATCTG 60.006 63.158 0.00 0.00 0.00 2.90
1689 1851 1.003580 ACCAGATTACTGCCACACTGG 59.996 52.381 0.00 0.00 46.78 4.00
1702 2210 3.307480 GCCACACTGGTATCCTAAACTGT 60.307 47.826 0.00 0.00 40.46 3.55
1767 2275 4.709886 TCAGTAATAGGAGCACTGCAGTTA 59.290 41.667 18.94 7.19 39.60 2.24
1769 2277 2.611225 ATAGGAGCACTGCAGTTAGC 57.389 50.000 18.94 18.87 45.96 3.09
1808 2316 3.551846 AGCAATGCATGATGACTGATGA 58.448 40.909 8.35 0.00 0.00 2.92
1826 2334 6.068461 TGATGAGTACTCCAGAGTAGAGTT 57.932 41.667 20.11 0.00 41.87 3.01
1834 2342 4.018779 ACTCCAGAGTAGAGTTGTAGCTCT 60.019 45.833 0.00 3.75 41.87 4.09
1868 2376 0.242825 CAATGGGAGCACTGCACTTG 59.757 55.000 3.30 0.00 0.00 3.16
1879 2387 0.963962 CTGCACTTGGACAAAGCCAT 59.036 50.000 6.67 0.00 39.76 4.40
1933 2444 1.078426 ATGTACCTGCCGAAGTGCC 60.078 57.895 0.00 0.00 0.00 5.01
1938 2449 1.973281 CCTGCCGAAGTGCCAACAT 60.973 57.895 0.00 0.00 0.00 2.71
1945 2456 3.340034 CCGAAGTGCCAACATAGGTTAA 58.660 45.455 0.00 0.00 34.87 2.01
1990 2502 2.365408 ACTTGAACCAGCGTAGTAGC 57.635 50.000 0.00 0.00 37.41 3.58
1996 2511 0.731417 ACCAGCGTAGTAGCACGTAG 59.269 55.000 0.00 0.00 43.79 3.51
1999 2514 1.664659 CAGCGTAGTAGCACGTAGAGT 59.335 52.381 0.00 0.00 43.79 3.24
2080 2595 6.936335 TGACTACACACAATCAATGAATCTGT 59.064 34.615 0.00 0.00 0.00 3.41
2096 2612 0.107508 CTGTAGTGGATGTGCCTGGG 60.108 60.000 0.00 0.00 37.63 4.45
2097 2613 1.452108 GTAGTGGATGTGCCTGGGC 60.452 63.158 4.43 4.43 42.35 5.36
2098 2614 2.679342 TAGTGGATGTGCCTGGGCC 61.679 63.158 9.28 0.00 41.09 5.80
2099 2615 4.052518 GTGGATGTGCCTGGGCCT 62.053 66.667 4.53 0.00 41.09 5.19
2119 2635 0.239347 GCCTGCATGCGTTATGATCC 59.761 55.000 14.09 0.00 39.21 3.36
2120 2636 1.596603 CCTGCATGCGTTATGATCCA 58.403 50.000 14.09 0.00 39.21 3.41
2121 2637 2.156917 CCTGCATGCGTTATGATCCAT 58.843 47.619 14.09 0.00 39.21 3.41
2122 2638 2.161012 CCTGCATGCGTTATGATCCATC 59.839 50.000 14.09 0.00 39.21 3.51
2198 2714 0.319727 GATGATCAGCTCAGCTCGGG 60.320 60.000 3.07 0.00 36.40 5.14
2216 2814 6.313905 AGCTCGGGCAGATATTATATTTTTCG 59.686 38.462 11.40 0.00 41.70 3.46
2220 2818 8.525316 TCGGGCAGATATTATATTTTTCGACTA 58.475 33.333 0.00 0.00 0.00 2.59
2237 2835 3.430931 GACTAAGCGAGACATGTGAGTC 58.569 50.000 1.15 0.92 38.81 3.36
2265 2864 2.650608 GCTGAAAAAGTAGCACCAACG 58.349 47.619 0.00 0.00 39.67 4.10
2278 2877 2.425773 CAACGCACGTTCAGCTGC 60.426 61.111 9.47 0.00 36.00 5.25
2297 2896 6.483974 CAGCTGCTCAAAAGATATGAAGAGAT 59.516 38.462 0.00 0.00 0.00 2.75
2351 2958 7.083875 AGATGAATACCGTTTTACATGGTTG 57.916 36.000 0.00 0.00 42.98 3.77
2365 2989 2.957491 TGGTTGGTTGCTTGTTGAAG 57.043 45.000 0.00 0.00 0.00 3.02
2414 3038 3.683847 GCTGGCTCTTGGTCTTGTATCAT 60.684 47.826 0.00 0.00 0.00 2.45
2420 3044 6.370994 GGCTCTTGGTCTTGTATCATATCATG 59.629 42.308 0.00 0.00 0.00 3.07
2421 3045 6.933521 GCTCTTGGTCTTGTATCATATCATGT 59.066 38.462 0.00 0.00 0.00 3.21
2423 3047 8.021898 TCTTGGTCTTGTATCATATCATGTGA 57.978 34.615 0.00 0.00 0.00 3.58
2454 3078 2.567497 GGTGGGGACGACGAGTGAA 61.567 63.158 0.00 0.00 0.00 3.18
2474 3098 4.916293 GATGGATCAGCCGGCGCA 62.916 66.667 23.20 12.42 40.66 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 7.956558 ACATTAACACCGATAAAAACGAGTAG 58.043 34.615 0.00 0.00 0.00 2.57
289 290 4.319549 GGCAAGAAAAGAGAAACAGGTACG 60.320 45.833 0.00 0.00 0.00 3.67
300 301 7.206981 TGAATTCAAGTAGGCAAGAAAAGAG 57.793 36.000 5.45 0.00 0.00 2.85
355 357 4.946160 ACCAGATCTTAACCCCATTCAA 57.054 40.909 0.00 0.00 0.00 2.69
363 365 8.771766 GGTAAATTTCGATACCAGATCTTAACC 58.228 37.037 7.87 0.00 33.04 2.85
369 371 7.787725 AACAGGTAAATTTCGATACCAGATC 57.212 36.000 13.92 0.00 35.15 2.75
450 452 3.913763 CCAAACGTGCAACATACTTCATG 59.086 43.478 0.00 0.00 40.78 3.07
451 453 3.611530 GCCAAACGTGCAACATACTTCAT 60.612 43.478 0.00 0.00 35.74 2.57
452 454 2.287308 GCCAAACGTGCAACATACTTCA 60.287 45.455 0.00 0.00 35.74 3.02
453 455 2.287308 TGCCAAACGTGCAACATACTTC 60.287 45.455 0.00 0.00 35.74 3.01
454 456 1.678627 TGCCAAACGTGCAACATACTT 59.321 42.857 0.00 0.00 35.74 2.24
455 457 1.313772 TGCCAAACGTGCAACATACT 58.686 45.000 0.00 0.00 35.74 2.12
456 458 1.984990 CATGCCAAACGTGCAACATAC 59.015 47.619 2.95 0.00 42.92 2.39
457 459 1.067985 CCATGCCAAACGTGCAACATA 60.068 47.619 2.95 0.00 42.92 2.29
578 647 7.065324 CGCTAGACAACCACTATAAAAATGGAA 59.935 37.037 0.00 0.00 36.94 3.53
579 648 6.537301 CGCTAGACAACCACTATAAAAATGGA 59.463 38.462 0.00 0.00 36.94 3.41
580 649 6.715464 CGCTAGACAACCACTATAAAAATGG 58.285 40.000 0.00 0.00 39.57 3.16
593 662 2.264813 TGATAAACGCGCTAGACAACC 58.735 47.619 5.73 0.00 0.00 3.77
595 664 4.994220 TTTTGATAAACGCGCTAGACAA 57.006 36.364 5.73 5.21 0.00 3.18
596 665 4.994220 TTTTTGATAAACGCGCTAGACA 57.006 36.364 5.73 0.00 0.00 3.41
619 688 3.818773 ACTGCGCTATACAACCACTTTTT 59.181 39.130 9.73 0.00 0.00 1.94
620 689 3.408634 ACTGCGCTATACAACCACTTTT 58.591 40.909 9.73 0.00 0.00 2.27
622 734 2.762535 ACTGCGCTATACAACCACTT 57.237 45.000 9.73 0.00 0.00 3.16
632 744 0.321298 ACGGGAACAAACTGCGCTAT 60.321 50.000 9.73 0.00 0.00 2.97
678 790 4.379082 CCACGATCTTTTTCTTTAACGGGG 60.379 45.833 0.00 0.00 36.78 5.73
679 791 4.453136 TCCACGATCTTTTTCTTTAACGGG 59.547 41.667 0.00 0.00 0.00 5.28
680 792 5.600908 TCCACGATCTTTTTCTTTAACGG 57.399 39.130 0.00 0.00 0.00 4.44
681 793 7.130269 AGTTTCCACGATCTTTTTCTTTAACG 58.870 34.615 0.00 0.00 0.00 3.18
682 794 8.743099 CAAGTTTCCACGATCTTTTTCTTTAAC 58.257 33.333 0.00 0.00 0.00 2.01
683 795 7.434013 GCAAGTTTCCACGATCTTTTTCTTTAA 59.566 33.333 0.00 0.00 0.00 1.52
684 796 6.915843 GCAAGTTTCCACGATCTTTTTCTTTA 59.084 34.615 0.00 0.00 0.00 1.85
685 797 5.748630 GCAAGTTTCCACGATCTTTTTCTTT 59.251 36.000 0.00 0.00 0.00 2.52
686 798 5.163561 TGCAAGTTTCCACGATCTTTTTCTT 60.164 36.000 0.00 0.00 0.00 2.52
687 799 4.338118 TGCAAGTTTCCACGATCTTTTTCT 59.662 37.500 0.00 0.00 0.00 2.52
688 800 4.606961 TGCAAGTTTCCACGATCTTTTTC 58.393 39.130 0.00 0.00 0.00 2.29
689 801 4.338118 TCTGCAAGTTTCCACGATCTTTTT 59.662 37.500 0.00 0.00 33.76 1.94
690 802 3.882888 TCTGCAAGTTTCCACGATCTTTT 59.117 39.130 0.00 0.00 33.76 2.27
691 803 3.476552 TCTGCAAGTTTCCACGATCTTT 58.523 40.909 0.00 0.00 33.76 2.52
692 804 3.070018 CTCTGCAAGTTTCCACGATCTT 58.930 45.455 0.00 0.00 33.76 2.40
693 805 2.613977 CCTCTGCAAGTTTCCACGATCT 60.614 50.000 0.00 0.00 33.76 2.75
694 806 1.734465 CCTCTGCAAGTTTCCACGATC 59.266 52.381 0.00 0.00 33.76 3.69
695 807 1.347707 TCCTCTGCAAGTTTCCACGAT 59.652 47.619 0.00 0.00 33.76 3.73
696 808 0.756294 TCCTCTGCAAGTTTCCACGA 59.244 50.000 0.00 0.00 33.76 4.35
697 809 1.813513 ATCCTCTGCAAGTTTCCACG 58.186 50.000 0.00 0.00 33.76 4.94
698 810 4.762251 ACTAAATCCTCTGCAAGTTTCCAC 59.238 41.667 0.00 0.00 33.76 4.02
699 811 4.985538 ACTAAATCCTCTGCAAGTTTCCA 58.014 39.130 0.00 0.00 33.76 3.53
700 812 5.003804 TGACTAAATCCTCTGCAAGTTTCC 58.996 41.667 0.00 0.00 33.76 3.13
701 813 6.749923 ATGACTAAATCCTCTGCAAGTTTC 57.250 37.500 0.00 0.00 33.76 2.78
702 814 9.331282 GTATATGACTAAATCCTCTGCAAGTTT 57.669 33.333 0.00 0.00 33.76 2.66
703 815 8.709308 AGTATATGACTAAATCCTCTGCAAGTT 58.291 33.333 0.00 0.00 36.27 2.66
704 816 8.147058 CAGTATATGACTAAATCCTCTGCAAGT 58.853 37.037 0.00 0.00 35.64 3.16
705 817 8.363390 TCAGTATATGACTAAATCCTCTGCAAG 58.637 37.037 0.00 0.00 35.64 4.01
706 818 8.250143 TCAGTATATGACTAAATCCTCTGCAA 57.750 34.615 0.00 0.00 35.64 4.08
707 819 7.725844 TCTCAGTATATGACTAAATCCTCTGCA 59.274 37.037 0.00 0.00 35.64 4.41
708 820 8.116651 TCTCAGTATATGACTAAATCCTCTGC 57.883 38.462 0.00 0.00 35.64 4.26
719 831 6.274436 TCCCAGATCTCTCTCAGTATATGACT 59.726 42.308 0.00 0.00 39.82 3.41
723 835 8.814931 CAAAATCCCAGATCTCTCTCAGTATAT 58.185 37.037 0.00 0.00 0.00 0.86
736 848 4.578105 GTGACCAGATCAAAATCCCAGATC 59.422 45.833 0.00 0.00 39.72 2.75
737 849 4.018141 TGTGACCAGATCAAAATCCCAGAT 60.018 41.667 0.00 0.00 39.72 2.90
921 1061 2.278849 TCGGGCAATTCTGTACCGA 58.721 52.632 0.00 0.00 45.56 4.69
932 1072 1.462616 CTGTGATTTGGATCGGGCAA 58.537 50.000 0.00 0.00 34.91 4.52
1513 1664 1.463674 ATGCAATTCTTGTCCCGTCC 58.536 50.000 0.00 0.00 0.00 4.79
1702 2210 1.405105 GCCTTTGTTCTTGTGCACTCA 59.595 47.619 19.41 3.62 0.00 3.41
1767 2275 0.322008 GCACCTGGCTTTGTCTAGCT 60.322 55.000 0.00 0.00 40.99 3.32
1769 2277 1.446907 CTGCACCTGGCTTTGTCTAG 58.553 55.000 0.00 0.00 45.15 2.43
1808 2316 5.045432 AGCTACAACTCTACTCTGGAGTACT 60.045 44.000 6.39 0.00 42.39 2.73
1826 2334 3.165071 TGACAAGATCACCAGAGCTACA 58.835 45.455 0.00 0.00 40.18 2.74
1834 2342 2.439409 CCATTGCTGACAAGATCACCA 58.561 47.619 0.00 0.00 39.69 4.17
1868 2376 1.105457 TGCTGCATATGGCTTTGTCC 58.895 50.000 4.56 0.00 45.15 4.02
1933 2444 6.737254 ACATTTCTCGGTTAACCTATGTTG 57.263 37.500 22.12 13.97 35.87 3.33
1938 2449 6.875195 CCAGTAAACATTTCTCGGTTAACCTA 59.125 38.462 22.12 10.88 0.00 3.08
1945 2456 3.134574 TGCCAGTAAACATTTCTCGGT 57.865 42.857 0.00 0.00 0.00 4.69
1990 2502 3.784701 AATGCTCTACCACTCTACGTG 57.215 47.619 0.00 0.00 43.41 4.49
1996 2511 7.330700 GCAGAGATAAATAATGCTCTACCACTC 59.669 40.741 0.00 0.00 36.06 3.51
1999 2514 6.043127 TGGCAGAGATAAATAATGCTCTACCA 59.957 38.462 0.00 0.00 44.56 3.25
2008 2523 5.439721 TGCACTGTGGCAGAGATAAATAAT 58.560 37.500 19.57 0.00 39.25 1.28
2059 2574 7.334171 CCACTACAGATTCATTGATTGTGTGTA 59.666 37.037 17.00 10.69 0.00 2.90
2080 2595 2.679342 GGCCCAGGCACATCCACTA 61.679 63.158 11.50 0.00 44.11 2.74
2097 2613 1.096967 TCATAACGCATGCAGGCAGG 61.097 55.000 24.53 10.53 34.35 4.85
2098 2614 0.949397 ATCATAACGCATGCAGGCAG 59.051 50.000 24.53 17.74 34.35 4.85
2099 2615 0.946528 GATCATAACGCATGCAGGCA 59.053 50.000 24.53 3.91 34.35 4.75
2163 2679 6.291849 GCTGATCATCAGTTGATTGTACGTAC 60.292 42.308 18.90 18.90 45.29 3.67
2164 2680 5.748630 GCTGATCATCAGTTGATTGTACGTA 59.251 40.000 16.28 0.00 45.29 3.57
2165 2681 4.568359 GCTGATCATCAGTTGATTGTACGT 59.432 41.667 16.28 0.00 45.29 3.57
2166 2682 4.807834 AGCTGATCATCAGTTGATTGTACG 59.192 41.667 16.28 0.00 45.29 3.67
2198 2714 9.676899 CGCTTAGTCGAAAAATATAATATCTGC 57.323 33.333 0.00 0.00 0.00 4.26
2216 2814 3.127895 AGACTCACATGTCTCGCTTAGTC 59.872 47.826 0.00 1.21 43.04 2.59
2220 2818 3.062763 CAAAGACTCACATGTCTCGCTT 58.937 45.455 0.00 0.00 45.49 4.68
2237 2835 2.721090 GCTACTTTTTCAGCGTGCAAAG 59.279 45.455 0.00 0.00 33.27 2.77
2265 2864 0.029300 TTTTGAGCAGCTGAACGTGC 59.971 50.000 20.43 0.47 40.17 5.34
2297 2896 2.230750 TGGATTGCATCACGATTTTGCA 59.769 40.909 0.00 0.00 44.12 4.08
2351 2958 5.869344 AGTTCTTTTTCTTCAACAAGCAACC 59.131 36.000 0.00 0.00 0.00 3.77
2414 3038 4.443857 GCGGCAGCTCACATGATA 57.556 55.556 0.00 0.00 41.01 2.15
2454 3078 2.865598 CGCCGGCTGATCCATCTCT 61.866 63.158 26.68 0.00 34.01 3.10
2474 3098 4.003788 CGGGTTGCCCTCACGACT 62.004 66.667 2.44 0.00 42.67 4.18


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

AutoCloner maintained by Alex Coulton.