Multiple sequence alignment - TraesCS7B01G227500

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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 TraesCS7B01G227500 chr7B 100.000 3231 0 0 1 3231 427713168 427709938 0 5967
1 TraesCS7B01G227500 chr7D 95.760 1698 42 11 1538 3231 413247698 413246027 0 2710
2 TraesCS7B01G227500 chr7D 93.432 746 35 10 806 1541 413248480 413247739 0 1094
3 TraesCS7B01G227500 chr7D 91.973 735 43 10 1 730 413249256 413248533 0 1016
4 TraesCS7B01G227500 chr7A 94.770 1721 55 8 1538 3231 474789722 474788010 0 2647
5 TraesCS7B01G227500 chr7A 90.102 1566 105 27 6 1541 474791308 474789763 0 1988


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 TraesCS7B01G227500 chr7B 427709938 427713168 3230 True 5967.000000 5967 100.000000 1 3231 1 chr7B.!!$R1 3230
1 TraesCS7B01G227500 chr7D 413246027 413249256 3229 True 1606.666667 2710 93.721667 1 3231 3 chr7D.!!$R1 3230
2 TraesCS7B01G227500 chr7A 474788010 474791308 3298 True 2317.500000 2647 92.436000 6 3231 2 chr7A.!!$R1 3225

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
722 732 0.387878 AGTGCTTCTGCTCGTTCGAG 60.388 55.0 16.47 16.47 40.48 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 2557 0.401738 CTGAAGCTCCCAAGGAACCA 59.598 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
51 52 2.332654 AAAGGGCGCACGATCAACC 61.333 57.895 10.83 0.00 0.00 3.77
65 66 2.178912 TCAACCAGAACCGTTGATCC 57.821 50.000 0.00 0.00 43.49 3.36
67 68 1.535462 CAACCAGAACCGTTGATCCAC 59.465 52.381 0.00 0.00 42.63 4.02
80 81 1.025812 GATCCACGATCAGACGGTCT 58.974 55.000 4.45 4.45 38.77 3.85
102 103 2.119801 TTTCTCAGATTGGCTGGAGC 57.880 50.000 0.00 0.00 44.98 4.70
118 119 4.511527 CTGGAGCCTGCAGTATATATTGG 58.488 47.826 13.81 0.00 30.66 3.16
131 134 2.603933 ATATTGGCCCCCACCCTTGC 62.604 60.000 0.00 0.00 30.78 4.01
259 264 1.606189 GTATACGACGTTCCTCCTCCC 59.394 57.143 5.50 0.00 0.00 4.30
266 271 2.042230 TTCCTCCTCCCCGCTACC 60.042 66.667 0.00 0.00 0.00 3.18
353 359 2.750888 GGCAGATCCGTTTGTCGCC 61.751 63.158 0.00 0.00 38.35 5.54
363 369 1.396815 CGTTTGTCGCCGTTCTTCTTC 60.397 52.381 0.00 0.00 0.00 2.87
364 370 1.865340 GTTTGTCGCCGTTCTTCTTCT 59.135 47.619 0.00 0.00 0.00 2.85
365 371 3.054878 GTTTGTCGCCGTTCTTCTTCTA 58.945 45.455 0.00 0.00 0.00 2.10
366 372 3.587797 TTGTCGCCGTTCTTCTTCTAT 57.412 42.857 0.00 0.00 0.00 1.98
367 373 2.876091 TGTCGCCGTTCTTCTTCTATG 58.124 47.619 0.00 0.00 0.00 2.23
392 398 6.466308 TCAGATGCGTATTATGAAATTCGG 57.534 37.500 0.88 0.00 36.66 4.30
420 426 7.427318 CGCCGTTTGTTAAAATAGGTTTAGATC 59.573 37.037 0.00 0.00 33.22 2.75
430 436 1.140816 GGTTTAGATCGCGATGCTCC 58.859 55.000 29.09 16.50 0.00 4.70
442 448 3.403038 GCGATGCTCCACTGGTATAAAT 58.597 45.455 0.00 0.00 0.00 1.40
447 453 4.714632 TGCTCCACTGGTATAAATAAGGC 58.285 43.478 0.00 0.00 0.00 4.35
484 490 6.398101 CGTTTCAATTTCACCGGTTAATTTCG 60.398 38.462 17.63 15.46 0.00 3.46
517 523 1.347707 TCTGGATTTCTCGTGGCTTGT 59.652 47.619 0.00 0.00 0.00 3.16
518 524 1.466167 CTGGATTTCTCGTGGCTTGTG 59.534 52.381 0.00 0.00 0.00 3.33
537 544 4.825422 TGTGCCTCTATTCTTGTTCTGAG 58.175 43.478 0.00 0.00 0.00 3.35
546 553 5.707242 ATTCTTGTTCTGAGTAGTCACGA 57.293 39.130 0.00 0.00 0.00 4.35
642 650 7.617041 ATCTACTTCAGATACCAAAAGCAAC 57.383 36.000 0.00 0.00 42.49 4.17
662 670 1.200020 CAAGAACGACCCAATTCCAGC 59.800 52.381 0.00 0.00 0.00 4.85
685 693 5.121454 GCACAAGATTCTTCTAGGTTGTCTG 59.879 44.000 0.00 0.00 0.00 3.51
699 709 4.948621 AGGTTGTCTGCTAGTACTACGAAT 59.051 41.667 0.00 0.00 0.00 3.34
720 730 1.651138 CTAAGTGCTTCTGCTCGTTCG 59.349 52.381 0.00 0.00 40.48 3.95
722 732 0.387878 AGTGCTTCTGCTCGTTCGAG 60.388 55.000 16.47 16.47 40.48 4.04
730 740 2.159503 TCTGCTCGTTCGAGATCAGTTC 60.160 50.000 23.47 6.60 34.40 3.01
731 741 1.539827 TGCTCGTTCGAGATCAGTTCA 59.460 47.619 23.47 8.87 34.40 3.18
739 764 1.646189 GAGATCAGTTCAAGGCGGAC 58.354 55.000 0.00 0.00 0.00 4.79
756 781 1.474077 GGACAATGCTTAGGTTGCCTG 59.526 52.381 0.00 0.00 34.61 4.85
769 832 2.677524 GCCTGCCAACTGATGCCA 60.678 61.111 0.00 0.00 0.00 4.92
770 833 2.277591 GCCTGCCAACTGATGCCAA 61.278 57.895 0.00 0.00 0.00 4.52
771 834 1.888018 CCTGCCAACTGATGCCAAG 59.112 57.895 0.00 0.00 0.00 3.61
772 835 1.601419 CCTGCCAACTGATGCCAAGG 61.601 60.000 0.00 0.00 0.00 3.61
773 836 0.609957 CTGCCAACTGATGCCAAGGA 60.610 55.000 0.00 0.00 0.00 3.36
774 837 0.895100 TGCCAACTGATGCCAAGGAC 60.895 55.000 0.00 0.00 0.00 3.85
775 838 0.610232 GCCAACTGATGCCAAGGACT 60.610 55.000 0.00 0.00 0.00 3.85
776 839 1.171308 CCAACTGATGCCAAGGACTG 58.829 55.000 0.00 0.00 0.00 3.51
777 840 1.271543 CCAACTGATGCCAAGGACTGA 60.272 52.381 0.00 0.00 0.00 3.41
778 841 2.507484 CAACTGATGCCAAGGACTGAA 58.493 47.619 0.00 0.00 0.00 3.02
779 842 2.486472 ACTGATGCCAAGGACTGAAG 57.514 50.000 0.00 0.00 0.00 3.02
780 843 1.701847 ACTGATGCCAAGGACTGAAGT 59.298 47.619 0.00 0.00 0.00 3.01
781 844 2.289945 ACTGATGCCAAGGACTGAAGTC 60.290 50.000 1.63 1.63 44.04 3.01
782 845 1.699083 TGATGCCAAGGACTGAAGTCA 59.301 47.619 12.32 0.00 46.47 3.41
783 846 2.106338 TGATGCCAAGGACTGAAGTCAA 59.894 45.455 12.32 0.00 46.47 3.18
784 847 2.957402 TGCCAAGGACTGAAGTCAAT 57.043 45.000 12.32 0.00 46.47 2.57
785 848 2.783135 TGCCAAGGACTGAAGTCAATC 58.217 47.619 12.32 0.00 46.47 2.67
786 849 2.373169 TGCCAAGGACTGAAGTCAATCT 59.627 45.455 12.32 0.00 46.47 2.40
787 850 3.181440 TGCCAAGGACTGAAGTCAATCTT 60.181 43.478 12.32 4.14 46.47 2.40
788 851 3.190118 GCCAAGGACTGAAGTCAATCTTG 59.810 47.826 12.32 14.20 46.47 3.02
789 852 4.392940 CCAAGGACTGAAGTCAATCTTGT 58.607 43.478 18.48 0.00 46.47 3.16
790 853 4.823989 CCAAGGACTGAAGTCAATCTTGTT 59.176 41.667 18.48 0.54 46.47 2.83
791 854 5.997746 CCAAGGACTGAAGTCAATCTTGTTA 59.002 40.000 18.48 0.00 46.47 2.41
792 855 6.148480 CCAAGGACTGAAGTCAATCTTGTTAG 59.852 42.308 18.48 7.29 46.47 2.34
793 856 6.426646 AGGACTGAAGTCAATCTTGTTAGT 57.573 37.500 12.32 0.00 46.47 2.24
794 857 6.831976 AGGACTGAAGTCAATCTTGTTAGTT 58.168 36.000 12.32 0.00 46.47 2.24
795 858 7.963532 AGGACTGAAGTCAATCTTGTTAGTTA 58.036 34.615 12.32 0.00 46.47 2.24
796 859 8.091449 AGGACTGAAGTCAATCTTGTTAGTTAG 58.909 37.037 12.32 0.00 46.47 2.34
797 860 7.873505 GGACTGAAGTCAATCTTGTTAGTTAGT 59.126 37.037 12.32 0.00 46.47 2.24
798 861 9.262358 GACTGAAGTCAATCTTGTTAGTTAGTT 57.738 33.333 5.58 0.00 44.18 2.24
799 862 9.046296 ACTGAAGTCAATCTTGTTAGTTAGTTG 57.954 33.333 0.00 0.00 36.40 3.16
800 863 8.958119 TGAAGTCAATCTTGTTAGTTAGTTGT 57.042 30.769 0.00 0.00 36.40 3.32
894 957 6.679327 AGGTTATCCTTTCGCAAATAACTC 57.321 37.500 0.00 0.00 42.12 3.01
944 1007 3.409570 GGTTGAAGAACCCCTTGTACTC 58.590 50.000 0.00 0.00 45.48 2.59
958 1021 1.488812 TGTACTCTTGTGCCAGGTTGT 59.511 47.619 0.00 0.00 0.00 3.32
982 1045 3.574826 CCCCCTTATAGCTACTGACAGTC 59.425 52.174 12.39 0.00 0.00 3.51
983 1046 4.215908 CCCCTTATAGCTACTGACAGTCA 58.784 47.826 12.39 2.48 0.00 3.41
1038 1101 2.556287 CGTTGCTTCGTTGGGAGC 59.444 61.111 0.00 0.00 0.00 4.70
1080 1143 1.936547 GTGGATCTGAAGGATGCGTTC 59.063 52.381 0.00 0.00 44.29 3.95
1114 1177 3.755378 TCGAGTTACTGAGACCAAGGTAC 59.245 47.826 0.00 0.00 0.00 3.34
1115 1178 3.119566 CGAGTTACTGAGACCAAGGTACC 60.120 52.174 2.73 2.73 0.00 3.34
1119 1183 5.368816 AGTTACTGAGACCAAGGTACCTTTT 59.631 40.000 24.99 14.56 33.42 2.27
1150 1214 1.829970 GGGCCTGGAATGCTTAGCC 60.830 63.158 0.84 0.00 39.73 3.93
1311 1382 9.473007 TGGTTAATCTATCATTCATTTGTCCAA 57.527 29.630 0.00 0.00 0.00 3.53
1321 1392 7.451732 TCATTCATTTGTCCAATTGGTGAATT 58.548 30.769 26.11 15.23 33.85 2.17
1333 1404 7.179872 TCCAATTGGTGAATTTGTCCATGAATA 59.820 33.333 23.76 0.00 36.34 1.75
1350 1423 9.419297 TCCATGAATATTACGCTTAGTATGAAC 57.581 33.333 0.00 0.00 34.88 3.18
1351 1424 9.203421 CCATGAATATTACGCTTAGTATGAACA 57.797 33.333 0.00 0.00 34.88 3.18
1364 1437 7.494625 GCTTAGTATGAACATGCACTAGGTTTA 59.505 37.037 0.00 0.00 32.65 2.01
1440 1513 5.249780 TCTTATGGTGGTGTGGTACAATT 57.750 39.130 0.00 0.00 44.16 2.32
1484 1557 4.701956 AAGGAATCTGTAAACATTGCCG 57.298 40.909 0.00 0.00 0.00 5.69
1547 1664 4.325972 TCATGCTACTGATTTGCAAGTCA 58.674 39.130 21.66 21.66 40.24 3.41
1559 1676 8.109705 TGATTTGCAAGTCAGTGTTATATGTT 57.890 30.769 19.55 0.00 0.00 2.71
1600 1717 5.833131 TCCTTATGTTTTCTCTGGCTTGTTT 59.167 36.000 0.00 0.00 0.00 2.83
1603 1720 7.040409 CCTTATGTTTTCTCTGGCTTGTTTACT 60.040 37.037 0.00 0.00 0.00 2.24
1608 1725 3.403038 TCTCTGGCTTGTTTACTCTTGC 58.597 45.455 0.00 0.00 0.00 4.01
1620 1737 0.689055 ACTCTTGCTGTCTGCCATGA 59.311 50.000 0.00 0.00 42.00 3.07
1625 1742 3.691118 TCTTGCTGTCTGCCATGATTTAC 59.309 43.478 0.00 0.00 42.00 2.01
1628 1745 4.779696 TGCTGTCTGCCATGATTTACATA 58.220 39.130 0.00 0.00 42.00 2.29
1982 2122 1.204786 TGGTGGGGACAGGTATGGTG 61.205 60.000 0.00 0.00 44.46 4.17
1983 2123 0.912487 GGTGGGGACAGGTATGGTGA 60.912 60.000 0.00 0.00 44.46 4.02
2080 2220 2.845659 AGGGATGACAAGTATGGTGGA 58.154 47.619 0.00 0.00 0.00 4.02
2137 2277 2.139118 GGTGATCGCTATTCTGGAAGC 58.861 52.381 6.18 0.00 35.33 3.86
2377 2519 2.906691 ATCCATGCTGACTAGTGCTC 57.093 50.000 0.00 0.00 0.00 4.26
2415 2557 5.191722 TCCTATCTGGATTTGGCTTGTAACT 59.808 40.000 0.00 0.00 40.56 2.24
2454 2596 4.083003 TCAGTGGATTGCGTTATTTTGTCC 60.083 41.667 0.00 0.00 0.00 4.02
2459 2601 4.379082 GGATTGCGTTATTTTGTCCGAGTT 60.379 41.667 0.00 0.00 0.00 3.01
2487 2629 1.133025 GGATCCATGTTTCTGCGTTGG 59.867 52.381 6.95 0.00 0.00 3.77
2515 2657 7.275183 TGATGGTAAAAGTCCTGTCATGATAG 58.725 38.462 12.27 12.27 0.00 2.08
2594 2736 5.624159 TGATGTCAAGGATGTTGAAGAACT 58.376 37.500 0.00 0.00 32.79 3.01
2690 2832 9.189156 CCTCCTTAAAATATTCCATCAGAAACA 57.811 33.333 0.00 0.00 38.21 2.83
2700 2842 4.665451 TCCATCAGAAACATGTGACCAAT 58.335 39.130 0.00 0.00 0.00 3.16
2846 2988 0.478072 TGCTGTTCAACCATGGGTCT 59.522 50.000 18.09 0.00 33.12 3.85
2926 3068 1.181098 GCTGGCATGGGTCACTTTGT 61.181 55.000 0.00 0.00 0.00 2.83
2993 3135 3.070748 GAGAACCTGGAAAGAGTTGCTC 58.929 50.000 0.00 0.00 0.00 4.26
2996 3138 0.603707 CCTGGAAAGAGTTGCTCGCA 60.604 55.000 0.00 0.00 35.36 5.10
3046 3188 2.620112 CCTGCTGCAACCCAAGTCG 61.620 63.158 3.02 0.00 0.00 4.18
3169 3313 4.097892 CCACACTTGCTTCTGGTTAACTTT 59.902 41.667 5.42 0.00 0.00 2.66
3176 3320 2.248280 TCTGGTTAACTTTCGCAGCA 57.752 45.000 5.42 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.927174 GATCGTGGATCAACGGTTCTG 59.073 52.381 22.15 0.00 43.73 3.02
102 103 2.357154 GGGGGCCAATATATACTGCAGG 60.357 54.545 19.93 0.00 0.00 4.85
131 134 2.959707 ACGAAGAGATAAGGCCTACAGG 59.040 50.000 5.16 0.00 38.53 4.00
134 137 3.058777 CGAGACGAAGAGATAAGGCCTAC 60.059 52.174 5.16 0.17 0.00 3.18
135 138 3.139850 CGAGACGAAGAGATAAGGCCTA 58.860 50.000 5.16 0.00 0.00 3.93
259 264 1.405821 ACGAAGAGATTGAGGTAGCGG 59.594 52.381 0.00 0.00 0.00 5.52
266 271 4.497340 GGACAGCTAGACGAAGAGATTGAG 60.497 50.000 0.00 0.00 0.00 3.02
344 350 1.865340 AGAAGAAGAACGGCGACAAAC 59.135 47.619 16.62 1.69 0.00 2.93
346 352 3.250744 CATAGAAGAAGAACGGCGACAA 58.749 45.455 16.62 0.00 0.00 3.18
348 354 1.588861 GCATAGAAGAAGAACGGCGAC 59.411 52.381 16.62 7.38 0.00 5.19
349 355 1.476891 AGCATAGAAGAAGAACGGCGA 59.523 47.619 16.62 0.00 0.00 5.54
350 356 1.855360 GAGCATAGAAGAAGAACGGCG 59.145 52.381 4.80 4.80 0.00 6.46
353 359 4.208873 GCATCTGAGCATAGAAGAAGAACG 59.791 45.833 0.00 0.00 0.00 3.95
363 369 7.586714 TTTCATAATACGCATCTGAGCATAG 57.413 36.000 0.00 0.00 0.00 2.23
364 370 8.552083 AATTTCATAATACGCATCTGAGCATA 57.448 30.769 0.00 0.00 0.00 3.14
365 371 7.444629 AATTTCATAATACGCATCTGAGCAT 57.555 32.000 0.00 0.00 0.00 3.79
366 372 6.346838 CGAATTTCATAATACGCATCTGAGCA 60.347 38.462 0.00 0.00 0.00 4.26
367 373 6.011879 CGAATTTCATAATACGCATCTGAGC 58.988 40.000 0.00 0.00 0.00 4.26
392 398 4.408993 ACCTATTTTAACAAACGGCGAC 57.591 40.909 16.62 0.00 0.00 5.19
406 412 4.632153 AGCATCGCGATCTAAACCTATTT 58.368 39.130 20.85 0.00 0.00 1.40
420 426 0.313987 TATACCAGTGGAGCATCGCG 59.686 55.000 18.40 0.00 34.37 5.87
430 436 4.632153 AGAGCGCCTTATTTATACCAGTG 58.368 43.478 2.29 0.00 0.00 3.66
447 453 3.813529 ATTGAAACGAAAAGGAGAGCG 57.186 42.857 0.00 0.00 0.00 5.03
517 523 5.717178 ACTACTCAGAACAAGAATAGAGGCA 59.283 40.000 0.00 0.00 0.00 4.75
518 524 6.127591 TGACTACTCAGAACAAGAATAGAGGC 60.128 42.308 0.00 0.00 0.00 4.70
537 544 2.985406 AAGTCTTCCGTCGTGACTAC 57.015 50.000 11.38 1.80 39.78 2.73
622 630 5.827797 TCTTGTTGCTTTTGGTATCTGAAGT 59.172 36.000 0.00 0.00 0.00 3.01
642 650 1.200020 GCTGGAATTGGGTCGTTCTTG 59.800 52.381 0.00 0.00 0.00 3.02
662 670 5.121454 GCAGACAACCTAGAAGAATCTTGTG 59.879 44.000 0.00 0.00 37.10 3.33
685 693 6.303021 AGCACTTAGATTCGTAGTACTAGC 57.697 41.667 1.87 0.00 0.00 3.42
699 709 2.668556 CGAACGAGCAGAAGCACTTAGA 60.669 50.000 0.00 0.00 45.49 2.10
720 730 1.066858 TGTCCGCCTTGAACTGATCTC 60.067 52.381 0.00 0.00 0.00 2.75
722 732 1.808411 TTGTCCGCCTTGAACTGATC 58.192 50.000 0.00 0.00 0.00 2.92
730 740 0.734889 CCTAAGCATTGTCCGCCTTG 59.265 55.000 0.00 0.00 0.00 3.61
731 741 0.328258 ACCTAAGCATTGTCCGCCTT 59.672 50.000 0.00 0.00 0.00 4.35
739 764 0.174162 GGCAGGCAACCTAAGCATTG 59.826 55.000 0.00 0.00 29.64 2.82
769 832 6.831976 ACTAACAAGATTGACTTCAGTCCTT 58.168 36.000 4.48 0.00 44.15 3.36
770 833 6.426646 ACTAACAAGATTGACTTCAGTCCT 57.573 37.500 4.48 0.00 44.15 3.85
771 834 7.873505 ACTAACTAACAAGATTGACTTCAGTCC 59.126 37.037 4.48 0.00 44.15 3.85
772 835 8.819643 ACTAACTAACAAGATTGACTTCAGTC 57.180 34.615 0.00 0.00 44.97 3.51
773 836 9.046296 CAACTAACTAACAAGATTGACTTCAGT 57.954 33.333 0.00 0.00 36.61 3.41
774 837 9.046296 ACAACTAACTAACAAGATTGACTTCAG 57.954 33.333 0.00 0.00 36.61 3.02
775 838 8.958119 ACAACTAACTAACAAGATTGACTTCA 57.042 30.769 0.00 0.00 36.61 3.02
843 906 1.865865 CACCCCGGATTGATTAGTCG 58.134 55.000 0.73 0.00 0.00 4.18
894 957 5.652744 AAAGTACTAGCGTTTGTGAGTTG 57.347 39.130 0.00 0.00 0.00 3.16
944 1007 0.893727 GGGGTACAACCTGGCACAAG 60.894 60.000 0.00 0.00 38.70 3.16
958 1021 4.169461 ACTGTCAGTAGCTATAAGGGGGTA 59.831 45.833 2.87 0.00 0.00 3.69
1038 1101 2.849942 TCAGTTGTGTTCCATGACAGG 58.150 47.619 0.00 0.00 0.00 4.00
1080 1143 3.124636 CAGTAACTCGACCAAATTTCCCG 59.875 47.826 0.00 0.00 0.00 5.14
1119 1183 4.329638 TCCAGGCCCATATGAAAAGAAA 57.670 40.909 3.65 0.00 0.00 2.52
1238 1302 3.006859 CACCATCACAAGTGTCTAGTGGA 59.993 47.826 13.58 0.00 34.17 4.02
1245 1309 4.272018 GCATATCTCACCATCACAAGTGTC 59.728 45.833 0.00 0.00 35.45 3.67
1297 1365 7.675962 AATTCACCAATTGGACAAATGAATG 57.324 32.000 31.22 14.76 38.94 2.67
1298 1366 7.720515 ACAAATTCACCAATTGGACAAATGAAT 59.279 29.630 31.22 26.99 38.94 2.57
1299 1367 7.052873 ACAAATTCACCAATTGGACAAATGAA 58.947 30.769 31.22 26.11 38.94 2.57
1300 1368 6.590068 ACAAATTCACCAATTGGACAAATGA 58.410 32.000 31.22 19.66 38.94 2.57
1301 1369 6.073112 GGACAAATTCACCAATTGGACAAATG 60.073 38.462 31.22 22.38 38.94 2.32
1302 1370 5.997129 GGACAAATTCACCAATTGGACAAAT 59.003 36.000 31.22 20.91 38.94 2.32
1303 1371 5.104776 TGGACAAATTCACCAATTGGACAAA 60.105 36.000 31.22 19.72 38.94 2.83
1304 1372 4.406972 TGGACAAATTCACCAATTGGACAA 59.593 37.500 31.22 20.91 38.94 3.18
1321 1392 9.203421 CATACTAAGCGTAATATTCATGGACAA 57.797 33.333 0.00 0.00 0.00 3.18
1333 1404 6.049149 AGTGCATGTTCATACTAAGCGTAAT 58.951 36.000 0.00 0.00 0.00 1.89
1350 1423 5.471456 GGAATCATCCTAAACCTAGTGCATG 59.529 44.000 0.00 0.00 42.93 4.06
1351 1424 5.625150 GGAATCATCCTAAACCTAGTGCAT 58.375 41.667 0.00 0.00 42.93 3.96
1411 1484 6.327386 ACCACACCACCATAAGATAAGAAT 57.673 37.500 0.00 0.00 0.00 2.40
1413 1486 5.722441 TGTACCACACCACCATAAGATAAGA 59.278 40.000 0.00 0.00 0.00 2.10
1415 1488 6.375830 TTGTACCACACCACCATAAGATAA 57.624 37.500 0.00 0.00 0.00 1.75
1461 1534 5.353123 TCGGCAATGTTTACAGATTCCTTAC 59.647 40.000 0.00 0.00 0.00 2.34
1484 1557 8.439286 GCATCGACATTCTCTATTATTTCCTTC 58.561 37.037 0.00 0.00 0.00 3.46
1504 1577 1.114627 ATGCCAGTGTCTAGCATCGA 58.885 50.000 0.00 0.00 43.58 3.59
1559 1676 7.001674 ACATAAGGAAAGTGGTGTATCAAACA 58.998 34.615 0.00 0.00 35.06 2.83
1603 1720 6.856421 TATGTAAATCATGGCAGACAGCAAGA 60.856 38.462 0.00 0.00 40.46 3.02
1608 1725 5.277683 GCAGTATGTAAATCATGGCAGACAG 60.278 44.000 0.00 0.00 39.31 3.51
1625 1742 3.375922 TGCACATTGAGACATGCAGTATG 59.624 43.478 0.00 0.00 42.92 2.39
1628 1745 1.900245 TGCACATTGAGACATGCAGT 58.100 45.000 0.00 0.00 42.92 4.40
1982 2122 4.218852 GCTACTATACCTGTCATCCCTGTC 59.781 50.000 0.00 0.00 0.00 3.51
1983 2123 4.153411 GCTACTATACCTGTCATCCCTGT 58.847 47.826 0.00 0.00 0.00 4.00
2080 2220 3.349006 CGACTGCTGCCGTTGCTT 61.349 61.111 0.00 0.00 38.71 3.91
2137 2277 2.202932 CGGCTTCCTCCATCACGG 60.203 66.667 0.00 0.00 0.00 4.94
2377 2519 4.574828 CCAGATAGGAACATTGGTAAACCG 59.425 45.833 0.00 0.00 41.22 4.44
2415 2557 0.401738 CTGAAGCTCCCAAGGAACCA 59.598 55.000 0.00 0.00 0.00 3.67
2454 2596 7.445402 AGAAACATGGATCCCAAATATAACTCG 59.555 37.037 9.90 0.00 36.95 4.18
2459 2601 5.473162 CGCAGAAACATGGATCCCAAATATA 59.527 40.000 9.90 0.00 36.95 0.86
2487 2629 4.894784 TGACAGGACTTTTACCATCAGAC 58.105 43.478 0.00 0.00 0.00 3.51
2515 2657 1.109323 AGAACAGCACCAAAGGCCAC 61.109 55.000 5.01 0.00 0.00 5.01
2594 2736 7.541091 CACAACGAGACTAAATAAAGAGCTGTA 59.459 37.037 0.00 0.00 0.00 2.74
2690 2832 5.549742 ACCATTTGTTTCATTGGTCACAT 57.450 34.783 0.00 0.00 38.00 3.21
2846 2988 4.808414 ACAGTACTAGAGCAAGCATTCA 57.192 40.909 0.00 0.00 0.00 2.57
2926 3068 3.565307 AGCCCAAAGAAGTGTTGATGAA 58.435 40.909 0.00 0.00 0.00 2.57
2996 3138 0.030297 AGAGAGCCCATCCCAGTGAT 60.030 55.000 0.00 0.00 0.00 3.06
3046 3188 0.405973 AGAACTTTCAAGGGCCCTCC 59.594 55.000 28.84 7.01 0.00 4.30
3095 3239 3.068165 CCCCCTTTGAGAAACACAGAAAC 59.932 47.826 0.00 0.00 0.00 2.78
3147 3291 4.900635 AAGTTAACCAGAAGCAAGTGTG 57.099 40.909 0.88 0.00 0.00 3.82
3169 3313 0.679505 ACTACACCTTCTTGCTGCGA 59.320 50.000 0.00 0.00 0.00 5.10
3188 3332 8.679100 CCGAACCCTACACATAAATATTTTCAA 58.321 33.333 5.91 0.00 0.00 2.69
3202 3346 2.036862 AGAAAGACACCGAACCCTACAC 59.963 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.