Multiple sequence alignment - TraesCS6B01G391100

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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 TraesCS6B01G391100 chr6B 100.000 5747 0 0 1 5747 665506900 665512646 0 10613
1 TraesCS6B01G391100 chr6B 89.286 728 70 7 2 726 504582836 504583558 0 905
2 TraesCS6B01G391100 chr6A 92.583 2373 108 31 2439 4753 588456901 588459263 0 3345
3 TraesCS6B01G391100 chr6A 91.803 1037 46 10 849 1876 588455254 588456260 0 1408
4 TraesCS6B01G391100 chr6A 91.825 1003 48 16 4770 5747 588459318 588460311 0 1367
5 TraesCS6B01G391100 chr6A 91.697 554 30 6 1884 2437 588456332 588456869 0 754
6 TraesCS6B01G391100 chr6D 93.851 2049 78 21 2439 4445 440365004 440367046 0 3042
7 TraesCS6B01G391100 chr6D 93.210 1031 35 11 851 1876 440363373 440364373 0 1483
8 TraesCS6B01G391100 chr6D 87.657 794 40 17 4981 5747 440367566 440368328 0 870
9 TraesCS6B01G391100 chr6D 92.922 551 21 8 1888 2437 440364440 440364973 0 785
10 TraesCS6B01G391100 chr6D 95.102 490 19 3 4448 4936 440367076 440367561 0 767
11 TraesCS6B01G391100 chr5D 90.128 780 66 5 2 771 407009888 407009110 0 1003
12 TraesCS6B01G391100 chr5B 89.345 779 66 7 3 771 488118586 488119357 0 963
13 TraesCS6B01G391100 chr5B 86.131 858 98 13 2 841 327054688 327053834 0 905
14 TraesCS6B01G391100 chr7B 90.577 711 65 2 2 711 488400989 488400280 0 941
15 TraesCS6B01G391100 chr1D 90.483 704 63 4 1 703 318550771 318551471 0 926
16 TraesCS6B01G391100 chr2D 89.430 719 72 4 2 718 629191390 629192106 0 904
17 TraesCS6B01G391100 chr3A 87.661 778 84 8 1 767 653957888 653958664 0 894
18 TraesCS6B01G391100 chr3D 89.121 717 73 5 4 718 72364939 72364226 0 887


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 TraesCS6B01G391100 chr6B 665506900 665512646 5746 False 10613.0 10613 100.0000 1 5747 1 chr6B.!!$F2 5746
1 TraesCS6B01G391100 chr6B 504582836 504583558 722 False 905.0 905 89.2860 2 726 1 chr6B.!!$F1 724
2 TraesCS6B01G391100 chr6A 588455254 588460311 5057 False 1718.5 3345 91.9770 849 5747 4 chr6A.!!$F1 4898
3 TraesCS6B01G391100 chr6D 440363373 440368328 4955 False 1389.4 3042 92.5484 851 5747 5 chr6D.!!$F1 4896
4 TraesCS6B01G391100 chr5D 407009110 407009888 778 True 1003.0 1003 90.1280 2 771 1 chr5D.!!$R1 769
5 TraesCS6B01G391100 chr5B 488118586 488119357 771 False 963.0 963 89.3450 3 771 1 chr5B.!!$F1 768
6 TraesCS6B01G391100 chr5B 327053834 327054688 854 True 905.0 905 86.1310 2 841 1 chr5B.!!$R1 839
7 TraesCS6B01G391100 chr7B 488400280 488400989 709 True 941.0 941 90.5770 2 711 1 chr7B.!!$R1 709
8 TraesCS6B01G391100 chr1D 318550771 318551471 700 False 926.0 926 90.4830 1 703 1 chr1D.!!$F1 702
9 TraesCS6B01G391100 chr2D 629191390 629192106 716 False 904.0 904 89.4300 2 718 1 chr2D.!!$F1 716
10 TraesCS6B01G391100 chr3A 653957888 653958664 776 False 894.0 894 87.6610 1 767 1 chr3A.!!$F1 766
11 TraesCS6B01G391100 chr3D 72364226 72364939 713 True 887.0 887 89.1210 4 718 1 chr3D.!!$R1 714

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
944 977 0.033208 AGCTGTCCCTCTCTCTGGAG 60.033 60.0 0.0 0.0 40.73 3.86 F
2473 2611 0.396974 GCATGGTGCCAAGGGGAATA 60.397 55.0 0.0 0.0 37.42 1.75 F
4289 4477 0.324738 TTGCCTCGGTCATCTCCTCT 60.325 55.0 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2487 2628 0.105760 TTGGCCCAAACTGATGGTGT 60.106 50.000 0.0 0.0 38.91 4.16 R
4424 4615 0.317160 CACTTCACTGTCTACCGCCA 59.683 55.000 0.0 0.0 0.00 5.69 R
5492 5780 1.876156 AGAAAGAGAGGCAAGCAAACG 59.124 47.619 0.0 0.0 0.00 3.60 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
181 183 6.428465 GTCGGAGAGAAGAGGAAAAGATTTTT 59.572 38.462 0.00 0.00 36.95 1.94
307 314 1.340405 GCTGTGGGAGGTGATGACAAT 60.340 52.381 0.00 0.00 0.00 2.71
364 371 1.665161 GCGTCCGGAATGTATCTACGG 60.665 57.143 5.23 0.00 45.52 4.02
382 389 4.160642 ACGGTCAAGGGTTTTAGTTTCT 57.839 40.909 0.00 0.00 0.00 2.52
384 391 4.131596 CGGTCAAGGGTTTTAGTTTCTGA 58.868 43.478 0.00 0.00 0.00 3.27
475 484 9.810231 GAAATGCACGATTTAAAAATTCACATT 57.190 25.926 0.00 0.00 34.18 2.71
478 487 8.357796 TGCACGATTTAAAAATTCACATTCAA 57.642 26.923 0.00 0.00 0.00 2.69
592 602 6.730960 TTTACTCGGCTTGTAAAACTATGG 57.269 37.500 8.69 0.00 37.07 2.74
651 668 6.919721 TGGGTGTGAAACTATGCTATTTTTC 58.080 36.000 0.00 0.00 38.04 2.29
685 704 7.441760 TGCTTGTGAAATAATGCAAAATGAGTT 59.558 29.630 0.00 0.00 0.00 3.01
711 731 3.439895 TTGTTTAAAAAGACCGGCCAC 57.560 42.857 0.00 0.00 0.00 5.01
712 740 2.376109 TGTTTAAAAAGACCGGCCACA 58.624 42.857 0.00 0.00 0.00 4.17
713 741 2.959707 TGTTTAAAAAGACCGGCCACAT 59.040 40.909 0.00 0.00 0.00 3.21
730 758 2.687425 CACATCGGCAAATATGGGTTGA 59.313 45.455 0.00 0.00 0.00 3.18
743 771 2.126888 GTTGACATGTTGGGCGCG 60.127 61.111 0.00 0.00 0.00 6.86
756 784 4.520846 GCGCGTTGCCGATCCAAG 62.521 66.667 8.43 0.00 37.76 3.61
778 806 4.771127 AAAAAGAGCGAGCGGACA 57.229 50.000 0.00 0.00 0.00 4.02
780 808 1.523758 AAAAAGAGCGAGCGGACAAT 58.476 45.000 0.00 0.00 0.00 2.71
785 814 1.009829 GAGCGAGCGGACAATCAAAT 58.990 50.000 0.00 0.00 0.00 2.32
787 816 0.726827 GCGAGCGGACAATCAAATGA 59.273 50.000 0.00 0.00 0.00 2.57
818 849 5.267776 ACAGATAAAAACACCGTTCGTTTG 58.732 37.500 0.00 0.00 36.71 2.93
819 850 5.064962 ACAGATAAAAACACCGTTCGTTTGA 59.935 36.000 0.00 0.00 36.71 2.69
820 851 5.966503 CAGATAAAAACACCGTTCGTTTGAA 59.033 36.000 0.00 0.00 36.71 2.69
826 857 1.523515 CACCGTTCGTTTGAATCGACA 59.476 47.619 0.00 0.00 36.29 4.35
832 863 2.461903 TCGTTTGAATCGACACGTTGA 58.538 42.857 0.00 0.00 34.24 3.18
841 872 0.232303 CGACACGTTGAAGTTGCTCC 59.768 55.000 0.00 0.00 0.00 4.70
842 873 1.583054 GACACGTTGAAGTTGCTCCT 58.417 50.000 0.00 0.00 0.00 3.69
843 874 2.750948 GACACGTTGAAGTTGCTCCTA 58.249 47.619 0.00 0.00 0.00 2.94
844 875 2.475487 GACACGTTGAAGTTGCTCCTAC 59.525 50.000 0.00 0.00 0.00 3.18
845 876 2.159014 ACACGTTGAAGTTGCTCCTACA 60.159 45.455 0.00 0.00 0.00 2.74
846 877 2.221055 CACGTTGAAGTTGCTCCTACAC 59.779 50.000 0.00 0.00 0.00 2.90
847 878 2.102588 ACGTTGAAGTTGCTCCTACACT 59.897 45.455 0.00 0.00 0.00 3.55
881 914 0.304705 GCAGACGTGGTTTCACAGTG 59.695 55.000 0.00 0.00 43.79 3.66
894 927 7.323656 GTGGTTTCACAGTGAAAAGAAATATCG 59.676 37.037 26.87 0.00 46.53 2.92
899 932 8.771920 TCACAGTGAAAAGAAATATCGTGTAT 57.228 30.769 0.00 0.00 0.00 2.29
930 963 2.955402 GACAGTCGTCGGAGCTGT 59.045 61.111 14.49 14.49 44.97 4.40
931 964 2.955402 ACAGTCGTCGGAGCTGTC 59.045 61.111 0.00 0.00 38.96 3.51
932 965 2.179517 CAGTCGTCGGAGCTGTCC 59.820 66.667 0.00 0.00 39.88 4.02
933 966 3.063084 AGTCGTCGGAGCTGTCCC 61.063 66.667 0.00 0.00 40.20 4.46
934 967 3.063084 GTCGTCGGAGCTGTCCCT 61.063 66.667 0.00 0.00 40.20 4.20
935 968 2.750637 TCGTCGGAGCTGTCCCTC 60.751 66.667 0.00 0.00 40.20 4.30
936 969 2.752238 CGTCGGAGCTGTCCCTCT 60.752 66.667 0.00 0.00 40.20 3.69
937 970 2.766400 CGTCGGAGCTGTCCCTCTC 61.766 68.421 0.00 0.00 40.20 3.20
938 971 1.379309 GTCGGAGCTGTCCCTCTCT 60.379 63.158 0.00 0.00 40.20 3.10
939 972 1.077357 TCGGAGCTGTCCCTCTCTC 60.077 63.158 0.00 0.00 40.20 3.20
940 973 1.077068 CGGAGCTGTCCCTCTCTCT 60.077 63.158 0.00 0.00 40.20 3.10
941 974 1.383456 CGGAGCTGTCCCTCTCTCTG 61.383 65.000 0.00 0.00 40.20 3.35
942 975 1.042559 GGAGCTGTCCCTCTCTCTGG 61.043 65.000 0.00 0.00 36.76 3.86
943 976 0.033601 GAGCTGTCCCTCTCTCTGGA 60.034 60.000 0.00 0.00 0.00 3.86
944 977 0.033208 AGCTGTCCCTCTCTCTGGAG 60.033 60.000 0.00 0.00 40.73 3.86
945 978 1.675720 GCTGTCCCTCTCTCTGGAGC 61.676 65.000 0.00 0.00 39.31 4.70
946 979 0.033208 CTGTCCCTCTCTCTGGAGCT 60.033 60.000 0.00 0.00 39.31 4.09
1014 1047 4.284550 GTCAACCCAGCCCAGCCA 62.285 66.667 0.00 0.00 0.00 4.75
1015 1048 3.970410 TCAACCCAGCCCAGCCAG 61.970 66.667 0.00 0.00 0.00 4.85
1016 1049 4.290622 CAACCCAGCCCAGCCAGT 62.291 66.667 0.00 0.00 0.00 4.00
1017 1050 3.971702 AACCCAGCCCAGCCAGTC 61.972 66.667 0.00 0.00 0.00 3.51
1036 1070 2.597510 GCCACCACCACCACCTTC 60.598 66.667 0.00 0.00 0.00 3.46
1441 1483 1.668151 GCTGTTCACTGACCGGTCC 60.668 63.158 31.19 15.23 0.00 4.46
1592 1635 3.814945 CTTTGTTCCGAGTTTCATCAGC 58.185 45.455 0.00 0.00 0.00 4.26
1603 1646 2.177394 TTCATCAGCCGCACTAACAA 57.823 45.000 0.00 0.00 0.00 2.83
1610 1653 2.096218 CAGCCGCACTAACAAAACTCTC 60.096 50.000 0.00 0.00 0.00 3.20
1876 1920 0.962489 CTTCACTCCGACCTGTCACT 59.038 55.000 0.00 0.00 0.00 3.41
1877 1921 0.673985 TTCACTCCGACCTGTCACTG 59.326 55.000 0.00 0.00 0.00 3.66
1878 1922 1.373497 CACTCCGACCTGTCACTGC 60.373 63.158 0.00 0.00 0.00 4.40
1880 1924 3.633094 CTCCGACCTGTCACTGCCG 62.633 68.421 0.00 0.00 0.00 5.69
1881 1925 3.680786 CCGACCTGTCACTGCCGA 61.681 66.667 0.00 0.00 0.00 5.54
1882 1926 2.338620 CGACCTGTCACTGCCGAA 59.661 61.111 0.00 0.00 0.00 4.30
1930 2038 2.360852 CACCAGCAGCAAGAGGGG 60.361 66.667 0.00 0.00 0.00 4.79
2101 2209 1.408422 CCGCTTTCGCCTTTTTCTTG 58.592 50.000 0.00 0.00 0.00 3.02
2138 2246 2.483538 GCAAAGCAAAGCAGGAAGGAAA 60.484 45.455 0.00 0.00 0.00 3.13
2228 2336 6.154534 ACAGAGTAAAGCTGGTGTATCATACA 59.845 38.462 0.00 0.00 37.69 2.29
2229 2337 7.147655 ACAGAGTAAAGCTGGTGTATCATACAT 60.148 37.037 0.00 0.00 37.63 2.29
2230 2338 8.360390 CAGAGTAAAGCTGGTGTATCATACATA 58.640 37.037 0.00 0.00 41.34 2.29
2231 2339 8.361139 AGAGTAAAGCTGGTGTATCATACATAC 58.639 37.037 0.00 0.00 41.34 2.39
2232 2340 8.251383 AGTAAAGCTGGTGTATCATACATACT 57.749 34.615 0.00 0.34 41.34 2.12
2233 2341 9.363401 AGTAAAGCTGGTGTATCATACATACTA 57.637 33.333 0.00 0.00 41.34 1.82
2234 2342 9.627395 GTAAAGCTGGTGTATCATACATACTAG 57.373 37.037 0.00 0.00 41.34 2.57
2353 2461 8.789762 GTTGGAGTTGTATGGTTAATTACACTT 58.210 33.333 0.00 0.00 0.00 3.16
2391 2499 2.465860 TAGGGTTGACATGTCGGTTG 57.534 50.000 20.54 0.00 0.00 3.77
2394 2502 0.872388 GGTTGACATGTCGGTTGTCC 59.128 55.000 20.54 11.85 42.25 4.02
2454 2592 5.683876 TTGGTAGGAAAAGAGAGATCAGG 57.316 43.478 0.00 0.00 0.00 3.86
2473 2611 0.396974 GCATGGTGCCAAGGGGAATA 60.397 55.000 0.00 0.00 37.42 1.75
2487 2628 7.147742 GCCAAGGGGAATAAGAATTGTTATTGA 60.148 37.037 21.53 0.00 33.60 2.57
2490 2631 8.293699 AGGGGAATAAGAATTGTTATTGACAC 57.706 34.615 21.53 15.67 38.18 3.67
2498 2639 7.765695 AGAATTGTTATTGACACCATCAGTT 57.234 32.000 0.00 0.00 38.99 3.16
2524 2665 0.905357 AAGGCCACAGCTAGTACCAG 59.095 55.000 5.01 0.00 39.73 4.00
2548 2689 6.315393 AGTTAGTGCAATTGTAGATAAACGGG 59.685 38.462 7.40 0.00 0.00 5.28
2618 2760 7.330946 TGATCATTTCACTAAACACTAGGTTCG 59.669 37.037 0.00 0.00 39.29 3.95
2663 2805 7.370905 TCATGAGGAGAATGACAGATGTATT 57.629 36.000 0.00 0.00 0.00 1.89
2798 2965 1.120530 TACTCCCGGAGCTTCCAATC 58.879 55.000 14.86 0.00 35.91 2.67
2816 2983 5.237127 TCCAATCGCACATGTGATATCTTTC 59.763 40.000 29.80 7.84 43.75 2.62
2880 3047 0.729116 CGAATGTCGATTGCTTGGCT 59.271 50.000 0.00 0.00 43.74 4.75
3113 3280 1.885233 CCCGGGTTACTACTAGCTAGC 59.115 57.143 20.91 6.62 0.00 3.42
3185 3352 1.415659 GTCCCTGATCAGATGTCCCAG 59.584 57.143 24.62 4.38 0.00 4.45
3269 3436 2.419297 GGCTTGTCATCAGAGGTACCTG 60.419 54.545 22.10 7.03 35.55 4.00
3617 3788 1.825474 GATCCCTCTTCAAGTCCACGA 59.175 52.381 0.00 0.00 0.00 4.35
3795 3983 0.892358 AGTGGATGCCAGCACAACAG 60.892 55.000 0.00 0.00 32.34 3.16
3838 4026 3.593942 TCTGGTTTAAGAACTGGAGGGA 58.406 45.455 0.00 0.00 36.03 4.20
3868 4056 1.157870 ACACGCCTGAAAAGTGACCG 61.158 55.000 1.63 0.00 39.04 4.79
3873 4061 1.948611 GCCTGAAAAGTGACCGCCATA 60.949 52.381 0.00 0.00 0.00 2.74
3900 4088 5.393962 CAAACTACCAATCAAGCAGTTAGC 58.606 41.667 0.00 0.00 46.19 3.09
4036 4224 5.874895 TTCTGTCAAGAAATCATCAGCTG 57.125 39.130 7.63 7.63 39.52 4.24
4039 4227 5.766670 TCTGTCAAGAAATCATCAGCTGTTT 59.233 36.000 14.67 6.68 0.00 2.83
4070 4258 1.241165 TCTGCTCAATTGCCACTGTG 58.759 50.000 0.00 0.00 0.00 3.66
4160 4348 1.372499 CGACGACGACAATGGTGGT 60.372 57.895 0.00 0.00 42.66 4.16
4289 4477 0.324738 TTGCCTCGGTCATCTCCTCT 60.325 55.000 0.00 0.00 0.00 3.69
4419 4610 2.366837 ATGGCTCCCGGACCATCA 60.367 61.111 15.49 2.97 43.26 3.07
4445 4636 1.014564 GCGGTAGACAGTGAAGTGGC 61.015 60.000 0.00 0.00 0.00 5.01
4582 4802 3.255888 GCCCTACCTTTTTCCTGTTCTTG 59.744 47.826 0.00 0.00 0.00 3.02
4793 5051 6.035542 AGGTACAAATGCAAAGTTGTTTTTCG 59.964 34.615 16.10 0.00 38.80 3.46
4842 5100 8.956426 GGTCAACAAATTGGAAGATAATCTACA 58.044 33.333 0.00 0.00 36.39 2.74
4908 5166 1.281419 TTCTTCCCGGATAACCAGCA 58.719 50.000 0.73 0.00 35.59 4.41
4927 5186 5.352569 CCAGCAAGTCAGATAACCTTAGTTG 59.647 44.000 0.00 0.00 36.68 3.16
4942 5201 4.387862 CCTTAGTTGTAGTGCGTTTACTGG 59.612 45.833 0.00 0.00 32.19 4.00
4943 5202 3.738830 AGTTGTAGTGCGTTTACTGGA 57.261 42.857 0.00 0.00 32.19 3.86
4976 5235 1.312371 AATGCTTACGCGCCAATGGT 61.312 50.000 5.73 0.00 39.65 3.55
4979 5238 1.917782 GCTTACGCGCCAATGGTTGA 61.918 55.000 5.73 0.00 0.00 3.18
5016 5275 3.973135 CACGGTTAATTAGACGATCCTCG 59.027 47.826 15.06 0.00 46.93 4.63
5031 5290 0.734253 CCTCGGAGCGTCAAGAACTG 60.734 60.000 0.00 0.00 0.00 3.16
5061 5320 1.820519 AGCCATGATGTTTGATGCGTT 59.179 42.857 0.00 0.00 0.00 4.84
5159 5425 2.224597 TGATGAACAAGGAGAAGCAGCA 60.225 45.455 0.00 0.00 0.00 4.41
5189 5455 2.962859 AGCATTTGAACAAGGGGAACT 58.037 42.857 0.00 0.00 0.00 3.01
5190 5456 3.308401 AGCATTTGAACAAGGGGAACTT 58.692 40.909 0.00 0.00 41.00 2.66
5194 5460 5.639082 GCATTTGAACAAGGGGAACTTAATG 59.361 40.000 0.00 0.00 37.29 1.90
5218 5485 2.277591 TGCAGAAATGCAGGTGGGC 61.278 57.895 0.00 0.00 40.23 5.36
5235 5502 1.523758 GGCGTCAGTTGGAAAGACAT 58.476 50.000 0.00 0.00 32.68 3.06
5241 5508 6.149633 GCGTCAGTTGGAAAGACATAAAAAT 58.850 36.000 0.00 0.00 32.68 1.82
5277 5544 6.206829 GTGCACCTAGAATTTTCAGGTTTACT 59.793 38.462 5.22 0.00 36.93 2.24
5357 5624 1.421410 CGCCGTGTTGATCAGTAGGC 61.421 60.000 17.94 17.94 38.24 3.93
5573 5861 1.996292 TCTTCGATGCTTCTGGTTCG 58.004 50.000 0.00 0.00 0.00 3.95
5653 5942 8.341892 AGGAAAAAGGAAACAGAGACAATATC 57.658 34.615 0.00 0.00 0.00 1.63
5703 5992 3.953612 GGGTGATGGCAAATCAACATAGA 59.046 43.478 16.02 0.00 37.47 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.615165 TAACATTCACCGGCGGGCTA 61.615 55.000 31.78 14.77 36.48 3.93
66 67 2.931325 TGTCGTAGTTGTGGTTGTTGAC 59.069 45.455 0.00 0.00 0.00 3.18
72 73 6.228258 AGTATCATTTGTCGTAGTTGTGGTT 58.772 36.000 0.00 0.00 0.00 3.67
181 183 3.923354 GCACTCTCTTGCTCTTGGA 57.077 52.632 0.00 0.00 39.59 3.53
220 222 3.629855 TCGAGATTGCAAAACACCAAAGA 59.370 39.130 1.71 0.00 0.00 2.52
272 279 3.261250 CAGCTTCTTGGTGCTCCAT 57.739 52.632 8.61 0.00 43.91 3.41
364 371 5.820947 TCACTCAGAAACTAAAACCCTTGAC 59.179 40.000 0.00 0.00 0.00 3.18
382 389 1.693606 TCAGGCACACATTCTCACTCA 59.306 47.619 0.00 0.00 0.00 3.41
384 391 1.610102 GCTCAGGCACACATTCTCACT 60.610 52.381 0.00 0.00 38.54 3.41
406 414 0.109132 CAAACATTGCCGCTCTTCCC 60.109 55.000 0.00 0.00 0.00 3.97
410 418 1.267806 CTGTTCAAACATTGCCGCTCT 59.732 47.619 0.00 0.00 38.41 4.09
457 465 8.486383 TGCAGTTGAATGTGAATTTTTAAATCG 58.514 29.630 0.00 0.00 0.00 3.34
462 470 9.932699 CATTTTGCAGTTGAATGTGAATTTTTA 57.067 25.926 0.00 0.00 0.00 1.52
463 471 8.675504 TCATTTTGCAGTTGAATGTGAATTTTT 58.324 25.926 11.42 0.00 33.60 1.94
475 484 5.668471 TCAACCAAATCATTTTGCAGTTGA 58.332 33.333 14.03 14.03 43.67 3.18
478 487 4.060205 GCTCAACCAAATCATTTTGCAGT 58.940 39.130 0.00 0.00 40.77 4.40
573 582 6.730960 TTAACCATAGTTTTACAAGCCGAG 57.269 37.500 0.00 0.00 37.42 4.63
616 626 5.983540 AGTTTCACACCCAAATAAAAGCAA 58.016 33.333 0.00 0.00 0.00 3.91
622 637 8.588290 AATAGCATAGTTTCACACCCAAATAA 57.412 30.769 0.00 0.00 0.00 1.40
651 668 7.197703 TGCATTATTTCACAAGCAGACATATG 58.802 34.615 0.00 0.00 0.00 1.78
685 704 6.015350 TGGCCGGTCTTTTTAAACAAATATGA 60.015 34.615 7.97 0.00 0.00 2.15
696 715 1.444836 CGATGTGGCCGGTCTTTTTA 58.555 50.000 7.97 0.00 0.00 1.52
711 731 2.687425 TGTCAACCCATATTTGCCGATG 59.313 45.455 0.00 0.00 0.00 3.84
712 740 3.011566 TGTCAACCCATATTTGCCGAT 57.988 42.857 0.00 0.00 0.00 4.18
713 741 2.498644 TGTCAACCCATATTTGCCGA 57.501 45.000 0.00 0.00 0.00 5.54
730 758 4.341502 GCAACGCGCCCAACATGT 62.342 61.111 5.73 0.00 32.94 3.21
743 771 3.363341 TTTTTGACTTGGATCGGCAAC 57.637 42.857 0.00 0.00 0.00 4.17
771 799 4.582701 TTTGTTCATTTGATTGTCCGCT 57.417 36.364 0.00 0.00 0.00 5.52
795 824 5.064962 TCAAACGAACGGTGTTTTTATCTGT 59.935 36.000 0.00 0.00 37.44 3.41
796 825 5.503498 TCAAACGAACGGTGTTTTTATCTG 58.497 37.500 0.00 0.00 37.44 2.90
797 826 5.738118 TCAAACGAACGGTGTTTTTATCT 57.262 34.783 0.00 0.00 37.44 1.98
798 827 6.183359 CGATTCAAACGAACGGTGTTTTTATC 60.183 38.462 0.00 4.80 37.44 1.75
799 828 5.622041 CGATTCAAACGAACGGTGTTTTTAT 59.378 36.000 0.00 0.00 37.44 1.40
800 829 4.962751 CGATTCAAACGAACGGTGTTTTTA 59.037 37.500 0.00 0.00 37.44 1.52
807 838 1.523934 GTGTCGATTCAAACGAACGGT 59.476 47.619 0.00 0.00 41.31 4.83
812 843 2.461903 TCAACGTGTCGATTCAAACGA 58.538 42.857 12.34 0.00 39.27 3.85
813 844 2.914816 TCAACGTGTCGATTCAAACG 57.085 45.000 0.00 0.00 41.64 3.60
818 849 2.221055 AGCAACTTCAACGTGTCGATTC 59.779 45.455 0.00 0.00 0.00 2.52
819 850 2.210116 AGCAACTTCAACGTGTCGATT 58.790 42.857 0.00 0.00 0.00 3.34
820 851 1.792949 GAGCAACTTCAACGTGTCGAT 59.207 47.619 0.00 0.00 0.00 3.59
826 857 2.102588 AGTGTAGGAGCAACTTCAACGT 59.897 45.455 0.00 0.00 0.00 3.99
832 863 6.415206 TGTAAACTAGTGTAGGAGCAACTT 57.585 37.500 0.00 0.00 0.00 2.66
894 927 7.610474 ACTGTCGTCACGGTTATGGATACAC 62.610 48.000 0.00 0.00 45.67 2.90
899 932 1.200716 GACTGTCGTCACGGTTATGGA 59.799 52.381 0.00 0.00 42.67 3.41
929 962 0.324275 ACAGCTCCAGAGAGAGGGAC 60.324 60.000 0.00 0.00 43.39 4.46
930 963 0.033601 GACAGCTCCAGAGAGAGGGA 60.034 60.000 0.00 0.00 43.39 4.20
931 964 1.042559 GGACAGCTCCAGAGAGAGGG 61.043 65.000 0.00 0.00 43.39 4.30
932 965 1.042559 GGGACAGCTCCAGAGAGAGG 61.043 65.000 0.00 0.00 43.39 3.69
933 966 0.033208 AGGGACAGCTCCAGAGAGAG 60.033 60.000 0.00 0.00 43.39 3.20
934 967 0.033601 GAGGGACAGCTCCAGAGAGA 60.034 60.000 0.00 0.00 43.39 3.10
935 968 0.033208 AGAGGGACAGCTCCAGAGAG 60.033 60.000 0.00 0.00 43.57 3.20
936 969 0.033601 GAGAGGGACAGCTCCAGAGA 60.034 60.000 0.00 0.00 38.52 3.10
937 970 0.033208 AGAGAGGGACAGCTCCAGAG 60.033 60.000 0.00 0.00 38.52 3.35
938 971 0.033601 GAGAGAGGGACAGCTCCAGA 60.034 60.000 0.00 0.00 38.52 3.86
939 972 0.033208 AGAGAGAGGGACAGCTCCAG 60.033 60.000 0.00 0.00 38.52 3.86
940 973 0.324183 CAGAGAGAGGGACAGCTCCA 60.324 60.000 0.00 0.00 38.52 3.86
941 974 1.675720 GCAGAGAGAGGGACAGCTCC 61.676 65.000 0.00 0.00 33.48 4.70
942 975 1.815866 GCAGAGAGAGGGACAGCTC 59.184 63.158 0.00 0.00 33.26 4.09
943 976 2.051518 CGCAGAGAGAGGGACAGCT 61.052 63.158 0.00 0.00 0.00 4.24
944 977 2.049185 TCGCAGAGAGAGGGACAGC 61.049 63.158 0.00 0.00 0.00 4.40
945 978 4.328041 TCGCAGAGAGAGGGACAG 57.672 61.111 0.00 0.00 0.00 3.51
1014 1047 2.772191 TGGTGGTGGTGGCTGACT 60.772 61.111 0.00 0.00 0.00 3.41
1015 1048 2.594592 GTGGTGGTGGTGGCTGAC 60.595 66.667 0.00 0.00 0.00 3.51
1016 1049 3.884774 GGTGGTGGTGGTGGCTGA 61.885 66.667 0.00 0.00 0.00 4.26
1017 1050 3.435525 AAGGTGGTGGTGGTGGCTG 62.436 63.158 0.00 0.00 0.00 4.85
1018 1051 3.103213 AAGGTGGTGGTGGTGGCT 61.103 61.111 0.00 0.00 0.00 4.75
1096 1138 1.745489 GGGCTGGCTACTTGGTTCG 60.745 63.158 0.00 0.00 0.00 3.95
1165 1207 1.079057 GAAGAAGTCGTCCTGCCCC 60.079 63.158 0.00 0.00 0.00 5.80
1166 1208 1.446272 CGAAGAAGTCGTCCTGCCC 60.446 63.158 0.00 0.00 45.09 5.36
1167 1209 4.170723 CGAAGAAGTCGTCCTGCC 57.829 61.111 0.00 0.00 45.09 4.85
1288 1330 4.047059 GCGGACTCGTCGAACCCA 62.047 66.667 11.62 0.00 38.89 4.51
1417 1459 2.031012 TCAGTGAACAGCGGCAGG 59.969 61.111 1.45 0.00 0.00 4.85
1534 1576 1.371183 CGGTTCTTGGCTCACCTGA 59.629 57.895 0.00 0.00 36.63 3.86
1581 1624 2.076863 GTTAGTGCGGCTGATGAAACT 58.923 47.619 0.00 0.00 0.00 2.66
1592 1635 1.804748 GGGAGAGTTTTGTTAGTGCGG 59.195 52.381 0.00 0.00 0.00 5.69
1603 1646 1.711375 GGGGGAAAGAAGGGAGAGTTT 59.289 52.381 0.00 0.00 0.00 2.66
1627 1670 2.215451 ATTGAGCCGGCCTTGGATGT 62.215 55.000 26.15 0.00 0.00 3.06
1769 1812 1.298953 TGATTGGGGGAGAAGGGAAG 58.701 55.000 0.00 0.00 0.00 3.46
1771 1814 2.000290 AATGATTGGGGGAGAAGGGA 58.000 50.000 0.00 0.00 0.00 4.20
1877 1921 4.668941 GCAAAAATGCCAGTAATTTTCGGC 60.669 41.667 5.08 5.08 45.11 5.54
1878 1922 4.690280 AGCAAAAATGCCAGTAATTTTCGG 59.310 37.500 0.00 0.00 36.46 4.30
1880 1924 6.783892 TGAGCAAAAATGCCAGTAATTTTC 57.216 33.333 0.00 0.00 36.46 2.29
1881 1925 7.565323 TTTGAGCAAAAATGCCAGTAATTTT 57.435 28.000 0.00 0.00 38.54 1.82
1882 1926 7.565323 TTTTGAGCAAAAATGCCAGTAATTT 57.435 28.000 5.95 0.00 37.35 1.82
1930 2038 0.729140 CGCACGGTTTCATTTCAGGC 60.729 55.000 0.00 0.00 0.00 4.85
1962 2070 3.430895 GCAGAGCAACACATGGAAAAATG 59.569 43.478 0.00 0.00 0.00 2.32
1989 2097 2.631580 CGCTATCCTCTCCCTCCGC 61.632 68.421 0.00 0.00 0.00 5.54
1990 2098 1.974343 CCGCTATCCTCTCCCTCCG 60.974 68.421 0.00 0.00 0.00 4.63
1992 2100 0.402504 TCTCCGCTATCCTCTCCCTC 59.597 60.000 0.00 0.00 0.00 4.30
2138 2246 3.563043 CCAGAATTCAGGGAAGGAAAGCT 60.563 47.826 8.99 0.00 0.00 3.74
2228 2336 7.446319 TGGCATCACACGTTATACTACTAGTAT 59.554 37.037 12.45 12.45 43.36 2.12
2229 2337 6.767423 TGGCATCACACGTTATACTACTAGTA 59.233 38.462 1.89 1.89 34.82 1.82
2230 2338 5.591472 TGGCATCACACGTTATACTACTAGT 59.409 40.000 0.00 0.00 0.00 2.57
2231 2339 6.068473 TGGCATCACACGTTATACTACTAG 57.932 41.667 0.00 0.00 0.00 2.57
2232 2340 6.443792 CATGGCATCACACGTTATACTACTA 58.556 40.000 0.00 0.00 0.00 1.82
2233 2341 4.994907 TGGCATCACACGTTATACTACT 57.005 40.909 0.00 0.00 0.00 2.57
2234 2342 4.084537 GCATGGCATCACACGTTATACTAC 60.085 45.833 0.00 0.00 0.00 2.73
2301 2409 4.589798 CCATCCATGCTTTCCAATTCCATA 59.410 41.667 0.00 0.00 0.00 2.74
2353 2461 6.893396 ACCCTATCCCCTGGATTACTTAATA 58.107 40.000 0.15 0.00 39.79 0.98
2354 2462 5.749293 ACCCTATCCCCTGGATTACTTAAT 58.251 41.667 0.15 0.00 39.79 1.40
2355 2463 5.179881 ACCCTATCCCCTGGATTACTTAA 57.820 43.478 0.15 0.00 39.79 1.85
2394 2502 0.736325 CTAAGCCAGACCGTCCAACG 60.736 60.000 0.00 0.00 42.11 4.10
2401 2509 5.519206 GTCACTAAATTACTAAGCCAGACCG 59.481 44.000 0.00 0.00 0.00 4.79
2403 2511 8.035984 AGAAGTCACTAAATTACTAAGCCAGAC 58.964 37.037 0.00 0.00 0.00 3.51
2437 2545 3.117963 CCATGCCTGATCTCTCTTTTCCT 60.118 47.826 0.00 0.00 0.00 3.36
2454 2592 0.396974 TATTCCCCTTGGCACCATGC 60.397 55.000 0.00 0.00 44.08 4.06
2473 2611 7.765695 ACTGATGGTGTCAATAACAATTCTT 57.234 32.000 0.00 0.00 40.31 2.52
2487 2628 0.105760 TTGGCCCAAACTGATGGTGT 60.106 50.000 0.00 0.00 38.91 4.16
2490 2631 1.891722 GCCTTGGCCCAAACTGATGG 61.892 60.000 0.00 0.00 40.35 3.51
2524 2665 6.457799 CCCCGTTTATCTACAATTGCACTAAC 60.458 42.308 5.05 2.52 0.00 2.34
2548 2689 2.976099 CCCCCTCAATTTGGTGTCC 58.024 57.895 0.00 0.00 0.00 4.02
2618 2760 9.481340 TCATGATGCTCAATATTGTAGTTCTAC 57.519 33.333 14.97 3.33 0.00 2.59
2798 2965 4.731961 GCAAAGAAAGATATCACATGTGCG 59.268 41.667 21.38 0.00 0.00 5.34
2816 2983 7.275341 TGAACAGTGAATAAAAGTTGTGCAAAG 59.725 33.333 0.00 0.00 0.00 2.77
3113 3280 3.189287 AGCAACATTCAGAAACTTAGCGG 59.811 43.478 0.00 0.00 0.00 5.52
3269 3436 6.088824 GTCAAAATGGAAGATCATGTCACAC 58.911 40.000 0.00 0.00 0.00 3.82
3315 3482 4.346418 GTCAGTGATGTAGGATTCCTCCAT 59.654 45.833 10.33 10.33 44.79 3.41
3648 3834 0.690192 TTTCAGTCCTCCGAATGCCA 59.310 50.000 0.00 0.00 34.06 4.92
3705 3893 5.186603 TGATGTGGTGCAATTTTTATAGGCA 59.813 36.000 0.00 0.00 0.00 4.75
3868 4056 6.515035 GCTTGATTGGTAGTTTGGTATATGGC 60.515 42.308 0.00 0.00 0.00 4.40
3873 4061 5.570320 ACTGCTTGATTGGTAGTTTGGTAT 58.430 37.500 0.00 0.00 0.00 2.73
3900 4088 1.896465 GTGGGCAGTAGCTCCTATAGG 59.104 57.143 13.07 13.07 41.98 2.57
3903 4091 3.235200 CTTAGTGGGCAGTAGCTCCTAT 58.765 50.000 0.00 0.00 41.98 2.57
4016 4204 5.624344 AACAGCTGATGATTTCTTGACAG 57.376 39.130 23.35 0.00 0.00 3.51
4027 4215 8.481314 AGATGACTCTTATAAAACAGCTGATGA 58.519 33.333 23.35 1.79 0.00 2.92
4036 4224 9.713740 CAATTGAGCAGATGACTCTTATAAAAC 57.286 33.333 0.00 0.00 35.12 2.43
4039 4227 6.484643 GGCAATTGAGCAGATGACTCTTATAA 59.515 38.462 10.34 0.00 35.12 0.98
4070 4258 3.127721 GCAAGGTGGACTCAGATTTTAGC 59.872 47.826 0.00 0.00 0.00 3.09
4337 4525 0.324460 CTTCGTGTAGGGGTCCTCCT 60.324 60.000 4.51 4.51 40.79 3.69
4419 4610 1.001760 ACTGTCTACCGCCATCCCT 59.998 57.895 0.00 0.00 0.00 4.20
4424 4615 0.317160 CACTTCACTGTCTACCGCCA 59.683 55.000 0.00 0.00 0.00 5.69
4459 4678 1.318576 GCAATTCTACCCCCGGAATG 58.681 55.000 0.73 0.00 33.19 2.67
4464 4683 1.823899 GCTGGCAATTCTACCCCCG 60.824 63.158 0.00 0.00 0.00 5.73
4681 4901 1.537202 GGAACGACAGCTCAGCAATTT 59.463 47.619 0.00 0.00 0.00 1.82
4682 4902 1.160137 GGAACGACAGCTCAGCAATT 58.840 50.000 0.00 0.00 0.00 2.32
4793 5051 2.989166 GCTTTGCATTTGTGCCTTCTAC 59.011 45.455 0.00 0.00 0.00 2.59
4842 5100 1.983691 CTCCTGGCTCCCACATGATAT 59.016 52.381 0.00 0.00 0.00 1.63
4908 5166 7.097834 GCACTACAACTAAGGTTATCTGACTT 58.902 38.462 0.00 0.00 33.88 3.01
4927 5186 2.159037 GGCTTTCCAGTAAACGCACTAC 59.841 50.000 0.00 0.00 0.00 2.73
4942 5201 1.745768 GCATTTCGCGCATGGCTTTC 61.746 55.000 8.75 0.32 40.44 2.62
4943 5202 1.806758 GCATTTCGCGCATGGCTTT 60.807 52.632 8.75 0.00 40.44 3.51
4967 5226 0.099968 CTGCATCTCAACCATTGGCG 59.900 55.000 1.54 0.00 0.00 5.69
4976 5235 2.778299 GTGTTACCACCTGCATCTCAA 58.222 47.619 0.00 0.00 35.44 3.02
4979 5238 0.036388 CCGTGTTACCACCTGCATCT 60.036 55.000 0.00 0.00 38.41 2.90
5016 5275 2.440539 TCTTCAGTTCTTGACGCTCC 57.559 50.000 0.00 0.00 34.94 4.70
5031 5290 9.622004 CATCAAACATCATGGCTTAATATCTTC 57.378 33.333 0.00 0.00 0.00 2.87
5061 5320 4.987408 TCTTCACCGGATCACGTAATTA 57.013 40.909 9.46 0.00 42.24 1.40
5121 5384 3.515104 TCATCAGAGTTGTCAGTGGCATA 59.485 43.478 0.00 0.00 0.00 3.14
5159 5425 5.106555 CCTTGTTCAAATGCTACAAGTCGAT 60.107 40.000 18.39 0.00 44.46 3.59
5218 5485 8.574196 AAATTTTTATGTCTTTCCAACTGACG 57.426 30.769 0.00 0.00 33.81 4.35
5277 5544 6.072508 GGCTGATTTAGTCTGAACATTTGTCA 60.073 38.462 0.00 0.00 0.00 3.58
5278 5545 6.072508 TGGCTGATTTAGTCTGAACATTTGTC 60.073 38.462 0.00 0.00 0.00 3.18
5357 5624 3.377172 CCCCCTGTTTGCTTTTCTATACG 59.623 47.826 0.00 0.00 0.00 3.06
5492 5780 1.876156 AGAAAGAGAGGCAAGCAAACG 59.124 47.619 0.00 0.00 0.00 3.60
5573 5861 5.921962 AAGATAAATTGAAAGGGTCTGCC 57.078 39.130 0.00 0.00 0.00 4.85
5653 5942 6.484540 CCTTCGATGTTCTTCATTGATTCTG 58.515 40.000 0.00 0.00 43.85 3.02


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

AutoCloner maintained by Alex Coulton.