Multiple sequence alignment - TraesCS4D01G330400

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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 TraesCS4D01G330400 chr4D 100.000 2880 0 0 1 2880 488606513 488609392 0.000000e+00 5319.0
1 TraesCS4D01G330400 chr4D 81.054 1594 231 38 859 2435 488513814 488515353 0.000000e+00 1205.0
2 TraesCS4D01G330400 chr4D 84.472 322 27 12 1 300 488516125 488516445 2.700000e-76 296.0
3 TraesCS4D01G330400 chr4D 92.029 138 9 1 291 426 488516476 488516613 3.640000e-45 193.0
4 TraesCS4D01G330400 chr4D 100.000 50 0 0 3524 3573 488610036 488610085 3.800000e-15 93.5
5 TraesCS4D01G330400 chr4B 92.389 2733 143 25 4 2686 625529679 625532396 0.000000e+00 3834.0
6 TraesCS4D01G330400 chr4B 80.623 1445 222 33 1015 2435 625400937 625402347 0.000000e+00 1064.0
7 TraesCS4D01G330400 chr4B 86.099 928 68 25 150 1043 625397878 625398778 0.000000e+00 942.0
8 TraesCS4D01G330400 chr4B 81.664 769 112 17 1668 2435 625382226 625382966 2.360000e-171 612.0
9 TraesCS4D01G330400 chr4B 80.340 824 124 17 868 1675 625380476 625381277 1.100000e-164 590.0
10 TraesCS4D01G330400 chr4B 78.557 499 100 6 1087 1584 625295383 625295875 4.450000e-84 322.0
11 TraesCS4D01G330400 chr4B 92.105 114 6 2 475 587 625403593 625403704 1.330000e-34 158.0
12 TraesCS4D01G330400 chr5A 80.424 1604 243 42 863 2436 670344701 670346263 0.000000e+00 1157.0
13 TraesCS4D01G330400 chr5A 86.228 334 25 9 1 315 670341451 670341782 3.420000e-90 342.0
14 TraesCS4D01G330400 chr5A 91.837 49 3 1 605 652 597792121 597792169 2.300000e-07 67.6
15 TraesCS4D01G330400 chr7B 80.376 1330 224 21 1118 2436 82444888 82446191 0.000000e+00 976.0
16 TraesCS4D01G330400 chr7B 91.489 47 3 1 611 656 157208746 157208792 2.980000e-06 63.9
17 TraesCS4D01G330400 chr7A 80.299 1340 224 28 1111 2436 125277584 125278897 0.000000e+00 976.0
18 TraesCS4D01G330400 chr7A 78.170 1333 227 40 1135 2435 19547555 19546255 0.000000e+00 791.0
19 TraesCS4D01G330400 chr7A 91.960 199 11 3 2465 2663 616078180 616078373 1.260000e-69 274.0
20 TraesCS4D01G330400 chr4A 77.566 1364 257 23 1087 2436 731237969 731239297 0.000000e+00 778.0
21 TraesCS4D01G330400 chr4A 82.449 245 41 2 2192 2435 713489515 713489758 2.790000e-51 213.0
22 TraesCS4D01G330400 chr3A 90.141 213 12 4 2451 2663 206527097 206527300 5.880000e-68 268.0
23 TraesCS4D01G330400 chr1A 100.000 35 0 0 612 646 494323076 494323042 8.280000e-07 65.8
24 TraesCS4D01G330400 chr6B 93.023 43 3 0 604 646 455424387 455424345 2.980000e-06 63.9
25 TraesCS4D01G330400 chr6A 97.368 38 0 1 611 647 191221938 191221975 2.980000e-06 63.9
26 TraesCS4D01G330400 chrUn 94.872 39 1 1 609 646 93828919 93828881 3.850000e-05 60.2
27 TraesCS4D01G330400 chr3B 92.683 41 3 0 607 647 669280958 669280998 3.850000e-05 60.2
28 TraesCS4D01G330400 chr1D 97.143 35 1 0 136 170 473769947 473769981 3.850000e-05 60.2


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 TraesCS4D01G330400 chr4D 488606513 488610085 3572 False 2706.250000 5319 100.000000 1 3573 2 chr4D.!!$F2 3572
1 TraesCS4D01G330400 chr4D 488513814 488516613 2799 False 564.666667 1205 85.851667 1 2435 3 chr4D.!!$F1 2434
2 TraesCS4D01G330400 chr4B 625529679 625532396 2717 False 3834.000000 3834 92.389000 4 2686 1 chr4B.!!$F2 2682
3 TraesCS4D01G330400 chr4B 625397878 625403704 5826 False 721.333333 1064 86.275667 150 2435 3 chr4B.!!$F4 2285
4 TraesCS4D01G330400 chr4B 625380476 625382966 2490 False 601.000000 612 81.002000 868 2435 2 chr4B.!!$F3 1567
5 TraesCS4D01G330400 chr5A 670341451 670346263 4812 False 749.500000 1157 83.326000 1 2436 2 chr5A.!!$F2 2435
6 TraesCS4D01G330400 chr7B 82444888 82446191 1303 False 976.000000 976 80.376000 1118 2436 1 chr7B.!!$F1 1318
7 TraesCS4D01G330400 chr7A 125277584 125278897 1313 False 976.000000 976 80.299000 1111 2436 1 chr7A.!!$F1 1325
8 TraesCS4D01G330400 chr7A 19546255 19547555 1300 True 791.000000 791 78.170000 1135 2435 1 chr7A.!!$R1 1300
9 TraesCS4D01G330400 chr4A 731237969 731239297 1328 False 778.000000 778 77.566000 1087 2436 1 chr4A.!!$F2 1349

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
986 5584 0.249322 ACAGGTCCAACTCAACGACG 60.249 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2805 9059 0.036448 CCTGATGCTGCCCTATCTGG 59.964 60.0 9.05 9.05 36.5 3.86 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
34 36 5.299148 TGAAAAAGGGCAAGAACAATCATG 58.701 37.500 0.00 0.00 0.00 3.07
40 42 3.236816 GGCAAGAACAATCATGTCGTTG 58.763 45.455 0.00 0.00 39.40 4.10
63 66 0.769247 ACCGGGTAGTGCCTCTTTTT 59.231 50.000 6.32 0.00 37.43 1.94
64 67 1.165270 CCGGGTAGTGCCTCTTTTTG 58.835 55.000 0.00 0.00 37.43 2.44
65 68 0.521735 CGGGTAGTGCCTCTTTTTGC 59.478 55.000 0.00 0.00 37.43 3.68
66 69 1.616159 GGGTAGTGCCTCTTTTTGCA 58.384 50.000 0.00 0.00 37.43 4.08
83 86 4.389890 TTGCACTGAAAAGACTGCAAAT 57.610 36.364 1.54 0.00 44.53 2.32
100 103 4.026393 TGCAAATATACCACGAAATCGACG 60.026 41.667 10.16 1.38 43.02 5.12
118 128 1.282248 CGCGAGACACACCGACAAAT 61.282 55.000 0.00 0.00 0.00 2.32
131 153 0.806868 GACAAATAGCAGCAGCAGCA 59.193 50.000 12.92 0.00 45.49 4.41
134 156 1.404035 CAAATAGCAGCAGCAGCATCA 59.596 47.619 12.92 0.00 45.49 3.07
194 216 5.512788 CGAGCAAACATGAAATCCACATTAC 59.487 40.000 0.00 0.00 0.00 1.89
209 236 5.103982 TCCACATTACCTCATCATTGTCCAT 60.104 40.000 0.00 0.00 0.00 3.41
226 257 2.114323 TCCATGGATAGGGATAGGCTGT 59.886 50.000 11.44 0.00 30.42 4.40
277 312 0.538118 GTGCCCAATGTGCCATTGAT 59.462 50.000 22.11 0.00 0.00 2.57
293 340 3.607163 ATGGTGCCTTTGCCATCG 58.393 55.556 0.00 0.00 41.24 3.84
300 347 1.986575 GCCTTTGCCATCGTCAGAGC 61.987 60.000 0.00 0.00 0.00 4.09
405 2425 1.028905 GAGGTCGAGTCTGATCCTGG 58.971 60.000 0.00 0.00 0.00 4.45
426 2446 5.165676 TGGATTTAGCACACAAGTAGTACG 58.834 41.667 0.00 0.00 0.00 3.67
435 2500 4.919754 CACACAAGTAGTACGTTCCCTTAC 59.080 45.833 0.00 0.00 0.00 2.34
713 3130 2.009042 GCATGTTTGACCGAGGAGAGG 61.009 57.143 0.00 0.00 0.00 3.69
771 3196 4.795970 GTGTGGATGTCGATTTCCATAC 57.204 45.455 21.88 21.88 43.76 2.39
831 3270 2.286067 GCATGTGCTTGAGCGAGTAATC 60.286 50.000 0.00 0.00 45.83 1.75
839 3278 1.268083 TGAGCGAGTAATCTTCGAGCG 60.268 52.381 0.00 0.00 0.00 5.03
840 3279 0.592754 AGCGAGTAATCTTCGAGCGC 60.593 55.000 0.00 0.00 42.88 5.92
953 5549 0.746204 TGCAAAGTTGACCTGCGTGA 60.746 50.000 0.00 0.00 38.97 4.35
969 5567 3.243226 CGTGACGTCGCTACATATACA 57.757 47.619 25.28 0.00 0.00 2.29
986 5584 0.249322 ACAGGTCCAACTCAACGACG 60.249 55.000 0.00 0.00 0.00 5.12
987 5585 1.300697 AGGTCCAACTCAACGACGC 60.301 57.895 0.00 0.00 0.00 5.19
1051 5708 1.538512 CCCAGTGCTGAATTGTGTGAG 59.461 52.381 0.02 0.00 0.00 3.51
1052 5709 1.068748 CCAGTGCTGAATTGTGTGAGC 60.069 52.381 0.02 0.00 0.00 4.26
2442 8130 1.340657 GACAAGCTGTGACGAGCGAG 61.341 60.000 0.00 0.00 44.24 5.03
2445 8133 4.760840 GCTGTGACGAGCGAGCGA 62.761 66.667 4.36 0.00 34.83 4.93
2455 8143 0.662970 GAGCGAGCGAGCCATAAGAG 60.663 60.000 2.87 0.00 38.01 2.85
2466 8154 1.538419 GCCATAAGAGCAGTACCGACC 60.538 57.143 0.00 0.00 0.00 4.79
2467 8155 1.269102 CCATAAGAGCAGTACCGACCG 60.269 57.143 0.00 0.00 0.00 4.79
2469 8157 2.048444 TAAGAGCAGTACCGACCGAT 57.952 50.000 0.00 0.00 0.00 4.18
2478 8166 2.098117 AGTACCGACCGATTAAGGAACG 59.902 50.000 0.00 0.00 35.71 3.95
2538 8289 3.274067 GGGGGCAAAGCAACTACG 58.726 61.111 0.00 0.00 0.00 3.51
2592 8350 6.322969 TGATCTGCCATGCATCTTTTCTTATT 59.677 34.615 0.00 0.00 38.13 1.40
2601 8359 5.931724 TGCATCTTTTCTTATTGTCTCGTCA 59.068 36.000 0.00 0.00 0.00 4.35
2625 8383 6.189677 ACAAGTTTTCATGTTCGTTCTCAA 57.810 33.333 0.00 0.00 0.00 3.02
2690 8944 1.905637 TCGCACTCTCAGTTCCACTA 58.094 50.000 0.00 0.00 0.00 2.74
2692 8946 2.229062 TCGCACTCTCAGTTCCACTAAG 59.771 50.000 0.00 0.00 0.00 2.18
2693 8947 2.229062 CGCACTCTCAGTTCCACTAAGA 59.771 50.000 0.00 0.00 0.00 2.10
2697 8951 5.788450 CACTCTCAGTTCCACTAAGATTGT 58.212 41.667 0.00 0.00 0.00 2.71
2700 8954 6.042093 ACTCTCAGTTCCACTAAGATTGTGAA 59.958 38.462 0.00 0.00 37.60 3.18
2702 8956 7.279615 TCTCAGTTCCACTAAGATTGTGAAAA 58.720 34.615 0.00 0.00 37.60 2.29
2703 8957 7.773224 TCTCAGTTCCACTAAGATTGTGAAAAA 59.227 33.333 0.00 0.00 37.60 1.94
2704 8958 8.463930 TCAGTTCCACTAAGATTGTGAAAAAT 57.536 30.769 0.00 0.00 37.60 1.82
2705 8959 8.912988 TCAGTTCCACTAAGATTGTGAAAAATT 58.087 29.630 0.00 0.00 37.60 1.82
2706 8960 8.971321 CAGTTCCACTAAGATTGTGAAAAATTG 58.029 33.333 0.00 0.00 37.60 2.32
2708 8962 9.185192 GTTCCACTAAGATTGTGAAAAATTGAG 57.815 33.333 0.00 0.00 37.60 3.02
2709 8963 8.463930 TCCACTAAGATTGTGAAAAATTGAGT 57.536 30.769 0.00 0.00 37.60 3.41
2711 8965 9.533253 CCACTAAGATTGTGAAAAATTGAGTTT 57.467 29.630 0.00 0.00 37.60 2.66
2713 8967 9.450807 ACTAAGATTGTGAAAAATTGAGTTTCG 57.549 29.630 0.00 0.00 37.72 3.46
2714 8968 9.663904 CTAAGATTGTGAAAAATTGAGTTTCGA 57.336 29.630 0.00 0.00 37.72 3.71
2720 8974 9.834628 TTGTGAAAAATTGAGTTTCGATATACC 57.165 29.630 0.00 0.00 37.72 2.73
2721 8975 9.226606 TGTGAAAAATTGAGTTTCGATATACCT 57.773 29.630 0.00 0.00 37.72 3.08
2724 8978 7.568199 AAAATTGAGTTTCGATATACCTGGG 57.432 36.000 0.00 0.00 0.00 4.45
2725 8979 6.494666 AATTGAGTTTCGATATACCTGGGA 57.505 37.500 0.00 0.00 0.00 4.37
2728 8982 6.097915 TGAGTTTCGATATACCTGGGAATC 57.902 41.667 0.00 0.00 0.00 2.52
2729 8983 5.839063 TGAGTTTCGATATACCTGGGAATCT 59.161 40.000 0.00 0.00 0.00 2.40
2732 8986 3.441101 TCGATATACCTGGGAATCTGGG 58.559 50.000 0.00 0.00 38.62 4.45
2733 8987 3.173965 CGATATACCTGGGAATCTGGGT 58.826 50.000 0.00 0.00 38.62 4.51
2734 8988 4.044952 TCGATATACCTGGGAATCTGGGTA 59.955 45.833 0.00 0.00 38.62 3.69
2735 8989 4.159879 CGATATACCTGGGAATCTGGGTAC 59.840 50.000 0.00 0.00 37.18 3.34
2751 9005 3.149005 GGTACCCAGAAAACCATGTGA 57.851 47.619 0.00 0.00 33.28 3.58
2752 9006 2.817844 GGTACCCAGAAAACCATGTGAC 59.182 50.000 0.00 0.00 33.28 3.67
2753 9007 2.746279 ACCCAGAAAACCATGTGACA 57.254 45.000 0.00 0.00 0.00 3.58
2754 9008 3.025322 ACCCAGAAAACCATGTGACAA 57.975 42.857 0.00 0.00 0.00 3.18
2755 9009 2.958355 ACCCAGAAAACCATGTGACAAG 59.042 45.455 0.00 0.00 0.00 3.16
2756 9010 2.288395 CCCAGAAAACCATGTGACAAGC 60.288 50.000 0.00 0.00 0.00 4.01
2757 9011 2.361757 CCAGAAAACCATGTGACAAGCA 59.638 45.455 0.00 0.00 0.00 3.91
2767 9021 2.405892 GTGACAAGCACACATGGAAC 57.594 50.000 0.00 0.00 46.91 3.62
2768 9022 0.943673 TGACAAGCACACATGGAACG 59.056 50.000 0.00 0.00 0.00 3.95
2769 9023 0.238289 GACAAGCACACATGGAACGG 59.762 55.000 0.00 0.00 0.00 4.44
2770 9024 0.465460 ACAAGCACACATGGAACGGT 60.465 50.000 0.00 0.00 0.00 4.83
2771 9025 0.040157 CAAGCACACATGGAACGGTG 60.040 55.000 0.00 0.00 41.12 4.94
2772 9026 1.172180 AAGCACACATGGAACGGTGG 61.172 55.000 0.00 0.00 39.93 4.61
2773 9027 2.953821 CACACATGGAACGGTGGC 59.046 61.111 0.00 0.00 39.93 5.01
2774 9028 1.896183 CACACATGGAACGGTGGCA 60.896 57.895 0.00 0.00 39.93 4.92
2775 9029 1.152860 ACACATGGAACGGTGGCAA 60.153 52.632 0.00 0.00 39.93 4.52
2776 9030 1.285641 CACATGGAACGGTGGCAAC 59.714 57.895 0.00 0.00 33.52 4.17
2787 9041 4.342427 TGGCAACATCCATCAGGC 57.658 55.556 0.00 0.00 46.17 4.85
2788 9042 1.693034 TGGCAACATCCATCAGGCT 59.307 52.632 0.00 0.00 46.17 4.58
2789 9043 0.040058 TGGCAACATCCATCAGGCTT 59.960 50.000 0.00 0.00 46.17 4.35
2790 9044 0.743097 GGCAACATCCATCAGGCTTC 59.257 55.000 0.00 0.00 33.74 3.86
2791 9045 1.466856 GCAACATCCATCAGGCTTCA 58.533 50.000 0.00 0.00 33.74 3.02
2792 9046 2.029623 GCAACATCCATCAGGCTTCAT 58.970 47.619 0.00 0.00 33.74 2.57
2793 9047 2.034305 GCAACATCCATCAGGCTTCATC 59.966 50.000 0.00 0.00 33.74 2.92
2794 9048 3.284617 CAACATCCATCAGGCTTCATCA 58.715 45.455 0.00 0.00 33.74 3.07
2795 9049 3.657398 ACATCCATCAGGCTTCATCAA 57.343 42.857 0.00 0.00 33.74 2.57
2796 9050 3.552875 ACATCCATCAGGCTTCATCAAG 58.447 45.455 0.00 0.00 33.74 3.02
2797 9051 2.723322 TCCATCAGGCTTCATCAAGG 57.277 50.000 0.00 0.00 33.74 3.61
2798 9052 2.199208 TCCATCAGGCTTCATCAAGGA 58.801 47.619 0.00 0.00 33.74 3.36
2799 9053 2.577563 TCCATCAGGCTTCATCAAGGAA 59.422 45.455 0.00 0.00 33.74 3.36
2800 9054 3.010472 TCCATCAGGCTTCATCAAGGAAA 59.990 43.478 0.00 0.00 33.74 3.13
2801 9055 3.958798 CCATCAGGCTTCATCAAGGAAAT 59.041 43.478 0.00 0.00 0.00 2.17
2802 9056 4.202121 CCATCAGGCTTCATCAAGGAAATG 60.202 45.833 0.00 0.00 0.00 2.32
2803 9057 3.359033 TCAGGCTTCATCAAGGAAATGG 58.641 45.455 0.00 0.00 0.00 3.16
2804 9058 2.429610 CAGGCTTCATCAAGGAAATGGG 59.570 50.000 0.00 0.00 0.00 4.00
2805 9059 1.137675 GGCTTCATCAAGGAAATGGGC 59.862 52.381 0.00 0.00 0.00 5.36
2806 9060 1.137675 GCTTCATCAAGGAAATGGGCC 59.862 52.381 0.00 0.00 0.00 5.80
2807 9061 2.459644 CTTCATCAAGGAAATGGGCCA 58.540 47.619 9.61 9.61 0.00 5.36
2808 9062 2.148446 TCATCAAGGAAATGGGCCAG 57.852 50.000 13.78 0.00 0.00 4.85
2809 9063 1.640149 TCATCAAGGAAATGGGCCAGA 59.360 47.619 13.78 1.43 0.00 3.86
2810 9064 2.245546 TCATCAAGGAAATGGGCCAGAT 59.754 45.455 13.78 4.19 0.00 2.90
2811 9065 3.462954 TCATCAAGGAAATGGGCCAGATA 59.537 43.478 13.78 0.00 0.00 1.98
2812 9066 3.582998 TCAAGGAAATGGGCCAGATAG 57.417 47.619 13.78 0.00 0.00 2.08
2831 9085 1.310933 GGGCAGCATCAGGTTCACAG 61.311 60.000 0.00 0.00 0.00 3.66
2832 9086 0.607489 GGCAGCATCAGGTTCACAGT 60.607 55.000 0.00 0.00 0.00 3.55
2833 9087 1.339055 GGCAGCATCAGGTTCACAGTA 60.339 52.381 0.00 0.00 0.00 2.74
2834 9088 1.734465 GCAGCATCAGGTTCACAGTAC 59.266 52.381 0.00 0.00 0.00 2.73
2836 9090 2.998670 CAGCATCAGGTTCACAGTACTG 59.001 50.000 21.44 21.44 0.00 2.74
2864 9152 2.751688 GTTTCCCACCGGGCAGTA 59.248 61.111 6.32 0.00 43.94 2.74
2865 9153 1.376812 GTTTCCCACCGGGCAGTAG 60.377 63.158 6.32 0.00 43.94 2.57
2866 9154 1.844289 TTTCCCACCGGGCAGTAGT 60.844 57.895 6.32 0.00 43.94 2.73
2867 9155 2.119484 TTTCCCACCGGGCAGTAGTG 62.119 60.000 6.32 0.00 43.94 2.74
3549 9837 9.416794 CACACACACATCTCTATTCCTAATATC 57.583 37.037 0.00 0.00 0.00 1.63
3550 9838 9.373450 ACACACACATCTCTATTCCTAATATCT 57.627 33.333 0.00 0.00 0.00 1.98
3551 9839 9.636879 CACACACATCTCTATTCCTAATATCTG 57.363 37.037 0.00 0.00 0.00 2.90
3552 9840 9.593565 ACACACATCTCTATTCCTAATATCTGA 57.406 33.333 0.00 0.00 0.00 3.27
3554 9842 9.821240 ACACATCTCTATTCCTAATATCTGAGT 57.179 33.333 0.00 0.00 0.00 3.41
3558 9846 9.836179 ATCTCTATTCCTAATATCTGAGTTGGT 57.164 33.333 0.00 0.00 0.00 3.67
3559 9847 9.083422 TCTCTATTCCTAATATCTGAGTTGGTG 57.917 37.037 0.00 0.00 0.00 4.17
3560 9848 9.083422 CTCTATTCCTAATATCTGAGTTGGTGA 57.917 37.037 0.00 0.00 0.00 4.02
3561 9849 9.434275 TCTATTCCTAATATCTGAGTTGGTGAA 57.566 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 67 6.030228 GGTATATTTGCAGTCTTTTCAGTGC 58.970 40.000 0.00 0.00 42.29 4.40
65 68 7.023575 GTGGTATATTTGCAGTCTTTTCAGTG 58.976 38.462 0.00 0.00 0.00 3.66
66 69 6.128282 CGTGGTATATTTGCAGTCTTTTCAGT 60.128 38.462 0.00 0.00 0.00 3.41
67 70 6.092122 TCGTGGTATATTTGCAGTCTTTTCAG 59.908 38.462 0.00 0.00 0.00 3.02
83 86 1.330213 TCGCGTCGATTTCGTGGTATA 59.670 47.619 5.77 0.00 40.80 1.47
100 103 1.654105 CTATTTGTCGGTGTGTCTCGC 59.346 52.381 0.00 0.00 0.00 5.03
118 128 0.179468 TCATGATGCTGCTGCTGCTA 59.821 50.000 27.67 16.66 40.48 3.49
131 153 2.292267 GGTGCTCGTCCATTTCATGAT 58.708 47.619 0.00 0.00 0.00 2.45
134 156 0.744414 CCGGTGCTCGTCCATTTCAT 60.744 55.000 0.00 0.00 37.11 2.57
194 216 4.567116 CCCTATCCATGGACAATGATGAGG 60.567 50.000 18.99 12.59 38.72 3.86
209 236 1.132721 AGCACAGCCTATCCCTATCCA 60.133 52.381 0.00 0.00 0.00 3.41
226 257 2.923121 CCTGCATCTAGGCTTTAAGCA 58.077 47.619 19.10 0.00 44.75 3.91
277 312 1.971167 GACGATGGCAAAGGCACCA 60.971 57.895 0.00 0.00 41.84 4.17
293 340 1.135746 GCTGCATCAACAAGCTCTGAC 60.136 52.381 0.00 0.00 0.00 3.51
300 347 1.269361 TGCTTGTGCTGCATCAACAAG 60.269 47.619 22.47 22.47 40.29 3.16
405 2425 6.183360 GGAACGTACTACTTGTGTGCTAAATC 60.183 42.308 0.00 0.00 0.00 2.17
435 2500 6.860080 TGAAAGGATTTGTAGTAGTACCTCG 58.140 40.000 5.26 0.00 39.27 4.63
646 3063 7.201911 CCTCTGTCCCAGTTCAAATTAAACTTT 60.202 37.037 3.94 0.00 34.79 2.66
647 3064 6.265422 CCTCTGTCCCAGTTCAAATTAAACTT 59.735 38.462 3.94 0.00 34.79 2.66
688 3105 1.335872 CCTCGGTCAAACATGCAAACC 60.336 52.381 0.00 0.00 0.00 3.27
692 3109 0.684535 TCTCCTCGGTCAAACATGCA 59.315 50.000 0.00 0.00 0.00 3.96
713 3130 1.757699 AGGGATACTCTTTGAGTCGGC 59.242 52.381 3.30 0.00 42.40 5.54
771 3196 6.559810 TCCACTGATTTTGTTGTTGTTACTG 58.440 36.000 0.00 0.00 0.00 2.74
831 3270 2.159421 TCTAAGTTACTGGCGCTCGAAG 60.159 50.000 7.64 2.70 0.00 3.79
839 3278 5.989777 TCTTGTCACTTTCTAAGTTACTGGC 59.010 40.000 5.73 0.00 40.46 4.85
840 3279 8.608844 AATCTTGTCACTTTCTAAGTTACTGG 57.391 34.615 5.73 0.00 40.46 4.00
886 3327 3.181463 CCCCAAAATTATCCATGCCACTG 60.181 47.826 0.00 0.00 0.00 3.66
926 5522 3.618150 CAGGTCAACTTTGCAAAAAGGTG 59.382 43.478 13.84 11.48 46.16 4.00
953 5549 2.551459 GGACCTGTATATGTAGCGACGT 59.449 50.000 0.00 0.00 0.00 4.34
969 5567 1.300697 GCGTCGTTGAGTTGGACCT 60.301 57.895 0.00 0.00 0.00 3.85
986 5584 3.428413 TTGTTGGTTTAGGACTAGGGC 57.572 47.619 0.00 0.00 0.00 5.19
987 5585 6.376299 GGTTATTTGTTGGTTTAGGACTAGGG 59.624 42.308 0.00 0.00 0.00 3.53
1435 6125 2.811317 GGCTGGTCGAAGCAGACG 60.811 66.667 11.06 0.00 45.98 4.18
2273 7958 3.443045 GCCGGTACCGTCCTCGAA 61.443 66.667 31.24 0.00 39.71 3.71
2442 8130 1.492720 GTACTGCTCTTATGGCTCGC 58.507 55.000 0.00 0.00 0.00 5.03
2445 8133 1.409427 GTCGGTACTGCTCTTATGGCT 59.591 52.381 0.00 0.00 0.00 4.75
2455 8143 1.406539 TCCTTAATCGGTCGGTACTGC 59.593 52.381 0.00 0.00 31.50 4.40
2466 8154 1.592110 CGCATGCACGTTCCTTAATCG 60.592 52.381 19.57 0.00 0.00 3.34
2467 8155 1.396996 ACGCATGCACGTTCCTTAATC 59.603 47.619 19.57 0.00 45.75 1.75
2469 8157 0.515127 CACGCATGCACGTTCCTTAA 59.485 50.000 19.57 0.00 45.75 1.85
2529 8280 2.227388 ACTGCTTACGTACGTAGTTGCT 59.773 45.455 30.63 19.42 37.78 3.91
2535 8286 7.009174 GGCTTAATTAAACTGCTTACGTACGTA 59.991 37.037 23.60 23.60 0.00 3.57
2536 8287 6.183360 GGCTTAATTAAACTGCTTACGTACGT 60.183 38.462 25.98 25.98 0.00 3.57
2537 8288 6.035327 AGGCTTAATTAAACTGCTTACGTACG 59.965 38.462 15.01 15.01 0.00 3.67
2538 8289 7.299787 AGGCTTAATTAAACTGCTTACGTAC 57.700 36.000 0.00 0.00 0.00 3.67
2592 8350 4.634004 ACATGAAAACTTGTTGACGAGACA 59.366 37.500 0.00 1.56 0.00 3.41
2601 8359 6.189677 TGAGAACGAACATGAAAACTTGTT 57.810 33.333 0.00 0.00 0.00 2.83
2625 8383 3.505680 TGGAATTGTTTTCGTAGCATGCT 59.494 39.130 25.99 25.99 0.00 3.79
2697 8951 8.673711 CCAGGTATATCGAAACTCAATTTTTCA 58.326 33.333 0.00 0.00 33.30 2.69
2700 8954 7.343357 TCCCAGGTATATCGAAACTCAATTTT 58.657 34.615 0.00 0.00 0.00 1.82
2702 8956 6.494666 TCCCAGGTATATCGAAACTCAATT 57.505 37.500 0.00 0.00 0.00 2.32
2703 8957 6.494666 TTCCCAGGTATATCGAAACTCAAT 57.505 37.500 0.00 0.00 0.00 2.57
2704 8958 5.943349 TTCCCAGGTATATCGAAACTCAA 57.057 39.130 0.00 0.00 0.00 3.02
2705 8959 5.839063 AGATTCCCAGGTATATCGAAACTCA 59.161 40.000 0.00 0.00 0.00 3.41
2706 8960 6.159988 CAGATTCCCAGGTATATCGAAACTC 58.840 44.000 0.00 0.00 0.00 3.01
2708 8962 5.238583 CCAGATTCCCAGGTATATCGAAAC 58.761 45.833 0.00 0.00 0.00 2.78
2709 8963 4.286032 CCCAGATTCCCAGGTATATCGAAA 59.714 45.833 0.00 0.00 0.00 3.46
2711 8965 3.181410 ACCCAGATTCCCAGGTATATCGA 60.181 47.826 0.00 0.00 0.00 3.59
2712 8966 3.173965 ACCCAGATTCCCAGGTATATCG 58.826 50.000 0.00 0.00 0.00 2.92
2713 8967 4.470304 GGTACCCAGATTCCCAGGTATATC 59.530 50.000 0.00 0.00 37.22 1.63
2714 8968 4.436079 GGTACCCAGATTCCCAGGTATAT 58.564 47.826 0.00 0.00 37.22 0.86
2715 8969 3.865571 GGTACCCAGATTCCCAGGTATA 58.134 50.000 0.00 0.00 37.22 1.47
2716 8970 2.702748 GGTACCCAGATTCCCAGGTAT 58.297 52.381 0.00 0.00 37.22 2.73
2717 8971 2.185663 GGTACCCAGATTCCCAGGTA 57.814 55.000 0.00 0.00 33.70 3.08
2732 8986 3.482436 TGTCACATGGTTTTCTGGGTAC 58.518 45.455 0.00 0.00 0.00 3.34
2733 8987 3.866703 TGTCACATGGTTTTCTGGGTA 57.133 42.857 0.00 0.00 0.00 3.69
2734 8988 2.746279 TGTCACATGGTTTTCTGGGT 57.254 45.000 0.00 0.00 0.00 4.51
2735 8989 2.288395 GCTTGTCACATGGTTTTCTGGG 60.288 50.000 0.00 0.00 0.00 4.45
2736 8990 2.361757 TGCTTGTCACATGGTTTTCTGG 59.638 45.455 0.00 0.00 0.00 3.86
2737 8991 3.374745 GTGCTTGTCACATGGTTTTCTG 58.625 45.455 0.00 0.00 44.98 3.02
2738 8992 3.715628 GTGCTTGTCACATGGTTTTCT 57.284 42.857 0.00 0.00 44.98 2.52
2748 9002 1.334059 CGTTCCATGTGTGCTTGTCAC 60.334 52.381 0.00 0.00 45.82 3.67
2749 9003 0.943673 CGTTCCATGTGTGCTTGTCA 59.056 50.000 0.00 0.00 0.00 3.58
2750 9004 0.238289 CCGTTCCATGTGTGCTTGTC 59.762 55.000 0.00 0.00 0.00 3.18
2751 9005 0.465460 ACCGTTCCATGTGTGCTTGT 60.465 50.000 0.00 0.00 0.00 3.16
2752 9006 0.040157 CACCGTTCCATGTGTGCTTG 60.040 55.000 0.00 0.00 0.00 4.01
2753 9007 1.172180 CCACCGTTCCATGTGTGCTT 61.172 55.000 0.00 0.00 0.00 3.91
2754 9008 1.600636 CCACCGTTCCATGTGTGCT 60.601 57.895 0.00 0.00 0.00 4.40
2755 9009 2.953821 CCACCGTTCCATGTGTGC 59.046 61.111 0.00 0.00 0.00 4.57
2756 9010 1.451337 TTGCCACCGTTCCATGTGTG 61.451 55.000 0.00 0.00 0.00 3.82
2757 9011 1.152860 TTGCCACCGTTCCATGTGT 60.153 52.632 0.00 0.00 0.00 3.72
2758 9012 1.285641 GTTGCCACCGTTCCATGTG 59.714 57.895 0.00 0.00 0.00 3.21
2759 9013 0.539438 ATGTTGCCACCGTTCCATGT 60.539 50.000 0.00 0.00 0.00 3.21
2760 9014 0.171007 GATGTTGCCACCGTTCCATG 59.829 55.000 0.00 0.00 0.00 3.66
2761 9015 0.965363 GGATGTTGCCACCGTTCCAT 60.965 55.000 0.00 0.00 0.00 3.41
2762 9016 1.602323 GGATGTTGCCACCGTTCCA 60.602 57.895 0.00 0.00 0.00 3.53
2763 9017 0.965363 ATGGATGTTGCCACCGTTCC 60.965 55.000 0.00 0.00 41.56 3.62
2764 9018 0.451783 GATGGATGTTGCCACCGTTC 59.548 55.000 0.00 0.00 41.56 3.95
2765 9019 0.251121 TGATGGATGTTGCCACCGTT 60.251 50.000 0.00 0.00 41.56 4.44
2766 9020 0.677731 CTGATGGATGTTGCCACCGT 60.678 55.000 0.00 0.00 41.56 4.83
2767 9021 1.378882 CCTGATGGATGTTGCCACCG 61.379 60.000 0.00 0.00 41.56 4.94
2768 9022 1.669999 GCCTGATGGATGTTGCCACC 61.670 60.000 0.00 0.00 41.56 4.61
2769 9023 0.682209 AGCCTGATGGATGTTGCCAC 60.682 55.000 0.00 0.00 41.56 5.01
2770 9024 0.040058 AAGCCTGATGGATGTTGCCA 59.960 50.000 0.00 0.00 43.23 4.92
2771 9025 0.743097 GAAGCCTGATGGATGTTGCC 59.257 55.000 0.00 0.00 34.57 4.52
2772 9026 1.466856 TGAAGCCTGATGGATGTTGC 58.533 50.000 0.00 0.00 34.57 4.17
2773 9027 3.284617 TGATGAAGCCTGATGGATGTTG 58.715 45.455 0.00 0.00 34.57 3.33
2774 9028 3.657398 TGATGAAGCCTGATGGATGTT 57.343 42.857 0.00 0.00 34.57 2.71
2775 9029 3.552875 CTTGATGAAGCCTGATGGATGT 58.447 45.455 0.00 0.00 34.57 3.06
2776 9030 2.885266 CCTTGATGAAGCCTGATGGATG 59.115 50.000 0.00 0.00 34.57 3.51
2777 9031 2.781757 TCCTTGATGAAGCCTGATGGAT 59.218 45.455 0.00 0.00 34.57 3.41
2778 9032 2.199208 TCCTTGATGAAGCCTGATGGA 58.801 47.619 0.00 0.00 34.57 3.41
2779 9033 2.723322 TCCTTGATGAAGCCTGATGG 57.277 50.000 0.00 0.00 0.00 3.51
2780 9034 4.202121 CCATTTCCTTGATGAAGCCTGATG 60.202 45.833 0.00 0.00 0.00 3.07
2781 9035 3.958798 CCATTTCCTTGATGAAGCCTGAT 59.041 43.478 0.00 0.00 0.00 2.90
2782 9036 3.359033 CCATTTCCTTGATGAAGCCTGA 58.641 45.455 0.00 0.00 0.00 3.86
2783 9037 2.429610 CCCATTTCCTTGATGAAGCCTG 59.570 50.000 0.00 0.00 0.00 4.85
2784 9038 2.743553 CCCATTTCCTTGATGAAGCCT 58.256 47.619 0.00 0.00 0.00 4.58
2785 9039 1.137675 GCCCATTTCCTTGATGAAGCC 59.862 52.381 0.00 0.00 0.00 4.35
2786 9040 1.137675 GGCCCATTTCCTTGATGAAGC 59.862 52.381 0.00 0.00 0.00 3.86
2787 9041 2.429610 CTGGCCCATTTCCTTGATGAAG 59.570 50.000 0.00 0.00 0.00 3.02
2788 9042 2.042842 TCTGGCCCATTTCCTTGATGAA 59.957 45.455 0.00 0.00 0.00 2.57
2789 9043 1.640149 TCTGGCCCATTTCCTTGATGA 59.360 47.619 0.00 0.00 0.00 2.92
2790 9044 2.148446 TCTGGCCCATTTCCTTGATG 57.852 50.000 0.00 0.00 0.00 3.07
2791 9045 3.181425 CCTATCTGGCCCATTTCCTTGAT 60.181 47.826 0.00 0.00 0.00 2.57
2792 9046 2.175499 CCTATCTGGCCCATTTCCTTGA 59.825 50.000 0.00 0.00 0.00 3.02
2793 9047 2.590821 CCTATCTGGCCCATTTCCTTG 58.409 52.381 0.00 0.00 0.00 3.61
2794 9048 1.500736 CCCTATCTGGCCCATTTCCTT 59.499 52.381 0.00 0.00 0.00 3.36
2795 9049 1.152649 CCCTATCTGGCCCATTTCCT 58.847 55.000 0.00 0.00 0.00 3.36
2796 9050 0.540597 GCCCTATCTGGCCCATTTCC 60.541 60.000 0.00 0.00 46.11 3.13
2797 9051 3.042481 GCCCTATCTGGCCCATTTC 57.958 57.895 0.00 0.00 46.11 2.17
2805 9059 0.036448 CCTGATGCTGCCCTATCTGG 59.964 60.000 9.05 9.05 36.50 3.86
2806 9060 0.763652 ACCTGATGCTGCCCTATCTG 59.236 55.000 0.00 0.00 0.00 2.90
2807 9061 1.419387 GAACCTGATGCTGCCCTATCT 59.581 52.381 0.00 0.00 0.00 1.98
2808 9062 1.141657 TGAACCTGATGCTGCCCTATC 59.858 52.381 0.00 0.00 0.00 2.08
2809 9063 1.133976 GTGAACCTGATGCTGCCCTAT 60.134 52.381 0.00 0.00 0.00 2.57
2810 9064 0.253044 GTGAACCTGATGCTGCCCTA 59.747 55.000 0.00 0.00 0.00 3.53
2811 9065 1.001641 GTGAACCTGATGCTGCCCT 60.002 57.895 0.00 0.00 0.00 5.19
2812 9066 1.303561 TGTGAACCTGATGCTGCCC 60.304 57.895 0.00 0.00 0.00 5.36
2831 9085 3.309954 GGGAAACGAGATGATTGCAGTAC 59.690 47.826 0.00 0.00 0.00 2.73
2832 9086 3.055458 TGGGAAACGAGATGATTGCAGTA 60.055 43.478 0.00 0.00 0.00 2.74
2833 9087 2.290260 TGGGAAACGAGATGATTGCAGT 60.290 45.455 0.00 0.00 0.00 4.40
2834 9088 2.096496 GTGGGAAACGAGATGATTGCAG 59.904 50.000 0.00 0.00 0.00 4.41
2836 9090 1.401905 GGTGGGAAACGAGATGATTGC 59.598 52.381 0.00 0.00 0.00 3.56
3523 9811 9.416794 GATATTAGGAATAGAGATGTGTGTGTG 57.583 37.037 0.00 0.00 0.00 3.82
3524 9812 9.373450 AGATATTAGGAATAGAGATGTGTGTGT 57.627 33.333 0.00 0.00 0.00 3.72
3526 9814 9.593565 TCAGATATTAGGAATAGAGATGTGTGT 57.406 33.333 0.00 0.00 0.00 3.72
3533 9821 9.083422 CACCAACTCAGATATTAGGAATAGAGA 57.917 37.037 0.00 0.00 0.00 3.10
3534 9822 9.083422 TCACCAACTCAGATATTAGGAATAGAG 57.917 37.037 0.00 0.00 0.00 2.43
3535 9823 9.434275 TTCACCAACTCAGATATTAGGAATAGA 57.566 33.333 0.00 0.00 0.00 1.98
3546 9834 9.476202 CGTGAATATTATTCACCAACTCAGATA 57.524 33.333 30.24 3.13 44.29 1.98
3547 9835 8.370493 CGTGAATATTATTCACCAACTCAGAT 57.630 34.615 30.24 0.00 44.29 2.90
3548 9836 7.770801 CGTGAATATTATTCACCAACTCAGA 57.229 36.000 30.24 3.70 44.29 3.27


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

AutoCloner maintained by Alex Coulton.