Multiple sequence alignment - TraesCS7B01G306800

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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 TraesCS7B01G306800 chr7B 100.000 2806 0 0 1 2806 550030709 550033514 0.000000e+00 5182.0
1 TraesCS7B01G306800 chr7A 91.198 1386 69 25 633 2001 592046998 592048347 0.000000e+00 1834.0
2 TraesCS7B01G306800 chr7A 91.564 569 21 6 1 564 592046270 592046816 0.000000e+00 760.0
3 TraesCS7B01G306800 chr7A 84.615 702 75 14 2071 2760 133044783 133044103 0.000000e+00 667.0
4 TraesCS7B01G306800 chr7A 89.441 161 17 0 2071 2231 133003285 133003445 1.320000e-48 204.0
5 TraesCS7B01G306800 chr7A 95.238 63 3 0 559 621 592046865 592046927 1.780000e-17 100.0
6 TraesCS7B01G306800 chr7D 92.256 1201 63 18 813 2001 517219859 517221041 0.000000e+00 1676.0
7 TraesCS7B01G306800 chr7D 93.357 572 21 8 1 564 517218974 517219536 0.000000e+00 830.0
8 TraesCS7B01G306800 chr7D 86.613 747 82 11 2017 2760 517221620 517222351 0.000000e+00 809.0
9 TraesCS7B01G306800 chr7D 85.385 520 44 11 2251 2760 134100169 134099672 6.930000e-141 510.0
10 TraesCS7B01G306800 chr7D 74.760 729 113 37 2071 2762 501814645 501813951 7.710000e-66 261.0
11 TraesCS7B01G306800 chr7D 78.035 346 46 19 2441 2760 638400066 638399725 1.030000e-44 191.0
12 TraesCS7B01G306800 chr7D 86.842 152 18 1 2071 2222 137910949 137910800 4.810000e-38 169.0
13 TraesCS7B01G306800 chr7D 86.842 152 19 1 2071 2222 137915071 137914921 4.810000e-38 169.0
14 TraesCS7B01G306800 chr7D 92.063 63 5 0 559 621 517219587 517219649 3.850000e-14 89.8
15 TraesCS7B01G306800 chr7D 95.918 49 2 0 2758 2806 134012260 134012212 2.320000e-11 80.5
16 TraesCS7B01G306800 chr4D 82.386 704 85 26 2069 2760 349137247 349137923 6.740000e-161 577.0
17 TraesCS7B01G306800 chr4D 77.681 345 52 14 2438 2760 51622683 51623024 1.330000e-43 187.0
18 TraesCS7B01G306800 chr3B 80.734 436 62 9 1 417 172958771 172958339 1.250000e-83 320.0
19 TraesCS7B01G306800 chr3B 74.965 715 126 31 2072 2760 738507213 738507900 2.130000e-71 279.0
20 TraesCS7B01G306800 chr1B 77.431 576 88 20 2070 2642 547599483 547600019 3.510000e-79 305.0
21 TraesCS7B01G306800 chr1B 75.872 344 55 19 2442 2760 542590662 542590322 1.740000e-32 150.0
22 TraesCS7B01G306800 chr1D 78.947 342 47 13 2441 2760 21632834 21632496 2.830000e-50 209.0
23 TraesCS7B01G306800 chr3A 82.902 193 32 1 2068 2260 688012141 688012332 3.720000e-39 172.0
24 TraesCS7B01G306800 chr3A 78.531 177 31 2 2070 2246 93331368 93331199 2.960000e-20 110.0
25 TraesCS7B01G306800 chr3A 77.401 177 33 2 2070 2246 93331935 93331766 6.400000e-17 99.0
26 TraesCS7B01G306800 chr2A 84.967 153 22 1 2071 2222 1683958 1684110 1.350000e-33 154.0
27 TraesCS7B01G306800 chr6B 86.014 143 18 2 2071 2212 52000608 52000749 4.840000e-33 152.0
28 TraesCS7B01G306800 chr1A 82.514 183 20 8 2589 2760 520397423 520397242 1.740000e-32 150.0
29 TraesCS7B01G306800 chr2D 79.769 173 34 1 2071 2243 584731258 584731087 1.060000e-24 124.0
30 TraesCS7B01G306800 chr5D 75.172 290 42 16 2497 2760 494285665 494285950 2.960000e-20 110.0


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 TraesCS7B01G306800 chr7B 550030709 550033514 2805 False 5182.0 5182 100.000000 1 2806 1 chr7B.!!$F1 2805
1 TraesCS7B01G306800 chr7A 592046270 592048347 2077 False 898.0 1834 92.666667 1 2001 3 chr7A.!!$F2 2000
2 TraesCS7B01G306800 chr7A 133044103 133044783 680 True 667.0 667 84.615000 2071 2760 1 chr7A.!!$R1 689
3 TraesCS7B01G306800 chr7D 517218974 517222351 3377 False 851.2 1676 91.072250 1 2760 4 chr7D.!!$F1 2759
4 TraesCS7B01G306800 chr7D 501813951 501814645 694 True 261.0 261 74.760000 2071 2762 1 chr7D.!!$R3 691
5 TraesCS7B01G306800 chr4D 349137247 349137923 676 False 577.0 577 82.386000 2069 2760 1 chr4D.!!$F2 691
6 TraesCS7B01G306800 chr3B 738507213 738507900 687 False 279.0 279 74.965000 2072 2760 1 chr3B.!!$F1 688
7 TraesCS7B01G306800 chr1B 547599483 547600019 536 False 305.0 305 77.431000 2070 2642 1 chr1B.!!$F1 572

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
779 912 0.250793 TGGAATTAAGCCGAAGCCGA 59.749 50.0 0.0 0.0 41.25 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2998 0.246635 GCCAGCTTCGTCCTAGTCAA 59.753 55.0 0.0 0.0 0.0 3.18 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
141 142 4.758251 CGATGCAGTCGCCCACCA 62.758 66.667 5.77 0.00 44.33 4.17
377 378 4.522114 TGCCATTACTACTTGCATGCTTA 58.478 39.130 20.33 6.07 0.00 3.09
395 396 5.445964 TGCTTATTTAGGACAGGGGAATTC 58.554 41.667 0.00 0.00 0.00 2.17
399 400 4.519906 TTTAGGACAGGGGAATTCCATC 57.480 45.455 25.67 16.46 37.91 3.51
453 459 2.416747 CAGTGCACTCAGAAATTCCGA 58.583 47.619 18.64 0.00 0.00 4.55
540 546 3.685139 TGATGACTGAAGAGGGTGTTC 57.315 47.619 0.00 0.00 0.00 3.18
598 663 7.287696 ACTTTTCCTTTGTATGAAGAACACCAT 59.712 33.333 0.00 0.00 0.00 3.55
614 679 1.153168 CATTAGACCACCCGGCCAG 60.153 63.158 2.24 0.00 34.57 4.85
660 792 7.827729 AGTCTTGTTCTGGTTGTAACTTTACTT 59.172 33.333 1.04 0.00 34.77 2.24
690 822 3.494626 TCAGTTTCGATGTGTTCTTGCTC 59.505 43.478 0.00 0.00 0.00 4.26
720 852 8.840833 TGTAAAATGCACTGTTAAGAGTATCA 57.159 30.769 4.74 7.09 37.82 2.15
721 853 8.935844 TGTAAAATGCACTGTTAAGAGTATCAG 58.064 33.333 4.74 0.00 37.82 2.90
774 907 1.353022 AGGTGGTGGAATTAAGCCGAA 59.647 47.619 0.00 0.00 0.00 4.30
775 908 1.743394 GGTGGTGGAATTAAGCCGAAG 59.257 52.381 0.00 0.00 0.00 3.79
776 909 1.132453 GTGGTGGAATTAAGCCGAAGC 59.868 52.381 0.00 0.00 40.32 3.86
777 910 0.738975 GGTGGAATTAAGCCGAAGCC 59.261 55.000 0.00 0.00 41.25 4.35
778 911 0.377203 GTGGAATTAAGCCGAAGCCG 59.623 55.000 0.00 0.00 41.25 5.52
779 912 0.250793 TGGAATTAAGCCGAAGCCGA 59.749 50.000 0.00 0.00 41.25 5.54
780 913 0.938008 GGAATTAAGCCGAAGCCGAG 59.062 55.000 0.00 0.00 41.25 4.63
781 914 0.938008 GAATTAAGCCGAAGCCGAGG 59.062 55.000 0.00 0.00 41.25 4.63
782 915 0.252197 AATTAAGCCGAAGCCGAGGT 59.748 50.000 0.00 0.00 41.25 3.85
783 916 0.462047 ATTAAGCCGAAGCCGAGGTG 60.462 55.000 0.00 0.00 41.25 4.00
784 917 1.823169 TTAAGCCGAAGCCGAGGTGT 61.823 55.000 0.00 0.00 41.25 4.16
785 918 2.501223 TAAGCCGAAGCCGAGGTGTG 62.501 60.000 0.00 0.00 41.25 3.82
786 919 4.373116 GCCGAAGCCGAGGTGTGA 62.373 66.667 0.00 0.00 38.22 3.58
787 920 2.432628 CCGAAGCCGAGGTGTGAC 60.433 66.667 0.00 0.00 38.22 3.67
788 921 2.651361 CGAAGCCGAGGTGTGACT 59.349 61.111 0.00 0.00 38.22 3.41
789 922 1.006102 CGAAGCCGAGGTGTGACTT 60.006 57.895 0.00 0.00 38.22 3.01
790 923 0.600255 CGAAGCCGAGGTGTGACTTT 60.600 55.000 0.00 0.00 38.22 2.66
791 924 1.594331 GAAGCCGAGGTGTGACTTTT 58.406 50.000 0.00 0.00 0.00 2.27
799 932 3.430218 CGAGGTGTGACTTTTCTTGCTAG 59.570 47.826 0.00 0.00 0.00 3.42
802 935 3.184581 GGTGTGACTTTTCTTGCTAGACG 59.815 47.826 0.00 0.00 0.00 4.18
807 940 3.654414 ACTTTTCTTGCTAGACGGTGAG 58.346 45.455 0.00 0.00 0.00 3.51
818 951 2.357517 CGGTGAGACTGTGTGCCC 60.358 66.667 0.00 0.00 0.00 5.36
826 959 4.007644 CTGTGTGCCCTGCCGAGA 62.008 66.667 0.00 0.00 0.00 4.04
828 961 4.008933 GTGTGCCCTGCCGAGAGT 62.009 66.667 0.00 0.00 0.00 3.24
845 985 7.933577 TGCCGAGAGTAATGAATGAAATATCTT 59.066 33.333 0.00 0.00 0.00 2.40
994 1142 0.537188 CTCACCGACTACCAGCCATT 59.463 55.000 0.00 0.00 0.00 3.16
1086 1234 1.391157 ATGCTCAGTCGCCTCTCTCC 61.391 60.000 0.00 0.00 0.00 3.71
1108 1256 2.047465 CTGCTCTCGCTTGCCAGT 60.047 61.111 0.00 0.00 36.97 4.00
1130 1281 3.831333 TGCAGATTCCTGGCACAAAAATA 59.169 39.130 0.00 0.00 40.72 1.40
1172 1323 4.557276 ATTGAAGTAGCGTCGTAAAACG 57.443 40.909 0.00 0.00 45.31 3.60
1209 1360 0.260523 AGCTCCCTCTCCCTGACTAC 59.739 60.000 0.00 0.00 0.00 2.73
1216 1367 2.183679 CTCTCCCTGACTACCTTTGCT 58.816 52.381 0.00 0.00 0.00 3.91
1238 1390 2.360350 CTCCGTGCAGGCAATGGT 60.360 61.111 12.00 0.00 40.77 3.55
1325 1477 6.260936 TCTTCCATTATTCTCTTCGGCAATTC 59.739 38.462 0.00 0.00 0.00 2.17
1364 1517 0.863144 TCTTGCACGCCGTCTTAAAC 59.137 50.000 0.00 0.00 0.00 2.01
1424 1578 3.546271 GGCGTTTTATCAAATTTCCGCTC 59.454 43.478 0.00 0.00 39.77 5.03
1481 1635 0.747283 CATGAGGCTCAAGTCCCTGC 60.747 60.000 22.84 0.00 0.00 4.85
1486 1640 2.811317 CTCAAGTCCCTGCGCGTC 60.811 66.667 8.43 0.00 0.00 5.19
1678 1833 1.880601 GAAGCGTGAGTGCGTGACTG 61.881 60.000 0.00 0.00 40.67 3.51
1790 1945 4.141620 ACCGCATTTATCATCTTCCAGTCT 60.142 41.667 0.00 0.00 0.00 3.24
1833 1988 2.187707 CTCCATGTTAATTTGCGCTGC 58.812 47.619 9.73 0.00 0.00 5.25
1934 2094 2.862140 GCGGGCATGGCATATTTTGTAC 60.862 50.000 22.06 0.00 0.00 2.90
1937 2097 4.458989 CGGGCATGGCATATTTTGTACTAT 59.541 41.667 22.06 0.00 0.00 2.12
1938 2098 5.048083 CGGGCATGGCATATTTTGTACTATT 60.048 40.000 22.06 0.00 0.00 1.73
1940 2100 7.538575 GGGCATGGCATATTTTGTACTATTAG 58.461 38.462 22.06 0.00 0.00 1.73
1942 2102 7.309133 GGCATGGCATATTTTGTACTATTAGCA 60.309 37.037 15.47 0.00 0.00 3.49
1943 2103 8.246180 GCATGGCATATTTTGTACTATTAGCAT 58.754 33.333 0.00 0.00 0.00 3.79
1944 2104 9.563898 CATGGCATATTTTGTACTATTAGCATG 57.436 33.333 0.00 0.00 0.00 4.06
1945 2105 8.690203 TGGCATATTTTGTACTATTAGCATGT 57.310 30.769 0.00 0.00 0.00 3.21
1946 2106 9.785982 TGGCATATTTTGTACTATTAGCATGTA 57.214 29.630 0.00 0.00 0.00 2.29
2005 2165 9.527157 TGACCAATCTAAATTGTTGATTCCTTA 57.473 29.630 0.00 0.00 40.63 2.69
2008 2168 9.252962 CCAATCTAAATTGTTGATTCCTTATGC 57.747 33.333 0.00 0.00 40.63 3.14
2012 2172 8.840321 TCTAAATTGTTGATTCCTTATGCTAGC 58.160 33.333 8.10 8.10 0.00 3.42
2013 2173 6.396829 AATTGTTGATTCCTTATGCTAGCC 57.603 37.500 13.29 0.00 0.00 3.93
2015 2175 4.199310 TGTTGATTCCTTATGCTAGCCAC 58.801 43.478 13.29 0.00 0.00 5.01
2024 2747 6.552932 TCCTTATGCTAGCCACTCTTCTATA 58.447 40.000 13.29 0.00 0.00 1.31
2025 2748 6.434652 TCCTTATGCTAGCCACTCTTCTATAC 59.565 42.308 13.29 0.00 0.00 1.47
2026 2749 6.209589 CCTTATGCTAGCCACTCTTCTATACA 59.790 42.308 13.29 0.00 0.00 2.29
2034 2757 5.248477 AGCCACTCTTCTATACAGTTTGGAA 59.752 40.000 0.00 0.00 0.00 3.53
2035 2758 5.351740 GCCACTCTTCTATACAGTTTGGAAC 59.648 44.000 0.00 0.00 0.00 3.62
2157 2881 6.930667 TTTTTACAAGTCAGTACCAACTCC 57.069 37.500 0.00 0.00 31.97 3.85
2175 2899 1.075374 TCCCAGCCTAAGTGTTGCAAT 59.925 47.619 0.59 0.00 0.00 3.56
2176 2900 1.203052 CCCAGCCTAAGTGTTGCAATG 59.797 52.381 0.59 0.00 0.00 2.82
2177 2901 1.888512 CCAGCCTAAGTGTTGCAATGT 59.111 47.619 0.59 0.00 0.00 2.71
2183 2907 3.569701 CCTAAGTGTTGCAATGTGGTCTT 59.430 43.478 0.59 4.50 0.00 3.01
2208 2932 5.032220 CAGTCGTATAAGCACGTATTGACA 58.968 41.667 0.00 0.00 42.51 3.58
2213 2937 5.287752 CGTATAAGCACGTATTGACAGTGTT 59.712 40.000 0.00 0.00 38.10 3.32
2290 3014 0.526662 CCGTTGACTAGGACGAAGCT 59.473 55.000 14.55 0.00 41.53 3.74
2310 3037 0.603975 GGCTCAGTCGTTCTTGGCTT 60.604 55.000 0.00 0.00 0.00 4.35
2359 3100 2.650322 CTAGCTCTCGTTTCCCTCTCT 58.350 52.381 0.00 0.00 0.00 3.10
2364 3105 2.682856 CTCTCGTTTCCCTCTCTCTCTG 59.317 54.545 0.00 0.00 0.00 3.35
2371 3112 1.077068 CCTCTCTCTCTGCCCTCGT 60.077 63.158 0.00 0.00 0.00 4.18
2398 3139 3.916544 CTCTGGCTATGGCGGCGA 61.917 66.667 12.98 0.00 39.81 5.54
2424 3173 4.250305 GGCAGTGGTGACGGTGGT 62.250 66.667 0.00 0.00 0.00 4.16
2425 3174 2.203153 GCAGTGGTGACGGTGGTT 60.203 61.111 0.00 0.00 0.00 3.67
2426 3175 2.542907 GCAGTGGTGACGGTGGTTG 61.543 63.158 0.00 0.00 0.00 3.77
2427 3176 1.153249 CAGTGGTGACGGTGGTTGT 60.153 57.895 0.00 0.00 0.00 3.32
2428 3177 0.105224 CAGTGGTGACGGTGGTTGTA 59.895 55.000 0.00 0.00 0.00 2.41
2429 3178 0.105408 AGTGGTGACGGTGGTTGTAC 59.895 55.000 0.00 0.00 0.00 2.90
2430 3179 0.881600 GTGGTGACGGTGGTTGTACC 60.882 60.000 0.00 0.00 39.22 3.34
2466 3216 1.226603 CGGCTACGAAGACCTTCCG 60.227 63.158 4.36 0.00 44.60 4.30
2470 3220 1.601419 CTACGAAGACCTTCCGGGCA 61.601 60.000 0.00 0.00 42.67 5.36
2525 3278 2.870411 GCGGCTCCAATTCGTATTACTT 59.130 45.455 0.00 0.00 0.00 2.24
2553 3309 3.290710 CGATGAGGGTTTGGATTTGGAT 58.709 45.455 0.00 0.00 0.00 3.41
2562 3321 1.453745 GGATTTGGATGAGGCGCCA 60.454 57.895 31.54 9.64 0.00 5.69
2577 3336 1.303561 GCCACTGTCCATGGAGCAA 60.304 57.895 16.81 2.86 39.87 3.91
2585 3344 2.040544 CCATGGAGCAACGGGTGAC 61.041 63.158 5.56 0.00 0.00 3.67
2622 3381 0.178885 TGGCCAACCCTACCACTAGT 60.179 55.000 0.61 0.00 33.59 2.57
2627 3386 2.434702 CCAACCCTACCACTAGTCATCC 59.565 54.545 0.00 0.00 0.00 3.51
2630 3389 3.136896 ACCCTACCACTAGTCATCCCTA 58.863 50.000 0.00 0.00 0.00 3.53
2634 3393 2.933573 ACCACTAGTCATCCCTAGACG 58.066 52.381 0.00 0.00 40.84 4.18
2649 3420 3.695060 CCTAGACGAGTGGAGTGTTGTAT 59.305 47.826 0.00 0.00 0.00 2.29
2692 3467 1.485124 CCTAGTTCAAATTGGGGGCC 58.515 55.000 0.00 0.00 0.00 5.80
2703 3478 0.477993 TTGGGGGCCAGGGTTAGTTA 60.478 55.000 4.39 0.00 33.81 2.24
2756 3533 6.422333 TGTAGTTTGGATGATGCTATTTGGA 58.578 36.000 0.00 0.00 0.00 3.53
2757 3534 7.062322 TGTAGTTTGGATGATGCTATTTGGAT 58.938 34.615 0.00 0.00 0.00 3.41
2758 3535 6.401047 AGTTTGGATGATGCTATTTGGATG 57.599 37.500 0.00 0.00 0.00 3.51
2759 3536 5.895534 AGTTTGGATGATGCTATTTGGATGT 59.104 36.000 0.00 0.00 0.00 3.06
2761 3538 4.067192 TGGATGATGCTATTTGGATGTCG 58.933 43.478 0.00 0.00 0.00 4.35
2762 3539 4.202346 TGGATGATGCTATTTGGATGTCGA 60.202 41.667 0.00 0.00 0.00 4.20
2764 3541 3.732212 TGATGCTATTTGGATGTCGAGG 58.268 45.455 0.00 0.00 0.00 4.63
2765 3542 2.620251 TGCTATTTGGATGTCGAGGG 57.380 50.000 0.00 0.00 0.00 4.30
2766 3543 2.115427 TGCTATTTGGATGTCGAGGGA 58.885 47.619 0.00 0.00 0.00 4.20
2767 3544 2.503765 TGCTATTTGGATGTCGAGGGAA 59.496 45.455 0.00 0.00 0.00 3.97
2768 3545 2.872858 GCTATTTGGATGTCGAGGGAAC 59.127 50.000 0.00 0.00 0.00 3.62
2786 3563 5.175388 GGAACCCTAATCACCAAAGTAGT 57.825 43.478 0.00 0.00 0.00 2.73
2787 3564 5.567430 GGAACCCTAATCACCAAAGTAGTT 58.433 41.667 0.00 0.00 0.00 2.24
2788 3565 5.414765 GGAACCCTAATCACCAAAGTAGTTG 59.585 44.000 0.00 0.00 36.94 3.16
2798 3575 1.967779 CAAAGTAGTTGGGTTTGGGGG 59.032 52.381 0.00 0.00 33.18 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 3.560251 AAGCAGTGGTGGGCGACT 61.560 61.111 0.00 0.00 33.87 4.18
141 142 3.289834 CCCGCAGTTGCAAGCAGT 61.290 61.111 0.00 0.00 42.21 4.40
377 378 4.482025 TGATGGAATTCCCCTGTCCTAAAT 59.518 41.667 21.90 4.22 34.29 1.40
395 396 0.104855 TCCTCGCGGAAATCTGATGG 59.895 55.000 6.13 0.00 36.03 3.51
399 400 5.639506 ACAATATAATCCTCGCGGAAATCTG 59.360 40.000 6.13 0.34 44.02 2.90
407 408 7.502339 CAAGAACTTACAATATAATCCTCGCG 58.498 38.462 0.00 0.00 0.00 5.87
453 459 4.503991 GGCAGAGAGATTAATCGAACCCAT 60.504 45.833 9.78 0.00 0.00 4.00
598 663 3.006728 CCTGGCCGGGTGGTCTAA 61.007 66.667 23.90 0.00 41.88 2.10
624 689 4.719369 ACAAGACTCCGCCGCGAC 62.719 66.667 15.93 0.00 0.00 5.19
625 690 3.909258 GAACAAGACTCCGCCGCGA 62.909 63.158 15.93 0.00 0.00 5.87
627 692 2.048127 AGAACAAGACTCCGCCGC 60.048 61.111 0.00 0.00 0.00 6.53
631 696 2.240493 ACAACCAGAACAAGACTCCG 57.760 50.000 0.00 0.00 0.00 4.63
634 758 7.336396 AGTAAAGTTACAACCAGAACAAGACT 58.664 34.615 4.14 0.00 36.12 3.24
673 805 1.800586 GCAGAGCAAGAACACATCGAA 59.199 47.619 0.00 0.00 0.00 3.71
690 822 3.648339 AACAGTGCATTTTACAGGCAG 57.352 42.857 0.00 0.00 38.38 4.85
720 852 9.247861 AGCCTTAACATGAATTCAATCTTTACT 57.752 29.630 13.09 1.89 0.00 2.24
721 853 9.860898 AAGCCTTAACATGAATTCAATCTTTAC 57.139 29.630 13.09 0.00 0.00 2.01
723 855 7.756722 CGAAGCCTTAACATGAATTCAATCTTT 59.243 33.333 13.09 5.92 0.00 2.52
774 907 0.759346 AGAAAAGTCACACCTCGGCT 59.241 50.000 0.00 0.00 0.00 5.52
775 908 1.264288 CAAGAAAAGTCACACCTCGGC 59.736 52.381 0.00 0.00 0.00 5.54
776 909 1.264288 GCAAGAAAAGTCACACCTCGG 59.736 52.381 0.00 0.00 0.00 4.63
777 910 2.213499 AGCAAGAAAAGTCACACCTCG 58.787 47.619 0.00 0.00 0.00 4.63
778 911 4.449405 GTCTAGCAAGAAAAGTCACACCTC 59.551 45.833 0.00 0.00 32.16 3.85
779 912 4.381411 GTCTAGCAAGAAAAGTCACACCT 58.619 43.478 0.00 0.00 32.16 4.00
780 913 3.184581 CGTCTAGCAAGAAAAGTCACACC 59.815 47.826 0.00 0.00 32.16 4.16
781 914 3.184581 CCGTCTAGCAAGAAAAGTCACAC 59.815 47.826 0.00 0.00 32.16 3.82
782 915 3.181469 ACCGTCTAGCAAGAAAAGTCACA 60.181 43.478 0.00 0.00 32.16 3.58
783 916 3.184581 CACCGTCTAGCAAGAAAAGTCAC 59.815 47.826 0.00 0.00 32.16 3.67
784 917 3.069016 TCACCGTCTAGCAAGAAAAGTCA 59.931 43.478 0.00 0.00 32.16 3.41
785 918 3.650139 TCACCGTCTAGCAAGAAAAGTC 58.350 45.455 0.00 0.00 32.16 3.01
786 919 3.321111 TCTCACCGTCTAGCAAGAAAAGT 59.679 43.478 0.00 0.00 32.16 2.66
787 920 3.675698 GTCTCACCGTCTAGCAAGAAAAG 59.324 47.826 0.00 0.00 32.16 2.27
788 921 3.321111 AGTCTCACCGTCTAGCAAGAAAA 59.679 43.478 0.00 0.00 32.16 2.29
789 922 2.891580 AGTCTCACCGTCTAGCAAGAAA 59.108 45.455 0.00 0.00 32.16 2.52
790 923 2.229062 CAGTCTCACCGTCTAGCAAGAA 59.771 50.000 0.00 0.00 32.16 2.52
791 924 1.813178 CAGTCTCACCGTCTAGCAAGA 59.187 52.381 0.00 0.00 0.00 3.02
799 932 1.664965 GGCACACAGTCTCACCGTC 60.665 63.158 0.00 0.00 0.00 4.79
802 935 1.302033 CAGGGCACACAGTCTCACC 60.302 63.158 0.00 0.00 0.00 4.02
807 940 4.314440 TCGGCAGGGCACACAGTC 62.314 66.667 0.00 0.00 0.00 3.51
818 951 5.998454 ATTTCATTCATTACTCTCGGCAG 57.002 39.130 0.00 0.00 0.00 4.85
860 1000 1.900498 GTTCAAGCAGTGCCTGGCT 60.900 57.895 21.03 0.00 43.46 4.75
994 1142 0.693430 AGGAGCTGAGCCATGGATGA 60.693 55.000 18.40 0.92 0.00 2.92
1108 1256 1.702182 TTTTGTGCCAGGAATCTGCA 58.298 45.000 0.00 0.00 39.61 4.41
1130 1281 0.036765 TCCTGCACGCGGATAAAAGT 60.037 50.000 12.47 0.00 0.00 2.66
1172 1323 1.079127 TAGCTCAAGAAGGCACGGC 60.079 57.895 0.00 0.00 0.00 5.68
1209 1360 1.301677 GCACGGAGAGGAAGCAAAGG 61.302 60.000 0.00 0.00 0.00 3.11
1216 1367 1.841302 ATTGCCTGCACGGAGAGGAA 61.841 55.000 6.40 0.00 33.16 3.36
1325 1477 6.348868 GCAAGAATAAACTGAAGGGAACAGAG 60.349 42.308 0.00 0.00 38.55 3.35
1364 1517 5.237815 TGGACTAGTGAAATTGCTACACAG 58.762 41.667 0.00 0.00 37.05 3.66
1410 1564 5.585047 GGTAAGTAGTGAGCGGAAATTTGAT 59.415 40.000 0.00 0.00 0.00 2.57
1424 1578 5.979288 ACCAAGTACAGAGGTAAGTAGTG 57.021 43.478 0.00 0.00 32.92 2.74
1486 1640 4.767255 GACCCCTGCTCGCACCTG 62.767 72.222 0.00 0.00 0.00 4.00
1585 1739 2.757980 GAAGCACCCCTTTGCCGGTA 62.758 60.000 1.90 0.00 44.14 4.02
1627 1781 3.395941 ACCATCAAACAGGGAAAGAGAGT 59.604 43.478 0.00 0.00 0.00 3.24
1678 1833 0.386478 CAGAGAAGCAAAGCAACGCC 60.386 55.000 0.00 0.00 0.00 5.68
1790 1945 3.653344 GATTGATCAATCCGACGATCCA 58.347 45.455 30.35 0.00 40.90 3.41
1851 2006 8.200792 AGCAAGAAAGACAACTCGAGATATATT 58.799 33.333 21.68 0.00 0.00 1.28
1852 2007 7.721402 AGCAAGAAAGACAACTCGAGATATAT 58.279 34.615 21.68 0.00 0.00 0.86
1853 2008 7.101652 AGCAAGAAAGACAACTCGAGATATA 57.898 36.000 21.68 0.00 0.00 0.86
1940 2100 9.837525 AGTAATACTTAATACGCTACTACATGC 57.162 33.333 0.00 0.00 0.00 4.06
2001 2161 5.736951 ATAGAAGAGTGGCTAGCATAAGG 57.263 43.478 18.24 0.00 0.00 2.69
2002 2162 7.040062 ACTGTATAGAAGAGTGGCTAGCATAAG 60.040 40.741 18.24 5.62 28.68 1.73
2005 2165 5.144100 ACTGTATAGAAGAGTGGCTAGCAT 58.856 41.667 18.24 0.89 28.68 3.79
2007 2167 5.523438 AACTGTATAGAAGAGTGGCTAGC 57.477 43.478 6.04 6.04 30.71 3.42
2008 2168 6.096987 TCCAAACTGTATAGAAGAGTGGCTAG 59.903 42.308 0.00 0.00 30.71 3.42
2011 2171 5.086104 TCCAAACTGTATAGAAGAGTGGC 57.914 43.478 0.00 0.00 30.71 5.01
2012 2172 6.702329 AGTTCCAAACTGTATAGAAGAGTGG 58.298 40.000 0.00 0.00 41.01 4.00
2026 2749 7.112779 CCTATCAGGTTTATCAGTTCCAAACT 58.887 38.462 0.00 0.00 44.06 2.66
2034 2757 2.368875 CCGGCCTATCAGGTTTATCAGT 59.631 50.000 0.00 0.00 37.80 3.41
2035 2758 2.289694 CCCGGCCTATCAGGTTTATCAG 60.290 54.545 0.00 0.00 37.80 2.90
2045 2768 1.546589 AAACACGTCCCGGCCTATCA 61.547 55.000 0.00 0.00 0.00 2.15
2048 2771 2.208619 TGAAACACGTCCCGGCCTA 61.209 57.895 0.00 0.00 0.00 3.93
2067 2790 5.066505 GGTAGTTCCATGCAATTAACTCCTG 59.933 44.000 12.52 0.00 33.41 3.86
2157 2881 1.888512 ACATTGCAACACTTAGGCTGG 59.111 47.619 0.00 0.00 0.00 4.85
2175 2899 4.460034 TGCTTATACGACTGTAAGACCACA 59.540 41.667 0.00 0.00 37.43 4.17
2176 2900 4.797349 GTGCTTATACGACTGTAAGACCAC 59.203 45.833 0.00 0.00 37.43 4.16
2177 2901 4.437794 CGTGCTTATACGACTGTAAGACCA 60.438 45.833 0.00 0.00 46.46 4.02
2183 2907 6.183360 TGTCAATACGTGCTTATACGACTGTA 60.183 38.462 0.00 0.00 46.46 2.74
2208 2932 1.006102 CCGCTCGGTCAGAAACACT 60.006 57.895 0.00 0.00 0.00 3.55
2274 2998 0.246635 GCCAGCTTCGTCCTAGTCAA 59.753 55.000 0.00 0.00 0.00 3.18
2290 3014 1.301716 GCCAAGAACGACTGAGCCA 60.302 57.895 0.00 0.00 0.00 4.75
2310 3037 1.227615 GTTGGAACCGGTTCGACCA 60.228 57.895 34.70 27.19 38.47 4.02
2388 3129 3.896133 GGAGTCGTCGCCGCCATA 61.896 66.667 0.00 0.00 0.00 2.74
2430 3179 2.747460 CCCACACCACCATCGCTG 60.747 66.667 0.00 0.00 0.00 5.18
2431 3180 4.722700 GCCCACACCACCATCGCT 62.723 66.667 0.00 0.00 0.00 4.93
2513 3266 4.282950 TCGTCGCTCAAGTAATACGAAT 57.717 40.909 0.00 0.00 36.53 3.34
2525 3278 0.389817 CAAACCCTCATCGTCGCTCA 60.390 55.000 0.00 0.00 0.00 4.26
2553 3309 3.321648 ATGGACAGTGGCGCCTCA 61.322 61.111 29.70 15.63 0.00 3.86
2562 3321 1.003355 CCGTTGCTCCATGGACAGT 60.003 57.895 11.44 0.00 0.00 3.55
2577 3336 2.994995 TCTGCCATCGTCACCCGT 60.995 61.111 0.00 0.00 37.94 5.28
2585 3344 1.019673 CACCCAAATCTCTGCCATCG 58.980 55.000 0.00 0.00 0.00 3.84
2587 3346 0.685458 GCCACCCAAATCTCTGCCAT 60.685 55.000 0.00 0.00 0.00 4.40
2622 3381 1.564818 ACTCCACTCGTCTAGGGATGA 59.435 52.381 0.00 0.00 36.25 2.92
2627 3386 1.887198 ACAACACTCCACTCGTCTAGG 59.113 52.381 0.00 0.00 0.00 3.02
2630 3389 2.891580 ACATACAACACTCCACTCGTCT 59.108 45.455 0.00 0.00 0.00 4.18
2634 3393 2.567615 AGGGACATACAACACTCCACTC 59.432 50.000 0.00 0.00 0.00 3.51
2649 3420 3.181417 TGAAAGAAGAGAGGAGAGGGACA 60.181 47.826 0.00 0.00 0.00 4.02
2703 3478 9.545105 TGACAGCAAAATTGAAAAATTCAGTAT 57.455 25.926 0.00 0.00 41.38 2.12
2756 3533 2.434702 GTGATTAGGGTTCCCTCGACAT 59.565 50.000 14.24 2.96 37.64 3.06
2757 3534 1.829222 GTGATTAGGGTTCCCTCGACA 59.171 52.381 14.24 9.63 37.64 4.35
2758 3535 1.138464 GGTGATTAGGGTTCCCTCGAC 59.862 57.143 14.24 7.30 37.64 4.20
2759 3536 1.273381 TGGTGATTAGGGTTCCCTCGA 60.273 52.381 14.24 5.09 37.64 4.04
2761 3538 3.010250 ACTTTGGTGATTAGGGTTCCCTC 59.990 47.826 14.24 1.24 37.64 4.30
2762 3539 2.993863 ACTTTGGTGATTAGGGTTCCCT 59.006 45.455 15.19 15.19 40.06 4.20
2764 3541 5.175388 ACTACTTTGGTGATTAGGGTTCC 57.825 43.478 0.00 0.00 0.00 3.62
2765 3542 6.496338 CAACTACTTTGGTGATTAGGGTTC 57.504 41.667 0.00 0.00 0.00 3.62
2778 3555 1.967779 CCCCCAAACCCAACTACTTTG 59.032 52.381 0.00 0.00 34.63 2.77
2779 3556 2.391926 CCCCCAAACCCAACTACTTT 57.608 50.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.