Multiple sequence alignment - TraesCS2B01G306500

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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 TraesCS2B01G306500 chr2B 100.000 3588 0 0 1 3588 437384041 437380454 0.000000e+00 6626.0
1 TraesCS2B01G306500 chr2B 87.097 62 8 0 1208 1269 438458658 438458719 1.790000e-08 71.3
2 TraesCS2B01G306500 chr2A 89.282 2771 175 53 59 2752 498842939 498840214 0.000000e+00 3360.0
3 TraesCS2B01G306500 chr2A 88.621 747 38 21 2878 3587 498839753 498839017 0.000000e+00 865.0
4 TraesCS2B01G306500 chr2A 90.043 231 23 0 1786 2016 188903341 188903111 2.090000e-77 300.0
5 TraesCS2B01G306500 chr2A 89.286 84 5 3 2769 2852 498840229 498840150 6.340000e-18 102.0
6 TraesCS2B01G306500 chr2A 87.097 62 8 0 1208 1269 499578769 499578830 1.790000e-08 71.3
7 TraesCS2B01G306500 chr2A 95.122 41 2 0 2 42 498842981 498842941 8.320000e-07 65.8
8 TraesCS2B01G306500 chr2D 92.335 2270 99 28 503 2752 368526801 368524587 0.000000e+00 3158.0
9 TraesCS2B01G306500 chr2D 86.936 865 37 33 2769 3587 368524602 368523768 0.000000e+00 902.0
10 TraesCS2B01G306500 chr2D 86.304 533 32 19 2 509 368527574 368527058 3.150000e-150 542.0
11 TraesCS2B01G306500 chr5D 89.787 235 23 1 1799 2033 28994477 28994710 2.090000e-77 300.0
12 TraesCS2B01G306500 chr5D 90.625 96 9 0 2157 2252 28994708 28994803 1.050000e-25 128.0
13 TraesCS2B01G306500 chr1A 90.043 231 23 0 1786 2016 464086768 464086538 2.090000e-77 300.0
14 TraesCS2B01G306500 chr1A 92.414 145 11 0 2157 2301 474165752 474165896 1.310000e-49 207.0
15 TraesCS2B01G306500 chr4B 89.177 231 23 1 1786 2016 211498271 211498499 1.630000e-73 287.0
16 TraesCS2B01G306500 chr6A 86.818 220 18 3 1807 2025 602928520 602928311 5.990000e-58 235.0
17 TraesCS2B01G306500 chrUn 93.103 145 10 0 2157 2301 77418651 77418795 2.810000e-51 213.0
18 TraesCS2B01G306500 chr7A 91.724 145 12 0 2157 2301 577614473 577614617 6.070000e-48 202.0
19 TraesCS2B01G306500 chr7A 91.034 145 13 0 2157 2301 49367114 49366970 2.830000e-46 196.0
20 TraesCS2B01G306500 chr7A 92.079 101 7 1 1822 1922 13394019 13394118 1.340000e-29 141.0
21 TraesCS2B01G306500 chr6B 91.724 145 12 0 2157 2301 574503330 574503474 6.070000e-48 202.0
22 TraesCS2B01G306500 chr6B 89.431 123 13 0 1908 2030 22888114 22888236 4.800000e-34 156.0
23 TraesCS2B01G306500 chr3B 90.244 123 12 0 1908 2030 739238672 739238794 1.030000e-35 161.0
24 TraesCS2B01G306500 chr3B 90.090 111 8 3 1822 1931 430931844 430931736 1.340000e-29 141.0
25 TraesCS2B01G306500 chr3B 92.000 100 8 0 1925 2024 754783846 754783945 1.340000e-29 141.0
26 TraesCS2B01G306500 chr4A 82.407 108 12 6 2171 2273 626700132 626700237 1.770000e-13 87.9


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 TraesCS2B01G306500 chr2B 437380454 437384041 3587 True 6626.0 6626 100.00000 1 3588 1 chr2B.!!$R1 3587
1 TraesCS2B01G306500 chr2A 498839017 498842981 3964 True 1098.2 3360 90.57775 2 3587 4 chr2A.!!$R2 3585
2 TraesCS2B01G306500 chr2D 368523768 368527574 3806 True 1534.0 3158 88.52500 2 3587 3 chr2D.!!$R1 3585

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
52 53 0.041238 TGGTTTGGTTTGGTGTGGGA 59.959 50.0 0.0 0.0 0.00 4.37 F
438 479 0.235665 CACACAAAGCCACGCTGTAG 59.764 55.0 0.0 0.0 39.62 2.74 F
1275 1627 0.389948 CTCAACGCCTACAGGTCCAC 60.390 60.0 0.0 0.0 37.57 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 2031 0.451135 CGCGAAGAAAAAGAGGCACG 60.451 55.0 0.00 0.0 0.00 5.34 R
1809 2173 0.539051 GCTCCACAGTAGCCATCACT 59.461 55.0 0.00 0.0 33.73 3.41 R
2656 3036 0.040336 GCCGATCATGCAGCATCTTG 60.040 55.0 4.38 0.0 0.00 3.02 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
42 43 0.899019 AACTGCGGTTTGGTTTGGTT 59.101 45.000 4.68 0.00 30.55 3.67
43 44 0.899019 ACTGCGGTTTGGTTTGGTTT 59.101 45.000 0.00 0.00 0.00 3.27
44 45 1.285578 CTGCGGTTTGGTTTGGTTTG 58.714 50.000 0.00 0.00 0.00 2.93
45 46 0.108138 TGCGGTTTGGTTTGGTTTGG 60.108 50.000 0.00 0.00 0.00 3.28
46 47 0.108089 GCGGTTTGGTTTGGTTTGGT 60.108 50.000 0.00 0.00 0.00 3.67
47 48 1.646189 CGGTTTGGTTTGGTTTGGTG 58.354 50.000 0.00 0.00 0.00 4.17
48 49 1.066787 CGGTTTGGTTTGGTTTGGTGT 60.067 47.619 0.00 0.00 0.00 4.16
49 50 2.351455 GGTTTGGTTTGGTTTGGTGTG 58.649 47.619 0.00 0.00 0.00 3.82
50 51 2.351455 GTTTGGTTTGGTTTGGTGTGG 58.649 47.619 0.00 0.00 0.00 4.17
51 52 0.905357 TTGGTTTGGTTTGGTGTGGG 59.095 50.000 0.00 0.00 0.00 4.61
52 53 0.041238 TGGTTTGGTTTGGTGTGGGA 59.959 50.000 0.00 0.00 0.00 4.37
53 54 1.196012 GGTTTGGTTTGGTGTGGGAA 58.804 50.000 0.00 0.00 0.00 3.97
54 55 1.765904 GGTTTGGTTTGGTGTGGGAAT 59.234 47.619 0.00 0.00 0.00 3.01
55 56 2.171659 GGTTTGGTTTGGTGTGGGAATT 59.828 45.455 0.00 0.00 0.00 2.17
56 57 3.371059 GGTTTGGTTTGGTGTGGGAATTT 60.371 43.478 0.00 0.00 0.00 1.82
57 58 3.828875 TTGGTTTGGTGTGGGAATTTC 57.171 42.857 0.00 0.00 0.00 2.17
142 157 3.429141 GACCGACGAGACGAGGCA 61.429 66.667 0.00 0.00 33.48 4.75
172 187 2.828095 CGGCCCGGCATTCAATGA 60.828 61.111 12.58 0.00 0.00 2.57
182 197 1.730121 GCATTCAATGACACGCCACTG 60.730 52.381 0.00 0.00 0.00 3.66
340 380 2.555757 ACATTTCTTTCAGGTGAGCTGC 59.444 45.455 6.80 0.00 0.00 5.25
388 428 3.569701 AGATCCAGTTGAAATTTGCGTGT 59.430 39.130 0.00 0.00 0.00 4.49
391 431 4.793071 TCCAGTTGAAATTTGCGTGTATG 58.207 39.130 0.00 0.00 0.00 2.39
435 476 2.003658 AACCACACAAAGCCACGCTG 62.004 55.000 0.00 0.00 39.62 5.18
438 479 0.235665 CACACAAAGCCACGCTGTAG 59.764 55.000 0.00 0.00 39.62 2.74
440 481 1.069513 ACACAAAGCCACGCTGTAGTA 59.930 47.619 0.00 0.00 39.62 1.82
442 483 2.742053 CACAAAGCCACGCTGTAGTATT 59.258 45.455 0.00 0.00 39.62 1.89
443 484 2.742053 ACAAAGCCACGCTGTAGTATTG 59.258 45.455 0.00 0.00 39.62 1.90
447 496 3.021695 AGCCACGCTGTAGTATTGTAGA 58.978 45.455 0.00 0.00 37.57 2.59
457 506 9.726232 CGCTGTAGTATTGTAGAGTAAATTACA 57.274 33.333 5.89 0.00 0.00 2.41
467 516 6.810182 TGTAGAGTAAATTACAGTCGGCTTTC 59.190 38.462 5.89 0.00 0.00 2.62
472 521 8.197988 AGTAAATTACAGTCGGCTTTCATAAG 57.802 34.615 5.89 0.00 34.36 1.73
477 526 7.681939 TTACAGTCGGCTTTCATAAGAAAAT 57.318 32.000 0.00 0.00 42.78 1.82
480 529 8.281212 ACAGTCGGCTTTCATAAGAAAATTAT 57.719 30.769 0.00 0.00 42.78 1.28
519 834 7.128331 TCTGAAACGTACGTATATTGTAGAGC 58.872 38.462 23.12 0.28 0.00 4.09
520 835 7.011763 TCTGAAACGTACGTATATTGTAGAGCT 59.988 37.037 23.12 0.00 0.00 4.09
541 859 8.569641 AGAGCTGTACATTACTGTAGCTATTAC 58.430 37.037 9.71 0.38 43.90 1.89
863 1186 5.338708 CGGAAAAGATAGGGAGATATGGCAT 60.339 44.000 4.88 4.88 0.00 4.40
864 1187 6.118852 GGAAAAGATAGGGAGATATGGCATC 58.881 44.000 1.65 0.00 0.00 3.91
865 1188 5.350504 AAAGATAGGGAGATATGGCATCG 57.649 43.478 1.65 0.00 0.00 3.84
866 1189 2.697751 AGATAGGGAGATATGGCATCGC 59.302 50.000 1.65 0.00 0.00 4.58
867 1190 1.937191 TAGGGAGATATGGCATCGCA 58.063 50.000 1.65 0.00 0.00 5.10
1036 1385 3.670629 CTCCTCCACGCCTCCTCCT 62.671 68.421 0.00 0.00 0.00 3.69
1154 1503 4.214327 CTTCTCCGCCTCGCCCTC 62.214 72.222 0.00 0.00 0.00 4.30
1155 1504 4.761058 TTCTCCGCCTCGCCCTCT 62.761 66.667 0.00 0.00 0.00 3.69
1162 1511 3.827898 CCTCGCCCTCTCCGTCAC 61.828 72.222 0.00 0.00 0.00 3.67
1163 1512 3.827898 CTCGCCCTCTCCGTCACC 61.828 72.222 0.00 0.00 0.00 4.02
1166 1515 3.319198 GCCCTCTCCGTCACCCAA 61.319 66.667 0.00 0.00 0.00 4.12
1167 1516 2.663196 CCCTCTCCGTCACCCAAC 59.337 66.667 0.00 0.00 0.00 3.77
1168 1517 1.913762 CCCTCTCCGTCACCCAACT 60.914 63.158 0.00 0.00 0.00 3.16
1200 1552 1.528586 CAAGATACATAGCGGTGCTGC 59.471 52.381 0.00 0.00 40.10 5.25
1275 1627 0.389948 CTCAACGCCTACAGGTCCAC 60.390 60.000 0.00 0.00 37.57 4.02
1407 1771 1.661178 GCTCACATGCAACGACAACTG 60.661 52.381 0.00 0.00 0.00 3.16
1667 2031 4.971125 GGCTCGAGGTATGCCCGC 62.971 72.222 15.58 0.00 40.71 6.13
1675 2039 4.530857 GTATGCCCGCGTGCCTCT 62.531 66.667 11.96 0.00 0.00 3.69
1702 2066 1.079405 GCGATTGGAGTCGGGTTGA 60.079 57.895 0.00 0.00 41.72 3.18
1813 2177 4.357947 GACACGCGAGGGCAGTGA 62.358 66.667 15.93 0.00 42.33 3.41
1912 2276 0.967887 CGAACTGGAGGAGAGGCTCA 60.968 60.000 18.26 0.00 31.08 4.26
2122 2486 4.680237 CGGCGTCCAAGGCAGTCA 62.680 66.667 0.00 0.00 36.37 3.41
2277 2641 0.468214 CCTCGCTCCATGTCCTCCTA 60.468 60.000 0.00 0.00 0.00 2.94
2280 2644 1.145945 TCGCTCCATGTCCTCCTATCT 59.854 52.381 0.00 0.00 0.00 1.98
2297 2661 4.080356 CCTATCTTGACCATCCAACTCCAA 60.080 45.833 0.00 0.00 0.00 3.53
2305 2669 0.040058 ATCCAACTCCAAGCCATGCA 59.960 50.000 0.00 0.00 0.00 3.96
2388 2752 9.766277 TGTTCTGCAATATTTGTTTTTGTTTTC 57.234 25.926 0.00 0.00 0.00 2.29
2404 2768 2.144833 TTTCGCTGCATGTGGGCTTG 62.145 55.000 0.00 0.00 34.04 4.01
2407 2771 1.975407 GCTGCATGTGGGCTTGAGT 60.975 57.895 0.00 0.00 34.04 3.41
2442 2806 0.612744 TCACGTGATCAGGCCATGAA 59.387 50.000 15.76 0.00 42.53 2.57
2506 2875 7.598759 TTTTTGTTTATTGGTAGGTTGCCTA 57.401 32.000 0.00 0.00 34.61 3.93
2507 2876 6.827586 TTTGTTTATTGGTAGGTTGCCTAG 57.172 37.500 0.00 0.00 36.71 3.02
2508 2877 5.508280 TGTTTATTGGTAGGTTGCCTAGT 57.492 39.130 0.00 0.00 36.71 2.57
2509 2878 6.623979 TGTTTATTGGTAGGTTGCCTAGTA 57.376 37.500 0.00 0.00 36.71 1.82
2512 2881 7.771826 TGTTTATTGGTAGGTTGCCTAGTATTC 59.228 37.037 0.00 0.00 36.71 1.75
2534 2912 6.599356 TCATGTGCTGAACTAACCTTAGTA 57.401 37.500 0.00 0.00 42.86 1.82
2535 2913 6.395629 TCATGTGCTGAACTAACCTTAGTAC 58.604 40.000 0.00 0.00 42.86 2.73
2536 2914 6.210784 TCATGTGCTGAACTAACCTTAGTACT 59.789 38.462 0.00 0.00 42.86 2.73
2537 2915 7.395206 TCATGTGCTGAACTAACCTTAGTACTA 59.605 37.037 0.00 0.00 42.86 1.82
2538 2916 7.154435 TGTGCTGAACTAACCTTAGTACTAG 57.846 40.000 2.23 0.00 42.86 2.57
2539 2917 6.035217 GTGCTGAACTAACCTTAGTACTAGC 58.965 44.000 2.23 14.91 42.86 3.42
2625 3005 2.034812 TGTATTGGAACCAAAACCGTGC 59.965 45.455 10.36 0.00 39.55 5.34
2634 3014 1.065109 AAAACCGTGCTGTTTCCGC 59.935 52.632 1.13 0.00 37.46 5.54
2642 3022 1.163420 TGCTGTTTCCGCGTGATTGT 61.163 50.000 4.92 0.00 0.00 2.71
2646 3026 0.452122 GTTTCCGCGTGATTGTTCCG 60.452 55.000 4.92 0.00 0.00 4.30
2654 3034 0.306533 GTGATTGTTCCGTGCGTGTT 59.693 50.000 0.00 0.00 0.00 3.32
2656 3036 0.110373 GATTGTTCCGTGCGTGTTCC 60.110 55.000 0.00 0.00 0.00 3.62
2668 3049 0.806868 CGTGTTCCAAGATGCTGCAT 59.193 50.000 16.20 16.20 0.00 3.96
2669 3050 1.466866 CGTGTTCCAAGATGCTGCATG 60.467 52.381 21.53 7.34 0.00 4.06
2670 3051 1.814394 GTGTTCCAAGATGCTGCATGA 59.186 47.619 21.53 8.10 0.00 3.07
2671 3052 2.426024 GTGTTCCAAGATGCTGCATGAT 59.574 45.455 21.53 5.44 0.00 2.45
2672 3053 2.686405 TGTTCCAAGATGCTGCATGATC 59.314 45.455 21.53 6.75 0.00 2.92
2673 3054 1.589803 TCCAAGATGCTGCATGATCG 58.410 50.000 21.53 5.47 0.00 3.69
2674 3055 0.591659 CCAAGATGCTGCATGATCGG 59.408 55.000 21.53 10.84 0.00 4.18
2675 3056 0.040336 CAAGATGCTGCATGATCGGC 60.040 55.000 21.53 4.15 38.78 5.54
2698 3079 6.458206 GGCTGATCGCAATATTTTACTGTCAA 60.458 38.462 10.82 0.00 41.67 3.18
2699 3080 6.630443 GCTGATCGCAATATTTTACTGTCAAG 59.370 38.462 4.93 0.00 38.92 3.02
2752 3133 2.288273 GCTTGAGTATACTCGCCGGATT 60.288 50.000 24.32 0.00 45.72 3.01
2753 3134 3.057736 GCTTGAGTATACTCGCCGGATTA 60.058 47.826 24.32 5.00 45.72 1.75
2754 3135 4.724303 CTTGAGTATACTCGCCGGATTAG 58.276 47.826 24.32 0.10 45.72 1.73
2755 3136 3.748083 TGAGTATACTCGCCGGATTAGT 58.252 45.455 24.32 7.38 45.72 2.24
2756 3137 4.139786 TGAGTATACTCGCCGGATTAGTT 58.860 43.478 24.32 0.00 45.72 2.24
2757 3138 4.581824 TGAGTATACTCGCCGGATTAGTTT 59.418 41.667 24.32 2.47 45.72 2.66
2758 3139 5.118642 AGTATACTCGCCGGATTAGTTTC 57.881 43.478 5.05 0.00 0.00 2.78
2759 3140 4.581824 AGTATACTCGCCGGATTAGTTTCA 59.418 41.667 5.05 0.00 0.00 2.69
2760 3141 2.754946 ACTCGCCGGATTAGTTTCAA 57.245 45.000 5.05 0.00 0.00 2.69
2761 3142 3.048337 ACTCGCCGGATTAGTTTCAAA 57.952 42.857 5.05 0.00 0.00 2.69
2762 3143 3.404899 ACTCGCCGGATTAGTTTCAAAA 58.595 40.909 5.05 0.00 0.00 2.44
2763 3144 3.816523 ACTCGCCGGATTAGTTTCAAAAA 59.183 39.130 5.05 0.00 0.00 1.94
2805 3186 5.542616 TCGTAGTAGTTCTACTTGAGCAC 57.457 43.478 16.10 8.28 44.80 4.40
2808 3189 5.335426 CGTAGTAGTTCTACTTGAGCACCAA 60.335 44.000 16.10 0.00 44.80 3.67
2811 3192 3.733337 AGTTCTACTTGAGCACCAACAG 58.267 45.455 0.00 0.00 0.00 3.16
2852 3238 4.035324 TCGATCGATCTTGACCAGTCTAAC 59.965 45.833 22.43 0.00 0.00 2.34
2860 3600 2.248248 TGACCAGTCTAACCTGTCCTG 58.752 52.381 0.00 0.00 0.00 3.86
2923 3680 0.884704 ACGGGTGAGTTGTCATGTGC 60.885 55.000 0.00 0.00 34.36 4.57
2924 3681 1.868997 GGGTGAGTTGTCATGTGCG 59.131 57.895 0.00 0.00 34.36 5.34
2950 3707 2.113139 CCCACTGTCGGTTTGCCT 59.887 61.111 0.00 0.00 0.00 4.75
2951 3708 1.122632 TCCCACTGTCGGTTTGCCTA 61.123 55.000 0.00 0.00 0.00 3.93
3105 3862 3.283684 CCCAAGGAACGCACGCAA 61.284 61.111 0.00 0.00 0.00 4.85
3126 3884 5.393962 CAACTGGTGCTTAGTAATTGCTTC 58.606 41.667 0.00 0.00 0.00 3.86
3131 3889 4.944317 GGTGCTTAGTAATTGCTTCCTCTT 59.056 41.667 0.00 0.00 0.00 2.85
3136 3894 6.038382 GCTTAGTAATTGCTTCCTCTTAACCC 59.962 42.308 0.00 0.00 0.00 4.11
3139 3897 0.326927 TTGCTTCCTCTTAACCCCCG 59.673 55.000 0.00 0.00 0.00 5.73
3164 3922 3.434299 CAGCCGTATCGTTTTTACCTGTT 59.566 43.478 0.00 0.00 0.00 3.16
3178 3944 1.682854 ACCTGTTGTGATGGCAAACTG 59.317 47.619 0.00 0.00 0.00 3.16
3200 3974 2.739913 CGCGAAATTCACAAGGTAGGAA 59.260 45.455 0.00 0.00 0.00 3.36
3209 3983 3.378112 TCACAAGGTAGGAATACGTACGG 59.622 47.826 21.06 1.43 37.99 4.02
3296 4090 1.818674 AGCAAAATTAGTGGGGAAGCG 59.181 47.619 0.00 0.00 0.00 4.68
3455 4254 3.349122 ATGCATGCATGGGAGGGA 58.651 55.556 31.74 1.06 35.03 4.20
3456 4255 1.153061 ATGCATGCATGGGAGGGAG 59.847 57.895 31.74 0.11 35.03 4.30
3457 4256 2.203451 GCATGCATGGGAGGGAGG 60.203 66.667 27.34 0.00 0.00 4.30
3458 4257 2.203451 CATGCATGGGAGGGAGGC 60.203 66.667 19.40 0.00 0.00 4.70
3459 4258 3.882326 ATGCATGGGAGGGAGGCG 61.882 66.667 0.00 0.00 0.00 5.52
3498 4297 1.376037 GCACCACAGCACTACCTCC 60.376 63.158 0.00 0.00 0.00 4.30
3504 4303 0.178932 ACAGCACTACCTCCACCTCA 60.179 55.000 0.00 0.00 0.00 3.86
3507 4306 0.685097 GCACTACCTCCACCTCAACA 59.315 55.000 0.00 0.00 0.00 3.33
3508 4307 1.338200 GCACTACCTCCACCTCAACAG 60.338 57.143 0.00 0.00 0.00 3.16
3509 4308 1.276421 CACTACCTCCACCTCAACAGG 59.724 57.143 0.00 0.00 46.87 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.625324 CGGATCTAGAAATTCCCACACCAA 60.625 45.833 0.00 0.00 0.00 3.67
43 44 3.118408 CGGATCTAGAAATTCCCACACCA 60.118 47.826 0.00 0.00 0.00 4.17
44 45 3.467803 CGGATCTAGAAATTCCCACACC 58.532 50.000 0.00 0.00 0.00 4.16
45 46 3.118371 ACCGGATCTAGAAATTCCCACAC 60.118 47.826 9.46 0.00 0.00 3.82
46 47 3.112263 ACCGGATCTAGAAATTCCCACA 58.888 45.455 9.46 0.00 0.00 4.17
47 48 3.840124 ACCGGATCTAGAAATTCCCAC 57.160 47.619 9.46 0.00 0.00 4.61
48 49 3.521937 ACAACCGGATCTAGAAATTCCCA 59.478 43.478 9.46 0.00 0.00 4.37
49 50 3.877508 CACAACCGGATCTAGAAATTCCC 59.122 47.826 9.46 0.00 0.00 3.97
50 51 3.877508 CCACAACCGGATCTAGAAATTCC 59.122 47.826 9.46 0.00 0.00 3.01
51 52 3.877508 CCCACAACCGGATCTAGAAATTC 59.122 47.826 9.46 0.00 0.00 2.17
52 53 3.371595 CCCCACAACCGGATCTAGAAATT 60.372 47.826 9.46 0.00 0.00 1.82
53 54 2.172717 CCCCACAACCGGATCTAGAAAT 59.827 50.000 9.46 0.00 0.00 2.17
54 55 1.557832 CCCCACAACCGGATCTAGAAA 59.442 52.381 9.46 0.00 0.00 2.52
55 56 1.200519 CCCCACAACCGGATCTAGAA 58.799 55.000 9.46 0.00 0.00 2.10
56 57 0.689745 CCCCCACAACCGGATCTAGA 60.690 60.000 9.46 0.00 0.00 2.43
57 58 0.689745 TCCCCCACAACCGGATCTAG 60.690 60.000 9.46 0.00 0.00 2.43
142 157 2.091541 CCGGGCCGCATTATTATTCAT 58.908 47.619 23.20 0.00 0.00 2.57
172 187 2.337532 GTCGTACCAGTGGCGTGT 59.662 61.111 9.78 0.00 0.00 4.49
182 197 0.598065 ACACAACCTACCGTCGTACC 59.402 55.000 0.00 0.00 0.00 3.34
282 302 9.902684 AGCTCTACTAGTACTAAATGTTGAGTA 57.097 33.333 21.69 12.64 34.65 2.59
285 305 8.803397 TCAGCTCTACTAGTACTAAATGTTGA 57.197 34.615 3.76 4.73 0.00 3.18
367 407 3.900941 ACACGCAAATTTCAACTGGATC 58.099 40.909 0.00 0.00 0.00 3.36
401 441 2.617274 GGTTCGTCAAGCAGGCACC 61.617 63.158 0.00 0.00 0.00 5.01
438 479 7.919621 AGCCGACTGTAATTTACTCTACAATAC 59.080 37.037 7.99 0.00 0.00 1.89
440 481 6.875076 AGCCGACTGTAATTTACTCTACAAT 58.125 36.000 7.99 0.00 0.00 2.71
442 483 5.909621 AGCCGACTGTAATTTACTCTACA 57.090 39.130 7.99 0.00 0.00 2.74
443 484 6.810182 TGAAAGCCGACTGTAATTTACTCTAC 59.190 38.462 7.99 0.00 0.00 2.59
447 496 8.038944 TCTTATGAAAGCCGACTGTAATTTACT 58.961 33.333 7.99 0.00 32.36 2.24
457 506 9.614792 ACTATAATTTTCTTATGAAAGCCGACT 57.385 29.630 4.22 0.00 42.34 4.18
541 859 3.428870 CGATACGGCCTACAAGCATTTAG 59.571 47.826 0.00 0.00 0.00 1.85
589 907 4.264128 CCTTTCCTTTCTCCCTCATTTCCT 60.264 45.833 0.00 0.00 0.00 3.36
694 1015 2.764128 GAGATGCGGGGGAGGACA 60.764 66.667 0.00 0.00 0.00 4.02
865 1188 2.709475 GTTGGACGGATGCGATGC 59.291 61.111 15.49 3.59 0.00 3.91
866 1189 2.180204 GGGTTGGACGGATGCGATG 61.180 63.158 15.49 0.00 0.00 3.84
867 1190 1.983119 ATGGGTTGGACGGATGCGAT 61.983 55.000 15.49 0.00 0.00 4.58
960 1294 1.751162 CGTTGGGTTGGGTGTGTGT 60.751 57.895 0.00 0.00 0.00 3.72
1036 1385 4.793201 TGGATAGAAAGAGAGATGGACGA 58.207 43.478 0.00 0.00 0.00 4.20
1151 1500 1.592223 GAGTTGGGTGACGGAGAGG 59.408 63.158 0.00 0.00 0.00 3.69
1152 1501 0.900647 AGGAGTTGGGTGACGGAGAG 60.901 60.000 0.00 0.00 0.00 3.20
1153 1502 0.898789 GAGGAGTTGGGTGACGGAGA 60.899 60.000 0.00 0.00 0.00 3.71
1154 1503 0.900647 AGAGGAGTTGGGTGACGGAG 60.901 60.000 0.00 0.00 0.00 4.63
1155 1504 0.898789 GAGAGGAGTTGGGTGACGGA 60.899 60.000 0.00 0.00 0.00 4.69
1156 1505 1.592223 GAGAGGAGTTGGGTGACGG 59.408 63.158 0.00 0.00 0.00 4.79
1157 1506 1.592223 GGAGAGGAGTTGGGTGACG 59.408 63.158 0.00 0.00 0.00 4.35
1158 1507 0.836400 TGGGAGAGGAGTTGGGTGAC 60.836 60.000 0.00 0.00 0.00 3.67
1159 1508 0.545309 CTGGGAGAGGAGTTGGGTGA 60.545 60.000 0.00 0.00 0.00 4.02
1160 1509 0.545309 TCTGGGAGAGGAGTTGGGTG 60.545 60.000 0.00 0.00 0.00 4.61
1161 1510 0.545548 GTCTGGGAGAGGAGTTGGGT 60.546 60.000 0.00 0.00 0.00 4.51
1162 1511 0.545309 TGTCTGGGAGAGGAGTTGGG 60.545 60.000 0.00 0.00 0.00 4.12
1163 1512 1.277557 CTTGTCTGGGAGAGGAGTTGG 59.722 57.143 0.00 0.00 0.00 3.77
1164 1513 2.251818 TCTTGTCTGGGAGAGGAGTTG 58.748 52.381 0.00 0.00 0.00 3.16
1165 1514 2.704190 TCTTGTCTGGGAGAGGAGTT 57.296 50.000 0.00 0.00 0.00 3.01
1166 1515 2.938428 ATCTTGTCTGGGAGAGGAGT 57.062 50.000 0.00 0.00 0.00 3.85
1167 1516 3.636679 TGTATCTTGTCTGGGAGAGGAG 58.363 50.000 0.00 0.00 0.00 3.69
1168 1517 3.757947 TGTATCTTGTCTGGGAGAGGA 57.242 47.619 0.00 0.00 0.00 3.71
1200 1552 4.124351 CAGCCATTGCCGCCACAG 62.124 66.667 0.00 0.00 38.69 3.66
1207 1559 3.455469 GCCTGGACAGCCATTGCC 61.455 66.667 0.00 0.00 44.91 4.52
1331 1695 2.435938 AATACACGGCACCGCTGG 60.436 61.111 9.43 1.60 44.19 4.85
1332 1696 2.749865 CCAATACACGGCACCGCTG 61.750 63.158 9.43 9.29 44.19 5.18
1333 1697 2.435938 CCAATACACGGCACCGCT 60.436 61.111 9.43 0.00 44.19 5.52
1334 1698 3.505184 CCCAATACACGGCACCGC 61.505 66.667 9.43 0.00 44.19 5.68
1335 1699 1.376166 TTCCCAATACACGGCACCG 60.376 57.895 7.71 7.71 46.03 4.94
1336 1700 0.606944 TGTTCCCAATACACGGCACC 60.607 55.000 0.00 0.00 0.00 5.01
1337 1701 1.068816 GTTGTTCCCAATACACGGCAC 60.069 52.381 0.00 0.00 32.11 5.01
1338 1702 1.240256 GTTGTTCCCAATACACGGCA 58.760 50.000 0.00 0.00 32.11 5.69
1339 1703 1.068816 GTGTTGTTCCCAATACACGGC 60.069 52.381 0.00 0.00 41.02 5.68
1340 1704 2.225491 CAGTGTTGTTCCCAATACACGG 59.775 50.000 5.36 0.00 43.04 4.94
1667 2031 0.451135 CGCGAAGAAAAAGAGGCACG 60.451 55.000 0.00 0.00 0.00 5.34
1669 2033 1.808411 ATCGCGAAGAAAAAGAGGCA 58.192 45.000 15.24 0.00 0.00 4.75
1675 2039 2.156891 CGACTCCAATCGCGAAGAAAAA 59.843 45.455 15.24 0.00 34.90 1.94
1702 2066 1.005294 CGTTCGACCAAACCGATCGT 61.005 55.000 15.09 0.00 41.46 3.73
1809 2173 0.539051 GCTCCACAGTAGCCATCACT 59.461 55.000 0.00 0.00 33.73 3.41
1813 2177 2.187946 GCGCTCCACAGTAGCCAT 59.812 61.111 0.00 0.00 36.60 4.40
1912 2276 2.729479 CCTCTGCGGTCATCTGCCT 61.729 63.158 0.00 0.00 44.62 4.75
2036 2400 2.509336 CGTCGGCATCACCCTCAC 60.509 66.667 0.00 0.00 33.26 3.51
2064 2428 2.347490 GGGGTCTCGAAGCAGCAA 59.653 61.111 0.00 0.00 0.00 3.91
2277 2641 3.875369 GCTTGGAGTTGGATGGTCAAGAT 60.875 47.826 0.00 0.00 35.08 2.40
2280 2644 1.547675 GGCTTGGAGTTGGATGGTCAA 60.548 52.381 0.00 0.00 0.00 3.18
2388 2752 3.047718 CTCAAGCCCACATGCAGCG 62.048 63.158 0.00 0.00 0.00 5.18
2487 2853 7.771826 TGAATACTAGGCAACCTACCAATAAAC 59.228 37.037 0.00 0.00 34.61 2.01
2493 2862 4.719773 ACATGAATACTAGGCAACCTACCA 59.280 41.667 0.00 0.00 34.61 3.25
2512 2881 6.398918 AGTACTAAGGTTAGTTCAGCACATG 58.601 40.000 7.68 0.00 40.96 3.21
2534 2912 1.285280 TTAGCCACCCACATGCTAGT 58.715 50.000 0.00 0.00 38.69 2.57
2535 2913 2.418368 TTTAGCCACCCACATGCTAG 57.582 50.000 0.00 0.00 38.69 3.42
2536 2914 3.380471 AATTTAGCCACCCACATGCTA 57.620 42.857 0.00 0.00 36.57 3.49
2537 2915 2.236489 AATTTAGCCACCCACATGCT 57.764 45.000 0.00 0.00 39.10 3.79
2538 2916 2.418609 GGAAATTTAGCCACCCACATGC 60.419 50.000 0.00 0.00 0.00 4.06
2539 2917 2.168313 GGGAAATTTAGCCACCCACATG 59.832 50.000 6.96 0.00 40.20 3.21
2604 2983 2.034812 GCACGGTTTTGGTTCCAATACA 59.965 45.455 20.42 0.21 32.30 2.29
2612 2991 1.134936 GGAAACAGCACGGTTTTGGTT 60.135 47.619 0.56 0.00 40.85 3.67
2625 3005 1.399727 GGAACAATCACGCGGAAACAG 60.400 52.381 12.47 0.00 0.00 3.16
2634 3014 1.154672 CACGCACGGAACAATCACG 60.155 57.895 0.00 0.00 0.00 4.35
2642 3022 0.250124 ATCTTGGAACACGCACGGAA 60.250 50.000 0.00 0.00 39.29 4.30
2646 3026 0.110056 CAGCATCTTGGAACACGCAC 60.110 55.000 0.00 0.00 39.29 5.34
2654 3034 1.589803 CGATCATGCAGCATCTTGGA 58.410 50.000 4.38 0.00 0.00 3.53
2656 3036 0.040336 GCCGATCATGCAGCATCTTG 60.040 55.000 4.38 0.00 0.00 3.02
2675 3056 6.630443 GCTTGACAGTAAAATATTGCGATCAG 59.370 38.462 0.00 0.00 0.00 2.90
2723 3104 4.560819 GCGAGTATACTCAAGCATAGCATC 59.439 45.833 28.00 2.36 43.00 3.91
2764 3145 3.181483 ACGATCCGGCGAGTATACTTTTT 60.181 43.478 9.30 0.00 34.83 1.94
2765 3146 2.360165 ACGATCCGGCGAGTATACTTTT 59.640 45.455 9.30 0.00 34.83 2.27
2766 3147 1.952296 ACGATCCGGCGAGTATACTTT 59.048 47.619 9.30 0.00 34.83 2.66
2767 3148 1.602311 ACGATCCGGCGAGTATACTT 58.398 50.000 9.30 0.00 34.83 2.24
2768 3149 2.289320 ACTACGATCCGGCGAGTATACT 60.289 50.000 9.30 4.68 34.83 2.12
2769 3150 2.072298 ACTACGATCCGGCGAGTATAC 58.928 52.381 9.30 0.00 34.83 1.47
2770 3151 2.462456 ACTACGATCCGGCGAGTATA 57.538 50.000 9.30 0.00 34.83 1.47
2771 3152 2.289320 ACTACTACGATCCGGCGAGTAT 60.289 50.000 9.30 0.00 34.83 2.12
2772 3153 1.069204 ACTACTACGATCCGGCGAGTA 59.931 52.381 9.30 6.06 34.83 2.59
2773 3154 0.179062 ACTACTACGATCCGGCGAGT 60.179 55.000 9.30 5.00 34.83 4.18
2774 3155 0.942962 AACTACTACGATCCGGCGAG 59.057 55.000 9.30 0.00 34.83 5.03
2775 3156 0.940126 GAACTACTACGATCCGGCGA 59.060 55.000 9.30 0.00 34.83 5.54
2776 3157 0.942962 AGAACTACTACGATCCGGCG 59.057 55.000 0.00 0.00 37.29 6.46
2777 3158 3.534524 GTAGAACTACTACGATCCGGC 57.465 52.381 0.00 0.00 41.36 6.13
2805 3186 3.436359 GGGCACAAAAATATTGCTGTTGG 59.564 43.478 0.94 0.00 36.46 3.77
2808 3189 2.298729 ACGGGCACAAAAATATTGCTGT 59.701 40.909 0.00 0.00 36.46 4.40
2811 3192 1.917303 CGACGGGCACAAAAATATTGC 59.083 47.619 0.00 0.00 35.40 3.56
2950 3707 1.675483 CCTGCCAATTTATGCGCTGTA 59.325 47.619 9.73 0.00 0.00 2.74
2951 3708 0.457035 CCTGCCAATTTATGCGCTGT 59.543 50.000 9.73 0.00 0.00 4.40
3028 3785 7.125755 CGTAAGTGAAACGTTCGATATACCTA 58.874 38.462 0.00 0.00 41.01 3.08
3029 3786 5.967674 CGTAAGTGAAACGTTCGATATACCT 59.032 40.000 0.00 0.00 41.01 3.08
3030 3787 5.172053 CCGTAAGTGAAACGTTCGATATACC 59.828 44.000 0.00 0.00 41.01 2.73
3105 3862 4.010349 GGAAGCAATTACTAAGCACCAGT 58.990 43.478 0.00 0.00 0.00 4.00
3114 3871 5.104235 GGGGGTTAAGAGGAAGCAATTACTA 60.104 44.000 0.00 0.00 0.00 1.82
3126 3884 3.012722 TGGCCGGGGGTTAAGAGG 61.013 66.667 2.18 0.00 0.00 3.69
3139 3897 1.063027 GTAAAAACGATACGGCTGGCC 59.937 52.381 0.00 0.00 0.00 5.36
3164 3922 2.644418 GCGCAGTTTGCCATCACA 59.356 55.556 0.30 0.00 41.12 3.58
3178 3944 1.202031 CCTACCTTGTGAATTTCGCGC 60.202 52.381 0.00 0.00 0.00 6.86
3217 3991 1.747355 CGTACGTACACCCCTCAAGAT 59.253 52.381 24.50 0.00 0.00 2.40
3218 3992 1.167851 CGTACGTACACCCCTCAAGA 58.832 55.000 24.50 0.00 0.00 3.02
3219 3993 0.883833 ACGTACGTACACCCCTCAAG 59.116 55.000 21.41 8.04 0.00 3.02
3296 4090 2.603173 CCTTTGTCTCTTTTGCTGCGTC 60.603 50.000 0.00 0.00 0.00 5.19
3394 4189 2.670905 CACGAAACGAATCATGCACCTA 59.329 45.455 0.00 0.00 0.00 3.08
3477 4276 3.423154 GTAGTGCTGTGGTGCCGC 61.423 66.667 0.00 0.00 0.00 6.53
3498 4297 0.036577 CTCTGCTCCCTGTTGAGGTG 60.037 60.000 0.00 0.00 37.73 4.00
3504 4303 0.178921 TCCACTCTCTGCTCCCTGTT 60.179 55.000 0.00 0.00 0.00 3.16
3507 4306 1.003646 TACTCCACTCTCTGCTCCCT 58.996 55.000 0.00 0.00 0.00 4.20
3508 4307 1.064314 TCTACTCCACTCTCTGCTCCC 60.064 57.143 0.00 0.00 0.00 4.30
3509 4308 2.428544 TCTACTCCACTCTCTGCTCC 57.571 55.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.