Multiple sequence alignment - TraesCS2A01G370300

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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 TraesCS2A01G370300 chr2A 100.000 4386 0 0 1 4386 613039949 613035564 0.000000e+00 8100.0
1 TraesCS2A01G370300 chr2A 93.827 648 39 1 2510 3157 613273668 613273022 0.000000e+00 974.0
2 TraesCS2A01G370300 chr2A 95.302 596 22 3 467 1061 613043257 613043847 0.000000e+00 941.0
3 TraesCS2A01G370300 chr2A 84.455 1010 96 34 2198 3162 613174590 613173597 0.000000e+00 939.0
4 TraesCS2A01G370300 chr2A 89.703 437 22 11 891 1316 613176037 613175613 1.800000e-148 536.0
5 TraesCS2A01G370300 chr2A 88.756 418 42 5 1 413 613180209 613179792 1.410000e-139 507.0
6 TraesCS2A01G370300 chr2A 84.884 516 46 17 827 1316 613275418 613274909 3.940000e-135 492.0
7 TraesCS2A01G370300 chr2A 82.857 455 59 12 1393 1843 613175546 613175107 1.480000e-104 390.0
8 TraesCS2A01G370300 chr2A 82.895 456 52 19 1344 1790 613274910 613274472 1.910000e-103 387.0
9 TraesCS2A01G370300 chr2A 81.711 339 44 11 1963 2297 613274313 613273989 2.600000e-67 267.0
10 TraesCS2A01G370300 chr2A 85.778 225 21 5 667 889 613176356 613176141 1.230000e-55 228.0
11 TraesCS2A01G370300 chr2A 86.869 99 5 3 2421 2517 613273798 613273706 2.160000e-18 104.0
12 TraesCS2A01G370300 chr2D 90.947 1900 78 32 667 2517 471374120 471372266 0.000000e+00 2470.0
13 TraesCS2A01G370300 chr2D 91.409 1164 57 18 2551 3699 471372092 471370957 0.000000e+00 1555.0
14 TraesCS2A01G370300 chr2D 88.606 667 56 9 2511 3162 471896206 471895545 0.000000e+00 793.0
15 TraesCS2A01G370300 chr2D 86.667 675 48 22 667 1316 471451826 471451169 0.000000e+00 710.0
16 TraesCS2A01G370300 chr2D 86.170 658 64 12 2524 3162 471448864 471448215 0.000000e+00 686.0
17 TraesCS2A01G370300 chr2D 86.036 666 59 13 3684 4333 471370941 471370294 0.000000e+00 684.0
18 TraesCS2A01G370300 chr2D 92.056 428 33 1 1 427 471389146 471388719 6.280000e-168 601.0
19 TraesCS2A01G370300 chr2D 82.286 525 65 16 1393 1912 471451102 471450601 3.130000e-116 429.0
20 TraesCS2A01G370300 chr2D 83.055 419 38 18 1414 1804 471896886 471896473 2.510000e-92 350.0
21 TraesCS2A01G370300 chr2D 94.578 166 9 0 1155 1320 471897075 471896910 1.570000e-64 257.0
22 TraesCS2A01G370300 chr2D 86.486 185 18 3 488 666 471454487 471454304 3.460000e-46 196.0
23 TraesCS2A01G370300 chr2D 81.132 212 18 13 767 973 471897453 471897259 2.730000e-32 150.0
24 TraesCS2A01G370300 chr2D 84.810 158 13 6 2145 2297 471450458 471450307 9.830000e-32 148.0
25 TraesCS2A01G370300 chr2D 89.744 117 5 6 2421 2533 471450045 471449932 4.570000e-30 143.0
26 TraesCS2A01G370300 chr2D 85.859 99 6 3 2421 2517 471896336 471896244 1.000000e-16 99.0
27 TraesCS2A01G370300 chr2B 84.820 1805 141 57 672 2381 550513056 550511290 0.000000e+00 1692.0
28 TraesCS2A01G370300 chr2B 87.318 1033 57 26 2552 3533 550510893 550509884 0.000000e+00 1114.0
29 TraesCS2A01G370300 chr2B 91.188 749 44 9 2421 3162 550857553 550856820 0.000000e+00 998.0
30 TraesCS2A01G370300 chr2B 83.554 1131 109 43 821 1910 550859513 550858419 0.000000e+00 987.0
31 TraesCS2A01G370300 chr2B 83.779 1048 111 38 2145 3162 550719756 550718738 0.000000e+00 939.0
32 TraesCS2A01G370300 chr2B 83.140 949 100 36 878 1791 550998196 550997273 0.000000e+00 811.0
33 TraesCS2A01G370300 chr2B 89.006 664 55 10 2510 3162 550996536 550995880 0.000000e+00 806.0
34 TraesCS2A01G370300 chr2B 93.290 462 31 0 1 462 550513699 550513238 0.000000e+00 682.0
35 TraesCS2A01G370300 chr2B 85.224 670 58 16 667 1315 550721220 550720571 0.000000e+00 651.0
36 TraesCS2A01G370300 chr2B 85.472 530 47 19 1393 1912 550720504 550719995 3.890000e-145 525.0
37 TraesCS2A01G370300 chr2B 87.640 445 49 5 1 440 550722283 550721840 3.030000e-141 512.0
38 TraesCS2A01G370300 chr2B 85.781 429 48 8 3528 3951 550485271 550484851 4.030000e-120 442.0
39 TraesCS2A01G370300 chr2B 88.780 205 16 4 3333 3536 550509873 550509675 1.220000e-60 244.0
40 TraesCS2A01G370300 chr2B 87.629 194 16 4 484 671 550861472 550861281 7.390000e-53 219.0
41 TraesCS2A01G370300 chr2B 79.121 273 26 13 2044 2296 550997054 550996793 4.540000e-35 159.0
42 TraesCS2A01G370300 chr2B 86.813 91 5 2 2428 2517 550996657 550996573 1.300000e-15 95.3


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 TraesCS2A01G370300 chr2A 613035564 613039949 4385 True 8100.000000 8100 100.000000 1 4386 1 chr2A.!!$R1 4385
1 TraesCS2A01G370300 chr2A 613043257 613043847 590 False 941.000000 941 95.302000 467 1061 1 chr2A.!!$F1 594
2 TraesCS2A01G370300 chr2A 613173597 613180209 6612 True 520.000000 939 86.309800 1 3162 5 chr2A.!!$R2 3161
3 TraesCS2A01G370300 chr2A 613273022 613275418 2396 True 444.800000 974 86.037200 827 3157 5 chr2A.!!$R3 2330
4 TraesCS2A01G370300 chr2D 471370294 471374120 3826 True 1569.666667 2470 89.464000 667 4333 3 chr2D.!!$R2 3666
5 TraesCS2A01G370300 chr2D 471448215 471454487 6272 True 385.333333 710 86.027167 488 3162 6 chr2D.!!$R3 2674
6 TraesCS2A01G370300 chr2D 471895545 471897453 1908 True 329.800000 793 86.646000 767 3162 5 chr2D.!!$R4 2395
7 TraesCS2A01G370300 chr2B 550509675 550513699 4024 True 933.000000 1692 88.552000 1 3536 4 chr2B.!!$R2 3535
8 TraesCS2A01G370300 chr2B 550856820 550861472 4652 True 734.666667 998 87.457000 484 3162 3 chr2B.!!$R4 2678
9 TraesCS2A01G370300 chr2B 550718738 550722283 3545 True 656.750000 939 85.528750 1 3162 4 chr2B.!!$R3 3161
10 TraesCS2A01G370300 chr2B 550995880 550998196 2316 True 467.825000 811 84.520000 878 3162 4 chr2B.!!$R5 2284

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
414 420 3.744426 CCCGGTAGGACATAATAAAAGCG 59.256 47.826 0.0 0.0 41.02 4.68 F
1806 9401 0.109723 TTTCCACCCCACCTTCTTCG 59.890 55.000 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 10442 0.933796 GGCTAGCGATTCTCAGTTGC 59.066 55.0 9.00 0.0 0.0 4.17 R
3601 13563 0.749049 ATACCTTAACCGACGGCCTC 59.251 55.0 15.39 0.0 0.0 4.70 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
113 116 4.083696 ACGGTTGGCAGTAAAATAAGAACG 60.084 41.667 0.00 0.00 0.00 3.95
265 271 4.660789 ATTAAGGACATTGGCATGAAGC 57.339 40.909 0.00 0.00 44.65 3.86
354 360 9.625747 TGCAAGTTAATTATTCCATGATAGACA 57.374 29.630 0.00 0.00 0.00 3.41
370 376 6.753180 TGATAGACATCCTCAATAAGCTCAC 58.247 40.000 0.00 0.00 0.00 3.51
414 420 3.744426 CCCGGTAGGACATAATAAAAGCG 59.256 47.826 0.00 0.00 41.02 4.68
415 421 4.374399 CCGGTAGGACATAATAAAAGCGT 58.626 43.478 0.00 0.00 41.02 5.07
815 8086 7.526041 TCCATGCCTTTTGGATTAGTATATGT 58.474 34.615 0.00 0.00 44.07 2.29
816 8087 8.004215 TCCATGCCTTTTGGATTAGTATATGTT 58.996 33.333 0.00 0.00 44.07 2.71
817 8088 9.295825 CCATGCCTTTTGGATTAGTATATGTTA 57.704 33.333 0.00 0.00 44.07 2.41
819 8090 8.373048 TGCCTTTTGGATTAGTATATGTTACG 57.627 34.615 0.00 0.00 44.07 3.18
870 8156 5.654603 TGAAAGAGCATTGCAGAAATCAT 57.345 34.783 11.91 0.00 0.00 2.45
875 8161 4.110482 GAGCATTGCAGAAATCATTGGAC 58.890 43.478 11.91 0.00 0.00 4.02
1395 8938 7.566760 TTTTCTTCTTGTCTACTTGCATTCA 57.433 32.000 0.00 0.00 0.00 2.57
1396 8939 7.750229 TTTCTTCTTGTCTACTTGCATTCAT 57.250 32.000 0.00 0.00 0.00 2.57
1445 9007 2.796651 CCGAGGCTCTGCAAATGC 59.203 61.111 13.50 0.00 42.50 3.56
1507 9072 1.633852 CTTGAGCTTCGTCTGCCTGC 61.634 60.000 0.00 0.00 0.00 4.85
1632 9227 1.352017 TGAATTGCAGGGCTTCAGAGA 59.648 47.619 0.00 0.00 0.00 3.10
1743 9338 2.603473 AGCCTCCACGCCACACTA 60.603 61.111 0.00 0.00 0.00 2.74
1806 9401 0.109723 TTTCCACCCCACCTTCTTCG 59.890 55.000 0.00 0.00 0.00 3.79
1808 9403 2.359975 CACCCCACCTTCTTCGGC 60.360 66.667 0.00 0.00 0.00 5.54
1930 9580 8.774546 TCATCTATAGTCATCCTCAGAAGTTT 57.225 34.615 0.00 0.00 0.00 2.66
1931 9581 9.868160 TCATCTATAGTCATCCTCAGAAGTTTA 57.132 33.333 0.00 0.00 0.00 2.01
2019 9712 0.944386 GCTGGCGAGTTGAGTTTCAA 59.056 50.000 0.00 0.00 33.32 2.69
2021 9714 0.944386 TGGCGAGTTGAGTTTCAAGC 59.056 50.000 0.00 0.00 37.00 4.01
2023 9716 0.582005 GCGAGTTGAGTTTCAAGCGT 59.418 50.000 12.47 0.00 37.00 5.07
2059 9764 6.718522 AAAAGGGAAAGAAAACGTATTCCA 57.281 33.333 14.75 0.00 42.50 3.53
2154 9884 0.519077 CCTGCGTTGGCTTCTCTTTC 59.481 55.000 0.00 0.00 40.82 2.62
2252 10427 4.213482 CGGTTAACCTCTTTTTGGACAGAG 59.787 45.833 22.12 0.00 36.96 3.35
2267 10442 3.580731 GACAGAGGAAAGGACGAAAGAG 58.419 50.000 0.00 0.00 0.00 2.85
2383 10806 6.913132 CGTCCTTGATCATAGTTAGTACTGTG 59.087 42.308 5.39 0.00 42.85 3.66
2390 10813 0.037605 AGTTAGTACTGTGCCGTGCC 60.038 55.000 5.39 0.00 31.99 5.01
2406 10842 4.095782 GCCGTGCCTAGTTTTGATAATGAA 59.904 41.667 0.00 0.00 0.00 2.57
2407 10843 5.730568 GCCGTGCCTAGTTTTGATAATGAAG 60.731 44.000 0.00 0.00 0.00 3.02
2408 10844 5.584649 CCGTGCCTAGTTTTGATAATGAAGA 59.415 40.000 0.00 0.00 0.00 2.87
2409 10845 6.260936 CCGTGCCTAGTTTTGATAATGAAGAT 59.739 38.462 0.00 0.00 0.00 2.40
2894 12565 4.722700 CCCGTGCTCCCCAAGGTG 62.723 72.222 0.00 0.00 40.97 4.00
2934 12611 0.875908 CATGGACATGGACTACGGCG 60.876 60.000 4.80 4.80 35.24 6.46
3050 12739 3.414700 GCCGTGGACTCGTTGCAG 61.415 66.667 0.00 0.00 0.00 4.41
3232 12937 4.135493 GCGAGCGGCGAAGTGTTC 62.135 66.667 12.98 0.00 44.57 3.18
3239 12944 3.345808 GCGAAGTGTTCTGCGGCA 61.346 61.111 1.29 1.29 42.55 5.69
3240 12945 2.892334 GCGAAGTGTTCTGCGGCAA 61.892 57.895 3.44 0.00 42.55 4.52
3241 12946 1.646540 CGAAGTGTTCTGCGGCAAA 59.353 52.632 3.44 0.00 38.93 3.68
3242 12947 0.384725 CGAAGTGTTCTGCGGCAAAG 60.385 55.000 3.44 0.00 38.93 2.77
3345 13074 6.620678 TCTTTTTGCCTATAATTGTGCAGTC 58.379 36.000 0.00 0.00 34.81 3.51
3351 13080 5.822519 TGCCTATAATTGTGCAGTCTTAAGG 59.177 40.000 1.85 0.00 0.00 2.69
3366 13124 5.709164 AGTCTTAAGGTTTAGAGTGTAGCGA 59.291 40.000 1.85 0.00 0.00 4.93
3377 13135 1.937899 AGTGTAGCGAACAAAGCGTTT 59.062 42.857 0.00 0.00 40.63 3.60
3379 13137 3.556775 AGTGTAGCGAACAAAGCGTTTAA 59.443 39.130 0.00 0.00 40.63 1.52
3439 13401 5.232838 CGGGGAACGTGTATACAGAAATAAC 59.767 44.000 5.62 0.00 37.93 1.89
3483 13445 3.992943 TCATGGTTTCATAGGTTCCGT 57.007 42.857 0.00 0.00 31.33 4.69
3507 13469 4.002982 TCCGATTGGTGTCTGAATTTCTG 58.997 43.478 0.00 0.00 36.30 3.02
3508 13470 3.127548 CCGATTGGTGTCTGAATTTCTGG 59.872 47.826 3.79 0.00 0.00 3.86
3526 13488 2.820197 CTGGATGAGAATGCATCATGGG 59.180 50.000 6.02 0.00 45.03 4.00
3544 13506 1.675116 GGGACCTCGAGTTGTTAAGGC 60.675 57.143 12.31 0.00 31.79 4.35
3601 13563 1.626654 AAATCGAACCGCTGACGCTG 61.627 55.000 0.00 0.00 38.22 5.18
3602 13564 2.486636 AATCGAACCGCTGACGCTGA 62.487 55.000 0.00 0.00 38.22 4.26
3603 13565 2.874010 ATCGAACCGCTGACGCTGAG 62.874 60.000 0.00 0.00 38.22 3.35
3604 13566 2.811317 GAACCGCTGACGCTGAGG 60.811 66.667 5.37 5.37 38.22 3.86
3674 13636 9.423061 AGGATATTTTTCAAAATTTTGACCTCG 57.577 29.630 28.78 5.34 45.99 4.63
3675 13637 9.418045 GGATATTTTTCAAAATTTTGACCTCGA 57.582 29.630 28.78 14.27 45.99 4.04
3737 13738 7.539034 AATAATTCATAAGGTGGTATTGGCC 57.461 36.000 0.00 0.00 0.00 5.36
3782 13783 4.948004 CCTCAAGGTTAGGTGTTTAATCCC 59.052 45.833 0.00 0.00 0.00 3.85
3783 13784 5.515886 CCTCAAGGTTAGGTGTTTAATCCCA 60.516 44.000 0.00 0.00 0.00 4.37
3786 13787 4.930696 AGGTTAGGTGTTTAATCCCAAGG 58.069 43.478 0.00 0.00 0.00 3.61
3864 13871 4.814771 CCTTAAAAGGTAGGCAAGATACCG 59.185 45.833 0.24 0.00 46.14 4.02
3877 13884 3.801307 AGATACCGGTTCCTGGTTTTT 57.199 42.857 15.04 0.00 40.96 1.94
3879 13886 2.275134 TACCGGTTCCTGGTTTTTCC 57.725 50.000 15.04 0.00 40.96 3.13
3893 13900 0.671163 TTTTCCGGTCGAATCGGTGG 60.671 55.000 22.41 2.56 46.82 4.61
3971 13979 3.782889 GCCTAGGGCTAAACATGTTTG 57.217 47.619 29.72 20.60 46.69 2.93
3983 13992 2.686491 ATGTTTGGCATGGCATGGT 58.314 47.368 27.48 6.95 36.26 3.55
3991 14000 3.469970 ATGGCATGGTCCGCGAGA 61.470 61.111 8.23 0.00 0.00 4.04
4012 14021 1.001641 ACGTCTAGTACACGGGCCT 60.002 57.895 0.84 0.00 41.73 5.19
4074 14083 1.002468 GGCACTGCATGTAAATAGGCG 60.002 52.381 2.82 0.00 0.00 5.52
4102 14111 2.046285 GCATGTTTAGCCCGCCAGT 61.046 57.895 0.00 0.00 0.00 4.00
4103 14112 1.993369 GCATGTTTAGCCCGCCAGTC 61.993 60.000 0.00 0.00 0.00 3.51
4104 14113 1.077716 ATGTTTAGCCCGCCAGTCC 60.078 57.895 0.00 0.00 0.00 3.85
4106 14115 3.315949 TTTAGCCCGCCAGTCCGT 61.316 61.111 0.00 0.00 0.00 4.69
4126 14135 6.704493 GTCCGTGTATTATTCAGCCTATTTGA 59.296 38.462 0.00 0.00 0.00 2.69
4156 14165 3.369997 GGGCCTATATTCAGCCTCTTAGC 60.370 52.174 0.84 0.00 46.31 3.09
4159 14168 5.187967 GGCCTATATTCAGCCTCTTAGCTTA 59.812 44.000 0.00 0.00 42.61 3.09
4161 14170 7.070074 GGCCTATATTCAGCCTCTTAGCTTATA 59.930 40.741 0.00 0.00 42.61 0.98
4183 14192 1.815817 AAAAAGGTCGTGCCATGCCC 61.816 55.000 0.00 0.00 40.61 5.36
4184 14193 4.740822 AAGGTCGTGCCATGCCCC 62.741 66.667 0.00 0.00 40.61 5.80
4210 14219 3.303135 TGCTCAACCTCGCGTCCT 61.303 61.111 5.77 0.00 0.00 3.85
4212 14221 1.214589 GCTCAACCTCGCGTCCTAA 59.785 57.895 5.77 0.00 0.00 2.69
4333 14342 3.849953 GTCGCCGCTTAGCAACCG 61.850 66.667 4.70 3.43 0.00 4.44
4340 14349 3.864686 CTTAGCAACCGCGCGCAT 61.865 61.111 32.61 16.29 45.49 4.73
4341 14350 2.509561 TTAGCAACCGCGCGCATA 60.510 55.556 32.61 10.28 45.49 3.14
4342 14351 2.680427 CTTAGCAACCGCGCGCATAC 62.680 60.000 32.61 14.97 45.49 2.39
4353 14362 2.030412 CGCATACCCCGCTATGCA 59.970 61.111 14.01 0.00 46.48 3.96
4354 14363 2.317609 CGCATACCCCGCTATGCAC 61.318 63.158 14.01 0.00 46.48 4.57
4355 14364 2.317609 GCATACCCCGCTATGCACG 61.318 63.158 10.01 0.00 45.76 5.34
4356 14365 1.069090 CATACCCCGCTATGCACGT 59.931 57.895 0.00 0.00 0.00 4.49
4357 14366 0.531974 CATACCCCGCTATGCACGTT 60.532 55.000 0.00 0.00 0.00 3.99
4358 14367 0.531974 ATACCCCGCTATGCACGTTG 60.532 55.000 0.00 0.00 0.00 4.10
4359 14368 1.890625 TACCCCGCTATGCACGTTGT 61.891 55.000 0.00 0.00 0.00 3.32
4360 14369 2.749865 CCCCGCTATGCACGTTGTG 61.750 63.158 0.00 0.00 36.51 3.33
4361 14370 2.032634 CCCGCTATGCACGTTGTGT 61.033 57.895 0.00 0.00 35.75 3.72
4362 14371 1.573829 CCCGCTATGCACGTTGTGTT 61.574 55.000 0.00 0.00 35.75 3.32
4363 14372 0.452618 CCGCTATGCACGTTGTGTTG 60.453 55.000 0.00 0.00 35.75 3.33
4364 14373 0.452618 CGCTATGCACGTTGTGTTGG 60.453 55.000 0.00 0.00 35.75 3.77
4365 14374 0.591170 GCTATGCACGTTGTGTTGGT 59.409 50.000 0.00 0.00 35.75 3.67
4366 14375 1.001815 GCTATGCACGTTGTGTTGGTT 60.002 47.619 0.00 0.00 35.75 3.67
4367 14376 2.542824 GCTATGCACGTTGTGTTGGTTT 60.543 45.455 0.00 0.00 35.75 3.27
4368 14377 1.919918 ATGCACGTTGTGTTGGTTTG 58.080 45.000 0.00 0.00 35.75 2.93
4369 14378 0.109086 TGCACGTTGTGTTGGTTTGG 60.109 50.000 0.00 0.00 35.75 3.28
4370 14379 0.804156 GCACGTTGTGTTGGTTTGGG 60.804 55.000 0.00 0.00 35.75 4.12
4371 14380 0.804156 CACGTTGTGTTGGTTTGGGC 60.804 55.000 0.00 0.00 0.00 5.36
4372 14381 1.227118 CGTTGTGTTGGTTTGGGCC 60.227 57.895 0.00 0.00 0.00 5.80
4373 14382 1.227118 GTTGTGTTGGTTTGGGCCG 60.227 57.895 0.00 0.00 0.00 6.13
4374 14383 2.427245 TTGTGTTGGTTTGGGCCGG 61.427 57.895 0.00 0.00 0.00 6.13
4375 14384 4.293648 GTGTTGGTTTGGGCCGGC 62.294 66.667 21.18 21.18 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.171754 GAGAAATGCTTTGAGGTGATTGC 58.828 43.478 0.00 0.00 0.00 3.56
113 116 2.623416 ACTGTCTTACTTGGGCTTTTGC 59.377 45.455 0.00 0.00 46.64 3.68
182 187 9.801714 CAAAAAGCTGCATAAAGTAATTTTCAG 57.198 29.630 1.02 1.31 0.00 3.02
235 241 5.102313 GCCAATGTCCTTAATTAACTGCAC 58.898 41.667 0.00 0.00 0.00 4.57
265 271 1.956477 CAACCCTCAAACCTCAAGTGG 59.044 52.381 0.00 0.00 0.00 4.00
353 359 5.885230 TTTGTGTGAGCTTATTGAGGATG 57.115 39.130 0.00 0.00 0.00 3.51
354 360 6.182627 TGATTTGTGTGAGCTTATTGAGGAT 58.817 36.000 0.00 0.00 0.00 3.24
370 376 7.436080 CCGGGATATTCTTGAAAATGATTTGTG 59.564 37.037 0.00 0.00 0.00 3.33
678 6396 6.739331 ATGGAAAGTAAAACCATGGACAAA 57.261 33.333 21.47 0.00 41.96 2.83
692 6410 4.522789 GTCCTTTTTGAGCCATGGAAAGTA 59.477 41.667 18.40 0.00 0.00 2.24
742 6465 4.386424 GGAGGCACCCAATTATAAGTCCTT 60.386 45.833 0.00 0.00 0.00 3.36
849 8135 5.291128 CCAATGATTTCTGCAATGCTCTTTC 59.709 40.000 6.82 0.00 0.00 2.62
870 8156 5.426689 ACTCTTTGAGATAGCATGTCCAA 57.573 39.130 1.25 0.00 33.32 3.53
875 8161 6.732531 TCACAAACTCTTTGAGATAGCATG 57.267 37.500 0.00 0.00 43.26 4.06
1008 8460 1.069090 TGCACTGTTCTGTCGGTCC 59.931 57.895 0.00 0.00 0.00 4.46
1104 8597 2.894387 GCAGGACCAGCGATGCTC 60.894 66.667 0.00 0.00 36.40 4.26
1395 8938 2.170397 GGGAAATTCGGAATTTGGGCAT 59.830 45.455 28.09 7.94 40.97 4.40
1396 8939 1.552792 GGGAAATTCGGAATTTGGGCA 59.447 47.619 28.09 0.00 40.97 5.36
1401 8962 5.104941 GGAAATCAGGGGAAATTCGGAATTT 60.105 40.000 24.50 24.50 43.43 1.82
1445 9007 3.649277 CTTCCCACGAGCCGAGGTG 62.649 68.421 9.41 0.00 35.94 4.00
1467 9029 8.525290 TCAAGAGAAATTAATTCCCCATCTTC 57.475 34.615 0.10 0.00 38.94 2.87
1710 9305 1.439644 GCTCATGACGGTCTCCTCC 59.560 63.158 9.88 0.00 0.00 4.30
1743 9338 1.075374 TGGGATGCTTACTTGTTGCCT 59.925 47.619 0.00 0.00 0.00 4.75
1853 9465 8.715191 ATACTCTCTGACTGATTCAATTCAAC 57.285 34.615 0.67 0.00 32.21 3.18
1939 9589 8.379331 AGCAAGAATACTCTACTTTTCTTCCTT 58.621 33.333 0.00 0.00 36.54 3.36
2019 9712 6.235664 TCCCTTTTATTTCACTTTCTACGCT 58.764 36.000 0.00 0.00 0.00 5.07
2021 9714 8.780249 TCTTTCCCTTTTATTTCACTTTCTACG 58.220 33.333 0.00 0.00 0.00 3.51
2057 9762 1.036707 TTCCTTTTGTTTCCGCCTGG 58.963 50.000 0.00 0.00 0.00 4.45
2059 9764 2.547855 GCATTTCCTTTTGTTTCCGCCT 60.548 45.455 0.00 0.00 0.00 5.52
2154 9884 1.227823 TCACCAAACCAGCACTCGG 60.228 57.895 0.00 0.00 0.00 4.63
2252 10427 2.224314 CAGTTGCTCTTTCGTCCTTTCC 59.776 50.000 0.00 0.00 0.00 3.13
2267 10442 0.933796 GGCTAGCGATTCTCAGTTGC 59.066 55.000 9.00 0.00 0.00 4.17
2383 10806 3.625764 TCATTATCAAAACTAGGCACGGC 59.374 43.478 0.00 0.00 0.00 5.68
2471 10909 5.714333 TGTTACACTATCATTGCCCATTGTT 59.286 36.000 0.00 0.00 0.00 2.83
2894 12565 2.125512 AGCCAGTCCGCGAACATC 60.126 61.111 8.23 0.00 0.00 3.06
3201 12906 3.097137 CTCGCTCGATCACGACGGT 62.097 63.158 0.00 0.00 43.81 4.83
3239 12944 4.922026 AACACCCCGCGACGCTTT 62.922 61.111 19.02 0.00 0.00 3.51
3240 12945 4.922026 AAACACCCCGCGACGCTT 62.922 61.111 19.02 0.59 0.00 4.68
3250 12955 2.603652 CGGAACAACGAATCAAACACCC 60.604 50.000 0.00 0.00 35.47 4.61
3318 13044 7.599998 ACTGCACAATTATAGGCAAAAAGAAAG 59.400 33.333 0.00 0.00 35.59 2.62
3345 13074 6.154445 TGTTCGCTACACTCTAAACCTTAAG 58.846 40.000 0.00 0.00 0.00 1.85
3351 13080 4.663389 CGCTTTGTTCGCTACACTCTAAAC 60.663 45.833 0.00 0.00 36.21 2.01
3357 13114 1.578583 AACGCTTTGTTCGCTACACT 58.421 45.000 0.00 0.00 35.27 3.55
3366 13124 8.124199 TCTTACGAAGAAATTAAACGCTTTGTT 58.876 29.630 10.72 0.00 37.14 2.83
3377 13135 7.332678 GGGCTACAAACTCTTACGAAGAAATTA 59.667 37.037 0.00 0.00 37.02 1.40
3379 13137 5.642491 GGGCTACAAACTCTTACGAAGAAAT 59.358 40.000 0.00 0.00 37.02 2.17
3418 13179 7.062138 TCGTTGTTATTTCTGTATACACGTTCC 59.938 37.037 0.08 0.00 0.00 3.62
3483 13445 5.817296 CAGAAATTCAGACACCAATCGGATA 59.183 40.000 0.00 0.00 35.59 2.59
3507 13469 2.818432 GTCCCATGATGCATTCTCATCC 59.182 50.000 0.00 0.00 41.54 3.51
3508 13470 2.818432 GGTCCCATGATGCATTCTCATC 59.182 50.000 0.00 0.00 42.33 2.92
3526 13488 2.067013 GTGCCTTAACAACTCGAGGTC 58.933 52.381 18.41 0.00 0.00 3.85
3597 13559 3.636313 TTAACCGACGGCCTCAGCG 62.636 63.158 15.39 0.00 41.24 5.18
3598 13560 1.810030 CTTAACCGACGGCCTCAGC 60.810 63.158 15.39 0.00 38.76 4.26
3601 13563 0.749049 ATACCTTAACCGACGGCCTC 59.251 55.000 15.39 0.00 0.00 4.70
3602 13564 1.197812 AATACCTTAACCGACGGCCT 58.802 50.000 15.39 3.77 0.00 5.19
3603 13565 2.028420 AAATACCTTAACCGACGGCC 57.972 50.000 15.39 0.00 0.00 6.13
3604 13566 2.866156 GGTAAATACCTTAACCGACGGC 59.134 50.000 15.39 0.00 43.10 5.68
3605 13567 3.115554 CGGTAAATACCTTAACCGACGG 58.884 50.000 13.61 13.61 44.25 4.79
3606 13568 3.791353 GTCGGTAAATACCTTAACCGACG 59.209 47.826 24.58 0.00 44.57 5.12
3659 13621 7.928908 TCTTTGATTCGAGGTCAAAATTTTG 57.071 32.000 22.40 22.40 42.91 2.44
3664 13626 8.073768 GTGTATTTCTTTGATTCGAGGTCAAAA 58.926 33.333 21.07 12.11 42.91 2.44
3665 13627 7.227711 TGTGTATTTCTTTGATTCGAGGTCAAA 59.772 33.333 20.12 20.12 41.75 2.69
3718 13711 4.724798 ACTAGGCCAATACCACCTTATGAA 59.275 41.667 5.01 0.00 34.92 2.57
3729 13730 5.067283 CACCAATAACCAACTAGGCCAATAC 59.933 44.000 5.01 0.00 43.14 1.89
3843 13850 4.225717 ACCGGTATCTTGCCTACCTTTTAA 59.774 41.667 4.49 0.00 37.15 1.52
3844 13851 3.776417 ACCGGTATCTTGCCTACCTTTTA 59.224 43.478 4.49 0.00 37.15 1.52
3845 13852 2.574824 ACCGGTATCTTGCCTACCTTTT 59.425 45.455 4.49 0.00 37.15 2.27
3847 13854 1.875488 ACCGGTATCTTGCCTACCTT 58.125 50.000 4.49 0.00 37.15 3.50
3848 13855 1.761198 GAACCGGTATCTTGCCTACCT 59.239 52.381 8.00 0.00 37.15 3.08
3849 13856 1.202615 GGAACCGGTATCTTGCCTACC 60.203 57.143 8.00 0.00 36.15 3.18
3850 13857 1.761198 AGGAACCGGTATCTTGCCTAC 59.239 52.381 8.00 0.00 0.00 3.18
3851 13858 1.760613 CAGGAACCGGTATCTTGCCTA 59.239 52.381 8.00 0.00 0.00 3.93
3852 13859 0.541863 CAGGAACCGGTATCTTGCCT 59.458 55.000 8.00 5.34 0.00 4.75
3853 13860 0.463833 CCAGGAACCGGTATCTTGCC 60.464 60.000 8.00 2.79 0.00 4.52
3854 13861 0.252197 ACCAGGAACCGGTATCTTGC 59.748 55.000 8.00 0.00 34.02 4.01
3855 13862 2.781681 AACCAGGAACCGGTATCTTG 57.218 50.000 8.00 14.01 34.99 3.02
3856 13863 3.801307 AAAACCAGGAACCGGTATCTT 57.199 42.857 8.00 1.08 34.99 2.40
3857 13864 3.560668 GGAAAAACCAGGAACCGGTATCT 60.561 47.826 8.00 5.52 34.99 1.98
3858 13865 2.751259 GGAAAAACCAGGAACCGGTATC 59.249 50.000 8.00 7.93 34.99 2.24
3859 13866 2.799017 GGAAAAACCAGGAACCGGTAT 58.201 47.619 8.00 0.00 34.99 2.73
3860 13867 1.542987 CGGAAAAACCAGGAACCGGTA 60.543 52.381 8.00 0.00 34.99 4.02
3861 13868 0.820482 CGGAAAAACCAGGAACCGGT 60.820 55.000 0.00 0.00 38.85 5.28
3862 13869 1.953772 CGGAAAAACCAGGAACCGG 59.046 57.895 0.00 0.00 38.90 5.28
3863 13870 0.820482 ACCGGAAAAACCAGGAACCG 60.820 55.000 9.46 0.00 38.90 4.44
3864 13871 0.956633 GACCGGAAAAACCAGGAACC 59.043 55.000 9.46 0.00 38.90 3.62
3879 13886 2.202703 GGACCACCGATTCGACCG 60.203 66.667 7.83 0.00 0.00 4.79
3893 13900 7.388776 ACCATAGTTTTAAAAACTAGACCGGAC 59.611 37.037 9.46 0.10 36.33 4.79
3902 13909 7.719633 TCTGCTGAGACCATAGTTTTAAAAACT 59.280 33.333 1.31 0.00 0.00 2.66
3965 13973 0.538118 GACCATGCCATGCCAAACAT 59.462 50.000 0.00 0.00 40.66 2.71
3969 13977 2.755064 CGGACCATGCCATGCCAA 60.755 61.111 0.00 0.00 0.00 4.52
3973 13981 3.274586 CTCGCGGACCATGCCATG 61.275 66.667 6.13 0.00 0.00 3.66
3987 13996 1.266940 CGTGTACTAGACGTGCTCTCG 60.267 57.143 0.00 0.00 32.06 4.04
3991 14000 1.930908 GCCCGTGTACTAGACGTGCT 61.931 60.000 6.04 0.00 37.26 4.40
3998 14007 0.179145 CGACAAGGCCCGTGTACTAG 60.179 60.000 9.59 0.00 0.00 2.57
4060 14069 0.875059 GAGCCCGCCTATTTACATGC 59.125 55.000 0.00 0.00 0.00 4.06
4063 14072 0.179468 GGTGAGCCCGCCTATTTACA 59.821 55.000 0.00 0.00 39.82 2.41
4074 14083 1.376609 CTAAACATGCCGGTGAGCCC 61.377 60.000 1.90 0.00 0.00 5.19
4102 14111 6.822442 TCAAATAGGCTGAATAATACACGGA 58.178 36.000 0.00 0.00 0.00 4.69
4103 14112 7.672983 ATCAAATAGGCTGAATAATACACGG 57.327 36.000 0.00 0.00 0.00 4.94
4104 14113 8.559536 ACAATCAAATAGGCTGAATAATACACG 58.440 33.333 0.00 0.00 0.00 4.49
4126 14135 4.344968 GGCTGAATATAGGCCCAAAACAAT 59.655 41.667 0.00 0.00 39.96 2.71
4183 14192 3.041940 GTTGAGCACGTGTCCCGG 61.042 66.667 18.38 0.00 42.24 5.73
4184 14193 3.041940 GGTTGAGCACGTGTCCCG 61.042 66.667 18.38 0.00 44.03 5.14
4185 14194 1.668151 GAGGTTGAGCACGTGTCCC 60.668 63.158 18.38 9.84 0.00 4.46
4186 14195 2.022129 CGAGGTTGAGCACGTGTCC 61.022 63.158 18.38 9.77 0.00 4.02
4187 14196 2.658707 GCGAGGTTGAGCACGTGTC 61.659 63.158 18.38 13.53 0.00 3.67
4210 14219 1.227438 GCTAATCGGGCCGTGCTTA 60.227 57.895 27.32 19.25 0.00 3.09
4212 14221 4.547367 GGCTAATCGGGCCGTGCT 62.547 66.667 27.32 13.76 40.19 4.40
4272 14281 0.325203 ACAAACCTGGCCACTTGGTT 60.325 50.000 19.57 19.57 44.92 3.67
4273 14282 1.042559 CACAAACCTGGCCACTTGGT 61.043 55.000 9.34 9.34 37.57 3.67
4334 14343 3.112075 CATAGCGGGGTATGCGCG 61.112 66.667 0.00 0.00 37.44 6.86
4335 14344 3.423154 GCATAGCGGGGTATGCGC 61.423 66.667 22.32 0.00 44.36 6.09
4338 14347 0.531974 AACGTGCATAGCGGGGTATG 60.532 55.000 12.31 12.31 34.07 2.39
4339 14348 0.531974 CAACGTGCATAGCGGGGTAT 60.532 55.000 0.00 0.00 0.00 2.73
4340 14349 1.153529 CAACGTGCATAGCGGGGTA 60.154 57.895 0.00 0.00 0.00 3.69
4341 14350 2.435938 CAACGTGCATAGCGGGGT 60.436 61.111 0.00 0.00 0.00 4.95
4342 14351 2.435938 ACAACGTGCATAGCGGGG 60.436 61.111 0.00 0.00 0.00 5.73
4343 14352 1.573829 AACACAACGTGCATAGCGGG 61.574 55.000 0.00 0.00 36.98 6.13
4344 14353 0.452618 CAACACAACGTGCATAGCGG 60.453 55.000 0.00 0.00 36.98 5.52
4345 14354 0.452618 CCAACACAACGTGCATAGCG 60.453 55.000 0.00 0.00 36.98 4.26
4346 14355 0.591170 ACCAACACAACGTGCATAGC 59.409 50.000 0.00 0.00 36.98 2.97
4347 14356 3.042189 CAAACCAACACAACGTGCATAG 58.958 45.455 0.00 0.00 36.98 2.23
4348 14357 2.223595 CCAAACCAACACAACGTGCATA 60.224 45.455 0.00 0.00 36.98 3.14
4349 14358 1.470632 CCAAACCAACACAACGTGCAT 60.471 47.619 0.00 0.00 36.98 3.96
4350 14359 0.109086 CCAAACCAACACAACGTGCA 60.109 50.000 0.00 0.00 36.98 4.57
4351 14360 0.804156 CCCAAACCAACACAACGTGC 60.804 55.000 0.00 0.00 36.98 5.34
4352 14361 0.804156 GCCCAAACCAACACAACGTG 60.804 55.000 0.00 0.00 39.75 4.49
4353 14362 1.513622 GCCCAAACCAACACAACGT 59.486 52.632 0.00 0.00 0.00 3.99
4354 14363 1.227118 GGCCCAAACCAACACAACG 60.227 57.895 0.00 0.00 0.00 4.10
4355 14364 1.227118 CGGCCCAAACCAACACAAC 60.227 57.895 0.00 0.00 0.00 3.32
4356 14365 2.427245 CCGGCCCAAACCAACACAA 61.427 57.895 0.00 0.00 0.00 3.33
4357 14366 2.835431 CCGGCCCAAACCAACACA 60.835 61.111 0.00 0.00 0.00 3.72
4358 14367 4.293648 GCCGGCCCAAACCAACAC 62.294 66.667 18.11 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.