Multiple sequence alignment - TraesCS7A01G252400

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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 TraesCS7A01G252400 chr7A 100.000 6317 0 0 1 6317 237510019 237503703 0.000000e+00 11666.0
1 TraesCS7A01G252400 chr7A 99.288 281 2 0 1685 1965 237507364 237507644 5.650000e-140 508.0
2 TraesCS7A01G252400 chr7A 79.920 249 36 10 2041 2275 105863567 105863319 3.030000e-38 171.0
3 TraesCS7A01G252400 chr7B 95.807 3053 108 14 2656 5694 174067993 174071039 0.000000e+00 4911.0
4 TraesCS7A01G252400 chr7B 95.205 855 27 8 837 1684 174067155 174068002 0.000000e+00 1339.0
5 TraesCS7A01G252400 chr7B 96.624 622 16 2 5696 6317 174071137 174071753 0.000000e+00 1027.0
6 TraesCS7A01G252400 chr7B 97.612 335 8 0 2327 2661 41193836 41193502 5.490000e-160 575.0
7 TraesCS7A01G252400 chr7B 94.551 312 14 3 1686 1996 713751501 713751810 4.430000e-131 479.0
8 TraesCS7A01G252400 chr7B 87.273 440 29 12 305 723 174047267 174047700 1.590000e-130 477.0
9 TraesCS7A01G252400 chr7B 91.772 316 17 5 1 307 174046911 174047226 1.260000e-116 431.0
10 TraesCS7A01G252400 chr7B 79.116 249 38 8 2041 2275 59311777 59311529 6.550000e-35 159.0
11 TraesCS7A01G252400 chr7D 94.880 2207 72 20 4129 6317 222520152 222517969 0.000000e+00 3411.0
12 TraesCS7A01G252400 chr7D 95.774 1396 53 5 2656 4046 222521566 222520172 0.000000e+00 2246.0
13 TraesCS7A01G252400 chr7D 95.070 852 29 4 843 1684 222522405 222521557 0.000000e+00 1328.0
14 TraesCS7A01G252400 chr7D 92.480 758 39 8 3 758 222524646 222523905 0.000000e+00 1068.0
15 TraesCS7A01G252400 chr7D 79.116 249 38 9 2041 2275 101806970 101806722 6.550000e-35 159.0
16 TraesCS7A01G252400 chr7D 97.917 48 1 0 758 805 222522514 222522467 4.060000e-12 84.2
17 TraesCS7A01G252400 chr2B 97.328 973 25 1 1684 2656 571767632 571768603 0.000000e+00 1652.0
18 TraesCS7A01G252400 chr2B 98.494 332 5 0 2326 2657 573128532 573128863 2.540000e-163 586.0
19 TraesCS7A01G252400 chr2B 95.570 316 10 4 1682 1996 573127901 573128213 2.630000e-138 503.0
20 TraesCS7A01G252400 chr2B 98.246 285 5 0 1681 1965 573128866 573128582 3.400000e-137 499.0
21 TraesCS7A01G252400 chr1D 91.105 697 46 8 2683 3366 59066343 59065650 0.000000e+00 929.0
22 TraesCS7A01G252400 chr4A 98.140 430 8 0 1683 2112 737844762 737844333 0.000000e+00 750.0
23 TraesCS7A01G252400 chr5A 90.385 572 40 5 2657 3215 466800251 466800820 0.000000e+00 737.0
24 TraesCS7A01G252400 chr5A 92.029 138 11 0 3229 3366 466801204 466801341 1.800000e-45 195.0
25 TraesCS7A01G252400 chr5A 82.313 147 22 4 3974 4118 588015992 588015848 2.390000e-24 124.0
26 TraesCS7A01G252400 chr2A 97.229 397 9 2 1685 2080 419653190 419652795 0.000000e+00 671.0
27 TraesCS7A01G252400 chr3A 98.498 333 5 0 2326 2658 49472880 49472548 7.050000e-164 588.0
28 TraesCS7A01G252400 chr6A 98.485 330 5 0 2328 2657 435591853 435592182 3.280000e-162 582.0
29 TraesCS7A01G252400 chr6A 89.053 338 33 4 1994 2331 584911792 584912125 3.520000e-112 416.0
30 TraesCS7A01G252400 chr4B 98.485 330 5 0 2327 2656 301872621 301872292 3.280000e-162 582.0
31 TraesCS7A01G252400 chr4B 98.182 330 6 0 2327 2656 301904648 301904319 1.530000e-160 577.0
32 TraesCS7A01G252400 chr4B 98.171 328 6 0 2329 2656 301791687 301791360 1.980000e-159 573.0
33 TraesCS7A01G252400 chr4B 97.872 282 6 0 1684 1965 301872291 301872572 7.360000e-134 488.0
34 TraesCS7A01G252400 chr4B 95.631 206 5 2 1875 2080 612330139 612329938 1.700000e-85 327.0
35 TraesCS7A01G252400 chr3B 97.885 331 7 0 2326 2656 52652239 52652569 1.980000e-159 573.0
36 TraesCS7A01G252400 chr3B 97.880 283 6 0 1683 1965 52652571 52652289 2.050000e-134 490.0
37 TraesCS7A01G252400 chr3B 80.537 149 18 6 3974 4118 242890342 242890201 3.120000e-18 104.0
38 TraesCS7A01G252400 chr6D 91.150 339 21 5 1994 2331 436716634 436716964 9.660000e-123 451.0
39 TraesCS7A01G252400 chr6B 90.778 347 19 4 1994 2331 659936284 659936626 9.660000e-123 451.0
40 TraesCS7A01G252400 chr6B 79.444 180 27 6 3974 4144 619023555 619023377 1.110000e-22 119.0
41 TraesCS7A01G252400 chr2D 83.230 161 18 6 3974 4129 372816306 372816150 8.540000e-29 139.0
42 TraesCS7A01G252400 chr5D 78.061 196 36 7 4197 4387 398767182 398766989 4.000000e-22 117.0
43 TraesCS7A01G252400 chr5D 81.818 77 12 2 3974 4049 27545609 27545684 5.290000e-06 63.9
44 TraesCS7A01G252400 chr5B 80.745 161 22 8 3974 4129 61373953 61374109 4.000000e-22 117.0
45 TraesCS7A01G252400 chr5B 77.619 210 34 8 4190 4387 478739831 478739623 1.440000e-21 115.0


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 TraesCS7A01G252400 chr7A 237503703 237510019 6316 True 11666.000000 11666 100.000000 1 6317 1 chr7A.!!$R2 6316
1 TraesCS7A01G252400 chr7B 174067155 174071753 4598 False 2425.666667 4911 95.878667 837 6317 3 chr7B.!!$F3 5480
2 TraesCS7A01G252400 chr7B 174046911 174047700 789 False 454.000000 477 89.522500 1 723 2 chr7B.!!$F2 722
3 TraesCS7A01G252400 chr7D 222517969 222524646 6677 True 1627.440000 3411 95.224200 3 6317 5 chr7D.!!$R2 6314
4 TraesCS7A01G252400 chr2B 571767632 571768603 971 False 1652.000000 1652 97.328000 1684 2656 1 chr2B.!!$F1 972
5 TraesCS7A01G252400 chr2B 573127901 573128863 962 False 544.500000 586 97.032000 1682 2657 2 chr2B.!!$F2 975
6 TraesCS7A01G252400 chr1D 59065650 59066343 693 True 929.000000 929 91.105000 2683 3366 1 chr1D.!!$R1 683
7 TraesCS7A01G252400 chr5A 466800251 466801341 1090 False 466.000000 737 91.207000 2657 3366 2 chr5A.!!$F1 709

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
829 2293 0.181587 TTTTGAGACAACCCGAGGCA 59.818 50.000 0.00 0.00 0.00 4.75 F
1350 2846 0.032678 CGCACTCTATACAGGCCCTG 59.967 60.000 9.83 9.83 37.52 4.45 F
1941 3442 0.753848 CCTCCTTCTCCTCCTCGTCC 60.754 65.000 0.00 0.00 0.00 4.79 F
3562 5535 1.133513 AGTGGTTTGCTGTTGATGGGA 60.134 47.619 0.00 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 3309 2.985282 CCCAGGCAAAGCGAGCAA 60.985 61.111 0.00 0.0 0.0 3.91 R
3184 4784 2.953020 TGTGAATGGCATTTTTACGGC 58.047 42.857 14.93 0.0 0.0 5.68 R
3768 5741 1.338579 TGCACGTATGATTCACAGGCA 60.339 47.619 0.00 0.0 0.0 4.75 R
5515 7514 1.019673 ATGCCAGCTGCTACAAATCG 58.980 50.000 8.66 0.0 42.0 3.34 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
24 25 2.453983 AAACCGTCCCAATTTGCATG 57.546 45.000 0.00 0.00 0.00 4.06
281 291 3.961414 GGCTGGAACCCCGGACAA 61.961 66.667 0.73 0.00 46.69 3.18
449 514 3.561217 TTGTGCGACGCTCGGCTAA 62.561 57.895 22.08 4.88 40.84 3.09
479 548 1.442813 CGTTTTCGACGTGCATTGTTG 59.557 47.619 0.00 0.00 46.49 3.33
500 569 1.674611 GGTCTCGCGTGATGTGAACG 61.675 60.000 14.59 0.00 43.81 3.95
530 602 7.913674 TTCCTCAGAAATAGAAGAGAAAAGC 57.086 36.000 0.00 0.00 0.00 3.51
559 631 3.312973 TGAACATTTTCGGTGCTACGTTT 59.687 39.130 0.00 0.00 34.04 3.60
561 633 2.096614 ACATTTTCGGTGCTACGTTTCG 60.097 45.455 0.00 0.00 34.94 3.46
563 635 2.414058 TTTCGGTGCTACGTTTCGTA 57.586 45.000 0.00 2.23 41.54 3.43
656 729 1.004277 CTTCCTGGGATTTTCGGGACA 59.996 52.381 0.00 0.00 39.22 4.02
687 760 1.401670 CGAAGACAGAGACTGGGTTCG 60.402 57.143 16.74 16.74 41.03 3.95
697 770 1.139058 GACTGGGTTCGTATCCTGCAT 59.861 52.381 0.00 0.00 0.00 3.96
698 771 1.134401 ACTGGGTTCGTATCCTGCATG 60.134 52.381 0.00 0.00 0.00 4.06
699 772 0.463654 TGGGTTCGTATCCTGCATGC 60.464 55.000 11.82 11.82 0.00 4.06
700 773 0.463654 GGGTTCGTATCCTGCATGCA 60.464 55.000 21.29 21.29 0.00 3.96
770 2234 4.749245 ACTACAAATTGAACAAGCGGAG 57.251 40.909 0.00 0.00 0.00 4.63
805 2269 0.906775 TTTCCCGAGGCGATTACCTT 59.093 50.000 0.00 0.00 41.32 3.50
807 2271 0.906775 TCCCGAGGCGATTACCTTTT 59.093 50.000 0.00 0.00 41.32 2.27
808 2272 1.279846 TCCCGAGGCGATTACCTTTTT 59.720 47.619 0.00 0.00 41.32 1.94
829 2293 0.181587 TTTTGAGACAACCCGAGGCA 59.818 50.000 0.00 0.00 0.00 4.75
831 2295 0.400213 TTGAGACAACCCGAGGCAAT 59.600 50.000 0.00 0.00 0.00 3.56
832 2296 0.400213 TGAGACAACCCGAGGCAATT 59.600 50.000 0.00 0.00 0.00 2.32
833 2297 1.626321 TGAGACAACCCGAGGCAATTA 59.374 47.619 0.00 0.00 0.00 1.40
834 2298 2.007608 GAGACAACCCGAGGCAATTAC 58.992 52.381 0.00 0.00 0.00 1.89
896 2385 0.674895 GCCGTGCAGGATTGAGTTCT 60.675 55.000 8.24 0.00 45.00 3.01
947 2437 2.158813 AGGACGGCCCAGTTATGTAATG 60.159 50.000 1.76 0.00 37.41 1.90
1315 2811 1.137086 AGAGGCAGGTGCGTATTACTG 59.863 52.381 0.00 0.00 43.26 2.74
1343 2839 0.750546 ACGCCTCCGCACTCTATACA 60.751 55.000 0.00 0.00 38.22 2.29
1349 2845 1.115930 CCGCACTCTATACAGGCCCT 61.116 60.000 0.00 0.00 0.00 5.19
1350 2846 0.032678 CGCACTCTATACAGGCCCTG 59.967 60.000 9.83 9.83 37.52 4.45
1444 2940 4.401519 AGAATGGGATTGCATTGTTCTCAG 59.598 41.667 0.00 0.00 0.00 3.35
1485 2981 6.326583 TCAAAGTGTAGGCTATTATAGTGGCT 59.673 38.462 0.00 3.83 39.84 4.75
1675 3176 6.395426 TTTCAATCTGACATGAAAAGTGCT 57.605 33.333 14.53 0.00 41.26 4.40
1676 3177 5.366829 TCAATCTGACATGAAAAGTGCTG 57.633 39.130 0.00 0.00 0.00 4.41
1677 3178 3.844577 ATCTGACATGAAAAGTGCTGC 57.155 42.857 0.00 0.00 0.00 5.25
1678 3179 2.854963 TCTGACATGAAAAGTGCTGCT 58.145 42.857 0.00 0.00 0.00 4.24
1679 3180 4.006780 TCTGACATGAAAAGTGCTGCTA 57.993 40.909 0.00 0.00 0.00 3.49
1680 3181 4.582869 TCTGACATGAAAAGTGCTGCTAT 58.417 39.130 0.00 0.00 0.00 2.97
1681 3182 4.633126 TCTGACATGAAAAGTGCTGCTATC 59.367 41.667 0.00 0.00 0.00 2.08
1682 3183 4.582869 TGACATGAAAAGTGCTGCTATCT 58.417 39.130 0.00 0.00 0.00 1.98
1941 3442 0.753848 CCTCCTTCTCCTCCTCGTCC 60.754 65.000 0.00 0.00 0.00 4.79
2084 3594 1.519455 CGATGAAGGCCTGGTCGAC 60.519 63.158 23.01 7.13 34.46 4.20
3065 4652 2.556189 TGATTGCTGCCGTAACAAATGT 59.444 40.909 0.00 0.00 0.00 2.71
3562 5535 1.133513 AGTGGTTTGCTGTTGATGGGA 60.134 47.619 0.00 0.00 0.00 4.37
3714 5687 2.028839 TGATTGACATGCCCTTTTGCAG 60.029 45.455 0.00 0.00 45.93 4.41
3747 5720 7.358066 CCACTGATGTCTTGTATTATTGATGC 58.642 38.462 0.00 0.00 0.00 3.91
3768 5741 8.819845 TGATGCATCTTGTAGATATGGAATACT 58.180 33.333 26.32 0.00 32.12 2.12
4018 5991 1.749063 AGGGCATAACCGCTTTTTAGC 59.251 47.619 0.00 0.00 40.62 3.09
4118 6092 1.979855 TACAGCACCAAGTGTTGCAT 58.020 45.000 10.92 0.00 46.08 3.96
4122 6099 0.530211 GCACCAAGTGTTGCATTGCA 60.530 50.000 7.38 7.38 35.75 4.08
4195 6181 3.378427 ACCACAAGAAAACAGCTCACTTC 59.622 43.478 0.00 0.00 0.00 3.01
4259 6250 3.066203 GGCAACCGTGATGTATTTTAGGG 59.934 47.826 0.00 0.00 0.00 3.53
4312 6307 5.767816 ACATTTTTCGGCTATAATCCACC 57.232 39.130 0.00 0.00 0.00 4.61
4318 6313 4.764050 TCGGCTATAATCCACCTTTTGA 57.236 40.909 0.00 0.00 0.00 2.69
4402 6397 4.682859 GCTCTTAGCACTCTCATCAACCAT 60.683 45.833 0.00 0.00 41.89 3.55
4522 6517 3.366679 GGCAAGATTTGTCACATGTCCTG 60.367 47.826 0.00 0.00 34.79 3.86
4529 6524 3.576078 TGTCACATGTCCTGGTTTCTT 57.424 42.857 0.00 0.00 0.00 2.52
4715 6710 0.528684 GCATCAGGTAGTCTCACGGC 60.529 60.000 0.00 0.00 0.00 5.68
4837 6833 1.173913 CGATTTCCCCTTCAACACCC 58.826 55.000 0.00 0.00 0.00 4.61
4853 6850 4.359971 ACACCCGAGTTTGTTTTGTAAC 57.640 40.909 0.00 0.00 34.75 2.50
5142 7140 0.538287 AAGTCCCTTTGCTGCACCTC 60.538 55.000 0.00 0.00 0.00 3.85
5259 7257 3.490933 CGAATCTCCTAAGGTTCATCGCA 60.491 47.826 0.00 0.00 41.91 5.10
5386 7384 3.196254 GCATTTCATGATGTGACCCCTTT 59.804 43.478 10.96 0.00 36.32 3.11
5399 7397 3.056107 TGACCCCTTTAAGATCACTGACG 60.056 47.826 0.00 0.00 0.00 4.35
5452 7450 5.301045 CACATGGAGTGGCATATTCTGAAAT 59.699 40.000 0.00 0.00 44.69 2.17
5515 7514 3.486383 TCTTTGGGATTGTCAGGTTGTC 58.514 45.455 0.00 0.00 0.00 3.18
5546 7545 2.753452 CAGCTGGCATTTCAGAATCAGT 59.247 45.455 5.57 0.00 36.93 3.41
5549 7548 3.181499 GCTGGCATTTCAGAATCAGTGAG 60.181 47.826 0.00 0.00 36.93 3.51
5550 7549 4.259356 CTGGCATTTCAGAATCAGTGAGA 58.741 43.478 0.00 0.00 36.93 3.27
5560 7559 6.178324 TCAGAATCAGTGAGAAATTGATGCT 58.822 36.000 0.00 0.00 40.68 3.79
5571 7570 9.319143 GTGAGAAATTGATGCTAGTACTGTAAT 57.681 33.333 5.39 0.00 0.00 1.89
5604 7603 8.645110 AGGGAGATTATAAATCAAATTTGGCAG 58.355 33.333 17.90 0.00 33.82 4.85
5700 7798 3.992260 ACATCGTAGCATCTGGTACTC 57.008 47.619 15.29 0.00 44.35 2.59
5849 7947 3.217017 CGGCCGCCTCTAGCAGTA 61.217 66.667 14.67 0.00 44.04 2.74
6202 8300 2.994995 TTGGCCGCGAAGGAGAGA 60.995 61.111 8.23 0.00 45.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 228 2.116736 CTTTCGCGGCAACAAGCTCA 62.117 55.000 6.13 0.00 44.79 4.26
249 250 4.864334 GCCATGGGCGTGGAGGAG 62.864 72.222 15.13 0.00 42.02 3.69
449 514 0.027586 GTCGAAAACGTGCAGCAAGT 59.972 50.000 8.32 8.32 0.00 3.16
479 548 0.666274 TTCACATCACGCGAGACCAC 60.666 55.000 15.93 0.00 0.00 4.16
507 576 6.102663 CGCTTTTCTCTTCTATTTCTGAGGA 58.897 40.000 0.00 0.00 0.00 3.71
508 577 5.872070 ACGCTTTTCTCTTCTATTTCTGAGG 59.128 40.000 0.00 0.00 0.00 3.86
510 579 6.455647 TCACGCTTTTCTCTTCTATTTCTGA 58.544 36.000 0.00 0.00 0.00 3.27
511 580 6.712241 TCACGCTTTTCTCTTCTATTTCTG 57.288 37.500 0.00 0.00 0.00 3.02
513 582 6.958193 CACATCACGCTTTTCTCTTCTATTTC 59.042 38.462 0.00 0.00 0.00 2.17
517 586 5.134202 TCACATCACGCTTTTCTCTTCTA 57.866 39.130 0.00 0.00 0.00 2.10
524 596 5.386323 CGAAAATGTTCACATCACGCTTTTC 60.386 40.000 0.00 0.00 35.10 2.29
530 602 3.225548 CACCGAAAATGTTCACATCACG 58.774 45.455 0.00 0.65 35.10 4.35
656 729 3.070018 CTCTGTCTTCGAAAATGCCACT 58.930 45.455 0.00 0.00 0.00 4.00
687 760 4.136796 TCTATGGTTTGCATGCAGGATAC 58.863 43.478 21.50 16.28 0.00 2.24
698 771 9.952188 GGAAACTTAAATATCTCTATGGTTTGC 57.048 33.333 0.00 0.00 0.00 3.68
700 773 9.642343 GGGGAAACTTAAATATCTCTATGGTTT 57.358 33.333 0.00 0.00 0.00 3.27
723 796 1.940613 CGCTCTCGAAAAATAAGGGGG 59.059 52.381 0.00 0.00 38.10 5.40
736 809 0.809385 TTGTAGTTCTCCCGCTCTCG 59.191 55.000 0.00 0.00 0.00 4.04
770 2234 2.681344 GGGAAACGTACAATGATGGTCC 59.319 50.000 0.00 0.00 0.00 4.46
809 2273 1.314730 GCCTCGGGTTGTCTCAAAAA 58.685 50.000 0.00 0.00 0.00 1.94
810 2274 0.181587 TGCCTCGGGTTGTCTCAAAA 59.818 50.000 0.00 0.00 0.00 2.44
811 2275 0.181587 TTGCCTCGGGTTGTCTCAAA 59.818 50.000 0.00 0.00 0.00 2.69
812 2276 0.400213 ATTGCCTCGGGTTGTCTCAA 59.600 50.000 0.00 0.00 0.00 3.02
813 2277 0.400213 AATTGCCTCGGGTTGTCTCA 59.600 50.000 0.00 0.00 0.00 3.27
814 2278 2.007608 GTAATTGCCTCGGGTTGTCTC 58.992 52.381 0.00 0.00 0.00 3.36
815 2279 1.339727 GGTAATTGCCTCGGGTTGTCT 60.340 52.381 5.16 0.00 0.00 3.41
816 2280 1.092348 GGTAATTGCCTCGGGTTGTC 58.908 55.000 5.16 0.00 0.00 3.18
818 2282 1.094785 CAGGTAATTGCCTCGGGTTG 58.905 55.000 12.76 0.00 36.58 3.77
821 2285 0.810031 CGACAGGTAATTGCCTCGGG 60.810 60.000 12.76 4.50 36.58 5.14
822 2286 0.174845 TCGACAGGTAATTGCCTCGG 59.825 55.000 19.28 10.40 36.58 4.63
824 2288 2.427453 TCTCTCGACAGGTAATTGCCTC 59.573 50.000 12.76 1.88 36.58 4.70
825 2289 2.457598 TCTCTCGACAGGTAATTGCCT 58.542 47.619 9.62 9.62 39.99 4.75
826 2290 2.961526 TCTCTCGACAGGTAATTGCC 57.038 50.000 4.07 4.07 0.00 4.52
829 2293 5.335269 CGCTGATATCTCTCGACAGGTAATT 60.335 44.000 3.98 0.00 0.00 1.40
831 2295 3.498777 CGCTGATATCTCTCGACAGGTAA 59.501 47.826 3.98 0.00 0.00 2.85
832 2296 3.067833 CGCTGATATCTCTCGACAGGTA 58.932 50.000 3.98 0.00 0.00 3.08
833 2297 1.876799 CGCTGATATCTCTCGACAGGT 59.123 52.381 3.98 0.00 0.00 4.00
834 2298 1.876799 ACGCTGATATCTCTCGACAGG 59.123 52.381 15.12 0.00 0.00 4.00
896 2385 2.047655 CGTGAAGGCCCGTAAGCA 60.048 61.111 0.00 0.00 0.00 3.91
1086 2576 4.908687 TTGCTGTCCACGCGCACT 62.909 61.111 5.73 0.00 32.71 4.40
1343 2839 2.684927 GCAGATGATAACAACAGGGCCT 60.685 50.000 0.00 0.00 0.00 5.19
1349 2845 3.610040 AGACCGCAGATGATAACAACA 57.390 42.857 0.00 0.00 0.00 3.33
1350 2846 6.604735 AATAAGACCGCAGATGATAACAAC 57.395 37.500 0.00 0.00 0.00 3.32
1351 2847 8.773645 CATTAATAAGACCGCAGATGATAACAA 58.226 33.333 0.00 0.00 0.00 2.83
1415 2911 4.232221 CAATGCAATCCCATTCTTATCGC 58.768 43.478 0.00 0.00 33.35 4.58
1444 2940 5.750067 ACACTTTGAACAAGCAATTCACATC 59.250 36.000 0.00 0.00 35.82 3.06
1485 2981 7.104043 AGCATGAAAGCAGCTAAATCATTTA 57.896 32.000 13.11 0.00 36.73 1.40
1674 3175 8.506168 TTTTGGTTAAATACTCCAGATAGCAG 57.494 34.615 0.00 0.00 32.63 4.24
1675 3176 8.736244 GTTTTTGGTTAAATACTCCAGATAGCA 58.264 33.333 0.00 0.00 32.63 3.49
1676 3177 8.957466 AGTTTTTGGTTAAATACTCCAGATAGC 58.043 33.333 0.00 0.00 34.37 2.97
1679 3180 9.239551 GGTAGTTTTTGGTTAAATACTCCAGAT 57.760 33.333 0.00 0.00 38.47 2.90
1680 3181 8.219178 TGGTAGTTTTTGGTTAAATACTCCAGA 58.781 33.333 0.00 0.00 38.47 3.86
1681 3182 8.294577 GTGGTAGTTTTTGGTTAAATACTCCAG 58.705 37.037 0.00 0.00 38.47 3.86
1682 3183 7.778853 TGTGGTAGTTTTTGGTTAAATACTCCA 59.221 33.333 0.00 0.00 38.47 3.86
1808 3309 2.985282 CCCAGGCAAAGCGAGCAA 60.985 61.111 0.00 0.00 0.00 3.91
2154 3732 3.155167 GGAGGGAAGGACCGCGAT 61.155 66.667 8.23 0.00 40.11 4.58
2573 4160 4.155280 CGATTTTGTCCCGAAAACTACCAT 59.845 41.667 0.00 0.00 0.00 3.55
3092 4679 7.612677 AGTTAATTTACTGTACAGAGGTCAGG 58.387 38.462 29.30 1.10 34.02 3.86
3184 4784 2.953020 TGTGAATGGCATTTTTACGGC 58.047 42.857 14.93 0.00 0.00 5.68
3270 5241 8.893219 TTAGAAAGTTCAGCATACTATGATGG 57.107 34.615 13.16 0.00 46.10 3.51
3562 5535 4.515567 CGGGTAAAGCTTTCTCTTGTTCTT 59.484 41.667 16.57 0.00 0.00 2.52
3702 5675 2.099405 GGCTATTACTGCAAAAGGGCA 58.901 47.619 0.00 0.00 42.53 5.36
3714 5687 4.770795 ACAAGACATCAGTGGGCTATTAC 58.229 43.478 0.00 0.00 0.00 1.89
3747 5720 7.548427 CAGGCAGTATTCCATATCTACAAGATG 59.452 40.741 0.00 0.00 35.37 2.90
3758 5731 5.628797 TGATTCACAGGCAGTATTCCATA 57.371 39.130 0.00 0.00 0.00 2.74
3768 5741 1.338579 TGCACGTATGATTCACAGGCA 60.339 47.619 0.00 0.00 0.00 4.75
3961 5934 6.426328 CCTATTGGAGATGCAAAGATGACTAC 59.574 42.308 0.00 0.00 34.57 2.73
4018 5991 2.008697 CGTTTTTGCCCTTCGTGCG 61.009 57.895 0.00 0.00 0.00 5.34
4118 6092 0.382873 CAGCAGCTGAAGTGTTGCAA 59.617 50.000 20.43 0.00 44.71 4.08
4122 6099 0.383231 GCAACAGCAGCTGAAGTGTT 59.617 50.000 29.70 19.27 35.18 3.32
4229 6220 1.244019 ATCACGGTTGCCTTCTTGCC 61.244 55.000 0.00 0.00 0.00 4.52
4238 6229 3.942748 TCCCTAAAATACATCACGGTTGC 59.057 43.478 0.00 0.00 0.00 4.17
4259 6250 6.484977 TCAAACAATTGCCCTAAAATTGGTTC 59.515 34.615 5.05 0.00 46.79 3.62
4318 6313 7.651704 GTGTGCTTGGAGTAAAATTTACAACAT 59.348 33.333 17.00 0.00 0.00 2.71
4493 6488 7.215789 ACATGTGACAAATCTTGCCATTAAAA 58.784 30.769 0.00 0.00 0.00 1.52
4522 6517 5.612351 ACCTAGTTCAGTGAGAAAGAAACC 58.388 41.667 0.00 0.00 38.13 3.27
4529 6524 6.776116 TCAAGAAGTACCTAGTTCAGTGAGAA 59.224 38.462 0.00 0.00 37.94 2.87
4715 6710 8.718734 GTTTCACCAGTAAGAGTTAATTAGGTG 58.281 37.037 0.00 0.00 43.94 4.00
4837 6833 3.781846 CACCGTGTTACAAAACAAACTCG 59.218 43.478 0.00 0.00 46.84 4.18
5142 7140 1.825191 CACCATCTCCCGGCAATGG 60.825 63.158 20.40 20.40 44.54 3.16
5349 7347 6.372659 TCATGAAATGCAACTTAAGAGGAGTC 59.627 38.462 10.09 5.38 46.21 3.36
5515 7514 1.019673 ATGCCAGCTGCTACAAATCG 58.980 50.000 8.66 0.00 42.00 3.34
5546 7545 9.890629 AATTACAGTACTAGCATCAATTTCTCA 57.109 29.630 0.00 0.00 0.00 3.27
5604 7603 8.254508 ACTATGGAAGAGTCTTTGTAAGATGAC 58.745 37.037 6.88 0.00 40.18 3.06
5658 7660 6.894682 TGTACAGGGATGATTGTTATGCTAA 58.105 36.000 0.00 0.00 0.00 3.09
5659 7661 6.493189 TGTACAGGGATGATTGTTATGCTA 57.507 37.500 0.00 0.00 0.00 3.49
5660 7662 5.372343 TGTACAGGGATGATTGTTATGCT 57.628 39.130 0.00 0.00 0.00 3.79
5661 7663 5.106948 CGATGTACAGGGATGATTGTTATGC 60.107 44.000 0.33 0.00 0.00 3.14
5662 7664 5.991606 ACGATGTACAGGGATGATTGTTATG 59.008 40.000 0.33 0.00 0.00 1.90
5664 7666 5.607939 ACGATGTACAGGGATGATTGTTA 57.392 39.130 0.33 0.00 0.00 2.41
5665 7667 4.487714 ACGATGTACAGGGATGATTGTT 57.512 40.909 0.33 0.00 0.00 2.83
5666 7668 4.501571 GCTACGATGTACAGGGATGATTGT 60.502 45.833 0.33 0.00 0.00 2.71
5667 7669 3.990469 GCTACGATGTACAGGGATGATTG 59.010 47.826 0.33 0.00 0.00 2.67
5668 7670 3.641436 TGCTACGATGTACAGGGATGATT 59.359 43.478 0.33 0.00 0.00 2.57
5700 7798 3.402628 ACACTAGTGCAACAAGGTAGG 57.597 47.619 22.90 0.00 41.43 3.18
6202 8300 2.183679 CTGCTCTGGAACCTCTACCTT 58.816 52.381 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.