Multiple sequence alignment - TraesCS3D01G122800

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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 TraesCS3D01G122800 chr3D 100.000 3701 0 0 1 3701 80602388 80598688 0.000000e+00 6835.0
1 TraesCS3D01G122800 chr3D 89.688 2114 127 39 798 2859 80917744 80915670 0.000000e+00 2612.0
2 TraesCS3D01G122800 chr3D 89.969 1605 93 27 861 2439 80630627 80629065 0.000000e+00 2010.0
3 TraesCS3D01G122800 chr3D 95.548 629 26 1 1 627 586598358 586598986 0.000000e+00 1005.0
4 TraesCS3D01G122800 chr3D 81.034 580 87 11 891 1449 81057866 81057289 1.220000e-119 440.0
5 TraesCS3D01G122800 chr3D 80.801 599 81 7 889 1454 81122335 81121738 4.390000e-119 438.0
6 TraesCS3D01G122800 chr3D 95.000 40 1 1 680 719 80601672 80601634 1.110000e-05 62.1
7 TraesCS3D01G122800 chr3D 95.000 40 1 1 717 755 80601709 80601670 1.110000e-05 62.1
8 TraesCS3D01G122800 chr3D 100.000 31 0 0 3671 3701 416895320 416895350 1.440000e-04 58.4
9 TraesCS3D01G122800 chr3A 89.073 2114 129 38 793 2859 94859392 94857334 0.000000e+00 2531.0
10 TraesCS3D01G122800 chr3A 93.302 1687 77 8 842 2498 94255502 94253822 0.000000e+00 2457.0
11 TraesCS3D01G122800 chr3A 92.351 1242 60 17 2478 3701 94202596 94201372 0.000000e+00 1735.0
12 TraesCS3D01G122800 chr3A 92.045 1232 72 13 2478 3701 94246741 94245528 0.000000e+00 1709.0
13 TraesCS3D01G122800 chr3A 91.539 1241 64 15 2478 3701 94253560 94252344 0.000000e+00 1672.0
14 TraesCS3D01G122800 chr3A 91.000 1200 80 17 1235 2431 94384152 94382978 0.000000e+00 1592.0
15 TraesCS3D01G122800 chr3A 85.903 986 129 7 1487 2467 95359243 95358263 0.000000e+00 1042.0
16 TraesCS3D01G122800 chr3A 87.173 421 27 13 816 1227 94385138 94384736 1.570000e-123 453.0
17 TraesCS3D01G122800 chr3A 83.439 157 10 6 2551 2691 94253705 94253549 8.340000e-27 132.0
18 TraesCS3D01G122800 chr3A 83.333 156 11 9 2551 2691 94246885 94246730 3.000000e-26 130.0
19 TraesCS3D01G122800 chr3A 82.667 150 8 6 648 793 94255651 94255516 2.340000e-22 117.0
20 TraesCS3D01G122800 chr3A 84.000 100 14 2 3294 3392 581836185 581836087 1.090000e-15 95.3
21 TraesCS3D01G122800 chr3B 91.864 1770 63 26 827 2559 126401015 126399290 0.000000e+00 2396.0
22 TraesCS3D01G122800 chr3B 88.816 1672 128 28 801 2439 126459257 126457612 0.000000e+00 1997.0
23 TraesCS3D01G122800 chr3B 85.903 986 129 8 1487 2467 126733158 126732178 0.000000e+00 1042.0
24 TraesCS3D01G122800 chr3B 83.220 441 51 5 1032 1449 126664589 126664149 2.090000e-102 383.0
25 TraesCS3D01G122800 chr3B 94.681 94 3 1 648 741 126401193 126401102 1.070000e-30 145.0
26 TraesCS3D01G122800 chr3B 97.500 40 0 1 717 755 126401163 126401124 2.390000e-07 67.6
27 TraesCS3D01G122800 chr3B 86.154 65 5 4 3639 3701 543014445 543014507 2.390000e-07 67.6
28 TraesCS3D01G122800 chr2B 96.355 631 21 1 1 629 25740322 25740952 0.000000e+00 1037.0
29 TraesCS3D01G122800 chr2B 80.702 228 38 5 3007 3232 688463225 688463448 4.910000e-39 172.0
30 TraesCS3D01G122800 chr2B 87.143 70 6 3 3278 3347 689121714 689121780 3.960000e-10 76.8
31 TraesCS3D01G122800 chr7B 96.038 631 23 1 1 629 21256186 21255556 0.000000e+00 1026.0
32 TraesCS3D01G122800 chr6D 95.447 637 27 1 1 635 61139129 61139765 0.000000e+00 1014.0
33 TraesCS3D01G122800 chr6D 77.301 163 25 8 3232 3383 356768984 356769145 6.590000e-13 86.1
34 TraesCS3D01G122800 chr5D 95.866 629 22 2 1 627 36487797 36487171 0.000000e+00 1014.0
35 TraesCS3D01G122800 chr5D 100.000 29 0 0 3673 3701 395080632 395080604 2.000000e-03 54.7
36 TraesCS3D01G122800 chr5D 100.000 29 0 0 3673 3701 395083493 395083465 2.000000e-03 54.7
37 TraesCS3D01G122800 chr4B 95.548 629 26 2 1 627 510842218 510842846 0.000000e+00 1005.0
38 TraesCS3D01G122800 chr1D 95.411 632 25 4 1 630 53166348 53166977 0.000000e+00 1003.0
39 TraesCS3D01G122800 chr6B 95.253 632 28 1 1 630 132111460 132110829 0.000000e+00 1000.0
40 TraesCS3D01G122800 chr1B 95.390 629 27 1 1 627 566121627 566122255 0.000000e+00 1000.0
41 TraesCS3D01G122800 chr5A 90.000 70 5 2 3278 3347 457923750 457923817 5.090000e-14 89.8
42 TraesCS3D01G122800 chr4A 81.081 111 19 2 3278 3386 608227463 608227573 1.830000e-13 87.9
43 TraesCS3D01G122800 chr4D 100.000 29 0 0 3673 3701 178725283 178725255 2.000000e-03 54.7


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 TraesCS3D01G122800 chr3D 80598688 80602388 3700 True 2319.733333 6835 96.666667 1 3701 3 chr3D.!!$R5 3700
1 TraesCS3D01G122800 chr3D 80915670 80917744 2074 True 2612.000000 2612 89.688000 798 2859 1 chr3D.!!$R2 2061
2 TraesCS3D01G122800 chr3D 80629065 80630627 1562 True 2010.000000 2010 89.969000 861 2439 1 chr3D.!!$R1 1578
3 TraesCS3D01G122800 chr3D 586598358 586598986 628 False 1005.000000 1005 95.548000 1 627 1 chr3D.!!$F2 626
4 TraesCS3D01G122800 chr3D 81057289 81057866 577 True 440.000000 440 81.034000 891 1449 1 chr3D.!!$R3 558
5 TraesCS3D01G122800 chr3D 81121738 81122335 597 True 438.000000 438 80.801000 889 1454 1 chr3D.!!$R4 565
6 TraesCS3D01G122800 chr3A 94857334 94859392 2058 True 2531.000000 2531 89.073000 793 2859 1 chr3A.!!$R2 2066
7 TraesCS3D01G122800 chr3A 94201372 94202596 1224 True 1735.000000 1735 92.351000 2478 3701 1 chr3A.!!$R1 1223
8 TraesCS3D01G122800 chr3A 94252344 94255651 3307 True 1094.500000 2457 87.736750 648 3701 4 chr3A.!!$R6 3053
9 TraesCS3D01G122800 chr3A 95358263 95359243 980 True 1042.000000 1042 85.903000 1487 2467 1 chr3A.!!$R3 980
10 TraesCS3D01G122800 chr3A 94382978 94385138 2160 True 1022.500000 1592 89.086500 816 2431 2 chr3A.!!$R7 1615
11 TraesCS3D01G122800 chr3A 94245528 94246885 1357 True 919.500000 1709 87.689000 2478 3701 2 chr3A.!!$R5 1223
12 TraesCS3D01G122800 chr3B 126457612 126459257 1645 True 1997.000000 1997 88.816000 801 2439 1 chr3B.!!$R1 1638
13 TraesCS3D01G122800 chr3B 126732178 126733158 980 True 1042.000000 1042 85.903000 1487 2467 1 chr3B.!!$R3 980
14 TraesCS3D01G122800 chr3B 126399290 126401193 1903 True 869.533333 2396 94.681667 648 2559 3 chr3B.!!$R4 1911
15 TraesCS3D01G122800 chr2B 25740322 25740952 630 False 1037.000000 1037 96.355000 1 629 1 chr2B.!!$F1 628
16 TraesCS3D01G122800 chr7B 21255556 21256186 630 True 1026.000000 1026 96.038000 1 629 1 chr7B.!!$R1 628
17 TraesCS3D01G122800 chr6D 61139129 61139765 636 False 1014.000000 1014 95.447000 1 635 1 chr6D.!!$F1 634
18 TraesCS3D01G122800 chr5D 36487171 36487797 626 True 1014.000000 1014 95.866000 1 627 1 chr5D.!!$R1 626
19 TraesCS3D01G122800 chr4B 510842218 510842846 628 False 1005.000000 1005 95.548000 1 627 1 chr4B.!!$F1 626
20 TraesCS3D01G122800 chr1D 53166348 53166977 629 False 1003.000000 1003 95.411000 1 630 1 chr1D.!!$F1 629
21 TraesCS3D01G122800 chr6B 132110829 132111460 631 True 1000.000000 1000 95.253000 1 630 1 chr6B.!!$R1 629
22 TraesCS3D01G122800 chr1B 566121627 566122255 628 False 1000.000000 1000 95.390000 1 627 1 chr1B.!!$F1 626

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
97 98 0.601841 GCGAAAAGTGTCCCTTCCGA 60.602 55.000 0.0 0.0 31.27 4.55 F
650 653 0.719465 GGGCGTGTCGTTTGTATGAG 59.281 55.000 0.0 0.0 0.00 2.90 F
1319 2002 1.139058 GGCCATTCGAGTACCTGATGT 59.861 52.381 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 2321 0.454196 GGAGAGAAGTCTGCTCGTCC 59.546 60.000 1.9 6.42 38.12 4.79 R
2254 2949 0.883370 GGAACGTGTTCTCCGCCTTT 60.883 55.000 12.1 0.00 39.45 3.11 R
2883 3879 1.004745 TGGGCTTGTTGGATCTTCCTC 59.995 52.381 0.0 0.00 37.46 3.71 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
97 98 0.601841 GCGAAAAGTGTCCCTTCCGA 60.602 55.000 0.00 0.00 31.27 4.55
186 187 1.276859 ATCTCCCACCAGCATCAGCA 61.277 55.000 0.00 0.00 45.49 4.41
304 305 2.362369 CCAGTGCCGATGGACCTCT 61.362 63.158 0.00 0.00 40.51 3.69
316 317 3.484953 TGGACCTCTAACCACCATAGT 57.515 47.619 0.00 0.00 0.00 2.12
318 319 3.012502 TGGACCTCTAACCACCATAGTCT 59.987 47.826 0.00 0.00 0.00 3.24
366 367 0.978146 AACACCGCTGGCTCCTAGAT 60.978 55.000 0.00 0.00 0.00 1.98
646 649 3.037249 GCGGGCGTGTCGTTTGTA 61.037 61.111 0.00 0.00 0.00 2.41
647 650 2.385091 GCGGGCGTGTCGTTTGTAT 61.385 57.895 0.00 0.00 0.00 2.29
648 651 1.418367 CGGGCGTGTCGTTTGTATG 59.582 57.895 0.00 0.00 0.00 2.39
649 652 1.009903 CGGGCGTGTCGTTTGTATGA 61.010 55.000 0.00 0.00 0.00 2.15
650 653 0.719465 GGGCGTGTCGTTTGTATGAG 59.281 55.000 0.00 0.00 0.00 2.90
651 654 1.670674 GGGCGTGTCGTTTGTATGAGA 60.671 52.381 0.00 0.00 0.00 3.27
652 655 2.063266 GGCGTGTCGTTTGTATGAGAA 58.937 47.619 0.00 0.00 0.00 2.87
653 656 2.159881 GGCGTGTCGTTTGTATGAGAAC 60.160 50.000 0.00 0.00 0.00 3.01
654 657 2.473609 GCGTGTCGTTTGTATGAGAACA 59.526 45.455 0.00 0.00 0.00 3.18
655 658 3.060138 GCGTGTCGTTTGTATGAGAACAA 60.060 43.478 0.00 0.00 37.58 2.83
656 659 4.688063 CGTGTCGTTTGTATGAGAACAAG 58.312 43.478 0.00 0.00 40.29 3.16
657 660 4.376008 CGTGTCGTTTGTATGAGAACAAGG 60.376 45.833 0.00 0.00 40.29 3.61
789 830 5.087323 TGGGAGTACAAAATATTGCCCAAA 58.913 37.500 0.00 0.00 40.22 3.28
791 832 6.106003 GGGAGTACAAAATATTGCCCAAAAG 58.894 40.000 0.00 0.00 40.34 2.27
792 833 6.295632 GGGAGTACAAAATATTGCCCAAAAGT 60.296 38.462 0.00 0.00 40.34 2.66
793 834 6.811665 GGAGTACAAAATATTGCCCAAAAGTC 59.188 38.462 0.00 0.00 40.34 3.01
794 835 6.697395 AGTACAAAATATTGCCCAAAAGTCC 58.303 36.000 0.00 0.00 40.34 3.85
795 836 5.559148 ACAAAATATTGCCCAAAAGTCCA 57.441 34.783 0.00 0.00 40.34 4.02
798 839 5.405935 AAATATTGCCCAAAAGTCCAGTC 57.594 39.130 0.00 0.00 0.00 3.51
799 840 2.683211 ATTGCCCAAAAGTCCAGTCT 57.317 45.000 0.00 0.00 0.00 3.24
803 844 1.884067 GCCCAAAAGTCCAGTCTCAGG 60.884 57.143 0.00 0.00 0.00 3.86
812 853 2.093764 GTCCAGTCTCAGGTCTCCAATG 60.094 54.545 0.00 0.00 0.00 2.82
818 859 2.774234 TCTCAGGTCTCCAATGGAATCC 59.226 50.000 2.61 8.76 0.00 3.01
906 958 4.915667 CACAGTTCATACCATATACCGACG 59.084 45.833 0.00 0.00 0.00 5.12
935 987 4.561500 TTCGTCTCCCCATTAATCAACA 57.438 40.909 0.00 0.00 0.00 3.33
937 989 4.450976 TCGTCTCCCCATTAATCAACATG 58.549 43.478 0.00 0.00 0.00 3.21
1008 1079 1.612950 CAGCTACACACCATTGGCAAA 59.387 47.619 3.01 0.00 0.00 3.68
1319 2002 1.139058 GGCCATTCGAGTACCTGATGT 59.861 52.381 0.00 0.00 0.00 3.06
1587 2273 2.524394 GCTCCCCGATGCCTCCTA 60.524 66.667 0.00 0.00 0.00 2.94
1622 2308 4.166337 AGTGCAGGTATCTCTACTCCTACA 59.834 45.833 0.00 0.00 0.00 2.74
1648 2337 2.282958 TCCCGGACGAGCAGACTT 60.283 61.111 0.73 0.00 0.00 3.01
1736 2425 2.594962 AACGTCAACTTCGGCTGCG 61.595 57.895 0.00 0.00 0.00 5.18
1966 2655 1.661463 TCCCATCTGAAGTGAAGGCT 58.339 50.000 0.00 0.00 0.00 4.58
1979 2668 2.029649 GTGAAGGCTTACTACACCGTCA 60.030 50.000 0.00 0.00 39.23 4.35
2226 2915 3.991051 CCCTGACGTGACGCTGGT 61.991 66.667 4.25 0.00 0.00 4.00
2473 3168 2.796557 TCCGGCTCTCTGTATATCTGG 58.203 52.381 0.00 0.00 0.00 3.86
2503 3221 8.184192 GCATTACTAGTTGACATATTTGCTTGT 58.816 33.333 0.00 0.00 0.00 3.16
2559 3278 9.409949 GTAAAACATTACGAGAAATGAGATTCG 57.590 33.333 13.92 0.00 38.84 3.34
2570 3549 5.940470 AGAAATGAGATTCGTGCTACCTTTT 59.060 36.000 0.00 0.00 34.46 2.27
2606 3589 9.528018 AAAATTTGTCATGTTTCGAAGTGTTAT 57.472 25.926 0.00 0.00 0.00 1.89
2684 3670 5.011090 ACTAATCTGAAGCGAGTGCATTA 57.989 39.130 0.00 0.00 46.23 1.90
2912 3911 1.961277 AACAAGCCCAGTCGAAGCG 60.961 57.895 0.00 0.00 0.00 4.68
2938 3937 6.533367 TGCTCACTAAATTTTGGTTGTTTGTC 59.467 34.615 0.00 0.00 0.00 3.18
2947 3946 9.566530 AAATTTTGGTTGTTTGTCAATTTTAGC 57.433 25.926 0.00 0.00 38.38 3.09
3032 4031 3.326747 CGATCCCTAAATTTAGCGGAGG 58.673 50.000 26.12 19.29 35.24 4.30
3035 4034 5.561679 GATCCCTAAATTTAGCGGAGGAAT 58.438 41.667 26.12 16.80 35.24 3.01
3045 4044 9.719355 AAATTTAGCGGAGGAATATTTTGTTTT 57.281 25.926 0.00 0.00 0.00 2.43
3049 4048 4.679639 GCGGAGGAATATTTTGTTTTCCCC 60.680 45.833 0.00 0.00 39.83 4.81
3118 4117 8.816640 ATTAGCACACATCTTAAAAACCAAAG 57.183 30.769 0.00 0.00 0.00 2.77
3147 4155 0.179094 AAGGTTCACGCAGTTCACGA 60.179 50.000 0.00 0.00 41.61 4.35
3199 4207 9.191995 CTAAGTTATTGAAATTCAAACACACCC 57.808 33.333 12.75 0.00 40.12 4.61
3254 4263 4.098416 GCCGCTTCATCTTCAATTGTAAC 58.902 43.478 5.13 0.00 0.00 2.50
3255 4264 4.379394 GCCGCTTCATCTTCAATTGTAACA 60.379 41.667 5.13 0.00 0.00 2.41
3256 4265 5.698832 CCGCTTCATCTTCAATTGTAACAA 58.301 37.500 5.13 0.00 0.00 2.83
3350 4360 2.813908 GCGGTGGAGGCGTAACAG 60.814 66.667 0.00 0.00 0.00 3.16
3434 4444 3.555547 TGATATGATGCCAAGTTTCGTCG 59.444 43.478 0.00 0.00 0.00 5.12
3440 4450 1.267632 TGCCAAGTTTCGTCGTTTTCG 60.268 47.619 0.00 0.00 45.64 3.46
3456 4466 5.349270 TCGTTTTCGGACAACATTCGATATT 59.651 36.000 7.69 0.00 44.25 1.28
3498 4508 3.577667 CTTTCGCTCATTTCAATGGCAA 58.422 40.909 0.00 4.90 37.03 4.52
3499 4509 2.925578 TCGCTCATTTCAATGGCAAG 57.074 45.000 0.00 0.00 37.03 4.01
3500 4510 2.435422 TCGCTCATTTCAATGGCAAGA 58.565 42.857 0.00 0.00 37.03 3.02
3502 4512 3.255395 TCGCTCATTTCAATGGCAAGAAA 59.745 39.130 17.17 17.17 38.04 2.52
3503 4513 4.082081 TCGCTCATTTCAATGGCAAGAAAT 60.082 37.500 19.42 19.42 43.23 2.17
3504 4514 4.628333 CGCTCATTTCAATGGCAAGAAATT 59.372 37.500 21.41 9.95 41.20 1.82
3505 4515 5.220340 CGCTCATTTCAATGGCAAGAAATTC 60.220 40.000 21.41 14.86 41.20 2.17
3506 4516 5.640357 GCTCATTTCAATGGCAAGAAATTCA 59.360 36.000 21.41 13.62 41.20 2.57
3507 4517 6.315393 GCTCATTTCAATGGCAAGAAATTCAT 59.685 34.615 21.41 6.29 41.20 2.57
3508 4518 7.493320 GCTCATTTCAATGGCAAGAAATTCATA 59.507 33.333 21.41 11.21 41.20 2.15
3548 4558 3.849574 TGAATCAACCCAGAATAGTCCCA 59.150 43.478 0.00 0.00 0.00 4.37
3549 4559 4.290985 TGAATCAACCCAGAATAGTCCCAA 59.709 41.667 0.00 0.00 0.00 4.12
3554 4564 6.081356 TCAACCCAGAATAGTCCCAAATTTT 58.919 36.000 0.00 0.00 0.00 1.82
3611 4621 9.111613 TGTAGAAAAAGTTTAACGGAGAAATGA 57.888 29.630 0.00 0.00 0.00 2.57
3649 4659 6.647067 AGAATTCTCTTCTTCGTTCGAAACAT 59.353 34.615 0.88 0.00 0.00 2.71
3655 4665 5.292345 TCTTCTTCGTTCGAAACATTGACAA 59.708 36.000 0.00 0.00 0.00 3.18
3659 4669 5.411083 TCGTTCGAAACATTGACAATTCA 57.589 34.783 0.00 0.00 0.00 2.57
3668 4678 4.597004 ACATTGACAATTCATGAGAGGCT 58.403 39.130 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.124403 CCATGCCCTCTCAGTGCC 60.124 66.667 0.00 0.00 0.00 5.01
97 98 4.081917 GGATGACTCGAGTTCTCTTCCTTT 60.082 45.833 21.08 0.00 0.00 3.11
186 187 2.301583 GCTGTTCTTCTCCTTCCTCTGT 59.698 50.000 0.00 0.00 0.00 3.41
316 317 1.429927 GATCTCGTCGAGGTCGCAGA 61.430 60.000 19.18 0.08 39.60 4.26
318 319 2.470362 GGATCTCGTCGAGGTCGCA 61.470 63.158 25.21 6.26 40.42 5.10
402 403 2.613691 GCGTCGGAATAAGTTTCTCCA 58.386 47.619 0.00 0.00 0.00 3.86
635 638 4.510340 ACCTTGTTCTCATACAAACGACAC 59.490 41.667 0.00 0.00 37.55 3.67
636 639 4.699637 ACCTTGTTCTCATACAAACGACA 58.300 39.130 0.00 0.00 37.55 4.35
637 640 5.235616 TCAACCTTGTTCTCATACAAACGAC 59.764 40.000 0.00 0.00 37.55 4.34
638 641 5.361427 TCAACCTTGTTCTCATACAAACGA 58.639 37.500 0.00 0.00 37.55 3.85
639 642 5.666969 TCAACCTTGTTCTCATACAAACG 57.333 39.130 0.00 0.00 37.55 3.60
640 643 6.206498 GGTTCAACCTTGTTCTCATACAAAC 58.794 40.000 0.00 0.00 37.55 2.93
641 644 5.008217 CGGTTCAACCTTGTTCTCATACAAA 59.992 40.000 4.68 0.00 37.55 2.83
642 645 4.513692 CGGTTCAACCTTGTTCTCATACAA 59.486 41.667 4.68 0.00 35.66 2.41
643 646 4.062293 CGGTTCAACCTTGTTCTCATACA 58.938 43.478 4.68 0.00 35.66 2.29
644 647 4.062991 ACGGTTCAACCTTGTTCTCATAC 58.937 43.478 4.68 0.00 35.66 2.39
645 648 4.345859 ACGGTTCAACCTTGTTCTCATA 57.654 40.909 4.68 0.00 35.66 2.15
646 649 3.208747 ACGGTTCAACCTTGTTCTCAT 57.791 42.857 4.68 0.00 35.66 2.90
647 650 2.702592 ACGGTTCAACCTTGTTCTCA 57.297 45.000 4.68 0.00 35.66 3.27
648 651 3.460103 TGTACGGTTCAACCTTGTTCTC 58.540 45.455 4.68 0.00 35.66 2.87
649 652 3.547054 TGTACGGTTCAACCTTGTTCT 57.453 42.857 4.68 0.00 35.66 3.01
650 653 4.514066 AGATTGTACGGTTCAACCTTGTTC 59.486 41.667 4.68 0.00 35.66 3.18
651 654 4.274950 CAGATTGTACGGTTCAACCTTGTT 59.725 41.667 4.68 0.00 35.66 2.83
652 655 3.813166 CAGATTGTACGGTTCAACCTTGT 59.187 43.478 4.68 0.00 35.66 3.16
653 656 3.813166 ACAGATTGTACGGTTCAACCTTG 59.187 43.478 4.68 4.74 35.66 3.61
654 657 4.081322 ACAGATTGTACGGTTCAACCTT 57.919 40.909 4.68 0.00 35.66 3.50
655 658 3.764237 ACAGATTGTACGGTTCAACCT 57.236 42.857 4.68 0.00 35.66 3.50
656 659 3.187842 GGAACAGATTGTACGGTTCAACC 59.812 47.826 0.00 0.00 43.12 3.77
657 660 3.810941 TGGAACAGATTGTACGGTTCAAC 59.189 43.478 2.16 0.00 43.12 3.18
743 781 8.689972 CCCAGATTTCAGCTGTTTTATAAGATT 58.310 33.333 14.67 0.00 0.00 2.40
744 782 8.055181 TCCCAGATTTCAGCTGTTTTATAAGAT 58.945 33.333 14.67 0.00 0.00 2.40
745 783 7.402054 TCCCAGATTTCAGCTGTTTTATAAGA 58.598 34.615 14.67 1.48 0.00 2.10
746 784 7.337942 ACTCCCAGATTTCAGCTGTTTTATAAG 59.662 37.037 14.67 5.32 0.00 1.73
747 785 7.175104 ACTCCCAGATTTCAGCTGTTTTATAA 58.825 34.615 14.67 0.00 0.00 0.98
748 786 6.721318 ACTCCCAGATTTCAGCTGTTTTATA 58.279 36.000 14.67 0.00 0.00 0.98
749 787 5.574188 ACTCCCAGATTTCAGCTGTTTTAT 58.426 37.500 14.67 3.08 0.00 1.40
789 830 1.148027 TGGAGACCTGAGACTGGACTT 59.852 52.381 0.00 0.00 29.60 3.01
791 832 1.633774 TTGGAGACCTGAGACTGGAC 58.366 55.000 0.00 0.00 0.00 4.02
792 833 2.182827 CATTGGAGACCTGAGACTGGA 58.817 52.381 0.00 0.00 0.00 3.86
793 834 1.209019 CCATTGGAGACCTGAGACTGG 59.791 57.143 0.00 0.00 0.00 4.00
794 835 2.182827 TCCATTGGAGACCTGAGACTG 58.817 52.381 0.00 0.00 0.00 3.51
795 836 2.630889 TCCATTGGAGACCTGAGACT 57.369 50.000 0.00 0.00 0.00 3.24
798 839 2.507058 TGGATTCCATTGGAGACCTGAG 59.493 50.000 22.12 0.00 32.80 3.35
799 840 2.239654 GTGGATTCCATTGGAGACCTGA 59.760 50.000 22.12 3.98 35.28 3.86
803 844 1.566231 AGGGTGGATTCCATTGGAGAC 59.434 52.381 9.01 4.30 35.28 3.36
812 853 2.826674 TGGAATTCAGGGTGGATTCC 57.173 50.000 17.12 17.12 40.73 3.01
818 859 1.942657 CTACGCATGGAATTCAGGGTG 59.057 52.381 18.29 11.18 0.00 4.61
876 926 2.355197 TGGTATGAACTGTGATTGCGG 58.645 47.619 0.00 0.00 0.00 5.69
906 958 2.124695 GGGAGACGAATGGGGCAC 60.125 66.667 0.00 0.00 0.00 5.01
935 987 2.946329 TGGCGTACGATTAAAATGGCAT 59.054 40.909 21.65 0.00 30.63 4.40
937 989 3.408288 TTGGCGTACGATTAAAATGGC 57.592 42.857 21.65 0.00 0.00 4.40
992 1059 1.697284 TGCTTTGCCAATGGTGTGTA 58.303 45.000 0.00 0.00 0.00 2.90
1008 1079 0.674895 GACTCAACTGCGGGATTGCT 60.675 55.000 0.00 0.00 35.36 3.91
1286 1969 1.504275 AATGGCCTGGAGGTGAGCTT 61.504 55.000 3.32 0.00 37.57 3.74
1342 2025 3.807631 GATGGCGAGCATGCGGGTA 62.808 63.158 13.01 0.00 35.06 3.69
1587 2273 2.847234 TGCACTTGGAGTCGGGGT 60.847 61.111 0.00 0.00 0.00 4.95
1635 2321 0.454196 GGAGAGAAGTCTGCTCGTCC 59.546 60.000 1.90 6.42 38.12 4.79
1736 2425 3.272334 GCCGATCATGGTCGTGGC 61.272 66.667 25.71 19.01 39.89 5.01
1966 2655 4.084287 ACTGGAGATTGACGGTGTAGTAA 58.916 43.478 0.00 0.00 0.00 2.24
1979 2668 2.099921 CGATCTTGACGGACTGGAGATT 59.900 50.000 0.00 0.00 0.00 2.40
2003 2692 3.777925 CGCCGCGAAGGTCTTGTG 61.778 66.667 8.23 0.00 43.70 3.33
2254 2949 0.883370 GGAACGTGTTCTCCGCCTTT 60.883 55.000 12.10 0.00 39.45 3.11
2327 3022 3.305676 CCGATGATGGACACAGGAGTATC 60.306 52.174 0.00 0.00 32.53 2.24
2328 3023 2.630098 CCGATGATGGACACAGGAGTAT 59.370 50.000 0.00 0.00 32.53 2.12
2452 3147 3.157881 CCAGATATACAGAGAGCCGGAA 58.842 50.000 5.05 0.00 0.00 4.30
2473 3168 7.852945 GCAAATATGTCAACTAGTAATGCTGAC 59.147 37.037 14.93 14.93 37.50 3.51
2528 3246 9.582431 CTCATTTCTCGTAATGTTTTACTCCTA 57.418 33.333 0.00 0.00 36.37 2.94
2529 3247 8.311836 TCTCATTTCTCGTAATGTTTTACTCCT 58.688 33.333 0.00 0.00 36.37 3.69
2530 3248 8.475331 TCTCATTTCTCGTAATGTTTTACTCC 57.525 34.615 0.00 0.00 36.37 3.85
2533 3251 9.409949 CGAATCTCATTTCTCGTAATGTTTTAC 57.590 33.333 0.00 0.00 36.95 2.01
2606 3589 5.477607 TGGAACGAGAGAAAAACCTGATA 57.522 39.130 0.00 0.00 0.00 2.15
2784 3774 8.085909 CCATGATTGCTTTGATATTCATGCTAA 58.914 33.333 0.00 0.00 39.24 3.09
2881 3877 2.505819 GGGCTTGTTGGATCTTCCTCTA 59.494 50.000 0.00 0.00 37.46 2.43
2882 3878 1.283321 GGGCTTGTTGGATCTTCCTCT 59.717 52.381 0.00 0.00 37.46 3.69
2883 3879 1.004745 TGGGCTTGTTGGATCTTCCTC 59.995 52.381 0.00 0.00 37.46 3.71
2884 3880 1.005215 CTGGGCTTGTTGGATCTTCCT 59.995 52.381 0.00 0.00 37.46 3.36
2885 3881 1.272147 ACTGGGCTTGTTGGATCTTCC 60.272 52.381 0.00 0.00 36.96 3.46
2886 3882 2.087646 GACTGGGCTTGTTGGATCTTC 58.912 52.381 0.00 0.00 0.00 2.87
2887 3883 1.611673 CGACTGGGCTTGTTGGATCTT 60.612 52.381 0.00 0.00 0.00 2.40
2912 3911 6.312672 ACAAACAACCAAAATTTAGTGAGCAC 59.687 34.615 0.00 0.00 0.00 4.40
2916 3915 9.442047 AATTGACAAACAACCAAAATTTAGTGA 57.558 25.926 0.00 0.00 41.52 3.41
2938 3937 3.507786 GCTGTTTACCCCGCTAAAATTG 58.492 45.455 0.00 0.00 0.00 2.32
2947 3946 2.182732 TTACCCGGCTGTTTACCCCG 62.183 60.000 0.00 0.00 41.60 5.73
3002 4001 7.172703 CGCTAAATTTAGGGATCGGTTAGAAAT 59.827 37.037 29.10 0.00 43.92 2.17
3080 4079 8.213679 AGATGTGTGCTAATATGTAGTTGGAAT 58.786 33.333 0.00 0.00 0.00 3.01
3083 4082 7.792374 AAGATGTGTGCTAATATGTAGTTGG 57.208 36.000 0.00 0.00 0.00 3.77
3118 4117 8.609176 TGAACTGCGTGAACCTTAATTATTATC 58.391 33.333 0.00 0.00 0.00 1.75
3199 4207 9.588774 CATGCATTTACTTCATTTGAAACTTTG 57.411 29.630 0.00 0.00 33.07 2.77
3254 4263 5.241064 TGGCCAATTGAATTCAACCAAATTG 59.759 36.000 22.71 20.10 38.86 2.32
3255 4264 5.383476 TGGCCAATTGAATTCAACCAAATT 58.617 33.333 22.71 10.26 38.86 1.82
3256 4265 4.983053 TGGCCAATTGAATTCAACCAAAT 58.017 34.783 22.71 4.20 38.86 2.32
3350 4360 2.954753 CTGAACGTTGCCGGCAGAC 61.955 63.158 30.75 26.35 40.69 3.51
3434 4444 6.311723 ACAATATCGAATGTTGTCCGAAAAC 58.688 36.000 7.39 0.00 39.95 2.43
3548 4558 8.370182 ACCATTGAAAGTCTCATGCTAAAATTT 58.630 29.630 0.00 0.00 32.78 1.82
3549 4559 7.816031 CACCATTGAAAGTCTCATGCTAAAATT 59.184 33.333 0.00 0.00 32.78 1.82
3554 4564 4.910195 ACACCATTGAAAGTCTCATGCTA 58.090 39.130 0.00 0.00 32.78 3.49
3649 4659 4.564782 AGAGCCTCTCATGAATTGTCAA 57.435 40.909 0.00 0.00 37.30 3.18
3655 4665 4.840716 AACTGAAGAGCCTCTCATGAAT 57.159 40.909 0.00 0.00 32.06 2.57
3659 4669 4.284490 TGTACAAACTGAAGAGCCTCTCAT 59.716 41.667 0.00 0.00 32.06 2.90
3668 4678 4.697828 TGCACTTTGTGTACAAACTGAAGA 59.302 37.500 16.23 2.70 40.55 2.87


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

AutoCloner maintained by Alex Coulton.