Multiple sequence alignment - TraesCS2A01G419500

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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 TraesCS2A01G419500 chr2A 100.000 8318 0 0 1 8318 675087052 675078735 0.000000e+00 15361.0
1 TraesCS2A01G419500 chr2A 94.407 1037 52 4 5927 6960 675747930 675746897 0.000000e+00 1589.0
2 TraesCS2A01G419500 chr2A 80.827 1523 188 49 2500 3962 675751340 675749862 0.000000e+00 1099.0
3 TraesCS2A01G419500 chr2A 78.663 1017 177 33 5932 6931 675897503 675896510 2.530000e-179 640.0
4 TraesCS2A01G419500 chr2A 95.304 362 16 1 2137 2497 675751671 675751310 2.600000e-159 573.0
5 TraesCS2A01G419500 chr2A 79.897 582 75 25 3291 3853 675751670 675751112 1.010000e-103 388.0
6 TraesCS2A01G419500 chr2A 79.457 589 60 27 7611 8157 675745904 675745335 2.210000e-95 361.0
7 TraesCS2A01G419500 chr2A 93.458 107 6 1 142 247 29944882 29944776 3.110000e-34 158.0
8 TraesCS2A01G419500 chr2A 96.000 75 2 1 143 217 605567876 605567803 4.080000e-23 121.0
9 TraesCS2A01G419500 chr2D 97.283 6367 111 18 900 7246 530265035 530258711 0.000000e+00 10743.0
10 TraesCS2A01G419500 chr2D 91.699 1036 55 6 5928 6960 531264048 531263041 0.000000e+00 1408.0
11 TraesCS2A01G419500 chr2D 95.143 803 16 3 7539 8318 530258280 530257478 0.000000e+00 1245.0
12 TraesCS2A01G419500 chr2D 80.577 1524 188 51 2500 3962 531267448 531265972 0.000000e+00 1075.0
13 TraesCS2A01G419500 chr2D 87.676 641 36 25 286 903 102288832 102288212 0.000000e+00 706.0
14 TraesCS2A01G419500 chr2D 78.337 1034 180 37 5917 6931 531349075 531348067 5.480000e-176 628.0
15 TraesCS2A01G419500 chr2D 95.664 369 15 1 2130 2497 531267786 531267418 7.190000e-165 592.0
16 TraesCS2A01G419500 chr2D 94.087 389 11 4 7122 7500 530258790 530258404 1.560000e-161 580.0
17 TraesCS2A01G419500 chr2D 79.661 590 78 24 3283 3853 531267786 531267220 3.640000e-103 387.0
18 TraesCS2A01G419500 chr2D 85.044 341 31 9 7824 8157 531259720 531259393 6.220000e-86 329.0
19 TraesCS2A01G419500 chr2D 81.795 390 49 9 2128 2497 530262672 530262285 2.920000e-79 307.0
20 TraesCS2A01G419500 chr2D 87.603 242 28 1 1866 2105 531268024 531267783 6.360000e-71 279.0
21 TraesCS2A01G419500 chr2D 76.172 256 24 21 6996 7246 531262969 531262746 5.310000e-17 100.0
22 TraesCS2A01G419500 chr2B 94.378 3504 145 13 4005 7487 630138824 630135352 0.000000e+00 5332.0
23 TraesCS2A01G419500 chr2B 95.970 3102 83 13 900 3981 630141896 630138817 0.000000e+00 4998.0
24 TraesCS2A01G419500 chr2B 77.053 2898 491 113 2498 5294 631106358 631103534 0.000000e+00 1507.0
25 TraesCS2A01G419500 chr2B 89.192 1027 105 6 5928 6951 631102872 631101849 0.000000e+00 1277.0
26 TraesCS2A01G419500 chr2B 95.082 488 15 1 7840 8318 630134812 630134325 0.000000e+00 760.0
27 TraesCS2A01G419500 chr2B 79.014 1034 173 36 5917 6931 631203831 631202823 0.000000e+00 667.0
28 TraesCS2A01G419500 chr2B 95.317 363 16 1 286 648 753330814 753331175 7.240000e-160 575.0
29 TraesCS2A01G419500 chr2B 94.475 362 16 2 2137 2497 631106684 631106326 9.430000e-154 555.0
30 TraesCS2A01G419500 chr2B 96.516 287 6 1 7539 7821 630135241 630134955 9.770000e-129 472.0
31 TraesCS2A01G419500 chr2B 81.086 608 59 27 7611 8184 631101043 631100458 1.280000e-117 435.0
32 TraesCS2A01G419500 chr2B 80.388 515 69 16 3358 3853 631106631 631106130 6.140000e-96 363.0
33 TraesCS2A01G419500 chr2B 81.282 390 51 7 2128 2497 630139518 630139131 6.310000e-76 296.0
34 TraesCS2A01G419500 chr2B 76.680 253 32 16 6996 7246 631101777 631101550 1.900000e-21 115.0
35 TraesCS2A01G419500 chr4D 96.932 1271 36 2 2937 4205 410440054 410438785 0.000000e+00 2128.0
36 TraesCS2A01G419500 chr4D 82.781 453 49 13 7589 8021 47288636 47289079 2.190000e-100 377.0
37 TraesCS2A01G419500 chr4D 80.000 390 56 8 2128 2497 410439710 410439323 1.380000e-67 268.0
38 TraesCS2A01G419500 chr3D 97.403 924 21 2 2938 3859 554513152 554514074 0.000000e+00 1570.0
39 TraesCS2A01G419500 chr3D 95.745 329 12 2 3878 4205 554514061 554514388 5.720000e-146 529.0
40 TraesCS2A01G419500 chr3D 80.874 366 48 9 2128 2473 554513495 554513858 1.380000e-67 268.0
41 TraesCS2A01G419500 chr7A 92.214 899 33 8 37 899 66695259 66696156 0.000000e+00 1238.0
42 TraesCS2A01G419500 chr7A 97.333 75 1 1 143 217 610196167 610196240 8.760000e-25 126.0
43 TraesCS2A01G419500 chr4A 92.371 485 33 2 282 762 624930784 624930300 0.000000e+00 688.0
44 TraesCS2A01G419500 chr4A 95.041 363 18 0 286 648 619770625 619770263 9.370000e-159 571.0
45 TraesCS2A01G419500 chr4A 82.819 454 48 13 7589 8021 551215472 551215028 6.090000e-101 379.0
46 TraesCS2A01G419500 chr4A 97.143 105 3 0 143 247 46056379 46056275 2.390000e-40 178.0
47 TraesCS2A01G419500 chr4A 97.980 99 2 0 149 247 46063307 46063209 1.110000e-38 172.0
48 TraesCS2A01G419500 chr6A 91.757 461 33 3 302 762 11848404 11847949 3.270000e-178 636.0
49 TraesCS2A01G419500 chr1A 94.207 397 23 0 366 762 570149339 570149735 2.570000e-169 606.0
50 TraesCS2A01G419500 chr1A 94.026 385 16 3 315 692 540391945 540392329 2.010000e-160 577.0
51 TraesCS2A01G419500 chr1A 83.178 107 11 6 646 752 90458352 90458253 3.200000e-14 91.6
52 TraesCS2A01G419500 chr5B 95.041 363 14 1 286 648 207155892 207156250 1.210000e-157 568.0
53 TraesCS2A01G419500 chr7B 93.113 363 25 0 286 648 214471142 214471504 4.420000e-147 532.0
54 TraesCS2A01G419500 chr7B 89.109 101 7 4 633 731 427406211 427406309 1.130000e-23 122.0
55 TraesCS2A01G419500 chr3A 90.407 344 11 10 581 902 555114880 555114537 4.610000e-117 433.0
56 TraesCS2A01G419500 chr3A 99.048 105 1 0 143 247 693123475 693123579 1.100000e-43 189.0
57 TraesCS2A01G419500 chr3A 93.684 95 5 1 37 131 555116063 555115970 3.130000e-29 141.0
58 TraesCS2A01G419500 chr3B 96.183 131 5 0 1 131 697139965 697139835 1.820000e-51 215.0
59 TraesCS2A01G419500 chr3B 86.667 120 9 3 6733 6846 732058711 732058593 8.760000e-25 126.0
60 TraesCS2A01G419500 chr7D 92.029 138 4 1 1 131 42242686 42242549 3.960000e-43 187.0
61 TraesCS2A01G419500 chr7D 97.674 43 1 0 201 243 609272539 609272497 3.220000e-09 75.0
62 TraesCS2A01G419500 chr4B 87.248 149 14 5 3703 3849 58060771 58060626 1.860000e-36 165.0
63 TraesCS2A01G419500 chr4B 84.076 157 15 6 7820 7976 68670459 68670605 8.700000e-30 143.0
64 TraesCS2A01G419500 chr1D 89.922 129 6 4 9 130 426415056 426414928 8.640000e-35 159.0


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 TraesCS2A01G419500 chr2A 675078735 675087052 8317 True 15361.000000 15361 100.000000 1 8318 1 chr2A.!!$R3 8317
1 TraesCS2A01G419500 chr2A 675745335 675751671 6336 True 802.000000 1589 85.978400 2137 8157 5 chr2A.!!$R5 6020
2 TraesCS2A01G419500 chr2A 675896510 675897503 993 True 640.000000 640 78.663000 5932 6931 1 chr2A.!!$R4 999
3 TraesCS2A01G419500 chr2D 530257478 530265035 7557 True 3218.750000 10743 92.077000 900 8318 4 chr2D.!!$R3 7418
4 TraesCS2A01G419500 chr2D 102288212 102288832 620 True 706.000000 706 87.676000 286 903 1 chr2D.!!$R1 617
5 TraesCS2A01G419500 chr2D 531348067 531349075 1008 True 628.000000 628 78.337000 5917 6931 1 chr2D.!!$R2 1014
6 TraesCS2A01G419500 chr2D 531259393 531268024 8631 True 595.714286 1408 85.202857 1866 8157 7 chr2D.!!$R4 6291
7 TraesCS2A01G419500 chr2B 630134325 630141896 7571 True 2371.600000 5332 92.645600 900 8318 5 chr2B.!!$R2 7418
8 TraesCS2A01G419500 chr2B 631100458 631106684 6226 True 708.666667 1507 83.145667 2137 8184 6 chr2B.!!$R3 6047
9 TraesCS2A01G419500 chr2B 631202823 631203831 1008 True 667.000000 667 79.014000 5917 6931 1 chr2B.!!$R1 1014
10 TraesCS2A01G419500 chr4D 410438785 410440054 1269 True 1198.000000 2128 88.466000 2128 4205 2 chr4D.!!$R1 2077
11 TraesCS2A01G419500 chr3D 554513152 554514388 1236 False 789.000000 1570 91.340667 2128 4205 3 chr3D.!!$F1 2077
12 TraesCS2A01G419500 chr7A 66695259 66696156 897 False 1238.000000 1238 92.214000 37 899 1 chr7A.!!$F1 862
13 TraesCS2A01G419500 chr3A 555114537 555116063 1526 True 287.000000 433 92.045500 37 902 2 chr3A.!!$R1 865

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
864 1688 1.640917 AGTCTACCAGGAGGCGAAAA 58.359 50.000 0.00 0.0 39.06 2.29 F
1887 2724 0.660005 TGCGCTGTTTGATTTCACGC 60.660 50.000 9.73 0.0 44.70 5.34 F
2789 3678 0.820074 TGTTCGAAACATTGGCGGGT 60.820 50.000 0.00 0.0 36.25 5.28 F
2883 3776 1.261619 GTTGACTGAGGCGAGTTTGTG 59.738 52.381 0.00 0.0 0.00 3.33 F
4174 5107 3.237268 TGGGTGAACCACTTTAGCATT 57.763 42.857 1.16 0.0 46.80 3.56 F
5080 6025 1.098050 ATGTCCCGATTGAGCTTTGC 58.902 50.000 0.00 0.0 0.00 3.68 F
5646 6671 1.446907 AACAGAGGCGAGCAATTCAG 58.553 50.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2782 3671 0.035915 TTGATCGATCAAACCCGCCA 60.036 50.000 32.99 12.61 43.26 5.69 R
3773 4701 0.099436 GCATGAAGCAACCGATCCAC 59.901 55.000 0.00 0.00 44.79 4.02 R
4326 5259 1.614903 CCTTGCCATCAGAAGCAACAA 59.385 47.619 7.06 0.00 43.74 2.83 R
4453 5386 1.773054 GCACATGCTGATCAGAGCGG 61.773 60.000 27.04 13.69 42.32 5.52 R
5901 6965 0.535780 CACAAGGCTTGGCTCACAGA 60.536 55.000 29.26 0.00 34.12 3.41 R
6088 7155 0.546267 ACTGAGTCTGCATCCCCAGT 60.546 55.000 6.24 6.24 34.47 4.00 R
7511 11096 0.030504 TTGAAGAACGTACGACCGCA 59.969 50.000 24.41 12.80 0.00 5.69 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 4.101448 CTGCTTGCCGGCTACCCT 62.101 66.667 29.70 0.00 0.00 4.34
101 102 2.606519 TTGCCGGCTACCCTGAGT 60.607 61.111 29.70 0.00 0.00 3.41
219 498 2.580867 CGCAGGAGAGCACGTAGC 60.581 66.667 0.00 0.00 46.19 3.58
550 841 4.193334 CGCATCTCCGCTCGTCCA 62.193 66.667 0.00 0.00 0.00 4.02
751 1555 4.527583 CTCCCTGCCTGCTCGCTC 62.528 72.222 0.00 0.00 0.00 5.03
848 1672 3.431233 GGCTATATTTTTCGCCGGTAGTC 59.569 47.826 1.90 0.00 32.22 2.59
849 1673 4.304939 GCTATATTTTTCGCCGGTAGTCT 58.695 43.478 1.90 0.00 0.00 3.24
850 1674 5.464168 GCTATATTTTTCGCCGGTAGTCTA 58.536 41.667 1.90 0.00 0.00 2.59
851 1675 5.344396 GCTATATTTTTCGCCGGTAGTCTAC 59.656 44.000 1.90 0.95 0.00 2.59
852 1676 2.368655 TTTTTCGCCGGTAGTCTACC 57.631 50.000 17.94 17.94 45.52 3.18
861 1685 3.491208 GTAGTCTACCAGGAGGCGA 57.509 57.895 0.00 0.00 39.06 5.54
862 1686 1.760192 GTAGTCTACCAGGAGGCGAA 58.240 55.000 0.00 0.00 39.06 4.70
863 1687 2.097825 GTAGTCTACCAGGAGGCGAAA 58.902 52.381 0.00 0.00 39.06 3.46
864 1688 1.640917 AGTCTACCAGGAGGCGAAAA 58.359 50.000 0.00 0.00 39.06 2.29
865 1689 1.975680 AGTCTACCAGGAGGCGAAAAA 59.024 47.619 0.00 0.00 39.06 1.94
887 1711 3.221222 CCTCCTAGGGCTCAACGG 58.779 66.667 9.46 0.00 0.00 4.44
888 1712 2.501610 CTCCTAGGGCTCAACGGC 59.498 66.667 9.46 0.00 37.49 5.68
889 1713 2.038975 TCCTAGGGCTCAACGGCT 59.961 61.111 9.46 0.00 38.46 5.52
890 1714 2.187946 CCTAGGGCTCAACGGCTG 59.812 66.667 0.00 0.00 38.46 4.85
891 1715 2.187946 CTAGGGCTCAACGGCTGG 59.812 66.667 0.00 0.00 38.46 4.85
892 1716 2.284331 TAGGGCTCAACGGCTGGA 60.284 61.111 0.00 0.00 38.46 3.86
893 1717 2.303549 CTAGGGCTCAACGGCTGGAG 62.304 65.000 0.00 0.00 38.46 3.86
894 1718 2.798445 TAGGGCTCAACGGCTGGAGA 62.798 60.000 0.00 0.00 38.46 3.71
895 1719 2.586792 GGCTCAACGGCTGGAGAT 59.413 61.111 0.00 0.00 32.87 2.75
896 1720 1.817099 GGCTCAACGGCTGGAGATG 60.817 63.158 0.00 0.00 32.87 2.90
897 1721 2.467826 GCTCAACGGCTGGAGATGC 61.468 63.158 0.00 0.00 32.87 3.91
898 1722 1.817099 CTCAACGGCTGGAGATGCC 60.817 63.158 0.00 0.00 46.42 4.40
1413 2249 3.271706 TACGGCAGGGTCGACAACG 62.272 63.158 18.91 15.12 41.26 4.10
1437 2273 1.759459 CGGAAGATACCAGAGCCCCC 61.759 65.000 0.00 0.00 0.00 5.40
1850 2687 2.314071 TCGGTAGTTCCCCTCTGAAA 57.686 50.000 0.00 0.00 0.00 2.69
1887 2724 0.660005 TGCGCTGTTTGATTTCACGC 60.660 50.000 9.73 0.00 44.70 5.34
1972 2829 1.465777 GTGATTGCAATTTTGGCTGGC 59.534 47.619 14.33 0.00 0.00 4.85
2686 3575 2.353109 GCATGAAGAACTTTGGGCCTTC 60.353 50.000 4.53 0.00 36.48 3.46
2789 3678 0.820074 TGTTCGAAACATTGGCGGGT 60.820 50.000 0.00 0.00 36.25 5.28
2883 3776 1.261619 GTTGACTGAGGCGAGTTTGTG 59.738 52.381 0.00 0.00 0.00 3.33
3381 4283 8.202811 CCTCTCATTCTCTTGTATCTTGAATCA 58.797 37.037 0.00 0.00 0.00 2.57
3438 4340 5.239306 TCATTACAGTCCTGTTTTGCTTGAG 59.761 40.000 5.10 0.00 41.83 3.02
4174 5107 3.237268 TGGGTGAACCACTTTAGCATT 57.763 42.857 1.16 0.00 46.80 3.56
4326 5259 6.611613 TCAGAAGTCTCCACATTCATTAGT 57.388 37.500 0.00 0.00 0.00 2.24
4453 5386 2.048127 AAGGACGAGCTGCCGTTC 60.048 61.111 15.31 13.75 43.49 3.95
4932 5874 5.449588 CGGCTGAAAATGCTGAACAGATAAT 60.450 40.000 5.97 0.00 38.99 1.28
5030 5975 5.761726 CAGTATAAGATGCTTCCATGCTTGA 59.238 40.000 0.22 0.00 0.00 3.02
5045 5990 4.761235 TGCTTGATTTTGAGCAAGAGAG 57.239 40.909 8.43 0.00 45.19 3.20
5080 6025 1.098050 ATGTCCCGATTGAGCTTTGC 58.902 50.000 0.00 0.00 0.00 3.68
5189 6152 3.876914 TGAGCGAATGGTTAATGATGGAC 59.123 43.478 0.00 0.00 0.00 4.02
5314 6279 4.227512 TCACACAATTTACTTGCTGCTG 57.772 40.909 0.00 0.00 38.50 4.41
5319 6284 5.242393 ACACAATTTACTTGCTGCTGAGAAT 59.758 36.000 0.00 0.00 38.50 2.40
5414 6436 3.065786 ACAGCAGAACATGTGTGTGAAAG 59.934 43.478 0.00 0.00 38.92 2.62
5482 6504 5.172934 TGCCCACTTACGTAATTCTTACTG 58.827 41.667 8.76 0.00 33.98 2.74
5646 6671 1.446907 AACAGAGGCGAGCAATTCAG 58.553 50.000 0.00 0.00 0.00 3.02
5681 6706 2.700371 ACACAGATGACAGAAGTGACCA 59.300 45.455 9.94 0.00 34.47 4.02
5785 6822 7.128077 ACCTCCAGGATCACAAAATATTTGAT 58.872 34.615 9.62 1.05 38.94 2.57
5872 6936 5.243507 TGCCTTTATTGCAAAGATTGTCAGA 59.756 36.000 1.71 0.00 35.40 3.27
5901 6965 6.926826 TGCAATAATCTCGGTATTACGATGTT 59.073 34.615 0.00 0.00 42.62 2.71
6088 7155 3.633986 TGAAGCTGATCTGCGAGATAGAA 59.366 43.478 17.62 0.00 34.53 2.10
6097 7164 1.688735 TGCGAGATAGAACTGGGGATG 59.311 52.381 0.00 0.00 0.00 3.51
6103 7170 2.254152 TAGAACTGGGGATGCAGACT 57.746 50.000 0.00 0.00 0.00 3.24
6942 8015 2.298610 CTACTACGACAGCAGGATGGA 58.701 52.381 0.00 0.00 35.86 3.41
6943 8016 1.781786 ACTACGACAGCAGGATGGAT 58.218 50.000 0.00 0.00 35.86 3.41
7139 8386 1.536766 CCTGCTGTGTTGTGTACATGG 59.463 52.381 0.00 0.00 39.39 3.66
7147 8394 3.059868 GTGTTGTGTACATGGTCGTCAAG 60.060 47.826 0.00 0.00 39.39 3.02
7197 8446 1.331447 CATGCTCGCCGAATTGATTCA 59.669 47.619 4.75 0.00 36.61 2.57
7233 8483 0.457853 TCTGTACATGCTCGCCGAAC 60.458 55.000 0.00 0.00 0.00 3.95
7315 8567 8.148807 TGTGAATCAACAAAGAATAGTTTCGA 57.851 30.769 0.00 0.00 36.93 3.71
7506 8872 4.759782 ACTACTGCATAGTGATGGTTGAC 58.240 43.478 7.69 0.00 42.90 3.18
7507 8873 3.701205 ACTGCATAGTGATGGTTGACA 57.299 42.857 0.00 0.00 35.34 3.58
7508 8874 3.603532 ACTGCATAGTGATGGTTGACAG 58.396 45.455 0.00 0.00 35.34 3.51
7511 11096 3.244875 TGCATAGTGATGGTTGACAGGTT 60.245 43.478 0.00 0.00 33.26 3.50
7517 11102 0.889186 ATGGTTGACAGGTTGCGGTC 60.889 55.000 0.00 0.00 34.63 4.79
7535 11120 3.609175 CGGTCGTACGTTCTTCAAACCTA 60.609 47.826 16.05 0.00 0.00 3.08
7606 11237 3.305964 ACAAGTGATGTGAAGTCGTACG 58.694 45.455 9.53 9.53 41.93 3.67
7796 11451 3.307059 CCTGAGTCCGGACTTCAGAATTT 60.307 47.826 38.22 20.96 42.66 1.82
7798 11453 5.073311 TGAGTCCGGACTTCAGAATTTAG 57.927 43.478 36.55 0.00 42.66 1.85
7905 11684 3.469739 TCACTTGGGTTTCGGTTAGTTC 58.530 45.455 0.00 0.00 0.00 3.01
7989 11777 7.492669 CACAAGAACCTGATAACTAATCGACAT 59.507 37.037 0.00 0.00 37.42 3.06
8028 11816 5.624159 TCAAGAGATGAACACAAACCTGAT 58.376 37.500 0.00 0.00 34.30 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 2.031012 CAGAGCGGGTGCAACTCA 59.969 61.111 0.00 0.00 36.87 3.41
196 475 4.426112 TGCTCTCCTGCGACGCTG 62.426 66.667 22.08 20.24 35.36 5.18
270 549 3.058160 CCACGGCTTTGCTCCCTG 61.058 66.667 0.00 0.00 0.00 4.45
870 1694 3.095347 GCCGTTGAGCCCTAGGAGG 62.095 68.421 11.48 2.99 34.30 4.30
871 1695 2.060980 AGCCGTTGAGCCCTAGGAG 61.061 63.158 11.48 1.06 0.00 3.69
872 1696 2.038975 AGCCGTTGAGCCCTAGGA 59.961 61.111 11.48 0.00 0.00 2.94
873 1697 2.187946 CAGCCGTTGAGCCCTAGG 59.812 66.667 0.06 0.06 0.00 3.02
874 1698 2.187946 CCAGCCGTTGAGCCCTAG 59.812 66.667 0.00 0.00 0.00 3.02
875 1699 2.284331 TCCAGCCGTTGAGCCCTA 60.284 61.111 0.00 0.00 0.00 3.53
876 1700 3.710722 CTCCAGCCGTTGAGCCCT 61.711 66.667 0.00 0.00 0.00 5.19
877 1701 3.036429 ATCTCCAGCCGTTGAGCCC 62.036 63.158 0.00 0.00 0.00 5.19
878 1702 1.817099 CATCTCCAGCCGTTGAGCC 60.817 63.158 0.00 0.00 0.00 4.70
879 1703 2.467826 GCATCTCCAGCCGTTGAGC 61.468 63.158 0.00 0.00 0.00 4.26
880 1704 1.817099 GGCATCTCCAGCCGTTGAG 60.817 63.158 0.00 0.00 43.15 3.02
881 1705 2.268920 GGCATCTCCAGCCGTTGA 59.731 61.111 0.00 0.00 43.15 3.18
887 1711 1.137086 TCGTCTTTAGGCATCTCCAGC 59.863 52.381 0.00 0.00 37.29 4.85
888 1712 2.166459 TGTCGTCTTTAGGCATCTCCAG 59.834 50.000 0.00 0.00 37.29 3.86
889 1713 2.176045 TGTCGTCTTTAGGCATCTCCA 58.824 47.619 0.00 0.00 37.29 3.86
890 1714 2.961526 TGTCGTCTTTAGGCATCTCC 57.038 50.000 0.00 0.00 0.00 3.71
891 1715 4.026475 CGAAATGTCGTCTTTAGGCATCTC 60.026 45.833 0.00 0.00 42.53 2.75
892 1716 3.865745 CGAAATGTCGTCTTTAGGCATCT 59.134 43.478 0.00 0.00 42.53 2.90
893 1717 4.183539 CGAAATGTCGTCTTTAGGCATC 57.816 45.455 0.00 0.00 42.53 3.91
1302 2138 4.151582 GCCGCGGTACTGGCCTAA 62.152 66.667 28.70 0.00 45.73 2.69
1413 2249 2.546162 GGCTCTGGTATCTTCCGTAAGC 60.546 54.545 0.00 0.00 32.36 3.09
1477 2313 3.546714 CTTCCCGAACCACGCCCTT 62.547 63.158 0.00 0.00 41.07 3.95
1887 2724 0.180171 TCGCCCCTATCAACCACATG 59.820 55.000 0.00 0.00 0.00 3.21
1972 2829 0.179111 TCCTCTAAATCAGCACGCGG 60.179 55.000 12.47 0.00 0.00 6.46
2276 3136 4.074970 GTTCAACACCACATCTTCATCCT 58.925 43.478 0.00 0.00 0.00 3.24
2782 3671 0.035915 TTGATCGATCAAACCCGCCA 60.036 50.000 32.99 12.61 43.26 5.69
2883 3776 0.543749 ACTAGAACAGGGATGCCTGC 59.456 55.000 31.27 17.04 41.12 4.85
3132 4032 5.066375 GCAGCACATGGAACTTATCATACAA 59.934 40.000 0.00 0.00 0.00 2.41
3381 4283 7.923414 AACTAAGAATCAAACGCTTCCTATT 57.077 32.000 0.00 0.00 0.00 1.73
3438 4340 3.947834 CACCACATTATCCTCCCACTTTC 59.052 47.826 0.00 0.00 0.00 2.62
3773 4701 0.099436 GCATGAAGCAACCGATCCAC 59.901 55.000 0.00 0.00 44.79 4.02
4174 5107 5.319043 AGACAGTTGATTCCCCAAACTTA 57.681 39.130 0.00 0.00 0.00 2.24
4326 5259 1.614903 CCTTGCCATCAGAAGCAACAA 59.385 47.619 7.06 0.00 43.74 2.83
4453 5386 1.773054 GCACATGCTGATCAGAGCGG 61.773 60.000 27.04 13.69 42.32 5.52
4932 5874 9.090103 TCTTATCTACTTTGAACTCCTTGAAGA 57.910 33.333 0.00 0.00 0.00 2.87
5030 5975 4.630644 TGTCCTCTCTCTTGCTCAAAAT 57.369 40.909 0.00 0.00 0.00 1.82
5045 5990 3.010420 GGACATAGTTTGGCTTGTCCTC 58.990 50.000 12.49 0.00 43.74 3.71
5080 6025 5.021033 ACTTCTGACATCTATGAAGCCTG 57.979 43.478 0.00 0.00 39.39 4.85
5482 6504 9.468532 AAGAAAGAAAATGACAGCAAATACTTC 57.531 29.630 0.00 0.00 0.00 3.01
5646 6671 6.543465 TGTCATCTGTGTATCCAATGAAATCC 59.457 38.462 0.00 0.00 0.00 3.01
5681 6706 1.385206 GGGGGAGAAGGATCCTGCT 60.385 63.158 23.51 23.51 39.50 4.24
5785 6822 1.123861 AGCACTTGAGAGACTGGCCA 61.124 55.000 4.71 4.71 0.00 5.36
5872 6936 6.982141 TCGTAATACCGAGATTATTGCACTTT 59.018 34.615 0.00 0.00 32.18 2.66
5901 6965 0.535780 CACAAGGCTTGGCTCACAGA 60.536 55.000 29.26 0.00 34.12 3.41
6088 7155 0.546267 ACTGAGTCTGCATCCCCAGT 60.546 55.000 6.24 6.24 34.47 4.00
6942 8015 1.000396 GCCTGGAACTGCAGGGAAT 60.000 57.895 19.93 0.44 38.95 3.01
6943 8016 2.436109 GCCTGGAACTGCAGGGAA 59.564 61.111 19.93 0.00 38.95 3.97
7139 8386 1.719780 CGTAAGAGCCAACTTGACGAC 59.280 52.381 0.00 0.00 43.02 4.34
7147 8394 0.109735 GCAAAGCCGTAAGAGCCAAC 60.110 55.000 0.00 0.00 43.02 3.77
7233 8483 5.695851 AGAATGAGTTTGTAACAAGCCAG 57.304 39.130 0.00 0.00 0.00 4.85
7496 8862 0.888736 CCGCAACCTGTCAACCATCA 60.889 55.000 0.00 0.00 0.00 3.07
7497 8863 0.889186 ACCGCAACCTGTCAACCATC 60.889 55.000 0.00 0.00 0.00 3.51
7499 8865 1.525077 GACCGCAACCTGTCAACCA 60.525 57.895 0.00 0.00 0.00 3.67
7500 8866 2.604174 CGACCGCAACCTGTCAACC 61.604 63.158 0.00 0.00 0.00 3.77
7501 8867 0.598158 TACGACCGCAACCTGTCAAC 60.598 55.000 0.00 0.00 0.00 3.18
7503 8869 1.007038 GTACGACCGCAACCTGTCA 60.007 57.895 0.00 0.00 0.00 3.58
7504 8870 2.084681 CGTACGACCGCAACCTGTC 61.085 63.158 10.44 0.00 0.00 3.51
7505 8871 2.049802 CGTACGACCGCAACCTGT 60.050 61.111 10.44 0.00 0.00 4.00
7506 8872 1.611592 GAACGTACGACCGCAACCTG 61.612 60.000 24.41 0.00 0.00 4.00
7507 8873 1.372128 GAACGTACGACCGCAACCT 60.372 57.895 24.41 0.00 0.00 3.50
7508 8874 0.940991 AAGAACGTACGACCGCAACC 60.941 55.000 24.41 1.48 0.00 3.77
7511 11096 0.030504 TTGAAGAACGTACGACCGCA 59.969 50.000 24.41 12.80 0.00 5.69
7517 11102 3.671928 CCACTAGGTTTGAAGAACGTACG 59.328 47.826 15.01 15.01 0.00 3.67
7535 11120 2.281070 CGCAACCTGTCAGCCACT 60.281 61.111 0.00 0.00 0.00 4.00
7606 11237 2.076863 CGGTGTGGGATTTTCTCTGAC 58.923 52.381 0.00 0.00 0.00 3.51
7796 11451 8.033038 CACCACTTAATGAAGTAGTAGTTGCTA 58.967 37.037 0.00 0.00 44.39 3.49
7798 11453 6.872020 TCACCACTTAATGAAGTAGTAGTTGC 59.128 38.462 0.00 0.00 44.39 4.17
7821 11476 9.761504 TGTTTGATATCTTTTTGAAGCATTTCA 57.238 25.926 3.98 0.00 41.44 2.69
8028 11816 5.895928 TCGTGACAATTTGAACCATTTTGA 58.104 33.333 2.79 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.