Multiple sequence alignment - TraesCS1A01G179900

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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 TraesCS1A01G179900 chr1A 100.000 5416 0 0 1960 7375 324857891 324863306 0.000000e+00 10002
1 TraesCS1A01G179900 chr1A 100.000 1743 0 0 1 1743 324855932 324857674 0.000000e+00 3219
2 TraesCS1A01G179900 chr3B 98.171 2187 16 11 2956 5141 344311435 344309272 0.000000e+00 3795
3 TraesCS1A01G179900 chr3B 90.258 893 81 1 1 887 662166920 662167812 0.000000e+00 1162
4 TraesCS1A01G179900 chr3B 89.274 895 89 2 1 888 662461628 662460734 0.000000e+00 1114
5 TraesCS1A01G179900 chr3B 94.297 263 10 4 4876 5138 7305910 7305653 1.490000e-106 398
6 TraesCS1A01G179900 chr3B 85.146 377 14 20 4608 4967 713950944 713951295 1.520000e-91 348
7 TraesCS1A01G179900 chr2B 97.987 2186 22 1 2956 5141 673231060 673228897 0.000000e+00 3773
8 TraesCS1A01G179900 chr2B 93.173 2197 118 27 2953 5139 759270274 759272448 0.000000e+00 3197
9 TraesCS1A01G179900 chr2B 90.639 2190 181 22 2956 5141 19871261 19869092 0.000000e+00 2887
10 TraesCS1A01G179900 chr2B 87.704 2204 238 27 2953 5139 24254274 24256461 0.000000e+00 2538
11 TraesCS1A01G179900 chr2B 90.476 105 2 3 7243 7339 357236795 357236899 1.670000e-26 132
12 TraesCS1A01G179900 chr2B 90.476 105 2 3 7243 7339 391220532 391220636 1.670000e-26 132
13 TraesCS1A01G179900 chr1B 96.036 2195 60 22 2956 5142 673920207 673918032 0.000000e+00 3546
14 TraesCS1A01G179900 chr1B 87.840 2204 236 27 2953 5140 661048495 661050682 0.000000e+00 2556
15 TraesCS1A01G179900 chr1B 89.952 209 10 6 7142 7340 70268258 70268051 7.340000e-65 259
16 TraesCS1A01G179900 chr1B 90.566 106 2 3 7243 7340 672545986 672545881 4.640000e-27 134
17 TraesCS1A01G179900 chr7B 92.847 2195 128 27 2956 5141 665499691 665497517 0.000000e+00 3157
18 TraesCS1A01G179900 chr7B 90.476 105 2 3 7243 7339 54044466 54044570 1.670000e-26 132
19 TraesCS1A01G179900 chr6B 91.746 2193 153 23 2956 5140 21016561 21014389 0.000000e+00 3022
20 TraesCS1A01G179900 chr6B 90.476 105 2 3 7243 7339 596597146 596597250 1.670000e-26 132
21 TraesCS1A01G179900 chr1D 98.584 1695 22 1 5262 6954 265674233 265675927 0.000000e+00 2996
22 TraesCS1A01G179900 chr1D 97.721 1009 6 3 1962 2957 265673056 265674060 0.000000e+00 1720
23 TraesCS1A01G179900 chr1D 98.890 721 8 0 929 1649 265672260 265672980 0.000000e+00 1288
24 TraesCS1A01G179900 chr1D 96.744 430 10 4 6947 7375 265679285 265679711 0.000000e+00 713
25 TraesCS1A01G179900 chr1D 99.206 126 1 0 5138 5263 265674080 265674205 2.070000e-55 228
26 TraesCS1A01G179900 chr6A 97.500 1760 21 2 3378 5137 522053992 522055728 0.000000e+00 2985
27 TraesCS1A01G179900 chr3D 95.541 897 31 3 1 889 85276651 85275756 0.000000e+00 1426
28 TraesCS1A01G179900 chr6D 95.307 895 33 3 1 889 205057916 205058807 0.000000e+00 1411
29 TraesCS1A01G179900 chr4D 94.966 894 38 2 1 888 10398253 10397361 0.000000e+00 1395
30 TraesCS1A01G179900 chr2A 94.314 897 42 4 1 888 670672913 670673809 0.000000e+00 1365
31 TraesCS1A01G179900 chr3A 93.624 894 50 2 1 888 562357788 562356896 0.000000e+00 1328
32 TraesCS1A01G179900 chr5B 91.739 920 53 15 5522 6431 7704871 7705777 0.000000e+00 1256
33 TraesCS1A01G179900 chr5B 91.235 753 60 2 997 1743 7703512 7704264 0.000000e+00 1020
34 TraesCS1A01G179900 chr5B 88.351 558 56 6 1965 2521 7704322 7704871 0.000000e+00 662
35 TraesCS1A01G179900 chr5B 87.151 179 19 2 6861 7035 512980714 512980892 4.510000e-47 200
36 TraesCS1A01G179900 chr5B 91.071 112 10 0 943 1054 7703380 7703491 1.280000e-32 152
37 TraesCS1A01G179900 chr4B 89.721 895 82 5 1 887 68447954 68447062 0.000000e+00 1134
38 TraesCS1A01G179900 chr4B 85.246 183 22 3 6864 7041 641552882 641552700 4.540000e-42 183
39 TraesCS1A01G179900 chr4B 89.189 111 4 3 7243 7345 495572661 495572551 1.670000e-26 132
40 TraesCS1A01G179900 chr4A 90.678 826 77 0 1 826 733362531 733363356 0.000000e+00 1099
41 TraesCS1A01G179900 chr5A 90.378 582 49 3 1965 2546 4950870 4951444 0.000000e+00 758
42 TraesCS1A01G179900 chr5A 90.160 376 21 6 5421 5787 4951440 4951808 6.700000e-130 475
43 TraesCS1A01G179900 chr5A 91.642 335 26 1 1402 1736 4950046 4950378 5.210000e-126 462
44 TraesCS1A01G179900 chr5A 86.782 348 28 5 1068 1408 4944488 4944824 9.040000e-99 372
45 TraesCS1A01G179900 chr5A 92.920 113 8 0 946 1058 4943897 4944009 1.650000e-36 165
46 TraesCS1A01G179900 chrUn 89.189 111 4 3 7243 7345 171012998 171012888 1.670000e-26 132
47 TraesCS1A01G179900 chrUn 90.476 105 2 3 7243 7339 422870842 422870946 1.670000e-26 132


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 TraesCS1A01G179900 chr1A 324855932 324863306 7374 False 6610.5 10002 100.000000 1 7375 2 chr1A.!!$F1 7374
1 TraesCS1A01G179900 chr3B 344309272 344311435 2163 True 3795.0 3795 98.171000 2956 5141 1 chr3B.!!$R2 2185
2 TraesCS1A01G179900 chr3B 662166920 662167812 892 False 1162.0 1162 90.258000 1 887 1 chr3B.!!$F1 886
3 TraesCS1A01G179900 chr3B 662460734 662461628 894 True 1114.0 1114 89.274000 1 888 1 chr3B.!!$R3 887
4 TraesCS1A01G179900 chr2B 673228897 673231060 2163 True 3773.0 3773 97.987000 2956 5141 1 chr2B.!!$R2 2185
5 TraesCS1A01G179900 chr2B 759270274 759272448 2174 False 3197.0 3197 93.173000 2953 5139 1 chr2B.!!$F4 2186
6 TraesCS1A01G179900 chr2B 19869092 19871261 2169 True 2887.0 2887 90.639000 2956 5141 1 chr2B.!!$R1 2185
7 TraesCS1A01G179900 chr2B 24254274 24256461 2187 False 2538.0 2538 87.704000 2953 5139 1 chr2B.!!$F1 2186
8 TraesCS1A01G179900 chr1B 673918032 673920207 2175 True 3546.0 3546 96.036000 2956 5142 1 chr1B.!!$R3 2186
9 TraesCS1A01G179900 chr1B 661048495 661050682 2187 False 2556.0 2556 87.840000 2953 5140 1 chr1B.!!$F1 2187
10 TraesCS1A01G179900 chr7B 665497517 665499691 2174 True 3157.0 3157 92.847000 2956 5141 1 chr7B.!!$R1 2185
11 TraesCS1A01G179900 chr6B 21014389 21016561 2172 True 3022.0 3022 91.746000 2956 5140 1 chr6B.!!$R1 2184
12 TraesCS1A01G179900 chr1D 265672260 265679711 7451 False 1389.0 2996 98.229000 929 7375 5 chr1D.!!$F1 6446
13 TraesCS1A01G179900 chr6A 522053992 522055728 1736 False 2985.0 2985 97.500000 3378 5137 1 chr6A.!!$F1 1759
14 TraesCS1A01G179900 chr3D 85275756 85276651 895 True 1426.0 1426 95.541000 1 889 1 chr3D.!!$R1 888
15 TraesCS1A01G179900 chr6D 205057916 205058807 891 False 1411.0 1411 95.307000 1 889 1 chr6D.!!$F1 888
16 TraesCS1A01G179900 chr4D 10397361 10398253 892 True 1395.0 1395 94.966000 1 888 1 chr4D.!!$R1 887
17 TraesCS1A01G179900 chr2A 670672913 670673809 896 False 1365.0 1365 94.314000 1 888 1 chr2A.!!$F1 887
18 TraesCS1A01G179900 chr3A 562356896 562357788 892 True 1328.0 1328 93.624000 1 888 1 chr3A.!!$R1 887
19 TraesCS1A01G179900 chr5B 7703380 7705777 2397 False 772.5 1256 90.599000 943 6431 4 chr5B.!!$F2 5488
20 TraesCS1A01G179900 chr4B 68447062 68447954 892 True 1134.0 1134 89.721000 1 887 1 chr4B.!!$R1 886
21 TraesCS1A01G179900 chr4A 733362531 733363356 825 False 1099.0 1099 90.678000 1 826 1 chr4A.!!$F1 825
22 TraesCS1A01G179900 chr5A 4950046 4951808 1762 False 565.0 758 90.726667 1402 5787 3 chr5A.!!$F2 4385
23 TraesCS1A01G179900 chr5A 4943897 4944824 927 False 268.5 372 89.851000 946 1408 2 chr5A.!!$F1 462

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
41 42 0.529555 GGGCTCTCGCTGATGAAGAC 60.530 60.000 0.00 0.0 36.09 3.01 F
366 369 0.889186 CCCGCATGTAACTATGGGCC 60.889 60.000 0.00 0.0 39.05 5.80 F
552 555 1.123077 CCTGGATCCGGTGATTCTCA 58.877 55.000 19.51 0.0 0.00 3.27 F
1442 2010 1.153168 GTACACAGGCCCGCATCAT 60.153 57.895 0.00 0.0 0.00 2.45 F
2448 3282 0.460284 CTGGCTTAGGTCGAACGCAT 60.460 55.000 0.00 0.0 0.00 4.73 F
4281 5129 0.445829 CGTGATAACATGCGTGCCAA 59.554 50.000 5.64 0.0 0.00 4.52 F
4811 5663 0.531532 GGTCTGATGCCGGTCTGATG 60.532 60.000 1.90 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 2294 0.177836 CCATGGATCTGCACGTACCA 59.822 55.000 5.56 0.0 35.09 3.25 R
1960 2531 5.308759 ACCTTAAGCTTAAACTCCCAGTACA 59.691 40.000 19.10 0.0 0.00 2.90 R
2448 3282 4.161942 AGCATTAATTAAATGGCACCAGCA 59.838 37.500 16.99 0.0 44.45 4.41 R
2813 3660 1.888512 TGAAGAACAATGGCTGCTTCC 59.111 47.619 0.00 0.0 35.34 3.46 R
4400 5248 0.105593 GATCGAGGGCAGCAAGATGA 59.894 55.000 0.00 0.0 0.00 2.92 R
5282 6204 4.575236 AGCTAGGCCTTTAAATTTCGCTAC 59.425 41.667 12.58 0.0 0.00 3.58 R
6727 7665 1.537348 GCGTCACTTCCACTGTGTACA 60.537 52.381 7.08 0.0 36.83 2.90 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
41 42 0.529555 GGGCTCTCGCTGATGAAGAC 60.530 60.000 0.00 0.00 36.09 3.01
366 369 0.889186 CCCGCATGTAACTATGGGCC 60.889 60.000 0.00 0.00 39.05 5.80
374 377 1.562475 GTAACTATGGGCCCAGGACAA 59.438 52.381 31.97 12.84 0.00 3.18
509 512 2.681591 GGGAACTACCTTGGGGCC 59.318 66.667 0.00 0.00 38.98 5.80
548 551 1.700042 GCCTCCTGGATCCGGTGATT 61.700 60.000 19.51 0.00 34.57 2.57
552 555 1.123077 CCTGGATCCGGTGATTCTCA 58.877 55.000 19.51 0.00 0.00 3.27
599 604 1.534175 GCGCTCGCTACAGACTTACAT 60.534 52.381 0.00 0.00 38.26 2.29
660 665 3.274288 GTGACAAGGATCAAGGATGACC 58.726 50.000 0.00 0.00 38.69 4.02
704 709 6.954487 ATTCTGCAAGATATCAAGCATCAA 57.046 33.333 18.57 15.08 46.36 2.57
828 833 4.012374 CCATGTGTGGCTTTCTTCTATGT 58.988 43.478 0.00 0.00 39.01 2.29
829 834 4.460382 CCATGTGTGGCTTTCTTCTATGTT 59.540 41.667 0.00 0.00 39.01 2.71
950 961 2.744166 CGCATCCACATTCCACATCTCT 60.744 50.000 0.00 0.00 0.00 3.10
1220 1784 1.290203 GTCGACTACCCGTACATCGA 58.710 55.000 8.70 0.00 42.86 3.59
1264 1829 1.293498 CTGCTCTGCGGTTACACCT 59.707 57.895 0.00 0.00 35.66 4.00
1442 2010 1.153168 GTACACAGGCCCGCATCAT 60.153 57.895 0.00 0.00 0.00 2.45
1652 2223 2.202797 CCCGCATGTCTCTGACCG 60.203 66.667 0.00 0.00 0.00 4.79
1707 2278 3.190535 ACAAATACCGCTGCTTAAAGGTG 59.809 43.478 6.44 0.00 37.57 4.00
1719 2290 1.909700 TAAAGGTGAGCAAAGGCAGG 58.090 50.000 0.00 0.00 44.61 4.85
1721 2292 3.376918 GGTGAGCAAAGGCAGGCC 61.377 66.667 0.97 0.97 44.61 5.19
1723 2294 1.980772 GTGAGCAAAGGCAGGCCAT 60.981 57.895 13.63 0.00 44.61 4.40
2333 3167 9.763465 CTAAATTGCTTTAAAATGCTGATTTGG 57.237 29.630 15.93 12.44 31.83 3.28
2366 3200 9.008965 ACATAGTGCATGTTGTTATTGTTTCTA 57.991 29.630 0.00 0.00 46.01 2.10
2447 3281 1.080093 CTGGCTTAGGTCGAACGCA 60.080 57.895 0.00 0.00 0.00 5.24
2448 3282 0.460284 CTGGCTTAGGTCGAACGCAT 60.460 55.000 0.00 0.00 0.00 4.73
2449 3283 0.739462 TGGCTTAGGTCGAACGCATG 60.739 55.000 0.00 0.00 0.00 4.06
2614 3449 1.884579 ACGAGGTTCTTCGCTAAGACA 59.115 47.619 0.00 0.00 41.48 3.41
2689 3524 1.168407 TGCACAGCTCAAAGGCACTC 61.168 55.000 0.00 0.00 38.49 3.51
2813 3660 3.506810 TGTTTTCTTGCTGGAAACAACG 58.493 40.909 12.32 0.00 42.06 4.10
3341 4188 5.513788 GCTCTGCCTATGAAATATCTGGGAA 60.514 44.000 0.00 0.00 0.00 3.97
4165 5013 1.270907 ACGAGTGGCTGGAGAGAAAT 58.729 50.000 0.00 0.00 0.00 2.17
4249 5097 7.546778 TTTCCTTTGGCAACTATTTCAAAAC 57.453 32.000 0.00 0.00 37.61 2.43
4281 5129 0.445829 CGTGATAACATGCGTGCCAA 59.554 50.000 5.64 0.00 0.00 4.52
4803 5655 2.124983 CACTGGGGTCTGATGCCG 60.125 66.667 0.00 0.00 0.00 5.69
4804 5656 3.402681 ACTGGGGTCTGATGCCGG 61.403 66.667 0.00 0.00 0.00 6.13
4805 5657 3.402681 CTGGGGTCTGATGCCGGT 61.403 66.667 1.90 0.00 0.00 5.28
4806 5658 3.391665 CTGGGGTCTGATGCCGGTC 62.392 68.421 1.90 0.00 0.00 4.79
4807 5659 3.083997 GGGGTCTGATGCCGGTCT 61.084 66.667 1.90 0.00 0.00 3.85
4808 5660 2.187946 GGGTCTGATGCCGGTCTG 59.812 66.667 1.90 0.00 0.00 3.51
4809 5661 2.359169 GGGTCTGATGCCGGTCTGA 61.359 63.158 1.90 0.00 0.00 3.27
4810 5662 1.690219 GGGTCTGATGCCGGTCTGAT 61.690 60.000 1.90 0.00 0.00 2.90
4811 5663 0.531532 GGTCTGATGCCGGTCTGATG 60.532 60.000 1.90 0.00 0.00 3.07
4812 5664 1.144716 TCTGATGCCGGTCTGATGC 59.855 57.895 1.90 0.00 0.00 3.91
4813 5665 1.890979 CTGATGCCGGTCTGATGCC 60.891 63.158 1.90 0.00 0.00 4.40
4819 5671 2.202797 CGGTCTGATGCCGGTCTG 60.203 66.667 1.90 0.00 44.98 3.51
4820 5672 2.710902 CGGTCTGATGCCGGTCTGA 61.711 63.158 1.90 0.00 44.98 3.27
4821 5673 1.826024 GGTCTGATGCCGGTCTGAT 59.174 57.895 1.90 0.00 0.00 2.90
4822 5674 0.531532 GGTCTGATGCCGGTCTGATG 60.532 60.000 1.90 0.00 0.00 3.07
4823 5675 1.144716 TCTGATGCCGGTCTGATGC 59.855 57.895 1.90 0.00 0.00 3.91
4824 5676 1.890979 CTGATGCCGGTCTGATGCC 60.891 63.158 1.90 0.00 0.00 4.40
5282 6204 7.201688 CCCTTACAACAAACCTTGGAATTTTTG 60.202 37.037 0.00 1.41 35.49 2.44
5317 6239 2.079925 GGCCTAGCTTCACAAGACTTG 58.920 52.381 13.77 13.77 0.00 3.16
5523 6450 6.842676 ACCAAAAGGAGTATCTCTGTTTCTT 58.157 36.000 0.00 0.00 33.73 2.52
5604 6532 5.120208 GCGCAGTCTATTTAACAGAGAACAA 59.880 40.000 0.30 0.00 0.00 2.83
5771 6702 7.517614 TTAGTTCATGTGTTCTTGCCAAATA 57.482 32.000 0.00 0.00 0.00 1.40
6465 7401 3.270877 GTGACCACCATCCATCACTTAC 58.729 50.000 0.00 0.00 38.72 2.34
6727 7665 1.518056 CCTGCCTCATTGCAACACGT 61.518 55.000 0.00 0.00 41.51 4.49
6738 7676 0.303493 GCAACACGTGTACACAGTGG 59.697 55.000 33.45 25.68 38.86 4.00
6915 7853 3.703127 GCGTTCGGGGAAGGGTCT 61.703 66.667 0.96 0.00 0.00 3.85
6926 7864 1.545651 GGAAGGGTCTGACCACTTTGG 60.546 57.143 26.94 0.00 41.02 3.28
6934 7872 5.318630 GGTCTGACCACTTTGGGTTTATAA 58.681 41.667 21.70 0.00 43.37 0.98
6938 7876 7.608761 GTCTGACCACTTTGGGTTTATAATACA 59.391 37.037 0.00 0.00 43.37 2.29
6943 7881 6.405397 CCACTTTGGGTTTATAATACACAGCC 60.405 42.308 3.91 0.69 32.67 4.85
6949 7887 5.587443 GGGTTTATAATACACAGCCGTTCTT 59.413 40.000 0.00 0.00 0.00 2.52
6978 11280 4.899502 TCTGTAAGAGGCTCTTTTCAAGG 58.100 43.478 32.69 19.63 38.67 3.61
6979 11281 3.412386 TGTAAGAGGCTCTTTTCAAGGC 58.588 45.455 32.69 15.11 37.89 4.35
7015 11317 0.178981 ATGGTCACAAGGCAGCAACT 60.179 50.000 0.00 0.00 0.00 3.16
7024 11326 2.550606 CAAGGCAGCAACTTTACCGTTA 59.449 45.455 0.00 0.00 0.00 3.18
7124 11426 6.232581 TGCTTCTTTTTCATTTGAAAGGGA 57.767 33.333 5.92 6.06 43.90 4.20
7139 11441 0.198696 AGGGAAGGGGAGAAGGGAAA 59.801 55.000 0.00 0.00 0.00 3.13
7187 11489 5.048153 AGGCGCTAAGAAAAGTGAATTTC 57.952 39.130 7.64 0.00 39.16 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 6.908870 TTAGAGATGATTGTTTCCGTGATG 57.091 37.500 0.00 0.00 0.00 3.07
146 147 0.258484 CCCACCAGATTGCCCACATA 59.742 55.000 0.00 0.00 0.00 2.29
366 369 2.819595 CCGCATCGGTTGTCCTGG 60.820 66.667 0.00 0.00 42.73 4.45
509 512 2.029728 GCCTTCGACAATGATCGTTGAG 59.970 50.000 29.89 22.26 42.80 3.02
599 604 1.065491 GCCACACATATGGACTGGACA 60.065 52.381 16.04 0.00 43.02 4.02
660 665 1.969923 TGGGAAAAACTTGCATGGGAG 59.030 47.619 4.44 0.00 0.00 4.30
704 709 3.797559 ACTGCCCTAAAAGCTCTTCTT 57.202 42.857 0.00 0.00 36.34 2.52
750 755 5.573380 AAAGCATGAGCCTCTCCATTATA 57.427 39.130 0.00 0.00 43.56 0.98
828 833 8.956533 TGAACTGTCATTGGAATAATATCGAA 57.043 30.769 0.00 0.00 0.00 3.71
829 834 8.992073 CATGAACTGTCATTGGAATAATATCGA 58.008 33.333 0.00 0.00 42.03 3.59
895 906 8.772250 TCTGGATCCTCACTTTCAGTTATAAAT 58.228 33.333 14.23 0.00 0.00 1.40
896 907 8.146053 TCTGGATCCTCACTTTCAGTTATAAA 57.854 34.615 14.23 0.00 0.00 1.40
897 908 7.733773 TCTGGATCCTCACTTTCAGTTATAA 57.266 36.000 14.23 0.00 0.00 0.98
898 909 7.921041 ATCTGGATCCTCACTTTCAGTTATA 57.079 36.000 14.23 0.00 0.00 0.98
899 910 6.821616 ATCTGGATCCTCACTTTCAGTTAT 57.178 37.500 14.23 0.00 0.00 1.89
900 911 6.227298 GATCTGGATCCTCACTTTCAGTTA 57.773 41.667 14.23 0.00 31.76 2.24
901 912 5.096443 GATCTGGATCCTCACTTTCAGTT 57.904 43.478 14.23 0.00 31.76 3.16
902 913 4.751767 GATCTGGATCCTCACTTTCAGT 57.248 45.455 14.23 0.00 31.76 3.41
914 925 0.683973 ATGCGGTCTGGATCTGGATC 59.316 55.000 2.24 2.24 37.11 3.36
915 926 0.683973 GATGCGGTCTGGATCTGGAT 59.316 55.000 5.94 0.00 41.82 3.41
916 927 1.402896 GGATGCGGTCTGGATCTGGA 61.403 60.000 12.40 0.00 44.29 3.86
917 928 1.070445 GGATGCGGTCTGGATCTGG 59.930 63.158 12.40 0.00 44.29 3.86
918 929 0.531532 GTGGATGCGGTCTGGATCTG 60.532 60.000 12.40 0.00 44.29 2.90
919 930 0.977627 TGTGGATGCGGTCTGGATCT 60.978 55.000 12.40 0.00 44.29 2.75
920 931 0.107456 ATGTGGATGCGGTCTGGATC 59.893 55.000 4.61 4.61 44.14 3.36
921 932 0.548031 AATGTGGATGCGGTCTGGAT 59.452 50.000 0.00 0.00 0.00 3.41
922 933 0.107703 GAATGTGGATGCGGTCTGGA 60.108 55.000 0.00 0.00 0.00 3.86
923 934 1.097547 GGAATGTGGATGCGGTCTGG 61.098 60.000 0.00 0.00 0.00 3.86
924 935 0.392863 TGGAATGTGGATGCGGTCTG 60.393 55.000 0.00 0.00 0.00 3.51
925 936 0.392998 GTGGAATGTGGATGCGGTCT 60.393 55.000 0.00 0.00 0.00 3.85
926 937 0.676466 TGTGGAATGTGGATGCGGTC 60.676 55.000 0.00 0.00 0.00 4.79
927 938 0.034186 ATGTGGAATGTGGATGCGGT 60.034 50.000 0.00 0.00 0.00 5.68
930 941 2.617308 CAGAGATGTGGAATGTGGATGC 59.383 50.000 0.00 0.00 0.00 3.91
950 961 1.270947 GGGTTCCGTGTATTGTGGACA 60.271 52.381 0.00 0.00 0.00 4.02
1220 1784 2.178521 CGCAGTCGTCGGTAGCTT 59.821 61.111 0.00 0.00 0.00 3.74
1264 1829 1.547372 GTAGTAGGTGAGCCCGACAAA 59.453 52.381 0.00 0.00 41.03 2.83
1338 1903 1.896660 GGAGTGGCGGCTGTTGAAA 60.897 57.895 11.43 0.00 0.00 2.69
1442 2010 1.476891 GGTCAATCGTGCAGGAGAGTA 59.523 52.381 15.18 0.00 0.00 2.59
1499 2067 0.804989 CGGTTTTGTCTCCCTGATGC 59.195 55.000 0.00 0.00 0.00 3.91
1707 2278 2.718073 CCATGGCCTGCCTTTGCTC 61.718 63.158 9.97 0.00 38.71 4.26
1719 2290 1.160329 GGATCTGCACGTACCATGGC 61.160 60.000 13.04 0.00 0.00 4.40
1721 2292 2.245159 ATGGATCTGCACGTACCATG 57.755 50.000 0.00 0.00 39.45 3.66
1723 2294 0.177836 CCATGGATCTGCACGTACCA 59.822 55.000 5.56 0.00 35.09 3.25
1959 2530 5.642491 CCTTAAGCTTAAACTCCCAGTACAC 59.358 44.000 19.10 0.00 0.00 2.90
1960 2531 5.308759 ACCTTAAGCTTAAACTCCCAGTACA 59.691 40.000 19.10 0.00 0.00 2.90
2366 3200 5.625150 AGCTTCCTTGTTCATAGACAAAGT 58.375 37.500 0.00 0.00 38.90 2.66
2447 3281 5.058490 GCATTAATTAAATGGCACCAGCAT 58.942 37.500 1.21 0.00 44.45 3.79
2448 3282 4.161942 AGCATTAATTAAATGGCACCAGCA 59.838 37.500 16.99 0.00 44.45 4.41
2449 3283 4.696455 AGCATTAATTAAATGGCACCAGC 58.304 39.130 16.99 6.05 44.45 4.85
2614 3449 4.005650 CTCCGCCAAGTATGATGCATTAT 58.994 43.478 9.16 9.16 0.00 1.28
2813 3660 1.888512 TGAAGAACAATGGCTGCTTCC 59.111 47.619 0.00 0.00 35.34 3.46
3341 4188 7.453126 CCTGAGAGTAGAATATGTAACAGGGAT 59.547 40.741 0.00 0.00 37.91 3.85
4165 5013 8.778059 ACCATTTTATAATTAGGACCTGACAGA 58.222 33.333 3.53 0.00 0.00 3.41
4249 5097 3.050619 GTTATCACGAGTAAGGATGGCG 58.949 50.000 0.00 0.00 0.00 5.69
4281 5129 2.630232 TGGGATTTCCAGGCCATTTTT 58.370 42.857 5.01 0.00 41.46 1.94
4400 5248 0.105593 GATCGAGGGCAGCAAGATGA 59.894 55.000 0.00 0.00 0.00 2.92
4533 5381 3.991121 TCGAACGACATGCTTATCAAACA 59.009 39.130 0.00 0.00 0.00 2.83
4569 5417 1.317613 AGAGCATGCCGTGAAAACAA 58.682 45.000 15.66 0.00 0.00 2.83
4803 5655 0.531532 CATCAGACCGGCATCAGACC 60.532 60.000 0.00 0.00 0.00 3.85
4804 5656 1.156645 GCATCAGACCGGCATCAGAC 61.157 60.000 0.00 0.00 0.00 3.51
4805 5657 1.144716 GCATCAGACCGGCATCAGA 59.855 57.895 0.00 0.00 0.00 3.27
4806 5658 1.890979 GGCATCAGACCGGCATCAG 60.891 63.158 0.00 0.00 0.00 2.90
4807 5659 2.190313 GGCATCAGACCGGCATCA 59.810 61.111 0.00 0.00 0.00 3.07
4808 5660 2.592861 GGGCATCAGACCGGCATC 60.593 66.667 0.00 0.00 29.21 3.91
4814 5666 4.101448 ACCAGCGGGCATCAGACC 62.101 66.667 1.46 0.00 40.75 3.85
4815 5667 2.599645 ATCACCAGCGGGCATCAGAC 62.600 60.000 1.46 0.00 37.90 3.51
4816 5668 2.315781 GATCACCAGCGGGCATCAGA 62.316 60.000 1.46 0.00 37.90 3.27
4817 5669 1.890979 GATCACCAGCGGGCATCAG 60.891 63.158 1.46 0.00 37.90 2.90
4818 5670 2.190313 GATCACCAGCGGGCATCA 59.810 61.111 1.46 0.00 37.90 3.07
4819 5671 1.890979 CAGATCACCAGCGGGCATC 60.891 63.158 1.46 5.03 37.90 3.91
4820 5672 1.337384 TACAGATCACCAGCGGGCAT 61.337 55.000 1.46 0.00 37.90 4.40
4821 5673 1.987306 TACAGATCACCAGCGGGCA 60.987 57.895 1.46 0.00 37.90 5.36
4822 5674 1.521681 GTACAGATCACCAGCGGGC 60.522 63.158 1.46 0.00 37.90 6.13
4823 5675 0.179100 CAGTACAGATCACCAGCGGG 60.179 60.000 0.00 0.00 41.29 6.13
4824 5676 0.807667 GCAGTACAGATCACCAGCGG 60.808 60.000 0.00 0.00 0.00 5.52
5282 6204 4.575236 AGCTAGGCCTTTAAATTTCGCTAC 59.425 41.667 12.58 0.00 0.00 3.58
5317 6239 6.364165 CCAGCATATTAGTAATGTTTGCATGC 59.636 38.462 11.82 11.82 37.19 4.06
5523 6450 6.188400 TCACGCATGCATTATTAGTTCAAA 57.812 33.333 19.57 0.00 0.00 2.69
5771 6702 7.475137 TTTAGGGCAAAAGTAAGCAACATAT 57.525 32.000 0.00 0.00 0.00 1.78
6465 7401 2.135933 GAAGTGGAAGTGACAAGTCGG 58.864 52.381 0.00 0.00 0.00 4.79
6727 7665 1.537348 GCGTCACTTCCACTGTGTACA 60.537 52.381 7.08 0.00 36.83 2.90
6877 7815 1.717937 CGCAAGGAGCTACATGCAC 59.282 57.895 24.82 0.00 45.94 4.57
6907 7845 1.545651 CCCAAAGTGGTCAGACCCTTC 60.546 57.143 17.59 7.68 37.50 3.46
6915 7853 7.232188 TGTGTATTATAAACCCAAAGTGGTCA 58.768 34.615 0.00 0.00 37.76 4.02
6926 7864 6.673154 AAGAACGGCTGTGTATTATAAACC 57.327 37.500 0.00 0.00 0.00 3.27
6934 7872 7.769044 ACAGAAATATAAAGAACGGCTGTGTAT 59.231 33.333 0.00 0.00 33.32 2.29
6938 7876 8.038944 TCTTACAGAAATATAAAGAACGGCTGT 58.961 33.333 0.00 0.00 37.73 4.40
6943 7881 8.649973 AGCCTCTTACAGAAATATAAAGAACG 57.350 34.615 0.00 0.00 0.00 3.95
6973 11275 0.534203 GTCACGGGTTCAAGCCTTGA 60.534 55.000 10.64 10.64 40.97 3.02
6974 11276 1.515521 GGTCACGGGTTCAAGCCTTG 61.516 60.000 5.76 5.76 36.48 3.61
6976 11278 1.705997 AAGGTCACGGGTTCAAGCCT 61.706 55.000 3.64 0.00 32.48 4.58
6978 11280 1.737793 CATAAGGTCACGGGTTCAAGC 59.262 52.381 0.00 0.00 0.00 4.01
6979 11281 2.356135 CCATAAGGTCACGGGTTCAAG 58.644 52.381 0.00 0.00 0.00 3.02
7003 11305 0.951558 ACGGTAAAGTTGCTGCCTTG 59.048 50.000 0.00 0.00 0.00 3.61
7015 11317 1.431496 GAGCCTTGCGTAACGGTAAA 58.569 50.000 0.00 0.00 0.00 2.01
7024 11326 4.035102 GGAAGGGGAGCCTTGCGT 62.035 66.667 0.00 0.00 0.00 5.24
7098 11400 7.609532 TCCCTTTCAAATGAAAAAGAAGCAAAA 59.390 29.630 9.63 0.00 42.72 2.44
7124 11426 2.385263 ATCCTTTCCCTTCTCCCCTT 57.615 50.000 0.00 0.00 0.00 3.95
7187 11489 3.922240 GCACAGCAACAGTTCATTAATGG 59.078 43.478 15.36 1.99 0.00 3.16


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

AutoCloner maintained by Alex Coulton.