Multiple sequence alignment - TraesCS2A01G193400

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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 TraesCS2A01G193400 chr2A 100.000 4415 0 0 1 4415 161859306 161854892 0.000000e+00 8154.0
1 TraesCS2A01G193400 chr2A 82.075 106 11 6 342 447 610980700 610980603 2.830000e-12 84.2
2 TraesCS2A01G193400 chr2D 96.233 3212 91 16 912 4118 139057920 139061106 0.000000e+00 5234.0
3 TraesCS2A01G193400 chr2D 90.265 339 25 6 488 819 139057520 139057857 1.890000e-118 436.0
4 TraesCS2A01G193400 chr2D 90.789 76 6 1 327 401 53579725 53579650 2.810000e-17 100.0
5 TraesCS2A01G193400 chr2B 95.347 3202 107 14 1228 4415 197717836 197721009 0.000000e+00 5049.0
6 TraesCS2A01G193400 chr2B 89.939 825 59 14 1 819 197716517 197717323 0.000000e+00 1042.0
7 TraesCS2A01G193400 chr2B 91.724 145 5 2 847 984 197717311 197717455 1.250000e-45 195.0
8 TraesCS2A01G193400 chr4B 86.957 115 7 1 329 443 465734104 465733998 6.000000e-24 122.0
9 TraesCS2A01G193400 chr5D 85.714 112 8 1 332 443 255594293 255594396 1.300000e-20 111.0
10 TraesCS2A01G193400 chr4D 85.088 114 9 1 330 443 419441890 419441995 4.670000e-20 110.0
11 TraesCS2A01G193400 chr3D 85.586 111 8 1 334 444 551077967 551078069 4.670000e-20 110.0
12 TraesCS2A01G193400 chr5A 82.787 122 11 5 323 442 306496567 306496454 2.810000e-17 100.0
13 TraesCS2A01G193400 chr5A 97.297 37 1 0 3567 3603 390566761 390566725 3.690000e-06 63.9
14 TraesCS2A01G193400 chr6A 82.569 109 9 8 336 443 597695776 597695677 2.190000e-13 87.9
15 TraesCS2A01G193400 chr6D 88.889 54 6 0 3575 3628 315743996 315743943 2.850000e-07 67.6
16 TraesCS2A01G193400 chr5B 85.714 63 7 2 3567 3628 352131024 352131085 1.020000e-06 65.8
17 TraesCS2A01G193400 chr7D 87.273 55 5 2 3575 3628 633070964 633070911 1.330000e-05 62.1


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 TraesCS2A01G193400 chr2A 161854892 161859306 4414 True 8154.000000 8154 100.000000 1 4415 1 chr2A.!!$R1 4414
1 TraesCS2A01G193400 chr2D 139057520 139061106 3586 False 2835.000000 5234 93.249000 488 4118 2 chr2D.!!$F1 3630
2 TraesCS2A01G193400 chr2B 197716517 197721009 4492 False 2095.333333 5049 92.336667 1 4415 3 chr2B.!!$F1 4414

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
152 153 0.038744 CACTCCCATTGGCAAGGACT 59.961 55.000 14.30 0.0 0.0 3.85 F
1221 1248 0.034380 TCCACCTCTACACCCTCTCG 60.034 60.000 0.00 0.0 0.0 4.04 F
2037 2200 1.538419 GCGCTGGTGACCTTATACTCC 60.538 57.143 2.11 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1942 0.037790 TCGCATTCCACACGACATCA 60.038 50.0 0.0 0.0 0.0 3.07 R
2214 2377 0.177373 GACCTCCGTGAACATACCCC 59.823 60.0 0.0 0.0 0.0 4.95 R
3780 3949 0.668401 GTTCGTGGTTACTGGTCGGG 60.668 60.0 0.0 0.0 0.0 5.14 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
18 19 1.669440 AGACACAACGCCGGTACAT 59.331 52.632 1.90 0.00 0.00 2.29
22 23 2.046700 CAACGCCGGTACATGGGT 60.047 61.111 1.90 2.16 0.00 4.51
30 31 1.134610 CCGGTACATGGGTTAGGTGAC 60.135 57.143 0.00 0.00 0.00 3.67
46 47 3.775316 AGGTGACGAGAACCTTATTCCAT 59.225 43.478 0.00 0.00 46.14 3.41
62 63 3.074857 TCCATATTTAGGGAGCCACCT 57.925 47.619 2.05 2.05 44.75 4.00
76 77 2.031870 GCCACCTTCACCTTGTCTTTT 58.968 47.619 0.00 0.00 0.00 2.27
107 108 4.067896 ACACAAACCATAAGCAGACTCTG 58.932 43.478 1.21 1.21 34.12 3.35
108 109 4.202357 ACACAAACCATAAGCAGACTCTGA 60.202 41.667 10.45 0.00 32.44 3.27
109 110 4.756642 CACAAACCATAAGCAGACTCTGAA 59.243 41.667 10.45 0.00 32.44 3.02
110 111 5.239306 CACAAACCATAAGCAGACTCTGAAA 59.761 40.000 10.45 0.00 32.44 2.69
111 112 5.827797 ACAAACCATAAGCAGACTCTGAAAA 59.172 36.000 10.45 0.00 32.44 2.29
112 113 5.948992 AACCATAAGCAGACTCTGAAAAC 57.051 39.130 10.45 0.00 32.44 2.43
113 114 4.973168 ACCATAAGCAGACTCTGAAAACA 58.027 39.130 10.45 0.00 32.44 2.83
114 115 4.757149 ACCATAAGCAGACTCTGAAAACAC 59.243 41.667 10.45 0.00 32.44 3.32
115 116 4.154918 CCATAAGCAGACTCTGAAAACACC 59.845 45.833 10.45 0.00 32.44 4.16
116 117 3.567478 AAGCAGACTCTGAAAACACCT 57.433 42.857 10.45 0.00 32.44 4.00
122 123 5.971792 GCAGACTCTGAAAACACCTAAAAAC 59.028 40.000 10.45 0.00 32.44 2.43
129 130 5.837437 TGAAAACACCTAAAAACGATGCAT 58.163 33.333 0.00 0.00 0.00 3.96
152 153 0.038744 CACTCCCATTGGCAAGGACT 59.961 55.000 14.30 0.00 0.00 3.85
157 158 1.496429 CCCATTGGCAAGGACTAGGAT 59.504 52.381 14.30 0.00 0.00 3.24
165 166 1.392710 AAGGACTAGGATCCACCGCG 61.393 60.000 15.82 0.00 44.74 6.46
218 219 2.492012 CAGATAGGAAGCATCACCAGC 58.508 52.381 0.00 0.00 0.00 4.85
219 220 1.419387 AGATAGGAAGCATCACCAGCC 59.581 52.381 0.00 0.00 0.00 4.85
242 243 1.550976 AGGAGAAAAGTCCTAGGCACG 59.449 52.381 2.96 0.00 45.83 5.34
243 244 1.549170 GGAGAAAAGTCCTAGGCACGA 59.451 52.381 2.96 0.00 33.30 4.35
248 252 1.629043 AAGTCCTAGGCACGAAGTCA 58.371 50.000 2.96 0.00 41.61 3.41
258 262 4.245054 CGAAGTCACTCGTGGGTG 57.755 61.111 0.00 0.00 38.44 4.61
272 276 2.384828 GTGGGTGGGAGAAAAGTGTTT 58.615 47.619 0.00 0.00 0.00 2.83
274 278 2.024846 TGGGTGGGAGAAAAGTGTTTCA 60.025 45.455 2.35 0.00 44.82 2.69
280 284 4.340950 TGGGAGAAAAGTGTTTCATTGGAC 59.659 41.667 2.35 0.00 44.82 4.02
350 354 4.213674 GTCCGTTTGTATTGGTTTTCGTC 58.786 43.478 0.00 0.00 0.00 4.20
352 356 3.557508 CGTTTGTATTGGTTTTCGTCCC 58.442 45.455 0.00 0.00 0.00 4.46
359 363 2.847959 TGGTTTTCGTCCCGTTTTTC 57.152 45.000 0.00 0.00 0.00 2.29
373 377 4.408694 CCGTTTTTCGTAAATTAGCTGGG 58.591 43.478 0.00 0.00 37.94 4.45
381 385 4.574828 TCGTAAATTAGCTGGGCAATTCTC 59.425 41.667 0.00 0.00 0.00 2.87
387 391 2.720915 AGCTGGGCAATTCTCTTCTTC 58.279 47.619 0.00 0.00 0.00 2.87
438 442 4.570930 ACTTTTTGCCTCCGTTTTGAAAA 58.429 34.783 0.00 0.00 0.00 2.29
492 496 3.765026 CAACCCGAATTGATTTTACCCG 58.235 45.455 0.00 0.00 0.00 5.28
542 546 5.525012 TGGCATCTTCGAATTGTCTTCATAG 59.475 40.000 12.35 0.00 0.00 2.23
593 597 5.011635 GGGACATGGAAAACCAAACTACAAT 59.988 40.000 0.00 0.00 0.00 2.71
634 639 2.482839 GCCAACTTAGTTTGCTGCCAAA 60.483 45.455 13.00 0.00 38.56 3.28
647 652 2.874086 GCTGCCAAATTTTTGTCAAGCT 59.126 40.909 11.50 0.00 36.45 3.74
670 675 6.183360 GCTAGAGTAATTTTGCTTCCACTCAG 60.183 42.308 0.00 0.00 35.87 3.35
695 700 3.693300 TTCGTCGTCGTATTTTTCAGC 57.307 42.857 1.33 0.00 38.33 4.26
729 734 5.843673 TGCTCAAATTTGGTCTACACAAA 57.156 34.783 17.90 0.00 41.50 2.83
788 797 5.855045 GGTACCTCTCTTATACCACAATGG 58.145 45.833 4.06 0.00 45.02 3.16
796 805 9.613428 CTCTCTTATACCACAATGGACATTTTA 57.387 33.333 0.84 0.00 40.96 1.52
805 814 8.875168 ACCACAATGGACATTTTATTTTTAGGA 58.125 29.630 0.84 0.00 40.96 2.94
811 820 9.719355 ATGGACATTTTATTTTTAGGAAACCAC 57.281 29.630 0.00 0.00 0.00 4.16
812 821 8.705594 TGGACATTTTATTTTTAGGAAACCACA 58.294 29.630 0.00 0.00 0.00 4.17
813 822 9.719355 GGACATTTTATTTTTAGGAAACCACAT 57.281 29.630 0.00 0.00 0.00 3.21
822 831 9.625747 ATTTTTAGGAAACCACATGAACAAATT 57.374 25.926 0.00 0.00 0.00 1.82
823 832 9.454859 TTTTTAGGAAACCACATGAACAAATTT 57.545 25.926 0.00 0.00 0.00 1.82
824 833 9.454859 TTTTAGGAAACCACATGAACAAATTTT 57.545 25.926 0.00 0.00 0.00 1.82
828 837 9.625747 AGGAAACCACATGAACAAATTTTATTT 57.374 25.926 0.00 0.00 0.00 1.40
853 862 0.465460 TGAGGCAGAACCACCACAAC 60.465 55.000 0.00 0.00 43.14 3.32
897 906 2.560981 CGCCTAAACCCCAAACAAGATT 59.439 45.455 0.00 0.00 0.00 2.40
898 907 3.366985 CGCCTAAACCCCAAACAAGATTC 60.367 47.826 0.00 0.00 0.00 2.52
905 914 5.535753 ACCCCAAACAAGATTCTCAAAAG 57.464 39.130 0.00 0.00 0.00 2.27
1221 1248 0.034380 TCCACCTCTACACCCTCTCG 60.034 60.000 0.00 0.00 0.00 4.04
1257 1420 2.028337 GCGATCCTCTTCCGCTCC 59.972 66.667 0.00 0.00 44.83 4.70
1779 1942 4.090761 TGAAGAGGTTGATGCAGAGTTT 57.909 40.909 0.00 0.00 0.00 2.66
1806 1969 2.352651 CGTGTGGAATGCGATGATTTCT 59.647 45.455 0.00 0.00 0.00 2.52
1914 2077 1.541379 TTACTAGCGTCCTGAGTGCA 58.459 50.000 0.00 0.00 0.00 4.57
1938 2101 4.122046 GTGCAAATGCTGGTTTCTTTCTT 58.878 39.130 6.97 0.00 42.66 2.52
2037 2200 1.538419 GCGCTGGTGACCTTATACTCC 60.538 57.143 2.11 0.00 0.00 3.85
2196 2359 9.494271 GAGATGCCATATAAAAGTGAGTTATCA 57.506 33.333 0.00 0.00 0.00 2.15
2214 2377 3.683365 TCATGGATGGTGATGGTATCG 57.317 47.619 0.00 0.00 0.00 2.92
2223 2386 2.370849 GGTGATGGTATCGGGGTATGTT 59.629 50.000 0.00 0.00 0.00 2.71
2226 2389 3.070446 TGATGGTATCGGGGTATGTTCAC 59.930 47.826 0.00 0.00 0.00 3.18
2235 2398 1.136500 GGGTATGTTCACGGAGGTCTC 59.864 57.143 0.00 0.00 0.00 3.36
2236 2399 2.100989 GGTATGTTCACGGAGGTCTCT 58.899 52.381 0.00 0.00 0.00 3.10
2337 2500 1.608055 CTGCATGTGGTGAACTTGGA 58.392 50.000 0.00 0.00 35.10 3.53
2652 2815 2.758423 TCATGCTGGCTTAGTAGACGAA 59.242 45.455 0.00 0.00 29.01 3.85
2655 2818 1.749634 GCTGGCTTAGTAGACGAAGGA 59.250 52.381 4.94 0.00 29.01 3.36
2718 2881 2.038295 CCCTGGAGAAGATCACTATGCC 59.962 54.545 0.00 0.00 0.00 4.40
2735 2898 0.536006 GCCCGGCTGATAGATTTGCT 60.536 55.000 0.71 0.00 0.00 3.91
2752 2915 3.567579 CTTGGCCGGGCTGGAAGAA 62.568 63.158 29.87 12.74 42.00 2.52
2754 2917 2.517166 GGCCGGGCTGGAAGAATC 60.517 66.667 22.87 0.00 42.00 2.52
2871 3034 1.922135 AACTTGGTGCTTATGCGGCG 61.922 55.000 0.51 0.51 43.34 6.46
3006 3169 1.278127 GATCGTGGGGTGAAGAAGGAA 59.722 52.381 0.00 0.00 0.00 3.36
3066 3229 2.246789 GTGTTTGTTGTTGGTGACACG 58.753 47.619 0.00 0.00 42.67 4.49
3207 3370 5.338614 AGGAATACGTATTATTTGCGCAC 57.661 39.130 20.37 5.21 36.86 5.34
3243 3406 6.038936 TGGCAGTTAGTTTTGGACTTCTAAAC 59.961 38.462 0.00 0.00 39.86 2.01
3258 3421 2.639839 TCTAAACTTGCCTCTTGGAGCT 59.360 45.455 0.00 0.00 34.57 4.09
3648 3817 1.398390 CCGGCTCTCTTTTTGAATCCG 59.602 52.381 0.00 0.00 33.59 4.18
3780 3949 7.117956 GGACTGATCTTTTGTTTACTGTCCTAC 59.882 40.741 0.00 0.00 40.53 3.18
3787 3956 1.895131 GTTTACTGTCCTACCCGACCA 59.105 52.381 0.00 0.00 31.35 4.02
3802 3971 1.287041 GACCAGTAACCACGAACCGC 61.287 60.000 0.00 0.00 0.00 5.68
3824 3993 0.539986 GTTTCGTATGCCTCCCTCCA 59.460 55.000 0.00 0.00 0.00 3.86
3831 4000 2.043248 GCCTCCCTCCAGTCCGTA 60.043 66.667 0.00 0.00 0.00 4.02
3833 4002 1.465200 GCCTCCCTCCAGTCCGTATC 61.465 65.000 0.00 0.00 0.00 2.24
3834 4003 0.828343 CCTCCCTCCAGTCCGTATCC 60.828 65.000 0.00 0.00 0.00 2.59
3844 4013 3.576982 CCAGTCCGTATCCCAGCTTTATA 59.423 47.826 0.00 0.00 0.00 0.98
3938 4107 1.211949 CTGGCCGAAGAATTCCCCTTA 59.788 52.381 0.65 0.00 43.81 2.69
3944 4113 3.181469 CCGAAGAATTCCCCTTATCGTGA 60.181 47.826 0.65 0.00 43.81 4.35
3982 4159 3.866651 ACAGTCTATGGTTGATCTGTGC 58.133 45.455 0.00 0.00 35.32 4.57
4144 4321 0.872388 GTTAAGTTCAGGTGCCGTGG 59.128 55.000 0.00 0.00 0.00 4.94
4156 4333 2.867472 CCGTGGCACGTTCCATTC 59.133 61.111 34.74 0.00 40.58 2.67
4161 4338 2.356135 GTGGCACGTTCCATTCATAGT 58.644 47.619 10.90 0.00 38.57 2.12
4168 4345 4.634004 CACGTTCCATTCATAGTGCCTAAA 59.366 41.667 0.00 0.00 0.00 1.85
4246 4423 2.463589 TAGGCAAGGAACTGGTGGCG 62.464 60.000 0.00 0.00 44.92 5.69
4247 4424 4.043200 GCAAGGAACTGGTGGCGC 62.043 66.667 0.00 0.00 40.86 6.53
4248 4425 3.726517 CAAGGAACTGGTGGCGCG 61.727 66.667 0.00 0.00 40.86 6.86
4250 4427 3.767630 AAGGAACTGGTGGCGCGTT 62.768 57.895 8.43 0.00 40.86 4.84
4251 4428 2.357760 GGAACTGGTGGCGCGTTA 60.358 61.111 8.43 0.00 0.00 3.18
4252 4429 2.674084 GGAACTGGTGGCGCGTTAC 61.674 63.158 8.43 7.19 0.00 2.50
4253 4430 1.957186 GAACTGGTGGCGCGTTACA 60.957 57.895 8.43 1.47 0.00 2.41
4254 4431 1.897398 GAACTGGTGGCGCGTTACAG 61.897 60.000 8.43 13.73 35.40 2.74
4255 4432 3.788766 CTGGTGGCGCGTTACAGC 61.789 66.667 18.13 18.13 35.77 4.40
4256 4433 4.610714 TGGTGGCGCGTTACAGCA 62.611 61.111 21.83 21.83 42.15 4.41
4257 4434 3.788766 GGTGGCGCGTTACAGCAG 61.789 66.667 19.40 0.00 36.85 4.24
4258 4435 2.736995 GTGGCGCGTTACAGCAGA 60.737 61.111 8.43 0.00 36.85 4.26
4259 4436 2.100631 GTGGCGCGTTACAGCAGAT 61.101 57.895 8.43 0.00 36.85 2.90
4260 4437 2.100031 TGGCGCGTTACAGCAGATG 61.100 57.895 8.43 0.00 36.85 2.90
4301 4478 2.629137 AGTCATTTTCACAATGCTGGCA 59.371 40.909 0.00 0.00 0.00 4.92
4302 4479 3.259876 AGTCATTTTCACAATGCTGGCAT 59.740 39.130 1.86 1.86 38.46 4.40
4307 4484 1.141019 CACAATGCTGGCATGAGGC 59.859 57.895 8.91 0.00 43.74 4.70
4322 4499 1.134699 TGAGGCTGGAAAGATACTGCG 60.135 52.381 0.00 0.00 33.07 5.18
4342 4529 2.190578 GAGCTCCCCGGACAATGG 59.809 66.667 0.73 0.00 0.00 3.16
4343 4530 2.285368 AGCTCCCCGGACAATGGA 60.285 61.111 0.73 0.00 0.00 3.41
4344 4531 1.910580 GAGCTCCCCGGACAATGGAA 61.911 60.000 0.73 0.00 0.00 3.53
4345 4532 1.452108 GCTCCCCGGACAATGGAAG 60.452 63.158 0.73 0.00 0.00 3.46
4346 4533 1.224592 CTCCCCGGACAATGGAAGG 59.775 63.158 0.73 0.00 0.00 3.46
4347 4534 1.540367 TCCCCGGACAATGGAAGGT 60.540 57.895 0.73 0.00 0.00 3.50
4348 4535 0.252789 TCCCCGGACAATGGAAGGTA 60.253 55.000 0.73 0.00 0.00 3.08
4349 4536 0.107361 CCCCGGACAATGGAAGGTAC 60.107 60.000 0.73 0.00 0.00 3.34
4350 4537 0.616371 CCCGGACAATGGAAGGTACA 59.384 55.000 0.73 0.00 0.00 2.90
4351 4538 1.003812 CCCGGACAATGGAAGGTACAA 59.996 52.381 0.73 0.00 0.00 2.41
4355 4542 3.556213 CGGACAATGGAAGGTACAACTGA 60.556 47.826 0.00 0.00 0.00 3.41
4382 4569 5.688621 GTGTATACTTCATCAACGGCGAATA 59.311 40.000 16.62 0.00 0.00 1.75
4384 4571 2.967362 ACTTCATCAACGGCGAATACA 58.033 42.857 16.62 0.00 0.00 2.29
4387 4574 5.113383 ACTTCATCAACGGCGAATACATAA 58.887 37.500 16.62 0.00 0.00 1.90
4404 4591 8.627208 AATACATAATTTAGTGCCTGATCTGG 57.373 34.615 14.07 14.07 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.090210 TCTCGTCACCTAACCCATGTA 57.910 47.619 0.00 0.00 0.00 2.29
18 19 0.971386 GGTTCTCGTCACCTAACCCA 59.029 55.000 0.00 0.00 36.24 4.51
22 23 4.773674 TGGAATAAGGTTCTCGTCACCTAA 59.226 41.667 3.81 0.00 44.48 2.69
30 31 7.676947 TCCCTAAATATGGAATAAGGTTCTCG 58.323 38.462 0.00 0.00 29.06 4.04
46 47 2.508300 GGTGAAGGTGGCTCCCTAAATA 59.492 50.000 1.14 0.00 36.75 1.40
62 63 4.644234 TCATGCTCAAAAAGACAAGGTGAA 59.356 37.500 0.00 0.00 0.00 3.18
76 77 4.321156 GCTTATGGTTTGTGTCATGCTCAA 60.321 41.667 0.00 0.00 0.00 3.02
107 108 5.918011 TCATGCATCGTTTTTAGGTGTTTTC 59.082 36.000 0.00 0.00 0.00 2.29
108 109 5.837437 TCATGCATCGTTTTTAGGTGTTTT 58.163 33.333 0.00 0.00 0.00 2.43
109 110 5.446143 TCATGCATCGTTTTTAGGTGTTT 57.554 34.783 0.00 0.00 0.00 2.83
110 111 4.615912 GCTCATGCATCGTTTTTAGGTGTT 60.616 41.667 0.00 0.00 39.41 3.32
111 112 3.119849 GCTCATGCATCGTTTTTAGGTGT 60.120 43.478 0.00 0.00 39.41 4.16
112 113 3.119884 TGCTCATGCATCGTTTTTAGGTG 60.120 43.478 0.00 0.00 45.31 4.00
113 114 3.081061 TGCTCATGCATCGTTTTTAGGT 58.919 40.909 0.00 0.00 45.31 3.08
114 115 3.763097 TGCTCATGCATCGTTTTTAGG 57.237 42.857 0.00 0.00 45.31 2.69
129 130 0.609957 CTTGCCAATGGGAGTGCTCA 60.610 55.000 0.00 0.00 35.59 4.26
138 139 2.487986 GGATCCTAGTCCTTGCCAATGG 60.488 54.545 3.84 0.00 35.32 3.16
152 153 1.038681 TGTAAGCGCGGTGGATCCTA 61.039 55.000 13.41 0.00 0.00 2.94
157 158 2.125310 CCATGTAAGCGCGGTGGA 60.125 61.111 13.41 0.00 31.59 4.02
185 186 1.339610 CCTATCTGCCTCGTCTCTTGG 59.660 57.143 0.00 0.00 0.00 3.61
218 219 1.757699 CCTAGGACTTTTCTCCTCCGG 59.242 57.143 1.05 0.00 40.12 5.14
219 220 1.137282 GCCTAGGACTTTTCTCCTCCG 59.863 57.143 14.75 0.00 40.12 4.63
225 226 2.633481 ACTTCGTGCCTAGGACTTTTCT 59.367 45.455 14.75 0.00 0.00 2.52
242 243 1.004918 CCCACCCACGAGTGACTTC 60.005 63.158 4.59 0.00 40.34 3.01
243 244 1.458777 TCCCACCCACGAGTGACTT 60.459 57.895 4.59 0.00 40.34 3.01
248 252 0.396811 CTTTTCTCCCACCCACGAGT 59.603 55.000 0.00 0.00 0.00 4.18
257 261 4.340950 GTCCAATGAAACACTTTTCTCCCA 59.659 41.667 0.00 0.00 41.64 4.37
258 262 4.556699 CGTCCAATGAAACACTTTTCTCCC 60.557 45.833 0.00 0.00 41.64 4.30
272 276 0.795698 CAATGCGTCACGTCCAATGA 59.204 50.000 0.00 0.00 0.00 2.57
274 278 1.233950 TGCAATGCGTCACGTCCAAT 61.234 50.000 0.00 0.00 0.00 3.16
280 284 1.010935 AGTCTCTGCAATGCGTCACG 61.011 55.000 0.00 0.00 0.00 4.35
359 363 4.576463 AGAGAATTGCCCAGCTAATTTACG 59.424 41.667 0.00 0.00 0.00 3.18
542 546 8.570068 TTTTGTAGGGATATGTTAAGTTCCAC 57.430 34.615 0.00 0.00 0.00 4.02
559 563 5.478407 GTTTTCCATGTCCCATTTTGTAGG 58.522 41.667 0.00 0.00 0.00 3.18
593 597 5.057819 TGGCGTTAAGTTTTCACTACATCA 58.942 37.500 0.00 0.00 30.68 3.07
634 639 9.196552 GCAAAATTACTCTAGCTTGACAAAAAT 57.803 29.630 0.00 0.00 0.00 1.82
647 652 6.769512 ACTGAGTGGAAGCAAAATTACTCTA 58.230 36.000 0.00 0.00 36.43 2.43
670 675 5.189625 TGAAAAATACGACGACGAAACAAC 58.810 37.500 15.32 0.88 42.66 3.32
695 700 5.443170 CCAAATTTGAGCAAATAAACGAGCG 60.443 40.000 19.86 0.00 39.88 5.03
796 805 9.625747 AATTTGTTCATGTGGTTTCCTAAAAAT 57.374 25.926 0.00 0.00 0.00 1.82
821 830 9.267084 GTGGTTCTGCCTCAAAATAAAATAAAA 57.733 29.630 0.00 0.00 38.35 1.52
822 831 7.875554 GGTGGTTCTGCCTCAAAATAAAATAAA 59.124 33.333 0.00 0.00 38.35 1.40
823 832 7.015682 TGGTGGTTCTGCCTCAAAATAAAATAA 59.984 33.333 0.00 0.00 38.35 1.40
824 833 6.495181 TGGTGGTTCTGCCTCAAAATAAAATA 59.505 34.615 0.00 0.00 38.35 1.40
825 834 5.306678 TGGTGGTTCTGCCTCAAAATAAAAT 59.693 36.000 0.00 0.00 38.35 1.82
826 835 4.651503 TGGTGGTTCTGCCTCAAAATAAAA 59.348 37.500 0.00 0.00 38.35 1.52
827 836 4.038642 GTGGTGGTTCTGCCTCAAAATAAA 59.961 41.667 0.00 0.00 38.35 1.40
828 837 3.572255 GTGGTGGTTCTGCCTCAAAATAA 59.428 43.478 0.00 0.00 38.35 1.40
829 838 3.153919 GTGGTGGTTCTGCCTCAAAATA 58.846 45.455 0.00 0.00 38.35 1.40
830 839 1.963515 GTGGTGGTTCTGCCTCAAAAT 59.036 47.619 0.00 0.00 38.35 1.82
831 840 1.341482 TGTGGTGGTTCTGCCTCAAAA 60.341 47.619 0.00 0.00 38.35 2.44
832 841 0.257328 TGTGGTGGTTCTGCCTCAAA 59.743 50.000 0.00 0.00 38.35 2.69
833 842 0.257328 TTGTGGTGGTTCTGCCTCAA 59.743 50.000 0.00 0.00 36.34 3.02
834 843 0.465460 GTTGTGGTGGTTCTGCCTCA 60.465 55.000 0.00 0.00 38.35 3.86
835 844 1.507141 CGTTGTGGTGGTTCTGCCTC 61.507 60.000 0.00 0.00 38.35 4.70
836 845 1.525995 CGTTGTGGTGGTTCTGCCT 60.526 57.895 0.00 0.00 38.35 4.75
837 846 1.098712 TTCGTTGTGGTGGTTCTGCC 61.099 55.000 0.00 0.00 37.90 4.85
838 847 0.028902 GTTCGTTGTGGTGGTTCTGC 59.971 55.000 0.00 0.00 0.00 4.26
839 848 1.374560 TGTTCGTTGTGGTGGTTCTG 58.625 50.000 0.00 0.00 0.00 3.02
840 849 2.341846 ATGTTCGTTGTGGTGGTTCT 57.658 45.000 0.00 0.00 0.00 3.01
841 850 2.616842 AGAATGTTCGTTGTGGTGGTTC 59.383 45.455 0.00 0.00 0.00 3.62
842 851 2.650322 AGAATGTTCGTTGTGGTGGTT 58.350 42.857 0.00 0.00 0.00 3.67
843 852 2.341846 AGAATGTTCGTTGTGGTGGT 57.658 45.000 0.00 0.00 0.00 4.16
844 853 2.616376 TGAAGAATGTTCGTTGTGGTGG 59.384 45.455 0.00 0.00 0.00 4.61
845 854 3.559655 TCTGAAGAATGTTCGTTGTGGTG 59.440 43.478 0.00 0.00 0.00 4.17
853 862 5.387855 CGTTCTGAACTCTGAAGAATGTTCG 60.388 44.000 17.60 0.00 40.93 3.95
1234 1397 4.610714 GAAGAGGATCGCCGGGGC 62.611 72.222 14.85 0.00 42.67 5.80
1426 1589 2.182030 GGAGCGGAACACGGAGAG 59.818 66.667 0.00 0.00 44.51 3.20
1779 1942 0.037790 TCGCATTCCACACGACATCA 60.038 50.000 0.00 0.00 0.00 3.07
1806 1969 0.621082 TTCCCGATTGCACATACCCA 59.379 50.000 0.00 0.00 0.00 4.51
1914 2077 3.756933 AAGAAACCAGCATTTGCACAT 57.243 38.095 5.20 0.00 45.16 3.21
2037 2200 3.059352 ACAGAAATCTTCCCGGACTTG 57.941 47.619 0.73 0.00 0.00 3.16
2196 2359 1.630369 CCCGATACCATCACCATCCAT 59.370 52.381 0.00 0.00 0.00 3.41
2214 2377 0.177373 GACCTCCGTGAACATACCCC 59.823 60.000 0.00 0.00 0.00 4.95
2223 2386 1.351350 TCTTCTGAGAGACCTCCGTGA 59.649 52.381 0.00 0.00 38.66 4.35
2226 2389 1.066908 GCATCTTCTGAGAGACCTCCG 59.933 57.143 0.00 0.00 38.66 4.63
2337 2500 0.242017 GCTTTCCATGCTTCAACGCT 59.758 50.000 0.00 0.00 0.00 5.07
2378 2541 1.166531 GCTTGCCTCGAAACCACACT 61.167 55.000 0.00 0.00 0.00 3.55
2406 2569 4.270008 ACATGGTTAGTAGTGCATTTCCC 58.730 43.478 0.00 0.00 0.00 3.97
2652 2815 8.827832 TCATGGACTCAAAATATTGAAATCCT 57.172 30.769 16.43 5.87 44.64 3.24
2691 2854 3.390639 AGTGATCTTCTCCAGGGCTAATG 59.609 47.826 0.00 0.00 0.00 1.90
2718 2881 1.605710 CCAAGCAAATCTATCAGCCGG 59.394 52.381 0.00 0.00 0.00 6.13
2735 2898 2.837031 GATTCTTCCAGCCCGGCCAA 62.837 60.000 5.55 0.00 33.14 4.52
2752 2915 3.889815 TCAAATCCATTGCTTCTCCGAT 58.110 40.909 0.00 0.00 38.98 4.18
2754 2917 3.628942 TGATCAAATCCATTGCTTCTCCG 59.371 43.478 0.00 0.00 38.98 4.63
2817 2980 1.561643 TCCGACAGCCAGAGAGAATT 58.438 50.000 0.00 0.00 0.00 2.17
2871 3034 5.237048 GGTATCATCTCAAAGAGCTGATCC 58.763 45.833 14.47 12.19 40.16 3.36
3006 3169 1.762522 CTATCCAGCTGCATCCGGGT 61.763 60.000 8.66 0.00 0.00 5.28
3066 3229 2.098293 ATGCGCTTCCGGATGTTTC 58.902 52.632 17.82 8.47 44.11 2.78
3243 3406 1.277557 ACTGTAGCTCCAAGAGGCAAG 59.722 52.381 0.00 0.00 33.74 4.01
3773 3942 1.549203 GTTACTGGTCGGGTAGGACA 58.451 55.000 0.00 0.00 38.70 4.02
3780 3949 0.668401 GTTCGTGGTTACTGGTCGGG 60.668 60.000 0.00 0.00 0.00 5.14
3787 3956 2.048877 CGGCGGTTCGTGGTTACT 60.049 61.111 0.00 0.00 0.00 2.24
3802 3971 1.523032 GGGAGGCATACGAAACCGG 60.523 63.158 0.00 0.00 0.00 5.28
3824 3993 6.070938 GGTAATATAAAGCTGGGATACGGACT 60.071 42.308 0.00 0.00 37.60 3.85
3831 4000 5.850046 AGCTGGTAATATAAAGCTGGGAT 57.150 39.130 0.00 0.00 44.14 3.85
3833 4002 6.476378 ACATAGCTGGTAATATAAAGCTGGG 58.524 40.000 6.29 1.38 45.33 4.45
3834 4003 7.094634 CCAACATAGCTGGTAATATAAAGCTGG 60.095 40.741 6.29 1.70 45.33 4.85
3844 4013 7.954666 ATTTACAACCAACATAGCTGGTAAT 57.045 32.000 0.00 0.00 46.75 1.89
3879 4048 2.441750 GTGCCCCTGGATTAGAATGGTA 59.558 50.000 0.00 0.00 0.00 3.25
3886 4055 1.146263 GTCCGTGCCCCTGGATTAG 59.854 63.158 0.00 0.00 36.48 1.73
3887 4056 2.372074 GGTCCGTGCCCCTGGATTA 61.372 63.158 0.00 0.00 36.48 1.75
3938 4107 8.678593 TGTATAGTTAACAGATCTCTCACGAT 57.321 34.615 8.61 0.00 0.00 3.73
3982 4159 3.679980 CCATCTGTCACTTGTTTACGAGG 59.320 47.826 0.00 0.00 0.00 4.63
4099 4276 2.999355 GAGAAGAAAGCTACTGTGCCTG 59.001 50.000 0.00 0.00 0.00 4.85
4144 4321 1.064060 GGCACTATGAATGGAACGTGC 59.936 52.381 0.00 0.00 44.97 5.34
4147 4324 5.527214 TCATTTAGGCACTATGAATGGAACG 59.473 40.000 0.00 0.00 42.38 3.95
4156 4333 6.057533 TCCATTGTCTCATTTAGGCACTATG 58.942 40.000 0.00 0.00 40.31 2.23
4161 4338 6.064060 CCTTATCCATTGTCTCATTTAGGCA 58.936 40.000 0.00 0.00 38.31 4.75
4168 4345 7.384524 TTCATCTCCTTATCCATTGTCTCAT 57.615 36.000 0.00 0.00 0.00 2.90
4246 4423 1.927174 ACGATTCATCTGCTGTAACGC 59.073 47.619 0.00 0.00 0.00 4.84
4247 4424 3.179048 TCACGATTCATCTGCTGTAACG 58.821 45.455 0.00 0.00 0.00 3.18
4248 4425 5.496387 CATTCACGATTCATCTGCTGTAAC 58.504 41.667 0.00 0.00 0.00 2.50
4250 4427 4.122046 CCATTCACGATTCATCTGCTGTA 58.878 43.478 0.00 0.00 0.00 2.74
4251 4428 2.941064 CCATTCACGATTCATCTGCTGT 59.059 45.455 0.00 0.00 0.00 4.40
4252 4429 2.289820 CCCATTCACGATTCATCTGCTG 59.710 50.000 0.00 0.00 0.00 4.41
4253 4430 2.092753 ACCCATTCACGATTCATCTGCT 60.093 45.455 0.00 0.00 0.00 4.24
4254 4431 2.292267 ACCCATTCACGATTCATCTGC 58.708 47.619 0.00 0.00 0.00 4.26
4255 4432 4.201950 GGAAACCCATTCACGATTCATCTG 60.202 45.833 0.00 0.00 39.98 2.90
4256 4433 3.947834 GGAAACCCATTCACGATTCATCT 59.052 43.478 0.00 0.00 39.98 2.90
4257 4434 4.292977 GGAAACCCATTCACGATTCATC 57.707 45.455 0.00 0.00 39.98 2.92
4301 4478 2.484417 CGCAGTATCTTTCCAGCCTCAT 60.484 50.000 0.00 0.00 0.00 2.90
4302 4479 1.134699 CGCAGTATCTTTCCAGCCTCA 60.135 52.381 0.00 0.00 0.00 3.86
4307 4484 2.349886 GCTCAACGCAGTATCTTTCCAG 59.650 50.000 0.00 0.00 45.00 3.86
4322 4499 1.026718 CATTGTCCGGGGAGCTCAAC 61.027 60.000 17.19 7.62 0.00 3.18
4331 4508 0.616371 TGTACCTTCCATTGTCCGGG 59.384 55.000 0.00 0.00 0.00 5.73
4342 4529 8.773404 AAGTATACACAATCAGTTGTACCTTC 57.227 34.615 5.50 0.00 46.49 3.46
4343 4530 8.372459 TGAAGTATACACAATCAGTTGTACCTT 58.628 33.333 5.50 0.00 46.49 3.50
4344 4531 7.903145 TGAAGTATACACAATCAGTTGTACCT 58.097 34.615 5.50 0.00 46.49 3.08
4345 4532 8.718102 ATGAAGTATACACAATCAGTTGTACC 57.282 34.615 5.50 0.00 46.49 3.34
4346 4533 9.366216 TGATGAAGTATACACAATCAGTTGTAC 57.634 33.333 5.50 0.00 46.49 2.90
4347 4534 9.936759 TTGATGAAGTATACACAATCAGTTGTA 57.063 29.630 5.50 0.00 46.49 2.41
4349 4536 7.899841 CGTTGATGAAGTATACACAATCAGTTG 59.100 37.037 5.50 2.02 41.20 3.16
4350 4537 7.064609 CCGTTGATGAAGTATACACAATCAGTT 59.935 37.037 5.50 0.00 0.00 3.16
4351 4538 6.535150 CCGTTGATGAAGTATACACAATCAGT 59.465 38.462 5.50 0.00 0.00 3.41
4355 4542 4.270084 CGCCGTTGATGAAGTATACACAAT 59.730 41.667 5.50 0.00 0.00 2.71
4361 4548 5.834169 TGTATTCGCCGTTGATGAAGTATA 58.166 37.500 0.00 0.00 0.00 1.47
4373 4560 4.212636 GGCACTAAATTATGTATTCGCCGT 59.787 41.667 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.