Multiple sequence alignment - TraesCS3B01G301100

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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 TraesCS3B01G301100 chr3B 100.000 7337 0 0 1 7337 483000778 482993442 0.000000e+00 13549.0
1 TraesCS3B01G301100 chr3B 100.000 35 0 0 4669 4703 482996008 482995974 1.710000e-06 65.8
2 TraesCS3B01G301100 chr3B 100.000 35 0 0 4771 4805 482996110 482996076 1.710000e-06 65.8
3 TraesCS3B01G301100 chr3D 95.205 7278 153 58 22 7196 371897982 371890798 0.000000e+00 11326.0
4 TraesCS3B01G301100 chr3D 82.759 116 17 3 7190 7302 527004744 527004859 4.680000e-17 100.0
5 TraesCS3B01G301100 chr3D 100.000 35 0 0 4669 4703 371893242 371893208 1.710000e-06 65.8
6 TraesCS3B01G301100 chr3D 100.000 34 0 0 4771 4804 371893344 371893311 6.150000e-06 63.9
7 TraesCS3B01G301100 chr3A 91.142 4753 251 61 22 4714 493134566 493129924 0.000000e+00 6288.0
8 TraesCS3B01G301100 chr3A 90.453 2493 158 43 4708 7149 493129688 493127225 0.000000e+00 3212.0
9 TraesCS3B01G301100 chr3A 81.164 292 46 4 5993 6275 493128351 493128060 7.410000e-55 226.0
10 TraesCS3B01G301100 chr3A 78.744 207 31 10 6107 6305 493128387 493128186 7.730000e-25 126.0
11 TraesCS3B01G301100 chr3A 90.000 90 7 2 7191 7278 721240191 721240280 1.670000e-21 115.0
12 TraesCS3B01G301100 chr3A 100.000 35 0 0 4669 4703 493129626 493129592 1.710000e-06 65.8
13 TraesCS3B01G301100 chr3A 97.143 35 1 0 4771 4805 493129969 493129935 7.950000e-05 60.2
14 TraesCS3B01G301100 chr2A 87.052 363 15 5 175 533 740483824 740484158 1.490000e-101 381.0
15 TraesCS3B01G301100 chr2D 87.368 95 11 1 7193 7286 612704875 612704781 2.800000e-19 108.0
16 TraesCS3B01G301100 chr2D 86.316 95 12 1 7202 7295 14815818 14815724 1.300000e-17 102.0
17 TraesCS3B01G301100 chr7A 85.859 99 12 2 7193 7289 669410685 669410783 3.620000e-18 104.0
18 TraesCS3B01G301100 chr7A 87.640 89 10 1 7202 7289 615335476 615335564 1.300000e-17 102.0
19 TraesCS3B01G301100 chr2B 88.235 85 10 0 7202 7286 134608145 134608229 1.300000e-17 102.0
20 TraesCS3B01G301100 chr5D 83.962 106 13 4 7183 7286 557210930 557211033 1.680000e-16 99.0
21 TraesCS3B01G301100 chr7B 84.000 100 14 2 7193 7290 244219306 244219405 2.180000e-15 95.3
22 TraesCS3B01G301100 chr1A 95.349 43 2 0 4587 4629 537057576 537057534 1.320000e-07 69.4
23 TraesCS3B01G301100 chr5B 97.222 36 1 0 4587 4622 643906056 643906021 2.210000e-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 TraesCS3B01G301100 chr3B 482993442 483000778 7336 True 13549.00 13549 100.0000 1 7337 1 chr3B.!!$R1 7336
1 TraesCS3B01G301100 chr3D 371890798 371897982 7184 True 11326.00 11326 95.2050 22 7196 1 chr3D.!!$R1 7174
2 TraesCS3B01G301100 chr3A 493127225 493134566 7341 True 1983.56 6288 88.3006 22 7149 5 chr3A.!!$R2 7127

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
83 84 1.756538 CCAAAATATGCCTCGCCCTTT 59.243 47.619 0.00 0.00 0.00 3.11 F
1064 1093 0.178767 TGCTCCTTGTCCATCCATCG 59.821 55.000 0.00 0.00 0.00 3.84 F
1135 1169 0.322008 GGGGTTTGTCTGCTCTCTGG 60.322 60.000 0.00 0.00 0.00 3.86 F
1192 1234 0.663153 GCGGTTCCATTGCCATCTAC 59.337 55.000 0.00 0.00 0.00 2.59 F
2915 3009 1.356938 GGTCAAGCACCGTAGCTAAC 58.643 55.000 0.00 2.15 45.89 2.34 F
3516 3615 0.238289 ACGCAGCACAAAGTATGCAC 59.762 50.000 0.00 0.00 45.92 4.57 F
3743 3845 0.738389 CGTCCAGCAAGTTTGTGGTT 59.262 50.000 10.90 0.00 33.75 3.67 F
4049 4151 4.928661 TGAGCAAGCTTTATTCTTCGTC 57.071 40.909 0.00 0.00 0.00 4.20 F
5711 6066 2.233676 CCTGCGTATAGTGATATGCCCA 59.766 50.000 6.67 0.00 46.16 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 1203 0.178975 AATGGAACCGCCCAACTCAA 60.179 50.000 0.00 0.0 40.04 3.02 R
2423 2502 3.257393 CATTCGATCCAGCATAGTAGCC 58.743 50.000 0.00 0.0 34.23 3.93 R
3059 3158 3.944087 AGCAGTTCACCCTAGAATTGAC 58.056 45.455 3.79 0.0 37.40 3.18 R
3203 3302 9.555727 GGACTATAAGCAGTATAACCATTTTCA 57.444 33.333 0.00 0.0 0.00 2.69 R
3906 4008 0.478072 TCTGCTCCTGGGCTCAAAAA 59.522 50.000 8.32 0.0 0.00 1.94 R
4893 5242 3.001330 GTCGAAATTGAGGATTAGGCACG 59.999 47.826 0.00 0.0 0.00 5.34 R
4959 5308 3.451178 GCAATACCTCTTGAGTGTCCCTA 59.549 47.826 0.00 0.0 0.00 3.53 R
5726 6081 3.640498 TCCATGATGCCACAAAGTGAAAA 59.360 39.130 0.00 0.0 35.23 2.29 R
6855 7281 1.139256 GGAGATCTCCGGTCCCTTTTC 59.861 57.143 25.78 0.0 40.36 2.29 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
83 84 1.756538 CCAAAATATGCCTCGCCCTTT 59.243 47.619 0.00 0.00 0.00 3.11
151 152 3.490759 CAGGCCATCGTCACGCAC 61.491 66.667 5.01 0.00 0.00 5.34
155 156 2.815211 CCATCGTCACGCACCTGG 60.815 66.667 0.00 0.00 0.00 4.45
299 306 3.415212 CCAGGATCAAGAAAAGCACAGA 58.585 45.455 0.00 0.00 0.00 3.41
342 349 3.384789 AGCGATGGTAGTAGCTTTCATCA 59.615 43.478 0.00 0.00 36.41 3.07
343 350 3.738282 GCGATGGTAGTAGCTTTCATCAG 59.262 47.826 0.00 0.00 35.32 2.90
344 351 4.499865 GCGATGGTAGTAGCTTTCATCAGA 60.500 45.833 0.00 0.00 35.32 3.27
345 352 5.777802 CGATGGTAGTAGCTTTCATCAGAT 58.222 41.667 0.00 0.00 35.32 2.90
346 353 5.861251 CGATGGTAGTAGCTTTCATCAGATC 59.139 44.000 0.00 0.00 35.32 2.75
347 354 6.515696 CGATGGTAGTAGCTTTCATCAGATCA 60.516 42.308 0.00 0.00 35.32 2.92
348 355 6.154203 TGGTAGTAGCTTTCATCAGATCAG 57.846 41.667 0.00 0.00 0.00 2.90
349 356 5.893824 TGGTAGTAGCTTTCATCAGATCAGA 59.106 40.000 0.00 0.00 0.00 3.27
350 357 6.040278 TGGTAGTAGCTTTCATCAGATCAGAG 59.960 42.308 0.00 0.00 0.00 3.35
351 358 6.040391 GGTAGTAGCTTTCATCAGATCAGAGT 59.960 42.308 0.00 0.00 0.00 3.24
352 359 6.543430 AGTAGCTTTCATCAGATCAGAGTT 57.457 37.500 0.00 0.00 0.00 3.01
353 360 7.652524 AGTAGCTTTCATCAGATCAGAGTTA 57.347 36.000 0.00 0.00 0.00 2.24
354 361 8.072321 AGTAGCTTTCATCAGATCAGAGTTAA 57.928 34.615 0.00 0.00 0.00 2.01
355 362 8.535335 AGTAGCTTTCATCAGATCAGAGTTAAA 58.465 33.333 0.00 0.00 0.00 1.52
356 363 9.155975 GTAGCTTTCATCAGATCAGAGTTAAAA 57.844 33.333 0.00 0.00 0.00 1.52
357 364 8.627208 AGCTTTCATCAGATCAGAGTTAAAAA 57.373 30.769 0.00 0.00 0.00 1.94
382 389 6.576662 AGAAAGATCAGAGTTAGTTGACGA 57.423 37.500 0.00 0.00 0.00 4.20
445 452 4.020662 GCAACCACCAATATTTTCCTTCCA 60.021 41.667 0.00 0.00 0.00 3.53
483 493 5.300752 ACTGATAGTAATAGTGCCACATGC 58.699 41.667 0.00 0.00 41.77 4.06
502 513 3.254060 TGCTACGCTGTCTCTCATTTTC 58.746 45.455 0.00 0.00 0.00 2.29
585 600 7.123397 TGCTATGATTAACTCCTCCTATGCTAG 59.877 40.741 0.00 0.00 0.00 3.42
586 601 7.123547 GCTATGATTAACTCCTCCTATGCTAGT 59.876 40.741 0.00 0.00 0.00 2.57
603 618 3.919197 GCTAGTACCACTTTCGAGTTCAC 59.081 47.826 0.00 0.00 0.00 3.18
630 650 4.981389 CTCACGAGAGAAAAAGGTGAAG 57.019 45.455 3.49 0.00 44.98 3.02
808 837 2.682136 TTCCCAGCCGTCCGATCA 60.682 61.111 0.00 0.00 0.00 2.92
1064 1093 0.178767 TGCTCCTTGTCCATCCATCG 59.821 55.000 0.00 0.00 0.00 3.84
1126 1160 3.075882 TCTTGGATCAATGGGGTTTGTCT 59.924 43.478 0.00 0.00 0.00 3.41
1128 1162 1.478105 GGATCAATGGGGTTTGTCTGC 59.522 52.381 0.00 0.00 0.00 4.26
1129 1163 2.450476 GATCAATGGGGTTTGTCTGCT 58.550 47.619 0.00 0.00 0.00 4.24
1135 1169 0.322008 GGGGTTTGTCTGCTCTCTGG 60.322 60.000 0.00 0.00 0.00 3.86
1162 1201 5.277825 TGTTTTCATTTTCTAACCAGTGCG 58.722 37.500 0.00 0.00 0.00 5.34
1190 1232 3.924507 GCGGTTCCATTGCCATCT 58.075 55.556 0.00 0.00 0.00 2.90
1191 1233 3.094386 GCGGTTCCATTGCCATCTA 57.906 52.632 0.00 0.00 0.00 1.98
1192 1234 0.663153 GCGGTTCCATTGCCATCTAC 59.337 55.000 0.00 0.00 0.00 2.59
1202 1244 4.252073 CATTGCCATCTACTAGCTCCATC 58.748 47.826 0.00 0.00 0.00 3.51
1425 1473 4.620723 TCTGATCTGGCTTTAAGGGACTA 58.379 43.478 0.00 0.00 38.49 2.59
1525 1603 4.095483 CCCAGTTCAATCTGCTATTGACAC 59.905 45.833 12.71 13.08 37.71 3.67
1667 1745 5.045578 ACTCCCATTTATTGACAGCTACACT 60.046 40.000 0.00 0.00 0.00 3.55
1730 1808 2.032550 CCCTTATTGATCTGTTGCTGCG 59.967 50.000 0.00 0.00 0.00 5.18
2322 2400 8.088981 GGTACTATTATCCAGGTGTGTAGAATG 58.911 40.741 0.00 0.00 0.00 2.67
2423 2502 3.870538 TTGGAGGATGGGATGAGAATG 57.129 47.619 0.00 0.00 0.00 2.67
2783 2877 4.766373 ACCACACAATATGCTGTCATGAAA 59.234 37.500 0.00 0.00 34.22 2.69
2915 3009 1.356938 GGTCAAGCACCGTAGCTAAC 58.643 55.000 0.00 2.15 45.89 2.34
2927 3021 6.455246 GCACCGTAGCTAACTTAGTTTGATTC 60.455 42.308 10.47 1.58 0.00 2.52
3059 3158 7.513371 AGTTATTATCGAGTCCTTGGTCTAG 57.487 40.000 0.00 0.00 0.00 2.43
3203 3302 7.830201 TCTTATTTGTGTTATGTTCCGGGTTAT 59.170 33.333 0.00 0.00 0.00 1.89
3212 3311 3.768878 TGTTCCGGGTTATGAAAATGGT 58.231 40.909 0.00 0.00 0.00 3.55
3268 3367 3.181479 GGCGTGGATAGTCAGTATGTCAA 60.181 47.826 0.00 0.00 37.40 3.18
3299 3398 2.622064 ATTACTCCGCTGTGATTCCC 57.378 50.000 0.00 0.00 0.00 3.97
3455 3554 8.576442 CAAACAAACTACCCTACAAGATCAAAT 58.424 33.333 0.00 0.00 0.00 2.32
3516 3615 0.238289 ACGCAGCACAAAGTATGCAC 59.762 50.000 0.00 0.00 45.92 4.57
3576 3675 1.075374 TGCCAACCTCTGCCAATAACT 59.925 47.619 0.00 0.00 0.00 2.24
3743 3845 0.738389 CGTCCAGCAAGTTTGTGGTT 59.262 50.000 10.90 0.00 33.75 3.67
4049 4151 4.928661 TGAGCAAGCTTTATTCTTCGTC 57.071 40.909 0.00 0.00 0.00 4.20
4363 4467 7.624360 TTTCATATTTAGTGTGCCTTGGTAG 57.376 36.000 0.00 0.00 0.00 3.18
5029 5378 5.636965 CCGGTATGATCAGAGCTAGAATTTG 59.363 44.000 16.70 0.00 0.00 2.32
5227 5577 5.045797 ACCTATTTCCTTACCACCTTCAGTC 60.046 44.000 0.00 0.00 0.00 3.51
5670 6021 9.672086 GCAGTGTGTGTCTTGTTATTAATAAAA 57.328 29.630 9.48 1.55 0.00 1.52
5711 6066 2.233676 CCTGCGTATAGTGATATGCCCA 59.766 50.000 6.67 0.00 46.16 5.36
5882 6240 7.782049 TCGTTCATGATTAGTGATAGAAGGTT 58.218 34.615 0.00 0.00 0.00 3.50
6100 6509 1.134367 CAGATGTTGATGCAGCCAAGG 59.866 52.381 0.00 0.00 0.00 3.61
6214 6623 0.603569 GAGAAGCGAGGAGACCAACA 59.396 55.000 0.00 0.00 0.00 3.33
6215 6624 1.205893 GAGAAGCGAGGAGACCAACAT 59.794 52.381 0.00 0.00 0.00 2.71
6275 6684 2.742372 GAGCAACATGGTCGCCGT 60.742 61.111 0.00 0.00 35.04 5.68
6406 6821 2.088950 TAAACTTGCTACGTGGAGCC 57.911 50.000 1.81 0.00 42.11 4.70
6495 6914 2.483188 GCCGTCTTCCCGTGAGAAATAT 60.483 50.000 0.00 0.00 0.00 1.28
6502 6921 7.244192 GTCTTCCCGTGAGAAATATTTTTCAG 58.756 38.462 18.85 13.38 43.09 3.02
6532 6952 2.124277 AAAAGGGTTCGGAGGCATAC 57.876 50.000 0.00 0.00 0.00 2.39
6620 7040 7.545615 AGTGTTTCAACCATTTTTCTTCTTGTC 59.454 33.333 0.00 0.00 0.00 3.18
6754 7180 5.839063 AGGTAGAAAAAGGAAGGGGAAAAAG 59.161 40.000 0.00 0.00 0.00 2.27
6855 7281 4.997395 TCCATTGACGAGAAAAGGAGAAAG 59.003 41.667 0.00 0.00 0.00 2.62
6941 7383 1.094785 CCGAAATGGGCGTTTGATCT 58.905 50.000 0.00 0.00 0.00 2.75
6942 7384 1.202177 CCGAAATGGGCGTTTGATCTG 60.202 52.381 0.00 0.00 0.00 2.90
7041 7495 4.065789 AGAAATCACGTCCAGTCTTTTCC 58.934 43.478 0.00 0.00 34.08 3.13
7085 7545 3.610791 CTCGTTCTCGGCTCACGCA 62.611 63.158 0.00 0.00 43.86 5.24
7107 7567 2.612200 ACATGGCGTGTGTGTGTAC 58.388 52.632 12.39 0.00 40.28 2.90
7127 7592 7.018826 GTGTACAAATCGCTTTATTGTTGCTA 58.981 34.615 0.00 0.00 38.22 3.49
7163 7628 3.763897 TGTGTGCTTCACTAGATGCTAGA 59.236 43.478 8.36 0.00 46.27 2.43
7164 7629 4.109050 GTGTGCTTCACTAGATGCTAGAC 58.891 47.826 8.36 0.00 43.30 2.59
7165 7630 4.019858 TGTGCTTCACTAGATGCTAGACT 58.980 43.478 8.36 0.00 43.30 3.24
7168 7633 5.518487 GTGCTTCACTAGATGCTAGACTTTC 59.482 44.000 8.36 0.00 43.30 2.62
7174 7639 8.764524 TCACTAGATGCTAGACTTTCTTTTTC 57.235 34.615 8.36 0.00 0.00 2.29
7196 7661 4.282703 TCCCTTTGACACTTGACTAGTACC 59.717 45.833 0.00 0.00 34.56 3.34
7197 7662 4.562963 CCCTTTGACACTTGACTAGTACCC 60.563 50.000 0.00 0.00 34.56 3.69
7198 7663 4.039973 CCTTTGACACTTGACTAGTACCCA 59.960 45.833 0.00 0.00 34.56 4.51
7199 7664 5.280011 CCTTTGACACTTGACTAGTACCCAT 60.280 44.000 0.00 0.00 34.56 4.00
7200 7665 5.818678 TTGACACTTGACTAGTACCCATT 57.181 39.130 0.00 0.00 34.56 3.16
7201 7666 5.401531 TGACACTTGACTAGTACCCATTC 57.598 43.478 0.00 0.00 34.56 2.67
7202 7667 4.082408 TGACACTTGACTAGTACCCATTCG 60.082 45.833 0.00 0.00 34.56 3.34
7203 7668 3.830755 ACACTTGACTAGTACCCATTCGT 59.169 43.478 0.00 0.00 34.56 3.85
7204 7669 4.282703 ACACTTGACTAGTACCCATTCGTT 59.717 41.667 0.00 0.00 34.56 3.85
7205 7670 4.863131 CACTTGACTAGTACCCATTCGTTC 59.137 45.833 0.00 0.00 34.56 3.95
7206 7671 4.771054 ACTTGACTAGTACCCATTCGTTCT 59.229 41.667 0.00 0.00 34.56 3.01
7207 7672 5.948162 ACTTGACTAGTACCCATTCGTTCTA 59.052 40.000 0.00 0.00 34.56 2.10
7208 7673 6.435277 ACTTGACTAGTACCCATTCGTTCTAA 59.565 38.462 0.00 0.00 34.56 2.10
7209 7674 6.839124 TGACTAGTACCCATTCGTTCTAAA 57.161 37.500 0.00 0.00 0.00 1.85
7210 7675 7.230849 TGACTAGTACCCATTCGTTCTAAAA 57.769 36.000 0.00 0.00 0.00 1.52
7211 7676 7.844009 TGACTAGTACCCATTCGTTCTAAAAT 58.156 34.615 0.00 0.00 0.00 1.82
7212 7677 8.970020 TGACTAGTACCCATTCGTTCTAAAATA 58.030 33.333 0.00 0.00 0.00 1.40
7213 7678 9.460906 GACTAGTACCCATTCGTTCTAAAATAG 57.539 37.037 0.00 0.00 0.00 1.73
7214 7679 9.193806 ACTAGTACCCATTCGTTCTAAAATAGA 57.806 33.333 0.00 0.00 0.00 1.98
7216 7681 8.888579 AGTACCCATTCGTTCTAAAATAGATG 57.111 34.615 0.00 0.00 34.22 2.90
7217 7682 8.701895 AGTACCCATTCGTTCTAAAATAGATGA 58.298 33.333 0.00 0.00 34.22 2.92
7218 7683 7.787725 ACCCATTCGTTCTAAAATAGATGAC 57.212 36.000 0.00 0.00 34.22 3.06
7219 7684 7.565680 ACCCATTCGTTCTAAAATAGATGACT 58.434 34.615 0.00 0.00 34.22 3.41
7220 7685 7.711339 ACCCATTCGTTCTAAAATAGATGACTC 59.289 37.037 0.00 0.00 34.22 3.36
7221 7686 7.096023 CCCATTCGTTCTAAAATAGATGACTCG 60.096 40.741 0.00 0.00 34.22 4.18
7222 7687 7.648112 CCATTCGTTCTAAAATAGATGACTCGA 59.352 37.037 0.00 0.00 34.22 4.04
7223 7688 7.966157 TTCGTTCTAAAATAGATGACTCGAC 57.034 36.000 0.00 0.00 34.22 4.20
7224 7689 7.317842 TCGTTCTAAAATAGATGACTCGACT 57.682 36.000 0.00 0.00 34.22 4.18
7225 7690 7.759465 TCGTTCTAAAATAGATGACTCGACTT 58.241 34.615 0.00 0.00 34.22 3.01
7226 7691 8.242053 TCGTTCTAAAATAGATGACTCGACTTT 58.758 33.333 0.00 0.00 34.22 2.66
7227 7692 8.314635 CGTTCTAAAATAGATGACTCGACTTTG 58.685 37.037 0.00 0.00 34.22 2.77
7228 7693 9.141400 GTTCTAAAATAGATGACTCGACTTTGT 57.859 33.333 0.00 0.00 34.22 2.83
7230 7695 9.784680 TCTAAAATAGATGACTCGACTTTGTAC 57.215 33.333 0.00 0.00 0.00 2.90
7231 7696 9.790389 CTAAAATAGATGACTCGACTTTGTACT 57.210 33.333 0.00 0.00 0.00 2.73
7238 7703 9.490379 AGATGACTCGACTTTGTACTTATTTTT 57.510 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.497291 TGTGGTCCTAGTCACTGTTTTT 57.503 40.909 0.00 0.00 35.15 1.94
15 16 4.706842 ATGTGGTCCTAGTCACTGTTTT 57.293 40.909 0.00 0.00 35.15 2.43
16 17 7.676683 ATATATGTGGTCCTAGTCACTGTTT 57.323 36.000 0.00 0.00 35.15 2.83
17 18 7.565398 AGAATATATGTGGTCCTAGTCACTGTT 59.435 37.037 0.00 0.00 35.15 3.16
18 19 7.069986 AGAATATATGTGGTCCTAGTCACTGT 58.930 38.462 0.00 2.72 35.15 3.55
19 20 7.531857 AGAATATATGTGGTCCTAGTCACTG 57.468 40.000 0.00 0.00 35.15 3.66
20 21 7.785028 TGAAGAATATATGTGGTCCTAGTCACT 59.215 37.037 8.77 0.00 35.15 3.41
21 22 7.868415 GTGAAGAATATATGTGGTCCTAGTCAC 59.132 40.741 0.00 0.00 34.71 3.67
22 23 7.015292 GGTGAAGAATATATGTGGTCCTAGTCA 59.985 40.741 0.00 0.00 0.00 3.41
23 24 7.233757 AGGTGAAGAATATATGTGGTCCTAGTC 59.766 40.741 0.00 0.00 0.00 2.59
24 25 7.076446 AGGTGAAGAATATATGTGGTCCTAGT 58.924 38.462 0.00 0.00 0.00 2.57
25 26 7.453126 AGAGGTGAAGAATATATGTGGTCCTAG 59.547 40.741 0.00 0.00 0.00 3.02
26 27 7.306013 AGAGGTGAAGAATATATGTGGTCCTA 58.694 38.462 0.00 0.00 0.00 2.94
27 28 6.146760 AGAGGTGAAGAATATATGTGGTCCT 58.853 40.000 0.00 0.00 0.00 3.85
87 88 7.093552 CCAAGATGAGGAATATCGGACTCTAAT 60.094 40.741 0.00 0.00 0.00 1.73
151 152 6.045318 CACTAGATGTGTTTAGATCACCAGG 58.955 44.000 0.00 0.00 41.53 4.45
155 156 7.916450 GTCTACCACTAGATGTGTTTAGATCAC 59.084 40.741 0.00 0.00 44.81 3.06
200 205 5.774690 ACTACATCCAACCAACATGAACATT 59.225 36.000 0.00 0.00 0.00 2.71
299 306 1.589803 GGTTGTCAGTGGCGTAAACT 58.410 50.000 0.00 0.00 0.00 2.66
355 362 8.552034 CGTCAACTAACTCTGATCTTTCTTTTT 58.448 33.333 0.00 0.00 0.00 1.94
356 363 7.926555 TCGTCAACTAACTCTGATCTTTCTTTT 59.073 33.333 0.00 0.00 0.00 2.27
357 364 7.382759 GTCGTCAACTAACTCTGATCTTTCTTT 59.617 37.037 0.00 0.00 0.00 2.52
358 365 6.864165 GTCGTCAACTAACTCTGATCTTTCTT 59.136 38.462 0.00 0.00 0.00 2.52
359 366 6.016192 TGTCGTCAACTAACTCTGATCTTTCT 60.016 38.462 0.00 0.00 0.00 2.52
360 367 6.088350 GTGTCGTCAACTAACTCTGATCTTTC 59.912 42.308 0.00 0.00 0.00 2.62
361 368 5.921408 GTGTCGTCAACTAACTCTGATCTTT 59.079 40.000 0.00 0.00 0.00 2.52
362 369 5.462405 GTGTCGTCAACTAACTCTGATCTT 58.538 41.667 0.00 0.00 0.00 2.40
382 389 1.788308 CGTACGACCATGAAAACGTGT 59.212 47.619 10.44 0.00 39.28 4.49
483 493 5.406649 AGAAGAAAATGAGAGACAGCGTAG 58.593 41.667 0.00 0.00 0.00 3.51
585 600 3.315418 GAGGTGAACTCGAAAGTGGTAC 58.685 50.000 0.00 0.00 36.29 3.34
586 601 3.655276 GAGGTGAACTCGAAAGTGGTA 57.345 47.619 0.00 0.00 36.29 3.25
630 650 3.751175 TGTAGCCTTTCAGCACAATACAC 59.249 43.478 0.00 0.00 34.23 2.90
781 806 1.304617 GGCTGGGAAGGAAGGAAGG 59.695 63.158 0.00 0.00 0.00 3.46
782 807 1.078143 CGGCTGGGAAGGAAGGAAG 60.078 63.158 0.00 0.00 0.00 3.46
783 808 1.838073 GACGGCTGGGAAGGAAGGAA 61.838 60.000 0.00 0.00 0.00 3.36
784 809 2.203938 ACGGCTGGGAAGGAAGGA 60.204 61.111 0.00 0.00 0.00 3.36
1064 1093 2.902486 TCATGTATCAGATCCAGCTCCC 59.098 50.000 0.00 0.00 0.00 4.30
1126 1160 6.409524 AAATGAAAACAATTCCAGAGAGCA 57.590 33.333 0.00 0.00 0.00 4.26
1129 1163 9.965824 GTTAGAAAATGAAAACAATTCCAGAGA 57.034 29.630 0.00 0.00 0.00 3.10
1135 1169 8.275632 GCACTGGTTAGAAAATGAAAACAATTC 58.724 33.333 0.00 0.00 0.00 2.17
1162 1201 2.265904 GGAACCGCCCAACTCAACC 61.266 63.158 0.00 0.00 0.00 3.77
1164 1203 0.178975 AATGGAACCGCCCAACTCAA 60.179 50.000 0.00 0.00 40.04 3.02
1190 1232 5.417894 TCAAAGAGAAACGATGGAGCTAGTA 59.582 40.000 0.00 0.00 0.00 1.82
1191 1233 4.220821 TCAAAGAGAAACGATGGAGCTAGT 59.779 41.667 0.00 0.00 0.00 2.57
1192 1234 4.748892 TCAAAGAGAAACGATGGAGCTAG 58.251 43.478 0.00 0.00 0.00 3.42
1202 1244 3.575630 TCTGACGGATCAAAGAGAAACG 58.424 45.455 0.00 0.00 33.30 3.60
1425 1473 1.369091 GGAGCACGCACGGATCAAAT 61.369 55.000 0.00 0.00 0.00 2.32
1486 1534 1.927174 CTGGGTCGAACTAATTCAGCG 59.073 52.381 0.00 0.00 34.14 5.18
1525 1603 3.365969 GGTAGGACGGCAAAACTCAATTG 60.366 47.826 0.00 0.00 0.00 2.32
1730 1808 0.310543 TCATGGTTCGCAAACAGCAC 59.689 50.000 0.00 0.00 46.13 4.40
2055 2133 6.804295 CGCTAAGATAAGCAAGGACTATACTG 59.196 42.308 0.00 0.00 42.91 2.74
2294 2372 4.627015 ACACACCTGGATAATAGTACCCA 58.373 43.478 0.00 0.00 0.00 4.51
2423 2502 3.257393 CATTCGATCCAGCATAGTAGCC 58.743 50.000 0.00 0.00 34.23 3.93
2927 3021 7.563888 TTGGCTCTTCATCATTTAAGATCTG 57.436 36.000 0.00 0.00 31.60 2.90
3059 3158 3.944087 AGCAGTTCACCCTAGAATTGAC 58.056 45.455 3.79 0.00 37.40 3.18
3203 3302 9.555727 GGACTATAAGCAGTATAACCATTTTCA 57.444 33.333 0.00 0.00 0.00 2.69
3212 3311 7.255381 GGAACGACTGGACTATAAGCAGTATAA 60.255 40.741 0.00 0.00 0.00 0.98
3268 3367 3.134804 AGCGGAGTAATATGGCTCTTTGT 59.865 43.478 6.71 0.00 32.67 2.83
3299 3398 0.389948 GTGTAGAAGGGTCCTGCACG 60.390 60.000 0.00 0.00 37.47 5.34
3434 3533 7.832685 GGGTAATTTGATCTTGTAGGGTAGTTT 59.167 37.037 0.00 0.00 0.00 2.66
3455 3554 3.953612 CAGCATGCTTATTGGAAGGGTAA 59.046 43.478 19.98 0.00 0.00 2.85
3516 3615 0.107361 GATCCTTTGGTGGTACCCGG 60.107 60.000 10.07 0.00 37.50 5.73
3576 3675 9.806203 CTTATTTGCAAACTTTGATGATGGATA 57.194 29.630 15.41 0.00 0.00 2.59
3743 3845 5.572885 GCTTCCTTTCCCTTGGTTAGTATGA 60.573 44.000 0.00 0.00 0.00 2.15
3906 4008 0.478072 TCTGCTCCTGGGCTCAAAAA 59.522 50.000 8.32 0.00 0.00 1.94
3907 4009 0.700564 ATCTGCTCCTGGGCTCAAAA 59.299 50.000 8.32 0.00 0.00 2.44
4342 4446 5.527582 GTCCTACCAAGGCACACTAAATATG 59.472 44.000 0.00 0.00 43.31 1.78
4893 5242 3.001330 GTCGAAATTGAGGATTAGGCACG 59.999 47.826 0.00 0.00 0.00 5.34
4959 5308 3.451178 GCAATACCTCTTGAGTGTCCCTA 59.549 47.826 0.00 0.00 0.00 3.53
5029 5378 7.011857 GTCAAGATAATTGACCAACAGAGATCC 59.988 40.741 9.12 0.00 42.07 3.36
5227 5577 5.448225 CCATGACAAAGAACATGAGGAATCG 60.448 44.000 0.00 0.00 44.28 3.34
5415 5766 5.929992 CGTCCAGTTATGAGTCCAAACTTAA 59.070 40.000 4.84 0.00 35.28 1.85
5670 6021 7.033185 CGCAGGTAATAAAATTTAGCAAACCT 58.967 34.615 0.00 0.00 35.23 3.50
5726 6081 3.640498 TCCATGATGCCACAAAGTGAAAA 59.360 39.130 0.00 0.00 35.23 2.29
6100 6509 0.240411 CCTTTGCTCTGCTCACTTGC 59.760 55.000 0.00 0.00 0.00 4.01
6214 6623 2.865119 TCAACATCTGCTGTCACCAT 57.135 45.000 0.00 0.00 36.98 3.55
6215 6624 2.865119 ATCAACATCTGCTGTCACCA 57.135 45.000 0.00 0.00 36.98 4.17
6275 6684 3.701205 TCTTGGCTGTATCAAGCTTCA 57.299 42.857 0.00 0.00 43.06 3.02
6406 6821 5.932883 CAGGATGATTGACCATCTATCAGTG 59.067 44.000 8.52 3.67 40.73 3.66
6523 6943 1.228367 CCAGCCATGGTATGCCTCC 60.228 63.158 14.67 0.00 42.17 4.30
6532 6952 3.495806 GGAGAATTCTCTACCAGCCATGG 60.496 52.174 29.64 7.63 46.12 3.66
6620 7040 4.203828 CGACGACAACAGAAGAAACAATG 58.796 43.478 0.00 0.00 0.00 2.82
6855 7281 1.139256 GGAGATCTCCGGTCCCTTTTC 59.861 57.143 25.78 0.00 40.36 2.29
6999 7453 3.133003 TCTCTCCATCGATCAAAACCCTC 59.867 47.826 0.00 0.00 0.00 4.30
7003 7457 6.481984 GTGATTTCTCTCCATCGATCAAAAC 58.518 40.000 0.00 0.00 0.00 2.43
7041 7495 2.124570 CATGTGGCCTCCCTTCCG 60.125 66.667 3.32 0.00 0.00 4.30
7104 7564 7.110216 CGATAGCAACAATAAAGCGATTTGTAC 59.890 37.037 9.29 0.00 33.44 2.90
7105 7565 7.123190 CGATAGCAACAATAAAGCGATTTGTA 58.877 34.615 9.29 0.00 33.44 2.41
7107 7567 5.965334 ACGATAGCAACAATAAAGCGATTTG 59.035 36.000 9.29 0.00 42.67 2.32
7163 7628 6.210584 TCAAGTGTCAAAGGGAAAAAGAAAGT 59.789 34.615 0.00 0.00 0.00 2.66
7164 7629 6.531594 GTCAAGTGTCAAAGGGAAAAAGAAAG 59.468 38.462 0.00 0.00 0.00 2.62
7165 7630 6.210584 AGTCAAGTGTCAAAGGGAAAAAGAAA 59.789 34.615 0.00 0.00 0.00 2.52
7168 7633 5.582689 AGTCAAGTGTCAAAGGGAAAAAG 57.417 39.130 0.00 0.00 0.00 2.27
7174 7639 4.562963 GGGTACTAGTCAAGTGTCAAAGGG 60.563 50.000 0.00 0.00 39.39 3.95
7196 7661 7.648112 TCGAGTCATCTATTTTAGAACGAATGG 59.352 37.037 0.00 0.00 38.50 3.16
7197 7662 8.473016 GTCGAGTCATCTATTTTAGAACGAATG 58.527 37.037 0.00 0.00 38.50 2.67
7198 7663 8.407064 AGTCGAGTCATCTATTTTAGAACGAAT 58.593 33.333 0.00 0.00 38.50 3.34
7199 7664 7.759465 AGTCGAGTCATCTATTTTAGAACGAA 58.241 34.615 0.00 0.00 38.50 3.85
7200 7665 7.317842 AGTCGAGTCATCTATTTTAGAACGA 57.682 36.000 0.00 0.00 38.50 3.85
7201 7666 7.972623 AAGTCGAGTCATCTATTTTAGAACG 57.027 36.000 0.00 0.00 38.50 3.95
7202 7667 9.141400 ACAAAGTCGAGTCATCTATTTTAGAAC 57.859 33.333 0.00 0.00 38.50 3.01
7204 7669 9.784680 GTACAAAGTCGAGTCATCTATTTTAGA 57.215 33.333 0.00 0.00 39.50 2.10
7205 7670 9.790389 AGTACAAAGTCGAGTCATCTATTTTAG 57.210 33.333 0.00 0.00 0.00 1.85
7212 7677 9.490379 AAAAATAAGTACAAAGTCGAGTCATCT 57.510 29.630 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.