Multiple sequence alignment - TraesCS3D01G319200

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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 TraesCS3D01G319200 chr3D 100.000 6281 0 0 1 6281 433132441 433138721 0.000000e+00 11599.0
1 TraesCS3D01G319200 chr3D 78.947 190 26 11 350 526 608482316 608482128 3.980000e-22 117.0
2 TraesCS3D01G319200 chr3B 93.090 4356 180 40 1717 5993 565266408 565270721 0.000000e+00 6264.0
3 TraesCS3D01G319200 chr3B 91.463 1675 86 20 1 1643 565264647 565266296 0.000000e+00 2248.0
4 TraesCS3D01G319200 chr3B 95.349 258 7 3 5992 6247 565270881 565271135 7.580000e-109 405.0
5 TraesCS3D01G319200 chr3B 88.060 67 7 1 485 551 225369731 225369666 1.880000e-10 78.7
6 TraesCS3D01G319200 chr3A 95.882 3254 108 15 3044 6281 571177170 571180413 0.000000e+00 5243.0
7 TraesCS3D01G319200 chr3A 91.952 1342 60 19 1 1324 571173942 571175253 0.000000e+00 1836.0
8 TraesCS3D01G319200 chr3A 92.377 1220 63 10 1311 2526 571175284 571176477 0.000000e+00 1711.0
9 TraesCS3D01G319200 chr3A 93.987 449 22 2 2531 2975 571176541 571176988 0.000000e+00 675.0
10 TraesCS3D01G319200 chr3A 81.739 230 20 11 340 547 9747710 9747481 8.370000e-39 172.0
11 TraesCS3D01G319200 chr3A 82.609 138 14 8 355 484 729232384 729232249 5.150000e-21 113.0
12 TraesCS3D01G319200 chr3A 88.043 92 9 2 5342 5432 142884940 142884850 2.390000e-19 108.0
13 TraesCS3D01G319200 chr3A 86.047 86 12 0 5459 5544 593970002 593969917 6.700000e-15 93.5
14 TraesCS3D01G319200 chr7D 84.293 191 21 3 370 551 18282051 18282241 1.800000e-40 178.0
15 TraesCS3D01G319200 chr7D 88.372 86 10 0 5459 5544 419793198 419793113 3.100000e-18 104.0
16 TraesCS3D01G319200 chr2B 83.333 192 16 12 337 513 305325358 305325548 5.040000e-36 163.0
17 TraesCS3D01G319200 chr2B 84.444 180 12 12 349 513 305325767 305325945 5.040000e-36 163.0
18 TraesCS3D01G319200 chr5B 79.911 224 31 6 338 547 350159933 350159710 1.090000e-32 152.0
19 TraesCS3D01G319200 chr5B 88.764 89 9 1 5459 5547 680853425 680853338 2.390000e-19 108.0
20 TraesCS3D01G319200 chr5D 92.135 89 6 1 5459 5547 539150919 539150832 2.380000e-24 124.0
21 TraesCS3D01G319200 chr5A 89.000 100 9 2 5450 5549 569803298 569803201 8.550000e-24 122.0
22 TraesCS3D01G319200 chr4D 90.426 94 8 1 5459 5552 450203791 450203699 8.550000e-24 122.0
23 TraesCS3D01G319200 chr4D 78.889 180 22 12 378 548 501508413 501508585 2.390000e-19 108.0
24 TraesCS3D01G319200 chr4D 76.000 200 35 10 360 549 454765392 454765196 2.410000e-14 91.6
25 TraesCS3D01G319200 chr4A 90.244 82 7 1 5463 5544 629378659 629378739 8.610000e-19 106.0
26 TraesCS3D01G319200 chr4A 87.302 63 8 0 485 547 216690459 216690521 8.730000e-09 73.1


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 TraesCS3D01G319200 chr3D 433132441 433138721 6280 False 11599.000000 11599 100.000000 1 6281 1 chr3D.!!$F1 6280
1 TraesCS3D01G319200 chr3B 565264647 565271135 6488 False 2972.333333 6264 93.300667 1 6247 3 chr3B.!!$F1 6246
2 TraesCS3D01G319200 chr3A 571173942 571180413 6471 False 2366.250000 5243 93.549500 1 6281 4 chr3A.!!$F1 6280

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
130 131 1.210478 CCTATGGGTGAAGTGGGACTG 59.790 57.143 0.0 0.0 0.00 3.51 F
1026 1049 0.463654 GCAATCATGGTGGGCGTAGA 60.464 55.000 0.0 0.0 0.00 2.59 F
1774 1934 0.175989 CTCCCTACGAGCCAAAGTCC 59.824 60.000 0.0 0.0 0.00 3.85 F
3083 3454 0.586319 TCTTCGTTTGGCAGCTTTCG 59.414 50.000 0.0 0.0 0.00 3.46 F
3272 3643 0.036875 CTGTCCCTGGTGGTTCCTTC 59.963 60.000 0.0 0.0 37.07 3.46 F
4628 5008 0.884514 TGTGCAGTTCTCCTCTCTCG 59.115 55.000 0.0 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1677 0.743345 GGTGCCGACAAGATACACCC 60.743 60.000 0.00 0.00 44.04 4.61 R
2994 3336 0.106519 AGACTTGGCAACTTGGTGCT 60.107 50.000 10.60 0.00 44.31 4.40 R
3236 3607 1.229625 AGGCATCCACAGAGGTCCA 60.230 57.895 0.00 0.00 39.02 4.02 R
4868 5255 0.472471 GGTGGGCGGATCCTTCATAA 59.528 55.000 10.75 0.00 34.39 1.90 R
5231 5618 1.898863 ATAGAAGATGGGGTGGCTGT 58.101 50.000 0.00 0.00 0.00 4.40 R
5642 6032 2.050144 CTGACCATACATAGGCCAGGT 58.950 52.381 5.01 1.73 0.00 4.00 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
127 128 2.587060 ATCCTATGGGTGAAGTGGGA 57.413 50.000 0.00 0.00 0.00 4.37
130 131 1.210478 CCTATGGGTGAAGTGGGACTG 59.790 57.143 0.00 0.00 0.00 3.51
137 138 2.290960 GGTGAAGTGGGACTGGCTAATT 60.291 50.000 0.00 0.00 0.00 1.40
239 240 4.707030 TGCATCTCACCATTCACAAATC 57.293 40.909 0.00 0.00 0.00 2.17
321 322 7.287466 TGTGCCTTTAATGTGCAATATATCCTT 59.713 33.333 0.00 0.00 36.65 3.36
365 376 5.834204 ACATATGTCCTGGTTACTAGTCCTC 59.166 44.000 1.41 0.00 0.00 3.71
384 395 6.209391 AGTCCTCTTGTTTGGGTCATATTTTG 59.791 38.462 0.00 0.00 0.00 2.44
463 475 8.279800 TGCGAACTACATTTAAATATGAATCCG 58.720 33.333 0.00 1.81 0.00 4.18
505 526 7.601130 TGACAACATTTTGCTAGTCTAATACGT 59.399 33.333 0.00 0.00 36.00 3.57
575 596 7.640597 GGTAGTAACCATCAAGGCTATTTTT 57.359 36.000 0.00 0.00 45.98 1.94
865 888 4.408921 TGGATGGCTATATATAGGTGGCAC 59.591 45.833 19.19 9.70 36.10 5.01
958 981 4.212214 GTGGATAGATTCTGATTTGGTCGC 59.788 45.833 0.00 0.00 0.00 5.19
972 995 1.899814 TGGTCGCTAGATCAACTTGGT 59.100 47.619 0.00 0.00 33.95 3.67
1026 1049 0.463654 GCAATCATGGTGGGCGTAGA 60.464 55.000 0.00 0.00 0.00 2.59
1070 1093 8.915036 GTTTCCCTCATCTCTAATACTAGTTGA 58.085 37.037 0.00 0.00 0.00 3.18
1098 1121 2.489329 TCTTGCATGCTTTCTTGCTACC 59.511 45.455 20.33 0.00 42.07 3.18
1170 1201 3.968265 TGAGGGCTTGAATTTCTTAGGG 58.032 45.455 0.00 0.00 0.00 3.53
1200 1231 7.439157 TGAAATATATCTTGCAAATCCTCCG 57.561 36.000 0.00 0.00 0.00 4.63
1231 1262 2.544685 CAGAAGTGCTACCTCGGATTG 58.455 52.381 0.00 0.00 0.00 2.67
1274 1305 7.121168 ACATCAACTCGGACATGTTTTTCATAT 59.879 33.333 0.00 0.00 34.67 1.78
1362 1439 5.872617 CCATCATCTGTTTTGACATGCATTT 59.127 36.000 0.00 0.00 0.00 2.32
1384 1461 7.843490 TTTGTATTCTAATCCAGGTTCTTCG 57.157 36.000 0.00 0.00 0.00 3.79
1393 1470 2.367241 TCCAGGTTCTTCGTGTTCATGA 59.633 45.455 0.00 0.00 0.00 3.07
1394 1471 3.007940 TCCAGGTTCTTCGTGTTCATGAT 59.992 43.478 0.00 0.00 0.00 2.45
1395 1472 3.753272 CCAGGTTCTTCGTGTTCATGATT 59.247 43.478 0.00 0.00 0.00 2.57
1396 1473 4.216257 CCAGGTTCTTCGTGTTCATGATTT 59.784 41.667 0.00 0.00 0.00 2.17
1397 1474 5.278463 CCAGGTTCTTCGTGTTCATGATTTT 60.278 40.000 0.00 0.00 0.00 1.82
1426 1506 5.410924 TCTGAGAATCGTTCATGTAACCAG 58.589 41.667 0.00 0.00 38.61 4.00
1462 1542 6.720309 TGTAAATTCCTTGATCCAGTCATCA 58.280 36.000 0.00 0.00 36.54 3.07
1476 1556 5.366477 TCCAGTCATCAAGGTTATCATAGCA 59.634 40.000 0.00 0.00 0.00 3.49
1479 1559 6.018425 CAGTCATCAAGGTTATCATAGCACAC 60.018 42.308 0.00 0.00 0.00 3.82
1481 1561 6.201806 GTCATCAAGGTTATCATAGCACACTC 59.798 42.308 0.00 0.00 0.00 3.51
1611 1691 5.064707 CCAAACATAAGGGTGTATCTTGTCG 59.935 44.000 0.00 0.00 0.00 4.35
1657 1817 7.520614 GCCCATATATTGCAGTACTGAAGAAAC 60.521 40.741 27.08 7.97 0.00 2.78
1742 1902 3.260740 CTTTGCTTGTGTTTTCCTTGCA 58.739 40.909 0.00 0.00 0.00 4.08
1774 1934 0.175989 CTCCCTACGAGCCAAAGTCC 59.824 60.000 0.00 0.00 0.00 3.85
1985 2147 1.962807 CTGTGCCACCTGAAAATTCCA 59.037 47.619 0.00 0.00 0.00 3.53
2097 2262 7.786178 TTTGATATTTACAGCAGAGCGTAAT 57.214 32.000 0.00 0.00 31.83 1.89
2273 2441 1.202891 ACCCAAGTGCTTGAAGGGTAC 60.203 52.381 12.99 0.00 42.93 3.34
2315 2483 8.804688 TTTGGTTTAATGAATTTAACACCTCG 57.195 30.769 7.10 0.00 34.93 4.63
2317 2485 5.803461 GGTTTAATGAATTTAACACCTCGCC 59.197 40.000 7.10 0.00 32.62 5.54
2319 2487 2.871096 TGAATTTAACACCTCGCCCT 57.129 45.000 0.00 0.00 0.00 5.19
2320 2488 2.706890 TGAATTTAACACCTCGCCCTC 58.293 47.619 0.00 0.00 0.00 4.30
2321 2489 2.039216 TGAATTTAACACCTCGCCCTCA 59.961 45.455 0.00 0.00 0.00 3.86
2349 2517 3.492421 TCATTTTCCTCGCTTGAATGC 57.508 42.857 0.00 0.00 0.00 3.56
2420 2588 0.889638 TGAGCGAGTCGACAGGTCTT 60.890 55.000 29.54 8.33 33.96 3.01
2491 2659 5.522460 TGAAGGTCTGTTCTAAAACACTTCG 59.478 40.000 11.93 0.00 42.83 3.79
2493 2661 5.048507 AGGTCTGTTCTAAAACACTTCGAC 58.951 41.667 0.00 0.00 40.45 4.20
2499 2668 5.064198 TGTTCTAAAACACTTCGACTTGTGG 59.936 40.000 14.27 0.56 40.45 4.17
2627 2855 6.018994 GCTTATGGTGGTAATCGTTCTAACTG 60.019 42.308 0.00 0.00 0.00 3.16
2628 2856 3.592059 TGGTGGTAATCGTTCTAACTGC 58.408 45.455 0.00 0.00 0.00 4.40
2803 3031 2.985456 CTCTGGGGAGGTGCAGAC 59.015 66.667 0.00 0.00 36.03 3.51
2917 3148 7.202526 TCTAAACTTTGAAACATTTGGCAGAG 58.797 34.615 0.00 0.00 0.00 3.35
2919 3150 4.936891 ACTTTGAAACATTTGGCAGAGTC 58.063 39.130 0.00 0.00 0.00 3.36
2921 3152 4.836125 TTGAAACATTTGGCAGAGTCTC 57.164 40.909 0.00 0.00 0.00 3.36
2992 3334 7.504924 TGAAGTAACTTTGGTGGAACTATTG 57.495 36.000 0.00 0.00 36.74 1.90
2993 3335 7.057894 TGAAGTAACTTTGGTGGAACTATTGT 58.942 34.615 0.00 0.00 36.74 2.71
2994 3336 8.212312 TGAAGTAACTTTGGTGGAACTATTGTA 58.788 33.333 0.00 0.00 36.74 2.41
2996 3338 5.959618 AACTTTGGTGGAACTATTGTAGC 57.040 39.130 0.00 0.00 36.74 3.58
2998 3340 4.760204 ACTTTGGTGGAACTATTGTAGCAC 59.240 41.667 0.00 0.00 36.74 4.40
3059 3430 9.274065 GTTAATTTTCCGATTTACACTGATGTC 57.726 33.333 0.00 0.00 40.48 3.06
3083 3454 0.586319 TCTTCGTTTGGCAGCTTTCG 59.414 50.000 0.00 0.00 0.00 3.46
3218 3589 3.548201 TGCAATGCACGAGTTTGTG 57.452 47.368 2.72 0.00 42.81 3.33
3272 3643 0.036875 CTGTCCCTGGTGGTTCCTTC 59.963 60.000 0.00 0.00 37.07 3.46
3287 3658 1.148310 CCTTCGACGTGCTGAACAAT 58.852 50.000 0.00 0.00 0.00 2.71
3332 3703 2.350676 CGCAAGAAGCAGTGCAAATGTA 60.351 45.455 19.20 0.00 46.13 2.29
3445 3821 9.109393 TGTAAGTTGCCTATAAATCTTGTCATC 57.891 33.333 0.00 0.00 0.00 2.92
3487 3864 5.406175 CACACACAATTTGATCCCATTGTTC 59.594 40.000 14.15 0.00 40.85 3.18
3877 4257 2.271800 GGGACAGTGATCATCGTTGAC 58.728 52.381 0.00 0.00 33.85 3.18
3934 4314 3.355378 CCACAAAATGCCATCAGGAGTA 58.645 45.455 0.00 0.00 36.89 2.59
3990 4370 7.093465 CCAGGTATGGTAAAGAAGACTTGAGTA 60.093 40.741 0.00 0.00 42.17 2.59
4040 4420 1.687563 GCACCTTACCCAGTGTTTGT 58.312 50.000 0.00 0.00 36.35 2.83
4126 4506 2.202756 CGAGCTCTACCGCCCAAC 60.203 66.667 12.85 0.00 0.00 3.77
4305 4685 8.918202 ACATATCCTGAGAAACAAACAAGTTA 57.082 30.769 0.00 0.00 0.00 2.24
4318 4698 8.502161 AACAAACAAGTTATCTATTCGTTTGC 57.498 30.769 10.96 0.00 43.30 3.68
4561 4941 1.728971 GGTGACGTTTGATCTGCTCAG 59.271 52.381 0.00 0.00 34.68 3.35
4628 5008 0.884514 TGTGCAGTTCTCCTCTCTCG 59.115 55.000 0.00 0.00 0.00 4.04
4650 5035 2.927014 GCGGCTAGCCATGTATGTACTC 60.927 54.545 32.47 1.58 40.81 2.59
4792 5177 3.886505 TCAAGGTACCAAACACATCCAAC 59.113 43.478 15.94 0.00 0.00 3.77
4810 5195 2.810852 CAACTTCAGCTCCTCCAAGAAC 59.189 50.000 0.00 0.00 0.00 3.01
4868 5255 5.055144 TCGACTAACTCGAGTATGCATACT 58.945 41.667 34.12 34.12 46.75 2.12
4997 5384 5.055144 CCAACTGATGAACGAGATCATGAT 58.945 41.667 8.25 8.25 40.08 2.45
5010 5397 1.775385 TCATGATCCCTAGCGACACA 58.225 50.000 0.00 0.00 0.00 3.72
5231 5618 3.648067 ACCATCAAGAAGACTCTGACCAA 59.352 43.478 0.00 0.00 30.03 3.67
5320 5710 4.903049 TCTGGTTCCTGTTAAACTCCACTA 59.097 41.667 0.00 0.00 0.00 2.74
5321 5711 5.011738 TCTGGTTCCTGTTAAACTCCACTAG 59.988 44.000 0.00 0.00 0.00 2.57
5322 5712 4.657039 TGGTTCCTGTTAAACTCCACTAGT 59.343 41.667 0.00 0.00 41.49 2.57
5323 5713 5.221581 TGGTTCCTGTTAAACTCCACTAGTC 60.222 44.000 0.00 0.00 37.50 2.59
5324 5714 5.236282 GTTCCTGTTAAACTCCACTAGTCC 58.764 45.833 0.00 0.00 37.50 3.85
5325 5715 4.748701 TCCTGTTAAACTCCACTAGTCCT 58.251 43.478 0.00 0.00 37.50 3.85
5326 5716 4.771054 TCCTGTTAAACTCCACTAGTCCTC 59.229 45.833 0.00 0.00 37.50 3.71
5752 6142 4.434713 AGACCTGTTGTTGTTGTTGTTC 57.565 40.909 0.00 0.00 0.00 3.18
5768 6164 5.592054 TGTTGTTCTTGTTGTTGTTGTTGA 58.408 33.333 0.00 0.00 0.00 3.18
5956 6352 4.237349 ACATAAAAGAAAACCCTGCACG 57.763 40.909 0.00 0.00 0.00 5.34
5993 6391 5.379187 ACTACCATTGCATGCATCAGATAA 58.621 37.500 23.37 4.56 0.00 1.75
5994 6553 4.848562 ACCATTGCATGCATCAGATAAG 57.151 40.909 23.37 9.17 0.00 1.73
6175 6736 5.819991 AGGATAGCAAGTGATTTTTCAGGA 58.180 37.500 0.00 0.00 0.00 3.86
6177 6738 6.721208 AGGATAGCAAGTGATTTTTCAGGAAA 59.279 34.615 0.00 0.00 0.00 3.13
6178 6739 7.398332 AGGATAGCAAGTGATTTTTCAGGAAAT 59.602 33.333 0.00 0.00 32.16 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.804989 CACGCCTGAGTGGGAAAATC 59.195 55.000 0.00 0.00 38.40 2.17
201 202 5.609423 AGATGCAATGGTTAACAAAAGCAA 58.391 33.333 14.40 2.27 37.59 3.91
239 240 6.151648 ACATCCATTTGACCTTCAACACATAG 59.848 38.462 0.00 0.00 35.89 2.23
286 287 1.175983 TTAAAGGCACACAAGGCGGG 61.176 55.000 0.00 0.00 39.37 6.13
344 345 5.728937 AGAGGACTAGTAACCAGGACATA 57.271 43.478 0.00 0.00 0.00 2.29
439 451 9.793245 GTCGGATTCATATTTAAATGTAGTTCG 57.207 33.333 11.05 4.76 0.00 3.95
478 490 8.604035 CGTATTAGACTAGCAAAATGTTGTCAT 58.396 33.333 0.00 0.00 37.06 3.06
482 494 7.148474 ACCACGTATTAGACTAGCAAAATGTTG 60.148 37.037 0.00 0.00 37.83 3.33
562 583 5.757808 GCAAAAAGGACAAAAATAGCCTTGA 59.242 36.000 0.00 0.00 40.44 3.02
564 585 5.928976 AGCAAAAAGGACAAAAATAGCCTT 58.071 33.333 0.00 0.00 42.27 4.35
575 596 1.960689 GCAGGGTAAGCAAAAAGGACA 59.039 47.619 0.00 0.00 0.00 4.02
819 841 3.339093 GCCTTACCCCTGGCCTGT 61.339 66.667 3.32 0.00 43.11 4.00
865 888 2.374184 TGTGTTGTTTCCCCTTGTCTG 58.626 47.619 0.00 0.00 0.00 3.51
958 981 2.739932 CGCCCTCACCAAGTTGATCTAG 60.740 54.545 3.87 0.00 0.00 2.43
972 995 1.515954 GAAAGATCGGACGCCCTCA 59.484 57.895 0.00 0.00 0.00 3.86
1026 1049 5.126545 GGGAAACAATTATACCGCCTTTCTT 59.873 40.000 0.00 0.00 0.00 2.52
1070 1093 5.220719 GCAAGAAAGCATGCAAGAAAACTTT 60.221 36.000 21.98 8.75 42.12 2.66
1098 1121 5.299279 ACAAGACATGTTACAACTCTTTGGG 59.701 40.000 0.00 0.01 40.06 4.12
1170 1201 9.415544 GGATTTGCAAGATATATTTCAACATCC 57.584 33.333 14.31 14.31 0.00 3.51
1324 1401 7.886629 ACAGATGATGGTTATTTGCTGTAAT 57.113 32.000 0.00 0.00 33.99 1.89
1362 1439 6.070995 ACACGAAGAACCTGGATTAGAATACA 60.071 38.462 0.00 0.00 0.00 2.29
1462 1542 4.737855 ACGAGTGTGCTATGATAACCTT 57.262 40.909 0.00 0.00 0.00 3.50
1476 1556 5.416947 AGAACTTGTTAGAACAACGAGTGT 58.583 37.500 10.08 0.00 43.45 3.55
1479 1559 8.761497 TGATTAAGAACTTGTTAGAACAACGAG 58.239 33.333 3.71 3.37 43.45 4.18
1481 1561 9.710979 TTTGATTAAGAACTTGTTAGAACAACG 57.289 29.630 3.71 4.01 43.45 4.10
1554 1634 1.074084 TGTACCGCCTTTTCCATTCCA 59.926 47.619 0.00 0.00 0.00 3.53
1597 1677 0.743345 GGTGCCGACAAGATACACCC 60.743 60.000 0.00 0.00 44.04 4.61
1600 1680 0.981183 AAGGGTGCCGACAAGATACA 59.019 50.000 0.00 0.00 0.00 2.29
1627 1707 6.306199 TCAGTACTGCAATATATGGGCAAAT 58.694 36.000 18.45 7.25 37.06 2.32
1698 1858 4.188462 CACGATACTGGACAGGCAAATTA 58.812 43.478 4.14 0.00 0.00 1.40
1699 1859 3.009723 CACGATACTGGACAGGCAAATT 58.990 45.455 4.14 0.00 0.00 1.82
1700 1860 2.632377 CACGATACTGGACAGGCAAAT 58.368 47.619 4.14 0.00 0.00 2.32
1701 1861 1.943968 GCACGATACTGGACAGGCAAA 60.944 52.381 4.14 0.00 0.00 3.68
1705 1865 2.002586 CAAAGCACGATACTGGACAGG 58.997 52.381 4.14 0.00 0.00 4.00
1774 1934 6.667007 AGGCAAAAACAAAAGAATGAAGTG 57.333 33.333 0.00 0.00 0.00 3.16
1985 2147 3.370103 CCCATCATGCTTTGAATTGCCTT 60.370 43.478 0.00 0.00 38.03 4.35
2031 2194 6.959639 TGGAAGATGCCAATTAGTATTTCC 57.040 37.500 8.00 8.00 34.31 3.13
2157 2322 2.238942 TGTGATATGTCCACGGCATC 57.761 50.000 0.00 0.00 37.34 3.91
2161 2326 2.355197 TGCTTTGTGATATGTCCACGG 58.645 47.619 0.00 0.00 37.34 4.94
2163 2328 4.142600 GGAGTTGCTTTGTGATATGTCCAC 60.143 45.833 0.00 0.00 35.23 4.02
2273 2441 3.025287 CAAATTCTTTGGTGGGAACCG 57.975 47.619 0.00 0.00 44.52 4.44
2293 2461 5.803461 GGCGAGGTGTTAAATTCATTAAACC 59.197 40.000 0.00 0.00 35.33 3.27
2349 2517 3.500982 CACATATGCCGAAAAACCTGTG 58.499 45.455 1.58 0.00 0.00 3.66
2420 2588 2.455674 ACTTGACTTGCTGCATCGTA 57.544 45.000 1.84 0.00 0.00 3.43
2491 2659 3.743396 GTGTCACTGAGATTCCACAAGTC 59.257 47.826 0.00 0.00 0.00 3.01
2493 2661 3.732212 TGTGTCACTGAGATTCCACAAG 58.268 45.455 4.27 0.00 30.53 3.16
2499 2668 3.733337 ACCAACTGTGTCACTGAGATTC 58.267 45.455 15.96 0.00 0.00 2.52
2574 2802 3.715495 CATGTCAGATCCTACTGTGCTC 58.285 50.000 0.00 0.00 38.79 4.26
2741 2969 1.547372 CAGGAGGGGCAAAATGAAGTG 59.453 52.381 0.00 0.00 0.00 3.16
2803 3031 1.064654 GCTCATTTTCCTGCCTTAGCG 59.935 52.381 0.00 0.00 44.31 4.26
2943 3175 4.939052 ATAGGTACGTCTAGCATTGCTT 57.061 40.909 17.71 0.25 40.44 3.91
2987 3329 3.081061 TGGCAACTTGGTGCTACAATAG 58.919 45.455 10.60 0.00 44.31 1.73
2992 3334 1.266989 GACTTGGCAACTTGGTGCTAC 59.733 52.381 10.60 0.00 44.31 3.58
2993 3335 1.142870 AGACTTGGCAACTTGGTGCTA 59.857 47.619 10.60 1.08 44.31 3.49
2994 3336 0.106519 AGACTTGGCAACTTGGTGCT 60.107 50.000 10.60 0.00 44.31 4.40
2996 3338 2.948979 TGTAAGACTTGGCAACTTGGTG 59.051 45.455 12.00 0.00 37.61 4.17
2998 3340 4.338118 TCTTTGTAAGACTTGGCAACTTGG 59.662 41.667 12.00 0.00 31.20 3.61
3022 3367 4.566759 TCGGAAAATTAACTCGAGATGCAG 59.433 41.667 21.68 0.00 0.00 4.41
3059 3430 1.732259 AGCTGCCAAACGAAGAATACG 59.268 47.619 0.00 0.00 0.00 3.06
3236 3607 1.229625 AGGCATCCACAGAGGTCCA 60.230 57.895 0.00 0.00 39.02 4.02
3272 3643 1.267532 GCCATATTGTTCAGCACGTCG 60.268 52.381 0.00 0.00 0.00 5.12
3287 3658 5.681954 GCCAAATGTTTGAGCATAAGCCATA 60.682 40.000 7.04 0.00 40.55 2.74
3332 3703 4.021016 GCCTCGGTCATGAATCCTAGTATT 60.021 45.833 0.00 0.00 0.00 1.89
3394 3765 7.551974 CAGAATCCATGATATAGTCCACAATCC 59.448 40.741 0.00 0.00 0.00 3.01
3445 3821 6.128580 TGTGTGTGTGACTTGAAATATCATCG 60.129 38.462 0.00 0.00 34.96 3.84
3487 3864 2.005451 GTAGCACTCCTGCAGTCATTG 58.995 52.381 13.81 5.28 46.97 2.82
3621 3998 7.775120 CCAAACATCTCTTGGCTAAAACATAT 58.225 34.615 0.00 0.00 37.14 1.78
3679 4059 6.312918 TCAGGATATGCTTGTTTTCGTAAGTC 59.687 38.462 0.00 0.00 39.48 3.01
3683 4063 5.105106 TCCTCAGGATATGCTTGTTTTCGTA 60.105 40.000 0.00 0.00 0.00 3.43
3686 4066 5.431765 TCTCCTCAGGATATGCTTGTTTTC 58.568 41.667 0.00 0.00 0.00 2.29
3934 4314 0.693049 AATTCAGGCTCCGAACCAGT 59.307 50.000 0.00 0.00 0.00 4.00
3937 4317 2.781911 GGAATTCAGGCTCCGAACC 58.218 57.895 7.93 0.00 0.00 3.62
4126 4506 1.363744 GAACATCAGTCCGCTCAAGG 58.636 55.000 0.00 0.00 0.00 3.61
4191 4571 4.746729 CTGACAATGAAGAGGTCTCTCAG 58.253 47.826 0.51 0.00 42.34 3.35
4318 4698 1.962807 TCCCATTTGTGTTGCCTGAAG 59.037 47.619 0.00 0.00 0.00 3.02
4561 4941 0.535553 TGGGCGTAACAGGTTGTTCC 60.536 55.000 0.00 0.00 40.22 3.62
4650 5035 6.309436 CACTGTGTGAGTAAAACATAGCATG 58.691 40.000 0.00 0.00 39.58 4.06
4734 5119 4.398358 AGACAACATCATCAATTCCTGCTG 59.602 41.667 0.00 0.00 0.00 4.41
4792 5177 1.349026 TGGTTCTTGGAGGAGCTGAAG 59.651 52.381 0.00 0.00 0.00 3.02
4810 5195 1.059913 ACTGGAGGAGAAAGTGGTGG 58.940 55.000 0.00 0.00 0.00 4.61
4862 5249 3.003480 GGCGGATCCTTCATAAGTATGC 58.997 50.000 10.75 0.53 33.76 3.14
4868 5255 0.472471 GGTGGGCGGATCCTTCATAA 59.528 55.000 10.75 0.00 34.39 1.90
5010 5397 2.111878 ACCTTGTTGCTCTGCGCT 59.888 55.556 9.73 0.00 40.11 5.92
5014 5401 2.633860 GGGACACCTTGTTGCTCTG 58.366 57.895 0.00 0.00 0.00 3.35
5194 5581 4.439305 TGATGGTAGCAATGTTTTCTGC 57.561 40.909 0.00 0.00 38.91 4.26
5231 5618 1.898863 ATAGAAGATGGGGTGGCTGT 58.101 50.000 0.00 0.00 0.00 4.40
5301 5688 5.011840 AGGACTAGTGGAGTTTAACAGGAAC 59.988 44.000 0.00 0.00 39.06 3.62
5320 5710 2.856231 AGATAGGTGAGGACTGAGGACT 59.144 50.000 0.00 0.00 0.00 3.85
5321 5711 3.306472 AGATAGGTGAGGACTGAGGAC 57.694 52.381 0.00 0.00 0.00 3.85
5322 5712 4.048600 ACTAGATAGGTGAGGACTGAGGA 58.951 47.826 0.00 0.00 0.00 3.71
5323 5713 4.447138 ACTAGATAGGTGAGGACTGAGG 57.553 50.000 0.00 0.00 0.00 3.86
5324 5714 4.825085 GGAACTAGATAGGTGAGGACTGAG 59.175 50.000 0.00 0.00 0.00 3.35
5325 5715 4.386536 GGGAACTAGATAGGTGAGGACTGA 60.387 50.000 0.00 0.00 0.00 3.41
5326 5716 3.892588 GGGAACTAGATAGGTGAGGACTG 59.107 52.174 0.00 0.00 0.00 3.51
5632 6022 3.330701 ACATAGGCCAGGTTCTTTTCTCA 59.669 43.478 5.01 0.00 0.00 3.27
5642 6032 2.050144 CTGACCATACATAGGCCAGGT 58.950 52.381 5.01 1.73 0.00 4.00
5752 6142 6.464895 AACAACATCAACAACAACAACAAG 57.535 33.333 0.00 0.00 0.00 3.16
5956 6352 6.038161 TGCAATGGTAGTAACAATGTGCTATC 59.962 38.462 17.67 0.00 30.58 2.08
5993 6391 9.354673 CCAATTTATTGAACTGGTGGTATATCT 57.645 33.333 4.07 0.00 40.14 1.98
5994 6553 9.349713 TCCAATTTATTGAACTGGTGGTATATC 57.650 33.333 4.07 0.00 40.14 1.63
6069 6628 7.059788 TGGTGGAGTACATGCAAATATTATGT 58.940 34.615 7.35 7.35 38.48 2.29


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

AutoCloner maintained by Alex Coulton.