Multiple sequence alignment - TraesCS4D01G204800

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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 TraesCS4D01G204800 chr4D 100.000 5980 0 0 1 5980 352436595 352442574 0.000000e+00 11044.0
1 TraesCS4D01G204800 chr4D 84.694 98 13 2 2206 2302 503868678 503868582 4.930000e-16 97.1
2 TraesCS4D01G204800 chr4B 96.326 4709 127 24 749 5437 435908494 435913176 0.000000e+00 7696.0
3 TraesCS4D01G204800 chr4A 95.562 4777 130 22 556 5304 112939178 112934456 0.000000e+00 7572.0
4 TraesCS4D01G204800 chr4A 92.224 553 35 5 1 551 112993879 112993333 0.000000e+00 776.0
5 TraesCS4D01G204800 chr4A 88.889 153 7 7 5288 5437 112934282 112934137 4.760000e-41 180.0
6 TraesCS4D01G204800 chr5D 95.580 543 23 1 5438 5980 300724615 300724074 0.000000e+00 869.0
7 TraesCS4D01G204800 chr5D 87.114 551 59 9 7 551 420207984 420208528 1.100000e-171 614.0
8 TraesCS4D01G204800 chr2A 94.019 418 18 2 5570 5980 757538610 757538193 1.410000e-175 627.0
9 TraesCS4D01G204800 chr2A 98.485 132 0 1 5438 5567 757540193 757540062 1.300000e-56 231.0
10 TraesCS4D01G204800 chr3A 86.751 551 60 9 7 551 698890888 698890345 8.580000e-168 601.0
11 TraesCS4D01G204800 chr3D 86.594 552 60 11 7 551 157742573 157743117 1.110000e-166 597.0
12 TraesCS4D01G204800 chrUn 86.388 551 63 9 7 551 74786547 74787091 5.160000e-165 592.0
13 TraesCS4D01G204800 chr6B 86.413 552 59 13 7 551 673953265 673953807 1.860000e-164 590.0
14 TraesCS4D01G204800 chr5A 86.207 551 64 9 7 551 533850100 533850644 2.400000e-163 586.0
15 TraesCS4D01G204800 chr1D 86.207 551 64 10 7 551 470903318 470903862 2.400000e-163 586.0
16 TraesCS4D01G204800 chr7D 86.182 550 65 8 7 551 607000547 607000004 8.640000e-163 584.0
17 TraesCS4D01G204800 chr7D 95.753 259 10 1 5438 5696 628623526 628623783 3.330000e-112 416.0
18 TraesCS4D01G204800 chr7D 94.286 245 13 1 5736 5980 628623779 628624022 2.040000e-99 374.0
19 TraesCS4D01G204800 chr7B 84.848 99 11 4 2206 2302 326671226 326671130 4.930000e-16 97.1
20 TraesCS4D01G204800 chr7A 83.673 98 14 2 2206 2302 138739542 138739638 2.300000e-14 91.6
21 TraesCS4D01G204800 chr1B 94.872 39 2 0 2267 2305 406340841 406340803 1.800000e-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 TraesCS4D01G204800 chr4D 352436595 352442574 5979 False 11044 11044 100.0000 1 5980 1 chr4D.!!$F1 5979
1 TraesCS4D01G204800 chr4B 435908494 435913176 4682 False 7696 7696 96.3260 749 5437 1 chr4B.!!$F1 4688
2 TraesCS4D01G204800 chr4A 112934137 112939178 5041 True 3876 7572 92.2255 556 5437 2 chr4A.!!$R2 4881
3 TraesCS4D01G204800 chr4A 112993333 112993879 546 True 776 776 92.2240 1 551 1 chr4A.!!$R1 550
4 TraesCS4D01G204800 chr5D 300724074 300724615 541 True 869 869 95.5800 5438 5980 1 chr5D.!!$R1 542
5 TraesCS4D01G204800 chr5D 420207984 420208528 544 False 614 614 87.1140 7 551 1 chr5D.!!$F1 544
6 TraesCS4D01G204800 chr2A 757538193 757540193 2000 True 429 627 96.2520 5438 5980 2 chr2A.!!$R1 542
7 TraesCS4D01G204800 chr3A 698890345 698890888 543 True 601 601 86.7510 7 551 1 chr3A.!!$R1 544
8 TraesCS4D01G204800 chr3D 157742573 157743117 544 False 597 597 86.5940 7 551 1 chr3D.!!$F1 544
9 TraesCS4D01G204800 chrUn 74786547 74787091 544 False 592 592 86.3880 7 551 1 chrUn.!!$F1 544
10 TraesCS4D01G204800 chr6B 673953265 673953807 542 False 590 590 86.4130 7 551 1 chr6B.!!$F1 544
11 TraesCS4D01G204800 chr5A 533850100 533850644 544 False 586 586 86.2070 7 551 1 chr5A.!!$F1 544
12 TraesCS4D01G204800 chr1D 470903318 470903862 544 False 586 586 86.2070 7 551 1 chr1D.!!$F1 544
13 TraesCS4D01G204800 chr7D 607000004 607000547 543 True 584 584 86.1820 7 551 1 chr7D.!!$R1 544

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
639 645 0.370273 GCCGAGTTCAGCATGTAACG 59.630 55.000 0.00 0.0 37.40 3.18 F
1410 1451 0.315886 TACCACGAGCGCTTTCTTCA 59.684 50.000 13.26 0.0 0.00 3.02 F
2026 2087 0.901580 GGTACCGAACCTGTCCCTCA 60.902 60.000 0.00 0.0 45.75 3.86 F
2660 2721 3.539604 GCAAGAGTATTGCTGTCCAGAT 58.460 45.455 15.13 0.0 41.87 2.90 F
3751 3812 0.324738 TCAGCCTACTGGGAGTCTGG 60.325 60.000 0.00 0.0 44.59 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2293 2354 1.007238 TGCTTAGCTACCACTCCCTCT 59.993 52.381 5.6 0.00 0.00 3.69 R
2488 2549 2.951642 TGTGGAGGCTTTGAGAAAACAG 59.048 45.455 0.0 0.00 0.00 3.16 R
3291 3352 5.192923 TGGCCATAAGATAACCCAACTAGTT 59.807 40.000 0.0 1.12 0.00 2.24 R
4049 4110 1.929494 TCCTGGGGTAAGGAATGCAAT 59.071 47.619 0.0 0.00 43.57 3.56 R
5713 7420 0.168348 CAGTCGTCCATCTTCGTCGT 59.832 55.000 0.0 0.00 0.00 4.34 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
77 78 8.687242 ACAGAGAGATATCAGATTTTTACGTGA 58.313 33.333 5.32 0.00 0.00 4.35
85 86 6.702716 TCAGATTTTTACGTGAAAAACCCT 57.297 33.333 20.25 14.61 47.00 4.34
130 131 1.674322 CGACGCCACCCAAATCCTT 60.674 57.895 0.00 0.00 0.00 3.36
189 192 5.092554 TCTAGATAGCACTAGAGGATCGG 57.907 47.826 0.00 0.00 42.32 4.18
280 283 7.718753 GGAACAATCTCATCAAAGATAGTGGAT 59.281 37.037 0.00 0.00 34.90 3.41
332 335 2.571653 CTGGACTATCACAACCTTGGGA 59.428 50.000 0.00 0.00 46.01 4.37
365 368 6.000219 CCTTGTCTTCTTCCTTCAATCTTCA 59.000 40.000 0.00 0.00 0.00 3.02
374 377 7.683578 TCTTCCTTCAATCTTCATCTCTTTCA 58.316 34.615 0.00 0.00 0.00 2.69
411 417 6.566197 TTTCTCTTCTTCTTCAATGAAGGC 57.434 37.500 21.35 0.00 42.54 4.35
414 420 4.330250 TCTTCTTCTTCAATGAAGGCTGG 58.670 43.478 21.35 10.10 42.54 4.85
417 423 3.072915 TCTTCTTCAATGAAGGCTGGACA 59.927 43.478 21.35 0.00 42.54 4.02
424 430 4.834496 TCAATGAAGGCTGGACAGATTTTT 59.166 37.500 3.00 0.00 0.00 1.94
452 458 0.918258 TGGTAATGGCTGCTGGATGA 59.082 50.000 0.00 0.00 0.00 2.92
462 468 2.619074 GCTGCTGGATGAAGGGTAAAGT 60.619 50.000 0.00 0.00 0.00 2.66
498 504 7.431249 TCTCACGTACAAAGTCTAAAATGAGT 58.569 34.615 0.00 0.00 33.28 3.41
547 553 8.774183 TGGGTAATAGGCTTTTGTATCTCTTTA 58.226 33.333 0.00 0.00 0.00 1.85
551 557 4.527944 AGGCTTTTGTATCTCTTTAGGCC 58.472 43.478 0.00 0.00 36.51 5.19
552 558 3.312697 GGCTTTTGTATCTCTTTAGGCCG 59.687 47.826 0.00 0.00 0.00 6.13
553 559 4.189231 GCTTTTGTATCTCTTTAGGCCGA 58.811 43.478 0.00 0.00 0.00 5.54
554 560 4.816925 GCTTTTGTATCTCTTTAGGCCGAT 59.183 41.667 0.00 0.00 0.00 4.18
562 568 5.359194 TCTCTTTAGGCCGATCATTTTCT 57.641 39.130 0.00 0.00 0.00 2.52
573 579 3.185188 CGATCATTTTCTCATAGCCCACG 59.815 47.826 0.00 0.00 0.00 4.94
614 620 1.526225 GGAGTATTTGGGAGGGCGC 60.526 63.158 0.00 0.00 0.00 6.53
615 621 1.887707 GAGTATTTGGGAGGGCGCG 60.888 63.158 0.00 0.00 0.00 6.86
639 645 0.370273 GCCGAGTTCAGCATGTAACG 59.630 55.000 0.00 0.00 37.40 3.18
647 653 2.892374 TCAGCATGTAACGGATCACAG 58.108 47.619 0.00 0.00 37.40 3.66
657 663 1.279271 ACGGATCACAGGAGGGAAAAG 59.721 52.381 0.00 0.00 0.00 2.27
1074 1112 1.683707 ACTGCGGATGAGCTCTCCA 60.684 57.895 23.52 10.62 38.13 3.86
1107 1148 4.803426 GTCTGCTCCGCCTCCACG 62.803 72.222 0.00 0.00 0.00 4.94
1146 1187 4.610714 GCGCCGATCCTCCTTCCC 62.611 72.222 0.00 0.00 0.00 3.97
1152 1193 3.153270 GATCCTCCTTCCCGACGGC 62.153 68.421 8.86 0.00 0.00 5.68
1176 1217 1.908619 TGGAAGCAGGTGATTAGCTCA 59.091 47.619 0.00 0.00 37.70 4.26
1194 1235 0.387622 CAACCATTTGGCTGTGCTCG 60.388 55.000 0.00 0.00 39.32 5.03
1195 1236 1.526575 AACCATTTGGCTGTGCTCGG 61.527 55.000 0.00 0.00 39.32 4.63
1198 1239 4.927782 TTTGGCTGTGCTCGGCGT 62.928 61.111 13.11 0.00 46.03 5.68
1410 1451 0.315886 TACCACGAGCGCTTTCTTCA 59.684 50.000 13.26 0.00 0.00 3.02
1411 1452 1.222115 ACCACGAGCGCTTTCTTCAC 61.222 55.000 13.26 0.00 0.00 3.18
1412 1453 0.946221 CCACGAGCGCTTTCTTCACT 60.946 55.000 13.26 0.00 0.00 3.41
1413 1454 1.668919 CCACGAGCGCTTTCTTCACTA 60.669 52.381 13.26 0.00 0.00 2.74
1414 1455 1.651138 CACGAGCGCTTTCTTCACTAG 59.349 52.381 13.26 0.00 0.00 2.57
1415 1456 1.269998 ACGAGCGCTTTCTTCACTAGT 59.730 47.619 13.26 0.00 0.00 2.57
1416 1457 2.486982 ACGAGCGCTTTCTTCACTAGTA 59.513 45.455 13.26 0.00 0.00 1.82
1417 1458 2.847133 CGAGCGCTTTCTTCACTAGTAC 59.153 50.000 13.26 0.00 0.00 2.73
1418 1459 3.426426 CGAGCGCTTTCTTCACTAGTACT 60.426 47.826 13.26 0.00 0.00 2.73
1419 1460 3.839293 AGCGCTTTCTTCACTAGTACTG 58.161 45.455 2.64 0.00 0.00 2.74
1420 1461 3.506455 AGCGCTTTCTTCACTAGTACTGA 59.494 43.478 2.64 0.00 0.00 3.41
1421 1462 4.022242 AGCGCTTTCTTCACTAGTACTGAA 60.022 41.667 2.64 0.52 0.00 3.02
1422 1463 4.865365 GCGCTTTCTTCACTAGTACTGAAT 59.135 41.667 5.39 0.00 0.00 2.57
1423 1464 5.220303 GCGCTTTCTTCACTAGTACTGAATG 60.220 44.000 5.39 1.01 0.00 2.67
1424 1465 5.220303 CGCTTTCTTCACTAGTACTGAATGC 60.220 44.000 19.82 19.82 33.91 3.56
1425 1466 5.872070 GCTTTCTTCACTAGTACTGAATGCT 59.128 40.000 21.11 0.00 34.21 3.79
1426 1467 7.036220 GCTTTCTTCACTAGTACTGAATGCTA 58.964 38.462 21.11 4.85 34.21 3.49
1427 1468 7.009723 GCTTTCTTCACTAGTACTGAATGCTAC 59.990 40.741 21.11 3.41 34.21 3.58
1428 1469 7.462571 TTCTTCACTAGTACTGAATGCTACA 57.537 36.000 5.39 0.00 0.00 2.74
1476 1536 5.552870 AGGGAATTTCTATCAGCGTATGT 57.447 39.130 0.00 0.00 0.00 2.29
1479 1539 5.758296 GGGAATTTCTATCAGCGTATGTTCA 59.242 40.000 0.00 0.00 0.00 3.18
1480 1540 6.073548 GGGAATTTCTATCAGCGTATGTTCAG 60.074 42.308 0.00 0.00 0.00 3.02
1481 1541 6.480320 GGAATTTCTATCAGCGTATGTTCAGT 59.520 38.462 0.00 0.00 0.00 3.41
1482 1542 7.011482 GGAATTTCTATCAGCGTATGTTCAGTT 59.989 37.037 0.00 0.00 0.00 3.16
1505 1565 7.826252 AGTTAGTTGCTCACTATGATGAACAAT 59.174 33.333 1.62 0.00 37.11 2.71
1513 1573 7.468922 TCACTATGATGAACAATCGTGAATC 57.531 36.000 0.00 0.00 38.22 2.52
1873 1934 2.847327 TCTGCCTTTCTGGAGAACTG 57.153 50.000 0.00 0.00 38.35 3.16
1884 1945 4.876125 TCTGGAGAACTGAATATGATCGC 58.124 43.478 0.00 0.00 0.00 4.58
2004 2065 1.061711 GATAGTGCAGAAGCTGTTGCG 59.938 52.381 15.47 0.00 45.42 4.85
2026 2087 0.901580 GGTACCGAACCTGTCCCTCA 60.902 60.000 0.00 0.00 45.75 3.86
2227 2288 5.952947 AGGTACTCCCTCGGATTCATATTAG 59.047 44.000 0.00 0.00 40.71 1.73
2230 2291 6.102897 ACTCCCTCGGATTCATATTAGTTG 57.897 41.667 0.00 0.00 0.00 3.16
2396 2457 4.415596 TCTGGGTTTTAACAATGCAGGAT 58.584 39.130 0.00 0.00 0.00 3.24
2660 2721 3.539604 GCAAGAGTATTGCTGTCCAGAT 58.460 45.455 15.13 0.00 41.87 2.90
2909 2970 6.212840 TCTCTCATTTCCTCTCTATAGGCT 57.787 41.667 0.00 0.00 36.51 4.58
3029 3090 9.052759 TGAGTAGAAGTTTCAACCAAATTACTC 57.947 33.333 0.00 0.00 33.12 2.59
3039 3100 7.074653 TCAACCAAATTACTCTGAGTAACCT 57.925 36.000 27.41 17.07 42.78 3.50
3104 3165 7.876068 CACAACCTGTAAAGAACTTATGGAGTA 59.124 37.037 0.00 0.00 37.72 2.59
3105 3166 8.434392 ACAACCTGTAAAGAACTTATGGAGTAA 58.566 33.333 0.00 0.00 37.72 2.24
3242 3303 5.359194 TTTTGCACTGGGGTTTAATTTGA 57.641 34.783 0.00 0.00 0.00 2.69
3291 3352 8.565896 ACTTTGAGAATACATGAGCATTGTTA 57.434 30.769 0.00 0.00 0.00 2.41
3329 3390 5.786975 TCTTATGGCCATATGATCTCCTTGA 59.213 40.000 28.70 10.34 0.00 3.02
3330 3391 6.446110 TCTTATGGCCATATGATCTCCTTGAT 59.554 38.462 28.70 3.67 38.27 2.57
3751 3812 0.324738 TCAGCCTACTGGGAGTCTGG 60.325 60.000 0.00 0.00 44.59 3.86
3783 3844 3.191162 TCTTGCGAAAATGATGACTTGGG 59.809 43.478 0.00 0.00 0.00 4.12
3898 3959 6.015940 CACAATCTTCTAAAGTGCCCTTTTCT 60.016 38.462 0.00 0.00 41.18 2.52
4045 4106 6.074249 GGAGCATACGAGCATTACTAGTTTTC 60.074 42.308 0.00 0.00 35.63 2.29
4049 4110 7.861372 GCATACGAGCATTACTAGTTTTCTCTA 59.139 37.037 0.00 0.00 35.63 2.43
4116 4177 0.680921 GCCAGGCTGCTGTATTTGGA 60.681 55.000 9.56 0.00 0.00 3.53
4299 4360 9.878599 ATTCTAAATTTACTTGTTTGAGTCACG 57.121 29.630 0.00 0.00 0.00 4.35
4619 4681 7.548780 GCTGTATTTGCATTTAATCTTTTCCCA 59.451 33.333 0.00 0.00 0.00 4.37
4723 4785 4.021719 CCCTGAAATGAATGCTTTCACAGT 60.022 41.667 16.45 5.71 44.36 3.55
4807 4869 9.712305 CCCGAACAATCTGATACTCTATTTATT 57.288 33.333 0.00 0.00 0.00 1.40
4873 4936 6.466308 TGAAATTGTGAGACTGTCATTACG 57.534 37.500 10.88 0.00 37.56 3.18
5086 5149 7.392953 TGCATTTCTGAAAACTGTATCATACCA 59.607 33.333 6.95 0.00 0.00 3.25
5607 7314 1.218230 GACGCTCATGCCCGAAGATC 61.218 60.000 11.01 0.00 35.36 2.75
5619 7326 2.009774 CCGAAGATCGCCTTGTGAAAT 58.990 47.619 0.00 0.00 38.82 2.17
5713 7420 5.375773 TGATGACTTCCAAACAATCAGACA 58.624 37.500 0.00 0.00 0.00 3.41
5921 7628 6.089954 GCACCATCAGAATTAAGTTTTGCTTC 59.910 38.462 0.00 0.00 38.57 3.86
5963 7677 1.656441 CAGCAGCTTTCCTTTGCGT 59.344 52.632 0.00 0.00 42.47 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 2.023888 TGGTTTTTCCCCTCAAGTTGGA 60.024 45.455 2.34 0.00 34.77 3.53
130 131 9.952030 TTGTATCCCATATTTGATAATAGCGAA 57.048 29.630 0.00 0.00 30.10 4.70
206 209 9.829507 AAATTTTGTTGTGTTCATCCAAGATTA 57.170 25.926 0.00 0.00 29.03 1.75
280 283 2.454336 TATCTCCTTCAAGCTCCGGA 57.546 50.000 2.93 2.93 0.00 5.14
411 417 6.656693 ACCAAGAGTGATAAAAATCTGTCCAG 59.343 38.462 0.00 0.00 0.00 3.86
414 420 9.994432 CATTACCAAGAGTGATAAAAATCTGTC 57.006 33.333 0.00 0.00 0.00 3.51
417 423 7.836183 AGCCATTACCAAGAGTGATAAAAATCT 59.164 33.333 0.00 0.00 0.00 2.40
424 430 3.455910 AGCAGCCATTACCAAGAGTGATA 59.544 43.478 0.00 0.00 0.00 2.15
452 458 6.903534 TGAGAGAATGGAGATACTTTACCCTT 59.096 38.462 0.00 0.00 0.00 3.95
462 468 6.377429 ACTTTGTACGTGAGAGAATGGAGATA 59.623 38.462 0.00 0.00 0.00 1.98
498 504 7.189794 CCATTAGGGTTATGACCTAGGATAGA 58.810 42.308 17.98 0.00 42.77 1.98
547 553 3.406764 GCTATGAGAAAATGATCGGCCT 58.593 45.455 0.00 0.00 0.00 5.19
551 557 3.185188 CGTGGGCTATGAGAAAATGATCG 59.815 47.826 0.00 0.00 0.00 3.69
552 558 4.130118 ACGTGGGCTATGAGAAAATGATC 58.870 43.478 0.00 0.00 0.00 2.92
553 559 4.156455 ACGTGGGCTATGAGAAAATGAT 57.844 40.909 0.00 0.00 0.00 2.45
554 560 3.627395 ACGTGGGCTATGAGAAAATGA 57.373 42.857 0.00 0.00 0.00 2.57
562 568 2.673258 TCCTCATTACGTGGGCTATGA 58.327 47.619 0.00 0.00 0.00 2.15
573 579 7.907389 TCCTATGTGTTGGATATCCTCATTAC 58.093 38.462 22.35 13.73 36.82 1.89
639 645 4.779993 ATACTTTTCCCTCCTGTGATCC 57.220 45.455 0.00 0.00 0.00 3.36
647 653 3.542648 CCGGAAGAATACTTTTCCCTCC 58.457 50.000 0.00 0.00 39.76 4.30
657 663 4.275196 GCATAGTTTTCCCCGGAAGAATAC 59.725 45.833 0.73 11.07 35.38 1.89
705 711 0.543410 TCTTCGGCCCACTTCACCTA 60.543 55.000 0.00 0.00 0.00 3.08
708 714 1.648467 GCATCTTCGGCCCACTTCAC 61.648 60.000 0.00 0.00 0.00 3.18
709 715 1.377202 GCATCTTCGGCCCACTTCA 60.377 57.895 0.00 0.00 0.00 3.02
710 716 1.078143 AGCATCTTCGGCCCACTTC 60.078 57.895 0.00 0.00 0.00 3.01
711 717 1.377725 CAGCATCTTCGGCCCACTT 60.378 57.895 0.00 0.00 0.00 3.16
712 718 2.270205 CAGCATCTTCGGCCCACT 59.730 61.111 0.00 0.00 0.00 4.00
783 807 1.136147 CCGTGGACTCGTACTTCGG 59.864 63.158 0.00 0.00 40.32 4.30
784 808 1.513586 GCCGTGGACTCGTACTTCG 60.514 63.158 0.00 0.00 41.41 3.79
926 952 2.753043 GGAGTACCGGAGTGGCGA 60.753 66.667 9.46 0.00 43.94 5.54
1107 1148 2.508751 GGAGATGTACCCCTCGGCC 61.509 68.421 0.00 0.00 0.00 6.13
1146 1187 4.776322 TGCTTCCATGGGCCGTCG 62.776 66.667 13.02 0.00 0.00 5.12
1152 1193 2.579873 CTAATCACCTGCTTCCATGGG 58.420 52.381 13.02 0.00 0.00 4.00
1176 1217 1.526575 CCGAGCACAGCCAAATGGTT 61.527 55.000 0.71 0.00 37.57 3.67
1217 1258 1.743958 CAAGCAGATTCAGAGGGCAAG 59.256 52.381 0.00 0.00 0.00 4.01
1410 1451 6.546428 ACCATTGTAGCATTCAGTACTAGT 57.454 37.500 0.00 0.00 0.00 2.57
1411 1452 7.600375 CCATACCATTGTAGCATTCAGTACTAG 59.400 40.741 0.00 0.00 0.00 2.57
1412 1453 7.070696 ACCATACCATTGTAGCATTCAGTACTA 59.929 37.037 0.00 0.00 0.00 1.82
1413 1454 6.126768 ACCATACCATTGTAGCATTCAGTACT 60.127 38.462 0.00 0.00 0.00 2.73
1414 1455 6.055588 ACCATACCATTGTAGCATTCAGTAC 58.944 40.000 0.00 0.00 0.00 2.73
1415 1456 6.247229 ACCATACCATTGTAGCATTCAGTA 57.753 37.500 0.00 0.00 0.00 2.74
1416 1457 5.116084 ACCATACCATTGTAGCATTCAGT 57.884 39.130 0.00 0.00 0.00 3.41
1417 1458 6.291377 ACTACCATACCATTGTAGCATTCAG 58.709 40.000 0.00 0.00 36.31 3.02
1418 1459 6.126911 TGACTACCATACCATTGTAGCATTCA 60.127 38.462 0.00 0.00 36.31 2.57
1419 1460 6.288294 TGACTACCATACCATTGTAGCATTC 58.712 40.000 0.00 0.00 36.31 2.67
1420 1461 6.247229 TGACTACCATACCATTGTAGCATT 57.753 37.500 0.00 0.00 36.31 3.56
1421 1462 5.887214 TGACTACCATACCATTGTAGCAT 57.113 39.130 0.00 0.00 36.31 3.79
1422 1463 5.685520 TTGACTACCATACCATTGTAGCA 57.314 39.130 0.00 0.00 36.31 3.49
1423 1464 6.765989 TGAATTGACTACCATACCATTGTAGC 59.234 38.462 0.00 0.00 36.31 3.58
1424 1465 7.768582 TGTGAATTGACTACCATACCATTGTAG 59.231 37.037 0.00 0.00 38.31 2.74
1425 1466 7.625469 TGTGAATTGACTACCATACCATTGTA 58.375 34.615 0.00 0.00 0.00 2.41
1426 1467 6.480763 TGTGAATTGACTACCATACCATTGT 58.519 36.000 0.00 0.00 0.00 2.71
1427 1468 7.121168 AGTTGTGAATTGACTACCATACCATTG 59.879 37.037 6.06 0.00 0.00 2.82
1428 1469 7.175104 AGTTGTGAATTGACTACCATACCATT 58.825 34.615 6.06 0.00 0.00 3.16
1476 1536 6.935167 TCATCATAGTGAGCAACTAACTGAA 58.065 36.000 3.68 0.00 44.57 3.02
1479 1539 6.701340 TGTTCATCATAGTGAGCAACTAACT 58.299 36.000 3.68 0.00 44.57 2.24
1480 1540 6.968131 TGTTCATCATAGTGAGCAACTAAC 57.032 37.500 3.68 0.15 44.57 2.34
1481 1541 7.010460 CGATTGTTCATCATAGTGAGCAACTAA 59.990 37.037 8.04 0.00 46.93 2.24
1482 1542 6.476706 CGATTGTTCATCATAGTGAGCAACTA 59.523 38.462 8.04 2.17 46.93 2.24
1505 1565 4.756642 AGAAAGCAACAGAATGATTCACGA 59.243 37.500 8.03 0.00 39.69 4.35
1513 1573 7.310664 ACATTACATCAGAAAGCAACAGAATG 58.689 34.615 0.00 0.00 46.00 2.67
1746 1806 3.200825 CCCCTCAATGAATGACCACTACT 59.799 47.826 0.00 0.00 33.47 2.57
1873 1934 3.617706 CAGAGATGCTGGCGATCATATTC 59.382 47.826 0.00 0.00 41.07 1.75
1884 1945 5.163683 CCAAAATACAGTTCAGAGATGCTGG 60.164 44.000 0.00 0.00 44.98 4.85
2163 2224 6.042143 AGTGTAGATTTGTTGCAAAAACCTG 58.958 36.000 0.18 0.00 0.00 4.00
2227 2288 5.805994 AGAGTTATACTAAAGCAGCGACAAC 59.194 40.000 0.00 0.00 0.00 3.32
2230 2291 5.341617 ACAGAGTTATACTAAAGCAGCGAC 58.658 41.667 0.00 0.00 0.00 5.19
2293 2354 1.007238 TGCTTAGCTACCACTCCCTCT 59.993 52.381 5.60 0.00 0.00 3.69
2396 2457 6.426937 GTCTAGGAAGTGAATTTACAAGTGCA 59.573 38.462 2.93 0.00 0.00 4.57
2403 2464 6.371825 CCCACAAGTCTAGGAAGTGAATTTAC 59.628 42.308 0.00 0.00 32.14 2.01
2488 2549 2.951642 TGTGGAGGCTTTGAGAAAACAG 59.048 45.455 0.00 0.00 0.00 3.16
2758 2819 4.756564 TGATAGGCACTCCTCCAATCTAT 58.243 43.478 0.00 0.00 43.06 1.98
3029 3090 7.556275 ACATAAGAGAGAAGAGAGGTTACTCAG 59.444 40.741 0.00 0.00 46.44 3.35
3039 3100 7.395772 ACACTGATCAACATAAGAGAGAAGAGA 59.604 37.037 0.00 0.00 0.00 3.10
3265 3326 7.081526 ACAATGCTCATGTATTCTCAAAGTC 57.918 36.000 0.00 0.00 0.00 3.01
3269 3330 8.565896 AGTTAACAATGCTCATGTATTCTCAA 57.434 30.769 8.61 0.00 0.00 3.02
3291 3352 5.192923 TGGCCATAAGATAACCCAACTAGTT 59.807 40.000 0.00 1.12 0.00 2.24
3329 3390 8.635765 ACAGTTATGAGTTTTTGGTACATGAT 57.364 30.769 0.00 0.00 39.30 2.45
3330 3391 8.458573 AACAGTTATGAGTTTTTGGTACATGA 57.541 30.769 0.00 0.00 39.30 3.07
3679 3740 5.435686 TTATGCCACTGATCCACTTAACT 57.564 39.130 0.00 0.00 0.00 2.24
3898 3959 5.242434 CACCAGTTACAGTAACCTGCATAA 58.758 41.667 18.27 0.00 42.81 1.90
4045 4106 4.392940 CTGGGGTAAGGAATGCAATAGAG 58.607 47.826 0.00 0.00 0.00 2.43
4049 4110 1.929494 TCCTGGGGTAAGGAATGCAAT 59.071 47.619 0.00 0.00 43.57 3.56
4627 4689 8.330466 ACATCAATACCAATTCACGAAACTAA 57.670 30.769 0.00 0.00 0.00 2.24
4723 4785 3.694043 TCCCTTCACACGAATCAATGA 57.306 42.857 0.00 0.00 0.00 2.57
4818 4881 8.764524 ATAACCATCAATAGAGCGTATTCTTC 57.235 34.615 0.00 0.00 0.00 2.87
4891 4954 1.918253 CCTCCTCCATTCCCTGTGG 59.082 63.158 0.00 0.00 38.11 4.17
5607 7314 2.611292 GAGGATCTCATTTCACAAGGCG 59.389 50.000 0.00 0.00 0.00 5.52
5713 7420 0.168348 CAGTCGTCCATCTTCGTCGT 59.832 55.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.