Multiple sequence alignment - TraesCS6D01G309300

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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 TraesCS6D01G309300 chr6D 100.000 3644 0 0 1 3644 419881417 419885060 0.000000e+00 6730.0
1 TraesCS6D01G309300 chr6A 94.513 2260 95 13 618 2861 562933599 562935845 0.000000e+00 3459.0
2 TraesCS6D01G309300 chr6A 94.814 617 29 3 2870 3486 562935905 562936518 0.000000e+00 959.0
3 TraesCS6D01G309300 chr6A 88.664 494 38 8 1 477 562933097 562933589 1.460000e-163 586.0
4 TraesCS6D01G309300 chr6A 92.667 150 8 3 3498 3644 562936570 562936719 2.850000e-51 213.0
5 TraesCS6D01G309300 chr6A 87.603 121 15 0 472 592 27786396 27786276 1.360000e-29 141.0
6 TraesCS6D01G309300 chr6B 92.279 1334 64 11 618 1940 632877777 632879082 0.000000e+00 1857.0
7 TraesCS6D01G309300 chr6B 95.781 640 20 4 2026 2664 632879497 632880130 0.000000e+00 1026.0
8 TraesCS6D01G309300 chr6B 94.976 617 28 2 2870 3486 632880354 632880967 0.000000e+00 965.0
9 TraesCS6D01G309300 chr6B 88.947 380 30 6 212 588 632877209 632877579 3.320000e-125 459.0
10 TraesCS6D01G309300 chr6B 92.086 139 9 2 3507 3644 632881067 632881204 1.030000e-45 195.0
11 TraesCS6D01G309300 chr6B 100.000 33 0 0 2403 2435 632879838 632879870 1.090000e-05 62.1
12 TraesCS6D01G309300 chr5B 91.150 113 9 1 481 592 665813086 665813198 6.300000e-33 152.0
13 TraesCS6D01G309300 chr5D 90.179 112 11 0 481 592 279302713 279302824 2.930000e-31 147.0
14 TraesCS6D01G309300 chr4D 89.655 116 10 2 478 592 150632590 150632476 2.930000e-31 147.0
15 TraesCS6D01G309300 chr3D 90.351 114 7 3 481 592 566956753 566956864 2.930000e-31 147.0
16 TraesCS6D01G309300 chr3D 88.889 117 13 0 477 593 62169279 62169163 1.050000e-30 145.0
17 TraesCS6D01G309300 chr5A 89.565 115 10 2 479 592 688327210 688327097 1.050000e-30 145.0
18 TraesCS6D01G309300 chr2D 86.131 137 15 4 479 613 445721248 445721382 1.050000e-30 145.0


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 TraesCS6D01G309300 chr6D 419881417 419885060 3643 False 6730.000000 6730 100.0000 1 3644 1 chr6D.!!$F1 3643
1 TraesCS6D01G309300 chr6A 562933097 562936719 3622 False 1304.250000 3459 92.6645 1 3644 4 chr6A.!!$F1 3643
2 TraesCS6D01G309300 chr6B 632877209 632881204 3995 False 760.683333 1857 94.0115 212 3644 6 chr6B.!!$F1 3432

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
755 940 1.006998 CTTCCCAATTCCCATCCACCA 59.993 52.381 0.0 0.0 0.0 4.17 F
1245 1441 0.971386 TCGGTAAGGACGGCTTCTTT 59.029 50.000 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2713 0.444651 TTTCTTCATAAACGCCGCGG 59.555 50.0 24.05 24.05 0.0 6.46 R
3181 3774 0.679960 GACCTTGGGATTTGTCCGGG 60.680 60.0 0.00 0.00 0.0 5.73 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
26 27 6.631016 AGCACTCGTGTAAAGAAATCAGATA 58.369 36.000 0.00 0.00 0.00 1.98
58 59 1.160329 AGCATCGGCCAAATACGAGC 61.160 55.000 2.24 0.00 42.89 5.03
75 77 4.662145 ACGAGCAAGCATTTTAATACTGC 58.338 39.130 0.00 0.00 36.15 4.40
117 119 6.653320 ACATGATGTCACCTTGTACGTTTATT 59.347 34.615 0.00 0.00 0.00 1.40
197 203 1.376037 CTTTCCGACTCCACAGGCC 60.376 63.158 0.00 0.00 0.00 5.19
222 228 5.121811 AGATAAGAATGCGAGCAAAGTGAT 58.878 37.500 0.57 0.00 0.00 3.06
224 230 6.763135 AGATAAGAATGCGAGCAAAGTGATAA 59.237 34.615 0.57 0.00 0.00 1.75
243 249 3.683365 AACATGAAAGGGATGGCAAAC 57.317 42.857 0.00 0.00 0.00 2.93
271 280 6.543831 CCCTCAAGATCGAAAGTTCCATTAAT 59.456 38.462 0.00 0.00 0.00 1.40
334 343 3.945981 AACGGACCAAACAACAAAACT 57.054 38.095 0.00 0.00 0.00 2.66
361 370 1.191096 CAAATGCGCCGAACATAAGC 58.809 50.000 4.18 0.00 0.00 3.09
449 466 3.090952 AGCTAGCAGCACGAGATAAAG 57.909 47.619 18.83 0.00 45.56 1.85
466 483 7.464710 CGAGATAAAGGTTTTCCATCTCTTTCG 60.465 40.741 10.10 0.00 41.23 3.46
477 494 5.984725 TCCATCTCTTTCGGCATTAACTAA 58.015 37.500 0.00 0.00 0.00 2.24
478 495 6.411376 TCCATCTCTTTCGGCATTAACTAAA 58.589 36.000 0.00 0.00 0.00 1.85
479 496 6.315393 TCCATCTCTTTCGGCATTAACTAAAC 59.685 38.462 0.00 0.00 0.00 2.01
480 497 6.316390 CCATCTCTTTCGGCATTAACTAAACT 59.684 38.462 0.00 0.00 0.00 2.66
481 498 7.494625 CCATCTCTTTCGGCATTAACTAAACTA 59.505 37.037 0.00 0.00 0.00 2.24
505 522 2.367894 CCCTCCGTTCCTAAATACTCCC 59.632 54.545 0.00 0.00 0.00 4.30
506 523 2.035576 CCTCCGTTCCTAAATACTCCCG 59.964 54.545 0.00 0.00 0.00 5.14
513 530 6.376978 CGTTCCTAAATACTCCCGTATGTAG 58.623 44.000 3.69 3.69 40.99 2.74
515 532 7.572724 CGTTCCTAAATACTCCCGTATGTAGAG 60.573 44.444 10.01 0.00 42.70 2.43
551 568 8.557029 TGAACTACATACAGATGTACATAGACG 58.443 37.037 8.71 0.18 44.77 4.18
588 605 4.631813 AGATTCACTCATTTTGCTCCGTAC 59.368 41.667 0.00 0.00 0.00 3.67
601 775 3.181487 TGCTCCGTACGTATTTAGGAACC 60.181 47.826 15.21 1.71 0.00 3.62
603 777 2.357637 TCCGTACGTATTTAGGAACCGG 59.642 50.000 15.21 0.00 0.00 5.28
604 778 2.357637 CCGTACGTATTTAGGAACCGGA 59.642 50.000 9.46 0.00 35.04 5.14
605 779 3.548818 CCGTACGTATTTAGGAACCGGAG 60.549 52.174 9.46 0.00 35.04 4.63
686 871 8.801913 GCATGAAAGCAAACTAAATGATAGAAC 58.198 33.333 0.00 0.00 0.00 3.01
755 940 1.006998 CTTCCCAATTCCCATCCACCA 59.993 52.381 0.00 0.00 0.00 4.17
764 949 6.314120 CAATTCCCATCCACCATTCCTAATA 58.686 40.000 0.00 0.00 0.00 0.98
947 1143 3.117360 TCCAGCTCTGATGATCTCTACCA 60.117 47.826 0.00 0.00 0.00 3.25
966 1162 4.220724 ACCAACACTGACTAGTAACCTCA 58.779 43.478 0.00 0.00 34.74 3.86
968 1164 4.281182 CCAACACTGACTAGTAACCTCAGT 59.719 45.833 8.05 8.05 44.42 3.41
1142 1338 3.554692 CGCGTTGATCCTCGGTGC 61.555 66.667 0.00 0.00 0.00 5.01
1245 1441 0.971386 TCGGTAAGGACGGCTTCTTT 59.029 50.000 0.00 0.00 0.00 2.52
1286 1482 1.798626 TCAGCTATCTCCAGCCATGT 58.201 50.000 0.00 0.00 42.84 3.21
1349 1549 9.639601 TGCCATGAATCTAGATAGTAAAATACG 57.360 33.333 5.46 0.00 0.00 3.06
1362 1562 9.597170 GATAGTAAAATACGAAAACCTCCTTCT 57.403 33.333 0.00 0.00 0.00 2.85
1363 1563 7.902387 AGTAAAATACGAAAACCTCCTTCTC 57.098 36.000 0.00 0.00 0.00 2.87
1370 1570 6.600882 ACGAAAACCTCCTTCTCAGTAATA 57.399 37.500 0.00 0.00 0.00 0.98
1388 1588 9.952030 TCAGTAATAAACCATAGTCAACAATCA 57.048 29.630 0.00 0.00 0.00 2.57
1596 1796 2.440539 TTCAAGCCACTCGAGAAGAC 57.559 50.000 21.68 3.49 0.00 3.01
1597 1797 1.328279 TCAAGCCACTCGAGAAGACA 58.672 50.000 21.68 0.00 0.00 3.41
1599 1799 1.998315 CAAGCCACTCGAGAAGACATG 59.002 52.381 21.68 5.38 0.00 3.21
1655 1855 4.562347 CCGTCTCTATGCAGGCATTATTCT 60.562 45.833 12.54 0.00 37.82 2.40
1660 1860 4.758674 TCTATGCAGGCATTATTCTTGAGC 59.241 41.667 12.54 0.00 37.82 4.26
1717 1917 4.201910 CCAATAAACACCTCCATAAGTGCG 60.202 45.833 0.00 0.00 37.51 5.34
1909 2109 4.439305 TGCACAGCCTATTTTCAATGTC 57.561 40.909 0.00 0.00 0.00 3.06
2002 2202 3.834813 TGGATGAGGTACCATATGAGCTC 59.165 47.826 15.94 6.82 39.99 4.09
2027 2227 4.018960 CCCCCTTTCTACATCTCATATGGG 60.019 50.000 2.13 0.00 0.00 4.00
2184 2713 1.210722 GTTTCCCTCTCCCCAGATGAC 59.789 57.143 0.00 0.00 0.00 3.06
2185 2714 0.326618 TTCCCTCTCCCCAGATGACC 60.327 60.000 0.00 0.00 0.00 4.02
2186 2715 2.136878 CCCTCTCCCCAGATGACCG 61.137 68.421 0.00 0.00 0.00 4.79
2196 2728 1.143183 AGATGACCGCGGCGTTTAT 59.857 52.632 28.58 12.56 0.00 1.40
2369 2901 3.758023 TCATCTCCAACGCAAATGTCATT 59.242 39.130 0.00 0.00 0.00 2.57
2401 2933 2.295349 CCTCCATATTCACAGCCAATGC 59.705 50.000 0.00 0.00 37.95 3.56
2497 3029 6.397272 TGGATGAAACTAAATGCAACCAATC 58.603 36.000 0.00 0.00 31.45 2.67
2506 3038 1.226379 GCAACCAATCCACATCGCG 60.226 57.895 0.00 0.00 0.00 5.87
2516 3048 0.445829 CCACATCGCGTGTTAATGCA 59.554 50.000 5.77 0.00 44.78 3.96
2602 3134 1.134461 ACAAGCAAAGTGGCAATGCAA 60.134 42.857 19.26 0.00 42.45 4.08
2640 3172 3.585990 GCGCCATCATCCCAACCG 61.586 66.667 0.00 0.00 0.00 4.44
2647 3179 3.496160 GCCATCATCCCAACCGTAGTAAT 60.496 47.826 0.00 0.00 0.00 1.89
2648 3180 4.262721 GCCATCATCCCAACCGTAGTAATA 60.263 45.833 0.00 0.00 0.00 0.98
2649 3181 5.743714 GCCATCATCCCAACCGTAGTAATAA 60.744 44.000 0.00 0.00 0.00 1.40
2683 3215 3.425577 TGCTTTTGGATTCATCGATGC 57.574 42.857 20.81 7.15 0.00 3.91
2687 3219 4.676196 GCTTTTGGATTCATCGATGCAGTT 60.676 41.667 20.81 4.83 0.00 3.16
2696 3228 7.689812 GGATTCATCGATGCAGTTATTAAATCG 59.310 37.037 20.81 0.00 41.04 3.34
2774 3309 2.939103 GCCAATGCGTTCATCTCTTACT 59.061 45.455 0.00 0.00 31.27 2.24
2778 3313 6.403200 GCCAATGCGTTCATCTCTTACTTTAA 60.403 38.462 0.00 0.00 31.27 1.52
2780 3315 7.360861 CCAATGCGTTCATCTCTTACTTTAACA 60.361 37.037 0.00 0.00 31.27 2.41
2853 3395 8.706492 TTTTTAAAAAGAGGCTGCATGATATG 57.294 30.769 9.31 0.00 0.00 1.78
2861 3403 3.635373 AGGCTGCATGATATGAACAAAGG 59.365 43.478 0.50 0.00 0.00 3.11
2862 3404 3.633525 GGCTGCATGATATGAACAAAGGA 59.366 43.478 0.50 0.00 0.00 3.36
2863 3405 4.098349 GGCTGCATGATATGAACAAAGGAA 59.902 41.667 0.50 0.00 0.00 3.36
2864 3406 5.221382 GGCTGCATGATATGAACAAAGGAAT 60.221 40.000 0.50 0.00 0.00 3.01
2867 3409 7.254319 GCTGCATGATATGAACAAAGGAATTTG 60.254 37.037 0.00 0.00 37.89 2.32
2897 3490 7.071698 ACATTCATGAAGGTATACTGGTCTGAT 59.928 37.037 23.29 0.00 33.15 2.90
3162 3755 9.178758 AGAAATCTAGGCCAAGTTTAATTACAG 57.821 33.333 5.01 0.00 0.00 2.74
3165 3758 6.412214 TCTAGGCCAAGTTTAATTACAGACC 58.588 40.000 5.01 0.00 0.00 3.85
3181 3774 9.601217 AATTACAGACCTATACTCACATGAAAC 57.399 33.333 0.00 0.00 0.00 2.78
3183 3776 5.104900 ACAGACCTATACTCACATGAAACCC 60.105 44.000 0.00 0.00 0.00 4.11
3187 3780 2.754946 TACTCACATGAAACCCGGAC 57.245 50.000 0.73 0.00 0.00 4.79
3221 3814 8.492415 AGGTCCATGTATAGTAGAATTAGCAA 57.508 34.615 0.00 0.00 0.00 3.91
3243 3836 5.223449 AGTTACAGCTACAAAAGTGGCTA 57.777 39.130 6.17 0.00 39.16 3.93
3274 3867 8.400947 CCATATGTTCCTAAAGACATGTTCTTG 58.599 37.037 0.00 0.00 44.41 3.02
3292 3885 6.826231 TGTTCTTGGTTGTTTATCTGTTCAGA 59.174 34.615 4.96 4.96 0.00 3.27
3403 3996 4.194640 GCCTGAATCTTGCTTATGAGTCA 58.805 43.478 0.00 0.00 36.19 3.41
3486 4079 9.117145 CAGTATTGTAAGTTTTGCAACTGTATG 57.883 33.333 0.00 0.00 42.89 2.39
3488 4081 9.113876 GTATTGTAAGTTTTGCAACTGTATGTC 57.886 33.333 0.00 0.00 42.89 3.06
3489 4082 6.935741 TGTAAGTTTTGCAACTGTATGTCT 57.064 33.333 0.00 0.00 42.89 3.41
3490 4083 8.439993 TTGTAAGTTTTGCAACTGTATGTCTA 57.560 30.769 0.00 0.00 42.89 2.59
3491 4084 8.439993 TGTAAGTTTTGCAACTGTATGTCTAA 57.560 30.769 0.00 0.00 42.89 2.10
3493 4086 7.801716 AAGTTTTGCAACTGTATGTCTAAGA 57.198 32.000 0.00 0.00 42.89 2.10
3494 4087 7.986085 AGTTTTGCAACTGTATGTCTAAGAT 57.014 32.000 0.00 0.00 42.05 2.40
3496 4089 7.445402 AGTTTTGCAACTGTATGTCTAAGATGT 59.555 33.333 0.00 0.00 42.05 3.06
3505 4177 6.156519 TGTATGTCTAAGATGTCACACACAC 58.843 40.000 0.00 0.00 38.04 3.82
3512 4184 5.895636 AAGATGTCACACACACAGAAAAA 57.104 34.783 0.00 0.00 38.04 1.94
3551 4223 4.750098 TCTCGTGTTTTGGATGTTTCTCTC 59.250 41.667 0.00 0.00 0.00 3.20
3558 4230 8.567948 GTGTTTTGGATGTTTCTCTCTATGAAA 58.432 33.333 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.366111 GCTTGCTCGTATTTGGCCGA 61.366 55.000 0.00 0.00 0.00 5.54
87 89 5.446340 CGTACAAGGTGACATCATGTGAATG 60.446 44.000 6.83 0.00 0.00 2.67
98 100 7.874016 AGATTACAATAAACGTACAAGGTGACA 59.126 33.333 0.00 0.00 0.00 3.58
103 105 7.748847 AGCAAGATTACAATAAACGTACAAGG 58.251 34.615 0.00 0.00 0.00 3.61
105 107 8.542497 AGAGCAAGATTACAATAAACGTACAA 57.458 30.769 0.00 0.00 0.00 2.41
167 173 2.367567 AGTCGGAAAGCAAGGTCAGTTA 59.632 45.455 0.00 0.00 0.00 2.24
172 178 0.034896 TGGAGTCGGAAAGCAAGGTC 59.965 55.000 0.00 0.00 0.00 3.85
197 203 5.026462 CACTTTGCTCGCATTCTTATCTTG 58.974 41.667 0.00 0.00 0.00 3.02
222 228 3.513515 GGTTTGCCATCCCTTTCATGTTA 59.486 43.478 0.00 0.00 34.09 2.41
224 230 1.901833 GGTTTGCCATCCCTTTCATGT 59.098 47.619 0.00 0.00 34.09 3.21
277 286 4.142249 GGAACCCATTTTTGGATCTTACGG 60.142 45.833 0.00 0.00 0.00 4.02
449 466 2.159382 TGCCGAAAGAGATGGAAAACC 58.841 47.619 0.00 0.00 0.00 3.27
466 483 5.366460 GGAGGGAGTAGTTTAGTTAATGCC 58.634 45.833 0.00 0.00 0.00 4.40
477 494 3.463048 TTAGGAACGGAGGGAGTAGTT 57.537 47.619 0.00 0.00 0.00 2.24
478 495 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
479 496 5.139001 AGTATTTAGGAACGGAGGGAGTAG 58.861 45.833 0.00 0.00 0.00 2.57
480 497 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
481 498 3.959449 GAGTATTTAGGAACGGAGGGAGT 59.041 47.826 0.00 0.00 0.00 3.85
538 555 9.947669 ACACTCTAAAATACGTCTATGTACATC 57.052 33.333 12.68 0.00 0.00 3.06
588 605 2.034124 TCCCTCCGGTTCCTAAATACG 58.966 52.381 0.00 0.00 0.00 3.06
601 775 0.179009 TGTCCCGTATACTCCCTCCG 60.179 60.000 0.56 0.00 0.00 4.63
603 777 3.703052 TCTTTTGTCCCGTATACTCCCTC 59.297 47.826 0.56 0.00 0.00 4.30
604 778 3.716431 TCTTTTGTCCCGTATACTCCCT 58.284 45.455 0.56 0.00 0.00 4.20
605 779 4.100498 TCATCTTTTGTCCCGTATACTCCC 59.900 45.833 0.56 0.00 0.00 4.30
606 780 5.272283 TCATCTTTTGTCCCGTATACTCC 57.728 43.478 0.56 0.00 0.00 3.85
607 781 6.513180 TCATCATCTTTTGTCCCGTATACTC 58.487 40.000 0.56 0.00 0.00 2.59
608 782 6.479972 TCATCATCTTTTGTCCCGTATACT 57.520 37.500 0.56 0.00 0.00 2.12
609 783 7.730364 AATCATCATCTTTTGTCCCGTATAC 57.270 36.000 0.00 0.00 0.00 1.47
610 784 8.746052 AAAATCATCATCTTTTGTCCCGTATA 57.254 30.769 0.00 0.00 0.00 1.47
611 785 7.645058 AAAATCATCATCTTTTGTCCCGTAT 57.355 32.000 0.00 0.00 0.00 3.06
612 786 7.461182 AAAAATCATCATCTTTTGTCCCGTA 57.539 32.000 0.00 0.00 0.00 4.02
614 788 7.761409 TCTAAAAATCATCATCTTTTGTCCCG 58.239 34.615 0.00 0.00 0.00 5.14
615 789 9.525409 CATCTAAAAATCATCATCTTTTGTCCC 57.475 33.333 0.00 0.00 0.00 4.46
616 790 9.028185 GCATCTAAAAATCATCATCTTTTGTCC 57.972 33.333 0.00 0.00 0.00 4.02
686 871 3.063997 ACTTTTGCTCGTCTCACAACTTG 59.936 43.478 0.00 0.00 0.00 3.16
755 940 1.772453 CGGTGGGTGGGTATTAGGAAT 59.228 52.381 0.00 0.00 0.00 3.01
966 1162 1.190833 CCACAGGTCTCTCTGGCACT 61.191 60.000 0.00 0.00 38.98 4.40
968 1164 3.797331 CCACAGGTCTCTCTGGCA 58.203 61.111 0.00 0.00 38.98 4.92
1132 1328 3.823330 GACGACGGCACCGAGGAT 61.823 66.667 17.40 0.00 42.83 3.24
1245 1441 0.698238 ATGGCTGAAACCTGGTGCTA 59.302 50.000 0.00 0.00 0.00 3.49
1286 1482 0.112995 ATGGAGCTTTGGAAGGCACA 59.887 50.000 0.00 0.00 0.00 4.57
1349 1549 7.664318 TGGTTTATTACTGAGAAGGAGGTTTTC 59.336 37.037 0.00 0.00 0.00 2.29
1351 1551 7.086685 TGGTTTATTACTGAGAAGGAGGTTT 57.913 36.000 0.00 0.00 0.00 3.27
1362 1562 9.952030 TGATTGTTGACTATGGTTTATTACTGA 57.048 29.630 0.00 0.00 0.00 3.41
1370 1570 6.237901 TGTAGCTGATTGTTGACTATGGTTT 58.762 36.000 0.00 0.00 0.00 3.27
1504 1704 4.567159 CGGTTTATCTCTTGTTGTAGCTCC 59.433 45.833 0.00 0.00 0.00 4.70
1570 1770 1.893062 GAGTGGCTTGAATTGGGGC 59.107 57.895 0.00 0.00 0.00 5.80
1596 1796 3.119291 GTCTCGGTCAGTATTCAGCATG 58.881 50.000 0.00 0.00 37.54 4.06
1597 1797 2.760650 TGTCTCGGTCAGTATTCAGCAT 59.239 45.455 0.00 0.00 0.00 3.79
1599 1799 2.941453 TGTCTCGGTCAGTATTCAGC 57.059 50.000 0.00 0.00 0.00 4.26
1655 1855 6.542005 TCAAATTCTACAACAGTGAAGCTCAA 59.458 34.615 0.00 0.00 0.00 3.02
1660 1860 8.562892 AGAACATCAAATTCTACAACAGTGAAG 58.437 33.333 0.00 0.00 34.59 3.02
1909 2109 1.528400 CGAATGCTCATGTCAAGCGTG 60.528 52.381 0.71 0.00 42.83 5.34
2184 2713 0.444651 TTTCTTCATAAACGCCGCGG 59.555 50.000 24.05 24.05 0.00 6.46
2185 2714 2.101125 CATTTCTTCATAAACGCCGCG 58.899 47.619 12.14 12.14 0.00 6.46
2186 2715 2.450160 CCATTTCTTCATAAACGCCGC 58.550 47.619 0.00 0.00 0.00 6.53
2196 2728 1.371467 TCAGCCTCCCCATTTCTTCA 58.629 50.000 0.00 0.00 0.00 3.02
2223 2755 5.125097 ACTTGATTCTGTGATGATTTCAGCC 59.875 40.000 0.00 0.00 34.17 4.85
2369 2901 3.459227 TGAATATGGAGGCATGGAAGTGA 59.541 43.478 0.00 0.00 0.00 3.41
2401 2933 1.152368 GAGGCATGGAAGGGGATGG 59.848 63.158 0.00 0.00 0.00 3.51
2506 3038 4.846779 TTGGAGGAAGTTGCATTAACAC 57.153 40.909 0.00 0.00 41.88 3.32
2516 3048 5.250313 AGAGAGATTGTCATTGGAGGAAGTT 59.750 40.000 0.00 0.00 0.00 2.66
2607 3139 2.568090 GCAATGGAGGTTGGTGCG 59.432 61.111 0.00 0.00 0.00 5.34
2661 3193 4.579753 TGCATCGATGAATCCAAAAGCATA 59.420 37.500 29.20 0.00 0.00 3.14
2662 3194 3.382227 TGCATCGATGAATCCAAAAGCAT 59.618 39.130 29.20 0.00 0.00 3.79
2665 3197 4.627611 ACTGCATCGATGAATCCAAAAG 57.372 40.909 29.20 7.28 0.00 2.27
2666 3198 6.698008 ATAACTGCATCGATGAATCCAAAA 57.302 33.333 29.20 6.12 0.00 2.44
2668 3200 7.800155 TTAATAACTGCATCGATGAATCCAA 57.200 32.000 29.20 9.17 0.00 3.53
2672 3204 8.087982 ACGATTTAATAACTGCATCGATGAAT 57.912 30.769 29.20 15.09 39.26 2.57
2675 3207 7.850492 TCAAACGATTTAATAACTGCATCGATG 59.150 33.333 21.27 21.27 39.26 3.84
2677 3209 7.297229 TCAAACGATTTAATAACTGCATCGA 57.703 32.000 10.59 0.00 39.26 3.59
2757 3291 6.874134 AGTGTTAAAGTAAGAGATGAACGCAT 59.126 34.615 0.00 0.00 37.47 4.73
2826 3368 7.605410 ATCATGCAGCCTCTTTTTAAAAATG 57.395 32.000 13.55 9.74 0.00 2.32
2840 3382 3.633525 TCCTTTGTTCATATCATGCAGCC 59.366 43.478 0.00 0.00 0.00 4.85
2841 3383 4.906065 TCCTTTGTTCATATCATGCAGC 57.094 40.909 0.00 0.00 0.00 5.25
2842 3384 7.223971 CCAAATTCCTTTGTTCATATCATGCAG 59.776 37.037 0.00 0.00 40.15 4.41
2853 3395 9.090692 CATGAATGTATCCAAATTCCTTTGTTC 57.909 33.333 0.00 0.00 40.15 3.18
2864 3406 9.559732 CAGTATACCTTCATGAATGTATCCAAA 57.440 33.333 28.74 15.66 35.07 3.28
2867 3409 7.680730 ACCAGTATACCTTCATGAATGTATCC 58.319 38.462 28.74 21.68 35.07 2.59
2874 3467 7.437713 AATCAGACCAGTATACCTTCATGAA 57.562 36.000 8.12 8.12 0.00 2.57
2907 3500 8.918202 AGTACCTGAAGAAAATTCAACATACA 57.082 30.769 0.00 0.00 0.00 2.29
2908 3501 9.612620 CAAGTACCTGAAGAAAATTCAACATAC 57.387 33.333 0.00 0.00 0.00 2.39
2924 3517 2.486982 GCTCGACTGTACAAGTACCTGA 59.513 50.000 7.82 0.81 40.07 3.86
2995 3588 3.362706 ACATGCAAATTCTGATCTGCCT 58.637 40.909 0.00 0.00 33.78 4.75
3160 3753 5.360591 GGGTTTCATGTGAGTATAGGTCTG 58.639 45.833 0.00 0.00 0.00 3.51
3162 3755 4.369182 CGGGTTTCATGTGAGTATAGGTC 58.631 47.826 0.00 0.00 0.00 3.85
3165 3758 4.142026 TGTCCGGGTTTCATGTGAGTATAG 60.142 45.833 0.00 0.00 0.00 1.31
3181 3774 0.679960 GACCTTGGGATTTGTCCGGG 60.680 60.000 0.00 0.00 0.00 5.73
3183 3776 2.868253 GGACCTTGGGATTTGTCCG 58.132 57.895 0.00 0.00 38.07 4.79
3187 3780 5.694995 ACTATACATGGACCTTGGGATTTG 58.305 41.667 11.77 4.78 0.00 2.32
3221 3814 4.086706 AGCCACTTTTGTAGCTGTAACT 57.913 40.909 0.00 0.00 45.24 2.24
3243 3836 4.227300 TGTCTTTAGGAACATATGGTGGCT 59.773 41.667 7.80 0.00 0.00 4.75
3403 3996 4.397417 GCAAGGAGCATTTACAGAACATCT 59.603 41.667 0.00 0.00 44.79 2.90
3459 4052 7.328277 ACAGTTGCAAAACTTACAATACTGA 57.672 32.000 12.35 0.00 0.00 3.41
3460 4053 9.117145 CATACAGTTGCAAAACTTACAATACTG 57.883 33.333 0.00 2.70 0.00 2.74
3463 4056 9.062524 AGACATACAGTTGCAAAACTTACAATA 57.937 29.630 0.00 0.00 0.00 1.90
3486 4079 4.871513 TCTGTGTGTGTGACATCTTAGAC 58.128 43.478 0.00 0.00 36.78 2.59
3488 4081 6.603237 TTTTCTGTGTGTGTGACATCTTAG 57.397 37.500 0.00 0.00 36.78 2.18
3489 4082 6.993786 TTTTTCTGTGTGTGTGACATCTTA 57.006 33.333 0.00 0.00 36.78 2.10
3490 4083 5.895636 TTTTTCTGTGTGTGTGACATCTT 57.104 34.783 0.00 0.00 36.78 2.40
3518 4190 9.396022 ACATCCAAAACACGAGAAAGATATAAT 57.604 29.630 0.00 0.00 0.00 1.28
3522 4194 7.444183 AGAAACATCCAAAACACGAGAAAGATA 59.556 33.333 0.00 0.00 0.00 1.98
3558 4230 4.795268 ACGCGTGTCTTCATAATATCGAT 58.205 39.130 12.93 2.16 0.00 3.59
3567 4239 2.157834 TGGTTTACGCGTGTCTTCAT 57.842 45.000 24.59 0.00 0.00 2.57
3568 4240 1.937278 TTGGTTTACGCGTGTCTTCA 58.063 45.000 24.59 10.84 0.00 3.02
3576 4248 5.677936 TGTACATTTAGTTTGGTTTACGCG 58.322 37.500 3.53 3.53 0.00 6.01


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

AutoCloner maintained by Alex Coulton.