Multiple sequence alignment - TraesCS4B01G089100

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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 TraesCS4B01G089100 chr4B 100.000 8131 0 0 1 8131 90499719 90507849 0.000000e+00 15016.0
1 TraesCS4B01G089100 chr4A 95.517 8165 266 33 1 8131 535432622 535424524 0.000000e+00 12959.0
2 TraesCS4B01G089100 chr4D 94.990 5010 175 30 3166 8131 62100040 62095063 0.000000e+00 7792.0
3 TraesCS4B01G089100 chr4D 97.577 3178 54 10 1 3167 62103299 62100134 0.000000e+00 5421.0
4 TraesCS4B01G089100 chr4D 83.146 356 51 7 7778 8131 101549435 101549087 4.740000e-82 316.0
5 TraesCS4B01G089100 chr4D 82.865 356 52 7 7778 8131 485945202 485945550 2.200000e-80 311.0
6 TraesCS4B01G089100 chr2D 83.473 357 49 8 7778 8131 63088679 63089028 2.830000e-84 324.0
7 TraesCS4B01G089100 chr2D 83.146 356 51 7 7778 8131 505672479 505672131 4.740000e-82 316.0
8 TraesCS4B01G089100 chr3A 82.913 357 51 8 7778 8131 112477323 112476974 6.130000e-81 313.0
9 TraesCS4B01G089100 chr3D 82.817 355 54 5 7778 8131 39940535 39940883 2.200000e-80 311.0
10 TraesCS4B01G089100 chr6B 82.240 366 58 5 7766 8130 594755401 594755760 7.930000e-80 309.0
11 TraesCS4B01G089100 chr3B 100.000 37 0 0 5761 5797 646007758 646007722 1.460000e-07 69.4


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 TraesCS4B01G089100 chr4B 90499719 90507849 8130 False 15016.0 15016 100.0000 1 8131 1 chr4B.!!$F1 8130
1 TraesCS4B01G089100 chr4A 535424524 535432622 8098 True 12959.0 12959 95.5170 1 8131 1 chr4A.!!$R1 8130
2 TraesCS4B01G089100 chr4D 62095063 62103299 8236 True 6606.5 7792 96.2835 1 8131 2 chr4D.!!$R2 8130

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
247 248 1.597742 TCTGTCCTTTGCTGTGAAGC 58.402 50.000 0.00 0.0 0.00 3.86 F
1226 1230 0.251341 ACAGAAGTGCCCAATGTCCC 60.251 55.000 0.00 0.0 0.00 4.46 F
2675 2686 0.325933 CTGCTGGTTCCTGGTCATCA 59.674 55.000 0.00 0.0 0.00 3.07 F
3113 3125 0.729116 CACACGGCCTGAATAAGCTG 59.271 55.000 0.00 0.0 41.32 4.24 F
5012 5132 0.034089 GGGCATGGTGAAGCTTAGGT 60.034 55.000 0.00 0.0 0.00 3.08 F
5725 5860 1.404449 CCATTGCAACGTGGCATGAAT 60.404 47.619 20.37 6.6 44.48 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2152 1.893808 CGGCTTGTCAGTGGTTGCT 60.894 57.895 0.00 0.0 0.00 3.91 R
3096 3108 1.009829 GACAGCTTATTCAGGCCGTG 58.990 55.000 0.00 0.0 0.00 4.94 R
4034 4149 0.174845 TCCCTACGCCAGTTGATTCG 59.825 55.000 0.00 0.0 0.00 3.34 R
5038 5160 0.109723 TCCGCTACAAACCTTGGCTT 59.890 50.000 0.00 0.0 34.12 4.35 R
6019 6166 0.900182 CCACAGGGAAAAGGAAGGCC 60.900 60.000 0.00 0.0 35.59 5.19 R
7294 7453 1.414181 ACGGCCAGAAGATACCATCAG 59.586 52.381 2.24 0.0 0.00 2.90 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
190 191 9.443323 TTCTTCACATATTTCCTCGAAATGTTA 57.557 29.630 9.36 0.00 41.55 2.41
221 222 9.973450 ATATGACTAGTTGACAGCTAAACTATG 57.027 33.333 13.33 10.86 38.02 2.23
247 248 1.597742 TCTGTCCTTTGCTGTGAAGC 58.402 50.000 0.00 0.00 0.00 3.86
296 297 8.859090 TGACAAGATTGTAGTTTTCATGGATTT 58.141 29.630 0.00 0.00 42.43 2.17
300 301 8.538409 AGATTGTAGTTTTCATGGATTTTTGC 57.462 30.769 0.00 0.00 0.00 3.68
345 346 8.445275 TGACTTCTTAACTTGTGATTTTGCTA 57.555 30.769 0.00 0.00 0.00 3.49
446 447 9.624697 CGAATCAATTTTAACCAGAAGAATGAA 57.375 29.630 0.00 0.00 0.00 2.57
537 538 7.320443 TGCAGTTTTGATGGATTGTCTATAC 57.680 36.000 0.00 0.00 0.00 1.47
573 574 7.455641 TTTTGGTTGACTTCTTAACTTGTGA 57.544 32.000 0.00 0.00 0.00 3.58
574 575 6.677781 TTGGTTGACTTCTTAACTTGTGAG 57.322 37.500 0.00 0.00 0.00 3.51
672 674 5.184479 TGCTCTTGATGCTAGCTTCAAAATT 59.816 36.000 33.09 5.82 38.84 1.82
768 770 6.624423 AGTTAGAAATTGCAATCATGACCAC 58.376 36.000 13.38 4.45 0.00 4.16
1226 1230 0.251341 ACAGAAGTGCCCAATGTCCC 60.251 55.000 0.00 0.00 0.00 4.46
1598 1609 7.386851 TCAATTTCCCCGTTTTGCATTTATTA 58.613 30.769 0.00 0.00 0.00 0.98
2055 2066 6.183360 GCAAAGGAATTCTTCATCGTGACATA 60.183 38.462 5.23 0.00 33.94 2.29
2141 2152 6.317140 GCAACATTTTATGATCCTGAGAGTCA 59.683 38.462 0.00 0.00 0.00 3.41
2244 2255 3.706594 CTGTGGATATGTGGAGTACAGGT 59.293 47.826 0.00 0.00 43.80 4.00
2675 2686 0.325933 CTGCTGGTTCCTGGTCATCA 59.674 55.000 0.00 0.00 0.00 3.07
2813 2824 2.152016 GGGTCTGTTAACAGCAACCTC 58.848 52.381 30.65 22.13 43.46 3.85
3065 3076 3.196469 TGGACTAGATCTGAGCTTGGTTG 59.804 47.826 5.18 0.00 0.00 3.77
3113 3125 0.729116 CACACGGCCTGAATAAGCTG 59.271 55.000 0.00 0.00 41.32 4.24
3121 3133 4.708177 GGCCTGAATAAGCTGTCAGATTA 58.292 43.478 19.05 12.70 43.32 1.75
3215 3322 6.373005 TCTAACCTGGTGAAGATCATCAAA 57.627 37.500 1.48 0.00 37.00 2.69
3383 3496 2.158726 GGACTTACCAAAGTGTCCACCA 60.159 50.000 6.18 0.00 46.09 4.17
3436 3549 5.435291 AGAGGAAGCAAGAAGGTATGATTG 58.565 41.667 0.00 0.00 0.00 2.67
3445 3558 6.349115 GCAAGAAGGTATGATTGCATATCCTG 60.349 42.308 4.02 0.00 45.66 3.86
3552 3665 2.208431 GCAGAATCTGTTCGATCAGGG 58.792 52.381 20.51 8.82 39.38 4.45
3554 3667 3.679917 GCAGAATCTGTTCGATCAGGGAA 60.680 47.826 20.51 4.99 39.38 3.97
3575 3688 6.353082 GGGAATGAGAATCCTAGAGAAAACCA 60.353 42.308 0.00 0.00 37.14 3.67
3578 3691 6.627087 TGAGAATCCTAGAGAAAACCATGT 57.373 37.500 0.00 0.00 0.00 3.21
3661 3774 7.550906 AGATGCTTCCTTTCTGTGTATAGTTTC 59.449 37.037 0.00 0.00 0.00 2.78
3704 3817 3.751175 CAGAAGAAACGGAATGCCTTACA 59.249 43.478 0.00 0.00 0.00 2.41
3798 3913 5.921976 TGCATTATTTGACTCTGTTGCTTTG 59.078 36.000 0.00 0.00 0.00 2.77
3971 4086 4.328983 CACGAAGTACCTGAACGCAAATAT 59.671 41.667 0.00 0.00 41.61 1.28
4034 4149 2.492088 GGGCTCAGACATGTTTAAACCC 59.508 50.000 15.59 5.61 0.00 4.11
4040 4155 5.309638 TCAGACATGTTTAAACCCGAATCA 58.690 37.500 15.59 0.00 0.00 2.57
4087 4202 4.067896 GCTTCTCACAACAAAGAGATGGA 58.932 43.478 0.00 0.00 40.32 3.41
4222 4339 2.743636 TGTCAGTTAAGCTTCGAGGG 57.256 50.000 0.00 0.00 0.00 4.30
4261 4378 3.069016 CCCAGTGATACTGTTGGCGTATA 59.931 47.826 8.04 0.00 44.50 1.47
4422 4542 8.394971 TGAATTATTTTCTGCTGAGAGTTCAA 57.605 30.769 0.00 0.00 31.69 2.69
4605 4725 7.631717 AGGGTAAGAGCAAAATAGTCAATTC 57.368 36.000 0.00 0.00 0.00 2.17
4744 4864 1.759445 AGATGAGTGGGATCGAACTGG 59.241 52.381 3.81 0.00 0.00 4.00
4778 4898 6.239008 CCAGCATTTCAAAGTTCAAAGTCCTA 60.239 38.462 0.00 0.00 0.00 2.94
4789 4909 2.912956 TCAAAGTCCTAGGATGGCAGTT 59.087 45.455 16.27 0.00 0.00 3.16
5012 5132 0.034089 GGGCATGGTGAAGCTTAGGT 60.034 55.000 0.00 0.00 0.00 3.08
5034 5156 5.112686 GTGCTGGAGGTCTAAGAAATACAG 58.887 45.833 0.00 0.00 0.00 2.74
5035 5157 4.777896 TGCTGGAGGTCTAAGAAATACAGT 59.222 41.667 0.00 0.00 0.00 3.55
5036 5158 5.955959 TGCTGGAGGTCTAAGAAATACAGTA 59.044 40.000 0.00 0.00 0.00 2.74
5037 5159 6.127423 TGCTGGAGGTCTAAGAAATACAGTAC 60.127 42.308 0.00 0.00 0.00 2.73
5038 5160 6.127423 GCTGGAGGTCTAAGAAATACAGTACA 60.127 42.308 0.00 0.00 0.00 2.90
5079 5201 3.773418 TTTTGACGGTTCATGGTCCTA 57.227 42.857 0.00 0.00 32.19 2.94
5266 5392 2.845659 AGTCCAGTATCCCACCATGAA 58.154 47.619 0.00 0.00 0.00 2.57
5271 5397 3.563261 CCAGTATCCCACCATGAAAACCA 60.563 47.826 0.00 0.00 0.00 3.67
5273 5399 4.082245 CAGTATCCCACCATGAAAACCAAC 60.082 45.833 0.00 0.00 0.00 3.77
5317 5444 7.424803 CATGACAACTGAACAAACTCCAAATA 58.575 34.615 0.00 0.00 0.00 1.40
5318 5445 7.397892 TGACAACTGAACAAACTCCAAATAA 57.602 32.000 0.00 0.00 0.00 1.40
5451 5579 9.018582 AGTTCAATCTTCCTGAAAAATTAGGAG 57.981 33.333 0.00 0.00 43.54 3.69
5476 5604 4.128925 TGCAATGACCAGATCAGACTAC 57.871 45.455 0.00 0.00 41.91 2.73
5519 5653 1.444836 TGCCCCGTATCTTGAAAACG 58.555 50.000 0.00 0.00 36.42 3.60
5660 5794 1.990060 TGACTCCCTACCTGGCTGC 60.990 63.158 0.00 0.00 0.00 5.25
5725 5860 1.404449 CCATTGCAACGTGGCATGAAT 60.404 47.619 20.37 6.60 44.48 2.57
5726 5861 2.339418 CATTGCAACGTGGCATGAATT 58.661 42.857 20.37 0.00 44.48 2.17
5727 5862 2.522836 TTGCAACGTGGCATGAATTT 57.477 40.000 20.37 0.00 44.48 1.82
5728 5863 2.522836 TGCAACGTGGCATGAATTTT 57.477 40.000 15.19 0.00 39.25 1.82
5783 5918 7.428020 TGAAATTCAGGAAAGAATTCACACAG 58.572 34.615 8.44 0.00 44.96 3.66
5834 5969 3.146847 AGTTCGAAAACAACAGATCCCC 58.853 45.455 0.00 0.00 37.88 4.81
5877 6012 9.533253 ACTGAAAATGAATCAAAAGAAAATCGT 57.467 25.926 0.00 0.00 0.00 3.73
5894 6029 3.928727 TCGTAACATTCTTGTCCGTCT 57.071 42.857 0.00 0.00 34.06 4.18
5970 6105 7.865889 CCTTTTGGTTCTAAATCCTACAAACAC 59.134 37.037 0.00 0.00 34.07 3.32
5983 6118 9.871238 AATCCTACAAACACAGTAGTATAGTTG 57.129 33.333 0.00 0.00 37.78 3.16
5985 6120 9.519191 TCCTACAAACACAGTAGTATAGTTGTA 57.481 33.333 0.00 0.00 37.78 2.41
5986 6121 9.784680 CCTACAAACACAGTAGTATAGTTGTAG 57.215 37.037 11.46 11.46 37.78 2.74
5989 6124 9.472361 ACAAACACAGTAGTATAGTTGTAGTTG 57.528 33.333 0.00 0.00 0.00 3.16
6019 6166 1.203994 CTCTCAAGGGCAAAATGGCAG 59.796 52.381 6.25 0.00 45.76 4.85
6128 6275 1.122019 AGAAGCTGTCCTCCACCGTT 61.122 55.000 0.00 0.00 0.00 4.44
6167 6314 0.034896 ACACTTCCGTCTCGCCATTT 59.965 50.000 0.00 0.00 0.00 2.32
6251 6398 4.642488 TCTGGCACCCACCCCGTA 62.642 66.667 0.00 0.00 0.00 4.02
6287 6434 2.114625 ACGTCCCACTCCGTCTCA 59.885 61.111 0.00 0.00 30.05 3.27
6374 6521 1.692395 TGGATGATCCTTGGGCGGA 60.692 57.895 13.44 0.00 37.46 5.54
7009 7168 0.941542 TGTGTAGCACTTTCGGCAAC 59.058 50.000 0.90 0.00 35.11 4.17
7198 7357 4.744795 TTTGATTGGGAGCTACTCTCTC 57.255 45.455 0.00 0.00 42.82 3.20
7199 7358 3.678965 TGATTGGGAGCTACTCTCTCT 57.321 47.619 0.00 0.00 42.94 3.10
7200 7359 3.561143 TGATTGGGAGCTACTCTCTCTC 58.439 50.000 0.00 0.00 42.94 3.20
7201 7360 3.204158 TGATTGGGAGCTACTCTCTCTCT 59.796 47.826 0.00 0.00 42.94 3.10
7225 7384 7.783119 TCTCCCTTCACTATTACTAGCACAATA 59.217 37.037 0.00 0.00 0.00 1.90
7226 7385 8.492415 TCCCTTCACTATTACTAGCACAATAT 57.508 34.615 0.00 0.00 0.00 1.28
7244 7403 6.019398 CACAATATCCGTGCGTTACTATGAAA 60.019 38.462 0.00 0.00 0.00 2.69
7286 7445 2.666317 TGTCATCGGCTTAGGAGATCA 58.334 47.619 0.00 0.00 0.00 2.92
7294 7453 3.249559 CGGCTTAGGAGATCATCAAAAGC 59.750 47.826 14.94 14.94 42.31 3.51
7388 7550 6.425577 AGTAACTGAAGAGTATCGAGTGAC 57.574 41.667 0.00 0.00 42.67 3.67
7408 7570 3.951663 ACCATAGTAGGTCCTTTGCAAC 58.048 45.455 0.00 0.00 37.28 4.17
7417 7579 6.828785 AGTAGGTCCTTTGCAACATTTATAGG 59.171 38.462 0.00 0.98 0.00 2.57
7520 7682 6.014156 GCACAAGATGGTAGATTAGGTAGGAT 60.014 42.308 0.00 0.00 0.00 3.24
7574 7736 3.857157 TGTTTGCCCCCATCTACTATC 57.143 47.619 0.00 0.00 0.00 2.08
7611 7773 2.859165 TTGGCTGGGTAGAGAAACTG 57.141 50.000 0.00 0.00 0.00 3.16
7684 7848 5.761234 TGTGTTTCTACAATAGTGGTGTTCC 59.239 40.000 0.00 0.00 35.69 3.62
7725 7889 1.138859 TGGGATATCTCGCACCTTGTG 59.861 52.381 2.05 0.00 39.22 3.33
8015 8180 9.231297 CTAAGTCTTTCAGATGGGTTTATCAAA 57.769 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
221 222 3.189287 CACAGCAAAGGACAGAACCATAC 59.811 47.826 0.00 0.00 0.00 2.39
247 248 7.850982 GTCATACACAACTAATCAATTTAGGCG 59.149 37.037 0.00 0.00 41.46 5.52
296 297 1.187974 CATGAGCAAGGGATGGCAAA 58.812 50.000 0.00 0.00 0.00 3.68
300 301 1.843368 ACAACATGAGCAAGGGATGG 58.157 50.000 0.00 0.00 0.00 3.51
446 447 3.771479 TCTGAGGCTACATCATGAACTGT 59.229 43.478 0.00 2.99 0.00 3.55
553 554 6.093633 ACAACTCACAAGTTAAGAAGTCAACC 59.906 38.462 0.00 0.00 43.99 3.77
554 555 6.961554 CACAACTCACAAGTTAAGAAGTCAAC 59.038 38.462 0.00 0.00 43.99 3.18
568 569 5.391097 CGTAAACCAAAGTCACAACTCACAA 60.391 40.000 0.00 0.00 33.48 3.33
569 570 4.093703 CGTAAACCAAAGTCACAACTCACA 59.906 41.667 0.00 0.00 33.48 3.58
570 571 4.495184 CCGTAAACCAAAGTCACAACTCAC 60.495 45.833 0.00 0.00 33.48 3.51
571 572 3.623960 CCGTAAACCAAAGTCACAACTCA 59.376 43.478 0.00 0.00 33.48 3.41
572 573 3.872771 TCCGTAAACCAAAGTCACAACTC 59.127 43.478 0.00 0.00 33.48 3.01
573 574 3.876341 TCCGTAAACCAAAGTCACAACT 58.124 40.909 0.00 0.00 37.32 3.16
574 575 4.514066 AGATCCGTAAACCAAAGTCACAAC 59.486 41.667 0.00 0.00 0.00 3.32
672 674 4.220382 AGCCAAATGTGATCGAAATTCCAA 59.780 37.500 0.00 0.00 0.00 3.53
1226 1230 3.134458 AGAACTGGCTTCTCTTTCAACG 58.866 45.455 0.00 0.00 33.53 4.10
1463 1467 6.876257 ACTTAATCTCTCAAACGAATCAGCTT 59.124 34.615 0.00 0.00 0.00 3.74
1598 1609 5.510179 CCTTGTCCAATCTGCAACTCAAAAT 60.510 40.000 0.00 0.00 0.00 1.82
1926 1937 5.412640 TCATGTCATGCATTCCAATCAAAC 58.587 37.500 8.03 0.00 35.19 2.93
2055 2066 4.328118 AATCAAGAGATTGGAGCCCTTT 57.672 40.909 0.00 0.00 42.72 3.11
2080 2091 3.328505 CAATCTTCAAAACACCATGGCC 58.671 45.455 13.04 0.00 0.00 5.36
2083 2094 4.682860 GTCAGCAATCTTCAAAACACCATG 59.317 41.667 0.00 0.00 0.00 3.66
2141 2152 1.893808 CGGCTTGTCAGTGGTTGCT 60.894 57.895 0.00 0.00 0.00 3.91
2244 2255 3.147629 CAGCAATTCCCCAAAAATGCAA 58.852 40.909 0.00 0.00 36.65 4.08
2813 2824 7.348080 TGGTACTAGTCCTGATCAGTATTTG 57.652 40.000 21.11 6.36 0.00 2.32
3096 3108 1.009829 GACAGCTTATTCAGGCCGTG 58.990 55.000 0.00 0.00 0.00 4.94
3113 3125 8.462016 AGTTTATTCCAGCAAACATAATCTGAC 58.538 33.333 0.00 0.00 37.16 3.51
3121 3133 5.769662 TCTGACAGTTTATTCCAGCAAACAT 59.230 36.000 1.59 0.00 37.16 2.71
3236 3343 4.469945 ACTAGCCAGCTGACCTAATAAACA 59.530 41.667 17.39 0.00 0.00 2.83
3383 3496 6.709846 GGAGTCTAGCATCATATTCTTTGCTT 59.290 38.462 1.22 0.00 42.52 3.91
3436 3549 6.426328 CCTATGAACAGAAAGACAGGATATGC 59.574 42.308 0.00 0.00 0.00 3.14
3445 3558 5.363939 CATCCTCCCTATGAACAGAAAGAC 58.636 45.833 0.00 0.00 0.00 3.01
3552 3665 7.772757 ACATGGTTTTCTCTAGGATTCTCATTC 59.227 37.037 0.00 0.00 0.00 2.67
3554 3667 7.205515 ACATGGTTTTCTCTAGGATTCTCAT 57.794 36.000 0.00 0.00 0.00 2.90
3704 3817 4.122776 GACGTAGGAGTGCATCATTTCAT 58.877 43.478 0.00 0.00 0.00 2.57
3746 3859 9.733556 TCCTGTTATTAAAAAGAGTGCAGAATA 57.266 29.630 0.00 0.00 0.00 1.75
3787 3902 3.419943 TGTATGATGGCAAAGCAACAGA 58.580 40.909 0.00 0.00 0.00 3.41
3788 3903 3.441222 TCTGTATGATGGCAAAGCAACAG 59.559 43.478 11.73 11.73 35.54 3.16
3798 3913 2.492012 CTGAAGCCTCTGTATGATGGC 58.508 52.381 0.00 0.00 45.21 4.40
3909 4024 0.323725 CCTCCCTTGTTCCATGTGGG 60.324 60.000 0.00 0.00 39.22 4.61
4034 4149 0.174845 TCCCTACGCCAGTTGATTCG 59.825 55.000 0.00 0.00 0.00 3.34
4040 4155 3.541632 CATAATGTTCCCTACGCCAGTT 58.458 45.455 0.00 0.00 0.00 3.16
4087 4202 2.256306 CCACCATTGGGCCTTTTACTT 58.744 47.619 4.53 0.00 39.57 2.24
4261 4378 1.243342 TTGCAGCATAAACAGCGCCT 61.243 50.000 2.29 0.00 37.01 5.52
4370 4490 8.015087 TCTTAAATCAAGCACTCACAAATAACG 58.985 33.333 0.00 0.00 33.94 3.18
4422 4542 5.511202 CCCAACAAAGGACAACATAAGCATT 60.511 40.000 0.00 0.00 0.00 3.56
4563 4683 3.099905 CCCTTGTAGTCCTGATCAGACA 58.900 50.000 24.62 16.62 0.00 3.41
4605 4725 0.616111 AGTAGCCACTGGACCAGAGG 60.616 60.000 28.44 28.44 43.41 3.69
4744 4864 4.992951 ACTTTGAAATGCTGGAATCTTTGC 59.007 37.500 0.00 0.00 0.00 3.68
4778 4898 3.325716 AGAAAAATGCAAACTGCCATCCT 59.674 39.130 0.00 0.00 44.23 3.24
4789 4909 5.942236 AGAGATGCTCTGTAGAAAAATGCAA 59.058 36.000 0.00 0.00 39.62 4.08
4804 4924 4.654091 AGTTGCTCTTCTAGAGATGCTC 57.346 45.455 7.85 0.00 45.07 4.26
4860 4980 7.500892 TCTTCAGCTGTACAAAAATGGAAGTAA 59.499 33.333 14.67 0.00 33.02 2.24
4865 4985 6.003326 TGATCTTCAGCTGTACAAAAATGGA 58.997 36.000 14.67 0.00 0.00 3.41
5012 5132 4.777896 ACTGTATTTCTTAGACCTCCAGCA 59.222 41.667 0.00 0.00 0.00 4.41
5034 5156 2.095919 CGCTACAAACCTTGGCTTGTAC 60.096 50.000 10.53 7.88 37.05 2.90
5035 5157 2.147958 CGCTACAAACCTTGGCTTGTA 58.852 47.619 13.08 13.08 37.05 2.41
5036 5158 0.951558 CGCTACAAACCTTGGCTTGT 59.048 50.000 12.29 12.29 39.13 3.16
5037 5159 0.240945 CCGCTACAAACCTTGGCTTG 59.759 55.000 1.66 1.66 34.12 4.01
5038 5160 0.109723 TCCGCTACAAACCTTGGCTT 59.890 50.000 0.00 0.00 34.12 4.35
5266 5392 3.130340 GCATAATCATCCACCGTTGGTTT 59.870 43.478 0.00 0.00 44.35 3.27
5271 5397 2.358898 GCTTGCATAATCATCCACCGTT 59.641 45.455 0.00 0.00 0.00 4.44
5273 5399 1.948834 TGCTTGCATAATCATCCACCG 59.051 47.619 0.00 0.00 0.00 4.94
5317 5444 1.000396 GACTGAGGCAGGCCCAATT 60.000 57.895 6.70 0.00 32.43 2.32
5318 5445 2.233566 TGACTGAGGCAGGCCCAAT 61.234 57.895 6.70 0.00 39.07 3.16
5373 5500 1.460504 CAGCAGCATCATGGTTCAGT 58.539 50.000 0.00 0.00 0.00 3.41
5451 5579 4.639310 AGTCTGATCTGGTCATTGCATTTC 59.361 41.667 0.00 0.00 35.97 2.17
5476 5604 7.278135 CAATGGGGTATATGTCATAGGAGATG 58.722 42.308 0.00 0.00 0.00 2.90
5519 5653 5.104735 AGGATCAGATCTACAACCACCTTTC 60.105 44.000 10.36 0.00 0.00 2.62
5834 5969 9.793252 CATTTTCAGTTATAAACATGGGAAGAG 57.207 33.333 0.00 0.00 0.00 2.85
5869 6004 5.923665 ACGGACAAGAATGTTACGATTTTC 58.076 37.500 11.89 0.00 40.74 2.29
5870 6005 5.699458 AGACGGACAAGAATGTTACGATTTT 59.301 36.000 11.89 0.00 40.74 1.82
5876 6011 3.927142 CCTGAGACGGACAAGAATGTTAC 59.073 47.826 0.00 0.00 40.74 2.50
5877 6012 3.056107 CCCTGAGACGGACAAGAATGTTA 60.056 47.826 0.00 0.00 40.74 2.41
5894 6029 5.128499 TCTTGATTTCTTTTTGTTGCCCTGA 59.872 36.000 0.00 0.00 0.00 3.86
5981 6116 8.946085 CCTTGAGAGCAAAATATACAACTACAA 58.054 33.333 0.00 0.00 32.73 2.41
5983 6118 7.467403 GCCCTTGAGAGCAAAATATACAACTAC 60.467 40.741 0.00 0.00 32.73 2.73
5985 6120 5.358160 GCCCTTGAGAGCAAAATATACAACT 59.642 40.000 0.00 0.00 32.73 3.16
5986 6121 5.125417 TGCCCTTGAGAGCAAAATATACAAC 59.875 40.000 0.00 0.00 35.69 3.32
5987 6122 5.260424 TGCCCTTGAGAGCAAAATATACAA 58.740 37.500 0.00 0.00 35.69 2.41
5989 6124 5.835113 TTGCCCTTGAGAGCAAAATATAC 57.165 39.130 0.00 0.00 45.51 1.47
6019 6166 0.900182 CCACAGGGAAAAGGAAGGCC 60.900 60.000 0.00 0.00 35.59 5.19
6248 6395 4.508128 ATGGTGGACGCGCCTACG 62.508 66.667 18.14 0.00 44.07 3.51
6251 6398 3.740128 GATCATGGTGGACGCGCCT 62.740 63.158 18.14 0.00 37.63 5.52
6374 6521 3.699894 CCGGACTGCACTGCCTCT 61.700 66.667 0.00 0.00 0.00 3.69
7198 7357 5.594725 TGTGCTAGTAATAGTGAAGGGAGAG 59.405 44.000 0.00 0.00 0.00 3.20
7199 7358 5.516044 TGTGCTAGTAATAGTGAAGGGAGA 58.484 41.667 0.00 0.00 0.00 3.71
7200 7359 5.854010 TGTGCTAGTAATAGTGAAGGGAG 57.146 43.478 0.00 0.00 0.00 4.30
7201 7360 6.808321 ATTGTGCTAGTAATAGTGAAGGGA 57.192 37.500 0.00 0.00 0.00 4.20
7225 7384 4.689071 TGATTTCATAGTAACGCACGGAT 58.311 39.130 0.00 0.00 0.00 4.18
7226 7385 4.112716 TGATTTCATAGTAACGCACGGA 57.887 40.909 0.00 0.00 0.00 4.69
7271 7430 4.697514 CTTTTGATGATCTCCTAAGCCGA 58.302 43.478 0.00 0.00 0.00 5.54
7294 7453 1.414181 ACGGCCAGAAGATACCATCAG 59.586 52.381 2.24 0.00 0.00 2.90
7307 7466 2.267351 TGAACCATGCAACGGCCAG 61.267 57.895 2.24 0.00 40.13 4.85
7340 7500 9.494479 CTACAACATGATTTTGCACTATAGTTG 57.506 33.333 1.56 0.00 38.71 3.16
7351 7513 9.817365 CTCTTCAGTTACTACAACATGATTTTG 57.183 33.333 0.00 0.00 0.00 2.44
7388 7550 3.950397 TGTTGCAAAGGACCTACTATGG 58.050 45.455 0.00 0.00 0.00 2.74
7520 7682 3.953712 ACACGGTGATAGATGTTGTCA 57.046 42.857 16.29 0.00 0.00 3.58
7611 7773 4.510038 ACTCAAACATGGTCTTGATTGC 57.490 40.909 0.00 0.00 31.56 3.56
7657 7821 7.023197 ACACCACTATTGTAGAAACACAAAC 57.977 36.000 0.00 0.00 41.50 2.93
8000 8165 9.277783 CGAGATTAGATTTTGATAAACCCATCT 57.722 33.333 0.00 0.00 0.00 2.90
8003 8168 9.627123 ATTCGAGATTAGATTTTGATAAACCCA 57.373 29.630 0.00 0.00 0.00 4.51
8050 8215 9.077885 GAATTGGCTAAATACCAGAATAATCCA 57.922 33.333 0.00 0.00 38.73 3.41
8059 8224 3.815401 CTCCGGAATTGGCTAAATACCAG 59.185 47.826 5.23 0.00 38.73 4.00


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

AutoCloner maintained by Alex Coulton.