Multiple sequence alignment - TraesCS2D01G031400

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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 TraesCS2D01G031400 chr2D 100.000 5929 0 0 1 5929 12618687 12624615 0.000000e+00 10949
1 TraesCS2D01G031400 chr2D 90.895 637 48 9 5292 5924 12629868 12630498 0.000000e+00 846
2 TraesCS2D01G031400 chr2A 93.601 5735 256 56 244 5929 14675861 14681533 0.000000e+00 8455
3 TraesCS2D01G031400 chr2A 89.987 769 53 12 5168 5929 14706534 14707285 0.000000e+00 972
4 TraesCS2D01G031400 chr2A 87.136 583 41 17 5168 5746 14725567 14726119 1.080000e-176 630
5 TraesCS2D01G031400 chr2A 90.500 400 20 8 5168 5566 14694139 14694521 4.100000e-141 512
6 TraesCS2D01G031400 chr2A 89.600 375 34 3 5559 5929 14726122 14726495 6.960000e-129 472
7 TraesCS2D01G031400 chr2A 89.408 321 25 3 5134 5454 14716183 14716494 4.310000e-106 396
8 TraesCS2D01G031400 chr2A 87.725 334 33 3 5597 5926 14694520 14694849 3.350000e-102 383
9 TraesCS2D01G031400 chr2B 91.945 5984 341 61 4 5929 20154387 20148487 0.000000e+00 8250


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 TraesCS2D01G031400 chr2D 12618687 12624615 5928 False 10949.0 10949 100.0000 1 5929 1 chr2D.!!$F1 5928
1 TraesCS2D01G031400 chr2D 12629868 12630498 630 False 846.0 846 90.8950 5292 5924 1 chr2D.!!$F2 632
2 TraesCS2D01G031400 chr2A 14675861 14681533 5672 False 8455.0 8455 93.6010 244 5929 1 chr2A.!!$F1 5685
3 TraesCS2D01G031400 chr2A 14706534 14707285 751 False 972.0 972 89.9870 5168 5929 1 chr2A.!!$F2 761
4 TraesCS2D01G031400 chr2A 14725567 14726495 928 False 551.0 630 88.3680 5168 5929 2 chr2A.!!$F5 761
5 TraesCS2D01G031400 chr2A 14694139 14694849 710 False 447.5 512 89.1125 5168 5926 2 chr2A.!!$F4 758
6 TraesCS2D01G031400 chr2B 20148487 20154387 5900 True 8250.0 8250 91.9450 4 5929 1 chr2B.!!$R1 5925

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
898 921 0.252927 CCACCTTCCCTCCTCCTTCT 60.253 60.0 0.0 0.0 0.00 2.85 F
1537 1591 0.175989 TTTCGGTGGGGTTTTTGTGC 59.824 50.0 0.0 0.0 0.00 4.57 F
1540 1594 0.176910 CGGTGGGGTTTTTGTGCTTT 59.823 50.0 0.0 0.0 0.00 3.51 F
1613 1679 0.322546 GCTCGAATGGTCCTTTGGGT 60.323 55.0 0.0 0.0 0.00 4.51 F
3548 3641 0.173935 TAGTGGATGTAACACGCCCG 59.826 55.0 0.0 0.0 43.41 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2353 2433 1.004044 ACAGAGTGCAGCTAATTGCCT 59.996 47.619 0.00 0.0 43.43 4.75 R
2968 3052 1.135257 CCAACGAGGCTGAGACAGTAG 60.135 57.143 0.00 0.0 33.43 2.57 R
3538 3631 1.666553 CAAGACAGCGGGCGTGTTA 60.667 57.895 0.00 0.0 0.00 2.41 R
3639 3732 8.894768 AGTGTGCTTAAGATAGATTAATGGAC 57.105 34.615 6.67 0.0 0.00 4.02 R
5204 5308 0.401356 TGGATGGCTCAGTTGCTGAA 59.599 50.000 0.37 0.0 40.18 3.02 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
66 70 4.922206 ACCAGCAGAAAACAAGATATGGA 58.078 39.130 0.00 0.00 0.00 3.41
80 84 4.796606 AGATATGGACAATTCCCAACAGG 58.203 43.478 0.64 0.00 42.01 4.00
97 101 5.124457 CCAACAGGAAACAAGATATGGACAG 59.876 44.000 0.00 0.00 0.00 3.51
100 104 6.644347 ACAGGAAACAAGATATGGACAGTAG 58.356 40.000 0.00 0.00 0.00 2.57
109 113 8.424918 ACAAGATATGGACAGTAGACTTTATGG 58.575 37.037 0.00 0.00 0.00 2.74
111 115 8.964533 AGATATGGACAGTAGACTTTATGGAT 57.035 34.615 0.00 0.00 0.00 3.41
134 138 8.349245 GGATATATCTGTTGATCCTATCTCACG 58.651 40.741 12.42 0.00 35.86 4.35
135 139 8.815565 ATATATCTGTTGATCCTATCTCACGT 57.184 34.615 0.00 0.00 34.32 4.49
136 140 5.860941 ATCTGTTGATCCTATCTCACGTT 57.139 39.130 0.00 0.00 0.00 3.99
137 141 5.661056 TCTGTTGATCCTATCTCACGTTT 57.339 39.130 0.00 0.00 0.00 3.60
138 142 5.651530 TCTGTTGATCCTATCTCACGTTTC 58.348 41.667 0.00 0.00 0.00 2.78
140 144 5.977635 TGTTGATCCTATCTCACGTTTCAT 58.022 37.500 0.00 0.00 0.00 2.57
189 193 5.105513 TGTGTTCTTAGTCACAAGAGACACA 60.106 40.000 19.39 19.39 43.87 3.72
196 200 1.611977 TCACAAGAGACACACCTACGG 59.388 52.381 0.00 0.00 0.00 4.02
250 255 4.931661 TCCGTCACCCATTATCTAGTTC 57.068 45.455 0.00 0.00 0.00 3.01
269 274 1.012086 CCATCACCACATCTTCAGCG 58.988 55.000 0.00 0.00 0.00 5.18
276 281 1.369625 CACATCTTCAGCGTTACCCC 58.630 55.000 0.00 0.00 0.00 4.95
286 292 2.743538 GTTACCCCGCCAACCGTC 60.744 66.667 0.00 0.00 34.38 4.79
287 293 4.376176 TTACCCCGCCAACCGTCG 62.376 66.667 0.00 0.00 34.38 5.12
338 344 2.033424 AGAACTCAAAGCTTTTCGTGCC 59.967 45.455 9.53 5.74 0.00 5.01
359 365 2.125793 GGGCGGACGACCTTACAC 60.126 66.667 9.83 0.00 41.04 2.90
372 378 0.666274 CTTACACCGTTCTGCGCTCA 60.666 55.000 9.73 0.00 39.71 4.26
388 394 2.607635 CGCTCACGGCACTATTTACATT 59.392 45.455 0.00 0.00 41.91 2.71
400 417 7.218204 GGCACTATTTACATTCGAACAAATGTC 59.782 37.037 17.82 6.90 44.53 3.06
412 429 4.614284 CGAACAAATGTCTAGTTACGTCGT 59.386 41.667 2.21 2.21 0.00 4.34
413 430 5.116074 CGAACAAATGTCTAGTTACGTCGTT 59.884 40.000 1.78 0.00 0.00 3.85
430 447 4.560035 CGTCGTTACGTCTTAAACATCCAT 59.440 41.667 4.24 0.00 44.21 3.41
434 451 5.220340 CGTTACGTCTTAAACATCCATGTCC 60.220 44.000 0.00 0.00 40.80 4.02
438 455 4.340617 GTCTTAAACATCCATGTCCCCAA 58.659 43.478 0.00 0.00 40.80 4.12
512 531 0.693622 TCAATGCTTTCCGTACCCCA 59.306 50.000 0.00 0.00 0.00 4.96
519 538 0.472352 TTTCCGTACCCCACCAGTCT 60.472 55.000 0.00 0.00 0.00 3.24
522 541 1.305046 CGTACCCCACCAGTCTCCT 60.305 63.158 0.00 0.00 0.00 3.69
523 542 1.321074 CGTACCCCACCAGTCTCCTC 61.321 65.000 0.00 0.00 0.00 3.71
571 591 4.340950 CCCATTTATTATTCCAGCCAACGT 59.659 41.667 0.00 0.00 0.00 3.99
577 597 4.752661 TTATTCCAGCCAACGTAACAAC 57.247 40.909 0.00 0.00 0.00 3.32
580 602 1.572447 CAGCCAACGTAACAACGGG 59.428 57.895 2.76 0.00 37.45 5.28
586 608 2.925563 CCAACGTAACAACGGGAGTATC 59.074 50.000 2.76 0.00 46.69 2.24
636 658 1.053424 AACCTCCAACGGTAAGCTCA 58.947 50.000 0.00 0.00 35.89 4.26
686 708 2.879233 GCCCGCCTCCCATAATCGA 61.879 63.158 0.00 0.00 0.00 3.59
694 716 2.354103 CCTCCCATAATCGATGATGCGT 60.354 50.000 16.36 0.00 37.82 5.24
722 744 2.024226 GATTCGCGCATCGTCTTGCA 62.024 55.000 8.75 0.00 42.91 4.08
726 748 3.112075 CGCATCGTCTTGCACCGT 61.112 61.111 0.00 0.00 42.91 4.83
761 783 4.919754 GCAACAAACATTTGCCAAAAACAA 59.080 33.333 4.25 0.00 43.02 2.83
764 786 6.566197 ACAAACATTTGCCAAAAACAAGAA 57.434 29.167 4.25 0.00 41.79 2.52
783 805 6.653740 ACAAGAACCGAAAACCCTCTATAAAG 59.346 38.462 0.00 0.00 0.00 1.85
799 822 4.783764 ATAAAGCCCAAGAAAAACCTCG 57.216 40.909 0.00 0.00 0.00 4.63
804 827 2.031069 GCCCAAGAAAAACCTCGAGAAC 60.031 50.000 15.71 0.00 0.00 3.01
898 921 0.252927 CCACCTTCCCTCCTCCTTCT 60.253 60.000 0.00 0.00 0.00 2.85
1386 1432 2.538939 GCCGGTAAGTCAATCGAAATGC 60.539 50.000 1.90 0.00 0.00 3.56
1388 1434 3.242413 CCGGTAAGTCAATCGAAATGCAG 60.242 47.826 0.00 0.00 0.00 4.41
1451 1497 4.489795 GATGCTGCGTCGTGTGCG 62.490 66.667 6.05 0.00 39.92 5.34
1489 1542 1.139256 TCCTAGTGTTCGTTGCCACAA 59.861 47.619 0.00 0.00 33.99 3.33
1536 1590 2.900716 ATTTCGGTGGGGTTTTTGTG 57.099 45.000 0.00 0.00 0.00 3.33
1537 1591 0.175989 TTTCGGTGGGGTTTTTGTGC 59.824 50.000 0.00 0.00 0.00 4.57
1538 1592 0.684805 TTCGGTGGGGTTTTTGTGCT 60.685 50.000 0.00 0.00 0.00 4.40
1539 1593 0.684805 TCGGTGGGGTTTTTGTGCTT 60.685 50.000 0.00 0.00 0.00 3.91
1540 1594 0.176910 CGGTGGGGTTTTTGTGCTTT 59.823 50.000 0.00 0.00 0.00 3.51
1541 1595 1.804746 CGGTGGGGTTTTTGTGCTTTC 60.805 52.381 0.00 0.00 0.00 2.62
1542 1596 1.474320 GGTGGGGTTTTTGTGCTTTCC 60.474 52.381 0.00 0.00 0.00 3.13
1543 1597 1.484653 GTGGGGTTTTTGTGCTTTCCT 59.515 47.619 0.00 0.00 0.00 3.36
1544 1598 1.484240 TGGGGTTTTTGTGCTTTCCTG 59.516 47.619 0.00 0.00 0.00 3.86
1545 1599 1.484653 GGGGTTTTTGTGCTTTCCTGT 59.515 47.619 0.00 0.00 0.00 4.00
1546 1600 2.696187 GGGGTTTTTGTGCTTTCCTGTA 59.304 45.455 0.00 0.00 0.00 2.74
1547 1601 3.243737 GGGGTTTTTGTGCTTTCCTGTAG 60.244 47.826 0.00 0.00 0.00 2.74
1554 1620 1.953686 GTGCTTTCCTGTAGGTTTGCA 59.046 47.619 0.00 4.48 36.34 4.08
1613 1679 0.322546 GCTCGAATGGTCCTTTGGGT 60.323 55.000 0.00 0.00 0.00 4.51
1634 1700 5.221461 GGGTAGTGGTAATGTATCCAGTGAG 60.221 48.000 0.00 0.00 37.83 3.51
1635 1701 5.221461 GGTAGTGGTAATGTATCCAGTGAGG 60.221 48.000 0.00 0.00 37.83 3.86
1639 1705 4.405680 TGGTAATGTATCCAGTGAGGTCTG 59.594 45.833 0.00 0.00 39.02 3.51
1665 1731 6.428159 CCATGACTAAGGGCAATACTGTAATC 59.572 42.308 0.00 0.00 0.00 1.75
1759 1825 0.738389 ACAAACCTGCACTCCAAACG 59.262 50.000 0.00 0.00 0.00 3.60
1774 1840 4.565531 ACGTGAAATCGACGTCCC 57.434 55.556 10.58 0.00 46.85 4.46
1781 1847 2.289133 TGAAATCGACGTCCCATTGACA 60.289 45.455 10.58 9.64 44.71 3.58
1817 1883 3.454082 AGGGAACATCTCAGATGAAGACC 59.546 47.826 22.08 15.89 0.00 3.85
1909 1987 9.725019 TTTCTATGCACTTATCTTTCTCTTCAA 57.275 29.630 0.00 0.00 0.00 2.69
1977 2055 5.163437 GGTGACCCAGGTTGTCTAAGTATAG 60.163 48.000 0.00 0.00 33.83 1.31
1979 2057 6.604795 GTGACCCAGGTTGTCTAAGTATAGTA 59.395 42.308 0.00 0.00 33.83 1.82
1985 2063 8.838365 CCAGGTTGTCTAAGTATAGTAGTAGTG 58.162 40.741 0.00 0.00 0.00 2.74
2086 2164 2.969821 TATGACCTTTTGCACCTGGT 57.030 45.000 0.00 0.00 35.23 4.00
2091 2169 2.552743 GACCTTTTGCACCTGGTCTTAC 59.447 50.000 18.52 0.00 43.91 2.34
2128 2208 5.661312 TCCTGGTACTGAACTTATAGTGCAT 59.339 40.000 0.00 0.00 32.25 3.96
2188 2268 7.224753 ACTCTGTTTTTGCAGTGTATATATCCG 59.775 37.037 0.00 0.00 40.18 4.18
2315 2395 4.639135 TCAAGACTCATGGATGTCGTAG 57.361 45.455 0.00 0.00 38.16 3.51
2336 2416 9.653287 TCGTAGTTCATCTTTAGAAATGACATT 57.347 29.630 0.00 0.00 31.83 2.71
2340 2420 8.025445 AGTTCATCTTTAGAAATGACATTGTGC 58.975 33.333 0.34 0.00 31.83 4.57
2353 2433 8.978874 AATGACATTGTGCTCTAATATGGTTA 57.021 30.769 0.00 0.00 0.00 2.85
2421 2502 7.974501 AGACTATAAGTGTTACCAACATCTTCG 59.025 37.037 8.90 0.00 44.35 3.79
2638 2719 3.923412 ACAAAATATTCGATGTGCGTCG 58.077 40.909 7.42 7.42 42.74 5.12
2655 2739 3.602491 GCGTCGCTGTCATTTGATGATAC 60.602 47.826 10.68 0.00 42.04 2.24
2657 2741 4.268644 CGTCGCTGTCATTTGATGATACTT 59.731 41.667 0.00 0.00 42.04 2.24
2663 2747 6.510799 GCTGTCATTTGATGATACTTCTTCCG 60.511 42.308 0.00 0.00 42.04 4.30
2800 2884 5.890334 TGCTGTTGTTCTTCCAAAGTTAAG 58.110 37.500 0.00 0.00 0.00 1.85
3024 3108 3.674997 TCATTGTCTGGAGTTTAGTGCC 58.325 45.455 0.00 0.00 0.00 5.01
3209 3293 7.518161 TGTCGTAGCTTTTTACTGATGAAATG 58.482 34.615 0.00 0.00 0.00 2.32
3211 3295 7.900352 GTCGTAGCTTTTTACTGATGAAATGAG 59.100 37.037 0.00 0.00 32.05 2.90
3365 3450 7.930865 TCATGCTTTATATACATACACTGTGCA 59.069 33.333 7.90 0.00 38.92 4.57
3421 3514 6.726490 TTATAGAGGGACGTCTATTTGCTT 57.274 37.500 16.46 0.00 39.86 3.91
3486 3579 4.358214 TGACTAATCAGACCATGGGTGTA 58.642 43.478 18.09 0.00 35.25 2.90
3538 3631 5.105106 TGTGTACCGATGATTTAGTGGATGT 60.105 40.000 0.00 0.00 0.00 3.06
3548 3641 0.173935 TAGTGGATGTAACACGCCCG 59.826 55.000 0.00 0.00 43.41 6.13
3639 3732 7.172875 CCAGAGGAATAAAGCACATATCAGAAG 59.827 40.741 0.00 0.00 0.00 2.85
3706 3807 1.601412 GCCTTGCTCAAAGTTCACAGC 60.601 52.381 0.00 0.00 33.66 4.40
3711 3812 2.056577 GCTCAAAGTTCACAGCATTGC 58.943 47.619 0.00 0.00 0.00 3.56
3779 3881 1.817099 GCAGGCCCATCTTCTGACG 60.817 63.158 0.00 0.00 0.00 4.35
3785 3887 0.036010 CCCATCTTCTGACGGCAAGT 60.036 55.000 0.00 0.00 0.00 3.16
4147 4251 9.177608 TGTATCTTTCCAAGGAAGATATTTGTG 57.822 33.333 16.69 0.00 35.38 3.33
4217 4321 6.187727 TCTTCTTCCTGTAATCACAAAGGT 57.812 37.500 0.00 0.00 33.22 3.50
4233 4337 4.649218 ACAAAGGTATTTCAACAACTGCCT 59.351 37.500 0.00 0.00 29.74 4.75
4499 4603 6.184068 TGCTATTTGATAAGGTAAACTGCCA 58.816 36.000 0.00 0.00 0.00 4.92
4504 4608 6.909550 TTGATAAGGTAAACTGCCACAAAT 57.090 33.333 0.00 0.00 0.00 2.32
4740 4844 2.972625 ACCATCCAGTACACATGAACG 58.027 47.619 0.00 0.00 0.00 3.95
4745 4849 1.665679 CCAGTACACATGAACGGATGC 59.334 52.381 0.00 0.00 0.00 3.91
4965 5069 1.268032 CGTGGCGAAATAGCAATGACC 60.268 52.381 0.00 0.00 39.27 4.02
5040 5144 1.270839 CCTTCAGCGGGAGTCTTTCAA 60.271 52.381 0.00 0.00 0.00 2.69
5204 5308 8.574853 TGGTACATCTATATACATGGGATAGGT 58.425 37.037 0.00 0.00 0.00 3.08
5260 5364 0.465705 AGAGGGACTGTGTGTGTGTG 59.534 55.000 0.00 0.00 41.55 3.82
5261 5365 0.178068 GAGGGACTGTGTGTGTGTGT 59.822 55.000 0.00 0.00 41.55 3.72
5310 5414 1.064166 AGAGGAAGGCCAACATCCATG 60.064 52.381 5.01 0.00 35.62 3.66
5396 5503 2.501723 TCCTGACTGGCAACCTAGATTC 59.498 50.000 0.00 0.00 35.26 2.52
5515 5626 1.070786 AGCCTTTCTTTCGGTCGCA 59.929 52.632 0.00 0.00 0.00 5.10
5613 5895 0.904649 TGACATGGCATCTTCTCGGT 59.095 50.000 0.00 0.00 0.00 4.69
5726 6011 3.101437 TGCATGATCTTGGCCATTTCTT 58.899 40.909 6.09 0.00 0.00 2.52
5834 6121 7.544566 ACATTTCAGAAAGTGATGATCAATTGC 59.455 33.333 9.01 7.21 34.67 3.56
5869 6156 6.346477 TGTAGAACTAGCAACTCTTGTCAT 57.654 37.500 0.00 0.00 30.52 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.415701 TCCATATCTTGTTTTCTGCTGGTTC 59.584 40.000 0.00 0.00 0.00 3.62
43 44 5.183904 GTCCATATCTTGTTTTCTGCTGGTT 59.816 40.000 0.00 0.00 0.00 3.67
44 45 4.702131 GTCCATATCTTGTTTTCTGCTGGT 59.298 41.667 0.00 0.00 0.00 4.00
45 46 4.701651 TGTCCATATCTTGTTTTCTGCTGG 59.298 41.667 0.00 0.00 0.00 4.85
46 47 5.885230 TGTCCATATCTTGTTTTCTGCTG 57.115 39.130 0.00 0.00 0.00 4.41
47 48 7.363268 GGAATTGTCCATATCTTGTTTTCTGCT 60.363 37.037 0.00 0.00 44.26 4.24
80 84 8.779354 AAAGTCTACTGTCCATATCTTGTTTC 57.221 34.615 0.00 0.00 0.00 2.78
83 87 8.424918 CCATAAAGTCTACTGTCCATATCTTGT 58.575 37.037 0.00 0.00 0.00 3.16
109 113 8.898761 ACGTGAGATAGGATCAACAGATATATC 58.101 37.037 4.42 4.42 0.00 1.63
111 115 8.637196 AACGTGAGATAGGATCAACAGATATA 57.363 34.615 0.00 0.00 0.00 0.86
118 122 5.235186 CCATGAAACGTGAGATAGGATCAAC 59.765 44.000 0.00 0.00 0.00 3.18
119 123 5.128663 TCCATGAAACGTGAGATAGGATCAA 59.871 40.000 0.00 0.00 0.00 2.57
134 138 0.455815 GGCCGTCCATTCCATGAAAC 59.544 55.000 0.00 0.00 0.00 2.78
135 139 1.029408 CGGCCGTCCATTCCATGAAA 61.029 55.000 19.50 0.00 0.00 2.69
136 140 1.451207 CGGCCGTCCATTCCATGAA 60.451 57.895 19.50 0.00 0.00 2.57
137 141 2.189257 CGGCCGTCCATTCCATGA 59.811 61.111 19.50 0.00 0.00 3.07
138 142 3.585990 GCGGCCGTCCATTCCATG 61.586 66.667 28.70 0.00 0.00 3.66
150 154 2.224428 CACAAAACAATGTGCGGCC 58.776 52.632 0.00 0.00 43.67 6.13
196 200 5.232463 TGTAAAATGGTAAGAGTCGGTCAC 58.768 41.667 0.00 0.00 0.00 3.67
200 204 4.814771 GGGATGTAAAATGGTAAGAGTCGG 59.185 45.833 0.00 0.00 0.00 4.79
202 206 6.657541 TGTTGGGATGTAAAATGGTAAGAGTC 59.342 38.462 0.00 0.00 0.00 3.36
210 214 4.159506 ACGGATTGTTGGGATGTAAAATGG 59.840 41.667 0.00 0.00 0.00 3.16
213 217 4.216687 GTGACGGATTGTTGGGATGTAAAA 59.783 41.667 0.00 0.00 0.00 1.52
250 255 1.012086 CGCTGAAGATGTGGTGATGG 58.988 55.000 0.00 0.00 0.00 3.51
269 274 2.743538 GACGGTTGGCGGGGTAAC 60.744 66.667 0.00 0.00 0.00 2.50
276 281 2.274232 TACATCTCCGACGGTTGGCG 62.274 60.000 14.79 3.62 0.00 5.69
286 292 5.060662 ACATGGTCGATATTACATCTCCG 57.939 43.478 0.00 0.00 0.00 4.63
287 293 7.061905 CGTTAACATGGTCGATATTACATCTCC 59.938 40.741 6.39 0.00 0.00 3.71
338 344 2.642254 TAAGGTCGTCCGCCCTGTG 61.642 63.158 0.00 0.00 39.05 3.66
345 351 0.730494 GAACGGTGTAAGGTCGTCCG 60.730 60.000 0.00 0.00 45.53 4.79
351 357 1.666872 GCGCAGAACGGTGTAAGGT 60.667 57.895 0.30 0.00 43.93 3.50
372 378 4.247258 TGTTCGAATGTAAATAGTGCCGT 58.753 39.130 0.00 0.00 0.00 5.68
388 394 4.847757 CGACGTAACTAGACATTTGTTCGA 59.152 41.667 0.00 0.00 0.00 3.71
412 429 5.180271 GGGACATGGATGTTTAAGACGTAA 58.820 41.667 0.00 0.00 41.95 3.18
413 430 4.383335 GGGGACATGGATGTTTAAGACGTA 60.383 45.833 0.00 0.00 41.95 3.57
420 437 3.816398 TGTTGGGGACATGGATGTTTA 57.184 42.857 0.00 0.00 41.95 2.01
421 438 2.692709 TGTTGGGGACATGGATGTTT 57.307 45.000 0.00 0.00 41.95 2.83
430 447 2.753701 CGGGTGATGTTGGGGACA 59.246 61.111 0.00 0.00 43.71 4.02
434 451 4.358841 TGGCCGGGTGATGTTGGG 62.359 66.667 2.18 0.00 0.00 4.12
489 507 2.817844 GGGTACGGAAAGCATTGAGTTT 59.182 45.455 0.00 0.00 0.00 2.66
571 591 3.084039 AGTCGTGATACTCCCGTTGTTA 58.916 45.455 0.00 0.00 0.00 2.41
577 597 1.596464 GCGTAAGTCGTGATACTCCCG 60.596 57.143 0.00 0.00 42.13 5.14
686 708 4.166523 CGAATCGTTATCCTACGCATCAT 58.833 43.478 0.00 0.00 41.16 2.45
694 716 2.592194 GATGCGCGAATCGTTATCCTA 58.408 47.619 12.20 0.00 41.07 2.94
722 744 0.828022 TTGCCGAGATTATCCACGGT 59.172 50.000 21.92 0.00 45.91 4.83
726 748 3.680490 TGTTTGTTGCCGAGATTATCCA 58.320 40.909 0.00 0.00 0.00 3.41
761 783 5.183969 GCTTTATAGAGGGTTTTCGGTTCT 58.816 41.667 0.00 0.00 0.00 3.01
764 786 3.371273 GGGCTTTATAGAGGGTTTTCGGT 60.371 47.826 0.00 0.00 0.00 4.69
783 805 1.892209 TCTCGAGGTTTTTCTTGGGC 58.108 50.000 13.56 0.00 0.00 5.36
799 822 7.206687 TCTTTCTCTCTCTTGTTCTTGTTCTC 58.793 38.462 0.00 0.00 0.00 2.87
804 827 6.095432 TCCTCTTTCTCTCTCTTGTTCTTG 57.905 41.667 0.00 0.00 0.00 3.02
1489 1542 1.443407 CCAGGGCTGAACGATCGAT 59.557 57.895 24.34 10.66 0.00 3.59
1523 1576 1.484653 AGGAAAGCACAAAAACCCCAC 59.515 47.619 0.00 0.00 0.00 4.61
1536 1590 2.819608 TGATGCAAACCTACAGGAAAGC 59.180 45.455 1.29 3.27 38.94 3.51
1537 1591 4.691860 CTGATGCAAACCTACAGGAAAG 57.308 45.455 1.29 0.00 38.94 2.62
1541 1595 2.787473 TCCTGATGCAAACCTACAGG 57.213 50.000 0.00 0.00 46.33 4.00
1542 1596 3.937706 CTCTTCCTGATGCAAACCTACAG 59.062 47.826 0.00 0.00 0.00 2.74
1543 1597 3.327757 ACTCTTCCTGATGCAAACCTACA 59.672 43.478 0.00 0.00 0.00 2.74
1544 1598 3.944087 ACTCTTCCTGATGCAAACCTAC 58.056 45.455 0.00 0.00 0.00 3.18
1545 1599 4.640771 AACTCTTCCTGATGCAAACCTA 57.359 40.909 0.00 0.00 0.00 3.08
1546 1600 3.515602 AACTCTTCCTGATGCAAACCT 57.484 42.857 0.00 0.00 0.00 3.50
1547 1601 3.823304 AGAAACTCTTCCTGATGCAAACC 59.177 43.478 0.00 0.00 31.28 3.27
1554 1620 3.774216 AGCTAGCAGAAACTCTTCCTGAT 59.226 43.478 18.83 0.00 31.28 2.90
1634 1700 0.464554 GCCCTTAGTCATGGCAGACC 60.465 60.000 0.00 0.00 44.70 3.85
1635 1701 3.086733 GCCCTTAGTCATGGCAGAC 57.913 57.895 0.00 8.46 44.70 3.51
1639 1705 2.880890 CAGTATTGCCCTTAGTCATGGC 59.119 50.000 0.00 0.00 45.56 4.40
1656 1722 4.142093 GCTAACCGTGGGAAGATTACAGTA 60.142 45.833 0.00 0.00 0.00 2.74
1665 1731 1.734707 CGTACAGCTAACCGTGGGAAG 60.735 57.143 0.00 0.00 0.00 3.46
1759 1825 2.093783 GTCAATGGGACGTCGATTTCAC 59.906 50.000 9.92 5.91 36.65 3.18
1774 1840 4.482386 CTCCAAAACAGAGCATGTCAATG 58.518 43.478 0.00 0.00 43.00 2.82
1781 1847 2.158475 TGTTCCCTCCAAAACAGAGCAT 60.158 45.455 0.00 0.00 31.97 3.79
1909 1987 6.627087 ACATGCTACTATGGCCAGTTATAT 57.373 37.500 13.05 0.00 32.32 0.86
1977 2055 8.688151 AGGTGAGACTAAAATCATCACTACTAC 58.312 37.037 3.91 0.00 40.07 2.73
1979 2057 7.726033 AGGTGAGACTAAAATCATCACTACT 57.274 36.000 3.91 0.00 40.07 2.57
1985 2063 8.273780 ACATTCAAGGTGAGACTAAAATCATC 57.726 34.615 0.00 0.00 0.00 2.92
2086 2164 4.882427 CCAGGACAGTCTTATCTCGTAAGA 59.118 45.833 0.00 0.00 45.01 2.10
2091 2169 4.035792 CAGTACCAGGACAGTCTTATCTCG 59.964 50.000 0.00 0.00 0.00 4.04
2128 2208 1.378531 AAGAAAAGTGTGCACAGCGA 58.621 45.000 22.40 0.00 0.00 4.93
2188 2268 2.562738 CCAAGGGGTGAAAATGGAGTTC 59.437 50.000 0.00 0.00 32.82 3.01
2257 2337 5.108385 TGTGCTAACTTGCTAGCTTTTTC 57.892 39.130 17.23 0.03 43.96 2.29
2264 2344 3.557595 GGTATGCTGTGCTAACTTGCTAG 59.442 47.826 0.00 0.00 0.00 3.42
2315 2395 8.025445 AGCACAATGTCATTTCTAAAGATGAAC 58.975 33.333 0.00 0.00 34.34 3.18
2336 2416 5.366482 TTGCCTAACCATATTAGAGCACA 57.634 39.130 8.44 0.00 32.23 4.57
2340 2420 7.148340 GCAGCTAATTGCCTAACCATATTAGAG 60.148 40.741 0.00 0.00 44.23 2.43
2353 2433 1.004044 ACAGAGTGCAGCTAATTGCCT 59.996 47.619 0.00 0.00 43.43 4.75
2421 2502 8.948631 TCCTAAATCATGTGAAGAAGATACAC 57.051 34.615 0.00 0.00 35.45 2.90
2638 2719 6.510799 CGGAAGAAGTATCATCAAATGACAGC 60.511 42.308 0.00 0.00 43.01 4.40
2655 2739 7.385778 TGGTTCAATAATAAACCGGAAGAAG 57.614 36.000 9.46 0.00 46.49 2.85
2657 2741 7.762588 TTTGGTTCAATAATAAACCGGAAGA 57.237 32.000 9.46 0.00 46.49 2.87
2800 2884 7.533426 AGCAACAAACATACATCATCTCTTTC 58.467 34.615 0.00 0.00 0.00 2.62
2968 3052 1.135257 CCAACGAGGCTGAGACAGTAG 60.135 57.143 0.00 0.00 33.43 2.57
3209 3293 5.119694 GTCAAATCCCCTTCAGATGTACTC 58.880 45.833 0.00 0.00 0.00 2.59
3211 3295 4.843728 TGTCAAATCCCCTTCAGATGTAC 58.156 43.478 0.00 0.00 0.00 2.90
3401 3494 6.726490 AATAAGCAAATAGACGTCCCTCTA 57.274 37.500 13.01 0.00 0.00 2.43
3412 3505 9.624697 TGCAACTGTAGAAAAATAAGCAAATAG 57.375 29.630 0.00 0.00 0.00 1.73
3486 3579 3.313526 CACTACAGAAACACTTTGCTGCT 59.686 43.478 0.00 0.00 31.74 4.24
3538 3631 1.666553 CAAGACAGCGGGCGTGTTA 60.667 57.895 0.00 0.00 0.00 2.41
3639 3732 8.894768 AGTGTGCTTAAGATAGATTAATGGAC 57.105 34.615 6.67 0.00 0.00 4.02
3691 3784 2.056577 GCAATGCTGTGAACTTTGAGC 58.943 47.619 0.00 0.00 0.00 4.26
3841 3944 9.931698 TGAGTCTAGTTCCTCCTGTAATATAAA 57.068 33.333 0.00 0.00 0.00 1.40
4091 4194 8.822805 ACCTAAACAGAAATACATAAGGACTCA 58.177 33.333 0.00 0.00 0.00 3.41
4147 4251 5.657302 TCCTTACCTGTAAGTGAGGAATCTC 59.343 44.000 14.22 0.00 46.36 2.75
4217 4321 4.713553 TCAGTGAGGCAGTTGTTGAAATA 58.286 39.130 0.00 0.00 0.00 1.40
4233 4337 1.065199 GTGGATCCCTGCAATCAGTGA 60.065 52.381 9.90 0.00 38.66 3.41
4479 4583 6.909550 TTGTGGCAGTTTACCTTATCAAAT 57.090 33.333 0.00 0.00 0.00 2.32
4499 4603 6.649141 TGTGAGTTCTACAATAAGCGATTTGT 59.351 34.615 0.00 0.00 39.32 2.83
4504 4608 5.048294 TGAGTGTGAGTTCTACAATAAGCGA 60.048 40.000 0.00 0.00 0.00 4.93
4745 4849 3.941483 AGTACGATTTTCAGAATGCCAGG 59.059 43.478 0.00 0.00 34.76 4.45
4864 4968 1.863454 CGAGCCAGTAATCAGCATCAC 59.137 52.381 0.00 0.00 0.00 3.06
4965 5069 1.585517 TGCGAATGTGCATTGTGGG 59.414 52.632 1.77 0.00 40.62 4.61
5040 5144 2.291282 TGGAAAATCTGCGGTTACCCAT 60.291 45.455 0.00 0.00 0.00 4.00
5097 5201 1.417517 TCTCTCTGCTTTGCCAGTCAA 59.582 47.619 0.00 0.00 34.47 3.18
5187 5291 7.457852 AGTTGCTGAACCTATCCCATGTATATA 59.542 37.037 0.00 0.00 31.81 0.86
5188 5292 6.273260 AGTTGCTGAACCTATCCCATGTATAT 59.727 38.462 0.00 0.00 31.81 0.86
5204 5308 0.401356 TGGATGGCTCAGTTGCTGAA 59.599 50.000 0.37 0.00 40.18 3.02
5260 5364 5.758784 GTGTTGCCTTCCTATCTTGGTATAC 59.241 44.000 0.00 0.00 0.00 1.47
5261 5365 5.427157 TGTGTTGCCTTCCTATCTTGGTATA 59.573 40.000 0.00 0.00 0.00 1.47
5310 5414 1.027792 AACACAACACACACCGACCC 61.028 55.000 0.00 0.00 0.00 4.46
5396 5503 6.428159 GTGACCTTTATTGATATGCTACCAGG 59.572 42.308 0.00 0.00 0.00 4.45
5495 5606 1.497722 CGACCGAAAGAAAGGCTGC 59.502 57.895 0.00 0.00 0.00 5.25
5515 5626 1.229336 AGCTACACAGGAGCCCACT 60.229 57.895 0.00 0.00 41.06 4.00
5613 5895 0.822811 GAGAGATCAGACTGCAGGCA 59.177 55.000 24.55 0.95 0.00 4.75
5821 6108 2.300433 CGAAGGGGCAATTGATCATCA 58.700 47.619 10.34 0.00 0.00 3.07
5834 6121 5.048507 GCTAGTTCTACAAATACGAAGGGG 58.951 45.833 0.00 0.00 0.00 4.79
5869 6156 7.419711 AGTTATGGAGTTATCTTCGGAAAGA 57.580 36.000 0.00 0.00 45.36 2.52


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

AutoCloner maintained by Alex Coulton.