Multiple sequence alignment - TraesCS4A01G155200

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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 TraesCS4A01G155200 chr4A 100.000 2694 0 0 1 2694 310749234 310751927 0.000000 4975.0
1 TraesCS4A01G155200 chr3A 95.295 2678 111 2 1 2665 66004934 66002259 0.000000 4233.0
2 TraesCS4A01G155200 chr6D 95.219 2677 113 2 1 2664 389245623 389242949 0.000000 4220.0
3 TraesCS4A01G155200 chr6D 97.222 36 1 0 2659 2694 408963577 408963542 0.000008 62.1
4 TraesCS4A01G155200 chr5D 95.146 2678 114 3 1 2665 503245471 503248145 0.000000 4211.0
5 TraesCS4A01G155200 chr5D 95.146 2678 114 3 1 2665 503264577 503261903 0.000000 4211.0
6 TraesCS4A01G155200 chr2A 95.146 2678 115 2 1 2665 726906256 726903581 0.000000 4211.0
7 TraesCS4A01G155200 chr2A 97.297 37 1 0 2658 2694 98091200 98091164 0.000002 63.9
8 TraesCS4A01G155200 chr3D 95.108 2678 115 3 1 2665 589263327 589260653 0.000000 4205.0
9 TraesCS4A01G155200 chr2D 95.071 2678 117 4 1 2665 591984808 591987483 0.000000 4200.0
10 TraesCS4A01G155200 chr1D 94.959 2678 120 3 1 2665 459904518 459901843 0.000000 4183.0
11 TraesCS4A01G155200 chr1D 94.735 2678 127 2 1 2665 254525804 254528480 0.000000 4152.0
12 TraesCS4A01G155200 chr1D 97.222 36 1 0 2659 2694 123049944 123049909 0.000008 62.1
13 TraesCS4A01G155200 chr7D 93.713 1193 61 5 1486 2665 231606235 231605044 0.000000 1775.0
14 TraesCS4A01G155200 chrUn 93.497 1138 61 4 1541 2665 428085155 428084018 0.000000 1679.0
15 TraesCS4A01G155200 chrUn 93.551 1070 56 4 1609 2665 433989994 433991063 0.000000 1581.0
16 TraesCS4A01G155200 chrUn 97.222 36 1 0 2659 2694 53251085 53251050 0.000008 62.1
17 TraesCS4A01G155200 chrUn 97.222 36 1 0 2659 2694 382408506 382408541 0.000008 62.1
18 TraesCS4A01G155200 chrUn 97.222 36 1 0 2659 2694 382410251 382410286 0.000008 62.1
19 TraesCS4A01G155200 chrUn 97.222 36 1 0 2659 2694 394610840 394610875 0.000008 62.1
20 TraesCS4A01G155200 chr7A 97.297 37 1 0 2658 2694 554127496 554127532 0.000002 63.9
21 TraesCS4A01G155200 chr1A 97.297 37 1 0 2658 2694 456465765 456465801 0.000002 63.9


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 TraesCS4A01G155200 chr4A 310749234 310751927 2693 False 4975 4975 100.000 1 2694 1 chr4A.!!$F1 2693
1 TraesCS4A01G155200 chr3A 66002259 66004934 2675 True 4233 4233 95.295 1 2665 1 chr3A.!!$R1 2664
2 TraesCS4A01G155200 chr6D 389242949 389245623 2674 True 4220 4220 95.219 1 2664 1 chr6D.!!$R1 2663
3 TraesCS4A01G155200 chr5D 503245471 503248145 2674 False 4211 4211 95.146 1 2665 1 chr5D.!!$F1 2664
4 TraesCS4A01G155200 chr5D 503261903 503264577 2674 True 4211 4211 95.146 1 2665 1 chr5D.!!$R1 2664
5 TraesCS4A01G155200 chr2A 726903581 726906256 2675 True 4211 4211 95.146 1 2665 1 chr2A.!!$R2 2664
6 TraesCS4A01G155200 chr3D 589260653 589263327 2674 True 4205 4205 95.108 1 2665 1 chr3D.!!$R1 2664
7 TraesCS4A01G155200 chr2D 591984808 591987483 2675 False 4200 4200 95.071 1 2665 1 chr2D.!!$F1 2664
8 TraesCS4A01G155200 chr1D 459901843 459904518 2675 True 4183 4183 94.959 1 2665 1 chr1D.!!$R2 2664
9 TraesCS4A01G155200 chr1D 254525804 254528480 2676 False 4152 4152 94.735 1 2665 1 chr1D.!!$F1 2664
10 TraesCS4A01G155200 chr7D 231605044 231606235 1191 True 1775 1775 93.713 1486 2665 1 chr7D.!!$R1 1179
11 TraesCS4A01G155200 chrUn 428084018 428085155 1137 True 1679 1679 93.497 1541 2665 1 chrUn.!!$R2 1124
12 TraesCS4A01G155200 chrUn 433989994 433991063 1069 False 1581 1581 93.551 1609 2665 1 chrUn.!!$F2 1056

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
642 645 0.179009 CGGACCGACCATAGACCCTA 60.179 60.0 8.64 0.0 38.9 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 2335 0.036732 TTCATCTTCAGCGCAAGGGT 59.963 50.0 11.47 0.0 38.28 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
35 36 1.202099 TTGGTTGGATCGTAGGGGCA 61.202 55.000 0.00 0.00 0.00 5.36
49 50 4.821805 CGTAGGGGCAATGATTTACTTCAT 59.178 41.667 0.00 0.00 37.96 2.57
73 74 1.889829 CGAGGTCTCTGGTTCAAGTCT 59.110 52.381 0.00 0.00 0.00 3.24
90 91 2.691996 TAGGATGGCCCAGCTGCA 60.692 61.111 8.66 0.81 37.41 4.41
92 93 4.437587 GGATGGCCCAGCTGCACT 62.438 66.667 8.66 0.00 34.14 4.40
179 182 6.661805 GGATATAGCTTAGTTGGTAGAGCTCT 59.338 42.308 22.17 22.17 43.86 4.09
200 203 1.401539 GCTCTTGCAATTGGGTCGTTC 60.402 52.381 7.72 0.00 39.41 3.95
201 204 2.154462 CTCTTGCAATTGGGTCGTTCT 58.846 47.619 7.72 0.00 0.00 3.01
230 233 2.488153 GGTTGGCTGTCTAATTGTCCAC 59.512 50.000 0.00 0.00 0.00 4.02
311 314 2.107204 AGAGGACTGAAACATGCCACTT 59.893 45.455 0.00 0.00 0.00 3.16
312 315 2.227388 GAGGACTGAAACATGCCACTTG 59.773 50.000 0.00 0.00 0.00 3.16
324 327 4.772624 ACATGCCACTTGAAGACTCTACTA 59.227 41.667 0.00 0.00 0.00 1.82
344 347 5.140454 ACTAAGACAAAAAGATGGGCTGTT 58.860 37.500 0.00 0.00 0.00 3.16
366 369 6.212187 TGTTAAAAAGGTAGAGGAGGTAGGAC 59.788 42.308 0.00 0.00 0.00 3.85
369 372 0.842635 GGTAGAGGAGGTAGGACGGA 59.157 60.000 0.00 0.00 0.00 4.69
433 436 3.805497 TCGGCGGCTCTCCTAGGA 61.805 66.667 11.98 11.98 0.00 2.94
437 440 1.287503 GCGGCTCTCCTAGGATTCG 59.712 63.158 13.12 14.16 0.00 3.34
478 481 1.213296 GGAGGATCAAGTTGGCCCTA 58.787 55.000 14.29 0.00 36.25 3.53
602 605 1.924731 ACGAGATCACTCCAAGGACA 58.075 50.000 0.00 0.00 39.76 4.02
642 645 0.179009 CGGACCGACCATAGACCCTA 60.179 60.000 8.64 0.00 38.90 3.53
767 770 0.960861 CGGGCAGAAAAAGGGGAGAC 60.961 60.000 0.00 0.00 0.00 3.36
793 796 2.236395 CCGTTCCTGGTTCTCCTGTAAT 59.764 50.000 0.00 0.00 34.23 1.89
796 799 4.652822 GTTCCTGGTTCTCCTGTAATTGT 58.347 43.478 0.00 0.00 34.23 2.71
840 843 6.913369 AATCCTTAGAATGGGATTCCAACTCG 60.913 42.308 0.00 0.00 45.84 4.18
917 920 5.277297 CGATGAAAGTTGTAAGCTGTGTTCA 60.277 40.000 0.00 0.00 0.00 3.18
1008 1011 2.046988 CTGTGGCGGATGTCAGCA 60.047 61.111 7.40 0.00 38.83 4.41
1021 1024 2.811317 CAGCAGTTCGAGTCCGCC 60.811 66.667 0.00 0.00 35.37 6.13
1083 1086 3.124578 AGCACCGAATTTTGCCAATTT 57.875 38.095 4.51 0.00 39.75 1.82
1144 1147 7.680730 TGATAAGATCCTTCCATTTAGTAGCC 58.319 38.462 0.00 0.00 0.00 3.93
1176 1179 3.881089 GGCATAGCCTTAACGTTAATGGT 59.119 43.478 24.48 24.48 46.69 3.55
1237 1240 1.984570 CCAGAGACGAGGAAGGGCA 60.985 63.158 0.00 0.00 0.00 5.36
1241 1244 1.215673 AGAGACGAGGAAGGGCATAGA 59.784 52.381 0.00 0.00 0.00 1.98
1248 1251 1.771255 AGGAAGGGCATAGAAAGCGAT 59.229 47.619 0.00 0.00 0.00 4.58
1252 1255 2.565841 AGGGCATAGAAAGCGATGAAC 58.434 47.619 0.00 0.00 29.67 3.18
1355 1358 1.228245 GGCAAGAGACAACCTGGCA 60.228 57.895 0.00 0.00 0.00 4.92
1385 1388 5.606348 ACATCTTAGTAGCCAGAGGAAAG 57.394 43.478 0.00 0.00 0.00 2.62
1389 1392 5.281314 TCTTAGTAGCCAGAGGAAAGGAAT 58.719 41.667 0.00 0.00 0.00 3.01
1404 1407 2.170166 AGGAATGCAAAAGCGATTCCA 58.830 42.857 21.89 0.00 45.25 3.53
1571 1574 1.139947 GCTCTGACCCGAGTAGCAC 59.860 63.158 0.00 0.00 33.55 4.40
1603 1606 3.640029 GGAATCCCATGTGAATCAGCAAT 59.360 43.478 0.00 0.00 0.00 3.56
1638 1641 2.772515 GGCTAAATACTCCTGGGTGACT 59.227 50.000 0.00 0.00 0.00 3.41
1644 1647 4.816048 ATACTCCTGGGTGACTGATAGA 57.184 45.455 0.00 0.00 0.00 1.98
1710 1713 7.287927 TGGGTAGTGAAATAAAACATGAAACCA 59.712 33.333 0.00 0.00 0.00 3.67
1740 1743 1.303643 CAAGCAGTGGGAGGGGAAC 60.304 63.158 0.00 0.00 0.00 3.62
1752 1755 1.825474 GAGGGGAACGTGATCTCTGAA 59.175 52.381 0.00 0.00 0.00 3.02
1765 1768 0.666274 CTCTGAACGCGTGCCTGTTA 60.666 55.000 14.98 0.00 0.00 2.41
1777 1780 2.819608 GTGCCTGTTAAAGAATGAGCCA 59.180 45.455 0.00 0.00 0.00 4.75
1790 1793 0.395724 TGAGCCAGCGACTCATAGGA 60.396 55.000 2.72 0.00 39.21 2.94
1807 1810 1.780919 AGGAAGTGGCTTGGTTAAGGT 59.219 47.619 0.00 0.00 34.40 3.50
1811 1814 3.868619 AGTGGCTTGGTTAAGGTAACA 57.131 42.857 0.96 0.00 40.39 2.41
1853 1856 3.737047 CGAAAGCGAGTCTTAATAGGGCA 60.737 47.826 0.00 0.00 40.82 5.36
1871 1874 2.493278 GGCAATTGTCACTGCTTATGGT 59.507 45.455 4.85 0.00 38.65 3.55
1925 1928 5.882557 GGATGAAGCTTGGATGAAACTAAGA 59.117 40.000 2.10 0.00 31.56 2.10
1956 1959 4.152402 CGAACCGACTGATGTTGAAGAATT 59.848 41.667 0.00 0.00 0.00 2.17
1959 1962 5.794894 ACCGACTGATGTTGAAGAATTAGT 58.205 37.500 0.00 0.00 0.00 2.24
2007 2010 1.178276 CACTCGAACCCAGAGCTAGT 58.822 55.000 0.00 0.00 39.23 2.57
2031 2034 0.035598 TCTCCCCGAAATGCGTTGAA 59.964 50.000 0.00 0.00 38.67 2.69
2033 2036 0.250553 TCCCCGAAATGCGTTGAAGT 60.251 50.000 0.00 0.00 38.67 3.01
2076 2079 0.240145 GGGTAAAGCACTGTTTCGGC 59.760 55.000 0.00 0.00 0.00 5.54
2079 2082 1.160946 TAAAGCACTGTTTCGGCGCA 61.161 50.000 10.83 0.00 0.00 6.09
2132 2135 8.144478 GCAAACTCTGAATACTAGATATGACCA 58.856 37.037 0.00 0.00 0.00 4.02
2160 2163 3.728373 GGGGTCAAGGTCGGCCAT 61.728 66.667 9.71 0.00 37.19 4.40
2187 2190 2.038952 CGATGGGGGATAAGCTTCATCA 59.961 50.000 18.34 6.04 32.88 3.07
2202 2205 4.507710 CTTCATCATCGAGAGGGAAACAA 58.492 43.478 0.00 0.00 0.00 2.83
2233 2236 3.056080 TCAGCTAAGGCCCCTAAATGAT 58.944 45.455 0.00 0.00 39.73 2.45
2240 2243 1.230324 GCCCCTAAATGATCGCTCAC 58.770 55.000 0.00 0.00 33.22 3.51
2355 2371 0.672342 GAACGGGGCTAAGCGATCTA 59.328 55.000 0.00 0.00 0.00 1.98
2418 2435 1.084370 CGCCTTAGAGGGAAGCAACG 61.084 60.000 0.00 0.00 35.37 4.10
2420 2437 0.613777 CCTTAGAGGGAAGCAACGGT 59.386 55.000 0.00 0.00 0.00 4.83
2479 2496 4.379793 CAGCTTGAGTAACGAAAACATTGC 59.620 41.667 0.00 0.00 0.00 3.56
2538 2555 2.993264 GGTTCGTCCACGGAGGGA 60.993 66.667 5.97 0.00 40.29 4.20
2544 2561 2.045242 TCCACGGAGGGAGAGTCG 60.045 66.667 0.00 0.00 38.24 4.18
2545 2562 2.045242 CCACGGAGGGAGAGTCGA 60.045 66.667 0.00 0.00 0.00 4.20
2556 2573 2.312390 GGAGAGTCGAGGCCTAAGATT 58.688 52.381 4.42 5.16 0.00 2.40
2587 2604 1.135489 GCGTAGTCGATGGACAACAGA 60.135 52.381 10.69 0.00 45.92 3.41
2626 2643 0.909623 CCTTGTTGGTACGGAGGGAT 59.090 55.000 0.00 0.00 30.57 3.85
2665 2682 4.881850 AGCCGAAAGATGGTTATAGGTTTG 59.118 41.667 0.00 0.00 0.00 2.93
2666 2683 4.638865 GCCGAAAGATGGTTATAGGTTTGT 59.361 41.667 0.00 0.00 0.00 2.83
2667 2684 5.818857 GCCGAAAGATGGTTATAGGTTTGTA 59.181 40.000 0.00 0.00 0.00 2.41
2668 2685 6.316890 GCCGAAAGATGGTTATAGGTTTGTAA 59.683 38.462 0.00 0.00 0.00 2.41
2669 2686 7.677982 GCCGAAAGATGGTTATAGGTTTGTAAC 60.678 40.741 0.00 0.00 32.06 2.50
2670 2687 7.334921 CCGAAAGATGGTTATAGGTTTGTAACA 59.665 37.037 0.00 0.00 33.85 2.41
2671 2688 8.889717 CGAAAGATGGTTATAGGTTTGTAACAT 58.110 33.333 0.00 0.00 33.85 2.71
2673 2690 8.747538 AAGATGGTTATAGGTTTGTAACATCC 57.252 34.615 0.00 0.00 33.85 3.51
2674 2691 7.287810 AGATGGTTATAGGTTTGTAACATCCC 58.712 38.462 0.00 0.00 33.85 3.85
2675 2692 6.390048 TGGTTATAGGTTTGTAACATCCCA 57.610 37.500 0.00 0.00 33.85 4.37
2676 2693 6.791371 TGGTTATAGGTTTGTAACATCCCAA 58.209 36.000 0.00 0.00 33.85 4.12
2677 2694 7.239438 TGGTTATAGGTTTGTAACATCCCAAA 58.761 34.615 0.00 0.00 33.85 3.28
2678 2695 7.896496 TGGTTATAGGTTTGTAACATCCCAAAT 59.104 33.333 0.00 0.00 33.85 2.32
2679 2696 8.755028 GGTTATAGGTTTGTAACATCCCAAATT 58.245 33.333 0.00 0.00 33.85 1.82
2682 2699 5.304778 AGGTTTGTAACATCCCAAATTTGC 58.695 37.500 12.92 0.00 33.53 3.68
2683 2700 5.059833 GGTTTGTAACATCCCAAATTTGCA 58.940 37.500 12.92 1.64 33.53 4.08
2684 2701 5.529060 GGTTTGTAACATCCCAAATTTGCAA 59.471 36.000 12.92 0.00 33.53 4.08
2685 2702 6.206438 GGTTTGTAACATCCCAAATTTGCAAT 59.794 34.615 12.92 5.30 33.53 3.56
2686 2703 7.255416 GGTTTGTAACATCCCAAATTTGCAATT 60.255 33.333 12.92 0.00 33.53 2.32
2687 2704 7.814264 TTGTAACATCCCAAATTTGCAATTT 57.186 28.000 12.92 0.00 0.00 1.82
2688 2705 7.814264 TGTAACATCCCAAATTTGCAATTTT 57.186 28.000 12.92 12.38 0.00 1.82
2689 2706 7.646314 TGTAACATCCCAAATTTGCAATTTTG 58.354 30.769 27.95 27.95 33.58 2.44
2690 2707 6.956202 AACATCCCAAATTTGCAATTTTGA 57.044 29.167 32.89 21.53 35.34 2.69
2691 2708 6.956202 ACATCCCAAATTTGCAATTTTGAA 57.044 29.167 32.89 24.51 35.34 2.69
2692 2709 7.527568 ACATCCCAAATTTGCAATTTTGAAT 57.472 28.000 32.89 25.23 35.34 2.57
2693 2710 7.371936 ACATCCCAAATTTGCAATTTTGAATG 58.628 30.769 32.89 31.56 35.34 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.885297 CCTCGCCCATGAAGTAAATCATT 59.115 43.478 0.00 0.00 37.96 2.57
49 50 2.203788 AACCAGAGACCTCGCCCA 60.204 61.111 0.00 0.00 34.09 5.36
73 74 2.691996 TGCAGCTGGGCCATCCTA 60.692 61.111 17.12 0.00 36.20 2.94
90 91 7.259088 TGCTTCTTCTATTCTTTTCCCTAGT 57.741 36.000 0.00 0.00 0.00 2.57
92 93 7.989741 CAGATGCTTCTTCTATTCTTTTCCCTA 59.010 37.037 0.00 0.00 0.00 3.53
154 157 6.661805 AGAGCTCTACCAACTAAGCTATATCC 59.338 42.308 16.50 0.00 44.77 2.59
155 158 7.535139 CAGAGCTCTACCAACTAAGCTATATC 58.465 42.308 17.75 0.00 44.77 1.63
200 203 1.066143 AGACAGCCAACCCGTAATCAG 60.066 52.381 0.00 0.00 0.00 2.90
201 204 0.981183 AGACAGCCAACCCGTAATCA 59.019 50.000 0.00 0.00 0.00 2.57
230 233 5.798934 GGTACAAGATACTATCATTACCGCG 59.201 44.000 0.00 0.00 0.00 6.46
311 314 9.698309 CATCTTTTTGTCTTAGTAGAGTCTTCA 57.302 33.333 0.00 0.00 0.00 3.02
312 315 9.145865 CCATCTTTTTGTCTTAGTAGAGTCTTC 57.854 37.037 0.00 0.00 0.00 2.87
324 327 6.478512 TTTAACAGCCCATCTTTTTGTCTT 57.521 33.333 0.00 0.00 0.00 3.01
344 347 4.952335 CGTCCTACCTCCTCTACCTTTTTA 59.048 45.833 0.00 0.00 0.00 1.52
366 369 2.755655 ACTAGATCTGACCAACTGTCCG 59.244 50.000 5.18 0.00 43.78 4.79
369 372 5.519808 TCCATACTAGATCTGACCAACTGT 58.480 41.667 5.18 0.00 0.00 3.55
433 436 0.689623 GGGATCCCAGATGAGCGAAT 59.310 55.000 26.95 0.00 35.81 3.34
437 440 1.759881 CCAGGGATCCCAGATGAGC 59.240 63.158 32.69 2.64 38.92 4.26
459 462 1.141858 CTAGGGCCAACTTGATCCTCC 59.858 57.143 6.18 0.00 0.00 4.30
478 481 5.605534 AGATAGTGCATCAAGTTATTCGCT 58.394 37.500 0.00 0.00 35.96 4.93
642 645 7.394359 ACAGCTAATGTGTTCCACTTATTGAAT 59.606 33.333 0.00 0.00 41.91 2.57
793 796 1.065647 TGTGGTTCCGGGGAATACAA 58.934 50.000 0.00 0.00 36.45 2.41
796 799 1.659022 TCTTGTGGTTCCGGGGAATA 58.341 50.000 0.00 0.00 36.45 1.75
840 843 5.584251 TCAAAATCTCAAAACAAAAGGTGCC 59.416 36.000 0.00 0.00 0.00 5.01
1008 1011 1.310904 GAGATAGGCGGACTCGAACT 58.689 55.000 0.00 0.00 39.00 3.01
1021 1024 1.115467 AGTTCACGGGCTGGAGATAG 58.885 55.000 0.00 0.00 0.00 2.08
1083 1086 4.811024 GTGAAATCATAGATCGAACTGCCA 59.189 41.667 5.31 0.00 0.00 4.92
1176 1179 3.117512 AGCCTTTCCTCTTTTGAACCTCA 60.118 43.478 0.00 0.00 0.00 3.86
1248 1251 1.768275 TCAACTCCCTGAAGCAGTTCA 59.232 47.619 0.00 0.00 40.55 3.18
1252 1255 5.620879 GCTTATTTTCAACTCCCTGAAGCAG 60.621 44.000 0.00 0.00 36.69 4.24
1259 1262 7.001073 GGATCTATGCTTATTTTCAACTCCCT 58.999 38.462 0.00 0.00 0.00 4.20
1355 1358 6.769512 TCTGGCTACTAAGATGTTTCAGTTT 58.230 36.000 0.00 0.00 0.00 2.66
1404 1407 0.101759 TTTCGCTCGCCGCTACTATT 59.898 50.000 0.00 0.00 36.73 1.73
1494 1497 2.172483 CTAGGGTGCGGCACTCAACT 62.172 60.000 32.51 24.17 37.30 3.16
1547 1550 0.322277 ACTCGGGTCAGAGCGTAAGA 60.322 55.000 0.00 0.00 41.77 2.10
1571 1574 2.519302 GGGATTCCATGTGCCCCG 60.519 66.667 4.80 0.00 34.39 5.73
1589 1592 2.756760 GGTGGTCATTGCTGATTCACAT 59.243 45.455 11.55 0.00 38.78 3.21
1638 1641 6.102762 TCCCTCATGGTACTACTTCTCTATCA 59.897 42.308 0.00 0.00 34.77 2.15
1644 1647 4.717280 CCTTTCCCTCATGGTACTACTTCT 59.283 45.833 0.00 0.00 34.77 2.85
1740 1743 1.983907 CACGCGTTCAGAGATCACG 59.016 57.895 10.22 0.00 36.98 4.35
1752 1755 1.196808 CATTCTTTAACAGGCACGCGT 59.803 47.619 5.58 5.58 0.00 6.01
1765 1768 1.002430 TGAGTCGCTGGCTCATTCTTT 59.998 47.619 8.45 0.00 37.98 2.52
1777 1780 0.461961 GCCACTTCCTATGAGTCGCT 59.538 55.000 0.00 0.00 30.05 4.93
1790 1793 4.141344 TCTGTTACCTTAACCAAGCCACTT 60.141 41.667 0.00 0.00 37.88 3.16
1807 1810 1.675219 GCTCCGGTGGGTTCTGTTA 59.325 57.895 0.00 0.00 33.83 2.41
1811 1814 3.892104 TACGGCTCCGGTGGGTTCT 62.892 63.158 13.31 0.00 44.69 3.01
1853 1856 3.356290 GGGACCATAAGCAGTGACAATT 58.644 45.455 0.00 0.00 0.00 2.32
1925 1928 0.538977 TCAGTCGGTTCGGACCTCTT 60.539 55.000 12.11 0.00 44.20 2.85
1956 1959 3.517901 CCCTAACCACAACTCATCCACTA 59.482 47.826 0.00 0.00 0.00 2.74
1959 1962 1.633432 CCCCTAACCACAACTCATCCA 59.367 52.381 0.00 0.00 0.00 3.41
2007 2010 0.958382 CGCATTTCGGGGAGAACCAA 60.958 55.000 0.00 0.00 42.91 3.67
2031 2034 5.555017 AGATGTCTAGTCAATTGTTGCACT 58.445 37.500 5.13 4.10 0.00 4.40
2033 2036 6.108687 CCTAGATGTCTAGTCAATTGTTGCA 58.891 40.000 14.22 0.00 43.34 4.08
2040 2043 6.042208 GCTTTACCCCTAGATGTCTAGTCAAT 59.958 42.308 14.22 2.38 43.34 2.57
2047 2050 3.452627 CAGTGCTTTACCCCTAGATGTCT 59.547 47.826 0.00 0.00 0.00 3.41
2079 2082 4.436998 GTACCGCTCGTGCAGCCT 62.437 66.667 10.43 0.00 46.74 4.58
2086 2089 0.179145 CTCGATTTGGTACCGCTCGT 60.179 55.000 22.24 3.33 0.00 4.18
2160 2163 1.416401 GCTTATCCCCCATCGTCTCAA 59.584 52.381 0.00 0.00 0.00 3.02
2202 2205 1.419387 GCCTTAGCTGATGATCTGGGT 59.581 52.381 0.00 0.00 35.50 4.51
2206 2209 1.063183 GGGGCCTTAGCTGATGATCT 58.937 55.000 0.84 0.00 39.73 2.75
2212 2215 2.487775 TCATTTAGGGGCCTTAGCTGA 58.512 47.619 0.84 4.34 39.73 4.26
2240 2243 1.199327 CTGGCTGTCTTTGCACATCAG 59.801 52.381 0.00 0.00 0.00 2.90
2319 2335 0.036732 TTCATCTTCAGCGCAAGGGT 59.963 50.000 11.47 0.00 38.28 4.34
2355 2371 0.762418 TGACATCCCACAACTTCGGT 59.238 50.000 0.00 0.00 0.00 4.69
2437 2454 0.371645 GACATTCTCGCTTCCGCTTG 59.628 55.000 0.00 0.00 0.00 4.01
2457 2474 4.275936 AGCAATGTTTTCGTTACTCAAGCT 59.724 37.500 0.00 0.00 0.00 3.74
2479 2496 0.181114 TCGGGGCATTGGATTCTCAG 59.819 55.000 0.00 0.00 0.00 3.35
2538 2555 3.492337 CCTAATCTTAGGCCTCGACTCT 58.508 50.000 9.68 0.00 43.43 3.24
2587 2604 6.619852 ACAAGGGGTAGTACAGGAATATTGAT 59.380 38.462 2.06 0.00 0.00 2.57
2626 2643 3.225608 GCTAACCTAGCCTCCTCCA 57.774 57.895 0.00 0.00 45.95 3.86
2665 2682 7.869800 TCAAAATTGCAAATTTGGGATGTTAC 58.130 30.769 30.14 1.17 37.19 2.50
2666 2683 8.455903 TTCAAAATTGCAAATTTGGGATGTTA 57.544 26.923 30.14 13.43 37.19 2.41
2667 2684 6.956202 TCAAAATTGCAAATTTGGGATGTT 57.044 29.167 30.14 4.69 37.19 2.71
2668 2685 6.956202 TTCAAAATTGCAAATTTGGGATGT 57.044 29.167 30.14 0.45 37.19 3.06
2669 2686 7.804614 CATTCAAAATTGCAAATTTGGGATG 57.195 32.000 30.14 27.39 37.19 3.51


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

AutoCloner maintained by Alex Coulton.