Multiple sequence alignment - TraesCS3A01G096600

Loading Multiple Alignment...

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 TraesCS3A01G096600 chr3A 100.000 4822 0 0 1 4822 61477511 61482332 0.000000e+00 8905.0
1 TraesCS3A01G096600 chr3A 84.390 615 65 18 842 1451 61434225 61434813 4.190000e-160 575.0
2 TraesCS3A01G096600 chr3A 87.059 85 10 1 842 925 61433210 61433294 1.430000e-15 95.3
3 TraesCS3A01G096600 chr3B 93.039 4626 232 43 46 4638 78594152 78598720 0.000000e+00 6676.0
4 TraesCS3A01G096600 chr3D 94.725 3943 167 26 903 4819 49005238 49009165 0.000000e+00 6091.0
5 TraesCS3A01G096600 chr3D 88.815 599 45 13 254 846 49004661 49005243 0.000000e+00 715.0


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 TraesCS3A01G096600 chr3A 61477511 61482332 4821 False 8905.00 8905 100.0000 1 4822 1 chr3A.!!$F1 4821
1 TraesCS3A01G096600 chr3A 61433210 61434813 1603 False 335.15 575 85.7245 842 1451 2 chr3A.!!$F2 609
2 TraesCS3A01G096600 chr3B 78594152 78598720 4568 False 6676.00 6676 93.0390 46 4638 1 chr3B.!!$F1 4592
3 TraesCS3A01G096600 chr3D 49004661 49009165 4504 False 3403.00 6091 91.7700 254 4819 2 chr3D.!!$F1 4565

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
955 1132 0.462047 CCTCGATTGGGGGAACGAAG 60.462 60.000 0.00 0.0 34.50 3.79 F
1247 1428 0.249741 ACGCCGTGTACAAGAAGCTT 60.250 50.000 10.61 0.0 0.00 3.74 F
1960 2147 0.970427 GGTTGATGGGGTTGGCGAAT 60.970 55.000 0.00 0.0 0.00 3.34 F
2416 2603 1.004277 TCATACAGTTGGGGTTCTGCC 59.996 52.381 0.00 0.0 35.37 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 2792 1.073923 ACAACCCATCTGAGACCAACC 59.926 52.381 0.0 0.0 0.00 3.77 R
3030 3217 0.599558 CACTACGGACCTTTCCACGA 59.400 55.000 0.0 0.0 43.00 4.35 R
3497 3684 0.175760 TACATTCGCCTCTGGAGCAC 59.824 55.000 0.0 0.0 0.00 4.40 R
4306 4513 0.246635 CTGGGAGTAACCACCAGTCG 59.753 60.000 0.0 0.0 45.21 4.18 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
24 25 7.129109 CATAGTTTGTATTCAACACGGAGTT 57.871 36.000 0.00 0.00 41.61 3.01
38 39 1.730064 CGGAGTTGTATTTGTCCGTGG 59.270 52.381 1.43 0.00 45.62 4.94
39 40 2.610976 CGGAGTTGTATTTGTCCGTGGA 60.611 50.000 1.43 0.00 45.62 4.02
69 70 5.123344 CCACAAATCGGAAGTAAAGTTAGGG 59.877 44.000 0.00 0.00 0.00 3.53
90 91 3.270877 GAATGTTTGCGGTAGTCTGGAT 58.729 45.455 0.00 0.00 0.00 3.41
118 119 3.951775 TCACCAATTAAATGCCACCAC 57.048 42.857 0.00 0.00 0.00 4.16
131 132 1.401409 GCCACCACACACAATTGATCG 60.401 52.381 13.59 2.59 0.00 3.69
142 143 6.206634 ACACACAATTGATCGGTTATTTGACT 59.793 34.615 13.59 0.00 0.00 3.41
161 162 0.622136 TGGAGGATTGCAGCTCACAT 59.378 50.000 0.00 0.00 0.00 3.21
180 181 9.787532 GCTCACATGCTATTTTAAAGTTGATAA 57.212 29.630 0.00 0.00 0.00 1.75
213 216 9.184523 CATTTAAGGTATAAAGTTGGATGACCA 57.815 33.333 0.00 0.00 45.34 4.02
226 229 2.540101 GGATGACCAGCTTTCGTATTCG 59.460 50.000 0.00 0.00 35.97 3.34
252 255 5.375417 TTGTGAACACAATCATGGACATC 57.625 39.130 15.04 0.00 45.42 3.06
262 265 1.520120 ATGGACATCTGCGCTGTCG 60.520 57.895 18.52 11.72 43.16 4.35
296 299 1.000052 GCGTAGGAGATGCCCTAACTC 60.000 57.143 0.00 0.00 40.24 3.01
298 301 3.752665 CGTAGGAGATGCCCTAACTCTA 58.247 50.000 0.00 0.00 40.24 2.43
299 302 4.337145 CGTAGGAGATGCCCTAACTCTAT 58.663 47.826 0.00 0.00 40.24 1.98
301 304 5.944599 CGTAGGAGATGCCCTAACTCTATTA 59.055 44.000 0.00 0.00 40.24 0.98
303 306 7.122948 CGTAGGAGATGCCCTAACTCTATTATT 59.877 40.741 0.00 0.00 40.24 1.40
304 307 7.880265 AGGAGATGCCCTAACTCTATTATTT 57.120 36.000 0.00 0.00 37.37 1.40
305 308 7.912719 AGGAGATGCCCTAACTCTATTATTTC 58.087 38.462 0.00 0.00 37.37 2.17
306 309 7.737149 AGGAGATGCCCTAACTCTATTATTTCT 59.263 37.037 0.00 0.00 37.37 2.52
307 310 9.036980 GGAGATGCCCTAACTCTATTATTTCTA 57.963 37.037 0.00 0.00 0.00 2.10
340 343 7.895975 TTCATCTAGACACAACTTCTGAATG 57.104 36.000 0.00 0.00 0.00 2.67
346 349 2.942376 ACACAACTTCTGAATGTTCGCA 59.058 40.909 0.00 0.00 0.00 5.10
348 351 4.036734 ACACAACTTCTGAATGTTCGCAAT 59.963 37.500 0.00 0.00 0.00 3.56
385 388 3.513912 ACGGGAGAGTCATGTGTCATTTA 59.486 43.478 0.00 0.00 0.00 1.40
390 393 6.344500 GGAGAGTCATGTGTCATTTAGTCAT 58.656 40.000 0.00 0.00 0.00 3.06
393 396 8.261492 AGAGTCATGTGTCATTTAGTCATTTC 57.739 34.615 0.00 0.00 0.00 2.17
394 397 7.335422 AGAGTCATGTGTCATTTAGTCATTTCC 59.665 37.037 0.00 0.00 0.00 3.13
395 398 7.170965 AGTCATGTGTCATTTAGTCATTTCCT 58.829 34.615 0.00 0.00 0.00 3.36
396 399 7.667219 AGTCATGTGTCATTTAGTCATTTCCTT 59.333 33.333 0.00 0.00 0.00 3.36
397 400 8.946085 GTCATGTGTCATTTAGTCATTTCCTTA 58.054 33.333 0.00 0.00 0.00 2.69
398 401 8.946085 TCATGTGTCATTTAGTCATTTCCTTAC 58.054 33.333 0.00 0.00 0.00 2.34
421 424 3.555428 GCTGAACACTCCAGCGTC 58.445 61.111 0.00 0.00 46.03 5.19
442 445 2.050077 GACCAAAACCGCAGCAGC 60.050 61.111 0.00 0.00 37.42 5.25
529 532 2.671963 AACCCTTCCGCGCCTTTC 60.672 61.111 0.00 0.00 0.00 2.62
702 705 4.504916 CCTCTGTGAGCGGCGAGG 62.505 72.222 12.98 1.79 37.33 4.63
720 723 0.523519 GGACAAAGCTAGGCTGTTGC 59.476 55.000 0.00 0.00 39.62 4.17
771 786 1.547901 GGAGTGAAGTTGGGGGAAAGG 60.548 57.143 0.00 0.00 0.00 3.11
821 836 2.960129 GACGAACGGCGCCTATGG 60.960 66.667 26.68 16.34 46.04 2.74
850 1026 4.944317 GGGACCAAGAATCCTAGTTCTTTG 59.056 45.833 5.77 5.76 43.90 2.77
886 1063 6.399743 ACGAATCCTAGTTCTTTCCTTTCTC 58.600 40.000 0.00 0.00 0.00 2.87
925 1102 1.474143 GGCAATGGTGACTCCTCTAGC 60.474 57.143 0.00 0.00 37.07 3.42
926 1103 1.804372 GCAATGGTGACTCCTCTAGCG 60.804 57.143 0.00 0.00 37.07 4.26
955 1132 0.462047 CCTCGATTGGGGGAACGAAG 60.462 60.000 0.00 0.00 34.50 3.79
1028 1207 3.688185 ACTGACATGCTCATGAATCACAC 59.312 43.478 15.96 0.00 41.20 3.82
1031 1210 4.763279 TGACATGCTCATGAATCACACTTT 59.237 37.500 15.96 0.00 41.20 2.66
1033 1212 5.466819 ACATGCTCATGAATCACACTTTTG 58.533 37.500 15.96 0.00 41.20 2.44
1035 1214 3.890756 TGCTCATGAATCACACTTTTGGT 59.109 39.130 0.00 0.00 0.00 3.67
1040 1219 7.522073 GCTCATGAATCACACTTTTGGTTTAGA 60.522 37.037 0.00 0.00 0.00 2.10
1041 1220 8.408043 TCATGAATCACACTTTTGGTTTAGAT 57.592 30.769 0.00 0.00 0.00 1.98
1073 1254 4.067192 GCAAATTTGGGCACTCTTTGAAT 58.933 39.130 19.47 0.00 0.00 2.57
1077 1258 2.673775 TGGGCACTCTTTGAATTGGA 57.326 45.000 0.00 0.00 0.00 3.53
1098 1279 0.896923 GCATTCATGTTTGGCAGGGA 59.103 50.000 0.00 0.00 0.00 4.20
1247 1428 0.249741 ACGCCGTGTACAAGAAGCTT 60.250 50.000 10.61 0.00 0.00 3.74
1338 1519 3.812262 CACTTCATCATGGTGCCTATCA 58.188 45.455 0.00 0.00 0.00 2.15
1429 1610 3.701205 TTATGTTCAGGCAGAGAAGCA 57.299 42.857 0.00 0.00 35.83 3.91
1432 1613 1.627329 TGTTCAGGCAGAGAAGCATCT 59.373 47.619 0.00 0.00 39.10 2.90
1437 1618 3.573538 TCAGGCAGAGAAGCATCTATCTC 59.426 47.826 0.00 0.00 41.92 2.75
1529 1710 1.901085 GCGAGATCCAGAACAGGGT 59.099 57.895 0.00 0.00 0.00 4.34
1581 1762 1.959985 TCAATGCACCAACCGTTCATT 59.040 42.857 0.00 0.00 38.64 2.57
1674 1855 2.685106 AGAGGTTCAGTCTGGTCAGA 57.315 50.000 0.00 0.00 34.56 3.27
1714 1895 4.160626 AGGGACAGTTGATACAACTAGCTC 59.839 45.833 15.17 10.77 0.00 4.09
1776 1957 2.843701 CTTTAGCATCAGGCCAGGTAG 58.156 52.381 5.01 0.00 46.50 3.18
1797 1978 7.071698 AGGTAGATCAATGACAACCTGTATCAT 59.928 37.037 10.94 0.00 36.03 2.45
1960 2147 0.970427 GGTTGATGGGGTTGGCGAAT 60.970 55.000 0.00 0.00 0.00 3.34
2273 2460 2.362503 ATGCCGACGAGGAGACCA 60.363 61.111 0.00 0.00 45.00 4.02
2281 2468 2.223829 CGACGAGGAGACCATAAAGCAT 60.224 50.000 0.00 0.00 0.00 3.79
2353 2540 2.292257 TGCCTCTGGTGATAGGTACACT 60.292 50.000 0.00 0.00 38.20 3.55
2416 2603 1.004277 TCATACAGTTGGGGTTCTGCC 59.996 52.381 0.00 0.00 35.37 4.85
2690 2877 4.213482 AGCACTTTACAAATGAGTTCGACC 59.787 41.667 0.00 0.00 0.00 4.79
2941 3128 5.147330 ACGTCCAAAGATATGTCTGTTGA 57.853 39.130 12.57 0.00 34.13 3.18
3030 3217 3.890756 TCTGATGATTTTGCAGGTGTTGT 59.109 39.130 0.00 0.00 0.00 3.32
3445 3632 4.371624 TCTGACACCTCCATGTTTCATT 57.628 40.909 0.00 0.00 31.24 2.57
3497 3684 0.829182 AGGCAGCTTCACAAAAGGGG 60.829 55.000 0.00 0.00 0.00 4.79
3624 3811 5.673818 GCGGTTCCAGATTCAACAACTATTC 60.674 44.000 0.00 0.00 0.00 1.75
3641 3828 0.768221 TTCCAGCTGAACAGGGGTCT 60.768 55.000 17.39 0.00 0.00 3.85
3759 3946 3.691118 CCAGGTTGATCATACACAAGTGG 59.309 47.826 0.00 0.00 34.19 4.00
3803 3990 2.304831 AAGCAAGAGGAGGAGGGGC 61.305 63.158 0.00 0.00 0.00 5.80
3827 4014 2.912956 ACCAGCTCCAAGATGAAACCTA 59.087 45.455 0.00 0.00 32.38 3.08
3858 4047 2.828520 TGGTTCAGAAACAGTTTTGCCA 59.171 40.909 0.00 2.56 37.10 4.92
3873 4062 0.546122 TGCCACTCTTGTTGGACAGT 59.454 50.000 0.00 0.00 0.00 3.55
3877 4066 2.035449 CCACTCTTGTTGGACAGTCGTA 59.965 50.000 0.00 0.00 0.00 3.43
3883 4072 5.466819 TCTTGTTGGACAGTCGTAACATAG 58.533 41.667 17.73 16.55 33.56 2.23
3887 4076 4.445452 TGGACAGTCGTAACATAGTTCC 57.555 45.455 0.00 0.00 0.00 3.62
3896 4085 9.021863 CAGTCGTAACATAGTTCCTTCTATTTC 57.978 37.037 0.00 0.00 0.00 2.17
3911 4100 9.519191 TCCTTCTATTTCATCATGTTTTCTTCA 57.481 29.630 0.00 0.00 0.00 3.02
3925 4114 0.607112 TCTTCAGTCTGCCTCTGCTG 59.393 55.000 0.00 0.00 38.71 4.41
3935 4124 1.416030 TGCCTCTGCTGTAGTTGAACA 59.584 47.619 0.00 0.00 38.71 3.18
3938 4127 3.503748 GCCTCTGCTGTAGTTGAACAATT 59.496 43.478 0.00 0.00 33.53 2.32
3941 4130 3.882288 TCTGCTGTAGTTGAACAATTGCA 59.118 39.130 5.05 2.29 30.32 4.08
4300 4505 5.119694 GGACTGAAACTTGAAGTGAACTCT 58.880 41.667 0.00 0.00 0.00 3.24
4301 4506 5.235401 GGACTGAAACTTGAAGTGAACTCTC 59.765 44.000 0.00 0.00 0.00 3.20
4306 4513 4.875561 ACTTGAAGTGAACTCTCTACCC 57.124 45.455 0.00 0.00 0.00 3.69
4331 4538 1.631898 GGTGGTTACTCCCAGGCTTTA 59.368 52.381 0.00 0.00 34.43 1.85
4332 4539 2.617276 GGTGGTTACTCCCAGGCTTTAC 60.617 54.545 0.00 0.00 34.43 2.01
4345 4552 1.009829 GCTTTACTGTCCCTGATGCG 58.990 55.000 0.00 0.00 0.00 4.73
4484 4693 0.458543 GATCAGCTTCGCTTCGACCA 60.459 55.000 0.00 0.00 36.40 4.02
4548 4758 2.933573 TGTTCCCGCTTTTCTGGTTTA 58.066 42.857 0.00 0.00 0.00 2.01
4556 4766 4.100529 CGCTTTTCTGGTTTATGCATCAG 58.899 43.478 0.19 4.42 0.00 2.90
4638 4848 3.505680 TGTACTGAATTGGGCATGTTGAC 59.494 43.478 0.00 0.00 0.00 3.18
4639 4849 2.880443 ACTGAATTGGGCATGTTGACT 58.120 42.857 0.00 0.00 0.00 3.41
4640 4850 2.821969 ACTGAATTGGGCATGTTGACTC 59.178 45.455 0.00 0.00 0.00 3.36
4661 4871 1.216064 TGCATCTCCTTGGCCATAGT 58.784 50.000 6.09 0.00 0.00 2.12
4685 4895 5.921004 GCAATTTGCAAAACCAATACTGA 57.079 34.783 17.19 0.00 44.26 3.41
4688 4898 6.369615 GCAATTTGCAAAACCAATACTGATCT 59.630 34.615 17.19 0.00 44.26 2.75
4689 4899 7.622672 GCAATTTGCAAAACCAATACTGATCTG 60.623 37.037 17.19 0.00 44.26 2.90
4700 4910 6.989169 ACCAATACTGATCTGCAAGTATCTTC 59.011 38.462 8.80 0.00 33.76 2.87
4701 4911 6.426328 CCAATACTGATCTGCAAGTATCTTCC 59.574 42.308 8.80 0.00 33.76 3.46
4722 4932 1.975407 CCCAAACTGGCTGCTCCTG 60.975 63.158 0.00 0.00 35.79 3.86
4737 4947 5.055265 TGCTCCTGCTAGTATCTTAGACT 57.945 43.478 0.00 0.00 40.48 3.24
4741 4951 6.039941 GCTCCTGCTAGTATCTTAGACTGAAA 59.960 42.308 0.00 0.00 36.03 2.69
4771 4981 5.639757 TGTGCTAAATGATGTGTAATGTGC 58.360 37.500 0.00 0.00 0.00 4.57
4773 4983 6.597280 TGTGCTAAATGATGTGTAATGTGCTA 59.403 34.615 0.00 0.00 0.00 3.49
4776 4986 7.128331 GCTAAATGATGTGTAATGTGCTACTG 58.872 38.462 0.00 0.00 0.00 2.74
4819 5030 6.015434 ACAGGGAAAACATGGTAGAATTGAAC 60.015 38.462 0.00 0.00 34.56 3.18
4820 5031 5.480422 AGGGAAAACATGGTAGAATTGAACC 59.520 40.000 0.00 0.00 36.24 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.721571 ACTCCGTGTTGAATACAAACTATG 57.278 37.500 0.00 0.00 38.80 2.23
14 15 2.803956 CGGACAAATACAACTCCGTGTT 59.196 45.455 0.00 0.00 40.71 3.32
15 16 2.409975 CGGACAAATACAACTCCGTGT 58.590 47.619 0.00 0.00 40.71 4.49
19 20 2.740447 GTCCACGGACAAATACAACTCC 59.260 50.000 11.43 0.00 44.02 3.85
38 39 1.459592 CTTCCGATTTGTGGACGTGTC 59.540 52.381 0.00 0.00 34.56 3.67
39 40 1.202604 ACTTCCGATTTGTGGACGTGT 60.203 47.619 0.00 0.00 36.70 4.49
41 42 3.389925 TTACTTCCGATTTGTGGACGT 57.610 42.857 0.00 0.00 40.63 4.34
42 43 3.744426 ACTTTACTTCCGATTTGTGGACG 59.256 43.478 0.00 0.00 34.56 4.79
43 44 5.684550 AACTTTACTTCCGATTTGTGGAC 57.315 39.130 0.00 0.00 34.56 4.02
44 45 5.935789 CCTAACTTTACTTCCGATTTGTGGA 59.064 40.000 0.00 0.00 0.00 4.02
69 70 2.695359 TCCAGACTACCGCAAACATTC 58.305 47.619 0.00 0.00 0.00 2.67
90 91 3.366883 GCATTTAATTGGTGAAGCGGACA 60.367 43.478 0.00 0.00 0.00 4.02
118 119 6.524239 CAGTCAAATAACCGATCAATTGTGTG 59.476 38.462 5.13 0.00 0.00 3.82
131 132 4.016444 TGCAATCCTCCAGTCAAATAACC 58.984 43.478 0.00 0.00 0.00 2.85
142 143 0.622136 ATGTGAGCTGCAATCCTCCA 59.378 50.000 1.02 4.99 0.00 3.86
192 193 5.044846 AGCTGGTCATCCAACTTTATACCTT 60.045 40.000 0.00 0.00 43.81 3.50
208 211 2.288579 ACACGAATACGAAAGCTGGTCA 60.289 45.455 0.00 0.00 42.66 4.02
209 212 2.334838 ACACGAATACGAAAGCTGGTC 58.665 47.619 0.00 0.00 42.66 4.02
213 216 3.805422 TCACAAACACGAATACGAAAGCT 59.195 39.130 0.00 0.00 42.66 3.74
250 253 1.662629 CTCAAAATCGACAGCGCAGAT 59.337 47.619 11.47 5.99 37.46 2.90
252 255 0.095935 CCTCAAAATCGACAGCGCAG 59.904 55.000 11.47 3.33 37.46 5.18
262 265 3.541632 TCCTACGCAATCCCTCAAAATC 58.458 45.455 0.00 0.00 0.00 2.17
373 376 8.950210 AGTAAGGAAATGACTAAATGACACATG 58.050 33.333 0.00 0.00 0.00 3.21
385 388 4.705507 TCAGCGTCTAGTAAGGAAATGACT 59.294 41.667 0.00 0.00 0.00 3.41
390 393 4.280174 AGTGTTCAGCGTCTAGTAAGGAAA 59.720 41.667 0.00 0.00 0.00 3.13
393 396 3.427773 GGAGTGTTCAGCGTCTAGTAAGG 60.428 52.174 0.00 0.00 0.00 2.69
394 397 3.190744 TGGAGTGTTCAGCGTCTAGTAAG 59.809 47.826 0.00 0.00 0.00 2.34
395 398 3.151554 TGGAGTGTTCAGCGTCTAGTAA 58.848 45.455 0.00 0.00 0.00 2.24
396 399 2.747989 CTGGAGTGTTCAGCGTCTAGTA 59.252 50.000 0.00 0.00 0.00 1.82
397 400 1.542030 CTGGAGTGTTCAGCGTCTAGT 59.458 52.381 0.00 0.00 0.00 2.57
398 401 1.734047 GCTGGAGTGTTCAGCGTCTAG 60.734 57.143 0.21 0.00 46.33 2.43
421 424 2.966309 GCTGCGGTTTTGGTCTCCG 61.966 63.158 0.00 0.00 45.94 4.63
518 521 3.652539 CTTACCGGAAAGGCGCGGA 62.653 63.158 9.46 0.00 46.52 5.54
583 586 3.164269 AGGGCTATGGTGGCTCCG 61.164 66.667 0.53 0.00 39.52 4.63
696 699 1.815840 GCCTAGCTTTGTCCTCGCC 60.816 63.158 0.00 0.00 0.00 5.54
702 705 0.166814 CGCAACAGCCTAGCTTTGTC 59.833 55.000 0.00 0.00 36.40 3.18
720 723 0.824182 TAAACCAAGGGTGCCCAACG 60.824 55.000 10.26 0.00 35.34 4.10
771 786 1.740025 CTGCTGCAAACCCTAGCTAAC 59.260 52.381 3.02 0.00 38.25 2.34
821 836 3.372440 AGGATTCTTGGTCCCAATCAC 57.628 47.619 0.00 0.00 36.36 3.06
886 1063 0.108138 CTAGAACCACTCCAAGGGCG 60.108 60.000 0.00 0.00 0.00 6.13
955 1132 3.878160 TTGGACAACACCAAAAGGAAC 57.122 42.857 0.00 0.00 45.36 3.62
1052 1233 5.049267 CCAATTCAAAGAGTGCCCAAATTTG 60.049 40.000 11.40 11.40 33.25 2.32
1073 1254 2.302157 TGCCAAACATGAATGCATCCAA 59.698 40.909 0.00 0.00 30.68 3.53
1077 1258 1.208535 CCCTGCCAAACATGAATGCAT 59.791 47.619 0.00 0.00 34.29 3.96
1098 1279 3.724508 TCGCACAAATTTGTCCATTGT 57.275 38.095 20.85 0.00 39.91 2.71
1307 1488 0.249955 TGATGAAGTGCCGATGAGCA 59.750 50.000 0.00 0.00 41.46 4.26
1338 1519 2.376109 ACTCCAGGACATATCGTCGTT 58.624 47.619 0.00 0.00 46.42 3.85
1429 1610 2.390225 AACCGGCTCTGGAGATAGAT 57.610 50.000 0.00 0.00 0.00 1.98
1432 1613 1.120530 GGAAACCGGCTCTGGAGATA 58.879 55.000 0.00 0.00 0.00 1.98
1529 1710 2.549754 CGAAGGAGCAAAAAGAGAAGCA 59.450 45.455 0.00 0.00 0.00 3.91
1581 1762 2.081462 TCGTAGTCGAGCATGTTGAGA 58.919 47.619 0.00 0.00 41.35 3.27
1674 1855 0.109342 CCTGAAGCTCCACACTGGTT 59.891 55.000 0.00 0.00 39.03 3.67
1714 1895 5.584649 TCGTCATACAGCCCAATTAAAAGAG 59.415 40.000 0.00 0.00 0.00 2.85
1764 1945 2.435805 GTCATTGATCTACCTGGCCTGA 59.564 50.000 11.88 0.00 0.00 3.86
1817 2004 9.201989 ACAGAAATCAGTGGACTATCACTATAA 57.798 33.333 0.00 0.00 45.24 0.98
1960 2147 3.575506 CAGTCCAGCCCTGCAAATA 57.424 52.632 0.00 0.00 0.00 1.40
2273 2460 2.390696 TGCCCTTGCATGATGCTTTAT 58.609 42.857 19.19 0.00 45.31 1.40
2353 2540 1.860641 TCAGCGGAAAGGGATAGACA 58.139 50.000 0.00 0.00 0.00 3.41
2416 2603 3.257873 CCCTGTAGAGATATGCCAGAGTG 59.742 52.174 0.00 0.00 0.00 3.51
2605 2792 1.073923 ACAACCCATCTGAGACCAACC 59.926 52.381 0.00 0.00 0.00 3.77
2690 2877 7.362056 CCAAACAACCTGGTCATCTGTTAATAG 60.362 40.741 13.41 6.14 30.30 1.73
2818 3005 2.159382 GGTGTGTAAACCTCCACCATG 58.841 52.381 0.00 0.00 45.34 3.66
2920 3107 5.062683 CAGTCAACAGACATATCTTTGGACG 59.937 44.000 0.00 0.00 34.69 4.79
2941 3128 4.771590 ATCGAAAACAATCATGCACAGT 57.228 36.364 0.00 0.00 0.00 3.55
3030 3217 0.599558 CACTACGGACCTTTCCACGA 59.400 55.000 0.00 0.00 43.00 4.35
3445 3632 5.540337 AGAATAGTGAGTTTGTCAGTCTGGA 59.460 40.000 0.00 0.00 39.70 3.86
3497 3684 0.175760 TACATTCGCCTCTGGAGCAC 59.824 55.000 0.00 0.00 0.00 4.40
3624 3811 1.002868 CAGACCCCTGTTCAGCTGG 60.003 63.158 15.13 0.00 35.70 4.85
3641 3828 2.607750 GTGTCCCTCTGGCCCTCA 60.608 66.667 0.00 0.00 0.00 3.86
3759 3946 1.457346 CTTGAATGGACCCTGCTGTC 58.543 55.000 0.00 0.00 34.42 3.51
3827 4014 3.279434 GTTTCTGAACCACTCACCAAGT 58.721 45.455 0.00 0.00 39.44 3.16
3839 4026 4.105486 GAGTGGCAAAACTGTTTCTGAAC 58.895 43.478 6.20 8.96 36.29 3.18
3858 4047 3.131577 TGTTACGACTGTCCAACAAGAGT 59.868 43.478 16.05 3.83 0.00 3.24
3873 4062 9.745880 GATGAAATAGAAGGAACTATGTTACGA 57.254 33.333 0.00 0.00 38.49 3.43
3877 4066 9.911788 ACATGATGAAATAGAAGGAACTATGTT 57.088 29.630 0.00 0.00 38.49 2.71
3896 4085 4.458295 AGGCAGACTGAAGAAAACATGATG 59.542 41.667 6.65 0.00 0.00 3.07
3905 4094 1.001746 CAGCAGAGGCAGACTGAAGAA 59.998 52.381 6.65 0.00 44.61 2.52
3910 4099 0.894141 ACTACAGCAGAGGCAGACTG 59.106 55.000 0.00 0.00 44.61 3.51
3911 4100 1.274728 CAACTACAGCAGAGGCAGACT 59.725 52.381 0.00 0.00 44.61 3.24
3925 4114 7.642071 ATCATTTGTGCAATTGTTCAACTAC 57.358 32.000 7.40 0.00 0.00 2.73
3935 4124 5.221682 TGGTCCAAGAATCATTTGTGCAATT 60.222 36.000 0.00 0.00 0.00 2.32
3938 4127 3.229293 TGGTCCAAGAATCATTTGTGCA 58.771 40.909 0.00 0.00 0.00 4.57
3941 4130 9.039165 AGAAATAATGGTCCAAGAATCATTTGT 57.961 29.630 0.00 0.00 32.81 2.83
4306 4513 0.246635 CTGGGAGTAACCACCAGTCG 59.753 60.000 0.00 0.00 45.21 4.18
4331 4538 4.101448 GGGCGCATCAGGGACAGT 62.101 66.667 10.83 0.00 37.47 3.55
4484 4693 6.008331 GGTTACAACCTATCTGTTTTTCCCT 58.992 40.000 3.80 0.00 45.75 4.20
4514 4723 0.928229 GGAACATCGGACCGAATTCG 59.072 55.000 22.55 20.92 39.99 3.34
4516 4725 3.471354 GGGAACATCGGACCGAATT 57.529 52.632 22.55 18.01 39.99 2.17
4548 4758 4.471908 TCGCCGCCACTGATGCAT 62.472 61.111 0.00 0.00 0.00 3.96
4566 4776 0.179089 CTCATCCCCTGAAGCAGTCG 60.179 60.000 0.00 0.00 32.14 4.18
4638 4848 0.106868 TGGCCAAGGAGATGCATGAG 60.107 55.000 0.61 0.00 0.00 2.90
4639 4849 0.554305 ATGGCCAAGGAGATGCATGA 59.446 50.000 10.96 0.00 0.00 3.07
4640 4850 2.160205 CTATGGCCAAGGAGATGCATG 58.840 52.381 10.96 0.00 0.00 4.06
4644 4854 1.952296 GCAACTATGGCCAAGGAGATG 59.048 52.381 10.96 13.60 0.00 2.90
4717 4927 7.575414 TTTCAGTCTAAGATACTAGCAGGAG 57.425 40.000 0.00 0.00 0.00 3.69
4737 4947 9.356433 CACATCATTTAGCACAATACAATTTCA 57.644 29.630 0.00 0.00 0.00 2.69
4771 4981 8.310406 TGTACATGTGAATTCAAGAACAGTAG 57.690 34.615 10.35 1.70 0.00 2.57
4773 4983 6.205464 CCTGTACATGTGAATTCAAGAACAGT 59.795 38.462 22.64 14.44 31.05 3.55
4776 4986 5.705441 TCCCTGTACATGTGAATTCAAGAAC 59.295 40.000 10.35 5.37 0.00 3.01


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

AutoCloner maintained by Alex Coulton.