Multiple sequence alignment - TraesCS2D01G366700

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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 TraesCS2D01G366700 chr2D 100.000 7840 0 0 1 7840 471223405 471215566 0.000000e+00 14478
1 TraesCS2D01G366700 chr2D 88.356 146 12 4 4 145 39083734 39083878 3.760000e-38 171
2 TraesCS2D01G366700 chr2A 92.884 6043 279 67 2 5977 612852881 612846923 0.000000e+00 8637
3 TraesCS2D01G366700 chr2A 91.957 1840 92 25 6014 7840 612846928 612845132 0.000000e+00 2527
4 TraesCS2D01G366700 chr2B 92.591 3995 141 56 624 4585 550406307 550402435 0.000000e+00 5594
5 TraesCS2D01G366700 chr2B 96.060 2716 64 10 4616 7329 550402441 550399767 0.000000e+00 4383
6 TraesCS2D01G366700 chr2B 94.242 521 24 4 7322 7840 550399688 550399172 0.000000e+00 791
7 TraesCS2D01G366700 chr2B 90.493 568 49 5 2 567 550407214 550406650 0.000000e+00 745
8 TraesCS2D01G366700 chr2B 81.081 148 13 11 574 713 550406387 550406247 3.870000e-18 104
9 TraesCS2D01G366700 chr6A 81.850 573 77 19 5125 5693 446297731 446298280 2.580000e-124 457
10 TraesCS2D01G366700 chr6A 92.453 106 8 0 6209 6314 446299404 446299509 1.360000e-32 152
11 TraesCS2D01G366700 chr6B 87.649 251 31 0 3040 3290 477218768 477219018 7.690000e-75 292
12 TraesCS2D01G366700 chr6B 92.453 106 8 0 6209 6314 477222101 477222206 1.360000e-32 152
13 TraesCS2D01G366700 chr6D 86.614 254 34 0 3037 3290 309581223 309581476 1.670000e-71 281
14 TraesCS2D01G366700 chr6D 91.667 156 11 2 6990 7145 410398429 410398276 1.710000e-51 215
15 TraesCS2D01G366700 chr6D 92.453 106 8 0 6209 6314 309584581 309584686 1.360000e-32 152
16 TraesCS2D01G366700 chr3D 92.810 153 9 2 6993 7145 92123270 92123120 3.680000e-53 220
17 TraesCS2D01G366700 chr3D 92.157 153 10 2 6993 7145 92358162 92358012 1.710000e-51 215
18 TraesCS2D01G366700 chr3B 92.810 153 9 2 6993 7145 141862434 141862284 3.680000e-53 220
19 TraesCS2D01G366700 chr7B 91.250 160 12 2 6990 7148 505937316 505937474 4.760000e-52 217
20 TraesCS2D01G366700 chr7B 82.278 158 23 5 1 156 323500027 323499873 1.780000e-26 132
21 TraesCS2D01G366700 chr4D 91.720 157 11 2 6986 7141 74079349 74079504 4.760000e-52 217
22 TraesCS2D01G366700 chr1B 90.798 163 12 3 6993 7155 632021073 632020914 1.710000e-51 215
23 TraesCS2D01G366700 chr1B 82.632 190 26 5 1915 2101 32765923 32765738 2.260000e-35 161
24 TraesCS2D01G366700 chr1D 84.375 160 22 3 1 157 400363786 400363945 3.790000e-33 154
25 TraesCS2D01G366700 chr7D 81.609 174 24 2 13 185 364024579 364024413 3.820000e-28 137
26 TraesCS2D01G366700 chr1A 82.099 162 14 6 6585 6741 555805693 555805844 2.970000e-24 124


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 TraesCS2D01G366700 chr2D 471215566 471223405 7839 True 14478.0 14478 100.0000 1 7840 1 chr2D.!!$R1 7839
1 TraesCS2D01G366700 chr2A 612845132 612852881 7749 True 5582.0 8637 92.4205 2 7840 2 chr2A.!!$R1 7838
2 TraesCS2D01G366700 chr2B 550399172 550407214 8042 True 2323.4 5594 90.8934 2 7840 5 chr2B.!!$R1 7838
3 TraesCS2D01G366700 chr6A 446297731 446299509 1778 False 304.5 457 87.1515 5125 6314 2 chr6A.!!$F1 1189
4 TraesCS2D01G366700 chr6B 477218768 477222206 3438 False 222.0 292 90.0510 3040 6314 2 chr6B.!!$F1 3274
5 TraesCS2D01G366700 chr6D 309581223 309584686 3463 False 216.5 281 89.5335 3037 6314 2 chr6D.!!$F1 3277

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
567 570 0.377203 CCGAGAATTTTAGCCCGCAC 59.623 55.000 0.00 0.0 0.00 5.34 F
1473 1773 0.734942 ATGGGCGAAACTCGTGTACG 60.735 55.000 11.00 11.0 42.81 3.67 F
1734 2047 2.736400 GCATGTTTTGGAGGCTATGTGC 60.736 50.000 0.00 0.0 41.94 4.57 F
1897 2210 3.010138 TGGAACAGAGGGAAAATGTAGGG 59.990 47.826 0.00 0.0 0.00 3.53 F
2075 2393 3.133901 TCTTTGTGTCTACAGTTCCTGCA 59.866 43.478 0.00 0.0 38.23 4.41 F
2652 2994 3.191371 GCTGATAGTGTTCTTGGTTTGGG 59.809 47.826 0.00 0.0 0.00 4.12 F
4586 5232 0.097674 GTGGCATGCTCATCGTTGTC 59.902 55.000 18.92 0.0 0.00 3.18 F
4784 5430 0.321298 GCGTCTGTGAAGGGCCTAAA 60.321 55.000 6.41 0.0 0.00 1.85 F
4799 5445 2.355818 GCCTAAACGATTTCCAGAGGGT 60.356 50.000 0.00 0.0 34.93 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 2074 1.143684 CCAATGCAGTAGCCCTACCAT 59.856 52.381 0.00 0.00 41.13 3.55 R
2652 2994 1.145803 GTGTACGACTGGCTTGTTCC 58.854 55.000 0.00 0.00 0.00 3.62 R
2788 3130 2.601504 CCGCATGCGAGATTCAAATCTG 60.602 50.000 39.90 15.30 45.39 2.90 R
3310 3653 3.637432 TCACGAATTCCATGTGCAAAAC 58.363 40.909 0.00 0.00 33.69 2.43 R
3953 4387 2.485426 GGACATATTGTGGGCATCGATG 59.515 50.000 21.27 21.27 0.00 3.84 R
4593 5239 0.610687 GGACTTGCTGCTGTAGACCT 59.389 55.000 0.00 0.00 0.00 3.85 R
6156 8265 1.367346 TGACCCACCCAGCTTGATAA 58.633 50.000 0.00 0.00 0.00 1.75 R
6754 8967 1.491670 CTCAATCCGATACCTGTGCG 58.508 55.000 0.00 0.00 0.00 5.34 R
6860 9073 0.627469 ACTTCCAGGGTGGGGCATAT 60.627 55.000 0.00 0.00 38.32 1.78 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
23 24 4.748892 CTCACTGTGGAATCGACATACTT 58.251 43.478 8.11 0.00 0.00 2.24
45 46 3.173668 ACTTACCGCGAATTGCATAGA 57.826 42.857 8.23 0.00 46.97 1.98
47 48 2.882927 TACCGCGAATTGCATAGACT 57.117 45.000 8.23 0.00 46.97 3.24
75 77 3.304928 CCTCGCAAGTCATCAAGCTTTTT 60.305 43.478 0.00 0.00 39.48 1.94
115 117 2.095372 GCAAAAGCGCTCGGTTATTACT 59.905 45.455 12.06 0.00 35.18 2.24
120 122 2.167900 AGCGCTCGGTTATTACTTTCCT 59.832 45.455 2.64 0.00 0.00 3.36
266 268 7.276658 CGAGGTAATATGCATCTCAAATCCTAC 59.723 40.741 0.19 0.00 0.00 3.18
282 284 3.516586 TCCTACAGGGAAAGACATGTCA 58.483 45.455 27.02 2.67 41.91 3.58
292 294 6.666546 AGGGAAAGACATGTCATTTGATTCAT 59.333 34.615 27.02 10.52 0.00 2.57
335 337 7.175119 ACTGGGTCTATGCTAAGTTTTTCTTTC 59.825 37.037 0.00 0.00 37.56 2.62
412 414 1.478105 CAAACCAATGGAGGCCTTAGC 59.522 52.381 6.77 0.00 38.76 3.09
423 425 4.140900 TGGAGGCCTTAGCTAGTAGAGAAT 60.141 45.833 6.77 0.00 39.73 2.40
429 431 6.072119 GGCCTTAGCTAGTAGAGAATCTCTTC 60.072 46.154 18.78 13.31 42.24 2.87
460 463 9.868277 TTTCTATTAATGAAAATCGGTGCAAAT 57.132 25.926 0.00 0.00 31.45 2.32
513 516 5.305585 TGATGCGACCCTATTTCTATTTCC 58.694 41.667 0.00 0.00 0.00 3.13
528 531 6.049955 TCTATTTCCGATGGACCATAATCC 57.950 41.667 7.05 0.00 39.45 3.01
563 566 3.128764 CCTTGTTCCGAGAATTTTAGCCC 59.871 47.826 0.00 0.00 0.00 5.19
567 570 0.377203 CCGAGAATTTTAGCCCGCAC 59.623 55.000 0.00 0.00 0.00 5.34
569 572 2.546778 CGAGAATTTTAGCCCGCACTA 58.453 47.619 0.00 0.00 0.00 2.74
571 574 3.059597 CGAGAATTTTAGCCCGCACTATG 60.060 47.826 0.00 0.00 0.00 2.23
633 922 5.689383 TGCGAAAGAACTAAAGAAGCAAT 57.311 34.783 0.00 0.00 0.00 3.56
652 941 8.905103 AAGCAATGGAAACGTGTAAATATAAC 57.095 30.769 0.00 0.00 0.00 1.89
786 1081 2.109181 GCCGTCATCCTACCCTGC 59.891 66.667 0.00 0.00 0.00 4.85
818 1113 4.735132 CGCCTCGCCAGAACGGAA 62.735 66.667 0.00 0.00 36.56 4.30
819 1114 3.119096 GCCTCGCCAGAACGGAAC 61.119 66.667 0.00 0.00 36.56 3.62
907 1203 2.213499 CGTCCCTCCAAATCATAGCAC 58.787 52.381 0.00 0.00 0.00 4.40
980 1277 1.227292 GGTTCGATCCCGGAGAAGC 60.227 63.158 0.73 9.11 35.67 3.86
1098 1395 3.857854 CCGACGCAGCAGCATCAC 61.858 66.667 0.82 0.00 42.27 3.06
1101 1398 2.745100 ACGCAGCAGCATCACCAG 60.745 61.111 0.82 0.00 42.27 4.00
1106 1403 3.823330 GCAGCATCACCAGCAGCC 61.823 66.667 0.00 0.00 38.40 4.85
1108 1405 4.025858 AGCATCACCAGCAGCCGT 62.026 61.111 0.00 0.00 0.00 5.68
1363 1660 4.156922 TGCCTATTGTTTGGTATTGGTTCG 59.843 41.667 0.00 0.00 0.00 3.95
1374 1671 5.432645 TGGTATTGGTTCGAAATGCTCATA 58.567 37.500 0.00 0.00 0.00 2.15
1410 1707 3.186409 CGTTGACTTGGGATAGTTGTGTG 59.814 47.826 0.00 0.00 0.00 3.82
1459 1759 1.214589 CTGAAAGTGCAGCATGGGC 59.785 57.895 0.00 0.00 41.61 5.36
1473 1773 0.734942 ATGGGCGAAACTCGTGTACG 60.735 55.000 11.00 11.00 42.81 3.67
1663 1976 7.540474 TTCTCTTGGAGTAGTTCAGTGTTAT 57.460 36.000 0.00 0.00 0.00 1.89
1701 2014 3.692257 ACTGCTGAGCAACTAACAGAT 57.308 42.857 9.07 0.00 38.41 2.90
1734 2047 2.736400 GCATGTTTTGGAGGCTATGTGC 60.736 50.000 0.00 0.00 41.94 4.57
1761 2074 6.761242 GCTGTGGATGTTGTGTACTGAATATA 59.239 38.462 0.00 0.00 0.00 0.86
1894 2207 5.450453 TGTTTGGAACAGAGGGAAAATGTA 58.550 37.500 0.00 0.00 42.39 2.29
1897 2210 3.010138 TGGAACAGAGGGAAAATGTAGGG 59.990 47.826 0.00 0.00 0.00 3.53
1969 2286 4.646492 GGAACAGGAATTGCAATCCTACAT 59.354 41.667 22.21 14.66 45.59 2.29
1975 2292 5.595952 AGGAATTGCAATCCTACATTCCTTC 59.404 40.000 21.67 9.61 45.51 3.46
2069 2387 7.606456 TGTTTTCTTCTCTTTGTGTCTACAGTT 59.394 33.333 0.00 0.00 38.23 3.16
2071 2389 5.844004 TCTTCTCTTTGTGTCTACAGTTCC 58.156 41.667 0.00 0.00 38.23 3.62
2072 2390 5.598830 TCTTCTCTTTGTGTCTACAGTTCCT 59.401 40.000 0.00 0.00 38.23 3.36
2073 2391 5.201713 TCTCTTTGTGTCTACAGTTCCTG 57.798 43.478 0.00 0.00 38.23 3.86
2074 2392 3.728845 TCTTTGTGTCTACAGTTCCTGC 58.271 45.455 0.00 0.00 38.23 4.85
2075 2393 3.133901 TCTTTGTGTCTACAGTTCCTGCA 59.866 43.478 0.00 0.00 38.23 4.41
2076 2394 3.769739 TTGTGTCTACAGTTCCTGCAT 57.230 42.857 0.00 0.00 38.23 3.96
2183 2501 8.506168 TTTTGAAGTGAATATCCTGGATGTAC 57.494 34.615 19.42 8.64 0.00 2.90
2488 2817 5.496387 CATGAGCTATTGTCTTGCTTTACG 58.504 41.667 0.00 0.00 36.01 3.18
2495 2824 6.129457 GCTATTGTCTTGCTTTACGTGTTTTG 60.129 38.462 0.00 0.00 0.00 2.44
2582 2918 3.465742 AGCACATCGCAGTCAGATATT 57.534 42.857 0.00 0.00 46.13 1.28
2652 2994 3.191371 GCTGATAGTGTTCTTGGTTTGGG 59.809 47.826 0.00 0.00 0.00 4.12
2733 3075 8.376203 CACTTTATGTTCTACAGTTCAGATTCG 58.624 37.037 0.00 0.00 0.00 3.34
2788 3130 8.862550 AGTTATTATTTGCTAAATCTTGCTGC 57.137 30.769 0.00 0.00 32.38 5.25
2935 3277 6.351966 CCTCTACCTTCTTTCCGAAATACCTT 60.352 42.308 0.00 0.00 0.00 3.50
2936 3278 7.147776 CCTCTACCTTCTTTCCGAAATACCTTA 60.148 40.741 0.00 0.00 0.00 2.69
2941 3283 6.039382 CCTTCTTTCCGAAATACCTTATTGGG 59.961 42.308 0.00 0.00 41.11 4.12
3310 3653 6.424207 GGTTTCTTCTGGACTAGTAACTGTTG 59.576 42.308 2.69 0.00 0.00 3.33
3953 4387 1.519408 TGCCTTTTTACGTGGAGAGC 58.481 50.000 0.00 0.00 0.00 4.09
3984 4418 3.696051 CCACAATATGTCCTGAAGTTGGG 59.304 47.826 0.00 0.00 0.00 4.12
4001 4645 5.337788 AGTTGGGTTGGCCTTTGATAATAA 58.662 37.500 3.32 0.00 34.45 1.40
4131 4775 8.945481 TCCATTTAAGGTGCATATGAAAAATG 57.055 30.769 6.97 8.96 34.45 2.32
4192 4837 3.070734 ACTGCTGAAAGACATGAGTGAGT 59.929 43.478 0.00 0.00 34.07 3.41
4543 5189 0.107993 CATGACATGGTCCGCTGACT 60.108 55.000 7.60 0.00 41.47 3.41
4581 5227 1.089112 TCTTTGTGGCATGCTCATCG 58.911 50.000 18.92 10.75 0.00 3.84
4586 5232 0.097674 GTGGCATGCTCATCGTTGTC 59.902 55.000 18.92 0.00 0.00 3.18
4606 5252 1.734047 CGAAGTCAGGTCTACAGCAGC 60.734 57.143 0.00 0.00 0.00 5.25
4703 5349 1.153269 TTGTGCACACGAGAGCCAA 60.153 52.632 21.56 0.00 0.00 4.52
4784 5430 0.321298 GCGTCTGTGAAGGGCCTAAA 60.321 55.000 6.41 0.00 0.00 1.85
4799 5445 2.355818 GCCTAAACGATTTCCAGAGGGT 60.356 50.000 0.00 0.00 34.93 4.34
4814 5460 4.323562 CCAGAGGGTCTTAAGGGTAACTTG 60.324 50.000 1.85 0.00 40.37 3.16
4898 5547 3.879892 GGGACTTATGATCAAAGGCAGAC 59.120 47.826 18.94 9.41 33.32 3.51
4927 5576 7.448469 ACTTGTGTTGTATAATCAAAGGCTTCT 59.552 33.333 0.00 0.00 0.00 2.85
4930 5579 5.584649 TGTTGTATAATCAAAGGCTTCTCGG 59.415 40.000 0.00 0.00 0.00 4.63
5117 6455 7.910683 GCAGCTGTAGATTTGTCCTTTAATAAC 59.089 37.037 16.64 0.00 0.00 1.89
5715 7075 6.018180 GCATGGAACTATACCTTTTACCTTCG 60.018 42.308 0.00 0.00 0.00 3.79
6356 8567 8.995027 TTATATTTTGGTGTTCAGGCTATGAT 57.005 30.769 0.00 0.00 37.89 2.45
6374 8585 8.396390 GGCTATGATTAGTTCTAATGATGCATG 58.604 37.037 2.46 0.00 0.00 4.06
6464 8677 7.992033 TGGAAATTGGAAAATGAACACATCTTT 59.008 29.630 0.00 0.00 0.00 2.52
6708 8921 6.316390 GCAATTGTTTACAGGACTGCTATAGT 59.684 38.462 7.40 0.00 44.02 2.12
6893 9106 7.391620 CACCCTGGAAGTTATAAGACAACTTA 58.608 38.462 0.00 0.00 44.24 2.24
6930 9143 6.914757 GCTCATCAGGTATGTTTGCTTATTTC 59.085 38.462 0.00 0.00 36.89 2.17
6931 9144 7.201767 GCTCATCAGGTATGTTTGCTTATTTCT 60.202 37.037 0.00 0.00 36.89 2.52
6932 9145 8.579850 TCATCAGGTATGTTTGCTTATTTCTT 57.420 30.769 0.00 0.00 36.89 2.52
6933 9146 9.023962 TCATCAGGTATGTTTGCTTATTTCTTT 57.976 29.630 0.00 0.00 36.89 2.52
7191 9409 7.043565 GTGGCTGTTGATATTTTTCCAATCAT 58.956 34.615 0.00 0.00 30.17 2.45
7249 9467 4.564372 CACAGGATCACGTTCTTCATAGTG 59.436 45.833 0.00 0.00 36.06 2.74
7448 9754 9.862371 TTGCTTTTTCTGAAGTATTTTGTGTTA 57.138 25.926 0.00 0.00 0.00 2.41
7533 9839 1.164411 TTGTGCCATAACTTCAGCCG 58.836 50.000 0.00 0.00 0.00 5.52
7647 9953 5.537295 GGTGTATCTTAAGTTGTTTTGGGGT 59.463 40.000 1.63 0.00 0.00 4.95
7651 9957 4.794334 TCTTAAGTTGTTTTGGGGTGCTA 58.206 39.130 1.63 0.00 0.00 3.49
7691 9997 4.946478 AGCTAGCTCGTCTAATTTCCAT 57.054 40.909 12.68 0.00 0.00 3.41
7699 10005 2.864343 CGTCTAATTTCCATCGGACCAC 59.136 50.000 0.00 0.00 0.00 4.16
7703 10009 0.392461 ATTTCCATCGGACCACGTGG 60.392 55.000 32.83 32.83 44.69 4.94
7733 10039 7.320443 TGTATCATGGCTAAGCTAAAACTTG 57.680 36.000 0.00 0.00 0.00 3.16
7822 10130 8.960591 ACTGAAAGATCTCTTTTTCTTTTGACA 58.039 29.630 6.63 0.00 45.37 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.015736 ATGTCGATTCCACAGTGAGC 57.984 50.000 0.62 0.00 0.00 4.26
1 2 4.377839 AGTATGTCGATTCCACAGTGAG 57.622 45.455 0.62 0.00 0.00 3.51
2 3 4.801330 AAGTATGTCGATTCCACAGTGA 57.199 40.909 0.62 0.00 0.00 3.41
4 5 6.282199 AGTAAAGTATGTCGATTCCACAGT 57.718 37.500 0.00 0.00 0.00 3.55
23 24 4.505191 GTCTATGCAATTCGCGGTAAGTAA 59.495 41.667 6.13 0.00 46.97 2.24
115 117 9.906660 CAAAATAAACTATGTGTTAGCAGGAAA 57.093 29.630 0.00 0.00 38.03 3.13
178 180 7.040340 TCGTGTTAATCAAATGAGGCCTTTTTA 60.040 33.333 6.77 0.00 0.00 1.52
217 219 8.450578 TCGCATCCTATGTTTCTTTTATTCAT 57.549 30.769 0.00 0.00 0.00 2.57
227 229 6.183360 GCATATTACCTCGCATCCTATGTTTC 60.183 42.308 0.00 0.00 0.00 2.78
230 232 4.222810 TGCATATTACCTCGCATCCTATGT 59.777 41.667 0.00 0.00 0.00 2.29
238 240 4.335400 TTGAGATGCATATTACCTCGCA 57.665 40.909 0.00 0.00 39.01 5.10
266 268 5.909621 ATCAAATGACATGTCTTTCCCTG 57.090 39.130 25.55 18.92 0.00 4.45
335 337 9.578439 GAATCTTATTCCTTCACAATTCAAAGG 57.422 33.333 4.36 4.36 40.80 3.11
343 345 8.337118 AGGATAGGAATCTTATTCCTTCACAA 57.663 34.615 22.65 8.18 46.21 3.33
528 531 2.562738 GGAACAAGGGGAAAGGAATGTG 59.437 50.000 0.00 0.00 0.00 3.21
534 537 0.690762 TCTCGGAACAAGGGGAAAGG 59.309 55.000 0.00 0.00 0.00 3.11
563 566 0.175760 AGTGCTGGTACCATAGTGCG 59.824 55.000 16.75 3.36 0.00 5.34
567 570 7.050970 TCTGTATTTAGTGCTGGTACCATAG 57.949 40.000 16.75 5.85 0.00 2.23
569 572 5.950544 TCTGTATTTAGTGCTGGTACCAT 57.049 39.130 16.75 2.52 0.00 3.55
571 574 6.093633 CCTTTTCTGTATTTAGTGCTGGTACC 59.906 42.308 4.43 4.43 0.00 3.34
602 861 2.229792 AGTTCTTTCGCATGCCTTTGA 58.770 42.857 13.15 0.00 0.00 2.69
603 862 2.712057 AGTTCTTTCGCATGCCTTTG 57.288 45.000 13.15 0.00 0.00 2.77
804 1099 2.809601 CCGTTCCGTTCTGGCGAG 60.810 66.667 0.00 0.00 37.80 5.03
818 1113 1.061546 TCTAAACTTTGCCCCTCCGT 58.938 50.000 0.00 0.00 0.00 4.69
819 1114 2.194201 TTCTAAACTTTGCCCCTCCG 57.806 50.000 0.00 0.00 0.00 4.63
821 1116 3.427638 GCGATTTCTAAACTTTGCCCCTC 60.428 47.826 0.00 0.00 0.00 4.30
822 1117 2.492088 GCGATTTCTAAACTTTGCCCCT 59.508 45.455 0.00 0.00 0.00 4.79
823 1118 2.416836 GGCGATTTCTAAACTTTGCCCC 60.417 50.000 0.00 0.00 35.24 5.80
824 1119 2.876091 GGCGATTTCTAAACTTTGCCC 58.124 47.619 0.00 0.00 35.24 5.36
825 1120 2.416836 GGGGCGATTTCTAAACTTTGCC 60.417 50.000 0.00 0.00 40.48 4.52
826 1121 2.416836 GGGGGCGATTTCTAAACTTTGC 60.417 50.000 0.00 0.00 0.00 3.68
886 1182 1.140852 TGCTATGATTTGGAGGGACGG 59.859 52.381 0.00 0.00 0.00 4.79
935 1232 0.735632 GTTGTGCAGAGCGAGGAGAG 60.736 60.000 0.00 0.00 0.00 3.20
936 1233 1.290324 GTTGTGCAGAGCGAGGAGA 59.710 57.895 0.00 0.00 0.00 3.71
937 1234 1.739562 GGTTGTGCAGAGCGAGGAG 60.740 63.158 0.00 0.00 0.00 3.69
938 1235 1.830587 ATGGTTGTGCAGAGCGAGGA 61.831 55.000 0.00 0.00 0.00 3.71
939 1236 0.957395 AATGGTTGTGCAGAGCGAGG 60.957 55.000 0.00 0.00 0.00 4.63
940 1237 0.877071 AAATGGTTGTGCAGAGCGAG 59.123 50.000 0.00 0.00 0.00 5.03
980 1277 2.586792 CTTCAAGGAGCCCCGGAG 59.413 66.667 0.73 0.00 37.58 4.63
1168 1465 3.476646 CGAGTGCTGCGAGTGCTG 61.477 66.667 0.00 0.00 43.34 4.41
1171 1468 3.476646 CTGCGAGTGCTGCGAGTG 61.477 66.667 0.00 0.00 43.34 3.51
1374 1671 7.339212 TCCCAAGTCAACGAATCAAATCAATAT 59.661 33.333 0.00 0.00 0.00 1.28
1459 1759 1.854126 ACCAAACGTACACGAGTTTCG 59.146 47.619 9.04 0.00 46.93 3.46
1473 1773 1.263217 CTCACAGCGTTACCACCAAAC 59.737 52.381 0.00 0.00 0.00 2.93
1663 1976 6.542005 TCAGCAGTTATCTGAAAACAGTCAAA 59.458 34.615 4.94 0.00 43.76 2.69
1734 2047 2.481568 CAGTACACAACATCCACAGCTG 59.518 50.000 13.48 13.48 0.00 4.24
1761 2074 1.143684 CCAATGCAGTAGCCCTACCAT 59.856 52.381 0.00 0.00 41.13 3.55
1922 2235 8.296728 TCCAAATGGTACCAAAGGAACTTTTCT 61.297 37.037 20.76 0.00 46.24 2.52
1928 2245 4.342665 TGTTCCAAATGGTACCAAAGGAAC 59.657 41.667 38.21 38.21 45.11 3.62
1969 2286 6.237901 TCATTCCAGAAGAATTTCGAAGGAA 58.762 36.000 12.05 12.05 42.86 3.36
1975 2292 3.691118 TGCCTCATTCCAGAAGAATTTCG 59.309 43.478 0.00 0.00 42.86 3.46
2488 2817 6.144241 ACAACCAGAACGTTAAAACAAAACAC 59.856 34.615 0.00 0.00 0.00 3.32
2495 2824 7.412063 ACTTATGACAACCAGAACGTTAAAAC 58.588 34.615 0.00 0.00 0.00 2.43
2652 2994 1.145803 GTGTACGACTGGCTTGTTCC 58.854 55.000 0.00 0.00 0.00 3.62
2788 3130 2.601504 CCGCATGCGAGATTCAAATCTG 60.602 50.000 39.90 15.30 45.39 2.90
2935 3277 5.250200 ACTTGACATTTAACTCGCCCAATA 58.750 37.500 0.00 0.00 0.00 1.90
2936 3278 4.079253 ACTTGACATTTAACTCGCCCAAT 58.921 39.130 0.00 0.00 0.00 3.16
2941 3283 5.928153 AGCTAAACTTGACATTTAACTCGC 58.072 37.500 0.00 0.00 0.00 5.03
2999 3341 5.482175 AGACACTAACTTAGCAGGAGAATGT 59.518 40.000 0.00 0.00 0.00 2.71
3310 3653 3.637432 TCACGAATTCCATGTGCAAAAC 58.363 40.909 0.00 0.00 33.69 2.43
3742 4169 3.745975 GCCATGCCAAAAAGGTTCTTTAC 59.254 43.478 0.00 0.00 40.61 2.01
3929 4363 5.335348 GCTCTCCACGTAAAAAGGCAATTTA 60.335 40.000 0.00 0.00 0.00 1.40
3953 4387 2.485426 GGACATATTGTGGGCATCGATG 59.515 50.000 21.27 21.27 0.00 3.84
3961 4395 3.696051 CCAACTTCAGGACATATTGTGGG 59.304 47.826 0.00 0.00 0.00 4.61
3963 4397 4.335416 ACCCAACTTCAGGACATATTGTG 58.665 43.478 0.00 0.00 0.00 3.33
3984 4418 5.932619 AGGGTTTATTATCAAAGGCCAAC 57.067 39.130 5.01 0.00 0.00 3.77
4001 4645 3.525800 AATGCAGACCAACTTAGGGTT 57.474 42.857 0.00 0.00 39.19 4.11
4130 4774 3.319689 GCTAAAAAGGGGCAAACTGTACA 59.680 43.478 0.00 0.00 0.00 2.90
4131 4775 3.572682 AGCTAAAAAGGGGCAAACTGTAC 59.427 43.478 0.00 0.00 0.00 2.90
4192 4837 2.439507 ACAGAGCAAACCCTCAAGAGAA 59.560 45.455 0.00 0.00 34.26 2.87
4525 5171 0.615331 AAGTCAGCGGACCATGTCAT 59.385 50.000 13.67 0.00 45.48 3.06
4581 5227 3.566523 CTGTAGACCTGACTTCGACAAC 58.433 50.000 0.00 0.00 29.58 3.32
4586 5232 1.734047 GCTGCTGTAGACCTGACTTCG 60.734 57.143 0.00 0.00 0.00 3.79
4591 5237 1.273606 GACTTGCTGCTGTAGACCTGA 59.726 52.381 0.00 0.00 0.00 3.86
4592 5238 1.674221 GGACTTGCTGCTGTAGACCTG 60.674 57.143 0.00 0.00 0.00 4.00
4593 5239 0.610687 GGACTTGCTGCTGTAGACCT 59.389 55.000 0.00 0.00 0.00 3.85
4594 5240 0.737715 CGGACTTGCTGCTGTAGACC 60.738 60.000 0.00 5.03 0.00 3.85
4595 5241 0.737715 CCGGACTTGCTGCTGTAGAC 60.738 60.000 0.00 0.00 0.00 2.59
4606 5252 2.892425 GGCAGCGATCCGGACTTG 60.892 66.667 6.12 3.95 0.00 3.16
4703 5349 1.071699 ACAACGAGCAACTACCACCAT 59.928 47.619 0.00 0.00 0.00 3.55
4784 5430 3.197983 CCTTAAGACCCTCTGGAAATCGT 59.802 47.826 3.36 0.00 34.81 3.73
4799 5445 5.876357 ACAGATTGCAAGTTACCCTTAAGA 58.124 37.500 4.94 0.00 0.00 2.10
4814 5460 4.747810 CCCCTCACATTAAAACAGATTGC 58.252 43.478 0.00 0.00 0.00 3.56
4879 5528 4.574674 TGGTCTGCCTTTGATCATAAGT 57.425 40.909 0.00 0.00 35.27 2.24
4927 5576 0.263765 ACCCAGGGAACTATAGCCGA 59.736 55.000 14.54 0.00 40.21 5.54
4930 5579 4.163649 AGTGTTTACCCAGGGAACTATAGC 59.836 45.833 14.54 0.00 40.21 2.97
5906 7428 3.258622 ACTTCTACACTAAGTGGCTCCAC 59.741 47.826 10.96 10.96 46.50 4.02
5918 7440 4.524714 ACTACATGTGCTGACTTCTACACT 59.475 41.667 9.11 0.00 34.14 3.55
6156 8265 1.367346 TGACCCACCCAGCTTGATAA 58.633 50.000 0.00 0.00 0.00 1.75
6356 8567 9.448438 AACAACTACATGCATCATTAGAACTAA 57.552 29.630 11.71 0.00 0.00 2.24
6374 8585 9.465985 GTAGAGGATTATTCAGCTAACAACTAC 57.534 37.037 0.00 0.00 0.00 2.73
6464 8677 3.011821 ACACTCCTGAACTCCTGATAGGA 59.988 47.826 0.00 0.00 43.43 2.94
6754 8967 1.491670 CTCAATCCGATACCTGTGCG 58.508 55.000 0.00 0.00 0.00 5.34
6860 9073 0.627469 ACTTCCAGGGTGGGGCATAT 60.627 55.000 0.00 0.00 38.32 1.78
6893 9106 5.301835 ACCTGATGAGCTGCTATTTACAT 57.698 39.130 0.15 0.63 0.00 2.29
6934 9147 8.715088 GCAGTGATGCAAAAGAAATAAAGAAAT 58.285 29.630 0.00 0.00 34.41 2.17
6935 9148 7.710044 TGCAGTGATGCAAAAGAAATAAAGAAA 59.290 29.630 0.00 0.00 42.40 2.52
6936 9149 7.208777 TGCAGTGATGCAAAAGAAATAAAGAA 58.791 30.769 0.00 0.00 42.40 2.52
6937 9150 6.747125 TGCAGTGATGCAAAAGAAATAAAGA 58.253 32.000 0.00 0.00 42.40 2.52
7129 9346 6.215431 TGAAGAGAAAATGATACTTCCCTCCA 59.785 38.462 0.00 0.00 36.96 3.86
7162 9380 7.473735 TGGAAAAATATCAACAGCCACAATA 57.526 32.000 0.00 0.00 0.00 1.90
7191 9409 9.140874 CCTATATCTGCTATATGAAGTGGATCA 57.859 37.037 0.00 0.00 0.00 2.92
7456 9762 9.569167 CGAGATCAGTTGATAAAACAAGTAGTA 57.431 33.333 0.00 0.00 34.37 1.82
7457 9763 8.304596 TCGAGATCAGTTGATAAAACAAGTAGT 58.695 33.333 0.00 0.00 34.37 2.73
7458 9764 8.689251 TCGAGATCAGTTGATAAAACAAGTAG 57.311 34.615 0.00 0.00 34.37 2.57
7647 9953 1.985159 ACTTTCACCTGTCCCATAGCA 59.015 47.619 0.00 0.00 0.00 3.49
7651 9957 2.290323 GCTACACTTTCACCTGTCCCAT 60.290 50.000 0.00 0.00 0.00 4.00
7699 10005 0.950555 CCATGATACATCCGCCCACG 60.951 60.000 0.00 0.00 39.67 4.94
7703 10009 2.350522 CTTAGCCATGATACATCCGCC 58.649 52.381 0.00 0.00 0.00 6.13
7705 10011 3.325293 AGCTTAGCCATGATACATCCG 57.675 47.619 0.00 0.00 0.00 4.18
7733 10039 6.683974 ACATTAACTATTGTCAGTGATGGC 57.316 37.500 0.00 0.00 31.83 4.40
7809 10117 8.610896 CAGCCAATACATTTGTCAAAAGAAAAA 58.389 29.630 7.51 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.