Multiple sequence alignment - TraesCS2B01G470700

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 TraesCS2B01G470700 chr2B 100.000 3186 0 0 1 3186 667130481 667127296 0.000000e+00 5884.0
1 TraesCS2B01G470700 chr2A 89.292 3250 187 73 25 3184 699387111 699383933 0.000000e+00 3925.0
2 TraesCS2B01G470700 chr2D 92.636 1453 66 17 870 2297 558734331 558732895 0.000000e+00 2052.0
3 TraesCS2B01G470700 chr2D 89.251 521 31 8 277 773 558734877 558734358 2.090000e-176 628.0
4 TraesCS2B01G470700 chr2D 81.392 618 93 18 2577 3184 632462291 632461686 4.780000e-133 484.0
5 TraesCS2B01G470700 chr2D 93.182 44 3 0 800 843 558734373 558734330 7.380000e-07 65.8
6 TraesCS2B01G470700 chr3D 81.818 847 113 29 2355 3183 46962269 46961446 0.000000e+00 673.0
7 TraesCS2B01G470700 chr3D 76.549 823 136 34 2379 3186 343868632 343867852 6.400000e-107 398.0
8 TraesCS2B01G470700 chr7D 81.401 871 113 29 2345 3183 138504683 138505536 0.000000e+00 665.0
9 TraesCS2B01G470700 chr6A 79.857 839 111 40 2345 3163 100428268 100429068 7.720000e-156 560.0
10 TraesCS2B01G470700 chr7A 81.029 680 101 23 2523 3183 164820627 164821297 1.690000e-142 516.0
11 TraesCS2B01G470700 chr7A 90.909 66 6 0 8 73 190393656 190393721 4.380000e-14 89.8
12 TraesCS2B01G470700 chr3B 81.518 606 83 23 2589 3184 817599437 817598851 3.720000e-129 472.0
13 TraesCS2B01G470700 chr6D 80.000 660 98 26 2523 3174 450355951 450355318 1.040000e-124 457.0
14 TraesCS2B01G470700 chr4A 80.062 642 101 22 2559 3184 604028051 604027421 4.850000e-123 451.0
15 TraesCS2B01G470700 chr5D 78.509 228 35 9 2367 2590 448833878 448833661 1.540000e-28 137.0
16 TraesCS2B01G470700 chr4B 94.595 37 2 0 25 61 51840924 51840960 1.230000e-04 58.4


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 TraesCS2B01G470700 chr2B 667127296 667130481 3185 True 5884.000000 5884 100.000000 1 3186 1 chr2B.!!$R1 3185
1 TraesCS2B01G470700 chr2A 699383933 699387111 3178 True 3925.000000 3925 89.292000 25 3184 1 chr2A.!!$R1 3159
2 TraesCS2B01G470700 chr2D 558732895 558734877 1982 True 915.266667 2052 91.689667 277 2297 3 chr2D.!!$R2 2020
3 TraesCS2B01G470700 chr2D 632461686 632462291 605 True 484.000000 484 81.392000 2577 3184 1 chr2D.!!$R1 607
4 TraesCS2B01G470700 chr3D 46961446 46962269 823 True 673.000000 673 81.818000 2355 3183 1 chr3D.!!$R1 828
5 TraesCS2B01G470700 chr3D 343867852 343868632 780 True 398.000000 398 76.549000 2379 3186 1 chr3D.!!$R2 807
6 TraesCS2B01G470700 chr7D 138504683 138505536 853 False 665.000000 665 81.401000 2345 3183 1 chr7D.!!$F1 838
7 TraesCS2B01G470700 chr6A 100428268 100429068 800 False 560.000000 560 79.857000 2345 3163 1 chr6A.!!$F1 818
8 TraesCS2B01G470700 chr7A 164820627 164821297 670 False 516.000000 516 81.029000 2523 3183 1 chr7A.!!$F1 660
9 TraesCS2B01G470700 chr3B 817598851 817599437 586 True 472.000000 472 81.518000 2589 3184 1 chr3B.!!$R1 595
10 TraesCS2B01G470700 chr6D 450355318 450355951 633 True 457.000000 457 80.000000 2523 3174 1 chr6D.!!$R1 651
11 TraesCS2B01G470700 chr4A 604027421 604028051 630 True 451.000000 451 80.062000 2559 3184 1 chr4A.!!$R1 625

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
23 24 0.036388 AAAGACATCGTCACCGCCAT 60.036 50.0 0.0 0.0 34.60 4.40 F
1314 1371 0.038166 GTGTCCAAGGGATGCAGGAA 59.962 55.0 0.0 0.0 32.73 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 1926 0.834612 TTCAACCACCTTCACGACCT 59.165 50.0 0.00 0.0 0.00 3.85 R
2287 2392 0.524392 CGACACGCAAGGTTTTTGCA 60.524 50.0 11.83 0.0 45.14 4.08 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
19 20 0.708370 CGTGAAAGACATCGTCACCG 59.292 55.000 11.06 5.38 38.76 4.94
20 21 0.438830 GTGAAAGACATCGTCACCGC 59.561 55.000 7.25 0.00 36.48 5.68
21 22 0.669318 TGAAAGACATCGTCACCGCC 60.669 55.000 0.00 0.00 34.60 6.13
22 23 0.669318 GAAAGACATCGTCACCGCCA 60.669 55.000 0.00 0.00 34.60 5.69
23 24 0.036388 AAAGACATCGTCACCGCCAT 60.036 50.000 0.00 0.00 34.60 4.40
29 30 0.461339 ATCGTCACCGCCATACAACC 60.461 55.000 0.00 0.00 0.00 3.77
34 35 0.682855 CACCGCCATACAACCCCAAT 60.683 55.000 0.00 0.00 0.00 3.16
38 39 1.821753 CGCCATACAACCCCAATCAAA 59.178 47.619 0.00 0.00 0.00 2.69
42 43 3.257127 CCATACAACCCCAATCAAAACGT 59.743 43.478 0.00 0.00 0.00 3.99
43 44 4.262249 CCATACAACCCCAATCAAAACGTT 60.262 41.667 0.00 0.00 0.00 3.99
82 83 3.403558 GGAGTCCCTCCCACTGGC 61.404 72.222 0.00 0.00 44.36 4.85
126 127 1.103398 CCATGGTTCGAAGGCCATCC 61.103 60.000 15.44 5.44 40.43 3.51
127 128 1.103398 CATGGTTCGAAGGCCATCCC 61.103 60.000 15.44 4.76 40.43 3.85
137 138 2.903855 GCCATCCCATGCGAGGTG 60.904 66.667 0.00 0.00 0.00 4.00
143 144 4.838152 CCATGCGAGGTGGACCGG 62.838 72.222 0.00 0.00 42.08 5.28
173 174 1.466558 CGGCAAGAAGAGAAAGAAGGC 59.533 52.381 0.00 0.00 0.00 4.35
179 180 5.009510 GCAAGAAGAGAAAGAAGGCTTTTCT 59.990 40.000 12.75 12.75 44.10 2.52
195 196 3.275848 TTTCTTGAGGAGGAGGAGGAA 57.724 47.619 0.00 0.00 0.00 3.36
196 197 3.275848 TTCTTGAGGAGGAGGAGGAAA 57.724 47.619 0.00 0.00 0.00 3.13
197 198 2.826488 TCTTGAGGAGGAGGAGGAAAG 58.174 52.381 0.00 0.00 0.00 2.62
198 199 2.383683 TCTTGAGGAGGAGGAGGAAAGA 59.616 50.000 0.00 0.00 0.00 2.52
208 209 1.545706 GGAGGAAAGAGAGCCCGTGT 61.546 60.000 0.00 0.00 0.00 4.49
210 211 0.321996 AGGAAAGAGAGCCCGTGTTC 59.678 55.000 0.00 0.00 0.00 3.18
213 214 3.916392 AAGAGAGCCCGTGTTCGCG 62.916 63.158 0.00 0.00 35.54 5.87
225 226 0.241749 TGTTCGCGTGGACGTTATCT 59.758 50.000 5.77 0.00 42.22 1.98
227 228 1.723003 GTTCGCGTGGACGTTATCTTT 59.277 47.619 5.77 0.00 42.22 2.52
229 230 0.643820 CGCGTGGACGTTATCTTTCC 59.356 55.000 0.00 0.00 42.22 3.13
257 258 4.690748 TGCTTAGTACTGATGTTGACTTGC 59.309 41.667 5.39 0.00 0.00 4.01
272 273 2.814336 GACTTGCATTTCGACCCTTTCT 59.186 45.455 0.00 0.00 0.00 2.52
273 274 2.554032 ACTTGCATTTCGACCCTTTCTG 59.446 45.455 0.00 0.00 0.00 3.02
274 275 1.533625 TGCATTTCGACCCTTTCTGG 58.466 50.000 0.00 0.00 0.00 3.86
275 276 0.171231 GCATTTCGACCCTTTCTGGC 59.829 55.000 0.00 0.00 0.00 4.85
276 277 1.826385 CATTTCGACCCTTTCTGGCT 58.174 50.000 0.00 0.00 0.00 4.75
277 278 2.162681 CATTTCGACCCTTTCTGGCTT 58.837 47.619 0.00 0.00 0.00 4.35
278 279 2.358322 TTTCGACCCTTTCTGGCTTT 57.642 45.000 0.00 0.00 0.00 3.51
279 280 1.892209 TTCGACCCTTTCTGGCTTTC 58.108 50.000 0.00 0.00 0.00 2.62
368 384 2.773993 TCGGCCCGACTTCTATTTTT 57.226 45.000 0.00 0.00 0.00 1.94
378 394 4.473199 GACTTCTATTTTTGCCGTTGGAC 58.527 43.478 0.00 0.00 0.00 4.02
481 504 3.209410 GCCTTGGTAGGTCAATCATGAG 58.791 50.000 0.09 0.00 44.00 2.90
491 514 9.614792 GGTAGGTCAATCATGAGTACTTTAATT 57.385 33.333 0.09 0.00 35.88 1.40
621 650 3.230134 CACTTGGGGGAAACATTCTTGA 58.770 45.455 0.00 0.00 0.00 3.02
630 659 3.314080 GGAAACATTCTTGACGAACCACA 59.686 43.478 0.00 0.00 33.72 4.17
694 723 0.524816 CCGACGAACACATACCTCCG 60.525 60.000 0.00 0.00 0.00 4.63
720 749 2.930040 CGAAGTACATGCGAAGTGGATT 59.070 45.455 0.00 0.00 0.00 3.01
839 869 4.290155 CTCCAACAATTCTCCAACAAACG 58.710 43.478 0.00 0.00 0.00 3.60
860 890 4.175337 ACCCTGCGTGCACACACT 62.175 61.111 18.64 0.00 45.10 3.55
903 935 2.309764 CTGGAGCCGCGCACATTAAC 62.310 60.000 8.75 0.00 0.00 2.01
904 936 2.403586 GAGCCGCGCACATTAACC 59.596 61.111 8.75 0.00 0.00 2.85
1314 1371 0.038166 GTGTCCAAGGGATGCAGGAA 59.962 55.000 0.00 0.00 32.73 3.36
1395 1456 2.155155 GCACGAAAGAGGTAAACAGACG 59.845 50.000 0.00 0.00 0.00 4.18
1420 1485 9.311916 CGATCTCTCTATCTGAAAAGTGAAAAT 57.688 33.333 0.00 0.00 0.00 1.82
1455 1520 2.505866 GTTTCGTTTCGGTGCATCATC 58.494 47.619 0.00 0.00 0.00 2.92
1458 1523 0.096976 CGTTTCGGTGCATCATCCAC 59.903 55.000 0.00 0.00 0.00 4.02
1462 1527 2.516930 GGTGCATCATCCACCCCG 60.517 66.667 0.00 0.00 45.51 5.73
1636 1729 7.131565 TGATACGTGCACATGCTAATTAATTG 58.868 34.615 18.64 2.59 42.66 2.32
1641 1734 5.678483 GTGCACATGCTAATTAATTGTCGAG 59.322 40.000 13.17 1.38 42.66 4.04
1667 1760 2.872245 GCAGATATTTACGCTGCCAAGA 59.128 45.455 0.00 0.00 46.94 3.02
1675 1768 2.383527 CGCTGCCAAGACGGACTTC 61.384 63.158 0.00 0.00 36.61 3.01
1699 1792 3.363378 GCAAGAACACTTGTGTCATCGAG 60.363 47.826 6.88 2.50 41.85 4.04
1782 1875 3.312973 GTCATCGACAAGGTAGAGACGAT 59.687 47.826 0.00 0.00 40.26 3.73
1833 1926 4.284746 GGTGAAGAAGAAGAAAGAGGAGGA 59.715 45.833 0.00 0.00 0.00 3.71
1839 1932 2.172679 GAAGAAAGAGGAGGAGGTCGT 58.827 52.381 0.00 0.00 0.00 4.34
1849 1942 0.763223 AGGAGGTCGTGAAGGTGGTT 60.763 55.000 0.00 0.00 0.00 3.67
2056 2161 1.140252 GGTGGTTACGGTCATGGCTAT 59.860 52.381 0.00 0.00 0.00 2.97
2062 2167 1.893808 CGGTCATGGCTATGGTGGC 60.894 63.158 10.47 0.00 34.97 5.01
2089 2194 2.100749 TGGGTCATACAGTATGCACTCG 59.899 50.000 14.95 0.00 42.53 4.18
2128 2233 1.260561 GACACGTCGTTCTTGCATTGT 59.739 47.619 0.00 0.00 0.00 2.71
2313 2418 6.255215 CAAAAACCTTGCGTGTCGATATATT 58.745 36.000 0.00 0.00 0.00 1.28
2321 2426 4.763279 TGCGTGTCGATATATTAGAAGGGA 59.237 41.667 0.00 0.00 0.00 4.20
2322 2427 5.106277 TGCGTGTCGATATATTAGAAGGGAG 60.106 44.000 0.00 0.00 0.00 4.30
2338 2444 5.701290 AGAAGGGAGAAAACGAAATGTACAG 59.299 40.000 0.33 0.00 0.00 2.74
2482 2614 9.712410 CAATTTTCTTAAATCGACGAACATTTG 57.288 29.630 0.00 0.00 32.85 2.32
2485 2617 9.932699 TTTTCTTAAATCGACGAACATTTGTAA 57.067 25.926 0.00 0.00 0.00 2.41
2498 2665 7.485277 ACGAACATTTGTAAAATCAACGAACAA 59.515 29.630 0.00 0.00 0.00 2.83
2721 2918 9.823098 TTTTTGAATTGTCAACATTTTGTTCAG 57.177 25.926 0.00 0.00 43.52 3.02
2732 2929 9.868277 TCAACATTTTGTTCAGTTTCATTAACT 57.132 25.926 0.00 0.00 42.35 2.24
2806 3004 8.641499 TCCGAACATTTATTTTCAATATTGCC 57.359 30.769 10.76 0.00 0.00 4.52
2826 3026 4.524714 TGCCAACATTTTTCGAATAAGGGA 59.475 37.500 15.53 6.29 0.00 4.20
2978 3206 8.038351 AGGAAAAATGAGAACGGAAAAGAAAAA 58.962 29.630 0.00 0.00 0.00 1.94
3177 3426 3.348647 AATATTTTGCAACTTGGGGGC 57.651 42.857 0.00 0.00 0.00 5.80
3180 3429 0.842635 TTTTGCAACTTGGGGGCAAT 59.157 45.000 0.00 0.00 45.81 3.56
3183 3432 0.396060 TGCAACTTGGGGGCAATTTC 59.604 50.000 0.00 0.00 34.05 2.17
3184 3433 0.670239 GCAACTTGGGGGCAATTTCG 60.670 55.000 0.00 0.00 0.00 3.46
3185 3434 0.965439 CAACTTGGGGGCAATTTCGA 59.035 50.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.780107 TTGGGGTTGTATGGCGGTGA 61.780 55.000 0.00 0.00 0.00 4.02
15 16 0.682855 ATTGGGGTTGTATGGCGGTG 60.683 55.000 0.00 0.00 0.00 4.94
16 17 0.395173 GATTGGGGTTGTATGGCGGT 60.395 55.000 0.00 0.00 0.00 5.68
17 18 0.395036 TGATTGGGGTTGTATGGCGG 60.395 55.000 0.00 0.00 0.00 6.13
18 19 1.468985 TTGATTGGGGTTGTATGGCG 58.531 50.000 0.00 0.00 0.00 5.69
19 20 3.595173 GTTTTGATTGGGGTTGTATGGC 58.405 45.455 0.00 0.00 0.00 4.40
20 21 3.257127 ACGTTTTGATTGGGGTTGTATGG 59.743 43.478 0.00 0.00 0.00 2.74
21 22 4.513198 ACGTTTTGATTGGGGTTGTATG 57.487 40.909 0.00 0.00 0.00 2.39
22 23 4.585162 TCAACGTTTTGATTGGGGTTGTAT 59.415 37.500 0.00 0.00 36.79 2.29
23 24 3.952323 TCAACGTTTTGATTGGGGTTGTA 59.048 39.130 0.00 0.00 36.79 2.41
29 30 3.726291 AGGTTCAACGTTTTGATTGGG 57.274 42.857 0.00 0.00 41.50 4.12
34 35 7.813148 TCATTTTTGTTAGGTTCAACGTTTTGA 59.187 29.630 0.00 0.00 40.14 2.69
38 39 6.622549 TGTCATTTTTGTTAGGTTCAACGTT 58.377 32.000 0.00 0.00 0.00 3.99
42 43 6.263392 TCCGATGTCATTTTTGTTAGGTTCAA 59.737 34.615 0.00 0.00 0.00 2.69
43 44 5.765677 TCCGATGTCATTTTTGTTAGGTTCA 59.234 36.000 0.00 0.00 0.00 3.18
84 85 2.193248 CAGAGGATTTCGGCCCCC 59.807 66.667 0.00 0.00 0.00 5.40
90 91 0.250234 TGGAGGTGCAGAGGATTTCG 59.750 55.000 0.00 0.00 0.00 3.46
93 94 0.549950 CCATGGAGGTGCAGAGGATT 59.450 55.000 5.56 0.00 0.00 3.01
113 114 1.453745 GCATGGGATGGCCTTCGAA 60.454 57.895 12.20 0.00 0.00 3.71
114 115 2.192979 GCATGGGATGGCCTTCGA 59.807 61.111 12.20 2.33 0.00 3.71
116 117 1.895707 CTCGCATGGGATGGCCTTC 60.896 63.158 13.45 10.18 0.00 3.46
126 127 4.838152 CCGGTCCACCTCGCATGG 62.838 72.222 0.00 0.00 38.71 3.66
151 152 2.079925 CTTCTTTCTCTTCTTGCCGGG 58.920 52.381 2.18 0.00 0.00 5.73
152 153 2.079925 CCTTCTTTCTCTTCTTGCCGG 58.920 52.381 0.00 0.00 0.00 6.13
153 154 1.466558 GCCTTCTTTCTCTTCTTGCCG 59.533 52.381 0.00 0.00 0.00 5.69
154 155 2.789213 AGCCTTCTTTCTCTTCTTGCC 58.211 47.619 0.00 0.00 0.00 4.52
155 156 4.844998 AAAGCCTTCTTTCTCTTCTTGC 57.155 40.909 0.00 0.00 38.03 4.01
156 157 6.631971 AGAAAAGCCTTCTTTCTCTTCTTG 57.368 37.500 0.00 0.00 41.40 3.02
157 158 6.830838 TCAAGAAAAGCCTTCTTTCTCTTCTT 59.169 34.615 8.34 0.00 41.40 2.52
158 159 6.360618 TCAAGAAAAGCCTTCTTTCTCTTCT 58.639 36.000 8.34 0.00 41.40 2.85
161 162 5.069318 CCTCAAGAAAAGCCTTCTTTCTCT 58.931 41.667 8.34 0.00 41.40 3.10
173 174 3.177228 TCCTCCTCCTCCTCAAGAAAAG 58.823 50.000 0.00 0.00 0.00 2.27
179 180 2.383683 TCTCTTTCCTCCTCCTCCTCAA 59.616 50.000 0.00 0.00 0.00 3.02
195 196 2.048127 GCGAACACGGGCTCTCTT 60.048 61.111 0.00 0.00 0.00 2.85
196 197 4.421479 CGCGAACACGGGCTCTCT 62.421 66.667 0.00 0.00 33.76 3.10
197 198 4.719369 ACGCGAACACGGGCTCTC 62.719 66.667 15.93 0.00 42.24 3.20
208 209 1.987770 GAAAGATAACGTCCACGCGAA 59.012 47.619 15.93 0.00 44.43 4.70
210 211 0.643820 GGAAAGATAACGTCCACGCG 59.356 55.000 3.53 3.53 44.43 6.01
213 214 3.604875 TGGAGGAAAGATAACGTCCAC 57.395 47.619 0.00 0.00 43.14 4.02
225 226 5.189736 ACATCAGTACTAAGCATGGAGGAAA 59.810 40.000 0.00 0.00 0.00 3.13
227 228 4.290093 ACATCAGTACTAAGCATGGAGGA 58.710 43.478 0.00 0.00 0.00 3.71
229 230 5.521735 GTCAACATCAGTACTAAGCATGGAG 59.478 44.000 0.00 0.00 0.00 3.86
272 273 7.285401 ACATTGTAAAGAAGAAGAAGAAAGCCA 59.715 33.333 0.00 0.00 0.00 4.75
273 274 7.652727 ACATTGTAAAGAAGAAGAAGAAAGCC 58.347 34.615 0.00 0.00 0.00 4.35
274 275 9.175060 GAACATTGTAAAGAAGAAGAAGAAAGC 57.825 33.333 0.00 0.00 0.00 3.51
277 278 9.173021 TGTGAACATTGTAAAGAAGAAGAAGAA 57.827 29.630 0.00 0.00 0.00 2.52
278 279 8.731275 TGTGAACATTGTAAAGAAGAAGAAGA 57.269 30.769 0.00 0.00 0.00 2.87
279 280 9.390795 CATGTGAACATTGTAAAGAAGAAGAAG 57.609 33.333 0.00 0.00 33.61 2.85
378 394 1.393539 CAAAGTTCTATGGTGACGGCG 59.606 52.381 4.80 4.80 0.00 6.46
386 402 1.006832 CGGACGGCAAAGTTCTATGG 58.993 55.000 0.00 0.00 0.00 2.74
444 467 2.789723 GCGAAAACGTTGACGGCG 60.790 61.111 22.10 4.80 44.95 6.46
581 610 0.889186 GGTTGGGCTGTCGTGTGATT 60.889 55.000 0.00 0.00 0.00 2.57
621 650 2.878406 CAATCCAAACTCTGTGGTTCGT 59.122 45.455 0.00 0.00 37.43 3.85
630 659 4.099419 GTGGGTTTTGTCAATCCAAACTCT 59.901 41.667 8.80 0.00 34.23 3.24
676 705 1.138047 GCGGAGGTATGTGTTCGTCG 61.138 60.000 0.00 0.00 0.00 5.12
694 723 2.615618 CGCATGTACTTCGAGCGC 59.384 61.111 0.00 0.00 41.95 5.92
720 749 2.833582 GCTCGGAGGGTCGGATCA 60.834 66.667 7.20 0.00 0.00 2.92
753 783 2.293399 GGGGTTCACATCACTTGTTGAC 59.707 50.000 0.00 0.00 36.92 3.18
756 786 1.142060 TCGGGGTTCACATCACTTGTT 59.858 47.619 0.00 0.00 36.00 2.83
762 792 1.052617 TTGAGTCGGGGTTCACATCA 58.947 50.000 0.00 0.00 0.00 3.07
786 816 5.062058 CGCATCACTTGTTTCTTTGTTTTGT 59.938 36.000 0.00 0.00 0.00 2.83
795 825 2.290641 GTGGTTCGCATCACTTGTTTCT 59.709 45.455 0.00 0.00 0.00 2.52
796 826 2.604614 GGTGGTTCGCATCACTTGTTTC 60.605 50.000 0.00 0.00 34.57 2.78
860 890 0.764369 AGGCTTCAGGTGTGAGGTGA 60.764 55.000 0.00 0.00 32.32 4.02
904 936 0.385390 GCATAACGCATTCAAGGGGG 59.615 55.000 0.00 0.00 41.79 5.40
1140 1189 8.351495 TGCTATAAAAACAAAGCAAAACAGAG 57.649 30.769 0.00 0.00 41.74 3.35
1314 1371 2.165845 GGAGGTATGTACTCAACGTGCT 59.834 50.000 0.00 0.00 36.70 4.40
1462 1527 3.442273 TCCTGCATTATGAAACGGGAAAC 59.558 43.478 0.00 0.00 34.63 2.78
1533 1598 2.305928 AGGATCTCTCTGACCATGACG 58.694 52.381 0.00 0.00 0.00 4.35
1574 1639 5.551233 ACGAATTTGTGAGAGAGGAAATGA 58.449 37.500 0.00 0.00 0.00 2.57
1575 1640 5.163814 GGACGAATTTGTGAGAGAGGAAATG 60.164 44.000 2.13 0.00 0.00 2.32
1576 1641 4.938226 GGACGAATTTGTGAGAGAGGAAAT 59.062 41.667 2.13 0.00 0.00 2.17
1577 1642 4.040461 AGGACGAATTTGTGAGAGAGGAAA 59.960 41.667 2.13 0.00 0.00 3.13
1578 1643 3.578716 AGGACGAATTTGTGAGAGAGGAA 59.421 43.478 2.13 0.00 0.00 3.36
1636 1729 5.629849 AGCGTAAATATCTGCATTACTCGAC 59.370 40.000 5.80 0.00 0.00 4.20
1667 1760 0.878961 GTGTTCTTGCCGAAGTCCGT 60.879 55.000 0.00 0.00 36.31 4.69
1699 1792 1.066587 CTTCTCCTCGATGACGCCC 59.933 63.158 0.00 0.00 39.58 6.13
1782 1875 4.758251 CCTCCACGATGCGCACCA 62.758 66.667 14.90 0.00 0.00 4.17
1833 1926 0.834612 TTCAACCACCTTCACGACCT 59.165 50.000 0.00 0.00 0.00 3.85
1839 1932 2.930950 CAACCTCTTCAACCACCTTCA 58.069 47.619 0.00 0.00 0.00 3.02
1849 1942 1.490490 ACAACCTCTGCAACCTCTTCA 59.510 47.619 0.00 0.00 0.00 3.02
2062 2167 0.821517 TACTGTATGACCCACAGCCG 59.178 55.000 2.51 0.00 45.96 5.52
2089 2194 1.045911 CCTGGTACCCTCTGAGCTCC 61.046 65.000 12.15 0.00 0.00 4.70
2116 2221 1.408422 GGTGCGAACAATGCAAGAAC 58.592 50.000 0.00 0.00 45.23 3.01
2128 2233 0.534203 GGAAGTCAACAGGGTGCGAA 60.534 55.000 0.00 0.00 0.00 4.70
2287 2392 0.524392 CGACACGCAAGGTTTTTGCA 60.524 50.000 11.83 0.00 45.14 4.08
2301 2406 9.194271 GTTTTCTCCCTTCTAATATATCGACAC 57.806 37.037 0.00 0.00 0.00 3.67
2313 2418 6.761312 TGTACATTTCGTTTTCTCCCTTCTA 58.239 36.000 0.00 0.00 0.00 2.10
2321 2426 3.818773 CACCCCTGTACATTTCGTTTTCT 59.181 43.478 0.00 0.00 0.00 2.52
2322 2427 3.566742 ACACCCCTGTACATTTCGTTTTC 59.433 43.478 0.00 0.00 0.00 2.29
2338 2444 0.582960 CGTAAACGTGTTCACACCCC 59.417 55.000 4.48 0.00 43.66 4.95
2466 2598 8.687301 GTTGATTTTACAAATGTTCGTCGATTT 58.313 29.630 0.00 0.00 0.00 2.17
2470 2602 5.841811 TCGTTGATTTTACAAATGTTCGTCG 59.158 36.000 0.00 0.00 0.00 5.12
2706 2903 9.868277 AGTTAATGAAACTGAACAAAATGTTGA 57.132 25.926 1.62 0.00 46.90 3.18
2781 2979 8.253810 TGGCAATATTGAAAATAAATGTTCGGA 58.746 29.630 19.73 0.00 0.00 4.55
2806 3004 8.532977 AATGTTCCCTTATTCGAAAAATGTTG 57.467 30.769 0.00 0.00 0.00 3.33
2980 3208 8.952979 CGGCCTGTTTTTAAATTTTCATTTTTC 58.047 29.630 0.00 0.00 34.29 2.29
3130 3379 7.000472 CCCACCAATGTCATCTATAAGTGATT 59.000 38.462 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.