Multiple sequence alignment - TraesCS1B01G341000

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 TraesCS1B01G341000 chr1B 100.000 3621 0 0 1 3621 568967022 568963402 0.000000e+00 6687.0
1 TraesCS1B01G341000 chr1B 81.657 338 45 11 1692 2016 50988713 50989046 7.710000e-67 265.0
2 TraesCS1B01G341000 chr1D 95.035 3424 104 35 210 3621 420653253 420649884 0.000000e+00 5321.0
3 TraesCS1B01G341000 chr1D 78.171 339 56 14 1692 2016 33605535 33605869 2.200000e-47 200.0
4 TraesCS1B01G341000 chr1D 83.893 149 16 7 1 146 420653395 420653252 6.310000e-28 135.0
5 TraesCS1B01G341000 chr1A 93.725 2263 92 20 36 2267 517100822 517098579 0.000000e+00 3347.0
6 TraesCS1B01G341000 chr1A 97.230 686 14 2 2269 2949 517098411 517097726 0.000000e+00 1157.0
7 TraesCS1B01G341000 chr1A 93.759 673 32 8 2954 3621 517097519 517096852 0.000000e+00 1002.0
8 TraesCS1B01G341000 chr1A 78.526 312 50 13 1719 2016 32187515 32187823 4.770000e-44 189.0
9 TraesCS1B01G341000 chr1A 93.976 83 4 1 2048 2129 311077344 311077262 1.370000e-24 124.0
10 TraesCS1B01G341000 chr1A 75.635 197 29 12 2099 2291 577833293 577833474 3.000000e-11 80.5
11 TraesCS1B01G341000 chr3D 95.181 83 3 1 2053 2134 105151047 105151129 2.930000e-26 130.0
12 TraesCS1B01G341000 chr3D 93.976 83 4 1 2053 2134 105182932 105183014 1.370000e-24 124.0
13 TraesCS1B01G341000 chr6B 89.899 99 3 3 2043 2134 216509750 216509848 1.770000e-23 121.0
14 TraesCS1B01G341000 chr2B 90.323 93 7 2 2042 2132 90401095 90401187 1.770000e-23 121.0
15 TraesCS1B01G341000 chr2B 86.250 80 6 1 2055 2129 508407899 508407978 8.330000e-12 82.4
16 TraesCS1B01G341000 chr2B 81.633 98 12 5 2048 2139 408297765 408297668 3.880000e-10 76.8
17 TraesCS1B01G341000 chr6D 78.974 195 26 9 2137 2328 459736380 459736562 6.350000e-23 119.0
18 TraesCS1B01G341000 chr3B 78.836 189 25 11 2146 2331 16048397 16048221 2.950000e-21 113.0
19 TraesCS1B01G341000 chr3B 77.500 200 32 10 2137 2334 501422515 501422327 1.370000e-19 108.0
20 TraesCS1B01G341000 chr5A 85.217 115 7 5 2025 2132 698639617 698639728 3.820000e-20 110.0
21 TraesCS1B01G341000 chr7D 77.041 196 32 11 2141 2334 29801294 29801110 2.300000e-17 100.0
22 TraesCS1B01G341000 chr7D 86.022 93 8 2 2139 2230 63657393 63657305 1.070000e-15 95.3
23 TraesCS1B01G341000 chr2D 88.095 84 5 4 2142 2224 36439033 36438954 1.070000e-15 95.3
24 TraesCS1B01G341000 chr7A 85.882 85 11 1 2249 2332 685384565 685384649 4.980000e-14 89.8
25 TraesCS1B01G341000 chr2A 85.263 95 5 4 2144 2237 526069868 526069782 4.980000e-14 89.8
26 TraesCS1B01G341000 chr7B 93.333 60 3 1 2267 2325 643198293 643198352 1.790000e-13 87.9


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 TraesCS1B01G341000 chr1B 568963402 568967022 3620 True 6687.000000 6687 100.000000 1 3621 1 chr1B.!!$R1 3620
1 TraesCS1B01G341000 chr1D 420649884 420653395 3511 True 2728.000000 5321 89.464000 1 3621 2 chr1D.!!$R1 3620
2 TraesCS1B01G341000 chr1A 517096852 517100822 3970 True 1835.333333 3347 94.904667 36 3621 3 chr1A.!!$R2 3585

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
139 141 0.105224 TCCTTTTGGACGAACGAGCA 59.895 50.000 0.14 0.00 45.19 4.26 F
490 494 0.527600 GCTCGTACATCGTGGCATGA 60.528 55.000 12.53 12.53 40.80 3.07 F
1488 1498 0.746063 TACGTAATGGGCGGACGATT 59.254 50.000 0.00 0.00 39.81 3.34 F
1528 1538 1.290009 GGTGGCATGTTTGACCAGC 59.710 57.895 3.26 3.26 38.99 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 1845 1.701847 GATCAGCATACCATCACCCCT 59.298 52.381 0.00 0.00 0.00 4.79 R
2300 2521 1.133407 GCTGGTCTCAGTCGACTAAGG 59.867 57.143 19.57 11.16 42.78 2.69 R
2599 2825 0.976641 AGAACAATCCGTCTCCTGCA 59.023 50.000 0.00 0.00 0.00 4.41 R
3177 3607 1.136828 AAACTGTCTACTGCCCACCA 58.863 50.000 0.00 0.00 0.00 4.17 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
110 112 0.249784 AGCAGTAGCATGATCCAGCG 60.250 55.000 0.00 0.00 45.49 5.18
130 132 2.034221 AGGCCGCTCCTTTTGGAC 59.966 61.111 0.00 0.00 44.75 4.02
136 138 0.942410 CGCTCCTTTTGGACGAACGA 60.942 55.000 0.14 0.00 45.19 3.85
139 141 0.105224 TCCTTTTGGACGAACGAGCA 59.895 50.000 0.14 0.00 45.19 4.26
141 143 1.217882 CTTTTGGACGAACGAGCAGT 58.782 50.000 0.14 0.00 0.00 4.40
200 202 3.055719 AAATGACGCCCCGTGCTG 61.056 61.111 0.00 0.00 41.37 4.41
231 233 7.472741 TCTGGATTTCCTATTGATTATGCCAT 58.527 34.615 0.00 0.00 36.82 4.40
271 273 7.238037 GCCAGTGCATTAGCTACTTAGCTTAT 61.238 42.308 15.79 9.71 46.94 1.73
324 326 2.172293 GACCTCATGGCAGAGATTCCTT 59.828 50.000 13.36 0.00 37.87 3.36
326 328 2.092538 CCTCATGGCAGAGATTCCTTGT 60.093 50.000 13.36 0.00 37.87 3.16
380 382 2.490115 CCTGAGTGTGTACCTGAGAGAC 59.510 54.545 0.00 0.00 0.00 3.36
479 483 9.642327 TTACTGAATAATAAACAAGCTCGTACA 57.358 29.630 0.00 0.00 0.00 2.90
490 494 0.527600 GCTCGTACATCGTGGCATGA 60.528 55.000 12.53 12.53 40.80 3.07
502 506 2.988493 CGTGGCATGACATTGGAAAAAG 59.012 45.455 3.50 0.00 0.00 2.27
553 558 2.681344 GTTCCATAATGTTGACCCCGTC 59.319 50.000 0.00 0.00 0.00 4.79
603 608 6.071728 CCATTTCAGGTGATAAAGAACAAGCT 60.072 38.462 0.00 0.00 0.00 3.74
604 609 6.560253 TTTCAGGTGATAAAGAACAAGCTC 57.440 37.500 0.00 0.00 0.00 4.09
605 610 5.489792 TCAGGTGATAAAGAACAAGCTCT 57.510 39.130 0.00 0.00 0.00 4.09
658 665 4.037446 TGTGTCTTTTGGCCATTGTACTTC 59.963 41.667 6.09 2.54 0.00 3.01
785 792 7.408756 TCAGCTGTTTTCCTAATGCATATTT 57.591 32.000 14.67 0.00 0.00 1.40
846 853 2.993899 ACACGTAAAAGGCTCAAGATCG 59.006 45.455 0.00 0.00 0.00 3.69
901 908 2.095212 GGGAACGATTGCTCTGGTTTTC 60.095 50.000 0.00 0.00 0.00 2.29
919 928 9.364989 CTGGTTTTCTTTTTGTTATGTTCAAGA 57.635 29.630 0.00 0.00 0.00 3.02
985 995 9.755064 ATATCATTTAAACGTTCTTTTGTCTCG 57.245 29.630 0.00 0.00 0.00 4.04
999 1009 3.349488 TGTCTCGGCATGTAGATTACG 57.651 47.619 0.00 0.00 0.00 3.18
1243 1253 4.909695 AGAAGGATGACATGGGTGATGATA 59.090 41.667 0.00 0.00 35.80 2.15
1452 1462 3.006112 TGTGGTAAAGTTGGACAAGCA 57.994 42.857 0.00 0.00 0.00 3.91
1455 1465 1.611977 GGTAAAGTTGGACAAGCACCC 59.388 52.381 0.00 0.00 0.00 4.61
1488 1498 0.746063 TACGTAATGGGCGGACGATT 59.254 50.000 0.00 0.00 39.81 3.34
1528 1538 1.290009 GGTGGCATGTTTGACCAGC 59.710 57.895 3.26 3.26 38.99 4.85
1717 1727 9.527157 TTGGATTTTATCTTCAGTTGGAACATA 57.473 29.630 0.00 0.00 39.30 2.29
1835 1845 8.333984 TCAGGAATATACCGGAGATCTGTATTA 58.666 37.037 9.46 0.00 34.73 0.98
2025 2035 2.042831 AGCCATGCGTTCTGCCTTC 61.043 57.895 0.00 0.00 45.60 3.46
2089 2099 7.201785 CCATAATATAAGGGCGTTTTTGACACT 60.202 37.037 0.00 0.00 0.00 3.55
2090 2100 8.832521 CATAATATAAGGGCGTTTTTGACACTA 58.167 33.333 0.00 0.00 0.00 2.74
2091 2101 6.920569 ATATAAGGGCGTTTTTGACACTAG 57.079 37.500 0.00 0.00 0.00 2.57
2092 2102 2.632987 AGGGCGTTTTTGACACTAGT 57.367 45.000 0.00 0.00 0.00 2.57
2093 2103 2.218603 AGGGCGTTTTTGACACTAGTG 58.781 47.619 21.44 21.44 0.00 2.74
2106 2116 4.957759 ACACTAGTGTCAAAAACGCTTT 57.042 36.364 22.95 0.00 46.62 3.51
2107 2117 5.305139 ACACTAGTGTCAAAAACGCTTTT 57.695 34.783 22.95 0.00 46.62 2.27
2108 2118 6.425577 ACACTAGTGTCAAAAACGCTTTTA 57.574 33.333 22.95 0.00 46.62 1.52
2109 2119 7.023197 ACACTAGTGTCAAAAACGCTTTTAT 57.977 32.000 22.95 0.00 46.62 1.40
2110 2120 8.145316 ACACTAGTGTCAAAAACGCTTTTATA 57.855 30.769 22.95 0.00 46.62 0.98
2111 2121 8.780249 ACACTAGTGTCAAAAACGCTTTTATAT 58.220 29.630 22.95 0.00 46.62 0.86
2112 2122 9.607285 CACTAGTGTCAAAAACGCTTTTATATT 57.393 29.630 15.06 0.00 46.62 1.28
2116 2126 9.567848 AGTGTCAAAAACGCTTTTATATTATGG 57.432 29.630 0.00 0.00 46.62 2.74
2117 2127 9.562583 GTGTCAAAAACGCTTTTATATTATGGA 57.437 29.630 0.00 0.00 32.85 3.41
2118 2128 9.562583 TGTCAAAAACGCTTTTATATTATGGAC 57.437 29.630 0.00 0.00 32.85 4.02
2119 2129 8.730427 GTCAAAAACGCTTTTATATTATGGACG 58.270 33.333 0.00 0.00 32.85 4.79
2120 2130 7.911205 TCAAAAACGCTTTTATATTATGGACGG 59.089 33.333 0.00 0.00 32.85 4.79
2121 2131 7.556733 AAAACGCTTTTATATTATGGACGGA 57.443 32.000 0.00 0.00 0.00 4.69
2122 2132 6.780706 AACGCTTTTATATTATGGACGGAG 57.219 37.500 0.00 0.00 0.00 4.63
2123 2133 5.235516 ACGCTTTTATATTATGGACGGAGG 58.764 41.667 0.00 0.00 0.00 4.30
2200 2255 3.072211 TCTCCGTCGATGCTATATTCGT 58.928 45.455 0.00 0.00 36.74 3.85
2201 2256 3.124806 TCTCCGTCGATGCTATATTCGTC 59.875 47.826 0.00 0.00 36.74 4.20
2202 2257 2.809696 TCCGTCGATGCTATATTCGTCA 59.190 45.455 0.00 0.00 36.74 4.35
2203 2258 3.251487 TCCGTCGATGCTATATTCGTCAA 59.749 43.478 0.00 0.00 36.74 3.18
2300 2521 5.504173 GCACTTGACTGAGACTTGGTTAAAC 60.504 44.000 0.00 0.00 0.00 2.01
2529 2755 5.680408 GCATTATGTGTTAGTCCACGGTCTA 60.680 44.000 0.00 0.00 38.20 2.59
2530 2756 5.981088 TTATGTGTTAGTCCACGGTCTAA 57.019 39.130 0.00 0.00 38.20 2.10
2599 2825 8.608185 AACCATGATAACAATAACCTTTGGAT 57.392 30.769 0.00 0.00 0.00 3.41
2632 2858 6.096423 ACGGATTGTTCTAGTTACAGCTATCA 59.904 38.462 0.00 0.00 0.00 2.15
2901 3127 4.101585 ACATCCACAATCGATACACATCCT 59.898 41.667 0.00 0.00 0.00 3.24
3257 3687 4.472833 AGTGAGATCCAGCTAGGTCAAATT 59.527 41.667 0.00 0.00 39.02 1.82
3268 3698 8.093927 CCAGCTAGGTCAAATTTTATTCCAAAA 58.906 33.333 0.00 0.00 0.00 2.44
3284 3714 4.277476 TCCAAAATTTCTGGCCGATATGT 58.723 39.130 0.00 0.00 33.63 2.29
3285 3715 4.097741 TCCAAAATTTCTGGCCGATATGTG 59.902 41.667 0.00 2.52 33.63 3.21
3286 3716 4.142182 CCAAAATTTCTGGCCGATATGTGT 60.142 41.667 0.00 0.00 0.00 3.72
3287 3717 5.410067 CAAAATTTCTGGCCGATATGTGTT 58.590 37.500 0.00 0.00 0.00 3.32
3288 3718 5.659440 AAATTTCTGGCCGATATGTGTTT 57.341 34.783 0.00 0.00 0.00 2.83
3289 3719 5.659440 AATTTCTGGCCGATATGTGTTTT 57.341 34.783 0.00 0.00 0.00 2.43
3290 3720 4.695217 TTTCTGGCCGATATGTGTTTTC 57.305 40.909 0.00 0.00 0.00 2.29
3291 3721 3.627395 TCTGGCCGATATGTGTTTTCT 57.373 42.857 0.00 0.00 0.00 2.52
3292 3722 3.531538 TCTGGCCGATATGTGTTTTCTC 58.468 45.455 0.00 0.00 0.00 2.87
3293 3723 3.197766 TCTGGCCGATATGTGTTTTCTCT 59.802 43.478 0.00 0.00 0.00 3.10
3334 3764 0.944386 GCAGAGTCGAACTGGCAAAA 59.056 50.000 18.21 0.00 36.09 2.44
3364 3794 8.707938 TGTTCACTCACTCTACATTATCATTG 57.292 34.615 0.00 0.00 0.00 2.82
3456 3886 7.346751 ACCAAAGACAAACAAATGTAGATGT 57.653 32.000 0.00 0.00 32.57 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.875933 GGTGACCGTTGAGACATTTCAA 59.124 45.455 0.00 0.00 34.83 2.69
38 39 3.706373 GCAGGGAGGGACGAAGCA 61.706 66.667 0.00 0.00 0.00 3.91
42 43 2.833582 GATCGCAGGGAGGGACGA 60.834 66.667 0.00 0.00 42.47 4.20
68 69 1.415672 GCCCGATTCCCACCATAGGA 61.416 60.000 0.00 0.00 0.00 2.94
69 70 1.073199 GCCCGATTCCCACCATAGG 59.927 63.158 0.00 0.00 0.00 2.57
130 132 4.717629 TCCCGCACTGCTCGTTCG 62.718 66.667 0.00 0.00 31.92 3.95
155 157 6.808008 TTAATTTTCTCTGCTCACTCCAAG 57.192 37.500 0.00 0.00 0.00 3.61
159 161 9.683069 TTTGATTTTAATTTTCTCTGCTCACTC 57.317 29.630 0.00 0.00 0.00 3.51
166 168 8.375465 GGCGTCATTTGATTTTAATTTTCTCTG 58.625 33.333 0.00 0.00 0.00 3.35
200 202 6.645790 ATCAATAGGAAATCCAGAATGCAC 57.354 37.500 1.67 0.00 38.89 4.57
231 233 1.985159 ACTGGCAGGTATGAACTCCAA 59.015 47.619 20.34 0.00 0.00 3.53
271 273 8.596271 TTTCTAGACGAACAACAATGACATAA 57.404 30.769 0.00 0.00 0.00 1.90
280 282 4.365723 GTCCACTTTCTAGACGAACAACA 58.634 43.478 0.00 0.00 0.00 3.33
324 326 6.488344 TGACATAAGCCTAAACACAAATGACA 59.512 34.615 0.00 0.00 0.00 3.58
326 328 6.939730 TCTGACATAAGCCTAAACACAAATGA 59.060 34.615 0.00 0.00 0.00 2.57
380 382 0.725784 GTGCGACGGCTTGAATTGTG 60.726 55.000 0.00 0.00 40.82 3.33
479 483 2.127271 TTCCAATGTCATGCCACGAT 57.873 45.000 0.00 0.00 0.00 3.73
490 494 5.067283 AGAGCGTTGTTACTTTTTCCAATGT 59.933 36.000 0.00 0.00 0.00 2.71
536 541 0.655733 GCGACGGGGTCAACATTATG 59.344 55.000 0.00 0.00 32.09 1.90
540 545 2.264794 GAGCGACGGGGTCAACAT 59.735 61.111 0.00 0.00 42.75 2.71
553 558 1.647545 AACAACGGATGGCATGAGCG 61.648 55.000 3.81 0.00 43.41 5.03
658 665 1.772182 AGAGACAGAGCGAAAACACG 58.228 50.000 0.00 0.00 0.00 4.49
801 808 8.946085 TGTCCAGTGTAATATTTTTCTAGCAAG 58.054 33.333 0.00 0.00 0.00 4.01
919 928 6.011096 TCACTGGAAAATACCCTTATTTCCCT 60.011 38.462 12.51 0.00 36.98 4.20
985 995 3.402628 ACCCATCGTAATCTACATGCC 57.597 47.619 0.00 0.00 0.00 4.40
999 1009 0.883833 CAGTGCCAACAGAACCCATC 59.116 55.000 0.00 0.00 0.00 3.51
1103 1113 5.695363 CCTCAGTATGACTGTGCTTATCATG 59.305 44.000 6.51 0.00 46.03 3.07
1452 1462 2.619646 ACGTAAAATTTTCTGCACGGGT 59.380 40.909 21.52 5.48 33.90 5.28
1455 1465 5.285134 CCCATTACGTAAAATTTTCTGCACG 59.715 40.000 12.81 17.89 35.62 5.34
1528 1538 1.817941 CCGCAGACCCAATTACCCG 60.818 63.158 0.00 0.00 0.00 5.28
1835 1845 1.701847 GATCAGCATACCATCACCCCT 59.298 52.381 0.00 0.00 0.00 4.79
2090 2100 9.567848 CCATAATATAAAAGCGTTTTTGACACT 57.432 29.630 18.77 3.85 37.12 3.55
2091 2101 9.562583 TCCATAATATAAAAGCGTTTTTGACAC 57.437 29.630 18.77 0.00 37.12 3.67
2092 2102 9.562583 GTCCATAATATAAAAGCGTTTTTGACA 57.437 29.630 18.77 5.33 37.12 3.58
2093 2103 8.730427 CGTCCATAATATAAAAGCGTTTTTGAC 58.270 33.333 18.77 13.14 37.12 3.18
2094 2104 7.911205 CCGTCCATAATATAAAAGCGTTTTTGA 59.089 33.333 18.77 8.06 37.12 2.69
2095 2105 7.911205 TCCGTCCATAATATAAAAGCGTTTTTG 59.089 33.333 18.77 2.23 37.12 2.44
2098 2108 6.204108 CCTCCGTCCATAATATAAAAGCGTTT 59.796 38.462 2.53 2.53 0.00 3.60
2100 2110 5.235516 CCTCCGTCCATAATATAAAAGCGT 58.764 41.667 0.00 0.00 0.00 5.07
2101 2111 4.630069 CCCTCCGTCCATAATATAAAAGCG 59.370 45.833 0.00 0.00 0.00 4.68
2102 2112 5.801380 TCCCTCCGTCCATAATATAAAAGC 58.199 41.667 0.00 0.00 0.00 3.51
2103 2113 7.005709 ACTCCCTCCGTCCATAATATAAAAG 57.994 40.000 0.00 0.00 0.00 2.27
2104 2114 7.731688 ACTACTCCCTCCGTCCATAATATAAAA 59.268 37.037 0.00 0.00 0.00 1.52
2105 2115 7.243824 ACTACTCCCTCCGTCCATAATATAAA 58.756 38.462 0.00 0.00 0.00 1.40
2106 2116 6.797707 ACTACTCCCTCCGTCCATAATATAA 58.202 40.000 0.00 0.00 0.00 0.98
2107 2117 6.398655 ACTACTCCCTCCGTCCATAATATA 57.601 41.667 0.00 0.00 0.00 0.86
2108 2118 5.272405 ACTACTCCCTCCGTCCATAATAT 57.728 43.478 0.00 0.00 0.00 1.28
2109 2119 4.736611 ACTACTCCCTCCGTCCATAATA 57.263 45.455 0.00 0.00 0.00 0.98
2110 2120 3.614568 ACTACTCCCTCCGTCCATAAT 57.385 47.619 0.00 0.00 0.00 1.28
2111 2121 3.393426 AACTACTCCCTCCGTCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
2112 2122 3.393426 AAACTACTCCCTCCGTCCATA 57.607 47.619 0.00 0.00 0.00 2.74
2113 2123 2.249309 AAACTACTCCCTCCGTCCAT 57.751 50.000 0.00 0.00 0.00 3.41
2114 2124 2.042162 AGTAAACTACTCCCTCCGTCCA 59.958 50.000 0.00 0.00 32.47 4.02
2115 2125 2.732763 AGTAAACTACTCCCTCCGTCC 58.267 52.381 0.00 0.00 32.47 4.79
2116 2126 6.939163 TGATATAGTAAACTACTCCCTCCGTC 59.061 42.308 0.00 0.00 40.14 4.79
2117 2127 6.845908 TGATATAGTAAACTACTCCCTCCGT 58.154 40.000 0.00 0.00 40.14 4.69
2118 2128 6.941436 ACTGATATAGTAAACTACTCCCTCCG 59.059 42.308 0.00 0.00 40.14 4.63
2119 2129 8.165397 AGACTGATATAGTAAACTACTCCCTCC 58.835 40.741 0.00 0.00 40.53 4.30
2120 2130 9.577222 AAGACTGATATAGTAAACTACTCCCTC 57.423 37.037 0.00 0.00 40.53 4.30
2121 2131 9.357161 CAAGACTGATATAGTAAACTACTCCCT 57.643 37.037 0.00 0.00 40.53 4.20
2122 2132 8.083462 GCAAGACTGATATAGTAAACTACTCCC 58.917 40.741 0.00 0.00 40.53 4.30
2123 2133 8.852135 AGCAAGACTGATATAGTAAACTACTCC 58.148 37.037 0.00 0.00 40.53 3.85
2174 2229 6.510879 AATATAGCATCGACGGAGACATAA 57.489 37.500 0.00 0.00 0.00 1.90
2300 2521 1.133407 GCTGGTCTCAGTCGACTAAGG 59.867 57.143 19.57 11.16 42.78 2.69
2529 2755 9.970395 CATATATCAGTATGCCAAACATTGTTT 57.030 29.630 8.97 8.97 40.38 2.83
2530 2756 9.135189 ACATATATCAGTATGCCAAACATTGTT 57.865 29.630 0.00 0.00 40.38 2.83
2599 2825 0.976641 AGAACAATCCGTCTCCTGCA 59.023 50.000 0.00 0.00 0.00 4.41
2632 2858 3.276857 CTGACCTGCTTATGCTGACATT 58.723 45.455 8.78 0.00 40.01 2.71
2901 3127 8.513774 ACTTTAAGGTCGTGAAAGTTGTAAAAA 58.486 29.630 2.64 0.00 39.75 1.94
3177 3607 1.136828 AAACTGTCTACTGCCCACCA 58.863 50.000 0.00 0.00 0.00 4.17
3257 3687 5.730296 TCGGCCAGAAATTTTGGAATAAA 57.270 34.783 18.07 0.00 37.96 1.40
3268 3698 4.949856 AGAAAACACATATCGGCCAGAAAT 59.050 37.500 2.24 0.00 0.00 2.17
3285 3715 4.036734 TGCTCAATGTGTTCCAGAGAAAAC 59.963 41.667 0.00 0.00 40.22 2.43
3286 3716 4.206375 TGCTCAATGTGTTCCAGAGAAAA 58.794 39.130 0.00 0.00 32.58 2.29
3287 3717 3.817084 CTGCTCAATGTGTTCCAGAGAAA 59.183 43.478 0.00 0.00 32.58 2.52
3288 3718 3.071457 TCTGCTCAATGTGTTCCAGAGAA 59.929 43.478 0.00 0.00 0.00 2.87
3289 3719 2.634453 TCTGCTCAATGTGTTCCAGAGA 59.366 45.455 0.00 0.00 0.00 3.10
3290 3720 3.049708 TCTGCTCAATGTGTTCCAGAG 57.950 47.619 0.00 0.00 0.00 3.35
3291 3721 3.490439 TTCTGCTCAATGTGTTCCAGA 57.510 42.857 0.00 0.00 0.00 3.86
3292 3722 4.778534 ATTTCTGCTCAATGTGTTCCAG 57.221 40.909 0.00 0.00 0.00 3.86
3293 3723 4.873817 CAATTTCTGCTCAATGTGTTCCA 58.126 39.130 0.00 0.00 0.00 3.53
3322 3752 4.675114 GTGAACAGTTATTTTGCCAGTTCG 59.325 41.667 0.00 0.00 37.34 3.95
3433 3863 8.567948 ACTACATCTACATTTGTTTGTCTTTGG 58.432 33.333 0.00 0.00 0.00 3.28
3574 4007 8.684655 GCAACATGTCAATTGTAAATATGATCG 58.315 33.333 5.13 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.