Multiple sequence alignment - TraesCS1D01G290500

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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 TraesCS1D01G290500 chr1D 100.000 4112 0 0 1 4112 388634707 388638818 0.000000e+00 7594.0
1 TraesCS1D01G290500 chr1A 93.061 1859 67 25 818 2642 487725286 487727116 0.000000e+00 2662.0
2 TraesCS1D01G290500 chr1A 94.206 535 26 3 2635 3164 487727246 487727780 0.000000e+00 811.0
3 TraesCS1D01G290500 chr1A 94.314 510 22 5 3190 3696 487728036 487728541 0.000000e+00 774.0
4 TraesCS1D01G290500 chr1A 93.678 348 13 4 3768 4112 487728534 487728875 2.830000e-141 512.0
5 TraesCS1D01G290500 chr1A 88.530 279 27 3 467 744 306675928 306676202 2.370000e-87 333.0
6 TraesCS1D01G290500 chr1B 94.575 1493 55 13 2638 4112 522009177 522010661 0.000000e+00 2285.0
7 TraesCS1D01G290500 chr1B 93.123 1076 46 15 1582 2642 522007981 522009043 0.000000e+00 1552.0
8 TraesCS1D01G290500 chr1B 91.017 757 42 11 818 1562 522007249 522007991 0.000000e+00 998.0
9 TraesCS1D01G290500 chr1B 94.737 38 0 2 797 834 522007202 522007237 1.600000e-04 58.4
10 TraesCS1D01G290500 chr3B 91.421 746 60 4 1 744 610206982 610207725 0.000000e+00 1020.0
11 TraesCS1D01G290500 chr3B 91.067 750 61 4 1 746 562919450 562920197 0.000000e+00 1009.0
12 TraesCS1D01G290500 chr7D 91.277 642 53 3 1 640 249491073 249490433 0.000000e+00 872.0
13 TraesCS1D01G290500 chr7D 91.781 73 4 2 676 747 249490085 249490014 2.620000e-17 100.0
14 TraesCS1D01G290500 chr2B 82.055 769 110 17 1 747 229442302 229443064 7.500000e-177 630.0
15 TraesCS1D01G290500 chr2D 84.641 599 87 5 1 597 575941109 575941704 3.540000e-165 592.0
16 TraesCS1D01G290500 chr5B 83.630 617 95 6 1 613 607864375 607864989 3.560000e-160 575.0
17 TraesCS1D01G290500 chr5B 83.172 618 94 8 1 613 704746070 704746682 1.290000e-154 556.0
18 TraesCS1D01G290500 chr5B 89.578 403 41 1 3 404 601392321 601392723 1.020000e-140 510.0
19 TraesCS1D01G290500 chr6B 89.556 383 39 1 1 382 130009401 130009783 6.180000e-133 484.0


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 TraesCS1D01G290500 chr1D 388634707 388638818 4111 False 7594.00 7594 100.00000 1 4112 1 chr1D.!!$F1 4111
1 TraesCS1D01G290500 chr1A 487725286 487728875 3589 False 1189.75 2662 93.81475 818 4112 4 chr1A.!!$F2 3294
2 TraesCS1D01G290500 chr1B 522007202 522010661 3459 False 1223.35 2285 93.36300 797 4112 4 chr1B.!!$F1 3315
3 TraesCS1D01G290500 chr3B 610206982 610207725 743 False 1020.00 1020 91.42100 1 744 1 chr3B.!!$F2 743
4 TraesCS1D01G290500 chr3B 562919450 562920197 747 False 1009.00 1009 91.06700 1 746 1 chr3B.!!$F1 745
5 TraesCS1D01G290500 chr7D 249490014 249491073 1059 True 486.00 872 91.52900 1 747 2 chr7D.!!$R1 746
6 TraesCS1D01G290500 chr2B 229442302 229443064 762 False 630.00 630 82.05500 1 747 1 chr2B.!!$F1 746
7 TraesCS1D01G290500 chr2D 575941109 575941704 595 False 592.00 592 84.64100 1 597 1 chr2D.!!$F1 596
8 TraesCS1D01G290500 chr5B 607864375 607864989 614 False 575.00 575 83.63000 1 613 1 chr5B.!!$F2 612
9 TraesCS1D01G290500 chr5B 704746070 704746682 612 False 556.00 556 83.17200 1 613 1 chr5B.!!$F3 612

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
753 1095 0.984230 AACGAGAGGGGATTGCTCAA 59.016 50.0 0.00 0.00 0.0 3.02 F
1432 1817 0.535780 CAGGCAGGAGTGTTGAGCAA 60.536 55.0 0.00 0.00 0.0 3.91 F
1433 1818 0.536006 AGGCAGGAGTGTTGAGCAAC 60.536 55.0 6.41 6.41 41.5 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 3042 0.700564 AGGATCCACTGCCAATGTGT 59.299 50.0 15.82 0.00 33.92 3.72 R
3081 3640 1.102978 GGTCAATTTGTGGGATCCCG 58.897 55.0 26.03 9.74 39.42 5.14 R
3166 3726 2.024176 TACCCTCCAGAAGAACAGCA 57.976 50.0 0.00 0.00 0.00 4.41 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
97 98 3.286404 CATGGCCTTCAACATGGGA 57.714 52.632 3.32 0.00 40.50 4.37
390 395 1.762957 GCAGTATGAACCCTAGCCAGA 59.237 52.381 0.00 0.00 39.69 3.86
404 409 1.153289 CCAGAGCCATCCAACGGAG 60.153 63.158 0.00 0.00 34.05 4.63
441 449 2.414806 GGTTCTTGTTCCTCGAAGACC 58.585 52.381 0.00 0.00 0.00 3.85
455 463 3.452264 TCGAAGACCACATCATCCAGATT 59.548 43.478 0.00 0.00 33.72 2.40
498 506 3.054213 TCTCCATCAATTCTGCCACATCA 60.054 43.478 0.00 0.00 0.00 3.07
568 578 1.838077 ACCCTAACCCGATGGAGAAAG 59.162 52.381 0.00 0.00 34.81 2.62
749 1091 3.688553 CCTAACGAGAGGGGATTGC 57.311 57.895 0.00 0.00 32.39 3.56
750 1092 1.123928 CCTAACGAGAGGGGATTGCT 58.876 55.000 0.00 0.00 32.39 3.91
751 1093 1.069358 CCTAACGAGAGGGGATTGCTC 59.931 57.143 0.00 0.00 32.39 4.26
752 1094 1.757118 CTAACGAGAGGGGATTGCTCA 59.243 52.381 0.00 0.00 0.00 4.26
753 1095 0.984230 AACGAGAGGGGATTGCTCAA 59.016 50.000 0.00 0.00 0.00 3.02
754 1096 1.207791 ACGAGAGGGGATTGCTCAAT 58.792 50.000 0.00 0.00 0.00 2.57
755 1097 1.139853 ACGAGAGGGGATTGCTCAATC 59.860 52.381 12.81 12.81 44.82 2.67
756 1098 1.415659 CGAGAGGGGATTGCTCAATCT 59.584 52.381 18.63 3.12 44.90 2.40
757 1099 2.547642 CGAGAGGGGATTGCTCAATCTC 60.548 54.545 18.63 15.87 45.32 2.75
763 1105 2.098770 GGGATTGCTCAATCTCAACTGC 59.901 50.000 18.63 4.16 45.37 4.40
764 1106 3.015327 GGATTGCTCAATCTCAACTGCT 58.985 45.455 18.63 0.00 44.90 4.24
765 1107 3.065095 GGATTGCTCAATCTCAACTGCTC 59.935 47.826 18.63 0.06 44.90 4.26
766 1108 2.105006 TGCTCAATCTCAACTGCTCC 57.895 50.000 0.00 0.00 0.00 4.70
767 1109 1.348696 TGCTCAATCTCAACTGCTCCA 59.651 47.619 0.00 0.00 0.00 3.86
768 1110 2.008329 GCTCAATCTCAACTGCTCCAG 58.992 52.381 0.00 0.00 37.52 3.86
834 1176 5.070580 GTGGACTAATATTACTGGGCTGTCT 59.929 44.000 8.04 0.00 0.00 3.41
835 1177 5.665812 TGGACTAATATTACTGGGCTGTCTT 59.334 40.000 8.04 0.00 0.00 3.01
839 1181 8.086143 ACTAATATTACTGGGCTGTCTTGTTA 57.914 34.615 0.00 0.00 0.00 2.41
841 1183 7.625828 AATATTACTGGGCTGTCTTGTTAAC 57.374 36.000 0.00 0.00 0.00 2.01
842 1184 4.699925 TTACTGGGCTGTCTTGTTAACT 57.300 40.909 7.22 0.00 0.00 2.24
845 1216 1.202879 TGGGCTGTCTTGTTAACTGGG 60.203 52.381 7.22 0.00 0.00 4.45
863 1234 1.068541 GGGCGTCCTGTCACAAATTTC 60.069 52.381 0.00 0.00 0.00 2.17
866 1237 2.604614 GCGTCCTGTCACAAATTTCACC 60.605 50.000 0.00 0.00 0.00 4.02
975 1352 3.584406 TCCACCCCAGCATTATCTCATAG 59.416 47.826 0.00 0.00 0.00 2.23
1322 1699 5.048643 GCGAAAGGATAGTAGTCTGCTATGA 60.049 44.000 14.46 0.00 30.09 2.15
1353 1738 1.139455 CGTGGTGGTCGGGGTTTATAT 59.861 52.381 0.00 0.00 0.00 0.86
1358 1743 1.418637 TGGTCGGGGTTTATATGAGGC 59.581 52.381 0.00 0.00 0.00 4.70
1408 1793 3.686726 GTGGTTCTAGAACTGGATTGCTG 59.313 47.826 29.66 0.00 40.94 4.41
1410 1795 3.686726 GGTTCTAGAACTGGATTGCTGTG 59.313 47.826 29.66 0.00 40.94 3.66
1426 1811 1.526917 GTGTGCAGGCAGGAGTGTT 60.527 57.895 0.00 0.00 0.00 3.32
1427 1812 1.526686 TGTGCAGGCAGGAGTGTTG 60.527 57.895 0.00 0.00 0.00 3.33
1428 1813 1.227943 GTGCAGGCAGGAGTGTTGA 60.228 57.895 0.00 0.00 0.00 3.18
1429 1814 1.071987 TGCAGGCAGGAGTGTTGAG 59.928 57.895 0.00 0.00 0.00 3.02
1430 1815 2.331132 GCAGGCAGGAGTGTTGAGC 61.331 63.158 0.00 0.00 0.00 4.26
1431 1816 1.071987 CAGGCAGGAGTGTTGAGCA 59.928 57.895 0.00 0.00 0.00 4.26
1432 1817 0.535780 CAGGCAGGAGTGTTGAGCAA 60.536 55.000 0.00 0.00 0.00 3.91
1433 1818 0.536006 AGGCAGGAGTGTTGAGCAAC 60.536 55.000 6.41 6.41 41.50 4.17
1454 1839 2.419324 CAGAGCAAGGTTCATTCTGAGC 59.581 50.000 0.00 0.00 37.96 4.26
1472 1857 3.887110 TGAGCATGATTTCTTAGGCATGG 59.113 43.478 0.00 0.00 38.75 3.66
1473 1858 2.626743 AGCATGATTTCTTAGGCATGGC 59.373 45.455 12.14 12.14 38.75 4.40
1642 2033 5.127031 GCATAACACATCACTATTTTGGGGT 59.873 40.000 0.00 0.00 0.00 4.95
1765 2156 1.546923 TGCATTGCTTTGACATGGAGG 59.453 47.619 10.49 0.00 0.00 4.30
2031 2430 5.390567 GGTTTGTCCTGTCGAACATTCATAC 60.391 44.000 0.00 0.00 34.44 2.39
2218 2617 7.781324 AAATAATGGACACTTTGTTCCTGAT 57.219 32.000 0.00 0.00 0.00 2.90
2339 2753 5.811796 TGTACAAGGTACACCATAACACT 57.188 39.130 5.18 0.00 38.89 3.55
2404 2818 7.581213 TTGATTTGGTGTCATCTACAACTTT 57.419 32.000 0.00 0.00 46.70 2.66
2412 2826 6.653320 GGTGTCATCTACAACTTTTATCCACA 59.347 38.462 0.00 0.00 42.96 4.17
2488 2903 4.986659 GCATATCCAAGATTGAAACCATGC 59.013 41.667 0.00 0.00 0.00 4.06
2491 2906 3.091545 TCCAAGATTGAAACCATGCCTC 58.908 45.455 0.00 0.00 0.00 4.70
2530 2945 8.122472 ACGATTGGAAACCATATCTTCTTTTT 57.878 30.769 0.00 0.00 31.53 1.94
2626 3042 4.977739 AGATTGAAACCAGATCTATGGGGA 59.022 41.667 6.01 0.00 45.25 4.81
2627 3043 4.503714 TTGAAACCAGATCTATGGGGAC 57.496 45.455 6.01 0.00 45.25 4.46
2628 3044 3.459828 TGAAACCAGATCTATGGGGACA 58.540 45.455 6.01 0.59 45.25 4.02
2639 3193 1.228521 TGGGGACACATTGGCAGTG 60.229 57.895 8.60 8.60 42.56 3.66
2657 3211 4.691175 CAGTGGATCCTAGTCTGTTCATG 58.309 47.826 14.23 0.00 0.00 3.07
2712 3271 7.224297 AGTTGAGCTGGTTCAGTTTTCTAATA 58.776 34.615 0.00 0.00 33.43 0.98
2913 3472 6.655078 AAAGTGGCACTGTTGATAAAATCT 57.345 33.333 22.83 0.00 0.00 2.40
3081 3640 2.034685 GCCAGAGTGGTTCCAAAGAAAC 59.965 50.000 0.00 0.00 40.46 2.78
3101 3660 1.102978 GGGATCCCACAAATTGACCG 58.897 55.000 26.95 0.00 35.81 4.79
3147 3707 6.006449 ACTCTGCAACTGAATTGGATTAGTT 58.994 36.000 0.00 0.00 38.08 2.24
3180 3743 2.645838 AAGCTTGCTGTTCTTCTGGA 57.354 45.000 0.00 0.00 0.00 3.86
3273 4063 3.861840 CCCGCAGAGAAGAAAGATGTAA 58.138 45.455 0.00 0.00 0.00 2.41
3275 4065 5.601662 CCCGCAGAGAAGAAAGATGTAATA 58.398 41.667 0.00 0.00 0.00 0.98
3393 4192 2.783135 ACGTGTACGAGGGAGTAAAGA 58.217 47.619 11.79 0.00 43.02 2.52
3407 4206 4.637534 GGAGTAAAGATCTGCAAAGCATGA 59.362 41.667 0.00 0.00 38.13 3.07
3457 4258 7.908827 TTATCGTTGTATAGCACTTTTTGGA 57.091 32.000 0.00 0.00 0.00 3.53
3470 4271 3.882888 ACTTTTTGGATGCTGACGAAAGA 59.117 39.130 0.00 0.00 0.00 2.52
3614 4415 0.107017 TTATCCTGCTTCTGCCCAGC 60.107 55.000 0.00 0.00 38.71 4.85
3636 4437 1.544825 TTCAGGAGCTTAGCGGCACT 61.545 55.000 1.45 0.00 34.17 4.40
3802 4604 7.885297 TGAACTGAATATCAAAACCTTCCAAG 58.115 34.615 0.00 0.00 0.00 3.61
3877 4679 3.634910 GGACTGCCTAAACCAAACTTGAA 59.365 43.478 0.00 0.00 0.00 2.69
4060 4864 4.655440 AAAAAGCCACACGAACAAAAAC 57.345 36.364 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 4.637534 CACGATCTTCCTGATGGATTTTGT 59.362 41.667 0.00 0.00 42.81 2.83
118 119 3.181451 TGGAGATATGGGCACAGATTCAC 60.181 47.826 0.00 0.00 0.00 3.18
390 395 3.390521 TCGCTCCGTTGGATGGCT 61.391 61.111 0.00 0.00 0.00 4.75
404 409 3.775654 CCCCTCCACCAGAGTCGC 61.776 72.222 0.00 0.00 41.47 5.19
441 449 5.066117 CCAAGAGAACAATCTGGATGATGTG 59.934 44.000 0.00 0.00 35.54 3.21
568 578 1.519455 CCTCAACAGCCCGATCGTC 60.519 63.158 15.09 5.42 0.00 4.20
717 1059 4.015084 CTCGTTAGGGTTTCTCCTACTCA 58.985 47.826 0.00 0.00 38.97 3.41
747 1089 1.348696 TGGAGCAGTTGAGATTGAGCA 59.651 47.619 0.00 0.00 0.00 4.26
748 1090 2.008329 CTGGAGCAGTTGAGATTGAGC 58.992 52.381 0.00 0.00 0.00 4.26
749 1091 3.331478 ACTGGAGCAGTTGAGATTGAG 57.669 47.619 0.00 0.00 42.59 3.02
798 1140 9.865321 GTAATATTAGTCCACTTGTGTTCTACA 57.135 33.333 0.00 0.00 37.56 2.74
801 1143 8.041323 CCAGTAATATTAGTCCACTTGTGTTCT 58.959 37.037 0.00 1.17 0.00 3.01
802 1144 7.280205 CCCAGTAATATTAGTCCACTTGTGTTC 59.720 40.741 0.00 0.00 0.00 3.18
803 1145 7.110155 CCCAGTAATATTAGTCCACTTGTGTT 58.890 38.462 0.00 0.00 0.00 3.32
834 1176 0.470766 ACAGGACGCCCAGTTAACAA 59.529 50.000 8.61 0.00 33.88 2.83
835 1177 0.034337 GACAGGACGCCCAGTTAACA 59.966 55.000 8.61 0.00 31.77 2.41
839 1181 1.978455 TTGTGACAGGACGCCCAGTT 61.978 55.000 0.00 0.00 31.77 3.16
841 1183 0.606401 ATTTGTGACAGGACGCCCAG 60.606 55.000 0.00 0.00 33.88 4.45
842 1184 0.179004 AATTTGTGACAGGACGCCCA 60.179 50.000 0.00 0.00 33.88 5.36
845 1216 2.604614 GGTGAAATTTGTGACAGGACGC 60.605 50.000 0.00 0.00 0.00 5.19
863 1234 3.834799 GGGCGAGGAGGTACGGTG 61.835 72.222 0.00 0.00 0.00 4.94
866 1237 4.189188 CGTGGGCGAGGAGGTACG 62.189 72.222 0.00 0.00 41.33 3.67
1342 1727 3.306780 CCACTAGCCTCATATAAACCCCG 60.307 52.174 0.00 0.00 0.00 5.73
1353 1738 1.974957 TGCAGTTAACCACTAGCCTCA 59.025 47.619 0.88 0.00 32.76 3.86
1358 1743 4.392138 GGTTTAGCTGCAGTTAACCACTAG 59.608 45.833 27.32 0.00 32.76 2.57
1408 1793 1.526917 AACACTCCTGCCTGCACAC 60.527 57.895 0.00 0.00 0.00 3.82
1410 1795 1.227943 TCAACACTCCTGCCTGCAC 60.228 57.895 0.00 0.00 0.00 4.57
1416 1801 0.590195 CTGTTGCTCAACACTCCTGC 59.410 55.000 11.03 0.00 45.42 4.85
1426 1811 1.134128 TGAACCTTGCTCTGTTGCTCA 60.134 47.619 0.00 0.00 0.00 4.26
1427 1812 1.597742 TGAACCTTGCTCTGTTGCTC 58.402 50.000 0.00 0.00 0.00 4.26
1428 1813 2.283145 ATGAACCTTGCTCTGTTGCT 57.717 45.000 0.00 0.00 0.00 3.91
1429 1814 2.555757 AGAATGAACCTTGCTCTGTTGC 59.444 45.455 0.00 0.00 0.00 4.17
1430 1815 3.817084 TCAGAATGAACCTTGCTCTGTTG 59.183 43.478 0.00 0.00 45.97 3.33
1431 1816 4.090761 TCAGAATGAACCTTGCTCTGTT 57.909 40.909 0.00 0.00 45.97 3.16
1432 1817 3.777106 TCAGAATGAACCTTGCTCTGT 57.223 42.857 0.00 0.00 45.97 3.41
1454 1839 5.300034 TGTTAGCCATGCCTAAGAAATCATG 59.700 40.000 0.00 0.00 36.86 3.07
1541 1931 9.719355 AAAAAGGACTTGATTTGTAAAACAACT 57.281 25.926 0.00 0.00 37.90 3.16
1600 1990 1.074752 GCAGTCAGAAAGGAAGCTCG 58.925 55.000 0.00 0.00 0.00 5.03
1642 2033 5.542635 AGTCCAACACTACCTGAAGATACAA 59.457 40.000 0.00 0.00 31.37 2.41
1765 2156 1.160137 GCCTTGTCGGATGATATGCC 58.840 55.000 0.00 0.00 33.16 4.40
1812 2204 9.613428 TGAGAACTTAACAACAATATCATAGGG 57.387 33.333 0.00 0.00 0.00 3.53
2051 2450 4.261825 GGAAGCGCAGATCAGTTAGATACT 60.262 45.833 11.47 0.00 37.00 2.12
2218 2617 3.706698 CGAGCACGAGAATTATCCTCAA 58.293 45.455 0.00 0.00 42.66 3.02
2422 2836 9.165035 CCTCCAATTTGCACAACATAATAAATT 57.835 29.630 0.00 0.00 0.00 1.82
2423 2837 8.320617 ACCTCCAATTTGCACAACATAATAAAT 58.679 29.630 0.00 0.00 0.00 1.40
2424 2838 7.675062 ACCTCCAATTTGCACAACATAATAAA 58.325 30.769 0.00 0.00 0.00 1.40
2425 2839 7.238486 ACCTCCAATTTGCACAACATAATAA 57.762 32.000 0.00 0.00 0.00 1.40
2426 2840 6.849085 ACCTCCAATTTGCACAACATAATA 57.151 33.333 0.00 0.00 0.00 0.98
2427 2841 5.743636 ACCTCCAATTTGCACAACATAAT 57.256 34.783 0.00 0.00 0.00 1.28
2499 2914 6.414732 AGATATGGTTTCCAATCGTTTCTGA 58.585 36.000 0.00 0.00 36.95 3.27
2500 2915 6.683974 AGATATGGTTTCCAATCGTTTCTG 57.316 37.500 0.00 0.00 36.95 3.02
2501 2916 7.112779 AGAAGATATGGTTTCCAATCGTTTCT 58.887 34.615 0.00 2.70 36.95 2.52
2502 2917 7.321745 AGAAGATATGGTTTCCAATCGTTTC 57.678 36.000 0.00 0.91 36.95 2.78
2504 2919 7.703058 AAAGAAGATATGGTTTCCAATCGTT 57.297 32.000 0.00 0.00 36.95 3.85
2505 2920 7.703058 AAAAGAAGATATGGTTTCCAATCGT 57.297 32.000 0.00 0.00 36.95 3.73
2506 2921 8.243426 TCAAAAAGAAGATATGGTTTCCAATCG 58.757 33.333 0.00 0.00 36.95 3.34
2510 2925 9.087871 TGATTCAAAAAGAAGATATGGTTTCCA 57.912 29.630 0.00 0.00 40.15 3.53
2511 2926 9.578439 CTGATTCAAAAAGAAGATATGGTTTCC 57.422 33.333 0.00 0.00 40.15 3.13
2530 2945 7.867403 GTGGCATTTTTCTAAGAAACTGATTCA 59.133 33.333 0.00 0.00 40.72 2.57
2626 3042 0.700564 AGGATCCACTGCCAATGTGT 59.299 50.000 15.82 0.00 33.92 3.72
2627 3043 2.092753 ACTAGGATCCACTGCCAATGTG 60.093 50.000 15.82 0.00 35.39 3.21
2628 3044 2.171448 GACTAGGATCCACTGCCAATGT 59.829 50.000 15.82 0.00 0.00 2.71
2629 3045 2.437281 AGACTAGGATCCACTGCCAATG 59.563 50.000 15.82 0.00 0.00 2.82
2630 3046 2.437281 CAGACTAGGATCCACTGCCAAT 59.563 50.000 15.82 0.00 0.00 3.16
2636 3190 3.133721 GCATGAACAGACTAGGATCCACT 59.866 47.826 15.82 4.77 0.00 4.00
2639 3193 3.244044 GGAGCATGAACAGACTAGGATCC 60.244 52.174 2.48 2.48 0.00 3.36
2657 3211 4.673841 GCAGAAAGCTTGATAAACAGGAGC 60.674 45.833 0.00 0.00 41.15 4.70
2937 3496 9.425248 AACATAATTGGATCAATAACACTGGAT 57.575 29.630 0.00 0.00 32.43 3.41
2942 3501 9.781834 TTTCGAACATAATTGGATCAATAACAC 57.218 29.630 0.00 0.00 32.43 3.32
3081 3640 1.102978 GGTCAATTTGTGGGATCCCG 58.897 55.000 26.03 9.74 39.42 5.14
3166 3726 2.024176 TACCCTCCAGAAGAACAGCA 57.976 50.000 0.00 0.00 0.00 4.41
3173 3733 5.657302 ACTGTACAAGTATACCCTCCAGAAG 59.343 44.000 0.00 0.00 37.36 2.85
3180 3743 9.359653 ACGAATATAACTGTACAAGTATACCCT 57.640 33.333 0.00 0.00 38.56 4.34
3348 4147 2.082231 CCATCAGCAAGGTTGTCTGAG 58.918 52.381 16.52 11.18 41.23 3.35
3393 4192 2.307768 CCCTGATCATGCTTTGCAGAT 58.692 47.619 0.00 2.04 43.65 2.90
3407 4206 5.965033 AATCACTGATGTAGAACCCTGAT 57.035 39.130 0.00 0.00 0.00 2.90
3438 4237 5.801947 CAGCATCCAAAAAGTGCTATACAAC 59.198 40.000 0.00 0.00 46.67 3.32
3457 4258 0.792640 CAAGCGTCTTTCGTCAGCAT 59.207 50.000 0.00 0.00 42.13 3.79
3470 4271 2.031157 GCATTGTAACTTCACCAAGCGT 60.031 45.455 0.00 0.00 32.09 5.07
3636 4437 3.038788 TGCTACTGATTCTTTGTCGCA 57.961 42.857 0.00 0.00 31.59 5.10
3732 4534 9.881773 AAAGCTCCAAAAATATATCCCTTATCA 57.118 29.630 0.00 0.00 0.00 2.15
3736 4538 7.126268 AGCAAAAGCTCCAAAAATATATCCCTT 59.874 33.333 0.00 0.00 0.00 3.95
3737 4539 6.612863 AGCAAAAGCTCCAAAAATATATCCCT 59.387 34.615 0.00 0.00 0.00 4.20
3802 4604 1.409661 GGATTGGGGGTATGTGTGTCC 60.410 57.143 0.00 0.00 0.00 4.02
3910 4712 9.959721 ATGGAGCTTTTTAAAATACTACTCTGA 57.040 29.630 0.55 0.00 0.00 3.27
3912 4714 9.959721 TGATGGAGCTTTTTAAAATACTACTCT 57.040 29.630 0.55 0.00 0.00 3.24
3914 4716 9.959721 TCTGATGGAGCTTTTTAAAATACTACT 57.040 29.630 0.55 0.00 0.00 2.57
4045 4849 0.818296 TGGGGTTTTTGTTCGTGTGG 59.182 50.000 0.00 0.00 0.00 4.17
4060 4864 1.703411 TCTTCCTTTTGCAACTGGGG 58.297 50.000 14.66 8.05 0.00 4.96


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

AutoCloner maintained by Alex Coulton.