Multiple sequence alignment - TraesCS2A01G209900

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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 TraesCS2A01G209900 chr2A 100.000 4310 0 0 1 4310 194121070 194125379 0.000000e+00 7960.0
1 TraesCS2A01G209900 chr2A 97.222 36 1 0 547 582 194122649 194122684 1.290000e-05 62.1
2 TraesCS2A01G209900 chr2D 96.057 2511 74 8 1802 4310 179662294 179664781 0.000000e+00 4065.0
3 TraesCS2A01G209900 chr2D 92.030 1744 87 16 69 1792 179660411 179662122 0.000000e+00 2403.0
4 TraesCS2A01G209900 chr2D 94.737 57 1 2 1 57 179660367 179660421 2.140000e-13 87.9
5 TraesCS2A01G209900 chr2B 96.645 1729 53 3 1802 3529 236457387 236459111 0.000000e+00 2867.0
6 TraesCS2A01G209900 chr2B 93.627 1020 52 5 777 1792 236456205 236457215 0.000000e+00 1511.0
7 TraesCS2A01G209900 chr2B 93.820 712 32 4 3528 4234 236459193 236459897 0.000000e+00 1061.0
8 TraesCS2A01G209900 chr2B 93.703 397 20 3 318 714 236455392 236455783 1.330000e-164 590.0
9 TraesCS2A01G209900 chr2B 88.545 323 13 12 1 313 236454795 236455103 1.890000e-98 370.0
10 TraesCS2A01G209900 chr2B 94.505 91 4 1 4220 4310 236459917 236460006 5.810000e-29 139.0
11 TraesCS2A01G209900 chr1B 83.817 896 109 17 913 1792 123968007 123967132 0.000000e+00 819.0
12 TraesCS2A01G209900 chr1A 83.212 822 113 15 973 1788 96462646 96463448 0.000000e+00 730.0
13 TraesCS2A01G209900 chr1A 84.756 656 81 11 997 1646 96470479 96471121 1.310000e-179 640.0
14 TraesCS2A01G209900 chr6A 81.215 905 130 20 913 1791 574778 573888 0.000000e+00 693.0
15 TraesCS2A01G209900 chr1D 85.600 625 73 8 1184 1792 78983060 78982437 1.310000e-179 640.0
16 TraesCS2A01G209900 chr6B 81.350 815 110 22 997 1792 3825577 3824786 3.660000e-175 625.0
17 TraesCS2A01G209900 chr5A 80.448 803 143 10 997 1789 617255276 617254478 6.170000e-168 601.0
18 TraesCS2A01G209900 chr5B 80.123 810 139 13 997 1789 610664610 610663806 6.210000e-163 584.0
19 TraesCS2A01G209900 chr4D 91.324 219 19 0 2170 2388 466320137 466320355 2.520000e-77 300.0
20 TraesCS2A01G209900 chr4D 90.667 225 21 0 2170 2394 471173434 471173210 2.520000e-77 300.0
21 TraesCS2A01G209900 chr7A 72.147 517 135 9 2399 2910 617703886 617703374 9.660000e-32 148.0
22 TraesCS2A01G209900 chr7A 93.333 90 4 2 3931 4020 728456547 728456634 9.730000e-27 132.0
23 TraesCS2A01G209900 chr7A 88.991 109 7 3 3912 4020 728239408 728239305 3.500000e-26 130.0
24 TraesCS2A01G209900 chr7D 90.826 109 5 3 3912 4020 637573305 637573202 1.620000e-29 141.0
25 TraesCS2A01G209900 chr4B 98.039 51 1 0 3861 3911 88872237 88872287 5.940000e-14 89.8


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 TraesCS2A01G209900 chr2A 194121070 194125379 4309 False 4011.050000 7960 98.611000 1 4310 2 chr2A.!!$F1 4309
1 TraesCS2A01G209900 chr2D 179660367 179664781 4414 False 2185.300000 4065 94.274667 1 4310 3 chr2D.!!$F1 4309
2 TraesCS2A01G209900 chr2B 236454795 236460006 5211 False 1089.666667 2867 93.474167 1 4310 6 chr2B.!!$F1 4309
3 TraesCS2A01G209900 chr1B 123967132 123968007 875 True 819.000000 819 83.817000 913 1792 1 chr1B.!!$R1 879
4 TraesCS2A01G209900 chr1A 96462646 96463448 802 False 730.000000 730 83.212000 973 1788 1 chr1A.!!$F1 815
5 TraesCS2A01G209900 chr1A 96470479 96471121 642 False 640.000000 640 84.756000 997 1646 1 chr1A.!!$F2 649
6 TraesCS2A01G209900 chr6A 573888 574778 890 True 693.000000 693 81.215000 913 1791 1 chr6A.!!$R1 878
7 TraesCS2A01G209900 chr1D 78982437 78983060 623 True 640.000000 640 85.600000 1184 1792 1 chr1D.!!$R1 608
8 TraesCS2A01G209900 chr6B 3824786 3825577 791 True 625.000000 625 81.350000 997 1792 1 chr6B.!!$R1 795
9 TraesCS2A01G209900 chr5A 617254478 617255276 798 True 601.000000 601 80.448000 997 1789 1 chr5A.!!$R1 792
10 TraesCS2A01G209900 chr5B 610663806 610664610 804 True 584.000000 584 80.123000 997 1789 1 chr5B.!!$R1 792

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
466 762 0.109735 TCGTCGACAGTCAGCATCAC 60.110 55.0 17.16 0.0 0.00 3.06 F
1880 2771 0.248825 CAGATCAACTCGAGCTCCGG 60.249 60.0 13.61 0.0 38.68 5.14 F
2415 3306 0.534412 CTGTGAAGAGGCTCGATGGT 59.466 55.0 9.22 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2235 3126 0.456221 TCCGATGAGTCCTTTCTCGC 59.544 55.0 0.0 0.0 37.28 5.03 R
3236 4127 0.523519 TGTTGTGCTGTTTTGCGTCA 59.476 45.0 0.0 0.0 35.36 4.35 R
3585 4562 0.660300 CGCCTTTTTCCAAGACACGC 60.660 55.0 0.0 0.0 0.00 5.34 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
61 62 0.963856 AGACGTATCAGTGGACGCCA 60.964 55.000 15.60 0.00 42.81 5.69
82 83 0.606604 TTACGCCTTCAGTGGAGACC 59.393 55.000 0.00 0.00 0.00 3.85
220 230 5.370679 AGATACCCGTTCTAGAAGAGAGAC 58.629 45.833 5.12 0.00 34.93 3.36
230 240 7.709182 CGTTCTAGAAGAGAGACAGAGATAGAA 59.291 40.741 5.12 0.00 34.93 2.10
269 279 0.395311 AACATCTGCCTGGCCATCTG 60.395 55.000 17.53 10.77 0.00 2.90
270 280 1.528542 CATCTGCCTGGCCATCTGG 60.529 63.158 17.53 5.27 37.51 3.86
271 281 1.695239 ATCTGCCTGGCCATCTGGA 60.695 57.895 17.53 7.31 36.68 3.86
272 282 1.284111 ATCTGCCTGGCCATCTGGAA 61.284 55.000 17.53 1.55 36.68 3.53
273 283 1.751927 CTGCCTGGCCATCTGGAAC 60.752 63.158 17.53 0.00 36.68 3.62
274 284 2.440980 GCCTGGCCATCTGGAACC 60.441 66.667 13.60 0.00 36.68 3.62
413 709 2.100087 TCAAAGCCGGAAAACCACTTTC 59.900 45.455 5.05 0.00 42.45 2.62
466 762 0.109735 TCGTCGACAGTCAGCATCAC 60.110 55.000 17.16 0.00 0.00 3.06
616 912 9.559958 AATAATTAAAGAAGCGAAAGTGACATG 57.440 29.630 0.00 0.00 0.00 3.21
644 940 7.524717 TCACTAACATCATAGCTATGCTACA 57.475 36.000 26.05 11.55 44.24 2.74
710 1006 4.221703 TCAAGCAAGGAAAAGAAAACACCA 59.778 37.500 0.00 0.00 0.00 4.17
719 1396 7.801104 AGGAAAAGAAAACACCATTAACCATT 58.199 30.769 0.00 0.00 0.00 3.16
738 1415 7.961325 ACCATTTGTCATAAATTTCAACACC 57.039 32.000 0.00 0.00 0.00 4.16
744 1421 9.829507 TTTGTCATAAATTTCAACACCAGATTT 57.170 25.926 0.00 0.00 0.00 2.17
906 1587 1.071385 CAGGCTGAGAAACCTCTGTGT 59.929 52.381 9.42 0.00 32.56 3.72
907 1588 1.346068 AGGCTGAGAAACCTCTGTGTC 59.654 52.381 0.00 0.00 33.69 3.67
908 1589 1.609320 GGCTGAGAAACCTCTGTGTCC 60.609 57.143 0.00 0.00 33.69 4.02
909 1590 1.070758 GCTGAGAAACCTCTGTGTCCA 59.929 52.381 0.00 0.00 33.69 4.02
910 1591 2.485479 GCTGAGAAACCTCTGTGTCCAA 60.485 50.000 0.00 0.00 33.69 3.53
911 1592 3.134458 CTGAGAAACCTCTGTGTCCAAC 58.866 50.000 0.00 0.00 27.85 3.77
968 1651 2.203126 CATCCTCGCTCAAGCCCC 60.203 66.667 0.00 0.00 37.91 5.80
1015 1706 3.431673 GATCCATGGATCCCTTCTTCC 57.568 52.381 35.69 14.64 43.71 3.46
1018 1709 1.423161 CCATGGATCCCTTCTTCCTCC 59.577 57.143 5.56 0.00 32.95 4.30
1035 1726 1.146152 CTCCTCCTCCTCCTATTCGGT 59.854 57.143 0.00 0.00 0.00 4.69
1116 1810 2.091278 ACAGAAGATCGTATCCCAGGGA 60.091 50.000 11.90 11.90 35.55 4.20
1227 1933 0.966179 ACATACGACTGCTGACCACA 59.034 50.000 0.00 0.00 0.00 4.17
1338 2052 1.220749 GAACCGGCAGCTATGGTCA 59.779 57.895 0.00 0.00 34.11 4.02
1342 2056 1.091771 CCGGCAGCTATGGTCAACTG 61.092 60.000 0.00 0.00 0.00 3.16
1401 2115 2.491022 GGACAGCGGTAGCCTCGAT 61.491 63.158 0.00 0.00 46.67 3.59
1404 2118 1.038130 ACAGCGGTAGCCTCGATCTT 61.038 55.000 0.00 0.00 46.67 2.40
1578 2298 3.704061 GGTTGTTCTCTCTGGAGCTAGAT 59.296 47.826 0.00 0.00 39.31 1.98
1686 2412 2.581354 GTGCCAGAGATGACGGCT 59.419 61.111 0.00 0.00 46.39 5.52
1792 2521 1.369625 GTTCATCATGGACGTGACCC 58.630 55.000 0.00 0.00 0.00 4.46
1793 2522 1.066143 GTTCATCATGGACGTGACCCT 60.066 52.381 0.00 0.00 0.00 4.34
1794 2523 0.824109 TCATCATGGACGTGACCCTC 59.176 55.000 0.00 0.00 0.00 4.30
1797 2526 0.617535 TCATGGACGTGACCCTCCAT 60.618 55.000 0.00 4.08 46.48 3.41
1798 2527 0.253044 CATGGACGTGACCCTCCATT 59.747 55.000 6.69 0.00 43.61 3.16
1799 2528 0.253044 ATGGACGTGACCCTCCATTG 59.747 55.000 0.00 0.00 43.61 2.82
1830 2721 3.471680 GGATCTTCAGGATTACAGTGGC 58.528 50.000 0.00 0.00 34.33 5.01
1845 2736 4.115199 GGCGGGTGCAGGAGGAAT 62.115 66.667 0.00 0.00 45.35 3.01
1880 2771 0.248825 CAGATCAACTCGAGCTCCGG 60.249 60.000 13.61 0.00 38.68 5.14
1904 2795 4.042187 ACAGACCAAGCCTGATAAGTTCTT 59.958 41.667 0.00 0.00 35.69 2.52
1906 2797 5.123027 CAGACCAAGCCTGATAAGTTCTTTC 59.877 44.000 0.00 0.00 33.65 2.62
1915 2806 4.671831 TGATAAGTTCTTTCCCATGGCAA 58.328 39.130 6.09 0.00 0.00 4.52
2106 2997 1.070758 GTTGGCACACTCTTCCTCAGA 59.929 52.381 0.00 0.00 39.29 3.27
2168 3059 1.270274 TGTGATCATTGGTGCAGTTGC 59.730 47.619 0.00 0.00 42.50 4.17
2172 3063 1.373748 CATTGGTGCAGTTGCTGGC 60.374 57.895 5.62 0.00 42.66 4.85
2202 3093 4.534168 CTGCAATTCTGATAATCCTTGCG 58.466 43.478 0.00 0.00 41.31 4.85
2241 3132 5.926542 CCTATATCAGAAATTTCGGCGAGAA 59.073 40.000 10.46 8.29 37.01 2.87
2249 3140 0.677288 TTTCGGCGAGAAAGGACTCA 59.323 50.000 10.46 0.00 43.35 3.41
2267 3158 5.207110 ACTCATCGGATATCAAAGACTGG 57.793 43.478 4.83 0.00 0.00 4.00
2277 3168 2.391130 AAAGACTGGTGGGGGCACA 61.391 57.895 0.00 0.00 0.00 4.57
2286 3177 1.078891 TGGGGGCACATTGATTGCT 59.921 52.632 0.00 0.00 40.07 3.91
2302 3193 4.937620 TGATTGCTTTCAGGTACAGTGATC 59.062 41.667 0.00 0.00 0.00 2.92
2319 3210 0.616891 ATCTGCAGCATGTCACCAGA 59.383 50.000 9.47 8.98 39.31 3.86
2388 3279 1.373570 GGAAGCTCCCAGATTCAACG 58.626 55.000 4.07 0.00 42.05 4.10
2391 3282 2.115291 GCTCCCAGATTCAACGGCC 61.115 63.158 0.00 0.00 0.00 6.13
2415 3306 0.534412 CTGTGAAGAGGCTCGATGGT 59.466 55.000 9.22 0.00 0.00 3.55
2494 3385 3.129638 GCATGTTAATTTGGTCCGCCTTA 59.870 43.478 0.00 0.00 35.27 2.69
2919 3810 1.556911 TCAGGCAGGAGGAATTCTGAC 59.443 52.381 5.23 0.00 39.23 3.51
3236 4127 1.349357 GTCTTCAAGCCAGACTTCCCT 59.651 52.381 0.00 0.00 38.14 4.20
3363 4254 5.580691 GGCCTTTATATGTTTGAAAAGTGCC 59.419 40.000 0.00 0.00 37.72 5.01
3375 4266 3.820467 TGAAAAGTGCCATGAGTAACTGG 59.180 43.478 0.00 0.00 35.53 4.00
3466 4359 2.434428 AGGCTCACAGCAGAATTGAAG 58.566 47.619 0.00 0.00 44.75 3.02
3585 4562 2.097466 AGTGTCTGCCTTTTCACAAACG 59.903 45.455 0.00 0.00 33.84 3.60
3646 4623 1.814394 TGCTATTTGGCAGAAGCACAG 59.186 47.619 14.15 0.00 44.61 3.66
3658 4635 4.441079 GCAGAAGCACAGCCATAATTTCAT 60.441 41.667 0.00 0.00 41.58 2.57
3775 4755 7.444183 GGTAATATGGACGGAAGAAATCAATGA 59.556 37.037 0.00 0.00 0.00 2.57
3776 4756 6.867662 ATATGGACGGAAGAAATCAATGAC 57.132 37.500 0.00 0.00 0.00 3.06
3791 4771 2.047179 GACCGTGTTGCCTCTCCC 60.047 66.667 0.00 0.00 0.00 4.30
3801 4781 0.401395 TGCCTCTCCCGGGGATATTT 60.401 55.000 23.50 0.00 0.00 1.40
3802 4782 0.771755 GCCTCTCCCGGGGATATTTT 59.228 55.000 23.50 0.00 0.00 1.82
3803 4783 1.145119 GCCTCTCCCGGGGATATTTTT 59.855 52.381 23.50 0.00 0.00 1.94
3961 4958 3.879892 GGCTAACCCTCTATTGCTTTCAG 59.120 47.826 0.00 0.00 0.00 3.02
4048 5047 5.992217 AGGTCAGGATTGATATTCGCTTTAC 59.008 40.000 0.00 0.00 35.39 2.01
4084 5083 9.730705 TCTCACTAAACAATCAAATCTCATTCT 57.269 29.630 0.00 0.00 0.00 2.40
4138 5137 3.482722 CATAGCAGTTCTGTGCCAAAG 57.517 47.619 1.78 0.00 45.20 2.77
4242 5275 4.585162 ACTAATACAATCTCCGGACTCCAG 59.415 45.833 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.117512 TCACCTTTTCCTTCTTTCCAGCT 60.118 43.478 0.00 0.00 0.00 4.24
61 62 2.354805 GGTCTCCACTGAAGGCGTAAAT 60.355 50.000 0.00 0.00 0.00 1.40
82 83 5.494863 TGTTAATAATCATCGTGATCGCG 57.505 39.130 22.36 22.36 35.76 5.87
220 230 4.120792 TGCTGCTGTTCTTCTATCTCTG 57.879 45.455 0.00 0.00 0.00 3.35
251 261 1.226542 CAGATGGCCAGGCAGATGT 59.773 57.895 15.19 0.00 0.00 3.06
252 262 1.528542 CCAGATGGCCAGGCAGATG 60.529 63.158 15.19 5.99 0.00 2.90
269 279 1.645710 TGGACTTCTCCTCTGGTTCC 58.354 55.000 0.00 0.00 37.48 3.62
270 280 3.990959 AATGGACTTCTCCTCTGGTTC 57.009 47.619 0.00 0.00 37.48 3.62
271 281 4.689062 TCTAATGGACTTCTCCTCTGGTT 58.311 43.478 0.00 0.00 37.48 3.67
272 282 4.285863 CTCTAATGGACTTCTCCTCTGGT 58.714 47.826 0.00 0.00 37.48 4.00
273 283 3.640967 CCTCTAATGGACTTCTCCTCTGG 59.359 52.174 0.00 0.00 37.48 3.86
274 284 4.285863 ACCTCTAATGGACTTCTCCTCTG 58.714 47.826 0.00 0.00 37.48 3.35
283 293 5.488919 TCCAGAATTCAACCTCTAATGGACT 59.511 40.000 8.44 0.00 29.63 3.85
326 622 8.908786 ATTTTAAGACTGACTTGTCATCTTGA 57.091 30.769 22.98 17.65 39.38 3.02
413 709 2.629617 AGAAAAATGGTGTGAAGCCAGG 59.370 45.455 0.00 0.00 39.65 4.45
450 746 1.212751 CCGTGATGCTGACTGTCGA 59.787 57.895 2.98 0.00 0.00 4.20
466 762 1.869767 GCCAATATCTGACTCTTGCCG 59.130 52.381 0.00 0.00 0.00 5.69
616 912 7.095910 AGCATAGCTATGATGTTAGTGATGTC 58.904 38.462 33.10 12.71 36.99 3.06
662 958 2.905075 TGTTGTGTCACCTCACTTCAG 58.095 47.619 0.00 0.00 38.90 3.02
719 1396 9.829507 AAAATCTGGTGTTGAAATTTATGACAA 57.170 25.926 0.00 0.00 0.00 3.18
906 1587 1.150536 GGCTGTGGTTGGAGTTGGA 59.849 57.895 0.00 0.00 0.00 3.53
907 1588 1.152777 TGGCTGTGGTTGGAGTTGG 60.153 57.895 0.00 0.00 0.00 3.77
908 1589 1.785041 CGTGGCTGTGGTTGGAGTTG 61.785 60.000 0.00 0.00 0.00 3.16
909 1590 1.525995 CGTGGCTGTGGTTGGAGTT 60.526 57.895 0.00 0.00 0.00 3.01
910 1591 2.111043 CGTGGCTGTGGTTGGAGT 59.889 61.111 0.00 0.00 0.00 3.85
911 1592 1.669115 CTCGTGGCTGTGGTTGGAG 60.669 63.158 0.00 0.00 0.00 3.86
968 1651 2.092753 TGGGAGCTTGGAAGAATAGCAG 60.093 50.000 0.00 0.00 37.37 4.24
1009 1700 1.398799 AGGAGGAGGAGGAGGAAGAA 58.601 55.000 0.00 0.00 0.00 2.52
1010 1701 2.305345 TAGGAGGAGGAGGAGGAAGA 57.695 55.000 0.00 0.00 0.00 2.87
1011 1702 3.506398 GAATAGGAGGAGGAGGAGGAAG 58.494 54.545 0.00 0.00 0.00 3.46
1015 1706 1.146152 ACCGAATAGGAGGAGGAGGAG 59.854 57.143 0.00 0.00 45.00 3.69
1018 1709 2.366640 TGACCGAATAGGAGGAGGAG 57.633 55.000 0.00 0.00 45.00 3.69
1035 1726 1.817357 CTGTGCAGAGCAGGATTTGA 58.183 50.000 0.00 0.00 40.08 2.69
1116 1810 2.841160 GCCCACGGCGAACTTGTTT 61.841 57.895 16.62 0.00 39.62 2.83
1205 1911 1.343142 TGGTCAGCAGTCGTATGTTGT 59.657 47.619 6.42 0.00 33.57 3.32
1214 1920 2.609825 CACACTGTGGTCAGCAGTC 58.390 57.895 13.09 0.00 44.43 3.51
1338 2052 6.384305 AGTTGGAGGCTATACTTACATCAGTT 59.616 38.462 0.00 0.00 0.00 3.16
1342 2056 5.304614 TGGAGTTGGAGGCTATACTTACATC 59.695 44.000 0.00 0.00 0.00 3.06
1578 2298 1.786937 ACTGTTTTGTGCCATTGGGA 58.213 45.000 4.53 0.00 35.59 4.37
1686 2412 8.126871 CGAATTGGAAGTCGTATCTGAAATTA 57.873 34.615 1.24 0.00 41.09 1.40
1792 2521 2.133281 TCCCAATCACTGCAATGGAG 57.867 50.000 0.00 0.00 34.82 3.86
1793 2522 2.242965 AGATCCCAATCACTGCAATGGA 59.757 45.455 0.00 0.00 34.82 3.41
1794 2523 2.662866 AGATCCCAATCACTGCAATGG 58.337 47.619 0.00 0.00 34.07 3.16
1797 2526 3.349927 CTGAAGATCCCAATCACTGCAA 58.650 45.455 0.00 0.00 34.07 4.08
1798 2527 2.356432 CCTGAAGATCCCAATCACTGCA 60.356 50.000 0.00 0.00 34.07 4.41
1799 2528 2.092753 TCCTGAAGATCCCAATCACTGC 60.093 50.000 0.00 0.00 34.07 4.40
1830 2721 0.462047 GTACATTCCTCCTGCACCCG 60.462 60.000 0.00 0.00 0.00 5.28
1880 2771 3.618690 ACTTATCAGGCTTGGTCTGTC 57.381 47.619 0.00 0.00 36.55 3.51
1904 2795 1.675310 CTCACGCTTGCCATGGGAA 60.675 57.895 18.59 18.59 0.00 3.97
1906 2797 3.136123 CCTCACGCTTGCCATGGG 61.136 66.667 15.13 0.00 0.00 4.00
2106 2997 2.667418 AGCTCGGATGCTGCAAGT 59.333 55.556 6.36 0.00 42.33 3.16
2141 3032 1.135199 CACCAATGATCACAGCCTTGC 60.135 52.381 0.00 0.00 0.00 4.01
2148 3039 1.270274 GCAACTGCACCAATGATCACA 59.730 47.619 0.00 0.00 41.59 3.58
2172 3063 1.213537 CAGAATTGCAGCAACCCCG 59.786 57.895 10.85 0.00 0.00 5.73
2175 3066 4.340381 AGGATTATCAGAATTGCAGCAACC 59.660 41.667 10.85 5.59 0.00 3.77
2231 3122 0.895530 ATGAGTCCTTTCTCGCCGAA 59.104 50.000 0.00 0.00 37.28 4.30
2235 3126 0.456221 TCCGATGAGTCCTTTCTCGC 59.544 55.000 0.00 0.00 37.28 5.03
2241 3132 5.600484 AGTCTTTGATATCCGATGAGTCCTT 59.400 40.000 0.00 0.00 0.00 3.36
2249 3140 3.071602 CCCACCAGTCTTTGATATCCGAT 59.928 47.826 0.00 0.00 0.00 4.18
2267 3158 1.218854 GCAATCAATGTGCCCCCAC 59.781 57.895 0.00 0.00 42.40 4.61
2277 3168 5.316167 TCACTGTACCTGAAAGCAATCAAT 58.684 37.500 0.00 0.00 0.00 2.57
2286 3177 3.866066 GCTGCAGATCACTGTACCTGAAA 60.866 47.826 20.43 0.00 45.04 2.69
2302 3193 1.068748 GTTTCTGGTGACATGCTGCAG 60.069 52.381 10.11 10.11 41.51 4.41
2355 3246 0.536460 GCTTCCCCTTGAACACCGAA 60.536 55.000 0.00 0.00 0.00 4.30
2388 3279 1.941999 GCCTCTTCACAGCAATGGCC 61.942 60.000 0.00 0.00 42.56 5.36
2391 3282 0.725686 CGAGCCTCTTCACAGCAATG 59.274 55.000 0.00 0.00 0.00 2.82
2415 3306 3.524095 TGCTTCTCCCCTTGATGAAAA 57.476 42.857 0.00 0.00 0.00 2.29
2494 3385 2.447047 ACCCTTCAGAACAGAACCCAAT 59.553 45.455 0.00 0.00 0.00 3.16
2919 3810 2.450320 CCTGCCCTCCTCTCCATGG 61.450 68.421 4.97 4.97 0.00 3.66
3236 4127 0.523519 TGTTGTGCTGTTTTGCGTCA 59.476 45.000 0.00 0.00 35.36 4.35
3466 4359 7.595130 ACAGAAATCTCGTTTTTATTTTGGCTC 59.405 33.333 0.00 0.00 0.00 4.70
3585 4562 0.660300 CGCCTTTTTCCAAGACACGC 60.660 55.000 0.00 0.00 0.00 5.34
3646 4623 7.781056 TGGACTTTCCTTTATGAAATTATGGC 58.219 34.615 0.00 0.00 37.46 4.40
3658 4635 5.454755 CCTCAGTTGACTGGACTTTCCTTTA 60.455 44.000 10.97 0.00 43.91 1.85
3775 4755 4.003788 CGGGAGAGGCAACACGGT 62.004 66.667 0.00 0.00 41.41 4.83
3776 4756 4.760047 CCGGGAGAGGCAACACGG 62.760 72.222 0.00 5.08 41.41 4.94
3801 4781 3.977999 TCCTGGAGAGGGTTAGTTCAAAA 59.022 43.478 0.00 0.00 40.25 2.44
3802 4782 3.583086 CTCCTGGAGAGGGTTAGTTCAAA 59.417 47.826 19.13 0.00 40.25 2.69
3803 4783 3.173965 CTCCTGGAGAGGGTTAGTTCAA 58.826 50.000 19.13 0.00 40.25 2.69
3804 4784 2.821437 CTCCTGGAGAGGGTTAGTTCA 58.179 52.381 19.13 0.00 40.25 3.18
3814 4794 1.677637 GGGCGTTACCTCCTGGAGAG 61.678 65.000 25.18 16.48 42.83 3.20
3815 4795 1.684734 GGGCGTTACCTCCTGGAGA 60.685 63.158 25.18 2.84 39.10 3.71
3816 4796 1.265454 AAGGGCGTTACCTCCTGGAG 61.265 60.000 17.02 17.02 40.87 3.86
4048 5047 8.893219 TGATTGTTTAGTGAGATTATAGGCAG 57.107 34.615 0.00 0.00 0.00 4.85
4110 5109 4.514441 GCACAGAACTGCTATGCAATATCT 59.486 41.667 9.80 0.00 38.41 1.98
4117 5116 1.167851 TTGGCACAGAACTGCTATGC 58.832 50.000 1.46 4.80 42.39 3.14
4138 5137 0.753111 ATCTTGCGAAAGGGCCATCC 60.753 55.000 6.18 0.00 0.00 3.51
4242 5275 3.629398 CAGTTGTATGATCAGAAAGGGGC 59.371 47.826 0.09 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.