Multiple sequence alignment - TraesCS2D01G291900

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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 TraesCS2D01G291900 chr2D 100.000 3521 0 0 1 3521 373877669 373881189 0.000000e+00 6503.0
1 TraesCS2D01G291900 chr2B 92.130 1474 63 26 1530 2960 443762512 443763975 0.000000e+00 2030.0
2 TraesCS2D01G291900 chr2B 85.856 1110 68 41 197 1265 443761209 443762270 0.000000e+00 1098.0
3 TraesCS2D01G291900 chr2B 98.410 566 9 0 2956 3521 509992897 509993462 0.000000e+00 996.0
4 TraesCS2D01G291900 chr2B 97.917 144 2 1 1 143 443761063 443761206 7.550000e-62 248.0
5 TraesCS2D01G291900 chr2B 84.536 97 4 3 1417 1506 443762435 443762527 6.260000e-13 86.1
6 TraesCS2D01G291900 chrUn 93.316 1152 46 16 1530 2663 229267960 229266822 0.000000e+00 1672.0
7 TraesCS2D01G291900 chrUn 98.934 563 6 0 2959 3521 415563109 415562547 0.000000e+00 1007.0
8 TraesCS2D01G291900 chrUn 86.489 903 42 26 646 1515 229268791 229267936 0.000000e+00 918.0
9 TraesCS2D01G291900 chrUn 88.889 684 29 20 8 655 229269640 229268968 0.000000e+00 798.0
10 TraesCS2D01G291900 chrUn 92.647 204 8 1 2753 2949 229266820 229266617 1.600000e-73 287.0
11 TraesCS2D01G291900 chr1D 99.291 564 3 1 2959 3521 70343920 70343357 0.000000e+00 1018.0
12 TraesCS2D01G291900 chr1D 98.584 565 8 0 2956 3520 28071851 28072415 0.000000e+00 1000.0
13 TraesCS2D01G291900 chr3D 99.112 563 5 0 2959 3521 136263123 136262561 0.000000e+00 1013.0
14 TraesCS2D01G291900 chr3D 98.587 566 8 0 2956 3521 370537442 370538007 0.000000e+00 1002.0
15 TraesCS2D01G291900 chr7D 98.934 563 6 0 2959 3521 252066540 252065978 0.000000e+00 1007.0
16 TraesCS2D01G291900 chr2A 98.401 563 9 0 2959 3521 677884326 677883764 0.000000e+00 990.0
17 TraesCS2D01G291900 chr1B 98.401 563 9 0 2959 3521 654268877 654268315 0.000000e+00 990.0


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 TraesCS2D01G291900 chr2D 373877669 373881189 3520 False 6503.000 6503 100.00000 1 3521 1 chr2D.!!$F1 3520
1 TraesCS2D01G291900 chr2B 509992897 509993462 565 False 996.000 996 98.41000 2956 3521 1 chr2B.!!$F1 565
2 TraesCS2D01G291900 chr2B 443761063 443763975 2912 False 865.525 2030 90.10975 1 2960 4 chr2B.!!$F2 2959
3 TraesCS2D01G291900 chrUn 415562547 415563109 562 True 1007.000 1007 98.93400 2959 3521 1 chrUn.!!$R1 562
4 TraesCS2D01G291900 chrUn 229266617 229269640 3023 True 918.750 1672 90.33525 8 2949 4 chrUn.!!$R2 2941
5 TraesCS2D01G291900 chr1D 70343357 70343920 563 True 1018.000 1018 99.29100 2959 3521 1 chr1D.!!$R1 562
6 TraesCS2D01G291900 chr1D 28071851 28072415 564 False 1000.000 1000 98.58400 2956 3520 1 chr1D.!!$F1 564
7 TraesCS2D01G291900 chr3D 136262561 136263123 562 True 1013.000 1013 99.11200 2959 3521 1 chr3D.!!$R1 562
8 TraesCS2D01G291900 chr3D 370537442 370538007 565 False 1002.000 1002 98.58700 2956 3521 1 chr3D.!!$F1 565
9 TraesCS2D01G291900 chr7D 252065978 252066540 562 True 1007.000 1007 98.93400 2959 3521 1 chr7D.!!$R1 562
10 TraesCS2D01G291900 chr2A 677883764 677884326 562 True 990.000 990 98.40100 2959 3521 1 chr2A.!!$R1 562
11 TraesCS2D01G291900 chr1B 654268315 654268877 562 True 990.000 990 98.40100 2959 3521 1 chr1B.!!$R1 562

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
643 694 0.433492 CGCGTACACAAGGAACGAAG 59.567 55.0 0.0 0.0 38.89 3.79 F
812 1059 0.467384 CATGAGAGCCTCCCATTCGT 59.533 55.0 0.0 0.0 0.00 3.85 F
1589 1925 0.466124 GGGTCTCCATGCTACAGTCC 59.534 60.0 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1847 0.035739 GAGGGTACGGCCTTGTTTCA 59.964 55.0 0.00 0.0 37.43 2.69 R
2090 2444 0.798776 GTGGAACAGCATTGAGGTCG 59.201 55.0 0.00 0.0 41.80 4.79 R
3258 3638 0.754957 CCCATTAGCAATTGGGCGGA 60.755 55.0 7.72 0.0 39.27 5.54 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
192 197 4.846940 GGAATATAGGAACAGGGATGGAGT 59.153 45.833 0.00 0.00 0.00 3.85
218 223 2.519780 GAGCGAGGACCCGGAGAT 60.520 66.667 0.73 0.00 0.00 2.75
303 309 1.811359 CCATCGTCGTATCCTCCTACC 59.189 57.143 0.00 0.00 0.00 3.18
304 310 2.552591 CCATCGTCGTATCCTCCTACCT 60.553 54.545 0.00 0.00 0.00 3.08
305 311 2.540265 TCGTCGTATCCTCCTACCTC 57.460 55.000 0.00 0.00 0.00 3.85
306 312 1.071385 TCGTCGTATCCTCCTACCTCC 59.929 57.143 0.00 0.00 0.00 4.30
345 357 2.959071 GCTCGCTCGCTGACCATC 60.959 66.667 0.00 0.00 0.00 3.51
346 358 2.279120 CTCGCTCGCTGACCATCC 60.279 66.667 0.00 0.00 0.00 3.51
347 359 3.781770 CTCGCTCGCTGACCATCCC 62.782 68.421 0.00 0.00 0.00 3.85
348 360 3.842923 CGCTCGCTGACCATCCCT 61.843 66.667 0.00 0.00 0.00 4.20
374 386 3.448469 TTGGGTTGGCCACCTAAAG 57.552 52.632 19.69 0.00 42.88 1.85
406 418 4.479786 AAATTACAGTGCCTCTCTCTCC 57.520 45.455 0.00 0.00 0.00 3.71
639 690 2.858158 GGCGCGTACACAAGGAAC 59.142 61.111 8.43 0.00 0.00 3.62
641 692 2.017783 GCGCGTACACAAGGAACGA 61.018 57.895 8.43 0.00 38.89 3.85
643 694 0.433492 CGCGTACACAAGGAACGAAG 59.567 55.000 0.00 0.00 38.89 3.79
650 885 2.224305 ACACAAGGAACGAAGGGAAGAG 60.224 50.000 0.00 0.00 0.00 2.85
655 890 3.240302 AGGAACGAAGGGAAGAGAGAAA 58.760 45.455 0.00 0.00 0.00 2.52
778 1021 3.288381 AGACCCCTCTGCCCCTCT 61.288 66.667 0.00 0.00 0.00 3.69
811 1058 0.755079 TCATGAGAGCCTCCCATTCG 59.245 55.000 0.00 0.00 0.00 3.34
812 1059 0.467384 CATGAGAGCCTCCCATTCGT 59.533 55.000 0.00 0.00 0.00 3.85
813 1060 1.688735 CATGAGAGCCTCCCATTCGTA 59.311 52.381 0.00 0.00 0.00 3.43
814 1061 1.112113 TGAGAGCCTCCCATTCGTAC 58.888 55.000 0.00 0.00 0.00 3.67
878 1126 4.320456 CCGCCTGTCAGCCACACT 62.320 66.667 0.00 0.00 0.00 3.55
919 1167 2.222227 CTGGAAGGGGAAAAAGGAGG 57.778 55.000 0.00 0.00 0.00 4.30
920 1168 0.783850 TGGAAGGGGAAAAAGGAGGG 59.216 55.000 0.00 0.00 0.00 4.30
926 1174 0.626382 GGGAAAAAGGAGGGAGGGAG 59.374 60.000 0.00 0.00 0.00 4.30
962 1210 0.755079 TAGCCTAGCTGCACTCCATG 59.245 55.000 1.02 0.00 40.10 3.66
1038 1286 1.376942 GCAGCAGGAGCACATCACT 60.377 57.895 0.00 0.00 45.49 3.41
1042 1290 2.113807 AGCAGGAGCACATCACTCATA 58.886 47.619 0.00 0.00 45.49 2.15
1043 1291 2.158986 AGCAGGAGCACATCACTCATAC 60.159 50.000 0.00 0.00 45.49 2.39
1078 1326 1.000827 CGACTTGATCCTCTCCATCCG 60.001 57.143 0.00 0.00 0.00 4.18
1155 1403 1.004560 TCCGACTCTGCCTTTGCTG 60.005 57.895 0.00 0.00 38.71 4.41
1157 1405 1.302033 CGACTCTGCCTTTGCTGGT 60.302 57.895 0.00 0.00 38.71 4.00
1199 1461 1.285078 AGCTCCAACAAGGTAATCCCC 59.715 52.381 0.00 0.00 39.02 4.81
1281 1564 1.273609 TGCAGCTCCCCTTTCCTAGTA 60.274 52.381 0.00 0.00 0.00 1.82
1287 1570 3.369576 GCTCCCCTTTCCTAGTAGTGTTG 60.370 52.174 0.00 0.00 0.00 3.33
1288 1571 3.838903 CTCCCCTTTCCTAGTAGTGTTGT 59.161 47.826 0.00 0.00 0.00 3.32
1289 1572 5.014534 TCCCCTTTCCTAGTAGTGTTGTA 57.985 43.478 0.00 0.00 0.00 2.41
1375 1682 6.532657 CCATGCCTTTGATTTGTTTATGTCTC 59.467 38.462 0.00 0.00 0.00 3.36
1382 1689 7.962964 TTGATTTGTTTATGTCTCGAGTCTT 57.037 32.000 13.13 7.79 0.00 3.01
1384 1691 6.368791 TGATTTGTTTATGTCTCGAGTCTTGG 59.631 38.462 13.13 0.00 0.00 3.61
1433 1758 8.853077 AATATATTCTGCTAGCAGTTGCAATA 57.147 30.769 36.99 30.92 45.16 1.90
1434 1759 6.798315 ATATTCTGCTAGCAGTTGCAATAG 57.202 37.500 36.99 15.38 45.16 1.73
1435 1760 2.910199 TCTGCTAGCAGTTGCAATAGG 58.090 47.619 36.99 14.68 45.16 2.57
1436 1761 2.501316 TCTGCTAGCAGTTGCAATAGGA 59.499 45.455 36.99 16.66 45.16 2.94
1457 1782 5.472137 AGGAAGCGTTAACATGTGTGTAAAT 59.528 36.000 0.00 0.00 37.67 1.40
1489 1821 1.698165 TTGCTTAGAACGAGCGAGTG 58.302 50.000 0.00 0.00 43.02 3.51
1497 1829 3.827898 CGAGCGAGTGACCCTCCC 61.828 72.222 0.00 0.00 36.82 4.30
1498 1830 2.680352 GAGCGAGTGACCCTCCCA 60.680 66.667 0.00 0.00 36.82 4.37
1506 1838 3.767711 GAGTGACCCTCCCATTTCTTTT 58.232 45.455 0.00 0.00 33.79 2.27
1507 1839 4.152647 GAGTGACCCTCCCATTTCTTTTT 58.847 43.478 0.00 0.00 33.79 1.94
1508 1840 4.152647 AGTGACCCTCCCATTTCTTTTTC 58.847 43.478 0.00 0.00 0.00 2.29
1511 1843 5.070446 GTGACCCTCCCATTTCTTTTTCTTT 59.930 40.000 0.00 0.00 0.00 2.52
1586 1922 1.489481 TCAGGGTCTCCATGCTACAG 58.511 55.000 0.00 0.00 34.83 2.74
1589 1925 0.466124 GGGTCTCCATGCTACAGTCC 59.534 60.000 0.00 0.00 0.00 3.85
1614 1950 5.880332 ACTGCTAGTGTTCTGTTTTTCTTCA 59.120 36.000 0.00 0.00 0.00 3.02
1619 1955 8.774586 GCTAGTGTTCTGTTTTTCTTCATCTTA 58.225 33.333 0.00 0.00 0.00 2.10
1718 2065 2.032549 CACTTCACTGTTTCTGCTTCCG 60.033 50.000 0.00 0.00 0.00 4.30
1736 2083 3.486383 TCCGTTTCTTCTTTTCCTGCAT 58.514 40.909 0.00 0.00 0.00 3.96
1749 2096 4.322080 TTCCTGCATTCATAGTAGGACG 57.678 45.455 0.00 0.00 45.67 4.79
1753 2100 3.392882 TGCATTCATAGTAGGACGCATG 58.607 45.455 4.44 0.00 0.00 4.06
1765 2112 2.943033 AGGACGCATGCAAGTTAATACC 59.057 45.455 19.57 5.49 0.00 2.73
1777 2124 1.727880 GTTAATACCAGTCGCGTGCAA 59.272 47.619 5.77 0.00 0.00 4.08
1780 2127 1.289109 ATACCAGTCGCGTGCAACAC 61.289 55.000 5.77 0.00 35.74 3.32
1782 2129 2.706432 CAGTCGCGTGCAACACAA 59.294 55.556 5.77 0.00 35.74 3.33
1788 2135 1.431440 GCGTGCAACACAACAGGAA 59.569 52.632 0.00 0.00 35.74 3.36
1810 2157 1.148310 AAACGAGAGCATTGTGACCG 58.852 50.000 0.00 0.00 0.00 4.79
2068 2419 4.263209 CGGCAACAGCAACGGCAA 62.263 61.111 0.00 0.00 44.61 4.52
2069 2420 2.658268 GGCAACAGCAACGGCAAC 60.658 61.111 0.00 0.00 44.61 4.17
2102 2456 2.370445 CCTCCCCGACCTCAATGCT 61.370 63.158 0.00 0.00 0.00 3.79
2104 2458 1.903877 CTCCCCGACCTCAATGCTGT 61.904 60.000 0.00 0.00 0.00 4.40
2172 2526 0.235926 GACTGTCGCAAACTGAAGCC 59.764 55.000 0.00 0.00 0.00 4.35
2208 2566 4.574674 TGGAGAACATATCCAGTGCTTT 57.425 40.909 0.00 0.00 41.96 3.51
2210 2568 4.019411 TGGAGAACATATCCAGTGCTTTCA 60.019 41.667 0.00 0.00 41.96 2.69
2211 2569 4.333926 GGAGAACATATCCAGTGCTTTCAC 59.666 45.833 0.00 0.00 43.44 3.18
2224 2582 3.191371 GTGCTTTCACTTCACCCATTAGG 59.809 47.826 0.00 0.00 40.03 2.69
2320 2684 0.671251 CGCTAAGGGTCTAGCTCTGG 59.329 60.000 0.00 0.00 41.86 3.86
2573 2944 2.099263 TCTAGTGCACGATGCTACCTTC 59.901 50.000 12.01 0.00 45.31 3.46
2650 3021 3.115554 CAAGTAAAGCAACCACAAGCAC 58.884 45.455 0.00 0.00 0.00 4.40
2709 3081 0.249322 AAGGTCGGTCACACGTCAAG 60.249 55.000 0.00 0.00 34.94 3.02
2750 3122 5.692115 TGCAGAAAATATACTGACCTCCA 57.308 39.130 0.00 0.00 36.38 3.86
2759 3131 1.294780 CTGACCTCCAGTCCAGCAC 59.705 63.158 0.00 0.00 45.68 4.40
2806 3178 1.202222 GCATTCGCAAGGGAATCAGTG 60.202 52.381 9.12 2.40 34.50 3.66
2838 3211 9.217278 ACTTCAGTCATCATGCATATTAATCTC 57.783 33.333 0.00 0.00 0.00 2.75
2839 3212 9.438228 CTTCAGTCATCATGCATATTAATCTCT 57.562 33.333 0.00 0.00 0.00 3.10
2846 3219 9.989869 CATCATGCATATTAATCTCTCAATGAC 57.010 33.333 0.00 0.00 0.00 3.06
2984 3364 2.754465 TGAAATACTTAGGCCTCCCGA 58.246 47.619 9.68 0.00 35.76 5.14
2990 3370 1.253100 CTTAGGCCTCCCGATCTCTC 58.747 60.000 9.68 0.00 35.76 3.20
3258 3638 3.568443 AGGTTAATTGGGACACCGTTTT 58.432 40.909 0.00 0.00 39.29 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 171 5.097234 CCATCCCTGTTCCTATATTCCTCT 58.903 45.833 0.00 0.00 0.00 3.69
192 197 0.461548 GGTCCTCGCTCATCATCACA 59.538 55.000 0.00 0.00 0.00 3.58
218 223 4.129380 CCAAGATTCGTAATGATGGCTCA 58.871 43.478 0.00 0.00 35.41 4.26
280 286 0.882474 GGAGGATACGACGATGGGAG 59.118 60.000 0.00 0.00 46.39 4.30
345 357 1.277842 GCCAACCCAAACCAAATAGGG 59.722 52.381 0.00 0.00 46.96 3.53
346 358 1.277842 GGCCAACCCAAACCAAATAGG 59.722 52.381 0.00 0.00 45.67 2.57
347 359 1.974236 TGGCCAACCCAAACCAAATAG 59.026 47.619 0.61 0.00 41.82 1.73
348 360 2.103153 TGGCCAACCCAAACCAAATA 57.897 45.000 0.61 0.00 41.82 1.40
374 386 3.052036 CACTGTAATTTTGTGCCAGTGC 58.948 45.455 5.30 0.00 44.33 4.40
406 418 8.988064 ATTATATTTATACTGCACGAGACAGG 57.012 34.615 8.50 0.00 39.55 4.00
655 890 1.285641 CCTCACGTGCCGCATTTTT 59.714 52.632 11.67 0.00 0.00 1.94
778 1021 0.690192 TCATGAGGCCTTTGAACGGA 59.310 50.000 6.77 0.00 0.00 4.69
878 1126 2.448926 TCGATCAAAAACCTCGAGCA 57.551 45.000 6.99 0.00 36.57 4.26
909 1157 0.626382 CCCTCCCTCCCTCCTTTTTC 59.374 60.000 0.00 0.00 0.00 2.29
912 1160 1.398234 CTCCCTCCCTCCCTCCTTT 59.602 63.158 0.00 0.00 0.00 3.11
913 1161 2.652113 CCTCCCTCCCTCCCTCCTT 61.652 68.421 0.00 0.00 0.00 3.36
914 1162 3.039526 CCTCCCTCCCTCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
915 1163 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
916 1164 2.613576 CTTCCCTCCCTCCCTCCCTC 62.614 70.000 0.00 0.00 0.00 4.30
917 1165 2.543637 TTCCCTCCCTCCCTCCCT 60.544 66.667 0.00 0.00 0.00 4.20
918 1166 2.040359 CTTCCCTCCCTCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
919 1167 1.979389 ATCCTTCCCTCCCTCCCTCC 61.979 65.000 0.00 0.00 0.00 4.30
920 1168 0.766288 CATCCTTCCCTCCCTCCCTC 60.766 65.000 0.00 0.00 0.00 4.30
926 1174 1.347062 CTAGCTCATCCTTCCCTCCC 58.653 60.000 0.00 0.00 0.00 4.30
962 1210 5.097529 TCGTTTCATACCAGTTCATCGTAC 58.902 41.667 0.00 0.00 0.00 3.67
1024 1272 3.193263 GTGTATGAGTGATGTGCTCCTG 58.807 50.000 0.00 0.00 32.31 3.86
1038 1286 2.620585 CGATCTCCTCTGCTGTGTATGA 59.379 50.000 0.00 0.00 0.00 2.15
1042 1290 0.814457 GTCGATCTCCTCTGCTGTGT 59.186 55.000 0.00 0.00 0.00 3.72
1043 1291 1.102154 AGTCGATCTCCTCTGCTGTG 58.898 55.000 0.00 0.00 0.00 3.66
1078 1326 0.884514 GGCAGGAAGAGAGGCAAAAC 59.115 55.000 0.00 0.00 0.00 2.43
1108 1356 3.133542 TGAGGCAATGAGATTCTGTCGAT 59.866 43.478 0.00 0.00 0.00 3.59
1109 1357 2.497273 TGAGGCAATGAGATTCTGTCGA 59.503 45.455 0.00 0.00 0.00 4.20
1111 1359 3.493877 CGATGAGGCAATGAGATTCTGTC 59.506 47.826 0.00 0.00 0.00 3.51
1112 1360 3.464907 CGATGAGGCAATGAGATTCTGT 58.535 45.455 0.00 0.00 0.00 3.41
1115 1363 1.194098 CGCGATGAGGCAATGAGATTC 59.806 52.381 0.00 0.00 0.00 2.52
1281 1564 5.763204 CCCAACTCAATGTTACTACAACACT 59.237 40.000 0.00 0.00 37.91 3.55
1287 1570 4.324267 AGCACCCAACTCAATGTTACTAC 58.676 43.478 0.00 0.00 37.07 2.73
1288 1571 4.634012 AGCACCCAACTCAATGTTACTA 57.366 40.909 0.00 0.00 37.07 1.82
1289 1572 3.508845 AGCACCCAACTCAATGTTACT 57.491 42.857 0.00 0.00 37.07 2.24
1403 1725 6.798315 ACTGCTAGCAGAATATATTTGCAG 57.202 37.500 43.42 18.65 46.30 4.41
1405 1727 5.855395 GCAACTGCTAGCAGAATATATTTGC 59.145 40.000 43.42 37.27 46.30 3.68
1407 1729 7.572523 TTGCAACTGCTAGCAGAATATATTT 57.427 32.000 43.42 25.81 46.30 1.40
1419 1744 2.286294 CGCTTCCTATTGCAACTGCTAG 59.714 50.000 0.00 0.00 42.66 3.42
1433 1758 2.846193 ACACACATGTTAACGCTTCCT 58.154 42.857 0.00 0.00 34.46 3.36
1434 1759 4.735662 TTACACACATGTTAACGCTTCC 57.264 40.909 0.00 0.00 40.48 3.46
1435 1760 7.269724 GGTTATTTACACACATGTTAACGCTTC 59.730 37.037 0.00 0.00 40.48 3.86
1436 1761 7.079475 GGTTATTTACACACATGTTAACGCTT 58.921 34.615 0.00 0.00 40.48 4.68
1457 1782 6.821160 TCGTTCTAAGCAAATCATGATGGTTA 59.179 34.615 9.46 13.79 38.19 2.85
1489 1821 5.808366 AAAGAAAAAGAAATGGGAGGGTC 57.192 39.130 0.00 0.00 0.00 4.46
1511 1843 2.101082 GGGTACGGCCTTGTTTCAAAAA 59.899 45.455 0.00 0.00 37.43 1.94
1515 1847 0.035739 GAGGGTACGGCCTTGTTTCA 59.964 55.000 0.00 0.00 37.43 2.69
1516 1848 0.675837 GGAGGGTACGGCCTTGTTTC 60.676 60.000 0.00 0.00 37.43 2.78
1517 1849 1.377612 GGAGGGTACGGCCTTGTTT 59.622 57.895 0.00 0.00 37.43 2.83
1518 1850 2.599757 GGGAGGGTACGGCCTTGTT 61.600 63.158 0.00 0.00 37.43 2.83
1519 1851 3.007323 GGGAGGGTACGGCCTTGT 61.007 66.667 0.00 0.00 37.43 3.16
1520 1852 1.921869 AATGGGAGGGTACGGCCTTG 61.922 60.000 0.00 0.00 37.43 3.61
1521 1853 1.212250 AAATGGGAGGGTACGGCCTT 61.212 55.000 0.00 0.00 37.43 4.35
1522 1854 1.618447 AAATGGGAGGGTACGGCCT 60.618 57.895 0.00 0.00 37.43 5.19
1523 1855 1.153025 GAAATGGGAGGGTACGGCC 60.153 63.158 0.00 0.00 0.00 6.13
1524 1856 0.255033 AAGAAATGGGAGGGTACGGC 59.745 55.000 0.00 0.00 0.00 5.68
1525 1857 2.801077 AAAGAAATGGGAGGGTACGG 57.199 50.000 0.00 0.00 0.00 4.02
1526 1858 5.291905 AGATAAAGAAATGGGAGGGTACG 57.708 43.478 0.00 0.00 0.00 3.67
1527 1859 6.424032 ACAAGATAAAGAAATGGGAGGGTAC 58.576 40.000 0.00 0.00 0.00 3.34
1528 1860 6.652205 ACAAGATAAAGAAATGGGAGGGTA 57.348 37.500 0.00 0.00 0.00 3.69
1614 1950 7.939588 GGCAACATCCTTAGGTAAGAATAAGAT 59.060 37.037 0.00 0.00 35.33 2.40
1619 1955 5.450818 TGGCAACATCCTTAGGTAAGAAT 57.549 39.130 0.00 0.00 46.17 2.40
1718 2065 7.597386 ACTATGAATGCAGGAAAAGAAGAAAC 58.403 34.615 0.00 0.00 0.00 2.78
1736 2083 3.118775 ACTTGCATGCGTCCTACTATGAA 60.119 43.478 14.09 0.00 0.00 2.57
1749 2096 3.788797 GCGACTGGTATTAACTTGCATGC 60.789 47.826 11.82 11.82 0.00 4.06
1753 2100 1.997606 ACGCGACTGGTATTAACTTGC 59.002 47.619 15.93 0.00 0.00 4.01
1765 2112 1.651132 GTTGTGTTGCACGCGACTG 60.651 57.895 15.93 1.64 39.34 3.51
1794 2141 0.994995 CTTCGGTCACAATGCTCTCG 59.005 55.000 0.00 0.00 0.00 4.04
1795 2142 2.086054 ACTTCGGTCACAATGCTCTC 57.914 50.000 0.00 0.00 0.00 3.20
1796 2143 2.037772 AGAACTTCGGTCACAATGCTCT 59.962 45.455 0.00 0.00 0.00 4.09
1800 2147 4.035091 TGTTTCAGAACTTCGGTCACAATG 59.965 41.667 0.00 0.00 36.70 2.82
1806 2153 2.143925 CCCTGTTTCAGAACTTCGGTC 58.856 52.381 0.00 0.00 36.70 4.79
1810 2157 1.248486 GGGCCCTGTTTCAGAACTTC 58.752 55.000 17.04 0.00 36.70 3.01
2090 2444 0.798776 GTGGAACAGCATTGAGGTCG 59.201 55.000 0.00 0.00 41.80 4.79
2224 2582 6.708054 ACATATCCAGTACCAGTACGTACTAC 59.292 42.308 26.95 20.91 45.65 2.73
2320 2684 3.244976 CGAAGCAAACATTCCCAACATC 58.755 45.455 0.00 0.00 0.00 3.06
2573 2944 4.095483 ACTTAGCAATCGAAGCCAGAATTG 59.905 41.667 9.31 0.00 0.00 2.32
2750 3122 3.580458 AGAGTAATCTGTTGTGCTGGACT 59.420 43.478 0.00 0.00 0.00 3.85
2751 3123 3.681897 CAGAGTAATCTGTTGTGCTGGAC 59.318 47.826 12.02 0.00 33.32 4.02
2752 3124 3.866066 GCAGAGTAATCTGTTGTGCTGGA 60.866 47.826 20.40 0.00 39.76 3.86
2753 3125 2.417933 GCAGAGTAATCTGTTGTGCTGG 59.582 50.000 20.40 0.00 39.76 4.85
2754 3126 2.417933 GGCAGAGTAATCTGTTGTGCTG 59.582 50.000 20.40 0.00 39.76 4.41
2759 3131 4.318332 TGTGAAGGCAGAGTAATCTGTTG 58.682 43.478 20.40 0.00 39.76 3.33
2806 3178 1.741706 CATGATGACTGAAGTGTGGCC 59.258 52.381 0.00 0.00 0.00 5.36
2984 3364 1.674764 CTGAGCCGCCACAGAGAGAT 61.675 60.000 8.86 0.00 36.38 2.75
2990 3370 2.435586 CTTCCTGAGCCGCCACAG 60.436 66.667 7.85 7.85 0.00 3.66
3258 3638 0.754957 CCCATTAGCAATTGGGCGGA 60.755 55.000 7.72 0.00 39.27 5.54


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

AutoCloner maintained by Alex Coulton.