Multiple sequence alignment - TraesCS2D01G455000

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 TraesCS2D01G455000 chr2D 100.000 2604 0 0 1 2604 563141820 563144423 0 4809
1 TraesCS2D01G455000 chr2A 88.692 2653 182 46 1 2602 703544735 703547320 0 3129
2 TraesCS2D01G455000 chr2B 92.631 1167 71 10 705 1864 673707516 673708674 0 1664
3 TraesCS2D01G455000 chr2B 84.825 771 53 24 1858 2602 673708890 673709622 0 717
4 TraesCS2D01G455000 chr2B 84.088 729 68 24 1 722 673706178 673706865 0 660


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 TraesCS2D01G455000 chr2D 563141820 563144423 2603 False 4809.000000 4809 100.000000 1 2604 1 chr2D.!!$F1 2603
1 TraesCS2D01G455000 chr2A 703544735 703547320 2585 False 3129.000000 3129 88.692000 1 2602 1 chr2A.!!$F1 2601
2 TraesCS2D01G455000 chr2B 673706178 673709622 3444 False 1013.666667 1664 87.181333 1 2602 3 chr2B.!!$F1 2601

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
486 498 0.033642 TCGACATTACCGTTGTGCCA 59.966 50.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2934 0.659427 TACGGTAGAGAACGGCGATG 59.341 55.0 16.62 0.0 31.81 3.84 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
42 43 2.287608 GGCTTTGCAACTTGGTCACTAC 60.288 50.000 0.00 0.00 0.00 2.73
90 98 0.889186 AAGGGTTTGTGCTAGTGGCG 60.889 55.000 0.00 0.00 45.43 5.69
98 106 4.137872 GCTAGTGGCGCGGTGGTA 62.138 66.667 8.83 0.00 0.00 3.25
125 133 3.572255 GTGCTATGTGGGTCCAAAAGAAA 59.428 43.478 0.00 0.00 0.00 2.52
126 134 4.038642 GTGCTATGTGGGTCCAAAAGAAAA 59.961 41.667 0.00 0.00 0.00 2.29
202 210 2.945008 ACTTGTGTTCACCAGATGTGTG 59.055 45.455 10.29 0.00 45.61 3.82
255 264 6.482898 TGCCAATGGAAGCACAATTATTAT 57.517 33.333 2.05 0.00 33.08 1.28
279 288 4.714851 GTTAACATGCAACGGTTAACGAT 58.285 39.130 24.00 0.00 45.16 3.73
377 388 4.406943 GGAACATCTCGAACTTTGATTGC 58.593 43.478 0.00 0.00 0.00 3.56
380 391 3.120060 ACATCTCGAACTTTGATTGCTGC 60.120 43.478 0.00 0.00 0.00 5.25
384 395 1.689959 GAACTTTGATTGCTGCCGTG 58.310 50.000 0.00 0.00 0.00 4.94
386 397 1.317613 ACTTTGATTGCTGCCGTGAA 58.682 45.000 0.00 0.00 0.00 3.18
400 411 1.334992 CGTGAACGAATGACGCGAGT 61.335 55.000 15.93 0.00 46.07 4.18
403 414 4.973659 CGTGAACGAATGACGCGAGTAAA 61.974 47.826 15.93 0.00 44.03 2.01
404 415 6.216117 CGTGAACGAATGACGCGAGTAAAT 62.216 45.833 15.93 0.00 44.03 1.40
417 428 7.700611 ACGCGAGTAAATTTCTTTTTATTCG 57.299 32.000 15.93 13.88 45.91 3.34
466 477 5.619086 GCGCAAAACTCATAACCATGTACTT 60.619 40.000 0.30 0.00 33.57 2.24
467 478 6.378582 CGCAAAACTCATAACCATGTACTTT 58.621 36.000 0.00 0.00 33.57 2.66
469 480 6.523201 GCAAAACTCATAACCATGTACTTTCG 59.477 38.462 0.00 0.00 33.57 3.46
474 486 7.103641 ACTCATAACCATGTACTTTCGACATT 58.896 34.615 0.00 0.00 35.31 2.71
486 498 0.033642 TCGACATTACCGTTGTGCCA 59.966 50.000 0.00 0.00 0.00 4.92
491 503 0.319083 ATTACCGTTGTGCCACTCGA 59.681 50.000 12.74 0.00 0.00 4.04
525 537 8.805175 ACATTACAATCATCCATGTTTTCAGAA 58.195 29.630 0.00 0.00 0.00 3.02
529 541 8.767478 ACAATCATCCATGTTTTCAGAAATTC 57.233 30.769 0.00 0.00 0.00 2.17
541 553 4.305989 TCAGAAATTCAAACACCAGCAC 57.694 40.909 0.00 0.00 0.00 4.40
566 578 6.903883 TTCGACAATATTTAGAGAAGGCAC 57.096 37.500 0.00 0.00 0.00 5.01
657 677 6.256321 AGTTGACATTTTCTTGAACATGTTGC 59.744 34.615 17.58 8.35 29.81 4.17
661 681 5.231991 ACATTTTCTTGAACATGTTGCGAAC 59.768 36.000 17.58 1.13 0.00 3.95
668 688 4.437239 TGAACATGTTGCGAACCATTTTT 58.563 34.783 17.58 0.00 0.00 1.94
671 691 6.703607 TGAACATGTTGCGAACCATTTTTATT 59.296 30.769 17.58 0.00 0.00 1.40
681 702 6.953189 GCGAACCATTTTTATTGTTACAATGC 59.047 34.615 19.55 6.82 0.00 3.56
692 713 8.755696 TTATTGTTACAATGCTGAAAATGTCC 57.244 30.769 19.55 0.00 0.00 4.02
694 715 4.021544 TGTTACAATGCTGAAAATGTCCCC 60.022 41.667 0.00 0.00 0.00 4.81
727 1416 6.237437 CCAATCATACAAAAATAACAACGCCG 60.237 38.462 0.00 0.00 0.00 6.46
731 1420 2.287728 ACAAAAATAACAACGCCGTCCC 60.288 45.455 0.00 0.00 0.00 4.46
732 1421 1.606903 AAAATAACAACGCCGTCCCA 58.393 45.000 0.00 0.00 0.00 4.37
862 1553 3.732048 AGAAATGGGAAATACACCGGT 57.268 42.857 0.00 0.00 0.00 5.28
866 1557 4.417426 AATGGGAAATACACCGGTAGAG 57.583 45.455 6.87 0.00 31.88 2.43
870 1561 2.223994 GGAAATACACCGGTAGAGCCTC 60.224 54.545 6.87 0.00 31.88 4.70
871 1562 2.154567 AATACACCGGTAGAGCCTCA 57.845 50.000 6.87 0.00 31.88 3.86
894 1585 4.202357 ACTCCACATCTTGAGTGCTAAACA 60.202 41.667 0.00 0.00 40.23 2.83
900 1591 7.699391 CCACATCTTGAGTGCTAAACATAATTG 59.301 37.037 0.00 0.00 35.69 2.32
901 1592 8.239314 CACATCTTGAGTGCTAAACATAATTGT 58.761 33.333 0.00 0.00 37.82 2.71
903 1594 9.708222 CATCTTGAGTGCTAAACATAATTGTAC 57.292 33.333 0.00 0.00 34.06 2.90
934 1626 3.227614 AGGGCCAAAATGAAAAGTACGT 58.772 40.909 6.18 0.00 0.00 3.57
973 1665 0.658897 GGGTCTCTCGCTTCTCTACG 59.341 60.000 0.00 0.00 0.00 3.51
1024 1716 4.827304 AGCTGAAAAGAAAGAGAAGCAC 57.173 40.909 0.00 0.00 0.00 4.40
1030 1722 6.299141 TGAAAAGAAAGAGAAGCACTACCAT 58.701 36.000 0.00 0.00 0.00 3.55
1033 1725 6.809630 AAGAAAGAGAAGCACTACCATTTC 57.190 37.500 0.00 0.00 0.00 2.17
1034 1726 6.120507 AGAAAGAGAAGCACTACCATTTCT 57.879 37.500 0.00 0.00 32.46 2.52
1035 1727 7.246171 AGAAAGAGAAGCACTACCATTTCTA 57.754 36.000 0.00 0.00 34.82 2.10
1282 1974 6.042777 ACATCTTCATGTACAGGTGAATACG 58.957 40.000 11.35 1.87 41.81 3.06
1292 1984 1.336125 AGGTGAATACGCGCTACTACC 59.664 52.381 5.73 10.31 0.00 3.18
1295 1989 0.670162 GAATACGCGCTACTACCCCA 59.330 55.000 5.73 0.00 0.00 4.96
1298 1992 0.964860 TACGCGCTACTACCCCAACA 60.965 55.000 5.73 0.00 0.00 3.33
1302 1996 1.614241 CGCTACTACCCCAACAGGCT 61.614 60.000 0.00 0.00 0.00 4.58
1485 2179 4.527583 GAGGAGCAGCGGCAGAGG 62.528 72.222 12.44 0.00 44.61 3.69
1552 2246 1.966762 CAGCTTTCCGGCAACCAAT 59.033 52.632 0.00 0.00 34.17 3.16
1580 2278 3.181516 CGTAGGATTTTCAGCAGCAGTTC 60.182 47.826 0.00 0.00 0.00 3.01
1581 2279 1.808945 AGGATTTTCAGCAGCAGTTCG 59.191 47.619 0.00 0.00 0.00 3.95
1602 2300 3.725895 CGTGAACAAAAGCTCGATGATGG 60.726 47.826 0.00 0.00 0.00 3.51
1609 2307 0.982852 AGCTCGATGATGGGTTGGGA 60.983 55.000 0.00 0.00 0.00 4.37
1612 2310 0.107214 TCGATGATGGGTTGGGAAGC 60.107 55.000 0.00 0.00 0.00 3.86
1674 2375 4.269523 GACCACCACCTGCAGGCA 62.270 66.667 33.06 0.00 39.32 4.75
1728 2429 1.450312 CGCAGGGATGGGTTCTCAC 60.450 63.158 0.00 0.00 0.00 3.51
1827 2529 2.802057 CGTAAGGTGTACCATAGCCTGC 60.802 54.545 3.56 0.00 38.89 4.85
1828 2530 0.546598 AAGGTGTACCATAGCCTGCC 59.453 55.000 3.56 0.00 38.89 4.85
1829 2531 0.326618 AGGTGTACCATAGCCTGCCT 60.327 55.000 3.56 0.00 38.89 4.75
1830 2532 0.179045 GGTGTACCATAGCCTGCCTG 60.179 60.000 0.00 0.00 35.64 4.85
1842 2545 1.869767 GCCTGCCTGTCGATATGAAAG 59.130 52.381 0.00 0.00 0.00 2.62
1879 2806 7.642669 CATAACAAAAGCTCTCTCAGTTTTCA 58.357 34.615 0.00 0.00 34.63 2.69
1880 2807 6.515272 AACAAAAGCTCTCTCAGTTTTCAA 57.485 33.333 0.00 0.00 34.63 2.69
1901 2828 4.825546 AATCAGTTCTGCTGTGTTCTTG 57.174 40.909 0.00 0.00 45.23 3.02
1905 2832 1.002033 GTTCTGCTGTGTTCTTGCCTG 60.002 52.381 0.00 0.00 0.00 4.85
1949 2884 1.262417 TCCGCTCATAACAGTGGACA 58.738 50.000 0.00 0.00 46.26 4.02
1996 2932 2.051703 CGTTTTGCCCCACGAACG 60.052 61.111 0.00 0.00 38.76 3.95
1998 2934 3.597728 TTTTGCCCCACGAACGCC 61.598 61.111 0.00 0.00 0.00 5.68
2010 2946 2.813908 AACGCCATCGCCGTTCTC 60.814 61.111 0.00 0.00 44.70 2.87
2014 2950 1.591863 GCCATCGCCGTTCTCTACC 60.592 63.158 0.00 0.00 0.00 3.18
2117 3060 1.537397 AGCAGAGGCAGAGGACCAA 60.537 57.895 0.00 0.00 44.61 3.67
2187 3130 5.126067 TGGAAAGTCCAGAGAGAAAACAAG 58.874 41.667 0.00 0.00 42.67 3.16
2190 3133 4.078639 AGTCCAGAGAGAAAACAAGTGG 57.921 45.455 0.00 0.00 0.00 4.00
2199 3142 0.744281 AAAACAAGTGGTGCCTTCCG 59.256 50.000 0.00 0.00 0.00 4.30
2235 3185 1.990799 TGATAGCCGTGAACGAGTTG 58.009 50.000 4.03 0.00 43.02 3.16
2265 3215 5.465935 AGACGTTTGCTTCAACAAGAAAAA 58.534 33.333 0.00 0.00 38.66 1.94
2367 3331 1.347707 TCTTCTCTTTCGGCCACACAT 59.652 47.619 2.24 0.00 0.00 3.21
2369 3333 0.389817 TCTCTTTCGGCCACACATCG 60.390 55.000 2.24 0.00 0.00 3.84
2398 3362 0.741221 ATTCGCGAGGCCTGTTTCTC 60.741 55.000 12.00 0.00 0.00 2.87
2410 3374 3.751698 GCCTGTTTCTCGGAAACTTACAT 59.248 43.478 21.90 0.00 0.00 2.29
2429 3393 1.671054 GAGGCAACGGCTAGCAACA 60.671 57.895 18.24 0.00 46.39 3.33
2430 3394 1.228124 AGGCAACGGCTAGCAACAA 60.228 52.632 18.24 0.00 46.39 2.83
2431 3395 0.821711 AGGCAACGGCTAGCAACAAA 60.822 50.000 18.24 0.00 46.39 2.83
2432 3396 0.031449 GGCAACGGCTAGCAACAAAA 59.969 50.000 18.24 0.00 40.87 2.44
2433 3397 1.537135 GGCAACGGCTAGCAACAAAAA 60.537 47.619 18.24 0.00 40.87 1.94
2471 3435 6.399986 GCGCATTTTACTTCACCATTTTTCTC 60.400 38.462 0.30 0.00 0.00 2.87
2472 3436 6.089417 CGCATTTTACTTCACCATTTTTCTCC 59.911 38.462 0.00 0.00 0.00 3.71
2502 3466 1.365633 GCCTGGCTAGTGGATCTCG 59.634 63.158 12.43 0.00 0.00 4.04
2503 3467 2.045280 CCTGGCTAGTGGATCTCGG 58.955 63.158 0.00 0.00 0.00 4.63
2504 3468 1.365633 CTGGCTAGTGGATCTCGGC 59.634 63.158 0.00 0.00 35.51 5.54
2508 3472 1.528542 CTAGTGGATCTCGGCCGGA 60.529 63.158 27.83 21.61 0.00 5.14
2534 3501 3.853698 TTACGTGCAAGGCCCACCC 62.854 63.158 0.00 0.00 36.11 4.61
2554 3521 1.599667 CGTCAGCTGCCGTCGTATTAT 60.600 52.381 9.38 0.00 0.00 1.28
2557 3524 4.046462 GTCAGCTGCCGTCGTATTATTAA 58.954 43.478 9.47 0.00 0.00 1.40
2558 3525 4.148348 GTCAGCTGCCGTCGTATTATTAAG 59.852 45.833 9.47 0.00 0.00 1.85
2559 3526 4.037089 TCAGCTGCCGTCGTATTATTAAGA 59.963 41.667 9.47 0.00 0.00 2.10
2562 3529 5.813672 AGCTGCCGTCGTATTATTAAGAAAA 59.186 36.000 0.00 0.00 0.00 2.29
2602 3578 5.444877 CGTGTAACATGTACCAATACGGTTG 60.445 44.000 0.00 0.00 41.62 3.77
2603 3579 5.163834 GTGTAACATGTACCAATACGGTTGG 60.164 44.000 17.27 17.27 41.20 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.249489 GACGGCCTAGGCACATACAG 60.249 60.000 34.09 17.23 44.11 2.74
90 98 2.223971 ACATAGCACATACTACCACCGC 60.224 50.000 0.00 0.00 0.00 5.68
92 100 3.494398 CCCACATAGCACATACTACCACC 60.494 52.174 0.00 0.00 0.00 4.61
93 101 3.134081 ACCCACATAGCACATACTACCAC 59.866 47.826 0.00 0.00 0.00 4.16
94 102 3.380393 ACCCACATAGCACATACTACCA 58.620 45.455 0.00 0.00 0.00 3.25
98 106 2.477245 TGGACCCACATAGCACATACT 58.523 47.619 0.00 0.00 0.00 2.12
125 133 2.158914 CCCCAGCTGCAAAAGACTTTTT 60.159 45.455 8.66 0.00 36.97 1.94
126 134 1.413812 CCCCAGCTGCAAAAGACTTTT 59.586 47.619 8.66 7.38 0.00 2.27
176 184 1.133823 TCTGGTGAACACAAGTGGCAT 60.134 47.619 8.87 0.00 34.02 4.40
202 210 4.729868 ACACATAATCCTAGGGCCAAATC 58.270 43.478 9.46 0.00 0.00 2.17
255 264 4.226113 GTTAACCGTTGCATGTTAACCA 57.774 40.909 23.33 0.00 45.53 3.67
279 288 3.660669 AGGGTATTTTGGTCTTTCTCCCA 59.339 43.478 0.00 0.00 35.31 4.37
365 376 1.266718 TCACGGCAGCAATCAAAGTTC 59.733 47.619 0.00 0.00 0.00 3.01
377 388 1.416049 CGTCATTCGTTCACGGCAG 59.584 57.895 0.00 0.00 40.29 4.85
380 391 1.998550 CTCGCGTCATTCGTTCACGG 61.999 60.000 5.77 0.00 42.13 4.94
384 395 3.901667 ATTTACTCGCGTCATTCGTTC 57.098 42.857 5.77 0.00 42.13 3.95
386 397 3.924686 AGAAATTTACTCGCGTCATTCGT 59.075 39.130 5.77 0.00 42.13 3.85
454 465 5.806502 CGGTAATGTCGAAAGTACATGGTTA 59.193 40.000 14.65 0.00 37.62 2.85
466 477 1.149987 GGCACAACGGTAATGTCGAA 58.850 50.000 0.00 0.00 0.00 3.71
467 478 0.033642 TGGCACAACGGTAATGTCGA 59.966 50.000 0.00 0.00 31.92 4.20
469 480 1.463444 GAGTGGCACAACGGTAATGTC 59.537 52.381 21.41 0.09 44.16 3.06
474 486 0.104487 TTTCGAGTGGCACAACGGTA 59.896 50.000 26.96 17.30 44.16 4.02
486 498 8.964476 ATGATTGTAATGTTCCTATTTCGAGT 57.036 30.769 0.00 0.00 0.00 4.18
491 503 9.425248 ACATGGATGATTGTAATGTTCCTATTT 57.575 29.630 0.00 0.00 0.00 1.40
525 537 3.380004 TCGAAAGTGCTGGTGTTTGAATT 59.620 39.130 0.00 0.00 0.00 2.17
529 541 1.400142 TGTCGAAAGTGCTGGTGTTTG 59.600 47.619 0.00 0.00 0.00 2.93
541 553 7.278868 AGTGCCTTCTCTAAATATTGTCGAAAG 59.721 37.037 0.00 0.00 0.00 2.62
587 600 1.956477 AGGTGTCAGGTGCATTGTTTC 59.044 47.619 0.00 0.00 0.00 2.78
596 609 3.096852 TGGTCTGTATAGGTGTCAGGTG 58.903 50.000 0.00 0.00 0.00 4.00
657 677 8.161610 CAGCATTGTAACAATAAAAATGGTTCG 58.838 33.333 0.00 0.00 36.97 3.95
668 688 7.319646 GGGACATTTTCAGCATTGTAACAATA 58.680 34.615 0.00 0.00 0.00 1.90
671 691 4.021544 GGGGACATTTTCAGCATTGTAACA 60.022 41.667 0.00 0.00 0.00 2.41
681 702 3.274288 GCTAGTCAGGGGACATTTTCAG 58.726 50.000 0.00 0.00 46.80 3.02
692 713 4.422073 TTGTATGATTGGCTAGTCAGGG 57.578 45.455 0.00 0.00 0.00 4.45
694 715 9.722056 GTTATTTTTGTATGATTGGCTAGTCAG 57.278 33.333 0.00 0.00 0.00 3.51
757 1448 4.460263 GTTTCCCAGCCCTTCAAATTTTT 58.540 39.130 0.00 0.00 0.00 1.94
758 1449 3.494223 CGTTTCCCAGCCCTTCAAATTTT 60.494 43.478 0.00 0.00 0.00 1.82
759 1450 2.037121 CGTTTCCCAGCCCTTCAAATTT 59.963 45.455 0.00 0.00 0.00 1.82
760 1451 1.618343 CGTTTCCCAGCCCTTCAAATT 59.382 47.619 0.00 0.00 0.00 1.82
761 1452 1.256812 CGTTTCCCAGCCCTTCAAAT 58.743 50.000 0.00 0.00 0.00 2.32
764 1455 2.282180 GCGTTTCCCAGCCCTTCA 60.282 61.111 0.00 0.00 0.00 3.02
855 1546 0.966370 GAGTGAGGCTCTACCGGTGT 60.966 60.000 19.93 0.00 46.52 4.16
862 1553 2.762887 CAAGATGTGGAGTGAGGCTCTA 59.237 50.000 16.72 0.00 43.62 2.43
866 1557 1.277557 ACTCAAGATGTGGAGTGAGGC 59.722 52.381 0.00 0.00 42.49 4.70
871 1562 4.202357 TGTTTAGCACTCAAGATGTGGAGT 60.202 41.667 0.00 0.00 44.84 3.85
894 1585 2.158813 CCTCTGTGGCGGGTACAATTAT 60.159 50.000 0.00 0.00 0.00 1.28
900 1591 4.468689 GCCCTCTGTGGCGGGTAC 62.469 72.222 0.00 0.00 42.54 3.34
1033 1725 6.438259 TCGATGGAGTAGTTTCTTCTGTAG 57.562 41.667 0.00 0.00 0.00 2.74
1034 1726 6.829298 AGATCGATGGAGTAGTTTCTTCTGTA 59.171 38.462 0.54 0.00 0.00 2.74
1035 1727 5.654650 AGATCGATGGAGTAGTTTCTTCTGT 59.345 40.000 0.54 0.00 0.00 3.41
1282 1974 1.153429 CCTGTTGGGGTAGTAGCGC 60.153 63.158 0.00 0.00 0.00 5.92
1292 1984 1.138661 GAGAGATCAGAGCCTGTTGGG 59.861 57.143 0.00 0.00 38.36 4.12
1295 1989 2.548464 AGGAGAGATCAGAGCCTGTT 57.452 50.000 0.00 0.00 32.61 3.16
1298 1992 3.586618 ACAAAAAGGAGAGATCAGAGCCT 59.413 43.478 0.00 0.00 0.00 4.58
1302 1996 4.594920 AGGTGACAAAAAGGAGAGATCAGA 59.405 41.667 0.00 0.00 0.00 3.27
1485 2179 3.041627 GCTCTGCTTCTGCTGCTGC 62.042 63.158 8.89 8.89 40.48 5.25
1518 2212 3.989698 CTGCTACCACGCCCAGACG 62.990 68.421 0.00 0.00 39.50 4.18
1552 2246 2.028839 TGCTGAAAATCCTACGTTCGGA 60.029 45.455 8.49 8.49 34.52 4.55
1580 2278 3.410850 CATCATCGAGCTTTTGTTCACG 58.589 45.455 0.00 0.00 0.00 4.35
1581 2279 3.426695 CCCATCATCGAGCTTTTGTTCAC 60.427 47.826 0.00 0.00 0.00 3.18
1602 2300 1.141858 CTGGATCTAGGCTTCCCAACC 59.858 57.143 0.00 0.00 0.00 3.77
1609 2307 2.122768 CCCTCAACTGGATCTAGGCTT 58.877 52.381 11.17 0.00 0.00 4.35
1612 2310 2.103941 GCTTCCCTCAACTGGATCTAGG 59.896 54.545 11.17 0.00 0.00 3.02
1691 2392 2.742053 GCGGTTCAGAGACAGCATAAAA 59.258 45.455 0.00 0.00 39.93 1.52
1692 2393 2.289382 TGCGGTTCAGAGACAGCATAAA 60.289 45.455 0.00 0.00 43.90 1.40
1728 2429 3.118261 TCCATCTTCGGAGATCAAAAGGG 60.118 47.826 2.21 0.88 40.67 3.95
1827 2529 6.333416 TCTCACTTTCTTTCATATCGACAGG 58.667 40.000 0.00 0.00 0.00 4.00
1828 2530 6.475076 CCTCTCACTTTCTTTCATATCGACAG 59.525 42.308 0.00 0.00 0.00 3.51
1829 2531 6.333416 CCTCTCACTTTCTTTCATATCGACA 58.667 40.000 0.00 0.00 0.00 4.35
1830 2532 5.233263 GCCTCTCACTTTCTTTCATATCGAC 59.767 44.000 0.00 0.00 0.00 4.20
1842 2545 5.048434 AGCTTTTGTTATGCCTCTCACTTTC 60.048 40.000 0.00 0.00 0.00 2.62
1996 2932 1.591863 GGTAGAGAACGGCGATGGC 60.592 63.158 16.62 0.00 38.90 4.40
1998 2934 0.659427 TACGGTAGAGAACGGCGATG 59.341 55.000 16.62 0.00 31.81 3.84
2010 2946 5.930569 GCCTTAAATTCCTATGGTACGGTAG 59.069 44.000 0.00 0.00 0.00 3.18
2014 2950 3.744426 CGGCCTTAAATTCCTATGGTACG 59.256 47.826 0.00 0.00 0.00 3.67
2052 2995 5.370679 GGCCTCCCGTAGTTTTGATTATTA 58.629 41.667 0.00 0.00 0.00 0.98
2053 2996 4.204799 GGCCTCCCGTAGTTTTGATTATT 58.795 43.478 0.00 0.00 0.00 1.40
2054 2997 3.816994 GGCCTCCCGTAGTTTTGATTAT 58.183 45.455 0.00 0.00 0.00 1.28
2055 2998 3.271055 GGCCTCCCGTAGTTTTGATTA 57.729 47.619 0.00 0.00 0.00 1.75
2154 3097 3.782656 TGGACTTTCCAGAGTTTACCC 57.217 47.619 0.00 0.00 42.67 3.69
2187 3130 1.534163 GTAAGAAACGGAAGGCACCAC 59.466 52.381 2.06 0.00 0.00 4.16
2190 3133 2.762745 TCAGTAAGAAACGGAAGGCAC 58.237 47.619 0.00 0.00 28.61 5.01
2235 3185 7.853929 TCTTGTTGAAGCAAACGTCTAATTAAC 59.146 33.333 0.00 0.00 32.47 2.01
2367 3331 2.030401 CGCGAATGAAACCACCCGA 61.030 57.895 0.00 0.00 0.00 5.14
2369 3333 1.644786 CCTCGCGAATGAAACCACCC 61.645 60.000 11.33 0.00 0.00 4.61
2398 3362 2.159707 CGTTGCCTCATGTAAGTTTCCG 60.160 50.000 0.00 0.00 0.00 4.30
2410 3374 1.671054 GTTGCTAGCCGTTGCCTCA 60.671 57.895 13.29 0.00 38.69 3.86
2435 3399 2.908688 AAAATGCGCCAGTCCTTTTT 57.091 40.000 4.18 0.00 0.00 1.94
2436 3400 2.890945 AGTAAAATGCGCCAGTCCTTTT 59.109 40.909 4.18 4.25 0.00 2.27
2437 3401 2.514803 AGTAAAATGCGCCAGTCCTTT 58.485 42.857 4.18 0.00 0.00 3.11
2471 3435 3.058160 CAGGCAGCTTTCGTGGGG 61.058 66.667 0.00 0.00 0.00 4.96
2472 3436 3.058160 CCAGGCAGCTTTCGTGGG 61.058 66.667 13.85 0.00 36.22 4.61
2502 3466 1.140375 CGTAAGGTGTACTCCGGCC 59.860 63.158 8.28 0.00 0.00 6.13
2503 3467 0.457337 CACGTAAGGTGTACTCCGGC 60.457 60.000 8.28 2.59 41.89 6.13
2504 3468 3.708195 CACGTAAGGTGTACTCCGG 57.292 57.895 8.28 0.00 41.89 5.14
2562 3529 2.282407 ACACGTACGAGCCTTTTGTTT 58.718 42.857 24.41 0.00 0.00 2.83
2565 3532 2.796031 TGTTACACGTACGAGCCTTTTG 59.204 45.455 24.41 10.30 0.00 2.44


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

AutoCloner maintained by Alex Coulton.