Multiple sequence alignment - TraesCS2B01G490000

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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 TraesCS2B01G490000 chr2B 100.000 2315 0 0 1 2315 687335206 687332892 0.000000e+00 4276.0
1 TraesCS2B01G490000 chr2A 91.195 1272 56 22 111 1334 711553299 711552036 0.000000e+00 1677.0
2 TraesCS2B01G490000 chr2A 93.043 115 8 0 4 118 711553488 711553374 3.960000e-38 169.0
3 TraesCS2B01G490000 chr2D 87.611 791 56 20 564 1334 572358104 572357336 0.000000e+00 880.0
4 TraesCS2B01G490000 chr2D 94.043 554 31 2 1 554 572358712 572358161 0.000000e+00 839.0
5 TraesCS2B01G490000 chr2D 89.784 509 29 3 1824 2311 572354464 572353958 4.200000e-177 630.0
6 TraesCS2B01G490000 chr2D 92.775 346 14 3 1478 1822 572357199 572356864 7.430000e-135 490.0
7 TraesCS2B01G490000 chr2D 84.091 132 9 6 1334 1463 572357298 572357177 1.450000e-22 117.0
8 TraesCS2B01G490000 chr5D 77.500 400 62 15 1823 2197 337181337 337180941 5.010000e-52 215.0
9 TraesCS2B01G490000 chr5D 76.531 392 64 17 1831 2196 125611923 125611534 3.040000e-44 189.0
10 TraesCS2B01G490000 chr5D 73.815 401 70 25 1824 2197 312121370 312121762 2.410000e-25 126.0
11 TraesCS2B01G490000 chr5D 81.333 150 21 5 1824 1967 94072838 94072690 5.230000e-22 115.0
12 TraesCS2B01G490000 chr4D 75.931 403 63 24 1824 2197 365857437 365857834 2.360000e-40 176.0
13 TraesCS2B01G490000 chr3A 75.696 395 63 20 1831 2197 717909156 717908767 1.420000e-37 167.0
14 TraesCS2B01G490000 chr1A 79.812 213 40 3 1987 2197 504583341 504583552 3.980000e-33 152.0
15 TraesCS2B01G490000 chr3B 78.673 211 44 1 1988 2197 772187825 772187615 3.100000e-29 139.0
16 TraesCS2B01G490000 chr4A 76.887 212 46 3 1988 2197 614613630 614613420 1.450000e-22 117.0
17 TraesCS2B01G490000 chr1B 73.008 389 77 20 1831 2197 533195648 533196030 6.760000e-21 111.0
18 TraesCS2B01G490000 chr6B 80.537 149 24 3 1824 1967 47106480 47106628 2.430000e-20 110.0
19 TraesCS2B01G490000 chr7A 76.056 213 37 8 1987 2197 461801728 461801928 5.260000e-17 99.0
20 TraesCS2B01G490000 chrUn 87.273 55 6 1 2262 2315 32160401 32160347 6.910000e-06 62.1


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 TraesCS2B01G490000 chr2B 687332892 687335206 2314 True 4276.0 4276 100.0000 1 2315 1 chr2B.!!$R1 2314
1 TraesCS2B01G490000 chr2A 711552036 711553488 1452 True 923.0 1677 92.1190 4 1334 2 chr2A.!!$R1 1330
2 TraesCS2B01G490000 chr2D 572353958 572358712 4754 True 591.2 880 89.6608 1 2311 5 chr2D.!!$R1 2310

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
153 238 0.393267 TCCCCGGAAATAAACAGCGG 60.393 55.0 0.73 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1684 0.028242 CGACGCTAGATGCTCGTTCT 59.972 55.0 0.0 0.0 40.11 3.01 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
31 32 2.099756 GGGTTGCCTGCACATTATTCTC 59.900 50.000 0.00 0.00 0.00 2.87
40 41 3.884693 TGCACATTATTCTCGATGCCAAT 59.115 39.130 1.31 0.00 32.02 3.16
41 42 4.224433 GCACATTATTCTCGATGCCAATG 58.776 43.478 7.85 7.85 0.00 2.82
153 238 0.393267 TCCCCGGAAATAAACAGCGG 60.393 55.000 0.73 0.00 0.00 5.52
156 241 1.131693 CCCGGAAATAAACAGCGGAAC 59.868 52.381 0.73 0.00 0.00 3.62
157 242 1.131693 CCGGAAATAAACAGCGGAACC 59.868 52.381 0.00 0.00 0.00 3.62
162 247 3.983044 AATAAACAGCGGAACCTCTCT 57.017 42.857 0.00 0.00 0.00 3.10
173 258 1.066908 GAACCTCTCTGCTCTCCGATG 59.933 57.143 0.00 0.00 0.00 3.84
238 331 0.437295 CCGCTCGAAGTAAACGTTGG 59.563 55.000 0.00 0.00 0.00 3.77
261 354 3.383761 CAACCAACTTGCTGATTTCACC 58.616 45.455 0.00 0.00 0.00 4.02
421 519 2.124151 ATGCCACCTTGATCGGCC 60.124 61.111 6.17 0.00 45.63 6.13
474 572 7.416964 TGAAAGAAACCCAAAGAGAAATGAA 57.583 32.000 0.00 0.00 0.00 2.57
489 587 5.757886 AGAAATGAAATCGTCGCAAAAAGA 58.242 33.333 0.00 0.00 0.00 2.52
490 588 6.205784 AGAAATGAAATCGTCGCAAAAAGAA 58.794 32.000 0.00 0.00 0.00 2.52
491 589 6.695278 AGAAATGAAATCGTCGCAAAAAGAAA 59.305 30.769 0.00 0.00 0.00 2.52
617 762 2.817844 ACTTTCAGGCGGGTTTGTATTC 59.182 45.455 0.00 0.00 0.00 1.75
618 763 2.871096 TTCAGGCGGGTTTGTATTCT 57.129 45.000 0.00 0.00 0.00 2.40
619 764 2.107950 TCAGGCGGGTTTGTATTCTG 57.892 50.000 0.00 0.00 0.00 3.02
620 765 1.626321 TCAGGCGGGTTTGTATTCTGA 59.374 47.619 0.00 0.00 0.00 3.27
621 766 1.737793 CAGGCGGGTTTGTATTCTGAC 59.262 52.381 0.00 0.00 0.00 3.51
622 767 1.628846 AGGCGGGTTTGTATTCTGACT 59.371 47.619 0.00 0.00 0.00 3.41
623 768 2.039879 AGGCGGGTTTGTATTCTGACTT 59.960 45.455 0.00 0.00 0.00 3.01
632 784 4.193826 TGTATTCTGACTTCTGAGCACC 57.806 45.455 0.00 0.00 0.00 5.01
696 848 6.127810 TGTATAGAAACAGTACTCGCGATT 57.872 37.500 10.36 6.77 0.00 3.34
721 882 6.551601 TGGGAGACTAATAATTCTCTGGTCTC 59.448 42.308 14.46 14.46 44.00 3.36
748 918 3.257127 GGCCTCACTCTCAGTCCATATAC 59.743 52.174 0.00 0.00 0.00 1.47
749 919 3.257127 GCCTCACTCTCAGTCCATATACC 59.743 52.174 0.00 0.00 0.00 2.73
750 920 4.735369 CCTCACTCTCAGTCCATATACCT 58.265 47.826 0.00 0.00 0.00 3.08
751 921 4.764823 CCTCACTCTCAGTCCATATACCTC 59.235 50.000 0.00 0.00 0.00 3.85
773 943 8.315482 ACCTCTTGTTATTAACCTCTCTTCTTC 58.685 37.037 4.17 0.00 0.00 2.87
774 944 8.536175 CCTCTTGTTATTAACCTCTCTTCTTCT 58.464 37.037 4.17 0.00 0.00 2.85
775 945 9.581099 CTCTTGTTATTAACCTCTCTTCTTCTC 57.419 37.037 4.17 0.00 0.00 2.87
810 980 6.633500 TTTTCTTCAGTTTAGTGGACCATG 57.367 37.500 0.00 0.00 0.00 3.66
825 995 3.962718 GGACCATGTTGATCCCAATGAAT 59.037 43.478 0.00 0.00 34.39 2.57
843 1013 8.509690 CCAATGAATACTGTGGCTCTATAAATG 58.490 37.037 0.00 0.00 0.00 2.32
883 1061 2.092914 ACCTCCCATAAGCTAGCACAAC 60.093 50.000 18.83 0.00 0.00 3.32
904 1082 0.679960 GAACCCACATGCCCCTACAC 60.680 60.000 0.00 0.00 0.00 2.90
910 1088 3.426615 CCACATGCCCCTACACTTTTAA 58.573 45.455 0.00 0.00 0.00 1.52
946 1124 1.271054 ACTGAAGTGCAAGCTACCCAG 60.271 52.381 0.00 0.00 0.00 4.45
951 1129 1.303561 TGCAAGCTACCCAGGCAAG 60.304 57.895 0.00 0.00 0.00 4.01
952 1130 2.704808 GCAAGCTACCCAGGCAAGC 61.705 63.158 3.52 3.52 36.48 4.01
974 1161 5.048434 AGCTGCAGGTTAAGTTTTGAGAATC 60.048 40.000 13.85 0.00 0.00 2.52
1032 1219 2.658593 GTCATCGCCCGGATCACG 60.659 66.667 0.73 0.58 43.80 4.35
1041 1228 4.185413 CGGATCACGGTTGAGGTG 57.815 61.111 0.00 0.00 39.42 4.00
1165 1358 3.737172 GCAACAATGCGACCGCCT 61.737 61.111 12.08 0.00 43.83 5.52
1194 1390 2.930562 GGGGACACCACTGGCTCT 60.931 66.667 0.00 0.00 39.85 4.09
1199 1395 2.100879 GACACCACTGGCTCTTCGGT 62.101 60.000 0.00 0.00 0.00 4.69
1329 1525 1.355971 CGTGATTGATTTCCGTCGGT 58.644 50.000 11.88 0.00 0.00 4.69
1341 1575 1.153706 CGTCGGTGGGGTGTATGAC 60.154 63.158 0.00 0.00 0.00 3.06
1346 1580 1.078708 GTGGGGTGTATGACGGTGG 60.079 63.158 0.00 0.00 0.00 4.61
1350 1584 0.672401 GGGTGTATGACGGTGGTGTG 60.672 60.000 0.00 0.00 0.00 3.82
1351 1585 0.034337 GGTGTATGACGGTGGTGTGT 59.966 55.000 0.00 0.00 0.00 3.72
1395 1629 0.678048 GGAATGGGCGAACTGCTTCT 60.678 55.000 0.00 0.00 45.43 2.85
1396 1630 0.449388 GAATGGGCGAACTGCTTCTG 59.551 55.000 0.00 0.00 45.43 3.02
1397 1631 0.250901 AATGGGCGAACTGCTTCTGT 60.251 50.000 0.00 0.00 45.43 3.41
1398 1632 0.250901 ATGGGCGAACTGCTTCTGTT 60.251 50.000 0.00 0.00 45.43 3.16
1399 1633 0.394938 TGGGCGAACTGCTTCTGTTA 59.605 50.000 0.00 0.00 45.43 2.41
1400 1634 0.796927 GGGCGAACTGCTTCTGTTAC 59.203 55.000 0.00 0.00 45.43 2.50
1401 1635 0.796927 GGCGAACTGCTTCTGTTACC 59.203 55.000 0.00 0.00 45.43 2.85
1402 1636 0.438830 GCGAACTGCTTCTGTTACCG 59.561 55.000 0.00 0.00 41.73 4.02
1403 1637 1.779569 CGAACTGCTTCTGTTACCGT 58.220 50.000 0.00 0.00 0.00 4.83
1404 1638 1.455786 CGAACTGCTTCTGTTACCGTG 59.544 52.381 0.00 0.00 0.00 4.94
1405 1639 2.480845 GAACTGCTTCTGTTACCGTGT 58.519 47.619 0.00 0.00 0.00 4.49
1406 1640 1.865865 ACTGCTTCTGTTACCGTGTG 58.134 50.000 0.00 0.00 0.00 3.82
1421 1655 1.003866 CGTGTGATCATCTAGCGTCGA 60.004 52.381 0.00 0.00 0.00 4.20
1445 1679 7.976734 CGAGTTCTCTTTCTATTTCCTGTATGT 59.023 37.037 0.00 0.00 0.00 2.29
1446 1680 9.660180 GAGTTCTCTTTCTATTTCCTGTATGTT 57.340 33.333 0.00 0.00 0.00 2.71
1456 1690 9.932207 TCTATTTCCTGTATGTTAAAAGAACGA 57.068 29.630 0.00 0.00 0.00 3.85
1458 1692 6.476243 TTCCTGTATGTTAAAAGAACGAGC 57.524 37.500 0.00 0.00 0.00 5.03
1459 1693 5.543714 TCCTGTATGTTAAAAGAACGAGCA 58.456 37.500 0.00 0.00 0.00 4.26
1460 1694 6.170506 TCCTGTATGTTAAAAGAACGAGCAT 58.829 36.000 0.00 0.00 0.00 3.79
1461 1695 6.312918 TCCTGTATGTTAAAAGAACGAGCATC 59.687 38.462 0.00 0.00 0.00 3.91
1462 1696 6.313905 CCTGTATGTTAAAAGAACGAGCATCT 59.686 38.462 0.00 0.00 0.00 2.90
1463 1697 7.491372 CCTGTATGTTAAAAGAACGAGCATCTA 59.509 37.037 0.00 0.00 0.00 1.98
1464 1698 8.407457 TGTATGTTAAAAGAACGAGCATCTAG 57.593 34.615 0.00 0.00 0.00 2.43
1465 1699 5.779806 TGTTAAAAGAACGAGCATCTAGC 57.220 39.130 0.00 0.00 46.19 3.42
1474 1708 2.353607 GCATCTAGCGTCGGACGG 60.354 66.667 29.30 14.72 42.82 4.79
1481 1715 2.699212 GCGTCGGACGGTTTATGC 59.301 61.111 29.30 9.20 42.82 3.14
1482 1716 2.992313 CGTCGGACGGTTTATGCG 59.008 61.111 22.18 0.00 38.08 4.73
1483 1717 1.802715 CGTCGGACGGTTTATGCGT 60.803 57.895 22.18 0.00 38.08 5.24
1484 1718 0.523125 CGTCGGACGGTTTATGCGTA 60.523 55.000 22.18 0.00 38.08 4.42
1485 1719 0.916581 GTCGGACGGTTTATGCGTAC 59.083 55.000 0.00 0.00 32.13 3.67
1511 1745 4.119442 ACGACAGTATGGACATGTAACC 57.881 45.455 0.00 0.00 43.62 2.85
1514 1748 4.442706 GACAGTATGGACATGTAACCCTG 58.557 47.826 0.00 4.49 43.62 4.45
1567 1801 6.594788 AATACAATGGATTGCAGTTTCAGT 57.405 33.333 0.00 0.00 41.38 3.41
1568 1802 4.510038 ACAATGGATTGCAGTTTCAGTC 57.490 40.909 0.00 0.00 41.38 3.51
1569 1803 3.890756 ACAATGGATTGCAGTTTCAGTCA 59.109 39.130 0.00 0.00 41.38 3.41
1570 1804 4.341806 ACAATGGATTGCAGTTTCAGTCAA 59.658 37.500 0.00 0.00 41.38 3.18
1571 1805 5.011329 ACAATGGATTGCAGTTTCAGTCAAT 59.989 36.000 0.00 0.00 41.38 2.57
1572 1806 4.508461 TGGATTGCAGTTTCAGTCAATG 57.492 40.909 0.00 0.00 30.19 2.82
1573 1807 4.143543 TGGATTGCAGTTTCAGTCAATGA 58.856 39.130 0.00 0.00 35.62 2.57
1574 1808 4.022935 TGGATTGCAGTTTCAGTCAATGAC 60.023 41.667 5.02 5.02 37.77 3.06
1575 1809 4.217118 GGATTGCAGTTTCAGTCAATGACT 59.783 41.667 10.56 10.56 44.44 3.41
1618 1852 3.129988 AGCCAGAGGTACGTGTTGTATAC 59.870 47.826 0.00 0.00 35.02 1.47
1749 1983 1.660607 CGTGATTATGCGAGCTGTGTT 59.339 47.619 0.00 0.00 0.00 3.32
1803 2038 3.949031 TTTTTCAAAACTCGGCCCG 57.051 47.368 0.00 0.00 0.00 6.13
1886 4519 3.626028 AGAAAATTCACAAGACGCACC 57.374 42.857 0.00 0.00 0.00 5.01
1887 4520 2.293399 AGAAAATTCACAAGACGCACCC 59.707 45.455 0.00 0.00 0.00 4.61
1932 4566 1.999071 GCAACCCACACAAGAACGCA 61.999 55.000 0.00 0.00 0.00 5.24
1941 4575 1.282570 CAAGAACGCACATGCCGTT 59.717 52.632 20.37 20.37 39.24 4.44
1945 4579 2.513065 GAACGCACATGCCGTTGAGG 62.513 60.000 23.84 1.39 44.97 3.86
2079 4733 1.317613 GCCAAACAGTCATCCACACA 58.682 50.000 0.00 0.00 0.00 3.72
2083 4737 2.682352 CAAACAGTCATCCACACACACA 59.318 45.455 0.00 0.00 0.00 3.72
2090 4744 0.767375 ATCCACACACACAGGCTTCT 59.233 50.000 0.00 0.00 0.00 2.85
2108 4762 0.457851 CTAAGCACCTCCCACTCTCG 59.542 60.000 0.00 0.00 0.00 4.04
2116 4770 1.605712 CCTCCCACTCTCGTGACAAAC 60.606 57.143 0.00 0.00 43.97 2.93
2126 4780 1.872952 TCGTGACAAACATTGCAGGAG 59.127 47.619 0.00 0.00 32.31 3.69
2134 4788 1.609208 ACATTGCAGGAGAAAAGCGT 58.391 45.000 0.00 0.00 0.00 5.07
2138 4792 0.465460 TGCAGGAGAAAAGCGTTGGT 60.465 50.000 0.00 0.00 0.00 3.67
2209 4863 1.593196 CGCAAGGAAGACCAAGTGAA 58.407 50.000 0.00 0.00 38.94 3.18
2242 4896 0.824109 TCGAACAAGCCGGATGAGAT 59.176 50.000 5.05 0.00 0.00 2.75
2254 4908 3.372954 CGGATGAGATCGACTACCAAAC 58.627 50.000 0.00 0.00 0.00 2.93
2301 4955 3.353029 CGCCATCGTTGCCACACA 61.353 61.111 0.00 0.00 0.00 3.72
2304 4958 1.302431 CCATCGTTGCCACACAGGA 60.302 57.895 0.00 0.00 41.22 3.86
2311 4965 3.414700 GCCACACAGGAAGTCGCG 61.415 66.667 0.00 0.00 41.22 5.87
2312 4966 3.414700 CCACACAGGAAGTCGCGC 61.415 66.667 0.00 0.00 41.22 6.86
2313 4967 2.661537 CACACAGGAAGTCGCGCA 60.662 61.111 8.75 0.00 0.00 6.09
2314 4968 2.108157 ACACAGGAAGTCGCGCAA 59.892 55.556 8.75 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.350197 GCATCGAGAATAATGTGCAGGC 60.350 50.000 0.00 0.00 33.09 4.85
40 41 2.108168 GTACTGATAGTCTGGTGCCCA 58.892 52.381 0.00 0.00 0.00 5.36
41 42 2.108168 TGTACTGATAGTCTGGTGCCC 58.892 52.381 0.00 0.00 0.00 5.36
46 47 4.500545 GCTGATGGTGTACTGATAGTCTGG 60.501 50.000 0.00 0.00 0.00 3.86
58 59 5.700832 CAGAAAACAGTAAGCTGATGGTGTA 59.299 40.000 1.30 0.00 45.28 2.90
60 61 4.756642 TCAGAAAACAGTAAGCTGATGGTG 59.243 41.667 1.30 0.00 45.28 4.17
153 238 1.066908 CATCGGAGAGCAGAGAGGTTC 59.933 57.143 0.00 0.00 43.63 3.62
156 241 0.667993 GACATCGGAGAGCAGAGAGG 59.332 60.000 0.00 0.00 43.63 3.69
157 242 0.307453 CGACATCGGAGAGCAGAGAG 59.693 60.000 0.00 0.00 43.63 3.20
162 247 1.241315 TGTGTCGACATCGGAGAGCA 61.241 55.000 23.12 9.36 43.63 4.26
173 258 3.501396 CATGGCCCATGTGTCGAC 58.499 61.111 15.89 9.11 37.12 4.20
261 354 3.131396 GAGCAACGTATGGGTTAGGATG 58.869 50.000 0.00 0.00 0.00 3.51
421 519 3.126001 TCTGCTTTGGTAGACAAGTGG 57.874 47.619 0.00 0.00 40.82 4.00
474 572 4.927422 TCCTTTTTCTTTTTGCGACGATT 58.073 34.783 0.00 0.00 0.00 3.34
489 587 6.993079 ACACTCAGTGTTCTTTTTCCTTTTT 58.007 32.000 3.98 0.00 45.08 1.94
490 588 6.590234 ACACTCAGTGTTCTTTTTCCTTTT 57.410 33.333 3.98 0.00 45.08 2.27
617 762 0.318441 TTCCGGTGCTCAGAAGTCAG 59.682 55.000 0.00 0.00 0.00 3.51
618 763 0.756294 TTTCCGGTGCTCAGAAGTCA 59.244 50.000 0.00 0.00 0.00 3.41
619 764 1.270358 ACTTTCCGGTGCTCAGAAGTC 60.270 52.381 0.00 0.00 0.00 3.01
620 765 0.759346 ACTTTCCGGTGCTCAGAAGT 59.241 50.000 0.00 0.00 0.00 3.01
621 766 2.611518 CTACTTTCCGGTGCTCAGAAG 58.388 52.381 0.00 0.00 0.00 2.85
622 767 1.337823 GCTACTTTCCGGTGCTCAGAA 60.338 52.381 0.00 0.00 0.00 3.02
623 768 0.246635 GCTACTTTCCGGTGCTCAGA 59.753 55.000 0.00 0.00 0.00 3.27
632 784 3.021269 TGGCATATACGCTACTTTCCG 57.979 47.619 0.00 0.00 0.00 4.30
696 848 6.444704 AGACCAGAGAATTATTAGTCTCCCA 58.555 40.000 5.62 0.00 44.53 4.37
721 882 0.614415 ACTGAGAGTGAGGCCAGAGG 60.614 60.000 5.01 0.00 0.00 3.69
748 918 8.536175 AGAAGAAGAGAGGTTAATAACAAGAGG 58.464 37.037 5.45 0.00 0.00 3.69
749 919 9.581099 GAGAAGAAGAGAGGTTAATAACAAGAG 57.419 37.037 5.45 0.00 0.00 2.85
750 920 8.532819 GGAGAAGAAGAGAGGTTAATAACAAGA 58.467 37.037 5.45 0.00 0.00 3.02
751 921 7.766738 GGGAGAAGAAGAGAGGTTAATAACAAG 59.233 40.741 5.45 0.00 0.00 3.16
793 963 4.698201 TCAACATGGTCCACTAAACTGA 57.302 40.909 0.00 0.00 0.00 3.41
810 980 4.202050 GCCACAGTATTCATTGGGATCAAC 60.202 45.833 0.00 0.00 35.48 3.18
825 995 4.368315 CGTGCATTTATAGAGCCACAGTA 58.632 43.478 0.00 0.00 0.00 2.74
843 1013 2.795973 GGTAATTTCGGGGCGTGC 59.204 61.111 0.00 0.00 0.00 5.34
883 1061 0.394352 GTAGGGGCATGTGGGTTCTG 60.394 60.000 0.00 0.00 0.00 3.02
904 1082 2.030805 GCTCCACACAGCAGGTTAAAAG 60.031 50.000 0.00 0.00 39.43 2.27
946 1124 0.961753 AACTTAACCTGCAGCTTGCC 59.038 50.000 8.66 0.00 44.23 4.52
951 1129 4.568152 TTCTCAAAACTTAACCTGCAGC 57.432 40.909 8.66 0.00 0.00 5.25
952 1130 6.016777 ACAGATTCTCAAAACTTAACCTGCAG 60.017 38.462 6.78 6.78 0.00 4.41
960 1138 6.542005 TGCAACTCACAGATTCTCAAAACTTA 59.458 34.615 0.00 0.00 0.00 2.24
961 1139 5.357878 TGCAACTCACAGATTCTCAAAACTT 59.642 36.000 0.00 0.00 0.00 2.66
962 1140 4.883585 TGCAACTCACAGATTCTCAAAACT 59.116 37.500 0.00 0.00 0.00 2.66
963 1141 4.972440 GTGCAACTCACAGATTCTCAAAAC 59.028 41.667 0.00 0.00 44.98 2.43
964 1142 4.260743 CGTGCAACTCACAGATTCTCAAAA 60.261 41.667 0.00 0.00 45.92 2.44
974 1161 4.032356 TGAGCGTGCAACTCACAG 57.968 55.556 14.95 0.00 45.92 3.66
1041 1228 2.969238 CTGATGATGGACGGCGCC 60.969 66.667 19.07 19.07 0.00 6.53
1329 1525 1.536907 ACCACCGTCATACACCCCA 60.537 57.895 0.00 0.00 0.00 4.96
1341 1575 0.249573 AACGTAGGAACACACCACCG 60.250 55.000 0.00 0.00 0.00 4.94
1346 1580 1.223187 CCCACAACGTAGGAACACAC 58.777 55.000 3.41 0.00 0.00 3.82
1350 1584 0.034337 TGAGCCCACAACGTAGGAAC 59.966 55.000 3.41 0.00 0.00 3.62
1351 1585 0.320374 CTGAGCCCACAACGTAGGAA 59.680 55.000 3.41 0.00 0.00 3.36
1395 1629 3.488553 CGCTAGATGATCACACGGTAACA 60.489 47.826 0.00 0.00 0.00 2.41
1396 1630 3.043586 CGCTAGATGATCACACGGTAAC 58.956 50.000 0.00 0.00 0.00 2.50
1397 1631 2.686405 ACGCTAGATGATCACACGGTAA 59.314 45.455 0.00 0.00 0.00 2.85
1398 1632 2.289820 GACGCTAGATGATCACACGGTA 59.710 50.000 0.00 0.00 0.00 4.02
1399 1633 1.065701 GACGCTAGATGATCACACGGT 59.934 52.381 0.00 0.00 0.00 4.83
1400 1634 1.759994 GACGCTAGATGATCACACGG 58.240 55.000 0.00 0.00 0.00 4.94
1401 1635 1.003866 TCGACGCTAGATGATCACACG 60.004 52.381 0.00 0.07 0.00 4.49
1402 1636 2.032302 ACTCGACGCTAGATGATCACAC 59.968 50.000 0.00 0.00 0.00 3.82
1403 1637 2.289565 ACTCGACGCTAGATGATCACA 58.710 47.619 0.00 0.00 0.00 3.58
1404 1638 3.002862 AGAACTCGACGCTAGATGATCAC 59.997 47.826 0.00 0.00 0.00 3.06
1405 1639 3.206964 AGAACTCGACGCTAGATGATCA 58.793 45.455 0.00 0.00 0.00 2.92
1406 1640 3.496884 AGAGAACTCGACGCTAGATGATC 59.503 47.826 0.00 0.00 34.09 2.92
1445 1679 4.491676 ACGCTAGATGCTCGTTCTTTTAA 58.508 39.130 0.00 0.00 40.11 1.52
1446 1680 4.103357 GACGCTAGATGCTCGTTCTTTTA 58.897 43.478 0.00 0.00 40.11 1.52
1447 1681 2.924290 GACGCTAGATGCTCGTTCTTTT 59.076 45.455 0.00 0.00 40.11 2.27
1449 1683 1.532090 CGACGCTAGATGCTCGTTCTT 60.532 52.381 0.00 0.00 40.11 2.52
1450 1684 0.028242 CGACGCTAGATGCTCGTTCT 59.972 55.000 0.00 0.00 40.11 3.01
1451 1685 0.930742 CCGACGCTAGATGCTCGTTC 60.931 60.000 0.00 0.00 39.15 3.95
1452 1686 1.064296 CCGACGCTAGATGCTCGTT 59.936 57.895 0.00 0.00 39.15 3.85
1453 1687 1.818363 TCCGACGCTAGATGCTCGT 60.818 57.895 0.00 0.00 39.15 4.18
1454 1688 1.369448 GTCCGACGCTAGATGCTCG 60.369 63.158 0.00 0.00 39.88 5.03
1455 1689 1.369448 CGTCCGACGCTAGATGCTC 60.369 63.158 8.21 0.00 40.11 4.26
1456 1690 2.716244 CGTCCGACGCTAGATGCT 59.284 61.111 8.21 0.00 40.11 3.79
1457 1691 2.353607 CCGTCCGACGCTAGATGC 60.354 66.667 15.64 0.00 40.91 3.91
1458 1692 0.179145 AAACCGTCCGACGCTAGATG 60.179 55.000 15.64 3.38 40.91 2.90
1459 1693 1.382522 TAAACCGTCCGACGCTAGAT 58.617 50.000 15.64 2.35 40.91 1.98
1460 1694 1.064505 CATAAACCGTCCGACGCTAGA 59.935 52.381 15.64 1.16 40.91 2.43
1461 1695 1.474017 CATAAACCGTCCGACGCTAG 58.526 55.000 15.64 4.83 40.91 3.42
1462 1696 0.526096 GCATAAACCGTCCGACGCTA 60.526 55.000 15.64 6.73 40.91 4.26
1463 1697 1.808390 GCATAAACCGTCCGACGCT 60.808 57.895 15.64 0.00 40.91 5.07
1464 1698 2.699212 GCATAAACCGTCCGACGC 59.301 61.111 15.64 0.00 40.91 5.19
1465 1699 0.523125 TACGCATAAACCGTCCGACG 60.523 55.000 14.15 14.15 42.11 5.12
1466 1700 0.916581 GTACGCATAAACCGTCCGAC 59.083 55.000 0.00 0.00 39.88 4.79
1467 1701 0.525311 TGTACGCATAAACCGTCCGA 59.475 50.000 0.00 0.00 39.88 4.55
1468 1702 1.322338 CTTGTACGCATAAACCGTCCG 59.678 52.381 0.00 0.00 39.88 4.79
1469 1703 2.340337 ACTTGTACGCATAAACCGTCC 58.660 47.619 0.00 0.00 39.88 4.79
1470 1704 3.001758 CGTACTTGTACGCATAAACCGTC 60.002 47.826 18.22 0.00 39.88 4.79
1471 1705 2.916716 CGTACTTGTACGCATAAACCGT 59.083 45.455 18.22 0.00 42.26 4.83
1472 1706 3.001758 GTCGTACTTGTACGCATAAACCG 60.002 47.826 23.41 2.74 42.62 4.44
1473 1707 3.919804 TGTCGTACTTGTACGCATAAACC 59.080 43.478 23.41 9.11 42.62 3.27
1474 1708 4.618489 ACTGTCGTACTTGTACGCATAAAC 59.382 41.667 23.41 17.32 42.62 2.01
1475 1709 4.797471 ACTGTCGTACTTGTACGCATAAA 58.203 39.130 23.41 7.74 42.62 1.40
1476 1710 4.424061 ACTGTCGTACTTGTACGCATAA 57.576 40.909 23.41 8.06 42.62 1.90
1477 1711 5.504392 CATACTGTCGTACTTGTACGCATA 58.496 41.667 23.41 17.40 42.62 3.14
1478 1712 4.348656 CATACTGTCGTACTTGTACGCAT 58.651 43.478 23.41 16.35 42.62 4.73
1479 1713 3.426560 CCATACTGTCGTACTTGTACGCA 60.427 47.826 23.41 21.49 42.62 5.24
1480 1714 3.103738 CCATACTGTCGTACTTGTACGC 58.896 50.000 23.41 18.93 42.62 4.42
1481 1715 4.142838 TGTCCATACTGTCGTACTTGTACG 60.143 45.833 22.55 22.55 44.11 3.67
1482 1716 5.300969 TGTCCATACTGTCGTACTTGTAC 57.699 43.478 1.13 1.13 0.00 2.90
1483 1717 5.416639 ACATGTCCATACTGTCGTACTTGTA 59.583 40.000 0.00 0.00 0.00 2.41
1484 1718 4.219944 ACATGTCCATACTGTCGTACTTGT 59.780 41.667 0.00 0.00 0.00 3.16
1485 1719 4.744570 ACATGTCCATACTGTCGTACTTG 58.255 43.478 0.00 0.00 0.00 3.16
1493 1727 3.844211 ACAGGGTTACATGTCCATACTGT 59.156 43.478 0.00 9.30 32.37 3.55
1498 1732 2.356125 GCAGACAGGGTTACATGTCCAT 60.356 50.000 0.00 0.00 45.61 3.41
1511 1745 2.983907 ATCAGACATGAGCAGACAGG 57.016 50.000 0.00 0.00 39.29 4.00
1514 1748 4.383850 ACTGTATCAGACATGAGCAGAC 57.616 45.455 0.00 0.00 41.30 3.51
1567 1801 1.339438 GCAGGAGGCAGAAGTCATTGA 60.339 52.381 0.00 0.00 43.97 2.57
1568 1802 1.093159 GCAGGAGGCAGAAGTCATTG 58.907 55.000 0.00 0.00 43.97 2.82
1569 1803 3.566130 GCAGGAGGCAGAAGTCATT 57.434 52.632 0.00 0.00 43.97 2.57
1618 1852 7.005380 CAGTTTAGCAAAAGCGAAATTCAATG 58.995 34.615 0.00 0.00 0.00 2.82
1678 1912 1.134753 GATCCCACGCATGCAAAATCA 59.865 47.619 19.57 0.00 0.00 2.57
1749 1983 5.296151 ACAAAAGATTCCTCAGTCTGACA 57.704 39.130 10.88 0.00 0.00 3.58
1790 2024 2.325082 CCTCACGGGCCGAGTTTTG 61.325 63.158 35.78 20.35 0.00 2.44
1791 2025 1.838073 ATCCTCACGGGCCGAGTTTT 61.838 55.000 35.78 6.54 34.39 2.43
1822 2057 3.763057 GGGCAACTCTTTTCCTCCTTTA 58.237 45.455 0.00 0.00 0.00 1.85
1827 4460 0.250770 ACCGGGCAACTCTTTTCCTC 60.251 55.000 6.32 0.00 0.00 3.71
1829 4462 0.313987 CAACCGGGCAACTCTTTTCC 59.686 55.000 6.32 0.00 0.00 3.13
1886 4519 1.672898 CCATGGTGCCCTGTTTTGG 59.327 57.895 2.57 0.00 0.00 3.28
1887 4520 1.672898 CCCATGGTGCCCTGTTTTG 59.327 57.895 11.73 0.00 0.00 2.44
1932 4566 2.154462 CTTTTCTCCTCAACGGCATGT 58.846 47.619 0.00 0.00 0.00 3.21
1941 4575 0.319555 CGACGGTGCTTTTCTCCTCA 60.320 55.000 0.00 0.00 0.00 3.86
1945 4579 0.319641 ACCTCGACGGTGCTTTTCTC 60.320 55.000 5.85 0.00 46.80 2.87
2068 4722 0.250467 AGCCTGTGTGTGTGGATGAC 60.250 55.000 0.00 0.00 0.00 3.06
2072 4726 1.419381 TAGAAGCCTGTGTGTGTGGA 58.581 50.000 0.00 0.00 0.00 4.02
2090 4744 0.251653 ACGAGAGTGGGAGGTGCTTA 60.252 55.000 0.00 0.00 46.97 3.09
2104 4758 1.872952 CCTGCAATGTTTGTCACGAGA 59.127 47.619 0.00 0.00 0.00 4.04
2108 4762 3.988379 TTCTCCTGCAATGTTTGTCAC 57.012 42.857 0.00 0.00 0.00 3.67
2116 4770 2.322161 CAACGCTTTTCTCCTGCAATG 58.678 47.619 0.00 0.00 0.00 2.82
2126 4780 2.783440 CGCAAGACCAACGCTTTTC 58.217 52.632 0.00 0.00 43.02 2.29
2138 4792 3.659092 CGTTGGCTTGGCGCAAGA 61.659 61.111 19.38 0.66 43.42 3.02
2147 4801 2.978010 CGGTTCTGGCGTTGGCTT 60.978 61.111 0.00 0.00 39.81 4.35
2173 4827 2.444624 CGGTGACAATGACGCGAGG 61.445 63.158 15.93 0.00 0.00 4.63
2242 4896 2.547218 GCAACTGAGGTTTGGTAGTCGA 60.547 50.000 0.00 0.00 32.73 4.20
2254 4908 3.409026 AGAGGTAGTTTGCAACTGAGG 57.591 47.619 0.00 0.00 42.84 3.86


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

AutoCloner maintained by Alex Coulton.