Multiple sequence alignment - TraesCS3A01G536500

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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 TraesCS3A01G536500 chr3A 100.000 2522 0 0 1 2522 747726745 747729266 0.000000e+00 4658.0
1 TraesCS3A01G536500 chr3A 88.933 253 26 2 187 437 747754180 747754432 6.770000e-81 311.0
2 TraesCS3A01G536500 chr3D 94.146 1230 50 5 545 1766 613075613 613076828 0.000000e+00 1853.0
3 TraesCS3A01G536500 chr3D 91.516 554 29 5 1799 2351 613076952 613077488 0.000000e+00 747.0
4 TraesCS3A01G536500 chr3D 84.615 481 60 11 785 1256 613115384 613115859 1.370000e-127 466.0
5 TraesCS3A01G536500 chr3D 89.180 305 10 4 187 490 613074819 613075101 2.390000e-95 359.0
6 TraesCS3A01G536500 chr3D 94.706 170 5 2 21 188 613074601 613074768 6.920000e-66 261.0
7 TraesCS3A01G536500 chr3D 90.196 102 9 1 337 437 613111530 613111631 5.660000e-27 132.0
8 TraesCS3A01G536500 chr3D 92.208 77 6 0 481 557 613075469 613075545 2.650000e-20 110.0
9 TraesCS3A01G536500 chr3D 88.043 92 11 0 187 278 613110899 613110990 2.650000e-20 110.0
10 TraesCS3A01G536500 chr3B 95.852 1133 34 6 611 1734 825971513 825970385 0.000000e+00 1820.0
11 TraesCS3A01G536500 chr3B 92.982 342 13 3 187 528 825971839 825971509 2.920000e-134 488.0
12 TraesCS3A01G536500 chr3B 87.879 165 16 4 276 437 825963084 825962921 9.210000e-45 191.0
13 TraesCS3A01G536500 chr3B 90.141 142 12 2 1820 1961 825970369 825970230 1.540000e-42 183.0
14 TraesCS3A01G536500 chr3B 88.776 98 11 0 187 284 825964091 825963994 1.230000e-23 121.0
15 TraesCS3A01G536500 chrUn 95.376 173 5 3 2352 2522 138271934 138272105 3.200000e-69 272.0
16 TraesCS3A01G536500 chrUn 94.798 173 7 2 2352 2522 171112601 171112429 4.140000e-68 268.0
17 TraesCS3A01G536500 chrUn 94.767 172 7 2 2352 2522 138345952 138346122 1.490000e-67 267.0
18 TraesCS3A01G536500 chr6A 95.376 173 5 3 2352 2522 558457705 558457534 3.200000e-69 272.0
19 TraesCS3A01G536500 chr6A 95.376 173 5 3 2352 2522 558461025 558460854 3.200000e-69 272.0
20 TraesCS3A01G536500 chr6A 94.798 173 6 3 2352 2522 558552762 558552591 1.490000e-67 267.0
21 TraesCS3A01G536500 chr5A 95.349 172 7 1 2352 2522 613741484 613741313 3.200000e-69 272.0
22 TraesCS3A01G536500 chr5A 87.500 88 7 2 1735 1818 532036125 532036038 5.740000e-17 99.0
23 TraesCS3A01G536500 chr6B 94.828 174 5 3 2352 2522 54191920 54192092 4.140000e-68 268.0
24 TraesCS3A01G536500 chr6B 89.024 82 9 0 1737 1818 22733660 22733741 4.440000e-18 102.0
25 TraesCS3A01G536500 chr5B 93.855 179 9 2 2346 2522 387765928 387765750 4.140000e-68 268.0
26 TraesCS3A01G536500 chr5B 92.958 71 5 0 2280 2350 592247487 592247417 1.230000e-18 104.0
27 TraesCS3A01G536500 chr1A 83.721 172 25 3 1515 1685 593391814 593391645 2.600000e-35 159.0
28 TraesCS3A01G536500 chr1A 94.366 71 4 0 2280 2350 534862915 534862845 2.650000e-20 110.0
29 TraesCS3A01G536500 chr4D 82.716 162 23 4 1512 1673 40579941 40580097 3.380000e-29 139.0
30 TraesCS3A01G536500 chr7B 92.405 79 5 1 1740 1818 589938035 589938112 7.370000e-21 111.0
31 TraesCS3A01G536500 chr7B 93.243 74 4 1 1746 1818 245982849 245982776 9.540000e-20 108.0
32 TraesCS3A01G536500 chr4B 93.151 73 5 0 1746 1818 13415759 13415687 9.540000e-20 108.0
33 TraesCS3A01G536500 chr2B 93.151 73 4 1 1746 1818 159968515 159968444 3.430000e-19 106.0
34 TraesCS3A01G536500 chr2B 90.909 77 7 0 1742 1818 376149173 376149249 1.230000e-18 104.0
35 TraesCS3A01G536500 chr2B 91.892 74 6 0 1745 1818 376149251 376149178 1.230000e-18 104.0
36 TraesCS3A01G536500 chr2B 91.549 71 6 0 2280 2350 567589466 567589536 5.740000e-17 99.0
37 TraesCS3A01G536500 chr7D 89.024 82 9 0 1737 1818 263033067 263033148 4.440000e-18 102.0
38 TraesCS3A01G536500 chr7D 90.000 60 4 2 1515 1574 326706367 326706310 2.690000e-10 76.8
39 TraesCS3A01G536500 chr1B 95.455 44 2 0 2307 2350 5533988 5533945 1.250000e-08 71.3


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 TraesCS3A01G536500 chr3A 747726745 747729266 2521 False 4658.000000 4658 100.000000 1 2522 1 chr3A.!!$F1 2521
1 TraesCS3A01G536500 chr3D 613074601 613077488 2887 False 666.000000 1853 92.351200 21 2351 5 chr3D.!!$F1 2330
2 TraesCS3A01G536500 chr3D 613110899 613115859 4960 False 236.000000 466 87.618000 187 1256 3 chr3D.!!$F2 1069
3 TraesCS3A01G536500 chr3B 825970230 825971839 1609 True 830.333333 1820 92.991667 187 1961 3 chr3B.!!$R2 1774
4 TraesCS3A01G536500 chr6A 558457534 558461025 3491 True 272.000000 272 95.376000 2352 2522 2 chr6A.!!$R2 170

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
566 1481 0.108019 GTGGAGAAGAACGTGGGGTT 59.892 55.0 0.0 0.0 42.96 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 6657 0.035056 AGTGGGTTAGTGCATGGCTC 60.035 55.0 0.0 0.0 0.0 4.7 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
32 33 0.613853 TACAAGCCCTGAGCCTACGT 60.614 55.000 0.00 0.00 45.47 3.57
40 41 3.181967 GAGCCTACGTGCACTGCG 61.182 66.667 16.19 4.23 0.00 5.18
47 48 4.059459 CGTGCACTGCGACGGTTC 62.059 66.667 16.19 0.00 32.64 3.62
51 52 2.029073 CACTGCGACGGTTCCTGT 59.971 61.111 0.00 0.00 0.00 4.00
137 138 3.322466 CACCTTCGGGCCCAGTCT 61.322 66.667 24.92 0.00 39.10 3.24
225 280 7.023575 TGACGTAACCTAGAATTAACGACTTC 58.976 38.462 0.00 0.00 0.00 3.01
262 317 1.268352 GGAGTAGCGATAGACTGCAGG 59.732 57.143 19.93 0.00 34.44 4.85
530 1445 3.060540 CGTATGCGCCATAGTTTACACAG 60.061 47.826 4.18 0.00 0.00 3.66
531 1446 1.732941 TGCGCCATAGTTTACACAGG 58.267 50.000 4.18 0.00 0.00 4.00
532 1447 1.014352 GCGCCATAGTTTACACAGGG 58.986 55.000 0.00 0.00 0.00 4.45
533 1448 1.014352 CGCCATAGTTTACACAGGGC 58.986 55.000 0.00 0.00 34.16 5.19
534 1449 1.014352 GCCATAGTTTACACAGGGCG 58.986 55.000 0.00 0.00 0.00 6.13
535 1450 1.014352 CCATAGTTTACACAGGGCGC 58.986 55.000 0.00 0.00 0.00 6.53
536 1451 0.650512 CATAGTTTACACAGGGCGCG 59.349 55.000 0.00 0.00 0.00 6.86
539 1454 2.735478 TTTACACAGGGCGCGTCG 60.735 61.111 8.43 0.00 0.00 5.12
540 1455 3.502990 TTTACACAGGGCGCGTCGT 62.503 57.895 8.43 3.05 0.00 4.34
541 1456 4.710695 TACACAGGGCGCGTCGTG 62.711 66.667 29.56 29.56 35.48 4.35
551 1466 2.964925 GCGTCGTGTGCAAGTGGA 60.965 61.111 0.00 0.00 0.00 4.02
552 1467 2.943345 GCGTCGTGTGCAAGTGGAG 61.943 63.158 0.00 0.00 0.00 3.86
553 1468 1.299850 CGTCGTGTGCAAGTGGAGA 60.300 57.895 0.00 0.00 0.00 3.71
555 1470 0.861837 GTCGTGTGCAAGTGGAGAAG 59.138 55.000 0.00 0.00 0.00 2.85
556 1471 0.750249 TCGTGTGCAAGTGGAGAAGA 59.250 50.000 0.00 0.00 0.00 2.87
558 1473 1.261619 CGTGTGCAAGTGGAGAAGAAC 59.738 52.381 0.00 0.00 0.00 3.01
559 1474 1.261619 GTGTGCAAGTGGAGAAGAACG 59.738 52.381 0.00 0.00 0.00 3.95
560 1475 1.134521 TGTGCAAGTGGAGAAGAACGT 60.135 47.619 0.00 0.00 0.00 3.99
563 1478 1.512926 CAAGTGGAGAAGAACGTGGG 58.487 55.000 0.00 0.00 0.00 4.61
564 1479 0.396811 AAGTGGAGAAGAACGTGGGG 59.603 55.000 0.00 0.00 0.00 4.96
566 1481 0.108019 GTGGAGAAGAACGTGGGGTT 59.892 55.000 0.00 0.00 42.96 4.11
567 1482 1.345415 GTGGAGAAGAACGTGGGGTTA 59.655 52.381 0.00 0.00 39.50 2.85
568 1483 2.027469 GTGGAGAAGAACGTGGGGTTAT 60.027 50.000 0.00 0.00 39.50 1.89
569 1484 2.640826 TGGAGAAGAACGTGGGGTTATT 59.359 45.455 0.00 0.00 42.44 1.40
570 1485 3.839490 TGGAGAAGAACGTGGGGTTATTA 59.161 43.478 0.00 0.00 40.00 0.98
571 1486 4.081309 TGGAGAAGAACGTGGGGTTATTAG 60.081 45.833 0.00 0.00 40.00 1.73
572 1487 4.081254 GGAGAAGAACGTGGGGTTATTAGT 60.081 45.833 0.00 0.00 40.00 2.24
573 1488 4.828829 AGAAGAACGTGGGGTTATTAGTG 58.171 43.478 0.00 0.00 40.00 2.74
574 1489 2.981898 AGAACGTGGGGTTATTAGTGC 58.018 47.619 0.00 0.00 39.50 4.40
575 1490 2.303600 AGAACGTGGGGTTATTAGTGCA 59.696 45.455 0.00 0.00 39.50 4.57
577 1492 2.639065 ACGTGGGGTTATTAGTGCATG 58.361 47.619 0.00 0.00 0.00 4.06
578 1493 2.237643 ACGTGGGGTTATTAGTGCATGA 59.762 45.455 0.00 0.00 0.00 3.07
580 1495 2.618709 GTGGGGTTATTAGTGCATGAGC 59.381 50.000 0.00 0.00 42.57 4.26
596 1511 3.501396 GCAGGTGCATGCATACGT 58.499 55.556 25.64 10.76 45.77 3.57
597 1512 1.063006 GCAGGTGCATGCATACGTG 59.937 57.895 25.64 22.52 45.77 4.49
598 1513 1.723273 CAGGTGCATGCATACGTGG 59.277 57.895 25.64 11.13 33.09 4.94
599 1514 1.451927 AGGTGCATGCATACGTGGG 60.452 57.895 25.64 0.00 33.09 4.61
600 1515 1.451207 GGTGCATGCATACGTGGGA 60.451 57.895 25.64 0.00 33.09 4.37
601 1516 1.439353 GGTGCATGCATACGTGGGAG 61.439 60.000 25.64 0.00 33.09 4.30
602 1517 0.461870 GTGCATGCATACGTGGGAGA 60.462 55.000 25.64 0.00 33.09 3.71
603 1518 0.251634 TGCATGCATACGTGGGAGAA 59.748 50.000 18.46 0.00 33.09 2.87
604 1519 0.940126 GCATGCATACGTGGGAGAAG 59.060 55.000 14.21 0.00 33.09 2.85
605 1520 1.473257 GCATGCATACGTGGGAGAAGA 60.473 52.381 14.21 0.00 33.09 2.87
606 1521 2.477825 CATGCATACGTGGGAGAAGAG 58.522 52.381 0.00 0.00 0.00 2.85
607 1522 1.847328 TGCATACGTGGGAGAAGAGA 58.153 50.000 0.00 0.00 0.00 3.10
608 1523 2.176045 TGCATACGTGGGAGAAGAGAA 58.824 47.619 0.00 0.00 0.00 2.87
609 1524 2.166459 TGCATACGTGGGAGAAGAGAAG 59.834 50.000 0.00 0.00 0.00 2.85
1051 5344 1.553248 CCATTACCCTCCTCGTTGTCA 59.447 52.381 0.00 0.00 0.00 3.58
1060 5353 0.613260 CCTCGTTGTCATTCCCTCCA 59.387 55.000 0.00 0.00 0.00 3.86
1112 5405 2.514013 GCGACGGCATTAGTGACCG 61.514 63.158 15.76 15.76 44.82 4.79
1148 5441 3.695606 GCTCAGCTCCGACCCACA 61.696 66.667 0.00 0.00 0.00 4.17
1294 5587 0.467290 GAAACTGGGGTTGGCACTGA 60.467 55.000 0.00 0.00 35.63 3.41
1302 5595 1.032014 GGTTGGCACTGAACATGTGT 58.968 50.000 0.00 0.00 37.70 3.72
1329 5622 0.324275 AATACAACCAAGCCGGCCAT 60.324 50.000 26.15 10.27 39.03 4.40
1356 5649 3.277742 GAACGCACGCACGGACTTC 62.278 63.158 2.61 0.00 37.37 3.01
1365 5658 1.671054 CACGGACTTCGGCAACCAT 60.671 57.895 0.00 0.00 44.45 3.55
1483 5776 9.381033 TCATGAAACAAATGAACAAGAAAATGT 57.619 25.926 0.00 0.00 31.17 2.71
1631 5924 4.137543 GTGGATCATGGACCCACTTTATC 58.862 47.826 18.48 1.37 45.08 1.75
1699 5998 8.523915 TGTTTTGTTCTTGCATATATGGATCT 57.476 30.769 14.51 0.00 0.00 2.75
1735 6036 4.601406 ACTTGGTATTATGGAGGCCAAA 57.399 40.909 5.01 0.00 38.54 3.28
1736 6037 4.941713 ACTTGGTATTATGGAGGCCAAAA 58.058 39.130 5.01 0.00 38.54 2.44
1749 6050 7.149202 TGGAGGCCAAAACTATCATATACTT 57.851 36.000 5.01 0.00 0.00 2.24
1753 6054 7.816411 AGGCCAAAACTATCATATACTTCCTT 58.184 34.615 5.01 0.00 0.00 3.36
1755 6056 7.719633 GGCCAAAACTATCATATACTTCCTTCA 59.280 37.037 0.00 0.00 0.00 3.02
1774 6075 9.973661 TTCCTTCATTCCAAAATAGATAACTCA 57.026 29.630 0.00 0.00 0.00 3.41
1775 6076 9.973661 TCCTTCATTCCAAAATAGATAACTCAA 57.026 29.630 0.00 0.00 0.00 3.02
1797 6189 8.589335 TCAAGTTAGTACAAAGTTGAGTCATC 57.411 34.615 0.00 0.00 41.57 2.92
1809 6201 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1812 6204 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1813 6205 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1818 6210 2.200373 ATTTTGGAACGGAGGGAGTG 57.800 50.000 0.00 0.00 0.00 3.51
1828 6220 2.026262 ACGGAGGGAGTGCAAAATACAT 60.026 45.455 0.00 0.00 0.00 2.29
1836 6228 5.883673 GGGAGTGCAAAATACATACCACTAA 59.116 40.000 0.00 0.00 34.05 2.24
1848 6240 6.903340 ACATACCACTAATAGAAAACCCCT 57.097 37.500 0.00 0.00 0.00 4.79
1868 6260 8.582891 ACCCCTTTATAGGATTTTCTCTACAT 57.417 34.615 0.00 0.00 45.05 2.29
1870 6262 8.440771 CCCCTTTATAGGATTTTCTCTACATGT 58.559 37.037 2.69 2.69 45.05 3.21
1880 6272 1.465777 TCTCTACATGTCGCGTTTCGA 59.534 47.619 5.77 0.00 46.29 3.71
1954 6346 3.306166 CAGGTTGAACGTCGTTGATATCC 59.694 47.826 16.75 10.08 0.00 2.59
1973 6365 1.133104 CCTAGTACTCCCTCCTTCCCC 60.133 61.905 0.00 0.00 0.00 4.81
2024 6416 2.693069 CTCCCATAATCTAAGGCGCAG 58.307 52.381 10.83 0.00 0.00 5.18
2041 6433 1.747924 GCAGATGCCTTTTTCTCTCCC 59.252 52.381 0.00 0.00 34.31 4.30
2077 6469 3.186909 TCCACTGACGATCGCTATTTTG 58.813 45.455 16.60 5.10 0.00 2.44
2087 6479 1.202114 TCGCTATTTTGCTGCAAAGGG 59.798 47.619 24.83 21.18 34.72 3.95
2136 6529 3.056891 GGATGCCTATCTCTCTACAGCAC 60.057 52.174 0.00 0.00 33.68 4.40
2141 6534 4.127907 CCTATCTCTCTACAGCACGTACA 58.872 47.826 0.00 0.00 0.00 2.90
2162 6555 6.240549 ACAATAGGTCAGGTAAGGATCAAG 57.759 41.667 0.00 0.00 0.00 3.02
2182 6575 1.322338 GACGCGCTAATTTTCGTGCTA 59.678 47.619 5.73 0.00 39.52 3.49
2183 6576 1.727880 ACGCGCTAATTTTCGTGCTAA 59.272 42.857 5.73 0.00 39.52 3.09
2184 6577 2.222729 ACGCGCTAATTTTCGTGCTAAG 60.223 45.455 5.73 0.00 39.52 2.18
2185 6578 2.028763 CGCGCTAATTTTCGTGCTAAGA 59.971 45.455 5.56 0.00 34.66 2.10
2186 6579 3.482923 CGCGCTAATTTTCGTGCTAAGAA 60.483 43.478 5.56 0.00 34.66 2.52
2187 6580 3.779238 GCGCTAATTTTCGTGCTAAGAAC 59.221 43.478 0.00 0.00 34.05 3.01
2188 6581 4.331962 CGCTAATTTTCGTGCTAAGAACC 58.668 43.478 0.00 0.00 0.00 3.62
2189 6582 4.142988 CGCTAATTTTCGTGCTAAGAACCA 60.143 41.667 0.00 0.00 0.00 3.67
2190 6583 5.615984 CGCTAATTTTCGTGCTAAGAACCAA 60.616 40.000 0.00 0.00 0.00 3.67
2191 6584 5.567915 GCTAATTTTCGTGCTAAGAACCAAC 59.432 40.000 0.00 0.00 0.00 3.77
2192 6585 5.508200 AATTTTCGTGCTAAGAACCAACA 57.492 34.783 0.00 0.00 0.00 3.33
2193 6586 3.955771 TTTCGTGCTAAGAACCAACAC 57.044 42.857 0.00 0.00 0.00 3.32
2195 6588 0.110823 CGTGCTAAGAACCAACACGC 60.111 55.000 0.63 0.00 46.11 5.34
2196 6589 0.237498 GTGCTAAGAACCAACACGCC 59.763 55.000 0.00 0.00 0.00 5.68
2197 6590 0.107831 TGCTAAGAACCAACACGCCT 59.892 50.000 0.00 0.00 0.00 5.52
2204 6597 1.534163 GAACCAACACGCCTAAGAACC 59.466 52.381 0.00 0.00 0.00 3.62
2215 6608 2.872842 GCCTAAGAACCAACACGCCTAA 60.873 50.000 0.00 0.00 0.00 2.69
2227 6620 1.232621 ACGCCTAAGAACCAAACGCC 61.233 55.000 0.00 0.00 0.00 5.68
2337 6730 0.957395 AGCTATATGCACGGCCATGC 60.957 55.000 18.86 18.86 45.94 4.06
2369 6762 2.439156 GATCCGGCTTGCCTGCTT 60.439 61.111 10.12 0.00 0.00 3.91
2415 10128 2.290071 CCCACTTCATCCTACGGTTGTT 60.290 50.000 0.00 0.00 0.00 2.83
2416 10129 3.000727 CCACTTCATCCTACGGTTGTTC 58.999 50.000 0.00 0.00 0.00 3.18
2473 10187 1.361197 CTGATTTTAAGGGGGTGGGGT 59.639 52.381 0.00 0.00 0.00 4.95
2487 10201 2.089201 GTGGGGTCGGACCTTATTTTG 58.911 52.381 25.39 0.00 38.64 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.291377 TCAGGGCTTGTACAATGATTCTATC 58.709 40.000 9.13 0.00 0.00 2.08
1 2 6.252599 TCAGGGCTTGTACAATGATTCTAT 57.747 37.500 9.13 0.00 0.00 1.98
2 3 5.674525 CTCAGGGCTTGTACAATGATTCTA 58.325 41.667 9.13 0.00 0.00 2.10
3 4 4.521146 CTCAGGGCTTGTACAATGATTCT 58.479 43.478 9.13 0.54 0.00 2.40
4 5 3.065925 GCTCAGGGCTTGTACAATGATTC 59.934 47.826 9.13 1.97 38.06 2.52
5 6 3.019564 GCTCAGGGCTTGTACAATGATT 58.980 45.455 9.13 0.00 38.06 2.57
6 7 2.648059 GCTCAGGGCTTGTACAATGAT 58.352 47.619 9.13 0.00 38.06 2.45
7 8 1.340017 GGCTCAGGGCTTGTACAATGA 60.340 52.381 9.13 8.95 41.46 2.57
8 9 1.098050 GGCTCAGGGCTTGTACAATG 58.902 55.000 9.13 4.65 41.46 2.82
9 10 0.995024 AGGCTCAGGGCTTGTACAAT 59.005 50.000 9.13 0.00 46.62 2.71
10 11 1.278127 GTAGGCTCAGGGCTTGTACAA 59.722 52.381 8.28 8.28 46.62 2.41
11 12 0.902531 GTAGGCTCAGGGCTTGTACA 59.097 55.000 0.00 0.00 46.62 2.90
12 13 0.179108 CGTAGGCTCAGGGCTTGTAC 60.179 60.000 0.00 0.00 46.62 2.90
13 14 0.613853 ACGTAGGCTCAGGGCTTGTA 60.614 55.000 0.00 0.00 46.62 2.41
14 15 1.913762 ACGTAGGCTCAGGGCTTGT 60.914 57.895 0.00 0.00 46.62 3.16
15 16 1.448540 CACGTAGGCTCAGGGCTTG 60.449 63.158 0.00 0.00 46.62 4.01
16 17 2.982130 CACGTAGGCTCAGGGCTT 59.018 61.111 0.00 0.00 46.62 4.35
18 19 4.082523 TGCACGTAGGCTCAGGGC 62.083 66.667 9.14 9.14 40.90 5.19
19 20 2.125512 GTGCACGTAGGCTCAGGG 60.126 66.667 0.00 0.00 34.04 4.45
32 33 3.923864 AGGAACCGTCGCAGTGCA 61.924 61.111 16.83 0.00 0.00 4.57
40 41 7.542025 TCTCTAAAATTACTACAGGAACCGTC 58.458 38.462 0.00 0.00 0.00 4.79
47 48 9.765795 CCCTTGTATCTCTAAAATTACTACAGG 57.234 37.037 0.00 0.00 0.00 4.00
51 52 8.139989 GTCGCCCTTGTATCTCTAAAATTACTA 58.860 37.037 0.00 0.00 0.00 1.82
137 138 2.027385 TGCCATGTGTTGTGCTTACAA 58.973 42.857 0.00 0.00 0.00 2.41
164 167 7.777425 ACGTTTTCATGTACGAGTTTACTAAC 58.223 34.615 19.14 0.00 40.03 2.34
165 168 7.928908 ACGTTTTCATGTACGAGTTTACTAA 57.071 32.000 19.14 0.00 40.03 2.24
225 280 5.800941 GCTACTCCCTAATATGAACGATTCG 59.199 44.000 4.14 4.14 0.00 3.34
351 887 9.696572 AAATATTTCATATCCATCATGAGGAGG 57.303 33.333 9.37 7.11 38.83 4.30
461 999 1.067212 GCCTCGATCAATACAGACGGT 59.933 52.381 0.00 0.00 0.00 4.83
523 1438 3.980989 ACGACGCGCCCTGTGTAA 61.981 61.111 5.73 0.00 42.62 2.41
524 1439 4.710695 CACGACGCGCCCTGTGTA 62.711 66.667 5.73 0.00 42.62 2.90
532 1447 4.993945 CACTTGCACACGACGCGC 62.994 66.667 5.73 0.00 0.00 6.86
533 1448 4.354212 CCACTTGCACACGACGCG 62.354 66.667 3.53 3.53 0.00 6.01
534 1449 2.943345 CTCCACTTGCACACGACGC 61.943 63.158 0.00 0.00 0.00 5.19
535 1450 0.874175 TTCTCCACTTGCACACGACG 60.874 55.000 0.00 0.00 0.00 5.12
536 1451 0.861837 CTTCTCCACTTGCACACGAC 59.138 55.000 0.00 0.00 0.00 4.34
539 1454 1.261619 CGTTCTTCTCCACTTGCACAC 59.738 52.381 0.00 0.00 0.00 3.82
540 1455 1.134521 ACGTTCTTCTCCACTTGCACA 60.135 47.619 0.00 0.00 0.00 4.57
541 1456 1.261619 CACGTTCTTCTCCACTTGCAC 59.738 52.381 0.00 0.00 0.00 4.57
543 1458 0.868406 CCACGTTCTTCTCCACTTGC 59.132 55.000 0.00 0.00 0.00 4.01
544 1459 1.512926 CCCACGTTCTTCTCCACTTG 58.487 55.000 0.00 0.00 0.00 3.16
545 1460 0.396811 CCCCACGTTCTTCTCCACTT 59.603 55.000 0.00 0.00 0.00 3.16
546 1461 0.763223 ACCCCACGTTCTTCTCCACT 60.763 55.000 0.00 0.00 0.00 4.00
547 1462 0.108019 AACCCCACGTTCTTCTCCAC 59.892 55.000 0.00 0.00 0.00 4.02
548 1463 1.719529 TAACCCCACGTTCTTCTCCA 58.280 50.000 0.00 0.00 35.79 3.86
549 1464 3.345508 AATAACCCCACGTTCTTCTCC 57.654 47.619 0.00 0.00 35.79 3.71
551 1466 4.828829 CACTAATAACCCCACGTTCTTCT 58.171 43.478 0.00 0.00 35.79 2.85
552 1467 3.373130 GCACTAATAACCCCACGTTCTTC 59.627 47.826 0.00 0.00 35.79 2.87
553 1468 3.244630 TGCACTAATAACCCCACGTTCTT 60.245 43.478 0.00 0.00 35.79 2.52
555 1470 2.702261 TGCACTAATAACCCCACGTTC 58.298 47.619 0.00 0.00 35.79 3.95
556 1471 2.863132 TGCACTAATAACCCCACGTT 57.137 45.000 0.00 0.00 38.57 3.99
558 1473 2.872245 CTCATGCACTAATAACCCCACG 59.128 50.000 0.00 0.00 0.00 4.94
559 1474 2.618709 GCTCATGCACTAATAACCCCAC 59.381 50.000 0.00 0.00 39.41 4.61
560 1475 2.240921 TGCTCATGCACTAATAACCCCA 59.759 45.455 0.00 0.00 45.31 4.96
563 1478 3.313526 CACCTGCTCATGCACTAATAACC 59.686 47.826 0.00 0.00 45.31 2.85
564 1479 3.242870 GCACCTGCTCATGCACTAATAAC 60.243 47.826 0.00 0.00 45.31 1.89
566 1481 2.093021 TGCACCTGCTCATGCACTAATA 60.093 45.455 5.40 0.00 46.63 0.98
567 1482 1.340308 TGCACCTGCTCATGCACTAAT 60.340 47.619 5.40 0.00 46.63 1.73
568 1483 0.036590 TGCACCTGCTCATGCACTAA 59.963 50.000 5.40 0.00 46.63 2.24
569 1484 1.678724 TGCACCTGCTCATGCACTA 59.321 52.632 5.40 0.00 46.63 2.74
570 1485 2.433004 TGCACCTGCTCATGCACT 59.567 55.556 5.40 0.00 46.63 4.40
574 1489 1.001706 GTATGCATGCACCTGCTCATG 60.002 52.381 25.37 0.00 42.75 3.07
575 1490 1.315690 GTATGCATGCACCTGCTCAT 58.684 50.000 25.37 7.00 42.75 2.90
577 1492 1.091771 ACGTATGCATGCACCTGCTC 61.092 55.000 25.37 8.80 42.75 4.26
578 1493 1.078214 ACGTATGCATGCACCTGCT 60.078 52.632 25.37 9.52 42.75 4.24
580 1495 1.717791 CCCACGTATGCATGCACCTG 61.718 60.000 25.37 17.38 0.00 4.00
581 1496 1.451927 CCCACGTATGCATGCACCT 60.452 57.895 25.37 11.24 0.00 4.00
582 1497 1.439353 CTCCCACGTATGCATGCACC 61.439 60.000 25.37 15.72 0.00 5.01
583 1498 0.461870 TCTCCCACGTATGCATGCAC 60.462 55.000 25.37 10.68 0.00 4.57
584 1499 0.251634 TTCTCCCACGTATGCATGCA 59.748 50.000 25.04 25.04 0.00 3.96
585 1500 0.940126 CTTCTCCCACGTATGCATGC 59.060 55.000 11.82 11.82 0.00 4.06
587 1502 2.388735 TCTCTTCTCCCACGTATGCAT 58.611 47.619 3.79 3.79 0.00 3.96
588 1503 1.847328 TCTCTTCTCCCACGTATGCA 58.153 50.000 0.00 0.00 0.00 3.96
589 1504 2.166664 ACTTCTCTTCTCCCACGTATGC 59.833 50.000 0.00 0.00 0.00 3.14
592 1507 4.401022 TGTAACTTCTCTTCTCCCACGTA 58.599 43.478 0.00 0.00 0.00 3.57
594 1509 3.256136 ACTGTAACTTCTCTTCTCCCACG 59.744 47.826 0.00 0.00 0.00 4.94
596 1511 4.480115 TGACTGTAACTTCTCTTCTCCCA 58.520 43.478 0.00 0.00 0.00 4.37
597 1512 5.221461 TGTTGACTGTAACTTCTCTTCTCCC 60.221 44.000 0.00 0.00 0.00 4.30
598 1513 5.844004 TGTTGACTGTAACTTCTCTTCTCC 58.156 41.667 0.00 0.00 0.00 3.71
599 1514 6.508777 ACTGTTGACTGTAACTTCTCTTCTC 58.491 40.000 0.00 0.00 0.00 2.87
600 1515 6.472686 ACTGTTGACTGTAACTTCTCTTCT 57.527 37.500 0.00 0.00 0.00 2.85
717 1796 7.272084 GGAGCGCAAATATTATTTCTGCATAAG 59.728 37.037 11.47 4.34 33.19 1.73
720 1799 5.242393 AGGAGCGCAAATATTATTTCTGCAT 59.758 36.000 11.47 6.34 33.19 3.96
1051 5344 2.427245 CGGCGAGAGTGGAGGGAAT 61.427 63.158 0.00 0.00 0.00 3.01
1060 5353 0.392998 AATTTGGCATCGGCGAGAGT 60.393 50.000 17.22 0.00 42.47 3.24
1112 5405 4.436998 CCTCCACGCAGTCGGGAC 62.437 72.222 0.00 0.00 42.95 4.46
1148 5441 1.738099 GTGGTCGCATTCACGCTCT 60.738 57.895 0.00 0.00 0.00 4.09
1294 5587 3.595173 TGTATTCGCTGCTACACATGTT 58.405 40.909 0.00 0.00 0.00 2.71
1302 5595 2.006888 GCTTGGTTGTATTCGCTGCTA 58.993 47.619 0.00 0.00 0.00 3.49
1329 5622 2.872557 CGTGCGTTCTCGAGGGTA 59.127 61.111 13.56 0.00 39.71 3.69
1392 5685 2.815308 GCTAAGCTAGCCTCGCCA 59.185 61.111 12.13 0.00 45.95 5.69
1483 5776 1.602920 GCAGATGTCGCACCGATCATA 60.603 52.381 0.00 0.00 38.42 2.15
1591 5884 4.464947 TCCACACACATGTATGTTTCCAA 58.535 39.130 7.12 0.00 39.39 3.53
1631 5924 7.011389 TGTTTATCCGTTCTTGAGCAATATCAG 59.989 37.037 0.00 0.00 0.00 2.90
1699 5998 9.914834 ATAATACCAAGTTGCTATTCCTAACAA 57.085 29.630 6.69 0.00 0.00 2.83
1726 6025 6.655425 GGAAGTATATGATAGTTTTGGCCTCC 59.345 42.308 3.32 0.00 0.00 4.30
1749 6050 9.973661 TTGAGTTATCTATTTTGGAATGAAGGA 57.026 29.630 0.00 0.00 0.00 3.36
1769 6070 8.038944 TGACTCAACTTTGTACTAACTTGAGTT 58.961 33.333 27.83 19.12 44.87 3.01
1770 6071 7.553334 TGACTCAACTTTGTACTAACTTGAGT 58.447 34.615 27.69 27.69 46.57 3.41
1773 6074 8.594881 AGATGACTCAACTTTGTACTAACTTG 57.405 34.615 0.00 0.00 0.00 3.16
1780 6081 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1781 6082 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1782 6083 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1783 6084 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1784 6085 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1785 6086 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1787 6088 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1789 6090 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1790 6091 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1793 6185 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1796 6188 3.055385 CACTCCCTCCGTTCCAAAATAGA 60.055 47.826 0.00 0.00 0.00 1.98
1797 6189 3.270877 CACTCCCTCCGTTCCAAAATAG 58.729 50.000 0.00 0.00 0.00 1.73
1803 6195 1.701031 TTTGCACTCCCTCCGTTCCA 61.701 55.000 0.00 0.00 0.00 3.53
1809 6201 3.883489 GGTATGTATTTTGCACTCCCTCC 59.117 47.826 0.00 0.00 0.00 4.30
1812 6204 4.270008 AGTGGTATGTATTTTGCACTCCC 58.730 43.478 0.00 0.00 0.00 4.30
1813 6205 6.995511 TTAGTGGTATGTATTTTGCACTCC 57.004 37.500 0.00 0.00 0.00 3.85
1848 6240 7.381408 CGCGACATGTAGAGAAAATCCTATAAA 59.619 37.037 10.44 0.00 0.00 1.40
1859 6251 2.095617 TCGAAACGCGACATGTAGAGAA 60.096 45.455 15.93 0.00 45.59 2.87
1880 6272 2.477176 TTGCCGCGTTCAGTTGCTT 61.477 52.632 4.92 0.00 0.00 3.91
1882 6274 1.837538 TAGTTGCCGCGTTCAGTTGC 61.838 55.000 4.92 0.00 0.00 4.17
1954 6346 1.574339 TGGGGAAGGAGGGAGTACTAG 59.426 57.143 0.00 0.00 0.00 2.57
1973 6365 1.802715 CTTGCGCGCCCAAGATTTG 60.803 57.895 30.77 2.84 43.79 2.32
1999 6391 2.810400 GCCTTAGATTATGGGAGCGCAA 60.810 50.000 11.47 0.00 0.00 4.85
2003 6395 1.270839 TGCGCCTTAGATTATGGGAGC 60.271 52.381 4.18 0.00 43.20 4.70
2024 6416 3.013219 GAGTGGGAGAGAAAAAGGCATC 58.987 50.000 0.00 0.00 0.00 3.91
2136 6529 5.301045 TGATCCTTACCTGACCTATTGTACG 59.699 44.000 0.00 0.00 0.00 3.67
2141 6534 5.069251 CGTCTTGATCCTTACCTGACCTATT 59.931 44.000 0.00 0.00 0.00 1.73
2162 6555 0.094730 AGCACGAAAATTAGCGCGTC 59.905 50.000 8.43 0.00 34.37 5.19
2182 6575 2.876550 GTTCTTAGGCGTGTTGGTTCTT 59.123 45.455 0.00 0.00 0.00 2.52
2183 6576 2.490991 GTTCTTAGGCGTGTTGGTTCT 58.509 47.619 0.00 0.00 0.00 3.01
2184 6577 1.534163 GGTTCTTAGGCGTGTTGGTTC 59.466 52.381 0.00 0.00 0.00 3.62
2185 6578 1.134037 TGGTTCTTAGGCGTGTTGGTT 60.134 47.619 0.00 0.00 0.00 3.67
2186 6579 0.470766 TGGTTCTTAGGCGTGTTGGT 59.529 50.000 0.00 0.00 0.00 3.67
2187 6580 1.265905 GTTGGTTCTTAGGCGTGTTGG 59.734 52.381 0.00 0.00 0.00 3.77
2188 6581 1.944024 TGTTGGTTCTTAGGCGTGTTG 59.056 47.619 0.00 0.00 0.00 3.33
2189 6582 1.944709 GTGTTGGTTCTTAGGCGTGTT 59.055 47.619 0.00 0.00 0.00 3.32
2190 6583 1.589803 GTGTTGGTTCTTAGGCGTGT 58.410 50.000 0.00 0.00 0.00 4.49
2191 6584 0.511221 CGTGTTGGTTCTTAGGCGTG 59.489 55.000 0.00 0.00 0.00 5.34
2192 6585 1.226030 GCGTGTTGGTTCTTAGGCGT 61.226 55.000 0.00 0.00 0.00 5.68
2193 6586 1.495951 GCGTGTTGGTTCTTAGGCG 59.504 57.895 0.00 0.00 0.00 5.52
2194 6587 0.605589 AGGCGTGTTGGTTCTTAGGC 60.606 55.000 0.00 0.00 0.00 3.93
2195 6588 2.754946 TAGGCGTGTTGGTTCTTAGG 57.245 50.000 0.00 0.00 0.00 2.69
2196 6589 3.921677 TCTTAGGCGTGTTGGTTCTTAG 58.078 45.455 0.00 0.00 0.00 2.18
2197 6590 4.060205 GTTCTTAGGCGTGTTGGTTCTTA 58.940 43.478 0.00 0.00 0.00 2.10
2204 6597 2.601266 CGTTTGGTTCTTAGGCGTGTTG 60.601 50.000 0.00 0.00 0.00 3.33
2215 6608 0.533308 TACTTGCGGCGTTTGGTTCT 60.533 50.000 9.37 0.00 0.00 3.01
2227 6620 1.656095 GCAGAGTGCTAAGTACTTGCG 59.344 52.381 18.56 9.99 40.96 4.85
2264 6657 0.035056 AGTGGGTTAGTGCATGGCTC 60.035 55.000 0.00 0.00 0.00 4.70
2337 6730 1.475034 CGGATCCATACAAGTGGTGGG 60.475 57.143 13.41 0.00 40.27 4.61
2369 6762 1.771746 GATGGGAGCATGGGGAGGA 60.772 63.158 0.00 0.00 0.00 3.71
2487 10201 3.244976 CGTGGCTTGATTTGATTGGAAC 58.755 45.455 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.