Multiple sequence alignment - TraesCS4B01G204400

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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 TraesCS4B01G204400 chr4B 100.000 2450 0 0 1 2450 436313303 436310854 0.000000e+00 4525.0
1 TraesCS4B01G204400 chr4D 90.711 2433 137 41 62 2450 352756486 352754099 0.000000e+00 3158.0
2 TraesCS4B01G204400 chr4D 91.266 458 30 4 994 1441 30195019 30195476 1.240000e-172 616.0
3 TraesCS4B01G204400 chr4A 93.226 1299 63 14 779 2069 112766953 112768234 0.000000e+00 1888.0
4 TraesCS4B01G204400 chr4A 91.778 450 28 3 1001 1441 572846014 572845565 3.460000e-173 617.0
5 TraesCS4B01G204400 chr4A 92.821 390 21 3 2063 2450 112768810 112769194 2.130000e-155 558.0
6 TraesCS4B01G204400 chr1A 90.949 453 30 6 999 1441 400955573 400956024 1.250000e-167 599.0
7 TraesCS4B01G204400 chr1A 88.300 453 30 14 999 1441 482767992 482768431 2.790000e-144 521.0
8 TraesCS4B01G204400 chr1B 90.769 455 30 5 999 1441 344375640 344375186 4.510000e-167 597.0
9 TraesCS4B01G204400 chr1B 90.769 455 31 6 997 1441 434429747 434429294 4.510000e-167 597.0
10 TraesCS4B01G204400 chr1D 90.728 453 31 6 999 1441 321710603 321710152 5.830000e-166 593.0
11 TraesCS4B01G204400 chr1D 89.451 455 36 6 999 1441 271837819 271837365 4.570000e-157 564.0
12 TraesCS4B01G204400 chr1D 87.919 447 32 10 1000 1441 382719801 382720230 7.820000e-140 507.0
13 TraesCS4B01G204400 chr1D 84.768 151 19 4 470 617 298009132 298009281 5.460000e-32 148.0
14 TraesCS4B01G204400 chr3D 93.478 46 0 1 1001 1043 462246628 462246583 5.650000e-07 65.8
15 TraesCS4B01G204400 chr3D 93.478 46 0 1 1001 1043 462455385 462455340 5.650000e-07 65.8
16 TraesCS4B01G204400 chr3B 93.478 46 0 1 1001 1043 613811866 613811821 5.650000e-07 65.8
17 TraesCS4B01G204400 chr3A 93.478 46 0 1 1001 1043 605241241 605241196 5.650000e-07 65.8


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 TraesCS4B01G204400 chr4B 436310854 436313303 2449 True 4525 4525 100.0000 1 2450 1 chr4B.!!$R1 2449
1 TraesCS4B01G204400 chr4D 352754099 352756486 2387 True 3158 3158 90.7110 62 2450 1 chr4D.!!$R1 2388
2 TraesCS4B01G204400 chr4A 112766953 112769194 2241 False 1223 1888 93.0235 779 2450 2 chr4A.!!$F1 1671

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
349 359 0.17899 AGAACCTTGGTGTTGCCTCC 60.179 55.0 0.0 0.0 38.35 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1612 0.035439 AGCCGTCCATTACAACCTGG 60.035 55.0 0.0 0.0 0.0 4.45 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
44 45 4.519540 TTTTTGCTACCTCTGGCATTTC 57.480 40.909 0.00 0.00 38.30 2.17
45 46 2.877097 TTGCTACCTCTGGCATTTCA 57.123 45.000 0.00 0.00 38.30 2.69
46 47 2.408271 TGCTACCTCTGGCATTTCAG 57.592 50.000 0.00 0.00 33.23 3.02
47 48 1.908619 TGCTACCTCTGGCATTTCAGA 59.091 47.619 0.00 0.00 41.03 3.27
48 49 2.507058 TGCTACCTCTGGCATTTCAGAT 59.493 45.455 0.00 0.00 42.19 2.90
49 50 3.054139 TGCTACCTCTGGCATTTCAGATT 60.054 43.478 0.00 0.00 42.19 2.40
50 51 3.950395 GCTACCTCTGGCATTTCAGATTT 59.050 43.478 0.00 0.00 42.19 2.17
51 52 4.201990 GCTACCTCTGGCATTTCAGATTTG 60.202 45.833 0.00 0.00 42.19 2.32
52 53 2.494870 ACCTCTGGCATTTCAGATTTGC 59.505 45.455 0.00 0.00 42.19 3.68
53 54 2.758979 CCTCTGGCATTTCAGATTTGCT 59.241 45.455 0.00 0.00 42.19 3.91
54 55 3.428999 CCTCTGGCATTTCAGATTTGCTG 60.429 47.826 0.00 0.00 46.31 4.41
55 56 2.494471 TCTGGCATTTCAGATTTGCTGG 59.506 45.455 0.00 0.66 44.98 4.85
56 57 2.494471 CTGGCATTTCAGATTTGCTGGA 59.506 45.455 0.00 0.00 44.98 3.86
57 58 2.898612 TGGCATTTCAGATTTGCTGGAA 59.101 40.909 5.37 0.00 45.96 3.53
58 59 3.256558 GGCATTTCAGATTTGCTGGAAC 58.743 45.455 5.37 0.00 44.74 3.62
59 60 3.256558 GCATTTCAGATTTGCTGGAACC 58.743 45.455 0.00 0.00 44.74 3.62
60 61 3.056322 GCATTTCAGATTTGCTGGAACCT 60.056 43.478 0.00 0.00 44.74 3.50
66 67 3.054802 CAGATTTGCTGGAACCTACTCCT 60.055 47.826 0.00 0.00 41.07 3.69
68 69 4.971924 AGATTTGCTGGAACCTACTCCTAT 59.028 41.667 0.00 0.00 36.35 2.57
83 84 9.969001 ACCTACTCCTATTTTGTTAATTTGCTA 57.031 29.630 0.00 0.00 0.00 3.49
112 113 1.273327 GTTTGGATTGCTGGAACCAGG 59.727 52.381 20.38 4.81 43.77 4.45
140 142 3.460857 TTTTGCTACAACCGGCATTTT 57.539 38.095 0.00 0.00 38.30 1.82
160 162 0.920664 GGTTTGCTGAAACAACGCAC 59.079 50.000 2.50 0.00 42.95 5.34
170 172 5.331532 GCTGAAACAACGCACAATTTTACTC 60.332 40.000 0.00 0.00 0.00 2.59
188 191 4.749245 ACTCTTTTTGCTACCAATGACG 57.251 40.909 0.00 0.00 0.00 4.35
212 216 1.484038 TGGTTTGCTGAGCCAACTTT 58.516 45.000 18.98 0.00 35.47 2.66
228 232 5.178623 GCCAACTTTAATTTTTGCTACCACC 59.821 40.000 0.00 0.00 0.00 4.61
269 273 4.346129 GAAACATCGTCCAATCTTGCATC 58.654 43.478 0.00 0.00 0.00 3.91
288 292 4.143263 GCATCTTTGCTTCCATCGTTTTTG 60.143 41.667 0.00 0.00 45.77 2.44
289 293 3.380142 TCTTTGCTTCCATCGTTTTTGC 58.620 40.909 0.00 0.00 0.00 3.68
291 295 2.420628 TGCTTCCATCGTTTTTGCTG 57.579 45.000 0.00 0.00 0.00 4.41
305 315 1.681538 TTGCTGGAACCAACGCTAAA 58.318 45.000 6.63 0.00 0.00 1.85
311 321 3.983741 TGGAACCAACGCTAAATTTTGG 58.016 40.909 0.00 0.00 44.66 3.28
330 340 3.632333 TGGTACCATTGTTGTTGGTTGA 58.368 40.909 11.60 0.00 45.19 3.18
331 341 3.634448 TGGTACCATTGTTGTTGGTTGAG 59.366 43.478 11.60 0.00 45.19 3.02
333 343 4.339814 GGTACCATTGTTGTTGGTTGAGAA 59.660 41.667 7.15 0.00 45.19 2.87
345 355 2.492019 GTTGAGAACCTTGGTGTTGC 57.508 50.000 0.00 0.00 0.00 4.17
349 359 0.178990 AGAACCTTGGTGTTGCCTCC 60.179 55.000 0.00 0.00 38.35 4.30
359 369 3.763360 TGGTGTTGCCTCCATTAATTCTG 59.237 43.478 0.00 0.00 38.35 3.02
360 370 3.131046 GGTGTTGCCTCCATTAATTCTGG 59.869 47.826 1.34 1.34 34.93 3.86
362 372 3.011144 TGTTGCCTCCATTAATTCTGGGA 59.989 43.478 7.04 0.54 34.36 4.37
401 418 2.595463 AGGGGTGAACGTCGACGA 60.595 61.111 41.52 19.40 43.02 4.20
437 454 0.889186 AAGACGGATGGGTGTTGTGC 60.889 55.000 0.00 0.00 0.00 4.57
456 473 3.966930 GACACGGAGGAGGAGGGCT 62.967 68.421 0.00 0.00 0.00 5.19
482 499 4.811557 CCATGTCTCCCGAGTTTTCTTATC 59.188 45.833 0.00 0.00 0.00 1.75
495 512 7.955324 CGAGTTTTCTTATCAGATTTTTACGCA 59.045 33.333 0.00 0.00 0.00 5.24
496 513 9.607285 GAGTTTTCTTATCAGATTTTTACGCAA 57.393 29.630 0.00 0.00 0.00 4.85
512 529 2.556622 ACGCAAAGACGATTGGGATTTT 59.443 40.909 18.39 0.81 43.65 1.82
513 530 3.171277 CGCAAAGACGATTGGGATTTTC 58.829 45.455 10.24 0.00 43.65 2.29
514 531 3.511699 GCAAAGACGATTGGGATTTTCC 58.488 45.455 0.00 0.00 35.23 3.13
523 540 6.826668 ACGATTGGGATTTTCCTTTTCTTTT 58.173 32.000 0.00 0.00 36.57 2.27
566 583 4.257731 TGTGATTTTATCCAACGCTAGCA 58.742 39.130 16.45 0.00 0.00 3.49
582 599 2.713967 GCATGCTGAACGGCCCAAT 61.714 57.895 11.37 0.00 0.00 3.16
585 602 0.532115 ATGCTGAACGGCCCAATTTC 59.468 50.000 0.00 0.00 0.00 2.17
586 603 1.154035 GCTGAACGGCCCAATTTCG 60.154 57.895 0.00 0.00 0.00 3.46
587 604 1.154035 CTGAACGGCCCAATTTCGC 60.154 57.895 0.00 0.00 0.00 4.70
588 605 2.180769 GAACGGCCCAATTTCGCC 59.819 61.111 0.00 2.87 42.05 5.54
593 610 3.822192 GCCCAATTTCGCCCGGTC 61.822 66.667 0.00 0.00 0.00 4.79
594 611 3.138128 CCCAATTTCGCCCGGTCC 61.138 66.667 0.00 0.00 0.00 4.46
613 631 2.526120 GCCGGTGTCTAGCATTCGC 61.526 63.158 1.90 0.00 38.99 4.70
673 694 6.622427 AGCTTTTTAGTAGAAAGGCTAGGA 57.378 37.500 13.43 0.00 46.15 2.94
677 698 6.930068 TTTTAGTAGAAAGGCTAGGAGTGT 57.070 37.500 0.00 0.00 0.00 3.55
684 705 4.347000 AGAAAGGCTAGGAGTGTGTTTACA 59.653 41.667 0.00 0.00 0.00 2.41
745 782 4.685924 GCCATCAATTTTGTCACCCATAG 58.314 43.478 0.00 0.00 0.00 2.23
751 788 0.623723 TTTGTCACCCATAGGAGCCC 59.376 55.000 0.00 0.00 36.73 5.19
753 790 2.064581 GTCACCCATAGGAGCCCGT 61.065 63.158 0.00 0.00 36.73 5.28
760 797 1.379527 CATAGGAGCCCGTGGAAAAC 58.620 55.000 0.00 0.00 0.00 2.43
761 798 0.255033 ATAGGAGCCCGTGGAAAACC 59.745 55.000 0.00 0.00 0.00 3.27
770 807 1.890510 GTGGAAAACCGAGGCACGT 60.891 57.895 3.22 0.00 40.78 4.49
777 814 1.827399 AACCGAGGCACGTCCATCTT 61.827 55.000 3.22 0.00 40.78 2.40
880 917 2.354729 CAATCCCCTTCCACCGCA 59.645 61.111 0.00 0.00 0.00 5.69
968 1005 1.750399 CGCCCATTTCCCTCCACAG 60.750 63.158 0.00 0.00 0.00 3.66
1076 1113 0.973496 GAGAAGGCCGAGAAGACCCT 60.973 60.000 0.00 0.00 0.00 4.34
1107 1144 4.394712 CCCAAGGCGGAGAAGCGT 62.395 66.667 0.00 0.00 36.56 5.07
1188 1225 1.629043 AGAGCGTGGAGACCTACAAA 58.371 50.000 0.00 0.00 0.00 2.83
1520 1557 2.292916 GCTTTTGTGTTGCCGTCGC 61.293 57.895 0.00 0.00 0.00 5.19
1522 1559 0.248458 CTTTTGTGTTGCCGTCGCTT 60.248 50.000 0.00 0.00 35.36 4.68
1535 1572 0.235665 GTCGCTTGTGTCCATGTGTG 59.764 55.000 0.00 0.00 0.00 3.82
1554 1591 4.578105 GTGTGTCGTTATAGGTAGGTAGCT 59.422 45.833 0.00 0.00 37.80 3.32
1557 1594 4.061596 GTCGTTATAGGTAGGTAGCTCGT 58.938 47.826 0.00 0.00 35.39 4.18
1575 1612 2.156891 TCGTCTGCTTTGTAAATCGTGC 59.843 45.455 0.00 0.00 0.00 5.34
1584 1621 3.404224 TGTAAATCGTGCCAGGTTGTA 57.596 42.857 0.00 0.00 0.00 2.41
1605 1642 3.855689 ATGGACGGCTTTGATTTCAAG 57.144 42.857 0.00 0.00 37.15 3.02
1608 1645 3.500680 TGGACGGCTTTGATTTCAAGTAC 59.499 43.478 0.00 0.00 37.15 2.73
1610 1647 4.933400 GGACGGCTTTGATTTCAAGTACTA 59.067 41.667 0.00 0.00 37.15 1.82
1611 1648 5.410439 GGACGGCTTTGATTTCAAGTACTAA 59.590 40.000 0.00 0.00 37.15 2.24
1612 1649 6.093633 GGACGGCTTTGATTTCAAGTACTAAT 59.906 38.462 0.00 0.00 37.15 1.73
1613 1650 6.842163 ACGGCTTTGATTTCAAGTACTAATG 58.158 36.000 0.00 0.00 37.15 1.90
1618 1655 7.336931 GCTTTGATTTCAAGTACTAATGGAGGA 59.663 37.037 0.00 0.00 37.15 3.71
1619 1656 8.792830 TTTGATTTCAAGTACTAATGGAGGAG 57.207 34.615 0.00 0.00 37.15 3.69
1620 1657 7.496346 TGATTTCAAGTACTAATGGAGGAGT 57.504 36.000 0.00 0.00 0.00 3.85
1625 1662 7.786046 TCAAGTACTAATGGAGGAGTTTGTA 57.214 36.000 0.00 0.00 27.90 2.41
1630 1667 5.186198 ACTAATGGAGGAGTTTGTATGTGC 58.814 41.667 0.00 0.00 0.00 4.57
1634 1671 3.181434 TGGAGGAGTTTGTATGTGCCTTT 60.181 43.478 0.00 0.00 0.00 3.11
1644 1681 2.642139 ATGTGCCTTTTCAATCTGCG 57.358 45.000 0.00 0.00 0.00 5.18
1654 1691 1.136147 CAATCTGCGAGCTGTTGCC 59.864 57.895 0.00 0.00 40.80 4.52
1663 1700 1.818642 GAGCTGTTGCCTCATTCTGT 58.181 50.000 0.00 0.00 40.80 3.41
1697 1735 3.375699 GATCTAGGGTTTGAGGGAGTGA 58.624 50.000 0.00 0.00 0.00 3.41
1706 1744 0.962855 TGAGGGAGTGAGTGCTCGAG 60.963 60.000 8.45 8.45 36.41 4.04
1707 1745 2.183046 GGGAGTGAGTGCTCGAGC 59.817 66.667 30.42 30.42 42.50 5.03
1708 1746 2.347322 GGGAGTGAGTGCTCGAGCT 61.347 63.158 35.27 18.95 42.66 4.09
1753 1791 0.877649 CCGATGATGTTGCGAGGAGG 60.878 60.000 0.00 0.00 0.00 4.30
1754 1792 0.877649 CGATGATGTTGCGAGGAGGG 60.878 60.000 0.00 0.00 0.00 4.30
1755 1793 0.465705 GATGATGTTGCGAGGAGGGA 59.534 55.000 0.00 0.00 0.00 4.20
1766 1804 0.030603 GAGGAGGGAGGAGGGTGATT 60.031 60.000 0.00 0.00 0.00 2.57
1808 1846 1.001641 GTCCCATGGCTTCAGCACT 60.002 57.895 6.09 0.00 44.36 4.40
1902 1944 4.009675 ACTTGTATGCGATGAATTGGTGT 58.990 39.130 0.00 0.00 0.00 4.16
1927 1973 8.822855 GTTGTGTGATTATGGTGACGATTATTA 58.177 33.333 0.00 0.00 0.00 0.98
1933 1979 8.093927 TGATTATGGTGACGATTATTATCTGCA 58.906 33.333 0.00 0.00 0.00 4.41
1936 1982 5.670485 TGGTGACGATTATTATCTGCAACT 58.330 37.500 0.00 0.00 0.00 3.16
2016 2062 0.254462 TTGAGCACTGGTTGGTGTGA 59.746 50.000 0.00 0.00 39.21 3.58
2082 2712 2.175499 AGCTTTAGCATGCCAGGGAATA 59.825 45.455 15.66 0.00 45.16 1.75
2102 2732 3.550437 ATTTCGAGCCTGCTACTGATT 57.450 42.857 0.00 0.00 0.00 2.57
2103 2733 3.334583 TTTCGAGCCTGCTACTGATTT 57.665 42.857 0.00 0.00 0.00 2.17
2206 2841 2.353610 GGCTGGATGGGTTTGCCTG 61.354 63.158 0.00 0.00 40.36 4.85
2211 2846 1.305930 GGATGGGTTTGCCTGACGTC 61.306 60.000 9.11 9.11 34.45 4.34
2220 2855 2.542020 TGCCTGACGTCATCTTTTCA 57.458 45.000 20.40 7.92 0.00 2.69
2243 2878 6.369890 TCATTGTTCTAGTGCTGATGAAGTTC 59.630 38.462 0.00 0.00 0.00 3.01
2253 2888 3.079578 CTGATGAAGTTCCACACATGCT 58.920 45.455 0.00 0.00 0.00 3.79
2316 2951 2.352388 GCCAGTACAATTTGTAGCCGA 58.648 47.619 9.49 0.00 32.84 5.54
2422 3057 3.873361 TCTTGGATGAAATGTCTGCGATC 59.127 43.478 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.894427 TGAAATGCCAGAGGTAGCAAAAA 59.106 39.130 0.00 0.00 43.36 1.94
24 25 3.495331 TGAAATGCCAGAGGTAGCAAAA 58.505 40.909 0.00 0.00 43.36 2.44
25 26 3.084039 CTGAAATGCCAGAGGTAGCAAA 58.916 45.455 0.00 0.00 43.36 3.68
26 27 2.305635 TCTGAAATGCCAGAGGTAGCAA 59.694 45.455 0.00 0.00 43.36 3.91
27 28 1.908619 TCTGAAATGCCAGAGGTAGCA 59.091 47.619 0.00 0.00 44.45 3.49
28 29 2.698855 TCTGAAATGCCAGAGGTAGC 57.301 50.000 0.00 0.00 38.18 3.58
29 30 4.201990 GCAAATCTGAAATGCCAGAGGTAG 60.202 45.833 6.74 0.00 45.27 3.18
30 31 3.696051 GCAAATCTGAAATGCCAGAGGTA 59.304 43.478 6.74 0.00 45.27 3.08
31 32 2.494870 GCAAATCTGAAATGCCAGAGGT 59.505 45.455 6.74 0.00 45.27 3.85
32 33 2.758979 AGCAAATCTGAAATGCCAGAGG 59.241 45.455 12.61 0.00 45.27 3.69
33 34 3.428999 CCAGCAAATCTGAAATGCCAGAG 60.429 47.826 12.61 3.66 45.27 3.35
34 35 2.494471 CCAGCAAATCTGAAATGCCAGA 59.506 45.455 12.61 0.00 45.72 3.86
35 36 2.494471 TCCAGCAAATCTGAAATGCCAG 59.506 45.455 12.61 7.43 45.72 4.85
36 37 2.527497 TCCAGCAAATCTGAAATGCCA 58.473 42.857 12.61 0.00 45.72 4.92
37 38 3.256558 GTTCCAGCAAATCTGAAATGCC 58.743 45.455 12.61 0.00 45.72 4.40
38 39 3.056322 AGGTTCCAGCAAATCTGAAATGC 60.056 43.478 9.29 9.29 45.72 3.56
39 40 4.796038 AGGTTCCAGCAAATCTGAAATG 57.204 40.909 0.00 0.00 45.72 2.32
40 41 5.574188 AGTAGGTTCCAGCAAATCTGAAAT 58.426 37.500 0.00 0.00 45.72 2.17
41 42 4.985538 AGTAGGTTCCAGCAAATCTGAAA 58.014 39.130 0.00 0.00 45.72 2.69
42 43 4.565652 GGAGTAGGTTCCAGCAAATCTGAA 60.566 45.833 0.00 0.00 45.72 3.02
43 44 3.055094 GGAGTAGGTTCCAGCAAATCTGA 60.055 47.826 0.00 0.00 45.72 3.27
44 45 3.054802 AGGAGTAGGTTCCAGCAAATCTG 60.055 47.826 0.00 0.00 39.84 2.90
45 46 3.185455 AGGAGTAGGTTCCAGCAAATCT 58.815 45.455 0.00 0.00 39.84 2.40
46 47 3.636153 AGGAGTAGGTTCCAGCAAATC 57.364 47.619 0.00 0.00 39.84 2.17
47 48 5.717119 AATAGGAGTAGGTTCCAGCAAAT 57.283 39.130 0.00 0.00 39.84 2.32
48 49 5.514500 AAATAGGAGTAGGTTCCAGCAAA 57.486 39.130 0.00 0.00 39.84 3.68
49 50 5.222048 ACAAAATAGGAGTAGGTTCCAGCAA 60.222 40.000 0.00 0.00 39.84 3.91
50 51 4.288626 ACAAAATAGGAGTAGGTTCCAGCA 59.711 41.667 0.00 0.00 39.84 4.41
51 52 4.844884 ACAAAATAGGAGTAGGTTCCAGC 58.155 43.478 0.00 0.00 39.84 4.85
52 53 9.462606 AATTAACAAAATAGGAGTAGGTTCCAG 57.537 33.333 0.00 0.00 39.84 3.86
53 54 9.816787 AAATTAACAAAATAGGAGTAGGTTCCA 57.183 29.630 0.00 0.00 39.84 3.53
55 56 9.569167 GCAAATTAACAAAATAGGAGTAGGTTC 57.431 33.333 0.00 0.00 0.00 3.62
56 57 9.309224 AGCAAATTAACAAAATAGGAGTAGGTT 57.691 29.630 0.00 0.00 0.00 3.50
57 58 8.879427 AGCAAATTAACAAAATAGGAGTAGGT 57.121 30.769 0.00 0.00 0.00 3.08
60 61 8.885722 CGGTAGCAAATTAACAAAATAGGAGTA 58.114 33.333 0.00 0.00 0.00 2.59
66 67 7.276658 CATTGGCGGTAGCAAATTAACAAAATA 59.723 33.333 0.00 0.00 44.23 1.40
68 69 5.406780 CATTGGCGGTAGCAAATTAACAAAA 59.593 36.000 0.00 0.00 44.23 2.44
133 135 2.941720 TGTTTCAGCAAACCAAAATGCC 59.058 40.909 0.00 0.00 43.57 4.40
140 142 0.528017 TGCGTTGTTTCAGCAAACCA 59.472 45.000 0.00 0.00 41.25 3.67
160 162 9.474920 TCATTGGTAGCAAAAAGAGTAAAATTG 57.525 29.630 12.00 0.81 0.00 2.32
170 172 6.410038 CAAAAACGTCATTGGTAGCAAAAAG 58.590 36.000 12.00 7.93 0.00 2.27
188 191 2.307934 TGGCTCAGCAAACCAAAAAC 57.692 45.000 0.00 0.00 0.00 2.43
212 216 3.488363 ACACCGGTGGTAGCAAAAATTA 58.512 40.909 36.47 0.00 32.11 1.40
247 251 3.829886 TGCAAGATTGGACGATGTTTC 57.170 42.857 0.00 0.00 0.00 2.78
248 252 4.012374 AGATGCAAGATTGGACGATGTTT 58.988 39.130 0.00 0.00 0.00 2.83
249 253 3.614092 AGATGCAAGATTGGACGATGTT 58.386 40.909 0.00 0.00 0.00 2.71
269 273 3.182972 CAGCAAAAACGATGGAAGCAAAG 59.817 43.478 0.00 0.00 0.00 2.77
288 292 3.297830 AAATTTAGCGTTGGTTCCAGC 57.702 42.857 0.00 0.00 0.00 4.85
289 293 3.987220 CCAAAATTTAGCGTTGGTTCCAG 59.013 43.478 0.00 0.00 37.59 3.86
330 340 3.421567 GAGGCAACACCAAGGTTCT 57.578 52.632 0.00 0.00 43.14 3.01
339 349 3.131046 CCCAGAATTAATGGAGGCAACAC 59.869 47.826 10.16 0.00 40.51 3.32
340 350 3.011144 TCCCAGAATTAATGGAGGCAACA 59.989 43.478 10.16 0.00 40.51 3.33
341 351 3.631250 TCCCAGAATTAATGGAGGCAAC 58.369 45.455 10.16 0.00 40.51 4.17
343 353 3.582998 CTCCCAGAATTAATGGAGGCA 57.417 47.619 10.16 0.00 40.59 4.75
401 418 0.732880 CTTTCGCTGTCGACCATCGT 60.733 55.000 14.12 0.00 45.43 3.73
414 431 0.953960 AACACCCATCCGTCTTTCGC 60.954 55.000 0.00 0.00 38.35 4.70
418 435 0.889186 GCACAACACCCATCCGTCTT 60.889 55.000 0.00 0.00 0.00 3.01
423 440 1.599518 TGTCGCACAACACCCATCC 60.600 57.895 0.00 0.00 0.00 3.51
437 454 3.141488 CCCTCCTCCTCCGTGTCG 61.141 72.222 0.00 0.00 0.00 4.35
456 473 1.488705 AAACTCGGGAGACATGGGCA 61.489 55.000 2.08 0.00 33.60 5.36
458 475 1.279271 AGAAAACTCGGGAGACATGGG 59.721 52.381 2.08 0.00 33.60 4.00
459 476 2.770164 AGAAAACTCGGGAGACATGG 57.230 50.000 2.08 0.00 33.60 3.66
482 499 5.283717 CCAATCGTCTTTGCGTAAAAATCTG 59.716 40.000 0.00 0.00 0.00 2.90
495 512 6.267699 AGAAAAGGAAAATCCCAATCGTCTTT 59.732 34.615 0.00 0.00 37.19 2.52
496 513 5.775195 AGAAAAGGAAAATCCCAATCGTCTT 59.225 36.000 0.00 0.00 37.19 3.01
512 529 7.316640 CGTCAGATCTAGAGAAAAGAAAAGGA 58.683 38.462 0.00 0.00 0.00 3.36
513 530 6.533367 CCGTCAGATCTAGAGAAAAGAAAAGG 59.467 42.308 0.00 0.00 0.00 3.11
514 531 7.093992 ACCGTCAGATCTAGAGAAAAGAAAAG 58.906 38.462 0.00 0.00 0.00 2.27
523 540 5.297029 CACATGTAACCGTCAGATCTAGAGA 59.703 44.000 0.00 0.00 0.00 3.10
533 550 6.174049 TGGATAAAATCACATGTAACCGTCA 58.826 36.000 0.00 0.00 0.00 4.35
566 583 0.532115 GAAATTGGGCCGTTCAGCAT 59.468 50.000 0.00 0.00 0.00 3.79
590 607 4.509737 GCTAGACACCGGCGGACC 62.510 72.222 35.78 19.95 0.00 4.46
592 609 2.292794 GAATGCTAGACACCGGCGGA 62.293 60.000 35.78 8.83 0.00 5.54
593 610 1.883084 GAATGCTAGACACCGGCGG 60.883 63.158 27.06 27.06 0.00 6.13
594 611 2.230940 CGAATGCTAGACACCGGCG 61.231 63.158 0.00 0.00 0.00 6.46
600 618 5.023533 AGAATTAAGGCGAATGCTAGACA 57.976 39.130 0.00 0.00 42.25 3.41
602 620 4.745125 CGAAGAATTAAGGCGAATGCTAGA 59.255 41.667 0.00 0.00 42.25 2.43
652 673 7.332182 CACACTCCTAGCCTTTCTACTAAAAAG 59.668 40.741 0.00 0.00 34.25 2.27
661 682 4.347000 TGTAAACACACTCCTAGCCTTTCT 59.653 41.667 0.00 0.00 0.00 2.52
690 711 6.146898 GCGTGGTATTTTTGCTTTCTTTCTA 58.853 36.000 0.00 0.00 0.00 2.10
745 782 3.053896 CGGTTTTCCACGGGCTCC 61.054 66.667 0.00 0.00 40.70 4.70
751 788 2.943653 GTGCCTCGGTTTTCCACG 59.056 61.111 0.00 0.00 40.70 4.94
753 790 1.595929 GACGTGCCTCGGTTTTCCA 60.596 57.895 0.00 0.00 44.69 3.53
760 797 1.519455 GAAGATGGACGTGCCTCGG 60.519 63.158 4.04 0.00 44.69 4.63
761 798 0.179100 ATGAAGATGGACGTGCCTCG 60.179 55.000 4.04 0.00 46.00 4.63
770 807 1.482182 CACGGTGGAGATGAAGATGGA 59.518 52.381 0.00 0.00 0.00 3.41
777 814 1.591703 GAGTGCACGGTGGAGATGA 59.408 57.895 12.01 0.00 0.00 2.92
806 843 2.359478 GTGTGGGGCGTCGGATTT 60.359 61.111 0.00 0.00 0.00 2.17
880 917 4.031611 GGAGGGGATTAATATAGAGGCGT 58.968 47.826 0.00 0.00 0.00 5.68
968 1005 2.743928 CTTGAGGTGTCGGGCTGC 60.744 66.667 0.00 0.00 0.00 5.25
1107 1144 4.373116 GACTTGGACGCCGGCAGA 62.373 66.667 28.98 2.98 0.00 4.26
1188 1225 5.426689 TGAGCACCTTGAAGATGTAGATT 57.573 39.130 0.00 0.00 0.00 2.40
1520 1557 1.581934 ACGACACACATGGACACAAG 58.418 50.000 0.00 0.00 0.00 3.16
1522 1559 2.892784 TAACGACACACATGGACACA 57.107 45.000 0.00 0.00 0.00 3.72
1535 1572 4.061596 ACGAGCTACCTACCTATAACGAC 58.938 47.826 0.00 0.00 0.00 4.34
1554 1591 2.156891 GCACGATTTACAAAGCAGACGA 59.843 45.455 0.00 0.00 0.00 4.20
1557 1594 2.483877 CTGGCACGATTTACAAAGCAGA 59.516 45.455 0.00 0.00 0.00 4.26
1575 1612 0.035439 AGCCGTCCATTACAACCTGG 60.035 55.000 0.00 0.00 0.00 4.45
1584 1621 3.573967 ACTTGAAATCAAAGCCGTCCATT 59.426 39.130 0.00 0.00 35.15 3.16
1605 1642 6.258068 GCACATACAAACTCCTCCATTAGTAC 59.742 42.308 0.00 0.00 0.00 2.73
1608 1645 4.576463 GGCACATACAAACTCCTCCATTAG 59.424 45.833 0.00 0.00 0.00 1.73
1610 1647 3.010584 AGGCACATACAAACTCCTCCATT 59.989 43.478 0.00 0.00 0.00 3.16
1611 1648 2.578021 AGGCACATACAAACTCCTCCAT 59.422 45.455 0.00 0.00 0.00 3.41
1612 1649 1.985159 AGGCACATACAAACTCCTCCA 59.015 47.619 0.00 0.00 0.00 3.86
1613 1650 2.789409 AGGCACATACAAACTCCTCC 57.211 50.000 0.00 0.00 0.00 4.30
1618 1655 6.449698 CAGATTGAAAAGGCACATACAAACT 58.550 36.000 0.00 0.00 0.00 2.66
1619 1656 5.119125 GCAGATTGAAAAGGCACATACAAAC 59.881 40.000 0.00 0.00 0.00 2.93
1620 1657 5.229423 GCAGATTGAAAAGGCACATACAAA 58.771 37.500 0.00 0.00 0.00 2.83
1625 1662 2.161855 TCGCAGATTGAAAAGGCACAT 58.838 42.857 0.00 0.00 0.00 3.21
1630 1667 1.808945 ACAGCTCGCAGATTGAAAAGG 59.191 47.619 0.00 0.00 33.89 3.11
1634 1671 0.518636 GCAACAGCTCGCAGATTGAA 59.481 50.000 0.00 0.00 33.89 2.69
1644 1681 1.736681 GACAGAATGAGGCAACAGCTC 59.263 52.381 0.00 0.00 39.69 4.09
1654 1691 7.504911 AGATCCCCAATTATTTGACAGAATGAG 59.495 37.037 0.00 0.00 41.26 2.90
1663 1700 6.606241 AACCCTAGATCCCCAATTATTTGA 57.394 37.500 0.00 0.00 34.60 2.69
1753 1791 1.679032 CCAAACGAATCACCCTCCTCC 60.679 57.143 0.00 0.00 0.00 4.30
1754 1792 1.739067 CCAAACGAATCACCCTCCTC 58.261 55.000 0.00 0.00 0.00 3.71
1755 1793 0.322546 GCCAAACGAATCACCCTCCT 60.323 55.000 0.00 0.00 0.00 3.69
1790 1828 1.001641 AGTGCTGAAGCCATGGGAC 60.002 57.895 15.13 0.00 41.18 4.46
1808 1846 5.733676 TGCTTACTGCTCACAAATATCTCA 58.266 37.500 0.00 0.00 43.37 3.27
1836 1874 2.041755 GGAATGGGGAGAAAACAGAGGT 59.958 50.000 0.00 0.00 0.00 3.85
1902 1944 7.857734 AATAATCGTCACCATAATCACACAA 57.142 32.000 0.00 0.00 0.00 3.33
1927 1973 2.490903 GCATGAACCAGAAGTTGCAGAT 59.509 45.455 0.00 0.00 39.40 2.90
1933 1979 2.300152 TCTCGAGCATGAACCAGAAGTT 59.700 45.455 7.81 0.00 43.07 2.66
1936 1982 1.895798 ACTCTCGAGCATGAACCAGAA 59.104 47.619 7.81 0.00 0.00 3.02
2016 2062 0.251341 AAAGCAAAGGAGACCGGCAT 60.251 50.000 0.00 0.00 0.00 4.40
2082 2712 3.550437 AATCAGTAGCAGGCTCGAAAT 57.450 42.857 0.00 0.00 0.00 2.17
2103 2733 9.784531 CAAAGGAATCATATTCTAAAGCTCCTA 57.215 33.333 0.00 0.00 30.60 2.94
2206 2841 7.230222 CACTAGAACAATGAAAAGATGACGTC 58.770 38.462 9.11 9.11 0.00 4.34
2211 2846 7.137490 TCAGCACTAGAACAATGAAAAGATG 57.863 36.000 0.00 0.00 0.00 2.90
2220 2855 5.645497 GGAACTTCATCAGCACTAGAACAAT 59.355 40.000 0.00 0.00 0.00 2.71
2243 2878 3.943381 ACATAATCAGTCAGCATGTGTGG 59.057 43.478 0.00 0.00 37.40 4.17
2253 2888 5.323371 TCATCGACACACATAATCAGTCA 57.677 39.130 0.00 0.00 0.00 3.41
2316 2951 3.893326 ACTTTTGGCAGAAGCAACTTT 57.107 38.095 16.88 0.00 44.61 2.66
2387 3022 4.129380 TCATCCAAGATGATAAAGTGCCG 58.871 43.478 3.17 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.