Multiple sequence alignment - TraesCS4D01G194300

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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 TraesCS4D01G194300 chr4D 100.000 5260 0 0 1 5260 337261201 337255942 0.000000e+00 9714
1 TraesCS4D01G194300 chr4D 84.307 548 78 6 4713 5260 496090630 496091169 3.610000e-146 529
2 TraesCS4D01G194300 chr4D 86.923 260 32 2 4718 4976 496096298 496096040 1.850000e-74 291
3 TraesCS4D01G194300 chr4D 86.517 267 31 5 4718 4984 337154176 337154437 6.660000e-74 289
4 TraesCS4D01G194300 chr4D 90.909 110 6 3 708 817 480824293 480824188 1.530000e-30 145
5 TraesCS4D01G194300 chr4B 93.901 3361 144 29 1548 4868 416439753 416436414 0.000000e+00 5014
6 TraesCS4D01G194300 chr4B 90.842 1365 52 28 3 1306 416441312 416439960 0.000000e+00 1760
7 TraesCS4D01G194300 chr4B 90.601 383 35 1 4878 5260 416415897 416415516 1.690000e-139 507
8 TraesCS4D01G194300 chr4B 86.154 260 35 1 4719 4977 416307243 416307502 4.010000e-71 279
9 TraesCS4D01G194300 chr4B 93.069 101 5 2 709 809 608669008 608668910 4.240000e-31 147
10 TraesCS4D01G194300 chr4A 92.760 2569 121 30 2740 5260 135357234 135359785 0.000000e+00 3653
11 TraesCS4D01G194300 chr4A 95.115 1310 44 12 1441 2748 135355675 135356966 0.000000e+00 2047
12 TraesCS4D01G194300 chr4A 92.921 1342 49 17 2 1306 135354200 135355532 0.000000e+00 1910
13 TraesCS4D01G194300 chr1B 82.792 523 82 5 4739 5260 139675687 139676202 1.330000e-125 460
14 TraesCS4D01G194300 chr2D 83.983 462 67 6 4803 5260 7147106 7146648 2.250000e-118 436
15 TraesCS4D01G194300 chr3D 87.200 250 30 2 4715 4963 554391410 554391658 3.100000e-72 283
16 TraesCS4D01G194300 chr3A 89.041 219 24 0 4718 4936 19637404 19637186 6.710000e-69 272
17 TraesCS4D01G194300 chr5B 82.323 198 28 6 5064 5260 429303847 429304038 1.170000e-36 165
18 TraesCS4D01G194300 chr6D 100.000 82 0 0 710 791 82588540 82588621 9.120000e-33 152
19 TraesCS4D01G194300 chr6D 100.000 82 0 0 710 791 82589113 82589194 9.120000e-33 152
20 TraesCS4D01G194300 chr6D 87.692 130 7 8 688 815 63710359 63710481 5.490000e-30 143
21 TraesCS4D01G194300 chr6B 92.381 105 7 1 685 788 136804229 136804333 1.180000e-31 148
22 TraesCS4D01G194300 chr5A 96.667 90 2 1 710 799 395758496 395758408 1.180000e-31 148


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 TraesCS4D01G194300 chr4D 337255942 337261201 5259 True 9714.000000 9714 100.000000 1 5260 1 chr4D.!!$R1 5259
1 TraesCS4D01G194300 chr4D 496090630 496091169 539 False 529.000000 529 84.307000 4713 5260 1 chr4D.!!$F2 547
2 TraesCS4D01G194300 chr4B 416436414 416441312 4898 True 3387.000000 5014 92.371500 3 4868 2 chr4B.!!$R3 4865
3 TraesCS4D01G194300 chr4A 135354200 135359785 5585 False 2536.666667 3653 93.598667 2 5260 3 chr4A.!!$F1 5258
4 TraesCS4D01G194300 chr1B 139675687 139676202 515 False 460.000000 460 82.792000 4739 5260 1 chr1B.!!$F1 521

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
508 521 1.740296 CGTCATGTTCGGGACCACC 60.740 63.158 0.00 0.00 0.00 4.61 F
1132 1202 1.153429 CTAAAACCCTAGCGCGCCT 60.153 57.895 30.33 17.79 0.00 5.52 F
1608 1731 0.036306 GTGAGTTGGGGTGATTCGGT 59.964 55.000 0.00 0.00 0.00 4.69 F
2921 3328 0.323360 GTGGAGGGGTTAATGCAGCA 60.323 55.000 0.00 0.00 0.00 4.41 F
3192 3599 0.698238 AACCATTGCCCAGAGCTACA 59.302 50.000 0.00 0.00 44.23 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1514 1637 0.177836 GGTGCCACTTTTTGCAAGGT 59.822 50.0 0.00 0.00 39.57 3.50 R
1936 2059 1.243342 CGCCCTGCACATTTCCTTCA 61.243 55.0 0.00 0.00 0.00 3.02 R
3174 3581 0.035056 GTGTAGCTCTGGGCAATGGT 60.035 55.0 0.74 0.00 44.79 3.55 R
4100 4529 0.179000 ACCTTAGCTCCATTGCGAGG 59.821 55.0 0.00 0.00 42.57 4.63 R
4313 4743 0.533755 CGATGTGGCCCATCCTTCTC 60.534 60.0 21.54 4.97 46.10 2.87 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
85 89 3.435186 GCGGAGGCACAGGAAAGC 61.435 66.667 0.00 0.00 39.62 3.51
259 263 4.016706 CCGGCGGACAAGAAGGGT 62.017 66.667 24.41 0.00 0.00 4.34
508 521 1.740296 CGTCATGTTCGGGACCACC 60.740 63.158 0.00 0.00 0.00 4.61
647 684 6.730960 ACACCGTGATTGTACGAATTAAAT 57.269 33.333 5.28 0.00 46.46 1.40
799 854 3.064958 CAGCAGCCACATCTCACTATTTG 59.935 47.826 0.00 0.00 0.00 2.32
858 925 4.526262 GGCTCTGATTAGCTCTTATGGAGA 59.474 45.833 0.00 0.00 44.45 3.71
1045 1114 2.892640 CCGCTCCATCGACTTCCA 59.107 61.111 0.00 0.00 0.00 3.53
1090 1160 2.202566 CCTTTTCCTCGTCTAATCGGC 58.797 52.381 0.00 0.00 0.00 5.54
1132 1202 1.153429 CTAAAACCCTAGCGCGCCT 60.153 57.895 30.33 17.79 0.00 5.52
1140 1210 3.477224 CTAGCGCGCCTCTGTCTCC 62.477 68.421 30.33 0.00 0.00 3.71
1158 1228 2.676471 AACCATTCCGTGCAGGCC 60.676 61.111 0.00 0.00 40.77 5.19
1160 1230 4.738998 CCATTCCGTGCAGGCCCA 62.739 66.667 0.00 0.00 40.77 5.36
1162 1232 4.431131 ATTCCGTGCAGGCCCAGG 62.431 66.667 0.00 0.00 40.77 4.45
1313 1435 2.343387 GTGCGCCCCATTGCTTTT 59.657 55.556 4.18 0.00 0.00 2.27
1321 1443 1.614317 CCCCATTGCTTTTCGTCTCCT 60.614 52.381 0.00 0.00 0.00 3.69
1336 1458 4.021104 TCGTCTCCTCTGTGAATTTGATGT 60.021 41.667 0.00 0.00 0.00 3.06
1337 1459 4.328440 CGTCTCCTCTGTGAATTTGATGTC 59.672 45.833 0.00 0.00 0.00 3.06
1338 1460 4.633565 GTCTCCTCTGTGAATTTGATGTCC 59.366 45.833 0.00 0.00 0.00 4.02
1339 1461 3.944015 CTCCTCTGTGAATTTGATGTCCC 59.056 47.826 0.00 0.00 0.00 4.46
1340 1462 3.330405 TCCTCTGTGAATTTGATGTCCCA 59.670 43.478 0.00 0.00 0.00 4.37
1341 1463 4.081406 CCTCTGTGAATTTGATGTCCCAA 58.919 43.478 0.00 0.00 0.00 4.12
1342 1464 4.082571 CCTCTGTGAATTTGATGTCCCAAC 60.083 45.833 0.00 0.00 0.00 3.77
1347 1469 4.761739 GTGAATTTGATGTCCCAACTCTCA 59.238 41.667 0.00 0.00 0.00 3.27
1361 1483 3.777106 ACTCTCAAGACAAGCATTCCA 57.223 42.857 0.00 0.00 0.00 3.53
1400 1522 4.406943 GTCATCTGATTCGGCTTTGAAAC 58.593 43.478 0.00 0.00 0.00 2.78
1449 1571 4.717233 TTTTGCGATGGATTGCATAACT 57.283 36.364 2.32 0.00 45.92 2.24
1450 1572 5.826601 TTTTGCGATGGATTGCATAACTA 57.173 34.783 2.32 0.00 45.92 2.24
1496 1619 6.026947 ACTGTAGTTTCAGTCTCATGGTAC 57.973 41.667 0.00 0.00 44.07 3.34
1497 1620 5.775701 ACTGTAGTTTCAGTCTCATGGTACT 59.224 40.000 0.00 0.00 44.07 2.73
1498 1621 6.946583 ACTGTAGTTTCAGTCTCATGGTACTA 59.053 38.462 0.00 0.00 44.07 1.82
1499 1622 7.450634 ACTGTAGTTTCAGTCTCATGGTACTAA 59.549 37.037 0.00 0.00 44.07 2.24
1530 1653 3.452755 ACTTACCTTGCAAAAAGTGGC 57.547 42.857 16.48 0.00 31.20 5.01
1531 1654 2.763448 ACTTACCTTGCAAAAAGTGGCA 59.237 40.909 16.48 0.00 38.46 4.92
1533 1656 0.177836 ACCTTGCAAAAAGTGGCACC 59.822 50.000 15.27 0.00 40.23 5.01
1534 1657 0.875474 CCTTGCAAAAAGTGGCACCG 60.875 55.000 15.27 0.00 40.23 4.94
1535 1658 1.489881 CTTGCAAAAAGTGGCACCGC 61.490 55.000 15.27 10.06 40.23 5.68
1536 1659 2.105930 GCAAAAAGTGGCACCGCA 59.894 55.556 15.27 0.00 0.00 5.69
1537 1660 1.300853 GCAAAAAGTGGCACCGCAT 60.301 52.632 15.27 0.00 0.00 4.73
1538 1661 1.559149 GCAAAAAGTGGCACCGCATG 61.559 55.000 15.27 10.13 0.00 4.06
1551 1674 1.402968 ACCGCATGCAAAAGCAGATAG 59.597 47.619 19.57 0.00 0.00 2.08
1568 1691 6.615088 GCAGATAGCATCTCAAAGTCAAAAA 58.385 36.000 0.00 0.00 44.79 1.94
1569 1692 7.256286 GCAGATAGCATCTCAAAGTCAAAAAT 58.744 34.615 0.00 0.00 44.79 1.82
1572 1695 7.613022 AGATAGCATCTCAAAGTCAAAAATCCA 59.387 33.333 0.00 0.00 33.42 3.41
1578 1701 8.715088 CATCTCAAAGTCAAAAATCCAAAATCC 58.285 33.333 0.00 0.00 0.00 3.01
1588 1711 8.266473 TCAAAAATCCAAAATCCTATTCCATGG 58.734 33.333 4.97 4.97 0.00 3.66
1591 1714 4.545678 TCCAAAATCCTATTCCATGGGTG 58.454 43.478 13.02 0.00 31.94 4.61
1608 1731 0.036306 GTGAGTTGGGGTGATTCGGT 59.964 55.000 0.00 0.00 0.00 4.69
1609 1732 0.768622 TGAGTTGGGGTGATTCGGTT 59.231 50.000 0.00 0.00 0.00 4.44
1624 1747 6.307077 GTGATTCGGTTAGTGCAATTTTTACC 59.693 38.462 0.00 0.00 0.00 2.85
1641 1764 9.791801 AATTTTTACCTGGCTTGAATGTTAATT 57.208 25.926 0.00 0.00 0.00 1.40
1643 1766 9.921637 TTTTTACCTGGCTTGAATGTTAATTAG 57.078 29.630 0.00 0.00 0.00 1.73
1647 1770 6.833416 ACCTGGCTTGAATGTTAATTAGCATA 59.167 34.615 14.31 0.00 31.54 3.14
1650 1773 8.462589 TGGCTTGAATGTTAATTAGCATATCA 57.537 30.769 14.31 15.32 31.54 2.15
1683 1806 3.499338 TCCAGCAATTGTGACAGGATTT 58.501 40.909 7.40 0.00 0.00 2.17
1697 1820 3.384467 ACAGGATTTTGTGTGGGTCTTTG 59.616 43.478 0.00 0.00 0.00 2.77
1793 1916 1.420138 TGAAGGAGGGAAAGAGCGTTT 59.580 47.619 0.00 0.00 0.00 3.60
2716 2840 4.571984 CGATGTGCAGGTTCTATCAAATGA 59.428 41.667 0.00 0.00 0.00 2.57
2831 3235 6.689178 TTTGTCTATCGCAAGCAAAAATTC 57.311 33.333 0.00 0.00 37.18 2.17
2843 3247 5.262455 AGCAAAAATTCTTAGGACCCTCT 57.738 39.130 0.00 0.00 0.00 3.69
2844 3248 6.388619 AGCAAAAATTCTTAGGACCCTCTA 57.611 37.500 0.00 0.00 0.00 2.43
2845 3249 6.974795 AGCAAAAATTCTTAGGACCCTCTAT 58.025 36.000 0.00 0.00 0.00 1.98
2846 3250 8.102484 AGCAAAAATTCTTAGGACCCTCTATA 57.898 34.615 0.00 0.00 0.00 1.31
2847 3251 8.214364 AGCAAAAATTCTTAGGACCCTCTATAG 58.786 37.037 0.00 0.00 0.00 1.31
2853 3260 0.941963 AGGACCCTCTATAGTGGCCA 59.058 55.000 14.33 0.00 0.00 5.36
2869 3276 3.868077 GTGGCCATCGAGATAATATCTGC 59.132 47.826 9.72 4.40 40.38 4.26
2921 3328 0.323360 GTGGAGGGGTTAATGCAGCA 60.323 55.000 0.00 0.00 0.00 4.41
3002 3409 2.037251 GAGACCTGGTAACTCTGTTGCA 59.963 50.000 0.00 0.00 37.61 4.08
3009 3416 2.808543 GGTAACTCTGTTGCAGTTCCAG 59.191 50.000 0.00 0.00 35.63 3.86
3083 3490 5.422970 ACATGTGCTTGGACCAAATATGAAT 59.577 36.000 17.73 2.95 0.00 2.57
3174 3581 7.903995 AATTCACTTTTTGAGAACTTTGCAA 57.096 28.000 0.00 0.00 34.94 4.08
3192 3599 0.698238 AACCATTGCCCAGAGCTACA 59.302 50.000 0.00 0.00 44.23 2.74
3281 3688 2.100879 AAACGAAGCGAGAGGGCAGT 62.101 55.000 0.00 0.00 34.64 4.40
3355 3764 0.952497 AGTCAACACCATGAGCGCAG 60.952 55.000 11.47 0.00 0.00 5.18
3445 3854 4.759183 AGAGGAAGACAACAAGAAGAATGC 59.241 41.667 0.00 0.00 0.00 3.56
3527 3936 5.392595 GCACCCAGAAAAATATAAGAACGCA 60.393 40.000 0.00 0.00 0.00 5.24
3542 3951 5.344743 AGAACGCAGATTCTATCCTTGAA 57.655 39.130 0.00 0.00 37.16 2.69
3644 4058 2.301009 TGCTCTTCTTGACATCTCAGCA 59.699 45.455 0.00 0.00 0.00 4.41
3650 4064 3.332919 TCTTGACATCTCAGCAAAGCTC 58.667 45.455 0.00 0.00 36.40 4.09
3666 4080 5.182760 GCAAAGCTCTTTATATATGCAGGCT 59.817 40.000 0.00 0.56 0.00 4.58
3731 4145 4.753233 TCTCTAGCAGATGTCAAGAAAGC 58.247 43.478 0.00 0.00 0.00 3.51
3812 4226 2.451490 AGAGGAAGACGCATCTCTGAA 58.549 47.619 0.00 0.00 35.52 3.02
3840 4254 5.047306 CAGGCTTGGATATCATTCGGTACTA 60.047 44.000 4.83 0.00 0.00 1.82
3848 4262 9.970553 TGGATATCATTCGGTACTACTATAACT 57.029 33.333 4.83 0.00 0.00 2.24
3875 4289 7.552459 AGTGTTTAACTGTTTATTGCCAACTT 58.448 30.769 0.00 0.00 37.88 2.66
3876 4290 8.038351 AGTGTTTAACTGTTTATTGCCAACTTT 58.962 29.630 0.00 0.00 37.88 2.66
3877 4291 8.113675 GTGTTTAACTGTTTATTGCCAACTTTG 58.886 33.333 0.00 0.00 0.00 2.77
3878 4292 7.819900 TGTTTAACTGTTTATTGCCAACTTTGT 59.180 29.630 0.00 0.00 0.00 2.83
3879 4293 7.763172 TTAACTGTTTATTGCCAACTTTGTG 57.237 32.000 0.00 0.00 0.00 3.33
3880 4294 5.590530 ACTGTTTATTGCCAACTTTGTGA 57.409 34.783 0.00 0.00 0.00 3.58
3882 4296 5.984926 ACTGTTTATTGCCAACTTTGTGATG 59.015 36.000 0.00 0.00 0.00 3.07
3977 4406 4.034510 GTCATAAGCCAGGATTTCAACTCG 59.965 45.833 0.00 0.00 0.00 4.18
4100 4529 3.557228 ATCAACCCTGATGAGAAGCTC 57.443 47.619 0.00 0.00 40.94 4.09
4245 4674 0.179240 GTCAGCTTCAACGATGCGTG 60.179 55.000 0.00 0.00 39.99 5.34
4268 4697 1.535015 GGCTGCAGTTAGAGCGTAGAG 60.535 57.143 16.64 0.00 35.95 2.43
4287 4717 2.483491 GAGCTAGCAGCATTATCCTTGC 59.517 50.000 18.83 0.00 45.56 4.01
4313 4743 5.365133 GCACATTTTACATTTCGTGCTTTG 58.635 37.500 0.00 0.00 44.77 2.77
4422 4852 4.323417 TGTTCATGTCCTATTTCGCACTT 58.677 39.130 0.00 0.00 0.00 3.16
4484 4915 4.392138 GGTTGACCTACTCACTAACATTGC 59.608 45.833 0.00 0.00 0.00 3.56
4677 5120 6.563422 TCAATTCAAAAGAACCAGACAGTTG 58.437 36.000 0.00 0.00 0.00 3.16
4681 5124 5.984725 TCAAAAGAACCAGACAGTTGAGTA 58.015 37.500 0.00 0.00 0.00 2.59
4687 5130 2.296471 ACCAGACAGTTGAGTAAGGACG 59.704 50.000 0.00 0.00 0.00 4.79
4748 5196 0.999712 CCCCAGGTATCCCAACTTGT 59.000 55.000 0.00 0.00 0.00 3.16
4813 5261 4.162131 TCCAGCATATCTCAACTTGCACTA 59.838 41.667 0.00 0.00 37.56 2.74
4846 5294 1.705997 GGTCCCCGGCCTATCACAAT 61.706 60.000 0.00 0.00 0.00 2.71
4868 5316 2.113774 CAAGTGGCAGCCAGGTGA 59.886 61.111 16.83 0.00 32.34 4.02
4936 5390 3.738830 TGTCTAATTAACCCGCGCTAT 57.261 42.857 5.56 0.00 0.00 2.97
4997 5451 0.377905 TCGTTCGAGAACACACGTGA 59.622 50.000 25.01 0.00 41.20 4.35
5008 5462 0.039527 CACACGTGATGTCCTGTCGA 60.040 55.000 25.01 0.00 40.64 4.20
5024 5478 2.054232 TCGAGGGCGATAAGAGTTCT 57.946 50.000 0.00 0.00 42.51 3.01
5189 5644 0.036577 TCTCCTCTGCTTTGCTCTGC 60.037 55.000 0.00 0.00 0.00 4.26
5191 5646 1.303074 CCTCTGCTTTGCTCTGCCA 60.303 57.895 0.00 0.00 0.00 4.92
5237 5692 2.959030 TCATAGCAGCTCTAATCGGTGT 59.041 45.455 0.00 0.00 32.75 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.829333 GAGCTCATTCTGAGGCCTCA 59.171 55.000 33.04 33.04 44.43 3.86
508 521 0.179161 CGAGCTTCCACACGAGGTAG 60.179 60.000 0.00 0.00 0.00 3.18
676 724 9.944376 ATCACACAGACAGTTTACTTAACATAT 57.056 29.630 0.00 0.00 39.30 1.78
677 725 9.203421 CATCACACAGACAGTTTACTTAACATA 57.797 33.333 0.00 0.00 39.30 2.29
678 726 7.715249 ACATCACACAGACAGTTTACTTAACAT 59.285 33.333 0.00 0.00 39.30 2.71
689 737 3.623060 GTGTTCAACATCACACAGACAGT 59.377 43.478 0.00 0.00 42.51 3.55
690 738 3.002656 GGTGTTCAACATCACACAGACAG 59.997 47.826 0.00 0.00 44.40 3.51
818 873 4.148871 CAGAGCCGTTAATCGTCATATGTG 59.851 45.833 1.90 0.00 37.94 3.21
819 874 4.037565 TCAGAGCCGTTAATCGTCATATGT 59.962 41.667 1.90 0.00 37.94 2.29
822 877 4.848562 ATCAGAGCCGTTAATCGTCATA 57.151 40.909 0.00 0.00 37.94 2.15
825 880 3.425858 GCTAATCAGAGCCGTTAATCGTC 59.574 47.826 0.00 0.00 36.38 4.20
858 925 2.520536 GGGGTCTGGCTGTCAGTGT 61.521 63.158 9.38 0.00 43.76 3.55
969 1038 1.000486 TCCAGAGGAGAGGAACCGG 60.000 63.158 0.00 0.00 0.00 5.28
1045 1114 0.252375 AAATCACCTGGGGCTGCAAT 60.252 50.000 0.50 0.00 0.00 3.56
1132 1202 1.001974 CACGGAATGGTTGGAGACAGA 59.998 52.381 0.00 0.00 44.54 3.41
1140 1210 2.568090 GCCTGCACGGAATGGTTG 59.432 61.111 6.40 0.00 33.16 3.77
1313 1435 4.021104 ACATCAAATTCACAGAGGAGACGA 60.021 41.667 0.00 0.00 0.00 4.20
1321 1443 4.728772 AGTTGGGACATCAAATTCACAGA 58.271 39.130 0.00 0.00 39.30 3.41
1336 1458 1.768275 TGCTTGTCTTGAGAGTTGGGA 59.232 47.619 0.00 0.00 0.00 4.37
1337 1459 2.260844 TGCTTGTCTTGAGAGTTGGG 57.739 50.000 0.00 0.00 0.00 4.12
1338 1460 3.190118 GGAATGCTTGTCTTGAGAGTTGG 59.810 47.826 0.00 0.00 0.00 3.77
1339 1461 3.817084 TGGAATGCTTGTCTTGAGAGTTG 59.183 43.478 0.00 0.00 0.00 3.16
1340 1462 4.090761 TGGAATGCTTGTCTTGAGAGTT 57.909 40.909 0.00 0.00 0.00 3.01
1341 1463 3.777106 TGGAATGCTTGTCTTGAGAGT 57.223 42.857 0.00 0.00 0.00 3.24
1342 1464 6.726230 CATTATGGAATGCTTGTCTTGAGAG 58.274 40.000 0.00 0.00 36.29 3.20
1375 1497 1.207791 AAGCCGAATCAGATGACCCT 58.792 50.000 0.00 0.00 0.00 4.34
1378 1500 4.154918 AGTTTCAAAGCCGAATCAGATGAC 59.845 41.667 0.00 0.00 0.00 3.06
1427 1549 5.070770 AGTTATGCAATCCATCGCAAAAA 57.929 34.783 0.00 0.00 42.37 1.94
1428 1550 4.717233 AGTTATGCAATCCATCGCAAAA 57.283 36.364 0.00 0.00 42.37 2.44
1429 1551 4.881273 ACTAGTTATGCAATCCATCGCAAA 59.119 37.500 0.00 0.00 42.37 3.68
1430 1552 4.450976 ACTAGTTATGCAATCCATCGCAA 58.549 39.130 0.00 0.00 42.37 4.85
1431 1553 4.071961 ACTAGTTATGCAATCCATCGCA 57.928 40.909 0.00 0.00 43.45 5.10
1432 1554 5.696724 AGTAACTAGTTATGCAATCCATCGC 59.303 40.000 18.03 1.38 35.34 4.58
1433 1555 6.146184 CCAGTAACTAGTTATGCAATCCATCG 59.854 42.308 18.03 0.00 35.34 3.84
1434 1556 7.217200 TCCAGTAACTAGTTATGCAATCCATC 58.783 38.462 18.03 2.05 35.34 3.51
1435 1557 7.136822 TCCAGTAACTAGTTATGCAATCCAT 57.863 36.000 18.03 0.00 37.97 3.41
1436 1558 6.553953 TCCAGTAACTAGTTATGCAATCCA 57.446 37.500 18.03 0.00 0.00 3.41
1437 1559 7.171678 GTGATCCAGTAACTAGTTATGCAATCC 59.828 40.741 18.03 4.10 0.00 3.01
1438 1560 7.710907 TGTGATCCAGTAACTAGTTATGCAATC 59.289 37.037 18.03 16.97 0.00 2.67
1439 1561 7.564793 TGTGATCCAGTAACTAGTTATGCAAT 58.435 34.615 18.03 10.08 0.00 3.56
1440 1562 6.941857 TGTGATCCAGTAACTAGTTATGCAA 58.058 36.000 18.03 6.01 0.00 4.08
1441 1563 6.538945 TGTGATCCAGTAACTAGTTATGCA 57.461 37.500 18.03 5.15 0.00 3.96
1442 1564 7.042335 ACTTGTGATCCAGTAACTAGTTATGC 58.958 38.462 18.03 6.85 0.00 3.14
1443 1565 9.436957 AAACTTGTGATCCAGTAACTAGTTATG 57.563 33.333 18.03 15.40 38.39 1.90
1444 1566 9.436957 CAAACTTGTGATCCAGTAACTAGTTAT 57.563 33.333 18.03 3.08 38.39 1.89
1445 1567 8.644216 TCAAACTTGTGATCCAGTAACTAGTTA 58.356 33.333 11.38 11.38 38.39 2.24
1446 1568 7.506114 TCAAACTTGTGATCCAGTAACTAGTT 58.494 34.615 13.68 13.68 40.13 2.24
1447 1569 7.062749 TCAAACTTGTGATCCAGTAACTAGT 57.937 36.000 0.00 0.00 32.47 2.57
1448 1570 7.962964 TTCAAACTTGTGATCCAGTAACTAG 57.037 36.000 0.00 0.00 0.00 2.57
1449 1571 7.990886 AGTTTCAAACTTGTGATCCAGTAACTA 59.009 33.333 0.00 0.00 39.04 2.24
1450 1572 6.828785 AGTTTCAAACTTGTGATCCAGTAACT 59.171 34.615 0.00 0.00 39.04 2.24
1508 1631 4.586841 TGCCACTTTTTGCAAGGTAAGTAT 59.413 37.500 17.71 1.42 33.87 2.12
1514 1637 0.177836 GGTGCCACTTTTTGCAAGGT 59.822 50.000 0.00 0.00 39.57 3.50
1539 1662 6.128090 TGACTTTGAGATGCTATCTGCTTTTG 60.128 38.462 3.76 0.00 40.38 2.44
1540 1663 5.942236 TGACTTTGAGATGCTATCTGCTTTT 59.058 36.000 3.76 0.00 40.38 2.27
1541 1664 5.494724 TGACTTTGAGATGCTATCTGCTTT 58.505 37.500 3.76 0.00 40.38 3.51
1542 1665 5.095145 TGACTTTGAGATGCTATCTGCTT 57.905 39.130 3.76 0.00 40.38 3.91
1543 1666 4.750021 TGACTTTGAGATGCTATCTGCT 57.250 40.909 3.76 0.00 40.38 4.24
1544 1667 5.808042 TTTGACTTTGAGATGCTATCTGC 57.192 39.130 3.76 0.00 40.38 4.26
1545 1668 7.914346 GGATTTTTGACTTTGAGATGCTATCTG 59.086 37.037 3.76 0.00 40.38 2.90
1546 1669 7.613022 TGGATTTTTGACTTTGAGATGCTATCT 59.387 33.333 0.00 0.00 43.70 1.98
1551 1674 7.481275 TTTTGGATTTTTGACTTTGAGATGC 57.519 32.000 0.00 0.00 0.00 3.91
1563 1686 7.499895 CCCATGGAATAGGATTTTGGATTTTTG 59.500 37.037 15.22 0.00 0.00 2.44
1568 1691 5.103129 TCACCCATGGAATAGGATTTTGGAT 60.103 40.000 15.22 0.00 0.00 3.41
1569 1692 4.231658 TCACCCATGGAATAGGATTTTGGA 59.768 41.667 15.22 0.00 0.00 3.53
1572 1695 5.472301 ACTCACCCATGGAATAGGATTTT 57.528 39.130 15.22 0.00 0.00 1.82
1578 1701 2.423373 CCCCAACTCACCCATGGAATAG 60.423 54.545 15.22 9.42 36.27 1.73
1588 1711 0.676782 CCGAATCACCCCAACTCACC 60.677 60.000 0.00 0.00 0.00 4.02
1591 1714 2.027469 ACTAACCGAATCACCCCAACTC 60.027 50.000 0.00 0.00 0.00 3.01
1608 1731 5.303078 TCAAGCCAGGTAAAAATTGCACTAA 59.697 36.000 0.00 0.00 0.00 2.24
1609 1732 4.830046 TCAAGCCAGGTAAAAATTGCACTA 59.170 37.500 0.00 0.00 0.00 2.74
1624 1747 8.570488 TGATATGCTAATTAACATTCAAGCCAG 58.430 33.333 6.67 0.00 0.00 4.85
1641 1764 6.422333 TGGAGTTTTGGTTGATGATATGCTA 58.578 36.000 0.00 0.00 0.00 3.49
1643 1766 5.581126 TGGAGTTTTGGTTGATGATATGC 57.419 39.130 0.00 0.00 0.00 3.14
1647 1770 3.499338 TGCTGGAGTTTTGGTTGATGAT 58.501 40.909 0.00 0.00 0.00 2.45
1650 1773 4.101430 ACAATTGCTGGAGTTTTGGTTGAT 59.899 37.500 5.05 0.00 0.00 2.57
1683 1806 2.520069 ACACAACAAAGACCCACACAA 58.480 42.857 0.00 0.00 0.00 3.33
1697 1820 7.681939 TTCCAATTGTATCCTAGAACACAAC 57.318 36.000 4.43 0.00 34.00 3.32
1793 1916 2.228582 CCAAGTTGCATCGGTCAATGAA 59.771 45.455 0.00 0.00 0.00 2.57
1936 2059 1.243342 CGCCCTGCACATTTCCTTCA 61.243 55.000 0.00 0.00 0.00 3.02
2509 2632 9.206870 GACAATATTCTTGATTTTTGGCTCAAA 57.793 29.630 0.00 0.00 31.40 2.69
2757 3157 7.175104 ACAAGGATAAAGCAGGATTCAAGTAA 58.825 34.615 0.00 0.00 0.00 2.24
2831 3235 3.166679 GGCCACTATAGAGGGTCCTAAG 58.833 54.545 16.83 0.00 0.00 2.18
2843 3247 7.255625 GCAGATATTATCTCGATGGCCACTATA 60.256 40.741 8.16 0.00 37.58 1.31
2844 3248 6.462207 GCAGATATTATCTCGATGGCCACTAT 60.462 42.308 8.16 0.00 37.58 2.12
2845 3249 5.163509 GCAGATATTATCTCGATGGCCACTA 60.164 44.000 8.16 0.00 37.58 2.74
2846 3250 4.382470 GCAGATATTATCTCGATGGCCACT 60.382 45.833 8.16 0.00 37.58 4.00
2847 3251 3.868077 GCAGATATTATCTCGATGGCCAC 59.132 47.826 8.16 0.47 37.58 5.01
2853 3260 7.928167 TGAAACACTTGCAGATATTATCTCGAT 59.072 33.333 3.10 0.00 37.58 3.59
2869 3276 2.233271 ACCTCCTGCATGAAACACTTG 58.767 47.619 0.00 0.00 0.00 3.16
3002 3409 3.498661 GGGAAGTTGATGGAACTGGAACT 60.499 47.826 0.00 0.00 44.68 3.01
3009 3416 2.716217 CAGAGGGGAAGTTGATGGAAC 58.284 52.381 0.00 0.00 34.40 3.62
3068 3475 4.037803 CGCATTGGATTCATATTTGGTCCA 59.962 41.667 6.96 6.96 36.73 4.02
3083 3490 1.278985 AGACAATCTGGACGCATTGGA 59.721 47.619 0.00 0.00 34.77 3.53
3174 3581 0.035056 GTGTAGCTCTGGGCAATGGT 60.035 55.000 0.74 0.00 44.79 3.55
3184 3591 0.901124 CTGCTTCCCTGTGTAGCTCT 59.099 55.000 0.00 0.00 35.93 4.09
3192 3599 3.726557 TTCATCATTCTGCTTCCCTGT 57.273 42.857 0.00 0.00 0.00 4.00
3281 3688 6.550854 ACTTTTTGGTCCTTTCAGAATCATCA 59.449 34.615 0.00 0.00 0.00 3.07
3355 3764 3.487120 AACTTAGTGTGTTGGTCCCTC 57.513 47.619 0.00 0.00 0.00 4.30
3445 3854 0.532862 AGTCTTGTTGGTGACCGCAG 60.533 55.000 0.00 0.00 34.02 5.18
3644 4058 8.924511 TTTAGCCTGCATATATAAAGAGCTTT 57.075 30.769 0.74 0.74 36.63 3.51
3650 4064 7.452880 TGCCTTTTAGCCTGCATATATAAAG 57.547 36.000 0.00 0.00 0.00 1.85
3666 4080 6.186957 AGATATCACCAACACATGCCTTTTA 58.813 36.000 5.32 0.00 0.00 1.52
3812 4226 4.384056 CGAATGATATCCAAGCCTGAACT 58.616 43.478 0.00 0.00 0.00 3.01
3868 4282 0.609662 ATGCCCATCACAAAGTTGGC 59.390 50.000 0.00 0.00 36.03 4.52
3875 4289 1.179152 CTTGCTCATGCCCATCACAA 58.821 50.000 0.00 0.00 38.71 3.33
3876 4290 0.328926 TCTTGCTCATGCCCATCACA 59.671 50.000 0.00 0.00 38.71 3.58
3877 4291 1.022735 CTCTTGCTCATGCCCATCAC 58.977 55.000 0.00 0.00 38.71 3.06
3878 4292 0.750546 GCTCTTGCTCATGCCCATCA 60.751 55.000 0.00 0.00 38.71 3.07
3879 4293 1.783031 CGCTCTTGCTCATGCCCATC 61.783 60.000 0.00 0.00 38.71 3.51
3880 4294 1.822613 CGCTCTTGCTCATGCCCAT 60.823 57.895 0.00 0.00 38.71 4.00
3882 4296 1.505477 GATCGCTCTTGCTCATGCCC 61.505 60.000 0.00 0.00 38.71 5.36
3910 4339 1.247567 CGGAACCTGCAGAAACCAAT 58.752 50.000 17.39 0.00 0.00 3.16
4070 4499 0.527817 CAGGGTTGATAGTCGCGGAC 60.528 60.000 6.13 3.09 0.00 4.79
4100 4529 0.179000 ACCTTAGCTCCATTGCGAGG 59.821 55.000 0.00 0.00 42.57 4.63
4245 4674 3.198489 GCTCTAACTGCAGCCCGC 61.198 66.667 15.27 5.97 42.89 6.13
4268 4697 2.224606 TGCAAGGATAATGCTGCTAGC 58.775 47.619 8.10 8.10 44.14 3.42
4269 4698 3.304525 GCTTGCAAGGATAATGCTGCTAG 60.305 47.826 27.10 0.00 44.14 3.42
4278 4708 6.338214 TGTAAAATGTGCTTGCAAGGATAA 57.662 33.333 27.10 17.21 0.00 1.75
4287 4717 4.933514 GCACGAAATGTAAAATGTGCTTG 58.066 39.130 7.80 0.00 46.69 4.01
4313 4743 0.533755 CGATGTGGCCCATCCTTCTC 60.534 60.000 21.54 4.97 46.10 2.87
4455 4885 3.314693 AGTGAGTAGGTCAACCCAAAGA 58.685 45.455 0.00 0.00 36.74 2.52
4484 4915 1.254284 CCCTCGCTGGCTATCCCTAG 61.254 65.000 0.00 0.00 0.00 3.02
4629 5061 7.125659 TGAACCTACATGAACATATCTTCCTGA 59.874 37.037 0.00 0.00 0.00 3.86
4677 5120 3.006247 ACTTCCGTACTCGTCCTTACTC 58.994 50.000 0.00 0.00 35.01 2.59
4681 5124 0.886563 CCACTTCCGTACTCGTCCTT 59.113 55.000 0.00 0.00 35.01 3.36
4687 5130 4.802563 GCACTATAAACCACTTCCGTACTC 59.197 45.833 0.00 0.00 0.00 2.59
4709 5157 4.441495 GGGGTGCTTTTAACTCATTATGGC 60.441 45.833 0.00 0.00 0.00 4.40
4794 5242 5.757320 ACATCTAGTGCAAGTTGAGATATGC 59.243 40.000 7.16 0.00 39.22 3.14
4846 5294 2.441717 TGGCTGCCACTTGTTGCA 60.442 55.556 19.30 0.00 35.86 4.08
4868 5316 2.264794 GGCGACGACCAATCCAGT 59.735 61.111 0.00 0.00 0.00 4.00
4874 5322 2.933878 AAAGTGCAGGCGACGACCAA 62.934 55.000 0.00 0.00 0.00 3.67
4875 5323 2.933878 AAAAGTGCAGGCGACGACCA 62.934 55.000 0.00 0.00 0.00 4.02
4903 5352 1.600023 TTAGACAAAACGGCAGGGTG 58.400 50.000 0.00 0.00 0.00 4.61
4936 5390 4.229582 ACAGATTTAATTCAGGTGCCCCTA 59.770 41.667 0.00 0.00 39.89 3.53
4993 5447 1.139734 CCCTCGACAGGACATCACG 59.860 63.158 0.00 0.00 43.65 4.35
4997 5451 2.362503 TCGCCCTCGACAGGACAT 60.363 61.111 0.76 0.00 43.65 3.06
5008 5462 1.033574 CCGAGAACTCTTATCGCCCT 58.966 55.000 0.41 0.00 42.57 5.19
5017 5471 3.764466 CGCCAGCCCGAGAACTCT 61.764 66.667 0.41 0.00 0.00 3.24
5024 5478 4.776322 CACCAATCGCCAGCCCGA 62.776 66.667 0.00 0.00 41.98 5.14
5066 5521 1.878522 GATGAACGCCAGCGACGAT 60.879 57.895 20.32 6.59 42.83 3.73
5077 5532 3.487202 CCACACCGCCGATGAACG 61.487 66.667 0.00 0.00 42.18 3.95
5131 5586 2.761208 CAGTAATCAGGAGGGAAGACGT 59.239 50.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.