Multiple sequence alignment - TraesCS6B01G248600

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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 TraesCS6B01G248600 chr6B 100.000 5189 0 0 1 5189 446055202 446050014 0.000000e+00 9583.0
1 TraesCS6B01G248600 chr6B 97.561 41 1 0 4380 4420 462028628 462028668 2.590000e-08 71.3
2 TraesCS6B01G248600 chr6A 95.523 3596 101 11 1543 5107 405663779 405660213 0.000000e+00 5694.0
3 TraesCS6B01G248600 chr6A 94.208 1554 45 18 1 1526 405665300 405663764 0.000000e+00 2329.0
4 TraesCS6B01G248600 chr6D 95.961 3169 106 13 1543 4700 285183691 285180534 0.000000e+00 5123.0
5 TraesCS6B01G248600 chr6D 93.718 1353 37 10 1 1345 285185232 285183920 0.000000e+00 1984.0
6 TraesCS6B01G248600 chr6D 92.343 431 17 3 4774 5189 285180511 285180082 2.670000e-167 599.0
7 TraesCS6B01G248600 chr6D 94.444 162 6 1 1365 1526 285183834 285183676 4.010000e-61 246.0
8 TraesCS6B01G248600 chr6D 76.849 311 40 14 2831 3112 9961356 9961663 4.190000e-31 147.0
9 TraesCS6B01G248600 chr6D 78.443 167 26 8 2931 3089 470900457 470900621 3.310000e-17 100.0
10 TraesCS6B01G248600 chr1B 79.762 252 37 10 4517 4763 359596477 359596719 2.480000e-38 171.0
11 TraesCS6B01G248600 chr1B 76.752 314 44 17 2824 3112 26466615 26466306 1.160000e-31 148.0
12 TraesCS6B01G248600 chr1D 82.584 178 27 4 2831 3005 246041961 246042137 2.500000e-33 154.0
13 TraesCS6B01G248600 chr4D 77.000 300 37 14 2831 3101 379345301 379345597 5.420000e-30 143.0
14 TraesCS6B01G248600 chr2D 77.000 300 37 14 2834 3104 617981092 617980796 5.420000e-30 143.0
15 TraesCS6B01G248600 chr2D 95.161 62 3 0 4702 4763 81632561 81632622 1.190000e-16 99.0
16 TraesCS6B01G248600 chr7D 81.421 183 20 9 2831 3011 87390102 87389932 2.520000e-28 137.0
17 TraesCS6B01G248600 chr7D 93.478 46 3 0 4372 4417 145832759 145832714 9.320000e-08 69.4
18 TraesCS6B01G248600 chr7B 80.769 182 29 5 2831 3011 36385102 36384926 2.520000e-28 137.0
19 TraesCS6B01G248600 chr5B 77.043 257 45 7 4517 4763 311849502 311849250 9.060000e-28 135.0
20 TraesCS6B01G248600 chr5A 76.866 268 32 14 4517 4763 506132751 506133009 1.960000e-24 124.0
21 TraesCS6B01G248600 chr3B 76.119 268 36 12 4517 4763 654346685 654346945 1.180000e-21 115.0
22 TraesCS6B01G248600 chr4A 75.746 268 35 14 4517 4763 632636557 632636815 1.980000e-19 108.0
23 TraesCS6B01G248600 chr1A 75.556 270 36 16 4517 4763 583536373 583536635 7.110000e-19 106.0
24 TraesCS6B01G248600 chr3D 95.161 62 3 0 4702 4763 540587598 540587537 1.190000e-16 99.0
25 TraesCS6B01G248600 chrUn 96.552 58 2 0 4706 4763 2744905 2744848 4.280000e-16 97.1
26 TraesCS6B01G248600 chr5D 95.122 41 2 0 4380 4420 509548523 509548483 1.210000e-06 65.8
27 TraesCS6B01G248600 chr3A 96.970 33 1 0 4387 4419 698863665 698863697 7.260000e-04 56.5
28 TraesCS6B01G248600 chr2A 100.000 29 0 0 4379 4407 303739168 303739196 3.000000e-03 54.7


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 TraesCS6B01G248600 chr6B 446050014 446055202 5188 True 9583.0 9583 100.0000 1 5189 1 chr6B.!!$R1 5188
1 TraesCS6B01G248600 chr6A 405660213 405665300 5087 True 4011.5 5694 94.8655 1 5107 2 chr6A.!!$R1 5106
2 TraesCS6B01G248600 chr6D 285180082 285185232 5150 True 1988.0 5123 94.1165 1 5189 4 chr6D.!!$R1 5188

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
768 775 0.466543 AGCTAACGTTGGTGGTGTCA 59.533 50.000 11.99 0.0 0.00 3.58 F
1244 1261 0.321122 CTCCGCTTCCTGCTTCACTT 60.321 55.000 0.00 0.0 40.11 3.16 F
1245 1262 0.603707 TCCGCTTCCTGCTTCACTTG 60.604 55.000 0.00 0.0 40.11 3.16 F
2255 2364 1.277557 GCAACACTCTGACAGGGATCT 59.722 52.381 9.98 0.0 0.00 2.75 F
3044 3153 0.182537 CAGAGGTTGGGTGTGGTTCA 59.817 55.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 2456 0.883833 CTTGTGGTGCCTGGTTCATC 59.116 55.0 0.00 0.00 0.00 2.92 R
2938 3047 0.960861 GCCCAGACGGAGGAAAAAGG 60.961 60.0 0.00 0.00 0.00 3.11 R
2954 3063 2.409948 ACAAGAGTGAAGCTATGCCC 57.590 50.0 0.00 0.00 0.00 5.36 R
3969 4085 1.752683 TTAGAGCTCTCCTGGTCGAC 58.247 55.0 22.17 7.13 39.21 4.20 R
4510 4627 0.468400 CCCCTCTCTCCCCTACTTCG 60.468 65.0 0.00 0.00 0.00 3.79 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
35 36 2.112297 GTGGCGAAGGGGTTGTCA 59.888 61.111 0.00 0.00 0.00 3.58
407 408 0.548682 AGCAGAAGTCCACCTCCCAT 60.549 55.000 0.00 0.00 0.00 4.00
486 493 1.202580 CCACATCATCCTCCTCGTTCC 60.203 57.143 0.00 0.00 0.00 3.62
505 512 3.535962 CTCGGCTGGCTCCTCCTC 61.536 72.222 0.00 0.00 35.26 3.71
762 769 2.032894 CACACAGAAGCTAACGTTGGTG 60.033 50.000 11.99 4.73 0.00 4.17
763 770 1.531149 CACAGAAGCTAACGTTGGTGG 59.469 52.381 11.99 0.00 0.00 4.61
764 771 1.140252 ACAGAAGCTAACGTTGGTGGT 59.860 47.619 11.99 3.89 0.00 4.16
765 772 1.531149 CAGAAGCTAACGTTGGTGGTG 59.469 52.381 11.99 1.29 0.00 4.17
766 773 1.140252 AGAAGCTAACGTTGGTGGTGT 59.860 47.619 11.99 0.00 0.00 4.16
767 774 1.529865 GAAGCTAACGTTGGTGGTGTC 59.470 52.381 11.99 0.00 0.00 3.67
768 775 0.466543 AGCTAACGTTGGTGGTGTCA 59.533 50.000 11.99 0.00 0.00 3.58
769 776 0.865769 GCTAACGTTGGTGGTGTCAG 59.134 55.000 11.99 0.00 0.00 3.51
770 777 1.808891 GCTAACGTTGGTGGTGTCAGT 60.809 52.381 11.99 0.00 0.00 3.41
871 879 1.338769 CCCACGTAAGACCCAAAGAGG 60.339 57.143 0.00 0.00 43.62 3.69
1164 1181 3.256558 TCACATCGATTCACTCTTGCTG 58.743 45.455 0.00 0.00 0.00 4.41
1197 1214 2.394563 GCTGCTCTGCTTCGGGTTC 61.395 63.158 0.00 0.00 0.00 3.62
1198 1215 1.004560 CTGCTCTGCTTCGGGTTCA 60.005 57.895 0.00 0.00 0.00 3.18
1244 1261 0.321122 CTCCGCTTCCTGCTTCACTT 60.321 55.000 0.00 0.00 40.11 3.16
1245 1262 0.603707 TCCGCTTCCTGCTTCACTTG 60.604 55.000 0.00 0.00 40.11 3.16
1351 1381 8.827177 AAATCGTTTTGTGATACTTCTCTGTA 57.173 30.769 0.00 0.00 0.00 2.74
1446 1544 1.677576 TGGGTACGATTGCCTACTACG 59.322 52.381 0.00 0.00 0.00 3.51
1535 1633 9.582431 TTGTAGAGTGATATACTTTTCTTTCCG 57.418 33.333 0.00 0.00 40.53 4.30
1536 1634 8.963725 TGTAGAGTGATATACTTTTCTTTCCGA 58.036 33.333 0.00 0.00 40.53 4.55
1537 1635 9.798994 GTAGAGTGATATACTTTTCTTTCCGAA 57.201 33.333 0.00 0.00 40.53 4.30
1539 1637 9.720769 AGAGTGATATACTTTTCTTTCCGAAAA 57.279 29.630 0.00 0.00 46.43 2.29
1548 1646 6.613755 TTTTCTTTCCGAAAAGGTGTAGAG 57.386 37.500 0.00 0.00 44.42 2.43
1549 1647 4.950205 TCTTTCCGAAAAGGTGTAGAGT 57.050 40.909 0.00 0.00 41.88 3.24
1550 1648 4.628074 TCTTTCCGAAAAGGTGTAGAGTG 58.372 43.478 0.00 0.00 41.88 3.51
1551 1649 4.342951 TCTTTCCGAAAAGGTGTAGAGTGA 59.657 41.667 0.00 0.00 41.88 3.41
1552 1650 4.884668 TTCCGAAAAGGTGTAGAGTGAT 57.115 40.909 0.00 0.00 41.99 3.06
1553 1651 5.988310 TTCCGAAAAGGTGTAGAGTGATA 57.012 39.130 0.00 0.00 41.99 2.15
1554 1652 6.540438 TTCCGAAAAGGTGTAGAGTGATAT 57.460 37.500 0.00 0.00 41.99 1.63
1555 1653 7.649533 TTCCGAAAAGGTGTAGAGTGATATA 57.350 36.000 0.00 0.00 41.99 0.86
1695 1793 2.043526 ACATCCTCTTGCCCATCCTTTT 59.956 45.455 0.00 0.00 0.00 2.27
1767 1865 4.083802 CCGAAAGTTCTGATTTGGTGAGAC 60.084 45.833 0.00 0.00 0.00 3.36
1908 2017 4.630069 ACACACCTTTGTATTCGTAGATGC 59.370 41.667 0.00 0.00 31.73 3.91
1917 2026 2.309528 TTCGTAGATGCACCATCCAC 57.690 50.000 0.00 0.00 41.36 4.02
2255 2364 1.277557 GCAACACTCTGACAGGGATCT 59.722 52.381 9.98 0.00 0.00 2.75
2487 2596 4.617959 CTGAAGGTTCGTTACTTCTGTCA 58.382 43.478 13.67 0.00 42.67 3.58
2732 2841 9.362539 ACAGATCAAGAATTTGTTAAATGATGC 57.637 29.630 0.00 0.00 35.73 3.91
2892 3001 1.641677 GTGCGGATATGGTCGTTGC 59.358 57.895 0.00 0.00 0.00 4.17
2938 3047 5.519722 TCATCGCTTTGGAGTTTTTCTTTC 58.480 37.500 0.00 0.00 0.00 2.62
2954 3063 3.740115 TCTTTCCTTTTTCCTCCGTCTG 58.260 45.455 0.00 0.00 0.00 3.51
2967 3076 0.811616 CCGTCTGGGCATAGCTTCAC 60.812 60.000 0.00 0.00 0.00 3.18
3006 3115 2.292103 TTGCTTGTGTGGTTCTTTGC 57.708 45.000 0.00 0.00 0.00 3.68
3040 3149 0.327924 TATGCAGAGGTTGGGTGTGG 59.672 55.000 0.00 0.00 0.00 4.17
3041 3150 1.719063 ATGCAGAGGTTGGGTGTGGT 61.719 55.000 0.00 0.00 0.00 4.16
3042 3151 1.152756 GCAGAGGTTGGGTGTGGTT 60.153 57.895 0.00 0.00 0.00 3.67
3043 3152 1.172812 GCAGAGGTTGGGTGTGGTTC 61.173 60.000 0.00 0.00 0.00 3.62
3044 3153 0.182537 CAGAGGTTGGGTGTGGTTCA 59.817 55.000 0.00 0.00 0.00 3.18
3101 3210 6.101332 TGAGTCAATAAAATCCAGCATTTGC 58.899 36.000 0.00 0.00 34.69 3.68
3173 3283 5.051708 GCGGTTCTTTGTTTTGTCTTGATTC 60.052 40.000 0.00 0.00 0.00 2.52
3245 3355 4.082125 ACAAAATGGAGGAAGCTAACCTG 58.918 43.478 15.70 4.78 37.93 4.00
3381 3492 6.320418 GTCTTATCGTGTTATTGGGGGAAATT 59.680 38.462 0.00 0.00 0.00 1.82
3829 3945 4.917415 CCGAGAAACACCAAAATTGCTTAG 59.083 41.667 0.00 0.00 0.00 2.18
3840 3956 5.569059 CCAAAATTGCTTAGCAGAACGTTAG 59.431 40.000 7.08 0.00 40.61 2.34
3969 4085 8.129211 ACTCTTGGAAGAATTTTGTAACTTTCG 58.871 33.333 0.00 0.00 34.03 3.46
4016 4132 3.007182 ACTTGCTGGATCCAACCAATTTG 59.993 43.478 21.39 14.99 39.59 2.32
4175 4292 5.843019 TCCCTTCCTTCTGAAAACTGTAT 57.157 39.130 0.00 0.00 31.06 2.29
4322 4439 9.914834 ATTTTGGTAGCTCAGGTATAAATTGTA 57.085 29.630 0.00 0.00 0.00 2.41
4556 4673 4.130857 CGCTGAGATAGAGAACTGACCTA 58.869 47.826 0.00 0.00 0.00 3.08
4589 4706 3.611358 TCCTTTGGGGTTAGGGTTTCTA 58.389 45.455 0.00 0.00 36.25 2.10
4635 4752 0.965363 CTGGGTTACATGGGCCACAC 60.965 60.000 9.28 3.08 0.00 3.82
4636 4753 1.075836 GGGTTACATGGGCCACACA 59.924 57.895 9.28 0.00 0.00 3.72
4637 4754 0.324275 GGGTTACATGGGCCACACAT 60.324 55.000 9.28 0.00 0.00 3.21
4638 4755 1.555967 GGTTACATGGGCCACACATT 58.444 50.000 9.28 0.00 0.00 2.71
4639 4756 1.204467 GGTTACATGGGCCACACATTG 59.796 52.381 9.28 5.22 0.00 2.82
4687 4804 4.804261 GCACAGAGAAGATACAACCCAACT 60.804 45.833 0.00 0.00 0.00 3.16
4688 4805 4.932200 CACAGAGAAGATACAACCCAACTC 59.068 45.833 0.00 0.00 0.00 3.01
4689 4806 4.020128 ACAGAGAAGATACAACCCAACTCC 60.020 45.833 0.00 0.00 0.00 3.85
4690 4807 3.519913 AGAGAAGATACAACCCAACTCCC 59.480 47.826 0.00 0.00 0.00 4.30
4691 4808 2.576648 AGAAGATACAACCCAACTCCCC 59.423 50.000 0.00 0.00 0.00 4.81
4692 4809 1.296002 AGATACAACCCAACTCCCCC 58.704 55.000 0.00 0.00 0.00 5.40
4693 4810 1.203570 AGATACAACCCAACTCCCCCT 60.204 52.381 0.00 0.00 0.00 4.79
4694 4811 1.212195 GATACAACCCAACTCCCCCTC 59.788 57.143 0.00 0.00 0.00 4.30
4695 4812 0.104356 TACAACCCAACTCCCCCTCA 60.104 55.000 0.00 0.00 0.00 3.86
4696 4813 0.996762 ACAACCCAACTCCCCCTCAA 60.997 55.000 0.00 0.00 0.00 3.02
4697 4814 0.409484 CAACCCAACTCCCCCTCAAT 59.591 55.000 0.00 0.00 0.00 2.57
4698 4815 1.638589 CAACCCAACTCCCCCTCAATA 59.361 52.381 0.00 0.00 0.00 1.90
4699 4816 1.596496 ACCCAACTCCCCCTCAATAG 58.404 55.000 0.00 0.00 0.00 1.73
4700 4817 1.203570 ACCCAACTCCCCCTCAATAGT 60.204 52.381 0.00 0.00 0.00 2.12
4704 4821 3.134804 CCAACTCCCCCTCAATAGTACTG 59.865 52.174 5.39 0.00 0.00 2.74
4821 4938 3.838271 GAGGCCTCGTCGGATGCA 61.838 66.667 19.06 0.00 35.74 3.96
4866 4983 3.257624 ACCTCTAGAAACGACGGAATGTT 59.742 43.478 0.00 0.00 0.00 2.71
4875 4992 2.940410 ACGACGGAATGTTGTTGTCTTT 59.060 40.909 0.00 0.00 42.86 2.52
4973 5104 0.522626 CACATCGATGTTTGGCTGCA 59.477 50.000 28.04 0.00 39.39 4.41
4996 5127 1.048601 TCTGGTTCTCCGAAAGCTGT 58.951 50.000 0.00 0.00 36.30 4.40
5121 5252 4.948004 GGTCGACCCCTCTTTTATGAAATT 59.052 41.667 24.75 0.00 0.00 1.82
5132 5263 4.799564 TTTATGAAATTCAGGTGGGTGC 57.200 40.909 1.10 0.00 0.00 5.01
5165 5296 7.420796 CCCTTCCCCCTTAAAAATTCAAAAAGA 60.421 37.037 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.350134 CTGCTGCTCTGGCTGGAA 59.650 61.111 0.00 0.00 37.30 3.53
548 555 2.764128 TGCCGGTCCATCTCCTCC 60.764 66.667 1.90 0.00 0.00 4.30
590 597 0.172803 CGCACTACCGCCTCTTAGTT 59.827 55.000 0.00 0.00 0.00 2.24
859 867 3.973472 AGGTTTTTCCTCTTTGGGTCT 57.027 42.857 0.00 0.00 44.42 3.85
871 879 3.934068 TCCGAGTCCACATAGGTTTTTC 58.066 45.455 0.00 0.00 39.02 2.29
1069 1086 1.374252 GAGCAACGGAGAAGCGGAA 60.374 57.895 0.00 0.00 36.17 4.30
1071 1088 1.807573 GAGAGCAACGGAGAAGCGG 60.808 63.158 0.00 0.00 36.17 5.52
1072 1089 2.155194 CGAGAGCAACGGAGAAGCG 61.155 63.158 0.00 0.00 36.17 4.68
1073 1090 3.773974 CGAGAGCAACGGAGAAGC 58.226 61.111 0.00 0.00 0.00 3.86
1213 1230 3.068873 AGGAAGCGGAGATGAACATACTC 59.931 47.826 0.00 0.00 0.00 2.59
1351 1381 4.621747 GCAGAGCACTTGGAACATACTACT 60.622 45.833 0.00 0.00 39.30 2.57
1415 1513 4.034048 GCAATCGTACCCACTAACATTCTG 59.966 45.833 0.00 0.00 0.00 3.02
1427 1525 1.678101 ACGTAGTAGGCAATCGTACCC 59.322 52.381 0.00 0.00 41.94 3.69
1446 1544 3.376540 CTTGCAGCTTATCTCGGAGTAC 58.623 50.000 4.69 0.00 0.00 2.73
1526 1624 5.526111 CACTCTACACCTTTTCGGAAAGAAA 59.474 40.000 18.12 0.00 46.22 2.52
1527 1625 5.054477 CACTCTACACCTTTTCGGAAAGAA 58.946 41.667 18.12 0.00 44.03 2.52
1528 1626 4.342951 TCACTCTACACCTTTTCGGAAAGA 59.657 41.667 18.12 0.00 44.03 2.52
1529 1627 4.628074 TCACTCTACACCTTTTCGGAAAG 58.372 43.478 9.39 9.39 41.56 2.62
1530 1628 4.675976 TCACTCTACACCTTTTCGGAAA 57.324 40.909 0.00 0.00 36.31 3.13
1531 1629 4.884668 ATCACTCTACACCTTTTCGGAA 57.115 40.909 0.00 0.00 36.31 4.30
1532 1630 6.832384 AGTATATCACTCTACACCTTTTCGGA 59.168 38.462 0.00 0.00 31.32 4.55
1533 1631 6.918569 CAGTATATCACTCTACACCTTTTCGG 59.081 42.308 0.00 0.00 34.26 4.30
1534 1632 6.918569 CCAGTATATCACTCTACACCTTTTCG 59.081 42.308 0.00 0.00 34.26 3.46
1535 1633 6.702282 GCCAGTATATCACTCTACACCTTTTC 59.298 42.308 0.00 0.00 34.26 2.29
1536 1634 6.408206 GGCCAGTATATCACTCTACACCTTTT 60.408 42.308 0.00 0.00 34.26 2.27
1537 1635 5.070580 GGCCAGTATATCACTCTACACCTTT 59.929 44.000 0.00 0.00 34.26 3.11
1538 1636 4.589374 GGCCAGTATATCACTCTACACCTT 59.411 45.833 0.00 0.00 34.26 3.50
1539 1637 4.153411 GGCCAGTATATCACTCTACACCT 58.847 47.826 0.00 0.00 34.26 4.00
1540 1638 3.057456 CGGCCAGTATATCACTCTACACC 60.057 52.174 2.24 0.00 34.26 4.16
1541 1639 3.612004 GCGGCCAGTATATCACTCTACAC 60.612 52.174 2.24 0.00 34.26 2.90
1542 1640 2.557056 GCGGCCAGTATATCACTCTACA 59.443 50.000 2.24 0.00 34.26 2.74
1543 1641 2.094649 GGCGGCCAGTATATCACTCTAC 60.095 54.545 15.62 0.00 34.26 2.59
1544 1642 2.168496 GGCGGCCAGTATATCACTCTA 58.832 52.381 15.62 0.00 34.26 2.43
1545 1643 0.969894 GGCGGCCAGTATATCACTCT 59.030 55.000 15.62 0.00 34.26 3.24
1546 1644 0.679505 TGGCGGCCAGTATATCACTC 59.320 55.000 19.77 0.00 34.26 3.51
1547 1645 0.393077 GTGGCGGCCAGTATATCACT 59.607 55.000 24.58 0.00 38.32 3.41
1548 1646 0.393077 AGTGGCGGCCAGTATATCAC 59.607 55.000 27.37 10.64 35.09 3.06
1549 1647 1.128200 AAGTGGCGGCCAGTATATCA 58.872 50.000 28.55 0.00 35.94 2.15
1550 1648 2.143925 GAAAGTGGCGGCCAGTATATC 58.856 52.381 28.55 21.52 35.94 1.63
1551 1649 1.202770 GGAAAGTGGCGGCCAGTATAT 60.203 52.381 28.55 17.85 35.94 0.86
1552 1650 0.179468 GGAAAGTGGCGGCCAGTATA 59.821 55.000 28.55 0.00 35.94 1.47
1553 1651 1.077716 GGAAAGTGGCGGCCAGTAT 60.078 57.895 28.55 14.47 35.94 2.12
1554 1652 2.180159 GAGGAAAGTGGCGGCCAGTA 62.180 60.000 28.55 0.81 35.94 2.74
1555 1653 3.553095 GAGGAAAGTGGCGGCCAGT 62.553 63.158 24.58 23.99 39.10 4.00
1664 1762 4.762251 GGGCAAGAGGATGTATATTTGGTC 59.238 45.833 0.00 0.00 0.00 4.02
1889 1998 4.189231 GGTGCATCTACGAATACAAAGGT 58.811 43.478 0.00 0.00 0.00 3.50
1908 2017 0.892755 ATTGCTTGCAGTGGATGGTG 59.107 50.000 0.00 0.00 0.00 4.17
1917 2026 1.667236 TATGTCCGGATTGCTTGCAG 58.333 50.000 7.81 0.00 0.00 4.41
2073 2182 8.641498 AACAGTGATCATTTCCATTTTCTACT 57.359 30.769 0.00 0.00 0.00 2.57
2347 2456 0.883833 CTTGTGGTGCCTGGTTCATC 59.116 55.000 0.00 0.00 0.00 2.92
2573 2682 6.780457 AAGAATTTCCCATTTCATCATCGT 57.220 33.333 0.00 0.00 0.00 3.73
2732 2841 4.627467 AGGATTTCGAGAGACATTCGTTTG 59.373 41.667 0.00 0.00 41.84 2.93
2892 3001 3.071786 ACAGCGATCGATGAAGTACAG 57.928 47.619 37.13 10.87 35.26 2.74
2938 3047 0.960861 GCCCAGACGGAGGAAAAAGG 60.961 60.000 0.00 0.00 0.00 3.11
2954 3063 2.409948 ACAAGAGTGAAGCTATGCCC 57.590 50.000 0.00 0.00 0.00 5.36
2967 3076 5.388944 GCAAAGAGCAAAGTCATACAAGAG 58.611 41.667 0.00 0.00 44.79 2.85
3006 3115 5.183014 TCTGCATAACTAGGATGTACACG 57.817 43.478 0.00 0.00 0.00 4.49
3040 3149 6.560253 AGGAGATACAAACACAATGTGAAC 57.440 37.500 21.34 0.00 36.96 3.18
3041 3150 7.581213 AAAGGAGATACAAACACAATGTGAA 57.419 32.000 21.34 0.31 36.96 3.18
3042 3151 8.729756 CATAAAGGAGATACAAACACAATGTGA 58.270 33.333 21.34 0.00 36.96 3.58
3043 3152 7.485913 GCATAAAGGAGATACAAACACAATGTG 59.514 37.037 12.40 12.40 39.75 3.21
3044 3153 7.394359 AGCATAAAGGAGATACAAACACAATGT 59.606 33.333 0.00 0.00 34.81 2.71
3173 3283 4.944962 TGAAGTAGACATGAAAATGGCG 57.055 40.909 0.00 0.00 33.96 5.69
3269 3379 2.301346 GGGGTCCATGTGAATGTCATC 58.699 52.381 0.00 0.00 0.00 2.92
3381 3492 2.685897 GCAATTGCATACGGGTCCTAAA 59.314 45.455 25.36 0.00 41.59 1.85
3829 3945 6.200475 GGTAGAACCATTATCTAACGTTCTGC 59.800 42.308 2.82 15.74 42.26 4.26
3840 3956 9.018582 ACGTATTAGTAGGGTAGAACCATTATC 57.981 37.037 0.00 0.00 41.02 1.75
3969 4085 1.752683 TTAGAGCTCTCCTGGTCGAC 58.247 55.000 22.17 7.13 39.21 4.20
4322 4439 5.573380 ACCACCAGAGCAACATCATATAT 57.427 39.130 0.00 0.00 0.00 0.86
4510 4627 0.468400 CCCCTCTCTCCCCTACTTCG 60.468 65.000 0.00 0.00 0.00 3.79
4556 4673 3.181412 ACCCCAAAGGAATACAACACCAT 60.181 43.478 0.00 0.00 39.89 3.55
4635 4752 1.869132 GTGCGCGCTTTAGCCAATG 60.869 57.895 33.29 0.00 37.91 2.82
4636 4753 2.331893 TGTGCGCGCTTTAGCCAAT 61.332 52.632 33.29 0.00 37.91 3.16
4637 4754 2.975248 TGTGCGCGCTTTAGCCAA 60.975 55.556 33.29 5.92 37.91 4.52
4638 4755 3.722295 GTGTGCGCGCTTTAGCCA 61.722 61.111 33.29 15.35 37.91 4.75
4639 4756 3.722295 TGTGTGCGCGCTTTAGCC 61.722 61.111 33.29 14.00 37.91 3.93
4640 4757 2.499732 GTGTGTGCGCGCTTTAGC 60.500 61.111 33.29 17.32 37.78 3.09
4687 4804 1.694693 GGGCAGTACTATTGAGGGGGA 60.695 57.143 0.00 0.00 0.00 4.81
4688 4805 0.765510 GGGCAGTACTATTGAGGGGG 59.234 60.000 0.00 0.00 0.00 5.40
4689 4806 0.765510 GGGGCAGTACTATTGAGGGG 59.234 60.000 0.00 0.00 0.00 4.79
4690 4807 1.694696 GAGGGGCAGTACTATTGAGGG 59.305 57.143 0.00 0.00 0.00 4.30
4691 4808 2.398588 TGAGGGGCAGTACTATTGAGG 58.601 52.381 0.00 0.00 0.00 3.86
4692 4809 3.706594 TCTTGAGGGGCAGTACTATTGAG 59.293 47.826 0.00 0.00 0.00 3.02
4693 4810 3.706594 CTCTTGAGGGGCAGTACTATTGA 59.293 47.826 0.00 0.00 0.00 2.57
4694 4811 3.181461 CCTCTTGAGGGGCAGTACTATTG 60.181 52.174 8.74 0.00 0.00 1.90
4695 4812 3.041946 CCTCTTGAGGGGCAGTACTATT 58.958 50.000 8.74 0.00 0.00 1.73
4696 4813 2.683768 CCTCTTGAGGGGCAGTACTAT 58.316 52.381 8.74 0.00 0.00 2.12
4697 4814 1.343075 CCCTCTTGAGGGGCAGTACTA 60.343 57.143 24.38 0.00 45.34 1.82
4698 4815 0.618968 CCCTCTTGAGGGGCAGTACT 60.619 60.000 24.38 0.00 45.34 2.73
4699 4816 1.908483 CCCTCTTGAGGGGCAGTAC 59.092 63.158 24.38 0.00 45.34 2.73
4700 4817 4.480480 CCCTCTTGAGGGGCAGTA 57.520 61.111 24.38 0.00 45.34 2.74
4704 4821 7.874550 GATATCTATCATCCCTCTTGAGGGGC 61.875 50.000 29.37 6.77 39.72 5.80
4760 4877 1.518903 GAGGTGGCCTTGTCACAAGC 61.519 60.000 12.49 7.65 40.26 4.01
4821 4938 4.079850 CAGCAGAGGAGCGCCACT 62.080 66.667 9.88 4.57 40.15 4.00
4850 4967 2.940410 ACAACAACATTCCGTCGTTTCT 59.060 40.909 0.00 0.00 0.00 2.52
4866 4983 2.143122 GTGGCATCTCGAAAGACAACA 58.857 47.619 0.00 0.00 33.32 3.33
4875 4992 3.838271 GAGGGCGTGGCATCTCGA 61.838 66.667 0.49 0.00 32.30 4.04
4973 5104 4.080863 ACAGCTTTCGGAGAACCAGAATAT 60.081 41.667 0.00 0.00 45.90 1.28
4996 5127 1.302511 GAAACAAGGCCGCTCAGGA 60.303 57.895 0.00 0.00 45.00 3.86
5142 5273 9.755122 TTTTCTTTTTGAATTTTTAAGGGGGAA 57.245 25.926 0.00 0.00 34.24 3.97


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

AutoCloner maintained by Alex Coulton.