Multiple sequence alignment - TraesCS3D01G380800

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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 TraesCS3D01G380800 chr3D 100.000 4154 0 0 833 4986 496943580 496947733 0.000000e+00 7672.0
1 TraesCS3D01G380800 chr3D 94.000 650 37 2 2131 2779 119531032 119531680 0.000000e+00 983.0
2 TraesCS3D01G380800 chr3D 100.000 454 0 0 1 454 496942748 496943201 0.000000e+00 839.0
3 TraesCS3D01G380800 chr3D 90.345 145 5 2 2811 2955 119548648 119548783 1.100000e-41 182.0
4 TraesCS3D01G380800 chr3B 96.149 3454 85 21 875 4313 656579555 656582975 0.000000e+00 5598.0
5 TraesCS3D01G380800 chr3B 95.814 430 17 1 26 454 656578855 656579284 0.000000e+00 693.0
6 TraesCS3D01G380800 chr3B 92.000 425 23 4 4572 4986 656583120 656583543 2.000000e-163 586.0
7 TraesCS3D01G380800 chr3B 97.826 46 1 0 4351 4396 656582987 656583032 4.140000e-11 80.5
8 TraesCS3D01G380800 chr3A 93.764 2309 109 22 2002 4294 637623306 637621017 0.000000e+00 3434.0
9 TraesCS3D01G380800 chr3A 94.283 1137 43 14 833 1961 637624425 637623303 0.000000e+00 1720.0
10 TraesCS3D01G380800 chr3A 93.968 431 20 3 26 454 637624878 637624452 0.000000e+00 647.0
11 TraesCS3D01G380800 chr3A 90.146 274 17 6 4713 4986 637615520 637615257 1.030000e-91 348.0
12 TraesCS3D01G380800 chr3A 86.000 100 5 6 4606 4705 637616546 637616456 1.140000e-16 99.0
13 TraesCS3D01G380800 chr2D 93.688 507 32 0 2087 2593 474294465 474293959 0.000000e+00 760.0
14 TraesCS3D01G380800 chr2D 95.833 216 9 0 2595 2810 474252864 474252649 2.860000e-92 350.0
15 TraesCS3D01G380800 chr2D 90.345 145 5 3 2811 2955 474251008 474250873 1.100000e-41 182.0
16 TraesCS3D01G380800 chr4D 87.805 82 9 1 3309 3390 183779609 183779689 1.480000e-15 95.3
17 TraesCS3D01G380800 chr6D 86.747 83 10 1 3309 3391 46227914 46227995 1.910000e-14 91.6
18 TraesCS3D01G380800 chr5D 86.747 83 10 1 3309 3391 391825421 391825502 1.910000e-14 91.6


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 TraesCS3D01G380800 chr3D 496942748 496947733 4985 False 4255.500000 7672 100.00000 1 4986 2 chr3D.!!$F3 4985
1 TraesCS3D01G380800 chr3D 119531032 119531680 648 False 983.000000 983 94.00000 2131 2779 1 chr3D.!!$F1 648
2 TraesCS3D01G380800 chr3B 656578855 656583543 4688 False 1739.375000 5598 95.44725 26 4986 4 chr3B.!!$F1 4960
3 TraesCS3D01G380800 chr3A 637621017 637624878 3861 True 1933.666667 3434 94.00500 26 4294 3 chr3A.!!$R2 4268
4 TraesCS3D01G380800 chr3A 637615257 637616546 1289 True 223.500000 348 88.07300 4606 4986 2 chr3A.!!$R1 380
5 TraesCS3D01G380800 chr2D 474293959 474294465 506 True 760.000000 760 93.68800 2087 2593 1 chr2D.!!$R1 506
6 TraesCS3D01G380800 chr2D 474250873 474252864 1991 True 266.000000 350 93.08900 2595 2955 2 chr2D.!!$R2 360

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
906 1110 0.250424 AAACCCTAACCACGGTTCGG 60.250 55.000 11.65 11.65 41.58 4.30 F
909 1113 0.671472 CCCTAACCACGGTTCGGTTC 60.671 60.000 16.06 0.00 43.36 3.62 F
2022 2234 0.747644 CCATGGGCTGTATGTGCGAA 60.748 55.000 2.85 0.00 0.00 4.70 F
2493 2706 1.063649 GCTTCTGCATGCCATCACG 59.936 57.895 16.68 0.00 39.41 4.35 F
3430 5291 1.148310 CAAAGGACTACACTGCACCG 58.852 55.000 0.00 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2177 0.662619 CTTCGCACAGCTGGAAAACA 59.337 50.000 19.93 0.0 0.00 2.83 R
2759 2973 1.135315 CATCCATGGCTGGTTTTGACG 60.135 52.381 6.96 0.0 43.61 4.35 R
3727 5588 0.873312 CACACGCCATCATCCTCTCG 60.873 60.000 0.00 0.0 0.00 4.04 R
3883 5744 1.645455 CATCTTCATTCTGCCGCCG 59.355 57.895 0.00 0.0 0.00 6.46 R
4563 6480 0.464036 ACAGCGTTGTCAAGTCTCCA 59.536 50.000 0.00 0.0 29.46 3.86 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
23 24 6.377327 CAACCATAGCCTACCACTATTTTG 57.623 41.667 0.00 0.00 0.00 2.44
24 25 5.968676 ACCATAGCCTACCACTATTTTGA 57.031 39.130 0.00 0.00 0.00 2.69
25 26 6.515512 ACCATAGCCTACCACTATTTTGAT 57.484 37.500 0.00 0.00 0.00 2.57
26 27 6.534634 ACCATAGCCTACCACTATTTTGATC 58.465 40.000 0.00 0.00 0.00 2.92
27 28 6.330250 ACCATAGCCTACCACTATTTTGATCT 59.670 38.462 0.00 0.00 0.00 2.75
28 29 6.876257 CCATAGCCTACCACTATTTTGATCTC 59.124 42.308 0.00 0.00 0.00 2.75
29 30 7.256475 CCATAGCCTACCACTATTTTGATCTCT 60.256 40.741 0.00 0.00 0.00 3.10
30 31 5.923204 AGCCTACCACTATTTTGATCTCTG 58.077 41.667 0.00 0.00 0.00 3.35
37 38 5.394663 CCACTATTTTGATCTCTGGACGTCT 60.395 44.000 16.46 0.00 0.00 4.18
112 113 2.693069 ACAGATCCAGAAAAGTGCGAG 58.307 47.619 0.00 0.00 0.00 5.03
150 151 1.131126 GCATTCAGGTCATTCCACGTG 59.869 52.381 9.08 9.08 39.02 4.49
194 195 1.067142 CAATCGTCCTCTCCGGAAACA 60.067 52.381 5.23 0.00 45.32 2.83
201 202 4.426313 CTCCGGAAACAGGGGGCC 62.426 72.222 5.23 0.00 0.00 5.80
433 435 1.143183 GCCAGGCCATTCATTGCAG 59.857 57.895 5.01 0.00 0.00 4.41
905 1109 0.869730 CAAACCCTAACCACGGTTCG 59.130 55.000 4.34 0.00 41.58 3.95
906 1110 0.250424 AAACCCTAACCACGGTTCGG 60.250 55.000 11.65 11.65 41.58 4.30
907 1111 1.410050 AACCCTAACCACGGTTCGGT 61.410 55.000 16.06 14.33 37.89 4.69
909 1113 0.671472 CCCTAACCACGGTTCGGTTC 60.671 60.000 16.06 0.00 43.36 3.62
944 1148 0.966370 ACGACGAGGAAGGAAGGAGG 60.966 60.000 0.00 0.00 0.00 4.30
1357 1561 3.186613 CGTAGGTGAGTTGCTTTCCTTTC 59.813 47.826 0.00 0.00 0.00 2.62
1900 2111 5.008316 AGTTCTTGGACAAAACGAACATACC 59.992 40.000 14.20 0.00 37.14 2.73
1914 2125 5.294306 ACGAACATACCTTTCTGCATGTATG 59.706 40.000 14.01 14.01 43.80 2.39
1963 2175 1.135527 CGATTGAACTGCATGCCCAAT 59.864 47.619 16.68 17.70 0.00 3.16
1965 2177 3.602483 GATTGAACTGCATGCCCAATTT 58.398 40.909 16.68 0.40 0.00 1.82
1975 2187 2.252976 TGCCCAATTTGTTTTCCAGC 57.747 45.000 0.00 0.00 0.00 4.85
1976 2188 1.767681 TGCCCAATTTGTTTTCCAGCT 59.232 42.857 0.00 0.00 0.00 4.24
1995 2207 3.316308 AGCTGTGCGAAGTTCTTGAATTT 59.684 39.130 0.56 0.00 0.00 1.82
2022 2234 0.747644 CCATGGGCTGTATGTGCGAA 60.748 55.000 2.85 0.00 0.00 4.70
2106 2318 1.734655 TTTCTTCTCCAGGTGCCTCT 58.265 50.000 0.00 0.00 0.00 3.69
2386 2598 4.397730 TGACCATTATTCAAACACCATCCG 59.602 41.667 0.00 0.00 0.00 4.18
2472 2685 4.228210 TCCAAGAAGCAAGGAATGGACTAT 59.772 41.667 0.00 0.00 32.28 2.12
2493 2706 1.063649 GCTTCTGCATGCCATCACG 59.936 57.895 16.68 0.00 39.41 4.35
2664 2877 4.022935 CCTTTGCAGAACACAATTGCTCTA 60.023 41.667 5.05 0.00 38.60 2.43
3021 4875 1.745115 TGCTGTCCGCTGCAATACC 60.745 57.895 0.00 0.00 44.61 2.73
3078 4933 6.183360 TGTTTCCAGTATGTTGCTCCAATTTT 60.183 34.615 0.00 0.00 0.00 1.82
3084 4939 6.583806 CAGTATGTTGCTCCAATTTTCAGAAC 59.416 38.462 0.00 0.00 0.00 3.01
3085 4940 5.796424 ATGTTGCTCCAATTTTCAGAACT 57.204 34.783 0.00 0.00 0.00 3.01
3430 5291 1.148310 CAAAGGACTACACTGCACCG 58.852 55.000 0.00 0.00 0.00 4.94
4154 6015 5.824904 AATCATCTGGTGTTCTGCATTAC 57.175 39.130 0.00 0.00 0.00 1.89
4234 6129 9.982651 AACATATATATGACGTTGAAGCTAAGT 57.017 29.630 26.05 0.00 37.15 2.24
4235 6130 9.627395 ACATATATATGACGTTGAAGCTAAGTC 57.373 33.333 26.05 0.00 37.15 3.01
4236 6131 9.077674 CATATATATGACGTTGAAGCTAAGTCC 57.922 37.037 16.44 0.00 35.75 3.85
4237 6132 3.678056 ATGACGTTGAAGCTAAGTCCA 57.322 42.857 0.00 0.00 0.00 4.02
4253 6148 8.136165 AGCTAAGTCCAATATTACTACTTCACG 58.864 37.037 10.76 0.00 32.85 4.35
4347 6242 7.782897 AAATGTAAGGATGAGATAGGATCGA 57.217 36.000 0.00 0.00 0.00 3.59
4348 6243 6.767524 ATGTAAGGATGAGATAGGATCGAC 57.232 41.667 0.00 0.00 0.00 4.20
4349 6244 5.631119 TGTAAGGATGAGATAGGATCGACA 58.369 41.667 0.00 0.00 0.00 4.35
4401 6298 9.180678 CTGGTTATGTGTTTAACTGTGAAAATC 57.819 33.333 0.00 0.00 33.49 2.17
4472 6369 8.405531 GCTAGGCACATCTGAAACATAAAAATA 58.594 33.333 0.00 0.00 0.00 1.40
4503 6420 9.248291 ACTGTTTCATGATAAACACAAAATGTC 57.752 29.630 8.57 0.00 42.78 3.06
4504 6421 9.247126 CTGTTTCATGATAAACACAAAATGTCA 57.753 29.630 8.57 0.00 42.78 3.58
4505 6422 9.591792 TGTTTCATGATAAACACAAAATGTCAA 57.408 25.926 8.57 0.00 42.78 3.18
4508 6425 9.761504 TTCATGATAAACACAAAATGTCAATGT 57.238 25.926 0.00 0.00 42.31 2.71
4562 6479 7.801716 AAAAGTAACATTGAAGCTACTGACA 57.198 32.000 0.00 0.00 0.00 3.58
4563 6480 7.986085 AAAGTAACATTGAAGCTACTGACAT 57.014 32.000 0.00 0.00 0.00 3.06
4564 6481 6.974932 AGTAACATTGAAGCTACTGACATG 57.025 37.500 0.00 0.00 0.00 3.21
4565 6482 5.877012 AGTAACATTGAAGCTACTGACATGG 59.123 40.000 0.00 0.00 0.00 3.66
4566 6483 4.558226 ACATTGAAGCTACTGACATGGA 57.442 40.909 0.00 0.00 0.00 3.41
4567 6484 4.511527 ACATTGAAGCTACTGACATGGAG 58.488 43.478 0.00 0.00 0.00 3.86
4568 6485 4.223700 ACATTGAAGCTACTGACATGGAGA 59.776 41.667 0.00 0.00 0.00 3.71
4569 6486 3.876274 TGAAGCTACTGACATGGAGAC 57.124 47.619 0.00 0.00 0.00 3.36
4570 6487 3.435275 TGAAGCTACTGACATGGAGACT 58.565 45.455 0.00 0.00 0.00 3.24
4571 6488 3.834813 TGAAGCTACTGACATGGAGACTT 59.165 43.478 0.00 0.39 0.00 3.01
4572 6489 3.883830 AGCTACTGACATGGAGACTTG 57.116 47.619 0.00 0.00 41.07 3.16
4573 6490 3.435275 AGCTACTGACATGGAGACTTGA 58.565 45.455 0.00 0.00 38.76 3.02
4574 6491 3.194542 AGCTACTGACATGGAGACTTGAC 59.805 47.826 0.00 0.00 38.76 3.18
4575 6492 3.056536 GCTACTGACATGGAGACTTGACA 60.057 47.826 0.00 0.00 37.70 3.58
4576 6493 4.561530 GCTACTGACATGGAGACTTGACAA 60.562 45.833 0.00 0.00 39.01 3.18
4577 6494 3.733337 ACTGACATGGAGACTTGACAAC 58.267 45.455 0.00 0.00 39.01 3.32
4593 6510 1.603802 ACAACGCTGTGAACTTCCATG 59.396 47.619 0.00 0.00 33.30 3.66
4726 7581 2.093764 TGAAAACTGCACAAACCCCAAG 60.094 45.455 0.00 0.00 0.00 3.61
4870 7725 6.003950 TGAAAGCAGAGGTACTAAGCAATTT 58.996 36.000 0.00 0.00 41.55 1.82
4904 7759 1.067821 GTGGAGATAGAACAGAGGGCG 59.932 57.143 0.00 0.00 0.00 6.13
4961 7816 5.539048 CTTCCTCGGGTTATCGATTAACAT 58.461 41.667 1.71 0.00 41.74 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.119536 TCAAAATAGTGGTAGGCTATGGTTG 58.880 40.000 0.00 0.00 32.15 3.77
1 2 6.321821 TCAAAATAGTGGTAGGCTATGGTT 57.678 37.500 0.00 0.00 30.38 3.67
2 3 5.968676 TCAAAATAGTGGTAGGCTATGGT 57.031 39.130 0.00 0.00 30.38 3.55
4 5 7.601886 CAGAGATCAAAATAGTGGTAGGCTATG 59.398 40.741 0.00 0.00 30.38 2.23
5 6 7.256475 CCAGAGATCAAAATAGTGGTAGGCTAT 60.256 40.741 0.00 0.00 0.00 2.97
6 7 6.042093 CCAGAGATCAAAATAGTGGTAGGCTA 59.958 42.308 0.00 0.00 0.00 3.93
7 8 5.163258 CCAGAGATCAAAATAGTGGTAGGCT 60.163 44.000 0.00 0.00 0.00 4.58
8 9 5.059833 CCAGAGATCAAAATAGTGGTAGGC 58.940 45.833 0.00 0.00 0.00 3.93
9 10 6.284459 GTCCAGAGATCAAAATAGTGGTAGG 58.716 44.000 0.00 0.00 0.00 3.18
10 11 5.980116 CGTCCAGAGATCAAAATAGTGGTAG 59.020 44.000 0.00 0.00 0.00 3.18
11 12 5.421056 ACGTCCAGAGATCAAAATAGTGGTA 59.579 40.000 0.00 0.00 0.00 3.25
12 13 4.223032 ACGTCCAGAGATCAAAATAGTGGT 59.777 41.667 0.00 0.00 0.00 4.16
13 14 4.759782 ACGTCCAGAGATCAAAATAGTGG 58.240 43.478 0.00 0.00 0.00 4.00
14 15 5.655488 AGACGTCCAGAGATCAAAATAGTG 58.345 41.667 13.01 0.00 0.00 2.74
15 16 5.923733 AGACGTCCAGAGATCAAAATAGT 57.076 39.130 13.01 0.00 0.00 2.12
16 17 6.036517 CCAAAGACGTCCAGAGATCAAAATAG 59.963 42.308 13.01 0.00 0.00 1.73
17 18 5.874810 CCAAAGACGTCCAGAGATCAAAATA 59.125 40.000 13.01 0.00 0.00 1.40
18 19 4.697352 CCAAAGACGTCCAGAGATCAAAAT 59.303 41.667 13.01 0.00 0.00 1.82
19 20 4.065088 CCAAAGACGTCCAGAGATCAAAA 58.935 43.478 13.01 0.00 0.00 2.44
20 21 3.664107 CCAAAGACGTCCAGAGATCAAA 58.336 45.455 13.01 0.00 0.00 2.69
21 22 2.612972 GCCAAAGACGTCCAGAGATCAA 60.613 50.000 13.01 0.00 0.00 2.57
22 23 1.066858 GCCAAAGACGTCCAGAGATCA 60.067 52.381 13.01 0.00 0.00 2.92
23 24 1.205893 AGCCAAAGACGTCCAGAGATC 59.794 52.381 13.01 0.00 0.00 2.75
24 25 1.066573 CAGCCAAAGACGTCCAGAGAT 60.067 52.381 13.01 0.00 0.00 2.75
25 26 0.318441 CAGCCAAAGACGTCCAGAGA 59.682 55.000 13.01 0.00 0.00 3.10
26 27 0.318441 TCAGCCAAAGACGTCCAGAG 59.682 55.000 13.01 0.00 0.00 3.35
27 28 0.033504 GTCAGCCAAAGACGTCCAGA 59.966 55.000 13.01 0.00 0.00 3.86
28 29 2.533318 GTCAGCCAAAGACGTCCAG 58.467 57.895 13.01 1.97 0.00 3.86
29 30 4.771127 GTCAGCCAAAGACGTCCA 57.229 55.556 13.01 0.00 0.00 4.02
112 113 2.356667 CCCTCTTGGTCTTGGGGC 59.643 66.667 0.00 0.00 36.15 5.80
158 159 1.532604 ATTGCGAGAGGTGGACGTGA 61.533 55.000 0.00 0.00 0.00 4.35
194 195 3.739613 GGTCATTTCGGGCCCCCT 61.740 66.667 18.66 0.00 0.00 4.79
201 202 0.670162 GGGCATGATGGTCATTTCGG 59.330 55.000 0.00 0.00 34.28 4.30
202 203 0.670162 GGGGCATGATGGTCATTTCG 59.330 55.000 0.00 0.00 34.28 3.46
272 274 1.231928 GGTTGGGTCTGGTTGGGTT 59.768 57.895 0.00 0.00 0.00 4.11
992 1196 1.021390 GTTCACCACCATCTCCGCTG 61.021 60.000 0.00 0.00 0.00 5.18
1203 1407 3.231736 AGCGACACCCTCCACGTT 61.232 61.111 0.00 0.00 0.00 3.99
1515 1726 0.390603 CGGCATTTACCCGTCACTCA 60.391 55.000 0.00 0.00 40.84 3.41
1545 1756 2.234414 AGGAAAACATGCGATGCCAAAT 59.766 40.909 0.00 0.00 0.00 2.32
1547 1758 1.067706 CAGGAAAACATGCGATGCCAA 60.068 47.619 0.00 0.00 0.00 4.52
1548 1759 0.527113 CAGGAAAACATGCGATGCCA 59.473 50.000 0.00 0.00 0.00 4.92
1549 1760 0.527565 ACAGGAAAACATGCGATGCC 59.472 50.000 0.00 0.00 0.00 4.40
1550 1761 3.698029 ATACAGGAAAACATGCGATGC 57.302 42.857 0.00 0.00 0.00 3.91
1591 1802 5.278218 GCAACACCCCAACAATAAAATTTGG 60.278 40.000 0.00 0.00 39.71 3.28
1900 2111 6.732531 TTCTTCAGACATACATGCAGAAAG 57.267 37.500 0.00 0.00 0.00 2.62
1936 2148 1.144969 TGCAGTTCAATCGTTCGGTC 58.855 50.000 0.00 0.00 0.00 4.79
1963 2175 1.098869 TCGCACAGCTGGAAAACAAA 58.901 45.000 19.93 0.00 0.00 2.83
1965 2177 0.662619 CTTCGCACAGCTGGAAAACA 59.337 50.000 19.93 0.00 0.00 2.83
1975 2187 4.601019 ACAAATTCAAGAACTTCGCACAG 58.399 39.130 0.00 0.00 0.00 3.66
1976 2188 4.630894 ACAAATTCAAGAACTTCGCACA 57.369 36.364 0.00 0.00 0.00 4.57
2106 2318 3.181477 CCTTCCATGTCAAAGTTGCACAA 60.181 43.478 0.00 0.00 0.00 3.33
2189 2401 1.300080 GCCGTTTGCATGCACAACT 60.300 52.632 27.54 0.00 40.77 3.16
2386 2598 5.008118 GGAATTCTTAGTGCTATTGCTGGAC 59.992 44.000 5.23 0.00 40.48 4.02
2664 2877 4.408921 TGTCGATCAGAAAGGGACCAATAT 59.591 41.667 0.00 0.00 0.00 1.28
2759 2973 1.135315 CATCCATGGCTGGTTTTGACG 60.135 52.381 6.96 0.00 43.61 4.35
3021 4875 2.532531 ATTCAATTGCGCTTGTCTCG 57.467 45.000 9.73 0.00 0.00 4.04
3078 4933 2.544721 AGGCCTGATGAAGAGTTCTGA 58.455 47.619 3.11 0.00 0.00 3.27
3084 4939 3.347077 AAGACAAGGCCTGATGAAGAG 57.653 47.619 5.69 0.00 0.00 2.85
3085 4940 3.072915 TCAAAGACAAGGCCTGATGAAGA 59.927 43.478 5.69 0.00 0.00 2.87
3341 5202 1.274703 GGGGGAGATTCTGGAGCACA 61.275 60.000 0.00 0.00 0.00 4.57
3430 5291 1.601166 AAAGTACAAGTTCCACCGGC 58.399 50.000 0.00 0.00 0.00 6.13
3727 5588 0.873312 CACACGCCATCATCCTCTCG 60.873 60.000 0.00 0.00 0.00 4.04
3883 5744 1.645455 CATCTTCATTCTGCCGCCG 59.355 57.895 0.00 0.00 0.00 6.46
4180 6051 8.780846 AAATGTGTAATTACTGAACCGTCATA 57.219 30.769 16.33 0.00 31.85 2.15
4215 6110 5.339008 TGGACTTAGCTTCAACGTCATAT 57.661 39.130 0.00 0.00 0.00 1.78
4216 6111 4.794278 TGGACTTAGCTTCAACGTCATA 57.206 40.909 0.00 0.00 0.00 2.15
4217 6112 3.678056 TGGACTTAGCTTCAACGTCAT 57.322 42.857 0.00 0.00 0.00 3.06
4218 6113 3.462483 TTGGACTTAGCTTCAACGTCA 57.538 42.857 0.00 0.00 0.00 4.35
4219 6114 6.663944 AATATTGGACTTAGCTTCAACGTC 57.336 37.500 0.00 0.00 0.00 4.34
4220 6115 7.328737 AGTAATATTGGACTTAGCTTCAACGT 58.671 34.615 0.00 0.00 0.00 3.99
4221 6116 7.772332 AGTAATATTGGACTTAGCTTCAACG 57.228 36.000 0.00 0.00 0.00 4.10
4222 6117 9.819267 AGTAGTAATATTGGACTTAGCTTCAAC 57.181 33.333 0.00 0.00 0.00 3.18
4226 6121 9.819267 GTGAAGTAGTAATATTGGACTTAGCTT 57.181 33.333 0.00 6.76 30.66 3.74
4227 6122 8.136165 CGTGAAGTAGTAATATTGGACTTAGCT 58.864 37.037 9.95 0.00 30.66 3.32
4228 6123 8.133627 TCGTGAAGTAGTAATATTGGACTTAGC 58.866 37.037 9.95 6.73 30.66 3.09
4229 6124 9.666626 CTCGTGAAGTAGTAATATTGGACTTAG 57.333 37.037 9.95 6.75 30.66 2.18
4230 6125 9.399797 TCTCGTGAAGTAGTAATATTGGACTTA 57.600 33.333 9.95 0.00 30.66 2.24
4231 6126 8.189460 GTCTCGTGAAGTAGTAATATTGGACTT 58.811 37.037 9.82 9.82 33.14 3.01
4232 6127 7.338703 TGTCTCGTGAAGTAGTAATATTGGACT 59.661 37.037 0.00 0.00 0.00 3.85
4233 6128 7.478322 TGTCTCGTGAAGTAGTAATATTGGAC 58.522 38.462 0.00 0.00 0.00 4.02
4234 6129 7.555195 TCTGTCTCGTGAAGTAGTAATATTGGA 59.445 37.037 0.00 0.00 0.00 3.53
4235 6130 7.704271 TCTGTCTCGTGAAGTAGTAATATTGG 58.296 38.462 0.00 0.00 0.00 3.16
4236 6131 9.737427 AATCTGTCTCGTGAAGTAGTAATATTG 57.263 33.333 0.00 0.00 0.00 1.90
4253 6148 7.369803 TGCTTCACTGAATTTAATCTGTCTC 57.630 36.000 0.00 0.00 30.16 3.36
4323 6218 7.233553 TGTCGATCCTATCTCATCCTTACATTT 59.766 37.037 0.00 0.00 0.00 2.32
4324 6219 6.721668 TGTCGATCCTATCTCATCCTTACATT 59.278 38.462 0.00 0.00 0.00 2.71
4325 6220 6.249192 TGTCGATCCTATCTCATCCTTACAT 58.751 40.000 0.00 0.00 0.00 2.29
4326 6221 5.631119 TGTCGATCCTATCTCATCCTTACA 58.369 41.667 0.00 0.00 0.00 2.41
4327 6222 6.601613 AGATGTCGATCCTATCTCATCCTTAC 59.398 42.308 13.29 0.00 38.16 2.34
4328 6223 6.726379 AGATGTCGATCCTATCTCATCCTTA 58.274 40.000 13.29 0.00 38.16 2.69
4329 6224 5.579047 AGATGTCGATCCTATCTCATCCTT 58.421 41.667 13.29 1.50 38.16 3.36
4330 6225 5.191727 AGATGTCGATCCTATCTCATCCT 57.808 43.478 13.29 0.00 38.16 3.24
4331 6226 5.417266 TCAAGATGTCGATCCTATCTCATCC 59.583 44.000 13.29 0.00 38.16 3.51
4332 6227 6.507958 TCAAGATGTCGATCCTATCTCATC 57.492 41.667 0.00 0.00 37.93 2.92
4333 6228 6.718912 TCTTCAAGATGTCGATCCTATCTCAT 59.281 38.462 0.00 0.00 31.16 2.90
4334 6229 6.016693 GTCTTCAAGATGTCGATCCTATCTCA 60.017 42.308 0.00 0.00 31.16 3.27
4335 6230 6.016693 TGTCTTCAAGATGTCGATCCTATCTC 60.017 42.308 0.00 0.00 31.16 2.75
4336 6231 5.830457 TGTCTTCAAGATGTCGATCCTATCT 59.170 40.000 0.00 0.00 32.80 1.98
4337 6232 6.078202 TGTCTTCAAGATGTCGATCCTATC 57.922 41.667 0.00 0.00 0.00 2.08
4338 6233 6.471233 TTGTCTTCAAGATGTCGATCCTAT 57.529 37.500 0.00 0.00 0.00 2.57
4339 6234 5.914898 TTGTCTTCAAGATGTCGATCCTA 57.085 39.130 0.00 0.00 0.00 2.94
4340 6235 4.808414 TTGTCTTCAAGATGTCGATCCT 57.192 40.909 0.00 0.00 0.00 3.24
4341 6236 7.539712 TTATTTGTCTTCAAGATGTCGATCC 57.460 36.000 0.00 0.00 34.88 3.36
4342 6237 9.430838 CATTTATTTGTCTTCAAGATGTCGATC 57.569 33.333 0.00 0.00 34.88 3.69
4343 6238 8.950210 ACATTTATTTGTCTTCAAGATGTCGAT 58.050 29.630 0.00 0.00 34.88 3.59
4344 6239 8.322906 ACATTTATTTGTCTTCAAGATGTCGA 57.677 30.769 0.00 0.00 34.88 4.20
4349 6244 9.846248 GCAGTTACATTTATTTGTCTTCAAGAT 57.154 29.630 0.00 0.00 34.88 2.40
4374 6269 5.682943 TCACAGTTAAACACATAACCAGC 57.317 39.130 0.00 0.00 36.62 4.85
4426 6323 9.706691 GCCTAGCTTATTATGAACATAACTACA 57.293 33.333 9.04 0.00 36.24 2.74
4427 6324 9.706691 TGCCTAGCTTATTATGAACATAACTAC 57.293 33.333 9.04 1.60 36.24 2.73
4428 6325 9.706691 GTGCCTAGCTTATTATGAACATAACTA 57.293 33.333 9.04 6.12 36.24 2.24
4429 6326 8.210946 TGTGCCTAGCTTATTATGAACATAACT 58.789 33.333 9.04 5.41 36.24 2.24
4430 6327 8.378172 TGTGCCTAGCTTATTATGAACATAAC 57.622 34.615 9.04 0.00 36.24 1.89
4431 6328 9.219603 GATGTGCCTAGCTTATTATGAACATAA 57.780 33.333 9.23 9.23 37.64 1.90
4432 6329 8.597167 AGATGTGCCTAGCTTATTATGAACATA 58.403 33.333 0.00 0.00 0.00 2.29
4433 6330 7.389884 CAGATGTGCCTAGCTTATTATGAACAT 59.610 37.037 0.00 0.00 0.00 2.71
4434 6331 6.707608 CAGATGTGCCTAGCTTATTATGAACA 59.292 38.462 0.00 0.00 0.00 3.18
4435 6332 6.931281 TCAGATGTGCCTAGCTTATTATGAAC 59.069 38.462 0.00 0.00 0.00 3.18
4436 6333 7.066307 TCAGATGTGCCTAGCTTATTATGAA 57.934 36.000 0.00 0.00 0.00 2.57
4437 6334 6.670695 TCAGATGTGCCTAGCTTATTATGA 57.329 37.500 0.00 0.00 0.00 2.15
4438 6335 7.227314 TGTTTCAGATGTGCCTAGCTTATTATG 59.773 37.037 0.00 0.00 0.00 1.90
4439 6336 7.282585 TGTTTCAGATGTGCCTAGCTTATTAT 58.717 34.615 0.00 0.00 0.00 1.28
4440 6337 6.649155 TGTTTCAGATGTGCCTAGCTTATTA 58.351 36.000 0.00 0.00 0.00 0.98
4441 6338 5.500234 TGTTTCAGATGTGCCTAGCTTATT 58.500 37.500 0.00 0.00 0.00 1.40
4478 6395 9.247126 TGACATTTTGTGTTTATCATGAAACAG 57.753 29.630 12.24 4.04 46.99 3.16
4537 6454 8.220755 TGTCAGTAGCTTCAATGTTACTTTTT 57.779 30.769 0.00 0.00 32.89 1.94
4538 6455 7.801716 TGTCAGTAGCTTCAATGTTACTTTT 57.198 32.000 0.00 0.00 32.89 2.27
4539 6456 7.094634 CCATGTCAGTAGCTTCAATGTTACTTT 60.095 37.037 0.00 0.00 32.89 2.66
4540 6457 6.372659 CCATGTCAGTAGCTTCAATGTTACTT 59.627 38.462 0.00 0.00 32.89 2.24
4541 6458 5.877012 CCATGTCAGTAGCTTCAATGTTACT 59.123 40.000 0.00 0.00 34.98 2.24
4542 6459 5.874810 TCCATGTCAGTAGCTTCAATGTTAC 59.125 40.000 0.00 0.00 0.00 2.50
4543 6460 6.048732 TCCATGTCAGTAGCTTCAATGTTA 57.951 37.500 0.00 0.00 0.00 2.41
4544 6461 4.910195 TCCATGTCAGTAGCTTCAATGTT 58.090 39.130 0.00 0.00 0.00 2.71
4545 6462 4.223700 TCTCCATGTCAGTAGCTTCAATGT 59.776 41.667 0.00 0.00 0.00 2.71
4546 6463 4.569966 GTCTCCATGTCAGTAGCTTCAATG 59.430 45.833 0.00 0.00 0.00 2.82
4547 6464 4.469227 AGTCTCCATGTCAGTAGCTTCAAT 59.531 41.667 0.00 0.00 0.00 2.57
4548 6465 3.834813 AGTCTCCATGTCAGTAGCTTCAA 59.165 43.478 0.00 0.00 0.00 2.69
4549 6466 3.435275 AGTCTCCATGTCAGTAGCTTCA 58.565 45.455 0.00 0.00 0.00 3.02
4550 6467 4.081972 TCAAGTCTCCATGTCAGTAGCTTC 60.082 45.833 0.00 0.00 0.00 3.86
4551 6468 3.834813 TCAAGTCTCCATGTCAGTAGCTT 59.165 43.478 0.00 0.00 0.00 3.74
4552 6469 3.194542 GTCAAGTCTCCATGTCAGTAGCT 59.805 47.826 0.00 0.00 0.00 3.32
4553 6470 3.056536 TGTCAAGTCTCCATGTCAGTAGC 60.057 47.826 0.00 0.00 0.00 3.58
4554 6471 4.790765 TGTCAAGTCTCCATGTCAGTAG 57.209 45.455 0.00 0.00 0.00 2.57
4555 6472 4.558697 CGTTGTCAAGTCTCCATGTCAGTA 60.559 45.833 0.00 0.00 0.00 2.74
4556 6473 3.733337 GTTGTCAAGTCTCCATGTCAGT 58.267 45.455 0.00 0.00 0.00 3.41
4557 6474 2.733552 CGTTGTCAAGTCTCCATGTCAG 59.266 50.000 0.00 0.00 0.00 3.51
4558 6475 2.754472 CGTTGTCAAGTCTCCATGTCA 58.246 47.619 0.00 0.00 0.00 3.58
4559 6476 1.461127 GCGTTGTCAAGTCTCCATGTC 59.539 52.381 0.00 0.00 0.00 3.06
4560 6477 1.070758 AGCGTTGTCAAGTCTCCATGT 59.929 47.619 0.00 0.00 0.00 3.21
4561 6478 1.462283 CAGCGTTGTCAAGTCTCCATG 59.538 52.381 0.00 0.00 0.00 3.66
4562 6479 1.070758 ACAGCGTTGTCAAGTCTCCAT 59.929 47.619 0.00 0.00 29.46 3.41
4563 6480 0.464036 ACAGCGTTGTCAAGTCTCCA 59.536 50.000 0.00 0.00 29.46 3.86
4564 6481 0.861837 CACAGCGTTGTCAAGTCTCC 59.138 55.000 0.32 0.00 34.62 3.71
4565 6482 1.852942 TCACAGCGTTGTCAAGTCTC 58.147 50.000 0.32 0.00 34.62 3.36
4566 6483 1.933853 GTTCACAGCGTTGTCAAGTCT 59.066 47.619 0.32 0.00 34.62 3.24
4567 6484 1.933853 AGTTCACAGCGTTGTCAAGTC 59.066 47.619 0.32 0.00 34.62 3.01
4568 6485 2.024176 AGTTCACAGCGTTGTCAAGT 57.976 45.000 0.32 0.00 34.62 3.16
4569 6486 2.286418 GGAAGTTCACAGCGTTGTCAAG 60.286 50.000 0.32 0.00 34.62 3.02
4570 6487 1.668751 GGAAGTTCACAGCGTTGTCAA 59.331 47.619 0.32 0.00 34.62 3.18
4571 6488 1.295792 GGAAGTTCACAGCGTTGTCA 58.704 50.000 0.32 0.00 34.62 3.58
4572 6489 1.295792 TGGAAGTTCACAGCGTTGTC 58.704 50.000 0.32 0.00 34.62 3.18
4573 6490 1.603802 CATGGAAGTTCACAGCGTTGT 59.396 47.619 0.00 0.00 38.31 3.32
4574 6491 1.872952 TCATGGAAGTTCACAGCGTTG 59.127 47.619 5.01 0.00 0.00 4.10
4575 6492 1.873591 GTCATGGAAGTTCACAGCGTT 59.126 47.619 5.01 0.00 0.00 4.84
4576 6493 1.202639 TGTCATGGAAGTTCACAGCGT 60.203 47.619 5.01 0.00 0.00 5.07
4577 6494 1.511850 TGTCATGGAAGTTCACAGCG 58.488 50.000 5.01 0.00 0.00 5.18
4593 6510 8.082242 ACTGCTATGACTTTTTGGTATTTTGTC 58.918 33.333 0.00 0.00 0.00 3.18
4644 6561 1.948834 TCATGGCATCATTAGGCGTTG 59.051 47.619 0.00 0.00 31.67 4.10
4645 6562 2.346766 TCATGGCATCATTAGGCGTT 57.653 45.000 0.00 0.00 31.67 4.84
4648 6565 3.439476 GTCTCATCATGGCATCATTAGGC 59.561 47.826 0.00 0.00 0.00 3.93
4649 6566 4.695928 CAGTCTCATCATGGCATCATTAGG 59.304 45.833 0.00 0.00 0.00 2.69
4726 7581 9.899226 AAGTAAGTTCTTTCACATTTAATCTGC 57.101 29.630 0.00 0.00 0.00 4.26
4766 7621 7.336931 TCAAGACAAGCTTCAACTTATTATCCC 59.663 37.037 0.00 0.00 33.60 3.85
4842 7697 2.409948 AGTACCTCTGCTTTCATGCC 57.590 50.000 0.00 0.00 0.00 4.40
4870 7725 1.621317 TCTCCACACTTACCATTCGCA 59.379 47.619 0.00 0.00 0.00 5.10
4904 7759 8.246180 TGTAGCGTAAATAAGGTATAGGTATGC 58.754 37.037 0.00 0.00 0.00 3.14
4932 7787 2.544069 CGATAACCCGAGGAAGCTCTTC 60.544 54.545 1.12 1.12 38.80 2.87
4961 7816 1.590525 GTTCGTCGCACACCTGTCA 60.591 57.895 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.