Multiple sequence alignment - TraesCS2B01G295800

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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 TraesCS2B01G295800 chr2B 100.000 3501 0 0 1 3501 412766975 412770475 0.000000e+00 6466.0
1 TraesCS2B01G295800 chr2B 90.769 65 6 0 76 140 166665590 166665654 1.730000e-13 87.9
2 TraesCS2B01G295800 chr2D 90.409 2127 97 45 643 2708 347463450 347465530 0.000000e+00 2699.0
3 TraesCS2B01G295800 chr2D 89.985 649 44 11 1 630 347462755 347463401 0.000000e+00 819.0
4 TraesCS2B01G295800 chr2D 95.575 226 10 0 2278 2503 532435140 532435365 2.570000e-96 363.0
5 TraesCS2B01G295800 chr2D 89.017 173 9 5 2533 2701 532436376 532436542 4.580000e-49 206.0
6 TraesCS2B01G295800 chr2D 87.778 90 9 2 278 365 623270047 623269958 1.720000e-18 104.0
7 TraesCS2B01G295800 chr2A 90.869 2026 66 43 716 2691 461153178 461155134 0.000000e+00 2606.0
8 TraesCS2B01G295800 chr2A 91.503 153 12 1 479 630 461151416 461151568 3.540000e-50 209.0
9 TraesCS2B01G295800 chr2A 96.364 55 2 0 1 55 461151074 461151128 1.340000e-14 91.6
10 TraesCS2B01G295800 chr4D 96.847 793 25 0 2709 3501 150967435 150966643 0.000000e+00 1327.0
11 TraesCS2B01G295800 chr1B 95.865 798 29 4 2705 3501 403125548 403124754 0.000000e+00 1288.0
12 TraesCS2B01G295800 chr7B 95.844 794 30 3 2709 3501 229837645 229836854 0.000000e+00 1280.0
13 TraesCS2B01G295800 chr7B 92.191 794 58 4 2710 3501 136003854 136003063 0.000000e+00 1120.0
14 TraesCS2B01G295800 chr1D 92.704 795 51 5 2710 3501 24544626 24543836 0.000000e+00 1140.0
15 TraesCS2B01G295800 chr1A 92.579 795 57 1 2709 3501 25556089 25555295 0.000000e+00 1140.0
16 TraesCS2B01G295800 chr3B 92.279 803 60 2 2699 3501 473749462 473748662 0.000000e+00 1138.0
17 TraesCS2B01G295800 chr3B 91.909 791 62 2 2711 3501 473739849 473739061 0.000000e+00 1105.0
18 TraesCS2B01G295800 chr3B 86.751 317 38 2 49 365 69617628 69617940 2.000000e-92 350.0
19 TraesCS2B01G295800 chr3B 89.041 146 13 1 2522 2664 207725596 207725741 9.990000e-41 178.0
20 TraesCS2B01G295800 chr6D 91.844 797 64 1 2705 3501 277141148 277141943 0.000000e+00 1110.0
21 TraesCS2B01G295800 chr5D 83.962 318 24 10 51 365 488836639 488836932 2.660000e-71 279.0
22 TraesCS2B01G295800 chr5B 87.151 179 22 1 51 228 602136951 602137129 5.930000e-48 202.0
23 TraesCS2B01G295800 chr6A 85.294 68 8 2 278 344 77058028 77058094 6.270000e-08 69.4


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 TraesCS2B01G295800 chr2B 412766975 412770475 3500 False 6466.000000 6466 100.000 1 3501 1 chr2B.!!$F2 3500
1 TraesCS2B01G295800 chr2D 347462755 347465530 2775 False 1759.000000 2699 90.197 1 2708 2 chr2D.!!$F1 2707
2 TraesCS2B01G295800 chr2D 532435140 532436542 1402 False 284.500000 363 92.296 2278 2701 2 chr2D.!!$F2 423
3 TraesCS2B01G295800 chr2A 461151074 461155134 4060 False 968.866667 2606 92.912 1 2691 3 chr2A.!!$F1 2690
4 TraesCS2B01G295800 chr4D 150966643 150967435 792 True 1327.000000 1327 96.847 2709 3501 1 chr4D.!!$R1 792
5 TraesCS2B01G295800 chr1B 403124754 403125548 794 True 1288.000000 1288 95.865 2705 3501 1 chr1B.!!$R1 796
6 TraesCS2B01G295800 chr7B 229836854 229837645 791 True 1280.000000 1280 95.844 2709 3501 1 chr7B.!!$R2 792
7 TraesCS2B01G295800 chr7B 136003063 136003854 791 True 1120.000000 1120 92.191 2710 3501 1 chr7B.!!$R1 791
8 TraesCS2B01G295800 chr1D 24543836 24544626 790 True 1140.000000 1140 92.704 2710 3501 1 chr1D.!!$R1 791
9 TraesCS2B01G295800 chr1A 25555295 25556089 794 True 1140.000000 1140 92.579 2709 3501 1 chr1A.!!$R1 792
10 TraesCS2B01G295800 chr3B 473748662 473749462 800 True 1138.000000 1138 92.279 2699 3501 1 chr3B.!!$R2 802
11 TraesCS2B01G295800 chr3B 473739061 473739849 788 True 1105.000000 1105 91.909 2711 3501 1 chr3B.!!$R1 790
12 TraesCS2B01G295800 chr6D 277141148 277141943 795 False 1110.000000 1110 91.844 2705 3501 1 chr6D.!!$F1 796

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
334 335 0.321653 GCCACTTCTTCCGTCCATGT 60.322 55.0 0.0 0.0 0.00 3.21 F
1669 3477 0.321346 TTTGACTGCTCTCCGATGCA 59.679 50.0 0.0 0.0 37.63 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 3691 0.322008 GACAGAGGGCAAGACCAAGG 60.322 60.0 0.00 0.0 42.05 3.61 R
2510 4358 0.346574 TGAATCCATGGAGGGAGGGA 59.653 55.0 21.33 0.0 41.08 4.20 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.875224 TCCCACTAAGATCACATTCAAACA 58.125 37.500 0.00 0.00 0.00 2.83
38 39 7.551974 CACTAAGATCACATTCAAACATCCTCT 59.448 37.037 0.00 0.00 0.00 3.69
56 57 5.202004 TCCTCTGAAAGTCCATAGTACTCC 58.798 45.833 0.00 0.00 33.76 3.85
75 76 2.704065 TCCCTTCGATCCCATTTACTCC 59.296 50.000 0.00 0.00 0.00 3.85
88 89 5.295045 CCCATTTACTCCGCGTATAACTTTT 59.705 40.000 4.92 0.00 0.00 2.27
111 112 5.132897 TGCCAAAATATCCGCAATATTCC 57.867 39.130 2.70 0.00 39.21 3.01
119 120 2.428491 TCCGCAATATTCCGTGTGTTT 58.572 42.857 0.00 0.00 0.00 2.83
124 125 5.464057 CCGCAATATTCCGTGTGTTTAGATA 59.536 40.000 0.00 0.00 0.00 1.98
127 128 8.067784 CGCAATATTCCGTGTGTTTAGATATTT 58.932 33.333 0.00 0.00 0.00 1.40
154 155 9.174166 AGCATATTCTTTACAGAAATACCGTTT 57.826 29.630 0.00 0.00 42.53 3.60
162 163 3.071892 ACAGAAATACCGTTTCACCTCCA 59.928 43.478 3.68 0.00 0.00 3.86
223 224 2.233186 TCAGAGAGACAACCATGCAGAG 59.767 50.000 0.00 0.00 0.00 3.35
225 226 2.902486 AGAGAGACAACCATGCAGAGAA 59.098 45.455 0.00 0.00 0.00 2.87
245 246 2.976350 CATCCCGCGCATGCAGAT 60.976 61.111 19.57 10.78 42.97 2.90
276 277 0.974383 GGGGAGAACGAAGAGGACAA 59.026 55.000 0.00 0.00 0.00 3.18
316 317 1.067354 GCATGGGGCATTTATAGCTGC 60.067 52.381 0.00 0.00 43.97 5.25
324 325 4.907879 GCATTTATAGCTGCCACTTCTT 57.092 40.909 0.00 0.00 32.15 2.52
327 328 2.890808 TATAGCTGCCACTTCTTCCG 57.109 50.000 0.00 0.00 0.00 4.30
334 335 0.321653 GCCACTTCTTCCGTCCATGT 60.322 55.000 0.00 0.00 0.00 3.21
348 350 1.890979 CATGTGCGCAGGGGATCTC 60.891 63.158 12.22 0.00 0.00 2.75
365 367 3.365265 CCGTCCACAAAGCAGGCC 61.365 66.667 0.00 0.00 0.00 5.19
367 369 3.365265 GTCCACAAAGCAGGCCGG 61.365 66.667 0.00 0.00 0.00 6.13
370 372 4.347453 CACAAAGCAGGCCGGTGC 62.347 66.667 8.91 8.91 44.35 5.01
424 426 9.183368 GGGAGTACTACTAAGTGTTATGTAGTT 57.817 37.037 4.77 0.00 41.65 2.24
917 2693 1.528309 ACCCGAGCAAACCACCAAG 60.528 57.895 0.00 0.00 0.00 3.61
942 2718 2.108976 ACCACACCAGCACTGACG 59.891 61.111 0.00 0.00 0.00 4.35
1606 3397 2.230750 ACAGAGTACGTAGCTCCCAAAC 59.769 50.000 16.53 0.00 33.69 2.93
1661 3469 0.761187 TGCACTCCTTTGACTGCTCT 59.239 50.000 0.00 0.00 33.15 4.09
1662 3470 1.270518 TGCACTCCTTTGACTGCTCTC 60.271 52.381 0.00 0.00 33.15 3.20
1663 3471 1.943507 GCACTCCTTTGACTGCTCTCC 60.944 57.143 0.00 0.00 30.39 3.71
1664 3472 0.605589 ACTCCTTTGACTGCTCTCCG 59.394 55.000 0.00 0.00 0.00 4.63
1665 3473 0.891373 CTCCTTTGACTGCTCTCCGA 59.109 55.000 0.00 0.00 0.00 4.55
1666 3474 1.480137 CTCCTTTGACTGCTCTCCGAT 59.520 52.381 0.00 0.00 0.00 4.18
1667 3475 1.205655 TCCTTTGACTGCTCTCCGATG 59.794 52.381 0.00 0.00 0.00 3.84
1668 3476 1.005340 CTTTGACTGCTCTCCGATGC 58.995 55.000 0.00 0.00 0.00 3.91
1669 3477 0.321346 TTTGACTGCTCTCCGATGCA 59.679 50.000 0.00 0.00 37.63 3.96
1670 3478 0.390340 TTGACTGCTCTCCGATGCAC 60.390 55.000 0.00 0.00 35.20 4.57
1671 3479 1.216444 GACTGCTCTCCGATGCACA 59.784 57.895 0.00 0.00 35.20 4.57
1674 3482 0.461516 CTGCTCTCCGATGCACACAT 60.462 55.000 0.00 0.00 39.98 3.21
1689 3497 6.635030 TGCACACATACATACTCCTACTAG 57.365 41.667 0.00 0.00 0.00 2.57
1705 3513 9.589461 ACTCCTACTAGTACATGCATTTATAGT 57.411 33.333 0.00 6.19 0.00 2.12
1740 3550 6.420588 TGAAAACACGTTTTATTACTCCACG 58.579 36.000 7.83 0.00 42.26 4.94
1754 3564 2.294233 ACTCCACGAAACGCTGTTACTA 59.706 45.455 0.00 0.00 0.00 1.82
1755 3565 2.660236 CTCCACGAAACGCTGTTACTAC 59.340 50.000 0.00 0.00 0.00 2.73
1756 3566 2.294233 TCCACGAAACGCTGTTACTACT 59.706 45.455 0.00 0.00 0.00 2.57
1757 3567 2.407361 CCACGAAACGCTGTTACTACTG 59.593 50.000 0.00 0.00 0.00 2.74
1758 3568 3.047796 CACGAAACGCTGTTACTACTGT 58.952 45.455 0.00 0.00 0.00 3.55
1759 3569 3.047796 ACGAAACGCTGTTACTACTGTG 58.952 45.455 0.00 0.00 39.00 3.66
1761 3571 3.119136 CGAAACGCTGTTACTACTGTGTC 59.881 47.826 0.00 0.00 43.40 3.67
1762 3572 4.296690 GAAACGCTGTTACTACTGTGTCT 58.703 43.478 0.00 0.00 43.40 3.41
1763 3573 4.317671 AACGCTGTTACTACTGTGTCTT 57.682 40.909 0.00 0.00 43.40 3.01
1764 3574 3.639538 ACGCTGTTACTACTGTGTCTTG 58.360 45.455 0.00 0.00 41.31 3.02
1765 3575 3.317149 ACGCTGTTACTACTGTGTCTTGA 59.683 43.478 0.00 0.00 41.31 3.02
1865 3684 2.108425 GTCTCCTTCCTTTCCCCTGTTT 59.892 50.000 0.00 0.00 0.00 2.83
1866 3685 3.329814 GTCTCCTTCCTTTCCCCTGTTTA 59.670 47.826 0.00 0.00 0.00 2.01
1870 3689 5.722290 TCCTTCCTTTCCCCTGTTTATTTT 58.278 37.500 0.00 0.00 0.00 1.82
1871 3690 5.778241 TCCTTCCTTTCCCCTGTTTATTTTC 59.222 40.000 0.00 0.00 0.00 2.29
1872 3691 5.046591 CCTTCCTTTCCCCTGTTTATTTTCC 60.047 44.000 0.00 0.00 0.00 3.13
1873 3692 4.422057 TCCTTTCCCCTGTTTATTTTCCC 58.578 43.478 0.00 0.00 0.00 3.97
1874 3693 4.108942 TCCTTTCCCCTGTTTATTTTCCCT 59.891 41.667 0.00 0.00 0.00 4.20
1913 3732 3.043713 CAGGTGCTTTGCGCGAGA 61.044 61.111 12.10 0.00 43.27 4.04
1931 3750 0.823356 GACCACAAGAGCCAAGGCAA 60.823 55.000 14.40 0.00 44.88 4.52
1935 3754 0.468771 ACAAGAGCCAAGGCAAAGCT 60.469 50.000 14.40 2.11 44.88 3.74
1942 3761 1.359833 CAAGGCAAAGCTTGTCGCA 59.640 52.632 15.28 0.00 41.01 5.10
1965 3784 1.666311 GCGGATGAGCTGGTATCGTAC 60.666 57.143 0.00 0.00 0.00 3.67
2017 3837 0.456142 CTTTGACTCGGTCGCATCGA 60.456 55.000 0.00 0.00 34.95 3.59
2127 3947 4.654412 CTAGCTAGCCTGCCGCGG 62.654 72.222 24.05 24.05 44.76 6.46
2224 4046 2.230025 GTCACCCTGATGATCGATCGAT 59.770 50.000 29.76 29.76 37.59 3.59
2244 4066 1.417517 TCGATCCATCCATCACAAGGG 59.582 52.381 0.00 0.00 0.00 3.95
2245 4067 1.417517 CGATCCATCCATCACAAGGGA 59.582 52.381 0.00 0.00 40.23 4.20
2246 4068 2.549563 CGATCCATCCATCACAAGGGAG 60.550 54.545 0.00 0.00 39.08 4.30
2299 4147 4.918360 TGGTGCAGGAGGTGGGGT 62.918 66.667 0.00 0.00 0.00 4.95
2327 4175 0.596083 CGTGGAGAGCGTGATGATCC 60.596 60.000 0.00 0.00 31.78 3.36
2333 4181 1.035923 GAGCGTGATGATCCAGAGGA 58.964 55.000 0.00 0.00 35.55 3.71
2484 4332 3.953775 CGTCCCCAAGCCACACCT 61.954 66.667 0.00 0.00 0.00 4.00
2501 4349 2.108970 ACCTACCACCACTAAGCTAGC 58.891 52.381 6.62 6.62 0.00 3.42
2502 4350 2.292323 ACCTACCACCACTAAGCTAGCT 60.292 50.000 12.68 12.68 0.00 3.32
2503 4351 3.053095 ACCTACCACCACTAAGCTAGCTA 60.053 47.826 19.70 5.71 0.00 3.32
2504 4352 3.570550 CCTACCACCACTAAGCTAGCTAG 59.429 52.174 19.70 16.84 0.00 3.42
2535 5384 2.135189 CCCTCCATGGATTCACCCTAA 58.865 52.381 16.63 0.00 38.35 2.69
2551 5400 3.523564 ACCCTAAACATCCAGCATACACT 59.476 43.478 0.00 0.00 0.00 3.55
2648 5506 5.340803 GTGTTCACCTCTCTTTTTGAAACC 58.659 41.667 0.00 0.00 30.00 3.27
2662 5520 7.340999 TCTTTTTGAAACCCAAAGCTTACTACT 59.659 33.333 0.00 0.00 44.67 2.57
2663 5521 8.522542 TTTTTGAAACCCAAAGCTTACTACTA 57.477 30.769 0.00 0.00 44.67 1.82
2664 5522 7.500720 TTTGAAACCCAAAGCTTACTACTAC 57.499 36.000 0.00 0.00 39.65 2.73
2737 5599 7.446001 TTTTGAAACAAGGCAAAAGATTTGT 57.554 28.000 4.90 0.00 38.60 2.83
2779 5641 7.039270 GGAAGAAAGTTTTAGACAAAAAGCCA 58.961 34.615 0.00 0.00 37.74 4.75
2786 5648 4.727507 TTAGACAAAAAGCCACAAAGCA 57.272 36.364 0.00 0.00 34.23 3.91
2852 5714 1.044790 GCACCTGCCATAGCCCAAAT 61.045 55.000 0.00 0.00 38.69 2.32
2969 5832 6.506538 AGACATAAGCATGAATAAGGAGGT 57.493 37.500 0.00 0.00 35.96 3.85
3022 5887 9.439500 CAATCACATTTTTAATCCACCAATCTT 57.561 29.630 0.00 0.00 0.00 2.40
3082 5947 2.224523 CCATGTAGGCCAATCCACGTAT 60.225 50.000 5.01 0.00 37.29 3.06
3119 5984 1.272313 ACGCTGGGAGAACCTACACTA 60.272 52.381 0.00 0.00 41.11 2.74
3283 6148 0.833949 GGCCCAAACCTTCCAAACAA 59.166 50.000 0.00 0.00 0.00 2.83
3322 6187 3.068560 GTTATGTGTCCCGCAAACTACA 58.931 45.455 0.00 0.00 0.00 2.74
3340 6205 2.384828 ACACCATATAGGCAGTCGACA 58.615 47.619 19.50 0.00 43.14 4.35
3369 6234 7.664589 AGGATTCTCCTTGAGAGGTGAACTTT 61.665 42.308 10.97 0.00 46.91 2.66
3461 6326 0.904865 TGTAGGTGCTCCAGGGTGAG 60.905 60.000 7.70 0.00 35.89 3.51
3462 6327 0.905337 GTAGGTGCTCCAGGGTGAGT 60.905 60.000 7.70 0.00 34.74 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.836358 GGAGTACTATGGACTTTCAGAGGAT 59.164 44.000 0.00 0.00 30.90 3.24
38 39 4.401519 CGAAGGGAGTACTATGGACTTTCA 59.598 45.833 0.00 0.00 0.00 2.69
56 57 2.755650 CGGAGTAAATGGGATCGAAGG 58.244 52.381 0.00 0.00 0.00 3.46
75 76 5.755330 ATTTTGGCAAAAAGTTATACGCG 57.245 34.783 27.25 3.53 38.62 6.01
88 89 8.128453 ACGGAATATTGCGGATATTTTGGCAA 62.128 38.462 29.18 0.00 46.70 4.52
127 128 9.826574 AACGGTATTTCTGTAAAGAATATGCTA 57.173 29.630 0.00 0.00 34.87 3.49
140 141 3.071892 TGGAGGTGAAACGGTATTTCTGT 59.928 43.478 1.48 0.00 38.12 3.41
141 142 3.435671 GTGGAGGTGAAACGGTATTTCTG 59.564 47.826 1.48 0.00 38.12 3.02
154 155 0.904865 ATGAGGCGAAGTGGAGGTGA 60.905 55.000 0.00 0.00 0.00 4.02
189 190 0.829990 TCTCTGACACAACCTGCACA 59.170 50.000 0.00 0.00 0.00 4.57
223 224 2.025156 CATGCGCGGGATGCTTTC 59.975 61.111 8.83 0.00 43.27 2.62
244 245 2.285069 TCCCCTACCCACGCACAT 60.285 61.111 0.00 0.00 0.00 3.21
245 246 3.000819 CTCCCCTACCCACGCACA 61.001 66.667 0.00 0.00 0.00 4.57
316 317 1.442769 CACATGGACGGAAGAAGTGG 58.557 55.000 0.00 0.00 0.00 4.00
317 318 0.798776 GCACATGGACGGAAGAAGTG 59.201 55.000 0.00 0.00 0.00 3.16
318 319 0.670546 CGCACATGGACGGAAGAAGT 60.671 55.000 0.00 0.00 0.00 3.01
324 325 4.758251 CCTGCGCACATGGACGGA 62.758 66.667 5.66 7.57 0.00 4.69
327 328 3.704231 ATCCCCTGCGCACATGGAC 62.704 63.158 17.34 0.00 33.64 4.02
348 350 3.365265 GGCCTGCTTTGTGGACGG 61.365 66.667 0.00 0.00 0.00 4.79
390 392 6.126652 ACACTTAGTAGTACTCCCTCCGATTA 60.127 42.308 5.96 0.00 31.96 1.75
475 687 4.953940 AGCCTCACTCCATCTCTTTATC 57.046 45.455 0.00 0.00 0.00 1.75
476 688 7.222872 CAAATAGCCTCACTCCATCTCTTTAT 58.777 38.462 0.00 0.00 0.00 1.40
477 689 6.408548 CCAAATAGCCTCACTCCATCTCTTTA 60.409 42.308 0.00 0.00 0.00 1.85
532 751 8.757164 AATTTCGTTTGGGACTTTCAATTATC 57.243 30.769 0.00 0.00 0.00 1.75
707 991 5.384063 ACACGAGGATGTCATCTATCATC 57.616 43.478 12.54 0.00 39.49 2.92
708 992 5.770162 TGTACACGAGGATGTCATCTATCAT 59.230 40.000 12.54 0.00 33.85 2.45
709 993 5.008712 GTGTACACGAGGATGTCATCTATCA 59.991 44.000 10.84 0.05 33.85 2.15
710 994 5.008712 TGTGTACACGAGGATGTCATCTATC 59.991 44.000 20.61 9.88 33.85 2.08
711 995 4.887655 TGTGTACACGAGGATGTCATCTAT 59.112 41.667 20.61 2.08 33.85 1.98
863 2638 4.435425 GGTTTTAAAAGTGGCCTCGTTTT 58.565 39.130 20.94 16.55 0.00 2.43
917 2693 2.193536 GCTGGTGTGGTGTGAACCC 61.194 63.158 0.00 0.00 32.70 4.11
1606 3397 2.259511 GCTTGCTTTGCTTCGGGG 59.740 61.111 0.00 0.00 0.00 5.73
1661 3469 3.243737 GGAGTATGTATGTGTGCATCGGA 60.244 47.826 0.00 0.00 36.58 4.55
1662 3470 3.059884 GGAGTATGTATGTGTGCATCGG 58.940 50.000 0.00 0.00 36.58 4.18
1663 3471 3.982475 AGGAGTATGTATGTGTGCATCG 58.018 45.455 0.00 0.00 36.58 3.84
1664 3472 6.090483 AGTAGGAGTATGTATGTGTGCATC 57.910 41.667 0.00 0.00 36.58 3.91
1665 3473 6.778069 ACTAGTAGGAGTATGTATGTGTGCAT 59.222 38.462 1.45 0.00 39.03 3.96
1666 3474 6.127101 ACTAGTAGGAGTATGTATGTGTGCA 58.873 40.000 1.45 0.00 0.00 4.57
1667 3475 6.636562 ACTAGTAGGAGTATGTATGTGTGC 57.363 41.667 1.45 0.00 0.00 4.57
1668 3476 8.672823 TGTACTAGTAGGAGTATGTATGTGTG 57.327 38.462 1.87 0.00 34.50 3.82
1669 3477 9.286170 CATGTACTAGTAGGAGTATGTATGTGT 57.714 37.037 1.87 0.00 34.50 3.72
1670 3478 8.237949 GCATGTACTAGTAGGAGTATGTATGTG 58.762 40.741 1.87 0.00 34.50 3.21
1671 3479 7.942894 TGCATGTACTAGTAGGAGTATGTATGT 59.057 37.037 1.87 0.00 34.50 2.29
1674 3482 8.935614 AATGCATGTACTAGTAGGAGTATGTA 57.064 34.615 1.87 4.07 34.50 2.29
1711 3519 6.604930 AGTAATAAAACGTGTTTTCATCGGG 58.395 36.000 13.53 0.00 41.39 5.14
1724 3534 4.076985 GCGTTTCGTGGAGTAATAAAACG 58.923 43.478 12.32 12.32 46.87 3.60
1740 3550 4.296690 AGACACAGTAGTAACAGCGTTTC 58.703 43.478 0.00 0.00 0.00 2.78
1758 3568 4.521639 ACCGAGTAATAGTGTGTCAAGACA 59.478 41.667 0.00 0.00 39.32 3.41
1759 3569 4.857588 CACCGAGTAATAGTGTGTCAAGAC 59.142 45.833 0.00 0.00 0.00 3.01
1761 3571 4.174009 CCACCGAGTAATAGTGTGTCAAG 58.826 47.826 0.00 0.00 0.00 3.02
1762 3572 3.575256 ACCACCGAGTAATAGTGTGTCAA 59.425 43.478 0.00 0.00 0.00 3.18
1763 3573 3.159472 ACCACCGAGTAATAGTGTGTCA 58.841 45.455 0.00 0.00 0.00 3.58
1764 3574 3.863142 ACCACCGAGTAATAGTGTGTC 57.137 47.619 0.00 0.00 0.00 3.67
1765 3575 4.612264 AAACCACCGAGTAATAGTGTGT 57.388 40.909 0.00 0.00 0.00 3.72
1865 3684 2.381961 AGGGCAAGACCAAGGGAAAATA 59.618 45.455 0.00 0.00 42.05 1.40
1866 3685 1.149923 AGGGCAAGACCAAGGGAAAAT 59.850 47.619 0.00 0.00 42.05 1.82
1870 3689 1.151810 AGAGGGCAAGACCAAGGGA 60.152 57.895 0.00 0.00 42.05 4.20
1871 3690 1.001641 CAGAGGGCAAGACCAAGGG 60.002 63.158 0.00 0.00 42.05 3.95
1872 3691 0.322008 GACAGAGGGCAAGACCAAGG 60.322 60.000 0.00 0.00 42.05 3.61
1873 3692 0.671781 CGACAGAGGGCAAGACCAAG 60.672 60.000 0.00 0.00 42.05 3.61
1874 3693 1.371183 CGACAGAGGGCAAGACCAA 59.629 57.895 0.00 0.00 42.05 3.67
1913 3732 0.396974 TTTGCCTTGGCTCTTGTGGT 60.397 50.000 13.18 0.00 0.00 4.16
1942 3761 0.965439 GATACCAGCTCATCCGCTCT 59.035 55.000 0.00 0.00 38.41 4.09
1965 3784 1.808945 CTACGTATACTGCCCCTACGG 59.191 57.143 0.00 0.00 41.80 4.02
2017 3837 5.478233 GGAACGGAAAATTTTGCTTTTGT 57.522 34.783 18.64 7.67 0.00 2.83
2139 3959 1.505353 GTCACAGGATTGCTGCTGC 59.495 57.895 8.89 8.89 44.13 5.25
2224 4046 1.417517 CCCTTGTGATGGATGGATCGA 59.582 52.381 0.00 0.00 0.00 3.59
2299 4147 2.997315 CTCTCCACGCACCCCTCA 60.997 66.667 0.00 0.00 0.00 3.86
2484 4332 2.957006 GCTAGCTAGCTTAGTGGTGGTA 59.043 50.000 33.71 0.00 45.62 3.25
2501 4349 1.155155 GAGGGAGGGAGGGAGCTAG 59.845 68.421 0.00 0.00 0.00 3.42
2502 4350 2.404750 GGAGGGAGGGAGGGAGCTA 61.405 68.421 0.00 0.00 0.00 3.32
2503 4351 3.773154 GGAGGGAGGGAGGGAGCT 61.773 72.222 0.00 0.00 0.00 4.09
2504 4352 3.418623 ATGGAGGGAGGGAGGGAGC 62.419 68.421 0.00 0.00 0.00 4.70
2505 4353 1.461075 CATGGAGGGAGGGAGGGAG 60.461 68.421 0.00 0.00 0.00 4.30
2506 4354 2.705410 CATGGAGGGAGGGAGGGA 59.295 66.667 0.00 0.00 0.00 4.20
2507 4355 2.352553 ATCCATGGAGGGAGGGAGGG 62.353 65.000 21.33 0.00 41.08 4.30
2508 4356 0.402566 AATCCATGGAGGGAGGGAGG 60.403 60.000 21.33 0.00 41.08 4.30
2509 4357 1.063183 GAATCCATGGAGGGAGGGAG 58.937 60.000 21.33 0.00 41.08 4.30
2510 4358 0.346574 TGAATCCATGGAGGGAGGGA 59.653 55.000 21.33 0.00 41.08 4.20
2511 4359 0.475906 GTGAATCCATGGAGGGAGGG 59.524 60.000 21.33 0.00 41.08 4.30
2512 4360 0.475906 GGTGAATCCATGGAGGGAGG 59.524 60.000 21.33 0.00 41.08 4.30
2535 5384 2.621338 CGTGAGTGTATGCTGGATGTT 58.379 47.619 0.00 0.00 0.00 2.71
2663 5521 9.032624 ACTCAGTATTAATGTACCAACTACAGT 57.967 33.333 0.00 0.00 38.80 3.55
2761 5623 5.580691 GCTTTGTGGCTTTTTGTCTAAAACT 59.419 36.000 0.00 0.00 35.62 2.66
2774 5636 0.396974 TGTTCCCTGCTTTGTGGCTT 60.397 50.000 0.00 0.00 0.00 4.35
2779 5641 3.365472 AGTTCTTTGTTCCCTGCTTTGT 58.635 40.909 0.00 0.00 0.00 2.83
2786 5648 3.306156 GCGAGAGTAGTTCTTTGTTCCCT 60.306 47.826 0.00 0.00 35.87 4.20
2852 5714 3.066208 AGATCAAAGAGGAGGCCCATA 57.934 47.619 0.00 0.00 33.88 2.74
2969 5832 3.369471 CGGAAACCAGAGAAAGGCTATCA 60.369 47.826 0.00 0.00 0.00 2.15
3022 5887 3.072915 TGGAGATTTGAGGCTTCAGTTCA 59.927 43.478 0.00 0.00 34.15 3.18
3082 5947 1.384525 CGTGTTTGGGTTGAGGTTGA 58.615 50.000 0.00 0.00 0.00 3.18
3119 5984 1.520342 GCGGCGCATCTTCTCTTCT 60.520 57.895 29.21 0.00 0.00 2.85
3322 6187 2.229062 CGATGTCGACTGCCTATATGGT 59.771 50.000 17.92 0.00 43.02 3.55
3369 6234 4.711846 AGTGTGCAAGATACTATCCACTGA 59.288 41.667 0.00 0.00 29.59 3.41
3461 6326 5.829924 AGTCAAATTGATACCCATCATGGAC 59.170 40.000 4.75 0.00 40.96 4.02
3462 6327 6.017211 AGTCAAATTGATACCCATCATGGA 57.983 37.500 4.75 0.00 40.96 3.41


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

AutoCloner maintained by Alex Coulton.