Multiple sequence alignment - TraesCS4A01G131600

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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 TraesCS4A01G131600 chr4A 100.000 4667 0 0 1 4667 175861770 175857104 0.000000e+00 8619
1 TraesCS4A01G131600 chr4A 95.588 612 14 7 58 661 175893538 175892932 0.000000e+00 968
2 TraesCS4A01G131600 chr4A 95.312 64 3 0 1 64 175895335 175895272 8.260000e-18 102
3 TraesCS4A01G131600 chr4B 95.504 2580 82 19 2104 4667 377935721 377938282 0.000000e+00 4091
4 TraesCS4A01G131600 chr4B 89.519 1746 123 22 381 2120 377932669 377934360 0.000000e+00 2156
5 TraesCS4A01G131600 chr4B 86.017 236 26 5 144 373 377932398 377932632 3.610000e-61 246
6 TraesCS4A01G131600 chr4D 95.790 2423 67 17 2258 4667 303516072 303518472 0.000000e+00 3877
7 TraesCS4A01G131600 chr4D 93.626 1208 56 12 921 2120 303512866 303514060 0.000000e+00 1784
8 TraesCS4A01G131600 chr4D 88.694 513 52 5 377 888 303512356 303512863 5.130000e-174 621
9 TraesCS4A01G131600 chr4D 88.859 377 38 3 1 376 303511953 303512326 1.180000e-125 460
10 TraesCS4A01G131600 chr3B 81.419 592 98 9 190 779 26575792 26575211 1.520000e-129 473
11 TraesCS4A01G131600 chr2D 80.449 624 82 25 181 769 429082298 429081680 1.540000e-119 440
12 TraesCS4A01G131600 chr2D 84.817 191 26 3 185 373 10735501 10735690 6.160000e-44 189
13 TraesCS4A01G131600 chr6D 85.396 404 57 2 377 779 394209960 394209558 7.220000e-113 418
14 TraesCS4A01G131600 chr7D 80.762 551 71 19 256 779 7205659 7206201 9.410000e-107 398
15 TraesCS4A01G131600 chr7D 79.051 611 103 16 185 780 178136422 178137022 3.380000e-106 396
16 TraesCS4A01G131600 chr7D 83.777 413 59 8 379 785 221997256 221996846 7.330000e-103 385
17 TraesCS4A01G131600 chr7D 83.416 404 65 2 377 779 573909072 573909474 1.590000e-99 374
18 TraesCS4A01G131600 chr7D 86.979 192 20 4 185 373 525360138 525360327 1.320000e-50 211
19 TraesCS4A01G131600 chr5D 84.406 404 61 2 377 779 487270341 487270743 3.380000e-106 396
20 TraesCS4A01G131600 chr2A 86.224 196 20 6 183 373 10379488 10379681 6.120000e-49 206
21 TraesCS4A01G131600 chr6A 85.641 195 25 2 185 377 438026749 438026556 7.920000e-48 202


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 TraesCS4A01G131600 chr4A 175857104 175861770 4666 True 8619.000000 8619 100.000000 1 4667 1 chr4A.!!$R1 4666
1 TraesCS4A01G131600 chr4A 175892932 175895335 2403 True 535.000000 968 95.450000 1 661 2 chr4A.!!$R2 660
2 TraesCS4A01G131600 chr4B 377932398 377938282 5884 False 2164.333333 4091 90.346667 144 4667 3 chr4B.!!$F1 4523
3 TraesCS4A01G131600 chr4D 303511953 303518472 6519 False 1685.500000 3877 91.742250 1 4667 4 chr4D.!!$F1 4666
4 TraesCS4A01G131600 chr3B 26575211 26575792 581 True 473.000000 473 81.419000 190 779 1 chr3B.!!$R1 589
5 TraesCS4A01G131600 chr2D 429081680 429082298 618 True 440.000000 440 80.449000 181 769 1 chr2D.!!$R1 588
6 TraesCS4A01G131600 chr7D 7205659 7206201 542 False 398.000000 398 80.762000 256 779 1 chr7D.!!$F1 523
7 TraesCS4A01G131600 chr7D 178136422 178137022 600 False 396.000000 396 79.051000 185 780 1 chr7D.!!$F2 595

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
912 2702 0.391263 GTAAACCACCAGAGCCGGAG 60.391 60.0 5.05 0.0 0.00 4.63 F
1718 3515 0.383231 GTATGTGCATTGGAGCAGGC 59.617 55.0 0.00 0.0 46.69 4.85 F
1952 3749 0.620556 TCCAGGGAGATGAAACTGCC 59.379 55.0 0.00 0.0 46.42 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 3776 1.065401 TGTTTGTTGCCGAAGCTTGAG 59.935 47.619 2.10 0.00 40.80 3.02 R
3492 7170 0.868406 GCAGGTACACAGTGTGAAGC 59.132 55.000 29.58 19.03 36.96 3.86 R
3892 7570 0.803380 CTGCAAAAGCTAATGCCGCC 60.803 55.000 18.00 0.00 41.87 6.13 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
72 73 4.460263 ACACGCCCATATTGTGTTCATAT 58.540 39.130 0.00 0.00 43.90 1.78
687 2470 4.276805 CGATGACAATGGTCGTTCGATGA 61.277 47.826 16.46 0.00 46.56 2.92
846 2629 4.215908 TCCGGCAGAATTCAGTATAGACT 58.784 43.478 8.44 0.00 35.80 3.24
849 2632 5.921408 CCGGCAGAATTCAGTATAGACTTAC 59.079 44.000 8.44 0.00 31.73 2.34
853 2636 7.419204 GCAGAATTCAGTATAGACTTACGAGT 58.581 38.462 8.44 0.00 39.32 4.18
888 2678 8.209917 ACGAATTAAAGGTCCATTCAGAATAC 57.790 34.615 0.00 0.00 0.00 1.89
889 2679 8.047310 ACGAATTAAAGGTCCATTCAGAATACT 58.953 33.333 0.00 0.00 0.00 2.12
890 2680 9.542462 CGAATTAAAGGTCCATTCAGAATACTA 57.458 33.333 0.00 0.00 0.00 1.82
892 2682 8.888579 ATTAAAGGTCCATTCAGAATACTACG 57.111 34.615 0.00 0.00 0.00 3.51
893 2683 4.939052 AGGTCCATTCAGAATACTACGG 57.061 45.455 0.00 0.00 0.00 4.02
894 2684 4.287552 AGGTCCATTCAGAATACTACGGT 58.712 43.478 0.00 0.00 0.00 4.83
895 2685 5.452255 AGGTCCATTCAGAATACTACGGTA 58.548 41.667 0.00 0.00 0.00 4.02
896 2686 5.895534 AGGTCCATTCAGAATACTACGGTAA 59.104 40.000 0.00 0.00 0.00 2.85
897 2687 6.381994 AGGTCCATTCAGAATACTACGGTAAA 59.618 38.462 0.00 0.00 0.00 2.01
898 2688 6.478016 GGTCCATTCAGAATACTACGGTAAAC 59.522 42.308 0.00 0.00 0.00 2.01
899 2689 6.478016 GTCCATTCAGAATACTACGGTAAACC 59.522 42.308 0.00 0.00 0.00 3.27
900 2690 6.154877 TCCATTCAGAATACTACGGTAAACCA 59.845 38.462 0.00 0.00 35.14 3.67
901 2691 6.257193 CCATTCAGAATACTACGGTAAACCAC 59.743 42.308 0.00 0.00 35.14 4.16
902 2692 5.329035 TCAGAATACTACGGTAAACCACC 57.671 43.478 0.00 0.00 44.75 4.61
910 2700 4.296265 GTAAACCACCAGAGCCGG 57.704 61.111 0.00 0.00 0.00 6.13
911 2701 1.675219 GTAAACCACCAGAGCCGGA 59.325 57.895 5.05 0.00 0.00 5.14
912 2702 0.391263 GTAAACCACCAGAGCCGGAG 60.391 60.000 5.05 0.00 0.00 4.63
913 2703 0.834687 TAAACCACCAGAGCCGGAGT 60.835 55.000 5.05 0.00 0.00 3.85
914 2704 0.834687 AAACCACCAGAGCCGGAGTA 60.835 55.000 5.05 0.00 0.00 2.59
915 2705 1.258445 AACCACCAGAGCCGGAGTAG 61.258 60.000 5.05 0.00 0.00 2.57
916 2706 1.379977 CCACCAGAGCCGGAGTAGA 60.380 63.158 5.05 0.00 0.00 2.59
917 2707 0.970937 CCACCAGAGCCGGAGTAGAA 60.971 60.000 5.05 0.00 0.00 2.10
918 2708 0.895530 CACCAGAGCCGGAGTAGAAA 59.104 55.000 5.05 0.00 0.00 2.52
1272 3067 2.979197 CTCCGACAACGACCTCGCT 61.979 63.158 0.00 0.00 44.43 4.93
1383 3178 2.494918 CGATCCTCTCGCGGGTTT 59.505 61.111 5.57 0.00 41.14 3.27
1392 3187 3.047877 CGCGGGTTTGAGTCCCAC 61.048 66.667 0.00 0.00 44.81 4.61
1404 3199 1.226773 GTCCCACGAATCGTACGGG 60.227 63.158 21.11 21.11 42.21 5.28
1406 3201 2.584143 CCACGAATCGTACGGGCC 60.584 66.667 16.52 0.00 38.32 5.80
1407 3202 2.584143 CACGAATCGTACGGGCCC 60.584 66.667 13.57 13.57 38.32 5.80
1426 3221 2.945668 CCCCTCTGCACTAACATTTAGC 59.054 50.000 0.00 0.00 0.00 3.09
1445 3242 2.317609 ACATCGTGGTGCGCAGAAC 61.318 57.895 12.22 11.75 41.07 3.01
1446 3243 2.029288 CATCGTGGTGCGCAGAACT 61.029 57.895 12.22 0.00 41.07 3.01
1447 3244 1.738099 ATCGTGGTGCGCAGAACTC 60.738 57.895 12.22 4.41 41.07 3.01
1448 3245 3.414700 CGTGGTGCGCAGAACTCC 61.415 66.667 12.22 9.06 0.00 3.85
1459 3256 1.527311 GCAGAACTCCGTGTCTGTTTC 59.473 52.381 2.90 0.00 33.17 2.78
1473 3270 3.804873 GTCTGTTTCAAGTCTCTGTGGTC 59.195 47.826 0.00 0.00 0.00 4.02
1570 3367 1.356527 GGTTCGTGTGGGCGTACATC 61.357 60.000 0.00 0.00 34.58 3.06
1603 3400 2.043248 GGTAGTGGGGAGAGGCGA 60.043 66.667 0.00 0.00 0.00 5.54
1614 3411 2.444895 GAGGCGAGAGGGGTGGAT 60.445 66.667 0.00 0.00 0.00 3.41
1655 3452 4.874970 TCTTCTCAACCCGTGTTTAGTAC 58.125 43.478 0.00 0.00 30.42 2.73
1657 3454 4.247267 TCTCAACCCGTGTTTAGTACTG 57.753 45.455 5.39 0.00 30.42 2.74
1682 3479 1.586028 CACGGCCATTTTCAGGTGG 59.414 57.895 2.24 0.00 38.55 4.61
1718 3515 0.383231 GTATGTGCATTGGAGCAGGC 59.617 55.000 0.00 0.00 46.69 4.85
1727 3524 2.603075 TTGGAGCAGGCCAAAATAGT 57.397 45.000 5.01 0.00 44.55 2.12
1728 3525 1.838112 TGGAGCAGGCCAAAATAGTG 58.162 50.000 5.01 0.00 34.31 2.74
1742 3539 5.224888 CAAAATAGTGTTGACTGCATTGCT 58.775 37.500 10.49 0.00 33.21 3.91
1814 3611 2.046892 CTTGGGCTGACACTCGGG 60.047 66.667 0.00 0.00 0.00 5.14
1896 3693 6.036470 GCAATTAACCATAAGCAGGTTCTTC 58.964 40.000 0.18 0.00 45.98 2.87
1952 3749 0.620556 TCCAGGGAGATGAAACTGCC 59.379 55.000 0.00 0.00 46.42 4.85
1990 3787 7.778470 ATTATTTCTTACTCTCAAGCTTCGG 57.222 36.000 0.00 0.00 0.00 4.30
2004 3801 3.081061 AGCTTCGGCAACAAACATGATA 58.919 40.909 0.00 0.00 44.74 2.15
2007 3804 5.008019 AGCTTCGGCAACAAACATGATATAG 59.992 40.000 0.00 0.00 44.74 1.31
2009 3806 3.563808 TCGGCAACAAACATGATATAGGC 59.436 43.478 0.00 0.00 0.00 3.93
2014 3811 6.381801 GCAACAAACATGATATAGGCCATAC 58.618 40.000 5.01 0.00 0.00 2.39
2086 3883 3.469771 TCCTGGGGTGTATAGTGGATACT 59.530 47.826 0.00 0.00 41.08 2.12
2169 5574 2.426522 TCAACAGTGAATGCCAGTAGC 58.573 47.619 0.00 0.00 44.14 3.58
2171 5576 0.692476 ACAGTGAATGCCAGTAGCCA 59.308 50.000 0.00 0.00 42.71 4.75
2223 5628 4.111375 ACAAATAGAGTAGGCTGTCACG 57.889 45.455 0.00 0.00 0.00 4.35
2442 6117 8.712285 TGGATTTTTATCTACTACAGTTTCCG 57.288 34.615 0.00 0.00 0.00 4.30
2500 6175 7.888021 TCCCTGTTCATATAGAGCTTTTCAAAA 59.112 33.333 0.00 0.00 0.00 2.44
2501 6176 8.689972 CCCTGTTCATATAGAGCTTTTCAAAAT 58.310 33.333 0.00 0.00 0.00 1.82
2527 6203 6.899393 TGTGATTCTATAAATTCATGGGCC 57.101 37.500 0.00 0.00 0.00 5.80
2528 6204 6.372104 TGTGATTCTATAAATTCATGGGCCA 58.628 36.000 9.61 9.61 0.00 5.36
2529 6205 7.011994 TGTGATTCTATAAATTCATGGGCCAT 58.988 34.615 14.78 14.78 0.00 4.40
2530 6206 7.039574 TGTGATTCTATAAATTCATGGGCCATG 60.040 37.037 35.67 35.67 42.60 3.66
2886 6564 4.591498 ACATGTTAACTCCACTGTCAGGTA 59.409 41.667 7.22 0.00 0.00 3.08
2913 6591 1.373570 GATTGGCTCCGTTTGAGAGG 58.626 55.000 0.00 0.00 44.42 3.69
2917 6595 1.375326 GCTCCGTTTGAGAGGGGTT 59.625 57.895 0.00 0.00 44.42 4.11
3105 6783 5.078411 TCCTCTATTCTCTGTTGAACAGC 57.922 43.478 19.99 0.00 45.54 4.40
3169 6847 4.520492 ACTGCTGGGTTGATACTCTTTTTG 59.480 41.667 0.00 0.00 0.00 2.44
3202 6880 9.855361 GTATATGTGATGTTTCTTTGATCTTCG 57.145 33.333 0.00 0.00 0.00 3.79
3231 6909 7.636259 TCTTTGTTTTATAATTGCAGTGCAC 57.364 32.000 19.58 9.40 38.71 4.57
3434 7112 3.353557 GTGGAAACTATGGAAAGGGGAC 58.646 50.000 0.00 0.00 0.00 4.46
3438 7116 3.345508 AACTATGGAAAGGGGACGAAC 57.654 47.619 0.00 0.00 0.00 3.95
3492 7170 3.313249 TGCCATTGTTATGCTCGATCTTG 59.687 43.478 0.00 0.00 0.00 3.02
3756 7434 5.411361 CCTTCTGTAACGGAATTGATTCACA 59.589 40.000 6.11 1.45 38.53 3.58
4017 7696 1.790818 ATCGGGGGAGAACTTAGGAC 58.209 55.000 0.00 0.00 0.00 3.85
4051 7730 8.229253 TGATCCAAATTCCTGACATAGAATTG 57.771 34.615 12.08 8.05 40.84 2.32
4070 7749 5.587388 ATTGGACTAGCAATGAAACATGG 57.413 39.130 0.00 0.00 0.00 3.66
4172 7852 1.069296 TGCAACAAATGTAGTGCGCTC 60.069 47.619 9.73 4.74 35.23 5.03
4246 7926 2.808933 CGTCTGGCAAAAGTTAGGACCA 60.809 50.000 0.00 0.00 0.00 4.02
4252 7932 5.636123 TGGCAAAAGTTAGGACCAATCTAA 58.364 37.500 0.00 0.00 0.00 2.10
4366 8046 9.659830 AAGTAACAACGTTTTGATTAGAACATC 57.340 29.630 0.00 0.00 36.48 3.06
4367 8047 8.007716 AGTAACAACGTTTTGATTAGAACATCG 58.992 33.333 0.00 0.00 36.48 3.84
4368 8048 5.144359 ACAACGTTTTGATTAGAACATCGC 58.856 37.500 0.00 0.00 36.48 4.58
4369 8049 4.336532 ACGTTTTGATTAGAACATCGCC 57.663 40.909 0.00 0.00 0.00 5.54
4370 8050 3.749088 ACGTTTTGATTAGAACATCGCCA 59.251 39.130 0.00 0.00 0.00 5.69
4371 8051 4.214545 ACGTTTTGATTAGAACATCGCCAA 59.785 37.500 0.00 0.00 0.00 4.52
4372 8052 5.106317 ACGTTTTGATTAGAACATCGCCAAT 60.106 36.000 0.00 0.00 0.00 3.16
4373 8053 5.452302 CGTTTTGATTAGAACATCGCCAATC 59.548 40.000 0.00 0.00 0.00 2.67
4489 8179 3.181429 TGCTGAGGAGGAAGAAAATGGTT 60.181 43.478 0.00 0.00 0.00 3.67
4504 8194 0.326595 TGGTTCGGCCAGCATAGAAA 59.673 50.000 2.24 0.00 43.61 2.52
4548 8238 2.143925 GGTTCGACCTTTGACTGGAAG 58.856 52.381 0.00 0.00 35.83 3.46
4596 8286 2.028658 TGAGTCTGTGCTCATGTCCTTC 60.029 50.000 0.00 0.00 40.23 3.46
4650 8343 1.415374 GAGCGCTTTTAGTGACGTCA 58.585 50.000 15.76 15.76 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.763652 CTGGCCTAGATGATGCCTGT 59.236 55.000 3.32 0.00 45.56 4.00
15 16 1.481871 GCTAGTGTACACCTGGCCTA 58.518 55.000 22.28 6.32 0.00 3.93
183 1920 2.028930 GTCGCCTTGAGAGAGAGGAAAA 60.029 50.000 0.00 0.00 34.91 2.29
210 1959 1.158007 TGGAGGGAAGGAAGGCTTTT 58.842 50.000 0.00 0.00 0.00 2.27
279 2031 4.590553 TCCTCCCCACCACCAGCA 62.591 66.667 0.00 0.00 0.00 4.41
359 2112 0.034477 GGACCACCATCCGTCCAAAT 60.034 55.000 1.38 0.00 46.59 2.32
722 2505 1.746220 CACCGGAAGTTCAAAACACCA 59.254 47.619 9.46 0.00 32.84 4.17
727 2510 5.845391 AAAGATTCACCGGAAGTTCAAAA 57.155 34.783 9.46 0.00 36.25 2.44
802 2585 9.146984 CCGGATATATTAGCACTTTTTCGATTA 57.853 33.333 0.00 0.00 0.00 1.75
893 2683 0.391263 CTCCGGCTCTGGTGGTTTAC 60.391 60.000 0.00 0.00 0.00 2.01
894 2684 0.834687 ACTCCGGCTCTGGTGGTTTA 60.835 55.000 0.00 0.00 0.00 2.01
895 2685 0.834687 TACTCCGGCTCTGGTGGTTT 60.835 55.000 0.00 0.00 0.00 3.27
896 2686 1.229082 TACTCCGGCTCTGGTGGTT 60.229 57.895 0.00 0.00 0.00 3.67
897 2687 1.682684 CTACTCCGGCTCTGGTGGT 60.683 63.158 0.00 2.69 0.00 4.16
898 2688 0.970937 TTCTACTCCGGCTCTGGTGG 60.971 60.000 0.00 0.00 0.00 4.61
899 2689 0.895530 TTTCTACTCCGGCTCTGGTG 59.104 55.000 0.00 0.00 0.00 4.17
900 2690 1.640917 TTTTCTACTCCGGCTCTGGT 58.359 50.000 0.00 0.00 0.00 4.00
901 2691 2.762535 TTTTTCTACTCCGGCTCTGG 57.237 50.000 0.00 0.00 0.00 3.86
943 2737 5.381757 ACTTGATTAGTTGCTGGTGGTTTA 58.618 37.500 0.00 0.00 31.29 2.01
1272 3067 0.685458 GGTAGTCGAGGCCCCAGTAA 60.685 60.000 0.00 0.00 0.00 2.24
1328 3123 2.514824 GGGAGGCGTTGATGAGGC 60.515 66.667 0.00 0.00 38.40 4.70
1356 3151 3.967335 GAGGATCGGAGGGCGACG 61.967 72.222 0.00 0.00 0.00 5.12
1383 3178 0.448990 CGTACGATTCGTGGGACTCA 59.551 55.000 21.40 0.00 41.39 3.41
1392 3187 3.495352 GAGGGGCCCGTACGATTCG 62.495 68.421 19.10 4.14 0.00 3.34
1404 3199 1.839424 AAATGTTAGTGCAGAGGGGC 58.161 50.000 0.00 0.00 0.00 5.80
1406 3201 3.375299 GTGCTAAATGTTAGTGCAGAGGG 59.625 47.826 0.00 0.00 34.15 4.30
1407 3202 4.002982 TGTGCTAAATGTTAGTGCAGAGG 58.997 43.478 0.00 0.00 34.15 3.69
1413 3208 4.391830 ACCACGATGTGCTAAATGTTAGTG 59.608 41.667 0.00 0.00 31.34 2.74
1445 3242 3.053455 GAGACTTGAAACAGACACGGAG 58.947 50.000 0.00 0.00 0.00 4.63
1446 3243 2.693591 AGAGACTTGAAACAGACACGGA 59.306 45.455 0.00 0.00 0.00 4.69
1447 3244 2.797156 CAGAGACTTGAAACAGACACGG 59.203 50.000 0.00 0.00 0.00 4.94
1448 3245 3.243877 CACAGAGACTTGAAACAGACACG 59.756 47.826 0.00 0.00 0.00 4.49
1459 3256 3.134458 GGAAACAGACCACAGAGACTTG 58.866 50.000 0.00 0.00 0.00 3.16
1570 3367 2.204865 TACCGCCAACCCCATCCTTG 62.205 60.000 0.00 0.00 0.00 3.61
1603 3400 2.125912 AGCCACATCCACCCCTCT 59.874 61.111 0.00 0.00 0.00 3.69
1655 3452 0.744414 AAATGGCCGTGGTCGATCAG 60.744 55.000 0.00 0.00 39.71 2.90
1657 3454 0.377203 GAAAATGGCCGTGGTCGATC 59.623 55.000 0.00 0.00 39.71 3.69
1682 3479 6.164176 GCACATACACCACTAGTATAATCCC 58.836 44.000 0.00 0.00 31.32 3.85
1718 3515 4.386652 GCAATGCAGTCAACACTATTTTGG 59.613 41.667 0.00 0.00 0.00 3.28
1721 3518 4.520111 TGAGCAATGCAGTCAACACTATTT 59.480 37.500 8.35 0.00 0.00 1.40
1722 3519 4.074259 TGAGCAATGCAGTCAACACTATT 58.926 39.130 8.35 0.00 0.00 1.73
1723 3520 3.678289 TGAGCAATGCAGTCAACACTAT 58.322 40.909 8.35 0.00 0.00 2.12
1724 3521 3.069289 CTGAGCAATGCAGTCAACACTA 58.931 45.455 8.35 0.00 0.00 2.74
1725 3522 1.878088 CTGAGCAATGCAGTCAACACT 59.122 47.619 8.35 0.00 0.00 3.55
1726 3523 1.605710 ACTGAGCAATGCAGTCAACAC 59.394 47.619 8.35 0.00 42.62 3.32
1727 3524 1.605232 CACTGAGCAATGCAGTCAACA 59.395 47.619 8.35 0.00 44.28 3.33
1728 3525 1.605710 ACACTGAGCAATGCAGTCAAC 59.394 47.619 8.35 0.00 44.28 3.18
1814 3611 1.599542 GACAGAATACCAGCAATCGCC 59.400 52.381 0.00 0.00 39.83 5.54
1923 3720 7.508977 AGTTTCATCTCCCTGGAAATAAAACAA 59.491 33.333 2.01 0.00 33.58 2.83
1979 3776 1.065401 TGTTTGTTGCCGAAGCTTGAG 59.935 47.619 2.10 0.00 40.80 3.02
1990 3787 4.916983 TGGCCTATATCATGTTTGTTGC 57.083 40.909 3.32 0.00 0.00 4.17
2004 3801 8.538701 CAAAGATCTCTAAGATGTATGGCCTAT 58.461 37.037 3.32 0.00 34.53 2.57
2007 3804 5.411053 GCAAAGATCTCTAAGATGTATGGCC 59.589 44.000 0.00 0.00 34.53 5.36
2009 3806 6.767456 AGGCAAAGATCTCTAAGATGTATGG 58.233 40.000 0.00 0.00 34.53 2.74
2014 3811 5.819059 GCAAAGGCAAAGATCTCTAAGATG 58.181 41.667 0.00 0.00 35.96 2.90
2061 3858 1.489230 CCACTATACACCCCAGGAACC 59.511 57.143 0.00 0.00 0.00 3.62
2086 3883 2.419667 GCAGTCGCTTGGGTTAAGTTA 58.580 47.619 0.00 0.00 38.70 2.24
2169 5574 4.499183 GATTGTCTCTTACAGGTCTGTGG 58.501 47.826 13.32 6.71 44.63 4.17
2171 5576 3.515901 GGGATTGTCTCTTACAGGTCTGT 59.484 47.826 8.74 8.74 46.87 3.41
2223 5628 2.129607 CCAACACTGCATGCACTTTTC 58.870 47.619 18.46 0.00 0.00 2.29
2311 5984 5.283763 TCCATCTCTAGCAGCCCATTATAT 58.716 41.667 0.00 0.00 0.00 0.86
2442 6117 6.093633 CAGGTTAGTTTTATGGAAGTAGTGCC 59.906 42.308 0.00 0.00 0.00 5.01
2501 6176 9.023962 GGCCCATGAATTTATAGAATCACAATA 57.976 33.333 0.00 0.00 0.00 1.90
2510 6186 6.838090 TCAAACATGGCCCATGAATTTATAGA 59.162 34.615 29.99 13.58 43.81 1.98
2610 6286 6.917533 AGTTTCATGATCTCAACAATTGGAC 58.082 36.000 10.83 0.00 0.00 4.02
2721 6397 7.199766 TGAACAACAAAATAACCAGATCACAC 58.800 34.615 0.00 0.00 0.00 3.82
2779 6455 9.877178 AGTAAGGAGATCACTACATTTTAGTTG 57.123 33.333 0.00 0.00 0.00 3.16
2913 6591 7.759489 TGCAACATAATCCTCATATAAACCC 57.241 36.000 0.00 0.00 0.00 4.11
3105 6783 7.857569 ACGAGAATAGATAGAAAGAGAACGAG 58.142 38.462 0.00 0.00 0.00 4.18
3120 6798 6.832384 AGAACATACCTTGGTACGAGAATAGA 59.168 38.462 1.13 0.00 0.00 1.98
3169 6847 8.853345 CAAAGAAACATCACATATACTTGCAAC 58.147 33.333 0.00 0.00 0.00 4.17
3202 6880 9.848172 CACTGCAATTATAAAACAAAGAAACAC 57.152 29.630 0.00 0.00 0.00 3.32
3438 7116 2.228582 TGCCATTGTTCCAGACGAAATG 59.771 45.455 0.00 0.00 30.39 2.32
3492 7170 0.868406 GCAGGTACACAGTGTGAAGC 59.132 55.000 29.58 19.03 36.96 3.86
3549 7227 4.778579 AGCAGATGAACATTATCAGTGCT 58.221 39.130 9.80 9.80 43.46 4.40
3892 7570 0.803380 CTGCAAAAGCTAATGCCGCC 60.803 55.000 18.00 0.00 41.87 6.13
3965 7644 0.249489 AGGCACACTGACTCGACAAC 60.249 55.000 0.00 0.00 18.29 3.32
4017 7696 6.261826 GTCAGGAATTTGGATCAGATTACCAG 59.738 42.308 0.00 0.00 35.08 4.00
4051 7730 2.754552 TGCCATGTTTCATTGCTAGTCC 59.245 45.455 7.19 0.00 0.00 3.85
4172 7852 8.013947 TGTTTCATCACACACAAAAATGTTTTG 58.986 29.630 11.02 11.02 35.64 2.44
4280 7960 9.571816 GTTCTGTATGAGTACTTATACCCTACT 57.428 37.037 26.37 0.00 32.87 2.57
4281 7961 9.571816 AGTTCTGTATGAGTACTTATACCCTAC 57.428 37.037 26.37 21.04 32.87 3.18
4282 7962 9.570468 CAGTTCTGTATGAGTACTTATACCCTA 57.430 37.037 26.37 14.11 30.21 3.53
4283 7963 8.060075 ACAGTTCTGTATGAGTACTTATACCCT 58.940 37.037 26.37 17.06 30.21 4.34
4288 7968 9.998106 AACAAACAGTTCTGTATGAGTACTTAT 57.002 29.630 5.39 5.39 34.74 1.73
4289 7969 9.826574 AAACAAACAGTTCTGTATGAGTACTTA 57.173 29.630 5.87 0.00 40.26 2.24
4300 7980 2.094234 GCCACCAAACAAACAGTTCTGT 60.094 45.455 0.00 0.00 40.26 3.41
4366 8046 2.223456 TGATTTTGTATGGCGATTGGCG 60.223 45.455 1.48 0.00 44.92 5.69
4367 8047 3.115554 GTGATTTTGTATGGCGATTGGC 58.884 45.455 0.00 0.00 42.51 4.52
4368 8048 4.336433 AGAGTGATTTTGTATGGCGATTGG 59.664 41.667 0.00 0.00 0.00 3.16
4369 8049 5.490139 AGAGTGATTTTGTATGGCGATTG 57.510 39.130 0.00 0.00 0.00 2.67
4370 8050 7.807977 ATTAGAGTGATTTTGTATGGCGATT 57.192 32.000 0.00 0.00 0.00 3.34
4371 8051 8.902540 TTATTAGAGTGATTTTGTATGGCGAT 57.097 30.769 0.00 0.00 0.00 4.58
4372 8052 8.201464 TCTTATTAGAGTGATTTTGTATGGCGA 58.799 33.333 0.00 0.00 0.00 5.54
4373 8053 8.365399 TCTTATTAGAGTGATTTTGTATGGCG 57.635 34.615 0.00 0.00 0.00 5.69
4489 8179 1.223487 GGGTTTCTATGCTGGCCGA 59.777 57.895 0.00 0.00 0.00 5.54
4504 8194 1.907255 GTAGCTGGTTTCTGGTAGGGT 59.093 52.381 0.00 0.00 0.00 4.34
4548 8238 2.095161 CGACTACAGCGGAGGATATTCC 60.095 54.545 0.00 0.00 36.58 3.01
4611 8304 1.005867 TCGCCACCCTTACAACGAC 60.006 57.895 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.