Multiple sequence alignment - TraesCS5B01G440100

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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 TraesCS5B01G440100 chr5B 100.000 2519 0 0 1 2519 612016077 612013559 0.000000e+00 4652
1 TraesCS5B01G440100 chr5B 89.180 305 30 3 1903 2206 303229099 303229401 6.580000e-101 377
2 TraesCS5B01G440100 chr5A 87.522 1683 115 38 4 1649 619477639 619476015 0.000000e+00 1857
3 TraesCS5B01G440100 chr5A 88.806 134 15 0 2386 2519 619475388 619475255 5.570000e-37 165
4 TraesCS5B01G440100 chr5A 93.333 105 7 0 2415 2519 619470079 619469975 3.360000e-34 156
5 TraesCS5B01G440100 chr5D 92.191 794 58 4 1024 1817 495373539 495372750 0.000000e+00 1120
6 TraesCS5B01G440100 chr5D 87.781 712 69 10 1818 2519 495369329 495368626 0.000000e+00 817
7 TraesCS5B01G440100 chr5D 89.439 303 17 9 107 400 495381025 495380729 3.960000e-98 368
8 TraesCS5B01G440100 chr5D 82.490 257 33 9 486 739 495380717 495380470 5.460000e-52 215
9 TraesCS5B01G440100 chr5D 94.231 104 6 0 6 109 495386431 495386328 2.590000e-35 159
10 TraesCS5B01G440100 chr3D 87.986 874 81 12 991 1859 438604274 438603420 0.000000e+00 1011
11 TraesCS5B01G440100 chr3D 83.333 978 80 38 4 953 438605432 438604510 0.000000e+00 826
12 TraesCS5B01G440100 chr3D 81.852 270 32 10 2250 2510 438603066 438602805 7.060000e-51 211
13 TraesCS5B01G440100 chr1D 87.805 574 59 9 1001 1567 17193966 17193397 0.000000e+00 662
14 TraesCS5B01G440100 chr1A 88.462 520 57 1 1001 1517 18487023 18486504 2.130000e-175 625
15 TraesCS5B01G440100 chr1A 88.710 310 30 5 1903 2211 285590026 285590331 8.510000e-100 374
16 TraesCS5B01G440100 chr1B 85.592 583 66 9 1001 1567 24989051 24988471 1.670000e-166 595
17 TraesCS5B01G440100 chr4B 90.252 318 26 5 1902 2216 396703703 396704018 6.490000e-111 411
18 TraesCS5B01G440100 chrUn 89.935 308 27 4 1903 2209 289820919 289820615 6.530000e-106 394
19 TraesCS5B01G440100 chr7B 89.644 309 30 2 1902 2209 59068742 59069049 2.350000e-105 392
20 TraesCS5B01G440100 chr7D 89.355 310 27 5 1901 2209 517003756 517004060 3.930000e-103 385
21 TraesCS5B01G440100 chr4D 89.286 308 28 5 1903 2209 421335214 421335517 5.080000e-102 381
22 TraesCS5B01G440100 chr4A 88.328 317 32 5 1902 2216 154521426 154521113 2.370000e-100 375


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 TraesCS5B01G440100 chr5B 612013559 612016077 2518 True 4652.000000 4652 100.000000 1 2519 1 chr5B.!!$R1 2518
1 TraesCS5B01G440100 chr5A 619475255 619477639 2384 True 1011.000000 1857 88.164000 4 2519 2 chr5A.!!$R2 2515
2 TraesCS5B01G440100 chr5D 495368626 495373539 4913 True 968.500000 1120 89.986000 1024 2519 2 chr5D.!!$R2 1495
3 TraesCS5B01G440100 chr5D 495380470 495381025 555 True 291.500000 368 85.964500 107 739 2 chr5D.!!$R3 632
4 TraesCS5B01G440100 chr3D 438602805 438605432 2627 True 682.666667 1011 84.390333 4 2510 3 chr3D.!!$R1 2506
5 TraesCS5B01G440100 chr1D 17193397 17193966 569 True 662.000000 662 87.805000 1001 1567 1 chr1D.!!$R1 566
6 TraesCS5B01G440100 chr1A 18486504 18487023 519 True 625.000000 625 88.462000 1001 1517 1 chr1A.!!$R1 516
7 TraesCS5B01G440100 chr1B 24988471 24989051 580 True 595.000000 595 85.592000 1001 1567 1 chr1B.!!$R1 566

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
799 860 0.104671 CCCAGGTGCTTTTGGTGTTG 59.895 55.0 0.0 0.0 32.4 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 6218 0.10576 TGCAACCAAACATGACCCCT 60.106 50.0 0.0 0.0 0.0 4.79 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
115 116 2.234296 CCCAACCTGAAGCCCTCCT 61.234 63.158 0.00 0.00 0.00 3.69
162 163 2.492090 CTCCTCGGGTGCTCTTCG 59.508 66.667 0.00 0.00 0.00 3.79
300 311 5.577945 CCAAATTCCGATCCTTCACAATTTG 59.422 40.000 7.61 7.61 38.62 2.32
340 371 7.123355 AGAGGAGAACAGAGGATAATTCTTG 57.877 40.000 0.00 0.00 31.58 3.02
343 374 7.563906 AGGAGAACAGAGGATAATTCTTGAAG 58.436 38.462 0.00 0.00 31.58 3.02
346 377 8.785329 AGAACAGAGGATAATTCTTGAAGTTC 57.215 34.615 0.00 0.00 0.00 3.01
355 386 8.830580 GGATAATTCTTGAAGTTCATCGATTGA 58.169 33.333 6.36 0.00 0.00 2.57
385 416 0.313672 TTGGCTGTTTGCATTCGTCC 59.686 50.000 0.00 0.00 45.15 4.79
394 425 0.107643 TGCATTCGTCCACTGGTTCA 59.892 50.000 0.00 0.00 0.00 3.18
436 467 0.895530 TAGAGCACAGTGGTAGTGGC 59.104 55.000 4.92 0.00 37.46 5.01
463 494 2.985957 AGAGGATCAAGAGAAGCAGC 57.014 50.000 0.00 0.00 37.82 5.25
523 554 8.333235 ACCTTTTTGTATCAACCATCCACTATA 58.667 33.333 0.00 0.00 0.00 1.31
524 555 9.354673 CCTTTTTGTATCAACCATCCACTATAT 57.645 33.333 0.00 0.00 0.00 0.86
576 610 7.287466 TCCATTTCTTATATTGTTCCCACCATG 59.713 37.037 0.00 0.00 0.00 3.66
577 611 7.436118 CATTTCTTATATTGTTCCCACCATGG 58.564 38.462 11.19 11.19 37.25 3.66
594 628 3.386726 CCATGGCCTGATTGAATGATTGT 59.613 43.478 3.32 0.00 0.00 2.71
670 709 2.025037 AGCCCAGCCAATCATCAACTTA 60.025 45.455 0.00 0.00 0.00 2.24
676 715 5.824624 CCAGCCAATCATCAACTTAGTATGT 59.175 40.000 0.00 0.00 0.00 2.29
701 740 8.971321 GTTTGTATCAATGCTTGCTAAATATGG 58.029 33.333 0.00 0.00 0.00 2.74
704 743 3.004629 TCAATGCTTGCTAAATATGGGCG 59.995 43.478 0.00 0.00 0.00 6.13
739 800 4.451900 ACTTGCTTGTTTAGTACTGCAGT 58.548 39.130 25.12 25.12 37.86 4.40
760 821 6.215121 CAGTCAAGGTGTTTGATTAAATGCA 58.785 36.000 0.00 0.00 46.85 3.96
774 835 8.283699 TGATTAAATGCATCTGAGATGAACAA 57.716 30.769 25.58 10.85 0.00 2.83
799 860 0.104671 CCCAGGTGCTTTTGGTGTTG 59.895 55.000 0.00 0.00 32.40 3.33
817 878 6.183360 TGGTGTTGGTAGATTGTTCTGTTTTC 60.183 38.462 0.00 0.00 33.17 2.29
909 971 3.516615 AGATTTCAGTACTTCGCTCTGC 58.483 45.455 0.00 0.00 0.00 4.26
918 980 6.037098 CAGTACTTCGCTCTGCTATTTTACT 58.963 40.000 0.00 0.00 0.00 2.24
919 981 6.531948 CAGTACTTCGCTCTGCTATTTTACTT 59.468 38.462 0.00 0.00 0.00 2.24
963 1027 4.049186 CAGGTTAATCCATCGTAGAACCG 58.951 47.826 0.00 0.00 43.58 4.44
979 1043 2.200373 ACCGCATAAAGAGGCTGTTT 57.800 45.000 14.46 14.46 41.55 2.83
984 1048 3.189287 CGCATAAAGAGGCTGTTTCAGTT 59.811 43.478 13.41 0.00 33.43 3.16
985 1049 4.479619 GCATAAAGAGGCTGTTTCAGTTG 58.520 43.478 13.41 8.50 33.43 3.16
986 1050 4.479619 CATAAAGAGGCTGTTTCAGTTGC 58.520 43.478 13.41 0.00 33.43 4.17
988 1052 0.886490 AGAGGCTGTTTCAGTTGCGG 60.886 55.000 0.00 0.00 33.43 5.69
989 1053 1.152963 AGGCTGTTTCAGTTGCGGT 60.153 52.632 0.00 0.00 33.43 5.68
1083 1356 1.153745 CTTCCCGTCTTCTCTGCCG 60.154 63.158 0.00 0.00 0.00 5.69
1228 1501 5.336372 CCGAATGATTACAAGAAGGCCAAAA 60.336 40.000 5.01 0.00 0.00 2.44
1247 1520 5.188359 CCAAAAAGGAATCTGATCCCAACAT 59.812 40.000 0.00 0.00 40.59 2.71
1254 1533 5.529060 GGAATCTGATCCCAACATTACTGAC 59.471 44.000 0.00 0.00 33.05 3.51
1260 1539 1.278127 CCCAACATTACTGACGAGGGT 59.722 52.381 0.00 0.00 0.00 4.34
1263 1542 3.930848 CCAACATTACTGACGAGGGTAAC 59.069 47.826 0.00 0.00 31.91 2.50
1271 1550 4.625028 ACTGACGAGGGTAACACTAAAAC 58.375 43.478 0.00 0.00 39.74 2.43
1449 1731 0.034896 TGGACGAGAAGGCTGGAAAC 59.965 55.000 0.00 0.00 0.00 2.78
1531 1820 6.408869 TCATCATCATGAGCTTGTTTCAGTA 58.591 36.000 0.09 0.00 33.80 2.74
1535 1824 5.868043 TCATGAGCTTGTTTCAGTATGTG 57.132 39.130 0.00 0.00 37.40 3.21
1539 1829 2.375174 AGCTTGTTTCAGTATGTGGGGA 59.625 45.455 0.00 0.00 37.40 4.81
1570 1860 3.006430 TCATTAGGACTCGCAGTTCAACA 59.994 43.478 0.00 0.00 0.00 3.33
1579 1869 2.160219 TCGCAGTTCAACATTCATGAGC 59.840 45.455 0.00 0.00 0.00 4.26
1673 1965 6.419484 TTTCTTTCATGTGTAGGTCTCTGA 57.581 37.500 0.00 0.00 0.00 3.27
1686 1978 6.719829 TGTAGGTCTCTGATCTTGTTTGTCTA 59.280 38.462 0.00 0.00 0.00 2.59
1694 1986 7.318893 TCTGATCTTGTTTGTCTACTGATCAG 58.681 38.462 21.37 21.37 45.20 2.90
1706 1998 6.127338 TGTCTACTGATCAGGGTTATGTGAAG 60.127 42.308 26.08 7.78 0.00 3.02
1732 2024 6.881602 TGTATTGTACATTGTTGCTATGGACA 59.118 34.615 0.00 4.88 43.35 4.02
1738 2030 6.832520 ACATTGTTGCTATGGACATTGTTA 57.167 33.333 0.00 0.00 37.17 2.41
1744 2036 4.776349 TGCTATGGACATTGTTATTCGGT 58.224 39.130 0.00 0.00 0.00 4.69
1760 2052 3.980646 TCGGTTTGTTTCAGTTGATGG 57.019 42.857 0.00 0.00 0.00 3.51
1761 2053 3.546724 TCGGTTTGTTTCAGTTGATGGA 58.453 40.909 0.00 0.00 0.00 3.41
1792 2084 8.655092 CAAACAAAAAGTGATGCTTAGACAAAA 58.345 29.630 0.00 0.00 36.17 2.44
1800 2092 7.869800 AGTGATGCTTAGACAAAAAGAAAGAG 58.130 34.615 0.00 0.00 0.00 2.85
1861 5572 5.866633 GCCGGTTGATTTTTCAATCATGTAA 59.133 36.000 1.90 0.00 46.68 2.41
1894 5625 4.142093 GGCATCCATGTGCAAACTCTAAAT 60.142 41.667 10.16 0.00 46.81 1.40
1910 5641 4.371681 TCTAAATTGAGGCCTACTCCCTT 58.628 43.478 4.42 0.00 46.01 3.95
1913 5644 0.252103 TTGAGGCCTACTCCCTTCGT 60.252 55.000 4.42 0.00 46.01 3.85
1918 5649 1.379576 CCTACTCCCTTCGTCCGGT 60.380 63.158 0.00 0.00 0.00 5.28
1923 5654 1.228644 TCCCTTCGTCCGGTGAAGA 60.229 57.895 28.83 15.05 44.42 2.87
1929 5660 3.568853 CCTTCGTCCGGTGAAGAGTATAT 59.431 47.826 28.83 0.00 44.42 0.86
1982 5714 5.755861 GTCTACTTCTATCTTCCCAATGCAC 59.244 44.000 0.00 0.00 0.00 4.57
1983 5715 4.851639 ACTTCTATCTTCCCAATGCACT 57.148 40.909 0.00 0.00 0.00 4.40
1986 5718 6.721318 ACTTCTATCTTCCCAATGCACTTTA 58.279 36.000 0.00 0.00 0.00 1.85
1988 5720 7.836183 ACTTCTATCTTCCCAATGCACTTTAAT 59.164 33.333 0.00 0.00 0.00 1.40
2022 5754 6.102663 AGAATGTTTCTCTCTTATCACACGG 58.897 40.000 0.00 0.00 34.07 4.94
2039 5771 5.640357 TCACACGGTAATCAAGACCAATAAC 59.360 40.000 0.00 0.00 36.72 1.89
2043 5775 7.825270 ACACGGTAATCAAGACCAATAACATTA 59.175 33.333 0.00 0.00 36.72 1.90
2052 5784 9.119418 TCAAGACCAATAACATTATACACATGG 57.881 33.333 0.00 0.00 0.00 3.66
2056 5788 8.677148 ACCAATAACATTATACACATGGTCTC 57.323 34.615 0.00 0.00 33.59 3.36
2057 5789 8.494433 ACCAATAACATTATACACATGGTCTCT 58.506 33.333 0.00 0.00 33.59 3.10
2085 5817 6.426980 TTTCTACATGCACTTAGCTCATTG 57.573 37.500 0.00 0.00 45.94 2.82
2086 5818 4.445453 TCTACATGCACTTAGCTCATTGG 58.555 43.478 0.00 0.00 45.94 3.16
2125 5857 0.175760 GCGAGAGATGGTGGCTTGTA 59.824 55.000 0.00 0.00 0.00 2.41
2131 5863 3.010420 GAGATGGTGGCTTGTACCTTTC 58.990 50.000 0.00 0.00 39.01 2.62
2137 5869 0.733150 GGCTTGTACCTTTCCGATGC 59.267 55.000 0.00 0.00 0.00 3.91
2214 5947 1.637553 AGGACGGAGGGAGTACTAACA 59.362 52.381 0.00 0.00 29.47 2.41
2215 5948 2.244252 AGGACGGAGGGAGTACTAACAT 59.756 50.000 0.00 0.00 29.47 2.71
2226 5959 4.221041 GGAGTACTAACATCCTCATAGGGC 59.779 50.000 0.00 0.00 35.59 5.19
2252 6218 6.512903 CGAGTTAGAAGTAGTCATGCCGATTA 60.513 42.308 0.00 0.00 0.00 1.75
2272 6238 0.755686 GGGGTCATGTTTGGTTGCAA 59.244 50.000 0.00 0.00 0.00 4.08
2332 6301 7.148507 CGATGTCTGCTATTCTCAAAACTCTTT 60.149 37.037 0.00 0.00 0.00 2.52
2335 6304 7.283127 TGTCTGCTATTCTCAAAACTCTTTGTT 59.717 33.333 0.00 0.00 42.26 2.83
2349 6378 8.959734 AAACTCTTTGTTGTTTACAAGTACAC 57.040 30.769 0.00 0.00 46.81 2.90
2369 6398 3.614176 CACACCATGAACACTACGATCAG 59.386 47.826 0.00 0.00 0.00 2.90
2370 6399 3.509967 ACACCATGAACACTACGATCAGA 59.490 43.478 0.00 0.00 0.00 3.27
2371 6400 4.160439 ACACCATGAACACTACGATCAGAT 59.840 41.667 0.00 0.00 0.00 2.90
2372 6401 5.359860 ACACCATGAACACTACGATCAGATA 59.640 40.000 0.00 0.00 0.00 1.98
2373 6402 5.917447 CACCATGAACACTACGATCAGATAG 59.083 44.000 0.00 0.00 0.00 2.08
2374 6403 5.594725 ACCATGAACACTACGATCAGATAGT 59.405 40.000 1.43 1.43 31.65 2.12
2375 6404 6.146216 CCATGAACACTACGATCAGATAGTC 58.854 44.000 0.00 0.00 28.91 2.59
2376 6405 5.752892 TGAACACTACGATCAGATAGTCC 57.247 43.478 0.00 0.00 28.91 3.85
2377 6406 4.579340 TGAACACTACGATCAGATAGTCCC 59.421 45.833 0.00 0.00 28.91 4.46
2378 6407 4.440826 ACACTACGATCAGATAGTCCCT 57.559 45.455 0.00 0.00 28.91 4.20
2379 6408 4.794334 ACACTACGATCAGATAGTCCCTT 58.206 43.478 0.00 0.00 28.91 3.95
2380 6409 5.938279 ACACTACGATCAGATAGTCCCTTA 58.062 41.667 0.00 0.00 28.91 2.69
2381 6410 6.544650 ACACTACGATCAGATAGTCCCTTAT 58.455 40.000 0.00 0.00 28.91 1.73
2382 6411 6.431543 ACACTACGATCAGATAGTCCCTTATG 59.568 42.308 0.00 0.00 28.91 1.90
2383 6412 6.655425 CACTACGATCAGATAGTCCCTTATGA 59.345 42.308 0.00 0.00 28.91 2.15
2384 6413 7.338196 CACTACGATCAGATAGTCCCTTATGAT 59.662 40.741 0.00 0.00 28.91 2.45
2512 6573 4.640771 AGACTTGATGTATGGTGGTTGT 57.359 40.909 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.764336 TTAGCGTCGCCGTCACCG 62.764 66.667 14.86 0.00 36.15 4.94
115 116 1.936436 ATCGTACGCCGGTGCTGTAA 61.936 55.000 16.69 0.00 37.11 2.41
225 236 4.717629 CCGTGGAGCGTGCTTCGA 62.718 66.667 13.46 0.00 42.86 3.71
228 239 4.927782 TTGCCGTGGAGCGTGCTT 62.928 61.111 0.00 0.00 39.32 3.91
300 311 2.084546 CCTCTCAACCGGGAAAATCAC 58.915 52.381 6.32 0.00 0.00 3.06
340 371 9.941664 ACAATGAATTATCAATCGATGAACTTC 57.058 29.630 0.00 5.02 42.54 3.01
343 374 8.961092 CCAACAATGAATTATCAATCGATGAAC 58.039 33.333 0.00 0.00 42.54 3.18
346 377 7.114388 CAGCCAACAATGAATTATCAATCGATG 59.886 37.037 0.00 0.00 39.49 3.84
355 386 5.549347 TGCAAACAGCCAACAATGAATTAT 58.451 33.333 0.00 0.00 44.83 1.28
356 387 4.953667 TGCAAACAGCCAACAATGAATTA 58.046 34.783 0.00 0.00 44.83 1.40
357 388 3.806380 TGCAAACAGCCAACAATGAATT 58.194 36.364 0.00 0.00 44.83 2.17
385 416 5.167121 TCAACACAACAAAATGAACCAGTG 58.833 37.500 0.00 0.00 0.00 3.66
394 425 4.466015 ACCCAAGTCTCAACACAACAAAAT 59.534 37.500 0.00 0.00 0.00 1.82
436 467 5.123661 GCTTCTCTTGATCCTCTTCTTTTGG 59.876 44.000 0.00 0.00 0.00 3.28
463 494 6.636666 AGCTGAAATGCATAAAATTCAACG 57.363 33.333 11.59 4.16 31.94 4.10
525 556 9.155975 GAAGTTCACAGTAATACAAGACATGAT 57.844 33.333 0.00 0.00 0.00 2.45
526 557 7.602644 GGAAGTTCACAGTAATACAAGACATGA 59.397 37.037 5.01 0.00 0.00 3.07
576 610 3.192466 GCAACAATCATTCAATCAGGCC 58.808 45.455 0.00 0.00 0.00 5.19
577 611 3.118884 AGGCAACAATCATTCAATCAGGC 60.119 43.478 0.00 0.00 41.41 4.85
594 628 0.885879 CATCTTCAGCAAGCAGGCAA 59.114 50.000 2.37 0.00 35.83 4.52
701 740 2.349532 GCAAGTAACAGAGTGTTTCGCC 60.350 50.000 0.00 0.00 41.45 5.54
704 743 5.485662 ACAAGCAAGTAACAGAGTGTTTC 57.514 39.130 0.00 0.00 41.45 2.78
760 821 3.054802 GGGTCCTGTTGTTCATCTCAGAT 60.055 47.826 0.00 0.00 0.00 2.90
774 835 0.468029 CAAAAGCACCTGGGTCCTGT 60.468 55.000 0.00 0.00 0.00 4.00
830 891 8.746530 ACAAGAACAAATCATTTCTGATGCTAT 58.253 29.630 0.00 0.00 41.34 2.97
909 971 8.564574 TGGTAAAGCACAAGACAAGTAAAATAG 58.435 33.333 0.00 0.00 0.00 1.73
918 980 3.820467 CTCCATGGTAAAGCACAAGACAA 59.180 43.478 12.58 0.00 0.00 3.18
919 981 3.411446 CTCCATGGTAAAGCACAAGACA 58.589 45.455 12.58 0.00 0.00 3.41
963 1027 4.479619 CAACTGAAACAGCCTCTTTATGC 58.520 43.478 0.00 0.00 34.37 3.14
988 1052 1.739067 AACTTCATTCCGGCTGCTAC 58.261 50.000 0.00 0.00 0.00 3.58
989 1053 2.489938 AAACTTCATTCCGGCTGCTA 57.510 45.000 0.00 0.00 0.00 3.49
1153 1426 1.424638 GAAGCCCCATACAGCCTAGA 58.575 55.000 0.00 0.00 0.00 2.43
1228 1501 6.069440 TCAGTAATGTTGGGATCAGATTCCTT 60.069 38.462 9.37 0.00 35.97 3.36
1247 1520 6.040842 AGTTTTAGTGTTACCCTCGTCAGTAA 59.959 38.462 0.00 0.00 0.00 2.24
1254 1533 4.450080 GGTTCAGTTTTAGTGTTACCCTCG 59.550 45.833 0.00 0.00 0.00 4.63
1260 1539 6.480981 GCACAGTAGGTTCAGTTTTAGTGTTA 59.519 38.462 0.00 0.00 29.63 2.41
1263 1542 5.057149 AGCACAGTAGGTTCAGTTTTAGTG 58.943 41.667 0.00 0.00 0.00 2.74
1271 1550 2.300152 TCCTCAAGCACAGTAGGTTCAG 59.700 50.000 0.00 0.00 0.00 3.02
1449 1731 1.973281 ATTGCCTTGCTGGTGACCG 60.973 57.895 0.00 0.00 38.35 4.79
1475 1757 1.095807 AGGCGACGTCGATGATCTCA 61.096 55.000 39.74 0.00 43.02 3.27
1531 1820 5.599656 CCTAATGATGACATTTTCCCCACAT 59.400 40.000 0.00 0.00 43.17 3.21
1535 1824 5.449553 AGTCCTAATGATGACATTTTCCCC 58.550 41.667 0.00 0.00 43.17 4.81
1539 1829 5.185454 TGCGAGTCCTAATGATGACATTTT 58.815 37.500 0.00 0.00 43.17 1.82
1570 1860 5.981315 CACAAACTGAAACAAGCTCATGAAT 59.019 36.000 0.00 0.00 0.00 2.57
1579 1869 3.129287 AGCTGTCCACAAACTGAAACAAG 59.871 43.478 0.00 0.00 0.00 3.16
1673 1965 5.249393 ACCCTGATCAGTAGACAAACAAGAT 59.751 40.000 21.11 0.00 0.00 2.40
1686 1978 4.287067 ACACTTCACATAACCCTGATCAGT 59.713 41.667 21.11 5.78 0.00 3.41
1694 1986 7.859325 ATGTACAATACACTTCACATAACCC 57.141 36.000 0.00 0.00 42.23 4.11
1706 1998 7.148323 TGTCCATAGCAACAATGTACAATACAC 60.148 37.037 0.00 0.00 42.23 2.90
1732 2024 7.484975 TCAACTGAAACAAACCGAATAACAAT 58.515 30.769 0.00 0.00 0.00 2.71
1738 2030 4.582656 TCCATCAACTGAAACAAACCGAAT 59.417 37.500 0.00 0.00 0.00 3.34
1744 2036 4.946772 TGTCTGTCCATCAACTGAAACAAA 59.053 37.500 0.00 0.00 0.00 2.83
1760 2052 5.343249 AGCATCACTTTTTGTTTGTCTGTC 58.657 37.500 0.00 0.00 0.00 3.51
1761 2053 5.329035 AGCATCACTTTTTGTTTGTCTGT 57.671 34.783 0.00 0.00 0.00 3.41
1812 2104 8.956426 GCAAGAGAGATCTAACTAGCATACTAT 58.044 37.037 0.00 0.00 0.00 2.12
1817 2109 4.022416 CGGCAAGAGAGATCTAACTAGCAT 60.022 45.833 0.00 0.00 0.00 3.79
1818 2110 3.316588 CGGCAAGAGAGATCTAACTAGCA 59.683 47.826 0.00 0.00 0.00 3.49
1820 2112 3.886505 ACCGGCAAGAGAGATCTAACTAG 59.113 47.826 0.00 0.00 0.00 2.57
1821 2113 3.899726 ACCGGCAAGAGAGATCTAACTA 58.100 45.455 0.00 0.00 0.00 2.24
1822 2114 2.741145 ACCGGCAAGAGAGATCTAACT 58.259 47.619 0.00 0.00 0.00 2.24
1823 2115 3.119101 TCAACCGGCAAGAGAGATCTAAC 60.119 47.826 0.00 0.00 0.00 2.34
1871 5602 1.180029 AGAGTTTGCACATGGATGCC 58.820 50.000 5.90 0.00 45.50 4.40
1894 5625 0.252103 ACGAAGGGAGTAGGCCTCAA 60.252 55.000 9.68 0.00 42.40 3.02
1910 5641 6.889301 AAATATATACTCTTCACCGGACGA 57.111 37.500 9.46 0.01 0.00 4.20
1913 5644 8.418597 AAGCTAAATATATACTCTTCACCGGA 57.581 34.615 9.46 0.00 0.00 5.14
1952 5684 8.437274 TTGGGAAGATAGAAGTAGACTCTTTT 57.563 34.615 0.00 0.00 0.00 2.27
1999 5731 5.869888 ACCGTGTGATAAGAGAGAAACATTC 59.130 40.000 0.00 0.00 0.00 2.67
2008 5740 6.405508 GGTCTTGATTACCGTGTGATAAGAGA 60.406 42.308 0.00 0.00 0.00 3.10
2016 5748 5.410132 TGTTATTGGTCTTGATTACCGTGTG 59.590 40.000 0.00 0.00 40.08 3.82
2051 5783 7.617041 AGTGCATGTAGAAATTAAAGAGACC 57.383 36.000 0.00 0.00 0.00 3.85
2054 5786 8.887717 AGCTAAGTGCATGTAGAAATTAAAGAG 58.112 33.333 10.04 0.00 45.94 2.85
2056 5788 8.668353 TGAGCTAAGTGCATGTAGAAATTAAAG 58.332 33.333 10.04 0.00 45.94 1.85
2057 5789 8.560355 TGAGCTAAGTGCATGTAGAAATTAAA 57.440 30.769 10.04 0.00 45.94 1.52
2085 5817 2.091499 CCTCCTTAATTACCCAACCCCC 60.091 54.545 0.00 0.00 0.00 5.40
2086 5818 2.688817 GCCTCCTTAATTACCCAACCCC 60.689 54.545 0.00 0.00 0.00 4.95
2177 5909 6.411376 TCCGTCCTGTGAAAAATGTACATAT 58.589 36.000 9.21 0.00 0.00 1.78
2181 5913 3.435671 CCTCCGTCCTGTGAAAAATGTAC 59.564 47.826 0.00 0.00 0.00 2.90
2186 5918 1.071699 CTCCCTCCGTCCTGTGAAAAA 59.928 52.381 0.00 0.00 0.00 1.94
2190 5922 0.323178 GTACTCCCTCCGTCCTGTGA 60.323 60.000 0.00 0.00 0.00 3.58
2193 5925 2.022934 GTTAGTACTCCCTCCGTCCTG 58.977 57.143 0.00 0.00 0.00 3.86
2194 5926 1.637553 TGTTAGTACTCCCTCCGTCCT 59.362 52.381 0.00 0.00 0.00 3.85
2195 5927 2.134789 TGTTAGTACTCCCTCCGTCC 57.865 55.000 0.00 0.00 0.00 4.79
2214 5947 2.110188 TCTAACTCGGCCCTATGAGGAT 59.890 50.000 9.79 1.87 37.67 3.24
2215 5948 1.497716 TCTAACTCGGCCCTATGAGGA 59.502 52.381 9.79 0.00 37.67 3.71
2226 5959 3.707793 GGCATGACTACTTCTAACTCGG 58.292 50.000 0.00 0.00 0.00 4.63
2252 6218 0.105760 TGCAACCAAACATGACCCCT 60.106 50.000 0.00 0.00 0.00 4.79
2332 6301 5.880887 TCATGGTGTGTACTTGTAAACAACA 59.119 36.000 20.09 20.09 43.83 3.33
2335 6304 5.880887 TGTTCATGGTGTGTACTTGTAAACA 59.119 36.000 0.03 0.03 0.00 2.83
2349 6378 4.110036 TCTGATCGTAGTGTTCATGGTG 57.890 45.455 0.00 0.00 0.00 4.17
2369 6398 8.652290 AGGAACAAGTTATCATAAGGGACTATC 58.348 37.037 0.00 0.00 38.49 2.08
2370 6399 8.568617 AGGAACAAGTTATCATAAGGGACTAT 57.431 34.615 0.00 0.00 38.49 2.12
2371 6400 7.989947 AGGAACAAGTTATCATAAGGGACTA 57.010 36.000 0.00 0.00 38.49 2.59
2373 6402 6.990939 GGTAGGAACAAGTTATCATAAGGGAC 59.009 42.308 0.00 0.00 0.00 4.46
2374 6403 6.674861 TGGTAGGAACAAGTTATCATAAGGGA 59.325 38.462 0.00 0.00 0.00 4.20
2375 6404 6.895782 TGGTAGGAACAAGTTATCATAAGGG 58.104 40.000 0.00 0.00 0.00 3.95
2376 6405 8.980481 ATTGGTAGGAACAAGTTATCATAAGG 57.020 34.615 0.00 0.00 0.00 2.69
2377 6406 8.765219 CGATTGGTAGGAACAAGTTATCATAAG 58.235 37.037 0.00 0.00 0.00 1.73
2378 6407 8.479689 TCGATTGGTAGGAACAAGTTATCATAA 58.520 33.333 0.00 0.00 0.00 1.90
2379 6408 8.014070 TCGATTGGTAGGAACAAGTTATCATA 57.986 34.615 0.00 0.00 0.00 2.15
2380 6409 6.884832 TCGATTGGTAGGAACAAGTTATCAT 58.115 36.000 0.00 0.00 0.00 2.45
2381 6410 6.288941 TCGATTGGTAGGAACAAGTTATCA 57.711 37.500 0.00 0.00 0.00 2.15
2382 6411 6.144080 CGATCGATTGGTAGGAACAAGTTATC 59.856 42.308 10.26 0.00 0.00 1.75
2383 6412 5.983720 CGATCGATTGGTAGGAACAAGTTAT 59.016 40.000 10.26 0.00 0.00 1.89
2384 6413 5.105635 ACGATCGATTGGTAGGAACAAGTTA 60.106 40.000 24.34 0.00 0.00 2.24
2429 6487 5.049749 CCTTCATGTGTTGTCATTACGTTCA 60.050 40.000 0.00 0.00 0.00 3.18
2432 6490 3.751175 CCCTTCATGTGTTGTCATTACGT 59.249 43.478 0.00 0.00 0.00 3.57
2439 6497 0.883833 CTGCCCCTTCATGTGTTGTC 59.116 55.000 0.00 0.00 0.00 3.18
2442 6503 1.705186 AGTACTGCCCCTTCATGTGTT 59.295 47.619 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.