Multiple sequence alignment - TraesCS1A01G039000

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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 TraesCS1A01G039000 chr1A 100.000 2506 0 0 1 2506 21280440 21277935 0.000000e+00 4628.0
1 TraesCS1A01G039000 chr1D 87.402 1659 169 17 1 1634 19874456 19872813 0.000000e+00 1869.0
2 TraesCS1A01G039000 chr1D 87.429 875 69 15 1640 2506 19872773 19871932 0.000000e+00 968.0
3 TraesCS1A01G039000 chr1B 84.630 1080 122 10 484 1523 31855528 31854453 0.000000e+00 1035.0
4 TraesCS1A01G039000 chr1B 81.614 756 76 31 1652 2364 31854401 31853666 3.620000e-158 568.0
5 TraesCS1A01G039000 chr5D 85.430 151 15 3 2362 2506 416798169 416798020 1.550000e-32 150.0
6 TraesCS1A01G039000 chr5A 82.803 157 21 5 2352 2506 462167411 462167259 4.350000e-28 135.0
7 TraesCS1A01G039000 chr5A 89.796 49 4 1 2405 2452 331861711 331861759 7.480000e-06 62.1
8 TraesCS1A01G039000 chr2A 84.677 124 18 1 2381 2504 7494926 7494804 3.390000e-24 122.0
9 TraesCS1A01G039000 chr7D 80.667 150 21 7 2362 2506 117545355 117545209 2.640000e-20 110.0
10 TraesCS1A01G039000 chr3A 80.851 141 26 1 2353 2492 606484536 606484676 2.640000e-20 110.0
11 TraesCS1A01G039000 chr7A 83.019 106 17 1 2394 2498 677661427 677661322 7.380000e-16 95.3
12 TraesCS1A01G039000 chr4A 82.524 103 17 1 2364 2466 728447870 728447971 3.430000e-14 89.8
13 TraesCS1A01G039000 chr3B 81.000 100 12 6 2362 2457 607195667 607195571 3.460000e-09 73.1


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 TraesCS1A01G039000 chr1A 21277935 21280440 2505 True 4628.0 4628 100.0000 1 2506 1 chr1A.!!$R1 2505
1 TraesCS1A01G039000 chr1D 19871932 19874456 2524 True 1418.5 1869 87.4155 1 2506 2 chr1D.!!$R1 2505
2 TraesCS1A01G039000 chr1B 31853666 31855528 1862 True 801.5 1035 83.1220 484 2364 2 chr1B.!!$R1 1880

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
544 553 0.317020 GTTTGTCTTGGTGTCGCTGC 60.317 55.0 0.0 0.0 0.0 5.25 F
1104 1130 0.590195 CAAGACACTGTTGCTCCTGC 59.410 55.0 0.0 0.0 40.2 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 1478 0.389391 CCGCATATTCCTCAGTCGGT 59.611 55.0 0.0 0.0 0.00 4.69 R
2341 2480 2.436173 AGCTCCTACAATGGCTAGAACC 59.564 50.0 0.0 0.0 32.94 3.62 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
28 29 1.848652 AGTAGTTCTAGCCCGAGCAA 58.151 50.000 0.00 0.00 43.56 3.91
80 81 4.946160 ATCACCAACATTAAGGAAGGGA 57.054 40.909 0.00 0.00 0.00 4.20
98 99 9.343994 AGGAAGGGAACATATATATGAGAACAT 57.656 33.333 26.05 10.17 40.16 2.71
180 181 2.691011 CCTCTACTTCACTAGGACCAGC 59.309 54.545 0.00 0.00 0.00 4.85
301 304 4.802051 GCGGCAGCCCTTCCATGA 62.802 66.667 5.63 0.00 37.42 3.07
307 310 3.346734 GCCCTTCCATGACCCCCA 61.347 66.667 0.00 0.00 0.00 4.96
309 312 1.930656 CCCTTCCATGACCCCCACT 60.931 63.158 0.00 0.00 0.00 4.00
326 329 0.874594 ACTCCCTCCATATGCCCCTA 59.125 55.000 0.00 0.00 0.00 3.53
327 330 1.203364 ACTCCCTCCATATGCCCCTAG 60.203 57.143 0.00 0.00 0.00 3.02
328 331 1.079490 CTCCCTCCATATGCCCCTAGA 59.921 57.143 0.00 0.00 0.00 2.43
332 335 1.078848 CCATATGCCCCTAGAGCGC 60.079 63.158 0.00 0.00 0.00 5.92
333 336 1.078848 CATATGCCCCTAGAGCGCC 60.079 63.158 2.29 0.00 0.00 6.53
335 338 3.802852 TATGCCCCTAGAGCGCCGA 62.803 63.158 2.29 0.00 0.00 5.54
338 341 3.291383 CCCCTAGAGCGCCGAGAG 61.291 72.222 2.29 0.00 0.00 3.20
354 357 4.094090 CGAGAGGAGGTGTAAACTGTAC 57.906 50.000 0.00 0.00 0.00 2.90
367 370 4.900635 AAACTGTACTGCTTCTGTTTGG 57.099 40.909 0.00 0.00 35.53 3.28
372 375 3.388024 TGTACTGCTTCTGTTTGGTCTCT 59.612 43.478 0.00 0.00 0.00 3.10
377 380 3.641436 TGCTTCTGTTTGGTCTCTGAGTA 59.359 43.478 4.32 0.00 0.00 2.59
390 393 2.102553 GAGTAGCGGTGGCGAGAC 59.897 66.667 0.00 0.00 46.35 3.36
393 396 2.827190 TAGCGGTGGCGAGACGAT 60.827 61.111 0.00 0.00 46.35 3.73
394 397 3.120979 TAGCGGTGGCGAGACGATG 62.121 63.158 0.00 0.00 46.35 3.84
428 431 4.809426 CGGTGTGGAATAAGGTATCTTCAC 59.191 45.833 0.00 0.00 34.59 3.18
453 456 2.307768 CTCTAGTTCCGATGGTGCCTA 58.692 52.381 0.00 0.00 0.00 3.93
455 458 2.891580 TCTAGTTCCGATGGTGCCTATC 59.108 50.000 0.00 0.00 0.00 2.08
456 459 0.759346 AGTTCCGATGGTGCCTATCC 59.241 55.000 0.00 0.00 0.00 2.59
459 468 0.832135 TCCGATGGTGCCTATCCTCC 60.832 60.000 0.00 0.00 0.00 4.30
494 503 1.694696 GATGGTGTGTCCCTAGATCCC 59.305 57.143 0.00 0.00 34.77 3.85
515 524 5.001232 CCCTTTCTCTGTGTCCGAATTTTA 58.999 41.667 0.00 0.00 0.00 1.52
519 528 7.255139 CCTTTCTCTGTGTCCGAATTTTACTTT 60.255 37.037 0.00 0.00 0.00 2.66
533 542 8.327429 CGAATTTTACTTTTGCATGTTTGTCTT 58.673 29.630 0.00 0.00 0.00 3.01
544 553 0.317020 GTTTGTCTTGGTGTCGCTGC 60.317 55.000 0.00 0.00 0.00 5.25
547 556 4.329545 TCTTGGTGTCGCTGCCCC 62.330 66.667 0.00 0.00 0.00 5.80
548 557 4.641645 CTTGGTGTCGCTGCCCCA 62.642 66.667 0.00 0.00 0.00 4.96
582 591 2.936498 CACGGATGTGTGTCTTAATCCC 59.064 50.000 0.00 0.00 41.34 3.85
589 598 3.591527 TGTGTGTCTTAATCCCCCATCTT 59.408 43.478 0.00 0.00 0.00 2.40
601 610 2.509548 CCCCCATCTTGAGTATTGACCA 59.490 50.000 0.00 0.00 0.00 4.02
607 616 6.377996 CCCATCTTGAGTATTGACCAATGAAA 59.622 38.462 5.56 0.00 32.50 2.69
612 621 7.719193 TCTTGAGTATTGACCAATGAAAGTTGA 59.281 33.333 5.56 0.00 32.50 3.18
630 639 2.677875 CCAGCCTTGGCCTTGACC 60.678 66.667 3.32 0.00 37.73 4.02
636 645 2.528127 TTGGCCTTGACCGGGAGA 60.528 61.111 6.32 0.00 0.00 3.71
663 672 5.296780 GTGAGATTTGTGTTCTTTGACTCCA 59.703 40.000 0.00 0.00 0.00 3.86
670 679 4.284490 TGTGTTCTTTGACTCCATCTAGCT 59.716 41.667 0.00 0.00 0.00 3.32
674 683 4.293494 TCTTTGACTCCATCTAGCTGGAT 58.707 43.478 15.53 6.78 44.23 3.41
702 711 2.159627 CGTTCTACAGGCACATTCCAAC 59.840 50.000 0.00 0.00 0.00 3.77
716 725 6.739565 GCACATTCCAACATTTTCCTTCTTCT 60.740 38.462 0.00 0.00 0.00 2.85
721 730 3.243359 ACATTTTCCTTCTTCTGGGCA 57.757 42.857 0.00 0.00 0.00 5.36
747 758 7.979865 GCGATTTGCTATACAGATCACTGTCC 61.980 46.154 6.15 0.00 46.54 4.02
774 785 6.461648 CGACATCTTCTGGTCTACATATTGGT 60.462 42.308 0.00 0.00 31.88 3.67
810 821 4.877323 ACTTCTGAGTTTCAACGGTTTC 57.123 40.909 0.00 0.00 29.87 2.78
815 826 1.865340 GAGTTTCAACGGTTTCGCTCT 59.135 47.619 0.00 0.00 40.63 4.09
835 846 0.966920 GTTGAGACGGAGACCCAGAA 59.033 55.000 0.00 0.00 0.00 3.02
850 862 1.610624 CCAGAAGGGCAACGAGCTTTA 60.611 52.381 0.00 0.00 44.79 1.85
858 870 1.779569 CAACGAGCTTTACTCACCGT 58.220 50.000 0.00 0.00 46.63 4.83
859 871 1.455786 CAACGAGCTTTACTCACCGTG 59.544 52.381 0.00 0.00 46.63 4.94
861 873 1.674611 CGAGCTTTACTCACCGTGCG 61.675 60.000 0.00 0.00 46.63 5.34
875 887 4.159901 TGCGCCGCTGATGGATGA 62.160 61.111 11.67 0.00 0.00 2.92
879 891 1.895707 GCCGCTGATGGATGAAGGG 60.896 63.158 0.00 0.00 0.00 3.95
881 893 1.895707 CGCTGATGGATGAAGGGGC 60.896 63.158 0.00 0.00 0.00 5.80
948 961 5.407407 TTTGCAAGGGTGTTTTTGTAAGA 57.593 34.783 0.00 0.00 32.06 2.10
971 989 9.988815 AAGAGTACATGCTACTCAATAATAAGG 57.011 33.333 24.65 0.00 44.66 2.69
1038 1058 1.870167 GCCTAAGCATCCACTCGCTAC 60.870 57.143 0.00 0.00 37.54 3.58
1039 1059 1.683917 CCTAAGCATCCACTCGCTACT 59.316 52.381 0.00 0.00 37.54 2.57
1050 1070 3.119291 CACTCGCTACTGATCATCCAAC 58.881 50.000 0.00 0.00 0.00 3.77
1060 1080 1.936547 GATCATCCAACACGAGGAAGC 59.063 52.381 0.00 0.00 38.93 3.86
1090 1116 2.604046 ACATACGAGATGGGCAAGAC 57.396 50.000 0.00 0.00 0.00 3.01
1104 1130 0.590195 CAAGACACTGTTGCTCCTGC 59.410 55.000 0.00 0.00 40.20 4.85
1112 1138 4.020617 TTGCTCCTGCCCGTCCTG 62.021 66.667 0.00 0.00 38.71 3.86
1135 1161 1.505425 GTCGCTTCCCGTAAGTGTTT 58.495 50.000 7.83 0.00 44.54 2.83
1142 1168 4.215613 GCTTCCCGTAAGTGTTTGAATTCT 59.784 41.667 7.05 0.00 37.53 2.40
1145 1171 5.556915 TCCCGTAAGTGTTTGAATTCTCAT 58.443 37.500 7.05 0.00 0.00 2.90
1148 1174 6.072728 CCCGTAAGTGTTTGAATTCTCATGAA 60.073 38.462 7.05 0.00 36.54 2.57
1269 1311 0.824595 GCATGGCCATGTGCATCCTA 60.825 55.000 39.08 0.00 43.89 2.94
1435 1478 0.319555 CGGCGACCTCACTTTCTTGA 60.320 55.000 0.00 0.00 0.00 3.02
1468 1511 2.583593 GCGGCGACATCCTCACTC 60.584 66.667 12.98 0.00 0.00 3.51
1477 1520 4.047822 CGACATCCTCACTCTCTTTATGC 58.952 47.826 0.00 0.00 0.00 3.14
1499 1549 2.193536 AAGCGTGAGTTGGGCCAAC 61.194 57.895 36.51 36.51 43.83 3.77
1524 1574 6.962182 TCCTGAATAAATGGACAAGATCTGT 58.038 36.000 0.00 0.00 42.61 3.41
1540 1590 5.808403 AGATCTGTCTAGTAGTTTTACGCG 58.192 41.667 3.53 3.53 34.88 6.01
1572 1622 6.817641 CCAAAAAGGATATGCATGTTTGCTAA 59.182 34.615 10.16 0.00 44.79 3.09
1573 1623 7.496591 CCAAAAAGGATATGCATGTTTGCTAAT 59.503 33.333 10.16 0.00 44.79 1.73
1604 1654 2.263077 ACTCGATCTTTTAGCTGCGTG 58.737 47.619 0.00 0.00 0.00 5.34
1636 1686 4.820744 ATGCAAAGGCCGGGCGAT 62.821 61.111 23.81 13.29 40.13 4.58
1638 1688 2.594592 GCAAAGGCCGGGCGATAT 60.595 61.111 23.81 7.63 0.00 1.63
1698 1795 0.821711 CTCCGGCTTCAAAACCACCA 60.822 55.000 0.00 0.00 0.00 4.17
1722 1819 4.582869 GGTTTTATCTAACCGTGTTCCCT 58.417 43.478 0.00 0.00 38.33 4.20
1727 1824 7.902920 TTTATCTAACCGTGTTCCCTATACT 57.097 36.000 0.00 0.00 0.00 2.12
1760 1857 8.712285 TTATCGCAAAGTTGTAAGCTAATACT 57.288 30.769 0.00 0.00 0.00 2.12
1773 1870 8.989131 TGTAAGCTAATACTATCAAAAGTCCCT 58.011 33.333 0.00 0.00 0.00 4.20
1795 1892 5.804473 CCTGTTTAATTGATTATGTGCGCAA 59.196 36.000 14.00 2.60 0.00 4.85
1839 1938 9.196552 GAAAAGTATTCCTGTTTTTCATCCAAG 57.803 33.333 4.26 0.00 38.65 3.61
1878 1981 1.469703 TGCGTCCTTTTCATGCAGATG 59.530 47.619 0.00 0.00 31.94 2.90
1911 2014 5.927954 ATTGTGTGGCATCAACATTTTTC 57.072 34.783 9.53 0.00 0.00 2.29
1920 2028 8.745837 GTGGCATCAACATTTTTCTAAATATCG 58.254 33.333 0.00 0.00 32.75 2.92
1966 2076 9.581289 TGGAAGTGATCAAAGAAATAAAAGGTA 57.419 29.630 0.00 0.00 0.00 3.08
2009 2120 6.192234 TCATCGTACTAGACTTTGTTCCTC 57.808 41.667 0.00 0.00 0.00 3.71
2317 2456 7.575332 TTTTGTTATATTTCCAAAGCTTCGC 57.425 32.000 0.00 0.00 30.51 4.70
2341 2480 0.107703 TGTGAGCTATGAAAGGGGCG 60.108 55.000 0.00 0.00 0.00 6.13
2368 2507 3.581101 AGCCATTGTAGGAGCTAGATGA 58.419 45.455 0.00 0.00 32.73 2.92
2369 2508 4.166539 AGCCATTGTAGGAGCTAGATGAT 58.833 43.478 0.00 0.00 32.73 2.45
2370 2509 5.336945 AGCCATTGTAGGAGCTAGATGATA 58.663 41.667 0.00 0.00 32.73 2.15
2371 2510 5.186797 AGCCATTGTAGGAGCTAGATGATAC 59.813 44.000 0.00 0.00 32.73 2.24
2372 2511 5.625656 GCCATTGTAGGAGCTAGATGATACC 60.626 48.000 0.00 0.00 0.00 2.73
2373 2512 5.105146 CCATTGTAGGAGCTAGATGATACCC 60.105 48.000 0.00 0.00 0.00 3.69
2374 2513 4.048970 TGTAGGAGCTAGATGATACCCC 57.951 50.000 0.00 0.00 0.00 4.95
2375 2514 3.401342 TGTAGGAGCTAGATGATACCCCA 59.599 47.826 0.00 0.00 0.00 4.96
2376 2515 2.896039 AGGAGCTAGATGATACCCCAC 58.104 52.381 0.00 0.00 0.00 4.61
2377 2516 2.180086 AGGAGCTAGATGATACCCCACA 59.820 50.000 0.00 0.00 0.00 4.17
2378 2517 2.300437 GGAGCTAGATGATACCCCACAC 59.700 54.545 0.00 0.00 0.00 3.82
2379 2518 2.965831 GAGCTAGATGATACCCCACACA 59.034 50.000 0.00 0.00 0.00 3.72
2380 2519 3.580458 GAGCTAGATGATACCCCACACAT 59.420 47.826 0.00 0.00 0.00 3.21
2381 2520 3.976654 AGCTAGATGATACCCCACACATT 59.023 43.478 0.00 0.00 0.00 2.71
2382 2521 4.067896 GCTAGATGATACCCCACACATTG 58.932 47.826 0.00 0.00 0.00 2.82
2402 2541 3.257393 TGTTGTGTGGACATTTTGCAAC 58.743 40.909 0.00 0.00 36.33 4.17
2421 2560 5.752955 TGCAACATATTTCGATGAGATTCGA 59.247 36.000 0.00 0.00 45.75 3.71
2430 2569 8.593492 ATTTCGATGAGATTCGATGTATGAAA 57.407 30.769 0.00 0.00 46.55 2.69
2483 2622 9.774742 GAGCTAAAAATCAAAATACGTCTGATT 57.225 29.630 0.00 0.00 40.62 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.848652 TGCTCGGGCTAGAACTACTT 58.151 50.000 9.62 0.00 39.59 2.24
13 14 2.167861 CGCTTGCTCGGGCTAGAAC 61.168 63.158 23.24 4.59 42.34 3.01
28 29 0.961019 ATTCAACAACATGTGCCGCT 59.039 45.000 0.00 0.00 0.00 5.52
37 38 8.132362 GTGATTAAGTAACACCATTCAACAACA 58.868 33.333 0.00 0.00 0.00 3.33
38 39 8.502161 GTGATTAAGTAACACCATTCAACAAC 57.498 34.615 0.00 0.00 0.00 3.32
153 154 6.159928 TGGTCCTAGTGAAGTAGAGGATAAGA 59.840 42.308 0.00 0.00 40.19 2.10
154 155 6.366340 TGGTCCTAGTGAAGTAGAGGATAAG 58.634 44.000 0.00 0.00 40.19 1.73
228 231 9.994432 CTTAGCTTAAGTGGTCTCATTAATTTG 57.006 33.333 4.02 0.00 0.00 2.32
229 232 9.959721 TCTTAGCTTAAGTGGTCTCATTAATTT 57.040 29.630 4.02 0.00 37.10 1.82
236 239 5.784177 CACTTCTTAGCTTAAGTGGTCTCA 58.216 41.667 20.38 0.00 45.68 3.27
268 271 3.541713 GCCTGCCTAGGTCGGGAG 61.542 72.222 26.38 7.60 46.41 4.30
273 276 4.537433 CTGCCGCCTGCCTAGGTC 62.537 72.222 11.31 3.32 46.41 3.85
287 290 2.440980 GGGTCATGGAAGGGCTGC 60.441 66.667 0.00 0.00 0.00 5.25
290 293 3.346734 TGGGGGTCATGGAAGGGC 61.347 66.667 0.00 0.00 0.00 5.19
294 297 1.928567 GGGAGTGGGGGTCATGGAA 60.929 63.158 0.00 0.00 0.00 3.53
298 301 2.042930 GGAGGGAGTGGGGGTCAT 59.957 66.667 0.00 0.00 0.00 3.06
299 302 1.532894 TATGGAGGGAGTGGGGGTCA 61.533 60.000 0.00 0.00 0.00 4.02
300 303 0.104409 ATATGGAGGGAGTGGGGGTC 60.104 60.000 0.00 0.00 0.00 4.46
301 304 0.401979 CATATGGAGGGAGTGGGGGT 60.402 60.000 0.00 0.00 0.00 4.95
307 310 0.874594 TAGGGGCATATGGAGGGAGT 59.125 55.000 4.56 0.00 0.00 3.85
309 312 1.079490 CTCTAGGGGCATATGGAGGGA 59.921 57.143 4.56 0.00 0.00 4.20
326 329 4.434354 ACCTCCTCTCGGCGCTCT 62.434 66.667 7.64 0.00 0.00 4.09
327 330 4.200283 CACCTCCTCTCGGCGCTC 62.200 72.222 7.64 0.00 0.00 5.03
328 331 3.640257 TACACCTCCTCTCGGCGCT 62.640 63.158 7.64 0.00 0.00 5.92
332 335 1.893801 ACAGTTTACACCTCCTCTCGG 59.106 52.381 0.00 0.00 0.00 4.63
333 336 3.757493 AGTACAGTTTACACCTCCTCTCG 59.243 47.826 0.00 0.00 0.00 4.04
335 338 3.258622 GCAGTACAGTTTACACCTCCTCT 59.741 47.826 0.00 0.00 0.00 3.69
338 341 3.679824 AGCAGTACAGTTTACACCTCC 57.320 47.619 0.00 0.00 0.00 4.30
345 348 5.433526 ACCAAACAGAAGCAGTACAGTTTA 58.566 37.500 0.00 0.00 0.00 2.01
347 350 3.877508 GACCAAACAGAAGCAGTACAGTT 59.122 43.478 0.00 0.00 0.00 3.16
349 352 3.733337 AGACCAAACAGAAGCAGTACAG 58.267 45.455 0.00 0.00 0.00 2.74
350 353 3.388024 AGAGACCAAACAGAAGCAGTACA 59.612 43.478 0.00 0.00 0.00 2.90
351 354 3.743396 CAGAGACCAAACAGAAGCAGTAC 59.257 47.826 0.00 0.00 0.00 2.73
352 355 3.641436 TCAGAGACCAAACAGAAGCAGTA 59.359 43.478 0.00 0.00 0.00 2.74
354 357 3.065655 CTCAGAGACCAAACAGAAGCAG 58.934 50.000 0.00 0.00 0.00 4.24
367 370 1.139947 GCCACCGCTACTCAGAGAC 59.860 63.158 3.79 0.00 0.00 3.36
372 375 2.360726 TCTCGCCACCGCTACTCA 60.361 61.111 0.00 0.00 0.00 3.41
377 380 4.498520 CATCGTCTCGCCACCGCT 62.499 66.667 0.00 0.00 0.00 5.52
428 431 1.482593 ACCATCGGAACTAGAGCAAGG 59.517 52.381 0.00 0.00 0.00 3.61
431 434 0.175760 GCACCATCGGAACTAGAGCA 59.824 55.000 0.00 0.00 0.00 4.26
437 440 0.759346 GGATAGGCACCATCGGAACT 59.241 55.000 0.00 0.00 0.00 3.01
438 441 0.759346 AGGATAGGCACCATCGGAAC 59.241 55.000 0.00 0.00 0.00 3.62
456 459 1.045350 TCCTCAGAATGCCTCCGGAG 61.045 60.000 25.36 25.36 34.76 4.63
459 468 0.250209 CCATCCTCAGAATGCCTCCG 60.250 60.000 0.00 0.00 34.76 4.63
469 478 1.759445 CTAGGGACACACCATCCTCAG 59.241 57.143 0.00 0.00 41.20 3.35
470 479 1.361197 TCTAGGGACACACCATCCTCA 59.639 52.381 0.00 0.00 41.20 3.86
494 503 6.787085 AGTAAAATTCGGACACAGAGAAAG 57.213 37.500 0.00 0.00 0.00 2.62
515 524 4.183101 CACCAAGACAAACATGCAAAAGT 58.817 39.130 0.00 0.00 0.00 2.66
519 528 2.223456 CGACACCAAGACAAACATGCAA 60.223 45.455 0.00 0.00 0.00 4.08
547 556 3.403057 CGTGTTGTCCGCTCCGTG 61.403 66.667 0.00 0.00 0.00 4.94
548 557 4.657824 CCGTGTTGTCCGCTCCGT 62.658 66.667 0.00 0.00 0.00 4.69
550 559 2.100631 CATCCGTGTTGTCCGCTCC 61.101 63.158 0.00 0.00 0.00 4.70
571 580 4.111577 ACTCAAGATGGGGGATTAAGACA 58.888 43.478 0.00 0.00 0.00 3.41
577 586 4.141158 GGTCAATACTCAAGATGGGGGATT 60.141 45.833 0.00 0.00 0.00 3.01
578 587 3.395941 GGTCAATACTCAAGATGGGGGAT 59.604 47.826 0.00 0.00 0.00 3.85
582 591 5.439721 TCATTGGTCAATACTCAAGATGGG 58.560 41.667 0.00 0.00 0.00 4.00
589 598 6.206634 GGTCAACTTTCATTGGTCAATACTCA 59.793 38.462 0.00 0.00 0.00 3.41
601 610 2.629617 CCAAGGCTGGTCAACTTTCATT 59.370 45.455 0.00 0.00 38.00 2.57
612 621 2.116125 GTCAAGGCCAAGGCTGGT 59.884 61.111 5.01 0.00 45.53 4.00
626 635 1.866015 ATCTCACAATCTCCCGGTCA 58.134 50.000 0.00 0.00 0.00 4.02
630 639 3.338249 ACACAAATCTCACAATCTCCCG 58.662 45.455 0.00 0.00 0.00 5.14
636 645 7.338800 AGTCAAAGAACACAAATCTCACAAT 57.661 32.000 0.00 0.00 0.00 2.71
663 672 1.198713 CGCCCCATATCCAGCTAGAT 58.801 55.000 0.00 0.00 0.00 1.98
670 679 1.691976 CTGTAGAACGCCCCATATCCA 59.308 52.381 0.00 0.00 0.00 3.41
674 683 0.978667 TGCCTGTAGAACGCCCCATA 60.979 55.000 0.00 0.00 0.00 2.74
702 711 2.094338 GCTGCCCAGAAGAAGGAAAATG 60.094 50.000 0.00 0.00 0.00 2.32
721 730 4.987285 CAGTGATCTGTATAGCAAATCGCT 59.013 41.667 0.00 0.00 44.25 4.93
741 752 1.821753 CCAGAAGATGTCGAGGACAGT 59.178 52.381 4.65 0.00 46.04 3.55
747 758 4.909696 ATGTAGACCAGAAGATGTCGAG 57.090 45.455 0.00 0.00 36.61 4.04
751 762 6.461648 CGACCAATATGTAGACCAGAAGATGT 60.462 42.308 0.00 0.00 0.00 3.06
774 785 5.241064 ACTCAGAAGTTTGTAGAACTAGCGA 59.759 40.000 0.00 0.00 28.74 4.93
805 816 0.784778 CGTCTCAACAGAGCGAAACC 59.215 55.000 0.00 0.00 33.68 3.27
810 821 0.455295 GTCTCCGTCTCAACAGAGCG 60.455 60.000 0.00 0.00 31.15 5.03
815 826 0.178973 TCTGGGTCTCCGTCTCAACA 60.179 55.000 0.00 0.00 35.24 3.33
835 846 3.534721 GAGTAAAGCTCGTTGCCCT 57.465 52.632 0.00 0.00 44.23 5.19
843 855 1.956620 GCGCACGGTGAGTAAAGCTC 61.957 60.000 13.29 0.00 44.36 4.09
858 870 3.678951 TTCATCCATCAGCGGCGCA 62.679 57.895 35.02 15.48 0.00 6.09
859 871 2.890109 CTTCATCCATCAGCGGCGC 61.890 63.158 26.86 26.86 0.00 6.53
861 873 1.895707 CCCTTCATCCATCAGCGGC 60.896 63.158 0.00 0.00 0.00 6.53
866 878 3.969466 TTATTGCCCCTTCATCCATCA 57.031 42.857 0.00 0.00 0.00 3.07
875 887 2.024464 TGCCACAGTATTATTGCCCCTT 60.024 45.455 0.00 0.00 0.00 3.95
879 891 1.681264 GGGTGCCACAGTATTATTGCC 59.319 52.381 0.00 0.00 0.00 4.52
881 893 3.011566 TGGGGTGCCACAGTATTATTG 57.988 47.619 0.00 0.00 0.00 1.90
923 935 6.370166 TCTTACAAAAACACCCTTGCAAAAAG 59.630 34.615 0.00 0.00 0.00 2.27
948 961 9.935241 CATCCTTATTATTGAGTAGCATGTACT 57.065 33.333 7.43 7.43 0.00 2.73
971 989 2.893489 GCATGGGGAAAGGGATAACATC 59.107 50.000 0.00 0.00 0.00 3.06
984 1002 0.870313 ATAGGAGGAGAGCATGGGGA 59.130 55.000 0.00 0.00 0.00 4.81
1038 1058 2.967599 TCCTCGTGTTGGATGATCAG 57.032 50.000 0.09 0.00 0.00 2.90
1039 1059 2.677902 GCTTCCTCGTGTTGGATGATCA 60.678 50.000 0.00 0.00 33.09 2.92
1050 1070 0.460987 GTCCTGGATGCTTCCTCGTG 60.461 60.000 18.67 7.20 43.07 4.35
1060 1080 4.082517 CCATCTCGTATGTAGTCCTGGATG 60.083 50.000 0.00 0.00 0.00 3.51
1069 1089 3.068165 TGTCTTGCCCATCTCGTATGTAG 59.932 47.826 1.02 0.00 0.00 2.74
1072 1092 2.159043 AGTGTCTTGCCCATCTCGTATG 60.159 50.000 0.00 0.00 0.00 2.39
1090 1116 3.052082 CGGGCAGGAGCAACAGTG 61.052 66.667 0.00 0.00 44.61 3.66
1098 1124 4.154347 GAGCAGGACGGGCAGGAG 62.154 72.222 0.00 0.00 0.00 3.69
1135 1161 6.293790 GCATCCGATTGATTCATGAGAATTCA 60.294 38.462 8.44 0.00 44.30 2.57
1142 1168 6.174760 TCATATGCATCCGATTGATTCATGA 58.825 36.000 0.19 0.00 37.78 3.07
1145 1171 7.457024 AATTCATATGCATCCGATTGATTCA 57.543 32.000 0.19 0.00 31.06 2.57
1148 1174 6.588756 GCAAAATTCATATGCATCCGATTGAT 59.411 34.615 0.19 0.00 39.81 2.57
1435 1478 0.389391 CCGCATATTCCTCAGTCGGT 59.611 55.000 0.00 0.00 0.00 4.69
1468 1511 3.620374 ACTCACGCTTGATGCATAAAGAG 59.380 43.478 25.59 23.79 43.06 2.85
1477 1520 1.503542 GCCCAACTCACGCTTGATG 59.496 57.895 0.00 0.00 0.00 3.07
1499 1549 7.052873 ACAGATCTTGTCCATTTATTCAGGAG 58.947 38.462 0.00 0.00 33.87 3.69
1524 1574 6.127925 TGGAAAGATCGCGTAAAACTACTAGA 60.128 38.462 5.77 0.00 0.00 2.43
1572 1622 3.482156 AGATCGAGTTGGCATAGCAAT 57.518 42.857 0.00 0.00 0.00 3.56
1573 1623 2.988010 AGATCGAGTTGGCATAGCAA 57.012 45.000 0.00 0.00 0.00 3.91
1574 1624 2.988010 AAGATCGAGTTGGCATAGCA 57.012 45.000 0.00 0.00 0.00 3.49
1575 1625 4.319118 GCTAAAAGATCGAGTTGGCATAGC 60.319 45.833 8.72 0.00 0.00 2.97
1576 1626 5.050499 CAGCTAAAAGATCGAGTTGGCATAG 60.050 44.000 13.80 1.00 31.75 2.23
1577 1627 4.811024 CAGCTAAAAGATCGAGTTGGCATA 59.189 41.667 13.80 0.00 31.75 3.14
1578 1628 3.624861 CAGCTAAAAGATCGAGTTGGCAT 59.375 43.478 13.80 1.36 31.75 4.40
1634 1684 4.537135 TCTTAGATGGCGGGTGAATATC 57.463 45.455 0.00 0.00 0.00 1.63
1635 1685 4.974645 TTCTTAGATGGCGGGTGAATAT 57.025 40.909 0.00 0.00 0.00 1.28
1636 1686 4.764050 TTTCTTAGATGGCGGGTGAATA 57.236 40.909 0.00 0.00 0.00 1.75
1638 1688 3.078837 GTTTTCTTAGATGGCGGGTGAA 58.921 45.455 0.00 0.00 0.00 3.18
1646 1730 7.396540 AGTTGGCATAAGTTTTCTTAGATGG 57.603 36.000 0.00 0.00 44.27 3.51
1647 1731 7.970614 GGAAGTTGGCATAAGTTTTCTTAGATG 59.029 37.037 0.00 0.00 44.27 2.90
1713 1810 5.320549 AGTGTGTAAGTATAGGGAACACG 57.679 43.478 0.00 0.00 42.58 4.49
1722 1819 8.865978 CAACTTTGCGATAAGTGTGTAAGTATA 58.134 33.333 3.74 0.00 38.33 1.47
1727 1824 5.994887 ACAACTTTGCGATAAGTGTGTAA 57.005 34.783 3.74 0.00 38.33 2.41
1773 1870 6.237781 GCATTGCGCACATAATCAATTAAACA 60.238 34.615 11.12 0.00 41.79 2.83
1795 1892 4.734398 TTTCCATTAAAAGGATGCGCAT 57.266 36.364 25.66 25.66 34.56 4.73
1811 1908 7.288852 TGGATGAAAAACAGGAATACTTTTCCA 59.711 33.333 7.10 0.00 41.00 3.53
1839 1938 3.545633 GCACGACATCAAACAAGAACTC 58.454 45.455 0.00 0.00 0.00 3.01
1878 1981 4.764679 TGCCACACAATTTGTAGATGTC 57.235 40.909 0.86 0.00 35.67 3.06
1925 2033 9.513906 TGATCACTTCCAACTCAACATAAATTA 57.486 29.630 0.00 0.00 0.00 1.40
1980 2090 9.530129 GAACAAAGTCTAGTACGATGAAAATTG 57.470 33.333 0.00 0.00 0.00 2.32
1981 2091 8.718734 GGAACAAAGTCTAGTACGATGAAAATT 58.281 33.333 0.00 0.00 0.00 1.82
1982 2093 8.095169 AGGAACAAAGTCTAGTACGATGAAAAT 58.905 33.333 0.00 0.00 0.00 1.82
2341 2480 2.436173 AGCTCCTACAATGGCTAGAACC 59.564 50.000 0.00 0.00 32.94 3.62
2364 2503 4.016444 ACAACAATGTGTGGGGTATCATC 58.984 43.478 0.00 0.00 38.69 2.92
2365 2504 4.046286 ACAACAATGTGTGGGGTATCAT 57.954 40.909 0.00 0.00 38.69 2.45
2366 2505 3.517296 ACAACAATGTGTGGGGTATCA 57.483 42.857 0.00 0.00 38.69 2.15
2377 2516 3.870419 GCAAAATGTCCACACAACAATGT 59.130 39.130 0.00 0.00 41.61 2.71
2378 2517 3.869832 TGCAAAATGTCCACACAACAATG 59.130 39.130 0.00 0.00 35.64 2.82
2379 2518 4.134379 TGCAAAATGTCCACACAACAAT 57.866 36.364 0.00 0.00 35.64 2.71
2380 2519 3.599730 TGCAAAATGTCCACACAACAA 57.400 38.095 0.00 0.00 35.64 2.83
2381 2520 3.257393 GTTGCAAAATGTCCACACAACA 58.743 40.909 0.00 0.00 35.64 3.33
2382 2521 3.257393 TGTTGCAAAATGTCCACACAAC 58.743 40.909 0.00 0.00 35.64 3.32
2388 2527 6.018589 TCGAAATATGTTGCAAAATGTCCA 57.981 33.333 12.62 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.