Multiple sequence alignment - TraesCS4A01G078200

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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 TraesCS4A01G078200 chr4A 100.000 2524 0 0 1 2524 78181448 78178925 0.000000e+00 4662
1 TraesCS4A01G078200 chr4D 93.003 786 35 6 1 781 396672214 396671444 0.000000e+00 1129
2 TraesCS4A01G078200 chr4D 88.251 732 60 11 863 1573 396671278 396670552 0.000000e+00 852
3 TraesCS4A01G078200 chr4D 80.441 997 139 30 1573 2524 396670517 396669532 0.000000e+00 710
4 TraesCS4A01G078200 chr4B 89.524 840 43 14 3 821 488679828 488679013 0.000000e+00 1022
5 TraesCS4A01G078200 chr4B 85.275 944 114 14 1601 2524 488618243 488617305 0.000000e+00 950
6 TraesCS4A01G078200 chr4B 89.969 319 28 2 1231 1546 488646281 488645964 2.340000e-110 409
7 TraesCS4A01G078200 chr4B 87.845 181 14 5 863 1039 488678135 488677959 3.290000e-49 206


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 TraesCS4A01G078200 chr4A 78178925 78181448 2523 True 4662 4662 100.000000 1 2524 1 chr4A.!!$R1 2523
1 TraesCS4A01G078200 chr4D 396669532 396672214 2682 True 897 1129 87.231667 1 2524 3 chr4D.!!$R1 2523
2 TraesCS4A01G078200 chr4B 488617305 488618243 938 True 950 950 85.275000 1601 2524 1 chr4B.!!$R1 923
3 TraesCS4A01G078200 chr4B 488677959 488679828 1869 True 614 1022 88.684500 3 1039 2 chr4B.!!$R3 1036

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
697 715 0.179137 TGCTCTGACTATGAACGGCG 60.179 55.0 4.8 4.8 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 3030 0.110486 GTTGTTTGGGAGGAGCAGGA 59.89 55.0 0.0 0.0 0.0 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
333 337 2.171237 CCAGAAGCATGATCCACAGGTA 59.829 50.000 0.00 0.00 32.48 3.08
337 341 1.134699 AGCATGATCCACAGGTACGTG 60.135 52.381 13.84 13.84 36.61 4.49
352 358 2.961522 ACGTGACGCCACAAATTTAG 57.038 45.000 4.25 0.00 43.34 1.85
355 361 3.223157 CGTGACGCCACAAATTTAGTTC 58.777 45.455 1.96 0.00 43.34 3.01
356 362 3.561503 GTGACGCCACAAATTTAGTTCC 58.438 45.455 0.00 0.00 42.72 3.62
357 363 2.224549 TGACGCCACAAATTTAGTTCCG 59.775 45.455 0.00 0.50 0.00 4.30
359 365 2.619646 ACGCCACAAATTTAGTTCCGTT 59.380 40.909 0.00 0.00 0.00 4.44
360 366 3.067040 ACGCCACAAATTTAGTTCCGTTT 59.933 39.130 0.00 0.00 0.00 3.60
361 367 3.666797 CGCCACAAATTTAGTTCCGTTTC 59.333 43.478 0.00 0.00 0.00 2.78
362 368 4.612943 GCCACAAATTTAGTTCCGTTTCA 58.387 39.130 0.00 0.00 0.00 2.69
365 371 5.567534 CCACAAATTTAGTTCCGTTTCATCG 59.432 40.000 0.00 0.00 0.00 3.84
387 393 4.202080 CGTCCTGGATTGATTGATTGCATT 60.202 41.667 0.00 0.00 0.00 3.56
389 395 3.807622 CCTGGATTGATTGATTGCATTGC 59.192 43.478 0.46 0.46 0.00 3.56
401 407 2.143008 TGCATTGCTGTTGCTGAAAG 57.857 45.000 10.49 0.00 40.77 2.62
402 408 1.682323 TGCATTGCTGTTGCTGAAAGA 59.318 42.857 10.49 0.00 40.77 2.52
403 409 2.056577 GCATTGCTGTTGCTGAAAGAC 58.943 47.619 0.16 0.00 40.48 3.01
404 410 2.288030 GCATTGCTGTTGCTGAAAGACT 60.288 45.455 0.16 0.00 40.48 3.24
405 411 3.305964 CATTGCTGTTGCTGAAAGACTG 58.694 45.455 0.00 0.00 40.48 3.51
406 412 2.330440 TGCTGTTGCTGAAAGACTGA 57.670 45.000 0.00 0.00 40.48 3.41
407 413 2.642427 TGCTGTTGCTGAAAGACTGAA 58.358 42.857 0.00 0.00 40.48 3.02
408 414 3.016031 TGCTGTTGCTGAAAGACTGAAA 58.984 40.909 0.00 0.00 40.48 2.69
501 507 2.745821 TCGACTACGACAGCTTGTACAT 59.254 45.455 0.00 0.00 43.81 2.29
503 509 3.179830 GACTACGACAGCTTGTACATGG 58.820 50.000 10.47 1.92 0.00 3.66
514 532 3.238497 TACATGGGATCGGCGGGG 61.238 66.667 7.21 0.00 0.00 5.73
573 591 3.991051 CGTCAGAGTGGGCGTGGT 61.991 66.667 0.00 0.00 0.00 4.16
688 706 1.754621 CTCCGGCCTGCTCTGACTA 60.755 63.158 0.00 0.00 0.00 2.59
696 714 1.565305 CTGCTCTGACTATGAACGGC 58.435 55.000 0.00 0.00 0.00 5.68
697 715 0.179137 TGCTCTGACTATGAACGGCG 60.179 55.000 4.80 4.80 0.00 6.46
710 728 2.591429 CGGCGGCATTCCAGCATA 60.591 61.111 10.53 0.00 34.88 3.14
715 733 0.514255 CGGCATTCCAGCATATCACG 59.486 55.000 0.00 0.00 35.83 4.35
722 740 0.602106 CCAGCATATCACGGAGCCAG 60.602 60.000 0.00 0.00 0.00 4.85
723 741 1.070445 AGCATATCACGGAGCCAGC 59.930 57.895 0.00 0.00 0.00 4.85
724 742 1.070445 GCATATCACGGAGCCAGCT 59.930 57.895 0.00 0.00 0.00 4.24
763 781 4.700365 CTCCAGACGTGACGCGCA 62.700 66.667 5.73 1.71 46.11 6.09
766 785 3.842126 CAGACGTGACGCGCATGG 61.842 66.667 21.11 12.64 46.11 3.66
767 786 4.050934 AGACGTGACGCGCATGGA 62.051 61.111 21.11 0.00 46.11 3.41
768 787 3.545481 GACGTGACGCGCATGGAG 61.545 66.667 21.11 0.00 46.11 3.86
769 788 3.964221 GACGTGACGCGCATGGAGA 62.964 63.158 21.11 0.00 46.11 3.71
771 790 2.167219 CGTGACGCGCATGGAGATT 61.167 57.895 5.73 0.00 0.00 2.40
772 791 0.869880 CGTGACGCGCATGGAGATTA 60.870 55.000 5.73 0.00 0.00 1.75
773 792 0.577269 GTGACGCGCATGGAGATTAC 59.423 55.000 5.73 0.00 0.00 1.89
774 793 0.459899 TGACGCGCATGGAGATTACT 59.540 50.000 5.73 0.00 0.00 2.24
775 794 1.132588 GACGCGCATGGAGATTACTC 58.867 55.000 5.73 0.00 41.94 2.59
776 795 0.747255 ACGCGCATGGAGATTACTCT 59.253 50.000 5.73 0.00 42.28 3.24
777 796 1.135046 CGCGCATGGAGATTACTCTG 58.865 55.000 8.75 0.00 42.28 3.35
778 797 1.536922 CGCGCATGGAGATTACTCTGT 60.537 52.381 8.75 0.00 42.28 3.41
779 798 2.555199 GCGCATGGAGATTACTCTGTT 58.445 47.619 0.30 0.00 42.28 3.16
780 799 2.286294 GCGCATGGAGATTACTCTGTTG 59.714 50.000 0.30 0.00 42.28 3.33
795 814 1.534163 CTGTTGTCTGCTGGATGTGTG 59.466 52.381 0.00 0.00 0.00 3.82
800 819 2.069273 GTCTGCTGGATGTGTGTGTAC 58.931 52.381 0.00 0.00 0.00 2.90
817 836 2.910319 TGTACACCCTTCTGCCTGTTAT 59.090 45.455 0.00 0.00 0.00 1.89
818 837 4.081309 GTGTACACCCTTCTGCCTGTTATA 60.081 45.833 15.42 0.00 0.00 0.98
819 838 4.719773 TGTACACCCTTCTGCCTGTTATAT 59.280 41.667 0.00 0.00 0.00 0.86
820 839 5.900699 TGTACACCCTTCTGCCTGTTATATA 59.099 40.000 0.00 0.00 0.00 0.86
821 840 5.552870 ACACCCTTCTGCCTGTTATATAG 57.447 43.478 0.00 0.00 0.00 1.31
822 841 5.216622 ACACCCTTCTGCCTGTTATATAGA 58.783 41.667 0.00 0.00 0.00 1.98
823 842 5.665812 ACACCCTTCTGCCTGTTATATAGAA 59.334 40.000 0.00 0.00 0.00 2.10
825 844 5.071923 ACCCTTCTGCCTGTTATATAGAACC 59.928 44.000 7.73 0.00 0.00 3.62
828 847 6.183361 CCTTCTGCCTGTTATATAGAACCACT 60.183 42.308 7.73 0.00 0.00 4.00
829 848 7.015292 CCTTCTGCCTGTTATATAGAACCACTA 59.985 40.741 7.73 0.00 35.42 2.74
830 849 7.907841 TCTGCCTGTTATATAGAACCACTAA 57.092 36.000 7.73 0.00 34.56 2.24
831 850 8.492415 TCTGCCTGTTATATAGAACCACTAAT 57.508 34.615 7.73 0.00 34.56 1.73
832 851 9.596308 TCTGCCTGTTATATAGAACCACTAATA 57.404 33.333 7.73 0.00 34.56 0.98
855 1718 3.525537 TGCTACTAAGAATGCTGCAGTC 58.474 45.455 21.29 21.29 0.00 3.51
856 1719 2.537625 GCTACTAAGAATGCTGCAGTCG 59.462 50.000 22.31 12.24 33.45 4.18
857 1720 2.751166 ACTAAGAATGCTGCAGTCGT 57.249 45.000 22.31 21.52 33.45 4.34
858 1721 2.341257 ACTAAGAATGCTGCAGTCGTG 58.659 47.619 24.48 19.01 33.45 4.35
951 1814 3.241530 TCCTCAGTTGCCACGCCT 61.242 61.111 0.00 0.00 0.00 5.52
969 1832 4.916870 CGCCTGCGTATACTGCTATATAA 58.083 43.478 16.71 0.44 34.35 0.98
977 1844 7.065443 TGCGTATACTGCTATATAACACGAGAT 59.935 37.037 16.71 0.00 0.00 2.75
1018 1885 4.993584 AGAACAGATGCAATATCGTCCATC 59.006 41.667 0.00 0.00 35.49 3.51
1029 1896 2.522638 CGTCCATCGTTTAGCCCGC 61.523 63.158 0.00 0.00 34.52 6.13
1039 1906 2.017049 GTTTAGCCCGCTTCATCATGT 58.983 47.619 0.00 0.00 0.00 3.21
1040 1907 2.418368 TTAGCCCGCTTCATCATGTT 57.582 45.000 0.00 0.00 0.00 2.71
1113 1992 2.435234 TCGCCGTATGTGTTGGCC 60.435 61.111 0.00 0.00 46.12 5.36
1118 1997 2.435234 GTATGTGTTGGCCGCCGA 60.435 61.111 4.58 0.00 0.00 5.54
1151 2030 1.825281 GCCGGAGAGATGGAGATGGG 61.825 65.000 5.05 0.00 0.00 4.00
1224 2103 2.576317 GACGACAGCGGCGACTAC 60.576 66.667 12.98 4.56 43.17 2.73
1269 2148 0.809241 CTCAAGCGGTCAGGATGCTC 60.809 60.000 0.00 0.00 38.17 4.26
1282 2161 0.605589 GATGCTCTGGGGGATACTCG 59.394 60.000 0.00 0.00 38.88 4.18
1293 2172 1.585521 GATACTCGCCCGTGTCGTG 60.586 63.158 0.00 0.00 0.00 4.35
1307 2186 3.706373 CGTGTGGAGGTGGAGGGG 61.706 72.222 0.00 0.00 0.00 4.79
1311 2190 4.649705 TGGAGGTGGAGGGGCGAA 62.650 66.667 0.00 0.00 0.00 4.70
1313 2192 3.787001 GAGGTGGAGGGGCGAAGG 61.787 72.222 0.00 0.00 0.00 3.46
1375 2254 3.458163 GGAGGCGGTCGTCATGGA 61.458 66.667 0.00 0.00 0.00 3.41
1386 2265 4.414956 TCATGGAGGCCGGACCCT 62.415 66.667 1.76 0.35 40.58 4.34
1429 2308 2.201436 CTGGTGCTAGCTGACGTCGT 62.201 60.000 17.23 0.00 0.00 4.34
1433 2312 1.124477 GTGCTAGCTGACGTCGTTTTC 59.876 52.381 17.23 0.00 0.00 2.29
1440 2319 3.001330 AGCTGACGTCGTTTTCTTCTTTG 59.999 43.478 11.62 0.00 0.00 2.77
1442 2321 4.026310 GCTGACGTCGTTTTCTTCTTTGTA 60.026 41.667 11.62 0.00 0.00 2.41
1449 2328 6.074005 GTCGTTTTCTTCTTTGTAGCTGATG 58.926 40.000 0.00 0.00 0.00 3.07
1463 2342 4.414337 AGCTGATGAAGGTATTGGAGAC 57.586 45.455 0.00 0.00 33.90 3.36
1468 2347 5.430886 TGATGAAGGTATTGGAGACACATG 58.569 41.667 0.00 0.00 42.67 3.21
1469 2348 4.220693 TGAAGGTATTGGAGACACATGG 57.779 45.455 0.00 0.00 42.67 3.66
1478 2357 1.133976 GGAGACACATGGGATTCAGGG 60.134 57.143 0.00 0.00 0.00 4.45
1504 2383 2.425312 TGTGTGCGTGGATTTTGAAGTT 59.575 40.909 0.00 0.00 0.00 2.66
1583 2500 3.054434 CAGTTGTTCTATGGTGGGATCCA 60.054 47.826 15.23 0.00 42.01 3.41
1590 2507 2.517919 GGTGGGATCCAGCCATCC 59.482 66.667 15.23 3.62 45.22 3.51
1591 2508 2.386100 GGTGGGATCCAGCCATCCA 61.386 63.158 15.23 0.00 45.22 3.41
1592 2509 1.150081 GTGGGATCCAGCCATCCAG 59.850 63.158 15.23 0.00 44.00 3.86
1593 2510 2.080536 TGGGATCCAGCCATCCAGG 61.081 63.158 15.23 0.00 44.00 4.45
1602 2519 3.177600 CCATCCAGGCGTTGTTCG 58.822 61.111 0.00 0.00 43.12 3.95
1603 2520 2.398554 CCATCCAGGCGTTGTTCGG 61.399 63.158 0.00 0.00 40.26 4.30
1604 2521 1.375396 CATCCAGGCGTTGTTCGGA 60.375 57.895 0.00 0.00 40.26 4.55
1629 2546 0.108329 ATAAGACACTCAACCGGCCG 60.108 55.000 21.04 21.04 0.00 6.13
1631 2548 4.681978 GACACTCAACCGGCCGCT 62.682 66.667 22.85 2.01 0.00 5.52
1648 2565 0.317854 GCTCCAAACGCACTCCAAAC 60.318 55.000 0.00 0.00 0.00 2.93
1704 2621 2.284625 TGGGATGGACCAGACGCT 60.285 61.111 15.64 0.00 41.20 5.07
1709 2626 3.694649 GGATGGACCAGACGCTTTCGT 62.695 57.143 0.00 0.00 44.73 3.85
1726 2643 3.051479 TACGCTCTGCCACGTCGA 61.051 61.111 0.00 0.00 42.46 4.20
1743 2671 0.521450 CGACTGTCTCACGATGTCCG 60.521 60.000 6.21 0.00 45.44 4.79
1747 2675 1.213013 GTCTCACGATGTCCGCACT 59.787 57.895 0.00 0.00 43.32 4.40
1756 2685 4.436998 GTCCGCACTCCTGTCCCG 62.437 72.222 0.00 0.00 0.00 5.14
1769 2698 0.179040 TGTCCCGACAAACACTTCCC 60.179 55.000 0.00 0.00 38.56 3.97
1771 2700 1.057851 TCCCGACAAACACTTCCCCT 61.058 55.000 0.00 0.00 0.00 4.79
1777 2707 0.187361 CAAACACTTCCCCTTCCCCA 59.813 55.000 0.00 0.00 0.00 4.96
1788 2718 0.040204 CCTTCCCCAGATGGCAAACT 59.960 55.000 0.00 0.00 31.13 2.66
1797 2727 4.326826 CCAGATGGCAAACTCTAGTCAAA 58.673 43.478 0.00 0.00 0.00 2.69
1803 2733 3.498777 GGCAAACTCTAGTCAAACTCACC 59.501 47.826 0.00 0.00 0.00 4.02
1817 2747 1.229209 TCACCCTCTCGCCCTCTTT 60.229 57.895 0.00 0.00 0.00 2.52
1836 2778 2.689034 CTCGCCTCCCCTTCCCTT 60.689 66.667 0.00 0.00 0.00 3.95
1844 2786 2.361567 CCCCTTCCCTTTGGCATGC 61.362 63.158 9.90 9.90 0.00 4.06
1918 2860 2.038295 CCAGAAGGACTTGAGCTTGTCT 59.962 50.000 12.80 0.00 36.89 3.41
1962 2904 2.203394 CCCCATTGCCCTCCATCG 60.203 66.667 0.00 0.00 0.00 3.84
1967 2909 2.735772 ATTGCCCTCCATCGCTCGT 61.736 57.895 0.00 0.00 0.00 4.18
1968 2910 2.650813 ATTGCCCTCCATCGCTCGTC 62.651 60.000 0.00 0.00 0.00 4.20
1982 2924 2.225791 CTCGTCGATGGACAAGGGCA 62.226 60.000 8.67 0.00 43.61 5.36
2007 2949 2.100631 CCACCTCGACGATGTTGCC 61.101 63.158 2.80 0.00 0.00 4.52
2009 2951 1.374252 ACCTCGACGATGTTGCCAC 60.374 57.895 0.00 0.00 0.00 5.01
2041 2983 2.527624 AGGTGCAGCTCCACTCCA 60.528 61.111 13.85 0.00 36.03 3.86
2045 2987 4.416738 GCAGCTCCACTCCACCCC 62.417 72.222 0.00 0.00 0.00 4.95
2062 3004 4.728102 CGCAACCGCCCTACGTCA 62.728 66.667 0.00 0.00 41.42 4.35
2078 3020 4.794648 CATCCGCGCCTTCCCCAA 62.795 66.667 0.00 0.00 0.00 4.12
2088 3030 1.064825 CCTTCCCCAACACTACCAGT 58.935 55.000 0.00 0.00 0.00 4.00
2102 3045 1.920325 CCAGTCCTGCTCCTCCCAA 60.920 63.158 0.00 0.00 0.00 4.12
2106 3049 0.110486 GTCCTGCTCCTCCCAAACAA 59.890 55.000 0.00 0.00 0.00 2.83
2131 3074 2.915659 TCCTCGTGTCCGCACCTT 60.916 61.111 0.00 0.00 42.39 3.50
2138 3081 4.070552 GTCCGCACCTTCGAGCCT 62.071 66.667 0.00 0.00 0.00 4.58
2170 3126 1.011904 CCGAAGCGCACATGAATCG 60.012 57.895 11.47 7.50 0.00 3.34
2291 3247 1.137872 GAGTCCCTCTGCGATGTCATT 59.862 52.381 0.00 0.00 0.00 2.57
2294 3250 1.278985 TCCCTCTGCGATGTCATTTGT 59.721 47.619 0.00 0.00 0.00 2.83
2312 3268 0.882927 GTCGCTTGTACACCTTGGCA 60.883 55.000 0.00 0.00 0.00 4.92
2350 3306 0.238289 CGACGCCAAGAAAATGCAGT 59.762 50.000 0.00 0.00 0.00 4.40
2445 3401 0.957362 GCTTGCAAGAGAGCAGGTTT 59.043 50.000 30.39 0.00 46.54 3.27
2483 3439 1.629297 GGGGGTCATCTCCTCCTCT 59.371 63.158 0.00 0.00 44.41 3.69
2485 3441 1.127343 GGGGTCATCTCCTCCTCTTG 58.873 60.000 0.00 0.00 0.00 3.02
2499 3458 0.749649 CTCTTGGAGAGCGGCACTAT 59.250 55.000 1.45 0.00 35.30 2.12
2506 3465 2.131183 GAGAGCGGCACTATTGATGAC 58.869 52.381 1.45 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 136 3.950794 GACCATCGGCGACTTGGCA 62.951 63.158 25.18 0.00 45.16 4.92
182 186 2.653953 CTTGGTGAACACGACCGGGT 62.654 60.000 6.32 0.00 36.12 5.28
246 250 1.152673 GGGGATGGGCTCCATGAAC 60.153 63.158 10.99 2.62 45.26 3.18
307 311 2.093288 GTGGATCATGCTTCTGGTCAGA 60.093 50.000 0.00 0.00 35.27 3.27
333 337 2.215196 ACTAAATTTGTGGCGTCACGT 58.785 42.857 16.50 1.92 46.42 4.49
337 341 2.224784 ACGGAACTAAATTTGTGGCGTC 59.775 45.455 0.00 0.00 0.00 5.19
352 358 1.076332 CCAGGACGATGAAACGGAAC 58.924 55.000 0.00 0.00 37.61 3.62
355 361 1.665679 CAATCCAGGACGATGAAACGG 59.334 52.381 0.00 0.00 37.61 4.44
356 362 2.616960 TCAATCCAGGACGATGAAACG 58.383 47.619 0.00 0.00 39.31 3.60
357 363 4.635765 TCAATCAATCCAGGACGATGAAAC 59.364 41.667 4.27 0.00 0.00 2.78
359 365 4.486125 TCAATCAATCCAGGACGATGAA 57.514 40.909 4.27 0.00 0.00 2.57
360 366 4.694760 ATCAATCAATCCAGGACGATGA 57.305 40.909 4.27 4.31 0.00 2.92
361 367 4.556104 GCAATCAATCAATCCAGGACGATG 60.556 45.833 4.27 0.00 0.00 3.84
362 368 3.567164 GCAATCAATCAATCCAGGACGAT 59.433 43.478 0.00 0.00 0.00 3.73
365 371 4.931661 ATGCAATCAATCAATCCAGGAC 57.068 40.909 0.00 0.00 0.00 3.85
387 393 2.330440 TCAGTCTTTCAGCAACAGCA 57.670 45.000 0.00 0.00 0.00 4.41
389 395 3.611517 CGTTTCAGTCTTTCAGCAACAG 58.388 45.455 0.00 0.00 0.00 3.16
401 407 1.955762 GCAGTTCATGCGTTTCAGTC 58.044 50.000 0.00 0.00 46.99 3.51
468 474 0.247974 GTAGTCGACGTCGTCCATGG 60.248 60.000 34.40 4.97 40.80 3.66
514 532 4.785453 CTGTCCCCGCCTTCCAGC 62.785 72.222 0.00 0.00 0.00 4.85
573 591 0.182061 GAAGATGCCCAGGCTGATGA 59.818 55.000 17.94 0.00 42.51 2.92
688 706 2.045438 TGGAATGCCGCCGTTCAT 60.045 55.556 0.33 0.00 38.47 2.57
696 714 0.514255 CGTGATATGCTGGAATGCCG 59.486 55.000 0.00 0.00 36.79 5.69
697 715 0.877071 CCGTGATATGCTGGAATGCC 59.123 55.000 0.00 0.00 0.00 4.40
710 728 3.790437 CCCAGCTGGCTCCGTGAT 61.790 66.667 28.39 0.00 0.00 3.06
723 741 3.664495 CAGAGTTGCTGTGCCCAG 58.336 61.111 0.00 0.00 39.85 4.45
741 759 0.039437 GCGTCACGTCTGGAGAGAAA 60.039 55.000 0.00 0.00 0.00 2.52
747 765 4.050934 ATGCGCGTCACGTCTGGA 62.051 61.111 8.43 0.00 46.11 3.86
763 781 4.469227 AGCAGACAACAGAGTAATCTCCAT 59.531 41.667 0.00 0.00 41.26 3.41
766 785 4.081972 TCCAGCAGACAACAGAGTAATCTC 60.082 45.833 0.00 0.00 40.70 2.75
767 786 3.834813 TCCAGCAGACAACAGAGTAATCT 59.165 43.478 0.00 0.00 0.00 2.40
768 787 4.193826 TCCAGCAGACAACAGAGTAATC 57.806 45.455 0.00 0.00 0.00 1.75
769 788 4.019860 ACATCCAGCAGACAACAGAGTAAT 60.020 41.667 0.00 0.00 0.00 1.89
771 790 2.899900 ACATCCAGCAGACAACAGAGTA 59.100 45.455 0.00 0.00 0.00 2.59
772 791 1.696336 ACATCCAGCAGACAACAGAGT 59.304 47.619 0.00 0.00 0.00 3.24
773 792 2.074576 CACATCCAGCAGACAACAGAG 58.925 52.381 0.00 0.00 0.00 3.35
774 793 1.417517 ACACATCCAGCAGACAACAGA 59.582 47.619 0.00 0.00 0.00 3.41
775 794 1.534163 CACACATCCAGCAGACAACAG 59.466 52.381 0.00 0.00 0.00 3.16
776 795 1.134128 ACACACATCCAGCAGACAACA 60.134 47.619 0.00 0.00 0.00 3.33
777 796 1.265095 CACACACATCCAGCAGACAAC 59.735 52.381 0.00 0.00 0.00 3.32
778 797 1.134128 ACACACACATCCAGCAGACAA 60.134 47.619 0.00 0.00 0.00 3.18
779 798 0.469494 ACACACACATCCAGCAGACA 59.531 50.000 0.00 0.00 0.00 3.41
780 799 2.069273 GTACACACACATCCAGCAGAC 58.931 52.381 0.00 0.00 0.00 3.51
795 814 0.396811 ACAGGCAGAAGGGTGTACAC 59.603 55.000 18.01 18.01 0.00 2.90
800 819 5.808366 TCTATATAACAGGCAGAAGGGTG 57.192 43.478 0.00 0.00 0.00 4.61
802 821 5.071788 TGGTTCTATATAACAGGCAGAAGGG 59.928 44.000 3.69 0.00 0.00 3.95
806 825 7.907841 TTAGTGGTTCTATATAACAGGCAGA 57.092 36.000 3.69 0.00 0.00 4.26
822 841 9.057089 GCATTCTTAGTAGCAATATTAGTGGTT 57.943 33.333 0.82 0.00 0.00 3.67
823 842 8.432805 AGCATTCTTAGTAGCAATATTAGTGGT 58.567 33.333 1.24 1.24 0.00 4.16
825 844 8.226448 GCAGCATTCTTAGTAGCAATATTAGTG 58.774 37.037 0.00 0.00 0.00 2.74
828 847 7.933577 ACTGCAGCATTCTTAGTAGCAATATTA 59.066 33.333 15.27 0.00 0.00 0.98
829 848 6.769822 ACTGCAGCATTCTTAGTAGCAATATT 59.230 34.615 15.27 0.00 0.00 1.28
830 849 6.294473 ACTGCAGCATTCTTAGTAGCAATAT 58.706 36.000 15.27 0.00 0.00 1.28
831 850 5.674525 ACTGCAGCATTCTTAGTAGCAATA 58.325 37.500 15.27 0.00 0.00 1.90
832 851 4.521146 ACTGCAGCATTCTTAGTAGCAAT 58.479 39.130 15.27 0.00 0.00 3.56
840 1703 1.078709 GCACGACTGCAGCATTCTTA 58.921 50.000 15.27 0.00 43.62 2.10
951 1814 6.369615 TCTCGTGTTATATAGCAGTATACGCA 59.630 38.462 17.70 7.81 0.00 5.24
977 1844 4.994217 TGTTCTTAACAGCACAATCGATGA 59.006 37.500 0.00 0.00 36.25 2.92
993 1860 5.912892 TGGACGATATTGCATCTGTTCTTA 58.087 37.500 0.00 0.00 0.00 2.10
1012 1879 0.743345 AAGCGGGCTAAACGATGGAC 60.743 55.000 0.00 0.00 0.00 4.02
1018 1885 1.003545 CATGATGAAGCGGGCTAAACG 60.004 52.381 0.00 0.00 0.00 3.60
1039 1906 1.078918 CCTCCTCAGCGTGCATCAA 60.079 57.895 0.00 0.00 0.00 2.57
1040 1907 1.953231 CTCCTCCTCAGCGTGCATCA 61.953 60.000 0.00 0.00 0.00 3.07
1049 1916 4.567385 GCGCGCTCTCCTCCTCAG 62.567 72.222 26.67 0.00 0.00 3.35
1135 2014 1.907936 CATCCCCATCTCCATCTCTCC 59.092 57.143 0.00 0.00 0.00 3.71
1137 2016 1.132462 AGCATCCCCATCTCCATCTCT 60.132 52.381 0.00 0.00 0.00 3.10
1251 2130 1.219124 GAGCATCCTGACCGCTTGA 59.781 57.895 0.00 0.00 35.75 3.02
1269 2148 3.616721 CGGGCGAGTATCCCCCAG 61.617 72.222 0.70 0.00 41.07 4.45
1307 2186 3.006706 CCGATTCTTCGCCTTCGC 58.993 61.111 0.00 0.00 44.12 4.70
1313 2192 3.929948 CTGGCGCCGATTCTTCGC 61.930 66.667 23.90 9.84 44.12 4.70
1345 2224 2.922234 CCTCCTCCCATTCCCAGC 59.078 66.667 0.00 0.00 0.00 4.85
1346 2225 2.922234 GCCTCCTCCCATTCCCAG 59.078 66.667 0.00 0.00 0.00 4.45
1347 2226 3.089874 CGCCTCCTCCCATTCCCA 61.090 66.667 0.00 0.00 0.00 4.37
1348 2227 3.878667 CCGCCTCCTCCCATTCCC 61.879 72.222 0.00 0.00 0.00 3.97
1355 2234 3.148279 ATGACGACCGCCTCCTCC 61.148 66.667 0.00 0.00 0.00 4.30
1371 2250 4.414956 TCAGGGTCCGGCCTCCAT 62.415 66.667 13.58 3.54 37.43 3.41
1429 2308 6.772716 ACCTTCATCAGCTACAAAGAAGAAAA 59.227 34.615 12.41 0.00 35.67 2.29
1433 2312 7.201679 CCAATACCTTCATCAGCTACAAAGAAG 60.202 40.741 0.00 0.00 33.96 2.85
1440 2319 5.163405 TGTCTCCAATACCTTCATCAGCTAC 60.163 44.000 0.00 0.00 0.00 3.58
1442 2321 3.776969 TGTCTCCAATACCTTCATCAGCT 59.223 43.478 0.00 0.00 0.00 4.24
1449 2328 3.199946 TCCCATGTGTCTCCAATACCTTC 59.800 47.826 0.00 0.00 0.00 3.46
1463 2342 3.216800 CACATACCCTGAATCCCATGTG 58.783 50.000 0.00 0.00 37.85 3.21
1468 2347 2.643551 CACACACATACCCTGAATCCC 58.356 52.381 0.00 0.00 0.00 3.85
1469 2348 2.017049 GCACACACATACCCTGAATCC 58.983 52.381 0.00 0.00 0.00 3.01
1478 2357 3.058570 TCAAAATCCACGCACACACATAC 60.059 43.478 0.00 0.00 0.00 2.39
1552 2434 6.878923 CCACCATAGAACAACTGAACAAGATA 59.121 38.462 0.00 0.00 0.00 1.98
1570 2452 1.067295 GATGGCTGGATCCCACCATA 58.933 55.000 27.35 8.65 41.70 2.74
1585 2502 2.398554 CCGAACAACGCCTGGATGG 61.399 63.158 0.00 0.00 41.07 3.51
1590 2507 0.878523 TTCTGTCCGAACAACGCCTG 60.879 55.000 0.00 0.00 41.07 4.85
1591 2508 0.179067 TTTCTGTCCGAACAACGCCT 60.179 50.000 0.00 0.00 41.07 5.52
1592 2509 0.872388 ATTTCTGTCCGAACAACGCC 59.128 50.000 0.00 0.00 41.07 5.68
1593 2510 3.430895 TCTTATTTCTGTCCGAACAACGC 59.569 43.478 0.00 0.00 41.07 4.84
1594 2511 4.446385 TGTCTTATTTCTGTCCGAACAACG 59.554 41.667 0.00 0.00 42.18 4.10
1597 2514 5.209818 AGTGTCTTATTTCTGTCCGAACA 57.790 39.130 0.00 0.00 0.00 3.18
1598 2515 5.227908 TGAGTGTCTTATTTCTGTCCGAAC 58.772 41.667 0.00 0.00 0.00 3.95
1599 2516 5.462530 TGAGTGTCTTATTTCTGTCCGAA 57.537 39.130 0.00 0.00 0.00 4.30
1600 2517 5.227908 GTTGAGTGTCTTATTTCTGTCCGA 58.772 41.667 0.00 0.00 0.00 4.55
1601 2518 4.389077 GGTTGAGTGTCTTATTTCTGTCCG 59.611 45.833 0.00 0.00 0.00 4.79
1602 2519 4.389077 CGGTTGAGTGTCTTATTTCTGTCC 59.611 45.833 0.00 0.00 0.00 4.02
1603 2520 4.389077 CCGGTTGAGTGTCTTATTTCTGTC 59.611 45.833 0.00 0.00 0.00 3.51
1604 2521 4.315803 CCGGTTGAGTGTCTTATTTCTGT 58.684 43.478 0.00 0.00 0.00 3.41
1629 2546 0.317854 GTTTGGAGTGCGTTTGGAGC 60.318 55.000 0.00 0.00 0.00 4.70
1631 2548 0.745128 ACGTTTGGAGTGCGTTTGGA 60.745 50.000 0.00 0.00 35.11 3.53
1661 2578 1.414158 GGCTGAGTATGGAGGTGCTA 58.586 55.000 0.00 0.00 0.00 3.49
1691 2608 4.598257 CGAAAGCGTCTGGTCCAT 57.402 55.556 0.00 0.00 0.00 3.41
1704 2621 1.731613 CGTGGCAGAGCGTACGAAA 60.732 57.895 21.65 0.00 40.37 3.46
1709 2626 3.051479 TCGACGTGGCAGAGCGTA 61.051 61.111 0.00 0.00 41.70 4.42
1712 2629 2.807045 CAGTCGACGTGGCAGAGC 60.807 66.667 10.46 0.00 0.00 4.09
1726 2643 1.213013 GCGGACATCGTGAGACAGT 59.787 57.895 0.00 0.00 46.97 3.55
1743 2671 1.070786 TTTGTCGGGACAGGAGTGC 59.929 57.895 1.37 0.00 42.94 4.40
1747 2675 0.834612 AAGTGTTTGTCGGGACAGGA 59.165 50.000 1.37 0.00 42.94 3.86
1756 2685 1.617322 GGGAAGGGGAAGTGTTTGTC 58.383 55.000 0.00 0.00 0.00 3.18
1771 2700 1.075601 AGAGTTTGCCATCTGGGGAA 58.924 50.000 0.00 0.00 46.41 3.97
1777 2707 5.221722 TGAGTTTGACTAGAGTTTGCCATCT 60.222 40.000 0.00 0.00 0.00 2.90
1788 2718 3.082548 CGAGAGGGTGAGTTTGACTAGA 58.917 50.000 0.00 0.00 0.00 2.43
1797 2727 2.363147 GAGGGCGAGAGGGTGAGT 60.363 66.667 0.00 0.00 0.00 3.41
1803 2733 1.153469 GAGCAAAGAGGGCGAGAGG 60.153 63.158 0.00 0.00 36.08 3.69
1901 2843 2.843701 CACAGACAAGCTCAAGTCCTT 58.156 47.619 9.50 0.00 35.38 3.36
1918 2860 3.220999 CTCCTTGTCGTCCGGCACA 62.221 63.158 0.00 0.00 0.00 4.57
1962 2904 1.519455 CCCTTGTCCATCGACGAGC 60.519 63.158 3.01 0.00 45.80 5.03
1967 2909 1.612146 TCCTGCCCTTGTCCATCGA 60.612 57.895 0.00 0.00 0.00 3.59
1968 2910 1.153289 CTCCTGCCCTTGTCCATCG 60.153 63.158 0.00 0.00 0.00 3.84
1982 2924 2.559922 ATCGTCGAGGTGGAGCTCCT 62.560 60.000 32.28 13.87 38.09 3.69
2016 2958 4.990910 AGCTGCACCTCCCCACCT 62.991 66.667 1.02 0.00 0.00 4.00
2045 2987 4.728102 TGACGTAGGGCGGTTGCG 62.728 66.667 0.00 0.00 46.52 4.85
2062 3004 4.796495 GTTGGGGAAGGCGCGGAT 62.796 66.667 8.83 0.00 0.00 4.18
2077 3019 0.977395 GGAGCAGGACTGGTAGTGTT 59.023 55.000 3.74 0.00 41.93 3.32
2078 3020 0.115349 AGGAGCAGGACTGGTAGTGT 59.885 55.000 3.74 0.00 41.93 3.55
2088 3030 0.110486 GTTGTTTGGGAGGAGCAGGA 59.890 55.000 0.00 0.00 0.00 3.86
2173 3129 2.052104 GCCGCCCTTTGCCTTGTAT 61.052 57.895 0.00 0.00 36.24 2.29
2256 3212 1.304217 ACTCATCGTCGTCCCTGGT 60.304 57.895 0.00 0.00 0.00 4.00
2291 3247 1.588674 CCAAGGTGTACAAGCGACAA 58.411 50.000 0.00 0.00 0.00 3.18
2294 3250 0.602638 CTGCCAAGGTGTACAAGCGA 60.603 55.000 0.00 0.00 0.00 4.93
2350 3306 3.372730 GCCCAATGTTGAGCGCCA 61.373 61.111 2.29 0.00 0.00 5.69
2483 3439 0.901827 TCAATAGTGCCGCTCTCCAA 59.098 50.000 0.00 0.00 0.00 3.53
2485 3441 1.069204 TCATCAATAGTGCCGCTCTCC 59.931 52.381 0.00 0.00 0.00 3.71
2499 3458 1.546029 CAGGGAGAGTGTCGTCATCAA 59.454 52.381 0.00 0.00 0.00 2.57
2506 3465 4.803426 GCGGCAGGGAGAGTGTCG 62.803 72.222 0.00 0.00 45.80 4.35


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

AutoCloner maintained by Alex Coulton.