Multiple sequence alignment - TraesCS5A01G538600

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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 TraesCS5A01G538600 chr5A 100.000 3295 0 0 1 3295 696927333 696924039 0.000000e+00 6085.0
1 TraesCS5A01G538600 chr4D 88.896 2999 123 93 2 2895 509059188 509056295 0.000000e+00 3500.0
2 TraesCS5A01G538600 chr4D 83.784 148 11 6 2910 3056 509045499 509045364 9.600000e-26 128.0
3 TraesCS5A01G538600 chr4D 93.939 66 4 0 3225 3290 509045267 509045202 2.090000e-17 100.0
4 TraesCS5A01G538600 chr4B 88.809 2368 108 69 347 2598 658210709 658213035 0.000000e+00 2760.0
5 TraesCS5A01G538600 chr4B 86.431 538 32 21 2594 3106 658213784 658214305 4.810000e-153 551.0
6 TraesCS5A01G538600 chr4B 90.794 315 12 11 4 302 658210255 658210568 3.960000e-109 405.0
7 TraesCS5A01G538600 chr4B 90.964 166 14 1 3126 3290 658446441 658446606 4.280000e-54 222.0
8 TraesCS5A01G538600 chr4B 73.004 263 55 13 3039 3295 178666638 178666890 9.800000e-11 78.7
9 TraesCS5A01G538600 chr4B 72.901 262 57 12 3039 3295 387517105 387517357 9.800000e-11 78.7
10 TraesCS5A01G538600 chr1D 77.156 661 88 41 1550 2169 310815746 310815108 3.170000e-85 326.0
11 TraesCS5A01G538600 chr1D 89.952 209 21 0 1936 2144 432319760 432319968 1.510000e-68 270.0
12 TraesCS5A01G538600 chr1D 72.332 253 61 8 3045 3295 22035906 22035661 1.640000e-08 71.3
13 TraesCS5A01G538600 chr1B 77.204 658 85 44 1550 2165 420685256 420685890 1.140000e-84 324.0
14 TraesCS5A01G538600 chr1B 89.474 209 22 0 1936 2144 583760667 583760875 7.010000e-67 265.0
15 TraesCS5A01G538600 chr1A 77.496 631 80 40 1564 2166 390709189 390709785 4.100000e-84 322.0
16 TraesCS5A01G538600 chr1A 89.952 209 21 0 1936 2144 530781648 530781856 1.510000e-68 270.0
17 TraesCS5A01G538600 chr1A 73.246 228 52 8 3070 3295 561566253 561566473 1.270000e-09 75.0
18 TraesCS5A01G538600 chr3D 88.889 207 22 1 1937 2143 380815056 380815261 1.520000e-63 254.0
19 TraesCS5A01G538600 chr6A 74.525 263 51 13 3039 3295 617085648 617085900 2.090000e-17 100.0
20 TraesCS5A01G538600 chr5B 73.047 256 55 12 3045 3295 461700355 461700109 9.800000e-11 78.7
21 TraesCS5A01G538600 chr2B 73.305 236 49 13 3064 3295 636553772 636553997 1.270000e-09 75.0


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 TraesCS5A01G538600 chr5A 696924039 696927333 3294 True 6085.000000 6085 100.000 1 3295 1 chr5A.!!$R1 3294
1 TraesCS5A01G538600 chr4D 509056295 509059188 2893 True 3500.000000 3500 88.896 2 2895 1 chr4D.!!$R1 2893
2 TraesCS5A01G538600 chr4B 658210255 658214305 4050 False 1238.666667 2760 88.678 4 3106 3 chr4B.!!$F4 3102
3 TraesCS5A01G538600 chr1D 310815108 310815746 638 True 326.000000 326 77.156 1550 2169 1 chr1D.!!$R2 619
4 TraesCS5A01G538600 chr1B 420685256 420685890 634 False 324.000000 324 77.204 1550 2165 1 chr1B.!!$F1 615
5 TraesCS5A01G538600 chr1A 390709189 390709785 596 False 322.000000 322 77.496 1564 2166 1 chr1A.!!$F1 602

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
874 1062 0.03392 CAGCTACAGCCACTGTCACA 59.966 55.0 3.01 0.0 41.21 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2696 3795 0.458716 GCTCACTCGCTTGACCTACC 60.459 60.0 0.0 0.0 0.0 3.18 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
68 69 2.814336 GGTTCCATTATTCCATCCGAGC 59.186 50.000 0.00 0.00 0.00 5.03
265 290 1.135373 GTGATCGATCGATATGCCCGT 60.135 52.381 29.45 6.96 34.60 5.28
302 327 7.977293 AGTAAATGTATCAACACATGCTACGTA 59.023 33.333 0.00 0.00 39.10 3.57
304 329 4.099824 TGTATCAACACATGCTACGTACG 58.900 43.478 15.01 15.01 34.14 3.67
305 330 2.710220 TCAACACATGCTACGTACGT 57.290 45.000 25.98 25.98 0.00 3.57
318 392 5.201181 GCTACGTACGTACAGAGAATTACC 58.799 45.833 23.60 4.36 0.00 2.85
322 396 5.874810 ACGTACGTACAGAGAATTACCACTA 59.125 40.000 21.41 0.00 0.00 2.74
335 449 7.996385 AGAATTACCACTAATAAACCATGCAC 58.004 34.615 0.00 0.00 0.00 4.57
336 450 7.613801 AGAATTACCACTAATAAACCATGCACA 59.386 33.333 0.00 0.00 0.00 4.57
369 494 8.738645 AAAGTAGCTAATTTAACTGATCCAGG 57.261 34.615 17.03 0.00 35.51 4.45
376 501 1.794714 TAACTGATCCAGGGAGAGGC 58.205 55.000 0.00 0.00 35.51 4.70
377 502 0.043940 AACTGATCCAGGGAGAGGCT 59.956 55.000 0.00 0.00 35.51 4.58
378 503 0.398381 ACTGATCCAGGGAGAGGCTC 60.398 60.000 6.34 6.34 35.51 4.70
379 504 0.398239 CTGATCCAGGGAGAGGCTCA 60.398 60.000 18.26 0.00 31.13 4.26
380 505 0.043183 TGATCCAGGGAGAGGCTCAA 59.957 55.000 18.26 0.00 29.03 3.02
430 564 2.828095 GTGGGGCGTGCATGCATA 60.828 61.111 30.79 14.27 36.28 3.14
431 565 2.195411 TGGGGCGTGCATGCATAT 59.805 55.556 30.79 0.00 36.28 1.78
432 566 2.194889 TGGGGCGTGCATGCATATG 61.195 57.895 30.79 17.51 37.36 1.78
455 589 4.581409 GCATGGCATATGGTATGCATATGA 59.419 41.667 25.61 0.00 46.21 2.15
470 604 3.799574 GCATATGAGTGAGTGAGCCTCTG 60.800 52.174 6.97 0.00 41.11 3.35
471 605 2.228545 ATGAGTGAGTGAGCCTCTGA 57.771 50.000 0.00 0.00 41.11 3.27
473 607 1.202989 TGAGTGAGTGAGCCTCTGAGT 60.203 52.381 3.66 0.00 41.11 3.41
474 608 2.040412 TGAGTGAGTGAGCCTCTGAGTA 59.960 50.000 3.66 0.00 41.11 2.59
475 609 2.422127 GAGTGAGTGAGCCTCTGAGTAC 59.578 54.545 3.66 0.00 41.11 2.73
476 610 1.131504 GTGAGTGAGCCTCTGAGTACG 59.868 57.143 3.66 0.00 41.11 3.67
477 611 0.736053 GAGTGAGCCTCTGAGTACGG 59.264 60.000 3.66 0.00 37.22 4.02
479 613 2.052690 TGAGCCTCTGAGTACGGGC 61.053 63.158 3.66 0.10 44.38 6.13
480 614 2.037367 AGCCTCTGAGTACGGGCA 59.963 61.111 15.14 3.65 46.23 5.36
481 615 2.010582 GAGCCTCTGAGTACGGGCAG 62.011 65.000 15.14 11.41 46.23 4.85
482 616 2.352032 GCCTCTGAGTACGGGCAGT 61.352 63.158 3.66 0.00 43.59 4.40
505 639 2.440980 GCATGGGCCCTGTTCCTC 60.441 66.667 25.70 0.99 0.00 3.71
665 835 2.022240 CTCCCCGGCTAGCTCAGTTC 62.022 65.000 15.72 0.00 0.00 3.01
762 944 8.045720 TCCTCCTCTATATTAATGGTTTTGCT 57.954 34.615 0.00 0.00 0.00 3.91
874 1062 0.033920 CAGCTACAGCCACTGTCACA 59.966 55.000 3.01 0.00 41.21 3.58
876 1064 0.034059 GCTACAGCCACTGTCACACT 59.966 55.000 3.01 0.00 41.21 3.55
878 1066 1.615883 CTACAGCCACTGTCACACTCT 59.384 52.381 3.01 0.00 41.21 3.24
880 1068 0.390492 CAGCCACTGTCACACTCTCA 59.610 55.000 0.00 0.00 0.00 3.27
882 1070 0.390860 GCCACTGTCACACTCTCACT 59.609 55.000 0.00 0.00 0.00 3.41
885 1073 2.030363 CCACTGTCACACTCTCACTCTC 60.030 54.545 0.00 0.00 0.00 3.20
886 1074 1.876799 ACTGTCACACTCTCACTCTCG 59.123 52.381 0.00 0.00 0.00 4.04
888 1076 0.878416 GTCACACTCTCACTCTCGCT 59.122 55.000 0.00 0.00 0.00 4.93
890 1078 0.877743 CACACTCTCACTCTCGCTCA 59.122 55.000 0.00 0.00 0.00 4.26
892 1080 1.164411 CACTCTCACTCTCGCTCAGT 58.836 55.000 0.00 0.00 0.00 3.41
893 1081 1.135717 CACTCTCACTCTCGCTCAGTG 60.136 57.143 2.72 2.72 42.40 3.66
926 1134 2.395654 GCCATTACTGCGAGCTACTAC 58.604 52.381 0.00 0.00 0.00 2.73
927 1135 2.034812 GCCATTACTGCGAGCTACTACT 59.965 50.000 0.00 0.00 0.00 2.57
928 1136 3.252701 GCCATTACTGCGAGCTACTACTA 59.747 47.826 0.00 0.00 0.00 1.82
962 1175 3.606662 ACTCCACTCGCTGCACGT 61.607 61.111 0.00 0.00 44.19 4.49
966 1179 2.661537 CACTCGCTGCACGTTCCA 60.662 61.111 0.00 0.00 44.19 3.53
1114 1336 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
1115 1337 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
1116 1338 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1119 1341 2.280797 CACCACCACCACCACTCG 60.281 66.667 0.00 0.00 0.00 4.18
1126 1348 2.203728 ACCACCACTCGGCCTACA 60.204 61.111 0.00 0.00 34.57 2.74
1230 1455 0.257328 AGATGCTCGACCTCTCCTCA 59.743 55.000 0.00 0.00 0.00 3.86
1412 1637 1.420138 CCTGCCTGTCCCGGTAATTAT 59.580 52.381 0.00 0.00 0.00 1.28
1414 1639 3.139077 CTGCCTGTCCCGGTAATTATTC 58.861 50.000 0.00 0.00 0.00 1.75
1423 1648 5.644636 GTCCCGGTAATTATTCACTTCAACA 59.355 40.000 0.00 0.00 0.00 3.33
1438 1684 0.442310 CAACATTCGATCGCGTGGTT 59.558 50.000 11.09 9.13 38.98 3.67
1450 1696 3.857052 TCGCGTGGTTGATCTTAATTCT 58.143 40.909 5.77 0.00 0.00 2.40
1484 1730 6.542005 TGTGTGAGAAACTGAGAATTAAGCAA 59.458 34.615 0.00 0.00 0.00 3.91
1495 1741 7.040409 ACTGAGAATTAAGCAACGGAAGAAATT 60.040 33.333 0.00 0.00 0.00 1.82
1520 1780 3.257873 TGATTGAGATCTAGCTAGCCAGC 59.742 47.826 16.35 2.60 39.38 4.85
1886 2208 2.815647 GGCGTCAAGAAGAGCGGG 60.816 66.667 0.00 0.00 0.00 6.13
1895 2217 3.591254 GAAGAGCGGGCTCGTGGTT 62.591 63.158 13.69 3.39 46.90 3.67
2153 2475 2.811317 CGGCAGAACGAGCTGGTC 60.811 66.667 0.40 0.00 36.41 4.02
2248 2573 2.430244 CGACTACGGCGTGTGCTT 60.430 61.111 24.86 1.18 42.25 3.91
2255 2580 2.048503 GGCGTGTGCTTACCGACT 60.049 61.111 0.00 0.00 42.25 4.18
2256 2581 2.092882 GGCGTGTGCTTACCGACTC 61.093 63.158 0.00 0.00 42.25 3.36
2257 2582 2.434134 GCGTGTGCTTACCGACTCG 61.434 63.158 0.00 0.00 38.39 4.18
2258 2583 1.208358 CGTGTGCTTACCGACTCGA 59.792 57.895 0.00 0.00 32.28 4.04
2294 2619 2.487762 CAGCAGCCTAGCTAGCTACTAG 59.512 54.545 20.67 12.90 44.54 2.57
2295 2620 2.107552 AGCAGCCTAGCTAGCTACTAGT 59.892 50.000 20.67 0.00 44.50 2.57
2351 2682 4.579647 CATGGATGGATATGGATGTGGA 57.420 45.455 0.00 0.00 0.00 4.02
2352 2683 5.125367 CATGGATGGATATGGATGTGGAT 57.875 43.478 0.00 0.00 0.00 3.41
2353 2684 4.579647 TGGATGGATATGGATGTGGATG 57.420 45.455 0.00 0.00 0.00 3.51
2354 2685 4.177546 TGGATGGATATGGATGTGGATGA 58.822 43.478 0.00 0.00 0.00 2.92
2355 2686 4.791880 TGGATGGATATGGATGTGGATGAT 59.208 41.667 0.00 0.00 0.00 2.45
2356 2687 5.104235 TGGATGGATATGGATGTGGATGATC 60.104 44.000 0.00 0.00 0.00 2.92
2357 2688 4.849813 TGGATATGGATGTGGATGATCC 57.150 45.455 4.05 4.05 40.04 3.36
2367 2698 2.549064 TGGATGATCCACATTAGCGG 57.451 50.000 10.75 0.00 42.67 5.52
2445 2782 3.422603 CGTGTACTATTTCGCGTTGCTTT 60.423 43.478 5.77 0.00 33.73 3.51
2446 2783 4.079710 GTGTACTATTTCGCGTTGCTTTC 58.920 43.478 5.77 0.00 0.00 2.62
2530 2871 3.574826 TGTTCAAAAACCCCGGGAATAAG 59.425 43.478 26.32 7.20 34.28 1.73
2542 2883 5.167845 CCCGGGAATAAGTTGAAAATGTTG 58.832 41.667 18.48 0.00 0.00 3.33
2548 2890 9.358872 GGGAATAAGTTGAAAATGTTGATCTTC 57.641 33.333 0.00 0.00 0.00 2.87
2552 2894 6.645790 AGTTGAAAATGTTGATCTTCTGCT 57.354 33.333 0.00 0.00 0.00 4.24
2554 2896 8.169977 AGTTGAAAATGTTGATCTTCTGCTTA 57.830 30.769 0.00 0.00 0.00 3.09
2600 3699 2.932083 CTGCACGCACACTGTCGAC 61.932 63.158 9.11 9.11 0.00 4.20
2643 3742 5.125417 GCAGAGTGAAGAGAAGAGTCAGTAT 59.875 44.000 0.00 0.00 0.00 2.12
2668 3767 2.241160 TGTGTATCGTACAGTGGTGGT 58.759 47.619 0.00 0.00 39.77 4.16
2677 3776 0.397941 ACAGTGGTGGTCATCAGTGG 59.602 55.000 19.47 5.78 44.94 4.00
2682 3781 1.276622 GGTGGTCATCAGTGGGTAGT 58.723 55.000 0.00 0.00 0.00 2.73
2683 3782 2.225420 TGGTGGTCATCAGTGGGTAGTA 60.225 50.000 0.00 0.00 0.00 1.82
2684 3783 2.431057 GGTGGTCATCAGTGGGTAGTAG 59.569 54.545 0.00 0.00 0.00 2.57
2685 3784 2.431057 GTGGTCATCAGTGGGTAGTAGG 59.569 54.545 0.00 0.00 0.00 3.18
2686 3785 2.313643 TGGTCATCAGTGGGTAGTAGGA 59.686 50.000 0.00 0.00 0.00 2.94
2688 3787 3.627747 GGTCATCAGTGGGTAGTAGGAGT 60.628 52.174 0.00 0.00 0.00 3.85
2689 3788 4.386088 GGTCATCAGTGGGTAGTAGGAGTA 60.386 50.000 0.00 0.00 0.00 2.59
2690 3789 4.579753 GTCATCAGTGGGTAGTAGGAGTAC 59.420 50.000 0.00 0.00 0.00 2.73
2691 3790 4.477581 TCATCAGTGGGTAGTAGGAGTACT 59.522 45.833 0.00 0.00 42.49 2.73
2692 3791 5.668991 TCATCAGTGGGTAGTAGGAGTACTA 59.331 44.000 0.00 0.00 40.23 1.82
2702 3801 4.143986 GTAGGAGTACTACGTGGTAGGT 57.856 50.000 12.49 2.75 42.39 3.08
2703 3802 3.274095 AGGAGTACTACGTGGTAGGTC 57.726 52.381 12.49 11.66 40.13 3.85
2704 3803 2.573462 AGGAGTACTACGTGGTAGGTCA 59.427 50.000 12.49 0.00 40.13 4.02
2756 3858 0.318762 AAAGGACGAGTGAGTGAGGC 59.681 55.000 0.00 0.00 0.00 4.70
2816 3918 1.659794 CAACTTTTGTCAGGCCGGG 59.340 57.895 2.18 0.00 0.00 5.73
2839 3941 1.102978 GCCGGGAACAATGCTATGTT 58.897 50.000 2.18 7.30 45.82 2.71
2895 4005 3.366396 CTCCTCCACTTGCTTCCTACTA 58.634 50.000 0.00 0.00 0.00 1.82
2896 4006 3.097614 TCCTCCACTTGCTTCCTACTAC 58.902 50.000 0.00 0.00 0.00 2.73
2897 4007 2.168728 CCTCCACTTGCTTCCTACTACC 59.831 54.545 0.00 0.00 0.00 3.18
2898 4008 3.100671 CTCCACTTGCTTCCTACTACCT 58.899 50.000 0.00 0.00 0.00 3.08
2900 4010 3.514309 TCCACTTGCTTCCTACTACCTTC 59.486 47.826 0.00 0.00 0.00 3.46
2901 4011 3.260884 CCACTTGCTTCCTACTACCTTCA 59.739 47.826 0.00 0.00 0.00 3.02
2903 4013 5.491982 CACTTGCTTCCTACTACCTTCATT 58.508 41.667 0.00 0.00 0.00 2.57
2904 4014 5.582665 CACTTGCTTCCTACTACCTTCATTC 59.417 44.000 0.00 0.00 0.00 2.67
2905 4015 5.485708 ACTTGCTTCCTACTACCTTCATTCT 59.514 40.000 0.00 0.00 0.00 2.40
2906 4016 6.668283 ACTTGCTTCCTACTACCTTCATTCTA 59.332 38.462 0.00 0.00 0.00 2.10
2908 4018 7.291411 TGCTTCCTACTACCTTCATTCTATC 57.709 40.000 0.00 0.00 0.00 2.08
2909 4019 6.839134 TGCTTCCTACTACCTTCATTCTATCA 59.161 38.462 0.00 0.00 0.00 2.15
2910 4020 7.510685 TGCTTCCTACTACCTTCATTCTATCAT 59.489 37.037 0.00 0.00 0.00 2.45
2911 4021 7.816995 GCTTCCTACTACCTTCATTCTATCATG 59.183 40.741 0.00 0.00 0.00 3.07
2913 4023 8.783660 TCCTACTACCTTCATTCTATCATGTT 57.216 34.615 0.00 0.00 0.00 2.71
2915 4025 9.482627 CCTACTACCTTCATTCTATCATGTTTC 57.517 37.037 0.00 0.00 0.00 2.78
2918 4028 9.553064 ACTACCTTCATTCTATCATGTTTCATC 57.447 33.333 0.00 0.00 0.00 2.92
2921 4031 9.471702 ACCTTCATTCTATCATGTTTCATCTTT 57.528 29.630 0.00 0.00 0.00 2.52
2970 4090 5.300034 AGTGATCATTTTCTGTTCTTGTGCA 59.700 36.000 0.00 0.00 0.00 4.57
2971 4091 6.015688 AGTGATCATTTTCTGTTCTTGTGCAT 60.016 34.615 0.00 0.00 0.00 3.96
2972 4092 6.643770 GTGATCATTTTCTGTTCTTGTGCATT 59.356 34.615 0.00 0.00 0.00 3.56
2973 4093 6.643360 TGATCATTTTCTGTTCTTGTGCATTG 59.357 34.615 0.00 0.00 0.00 2.82
2974 4094 5.291178 TCATTTTCTGTTCTTGTGCATTGG 58.709 37.500 0.00 0.00 0.00 3.16
2975 4095 4.998671 TTTTCTGTTCTTGTGCATTGGA 57.001 36.364 0.00 0.00 0.00 3.53
2980 4100 3.991773 CTGTTCTTGTGCATTGGAATTGG 59.008 43.478 0.00 0.00 0.00 3.16
2984 4104 5.486735 TCTTGTGCATTGGAATTGGAATT 57.513 34.783 0.00 0.00 0.00 2.17
2987 4107 4.567971 TGTGCATTGGAATTGGAATTGTC 58.432 39.130 0.00 0.00 0.00 3.18
3013 4133 9.748708 CGGTTCATTATTTATGATCAAACCAAT 57.251 29.630 16.42 8.38 42.69 3.16
3027 4148 6.339587 TCAAACCAATCCATGTTTAAGACC 57.660 37.500 0.00 0.00 33.57 3.85
3028 4149 5.835819 TCAAACCAATCCATGTTTAAGACCA 59.164 36.000 0.00 0.00 33.57 4.02
3029 4150 5.722021 AACCAATCCATGTTTAAGACCAC 57.278 39.130 0.00 0.00 0.00 4.16
3031 4152 3.427503 CCAATCCATGTTTAAGACCACGC 60.428 47.826 0.00 0.00 0.00 5.34
3042 4163 1.213537 GACCACGCGCAGTAGGTTA 59.786 57.895 5.73 0.00 35.43 2.85
3044 4165 0.033781 ACCACGCGCAGTAGGTTAAA 59.966 50.000 5.73 0.00 32.77 1.52
3046 4167 0.094730 CACGCGCAGTAGGTTAAAGC 59.905 55.000 5.73 0.00 0.00 3.51
3049 4170 2.380081 CGCAGTAGGTTAAAGCGGG 58.620 57.895 0.00 0.00 44.20 6.13
3087 4208 0.104120 CCAACATGGATGGCAGCATG 59.896 55.000 4.64 9.16 40.96 4.06
3095 4216 1.540267 GGATGGCAGCATGATCATCAC 59.460 52.381 4.86 0.85 44.43 3.06
3106 4227 1.138859 TGATCATCACATCGGTCCACC 59.861 52.381 0.00 0.00 0.00 4.61
3107 4228 1.138859 GATCATCACATCGGTCCACCA 59.861 52.381 0.00 0.00 35.14 4.17
3108 4229 0.980423 TCATCACATCGGTCCACCAA 59.020 50.000 0.00 0.00 35.14 3.67
3109 4230 1.086696 CATCACATCGGTCCACCAAC 58.913 55.000 0.00 0.00 35.14 3.77
3110 4231 0.984230 ATCACATCGGTCCACCAACT 59.016 50.000 0.00 0.00 35.14 3.16
3111 4232 0.320374 TCACATCGGTCCACCAACTC 59.680 55.000 0.00 0.00 35.14 3.01
3112 4233 0.321671 CACATCGGTCCACCAACTCT 59.678 55.000 0.00 0.00 35.14 3.24
3113 4234 0.321671 ACATCGGTCCACCAACTCTG 59.678 55.000 0.00 0.00 35.14 3.35
3114 4235 0.321671 CATCGGTCCACCAACTCTGT 59.678 55.000 0.00 0.00 35.14 3.41
3115 4236 0.608640 ATCGGTCCACCAACTCTGTC 59.391 55.000 0.00 0.00 35.14 3.51
3116 4237 1.372997 CGGTCCACCAACTCTGTCG 60.373 63.158 0.00 0.00 35.14 4.35
3117 4238 1.802337 CGGTCCACCAACTCTGTCGA 61.802 60.000 0.00 0.00 35.14 4.20
3118 4239 0.319641 GGTCCACCAACTCTGTCGAC 60.320 60.000 9.11 9.11 35.64 4.20
3119 4240 0.663568 GTCCACCAACTCTGTCGACG 60.664 60.000 11.62 6.07 0.00 5.12
3120 4241 0.820482 TCCACCAACTCTGTCGACGA 60.820 55.000 11.62 10.20 0.00 4.20
3121 4242 0.031585 CCACCAACTCTGTCGACGAA 59.968 55.000 11.62 0.00 0.00 3.85
3122 4243 1.409412 CACCAACTCTGTCGACGAAG 58.591 55.000 11.62 12.82 0.00 3.79
3123 4244 0.314302 ACCAACTCTGTCGACGAAGG 59.686 55.000 18.00 16.30 0.00 3.46
3124 4245 1.009389 CCAACTCTGTCGACGAAGGC 61.009 60.000 18.00 0.00 0.00 4.35
3125 4246 0.318699 CAACTCTGTCGACGAAGGCA 60.319 55.000 18.00 0.00 0.00 4.75
3126 4247 0.603569 AACTCTGTCGACGAAGGCAT 59.396 50.000 18.00 4.79 0.00 4.40
3127 4248 1.460504 ACTCTGTCGACGAAGGCATA 58.539 50.000 18.00 0.00 0.00 3.14
3128 4249 2.025155 ACTCTGTCGACGAAGGCATAT 58.975 47.619 18.00 0.00 0.00 1.78
3129 4250 2.427453 ACTCTGTCGACGAAGGCATATT 59.573 45.455 18.00 0.00 0.00 1.28
3130 4251 2.791560 CTCTGTCGACGAAGGCATATTG 59.208 50.000 11.62 0.00 0.00 1.90
3131 4252 2.165641 TCTGTCGACGAAGGCATATTGT 59.834 45.455 11.62 0.00 0.00 2.71
3132 4253 2.535984 CTGTCGACGAAGGCATATTGTC 59.464 50.000 11.62 0.00 0.00 3.18
3133 4254 2.165641 TGTCGACGAAGGCATATTGTCT 59.834 45.455 11.62 0.00 30.81 3.41
3134 4255 3.379057 TGTCGACGAAGGCATATTGTCTA 59.621 43.478 11.62 0.00 28.54 2.59
3135 4256 4.037565 TGTCGACGAAGGCATATTGTCTAT 59.962 41.667 11.62 0.00 28.54 1.98
3136 4257 4.617645 GTCGACGAAGGCATATTGTCTATC 59.382 45.833 0.00 0.00 28.54 2.08
3137 4258 3.921021 CGACGAAGGCATATTGTCTATCC 59.079 47.826 0.00 0.00 28.54 2.59
3138 4259 4.321304 CGACGAAGGCATATTGTCTATCCT 60.321 45.833 0.00 0.00 28.54 3.24
3139 4260 5.106277 CGACGAAGGCATATTGTCTATCCTA 60.106 44.000 0.00 0.00 28.54 2.94
3140 4261 6.404844 CGACGAAGGCATATTGTCTATCCTAT 60.405 42.308 0.00 0.00 28.54 2.57
3141 4262 7.201705 CGACGAAGGCATATTGTCTATCCTATA 60.202 40.741 0.00 0.00 28.54 1.31
3142 4263 8.540507 ACGAAGGCATATTGTCTATCCTATAT 57.459 34.615 0.00 0.00 28.54 0.86
3143 4264 8.417106 ACGAAGGCATATTGTCTATCCTATATG 58.583 37.037 0.00 0.00 28.54 1.78
3144 4265 8.633561 CGAAGGCATATTGTCTATCCTATATGA 58.366 37.037 0.00 0.00 34.43 2.15
3145 4266 9.757227 GAAGGCATATTGTCTATCCTATATGAC 57.243 37.037 0.00 0.00 38.63 3.06
3146 4267 9.499369 AAGGCATATTGTCTATCCTATATGACT 57.501 33.333 0.00 0.00 46.30 3.41
3147 4268 9.499369 AGGCATATTGTCTATCCTATATGACTT 57.501 33.333 0.00 0.00 43.45 3.01
3159 4280 7.477144 TCCTATATGACTTTATTGTTGCACG 57.523 36.000 0.00 0.00 0.00 5.34
3160 4281 7.045416 TCCTATATGACTTTATTGTTGCACGT 58.955 34.615 0.00 0.00 0.00 4.49
3161 4282 8.198778 TCCTATATGACTTTATTGTTGCACGTA 58.801 33.333 0.00 0.00 0.00 3.57
3162 4283 8.988934 CCTATATGACTTTATTGTTGCACGTAT 58.011 33.333 0.00 0.00 0.00 3.06
3163 4284 9.797473 CTATATGACTTTATTGTTGCACGTATG 57.203 33.333 0.00 0.00 0.00 2.39
3178 4299 5.511088 CACGTATGCTCGTTTTCTTACTT 57.489 39.130 0.00 0.00 42.27 2.24
3179 4300 5.912528 CACGTATGCTCGTTTTCTTACTTT 58.087 37.500 0.00 0.00 42.27 2.66
3180 4301 6.360329 CACGTATGCTCGTTTTCTTACTTTT 58.640 36.000 0.00 0.00 42.27 2.27
3181 4302 7.503991 CACGTATGCTCGTTTTCTTACTTTTA 58.496 34.615 0.00 0.00 42.27 1.52
3182 4303 8.166706 CACGTATGCTCGTTTTCTTACTTTTAT 58.833 33.333 0.00 0.00 42.27 1.40
3183 4304 8.715088 ACGTATGCTCGTTTTCTTACTTTTATT 58.285 29.630 0.00 0.00 41.37 1.40
3184 4305 9.537848 CGTATGCTCGTTTTCTTACTTTTATTT 57.462 29.630 0.00 0.00 0.00 1.40
3187 4308 8.056710 TGCTCGTTTTCTTACTTTTATTTTGC 57.943 30.769 0.00 0.00 0.00 3.68
3188 4309 7.168469 TGCTCGTTTTCTTACTTTTATTTTGCC 59.832 33.333 0.00 0.00 0.00 4.52
3189 4310 7.168469 GCTCGTTTTCTTACTTTTATTTTGCCA 59.832 33.333 0.00 0.00 0.00 4.92
3190 4311 8.568732 TCGTTTTCTTACTTTTATTTTGCCAG 57.431 30.769 0.00 0.00 0.00 4.85
3191 4312 8.407064 TCGTTTTCTTACTTTTATTTTGCCAGA 58.593 29.630 0.00 0.00 0.00 3.86
3192 4313 9.026074 CGTTTTCTTACTTTTATTTTGCCAGAA 57.974 29.630 0.00 0.00 0.00 3.02
3196 4317 9.691362 TTCTTACTTTTATTTTGCCAGAATGTC 57.309 29.630 0.00 0.00 0.00 3.06
3197 4318 8.303876 TCTTACTTTTATTTTGCCAGAATGTCC 58.696 33.333 0.00 0.00 0.00 4.02
3198 4319 6.418057 ACTTTTATTTTGCCAGAATGTCCA 57.582 33.333 0.00 0.00 0.00 4.02
3199 4320 7.008021 ACTTTTATTTTGCCAGAATGTCCAT 57.992 32.000 0.00 0.00 0.00 3.41
3200 4321 6.875195 ACTTTTATTTTGCCAGAATGTCCATG 59.125 34.615 0.00 0.00 0.00 3.66
3201 4322 5.999205 TTATTTTGCCAGAATGTCCATGT 57.001 34.783 0.00 0.00 0.00 3.21
3202 4323 4.895668 ATTTTGCCAGAATGTCCATGTT 57.104 36.364 0.00 0.00 0.00 2.71
3203 4324 4.686191 TTTTGCCAGAATGTCCATGTTT 57.314 36.364 0.00 0.00 0.00 2.83
3204 4325 3.663995 TTGCCAGAATGTCCATGTTTG 57.336 42.857 0.00 0.00 0.00 2.93
3205 4326 1.273048 TGCCAGAATGTCCATGTTTGC 59.727 47.619 0.00 0.00 0.00 3.68
3206 4327 1.547372 GCCAGAATGTCCATGTTTGCT 59.453 47.619 0.00 0.00 0.00 3.91
3207 4328 2.416431 GCCAGAATGTCCATGTTTGCTC 60.416 50.000 0.00 0.00 0.00 4.26
3208 4329 2.159476 CCAGAATGTCCATGTTTGCTCG 60.159 50.000 0.00 0.00 0.00 5.03
3209 4330 2.485426 CAGAATGTCCATGTTTGCTCGT 59.515 45.455 0.00 0.00 0.00 4.18
3210 4331 2.485426 AGAATGTCCATGTTTGCTCGTG 59.515 45.455 0.00 0.00 0.00 4.35
3211 4332 1.896220 ATGTCCATGTTTGCTCGTGT 58.104 45.000 0.00 0.00 0.00 4.49
3212 4333 0.943673 TGTCCATGTTTGCTCGTGTG 59.056 50.000 0.00 0.00 0.00 3.82
3213 4334 0.385974 GTCCATGTTTGCTCGTGTGC 60.386 55.000 0.00 0.00 0.00 4.57
3214 4335 0.817229 TCCATGTTTGCTCGTGTGCA 60.817 50.000 0.00 0.00 41.65 4.57
3215 4336 0.241749 CCATGTTTGCTCGTGTGCAT 59.758 50.000 0.00 0.00 42.96 3.96
3216 4337 1.609932 CATGTTTGCTCGTGTGCATC 58.390 50.000 0.00 0.00 42.96 3.91
3217 4338 1.198408 CATGTTTGCTCGTGTGCATCT 59.802 47.619 0.00 0.00 42.96 2.90
3218 4339 1.308047 TGTTTGCTCGTGTGCATCTT 58.692 45.000 0.00 0.00 42.96 2.40
3219 4340 2.488952 TGTTTGCTCGTGTGCATCTTA 58.511 42.857 0.00 0.00 42.96 2.10
3220 4341 2.480037 TGTTTGCTCGTGTGCATCTTAG 59.520 45.455 0.00 0.00 42.96 2.18
3221 4342 1.078709 TTGCTCGTGTGCATCTTAGC 58.921 50.000 0.00 0.00 42.96 3.09
3222 4343 0.247460 TGCTCGTGTGCATCTTAGCT 59.753 50.000 13.09 0.00 38.12 3.32
3223 4344 0.649475 GCTCGTGTGCATCTTAGCTG 59.351 55.000 0.00 0.00 34.99 4.24
3224 4345 2.001812 CTCGTGTGCATCTTAGCTGT 57.998 50.000 0.00 0.00 34.99 4.40
3225 4346 2.735444 GCTCGTGTGCATCTTAGCTGTA 60.735 50.000 0.00 0.00 34.99 2.74
3226 4347 2.854777 CTCGTGTGCATCTTAGCTGTAC 59.145 50.000 0.00 0.00 34.99 2.90
3227 4348 1.583856 CGTGTGCATCTTAGCTGTACG 59.416 52.381 0.00 0.00 32.62 3.67
3228 4349 1.927174 GTGTGCATCTTAGCTGTACGG 59.073 52.381 0.00 0.00 32.62 4.02
3229 4350 1.822371 TGTGCATCTTAGCTGTACGGA 59.178 47.619 5.68 0.00 32.62 4.69
3230 4351 2.159240 TGTGCATCTTAGCTGTACGGAG 60.159 50.000 5.68 0.00 32.62 4.63
3231 4352 1.409064 TGCATCTTAGCTGTACGGAGG 59.591 52.381 5.68 0.00 34.99 4.30
3232 4353 1.870167 GCATCTTAGCTGTACGGAGGC 60.870 57.143 5.68 0.00 0.00 4.70
3233 4354 1.683917 CATCTTAGCTGTACGGAGGCT 59.316 52.381 5.68 6.77 39.74 4.58
3234 4355 1.103803 TCTTAGCTGTACGGAGGCTG 58.896 55.000 5.68 0.00 37.50 4.85
3235 4356 0.103208 CTTAGCTGTACGGAGGCTGG 59.897 60.000 5.68 0.00 37.50 4.85
3236 4357 0.323999 TTAGCTGTACGGAGGCTGGA 60.324 55.000 5.68 0.00 37.50 3.86
3237 4358 0.106167 TAGCTGTACGGAGGCTGGAT 60.106 55.000 5.68 0.00 37.50 3.41
3238 4359 1.227380 GCTGTACGGAGGCTGGATG 60.227 63.158 5.68 0.00 0.00 3.51
3239 4360 1.961180 GCTGTACGGAGGCTGGATGT 61.961 60.000 5.68 0.00 0.00 3.06
3240 4361 0.537188 CTGTACGGAGGCTGGATGTT 59.463 55.000 0.00 0.00 0.00 2.71
3241 4362 0.249120 TGTACGGAGGCTGGATGTTG 59.751 55.000 0.00 0.00 0.00 3.33
3242 4363 1.090052 GTACGGAGGCTGGATGTTGC 61.090 60.000 0.00 0.00 0.00 4.17
3243 4364 1.264749 TACGGAGGCTGGATGTTGCT 61.265 55.000 0.00 0.00 0.00 3.91
3244 4365 1.817099 CGGAGGCTGGATGTTGCTC 60.817 63.158 0.00 0.00 0.00 4.26
3245 4366 1.300963 GGAGGCTGGATGTTGCTCA 59.699 57.895 0.00 0.00 0.00 4.26
3246 4367 0.106819 GGAGGCTGGATGTTGCTCAT 60.107 55.000 0.00 0.00 39.77 2.90
3260 4381 7.934855 ATGTTGCTCATCTTTCTTTGTATCT 57.065 32.000 0.00 0.00 29.76 1.98
3261 4382 7.137490 TGTTGCTCATCTTTCTTTGTATCTG 57.863 36.000 0.00 0.00 0.00 2.90
3262 4383 5.808042 TGCTCATCTTTCTTTGTATCTGC 57.192 39.130 0.00 0.00 0.00 4.26
3263 4384 5.494724 TGCTCATCTTTCTTTGTATCTGCT 58.505 37.500 0.00 0.00 0.00 4.24
3264 4385 5.942236 TGCTCATCTTTCTTTGTATCTGCTT 59.058 36.000 0.00 0.00 0.00 3.91
3265 4386 6.093219 TGCTCATCTTTCTTTGTATCTGCTTC 59.907 38.462 0.00 0.00 0.00 3.86
3266 4387 6.093219 GCTCATCTTTCTTTGTATCTGCTTCA 59.907 38.462 0.00 0.00 0.00 3.02
3267 4388 7.201714 GCTCATCTTTCTTTGTATCTGCTTCAT 60.202 37.037 0.00 0.00 0.00 2.57
3268 4389 7.982224 TCATCTTTCTTTGTATCTGCTTCATG 58.018 34.615 0.00 0.00 0.00 3.07
3269 4390 6.187125 TCTTTCTTTGTATCTGCTTCATGC 57.813 37.500 0.00 0.00 43.25 4.06
3270 4391 5.942236 TCTTTCTTTGTATCTGCTTCATGCT 59.058 36.000 0.00 0.00 43.37 3.79
3271 4392 7.105588 TCTTTCTTTGTATCTGCTTCATGCTA 58.894 34.615 0.00 0.00 43.37 3.49
3272 4393 6.668541 TTCTTTGTATCTGCTTCATGCTAC 57.331 37.500 0.00 0.00 43.37 3.58
3273 4394 5.733676 TCTTTGTATCTGCTTCATGCTACA 58.266 37.500 0.00 0.00 43.37 2.74
3274 4395 6.351711 TCTTTGTATCTGCTTCATGCTACAT 58.648 36.000 0.00 0.00 43.37 2.29
3275 4396 6.825213 TCTTTGTATCTGCTTCATGCTACATT 59.175 34.615 0.00 0.00 43.37 2.71
3276 4397 7.337689 TCTTTGTATCTGCTTCATGCTACATTT 59.662 33.333 0.00 0.00 43.37 2.32
3277 4398 6.367686 TGTATCTGCTTCATGCTACATTTG 57.632 37.500 0.00 0.00 43.37 2.32
3278 4399 4.913335 ATCTGCTTCATGCTACATTTGG 57.087 40.909 0.00 0.00 43.37 3.28
3279 4400 3.954200 TCTGCTTCATGCTACATTTGGA 58.046 40.909 0.00 0.00 43.37 3.53
3280 4401 3.943381 TCTGCTTCATGCTACATTTGGAG 59.057 43.478 0.00 0.00 43.37 3.86
3281 4402 3.689347 TGCTTCATGCTACATTTGGAGT 58.311 40.909 0.00 0.00 43.37 3.85
3282 4403 4.081406 TGCTTCATGCTACATTTGGAGTT 58.919 39.130 0.00 0.00 43.37 3.01
3283 4404 5.252547 TGCTTCATGCTACATTTGGAGTTA 58.747 37.500 0.00 0.00 43.37 2.24
3284 4405 5.709631 TGCTTCATGCTACATTTGGAGTTAA 59.290 36.000 0.00 0.00 43.37 2.01
3285 4406 6.377996 TGCTTCATGCTACATTTGGAGTTAAT 59.622 34.615 0.00 0.00 43.37 1.40
3286 4407 7.555914 TGCTTCATGCTACATTTGGAGTTAATA 59.444 33.333 0.00 0.00 43.37 0.98
3287 4408 8.405531 GCTTCATGCTACATTTGGAGTTAATAA 58.594 33.333 0.00 0.00 38.95 1.40
3291 4412 9.023967 CATGCTACATTTGGAGTTAATAAAAGC 57.976 33.333 0.00 0.00 0.00 3.51
3292 4413 7.247728 TGCTACATTTGGAGTTAATAAAAGCG 58.752 34.615 0.00 0.00 0.00 4.68
3293 4414 6.196538 GCTACATTTGGAGTTAATAAAAGCGC 59.803 38.462 0.00 0.00 0.00 5.92
3294 4415 5.407502 ACATTTGGAGTTAATAAAAGCGCC 58.592 37.500 2.29 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.896133 CCAGCGTGCATCATGGCC 61.896 66.667 0.00 0.00 0.00 5.36
68 69 3.855950 GGTCCTGTCAATTTACGTACTCG 59.144 47.826 0.00 0.00 43.34 4.18
265 290 2.483014 ACATTTACTTAGGCACGGCA 57.517 45.000 0.00 0.00 0.00 5.69
302 327 9.578439 GTTTATTAGTGGTAATTCTCTGTACGT 57.422 33.333 0.00 0.00 31.04 3.57
304 329 9.880157 TGGTTTATTAGTGGTAATTCTCTGTAC 57.120 33.333 0.00 0.00 31.04 2.90
318 392 4.402583 CGTGTGTGCATGGTTTATTAGTG 58.597 43.478 0.00 0.00 0.00 2.74
335 449 5.607119 AAATTAGCTACTTTCACCGTGTG 57.393 39.130 3.38 0.00 34.45 3.82
336 450 6.932960 AGTTAAATTAGCTACTTTCACCGTGT 59.067 34.615 11.91 0.00 0.00 4.49
369 494 3.557228 ATCATTGAGTTGAGCCTCTCC 57.443 47.619 0.00 0.00 32.50 3.71
376 501 5.392703 CCCATCACACAATCATTGAGTTGAG 60.393 44.000 3.79 8.95 32.03 3.02
377 502 4.460034 CCCATCACACAATCATTGAGTTGA 59.540 41.667 3.79 3.77 32.03 3.18
378 503 4.740268 CCCATCACACAATCATTGAGTTG 58.260 43.478 3.79 0.00 32.03 3.16
379 504 3.194116 GCCCATCACACAATCATTGAGTT 59.806 43.478 3.79 0.00 32.03 3.01
380 505 2.756760 GCCCATCACACAATCATTGAGT 59.243 45.455 3.79 0.00 34.76 3.41
470 604 1.738099 CACTGCACTGCCCGTACTC 60.738 63.158 0.00 0.00 0.00 2.59
471 605 2.343758 CACTGCACTGCCCGTACT 59.656 61.111 0.00 0.00 0.00 2.73
473 607 3.252627 ATGCACTGCACTGCCCGTA 62.253 57.895 14.65 0.00 43.04 4.02
474 608 4.648626 ATGCACTGCACTGCCCGT 62.649 61.111 14.65 0.10 43.04 5.28
475 609 4.111016 CATGCACTGCACTGCCCG 62.111 66.667 14.65 3.35 43.04 6.13
476 610 3.755628 CCATGCACTGCACTGCCC 61.756 66.667 14.65 0.00 43.04 5.36
477 611 3.755628 CCCATGCACTGCACTGCC 61.756 66.667 14.65 0.00 43.04 4.85
479 613 3.755628 GGCCCATGCACTGCACTG 61.756 66.667 5.67 6.21 43.04 3.66
552 705 1.502231 GTGTAGTGTGAGTGTGCAGG 58.498 55.000 0.00 0.00 0.00 4.85
559 712 2.551459 GGTGTAGACGTGTAGTGTGAGT 59.449 50.000 0.00 0.00 0.00 3.41
655 825 2.912956 ACATGAAAGGGGAACTGAGCTA 59.087 45.455 0.00 0.00 0.00 3.32
665 835 2.133281 TGATGAGCACATGAAAGGGG 57.867 50.000 0.00 0.00 36.82 4.79
736 914 8.502738 AGCAAAACCATTAATATAGAGGAGGAA 58.497 33.333 0.00 0.00 0.00 3.36
762 944 0.952010 GTAACAGGAAAGCCGCCGAA 60.952 55.000 0.00 0.00 39.96 4.30
859 1041 1.613925 GAGAGTGTGACAGTGGCTGTA 59.386 52.381 0.00 0.00 45.44 2.74
869 1057 0.878416 AGCGAGAGTGAGAGTGTGAC 59.122 55.000 0.00 0.00 0.00 3.67
874 1062 1.164411 CACTGAGCGAGAGTGAGAGT 58.836 55.000 6.91 0.00 43.04 3.24
876 1064 2.077627 GTACACTGAGCGAGAGTGAGA 58.922 52.381 16.64 4.65 43.04 3.27
878 1066 1.807142 CAGTACACTGAGCGAGAGTGA 59.193 52.381 16.64 1.96 46.59 3.41
880 1068 0.523966 GCAGTACACTGAGCGAGAGT 59.476 55.000 13.50 0.00 46.59 3.24
882 1070 0.893727 TGGCAGTACACTGAGCGAGA 60.894 55.000 13.50 0.00 46.59 4.04
885 1073 1.738099 GGTGGCAGTACACTGAGCG 60.738 63.158 13.50 0.00 46.59 5.03
886 1074 1.376037 GGGTGGCAGTACACTGAGC 60.376 63.158 13.50 3.00 46.59 4.26
888 1076 2.579657 CGGGGTGGCAGTACACTGA 61.580 63.158 13.50 0.00 46.59 3.41
890 1078 4.016706 GCGGGGTGGCAGTACACT 62.017 66.667 0.00 0.00 41.09 3.55
942 1150 2.917227 TGCAGCGAGTGGAGTGGA 60.917 61.111 0.00 0.00 0.00 4.02
1114 1336 2.227089 GAGTGGGTGTAGGCCGAGTG 62.227 65.000 0.00 0.00 0.00 3.51
1115 1337 1.982938 GAGTGGGTGTAGGCCGAGT 60.983 63.158 0.00 0.00 0.00 4.18
1116 1338 2.722201 GGAGTGGGTGTAGGCCGAG 61.722 68.421 0.00 0.00 0.00 4.63
1119 1341 2.609610 TGGGAGTGGGTGTAGGCC 60.610 66.667 0.00 0.00 0.00 5.19
1122 1344 2.670148 GGGCTGGGAGTGGGTGTAG 61.670 68.421 0.00 0.00 0.00 2.74
1335 1560 3.884774 TGGTGGTGCTGGTGGTCC 61.885 66.667 0.00 0.00 0.00 4.46
1412 1637 2.092055 CGCGATCGAATGTTGAAGTGAA 59.908 45.455 21.57 0.00 38.10 3.18
1414 1639 1.390123 ACGCGATCGAATGTTGAAGTG 59.610 47.619 21.57 0.00 39.41 3.16
1423 1648 1.202417 AGATCAACCACGCGATCGAAT 60.202 47.619 21.57 1.84 42.36 3.34
1450 1696 6.823182 TCTCAGTTTCTCACACATTTCTTCAA 59.177 34.615 0.00 0.00 0.00 2.69
1484 1730 4.651778 TCTCAATCACCAATTTCTTCCGT 58.348 39.130 0.00 0.00 0.00 4.69
1495 1741 3.576118 GGCTAGCTAGATCTCAATCACCA 59.424 47.826 25.15 0.00 34.07 4.17
1531 1792 6.824305 ACACATCAAGCATTTAAGTAAGCT 57.176 33.333 0.00 0.00 39.37 3.74
1532 1793 6.682863 CGTACACATCAAGCATTTAAGTAAGC 59.317 38.462 0.00 0.00 0.00 3.09
1682 1977 4.980805 TGCTTCACCACGACGCCC 62.981 66.667 0.00 0.00 38.10 6.13
1868 2181 2.048222 CCGCTCTTCTTGACGCCA 60.048 61.111 0.00 0.00 0.00 5.69
2348 2679 1.543208 GCCGCTAATGTGGATCATCCA 60.543 52.381 0.66 0.66 45.98 3.41
2349 2680 1.160137 GCCGCTAATGTGGATCATCC 58.840 55.000 0.00 0.00 46.34 3.51
2350 2681 1.532868 GTGCCGCTAATGTGGATCATC 59.467 52.381 0.00 0.00 46.34 2.92
2351 2682 1.597742 GTGCCGCTAATGTGGATCAT 58.402 50.000 0.00 0.00 46.34 2.45
2352 2683 0.809636 CGTGCCGCTAATGTGGATCA 60.810 55.000 0.00 0.00 46.34 2.92
2353 2684 0.529773 TCGTGCCGCTAATGTGGATC 60.530 55.000 0.00 0.00 46.34 3.36
2354 2685 0.810031 GTCGTGCCGCTAATGTGGAT 60.810 55.000 0.00 0.00 46.34 3.41
2355 2686 1.447140 GTCGTGCCGCTAATGTGGA 60.447 57.895 0.00 0.00 46.34 4.02
2356 2687 2.798501 CGTCGTGCCGCTAATGTGG 61.799 63.158 0.00 0.00 46.17 4.17
2357 2688 1.803922 TCGTCGTGCCGCTAATGTG 60.804 57.895 0.00 0.00 0.00 3.21
2358 2689 1.804326 GTCGTCGTGCCGCTAATGT 60.804 57.895 0.00 0.00 0.00 2.71
2359 2690 2.845739 CGTCGTCGTGCCGCTAATG 61.846 63.158 0.00 0.00 0.00 1.90
2367 2698 0.522705 TAAGCAGATCGTCGTCGTGC 60.523 55.000 7.78 7.78 37.02 5.34
2518 2858 3.767131 ACATTTTCAACTTATTCCCGGGG 59.233 43.478 23.50 6.77 0.00 5.73
2530 2871 8.801715 TTAAGCAGAAGATCAACATTTTCAAC 57.198 30.769 0.00 0.00 0.00 3.18
2542 2883 5.114780 TCAGCTCACATTAAGCAGAAGATC 58.885 41.667 0.00 0.00 42.35 2.75
2548 2890 3.692576 GCAATCAGCTCACATTAAGCAG 58.307 45.455 0.00 0.00 42.35 4.24
2552 2894 3.333804 TCACGCAATCAGCTCACATTAA 58.666 40.909 0.00 0.00 42.61 1.40
2554 2896 1.736126 CTCACGCAATCAGCTCACATT 59.264 47.619 0.00 0.00 42.61 2.71
2618 3717 2.227626 TGACTCTTCTCTTCACTCTGCG 59.772 50.000 0.00 0.00 0.00 5.18
2643 3742 3.258228 CCACTGTACGATACACATGCAA 58.742 45.455 0.00 0.00 34.46 4.08
2668 3767 4.477581 AGTACTCCTACTACCCACTGATGA 59.522 45.833 0.00 0.00 30.81 2.92
2682 3781 3.774766 TGACCTACCACGTAGTACTCCTA 59.225 47.826 0.00 0.00 41.61 2.94
2683 3782 2.573462 TGACCTACCACGTAGTACTCCT 59.427 50.000 0.00 0.00 41.61 3.69
2684 3783 2.991250 TGACCTACCACGTAGTACTCC 58.009 52.381 0.00 0.00 41.61 3.85
2685 3784 3.181502 GCTTGACCTACCACGTAGTACTC 60.182 52.174 0.00 0.00 41.61 2.59
2686 3785 2.751806 GCTTGACCTACCACGTAGTACT 59.248 50.000 0.00 0.00 41.61 2.73
2688 3787 1.739466 CGCTTGACCTACCACGTAGTA 59.261 52.381 0.00 0.00 41.61 1.82
2690 3789 0.806868 TCGCTTGACCTACCACGTAG 59.193 55.000 0.00 0.00 36.04 3.51
2691 3790 0.806868 CTCGCTTGACCTACCACGTA 59.193 55.000 0.00 0.00 0.00 3.57
2692 3791 1.177256 ACTCGCTTGACCTACCACGT 61.177 55.000 0.00 0.00 0.00 4.49
2693 3792 0.732880 CACTCGCTTGACCTACCACG 60.733 60.000 0.00 0.00 0.00 4.94
2694 3793 0.601558 TCACTCGCTTGACCTACCAC 59.398 55.000 0.00 0.00 0.00 4.16
2695 3794 0.888619 CTCACTCGCTTGACCTACCA 59.111 55.000 0.00 0.00 0.00 3.25
2696 3795 0.458716 GCTCACTCGCTTGACCTACC 60.459 60.000 0.00 0.00 0.00 3.18
2697 3796 0.528470 AGCTCACTCGCTTGACCTAC 59.472 55.000 0.00 0.00 36.74 3.18
2698 3797 2.962882 AGCTCACTCGCTTGACCTA 58.037 52.632 0.00 0.00 36.74 3.08
2699 3798 3.784573 AGCTCACTCGCTTGACCT 58.215 55.556 0.00 0.00 36.74 3.85
2728 3827 3.236896 TCACTCGTCCTTTACCTTTCCT 58.763 45.455 0.00 0.00 0.00 3.36
2839 3941 2.450243 GAGGTGAGGTGAGGGGGA 59.550 66.667 0.00 0.00 0.00 4.81
2895 4005 9.471702 AAAGATGAAACATGATAGAATGAAGGT 57.528 29.630 0.00 0.00 0.00 3.50
2920 4030 6.014156 TGTGGGAGGAAAAGAAAACAGAAAAA 60.014 34.615 0.00 0.00 0.00 1.94
2921 4031 5.482175 TGTGGGAGGAAAAGAAAACAGAAAA 59.518 36.000 0.00 0.00 0.00 2.29
2970 4090 4.526262 TGAACCGACAATTCCAATTCCAAT 59.474 37.500 0.00 0.00 0.00 3.16
2971 4091 3.891977 TGAACCGACAATTCCAATTCCAA 59.108 39.130 0.00 0.00 0.00 3.53
2972 4092 3.491342 TGAACCGACAATTCCAATTCCA 58.509 40.909 0.00 0.00 0.00 3.53
2973 4093 4.718940 ATGAACCGACAATTCCAATTCC 57.281 40.909 0.00 0.00 0.00 3.01
2974 4094 8.702163 AAATAATGAACCGACAATTCCAATTC 57.298 30.769 0.00 0.00 0.00 2.17
3001 4121 7.309744 GGTCTTAAACATGGATTGGTTTGATCA 60.310 37.037 0.00 0.00 36.41 2.92
3006 4126 5.278758 CGTGGTCTTAAACATGGATTGGTTT 60.279 40.000 0.00 0.00 36.41 3.27
3013 4133 1.434555 CGCGTGGTCTTAAACATGGA 58.565 50.000 0.00 0.00 0.00 3.41
3027 4148 0.094730 GCTTTAACCTACTGCGCGTG 59.905 55.000 8.43 3.52 0.00 5.34
3028 4149 1.349259 CGCTTTAACCTACTGCGCGT 61.349 55.000 8.43 6.51 40.15 6.01
3029 4150 1.343821 CGCTTTAACCTACTGCGCG 59.656 57.895 0.00 0.00 40.15 6.86
3031 4152 0.390735 ACCCGCTTTAACCTACTGCG 60.391 55.000 0.00 0.00 45.22 5.18
3046 4167 1.757118 TGAAATCTCTCTAGCCACCCG 59.243 52.381 0.00 0.00 0.00 5.28
3049 4170 4.679373 TGGATGAAATCTCTCTAGCCAC 57.321 45.455 0.00 0.00 44.71 5.01
3054 4175 6.813293 TCCATGTTGGATGAAATCTCTCTA 57.187 37.500 0.00 0.00 42.67 2.43
3077 4198 2.358322 TGTGATGATCATGCTGCCAT 57.642 45.000 14.30 0.00 0.00 4.40
3087 4208 1.138859 TGGTGGACCGATGTGATGATC 59.861 52.381 0.00 0.00 39.43 2.92
3095 4216 0.321671 ACAGAGTTGGTGGACCGATG 59.678 55.000 0.00 0.00 39.43 3.84
3106 4227 0.318699 TGCCTTCGTCGACAGAGTTG 60.319 55.000 17.16 7.27 0.00 3.16
3107 4228 0.603569 ATGCCTTCGTCGACAGAGTT 59.396 50.000 17.16 0.00 0.00 3.01
3108 4229 1.460504 TATGCCTTCGTCGACAGAGT 58.539 50.000 17.16 0.00 0.00 3.24
3109 4230 2.783828 ATATGCCTTCGTCGACAGAG 57.216 50.000 17.16 11.92 0.00 3.35
3110 4231 2.165641 ACAATATGCCTTCGTCGACAGA 59.834 45.455 17.16 10.99 0.00 3.41
3111 4232 2.535984 GACAATATGCCTTCGTCGACAG 59.464 50.000 17.16 6.13 0.00 3.51
3112 4233 2.165641 AGACAATATGCCTTCGTCGACA 59.834 45.455 17.16 0.00 0.00 4.35
3113 4234 2.810650 AGACAATATGCCTTCGTCGAC 58.189 47.619 5.18 5.18 0.00 4.20
3114 4235 4.321008 GGATAGACAATATGCCTTCGTCGA 60.321 45.833 0.00 0.00 0.00 4.20
3115 4236 3.921021 GGATAGACAATATGCCTTCGTCG 59.079 47.826 0.00 0.00 0.00 5.12
3116 4237 5.140747 AGGATAGACAATATGCCTTCGTC 57.859 43.478 0.00 0.00 0.00 4.20
3117 4238 6.859112 ATAGGATAGACAATATGCCTTCGT 57.141 37.500 0.00 0.00 0.00 3.85
3118 4239 8.633561 TCATATAGGATAGACAATATGCCTTCG 58.366 37.037 0.00 0.00 33.99 3.79
3119 4240 9.757227 GTCATATAGGATAGACAATATGCCTTC 57.243 37.037 0.00 0.00 33.99 3.46
3120 4241 9.499369 AGTCATATAGGATAGACAATATGCCTT 57.501 33.333 0.00 0.00 33.99 4.35
3121 4242 9.499369 AAGTCATATAGGATAGACAATATGCCT 57.501 33.333 0.00 0.00 33.99 4.75
3133 4254 9.203421 CGTGCAACAATAAAGTCATATAGGATA 57.797 33.333 0.00 0.00 35.74 2.59
3134 4255 7.715249 ACGTGCAACAATAAAGTCATATAGGAT 59.285 33.333 0.00 0.00 35.74 3.24
3135 4256 7.045416 ACGTGCAACAATAAAGTCATATAGGA 58.955 34.615 0.00 0.00 35.74 2.94
3136 4257 7.246674 ACGTGCAACAATAAAGTCATATAGG 57.753 36.000 0.00 0.00 35.74 2.57
3137 4258 9.797473 CATACGTGCAACAATAAAGTCATATAG 57.203 33.333 0.00 0.00 35.74 1.31
3156 4277 5.511088 AAGTAAGAAAACGAGCATACGTG 57.489 39.130 0.00 0.00 45.83 4.49
3158 4279 9.537848 AAATAAAAGTAAGAAAACGAGCATACG 57.462 29.630 0.00 0.00 39.31 3.06
3161 4282 8.699749 GCAAAATAAAAGTAAGAAAACGAGCAT 58.300 29.630 0.00 0.00 0.00 3.79
3162 4283 7.168469 GGCAAAATAAAAGTAAGAAAACGAGCA 59.832 33.333 0.00 0.00 0.00 4.26
3163 4284 7.168469 TGGCAAAATAAAAGTAAGAAAACGAGC 59.832 33.333 0.00 0.00 0.00 5.03
3164 4285 8.568732 TGGCAAAATAAAAGTAAGAAAACGAG 57.431 30.769 0.00 0.00 0.00 4.18
3165 4286 8.407064 TCTGGCAAAATAAAAGTAAGAAAACGA 58.593 29.630 0.00 0.00 0.00 3.85
3166 4287 8.568732 TCTGGCAAAATAAAAGTAAGAAAACG 57.431 30.769 0.00 0.00 0.00 3.60
3170 4291 9.691362 GACATTCTGGCAAAATAAAAGTAAGAA 57.309 29.630 0.00 0.00 0.00 2.52
3171 4292 8.303876 GGACATTCTGGCAAAATAAAAGTAAGA 58.696 33.333 0.00 0.00 0.00 2.10
3172 4293 8.087750 TGGACATTCTGGCAAAATAAAAGTAAG 58.912 33.333 0.00 0.00 0.00 2.34
3173 4294 7.957002 TGGACATTCTGGCAAAATAAAAGTAA 58.043 30.769 0.00 0.00 0.00 2.24
3174 4295 7.531857 TGGACATTCTGGCAAAATAAAAGTA 57.468 32.000 0.00 0.00 0.00 2.24
3175 4296 6.418057 TGGACATTCTGGCAAAATAAAAGT 57.582 33.333 0.00 0.00 0.00 2.66
3176 4297 6.875195 ACATGGACATTCTGGCAAAATAAAAG 59.125 34.615 0.00 0.00 0.00 2.27
3177 4298 6.767456 ACATGGACATTCTGGCAAAATAAAA 58.233 32.000 0.00 0.00 0.00 1.52
3178 4299 6.357579 ACATGGACATTCTGGCAAAATAAA 57.642 33.333 0.00 0.00 0.00 1.40
3179 4300 5.999205 ACATGGACATTCTGGCAAAATAA 57.001 34.783 0.00 0.00 0.00 1.40
3180 4301 5.999205 AACATGGACATTCTGGCAAAATA 57.001 34.783 0.00 0.00 0.00 1.40
3181 4302 4.895668 AACATGGACATTCTGGCAAAAT 57.104 36.364 0.00 0.00 0.00 1.82
3182 4303 4.378774 CAAACATGGACATTCTGGCAAAA 58.621 39.130 0.00 0.00 0.00 2.44
3183 4304 3.803021 GCAAACATGGACATTCTGGCAAA 60.803 43.478 0.00 0.00 0.00 3.68
3184 4305 2.288948 GCAAACATGGACATTCTGGCAA 60.289 45.455 0.00 0.00 0.00 4.52
3185 4306 1.273048 GCAAACATGGACATTCTGGCA 59.727 47.619 0.00 0.00 0.00 4.92
3186 4307 1.547372 AGCAAACATGGACATTCTGGC 59.453 47.619 0.00 0.00 0.00 4.85
3187 4308 2.159476 CGAGCAAACATGGACATTCTGG 60.159 50.000 0.00 0.00 0.00 3.86
3188 4309 2.485426 ACGAGCAAACATGGACATTCTG 59.515 45.455 0.00 0.00 0.00 3.02
3189 4310 2.485426 CACGAGCAAACATGGACATTCT 59.515 45.455 0.00 0.00 0.00 2.40
3190 4311 2.226437 ACACGAGCAAACATGGACATTC 59.774 45.455 0.00 0.00 0.00 2.67
3191 4312 2.030893 CACACGAGCAAACATGGACATT 60.031 45.455 0.00 0.00 0.00 2.71
3192 4313 1.536766 CACACGAGCAAACATGGACAT 59.463 47.619 0.00 0.00 0.00 3.06
3193 4314 0.943673 CACACGAGCAAACATGGACA 59.056 50.000 0.00 0.00 0.00 4.02
3194 4315 0.385974 GCACACGAGCAAACATGGAC 60.386 55.000 0.00 0.00 0.00 4.02
3195 4316 0.817229 TGCACACGAGCAAACATGGA 60.817 50.000 0.00 0.00 42.46 3.41
3196 4317 1.653667 TGCACACGAGCAAACATGG 59.346 52.632 0.00 0.00 42.46 3.66
3204 4325 0.649475 CAGCTAAGATGCACACGAGC 59.351 55.000 0.00 1.59 34.99 5.03
3205 4326 2.001812 ACAGCTAAGATGCACACGAG 57.998 50.000 0.00 0.00 34.99 4.18
3206 4327 2.731027 CGTACAGCTAAGATGCACACGA 60.731 50.000 0.00 0.00 36.49 4.35
3207 4328 1.583856 CGTACAGCTAAGATGCACACG 59.416 52.381 0.00 0.00 34.99 4.49
3208 4329 1.927174 CCGTACAGCTAAGATGCACAC 59.073 52.381 0.00 0.00 34.99 3.82
3209 4330 1.822371 TCCGTACAGCTAAGATGCACA 59.178 47.619 0.00 0.00 34.99 4.57
3210 4331 2.464865 CTCCGTACAGCTAAGATGCAC 58.535 52.381 0.00 0.00 34.99 4.57
3211 4332 1.409064 CCTCCGTACAGCTAAGATGCA 59.591 52.381 0.00 0.00 34.99 3.96
3212 4333 1.870167 GCCTCCGTACAGCTAAGATGC 60.870 57.143 0.00 0.00 0.00 3.91
3213 4334 1.683917 AGCCTCCGTACAGCTAAGATG 59.316 52.381 0.00 0.00 34.38 2.90
3214 4335 1.683917 CAGCCTCCGTACAGCTAAGAT 59.316 52.381 0.00 0.00 34.38 2.40
3215 4336 1.103803 CAGCCTCCGTACAGCTAAGA 58.896 55.000 0.00 0.00 34.38 2.10
3216 4337 0.103208 CCAGCCTCCGTACAGCTAAG 59.897 60.000 0.00 0.00 34.38 2.18
3217 4338 0.323999 TCCAGCCTCCGTACAGCTAA 60.324 55.000 0.00 0.00 34.38 3.09
3218 4339 0.106167 ATCCAGCCTCCGTACAGCTA 60.106 55.000 0.00 0.00 34.38 3.32
3219 4340 1.381872 ATCCAGCCTCCGTACAGCT 60.382 57.895 0.00 0.00 37.32 4.24
3220 4341 1.227380 CATCCAGCCTCCGTACAGC 60.227 63.158 0.00 0.00 0.00 4.40
3221 4342 0.537188 AACATCCAGCCTCCGTACAG 59.463 55.000 0.00 0.00 0.00 2.74
3222 4343 0.249120 CAACATCCAGCCTCCGTACA 59.751 55.000 0.00 0.00 0.00 2.90
3223 4344 1.090052 GCAACATCCAGCCTCCGTAC 61.090 60.000 0.00 0.00 0.00 3.67
3224 4345 1.220749 GCAACATCCAGCCTCCGTA 59.779 57.895 0.00 0.00 0.00 4.02
3225 4346 2.045926 GCAACATCCAGCCTCCGT 60.046 61.111 0.00 0.00 0.00 4.69
3226 4347 1.817099 GAGCAACATCCAGCCTCCG 60.817 63.158 0.00 0.00 0.00 4.63
3227 4348 0.106819 ATGAGCAACATCCAGCCTCC 60.107 55.000 0.00 0.00 33.46 4.30
3228 4349 1.307097 GATGAGCAACATCCAGCCTC 58.693 55.000 11.25 0.00 46.78 4.70
3229 4350 3.491208 GATGAGCAACATCCAGCCT 57.509 52.632 11.25 0.00 46.78 4.58
3236 4357 7.627939 GCAGATACAAAGAAAGATGAGCAACAT 60.628 37.037 0.00 0.00 42.47 2.71
3237 4358 6.348786 GCAGATACAAAGAAAGATGAGCAACA 60.349 38.462 0.00 0.00 0.00 3.33
3238 4359 6.026513 GCAGATACAAAGAAAGATGAGCAAC 58.973 40.000 0.00 0.00 0.00 4.17
3239 4360 5.942236 AGCAGATACAAAGAAAGATGAGCAA 59.058 36.000 0.00 0.00 0.00 3.91
3240 4361 5.494724 AGCAGATACAAAGAAAGATGAGCA 58.505 37.500 0.00 0.00 0.00 4.26
3241 4362 6.093219 TGAAGCAGATACAAAGAAAGATGAGC 59.907 38.462 0.00 0.00 0.00 4.26
3242 4363 7.606858 TGAAGCAGATACAAAGAAAGATGAG 57.393 36.000 0.00 0.00 0.00 2.90
3243 4364 7.414873 GCATGAAGCAGATACAAAGAAAGATGA 60.415 37.037 0.00 0.00 44.79 2.92
3244 4365 6.691818 GCATGAAGCAGATACAAAGAAAGATG 59.308 38.462 0.00 0.00 44.79 2.90
3245 4366 6.793349 GCATGAAGCAGATACAAAGAAAGAT 58.207 36.000 0.00 0.00 44.79 2.40
3246 4367 6.187125 GCATGAAGCAGATACAAAGAAAGA 57.813 37.500 0.00 0.00 44.79 2.52
3261 4382 4.708726 AACTCCAAATGTAGCATGAAGC 57.291 40.909 0.00 0.00 46.19 3.86
3265 4386 9.023967 GCTTTTATTAACTCCAAATGTAGCATG 57.976 33.333 0.00 0.00 0.00 4.06
3266 4387 7.915397 CGCTTTTATTAACTCCAAATGTAGCAT 59.085 33.333 0.00 0.00 0.00 3.79
3267 4388 7.247728 CGCTTTTATTAACTCCAAATGTAGCA 58.752 34.615 0.00 0.00 0.00 3.49
3268 4389 6.196538 GCGCTTTTATTAACTCCAAATGTAGC 59.803 38.462 0.00 0.00 0.00 3.58
3269 4390 6.691388 GGCGCTTTTATTAACTCCAAATGTAG 59.309 38.462 7.64 0.00 0.00 2.74
3270 4391 6.557110 GGCGCTTTTATTAACTCCAAATGTA 58.443 36.000 7.64 0.00 0.00 2.29
3271 4392 5.407502 GGCGCTTTTATTAACTCCAAATGT 58.592 37.500 7.64 0.00 0.00 2.71
3272 4393 5.949233 GGCGCTTTTATTAACTCCAAATG 57.051 39.130 7.64 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.