Multiple sequence alignment - TraesCS6A01G315700

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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 TraesCS6A01G315700 chr6A 100.000 3156 0 0 1 3156 552263687 552266842 0.000000e+00 5829.0
1 TraesCS6A01G315700 chr6A 100.000 401 0 0 3395 3795 552267081 552267481 0.000000e+00 741.0
2 TraesCS6A01G315700 chr6B 90.984 2440 99 49 642 3013 609886124 609888510 0.000000e+00 3175.0
3 TraesCS6A01G315700 chr6B 88.832 197 18 2 3603 3795 609888661 609888857 4.900000e-59 239.0
4 TraesCS6A01G315700 chr6D 91.011 2325 75 51 750 3017 405672402 405674649 0.000000e+00 3013.0
5 TraesCS6A01G315700 chr6D 95.345 537 24 1 1 536 144616519 144617055 0.000000e+00 852.0
6 TraesCS6A01G315700 chr6D 93.810 210 12 1 537 745 405671997 405672206 7.910000e-82 315.0
7 TraesCS6A01G315700 chr1A 96.269 536 20 0 1 536 62138170 62137635 0.000000e+00 880.0
8 TraesCS6A01G315700 chr2B 96.089 537 19 2 1 536 765796769 765797304 0.000000e+00 874.0
9 TraesCS6A01G315700 chr5A 95.896 536 22 0 1 536 487616530 487615995 0.000000e+00 869.0
10 TraesCS6A01G315700 chr5A 85.714 77 11 0 2036 2112 462145666 462145742 8.740000e-12 82.4
11 TraesCS6A01G315700 chr4D 95.345 537 23 2 1 536 339397071 339396536 0.000000e+00 852.0
12 TraesCS6A01G315700 chr4A 95.345 537 23 2 1 536 460501598 460502133 0.000000e+00 852.0
13 TraesCS6A01G315700 chr5D 94.972 537 26 1 1 536 548043758 548044294 0.000000e+00 841.0
14 TraesCS6A01G315700 chr5D 94.796 538 26 1 1 536 90145714 90146251 0.000000e+00 837.0
15 TraesCS6A01G315700 chr5D 84.524 84 13 0 2036 2119 361606928 361607011 2.430000e-12 84.2
16 TraesCS6A01G315700 chr2A 94.776 536 28 0 1 536 765577363 765576828 0.000000e+00 835.0
17 TraesCS6A01G315700 chr2A 91.892 74 6 0 3083 3156 667011876 667011949 1.860000e-18 104.0
18 TraesCS6A01G315700 chr5B 91.781 73 6 0 3083 3155 490235508 490235580 6.710000e-18 102.0
19 TraesCS6A01G315700 chr5B 86.441 59 8 0 2036 2094 427239252 427239310 8.800000e-07 65.8


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 TraesCS6A01G315700 chr6A 552263687 552267481 3794 False 3285 5829 100.0000 1 3795 2 chr6A.!!$F1 3794
1 TraesCS6A01G315700 chr6B 609886124 609888857 2733 False 1707 3175 89.9080 642 3795 2 chr6B.!!$F1 3153
2 TraesCS6A01G315700 chr6D 405671997 405674649 2652 False 1664 3013 92.4105 537 3017 2 chr6D.!!$F2 2480
3 TraesCS6A01G315700 chr6D 144616519 144617055 536 False 852 852 95.3450 1 536 1 chr6D.!!$F1 535
4 TraesCS6A01G315700 chr1A 62137635 62138170 535 True 880 880 96.2690 1 536 1 chr1A.!!$R1 535
5 TraesCS6A01G315700 chr2B 765796769 765797304 535 False 874 874 96.0890 1 536 1 chr2B.!!$F1 535
6 TraesCS6A01G315700 chr5A 487615995 487616530 535 True 869 869 95.8960 1 536 1 chr5A.!!$R1 535
7 TraesCS6A01G315700 chr4D 339396536 339397071 535 True 852 852 95.3450 1 536 1 chr4D.!!$R1 535
8 TraesCS6A01G315700 chr4A 460501598 460502133 535 False 852 852 95.3450 1 536 1 chr4A.!!$F1 535
9 TraesCS6A01G315700 chr5D 548043758 548044294 536 False 841 841 94.9720 1 536 1 chr5D.!!$F3 535
10 TraesCS6A01G315700 chr5D 90145714 90146251 537 False 837 837 94.7960 1 536 1 chr5D.!!$F1 535
11 TraesCS6A01G315700 chr2A 765576828 765577363 535 True 835 835 94.7760 1 536 1 chr2A.!!$R1 535

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
582 585 0.039618 TTCAAGGAATGGCAGGGGTC 59.960 55.0 0.00 0.0 0.0 4.46 F
1257 1462 0.036388 CAAGAAGAGGCGGCCAACTA 60.036 55.0 23.09 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2711 0.320683 TGGAACAGAGTGCGGATGTG 60.321 55.0 0.0 0.0 0.0 3.21 R
3092 3380 0.995803 AGCCCCTTCCTTCTCCTTTC 59.004 55.0 0.0 0.0 0.0 2.62 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
106 107 6.099269 TGGAATTTCCGTTTCTACTATAGGCT 59.901 38.462 10.79 0.00 40.17 4.58
151 152 4.734398 ACCAAACAACACACAATGACAT 57.266 36.364 0.00 0.00 0.00 3.06
209 210 3.879295 ACTTCCACACACATTCTCAACTG 59.121 43.478 0.00 0.00 0.00 3.16
415 416 1.469703 TCGCTCCGTATCTGTTTTCGA 59.530 47.619 0.00 0.00 0.00 3.71
506 509 9.855021 GAAAACAAATATGGTAGCATACAGTTT 57.145 29.630 22.39 22.39 45.43 2.66
574 577 7.623770 CATTTTTATGCGATTTCAAGGAATGG 58.376 34.615 0.00 0.00 0.00 3.16
575 578 2.877043 ATGCGATTTCAAGGAATGGC 57.123 45.000 1.57 1.57 40.02 4.40
582 585 0.039618 TTCAAGGAATGGCAGGGGTC 59.960 55.000 0.00 0.00 0.00 4.46
588 591 3.721370 AATGGCAGGGGTCATCGGC 62.721 63.158 0.00 0.00 38.73 5.54
592 595 2.700773 GCAGGGGTCATCGGCAAAC 61.701 63.158 0.00 0.00 0.00 2.93
603 606 3.627123 TCATCGGCAAACTTCCATACATG 59.373 43.478 0.00 0.00 0.00 3.21
626 629 0.366871 CAGAGCCGATTTGACGAACG 59.633 55.000 0.00 0.00 35.09 3.95
628 631 0.093026 GAGCCGATTTGACGAACGTG 59.907 55.000 4.19 0.00 35.09 4.49
691 695 5.971895 ATTGCATTTTACGATTTCATGGC 57.028 34.783 0.00 0.00 0.00 4.40
745 750 4.242475 TCGTGAAAGTCGAGTGCAATTAT 58.758 39.130 0.00 0.00 33.38 1.28
746 751 4.091365 TCGTGAAAGTCGAGTGCAATTATG 59.909 41.667 0.00 0.00 33.38 1.90
748 753 3.126858 TGAAAGTCGAGTGCAATTATGGC 59.873 43.478 0.00 0.00 0.00 4.40
778 974 2.260639 ATATCTCCTGCCCCATCGAT 57.739 50.000 0.00 0.00 0.00 3.59
909 1106 0.250513 ACTTGCATCCGTCCTTCCTC 59.749 55.000 0.00 0.00 0.00 3.71
982 1181 0.179124 CTGAGCGTGACCTAGCTTCC 60.179 60.000 0.00 0.00 44.69 3.46
1030 1229 3.214328 TCTTCTTGTTCTTGGCTTCACC 58.786 45.455 0.00 0.00 39.84 4.02
1038 1237 0.673644 CTTGGCTTCACCGGGTAGTG 60.674 60.000 6.32 0.00 43.94 2.74
1040 1239 2.590114 GGCTTCACCGGGTAGTGGT 61.590 63.158 6.32 0.00 41.47 4.16
1204 1403 2.486504 CGCGGCATCAGCATTGTT 59.513 55.556 0.00 0.00 44.61 2.83
1248 1453 0.957888 GTGGTGCTCCAAGAAGAGGC 60.958 60.000 9.53 0.00 46.15 4.70
1250 1455 1.743252 GTGCTCCAAGAAGAGGCGG 60.743 63.158 0.00 0.00 34.26 6.13
1253 1458 2.927856 TCCAAGAAGAGGCGGCCA 60.928 61.111 23.09 0.00 0.00 5.36
1254 1459 2.034066 CCAAGAAGAGGCGGCCAA 59.966 61.111 23.09 0.00 0.00 4.52
1256 1461 1.302832 CAAGAAGAGGCGGCCAACT 60.303 57.895 23.09 16.72 0.00 3.16
1257 1462 0.036388 CAAGAAGAGGCGGCCAACTA 60.036 55.000 23.09 0.00 0.00 2.24
1576 1793 2.202743 CACGACGCATCATCGGGT 60.203 61.111 0.00 0.00 43.95 5.28
1597 1814 0.234884 GTACACCTTTCACTGTGCGC 59.765 55.000 0.00 0.00 35.90 6.09
1817 2057 2.751036 TCCCCATGCATGCACACG 60.751 61.111 25.37 14.44 0.00 4.49
2018 2258 5.670792 AATCAATCAATGGCATGTTCTGT 57.329 34.783 0.00 0.00 0.00 3.41
2108 2348 4.586618 CAGCTACTGCAGTCGCTT 57.413 55.556 35.61 21.67 43.34 4.68
2114 2354 2.507110 TACTGCAGTCGCTTGAGGCC 62.507 60.000 25.56 0.00 39.64 5.19
2188 2434 0.251077 ACGTTCCCTCAGTACTCCGT 60.251 55.000 0.00 0.00 0.00 4.69
2290 2557 1.069765 CGAGTGTGAAGGTGCTGGT 59.930 57.895 0.00 0.00 0.00 4.00
2444 2711 2.353889 CAGACACATTACTCTGCCATGC 59.646 50.000 0.00 0.00 0.00 4.06
2465 2732 1.012086 CATCCGCACTCTGTTCCATG 58.988 55.000 0.00 0.00 0.00 3.66
2466 2733 0.745845 ATCCGCACTCTGTTCCATGC 60.746 55.000 0.00 0.00 34.66 4.06
2467 2734 2.401766 CCGCACTCTGTTCCATGCC 61.402 63.158 0.00 0.00 34.49 4.40
2468 2735 2.743752 CGCACTCTGTTCCATGCCG 61.744 63.158 0.00 0.00 34.49 5.69
2469 2736 1.672356 GCACTCTGTTCCATGCCGT 60.672 57.895 0.00 0.00 31.71 5.68
2470 2737 1.915614 GCACTCTGTTCCATGCCGTG 61.916 60.000 0.00 0.00 31.71 4.94
2471 2738 1.672356 ACTCTGTTCCATGCCGTGC 60.672 57.895 0.00 0.00 0.00 5.34
2472 2739 1.672030 CTCTGTTCCATGCCGTGCA 60.672 57.895 1.01 1.01 44.86 4.57
2473 2740 1.642037 CTCTGTTCCATGCCGTGCAG 61.642 60.000 4.90 0.00 43.65 4.41
2474 2741 2.672651 TGTTCCATGCCGTGCAGG 60.673 61.111 0.00 0.00 43.65 4.85
2503 2770 2.536130 CCGTGATTAAATGACGCCGTTC 60.536 50.000 0.00 0.00 38.57 3.95
2697 2973 1.813753 CGTGCATGGGTAACTCCGG 60.814 63.158 0.00 0.00 37.00 5.14
2698 2974 2.112815 GTGCATGGGTAACTCCGGC 61.113 63.158 0.00 0.00 37.00 6.13
2699 2975 2.516225 GCATGGGTAACTCCGGCC 60.516 66.667 0.00 0.00 37.00 6.13
2700 2976 2.203015 CATGGGTAACTCCGGCCG 60.203 66.667 21.04 21.04 37.00 6.13
2885 3173 4.041740 CGTTCATCACCGGATAAGAAGA 57.958 45.455 9.46 0.00 30.87 2.87
2886 3174 4.430007 CGTTCATCACCGGATAAGAAGAA 58.570 43.478 9.46 6.50 30.87 2.52
2901 3189 2.019984 GAAGAACCATGGAGATGTGGC 58.980 52.381 21.47 0.00 39.13 5.01
2917 3205 2.677228 GCTCCCTGGCTGGCTTAA 59.323 61.111 4.64 0.00 0.00 1.85
2919 3207 1.077429 CTCCCTGGCTGGCTTAACC 60.077 63.158 4.64 0.00 39.84 2.85
2999 3287 7.595130 TCAACGATCATGTATGTAGAATAGTGC 59.405 37.037 0.00 0.00 0.00 4.40
3013 3301 3.492102 ATAGTGCTGTGTTCTTGGTGT 57.508 42.857 0.00 0.00 0.00 4.16
3017 3305 0.814010 GCTGTGTTCTTGGTGTCCGT 60.814 55.000 0.00 0.00 0.00 4.69
3019 3307 1.597663 CTGTGTTCTTGGTGTCCGTTC 59.402 52.381 0.00 0.00 0.00 3.95
3020 3308 1.066071 TGTGTTCTTGGTGTCCGTTCA 60.066 47.619 0.00 0.00 0.00 3.18
3021 3309 1.329599 GTGTTCTTGGTGTCCGTTCAC 59.670 52.381 0.00 0.00 37.57 3.18
3023 3311 2.218603 GTTCTTGGTGTCCGTTCACAT 58.781 47.619 8.92 0.00 39.76 3.21
3024 3312 2.616842 GTTCTTGGTGTCCGTTCACATT 59.383 45.455 8.92 0.00 39.76 2.71
3025 3313 3.755112 TCTTGGTGTCCGTTCACATTA 57.245 42.857 8.92 0.00 39.76 1.90
3026 3314 3.659786 TCTTGGTGTCCGTTCACATTAG 58.340 45.455 8.92 3.98 39.76 1.73
3028 3316 3.478857 TGGTGTCCGTTCACATTAGTT 57.521 42.857 8.92 0.00 39.76 2.24
3029 3317 4.603989 TGGTGTCCGTTCACATTAGTTA 57.396 40.909 8.92 0.00 39.76 2.24
3030 3318 4.958509 TGGTGTCCGTTCACATTAGTTAA 58.041 39.130 8.92 0.00 39.76 2.01
3031 3319 5.366460 TGGTGTCCGTTCACATTAGTTAAA 58.634 37.500 8.92 0.00 39.76 1.52
3032 3320 5.998981 TGGTGTCCGTTCACATTAGTTAAAT 59.001 36.000 8.92 0.00 39.76 1.40
3034 3322 6.148150 GGTGTCCGTTCACATTAGTTAAATGA 59.852 38.462 4.82 0.00 46.81 2.57
3035 3323 7.013529 GTGTCCGTTCACATTAGTTAAATGAC 58.986 38.462 4.82 0.00 46.81 3.06
3038 3326 8.234546 GTCCGTTCACATTAGTTAAATGACAAT 58.765 33.333 4.82 0.00 46.81 2.71
3040 3328 8.849490 CCGTTCACATTAGTTAAATGACAATTG 58.151 33.333 3.24 3.24 46.81 2.32
3041 3329 9.605955 CGTTCACATTAGTTAAATGACAATTGA 57.394 29.630 13.59 0.00 46.81 2.57
3060 3348 8.992073 ACAATTGACTGAATTTCAAATTAAGCC 58.008 29.630 13.59 0.00 36.57 4.35
3061 3349 8.445493 CAATTGACTGAATTTCAAATTAAGCCC 58.555 33.333 7.10 1.23 36.57 5.19
3062 3350 6.662865 TGACTGAATTTCAAATTAAGCCCA 57.337 33.333 7.10 3.59 0.00 5.36
3064 3352 6.267471 TGACTGAATTTCAAATTAAGCCCAGT 59.733 34.615 11.89 11.89 34.34 4.00
3067 3355 7.060383 TGAATTTCAAATTAAGCCCAGTCAA 57.940 32.000 0.00 0.00 0.00 3.18
3068 3356 7.678837 TGAATTTCAAATTAAGCCCAGTCAAT 58.321 30.769 0.00 0.00 0.00 2.57
3069 3357 8.156165 TGAATTTCAAATTAAGCCCAGTCAATT 58.844 29.630 0.00 0.00 0.00 2.32
3070 3358 8.922931 AATTTCAAATTAAGCCCAGTCAATTT 57.077 26.923 0.00 0.00 32.29 1.82
3071 3359 8.922931 ATTTCAAATTAAGCCCAGTCAATTTT 57.077 26.923 0.00 0.00 30.27 1.82
3072 3360 8.744568 TTTCAAATTAAGCCCAGTCAATTTTT 57.255 26.923 0.00 0.00 30.27 1.94
3102 3390 2.682155 CGGAGGGAAGAAAGGAGAAG 57.318 55.000 0.00 0.00 0.00 2.85
3103 3391 1.208293 CGGAGGGAAGAAAGGAGAAGG 59.792 57.143 0.00 0.00 0.00 3.46
3104 3392 2.552367 GGAGGGAAGAAAGGAGAAGGA 58.448 52.381 0.00 0.00 0.00 3.36
3106 3394 3.054728 GGAGGGAAGAAAGGAGAAGGAAG 60.055 52.174 0.00 0.00 0.00 3.46
3107 3395 2.916269 AGGGAAGAAAGGAGAAGGAAGG 59.084 50.000 0.00 0.00 0.00 3.46
3108 3396 2.025793 GGGAAGAAAGGAGAAGGAAGGG 60.026 54.545 0.00 0.00 0.00 3.95
3110 3398 0.995803 AGAAAGGAGAAGGAAGGGGC 59.004 55.000 0.00 0.00 0.00 5.80
3111 3399 0.995803 GAAAGGAGAAGGAAGGGGCT 59.004 55.000 0.00 0.00 0.00 5.19
3112 3400 0.995803 AAAGGAGAAGGAAGGGGCTC 59.004 55.000 0.00 0.00 0.00 4.70
3113 3401 1.268283 AAGGAGAAGGAAGGGGCTCG 61.268 60.000 0.00 0.00 0.00 5.03
3114 3402 2.188207 GAGAAGGAAGGGGCTCGC 59.812 66.667 0.00 0.00 0.00 5.03
3115 3403 3.393149 GAGAAGGAAGGGGCTCGCC 62.393 68.421 0.00 0.00 0.00 5.54
3116 3404 4.840005 GAAGGAAGGGGCTCGCCG 62.840 72.222 1.24 0.00 36.85 6.46
3126 3414 4.874977 GCTCGCCGGAGTGCTACC 62.875 72.222 22.65 0.00 42.53 3.18
3127 3415 4.208686 CTCGCCGGAGTGCTACCC 62.209 72.222 5.05 0.00 35.48 3.69
3134 3422 1.002087 CCGGAGTGCTACCCCATTATC 59.998 57.143 0.00 0.00 0.00 1.75
3136 3424 3.162666 CGGAGTGCTACCCCATTATCTA 58.837 50.000 0.00 0.00 0.00 1.98
3137 3425 3.056749 CGGAGTGCTACCCCATTATCTAC 60.057 52.174 0.00 0.00 0.00 2.59
3139 3427 4.161102 GAGTGCTACCCCATTATCTACCT 58.839 47.826 0.00 0.00 0.00 3.08
3140 3428 4.567857 AGTGCTACCCCATTATCTACCTT 58.432 43.478 0.00 0.00 0.00 3.50
3141 3429 5.723355 AGTGCTACCCCATTATCTACCTTA 58.277 41.667 0.00 0.00 0.00 2.69
3142 3430 5.780793 AGTGCTACCCCATTATCTACCTTAG 59.219 44.000 0.00 0.00 0.00 2.18
3145 3433 5.965091 GCTACCCCATTATCTACCTTAGGAT 59.035 44.000 4.77 0.00 0.00 3.24
3146 3434 6.444171 GCTACCCCATTATCTACCTTAGGATT 59.556 42.308 4.77 0.00 0.00 3.01
3149 3437 8.450780 ACCCCATTATCTACCTTAGGATTTAG 57.549 38.462 4.77 0.00 0.00 1.85
3150 3438 7.461363 ACCCCATTATCTACCTTAGGATTTAGG 59.539 40.741 4.77 0.00 37.56 2.69
3152 3440 9.285359 CCCATTATCTACCTTAGGATTTAGGAT 57.715 37.037 4.77 2.08 35.45 3.24
3411 3699 4.029809 CGGGGGTGGTGGAAGACC 62.030 72.222 0.00 0.00 46.37 3.85
3420 3708 4.761163 TGGAAGACCAACAGGGGA 57.239 55.556 0.00 0.00 43.91 4.81
3421 3709 2.463441 TGGAAGACCAACAGGGGAG 58.537 57.895 0.00 0.00 43.91 4.30
3422 3710 1.133809 TGGAAGACCAACAGGGGAGG 61.134 60.000 0.00 0.00 43.91 4.30
3423 3711 1.685820 GAAGACCAACAGGGGAGGG 59.314 63.158 0.00 0.00 42.91 4.30
3424 3712 1.852626 AAGACCAACAGGGGAGGGG 60.853 63.158 0.00 0.00 42.91 4.79
3425 3713 3.339093 GACCAACAGGGGAGGGGG 61.339 72.222 0.00 0.00 42.91 5.40
3490 3778 4.043100 GCCGGGGGCCAGTAGTTT 62.043 66.667 4.39 0.00 44.06 2.66
3491 3779 2.045340 CCGGGGGCCAGTAGTTTG 60.045 66.667 4.39 0.00 0.00 2.93
3492 3780 2.045340 CGGGGGCCAGTAGTTTGG 60.045 66.667 4.39 0.00 41.35 3.28
3498 3786 3.870606 CCAGTAGTTTGGCCGACG 58.129 61.111 0.00 0.00 0.00 5.12
3499 3787 1.740296 CCAGTAGTTTGGCCGACGG 60.740 63.158 10.29 10.29 0.00 4.79
3520 3808 4.783621 GTGCGATGGCCTGCTGGA 62.784 66.667 14.77 0.00 38.85 3.86
3521 3809 4.478371 TGCGATGGCCTGCTGGAG 62.478 66.667 14.77 0.00 38.85 3.86
3522 3810 4.166888 GCGATGGCCTGCTGGAGA 62.167 66.667 14.77 0.00 34.57 3.71
3523 3811 2.586245 CGATGGCCTGCTGGAGAA 59.414 61.111 14.77 0.00 34.57 2.87
3524 3812 1.523258 CGATGGCCTGCTGGAGAAG 60.523 63.158 14.77 0.00 34.57 2.85
3525 3813 1.910722 GATGGCCTGCTGGAGAAGA 59.089 57.895 14.77 0.00 34.57 2.87
3526 3814 0.254178 GATGGCCTGCTGGAGAAGAA 59.746 55.000 14.77 0.00 34.57 2.52
3527 3815 0.255318 ATGGCCTGCTGGAGAAGAAG 59.745 55.000 14.77 0.00 34.57 2.85
3528 3816 0.837691 TGGCCTGCTGGAGAAGAAGA 60.838 55.000 14.77 0.00 32.35 2.87
3529 3817 0.326264 GGCCTGCTGGAGAAGAAGAA 59.674 55.000 14.77 0.00 32.35 2.52
3530 3818 1.678425 GGCCTGCTGGAGAAGAAGAAG 60.678 57.143 14.77 0.00 32.35 2.85
3531 3819 1.277557 GCCTGCTGGAGAAGAAGAAGA 59.722 52.381 14.77 0.00 32.35 2.87
3532 3820 2.677613 GCCTGCTGGAGAAGAAGAAGAG 60.678 54.545 14.77 0.00 32.35 2.85
3533 3821 2.566724 CCTGCTGGAGAAGAAGAAGAGT 59.433 50.000 2.92 0.00 32.35 3.24
3534 3822 3.007831 CCTGCTGGAGAAGAAGAAGAGTT 59.992 47.826 2.92 0.00 32.35 3.01
3535 3823 4.221703 CCTGCTGGAGAAGAAGAAGAGTTA 59.778 45.833 2.92 0.00 32.35 2.24
3536 3824 5.398603 TGCTGGAGAAGAAGAAGAGTTAG 57.601 43.478 0.00 0.00 0.00 2.34
3537 3825 4.221703 TGCTGGAGAAGAAGAAGAGTTAGG 59.778 45.833 0.00 0.00 0.00 2.69
3538 3826 4.464597 GCTGGAGAAGAAGAAGAGTTAGGA 59.535 45.833 0.00 0.00 0.00 2.94
3539 3827 5.394115 GCTGGAGAAGAAGAAGAGTTAGGAG 60.394 48.000 0.00 0.00 0.00 3.69
3540 3828 5.893500 TGGAGAAGAAGAAGAGTTAGGAGA 58.106 41.667 0.00 0.00 0.00 3.71
3541 3829 5.712917 TGGAGAAGAAGAAGAGTTAGGAGAC 59.287 44.000 0.00 0.00 0.00 3.36
3542 3830 5.163693 GGAGAAGAAGAAGAGTTAGGAGACG 60.164 48.000 0.00 0.00 0.00 4.18
3543 3831 5.318630 AGAAGAAGAAGAGTTAGGAGACGT 58.681 41.667 0.00 0.00 0.00 4.34
3544 3832 6.474630 AGAAGAAGAAGAGTTAGGAGACGTA 58.525 40.000 0.00 0.00 0.00 3.57
3545 3833 6.941436 AGAAGAAGAAGAGTTAGGAGACGTAA 59.059 38.462 0.00 0.00 0.00 3.18
3546 3834 7.447853 AGAAGAAGAAGAGTTAGGAGACGTAAA 59.552 37.037 0.00 0.00 0.00 2.01
3547 3835 7.521871 AGAAGAAGAGTTAGGAGACGTAAAA 57.478 36.000 0.00 0.00 0.00 1.52
3548 3836 8.124808 AGAAGAAGAGTTAGGAGACGTAAAAT 57.875 34.615 0.00 0.00 0.00 1.82
3549 3837 8.245491 AGAAGAAGAGTTAGGAGACGTAAAATC 58.755 37.037 0.00 0.00 0.00 2.17
3550 3838 7.706100 AGAAGAGTTAGGAGACGTAAAATCT 57.294 36.000 0.00 0.00 31.43 2.40
3551 3839 7.540299 AGAAGAGTTAGGAGACGTAAAATCTG 58.460 38.462 0.00 0.00 30.90 2.90
3552 3840 5.652518 AGAGTTAGGAGACGTAAAATCTGC 58.347 41.667 0.00 0.00 34.92 4.26
3553 3841 5.185249 AGAGTTAGGAGACGTAAAATCTGCA 59.815 40.000 0.00 0.00 37.02 4.41
3554 3842 5.978814 AGTTAGGAGACGTAAAATCTGCAT 58.021 37.500 0.00 0.00 37.02 3.96
3555 3843 6.043411 AGTTAGGAGACGTAAAATCTGCATC 58.957 40.000 0.00 0.00 37.02 3.91
3556 3844 4.744795 AGGAGACGTAAAATCTGCATCT 57.255 40.909 0.00 0.00 37.02 2.90
3557 3845 5.854010 AGGAGACGTAAAATCTGCATCTA 57.146 39.130 0.00 0.00 37.02 1.98
3558 3846 6.222038 AGGAGACGTAAAATCTGCATCTAA 57.778 37.500 0.00 0.00 37.02 2.10
3559 3847 6.821388 AGGAGACGTAAAATCTGCATCTAAT 58.179 36.000 0.00 0.00 37.02 1.73
3560 3848 6.703607 AGGAGACGTAAAATCTGCATCTAATG 59.296 38.462 0.00 0.00 37.02 1.90
3561 3849 6.073548 GGAGACGTAAAATCTGCATCTAATGG 60.074 42.308 0.00 0.00 34.84 3.16
3562 3850 6.349300 AGACGTAAAATCTGCATCTAATGGT 58.651 36.000 0.00 0.00 0.00 3.55
3563 3851 6.480320 AGACGTAAAATCTGCATCTAATGGTC 59.520 38.462 0.00 0.00 0.00 4.02
3564 3852 6.349300 ACGTAAAATCTGCATCTAATGGTCT 58.651 36.000 0.00 0.00 0.00 3.85
3565 3853 6.258727 ACGTAAAATCTGCATCTAATGGTCTG 59.741 38.462 0.00 0.00 0.00 3.51
3566 3854 6.479990 CGTAAAATCTGCATCTAATGGTCTGA 59.520 38.462 0.00 0.00 0.00 3.27
3567 3855 7.011389 CGTAAAATCTGCATCTAATGGTCTGAA 59.989 37.037 0.00 0.00 0.00 3.02
3568 3856 7.707624 AAAATCTGCATCTAATGGTCTGAAA 57.292 32.000 0.00 0.00 0.00 2.69
3569 3857 7.893124 AAATCTGCATCTAATGGTCTGAAAT 57.107 32.000 0.00 0.00 0.00 2.17
3570 3858 6.879276 ATCTGCATCTAATGGTCTGAAATG 57.121 37.500 0.00 0.00 0.00 2.32
3571 3859 5.128205 TCTGCATCTAATGGTCTGAAATGG 58.872 41.667 0.00 0.00 0.00 3.16
3572 3860 4.858850 TGCATCTAATGGTCTGAAATGGT 58.141 39.130 0.00 0.00 0.00 3.55
3573 3861 4.883585 TGCATCTAATGGTCTGAAATGGTC 59.116 41.667 0.00 0.00 0.00 4.02
3574 3862 4.024556 GCATCTAATGGTCTGAAATGGTCG 60.025 45.833 0.00 0.00 0.00 4.79
3575 3863 5.359756 CATCTAATGGTCTGAAATGGTCGA 58.640 41.667 0.00 0.00 0.00 4.20
3576 3864 4.755411 TCTAATGGTCTGAAATGGTCGAC 58.245 43.478 7.13 7.13 32.43 4.20
3577 3865 3.703001 AATGGTCTGAAATGGTCGACT 57.297 42.857 16.46 0.00 33.22 4.18
3578 3866 2.455674 TGGTCTGAAATGGTCGACTG 57.544 50.000 16.46 0.00 33.22 3.51
3579 3867 1.691976 TGGTCTGAAATGGTCGACTGT 59.308 47.619 16.46 1.11 33.22 3.55
3580 3868 2.288825 TGGTCTGAAATGGTCGACTGTC 60.289 50.000 16.46 8.25 33.22 3.51
3581 3869 2.338500 GTCTGAAATGGTCGACTGTCC 58.662 52.381 16.46 0.00 31.31 4.02
3582 3870 1.275291 TCTGAAATGGTCGACTGTCCC 59.725 52.381 16.46 0.00 0.00 4.46
3583 3871 1.001974 CTGAAATGGTCGACTGTCCCA 59.998 52.381 16.46 4.65 0.00 4.37
3584 3872 1.418264 TGAAATGGTCGACTGTCCCAA 59.582 47.619 16.46 0.00 0.00 4.12
3585 3873 2.158740 TGAAATGGTCGACTGTCCCAAA 60.159 45.455 16.46 0.00 0.00 3.28
3586 3874 2.879103 AATGGTCGACTGTCCCAAAT 57.121 45.000 16.46 0.00 0.00 2.32
3587 3875 3.992943 AATGGTCGACTGTCCCAAATA 57.007 42.857 16.46 0.00 0.00 1.40
3588 3876 3.992943 ATGGTCGACTGTCCCAAATAA 57.007 42.857 16.46 0.00 0.00 1.40
3589 3877 3.992943 TGGTCGACTGTCCCAAATAAT 57.007 42.857 16.46 0.00 0.00 1.28
3590 3878 5.623956 ATGGTCGACTGTCCCAAATAATA 57.376 39.130 16.46 0.00 0.00 0.98
3591 3879 5.623956 TGGTCGACTGTCCCAAATAATAT 57.376 39.130 16.46 0.00 0.00 1.28
3592 3880 5.607477 TGGTCGACTGTCCCAAATAATATC 58.393 41.667 16.46 0.00 0.00 1.63
3593 3881 4.684703 GGTCGACTGTCCCAAATAATATCG 59.315 45.833 16.46 0.00 0.00 2.92
3594 3882 4.684703 GTCGACTGTCCCAAATAATATCGG 59.315 45.833 8.70 0.00 0.00 4.18
3595 3883 4.585581 TCGACTGTCCCAAATAATATCGGA 59.414 41.667 1.55 0.00 0.00 4.55
3596 3884 5.069383 TCGACTGTCCCAAATAATATCGGAA 59.931 40.000 1.55 0.00 0.00 4.30
3600 3888 7.940850 ACTGTCCCAAATAATATCGGAATTTG 58.059 34.615 6.08 6.08 39.31 2.32
3601 3889 7.777910 ACTGTCCCAAATAATATCGGAATTTGA 59.222 33.333 12.27 0.00 41.14 2.69
3610 3898 8.703604 ATAATATCGGAATTTGACTATCACGG 57.296 34.615 0.00 0.00 0.00 4.94
3617 3905 5.520649 GGAATTTGACTATCACGGAGAGAAC 59.479 44.000 3.08 0.00 0.00 3.01
3619 3907 5.462530 TTTGACTATCACGGAGAGAACAA 57.537 39.130 3.08 5.98 0.00 2.83
3630 3918 6.368791 TCACGGAGAGAACAATTAATCAACTG 59.631 38.462 0.00 0.00 0.00 3.16
3636 3924 8.545229 AGAGAACAATTAATCAACTGACTCTG 57.455 34.615 13.12 0.00 31.10 3.35
3637 3925 8.370940 AGAGAACAATTAATCAACTGACTCTGA 58.629 33.333 13.12 0.00 31.10 3.27
3638 3926 9.160496 GAGAACAATTAATCAACTGACTCTGAT 57.840 33.333 0.00 0.00 33.66 2.90
3639 3927 8.944029 AGAACAATTAATCAACTGACTCTGATG 58.056 33.333 0.00 0.00 32.60 3.07
3643 3933 2.643933 TCAACTGACTCTGATGCTCG 57.356 50.000 0.00 0.00 0.00 5.03
3654 3944 0.179137 TGATGCTCGCTGTAAGGTCG 60.179 55.000 0.00 0.00 0.00 4.79
3661 3951 2.617308 CTCGCTGTAAGGTCGGAATCTA 59.383 50.000 0.00 0.00 0.00 1.98
3665 3955 4.551388 GCTGTAAGGTCGGAATCTATGAG 58.449 47.826 0.00 0.00 0.00 2.90
3675 3965 6.234177 GTCGGAATCTATGAGGGAATGAAAT 58.766 40.000 0.00 0.00 0.00 2.17
3698 3990 4.647853 TGGGCTTTACATACTCTATCGTGT 59.352 41.667 0.00 0.00 0.00 4.49
3728 4020 1.250840 GGAGGGCCGTCAAAGCAAAT 61.251 55.000 25.86 0.00 0.00 2.32
3732 4024 1.081509 GCCGTCAAAGCAAATCGCA 60.082 52.632 0.00 0.00 46.13 5.10
3733 4025 0.662970 GCCGTCAAAGCAAATCGCAA 60.663 50.000 0.00 0.00 46.13 4.85
3751 4043 2.736978 CAAGAGAACGGATCGAGATGG 58.263 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 152 5.993055 TCAAATGATCCAGTCTGCTCATTA 58.007 37.500 20.48 10.01 37.35 1.90
209 210 1.944024 TGACAATTCCGTGTTGTGTCC 59.056 47.619 2.59 0.00 39.72 4.02
569 572 1.526917 CCGATGACCCCTGCCATTC 60.527 63.158 0.00 0.00 0.00 2.67
574 577 2.361104 TTTGCCGATGACCCCTGC 60.361 61.111 0.00 0.00 0.00 4.85
575 578 0.609131 AAGTTTGCCGATGACCCCTG 60.609 55.000 0.00 0.00 0.00 4.45
582 585 3.956233 CATGTATGGAAGTTTGCCGATG 58.044 45.455 0.00 0.00 0.00 3.84
603 606 0.721718 CGTCAAATCGGCTCTGAACC 59.278 55.000 0.00 0.00 0.00 3.62
609 612 0.093026 CACGTTCGTCAAATCGGCTC 59.907 55.000 0.00 0.00 0.00 4.70
691 695 3.164268 TGGGTTCATTTTGGTCCATGAG 58.836 45.455 0.00 0.00 31.04 2.90
745 750 5.684704 CAGGAGATATTCTTTAGTTGGCCA 58.315 41.667 0.00 0.00 0.00 5.36
746 751 4.517075 GCAGGAGATATTCTTTAGTTGGCC 59.483 45.833 0.00 0.00 0.00 5.36
748 753 5.066593 GGGCAGGAGATATTCTTTAGTTGG 58.933 45.833 0.00 0.00 0.00 3.77
765 961 4.996434 GCCGATCGATGGGGCAGG 62.996 72.222 25.55 9.73 46.13 4.85
909 1106 1.380280 TATGGAGGAGAGGGGGAGGG 61.380 65.000 0.00 0.00 0.00 4.30
968 1167 1.550130 TTGGGGGAAGCTAGGTCACG 61.550 60.000 0.00 0.00 0.00 4.35
970 1169 1.213296 GATTGGGGGAAGCTAGGTCA 58.787 55.000 0.00 0.00 0.00 4.02
982 1181 1.070758 CCTATGGACACGAGATTGGGG 59.929 57.143 0.00 0.00 0.00 4.96
1030 1229 1.136305 CTCACACCATACCACTACCCG 59.864 57.143 0.00 0.00 0.00 5.28
1038 1237 1.224592 CCCAGCCTCACACCATACC 59.775 63.158 0.00 0.00 0.00 2.73
1040 1239 0.252696 AGACCCAGCCTCACACCATA 60.253 55.000 0.00 0.00 0.00 2.74
1105 1304 2.358125 TCATGCGGGAACACCACG 60.358 61.111 0.00 0.00 40.22 4.94
1204 1403 1.166129 CCTTCTCCTCGAACTCGTCA 58.834 55.000 0.00 0.00 40.80 4.35
1517 1734 3.161450 GTAGGAGGGCGGCATGGA 61.161 66.667 12.47 0.00 0.00 3.41
1575 1792 2.729882 CGCACAGTGAAAGGTGTACTAC 59.270 50.000 4.15 0.00 37.35 2.73
1576 1793 2.864882 GCGCACAGTGAAAGGTGTACTA 60.865 50.000 4.15 0.00 37.35 1.82
2018 2258 1.653667 CTGCATCACACGGCACAAA 59.346 52.632 0.00 0.00 35.86 2.83
2096 2336 2.358003 GCCTCAAGCGACTGCAGT 60.358 61.111 21.88 21.88 46.23 4.40
2276 2543 2.203337 GGCACCAGCACCTTCACA 60.203 61.111 0.00 0.00 44.61 3.58
2345 2612 3.941657 GAGGTGGAGCACGGTGAGC 62.942 68.421 13.29 2.09 34.83 4.26
2444 2711 0.320683 TGGAACAGAGTGCGGATGTG 60.321 55.000 0.00 0.00 0.00 3.21
2474 2741 2.618241 TCATTTAATCACGGCATCAGGC 59.382 45.455 0.00 0.00 43.74 4.85
2475 2742 3.303329 CGTCATTTAATCACGGCATCAGG 60.303 47.826 0.00 0.00 0.00 3.86
2476 2743 3.846023 GCGTCATTTAATCACGGCATCAG 60.846 47.826 3.29 0.00 34.04 2.90
2477 2744 2.031560 GCGTCATTTAATCACGGCATCA 59.968 45.455 3.29 0.00 34.04 3.07
2478 2745 2.639751 GCGTCATTTAATCACGGCATC 58.360 47.619 3.29 0.00 34.04 3.91
2479 2746 2.755836 GCGTCATTTAATCACGGCAT 57.244 45.000 3.29 0.00 34.04 4.40
2884 3172 1.673168 GAGCCACATCTCCATGGTTC 58.327 55.000 12.58 0.00 38.77 3.62
2885 3173 3.890527 GAGCCACATCTCCATGGTT 57.109 52.632 12.58 0.00 38.34 3.67
2901 3189 1.077429 GGTTAAGCCAGCCAGGGAG 60.077 63.158 0.00 0.00 38.09 4.30
2917 3205 2.616842 GCCAATCCGATTATCAAACGGT 59.383 45.455 7.37 0.00 45.71 4.83
2919 3207 2.031157 GGGCCAATCCGATTATCAAACG 60.031 50.000 4.39 0.00 34.94 3.60
2999 3287 1.597663 GAACGGACACCAAGAACACAG 59.402 52.381 0.00 0.00 0.00 3.66
3013 3301 7.731882 TTGTCATTTAACTAATGTGAACGGA 57.268 32.000 0.00 0.00 43.41 4.69
3034 3322 8.992073 GGCTTAATTTGAAATTCAGTCAATTGT 58.008 29.630 6.40 0.00 34.69 2.71
3035 3323 8.445493 GGGCTTAATTTGAAATTCAGTCAATTG 58.555 33.333 15.68 0.00 34.69 2.32
3038 3326 7.060383 TGGGCTTAATTTGAAATTCAGTCAA 57.940 32.000 15.68 4.48 33.21 3.18
3040 3328 6.691508 ACTGGGCTTAATTTGAAATTCAGTC 58.308 36.000 6.40 7.13 0.00 3.51
3041 3329 6.267471 TGACTGGGCTTAATTTGAAATTCAGT 59.733 34.615 16.77 16.77 34.91 3.41
3043 3331 6.662865 TGACTGGGCTTAATTTGAAATTCA 57.337 33.333 6.40 0.00 0.00 2.57
3045 3333 8.922931 AAATTGACTGGGCTTAATTTGAAATT 57.077 26.923 8.35 8.35 33.05 1.82
3046 3334 8.922931 AAAATTGACTGGGCTTAATTTGAAAT 57.077 26.923 0.00 0.00 34.16 2.17
3069 3357 5.307716 TCTTCCCTCCGGTAAACTCTAAAAA 59.692 40.000 0.00 0.00 0.00 1.94
3070 3358 4.840115 TCTTCCCTCCGGTAAACTCTAAAA 59.160 41.667 0.00 0.00 0.00 1.52
3071 3359 4.419282 TCTTCCCTCCGGTAAACTCTAAA 58.581 43.478 0.00 0.00 0.00 1.85
3072 3360 4.051661 TCTTCCCTCCGGTAAACTCTAA 57.948 45.455 0.00 0.00 0.00 2.10
3074 3362 2.617840 TCTTCCCTCCGGTAAACTCT 57.382 50.000 0.00 0.00 0.00 3.24
3075 3363 3.597255 CTTTCTTCCCTCCGGTAAACTC 58.403 50.000 0.00 0.00 0.00 3.01
3077 3365 2.303890 TCCTTTCTTCCCTCCGGTAAAC 59.696 50.000 0.00 0.00 0.00 2.01
3078 3366 2.570302 CTCCTTTCTTCCCTCCGGTAAA 59.430 50.000 0.00 0.00 0.00 2.01
3079 3367 2.185387 CTCCTTTCTTCCCTCCGGTAA 58.815 52.381 0.00 0.00 0.00 2.85
3080 3368 1.360162 TCTCCTTTCTTCCCTCCGGTA 59.640 52.381 0.00 0.00 0.00 4.02
3082 3370 1.208293 CTTCTCCTTTCTTCCCTCCGG 59.792 57.143 0.00 0.00 0.00 5.14
3083 3371 1.208293 CCTTCTCCTTTCTTCCCTCCG 59.792 57.143 0.00 0.00 0.00 4.63
3085 3373 3.054728 CCTTCCTTCTCCTTTCTTCCCTC 60.055 52.174 0.00 0.00 0.00 4.30
3086 3374 2.916269 CCTTCCTTCTCCTTTCTTCCCT 59.084 50.000 0.00 0.00 0.00 4.20
3087 3375 2.025793 CCCTTCCTTCTCCTTTCTTCCC 60.026 54.545 0.00 0.00 0.00 3.97
3088 3376 2.025793 CCCCTTCCTTCTCCTTTCTTCC 60.026 54.545 0.00 0.00 0.00 3.46
3089 3377 2.619332 GCCCCTTCCTTCTCCTTTCTTC 60.619 54.545 0.00 0.00 0.00 2.87
3092 3380 0.995803 AGCCCCTTCCTTCTCCTTTC 59.004 55.000 0.00 0.00 0.00 2.62
3093 3381 0.995803 GAGCCCCTTCCTTCTCCTTT 59.004 55.000 0.00 0.00 0.00 3.11
3094 3382 1.268283 CGAGCCCCTTCCTTCTCCTT 61.268 60.000 0.00 0.00 0.00 3.36
3095 3383 1.687493 CGAGCCCCTTCCTTCTCCT 60.687 63.158 0.00 0.00 0.00 3.69
3096 3384 2.904131 CGAGCCCCTTCCTTCTCC 59.096 66.667 0.00 0.00 0.00 3.71
3097 3385 2.188207 GCGAGCCCCTTCCTTCTC 59.812 66.667 0.00 0.00 0.00 2.87
3098 3386 3.403558 GGCGAGCCCCTTCCTTCT 61.404 66.667 1.97 0.00 0.00 2.85
3099 3387 4.840005 CGGCGAGCCCCTTCCTTC 62.840 72.222 0.00 0.00 0.00 3.46
3108 3396 4.874977 GTAGCACTCCGGCGAGCC 62.875 72.222 9.30 3.59 40.03 4.70
3110 3398 4.208686 GGGTAGCACTCCGGCGAG 62.209 72.222 9.30 6.64 42.32 5.03
3113 3401 1.692173 TAATGGGGTAGCACTCCGGC 61.692 60.000 0.00 0.00 43.44 6.13
3114 3402 1.002087 GATAATGGGGTAGCACTCCGG 59.998 57.143 0.00 0.00 43.44 5.14
3115 3403 1.971357 AGATAATGGGGTAGCACTCCG 59.029 52.381 0.00 0.00 43.44 4.63
3116 3404 3.261137 GGTAGATAATGGGGTAGCACTCC 59.739 52.174 0.00 0.00 39.92 3.85
3117 3405 4.161102 AGGTAGATAATGGGGTAGCACTC 58.839 47.826 0.00 0.00 0.00 3.51
3118 3406 4.214993 AGGTAGATAATGGGGTAGCACT 57.785 45.455 0.00 0.00 0.00 4.40
3119 3407 4.976540 AAGGTAGATAATGGGGTAGCAC 57.023 45.455 0.00 0.00 0.00 4.40
3121 3409 5.339477 TCCTAAGGTAGATAATGGGGTAGC 58.661 45.833 0.00 0.00 0.00 3.58
3122 3410 8.450780 AAATCCTAAGGTAGATAATGGGGTAG 57.549 38.462 0.00 0.00 0.00 3.18
3124 3412 7.461363 CCTAAATCCTAAGGTAGATAATGGGGT 59.539 40.741 0.00 0.00 0.00 4.95
3126 3414 8.680820 TCCTAAATCCTAAGGTAGATAATGGG 57.319 38.462 0.00 0.00 34.30 4.00
3129 3417 9.285359 CCCATCCTAAATCCTAAGGTAGATAAT 57.715 37.037 0.00 0.00 34.30 1.28
3394 3682 4.029809 GGTCTTCCACCACCCCCG 62.030 72.222 0.00 0.00 45.98 5.73
3401 3689 1.074951 CCCCTGTTGGTCTTCCACC 59.925 63.158 0.00 0.00 44.22 4.61
3402 3690 0.036875 CTCCCCTGTTGGTCTTCCAC 59.963 60.000 0.00 0.00 44.22 4.02
3403 3691 1.133809 CCTCCCCTGTTGGTCTTCCA 61.134 60.000 0.00 0.00 42.66 3.53
3404 3692 1.685820 CCTCCCCTGTTGGTCTTCC 59.314 63.158 0.00 0.00 0.00 3.46
3405 3693 1.685820 CCCTCCCCTGTTGGTCTTC 59.314 63.158 0.00 0.00 0.00 2.87
3406 3694 1.852626 CCCCTCCCCTGTTGGTCTT 60.853 63.158 0.00 0.00 0.00 3.01
3407 3695 2.204151 CCCCTCCCCTGTTGGTCT 60.204 66.667 0.00 0.00 0.00 3.85
3408 3696 3.339093 CCCCCTCCCCTGTTGGTC 61.339 72.222 0.00 0.00 0.00 4.02
3474 3762 2.045340 CAAACTACTGGCCCCCGG 60.045 66.667 0.00 0.00 35.68 5.73
3475 3763 2.045340 CCAAACTACTGGCCCCCG 60.045 66.667 0.00 0.00 0.00 5.73
3481 3769 1.740296 CCGTCGGCCAAACTACTGG 60.740 63.158 2.24 0.00 39.71 4.00
3482 3770 2.388232 GCCGTCGGCCAAACTACTG 61.388 63.158 26.23 0.00 44.06 2.74
3483 3771 2.047560 GCCGTCGGCCAAACTACT 60.048 61.111 26.23 0.00 44.06 2.57
3503 3791 4.783621 TCCAGCAGGCCATCGCAC 62.784 66.667 5.01 0.00 36.38 5.34
3504 3792 4.478371 CTCCAGCAGGCCATCGCA 62.478 66.667 5.01 0.00 36.38 5.10
3505 3793 3.687321 TTCTCCAGCAGGCCATCGC 62.687 63.158 5.01 4.26 33.74 4.58
3506 3794 1.523258 CTTCTCCAGCAGGCCATCG 60.523 63.158 5.01 0.00 33.74 3.84
3507 3795 0.254178 TTCTTCTCCAGCAGGCCATC 59.746 55.000 5.01 0.00 33.74 3.51
3508 3796 0.255318 CTTCTTCTCCAGCAGGCCAT 59.745 55.000 5.01 0.00 33.74 4.40
3509 3797 0.837691 TCTTCTTCTCCAGCAGGCCA 60.838 55.000 5.01 0.00 33.74 5.36
3510 3798 0.326264 TTCTTCTTCTCCAGCAGGCC 59.674 55.000 0.00 0.00 33.74 5.19
3511 3799 1.277557 TCTTCTTCTTCTCCAGCAGGC 59.722 52.381 0.00 0.00 33.74 4.85
3512 3800 2.566724 ACTCTTCTTCTTCTCCAGCAGG 59.433 50.000 0.00 0.00 0.00 4.85
3513 3801 3.959535 ACTCTTCTTCTTCTCCAGCAG 57.040 47.619 0.00 0.00 0.00 4.24
3514 3802 4.221703 CCTAACTCTTCTTCTTCTCCAGCA 59.778 45.833 0.00 0.00 0.00 4.41
3515 3803 4.464597 TCCTAACTCTTCTTCTTCTCCAGC 59.535 45.833 0.00 0.00 0.00 4.85
3516 3804 5.949354 TCTCCTAACTCTTCTTCTTCTCCAG 59.051 44.000 0.00 0.00 0.00 3.86
3517 3805 5.712917 GTCTCCTAACTCTTCTTCTTCTCCA 59.287 44.000 0.00 0.00 0.00 3.86
3518 3806 5.163693 CGTCTCCTAACTCTTCTTCTTCTCC 60.164 48.000 0.00 0.00 0.00 3.71
3519 3807 5.413523 ACGTCTCCTAACTCTTCTTCTTCTC 59.586 44.000 0.00 0.00 0.00 2.87
3520 3808 5.318630 ACGTCTCCTAACTCTTCTTCTTCT 58.681 41.667 0.00 0.00 0.00 2.85
3521 3809 5.632244 ACGTCTCCTAACTCTTCTTCTTC 57.368 43.478 0.00 0.00 0.00 2.87
3522 3810 7.521871 TTTACGTCTCCTAACTCTTCTTCTT 57.478 36.000 0.00 0.00 0.00 2.52
3523 3811 7.521871 TTTTACGTCTCCTAACTCTTCTTCT 57.478 36.000 0.00 0.00 0.00 2.85
3524 3812 8.245491 AGATTTTACGTCTCCTAACTCTTCTTC 58.755 37.037 0.00 0.00 0.00 2.87
3525 3813 8.030106 CAGATTTTACGTCTCCTAACTCTTCTT 58.970 37.037 0.00 0.00 0.00 2.52
3526 3814 7.540299 CAGATTTTACGTCTCCTAACTCTTCT 58.460 38.462 0.00 0.00 0.00 2.85
3527 3815 6.253942 GCAGATTTTACGTCTCCTAACTCTTC 59.746 42.308 0.00 0.00 0.00 2.87
3528 3816 6.100668 GCAGATTTTACGTCTCCTAACTCTT 58.899 40.000 0.00 0.00 0.00 2.85
3529 3817 5.185249 TGCAGATTTTACGTCTCCTAACTCT 59.815 40.000 0.00 0.00 0.00 3.24
3530 3818 5.408356 TGCAGATTTTACGTCTCCTAACTC 58.592 41.667 0.00 0.00 0.00 3.01
3531 3819 5.401531 TGCAGATTTTACGTCTCCTAACT 57.598 39.130 0.00 0.00 0.00 2.24
3532 3820 6.043411 AGATGCAGATTTTACGTCTCCTAAC 58.957 40.000 0.00 0.00 0.00 2.34
3533 3821 6.222038 AGATGCAGATTTTACGTCTCCTAA 57.778 37.500 0.00 0.00 0.00 2.69
3534 3822 5.854010 AGATGCAGATTTTACGTCTCCTA 57.146 39.130 0.00 0.00 0.00 2.94
3535 3823 4.744795 AGATGCAGATTTTACGTCTCCT 57.255 40.909 0.00 0.00 0.00 3.69
3536 3824 6.073548 CCATTAGATGCAGATTTTACGTCTCC 60.074 42.308 0.00 0.00 32.16 3.71
3537 3825 6.480320 ACCATTAGATGCAGATTTTACGTCTC 59.520 38.462 0.00 0.00 32.16 3.36
3538 3826 6.349300 ACCATTAGATGCAGATTTTACGTCT 58.651 36.000 0.00 0.00 34.21 4.18
3539 3827 6.480320 AGACCATTAGATGCAGATTTTACGTC 59.520 38.462 0.00 0.00 0.00 4.34
3540 3828 6.258727 CAGACCATTAGATGCAGATTTTACGT 59.741 38.462 0.00 0.00 0.00 3.57
3541 3829 6.479990 TCAGACCATTAGATGCAGATTTTACG 59.520 38.462 0.00 0.00 0.00 3.18
3542 3830 7.792374 TCAGACCATTAGATGCAGATTTTAC 57.208 36.000 0.00 0.00 0.00 2.01
3543 3831 8.806429 TTTCAGACCATTAGATGCAGATTTTA 57.194 30.769 0.00 0.00 0.00 1.52
3544 3832 7.707624 TTTCAGACCATTAGATGCAGATTTT 57.292 32.000 0.00 0.00 0.00 1.82
3545 3833 7.201884 CCATTTCAGACCATTAGATGCAGATTT 60.202 37.037 0.00 0.00 0.00 2.17
3546 3834 6.264744 CCATTTCAGACCATTAGATGCAGATT 59.735 38.462 0.00 0.00 0.00 2.40
3547 3835 5.768662 CCATTTCAGACCATTAGATGCAGAT 59.231 40.000 0.00 0.00 0.00 2.90
3548 3836 5.128205 CCATTTCAGACCATTAGATGCAGA 58.872 41.667 0.00 0.00 0.00 4.26
3549 3837 4.885907 ACCATTTCAGACCATTAGATGCAG 59.114 41.667 0.00 0.00 0.00 4.41
3550 3838 4.858850 ACCATTTCAGACCATTAGATGCA 58.141 39.130 0.00 0.00 0.00 3.96
3551 3839 4.024556 CGACCATTTCAGACCATTAGATGC 60.025 45.833 0.00 0.00 0.00 3.91
3552 3840 5.235186 GTCGACCATTTCAGACCATTAGATG 59.765 44.000 3.51 0.00 0.00 2.90
3553 3841 5.129485 AGTCGACCATTTCAGACCATTAGAT 59.871 40.000 13.01 0.00 34.41 1.98
3554 3842 4.466370 AGTCGACCATTTCAGACCATTAGA 59.534 41.667 13.01 0.00 34.41 2.10
3555 3843 4.568359 CAGTCGACCATTTCAGACCATTAG 59.432 45.833 13.01 0.00 34.41 1.73
3556 3844 4.020573 ACAGTCGACCATTTCAGACCATTA 60.021 41.667 13.01 0.00 34.41 1.90
3557 3845 3.244561 ACAGTCGACCATTTCAGACCATT 60.245 43.478 13.01 0.00 34.41 3.16
3558 3846 2.303022 ACAGTCGACCATTTCAGACCAT 59.697 45.455 13.01 0.00 34.41 3.55
3559 3847 1.691976 ACAGTCGACCATTTCAGACCA 59.308 47.619 13.01 0.00 34.41 4.02
3560 3848 2.338500 GACAGTCGACCATTTCAGACC 58.662 52.381 13.01 0.00 34.41 3.85
3561 3849 2.338500 GGACAGTCGACCATTTCAGAC 58.662 52.381 13.01 0.00 0.00 3.51
3562 3850 1.275291 GGGACAGTCGACCATTTCAGA 59.725 52.381 13.01 0.00 0.00 3.27
3563 3851 1.001974 TGGGACAGTCGACCATTTCAG 59.998 52.381 13.01 0.00 0.00 3.02
3564 3852 1.052617 TGGGACAGTCGACCATTTCA 58.947 50.000 13.01 3.14 0.00 2.69
3565 3853 2.178912 TTGGGACAGTCGACCATTTC 57.821 50.000 13.01 3.37 42.39 2.17
3566 3854 2.649531 TTTGGGACAGTCGACCATTT 57.350 45.000 13.01 0.00 42.39 2.32
3567 3855 2.879103 ATTTGGGACAGTCGACCATT 57.121 45.000 13.01 0.00 42.39 3.16
3568 3856 3.992943 TTATTTGGGACAGTCGACCAT 57.007 42.857 13.01 0.00 42.39 3.55
3569 3857 3.992943 ATTATTTGGGACAGTCGACCA 57.007 42.857 13.01 0.00 42.39 4.02
3570 3858 4.684703 CGATATTATTTGGGACAGTCGACC 59.315 45.833 13.01 0.00 42.39 4.79
3571 3859 4.684703 CCGATATTATTTGGGACAGTCGAC 59.315 45.833 7.70 7.70 42.39 4.20
3572 3860 4.585581 TCCGATATTATTTGGGACAGTCGA 59.414 41.667 0.00 0.00 42.39 4.20
3573 3861 4.878439 TCCGATATTATTTGGGACAGTCG 58.122 43.478 0.00 0.00 42.39 4.18
3574 3862 7.745620 AATTCCGATATTATTTGGGACAGTC 57.254 36.000 0.00 0.00 42.39 3.51
3575 3863 7.777910 TCAAATTCCGATATTATTTGGGACAGT 59.222 33.333 0.00 0.00 42.39 3.55
3576 3864 8.076178 GTCAAATTCCGATATTATTTGGGACAG 58.924 37.037 0.00 0.00 42.39 3.51
3577 3865 7.777910 AGTCAAATTCCGATATTATTTGGGACA 59.222 33.333 0.00 0.00 38.91 4.02
3578 3866 8.166422 AGTCAAATTCCGATATTATTTGGGAC 57.834 34.615 0.00 0.00 38.91 4.46
3584 3872 9.151471 CCGTGATAGTCAAATTCCGATATTATT 57.849 33.333 0.00 0.00 0.00 1.40
3585 3873 8.528643 TCCGTGATAGTCAAATTCCGATATTAT 58.471 33.333 0.00 0.00 0.00 1.28
3586 3874 7.888424 TCCGTGATAGTCAAATTCCGATATTA 58.112 34.615 0.00 0.00 0.00 0.98
3587 3875 6.755206 TCCGTGATAGTCAAATTCCGATATT 58.245 36.000 0.00 0.00 0.00 1.28
3588 3876 6.208797 TCTCCGTGATAGTCAAATTCCGATAT 59.791 38.462 0.00 0.00 0.00 1.63
3589 3877 5.533528 TCTCCGTGATAGTCAAATTCCGATA 59.466 40.000 0.00 0.00 0.00 2.92
3590 3878 4.341235 TCTCCGTGATAGTCAAATTCCGAT 59.659 41.667 0.00 0.00 0.00 4.18
3591 3879 3.697542 TCTCCGTGATAGTCAAATTCCGA 59.302 43.478 0.00 0.00 0.00 4.55
3592 3880 4.041740 TCTCCGTGATAGTCAAATTCCG 57.958 45.455 0.00 0.00 0.00 4.30
3593 3881 5.263968 TCTCTCCGTGATAGTCAAATTCC 57.736 43.478 0.00 0.00 0.00 3.01
3594 3882 6.100004 TGTTCTCTCCGTGATAGTCAAATTC 58.900 40.000 0.00 0.00 0.00 2.17
3595 3883 6.037786 TGTTCTCTCCGTGATAGTCAAATT 57.962 37.500 0.00 0.00 0.00 1.82
3596 3884 5.661056 TGTTCTCTCCGTGATAGTCAAAT 57.339 39.130 0.00 0.00 0.00 2.32
3600 3888 7.921214 TGATTAATTGTTCTCTCCGTGATAGTC 59.079 37.037 0.00 0.00 0.00 2.59
3601 3889 7.782049 TGATTAATTGTTCTCTCCGTGATAGT 58.218 34.615 0.00 0.00 0.00 2.12
3610 3898 8.655092 CAGAGTCAGTTGATTAATTGTTCTCTC 58.345 37.037 14.32 9.14 35.83 3.20
3617 3905 7.317842 AGCATCAGAGTCAGTTGATTAATTG 57.682 36.000 0.00 0.00 31.91 2.32
3619 3907 5.752472 CGAGCATCAGAGTCAGTTGATTAAT 59.248 40.000 0.00 0.00 31.91 1.40
3630 3918 2.458951 CTTACAGCGAGCATCAGAGTC 58.541 52.381 0.00 0.00 33.17 3.36
3636 3924 0.872021 CCGACCTTACAGCGAGCATC 60.872 60.000 0.00 0.00 0.00 3.91
3637 3925 1.141881 CCGACCTTACAGCGAGCAT 59.858 57.895 0.00 0.00 0.00 3.79
3638 3926 1.529152 TTCCGACCTTACAGCGAGCA 61.529 55.000 0.00 0.00 0.00 4.26
3639 3927 0.179108 ATTCCGACCTTACAGCGAGC 60.179 55.000 0.00 0.00 0.00 5.03
3643 3933 4.551388 CTCATAGATTCCGACCTTACAGC 58.449 47.826 0.00 0.00 0.00 4.40
3654 3944 5.713861 CCCATTTCATTCCCTCATAGATTCC 59.286 44.000 0.00 0.00 0.00 3.01
3661 3951 3.409804 AAGCCCATTTCATTCCCTCAT 57.590 42.857 0.00 0.00 0.00 2.90
3665 3955 5.598417 AGTATGTAAAGCCCATTTCATTCCC 59.402 40.000 0.00 0.00 32.01 3.97
3675 3965 4.647853 ACACGATAGAGTATGTAAAGCCCA 59.352 41.667 0.00 0.00 38.43 5.36
3698 3990 3.319198 GCCCTCCGTCCACAAGGA 61.319 66.667 0.00 0.00 43.21 3.36
3714 4006 0.662970 TTGCGATTTGCTTTGACGGC 60.663 50.000 0.00 0.00 46.63 5.68
3728 4020 0.098905 CTCGATCCGTTCTCTTGCGA 59.901 55.000 0.00 0.00 0.00 5.10
3732 4024 2.656002 TCCATCTCGATCCGTTCTCTT 58.344 47.619 0.00 0.00 0.00 2.85
3733 4025 2.350057 TCCATCTCGATCCGTTCTCT 57.650 50.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.