Multiple sequence alignment - TraesCS1D01G200000

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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 TraesCS1D01G200000 chr1D 100.000 4407 0 0 1 4407 282949407 282945001 0.000000e+00 8139.0
1 TraesCS1D01G200000 chr1B 91.371 2735 150 43 6 2712 384299193 384296517 0.000000e+00 3664.0
2 TraesCS1D01G200000 chr1B 89.520 1126 70 26 2700 3811 384296499 384295408 0.000000e+00 1382.0
3 TraesCS1D01G200000 chr1B 87.500 336 30 5 4 338 34777392 34777716 1.160000e-100 377.0
4 TraesCS1D01G200000 chr1B 87.500 336 30 5 4 338 34794720 34795044 1.160000e-100 377.0
5 TraesCS1D01G200000 chr1B 90.000 200 20 0 3808 4007 384249575 384249376 4.370000e-65 259.0
6 TraesCS1D01G200000 chr1B 88.557 201 21 1 4125 4323 384249361 384249161 4.400000e-60 243.0
7 TraesCS1D01G200000 chr1A 91.471 2732 105 50 6 2674 354938532 354935866 0.000000e+00 3637.0
8 TraesCS1D01G200000 chr1A 92.487 985 57 5 2700 3684 354935640 354934673 0.000000e+00 1393.0
9 TraesCS1D01G200000 chr1A 85.489 634 60 9 3696 4321 354934695 354934086 2.240000e-177 632.0
10 TraesCS1D01G200000 chr2B 85.811 296 31 6 2 295 65473130 65473416 1.990000e-78 303.0
11 TraesCS1D01G200000 chr2B 94.565 92 5 0 4316 4407 519180654 519180745 4.590000e-30 143.0
12 TraesCS1D01G200000 chr2B 85.526 76 10 1 4042 4116 714500943 714500868 1.310000e-10 78.7
13 TraesCS1D01G200000 chr2B 84.810 79 8 2 4042 4116 489937877 489937799 4.730000e-10 76.8
14 TraesCS1D01G200000 chr4A 83.203 256 26 6 2 257 196609495 196609257 7.420000e-53 219.0
15 TraesCS1D01G200000 chr4A 91.667 120 9 1 342 460 196609226 196609107 9.810000e-37 165.0
16 TraesCS1D01G200000 chr5B 87.500 144 14 3 341 483 397964580 397964720 3.530000e-36 163.0
17 TraesCS1D01G200000 chr3D 97.872 94 1 1 4315 4407 582989972 582989879 1.270000e-35 161.0
18 TraesCS1D01G200000 chr4D 98.824 85 1 0 4323 4407 32357082 32357166 7.630000e-33 152.0
19 TraesCS1D01G200000 chr4D 98.824 85 1 0 4323 4407 292912531 292912615 7.630000e-33 152.0
20 TraesCS1D01G200000 chr2D 97.727 88 2 0 4320 4407 83920433 83920520 7.630000e-33 152.0
21 TraesCS1D01G200000 chr7B 93.137 102 5 2 4307 4407 429268592 429268692 9.880000e-32 148.0
22 TraesCS1D01G200000 chr7B 82.278 79 10 2 4042 4116 530441561 530441639 1.020000e-06 65.8
23 TraesCS1D01G200000 chr7D 97.647 85 2 0 4323 4407 60706390 60706306 3.550000e-31 147.0
24 TraesCS1D01G200000 chr7D 96.552 87 3 0 4321 4407 171307988 171308074 1.280000e-30 145.0
25 TraesCS1D01G200000 chr6D 96.552 87 3 0 4321 4407 24998360 24998274 1.280000e-30 145.0
26 TraesCS1D01G200000 chr6B 84.810 79 8 2 4042 4116 481793348 481793270 4.730000e-10 76.8
27 TraesCS1D01G200000 chr6B 83.544 79 9 2 4042 4116 157860531 157860609 2.200000e-08 71.3
28 TraesCS1D01G200000 chr3B 83.544 79 9 2 4042 4116 228676842 228676764 2.200000e-08 71.3
29 TraesCS1D01G200000 chr2A 89.655 58 2 2 4042 4095 133562016 133562073 2.200000e-08 71.3
30 TraesCS1D01G200000 chr5D 91.667 48 2 2 4042 4087 135710510 135710463 1.020000e-06 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 TraesCS1D01G200000 chr1D 282945001 282949407 4406 True 8139.000000 8139 100.000000 1 4407 1 chr1D.!!$R1 4406
1 TraesCS1D01G200000 chr1B 384295408 384299193 3785 True 2523.000000 3664 90.445500 6 3811 2 chr1B.!!$R2 3805
2 TraesCS1D01G200000 chr1A 354934086 354938532 4446 True 1887.333333 3637 89.815667 6 4321 3 chr1A.!!$R1 4315

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
583 594 0.027324 CGGTCGAGCGTCTTACCTAC 59.973 60.000 27.67 0.0 0.0 3.18 F
887 936 0.443869 GCCACATACACTTGCGTCAG 59.556 55.000 0.00 0.0 0.0 3.51 F
1814 1866 1.080230 CACTCAGTCCTGTCCTGCG 60.080 63.158 0.00 0.0 0.0 5.18 F
2761 3051 0.107410 AACTTGTGTCGCTGTGGGAA 60.107 50.000 0.00 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2304 1.479730 AGCCGTAGTACTAAACCCTGC 59.520 52.381 3.61 0.58 0.00 4.85 R
2594 2668 0.251787 ACCCCAGAAAACCCATCAGC 60.252 55.000 0.00 0.00 0.00 4.26 R
3052 3343 1.437089 CGTCAGCGAAGTGTTTGCG 60.437 57.895 0.00 0.00 44.92 4.85 R
4084 4388 0.036732 CCTGTCAGCTAACTGGGCAA 59.963 55.000 4.99 0.00 44.59 4.52 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
79 80 3.810896 GCGGATCGTTGGGTTGCC 61.811 66.667 0.00 0.00 0.00 4.52
160 161 9.279904 CTTAAAATCTACGAACAGAGTAGTCAG 57.720 37.037 0.00 0.00 41.55 3.51
166 167 3.750639 GAACAGAGTAGTCAGGTCGAG 57.249 52.381 0.00 0.00 0.00 4.04
197 198 7.673641 ATTCAGGAGAAAGAGACATACTGAT 57.326 36.000 0.00 0.00 37.29 2.90
284 285 3.384532 CAGGCGGGCAAAGGCATT 61.385 61.111 3.78 0.00 43.71 3.56
357 358 2.639065 GTCTTGGTGAAGGTGTGAACA 58.361 47.619 0.00 0.00 0.00 3.18
497 502 1.046472 TGGAGGAGGACGTGTGTGTT 61.046 55.000 0.00 0.00 0.00 3.32
566 577 1.429148 GCAGAGGCGTTTGGTATCGG 61.429 60.000 0.00 0.00 0.00 4.18
583 594 0.027324 CGGTCGAGCGTCTTACCTAC 59.973 60.000 27.67 0.00 0.00 3.18
584 595 1.377536 GGTCGAGCGTCTTACCTACT 58.622 55.000 0.00 0.00 0.00 2.57
585 596 1.742268 GGTCGAGCGTCTTACCTACTT 59.258 52.381 0.00 0.00 0.00 2.24
586 597 2.939103 GGTCGAGCGTCTTACCTACTTA 59.061 50.000 0.00 0.00 0.00 2.24
617 628 6.126710 TGGAGAGAGTTTTGTTACCCTTGTTA 60.127 38.462 0.00 0.00 0.00 2.41
619 630 7.447545 GGAGAGAGTTTTGTTACCCTTGTTATT 59.552 37.037 0.00 0.00 0.00 1.40
626 637 8.631797 GTTTTGTTACCCTTGTTATTTGTAGGA 58.368 33.333 0.00 0.00 0.00 2.94
668 679 7.205992 AGAGAAAAGAAGTTGCTCCATTTTTC 58.794 34.615 0.00 0.00 34.79 2.29
672 683 3.004734 AGAAGTTGCTCCATTTTTCGTGG 59.995 43.478 0.00 0.00 38.11 4.94
678 689 4.643463 TGCTCCATTTTTCGTGGTTACTA 58.357 39.130 0.00 0.00 37.96 1.82
738 755 6.909550 TTTTGTAACCCATCAAGTATGCTT 57.090 33.333 0.00 0.00 33.92 3.91
739 756 6.909550 TTTGTAACCCATCAAGTATGCTTT 57.090 33.333 0.00 0.00 33.92 3.51
741 758 6.909550 TGTAACCCATCAAGTATGCTTTTT 57.090 33.333 0.00 0.00 33.92 1.94
780 821 1.946768 GTTGGTGTTGAACAGCTGCTA 59.053 47.619 25.31 5.21 46.03 3.49
822 871 2.036256 GGTGCCCTGCTGAATGGT 59.964 61.111 0.00 0.00 0.00 3.55
861 910 1.674057 GATACATCCTGGCCTCGGG 59.326 63.158 3.32 3.76 40.84 5.14
879 928 1.604378 GCTCCTGGCCACATACACT 59.396 57.895 0.00 0.00 34.27 3.55
883 932 1.647545 CCTGGCCACATACACTTGCG 61.648 60.000 0.00 0.00 0.00 4.85
887 936 0.443869 GCCACATACACTTGCGTCAG 59.556 55.000 0.00 0.00 0.00 3.51
891 940 2.409715 CACATACACTTGCGTCAGACAG 59.590 50.000 0.41 0.00 0.00 3.51
897 946 1.137086 ACTTGCGTCAGACAGAACACT 59.863 47.619 0.41 0.00 0.00 3.55
907 956 5.006165 GTCAGACAGAACACTGAAAAGTCTG 59.994 44.000 12.12 12.12 43.29 3.51
908 957 3.873952 AGACAGAACACTGAAAAGTCTGC 59.126 43.478 0.00 0.00 35.80 4.26
910 959 2.291741 CAGAACACTGAAAAGTCTGCCC 59.708 50.000 0.00 0.00 33.94 5.36
1123 1172 4.379243 ACCAACCCAGCTCGCTCG 62.379 66.667 0.00 0.00 0.00 5.03
1197 1246 4.426313 TCCTCTCCTCGCGCCTCA 62.426 66.667 0.00 0.00 0.00 3.86
1355 1407 2.043852 TGCTCGTCCTCCTCCTCC 60.044 66.667 0.00 0.00 0.00 4.30
1406 1458 6.746822 CGTCGACGACAGATAGTAGATAGTAT 59.253 42.308 33.35 0.00 43.02 2.12
1407 1459 7.907563 CGTCGACGACAGATAGTAGATAGTATA 59.092 40.741 33.35 0.00 43.02 1.47
1408 1460 9.734620 GTCGACGACAGATAGTAGATAGTATAT 57.265 37.037 22.66 0.00 32.09 0.86
1782 1834 2.565391 CACATGTACTCTACCACCACCA 59.435 50.000 0.00 0.00 0.00 4.17
1783 1835 2.565834 ACATGTACTCTACCACCACCAC 59.434 50.000 0.00 0.00 0.00 4.16
1814 1866 1.080230 CACTCAGTCCTGTCCTGCG 60.080 63.158 0.00 0.00 0.00 5.18
2252 2317 5.511234 ACTATACTACGTGCAGGGTTTAG 57.489 43.478 11.67 10.50 0.00 1.85
2259 2324 2.095059 ACGTGCAGGGTTTAGTACTACG 60.095 50.000 11.67 4.81 35.40 3.51
2260 2325 2.733227 CGTGCAGGGTTTAGTACTACGG 60.733 54.545 0.91 0.00 0.00 4.02
2289 2354 4.280425 TCATTTGCATTTGCCTGACTACAA 59.720 37.500 0.00 0.00 41.18 2.41
2294 2359 4.155826 TGCATTTGCCTGACTACAACATAC 59.844 41.667 0.00 0.00 41.18 2.39
2298 2363 3.872696 TGCCTGACTACAACATACATGG 58.127 45.455 0.00 0.00 0.00 3.66
2487 2553 7.987458 TCTGAATTCTTCTGTAGTTTCACAACT 59.013 33.333 7.05 0.00 45.73 3.16
2508 2574 2.102161 GCCTTGTAATTGCGGCCG 59.898 61.111 24.05 24.05 36.56 6.13
2518 2584 3.671008 AATTGCGGCCGTATATACTCA 57.329 42.857 28.70 10.63 0.00 3.41
2594 2668 1.892819 ATCCTGGAGCTGGTGACGTG 61.893 60.000 1.52 0.00 0.00 4.49
2603 2677 2.347490 GGTGACGTGCTGATGGGT 59.653 61.111 0.00 0.00 0.00 4.51
2609 2683 1.197721 GACGTGCTGATGGGTTTTCTG 59.802 52.381 0.00 0.00 0.00 3.02
2661 2735 5.470098 TCAATGTTCAAGCAGAGAAAGGTAC 59.530 40.000 0.00 0.00 0.00 3.34
2676 2750 3.577805 AGGTACATGTAATTCCCAGCC 57.422 47.619 7.25 1.92 0.00 4.85
2678 2752 3.117888 AGGTACATGTAATTCCCAGCCAG 60.118 47.826 7.25 0.00 0.00 4.85
2685 2759 1.511613 AATTCCCAGCCAGCTAGCTA 58.488 50.000 18.86 0.00 42.61 3.32
2686 2760 1.511613 ATTCCCAGCCAGCTAGCTAA 58.488 50.000 18.86 6.61 42.61 3.09
2687 2761 0.833287 TTCCCAGCCAGCTAGCTAAG 59.167 55.000 18.86 13.21 42.61 2.18
2737 3027 2.128035 GGTTGCTCTGTATCGAATCCG 58.872 52.381 0.00 0.00 37.07 4.18
2739 3029 3.243301 GGTTGCTCTGTATCGAATCCGTA 60.243 47.826 0.00 0.00 37.05 4.02
2746 3036 6.862090 GCTCTGTATCGAATCCGTAATAACTT 59.138 38.462 0.00 0.00 37.05 2.66
2757 3047 3.181534 CCGTAATAACTTGTGTCGCTGTG 60.182 47.826 0.00 0.00 0.00 3.66
2759 3049 1.808411 ATAACTTGTGTCGCTGTGGG 58.192 50.000 0.00 0.00 0.00 4.61
2761 3051 0.107410 AACTTGTGTCGCTGTGGGAA 60.107 50.000 0.00 0.00 0.00 3.97
2762 3052 0.108585 ACTTGTGTCGCTGTGGGAAT 59.891 50.000 0.00 0.00 0.00 3.01
2763 3053 1.238439 CTTGTGTCGCTGTGGGAATT 58.762 50.000 0.00 0.00 0.00 2.17
2840 3130 1.825474 ACATTCTCCCTGTACTCCACG 59.175 52.381 0.00 0.00 0.00 4.94
2891 3181 2.684881 GCCAACATTGACCATCTCGATT 59.315 45.455 0.00 0.00 0.00 3.34
2903 3193 0.881118 TCTCGATTTTGCCAAGGTGC 59.119 50.000 0.00 0.00 0.00 5.01
2949 3239 4.092091 GCATAGTGTCTTTCTTCGAAGGTG 59.908 45.833 24.37 14.38 0.00 4.00
2959 3249 8.171840 GTCTTTCTTCGAAGGTGATTAAATGAG 58.828 37.037 24.37 5.77 0.00 2.90
3046 3337 0.451135 GTGCTTTGTGCGTCGATGAC 60.451 55.000 9.31 4.64 46.63 3.06
3154 3445 1.202099 TTGGCCTCAACGACCCCATA 61.202 55.000 3.32 0.00 0.00 2.74
3157 3448 1.972660 GCCTCAACGACCCCATAGCT 61.973 60.000 0.00 0.00 0.00 3.32
3204 3495 6.609616 AGGTAAACTTGATGAAACTTTGGGAA 59.390 34.615 0.00 0.00 0.00 3.97
3220 3511 1.566018 GGAACCTGTCCTTGCGTTCG 61.566 60.000 0.00 0.00 43.98 3.95
3266 3563 3.446570 GGTGCAGTGCTCATGGGC 61.447 66.667 17.60 11.75 0.00 5.36
3367 3664 0.104671 GCTCACTGATCTGCTCCTCC 59.895 60.000 0.00 0.00 0.00 4.30
3373 3670 4.804420 ATCTGCTCCTCCCCGGCA 62.804 66.667 0.00 0.00 34.66 5.69
3417 3716 1.694150 AGCCGGCTGACACACATATAT 59.306 47.619 32.33 0.00 0.00 0.86
3620 3921 7.466320 GCAAAATGTTCAGTGATTGCTTTTCTT 60.466 33.333 17.28 0.00 39.87 2.52
3629 3930 6.308041 CAGTGATTGCTTTTCTTCATGTGATG 59.692 38.462 0.00 0.00 0.00 3.07
3633 3934 7.711772 TGATTGCTTTTCTTCATGTGATGTTTT 59.288 29.630 0.00 0.00 0.00 2.43
3660 3961 8.834004 TCTAAAGGAACAAGAGTAATAGCCTA 57.166 34.615 0.00 0.00 0.00 3.93
3665 3966 6.768381 AGGAACAAGAGTAATAGCCTAATTGC 59.232 38.462 0.00 0.00 0.00 3.56
3670 3971 7.829211 ACAAGAGTAATAGCCTAATTGCTTTGA 59.171 33.333 15.07 0.00 42.75 2.69
3695 3996 5.341872 CCAACAATTGGCATTCCTATCAA 57.658 39.130 10.83 0.00 45.17 2.57
3696 3997 5.920903 CCAACAATTGGCATTCCTATCAAT 58.079 37.500 10.83 0.00 45.17 2.57
3697 3998 6.350906 CCAACAATTGGCATTCCTATCAATT 58.649 36.000 10.83 0.00 45.17 2.32
3700 4001 5.920903 CAATTGGCATTCCTATCAATTGGT 58.079 37.500 15.64 0.00 45.91 3.67
3709 4010 2.830923 CCTATCAATTGGTTGGTTGGCA 59.169 45.455 10.68 0.00 35.18 4.92
3716 4017 6.430283 TCAATTGGTTGGTTGGCAACAAATC 61.430 40.000 29.63 25.46 45.72 2.17
3739 4041 1.106285 CTTGCCTCTTTACATGGCCC 58.894 55.000 0.00 0.00 45.56 5.80
3754 4056 1.555967 GGCCCTTTTTGCCTATGTGA 58.444 50.000 0.00 0.00 45.70 3.58
3758 4060 2.094026 CCCTTTTTGCCTATGTGAAGCC 60.094 50.000 0.00 0.00 0.00 4.35
3790 4092 5.309638 AGTAAAAAGGAAGGAAGTGAGCTC 58.690 41.667 6.82 6.82 0.00 4.09
3796 4098 2.278854 GAAGGAAGTGAGCTCTCATGC 58.721 52.381 16.19 9.85 42.18 4.06
3804 4108 1.622312 TGAGCTCTCATGCAAGTCAGT 59.378 47.619 16.19 0.00 34.14 3.41
3817 4121 5.204292 TGCAAGTCAGTCTCTATATGTCCT 58.796 41.667 0.00 0.00 0.00 3.85
3833 4137 2.634453 TGTCCTCTCATGCAAGAGTCAA 59.366 45.455 17.84 2.85 41.06 3.18
3834 4138 3.262660 TGTCCTCTCATGCAAGAGTCAAT 59.737 43.478 17.84 0.00 41.06 2.57
3857 4161 5.434408 TCTCTACACGTGCTCCTAGATAAA 58.566 41.667 17.22 1.80 0.00 1.40
3911 4215 5.947443 TCACTAACTTAAGAGCGACCTTAC 58.053 41.667 10.09 0.00 0.00 2.34
3912 4216 5.474532 TCACTAACTTAAGAGCGACCTTACA 59.525 40.000 10.09 0.00 0.00 2.41
3935 4239 6.599244 ACAACCAACCATATTGTATGAGTGAG 59.401 38.462 0.00 0.00 34.84 3.51
3976 4280 9.987272 TTTGATGACATGACAGTCTTATATAGG 57.013 33.333 0.00 0.00 39.27 2.57
3977 4281 7.606349 TGATGACATGACAGTCTTATATAGGC 58.394 38.462 0.00 0.00 39.27 3.93
3978 4282 6.976934 TGACATGACAGTCTTATATAGGCA 57.023 37.500 0.00 0.00 39.27 4.75
3979 4283 6.986250 TGACATGACAGTCTTATATAGGCAG 58.014 40.000 0.00 0.00 39.27 4.85
3980 4284 6.551227 TGACATGACAGTCTTATATAGGCAGT 59.449 38.462 0.00 0.00 39.27 4.40
3981 4285 7.069950 TGACATGACAGTCTTATATAGGCAGTT 59.930 37.037 0.00 0.00 39.27 3.16
3982 4286 7.212976 ACATGACAGTCTTATATAGGCAGTTG 58.787 38.462 0.00 0.00 27.12 3.16
3983 4287 6.791867 TGACAGTCTTATATAGGCAGTTGT 57.208 37.500 1.31 0.00 27.12 3.32
3984 4288 7.182817 TGACAGTCTTATATAGGCAGTTGTT 57.817 36.000 1.31 0.00 27.12 2.83
3985 4289 7.041721 TGACAGTCTTATATAGGCAGTTGTTG 58.958 38.462 1.31 0.00 27.12 3.33
3986 4290 6.349300 ACAGTCTTATATAGGCAGTTGTTGG 58.651 40.000 0.00 0.00 0.00 3.77
4065 4369 3.181506 CGGAGCTAAAGTTTTGCCTCATC 60.182 47.826 16.79 8.88 0.00 2.92
4081 4385 9.425248 TTTGCCTCATCCATTAATTAAGAAGAT 57.575 29.630 3.94 3.36 0.00 2.40
4083 4387 9.730705 TGCCTCATCCATTAATTAAGAAGATAG 57.269 33.333 3.94 0.00 0.00 2.08
4084 4388 9.732130 GCCTCATCCATTAATTAAGAAGATAGT 57.268 33.333 3.94 0.00 0.00 2.12
4089 4393 8.691661 TCCATTAATTAAGAAGATAGTTGCCC 57.308 34.615 3.94 0.00 0.00 5.36
4090 4394 8.278639 TCCATTAATTAAGAAGATAGTTGCCCA 58.721 33.333 3.94 0.00 0.00 5.36
4095 4399 8.738645 AATTAAGAAGATAGTTGCCCAGTTAG 57.261 34.615 0.00 0.00 0.00 2.34
4101 4405 0.764890 AGTTGCCCAGTTAGCTGACA 59.235 50.000 11.65 3.27 45.28 3.58
4103 4407 0.036732 TTGCCCAGTTAGCTGACAGG 59.963 55.000 12.58 12.58 45.28 4.00
4111 4415 2.039084 AGTTAGCTGACAGGAAACCAGG 59.961 50.000 11.65 0.00 0.00 4.45
4116 4420 0.534203 TGACAGGAAACCAGGCGAAC 60.534 55.000 0.00 0.00 0.00 3.95
4117 4421 1.228154 ACAGGAAACCAGGCGAACC 60.228 57.895 0.00 0.00 0.00 3.62
4142 4446 5.129634 TGTTACAATCTTGACCACACATGT 58.870 37.500 0.00 0.00 0.00 3.21
4155 4459 3.685139 ACACATGTGAACTACTCCCAG 57.315 47.619 31.94 0.88 0.00 4.45
4162 4466 4.930696 TGTGAACTACTCCCAGACTATGA 58.069 43.478 0.00 0.00 0.00 2.15
4181 4485 1.824852 GAACCCACATGAATCCCCAAC 59.175 52.381 0.00 0.00 0.00 3.77
4189 4493 3.069443 ACATGAATCCCCAACAAACACAC 59.931 43.478 0.00 0.00 0.00 3.82
4191 4495 2.955660 TGAATCCCCAACAAACACACTC 59.044 45.455 0.00 0.00 0.00 3.51
4201 4505 4.419522 ACAAACACACTCAACACAGAAC 57.580 40.909 0.00 0.00 0.00 3.01
4208 4512 1.837439 ACTCAACACAGAACCAGTCCA 59.163 47.619 0.00 0.00 0.00 4.02
4209 4513 2.158900 ACTCAACACAGAACCAGTCCAG 60.159 50.000 0.00 0.00 0.00 3.86
4217 4521 0.467290 GAACCAGTCCAGCACCCAAA 60.467 55.000 0.00 0.00 0.00 3.28
4220 4524 0.540365 CCAGTCCAGCACCCAAACAT 60.540 55.000 0.00 0.00 0.00 2.71
4291 4597 8.358148 GGATATAAAGATAGAGACAACGGACAA 58.642 37.037 0.00 0.00 0.00 3.18
4300 4606 2.037772 AGACAACGGACAAATCTGAGCT 59.962 45.455 0.00 0.00 34.98 4.09
4305 4611 0.723981 GGACAAATCTGAGCTCACGC 59.276 55.000 13.74 0.00 0.00 5.34
4306 4612 0.368227 GACAAATCTGAGCTCACGCG 59.632 55.000 13.74 3.53 42.32 6.01
4308 4614 0.094216 CAAATCTGAGCTCACGCGTG 59.906 55.000 32.76 32.76 42.32 5.34
4321 4627 1.219522 ACGCGTGCAACCTAGACAAC 61.220 55.000 12.93 0.00 0.00 3.32
4322 4628 0.944311 CGCGTGCAACCTAGACAACT 60.944 55.000 0.00 0.00 0.00 3.16
4323 4629 1.667756 CGCGTGCAACCTAGACAACTA 60.668 52.381 0.00 0.00 0.00 2.24
4324 4630 1.725164 GCGTGCAACCTAGACAACTAC 59.275 52.381 0.00 0.00 0.00 2.73
4325 4631 2.609737 GCGTGCAACCTAGACAACTACT 60.610 50.000 0.00 0.00 0.00 2.57
4326 4632 3.650139 CGTGCAACCTAGACAACTACTT 58.350 45.455 0.00 0.00 0.00 2.24
4327 4633 3.673809 CGTGCAACCTAGACAACTACTTC 59.326 47.826 0.00 0.00 0.00 3.01
4328 4634 3.995048 GTGCAACCTAGACAACTACTTCC 59.005 47.826 0.00 0.00 0.00 3.46
4329 4635 3.901844 TGCAACCTAGACAACTACTTCCT 59.098 43.478 0.00 0.00 0.00 3.36
4330 4636 4.021368 TGCAACCTAGACAACTACTTCCTC 60.021 45.833 0.00 0.00 0.00 3.71
4331 4637 4.621038 GCAACCTAGACAACTACTTCCTCC 60.621 50.000 0.00 0.00 0.00 4.30
4332 4638 3.354467 ACCTAGACAACTACTTCCTCCG 58.646 50.000 0.00 0.00 0.00 4.63
4333 4639 3.245193 ACCTAGACAACTACTTCCTCCGT 60.245 47.826 0.00 0.00 0.00 4.69
4334 4640 3.762823 CCTAGACAACTACTTCCTCCGTT 59.237 47.826 0.00 0.00 0.00 4.44
4335 4641 3.938289 AGACAACTACTTCCTCCGTTC 57.062 47.619 0.00 0.00 0.00 3.95
4336 4642 2.561858 AGACAACTACTTCCTCCGTTCC 59.438 50.000 0.00 0.00 0.00 3.62
4337 4643 2.561858 GACAACTACTTCCTCCGTTCCT 59.438 50.000 0.00 0.00 0.00 3.36
4338 4644 3.760684 GACAACTACTTCCTCCGTTCCTA 59.239 47.826 0.00 0.00 0.00 2.94
4339 4645 4.154942 ACAACTACTTCCTCCGTTCCTAA 58.845 43.478 0.00 0.00 0.00 2.69
4340 4646 4.590222 ACAACTACTTCCTCCGTTCCTAAA 59.410 41.667 0.00 0.00 0.00 1.85
4341 4647 5.247792 ACAACTACTTCCTCCGTTCCTAAAT 59.752 40.000 0.00 0.00 0.00 1.40
4342 4648 6.438425 ACAACTACTTCCTCCGTTCCTAAATA 59.562 38.462 0.00 0.00 0.00 1.40
4343 4649 7.125356 ACAACTACTTCCTCCGTTCCTAAATAT 59.875 37.037 0.00 0.00 0.00 1.28
4344 4650 8.636213 CAACTACTTCCTCCGTTCCTAAATATA 58.364 37.037 0.00 0.00 0.00 0.86
4345 4651 8.773033 ACTACTTCCTCCGTTCCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
4346 4652 8.858094 ACTACTTCCTCCGTTCCTAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
4347 4653 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
4348 4654 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
4349 4655 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
4350 4656 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
4351 4657 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
4352 4658 8.202137 TCCTCCGTTCCTAAATATAAGTCTTTG 58.798 37.037 0.00 0.00 0.00 2.77
4353 4659 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
4368 4674 6.783708 AGTCTTTGTAGAGATTCCACTAGG 57.216 41.667 0.00 0.00 0.00 3.02
4369 4675 6.257586 AGTCTTTGTAGAGATTCCACTAGGT 58.742 40.000 0.00 0.00 35.89 3.08
4370 4676 6.153680 AGTCTTTGTAGAGATTCCACTAGGTG 59.846 42.308 0.00 0.00 35.89 4.00
4385 4691 5.940595 CACTAGGTGGACTATATACGAAGC 58.059 45.833 0.00 0.00 0.00 3.86
4386 4692 5.472478 CACTAGGTGGACTATATACGAAGCA 59.528 44.000 0.00 0.00 0.00 3.91
4387 4693 6.016527 CACTAGGTGGACTATATACGAAGCAA 60.017 42.308 0.00 0.00 0.00 3.91
4388 4694 5.864418 AGGTGGACTATATACGAAGCAAA 57.136 39.130 0.00 0.00 0.00 3.68
4389 4695 6.229936 AGGTGGACTATATACGAAGCAAAA 57.770 37.500 0.00 0.00 0.00 2.44
4390 4696 6.827727 AGGTGGACTATATACGAAGCAAAAT 58.172 36.000 0.00 0.00 0.00 1.82
4391 4697 6.706270 AGGTGGACTATATACGAAGCAAAATG 59.294 38.462 0.00 0.00 0.00 2.32
4392 4698 6.704493 GGTGGACTATATACGAAGCAAAATGA 59.296 38.462 0.00 0.00 0.00 2.57
4393 4699 7.225931 GGTGGACTATATACGAAGCAAAATGAA 59.774 37.037 0.00 0.00 0.00 2.57
4394 4700 8.774586 GTGGACTATATACGAAGCAAAATGAAT 58.225 33.333 0.00 0.00 0.00 2.57
4395 4701 8.773645 TGGACTATATACGAAGCAAAATGAATG 58.226 33.333 0.00 0.00 0.00 2.67
4396 4702 8.988934 GGACTATATACGAAGCAAAATGAATGA 58.011 33.333 0.00 0.00 0.00 2.57
4403 4709 7.144722 ACGAAGCAAAATGAATGAATCTACA 57.855 32.000 0.00 0.00 0.00 2.74
4404 4710 7.023575 ACGAAGCAAAATGAATGAATCTACAC 58.976 34.615 0.00 0.00 0.00 2.90
4405 4711 7.094634 ACGAAGCAAAATGAATGAATCTACACT 60.095 33.333 0.00 0.00 0.00 3.55
4406 4712 7.752239 CGAAGCAAAATGAATGAATCTACACTT 59.248 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.413634 GCCACCGTTTGCAACTACATAC 60.414 50.000 0.00 0.00 0.00 2.39
1 2 1.807742 GCCACCGTTTGCAACTACATA 59.192 47.619 0.00 0.00 0.00 2.29
2 3 0.596082 GCCACCGTTTGCAACTACAT 59.404 50.000 0.00 0.00 0.00 2.29
3 4 1.777030 CGCCACCGTTTGCAACTACA 61.777 55.000 0.00 0.00 0.00 2.74
4 5 1.082366 CGCCACCGTTTGCAACTAC 60.082 57.895 0.00 0.00 0.00 2.73
70 71 3.897122 AGGAAGCCGGCAACCCAA 61.897 61.111 31.54 0.00 0.00 4.12
76 77 2.927856 TTCTCCAGGAAGCCGGCA 60.928 61.111 31.54 4.35 0.00 5.69
146 147 2.159490 GCTCGACCTGACTACTCTGTTC 60.159 54.545 0.00 0.00 0.00 3.18
160 161 2.611292 CTCCTGAATTTCATGCTCGACC 59.389 50.000 0.00 0.00 0.00 4.79
166 167 5.413833 TGTCTCTTTCTCCTGAATTTCATGC 59.586 40.000 0.00 0.00 31.56 4.06
197 198 2.112380 TTATTACAGCAGCAGCAGCA 57.888 45.000 12.92 0.00 45.49 4.41
357 358 0.391597 TTCTCGCTTCCTCGGTGTTT 59.608 50.000 0.00 0.00 0.00 2.83
367 368 5.198274 CACAACTAAACAACTTCTCGCTTC 58.802 41.667 0.00 0.00 0.00 3.86
468 473 2.685897 CGTCCTCCTCCAACAACAAAAA 59.314 45.455 0.00 0.00 0.00 1.94
473 478 0.106149 ACACGTCCTCCTCCAACAAC 59.894 55.000 0.00 0.00 0.00 3.32
481 486 0.539986 ACAAACACACACGTCCTCCT 59.460 50.000 0.00 0.00 0.00 3.69
488 493 1.069568 ACACACACACAAACACACACG 60.070 47.619 0.00 0.00 0.00 4.49
497 502 3.633235 GTGAAACAACACACACACACAA 58.367 40.909 0.00 0.00 40.11 3.33
562 573 0.747283 AGGTAAGACGCTCGACCGAT 60.747 55.000 7.21 0.00 33.97 4.18
566 577 3.620821 AGTAAGTAGGTAAGACGCTCGAC 59.379 47.826 0.00 0.00 0.00 4.20
583 594 9.141400 GTAACAAAACTCTCTCCACATAGTAAG 57.859 37.037 0.00 0.00 0.00 2.34
584 595 8.092687 GGTAACAAAACTCTCTCCACATAGTAA 58.907 37.037 0.00 0.00 0.00 2.24
585 596 7.310237 GGGTAACAAAACTCTCTCCACATAGTA 60.310 40.741 0.00 0.00 39.74 1.82
586 597 6.465084 GGTAACAAAACTCTCTCCACATAGT 58.535 40.000 0.00 0.00 0.00 2.12
637 648 7.170965 TGGAGCAACTTCTTTTCTCTCATTAT 58.829 34.615 0.00 0.00 0.00 1.28
668 679 6.875195 TCCCTTTTTCTTATGTAGTAACCACG 59.125 38.462 0.00 0.00 0.00 4.94
672 683 7.389607 TGTGCTCCCTTTTTCTTATGTAGTAAC 59.610 37.037 0.00 0.00 0.00 2.50
678 689 5.385198 TCTTGTGCTCCCTTTTTCTTATGT 58.615 37.500 0.00 0.00 0.00 2.29
739 756 6.588373 CCAACGTTCTTTTCTTCCTTCAAAAA 59.412 34.615 0.00 0.00 0.00 1.94
741 758 5.184287 ACCAACGTTCTTTTCTTCCTTCAAA 59.816 36.000 0.00 0.00 0.00 2.69
744 761 4.095932 ACACCAACGTTCTTTTCTTCCTTC 59.904 41.667 0.00 0.00 0.00 3.46
745 762 4.014406 ACACCAACGTTCTTTTCTTCCTT 58.986 39.130 0.00 0.00 0.00 3.36
746 763 3.617284 ACACCAACGTTCTTTTCTTCCT 58.383 40.909 0.00 0.00 0.00 3.36
780 821 2.189594 CACATCACCACTCCATGTGT 57.810 50.000 3.57 0.00 44.81 3.72
822 871 2.366266 CCGGATTGGTATCCTTCGGTTA 59.634 50.000 0.00 0.00 46.97 2.85
861 910 0.035056 AAGTGTATGTGGCCAGGAGC 60.035 55.000 5.11 0.00 42.60 4.70
879 928 1.136110 TCAGTGTTCTGTCTGACGCAA 59.864 47.619 2.98 0.00 41.91 4.85
883 932 5.006165 CAGACTTTTCAGTGTTCTGTCTGAC 59.994 44.000 22.09 0.00 39.77 3.51
887 936 3.002759 GGCAGACTTTTCAGTGTTCTGTC 59.997 47.826 0.00 0.00 41.91 3.51
891 940 1.264288 CGGGCAGACTTTTCAGTGTTC 59.736 52.381 0.00 0.00 31.22 3.18
897 946 0.882927 CGAACCGGGCAGACTTTTCA 60.883 55.000 6.32 0.00 0.00 2.69
926 975 3.710722 AGGGTTGGCTGCCTCTCG 61.711 66.667 21.03 0.00 0.00 4.04
927 976 2.045536 CAGGGTTGGCTGCCTCTC 60.046 66.667 21.03 12.79 0.00 3.20
928 977 4.357279 GCAGGGTTGGCTGCCTCT 62.357 66.667 21.03 9.17 40.40 3.69
929 978 4.357279 AGCAGGGTTGGCTGCCTC 62.357 66.667 21.03 12.58 46.79 4.70
1406 1458 7.646548 AGCGCAGAGGATAAGAATATACATA 57.353 36.000 11.47 0.00 0.00 2.29
1407 1459 6.537453 AGCGCAGAGGATAAGAATATACAT 57.463 37.500 11.47 0.00 0.00 2.29
1408 1460 5.984695 AGCGCAGAGGATAAGAATATACA 57.015 39.130 11.47 0.00 0.00 2.29
1428 1480 9.706691 ACAACCTATACATACATACATACAAGC 57.293 33.333 0.00 0.00 0.00 4.01
1814 1866 9.107367 CGTCAGTGAAGAAAAATAAATCTTGTC 57.893 33.333 0.00 0.00 36.08 3.18
1824 1876 3.059597 CGACAGCGTCAGTGAAGAAAAAT 60.060 43.478 10.48 0.00 32.09 1.82
1827 1879 1.487482 CGACAGCGTCAGTGAAGAAA 58.513 50.000 10.48 0.00 32.09 2.52
1849 1901 2.927553 AGGAAAAATGCAGCATCGAC 57.072 45.000 8.77 1.07 0.00 4.20
2232 2294 6.122277 AGTACTAAACCCTGCACGTAGTATA 58.878 40.000 0.00 0.00 41.61 1.47
2233 2295 4.952335 AGTACTAAACCCTGCACGTAGTAT 59.048 41.667 0.00 0.00 41.61 2.12
2239 2301 2.523015 CGTAGTACTAAACCCTGCACG 58.477 52.381 3.61 0.00 0.00 5.34
2242 2304 1.479730 AGCCGTAGTACTAAACCCTGC 59.520 52.381 3.61 0.58 0.00 4.85
2252 2317 4.178540 TGCAAATGAAGTAGCCGTAGTAC 58.821 43.478 0.00 0.00 0.00 2.73
2259 2324 2.931969 GGCAAATGCAAATGAAGTAGCC 59.068 45.455 7.80 0.00 44.36 3.93
2260 2325 3.615496 CAGGCAAATGCAAATGAAGTAGC 59.385 43.478 7.80 0.00 44.36 3.58
2322 2388 6.657541 GGGTGTAACAATTTCTTGATACCAGA 59.342 38.462 0.00 0.00 38.93 3.86
2372 2438 1.582610 ATGCGACCGCCGACAAATTT 61.583 50.000 12.08 0.00 41.76 1.82
2508 2574 9.239002 CACTTGTGTTAAGAGCTGAGTATATAC 57.761 37.037 4.60 4.60 0.00 1.47
2518 2584 3.214328 CCAACCACTTGTGTTAAGAGCT 58.786 45.455 0.00 0.00 0.00 4.09
2594 2668 0.251787 ACCCCAGAAAACCCATCAGC 60.252 55.000 0.00 0.00 0.00 4.26
2603 2677 5.250543 TGATAAGATGACAGACCCCAGAAAA 59.749 40.000 0.00 0.00 0.00 2.29
2609 2683 4.276926 GCAAATGATAAGATGACAGACCCC 59.723 45.833 0.00 0.00 0.00 4.95
2661 2735 2.062971 AGCTGGCTGGGAATTACATG 57.937 50.000 0.00 0.00 0.00 3.21
2685 2759 5.183713 TGTTGCAAGATAACAATGCTAGCTT 59.816 36.000 17.23 6.81 40.66 3.74
2686 2760 4.701651 TGTTGCAAGATAACAATGCTAGCT 59.298 37.500 17.23 0.00 40.66 3.32
2687 2761 4.795278 GTGTTGCAAGATAACAATGCTAGC 59.205 41.667 8.10 8.10 39.50 3.42
2688 2762 6.025896 CAGTGTTGCAAGATAACAATGCTAG 58.974 40.000 0.00 0.00 43.89 3.42
2690 2764 4.801891 CAGTGTTGCAAGATAACAATGCT 58.198 39.130 0.00 0.00 43.89 3.79
2693 2767 6.370593 CGTAACAGTGTTGCAAGATAACAAT 58.629 36.000 21.69 0.00 39.50 2.71
2694 2768 5.277586 CCGTAACAGTGTTGCAAGATAACAA 60.278 40.000 21.69 0.00 39.50 2.83
2696 2770 4.212636 ACCGTAACAGTGTTGCAAGATAAC 59.787 41.667 21.69 7.84 0.00 1.89
2737 3027 3.124636 CCCACAGCGACACAAGTTATTAC 59.875 47.826 0.00 0.00 0.00 1.89
2739 3029 2.151202 CCCACAGCGACACAAGTTATT 58.849 47.619 0.00 0.00 0.00 1.40
2746 3036 1.606668 GAAAATTCCCACAGCGACACA 59.393 47.619 0.00 0.00 0.00 3.72
2763 3053 2.479389 CGTGCCTTTTCACAAGCTGAAA 60.479 45.455 0.00 0.00 45.48 2.69
2777 3067 1.805428 AAATTTCTGCCGCGTGCCTT 61.805 50.000 15.40 1.47 40.16 4.35
2903 3193 1.977594 GAGCCAACGCCACGGTTATG 61.978 60.000 0.00 0.00 34.57 1.90
2949 3239 6.492772 AGAATGCAAGGGGATCTCATTTAATC 59.507 38.462 0.00 0.00 0.00 1.75
2959 3249 3.212685 CAGAAGAGAATGCAAGGGGATC 58.787 50.000 0.00 0.00 0.00 3.36
3052 3343 1.437089 CGTCAGCGAAGTGTTTGCG 60.437 57.895 0.00 0.00 44.92 4.85
3154 3445 1.698506 CTGTTCCGATCCCTCTAGCT 58.301 55.000 0.00 0.00 0.00 3.32
3157 3448 2.032620 GAAGCTGTTCCGATCCCTCTA 58.967 52.381 0.00 0.00 0.00 2.43
3204 3495 2.665185 GCGAACGCAAGGACAGGT 60.665 61.111 14.26 0.00 46.39 4.00
3367 3664 3.058160 CTTTGCCTGACTGCCGGG 61.058 66.667 2.18 0.00 44.49 5.73
3417 3716 4.250464 GCTGTTGTTGCTGTATACCAGTA 58.750 43.478 0.00 0.00 43.55 2.74
3475 3775 7.595819 TTTGTTCTCCAATCACTTACCATTT 57.404 32.000 0.00 0.00 31.81 2.32
3487 3787 7.201723 GGAAATTTTGCACTTTTGTTCTCCAAT 60.202 33.333 0.00 0.00 31.81 3.16
3539 3840 2.964464 TGACTTGTTGCAACCATCCATT 59.036 40.909 26.14 4.05 0.00 3.16
3633 3934 8.603304 AGGCTATTACTCTTGTTCCTTTAGAAA 58.397 33.333 0.00 0.00 35.85 2.52
3660 3961 4.216687 CCAATTGTTGGCATCAAAGCAATT 59.783 37.500 14.40 9.12 45.17 2.32
3685 3986 4.162131 GCCAACCAACCAATTGATAGGAAT 59.838 41.667 7.12 0.00 38.15 3.01
3686 3987 3.513515 GCCAACCAACCAATTGATAGGAA 59.486 43.478 7.12 0.00 38.15 3.36
3687 3988 3.096092 GCCAACCAACCAATTGATAGGA 58.904 45.455 7.12 0.00 38.15 2.94
3688 3989 2.830923 TGCCAACCAACCAATTGATAGG 59.169 45.455 7.12 7.68 38.15 2.57
3689 3990 4.244862 GTTGCCAACCAACCAATTGATAG 58.755 43.478 7.12 0.00 46.44 2.08
3690 3991 4.264460 GTTGCCAACCAACCAATTGATA 57.736 40.909 7.12 0.00 46.44 2.15
3691 3992 3.124578 GTTGCCAACCAACCAATTGAT 57.875 42.857 7.12 0.00 46.44 2.57
3692 3993 2.611225 GTTGCCAACCAACCAATTGA 57.389 45.000 7.12 0.00 46.44 2.57
3700 4001 2.428890 AGAACGATTTGTTGCCAACCAA 59.571 40.909 4.90 0.19 42.09 3.67
3709 4010 4.918810 AAAGAGGCAAGAACGATTTGTT 57.081 36.364 0.00 0.00 45.61 2.83
3716 4017 3.747099 CCATGTAAAGAGGCAAGAACG 57.253 47.619 0.00 0.00 0.00 3.95
3739 4041 2.487762 TCGGCTTCACATAGGCAAAAAG 59.512 45.455 0.00 0.00 40.49 2.27
3754 4056 4.065789 CCTTTTTACTTGTCTCTCGGCTT 58.934 43.478 0.00 0.00 0.00 4.35
3758 4060 5.539048 TCCTTCCTTTTTACTTGTCTCTCG 58.461 41.667 0.00 0.00 0.00 4.04
3790 4092 6.747125 ACATATAGAGACTGACTTGCATGAG 58.253 40.000 6.60 0.00 0.00 2.90
3796 4098 6.770303 TGAGAGGACATATAGAGACTGACTTG 59.230 42.308 0.00 0.00 0.00 3.16
3804 4108 6.310149 TCTTGCATGAGAGGACATATAGAGA 58.690 40.000 0.00 0.00 0.00 3.10
3833 4137 3.562343 TCTAGGAGCACGTGTAGAGAT 57.438 47.619 18.38 1.54 0.00 2.75
3834 4138 3.562343 ATCTAGGAGCACGTGTAGAGA 57.438 47.619 18.38 12.83 0.00 3.10
3857 4161 5.300539 GCACTTTCTCTTTTTCTCCTTCCTT 59.699 40.000 0.00 0.00 0.00 3.36
3887 4191 5.662674 AAGGTCGCTCTTAAGTTAGTGAT 57.337 39.130 9.81 0.00 34.94 3.06
3911 4215 6.599244 ACTCACTCATACAATATGGTTGGTTG 59.401 38.462 0.00 0.00 0.00 3.77
3912 4216 6.721318 ACTCACTCATACAATATGGTTGGTT 58.279 36.000 0.00 0.00 0.00 3.67
3947 4251 9.896645 ATATAAGACTGTCATGTCATCAAAAGT 57.103 29.630 10.88 0.00 39.27 2.66
3974 4278 7.777910 TGTTAATAATATAGCCAACAACTGCCT 59.222 33.333 0.00 0.00 0.00 4.75
3975 4279 7.936584 TGTTAATAATATAGCCAACAACTGCC 58.063 34.615 0.00 0.00 0.00 4.85
3976 4280 9.965824 AATGTTAATAATATAGCCAACAACTGC 57.034 29.630 0.00 0.00 30.48 4.40
3978 4282 9.965824 GCAATGTTAATAATATAGCCAACAACT 57.034 29.630 0.00 0.00 30.48 3.16
3979 4283 9.965824 AGCAATGTTAATAATATAGCCAACAAC 57.034 29.630 0.00 0.00 30.48 3.32
3981 4285 9.573166 AGAGCAATGTTAATAATATAGCCAACA 57.427 29.630 0.00 0.00 0.00 3.33
4038 4342 3.476181 GCAAAACTTTAGCTCCGTTACG 58.524 45.455 0.00 0.00 0.00 3.18
4039 4343 3.501062 AGGCAAAACTTTAGCTCCGTTAC 59.499 43.478 0.00 0.00 0.00 2.50
4040 4344 3.746940 AGGCAAAACTTTAGCTCCGTTA 58.253 40.909 0.00 0.00 0.00 3.18
4043 4347 2.151202 TGAGGCAAAACTTTAGCTCCG 58.849 47.619 0.00 0.00 0.00 4.63
4044 4348 3.129462 GGATGAGGCAAAACTTTAGCTCC 59.871 47.826 0.00 0.00 0.00 4.70
4046 4350 3.766545 TGGATGAGGCAAAACTTTAGCT 58.233 40.909 0.00 0.00 0.00 3.32
4047 4351 4.725790 ATGGATGAGGCAAAACTTTAGC 57.274 40.909 0.00 0.00 0.00 3.09
4050 4354 9.657419 CTTAATTAATGGATGAGGCAAAACTTT 57.343 29.630 0.00 0.00 0.00 2.66
4051 4355 9.034800 TCTTAATTAATGGATGAGGCAAAACTT 57.965 29.630 0.00 0.00 0.00 2.66
4052 4356 8.593945 TCTTAATTAATGGATGAGGCAAAACT 57.406 30.769 0.00 0.00 0.00 2.66
4065 4369 8.463930 TGGGCAACTATCTTCTTAATTAATGG 57.536 34.615 0.00 0.00 0.00 3.16
4081 4385 1.974957 TGTCAGCTAACTGGGCAACTA 59.025 47.619 0.00 0.00 44.59 2.24
4083 4387 1.160137 CTGTCAGCTAACTGGGCAAC 58.840 55.000 0.00 0.00 44.59 4.17
4084 4388 0.036732 CCTGTCAGCTAACTGGGCAA 59.963 55.000 4.99 0.00 44.59 4.52
4085 4389 0.835971 TCCTGTCAGCTAACTGGGCA 60.836 55.000 12.70 0.00 44.59 5.36
4087 4391 2.427506 GTTTCCTGTCAGCTAACTGGG 58.572 52.381 12.70 3.43 44.59 4.45
4088 4392 2.224523 TGGTTTCCTGTCAGCTAACTGG 60.225 50.000 6.59 6.59 44.59 4.00
4089 4393 3.070018 CTGGTTTCCTGTCAGCTAACTG 58.930 50.000 12.34 0.00 45.95 3.16
4090 4394 2.039084 CCTGGTTTCCTGTCAGCTAACT 59.961 50.000 12.34 0.00 0.00 2.24
4095 4399 2.328099 CGCCTGGTTTCCTGTCAGC 61.328 63.158 0.00 0.00 0.00 4.26
4101 4405 2.154074 AGGGTTCGCCTGGTTTCCT 61.154 57.895 0.00 0.00 37.45 3.36
4103 4407 0.822121 AACAGGGTTCGCCTGGTTTC 60.822 55.000 11.61 0.00 39.38 2.78
4111 4415 3.071479 TCAAGATTGTAACAGGGTTCGC 58.929 45.455 0.00 0.00 0.00 4.70
4116 4420 3.502211 GTGTGGTCAAGATTGTAACAGGG 59.498 47.826 0.00 0.00 0.00 4.45
4117 4421 4.133820 TGTGTGGTCAAGATTGTAACAGG 58.866 43.478 0.00 0.00 0.00 4.00
4119 4423 5.008514 CACATGTGTGGTCAAGATTGTAACA 59.991 40.000 18.03 0.00 42.10 2.41
4122 4426 4.967036 TCACATGTGTGGTCAAGATTGTA 58.033 39.130 24.63 0.00 45.65 2.41
4124 4428 4.276678 AGTTCACATGTGTGGTCAAGATTG 59.723 41.667 24.63 0.00 45.65 2.67
4142 4446 4.710375 GGTTCATAGTCTGGGAGTAGTTCA 59.290 45.833 0.00 0.00 0.00 3.18
4155 4459 4.137543 GGGATTCATGTGGGTTCATAGTC 58.862 47.826 0.00 0.00 0.00 2.59
4162 4466 1.148867 TGTTGGGGATTCATGTGGGTT 59.851 47.619 0.00 0.00 0.00 4.11
4181 4485 3.190327 TGGTTCTGTGTTGAGTGTGTTTG 59.810 43.478 0.00 0.00 0.00 2.93
4189 4493 2.487934 CTGGACTGGTTCTGTGTTGAG 58.512 52.381 0.00 0.00 0.00 3.02
4191 4495 0.947244 GCTGGACTGGTTCTGTGTTG 59.053 55.000 0.00 0.00 0.00 3.33
4201 4505 0.540365 ATGTTTGGGTGCTGGACTGG 60.540 55.000 0.00 0.00 0.00 4.00
4208 4512 2.114616 TGACCAAAATGTTTGGGTGCT 58.885 42.857 20.78 3.05 44.48 4.40
4209 4513 2.209273 GTGACCAAAATGTTTGGGTGC 58.791 47.619 20.78 11.74 44.48 5.01
4273 4579 5.419155 TCAGATTTGTCCGTTGTCTCTATCT 59.581 40.000 0.00 0.00 0.00 1.98
4276 4582 4.618460 GCTCAGATTTGTCCGTTGTCTCTA 60.618 45.833 0.00 0.00 0.00 2.43
4300 4606 1.372499 GTCTAGGTTGCACGCGTGA 60.372 57.895 41.19 23.48 0.00 4.35
4305 4611 3.299340 AGTAGTTGTCTAGGTTGCACG 57.701 47.619 0.00 0.00 0.00 5.34
4306 4612 3.995048 GGAAGTAGTTGTCTAGGTTGCAC 59.005 47.826 0.00 0.00 0.00 4.57
4308 4614 4.496360 GAGGAAGTAGTTGTCTAGGTTGC 58.504 47.826 0.00 0.00 0.00 4.17
4321 4627 8.858094 ACTTATATTTAGGAACGGAGGAAGTAG 58.142 37.037 0.00 0.00 0.00 2.57
4322 4628 8.773033 ACTTATATTTAGGAACGGAGGAAGTA 57.227 34.615 0.00 0.00 0.00 2.24
4323 4629 7.564292 AGACTTATATTTAGGAACGGAGGAAGT 59.436 37.037 0.00 0.00 0.00 3.01
4324 4630 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
4325 4631 7.909485 AGACTTATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
4326 4632 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
4327 4633 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
4328 4634 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
4342 4648 8.919145 CCTAGTGGAATCTCTACAAAGACTTAT 58.081 37.037 0.00 0.00 34.57 1.73
4343 4649 7.894364 ACCTAGTGGAATCTCTACAAAGACTTA 59.106 37.037 0.00 0.00 37.04 2.24
4344 4650 6.726764 ACCTAGTGGAATCTCTACAAAGACTT 59.273 38.462 0.00 0.00 37.04 3.01
4345 4651 6.153680 CACCTAGTGGAATCTCTACAAAGACT 59.846 42.308 0.00 0.00 37.04 3.24
4346 4652 6.334202 CACCTAGTGGAATCTCTACAAAGAC 58.666 44.000 0.00 0.00 37.04 3.01
4347 4653 6.531503 CACCTAGTGGAATCTCTACAAAGA 57.468 41.667 0.00 0.00 37.04 2.52
4362 4668 5.472478 TGCTTCGTATATAGTCCACCTAGTG 59.528 44.000 0.00 0.00 0.00 2.74
4363 4669 5.628130 TGCTTCGTATATAGTCCACCTAGT 58.372 41.667 0.00 0.00 0.00 2.57
4364 4670 6.570672 TTGCTTCGTATATAGTCCACCTAG 57.429 41.667 0.00 0.00 0.00 3.02
4365 4671 6.964807 TTTGCTTCGTATATAGTCCACCTA 57.035 37.500 0.00 0.00 0.00 3.08
4366 4672 5.864418 TTTGCTTCGTATATAGTCCACCT 57.136 39.130 0.00 0.00 0.00 4.00
4367 4673 6.704493 TCATTTTGCTTCGTATATAGTCCACC 59.296 38.462 0.00 0.00 0.00 4.61
4368 4674 7.709269 TCATTTTGCTTCGTATATAGTCCAC 57.291 36.000 0.00 0.00 0.00 4.02
4369 4675 8.773645 CATTCATTTTGCTTCGTATATAGTCCA 58.226 33.333 0.00 0.00 0.00 4.02
4370 4676 8.988934 TCATTCATTTTGCTTCGTATATAGTCC 58.011 33.333 0.00 0.00 0.00 3.85
4377 4683 8.892723 TGTAGATTCATTCATTTTGCTTCGTAT 58.107 29.630 0.00 0.00 0.00 3.06
4378 4684 8.175069 GTGTAGATTCATTCATTTTGCTTCGTA 58.825 33.333 0.00 0.00 0.00 3.43
4379 4685 7.023575 GTGTAGATTCATTCATTTTGCTTCGT 58.976 34.615 0.00 0.00 0.00 3.85
4380 4686 7.246311 AGTGTAGATTCATTCATTTTGCTTCG 58.754 34.615 0.00 0.00 0.00 3.79
4381 4687 8.976986 AAGTGTAGATTCATTCATTTTGCTTC 57.023 30.769 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.