Multiple sequence alignment - TraesCS3D01G533900

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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 TraesCS3D01G533900 chr3D 100.000 3097 0 0 1 3097 609121976 609118880 0.000000e+00 5720.0
1 TraesCS3D01G533900 chr3A 94.213 2523 91 26 1 2508 742468728 742466246 0.000000e+00 3799.0
2 TraesCS3D01G533900 chr3A 97.887 142 3 0 2724 2865 742466246 742466105 2.390000e-61 246.0
3 TraesCS3D01G533900 chr1B 86.940 1317 111 27 865 2142 685621071 685619777 0.000000e+00 1423.0
4 TraesCS3D01G533900 chr1B 84.637 1393 105 49 848 2142 688121832 688123213 0.000000e+00 1286.0
5 TraesCS3D01G533900 chr1B 84.722 72 5 3 657 727 688121731 688121797 1.990000e-07 67.6
6 TraesCS3D01G533900 chr3B 85.629 501 63 8 2158 2653 819856387 819855891 4.580000e-143 518.0
7 TraesCS3D01G533900 chr3B 84.000 175 24 3 1 173 819857444 819857272 6.870000e-37 165.0
8 TraesCS3D01G533900 chr1D 89.267 382 39 2 1771 2151 495022189 495022569 7.770000e-131 477.0
9 TraesCS3D01G533900 chr1D 81.688 557 78 16 961 1499 495021601 495022151 2.830000e-120 442.0
10 TraesCS3D01G533900 chr2D 97.009 234 5 1 2866 3097 10959902 10959669 2.900000e-105 392.0
11 TraesCS3D01G533900 chr2D 95.708 233 7 2 2867 3097 63320561 63320330 3.770000e-99 372.0
12 TraesCS3D01G533900 chr1A 96.170 235 5 3 2867 3097 294183334 294183568 6.270000e-102 381.0
13 TraesCS3D01G533900 chr5A 96.154 234 5 3 2867 3097 399038074 399037842 2.250000e-101 379.0
14 TraesCS3D01G533900 chr5A 96.137 233 6 2 2867 3097 525020836 525021067 8.110000e-101 377.0
15 TraesCS3D01G533900 chr7A 95.726 234 6 3 2867 3097 565135569 565135337 1.050000e-99 374.0
16 TraesCS3D01G533900 chr5B 95.745 235 5 4 2867 3097 633254296 633254063 1.050000e-99 374.0
17 TraesCS3D01G533900 chr4A 95.339 236 7 3 2865 3097 536899795 536900029 3.770000e-99 372.0
18 TraesCS3D01G533900 chr2A 95.708 233 7 2 2867 3097 672007591 672007360 3.770000e-99 372.0
19 TraesCS3D01G533900 chr4D 82.667 75 13 0 2654 2728 20124918 20124992 1.990000e-07 67.6


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 TraesCS3D01G533900 chr3D 609118880 609121976 3096 True 5720.0 5720 100.0000 1 3097 1 chr3D.!!$R1 3096
1 TraesCS3D01G533900 chr3A 742466105 742468728 2623 True 2022.5 3799 96.0500 1 2865 2 chr3A.!!$R1 2864
2 TraesCS3D01G533900 chr1B 685619777 685621071 1294 True 1423.0 1423 86.9400 865 2142 1 chr1B.!!$R1 1277
3 TraesCS3D01G533900 chr1B 688121731 688123213 1482 False 676.8 1286 84.6795 657 2142 2 chr1B.!!$F1 1485
4 TraesCS3D01G533900 chr3B 819855891 819857444 1553 True 341.5 518 84.8145 1 2653 2 chr3B.!!$R1 2652
5 TraesCS3D01G533900 chr1D 495021601 495022569 968 False 459.5 477 85.4775 961 2151 2 chr1D.!!$F1 1190

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
252 338 0.345502 AGTGGGCCTAGGGTATCCAA 59.654 55.0 11.72 0.0 34.83 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2688 0.323178 TGGTCGTCTCTACAGGGACC 60.323 60.0 3.67 1.68 40.96 4.46 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
62 64 1.244816 TGACCAGATCGACGAGTTGT 58.755 50.000 3.01 0.00 0.00 3.32
252 338 0.345502 AGTGGGCCTAGGGTATCCAA 59.654 55.000 11.72 0.00 34.83 3.53
426 518 3.133901 AGATATGTACCCGCATGTGTTCA 59.866 43.478 5.38 0.26 0.00 3.18
526 618 7.281100 GGAGAAAGTGGAGACATATTTAACTGG 59.719 40.741 0.00 0.00 46.14 4.00
623 716 3.064820 ACAACGTCTTGGAATTGTGTGAC 59.935 43.478 0.00 0.00 34.08 3.67
711 804 1.686110 AGCCCAACTACTAGCCGCT 60.686 57.895 0.00 0.00 0.00 5.52
730 823 2.852281 GCCCCTCCCCTCAAAACCA 61.852 63.158 0.00 0.00 0.00 3.67
731 824 1.076727 CCCCTCCCCTCAAAACCAC 59.923 63.158 0.00 0.00 0.00 4.16
732 825 1.435346 CCCCTCCCCTCAAAACCACT 61.435 60.000 0.00 0.00 0.00 4.00
897 1015 2.672996 GCCGCCAGAAGCCAGAAA 60.673 61.111 0.00 0.00 38.78 2.52
1025 1180 4.079253 GCCCAAGTCAGAATAGTTTCCAA 58.921 43.478 0.00 0.00 31.84 3.53
1043 1198 2.559668 CCAACCTTGCTGATGTTGATGT 59.440 45.455 3.35 0.00 41.38 3.06
1307 1462 1.160137 GGAGTTGAAGCAAGCATCGT 58.840 50.000 0.00 0.00 0.00 3.73
1419 1584 4.533707 CCATCTATCCACACCCTCATGTAT 59.466 45.833 0.00 0.00 0.00 2.29
1493 1996 4.512944 ACATCTTATATGTTCGCTTGCCTG 59.487 41.667 0.00 0.00 0.00 4.85
1502 2005 2.554636 CGCTTGCCTGCTGTTGGAA 61.555 57.895 0.00 0.00 0.00 3.53
1507 2019 3.777478 CTTGCCTGCTGTTGGAAATATG 58.223 45.455 0.00 0.00 0.00 1.78
1665 2195 9.065871 GTGCATTTCATTGAGATAACAACTTAC 57.934 33.333 0.00 0.00 32.50 2.34
1674 2204 7.905604 TGAGATAACAACTTACAACCAGATG 57.094 36.000 0.00 0.00 0.00 2.90
1763 2293 9.502091 TGTGCTATTGTTTGTCTAGAAAACTAT 57.498 29.630 20.94 20.35 38.17 2.12
1816 2346 7.490402 GCATTTTTCTCATTATCAGTTCCCAAG 59.510 37.037 0.00 0.00 0.00 3.61
1825 2355 8.556589 TCATTATCAGTTCCCAAGATTTCCTAA 58.443 33.333 0.00 0.00 0.00 2.69
1857 2387 0.678395 CACACACCAGCAGAGAGTCT 59.322 55.000 0.00 0.00 0.00 3.24
1869 2399 5.534278 CAGCAGAGAGTCTCATATCAACCTA 59.466 44.000 22.05 0.00 32.06 3.08
2044 2574 5.488919 AGTTCAAGAGGATTATGGAGGAACA 59.511 40.000 0.00 0.00 35.73 3.18
2090 2620 4.743651 GCGGATGATGAATTTCCTCCACTA 60.744 45.833 3.34 0.00 31.84 2.74
2527 3069 7.907389 TGGTGTATTTATTGGTTTTGGCATAA 58.093 30.769 0.00 0.00 0.00 1.90
2586 3128 7.914427 ATATGATTGTCTACCTTACCTCACA 57.086 36.000 0.00 0.00 0.00 3.58
2605 3147 9.632638 ACCTCACATGCAAGTAAATAGATAATT 57.367 29.630 0.00 0.00 0.00 1.40
2631 3173 8.749354 TCTAGATTGTGTATGTAAGTGATGTGT 58.251 33.333 0.00 0.00 0.00 3.72
2632 3174 7.601073 AGATTGTGTATGTAAGTGATGTGTG 57.399 36.000 0.00 0.00 0.00 3.82
2640 3182 5.984233 TGTAAGTGATGTGTGTGTTTCTC 57.016 39.130 0.00 0.00 0.00 2.87
2641 3183 4.814234 TGTAAGTGATGTGTGTGTTTCTCC 59.186 41.667 0.00 0.00 0.00 3.71
2645 3187 3.627577 GTGATGTGTGTGTTTCTCCAAGT 59.372 43.478 0.00 0.00 0.00 3.16
2653 3195 4.156008 GTGTGTTTCTCCAAGTGACTTGTT 59.844 41.667 22.40 0.00 39.58 2.83
2654 3196 4.155826 TGTGTTTCTCCAAGTGACTTGTTG 59.844 41.667 22.40 14.66 39.58 3.33
2655 3197 3.694072 TGTTTCTCCAAGTGACTTGTTGG 59.306 43.478 22.40 9.85 44.08 3.77
2656 3198 1.967319 TCTCCAAGTGACTTGTTGGC 58.033 50.000 22.40 0.00 42.67 4.52
2657 3199 0.954452 CTCCAAGTGACTTGTTGGCC 59.046 55.000 22.40 0.00 42.67 5.36
2658 3200 0.550914 TCCAAGTGACTTGTTGGCCT 59.449 50.000 22.40 0.00 42.67 5.19
2659 3201 1.771854 TCCAAGTGACTTGTTGGCCTA 59.228 47.619 22.40 0.00 42.67 3.93
2660 3202 2.154462 CCAAGTGACTTGTTGGCCTAG 58.846 52.381 22.40 2.43 39.58 3.02
2661 3203 2.224523 CCAAGTGACTTGTTGGCCTAGA 60.225 50.000 22.40 0.00 39.58 2.43
2662 3204 3.476552 CAAGTGACTTGTTGGCCTAGAA 58.523 45.455 16.84 0.00 36.79 2.10
2663 3205 4.074970 CAAGTGACTTGTTGGCCTAGAAT 58.925 43.478 16.84 0.00 36.79 2.40
2664 3206 5.245531 CAAGTGACTTGTTGGCCTAGAATA 58.754 41.667 16.84 0.00 36.79 1.75
2665 3207 4.833390 AGTGACTTGTTGGCCTAGAATAC 58.167 43.478 3.32 1.49 0.00 1.89
2666 3208 4.286032 AGTGACTTGTTGGCCTAGAATACA 59.714 41.667 3.32 1.89 0.00 2.29
2667 3209 5.045578 AGTGACTTGTTGGCCTAGAATACAT 60.046 40.000 3.32 0.00 0.00 2.29
2668 3210 5.065218 GTGACTTGTTGGCCTAGAATACATG 59.935 44.000 3.32 0.00 0.00 3.21
2669 3211 4.526970 ACTTGTTGGCCTAGAATACATGG 58.473 43.478 3.32 0.00 0.00 3.66
2670 3212 4.018415 ACTTGTTGGCCTAGAATACATGGT 60.018 41.667 3.32 0.00 0.00 3.55
2671 3213 4.150897 TGTTGGCCTAGAATACATGGTC 57.849 45.455 3.32 0.00 0.00 4.02
2672 3214 3.131396 GTTGGCCTAGAATACATGGTCG 58.869 50.000 3.32 0.00 0.00 4.79
2673 3215 2.673258 TGGCCTAGAATACATGGTCGA 58.327 47.619 3.32 0.00 0.00 4.20
2674 3216 2.628178 TGGCCTAGAATACATGGTCGAG 59.372 50.000 3.32 0.00 0.00 4.04
2675 3217 2.891580 GGCCTAGAATACATGGTCGAGA 59.108 50.000 0.00 0.00 0.00 4.04
2676 3218 3.321111 GGCCTAGAATACATGGTCGAGAA 59.679 47.826 0.00 0.00 0.00 2.87
2677 3219 4.551388 GCCTAGAATACATGGTCGAGAAG 58.449 47.826 0.00 0.00 0.00 2.85
2678 3220 4.551388 CCTAGAATACATGGTCGAGAAGC 58.449 47.826 0.00 0.00 0.00 3.86
2679 3221 4.279671 CCTAGAATACATGGTCGAGAAGCT 59.720 45.833 0.00 0.00 0.00 3.74
2680 3222 4.314740 AGAATACATGGTCGAGAAGCTC 57.685 45.455 0.00 0.00 0.00 4.09
2689 3231 2.577378 GAGAAGCTCGGCGTCGAC 60.577 66.667 8.66 5.18 41.56 4.20
2690 3232 3.324099 GAGAAGCTCGGCGTCGACA 62.324 63.158 8.66 0.00 41.56 4.35
2691 3233 2.430244 GAAGCTCGGCGTCGACAA 60.430 61.111 8.66 0.00 40.88 3.18
2692 3234 2.430921 AAGCTCGGCGTCGACAAG 60.431 61.111 8.66 0.00 40.88 3.16
2693 3235 2.797866 GAAGCTCGGCGTCGACAAGA 62.798 60.000 8.66 10.12 40.88 3.02
2694 3236 2.804368 AAGCTCGGCGTCGACAAGAG 62.804 60.000 8.66 19.35 40.88 2.85
2695 3237 2.876645 CTCGGCGTCGACAAGAGC 60.877 66.667 8.66 10.48 40.88 4.09
2696 3238 4.753877 TCGGCGTCGACAAGAGCG 62.754 66.667 8.66 0.89 40.88 5.03
2698 3240 3.173240 GGCGTCGACAAGAGCGTC 61.173 66.667 17.16 0.00 0.00 5.19
2699 3241 2.428569 GCGTCGACAAGAGCGTCA 60.429 61.111 17.16 0.00 35.54 4.35
2700 3242 2.014554 GCGTCGACAAGAGCGTCAA 61.015 57.895 17.16 0.00 35.54 3.18
2701 3243 1.767388 CGTCGACAAGAGCGTCAAC 59.233 57.895 17.16 0.00 35.54 3.18
2702 3244 1.606350 CGTCGACAAGAGCGTCAACC 61.606 60.000 17.16 0.00 35.54 3.77
2703 3245 0.318784 GTCGACAAGAGCGTCAACCT 60.319 55.000 11.55 0.00 35.54 3.50
2704 3246 0.039437 TCGACAAGAGCGTCAACCTC 60.039 55.000 0.00 0.00 35.54 3.85
2705 3247 1.337817 CGACAAGAGCGTCAACCTCG 61.338 60.000 0.00 0.00 35.54 4.63
2706 3248 0.039437 GACAAGAGCGTCAACCTCGA 60.039 55.000 0.00 0.00 35.88 4.04
2707 3249 0.039074 ACAAGAGCGTCAACCTCGAG 60.039 55.000 5.13 5.13 34.56 4.04
2708 3250 1.080434 AAGAGCGTCAACCTCGAGC 60.080 57.895 6.99 0.00 34.56 5.03
2709 3251 1.528292 AAGAGCGTCAACCTCGAGCT 61.528 55.000 6.99 0.00 41.29 4.09
2710 3252 1.515304 GAGCGTCAACCTCGAGCTC 60.515 63.158 6.99 2.73 45.74 4.09
2711 3253 1.974343 AGCGTCAACCTCGAGCTCT 60.974 57.895 12.85 0.00 31.94 4.09
2712 3254 1.803519 GCGTCAACCTCGAGCTCTG 60.804 63.158 12.85 5.69 0.00 3.35
2713 3255 1.153939 CGTCAACCTCGAGCTCTGG 60.154 63.158 12.85 15.70 0.00 3.86
2714 3256 1.587043 CGTCAACCTCGAGCTCTGGA 61.587 60.000 23.70 9.84 0.00 3.86
2715 3257 0.820871 GTCAACCTCGAGCTCTGGAT 59.179 55.000 23.70 12.92 0.00 3.41
2716 3258 1.107114 TCAACCTCGAGCTCTGGATC 58.893 55.000 23.70 0.00 0.00 3.36
2717 3259 0.103937 CAACCTCGAGCTCTGGATCC 59.896 60.000 23.70 4.20 0.00 3.36
2718 3260 0.032615 AACCTCGAGCTCTGGATCCT 60.033 55.000 23.70 4.23 0.00 3.24
2719 3261 0.754957 ACCTCGAGCTCTGGATCCTG 60.755 60.000 23.70 13.20 0.00 3.86
2720 3262 1.363443 CTCGAGCTCTGGATCCTGC 59.637 63.158 14.23 14.25 0.00 4.85
2721 3263 1.076412 TCGAGCTCTGGATCCTGCT 60.076 57.895 21.39 21.39 38.59 4.24
2722 3264 1.106351 TCGAGCTCTGGATCCTGCTC 61.106 60.000 28.72 28.72 45.79 4.26
2723 3265 1.108727 CGAGCTCTGGATCCTGCTCT 61.109 60.000 31.78 22.78 46.70 4.09
2754 3296 3.256960 AACCACCATGGCCGGTCT 61.257 61.111 23.23 12.75 42.67 3.85
2803 3345 6.767423 ACCGTAAAGCCTAGTTCTTTTGTTTA 59.233 34.615 11.07 0.00 35.58 2.01
2865 3407 0.033781 AGGCCGTTGCGTAACAGTTA 59.966 50.000 16.69 0.00 38.85 2.24
2866 3408 1.081094 GGCCGTTGCGTAACAGTTAT 58.919 50.000 16.69 0.00 38.85 1.89
2867 3409 1.201987 GGCCGTTGCGTAACAGTTATG 60.202 52.381 16.69 8.04 38.85 1.90
2868 3410 1.727880 GCCGTTGCGTAACAGTTATGA 59.272 47.619 16.69 0.00 36.58 2.15
2869 3411 2.158058 GCCGTTGCGTAACAGTTATGAA 59.842 45.455 16.69 2.87 36.58 2.57
2870 3412 3.723835 GCCGTTGCGTAACAGTTATGAAG 60.724 47.826 16.69 4.06 36.58 3.02
2871 3413 3.181524 CCGTTGCGTAACAGTTATGAAGG 60.182 47.826 16.69 11.41 36.58 3.46
2872 3414 3.676172 CGTTGCGTAACAGTTATGAAGGA 59.324 43.478 16.69 0.00 36.58 3.36
2873 3415 4.150980 CGTTGCGTAACAGTTATGAAGGAA 59.849 41.667 16.69 4.37 36.58 3.36
2874 3416 5.333492 CGTTGCGTAACAGTTATGAAGGAAA 60.333 40.000 16.69 0.43 36.58 3.13
2875 3417 6.608610 GTTGCGTAACAGTTATGAAGGAAAT 58.391 36.000 15.65 0.00 36.78 2.17
2876 3418 7.412129 CGTTGCGTAACAGTTATGAAGGAAATA 60.412 37.037 16.69 0.00 36.58 1.40
2877 3419 8.395633 GTTGCGTAACAGTTATGAAGGAAATAT 58.604 33.333 15.65 0.00 36.78 1.28
2878 3420 7.915508 TGCGTAACAGTTATGAAGGAAATATG 58.084 34.615 15.65 0.00 0.00 1.78
2879 3421 6.851330 GCGTAACAGTTATGAAGGAAATATGC 59.149 38.462 15.65 0.00 0.00 3.14
2880 3422 7.352739 CGTAACAGTTATGAAGGAAATATGCC 58.647 38.462 6.69 0.00 0.00 4.40
2881 3423 6.715347 AACAGTTATGAAGGAAATATGCCC 57.285 37.500 0.00 0.00 0.00 5.36
2882 3424 6.018433 ACAGTTATGAAGGAAATATGCCCT 57.982 37.500 0.00 0.00 0.00 5.19
2883 3425 7.149202 ACAGTTATGAAGGAAATATGCCCTA 57.851 36.000 0.00 0.00 31.36 3.53
2884 3426 7.227156 ACAGTTATGAAGGAAATATGCCCTAG 58.773 38.462 0.00 0.00 31.36 3.02
2885 3427 7.072454 ACAGTTATGAAGGAAATATGCCCTAGA 59.928 37.037 0.00 0.00 31.36 2.43
2886 3428 7.605691 CAGTTATGAAGGAAATATGCCCTAGAG 59.394 40.741 0.00 0.00 31.36 2.43
2887 3429 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
2929 3471 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
2930 3472 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
2931 3473 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
2932 3474 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
2933 3475 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
2934 3476 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
2935 3477 7.554835 TGCTAGAATTGTATTAACCGGAAACAT 59.445 33.333 9.46 0.00 0.00 2.71
2936 3478 7.855904 GCTAGAATTGTATTAACCGGAAACATG 59.144 37.037 9.46 0.00 0.00 3.21
2937 3479 7.931578 AGAATTGTATTAACCGGAAACATGA 57.068 32.000 9.46 0.00 0.00 3.07
2938 3480 8.519799 AGAATTGTATTAACCGGAAACATGAT 57.480 30.769 9.46 0.00 0.00 2.45
2939 3481 9.621629 AGAATTGTATTAACCGGAAACATGATA 57.378 29.630 9.46 0.00 0.00 2.15
2940 3482 9.659830 GAATTGTATTAACCGGAAACATGATAC 57.340 33.333 9.46 7.13 0.00 2.24
2941 3483 8.740123 ATTGTATTAACCGGAAACATGATACA 57.260 30.769 9.46 9.57 0.00 2.29
2942 3484 8.740123 TTGTATTAACCGGAAACATGATACAT 57.260 30.769 9.46 0.00 31.27 2.29
2943 3485 8.148807 TGTATTAACCGGAAACATGATACATG 57.851 34.615 9.46 9.72 0.00 3.21
2944 3486 7.771361 TGTATTAACCGGAAACATGATACATGT 59.229 33.333 9.46 10.94 0.00 3.21
2945 3487 4.963276 AACCGGAAACATGATACATGTG 57.037 40.909 9.46 7.59 31.80 3.21
2946 3488 3.950397 ACCGGAAACATGATACATGTGT 58.050 40.909 9.46 11.88 31.80 3.72
2947 3489 3.689161 ACCGGAAACATGATACATGTGTG 59.311 43.478 9.46 4.81 31.80 3.82
2948 3490 3.938334 CCGGAAACATGATACATGTGTGA 59.062 43.478 16.29 0.00 31.80 3.58
2949 3491 4.394610 CCGGAAACATGATACATGTGTGAA 59.605 41.667 16.29 0.00 31.80 3.18
2950 3492 5.066375 CCGGAAACATGATACATGTGTGAAT 59.934 40.000 16.29 0.00 31.80 2.57
2951 3493 6.259829 CCGGAAACATGATACATGTGTGAATA 59.740 38.462 16.29 0.00 31.80 1.75
2952 3494 7.125755 CGGAAACATGATACATGTGTGAATAC 58.874 38.462 16.29 1.40 31.80 1.89
2953 3495 7.201600 CGGAAACATGATACATGTGTGAATACA 60.202 37.037 16.29 0.00 34.63 2.29
2954 3496 8.623903 GGAAACATGATACATGTGTGAATACAT 58.376 33.333 16.29 0.00 41.77 2.29
2958 3500 9.481340 ACATGATACATGTGTGAATACATAGAC 57.519 33.333 15.11 0.00 39.17 2.59
2959 3501 9.480053 CATGATACATGTGTGAATACATAGACA 57.520 33.333 9.11 0.00 39.17 3.41
2961 3503 9.883142 TGATACATGTGTGAATACATAGACAAA 57.117 29.630 9.11 0.00 39.17 2.83
2963 3505 7.977789 ACATGTGTGAATACATAGACAAACA 57.022 32.000 0.00 0.00 39.17 2.83
2964 3506 8.032952 ACATGTGTGAATACATAGACAAACAG 57.967 34.615 0.00 0.00 39.17 3.16
2965 3507 7.661437 ACATGTGTGAATACATAGACAAACAGT 59.339 33.333 0.00 0.00 39.17 3.55
2966 3508 7.420184 TGTGTGAATACATAGACAAACAGTG 57.580 36.000 0.00 0.00 39.39 3.66
2967 3509 6.989759 TGTGTGAATACATAGACAAACAGTGT 59.010 34.615 0.00 0.00 40.53 3.55
2968 3510 7.170828 TGTGTGAATACATAGACAAACAGTGTC 59.829 37.037 0.00 0.00 46.76 3.67
2980 3522 6.406692 ACAAACAGTGTCACTAGTATGTCT 57.593 37.500 4.85 0.00 34.38 3.41
2981 3523 6.448006 ACAAACAGTGTCACTAGTATGTCTC 58.552 40.000 4.85 0.00 34.38 3.36
2982 3524 6.265649 ACAAACAGTGTCACTAGTATGTCTCT 59.734 38.462 4.85 0.00 34.38 3.10
2983 3525 7.447545 ACAAACAGTGTCACTAGTATGTCTCTA 59.552 37.037 4.85 0.00 34.38 2.43
2984 3526 6.988622 ACAGTGTCACTAGTATGTCTCTAC 57.011 41.667 4.85 0.00 0.00 2.59
2985 3527 6.713276 ACAGTGTCACTAGTATGTCTCTACT 58.287 40.000 4.85 0.00 36.04 2.57
2986 3528 7.169591 ACAGTGTCACTAGTATGTCTCTACTT 58.830 38.462 4.85 0.00 33.96 2.24
2987 3529 7.119992 ACAGTGTCACTAGTATGTCTCTACTTG 59.880 40.741 4.85 0.00 33.96 3.16
2988 3530 7.334671 CAGTGTCACTAGTATGTCTCTACTTGA 59.665 40.741 4.85 0.00 33.96 3.02
2989 3531 7.334921 AGTGTCACTAGTATGTCTCTACTTGAC 59.665 40.741 2.87 8.24 38.64 3.18
2990 3532 7.334921 GTGTCACTAGTATGTCTCTACTTGACT 59.665 40.741 13.21 0.00 38.79 3.41
2991 3533 8.537858 TGTCACTAGTATGTCTCTACTTGACTA 58.462 37.037 13.21 0.00 38.79 2.59
2992 3534 9.037737 GTCACTAGTATGTCTCTACTTGACTAG 57.962 40.741 0.00 0.00 36.95 2.57
2993 3535 7.711772 TCACTAGTATGTCTCTACTTGACTAGC 59.288 40.741 0.00 0.00 38.86 3.42
2994 3536 7.713507 CACTAGTATGTCTCTACTTGACTAGCT 59.286 40.741 0.00 0.00 38.86 3.32
2995 3537 7.929785 ACTAGTATGTCTCTACTTGACTAGCTC 59.070 40.741 0.00 0.00 38.86 4.09
2996 3538 5.756347 AGTATGTCTCTACTTGACTAGCTCG 59.244 44.000 0.00 0.00 35.63 5.03
2997 3539 3.940319 TGTCTCTACTTGACTAGCTCGT 58.060 45.455 0.00 0.00 35.63 4.18
2998 3540 4.325119 TGTCTCTACTTGACTAGCTCGTT 58.675 43.478 0.00 0.00 35.63 3.85
2999 3541 4.154375 TGTCTCTACTTGACTAGCTCGTTG 59.846 45.833 0.00 0.00 35.63 4.10
3000 3542 4.392445 GTCTCTACTTGACTAGCTCGTTGA 59.608 45.833 0.00 0.00 0.00 3.18
3001 3543 5.065474 GTCTCTACTTGACTAGCTCGTTGAT 59.935 44.000 0.00 0.00 0.00 2.57
3002 3544 5.294799 TCTCTACTTGACTAGCTCGTTGATC 59.705 44.000 0.00 0.00 0.00 2.92
3003 3545 4.941873 TCTACTTGACTAGCTCGTTGATCA 59.058 41.667 0.00 0.00 0.00 2.92
3004 3546 4.521130 ACTTGACTAGCTCGTTGATCAA 57.479 40.909 3.38 3.38 0.00 2.57
3005 3547 4.883083 ACTTGACTAGCTCGTTGATCAAA 58.117 39.130 10.35 0.00 0.00 2.69
3006 3548 4.926238 ACTTGACTAGCTCGTTGATCAAAG 59.074 41.667 10.35 12.64 0.00 2.77
3007 3549 4.783764 TGACTAGCTCGTTGATCAAAGA 57.216 40.909 20.62 20.62 0.00 2.52
3008 3550 5.330455 TGACTAGCTCGTTGATCAAAGAT 57.670 39.130 21.83 12.82 0.00 2.40
3009 3551 5.105063 TGACTAGCTCGTTGATCAAAGATG 58.895 41.667 21.83 16.63 0.00 2.90
3010 3552 4.437239 ACTAGCTCGTTGATCAAAGATGG 58.563 43.478 21.83 14.18 0.00 3.51
3011 3553 3.340814 AGCTCGTTGATCAAAGATGGT 57.659 42.857 21.83 17.63 0.00 3.55
3012 3554 3.679389 AGCTCGTTGATCAAAGATGGTT 58.321 40.909 21.83 8.86 0.00 3.67
3013 3555 4.832248 AGCTCGTTGATCAAAGATGGTTA 58.168 39.130 21.83 1.90 0.00 2.85
3014 3556 5.431765 AGCTCGTTGATCAAAGATGGTTAT 58.568 37.500 21.83 4.91 0.00 1.89
3015 3557 5.295292 AGCTCGTTGATCAAAGATGGTTATG 59.705 40.000 21.83 11.16 0.00 1.90
3016 3558 5.065218 GCTCGTTGATCAAAGATGGTTATGT 59.935 40.000 21.83 0.00 0.00 2.29
3017 3559 6.403636 GCTCGTTGATCAAAGATGGTTATGTT 60.404 38.462 21.83 0.00 0.00 2.71
3018 3560 7.447374 TCGTTGATCAAAGATGGTTATGTTT 57.553 32.000 18.50 0.00 30.61 2.83
3019 3561 7.526608 TCGTTGATCAAAGATGGTTATGTTTC 58.473 34.615 18.50 0.00 28.23 2.78
3020 3562 6.747280 CGTTGATCAAAGATGGTTATGTTTCC 59.253 38.462 15.34 0.00 28.23 3.13
3021 3563 7.362056 CGTTGATCAAAGATGGTTATGTTTCCT 60.362 37.037 15.34 0.00 28.23 3.36
3022 3564 8.956426 GTTGATCAAAGATGGTTATGTTTCCTA 58.044 33.333 10.35 0.00 28.23 2.94
3023 3565 8.737168 TGATCAAAGATGGTTATGTTTCCTAG 57.263 34.615 0.00 0.00 28.23 3.02
3024 3566 7.283127 TGATCAAAGATGGTTATGTTTCCTAGC 59.717 37.037 0.00 0.00 28.23 3.42
3025 3567 5.885912 TCAAAGATGGTTATGTTTCCTAGCC 59.114 40.000 0.00 0.00 28.23 3.93
3026 3568 5.450818 AAGATGGTTATGTTTCCTAGCCA 57.549 39.130 0.00 0.00 34.50 4.75
3027 3569 5.653255 AGATGGTTATGTTTCCTAGCCAT 57.347 39.130 0.00 0.00 41.28 4.40
3028 3570 6.763715 AGATGGTTATGTTTCCTAGCCATA 57.236 37.500 0.00 0.00 39.44 2.74
3029 3571 6.773638 AGATGGTTATGTTTCCTAGCCATAG 58.226 40.000 0.00 0.00 39.44 2.23
3030 3572 6.558775 AGATGGTTATGTTTCCTAGCCATAGA 59.441 38.462 0.00 0.00 39.44 1.98
3031 3573 5.925509 TGGTTATGTTTCCTAGCCATAGAC 58.074 41.667 0.00 0.00 0.00 2.59
3032 3574 5.427157 TGGTTATGTTTCCTAGCCATAGACA 59.573 40.000 0.00 0.00 0.00 3.41
3033 3575 6.069905 TGGTTATGTTTCCTAGCCATAGACAA 60.070 38.462 0.00 0.00 0.00 3.18
3034 3576 6.826741 GGTTATGTTTCCTAGCCATAGACAAA 59.173 38.462 0.00 0.00 0.00 2.83
3035 3577 7.012421 GGTTATGTTTCCTAGCCATAGACAAAG 59.988 40.741 0.00 0.00 0.00 2.77
3036 3578 5.755409 TGTTTCCTAGCCATAGACAAAGA 57.245 39.130 0.00 0.00 0.00 2.52
3037 3579 5.734720 TGTTTCCTAGCCATAGACAAAGAG 58.265 41.667 0.00 0.00 0.00 2.85
3038 3580 5.248477 TGTTTCCTAGCCATAGACAAAGAGT 59.752 40.000 0.00 0.00 0.00 3.24
3039 3581 6.174049 GTTTCCTAGCCATAGACAAAGAGTT 58.826 40.000 0.00 0.00 0.00 3.01
3040 3582 5.344743 TCCTAGCCATAGACAAAGAGTTG 57.655 43.478 0.00 0.00 40.84 3.16
3055 3597 7.138736 ACAAAGAGTTGTCATTTGATTAACGG 58.861 34.615 4.08 0.00 45.00 4.44
3056 3598 5.880054 AGAGTTGTCATTTGATTAACGGG 57.120 39.130 0.00 0.00 32.73 5.28
3057 3599 5.556915 AGAGTTGTCATTTGATTAACGGGA 58.443 37.500 0.00 0.00 32.73 5.14
3058 3600 6.180472 AGAGTTGTCATTTGATTAACGGGAT 58.820 36.000 0.00 0.00 32.73 3.85
3059 3601 6.316390 AGAGTTGTCATTTGATTAACGGGATC 59.684 38.462 0.00 0.00 32.73 3.36
3060 3602 5.943416 AGTTGTCATTTGATTAACGGGATCA 59.057 36.000 0.00 0.00 32.73 2.92
3061 3603 5.811399 TGTCATTTGATTAACGGGATCAC 57.189 39.130 0.00 0.00 33.51 3.06
3062 3604 5.249420 TGTCATTTGATTAACGGGATCACA 58.751 37.500 0.00 0.00 33.51 3.58
3063 3605 5.885352 TGTCATTTGATTAACGGGATCACAT 59.115 36.000 0.00 0.00 33.51 3.21
3064 3606 6.038161 TGTCATTTGATTAACGGGATCACATC 59.962 38.462 0.00 0.00 33.51 3.06
3065 3607 6.038161 GTCATTTGATTAACGGGATCACATCA 59.962 38.462 0.00 0.00 33.51 3.07
3066 3608 6.772233 TCATTTGATTAACGGGATCACATCAT 59.228 34.615 0.00 0.00 33.51 2.45
3067 3609 7.285172 TCATTTGATTAACGGGATCACATCATT 59.715 33.333 0.00 0.00 33.51 2.57
3068 3610 8.567104 CATTTGATTAACGGGATCACATCATTA 58.433 33.333 0.00 0.00 33.51 1.90
3069 3611 7.728847 TTGATTAACGGGATCACATCATTAG 57.271 36.000 0.00 0.00 33.51 1.73
3070 3612 6.230472 TGATTAACGGGATCACATCATTAGG 58.770 40.000 0.00 0.00 0.00 2.69
3071 3613 5.880164 TTAACGGGATCACATCATTAGGA 57.120 39.130 0.00 0.00 0.00 2.94
3072 3614 4.342862 AACGGGATCACATCATTAGGAG 57.657 45.455 0.00 0.00 0.00 3.69
3073 3615 3.576861 ACGGGATCACATCATTAGGAGA 58.423 45.455 0.00 0.00 0.00 3.71
3074 3616 3.967326 ACGGGATCACATCATTAGGAGAA 59.033 43.478 0.00 0.00 0.00 2.87
3075 3617 4.594920 ACGGGATCACATCATTAGGAGAAT 59.405 41.667 0.00 0.00 0.00 2.40
3076 3618 4.934001 CGGGATCACATCATTAGGAGAATG 59.066 45.833 0.00 0.00 0.00 2.67
3077 3619 5.279657 CGGGATCACATCATTAGGAGAATGA 60.280 44.000 0.00 2.66 40.50 2.57
3078 3620 6.575847 CGGGATCACATCATTAGGAGAATGAT 60.576 42.308 6.90 6.90 45.40 2.45
3087 3629 8.618702 ATCATTAGGAGAATGATGTGATTGAC 57.381 34.615 11.08 0.00 43.52 3.18
3088 3630 7.799081 TCATTAGGAGAATGATGTGATTGACT 58.201 34.615 0.00 0.00 32.21 3.41
3089 3631 8.270030 TCATTAGGAGAATGATGTGATTGACTT 58.730 33.333 0.00 0.00 32.21 3.01
3090 3632 7.854557 TTAGGAGAATGATGTGATTGACTTG 57.145 36.000 0.00 0.00 0.00 3.16
3091 3633 6.058553 AGGAGAATGATGTGATTGACTTGA 57.941 37.500 0.00 0.00 0.00 3.02
3092 3634 5.879223 AGGAGAATGATGTGATTGACTTGAC 59.121 40.000 0.00 0.00 0.00 3.18
3093 3635 5.065731 GGAGAATGATGTGATTGACTTGACC 59.934 44.000 0.00 0.00 0.00 4.02
3094 3636 4.946157 AGAATGATGTGATTGACTTGACCC 59.054 41.667 0.00 0.00 0.00 4.46
3095 3637 3.786368 TGATGTGATTGACTTGACCCA 57.214 42.857 0.00 0.00 0.00 4.51
3096 3638 4.305539 TGATGTGATTGACTTGACCCAT 57.694 40.909 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
711 804 2.851045 GTTTTGAGGGGAGGGGCA 59.149 61.111 0.00 0.00 0.00 5.36
740 843 3.151022 GAGGGCGAGGCTGCTAGT 61.151 66.667 0.00 0.00 34.52 2.57
897 1015 3.295973 GAAGAGTATGAGGAGGAGCACT 58.704 50.000 0.00 0.00 0.00 4.40
1025 1180 2.029649 GCAACATCAACATCAGCAAGGT 60.030 45.455 0.00 0.00 0.00 3.50
1043 1198 0.518636 GTGCAGATCTTGAAGCGCAA 59.481 50.000 11.47 0.00 37.44 4.85
1130 1285 4.219288 GGGTCTTCACATTGATCTTTGCTT 59.781 41.667 0.00 0.00 0.00 3.91
1363 1527 3.326588 TCCCCGATTTCTTTCAGAAGTGA 59.673 43.478 0.00 0.00 35.37 3.41
1419 1584 9.581289 TTTATTATCCCAAGAAAGAGAACAACA 57.419 29.630 0.00 0.00 0.00 3.33
1493 1996 4.708726 AACAGAGCATATTTCCAACAGC 57.291 40.909 0.00 0.00 0.00 4.40
1763 2293 4.890581 ACTAAGCAAACATACCACAACCAA 59.109 37.500 0.00 0.00 0.00 3.67
1816 2346 5.521372 GTGCCATGCTCAAAATTAGGAAATC 59.479 40.000 0.00 0.00 0.00 2.17
1825 2355 1.001181 GGTGTGTGCCATGCTCAAAAT 59.999 47.619 0.00 0.00 33.88 1.82
1857 2387 8.541899 TGTGTACCATAAGTAGGTTGATATGA 57.458 34.615 0.00 0.00 40.54 2.15
1869 2399 5.280011 CCCTCTCTTGTTGTGTACCATAAGT 60.280 44.000 0.00 0.00 0.00 2.24
1925 2455 2.274760 GCATGCCAGAGAGCCCTT 59.725 61.111 6.36 0.00 0.00 3.95
2044 2574 1.972588 ACCAGCCCCTAAGTCAGATT 58.027 50.000 0.00 0.00 0.00 2.40
2144 2681 2.133520 TCTCTACAGGGACCGGAGTAT 58.866 52.381 9.46 0.00 0.00 2.12
2151 2688 0.323178 TGGTCGTCTCTACAGGGACC 60.323 60.000 3.67 1.68 40.96 4.46
2156 2693 4.193090 AGTAGTCATGGTCGTCTCTACAG 58.807 47.826 0.00 0.00 32.82 2.74
2515 3057 9.884636 AAAGATATTAAAGGTTATGCCAAAACC 57.115 29.630 4.26 4.26 45.65 3.27
2562 3104 7.914427 TGTGAGGTAAGGTAGACAATCATAT 57.086 36.000 0.00 0.00 0.00 1.78
2579 3121 9.632638 AATTATCTATTTACTTGCATGTGAGGT 57.367 29.630 15.08 6.23 0.00 3.85
2605 3147 8.749354 ACACATCACTTACATACACAATCTAGA 58.251 33.333 0.00 0.00 0.00 2.43
2612 3154 5.606505 ACACACACATCACTTACATACACA 58.393 37.500 0.00 0.00 0.00 3.72
2615 3157 7.360101 GGAGAAACACACACATCACTTACATAC 60.360 40.741 0.00 0.00 0.00 2.39
2617 3159 5.470098 GGAGAAACACACACATCACTTACAT 59.530 40.000 0.00 0.00 0.00 2.29
2618 3160 4.814234 GGAGAAACACACACATCACTTACA 59.186 41.667 0.00 0.00 0.00 2.41
2619 3161 4.814234 TGGAGAAACACACACATCACTTAC 59.186 41.667 0.00 0.00 0.00 2.34
2629 3171 3.627395 AGTCACTTGGAGAAACACACA 57.373 42.857 0.00 0.00 0.00 3.72
2631 3173 3.950397 ACAAGTCACTTGGAGAAACACA 58.050 40.909 21.71 0.00 44.81 3.72
2632 3174 4.438744 CCAACAAGTCACTTGGAGAAACAC 60.439 45.833 21.71 0.00 44.81 3.32
2640 3182 2.154462 CTAGGCCAACAAGTCACTTGG 58.846 52.381 21.71 6.05 44.81 3.61
2641 3183 3.126001 TCTAGGCCAACAAGTCACTTG 57.874 47.619 16.42 16.42 45.85 3.16
2645 3187 4.901197 TGTATTCTAGGCCAACAAGTCA 57.099 40.909 5.01 0.00 0.00 3.41
2653 3195 2.628178 CTCGACCATGTATTCTAGGCCA 59.372 50.000 5.01 0.00 0.00 5.36
2654 3196 2.891580 TCTCGACCATGTATTCTAGGCC 59.108 50.000 0.00 0.00 0.00 5.19
2655 3197 4.551388 CTTCTCGACCATGTATTCTAGGC 58.449 47.826 0.00 0.00 0.00 3.93
2656 3198 4.279671 AGCTTCTCGACCATGTATTCTAGG 59.720 45.833 0.00 0.00 0.00 3.02
2657 3199 5.446143 AGCTTCTCGACCATGTATTCTAG 57.554 43.478 0.00 0.00 0.00 2.43
2658 3200 5.440234 GAGCTTCTCGACCATGTATTCTA 57.560 43.478 0.00 0.00 0.00 2.10
2659 3201 4.314740 GAGCTTCTCGACCATGTATTCT 57.685 45.455 0.00 0.00 0.00 2.40
2672 3214 2.577378 GTCGACGCCGAGCTTCTC 60.577 66.667 0.00 0.00 46.52 2.87
2673 3215 2.804368 CTTGTCGACGCCGAGCTTCT 62.804 60.000 11.62 0.00 46.52 2.85
2674 3216 2.430244 TTGTCGACGCCGAGCTTC 60.430 61.111 11.62 0.00 46.52 3.86
2675 3217 2.430921 CTTGTCGACGCCGAGCTT 60.431 61.111 11.62 0.00 46.52 3.74
2676 3218 3.329688 CTCTTGTCGACGCCGAGCT 62.330 63.158 11.62 0.00 46.52 4.09
2677 3219 2.876645 CTCTTGTCGACGCCGAGC 60.877 66.667 11.62 0.00 46.52 5.03
2678 3220 2.876645 GCTCTTGTCGACGCCGAG 60.877 66.667 18.58 18.58 46.52 4.63
2679 3221 4.753877 CGCTCTTGTCGACGCCGA 62.754 66.667 11.62 6.10 43.35 5.54
2681 3223 3.173240 GACGCTCTTGTCGACGCC 61.173 66.667 11.62 0.00 0.00 5.68
2682 3224 2.014554 TTGACGCTCTTGTCGACGC 61.015 57.895 11.62 7.09 41.87 5.19
2683 3225 1.767388 GTTGACGCTCTTGTCGACG 59.233 57.895 11.62 0.00 41.90 5.12
2685 3227 0.039437 GAGGTTGACGCTCTTGTCGA 60.039 55.000 0.00 0.00 41.87 4.20
2686 3228 1.337817 CGAGGTTGACGCTCTTGTCG 61.338 60.000 0.00 0.00 41.87 4.35
2687 3229 0.039437 TCGAGGTTGACGCTCTTGTC 60.039 55.000 0.00 0.00 39.37 3.18
2688 3230 0.039074 CTCGAGGTTGACGCTCTTGT 60.039 55.000 3.91 0.00 0.00 3.16
2689 3231 1.347817 GCTCGAGGTTGACGCTCTTG 61.348 60.000 15.58 0.00 0.00 3.02
2690 3232 1.080434 GCTCGAGGTTGACGCTCTT 60.080 57.895 15.58 0.00 0.00 2.85
2691 3233 1.928706 GAGCTCGAGGTTGACGCTCT 61.929 60.000 19.66 0.37 42.72 4.09
2692 3234 1.515304 GAGCTCGAGGTTGACGCTC 60.515 63.158 19.66 11.59 40.07 5.03
2693 3235 1.974343 AGAGCTCGAGGTTGACGCT 60.974 57.895 19.66 7.79 0.00 5.07
2694 3236 1.803519 CAGAGCTCGAGGTTGACGC 60.804 63.158 19.66 5.33 0.00 5.19
2695 3237 1.153939 CCAGAGCTCGAGGTTGACG 60.154 63.158 19.66 7.48 0.00 4.35
2696 3238 0.820871 ATCCAGAGCTCGAGGTTGAC 59.179 55.000 19.66 6.12 0.00 3.18
2697 3239 1.107114 GATCCAGAGCTCGAGGTTGA 58.893 55.000 19.66 15.50 0.00 3.18
2698 3240 0.103937 GGATCCAGAGCTCGAGGTTG 59.896 60.000 19.66 17.03 0.00 3.77
2699 3241 0.032615 AGGATCCAGAGCTCGAGGTT 60.033 55.000 19.66 16.62 0.00 3.50
2700 3242 0.754957 CAGGATCCAGAGCTCGAGGT 60.755 60.000 18.67 18.67 0.00 3.85
2701 3243 2.040330 CAGGATCCAGAGCTCGAGG 58.960 63.158 15.82 18.85 0.00 4.63
2702 3244 1.108727 AGCAGGATCCAGAGCTCGAG 61.109 60.000 15.82 8.45 30.05 4.04
2703 3245 1.076412 AGCAGGATCCAGAGCTCGA 60.076 57.895 15.82 0.22 30.05 4.04
2704 3246 1.363443 GAGCAGGATCCAGAGCTCG 59.637 63.158 27.25 3.24 43.27 5.03
2706 3248 1.122227 GAAGAGCAGGATCCAGAGCT 58.878 55.000 21.73 21.73 40.60 4.09
2707 3249 1.122227 AGAAGAGCAGGATCCAGAGC 58.878 55.000 15.82 14.76 0.00 4.09
2719 3261 7.919724 GGTGGTTCCATAGTGCTAGAAGAGC 62.920 52.000 0.00 0.00 43.20 4.09
2720 3262 4.442192 GGTGGTTCCATAGTGCTAGAAGAG 60.442 50.000 0.00 0.00 35.97 2.85
2721 3263 3.451178 GGTGGTTCCATAGTGCTAGAAGA 59.549 47.826 0.00 0.00 35.97 2.87
2722 3264 3.197766 TGGTGGTTCCATAGTGCTAGAAG 59.802 47.826 0.00 0.00 41.93 2.85
2723 3265 3.178046 TGGTGGTTCCATAGTGCTAGAA 58.822 45.455 0.00 0.00 41.93 2.10
2754 3296 0.753848 TCAGATCATACGGACCCGCA 60.754 55.000 8.55 0.00 44.19 5.69
2803 3345 7.015680 AGACATCCATGGTCAATACTAGAGAT 58.984 38.462 12.58 0.00 37.74 2.75
2859 3401 6.018433 AGGGCATATTTCCTTCATAACTGT 57.982 37.500 0.00 0.00 0.00 3.55
2865 3407 5.511386 CCTCTAGGGCATATTTCCTTCAT 57.489 43.478 0.00 0.00 34.75 2.57
2866 3408 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
2878 3420 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
2903 3445 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
2904 3446 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
2905 3447 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
2906 3448 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
2907 3449 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
2908 3450 7.554835 TGTTTCCGGTTAATACAATTCTAGCAT 59.445 33.333 0.00 0.00 0.00 3.79
2909 3451 6.879993 TGTTTCCGGTTAATACAATTCTAGCA 59.120 34.615 0.00 0.00 0.00 3.49
2910 3452 7.311364 TGTTTCCGGTTAATACAATTCTAGC 57.689 36.000 0.00 0.00 0.00 3.42
2911 3453 9.104965 TCATGTTTCCGGTTAATACAATTCTAG 57.895 33.333 0.00 0.00 0.00 2.43
2912 3454 9.621629 ATCATGTTTCCGGTTAATACAATTCTA 57.378 29.630 0.00 0.00 0.00 2.10
2913 3455 7.931578 TCATGTTTCCGGTTAATACAATTCT 57.068 32.000 0.00 0.00 0.00 2.40
2914 3456 9.659830 GTATCATGTTTCCGGTTAATACAATTC 57.340 33.333 0.00 0.00 0.00 2.17
2915 3457 9.179909 TGTATCATGTTTCCGGTTAATACAATT 57.820 29.630 0.00 0.00 0.00 2.32
2916 3458 8.740123 TGTATCATGTTTCCGGTTAATACAAT 57.260 30.769 0.00 0.00 0.00 2.71
2917 3459 8.616942 CATGTATCATGTTTCCGGTTAATACAA 58.383 33.333 0.00 0.00 33.52 2.41
2918 3460 7.771361 ACATGTATCATGTTTCCGGTTAATACA 59.229 33.333 0.00 7.97 34.10 2.29
2919 3461 8.067784 CACATGTATCATGTTTCCGGTTAATAC 58.932 37.037 11.89 2.60 0.00 1.89
2920 3462 7.771361 ACACATGTATCATGTTTCCGGTTAATA 59.229 33.333 11.89 0.00 0.00 0.98
2921 3463 6.601613 ACACATGTATCATGTTTCCGGTTAAT 59.398 34.615 11.89 0.00 0.00 1.40
2922 3464 5.941058 ACACATGTATCATGTTTCCGGTTAA 59.059 36.000 11.89 0.00 0.00 2.01
2923 3465 5.352846 CACACATGTATCATGTTTCCGGTTA 59.647 40.000 11.89 0.00 0.00 2.85
2924 3466 4.155826 CACACATGTATCATGTTTCCGGTT 59.844 41.667 11.89 0.00 0.00 4.44
2925 3467 3.689161 CACACATGTATCATGTTTCCGGT 59.311 43.478 11.89 5.17 0.00 5.28
2926 3468 3.938334 TCACACATGTATCATGTTTCCGG 59.062 43.478 11.89 0.00 0.00 5.14
2927 3469 5.544136 TTCACACATGTATCATGTTTCCG 57.456 39.130 11.89 4.94 0.00 4.30
2928 3470 7.984391 TGTATTCACACATGTATCATGTTTCC 58.016 34.615 11.89 0.00 0.00 3.13
2932 3474 9.481340 GTCTATGTATTCACACATGTATCATGT 57.519 33.333 9.21 9.21 39.46 3.21
2933 3475 9.480053 TGTCTATGTATTCACACATGTATCATG 57.520 33.333 0.00 7.99 39.46 3.07
2935 3477 9.883142 TTTGTCTATGTATTCACACATGTATCA 57.117 29.630 0.00 0.00 39.46 2.15
2937 3479 9.665719 TGTTTGTCTATGTATTCACACATGTAT 57.334 29.630 0.00 0.00 39.46 2.29
2938 3480 9.150348 CTGTTTGTCTATGTATTCACACATGTA 57.850 33.333 0.00 0.00 39.46 2.29
2939 3481 7.661437 ACTGTTTGTCTATGTATTCACACATGT 59.339 33.333 0.00 0.00 39.46 3.21
2940 3482 7.959109 CACTGTTTGTCTATGTATTCACACATG 59.041 37.037 0.00 0.00 39.46 3.21
2941 3483 7.661437 ACACTGTTTGTCTATGTATTCACACAT 59.339 33.333 0.00 0.00 37.06 3.21
2942 3484 6.989759 ACACTGTTTGTCTATGTATTCACACA 59.010 34.615 0.00 0.00 32.51 3.72
2943 3485 7.421530 ACACTGTTTGTCTATGTATTCACAC 57.578 36.000 0.00 0.00 32.51 3.82
2957 3499 6.265649 AGAGACATACTAGTGACACTGTTTGT 59.734 38.462 18.58 20.66 43.10 2.83
2958 3500 6.682746 AGAGACATACTAGTGACACTGTTTG 58.317 40.000 18.58 18.21 0.00 2.93
2959 3501 6.902771 AGAGACATACTAGTGACACTGTTT 57.097 37.500 18.58 3.13 0.00 2.83
2960 3502 7.169591 AGTAGAGACATACTAGTGACACTGTT 58.830 38.462 18.58 7.15 34.21 3.16
2961 3503 6.713276 AGTAGAGACATACTAGTGACACTGT 58.287 40.000 18.58 15.25 34.21 3.55
2962 3504 7.334671 TCAAGTAGAGACATACTAGTGACACTG 59.665 40.741 18.58 10.41 34.90 3.66
2963 3505 7.334921 GTCAAGTAGAGACATACTAGTGACACT 59.665 40.741 13.68 13.68 40.28 3.55
2964 3506 7.334921 AGTCAAGTAGAGACATACTAGTGACAC 59.665 40.741 5.39 0.00 41.63 3.67
2965 3507 7.395617 AGTCAAGTAGAGACATACTAGTGACA 58.604 38.462 5.39 0.00 41.63 3.58
2966 3508 7.852971 AGTCAAGTAGAGACATACTAGTGAC 57.147 40.000 5.39 9.26 40.57 3.67
2967 3509 7.711772 GCTAGTCAAGTAGAGACATACTAGTGA 59.288 40.741 5.39 0.00 37.08 3.41
2968 3510 7.713507 AGCTAGTCAAGTAGAGACATACTAGTG 59.286 40.741 5.39 0.00 37.08 2.74
2969 3511 7.798071 AGCTAGTCAAGTAGAGACATACTAGT 58.202 38.462 0.00 0.00 37.08 2.57
2970 3512 7.115805 CGAGCTAGTCAAGTAGAGACATACTAG 59.884 44.444 0.00 0.00 38.46 2.57
2971 3513 6.924612 CGAGCTAGTCAAGTAGAGACATACTA 59.075 42.308 0.00 0.00 38.46 1.82
2972 3514 5.756347 CGAGCTAGTCAAGTAGAGACATACT 59.244 44.000 0.00 0.00 38.46 2.12
2973 3515 5.524646 ACGAGCTAGTCAAGTAGAGACATAC 59.475 44.000 0.00 0.00 38.46 2.39
2974 3516 5.672503 ACGAGCTAGTCAAGTAGAGACATA 58.327 41.667 0.00 0.00 38.46 2.29
2975 3517 4.519213 ACGAGCTAGTCAAGTAGAGACAT 58.481 43.478 0.00 0.00 38.46 3.06
2976 3518 3.940319 ACGAGCTAGTCAAGTAGAGACA 58.060 45.455 0.00 0.00 38.46 3.41
2977 3519 4.392445 TCAACGAGCTAGTCAAGTAGAGAC 59.608 45.833 0.00 0.00 36.26 3.36
2978 3520 4.576879 TCAACGAGCTAGTCAAGTAGAGA 58.423 43.478 0.00 0.00 0.00 3.10
2979 3521 4.948608 TCAACGAGCTAGTCAAGTAGAG 57.051 45.455 0.00 0.00 0.00 2.43
2980 3522 4.941873 TGATCAACGAGCTAGTCAAGTAGA 59.058 41.667 0.00 0.00 0.00 2.59
2981 3523 5.236655 TGATCAACGAGCTAGTCAAGTAG 57.763 43.478 0.00 0.00 0.00 2.57
2982 3524 5.638596 TTGATCAACGAGCTAGTCAAGTA 57.361 39.130 3.38 0.00 0.00 2.24
2983 3525 4.521130 TTGATCAACGAGCTAGTCAAGT 57.479 40.909 3.38 0.00 0.00 3.16
2984 3526 5.164233 TCTTTGATCAACGAGCTAGTCAAG 58.836 41.667 7.89 0.00 0.00 3.02
2985 3527 5.134202 TCTTTGATCAACGAGCTAGTCAA 57.866 39.130 7.89 0.00 0.00 3.18
2986 3528 4.783764 TCTTTGATCAACGAGCTAGTCA 57.216 40.909 7.89 0.00 0.00 3.41
2987 3529 4.505922 CCATCTTTGATCAACGAGCTAGTC 59.494 45.833 18.24 0.00 0.00 2.59
2988 3530 4.081420 ACCATCTTTGATCAACGAGCTAGT 60.081 41.667 18.24 10.56 0.00 2.57
2989 3531 4.437239 ACCATCTTTGATCAACGAGCTAG 58.563 43.478 18.24 8.24 0.00 3.42
2990 3532 4.471904 ACCATCTTTGATCAACGAGCTA 57.528 40.909 18.24 0.00 0.00 3.32
2991 3533 3.340814 ACCATCTTTGATCAACGAGCT 57.659 42.857 18.24 2.03 0.00 4.09
2992 3534 5.065218 ACATAACCATCTTTGATCAACGAGC 59.935 40.000 18.24 0.00 0.00 5.03
2993 3535 6.668541 ACATAACCATCTTTGATCAACGAG 57.331 37.500 18.24 10.23 0.00 4.18
2994 3536 7.361713 GGAAACATAACCATCTTTGATCAACGA 60.362 37.037 16.08 16.08 0.00 3.85
2995 3537 6.747280 GGAAACATAACCATCTTTGATCAACG 59.253 38.462 7.89 6.62 0.00 4.10
2996 3538 7.830739 AGGAAACATAACCATCTTTGATCAAC 58.169 34.615 7.89 0.00 0.00 3.18
2997 3539 9.177608 CTAGGAAACATAACCATCTTTGATCAA 57.822 33.333 3.38 3.38 0.00 2.57
2998 3540 7.283127 GCTAGGAAACATAACCATCTTTGATCA 59.717 37.037 0.00 0.00 0.00 2.92
2999 3541 7.255277 GGCTAGGAAACATAACCATCTTTGATC 60.255 40.741 0.00 0.00 0.00 2.92
3000 3542 6.547510 GGCTAGGAAACATAACCATCTTTGAT 59.452 38.462 0.00 0.00 0.00 2.57
3001 3543 5.885912 GGCTAGGAAACATAACCATCTTTGA 59.114 40.000 0.00 0.00 0.00 2.69
3002 3544 5.652014 TGGCTAGGAAACATAACCATCTTTG 59.348 40.000 0.00 0.00 0.00 2.77
3003 3545 5.826643 TGGCTAGGAAACATAACCATCTTT 58.173 37.500 0.00 0.00 0.00 2.52
3004 3546 5.450818 TGGCTAGGAAACATAACCATCTT 57.549 39.130 0.00 0.00 0.00 2.40
3005 3547 5.653255 ATGGCTAGGAAACATAACCATCT 57.347 39.130 0.00 0.00 30.76 2.90
3006 3548 6.651225 GTCTATGGCTAGGAAACATAACCATC 59.349 42.308 0.00 0.00 37.58 3.51
3007 3549 6.101150 TGTCTATGGCTAGGAAACATAACCAT 59.899 38.462 0.00 0.00 39.62 3.55
3008 3550 5.427157 TGTCTATGGCTAGGAAACATAACCA 59.573 40.000 0.00 0.00 0.00 3.67
3009 3551 5.925509 TGTCTATGGCTAGGAAACATAACC 58.074 41.667 0.00 0.00 0.00 2.85
3010 3552 7.769044 TCTTTGTCTATGGCTAGGAAACATAAC 59.231 37.037 0.00 0.00 0.00 1.89
3011 3553 7.857456 TCTTTGTCTATGGCTAGGAAACATAA 58.143 34.615 0.00 0.00 0.00 1.90
3012 3554 7.125811 ACTCTTTGTCTATGGCTAGGAAACATA 59.874 37.037 0.00 0.00 0.00 2.29
3013 3555 6.069963 ACTCTTTGTCTATGGCTAGGAAACAT 60.070 38.462 0.00 0.00 0.00 2.71
3014 3556 5.248477 ACTCTTTGTCTATGGCTAGGAAACA 59.752 40.000 0.00 0.00 0.00 2.83
3015 3557 5.735766 ACTCTTTGTCTATGGCTAGGAAAC 58.264 41.667 0.00 0.00 0.00 2.78
3016 3558 6.173339 CAACTCTTTGTCTATGGCTAGGAAA 58.827 40.000 0.00 0.00 0.00 3.13
3017 3559 5.248477 ACAACTCTTTGTCTATGGCTAGGAA 59.752 40.000 0.00 0.00 42.67 3.36
3018 3560 4.777896 ACAACTCTTTGTCTATGGCTAGGA 59.222 41.667 0.00 0.00 42.67 2.94
3019 3561 5.091261 ACAACTCTTTGTCTATGGCTAGG 57.909 43.478 0.00 0.00 42.67 3.02
3031 3573 6.582295 CCCGTTAATCAAATGACAACTCTTTG 59.418 38.462 7.65 0.00 38.83 2.77
3032 3574 6.488683 TCCCGTTAATCAAATGACAACTCTTT 59.511 34.615 7.65 0.00 0.00 2.52
3033 3575 6.001460 TCCCGTTAATCAAATGACAACTCTT 58.999 36.000 7.65 0.00 0.00 2.85
3034 3576 5.556915 TCCCGTTAATCAAATGACAACTCT 58.443 37.500 7.65 0.00 0.00 3.24
3035 3577 5.873179 TCCCGTTAATCAAATGACAACTC 57.127 39.130 7.65 0.00 0.00 3.01
3036 3578 5.943416 TGATCCCGTTAATCAAATGACAACT 59.057 36.000 0.00 0.00 30.37 3.16
3037 3579 6.027749 GTGATCCCGTTAATCAAATGACAAC 58.972 40.000 0.00 0.00 35.04 3.32
3038 3580 5.707764 TGTGATCCCGTTAATCAAATGACAA 59.292 36.000 0.00 0.00 35.04 3.18
3039 3581 5.249420 TGTGATCCCGTTAATCAAATGACA 58.751 37.500 0.00 0.00 35.04 3.58
3040 3582 5.811399 TGTGATCCCGTTAATCAAATGAC 57.189 39.130 0.00 0.00 35.04 3.06
3041 3583 6.118852 TGATGTGATCCCGTTAATCAAATGA 58.881 36.000 0.00 0.00 32.39 2.57
3042 3584 6.375945 TGATGTGATCCCGTTAATCAAATG 57.624 37.500 0.00 0.00 32.39 2.32
3043 3585 7.587037 AATGATGTGATCCCGTTAATCAAAT 57.413 32.000 0.00 0.00 34.46 2.32
3044 3586 7.228507 CCTAATGATGTGATCCCGTTAATCAAA 59.771 37.037 0.00 0.00 35.04 2.69
3045 3587 6.710295 CCTAATGATGTGATCCCGTTAATCAA 59.290 38.462 0.00 0.00 35.04 2.57
3046 3588 6.042666 TCCTAATGATGTGATCCCGTTAATCA 59.957 38.462 0.00 0.00 0.00 2.57
3047 3589 6.464222 TCCTAATGATGTGATCCCGTTAATC 58.536 40.000 0.00 0.00 0.00 1.75
3048 3590 6.270000 TCTCCTAATGATGTGATCCCGTTAAT 59.730 38.462 0.00 0.00 0.00 1.40
3049 3591 5.600898 TCTCCTAATGATGTGATCCCGTTAA 59.399 40.000 0.00 0.00 0.00 2.01
3050 3592 5.144832 TCTCCTAATGATGTGATCCCGTTA 58.855 41.667 0.00 0.00 0.00 3.18
3051 3593 3.967326 TCTCCTAATGATGTGATCCCGTT 59.033 43.478 0.00 0.00 0.00 4.44
3052 3594 3.576861 TCTCCTAATGATGTGATCCCGT 58.423 45.455 0.00 0.00 0.00 5.28
3053 3595 4.607293 TTCTCCTAATGATGTGATCCCG 57.393 45.455 0.00 0.00 0.00 5.14
3054 3596 6.119240 TCATTCTCCTAATGATGTGATCCC 57.881 41.667 0.00 0.00 32.21 3.85
3062 3604 8.438373 AGTCAATCACATCATTCTCCTAATGAT 58.562 33.333 7.28 7.28 45.40 2.45
3063 3605 7.799081 AGTCAATCACATCATTCTCCTAATGA 58.201 34.615 3.13 3.13 40.50 2.57
3064 3606 8.343366 CAAGTCAATCACATCATTCTCCTAATG 58.657 37.037 0.00 0.00 0.00 1.90
3065 3607 8.270030 TCAAGTCAATCACATCATTCTCCTAAT 58.730 33.333 0.00 0.00 0.00 1.73
3066 3608 7.550551 GTCAAGTCAATCACATCATTCTCCTAA 59.449 37.037 0.00 0.00 0.00 2.69
3067 3609 7.044181 GTCAAGTCAATCACATCATTCTCCTA 58.956 38.462 0.00 0.00 0.00 2.94
3068 3610 5.879223 GTCAAGTCAATCACATCATTCTCCT 59.121 40.000 0.00 0.00 0.00 3.69
3069 3611 5.065731 GGTCAAGTCAATCACATCATTCTCC 59.934 44.000 0.00 0.00 0.00 3.71
3070 3612 5.065731 GGGTCAAGTCAATCACATCATTCTC 59.934 44.000 0.00 0.00 0.00 2.87
3071 3613 4.946157 GGGTCAAGTCAATCACATCATTCT 59.054 41.667 0.00 0.00 0.00 2.40
3072 3614 4.701651 TGGGTCAAGTCAATCACATCATTC 59.298 41.667 0.00 0.00 0.00 2.67
3073 3615 4.665451 TGGGTCAAGTCAATCACATCATT 58.335 39.130 0.00 0.00 0.00 2.57
3074 3616 4.305539 TGGGTCAAGTCAATCACATCAT 57.694 40.909 0.00 0.00 0.00 2.45
3075 3617 3.786368 TGGGTCAAGTCAATCACATCA 57.214 42.857 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.