Multiple sequence alignment - TraesCS2B01G375500

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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 TraesCS2B01G375500 chr2B 100.000 3356 0 0 1 3356 538013174 538009819 0.000000e+00 6198
1 TraesCS2B01G375500 chr2B 96.739 92 2 1 1 91 770605435 770605526 5.800000e-33 152
2 TraesCS2B01G375500 chr2D 93.808 3004 97 38 79 3033 457256740 457253777 0.000000e+00 4434
3 TraesCS2B01G375500 chr2D 95.575 113 4 1 3147 3259 457253711 457253600 2.660000e-41 180
4 TraesCS2B01G375500 chr2A 94.869 2553 83 12 79 2604 600530907 600528376 0.000000e+00 3945
5 TraesCS2B01G375500 chr2A 93.187 411 22 5 2624 3033 600527177 600526772 1.720000e-167 599
6 TraesCS2B01G375500 chr2A 94.958 119 6 0 3234 3352 600519410 600519292 1.590000e-43 187
7 TraesCS2B01G375500 chr2A 92.308 91 6 1 3147 3237 600526702 600526613 9.770000e-26 128
8 TraesCS2B01G375500 chr6D 83.607 1342 194 18 1023 2357 288541795 288540473 0.000000e+00 1236
9 TraesCS2B01G375500 chr6B 82.861 1342 204 18 1023 2357 448668256 448666934 0.000000e+00 1181
10 TraesCS2B01G375500 chr6A 82.674 1339 203 21 1023 2354 437021235 437022551 0.000000e+00 1160
11 TraesCS2B01G375500 chrUn 100.000 395 0 0 1148 1542 479365959 479365565 0.000000e+00 730
12 TraesCS2B01G375500 chr1A 75.915 328 56 19 1173 1487 551680384 551680067 2.700000e-31 147


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 TraesCS2B01G375500 chr2B 538009819 538013174 3355 True 6198.000000 6198 100.000000 1 3356 1 chr2B.!!$R1 3355
1 TraesCS2B01G375500 chr2D 457253600 457256740 3140 True 2307.000000 4434 94.691500 79 3259 2 chr2D.!!$R1 3180
2 TraesCS2B01G375500 chr2A 600526613 600530907 4294 True 1557.333333 3945 93.454667 79 3237 3 chr2A.!!$R2 3158
3 TraesCS2B01G375500 chr6D 288540473 288541795 1322 True 1236.000000 1236 83.607000 1023 2357 1 chr6D.!!$R1 1334
4 TraesCS2B01G375500 chr6B 448666934 448668256 1322 True 1181.000000 1181 82.861000 1023 2357 1 chr6B.!!$R1 1334
5 TraesCS2B01G375500 chr6A 437021235 437022551 1316 False 1160.000000 1160 82.674000 1023 2354 1 chr6A.!!$F1 1331

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
681 709 0.170339 GCGAAAAATTCCACTCCGGG 59.830 55.000 0.0 0.0 34.36 5.73 F
1785 1849 1.374758 CGAGCAGGCCGACTTCTTT 60.375 57.895 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1966 0.618458 TCTTGTCCCGGAAATCCAGG 59.382 55.0 0.73 0.0 34.8 4.45 R
3321 4609 0.036732 GACCTGTCATGTGCCTTCCA 59.963 55.0 0.00 0.0 0.0 3.53 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
24 25 5.464069 ACCATTTTTCTGGGGTTTTCTAGT 58.536 37.500 0.00 0.00 40.85 2.57
25 26 5.903010 ACCATTTTTCTGGGGTTTTCTAGTT 59.097 36.000 0.00 0.00 40.85 2.24
26 27 6.385759 ACCATTTTTCTGGGGTTTTCTAGTTT 59.614 34.615 0.00 0.00 40.85 2.66
27 28 7.092623 ACCATTTTTCTGGGGTTTTCTAGTTTT 60.093 33.333 0.00 0.00 40.85 2.43
28 29 7.773224 CCATTTTTCTGGGGTTTTCTAGTTTTT 59.227 33.333 0.00 0.00 32.28 1.94
29 30 8.611757 CATTTTTCTGGGGTTTTCTAGTTTTTG 58.388 33.333 0.00 0.00 0.00 2.44
30 31 6.860790 TTTCTGGGGTTTTCTAGTTTTTGT 57.139 33.333 0.00 0.00 0.00 2.83
31 32 7.957992 TTTCTGGGGTTTTCTAGTTTTTGTA 57.042 32.000 0.00 0.00 0.00 2.41
32 33 8.541899 TTTCTGGGGTTTTCTAGTTTTTGTAT 57.458 30.769 0.00 0.00 0.00 2.29
33 34 7.519032 TCTGGGGTTTTCTAGTTTTTGTATG 57.481 36.000 0.00 0.00 0.00 2.39
34 35 7.291566 TCTGGGGTTTTCTAGTTTTTGTATGA 58.708 34.615 0.00 0.00 0.00 2.15
35 36 7.947890 TCTGGGGTTTTCTAGTTTTTGTATGAT 59.052 33.333 0.00 0.00 0.00 2.45
36 37 8.485578 TGGGGTTTTCTAGTTTTTGTATGATT 57.514 30.769 0.00 0.00 0.00 2.57
37 38 8.581578 TGGGGTTTTCTAGTTTTTGTATGATTC 58.418 33.333 0.00 0.00 0.00 2.52
38 39 8.803235 GGGGTTTTCTAGTTTTTGTATGATTCT 58.197 33.333 0.00 0.00 0.00 2.40
39 40 9.626045 GGGTTTTCTAGTTTTTGTATGATTCTG 57.374 33.333 0.00 0.00 0.00 3.02
48 49 8.015658 AGTTTTTGTATGATTCTGTTAGTTCGC 58.984 33.333 0.00 0.00 0.00 4.70
49 50 7.667043 TTTTGTATGATTCTGTTAGTTCGCT 57.333 32.000 0.00 0.00 0.00 4.93
50 51 6.647212 TTGTATGATTCTGTTAGTTCGCTG 57.353 37.500 0.00 0.00 0.00 5.18
51 52 4.566759 TGTATGATTCTGTTAGTTCGCTGC 59.433 41.667 0.00 0.00 0.00 5.25
52 53 3.038788 TGATTCTGTTAGTTCGCTGCA 57.961 42.857 0.00 0.00 0.00 4.41
53 54 3.398406 TGATTCTGTTAGTTCGCTGCAA 58.602 40.909 0.00 0.00 0.00 4.08
54 55 3.433274 TGATTCTGTTAGTTCGCTGCAAG 59.567 43.478 0.00 0.00 0.00 4.01
55 56 2.526304 TCTGTTAGTTCGCTGCAAGT 57.474 45.000 0.00 0.00 35.30 3.16
56 57 2.833794 TCTGTTAGTTCGCTGCAAGTT 58.166 42.857 0.00 0.00 35.30 2.66
57 58 3.202906 TCTGTTAGTTCGCTGCAAGTTT 58.797 40.909 0.00 0.00 35.30 2.66
58 59 3.625764 TCTGTTAGTTCGCTGCAAGTTTT 59.374 39.130 0.00 0.00 35.30 2.43
59 60 4.095782 TCTGTTAGTTCGCTGCAAGTTTTT 59.904 37.500 0.00 0.00 35.30 1.94
60 61 4.101942 TGTTAGTTCGCTGCAAGTTTTTG 58.898 39.130 0.00 0.00 35.30 2.44
61 62 2.939460 AGTTCGCTGCAAGTTTTTGT 57.061 40.000 0.00 0.00 36.65 2.83
62 63 5.163744 TGTTAGTTCGCTGCAAGTTTTTGTA 60.164 36.000 0.00 0.00 36.65 2.41
63 64 3.691498 AGTTCGCTGCAAGTTTTTGTAC 58.309 40.909 0.00 0.00 36.65 2.90
64 65 3.377172 AGTTCGCTGCAAGTTTTTGTACT 59.623 39.130 0.00 0.00 36.65 2.73
65 66 4.573201 AGTTCGCTGCAAGTTTTTGTACTA 59.427 37.500 0.00 0.00 36.65 1.82
66 67 4.461992 TCGCTGCAAGTTTTTGTACTAC 57.538 40.909 0.00 0.00 36.65 2.73
67 68 3.872182 TCGCTGCAAGTTTTTGTACTACA 59.128 39.130 0.00 0.00 36.65 2.74
68 69 4.025229 TCGCTGCAAGTTTTTGTACTACAG 60.025 41.667 0.00 0.00 36.38 2.74
69 70 4.025229 CGCTGCAAGTTTTTGTACTACAGA 60.025 41.667 0.00 0.00 35.81 3.41
70 71 5.334105 CGCTGCAAGTTTTTGTACTACAGAT 60.334 40.000 0.00 0.00 35.81 2.90
71 72 5.853282 GCTGCAAGTTTTTGTACTACAGATG 59.147 40.000 0.00 0.00 35.81 2.90
72 73 6.513393 GCTGCAAGTTTTTGTACTACAGATGT 60.513 38.462 0.00 0.00 35.81 3.06
73 74 7.307751 GCTGCAAGTTTTTGTACTACAGATGTA 60.308 37.037 0.00 0.00 35.81 2.29
74 75 8.439993 TGCAAGTTTTTGTACTACAGATGTAA 57.560 30.769 0.00 0.00 36.65 2.41
75 76 9.062524 TGCAAGTTTTTGTACTACAGATGTAAT 57.937 29.630 0.00 0.00 36.65 1.89
76 77 9.893305 GCAAGTTTTTGTACTACAGATGTAATT 57.107 29.630 0.00 0.00 36.65 1.40
122 123 1.172180 CGCAGAGGGGAAAGCAAACA 61.172 55.000 0.00 0.00 0.00 2.83
130 131 1.069049 GGGAAAGCAAACATGCAGTGT 59.931 47.619 3.41 0.00 44.84 3.55
186 187 1.153289 CCCGACAGGAGCAGGAATG 60.153 63.158 0.00 0.00 41.02 2.67
615 643 7.509050 TGATTGATGAAAATGTTATGCGTTG 57.491 32.000 0.00 0.00 0.00 4.10
620 648 5.384063 TGAAAATGTTATGCGTTGGACAT 57.616 34.783 0.00 0.00 34.41 3.06
626 654 3.000041 GTTATGCGTTGGACATGACAGA 59.000 45.455 0.00 0.00 34.95 3.41
664 692 0.749649 ACTAGATTCAGGCAGGAGCG 59.250 55.000 0.00 0.00 43.41 5.03
681 709 0.170339 GCGAAAAATTCCACTCCGGG 59.830 55.000 0.00 0.00 34.36 5.73
1134 1192 3.082579 GCTCGACGCCTCCTGGAAT 62.083 63.158 0.00 0.00 34.57 3.01
1731 1795 1.377725 CTGCAAGGGCCGACTCAAT 60.378 57.895 0.00 0.00 40.13 2.57
1785 1849 1.374758 CGAGCAGGCCGACTTCTTT 60.375 57.895 0.00 0.00 0.00 2.52
1794 1858 1.938016 GCCGACTTCTTTTACGAGCCA 60.938 52.381 0.00 0.00 0.00 4.75
1800 1864 1.743995 CTTTTACGAGCCACCCGGG 60.744 63.158 22.25 22.25 40.85 5.73
1902 1966 0.321653 ACAACTGTTCCATCGGCCTC 60.322 55.000 0.00 0.00 0.00 4.70
2068 2132 1.298014 CTGGACCTGAGGAGCAACC 59.702 63.158 4.99 1.06 39.35 3.77
2403 2470 3.482783 GCTCGCCGTGACTTGAGC 61.483 66.667 5.15 5.15 45.95 4.26
2449 2521 6.310956 CACTCAGCAGAAGAAAAGAGATACTG 59.689 42.308 0.00 0.00 0.00 2.74
2498 2570 4.428294 ACACCTAACTGATGATGATGGG 57.572 45.455 0.00 0.00 0.00 4.00
2638 3890 1.745087 CCTTTTACGCATGCCATCACT 59.255 47.619 13.15 0.00 0.00 3.41
2649 3901 5.559608 CGCATGCCATCACTAGTAGATTTTG 60.560 44.000 13.15 0.00 0.00 2.44
2660 3912 3.092301 AGTAGATTTTGCTTGCCCTTCC 58.908 45.455 0.00 0.00 0.00 3.46
2683 3935 5.340803 CAATTCTTCTCGTCGGAACATCTA 58.659 41.667 0.00 0.00 0.00 1.98
2741 3993 3.005155 ACAAGGTTGATTCTCAGCAAAGC 59.995 43.478 0.00 0.00 28.47 3.51
2781 4033 2.831333 AGATATCTTCCGCTGCACTTG 58.169 47.619 0.00 0.00 0.00 3.16
2784 4036 1.376543 ATCTTCCGCTGCACTTGATG 58.623 50.000 0.00 0.00 0.00 3.07
2859 4111 5.295431 TGCATTTTAGAATTGGTGACTCG 57.705 39.130 0.00 0.00 0.00 4.18
2913 4165 0.457166 CAGCAATGTCGGCCACAATG 60.457 55.000 15.15 15.15 38.97 2.82
2922 4174 2.094752 GTCGGCCACAATGTTTAATGCT 60.095 45.455 2.24 0.00 0.00 3.79
2962 4218 6.260936 CCCCTATCTGTTTCACATACACATTC 59.739 42.308 0.00 0.00 0.00 2.67
2974 4230 1.502231 ACACATTCTCTGTCACGTGC 58.498 50.000 11.67 6.86 35.29 5.34
3061 4349 1.410050 TTCAGAGGCAGTCACAGGCA 61.410 55.000 0.00 0.00 0.00 4.75
3076 4364 2.206576 AGGCACTGGTTTGGAATCTC 57.793 50.000 0.00 0.00 37.18 2.75
3077 4365 1.177401 GGCACTGGTTTGGAATCTCC 58.823 55.000 0.00 0.00 36.96 3.71
3078 4366 1.272147 GGCACTGGTTTGGAATCTCCT 60.272 52.381 0.00 0.00 37.46 3.69
3079 4367 1.815003 GCACTGGTTTGGAATCTCCTG 59.185 52.381 0.00 0.00 37.46 3.86
3080 4368 2.440409 CACTGGTTTGGAATCTCCTGG 58.560 52.381 0.00 0.00 37.46 4.45
3081 4369 1.272147 ACTGGTTTGGAATCTCCTGGC 60.272 52.381 0.00 0.00 37.46 4.85
3082 4370 0.039618 TGGTTTGGAATCTCCTGGCC 59.960 55.000 0.00 0.00 37.46 5.36
3083 4371 0.684479 GGTTTGGAATCTCCTGGCCC 60.684 60.000 0.00 0.00 37.46 5.80
3084 4372 0.332972 GTTTGGAATCTCCTGGCCCT 59.667 55.000 0.00 0.00 37.46 5.19
3085 4373 1.564348 GTTTGGAATCTCCTGGCCCTA 59.436 52.381 0.00 0.00 37.46 3.53
3086 4374 1.511613 TTGGAATCTCCTGGCCCTAG 58.488 55.000 0.00 0.00 37.46 3.02
3087 4375 1.056700 TGGAATCTCCTGGCCCTAGC 61.057 60.000 0.00 0.00 37.46 3.42
3088 4376 1.056700 GGAATCTCCTGGCCCTAGCA 61.057 60.000 0.00 0.00 35.28 3.49
3089 4377 0.396060 GAATCTCCTGGCCCTAGCAG 59.604 60.000 0.00 0.00 42.56 4.24
3090 4378 0.327000 AATCTCCTGGCCCTAGCAGT 60.327 55.000 0.00 0.00 42.56 4.40
3091 4379 0.563173 ATCTCCTGGCCCTAGCAGTA 59.437 55.000 0.00 0.00 42.56 2.74
3092 4380 0.105964 TCTCCTGGCCCTAGCAGTAG 60.106 60.000 0.00 0.00 42.56 2.57
3093 4381 1.753368 CTCCTGGCCCTAGCAGTAGC 61.753 65.000 0.00 0.00 42.56 3.58
3094 4382 2.066393 CCTGGCCCTAGCAGTAGCA 61.066 63.158 0.00 0.00 45.49 3.49
3095 4383 1.445095 CTGGCCCTAGCAGTAGCAG 59.555 63.158 0.00 0.00 45.49 4.24
3096 4384 2.110006 GGCCCTAGCAGTAGCAGC 59.890 66.667 0.00 0.00 45.49 5.25
3097 4385 2.735772 GGCCCTAGCAGTAGCAGCA 61.736 63.158 0.00 0.00 45.49 4.41
3098 4386 1.221840 GCCCTAGCAGTAGCAGCAA 59.778 57.895 0.00 0.00 45.49 3.91
3099 4387 0.179034 GCCCTAGCAGTAGCAGCAAT 60.179 55.000 0.00 0.00 45.49 3.56
3100 4388 1.590932 CCCTAGCAGTAGCAGCAATG 58.409 55.000 0.00 0.00 45.49 2.82
3101 4389 0.942962 CCTAGCAGTAGCAGCAATGC 59.057 55.000 0.00 0.00 45.49 3.56
3102 4390 0.942962 CTAGCAGTAGCAGCAATGCC 59.057 55.000 0.00 0.00 45.49 4.40
3103 4391 0.252761 TAGCAGTAGCAGCAATGCCA 59.747 50.000 0.00 0.00 45.49 4.92
3104 4392 1.030488 AGCAGTAGCAGCAATGCCAG 61.030 55.000 0.00 0.00 45.49 4.85
3105 4393 1.310933 GCAGTAGCAGCAATGCCAGT 61.311 55.000 0.00 0.00 41.58 4.00
3106 4394 0.450583 CAGTAGCAGCAATGCCAGTG 59.549 55.000 0.00 0.00 34.90 3.66
3107 4395 0.037303 AGTAGCAGCAATGCCAGTGT 59.963 50.000 0.00 0.00 34.90 3.55
3108 4396 0.169672 GTAGCAGCAATGCCAGTGTG 59.830 55.000 0.00 0.00 34.90 3.82
3109 4397 0.036590 TAGCAGCAATGCCAGTGTGA 59.963 50.000 0.00 0.00 34.90 3.58
3110 4398 0.611062 AGCAGCAATGCCAGTGTGAT 60.611 50.000 0.00 0.00 34.90 3.06
3111 4399 0.245539 GCAGCAATGCCAGTGTGATT 59.754 50.000 0.00 0.00 0.00 2.57
3112 4400 1.990799 CAGCAATGCCAGTGTGATTG 58.009 50.000 0.00 6.89 0.00 2.67
3113 4401 1.271379 CAGCAATGCCAGTGTGATTGT 59.729 47.619 0.00 0.00 31.03 2.71
3114 4402 1.271379 AGCAATGCCAGTGTGATTGTG 59.729 47.619 0.00 0.00 31.03 3.33
3115 4403 1.270274 GCAATGCCAGTGTGATTGTGA 59.730 47.619 0.00 0.00 31.03 3.58
3116 4404 2.094390 GCAATGCCAGTGTGATTGTGAT 60.094 45.455 0.00 0.00 31.03 3.06
3117 4405 3.507786 CAATGCCAGTGTGATTGTGATG 58.492 45.455 4.04 0.00 0.00 3.07
3118 4406 0.883153 TGCCAGTGTGATTGTGATGC 59.117 50.000 0.00 0.00 0.00 3.91
3119 4407 1.171308 GCCAGTGTGATTGTGATGCT 58.829 50.000 0.00 0.00 0.00 3.79
3120 4408 1.135489 GCCAGTGTGATTGTGATGCTG 60.135 52.381 0.00 0.00 0.00 4.41
3121 4409 1.135489 CCAGTGTGATTGTGATGCTGC 60.135 52.381 0.00 0.00 0.00 5.25
3122 4410 1.810755 CAGTGTGATTGTGATGCTGCT 59.189 47.619 0.00 0.00 0.00 4.24
3123 4411 2.082231 AGTGTGATTGTGATGCTGCTC 58.918 47.619 0.00 0.00 0.00 4.26
3124 4412 1.131883 GTGTGATTGTGATGCTGCTCC 59.868 52.381 0.00 0.00 0.00 4.70
3125 4413 1.271488 TGTGATTGTGATGCTGCTCCA 60.271 47.619 0.00 0.00 0.00 3.86
3126 4414 2.022195 GTGATTGTGATGCTGCTCCAT 58.978 47.619 0.00 0.00 0.00 3.41
3127 4415 3.208594 GTGATTGTGATGCTGCTCCATA 58.791 45.455 0.00 0.00 0.00 2.74
3128 4416 3.628942 GTGATTGTGATGCTGCTCCATAA 59.371 43.478 0.00 4.03 0.00 1.90
3129 4417 3.628942 TGATTGTGATGCTGCTCCATAAC 59.371 43.478 0.00 0.00 0.00 1.89
3130 4418 3.354948 TTGTGATGCTGCTCCATAACT 57.645 42.857 0.00 0.00 29.48 2.24
3131 4419 2.910199 TGTGATGCTGCTCCATAACTC 58.090 47.619 0.00 0.00 29.48 3.01
3132 4420 2.236893 TGTGATGCTGCTCCATAACTCA 59.763 45.455 0.00 0.00 29.48 3.41
3133 4421 3.118149 TGTGATGCTGCTCCATAACTCAT 60.118 43.478 0.00 0.00 29.48 2.90
3134 4422 3.497640 GTGATGCTGCTCCATAACTCATC 59.502 47.826 0.00 0.00 0.00 2.92
3135 4423 3.135167 TGATGCTGCTCCATAACTCATCA 59.865 43.478 0.00 0.00 37.20 3.07
3136 4424 3.189618 TGCTGCTCCATAACTCATCAG 57.810 47.619 0.00 0.00 0.00 2.90
3137 4425 1.872313 GCTGCTCCATAACTCATCAGC 59.128 52.381 0.00 0.00 38.62 4.26
3138 4426 2.133553 CTGCTCCATAACTCATCAGCG 58.866 52.381 0.00 0.00 0.00 5.18
3139 4427 1.756538 TGCTCCATAACTCATCAGCGA 59.243 47.619 0.00 0.00 0.00 4.93
3140 4428 2.223900 TGCTCCATAACTCATCAGCGAG 60.224 50.000 0.00 0.00 39.05 5.03
3141 4429 2.035193 GCTCCATAACTCATCAGCGAGA 59.965 50.000 0.00 0.00 36.47 4.04
3142 4430 3.491619 GCTCCATAACTCATCAGCGAGAA 60.492 47.826 0.00 0.00 36.47 2.87
3143 4431 4.297510 CTCCATAACTCATCAGCGAGAAG 58.702 47.826 0.00 0.00 36.47 2.85
3158 4446 0.972134 AGAAGCTGCAGCACTGTCTA 59.028 50.000 38.24 0.00 45.16 2.59
3173 4461 8.671921 CAGCACTGTCTATAATCTTTCATTTGT 58.328 33.333 0.00 0.00 0.00 2.83
3180 4468 9.860898 GTCTATAATCTTTCATTTGTGGCTTTT 57.139 29.630 0.00 0.00 0.00 2.27
3254 4542 8.590470 GCTTTTTAGAGTTGGTAACGAGTATAC 58.410 37.037 0.00 0.00 42.51 1.47
3255 4543 9.852091 CTTTTTAGAGTTGGTAACGAGTATACT 57.148 33.333 4.68 4.68 42.51 2.12
3258 4546 9.672673 TTTAGAGTTGGTAACGAGTATACTAGT 57.327 33.333 12.36 12.36 42.51 2.57
3261 4549 9.487790 AGAGTTGGTAACGAGTATACTAGTATC 57.512 37.037 18.68 13.19 42.51 2.24
3262 4550 9.265901 GAGTTGGTAACGAGTATACTAGTATCA 57.734 37.037 18.68 13.12 42.51 2.15
3263 4551 9.790344 AGTTGGTAACGAGTATACTAGTATCAT 57.210 33.333 18.68 8.87 42.51 2.45
3267 4555 9.752274 GGTAACGAGTATACTAGTATCATTTCG 57.248 37.037 18.68 21.36 31.54 3.46
3271 4559 9.656040 ACGAGTATACTAGTATCATTTCGATCT 57.344 33.333 27.05 13.90 35.39 2.75
3272 4560 9.909043 CGAGTATACTAGTATCATTTCGATCTG 57.091 37.037 18.68 0.00 35.39 2.90
3274 4562 9.179909 AGTATACTAGTATCATTTCGATCTGGG 57.820 37.037 18.68 0.00 35.39 4.45
3275 4563 5.140747 ACTAGTATCATTTCGATCTGGGC 57.859 43.478 0.00 0.00 35.39 5.36
3276 4564 3.032017 AGTATCATTTCGATCTGGGCG 57.968 47.619 0.00 0.00 35.39 6.13
3277 4565 1.461127 GTATCATTTCGATCTGGGCGC 59.539 52.381 0.00 0.00 35.39 6.53
3278 4566 0.179048 ATCATTTCGATCTGGGCGCA 60.179 50.000 10.83 2.47 0.00 6.09
3279 4567 0.179048 TCATTTCGATCTGGGCGCAT 60.179 50.000 10.83 0.00 0.00 4.73
3280 4568 0.236711 CATTTCGATCTGGGCGCATC 59.763 55.000 10.83 1.99 0.00 3.91
3281 4569 0.179048 ATTTCGATCTGGGCGCATCA 60.179 50.000 10.83 6.07 0.00 3.07
3282 4570 0.179048 TTTCGATCTGGGCGCATCAT 60.179 50.000 10.83 0.00 0.00 2.45
3283 4571 0.678950 TTCGATCTGGGCGCATCATA 59.321 50.000 10.83 0.00 0.00 2.15
3284 4572 0.897621 TCGATCTGGGCGCATCATAT 59.102 50.000 10.83 5.11 0.00 1.78
3285 4573 1.134995 TCGATCTGGGCGCATCATATC 60.135 52.381 10.83 13.08 0.00 1.63
3286 4574 1.661341 GATCTGGGCGCATCATATCC 58.339 55.000 10.83 0.00 0.00 2.59
3287 4575 0.986527 ATCTGGGCGCATCATATCCA 59.013 50.000 10.83 4.16 0.00 3.41
3288 4576 0.764271 TCTGGGCGCATCATATCCAA 59.236 50.000 10.83 0.00 0.00 3.53
3289 4577 1.352017 TCTGGGCGCATCATATCCAAT 59.648 47.619 10.83 0.00 0.00 3.16
3290 4578 1.741706 CTGGGCGCATCATATCCAATC 59.258 52.381 10.83 0.00 0.00 2.67
3291 4579 1.098050 GGGCGCATCATATCCAATCC 58.902 55.000 10.83 0.00 0.00 3.01
3292 4580 1.614051 GGGCGCATCATATCCAATCCA 60.614 52.381 10.83 0.00 0.00 3.41
3293 4581 2.161855 GGCGCATCATATCCAATCCAA 58.838 47.619 10.83 0.00 0.00 3.53
3294 4582 2.095059 GGCGCATCATATCCAATCCAAC 60.095 50.000 10.83 0.00 0.00 3.77
3295 4583 2.553602 GCGCATCATATCCAATCCAACA 59.446 45.455 0.30 0.00 0.00 3.33
3296 4584 3.192001 GCGCATCATATCCAATCCAACAT 59.808 43.478 0.30 0.00 0.00 2.71
3297 4585 4.673580 GCGCATCATATCCAATCCAACATC 60.674 45.833 0.30 0.00 0.00 3.06
3298 4586 4.698780 CGCATCATATCCAATCCAACATCT 59.301 41.667 0.00 0.00 0.00 2.90
3299 4587 5.182570 CGCATCATATCCAATCCAACATCTT 59.817 40.000 0.00 0.00 0.00 2.40
3300 4588 6.387465 GCATCATATCCAATCCAACATCTTG 58.613 40.000 0.00 0.00 0.00 3.02
3301 4589 6.015688 GCATCATATCCAATCCAACATCTTGT 60.016 38.462 0.00 0.00 0.00 3.16
3302 4590 7.591165 CATCATATCCAATCCAACATCTTGTC 58.409 38.462 0.00 0.00 0.00 3.18
3303 4591 6.064060 TCATATCCAATCCAACATCTTGTCC 58.936 40.000 0.00 0.00 0.00 4.02
3304 4592 4.598036 ATCCAATCCAACATCTTGTCCT 57.402 40.909 0.00 0.00 0.00 3.85
3305 4593 3.955471 TCCAATCCAACATCTTGTCCTC 58.045 45.455 0.00 0.00 0.00 3.71
3306 4594 3.588842 TCCAATCCAACATCTTGTCCTCT 59.411 43.478 0.00 0.00 0.00 3.69
3307 4595 4.782691 TCCAATCCAACATCTTGTCCTCTA 59.217 41.667 0.00 0.00 0.00 2.43
3308 4596 4.878397 CCAATCCAACATCTTGTCCTCTAC 59.122 45.833 0.00 0.00 0.00 2.59
3309 4597 5.338708 CCAATCCAACATCTTGTCCTCTACT 60.339 44.000 0.00 0.00 0.00 2.57
3310 4598 6.176183 CAATCCAACATCTTGTCCTCTACTT 58.824 40.000 0.00 0.00 0.00 2.24
3311 4599 5.152623 TCCAACATCTTGTCCTCTACTTG 57.847 43.478 0.00 0.00 0.00 3.16
3312 4600 4.020218 TCCAACATCTTGTCCTCTACTTGG 60.020 45.833 0.00 0.00 30.74 3.61
3313 4601 4.020218 CCAACATCTTGTCCTCTACTTGGA 60.020 45.833 0.00 0.00 30.96 3.53
3314 4602 5.513094 CCAACATCTTGTCCTCTACTTGGAA 60.513 44.000 0.00 0.00 35.10 3.53
3315 4603 6.176183 CAACATCTTGTCCTCTACTTGGAAT 58.824 40.000 0.00 0.00 35.10 3.01
3316 4604 6.380079 ACATCTTGTCCTCTACTTGGAATT 57.620 37.500 0.00 0.00 35.10 2.17
3317 4605 6.176183 ACATCTTGTCCTCTACTTGGAATTG 58.824 40.000 0.00 0.00 35.10 2.32
3318 4606 5.165961 TCTTGTCCTCTACTTGGAATTGG 57.834 43.478 0.00 0.00 35.10 3.16
3319 4607 4.844085 TCTTGTCCTCTACTTGGAATTGGA 59.156 41.667 0.00 0.00 35.10 3.53
3320 4608 5.309543 TCTTGTCCTCTACTTGGAATTGGAA 59.690 40.000 0.00 0.00 35.10 3.53
3321 4609 5.779241 TGTCCTCTACTTGGAATTGGAAT 57.221 39.130 0.00 0.00 35.10 3.01
3322 4610 5.500234 TGTCCTCTACTTGGAATTGGAATG 58.500 41.667 0.00 0.00 35.10 2.67
3323 4611 4.884164 GTCCTCTACTTGGAATTGGAATGG 59.116 45.833 0.00 0.00 35.10 3.16
3324 4612 4.788075 TCCTCTACTTGGAATTGGAATGGA 59.212 41.667 0.00 0.00 0.00 3.41
3325 4613 5.252863 TCCTCTACTTGGAATTGGAATGGAA 59.747 40.000 0.00 0.00 0.00 3.53
3326 4614 5.591877 CCTCTACTTGGAATTGGAATGGAAG 59.408 44.000 0.00 0.00 0.00 3.46
3327 4615 5.509498 TCTACTTGGAATTGGAATGGAAGG 58.491 41.667 0.00 0.00 0.00 3.46
3328 4616 2.833943 ACTTGGAATTGGAATGGAAGGC 59.166 45.455 0.00 0.00 0.00 4.35
3329 4617 2.619697 TGGAATTGGAATGGAAGGCA 57.380 45.000 0.00 0.00 0.00 4.75
3330 4618 2.178580 TGGAATTGGAATGGAAGGCAC 58.821 47.619 0.00 0.00 0.00 5.01
3331 4619 2.178580 GGAATTGGAATGGAAGGCACA 58.821 47.619 0.00 0.00 0.00 4.57
3332 4620 2.767960 GGAATTGGAATGGAAGGCACAT 59.232 45.455 0.00 0.00 0.00 3.21
3333 4621 3.431207 GGAATTGGAATGGAAGGCACATG 60.431 47.826 0.00 0.00 0.00 3.21
3334 4622 2.601240 TTGGAATGGAAGGCACATGA 57.399 45.000 0.00 0.00 0.00 3.07
3335 4623 1.838112 TGGAATGGAAGGCACATGAC 58.162 50.000 0.00 0.00 0.00 3.06
3336 4624 1.075212 TGGAATGGAAGGCACATGACA 59.925 47.619 0.00 0.00 0.00 3.58
3337 4625 1.747355 GGAATGGAAGGCACATGACAG 59.253 52.381 0.00 0.00 0.00 3.51
3338 4626 1.747355 GAATGGAAGGCACATGACAGG 59.253 52.381 0.00 0.00 0.00 4.00
3339 4627 0.700564 ATGGAAGGCACATGACAGGT 59.299 50.000 0.00 0.00 0.00 4.00
3340 4628 0.036732 TGGAAGGCACATGACAGGTC 59.963 55.000 0.00 0.00 0.00 3.85
3341 4629 1.021390 GGAAGGCACATGACAGGTCG 61.021 60.000 0.00 0.00 0.00 4.79
3342 4630 1.003355 AAGGCACATGACAGGTCGG 60.003 57.895 0.00 0.00 0.00 4.79
3343 4631 1.480212 AAGGCACATGACAGGTCGGA 61.480 55.000 0.00 0.00 0.00 4.55
3344 4632 1.448540 GGCACATGACAGGTCGGAG 60.449 63.158 0.00 0.00 0.00 4.63
3345 4633 1.293498 GCACATGACAGGTCGGAGT 59.707 57.895 0.00 0.00 0.00 3.85
3346 4634 0.530744 GCACATGACAGGTCGGAGTA 59.469 55.000 0.00 0.00 0.00 2.59
3347 4635 1.469940 GCACATGACAGGTCGGAGTAG 60.470 57.143 0.00 0.00 0.00 2.57
3348 4636 1.819288 CACATGACAGGTCGGAGTAGT 59.181 52.381 0.00 0.00 0.00 2.73
3349 4637 3.014623 CACATGACAGGTCGGAGTAGTA 58.985 50.000 0.00 0.00 0.00 1.82
3350 4638 3.015327 ACATGACAGGTCGGAGTAGTAC 58.985 50.000 0.00 0.00 0.00 2.73
3351 4639 3.280295 CATGACAGGTCGGAGTAGTACT 58.720 50.000 1.37 1.37 0.00 2.73
3352 4640 2.708051 TGACAGGTCGGAGTAGTACTG 58.292 52.381 7.76 0.00 0.00 2.74
3353 4641 1.401199 GACAGGTCGGAGTAGTACTGC 59.599 57.143 7.76 9.89 32.81 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.616577 ACTAGAAAACCCCAGAAAAATGGTA 58.383 36.000 0.00 0.00 38.81 3.25
1 2 5.464069 ACTAGAAAACCCCAGAAAAATGGT 58.536 37.500 0.00 0.00 38.81 3.55
2 3 6.419484 AACTAGAAAACCCCAGAAAAATGG 57.581 37.500 0.00 0.00 40.29 3.16
3 4 8.611757 CAAAAACTAGAAAACCCCAGAAAAATG 58.388 33.333 0.00 0.00 0.00 2.32
4 5 8.325787 ACAAAAACTAGAAAACCCCAGAAAAAT 58.674 29.630 0.00 0.00 0.00 1.82
5 6 7.681679 ACAAAAACTAGAAAACCCCAGAAAAA 58.318 30.769 0.00 0.00 0.00 1.94
6 7 7.247456 ACAAAAACTAGAAAACCCCAGAAAA 57.753 32.000 0.00 0.00 0.00 2.29
7 8 6.860790 ACAAAAACTAGAAAACCCCAGAAA 57.139 33.333 0.00 0.00 0.00 2.52
8 9 7.780745 TCATACAAAAACTAGAAAACCCCAGAA 59.219 33.333 0.00 0.00 0.00 3.02
9 10 7.291566 TCATACAAAAACTAGAAAACCCCAGA 58.708 34.615 0.00 0.00 0.00 3.86
10 11 7.519032 TCATACAAAAACTAGAAAACCCCAG 57.481 36.000 0.00 0.00 0.00 4.45
11 12 8.485578 AATCATACAAAAACTAGAAAACCCCA 57.514 30.769 0.00 0.00 0.00 4.96
12 13 8.803235 AGAATCATACAAAAACTAGAAAACCCC 58.197 33.333 0.00 0.00 0.00 4.95
13 14 9.626045 CAGAATCATACAAAAACTAGAAAACCC 57.374 33.333 0.00 0.00 0.00 4.11
22 23 8.015658 GCGAACTAACAGAATCATACAAAAACT 58.984 33.333 0.00 0.00 0.00 2.66
23 24 8.015658 AGCGAACTAACAGAATCATACAAAAAC 58.984 33.333 0.00 0.00 0.00 2.43
24 25 8.015087 CAGCGAACTAACAGAATCATACAAAAA 58.985 33.333 0.00 0.00 0.00 1.94
25 26 7.518161 CAGCGAACTAACAGAATCATACAAAA 58.482 34.615 0.00 0.00 0.00 2.44
26 27 6.402118 GCAGCGAACTAACAGAATCATACAAA 60.402 38.462 0.00 0.00 0.00 2.83
27 28 5.063438 GCAGCGAACTAACAGAATCATACAA 59.937 40.000 0.00 0.00 0.00 2.41
28 29 4.566759 GCAGCGAACTAACAGAATCATACA 59.433 41.667 0.00 0.00 0.00 2.29
29 30 4.566759 TGCAGCGAACTAACAGAATCATAC 59.433 41.667 0.00 0.00 0.00 2.39
30 31 4.754322 TGCAGCGAACTAACAGAATCATA 58.246 39.130 0.00 0.00 0.00 2.15
31 32 3.599343 TGCAGCGAACTAACAGAATCAT 58.401 40.909 0.00 0.00 0.00 2.45
32 33 3.038788 TGCAGCGAACTAACAGAATCA 57.961 42.857 0.00 0.00 0.00 2.57
33 34 3.433615 ACTTGCAGCGAACTAACAGAATC 59.566 43.478 0.00 0.00 0.00 2.52
34 35 3.403038 ACTTGCAGCGAACTAACAGAAT 58.597 40.909 0.00 0.00 0.00 2.40
35 36 2.833794 ACTTGCAGCGAACTAACAGAA 58.166 42.857 0.00 0.00 0.00 3.02
36 37 2.526304 ACTTGCAGCGAACTAACAGA 57.474 45.000 0.00 0.00 0.00 3.41
37 38 3.609103 AAACTTGCAGCGAACTAACAG 57.391 42.857 0.00 0.00 0.00 3.16
38 39 4.101942 CAAAAACTTGCAGCGAACTAACA 58.898 39.130 0.00 0.00 0.00 2.41
39 40 4.102649 ACAAAAACTTGCAGCGAACTAAC 58.897 39.130 0.00 0.00 0.00 2.34
40 41 4.364415 ACAAAAACTTGCAGCGAACTAA 57.636 36.364 0.00 0.00 0.00 2.24
41 42 4.573201 AGTACAAAAACTTGCAGCGAACTA 59.427 37.500 0.00 0.00 0.00 2.24
42 43 2.939460 ACAAAAACTTGCAGCGAACT 57.061 40.000 0.00 0.00 0.00 3.01
43 44 3.691498 AGTACAAAAACTTGCAGCGAAC 58.309 40.909 0.00 0.00 0.00 3.95
44 45 4.333095 TGTAGTACAAAAACTTGCAGCGAA 59.667 37.500 0.00 0.00 0.00 4.70
45 46 3.872182 TGTAGTACAAAAACTTGCAGCGA 59.128 39.130 0.00 0.00 0.00 4.93
46 47 4.025229 TCTGTAGTACAAAAACTTGCAGCG 60.025 41.667 4.21 0.00 34.26 5.18
47 48 5.418310 TCTGTAGTACAAAAACTTGCAGC 57.582 39.130 4.21 0.00 34.26 5.25
48 49 6.959361 ACATCTGTAGTACAAAAACTTGCAG 58.041 36.000 4.21 0.00 34.93 4.41
49 50 6.935741 ACATCTGTAGTACAAAAACTTGCA 57.064 33.333 4.21 0.00 0.00 4.08
50 51 9.893305 AATTACATCTGTAGTACAAAAACTTGC 57.107 29.630 4.21 0.00 0.00 4.01
74 75 8.565416 CGTTGGGACTTTTTCTAAAGAGTTAAT 58.435 33.333 4.77 0.00 42.78 1.40
75 76 7.769970 TCGTTGGGACTTTTTCTAAAGAGTTAA 59.230 33.333 4.77 0.00 42.78 2.01
76 77 7.225341 GTCGTTGGGACTTTTTCTAAAGAGTTA 59.775 37.037 4.77 0.00 42.78 2.24
77 78 6.037940 GTCGTTGGGACTTTTTCTAAAGAGTT 59.962 38.462 4.77 0.00 42.78 3.01
78 79 5.526479 GTCGTTGGGACTTTTTCTAAAGAGT 59.474 40.000 4.77 0.00 42.78 3.24
79 80 5.049612 GGTCGTTGGGACTTTTTCTAAAGAG 60.050 44.000 4.77 0.00 45.35 2.85
80 81 4.818005 GGTCGTTGGGACTTTTTCTAAAGA 59.182 41.667 4.77 0.00 45.35 2.52
81 82 4.319261 CGGTCGTTGGGACTTTTTCTAAAG 60.319 45.833 0.00 0.00 45.35 1.85
93 94 3.691342 CCTCTGCGGTCGTTGGGA 61.691 66.667 0.00 0.00 0.00 4.37
122 123 4.838152 CGGCGGCCTACACTGCAT 62.838 66.667 18.34 0.00 44.09 3.96
153 154 4.547367 GGGATCGTGGCCGGGAAG 62.547 72.222 2.18 0.00 33.95 3.46
186 187 0.629058 TGTTGGCCTATTTCCCCTCC 59.371 55.000 3.32 0.00 0.00 4.30
222 223 2.268167 ATCTTCCTGCCTGCCTCTGC 62.268 60.000 0.00 0.00 38.26 4.26
604 632 2.741517 CTGTCATGTCCAACGCATAACA 59.258 45.455 0.00 0.00 0.00 2.41
620 648 3.311486 TCGTGCATTACATGTCTGTCA 57.689 42.857 0.00 1.90 36.79 3.58
636 664 2.286294 GCCTGAATCTAGTGCAATCGTG 59.714 50.000 0.00 0.00 0.00 4.35
664 692 2.092323 CTCCCCGGAGTGGAATTTTTC 58.908 52.381 0.73 0.00 42.00 2.29
681 709 0.603569 TCACAAGTCTCCGCTTCTCC 59.396 55.000 0.00 0.00 0.00 3.71
740 790 0.240411 GAGAAGGTGCTGCTTGCTTG 59.760 55.000 0.00 0.00 43.37 4.01
755 805 2.614013 GGGGAGGGGGCAAGAGAA 60.614 66.667 0.00 0.00 0.00 2.87
984 1042 2.437895 ATCGAGCCGACAGACCGA 60.438 61.111 0.00 0.00 39.18 4.69
985 1043 2.278206 CATCGAGCCGACAGACCG 60.278 66.667 0.00 0.00 39.18 4.79
986 1044 2.105128 CCATCGAGCCGACAGACC 59.895 66.667 0.00 0.00 39.18 3.85
987 1045 2.583593 GCCATCGAGCCGACAGAC 60.584 66.667 0.00 0.00 39.18 3.51
988 1046 4.193334 CGCCATCGAGCCGACAGA 62.193 66.667 0.00 0.00 39.18 3.41
1656 1720 2.434359 CCGGCGGTGAAGGACTTC 60.434 66.667 19.97 5.14 39.91 3.01
1725 1789 1.202417 CCGATGCCGTACTCATTGAGT 60.202 52.381 22.16 22.16 45.54 3.41
1731 1795 3.405592 GACGCCGATGCCGTACTCA 62.406 63.158 0.00 0.00 39.30 3.41
1785 1849 3.697747 CACCCGGGTGGCTCGTAA 61.698 66.667 41.16 0.00 42.00 3.18
1902 1966 0.618458 TCTTGTCCCGGAAATCCAGG 59.382 55.000 0.73 0.00 34.80 4.45
2022 2086 1.471684 AGGTCGTCGTACTGGTTGATC 59.528 52.381 0.00 0.00 0.00 2.92
2403 2470 1.298563 CACAACAAGTGCAGTGCGG 60.299 57.895 11.20 2.46 42.15 5.69
2430 2502 6.102663 TGTAGCAGTATCTCTTTTCTTCTGC 58.897 40.000 0.00 0.00 44.44 4.26
2449 2521 6.926272 CCATTCCTTCTGAATACTACTGTAGC 59.074 42.308 14.55 0.00 41.85 3.58
2523 2595 4.505922 GTGCTCCAGTTAAGATTGATCGAG 59.494 45.833 0.00 0.00 0.00 4.04
2638 3890 4.263727 TGGAAGGGCAAGCAAAATCTACTA 60.264 41.667 0.00 0.00 0.00 1.82
2649 3901 2.165234 GAGAAGAATTGGAAGGGCAAGC 59.835 50.000 0.00 0.00 0.00 4.01
2660 3912 4.177026 AGATGTTCCGACGAGAAGAATTG 58.823 43.478 0.00 0.00 0.00 2.32
2683 3935 1.377202 AACGCCTGATGCCGACAAT 60.377 52.632 0.00 0.00 36.24 2.71
2707 3959 7.117397 AGAATCAACCTTGTGATGATCTTGAT 58.883 34.615 0.00 0.00 38.28 2.57
2761 4013 2.432146 TCAAGTGCAGCGGAAGATATCT 59.568 45.455 0.00 0.00 0.00 1.98
2770 4022 1.078918 TCCTCATCAAGTGCAGCGG 60.079 57.895 0.00 0.00 0.00 5.52
2781 4033 2.857744 CGTACGGGGCCTCCTCATC 61.858 68.421 7.57 0.00 0.00 2.92
2859 4111 0.107945 AGCCAAATCTGTCCTCGAGC 60.108 55.000 6.99 0.00 0.00 5.03
2913 4165 5.119125 GCACTGTTCCAATTCAGCATTAAAC 59.881 40.000 0.00 0.00 35.37 2.01
2922 4174 0.482446 AGGGGCACTGTTCCAATTCA 59.518 50.000 0.00 0.00 0.00 2.57
2962 4218 2.748605 AGAAAGAAGCACGTGACAGAG 58.251 47.619 22.23 0.00 0.00 3.35
3014 4271 8.281212 ACAGCAGAAACTCTTTTAAAGAAAGA 57.719 30.769 8.82 1.75 37.02 2.52
3023 4280 5.882557 TCTGAAGAACAGCAGAAACTCTTTT 59.117 36.000 0.00 0.00 45.38 2.27
3033 4290 1.270732 ACTGCCTCTGAAGAACAGCAG 60.271 52.381 18.18 18.18 45.38 4.24
3034 4291 0.761187 ACTGCCTCTGAAGAACAGCA 59.239 50.000 9.02 5.08 45.38 4.41
3035 4292 1.270518 TGACTGCCTCTGAAGAACAGC 60.271 52.381 9.02 1.32 45.38 4.40
3036 4293 2.224137 TGTGACTGCCTCTGAAGAACAG 60.224 50.000 7.96 7.96 46.97 3.16
3061 4349 1.272147 GCCAGGAGATTCCAAACCAGT 60.272 52.381 0.00 0.00 39.61 4.00
3065 4353 0.332972 AGGGCCAGGAGATTCCAAAC 59.667 55.000 6.18 0.00 39.61 2.93
3067 4355 1.511613 CTAGGGCCAGGAGATTCCAA 58.488 55.000 6.18 0.00 39.61 3.53
3068 4356 1.056700 GCTAGGGCCAGGAGATTCCA 61.057 60.000 6.18 0.00 39.61 3.53
3069 4357 1.056700 TGCTAGGGCCAGGAGATTCC 61.057 60.000 6.18 0.00 37.74 3.01
3070 4358 0.396060 CTGCTAGGGCCAGGAGATTC 59.604 60.000 15.84 0.00 36.15 2.52
3071 4359 0.327000 ACTGCTAGGGCCAGGAGATT 60.327 55.000 23.78 6.64 37.43 2.40
3072 4360 0.563173 TACTGCTAGGGCCAGGAGAT 59.437 55.000 23.78 13.98 37.43 2.75
3073 4361 0.105964 CTACTGCTAGGGCCAGGAGA 60.106 60.000 23.78 11.41 37.43 3.71
3074 4362 1.753368 GCTACTGCTAGGGCCAGGAG 61.753 65.000 18.15 18.15 39.69 3.69
3075 4363 1.762460 GCTACTGCTAGGGCCAGGA 60.762 63.158 6.18 1.27 37.74 3.86
3076 4364 2.037620 CTGCTACTGCTAGGGCCAGG 62.038 65.000 6.18 0.00 40.48 4.45
3077 4365 1.445095 CTGCTACTGCTAGGGCCAG 59.555 63.158 6.18 2.03 40.48 4.85
3078 4366 2.735772 GCTGCTACTGCTAGGGCCA 61.736 63.158 6.18 0.00 40.48 5.36
3079 4367 2.110006 GCTGCTACTGCTAGGGCC 59.890 66.667 0.00 0.00 40.48 5.80
3080 4368 0.179034 ATTGCTGCTACTGCTAGGGC 60.179 55.000 0.00 0.00 40.48 5.19
3081 4369 1.590932 CATTGCTGCTACTGCTAGGG 58.409 55.000 0.00 0.00 40.48 3.53
3082 4370 0.942962 GCATTGCTGCTACTGCTAGG 59.057 55.000 0.16 0.00 45.32 3.02
3093 4381 1.271379 ACAATCACACTGGCATTGCTG 59.729 47.619 8.82 1.61 31.74 4.41
3094 4382 1.271379 CACAATCACACTGGCATTGCT 59.729 47.619 8.82 0.00 31.74 3.91
3095 4383 1.270274 TCACAATCACACTGGCATTGC 59.730 47.619 4.57 0.00 31.74 3.56
3096 4384 3.507786 CATCACAATCACACTGGCATTG 58.492 45.455 2.97 2.97 34.29 2.82
3097 4385 2.094390 GCATCACAATCACACTGGCATT 60.094 45.455 0.00 0.00 0.00 3.56
3098 4386 1.475280 GCATCACAATCACACTGGCAT 59.525 47.619 0.00 0.00 0.00 4.40
3099 4387 0.883153 GCATCACAATCACACTGGCA 59.117 50.000 0.00 0.00 0.00 4.92
3100 4388 1.135489 CAGCATCACAATCACACTGGC 60.135 52.381 0.00 0.00 0.00 4.85
3101 4389 1.135489 GCAGCATCACAATCACACTGG 60.135 52.381 0.00 0.00 0.00 4.00
3102 4390 1.810755 AGCAGCATCACAATCACACTG 59.189 47.619 0.00 0.00 0.00 3.66
3103 4391 2.082231 GAGCAGCATCACAATCACACT 58.918 47.619 0.00 0.00 0.00 3.55
3104 4392 1.131883 GGAGCAGCATCACAATCACAC 59.868 52.381 0.00 0.00 0.00 3.82
3105 4393 1.271488 TGGAGCAGCATCACAATCACA 60.271 47.619 0.00 0.00 0.00 3.58
3106 4394 1.456296 TGGAGCAGCATCACAATCAC 58.544 50.000 0.00 0.00 0.00 3.06
3107 4395 2.430248 ATGGAGCAGCATCACAATCA 57.570 45.000 0.00 0.00 0.00 2.57
3108 4396 3.881688 AGTTATGGAGCAGCATCACAATC 59.118 43.478 0.00 0.00 0.00 2.67
3109 4397 3.881688 GAGTTATGGAGCAGCATCACAAT 59.118 43.478 0.00 0.00 0.00 2.71
3110 4398 3.273434 GAGTTATGGAGCAGCATCACAA 58.727 45.455 0.00 0.00 0.00 3.33
3111 4399 2.236893 TGAGTTATGGAGCAGCATCACA 59.763 45.455 0.00 0.00 0.00 3.58
3112 4400 2.910199 TGAGTTATGGAGCAGCATCAC 58.090 47.619 0.00 0.00 0.00 3.06
3113 4401 3.135167 TGATGAGTTATGGAGCAGCATCA 59.865 43.478 0.00 0.00 38.51 3.07
3114 4402 3.736720 TGATGAGTTATGGAGCAGCATC 58.263 45.455 0.00 0.00 33.24 3.91
3115 4403 3.741249 CTGATGAGTTATGGAGCAGCAT 58.259 45.455 0.00 0.00 0.00 3.79
3116 4404 2.744166 GCTGATGAGTTATGGAGCAGCA 60.744 50.000 0.00 0.00 44.72 4.41
3117 4405 1.872313 GCTGATGAGTTATGGAGCAGC 59.128 52.381 0.00 0.00 40.15 5.25
3118 4406 2.133553 CGCTGATGAGTTATGGAGCAG 58.866 52.381 0.00 0.00 0.00 4.24
3119 4407 1.756538 TCGCTGATGAGTTATGGAGCA 59.243 47.619 0.00 0.00 0.00 4.26
3120 4408 2.035193 TCTCGCTGATGAGTTATGGAGC 59.965 50.000 0.00 0.00 37.28 4.70
3121 4409 3.998099 TCTCGCTGATGAGTTATGGAG 57.002 47.619 0.00 0.00 37.28 3.86
3122 4410 3.491619 GCTTCTCGCTGATGAGTTATGGA 60.492 47.826 0.00 0.00 37.28 3.41
3123 4411 2.799412 GCTTCTCGCTGATGAGTTATGG 59.201 50.000 0.00 0.00 37.28 2.74
3136 4424 2.741598 AGTGCTGCAGCTTCTCGC 60.742 61.111 36.61 19.58 42.66 5.03
3137 4425 1.624865 GACAGTGCTGCAGCTTCTCG 61.625 60.000 36.61 26.03 42.66 4.04
3138 4426 0.320596 AGACAGTGCTGCAGCTTCTC 60.321 55.000 36.61 24.22 42.66 2.87
3139 4427 0.972134 TAGACAGTGCTGCAGCTTCT 59.028 50.000 36.61 29.94 42.66 2.85
3140 4428 2.021355 ATAGACAGTGCTGCAGCTTC 57.979 50.000 36.61 27.90 42.66 3.86
3141 4429 3.616956 TTATAGACAGTGCTGCAGCTT 57.383 42.857 36.61 23.21 42.66 3.74
3142 4430 3.387374 AGATTATAGACAGTGCTGCAGCT 59.613 43.478 36.61 19.14 42.66 4.24
3143 4431 3.726607 AGATTATAGACAGTGCTGCAGC 58.273 45.455 31.89 31.89 42.50 5.25
3144 4432 5.814188 TGAAAGATTATAGACAGTGCTGCAG 59.186 40.000 10.11 10.11 0.00 4.41
3145 4433 5.733676 TGAAAGATTATAGACAGTGCTGCA 58.266 37.500 0.00 0.00 0.00 4.41
3152 4440 8.218338 AGCCACAAATGAAAGATTATAGACAG 57.782 34.615 0.00 0.00 0.00 3.51
3173 4461 2.038952 TGAGCAGAGCTAAGAAAAGCCA 59.961 45.455 0.00 0.00 43.86 4.75
3254 4542 4.169508 CGCCCAGATCGAAATGATACTAG 58.830 47.826 0.00 0.00 37.47 2.57
3255 4543 3.614150 GCGCCCAGATCGAAATGATACTA 60.614 47.826 0.00 0.00 37.47 1.82
3256 4544 2.868044 GCGCCCAGATCGAAATGATACT 60.868 50.000 0.00 0.00 37.47 2.12
3257 4545 1.461127 GCGCCCAGATCGAAATGATAC 59.539 52.381 0.00 0.00 37.47 2.24
3258 4546 1.069978 TGCGCCCAGATCGAAATGATA 59.930 47.619 4.18 0.00 37.47 2.15
3259 4547 0.179048 TGCGCCCAGATCGAAATGAT 60.179 50.000 4.18 0.00 41.06 2.45
3260 4548 0.179048 ATGCGCCCAGATCGAAATGA 60.179 50.000 4.18 0.00 0.00 2.57
3261 4549 0.236711 GATGCGCCCAGATCGAAATG 59.763 55.000 4.18 0.00 0.00 2.32
3262 4550 0.179048 TGATGCGCCCAGATCGAAAT 60.179 50.000 4.18 0.00 0.00 2.17
3263 4551 0.179048 ATGATGCGCCCAGATCGAAA 60.179 50.000 4.18 0.00 0.00 3.46
3264 4552 0.678950 TATGATGCGCCCAGATCGAA 59.321 50.000 4.18 0.00 0.00 3.71
3265 4553 0.897621 ATATGATGCGCCCAGATCGA 59.102 50.000 4.18 0.00 0.00 3.59
3266 4554 1.284657 GATATGATGCGCCCAGATCG 58.715 55.000 15.39 0.00 0.00 3.69
3267 4555 1.065926 TGGATATGATGCGCCCAGATC 60.066 52.381 19.73 19.73 33.00 2.75
3268 4556 0.986527 TGGATATGATGCGCCCAGAT 59.013 50.000 4.18 5.76 0.00 2.90
3269 4557 0.764271 TTGGATATGATGCGCCCAGA 59.236 50.000 4.18 0.00 0.00 3.86
3270 4558 1.741706 GATTGGATATGATGCGCCCAG 59.258 52.381 4.18 0.00 0.00 4.45
3271 4559 1.614051 GGATTGGATATGATGCGCCCA 60.614 52.381 4.18 2.91 0.00 5.36
3272 4560 1.098050 GGATTGGATATGATGCGCCC 58.902 55.000 4.18 0.00 0.00 6.13
3273 4561 1.825090 TGGATTGGATATGATGCGCC 58.175 50.000 4.18 0.00 0.00 6.53
3274 4562 2.553602 TGTTGGATTGGATATGATGCGC 59.446 45.455 0.00 0.00 0.00 6.09
3275 4563 4.698780 AGATGTTGGATTGGATATGATGCG 59.301 41.667 0.00 0.00 0.00 4.73
3276 4564 6.015688 ACAAGATGTTGGATTGGATATGATGC 60.016 38.462 7.59 0.00 38.07 3.91
3277 4565 7.309012 GGACAAGATGTTGGATTGGATATGATG 60.309 40.741 7.59 0.00 38.07 3.07
3278 4566 6.718454 GGACAAGATGTTGGATTGGATATGAT 59.282 38.462 7.59 0.00 38.07 2.45
3279 4567 6.064060 GGACAAGATGTTGGATTGGATATGA 58.936 40.000 7.59 0.00 38.07 2.15
3280 4568 6.066690 AGGACAAGATGTTGGATTGGATATG 58.933 40.000 7.59 0.00 38.07 1.78
3281 4569 6.102321 AGAGGACAAGATGTTGGATTGGATAT 59.898 38.462 7.59 0.00 38.07 1.63
3282 4570 5.429762 AGAGGACAAGATGTTGGATTGGATA 59.570 40.000 7.59 0.00 38.07 2.59
3283 4571 4.229123 AGAGGACAAGATGTTGGATTGGAT 59.771 41.667 7.59 0.00 38.07 3.41
3284 4572 3.588842 AGAGGACAAGATGTTGGATTGGA 59.411 43.478 7.59 0.00 38.07 3.53
3285 4573 3.960571 AGAGGACAAGATGTTGGATTGG 58.039 45.455 7.59 0.00 38.07 3.16
3286 4574 5.738909 AGTAGAGGACAAGATGTTGGATTG 58.261 41.667 7.59 0.00 38.07 2.67
3287 4575 6.176183 CAAGTAGAGGACAAGATGTTGGATT 58.824 40.000 7.59 0.00 38.07 3.01
3288 4576 5.338708 CCAAGTAGAGGACAAGATGTTGGAT 60.339 44.000 7.59 0.00 38.07 3.41
3289 4577 4.020218 CCAAGTAGAGGACAAGATGTTGGA 60.020 45.833 7.59 0.00 38.07 3.53
3290 4578 4.020218 TCCAAGTAGAGGACAAGATGTTGG 60.020 45.833 7.59 0.00 38.07 3.77
3291 4579 5.152623 TCCAAGTAGAGGACAAGATGTTG 57.847 43.478 0.13 0.13 39.82 3.33
3292 4580 5.825593 TTCCAAGTAGAGGACAAGATGTT 57.174 39.130 0.00 0.00 34.19 2.71
3293 4581 6.176183 CAATTCCAAGTAGAGGACAAGATGT 58.824 40.000 0.00 0.00 34.19 3.06
3294 4582 5.587844 CCAATTCCAAGTAGAGGACAAGATG 59.412 44.000 0.00 0.00 34.19 2.90
3295 4583 5.488919 TCCAATTCCAAGTAGAGGACAAGAT 59.511 40.000 0.00 0.00 34.19 2.40
3296 4584 4.844085 TCCAATTCCAAGTAGAGGACAAGA 59.156 41.667 0.00 0.00 34.19 3.02
3297 4585 5.165961 TCCAATTCCAAGTAGAGGACAAG 57.834 43.478 0.00 0.00 34.19 3.16
3298 4586 5.576563 TTCCAATTCCAAGTAGAGGACAA 57.423 39.130 0.00 0.00 34.19 3.18
3299 4587 5.500234 CATTCCAATTCCAAGTAGAGGACA 58.500 41.667 0.00 0.00 34.19 4.02
3300 4588 4.884164 CCATTCCAATTCCAAGTAGAGGAC 59.116 45.833 0.00 0.00 34.19 3.85
3301 4589 4.788075 TCCATTCCAATTCCAAGTAGAGGA 59.212 41.667 0.00 0.00 0.00 3.71
3302 4590 5.116084 TCCATTCCAATTCCAAGTAGAGG 57.884 43.478 0.00 0.00 0.00 3.69
3303 4591 5.591877 CCTTCCATTCCAATTCCAAGTAGAG 59.408 44.000 0.00 0.00 0.00 2.43
3304 4592 5.509498 CCTTCCATTCCAATTCCAAGTAGA 58.491 41.667 0.00 0.00 0.00 2.59
3305 4593 4.098501 GCCTTCCATTCCAATTCCAAGTAG 59.901 45.833 0.00 0.00 0.00 2.57
3306 4594 4.023291 GCCTTCCATTCCAATTCCAAGTA 58.977 43.478 0.00 0.00 0.00 2.24
3307 4595 2.833943 GCCTTCCATTCCAATTCCAAGT 59.166 45.455 0.00 0.00 0.00 3.16
3308 4596 2.833338 TGCCTTCCATTCCAATTCCAAG 59.167 45.455 0.00 0.00 0.00 3.61
3309 4597 2.566724 GTGCCTTCCATTCCAATTCCAA 59.433 45.455 0.00 0.00 0.00 3.53
3310 4598 2.178580 GTGCCTTCCATTCCAATTCCA 58.821 47.619 0.00 0.00 0.00 3.53
3311 4599 2.178580 TGTGCCTTCCATTCCAATTCC 58.821 47.619 0.00 0.00 0.00 3.01
3312 4600 3.448301 TCATGTGCCTTCCATTCCAATTC 59.552 43.478 0.00 0.00 0.00 2.17
3313 4601 3.196254 GTCATGTGCCTTCCATTCCAATT 59.804 43.478 0.00 0.00 0.00 2.32
3314 4602 2.762327 GTCATGTGCCTTCCATTCCAAT 59.238 45.455 0.00 0.00 0.00 3.16
3315 4603 2.170166 GTCATGTGCCTTCCATTCCAA 58.830 47.619 0.00 0.00 0.00 3.53
3316 4604 1.075212 TGTCATGTGCCTTCCATTCCA 59.925 47.619 0.00 0.00 0.00 3.53
3317 4605 1.747355 CTGTCATGTGCCTTCCATTCC 59.253 52.381 0.00 0.00 0.00 3.01
3318 4606 1.747355 CCTGTCATGTGCCTTCCATTC 59.253 52.381 0.00 0.00 0.00 2.67
3319 4607 1.076024 ACCTGTCATGTGCCTTCCATT 59.924 47.619 0.00 0.00 0.00 3.16
3320 4608 0.700564 ACCTGTCATGTGCCTTCCAT 59.299 50.000 0.00 0.00 0.00 3.41
3321 4609 0.036732 GACCTGTCATGTGCCTTCCA 59.963 55.000 0.00 0.00 0.00 3.53
3322 4610 1.021390 CGACCTGTCATGTGCCTTCC 61.021 60.000 0.00 0.00 0.00 3.46
3323 4611 1.021390 CCGACCTGTCATGTGCCTTC 61.021 60.000 0.00 0.00 0.00 3.46
3324 4612 1.003355 CCGACCTGTCATGTGCCTT 60.003 57.895 0.00 0.00 0.00 4.35
3325 4613 1.892819 CTCCGACCTGTCATGTGCCT 61.893 60.000 0.00 0.00 0.00 4.75
3326 4614 1.448540 CTCCGACCTGTCATGTGCC 60.449 63.158 0.00 0.00 0.00 5.01
3327 4615 0.530744 TACTCCGACCTGTCATGTGC 59.469 55.000 0.00 0.00 0.00 4.57
3328 4616 1.819288 ACTACTCCGACCTGTCATGTG 59.181 52.381 0.00 0.00 0.00 3.21
3329 4617 2.217510 ACTACTCCGACCTGTCATGT 57.782 50.000 0.00 0.00 0.00 3.21
3330 4618 3.065510 CAGTACTACTCCGACCTGTCATG 59.934 52.174 0.00 0.00 0.00 3.07
3331 4619 3.280295 CAGTACTACTCCGACCTGTCAT 58.720 50.000 0.00 0.00 0.00 3.06
3332 4620 2.708051 CAGTACTACTCCGACCTGTCA 58.292 52.381 0.00 0.00 0.00 3.58
3333 4621 1.401199 GCAGTACTACTCCGACCTGTC 59.599 57.143 0.00 0.00 0.00 3.51
3334 4622 1.461559 GCAGTACTACTCCGACCTGT 58.538 55.000 0.00 0.00 0.00 4.00
3335 4623 0.377554 CGCAGTACTACTCCGACCTG 59.622 60.000 0.00 0.00 0.00 4.00
3336 4624 0.747283 CCGCAGTACTACTCCGACCT 60.747 60.000 0.82 0.00 0.00 3.85
3337 4625 1.726265 CCGCAGTACTACTCCGACC 59.274 63.158 0.82 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.