Multiple sequence alignment - TraesCS1A01G292500

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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 TraesCS1A01G292500 chr1A 100.000 3530 0 0 1 3530 488096618 488100147 0.000000e+00 6519.0
1 TraesCS1A01G292500 chr1A 80.345 1450 245 28 1086 2521 319447392 319445969 0.000000e+00 1062.0
2 TraesCS1A01G292500 chr1A 80.165 1457 243 33 1081 2520 319889304 319887877 0.000000e+00 1048.0
3 TraesCS1A01G292500 chr1A 75.062 401 71 22 1080 1478 320155974 320155601 3.650000e-35 159.0
4 TraesCS1A01G292500 chr1B 93.165 2970 108 35 1 2918 522745842 522742916 0.000000e+00 4272.0
5 TraesCS1A01G292500 chr1B 80.150 1466 247 35 1072 2521 364504992 364506429 0.000000e+00 1055.0
6 TraesCS1A01G292500 chr1B 77.346 1492 266 46 1080 2523 364423137 364424604 0.000000e+00 817.0
7 TraesCS1A01G292500 chr1B 82.412 597 91 13 1926 2521 364812164 364812747 3.140000e-140 508.0
8 TraesCS1A01G292500 chr1B 86.000 400 21 14 2975 3355 522742759 522742376 2.550000e-106 396.0
9 TraesCS1A01G292500 chr1B 78.131 503 62 30 2891 3355 522837572 522838064 3.470000e-70 276.0
10 TraesCS1A01G292500 chr1B 94.118 102 4 2 3392 3491 17268190 17268089 1.700000e-33 154.0
11 TraesCS1A01G292500 chr1D 93.015 2348 85 37 1058 3355 389489281 389491599 0.000000e+00 3354.0
12 TraesCS1A01G292500 chr1D 81.007 1469 229 38 1072 2521 249755541 249754104 0.000000e+00 1122.0
13 TraesCS1A01G292500 chr1D 80.577 1457 239 38 1081 2521 250070706 250069278 0.000000e+00 1083.0
14 TraesCS1A01G292500 chr1D 78.057 1472 267 47 1080 2520 442798167 442799613 0.000000e+00 878.0
15 TraesCS1A01G292500 chr1D 76.530 1487 273 53 1082 2521 467607383 467605926 0.000000e+00 743.0
16 TraesCS1A01G292500 chr1D 93.766 401 21 4 1 400 389488556 389488953 1.810000e-167 599.0
17 TraesCS1A01G292500 chr1D 85.328 259 14 12 584 830 389489023 389489269 2.720000e-61 246.0
18 TraesCS1A01G292500 chr1D 79.083 349 35 14 3017 3355 389809328 389809648 4.620000e-49 206.0
19 TraesCS1A01G292500 chr1D 82.609 207 20 9 3017 3214 389246901 389246702 6.060000e-38 169.0
20 TraesCS1A01G292500 chr1D 89.147 129 12 2 3229 3356 389246611 389246484 3.650000e-35 159.0
21 TraesCS1A01G292500 chr1D 77.070 157 19 8 3017 3164 389353970 389353822 1.360000e-09 75.0
22 TraesCS1A01G292500 chrUn 77.370 1498 241 66 1086 2527 28754123 28752668 0.000000e+00 798.0
23 TraesCS1A01G292500 chrUn 96.429 140 4 1 3392 3530 94243197 94243058 2.740000e-56 230.0
24 TraesCS1A01G292500 chr7A 81.250 320 45 11 82 391 550051243 550050929 9.790000e-61 244.0
25 TraesCS1A01G292500 chr7A 80.180 333 52 10 51 379 35393675 35393353 1.640000e-58 237.0
26 TraesCS1A01G292500 chr2A 97.163 141 3 1 3391 3530 758938212 758938072 1.640000e-58 237.0
27 TraesCS1A01G292500 chr2A 87.413 143 15 2 3391 3530 43178855 43178997 1.010000e-35 161.0
28 TraesCS1A01G292500 chr3A 80.119 337 48 15 70 393 696282548 696282878 2.120000e-57 233.0
29 TraesCS1A01G292500 chr3A 89.552 134 9 3 3392 3523 53296719 53296849 7.840000e-37 165.0
30 TraesCS1A01G292500 chr4A 83.936 249 29 9 151 391 689667257 689667012 9.860000e-56 228.0
31 TraesCS1A01G292500 chr5B 94.326 141 6 2 3392 3530 2624129 2624269 7.670000e-52 215.0
32 TraesCS1A01G292500 chr5B 87.838 148 9 5 3389 3530 711991968 711992112 7.840000e-37 165.0
33 TraesCS1A01G292500 chr3B 78.512 363 52 21 51 393 744312611 744312967 7.670000e-52 215.0
34 TraesCS1A01G292500 chr3B 80.695 259 35 14 50 298 736667660 736667407 1.670000e-43 187.0
35 TraesCS1A01G292500 chr3B 78.049 164 24 9 224 379 752670124 752670283 3.750000e-15 93.5
36 TraesCS1A01G292500 chr3D 79.355 310 44 11 96 388 560119493 560119799 2.150000e-47 200.0
37 TraesCS1A01G292500 chr6D 95.833 120 4 1 3412 3530 115770619 115770738 3.600000e-45 193.0
38 TraesCS1A01G292500 chr2B 90.210 143 10 2 3392 3530 635080439 635080581 2.160000e-42 183.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G292500 chr1A 488096618 488100147 3529 False 6519.000000 6519 100.0000 1 3530 1 chr1A.!!$F1 3529
1 TraesCS1A01G292500 chr1A 319445969 319447392 1423 True 1062.000000 1062 80.3450 1086 2521 1 chr1A.!!$R1 1435
2 TraesCS1A01G292500 chr1A 319887877 319889304 1427 True 1048.000000 1048 80.1650 1081 2520 1 chr1A.!!$R2 1439
3 TraesCS1A01G292500 chr1B 522742376 522745842 3466 True 2334.000000 4272 89.5825 1 3355 2 chr1B.!!$R2 3354
4 TraesCS1A01G292500 chr1B 364504992 364506429 1437 False 1055.000000 1055 80.1500 1072 2521 1 chr1B.!!$F2 1449
5 TraesCS1A01G292500 chr1B 364423137 364424604 1467 False 817.000000 817 77.3460 1080 2523 1 chr1B.!!$F1 1443
6 TraesCS1A01G292500 chr1B 364812164 364812747 583 False 508.000000 508 82.4120 1926 2521 1 chr1B.!!$F3 595
7 TraesCS1A01G292500 chr1D 389488556 389491599 3043 False 1399.666667 3354 90.7030 1 3355 3 chr1D.!!$F3 3354
8 TraesCS1A01G292500 chr1D 249754104 249755541 1437 True 1122.000000 1122 81.0070 1072 2521 1 chr1D.!!$R1 1449
9 TraesCS1A01G292500 chr1D 250069278 250070706 1428 True 1083.000000 1083 80.5770 1081 2521 1 chr1D.!!$R2 1440
10 TraesCS1A01G292500 chr1D 442798167 442799613 1446 False 878.000000 878 78.0570 1080 2520 1 chr1D.!!$F2 1440
11 TraesCS1A01G292500 chr1D 467605926 467607383 1457 True 743.000000 743 76.5300 1082 2521 1 chr1D.!!$R4 1439
12 TraesCS1A01G292500 chrUn 28752668 28754123 1455 True 798.000000 798 77.3700 1086 2527 1 chrUn.!!$R1 1441

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
492 502 0.030235 TATCCACACGAATCTCCGCG 59.970 55.000 0.00 0.0 0.00 6.46 F
495 505 0.866061 CCACACGAATCTCCGCGTAG 60.866 60.000 4.92 0.0 38.92 3.51 F
1048 1098 1.150536 CTCCTCCTCCTCTCCCTCG 59.849 68.421 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1332 1397 1.705337 CGCGGGTGATGATGTTGTCC 61.705 60.000 0.00 0.0 0.0 4.02 R
1980 2100 3.604629 TCGTAGAGCCTGTCCTGC 58.395 61.111 0.00 0.0 0.0 4.85 R
2749 2899 2.092592 CCCATGGGTAACTTAGGTCACC 60.093 54.545 23.93 0.0 0.0 4.02 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
73 79 4.113354 CTCCTTCCTCGATTTTTACTCCG 58.887 47.826 0.00 0.00 0.00 4.63
127 133 3.102052 TGTTTGGTACTCTCAACCGAC 57.898 47.619 0.00 0.00 40.08 4.79
251 261 7.885297 TCAAATCTTCCCAAATTCACAACTAG 58.115 34.615 0.00 0.00 0.00 2.57
273 283 6.656632 AGATCCAAACTTTCCTTTTCTTCC 57.343 37.500 0.00 0.00 0.00 3.46
281 291 7.855784 AACTTTCCTTTTCTTCCCATACAAT 57.144 32.000 0.00 0.00 0.00 2.71
318 328 9.710900 AAATCAAATCTTACCAAAATCTCAACC 57.289 29.630 0.00 0.00 0.00 3.77
351 361 1.215173 TCCTTGCATTCCCTACCCATG 59.785 52.381 0.00 0.00 0.00 3.66
406 416 9.298250 TCTAGAATATGTGTTAGATACAGGGTC 57.702 37.037 0.00 0.00 37.45 4.46
409 419 3.887621 TGTGTTAGATACAGGGTCTGC 57.112 47.619 0.00 0.00 37.45 4.26
451 461 5.961272 TCGCACATCTAAGTGACTTAATCA 58.039 37.500 6.51 0.00 42.05 2.57
466 476 9.346725 GTGACTTAATCAAAGCATAAAAGGAAG 57.653 33.333 0.00 0.00 39.72 3.46
468 478 9.561270 GACTTAATCAAAGCATAAAAGGAAGAC 57.439 33.333 0.00 0.00 38.93 3.01
482 492 5.880054 AAGGAAGACAAAATATCCACACG 57.120 39.130 0.00 0.00 34.30 4.49
492 502 0.030235 TATCCACACGAATCTCCGCG 59.970 55.000 0.00 0.00 0.00 6.46
495 505 0.866061 CCACACGAATCTCCGCGTAG 60.866 60.000 4.92 0.00 38.92 3.51
525 535 2.052590 CGCCCGTTGAAACACACG 60.053 61.111 0.00 0.00 0.00 4.49
604 614 9.987272 AAAGGAGAGATAAGAAAAACCAAAATG 57.013 29.630 0.00 0.00 0.00 2.32
636 660 8.368668 GCATGTAGGAGTAGATACCTATTTTGT 58.631 37.037 0.00 0.00 40.27 2.83
724 751 5.023533 TCAAGAACGAGATAGATTTGGGG 57.976 43.478 0.00 0.00 0.00 4.96
734 761 7.093992 CGAGATAGATTTGGGGTTCTAGATTC 58.906 42.308 0.00 0.00 0.00 2.52
767 795 2.654863 CAAACCCACCACAACTCTTCT 58.345 47.619 0.00 0.00 0.00 2.85
768 796 3.023832 CAAACCCACCACAACTCTTCTT 58.976 45.455 0.00 0.00 0.00 2.52
769 797 2.640316 ACCCACCACAACTCTTCTTC 57.360 50.000 0.00 0.00 0.00 2.87
770 798 1.843851 ACCCACCACAACTCTTCTTCA 59.156 47.619 0.00 0.00 0.00 3.02
771 799 2.241176 ACCCACCACAACTCTTCTTCAA 59.759 45.455 0.00 0.00 0.00 2.69
772 800 3.287222 CCCACCACAACTCTTCTTCAAA 58.713 45.455 0.00 0.00 0.00 2.69
773 801 3.891366 CCCACCACAACTCTTCTTCAAAT 59.109 43.478 0.00 0.00 0.00 2.32
774 802 4.022849 CCCACCACAACTCTTCTTCAAATC 60.023 45.833 0.00 0.00 0.00 2.17
835 863 2.163412 TCCCGCCTTTGAATTGAATTCG 59.837 45.455 12.72 1.04 42.15 3.34
836 864 1.919918 CCGCCTTTGAATTGAATTCGC 59.080 47.619 12.72 8.93 42.15 4.70
889 918 3.632107 TTGCACGCACGAACGTCC 61.632 61.111 4.58 0.00 46.34 4.79
935 984 1.685491 GGTCTCGTACATCTCCACCCT 60.685 57.143 0.00 0.00 0.00 4.34
936 985 1.677052 GTCTCGTACATCTCCACCCTC 59.323 57.143 0.00 0.00 0.00 4.30
1044 1094 2.123033 GCCCTCCTCCTCCTCTCC 60.123 72.222 0.00 0.00 0.00 3.71
1048 1098 1.150536 CTCCTCCTCCTCTCCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
1052 1102 3.213402 CCTCCTCTCCCTCGTCGC 61.213 72.222 0.00 0.00 0.00 5.19
1201 1257 3.467226 AGTACGGCCCCATCGTGG 61.467 66.667 0.00 0.00 41.24 4.94
1648 1740 3.296322 AGCTCACTGTCTTCTTCTTCG 57.704 47.619 0.00 0.00 0.00 3.79
1980 2100 3.047877 GTCAAGAACCCGGCCGTG 61.048 66.667 26.12 16.88 0.00 4.94
2570 2705 7.581011 ATTTCCTTTTAGCTTAATTTGCACG 57.419 32.000 0.00 0.00 0.00 5.34
2596 2735 5.431420 TGTTTTGCGTGTGTGATTAGATT 57.569 34.783 0.00 0.00 0.00 2.40
2680 2830 3.299503 AGCAAGGAACATTGTTGGAGTT 58.700 40.909 6.80 0.00 32.56 3.01
2721 2871 5.772672 TGTCTAGGTTTGCCAATTGTAATGT 59.227 36.000 4.43 0.00 37.19 2.71
2749 2899 9.695526 TTTTGTTTCCTGATTCAGATTACAATG 57.304 29.630 15.36 0.00 32.44 2.82
2775 2925 0.107410 TAAGTTACCCATGGGCAGCG 60.107 55.000 31.73 7.08 39.32 5.18
2777 2927 3.012119 TTACCCATGGGCAGCGGA 61.012 61.111 31.73 7.45 39.32 5.54
2823 2973 6.592798 AACAAAAGCATTCATCAACACAAG 57.407 33.333 0.00 0.00 0.00 3.16
2826 2976 6.643770 ACAAAAGCATTCATCAACACAAGATC 59.356 34.615 0.00 0.00 0.00 2.75
2827 2977 6.585695 AAAGCATTCATCAACACAAGATCT 57.414 33.333 0.00 0.00 0.00 2.75
2828 2978 7.692460 AAAGCATTCATCAACACAAGATCTA 57.308 32.000 0.00 0.00 0.00 1.98
2829 2979 7.876936 AAGCATTCATCAACACAAGATCTAT 57.123 32.000 0.00 0.00 0.00 1.98
2830 2980 7.260558 AGCATTCATCAACACAAGATCTATG 57.739 36.000 0.00 0.00 0.00 2.23
2831 2981 7.052248 AGCATTCATCAACACAAGATCTATGA 58.948 34.615 12.66 6.05 0.00 2.15
2832 2982 7.555195 AGCATTCATCAACACAAGATCTATGAA 59.445 33.333 14.21 14.21 36.59 2.57
2859 3015 4.754114 GGAAAAGATCCCATTCTGATCTCG 59.246 45.833 3.46 0.00 46.29 4.04
2921 3080 6.327279 AGGTTGTTTGTAATTTACCTCTGC 57.673 37.500 4.17 0.00 30.42 4.26
2922 3081 5.830991 AGGTTGTTTGTAATTTACCTCTGCA 59.169 36.000 4.17 0.00 30.42 4.41
2923 3082 6.493458 AGGTTGTTTGTAATTTACCTCTGCAT 59.507 34.615 4.17 0.00 30.42 3.96
2924 3083 6.806739 GGTTGTTTGTAATTTACCTCTGCATC 59.193 38.462 4.17 0.00 0.00 3.91
2925 3084 7.367285 GTTGTTTGTAATTTACCTCTGCATCA 58.633 34.615 4.17 0.00 0.00 3.07
2926 3085 7.701539 TGTTTGTAATTTACCTCTGCATCAT 57.298 32.000 4.17 0.00 0.00 2.45
2927 3086 7.537715 TGTTTGTAATTTACCTCTGCATCATG 58.462 34.615 4.17 0.00 0.00 3.07
2928 3087 7.392953 TGTTTGTAATTTACCTCTGCATCATGA 59.607 33.333 0.00 0.00 0.00 3.07
2929 3088 6.925610 TGTAATTTACCTCTGCATCATGAC 57.074 37.500 0.00 0.00 0.00 3.06
2930 3089 6.653020 TGTAATTTACCTCTGCATCATGACT 58.347 36.000 0.00 0.00 0.00 3.41
2931 3090 7.112122 TGTAATTTACCTCTGCATCATGACTT 58.888 34.615 0.00 0.00 0.00 3.01
2932 3091 8.264347 TGTAATTTACCTCTGCATCATGACTTA 58.736 33.333 0.00 0.00 0.00 2.24
2933 3092 7.559590 AATTTACCTCTGCATCATGACTTAC 57.440 36.000 0.00 0.00 0.00 2.34
3007 3283 8.827832 AATCATACATTTTTCCTCCTTCATCA 57.172 30.769 0.00 0.00 0.00 3.07
3008 3284 8.827832 ATCATACATTTTTCCTCCTTCATCAA 57.172 30.769 0.00 0.00 0.00 2.57
3056 3332 6.358974 TCAGTCATCCAATCTAGAACACAA 57.641 37.500 0.00 0.00 0.00 3.33
3061 3337 6.763135 GTCATCCAATCTAGAACACAAGCATA 59.237 38.462 0.00 0.00 0.00 3.14
3067 3352 8.986847 CCAATCTAGAACACAAGCATATTCTAG 58.013 37.037 11.83 11.83 46.38 2.43
3073 3361 6.482641 AGAACACAAGCATATTCTAGCATGAG 59.517 38.462 0.00 0.00 33.97 2.90
3104 3392 9.401058 GCTTTATATTGGATATGGCAGATAACT 57.599 33.333 0.00 0.00 0.00 2.24
3163 3451 8.603242 ACCGTGATAACCAATACTATCAAATC 57.397 34.615 0.00 0.00 36.53 2.17
3286 3582 7.392673 AGCATATCCCAGATTTGATGAATACAC 59.607 37.037 0.02 0.00 0.00 2.90
3291 3587 4.260907 CCAGATTTGATGAATACACAGCGG 60.261 45.833 0.00 0.00 0.00 5.52
3331 3629 6.616774 ACACTTTGGGCAATAACATTTTTG 57.383 33.333 0.00 0.00 0.00 2.44
3348 3646 7.799784 ACATTTTTGCAAAGAACATAAGCATC 58.200 30.769 12.41 0.00 34.87 3.91
3355 3653 6.037940 TGCAAAGAACATAAGCATCATCTCTC 59.962 38.462 0.00 0.00 0.00 3.20
3356 3654 6.260493 GCAAAGAACATAAGCATCATCTCTCT 59.740 38.462 0.00 0.00 0.00 3.10
3357 3655 7.518689 GCAAAGAACATAAGCATCATCTCTCTC 60.519 40.741 0.00 0.00 0.00 3.20
3358 3656 6.982160 AGAACATAAGCATCATCTCTCTCT 57.018 37.500 0.00 0.00 0.00 3.10
3359 3657 6.985117 AGAACATAAGCATCATCTCTCTCTC 58.015 40.000 0.00 0.00 0.00 3.20
3360 3658 6.779049 AGAACATAAGCATCATCTCTCTCTCT 59.221 38.462 0.00 0.00 0.00 3.10
3361 3659 6.579666 ACATAAGCATCATCTCTCTCTCTC 57.420 41.667 0.00 0.00 0.00 3.20
3362 3660 6.309357 ACATAAGCATCATCTCTCTCTCTCT 58.691 40.000 0.00 0.00 0.00 3.10
3363 3661 6.432162 ACATAAGCATCATCTCTCTCTCTCTC 59.568 42.308 0.00 0.00 0.00 3.20
3364 3662 3.405831 AGCATCATCTCTCTCTCTCTCG 58.594 50.000 0.00 0.00 0.00 4.04
3365 3663 2.095567 GCATCATCTCTCTCTCTCTCGC 60.096 54.545 0.00 0.00 0.00 5.03
3366 3664 2.998316 TCATCTCTCTCTCTCTCGCA 57.002 50.000 0.00 0.00 0.00 5.10
3367 3665 2.837498 TCATCTCTCTCTCTCTCGCAG 58.163 52.381 0.00 0.00 0.00 5.18
3368 3666 1.265095 CATCTCTCTCTCTCTCGCAGC 59.735 57.143 0.00 0.00 0.00 5.25
3369 3667 0.541392 TCTCTCTCTCTCTCGCAGCT 59.459 55.000 0.00 0.00 0.00 4.24
3370 3668 0.940126 CTCTCTCTCTCTCGCAGCTC 59.060 60.000 0.00 0.00 0.00 4.09
3371 3669 0.251634 TCTCTCTCTCTCGCAGCTCA 59.748 55.000 0.00 0.00 0.00 4.26
3372 3670 0.378257 CTCTCTCTCTCGCAGCTCAC 59.622 60.000 0.00 0.00 0.00 3.51
3373 3671 0.322008 TCTCTCTCTCGCAGCTCACA 60.322 55.000 0.00 0.00 0.00 3.58
3374 3672 0.525311 CTCTCTCTCGCAGCTCACAA 59.475 55.000 0.00 0.00 0.00 3.33
3375 3673 0.525311 TCTCTCTCGCAGCTCACAAG 59.475 55.000 0.00 0.00 0.00 3.16
3376 3674 0.243365 CTCTCTCGCAGCTCACAAGT 59.757 55.000 0.00 0.00 0.00 3.16
3377 3675 1.470494 CTCTCTCGCAGCTCACAAGTA 59.530 52.381 0.00 0.00 0.00 2.24
3378 3676 1.470494 TCTCTCGCAGCTCACAAGTAG 59.530 52.381 0.00 0.00 0.00 2.57
3379 3677 0.109086 TCTCGCAGCTCACAAGTAGC 60.109 55.000 0.00 0.00 40.40 3.58
3380 3678 1.409227 CTCGCAGCTCACAAGTAGCG 61.409 60.000 4.59 4.59 44.87 4.26
3381 3679 1.734477 CGCAGCTCACAAGTAGCGT 60.734 57.895 2.94 0.00 44.87 5.07
3382 3680 1.284982 CGCAGCTCACAAGTAGCGTT 61.285 55.000 2.94 0.00 44.87 4.84
3383 3681 0.164647 GCAGCTCACAAGTAGCGTTG 59.835 55.000 0.00 0.00 44.87 4.10
3384 3682 0.792640 CAGCTCACAAGTAGCGTTGG 59.207 55.000 0.00 0.00 44.87 3.77
3385 3683 0.679505 AGCTCACAAGTAGCGTTGGA 59.320 50.000 0.00 0.00 44.87 3.53
3386 3684 1.276421 AGCTCACAAGTAGCGTTGGAT 59.724 47.619 0.00 0.00 44.87 3.41
3387 3685 2.076863 GCTCACAAGTAGCGTTGGATT 58.923 47.619 2.25 0.00 0.00 3.01
3388 3686 2.484264 GCTCACAAGTAGCGTTGGATTT 59.516 45.455 2.25 0.00 0.00 2.17
3389 3687 3.058224 GCTCACAAGTAGCGTTGGATTTT 60.058 43.478 2.25 0.00 0.00 1.82
3390 3688 4.712763 CTCACAAGTAGCGTTGGATTTTC 58.287 43.478 2.25 0.00 0.00 2.29
3391 3689 3.185594 TCACAAGTAGCGTTGGATTTTCG 59.814 43.478 2.25 0.00 0.00 3.46
3392 3690 3.185594 CACAAGTAGCGTTGGATTTTCGA 59.814 43.478 2.25 0.00 0.00 3.71
3393 3691 3.432252 ACAAGTAGCGTTGGATTTTCGAG 59.568 43.478 2.25 0.00 0.00 4.04
3394 3692 3.587797 AGTAGCGTTGGATTTTCGAGA 57.412 42.857 0.00 0.00 0.00 4.04
3395 3693 3.921677 AGTAGCGTTGGATTTTCGAGAA 58.078 40.909 0.00 0.00 0.00 2.87
3396 3694 4.312443 AGTAGCGTTGGATTTTCGAGAAA 58.688 39.130 0.00 0.00 0.00 2.52
3397 3695 4.753107 AGTAGCGTTGGATTTTCGAGAAAA 59.247 37.500 12.61 12.61 43.48 2.29
3398 3696 4.147219 AGCGTTGGATTTTCGAGAAAAG 57.853 40.909 15.03 3.69 42.72 2.27
3399 3697 2.656897 GCGTTGGATTTTCGAGAAAAGC 59.343 45.455 15.65 15.65 42.72 3.51
3400 3698 3.609409 GCGTTGGATTTTCGAGAAAAGCT 60.609 43.478 20.95 5.56 43.77 3.74
3401 3699 4.378046 GCGTTGGATTTTCGAGAAAAGCTA 60.378 41.667 20.95 15.04 43.77 3.32
3402 3700 5.685841 CGTTGGATTTTCGAGAAAAGCTAA 58.314 37.500 20.95 19.04 43.77 3.09
3403 3701 6.314784 CGTTGGATTTTCGAGAAAAGCTAAT 58.685 36.000 21.57 5.22 44.52 1.73
3404 3702 6.466097 CGTTGGATTTTCGAGAAAAGCTAATC 59.534 38.462 21.57 15.80 44.52 1.75
3405 3703 7.530863 GTTGGATTTTCGAGAAAAGCTAATCT 58.469 34.615 21.57 1.02 44.52 2.40
3406 3704 7.308782 TGGATTTTCGAGAAAAGCTAATCTC 57.691 36.000 20.95 15.42 43.77 2.75
3407 3705 6.316390 TGGATTTTCGAGAAAAGCTAATCTCC 59.684 38.462 20.95 17.02 43.77 3.71
3408 3706 6.238511 GGATTTTCGAGAAAAGCTAATCTCCC 60.239 42.308 20.95 11.18 43.77 4.30
3409 3707 4.819105 TTCGAGAAAAGCTAATCTCCCA 57.181 40.909 18.18 6.89 39.09 4.37
3410 3708 5.359194 TTCGAGAAAAGCTAATCTCCCAT 57.641 39.130 18.18 0.00 39.09 4.00
3411 3709 4.697514 TCGAGAAAAGCTAATCTCCCATG 58.302 43.478 18.18 8.30 39.09 3.66
3412 3710 3.249559 CGAGAAAAGCTAATCTCCCATGC 59.750 47.826 18.18 0.00 39.09 4.06
3413 3711 4.202441 GAGAAAAGCTAATCTCCCATGCA 58.798 43.478 14.77 0.00 36.83 3.96
3414 3712 3.950395 AGAAAAGCTAATCTCCCATGCAC 59.050 43.478 0.00 0.00 0.00 4.57
3415 3713 2.355010 AAGCTAATCTCCCATGCACC 57.645 50.000 0.00 0.00 0.00 5.01
3416 3714 0.107456 AGCTAATCTCCCATGCACCG 59.893 55.000 0.00 0.00 0.00 4.94
3417 3715 0.886490 GCTAATCTCCCATGCACCGG 60.886 60.000 0.00 0.00 0.00 5.28
3418 3716 0.758734 CTAATCTCCCATGCACCGGA 59.241 55.000 9.46 4.55 0.00 5.14
3419 3717 0.758734 TAATCTCCCATGCACCGGAG 59.241 55.000 20.37 20.37 46.07 4.63
3433 3731 2.267642 GGAGGTACCGTGCATGCA 59.732 61.111 18.46 18.46 0.00 3.96
3434 3732 1.153168 GGAGGTACCGTGCATGCAT 60.153 57.895 25.64 10.90 0.00 3.96
3435 3733 1.439353 GGAGGTACCGTGCATGCATG 61.439 60.000 29.36 29.36 0.00 4.06
3445 3743 4.118995 CATGCATGCGCCGTTGGT 62.119 61.111 14.93 0.00 37.32 3.67
3446 3744 3.372730 ATGCATGCGCCGTTGGTT 61.373 55.556 14.09 0.00 37.32 3.67
3447 3745 2.929903 ATGCATGCGCCGTTGGTTT 61.930 52.632 14.09 0.00 37.32 3.27
3448 3746 3.105157 GCATGCGCCGTTGGTTTG 61.105 61.111 4.18 0.00 0.00 2.93
3449 3747 3.105157 CATGCGCCGTTGGTTTGC 61.105 61.111 4.18 0.00 0.00 3.68
3450 3748 3.294493 ATGCGCCGTTGGTTTGCT 61.294 55.556 4.18 0.00 0.00 3.91
3451 3749 2.855514 ATGCGCCGTTGGTTTGCTT 61.856 52.632 4.18 0.00 0.00 3.91
3452 3750 3.029735 GCGCCGTTGGTTTGCTTG 61.030 61.111 0.00 0.00 0.00 4.01
3453 3751 2.354539 CGCCGTTGGTTTGCTTGG 60.355 61.111 0.00 0.00 0.00 3.61
3454 3752 2.840066 CGCCGTTGGTTTGCTTGGA 61.840 57.895 0.00 0.00 0.00 3.53
3455 3753 1.007387 GCCGTTGGTTTGCTTGGAG 60.007 57.895 0.00 0.00 0.00 3.86
3456 3754 1.452145 GCCGTTGGTTTGCTTGGAGA 61.452 55.000 0.00 0.00 0.00 3.71
3457 3755 1.247567 CCGTTGGTTTGCTTGGAGAT 58.752 50.000 0.00 0.00 0.00 2.75
3458 3756 1.200020 CCGTTGGTTTGCTTGGAGATC 59.800 52.381 0.00 0.00 0.00 2.75
3459 3757 1.135972 CGTTGGTTTGCTTGGAGATCG 60.136 52.381 0.00 0.00 0.00 3.69
3460 3758 2.151202 GTTGGTTTGCTTGGAGATCGA 58.849 47.619 0.00 0.00 0.00 3.59
3461 3759 2.749621 GTTGGTTTGCTTGGAGATCGAT 59.250 45.455 0.00 0.00 0.00 3.59
3462 3760 2.358957 TGGTTTGCTTGGAGATCGATG 58.641 47.619 0.54 0.00 0.00 3.84
3463 3761 1.064654 GGTTTGCTTGGAGATCGATGC 59.935 52.381 0.54 0.00 0.00 3.91
3464 3762 1.064654 GTTTGCTTGGAGATCGATGCC 59.935 52.381 0.54 4.63 0.00 4.40
3465 3763 0.252761 TTGCTTGGAGATCGATGCCA 59.747 50.000 0.54 7.65 0.00 4.92
3466 3764 0.471191 TGCTTGGAGATCGATGCCAT 59.529 50.000 15.23 0.00 0.00 4.40
3467 3765 0.873054 GCTTGGAGATCGATGCCATG 59.127 55.000 15.23 16.96 0.00 3.66
3468 3766 0.873054 CTTGGAGATCGATGCCATGC 59.127 55.000 15.23 0.37 0.00 4.06
3469 3767 0.180878 TTGGAGATCGATGCCATGCA 59.819 50.000 15.23 0.00 44.86 3.96
3480 3778 1.979855 TGCCATGCATTTATACCGCT 58.020 45.000 0.00 0.00 31.71 5.52
3481 3779 1.608109 TGCCATGCATTTATACCGCTG 59.392 47.619 0.00 0.00 31.71 5.18
3482 3780 1.068333 GCCATGCATTTATACCGCTGG 60.068 52.381 0.00 0.00 0.00 4.85
3483 3781 1.068333 CCATGCATTTATACCGCTGGC 60.068 52.381 0.00 0.00 0.00 4.85
3484 3782 1.608109 CATGCATTTATACCGCTGGCA 59.392 47.619 0.00 0.00 0.00 4.92
3485 3783 1.308047 TGCATTTATACCGCTGGCAG 58.692 50.000 10.94 10.94 0.00 4.85
3486 3784 1.308998 GCATTTATACCGCTGGCAGT 58.691 50.000 17.16 0.00 0.00 4.40
3487 3785 1.676006 GCATTTATACCGCTGGCAGTT 59.324 47.619 17.16 3.51 0.00 3.16
3488 3786 2.875933 GCATTTATACCGCTGGCAGTTA 59.124 45.455 17.16 5.76 0.00 2.24
3489 3787 3.058914 GCATTTATACCGCTGGCAGTTAG 60.059 47.826 17.16 7.65 0.00 2.34
3490 3788 3.899052 TTTATACCGCTGGCAGTTAGT 57.101 42.857 17.16 13.13 0.00 2.24
3491 3789 3.899052 TTATACCGCTGGCAGTTAGTT 57.101 42.857 17.16 1.65 0.00 2.24
3492 3790 5.341872 TTTATACCGCTGGCAGTTAGTTA 57.658 39.130 17.16 1.65 0.00 2.24
3493 3791 2.953466 TACCGCTGGCAGTTAGTTAG 57.047 50.000 17.16 0.10 0.00 2.34
3494 3792 0.974383 ACCGCTGGCAGTTAGTTAGT 59.026 50.000 17.16 0.72 0.00 2.24
3495 3793 1.346722 ACCGCTGGCAGTTAGTTAGTT 59.653 47.619 17.16 0.00 0.00 2.24
3496 3794 2.564062 ACCGCTGGCAGTTAGTTAGTTA 59.436 45.455 17.16 0.00 0.00 2.24
3497 3795 3.197116 ACCGCTGGCAGTTAGTTAGTTAT 59.803 43.478 17.16 0.00 0.00 1.89
3498 3796 4.189231 CCGCTGGCAGTTAGTTAGTTATT 58.811 43.478 17.16 0.00 0.00 1.40
3499 3797 4.634443 CCGCTGGCAGTTAGTTAGTTATTT 59.366 41.667 17.16 0.00 0.00 1.40
3500 3798 5.220605 CCGCTGGCAGTTAGTTAGTTATTTC 60.221 44.000 17.16 0.00 0.00 2.17
3501 3799 5.581085 CGCTGGCAGTTAGTTAGTTATTTCT 59.419 40.000 17.16 0.00 0.00 2.52
3502 3800 6.237861 CGCTGGCAGTTAGTTAGTTATTTCTC 60.238 42.308 17.16 0.00 0.00 2.87
3503 3801 6.819146 GCTGGCAGTTAGTTAGTTATTTCTCT 59.181 38.462 17.16 0.00 0.00 3.10
3504 3802 7.010645 GCTGGCAGTTAGTTAGTTATTTCTCTC 59.989 40.741 17.16 0.00 0.00 3.20
3505 3803 7.903145 TGGCAGTTAGTTAGTTATTTCTCTCA 58.097 34.615 0.00 0.00 0.00 3.27
3506 3804 8.540388 TGGCAGTTAGTTAGTTATTTCTCTCAT 58.460 33.333 0.00 0.00 0.00 2.90
3507 3805 9.036671 GGCAGTTAGTTAGTTATTTCTCTCATC 57.963 37.037 0.00 0.00 0.00 2.92
3508 3806 9.587772 GCAGTTAGTTAGTTATTTCTCTCATCA 57.412 33.333 0.00 0.00 0.00 3.07
3513 3811 8.430801 AGTTAGTTATTTCTCTCATCACATGC 57.569 34.615 0.00 0.00 0.00 4.06
3514 3812 8.043113 AGTTAGTTATTTCTCTCATCACATGCA 58.957 33.333 0.00 0.00 0.00 3.96
3515 3813 8.668353 GTTAGTTATTTCTCTCATCACATGCAA 58.332 33.333 0.00 0.00 0.00 4.08
3516 3814 7.317842 AGTTATTTCTCTCATCACATGCAAG 57.682 36.000 0.00 0.00 0.00 4.01
3517 3815 6.883217 AGTTATTTCTCTCATCACATGCAAGT 59.117 34.615 0.00 0.00 0.00 3.16
3518 3816 8.043113 AGTTATTTCTCTCATCACATGCAAGTA 58.957 33.333 0.00 0.00 0.00 2.24
3519 3817 6.674694 ATTTCTCTCATCACATGCAAGTAC 57.325 37.500 0.00 0.00 0.00 2.73
3520 3818 4.806640 TCTCTCATCACATGCAAGTACA 57.193 40.909 0.00 0.00 0.00 2.90
3521 3819 4.498241 TCTCTCATCACATGCAAGTACAC 58.502 43.478 0.00 0.00 0.00 2.90
3522 3820 4.221482 TCTCTCATCACATGCAAGTACACT 59.779 41.667 0.00 0.00 0.00 3.55
3523 3821 4.248058 TCTCATCACATGCAAGTACACTG 58.752 43.478 0.00 0.00 0.00 3.66
3524 3822 3.999001 CTCATCACATGCAAGTACACTGT 59.001 43.478 0.00 0.00 0.00 3.55
3525 3823 4.388485 TCATCACATGCAAGTACACTGTT 58.612 39.130 0.00 0.00 0.00 3.16
3526 3824 4.821260 TCATCACATGCAAGTACACTGTTT 59.179 37.500 0.00 0.00 0.00 2.83
3527 3825 4.811555 TCACATGCAAGTACACTGTTTC 57.188 40.909 0.00 0.00 0.00 2.78
3528 3826 4.195416 TCACATGCAAGTACACTGTTTCA 58.805 39.130 0.00 0.00 0.00 2.69
3529 3827 4.035091 TCACATGCAAGTACACTGTTTCAC 59.965 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.601130 GGTATTTGTATGGGAGGAAAAACAAAC 59.399 37.037 0.00 0.00 39.01 2.93
108 114 2.056577 CGTCGGTTGAGAGTACCAAAC 58.943 52.381 0.00 0.00 35.31 2.93
127 133 5.858475 TGTTGGTTTTAATTTTGTGCAACG 58.142 33.333 0.00 0.00 42.39 4.10
208 218 8.176814 AGATTTGATTTGATTGTGTTAATGCG 57.823 30.769 0.00 0.00 0.00 4.73
251 261 5.304357 TGGGAAGAAAAGGAAAGTTTGGATC 59.696 40.000 0.00 0.00 0.00 3.36
273 283 6.876155 TGATTTGATTTGGGTGATTGTATGG 58.124 36.000 0.00 0.00 0.00 2.74
281 291 7.234371 TGGTAAGATTTGATTTGATTTGGGTGA 59.766 33.333 0.00 0.00 0.00 4.02
318 328 7.445096 AGGGAATGCAAGGAAAGTTTTAATTTG 59.555 33.333 0.00 0.00 0.00 2.32
379 389 9.830186 ACCCTGTATCTAACACATATTCTAGAT 57.170 33.333 0.00 0.00 35.70 1.98
409 419 3.367498 GCGATAACTAGATGTGCCCTAGG 60.367 52.174 0.06 0.06 38.28 3.02
428 438 5.961272 TGATTAAGTCACTTAGATGTGCGA 58.039 37.500 0.00 0.00 37.81 5.10
429 439 6.647212 TTGATTAAGTCACTTAGATGTGCG 57.353 37.500 0.00 0.00 36.32 5.34
451 461 9.875691 GGATATTTTGTCTTCCTTTTATGCTTT 57.124 29.630 0.00 0.00 0.00 3.51
466 476 5.276868 CGGAGATTCGTGTGGATATTTTGTC 60.277 44.000 0.00 0.00 0.00 3.18
468 478 4.552767 GCGGAGATTCGTGTGGATATTTTG 60.553 45.833 0.00 0.00 0.00 2.44
492 502 2.629051 GGGCGCCATACATAATCCTAC 58.371 52.381 30.85 0.45 0.00 3.18
495 505 0.321298 ACGGGCGCCATACATAATCC 60.321 55.000 30.85 5.23 0.00 3.01
506 516 3.587933 TGTGTTTCAACGGGCGCC 61.588 61.111 21.18 21.18 0.00 6.53
525 535 2.973406 ACTGCTACTAGCTAATTCCCCC 59.027 50.000 9.49 0.00 42.97 5.40
555 565 2.358322 TTGCGGGGAGTTTCTTTTCT 57.642 45.000 0.00 0.00 0.00 2.52
604 614 5.409826 GGTATCTACTCCTACATGCATTTGC 59.590 44.000 0.00 0.00 42.50 3.68
636 660 2.315925 TGCATTCCCGCAAAACAAAA 57.684 40.000 0.00 0.00 39.45 2.44
734 761 1.908299 GGTTTGGGTTCCTGGCAGG 60.908 63.158 28.01 28.01 36.46 4.85
767 795 8.333908 CGGTTGTTTGATTTGATTTGATTTGAA 58.666 29.630 0.00 0.00 0.00 2.69
768 796 7.708322 TCGGTTGTTTGATTTGATTTGATTTGA 59.292 29.630 0.00 0.00 0.00 2.69
769 797 7.793427 GTCGGTTGTTTGATTTGATTTGATTTG 59.207 33.333 0.00 0.00 0.00 2.32
770 798 7.493971 TGTCGGTTGTTTGATTTGATTTGATTT 59.506 29.630 0.00 0.00 0.00 2.17
771 799 6.983307 TGTCGGTTGTTTGATTTGATTTGATT 59.017 30.769 0.00 0.00 0.00 2.57
772 800 6.511416 TGTCGGTTGTTTGATTTGATTTGAT 58.489 32.000 0.00 0.00 0.00 2.57
773 801 5.895928 TGTCGGTTGTTTGATTTGATTTGA 58.104 33.333 0.00 0.00 0.00 2.69
774 802 6.768029 ATGTCGGTTGTTTGATTTGATTTG 57.232 33.333 0.00 0.00 0.00 2.32
835 863 5.936956 CAGAAGGGTAATCTTATCTGATGGC 59.063 44.000 0.00 0.00 0.00 4.40
836 864 6.270927 TCCAGAAGGGTAATCTTATCTGATGG 59.729 42.308 0.00 0.00 38.11 3.51
889 918 2.728817 GCGGAGGAGATGTACGGG 59.271 66.667 0.00 0.00 0.00 5.28
890 919 0.536687 TAGGCGGAGGAGATGTACGG 60.537 60.000 0.00 0.00 0.00 4.02
916 965 1.677052 GAGGGTGGAGATGTACGAGAC 59.323 57.143 0.00 0.00 0.00 3.36
935 984 1.592400 GATGTCGTGGACTCGTGGGA 61.592 60.000 0.00 0.00 33.15 4.37
936 985 1.153823 GATGTCGTGGACTCGTGGG 60.154 63.158 0.00 0.00 33.15 4.61
1332 1397 1.705337 CGCGGGTGATGATGTTGTCC 61.705 60.000 0.00 0.00 0.00 4.02
1980 2100 3.604629 TCGTAGAGCCTGTCCTGC 58.395 61.111 0.00 0.00 0.00 4.85
2570 2705 3.542712 ATCACACACGCAAAACATCTC 57.457 42.857 0.00 0.00 0.00 2.75
2636 2775 7.038659 GCTAGCTCTAAACATTTCTCTCTGAA 58.961 38.462 7.70 0.00 0.00 3.02
2680 2830 7.620880 ACCTAGACACTGCATTATAAACTGAA 58.379 34.615 0.00 0.00 0.00 3.02
2749 2899 2.092592 CCCATGGGTAACTTAGGTCACC 60.093 54.545 23.93 0.00 0.00 4.02
2795 2945 9.926158 TGTGTTGATGAATGCTTTTGTTATTAT 57.074 25.926 0.00 0.00 0.00 1.28
2805 2955 7.555195 TCATAGATCTTGTGTTGATGAATGCTT 59.445 33.333 0.00 0.00 0.00 3.91
2807 2957 7.255491 TCATAGATCTTGTGTTGATGAATGC 57.745 36.000 0.00 0.00 0.00 3.56
2823 2973 9.972106 ATGGGATCTTTTCCTAATTCATAGATC 57.028 33.333 0.00 0.00 44.75 2.75
2826 2976 9.804977 AGAATGGGATCTTTTCCTAATTCATAG 57.195 33.333 16.08 0.00 43.16 2.23
2827 2977 9.578576 CAGAATGGGATCTTTTCCTAATTCATA 57.421 33.333 16.08 0.00 43.16 2.15
2828 2978 8.284435 TCAGAATGGGATCTTTTCCTAATTCAT 58.716 33.333 16.08 1.23 43.16 2.57
2829 2979 7.642186 TCAGAATGGGATCTTTTCCTAATTCA 58.358 34.615 16.08 0.00 43.16 2.57
2830 2980 8.703378 ATCAGAATGGGATCTTTTCCTAATTC 57.297 34.615 0.00 10.22 44.75 2.17
2831 2981 8.703378 GATCAGAATGGGATCTTTTCCTAATT 57.297 34.615 0.00 0.00 44.75 1.40
2918 3077 6.726258 TTGTGTTAGTAAGTCATGATGCAG 57.274 37.500 0.00 0.00 0.00 4.41
2920 3079 8.970691 AAAATTGTGTTAGTAAGTCATGATGC 57.029 30.769 0.00 0.00 0.00 3.91
2923 3082 9.114952 TGTGAAAATTGTGTTAGTAAGTCATGA 57.885 29.630 0.00 0.00 0.00 3.07
2924 3083 9.385902 CTGTGAAAATTGTGTTAGTAAGTCATG 57.614 33.333 0.00 0.00 0.00 3.07
2925 3084 9.120538 ACTGTGAAAATTGTGTTAGTAAGTCAT 57.879 29.630 0.00 0.00 0.00 3.06
2926 3085 8.500753 ACTGTGAAAATTGTGTTAGTAAGTCA 57.499 30.769 0.00 0.00 0.00 3.41
2928 3087 9.052759 CCTACTGTGAAAATTGTGTTAGTAAGT 57.947 33.333 0.00 0.00 0.00 2.24
2929 3088 8.015658 GCCTACTGTGAAAATTGTGTTAGTAAG 58.984 37.037 0.00 0.00 0.00 2.34
2930 3089 7.499563 TGCCTACTGTGAAAATTGTGTTAGTAA 59.500 33.333 0.00 0.00 0.00 2.24
2931 3090 6.993308 TGCCTACTGTGAAAATTGTGTTAGTA 59.007 34.615 0.00 0.00 0.00 1.82
2932 3091 5.825679 TGCCTACTGTGAAAATTGTGTTAGT 59.174 36.000 0.00 0.00 0.00 2.24
2933 3092 6.204688 TCTGCCTACTGTGAAAATTGTGTTAG 59.795 38.462 0.00 0.00 0.00 2.34
2995 3271 9.546428 GAAAATTTTCTTTTTGATGAAGGAGGA 57.454 29.630 21.21 0.00 34.41 3.71
3056 3332 4.996122 GCAGAACTCATGCTAGAATATGCT 59.004 41.667 0.00 0.00 40.59 3.79
3067 3352 6.624352 TCCAATATAAAGCAGAACTCATGC 57.376 37.500 0.00 0.00 44.18 4.06
3073 3361 7.391554 TCTGCCATATCCAATATAAAGCAGAAC 59.608 37.037 17.38 0.00 42.58 3.01
3111 3399 6.714810 TGTGTTGATGTAGAGCATACCTTTTT 59.285 34.615 0.00 0.00 38.06 1.94
3163 3451 2.941064 CCTCTCACTGGCATACATGTTG 59.059 50.000 2.30 3.61 0.00 3.33
3220 3508 3.128242 GCTGATGATGGGAAACTTGTGAG 59.872 47.826 0.00 0.00 0.00 3.51
3221 3509 3.084039 GCTGATGATGGGAAACTTGTGA 58.916 45.455 0.00 0.00 0.00 3.58
3222 3510 2.821378 TGCTGATGATGGGAAACTTGTG 59.179 45.455 0.00 0.00 0.00 3.33
3223 3511 3.159213 TGCTGATGATGGGAAACTTGT 57.841 42.857 0.00 0.00 0.00 3.16
3224 3512 3.737047 GCATGCTGATGATGGGAAACTTG 60.737 47.826 11.37 0.00 0.00 3.16
3286 3582 1.511850 TGTTCTGACATGTTCCGCTG 58.488 50.000 0.00 0.00 0.00 5.18
3291 3587 6.034898 CCAAAGTGTTTTGTTCTGACATGTTC 59.965 38.462 0.00 0.00 41.68 3.18
3331 3629 6.260493 AGAGAGATGATGCTTATGTTCTTTGC 59.740 38.462 0.00 0.00 0.00 3.68
3348 3646 1.265095 GCTGCGAGAGAGAGAGAGATG 59.735 57.143 0.00 0.00 0.00 2.90
3355 3653 0.525311 TTGTGAGCTGCGAGAGAGAG 59.475 55.000 0.00 0.00 0.00 3.20
3356 3654 0.525311 CTTGTGAGCTGCGAGAGAGA 59.475 55.000 0.00 0.00 0.00 3.10
3357 3655 0.243365 ACTTGTGAGCTGCGAGAGAG 59.757 55.000 0.00 0.00 0.00 3.20
3358 3656 1.470494 CTACTTGTGAGCTGCGAGAGA 59.530 52.381 0.00 0.00 0.00 3.10
3359 3657 1.906757 CTACTTGTGAGCTGCGAGAG 58.093 55.000 0.00 0.00 0.00 3.20
3360 3658 0.109086 GCTACTTGTGAGCTGCGAGA 60.109 55.000 0.00 0.00 36.96 4.04
3361 3659 1.409227 CGCTACTTGTGAGCTGCGAG 61.409 60.000 4.96 3.14 44.87 5.03
3362 3660 1.444383 CGCTACTTGTGAGCTGCGA 60.444 57.895 4.96 0.00 44.87 5.10
3363 3661 1.284982 AACGCTACTTGTGAGCTGCG 61.285 55.000 8.99 8.99 46.31 5.18
3364 3662 0.164647 CAACGCTACTTGTGAGCTGC 59.835 55.000 0.00 0.00 37.81 5.25
3365 3663 0.792640 CCAACGCTACTTGTGAGCTG 59.207 55.000 0.00 0.00 37.81 4.24
3366 3664 0.679505 TCCAACGCTACTTGTGAGCT 59.320 50.000 0.00 0.00 37.81 4.09
3367 3665 1.726853 ATCCAACGCTACTTGTGAGC 58.273 50.000 0.00 0.00 36.54 4.26
3368 3666 4.666655 CGAAAATCCAACGCTACTTGTGAG 60.667 45.833 0.00 0.00 0.00 3.51
3369 3667 3.185594 CGAAAATCCAACGCTACTTGTGA 59.814 43.478 0.00 0.00 0.00 3.58
3370 3668 3.185594 TCGAAAATCCAACGCTACTTGTG 59.814 43.478 0.00 0.00 0.00 3.33
3371 3669 3.395639 TCGAAAATCCAACGCTACTTGT 58.604 40.909 0.00 0.00 0.00 3.16
3372 3670 3.678072 TCTCGAAAATCCAACGCTACTTG 59.322 43.478 0.00 0.00 0.00 3.16
3373 3671 3.921677 TCTCGAAAATCCAACGCTACTT 58.078 40.909 0.00 0.00 0.00 2.24
3374 3672 3.587797 TCTCGAAAATCCAACGCTACT 57.412 42.857 0.00 0.00 0.00 2.57
3375 3673 4.657075 TTTCTCGAAAATCCAACGCTAC 57.343 40.909 0.00 0.00 0.00 3.58
3376 3674 4.378046 GCTTTTCTCGAAAATCCAACGCTA 60.378 41.667 5.39 0.00 39.29 4.26
3377 3675 3.609409 GCTTTTCTCGAAAATCCAACGCT 60.609 43.478 5.39 0.00 39.29 5.07
3378 3676 2.656897 GCTTTTCTCGAAAATCCAACGC 59.343 45.455 5.39 1.73 39.29 4.84
3379 3677 4.147219 AGCTTTTCTCGAAAATCCAACG 57.853 40.909 5.39 0.00 39.29 4.10
3380 3678 7.530863 AGATTAGCTTTTCTCGAAAATCCAAC 58.469 34.615 5.39 0.00 39.29 3.77
3381 3679 7.148239 GGAGATTAGCTTTTCTCGAAAATCCAA 60.148 37.037 15.49 0.00 39.42 3.53
3382 3680 6.316390 GGAGATTAGCTTTTCTCGAAAATCCA 59.684 38.462 15.49 0.00 39.42 3.41
3383 3681 6.238511 GGGAGATTAGCTTTTCTCGAAAATCC 60.239 42.308 15.49 7.44 39.42 3.01
3384 3682 6.316390 TGGGAGATTAGCTTTTCTCGAAAATC 59.684 38.462 15.49 5.93 39.42 2.17
3385 3683 6.180472 TGGGAGATTAGCTTTTCTCGAAAAT 58.820 36.000 15.49 0.00 39.42 1.82
3386 3684 5.556915 TGGGAGATTAGCTTTTCTCGAAAA 58.443 37.500 15.49 4.90 39.42 2.29
3387 3685 5.160607 TGGGAGATTAGCTTTTCTCGAAA 57.839 39.130 15.49 5.14 39.42 3.46
3388 3686 4.819105 TGGGAGATTAGCTTTTCTCGAA 57.181 40.909 15.49 6.97 39.42 3.71
3389 3687 4.697514 CATGGGAGATTAGCTTTTCTCGA 58.302 43.478 15.49 8.21 39.42 4.04
3390 3688 3.249559 GCATGGGAGATTAGCTTTTCTCG 59.750 47.826 15.49 6.66 39.42 4.04
3391 3689 4.036144 GTGCATGGGAGATTAGCTTTTCTC 59.964 45.833 14.26 14.26 38.10 2.87
3392 3690 3.950395 GTGCATGGGAGATTAGCTTTTCT 59.050 43.478 0.00 0.00 0.00 2.52
3393 3691 3.067320 GGTGCATGGGAGATTAGCTTTTC 59.933 47.826 0.00 0.00 0.00 2.29
3394 3692 3.026694 GGTGCATGGGAGATTAGCTTTT 58.973 45.455 0.00 0.00 0.00 2.27
3395 3693 2.659428 GGTGCATGGGAGATTAGCTTT 58.341 47.619 0.00 0.00 0.00 3.51
3396 3694 1.475751 CGGTGCATGGGAGATTAGCTT 60.476 52.381 0.00 0.00 0.00 3.74
3397 3695 0.107456 CGGTGCATGGGAGATTAGCT 59.893 55.000 0.00 0.00 0.00 3.32
3398 3696 0.886490 CCGGTGCATGGGAGATTAGC 60.886 60.000 0.00 0.00 0.00 3.09
3399 3697 0.758734 TCCGGTGCATGGGAGATTAG 59.241 55.000 0.00 0.00 0.00 1.73
3400 3698 2.923619 TCCGGTGCATGGGAGATTA 58.076 52.632 0.00 0.00 0.00 1.75
3401 3699 3.739922 TCCGGTGCATGGGAGATT 58.260 55.556 0.00 0.00 0.00 2.40
3405 3703 2.039787 TACCTCCGGTGCATGGGA 59.960 61.111 0.00 8.25 36.19 4.37
3406 3704 2.189521 GTACCTCCGGTGCATGGG 59.810 66.667 0.00 4.03 38.20 4.00
3407 3705 2.189521 GGTACCTCCGGTGCATGG 59.810 66.667 4.06 1.64 40.07 3.66
3416 3714 1.153168 ATGCATGCACGGTACCTCC 60.153 57.895 25.37 0.00 0.00 4.30
3417 3715 2.016961 CATGCATGCACGGTACCTC 58.983 57.895 25.37 0.00 0.00 3.85
3418 3716 4.223800 CATGCATGCACGGTACCT 57.776 55.556 25.37 1.29 0.00 3.08
3428 3726 3.629883 AACCAACGGCGCATGCATG 62.630 57.895 22.70 22.70 45.35 4.06
3429 3727 2.929903 AAACCAACGGCGCATGCAT 61.930 52.632 19.57 0.00 45.35 3.96
3430 3728 3.600694 AAACCAACGGCGCATGCA 61.601 55.556 19.57 0.00 45.35 3.96
3431 3729 3.105157 CAAACCAACGGCGCATGC 61.105 61.111 10.83 7.91 41.71 4.06
3432 3730 3.105157 GCAAACCAACGGCGCATG 61.105 61.111 10.83 6.55 0.00 4.06
3433 3731 2.855514 AAGCAAACCAACGGCGCAT 61.856 52.632 10.83 0.00 0.00 4.73
3434 3732 3.522731 AAGCAAACCAACGGCGCA 61.523 55.556 10.83 0.00 0.00 6.09
3435 3733 3.029735 CAAGCAAACCAACGGCGC 61.030 61.111 6.90 0.00 0.00 6.53
3436 3734 2.354539 CCAAGCAAACCAACGGCG 60.355 61.111 4.80 4.80 0.00 6.46
3437 3735 1.007387 CTCCAAGCAAACCAACGGC 60.007 57.895 0.00 0.00 0.00 5.68
3438 3736 1.200020 GATCTCCAAGCAAACCAACGG 59.800 52.381 0.00 0.00 0.00 4.44
3439 3737 1.135972 CGATCTCCAAGCAAACCAACG 60.136 52.381 0.00 0.00 0.00 4.10
3440 3738 2.151202 TCGATCTCCAAGCAAACCAAC 58.849 47.619 0.00 0.00 0.00 3.77
3441 3739 2.559698 TCGATCTCCAAGCAAACCAA 57.440 45.000 0.00 0.00 0.00 3.67
3442 3740 2.358957 CATCGATCTCCAAGCAAACCA 58.641 47.619 0.00 0.00 0.00 3.67
3443 3741 1.064654 GCATCGATCTCCAAGCAAACC 59.935 52.381 0.00 0.00 0.00 3.27
3444 3742 1.064654 GGCATCGATCTCCAAGCAAAC 59.935 52.381 0.00 0.00 0.00 2.93
3445 3743 1.339920 TGGCATCGATCTCCAAGCAAA 60.340 47.619 12.23 0.00 0.00 3.68
3446 3744 0.252761 TGGCATCGATCTCCAAGCAA 59.747 50.000 12.23 0.00 0.00 3.91
3447 3745 0.471191 ATGGCATCGATCTCCAAGCA 59.529 50.000 17.06 0.47 33.04 3.91
3448 3746 0.873054 CATGGCATCGATCTCCAAGC 59.127 55.000 17.06 7.21 33.04 4.01
3449 3747 0.873054 GCATGGCATCGATCTCCAAG 59.127 55.000 17.06 14.36 33.04 3.61
3450 3748 0.180878 TGCATGGCATCGATCTCCAA 59.819 50.000 17.06 2.05 31.71 3.53
3451 3749 1.831527 TGCATGGCATCGATCTCCA 59.168 52.632 15.86 15.86 31.71 3.86
3452 3750 4.785767 TGCATGGCATCGATCTCC 57.214 55.556 0.00 0.00 31.71 3.71
3461 3759 1.608109 CAGCGGTATAAATGCATGGCA 59.392 47.619 0.00 0.00 44.86 4.92
3462 3760 1.068333 CCAGCGGTATAAATGCATGGC 60.068 52.381 0.00 0.00 0.00 4.40
3463 3761 1.068333 GCCAGCGGTATAAATGCATGG 60.068 52.381 0.00 0.00 33.15 3.66
3464 3762 1.608109 TGCCAGCGGTATAAATGCATG 59.392 47.619 0.00 0.00 0.00 4.06
3465 3763 1.881973 CTGCCAGCGGTATAAATGCAT 59.118 47.619 0.00 0.00 0.00 3.96
3466 3764 1.308047 CTGCCAGCGGTATAAATGCA 58.692 50.000 0.00 0.00 0.00 3.96
3467 3765 1.308998 ACTGCCAGCGGTATAAATGC 58.691 50.000 1.31 0.00 33.13 3.56
3468 3766 4.127171 ACTAACTGCCAGCGGTATAAATG 58.873 43.478 4.19 0.00 34.70 2.32
3469 3767 4.417426 ACTAACTGCCAGCGGTATAAAT 57.583 40.909 4.19 0.00 34.70 1.40
3470 3768 3.899052 ACTAACTGCCAGCGGTATAAA 57.101 42.857 4.19 0.00 34.70 1.40
3471 3769 3.899052 AACTAACTGCCAGCGGTATAA 57.101 42.857 4.19 0.00 34.70 0.98
3472 3770 3.956199 ACTAACTAACTGCCAGCGGTATA 59.044 43.478 4.19 0.00 34.70 1.47
3473 3771 2.764572 ACTAACTAACTGCCAGCGGTAT 59.235 45.455 4.19 0.00 34.70 2.73
3474 3772 2.173519 ACTAACTAACTGCCAGCGGTA 58.826 47.619 4.19 0.00 34.70 4.02
3475 3773 0.974383 ACTAACTAACTGCCAGCGGT 59.026 50.000 0.00 0.00 37.08 5.68
3476 3774 2.094762 AACTAACTAACTGCCAGCGG 57.905 50.000 0.00 0.00 0.00 5.52
3477 3775 5.581085 AGAAATAACTAACTAACTGCCAGCG 59.419 40.000 0.00 0.00 0.00 5.18
3478 3776 6.819146 AGAGAAATAACTAACTAACTGCCAGC 59.181 38.462 0.00 0.00 0.00 4.85
3479 3777 8.035394 TGAGAGAAATAACTAACTAACTGCCAG 58.965 37.037 0.00 0.00 0.00 4.85
3480 3778 7.903145 TGAGAGAAATAACTAACTAACTGCCA 58.097 34.615 0.00 0.00 0.00 4.92
3481 3779 8.950208 ATGAGAGAAATAACTAACTAACTGCC 57.050 34.615 0.00 0.00 0.00 4.85
3482 3780 9.587772 TGATGAGAGAAATAACTAACTAACTGC 57.412 33.333 0.00 0.00 0.00 4.40
3487 3785 9.534565 GCATGTGATGAGAGAAATAACTAACTA 57.465 33.333 0.00 0.00 0.00 2.24
3488 3786 8.043113 TGCATGTGATGAGAGAAATAACTAACT 58.957 33.333 0.00 0.00 0.00 2.24
3489 3787 8.201554 TGCATGTGATGAGAGAAATAACTAAC 57.798 34.615 0.00 0.00 0.00 2.34
3490 3788 8.791327 TTGCATGTGATGAGAGAAATAACTAA 57.209 30.769 0.00 0.00 0.00 2.24
3491 3789 8.043113 ACTTGCATGTGATGAGAGAAATAACTA 58.957 33.333 4.14 0.00 0.00 2.24
3492 3790 6.883217 ACTTGCATGTGATGAGAGAAATAACT 59.117 34.615 4.14 0.00 0.00 2.24
3493 3791 7.081526 ACTTGCATGTGATGAGAGAAATAAC 57.918 36.000 4.14 0.00 0.00 1.89
3494 3792 7.823799 TGTACTTGCATGTGATGAGAGAAATAA 59.176 33.333 15.08 0.00 0.00 1.40
3495 3793 7.278646 GTGTACTTGCATGTGATGAGAGAAATA 59.721 37.037 15.08 0.00 0.00 1.40
3496 3794 6.093219 GTGTACTTGCATGTGATGAGAGAAAT 59.907 38.462 15.08 0.00 0.00 2.17
3497 3795 5.409520 GTGTACTTGCATGTGATGAGAGAAA 59.590 40.000 15.08 0.00 0.00 2.52
3498 3796 4.931601 GTGTACTTGCATGTGATGAGAGAA 59.068 41.667 15.08 0.00 0.00 2.87
3499 3797 4.221482 AGTGTACTTGCATGTGATGAGAGA 59.779 41.667 15.08 0.00 0.00 3.10
3500 3798 4.329256 CAGTGTACTTGCATGTGATGAGAG 59.671 45.833 15.08 0.00 0.00 3.20
3501 3799 4.248058 CAGTGTACTTGCATGTGATGAGA 58.752 43.478 15.08 0.00 0.00 3.27
3502 3800 3.999001 ACAGTGTACTTGCATGTGATGAG 59.001 43.478 15.08 5.39 0.00 2.90
3503 3801 4.006780 ACAGTGTACTTGCATGTGATGA 57.993 40.909 15.08 0.00 0.00 2.92
3504 3802 4.754372 AACAGTGTACTTGCATGTGATG 57.246 40.909 15.08 10.11 0.00 3.07
3505 3803 4.821260 TGAAACAGTGTACTTGCATGTGAT 59.179 37.500 15.08 0.00 0.00 3.06
3506 3804 4.035091 GTGAAACAGTGTACTTGCATGTGA 59.965 41.667 15.08 0.00 36.32 3.58
3507 3805 4.282068 GTGAAACAGTGTACTTGCATGTG 58.718 43.478 15.08 0.95 36.32 3.21
3508 3806 4.552166 GTGAAACAGTGTACTTGCATGT 57.448 40.909 10.40 10.40 36.32 3.21


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

AutoCloner maintained by Alex Coulton.