Multiple sequence alignment - TraesCS7D01G336000

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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 TraesCS7D01G336000 chr7D 100.000 3993 0 0 1 3993 427908090 427904098 0.000000e+00 7374.0
1 TraesCS7D01G336000 chr7B 90.840 2500 106 42 1 2439 445659791 445657354 0.000000e+00 3234.0
2 TraesCS7D01G336000 chr7B 91.781 876 53 10 2718 3581 445656906 445656038 0.000000e+00 1201.0
3 TraesCS7D01G336000 chr7B 89.655 348 26 6 3581 3927 445656157 445655819 6.130000e-118 435.0
4 TraesCS7D01G336000 chr7B 93.939 66 2 2 3929 3992 191731104 191731039 9.130000e-17 99.0
5 TraesCS7D01G336000 chr7B 87.500 48 4 2 3382 3429 436642133 436642178 2.000000e-03 54.7
6 TraesCS7D01G336000 chr7A 82.917 1042 95 43 375 1358 504732184 504733200 0.000000e+00 861.0
7 TraesCS7D01G336000 chr7A 91.906 593 28 9 2722 3298 504734344 504734932 0.000000e+00 811.0
8 TraesCS7D01G336000 chr7A 88.869 557 44 8 3311 3861 504735113 504735657 0.000000e+00 669.0
9 TraesCS7D01G336000 chr7A 82.125 593 43 18 1883 2435 504733585 504734154 2.190000e-122 449.0
10 TraesCS7D01G336000 chr7A 86.667 165 20 1 1568 1732 504733399 504733561 8.820000e-42 182.0
11 TraesCS7D01G336000 chr7A 89.147 129 8 2 3578 3706 504735264 504735386 5.340000e-34 156.0
12 TraesCS7D01G336000 chr7A 87.059 85 9 2 3845 3928 504735727 504735810 1.180000e-15 95.3
13 TraesCS7D01G336000 chr7A 83.117 77 13 0 1413 1489 504733280 504733356 1.990000e-08 71.3
14 TraesCS7D01G336000 chr7A 100.000 29 0 0 3400 3428 589769047 589769019 2.000000e-03 54.7
15 TraesCS7D01G336000 chr6B 95.385 65 2 1 3929 3992 703017500 703017436 7.060000e-18 102.0
16 TraesCS7D01G336000 chr2A 94.030 67 2 1 3929 3993 137133578 137133644 2.540000e-17 100.0
17 TraesCS7D01G336000 chrUn 92.754 69 3 2 3926 3992 336471278 336471346 9.130000e-17 99.0
18 TraesCS7D01G336000 chrUn 100.000 28 0 0 3401 3428 318936234 318936207 7.000000e-03 52.8
19 TraesCS7D01G336000 chr5D 94.030 67 1 3 3929 3993 472219816 472219751 9.130000e-17 99.0
20 TraesCS7D01G336000 chr5D 100.000 28 0 0 3401 3428 100855852 100855825 7.000000e-03 52.8
21 TraesCS7D01G336000 chr4D 93.750 64 4 0 3929 3992 507897435 507897498 3.280000e-16 97.1
22 TraesCS7D01G336000 chr4D 87.952 83 6 4 3913 3993 480297640 480297560 1.180000e-15 95.3
23 TraesCS7D01G336000 chr5B 91.549 71 3 3 3924 3992 387903093 387903024 1.180000e-15 95.3
24 TraesCS7D01G336000 chr4B 89.189 74 7 1 3919 3992 664067666 664067594 1.530000e-14 91.6
25 TraesCS7D01G336000 chr4B 94.286 35 2 0 3401 3435 623034161 623034127 2.000000e-03 54.7
26 TraesCS7D01G336000 chr3D 81.818 110 18 2 2728 2836 330053440 330053548 1.530000e-14 91.6
27 TraesCS7D01G336000 chr3B 81.818 110 18 2 2728 2836 427585057 427585165 1.530000e-14 91.6
28 TraesCS7D01G336000 chr3A 81.818 110 18 2 2728 2836 445268559 445268667 1.530000e-14 91.6
29 TraesCS7D01G336000 chr2D 94.286 35 2 0 3401 3435 376818601 376818635 2.000000e-03 54.7
30 TraesCS7D01G336000 chr6D 100.000 28 0 0 3401 3428 190277626 190277653 7.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G336000 chr7D 427904098 427908090 3992 True 7374.000000 7374 100.000000 1 3993 1 chr7D.!!$R1 3992
1 TraesCS7D01G336000 chr7B 445655819 445659791 3972 True 1623.333333 3234 90.758667 1 3927 3 chr7B.!!$R2 3926
2 TraesCS7D01G336000 chr7A 504732184 504735810 3626 False 411.825000 861 86.475875 375 3928 8 chr7A.!!$F1 3553

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
305 324 0.035820 AACGTGGTGGCATATTCGGT 60.036 50.0 0.0 0.0 0.0 4.69 F
1353 1450 0.671251 TGTGTTTTCCGGCATTGACC 59.329 50.0 0.0 0.0 0.0 4.02 F
2271 2447 0.401738 CCCTTGGTCTGCTTCCTTGA 59.598 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2388 0.310854 GGGAAGTGCAAACCAACTCG 59.689 55.0 0.00 0.00 0.0 4.18 R
2735 3090 0.250038 CGATGCCCTGGTCAATCGAT 60.250 55.0 14.25 0.00 33.9 3.59 R
3801 4472 0.107945 CTGGAGCAGCTGTTAGGGTC 60.108 60.0 16.64 3.46 0.0 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
68 70 7.008628 CGTTTGAAAATAACATCTTGGAGCATC 59.991 37.037 0.00 0.00 0.00 3.91
108 118 7.912056 TTTCAAAAATGTCATTTGGTGTTGA 57.088 28.000 11.54 13.50 38.12 3.18
113 123 9.570488 CAAAAATGTCATTTGGTGTTGAAATTT 57.430 25.926 11.54 0.00 40.06 1.82
117 127 7.456684 TGTCATTTGGTGTTGAAATTTTACG 57.543 32.000 0.00 0.00 0.00 3.18
118 128 6.477033 TGTCATTTGGTGTTGAAATTTTACGG 59.523 34.615 0.00 0.00 0.00 4.02
126 136 9.233649 TGGTGTTGAAATTTTACGGACTATTAT 57.766 29.630 0.00 0.00 0.00 1.28
152 162 6.437928 ACATATGTCAATGTTTCACACACAC 58.562 36.000 1.41 0.00 38.61 3.82
153 163 4.979943 ATGTCAATGTTTCACACACACA 57.020 36.364 0.00 0.00 38.61 3.72
154 164 4.773323 TGTCAATGTTTCACACACACAA 57.227 36.364 0.00 0.00 38.61 3.33
155 165 5.321959 TGTCAATGTTTCACACACACAAT 57.678 34.783 0.00 0.00 38.61 2.71
157 167 6.856895 TGTCAATGTTTCACACACACAATAA 58.143 32.000 0.00 0.00 38.61 1.40
158 168 7.487484 TGTCAATGTTTCACACACACAATAAT 58.513 30.769 0.00 0.00 38.61 1.28
159 169 8.624776 TGTCAATGTTTCACACACACAATAATA 58.375 29.630 0.00 0.00 38.61 0.98
160 170 9.457110 GTCAATGTTTCACACACACAATAATAA 57.543 29.630 0.00 0.00 38.61 1.40
201 211 7.748691 TTTTAATTTACTGTTTACCCGAGCT 57.251 32.000 0.00 0.00 0.00 4.09
202 212 6.973229 TTAATTTACTGTTTACCCGAGCTC 57.027 37.500 2.73 2.73 0.00 4.09
203 213 4.546829 ATTTACTGTTTACCCGAGCTCA 57.453 40.909 15.40 0.00 0.00 4.26
204 214 3.308438 TTACTGTTTACCCGAGCTCAC 57.692 47.619 15.40 3.47 0.00 3.51
205 215 0.038526 ACTGTTTACCCGAGCTCACG 60.039 55.000 15.40 4.93 0.00 4.35
206 216 0.038526 CTGTTTACCCGAGCTCACGT 60.039 55.000 15.40 11.07 0.00 4.49
209 219 0.242825 TTTACCCGAGCTCACGTGAG 59.757 55.000 35.80 35.80 44.75 3.51
218 228 1.064946 CTCACGTGAGCTCGGGATC 59.935 63.158 31.00 0.00 42.38 3.36
223 233 0.526524 CGTGAGCTCGGGATCAGAAC 60.527 60.000 1.92 0.00 38.62 3.01
226 236 0.179097 GAGCTCGGGATCAGAACACC 60.179 60.000 0.00 0.00 0.00 4.16
227 237 1.153349 GCTCGGGATCAGAACACCC 60.153 63.158 0.00 0.00 40.17 4.61
244 263 0.956902 CCCGTGTCCCCCTTTAAACG 60.957 60.000 0.00 0.00 0.00 3.60
271 290 6.384305 TGTTTCAAAGTTTGGGATCCCTAAAA 59.616 34.615 31.05 20.73 33.07 1.52
305 324 0.035820 AACGTGGTGGCATATTCGGT 60.036 50.000 0.00 0.00 0.00 4.69
315 335 4.093408 GTGGCATATTCGGTGCACATATAG 59.907 45.833 20.43 9.20 44.25 1.31
405 425 1.530720 CATACACTGAAACACTGCGCA 59.469 47.619 10.98 10.98 0.00 6.09
514 535 4.676951 CACAACGGGCCCCACCAT 62.677 66.667 18.66 0.00 42.05 3.55
710 744 4.675303 CTCCTCCCCACCACCCCA 62.675 72.222 0.00 0.00 0.00 4.96
833 876 1.137086 CGAATCTGTCCCCACGAATCT 59.863 52.381 0.00 0.00 0.00 2.40
913 969 2.476499 GGCGCTGCTCGTTTCTTC 59.524 61.111 7.64 0.00 41.07 2.87
1155 1245 4.507916 CCGAGGGAGGAGAGGCGA 62.508 72.222 0.00 0.00 0.00 5.54
1156 1246 2.440430 CGAGGGAGGAGAGGCGAA 60.440 66.667 0.00 0.00 0.00 4.70
1157 1247 2.776913 CGAGGGAGGAGAGGCGAAC 61.777 68.421 0.00 0.00 0.00 3.95
1158 1248 2.364448 AGGGAGGAGAGGCGAACC 60.364 66.667 0.00 0.00 0.00 3.62
1159 1249 3.839432 GGGAGGAGAGGCGAACCG 61.839 72.222 0.00 0.00 42.76 4.44
1160 1250 2.754658 GGAGGAGAGGCGAACCGA 60.755 66.667 0.00 0.00 42.76 4.69
1161 1251 2.776913 GGAGGAGAGGCGAACCGAG 61.777 68.421 0.00 0.00 42.76 4.63
1162 1252 2.756283 AGGAGAGGCGAACCGAGG 60.756 66.667 0.00 0.00 42.76 4.63
1163 1253 2.754658 GGAGAGGCGAACCGAGGA 60.755 66.667 0.00 0.00 42.76 3.71
1164 1254 2.348888 GGAGAGGCGAACCGAGGAA 61.349 63.158 0.00 0.00 42.76 3.36
1353 1450 0.671251 TGTGTTTTCCGGCATTGACC 59.329 50.000 0.00 0.00 0.00 4.02
1364 1498 1.727467 CATTGACCGGCGAATTCCC 59.273 57.895 9.30 1.46 0.00 3.97
1409 1543 1.745087 TCCTCATTCCATTTCGCTTGC 59.255 47.619 0.00 0.00 0.00 4.01
1776 1917 8.246871 TCTAATGACACTTGACATCTCTTACTG 58.753 37.037 0.00 0.00 30.61 2.74
1777 1918 5.139435 TGACACTTGACATCTCTTACTGG 57.861 43.478 0.00 0.00 0.00 4.00
1778 1919 4.588951 TGACACTTGACATCTCTTACTGGT 59.411 41.667 0.00 0.00 0.00 4.00
1779 1920 5.773176 TGACACTTGACATCTCTTACTGGTA 59.227 40.000 0.00 0.00 0.00 3.25
1780 1921 6.071896 TGACACTTGACATCTCTTACTGGTAG 60.072 42.308 0.00 0.00 0.00 3.18
1781 1922 5.775701 ACACTTGACATCTCTTACTGGTAGT 59.224 40.000 0.00 0.00 0.00 2.73
1782 1923 6.071840 ACACTTGACATCTCTTACTGGTAGTC 60.072 42.308 0.00 0.00 0.00 2.59
1783 1924 6.151985 CACTTGACATCTCTTACTGGTAGTCT 59.848 42.308 0.00 0.00 0.00 3.24
1784 1925 6.151985 ACTTGACATCTCTTACTGGTAGTCTG 59.848 42.308 0.00 0.00 0.00 3.51
1806 1947 5.496556 TGGTACATGTCAATTTGGTAGAGG 58.503 41.667 0.00 0.00 0.00 3.69
1808 1949 4.307032 ACATGTCAATTTGGTAGAGGCT 57.693 40.909 0.00 0.00 0.00 4.58
1812 1953 3.582647 TGTCAATTTGGTAGAGGCTGAGA 59.417 43.478 0.00 0.00 0.00 3.27
1879 2023 4.332428 AAGTCAAGTAGCCGTGTTAGTT 57.668 40.909 0.00 0.00 0.00 2.24
1938 2082 4.456280 TGTGACTGACTTATGCACTAGG 57.544 45.455 0.00 0.00 0.00 3.02
1956 2100 6.144563 GCACTAGGCTGAAAAAGTTCAATTTC 59.855 38.462 0.00 0.00 43.18 2.17
2042 2205 9.740239 ACACATGTTTGATGCAATATATTCTTC 57.260 29.630 0.00 0.73 0.00 2.87
2070 2239 7.938140 AAATCGATTAGAAGGAATGTGGAAA 57.062 32.000 11.83 0.00 0.00 3.13
2212 2388 2.168728 CCTCCTTTCTGGTGTACTAGCC 59.831 54.545 0.00 0.00 37.07 3.93
2271 2447 0.401738 CCCTTGGTCTGCTTCCTTGA 59.598 55.000 0.00 0.00 0.00 3.02
2373 2552 5.751680 TCTTGAAAGCGACTTCAAATTCTG 58.248 37.500 11.87 3.07 43.03 3.02
2392 2574 9.442047 AAATTCTGGAAGTAAATGTCTGACTAG 57.558 33.333 9.51 0.00 33.76 2.57
2435 2617 5.575157 TCCTGTTCTAATGCCCACAAAATA 58.425 37.500 0.00 0.00 0.00 1.40
2438 2620 7.836685 TCCTGTTCTAATGCCCACAAAATATTA 59.163 33.333 0.00 0.00 0.00 0.98
2439 2621 8.137437 CCTGTTCTAATGCCCACAAAATATTAG 58.863 37.037 0.00 0.00 34.33 1.73
2441 2623 9.688091 TGTTCTAATGCCCACAAAATATTAGTA 57.312 29.630 0.00 0.00 34.54 1.82
2468 2650 5.496133 TTTTTGTTTTCCATGCAACATGG 57.504 34.783 18.57 18.57 40.48 3.66
2479 2716 3.435105 TGCAACATGGAAGTGACAAAC 57.565 42.857 0.00 0.00 0.00 2.93
2480 2717 2.757314 TGCAACATGGAAGTGACAAACA 59.243 40.909 0.00 0.00 0.00 2.83
2481 2718 3.384146 TGCAACATGGAAGTGACAAACAT 59.616 39.130 0.00 0.00 0.00 2.71
2492 2729 3.947834 AGTGACAAACATGCTATTAGCCC 59.052 43.478 13.01 0.00 41.51 5.19
2500 2737 1.602041 GCTATTAGCCCTGCTGCCC 60.602 63.158 4.21 0.00 40.10 5.36
2501 2738 1.839191 CTATTAGCCCTGCTGCCCA 59.161 57.895 0.00 0.00 40.10 5.36
2502 2739 0.403271 CTATTAGCCCTGCTGCCCAT 59.597 55.000 0.00 0.00 40.10 4.00
2513 2750 0.952280 GCTGCCCATCATCATGACAG 59.048 55.000 0.00 0.00 37.20 3.51
2527 2764 8.442632 TCATCATGACAGCTAAGAATTTTAGG 57.557 34.615 0.00 0.00 0.00 2.69
2533 2770 4.576463 ACAGCTAAGAATTTTAGGCATCCG 59.424 41.667 0.00 0.00 0.00 4.18
2536 2773 6.260050 CAGCTAAGAATTTTAGGCATCCGTTA 59.740 38.462 0.00 0.00 0.00 3.18
2538 2775 7.012421 AGCTAAGAATTTTAGGCATCCGTTAAG 59.988 37.037 0.00 0.00 0.00 1.85
2542 2779 3.598019 TTTAGGCATCCGTTAAGTCGT 57.402 42.857 0.00 0.00 0.00 4.34
2549 2786 3.734293 GCATCCGTTAAGTCGTAGCTCTT 60.734 47.826 0.00 0.00 0.00 2.85
2552 2789 3.120060 TCCGTTAAGTCGTAGCTCTTGTC 60.120 47.826 0.00 0.00 0.00 3.18
2568 2805 0.533085 TGTCGTCGGTCAATTGGCAA 60.533 50.000 12.93 0.68 0.00 4.52
2570 2807 0.871722 TCGTCGGTCAATTGGCAAAG 59.128 50.000 12.93 2.76 0.00 2.77
2571 2808 0.871722 CGTCGGTCAATTGGCAAAGA 59.128 50.000 12.93 5.24 0.00 2.52
2572 2809 1.468520 CGTCGGTCAATTGGCAAAGAT 59.531 47.619 12.93 0.00 0.00 2.40
2573 2810 2.728846 CGTCGGTCAATTGGCAAAGATG 60.729 50.000 12.93 9.40 0.00 2.90
2575 2812 2.487762 TCGGTCAATTGGCAAAGATGAC 59.512 45.455 24.33 24.33 36.25 3.06
2576 2813 2.228582 CGGTCAATTGGCAAAGATGACA 59.771 45.455 29.05 7.17 44.97 3.58
2588 2880 5.182760 GGCAAAGATGACAGATGAACTTTCT 59.817 40.000 0.00 0.00 33.41 2.52
2618 2928 6.265196 TCCATTTTCAAGCACACTCAGTTATT 59.735 34.615 0.00 0.00 0.00 1.40
2627 2937 5.009010 AGCACACTCAGTTATTTTTCACCAG 59.991 40.000 0.00 0.00 0.00 4.00
2630 2940 6.912591 CACACTCAGTTATTTTTCACCAGAAC 59.087 38.462 0.00 0.00 32.39 3.01
2634 2944 5.591067 TCAGTTATTTTTCACCAGAACCGTT 59.409 36.000 0.00 0.00 32.39 4.44
2638 2948 7.499895 AGTTATTTTTCACCAGAACCGTTTAGA 59.500 33.333 0.00 0.00 32.39 2.10
2700 3010 2.490903 CAAGCTTCATTCTGGTCCCTTG 59.509 50.000 0.00 0.00 0.00 3.61
2705 3015 4.949856 GCTTCATTCTGGTCCCTTGATTTA 59.050 41.667 0.00 0.00 0.00 1.40
2706 3016 5.595952 GCTTCATTCTGGTCCCTTGATTTAT 59.404 40.000 0.00 0.00 0.00 1.40
2709 3019 9.189156 CTTCATTCTGGTCCCTTGATTTATTTA 57.811 33.333 0.00 0.00 0.00 1.40
2710 3020 9.713684 TTCATTCTGGTCCCTTGATTTATTTAT 57.286 29.630 0.00 0.00 0.00 1.40
2735 3090 0.746204 TTCTGTTTCACGCAGGCACA 60.746 50.000 0.00 0.00 34.89 4.57
2750 3105 1.718757 GCACATCGATTGACCAGGGC 61.719 60.000 0.00 0.00 0.00 5.19
2922 3286 1.130373 GTGTGTGTGTGTGGTGTTCTG 59.870 52.381 0.00 0.00 0.00 3.02
3031 3400 8.737168 AGTTCATGCTAATGTGTGTATGTATT 57.263 30.769 0.00 0.00 35.15 1.89
3032 3401 9.830975 AGTTCATGCTAATGTGTGTATGTATTA 57.169 29.630 0.00 0.00 35.15 0.98
3077 3448 4.152625 GTGCTGCGATGCGTGGTC 62.153 66.667 0.00 0.00 35.36 4.02
3102 3473 3.446873 TCTGGTTTTGCAAGTTGTGTGAT 59.553 39.130 4.48 0.00 0.00 3.06
3103 3474 4.642437 TCTGGTTTTGCAAGTTGTGTGATA 59.358 37.500 4.48 0.00 0.00 2.15
3104 3475 4.677584 TGGTTTTGCAAGTTGTGTGATAC 58.322 39.130 4.48 0.00 0.00 2.24
3105 3476 3.728718 GGTTTTGCAAGTTGTGTGATACG 59.271 43.478 4.48 0.00 0.00 3.06
3106 3477 4.347813 GTTTTGCAAGTTGTGTGATACGT 58.652 39.130 4.48 0.00 0.00 3.57
3134 3505 0.033796 CCCATGTGGATGCTTGTCCT 60.034 55.000 0.00 0.00 39.12 3.85
3255 3632 3.583806 AGTTGAGTGATTCGCTTCTCTG 58.416 45.455 0.47 0.00 0.00 3.35
3256 3633 3.256879 AGTTGAGTGATTCGCTTCTCTGA 59.743 43.478 0.47 0.00 0.00 3.27
3264 3641 1.304254 TCGCTTCTCTGATCTCCTCG 58.696 55.000 0.00 0.00 0.00 4.63
3275 3652 5.982356 TCTGATCTCCTCGTGATGAATTTT 58.018 37.500 0.00 0.00 0.00 1.82
3305 3845 4.333913 ACTGCCTATGTGAGATGTCATC 57.666 45.455 4.52 4.52 34.36 2.92
3306 3846 3.070734 ACTGCCTATGTGAGATGTCATCC 59.929 47.826 9.29 2.20 34.36 3.51
3356 3901 5.167845 CAACTTGCAAGTACTGTTTTTGGT 58.832 37.500 31.31 9.28 38.57 3.67
3376 3921 7.976414 TTGGTTGGATGGATTGAATTTCTAT 57.024 32.000 0.00 0.00 0.00 1.98
3393 3938 9.269415 GAATTTCTATTGCAAATTTGATTGTGC 57.731 29.630 22.31 6.48 34.30 4.57
3394 3939 7.725818 TTTCTATTGCAAATTTGATTGTGCA 57.274 28.000 22.31 9.25 44.85 4.57
3454 4005 0.664761 CAAATGCCTACATCAGCCGG 59.335 55.000 0.00 0.00 34.62 6.13
3455 4006 0.255890 AAATGCCTACATCAGCCGGT 59.744 50.000 1.90 0.00 34.62 5.28
3456 4007 1.128200 AATGCCTACATCAGCCGGTA 58.872 50.000 1.90 0.00 34.62 4.02
3457 4008 1.352083 ATGCCTACATCAGCCGGTAT 58.648 50.000 1.90 0.00 0.00 2.73
3458 4009 0.392706 TGCCTACATCAGCCGGTATG 59.607 55.000 1.90 7.67 0.00 2.39
3459 4010 0.320771 GCCTACATCAGCCGGTATGG 60.321 60.000 1.90 0.00 42.50 2.74
3460 4011 1.048601 CCTACATCAGCCGGTATGGT 58.951 55.000 1.90 0.00 41.21 3.55
3461 4012 2.244695 CCTACATCAGCCGGTATGGTA 58.755 52.381 1.90 1.02 41.21 3.25
3462 4013 2.231478 CCTACATCAGCCGGTATGGTAG 59.769 54.545 1.90 10.07 41.21 3.18
3463 4014 0.393077 ACATCAGCCGGTATGGTAGC 59.607 55.000 1.90 0.00 41.21 3.58
3464 4015 0.392706 CATCAGCCGGTATGGTAGCA 59.607 55.000 1.90 0.00 41.21 3.49
3465 4016 1.128200 ATCAGCCGGTATGGTAGCAA 58.872 50.000 1.90 0.00 41.21 3.91
3466 4017 1.128200 TCAGCCGGTATGGTAGCAAT 58.872 50.000 1.90 0.00 41.21 3.56
3467 4018 1.070134 TCAGCCGGTATGGTAGCAATC 59.930 52.381 1.90 0.00 41.21 2.67
3468 4019 1.070758 CAGCCGGTATGGTAGCAATCT 59.929 52.381 1.90 0.00 41.21 2.40
3469 4020 2.299013 CAGCCGGTATGGTAGCAATCTA 59.701 50.000 1.90 0.00 41.21 1.98
3470 4021 2.299297 AGCCGGTATGGTAGCAATCTAC 59.701 50.000 1.90 0.00 43.43 2.59
3479 4030 3.199880 GTAGCAATCTACCTGGCATGT 57.800 47.619 0.10 0.10 39.36 3.21
3480 4031 2.338577 AGCAATCTACCTGGCATGTC 57.661 50.000 0.00 0.00 0.00 3.06
3481 4032 1.133976 AGCAATCTACCTGGCATGTCC 60.134 52.381 0.00 0.00 0.00 4.02
3482 4033 1.408683 GCAATCTACCTGGCATGTCCA 60.409 52.381 0.00 8.33 44.18 4.02
3483 4034 2.292267 CAATCTACCTGGCATGTCCAC 58.708 52.381 0.00 0.00 40.72 4.02
3484 4035 1.583556 ATCTACCTGGCATGTCCACA 58.416 50.000 0.00 0.00 40.72 4.17
3485 4036 1.357137 TCTACCTGGCATGTCCACAA 58.643 50.000 0.00 0.00 40.72 3.33
3486 4037 1.278985 TCTACCTGGCATGTCCACAAG 59.721 52.381 0.00 3.98 40.72 3.16
3487 4038 1.278985 CTACCTGGCATGTCCACAAGA 59.721 52.381 0.00 0.00 40.72 3.02
3488 4039 0.700564 ACCTGGCATGTCCACAAGAT 59.299 50.000 4.93 0.00 40.72 2.40
3489 4040 1.340405 ACCTGGCATGTCCACAAGATC 60.340 52.381 4.93 0.00 40.72 2.75
3490 4041 1.340308 CCTGGCATGTCCACAAGATCA 60.340 52.381 4.93 0.00 40.72 2.92
3491 4042 2.014857 CTGGCATGTCCACAAGATCAG 58.985 52.381 4.93 0.00 40.72 2.90
3492 4043 0.737219 GGCATGTCCACAAGATCAGC 59.263 55.000 0.00 0.00 34.01 4.26
3493 4044 1.456296 GCATGTCCACAAGATCAGCA 58.544 50.000 0.00 0.00 0.00 4.41
3494 4045 2.022195 GCATGTCCACAAGATCAGCAT 58.978 47.619 0.00 0.00 0.00 3.79
3495 4046 2.223502 GCATGTCCACAAGATCAGCATG 60.224 50.000 0.00 0.00 36.35 4.06
3496 4047 2.865119 TGTCCACAAGATCAGCATGT 57.135 45.000 0.00 0.00 37.40 3.21
3497 4048 2.429478 TGTCCACAAGATCAGCATGTG 58.571 47.619 11.68 11.68 43.81 3.21
3498 4049 2.224597 TGTCCACAAGATCAGCATGTGT 60.225 45.455 15.29 0.00 42.94 3.72
3499 4050 3.007831 TGTCCACAAGATCAGCATGTGTA 59.992 43.478 15.29 2.64 42.94 2.90
3500 4051 3.372206 GTCCACAAGATCAGCATGTGTAC 59.628 47.826 15.29 9.25 42.94 2.90
3501 4052 3.261643 TCCACAAGATCAGCATGTGTACT 59.738 43.478 15.29 0.00 42.94 2.73
3502 4053 3.373130 CCACAAGATCAGCATGTGTACTG 59.627 47.826 15.29 0.00 42.94 2.74
3503 4054 3.005554 ACAAGATCAGCATGTGTACTGC 58.994 45.455 0.00 0.00 39.97 4.40
3505 4056 3.176552 AGATCAGCATGTGTACTGCTC 57.823 47.619 5.19 0.00 46.79 4.26
3506 4057 2.158986 AGATCAGCATGTGTACTGCTCC 60.159 50.000 5.19 0.00 46.79 4.70
3507 4058 1.269958 TCAGCATGTGTACTGCTCCT 58.730 50.000 5.19 0.00 46.79 3.69
3508 4059 1.066645 TCAGCATGTGTACTGCTCCTG 60.067 52.381 5.19 1.93 46.79 3.86
3509 4060 0.979665 AGCATGTGTACTGCTCCTGT 59.020 50.000 2.41 0.00 46.79 4.00
3510 4061 2.094026 CAGCATGTGTACTGCTCCTGTA 60.094 50.000 5.19 0.00 46.79 2.74
3511 4062 2.768527 AGCATGTGTACTGCTCCTGTAT 59.231 45.455 2.41 0.00 46.79 2.29
3512 4063 3.198635 AGCATGTGTACTGCTCCTGTATT 59.801 43.478 2.41 0.00 46.79 1.89
3513 4064 3.557595 GCATGTGTACTGCTCCTGTATTC 59.442 47.826 0.00 0.00 36.68 1.75
3514 4065 3.887621 TGTGTACTGCTCCTGTATTCC 57.112 47.619 0.00 0.00 0.00 3.01
3515 4066 3.441101 TGTGTACTGCTCCTGTATTCCT 58.559 45.455 0.00 0.00 0.00 3.36
3516 4067 4.606210 TGTGTACTGCTCCTGTATTCCTA 58.394 43.478 0.00 0.00 0.00 2.94
3517 4068 5.020795 TGTGTACTGCTCCTGTATTCCTAA 58.979 41.667 0.00 0.00 0.00 2.69
3518 4069 5.482526 TGTGTACTGCTCCTGTATTCCTAAA 59.517 40.000 0.00 0.00 0.00 1.85
3519 4070 6.156256 TGTGTACTGCTCCTGTATTCCTAAAT 59.844 38.462 0.00 0.00 0.00 1.40
3520 4071 6.702282 GTGTACTGCTCCTGTATTCCTAAATC 59.298 42.308 0.00 0.00 0.00 2.17
3521 4072 6.611642 TGTACTGCTCCTGTATTCCTAAATCT 59.388 38.462 0.00 0.00 0.00 2.40
3522 4073 7.783119 TGTACTGCTCCTGTATTCCTAAATCTA 59.217 37.037 0.00 0.00 0.00 1.98
3523 4074 7.676683 ACTGCTCCTGTATTCCTAAATCTAA 57.323 36.000 0.00 0.00 0.00 2.10
3524 4075 8.090788 ACTGCTCCTGTATTCCTAAATCTAAA 57.909 34.615 0.00 0.00 0.00 1.85
3525 4076 8.718656 ACTGCTCCTGTATTCCTAAATCTAAAT 58.281 33.333 0.00 0.00 0.00 1.40
3526 4077 8.908786 TGCTCCTGTATTCCTAAATCTAAATG 57.091 34.615 0.00 0.00 0.00 2.32
3527 4078 7.445402 TGCTCCTGTATTCCTAAATCTAAATGC 59.555 37.037 0.00 0.00 0.00 3.56
3528 4079 7.663493 GCTCCTGTATTCCTAAATCTAAATGCT 59.337 37.037 0.00 0.00 0.00 3.79
3531 4082 8.940952 CCTGTATTCCTAAATCTAAATGCTAGC 58.059 37.037 8.10 8.10 0.00 3.42
3532 4083 9.494271 CTGTATTCCTAAATCTAAATGCTAGCA 57.506 33.333 21.85 21.85 0.00 3.49
3533 4084 9.494271 TGTATTCCTAAATCTAAATGCTAGCAG 57.506 33.333 23.89 9.50 0.00 4.24
3534 4085 9.712305 GTATTCCTAAATCTAAATGCTAGCAGA 57.288 33.333 23.89 14.88 0.00 4.26
3535 4086 8.614469 ATTCCTAAATCTAAATGCTAGCAGAC 57.386 34.615 23.89 0.00 0.00 3.51
3536 4087 6.216569 TCCTAAATCTAAATGCTAGCAGACG 58.783 40.000 23.89 11.16 0.00 4.18
3537 4088 4.802876 AAATCTAAATGCTAGCAGACGC 57.197 40.909 23.89 0.00 38.99 5.19
3538 4089 1.840181 TCTAAATGCTAGCAGACGCG 58.160 50.000 23.89 3.53 45.49 6.01
3539 4090 0.855349 CTAAATGCTAGCAGACGCGG 59.145 55.000 23.89 7.13 45.49 6.46
3540 4091 0.458260 TAAATGCTAGCAGACGCGGA 59.542 50.000 23.89 0.00 45.49 5.54
3541 4092 1.084370 AAATGCTAGCAGACGCGGAC 61.084 55.000 23.89 3.93 45.49 4.79
3542 4093 2.907897 AATGCTAGCAGACGCGGACC 62.908 60.000 23.89 0.00 45.49 4.46
3543 4094 4.129737 GCTAGCAGACGCGGACCA 62.130 66.667 12.47 0.00 45.49 4.02
3544 4095 2.808315 CTAGCAGACGCGGACCAT 59.192 61.111 12.47 0.00 45.49 3.55
3545 4096 1.589993 CTAGCAGACGCGGACCATG 60.590 63.158 12.47 2.27 45.49 3.66
3546 4097 2.004808 CTAGCAGACGCGGACCATGA 62.005 60.000 12.47 0.00 45.49 3.07
3547 4098 1.600511 TAGCAGACGCGGACCATGAA 61.601 55.000 12.47 0.00 45.49 2.57
3548 4099 2.740714 GCAGACGCGGACCATGAAC 61.741 63.158 12.47 0.00 0.00 3.18
3549 4100 1.079819 CAGACGCGGACCATGAACT 60.080 57.895 12.47 0.00 0.00 3.01
3550 4101 0.670546 CAGACGCGGACCATGAACTT 60.671 55.000 12.47 0.00 0.00 2.66
3551 4102 0.892755 AGACGCGGACCATGAACTTA 59.107 50.000 12.47 0.00 0.00 2.24
3552 4103 1.274167 AGACGCGGACCATGAACTTAA 59.726 47.619 12.47 0.00 0.00 1.85
3553 4104 1.392510 GACGCGGACCATGAACTTAAC 59.607 52.381 12.47 0.00 0.00 2.01
3554 4105 1.270412 ACGCGGACCATGAACTTAACA 60.270 47.619 12.47 0.00 0.00 2.41
3555 4106 1.393539 CGCGGACCATGAACTTAACAG 59.606 52.381 0.00 0.00 0.00 3.16
3556 4107 1.737793 GCGGACCATGAACTTAACAGG 59.262 52.381 0.00 0.00 0.00 4.00
3557 4108 2.614481 GCGGACCATGAACTTAACAGGA 60.614 50.000 0.00 0.00 0.00 3.86
3558 4109 3.670625 CGGACCATGAACTTAACAGGAA 58.329 45.455 0.00 0.00 0.00 3.36
3559 4110 3.435671 CGGACCATGAACTTAACAGGAAC 59.564 47.826 0.00 0.00 0.00 3.62
3560 4111 4.652822 GGACCATGAACTTAACAGGAACT 58.347 43.478 0.00 0.00 43.88 3.01
3576 4127 5.441718 AGGAACTGATATTGCTCCTTGAA 57.558 39.130 0.00 0.00 37.18 2.69
3628 4179 3.876274 CAGCATGTGTACTACTCCTGT 57.124 47.619 0.00 0.00 0.00 4.00
3636 4187 4.763793 TGTGTACTACTCCTGTTCCTGTAC 59.236 45.833 0.00 0.00 0.00 2.90
3709 4379 2.743636 TTGCTCCTTGAAGGTACGAG 57.256 50.000 11.60 2.08 36.53 4.18
3710 4380 1.919240 TGCTCCTTGAAGGTACGAGA 58.081 50.000 11.60 0.00 36.53 4.04
3743 4413 4.217767 AGCGAGTACATTGTCTCTGTGTTA 59.782 41.667 0.00 0.00 0.00 2.41
3792 4463 4.955811 ACCACTTCTGTCAGTGTATTCA 57.044 40.909 0.00 0.00 42.45 2.57
3801 4472 3.081804 GTCAGTGTATTCAACCCCCTTG 58.918 50.000 0.00 0.00 0.00 3.61
3810 4481 0.774908 CAACCCCCTTGACCCTAACA 59.225 55.000 0.00 0.00 30.42 2.41
3811 4482 1.073098 AACCCCCTTGACCCTAACAG 58.927 55.000 0.00 0.00 0.00 3.16
3872 4628 0.804989 GGTGTTTCCTGGCTGATTCG 59.195 55.000 0.00 0.00 0.00 3.34
3911 4667 4.291815 TGCCTGGTTGCAAATGGT 57.708 50.000 0.00 0.00 38.56 3.55
3927 4683 5.006358 GCAAATGGTTTGAGATGCATGATTC 59.994 40.000 2.46 0.00 43.26 2.52
3928 4684 5.925506 AATGGTTTGAGATGCATGATTCA 57.074 34.783 2.46 2.16 0.00 2.57
3929 4685 4.976224 TGGTTTGAGATGCATGATTCAG 57.024 40.909 2.46 0.00 0.00 3.02
3930 4686 4.591929 TGGTTTGAGATGCATGATTCAGA 58.408 39.130 2.46 0.00 0.00 3.27
3931 4687 4.638865 TGGTTTGAGATGCATGATTCAGAG 59.361 41.667 2.46 0.00 0.00 3.35
3932 4688 4.497674 GGTTTGAGATGCATGATTCAGAGC 60.498 45.833 2.46 6.67 0.00 4.09
3933 4689 3.553828 TGAGATGCATGATTCAGAGCA 57.446 42.857 2.46 16.01 41.73 4.26
3946 4702 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
3966 4722 2.348243 CCCCAGGGACGCGTAAAA 59.652 61.111 13.97 0.00 37.50 1.52
3967 4723 1.078001 CCCCAGGGACGCGTAAAAT 60.078 57.895 13.97 0.00 37.50 1.82
3968 4724 1.093496 CCCCAGGGACGCGTAAAATC 61.093 60.000 13.97 0.00 37.50 2.17
3969 4725 1.426041 CCCAGGGACGCGTAAAATCG 61.426 60.000 13.97 0.00 0.00 3.34
3977 4733 2.707039 CGTAAAATCGCCGCCTGG 59.293 61.111 0.00 0.00 38.77 4.45
3978 4734 2.819552 CGTAAAATCGCCGCCTGGG 61.820 63.158 0.00 0.00 39.58 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.163774 ACGCATTTTGAAGCAACAATTTTGT 60.164 32.000 0.00 0.00 44.72 2.83
182 192 4.251268 GTGAGCTCGGGTAAACAGTAAAT 58.749 43.478 9.64 0.00 0.00 1.40
192 202 3.587095 CTCACGTGAGCTCGGGTA 58.413 61.111 31.00 0.00 35.13 3.69
200 210 1.064946 GATCCCGAGCTCACGTGAG 59.935 63.158 35.80 35.80 44.75 3.51
201 211 1.657751 CTGATCCCGAGCTCACGTGA 61.658 60.000 18.88 18.88 0.00 4.35
202 212 1.226802 CTGATCCCGAGCTCACGTG 60.227 63.158 15.40 9.94 0.00 4.49
203 213 0.965866 TTCTGATCCCGAGCTCACGT 60.966 55.000 15.40 0.00 0.00 4.49
204 214 0.526524 GTTCTGATCCCGAGCTCACG 60.527 60.000 15.40 0.37 0.00 4.35
205 215 0.532573 TGTTCTGATCCCGAGCTCAC 59.467 55.000 15.40 1.13 0.00 3.51
206 216 0.532573 GTGTTCTGATCCCGAGCTCA 59.467 55.000 15.40 0.00 0.00 4.26
209 219 1.153349 GGGTGTTCTGATCCCGAGC 60.153 63.158 0.00 0.00 0.00 5.03
214 224 0.391263 GGACACGGGTGTTCTGATCC 60.391 60.000 0.00 0.00 45.05 3.36
218 228 2.032071 GGGGACACGGGTGTTCTG 59.968 66.667 9.93 0.00 45.05 3.02
223 233 0.110869 TTTAAAGGGGGACACGGGTG 59.889 55.000 0.00 0.00 0.00 4.61
226 236 0.250424 ACGTTTAAAGGGGGACACGG 60.250 55.000 12.21 0.00 31.93 4.94
227 237 1.264826 CAACGTTTAAAGGGGGACACG 59.735 52.381 12.21 2.02 0.00 4.49
244 263 4.100963 AGGGATCCCAAACTTTGAAACAAC 59.899 41.667 32.69 0.00 38.92 3.32
289 308 1.029408 TGCACCGAATATGCCACCAC 61.029 55.000 0.00 0.00 42.69 4.16
291 310 1.029408 TGTGCACCGAATATGCCACC 61.029 55.000 15.69 0.00 42.69 4.61
292 311 1.024271 ATGTGCACCGAATATGCCAC 58.976 50.000 15.69 0.00 42.69 5.01
305 324 3.487376 GCAAAAGCGCTTCTATATGTGCA 60.487 43.478 25.24 0.00 41.57 4.57
315 335 0.039256 TCCACATGCAAAAGCGCTTC 60.039 50.000 25.24 11.96 0.00 3.86
356 376 1.990060 CATCCAGAGTCCGGTGGGT 60.990 63.158 8.84 0.00 34.27 4.51
513 534 1.133482 GTTATTACTGGGCAGGGGCAT 60.133 52.381 0.00 0.00 43.71 4.40
514 535 0.257616 GTTATTACTGGGCAGGGGCA 59.742 55.000 0.00 0.00 43.71 5.36
637 658 2.114670 CGATGCCATGTCGCCCTTT 61.115 57.895 0.00 0.00 31.85 3.11
710 744 4.636435 CGGGCGTGGGAGTTGGTT 62.636 66.667 0.00 0.00 0.00 3.67
833 876 2.181777 GATCACCTCTGTGCGCGA 59.818 61.111 12.10 0.00 42.46 5.87
913 969 0.738762 CGGCATCAGTCAGTGAGTGG 60.739 60.000 24.47 12.70 39.07 4.00
1155 1245 0.676782 CGCCATTTCCTTCCTCGGTT 60.677 55.000 0.00 0.00 0.00 4.44
1156 1246 1.078426 CGCCATTTCCTTCCTCGGT 60.078 57.895 0.00 0.00 0.00 4.69
1157 1247 1.819632 CCGCCATTTCCTTCCTCGG 60.820 63.158 0.00 0.00 0.00 4.63
1158 1248 2.472909 GCCGCCATTTCCTTCCTCG 61.473 63.158 0.00 0.00 0.00 4.63
1159 1249 2.472909 CGCCGCCATTTCCTTCCTC 61.473 63.158 0.00 0.00 0.00 3.71
1160 1250 2.438434 CGCCGCCATTTCCTTCCT 60.438 61.111 0.00 0.00 0.00 3.36
1161 1251 2.750237 ACGCCGCCATTTCCTTCC 60.750 61.111 0.00 0.00 0.00 3.46
1162 1252 2.485122 CACGCCGCCATTTCCTTC 59.515 61.111 0.00 0.00 0.00 3.46
1163 1253 3.061848 CCACGCCGCCATTTCCTT 61.062 61.111 0.00 0.00 0.00 3.36
1164 1254 4.028490 TCCACGCCGCCATTTCCT 62.028 61.111 0.00 0.00 0.00 3.36
1409 1543 1.512996 TTACCGCCGCGAGAGGATAG 61.513 60.000 15.93 0.00 33.81 2.08
1572 1712 5.805486 TGAGCGTGACAATACTATTCAAGTC 59.195 40.000 0.00 0.00 39.80 3.01
1573 1713 5.720202 TGAGCGTGACAATACTATTCAAGT 58.280 37.500 0.00 0.00 42.62 3.16
1574 1714 6.834959 ATGAGCGTGACAATACTATTCAAG 57.165 37.500 0.00 0.00 0.00 3.02
1576 1716 7.762159 TGTTTATGAGCGTGACAATACTATTCA 59.238 33.333 0.00 0.00 0.00 2.57
1577 1717 8.126871 TGTTTATGAGCGTGACAATACTATTC 57.873 34.615 0.00 0.00 0.00 1.75
1578 1718 8.487313 TTGTTTATGAGCGTGACAATACTATT 57.513 30.769 0.00 0.00 0.00 1.73
1705 1846 6.681865 GCAACTTTGAAGGGCTAGTGTAAAAA 60.682 38.462 0.00 0.00 0.00 1.94
1744 1885 6.922407 AGATGTCAAGTGTCATTAGATCATCG 59.078 38.462 0.00 0.00 34.92 3.84
1776 1917 5.354234 CCAAATTGACATGTACCAGACTACC 59.646 44.000 0.00 0.00 0.00 3.18
1777 1918 5.938125 ACCAAATTGACATGTACCAGACTAC 59.062 40.000 0.00 0.00 0.00 2.73
1778 1919 6.121776 ACCAAATTGACATGTACCAGACTA 57.878 37.500 0.00 0.00 0.00 2.59
1779 1920 4.985538 ACCAAATTGACATGTACCAGACT 58.014 39.130 0.00 0.00 0.00 3.24
1780 1921 6.170506 TCTACCAAATTGACATGTACCAGAC 58.829 40.000 0.00 0.00 0.00 3.51
1781 1922 6.367374 TCTACCAAATTGACATGTACCAGA 57.633 37.500 0.00 0.00 0.00 3.86
1782 1923 5.586243 CCTCTACCAAATTGACATGTACCAG 59.414 44.000 0.00 0.00 0.00 4.00
1783 1924 5.496556 CCTCTACCAAATTGACATGTACCA 58.503 41.667 0.00 0.00 0.00 3.25
1784 1925 4.335594 GCCTCTACCAAATTGACATGTACC 59.664 45.833 0.00 0.00 0.00 3.34
1806 1947 3.876274 TCTGTAACCAGATGTCTCAGC 57.124 47.619 0.00 0.00 42.80 4.26
1844 1985 4.319177 ACTTGACTTATTCAGCACAGTCC 58.681 43.478 0.00 0.00 35.71 3.85
1847 1988 4.331168 GGCTACTTGACTTATTCAGCACAG 59.669 45.833 0.00 0.00 34.94 3.66
1879 2023 7.756272 CAGCTAATTGTTTGTCAAGATATGCAA 59.244 33.333 0.00 0.00 39.55 4.08
1938 2082 7.704789 ACTGATGAAATTGAACTTTTTCAGC 57.295 32.000 6.68 6.68 44.41 4.26
1967 2111 2.524306 AGAGACAGTTCCTCCTCACAG 58.476 52.381 0.00 0.00 0.00 3.66
2040 2203 8.600625 CACATTCCTTCTAATCGATTTTACGAA 58.399 33.333 17.19 11.83 45.16 3.85
2041 2204 7.223971 CCACATTCCTTCTAATCGATTTTACGA 59.776 37.037 17.19 5.59 46.04 3.43
2042 2205 7.223971 TCCACATTCCTTCTAATCGATTTTACG 59.776 37.037 17.19 2.72 0.00 3.18
2047 2210 6.318900 GGTTTCCACATTCCTTCTAATCGATT 59.681 38.462 16.15 16.15 0.00 3.34
2070 2239 6.090358 CGAACTTATCTTGTACAACGAATGGT 59.910 38.462 3.59 0.00 0.00 3.55
2212 2388 0.310854 GGGAAGTGCAAACCAACTCG 59.689 55.000 0.00 0.00 0.00 4.18
2271 2447 9.277783 GTATCATGTATTTCAATGGAAGCTACT 57.722 33.333 0.00 0.00 33.82 2.57
2392 2574 3.379688 GGAAGGCCTGAAATTGATGACTC 59.620 47.826 5.69 0.00 0.00 3.36
2448 2630 4.412796 TCCATGTTGCATGGAAAACAAA 57.587 36.364 23.75 4.31 44.54 2.83
2455 2637 2.161855 GTCACTTCCATGTTGCATGGA 58.838 47.619 22.58 22.58 45.71 3.41
2457 2639 3.646611 TTGTCACTTCCATGTTGCATG 57.353 42.857 2.38 2.38 0.00 4.06
2458 2640 3.384146 TGTTTGTCACTTCCATGTTGCAT 59.616 39.130 0.00 0.00 0.00 3.96
2459 2641 2.757314 TGTTTGTCACTTCCATGTTGCA 59.243 40.909 0.00 0.00 0.00 4.08
2460 2642 3.435105 TGTTTGTCACTTCCATGTTGC 57.565 42.857 0.00 0.00 0.00 4.17
2463 2645 3.225104 AGCATGTTTGTCACTTCCATGT 58.775 40.909 0.00 0.00 36.23 3.21
2465 2647 6.183360 GCTAATAGCATGTTTGTCACTTCCAT 60.183 38.462 7.49 0.00 41.89 3.41
2466 2648 5.123820 GCTAATAGCATGTTTGTCACTTCCA 59.876 40.000 7.49 0.00 41.89 3.53
2468 2650 5.449177 GGGCTAATAGCATGTTTGTCACTTC 60.449 44.000 14.76 0.00 44.75 3.01
2470 2652 3.947834 GGGCTAATAGCATGTTTGTCACT 59.052 43.478 14.76 0.00 44.75 3.41
2471 2653 3.947834 AGGGCTAATAGCATGTTTGTCAC 59.052 43.478 14.76 0.00 44.75 3.67
2472 2654 3.947196 CAGGGCTAATAGCATGTTTGTCA 59.053 43.478 14.76 0.00 44.75 3.58
2473 2655 3.243201 GCAGGGCTAATAGCATGTTTGTC 60.243 47.826 14.76 0.00 44.75 3.18
2479 2716 0.879765 GCAGCAGGGCTAATAGCATG 59.120 55.000 14.76 12.64 44.75 4.06
2480 2717 0.251077 GGCAGCAGGGCTAATAGCAT 60.251 55.000 14.76 0.00 44.75 3.79
2481 2718 1.149174 GGCAGCAGGGCTAATAGCA 59.851 57.895 14.76 0.00 44.75 3.49
2500 2737 9.880064 CTAAAATTCTTAGCTGTCATGATGATG 57.120 33.333 0.00 0.00 0.00 3.07
2501 2738 9.064706 CCTAAAATTCTTAGCTGTCATGATGAT 57.935 33.333 0.00 0.00 0.00 2.45
2502 2739 7.012704 GCCTAAAATTCTTAGCTGTCATGATGA 59.987 37.037 0.00 0.00 0.00 2.92
2513 2750 5.500645 AACGGATGCCTAAAATTCTTAGC 57.499 39.130 0.00 0.00 0.00 3.09
2527 2764 2.117910 GAGCTACGACTTAACGGATGC 58.882 52.381 0.00 0.00 37.61 3.91
2533 2770 3.819537 ACGACAAGAGCTACGACTTAAC 58.180 45.455 0.00 0.00 0.00 2.01
2536 2773 1.136029 CGACGACAAGAGCTACGACTT 60.136 52.381 0.00 0.00 0.00 3.01
2538 2775 0.520827 CCGACGACAAGAGCTACGAC 60.521 60.000 0.00 0.00 0.00 4.34
2542 2779 1.241165 TTGACCGACGACAAGAGCTA 58.759 50.000 0.00 0.00 0.00 3.32
2549 2786 0.533085 TTGCCAATTGACCGACGACA 60.533 50.000 7.12 0.00 0.00 4.35
2552 2789 0.871722 TCTTTGCCAATTGACCGACG 59.128 50.000 7.12 0.00 0.00 5.12
2568 2805 6.767456 ACTCAGAAAGTTCATCTGTCATCTT 58.233 36.000 4.82 0.00 43.77 2.40
2588 2880 3.953612 AGTGTGCTTGAAAATGGAACTCA 59.046 39.130 0.00 0.00 0.00 3.41
2618 2928 3.556775 CGTCTAAACGGTTCTGGTGAAAA 59.443 43.478 0.00 0.00 45.21 2.29
2645 2955 9.757227 CAGGTTAGAAATAACAATTTGGTTTCA 57.243 29.630 18.13 8.28 32.66 2.69
2674 2984 4.039124 GGGACCAGAATGAAGCTTGAAAAA 59.961 41.667 2.10 0.00 39.69 1.94
2705 3015 6.276847 TGCGTGAAACAGAAACCAAATAAAT 58.723 32.000 0.00 0.00 35.74 1.40
2706 3016 5.651530 TGCGTGAAACAGAAACCAAATAAA 58.348 33.333 0.00 0.00 35.74 1.40
2709 3019 3.490761 CCTGCGTGAAACAGAAACCAAAT 60.491 43.478 0.00 0.00 37.32 2.32
2710 3020 2.159310 CCTGCGTGAAACAGAAACCAAA 60.159 45.455 0.00 0.00 37.32 3.28
2713 3023 0.317854 GCCTGCGTGAAACAGAAACC 60.318 55.000 0.00 0.00 37.32 3.27
2724 3079 1.061411 CAATCGATGTGCCTGCGTG 59.939 57.895 0.00 0.00 0.00 5.34
2735 3090 0.250038 CGATGCCCTGGTCAATCGAT 60.250 55.000 14.25 0.00 33.90 3.59
2922 3286 2.587612 TCTGACGCGCATACAAAAAC 57.412 45.000 5.73 0.00 0.00 2.43
3031 3400 2.170738 GCACAGCGCCAGTGAAATA 58.829 52.632 28.35 0.00 39.30 1.40
3032 3401 2.956987 GCACAGCGCCAGTGAAAT 59.043 55.556 28.35 0.00 39.30 2.17
3077 3448 1.134175 ACAACTTGCAAAACCAGACCG 59.866 47.619 0.00 0.00 0.00 4.79
3102 3473 3.201930 TCCACATGGGTAGTAGGTACGTA 59.798 47.826 0.00 0.00 38.11 3.57
3103 3474 2.025037 TCCACATGGGTAGTAGGTACGT 60.025 50.000 0.00 0.00 38.11 3.57
3104 3475 2.658285 TCCACATGGGTAGTAGGTACG 58.342 52.381 0.00 0.00 38.11 3.67
3105 3476 3.244112 GCATCCACATGGGTAGTAGGTAC 60.244 52.174 0.00 0.00 38.11 3.34
3106 3477 2.969950 GCATCCACATGGGTAGTAGGTA 59.030 50.000 0.00 0.00 38.11 3.08
3255 3632 6.668541 TTCAAAATTCATCACGAGGAGATC 57.331 37.500 0.00 0.00 0.00 2.75
3256 3633 7.337689 TCATTTCAAAATTCATCACGAGGAGAT 59.662 33.333 0.00 0.00 0.00 2.75
3264 3641 7.172019 AGGCAGTTTCATTTCAAAATTCATCAC 59.828 33.333 0.00 0.00 0.00 3.06
3275 3652 5.559770 TCTCACATAGGCAGTTTCATTTCA 58.440 37.500 0.00 0.00 0.00 2.69
3305 3845 3.839432 GGAGAGGGGTCGAAGCGG 61.839 72.222 0.00 0.00 0.00 5.52
3306 3846 4.194720 CGGAGAGGGGTCGAAGCG 62.195 72.222 0.00 0.00 0.00 4.68
3345 3890 4.653341 TCAATCCATCCAACCAAAAACAGT 59.347 37.500 0.00 0.00 0.00 3.55
3356 3901 7.421087 TGCAATAGAAATTCAATCCATCCAA 57.579 32.000 0.00 0.00 0.00 3.53
3459 4010 3.134458 GACATGCCAGGTAGATTGCTAC 58.866 50.000 0.00 0.00 45.04 3.58
3460 4011 2.104792 GGACATGCCAGGTAGATTGCTA 59.895 50.000 0.00 0.00 36.34 3.49
3461 4012 1.133976 GGACATGCCAGGTAGATTGCT 60.134 52.381 0.00 0.00 36.34 3.91
3462 4013 1.312815 GGACATGCCAGGTAGATTGC 58.687 55.000 0.00 0.00 36.34 3.56
3463 4014 2.715749 TGGACATGCCAGGTAGATTG 57.284 50.000 4.93 0.00 43.33 2.67
3472 4023 1.951895 GCTGATCTTGTGGACATGCCA 60.952 52.381 4.93 4.93 46.96 4.92
3473 4024 0.737219 GCTGATCTTGTGGACATGCC 59.263 55.000 0.00 0.00 37.10 4.40
3474 4025 1.456296 TGCTGATCTTGTGGACATGC 58.544 50.000 0.00 0.00 0.00 4.06
3475 4026 3.014623 ACATGCTGATCTTGTGGACATG 58.985 45.455 0.00 0.00 39.38 3.21
3476 4027 3.014623 CACATGCTGATCTTGTGGACAT 58.985 45.455 0.00 0.00 43.31 3.06
3477 4028 2.429478 CACATGCTGATCTTGTGGACA 58.571 47.619 0.00 0.00 43.31 4.02
3482 4033 3.005554 GCAGTACACATGCTGATCTTGT 58.994 45.455 0.00 0.00 40.79 3.16
3483 4034 3.670311 GCAGTACACATGCTGATCTTG 57.330 47.619 0.00 0.00 40.79 3.02
3491 4042 2.672961 TACAGGAGCAGTACACATGC 57.327 50.000 0.00 0.00 44.18 4.06
3492 4043 4.122776 GGAATACAGGAGCAGTACACATG 58.877 47.826 0.00 0.00 0.00 3.21
3493 4044 4.033709 AGGAATACAGGAGCAGTACACAT 58.966 43.478 0.00 0.00 0.00 3.21
3494 4045 3.441101 AGGAATACAGGAGCAGTACACA 58.559 45.455 0.00 0.00 0.00 3.72
3495 4046 5.593679 TTAGGAATACAGGAGCAGTACAC 57.406 43.478 0.00 0.00 0.00 2.90
3496 4047 6.611642 AGATTTAGGAATACAGGAGCAGTACA 59.388 38.462 0.00 0.00 0.00 2.90
3497 4048 7.056844 AGATTTAGGAATACAGGAGCAGTAC 57.943 40.000 0.00 0.00 0.00 2.73
3498 4049 8.777578 TTAGATTTAGGAATACAGGAGCAGTA 57.222 34.615 0.00 0.00 0.00 2.74
3499 4050 7.676683 TTAGATTTAGGAATACAGGAGCAGT 57.323 36.000 0.00 0.00 0.00 4.40
3500 4051 8.997323 CATTTAGATTTAGGAATACAGGAGCAG 58.003 37.037 0.00 0.00 0.00 4.24
3501 4052 7.445402 GCATTTAGATTTAGGAATACAGGAGCA 59.555 37.037 0.00 0.00 0.00 4.26
3502 4053 7.663493 AGCATTTAGATTTAGGAATACAGGAGC 59.337 37.037 0.00 0.00 0.00 4.70
3505 4056 8.940952 GCTAGCATTTAGATTTAGGAATACAGG 58.059 37.037 10.63 0.00 0.00 4.00
3506 4057 9.494271 TGCTAGCATTTAGATTTAGGAATACAG 57.506 33.333 14.93 0.00 0.00 2.74
3507 4058 9.494271 CTGCTAGCATTTAGATTTAGGAATACA 57.506 33.333 19.72 0.00 0.00 2.29
3508 4059 9.712305 TCTGCTAGCATTTAGATTTAGGAATAC 57.288 33.333 19.72 0.00 0.00 1.89
3509 4060 9.712305 GTCTGCTAGCATTTAGATTTAGGAATA 57.288 33.333 19.72 0.00 0.00 1.75
3510 4061 7.386299 CGTCTGCTAGCATTTAGATTTAGGAAT 59.614 37.037 19.72 0.00 0.00 3.01
3511 4062 6.701841 CGTCTGCTAGCATTTAGATTTAGGAA 59.298 38.462 19.72 0.00 0.00 3.36
3512 4063 6.216569 CGTCTGCTAGCATTTAGATTTAGGA 58.783 40.000 19.72 4.25 0.00 2.94
3513 4064 5.107298 GCGTCTGCTAGCATTTAGATTTAGG 60.107 44.000 19.72 1.57 38.39 2.69
3514 4065 5.387855 CGCGTCTGCTAGCATTTAGATTTAG 60.388 44.000 19.72 2.14 39.65 1.85
3515 4066 4.444388 CGCGTCTGCTAGCATTTAGATTTA 59.556 41.667 19.72 0.00 39.65 1.40
3516 4067 3.246226 CGCGTCTGCTAGCATTTAGATTT 59.754 43.478 19.72 0.00 39.65 2.17
3517 4068 2.797156 CGCGTCTGCTAGCATTTAGATT 59.203 45.455 19.72 0.00 39.65 2.40
3518 4069 2.398498 CGCGTCTGCTAGCATTTAGAT 58.602 47.619 19.72 0.00 39.65 1.98
3519 4070 1.536072 CCGCGTCTGCTAGCATTTAGA 60.536 52.381 19.72 9.22 39.65 2.10
3520 4071 0.855349 CCGCGTCTGCTAGCATTTAG 59.145 55.000 19.72 11.18 39.65 1.85
3521 4072 0.458260 TCCGCGTCTGCTAGCATTTA 59.542 50.000 19.72 4.03 39.65 1.40
3522 4073 1.084370 GTCCGCGTCTGCTAGCATTT 61.084 55.000 19.72 0.00 39.65 2.32
3523 4074 1.519455 GTCCGCGTCTGCTAGCATT 60.519 57.895 19.72 0.00 39.65 3.56
3524 4075 2.105128 GTCCGCGTCTGCTAGCAT 59.895 61.111 19.72 0.00 39.65 3.79
3525 4076 4.129737 GGTCCGCGTCTGCTAGCA 62.130 66.667 18.22 18.22 39.65 3.49
3526 4077 3.432051 ATGGTCCGCGTCTGCTAGC 62.432 63.158 8.10 8.10 39.65 3.42
3527 4078 1.589993 CATGGTCCGCGTCTGCTAG 60.590 63.158 4.92 0.00 39.65 3.42
3528 4079 1.600511 TTCATGGTCCGCGTCTGCTA 61.601 55.000 4.92 0.00 39.65 3.49
3529 4080 2.942796 TTCATGGTCCGCGTCTGCT 61.943 57.895 4.92 0.00 39.65 4.24
3530 4081 2.434185 TTCATGGTCCGCGTCTGC 60.434 61.111 4.92 0.00 37.91 4.26
3531 4082 0.670546 AAGTTCATGGTCCGCGTCTG 60.671 55.000 4.92 0.00 0.00 3.51
3532 4083 0.892755 TAAGTTCATGGTCCGCGTCT 59.107 50.000 4.92 0.00 0.00 4.18
3533 4084 1.392510 GTTAAGTTCATGGTCCGCGTC 59.607 52.381 4.92 0.00 0.00 5.19
3534 4085 1.270412 TGTTAAGTTCATGGTCCGCGT 60.270 47.619 4.92 0.00 0.00 6.01
3535 4086 1.393539 CTGTTAAGTTCATGGTCCGCG 59.606 52.381 0.00 0.00 0.00 6.46
3536 4087 1.737793 CCTGTTAAGTTCATGGTCCGC 59.262 52.381 0.00 0.00 0.00 5.54
3537 4088 3.328382 TCCTGTTAAGTTCATGGTCCG 57.672 47.619 0.00 0.00 0.00 4.79
3538 4089 4.455877 CAGTTCCTGTTAAGTTCATGGTCC 59.544 45.833 0.00 0.00 0.00 4.46
3539 4090 5.305585 TCAGTTCCTGTTAAGTTCATGGTC 58.694 41.667 0.00 0.00 32.61 4.02
3540 4091 5.304686 TCAGTTCCTGTTAAGTTCATGGT 57.695 39.130 0.00 0.00 32.61 3.55
3541 4092 8.400947 CAATATCAGTTCCTGTTAAGTTCATGG 58.599 37.037 0.00 0.00 32.61 3.66
3542 4093 7.912250 GCAATATCAGTTCCTGTTAAGTTCATG 59.088 37.037 0.00 0.00 32.61 3.07
3543 4094 7.831193 AGCAATATCAGTTCCTGTTAAGTTCAT 59.169 33.333 0.00 0.00 32.61 2.57
3544 4095 7.168219 AGCAATATCAGTTCCTGTTAAGTTCA 58.832 34.615 0.00 0.00 32.61 3.18
3545 4096 7.201652 GGAGCAATATCAGTTCCTGTTAAGTTC 60.202 40.741 4.41 0.00 34.02 3.01
3546 4097 6.599638 GGAGCAATATCAGTTCCTGTTAAGTT 59.400 38.462 4.41 0.00 34.02 2.66
3547 4098 6.069963 AGGAGCAATATCAGTTCCTGTTAAGT 60.070 38.462 11.22 0.00 43.86 2.24
3548 4099 6.352516 AGGAGCAATATCAGTTCCTGTTAAG 58.647 40.000 11.22 0.00 43.86 1.85
3549 4100 6.313519 AGGAGCAATATCAGTTCCTGTTAA 57.686 37.500 11.22 0.00 43.86 2.01
3550 4101 5.957771 AGGAGCAATATCAGTTCCTGTTA 57.042 39.130 11.22 0.00 43.86 2.41
3551 4102 4.851639 AGGAGCAATATCAGTTCCTGTT 57.148 40.909 11.22 0.00 43.86 3.16
3552 4103 4.225942 TCAAGGAGCAATATCAGTTCCTGT 59.774 41.667 12.32 3.54 44.63 4.00
3553 4104 4.774124 TCAAGGAGCAATATCAGTTCCTG 58.226 43.478 12.32 8.29 44.63 3.86
3554 4105 5.435291 CTTCAAGGAGCAATATCAGTTCCT 58.565 41.667 7.45 7.45 46.94 3.36
3555 4106 4.578105 CCTTCAAGGAGCAATATCAGTTCC 59.422 45.833 0.00 3.65 37.67 3.62
3556 4107 5.189180 ACCTTCAAGGAGCAATATCAGTTC 58.811 41.667 11.59 0.00 37.67 3.01
3557 4108 5.184892 ACCTTCAAGGAGCAATATCAGTT 57.815 39.130 11.59 0.00 37.67 3.16
3558 4109 4.851639 ACCTTCAAGGAGCAATATCAGT 57.148 40.909 11.59 0.00 37.67 3.41
3559 4110 4.754114 GCTACCTTCAAGGAGCAATATCAG 59.246 45.833 11.59 0.00 37.67 2.90
3560 4111 4.164030 TGCTACCTTCAAGGAGCAATATCA 59.836 41.667 21.53 0.53 41.86 2.15
3561 4112 4.708177 TGCTACCTTCAAGGAGCAATATC 58.292 43.478 21.53 0.00 41.86 1.63
3562 4113 4.164988 ACTGCTACCTTCAAGGAGCAATAT 59.835 41.667 23.00 13.54 43.10 1.28
3563 4114 3.519510 ACTGCTACCTTCAAGGAGCAATA 59.480 43.478 23.00 8.33 43.10 1.90
3564 4115 2.307098 ACTGCTACCTTCAAGGAGCAAT 59.693 45.455 23.00 15.40 43.10 3.56
3565 4116 1.699634 ACTGCTACCTTCAAGGAGCAA 59.300 47.619 23.00 12.44 43.10 3.91
3566 4117 1.276421 GACTGCTACCTTCAAGGAGCA 59.724 52.381 22.05 22.05 42.24 4.26
3567 4118 1.552792 AGACTGCTACCTTCAAGGAGC 59.447 52.381 11.59 14.94 37.67 4.70
3568 4119 3.764434 TGTAGACTGCTACCTTCAAGGAG 59.236 47.826 11.59 4.46 45.15 3.69
3569 4120 3.774734 TGTAGACTGCTACCTTCAAGGA 58.225 45.455 11.59 0.00 45.15 3.36
3570 4121 4.437239 CATGTAGACTGCTACCTTCAAGG 58.563 47.826 0.22 0.22 45.15 3.61
3571 4122 4.437239 CCATGTAGACTGCTACCTTCAAG 58.563 47.826 0.00 0.00 45.15 3.02
3572 4123 3.369471 GCCATGTAGACTGCTACCTTCAA 60.369 47.826 0.00 0.00 45.15 2.69
3573 4124 2.168521 GCCATGTAGACTGCTACCTTCA 59.831 50.000 0.00 0.00 45.15 3.02
3574 4125 2.168521 TGCCATGTAGACTGCTACCTTC 59.831 50.000 0.00 0.00 45.15 3.46
3575 4126 2.187958 TGCCATGTAGACTGCTACCTT 58.812 47.619 0.00 0.00 45.15 3.50
3576 4127 1.866015 TGCCATGTAGACTGCTACCT 58.134 50.000 0.00 0.00 45.15 3.08
3623 4174 5.590818 AGATTTAGGAGTACAGGAACAGGA 58.409 41.667 0.00 0.00 0.00 3.86
3624 4175 5.941555 AGATTTAGGAGTACAGGAACAGG 57.058 43.478 0.00 0.00 0.00 4.00
3625 4176 9.319143 CATTTAGATTTAGGAGTACAGGAACAG 57.681 37.037 0.00 0.00 0.00 3.16
3626 4177 7.769044 GCATTTAGATTTAGGAGTACAGGAACA 59.231 37.037 0.00 0.00 0.00 3.18
3627 4178 7.988028 AGCATTTAGATTTAGGAGTACAGGAAC 59.012 37.037 0.00 0.00 0.00 3.62
3628 4179 8.090788 AGCATTTAGATTTAGGAGTACAGGAA 57.909 34.615 0.00 0.00 0.00 3.36
3636 4187 7.441017 AGTCTGCTAGCATTTAGATTTAGGAG 58.559 38.462 19.72 0.87 32.94 3.69
3709 4379 1.540267 TGTACTCGCTCACCAGTTCTC 59.460 52.381 0.00 0.00 0.00 2.87
3710 4380 1.617322 TGTACTCGCTCACCAGTTCT 58.383 50.000 0.00 0.00 0.00 3.01
3743 4413 3.480133 GGTAGAGCGGCCCATGGT 61.480 66.667 11.73 0.00 0.00 3.55
3792 4463 1.073098 CTGTTAGGGTCAAGGGGGTT 58.927 55.000 0.00 0.00 0.00 4.11
3801 4472 0.107945 CTGGAGCAGCTGTTAGGGTC 60.108 60.000 16.64 3.46 0.00 4.46
3911 4667 4.266714 TGCTCTGAATCATGCATCTCAAA 58.733 39.130 0.00 0.00 0.00 2.69
3927 4683 1.088340 CAACGGCTGGAGATGCTCTG 61.088 60.000 0.00 0.00 0.00 3.35
3928 4684 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
3929 4685 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
3948 4704 2.546114 ATTTTACGCGTCCCTGGGGG 62.546 60.000 18.63 6.62 46.11 5.40
3949 4705 1.078001 ATTTTACGCGTCCCTGGGG 60.078 57.895 18.63 2.42 0.00 4.96
3950 4706 1.426041 CGATTTTACGCGTCCCTGGG 61.426 60.000 18.63 6.33 0.00 4.45
3951 4707 2.003672 CGATTTTACGCGTCCCTGG 58.996 57.895 18.63 0.00 0.00 4.45
3960 4716 2.707039 CCAGGCGGCGATTTTACG 59.293 61.111 12.98 0.00 0.00 3.18
3961 4717 2.478033 CCCCAGGCGGCGATTTTAC 61.478 63.158 12.98 0.00 0.00 2.01
3962 4718 2.124487 CCCCAGGCGGCGATTTTA 60.124 61.111 12.98 0.00 0.00 1.52
3963 4719 4.041762 TCCCCAGGCGGCGATTTT 62.042 61.111 12.98 0.00 0.00 1.82
3964 4720 4.796495 GTCCCCAGGCGGCGATTT 62.796 66.667 12.98 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.