Multiple sequence alignment - TraesCS6B01G413000

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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 TraesCS6B01G413000 chr6B 100.000 6416 0 0 1 6416 686371050 686364635 0.000000e+00 11849.0
1 TraesCS6B01G413000 chr6B 91.304 115 7 1 865 979 595377305 595377416 3.100000e-33 154.0
2 TraesCS6B01G413000 chr6D 91.207 4458 227 77 27 4431 451901244 451896899 0.000000e+00 5908.0
3 TraesCS6B01G413000 chr6D 94.691 1375 41 13 4427 5793 451896867 451895517 0.000000e+00 2106.0
4 TraesCS6B01G413000 chr6D 94.262 488 27 1 5929 6416 451895413 451894927 0.000000e+00 745.0
5 TraesCS6B01G413000 chr6D 90.196 51 5 0 5810 5860 438896962 438897012 4.150000e-07 67.6
6 TraesCS6B01G413000 chr6A 91.971 4210 217 55 68 4237 597795641 597791513 0.000000e+00 5790.0
7 TraesCS6B01G413000 chr6A 94.208 1502 41 16 4299 5783 597791343 597789871 0.000000e+00 2250.0
8 TraesCS6B01G413000 chr6A 95.492 488 22 0 5929 6416 597789776 597789289 0.000000e+00 780.0
9 TraesCS6B01G413000 chr6A 96.273 161 6 0 4225 4385 597791495 597791335 1.370000e-66 265.0
10 TraesCS6B01G413000 chr6A 93.103 87 6 0 4299 4385 597791382 597791296 1.880000e-25 128.0
11 TraesCS6B01G413000 chrUn 94.103 390 20 1 2650 3036 479996814 479997203 1.990000e-164 590.0
12 TraesCS6B01G413000 chrUn 79.266 463 83 5 5955 6406 15346872 15346412 1.740000e-80 311.0
13 TraesCS6B01G413000 chrUn 79.266 463 83 5 5955 6406 272742794 272743254 1.740000e-80 311.0
14 TraesCS6B01G413000 chrUn 95.652 46 2 0 5815 5860 288298338 288298383 2.480000e-09 75.0
15 TraesCS6B01G413000 chrUn 95.652 46 2 0 5815 5860 293843155 293843200 2.480000e-09 75.0
16 TraesCS6B01G413000 chr7B 86.066 488 67 1 5929 6416 679361006 679360520 2.050000e-144 523.0
17 TraesCS6B01G413000 chr2A 84.632 462 71 0 5955 6416 723626652 723626191 1.630000e-125 460.0
18 TraesCS6B01G413000 chr4B 89.565 115 9 1 865 979 556509258 556509147 6.710000e-30 143.0
19 TraesCS6B01G413000 chr4D 92.593 54 2 2 5816 5868 379335677 379335729 6.900000e-10 76.8
20 TraesCS6B01G413000 chr2B 95.652 46 2 0 5815 5860 28424565 28424610 2.480000e-09 75.0
21 TraesCS6B01G413000 chr2B 95.556 45 2 0 5816 5860 28424681 28424637 8.920000e-09 73.1
22 TraesCS6B01G413000 chr5B 90.741 54 3 2 5816 5868 57496908 57496856 3.210000e-08 71.3
23 TraesCS6B01G413000 chr3B 92.000 50 4 0 5816 5865 20026625 20026576 3.210000e-08 71.3
24 TraesCS6B01G413000 chr1D 88.679 53 6 0 5816 5868 452260461 452260409 1.490000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G413000 chr6B 686364635 686371050 6415 True 11849.000000 11849 100.000000 1 6416 1 chr6B.!!$R1 6415
1 TraesCS6B01G413000 chr6D 451894927 451901244 6317 True 2919.666667 5908 93.386667 27 6416 3 chr6D.!!$R1 6389
2 TraesCS6B01G413000 chr6A 597789289 597795641 6352 True 1842.600000 5790 94.209400 68 6416 5 chr6A.!!$R1 6348

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
937 984 0.178973 GGAGGAGGACTAGGAGGAGC 60.179 65.0 0.00 0.0 0.00 4.70 F
1252 1302 0.240678 TTACGCATGCTGTTGCCAAG 59.759 50.0 17.13 0.0 39.52 3.61 F
2256 2328 0.389757 GCTATGGGAGGGAACGAGAC 59.610 60.0 0.00 0.0 0.00 3.36 F
4011 4104 0.329261 TTCATTCCAGGCCACAGGAG 59.671 55.0 5.01 0.0 33.44 3.69 F
4801 5040 0.179006 CCCTGGCTGCCTATTTCTCC 60.179 60.0 21.03 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2768 2840 0.042581 TGTCCTGGGTATCTCCTGCA 59.957 55.000 0.00 0.0 36.25 4.41 R
2769 2841 1.134371 GTTGTCCTGGGTATCTCCTGC 60.134 57.143 0.00 0.0 36.25 4.85 R
4223 4316 0.393944 ACATGGGAGCAGCATGAGTG 60.394 55.000 0.00 0.0 39.69 3.51 R
5077 5316 0.106719 ATTCCGCCACCATAACCAGG 60.107 55.000 0.00 0.0 0.00 4.45 R
6240 6528 0.443869 GTCGACGACGCCTACTACAA 59.556 55.000 12.94 0.0 39.58 2.41 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 7.539712 GCTTGTATCTGTACTCATGCTAAAA 57.460 36.000 0.00 0.00 0.00 1.52
25 26 7.974675 GCTTGTATCTGTACTCATGCTAAAAA 58.025 34.615 0.00 0.00 0.00 1.94
43 44 3.531262 AAAAACGAGCATGAACCGTAC 57.469 42.857 0.00 0.00 35.28 3.67
52 53 3.451178 AGCATGAACCGTACCAGATTAGT 59.549 43.478 0.00 0.00 0.00 2.24
53 54 4.647853 AGCATGAACCGTACCAGATTAGTA 59.352 41.667 0.00 0.00 0.00 1.82
54 55 4.982916 GCATGAACCGTACCAGATTAGTAG 59.017 45.833 0.00 0.00 0.00 2.57
55 56 5.221185 GCATGAACCGTACCAGATTAGTAGA 60.221 44.000 0.00 0.00 0.00 2.59
56 57 6.516860 GCATGAACCGTACCAGATTAGTAGAT 60.517 42.308 0.00 0.00 0.00 1.98
127 128 1.539827 CTGTCCGGTTCACCCATTTTC 59.460 52.381 0.00 0.00 0.00 2.29
166 175 2.876368 ATTAGCCGAGCACCAGCACC 62.876 60.000 0.00 0.00 45.49 5.01
170 179 4.994471 CGAGCACCAGCACCAGCA 62.994 66.667 0.00 0.00 45.49 4.41
171 180 3.360340 GAGCACCAGCACCAGCAC 61.360 66.667 0.00 0.00 45.49 4.40
176 185 3.667282 CCAGCACCAGCACAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
230 239 7.021196 GCAGCACAAAAGAAACGAGATTATTA 58.979 34.615 0.00 0.00 0.00 0.98
239 248 7.948278 AGAAACGAGATTATTATTCTTCCCG 57.052 36.000 0.00 0.00 0.00 5.14
240 249 6.424207 AGAAACGAGATTATTATTCTTCCCGC 59.576 38.462 0.00 0.00 0.00 6.13
241 250 5.209818 ACGAGATTATTATTCTTCCCGCA 57.790 39.130 0.00 0.00 0.00 5.69
273 286 3.962421 CGCCTACCCTCCGTAGCG 61.962 72.222 0.00 0.00 42.85 4.26
285 298 2.580867 GTAGCGAGCCAGCGACAG 60.581 66.667 8.87 0.00 41.39 3.51
345 363 2.405594 CCGTTCCTCGCTCTCTCG 59.594 66.667 0.00 0.00 38.35 4.04
354 372 3.894947 GCTCTCTCGCGGACCTCC 61.895 72.222 6.13 0.00 0.00 4.30
355 373 3.213402 CTCTCTCGCGGACCTCCC 61.213 72.222 6.13 0.00 0.00 4.30
356 374 3.997400 CTCTCTCGCGGACCTCCCA 62.997 68.421 6.13 0.00 34.14 4.37
357 375 3.827898 CTCTCGCGGACCTCCCAC 61.828 72.222 6.13 0.00 34.14 4.61
491 509 2.716017 CCGCCTCCTCACTCAGGTC 61.716 68.421 0.00 0.00 43.95 3.85
500 518 2.118513 ACTCAGGTCCGTCCAGCT 59.881 61.111 0.00 0.00 39.02 4.24
501 519 2.279069 ACTCAGGTCCGTCCAGCTG 61.279 63.158 6.78 6.78 42.29 4.24
502 520 3.655810 CTCAGGTCCGTCCAGCTGC 62.656 68.421 8.66 0.00 40.97 5.25
503 521 3.699894 CAGGTCCGTCCAGCTGCT 61.700 66.667 8.66 0.00 35.22 4.24
504 522 3.386237 AGGTCCGTCCAGCTGCTC 61.386 66.667 8.66 2.05 39.02 4.26
506 524 3.386237 GTCCGTCCAGCTGCTCCT 61.386 66.667 8.66 0.00 0.00 3.69
509 527 3.073735 CGTCCAGCTGCTCCTCCT 61.074 66.667 8.66 0.00 0.00 3.69
510 528 2.899505 GTCCAGCTGCTCCTCCTC 59.100 66.667 8.66 0.00 0.00 3.71
511 529 2.364842 TCCAGCTGCTCCTCCTCC 60.365 66.667 8.66 0.00 0.00 4.30
512 530 2.365370 CCAGCTGCTCCTCCTCCT 60.365 66.667 8.66 0.00 0.00 3.69
513 531 2.433994 CCAGCTGCTCCTCCTCCTC 61.434 68.421 8.66 0.00 0.00 3.71
516 534 2.366167 CTGCTCCTCCTCCTCCCA 59.634 66.667 0.00 0.00 0.00 4.37
520 538 1.382420 CTCCTCCTCCTCCCACCAG 60.382 68.421 0.00 0.00 0.00 4.00
521 539 2.174876 CTCCTCCTCCTCCCACCAGT 62.175 65.000 0.00 0.00 0.00 4.00
522 540 0.854039 TCCTCCTCCTCCCACCAGTA 60.854 60.000 0.00 0.00 0.00 2.74
524 544 0.336737 CTCCTCCTCCCACCAGTACT 59.663 60.000 0.00 0.00 0.00 2.73
527 547 1.612442 TCCTCCCACCAGTACTGCC 60.612 63.158 17.86 0.00 0.00 4.85
528 548 1.613630 CCTCCCACCAGTACTGCCT 60.614 63.158 17.86 1.25 0.00 4.75
539 559 1.080995 GTACTGCCTCTGCTTGCTCG 61.081 60.000 0.00 0.00 38.71 5.03
540 560 2.842394 TACTGCCTCTGCTTGCTCGC 62.842 60.000 0.00 0.00 38.71 5.03
702 746 4.593864 GCGGATCTCCTGCCCGTC 62.594 72.222 0.00 0.00 44.63 4.79
705 749 2.503382 GGATCTCCTGCCCGTCTCC 61.503 68.421 0.00 0.00 0.00 3.71
711 755 4.803426 CTGCCCGTCTCCGCTGTC 62.803 72.222 0.00 0.00 0.00 3.51
743 787 1.136774 GCTTTTCGTGCCGGATTCC 59.863 57.895 5.05 0.00 0.00 3.01
760 804 2.045536 CCCCCTGCTGCTCTGTTC 60.046 66.667 0.00 0.00 0.00 3.18
761 805 2.435586 CCCCTGCTGCTCTGTTCG 60.436 66.667 0.00 0.00 0.00 3.95
762 806 2.435586 CCCTGCTGCTCTGTTCGG 60.436 66.667 0.00 0.00 0.00 4.30
763 807 3.123620 CCTGCTGCTCTGTTCGGC 61.124 66.667 0.00 0.00 36.41 5.54
764 808 2.047465 CTGCTGCTCTGTTCGGCT 60.047 61.111 0.00 0.00 36.79 5.52
788 832 2.991190 TGTTAGGATCGTTCGCTGTTTC 59.009 45.455 0.00 0.00 0.00 2.78
821 865 2.313172 GCGATGCTATGCCTGTCCG 61.313 63.158 0.00 0.00 0.00 4.79
874 918 4.814294 GCGTCTGGGTAGGTGGCG 62.814 72.222 0.00 0.00 0.00 5.69
894 938 0.807496 GCTTGGATCTCACCAGCAAC 59.193 55.000 0.00 0.00 41.19 4.17
895 939 1.612726 GCTTGGATCTCACCAGCAACT 60.613 52.381 0.00 0.00 41.19 3.16
913 957 1.701847 ACTGATTGTGCAGGTCTCCTT 59.298 47.619 0.00 0.00 40.20 3.36
937 984 0.178973 GGAGGAGGACTAGGAGGAGC 60.179 65.000 0.00 0.00 0.00 4.70
940 987 0.469144 GGAGGACTAGGAGGAGCAGG 60.469 65.000 0.00 0.00 0.00 4.85
956 1003 4.890306 GGAGGAGGAGGGGAGGCC 62.890 77.778 0.00 0.00 0.00 5.19
957 1004 3.773154 GAGGAGGAGGGGAGGCCT 61.773 72.222 3.86 3.86 37.18 5.19
958 1005 4.101077 AGGAGGAGGGGAGGCCTG 62.101 72.222 12.00 0.00 33.84 4.85
960 1007 4.814041 GAGGAGGGGAGGCCTGCT 62.814 72.222 24.77 4.69 38.63 4.24
991 1041 0.245266 GGAGGCTAGCTAGATTCGGC 59.755 60.000 25.15 10.10 0.00 5.54
1023 1073 3.132289 TGAAGAAAGTGTTCGACCAGACT 59.868 43.478 0.00 0.00 38.90 3.24
1061 1111 0.835941 ACCTCCATGCCATCTGTCTC 59.164 55.000 0.00 0.00 0.00 3.36
1068 1118 2.462456 TGCCATCTGTCTCTGTTCAC 57.538 50.000 0.00 0.00 0.00 3.18
1218 1268 0.244721 GGCCCTCTTTCATGCACAAC 59.755 55.000 0.00 0.00 0.00 3.32
1252 1302 0.240678 TTACGCATGCTGTTGCCAAG 59.759 50.000 17.13 0.00 39.52 3.61
1321 1371 7.416964 AATCTTAGTATGAGTCTGCTCTTGT 57.583 36.000 0.00 0.00 42.13 3.16
1322 1372 8.526667 AATCTTAGTATGAGTCTGCTCTTGTA 57.473 34.615 0.00 0.00 42.13 2.41
1450 1509 3.181478 ACATAACTAGTACGCCTTCTGCC 60.181 47.826 0.00 0.00 36.24 4.85
1611 1670 5.047306 TGTGTACAAGGTATGGTCTTCTCTG 60.047 44.000 0.00 0.00 0.00 3.35
1657 1719 2.677836 TCTTGATAATGCGTTGGACAGC 59.322 45.455 0.08 0.00 0.00 4.40
1805 1877 4.096681 TCAATCCTCTACTTCCTGCTTCA 58.903 43.478 0.00 0.00 0.00 3.02
1806 1878 4.718774 TCAATCCTCTACTTCCTGCTTCAT 59.281 41.667 0.00 0.00 0.00 2.57
1807 1879 4.953940 ATCCTCTACTTCCTGCTTCATC 57.046 45.455 0.00 0.00 0.00 2.92
1841 1913 6.018098 CACAAGCATCTCATCTTATGTTCCTC 60.018 42.308 0.00 0.00 0.00 3.71
1842 1914 6.126825 ACAAGCATCTCATCTTATGTTCCTCT 60.127 38.462 0.00 0.00 0.00 3.69
1866 1938 8.591940 TCTATCATACTTGCTTGATGCTCTAAT 58.408 33.333 0.00 0.00 43.37 1.73
1869 1941 8.599055 TCATACTTGCTTGATGCTCTAATAAG 57.401 34.615 0.00 0.00 43.37 1.73
1943 2015 4.376146 GGAGAGATCAAGGTAGCAATGTC 58.624 47.826 0.00 0.00 0.00 3.06
2070 2142 9.944663 TTCGTATTATGTTTGCTTCAAATATCC 57.055 29.630 5.10 0.00 36.73 2.59
2157 2229 0.608856 ATCGGAGTGCATTTGCCACA 60.609 50.000 0.00 0.00 41.18 4.17
2178 2250 2.657237 GGACCACACAGGAGTCCG 59.343 66.667 2.76 1.29 40.65 4.79
2199 2271 1.873591 GGTGGATATGACAATGACCGC 59.126 52.381 0.00 0.00 0.00 5.68
2256 2328 0.389757 GCTATGGGAGGGAACGAGAC 59.610 60.000 0.00 0.00 0.00 3.36
2259 2331 2.362120 GGGAGGGAACGAGACGGA 60.362 66.667 0.00 0.00 0.00 4.69
2298 2370 1.517361 CAGTGGCGCTGGAGATACA 59.483 57.895 20.17 0.00 41.42 2.29
2363 2435 3.689161 CGCAACAGGGAAGATGAATACAA 59.311 43.478 0.00 0.00 0.00 2.41
2364 2436 4.437390 CGCAACAGGGAAGATGAATACAAC 60.437 45.833 0.00 0.00 0.00 3.32
2365 2437 4.458989 GCAACAGGGAAGATGAATACAACA 59.541 41.667 0.00 0.00 0.00 3.33
2409 2481 1.630126 ATGCAGAAGGATCAGGCCGT 61.630 55.000 0.00 0.00 0.00 5.68
2497 2569 7.390027 ACATTCTTAAGCGCTGATTATAGGAT 58.610 34.615 12.58 0.00 0.00 3.24
2505 2577 3.997021 CGCTGATTATAGGATGGTCAACC 59.003 47.826 0.00 0.00 0.00 3.77
2520 2592 4.215399 TGGTCAACCGATGATTTTCAAGAC 59.785 41.667 0.00 0.00 40.97 3.01
2550 2622 9.563748 TTTTGTGTATTACTAATATAGTGCCCC 57.436 33.333 0.37 0.00 39.81 5.80
2579 2651 6.039270 TGTTAAACATCCTCCTGTTTCTGTTG 59.961 38.462 5.54 0.00 43.98 3.33
2665 2737 5.941948 TGAGTTCTTACCTTTTAGCTTGC 57.058 39.130 0.00 0.00 0.00 4.01
2670 2742 4.736473 TCTTACCTTTTAGCTTGCCCTTT 58.264 39.130 0.00 0.00 0.00 3.11
2671 2743 5.144832 TCTTACCTTTTAGCTTGCCCTTTT 58.855 37.500 0.00 0.00 0.00 2.27
2673 2745 3.038280 ACCTTTTAGCTTGCCCTTTTGT 58.962 40.909 0.00 0.00 0.00 2.83
2681 2753 1.745653 CTTGCCCTTTTGTAGCTAGCC 59.254 52.381 12.13 0.00 0.00 3.93
2755 2827 1.068055 GCAGATTGCTTCACCACCAAG 60.068 52.381 0.00 0.00 40.96 3.61
2768 2840 2.038557 ACCACCAAGCTACGAAGATGTT 59.961 45.455 0.00 0.00 0.00 2.71
2769 2841 2.416547 CCACCAAGCTACGAAGATGTTG 59.583 50.000 0.00 0.00 0.00 3.33
2789 2861 1.134371 GCAGGAGATACCCAGGACAAC 60.134 57.143 0.00 0.00 40.05 3.32
2808 2880 4.460382 ACAACCATCATGATGAAAGGTGAC 59.540 41.667 32.71 0.00 38.38 3.67
2821 2893 6.785337 TGAAAGGTGACGATTCTATCCTAA 57.215 37.500 0.00 0.00 33.77 2.69
2915 2990 2.913578 CCTGCTGCACCAAAGGCA 60.914 61.111 0.00 0.00 39.32 4.75
2924 2999 1.467920 CACCAAAGGCATCTTCTCCC 58.532 55.000 0.00 0.00 31.82 4.30
2930 3005 2.856760 AGGCATCTTCTCCCTCTGTA 57.143 50.000 0.00 0.00 0.00 2.74
3003 3078 0.458716 GCCTGTCGAGGTTGTAGCTC 60.459 60.000 0.00 0.00 42.15 4.09
3038 3113 2.908940 GCTGCACAACCACCTGCT 60.909 61.111 0.00 0.00 34.29 4.24
3099 3174 5.068723 CGTGGATCAGTACCAGGTATAGTTT 59.931 44.000 1.54 0.00 38.14 2.66
3143 3218 4.515191 TGTGCTCATGACTAAACCAAAGTC 59.485 41.667 0.00 0.00 43.04 3.01
3158 3233 6.418057 ACCAAAGTCATGGAAAATAGCAAA 57.582 33.333 0.00 0.00 43.54 3.68
3159 3234 7.008021 ACCAAAGTCATGGAAAATAGCAAAT 57.992 32.000 0.00 0.00 43.54 2.32
3160 3235 6.875195 ACCAAAGTCATGGAAAATAGCAAATG 59.125 34.615 0.00 0.00 43.54 2.32
3161 3236 7.098477 CCAAAGTCATGGAAAATAGCAAATGA 58.902 34.615 0.00 0.00 43.54 2.57
3203 3278 9.813080 CTTTATAAACTGTACAAGAAGAACAGC 57.187 33.333 0.00 0.00 43.53 4.40
3250 3325 6.591062 ACTGGCATGTTGCTGTTATAAATTTG 59.409 34.615 0.00 0.00 44.28 2.32
3397 3472 0.385390 CGCTGGCTTTGGTTTCTGTT 59.615 50.000 0.00 0.00 0.00 3.16
3487 3562 1.379642 GCATGCCACCTGCTTCTACC 61.380 60.000 6.36 0.00 42.00 3.18
3490 3565 2.584608 CCACCTGCTTCTACCGGG 59.415 66.667 6.32 0.00 34.80 5.73
3512 3587 5.491982 GGTTCAGTGAGGTATGAATCTGTT 58.508 41.667 0.00 0.00 37.72 3.16
3577 3660 5.642491 GGGGATAAGATACAATTTAGACCGC 59.358 44.000 0.00 0.00 0.00 5.68
3588 3671 5.067283 ACAATTTAGACCGCACTGTTTCTTT 59.933 36.000 0.00 0.00 0.00 2.52
3600 3683 7.352739 CGCACTGTTTCTTTAATTCTAGTGTT 58.647 34.615 0.00 0.00 37.28 3.32
3671 3764 9.461312 AATTTGACATACTGGATAAGTTAAGCA 57.539 29.630 0.00 0.00 40.56 3.91
3672 3765 7.843490 TTGACATACTGGATAAGTTAAGCAC 57.157 36.000 0.00 0.00 40.56 4.40
3673 3766 7.182817 TGACATACTGGATAAGTTAAGCACT 57.817 36.000 0.00 0.00 40.56 4.40
3674 3767 8.301252 TGACATACTGGATAAGTTAAGCACTA 57.699 34.615 0.00 0.00 40.56 2.74
3675 3768 8.414003 TGACATACTGGATAAGTTAAGCACTAG 58.586 37.037 0.00 0.00 40.56 2.57
3676 3769 8.307582 ACATACTGGATAAGTTAAGCACTAGT 57.692 34.615 0.00 0.00 40.56 2.57
3677 3770 9.417561 ACATACTGGATAAGTTAAGCACTAGTA 57.582 33.333 0.00 0.00 40.56 1.82
3757 3850 4.993905 AGTAATGTTGGCTAAATTTCGGC 58.006 39.130 9.08 9.08 0.00 5.54
3792 3885 5.570262 TCTGAATTAAACGTGAAGTGACG 57.430 39.130 0.00 0.00 45.09 4.35
3853 3946 7.834068 AATATAGTCATAATAGCCAACGCAG 57.166 36.000 0.00 0.00 37.52 5.18
3963 4056 5.629097 CAGTTCAAGAAGAGAATCATGCAC 58.371 41.667 0.00 0.00 37.82 4.57
3986 4079 1.361668 CTCAGACAAATGCGACCCCG 61.362 60.000 0.00 0.00 39.16 5.73
4011 4104 0.329261 TTCATTCCAGGCCACAGGAG 59.671 55.000 5.01 0.00 33.44 3.69
4327 4528 0.694771 TCATTTGCTCCTCCACAGCT 59.305 50.000 0.00 0.00 37.79 4.24
4513 4750 0.327591 CCTCAGCAAAGCTTCCTCCT 59.672 55.000 0.00 0.00 36.40 3.69
4523 4760 1.003696 AGCTTCCTCCTACAAACTGCC 59.996 52.381 0.00 0.00 0.00 4.85
4580 4817 1.542492 CATCTCAGCCTTTTGGTGCT 58.458 50.000 0.00 0.00 42.30 4.40
4773 5010 0.605319 TTCTGGCGGTAAGTGGCTTG 60.605 55.000 0.00 0.00 0.00 4.01
4784 5023 2.124736 TGGCTTGTCTATGCGCCC 60.125 61.111 4.18 0.00 41.80 6.13
4785 5024 2.190578 GGCTTGTCTATGCGCCCT 59.809 61.111 4.18 0.00 36.56 5.19
4786 5025 2.182842 GGCTTGTCTATGCGCCCTG 61.183 63.158 4.18 0.00 36.56 4.45
4787 5026 2.182842 GCTTGTCTATGCGCCCTGG 61.183 63.158 4.18 0.00 0.00 4.45
4788 5027 2.124736 TTGTCTATGCGCCCTGGC 60.125 61.111 4.18 0.00 37.85 4.85
4791 5030 4.552365 TCTATGCGCCCTGGCTGC 62.552 66.667 4.18 15.03 39.63 5.25
4796 5035 4.883354 GCGCCCTGGCTGCCTATT 62.883 66.667 21.03 0.00 39.32 1.73
4797 5036 2.124151 CGCCCTGGCTGCCTATTT 60.124 61.111 21.03 0.00 39.32 1.40
4798 5037 2.189499 CGCCCTGGCTGCCTATTTC 61.189 63.158 21.03 4.50 39.32 2.17
4799 5038 1.228510 GCCCTGGCTGCCTATTTCT 59.771 57.895 21.03 0.00 38.26 2.52
4800 5039 0.821301 GCCCTGGCTGCCTATTTCTC 60.821 60.000 21.03 0.00 38.26 2.87
4801 5040 0.179006 CCCTGGCTGCCTATTTCTCC 60.179 60.000 21.03 0.00 0.00 3.71
4802 5041 0.548031 CCTGGCTGCCTATTTCTCCA 59.452 55.000 21.03 0.00 0.00 3.86
4803 5042 1.476471 CCTGGCTGCCTATTTCTCCAG 60.476 57.143 21.03 5.06 40.43 3.86
4804 5043 1.211457 CTGGCTGCCTATTTCTCCAGT 59.789 52.381 21.03 0.00 37.05 4.00
4805 5044 1.065199 TGGCTGCCTATTTCTCCAGTG 60.065 52.381 21.03 0.00 0.00 3.66
4806 5045 1.065126 GGCTGCCTATTTCTCCAGTGT 60.065 52.381 12.43 0.00 0.00 3.55
4807 5046 2.284190 GCTGCCTATTTCTCCAGTGTC 58.716 52.381 0.00 0.00 0.00 3.67
4808 5047 2.911484 CTGCCTATTTCTCCAGTGTCC 58.089 52.381 0.00 0.00 0.00 4.02
4809 5048 2.237143 CTGCCTATTTCTCCAGTGTCCA 59.763 50.000 0.00 0.00 0.00 4.02
4850 5089 8.015658 GTGTTCTGACCTAATTGTATGTTGTTC 58.984 37.037 0.00 0.00 0.00 3.18
5077 5316 0.392060 GGGTGTCGGTATTGGTGGTC 60.392 60.000 0.00 0.00 0.00 4.02
5109 5348 0.746563 GCGGAATGGGAATGAACCGA 60.747 55.000 0.00 0.00 42.40 4.69
5152 5397 1.062886 TGAACCAACAACCCATGGGAA 60.063 47.619 38.07 6.13 41.17 3.97
5167 5412 1.466526 GGAATGGGGATGGGGATGG 59.533 63.158 0.00 0.00 0.00 3.51
5168 5413 1.466526 GAATGGGGATGGGGATGGG 59.533 63.158 0.00 0.00 0.00 4.00
5198 5443 2.524306 GATGGGGATGAACCAACAACA 58.476 47.619 0.00 0.00 42.17 3.33
5199 5444 1.993956 TGGGGATGAACCAACAACAG 58.006 50.000 0.00 0.00 41.20 3.16
5373 5618 1.302949 TGGCTACAACCAGATGGGC 59.697 57.895 3.48 0.00 42.05 5.36
5557 5812 8.101309 TCACTATTCTTTTTCCTATCCATCCA 57.899 34.615 0.00 0.00 0.00 3.41
5558 5813 8.727149 TCACTATTCTTTTTCCTATCCATCCAT 58.273 33.333 0.00 0.00 0.00 3.41
5559 5814 9.007901 CACTATTCTTTTTCCTATCCATCCATC 57.992 37.037 0.00 0.00 0.00 3.51
5640 5895 0.392336 TGTGTTTGGATGCAAAGCCC 59.608 50.000 13.15 2.30 0.00 5.19
5764 6019 6.911308 AGGCAATAAAAGGATGTACTACCAT 58.089 36.000 10.50 0.00 0.00 3.55
5793 6054 5.452078 TGAATTTCTGTTCGCTCCATTTT 57.548 34.783 0.00 0.00 0.00 1.82
5794 6055 5.841810 TGAATTTCTGTTCGCTCCATTTTT 58.158 33.333 0.00 0.00 0.00 1.94
5796 6057 4.909696 TTTCTGTTCGCTCCATTTTTGA 57.090 36.364 0.00 0.00 0.00 2.69
5797 6058 5.452078 TTTCTGTTCGCTCCATTTTTGAT 57.548 34.783 0.00 0.00 0.00 2.57
5798 6059 5.452078 TTCTGTTCGCTCCATTTTTGATT 57.548 34.783 0.00 0.00 0.00 2.57
5799 6060 6.567687 TTCTGTTCGCTCCATTTTTGATTA 57.432 33.333 0.00 0.00 0.00 1.75
5804 6065 6.094742 TGTTCGCTCCATTTTTGATTAGCATA 59.905 34.615 0.00 0.00 0.00 3.14
5806 6067 5.588246 TCGCTCCATTTTTGATTAGCATACA 59.412 36.000 0.00 0.00 0.00 2.29
5807 6068 5.682862 CGCTCCATTTTTGATTAGCATACAC 59.317 40.000 0.00 0.00 0.00 2.90
5808 6069 6.563422 GCTCCATTTTTGATTAGCATACACA 58.437 36.000 0.00 0.00 0.00 3.72
5809 6070 6.694411 GCTCCATTTTTGATTAGCATACACAG 59.306 38.462 0.00 0.00 0.00 3.66
5812 6073 8.970020 TCCATTTTTGATTAGCATACACAGATT 58.030 29.630 0.00 0.00 0.00 2.40
5814 6075 9.027129 CATTTTTGATTAGCATACACAGATTGG 57.973 33.333 0.00 0.00 0.00 3.16
5817 6078 7.786178 TTGATTAGCATACACAGATTGGTAC 57.214 36.000 0.00 0.00 0.00 3.34
5818 6079 7.124573 TGATTAGCATACACAGATTGGTACT 57.875 36.000 0.00 0.00 0.00 2.73
5819 6080 7.210174 TGATTAGCATACACAGATTGGTACTC 58.790 38.462 0.00 0.00 0.00 2.59
5820 6081 4.408182 AGCATACACAGATTGGTACTCC 57.592 45.455 0.00 0.00 0.00 3.85
5821 6082 3.134804 AGCATACACAGATTGGTACTCCC 59.865 47.826 0.00 0.00 0.00 4.30
5822 6083 3.134804 GCATACACAGATTGGTACTCCCT 59.865 47.826 0.00 0.00 0.00 4.20
5823 6084 4.740934 GCATACACAGATTGGTACTCCCTC 60.741 50.000 0.00 0.00 0.00 4.30
5824 6085 2.188817 ACACAGATTGGTACTCCCTCC 58.811 52.381 0.00 0.00 0.00 4.30
5825 6086 1.137086 CACAGATTGGTACTCCCTCCG 59.863 57.143 0.00 0.00 0.00 4.63
5826 6087 1.273098 ACAGATTGGTACTCCCTCCGT 60.273 52.381 0.00 0.00 0.00 4.69
5827 6088 1.831736 CAGATTGGTACTCCCTCCGTT 59.168 52.381 0.00 0.00 0.00 4.44
5828 6089 2.236395 CAGATTGGTACTCCCTCCGTTT 59.764 50.000 0.00 0.00 0.00 3.60
5829 6090 2.500504 AGATTGGTACTCCCTCCGTTTC 59.499 50.000 0.00 0.00 0.00 2.78
5830 6091 1.719529 TTGGTACTCCCTCCGTTTCA 58.280 50.000 0.00 0.00 0.00 2.69
5831 6092 1.719529 TGGTACTCCCTCCGTTTCAA 58.280 50.000 0.00 0.00 0.00 2.69
5832 6093 2.048601 TGGTACTCCCTCCGTTTCAAA 58.951 47.619 0.00 0.00 0.00 2.69
5833 6094 2.438763 TGGTACTCCCTCCGTTTCAAAA 59.561 45.455 0.00 0.00 0.00 2.44
5834 6095 3.073356 TGGTACTCCCTCCGTTTCAAAAT 59.927 43.478 0.00 0.00 0.00 1.82
5835 6096 4.077108 GGTACTCCCTCCGTTTCAAAATT 58.923 43.478 0.00 0.00 0.00 1.82
5836 6097 5.221884 TGGTACTCCCTCCGTTTCAAAATTA 60.222 40.000 0.00 0.00 0.00 1.40
5837 6098 5.884232 GGTACTCCCTCCGTTTCAAAATTAT 59.116 40.000 0.00 0.00 0.00 1.28
5838 6099 6.376299 GGTACTCCCTCCGTTTCAAAATTATT 59.624 38.462 0.00 0.00 0.00 1.40
5839 6100 6.267496 ACTCCCTCCGTTTCAAAATTATTG 57.733 37.500 0.00 0.00 0.00 1.90
5840 6101 5.773176 ACTCCCTCCGTTTCAAAATTATTGT 59.227 36.000 0.00 0.00 0.00 2.71
5841 6102 6.072119 ACTCCCTCCGTTTCAAAATTATTGTC 60.072 38.462 0.00 0.00 0.00 3.18
5842 6103 5.092781 CCCTCCGTTTCAAAATTATTGTCG 58.907 41.667 0.00 0.00 0.00 4.35
5843 6104 5.335348 CCCTCCGTTTCAAAATTATTGTCGT 60.335 40.000 0.00 0.00 0.00 4.34
5844 6105 5.567534 CCTCCGTTTCAAAATTATTGTCGTG 59.432 40.000 0.00 0.00 0.00 4.35
5845 6106 5.453648 TCCGTTTCAAAATTATTGTCGTGG 58.546 37.500 0.00 0.00 0.00 4.94
5846 6107 5.008811 TCCGTTTCAAAATTATTGTCGTGGT 59.991 36.000 0.00 0.00 0.00 4.16
5847 6108 5.688176 CCGTTTCAAAATTATTGTCGTGGTT 59.312 36.000 0.00 0.00 0.00 3.67
5848 6109 6.199342 CCGTTTCAAAATTATTGTCGTGGTTT 59.801 34.615 0.00 0.00 0.00 3.27
5849 6110 7.254151 CCGTTTCAAAATTATTGTCGTGGTTTT 60.254 33.333 0.00 0.00 0.00 2.43
5850 6111 8.744011 CGTTTCAAAATTATTGTCGTGGTTTTA 58.256 29.630 0.00 0.00 0.00 1.52
5852 6113 9.804758 TTTCAAAATTATTGTCGTGGTTTTAGT 57.195 25.926 0.00 0.00 0.00 2.24
5853 6114 9.804758 TTCAAAATTATTGTCGTGGTTTTAGTT 57.195 25.926 0.00 0.00 0.00 2.24
5854 6115 9.453325 TCAAAATTATTGTCGTGGTTTTAGTTC 57.547 29.630 0.00 0.00 0.00 3.01
5855 6116 9.239002 CAAAATTATTGTCGTGGTTTTAGTTCA 57.761 29.630 0.00 0.00 0.00 3.18
5856 6117 9.804758 AAAATTATTGTCGTGGTTTTAGTTCAA 57.195 25.926 0.00 0.00 0.00 2.69
5857 6118 9.804758 AAATTATTGTCGTGGTTTTAGTTCAAA 57.195 25.926 0.00 0.00 0.00 2.69
5858 6119 9.974980 AATTATTGTCGTGGTTTTAGTTCAAAT 57.025 25.926 0.00 0.00 0.00 2.32
5859 6120 9.974980 ATTATTGTCGTGGTTTTAGTTCAAATT 57.025 25.926 0.00 0.00 0.00 1.82
5862 6123 6.961576 TGTCGTGGTTTTAGTTCAAATTAGG 58.038 36.000 0.00 0.00 0.00 2.69
5863 6124 6.016943 TGTCGTGGTTTTAGTTCAAATTAGGG 60.017 38.462 0.00 0.00 0.00 3.53
5864 6125 6.205270 GTCGTGGTTTTAGTTCAAATTAGGGA 59.795 38.462 0.00 0.00 0.00 4.20
5865 6126 6.428771 TCGTGGTTTTAGTTCAAATTAGGGAG 59.571 38.462 0.00 0.00 0.00 4.30
5866 6127 6.206048 CGTGGTTTTAGTTCAAATTAGGGAGT 59.794 38.462 0.00 0.00 0.00 3.85
5867 6128 7.388500 CGTGGTTTTAGTTCAAATTAGGGAGTA 59.612 37.037 0.00 0.00 0.00 2.59
5877 6138 8.880750 GTTCAAATTAGGGAGTAATGTGTACTC 58.119 37.037 5.16 5.16 37.54 2.59
5892 6153 5.220381 TGTGTACTCGATGAAACAAGACTC 58.780 41.667 0.00 0.00 0.00 3.36
5906 6168 4.962155 ACAAGACTCGAAACTGAGGAAAT 58.038 39.130 0.00 0.00 40.39 2.17
5911 6173 6.994221 AGACTCGAAACTGAGGAAATAAGAA 58.006 36.000 0.00 0.00 40.39 2.52
5921 6183 7.234355 ACTGAGGAAATAAGAACTGGAACATT 58.766 34.615 0.00 0.00 38.20 2.71
5922 6184 7.175641 ACTGAGGAAATAAGAACTGGAACATTG 59.824 37.037 0.00 0.00 38.20 2.82
5924 6186 6.314917 AGGAAATAAGAACTGGAACATTGGT 58.685 36.000 0.00 0.00 38.20 3.67
5925 6187 6.209391 AGGAAATAAGAACTGGAACATTGGTG 59.791 38.462 0.00 0.00 38.20 4.17
5926 6188 6.208599 GGAAATAAGAACTGGAACATTGGTGA 59.791 38.462 0.00 0.00 38.20 4.02
5927 6189 6.575162 AATAAGAACTGGAACATTGGTGAC 57.425 37.500 0.00 0.00 38.20 3.67
5953 6241 0.678048 AGTTTTGAGAGGCCGGATGC 60.678 55.000 5.05 0.00 40.16 3.91
6240 6528 0.173708 GGCGAAGTCGATGAAGGACT 59.826 55.000 4.59 0.00 46.27 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.539712 TTTTAGCATGAGTACAGATACAAGC 57.460 36.000 0.00 0.00 33.30 4.01
23 24 2.224784 GGTACGGTTCATGCTCGTTTTT 59.775 45.455 11.66 0.00 38.19 1.94
24 25 1.802365 GGTACGGTTCATGCTCGTTTT 59.198 47.619 11.66 0.00 38.19 2.43
25 26 1.270412 TGGTACGGTTCATGCTCGTTT 60.270 47.619 11.66 0.00 38.19 3.60
32 33 6.387041 TCTACTAATCTGGTACGGTTCATG 57.613 41.667 0.00 0.00 35.30 3.07
63 64 1.152510 TCAGTTGCGCGCATCTTAAA 58.847 45.000 35.25 22.96 0.00 1.52
66 67 1.020861 TGATCAGTTGCGCGCATCTT 61.021 50.000 35.25 24.97 0.00 2.40
67 68 1.448365 TGATCAGTTGCGCGCATCT 60.448 52.632 36.83 34.63 0.00 2.90
70 71 3.776849 CGTGATCAGTTGCGCGCA 61.777 61.111 33.09 33.09 0.00 6.09
110 111 0.397187 TCGAAAATGGGTGAACCGGA 59.603 50.000 9.46 0.00 44.64 5.14
166 175 4.039357 GGCTGCTGTGCTGTGCTG 62.039 66.667 0.00 0.00 0.00 4.41
167 176 4.574271 TGGCTGCTGTGCTGTGCT 62.574 61.111 0.00 0.00 0.00 4.40
168 177 4.039357 CTGGCTGCTGTGCTGTGC 62.039 66.667 0.00 0.00 0.00 4.57
169 178 4.039357 GCTGGCTGCTGTGCTGTG 62.039 66.667 9.31 0.00 38.95 3.66
170 179 4.574271 TGCTGGCTGCTGTGCTGT 62.574 61.111 17.45 0.00 43.37 4.40
171 180 3.738246 CTGCTGGCTGCTGTGCTG 61.738 66.667 17.45 2.46 43.37 4.41
176 185 2.258591 CTTTGCTGCTGGCTGCTG 59.741 61.111 21.19 17.16 43.37 4.41
202 211 1.065401 TCGTTTCTTTTGTGCTGCCTG 59.935 47.619 0.00 0.00 0.00 4.85
204 213 1.333619 TCTCGTTTCTTTTGTGCTGCC 59.666 47.619 0.00 0.00 0.00 4.85
230 239 2.680370 GGGGAGGTGCGGGAAGAAT 61.680 63.158 0.00 0.00 0.00 2.40
285 298 1.711060 CTCGTCTCGTCTCCCTGAGC 61.711 65.000 0.00 0.00 32.20 4.26
347 365 2.365768 GAGGAGGGTGGGAGGTCC 60.366 72.222 0.00 0.00 0.00 4.46
348 366 2.760385 CGAGGAGGGTGGGAGGTC 60.760 72.222 0.00 0.00 0.00 3.85
491 509 4.154347 GGAGGAGCAGCTGGACGG 62.154 72.222 17.12 0.00 0.00 4.79
500 518 2.039624 GTGGGAGGAGGAGGAGCA 59.960 66.667 0.00 0.00 0.00 4.26
501 519 2.766229 GGTGGGAGGAGGAGGAGC 60.766 72.222 0.00 0.00 0.00 4.70
502 520 1.382420 CTGGTGGGAGGAGGAGGAG 60.382 68.421 0.00 0.00 0.00 3.69
503 521 0.854039 TACTGGTGGGAGGAGGAGGA 60.854 60.000 0.00 0.00 0.00 3.71
504 522 0.688087 GTACTGGTGGGAGGAGGAGG 60.688 65.000 0.00 0.00 0.00 4.30
506 524 0.041238 CAGTACTGGTGGGAGGAGGA 59.959 60.000 15.49 0.00 0.00 3.71
509 527 1.612442 GGCAGTACTGGTGGGAGGA 60.612 63.158 23.95 0.00 0.00 3.71
510 528 1.613630 AGGCAGTACTGGTGGGAGG 60.614 63.158 23.95 0.00 0.00 4.30
511 529 0.616111 AGAGGCAGTACTGGTGGGAG 60.616 60.000 23.95 0.00 0.00 4.30
512 530 0.904865 CAGAGGCAGTACTGGTGGGA 60.905 60.000 23.95 0.00 0.00 4.37
513 531 1.599047 CAGAGGCAGTACTGGTGGG 59.401 63.158 23.95 0.00 0.00 4.61
516 534 0.322975 CAAGCAGAGGCAGTACTGGT 59.677 55.000 23.95 0.49 44.83 4.00
520 538 1.080995 CGAGCAAGCAGAGGCAGTAC 61.081 60.000 0.00 0.00 44.61 2.73
521 539 1.216444 CGAGCAAGCAGAGGCAGTA 59.784 57.895 0.00 0.00 44.61 2.74
522 540 2.047465 CGAGCAAGCAGAGGCAGT 60.047 61.111 0.00 0.00 44.61 4.40
527 547 1.347564 CAATCGCGAGCAAGCAGAG 59.652 57.895 16.66 0.00 36.85 3.35
528 548 2.743752 GCAATCGCGAGCAAGCAGA 61.744 57.895 16.66 3.09 36.85 4.26
679 723 2.167861 GCAGGAGATCCGCGTGAAC 61.168 63.158 4.92 0.74 42.08 3.18
743 787 2.045536 GAACAGAGCAGCAGGGGG 60.046 66.667 0.00 0.00 0.00 5.40
747 791 2.047465 AGCCGAACAGAGCAGCAG 60.047 61.111 0.00 0.00 0.00 4.24
748 792 2.357881 CAGCCGAACAGAGCAGCA 60.358 61.111 0.00 0.00 0.00 4.41
749 793 1.963338 AACAGCCGAACAGAGCAGC 60.963 57.895 0.00 0.00 0.00 5.25
750 794 0.882042 ACAACAGCCGAACAGAGCAG 60.882 55.000 0.00 0.00 0.00 4.24
751 795 0.463654 AACAACAGCCGAACAGAGCA 60.464 50.000 0.00 0.00 0.00 4.26
752 796 1.461127 CTAACAACAGCCGAACAGAGC 59.539 52.381 0.00 0.00 0.00 4.09
753 797 2.069273 CCTAACAACAGCCGAACAGAG 58.931 52.381 0.00 0.00 0.00 3.35
755 799 2.163818 TCCTAACAACAGCCGAACAG 57.836 50.000 0.00 0.00 0.00 3.16
758 802 1.274167 ACGATCCTAACAACAGCCGAA 59.726 47.619 0.00 0.00 0.00 4.30
759 803 0.892755 ACGATCCTAACAACAGCCGA 59.107 50.000 0.00 0.00 0.00 5.54
760 804 1.659098 GAACGATCCTAACAACAGCCG 59.341 52.381 0.00 0.00 0.00 5.52
761 805 1.659098 CGAACGATCCTAACAACAGCC 59.341 52.381 0.00 0.00 0.00 4.85
762 806 1.060698 GCGAACGATCCTAACAACAGC 59.939 52.381 0.00 0.00 0.00 4.40
763 807 2.345641 CAGCGAACGATCCTAACAACAG 59.654 50.000 0.00 0.00 0.00 3.16
764 808 2.288579 ACAGCGAACGATCCTAACAACA 60.289 45.455 0.00 0.00 0.00 3.33
874 918 0.322816 TTGCTGGTGAGATCCAAGCC 60.323 55.000 0.00 0.00 37.01 4.35
894 938 2.354259 GAAGGAGACCTGCACAATCAG 58.646 52.381 0.00 0.00 32.13 2.90
895 939 1.003580 GGAAGGAGACCTGCACAATCA 59.996 52.381 0.00 0.00 32.13 2.57
913 957 0.327287 TCCTAGTCCTCCTCCTCGGA 60.327 60.000 0.00 0.00 40.30 4.55
927 971 0.178964 CCTCCTCCTGCTCCTCCTAG 60.179 65.000 0.00 0.00 0.00 3.02
928 972 0.627768 TCCTCCTCCTGCTCCTCCTA 60.628 60.000 0.00 0.00 0.00 2.94
937 984 2.285180 CCTCCCCTCCTCCTCCTG 59.715 72.222 0.00 0.00 0.00 3.86
940 987 3.773154 AGGCCTCCCCTCCTCCTC 61.773 72.222 0.00 0.00 41.21 3.71
974 1024 0.965439 CTGCCGAATCTAGCTAGCCT 59.035 55.000 16.35 5.00 0.00 4.58
991 1041 0.962356 ACTTTCTTCATGGCGCCCTG 60.962 55.000 26.77 25.33 0.00 4.45
1023 1073 2.115910 ACGTACAGGTCCCGGACA 59.884 61.111 19.43 0.00 33.68 4.02
1061 1111 3.252215 ACAAGTCTCTCTCGAGTGAACAG 59.748 47.826 17.19 14.94 38.45 3.16
1068 1118 3.546002 ACGAAACAAGTCTCTCTCGAG 57.454 47.619 5.93 5.93 38.67 4.04
1079 1129 9.567848 AATACTATTATTGGCAAACGAAACAAG 57.432 29.630 3.01 2.27 0.00 3.16
1252 1302 1.127582 GCAGTGAGCAATCAGACGAAC 59.872 52.381 0.00 0.00 44.79 3.95
1304 1354 9.413048 GGTTAATATACAAGAGCAGACTCATAC 57.587 37.037 0.00 0.00 46.09 2.39
1311 1361 5.864418 ACGGGTTAATATACAAGAGCAGA 57.136 39.130 0.00 0.00 0.00 4.26
1383 1434 4.290622 GATCCATGCGGGCCCCAT 62.291 66.667 18.66 17.90 36.21 4.00
1392 1443 2.114838 GCCAGGAGGGATCCATGC 59.885 66.667 15.23 12.74 40.01 4.06
1611 1670 2.480555 CCATCCACTCGCGTTTGC 59.519 61.111 5.77 0.00 37.91 3.68
1629 1691 5.758296 TCCAACGCATTATCAAGATTAGTCC 59.242 40.000 0.00 0.00 0.00 3.85
1657 1719 6.038382 AGAGCAAAATACAGCATCAGATTCAG 59.962 38.462 0.00 0.00 0.00 3.02
1805 1877 2.089980 GATGCTTGTGTGGCTCTTGAT 58.910 47.619 0.00 0.00 0.00 2.57
1806 1878 1.072806 AGATGCTTGTGTGGCTCTTGA 59.927 47.619 0.00 0.00 0.00 3.02
1807 1879 1.467734 GAGATGCTTGTGTGGCTCTTG 59.532 52.381 0.00 0.00 0.00 3.02
1866 1938 5.468746 GTGCCTGCAATTCCGATTATACTTA 59.531 40.000 0.00 0.00 0.00 2.24
1869 1941 3.815401 AGTGCCTGCAATTCCGATTATAC 59.185 43.478 0.00 0.00 0.00 1.47
1943 2015 1.521681 GCTCTGGGATTTCCGTCGG 60.522 63.158 4.39 4.39 38.76 4.79
2046 2118 8.279800 TCGGATATTTGAAGCAAACATAATACG 58.720 33.333 0.00 0.00 36.13 3.06
2050 2122 7.351981 CGATCGGATATTTGAAGCAAACATAA 58.648 34.615 7.38 0.00 36.13 1.90
2104 2176 4.732285 ACACAGAAAACTAATCAGCACG 57.268 40.909 0.00 0.00 0.00 5.34
2157 2229 0.759346 GACTCCTGTGTGGTCCACTT 59.241 55.000 22.56 0.00 44.81 3.16
2178 2250 2.494059 CGGTCATTGTCATATCCACCC 58.506 52.381 0.00 0.00 0.00 4.61
2199 2271 1.194997 CTACCTCCTTCGTAGCGATCG 59.805 57.143 11.69 11.69 35.23 3.69
2256 2328 8.443953 TGTATCTGTCATCATCTCTATATCCG 57.556 38.462 0.00 0.00 0.00 4.18
2259 2331 9.187996 CCACTGTATCTGTCATCATCTCTATAT 57.812 37.037 0.00 0.00 0.00 0.86
2363 2435 4.080863 CAGGGTTGCTATTACTTCCTCTGT 60.081 45.833 0.00 0.00 0.00 3.41
2364 2436 4.162320 TCAGGGTTGCTATTACTTCCTCTG 59.838 45.833 0.00 0.00 0.00 3.35
2365 2437 4.362677 TCAGGGTTGCTATTACTTCCTCT 58.637 43.478 0.00 0.00 0.00 3.69
2409 2481 0.112606 CCTCATCCCCGTAGCTCCTA 59.887 60.000 0.00 0.00 0.00 2.94
2497 2569 4.215399 GTCTTGAAAATCATCGGTTGACCA 59.785 41.667 0.51 0.00 37.11 4.02
2505 2577 7.220683 ACACAAAAACAGTCTTGAAAATCATCG 59.779 33.333 2.98 0.00 0.00 3.84
2544 2616 4.278310 AGGATGTTTAACATAAGGGGCAC 58.722 43.478 10.82 0.00 39.27 5.01
2607 2679 4.883021 TTACCTCTCATCCTGAGTAGGT 57.117 45.455 21.26 21.26 46.61 3.08
2665 2737 1.207329 AGACGGCTAGCTACAAAAGGG 59.793 52.381 15.72 0.00 0.00 3.95
2670 2742 4.461781 AGAACTTAAGACGGCTAGCTACAA 59.538 41.667 15.72 0.17 0.00 2.41
2671 2743 4.015084 AGAACTTAAGACGGCTAGCTACA 58.985 43.478 15.72 0.00 0.00 2.74
2673 2745 4.578105 GGTAGAACTTAAGACGGCTAGCTA 59.422 45.833 15.72 0.00 0.00 3.32
2681 2753 6.643770 TGTTAAAGCAGGTAGAACTTAAGACG 59.356 38.462 10.09 0.00 0.00 4.18
2755 2827 1.929836 CTCCTGCAACATCTTCGTAGC 59.070 52.381 0.00 0.00 0.00 3.58
2768 2840 0.042581 TGTCCTGGGTATCTCCTGCA 59.957 55.000 0.00 0.00 36.25 4.41
2769 2841 1.134371 GTTGTCCTGGGTATCTCCTGC 60.134 57.143 0.00 0.00 36.25 4.85
2789 2861 3.534554 TCGTCACCTTTCATCATGATGG 58.465 45.455 30.54 19.41 39.24 3.51
2850 2922 2.173356 TGGATGGCTCAGATTTCCGATT 59.827 45.455 0.00 0.00 0.00 3.34
2856 2928 3.897657 ATGGATGGATGGCTCAGATTT 57.102 42.857 0.00 0.00 0.00 2.17
2914 2989 5.055265 TCTAGGTACAGAGGGAGAAGATG 57.945 47.826 0.00 0.00 0.00 2.90
2915 2990 5.044030 TGTTCTAGGTACAGAGGGAGAAGAT 60.044 44.000 0.00 0.00 0.00 2.40
2924 2999 5.172205 GGAAAGCTTGTTCTAGGTACAGAG 58.828 45.833 0.00 0.00 0.00 3.35
2930 3005 1.354705 GGGGGAAAGCTTGTTCTAGGT 59.645 52.381 0.00 0.00 0.00 3.08
3003 3078 1.601759 CAGGAGCAGGTGGTTGTGG 60.602 63.158 0.00 0.00 0.00 4.17
3038 3113 2.066340 ACCATTCGGTTCAGCAGGA 58.934 52.632 0.00 0.00 46.31 3.86
3099 3174 6.293407 GCACATTGACTGCTAAAAGAGTACAA 60.293 38.462 0.00 0.00 0.00 2.41
3203 3278 6.805271 CAGTTAGTCAAAATTCTTCCATGCAG 59.195 38.462 0.00 0.00 0.00 4.41
3337 3412 4.927425 CCAAACAAATCCATCTCAAAGCTG 59.073 41.667 0.00 0.00 0.00 4.24
3487 3562 3.133003 AGATTCATACCTCACTGAACCCG 59.867 47.826 0.00 0.00 34.43 5.28
3490 3565 6.166279 TCAACAGATTCATACCTCACTGAAC 58.834 40.000 0.00 0.00 34.43 3.18
3534 3617 2.609459 CCCATTATCATCGGCGCTAATC 59.391 50.000 7.64 0.00 0.00 1.75
3626 3709 7.440856 GTCAAATTTCAAGGAATTGTAAGGCAA 59.559 33.333 0.00 0.00 41.89 4.52
3792 3885 4.520492 ACAGTCATTCCATCACAAAAGGAC 59.480 41.667 0.00 0.00 34.77 3.85
3834 3927 2.838736 CCTGCGTTGGCTATTATGACT 58.161 47.619 0.00 0.00 40.82 3.41
3853 3946 3.505293 AGAGAAAAAGCTGAATGTCTGCC 59.495 43.478 3.79 0.00 41.50 4.85
3963 4056 1.734465 GGTCGCATTTGTCTGAGAAGG 59.266 52.381 0.00 0.00 0.00 3.46
4011 4104 2.648059 AGGATTTACATCTGCACCAGC 58.352 47.619 0.00 0.00 42.57 4.85
4190 4283 0.918983 CCTGGGAGGGAACATAAGCA 59.081 55.000 0.00 0.00 0.00 3.91
4223 4316 0.393944 ACATGGGAGCAGCATGAGTG 60.394 55.000 0.00 0.00 39.69 3.51
4327 4528 0.399833 TGGTGCAGCATGTTGAGGTA 59.600 50.000 15.99 0.00 39.31 3.08
4513 4750 2.258013 GCTGGTGCGGCAGTTTGTA 61.258 57.895 1.18 0.00 35.55 2.41
4580 4817 2.225091 ACCAGATGGCACTGAATTTGGA 60.225 45.455 15.61 0.00 39.94 3.53
4706 4943 5.931532 GTCAATGTATCAGACCAAACTGTG 58.068 41.667 0.00 0.00 38.79 3.66
4784 5023 1.211457 ACTGGAGAAATAGGCAGCCAG 59.789 52.381 15.80 0.00 46.30 4.85
4785 5024 1.065199 CACTGGAGAAATAGGCAGCCA 60.065 52.381 15.80 0.00 0.00 4.75
4786 5025 1.065126 ACACTGGAGAAATAGGCAGCC 60.065 52.381 1.84 1.84 0.00 4.85
4787 5026 2.284190 GACACTGGAGAAATAGGCAGC 58.716 52.381 0.00 0.00 0.00 5.25
4788 5027 2.237143 TGGACACTGGAGAAATAGGCAG 59.763 50.000 0.00 0.00 0.00 4.85
4791 5030 3.981071 TGTGGACACTGGAGAAATAGG 57.019 47.619 3.91 0.00 0.00 2.57
4793 5032 5.491070 CAGAATGTGGACACTGGAGAAATA 58.509 41.667 3.91 0.00 0.00 1.40
4794 5033 4.330250 CAGAATGTGGACACTGGAGAAAT 58.670 43.478 3.91 0.00 0.00 2.17
4795 5034 3.743521 CAGAATGTGGACACTGGAGAAA 58.256 45.455 3.91 0.00 0.00 2.52
4796 5035 3.407424 CAGAATGTGGACACTGGAGAA 57.593 47.619 3.91 0.00 0.00 2.87
4850 5089 5.814705 TGTGGATTGGTTTTTGCTGTAAAAG 59.185 36.000 3.96 0.00 39.29 2.27
4923 5162 6.018832 GTGCTTGAGAGATCTTCTTATCTTGC 60.019 42.308 0.00 1.50 36.33 4.01
4929 5168 4.774726 ACAGGTGCTTGAGAGATCTTCTTA 59.225 41.667 0.00 0.00 35.87 2.10
5077 5316 0.106719 ATTCCGCCACCATAACCAGG 60.107 55.000 0.00 0.00 0.00 4.45
5109 5348 0.265553 CCATTCCCATCCCCATTGGT 59.734 55.000 1.20 0.00 34.77 3.67
5152 5397 3.195632 GCCCATCCCCATCCCCAT 61.196 66.667 0.00 0.00 0.00 4.00
5168 5413 3.721370 ATCCCCATCGGTTGCTGGC 62.721 63.158 0.00 0.00 29.69 4.85
5198 5443 1.545211 CCCATGCCCATTCCCATCT 59.455 57.895 0.00 0.00 0.00 2.90
5199 5444 1.534717 CCCCATGCCCATTCCCATC 60.535 63.158 0.00 0.00 0.00 3.51
5349 5594 4.715523 TGGTTGTAGCCAGCGCCC 62.716 66.667 2.29 0.00 33.97 6.13
5559 5814 9.025041 TCAGTAGATACAGTATATCCAACATGG 57.975 37.037 0.00 0.00 39.43 3.66
5640 5895 6.127647 ACCAACCAAGCTTGTAATATCATGTG 60.128 38.462 24.35 7.46 0.00 3.21
5764 6019 5.518487 GGAGCGAACAGAAATTCAACAAAAA 59.482 36.000 0.00 0.00 0.00 1.94
5793 6054 7.564793 AGTACCAATCTGTGTATGCTAATCAA 58.435 34.615 0.00 0.00 0.00 2.57
5794 6055 7.124573 AGTACCAATCTGTGTATGCTAATCA 57.875 36.000 0.00 0.00 0.00 2.57
5796 6057 6.464465 GGGAGTACCAATCTGTGTATGCTAAT 60.464 42.308 0.00 0.00 39.85 1.73
5797 6058 5.163343 GGGAGTACCAATCTGTGTATGCTAA 60.163 44.000 0.00 0.00 39.85 3.09
5798 6059 4.344102 GGGAGTACCAATCTGTGTATGCTA 59.656 45.833 0.00 0.00 39.85 3.49
5799 6060 3.134804 GGGAGTACCAATCTGTGTATGCT 59.865 47.826 0.00 0.00 39.85 3.79
5804 6065 2.188817 GGAGGGAGTACCAATCTGTGT 58.811 52.381 0.00 0.00 43.89 3.72
5806 6067 1.273098 ACGGAGGGAGTACCAATCTGT 60.273 52.381 0.00 0.00 43.89 3.41
5807 6068 1.486211 ACGGAGGGAGTACCAATCTG 58.514 55.000 0.00 0.00 43.89 2.90
5808 6069 2.249309 AACGGAGGGAGTACCAATCT 57.751 50.000 0.00 0.00 43.89 2.40
5809 6070 2.235402 TGAAACGGAGGGAGTACCAATC 59.765 50.000 0.00 0.00 43.89 2.67
5812 6073 1.719529 TTGAAACGGAGGGAGTACCA 58.280 50.000 0.00 0.00 43.89 3.25
5814 6075 6.997239 ATAATTTTGAAACGGAGGGAGTAC 57.003 37.500 0.00 0.00 0.00 2.73
5817 6078 6.267496 ACAATAATTTTGAAACGGAGGGAG 57.733 37.500 7.18 0.00 0.00 4.30
5818 6079 5.106475 CGACAATAATTTTGAAACGGAGGGA 60.106 40.000 7.18 0.00 0.00 4.20
5819 6080 5.092781 CGACAATAATTTTGAAACGGAGGG 58.907 41.667 7.18 0.00 0.00 4.30
5820 6081 5.567534 CACGACAATAATTTTGAAACGGAGG 59.432 40.000 0.00 0.00 0.00 4.30
5821 6082 5.567534 CCACGACAATAATTTTGAAACGGAG 59.432 40.000 0.00 0.00 0.00 4.63
5822 6083 5.008811 ACCACGACAATAATTTTGAAACGGA 59.991 36.000 0.00 0.00 0.00 4.69
5823 6084 5.216648 ACCACGACAATAATTTTGAAACGG 58.783 37.500 0.00 0.00 0.00 4.44
5824 6085 6.741448 AACCACGACAATAATTTTGAAACG 57.259 33.333 0.00 0.00 0.00 3.60
5826 6087 9.804758 ACTAAAACCACGACAATAATTTTGAAA 57.195 25.926 0.00 0.00 0.00 2.69
5827 6088 9.804758 AACTAAAACCACGACAATAATTTTGAA 57.195 25.926 0.00 0.00 0.00 2.69
5828 6089 9.453325 GAACTAAAACCACGACAATAATTTTGA 57.547 29.630 0.00 0.00 0.00 2.69
5829 6090 9.239002 TGAACTAAAACCACGACAATAATTTTG 57.761 29.630 0.00 0.00 0.00 2.44
5830 6091 9.804758 TTGAACTAAAACCACGACAATAATTTT 57.195 25.926 0.00 0.00 0.00 1.82
5831 6092 9.804758 TTTGAACTAAAACCACGACAATAATTT 57.195 25.926 0.00 0.00 0.00 1.82
5832 6093 9.974980 ATTTGAACTAAAACCACGACAATAATT 57.025 25.926 0.00 0.00 0.00 1.40
5833 6094 9.974980 AATTTGAACTAAAACCACGACAATAAT 57.025 25.926 0.00 0.00 0.00 1.28
5836 6097 8.079809 CCTAATTTGAACTAAAACCACGACAAT 58.920 33.333 0.00 0.00 0.00 2.71
5837 6098 7.419204 CCTAATTTGAACTAAAACCACGACAA 58.581 34.615 0.00 0.00 0.00 3.18
5838 6099 6.016943 CCCTAATTTGAACTAAAACCACGACA 60.017 38.462 0.00 0.00 0.00 4.35
5839 6100 6.205270 TCCCTAATTTGAACTAAAACCACGAC 59.795 38.462 0.00 0.00 0.00 4.34
5840 6101 6.297582 TCCCTAATTTGAACTAAAACCACGA 58.702 36.000 0.00 0.00 0.00 4.35
5841 6102 6.206048 ACTCCCTAATTTGAACTAAAACCACG 59.794 38.462 0.00 0.00 0.00 4.94
5842 6103 7.520451 ACTCCCTAATTTGAACTAAAACCAC 57.480 36.000 0.00 0.00 0.00 4.16
5843 6104 9.816787 ATTACTCCCTAATTTGAACTAAAACCA 57.183 29.630 0.00 0.00 0.00 3.67
5847 6108 9.802039 ACACATTACTCCCTAATTTGAACTAAA 57.198 29.630 0.00 0.00 30.11 1.85
5849 6110 9.880157 GTACACATTACTCCCTAATTTGAACTA 57.120 33.333 0.00 0.00 30.11 2.24
5850 6111 8.603304 AGTACACATTACTCCCTAATTTGAACT 58.397 33.333 0.00 0.00 30.11 3.01
5851 6112 8.788325 AGTACACATTACTCCCTAATTTGAAC 57.212 34.615 0.00 0.00 30.11 3.18
5852 6113 7.762615 CGAGTACACATTACTCCCTAATTTGAA 59.237 37.037 5.98 0.00 40.48 2.69
5853 6114 7.123098 TCGAGTACACATTACTCCCTAATTTGA 59.877 37.037 5.98 0.00 40.48 2.69
5854 6115 7.262772 TCGAGTACACATTACTCCCTAATTTG 58.737 38.462 5.98 0.00 40.48 2.32
5855 6116 7.414222 TCGAGTACACATTACTCCCTAATTT 57.586 36.000 5.98 0.00 40.48 1.82
5856 6117 7.287005 TCATCGAGTACACATTACTCCCTAATT 59.713 37.037 5.98 0.00 40.48 1.40
5857 6118 6.776116 TCATCGAGTACACATTACTCCCTAAT 59.224 38.462 5.98 0.00 40.48 1.73
5858 6119 6.124340 TCATCGAGTACACATTACTCCCTAA 58.876 40.000 5.98 0.00 40.48 2.69
5859 6120 5.687780 TCATCGAGTACACATTACTCCCTA 58.312 41.667 5.98 0.00 40.48 3.53
5860 6121 4.533815 TCATCGAGTACACATTACTCCCT 58.466 43.478 5.98 0.00 40.48 4.20
5861 6122 4.913335 TCATCGAGTACACATTACTCCC 57.087 45.455 5.98 0.00 40.48 4.30
5862 6123 6.097356 TGTTTCATCGAGTACACATTACTCC 58.903 40.000 5.98 0.00 40.48 3.85
5863 6124 7.541091 TCTTGTTTCATCGAGTACACATTACTC 59.459 37.037 0.00 1.94 40.26 2.59
5864 6125 7.328737 GTCTTGTTTCATCGAGTACACATTACT 59.671 37.037 0.00 0.00 0.00 2.24
5865 6126 7.328737 AGTCTTGTTTCATCGAGTACACATTAC 59.671 37.037 0.00 0.00 0.00 1.89
5866 6127 7.375834 AGTCTTGTTTCATCGAGTACACATTA 58.624 34.615 0.00 0.00 0.00 1.90
5867 6128 6.223852 AGTCTTGTTTCATCGAGTACACATT 58.776 36.000 0.00 0.00 0.00 2.71
5870 6131 4.321217 CGAGTCTTGTTTCATCGAGTACAC 59.679 45.833 0.00 0.00 35.47 2.90
5877 6138 4.444388 TCAGTTTCGAGTCTTGTTTCATCG 59.556 41.667 0.00 0.00 34.80 3.84
5892 6153 5.932303 TCCAGTTCTTATTTCCTCAGTTTCG 59.068 40.000 0.00 0.00 0.00 3.46
5906 6168 5.042463 TGTCACCAATGTTCCAGTTCTTA 57.958 39.130 0.00 0.00 0.00 2.10
5911 6173 3.795688 AGATGTCACCAATGTTCCAGT 57.204 42.857 0.00 0.00 0.00 4.00
5921 6183 5.047021 CCTCTCAAAACTCTAGATGTCACCA 60.047 44.000 0.00 0.00 0.00 4.17
5922 6184 5.415221 CCTCTCAAAACTCTAGATGTCACC 58.585 45.833 0.00 0.00 0.00 4.02
5924 6186 4.081420 GGCCTCTCAAAACTCTAGATGTCA 60.081 45.833 0.00 0.00 0.00 3.58
5925 6187 4.438148 GGCCTCTCAAAACTCTAGATGTC 58.562 47.826 0.00 0.00 0.00 3.06
5926 6188 3.118956 CGGCCTCTCAAAACTCTAGATGT 60.119 47.826 0.00 0.00 0.00 3.06
5927 6189 3.452474 CGGCCTCTCAAAACTCTAGATG 58.548 50.000 0.00 0.00 0.00 2.90
5953 6241 3.121030 CCTTCCGGAACTGCTGCG 61.121 66.667 14.35 1.06 38.86 5.18
5965 6253 2.537560 CGCGACATGGATGCCTTCC 61.538 63.158 0.00 0.00 45.69 3.46
6029 6317 3.056328 GCCTTCCTTGTGGCGTCC 61.056 66.667 0.00 0.00 39.71 4.79
6113 6401 1.153881 GGTGCGTCTCCCGTTCTAC 60.154 63.158 0.00 0.00 39.32 2.59
6240 6528 0.443869 GTCGACGACGCCTACTACAA 59.556 55.000 12.94 0.00 39.58 2.41


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

AutoCloner maintained by Alex Coulton.