Multiple sequence alignment - TraesCS7B01G054700

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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 TraesCS7B01G054700 chr7B 100.000 4130 0 0 1 4130 57911617 57915746 0.000000e+00 7627.0
1 TraesCS7B01G054700 chr7B 93.999 3233 149 20 67 3265 58241995 58245216 0.000000e+00 4854.0
2 TraesCS7B01G054700 chr7B 85.130 538 70 7 3266 3801 57993661 57994190 3.630000e-150 542.0
3 TraesCS7B01G054700 chr7B 95.410 305 14 0 3826 4130 442168082 442168386 1.730000e-133 486.0
4 TraesCS7B01G054700 chrUn 90.610 3131 235 36 67 3180 91486111 91483023 0.000000e+00 4098.0
5 TraesCS7B01G054700 chr7A 89.732 3214 270 37 67 3265 91017800 91020968 0.000000e+00 4052.0
6 TraesCS7B01G054700 chr7A 88.972 2548 214 46 67 2594 105928167 105930667 0.000000e+00 3086.0
7 TraesCS7B01G054700 chr7A 88.878 1987 177 28 67 2040 104497943 104499898 0.000000e+00 2405.0
8 TraesCS7B01G054700 chr7A 90.208 1011 74 19 67 1067 104780056 104781051 0.000000e+00 1295.0
9 TraesCS7B01G054700 chr7A 90.226 931 77 6 2166 3092 104800624 104801544 0.000000e+00 1203.0
10 TraesCS7B01G054700 chr7A 88.514 949 100 7 361 1303 103997185 103998130 0.000000e+00 1140.0
11 TraesCS7B01G054700 chr7A 86.058 832 90 15 2441 3265 104535837 104536649 0.000000e+00 870.0
12 TraesCS7B01G054700 chr7A 86.217 682 67 3 2585 3265 105932391 105933046 0.000000e+00 713.0
13 TraesCS7B01G054700 chr7A 90.754 411 34 4 2050 2458 104507216 104507624 2.810000e-151 545.0
14 TraesCS7B01G054700 chr7A 93.333 180 10 1 67 244 103996936 103997115 8.800000e-67 265.0
15 TraesCS7B01G054700 chr7A 95.833 48 2 0 247 294 103997137 103997184 1.230000e-10 78.7
16 TraesCS7B01G054700 chr7D 90.185 3138 219 45 67 3166 101391129 101394215 0.000000e+00 4006.0
17 TraesCS7B01G054700 chr5D 86.387 1572 155 32 1073 2631 402711229 402712754 0.000000e+00 1663.0
18 TraesCS7B01G054700 chr5D 81.925 852 136 14 1061 1906 402417248 402418087 0.000000e+00 704.0
19 TraesCS7B01G054700 chr5D 81.925 852 136 14 1061 1906 402421089 402421928 0.000000e+00 704.0
20 TraesCS7B01G054700 chr5D 86.667 540 61 8 2630 3169 402712784 402713312 4.600000e-164 588.0
21 TraesCS7B01G054700 chr5D 82.114 123 20 2 2452 2574 402722802 402722922 2.030000e-18 104.0
22 TraesCS7B01G054700 chr5B 85.887 1573 163 31 1071 2630 482175777 482177303 0.000000e+00 1620.0
23 TraesCS7B01G054700 chr5B 81.893 845 136 17 1061 1900 481948679 481949511 0.000000e+00 697.0
24 TraesCS7B01G054700 chr5B 89.438 445 36 7 2725 3169 482177458 482177891 6.030000e-153 551.0
25 TraesCS7B01G054700 chr5B 96.333 300 10 1 3826 4125 404384933 404385231 3.710000e-135 492.0
26 TraesCS7B01G054700 chr5B 83.140 172 26 3 2452 2622 482180763 482180932 1.990000e-33 154.0
27 TraesCS7B01G054700 chr5A 89.485 447 39 5 2725 3169 508619884 508620324 3.610000e-155 558.0
28 TraesCS7B01G054700 chr5A 90.464 388 36 1 1907 2293 508619000 508619387 1.020000e-140 510.0
29 TraesCS7B01G054700 chr1B 95.541 314 12 2 3818 4130 320067929 320067617 6.160000e-138 501.0
30 TraesCS7B01G054700 chr4D 95.752 306 12 1 3826 4130 417885594 417885899 3.710000e-135 492.0
31 TraesCS7B01G054700 chr4D 95.410 305 12 1 3826 4130 417892313 417892615 6.210000e-133 484.0
32 TraesCS7B01G054700 chr3B 95.738 305 12 1 3826 4130 638267591 638267894 1.330000e-134 490.0
33 TraesCS7B01G054700 chr2B 95.724 304 11 2 3827 4130 45959788 45960089 4.800000e-134 488.0
34 TraesCS7B01G054700 chr2B 94.304 316 17 1 3816 4130 131667087 131667402 2.230000e-132 483.0
35 TraesCS7B01G054700 chr2B 80.583 103 12 5 3266 3360 773882055 773881953 5.730000e-09 73.1
36 TraesCS7B01G054700 chr4B 95.410 305 13 1 3826 4130 185256513 185256210 6.210000e-133 484.0
37 TraesCS7B01G054700 chr3D 84.290 331 41 7 3397 3719 371859965 371859638 3.100000e-81 313.0
38 TraesCS7B01G054700 chr3A 85.776 232 28 4 3488 3717 492685753 492685525 1.480000e-59 241.0
39 TraesCS7B01G054700 chr2A 87.603 121 15 0 122 242 741021038 741020918 1.550000e-29 141.0


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 TraesCS7B01G054700 chr7B 57911617 57915746 4129 False 7627.000000 7627 100.0000 1 4130 1 chr7B.!!$F1 4129
1 TraesCS7B01G054700 chr7B 58241995 58245216 3221 False 4854.000000 4854 93.9990 67 3265 1 chr7B.!!$F3 3198
2 TraesCS7B01G054700 chr7B 57993661 57994190 529 False 542.000000 542 85.1300 3266 3801 1 chr7B.!!$F2 535
3 TraesCS7B01G054700 chrUn 91483023 91486111 3088 True 4098.000000 4098 90.6100 67 3180 1 chrUn.!!$R1 3113
4 TraesCS7B01G054700 chr7A 91017800 91020968 3168 False 4052.000000 4052 89.7320 67 3265 1 chr7A.!!$F1 3198
5 TraesCS7B01G054700 chr7A 104497943 104499898 1955 False 2405.000000 2405 88.8780 67 2040 1 chr7A.!!$F2 1973
6 TraesCS7B01G054700 chr7A 105928167 105933046 4879 False 1899.500000 3086 87.5945 67 3265 2 chr7A.!!$F8 3198
7 TraesCS7B01G054700 chr7A 104780056 104781051 995 False 1295.000000 1295 90.2080 67 1067 1 chr7A.!!$F5 1000
8 TraesCS7B01G054700 chr7A 104800624 104801544 920 False 1203.000000 1203 90.2260 2166 3092 1 chr7A.!!$F6 926
9 TraesCS7B01G054700 chr7A 104535837 104536649 812 False 870.000000 870 86.0580 2441 3265 1 chr7A.!!$F4 824
10 TraesCS7B01G054700 chr7A 103996936 103998130 1194 False 494.566667 1140 92.5600 67 1303 3 chr7A.!!$F7 1236
11 TraesCS7B01G054700 chr7D 101391129 101394215 3086 False 4006.000000 4006 90.1850 67 3166 1 chr7D.!!$F1 3099
12 TraesCS7B01G054700 chr5D 402711229 402713312 2083 False 1125.500000 1663 86.5270 1073 3169 2 chr5D.!!$F3 2096
13 TraesCS7B01G054700 chr5D 402417248 402421928 4680 False 704.000000 704 81.9250 1061 1906 2 chr5D.!!$F2 845
14 TraesCS7B01G054700 chr5B 482175777 482180932 5155 False 775.000000 1620 86.1550 1071 3169 3 chr5B.!!$F3 2098
15 TraesCS7B01G054700 chr5B 481948679 481949511 832 False 697.000000 697 81.8930 1061 1900 1 chr5B.!!$F2 839
16 TraesCS7B01G054700 chr5A 508619000 508620324 1324 False 534.000000 558 89.9745 1907 3169 2 chr5A.!!$F1 1262

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
316 341 0.096976 GTGTGTGTGTGTGTGTCTGC 59.903 55.0 0.00 0.00 0.00 4.26 F
950 1015 0.098200 CTCGCCGTCGTAATCACAGA 59.902 55.0 0.00 0.00 36.96 3.41 F
2786 8641 0.970640 ATGTACCACGCCAGTGTACA 59.029 50.0 4.42 4.42 46.56 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 6145 1.074471 AGTATCCAGTCGGCCCCAT 60.074 57.895 0.00 0.0 0.00 4.00 R
2908 8769 3.450904 TGCATCAGGTACCCTACTCTTT 58.549 45.455 8.74 0.0 29.64 2.52 R
4077 12159 0.033504 GCTTCTTGACGTCCACTCCA 59.966 55.000 14.12 0.0 0.00 3.86 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
277 302 2.911484 TGTGTGTGCAGTGAACATGTA 58.089 42.857 7.35 0.00 0.00 2.29
313 338 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
314 339 1.270571 TGTGTGTGTGTGTGTGTGTCT 60.271 47.619 0.00 0.00 0.00 3.41
316 341 0.096976 GTGTGTGTGTGTGTGTCTGC 59.903 55.000 0.00 0.00 0.00 4.26
318 343 1.079474 TGTGTGTGTGTGTCTGCGT 60.079 52.632 0.00 0.00 0.00 5.24
319 344 1.348250 GTGTGTGTGTGTCTGCGTG 59.652 57.895 0.00 0.00 0.00 5.34
320 345 1.079474 TGTGTGTGTGTCTGCGTGT 60.079 52.632 0.00 0.00 0.00 4.49
321 346 1.348250 GTGTGTGTGTCTGCGTGTG 59.652 57.895 0.00 0.00 0.00 3.82
322 347 1.079474 TGTGTGTGTCTGCGTGTGT 60.079 52.632 0.00 0.00 0.00 3.72
323 348 1.348250 GTGTGTGTCTGCGTGTGTG 59.652 57.895 0.00 0.00 0.00 3.82
324 349 1.079474 TGTGTGTCTGCGTGTGTGT 60.079 52.632 0.00 0.00 0.00 3.72
325 350 1.348250 GTGTGTCTGCGTGTGTGTG 59.652 57.895 0.00 0.00 0.00 3.82
326 351 1.079474 TGTGTCTGCGTGTGTGTGT 60.079 52.632 0.00 0.00 0.00 3.72
339 370 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
351 382 4.122776 GTGTGTGTGTTTGTGAGAGAGAT 58.877 43.478 0.00 0.00 0.00 2.75
359 390 6.889177 TGTGTTTGTGAGAGAGATAGAGAGAT 59.111 38.462 0.00 0.00 0.00 2.75
421 460 0.909623 GCCAGCCCCTTAGTGTTCTA 59.090 55.000 0.00 0.00 0.00 2.10
460 501 1.577328 CTCTTTCCGCACGCCAACAT 61.577 55.000 0.00 0.00 0.00 2.71
461 502 0.320858 TCTTTCCGCACGCCAACATA 60.321 50.000 0.00 0.00 0.00 2.29
495 536 1.078848 GGCAGATCTGGTGAGCGTT 60.079 57.895 23.89 0.00 33.18 4.84
554 595 0.107214 GGAATCAACCAGATCCGCCA 60.107 55.000 0.00 0.00 35.39 5.69
739 802 1.614226 CGTAGAAACCCCCTCCCCA 60.614 63.158 0.00 0.00 0.00 4.96
763 826 2.032528 CTCTTTCCAGCCCACGCA 59.967 61.111 0.00 0.00 37.52 5.24
924 989 1.228367 CCTGCAACTGCTCAACCCT 60.228 57.895 2.95 0.00 42.66 4.34
948 1013 1.515519 GCTCGCCGTCGTAATCACA 60.516 57.895 0.00 0.00 36.96 3.58
949 1014 1.472276 GCTCGCCGTCGTAATCACAG 61.472 60.000 0.00 0.00 36.96 3.66
950 1015 0.098200 CTCGCCGTCGTAATCACAGA 59.902 55.000 0.00 0.00 36.96 3.41
1014 1079 1.742761 ATTGCTCTGACCCAACGATG 58.257 50.000 0.00 0.00 0.00 3.84
1017 1082 1.599047 CTCTGACCCAACGATGCCT 59.401 57.895 0.00 0.00 0.00 4.75
1261 1331 4.003648 ACTTAAGATCCGTGCTTTGGAAG 58.996 43.478 10.09 0.00 39.39 3.46
1315 1386 3.850173 TCAGATAAACCTACCCAAGCCTT 59.150 43.478 0.00 0.00 0.00 4.35
1369 1441 7.074653 TCCCAAGTTCTTACTCTATGTGTTT 57.925 36.000 0.00 0.00 31.99 2.83
1437 1509 4.512944 GCCAGATAGATGATTCGCTGAAAA 59.487 41.667 0.00 0.00 0.00 2.29
1803 5721 6.558771 TGTATCACACTTTTCATTGTGGAG 57.441 37.500 2.10 0.00 42.88 3.86
2064 5996 3.009363 TCATCTTGCTTTGGAGATGGTGA 59.991 43.478 11.99 0.00 45.86 4.02
2212 6145 3.132467 CAGGAGCTTGATCTGATCTGTCA 59.868 47.826 17.82 0.00 0.00 3.58
2220 6153 1.227764 CTGATCTGTCATGGGGCCG 60.228 63.158 0.00 0.00 32.98 6.13
2254 6187 7.182206 ACTCCCAAGATACACAGTATTACCTTT 59.818 37.037 0.00 0.00 0.00 3.11
2425 6447 5.480772 TCGAATTCAATCCCTATAGGTCCTC 59.519 44.000 17.72 2.30 36.75 3.71
2435 6457 4.382362 CCCTATAGGTCCTCGTTCGTTTTT 60.382 45.833 17.72 0.00 0.00 1.94
2493 6515 5.294552 GCTAACCATGCTTAGACGAAAAGAT 59.705 40.000 11.28 0.00 0.00 2.40
2516 6538 9.471702 AGATTTTTCAAGGTGTCAGATCAATAT 57.528 29.630 0.00 0.00 0.00 1.28
2520 6542 5.687780 TCAAGGTGTCAGATCAATATGCAT 58.312 37.500 3.79 3.79 0.00 3.96
2522 6544 5.300411 AGGTGTCAGATCAATATGCATGA 57.700 39.130 10.16 0.00 0.00 3.07
2551 6576 6.536582 GCTCTCTTGATGTCAAAGTAGCAATA 59.463 38.462 13.54 0.00 35.15 1.90
2637 8427 9.953697 AACATTCGATCAGTAGTTATCTTAGAC 57.046 33.333 0.00 0.00 0.00 2.59
2786 8641 0.970640 ATGTACCACGCCAGTGTACA 59.029 50.000 4.42 4.42 46.56 2.90
2908 8769 1.238439 CAAGAAGGCGGAAGAGCAAA 58.762 50.000 0.00 0.00 39.27 3.68
2954 8815 6.884280 AATCACCTTGTTAAACTCCTGAAG 57.116 37.500 0.00 0.00 0.00 3.02
2962 8823 0.698818 AAACTCCTGAAGCCGGGAAT 59.301 50.000 2.18 0.00 46.70 3.01
2964 8825 0.909610 ACTCCTGAAGCCGGGAATCA 60.910 55.000 2.18 0.00 46.70 2.57
2967 8828 1.078214 CTGAAGCCGGGAATCAGCA 60.078 57.895 14.13 0.00 34.72 4.41
3054 8917 4.392138 GTGTTGGTACCTTGTTGATAGCTC 59.608 45.833 14.36 0.00 0.00 4.09
3101 8967 6.491745 TCCATGTGTTGTTGTTGGTATTATGT 59.508 34.615 0.00 0.00 0.00 2.29
3169 9037 4.002982 TCTATGATGTTTCAGTTGCGCTT 58.997 39.130 9.73 0.00 34.73 4.68
3180 9048 8.937884 TGTTTCAGTTGCGCTTACTATTTTATA 58.062 29.630 9.73 0.00 0.00 0.98
3190 9058 6.091713 CGCTTACTATTTTATAATGGGACCCG 59.908 42.308 5.91 0.00 0.00 5.28
3207 9075 1.736282 CGCACTGATGTGTACCGCA 60.736 57.895 0.00 0.00 45.44 5.69
3232 9100 3.349006 CGAGGCTTGCGTGTGCTT 61.349 61.111 0.00 0.00 43.34 3.91
3236 9104 2.425773 GCTTGCGTGTGCTTGACG 60.426 61.111 0.00 0.00 43.34 4.35
3242 9110 2.546321 GTGTGCTTGACGTCAGCG 59.454 61.111 24.75 18.80 44.93 5.18
3243 9111 2.661537 TGTGCTTGACGTCAGCGG 60.662 61.111 24.75 17.87 43.45 5.52
3305 9173 2.039879 CCCCTAGCTCTACCTCTCTCTC 59.960 59.091 0.00 0.00 0.00 3.20
3306 9174 2.979678 CCCTAGCTCTACCTCTCTCTCT 59.020 54.545 0.00 0.00 0.00 3.10
3312 9180 3.244249 GCTCTACCTCTCTCTCTCTCTCC 60.244 56.522 0.00 0.00 0.00 3.71
3321 9189 6.270000 CCTCTCTCTCTCTCTCCTCTATAACA 59.730 46.154 0.00 0.00 0.00 2.41
3332 9200 5.182190 TCTCCTCTATAACATTGCTCTAGCG 59.818 44.000 0.00 0.00 45.83 4.26
3333 9201 3.923461 CCTCTATAACATTGCTCTAGCGC 59.077 47.826 0.00 0.00 45.83 5.92
3340 9208 0.807667 ATTGCTCTAGCGCGAACCAG 60.808 55.000 12.10 0.00 45.83 4.00
3344 9212 0.452184 CTCTAGCGCGAACCAGAAGA 59.548 55.000 12.10 0.00 0.00 2.87
3352 9220 1.673329 GCGAACCAGAAGAAGGAGGAC 60.673 57.143 0.00 0.00 0.00 3.85
3375 9243 2.579873 AGAAGCAAACACAGAGCACAT 58.420 42.857 0.00 0.00 0.00 3.21
3385 9253 1.970640 ACAGAGCACATAGTGGACACA 59.029 47.619 5.14 0.00 33.64 3.72
3387 9255 2.738846 CAGAGCACATAGTGGACACAAC 59.261 50.000 5.14 0.00 33.64 3.32
3388 9256 2.368548 AGAGCACATAGTGGACACAACA 59.631 45.455 5.14 0.00 33.64 3.33
3395 9263 4.578928 ACATAGTGGACACAACAAGGTTTC 59.421 41.667 5.14 0.00 0.00 2.78
3398 9266 0.666374 GGACACAACAAGGTTTCCCG 59.334 55.000 0.00 0.00 32.61 5.14
3400 9268 0.753848 ACACAACAAGGTTTCCCGGG 60.754 55.000 16.85 16.85 35.12 5.73
3437 9305 1.463528 CGCCCGAACGACATTTTTCTC 60.464 52.381 0.00 0.00 34.06 2.87
3467 9335 1.069765 CACGAACTCAGCCCACACT 59.930 57.895 0.00 0.00 0.00 3.55
3476 9381 3.380320 ACTCAGCCCACACTTGTTAAAAC 59.620 43.478 0.00 0.00 0.00 2.43
3510 9415 1.974028 TCTTTATACCCTGGGCCACA 58.026 50.000 14.08 0.00 0.00 4.17
3512 9417 2.856231 TCTTTATACCCTGGGCCACATT 59.144 45.455 14.08 0.00 0.00 2.71
3540 9445 4.016706 CCCCACGTCCCAGTCCAC 62.017 72.222 0.00 0.00 0.00 4.02
3567 9472 3.965539 CTTGGTCCAGCCCGCTCTG 62.966 68.421 0.00 0.00 36.04 3.35
3628 9533 1.973812 GCCTGCCTTGGACCAACTC 60.974 63.158 1.69 0.00 0.00 3.01
3630 9535 1.763770 CTGCCTTGGACCAACTCCT 59.236 57.895 1.69 0.00 40.26 3.69
3631 9536 0.322008 CTGCCTTGGACCAACTCCTC 60.322 60.000 1.69 0.00 40.26 3.71
3642 9547 1.229400 AACTCCTCGCACCCCCTAA 60.229 57.895 0.00 0.00 0.00 2.69
3647 9552 1.048724 CCTCGCACCCCCTAATCTCA 61.049 60.000 0.00 0.00 0.00 3.27
3654 9559 1.916181 ACCCCCTAATCTCACCAACAG 59.084 52.381 0.00 0.00 0.00 3.16
3662 9567 1.896220 TCTCACCAACAGAATGCACC 58.104 50.000 0.00 0.00 42.53 5.01
3667 9572 2.485426 CACCAACAGAATGCACCTACAG 59.515 50.000 0.00 0.00 42.53 2.74
3668 9573 2.106511 ACCAACAGAATGCACCTACAGT 59.893 45.455 0.00 0.00 42.53 3.55
3674 9579 1.014044 AATGCACCTACAGTCACGCG 61.014 55.000 3.53 3.53 0.00 6.01
3677 9582 1.446099 CACCTACAGTCACGCGCAT 60.446 57.895 5.73 0.00 0.00 4.73
3683 9892 1.736282 CAGTCACGCGCATGGTGTA 60.736 57.895 5.73 0.00 37.23 2.90
3741 10302 0.179070 ACATGCACACGTACACCACA 60.179 50.000 0.00 0.00 0.00 4.17
3746 10307 0.387929 CACACGTACACCACAGACCT 59.612 55.000 0.00 0.00 0.00 3.85
3748 10309 0.671796 CACGTACACCACAGACCTGA 59.328 55.000 3.76 0.00 0.00 3.86
3751 10312 0.666577 GTACACCACAGACCTGACGC 60.667 60.000 3.76 0.00 0.00 5.19
3752 10313 1.110518 TACACCACAGACCTGACGCA 61.111 55.000 3.76 0.00 0.00 5.24
3816 11437 2.519302 GCCATGGCCACGGCTTAT 60.519 61.111 35.01 0.00 45.29 1.73
3818 11439 1.675720 GCCATGGCCACGGCTTATTT 61.676 55.000 35.01 0.00 45.29 1.40
3819 11440 0.102844 CCATGGCCACGGCTTATTTG 59.897 55.000 8.16 0.00 41.60 2.32
3820 11441 0.528249 CATGGCCACGGCTTATTTGC 60.528 55.000 8.16 0.00 41.60 3.68
3831 11452 3.900941 GGCTTATTTGCCCAATGATACG 58.099 45.455 0.00 0.00 46.82 3.06
3832 11453 3.317993 GGCTTATTTGCCCAATGATACGT 59.682 43.478 0.00 0.00 46.82 3.57
3833 11454 4.537015 GCTTATTTGCCCAATGATACGTC 58.463 43.478 0.00 0.00 0.00 4.34
3834 11455 4.275936 GCTTATTTGCCCAATGATACGTCT 59.724 41.667 0.00 0.00 0.00 4.18
3835 11456 5.560953 GCTTATTTGCCCAATGATACGTCTC 60.561 44.000 0.00 0.00 0.00 3.36
3836 11457 2.325583 TTGCCCAATGATACGTCTCC 57.674 50.000 0.00 0.00 0.00 3.71
3837 11458 1.199615 TGCCCAATGATACGTCTCCA 58.800 50.000 0.00 0.00 0.00 3.86
3838 11459 1.557371 TGCCCAATGATACGTCTCCAA 59.443 47.619 0.00 0.00 0.00 3.53
3839 11460 1.940613 GCCCAATGATACGTCTCCAAC 59.059 52.381 0.00 0.00 0.00 3.77
3884 11624 9.860650 TGTTCCATGCTATTATATTACCTGTTT 57.139 29.630 0.00 0.00 0.00 2.83
3887 11627 9.295825 TCCATGCTATTATATTACCTGTTTTGG 57.704 33.333 0.00 0.00 0.00 3.28
3888 11628 9.295825 CCATGCTATTATATTACCTGTTTTGGA 57.704 33.333 0.00 0.00 0.00 3.53
3891 11631 9.860650 TGCTATTATATTACCTGTTTTGGATGT 57.139 29.630 0.00 0.00 0.00 3.06
3898 11638 6.597832 TTACCTGTTTTGGATGTTTATGGG 57.402 37.500 0.00 0.00 0.00 4.00
3902 11642 5.512921 CCTGTTTTGGATGTTTATGGGCTTT 60.513 40.000 0.00 0.00 0.00 3.51
3903 11643 6.295575 CCTGTTTTGGATGTTTATGGGCTTTA 60.296 38.462 0.00 0.00 0.00 1.85
3904 11644 6.459923 TGTTTTGGATGTTTATGGGCTTTAC 58.540 36.000 0.00 0.00 0.00 2.01
3905 11645 6.268847 TGTTTTGGATGTTTATGGGCTTTACT 59.731 34.615 0.00 0.00 0.00 2.24
3907 11647 6.926630 TTGGATGTTTATGGGCTTTACTTT 57.073 33.333 0.00 0.00 0.00 2.66
3921 12003 9.742144 TGGGCTTTACTTTACACTTTTATATCA 57.258 29.630 0.00 0.00 0.00 2.15
3944 12026 7.170277 TCATTTTTGGGACTAACCTACTAACC 58.830 38.462 0.00 0.00 38.98 2.85
3945 12027 4.806640 TTTGGGACTAACCTACTAACCG 57.193 45.455 0.00 0.00 38.98 4.44
3946 12028 2.738743 TGGGACTAACCTACTAACCGG 58.261 52.381 0.00 0.00 38.98 5.28
3950 12032 4.805044 GGACTAACCTACTAACCGGAGGC 61.805 56.522 9.46 0.00 44.44 4.70
3966 12048 2.124320 GCCCAGCCCGAATTGCTA 60.124 61.111 0.00 0.00 36.81 3.49
3967 12049 1.529244 GCCCAGCCCGAATTGCTAT 60.529 57.895 0.00 0.00 36.81 2.97
3968 12050 1.109323 GCCCAGCCCGAATTGCTATT 61.109 55.000 0.00 0.00 36.81 1.73
3969 12051 1.402787 CCCAGCCCGAATTGCTATTT 58.597 50.000 0.00 0.00 36.81 1.40
3970 12052 1.756538 CCCAGCCCGAATTGCTATTTT 59.243 47.619 0.00 0.00 36.81 1.82
3971 12053 2.168313 CCCAGCCCGAATTGCTATTTTT 59.832 45.455 0.00 0.00 36.81 1.94
3994 12076 5.759506 TTTTGCCTATTTCAGTGTTTCGA 57.240 34.783 0.00 0.00 0.00 3.71
3998 12080 5.060506 TGCCTATTTCAGTGTTTCGAAGAA 58.939 37.500 0.00 0.00 45.90 2.52
3999 12081 5.529430 TGCCTATTTCAGTGTTTCGAAGAAA 59.471 36.000 10.72 10.72 45.90 2.52
4010 12092 8.289618 CAGTGTTTCGAAGAAAAGGAATATCAA 58.710 33.333 0.00 0.00 45.90 2.57
4012 12094 9.458374 GTGTTTCGAAGAAAAGGAATATCAAAA 57.542 29.630 0.00 0.00 45.90 2.44
4014 12096 9.129209 GTTTCGAAGAAAAGGAATATCAAAAGG 57.871 33.333 0.00 0.00 45.90 3.11
4016 12098 8.268850 TCGAAGAAAAGGAATATCAAAAGGAG 57.731 34.615 0.00 0.00 0.00 3.69
4017 12099 7.883311 TCGAAGAAAAGGAATATCAAAAGGAGT 59.117 33.333 0.00 0.00 0.00 3.85
4018 12100 8.178313 CGAAGAAAAGGAATATCAAAAGGAGTC 58.822 37.037 0.00 0.00 0.00 3.36
4019 12101 7.946381 AGAAAAGGAATATCAAAAGGAGTCC 57.054 36.000 0.00 0.00 0.00 3.85
4020 12102 7.470192 AGAAAAGGAATATCAAAAGGAGTCCA 58.530 34.615 12.86 0.00 30.78 4.02
4021 12103 7.950124 AGAAAAGGAATATCAAAAGGAGTCCAA 59.050 33.333 12.86 0.00 30.78 3.53
4022 12104 8.491045 AAAAGGAATATCAAAAGGAGTCCAAA 57.509 30.769 12.86 0.00 30.78 3.28
4023 12105 7.468141 AAGGAATATCAAAAGGAGTCCAAAC 57.532 36.000 12.86 0.00 30.78 2.93
4025 12107 5.163652 GGAATATCAAAAGGAGTCCAAACGG 60.164 44.000 12.86 0.00 0.00 4.44
4026 12108 3.502123 ATCAAAAGGAGTCCAAACGGA 57.498 42.857 12.86 2.49 0.00 4.69
4027 12109 3.284793 TCAAAAGGAGTCCAAACGGAA 57.715 42.857 12.86 0.00 33.16 4.30
4028 12110 3.827722 TCAAAAGGAGTCCAAACGGAAT 58.172 40.909 12.86 0.00 33.16 3.01
4029 12111 3.568007 TCAAAAGGAGTCCAAACGGAATG 59.432 43.478 12.86 0.00 33.16 2.67
4030 12112 3.502123 AAAGGAGTCCAAACGGAATGA 57.498 42.857 12.86 0.00 33.16 2.57
4031 12113 3.502123 AAGGAGTCCAAACGGAATGAA 57.498 42.857 12.86 0.00 33.16 2.57
4032 12114 3.502123 AGGAGTCCAAACGGAATGAAA 57.498 42.857 12.86 0.00 33.16 2.69
4035 12117 3.146847 GAGTCCAAACGGAATGAAACCT 58.853 45.455 0.00 0.00 33.16 3.50
4036 12118 3.562182 AGTCCAAACGGAATGAAACCTT 58.438 40.909 0.00 0.00 33.16 3.50
4037 12119 3.958147 AGTCCAAACGGAATGAAACCTTT 59.042 39.130 0.00 0.00 33.16 3.11
4038 12120 4.048504 GTCCAAACGGAATGAAACCTTTG 58.951 43.478 0.00 0.00 33.16 2.77
4039 12121 3.068873 TCCAAACGGAATGAAACCTTTGG 59.931 43.478 2.76 2.76 41.41 3.28
4040 12122 3.389221 CAAACGGAATGAAACCTTTGGG 58.611 45.455 0.00 0.00 38.88 4.12
4042 12124 2.514803 ACGGAATGAAACCTTTGGGAG 58.485 47.619 0.00 0.00 36.25 4.30
4043 12125 1.202348 CGGAATGAAACCTTTGGGAGC 59.798 52.381 0.00 0.00 36.25 4.70
4044 12126 1.202348 GGAATGAAACCTTTGGGAGCG 59.798 52.381 0.00 0.00 36.25 5.03
4045 12127 2.159382 GAATGAAACCTTTGGGAGCGA 58.841 47.619 0.00 0.00 36.25 4.93
4046 12128 2.514458 ATGAAACCTTTGGGAGCGAT 57.486 45.000 0.00 0.00 36.25 4.58
4047 12129 3.644966 ATGAAACCTTTGGGAGCGATA 57.355 42.857 0.00 0.00 36.25 2.92
4048 12130 3.644966 TGAAACCTTTGGGAGCGATAT 57.355 42.857 0.00 0.00 36.25 1.63
4051 12133 4.770010 TGAAACCTTTGGGAGCGATATTTT 59.230 37.500 0.00 0.00 36.25 1.82
4053 12135 6.434652 TGAAACCTTTGGGAGCGATATTTTTA 59.565 34.615 0.00 0.00 36.25 1.52
4054 12136 6.451064 AACCTTTGGGAGCGATATTTTTAG 57.549 37.500 0.00 0.00 36.25 1.85
4055 12137 5.751586 ACCTTTGGGAGCGATATTTTTAGA 58.248 37.500 0.00 0.00 36.25 2.10
4058 12140 6.094881 CCTTTGGGAGCGATATTTTTAGAACA 59.905 38.462 0.00 0.00 33.58 3.18
4059 12141 7.362574 CCTTTGGGAGCGATATTTTTAGAACAA 60.363 37.037 0.00 0.00 33.58 2.83
4061 12143 7.639113 TGGGAGCGATATTTTTAGAACAAAT 57.361 32.000 0.00 0.00 0.00 2.32
4062 12144 7.479980 TGGGAGCGATATTTTTAGAACAAATG 58.520 34.615 0.00 0.00 0.00 2.32
4063 12145 6.417930 GGGAGCGATATTTTTAGAACAAATGC 59.582 38.462 0.00 0.00 0.00 3.56
4064 12146 6.972328 GGAGCGATATTTTTAGAACAAATGCA 59.028 34.615 0.00 0.00 0.00 3.96
4065 12147 7.487829 GGAGCGATATTTTTAGAACAAATGCAA 59.512 33.333 0.00 0.00 0.00 4.08
4066 12148 8.931385 AGCGATATTTTTAGAACAAATGCAAT 57.069 26.923 0.00 0.00 0.00 3.56
4067 12149 9.023967 AGCGATATTTTTAGAACAAATGCAATC 57.976 29.630 0.00 0.00 0.00 2.67
4068 12150 8.268738 GCGATATTTTTAGAACAAATGCAATCC 58.731 33.333 0.00 0.00 0.00 3.01
4069 12151 9.299963 CGATATTTTTAGAACAAATGCAATCCA 57.700 29.630 0.00 0.00 0.00 3.41
4071 12153 7.910441 ATTTTTAGAACAAATGCAATCCAGG 57.090 32.000 0.00 0.00 0.00 4.45
4072 12154 6.662865 TTTTAGAACAAATGCAATCCAGGA 57.337 33.333 0.00 0.00 0.00 3.86
4074 12156 4.038271 AGAACAAATGCAATCCAGGAGA 57.962 40.909 0.00 0.00 0.00 3.71
4075 12157 3.760684 AGAACAAATGCAATCCAGGAGAC 59.239 43.478 0.00 0.00 0.00 3.36
4076 12158 3.446442 ACAAATGCAATCCAGGAGACT 57.554 42.857 0.00 0.00 46.44 3.24
4077 12159 3.771216 ACAAATGCAATCCAGGAGACTT 58.229 40.909 0.00 0.00 40.21 3.01
4078 12160 3.508793 ACAAATGCAATCCAGGAGACTTG 59.491 43.478 0.00 0.00 40.21 3.16
4079 12161 2.431954 ATGCAATCCAGGAGACTTGG 57.568 50.000 0.00 0.00 40.21 3.61
4080 12162 1.361204 TGCAATCCAGGAGACTTGGA 58.639 50.000 5.16 5.16 40.21 3.53
4081 12163 1.280133 TGCAATCCAGGAGACTTGGAG 59.720 52.381 8.43 0.00 39.78 3.86
4083 12165 2.938756 GCAATCCAGGAGACTTGGAGTG 60.939 54.545 20.22 20.22 46.73 3.51
4085 12167 0.487325 TCCAGGAGACTTGGAGTGGA 59.513 55.000 0.00 0.00 40.21 4.02
4086 12168 0.610687 CCAGGAGACTTGGAGTGGAC 59.389 60.000 0.00 0.00 40.21 4.02
4087 12169 0.244994 CAGGAGACTTGGAGTGGACG 59.755 60.000 0.00 0.00 40.21 4.79
4088 12170 0.178958 AGGAGACTTGGAGTGGACGT 60.179 55.000 0.00 0.00 37.44 4.34
4089 12171 0.244178 GGAGACTTGGAGTGGACGTC 59.756 60.000 7.13 7.13 0.00 4.34
4091 12173 1.340248 GAGACTTGGAGTGGACGTCAA 59.660 52.381 18.91 2.10 0.00 3.18
4092 12174 1.341531 AGACTTGGAGTGGACGTCAAG 59.658 52.381 18.91 13.77 41.46 3.02
4093 12175 1.340248 GACTTGGAGTGGACGTCAAGA 59.660 52.381 18.91 0.00 38.96 3.02
4095 12177 2.224066 ACTTGGAGTGGACGTCAAGAAG 60.224 50.000 18.91 11.67 38.96 2.85
4096 12178 0.033504 TGGAGTGGACGTCAAGAAGC 59.966 55.000 18.91 0.00 0.00 3.86
4097 12179 0.033504 GGAGTGGACGTCAAGAAGCA 59.966 55.000 18.91 1.46 0.00 3.91
4098 12180 1.423395 GAGTGGACGTCAAGAAGCAG 58.577 55.000 18.91 0.00 0.00 4.24
4099 12181 0.601311 AGTGGACGTCAAGAAGCAGC 60.601 55.000 18.91 0.00 0.00 5.25
4100 12182 1.301716 TGGACGTCAAGAAGCAGCC 60.302 57.895 18.91 0.00 0.00 4.85
4101 12183 1.004440 GGACGTCAAGAAGCAGCCT 60.004 57.895 18.91 0.00 0.00 4.58
4102 12184 0.246635 GGACGTCAAGAAGCAGCCTA 59.753 55.000 18.91 0.00 0.00 3.93
4104 12186 0.247736 ACGTCAAGAAGCAGCCTAGG 59.752 55.000 3.67 3.67 0.00 3.02
4105 12187 1.086634 CGTCAAGAAGCAGCCTAGGC 61.087 60.000 27.19 27.19 42.33 3.93
4107 12189 0.914644 TCAAGAAGCAGCCTAGGCAT 59.085 50.000 34.70 17.82 44.88 4.40
4108 12190 1.134280 TCAAGAAGCAGCCTAGGCATC 60.134 52.381 34.70 24.21 44.88 3.91
4110 12192 0.984961 AGAAGCAGCCTAGGCATCCA 60.985 55.000 34.70 0.00 44.88 3.41
4111 12193 0.817229 GAAGCAGCCTAGGCATCCAC 60.817 60.000 34.70 18.57 44.88 4.02
4112 12194 2.590007 GCAGCCTAGGCATCCACG 60.590 66.667 34.70 16.13 44.88 4.94
4113 12195 3.094062 GCAGCCTAGGCATCCACGA 62.094 63.158 34.70 0.00 44.88 4.35
4114 12196 1.068753 CAGCCTAGGCATCCACGAG 59.931 63.158 34.70 10.29 44.88 4.18
4115 12197 2.136878 AGCCTAGGCATCCACGAGG 61.137 63.158 34.70 0.00 44.88 4.63
4116 12198 2.423446 CCTAGGCATCCACGAGGC 59.577 66.667 0.00 0.00 38.72 4.70
4117 12199 2.434843 CCTAGGCATCCACGAGGCA 61.435 63.158 0.00 0.00 41.39 4.75
4118 12200 1.068753 CTAGGCATCCACGAGGCAG 59.931 63.158 0.41 0.00 41.39 4.85
4119 12201 2.374830 CTAGGCATCCACGAGGCAGG 62.375 65.000 0.41 0.00 41.39 4.85
4120 12202 2.871795 TAGGCATCCACGAGGCAGGA 62.872 60.000 0.41 0.00 41.39 3.86
4121 12203 2.202987 GCATCCACGAGGCAGGAG 60.203 66.667 0.00 0.00 39.28 3.69
4122 12204 2.503061 CATCCACGAGGCAGGAGG 59.497 66.667 0.00 0.00 37.34 4.30
4123 12205 2.765807 ATCCACGAGGCAGGAGGG 60.766 66.667 0.00 0.00 37.34 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 9.864976 TCCTAGTCCTAGTCTACCCTAATAATA 57.135 37.037 0.96 0.00 0.00 0.98
53 54 8.769566 TCCTAGTCCTAGTCTACCCTAATAAT 57.230 38.462 0.96 0.00 0.00 1.28
54 55 8.587202 TTCCTAGTCCTAGTCTACCCTAATAA 57.413 38.462 0.96 0.00 0.00 1.40
55 56 8.587202 TTTCCTAGTCCTAGTCTACCCTAATA 57.413 38.462 0.96 0.00 0.00 0.98
56 57 7.477345 TTTCCTAGTCCTAGTCTACCCTAAT 57.523 40.000 0.96 0.00 0.00 1.73
57 58 6.915468 TTTCCTAGTCCTAGTCTACCCTAA 57.085 41.667 0.96 0.00 0.00 2.69
58 59 6.915468 TTTTCCTAGTCCTAGTCTACCCTA 57.085 41.667 0.96 0.00 0.00 3.53
59 60 5.810456 TTTTCCTAGTCCTAGTCTACCCT 57.190 43.478 0.96 0.00 0.00 4.34
277 302 3.081061 ACACACACACACACACAAAGAT 58.919 40.909 0.00 0.00 0.00 2.40
313 338 1.060779 CACACACACACACACGCAG 59.939 57.895 0.00 0.00 0.00 5.18
314 339 1.669437 ACACACACACACACACGCA 60.669 52.632 0.00 0.00 0.00 5.24
316 341 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
318 343 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
319 344 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
320 345 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
321 346 2.287308 ACAAACACACACACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
322 347 1.950216 ACAAACACACACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
323 348 2.031595 TCACAAACACACACACACACAC 60.032 45.455 0.00 0.00 0.00 3.82
324 349 2.222027 TCACAAACACACACACACACA 58.778 42.857 0.00 0.00 0.00 3.72
325 350 2.482336 TCTCACAAACACACACACACAC 59.518 45.455 0.00 0.00 0.00 3.82
326 351 2.741517 CTCTCACAAACACACACACACA 59.258 45.455 0.00 0.00 0.00 3.72
339 370 8.491045 TCTCTATCTCTCTATCTCTCTCACAA 57.509 38.462 0.00 0.00 0.00 3.33
351 382 9.607333 AATTCTCTCTCTCTCTCTATCTCTCTA 57.393 37.037 0.00 0.00 0.00 2.43
359 390 5.815222 CACGTGAATTCTCTCTCTCTCTCTA 59.185 44.000 10.90 0.00 0.00 2.43
421 460 2.341176 GAGGTTACGTGCGTGGGT 59.659 61.111 7.55 0.00 0.00 4.51
460 501 3.023118 CGACGCTGAGATCGGCTA 58.977 61.111 11.65 0.00 45.75 3.93
495 536 0.693049 GGCTTGTTCTTCTCCTCCCA 59.307 55.000 0.00 0.00 0.00 4.37
567 608 0.602905 GTCACCGTGTTCCCTTCCTG 60.603 60.000 0.00 0.00 0.00 3.86
739 802 2.433318 GCTGGAAAGAGCGAGCGT 60.433 61.111 0.00 0.00 30.15 5.07
763 826 1.380650 GGAAGGAGTCGGAGAGGCT 60.381 63.158 0.00 0.00 36.95 4.58
924 989 1.579964 TTACGACGGCGAGCTTCTCA 61.580 55.000 22.49 0.00 41.64 3.27
948 1013 0.173708 GATGCGAGGAAGACGGTTCT 59.826 55.000 0.00 0.00 0.00 3.01
949 1014 0.173708 AGATGCGAGGAAGACGGTTC 59.826 55.000 0.00 0.00 0.00 3.62
950 1015 0.608640 AAGATGCGAGGAAGACGGTT 59.391 50.000 0.00 0.00 0.00 4.44
1014 1079 1.866015 AAAATAGCAAGGGGGAAGGC 58.134 50.000 0.00 0.00 0.00 4.35
1261 1331 8.761575 TCTTCAGACATTTCAATATTTTTGCC 57.238 30.769 0.00 0.00 0.00 4.52
1369 1441 5.584251 GTGGCACCTTCAAAGAAAATTTTGA 59.416 36.000 8.47 0.00 43.32 2.69
1437 1509 7.461182 TTTCATCCCGTATTTTCTGAATTGT 57.539 32.000 0.00 0.00 0.00 2.71
1538 1612 6.894654 AGAGAGAATAGGAGAGTTCACATCAA 59.105 38.462 0.00 0.00 0.00 2.57
1610 1685 3.134623 TGTCTGGATGTCCATATCACACC 59.865 47.826 1.54 0.00 46.46 4.16
2064 5996 6.978674 TCTTCCTATTAGTGATCGATTGGT 57.021 37.500 0.00 0.00 0.00 3.67
2212 6145 1.074471 AGTATCCAGTCGGCCCCAT 60.074 57.895 0.00 0.00 0.00 4.00
2493 6515 7.039853 TGCATATTGATCTGACACCTTGAAAAA 60.040 33.333 0.00 0.00 0.00 1.94
2516 6538 9.132385 TTTGACATCAAGAGAGCAAATCATGCA 62.132 37.037 3.01 0.00 46.41 3.96
2520 6542 5.766670 ACTTTGACATCAAGAGAGCAAATCA 59.233 36.000 9.39 0.00 37.15 2.57
2522 6544 6.128063 GCTACTTTGACATCAAGAGAGCAAAT 60.128 38.462 14.15 0.00 37.15 2.32
2625 8383 8.062536 ACCTAATCAGTCTGGTCTAAGATAACT 58.937 37.037 0.00 0.00 0.00 2.24
2786 8641 5.266788 TCTCAAAATCTGGGCATCTCAAAT 58.733 37.500 0.00 0.00 0.00 2.32
2908 8769 3.450904 TGCATCAGGTACCCTACTCTTT 58.549 45.455 8.74 0.00 29.64 2.52
2967 8828 1.151450 CAACTGGTTCCAGCCACCT 59.849 57.895 17.55 0.00 37.57 4.00
3079 8942 7.759489 AGACATAATACCAACAACAACACAT 57.241 32.000 0.00 0.00 0.00 3.21
3101 8967 9.768662 GGGTTTATCACGACCTTAATAAATAGA 57.231 33.333 0.00 0.00 36.18 1.98
3169 9037 6.043474 AGTGCGGGTCCCATTATAAAATAGTA 59.957 38.462 9.12 0.00 0.00 1.82
3180 9048 1.077501 CATCAGTGCGGGTCCCATT 60.078 57.895 9.12 0.00 0.00 3.16
3222 9090 2.202810 TGACGTCAAGCACACGCA 60.203 55.556 17.62 0.00 41.10 5.24
3226 9094 2.661537 CCGCTGACGTCAAGCACA 60.662 61.111 27.61 6.52 37.70 4.57
3242 9110 2.104928 GCTTGCCATAAAGCCGCC 59.895 61.111 0.00 0.00 45.60 6.13
3305 9173 6.899393 AGAGCAATGTTATAGAGGAGAGAG 57.101 41.667 0.00 0.00 0.00 3.20
3306 9174 6.432783 GCTAGAGCAATGTTATAGAGGAGAGA 59.567 42.308 2.96 0.00 41.59 3.10
3312 9180 3.605916 CGCGCTAGAGCAATGTTATAGAG 59.394 47.826 18.87 0.84 42.21 2.43
3321 9189 0.807667 CTGGTTCGCGCTAGAGCAAT 60.808 55.000 18.87 0.00 42.21 3.56
3332 9200 0.608640 TCCTCCTTCTTCTGGTTCGC 59.391 55.000 0.00 0.00 0.00 4.70
3333 9201 1.402984 CGTCCTCCTTCTTCTGGTTCG 60.403 57.143 0.00 0.00 0.00 3.95
3340 9208 2.028930 TGCTTCTTCGTCCTCCTTCTTC 60.029 50.000 0.00 0.00 0.00 2.87
3344 9212 2.158813 TGTTTGCTTCTTCGTCCTCCTT 60.159 45.455 0.00 0.00 0.00 3.36
3352 9220 1.599071 TGCTCTGTGTTTGCTTCTTCG 59.401 47.619 0.00 0.00 0.00 3.79
3375 9243 3.547746 GGAAACCTTGTTGTGTCCACTA 58.452 45.455 0.00 0.00 41.57 2.74
3417 9285 0.515564 AGAAAAATGTCGTTCGGGCG 59.484 50.000 0.00 0.00 0.00 6.13
3425 9293 9.107367 GTGATCAAGTAAAAGAGAAAAATGTCG 57.893 33.333 0.00 0.00 0.00 4.35
3427 9295 8.836413 TCGTGATCAAGTAAAAGAGAAAAATGT 58.164 29.630 8.54 0.00 0.00 2.71
3429 9297 9.665264 GTTCGTGATCAAGTAAAAGAGAAAAAT 57.335 29.630 8.54 0.00 0.00 1.82
3437 9305 5.389935 GGCTGAGTTCGTGATCAAGTAAAAG 60.390 44.000 8.54 3.40 0.00 2.27
3467 9335 3.697045 CCCTCCCATATGCGTTTTAACAA 59.303 43.478 0.00 0.00 0.00 2.83
3476 9381 2.348411 AAAGAACCCTCCCATATGCG 57.652 50.000 0.00 0.00 0.00 4.73
3593 9498 2.202797 CTCGCCATGACCCAGACG 60.203 66.667 0.00 0.00 0.00 4.18
3596 9501 3.790437 AGGCTCGCCATGACCCAG 61.790 66.667 11.02 0.00 38.92 4.45
3597 9502 4.100084 CAGGCTCGCCATGACCCA 62.100 66.667 11.02 0.00 38.92 4.51
3628 9533 1.048724 TGAGATTAGGGGGTGCGAGG 61.049 60.000 0.00 0.00 0.00 4.63
3630 9535 1.335132 GGTGAGATTAGGGGGTGCGA 61.335 60.000 0.00 0.00 0.00 5.10
3631 9536 1.146263 GGTGAGATTAGGGGGTGCG 59.854 63.158 0.00 0.00 0.00 5.34
3642 9547 2.040813 AGGTGCATTCTGTTGGTGAGAT 59.959 45.455 0.00 0.00 0.00 2.75
3647 9552 2.106511 ACTGTAGGTGCATTCTGTTGGT 59.893 45.455 0.00 0.00 0.00 3.67
3654 9559 0.721718 GCGTGACTGTAGGTGCATTC 59.278 55.000 0.00 0.00 0.00 2.67
3662 9567 1.446099 ACCATGCGCGTGACTGTAG 60.446 57.895 30.68 14.86 0.00 2.74
3667 9572 1.683790 GAGTACACCATGCGCGTGAC 61.684 60.000 30.68 19.70 35.17 3.67
3668 9573 1.445410 GAGTACACCATGCGCGTGA 60.445 57.895 30.68 7.99 35.17 4.35
3683 9892 4.108673 GGGTGACCGTGTAGGAGT 57.891 61.111 0.00 0.00 45.00 3.85
3720 10281 1.206578 GGTGTACGTGTGCATGTGC 59.793 57.895 0.00 6.50 42.50 4.57
3721 10282 0.234625 GTGGTGTACGTGTGCATGTG 59.765 55.000 0.00 0.00 0.00 3.21
3722 10283 0.179070 TGTGGTGTACGTGTGCATGT 60.179 50.000 0.00 2.46 0.00 3.21
3724 10285 0.391228 TCTGTGGTGTACGTGTGCAT 59.609 50.000 0.00 0.00 0.00 3.96
3725 10286 0.528901 GTCTGTGGTGTACGTGTGCA 60.529 55.000 0.00 0.00 0.00 4.57
3732 10293 0.666577 GCGTCAGGTCTGTGGTGTAC 60.667 60.000 0.00 0.00 0.00 2.90
3735 10296 1.004560 ATGCGTCAGGTCTGTGGTG 60.005 57.895 0.00 0.00 0.00 4.17
3741 10302 1.977009 TGTCGGATGCGTCAGGTCT 60.977 57.895 6.49 0.00 0.00 3.85
3751 10312 4.758251 TGCTGGGCGTGTCGGATG 62.758 66.667 0.00 0.00 0.00 3.51
3752 10313 4.760047 GTGCTGGGCGTGTCGGAT 62.760 66.667 0.00 0.00 0.00 4.18
3801 11422 0.528249 GCAAATAAGCCGTGGCCATG 60.528 55.000 18.73 18.73 43.17 3.66
3802 11423 1.675720 GGCAAATAAGCCGTGGCCAT 61.676 55.000 9.72 0.00 46.12 4.40
3803 11424 2.347322 GGCAAATAAGCCGTGGCCA 61.347 57.895 0.00 0.00 46.12 5.36
3804 11425 2.494445 GGCAAATAAGCCGTGGCC 59.506 61.111 7.39 0.00 46.12 5.36
3811 11432 4.275936 AGACGTATCATTGGGCAAATAAGC 59.724 41.667 0.00 0.00 0.00 3.09
3813 11434 4.819630 GGAGACGTATCATTGGGCAAATAA 59.180 41.667 12.92 0.00 0.00 1.40
3815 11436 3.214328 GGAGACGTATCATTGGGCAAAT 58.786 45.455 12.92 0.00 0.00 2.32
3816 11437 2.026729 TGGAGACGTATCATTGGGCAAA 60.027 45.455 12.92 0.00 0.00 3.68
3818 11439 1.199615 TGGAGACGTATCATTGGGCA 58.800 50.000 12.92 0.00 0.00 5.36
3819 11440 1.940613 GTTGGAGACGTATCATTGGGC 59.059 52.381 12.92 0.00 0.00 5.36
3820 11441 2.201732 CGTTGGAGACGTATCATTGGG 58.798 52.381 12.92 0.00 46.49 4.12
3861 11601 9.295825 CCAAAACAGGTAATATAATAGCATGGA 57.704 33.333 0.00 0.00 0.00 3.41
3862 11602 9.295825 TCCAAAACAGGTAATATAATAGCATGG 57.704 33.333 0.00 0.00 0.00 3.66
3865 11605 9.860650 ACATCCAAAACAGGTAATATAATAGCA 57.139 29.630 0.17 0.00 0.00 3.49
3872 11612 8.923270 CCCATAAACATCCAAAACAGGTAATAT 58.077 33.333 0.00 0.00 0.00 1.28
3874 11614 6.351796 GCCCATAAACATCCAAAACAGGTAAT 60.352 38.462 0.00 0.00 0.00 1.89
3875 11615 5.046950 GCCCATAAACATCCAAAACAGGTAA 60.047 40.000 0.00 0.00 0.00 2.85
3876 11616 4.464597 GCCCATAAACATCCAAAACAGGTA 59.535 41.667 0.00 0.00 0.00 3.08
3880 11620 5.559148 AAAGCCCATAAACATCCAAAACA 57.441 34.783 0.00 0.00 0.00 2.83
3881 11621 6.697395 AGTAAAGCCCATAAACATCCAAAAC 58.303 36.000 0.00 0.00 0.00 2.43
3882 11622 6.926630 AGTAAAGCCCATAAACATCCAAAA 57.073 33.333 0.00 0.00 0.00 2.44
3884 11624 6.926630 AAAGTAAAGCCCATAAACATCCAA 57.073 33.333 0.00 0.00 0.00 3.53
3886 11626 7.122204 AGTGTAAAGTAAAGCCCATAAACATCC 59.878 37.037 0.00 0.00 0.00 3.51
3887 11627 8.051901 AGTGTAAAGTAAAGCCCATAAACATC 57.948 34.615 0.00 0.00 0.00 3.06
3888 11628 8.417273 AAGTGTAAAGTAAAGCCCATAAACAT 57.583 30.769 0.00 0.00 0.00 2.71
3895 11635 9.742144 TGATATAAAAGTGTAAAGTAAAGCCCA 57.258 29.630 0.00 0.00 0.00 5.36
3918 12000 7.832685 GGTTAGTAGGTTAGTCCCAAAAATGAT 59.167 37.037 0.00 0.00 36.75 2.45
3921 12003 6.175471 CGGTTAGTAGGTTAGTCCCAAAAAT 58.825 40.000 0.00 0.00 36.75 1.82
3924 12006 3.515104 CCGGTTAGTAGGTTAGTCCCAAA 59.485 47.826 0.00 0.00 36.75 3.28
3925 12007 3.099141 CCGGTTAGTAGGTTAGTCCCAA 58.901 50.000 0.00 0.00 36.75 4.12
3927 12009 2.954989 CTCCGGTTAGTAGGTTAGTCCC 59.045 54.545 0.00 0.00 36.75 4.46
3928 12010 2.954989 CCTCCGGTTAGTAGGTTAGTCC 59.045 54.545 0.00 0.00 0.00 3.85
3929 12011 2.360483 GCCTCCGGTTAGTAGGTTAGTC 59.640 54.545 0.00 0.00 32.67 2.59
3930 12012 2.382882 GCCTCCGGTTAGTAGGTTAGT 58.617 52.381 0.00 0.00 32.67 2.24
3931 12013 1.685517 GGCCTCCGGTTAGTAGGTTAG 59.314 57.143 0.00 0.00 32.67 2.34
3932 12014 1.689258 GGGCCTCCGGTTAGTAGGTTA 60.689 57.143 0.84 0.00 32.67 2.85
3933 12015 0.979709 GGGCCTCCGGTTAGTAGGTT 60.980 60.000 0.84 0.00 32.67 3.50
3935 12017 1.382146 TGGGCCTCCGGTTAGTAGG 60.382 63.158 4.53 0.51 35.24 3.18
3936 12018 2.029307 GCTGGGCCTCCGGTTAGTAG 62.029 65.000 4.53 0.00 41.53 2.57
3937 12019 2.062177 GCTGGGCCTCCGGTTAGTA 61.062 63.158 4.53 0.00 41.53 1.82
3938 12020 3.400054 GCTGGGCCTCCGGTTAGT 61.400 66.667 4.53 0.00 41.53 2.24
3950 12032 1.402787 AAATAGCAATTCGGGCTGGG 58.597 50.000 0.00 0.00 42.62 4.45
3971 12053 6.137794 TCGAAACACTGAAATAGGCAAAAA 57.862 33.333 0.00 0.00 0.00 1.94
3972 12054 5.759506 TCGAAACACTGAAATAGGCAAAA 57.240 34.783 0.00 0.00 0.00 2.44
3973 12055 5.529430 TCTTCGAAACACTGAAATAGGCAAA 59.471 36.000 0.00 0.00 0.00 3.68
3974 12056 5.060506 TCTTCGAAACACTGAAATAGGCAA 58.939 37.500 0.00 0.00 0.00 4.52
3975 12057 4.637276 TCTTCGAAACACTGAAATAGGCA 58.363 39.130 0.00 0.00 0.00 4.75
3976 12058 5.607119 TTCTTCGAAACACTGAAATAGGC 57.393 39.130 0.00 0.00 0.00 3.93
3977 12059 7.041372 TCCTTTTCTTCGAAACACTGAAATAGG 60.041 37.037 18.83 18.83 32.66 2.57
3978 12060 7.861630 TCCTTTTCTTCGAAACACTGAAATAG 58.138 34.615 9.49 9.48 0.00 1.73
3979 12061 7.795482 TCCTTTTCTTCGAAACACTGAAATA 57.205 32.000 9.49 2.77 0.00 1.40
3980 12062 6.693315 TCCTTTTCTTCGAAACACTGAAAT 57.307 33.333 9.49 0.00 0.00 2.17
3981 12063 6.503589 TTCCTTTTCTTCGAAACACTGAAA 57.496 33.333 0.00 2.34 0.00 2.69
3982 12064 6.693315 ATTCCTTTTCTTCGAAACACTGAA 57.307 33.333 0.00 0.00 0.00 3.02
3983 12065 7.659799 TGATATTCCTTTTCTTCGAAACACTGA 59.340 33.333 0.00 0.00 0.00 3.41
3984 12066 7.806690 TGATATTCCTTTTCTTCGAAACACTG 58.193 34.615 0.00 0.00 0.00 3.66
3985 12067 7.979444 TGATATTCCTTTTCTTCGAAACACT 57.021 32.000 0.00 0.00 0.00 3.55
3986 12068 9.458374 TTTTGATATTCCTTTTCTTCGAAACAC 57.542 29.630 0.00 0.00 0.00 3.32
3987 12069 9.677567 CTTTTGATATTCCTTTTCTTCGAAACA 57.322 29.630 0.00 0.00 0.00 2.83
3988 12070 9.129209 CCTTTTGATATTCCTTTTCTTCGAAAC 57.871 33.333 0.00 0.00 0.00 2.78
3989 12071 9.073475 TCCTTTTGATATTCCTTTTCTTCGAAA 57.927 29.630 0.00 0.00 0.00 3.46
3990 12072 8.630054 TCCTTTTGATATTCCTTTTCTTCGAA 57.370 30.769 0.00 0.00 0.00 3.71
3991 12073 7.883311 ACTCCTTTTGATATTCCTTTTCTTCGA 59.117 33.333 0.00 0.00 0.00 3.71
3992 12074 8.045176 ACTCCTTTTGATATTCCTTTTCTTCG 57.955 34.615 0.00 0.00 0.00 3.79
3993 12075 8.462811 GGACTCCTTTTGATATTCCTTTTCTTC 58.537 37.037 0.00 0.00 0.00 2.87
3994 12076 7.950124 TGGACTCCTTTTGATATTCCTTTTCTT 59.050 33.333 0.00 0.00 0.00 2.52
3998 12080 7.309194 CGTTTGGACTCCTTTTGATATTCCTTT 60.309 37.037 0.00 0.00 0.00 3.11
3999 12081 6.151144 CGTTTGGACTCCTTTTGATATTCCTT 59.849 38.462 0.00 0.00 0.00 3.36
4010 12092 3.502123 TCATTCCGTTTGGACTCCTTT 57.498 42.857 0.00 0.00 46.45 3.11
4012 12094 3.146847 GTTTCATTCCGTTTGGACTCCT 58.853 45.455 0.00 0.00 46.45 3.69
4014 12096 3.146847 AGGTTTCATTCCGTTTGGACTC 58.853 45.455 0.00 0.00 46.45 3.36
4016 12098 4.048504 CAAAGGTTTCATTCCGTTTGGAC 58.951 43.478 0.00 0.00 46.45 4.02
4017 12099 3.068873 CCAAAGGTTTCATTCCGTTTGGA 59.931 43.478 15.17 0.00 44.61 3.53
4018 12100 3.389221 CCAAAGGTTTCATTCCGTTTGG 58.611 45.455 8.80 8.80 37.15 3.28
4019 12101 3.068873 TCCCAAAGGTTTCATTCCGTTTG 59.931 43.478 0.00 0.00 0.00 2.93
4020 12102 3.301274 TCCCAAAGGTTTCATTCCGTTT 58.699 40.909 0.00 0.00 0.00 3.60
4021 12103 2.890945 CTCCCAAAGGTTTCATTCCGTT 59.109 45.455 0.00 0.00 0.00 4.44
4022 12104 2.514803 CTCCCAAAGGTTTCATTCCGT 58.485 47.619 0.00 0.00 0.00 4.69
4023 12105 1.202348 GCTCCCAAAGGTTTCATTCCG 59.798 52.381 0.00 0.00 0.00 4.30
4025 12107 2.159382 TCGCTCCCAAAGGTTTCATTC 58.841 47.619 0.00 0.00 0.00 2.67
4026 12108 2.286365 TCGCTCCCAAAGGTTTCATT 57.714 45.000 0.00 0.00 0.00 2.57
4027 12109 2.514458 ATCGCTCCCAAAGGTTTCAT 57.486 45.000 0.00 0.00 0.00 2.57
4028 12110 3.644966 ATATCGCTCCCAAAGGTTTCA 57.355 42.857 0.00 0.00 0.00 2.69
4029 12111 4.983671 AAATATCGCTCCCAAAGGTTTC 57.016 40.909 0.00 0.00 0.00 2.78
4030 12112 5.738619 AAAAATATCGCTCCCAAAGGTTT 57.261 34.783 0.00 0.00 0.00 3.27
4031 12113 6.184789 TCTAAAAATATCGCTCCCAAAGGTT 58.815 36.000 0.00 0.00 0.00 3.50
4032 12114 5.751586 TCTAAAAATATCGCTCCCAAAGGT 58.248 37.500 0.00 0.00 0.00 3.50
4035 12117 7.455641 TTGTTCTAAAAATATCGCTCCCAAA 57.544 32.000 0.00 0.00 0.00 3.28
4036 12118 7.455641 TTTGTTCTAAAAATATCGCTCCCAA 57.544 32.000 0.00 0.00 0.00 4.12
4037 12119 7.479980 CATTTGTTCTAAAAATATCGCTCCCA 58.520 34.615 0.00 0.00 0.00 4.37
4038 12120 6.417930 GCATTTGTTCTAAAAATATCGCTCCC 59.582 38.462 0.00 0.00 0.00 4.30
4039 12121 6.972328 TGCATTTGTTCTAAAAATATCGCTCC 59.028 34.615 0.00 0.00 0.00 4.70
4040 12122 7.969387 TGCATTTGTTCTAAAAATATCGCTC 57.031 32.000 0.00 0.00 0.00 5.03
4042 12124 8.268738 GGATTGCATTTGTTCTAAAAATATCGC 58.731 33.333 0.00 0.00 0.00 4.58
4043 12125 9.299963 TGGATTGCATTTGTTCTAAAAATATCG 57.700 29.630 0.00 0.00 0.00 2.92
4045 12127 9.603921 CCTGGATTGCATTTGTTCTAAAAATAT 57.396 29.630 0.00 0.00 0.00 1.28
4046 12128 8.811017 TCCTGGATTGCATTTGTTCTAAAAATA 58.189 29.630 0.00 0.00 0.00 1.40
4047 12129 7.678837 TCCTGGATTGCATTTGTTCTAAAAAT 58.321 30.769 0.00 0.00 0.00 1.82
4048 12130 7.015098 TCTCCTGGATTGCATTTGTTCTAAAAA 59.985 33.333 0.00 0.00 0.00 1.94
4051 12133 5.415701 GTCTCCTGGATTGCATTTGTTCTAA 59.584 40.000 0.00 0.00 0.00 2.10
4053 12135 3.760684 GTCTCCTGGATTGCATTTGTTCT 59.239 43.478 0.00 0.00 0.00 3.01
4054 12136 3.760684 AGTCTCCTGGATTGCATTTGTTC 59.239 43.478 0.00 0.00 0.00 3.18
4055 12137 3.771216 AGTCTCCTGGATTGCATTTGTT 58.229 40.909 0.00 0.00 0.00 2.83
4058 12140 3.094572 CCAAGTCTCCTGGATTGCATTT 58.905 45.455 0.00 0.00 0.00 2.32
4059 12141 2.309755 TCCAAGTCTCCTGGATTGCATT 59.690 45.455 0.00 0.00 0.00 3.56
4061 12143 1.280133 CTCCAAGTCTCCTGGATTGCA 59.720 52.381 0.00 0.00 0.00 4.08
4062 12144 1.280421 ACTCCAAGTCTCCTGGATTGC 59.720 52.381 0.00 0.00 0.00 3.56
4063 12145 2.355513 CCACTCCAAGTCTCCTGGATTG 60.356 54.545 0.00 0.00 33.75 2.67
4064 12146 1.912043 CCACTCCAAGTCTCCTGGATT 59.088 52.381 0.00 0.00 0.00 3.01
4065 12147 1.079490 TCCACTCCAAGTCTCCTGGAT 59.921 52.381 0.00 0.00 0.00 3.41
4066 12148 0.487325 TCCACTCCAAGTCTCCTGGA 59.513 55.000 0.00 0.00 0.00 3.86
4067 12149 0.610687 GTCCACTCCAAGTCTCCTGG 59.389 60.000 0.00 0.00 0.00 4.45
4068 12150 0.244994 CGTCCACTCCAAGTCTCCTG 59.755 60.000 0.00 0.00 0.00 3.86
4069 12151 0.178958 ACGTCCACTCCAAGTCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
4070 12152 0.244178 GACGTCCACTCCAAGTCTCC 59.756 60.000 3.51 0.00 0.00 3.71
4071 12153 0.959553 TGACGTCCACTCCAAGTCTC 59.040 55.000 14.12 0.00 33.40 3.36
4072 12154 1.341531 CTTGACGTCCACTCCAAGTCT 59.658 52.381 14.12 0.00 33.34 3.24
4074 12156 1.410004 TCTTGACGTCCACTCCAAGT 58.590 50.000 14.12 0.00 37.74 3.16
4075 12157 2.408050 CTTCTTGACGTCCACTCCAAG 58.592 52.381 14.12 9.50 37.82 3.61
4076 12158 1.540363 GCTTCTTGACGTCCACTCCAA 60.540 52.381 14.12 0.00 0.00 3.53
4077 12159 0.033504 GCTTCTTGACGTCCACTCCA 59.966 55.000 14.12 0.00 0.00 3.86
4078 12160 0.033504 TGCTTCTTGACGTCCACTCC 59.966 55.000 14.12 0.00 0.00 3.85
4079 12161 1.423395 CTGCTTCTTGACGTCCACTC 58.577 55.000 14.12 0.00 0.00 3.51
4080 12162 0.601311 GCTGCTTCTTGACGTCCACT 60.601 55.000 14.12 0.00 0.00 4.00
4081 12163 1.569479 GGCTGCTTCTTGACGTCCAC 61.569 60.000 14.12 0.00 0.00 4.02
4083 12165 0.246635 TAGGCTGCTTCTTGACGTCC 59.753 55.000 14.12 0.00 0.00 4.79
4085 12167 0.247736 CCTAGGCTGCTTCTTGACGT 59.752 55.000 0.00 0.00 0.00 4.34
4086 12168 1.086634 GCCTAGGCTGCTTCTTGACG 61.087 60.000 27.17 0.00 38.26 4.35
4087 12169 0.036010 TGCCTAGGCTGCTTCTTGAC 60.036 55.000 33.07 1.38 42.51 3.18
4088 12170 0.914644 ATGCCTAGGCTGCTTCTTGA 59.085 50.000 33.07 11.23 42.51 3.02
4089 12171 1.307097 GATGCCTAGGCTGCTTCTTG 58.693 55.000 33.07 0.00 42.51 3.02
4091 12173 0.984961 TGGATGCCTAGGCTGCTTCT 60.985 55.000 33.07 11.65 42.51 2.85
4092 12174 0.817229 GTGGATGCCTAGGCTGCTTC 60.817 60.000 33.07 22.35 42.51 3.86
4093 12175 1.225704 GTGGATGCCTAGGCTGCTT 59.774 57.895 33.07 16.02 42.51 3.91
4095 12177 2.590007 CGTGGATGCCTAGGCTGC 60.590 66.667 33.07 23.56 42.51 5.25
4096 12178 1.068753 CTCGTGGATGCCTAGGCTG 59.931 63.158 33.07 15.93 42.51 4.85
4097 12179 2.136878 CCTCGTGGATGCCTAGGCT 61.137 63.158 33.07 19.27 37.52 4.58
4098 12180 2.423446 CCTCGTGGATGCCTAGGC 59.577 66.667 27.71 27.71 37.27 3.93
4099 12181 2.374830 CTGCCTCGTGGATGCCTAGG 62.375 65.000 7.92 3.67 34.57 3.02
4100 12182 1.068753 CTGCCTCGTGGATGCCTAG 59.931 63.158 7.92 0.00 34.57 3.02
4101 12183 2.434843 CCTGCCTCGTGGATGCCTA 61.435 63.158 7.92 0.00 34.57 3.93
4102 12184 3.790437 CCTGCCTCGTGGATGCCT 61.790 66.667 7.92 0.00 34.57 4.75
4104 12186 2.202987 CTCCTGCCTCGTGGATGC 60.203 66.667 7.92 0.00 34.57 3.91
4105 12187 2.503061 CCTCCTGCCTCGTGGATG 59.497 66.667 7.92 0.00 34.57 3.51


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

AutoCloner maintained by Alex Coulton.