Multiple sequence alignment - TraesCS3B01G332000

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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 TraesCS3B01G332000 chr3B 100.000 3484 0 0 1 3484 537436969 537433486 0.000000e+00 6434
1 TraesCS3B01G332000 chr3B 100.000 185 0 0 3796 3980 537433174 537432990 3.810000e-90 342
2 TraesCS3B01G332000 chr3B 90.566 106 9 1 3876 3980 48706230 48706125 5.360000e-29 139
3 TraesCS3B01G332000 chr3D 95.011 2205 90 11 1103 3293 410993145 410990947 0.000000e+00 3445
4 TraesCS3B01G332000 chr3D 91.343 566 43 3 1 563 410997336 410996774 0.000000e+00 769
5 TraesCS3B01G332000 chr3D 92.000 525 28 8 587 1104 410993851 410993334 0.000000e+00 725
6 TraesCS3B01G332000 chr3A 92.679 1284 66 11 2040 3315 540660687 540661950 0.000000e+00 1825
7 TraesCS3B01G332000 chr3A 96.484 910 32 0 1108 2017 540659710 540660619 0.000000e+00 1504
8 TraesCS3B01G332000 chr3A 92.504 627 35 5 485 1105 540658909 540659529 0.000000e+00 887
9 TraesCS3B01G332000 chr3A 90.411 511 36 8 1 499 540658354 540658863 0.000000e+00 660
10 TraesCS3B01G332000 chr5B 93.578 109 5 2 3874 3980 399219860 399219752 1.140000e-35 161
11 TraesCS3B01G332000 chr5B 90.566 106 9 1 3876 3980 251910958 251911063 5.360000e-29 139
12 TraesCS3B01G332000 chr5B 89.815 108 10 1 3872 3979 328245444 328245338 1.930000e-28 137
13 TraesCS3B01G332000 chr1D 87.879 132 10 4 3315 3441 470346566 470346696 2.480000e-32 150
14 TraesCS3B01G332000 chr1B 90.909 110 7 3 3874 3980 14626706 14626597 1.150000e-30 145
15 TraesCS3B01G332000 chr1B 92.929 99 6 1 3883 3980 593151279 593151377 4.150000e-30 143
16 TraesCS3B01G332000 chrUn 90.566 106 9 1 3876 3980 3842338 3842233 5.360000e-29 139
17 TraesCS3B01G332000 chr2B 90.000 110 8 3 3872 3980 551488880 551488773 5.360000e-29 139
18 TraesCS3B01G332000 chr6B 89.908 109 7 3 3876 3980 234735308 234735416 1.930000e-28 137


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 TraesCS3B01G332000 chr3B 537432990 537436969 3979 True 3388.000000 6434 100.000000 1 3980 2 chr3B.!!$R2 3979
1 TraesCS3B01G332000 chr3D 410990947 410997336 6389 True 1646.333333 3445 92.784667 1 3293 3 chr3D.!!$R1 3292
2 TraesCS3B01G332000 chr3A 540658354 540661950 3596 False 1219.000000 1825 93.019500 1 3315 4 chr3A.!!$F1 3314

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
274 281 0.036010 GCAAGGCAAGAGCTCTACCA 60.036 55.0 28.47 0.0 41.70 3.25 F
1046 4024 0.031857 AGCTCTGAATCCGATGCTCG 59.968 55.0 0.00 0.0 40.07 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 4357 0.179004 TGTTGGTGTTGAGCCCGAAT 60.179 50.0 0.00 0.0 0.0 3.34 R
3003 6221 0.242555 ACGTTAAAAATGGCCTGCGG 59.757 50.0 3.32 0.0 0.0 5.69 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
27 28 5.744171 TGTTGTATGTTCATGCCTCAGTAT 58.256 37.500 0.00 0.00 0.00 2.12
30 31 7.495606 TGTTGTATGTTCATGCCTCAGTATTAG 59.504 37.037 0.00 0.00 0.00 1.73
34 35 1.699634 TCATGCCTCAGTATTAGGGCC 59.300 52.381 0.00 0.00 43.50 5.80
35 36 1.701847 CATGCCTCAGTATTAGGGCCT 59.298 52.381 12.58 12.58 43.50 5.19
37 38 3.275848 TGCCTCAGTATTAGGGCCTAT 57.724 47.619 15.37 7.37 43.50 2.57
75 76 7.437565 GGTAAAGGACGACTACATTATTCCTTC 59.562 40.741 1.28 0.00 41.61 3.46
77 78 5.903810 AGGACGACTACATTATTCCTTCAC 58.096 41.667 0.00 0.00 28.60 3.18
97 98 1.875514 CGAATATGCCCATGTGGTCTG 59.124 52.381 0.00 0.00 36.04 3.51
124 131 5.163519 GGTAAAATACCCTACGCTGTAGTGA 60.164 44.000 12.54 1.57 43.18 3.41
135 142 3.189910 ACGCTGTAGTGATTGAAGTCGTA 59.810 43.478 0.00 0.00 0.00 3.43
151 158 1.526464 TCGTAACTTTTTCGCCGGAAC 59.474 47.619 5.05 0.00 0.00 3.62
152 159 1.398832 CGTAACTTTTTCGCCGGAACC 60.399 52.381 5.05 0.00 0.00 3.62
164 171 1.270358 GCCGGAACCTATAGGAGCAAG 60.270 57.143 26.01 11.43 38.94 4.01
213 220 2.952310 GGATCTTGCCCATGGAACTAAC 59.048 50.000 15.22 0.00 0.00 2.34
274 281 0.036010 GCAAGGCAAGAGCTCTACCA 60.036 55.000 28.47 0.00 41.70 3.25
275 282 1.407989 GCAAGGCAAGAGCTCTACCAT 60.408 52.381 28.47 18.98 41.70 3.55
281 288 3.127721 GGCAAGAGCTCTACCATTTTCAC 59.872 47.826 24.25 1.73 41.70 3.18
343 352 5.435686 TGCCATCCTACTATTGTTGAAGT 57.564 39.130 0.00 0.00 0.00 3.01
446 459 0.385390 AGGTGGCAAGTTTGAAAGCG 59.615 50.000 0.00 0.00 0.00 4.68
500 573 6.540189 ACATGGGTCTAATTTCAAAGATCTCG 59.460 38.462 0.00 0.00 0.00 4.04
563 636 7.516312 CGAATTAACGGTATGAGAGCTAAAACC 60.516 40.741 0.00 0.00 0.00 3.27
597 2027 6.250344 TCAAGAGAAGCATTTGAAGTGATG 57.750 37.500 0.00 0.00 0.00 3.07
605 3577 7.555195 AGAAGCATTTGAAGTGATGATACATGA 59.445 33.333 0.00 0.00 0.00 3.07
680 3652 5.570205 TCCTCCTGTGTGTTGGTTTTATA 57.430 39.130 0.00 0.00 0.00 0.98
826 3803 1.094073 CCAAGGAGAATGCAGGAGCG 61.094 60.000 0.00 0.00 46.23 5.03
839 3816 1.001406 CAGGAGCGTGTTCTTTCCTCT 59.999 52.381 0.00 0.00 37.97 3.69
841 3818 0.793250 GAGCGTGTTCTTTCCTCTGC 59.207 55.000 0.00 0.00 0.00 4.26
852 3829 2.079170 TTCCTCTGCCGATCTCAGAT 57.921 50.000 12.89 0.00 39.56 2.90
862 3839 3.314635 GCCGATCTCAGATTTGCATTTCT 59.685 43.478 4.84 0.00 0.00 2.52
916 3894 0.886490 CCTCTCGGCAAGCAACAACT 60.886 55.000 0.00 0.00 0.00 3.16
1046 4024 0.031857 AGCTCTGAATCCGATGCTCG 59.968 55.000 0.00 0.00 40.07 5.03
1080 4058 1.217183 AGAGGTGGATTCGTAGCCCTA 59.783 52.381 0.00 0.00 0.00 3.53
1129 4298 6.321945 TCATCCCTTCAATTTGTGATGGTATG 59.678 38.462 14.64 7.22 45.92 2.39
1188 4357 0.181587 TGTTGGAGAAAGTTGCGGGA 59.818 50.000 0.00 0.00 0.00 5.14
1230 4399 3.008923 TGATCATGTACCTCACCAAGCAA 59.991 43.478 0.00 0.00 0.00 3.91
1384 4553 1.020861 CGCATGCCTAACAGTGAGCA 61.021 55.000 13.15 0.41 40.00 4.26
1436 4609 3.574284 TCACTTGCGCTAAATTTGCAT 57.426 38.095 9.73 0.00 38.60 3.96
1442 4615 3.244156 TGCGCTAAATTTGCATCACTTG 58.756 40.909 9.73 0.00 32.86 3.16
1769 4942 3.712881 GTGCAGGACAACGTCGGC 61.713 66.667 0.00 0.00 35.26 5.54
1830 5003 3.764466 CCGCGGTGAGCTTCCTCT 61.764 66.667 19.50 0.00 45.59 3.69
2035 5215 1.936547 GAGTGAAAGGCATGATCGACC 59.063 52.381 0.00 0.00 0.00 4.79
2038 5218 1.212688 TGAAAGGCATGATCGACCCAT 59.787 47.619 0.00 0.00 0.00 4.00
2049 5229 3.940852 TGATCGACCCATTGATTGTTCAG 59.059 43.478 0.00 0.00 32.27 3.02
2083 5301 3.427503 GGCGATGTTTGATTTGAATCCGT 60.428 43.478 1.56 0.00 34.50 4.69
2120 5338 0.179145 GCCTGCATGATCAGCAACAC 60.179 55.000 16.93 8.62 42.17 3.32
2129 5347 4.454948 CAGCAACACTGGGAACGA 57.545 55.556 0.00 0.00 43.19 3.85
2134 5352 0.393077 CAACACTGGGAACGAGGACT 59.607 55.000 0.00 0.00 0.00 3.85
2135 5353 1.129058 AACACTGGGAACGAGGACTT 58.871 50.000 0.00 0.00 0.00 3.01
2136 5354 0.393077 ACACTGGGAACGAGGACTTG 59.607 55.000 0.00 0.00 0.00 3.16
2147 5365 0.035739 GAGGACTTGTTACCCGGCAA 59.964 55.000 0.00 0.00 0.00 4.52
2205 5423 2.603473 AGGAGGCTGTGCACGGTA 60.603 61.111 26.00 0.90 0.00 4.02
2880 6098 1.074775 TCTGGGCGCCATGAACTTT 59.925 52.632 30.85 0.00 30.82 2.66
2999 6217 3.664107 AGTTTTGTAATGCTGAGCTCGA 58.336 40.909 9.64 0.00 0.00 4.04
3003 6221 0.926846 GTAATGCTGAGCTCGAGTGC 59.073 55.000 15.13 13.49 0.00 4.40
3005 6223 3.713205 ATGCTGAGCTCGAGTGCCG 62.713 63.158 15.13 4.16 40.25 5.69
3043 6265 1.470890 GAGTCTGAACTCGGAGGACAG 59.529 57.143 19.98 19.98 42.42 3.51
3045 6267 1.470890 GTCTGAACTCGGAGGACAGAG 59.529 57.143 25.24 9.73 42.42 3.35
3046 6268 0.172352 CTGAACTCGGAGGACAGAGC 59.828 60.000 20.85 1.24 40.90 4.09
3096 6319 3.326006 TCTCTGAACCAACTGCTCTGAAT 59.674 43.478 0.00 0.00 0.00 2.57
3170 6393 1.741706 CTTGCCATTCATCAGCGAAGT 59.258 47.619 0.00 0.00 0.00 3.01
3182 6405 1.402259 CAGCGAAGTCGGAGTCTACAT 59.598 52.381 2.47 0.00 40.23 2.29
3185 6408 1.065701 CGAAGTCGGAGTCTACATGGG 59.934 57.143 0.00 0.00 35.37 4.00
3187 6410 2.233305 AGTCGGAGTCTACATGGGTT 57.767 50.000 0.00 0.00 0.00 4.11
3222 6446 8.467598 GGGAAATGTTTACCTTATTCTTCTTCC 58.532 37.037 0.00 0.00 38.19 3.46
3228 6452 7.780745 TGTTTACCTTATTCTTCTTCCCAACAA 59.219 33.333 0.00 0.00 0.00 2.83
3277 6501 7.444183 AGAAACTTCGGTCATCTAATTTCAACA 59.556 33.333 0.00 0.00 0.00 3.33
3286 6510 6.299966 GTCATCTAATTTCAACAAACGACACG 59.700 38.462 0.00 0.00 0.00 4.49
3323 6551 8.755696 TGATTGGTTAAATGAAACACAATAGC 57.244 30.769 0.00 0.00 33.24 2.97
3324 6552 8.584157 TGATTGGTTAAATGAAACACAATAGCT 58.416 29.630 0.00 0.00 33.24 3.32
3328 6556 9.906660 TGGTTAAATGAAACACAATAGCTAAAG 57.093 29.630 0.00 0.00 26.28 1.85
3329 6557 9.353999 GGTTAAATGAAACACAATAGCTAAAGG 57.646 33.333 0.00 0.00 0.00 3.11
3330 6558 9.908152 GTTAAATGAAACACAATAGCTAAAGGT 57.092 29.630 0.00 0.00 0.00 3.50
3332 6560 7.759489 AATGAAACACAATAGCTAAAGGTCA 57.241 32.000 0.00 0.00 0.00 4.02
3333 6561 6.801539 TGAAACACAATAGCTAAAGGTCAG 57.198 37.500 0.00 0.00 0.00 3.51
3334 6562 6.296026 TGAAACACAATAGCTAAAGGTCAGT 58.704 36.000 0.00 0.00 0.00 3.41
3335 6563 6.426937 TGAAACACAATAGCTAAAGGTCAGTC 59.573 38.462 0.00 0.00 0.00 3.51
3336 6564 4.495422 ACACAATAGCTAAAGGTCAGTCG 58.505 43.478 0.00 0.00 0.00 4.18
3337 6565 4.219944 ACACAATAGCTAAAGGTCAGTCGA 59.780 41.667 0.00 0.00 0.00 4.20
3338 6566 4.563184 CACAATAGCTAAAGGTCAGTCGAC 59.437 45.833 7.70 7.70 41.80 4.20
3339 6567 4.463186 ACAATAGCTAAAGGTCAGTCGACT 59.537 41.667 13.58 13.58 42.21 4.18
3340 6568 4.640789 ATAGCTAAAGGTCAGTCGACTG 57.359 45.455 34.76 34.76 45.08 3.51
3375 6603 8.732413 TTTTGATCAATCGATTCAGTTTTGAG 57.268 30.769 9.40 0.00 34.15 3.02
3376 6604 7.671495 TTGATCAATCGATTCAGTTTTGAGA 57.329 32.000 7.92 0.00 34.15 3.27
3377 6605 7.671495 TGATCAATCGATTCAGTTTTGAGAA 57.329 32.000 7.92 0.00 34.15 2.87
3378 6606 7.745972 TGATCAATCGATTCAGTTTTGAGAAG 58.254 34.615 7.92 0.00 34.15 2.85
3379 6607 6.486253 TCAATCGATTCAGTTTTGAGAAGG 57.514 37.500 7.92 0.00 34.15 3.46
3380 6608 6.230472 TCAATCGATTCAGTTTTGAGAAGGA 58.770 36.000 7.92 0.00 34.15 3.36
3381 6609 6.710295 TCAATCGATTCAGTTTTGAGAAGGAA 59.290 34.615 7.92 0.00 34.15 3.36
3382 6610 6.734104 ATCGATTCAGTTTTGAGAAGGAAG 57.266 37.500 0.00 0.00 34.15 3.46
3383 6611 5.853936 TCGATTCAGTTTTGAGAAGGAAGA 58.146 37.500 0.00 0.00 34.15 2.87
3384 6612 6.288294 TCGATTCAGTTTTGAGAAGGAAGAA 58.712 36.000 0.00 0.00 34.15 2.52
3385 6613 6.425114 TCGATTCAGTTTTGAGAAGGAAGAAG 59.575 38.462 0.00 0.00 34.15 2.85
3386 6614 6.348050 CGATTCAGTTTTGAGAAGGAAGAAGG 60.348 42.308 0.00 0.00 34.15 3.46
3387 6615 5.630415 TCAGTTTTGAGAAGGAAGAAGGA 57.370 39.130 0.00 0.00 0.00 3.36
3388 6616 6.001449 TCAGTTTTGAGAAGGAAGAAGGAA 57.999 37.500 0.00 0.00 0.00 3.36
3389 6617 6.058183 TCAGTTTTGAGAAGGAAGAAGGAAG 58.942 40.000 0.00 0.00 0.00 3.46
3390 6618 4.824537 AGTTTTGAGAAGGAAGAAGGAAGC 59.175 41.667 0.00 0.00 0.00 3.86
3391 6619 4.437682 TTTGAGAAGGAAGAAGGAAGCA 57.562 40.909 0.00 0.00 0.00 3.91
3392 6620 3.409026 TGAGAAGGAAGAAGGAAGCAC 57.591 47.619 0.00 0.00 0.00 4.40
3393 6621 2.039084 TGAGAAGGAAGAAGGAAGCACC 59.961 50.000 0.00 0.00 39.35 5.01
3394 6622 2.039084 GAGAAGGAAGAAGGAAGCACCA 59.961 50.000 2.96 0.00 42.04 4.17
3395 6623 2.443255 AGAAGGAAGAAGGAAGCACCAA 59.557 45.455 2.96 0.00 42.04 3.67
3396 6624 2.575805 AGGAAGAAGGAAGCACCAAG 57.424 50.000 2.96 0.00 42.04 3.61
3397 6625 2.057922 AGGAAGAAGGAAGCACCAAGA 58.942 47.619 2.96 0.00 42.04 3.02
3398 6626 2.155279 GGAAGAAGGAAGCACCAAGAC 58.845 52.381 2.96 0.00 42.04 3.01
3399 6627 2.487265 GGAAGAAGGAAGCACCAAGACA 60.487 50.000 2.96 0.00 42.04 3.41
3400 6628 2.557920 AGAAGGAAGCACCAAGACAG 57.442 50.000 2.96 0.00 42.04 3.51
3401 6629 2.050144 AGAAGGAAGCACCAAGACAGA 58.950 47.619 2.96 0.00 42.04 3.41
3402 6630 2.038295 AGAAGGAAGCACCAAGACAGAG 59.962 50.000 2.96 0.00 42.04 3.35
3403 6631 0.689623 AGGAAGCACCAAGACAGAGG 59.310 55.000 2.96 0.00 42.04 3.69
3404 6632 0.687354 GGAAGCACCAAGACAGAGGA 59.313 55.000 0.00 0.00 38.79 3.71
3405 6633 1.072331 GGAAGCACCAAGACAGAGGAA 59.928 52.381 0.00 0.00 38.79 3.36
3406 6634 2.421619 GAAGCACCAAGACAGAGGAAG 58.578 52.381 0.00 0.00 0.00 3.46
3407 6635 0.689623 AGCACCAAGACAGAGGAAGG 59.310 55.000 0.00 0.00 0.00 3.46
3408 6636 0.687354 GCACCAAGACAGAGGAAGGA 59.313 55.000 0.00 0.00 0.00 3.36
3409 6637 1.338579 GCACCAAGACAGAGGAAGGAG 60.339 57.143 0.00 0.00 0.00 3.69
3410 6638 2.251818 CACCAAGACAGAGGAAGGAGA 58.748 52.381 0.00 0.00 0.00 3.71
3411 6639 2.028567 CACCAAGACAGAGGAAGGAGAC 60.029 54.545 0.00 0.00 0.00 3.36
3412 6640 1.203523 CCAAGACAGAGGAAGGAGACG 59.796 57.143 0.00 0.00 0.00 4.18
3413 6641 1.203523 CAAGACAGAGGAAGGAGACGG 59.796 57.143 0.00 0.00 0.00 4.79
3414 6642 0.968393 AGACAGAGGAAGGAGACGGC 60.968 60.000 0.00 0.00 0.00 5.68
3415 6643 2.272918 GACAGAGGAAGGAGACGGCG 62.273 65.000 4.80 4.80 0.00 6.46
3416 6644 2.046864 CAGAGGAAGGAGACGGCGA 61.047 63.158 16.62 0.00 0.00 5.54
3417 6645 1.751162 AGAGGAAGGAGACGGCGAG 60.751 63.158 16.62 0.00 0.00 5.03
3418 6646 2.756283 AGGAAGGAGACGGCGAGG 60.756 66.667 16.62 0.00 0.00 4.63
3419 6647 4.516195 GGAAGGAGACGGCGAGGC 62.516 72.222 16.62 1.94 0.00 4.70
3420 6648 4.516195 GAAGGAGACGGCGAGGCC 62.516 72.222 16.62 11.36 46.75 5.19
3443 6671 2.671619 CGCCGGGGAAAGAAGCAA 60.672 61.111 14.46 0.00 0.00 3.91
3444 6672 2.962569 GCCGGGGAAAGAAGCAAC 59.037 61.111 2.18 0.00 0.00 4.17
3445 6673 2.636412 GCCGGGGAAAGAAGCAACC 61.636 63.158 2.18 0.00 0.00 3.77
3446 6674 1.977009 CCGGGGAAAGAAGCAACCC 60.977 63.158 0.00 0.00 41.41 4.11
3447 6675 1.228429 CGGGGAAAGAAGCAACCCA 60.228 57.895 0.00 0.00 43.67 4.51
3448 6676 0.825840 CGGGGAAAGAAGCAACCCAA 60.826 55.000 0.00 0.00 43.67 4.12
3449 6677 1.644509 GGGGAAAGAAGCAACCCAAT 58.355 50.000 0.00 0.00 43.67 3.16
3450 6678 1.550524 GGGGAAAGAAGCAACCCAATC 59.449 52.381 0.00 0.00 43.67 2.67
3451 6679 2.529632 GGGAAAGAAGCAACCCAATCT 58.470 47.619 0.00 0.00 41.72 2.40
3452 6680 2.899900 GGGAAAGAAGCAACCCAATCTT 59.100 45.455 0.00 0.00 41.72 2.40
3453 6681 4.086457 GGGAAAGAAGCAACCCAATCTTA 58.914 43.478 0.00 0.00 41.72 2.10
3454 6682 4.526650 GGGAAAGAAGCAACCCAATCTTAA 59.473 41.667 0.00 0.00 41.72 1.85
3455 6683 5.336770 GGGAAAGAAGCAACCCAATCTTAAG 60.337 44.000 0.00 0.00 41.72 1.85
3456 6684 5.336770 GGAAAGAAGCAACCCAATCTTAAGG 60.337 44.000 1.85 0.00 32.13 2.69
3465 6693 2.456577 CCAATCTTAAGGGTGTTGGGG 58.543 52.381 15.84 1.47 36.53 4.96
3466 6694 2.456577 CAATCTTAAGGGTGTTGGGGG 58.543 52.381 1.85 0.00 0.00 5.40
3467 6695 1.768265 ATCTTAAGGGTGTTGGGGGT 58.232 50.000 1.85 0.00 0.00 4.95
3468 6696 0.774908 TCTTAAGGGTGTTGGGGGTG 59.225 55.000 1.85 0.00 0.00 4.61
3469 6697 0.774908 CTTAAGGGTGTTGGGGGTGA 59.225 55.000 0.00 0.00 0.00 4.02
3470 6698 1.146152 CTTAAGGGTGTTGGGGGTGAA 59.854 52.381 0.00 0.00 0.00 3.18
3471 6699 0.774908 TAAGGGTGTTGGGGGTGAAG 59.225 55.000 0.00 0.00 0.00 3.02
3472 6700 2.018884 AAGGGTGTTGGGGGTGAAGG 62.019 60.000 0.00 0.00 0.00 3.46
3473 6701 2.774633 GGGTGTTGGGGGTGAAGGT 61.775 63.158 0.00 0.00 0.00 3.50
3474 6702 1.530655 GGTGTTGGGGGTGAAGGTG 60.531 63.158 0.00 0.00 0.00 4.00
3475 6703 2.197324 TGTTGGGGGTGAAGGTGC 59.803 61.111 0.00 0.00 0.00 5.01
3476 6704 2.197324 GTTGGGGGTGAAGGTGCA 59.803 61.111 0.00 0.00 0.00 4.57
3477 6705 1.903404 GTTGGGGGTGAAGGTGCAG 60.903 63.158 0.00 0.00 0.00 4.41
3478 6706 2.391130 TTGGGGGTGAAGGTGCAGT 61.391 57.895 0.00 0.00 0.00 4.40
3479 6707 1.943730 TTGGGGGTGAAGGTGCAGTT 61.944 55.000 0.00 0.00 0.00 3.16
3480 6708 1.603739 GGGGGTGAAGGTGCAGTTC 60.604 63.158 0.00 0.00 0.00 3.01
3481 6709 1.966451 GGGGTGAAGGTGCAGTTCG 60.966 63.158 0.00 0.00 0.00 3.95
3482 6710 2.617274 GGGTGAAGGTGCAGTTCGC 61.617 63.158 12.07 12.07 42.89 4.70
3483 6711 2.617274 GGTGAAGGTGCAGTTCGCC 61.617 63.158 20.26 20.26 44.96 5.54
3812 7040 3.966543 AGGGCGGGGTGGTGAAAG 61.967 66.667 0.00 0.00 0.00 2.62
3813 7041 4.280019 GGGCGGGGTGGTGAAAGT 62.280 66.667 0.00 0.00 0.00 2.66
3814 7042 2.983592 GGCGGGGTGGTGAAAGTG 60.984 66.667 0.00 0.00 0.00 3.16
3815 7043 2.983592 GCGGGGTGGTGAAAGTGG 60.984 66.667 0.00 0.00 0.00 4.00
3816 7044 2.983592 CGGGGTGGTGAAAGTGGC 60.984 66.667 0.00 0.00 0.00 5.01
3817 7045 2.197324 GGGGTGGTGAAAGTGGCA 59.803 61.111 0.00 0.00 0.00 4.92
3818 7046 1.228862 GGGGTGGTGAAAGTGGCAT 60.229 57.895 0.00 0.00 0.00 4.40
3819 7047 1.535204 GGGGTGGTGAAAGTGGCATG 61.535 60.000 0.00 0.00 0.00 4.06
3820 7048 1.535204 GGGTGGTGAAAGTGGCATGG 61.535 60.000 0.00 0.00 0.00 3.66
3821 7049 0.827507 GGTGGTGAAAGTGGCATGGT 60.828 55.000 0.00 0.00 0.00 3.55
3822 7050 1.546773 GGTGGTGAAAGTGGCATGGTA 60.547 52.381 0.00 0.00 0.00 3.25
3823 7051 1.812571 GTGGTGAAAGTGGCATGGTAG 59.187 52.381 0.00 0.00 0.00 3.18
3824 7052 1.271871 TGGTGAAAGTGGCATGGTAGG 60.272 52.381 0.00 0.00 0.00 3.18
3825 7053 0.811281 GTGAAAGTGGCATGGTAGGC 59.189 55.000 0.00 0.00 0.00 3.93
3831 7059 4.175337 GGCATGGTAGGCCGCTGA 62.175 66.667 0.00 0.00 42.39 4.26
3832 7060 2.897350 GCATGGTAGGCCGCTGAC 60.897 66.667 0.00 0.00 37.67 3.51
3833 7061 2.203070 CATGGTAGGCCGCTGACC 60.203 66.667 11.08 11.08 37.67 4.02
3834 7062 3.849951 ATGGTAGGCCGCTGACCG 61.850 66.667 12.62 0.00 35.91 4.79
3851 7079 4.221422 GCGGGCGGCAGTAGATCA 62.221 66.667 12.47 0.00 42.87 2.92
3852 7080 2.028190 CGGGCGGCAGTAGATCAG 59.972 66.667 12.47 0.00 0.00 2.90
3853 7081 2.423446 GGGCGGCAGTAGATCAGG 59.577 66.667 12.47 0.00 0.00 3.86
3854 7082 2.280457 GGCGGCAGTAGATCAGGC 60.280 66.667 3.07 0.00 0.00 4.85
3856 7084 2.028190 CGGCAGTAGATCAGGCGG 59.972 66.667 13.06 4.11 44.93 6.13
3857 7085 2.786495 CGGCAGTAGATCAGGCGGT 61.786 63.158 13.06 0.00 44.93 5.68
3858 7086 1.522569 GGCAGTAGATCAGGCGGTT 59.477 57.895 0.00 0.00 0.00 4.44
3859 7087 0.530870 GGCAGTAGATCAGGCGGTTC 60.531 60.000 0.00 0.00 0.00 3.62
3860 7088 0.872021 GCAGTAGATCAGGCGGTTCG 60.872 60.000 0.00 0.00 0.00 3.95
3861 7089 0.738975 CAGTAGATCAGGCGGTTCGA 59.261 55.000 0.00 0.00 0.00 3.71
3862 7090 1.025812 AGTAGATCAGGCGGTTCGAG 58.974 55.000 0.00 0.00 0.00 4.04
3863 7091 0.030908 GTAGATCAGGCGGTTCGAGG 59.969 60.000 0.00 0.00 0.00 4.63
3864 7092 0.395311 TAGATCAGGCGGTTCGAGGT 60.395 55.000 0.00 0.00 0.00 3.85
3865 7093 0.395311 AGATCAGGCGGTTCGAGGTA 60.395 55.000 0.00 0.00 0.00 3.08
3866 7094 0.030908 GATCAGGCGGTTCGAGGTAG 59.969 60.000 0.00 0.00 0.00 3.18
3867 7095 0.395311 ATCAGGCGGTTCGAGGTAGA 60.395 55.000 0.00 0.00 0.00 2.59
3868 7096 0.609957 TCAGGCGGTTCGAGGTAGAA 60.610 55.000 0.00 0.00 0.00 2.10
3869 7097 0.179134 CAGGCGGTTCGAGGTAGAAG 60.179 60.000 0.00 0.00 0.00 2.85
3870 7098 0.323178 AGGCGGTTCGAGGTAGAAGA 60.323 55.000 0.00 0.00 0.00 2.87
3871 7099 0.745468 GGCGGTTCGAGGTAGAAGAT 59.255 55.000 0.00 0.00 0.00 2.40
3872 7100 1.136500 GGCGGTTCGAGGTAGAAGATT 59.864 52.381 0.00 0.00 0.00 2.40
3873 7101 2.418334 GGCGGTTCGAGGTAGAAGATTT 60.418 50.000 0.00 0.00 0.00 2.17
3874 7102 3.181483 GGCGGTTCGAGGTAGAAGATTTA 60.181 47.826 0.00 0.00 0.00 1.40
3875 7103 4.501058 GGCGGTTCGAGGTAGAAGATTTAT 60.501 45.833 0.00 0.00 0.00 1.40
3876 7104 5.048507 GCGGTTCGAGGTAGAAGATTTATT 58.951 41.667 0.00 0.00 0.00 1.40
3877 7105 5.522824 GCGGTTCGAGGTAGAAGATTTATTT 59.477 40.000 0.00 0.00 0.00 1.40
3878 7106 6.036844 GCGGTTCGAGGTAGAAGATTTATTTT 59.963 38.462 0.00 0.00 0.00 1.82
3879 7107 7.413767 GCGGTTCGAGGTAGAAGATTTATTTTT 60.414 37.037 0.00 0.00 0.00 1.94
3908 7136 3.737702 GGTTACCCCAGTCTTTGCA 57.262 52.632 0.00 0.00 0.00 4.08
3909 7137 2.215942 GGTTACCCCAGTCTTTGCAT 57.784 50.000 0.00 0.00 0.00 3.96
3910 7138 2.092323 GGTTACCCCAGTCTTTGCATC 58.908 52.381 0.00 0.00 0.00 3.91
3911 7139 2.554344 GGTTACCCCAGTCTTTGCATCA 60.554 50.000 0.00 0.00 0.00 3.07
3912 7140 2.749621 GTTACCCCAGTCTTTGCATCAG 59.250 50.000 0.00 0.00 0.00 2.90
3913 7141 1.067295 ACCCCAGTCTTTGCATCAGA 58.933 50.000 0.00 0.00 0.00 3.27
3914 7142 1.425066 ACCCCAGTCTTTGCATCAGAA 59.575 47.619 0.00 0.00 0.00 3.02
3915 7143 2.158475 ACCCCAGTCTTTGCATCAGAAA 60.158 45.455 0.00 0.00 0.00 2.52
3916 7144 2.490903 CCCCAGTCTTTGCATCAGAAAG 59.509 50.000 0.00 0.00 0.00 2.62
3917 7145 3.415212 CCCAGTCTTTGCATCAGAAAGA 58.585 45.455 0.00 0.00 37.15 2.52
3918 7146 4.015084 CCCAGTCTTTGCATCAGAAAGAT 58.985 43.478 1.34 0.00 40.60 2.40
3927 7155 3.532892 CATCAGAAAGATGCATACGGC 57.467 47.619 0.00 0.00 46.90 5.68
3928 7156 2.988010 TCAGAAAGATGCATACGGCT 57.012 45.000 0.00 0.00 45.15 5.52
3929 7157 2.826428 TCAGAAAGATGCATACGGCTC 58.174 47.619 0.00 0.00 45.15 4.70
3930 7158 2.168313 TCAGAAAGATGCATACGGCTCA 59.832 45.455 0.00 0.00 45.15 4.26
3931 7159 3.136763 CAGAAAGATGCATACGGCTCAT 58.863 45.455 0.00 0.00 45.15 2.90
3932 7160 4.039124 TCAGAAAGATGCATACGGCTCATA 59.961 41.667 0.00 0.00 45.15 2.15
3933 7161 4.934001 CAGAAAGATGCATACGGCTCATAT 59.066 41.667 0.00 0.00 45.15 1.78
3934 7162 5.410746 CAGAAAGATGCATACGGCTCATATT 59.589 40.000 0.00 0.00 45.15 1.28
3935 7163 6.591448 CAGAAAGATGCATACGGCTCATATTA 59.409 38.462 0.00 0.00 45.15 0.98
3936 7164 7.279536 CAGAAAGATGCATACGGCTCATATTAT 59.720 37.037 0.00 0.00 45.15 1.28
3937 7165 7.826252 AGAAAGATGCATACGGCTCATATTATT 59.174 33.333 0.00 0.00 45.15 1.40
3938 7166 9.098355 GAAAGATGCATACGGCTCATATTATTA 57.902 33.333 0.00 0.00 45.15 0.98
3939 7167 9.448438 AAAGATGCATACGGCTCATATTATTAA 57.552 29.630 0.00 0.00 45.15 1.40
3940 7168 9.448438 AAGATGCATACGGCTCATATTATTAAA 57.552 29.630 0.00 0.00 45.15 1.52
3941 7169 9.448438 AGATGCATACGGCTCATATTATTAAAA 57.552 29.630 0.00 0.00 45.15 1.52
3942 7170 9.708222 GATGCATACGGCTCATATTATTAAAAG 57.292 33.333 0.00 0.00 45.15 2.27
3943 7171 7.526608 TGCATACGGCTCATATTATTAAAAGC 58.473 34.615 0.00 0.00 45.15 3.51
3944 7172 7.174080 TGCATACGGCTCATATTATTAAAAGCA 59.826 33.333 0.00 0.00 45.15 3.91
3945 7173 8.020819 GCATACGGCTCATATTATTAAAAGCAA 58.979 33.333 0.00 0.00 40.25 3.91
3946 7174 9.891828 CATACGGCTCATATTATTAAAAGCAAA 57.108 29.630 0.00 0.00 0.00 3.68
3948 7176 8.628882 ACGGCTCATATTATTAAAAGCAAAAC 57.371 30.769 0.00 0.00 0.00 2.43
3949 7177 7.704899 ACGGCTCATATTATTAAAAGCAAAACC 59.295 33.333 0.00 0.00 0.00 3.27
3950 7178 7.704472 CGGCTCATATTATTAAAAGCAAAACCA 59.296 33.333 0.00 0.00 0.00 3.67
3951 7179 9.034544 GGCTCATATTATTAAAAGCAAAACCAG 57.965 33.333 0.00 0.00 0.00 4.00
3952 7180 9.586435 GCTCATATTATTAAAAGCAAAACCAGT 57.414 29.630 0.00 0.00 0.00 4.00
3961 7189 8.865590 TTAAAAGCAAAACCAGTATCAAAGTC 57.134 30.769 0.00 0.00 0.00 3.01
3962 7190 6.715347 AAAGCAAAACCAGTATCAAAGTCT 57.285 33.333 0.00 0.00 0.00 3.24
3963 7191 5.948992 AGCAAAACCAGTATCAAAGTCTC 57.051 39.130 0.00 0.00 0.00 3.36
3964 7192 4.762251 AGCAAAACCAGTATCAAAGTCTCC 59.238 41.667 0.00 0.00 0.00 3.71
3965 7193 4.762251 GCAAAACCAGTATCAAAGTCTCCT 59.238 41.667 0.00 0.00 0.00 3.69
3966 7194 5.335191 GCAAAACCAGTATCAAAGTCTCCTG 60.335 44.000 0.00 0.00 0.00 3.86
3967 7195 5.568620 AAACCAGTATCAAAGTCTCCTGT 57.431 39.130 0.00 0.00 0.00 4.00
3968 7196 4.543590 ACCAGTATCAAAGTCTCCTGTG 57.456 45.455 0.00 0.00 0.00 3.66
3969 7197 3.904339 ACCAGTATCAAAGTCTCCTGTGT 59.096 43.478 0.00 0.00 0.00 3.72
3970 7198 4.021016 ACCAGTATCAAAGTCTCCTGTGTC 60.021 45.833 0.00 0.00 0.00 3.67
3971 7199 4.221703 CCAGTATCAAAGTCTCCTGTGTCT 59.778 45.833 0.00 0.00 0.00 3.41
3972 7200 5.406649 CAGTATCAAAGTCTCCTGTGTCTC 58.593 45.833 0.00 0.00 0.00 3.36
3973 7201 5.047731 CAGTATCAAAGTCTCCTGTGTCTCA 60.048 44.000 0.00 0.00 0.00 3.27
3974 7202 4.963318 ATCAAAGTCTCCTGTGTCTCAA 57.037 40.909 0.00 0.00 0.00 3.02
3975 7203 4.753516 TCAAAGTCTCCTGTGTCTCAAA 57.246 40.909 0.00 0.00 0.00 2.69
3976 7204 4.697514 TCAAAGTCTCCTGTGTCTCAAAG 58.302 43.478 0.00 0.00 0.00 2.77
3977 7205 4.162320 TCAAAGTCTCCTGTGTCTCAAAGT 59.838 41.667 0.00 0.00 0.00 2.66
3978 7206 5.362717 TCAAAGTCTCCTGTGTCTCAAAGTA 59.637 40.000 0.00 0.00 0.00 2.24
3979 7207 4.857509 AGTCTCCTGTGTCTCAAAGTAC 57.142 45.455 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.040461 CCGAGAGAAAATCATAGGCCCTAA 59.960 45.833 0.00 0.00 0.00 2.69
30 31 2.104963 ACCGAGAGAAAATCATAGGCCC 59.895 50.000 0.00 0.00 0.00 5.80
34 35 6.418226 CGTCCTTTACCGAGAGAAAATCATAG 59.582 42.308 0.00 0.00 0.00 2.23
35 36 6.095860 TCGTCCTTTACCGAGAGAAAATCATA 59.904 38.462 0.00 0.00 0.00 2.15
37 38 4.219070 TCGTCCTTTACCGAGAGAAAATCA 59.781 41.667 0.00 0.00 0.00 2.57
75 76 1.603802 GACCACATGGGCATATTCGTG 59.396 52.381 0.00 0.00 44.76 4.35
113 114 2.030185 ACGACTTCAATCACTACAGCGT 60.030 45.455 0.00 0.00 0.00 5.07
124 131 4.609783 CGGCGAAAAAGTTACGACTTCAAT 60.610 41.667 0.00 0.00 45.18 2.57
135 142 2.259266 TAGGTTCCGGCGAAAAAGTT 57.741 45.000 9.30 0.00 0.00 2.66
151 158 2.641815 AGGGAATGCTTGCTCCTATAGG 59.358 50.000 13.07 13.07 31.88 2.57
152 159 3.326006 TGAGGGAATGCTTGCTCCTATAG 59.674 47.826 0.00 0.00 31.88 1.31
164 171 3.248602 CGCTAAACATAGTGAGGGAATGC 59.751 47.826 0.00 0.00 0.00 3.56
209 216 4.733850 TGAAGATGCTCTACACACGTTAG 58.266 43.478 0.00 0.00 0.00 2.34
213 220 2.862536 CCATGAAGATGCTCTACACACG 59.137 50.000 0.00 0.00 0.00 4.49
370 379 4.575645 CCAAACTTTGGCATCAACACATTT 59.424 37.500 7.63 0.00 45.17 2.32
520 593 7.853929 CGTTAATTCGATTTACAATCCGGATTT 59.146 33.333 27.21 19.26 33.01 2.17
605 3577 1.917782 AAACGCGCGGTGCATGTATT 61.918 50.000 35.22 12.97 46.97 1.89
680 3652 4.579869 ACTCGTGACCTTCTTGCATAAAT 58.420 39.130 0.00 0.00 0.00 1.40
792 3769 2.109834 TCCTTGGGAATTGGCAGAAAGA 59.890 45.455 0.00 0.00 0.00 2.52
806 3783 0.750911 GCTCCTGCATTCTCCTTGGG 60.751 60.000 0.00 0.00 39.41 4.12
826 3803 2.003301 GATCGGCAGAGGAAAGAACAC 58.997 52.381 0.00 0.00 0.00 3.32
839 3816 2.336945 ATGCAAATCTGAGATCGGCA 57.663 45.000 18.93 18.93 0.00 5.69
841 3818 4.573607 TGAGAAATGCAAATCTGAGATCGG 59.426 41.667 9.14 0.00 0.00 4.18
852 3829 1.330234 TGCCTGCTGAGAAATGCAAA 58.670 45.000 0.00 0.00 38.81 3.68
916 3894 1.445410 CCCGTGCTCGATCGTTTCA 60.445 57.895 15.94 8.65 39.71 2.69
950 3928 2.201708 GGTAGGTAGCCGAGGGAGC 61.202 68.421 0.00 0.00 0.00 4.70
1046 4024 1.882623 CACCTCTCCCTTTCACTTTGC 59.117 52.381 0.00 0.00 0.00 3.68
1080 4058 9.031537 TGATATTACATACCTATGATGAACGGT 57.968 33.333 0.00 0.00 37.15 4.83
1129 4298 3.991121 GCAAAGGTCAGAGAGAACACTAC 59.009 47.826 0.00 0.00 35.97 2.73
1188 4357 0.179004 TGTTGGTGTTGAGCCCGAAT 60.179 50.000 0.00 0.00 0.00 3.34
1230 4399 0.973632 TGACGTTGCTCAGGTGGTAT 59.026 50.000 0.00 0.00 0.00 2.73
1384 4553 3.572255 ACGCTCATATTTGGTGGTTTTGT 59.428 39.130 0.00 0.00 0.00 2.83
1436 4609 0.609957 CAATCCCCTGCAGCAAGTGA 60.610 55.000 8.66 0.00 0.00 3.41
1442 4615 0.247460 GGAAAACAATCCCCTGCAGC 59.753 55.000 8.66 0.00 33.05 5.25
1908 5081 0.685097 TGCACCCTGTAGTTCCTGAC 59.315 55.000 0.00 0.00 0.00 3.51
2035 5215 4.713824 ATGTCAGCTGAACAATCAATGG 57.286 40.909 20.19 0.00 34.49 3.16
2038 5218 6.016860 GCCATATATGTCAGCTGAACAATCAA 60.017 38.462 20.19 5.19 34.49 2.57
2049 5229 4.452114 TCAAACATCGCCATATATGTCAGC 59.548 41.667 11.73 7.10 35.30 4.26
2120 5338 2.612221 GGTAACAAGTCCTCGTTCCCAG 60.612 54.545 0.00 0.00 0.00 4.45
2125 5343 0.319405 CCGGGTAACAAGTCCTCGTT 59.681 55.000 0.00 0.00 39.74 3.85
2126 5344 1.969862 CCGGGTAACAAGTCCTCGT 59.030 57.895 0.00 0.00 39.74 4.18
2129 5347 0.696501 ATTGCCGGGTAACAAGTCCT 59.303 50.000 2.18 0.00 39.74 3.85
2134 5352 2.336478 CGCCATTGCCGGGTAACAA 61.336 57.895 2.18 0.00 39.74 2.83
2135 5353 2.748251 CGCCATTGCCGGGTAACA 60.748 61.111 2.18 0.00 39.74 2.41
2136 5354 4.187810 GCGCCATTGCCGGGTAAC 62.188 66.667 2.18 0.00 0.00 2.50
2205 5423 2.203907 AGCTGCTCCACCTGGTCT 60.204 61.111 0.00 0.00 36.34 3.85
2241 5459 0.687427 TGGATGACCAGATCGGCAGA 60.687 55.000 3.85 0.00 41.77 4.26
2872 6090 5.163195 ACCAGAGGAAGTACACAAAGTTCAT 60.163 40.000 0.00 0.00 31.56 2.57
2874 6092 4.511826 CACCAGAGGAAGTACACAAAGTTC 59.488 45.833 0.00 0.00 0.00 3.01
2880 6098 0.317160 CGCACCAGAGGAAGTACACA 59.683 55.000 0.00 0.00 0.00 3.72
3003 6221 0.242555 ACGTTAAAAATGGCCTGCGG 59.757 50.000 3.32 0.00 0.00 5.69
3005 6223 2.030274 ACTCACGTTAAAAATGGCCTGC 60.030 45.455 3.32 0.00 0.00 4.85
3035 6257 2.726351 CCTTCGGGCTCTGTCCTCC 61.726 68.421 0.00 0.00 0.00 4.30
3040 6262 2.032681 GCAACCTTCGGGCTCTGT 59.967 61.111 0.00 0.00 39.10 3.41
3050 6272 1.830847 GAACCAACCCGGCAACCTT 60.831 57.895 0.00 0.00 39.03 3.50
3058 6280 1.896465 AGAGAAGAGAGAACCAACCCG 59.104 52.381 0.00 0.00 0.00 5.28
3096 6319 6.342111 GGGAACTTTGAAACATTAACCACAA 58.658 36.000 0.00 0.00 0.00 3.33
3196 6419 8.467598 GGAAGAAGAATAAGGTAAACATTTCCC 58.532 37.037 0.00 0.00 0.00 3.97
3197 6420 8.467598 GGGAAGAAGAATAAGGTAAACATTTCC 58.532 37.037 0.00 0.00 0.00 3.13
3211 6435 5.010282 GCCTCTTTGTTGGGAAGAAGAATA 58.990 41.667 0.00 0.00 33.10 1.75
3222 6446 0.961753 GGAACTGGCCTCTTTGTTGG 59.038 55.000 3.32 0.00 0.00 3.77
3244 6468 2.578786 TGACCGAAGTTTCTTTTCCCC 58.421 47.619 0.00 0.00 0.00 4.81
3246 6470 6.796705 TTAGATGACCGAAGTTTCTTTTCC 57.203 37.500 0.00 0.00 0.00 3.13
3252 6476 7.581476 TGTTGAAATTAGATGACCGAAGTTTC 58.419 34.615 0.00 0.00 0.00 2.78
3255 6479 7.360361 GTTTGTTGAAATTAGATGACCGAAGT 58.640 34.615 0.00 0.00 0.00 3.01
3315 6543 4.563184 GTCGACTGACCTTTAGCTATTGTG 59.437 45.833 8.70 0.00 39.30 3.33
3316 6544 4.463186 AGTCGACTGACCTTTAGCTATTGT 59.537 41.667 19.30 0.00 46.74 2.71
3317 6545 4.800993 CAGTCGACTGACCTTTAGCTATTG 59.199 45.833 36.73 7.78 46.74 1.90
3318 6546 5.000012 CAGTCGACTGACCTTTAGCTATT 58.000 43.478 36.73 0.00 46.74 1.73
3319 6547 4.640789 CAGTCGACTGACCTTTAGCTAT 57.359 45.455 36.73 0.00 46.74 2.97
3349 6577 9.184062 CTCAAAACTGAATCGATTGATCAAAAA 57.816 29.630 16.96 1.16 32.24 1.94
3350 6578 8.567104 TCTCAAAACTGAATCGATTGATCAAAA 58.433 29.630 16.96 1.54 32.24 2.44
3351 6579 8.098220 TCTCAAAACTGAATCGATTGATCAAA 57.902 30.769 16.96 0.00 32.24 2.69
3352 6580 7.671495 TCTCAAAACTGAATCGATTGATCAA 57.329 32.000 16.96 11.26 32.24 2.57
3353 6581 7.148356 CCTTCTCAAAACTGAATCGATTGATCA 60.148 37.037 16.96 6.74 32.24 2.92
3354 6582 7.065085 TCCTTCTCAAAACTGAATCGATTGATC 59.935 37.037 16.96 1.49 32.24 2.92
3355 6583 6.881065 TCCTTCTCAAAACTGAATCGATTGAT 59.119 34.615 16.96 0.00 35.98 2.57
3356 6584 6.230472 TCCTTCTCAAAACTGAATCGATTGA 58.770 36.000 16.96 6.19 0.00 2.57
3357 6585 6.486253 TCCTTCTCAAAACTGAATCGATTG 57.514 37.500 16.96 4.53 0.00 2.67
3358 6586 6.936900 TCTTCCTTCTCAAAACTGAATCGATT 59.063 34.615 11.20 11.20 0.00 3.34
3359 6587 6.467677 TCTTCCTTCTCAAAACTGAATCGAT 58.532 36.000 0.00 0.00 0.00 3.59
3360 6588 5.853936 TCTTCCTTCTCAAAACTGAATCGA 58.146 37.500 0.00 0.00 0.00 3.59
3361 6589 6.348050 CCTTCTTCCTTCTCAAAACTGAATCG 60.348 42.308 0.00 0.00 0.00 3.34
3362 6590 6.712547 TCCTTCTTCCTTCTCAAAACTGAATC 59.287 38.462 0.00 0.00 0.00 2.52
3363 6591 6.605119 TCCTTCTTCCTTCTCAAAACTGAAT 58.395 36.000 0.00 0.00 0.00 2.57
3364 6592 6.001449 TCCTTCTTCCTTCTCAAAACTGAA 57.999 37.500 0.00 0.00 0.00 3.02
3365 6593 5.630415 TCCTTCTTCCTTCTCAAAACTGA 57.370 39.130 0.00 0.00 0.00 3.41
3366 6594 5.278218 GCTTCCTTCTTCCTTCTCAAAACTG 60.278 44.000 0.00 0.00 0.00 3.16
3367 6595 4.824537 GCTTCCTTCTTCCTTCTCAAAACT 59.175 41.667 0.00 0.00 0.00 2.66
3368 6596 4.580580 TGCTTCCTTCTTCCTTCTCAAAAC 59.419 41.667 0.00 0.00 0.00 2.43
3369 6597 4.580580 GTGCTTCCTTCTTCCTTCTCAAAA 59.419 41.667 0.00 0.00 0.00 2.44
3370 6598 4.137543 GTGCTTCCTTCTTCCTTCTCAAA 58.862 43.478 0.00 0.00 0.00 2.69
3371 6599 3.496870 GGTGCTTCCTTCTTCCTTCTCAA 60.497 47.826 0.00 0.00 0.00 3.02
3372 6600 2.039084 GGTGCTTCCTTCTTCCTTCTCA 59.961 50.000 0.00 0.00 0.00 3.27
3373 6601 2.039084 TGGTGCTTCCTTCTTCCTTCTC 59.961 50.000 0.80 0.00 37.07 2.87
3374 6602 2.057922 TGGTGCTTCCTTCTTCCTTCT 58.942 47.619 0.80 0.00 37.07 2.85
3375 6603 2.568623 TGGTGCTTCCTTCTTCCTTC 57.431 50.000 0.80 0.00 37.07 3.46
3376 6604 2.443255 TCTTGGTGCTTCCTTCTTCCTT 59.557 45.455 0.80 0.00 37.07 3.36
3377 6605 2.057922 TCTTGGTGCTTCCTTCTTCCT 58.942 47.619 0.80 0.00 37.07 3.36
3378 6606 2.155279 GTCTTGGTGCTTCCTTCTTCC 58.845 52.381 0.80 0.00 37.07 3.46
3379 6607 2.810852 CTGTCTTGGTGCTTCCTTCTTC 59.189 50.000 0.80 0.00 37.07 2.87
3380 6608 2.439507 TCTGTCTTGGTGCTTCCTTCTT 59.560 45.455 0.80 0.00 37.07 2.52
3381 6609 2.038295 CTCTGTCTTGGTGCTTCCTTCT 59.962 50.000 0.80 0.00 37.07 2.85
3382 6610 2.421619 CTCTGTCTTGGTGCTTCCTTC 58.578 52.381 0.80 0.00 37.07 3.46
3383 6611 1.072965 CCTCTGTCTTGGTGCTTCCTT 59.927 52.381 0.80 0.00 37.07 3.36
3384 6612 0.689623 CCTCTGTCTTGGTGCTTCCT 59.310 55.000 0.80 0.00 37.07 3.36
3385 6613 0.687354 TCCTCTGTCTTGGTGCTTCC 59.313 55.000 0.00 0.00 0.00 3.46
3386 6614 2.421619 CTTCCTCTGTCTTGGTGCTTC 58.578 52.381 0.00 0.00 0.00 3.86
3387 6615 1.072965 CCTTCCTCTGTCTTGGTGCTT 59.927 52.381 0.00 0.00 0.00 3.91
3388 6616 0.689623 CCTTCCTCTGTCTTGGTGCT 59.310 55.000 0.00 0.00 0.00 4.40
3389 6617 0.687354 TCCTTCCTCTGTCTTGGTGC 59.313 55.000 0.00 0.00 0.00 5.01
3390 6618 2.028567 GTCTCCTTCCTCTGTCTTGGTG 60.029 54.545 0.00 0.00 0.00 4.17
3391 6619 2.252714 GTCTCCTTCCTCTGTCTTGGT 58.747 52.381 0.00 0.00 0.00 3.67
3392 6620 1.203523 CGTCTCCTTCCTCTGTCTTGG 59.796 57.143 0.00 0.00 0.00 3.61
3393 6621 1.203523 CCGTCTCCTTCCTCTGTCTTG 59.796 57.143 0.00 0.00 0.00 3.02
3394 6622 1.551452 CCGTCTCCTTCCTCTGTCTT 58.449 55.000 0.00 0.00 0.00 3.01
3395 6623 0.968393 GCCGTCTCCTTCCTCTGTCT 60.968 60.000 0.00 0.00 0.00 3.41
3396 6624 1.513622 GCCGTCTCCTTCCTCTGTC 59.486 63.158 0.00 0.00 0.00 3.51
3397 6625 2.344203 CGCCGTCTCCTTCCTCTGT 61.344 63.158 0.00 0.00 0.00 3.41
3398 6626 1.999071 CTCGCCGTCTCCTTCCTCTG 61.999 65.000 0.00 0.00 0.00 3.35
3399 6627 1.751162 CTCGCCGTCTCCTTCCTCT 60.751 63.158 0.00 0.00 0.00 3.69
3400 6628 2.776913 CCTCGCCGTCTCCTTCCTC 61.777 68.421 0.00 0.00 0.00 3.71
3401 6629 2.756283 CCTCGCCGTCTCCTTCCT 60.756 66.667 0.00 0.00 0.00 3.36
3402 6630 4.516195 GCCTCGCCGTCTCCTTCC 62.516 72.222 0.00 0.00 0.00 3.46
3403 6631 4.516195 GGCCTCGCCGTCTCCTTC 62.516 72.222 0.00 0.00 39.62 3.46
3426 6654 2.671619 TTGCTTCTTTCCCCGGCG 60.672 61.111 0.00 0.00 0.00 6.46
3427 6655 2.636412 GGTTGCTTCTTTCCCCGGC 61.636 63.158 0.00 0.00 0.00 6.13
3428 6656 1.977009 GGGTTGCTTCTTTCCCCGG 60.977 63.158 0.00 0.00 34.32 5.73
3429 6657 0.825840 TTGGGTTGCTTCTTTCCCCG 60.826 55.000 0.00 0.00 39.20 5.73
3430 6658 1.550524 GATTGGGTTGCTTCTTTCCCC 59.449 52.381 0.00 0.00 39.20 4.81
3431 6659 2.529632 AGATTGGGTTGCTTCTTTCCC 58.470 47.619 0.00 0.00 40.26 3.97
3432 6660 5.336770 CCTTAAGATTGGGTTGCTTCTTTCC 60.337 44.000 3.36 0.00 31.29 3.13
3433 6661 5.336770 CCCTTAAGATTGGGTTGCTTCTTTC 60.337 44.000 3.36 0.00 38.65 2.62
3434 6662 4.528206 CCCTTAAGATTGGGTTGCTTCTTT 59.472 41.667 3.36 0.00 38.65 2.52
3435 6663 4.089361 CCCTTAAGATTGGGTTGCTTCTT 58.911 43.478 3.36 0.00 38.65 2.52
3436 6664 3.701664 CCCTTAAGATTGGGTTGCTTCT 58.298 45.455 3.36 0.00 38.65 2.85
3445 6673 2.456577 CCCCAACACCCTTAAGATTGG 58.543 52.381 3.36 11.46 39.67 3.16
3446 6674 2.225267 ACCCCCAACACCCTTAAGATTG 60.225 50.000 3.36 2.92 0.00 2.67
3447 6675 2.078611 ACCCCCAACACCCTTAAGATT 58.921 47.619 3.36 0.00 0.00 2.40
3448 6676 1.357761 CACCCCCAACACCCTTAAGAT 59.642 52.381 3.36 0.00 0.00 2.40
3449 6677 0.774908 CACCCCCAACACCCTTAAGA 59.225 55.000 3.36 0.00 0.00 2.10
3450 6678 0.774908 TCACCCCCAACACCCTTAAG 59.225 55.000 0.00 0.00 0.00 1.85
3451 6679 1.146152 CTTCACCCCCAACACCCTTAA 59.854 52.381 0.00 0.00 0.00 1.85
3452 6680 0.774908 CTTCACCCCCAACACCCTTA 59.225 55.000 0.00 0.00 0.00 2.69
3453 6681 1.541672 CTTCACCCCCAACACCCTT 59.458 57.895 0.00 0.00 0.00 3.95
3454 6682 2.469765 CCTTCACCCCCAACACCCT 61.470 63.158 0.00 0.00 0.00 4.34
3455 6683 2.117423 CCTTCACCCCCAACACCC 59.883 66.667 0.00 0.00 0.00 4.61
3456 6684 1.530655 CACCTTCACCCCCAACACC 60.531 63.158 0.00 0.00 0.00 4.16
3457 6685 2.200337 GCACCTTCACCCCCAACAC 61.200 63.158 0.00 0.00 0.00 3.32
3458 6686 2.197324 GCACCTTCACCCCCAACA 59.803 61.111 0.00 0.00 0.00 3.33
3459 6687 1.903404 CTGCACCTTCACCCCCAAC 60.903 63.158 0.00 0.00 0.00 3.77
3460 6688 1.943730 AACTGCACCTTCACCCCCAA 61.944 55.000 0.00 0.00 0.00 4.12
3461 6689 2.351924 GAACTGCACCTTCACCCCCA 62.352 60.000 0.00 0.00 0.00 4.96
3462 6690 1.603739 GAACTGCACCTTCACCCCC 60.604 63.158 0.00 0.00 0.00 5.40
3463 6691 1.966451 CGAACTGCACCTTCACCCC 60.966 63.158 0.00 0.00 0.00 4.95
3464 6692 2.617274 GCGAACTGCACCTTCACCC 61.617 63.158 0.00 0.00 45.45 4.61
3465 6693 2.946762 GCGAACTGCACCTTCACC 59.053 61.111 0.00 0.00 45.45 4.02
3795 7023 3.966543 CTTTCACCACCCCGCCCT 61.967 66.667 0.00 0.00 0.00 5.19
3796 7024 4.280019 ACTTTCACCACCCCGCCC 62.280 66.667 0.00 0.00 0.00 6.13
3797 7025 2.983592 CACTTTCACCACCCCGCC 60.984 66.667 0.00 0.00 0.00 6.13
3798 7026 2.983592 CCACTTTCACCACCCCGC 60.984 66.667 0.00 0.00 0.00 6.13
3799 7027 2.983592 GCCACTTTCACCACCCCG 60.984 66.667 0.00 0.00 0.00 5.73
3800 7028 1.228862 ATGCCACTTTCACCACCCC 60.229 57.895 0.00 0.00 0.00 4.95
3801 7029 1.535204 CCATGCCACTTTCACCACCC 61.535 60.000 0.00 0.00 0.00 4.61
3802 7030 0.827507 ACCATGCCACTTTCACCACC 60.828 55.000 0.00 0.00 0.00 4.61
3803 7031 1.812571 CTACCATGCCACTTTCACCAC 59.187 52.381 0.00 0.00 0.00 4.16
3804 7032 1.271871 CCTACCATGCCACTTTCACCA 60.272 52.381 0.00 0.00 0.00 4.17
3805 7033 1.463674 CCTACCATGCCACTTTCACC 58.536 55.000 0.00 0.00 0.00 4.02
3806 7034 0.811281 GCCTACCATGCCACTTTCAC 59.189 55.000 0.00 0.00 0.00 3.18
3807 7035 3.264574 GCCTACCATGCCACTTTCA 57.735 52.632 0.00 0.00 0.00 2.69
3814 7042 4.175337 TCAGCGGCCTACCATGCC 62.175 66.667 0.00 0.00 45.70 4.40
3815 7043 2.897350 GTCAGCGGCCTACCATGC 60.897 66.667 0.00 0.00 34.57 4.06
3816 7044 2.203070 GGTCAGCGGCCTACCATG 60.203 66.667 14.56 0.00 34.57 3.66
3817 7045 3.849951 CGGTCAGCGGCCTACCAT 61.850 66.667 18.20 0.00 34.57 3.55
3834 7062 4.221422 TGATCTACTGCCGCCCGC 62.221 66.667 0.00 0.00 38.31 6.13
3835 7063 2.028190 CTGATCTACTGCCGCCCG 59.972 66.667 0.00 0.00 0.00 6.13
3836 7064 2.423446 CCTGATCTACTGCCGCCC 59.577 66.667 0.00 0.00 0.00 6.13
3837 7065 2.280457 GCCTGATCTACTGCCGCC 60.280 66.667 0.00 0.00 0.00 6.13
3838 7066 2.659897 CGCCTGATCTACTGCCGC 60.660 66.667 0.00 0.00 0.00 6.53
3839 7067 2.028190 CCGCCTGATCTACTGCCG 59.972 66.667 0.00 0.00 0.00 5.69
3840 7068 0.530870 GAACCGCCTGATCTACTGCC 60.531 60.000 0.00 0.00 0.00 4.85
3841 7069 0.872021 CGAACCGCCTGATCTACTGC 60.872 60.000 0.00 0.00 0.00 4.40
3842 7070 0.738975 TCGAACCGCCTGATCTACTG 59.261 55.000 0.00 0.00 0.00 2.74
3843 7071 1.025812 CTCGAACCGCCTGATCTACT 58.974 55.000 0.00 0.00 0.00 2.57
3844 7072 0.030908 CCTCGAACCGCCTGATCTAC 59.969 60.000 0.00 0.00 0.00 2.59
3845 7073 0.395311 ACCTCGAACCGCCTGATCTA 60.395 55.000 0.00 0.00 0.00 1.98
3846 7074 0.395311 TACCTCGAACCGCCTGATCT 60.395 55.000 0.00 0.00 0.00 2.75
3847 7075 0.030908 CTACCTCGAACCGCCTGATC 59.969 60.000 0.00 0.00 0.00 2.92
3848 7076 0.395311 TCTACCTCGAACCGCCTGAT 60.395 55.000 0.00 0.00 0.00 2.90
3849 7077 0.609957 TTCTACCTCGAACCGCCTGA 60.610 55.000 0.00 0.00 0.00 3.86
3850 7078 0.179134 CTTCTACCTCGAACCGCCTG 60.179 60.000 0.00 0.00 0.00 4.85
3851 7079 0.323178 TCTTCTACCTCGAACCGCCT 60.323 55.000 0.00 0.00 0.00 5.52
3852 7080 0.745468 ATCTTCTACCTCGAACCGCC 59.255 55.000 0.00 0.00 0.00 6.13
3853 7081 2.580966 AATCTTCTACCTCGAACCGC 57.419 50.000 0.00 0.00 0.00 5.68
3854 7082 7.535489 AAAATAAATCTTCTACCTCGAACCG 57.465 36.000 0.00 0.00 0.00 4.44
3891 7119 2.749621 CTGATGCAAAGACTGGGGTAAC 59.250 50.000 0.00 0.00 0.00 2.50
3892 7120 2.642311 TCTGATGCAAAGACTGGGGTAA 59.358 45.455 0.00 0.00 0.00 2.85
3893 7121 2.265367 TCTGATGCAAAGACTGGGGTA 58.735 47.619 0.00 0.00 0.00 3.69
3894 7122 1.067295 TCTGATGCAAAGACTGGGGT 58.933 50.000 0.00 0.00 0.00 4.95
3895 7123 2.205022 TTCTGATGCAAAGACTGGGG 57.795 50.000 2.11 0.00 0.00 4.96
3896 7124 3.415212 TCTTTCTGATGCAAAGACTGGG 58.585 45.455 2.11 0.00 35.40 4.45
3897 7125 4.982999 CATCTTTCTGATGCAAAGACTGG 58.017 43.478 0.00 0.00 44.96 4.00
3908 7136 3.181462 TGAGCCGTATGCATCTTTCTGAT 60.181 43.478 0.19 0.00 44.83 2.90
3909 7137 2.168313 TGAGCCGTATGCATCTTTCTGA 59.832 45.455 0.19 0.00 44.83 3.27
3910 7138 2.554142 TGAGCCGTATGCATCTTTCTG 58.446 47.619 0.19 0.00 44.83 3.02
3911 7139 2.988010 TGAGCCGTATGCATCTTTCT 57.012 45.000 0.19 0.00 44.83 2.52
3912 7140 5.869753 AATATGAGCCGTATGCATCTTTC 57.130 39.130 0.19 0.00 44.83 2.62
3913 7141 7.928307 AATAATATGAGCCGTATGCATCTTT 57.072 32.000 0.19 0.00 44.83 2.52
3914 7142 9.448438 TTTAATAATATGAGCCGTATGCATCTT 57.552 29.630 0.19 0.00 44.83 2.40
3915 7143 9.448438 TTTTAATAATATGAGCCGTATGCATCT 57.552 29.630 0.19 0.00 44.83 2.90
3916 7144 9.708222 CTTTTAATAATATGAGCCGTATGCATC 57.292 33.333 0.19 0.00 44.83 3.91
3917 7145 8.184192 GCTTTTAATAATATGAGCCGTATGCAT 58.816 33.333 3.79 3.79 44.83 3.96
3918 7146 7.174080 TGCTTTTAATAATATGAGCCGTATGCA 59.826 33.333 0.00 0.00 44.83 3.96
3919 7147 7.526608 TGCTTTTAATAATATGAGCCGTATGC 58.473 34.615 0.00 0.00 41.71 3.14
3920 7148 9.891828 TTTGCTTTTAATAATATGAGCCGTATG 57.108 29.630 0.00 0.00 0.00 2.39
3922 7150 9.724839 GTTTTGCTTTTAATAATATGAGCCGTA 57.275 29.630 0.00 0.00 0.00 4.02
3923 7151 7.704899 GGTTTTGCTTTTAATAATATGAGCCGT 59.295 33.333 0.00 0.00 0.00 5.68
3924 7152 7.704472 TGGTTTTGCTTTTAATAATATGAGCCG 59.296 33.333 0.00 0.00 0.00 5.52
3925 7153 8.940768 TGGTTTTGCTTTTAATAATATGAGCC 57.059 30.769 0.00 0.00 0.00 4.70
3926 7154 9.586435 ACTGGTTTTGCTTTTAATAATATGAGC 57.414 29.630 0.00 0.00 0.00 4.26
3935 7163 9.476202 GACTTTGATACTGGTTTTGCTTTTAAT 57.524 29.630 0.00 0.00 0.00 1.40
3936 7164 8.691797 AGACTTTGATACTGGTTTTGCTTTTAA 58.308 29.630 0.00 0.00 0.00 1.52
3937 7165 8.232913 AGACTTTGATACTGGTTTTGCTTTTA 57.767 30.769 0.00 0.00 0.00 1.52
3938 7166 7.112452 AGACTTTGATACTGGTTTTGCTTTT 57.888 32.000 0.00 0.00 0.00 2.27
3939 7167 6.239036 GGAGACTTTGATACTGGTTTTGCTTT 60.239 38.462 0.00 0.00 0.00 3.51
3940 7168 5.241728 GGAGACTTTGATACTGGTTTTGCTT 59.758 40.000 0.00 0.00 0.00 3.91
3941 7169 4.762251 GGAGACTTTGATACTGGTTTTGCT 59.238 41.667 0.00 0.00 0.00 3.91
3942 7170 4.762251 AGGAGACTTTGATACTGGTTTTGC 59.238 41.667 0.00 0.00 37.44 3.68
3943 7171 5.765182 ACAGGAGACTTTGATACTGGTTTTG 59.235 40.000 0.00 0.00 40.21 2.44
3944 7172 5.765182 CACAGGAGACTTTGATACTGGTTTT 59.235 40.000 0.00 0.00 40.68 2.43
3945 7173 5.163195 ACACAGGAGACTTTGATACTGGTTT 60.163 40.000 0.00 0.00 40.68 3.27
3946 7174 4.348168 ACACAGGAGACTTTGATACTGGTT 59.652 41.667 0.00 0.00 40.68 3.67
3947 7175 3.904339 ACACAGGAGACTTTGATACTGGT 59.096 43.478 0.00 0.00 40.68 4.00
3948 7176 4.221703 AGACACAGGAGACTTTGATACTGG 59.778 45.833 0.00 0.00 40.68 4.00
3949 7177 5.047731 TGAGACACAGGAGACTTTGATACTG 60.048 44.000 0.00 0.00 40.68 2.74
3950 7178 5.080337 TGAGACACAGGAGACTTTGATACT 58.920 41.667 0.00 0.00 40.68 2.12
3951 7179 5.392767 TGAGACACAGGAGACTTTGATAC 57.607 43.478 0.00 0.00 40.68 2.24
3952 7180 6.042093 ACTTTGAGACACAGGAGACTTTGATA 59.958 38.462 0.00 0.00 40.68 2.15
3953 7181 4.963318 TTGAGACACAGGAGACTTTGAT 57.037 40.909 0.00 0.00 40.68 2.57
3954 7182 4.162320 ACTTTGAGACACAGGAGACTTTGA 59.838 41.667 0.00 0.00 40.68 2.69
3955 7183 4.446371 ACTTTGAGACACAGGAGACTTTG 58.554 43.478 0.00 0.00 43.85 2.77
3956 7184 4.762289 ACTTTGAGACACAGGAGACTTT 57.238 40.909 0.00 0.00 40.21 2.66
3957 7185 5.203060 GTACTTTGAGACACAGGAGACTT 57.797 43.478 0.00 0.00 40.21 3.01
3958 7186 4.857509 GTACTTTGAGACACAGGAGACT 57.142 45.455 0.00 0.00 46.44 3.24


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

AutoCloner maintained by Alex Coulton.