Multiple sequence alignment - TraesCS7B01G168000

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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 TraesCS7B01G168000 chr7B 100.000 6876 0 0 1 6876 234597569 234590694 0.000000e+00 12698.0
1 TraesCS7B01G168000 chr7B 84.836 732 77 21 4957 5672 576673339 576674052 0.000000e+00 706.0
2 TraesCS7B01G168000 chr7B 93.233 399 19 4 238 628 677353854 677353456 1.290000e-161 580.0
3 TraesCS7B01G168000 chr7B 80.702 627 82 23 18 628 730110273 730110876 1.050000e-122 451.0
4 TraesCS7B01G168000 chr7B 83.333 72 4 1 586 657 438398571 438398634 7.450000e-05 60.2
5 TraesCS7B01G168000 chr7B 100.000 28 0 0 622 649 677353470 677353443 1.200000e-02 52.8
6 TraesCS7B01G168000 chr7A 93.436 5667 270 48 649 6278 275922647 275917046 0.000000e+00 8311.0
7 TraesCS7B01G168000 chr7A 91.460 363 17 6 6522 6876 275916885 275916529 2.880000e-133 486.0
8 TraesCS7B01G168000 chr7D 94.884 4652 186 28 661 5286 255975557 255970932 0.000000e+00 7225.0
9 TraesCS7B01G168000 chr7D 93.968 1575 62 13 5316 6876 255970938 255969383 0.000000e+00 2351.0
10 TraesCS7B01G168000 chr7D 90.581 637 46 7 1 626 21709422 21708789 0.000000e+00 832.0
11 TraesCS7B01G168000 chr3B 93.997 633 29 5 4 628 772409700 772409069 0.000000e+00 950.0
12 TraesCS7B01G168000 chr3B 94.444 36 1 1 622 656 805376948 805376983 3.000000e-03 54.7
13 TraesCS7B01G168000 chr4B 93.060 634 32 6 1 623 91133411 91134043 0.000000e+00 917.0
14 TraesCS7B01G168000 chr4B 80.763 629 78 25 18 628 3760709 3760106 1.050000e-122 451.0
15 TraesCS7B01G168000 chr5B 86.008 729 72 17 4957 5672 704404084 704403373 0.000000e+00 754.0
16 TraesCS7B01G168000 chrUn 94.221 398 17 3 237 628 236404298 236403901 2.740000e-168 603.0
17 TraesCS7B01G168000 chrUn 100.000 29 0 0 622 650 236403915 236403887 3.000000e-03 54.7
18 TraesCS7B01G168000 chr2B 93.750 400 17 4 237 628 207484413 207484014 1.650000e-165 593.0
19 TraesCS7B01G168000 chr2B 93.734 399 18 3 237 628 786212673 786213071 5.940000e-165 592.0
20 TraesCS7B01G168000 chr1B 85.374 588 64 13 4957 5532 570095130 570094553 2.140000e-164 590.0
21 TraesCS7B01G168000 chr1B 81.659 229 32 7 407 628 89473506 89473281 1.520000e-41 182.0
22 TraesCS7B01G168000 chr4A 81.180 627 79 22 18 628 475901730 475901127 1.040000e-127 468.0
23 TraesCS7B01G168000 chr6A 80.702 627 82 22 18 628 466658408 466659011 1.050000e-122 451.0
24 TraesCS7B01G168000 chr6B 80.542 627 79 26 18 628 42474187 42474786 6.330000e-120 442.0
25 TraesCS7B01G168000 chr3A 81.638 403 61 9 10 407 70548955 70548561 8.600000e-84 322.0
26 TraesCS7B01G168000 chr6D 88.258 264 31 0 2265 2528 87273199 87272936 4.000000e-82 316.0
27 TraesCS7B01G168000 chr3D 82.609 299 37 11 341 628 80594225 80594519 4.120000e-62 250.0
28 TraesCS7B01G168000 chr5A 88.421 190 21 1 2339 2528 340402352 340402164 1.930000e-55 228.0
29 TraesCS7B01G168000 chr5A 89.011 91 10 0 996 1086 524247128 524247038 5.640000e-21 113.0
30 TraesCS7B01G168000 chr2A 86.164 159 19 1 2276 2434 526302056 526302211 1.190000e-37 169.0
31 TraesCS7B01G168000 chr1A 92.632 95 7 0 2434 2528 82131694 82131600 3.340000e-28 137.0
32 TraesCS7B01G168000 chr1A 84.286 140 12 1 2434 2573 42506882 42507011 2.010000e-25 128.0
33 TraesCS7B01G168000 chr5D 89.011 91 10 0 996 1086 412367336 412367246 5.640000e-21 113.0


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 TraesCS7B01G168000 chr7B 234590694 234597569 6875 True 12698.0 12698 100.000 1 6876 1 chr7B.!!$R1 6875
1 TraesCS7B01G168000 chr7B 576673339 576674052 713 False 706.0 706 84.836 4957 5672 1 chr7B.!!$F2 715
2 TraesCS7B01G168000 chr7B 730110273 730110876 603 False 451.0 451 80.702 18 628 1 chr7B.!!$F3 610
3 TraesCS7B01G168000 chr7A 275916529 275922647 6118 True 4398.5 8311 92.448 649 6876 2 chr7A.!!$R1 6227
4 TraesCS7B01G168000 chr7D 255969383 255975557 6174 True 4788.0 7225 94.426 661 6876 2 chr7D.!!$R2 6215
5 TraesCS7B01G168000 chr7D 21708789 21709422 633 True 832.0 832 90.581 1 626 1 chr7D.!!$R1 625
6 TraesCS7B01G168000 chr3B 772409069 772409700 631 True 950.0 950 93.997 4 628 1 chr3B.!!$R1 624
7 TraesCS7B01G168000 chr4B 91133411 91134043 632 False 917.0 917 93.060 1 623 1 chr4B.!!$F1 622
8 TraesCS7B01G168000 chr4B 3760106 3760709 603 True 451.0 451 80.763 18 628 1 chr4B.!!$R1 610
9 TraesCS7B01G168000 chr5B 704403373 704404084 711 True 754.0 754 86.008 4957 5672 1 chr5B.!!$R1 715
10 TraesCS7B01G168000 chr1B 570094553 570095130 577 True 590.0 590 85.374 4957 5532 1 chr1B.!!$R2 575
11 TraesCS7B01G168000 chr4A 475901127 475901730 603 True 468.0 468 81.180 18 628 1 chr4A.!!$R1 610
12 TraesCS7B01G168000 chr6A 466658408 466659011 603 False 451.0 451 80.702 18 628 1 chr6A.!!$F1 610
13 TraesCS7B01G168000 chr6B 42474187 42474786 599 False 442.0 442 80.542 18 628 1 chr6B.!!$F1 610

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
797 821 0.321564 CGGCCCACTTGATCTCAACA 60.322 55.0 0.00 0.00 0.00 3.33 F
1681 1713 0.034089 TCTCTGGATGTGCCGAGAGA 60.034 55.0 0.00 0.00 42.98 3.10 F
3107 3149 0.749454 AAGAGGGAATGCATGCGGTC 60.749 55.0 14.09 12.36 0.00 4.79 F
3600 3642 0.034380 AAGCAGTGCAGATGGCTGAT 60.034 50.0 19.20 0.00 45.17 2.90 F
3891 3942 0.325296 TCTCAACTGGCTATCCCCGT 60.325 55.0 0.00 0.00 31.66 5.28 F
5258 5319 0.108774 TTGGTTATCCACACGGCACA 59.891 50.0 0.00 0.00 44.22 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2620 2658 0.324943 AACAGTCCCATGAACCTCCG 59.675 55.000 0.00 0.0 0.00 4.63 R
3570 3612 1.529010 CACTGCTTCTGTTGGCCCA 60.529 57.895 0.00 0.0 0.00 5.36 R
4295 4347 0.326048 AGCTAGGCCCATGACACTCT 60.326 55.000 0.00 0.0 0.00 3.24 R
5254 5315 0.902531 TTCCCCTACAGCTAGTGTGC 59.097 55.000 7.85 0.0 40.69 4.57 R
5638 5710 1.134367 CGTGCTCGGTCTTCCATAGAA 59.866 52.381 0.00 0.0 33.81 2.10 R
6474 6570 1.198408 CACCTTCGAGCACTACGTACA 59.802 52.381 0.00 0.0 0.00 2.90 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
87 89 6.271488 TGCTACATCCATTCTTTTTCAAGG 57.729 37.500 0.00 0.00 0.00 3.61
170 173 1.594293 CTGCAACCGTTGTCTCCGT 60.594 57.895 12.77 0.00 0.00 4.69
273 276 1.538047 ACCGACGGTAACAAGAGCTA 58.462 50.000 20.23 0.00 32.11 3.32
364 368 1.730451 CCCACCGGCGAACTTTTTGT 61.730 55.000 9.30 0.00 0.00 2.83
389 393 1.883732 CGTGGATCCGGCGAGATAT 59.116 57.895 19.81 0.00 0.00 1.63
398 405 3.951663 TCCGGCGAGATATATGAGAGAA 58.048 45.455 9.30 0.00 0.00 2.87
430 437 2.435586 GCGAGTGCAGCATCCAGT 60.436 61.111 0.00 0.00 42.15 4.00
435 442 1.448540 GTGCAGCATCCAGTAGCGT 60.449 57.895 0.00 0.00 35.48 5.07
695 719 6.809630 GAGTATCCATAGAGGGCAAAAATC 57.190 41.667 0.00 0.00 38.24 2.17
709 733 7.966812 AGGGCAAAAATCTAAATGTCTTCTTT 58.033 30.769 0.00 0.00 0.00 2.52
711 735 9.705290 GGGCAAAAATCTAAATGTCTTCTTTTA 57.295 29.630 0.00 0.00 0.00 1.52
724 748 5.600484 TGTCTTCTTTTATTTTGAGGGGCAA 59.400 36.000 0.00 0.00 33.88 4.52
797 821 0.321564 CGGCCCACTTGATCTCAACA 60.322 55.000 0.00 0.00 0.00 3.33
1127 1154 3.975670 CACAACTTCGTCTGTACTGTCTC 59.024 47.826 0.00 0.00 0.00 3.36
1137 1164 4.765856 GTCTGTACTGTCTCTTGTCCCTTA 59.234 45.833 0.00 0.00 0.00 2.69
1147 1174 1.005569 CTTGTCCCTTACCTTTCCCCC 59.994 57.143 0.00 0.00 0.00 5.40
1159 1188 2.234661 CCTTTCCCCCTGAAAAATCTGC 59.765 50.000 0.00 0.00 42.25 4.26
1180 1209 0.828022 CCAGGGGCTACGTTCATGTA 59.172 55.000 0.00 0.00 0.00 2.29
1187 1216 4.439057 GGGCTACGTTCATGTAGATTTGA 58.561 43.478 9.94 0.00 43.65 2.69
1259 1288 4.545706 GCGATGCGGTGGGATGGA 62.546 66.667 0.00 0.00 0.00 3.41
1267 1296 3.017581 GTGGGATGGAGGCTGGGT 61.018 66.667 0.00 0.00 0.00 4.51
1275 1304 1.063070 TGGAGGCTGGGTGGTTTGTA 61.063 55.000 0.00 0.00 0.00 2.41
1277 1306 1.562475 GGAGGCTGGGTGGTTTGTATA 59.438 52.381 0.00 0.00 0.00 1.47
1295 1324 5.351458 TGTATATGTGTGACTCAGCATCAC 58.649 41.667 0.00 0.00 45.58 3.06
1380 1411 2.092323 GGTTTCTGGAGTGTAATGCCC 58.908 52.381 0.00 0.00 0.00 5.36
1382 1413 0.392461 TTCTGGAGTGTAATGCCCGC 60.392 55.000 0.00 0.00 0.00 6.13
1384 1415 2.185867 GGAGTGTAATGCCCGCGA 59.814 61.111 8.23 0.00 0.00 5.87
1389 1420 0.249489 GTGTAATGCCCGCGATCTCT 60.249 55.000 8.23 0.00 0.00 3.10
1403 1434 3.651206 CGATCTCTGATTGCTGCATACT 58.349 45.455 1.84 0.00 0.00 2.12
1408 1439 5.840715 TCTCTGATTGCTGCATACTCTTAG 58.159 41.667 1.84 3.81 0.00 2.18
1415 1446 2.543430 GCTGCATACTCTTAGCTTCTGC 59.457 50.000 0.00 0.00 40.05 4.26
1432 1463 5.332808 GCTTCTGCTTTATGTTTGTGCTTTG 60.333 40.000 0.00 0.00 36.03 2.77
1434 1465 6.088016 TCTGCTTTATGTTTGTGCTTTGAT 57.912 33.333 0.00 0.00 0.00 2.57
1441 1472 9.248291 CTTTATGTTTGTGCTTTGATTAACACT 57.752 29.630 0.00 0.00 34.14 3.55
1447 1478 5.688823 TGTGCTTTGATTAACACTGAATCG 58.311 37.500 0.00 0.00 36.30 3.34
1464 1495 7.065085 CACTGAATCGTCAATGGATTAGAGTTT 59.935 37.037 0.00 0.00 34.41 2.66
1473 1504 3.533146 TGGATTAGAGTTTGGGGGTGTA 58.467 45.455 0.00 0.00 0.00 2.90
1499 1530 6.343703 TCGATCTCATAAATGATATGGCTGG 58.656 40.000 0.00 0.00 36.02 4.85
1538 1570 2.229784 GCAGTGGGAGGACTGAATTTTG 59.770 50.000 4.86 0.00 45.39 2.44
1562 1594 2.479566 ATCTGTCCAGATGTTTGCGT 57.520 45.000 8.95 0.00 45.77 5.24
1567 1599 1.131126 GTCCAGATGTTTGCGTCATGG 59.869 52.381 0.00 0.00 33.80 3.66
1570 1602 2.079158 CAGATGTTTGCGTCATGGACT 58.921 47.619 0.00 0.00 33.18 3.85
1606 1638 5.121142 CACGGTAGTGGTTAGTTGTATTTGG 59.879 44.000 0.00 0.00 44.34 3.28
1638 1670 1.186200 GGGGCAAGAGGGAAAACATC 58.814 55.000 0.00 0.00 0.00 3.06
1676 1708 2.887568 GCGTCTCTGGATGTGCCG 60.888 66.667 0.00 0.00 40.66 5.69
1681 1713 0.034089 TCTCTGGATGTGCCGAGAGA 60.034 55.000 0.00 0.00 42.98 3.10
1696 1728 4.799428 GCCGAGAGACTATGTTAACTGAAC 59.201 45.833 7.22 0.00 38.65 3.18
1742 1774 6.092807 GCTTTTTCAGGAGATTTATGTCGACT 59.907 38.462 17.92 4.95 0.00 4.18
1931 1966 1.303309 GTGCTGCACCTTATAGGCTG 58.697 55.000 21.78 0.00 39.63 4.85
1938 1973 2.907042 GCACCTTATAGGCTGGGATACT 59.093 50.000 0.00 0.00 39.63 2.12
1939 1974 3.055747 GCACCTTATAGGCTGGGATACTC 60.056 52.174 0.00 0.00 39.63 2.59
2052 2087 6.142817 ACAGCTATTGTTTTCGTCATGTTTC 58.857 36.000 0.00 0.00 36.31 2.78
2120 2158 5.045869 TGTGTATTACTAGCTTTCTGGGCTT 60.046 40.000 0.00 0.00 40.74 4.35
2123 2161 7.171678 GTGTATTACTAGCTTTCTGGGCTTATG 59.828 40.741 0.00 0.00 40.74 1.90
2170 2208 1.893137 TGTACATAGGAGCATAGCGGG 59.107 52.381 0.00 0.00 0.00 6.13
2263 2301 3.258372 TCTGTTCTCTTTCTGGTATGCGT 59.742 43.478 0.00 0.00 0.00 5.24
2277 2315 5.549347 TGGTATGCGTTTTAGTGTCCTAAA 58.451 37.500 0.00 0.00 40.53 1.85
2311 2349 3.892588 TCCCTCCACAAAATGTAACCAAC 59.107 43.478 0.00 0.00 0.00 3.77
2349 2387 4.643784 GCACCAGAATCAATCAGAATCCTT 59.356 41.667 0.00 0.00 0.00 3.36
2399 2437 2.122783 TGGACGAACCATTTGATCCC 57.877 50.000 0.00 0.00 44.64 3.85
2462 2500 3.217626 CCCAAGTTTTGTTGAGAGAGCT 58.782 45.455 0.00 0.00 0.00 4.09
2603 2641 5.350365 TGTTATTGAAGATGTTACTGGACGC 59.650 40.000 0.00 0.00 0.00 5.19
2620 2658 3.366440 ACGCGAGTCTTTATATGGTCC 57.634 47.619 15.93 0.00 44.19 4.46
2642 2680 2.489073 GGAGGTTCATGGGACTGTTGTT 60.489 50.000 0.00 0.00 0.00 2.83
2643 2681 2.554032 GAGGTTCATGGGACTGTTGTTG 59.446 50.000 0.00 0.00 0.00 3.33
2716 2754 6.183360 CCAAGAAATACTCCAAGCACATACAG 60.183 42.308 0.00 0.00 0.00 2.74
2864 2902 6.203723 GCTTCGACTTATTGGATATCTTGCTT 59.796 38.462 2.05 0.00 0.00 3.91
2951 2989 3.313526 GGTGCATGTGAGAATGTATCACC 59.686 47.826 3.82 0.00 45.24 4.02
2952 2990 4.194640 GTGCATGTGAGAATGTATCACCT 58.805 43.478 3.82 0.00 45.24 4.00
2970 3008 7.615039 ATCACCTGTCAGAGATAATGATCTT 57.385 36.000 0.00 0.00 42.80 2.40
2975 3013 5.981174 TGTCAGAGATAATGATCTTGCACA 58.019 37.500 0.00 0.00 42.80 4.57
2977 3015 6.880529 TGTCAGAGATAATGATCTTGCACAAA 59.119 34.615 0.00 0.00 42.80 2.83
3000 3038 1.807142 GTTTCTCTTTCCTTGGAGGCG 59.193 52.381 0.00 0.00 34.61 5.52
3007 3045 1.125093 TTCCTTGGAGGCGGTTCTCA 61.125 55.000 0.00 0.00 34.61 3.27
3008 3046 1.078848 CCTTGGAGGCGGTTCTCAG 60.079 63.158 0.00 0.00 35.58 3.35
3014 3055 1.373570 GAGGCGGTTCTCAGATTTGG 58.626 55.000 0.00 0.00 34.13 3.28
3107 3149 0.749454 AAGAGGGAATGCATGCGGTC 60.749 55.000 14.09 12.36 0.00 4.79
3175 3217 1.239347 GAGGCAGTTGAAAGGTGACC 58.761 55.000 0.00 0.00 0.00 4.02
3244 3286 2.554032 ACAAATTGCTCGGTTTCTCAGG 59.446 45.455 0.00 0.00 0.00 3.86
3253 3295 4.319177 CTCGGTTTCTCAGGAATGTTTCT 58.681 43.478 0.00 0.00 0.00 2.52
3283 3325 4.616835 GCTCAGTTTCCATTGTTCCATCAC 60.617 45.833 0.00 0.00 0.00 3.06
3287 3329 5.006386 AGTTTCCATTGTTCCATCACTCTC 58.994 41.667 0.00 0.00 0.00 3.20
3306 3348 5.827797 ACTCTCCAGTTTCAAAAGCATTGTA 59.172 36.000 2.69 0.00 0.00 2.41
3334 3376 5.458779 GTGCTATTTTGACACAAGTTTGACC 59.541 40.000 0.00 0.00 34.43 4.02
3341 3383 2.682856 GACACAAGTTTGACCAGCTGAA 59.317 45.455 17.39 0.00 0.00 3.02
3381 3423 5.241064 TCCTAGCGTAATAGCCTTGAACTAG 59.759 44.000 0.00 0.00 38.01 2.57
3389 3431 3.342377 AGCCTTGAACTAGCCTTTCTC 57.658 47.619 0.00 0.00 0.00 2.87
3405 3447 8.177119 AGCCTTTCTCTATCTAGTGATAACTG 57.823 38.462 0.00 0.00 35.04 3.16
3480 3522 4.843728 CTGGAACTTCTAGGCAATTGGTA 58.156 43.478 7.72 0.00 0.00 3.25
3489 3531 6.560003 TCTAGGCAATTGGTAGATGAAGAA 57.440 37.500 7.72 0.00 0.00 2.52
3570 3612 2.675317 GCGTGTTCTATCTGGAACTGCT 60.675 50.000 7.76 0.00 44.02 4.24
3591 3633 1.285023 GCCAACAGAAGCAGTGCAG 59.715 57.895 19.20 6.61 0.00 4.41
3593 3635 1.531423 CCAACAGAAGCAGTGCAGAT 58.469 50.000 19.20 2.42 0.00 2.90
3600 3642 0.034380 AAGCAGTGCAGATGGCTGAT 60.034 50.000 19.20 0.00 45.17 2.90
3603 3645 1.227639 CAGTGCAGATGGCTGATAGC 58.772 55.000 0.00 0.00 45.17 2.97
3714 3756 3.008485 CCTCTAGGAGGCTTCTGTTTTGT 59.992 47.826 5.28 0.00 43.29 2.83
3722 3764 3.891366 AGGCTTCTGTTTTGTTGCACTAT 59.109 39.130 0.00 0.00 0.00 2.12
3737 3783 5.675684 TGCACTATAGTTTCTCCATCACA 57.324 39.130 1.56 0.00 0.00 3.58
3789 3840 3.424170 GCATTTCTTCTGAAGAGCACGAC 60.424 47.826 18.58 6.00 39.03 4.34
3891 3942 0.325296 TCTCAACTGGCTATCCCCGT 60.325 55.000 0.00 0.00 31.66 5.28
3892 3943 1.063492 TCTCAACTGGCTATCCCCGTA 60.063 52.381 0.00 0.00 30.01 4.02
4001 4052 5.565509 TGGATTGACTATTGCACCTAACAA 58.434 37.500 0.00 0.00 0.00 2.83
4109 4160 4.036971 TGAGCTCCGTAGATTAGAAGAAGC 59.963 45.833 12.15 0.00 0.00 3.86
4119 4170 2.105006 TAGAAGAAGCTGCTGCAAGG 57.895 50.000 18.42 0.00 42.74 3.61
4245 4296 2.541466 AGTTCCGGAATTCACTCCTCT 58.459 47.619 22.04 6.24 32.82 3.69
4324 4376 1.633432 TGGGCCTAGCTTAACACACAT 59.367 47.619 4.53 0.00 0.00 3.21
4325 4377 2.289565 GGGCCTAGCTTAACACACATC 58.710 52.381 0.84 0.00 0.00 3.06
4326 4378 2.289565 GGCCTAGCTTAACACACATCC 58.710 52.381 0.00 0.00 0.00 3.51
4328 4380 2.550978 CCTAGCTTAACACACATCCCG 58.449 52.381 0.00 0.00 0.00 5.14
4329 4381 2.167693 CCTAGCTTAACACACATCCCGA 59.832 50.000 0.00 0.00 0.00 5.14
4330 4382 3.181465 CCTAGCTTAACACACATCCCGAT 60.181 47.826 0.00 0.00 0.00 4.18
4372 4426 5.413833 CCACATAATATGCTGGGATGTCTTC 59.586 44.000 11.52 0.00 31.84 2.87
4373 4427 5.999600 CACATAATATGCTGGGATGTCTTCA 59.000 40.000 0.00 0.00 0.00 3.02
4374 4428 6.657966 CACATAATATGCTGGGATGTCTTCAT 59.342 38.462 0.00 0.00 36.95 2.57
4375 4429 6.657966 ACATAATATGCTGGGATGTCTTCATG 59.342 38.462 0.00 0.00 34.06 3.07
4376 4430 1.688772 ATGCTGGGATGTCTTCATGC 58.311 50.000 0.00 0.00 40.81 4.06
4399 4453 1.331756 GGATTACGCTTGGATGCTGTG 59.668 52.381 0.00 0.00 0.00 3.66
4403 4457 2.330372 CGCTTGGATGCTGTGCTGT 61.330 57.895 0.00 0.00 0.00 4.40
4459 4513 1.659794 GCGGATGTGGCAAACTGTT 59.340 52.632 0.00 0.00 0.00 3.16
4473 4527 9.503427 GTGGCAAACTGTTAATTAATATGAGTC 57.497 33.333 0.31 0.00 0.00 3.36
4530 4584 6.753180 TCTGTAAGATATGCCTGAGATTGTC 58.247 40.000 0.00 0.00 38.67 3.18
4538 4592 2.037121 TGCCTGAGATTGTCGAACTTCA 59.963 45.455 0.00 0.00 0.00 3.02
4688 4742 5.982356 TGCTATTTCTTGCTGTGACTATCT 58.018 37.500 0.00 0.00 0.00 1.98
4729 4788 9.638176 AAGAAGCATGTAATATTTCTTCTCCAT 57.362 29.630 7.97 0.00 39.23 3.41
4744 4803 7.246171 TCTTCTCCATACTCTGTTAAAGCTT 57.754 36.000 0.00 0.00 0.00 3.74
4787 4846 5.620822 CGATGAACATGTTATATTTGGCACG 59.379 40.000 11.95 4.63 0.00 5.34
4853 4912 2.758089 GGAGTCCATGCTTGCAGCG 61.758 63.158 3.60 0.00 46.26 5.18
5246 5307 3.543680 ATAGCGACAGTGCTTGGTTAT 57.456 42.857 3.27 0.00 44.46 1.89
5253 5314 1.464608 CAGTGCTTGGTTATCCACACG 59.535 52.381 7.55 0.00 44.22 4.49
5254 5315 0.802494 GTGCTTGGTTATCCACACGG 59.198 55.000 0.00 0.00 44.22 4.94
5255 5316 0.958382 TGCTTGGTTATCCACACGGC 60.958 55.000 0.00 0.00 44.22 5.68
5257 5318 0.802494 CTTGGTTATCCACACGGCAC 59.198 55.000 0.00 0.00 44.22 5.01
5258 5319 0.108774 TTGGTTATCCACACGGCACA 59.891 50.000 0.00 0.00 44.22 4.57
5259 5320 0.604243 TGGTTATCCACACGGCACAC 60.604 55.000 0.00 0.00 39.03 3.82
5260 5321 0.321298 GGTTATCCACACGGCACACT 60.321 55.000 0.00 0.00 0.00 3.55
5262 5323 2.268298 GTTATCCACACGGCACACTAG 58.732 52.381 0.00 0.00 0.00 2.57
5263 5324 0.174845 TATCCACACGGCACACTAGC 59.825 55.000 0.00 0.00 0.00 3.42
5264 5325 1.544825 ATCCACACGGCACACTAGCT 61.545 55.000 0.00 0.00 34.17 3.32
5265 5326 2.029288 CCACACGGCACACTAGCTG 61.029 63.158 0.00 0.00 46.31 4.24
5478 5547 6.922247 ATGATGATTGATCGCATAGAATCC 57.078 37.500 0.00 0.00 33.17 3.01
5638 5710 6.597672 TGGAATTTGTGATGACGTAGCTAAAT 59.402 34.615 0.00 0.00 0.00 1.40
5857 5929 1.986882 AACAGGAGGCCTTGTTTCTG 58.013 50.000 15.74 15.27 0.00 3.02
5899 5971 7.861629 AGTGTGAAGGATTTAGTAATGGATGA 58.138 34.615 0.00 0.00 0.00 2.92
5985 6057 2.979197 CTCGTGAACCTCCGCGTCT 61.979 63.158 4.92 0.00 40.53 4.18
6010 6082 9.541143 CTAGAAAGGTCTCATTATCCTCTTTTC 57.459 37.037 0.00 0.00 35.12 2.29
6038 6110 0.174845 TCCGGTGATAGCAAGTTCCG 59.825 55.000 0.00 1.07 38.05 4.30
6097 6169 7.577616 GCATGCAGTCAGGATGTATATACAGTA 60.578 40.741 19.80 5.01 46.68 2.74
6098 6170 7.215719 TGCAGTCAGGATGTATATACAGTAC 57.784 40.000 19.80 12.40 39.92 2.73
6099 6171 6.775629 TGCAGTCAGGATGTATATACAGTACA 59.224 38.462 19.80 0.00 39.92 2.90
6100 6172 7.040409 TGCAGTCAGGATGTATATACAGTACAG 60.040 40.741 19.80 9.98 39.92 2.74
6101 6173 7.040340 GCAGTCAGGATGTATATACAGTACAGT 60.040 40.741 19.80 3.11 39.92 3.55
6151 6223 5.041951 TGCATGGTATGTTTTTCGAGTTC 57.958 39.130 0.00 0.00 0.00 3.01
6167 6239 3.241553 CGAGTTCGCAGACATCATGTTAG 59.758 47.826 0.00 0.00 34.32 2.34
6168 6240 4.177026 GAGTTCGCAGACATCATGTTAGT 58.823 43.478 0.00 0.00 34.32 2.24
6270 6342 1.975407 GTGGCCAGCTTGCATCAGT 60.975 57.895 5.11 0.00 0.00 3.41
6474 6570 3.063997 CCGAGCTTAAAGTGAAATCGCAT 59.936 43.478 0.00 0.00 0.00 4.73
6479 6575 4.723862 GCTTAAAGTGAAATCGCATGTACG 59.276 41.667 0.00 0.00 0.00 3.67
6487 6583 2.121116 ATCGCATGTACGTAGTGCTC 57.879 50.000 22.93 2.89 45.46 4.26
6496 6592 1.080772 CGTAGTGCTCGAAGGTGCA 60.081 57.895 0.00 0.00 35.45 4.57
6499 6595 2.734175 CGTAGTGCTCGAAGGTGCATAA 60.734 50.000 0.05 0.00 39.13 1.90
6518 6614 5.589050 GCATAAAAGGAAGGAAATCGGTAGT 59.411 40.000 0.00 0.00 0.00 2.73
6551 6647 6.076298 CGTCAAATCGTCCATTTTATTAACGC 60.076 38.462 0.00 0.00 31.79 4.84
6579 6675 1.376942 GACAGCAGCAGCAGGACAT 60.377 57.895 3.17 0.00 45.49 3.06
6604 6700 4.569564 ACAGACTGGACAAACGAAAACTAC 59.430 41.667 7.51 0.00 0.00 2.73
6612 6708 0.317770 AACGAAAACTACGACGGCGA 60.318 50.000 22.49 0.00 41.64 5.54
6668 6770 7.907389 ACAACCTTCATTATTAGTCACTCTGA 58.093 34.615 0.00 0.00 0.00 3.27
6752 6856 8.093659 AGACAGAATCAAGCTTAGAAAACTTC 57.906 34.615 0.00 0.99 0.00 3.01
6756 6860 6.370166 AGAATCAAGCTTAGAAAACTTCGGAG 59.630 38.462 0.00 0.00 34.02 4.63
6779 6883 4.698304 GGCATAAACAAAGCAGTGGTAGTA 59.302 41.667 0.00 0.00 0.00 1.82
6810 6914 3.293337 TGAAGAAGGAATGATGCATGGG 58.707 45.455 2.46 0.00 0.00 4.00
6812 6916 0.677842 GAAGGAATGATGCATGGGGC 59.322 55.000 2.46 0.00 45.13 5.80
6813 6917 0.761702 AAGGAATGATGCATGGGGCC 60.762 55.000 2.46 0.00 43.89 5.80
6814 6918 1.458020 GGAATGATGCATGGGGCCA 60.458 57.895 2.46 0.00 43.89 5.36
6845 6949 2.169832 TGGCTTACAGCAGTTGACTC 57.830 50.000 0.00 0.00 44.75 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 115 3.755628 GTCGCCCGGTGTAGCTCA 61.756 66.667 0.00 0.00 0.00 4.26
170 173 2.691571 TTGCACGGTCGTAGCAAAA 58.308 47.368 21.26 8.52 44.39 2.44
273 276 0.460987 GTTGCAGCTCCGCTAGATGT 60.461 55.000 0.00 0.00 43.78 3.06
364 368 1.522806 GCCGGATCCACGCATGTAA 60.523 57.895 13.41 0.00 0.00 2.41
389 393 1.734137 GTCGCCGCCTTCTCTCATA 59.266 57.895 0.00 0.00 0.00 2.15
435 442 4.082523 CTTTCTCCGCCGCTCCCA 62.083 66.667 0.00 0.00 0.00 4.37
634 658 0.316204 TTATAAGGGCGACGCTAGGC 59.684 55.000 20.77 2.15 0.00 3.93
635 659 4.650754 ATATTATAAGGGCGACGCTAGG 57.349 45.455 20.77 0.00 0.00 3.02
636 660 5.506982 GGGTATATTATAAGGGCGACGCTAG 60.507 48.000 20.77 0.00 0.00 3.42
637 661 4.339247 GGGTATATTATAAGGGCGACGCTA 59.661 45.833 20.77 4.64 0.00 4.26
638 662 3.131755 GGGTATATTATAAGGGCGACGCT 59.868 47.826 20.77 2.06 0.00 5.07
639 663 3.451526 GGGTATATTATAAGGGCGACGC 58.548 50.000 12.43 12.43 0.00 5.19
640 664 3.703052 AGGGGTATATTATAAGGGCGACG 59.297 47.826 0.00 0.00 0.00 5.12
641 665 6.131961 TCTAGGGGTATATTATAAGGGCGAC 58.868 44.000 0.00 0.00 0.00 5.19
642 666 6.345646 TCTAGGGGTATATTATAAGGGCGA 57.654 41.667 0.00 0.00 0.00 5.54
643 667 6.781014 TCATCTAGGGGTATATTATAAGGGCG 59.219 42.308 0.00 0.00 0.00 6.13
644 668 8.562949 TTCATCTAGGGGTATATTATAAGGGC 57.437 38.462 0.00 0.00 0.00 5.19
645 669 9.160412 CCTTCATCTAGGGGTATATTATAAGGG 57.840 40.741 0.00 0.00 0.00 3.95
672 696 6.538263 AGATTTTTGCCCTCTATGGATACTC 58.462 40.000 0.00 0.00 38.35 2.59
695 719 9.860898 CCCCTCAAAATAAAAGAAGACATTTAG 57.139 33.333 0.00 0.00 0.00 1.85
709 733 5.306678 ACATTCTTGTTGCCCCTCAAAATAA 59.693 36.000 0.00 0.00 36.26 1.40
711 735 3.647590 ACATTCTTGTTGCCCCTCAAAAT 59.352 39.130 0.00 0.00 36.26 1.82
724 748 5.182001 GGCTGACAGACATTTACATTCTTGT 59.818 40.000 6.65 0.00 39.98 3.16
797 821 2.550978 CCATTCGCATTCTCGGTAGTT 58.449 47.619 0.00 0.00 0.00 2.24
849 876 2.349532 GGAGCCGTGCTTATTAATTCGC 60.350 50.000 0.00 0.00 39.88 4.70
1127 1154 1.005569 GGGGGAAAGGTAAGGGACAAG 59.994 57.143 0.00 0.00 0.00 3.16
1137 1164 3.510459 CAGATTTTTCAGGGGGAAAGGT 58.490 45.455 0.00 0.00 45.70 3.50
1147 1174 0.171903 CCCTGGCGCAGATTTTTCAG 59.828 55.000 10.83 4.21 32.44 3.02
1180 1209 2.493278 CAACCCGAAAGCCATCAAATCT 59.507 45.455 0.00 0.00 0.00 2.40
1187 1216 2.618045 CCTAACTCAACCCGAAAGCCAT 60.618 50.000 0.00 0.00 0.00 4.40
1236 1265 2.969238 CCACCGCATCGCCATCTC 60.969 66.667 0.00 0.00 0.00 2.75
1259 1288 2.580783 ACATATACAAACCACCCAGCCT 59.419 45.455 0.00 0.00 0.00 4.58
1267 1296 4.935205 GCTGAGTCACACATATACAAACCA 59.065 41.667 0.00 0.00 0.00 3.67
1275 1304 3.739209 CGGTGATGCTGAGTCACACATAT 60.739 47.826 12.19 0.00 45.99 1.78
1277 1306 1.673923 CGGTGATGCTGAGTCACACAT 60.674 52.381 12.19 8.36 45.99 3.21
1295 1324 4.480541 GACTCTGCATACTGATCATACGG 58.519 47.826 0.00 0.00 0.00 4.02
1380 1411 1.149964 TGCAGCAATCAGAGATCGCG 61.150 55.000 0.00 0.00 0.00 5.87
1382 1413 3.651206 AGTATGCAGCAATCAGAGATCG 58.349 45.455 0.00 0.00 0.00 3.69
1384 1415 4.959560 AGAGTATGCAGCAATCAGAGAT 57.040 40.909 0.00 0.00 0.00 2.75
1389 1420 4.412796 AGCTAAGAGTATGCAGCAATCA 57.587 40.909 0.00 0.00 36.47 2.57
1408 1439 3.905784 AGCACAAACATAAAGCAGAAGC 58.094 40.909 0.00 0.00 42.56 3.86
1415 1446 9.248291 AGTGTTAATCAAAGCACAAACATAAAG 57.752 29.630 0.00 0.00 34.59 1.85
1432 1463 6.662414 TCCATTGACGATTCAGTGTTAATC 57.338 37.500 0.00 0.00 37.69 1.75
1434 1465 8.038351 TCTAATCCATTGACGATTCAGTGTTAA 58.962 33.333 0.00 0.00 37.69 2.01
1441 1472 6.316140 CCAAACTCTAATCCATTGACGATTCA 59.684 38.462 0.00 0.00 32.32 2.57
1447 1478 3.954258 CCCCCAAACTCTAATCCATTGAC 59.046 47.826 0.00 0.00 0.00 3.18
1464 1495 2.168458 TGAGATCGAATACACCCCCA 57.832 50.000 0.00 0.00 0.00 4.96
1473 1504 7.498239 CCAGCCATATCATTTATGAGATCGAAT 59.502 37.037 0.00 0.00 36.67 3.34
1499 1530 5.176223 CCACTGCACAAATCAACTCAATTTC 59.824 40.000 0.00 0.00 0.00 2.17
1562 1594 1.689575 GCTCCTCCCTACAGTCCATGA 60.690 57.143 0.00 0.00 0.00 3.07
1567 1599 1.668101 CCGTGCTCCTCCCTACAGTC 61.668 65.000 0.00 0.00 0.00 3.51
1570 1602 0.395311 CTACCGTGCTCCTCCCTACA 60.395 60.000 0.00 0.00 0.00 2.74
1591 1623 7.013942 ACTCCAAAAGTCCAAATACAACTAACC 59.986 37.037 0.00 0.00 30.02 2.85
1606 1638 2.039879 TCTTGCCCCTACTCCAAAAGTC 59.960 50.000 0.00 0.00 39.55 3.01
1647 1679 3.449377 TCCAGAGACGCCATACATGTTTA 59.551 43.478 2.30 0.00 0.00 2.01
1656 1688 1.153289 GCACATCCAGAGACGCCAT 60.153 57.895 0.00 0.00 0.00 4.40
1659 1691 2.887568 CGGCACATCCAGAGACGC 60.888 66.667 0.00 0.00 31.16 5.19
1676 1708 4.799428 GCCGTTCAGTTAACATAGTCTCTC 59.201 45.833 8.61 0.00 38.03 3.20
1681 1713 4.530710 TCAGCCGTTCAGTTAACATAGT 57.469 40.909 8.61 0.00 38.03 2.12
1696 1728 1.808945 AGATCTGCAAAACTTCAGCCG 59.191 47.619 0.00 0.00 0.00 5.52
1736 1768 6.093404 TCTGTTCATCAAATACTCAGTCGAC 58.907 40.000 7.70 7.70 0.00 4.20
1820 1852 6.541641 TCCAAATTGCTTTGTTTTTACAGCAT 59.458 30.769 0.00 0.00 41.80 3.79
2120 2158 6.573712 TGGCCAGCCATTATCATATACATA 57.426 37.500 7.43 0.00 41.89 2.29
2123 2161 5.887598 TCATTGGCCAGCCATTATCATATAC 59.112 40.000 13.10 0.00 46.64 1.47
2170 2208 2.396590 TCACCGCTTCATTTAGGTCC 57.603 50.000 0.00 0.00 34.25 4.46
2232 2270 6.951198 ACCAGAAAGAGAACAGATAAGAGAGA 59.049 38.462 0.00 0.00 0.00 3.10
2239 2277 5.127194 ACGCATACCAGAAAGAGAACAGATA 59.873 40.000 0.00 0.00 0.00 1.98
2294 2332 4.664150 ACAGGTTGGTTACATTTTGTGG 57.336 40.909 0.00 0.00 0.00 4.17
2295 2333 6.976088 TCATACAGGTTGGTTACATTTTGTG 58.024 36.000 0.00 0.00 0.00 3.33
2311 2349 4.264253 TCTGGTGCTGAAAATCATACAGG 58.736 43.478 0.00 0.00 33.00 4.00
2349 2387 9.933723 CATAATATCATCATGACTGTCAGGTAA 57.066 33.333 20.30 8.95 29.15 2.85
2399 2437 2.744202 GCCCATAGATCGGCTAAACATG 59.256 50.000 2.39 0.00 42.21 3.21
2462 2500 1.032014 GACCAAAGAAACCAGCAGCA 58.968 50.000 0.00 0.00 0.00 4.41
2603 2641 3.057456 CCTCCGGACCATATAAAGACTCG 60.057 52.174 0.00 0.00 0.00 4.18
2620 2658 0.324943 AACAGTCCCATGAACCTCCG 59.675 55.000 0.00 0.00 0.00 4.63
2642 2680 5.625568 AGTCATCATCATCCTCATCAACA 57.374 39.130 0.00 0.00 0.00 3.33
2643 2681 5.277876 GCAAGTCATCATCATCCTCATCAAC 60.278 44.000 0.00 0.00 0.00 3.18
2899 2937 4.351874 AAGCCTAAACACAGCAGACTTA 57.648 40.909 0.00 0.00 0.00 2.24
2951 2989 6.047231 TGTGCAAGATCATTATCTCTGACAG 58.953 40.000 0.00 0.00 41.81 3.51
2952 2990 5.981174 TGTGCAAGATCATTATCTCTGACA 58.019 37.500 0.00 0.00 41.81 3.58
2970 3008 4.016444 AGGAAAGAGAAACTGTTTGTGCA 58.984 39.130 11.03 0.00 27.07 4.57
2975 3013 4.889995 CCTCCAAGGAAAGAGAAACTGTTT 59.110 41.667 5.29 5.29 37.67 2.83
2977 3015 3.748989 GCCTCCAAGGAAAGAGAAACTGT 60.749 47.826 0.00 0.00 37.67 3.55
3000 3038 2.751806 CAAGAGCCCAAATCTGAGAACC 59.248 50.000 0.00 0.00 0.00 3.62
3007 3045 3.493176 GCACAAAACAAGAGCCCAAATCT 60.493 43.478 0.00 0.00 0.00 2.40
3008 3046 2.802247 GCACAAAACAAGAGCCCAAATC 59.198 45.455 0.00 0.00 0.00 2.17
3014 3055 2.514205 ACATGCACAAAACAAGAGCC 57.486 45.000 0.00 0.00 0.00 4.70
3064 3106 4.216411 AGTAGAACTCTCTCTCGCTCTT 57.784 45.455 0.00 0.00 32.70 2.85
3224 3266 2.813754 TCCTGAGAAACCGAGCAATTTG 59.186 45.455 0.00 0.00 0.00 2.32
3227 3269 2.859165 TTCCTGAGAAACCGAGCAAT 57.141 45.000 0.00 0.00 0.00 3.56
3244 3286 5.429957 ACTGAGCAAGTGAAGAAACATTC 57.570 39.130 0.00 0.00 37.88 2.67
3253 3295 3.953612 ACAATGGAAACTGAGCAAGTGAA 59.046 39.130 0.00 0.00 39.81 3.18
3283 3325 5.192327 ACAATGCTTTTGAAACTGGAGAG 57.808 39.130 6.92 0.00 0.00 3.20
3287 3329 7.346695 CACAAATACAATGCTTTTGAAACTGG 58.653 34.615 13.21 0.00 35.03 4.00
3320 3362 2.288666 TCAGCTGGTCAAACTTGTGTC 58.711 47.619 15.13 0.00 0.00 3.67
3334 3376 2.287970 ACACAATGTGCATGTTCAGCTG 60.288 45.455 14.01 7.63 36.98 4.24
3362 3404 2.801111 GGCTAGTTCAAGGCTATTACGC 59.199 50.000 0.00 0.00 38.92 4.42
3381 3423 8.172352 TCAGTTATCACTAGATAGAGAAAGGC 57.828 38.462 0.00 0.00 37.97 4.35
3405 3447 7.454260 ACAAGAAAGGACAATACAAGGAATC 57.546 36.000 0.00 0.00 0.00 2.52
3489 3531 7.607991 ACATCTTCAATATCGTCTTGGAAGTTT 59.392 33.333 0.00 0.00 0.00 2.66
3570 3612 1.529010 CACTGCTTCTGTTGGCCCA 60.529 57.895 0.00 0.00 0.00 5.36
3603 3645 4.421554 TGAGGGCCTGAGGGAGGG 62.422 72.222 12.95 0.00 43.07 4.30
3629 3671 3.754188 GCTGGTGAGCATTTTGAGTAG 57.246 47.619 0.00 0.00 45.46 2.57
3651 3693 1.561542 TCTGAGGGGAAAGCTCCATTC 59.438 52.381 0.00 0.00 44.51 2.67
3714 3756 6.048732 TGTGATGGAGAAACTATAGTGCAA 57.951 37.500 6.06 0.00 0.00 4.08
3722 3764 5.808366 ACAGAACTGTGATGGAGAAACTA 57.192 39.130 6.67 0.00 43.11 2.24
3870 3921 1.001406 CGGGGATAGCCAGTTGAGATC 59.999 57.143 0.00 0.00 35.15 2.75
3891 3942 3.586429 TGGTGATGGAGGATGTGCTATA 58.414 45.455 0.00 0.00 0.00 1.31
3892 3943 2.411583 TGGTGATGGAGGATGTGCTAT 58.588 47.619 0.00 0.00 0.00 2.97
4011 4062 9.494271 GCAAGATACTCATCATCCTGTAATTTA 57.506 33.333 0.00 0.00 33.21 1.40
4109 4160 2.991076 GCAGCTTCCCTTGCAGCAG 61.991 63.158 0.00 0.00 41.54 4.24
4119 4170 4.989279 TTCCATTTCAATAGCAGCTTCC 57.011 40.909 0.00 0.00 0.00 3.46
4230 4281 8.798402 AGAATACTAATAGAGGAGTGAATTCCG 58.202 37.037 2.27 0.00 42.29 4.30
4295 4347 0.326048 AGCTAGGCCCATGACACTCT 60.326 55.000 0.00 0.00 0.00 3.24
4296 4348 0.543749 AAGCTAGGCCCATGACACTC 59.456 55.000 0.00 0.00 0.00 3.51
4324 4376 5.709164 GCCTCTTATACTGTTAGTATCGGGA 59.291 44.000 4.86 2.86 40.37 5.14
4325 4377 5.105837 GGCCTCTTATACTGTTAGTATCGGG 60.106 48.000 4.86 5.39 40.37 5.14
4326 4378 5.475909 TGGCCTCTTATACTGTTAGTATCGG 59.524 44.000 3.32 4.28 40.37 4.18
4328 4380 7.286215 TGTGGCCTCTTATACTGTTAGTATC 57.714 40.000 3.32 0.00 40.37 2.24
4329 4381 7.857404 ATGTGGCCTCTTATACTGTTAGTAT 57.143 36.000 3.32 6.70 43.36 2.12
4330 4382 8.771521 TTATGTGGCCTCTTATACTGTTAGTA 57.228 34.615 3.32 0.00 34.82 1.82
4359 4413 1.337071 CATGCATGAAGACATCCCAGC 59.663 52.381 22.59 0.00 34.15 4.85
4372 4426 1.948834 TCCAAGCGTAATCCATGCATG 59.051 47.619 20.19 20.19 42.04 4.06
4373 4427 2.346766 TCCAAGCGTAATCCATGCAT 57.653 45.000 0.00 0.00 42.04 3.96
4374 4428 1.948834 CATCCAAGCGTAATCCATGCA 59.051 47.619 0.00 0.00 42.04 3.96
4375 4429 1.335324 GCATCCAAGCGTAATCCATGC 60.335 52.381 0.00 0.00 39.67 4.06
4376 4430 2.031420 CAGCATCCAAGCGTAATCCATG 60.031 50.000 0.00 0.00 40.15 3.66
4399 4453 1.745653 GATGAGCAACCCCTAAACAGC 59.254 52.381 0.00 0.00 0.00 4.40
4403 4457 2.274542 TCCTGATGAGCAACCCCTAAA 58.725 47.619 0.00 0.00 0.00 1.85
4440 4494 2.128853 AACAGTTTGCCACATCCGCG 62.129 55.000 0.00 0.00 0.00 6.46
4473 4527 9.748708 TTCATTCCACTCTTGTTCAAAATTAAG 57.251 29.630 0.00 0.00 0.00 1.85
4507 4561 5.632764 CGACAATCTCAGGCATATCTTACAG 59.367 44.000 0.00 0.00 0.00 2.74
4530 4584 8.928270 AGTAAAGGAACATACTATGAAGTTCG 57.072 34.615 2.90 0.00 40.83 3.95
4638 4692 5.381757 ACCCTACACAACTTTGATGCTAAA 58.618 37.500 0.00 0.00 0.00 1.85
4688 4742 8.565896 ACATGCTTCTTATCACTTATTTGACA 57.434 30.769 0.00 0.00 0.00 3.58
4726 4785 9.167311 ACTAATCAAAGCTTTAACAGAGTATGG 57.833 33.333 12.25 1.29 0.00 2.74
4771 4830 2.289547 GTCGCCGTGCCAAATATAACAT 59.710 45.455 0.00 0.00 0.00 2.71
4787 4846 5.748152 ACAAATGCATAATAAATGTGTCGCC 59.252 36.000 0.00 0.00 0.00 5.54
4819 4878 6.884472 TGGACTCCAACTCCTATTTTCATA 57.116 37.500 0.00 0.00 0.00 2.15
4853 4912 3.242870 CCTTTGGTAATGATGCTCGCTTC 60.243 47.826 0.00 0.00 0.00 3.86
5246 5307 2.207229 AGCTAGTGTGCCGTGTGGA 61.207 57.895 0.00 0.00 37.49 4.02
5253 5314 0.976073 TCCCCTACAGCTAGTGTGCC 60.976 60.000 7.85 0.00 40.69 5.01
5254 5315 0.902531 TTCCCCTACAGCTAGTGTGC 59.097 55.000 7.85 0.00 40.69 4.57
5255 5316 2.567615 AGTTTCCCCTACAGCTAGTGTG 59.432 50.000 7.85 1.36 40.69 3.82
5257 5318 6.493802 TGATATAGTTTCCCCTACAGCTAGTG 59.506 42.308 0.00 0.00 0.00 2.74
5258 5319 6.621394 TGATATAGTTTCCCCTACAGCTAGT 58.379 40.000 0.00 0.00 0.00 2.57
5259 5320 7.179338 ACATGATATAGTTTCCCCTACAGCTAG 59.821 40.741 0.00 0.00 0.00 3.42
5260 5321 7.016914 ACATGATATAGTTTCCCCTACAGCTA 58.983 38.462 0.00 0.00 0.00 3.32
5262 5323 6.115448 ACATGATATAGTTTCCCCTACAGC 57.885 41.667 0.00 0.00 0.00 4.40
5263 5324 8.608844 GAAACATGATATAGTTTCCCCTACAG 57.391 38.462 0.00 0.00 44.75 2.74
5304 5366 7.595130 GCACTAATACATAGATGTTGATGACGA 59.405 37.037 0.00 0.00 41.97 4.20
5349 5411 7.775053 ATGGGAATTCAAGCTTTGTTTAGTA 57.225 32.000 7.93 0.00 0.00 1.82
5478 5547 1.806542 CAGAAACGGTTGGGAGTCATG 59.193 52.381 0.00 0.00 0.00 3.07
5638 5710 1.134367 CGTGCTCGGTCTTCCATAGAA 59.866 52.381 0.00 0.00 33.81 2.10
5857 5929 6.817765 TCACACTATCCTGAAATTTGTTCC 57.182 37.500 0.00 0.00 0.00 3.62
5899 5971 5.456921 AGTATGAATCCCCAGTTGAATGT 57.543 39.130 0.00 0.00 0.00 2.71
5946 6018 6.039382 ACGAGAAACCTTGCTAACTTTTCATT 59.961 34.615 0.00 0.00 0.00 2.57
5985 6057 9.273137 AGAAAAGAGGATAATGAGACCTTTCTA 57.727 33.333 0.00 0.00 33.89 2.10
6010 6082 5.760253 ACTTGCTATCACCGGATCATAAAAG 59.240 40.000 9.46 7.01 34.89 2.27
6038 6110 4.735662 TTTGCGACACCAAGTACATAAC 57.264 40.909 0.00 0.00 0.00 1.89
6097 6169 4.453819 GCTTAGATCACAAAAGAGCACTGT 59.546 41.667 0.00 0.00 0.00 3.55
6098 6170 4.694509 AGCTTAGATCACAAAAGAGCACTG 59.305 41.667 0.00 0.00 0.00 3.66
6099 6171 4.904241 AGCTTAGATCACAAAAGAGCACT 58.096 39.130 0.00 0.00 0.00 4.40
6100 6172 6.727824 TTAGCTTAGATCACAAAAGAGCAC 57.272 37.500 0.00 0.00 0.00 4.40
6101 6173 6.317140 CCATTAGCTTAGATCACAAAAGAGCA 59.683 38.462 0.00 0.00 0.00 4.26
6151 6223 3.928992 AGAACACTAACATGATGTCTGCG 59.071 43.478 0.00 0.00 0.00 5.18
6206 6278 1.257750 CCGAGGTGACCATGAGTCCA 61.258 60.000 3.63 0.00 45.68 4.02
6403 6475 3.531538 AGTAAATCCACATAGCCACGTG 58.468 45.455 9.08 9.08 0.00 4.49
6474 6570 1.198408 CACCTTCGAGCACTACGTACA 59.802 52.381 0.00 0.00 0.00 2.90
6479 6575 2.579207 TATGCACCTTCGAGCACTAC 57.421 50.000 0.00 0.00 44.49 2.73
6487 6583 3.343617 TCCTTCCTTTTATGCACCTTCG 58.656 45.455 0.00 0.00 0.00 3.79
6496 6592 6.822170 GTCACTACCGATTTCCTTCCTTTTAT 59.178 38.462 0.00 0.00 0.00 1.40
6499 6595 4.565028 GGTCACTACCGATTTCCTTCCTTT 60.565 45.833 0.00 0.00 35.62 3.11
6579 6675 2.971660 TTCGTTTGTCCAGTCTGTCA 57.028 45.000 0.00 0.00 0.00 3.58
6604 6700 2.956964 GCCTCTTCATCGCCGTCG 60.957 66.667 0.00 0.00 0.00 5.12
6612 6708 2.042831 GTTGCGGCTGCCTCTTCAT 61.043 57.895 16.57 0.00 41.78 2.57
6668 6770 2.223377 GGAACGAAGAAACGATGCAAGT 59.777 45.455 0.00 0.00 37.03 3.16
6669 6771 2.839474 GGAACGAAGAAACGATGCAAG 58.161 47.619 0.00 0.00 37.03 4.01
6670 6772 2.961522 GGAACGAAGAAACGATGCAA 57.038 45.000 0.00 0.00 37.03 4.08
6752 6856 1.812571 ACTGCTTTGTTTATGCCTCCG 59.187 47.619 0.00 0.00 0.00 4.63
6756 6860 3.506067 ACTACCACTGCTTTGTTTATGCC 59.494 43.478 0.00 0.00 0.00 4.40
6817 6921 2.653557 CTGTAAGCCAACAACCCCC 58.346 57.895 0.00 0.00 0.00 5.40
6845 6949 3.853330 CCGCTGCAACATCGGACG 61.853 66.667 3.90 0.00 44.57 4.79


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

AutoCloner maintained by Alex Coulton.