Multiple sequence alignment - TraesCS5D01G520200

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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 TraesCS5D01G520200 chr5D 100.000 5969 0 0 1 5969 541606604 541612572 0.000000e+00 11023.0
1 TraesCS5D01G520200 chr5D 86.059 373 22 17 14 377 541598006 541598357 2.030000e-99 374.0
2 TraesCS5D01G520200 chr5D 76.875 160 18 10 998 1156 541579112 541579253 8.300000e-09 73.1
3 TraesCS5D01G520200 chr4A 94.733 3968 145 20 1578 5525 627519751 627515828 0.000000e+00 6111.0
4 TraesCS5D01G520200 chr4A 87.458 598 27 19 756 1339 627520959 627520396 0.000000e+00 645.0
5 TraesCS5D01G520200 chr4A 86.538 312 14 7 5661 5964 627515808 627515517 9.650000e-83 318.0
6 TraesCS5D01G520200 chr4A 82.911 316 24 11 14 316 627521944 627521646 2.130000e-64 257.0
7 TraesCS5D01G520200 chr4A 81.910 199 15 8 550 745 627521330 627521150 1.340000e-31 148.0
8 TraesCS5D01G520200 chr4A 93.750 48 2 1 330 377 627521474 627521428 2.980000e-08 71.3
9 TraesCS5D01G520200 chr4A 100.000 28 0 0 3243 3270 742155683 742155710 1.100000e-02 52.8
10 TraesCS5D01G520200 chr5B 94.025 3297 136 16 1734 5015 683516916 683520166 0.000000e+00 4940.0
11 TraesCS5D01G520200 chr5B 82.007 867 67 45 510 1354 683515087 683515886 0.000000e+00 654.0
12 TraesCS5D01G520200 chr5B 91.036 357 21 5 5619 5969 683520723 683521074 7.000000e-129 472.0
13 TraesCS5D01G520200 chr5B 88.660 291 25 6 10 297 683514591 683514876 1.230000e-91 348.0
14 TraesCS5D01G520200 chr5B 88.112 286 17 7 5034 5314 683520219 683520492 2.070000e-84 324.0
15 TraesCS5D01G520200 chr5B 81.646 316 34 12 10 311 683506641 683506946 2.150000e-59 241.0
16 TraesCS5D01G520200 chr5B 99.160 119 1 0 1585 1703 683516543 683516661 1.300000e-51 215.0
17 TraesCS5D01G520200 chr6B 86.753 1087 111 19 3283 4359 197772588 197771525 0.000000e+00 1179.0


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 TraesCS5D01G520200 chr5D 541606604 541612572 5968 False 11023.000000 11023 100.000000 1 5969 1 chr5D.!!$F3 5968
1 TraesCS5D01G520200 chr4A 627515517 627521944 6427 True 1258.383333 6111 87.883333 14 5964 6 chr4A.!!$R1 5950
2 TraesCS5D01G520200 chr5B 683514591 683521074 6483 False 1158.833333 4940 90.500000 10 5969 6 chr5B.!!$F2 5959
3 TraesCS5D01G520200 chr6B 197771525 197772588 1063 True 1179.000000 1179 86.753000 3283 4359 1 chr6B.!!$R1 1076

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
392 614 0.034089 AAAGGGCAGCATCCAGTACC 60.034 55.000 0.0 0.0 0.00 3.34 F
1511 2390 0.106918 AAACCGCACCAGAACCAGAA 60.107 50.000 0.0 0.0 0.00 3.02 F
1770 2918 0.108186 CTCGGTGCTTGCCACTATCA 60.108 55.000 0.0 0.0 44.08 2.15 F
2276 3431 0.179100 AAGATGTGGTCGCCGATCTG 60.179 55.000 0.0 0.0 29.39 2.90 F
2699 3854 1.219522 AACGTTCTTCTTCCGCCGTG 61.220 55.000 0.0 0.0 0.00 4.94 F
2980 4135 2.554032 GTGATTCCACTTCCACTGTTGG 59.446 50.000 0.0 0.0 41.13 3.77 F
4688 5899 1.679680 CATGAAAATCATCGCTGCCCT 59.320 47.619 0.0 0.0 34.28 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 3311 0.321671 CAGGTTCCACACTCGATGGT 59.678 55.000 3.55 0.00 38.47 3.55 R
2930 4085 0.250124 CACCGTGCAACCTTGGACTA 60.250 55.000 7.91 0.00 45.83 2.59 R
2936 4091 1.202758 TCTGAATCACCGTGCAACCTT 60.203 47.619 0.00 0.00 0.00 3.50 R
3844 5017 2.161609 GCTTACGCATTAAGGCACTTGT 59.838 45.455 13.17 4.35 42.58 3.16 R
4375 5581 1.082300 CAGAGCAAGTGCAGCAACG 60.082 57.895 6.00 0.00 45.16 4.10 R
4731 5942 0.610232 CCCCCTCAAGCAGTTTCAGG 60.610 60.000 0.00 0.00 0.00 3.86 R
5653 6926 0.179070 TTGTCGCTGCACAGTACCAA 60.179 50.000 0.00 0.00 0.00 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.002791 AGCGTACACAGATGACCAAATG 58.997 45.455 0.00 0.00 0.00 2.32
25 26 2.095853 GCGTACACAGATGACCAAATGG 59.904 50.000 0.00 0.00 42.17 3.16
36 37 2.635443 CCAAATGGAAAGCGCGGGT 61.635 57.895 8.83 0.00 37.39 5.28
91 94 1.305219 TGCCACTATTTGCCAGCGAC 61.305 55.000 0.00 0.00 0.00 5.19
180 193 3.633525 AGCAGATCAAAAAGTTGACAGCA 59.366 39.130 0.00 0.00 46.40 4.41
222 237 3.526197 CGTACGTACGTATGCTGTAGAC 58.474 50.000 33.95 16.22 44.13 2.59
230 245 0.459899 TATGCTGTAGACACCGGCAG 59.540 55.000 0.00 0.00 36.38 4.85
298 363 2.039879 GGTTGGCCAAAAGGAGAGAGTA 59.960 50.000 22.47 0.00 34.09 2.59
299 364 3.075148 GTTGGCCAAAAGGAGAGAGTAC 58.925 50.000 22.47 0.00 0.00 2.73
313 378 1.134907 AGAGTACCCGCACATTTACCG 60.135 52.381 0.00 0.00 0.00 4.02
320 385 3.243636 ACCCGCACATTTACCGTATCTAG 60.244 47.826 0.00 0.00 0.00 2.43
323 388 4.498513 CCGCACATTTACCGTATCTAGTCA 60.499 45.833 0.00 0.00 0.00 3.41
324 389 5.220381 CGCACATTTACCGTATCTAGTCAT 58.780 41.667 0.00 0.00 0.00 3.06
372 594 5.088739 GTGTGAATAAAAATCAGTCGGCAG 58.911 41.667 0.00 0.00 0.00 4.85
379 601 0.678048 AATCAGTCGGCAGAAAGGGC 60.678 55.000 0.00 0.00 0.00 5.19
381 603 2.037136 CAGTCGGCAGAAAGGGCAG 61.037 63.158 0.00 0.00 0.00 4.85
382 604 3.435186 GTCGGCAGAAAGGGCAGC 61.435 66.667 0.00 0.00 0.00 5.25
383 605 3.952508 TCGGCAGAAAGGGCAGCA 61.953 61.111 0.00 0.00 0.00 4.41
384 606 2.753043 CGGCAGAAAGGGCAGCAT 60.753 61.111 0.00 0.00 0.00 3.79
385 607 2.768492 CGGCAGAAAGGGCAGCATC 61.768 63.158 0.00 0.00 0.00 3.91
387 609 1.679977 GCAGAAAGGGCAGCATCCA 60.680 57.895 0.00 0.00 0.00 3.41
388 610 1.664321 GCAGAAAGGGCAGCATCCAG 61.664 60.000 0.00 0.00 0.00 3.86
389 611 0.323178 CAGAAAGGGCAGCATCCAGT 60.323 55.000 0.00 0.00 0.00 4.00
390 612 1.065199 CAGAAAGGGCAGCATCCAGTA 60.065 52.381 0.00 0.00 0.00 2.74
391 613 1.065126 AGAAAGGGCAGCATCCAGTAC 60.065 52.381 0.00 0.00 0.00 2.73
392 614 0.034089 AAAGGGCAGCATCCAGTACC 60.034 55.000 0.00 0.00 0.00 3.34
393 615 2.203070 GGGCAGCATCCAGTACCG 60.203 66.667 0.00 0.00 0.00 4.02
394 616 2.584608 GGCAGCATCCAGTACCGT 59.415 61.111 0.00 0.00 0.00 4.83
395 617 1.078426 GGCAGCATCCAGTACCGTT 60.078 57.895 0.00 0.00 0.00 4.44
397 619 1.571919 GCAGCATCCAGTACCGTTAG 58.428 55.000 0.00 0.00 0.00 2.34
398 620 1.571919 CAGCATCCAGTACCGTTAGC 58.428 55.000 0.00 0.00 0.00 3.09
399 621 1.134818 CAGCATCCAGTACCGTTAGCA 60.135 52.381 0.00 0.00 0.00 3.49
400 622 1.137086 AGCATCCAGTACCGTTAGCAG 59.863 52.381 0.00 0.00 0.00 4.24
416 638 3.409026 AGCAGTCCAAGAAAATCGACT 57.591 42.857 0.00 0.00 36.00 4.18
419 641 4.580580 AGCAGTCCAAGAAAATCGACTTTT 59.419 37.500 0.00 0.00 39.78 2.27
479 701 7.946381 AGACATTCTCTTTTTATTTCCCTCC 57.054 36.000 0.00 0.00 0.00 4.30
483 705 8.367911 ACATTCTCTTTTTATTTCCCTCCAAAC 58.632 33.333 0.00 0.00 0.00 2.93
543 781 8.932945 AGAAAAGAAAAGCAGTAAAGGAAAAG 57.067 30.769 0.00 0.00 0.00 2.27
544 782 7.981789 AGAAAAGAAAAGCAGTAAAGGAAAAGG 59.018 33.333 0.00 0.00 0.00 3.11
545 783 5.201713 AGAAAAGCAGTAAAGGAAAAGGC 57.798 39.130 0.00 0.00 0.00 4.35
546 784 4.039245 AGAAAAGCAGTAAAGGAAAAGGCC 59.961 41.667 0.00 0.00 0.00 5.19
547 785 1.924731 AGCAGTAAAGGAAAAGGCCC 58.075 50.000 0.00 0.00 0.00 5.80
548 786 1.146982 AGCAGTAAAGGAAAAGGCCCA 59.853 47.619 0.00 0.00 0.00 5.36
582 821 4.039124 GGGTATATTCGGTAAGAAACGGGA 59.961 45.833 0.00 0.00 42.91 5.14
583 822 5.453198 GGGTATATTCGGTAAGAAACGGGAA 60.453 44.000 0.00 0.00 42.91 3.97
637 879 0.766288 AAACAAATGGTGGGGTGGGG 60.766 55.000 0.00 0.00 0.00 4.96
638 880 3.002583 CAAATGGTGGGGTGGGGC 61.003 66.667 0.00 0.00 0.00 5.80
653 895 1.621672 GGGGCTGTGGGAGAGAGAAG 61.622 65.000 0.00 0.00 0.00 2.85
665 907 0.391793 GAGAGAAGCCCGAACCCAAG 60.392 60.000 0.00 0.00 0.00 3.61
666 908 1.128188 AGAGAAGCCCGAACCCAAGT 61.128 55.000 0.00 0.00 0.00 3.16
667 909 0.611714 GAGAAGCCCGAACCCAAGTA 59.388 55.000 0.00 0.00 0.00 2.24
670 912 2.045634 GCCCGAACCCAAGTACCC 60.046 66.667 0.00 0.00 0.00 3.69
672 914 1.996086 CCCGAACCCAAGTACCCAT 59.004 57.895 0.00 0.00 0.00 4.00
677 923 0.999712 AACCCAAGTACCCATCCCAG 59.000 55.000 0.00 0.00 0.00 4.45
681 927 1.084842 AAGTACCCATCCCAGCCCT 59.915 57.895 0.00 0.00 0.00 5.19
745 991 2.888998 GCACGAACCAACACGACCC 61.889 63.158 0.00 0.00 0.00 4.46
746 992 1.521906 CACGAACCAACACGACCCA 60.522 57.895 0.00 0.00 0.00 4.51
747 993 0.882927 CACGAACCAACACGACCCAT 60.883 55.000 0.00 0.00 0.00 4.00
749 995 1.296056 CGAACCAACACGACCCATCC 61.296 60.000 0.00 0.00 0.00 3.51
752 998 2.435938 CAACACGACCCATCCCCG 60.436 66.667 0.00 0.00 0.00 5.73
774 1031 0.744281 CGGAGGAGAGAGAGAAAGGC 59.256 60.000 0.00 0.00 0.00 4.35
777 1034 1.142965 GGAGAGAGAGAAAGGCCGC 59.857 63.158 0.00 0.00 0.00 6.53
778 1035 1.226831 GAGAGAGAGAAAGGCCGCG 60.227 63.158 0.00 0.00 0.00 6.46
1115 1577 4.467107 GGAGGAGGAGGAGGCGGT 62.467 72.222 0.00 0.00 0.00 5.68
1215 1677 2.332654 GGCCTTCGTCAATGCCGTT 61.333 57.895 0.00 0.00 34.07 4.44
1346 1808 2.743928 CAAGCAGGTCGGTCAGCC 60.744 66.667 0.00 0.00 0.00 4.85
1394 2264 7.043961 TGCACTCTATTCTAATCAGATCGTT 57.956 36.000 0.00 0.00 0.00 3.85
1416 2286 2.250031 TGACCCATGCTGCAAAGATTT 58.750 42.857 6.36 0.00 0.00 2.17
1457 2327 5.549742 TGCTCTTCATTTTGGTGGATTTT 57.450 34.783 0.00 0.00 0.00 1.82
1481 2360 3.950397 TCTGTAATCCTGCCGATTTGTT 58.050 40.909 1.84 0.00 41.58 2.83
1496 2375 1.931635 TTGTTCCCCCATAGCAAACC 58.068 50.000 0.00 0.00 0.00 3.27
1499 2378 2.044451 CCCCCATAGCAAACCGCA 60.044 61.111 0.00 0.00 46.13 5.69
1500 2379 2.414785 CCCCCATAGCAAACCGCAC 61.415 63.158 0.00 0.00 46.13 5.34
1506 2385 1.135689 CATAGCAAACCGCACCAGAAC 60.136 52.381 0.00 0.00 46.13 3.01
1507 2386 0.887387 TAGCAAACCGCACCAGAACC 60.887 55.000 0.00 0.00 46.13 3.62
1508 2387 2.485795 GCAAACCGCACCAGAACCA 61.486 57.895 0.00 0.00 41.79 3.67
1509 2388 1.654220 CAAACCGCACCAGAACCAG 59.346 57.895 0.00 0.00 0.00 4.00
1510 2389 0.817634 CAAACCGCACCAGAACCAGA 60.818 55.000 0.00 0.00 0.00 3.86
1511 2390 0.106918 AAACCGCACCAGAACCAGAA 60.107 50.000 0.00 0.00 0.00 3.02
1512 2391 0.110486 AACCGCACCAGAACCAGAAT 59.890 50.000 0.00 0.00 0.00 2.40
1513 2392 0.110486 ACCGCACCAGAACCAGAATT 59.890 50.000 0.00 0.00 0.00 2.17
1514 2393 1.247567 CCGCACCAGAACCAGAATTT 58.752 50.000 0.00 0.00 0.00 1.82
1516 2395 1.135972 CGCACCAGAACCAGAATTTCG 60.136 52.381 0.00 0.00 0.00 3.46
1517 2396 1.401539 GCACCAGAACCAGAATTTCGC 60.402 52.381 0.00 0.00 0.00 4.70
1518 2397 1.200020 CACCAGAACCAGAATTTCGCC 59.800 52.381 0.00 0.00 0.00 5.54
1519 2398 0.811281 CCAGAACCAGAATTTCGCCC 59.189 55.000 0.00 0.00 0.00 6.13
1520 2399 0.811281 CAGAACCAGAATTTCGCCCC 59.189 55.000 0.00 0.00 0.00 5.80
1543 2422 1.732259 GTTCTGATGCGGTTACCACAG 59.268 52.381 1.13 5.50 0.00 3.66
1544 2423 1.262417 TCTGATGCGGTTACCACAGA 58.738 50.000 1.13 7.70 33.06 3.41
1548 2427 2.205074 GATGCGGTTACCACAGAGATG 58.795 52.381 1.13 0.00 0.00 2.90
1549 2428 1.262417 TGCGGTTACCACAGAGATGA 58.738 50.000 1.13 0.00 0.00 2.92
1570 2454 8.216423 AGATGATGAATTTGCCATCTAGTACTT 58.784 33.333 0.00 0.00 42.57 2.24
1571 2455 9.494271 GATGATGAATTTGCCATCTAGTACTTA 57.506 33.333 0.00 0.00 40.65 2.24
1572 2456 8.662781 TGATGAATTTGCCATCTAGTACTTAC 57.337 34.615 0.00 0.00 40.65 2.34
1573 2457 8.486210 TGATGAATTTGCCATCTAGTACTTACT 58.514 33.333 0.00 0.00 40.65 2.24
1574 2458 9.982651 GATGAATTTGCCATCTAGTACTTACTA 57.017 33.333 0.00 0.00 37.88 1.82
1576 2460 9.595823 TGAATTTGCCATCTAGTACTTACTAAC 57.404 33.333 0.00 0.00 38.24 2.34
1580 2501 5.068723 TGCCATCTAGTACTTACTAACTGCC 59.931 44.000 0.00 0.00 38.24 4.85
1713 2637 0.962356 CCAAGAGGAAGCGCACCATT 60.962 55.000 21.98 14.48 36.89 3.16
1770 2918 0.108186 CTCGGTGCTTGCCACTATCA 60.108 55.000 0.00 0.00 44.08 2.15
2021 3173 4.228567 TGTGTGCTGCCGTTCGGA 62.229 61.111 15.69 0.00 0.00 4.55
2082 3234 0.250684 TGAACCGAGCAAAGATGGCA 60.251 50.000 0.00 0.00 0.00 4.92
2083 3235 0.449388 GAACCGAGCAAAGATGGCAG 59.551 55.000 0.00 0.00 0.00 4.85
2085 3237 2.768492 CCGAGCAAAGATGGCAGCC 61.768 63.158 3.66 3.66 0.00 4.85
2089 3241 2.045045 CAAAGATGGCAGCCCCGA 60.045 61.111 9.64 0.00 35.87 5.14
2090 3242 1.454479 CAAAGATGGCAGCCCCGAT 60.454 57.895 9.64 0.00 35.87 4.18
2139 3291 2.125753 GCAGTCAGCCAGAGGACG 60.126 66.667 0.00 0.00 39.01 4.79
2140 3292 2.936912 GCAGTCAGCCAGAGGACGT 61.937 63.158 0.00 0.00 39.01 4.34
2141 3293 1.214062 CAGTCAGCCAGAGGACGTC 59.786 63.158 7.13 7.13 39.01 4.34
2142 3294 2.179517 GTCAGCCAGAGGACGTCG 59.820 66.667 9.92 0.00 0.00 5.12
2143 3295 2.282251 TCAGCCAGAGGACGTCGT 60.282 61.111 11.12 11.12 0.00 4.34
2144 3296 2.179517 CAGCCAGAGGACGTCGTC 59.820 66.667 26.58 26.58 0.00 4.20
2145 3297 3.432588 AGCCAGAGGACGTCGTCG 61.433 66.667 27.13 21.72 43.34 5.12
2147 3299 3.432588 CCAGAGGACGTCGTCGCT 61.433 66.667 27.13 16.01 41.18 4.93
2223 3378 1.207570 AGACTGAAGCAGCAGATCCTG 59.792 52.381 12.11 0.00 39.20 3.86
2241 3396 0.250467 TGCTGACAGGGACAAAGAGC 60.250 55.000 4.26 0.00 0.00 4.09
2250 3405 2.158475 AGGGACAAAGAGCCAACAATGA 60.158 45.455 0.00 0.00 0.00 2.57
2276 3431 0.179100 AAGATGTGGTCGCCGATCTG 60.179 55.000 0.00 0.00 29.39 2.90
2282 3437 4.148825 GTCGCCGATCTGCCAGGT 62.149 66.667 3.31 0.00 0.00 4.00
2310 3465 1.956170 AGTGTGCTGTACTGCGTGC 60.956 57.895 18.40 12.02 35.36 5.34
2323 3478 4.069232 CGTGCTGCCGGAGAGGAA 62.069 66.667 5.05 0.00 45.00 3.36
2357 3512 1.337821 CAAGTACTTCGAGTCGGCAC 58.662 55.000 13.54 5.74 0.00 5.01
2408 3563 2.248686 AGGGGATGGAGATCTGTACTGT 59.751 50.000 0.00 0.00 0.00 3.55
2525 3680 2.030805 GCTGTCAAAGAATGGTGGACAC 60.031 50.000 0.00 0.00 34.97 3.67
2699 3854 1.219522 AACGTTCTTCTTCCGCCGTG 61.220 55.000 0.00 0.00 0.00 4.94
2930 4085 8.641498 ACAACAAATCCTTGAAATCTGATACT 57.359 30.769 0.00 0.00 36.33 2.12
2936 4091 7.921041 ATCCTTGAAATCTGATACTAGTCCA 57.079 36.000 0.00 0.00 0.00 4.02
2944 4099 4.093743 TCTGATACTAGTCCAAGGTTGCA 58.906 43.478 0.00 0.00 0.00 4.08
2945 4100 4.081642 TCTGATACTAGTCCAAGGTTGCAC 60.082 45.833 0.00 0.00 0.00 4.57
2977 4132 3.795688 ATGTGATTCCACTTCCACTGT 57.204 42.857 0.00 0.00 43.55 3.55
2980 4135 2.554032 GTGATTCCACTTCCACTGTTGG 59.446 50.000 0.00 0.00 41.13 3.77
2981 4136 3.747388 GTGATTCCACTTCCACTGTTGGA 60.747 47.826 0.00 0.00 43.69 3.53
3077 4232 8.998277 AAGAGTATTCTTCAGTATGTAGGCTA 57.002 34.615 0.00 0.00 39.46 3.93
3101 4256 7.856145 ATTTAGTTATGAGGAGCTGAAACTG 57.144 36.000 0.00 0.00 0.00 3.16
3158 4313 5.893687 TGGCATCTACATTGCTTTGTTATG 58.106 37.500 0.00 4.56 40.03 1.90
3175 4333 8.549777 TTTGTTATGTACGTTTGTTTTAGCAG 57.450 30.769 0.00 0.00 0.00 4.24
3275 4435 2.735259 TTGGGAAGGGAGGAACTAGT 57.265 50.000 0.00 0.00 41.55 2.57
3398 4558 4.281688 ACTGTAACCAGCTTGCAAAATGAT 59.718 37.500 11.20 3.96 42.81 2.45
3614 4779 3.289407 GCCTTAGCTGGGAAAAGAGAT 57.711 47.619 11.11 0.00 35.50 2.75
3754 4919 5.610982 TGAGGCCCAGGTATAAATATTCAGT 59.389 40.000 0.00 0.00 0.00 3.41
3882 5080 4.333649 CGTAAGCAGTGATGGATGAATTGT 59.666 41.667 0.00 0.00 0.00 2.71
3895 5093 5.948758 TGGATGAATTGTGGTTAGCATGTAA 59.051 36.000 0.00 0.00 0.00 2.41
4329 5535 3.195610 TCGGAACAGTAACATGCTCTGAT 59.804 43.478 15.82 7.00 28.18 2.90
4578 5784 3.640498 GTGATGAGATGGAGAGGATGACA 59.360 47.826 0.00 0.00 0.00 3.58
4688 5899 1.679680 CATGAAAATCATCGCTGCCCT 59.320 47.619 0.00 0.00 34.28 5.19
4713 5924 9.255304 CTAGATATCTGACTTGGCTAAACTTTC 57.745 37.037 15.79 0.00 0.00 2.62
4731 5942 3.934391 CTCCACGCGAACCCAGGTC 62.934 68.421 15.93 0.00 0.00 3.85
4737 5948 1.072505 GCGAACCCAGGTCCTGAAA 59.927 57.895 21.23 0.00 32.44 2.69
4752 5963 1.005215 CTGAAACTGCTTGAGGGGGAT 59.995 52.381 0.00 0.00 0.00 3.85
4767 5978 1.433879 GGATGACGAGACGGTCCAG 59.566 63.158 4.14 1.66 36.07 3.86
5037 6287 3.016971 TGGCATCTGGACTGGGGG 61.017 66.667 0.00 0.00 0.00 5.40
5138 6388 0.450983 CATGTGTGTGTGTGTGTGCA 59.549 50.000 0.00 0.00 0.00 4.57
5139 6389 0.734309 ATGTGTGTGTGTGTGTGCAG 59.266 50.000 0.00 0.00 0.00 4.41
5140 6390 1.304509 TGTGTGTGTGTGTGTGCAGG 61.305 55.000 0.00 0.00 0.00 4.85
5141 6391 1.748500 TGTGTGTGTGTGTGCAGGG 60.749 57.895 0.00 0.00 0.00 4.45
5144 6394 1.146041 GTGTGTGTGTGCAGGGAGA 59.854 57.895 0.00 0.00 0.00 3.71
5155 6405 0.675633 GCAGGGAGAGAGAGAGATGC 59.324 60.000 0.00 0.00 0.00 3.91
5297 6551 6.624352 ATGAGGAATGAATGTATGGTTTCG 57.376 37.500 0.00 0.00 0.00 3.46
5429 6698 2.151502 TTACCTGCCCTCTCTCTCTG 57.848 55.000 0.00 0.00 0.00 3.35
5437 6706 2.091541 CCCTCTCTCTCTGTGACACTC 58.908 57.143 7.20 0.00 0.00 3.51
5467 6736 9.475620 TCTGAAGATACTACCAAATCTGAGTTA 57.524 33.333 0.00 0.00 32.79 2.24
5480 6749 7.959651 CCAAATCTGAGTTAATCTTTTCAGACG 59.040 37.037 5.29 0.00 46.12 4.18
5482 6751 4.929808 TCTGAGTTAATCTTTTCAGACGGC 59.070 41.667 0.00 0.00 40.65 5.68
5508 6777 7.547019 CAGAGAAGAACAGTTCATTATAGTGCA 59.453 37.037 15.85 0.00 0.00 4.57
5509 6778 8.097038 AGAGAAGAACAGTTCATTATAGTGCAA 58.903 33.333 15.85 0.00 0.00 4.08
5510 6779 8.621532 AGAAGAACAGTTCATTATAGTGCAAA 57.378 30.769 15.85 0.00 0.00 3.68
5511 6780 8.507249 AGAAGAACAGTTCATTATAGTGCAAAC 58.493 33.333 15.85 0.00 0.00 2.93
5513 6782 7.810658 AGAACAGTTCATTATAGTGCAAACTG 58.189 34.615 19.65 19.65 45.58 3.16
5514 6783 5.942872 ACAGTTCATTATAGTGCAAACTGC 58.057 37.500 20.52 0.00 44.55 4.40
5527 6796 4.926860 GCAAACTGCAAAGTTTTTCTGT 57.073 36.364 1.55 0.00 44.26 3.41
5528 6797 4.640956 GCAAACTGCAAAGTTTTTCTGTG 58.359 39.130 1.55 0.00 44.26 3.66
5529 6798 4.435917 GCAAACTGCAAAGTTTTTCTGTGG 60.436 41.667 1.55 0.00 44.26 4.17
5530 6799 2.892374 ACTGCAAAGTTTTTCTGTGGC 58.108 42.857 0.00 0.00 32.27 5.01
5531 6800 2.497273 ACTGCAAAGTTTTTCTGTGGCT 59.503 40.909 0.00 0.00 32.27 4.75
5532 6801 2.861935 CTGCAAAGTTTTTCTGTGGCTG 59.138 45.455 0.00 0.00 32.27 4.85
5533 6802 2.233431 TGCAAAGTTTTTCTGTGGCTGT 59.767 40.909 0.00 0.00 32.27 4.40
5534 6803 3.445450 TGCAAAGTTTTTCTGTGGCTGTA 59.555 39.130 0.00 0.00 32.27 2.74
5535 6804 4.099266 TGCAAAGTTTTTCTGTGGCTGTAT 59.901 37.500 0.00 0.00 32.27 2.29
5536 6805 4.445385 GCAAAGTTTTTCTGTGGCTGTATG 59.555 41.667 0.00 0.00 32.27 2.39
5537 6806 3.923017 AGTTTTTCTGTGGCTGTATGC 57.077 42.857 0.00 0.00 41.94 3.14
5538 6807 3.221771 AGTTTTTCTGTGGCTGTATGCA 58.778 40.909 0.00 0.00 45.15 3.96
5539 6808 3.828451 AGTTTTTCTGTGGCTGTATGCAT 59.172 39.130 3.79 3.79 45.15 3.96
5540 6809 4.082571 AGTTTTTCTGTGGCTGTATGCATC 60.083 41.667 0.19 0.00 45.15 3.91
5541 6810 1.655484 TTCTGTGGCTGTATGCATCG 58.345 50.000 0.19 0.00 45.15 3.84
5542 6811 0.536724 TCTGTGGCTGTATGCATCGT 59.463 50.000 0.19 0.00 45.15 3.73
5543 6812 1.066215 TCTGTGGCTGTATGCATCGTT 60.066 47.619 0.19 0.00 45.15 3.85
5544 6813 1.328680 CTGTGGCTGTATGCATCGTTC 59.671 52.381 0.19 0.00 45.15 3.95
5545 6814 1.066215 TGTGGCTGTATGCATCGTTCT 60.066 47.619 0.19 0.00 45.15 3.01
5546 6815 1.328680 GTGGCTGTATGCATCGTTCTG 59.671 52.381 0.19 0.00 45.15 3.02
5547 6816 1.206849 TGGCTGTATGCATCGTTCTGA 59.793 47.619 0.19 0.00 45.15 3.27
5548 6817 1.594862 GGCTGTATGCATCGTTCTGAC 59.405 52.381 0.19 0.00 45.15 3.51
5549 6818 2.270923 GCTGTATGCATCGTTCTGACA 58.729 47.619 0.19 0.00 42.31 3.58
5550 6819 2.283617 GCTGTATGCATCGTTCTGACAG 59.716 50.000 15.93 15.93 42.31 3.51
5551 6820 3.774066 CTGTATGCATCGTTCTGACAGA 58.226 45.455 15.39 0.00 35.87 3.41
5552 6821 3.774066 TGTATGCATCGTTCTGACAGAG 58.226 45.455 0.19 0.00 0.00 3.35
5553 6822 2.306341 ATGCATCGTTCTGACAGAGG 57.694 50.000 5.10 2.43 0.00 3.69
5554 6823 0.390340 TGCATCGTTCTGACAGAGGC 60.390 55.000 5.10 10.11 41.39 4.70
5555 6824 1.086634 GCATCGTTCTGACAGAGGCC 61.087 60.000 5.10 0.00 35.91 5.19
5556 6825 0.803768 CATCGTTCTGACAGAGGCCG 60.804 60.000 5.10 9.61 0.00 6.13
5557 6826 1.949847 ATCGTTCTGACAGAGGCCGG 61.950 60.000 16.34 0.00 0.00 6.13
5558 6827 2.266055 GTTCTGACAGAGGCCGGG 59.734 66.667 2.18 0.00 0.00 5.73
5559 6828 3.003173 TTCTGACAGAGGCCGGGG 61.003 66.667 2.18 0.00 0.00 5.73
5560 6829 3.539593 TTCTGACAGAGGCCGGGGA 62.540 63.158 2.18 0.00 0.00 4.81
5561 6830 3.465403 CTGACAGAGGCCGGGGAG 61.465 72.222 2.18 0.00 0.00 4.30
5562 6831 4.316823 TGACAGAGGCCGGGGAGT 62.317 66.667 2.18 0.00 0.00 3.85
5563 6832 3.462678 GACAGAGGCCGGGGAGTC 61.463 72.222 2.18 0.00 0.00 3.36
5577 6846 2.265589 GGAGTCCCCTTGTCGAAAAA 57.734 50.000 0.00 0.00 0.00 1.94
5597 6866 3.633058 AAAACTGCAAAGTTTTTCGCG 57.367 38.095 10.18 0.00 46.15 5.87
5643 6916 7.020602 CAGAAGTAGATCGAGCTGTATGTATG 58.979 42.308 14.67 0.00 0.00 2.39
5645 6918 7.878644 AGAAGTAGATCGAGCTGTATGTATGTA 59.121 37.037 14.67 0.00 0.00 2.29
5646 6919 8.568676 AAGTAGATCGAGCTGTATGTATGTAT 57.431 34.615 14.67 0.00 0.00 2.29
5647 6920 7.980062 AGTAGATCGAGCTGTATGTATGTATG 58.020 38.462 14.67 0.00 0.00 2.39
5648 6921 6.825944 AGATCGAGCTGTATGTATGTATGT 57.174 37.500 0.39 0.00 0.00 2.29
5649 6922 6.616017 AGATCGAGCTGTATGTATGTATGTG 58.384 40.000 0.39 0.00 0.00 3.21
5650 6923 5.121221 TCGAGCTGTATGTATGTATGTGG 57.879 43.478 0.00 0.00 0.00 4.17
5651 6924 3.675225 CGAGCTGTATGTATGTATGTGGC 59.325 47.826 0.00 0.00 0.00 5.01
5652 6925 3.997021 GAGCTGTATGTATGTATGTGGCC 59.003 47.826 0.00 0.00 0.00 5.36
5653 6926 3.648067 AGCTGTATGTATGTATGTGGCCT 59.352 43.478 3.32 0.00 0.00 5.19
5698 6973 1.417890 ACTGTGGCTGCTTGAGTAGTT 59.582 47.619 0.00 0.00 0.00 2.24
5739 7014 4.556104 GCTAGTATGTGGAGCATGCATTTG 60.556 45.833 21.98 0.00 39.99 2.32
5740 7015 2.691526 AGTATGTGGAGCATGCATTTGG 59.308 45.455 21.98 0.00 39.99 3.28
5741 7016 0.828022 ATGTGGAGCATGCATTTGGG 59.172 50.000 21.98 0.00 39.99 4.12
5742 7017 1.259142 TGTGGAGCATGCATTTGGGG 61.259 55.000 21.98 0.00 39.99 4.96
5758 7033 3.195632 GGGGGCATGGGGATGGAT 61.196 66.667 0.00 0.00 0.00 3.41
5853 7128 1.517832 GATCCCACGAGGTGTCCTG 59.482 63.158 0.00 0.00 31.76 3.86
5935 7218 0.593128 ATGACCACGCTGTTTTCTGC 59.407 50.000 0.00 0.00 40.57 4.26
5945 7228 1.301479 GTTTTCTGCTCCCGTCCGT 60.301 57.895 0.00 0.00 0.00 4.69
5951 7234 3.379445 GCTCCCGTCCGTCCAGAA 61.379 66.667 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.336795 TGGTCATCTGTGTACGCTGTG 60.337 52.381 8.10 8.36 0.00 3.66
1 2 0.966179 TGGTCATCTGTGTACGCTGT 59.034 50.000 8.10 0.00 0.00 4.40
2 3 2.078849 TTGGTCATCTGTGTACGCTG 57.921 50.000 8.10 7.49 0.00 5.18
3 4 2.831685 TTTGGTCATCTGTGTACGCT 57.168 45.000 8.10 0.00 0.00 5.07
4 5 2.095853 CCATTTGGTCATCTGTGTACGC 59.904 50.000 0.00 0.00 0.00 4.42
5 6 3.595173 TCCATTTGGTCATCTGTGTACG 58.405 45.455 0.00 0.00 36.34 3.67
6 7 5.619981 GCTTTCCATTTGGTCATCTGTGTAC 60.620 44.000 0.00 0.00 36.34 2.90
7 8 4.458989 GCTTTCCATTTGGTCATCTGTGTA 59.541 41.667 0.00 0.00 36.34 2.90
8 9 3.256631 GCTTTCCATTTGGTCATCTGTGT 59.743 43.478 0.00 0.00 36.34 3.72
41 42 5.769835 AGGATTATCATTTGGCAAAGGAGA 58.230 37.500 28.01 22.80 34.39 3.71
43 44 7.784073 TGATTAGGATTATCATTTGGCAAAGGA 59.216 33.333 26.87 26.87 35.48 3.36
51 52 6.017192 TGGCACGTGATTAGGATTATCATTTG 60.017 38.462 22.23 0.00 34.75 2.32
180 193 3.120580 CGTACGCCGGAATAACTTTGTTT 60.121 43.478 5.05 0.00 0.00 2.83
222 237 4.790962 AGATGCTGCCTGCCGGTG 62.791 66.667 1.90 0.00 42.00 4.94
240 255 2.737783 CCATCGCACAGGTACGTAAAAA 59.262 45.455 0.00 0.00 0.00 1.94
298 363 1.483415 AGATACGGTAAATGTGCGGGT 59.517 47.619 0.00 0.00 0.00 5.28
299 364 2.234300 AGATACGGTAAATGTGCGGG 57.766 50.000 0.00 0.00 0.00 6.13
320 385 9.713740 CTTTTCTGCAGATAGATGTAAAATGAC 57.286 33.333 19.04 0.00 0.00 3.06
324 389 9.944376 ACTACTTTTCTGCAGATAGATGTAAAA 57.056 29.630 25.04 16.05 0.00 1.52
329 394 7.038048 TCACACTACTTTTCTGCAGATAGATG 58.962 38.462 25.04 20.34 0.00 2.90
334 399 8.621532 TTTATTCACACTACTTTTCTGCAGAT 57.378 30.769 19.04 4.84 0.00 2.90
336 401 9.683069 ATTTTTATTCACACTACTTTTCTGCAG 57.317 29.630 7.63 7.63 0.00 4.41
337 402 9.677567 GATTTTTATTCACACTACTTTTCTGCA 57.322 29.630 0.00 0.00 0.00 4.41
372 594 1.383523 GTACTGGATGCTGCCCTTTC 58.616 55.000 0.00 0.00 0.00 2.62
379 601 1.134818 TGCTAACGGTACTGGATGCTG 60.135 52.381 6.65 0.00 0.00 4.41
381 603 1.134788 ACTGCTAACGGTACTGGATGC 60.135 52.381 6.65 7.31 31.99 3.91
382 604 2.481449 GGACTGCTAACGGTACTGGATG 60.481 54.545 6.65 0.00 34.75 3.51
383 605 1.755380 GGACTGCTAACGGTACTGGAT 59.245 52.381 6.65 0.00 34.75 3.41
384 606 1.180029 GGACTGCTAACGGTACTGGA 58.820 55.000 6.65 0.00 34.75 3.86
385 607 0.892755 TGGACTGCTAACGGTACTGG 59.107 55.000 6.65 0.00 36.88 4.00
387 609 2.522185 TCTTGGACTGCTAACGGTACT 58.478 47.619 0.00 0.00 36.88 2.73
388 610 3.308438 TTCTTGGACTGCTAACGGTAC 57.692 47.619 0.00 0.00 36.42 3.34
389 611 4.339872 TTTTCTTGGACTGCTAACGGTA 57.660 40.909 0.00 0.00 34.75 4.02
390 612 2.922740 TTTCTTGGACTGCTAACGGT 57.077 45.000 0.00 0.00 38.42 4.83
391 613 3.181520 CGATTTTCTTGGACTGCTAACGG 60.182 47.826 0.00 0.00 0.00 4.44
392 614 3.678072 TCGATTTTCTTGGACTGCTAACG 59.322 43.478 0.00 0.00 0.00 3.18
393 615 4.691216 AGTCGATTTTCTTGGACTGCTAAC 59.309 41.667 0.00 0.00 38.27 2.34
394 616 4.894784 AGTCGATTTTCTTGGACTGCTAA 58.105 39.130 0.00 0.00 38.27 3.09
395 617 4.537135 AGTCGATTTTCTTGGACTGCTA 57.463 40.909 0.00 0.00 38.27 3.49
397 619 4.489679 AAAGTCGATTTTCTTGGACTGC 57.510 40.909 0.00 0.00 39.53 4.40
434 656 9.665719 ATGTCTATTTTCTTCTTCTTCTTCCTC 57.334 33.333 0.00 0.00 0.00 3.71
474 696 1.006220 GCCGCTTTTGTTTGGAGGG 60.006 57.895 0.00 0.00 0.00 4.30
479 701 1.117234 GTACGTGCCGCTTTTGTTTG 58.883 50.000 0.00 0.00 0.00 2.93
483 705 3.413558 GAATTAGTACGTGCCGCTTTTG 58.586 45.455 0.00 0.00 0.00 2.44
535 773 2.487746 TTCCTTTGGGCCTTTTCCTT 57.512 45.000 4.53 0.00 0.00 3.36
543 781 3.955145 CCCATTTTTCCTTTGGGCC 57.045 52.632 0.00 0.00 43.45 5.80
546 784 6.097696 ACCGAATATACCCATTTTTCCTTTGG 59.902 38.462 0.00 0.00 0.00 3.28
547 785 7.107639 ACCGAATATACCCATTTTTCCTTTG 57.892 36.000 0.00 0.00 0.00 2.77
548 786 8.826293 TTACCGAATATACCCATTTTTCCTTT 57.174 30.769 0.00 0.00 0.00 3.11
582 821 4.211164 GCAACTGCCGCTCTTTTTATTTTT 59.789 37.500 0.00 0.00 34.31 1.94
583 822 3.740832 GCAACTGCCGCTCTTTTTATTTT 59.259 39.130 0.00 0.00 34.31 1.82
637 879 1.220477 GGCTTCTCTCTCCCACAGC 59.780 63.158 0.00 0.00 0.00 4.40
638 880 1.904032 GGGCTTCTCTCTCCCACAG 59.096 63.158 0.00 0.00 39.82 3.66
653 895 2.045634 GGGTACTTGGGTTCGGGC 60.046 66.667 0.00 0.00 0.00 6.13
665 907 1.692749 TGAGGGCTGGGATGGGTAC 60.693 63.158 0.00 0.00 0.00 3.34
666 908 1.692749 GTGAGGGCTGGGATGGGTA 60.693 63.158 0.00 0.00 0.00 3.69
667 909 3.017581 GTGAGGGCTGGGATGGGT 61.018 66.667 0.00 0.00 0.00 4.51
752 998 0.684805 TTTCTCTCTCTCCTCCGGGC 60.685 60.000 0.00 0.00 0.00 6.13
786 1220 1.082104 CCTTTGTTCCGTTGCTCGC 60.082 57.895 0.00 0.00 38.35 5.03
845 1285 0.043334 TTCCTCCCTCCCTCTCCTTG 59.957 60.000 0.00 0.00 0.00 3.61
918 1358 4.539881 GTCGCCTCGTCCTCTCGC 62.540 72.222 0.00 0.00 0.00 5.03
919 1359 4.225340 CGTCGCCTCGTCCTCTCG 62.225 72.222 0.00 0.00 0.00 4.04
920 1360 3.878519 CCGTCGCCTCGTCCTCTC 61.879 72.222 0.00 0.00 0.00 3.20
967 1407 2.664518 GCCGAGCCTATCTGCTGC 60.665 66.667 0.00 0.00 42.95 5.25
1043 1502 0.341609 CTCCTTCCCCTCTTCCTCCT 59.658 60.000 0.00 0.00 0.00 3.69
1046 1505 0.341609 CTCCTCCTTCCCCTCTTCCT 59.658 60.000 0.00 0.00 0.00 3.36
1052 1511 2.978674 ATGGCCTCCTCCTTCCCCT 61.979 63.158 3.32 0.00 0.00 4.79
1281 1743 2.100631 CATGCCGTCGAAGTCCACC 61.101 63.158 0.00 0.00 0.00 4.61
1366 1828 9.631452 CGATCTGATTAGAATAGAGTGCAATTA 57.369 33.333 0.00 0.00 36.32 1.40
1367 1829 8.147058 ACGATCTGATTAGAATAGAGTGCAATT 58.853 33.333 0.00 0.00 36.32 2.32
1368 1830 7.665690 ACGATCTGATTAGAATAGAGTGCAAT 58.334 34.615 0.00 0.00 36.32 3.56
1371 1833 7.938563 AAACGATCTGATTAGAATAGAGTGC 57.061 36.000 0.00 0.00 36.32 4.40
1374 1836 8.973378 GGTCAAAACGATCTGATTAGAATAGAG 58.027 37.037 0.00 0.00 36.32 2.43
1375 1837 7.926555 GGGTCAAAACGATCTGATTAGAATAGA 59.073 37.037 0.00 0.00 36.32 1.98
1394 2264 1.702182 TCTTTGCAGCATGGGTCAAA 58.298 45.000 0.00 0.00 35.86 2.69
1425 2295 8.663911 CACCAAAATGAAGAGCAAAACTAAAAA 58.336 29.630 0.00 0.00 0.00 1.94
1426 2296 7.279758 CCACCAAAATGAAGAGCAAAACTAAAA 59.720 33.333 0.00 0.00 0.00 1.52
1427 2297 6.760770 CCACCAAAATGAAGAGCAAAACTAAA 59.239 34.615 0.00 0.00 0.00 1.85
1428 2298 6.097554 TCCACCAAAATGAAGAGCAAAACTAA 59.902 34.615 0.00 0.00 0.00 2.24
1429 2299 5.596361 TCCACCAAAATGAAGAGCAAAACTA 59.404 36.000 0.00 0.00 0.00 2.24
1430 2300 4.405358 TCCACCAAAATGAAGAGCAAAACT 59.595 37.500 0.00 0.00 0.00 2.66
1431 2301 4.692228 TCCACCAAAATGAAGAGCAAAAC 58.308 39.130 0.00 0.00 0.00 2.43
1436 2306 5.787380 AGAAAATCCACCAAAATGAAGAGC 58.213 37.500 0.00 0.00 0.00 4.09
1440 2310 7.123355 ACAGAAGAAAATCCACCAAAATGAA 57.877 32.000 0.00 0.00 0.00 2.57
1446 2316 6.834168 GGATTACAGAAGAAAATCCACCAA 57.166 37.500 8.15 0.00 45.31 3.67
1457 2327 4.191544 CAAATCGGCAGGATTACAGAAGA 58.808 43.478 3.05 0.00 44.59 2.87
1481 2360 2.274104 GCGGTTTGCTATGGGGGA 59.726 61.111 0.00 0.00 41.73 4.81
1496 2375 1.135972 CGAAATTCTGGTTCTGGTGCG 60.136 52.381 0.00 0.00 0.00 5.34
1499 2378 1.534729 GGCGAAATTCTGGTTCTGGT 58.465 50.000 0.00 0.00 0.00 4.00
1500 2379 0.811281 GGGCGAAATTCTGGTTCTGG 59.189 55.000 0.00 0.00 0.00 3.86
1528 2407 2.159099 TCATCTCTGTGGTAACCGCATC 60.159 50.000 0.00 0.00 43.46 3.91
1530 2409 1.262417 TCATCTCTGTGGTAACCGCA 58.738 50.000 0.00 0.00 42.15 5.69
1543 2422 7.877097 AGTACTAGATGGCAAATTCATCATCTC 59.123 37.037 15.85 6.80 43.41 2.75
1544 2423 7.743749 AGTACTAGATGGCAAATTCATCATCT 58.256 34.615 16.34 16.34 45.48 2.90
1548 2427 8.894768 AGTAAGTACTAGATGGCAAATTCATC 57.105 34.615 0.00 0.00 40.79 2.92
1570 2454 5.046663 TCTGTTCATCACATGGCAGTTAGTA 60.047 40.000 0.00 0.00 36.14 1.82
1571 2455 4.005650 CTGTTCATCACATGGCAGTTAGT 58.994 43.478 0.00 0.00 33.76 2.24
1572 2456 4.256110 TCTGTTCATCACATGGCAGTTAG 58.744 43.478 0.00 0.00 36.14 2.34
1573 2457 4.284829 TCTGTTCATCACATGGCAGTTA 57.715 40.909 0.00 0.00 36.14 2.24
1574 2458 3.144657 TCTGTTCATCACATGGCAGTT 57.855 42.857 0.00 0.00 36.14 3.16
1575 2459 2.865119 TCTGTTCATCACATGGCAGT 57.135 45.000 0.00 0.00 36.14 4.40
1576 2460 3.275999 TGATCTGTTCATCACATGGCAG 58.724 45.455 0.00 0.00 33.76 4.85
1580 2501 6.920569 TGAGATTGATCTGTTCATCACATG 57.079 37.500 0.00 0.00 37.25 3.21
1721 2645 3.797353 CCGTGATGGTGGGGGAGG 61.797 72.222 0.00 0.00 0.00 4.30
1722 2646 2.257409 CTTCCGTGATGGTGGGGGAG 62.257 65.000 0.00 0.00 39.52 4.30
1970 3122 2.046892 CCACAGGCAGGAACCTCG 60.047 66.667 0.00 0.00 38.26 4.63
2021 3173 1.831652 CTTCACCCTTCTGACGGGCT 61.832 60.000 18.45 4.09 46.04 5.19
2031 3183 1.548269 CTCGCTCTCTTCTTCACCCTT 59.452 52.381 0.00 0.00 0.00 3.95
2082 3234 1.218316 GTTCTTCGTCATCGGGGCT 59.782 57.895 0.00 0.00 37.69 5.19
2083 3235 1.079405 TGTTCTTCGTCATCGGGGC 60.079 57.895 0.00 0.00 37.69 5.80
2085 3237 0.389817 TGCTGTTCTTCGTCATCGGG 60.390 55.000 0.00 0.00 37.69 5.14
2089 3241 3.603532 ACATCATGCTGTTCTTCGTCAT 58.396 40.909 0.00 0.00 0.00 3.06
2090 3242 3.044235 ACATCATGCTGTTCTTCGTCA 57.956 42.857 0.00 0.00 0.00 4.35
2136 3288 0.659417 TGTTCTTCAGCGACGACGTC 60.659 55.000 18.04 18.04 41.98 4.34
2137 3289 0.660595 CTGTTCTTCAGCGACGACGT 60.661 55.000 9.33 0.00 41.98 4.34
2138 3290 2.054801 CTGTTCTTCAGCGACGACG 58.945 57.895 2.12 2.12 42.93 5.12
2146 3298 2.414481 CTCGATGGTTGCTGTTCTTCAG 59.586 50.000 0.00 0.00 46.12 3.02
2147 3299 2.224281 ACTCGATGGTTGCTGTTCTTCA 60.224 45.455 0.00 0.00 0.00 3.02
2159 3311 0.321671 CAGGTTCCACACTCGATGGT 59.678 55.000 3.55 0.00 38.47 3.55
2223 3378 0.957888 GGCTCTTTGTCCCTGTCAGC 60.958 60.000 0.00 0.00 0.00 4.26
2241 3396 3.508793 ACATCTTTCTGGCTCATTGTTGG 59.491 43.478 0.00 0.00 0.00 3.77
2250 3405 0.674895 GCGACCACATCTTTCTGGCT 60.675 55.000 0.00 0.00 0.00 4.75
2276 3431 4.729918 CTGGCACCCTCACCTGGC 62.730 72.222 0.00 0.00 0.00 4.85
2282 3437 3.170672 AGCACACTGGCACCCTCA 61.171 61.111 0.00 0.00 35.83 3.86
2310 3465 1.144936 GGTCATTCCTCTCCGGCAG 59.855 63.158 0.00 0.00 0.00 4.85
2323 3478 4.655963 AGTACTTGCAACTGAATGGTCAT 58.344 39.130 0.00 0.00 31.85 3.06
2357 3512 1.332178 GCTCAGTCGAGTCACTTTCG 58.668 55.000 0.00 0.00 41.71 3.46
2408 3563 3.796111 TCCATTTCTTGGGGGCAATAAA 58.204 40.909 0.00 0.00 46.45 1.40
2525 3680 1.557269 CCCCAGAACTCCCACCTGAG 61.557 65.000 0.00 0.00 38.37 3.35
2699 3854 3.522553 CAAATCCTCAGGTTCCGTAGAC 58.477 50.000 0.00 0.00 0.00 2.59
2744 3899 1.558756 AGCCTTCTCAGAGACATTGGG 59.441 52.381 0.00 0.00 0.00 4.12
2930 4085 0.250124 CACCGTGCAACCTTGGACTA 60.250 55.000 7.91 0.00 45.83 2.59
2936 4091 1.202758 TCTGAATCACCGTGCAACCTT 60.203 47.619 0.00 0.00 0.00 3.50
2944 4099 3.941483 GGAATCACATTCTGAATCACCGT 59.059 43.478 0.00 0.00 39.24 4.83
2945 4100 3.940852 TGGAATCACATTCTGAATCACCG 59.059 43.478 0.00 0.00 39.24 4.94
3077 4232 6.825721 CCAGTTTCAGCTCCTCATAACTAAAT 59.174 38.462 0.00 0.00 0.00 1.40
3101 4256 3.674997 TGGTGAGAAGTTTGATGTAGCC 58.325 45.455 0.00 0.00 0.00 3.93
3158 4313 3.249080 TCCAGCTGCTAAAACAAACGTAC 59.751 43.478 8.66 0.00 0.00 3.67
3175 4333 2.989166 CGAAAGAAAATTGGCTTCCAGC 59.011 45.455 0.00 0.00 41.46 4.85
3275 4435 2.319136 ACTGTGCCTTGTAAACGTGA 57.681 45.000 0.00 0.00 0.00 4.35
3416 4576 5.234466 AGTAGTTGTCAAAGCTGAATCCT 57.766 39.130 0.00 0.00 31.88 3.24
3754 4919 4.713553 TCTTGGTACTTGCAAACAGATCA 58.286 39.130 0.00 0.00 0.00 2.92
3844 5017 2.161609 GCTTACGCATTAAGGCACTTGT 59.838 45.455 13.17 4.35 42.58 3.16
3871 5069 4.343231 ACATGCTAACCACAATTCATCCA 58.657 39.130 0.00 0.00 0.00 3.41
3872 5070 4.989279 ACATGCTAACCACAATTCATCC 57.011 40.909 0.00 0.00 0.00 3.51
3873 5071 7.088589 AGTTACATGCTAACCACAATTCATC 57.911 36.000 11.94 0.00 0.00 2.92
3874 5072 7.039784 ACAAGTTACATGCTAACCACAATTCAT 60.040 33.333 11.94 0.00 0.00 2.57
3882 5080 6.892658 ATTTGACAAGTTACATGCTAACCA 57.107 33.333 11.94 4.04 0.00 3.67
3895 5093 3.825328 ACCAGAGCAGAATTTGACAAGT 58.175 40.909 0.00 0.00 0.00 3.16
4375 5581 1.082300 CAGAGCAAGTGCAGCAACG 60.082 57.895 6.00 0.00 45.16 4.10
4578 5784 4.731612 CACAGCGAGGCAGCGAGT 62.732 66.667 3.93 2.71 43.00 4.18
4623 5829 1.319669 GTTCTTACTAGCGGCGTTTCG 59.680 52.381 9.37 0.00 0.00 3.46
4680 5891 2.166829 AGTCAGATATCTAGGGCAGCG 58.833 52.381 4.54 0.00 0.00 5.18
4688 5899 8.982723 AGAAAGTTTAGCCAAGTCAGATATCTA 58.017 33.333 4.54 0.00 0.00 1.98
4713 5924 3.934391 GACCTGGGTTCGCGTGGAG 62.934 68.421 5.77 0.00 0.00 3.86
4731 5942 0.610232 CCCCCTCAAGCAGTTTCAGG 60.610 60.000 0.00 0.00 0.00 3.86
4737 5948 1.903877 CGTCATCCCCCTCAAGCAGT 61.904 60.000 0.00 0.00 0.00 4.40
4752 5963 2.265904 CCACTGGACCGTCTCGTCA 61.266 63.158 0.00 0.00 34.24 4.35
5037 6287 0.251787 AGCACCCACCAAAGAATCCC 60.252 55.000 0.00 0.00 0.00 3.85
5038 6288 1.273327 CAAGCACCCACCAAAGAATCC 59.727 52.381 0.00 0.00 0.00 3.01
5138 6388 1.133388 CAGGCATCTCTCTCTCTCCCT 60.133 57.143 0.00 0.00 0.00 4.20
5139 6389 1.133513 TCAGGCATCTCTCTCTCTCCC 60.134 57.143 0.00 0.00 0.00 4.30
5140 6390 2.363306 TCAGGCATCTCTCTCTCTCC 57.637 55.000 0.00 0.00 0.00 3.71
5141 6391 2.029649 GCATCAGGCATCTCTCTCTCTC 60.030 54.545 0.00 0.00 43.97 3.20
5155 6405 1.816835 AGCATCAACAACAGCATCAGG 59.183 47.619 0.00 0.00 0.00 3.86
5297 6551 3.444742 TCATTCCAATCTTGATGCACCAC 59.555 43.478 0.00 0.00 0.00 4.16
5429 6698 6.019779 AGTATCTTCAGACTTGAGTGTCAC 57.980 41.667 0.00 0.00 39.27 3.67
5437 6706 8.253810 TCAGATTTGGTAGTATCTTCAGACTTG 58.746 37.037 0.00 0.00 0.00 3.16
5467 6736 3.685139 TCTCTGCCGTCTGAAAAGATT 57.315 42.857 0.00 0.00 0.00 2.40
5480 6749 7.010923 CACTATAATGAACTGTTCTTCTCTGCC 59.989 40.741 20.18 0.00 0.00 4.85
5482 6751 7.547019 TGCACTATAATGAACTGTTCTTCTCTG 59.453 37.037 20.18 9.84 0.00 3.35
5509 6778 3.055891 AGCCACAGAAAAACTTTGCAGTT 60.056 39.130 0.00 0.00 45.89 3.16
5510 6779 2.497273 AGCCACAGAAAAACTTTGCAGT 59.503 40.909 0.00 0.00 33.11 4.40
5511 6780 2.861935 CAGCCACAGAAAAACTTTGCAG 59.138 45.455 0.00 0.00 0.00 4.41
5513 6782 2.892374 ACAGCCACAGAAAAACTTTGC 58.108 42.857 0.00 0.00 0.00 3.68
5514 6783 4.445385 GCATACAGCCACAGAAAAACTTTG 59.555 41.667 0.00 0.00 37.23 2.77
5515 6784 4.099266 TGCATACAGCCACAGAAAAACTTT 59.901 37.500 0.00 0.00 44.83 2.66
5516 6785 3.636300 TGCATACAGCCACAGAAAAACTT 59.364 39.130 0.00 0.00 44.83 2.66
5517 6786 3.221771 TGCATACAGCCACAGAAAAACT 58.778 40.909 0.00 0.00 44.83 2.66
5518 6787 3.641437 TGCATACAGCCACAGAAAAAC 57.359 42.857 0.00 0.00 44.83 2.43
5520 6789 2.419673 CGATGCATACAGCCACAGAAAA 59.580 45.455 0.00 0.00 44.83 2.29
5521 6790 2.009051 CGATGCATACAGCCACAGAAA 58.991 47.619 0.00 0.00 44.83 2.52
5522 6791 1.066215 ACGATGCATACAGCCACAGAA 60.066 47.619 0.00 0.00 44.83 3.02
5523 6792 0.536724 ACGATGCATACAGCCACAGA 59.463 50.000 0.00 0.00 44.83 3.41
5524 6793 1.328680 GAACGATGCATACAGCCACAG 59.671 52.381 0.00 0.00 44.83 3.66
5525 6794 1.066215 AGAACGATGCATACAGCCACA 60.066 47.619 0.00 0.00 44.83 4.17
5526 6795 1.328680 CAGAACGATGCATACAGCCAC 59.671 52.381 0.00 0.00 44.83 5.01
5527 6796 1.206849 TCAGAACGATGCATACAGCCA 59.793 47.619 0.00 0.00 44.83 4.75
5528 6797 1.594862 GTCAGAACGATGCATACAGCC 59.405 52.381 0.00 0.00 44.83 4.85
5529 6798 2.270923 TGTCAGAACGATGCATACAGC 58.729 47.619 0.00 0.00 45.96 4.40
5530 6799 3.774066 TCTGTCAGAACGATGCATACAG 58.226 45.455 14.62 14.62 35.36 2.74
5531 6800 3.429410 CCTCTGTCAGAACGATGCATACA 60.429 47.826 0.00 0.00 0.00 2.29
5532 6801 3.119291 CCTCTGTCAGAACGATGCATAC 58.881 50.000 0.00 0.00 0.00 2.39
5533 6802 2.481969 GCCTCTGTCAGAACGATGCATA 60.482 50.000 0.00 0.00 0.00 3.14
5534 6803 1.741732 GCCTCTGTCAGAACGATGCAT 60.742 52.381 0.00 0.00 0.00 3.96
5535 6804 0.390340 GCCTCTGTCAGAACGATGCA 60.390 55.000 3.67 0.00 0.00 3.96
5536 6805 1.086634 GGCCTCTGTCAGAACGATGC 61.087 60.000 3.67 2.31 0.00 3.91
5537 6806 0.803768 CGGCCTCTGTCAGAACGATG 60.804 60.000 13.15 0.00 0.00 3.84
5538 6807 1.513158 CGGCCTCTGTCAGAACGAT 59.487 57.895 13.15 0.00 0.00 3.73
5539 6808 2.636412 CCGGCCTCTGTCAGAACGA 61.636 63.158 17.77 0.00 0.00 3.85
5540 6809 2.125912 CCGGCCTCTGTCAGAACG 60.126 66.667 3.67 8.80 0.00 3.95
5541 6810 2.266055 CCCGGCCTCTGTCAGAAC 59.734 66.667 3.67 0.00 0.00 3.01
5542 6811 3.003173 CCCCGGCCTCTGTCAGAA 61.003 66.667 3.67 0.00 0.00 3.02
5543 6812 3.965026 CTCCCCGGCCTCTGTCAGA 62.965 68.421 0.00 1.78 0.00 3.27
5544 6813 3.465403 CTCCCCGGCCTCTGTCAG 61.465 72.222 0.00 0.00 0.00 3.51
5545 6814 4.316823 ACTCCCCGGCCTCTGTCA 62.317 66.667 0.00 0.00 0.00 3.58
5546 6815 3.462678 GACTCCCCGGCCTCTGTC 61.463 72.222 0.00 0.00 0.00 3.51
5558 6827 2.265589 TTTTTCGACAAGGGGACTCC 57.734 50.000 0.00 0.00 42.68 3.85
5597 6866 6.576185 TCTGTCCACCTTCGGTTATTATTAC 58.424 40.000 0.00 0.00 31.02 1.89
5617 6886 4.884744 ACATACAGCTCGATCTACTTCTGT 59.115 41.667 0.00 0.00 38.24 3.41
5625 6898 6.349694 CCACATACATACATACAGCTCGATCT 60.350 42.308 0.00 0.00 0.00 2.75
5643 6916 2.356135 CACAGTACCAAGGCCACATAC 58.644 52.381 5.01 1.61 0.00 2.39
5645 6918 0.609131 GCACAGTACCAAGGCCACAT 60.609 55.000 5.01 0.00 0.00 3.21
5646 6919 1.228124 GCACAGTACCAAGGCCACA 60.228 57.895 5.01 0.00 0.00 4.17
5647 6920 1.228124 TGCACAGTACCAAGGCCAC 60.228 57.895 5.01 0.00 0.00 5.01
5648 6921 1.073025 CTGCACAGTACCAAGGCCA 59.927 57.895 5.01 0.00 0.00 5.36
5649 6922 2.335712 GCTGCACAGTACCAAGGCC 61.336 63.158 0.00 0.00 0.00 5.19
5650 6923 2.680913 CGCTGCACAGTACCAAGGC 61.681 63.158 0.00 0.00 0.00 4.35
5651 6924 1.005037 TCGCTGCACAGTACCAAGG 60.005 57.895 0.00 0.00 0.00 3.61
5652 6925 0.599991 TGTCGCTGCACAGTACCAAG 60.600 55.000 0.00 0.00 0.00 3.61
5653 6926 0.179070 TTGTCGCTGCACAGTACCAA 60.179 50.000 0.00 0.00 0.00 3.67
5698 6973 0.953727 GCAAACATCTCACACCTGCA 59.046 50.000 0.00 0.00 0.00 4.41
5741 7016 2.793669 AATCCATCCCCATGCCCCC 61.794 63.158 0.00 0.00 0.00 5.40
5742 7017 1.534717 CAATCCATCCCCATGCCCC 60.535 63.158 0.00 0.00 0.00 5.80
5758 7033 1.764571 CTCTGGTGTCCCCGTTCCAA 61.765 60.000 0.00 0.00 35.15 3.53
5928 7211 1.005394 GACGGACGGGAGCAGAAAA 60.005 57.895 0.00 0.00 0.00 2.29
5935 7218 1.935327 GACTTCTGGACGGACGGGAG 61.935 65.000 0.00 0.00 0.00 4.30
5945 7228 0.251354 GGCAGCATCAGACTTCTGGA 59.749 55.000 6.40 0.00 43.91 3.86


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

AutoCloner maintained by Alex Coulton.