Multiple sequence alignment - TraesCS6B01G282200

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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 TraesCS6B01G282200 chr6B 100.000 4289 0 0 1 4289 508604166 508608454 0.000000e+00 7921.0
1 TraesCS6B01G282200 chr6B 84.722 72 5 5 570 639 565208008 565207941 2.770000e-07 67.6
2 TraesCS6B01G282200 chr6B 82.540 63 11 0 1247 1309 120651980 120651918 5.990000e-04 56.5
3 TraesCS6B01G282200 chr6D 92.006 1989 122 19 494 2458 316104506 316102531 0.000000e+00 2758.0
4 TraesCS6B01G282200 chr6D 93.032 1550 57 19 2766 4289 316101860 316100336 0.000000e+00 2217.0
5 TraesCS6B01G282200 chr6D 83.807 352 49 6 139 488 336544835 336544490 1.150000e-85 327.0
6 TraesCS6B01G282200 chr6D 93.293 164 11 0 2494 2657 316102529 316102366 4.280000e-60 243.0
7 TraesCS6B01G282200 chr6D 95.506 89 3 1 2645 2733 316101946 316101859 1.610000e-29 141.0
8 TraesCS6B01G282200 chr6A 94.242 1754 68 16 787 2532 453911883 453910155 0.000000e+00 2649.0
9 TraesCS6B01G282200 chr6A 92.866 799 25 10 2766 3556 453909170 453908396 0.000000e+00 1131.0
10 TraesCS6B01G282200 chr6A 86.918 795 50 31 3538 4289 453908380 453907597 0.000000e+00 843.0
11 TraesCS6B01G282200 chr6A 93.810 210 10 1 2524 2733 453909375 453909169 3.220000e-81 313.0
12 TraesCS6B01G282200 chr2D 85.081 496 56 11 2 484 459286563 459287053 1.390000e-134 490.0
13 TraesCS6B01G282200 chr2D 80.214 187 32 4 493 677 317939501 317939684 7.480000e-28 135.0
14 TraesCS6B01G282200 chr2A 81.481 513 60 12 2 484 602436566 602437073 5.200000e-104 388.0
15 TraesCS6B01G282200 chr2A 80.242 496 83 12 6 488 128194268 128193775 4.080000e-95 359.0
16 TraesCS6B01G282200 chr2A 86.747 83 10 1 1 82 195307320 195307402 1.640000e-14 91.6
17 TraesCS6B01G282200 chr4D 85.143 350 47 4 139 484 69573933 69574281 1.900000e-93 353.0
18 TraesCS6B01G282200 chrUn 84.615 351 53 1 139 488 56334730 56334380 8.830000e-92 348.0
19 TraesCS6B01G282200 chrUn 79.956 459 68 17 2 440 423046702 423047156 2.490000e-82 316.0
20 TraesCS6B01G282200 chrUn 85.577 104 12 2 579 681 3696357 3696256 5.870000e-19 106.0
21 TraesCS6B01G282200 chr4A 84.900 351 43 6 139 487 158471402 158471744 3.170000e-91 346.0
22 TraesCS6B01G282200 chr4A 84.046 351 48 7 139 487 158496631 158496975 8.890000e-87 331.0
23 TraesCS6B01G282200 chr4A 75.591 254 47 13 496 743 934895 934651 1.260000e-20 111.0
24 TraesCS6B01G282200 chr2B 79.079 521 71 18 1 488 427566915 427566400 1.490000e-84 324.0
25 TraesCS6B01G282200 chr3D 77.947 263 45 9 493 751 407219786 407220039 7.430000e-33 152.0
26 TraesCS6B01G282200 chr7A 79.787 188 33 4 493 678 646843357 646843541 9.680000e-27 132.0
27 TraesCS6B01G282200 chr1A 79.255 188 34 4 493 678 504003754 504003938 4.500000e-25 126.0
28 TraesCS6B01G282200 chr5D 85.185 54 6 1 36 89 311380060 311380009 2.000000e-03 54.7
29 TraesCS6B01G282200 chr3B 100.000 28 0 0 606 633 787838300 787838327 8.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G282200 chr6B 508604166 508608454 4288 False 7921.00 7921 100.00000 1 4289 1 chr6B.!!$F1 4288
1 TraesCS6B01G282200 chr6D 316100336 316104506 4170 True 1339.75 2758 93.45925 494 4289 4 chr6D.!!$R2 3795
2 TraesCS6B01G282200 chr6A 453907597 453911883 4286 True 1234.00 2649 91.95900 787 4289 4 chr6A.!!$R1 3502
3 TraesCS6B01G282200 chr2A 602436566 602437073 507 False 388.00 388 81.48100 2 484 1 chr2A.!!$F2 482
4 TraesCS6B01G282200 chr2B 427566400 427566915 515 True 324.00 324 79.07900 1 488 1 chr2B.!!$R1 487

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
584 616 0.319641 ACGAGGAACCAAACGAGCTC 60.320 55.0 2.73 2.73 0.00 4.09 F
640 687 0.323629 TGGATTTGAGGTGTCCGGTC 59.676 55.0 0.00 0.00 34.72 4.79 F
1470 1521 0.400093 AGTAGGCCATGGAGGGGTAC 60.400 60.0 18.40 8.46 38.09 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 1507 0.261696 AAATGGTACCCCTCCATGGC 59.738 55.000 10.07 0.0 43.85 4.40 R
1703 1755 1.289530 AGAAACCCAAGGAACCACCAA 59.710 47.619 0.00 0.0 42.04 3.67 R
3446 4726 0.192566 ACAAGTACACTCCTCCCCCA 59.807 55.000 0.00 0.0 0.00 4.96 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
55 57 3.760035 CCGCAGTACCGCTGGAGT 61.760 66.667 6.20 0.00 45.14 3.85
84 86 2.393768 CGCTGAACTGCCGCTCAAT 61.394 57.895 0.00 0.00 0.00 2.57
91 93 3.155470 CTGCCGCTCAATTACCGCG 62.155 63.158 0.00 0.00 45.86 6.46
123 125 3.011119 ACACACAAAACAAGCGGAAGTA 58.989 40.909 0.00 0.00 0.00 2.24
158 188 1.518133 GCTGAGCAGAGCGGTACTG 60.518 63.158 0.00 0.00 38.27 2.74
171 201 0.321671 GGTACTGCTGCTGAGGTTGA 59.678 55.000 13.69 0.00 0.00 3.18
207 238 2.149578 CACAAGGAAGGACAAGCTCAG 58.850 52.381 0.00 0.00 0.00 3.35
211 242 4.042187 ACAAGGAAGGACAAGCTCAGTTAT 59.958 41.667 0.00 0.00 0.00 1.89
246 277 3.838317 AGGGTGCAAAGAGATAGTGTACA 59.162 43.478 0.00 0.00 30.43 2.90
259 290 6.946340 AGATAGTGTACATGTTGATTCCACA 58.054 36.000 2.30 0.00 0.00 4.17
269 300 5.413309 TGTTGATTCCACACAAACCTTTT 57.587 34.783 0.00 0.00 0.00 2.27
275 306 3.611970 TCCACACAAACCTTTTCGAAGA 58.388 40.909 0.00 0.00 0.00 2.87
304 336 4.630069 CCTCTTAATTGTACGGTGTTCCTG 59.370 45.833 0.00 0.00 0.00 3.86
330 362 6.345096 ACTCAAATCCACCGAAAATGAAAT 57.655 33.333 0.00 0.00 0.00 2.17
335 367 6.588719 AATCCACCGAAAATGAAATGAAGA 57.411 33.333 0.00 0.00 0.00 2.87
363 395 6.589830 ACATCATCTTCACAATAGTTACGC 57.410 37.500 0.00 0.00 0.00 4.42
430 462 1.327460 CAATGCACACGATTAGTCCGG 59.673 52.381 0.00 0.00 0.00 5.14
435 467 2.481185 GCACACGATTAGTCCGGAAAAA 59.519 45.455 5.23 3.49 0.00 1.94
442 474 7.120138 ACACGATTAGTCCGGAAAAACATTATT 59.880 33.333 5.23 0.00 0.00 1.40
465 497 8.877864 ATTATCAATCACCAAAACCACTAAGA 57.122 30.769 0.00 0.00 0.00 2.10
475 507 9.667107 CACCAAAACCACTAAGAGAGAAATATA 57.333 33.333 0.00 0.00 0.00 0.86
491 523 9.710818 AGAGAAATATACCCTAACAGTCTAACA 57.289 33.333 0.00 0.00 0.00 2.41
492 524 9.747293 GAGAAATATACCCTAACAGTCTAACAC 57.253 37.037 0.00 0.00 0.00 3.32
513 545 2.505819 CCATGCCCTACTCTACCTTGTT 59.494 50.000 0.00 0.00 0.00 2.83
514 546 3.535561 CATGCCCTACTCTACCTTGTTG 58.464 50.000 0.00 0.00 0.00 3.33
533 565 0.608640 GGTGATCGGACCAACACTCT 59.391 55.000 10.88 0.00 35.88 3.24
534 566 1.822990 GGTGATCGGACCAACACTCTA 59.177 52.381 10.88 0.00 35.88 2.43
538 570 1.263356 TCGGACCAACACTCTAAGGG 58.737 55.000 0.00 0.00 0.00 3.95
571 603 1.745890 CCGAATATGGGCACGAGGA 59.254 57.895 0.00 0.00 0.00 3.71
573 605 1.217882 CGAATATGGGCACGAGGAAC 58.782 55.000 0.00 0.00 0.00 3.62
575 607 0.916086 AATATGGGCACGAGGAACCA 59.084 50.000 0.00 0.00 37.41 3.67
576 608 0.916086 ATATGGGCACGAGGAACCAA 59.084 50.000 0.00 0.00 36.44 3.67
577 609 0.693622 TATGGGCACGAGGAACCAAA 59.306 50.000 0.00 0.00 36.44 3.28
578 610 0.893727 ATGGGCACGAGGAACCAAAC 60.894 55.000 0.00 0.00 36.44 2.93
579 611 2.613506 GGGCACGAGGAACCAAACG 61.614 63.158 0.00 0.00 0.00 3.60
580 612 1.595929 GGCACGAGGAACCAAACGA 60.596 57.895 0.00 0.00 0.00 3.85
581 613 1.566018 GGCACGAGGAACCAAACGAG 61.566 60.000 0.00 0.00 0.00 4.18
582 614 1.860078 CACGAGGAACCAAACGAGC 59.140 57.895 0.00 0.00 0.00 5.03
583 615 0.600255 CACGAGGAACCAAACGAGCT 60.600 55.000 0.00 0.00 0.00 4.09
584 616 0.319641 ACGAGGAACCAAACGAGCTC 60.320 55.000 2.73 2.73 0.00 4.09
608 641 7.918643 TCCGTTTAAAGATGAGTTTTACGTTT 58.081 30.769 0.00 0.00 30.48 3.60
637 684 7.659799 TGTAATAATATGGATTTGAGGTGTCCG 59.340 37.037 0.00 0.00 34.72 4.79
640 687 0.323629 TGGATTTGAGGTGTCCGGTC 59.676 55.000 0.00 0.00 34.72 4.79
659 706 8.985805 GTCCGGTCGTAGAATCAAATATTTAAT 58.014 33.333 0.00 0.00 39.69 1.40
660 707 8.984764 TCCGGTCGTAGAATCAAATATTTAATG 58.015 33.333 0.00 0.00 39.69 1.90
662 709 8.279800 CGGTCGTAGAATCAAATATTTAATGCA 58.720 33.333 0.00 0.00 39.69 3.96
673 720 5.689383 ATATTTAATGCATGACCGGTCAC 57.311 39.130 38.46 26.54 43.11 3.67
678 725 1.293498 GCATGACCGGTCACTGTCT 59.707 57.895 38.46 20.57 43.11 3.41
684 731 1.188219 ACCGGTCACTGTCTGCTGAT 61.188 55.000 0.00 0.00 0.00 2.90
687 734 1.023513 GGTCACTGTCTGCTGATGCC 61.024 60.000 0.00 0.00 38.71 4.40
691 738 2.046988 TGTCTGCTGATGCCGGTG 60.047 61.111 1.90 0.00 38.71 4.94
693 740 4.100084 TCTGCTGATGCCGGTGGG 62.100 66.667 1.90 0.00 38.71 4.61
694 741 4.415150 CTGCTGATGCCGGTGGGT 62.415 66.667 1.90 0.00 38.71 4.51
706 753 4.295119 GTGGGTGCGTCCACGAGT 62.295 66.667 11.68 0.00 46.31 4.18
714 761 0.596600 GCGTCCACGAGTGTTTGAGA 60.597 55.000 2.58 0.00 43.02 3.27
716 763 1.784525 GTCCACGAGTGTTTGAGAGG 58.215 55.000 2.36 0.00 0.00 3.69
720 767 1.001706 CACGAGTGTTTGAGAGGTCGA 60.002 52.381 0.00 0.00 0.00 4.20
723 770 3.243771 ACGAGTGTTTGAGAGGTCGAATT 60.244 43.478 0.00 0.00 0.00 2.17
726 773 3.251004 AGTGTTTGAGAGGTCGAATTTGC 59.749 43.478 0.00 0.00 0.00 3.68
727 774 2.552315 TGTTTGAGAGGTCGAATTTGCC 59.448 45.455 0.00 0.00 0.00 4.52
732 779 1.625818 AGAGGTCGAATTTGCCAGTCT 59.374 47.619 8.35 2.22 0.00 3.24
735 782 1.610624 GGTCGAATTTGCCAGTCTGGA 60.611 52.381 23.77 1.66 40.96 3.86
737 784 2.096496 GTCGAATTTGCCAGTCTGGATG 59.904 50.000 23.77 3.40 40.96 3.51
766 813 2.321263 TAACCCGCACCCAAACACGA 62.321 55.000 0.00 0.00 0.00 4.35
785 832 1.303236 CGGGTGGCATGGTGAGAAA 60.303 57.895 0.00 0.00 0.00 2.52
905 955 5.240844 CCTCCAACAAAAAGGATAACGTTCT 59.759 40.000 2.82 0.00 32.53 3.01
911 961 4.376225 AAAAGGATAACGTTCTTCCCCA 57.624 40.909 20.77 0.00 0.00 4.96
913 963 4.586306 AAGGATAACGTTCTTCCCCAAT 57.414 40.909 20.77 1.66 0.00 3.16
914 964 4.152284 AGGATAACGTTCTTCCCCAATC 57.848 45.455 20.77 9.83 0.00 2.67
916 966 3.118000 GGATAACGTTCTTCCCCAATCCT 60.118 47.826 15.91 0.00 31.05 3.24
917 967 2.491675 AACGTTCTTCCCCAATCCTC 57.508 50.000 0.00 0.00 0.00 3.71
1059 1110 2.835764 ACTTCTTCCCCACGCACTATTA 59.164 45.455 0.00 0.00 0.00 0.98
1470 1521 0.400093 AGTAGGCCATGGAGGGGTAC 60.400 60.000 18.40 8.46 38.09 3.34
1546 1597 2.677199 TCTGTTGAGTTGCTAGAAGCG 58.323 47.619 0.00 0.00 46.26 4.68
1655 1706 8.657387 TTAGGGTTCAGATAGGAGAAGATATG 57.343 38.462 0.00 0.00 0.00 1.78
1701 1753 2.948115 CATTAGCATGGGTGGATGGAA 58.052 47.619 0.00 0.00 0.00 3.53
1703 1755 3.686227 TTAGCATGGGTGGATGGAATT 57.314 42.857 0.00 0.00 0.00 2.17
1732 1784 6.272792 TGGTTCCTTGGGTTTCTGTATACTTA 59.727 38.462 4.17 0.00 0.00 2.24
1887 1943 1.818674 GATTTGAAGCCCGGTGACATT 59.181 47.619 0.00 0.00 0.00 2.71
1909 1965 3.784701 TCGAGCTTAGAATGGTGAGAC 57.215 47.619 0.00 0.00 0.00 3.36
1914 1970 4.826556 AGCTTAGAATGGTGAGACTGTTC 58.173 43.478 0.00 0.00 0.00 3.18
1938 1994 7.324935 TCGCTACTCTTGAATGTGGTTTTATA 58.675 34.615 0.00 0.00 0.00 0.98
1991 2048 1.431440 GTTGTTGCAGCAACGTCCA 59.569 52.632 27.16 12.31 46.13 4.02
2181 2238 8.435982 TGTGGATACCATCACATGTATCAAATA 58.564 33.333 0.00 0.00 38.75 1.40
2193 2250 7.547019 CACATGTATCAAATAGTGACAGTGAGT 59.453 37.037 0.00 0.00 39.72 3.41
2249 2306 7.254227 TGTGTATCTTTTGTTCGCTTTAACT 57.746 32.000 0.00 0.00 0.00 2.24
2250 2307 8.367943 TGTGTATCTTTTGTTCGCTTTAACTA 57.632 30.769 0.00 0.00 0.00 2.24
2251 2308 8.277713 TGTGTATCTTTTGTTCGCTTTAACTAC 58.722 33.333 0.00 0.00 0.00 2.73
2301 2359 6.382869 TTCTACGGCATACTAACCTTAGTC 57.617 41.667 0.85 0.00 42.66 2.59
2353 2412 1.135689 CGTTGGCCTTCACATACTTGC 60.136 52.381 3.32 0.00 0.00 4.01
2369 2428 4.195225 ACTTGCTCTCAGGTACTTTAGC 57.805 45.455 0.00 0.00 34.60 3.09
2393 2452 8.870116 AGCTTTTCTAATGTCCACCTTAAAATT 58.130 29.630 0.00 0.00 0.00 1.82
2402 2461 7.130681 TGTCCACCTTAAAATTGGTTGAATT 57.869 32.000 0.00 0.00 35.65 2.17
2438 2497 1.075542 TTACAATGAACTGAGCGCCG 58.924 50.000 2.29 0.00 0.00 6.46
2444 2503 0.737367 TGAACTGAGCGCCGAAGATG 60.737 55.000 2.29 0.00 0.00 2.90
2458 2517 4.676196 GCCGAAGATGCTTTTGTCATGATT 60.676 41.667 0.00 0.00 0.00 2.57
2459 2518 5.449041 GCCGAAGATGCTTTTGTCATGATTA 60.449 40.000 0.00 0.00 0.00 1.75
2460 2519 6.554419 CCGAAGATGCTTTTGTCATGATTAA 58.446 36.000 0.00 0.00 0.00 1.40
2461 2520 7.198390 CCGAAGATGCTTTTGTCATGATTAAT 58.802 34.615 0.00 0.00 0.00 1.40
2462 2521 8.344831 CCGAAGATGCTTTTGTCATGATTAATA 58.655 33.333 0.00 0.00 0.00 0.98
2463 2522 9.720667 CGAAGATGCTTTTGTCATGATTAATAA 57.279 29.630 0.00 0.00 0.00 1.40
2541 3388 6.593382 CCTTTGAATGTTTGAAAGGTGTGAAA 59.407 34.615 9.28 0.00 40.56 2.69
2572 3419 5.411361 TGCTCAAAATGCATTACTTACGTCT 59.589 36.000 13.39 0.00 35.31 4.18
2573 3420 5.734498 GCTCAAAATGCATTACTTACGTCTG 59.266 40.000 13.39 0.14 0.00 3.51
2575 3422 7.197071 TCAAAATGCATTACTTACGTCTGTT 57.803 32.000 13.39 0.00 0.00 3.16
2606 3453 7.709182 AGAGGCAAATTTACAAAACCAGTTAAC 59.291 33.333 0.00 0.00 0.00 2.01
2610 3457 8.325282 GCAAATTTACAAAACCAGTTAACTGAC 58.675 33.333 32.50 0.00 46.59 3.51
2729 4008 1.327303 TTGCGGAATTCTGTTTGGCT 58.673 45.000 15.63 0.00 0.00 4.75
2733 4012 2.676076 CGGAATTCTGTTTGGCTTTGG 58.324 47.619 6.08 0.00 0.00 3.28
2734 4013 2.295909 CGGAATTCTGTTTGGCTTTGGA 59.704 45.455 6.08 0.00 0.00 3.53
2735 4014 3.056607 CGGAATTCTGTTTGGCTTTGGAT 60.057 43.478 6.08 0.00 0.00 3.41
2736 4015 4.561326 CGGAATTCTGTTTGGCTTTGGATT 60.561 41.667 6.08 0.00 0.00 3.01
2737 4016 5.336372 CGGAATTCTGTTTGGCTTTGGATTA 60.336 40.000 6.08 0.00 0.00 1.75
2738 4017 6.463360 GGAATTCTGTTTGGCTTTGGATTAA 58.537 36.000 5.23 0.00 0.00 1.40
2739 4018 7.105588 GGAATTCTGTTTGGCTTTGGATTAAT 58.894 34.615 5.23 0.00 0.00 1.40
2740 4019 7.278646 GGAATTCTGTTTGGCTTTGGATTAATC 59.721 37.037 6.93 6.93 0.00 1.75
2741 4020 5.309323 TCTGTTTGGCTTTGGATTAATCG 57.691 39.130 9.32 0.00 0.00 3.34
2742 4021 3.843999 TGTTTGGCTTTGGATTAATCGC 58.156 40.909 9.32 6.90 0.00 4.58
2743 4022 3.186909 GTTTGGCTTTGGATTAATCGCC 58.813 45.455 19.55 19.55 36.38 5.54
2744 4023 1.021202 TGGCTTTGGATTAATCGCCG 58.979 50.000 20.41 7.57 37.78 6.46
2745 4024 1.305201 GGCTTTGGATTAATCGCCGA 58.695 50.000 14.00 0.00 0.00 5.54
2746 4025 1.880027 GGCTTTGGATTAATCGCCGAT 59.120 47.619 14.00 0.00 0.00 4.18
2747 4026 3.071479 GGCTTTGGATTAATCGCCGATA 58.929 45.455 14.00 0.00 0.00 2.92
2748 4027 3.120304 GGCTTTGGATTAATCGCCGATAC 60.120 47.826 14.00 0.00 0.00 2.24
2749 4028 3.496884 GCTTTGGATTAATCGCCGATACA 59.503 43.478 0.00 0.00 0.00 2.29
2750 4029 4.377431 GCTTTGGATTAATCGCCGATACAG 60.377 45.833 0.00 0.00 0.00 2.74
2751 4030 4.330944 TTGGATTAATCGCCGATACAGT 57.669 40.909 0.00 0.00 0.00 3.55
2752 4031 3.649073 TGGATTAATCGCCGATACAGTG 58.351 45.455 0.00 0.00 0.00 3.66
2753 4032 3.069016 TGGATTAATCGCCGATACAGTGT 59.931 43.478 0.00 0.00 0.00 3.55
2754 4033 4.056050 GGATTAATCGCCGATACAGTGTT 58.944 43.478 0.00 0.00 0.00 3.32
2755 4034 4.510340 GGATTAATCGCCGATACAGTGTTT 59.490 41.667 0.00 0.00 0.00 2.83
2756 4035 4.850859 TTAATCGCCGATACAGTGTTTG 57.149 40.909 0.00 0.00 0.00 2.93
2757 4036 1.651987 ATCGCCGATACAGTGTTTGG 58.348 50.000 0.00 2.20 0.00 3.28
2758 4037 1.017177 TCGCCGATACAGTGTTTGGC 61.017 55.000 18.21 18.21 39.10 4.52
2759 4038 1.019278 CGCCGATACAGTGTTTGGCT 61.019 55.000 22.76 0.00 40.31 4.75
2760 4039 1.165270 GCCGATACAGTGTTTGGCTT 58.835 50.000 19.95 0.00 39.38 4.35
2761 4040 1.539827 GCCGATACAGTGTTTGGCTTT 59.460 47.619 19.95 0.00 39.38 3.51
2762 4041 2.030274 GCCGATACAGTGTTTGGCTTTT 60.030 45.455 19.95 0.00 39.38 2.27
2763 4042 3.564511 CCGATACAGTGTTTGGCTTTTG 58.435 45.455 0.00 0.00 0.00 2.44
2764 4043 2.979813 CGATACAGTGTTTGGCTTTTGC 59.020 45.455 0.00 0.00 46.64 3.68
2778 4057 2.803956 GCTTTTGCTGACATTGTTGCAT 59.196 40.909 15.64 0.00 43.35 3.96
2826 4105 4.075963 AGCAAGTACCTTTTCCGTTACA 57.924 40.909 0.00 0.00 0.00 2.41
2943 4223 3.938289 TGCATATTGCTGCTGTTGAAA 57.062 38.095 0.00 0.00 45.31 2.69
2963 4243 4.503741 AAGTGTTTATTTGCACGCATCT 57.496 36.364 0.00 0.00 40.26 2.90
2966 4246 5.288804 AGTGTTTATTTGCACGCATCTTTT 58.711 33.333 0.00 0.00 40.26 2.27
3012 4292 4.671766 GCCCATCGTCTCATGTGTAAAAAC 60.672 45.833 0.00 0.00 0.00 2.43
3116 4396 2.103263 AGACCAAACACTGTCCAGACTC 59.897 50.000 0.40 0.00 31.76 3.36
3117 4397 2.103263 GACCAAACACTGTCCAGACTCT 59.897 50.000 0.40 0.00 0.00 3.24
3118 4398 2.158900 ACCAAACACTGTCCAGACTCTG 60.159 50.000 0.40 0.00 0.00 3.35
3119 4399 1.869767 CAAACACTGTCCAGACTCTGC 59.130 52.381 0.40 0.00 0.00 4.26
3120 4400 1.418334 AACACTGTCCAGACTCTGCT 58.582 50.000 0.40 0.00 0.00 4.24
3121 4401 2.294449 ACACTGTCCAGACTCTGCTA 57.706 50.000 0.40 0.00 0.00 3.49
3122 4402 1.889829 ACACTGTCCAGACTCTGCTAC 59.110 52.381 0.40 2.22 0.00 3.58
3123 4403 2.166829 CACTGTCCAGACTCTGCTACT 58.833 52.381 0.40 0.00 0.00 2.57
3124 4404 2.094803 CACTGTCCAGACTCTGCTACTG 60.095 54.545 0.40 7.56 0.00 2.74
3125 4405 0.891373 TGTCCAGACTCTGCTACTGC 59.109 55.000 0.00 0.00 40.20 4.40
3126 4406 1.181786 GTCCAGACTCTGCTACTGCT 58.818 55.000 0.00 0.00 40.48 4.24
3127 4407 1.134175 GTCCAGACTCTGCTACTGCTC 59.866 57.143 0.00 0.00 40.48 4.26
3128 4408 1.180907 CCAGACTCTGCTACTGCTCA 58.819 55.000 0.00 0.00 40.48 4.26
3129 4409 1.134753 CCAGACTCTGCTACTGCTCAG 59.865 57.143 0.00 0.00 40.48 3.35
3130 4410 2.090760 CAGACTCTGCTACTGCTCAGA 58.909 52.381 3.60 0.00 40.48 3.27
3146 4426 3.056322 GCTCAGAATCCCTGCAACAAAAT 60.056 43.478 0.00 0.00 42.62 1.82
3346 4626 2.218603 TCTCCTTGGCAAACGAGTTTC 58.781 47.619 18.40 0.00 0.00 2.78
3354 4634 2.293399 GGCAAACGAGTTTCCACAATCT 59.707 45.455 0.00 0.00 0.00 2.40
3356 4636 4.023536 GGCAAACGAGTTTCCACAATCTTA 60.024 41.667 0.00 0.00 0.00 2.10
3399 4679 3.451141 AATGATCTCTGAACCTCGAGC 57.549 47.619 6.99 0.00 0.00 5.03
3446 4726 5.989168 TCGATTGGCATATATTTCGTCTTGT 59.011 36.000 0.00 0.00 0.00 3.16
3449 4729 4.133820 TGGCATATATTTCGTCTTGTGGG 58.866 43.478 0.00 0.00 0.00 4.61
3483 4764 9.214957 TGTACTTGTGAGTGTATAAAATTCCTG 57.785 33.333 0.00 0.00 36.60 3.86
3541 4829 1.078426 CTTTCCCAGCTACCCACCG 60.078 63.158 0.00 0.00 0.00 4.94
3694 5019 3.006940 GTTGGTTTGATGGCGAGTCATA 58.993 45.455 0.00 0.00 0.00 2.15
3695 5020 3.558931 TGGTTTGATGGCGAGTCATAT 57.441 42.857 0.00 0.00 0.00 1.78
3696 5021 3.466836 TGGTTTGATGGCGAGTCATATC 58.533 45.455 0.00 0.00 0.00 1.63
3699 5024 4.295870 GTTTGATGGCGAGTCATATCGTA 58.704 43.478 0.00 0.00 44.53 3.43
3717 5042 9.066939 CATATCGTAGTATCAATTTTCTCTCCG 57.933 37.037 0.00 0.00 0.00 4.63
3731 5056 2.904434 TCTCTCCGGCTTAGGAAACTTT 59.096 45.455 0.00 0.00 43.67 2.66
3732 5057 3.003480 CTCTCCGGCTTAGGAAACTTTG 58.997 50.000 0.00 0.00 43.67 2.77
3733 5058 1.468914 CTCCGGCTTAGGAAACTTTGC 59.531 52.381 0.00 0.00 43.67 3.68
3734 5059 1.202830 TCCGGCTTAGGAAACTTTGCA 60.203 47.619 0.00 0.00 43.67 4.08
3735 5060 1.818674 CCGGCTTAGGAAACTTTGCAT 59.181 47.619 0.00 0.00 43.67 3.96
3746 5071 2.215942 ACTTTGCATCCAGGGGTTAC 57.784 50.000 0.00 0.00 0.00 2.50
3842 5175 9.705290 AAACACAATAAAAGTTTCACTCAGTTT 57.295 25.926 0.00 0.00 30.19 2.66
3886 5225 0.830648 TCAGGCCATGCTAGGTGTAC 59.169 55.000 5.01 0.00 0.00 2.90
3897 5236 7.913821 GCCATGCTAGGTGTACTTTTTATTTAC 59.086 37.037 0.00 0.00 0.00 2.01
3970 5343 4.154918 CACATCCAAGTTTGAGCCTAAGTC 59.845 45.833 0.00 0.00 0.00 3.01
3975 5348 3.897141 AGTTTGAGCCTAAGTCTAGCC 57.103 47.619 0.00 0.00 0.00 3.93
4067 5440 5.571784 TGTTCTCGTGTCTTATCCGTAAT 57.428 39.130 0.00 0.00 0.00 1.89
4281 5660 8.141909 TGTGCAATGTAGGAGTATAATCACTAC 58.858 37.037 15.83 15.83 35.71 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.244450 CACTACCGCGGGTTTACTGA 59.756 55.000 31.76 2.62 37.09 3.41
29 31 1.153429 GGTACTGCGGCCCTAACTG 60.153 63.158 0.00 0.00 0.00 3.16
51 53 2.103736 GCGCGGTAGTACCACTCC 59.896 66.667 19.41 3.56 38.47 3.85
55 57 1.213537 GTTCAGCGCGGTAGTACCA 59.786 57.895 19.41 0.00 38.47 3.25
82 84 4.151157 GTGTTCTGTAAACTCGCGGTAATT 59.849 41.667 6.13 0.00 0.00 1.40
84 86 3.052036 GTGTTCTGTAAACTCGCGGTAA 58.948 45.455 6.13 0.00 0.00 2.85
91 93 6.033513 GCTTGTTTTGTGTGTTCTGTAAACTC 59.966 38.462 0.00 0.00 0.00 3.01
92 94 5.861787 GCTTGTTTTGTGTGTTCTGTAAACT 59.138 36.000 0.00 0.00 0.00 2.66
123 125 1.003718 GCGGAACAGTGCTACCCTT 60.004 57.895 0.00 0.00 0.00 3.95
158 188 2.105006 TTCAGATCAACCTCAGCAGC 57.895 50.000 0.00 0.00 0.00 5.25
160 190 2.816087 GCTTTTCAGATCAACCTCAGCA 59.184 45.455 0.00 0.00 0.00 4.41
164 194 4.379290 GCTTGAGCTTTTCAGATCAACCTC 60.379 45.833 0.00 0.00 46.22 3.85
166 196 3.254166 TGCTTGAGCTTTTCAGATCAACC 59.746 43.478 4.44 0.00 46.22 3.77
171 201 3.255149 CCTTGTGCTTGAGCTTTTCAGAT 59.745 43.478 4.44 0.00 42.66 2.90
207 238 2.364647 ACCCTCGATCTTTCCCGATAAC 59.635 50.000 0.00 0.00 34.08 1.89
211 242 1.956629 GCACCCTCGATCTTTCCCGA 61.957 60.000 0.00 0.00 0.00 5.14
246 277 5.612725 AAAGGTTTGTGTGGAATCAACAT 57.387 34.783 0.00 0.00 0.00 2.71
259 290 3.211865 GGTCCTCTTCGAAAAGGTTTGT 58.788 45.455 17.01 0.00 34.12 2.83
275 306 2.770232 CCGTACAATTAAGAGGGGTCCT 59.230 50.000 0.00 0.00 36.03 3.85
290 322 1.007038 GTCGCAGGAACACCGTACA 60.007 57.895 0.00 0.00 0.00 2.90
304 336 1.153353 TTTCGGTGGATTTGAGTCGC 58.847 50.000 0.00 0.00 0.00 5.19
343 375 4.109766 CCGCGTAACTATTGTGAAGATGA 58.890 43.478 4.92 0.00 0.00 2.92
358 390 2.509786 GATTCGTGCCCCGCGTAA 60.510 61.111 4.92 0.00 38.57 3.18
360 392 4.388499 AAGATTCGTGCCCCGCGT 62.388 61.111 4.92 0.00 38.57 6.01
363 395 0.673644 ACAAGAAGATTCGTGCCCCG 60.674 55.000 8.18 0.00 39.76 5.73
408 440 2.670905 CGGACTAATCGTGTGCATTGAA 59.329 45.455 0.00 0.00 0.00 2.69
435 467 9.034800 AGTGGTTTTGGTGATTGATAATAATGT 57.965 29.630 0.00 0.00 0.00 2.71
442 474 7.685481 TCTCTTAGTGGTTTTGGTGATTGATA 58.315 34.615 0.00 0.00 0.00 2.15
465 497 9.710818 TGTTAGACTGTTAGGGTATATTTCTCT 57.289 33.333 0.00 0.00 0.00 3.10
475 507 3.307480 GCATGGTGTTAGACTGTTAGGGT 60.307 47.826 0.00 0.00 0.00 4.34
484 516 2.766828 AGAGTAGGGCATGGTGTTAGAC 59.233 50.000 0.00 0.00 0.00 2.59
488 520 1.838077 GGTAGAGTAGGGCATGGTGTT 59.162 52.381 0.00 0.00 0.00 3.32
489 521 1.008449 AGGTAGAGTAGGGCATGGTGT 59.992 52.381 0.00 0.00 0.00 4.16
490 522 1.794714 AGGTAGAGTAGGGCATGGTG 58.205 55.000 0.00 0.00 0.00 4.17
491 523 2.119495 CAAGGTAGAGTAGGGCATGGT 58.881 52.381 0.00 0.00 0.00 3.55
492 524 2.119495 ACAAGGTAGAGTAGGGCATGG 58.881 52.381 0.00 0.00 0.00 3.66
513 545 0.320374 GAGTGTTGGTCCGATCACCA 59.680 55.000 0.79 0.79 45.25 4.17
514 546 0.608640 AGAGTGTTGGTCCGATCACC 59.391 55.000 0.00 0.00 36.90 4.02
516 548 2.496070 CCTTAGAGTGTTGGTCCGATCA 59.504 50.000 0.00 0.00 0.00 2.92
521 553 1.066071 GCTCCCTTAGAGTGTTGGTCC 60.066 57.143 0.00 0.00 45.21 4.46
522 554 1.404315 CGCTCCCTTAGAGTGTTGGTC 60.404 57.143 0.00 0.00 46.25 4.02
524 556 3.442996 CGCTCCCTTAGAGTGTTGG 57.557 57.895 0.00 0.00 46.25 3.77
533 565 2.797278 GGCTAGCTGCGCTCCCTTA 61.797 63.158 15.72 0.00 44.05 2.69
534 566 4.168291 GGCTAGCTGCGCTCCCTT 62.168 66.667 15.72 0.00 44.05 3.95
547 579 2.345991 GCCCATATTCGGCGGCTA 59.654 61.111 7.21 0.00 38.41 3.93
556 588 0.916086 TGGTTCCTCGTGCCCATATT 59.084 50.000 0.00 0.00 0.00 1.28
558 590 0.693622 TTTGGTTCCTCGTGCCCATA 59.306 50.000 0.00 0.00 0.00 2.74
567 599 1.014564 CGGAGCTCGTTTGGTTCCTC 61.015 60.000 7.83 0.00 32.94 3.71
568 600 1.004918 CGGAGCTCGTTTGGTTCCT 60.005 57.895 7.83 0.00 32.94 3.36
569 601 3.562635 CGGAGCTCGTTTGGTTCC 58.437 61.111 7.83 0.00 0.00 3.62
578 610 3.512680 ACTCATCTTTAAACGGAGCTCG 58.487 45.455 7.83 5.83 45.88 5.03
579 611 5.864628 AAACTCATCTTTAAACGGAGCTC 57.135 39.130 4.71 4.71 0.00 4.09
580 612 6.128634 CGTAAAACTCATCTTTAAACGGAGCT 60.129 38.462 0.00 0.00 0.00 4.09
581 613 6.013689 CGTAAAACTCATCTTTAAACGGAGC 58.986 40.000 6.12 0.00 0.00 4.70
582 614 7.113704 ACGTAAAACTCATCTTTAAACGGAG 57.886 36.000 0.00 5.07 31.65 4.63
583 615 7.481275 AACGTAAAACTCATCTTTAAACGGA 57.519 32.000 0.00 0.00 31.65 4.69
584 616 7.851963 TGAAACGTAAAACTCATCTTTAAACGG 59.148 33.333 0.00 0.00 31.65 4.44
623 656 0.037605 ACGACCGGACACCTCAAATC 60.038 55.000 9.46 0.00 0.00 2.17
628 675 1.065251 GATTCTACGACCGGACACCTC 59.935 57.143 9.46 0.00 0.00 3.85
635 682 7.744715 GCATTAAATATTTGATTCTACGACCGG 59.255 37.037 11.05 0.00 0.00 5.28
659 706 1.005037 GACAGTGACCGGTCATGCA 60.005 57.895 38.11 15.45 42.18 3.96
660 707 1.016130 CAGACAGTGACCGGTCATGC 61.016 60.000 38.11 26.39 42.18 4.06
662 709 1.188219 AGCAGACAGTGACCGGTCAT 61.188 55.000 38.11 24.17 42.18 3.06
673 720 2.104859 CACCGGCATCAGCAGACAG 61.105 63.158 0.00 0.00 44.61 3.51
678 725 4.720902 CACCCACCGGCATCAGCA 62.721 66.667 0.00 0.00 44.61 4.41
691 738 3.802418 AACACTCGTGGACGCACCC 62.802 63.158 1.77 0.00 39.60 4.61
693 740 1.149361 TCAAACACTCGTGGACGCAC 61.149 55.000 1.77 0.00 39.60 5.34
694 741 0.874175 CTCAAACACTCGTGGACGCA 60.874 55.000 1.77 0.00 39.60 5.24
704 751 3.251004 GCAAATTCGACCTCTCAAACACT 59.749 43.478 0.00 0.00 0.00 3.55
705 752 3.555518 GCAAATTCGACCTCTCAAACAC 58.444 45.455 0.00 0.00 0.00 3.32
706 753 2.552315 GGCAAATTCGACCTCTCAAACA 59.448 45.455 0.00 0.00 0.00 2.83
714 761 1.611673 CCAGACTGGCAAATTCGACCT 60.612 52.381 8.99 0.00 0.00 3.85
716 763 1.808411 TCCAGACTGGCAAATTCGAC 58.192 50.000 17.33 0.00 37.47 4.20
720 767 4.574674 TCTACATCCAGACTGGCAAATT 57.425 40.909 17.33 1.74 37.47 1.82
723 770 2.420547 GCATCTACATCCAGACTGGCAA 60.421 50.000 17.33 0.31 37.47 4.52
726 773 3.383620 GAGCATCTACATCCAGACTGG 57.616 52.381 15.99 15.99 39.43 4.00
766 813 2.063015 TTTCTCACCATGCCACCCGT 62.063 55.000 0.00 0.00 0.00 5.28
905 955 2.694616 CGGGGGAGGATTGGGGAA 60.695 66.667 0.00 0.00 0.00 3.97
1059 1110 2.125106 GGAGGCGAGCGGTGATTT 60.125 61.111 0.00 0.00 0.00 2.17
1200 1251 3.847602 CCCTCAGGAGCAGGCTCG 61.848 72.222 14.56 2.82 43.59 5.03
1329 1380 1.788229 TGCTTACCCCGATGATCTCA 58.212 50.000 0.00 0.00 0.00 3.27
1396 1447 4.385358 ACAATTTCGCCAAACTTGACTT 57.615 36.364 4.29 0.00 0.00 3.01
1450 1501 0.399949 TACCCCTCCATGGCCTACTG 60.400 60.000 6.96 0.00 0.00 2.74
1451 1502 0.400093 GTACCCCTCCATGGCCTACT 60.400 60.000 6.96 0.00 0.00 2.57
1453 1504 1.074014 GGTACCCCTCCATGGCCTA 60.074 63.158 6.96 0.00 0.00 3.93
1454 1505 2.368329 GGTACCCCTCCATGGCCT 60.368 66.667 6.96 0.00 0.00 5.19
1455 1506 1.655114 AATGGTACCCCTCCATGGCC 61.655 60.000 10.07 0.00 43.85 5.36
1456 1507 0.261696 AAATGGTACCCCTCCATGGC 59.738 55.000 10.07 0.00 43.85 4.40
1458 1509 3.669939 AAGAAATGGTACCCCTCCATG 57.330 47.619 10.07 0.00 43.85 3.66
1546 1597 2.803451 CGATGGTGCTCAAGAGACTAC 58.197 52.381 0.32 0.00 0.00 2.73
1655 1706 7.254218 GCAATCATGAAACTTATTTAGCAAGCC 60.254 37.037 0.00 0.00 0.00 4.35
1691 1743 1.937191 ACCACCAAATTCCATCCACC 58.063 50.000 0.00 0.00 0.00 4.61
1701 1753 2.487746 AACCCAAGGAACCACCAAAT 57.512 45.000 0.00 0.00 42.04 2.32
1703 1755 1.289530 AGAAACCCAAGGAACCACCAA 59.710 47.619 0.00 0.00 42.04 3.67
1732 1784 9.912634 CAAAATGGTCTTGAATGTAACAAGTAT 57.087 29.630 0.00 0.00 43.30 2.12
1887 1943 5.009110 CAGTCTCACCATTCTAAGCTCGATA 59.991 44.000 0.00 0.00 0.00 2.92
1909 1965 3.369147 CCACATTCAAGAGTAGCGAACAG 59.631 47.826 0.00 0.00 0.00 3.16
1914 1970 4.749245 AAAACCACATTCAAGAGTAGCG 57.251 40.909 0.00 0.00 0.00 4.26
1938 1994 7.290014 GGACATCAATAACCCCCAAATAAGAAT 59.710 37.037 0.00 0.00 0.00 2.40
2168 2225 7.615403 ACTCACTGTCACTATTTGATACATGT 58.385 34.615 2.69 2.69 36.32 3.21
2181 2238 7.716998 AGATTCAATACAAAACTCACTGTCACT 59.283 33.333 0.00 0.00 0.00 3.41
2249 2306 7.176515 ACATGTGCATAGTCCAAATTTCTTGTA 59.823 33.333 0.00 0.00 0.00 2.41
2250 2307 6.015180 ACATGTGCATAGTCCAAATTTCTTGT 60.015 34.615 0.00 0.00 0.00 3.16
2251 2308 6.392354 ACATGTGCATAGTCCAAATTTCTTG 58.608 36.000 0.00 0.00 0.00 3.02
2353 2412 9.092876 CATTAGAAAAGCTAAAGTACCTGAGAG 57.907 37.037 0.00 0.00 42.10 3.20
2369 2428 9.423061 CCAATTTTAAGGTGGACATTAGAAAAG 57.577 33.333 0.00 0.00 34.05 2.27
2410 2469 7.645340 GCGCTCAGTTCATTGTAAAATTGATAT 59.355 33.333 0.00 0.00 0.00 1.63
2429 2488 1.364626 AAAGCATCTTCGGCGCTCAG 61.365 55.000 7.64 0.41 34.11 3.35
2435 2494 2.162208 TCATGACAAAAGCATCTTCGGC 59.838 45.455 0.00 0.00 0.00 5.54
2459 2518 9.388506 CTTAGACCAAACAGATCATGAGTTATT 57.611 33.333 0.09 0.00 0.00 1.40
2460 2519 8.762645 TCTTAGACCAAACAGATCATGAGTTAT 58.237 33.333 0.09 0.00 0.00 1.89
2461 2520 8.134202 TCTTAGACCAAACAGATCATGAGTTA 57.866 34.615 0.09 0.00 0.00 2.24
2462 2521 7.009179 TCTTAGACCAAACAGATCATGAGTT 57.991 36.000 0.09 0.00 0.00 3.01
2463 2522 6.611613 TCTTAGACCAAACAGATCATGAGT 57.388 37.500 0.09 0.00 0.00 3.41
2468 2527 8.687242 CACTAGTATCTTAGACCAAACAGATCA 58.313 37.037 0.00 0.00 0.00 2.92
2572 3419 4.138290 TGTAAATTTGCCTCTTCCGAACA 58.862 39.130 0.00 0.00 0.00 3.18
2573 3420 4.759516 TGTAAATTTGCCTCTTCCGAAC 57.240 40.909 0.00 0.00 0.00 3.95
2575 3422 5.508320 GGTTTTGTAAATTTGCCTCTTCCGA 60.508 40.000 0.00 0.00 0.00 4.55
2606 3453 4.228912 AGAAAATTCCAAGTTGCGTCAG 57.771 40.909 0.00 0.00 0.00 3.51
2610 3457 5.801947 CCTTCATAGAAAATTCCAAGTTGCG 59.198 40.000 0.00 0.00 0.00 4.85
2729 4008 4.509970 CACTGTATCGGCGATTAATCCAAA 59.490 41.667 28.93 3.90 0.00 3.28
2733 4012 5.432157 CAAACACTGTATCGGCGATTAATC 58.568 41.667 28.93 15.69 0.00 1.75
2734 4013 4.272504 CCAAACACTGTATCGGCGATTAAT 59.727 41.667 28.93 6.86 0.00 1.40
2735 4014 3.619483 CCAAACACTGTATCGGCGATTAA 59.381 43.478 28.93 15.23 0.00 1.40
2736 4015 3.191669 CCAAACACTGTATCGGCGATTA 58.808 45.455 28.93 16.15 0.00 1.75
2737 4016 2.006888 CCAAACACTGTATCGGCGATT 58.993 47.619 28.93 12.14 0.00 3.34
2738 4017 1.651987 CCAAACACTGTATCGGCGAT 58.348 50.000 26.95 26.95 0.00 4.58
2739 4018 1.017177 GCCAAACACTGTATCGGCGA 61.017 55.000 13.87 13.87 0.00 5.54
2740 4019 1.019278 AGCCAAACACTGTATCGGCG 61.019 55.000 0.00 0.00 44.34 6.46
2741 4020 1.165270 AAGCCAAACACTGTATCGGC 58.835 50.000 7.91 7.91 39.90 5.54
2742 4021 3.564511 CAAAAGCCAAACACTGTATCGG 58.435 45.455 0.00 0.00 0.00 4.18
2743 4022 2.979813 GCAAAAGCCAAACACTGTATCG 59.020 45.455 0.00 0.00 0.00 2.92
2744 4023 3.983344 CAGCAAAAGCCAAACACTGTATC 59.017 43.478 0.00 0.00 0.00 2.24
2745 4024 3.636300 TCAGCAAAAGCCAAACACTGTAT 59.364 39.130 0.00 0.00 0.00 2.29
2746 4025 3.020274 TCAGCAAAAGCCAAACACTGTA 58.980 40.909 0.00 0.00 0.00 2.74
2747 4026 1.824230 TCAGCAAAAGCCAAACACTGT 59.176 42.857 0.00 0.00 0.00 3.55
2748 4027 2.195922 GTCAGCAAAAGCCAAACACTG 58.804 47.619 0.00 0.00 0.00 3.66
2749 4028 1.824230 TGTCAGCAAAAGCCAAACACT 59.176 42.857 0.00 0.00 0.00 3.55
2750 4029 2.292103 TGTCAGCAAAAGCCAAACAC 57.708 45.000 0.00 0.00 0.00 3.32
2751 4030 3.196463 CAATGTCAGCAAAAGCCAAACA 58.804 40.909 0.00 0.00 0.00 2.83
2752 4031 3.197265 ACAATGTCAGCAAAAGCCAAAC 58.803 40.909 0.00 0.00 0.00 2.93
2753 4032 3.540314 ACAATGTCAGCAAAAGCCAAA 57.460 38.095 0.00 0.00 0.00 3.28
2754 4033 3.196463 CAACAATGTCAGCAAAAGCCAA 58.804 40.909 0.00 0.00 0.00 4.52
2755 4034 2.823984 CAACAATGTCAGCAAAAGCCA 58.176 42.857 0.00 0.00 0.00 4.75
2756 4035 1.528161 GCAACAATGTCAGCAAAAGCC 59.472 47.619 6.00 0.00 0.00 4.35
2757 4036 2.203401 TGCAACAATGTCAGCAAAAGC 58.797 42.857 10.35 0.00 33.48 3.51
2758 4037 6.366604 TGATAATGCAACAATGTCAGCAAAAG 59.633 34.615 15.46 0.00 40.76 2.27
2759 4038 6.221659 TGATAATGCAACAATGTCAGCAAAA 58.778 32.000 15.46 8.55 40.76 2.44
2760 4039 5.780984 TGATAATGCAACAATGTCAGCAAA 58.219 33.333 15.46 8.84 40.76 3.68
2761 4040 5.388408 TGATAATGCAACAATGTCAGCAA 57.612 34.783 15.46 3.30 40.76 3.91
2762 4041 5.125739 TCATGATAATGCAACAATGTCAGCA 59.874 36.000 14.20 14.20 41.73 4.41
2763 4042 5.584442 TCATGATAATGCAACAATGTCAGC 58.416 37.500 0.00 4.17 0.00 4.26
2764 4043 7.704899 ACATTCATGATAATGCAACAATGTCAG 59.295 33.333 7.21 0.00 39.93 3.51
2826 4105 9.787435 CCTATCTGAGTAGTGAGTAGAATAAGT 57.213 37.037 0.00 0.00 0.00 2.24
2899 4179 9.472361 GCAAAGTGAATCATATTGCAAATAGAT 57.528 29.630 22.38 4.09 44.29 1.98
2943 4223 4.503741 AAGATGCGTGCAAATAAACACT 57.496 36.364 0.00 0.00 34.58 3.55
2970 4250 1.334689 GCCAGCTGTTTTCACGTTACC 60.335 52.381 13.81 0.00 0.00 2.85
2977 4257 1.243342 CGATGGGCCAGCTGTTTTCA 61.243 55.000 20.97 5.89 0.00 2.69
3012 4292 2.295349 GCCACTGCCCATATGATTTCAG 59.705 50.000 3.65 7.89 0.00 3.02
3116 4396 1.761784 AGGGATTCTGAGCAGTAGCAG 59.238 52.381 0.00 0.00 45.49 4.24
3117 4397 1.483827 CAGGGATTCTGAGCAGTAGCA 59.516 52.381 0.00 0.00 46.18 3.49
3118 4398 1.809651 GCAGGGATTCTGAGCAGTAGC 60.810 57.143 0.00 0.00 46.18 3.58
3119 4399 1.483827 TGCAGGGATTCTGAGCAGTAG 59.516 52.381 0.00 0.00 46.18 2.57
3120 4400 1.571955 TGCAGGGATTCTGAGCAGTA 58.428 50.000 0.00 0.00 46.18 2.74
3121 4401 0.694771 TTGCAGGGATTCTGAGCAGT 59.305 50.000 0.00 0.00 46.18 4.40
3122 4402 1.093159 GTTGCAGGGATTCTGAGCAG 58.907 55.000 0.00 0.00 46.18 4.24
3123 4403 0.401356 TGTTGCAGGGATTCTGAGCA 59.599 50.000 0.00 0.00 46.18 4.26
3124 4404 1.538047 TTGTTGCAGGGATTCTGAGC 58.462 50.000 0.00 0.00 46.18 4.26
3125 4405 4.796038 ATTTTGTTGCAGGGATTCTGAG 57.204 40.909 0.00 0.00 46.18 3.35
3126 4406 4.588106 TCAATTTTGTTGCAGGGATTCTGA 59.412 37.500 0.00 0.00 46.18 3.27
3127 4407 4.885413 TCAATTTTGTTGCAGGGATTCTG 58.115 39.130 0.00 0.00 46.03 3.02
3128 4408 5.750352 ATCAATTTTGTTGCAGGGATTCT 57.250 34.783 0.00 0.00 0.00 2.40
3129 4409 6.633856 AGTATCAATTTTGTTGCAGGGATTC 58.366 36.000 0.00 0.00 0.00 2.52
3130 4410 6.610075 AGTATCAATTTTGTTGCAGGGATT 57.390 33.333 0.00 0.00 0.00 3.01
3146 4426 8.585881 GGAATGTATAGGCTCAGTAAGTATCAA 58.414 37.037 0.00 0.00 0.00 2.57
3346 4626 5.587443 TGCACAGATCTGAATAAGATTGTGG 59.413 40.000 29.27 0.00 46.12 4.17
3354 4634 5.121105 CAGTGGATGCACAGATCTGAATAA 58.879 41.667 29.27 11.56 0.00 1.40
3356 4636 3.054582 ACAGTGGATGCACAGATCTGAAT 60.055 43.478 29.27 17.87 0.00 2.57
3446 4726 0.192566 ACAAGTACACTCCTCCCCCA 59.807 55.000 0.00 0.00 0.00 4.96
3449 4729 2.028930 CACTCACAAGTACACTCCTCCC 60.029 54.545 0.00 0.00 33.25 4.30
3483 4764 2.996168 ATTCATACCGGAGCGCTGGC 62.996 60.000 18.48 0.00 44.98 4.85
3600 4925 3.995636 AGAGCCCAGACCTACTATTTCA 58.004 45.455 0.00 0.00 0.00 2.69
3694 5019 6.448006 CCGGAGAGAAAATTGATACTACGAT 58.552 40.000 0.00 0.00 34.22 3.73
3695 5020 5.735354 GCCGGAGAGAAAATTGATACTACGA 60.735 44.000 5.05 0.00 34.22 3.43
3696 5021 4.444720 GCCGGAGAGAAAATTGATACTACG 59.555 45.833 5.05 0.00 0.00 3.51
3699 5024 4.762289 AGCCGGAGAGAAAATTGATACT 57.238 40.909 5.05 0.00 0.00 2.12
3717 5042 2.825532 TGGATGCAAAGTTTCCTAAGCC 59.174 45.455 4.96 0.00 0.00 4.35
3731 5056 1.195442 TCGTGTAACCCCTGGATGCA 61.195 55.000 0.00 0.00 0.00 3.96
3732 5057 0.743345 GTCGTGTAACCCCTGGATGC 60.743 60.000 0.00 0.00 0.00 3.91
3733 5058 0.611200 TGTCGTGTAACCCCTGGATG 59.389 55.000 0.00 0.00 0.00 3.51
3734 5059 1.580059 ATGTCGTGTAACCCCTGGAT 58.420 50.000 0.00 0.00 0.00 3.41
3735 5060 1.002659 CAATGTCGTGTAACCCCTGGA 59.997 52.381 0.00 0.00 0.00 3.86
3782 5107 0.890683 CAATGTGAGTTTCCAGGGCC 59.109 55.000 0.00 0.00 0.00 5.80
3842 5175 4.096833 GCTTCCATGTCATACAGATTTGCA 59.903 41.667 0.00 0.00 0.00 4.08
3970 5343 6.879400 TCTTTCTTCTTAGCTTAAGGGCTAG 58.121 40.000 4.29 0.00 44.23 3.42
4008 5381 6.096282 GGACCCAGTTATTGCTTGCTTTAATA 59.904 38.462 0.00 0.00 0.00 0.98
4067 5440 4.555262 GAGGTTTTCAATCATTTTCGCCA 58.445 39.130 0.00 0.00 0.00 5.69
4168 5541 1.462283 CGTTCGGTACTCTTCTCGACA 59.538 52.381 0.00 0.00 0.00 4.35
4171 5544 2.888513 TTCGTTCGGTACTCTTCTCG 57.111 50.000 0.00 0.00 0.00 4.04
4227 5600 7.956328 ATTAAGAAGTACAAAAAGGGGATCC 57.044 36.000 1.92 1.92 0.00 3.36


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

AutoCloner maintained by Alex Coulton.