Multiple sequence alignment - TraesCS3B01G437400

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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 TraesCS3B01G437400 chr3B 100.000 6063 0 0 1 6063 676276774 676270712 0.000000e+00 11197.0
1 TraesCS3B01G437400 chr3D 93.066 5408 201 70 629 5917 513953571 513948219 0.000000e+00 7749.0
2 TraesCS3B01G437400 chr3D 87.821 624 66 7 1 617 513954176 513953556 0.000000e+00 723.0
3 TraesCS3B01G437400 chr3D 97.500 40 1 0 5760 5799 513948337 513948298 1.090000e-07 69.4
4 TraesCS3B01G437400 chr3A 94.782 2319 88 13 2830 5131 648870447 648868145 0.000000e+00 3581.0
5 TraesCS3B01G437400 chr3A 90.771 1972 96 33 638 2561 648872702 648870769 0.000000e+00 2555.0
6 TraesCS3B01G437400 chr3A 85.667 900 48 34 5085 5931 648868150 648867279 0.000000e+00 872.0
7 TraesCS3B01G437400 chr3A 82.835 635 88 13 1 617 648874410 648873779 3.190000e-152 549.0
8 TraesCS3B01G437400 chr3A 96.694 242 5 2 2591 2831 648870768 648870529 3.400000e-107 399.0
9 TraesCS3B01G437400 chr3A 80.897 513 84 8 109 609 648873511 648873001 5.700000e-105 392.0
10 TraesCS3B01G437400 chr3A 95.918 49 2 0 5760 5808 648867407 648867359 5.040000e-11 80.5
11 TraesCS3B01G437400 chr6B 89.157 83 9 0 2446 2528 10313869 10313787 2.990000e-18 104.0
12 TraesCS3B01G437400 chr1D 92.000 75 5 1 4325 4398 356154912 356154838 2.990000e-18 104.0
13 TraesCS3B01G437400 chr1A 92.000 75 5 1 4325 4398 456941372 456941298 2.990000e-18 104.0
14 TraesCS3B01G437400 chr1A 91.837 49 3 1 2445 2492 45840206 45840254 3.920000e-07 67.6
15 TraesCS3B01G437400 chr5A 92.453 53 4 0 2445 2497 505496758 505496810 6.520000e-10 76.8
16 TraesCS3B01G437400 chr2D 86.154 65 5 4 2477 2539 291859396 291859334 3.920000e-07 67.6
17 TraesCS3B01G437400 chr6D 89.130 46 5 0 2495 2540 150786062 150786017 2.360000e-04 58.4
18 TraesCS3B01G437400 chr6D 88.889 45 5 0 2445 2489 157659514 157659470 8.490000e-04 56.5
19 TraesCS3B01G437400 chr7B 100.000 28 0 0 2442 2469 693954271 693954298 1.100000e-02 52.8
20 TraesCS3B01G437400 chr7A 100.000 28 0 0 2445 2472 716231985 716231958 1.100000e-02 52.8
21 TraesCS3B01G437400 chr4A 100.000 28 0 0 2441 2468 546196560 546196587 1.100000e-02 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 TraesCS3B01G437400 chr3B 676270712 676276774 6062 True 11197.000000 11197 100.000 1 6063 1 chr3B.!!$R1 6062
1 TraesCS3B01G437400 chr3D 513948219 513953571 5352 True 7749.000000 7749 93.066 629 5917 1 chr3D.!!$R1 5288
2 TraesCS3B01G437400 chr3D 513953556 513954176 620 True 723.000000 723 87.821 1 617 1 chr3D.!!$R3 616
3 TraesCS3B01G437400 chr3A 648867279 648874410 7131 True 1204.071429 3581 89.652 1 5931 7 chr3A.!!$R1 5930

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
856 1955 1.027357 CTCCATCTTGGCATTTCCGG 58.973 55.0 0.00 0.0 37.47 5.14 F
1224 2337 0.108992 GGAAGTACGTGGTCGATGCA 60.109 55.0 0.00 0.0 40.62 3.96 F
2339 3491 0.396435 CCCGGGTGCTATTGCTATCA 59.604 55.0 14.18 0.0 40.48 2.15 F
2713 3866 1.059098 TGTGATTGTGGTCCTGCTCT 58.941 50.0 0.00 0.0 0.00 4.09 F
4280 5529 0.033504 TCTGACTGTGGTCCTTTCGC 59.966 55.0 0.00 0.0 41.47 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 3197 2.009774 CCTGCAGCCATAGTGTGTAAC 58.990 52.381 8.66 0.00 37.35 2.50 R
3146 4380 1.215647 GGTGCGAGTTGAGGTCGAT 59.784 57.895 0.00 0.00 39.92 3.59 R
3611 4851 0.106708 GCACAACAGACCTCACCTGA 59.893 55.000 0.00 0.00 35.69 3.86 R
4537 5788 0.038801 GCTTTGCTTGGTCCTTGAGC 60.039 55.000 5.76 5.76 36.95 4.26 R
5992 7414 0.036105 GGGGTGTATTTCGACCGGTT 60.036 55.000 9.42 0.00 32.48 4.44 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
41 42 2.045926 GACCCTCTTGGCGTGCAT 60.046 61.111 0.00 0.00 37.83 3.96
42 43 1.675641 GACCCTCTTGGCGTGCATT 60.676 57.895 0.00 0.00 37.83 3.56
64 67 3.300388 TGCTCATCTCTCCCTCGTAAAT 58.700 45.455 0.00 0.00 0.00 1.40
128 131 4.799949 TGCGTGTATTATCGTGTTAACTCC 59.200 41.667 7.22 0.00 0.00 3.85
132 135 6.634436 CGTGTATTATCGTGTTAACTCCCTAC 59.366 42.308 7.22 0.00 0.00 3.18
134 137 2.573941 ATCGTGTTAACTCCCTACGC 57.426 50.000 7.22 0.00 34.98 4.42
259 262 1.450312 CACCATCCCGAGGAGCAAC 60.450 63.158 0.00 0.00 34.05 4.17
291 294 5.407387 TGTAAAGATAGTGGCGTTTCAACTC 59.593 40.000 0.00 0.00 0.00 3.01
294 297 2.922740 TAGTGGCGTTTCAACTCCTT 57.077 45.000 0.61 0.00 34.89 3.36
313 318 2.588027 TGTGTCTGTAGCGTTCACAA 57.412 45.000 0.00 0.00 36.34 3.33
315 320 2.799978 TGTGTCTGTAGCGTTCACAATG 59.200 45.455 0.00 0.00 36.34 2.82
327 338 3.241773 CGTTCACAATGTCGCACTAGATG 60.242 47.826 0.00 0.00 0.00 2.90
382 394 8.732531 TCTTTATAAACTTTCAATAACCACCGG 58.267 33.333 0.00 0.00 0.00 5.28
403 415 2.006888 CGCGTGGATTCCAGTAACAAT 58.993 47.619 5.39 0.00 32.34 2.71
409 421 5.123936 GTGGATTCCAGTAACAATCTACCC 58.876 45.833 5.39 0.00 35.51 3.69
410 422 4.785914 TGGATTCCAGTAACAATCTACCCA 59.214 41.667 0.00 0.00 30.85 4.51
414 426 3.262405 TCCAGTAACAATCTACCCACCAC 59.738 47.826 0.00 0.00 0.00 4.16
417 429 4.454504 CAGTAACAATCTACCCACCACAAC 59.545 45.833 0.00 0.00 0.00 3.32
425 437 5.353394 TCTACCCACCACAACTATTCATC 57.647 43.478 0.00 0.00 0.00 2.92
438 450 2.532531 ATTCATCGCGTGCAAGAAAG 57.467 45.000 5.77 0.00 0.00 2.62
441 453 2.409012 TCATCGCGTGCAAGAAAGTAA 58.591 42.857 5.77 0.00 0.00 2.24
450 462 5.275741 GCGTGCAAGAAAGTAAGTTTTCAAC 60.276 40.000 2.99 0.00 39.08 3.18
454 466 4.205323 AGAAAGTAAGTTTTCAACCGCG 57.795 40.909 0.00 0.00 39.08 6.46
460 472 3.757745 AAGTTTTCAACCGCGGATATG 57.242 42.857 35.90 25.84 0.00 1.78
462 474 2.676342 AGTTTTCAACCGCGGATATGTC 59.324 45.455 35.90 15.65 0.00 3.06
506 519 1.295357 CGCAACTGGATAACCACGCA 61.295 55.000 0.00 0.00 41.77 5.24
539 553 4.108501 ACCATCTTTCCCCGTAAACTTT 57.891 40.909 0.00 0.00 0.00 2.66
546 560 8.466798 CATCTTTCCCCGTAAACTTTCAATAAT 58.533 33.333 0.00 0.00 0.00 1.28
554 568 7.201574 CCCGTAAACTTTCAATAATCATCGACA 60.202 37.037 0.00 0.00 0.00 4.35
563 577 6.290605 TCAATAATCATCGACATGTGGATGT 58.709 36.000 35.29 25.44 46.01 3.06
612 626 4.515191 AGTCATTGCGTGTAAGACAATTGT 59.485 37.500 11.78 11.78 31.82 2.71
856 1955 1.027357 CTCCATCTTGGCATTTCCGG 58.973 55.000 0.00 0.00 37.47 5.14
1027 2137 4.856801 CGGTGGGGATCAAGCGGG 62.857 72.222 0.00 0.00 33.85 6.13
1197 2310 2.443016 CTCGAGGAGGTGGAGGGG 60.443 72.222 3.91 0.00 0.00 4.79
1218 2331 1.735559 GCGGTGGAAGTACGTGGTC 60.736 63.158 0.00 0.00 0.00 4.02
1224 2337 0.108992 GGAAGTACGTGGTCGATGCA 60.109 55.000 0.00 0.00 40.62 3.96
1338 2457 2.668550 GCCGAGGTGAGCCGTTTT 60.669 61.111 0.00 0.00 40.50 2.43
1344 2463 2.561037 GGTGAGCCGTTTTGGTGGG 61.561 63.158 0.00 0.00 41.21 4.61
1422 2541 0.901580 TCCTCCGCGTTAGGTTTCCT 60.902 55.000 20.46 0.00 37.71 3.36
1437 2556 2.969262 GTTTCCTGTTTGATTTGGGGGA 59.031 45.455 0.00 0.00 0.00 4.81
1468 2588 2.336667 GATTTTGGGCGATTTGGTGTG 58.663 47.619 0.00 0.00 0.00 3.82
1557 2677 1.474330 TCTCAGGATGCACGCTCTAA 58.526 50.000 0.00 0.00 34.76 2.10
1561 2681 2.432146 TCAGGATGCACGCTCTAATTCT 59.568 45.455 0.00 0.00 34.76 2.40
1653 2774 1.611977 TGTGTCGTACTTCCAGGACTG 59.388 52.381 0.00 0.00 35.01 3.51
1717 2842 4.506838 TTGTTTTCGCCGTCAATTTTTG 57.493 36.364 0.00 0.00 0.00 2.44
1737 2862 4.628963 TGGTTGGGACTAAGGTAGTTTC 57.371 45.455 0.00 0.00 39.59 2.78
1784 2909 5.804639 ACTACACATGCCAGATTAAGTTGA 58.195 37.500 0.00 0.00 0.00 3.18
1892 3018 7.976414 TTGGGATTAATGGAATTCATTCTGT 57.024 32.000 7.93 0.00 44.32 3.41
1905 3031 7.750903 GGAATTCATTCTGTAGTTAAGTTGTGC 59.249 37.037 7.93 0.00 37.00 4.57
1968 3099 7.445402 ACTGTTATGTGAAGATTAAAGTGCTGT 59.555 33.333 0.00 0.00 0.00 4.40
1982 3113 1.599542 GTGCTGTGTGGAGAGTTGAAC 59.400 52.381 0.00 0.00 0.00 3.18
2049 3197 7.414436 CCATACAGGTTTGATAAATAACACCG 58.586 38.462 0.00 0.00 0.00 4.94
2208 3360 4.453478 TGTTCAGCACTGTCTTGATTCATC 59.547 41.667 0.00 0.00 0.00 2.92
2329 3481 2.530916 AAGGTTACCCCGGGTGCT 60.531 61.111 21.85 3.47 36.19 4.40
2339 3491 0.396435 CCCGGGTGCTATTGCTATCA 59.604 55.000 14.18 0.00 40.48 2.15
2451 3603 9.358872 GACAAATCAAAAATTTATCACTCCCTC 57.641 33.333 0.00 0.00 0.00 4.30
2470 3622 5.546110 TCCCTCCGATCCATATTAATTGACA 59.454 40.000 0.00 0.00 0.00 3.58
2474 3626 5.995282 TCCGATCCATATTAATTGACACACC 59.005 40.000 0.00 0.00 0.00 4.16
2485 3637 8.927675 ATTAATTGACACACCCTTAGTACAAA 57.072 30.769 0.00 0.00 0.00 2.83
2513 3665 7.156000 TGTACTAAAGTTGTACTAAGCATGCA 58.844 34.615 21.98 0.00 40.44 3.96
2530 3682 6.646267 AGCATGCATCAATTAATTTTGACCT 58.354 32.000 21.98 0.00 38.37 3.85
2589 3741 7.411486 TGAACCTGAAGTCTTATCCTTCTAG 57.589 40.000 0.00 0.00 39.24 2.43
2713 3866 1.059098 TGTGATTGTGGTCCTGCTCT 58.941 50.000 0.00 0.00 0.00 4.09
3031 4265 4.131088 GGTCTGTCCTCGCCGGTC 62.131 72.222 1.90 0.00 0.00 4.79
3043 4277 1.281656 GCCGGTCGTTCAAAGTTGG 59.718 57.895 1.90 0.00 0.00 3.77
3146 4380 2.455674 AGAATGTCGCTGCTGTTACA 57.544 45.000 0.00 0.00 0.00 2.41
3209 4443 7.716998 GCAAGAGGAGAAAATATTGGAGATGTA 59.283 37.037 0.00 0.00 0.00 2.29
3227 4461 2.500098 TGTAACTGCTAAGGGCGAATCT 59.500 45.455 0.00 0.00 45.43 2.40
3253 4487 3.378427 GGGAACATTGCAGATCTGGTAAC 59.622 47.826 23.89 7.91 0.00 2.50
3299 4533 1.270971 GCGCAAGTGGCACATTAATG 58.729 50.000 21.41 14.01 44.52 1.90
3329 4563 4.022849 GCAACTGAGTTGGCTGATTTACTT 60.023 41.667 25.00 0.00 42.99 2.24
3335 4569 5.355071 TGAGTTGGCTGATTTACTTGCATAG 59.645 40.000 0.00 0.00 0.00 2.23
3338 4572 5.565592 TGGCTGATTTACTTGCATAGTTG 57.434 39.130 6.82 0.00 38.33 3.16
3342 4576 6.433766 GCTGATTTACTTGCATAGTTGGATC 58.566 40.000 6.82 8.42 38.33 3.36
3544 4784 5.674525 TGAGTTCATATCATGAGGTTCACC 58.325 41.667 0.09 0.00 40.94 4.02
3573 4813 5.842907 ACTTTATTTCTTGGGTCTTGTTGC 58.157 37.500 0.00 0.00 0.00 4.17
3909 5149 7.542025 AGGCATAGCAAAGTAAGAATTCAAAG 58.458 34.615 8.44 0.00 0.00 2.77
3973 5221 4.853924 ACCATGGTGAAAACATGAACTC 57.146 40.909 18.99 0.00 46.60 3.01
3983 5231 5.883115 TGAAAACATGAACTCTTGGTGTGTA 59.117 36.000 0.00 0.00 0.00 2.90
4006 5254 2.164219 CAGCACAATGGGTTGGACATAC 59.836 50.000 0.00 0.00 39.70 2.39
4072 5320 7.051000 GCCATATGGAACTTTTAGAGTCTCTT 58.949 38.462 26.47 0.00 34.65 2.85
4280 5529 0.033504 TCTGACTGTGGTCCTTTCGC 59.966 55.000 0.00 0.00 41.47 4.70
4372 5621 2.693074 AGAACCCGTTTCATTTGTTGCT 59.307 40.909 0.00 0.00 36.57 3.91
4403 5652 1.004277 TGTTTGAGGTACATCCCCAGC 59.996 52.381 4.87 0.00 36.75 4.85
4534 5785 7.122715 ACCCAACAAAGGATAAAGTATATGCA 58.877 34.615 0.00 0.00 0.00 3.96
4537 5788 9.467258 CCAACAAAGGATAAAGTATATGCATTG 57.533 33.333 3.54 0.00 32.73 2.82
4756 6007 5.079643 TCCAATCGATCAGATCACTATGGA 58.920 41.667 15.35 15.35 38.34 3.41
4828 6079 6.127535 CCTGCAAAATTGTGTCATCCTCTTAT 60.128 38.462 0.00 0.00 0.00 1.73
4956 6208 1.438651 CGCTTGATTGAAACCCTCGA 58.561 50.000 0.00 0.00 0.00 4.04
4981 6233 6.976934 ACATGACTAACCACATTCCTTTTT 57.023 33.333 0.00 0.00 0.00 1.94
4989 6241 4.779696 ACCACATTCCTTTTTGTTGCATT 58.220 34.783 0.00 0.00 0.00 3.56
4996 6248 2.549329 CCTTTTTGTTGCATTTCAGGGC 59.451 45.455 0.00 0.00 0.00 5.19
5008 6260 4.209538 CATTTCAGGGCTGGATAATGTCA 58.790 43.478 0.00 0.00 0.00 3.58
5200 6493 3.400054 GAGCCCGGCCTAGGTGTT 61.400 66.667 11.31 0.00 0.00 3.32
5215 6508 2.696506 GGTGTTAACCAGTGAGCCTAC 58.303 52.381 2.48 0.00 46.75 3.18
5234 6528 0.462047 CCATCTCGTGCAACCCCTAC 60.462 60.000 0.00 0.00 0.00 3.18
5235 6529 0.537188 CATCTCGTGCAACCCCTACT 59.463 55.000 0.00 0.00 0.00 2.57
5291 6586 4.021368 ACACCAAGAAGCTGTAAGTCGTAT 60.021 41.667 0.00 0.00 35.30 3.06
5325 6620 5.074115 CCCCTTGACTTGTATTTACACCAA 58.926 41.667 0.00 0.00 35.64 3.67
5336 6631 7.938563 TGTATTTACACCAAAAATCTGTTGC 57.061 32.000 0.00 0.00 0.00 4.17
5339 6634 5.843673 TTACACCAAAAATCTGTTGCTGA 57.156 34.783 0.00 0.00 0.00 4.26
5381 6703 2.105128 GTCAGGTATGCTCGCGCT 59.895 61.111 5.56 0.00 36.97 5.92
5397 6719 0.175302 CGCTGAGCCATGAGAAGACT 59.825 55.000 0.00 0.00 0.00 3.24
5439 6761 2.032620 ACTGCATAGGAGTAGGTTCCG 58.967 52.381 0.00 0.00 42.29 4.30
5517 6841 4.120589 GCTAACTGTATGTAGCCTGTTCC 58.879 47.826 0.00 0.00 0.00 3.62
5531 6855 0.828022 TGTTCCTGAGTGGTGTTCGT 59.172 50.000 0.00 0.00 37.07 3.85
5532 6856 1.202486 TGTTCCTGAGTGGTGTTCGTC 60.202 52.381 0.00 0.00 37.07 4.20
5533 6857 0.031585 TTCCTGAGTGGTGTTCGTCG 59.968 55.000 0.00 0.00 37.07 5.12
5534 6858 1.372997 CCTGAGTGGTGTTCGTCGG 60.373 63.158 0.00 0.00 0.00 4.79
5535 6859 2.022129 CTGAGTGGTGTTCGTCGGC 61.022 63.158 0.00 0.00 0.00 5.54
5536 6860 2.338984 GAGTGGTGTTCGTCGGCT 59.661 61.111 0.00 0.00 0.00 5.52
5537 6861 2.022129 GAGTGGTGTTCGTCGGCTG 61.022 63.158 0.00 0.00 0.00 4.85
5538 6862 3.712881 GTGGTGTTCGTCGGCTGC 61.713 66.667 0.00 0.00 0.00 5.25
5542 6866 4.717629 TGTTCGTCGGCTGCGGAG 62.718 66.667 10.36 0.00 0.00 4.63
5543 6867 4.719369 GTTCGTCGGCTGCGGAGT 62.719 66.667 10.36 0.00 0.00 3.85
5544 6868 4.415332 TTCGTCGGCTGCGGAGTC 62.415 66.667 10.36 0.75 0.00 3.36
5649 7008 5.220397 GCTTGTTGTAAGTTGCAGTTTTTCC 60.220 40.000 0.00 0.00 0.00 3.13
5651 7010 3.701532 TGTAAGTTGCAGTTTTTCCGG 57.298 42.857 0.00 0.00 0.00 5.14
5652 7011 2.359531 TGTAAGTTGCAGTTTTTCCGGG 59.640 45.455 0.00 0.00 0.00 5.73
5749 7111 9.729023 CTGTTGAGTTAAATTTTGTGTGATGTA 57.271 29.630 0.00 0.00 0.00 2.29
5750 7112 9.729023 TGTTGAGTTAAATTTTGTGTGATGTAG 57.271 29.630 0.00 0.00 0.00 2.74
5751 7113 9.730420 GTTGAGTTAAATTTTGTGTGATGTAGT 57.270 29.630 0.00 0.00 0.00 2.73
5790 7206 4.773323 AAAGCATTTTCTGGTACTCTGC 57.227 40.909 0.00 0.00 31.62 4.26
5791 7207 3.710209 AGCATTTTCTGGTACTCTGCT 57.290 42.857 0.00 0.00 32.64 4.24
5792 7208 3.341823 AGCATTTTCTGGTACTCTGCTG 58.658 45.455 0.00 0.00 37.13 4.41
5793 7209 2.159462 GCATTTTCTGGTACTCTGCTGC 60.159 50.000 0.00 0.00 0.00 5.25
5794 7210 2.928801 TTTTCTGGTACTCTGCTGCA 57.071 45.000 0.88 0.88 0.00 4.41
5795 7211 3.423539 TTTTCTGGTACTCTGCTGCAT 57.576 42.857 1.31 0.00 0.00 3.96
5796 7212 2.680312 TTCTGGTACTCTGCTGCATC 57.320 50.000 1.31 0.00 0.00 3.91
5797 7213 1.857965 TCTGGTACTCTGCTGCATCT 58.142 50.000 1.31 0.00 0.00 2.90
5798 7214 1.479730 TCTGGTACTCTGCTGCATCTG 59.520 52.381 1.31 0.00 0.00 2.90
5799 7215 0.538584 TGGTACTCTGCTGCATCTGG 59.461 55.000 1.31 0.00 0.00 3.86
5800 7216 0.179062 GGTACTCTGCTGCATCTGGG 60.179 60.000 1.31 0.00 0.00 4.45
5801 7217 0.539051 GTACTCTGCTGCATCTGGGT 59.461 55.000 1.31 5.27 0.00 4.51
5802 7218 1.065854 GTACTCTGCTGCATCTGGGTT 60.066 52.381 5.23 0.00 0.00 4.11
5803 7219 1.279496 ACTCTGCTGCATCTGGGTTA 58.721 50.000 1.31 0.00 0.00 2.85
5804 7220 1.209019 ACTCTGCTGCATCTGGGTTAG 59.791 52.381 1.31 0.00 0.00 2.34
5805 7221 1.209019 CTCTGCTGCATCTGGGTTAGT 59.791 52.381 1.31 0.00 0.00 2.24
5806 7222 2.432146 CTCTGCTGCATCTGGGTTAGTA 59.568 50.000 1.31 0.00 0.00 1.82
5807 7223 2.168521 TCTGCTGCATCTGGGTTAGTAC 59.831 50.000 1.31 0.00 0.00 2.73
5808 7224 1.905894 TGCTGCATCTGGGTTAGTACA 59.094 47.619 0.00 0.00 0.00 2.90
5809 7225 2.304470 TGCTGCATCTGGGTTAGTACAA 59.696 45.455 0.00 0.00 0.00 2.41
5810 7226 2.678336 GCTGCATCTGGGTTAGTACAAC 59.322 50.000 0.00 0.00 0.00 3.32
5811 7227 3.868369 GCTGCATCTGGGTTAGTACAACA 60.868 47.826 0.00 0.00 0.00 3.33
5812 7228 3.935203 CTGCATCTGGGTTAGTACAACAG 59.065 47.826 0.00 0.00 34.18 3.16
5813 7229 2.678336 GCATCTGGGTTAGTACAACAGC 59.322 50.000 0.00 0.00 33.41 4.40
5814 7230 3.868369 GCATCTGGGTTAGTACAACAGCA 60.868 47.826 0.00 0.00 33.41 4.41
5815 7231 4.517285 CATCTGGGTTAGTACAACAGCAT 58.483 43.478 0.00 0.00 33.41 3.79
5816 7232 4.634012 TCTGGGTTAGTACAACAGCATT 57.366 40.909 0.00 0.00 33.41 3.56
5817 7233 4.980573 TCTGGGTTAGTACAACAGCATTT 58.019 39.130 0.00 0.00 33.41 2.32
5818 7234 5.381757 TCTGGGTTAGTACAACAGCATTTT 58.618 37.500 0.00 0.00 33.41 1.82
5819 7235 5.472137 TCTGGGTTAGTACAACAGCATTTTC 59.528 40.000 0.00 0.00 33.41 2.29
5820 7236 4.521256 TGGGTTAGTACAACAGCATTTTCC 59.479 41.667 0.00 0.00 0.00 3.13
5874 7296 2.677979 GGGGCGAAACGAGCTGTTC 61.678 63.158 0.00 0.00 40.84 3.18
5885 7307 0.234884 GAGCTGTTCCGTTCCGTTTG 59.765 55.000 0.00 0.00 0.00 2.93
5911 7333 4.397730 GCTGGATCCTTTTCTTCTTCTTCC 59.602 45.833 14.23 0.00 0.00 3.46
5918 7340 7.713734 TCCTTTTCTTCTTCTTCCGAGTATA 57.286 36.000 0.00 0.00 0.00 1.47
5919 7341 8.307582 TCCTTTTCTTCTTCTTCCGAGTATAT 57.692 34.615 0.00 0.00 0.00 0.86
5920 7342 8.759782 TCCTTTTCTTCTTCTTCCGAGTATATT 58.240 33.333 0.00 0.00 0.00 1.28
5952 7374 9.981114 AATAGAAAAGTTAACATTTCAACCCTG 57.019 29.630 28.37 0.00 36.38 4.45
5953 7375 7.654022 AGAAAAGTTAACATTTCAACCCTGA 57.346 32.000 28.37 0.00 36.38 3.86
5954 7376 8.073467 AGAAAAGTTAACATTTCAACCCTGAA 57.927 30.769 28.37 0.00 39.87 3.02
5955 7377 7.979537 AGAAAAGTTAACATTTCAACCCTGAAC 59.020 33.333 28.37 7.37 41.34 3.18
5956 7378 7.418337 AAAGTTAACATTTCAACCCTGAACT 57.582 32.000 8.61 0.00 41.34 3.01
5957 7379 8.528044 AAAGTTAACATTTCAACCCTGAACTA 57.472 30.769 8.61 0.00 41.34 2.24
5958 7380 8.528044 AAGTTAACATTTCAACCCTGAACTAA 57.472 30.769 8.61 0.00 41.34 2.24
5959 7381 7.937649 AGTTAACATTTCAACCCTGAACTAAC 58.062 34.615 8.61 0.00 41.34 2.34
5960 7382 5.784578 AACATTTCAACCCTGAACTAACC 57.215 39.130 0.00 0.00 41.34 2.85
5961 7383 4.798882 ACATTTCAACCCTGAACTAACCA 58.201 39.130 0.00 0.00 41.34 3.67
5962 7384 5.393866 ACATTTCAACCCTGAACTAACCAT 58.606 37.500 0.00 0.00 41.34 3.55
5963 7385 5.838521 ACATTTCAACCCTGAACTAACCATT 59.161 36.000 0.00 0.00 41.34 3.16
5964 7386 6.326323 ACATTTCAACCCTGAACTAACCATTT 59.674 34.615 0.00 0.00 41.34 2.32
5965 7387 5.782893 TTCAACCCTGAACTAACCATTTG 57.217 39.130 0.00 0.00 36.62 2.32
5966 7388 4.148838 TCAACCCTGAACTAACCATTTGG 58.851 43.478 0.00 0.00 42.17 3.28
5967 7389 5.870780 TTCAACCCTGAACTAACCATTTGGT 60.871 40.000 0.00 0.00 42.74 3.67
5968 7390 7.316955 TTCAACCCTGAACTAACCATTTGGTT 61.317 38.462 18.37 18.37 46.71 3.67
5969 7391 8.729733 TTCAACCCTGAACTAACCATTTGGTTT 61.730 37.037 19.41 2.66 44.84 3.27
5997 7419 7.868906 TTATAACCCTGATCTTTAAAACCGG 57.131 36.000 0.00 0.00 0.00 5.28
5998 7420 3.801307 ACCCTGATCTTTAAAACCGGT 57.199 42.857 0.00 0.00 0.00 5.28
5999 7421 3.682696 ACCCTGATCTTTAAAACCGGTC 58.317 45.455 8.04 0.00 0.00 4.79
6000 7422 2.676342 CCCTGATCTTTAAAACCGGTCG 59.324 50.000 8.04 0.00 0.00 4.79
6001 7423 3.592059 CCTGATCTTTAAAACCGGTCGA 58.408 45.455 8.04 0.00 0.00 4.20
6002 7424 3.998341 CCTGATCTTTAAAACCGGTCGAA 59.002 43.478 8.04 0.00 0.00 3.71
6003 7425 4.453136 CCTGATCTTTAAAACCGGTCGAAA 59.547 41.667 8.04 7.95 0.00 3.46
6004 7426 5.123344 CCTGATCTTTAAAACCGGTCGAAAT 59.877 40.000 8.04 0.00 0.00 2.17
6005 7427 6.314400 CCTGATCTTTAAAACCGGTCGAAATA 59.686 38.462 8.04 1.95 0.00 1.40
6006 7428 7.064060 TGATCTTTAAAACCGGTCGAAATAC 57.936 36.000 8.04 4.31 0.00 1.89
6007 7429 6.649973 TGATCTTTAAAACCGGTCGAAATACA 59.350 34.615 8.04 6.60 0.00 2.29
6008 7430 6.226988 TCTTTAAAACCGGTCGAAATACAC 57.773 37.500 8.04 0.00 0.00 2.90
6009 7431 5.179182 TCTTTAAAACCGGTCGAAATACACC 59.821 40.000 8.04 0.00 0.00 4.16
6010 7432 1.812235 AAACCGGTCGAAATACACCC 58.188 50.000 8.04 0.00 0.00 4.61
6011 7433 0.036105 AACCGGTCGAAATACACCCC 60.036 55.000 8.04 0.00 0.00 4.95
6012 7434 1.519898 CCGGTCGAAATACACCCCG 60.520 63.158 0.00 0.24 35.32 5.73
6013 7435 1.512230 CGGTCGAAATACACCCCGA 59.488 57.895 0.91 0.00 37.66 5.14
6014 7436 0.108709 CGGTCGAAATACACCCCGAA 60.109 55.000 0.91 0.00 37.66 4.30
6015 7437 1.472026 CGGTCGAAATACACCCCGAAT 60.472 52.381 0.91 0.00 37.66 3.34
6016 7438 2.207590 GGTCGAAATACACCCCGAATC 58.792 52.381 0.00 0.00 32.60 2.52
6017 7439 2.419021 GGTCGAAATACACCCCGAATCA 60.419 50.000 0.00 0.00 32.60 2.57
6018 7440 2.606272 GTCGAAATACACCCCGAATCAC 59.394 50.000 0.00 0.00 32.60 3.06
6019 7441 2.234168 TCGAAATACACCCCGAATCACA 59.766 45.455 0.00 0.00 0.00 3.58
6020 7442 2.350498 CGAAATACACCCCGAATCACAC 59.650 50.000 0.00 0.00 0.00 3.82
6021 7443 3.340034 GAAATACACCCCGAATCACACA 58.660 45.455 0.00 0.00 0.00 3.72
6022 7444 3.644966 AATACACCCCGAATCACACAT 57.355 42.857 0.00 0.00 0.00 3.21
6023 7445 2.394930 TACACCCCGAATCACACATG 57.605 50.000 0.00 0.00 0.00 3.21
6024 7446 0.690192 ACACCCCGAATCACACATGA 59.310 50.000 0.00 0.00 39.83 3.07
6025 7447 1.339055 ACACCCCGAATCACACATGAG 60.339 52.381 0.00 0.00 38.57 2.90
6026 7448 0.984230 ACCCCGAATCACACATGAGT 59.016 50.000 0.00 0.00 38.57 3.41
6027 7449 1.351017 ACCCCGAATCACACATGAGTT 59.649 47.619 0.00 0.00 38.57 3.01
6028 7450 2.009774 CCCCGAATCACACATGAGTTC 58.990 52.381 0.00 0.00 38.57 3.01
6029 7451 2.615240 CCCCGAATCACACATGAGTTCA 60.615 50.000 0.00 0.00 38.57 3.18
6030 7452 3.073678 CCCGAATCACACATGAGTTCAA 58.926 45.455 0.00 0.00 38.57 2.69
6031 7453 3.501828 CCCGAATCACACATGAGTTCAAA 59.498 43.478 0.00 0.00 38.57 2.69
6032 7454 4.023279 CCCGAATCACACATGAGTTCAAAA 60.023 41.667 0.00 0.00 38.57 2.44
6033 7455 4.911610 CCGAATCACACATGAGTTCAAAAC 59.088 41.667 0.00 0.00 38.57 2.43
6034 7456 5.277974 CCGAATCACACATGAGTTCAAAACT 60.278 40.000 0.00 0.00 46.38 2.66
6045 7467 4.639135 AGTTCAAAACTCAAACCTGCTC 57.361 40.909 0.00 0.00 37.02 4.26
6046 7468 4.273318 AGTTCAAAACTCAAACCTGCTCT 58.727 39.130 0.00 0.00 37.02 4.09
6047 7469 4.336713 AGTTCAAAACTCAAACCTGCTCTC 59.663 41.667 0.00 0.00 37.02 3.20
6048 7470 2.872245 TCAAAACTCAAACCTGCTCTCG 59.128 45.455 0.00 0.00 0.00 4.04
6049 7471 1.884235 AAACTCAAACCTGCTCTCGG 58.116 50.000 0.00 0.00 0.00 4.63
6050 7472 0.759346 AACTCAAACCTGCTCTCGGT 59.241 50.000 0.00 0.00 35.97 4.69
6051 7473 0.759346 ACTCAAACCTGCTCTCGGTT 59.241 50.000 0.00 0.00 46.27 4.44
6056 7478 1.884235 AACCTGCTCTCGGTTTTGAG 58.116 50.000 0.00 0.00 41.83 3.02
6057 7479 0.759346 ACCTGCTCTCGGTTTTGAGT 59.241 50.000 0.00 0.00 37.28 3.41
6058 7480 1.141053 ACCTGCTCTCGGTTTTGAGTT 59.859 47.619 0.00 0.00 37.28 3.01
6059 7481 1.532868 CCTGCTCTCGGTTTTGAGTTG 59.467 52.381 0.00 0.00 37.28 3.16
6060 7482 1.532868 CTGCTCTCGGTTTTGAGTTGG 59.467 52.381 0.00 0.00 37.28 3.77
6061 7483 1.134220 TGCTCTCGGTTTTGAGTTGGT 60.134 47.619 0.00 0.00 37.28 3.67
6062 7484 1.531578 GCTCTCGGTTTTGAGTTGGTC 59.468 52.381 0.00 0.00 37.28 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.142097 GCCAAGAGGGTCGTCTAGC 59.858 63.158 0.00 0.00 39.65 3.42
30 31 0.108992 ATGAGCAAATGCACGCCAAG 60.109 50.000 8.28 0.00 45.16 3.61
41 42 1.561643 ACGAGGGAGAGATGAGCAAA 58.438 50.000 0.00 0.00 0.00 3.68
42 43 2.437085 TACGAGGGAGAGATGAGCAA 57.563 50.000 0.00 0.00 0.00 3.91
64 67 2.517402 GCCGGTGGTTGTTGGACA 60.517 61.111 1.90 0.00 0.00 4.02
147 150 3.127376 GGGTAGTGTGACAACAAAAACGT 59.873 43.478 0.00 0.00 38.27 3.99
259 262 3.242739 GCCACTATCTTTACACGCAATGG 60.243 47.826 0.00 0.00 0.00 3.16
291 294 1.792949 GTGAACGCTACAGACACAAGG 59.207 52.381 0.00 0.00 0.00 3.61
294 297 2.588027 TTGTGAACGCTACAGACACA 57.412 45.000 0.00 0.00 39.22 3.72
313 318 2.752121 CATGCTCATCTAGTGCGACAT 58.248 47.619 0.00 0.00 39.54 3.06
315 320 0.857935 GCATGCTCATCTAGTGCGAC 59.142 55.000 11.37 0.00 39.54 5.19
319 324 1.227639 GCCAGCATGCTCATCTAGTG 58.772 55.000 19.68 4.63 31.97 2.74
357 368 7.486870 GCCGGTGGTTATTGAAAGTTTATAAAG 59.513 37.037 1.90 0.00 0.00 1.85
358 369 7.314393 GCCGGTGGTTATTGAAAGTTTATAAA 58.686 34.615 1.90 0.00 0.00 1.40
359 370 6.403418 CGCCGGTGGTTATTGAAAGTTTATAA 60.403 38.462 7.26 0.00 0.00 0.98
360 371 5.064962 CGCCGGTGGTTATTGAAAGTTTATA 59.935 40.000 7.26 0.00 0.00 0.98
361 372 4.142556 CGCCGGTGGTTATTGAAAGTTTAT 60.143 41.667 7.26 0.00 0.00 1.40
366 377 0.179174 GCGCCGGTGGTTATTGAAAG 60.179 55.000 18.41 0.00 0.00 2.62
369 381 2.816083 CGCGCCGGTGGTTATTGA 60.816 61.111 18.41 0.00 0.00 2.57
382 394 1.017177 TGTTACTGGAATCCACGCGC 61.017 55.000 5.73 0.00 0.00 6.86
403 415 4.142026 CGATGAATAGTTGTGGTGGGTAGA 60.142 45.833 0.00 0.00 0.00 2.59
409 421 1.999735 ACGCGATGAATAGTTGTGGTG 59.000 47.619 15.93 0.00 0.00 4.17
410 422 1.999735 CACGCGATGAATAGTTGTGGT 59.000 47.619 15.93 0.00 0.00 4.16
414 426 2.348362 TCTTGCACGCGATGAATAGTTG 59.652 45.455 15.93 0.00 0.00 3.16
417 429 3.062639 ACTTTCTTGCACGCGATGAATAG 59.937 43.478 15.93 10.96 0.00 1.73
425 437 2.663279 AACTTACTTTCTTGCACGCG 57.337 45.000 3.53 3.53 0.00 6.01
450 462 0.809636 TGCAACAGACATATCCGCGG 60.810 55.000 22.12 22.12 0.00 6.46
454 466 5.165911 CATGAACTGCAACAGACATATCC 57.834 43.478 0.78 0.00 33.83 2.59
514 527 0.034863 TACGGGGAAAGATGGTTGGC 60.035 55.000 0.00 0.00 0.00 4.52
539 553 6.290605 ACATCCACATGTCGATGATTATTGA 58.709 36.000 31.94 4.62 39.15 2.57
563 577 0.108963 CGGGGTAGGGTTGTTTGTGA 59.891 55.000 0.00 0.00 0.00 3.58
617 631 3.822735 CCAATTGTCTCAGCCTCAAAGAA 59.177 43.478 4.43 0.00 0.00 2.52
618 632 3.181440 ACCAATTGTCTCAGCCTCAAAGA 60.181 43.478 4.43 0.00 0.00 2.52
619 633 3.152341 ACCAATTGTCTCAGCCTCAAAG 58.848 45.455 4.43 0.00 0.00 2.77
620 634 3.228188 ACCAATTGTCTCAGCCTCAAA 57.772 42.857 4.43 0.00 0.00 2.69
621 635 2.957402 ACCAATTGTCTCAGCCTCAA 57.043 45.000 4.43 0.00 0.00 3.02
622 636 2.957402 AACCAATTGTCTCAGCCTCA 57.043 45.000 4.43 0.00 0.00 3.86
623 637 3.569701 TGAAAACCAATTGTCTCAGCCTC 59.430 43.478 4.43 0.00 0.00 4.70
624 638 3.565307 TGAAAACCAATTGTCTCAGCCT 58.435 40.909 4.43 0.00 0.00 4.58
625 639 4.051237 GTTGAAAACCAATTGTCTCAGCC 58.949 43.478 4.43 0.00 42.21 4.85
765 1862 0.687757 TCTCTTGCTCCGCTATGGGT 60.688 55.000 0.00 0.00 38.76 4.51
769 1866 1.036707 GGTCTCTCTTGCTCCGCTAT 58.963 55.000 0.00 0.00 0.00 2.97
932 2031 2.348998 GCACAGGACAGGACAGGG 59.651 66.667 0.00 0.00 0.00 4.45
1197 2310 4.729856 ACGTACTTCCACCGCCGC 62.730 66.667 0.00 0.00 0.00 6.53
1422 2541 3.321950 ACCAATTCCCCCAAATCAAACA 58.678 40.909 0.00 0.00 0.00 2.83
1437 2556 2.549778 CGCCCAAAATCCACAACCAATT 60.550 45.455 0.00 0.00 0.00 2.32
1479 2599 1.953559 TCTACAATTCGCAGATGGCC 58.046 50.000 0.00 0.00 40.31 5.36
1557 2677 1.556911 CAGTACACTCCTGGGCAGAAT 59.443 52.381 0.00 0.00 0.00 2.40
1561 2681 0.178932 AGTCAGTACACTCCTGGGCA 60.179 55.000 0.00 0.00 0.00 5.36
1717 2842 4.904895 AGAAACTACCTTAGTCCCAACC 57.095 45.455 0.00 0.00 38.26 3.77
1737 2862 9.125026 AGTCCACTGCAATATTAAATTTCCTAG 57.875 33.333 0.00 0.00 0.00 3.02
1784 2909 6.044682 CCAAAAAGAACTTTCAGTCAGCAAT 58.955 36.000 0.21 0.00 31.45 3.56
1807 2932 6.095021 GGACAACTTCCACAGGTAATAATTCC 59.905 42.308 0.00 0.00 45.10 3.01
1889 3015 3.809832 ACTGCTGCACAACTTAACTACAG 59.190 43.478 0.00 0.00 0.00 2.74
1892 3018 4.196193 ACAACTGCTGCACAACTTAACTA 58.804 39.130 0.00 0.00 0.00 2.24
1939 3070 8.076178 GCACTTTAATCTTCACATAACAGTGTT 58.924 33.333 14.05 14.05 40.37 3.32
1968 3099 2.365617 GGAGTGAGTTCAACTCTCCACA 59.634 50.000 18.49 0.00 45.27 4.17
1982 3113 8.420222 AGAGATAGAACATAAATGTGGAGTGAG 58.580 37.037 0.00 0.00 41.61 3.51
2049 3197 2.009774 CCTGCAGCCATAGTGTGTAAC 58.990 52.381 8.66 0.00 37.35 2.50
2208 3360 6.018425 AGCGAACAAATCTTAGCATGATACAG 60.018 38.462 0.00 0.00 0.00 2.74
2329 3481 6.499106 TGAGGATCCAGTTTGATAGCAATA 57.501 37.500 15.82 0.00 33.25 1.90
2339 3491 5.319043 TGTTTACCTTGAGGATCCAGTTT 57.681 39.130 15.82 0.00 38.94 2.66
2434 3586 5.104109 TGGATCGGAGGGAGTGATAAATTTT 60.104 40.000 0.00 0.00 0.00 1.82
2443 3595 5.683876 ATTAATATGGATCGGAGGGAGTG 57.316 43.478 0.00 0.00 0.00 3.51
2451 3603 5.181245 GGGTGTGTCAATTAATATGGATCGG 59.819 44.000 0.00 0.00 0.00 4.18
2508 3660 7.223971 CCTCAGGTCAAAATTAATTGATGCATG 59.776 37.037 2.46 8.52 41.09 4.06
2513 3665 7.184862 ACTCCCTCAGGTCAAAATTAATTGAT 58.815 34.615 0.39 0.00 41.09 2.57
2589 3741 7.976135 ATTGCTATCAGATGACCAATAACTC 57.024 36.000 0.00 0.00 0.00 3.01
2685 3838 5.528690 CAGGACCACAATCACAACTATATGG 59.471 44.000 0.00 0.00 0.00 2.74
2713 3866 2.282674 ACGTCCAGCACCGTCCTA 60.283 61.111 0.00 0.00 30.05 2.94
3028 4262 5.449304 CAATTACTCCAACTTTGAACGACC 58.551 41.667 0.00 0.00 0.00 4.79
3031 4265 5.682943 TCCAATTACTCCAACTTTGAACG 57.317 39.130 0.00 0.00 0.00 3.95
3066 4300 5.713822 ACTTTCAAAACAGTGTCGAGTAC 57.286 39.130 0.00 0.00 0.00 2.73
3146 4380 1.215647 GGTGCGAGTTGAGGTCGAT 59.784 57.895 0.00 0.00 39.92 3.59
3209 4443 1.279271 ACAGATTCGCCCTTAGCAGTT 59.721 47.619 0.00 0.00 44.04 3.16
3227 4461 1.278985 AGATCTGCAATGTTCCCGACA 59.721 47.619 0.00 0.00 43.71 4.35
3299 4533 0.524862 CCAACTCAGTTGCATGCCTC 59.475 55.000 16.68 8.19 41.62 4.70
3329 4563 2.616960 GTCACACGATCCAACTATGCA 58.383 47.619 0.00 0.00 0.00 3.96
3335 4569 1.714794 CTCAGGTCACACGATCCAAC 58.285 55.000 0.00 0.00 0.00 3.77
3338 4572 0.247736 AAGCTCAGGTCACACGATCC 59.752 55.000 0.00 0.00 0.00 3.36
3342 4576 0.532862 ACCAAAGCTCAGGTCACACG 60.533 55.000 4.29 0.00 30.79 4.49
3397 4634 8.143193 TCAACAAAATAATGTCAGAATTGCTGT 58.857 29.630 0.00 0.00 45.14 4.40
3544 4784 9.014297 ACAAGACCCAAGAAATAAAGTATTGAG 57.986 33.333 0.00 0.00 32.40 3.02
3573 4813 3.834489 ACATATGACTTGCAGAGGGAG 57.166 47.619 10.38 0.00 0.00 4.30
3611 4851 0.106708 GCACAACAGACCTCACCTGA 59.893 55.000 0.00 0.00 35.69 3.86
3735 4975 8.507249 AGTATGTTTGCACTTTCTAGAACAATC 58.493 33.333 4.18 6.24 31.69 2.67
3824 5064 7.549842 TCACAAATATAAGTGCCGCTTTACTAA 59.450 33.333 0.00 0.00 38.57 2.24
3825 5065 7.042950 TCACAAATATAAGTGCCGCTTTACTA 58.957 34.615 0.00 0.00 38.57 1.82
3826 5066 5.878116 TCACAAATATAAGTGCCGCTTTACT 59.122 36.000 0.00 0.00 38.57 2.24
3827 5067 6.114221 TCACAAATATAAGTGCCGCTTTAC 57.886 37.500 0.00 0.00 38.57 2.01
3828 5068 6.745159 TTCACAAATATAAGTGCCGCTTTA 57.255 33.333 0.00 0.00 38.57 1.85
3829 5069 5.637006 TTCACAAATATAAGTGCCGCTTT 57.363 34.783 0.00 0.00 38.57 3.51
3830 5070 5.637006 TTTCACAAATATAAGTGCCGCTT 57.363 34.783 0.00 0.00 41.05 4.68
3909 5149 6.332735 ACTGTCAAATCTTTTCTAAAGCCC 57.667 37.500 0.00 0.00 0.00 5.19
3983 5231 1.203038 TGTCCAACCCATTGTGCTGAT 60.203 47.619 0.00 0.00 33.60 2.90
4006 5254 4.159321 TGTGAGTGCAAGGATAGAAGAGAG 59.841 45.833 0.00 0.00 0.00 3.20
4072 5320 9.273016 CTAAAAGAGACCACAATTAGAACTTCA 57.727 33.333 0.00 0.00 0.00 3.02
4319 5568 4.905429 TCTCCAAATCGTGATCCTGAAAA 58.095 39.130 0.00 0.00 0.00 2.29
4516 5767 8.696043 TGAGCAATGCATATACTTTATCCTTT 57.304 30.769 8.35 0.00 0.00 3.11
4534 5785 3.751767 TGCTTGGTCCTTGAGCAAT 57.248 47.368 8.92 0.00 46.49 3.56
4537 5788 0.038801 GCTTTGCTTGGTCCTTGAGC 60.039 55.000 5.76 5.76 36.95 4.26
4828 6079 3.831323 TGCTTTCTTCCTGAATGTTCCA 58.169 40.909 0.00 0.00 34.24 3.53
4956 6208 8.522830 CAAAAAGGAATGTGGTTAGTCATGTAT 58.477 33.333 0.00 0.00 0.00 2.29
4981 6233 0.178967 TCCAGCCCTGAAATGCAACA 60.179 50.000 0.00 0.00 0.00 3.33
4989 6241 3.114606 TCTGACATTATCCAGCCCTGAA 58.885 45.455 0.00 0.00 0.00 3.02
4996 6248 6.219417 AGAAGTGACTCTGACATTATCCAG 57.781 41.667 0.00 0.00 0.00 3.86
5008 6260 2.907042 CCCAGGGTTAAGAAGTGACTCT 59.093 50.000 0.00 0.00 0.00 3.24
5200 6493 3.031736 GAGATGGTAGGCTCACTGGTTA 58.968 50.000 0.00 0.00 0.00 2.85
5207 6500 0.970427 TGCACGAGATGGTAGGCTCA 60.970 55.000 0.00 0.00 0.00 4.26
5215 6508 0.462047 GTAGGGGTTGCACGAGATGG 60.462 60.000 0.00 0.00 0.00 3.51
5305 6600 9.965824 AGATTTTTGGTGTAAATACAAGTCAAG 57.034 29.630 0.00 0.00 38.04 3.02
5325 6620 5.733620 ATGATTGGTCAGCAACAGATTTT 57.266 34.783 0.00 0.00 37.87 1.82
5358 6653 1.927895 CGAGCATACCTGACAAGTCC 58.072 55.000 0.00 0.00 0.00 3.85
5381 6703 1.829849 CCTCAGTCTTCTCATGGCTCA 59.170 52.381 0.00 0.00 0.00 4.26
5414 6736 7.731666 GGAACCTACTCCTATGCAGTTAGCG 62.732 52.000 0.00 0.00 38.13 4.26
5439 6761 6.365518 GCAAGCTTAAATATACGTCCCTCTAC 59.634 42.308 0.00 0.00 0.00 2.59
5517 6841 2.022129 GCCGACGAACACCACTCAG 61.022 63.158 0.00 0.00 0.00 3.35
5531 6855 3.509137 AAAACGACTCCGCAGCCGA 62.509 57.895 0.00 0.00 39.95 5.54
5532 6856 3.011760 GAAAACGACTCCGCAGCCG 62.012 63.158 0.00 0.00 39.95 5.52
5533 6857 2.861006 GAAAACGACTCCGCAGCC 59.139 61.111 0.00 0.00 39.95 4.85
5534 6858 2.470286 CGAAAACGACTCCGCAGC 59.530 61.111 0.00 0.00 39.95 5.25
5535 6859 0.942410 TTCCGAAAACGACTCCGCAG 60.942 55.000 0.00 0.00 39.95 5.18
5536 6860 0.320073 ATTCCGAAAACGACTCCGCA 60.320 50.000 0.00 0.00 39.95 5.69
5537 6861 0.094730 CATTCCGAAAACGACTCCGC 59.905 55.000 0.00 0.00 39.95 5.54
5538 6862 1.425412 ACATTCCGAAAACGACTCCG 58.575 50.000 0.00 0.00 42.50 4.63
5539 6863 2.928116 CCTACATTCCGAAAACGACTCC 59.072 50.000 0.00 0.00 0.00 3.85
5540 6864 3.841643 TCCTACATTCCGAAAACGACTC 58.158 45.455 0.00 0.00 0.00 3.36
5541 6865 3.947910 TCCTACATTCCGAAAACGACT 57.052 42.857 0.00 0.00 0.00 4.18
5542 6866 4.240096 TCTTCCTACATTCCGAAAACGAC 58.760 43.478 0.00 0.00 0.00 4.34
5543 6867 4.491676 CTCTTCCTACATTCCGAAAACGA 58.508 43.478 0.00 0.00 0.00 3.85
5544 6868 3.062234 GCTCTTCCTACATTCCGAAAACG 59.938 47.826 0.00 0.00 0.00 3.60
5545 6869 4.093556 CAGCTCTTCCTACATTCCGAAAAC 59.906 45.833 0.00 0.00 0.00 2.43
5546 6870 4.253685 CAGCTCTTCCTACATTCCGAAAA 58.746 43.478 0.00 0.00 0.00 2.29
5547 6871 3.260884 ACAGCTCTTCCTACATTCCGAAA 59.739 43.478 0.00 0.00 0.00 3.46
5548 6872 2.832129 ACAGCTCTTCCTACATTCCGAA 59.168 45.455 0.00 0.00 0.00 4.30
5649 7008 3.408634 ACATAAAAACACTCTCCACCCG 58.591 45.455 0.00 0.00 0.00 5.28
5651 7010 4.312443 TCGACATAAAAACACTCTCCACC 58.688 43.478 0.00 0.00 0.00 4.61
5652 7011 5.671329 GCATCGACATAAAAACACTCTCCAC 60.671 44.000 0.00 0.00 0.00 4.02
5749 7111 2.997899 GCAGCGGCAATGAGATACT 58.002 52.632 3.18 0.00 40.72 2.12
5770 7186 3.755378 CAGCAGAGTACCAGAAAATGCTT 59.245 43.478 0.00 0.00 40.35 3.91
5781 7197 0.179062 CCCAGATGCAGCAGAGTACC 60.179 60.000 4.07 0.00 0.00 3.34
5782 7198 0.539051 ACCCAGATGCAGCAGAGTAC 59.461 55.000 4.07 0.00 0.00 2.73
5783 7199 1.279496 AACCCAGATGCAGCAGAGTA 58.721 50.000 4.07 0.00 0.00 2.59
5784 7200 1.209019 CTAACCCAGATGCAGCAGAGT 59.791 52.381 4.07 0.00 0.00 3.24
5785 7201 1.209019 ACTAACCCAGATGCAGCAGAG 59.791 52.381 4.07 0.00 0.00 3.35
5786 7202 1.279496 ACTAACCCAGATGCAGCAGA 58.721 50.000 4.07 0.00 0.00 4.26
5787 7203 2.093500 TGTACTAACCCAGATGCAGCAG 60.093 50.000 4.07 0.00 0.00 4.24
5788 7204 1.905894 TGTACTAACCCAGATGCAGCA 59.094 47.619 4.07 0.00 0.00 4.41
5789 7205 2.678336 GTTGTACTAACCCAGATGCAGC 59.322 50.000 0.00 0.00 0.00 5.25
5790 7206 3.935203 CTGTTGTACTAACCCAGATGCAG 59.065 47.826 0.00 0.00 0.00 4.41
5791 7207 3.868369 GCTGTTGTACTAACCCAGATGCA 60.868 47.826 0.00 0.00 0.00 3.96
5792 7208 2.678336 GCTGTTGTACTAACCCAGATGC 59.322 50.000 0.00 0.00 0.00 3.91
5793 7209 3.937814 TGCTGTTGTACTAACCCAGATG 58.062 45.455 0.00 0.00 0.00 2.90
5794 7210 4.844349 ATGCTGTTGTACTAACCCAGAT 57.156 40.909 0.00 0.00 0.00 2.90
5795 7211 4.634012 AATGCTGTTGTACTAACCCAGA 57.366 40.909 0.00 0.00 0.00 3.86
5796 7212 5.335661 GGAAAATGCTGTTGTACTAACCCAG 60.336 44.000 0.00 0.00 0.00 4.45
5797 7213 4.521256 GGAAAATGCTGTTGTACTAACCCA 59.479 41.667 0.00 0.00 0.00 4.51
5798 7214 4.379082 CGGAAAATGCTGTTGTACTAACCC 60.379 45.833 0.00 0.00 0.00 4.11
5799 7215 4.379082 CCGGAAAATGCTGTTGTACTAACC 60.379 45.833 0.00 0.00 0.00 2.85
5800 7216 4.214758 ACCGGAAAATGCTGTTGTACTAAC 59.785 41.667 9.46 0.00 0.00 2.34
5801 7217 4.391155 ACCGGAAAATGCTGTTGTACTAA 58.609 39.130 9.46 0.00 0.00 2.24
5802 7218 4.010667 ACCGGAAAATGCTGTTGTACTA 57.989 40.909 9.46 0.00 0.00 1.82
5803 7219 2.858745 ACCGGAAAATGCTGTTGTACT 58.141 42.857 9.46 0.00 0.00 2.73
5804 7220 3.749609 AGTACCGGAAAATGCTGTTGTAC 59.250 43.478 9.46 0.00 0.00 2.90
5805 7221 3.998341 GAGTACCGGAAAATGCTGTTGTA 59.002 43.478 9.46 0.00 0.00 2.41
5806 7222 2.812011 GAGTACCGGAAAATGCTGTTGT 59.188 45.455 9.46 0.00 0.00 3.32
5807 7223 3.074412 AGAGTACCGGAAAATGCTGTTG 58.926 45.455 9.46 0.00 0.00 3.33
5808 7224 3.074412 CAGAGTACCGGAAAATGCTGTT 58.926 45.455 9.46 0.00 0.00 3.16
5809 7225 2.699954 CAGAGTACCGGAAAATGCTGT 58.300 47.619 9.46 0.00 0.00 4.40
5810 7226 1.398390 GCAGAGTACCGGAAAATGCTG 59.602 52.381 9.46 8.88 0.00 4.41
5811 7227 1.279271 AGCAGAGTACCGGAAAATGCT 59.721 47.619 9.46 14.13 37.69 3.79
5812 7228 1.398390 CAGCAGAGTACCGGAAAATGC 59.602 52.381 9.46 11.88 0.00 3.56
5813 7229 1.398390 GCAGCAGAGTACCGGAAAATG 59.602 52.381 9.46 0.74 0.00 2.32
5814 7230 1.003118 TGCAGCAGAGTACCGGAAAAT 59.997 47.619 9.46 0.00 0.00 1.82
5815 7231 0.394938 TGCAGCAGAGTACCGGAAAA 59.605 50.000 9.46 0.00 0.00 2.29
5816 7232 0.613260 ATGCAGCAGAGTACCGGAAA 59.387 50.000 9.46 0.00 0.00 3.13
5817 7233 0.175760 GATGCAGCAGAGTACCGGAA 59.824 55.000 9.46 0.00 0.00 4.30
5818 7234 0.684479 AGATGCAGCAGAGTACCGGA 60.684 55.000 9.46 0.00 0.00 5.14
5819 7235 0.529337 CAGATGCAGCAGAGTACCGG 60.529 60.000 4.07 0.00 0.00 5.28
5820 7236 0.529337 CCAGATGCAGCAGAGTACCG 60.529 60.000 4.07 0.00 0.00 4.02
5885 7307 3.078891 AGAAGAAAAGGATCCAGCCAC 57.921 47.619 15.82 1.21 0.00 5.01
5926 7348 9.981114 CAGGGTTGAAATGTTAACTTTTCTATT 57.019 29.630 31.04 18.57 39.39 1.73
5928 7350 8.754991 TCAGGGTTGAAATGTTAACTTTTCTA 57.245 30.769 31.04 25.60 39.39 2.10
5929 7351 7.654022 TCAGGGTTGAAATGTTAACTTTTCT 57.346 32.000 31.04 17.71 39.39 2.52
5930 7352 7.979537 AGTTCAGGGTTGAAATGTTAACTTTTC 59.020 33.333 27.64 27.64 44.49 2.29
5931 7353 7.847096 AGTTCAGGGTTGAAATGTTAACTTTT 58.153 30.769 16.80 16.80 44.49 2.27
5932 7354 7.418337 AGTTCAGGGTTGAAATGTTAACTTT 57.582 32.000 7.22 3.94 44.49 2.66
5933 7355 8.410912 GTTAGTTCAGGGTTGAAATGTTAACTT 58.589 33.333 7.22 0.00 44.49 2.66
5934 7356 7.013942 GGTTAGTTCAGGGTTGAAATGTTAACT 59.986 37.037 7.22 0.00 44.49 2.24
5935 7357 7.143340 GGTTAGTTCAGGGTTGAAATGTTAAC 58.857 38.462 0.00 0.00 44.49 2.01
5936 7358 6.834451 TGGTTAGTTCAGGGTTGAAATGTTAA 59.166 34.615 1.00 0.00 44.49 2.01
5937 7359 6.366340 TGGTTAGTTCAGGGTTGAAATGTTA 58.634 36.000 1.00 0.00 44.49 2.41
5938 7360 5.205056 TGGTTAGTTCAGGGTTGAAATGTT 58.795 37.500 1.00 0.00 44.49 2.71
5939 7361 4.798882 TGGTTAGTTCAGGGTTGAAATGT 58.201 39.130 1.00 0.00 44.49 2.71
5940 7362 5.982890 ATGGTTAGTTCAGGGTTGAAATG 57.017 39.130 1.00 0.00 44.49 2.32
5941 7363 6.239572 CCAAATGGTTAGTTCAGGGTTGAAAT 60.240 38.462 0.00 0.00 44.49 2.17
5942 7364 5.069781 CCAAATGGTTAGTTCAGGGTTGAAA 59.930 40.000 0.00 0.00 44.49 2.69
5943 7365 4.586841 CCAAATGGTTAGTTCAGGGTTGAA 59.413 41.667 0.00 0.00 40.92 2.69
5944 7366 4.148838 CCAAATGGTTAGTTCAGGGTTGA 58.851 43.478 0.00 0.00 0.00 3.18
5945 7367 4.519540 CCAAATGGTTAGTTCAGGGTTG 57.480 45.455 0.00 0.00 0.00 3.77
5971 7393 8.909923 CCGGTTTTAAAGATCAGGGTTATAAAT 58.090 33.333 0.00 0.00 0.00 1.40
5972 7394 7.889600 ACCGGTTTTAAAGATCAGGGTTATAAA 59.110 33.333 0.00 0.00 0.00 1.40
5973 7395 7.404481 ACCGGTTTTAAAGATCAGGGTTATAA 58.596 34.615 0.00 0.00 0.00 0.98
5974 7396 6.961042 ACCGGTTTTAAAGATCAGGGTTATA 58.039 36.000 0.00 0.00 0.00 0.98
5975 7397 5.823312 ACCGGTTTTAAAGATCAGGGTTAT 58.177 37.500 0.00 0.00 0.00 1.89
5976 7398 5.245584 ACCGGTTTTAAAGATCAGGGTTA 57.754 39.130 0.00 0.00 0.00 2.85
5977 7399 4.077108 GACCGGTTTTAAAGATCAGGGTT 58.923 43.478 9.42 0.00 0.00 4.11
5978 7400 3.682696 GACCGGTTTTAAAGATCAGGGT 58.317 45.455 9.42 0.00 0.00 4.34
5979 7401 2.676342 CGACCGGTTTTAAAGATCAGGG 59.324 50.000 9.42 0.00 0.00 4.45
5980 7402 3.592059 TCGACCGGTTTTAAAGATCAGG 58.408 45.455 9.42 0.00 0.00 3.86
5981 7403 5.600908 TTTCGACCGGTTTTAAAGATCAG 57.399 39.130 9.42 0.00 0.00 2.90
5982 7404 6.649973 TGTATTTCGACCGGTTTTAAAGATCA 59.350 34.615 9.42 7.82 0.00 2.92
5983 7405 6.957635 GTGTATTTCGACCGGTTTTAAAGATC 59.042 38.462 9.42 5.59 0.00 2.75
5984 7406 6.128200 GGTGTATTTCGACCGGTTTTAAAGAT 60.128 38.462 9.42 0.00 0.00 2.40
5985 7407 5.179182 GGTGTATTTCGACCGGTTTTAAAGA 59.821 40.000 9.42 4.47 0.00 2.52
5986 7408 5.384787 GGTGTATTTCGACCGGTTTTAAAG 58.615 41.667 9.42 0.00 0.00 1.85
5987 7409 4.215185 GGGTGTATTTCGACCGGTTTTAAA 59.785 41.667 9.42 10.46 32.48 1.52
5988 7410 3.750652 GGGTGTATTTCGACCGGTTTTAA 59.249 43.478 9.42 3.35 32.48 1.52
5989 7411 3.333804 GGGTGTATTTCGACCGGTTTTA 58.666 45.455 9.42 0.00 32.48 1.52
5990 7412 2.153645 GGGTGTATTTCGACCGGTTTT 58.846 47.619 9.42 0.00 32.48 2.43
5991 7413 1.611410 GGGGTGTATTTCGACCGGTTT 60.611 52.381 9.42 0.00 32.48 3.27
5992 7414 0.036105 GGGGTGTATTTCGACCGGTT 60.036 55.000 9.42 0.00 32.48 4.44
5993 7415 1.598517 GGGGTGTATTTCGACCGGT 59.401 57.895 6.92 6.92 32.48 5.28
5994 7416 1.519898 CGGGGTGTATTTCGACCGG 60.520 63.158 0.00 0.00 37.80 5.28
5995 7417 0.108709 TTCGGGGTGTATTTCGACCG 60.109 55.000 0.76 0.76 42.45 4.79
5996 7418 2.207590 GATTCGGGGTGTATTTCGACC 58.792 52.381 0.00 0.00 0.00 4.79
5997 7419 2.606272 GTGATTCGGGGTGTATTTCGAC 59.394 50.000 0.00 0.00 0.00 4.20
5998 7420 2.234168 TGTGATTCGGGGTGTATTTCGA 59.766 45.455 0.00 0.00 0.00 3.71
5999 7421 2.350498 GTGTGATTCGGGGTGTATTTCG 59.650 50.000 0.00 0.00 0.00 3.46
6000 7422 3.340034 TGTGTGATTCGGGGTGTATTTC 58.660 45.455 0.00 0.00 0.00 2.17
6001 7423 3.426787 TGTGTGATTCGGGGTGTATTT 57.573 42.857 0.00 0.00 0.00 1.40
6002 7424 3.054728 TCATGTGTGATTCGGGGTGTATT 60.055 43.478 0.00 0.00 0.00 1.89
6003 7425 2.503765 TCATGTGTGATTCGGGGTGTAT 59.496 45.455 0.00 0.00 0.00 2.29
6004 7426 1.903183 TCATGTGTGATTCGGGGTGTA 59.097 47.619 0.00 0.00 0.00 2.90
6005 7427 0.690192 TCATGTGTGATTCGGGGTGT 59.310 50.000 0.00 0.00 0.00 4.16
6006 7428 1.339055 ACTCATGTGTGATTCGGGGTG 60.339 52.381 0.00 0.00 32.98 4.61
6007 7429 0.984230 ACTCATGTGTGATTCGGGGT 59.016 50.000 0.00 0.00 32.98 4.95
6008 7430 2.009774 GAACTCATGTGTGATTCGGGG 58.990 52.381 0.31 0.00 32.98 5.73
6009 7431 2.698803 TGAACTCATGTGTGATTCGGG 58.301 47.619 0.31 0.00 32.98 5.14
6010 7432 4.747540 TTTGAACTCATGTGTGATTCGG 57.252 40.909 0.31 0.00 32.98 4.30
6011 7433 5.751680 AGTTTTGAACTCATGTGTGATTCG 58.248 37.500 0.31 0.00 37.02 3.34
6024 7446 4.273318 AGAGCAGGTTTGAGTTTTGAACT 58.727 39.130 0.00 0.00 46.38 3.01
6025 7447 4.602006 GAGAGCAGGTTTGAGTTTTGAAC 58.398 43.478 0.00 0.00 0.00 3.18
6026 7448 3.312421 CGAGAGCAGGTTTGAGTTTTGAA 59.688 43.478 0.00 0.00 0.00 2.69
6027 7449 2.872245 CGAGAGCAGGTTTGAGTTTTGA 59.128 45.455 0.00 0.00 0.00 2.69
6028 7450 2.031682 CCGAGAGCAGGTTTGAGTTTTG 60.032 50.000 0.00 0.00 0.00 2.44
6029 7451 2.222027 CCGAGAGCAGGTTTGAGTTTT 58.778 47.619 0.00 0.00 0.00 2.43
6030 7452 1.141053 ACCGAGAGCAGGTTTGAGTTT 59.859 47.619 0.00 0.00 39.29 2.66
6031 7453 0.759346 ACCGAGAGCAGGTTTGAGTT 59.241 50.000 0.00 0.00 39.29 3.01
6032 7454 2.442056 ACCGAGAGCAGGTTTGAGT 58.558 52.632 0.00 0.00 39.29 3.41
6038 7460 0.759346 ACTCAAAACCGAGAGCAGGT 59.241 50.000 0.00 0.00 45.29 4.00
6039 7461 1.532868 CAACTCAAAACCGAGAGCAGG 59.467 52.381 0.00 0.00 36.47 4.85
6040 7462 1.532868 CCAACTCAAAACCGAGAGCAG 59.467 52.381 0.00 0.00 36.47 4.24
6041 7463 1.134220 ACCAACTCAAAACCGAGAGCA 60.134 47.619 0.00 0.00 36.47 4.26
6042 7464 1.531578 GACCAACTCAAAACCGAGAGC 59.468 52.381 0.00 0.00 36.47 4.09


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

AutoCloner maintained by Alex Coulton.