Multiple sequence alignment - TraesCS3A01G530100

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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 TraesCS3A01G530100 chr3A 100.000 4401 0 0 1 4401 743276118 743271718 0.000000e+00 8128.0
1 TraesCS3A01G530100 chr3A 85.616 146 15 3 2727 2866 743257028 743256883 9.860000e-32 148.0
2 TraesCS3A01G530100 chr3A 90.123 81 7 1 4 84 743374498 743374419 2.170000e-18 104.0
3 TraesCS3A01G530100 chr3B 92.472 1873 110 14 2549 4401 820894518 820892657 0.000000e+00 2649.0
4 TraesCS3A01G530100 chr3B 90.830 1603 107 19 893 2460 820896112 820894515 0.000000e+00 2109.0
5 TraesCS3A01G530100 chr3B 91.136 801 62 5 4 800 820897195 820896400 0.000000e+00 1077.0
6 TraesCS3A01G530100 chr3B 83.234 334 40 4 2743 3071 820535075 820534753 4.310000e-75 292.0
7 TraesCS3A01G530100 chr3B 78.512 363 60 13 2918 3277 820889505 820889158 5.730000e-54 222.0
8 TraesCS3A01G530100 chr3B 83.333 204 24 5 2727 2920 820890378 820890175 3.500000e-41 180.0
9 TraesCS3A01G530100 chr3D 86.667 1620 144 31 2549 4145 609705506 609703936 0.000000e+00 1729.0
10 TraesCS3A01G530100 chr3D 91.003 1256 86 17 1225 2460 609706751 609705503 0.000000e+00 1668.0
11 TraesCS3A01G530100 chr3D 89.714 350 17 6 836 1169 609707333 609706987 3.150000e-116 429.0
12 TraesCS3A01G530100 chr6D 84.071 226 30 3 4153 4374 441538794 441538571 3.450000e-51 213.0
13 TraesCS3A01G530100 chr5B 89.062 64 5 2 4055 4116 526647932 526647869 1.310000e-10 78.7
14 TraesCS3A01G530100 chr5B 88.372 43 5 0 2456 2498 696437604 696437562 8.000000e-03 52.8
15 TraesCS3A01G530100 chr2A 86.667 75 5 3 4201 4271 58670508 58670435 1.310000e-10 78.7
16 TraesCS3A01G530100 chr2A 79.381 97 17 2 2457 2550 62725760 62725664 1.020000e-06 65.8
17 TraesCS3A01G530100 chr4A 92.157 51 3 1 2457 2507 97258657 97258706 2.200000e-08 71.3
18 TraesCS3A01G530100 chr4A 89.130 46 5 0 2454 2499 33860970 33861015 1.710000e-04 58.4
19 TraesCS3A01G530100 chr5A 78.846 104 14 6 2456 2554 25890693 25890593 3.670000e-06 63.9
20 TraesCS3A01G530100 chr1B 91.489 47 2 2 2453 2498 68933962 68933917 3.670000e-06 63.9
21 TraesCS3A01G530100 chr7B 78.788 99 14 5 2457 2550 377903137 377903233 4.750000e-05 60.2
22 TraesCS3A01G530100 chr2D 100.000 29 0 0 2455 2483 30406646 30406674 2.000000e-03 54.7
23 TraesCS3A01G530100 chr2B 77.228 101 16 6 2456 2551 26228366 26228268 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 TraesCS3A01G530100 chr3A 743271718 743276118 4400 True 8128.000000 8128 100.0000 1 4401 1 chr3A.!!$R2 4400
1 TraesCS3A01G530100 chr3B 820889158 820897195 8037 True 1247.400000 2649 87.2566 4 4401 5 chr3B.!!$R2 4397
2 TraesCS3A01G530100 chr3D 609703936 609707333 3397 True 1275.333333 1729 89.1280 836 4145 3 chr3D.!!$R1 3309

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
809 814 0.098376 CTTACTACCGAGCGTTCGCT 59.902 55.0 19.46 19.46 45.38 4.93 F
1333 1725 0.106619 AGGTCGAGGAGTTCGCCTAT 60.107 55.0 9.62 0.00 46.64 2.57 F
2473 2885 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.0 0.00 0.00 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2568 0.392193 CTGAGCTCAAGGGAACGCAT 60.392 55.0 18.85 0.0 0.00 4.73 R
2976 3390 0.592637 CAGCGTGTGCCTTTTCATCA 59.407 50.0 0.00 0.0 44.31 3.07 R
3993 4428 0.623723 GGAAGTATGTCTTGGGGGCA 59.376 55.0 0.00 0.0 36.40 5.36 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
36 37 2.030893 ACGTGATTGGTGCTCAACATTG 60.031 45.455 0.00 0.00 38.31 2.82
39 40 1.205417 GATTGGTGCTCAACATTGGGG 59.795 52.381 0.00 0.00 38.31 4.96
95 96 4.894114 TGTTCTGATCTAGTAGGCTAACCC 59.106 45.833 0.00 0.00 36.11 4.11
104 105 8.686739 ATCTAGTAGGCTAACCCATGATTTAT 57.313 34.615 0.00 0.00 36.11 1.40
142 143 3.704381 TGTGACCGTGCACAAAAAC 57.296 47.368 18.64 9.98 45.08 2.43
154 155 8.023706 ACCGTGCACAAAAACAAAATTTTATTT 58.976 25.926 18.64 1.83 31.54 1.40
213 214 7.972832 ATTCTATTTGGTAAGACAACACGAA 57.027 32.000 0.00 0.00 0.00 3.85
258 259 2.037121 GTGAAACACATGGGGAAAAGGG 59.963 50.000 0.00 0.00 36.32 3.95
328 329 7.120923 ACGAGCCAATTTAGGAGATAAACTA 57.879 36.000 0.00 0.00 36.20 2.24
331 332 6.299922 AGCCAATTTAGGAGATAAACTAGGC 58.700 40.000 0.00 0.00 42.50 3.93
346 347 2.143122 CTAGGCGAGAAAAGCACACAA 58.857 47.619 0.00 0.00 36.08 3.33
347 348 1.388547 AGGCGAGAAAAGCACACAAA 58.611 45.000 0.00 0.00 36.08 2.83
348 349 1.334869 AGGCGAGAAAAGCACACAAAG 59.665 47.619 0.00 0.00 36.08 2.77
354 355 4.143030 CGAGAAAAGCACACAAAGATCGAT 60.143 41.667 0.00 0.00 0.00 3.59
356 357 2.907910 AAGCACACAAAGATCGATGC 57.092 45.000 0.54 0.00 0.00 3.91
362 363 4.034394 GCACACAAAGATCGATGCATTAGA 59.966 41.667 0.54 4.30 33.27 2.10
367 368 5.757320 ACAAAGATCGATGCATTAGAAGGAG 59.243 40.000 0.54 0.00 0.00 3.69
368 369 4.533919 AGATCGATGCATTAGAAGGAGG 57.466 45.455 0.54 0.00 0.00 4.30
369 370 4.155709 AGATCGATGCATTAGAAGGAGGA 58.844 43.478 0.54 0.00 0.00 3.71
370 371 4.590647 AGATCGATGCATTAGAAGGAGGAA 59.409 41.667 0.54 0.00 0.00 3.36
371 372 4.060038 TCGATGCATTAGAAGGAGGAAC 57.940 45.455 0.00 0.00 0.00 3.62
422 423 4.479993 AGAGCACCGCCCATGAGC 62.480 66.667 0.00 0.00 0.00 4.26
424 425 4.349503 AGCACCGCCCATGAGCAA 62.350 61.111 0.00 0.00 0.00 3.91
427 428 1.973281 CACCGCCCATGAGCAAACT 60.973 57.895 0.00 0.00 0.00 2.66
440 441 1.134521 AGCAAACTCCGAGACACAACA 60.135 47.619 1.33 0.00 0.00 3.33
460 461 1.313091 ACACATGCGGACGAGCTAGA 61.313 55.000 0.00 0.00 38.13 2.43
472 473 2.291024 ACGAGCTAGATATCCCCACGAT 60.291 50.000 0.00 0.00 34.73 3.73
485 486 2.558795 CCCCACGATGTGATACTAGAGG 59.441 54.545 0.00 0.00 35.23 3.69
490 491 5.163550 CCACGATGTGATACTAGAGGAAACA 60.164 44.000 0.00 0.00 35.23 2.83
491 492 5.744345 CACGATGTGATACTAGAGGAAACAC 59.256 44.000 0.00 0.00 35.23 3.32
499 500 6.811665 TGATACTAGAGGAAACACAATCAACG 59.188 38.462 0.00 0.00 0.00 4.10
508 509 5.499139 AAACACAATCAACGAGTGTCATT 57.501 34.783 0.00 0.00 44.99 2.57
523 524 3.061322 TGTCATTGACCGTAAAACTCCG 58.939 45.455 14.05 0.00 0.00 4.63
525 526 1.801771 CATTGACCGTAAAACTCCGCA 59.198 47.619 0.00 0.00 0.00 5.69
531 532 1.002251 CCGTAAAACTCCGCAGCAAAA 60.002 47.619 0.00 0.00 0.00 2.44
535 536 2.087462 AAACTCCGCAGCAAAAGGGC 62.087 55.000 0.00 0.00 0.00 5.19
543 544 1.453155 CAGCAAAAGGGCGTGATACT 58.547 50.000 0.00 0.00 39.27 2.12
554 555 1.328680 GCGTGATACTGGACAATGCAG 59.671 52.381 0.00 0.00 41.93 4.41
612 613 2.615227 CTAGCTGCCATTCCGCCCTT 62.615 60.000 0.00 0.00 0.00 3.95
626 627 1.813862 CGCCCTTGAAGTCCAACTCAA 60.814 52.381 0.00 0.00 0.00 3.02
628 629 2.229784 GCCCTTGAAGTCCAACTCAATG 59.770 50.000 0.00 0.00 0.00 2.82
658 659 4.649692 AGCCAAGATCATCATCCATGTAC 58.350 43.478 0.00 0.00 33.66 2.90
663 664 5.883685 AGATCATCATCCATGTACTGTGT 57.116 39.130 0.00 0.00 33.66 3.72
673 674 3.629855 CCATGTACTGTGTCAAACAACCA 59.370 43.478 0.00 0.00 38.67 3.67
686 687 5.178623 GTCAAACAACCAACGACATATCTCA 59.821 40.000 0.00 0.00 0.00 3.27
697 698 7.172190 CCAACGACATATCTCATTGCTAATTCT 59.828 37.037 0.00 0.00 0.00 2.40
701 703 9.591404 CGACATATCTCATTGCTAATTCTTTTC 57.409 33.333 0.00 0.00 0.00 2.29
756 761 6.795098 AAAACCAAAAGGAGAAAACACAAC 57.205 33.333 0.00 0.00 0.00 3.32
757 762 5.476091 AACCAAAAGGAGAAAACACAACA 57.524 34.783 0.00 0.00 0.00 3.33
758 763 5.675684 ACCAAAAGGAGAAAACACAACAT 57.324 34.783 0.00 0.00 0.00 2.71
759 764 5.418676 ACCAAAAGGAGAAAACACAACATG 58.581 37.500 0.00 0.00 0.00 3.21
772 777 5.091261 ACACAACATGGCCTTAAAACAAA 57.909 34.783 3.32 0.00 0.00 2.83
800 805 2.094545 GCTCCCGAAAACTTACTACCGA 60.095 50.000 0.00 0.00 0.00 4.69
801 806 3.767278 CTCCCGAAAACTTACTACCGAG 58.233 50.000 0.00 0.00 0.00 4.63
802 807 2.094545 TCCCGAAAACTTACTACCGAGC 60.095 50.000 0.00 0.00 0.00 5.03
803 808 1.916000 CCGAAAACTTACTACCGAGCG 59.084 52.381 0.00 0.00 0.00 5.03
804 809 2.589014 CGAAAACTTACTACCGAGCGT 58.411 47.619 0.00 0.00 0.00 5.07
805 810 2.982470 CGAAAACTTACTACCGAGCGTT 59.018 45.455 0.00 0.00 0.00 4.84
806 811 3.058651 CGAAAACTTACTACCGAGCGTTC 59.941 47.826 0.00 0.00 0.00 3.95
807 812 2.253392 AACTTACTACCGAGCGTTCG 57.747 50.000 15.26 15.26 46.29 3.95
808 813 0.179179 ACTTACTACCGAGCGTTCGC 60.179 55.000 16.81 9.24 45.38 4.70
809 814 0.098376 CTTACTACCGAGCGTTCGCT 59.902 55.000 19.46 19.46 45.38 4.93
810 815 1.328680 CTTACTACCGAGCGTTCGCTA 59.671 52.381 19.41 6.33 45.38 4.26
811 816 1.586422 TACTACCGAGCGTTCGCTAT 58.414 50.000 19.41 10.75 45.38 2.97
812 817 0.307146 ACTACCGAGCGTTCGCTATC 59.693 55.000 19.41 7.90 45.38 2.08
813 818 0.306840 CTACCGAGCGTTCGCTATCA 59.693 55.000 19.41 5.15 45.38 2.15
814 819 0.734309 TACCGAGCGTTCGCTATCAA 59.266 50.000 19.41 4.00 45.38 2.57
815 820 0.801067 ACCGAGCGTTCGCTATCAAC 60.801 55.000 19.41 6.27 45.38 3.18
816 821 0.800683 CCGAGCGTTCGCTATCAACA 60.801 55.000 19.41 0.00 45.38 3.33
817 822 1.200483 CGAGCGTTCGCTATCAACAT 58.800 50.000 19.41 0.00 42.08 2.71
818 823 1.188138 CGAGCGTTCGCTATCAACATC 59.812 52.381 19.41 4.46 42.08 3.06
819 824 1.188138 GAGCGTTCGCTATCAACATCG 59.812 52.381 19.41 0.00 42.08 3.84
820 825 0.921347 GCGTTCGCTATCAACATCGT 59.079 50.000 9.99 0.00 0.00 3.73
821 826 1.072089 GCGTTCGCTATCAACATCGTC 60.072 52.381 9.99 0.00 0.00 4.20
822 827 1.517276 CGTTCGCTATCAACATCGTCC 59.483 52.381 0.00 0.00 0.00 4.79
823 828 1.859080 GTTCGCTATCAACATCGTCCC 59.141 52.381 0.00 0.00 0.00 4.46
824 829 1.107945 TCGCTATCAACATCGTCCCA 58.892 50.000 0.00 0.00 0.00 4.37
825 830 1.478916 TCGCTATCAACATCGTCCCAA 59.521 47.619 0.00 0.00 0.00 4.12
826 831 1.860950 CGCTATCAACATCGTCCCAAG 59.139 52.381 0.00 0.00 0.00 3.61
827 832 2.481276 CGCTATCAACATCGTCCCAAGA 60.481 50.000 0.00 0.00 0.00 3.02
828 833 3.531538 GCTATCAACATCGTCCCAAGAA 58.468 45.455 0.00 0.00 0.00 2.52
829 834 3.938963 GCTATCAACATCGTCCCAAGAAA 59.061 43.478 0.00 0.00 0.00 2.52
830 835 4.394920 GCTATCAACATCGTCCCAAGAAAA 59.605 41.667 0.00 0.00 0.00 2.29
831 836 5.106317 GCTATCAACATCGTCCCAAGAAAAA 60.106 40.000 0.00 0.00 0.00 1.94
884 893 2.029743 CCGTCCACACCACCAAAAG 58.970 57.895 0.00 0.00 0.00 2.27
891 900 0.454196 ACACCACCAAAAGCGTTCAC 59.546 50.000 0.00 0.00 0.00 3.18
924 1125 1.367471 GCAGGTGAAAGGCCCAAAC 59.633 57.895 0.00 0.00 0.00 2.93
932 1133 1.396607 AAAGGCCCAAACCGAACACC 61.397 55.000 0.00 0.00 33.69 4.16
1166 1378 0.108138 CTCGGCCAGGTAACCAAGAG 60.108 60.000 2.24 0.00 37.17 2.85
1173 1385 2.234908 CCAGGTAACCAAGAGACCAGAG 59.765 54.545 0.00 0.00 35.56 3.35
1223 1446 1.903860 TCTTACCTTCCCTGCGCTTTA 59.096 47.619 9.73 0.00 0.00 1.85
1273 1665 3.134127 CAGCAAAGCTACCGGGGC 61.134 66.667 6.32 10.29 36.40 5.80
1318 1710 1.973812 GAACAGGGCCAAGCAGGTC 60.974 63.158 6.18 0.00 43.09 3.85
1333 1725 0.106619 AGGTCGAGGAGTTCGCCTAT 60.107 55.000 9.62 0.00 46.64 2.57
1345 1737 2.203070 GCCTATGGTGAGTGCCCG 60.203 66.667 0.00 0.00 0.00 6.13
1346 1738 2.203070 CCTATGGTGAGTGCCCGC 60.203 66.667 0.00 0.00 0.00 6.13
1347 1739 2.203070 CTATGGTGAGTGCCCGCC 60.203 66.667 0.00 0.00 37.23 6.13
1396 1788 4.821589 CCTCGGCCGCTCTTGTCC 62.822 72.222 23.51 0.00 0.00 4.02
1473 1865 3.059386 GTTGGCGCGGGATGGAAA 61.059 61.111 8.83 0.00 0.00 3.13
1548 1953 6.239176 CCAAGGTAGGTTAAAGCATTGTGAAA 60.239 38.462 0.00 0.00 0.00 2.69
1551 1956 6.027749 GGTAGGTTAAAGCATTGTGAAATCG 58.972 40.000 0.00 0.00 0.00 3.34
1552 1957 5.957842 AGGTTAAAGCATTGTGAAATCGA 57.042 34.783 0.00 0.00 0.00 3.59
1557 1962 5.437289 AAAGCATTGTGAAATCGAAGACA 57.563 34.783 0.00 0.00 42.51 3.41
1563 1968 3.565516 TGTGAAATCGAAGACAGAGTCG 58.434 45.455 0.00 0.00 42.51 4.18
1571 1976 2.350484 CGAAGACAGAGTCGTGTGCTTA 60.350 50.000 0.71 0.00 37.67 3.09
1574 1979 3.409570 AGACAGAGTCGTGTGCTTAGTA 58.590 45.455 0.71 0.00 37.67 1.82
1576 1981 4.277672 AGACAGAGTCGTGTGCTTAGTAAA 59.722 41.667 0.71 0.00 37.67 2.01
1577 1982 4.296690 ACAGAGTCGTGTGCTTAGTAAAC 58.703 43.478 0.00 0.00 0.00 2.01
1583 1988 3.319972 TCGTGTGCTTAGTAAACTGGAGT 59.680 43.478 0.00 0.00 0.00 3.85
1589 1994 3.512680 CTTAGTAAACTGGAGTGGCTCG 58.487 50.000 0.00 0.00 0.00 5.03
1597 2009 1.066303 CTGGAGTGGCTCGTGACTATC 59.934 57.143 0.00 0.00 0.00 2.08
1600 2012 2.166664 GGAGTGGCTCGTGACTATCTTT 59.833 50.000 0.00 0.00 0.00 2.52
1605 2017 2.541556 GCTCGTGACTATCTTTGTCCC 58.458 52.381 0.00 0.00 33.83 4.46
1615 2027 2.879103 TCTTTGTCCCATGGTCCTTC 57.121 50.000 11.73 0.00 0.00 3.46
1616 2028 1.354368 TCTTTGTCCCATGGTCCTTCC 59.646 52.381 11.73 0.00 0.00 3.46
1617 2029 1.355720 CTTTGTCCCATGGTCCTTCCT 59.644 52.381 11.73 0.00 37.07 3.36
1618 2030 1.455822 TTGTCCCATGGTCCTTCCTT 58.544 50.000 11.73 0.00 37.07 3.36
1635 2047 3.866651 TCCTTGCAGATACTTCTCAAGC 58.133 45.455 0.00 0.00 36.65 4.01
1673 2085 2.041819 GAGACGGTGGGGATCCCT 60.042 66.667 30.08 10.28 45.70 4.20
1700 2112 4.475444 AGGGGCACGCCTAGGCTA 62.475 66.667 30.55 0.00 44.92 3.93
1732 2144 2.034879 CGTCGCAGGTGCTTTGGAT 61.035 57.895 0.00 0.00 39.32 3.41
1761 2173 3.429085 CGTTTGATGCTATTGCTGGTTC 58.571 45.455 0.00 0.00 40.48 3.62
1785 2197 4.122776 ACTAGCTCAGTGTTGTTGACAAG 58.877 43.478 0.00 0.00 40.65 3.16
1885 2297 2.618045 CCTTAAGGGGCACGAGATTGTT 60.618 50.000 14.25 0.00 0.00 2.83
1917 2329 1.197430 CCTCTCTCCCAGCAACCTGT 61.197 60.000 0.00 0.00 37.38 4.00
1964 2376 5.899299 AGATCATTGCAAATAAGCTGAACC 58.101 37.500 1.71 0.00 34.99 3.62
1984 2396 1.263217 CCGTGTTCTTTTCTGTTCCGG 59.737 52.381 0.00 0.00 0.00 5.14
2109 2521 0.767375 TCAAAGCAGTTCTGGAGGCT 59.233 50.000 1.97 0.00 38.45 4.58
2151 2563 2.382882 TGTTGAATTGGCAAGTCACCA 58.617 42.857 27.79 24.44 34.93 4.17
2156 2568 3.892633 TTGGCAAGTCACCAAGTCA 57.107 47.368 0.00 0.00 42.23 3.41
2159 2571 0.242017 GGCAAGTCACCAAGTCATGC 59.758 55.000 0.00 0.00 0.00 4.06
2406 2818 7.392113 AGGTACGATGTCAAAATATTCCAAACA 59.608 33.333 0.00 0.00 0.00 2.83
2460 2872 4.575236 GGCCTTGGTTTATGCTTACTACTC 59.425 45.833 0.00 0.00 0.00 2.59
2461 2873 4.575236 GCCTTGGTTTATGCTTACTACTCC 59.425 45.833 0.00 0.00 0.00 3.85
2462 2874 5.123936 CCTTGGTTTATGCTTACTACTCCC 58.876 45.833 0.00 0.00 0.00 4.30
2463 2875 5.104485 CCTTGGTTTATGCTTACTACTCCCT 60.104 44.000 0.00 0.00 0.00 4.20
2464 2876 5.609533 TGGTTTATGCTTACTACTCCCTC 57.390 43.478 0.00 0.00 0.00 4.30
2465 2877 4.407945 TGGTTTATGCTTACTACTCCCTCC 59.592 45.833 0.00 0.00 0.00 4.30
2466 2878 4.501058 GGTTTATGCTTACTACTCCCTCCG 60.501 50.000 0.00 0.00 0.00 4.63
2467 2879 2.456073 ATGCTTACTACTCCCTCCGT 57.544 50.000 0.00 0.00 0.00 4.69
2468 2880 1.760192 TGCTTACTACTCCCTCCGTC 58.240 55.000 0.00 0.00 0.00 4.79
2469 2881 1.031235 GCTTACTACTCCCTCCGTCC 58.969 60.000 0.00 0.00 0.00 4.79
2470 2882 1.689984 CTTACTACTCCCTCCGTCCC 58.310 60.000 0.00 0.00 0.00 4.46
2471 2883 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2472 2884 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
2473 2885 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2474 2886 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
2475 2887 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
2476 2888 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2477 2889 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2478 2890 2.026542 ACTCCCTCCGTCCCAAAATAAC 60.027 50.000 0.00 0.00 0.00 1.89
2479 2891 2.238898 CTCCCTCCGTCCCAAAATAACT 59.761 50.000 0.00 0.00 0.00 2.24
2480 2892 2.026636 TCCCTCCGTCCCAAAATAACTG 60.027 50.000 0.00 0.00 0.00 3.16
2481 2893 2.290705 CCCTCCGTCCCAAAATAACTGT 60.291 50.000 0.00 0.00 0.00 3.55
2482 2894 3.007635 CCTCCGTCCCAAAATAACTGTC 58.992 50.000 0.00 0.00 0.00 3.51
2483 2895 2.671396 CTCCGTCCCAAAATAACTGTCG 59.329 50.000 0.00 0.00 0.00 4.35
2484 2896 1.129811 CCGTCCCAAAATAACTGTCGC 59.870 52.381 0.00 0.00 0.00 5.19
2485 2897 2.073816 CGTCCCAAAATAACTGTCGCT 58.926 47.619 0.00 0.00 0.00 4.93
2486 2898 2.159707 CGTCCCAAAATAACTGTCGCTG 60.160 50.000 0.00 0.00 0.00 5.18
2487 2899 3.071479 GTCCCAAAATAACTGTCGCTGA 58.929 45.455 0.00 0.00 0.00 4.26
2488 2900 3.689649 GTCCCAAAATAACTGTCGCTGAT 59.310 43.478 0.00 0.00 0.00 2.90
2489 2901 4.156008 GTCCCAAAATAACTGTCGCTGATT 59.844 41.667 0.00 0.00 0.00 2.57
2490 2902 4.764823 TCCCAAAATAACTGTCGCTGATTT 59.235 37.500 0.00 0.00 0.00 2.17
2491 2903 5.941058 TCCCAAAATAACTGTCGCTGATTTA 59.059 36.000 0.00 0.00 0.00 1.40
2492 2904 6.093495 TCCCAAAATAACTGTCGCTGATTTAG 59.907 38.462 0.00 0.00 0.00 1.85
2493 2905 6.128007 CCCAAAATAACTGTCGCTGATTTAGT 60.128 38.462 0.00 0.00 0.00 2.24
2494 2906 7.065324 CCCAAAATAACTGTCGCTGATTTAGTA 59.935 37.037 0.00 0.00 0.00 1.82
2495 2907 7.903431 CCAAAATAACTGTCGCTGATTTAGTAC 59.097 37.037 0.00 0.00 0.00 2.73
2496 2908 8.440059 CAAAATAACTGTCGCTGATTTAGTACA 58.560 33.333 0.00 0.00 0.00 2.90
2497 2909 8.542497 AAATAACTGTCGCTGATTTAGTACAA 57.458 30.769 0.00 0.00 0.00 2.41
2498 2910 8.542497 AATAACTGTCGCTGATTTAGTACAAA 57.458 30.769 0.00 0.00 0.00 2.83
2499 2911 6.467723 AACTGTCGCTGATTTAGTACAAAG 57.532 37.500 0.00 0.00 0.00 2.77
2500 2912 4.389077 ACTGTCGCTGATTTAGTACAAAGC 59.611 41.667 0.00 0.00 0.00 3.51
2501 2913 4.566004 TGTCGCTGATTTAGTACAAAGCT 58.434 39.130 0.00 0.00 0.00 3.74
2502 2914 5.716094 TGTCGCTGATTTAGTACAAAGCTA 58.284 37.500 0.00 0.00 0.00 3.32
2503 2915 5.805486 TGTCGCTGATTTAGTACAAAGCTAG 59.195 40.000 0.00 0.00 0.00 3.42
2504 2916 5.805994 GTCGCTGATTTAGTACAAAGCTAGT 59.194 40.000 0.00 0.00 0.00 2.57
2505 2917 6.971184 GTCGCTGATTTAGTACAAAGCTAGTA 59.029 38.462 0.00 0.00 0.00 1.82
2506 2918 6.971184 TCGCTGATTTAGTACAAAGCTAGTAC 59.029 38.462 17.29 17.29 41.59 2.73
2507 2919 6.750501 CGCTGATTTAGTACAAAGCTAGTACA 59.249 38.462 23.49 11.97 43.24 2.90
2508 2920 7.274904 CGCTGATTTAGTACAAAGCTAGTACAA 59.725 37.037 23.49 14.39 43.24 2.41
2509 2921 8.381387 GCTGATTTAGTACAAAGCTAGTACAAC 58.619 37.037 23.49 13.55 43.24 3.32
2510 2922 9.640963 CTGATTTAGTACAAAGCTAGTACAACT 57.359 33.333 23.49 12.61 43.24 3.16
2511 2923 9.991906 TGATTTAGTACAAAGCTAGTACAACTT 57.008 29.630 23.49 11.03 43.24 2.66
2540 2952 8.464770 ACATCAATGACATTTATTTTTGGACG 57.535 30.769 0.00 0.00 0.00 4.79
2541 2953 7.545265 ACATCAATGACATTTATTTTTGGACGG 59.455 33.333 0.00 0.00 0.00 4.79
2542 2954 7.220741 TCAATGACATTTATTTTTGGACGGA 57.779 32.000 0.00 0.00 0.00 4.69
2543 2955 7.312154 TCAATGACATTTATTTTTGGACGGAG 58.688 34.615 0.00 0.00 0.00 4.63
2628 3040 2.054799 TGTCCAAACCCTGAGCTTAGT 58.945 47.619 4.63 0.00 0.00 2.24
2642 3054 6.706270 CCTGAGCTTAGTTGAAAGAAACTGTA 59.294 38.462 4.63 0.00 40.58 2.74
2693 3105 8.947055 AATTTGTTTTCTGACTATTTTGCTGT 57.053 26.923 0.00 0.00 0.00 4.40
2696 3108 9.677567 TTTGTTTTCTGACTATTTTGCTGTATC 57.322 29.630 0.00 0.00 0.00 2.24
2732 3144 0.609131 CCCCAAATCAGAGGTTGCGT 60.609 55.000 0.00 0.00 0.00 5.24
2753 3165 4.180057 GTGAAACAATTGTTCCAAGTGCA 58.820 39.130 23.47 3.24 37.25 4.57
2822 3234 2.027625 CGAAACTGGACGCAGGGTC 61.028 63.158 9.16 9.16 45.31 4.46
2837 3249 0.816373 GGGTCTCCTTCGAGTACACC 59.184 60.000 0.00 0.00 37.40 4.16
2840 3252 2.356535 GGTCTCCTTCGAGTACACCCTA 60.357 54.545 0.00 0.00 37.40 3.53
2851 3264 5.367937 TCGAGTACACCCTACTAGGTAATCT 59.632 44.000 1.25 0.00 38.39 2.40
2884 3297 7.520131 GCTTTCACACTGAATGATCCATCTATG 60.520 40.741 0.00 0.00 36.11 2.23
2888 3301 6.935208 CACACTGAATGATCCATCTATGTGAT 59.065 38.462 17.52 0.00 36.65 3.06
2899 3312 4.778579 CATCTATGTGATGGGGATGGATC 58.221 47.826 0.00 0.00 46.55 3.36
2902 3315 3.803186 ATGTGATGGGGATGGATCTTC 57.197 47.619 0.00 0.00 0.00 2.87
2906 3319 4.264307 TGTGATGGGGATGGATCTTCAAAA 60.264 41.667 0.00 0.00 0.00 2.44
2907 3320 4.897670 GTGATGGGGATGGATCTTCAAAAT 59.102 41.667 0.00 0.00 0.00 1.82
2917 3330 8.145767 GGATGGATCTTCAAAATTGCATTATGA 58.854 33.333 0.00 0.00 0.00 2.15
2931 3344 5.593968 TGCATTATGATTTCAGCCATTGTC 58.406 37.500 0.00 0.00 0.00 3.18
2936 3349 2.821378 TGATTTCAGCCATTGTCACCTG 59.179 45.455 0.00 0.00 0.00 4.00
2959 3372 6.680810 TGACATGATTGAACTGTTCCATTTC 58.319 36.000 17.26 14.73 0.00 2.17
2960 3373 6.029346 ACATGATTGAACTGTTCCATTTCC 57.971 37.500 17.26 2.20 0.00 3.13
3030 3444 2.050350 GCTGCATGCATGTGGAGGT 61.050 57.895 26.79 0.00 42.31 3.85
3112 3526 6.715464 CCTTACAGAAAAGCGGTATGTTATG 58.285 40.000 0.00 0.00 0.00 1.90
3331 3745 3.196469 AGAATCCTCTGCTTGAATCGTCA 59.804 43.478 0.00 0.00 0.00 4.35
3376 3790 1.748122 GGAGTCGTCTACGCCCTCA 60.748 63.158 17.66 0.00 41.93 3.86
3388 3802 2.730524 GCCCTCAGAGTCCAGCCTC 61.731 68.421 0.00 0.00 0.00 4.70
3452 3867 5.611796 TCGAGATTGTTGTGAATTTCTGG 57.388 39.130 0.00 0.00 0.00 3.86
3576 4007 1.620819 TGAGAGGCTCCTGTTCAGTTC 59.379 52.381 11.71 0.00 0.00 3.01
3616 4047 5.578336 TCTTTGAGATATGAAGTGTTCTGCG 59.422 40.000 0.00 0.00 0.00 5.18
3624 4055 3.787785 TGAAGTGTTCTGCGTGAAGTTA 58.212 40.909 0.00 0.00 35.01 2.24
3626 4057 2.755650 AGTGTTCTGCGTGAAGTTAGG 58.244 47.619 0.00 0.00 35.01 2.69
3638 4069 7.269316 TGCGTGAAGTTAGGATATGTATTTGA 58.731 34.615 0.00 0.00 0.00 2.69
3711 4143 6.380846 TGGTATTGAAGCTGCCAAATCTTATT 59.619 34.615 5.98 0.00 0.00 1.40
3718 4150 7.123997 TGAAGCTGCCAAATCTTATTCCATTAA 59.876 33.333 0.00 0.00 0.00 1.40
3852 4284 9.342308 TCTGTTCAAGTATGAAAGTTCTGAAAT 57.658 29.630 0.00 0.00 46.66 2.17
3929 4361 5.989168 TCTGTTTCTTTAGATCAAACGAGCA 59.011 36.000 0.00 0.00 33.48 4.26
3944 4376 1.701024 AGCATCCAGGCCCCCATTA 60.701 57.895 0.00 0.00 0.00 1.90
3948 4380 1.147608 CATCCAGGCCCCCATTATCAA 59.852 52.381 0.00 0.00 0.00 2.57
3961 4393 7.505923 GCCCCCATTATCAACTAAGAAAATAGT 59.494 37.037 0.00 0.00 37.73 2.12
3993 4428 7.928167 TCAGAAGACGAAGCAATAACATCATAT 59.072 33.333 0.00 0.00 0.00 1.78
3994 4429 8.008279 CAGAAGACGAAGCAATAACATCATATG 58.992 37.037 0.00 0.00 0.00 1.78
4022 4457 5.070446 CCAAGACATACTTCCTGCCTACATA 59.930 44.000 0.00 0.00 36.61 2.29
4027 4462 3.130734 ACTTCCTGCCTACATAAGGGA 57.869 47.619 0.00 0.00 46.65 4.20
4034 4469 4.564406 CCTGCCTACATAAGGGATGCTAAG 60.564 50.000 0.00 0.00 46.01 2.18
4038 4473 5.376625 CCTACATAAGGGATGCTAAGCAAA 58.623 41.667 0.00 0.00 41.32 3.68
4118 4553 4.172505 CTCTACAGAAGCATCACACACTC 58.827 47.826 0.00 0.00 0.00 3.51
4199 4634 6.639632 ACAGTGAAATCATGTAGCAAAGTT 57.360 33.333 0.00 0.00 0.00 2.66
4286 4721 2.140065 TCACTCGTCAGTTGAGCAAG 57.860 50.000 0.00 0.00 36.94 4.01
4337 4772 4.478206 TGCTATCCTCTTTTCTGTGGAG 57.522 45.455 0.00 0.00 33.79 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.594529 ATCACGTTTTAGCACGCAAG 57.405 45.000 0.00 0.00 44.37 4.01
6 7 2.570169 CACCAATCACGTTTTAGCACG 58.430 47.619 0.00 0.00 46.04 5.34
17 18 2.353011 CCCAATGTTGAGCACCAATCAC 60.353 50.000 0.00 0.00 37.08 3.06
36 37 4.543590 ATCACATCGATCTAATCACCCC 57.456 45.455 0.00 0.00 0.00 4.95
39 40 7.468922 TGTCAAATCACATCGATCTAATCAC 57.531 36.000 0.00 0.00 31.11 3.06
77 78 5.074746 TCATGGGTTAGCCTACTAGATCA 57.925 43.478 1.07 0.00 34.45 2.92
84 85 6.371825 GCTACATAAATCATGGGTTAGCCTAC 59.628 42.308 1.07 0.00 39.13 3.18
104 105 7.812191 GGTCACATTAACAATCAAAATGCTACA 59.188 33.333 0.00 0.00 34.63 2.74
154 155 8.948631 TTTGCAAAATCAATAAGTGTTTACCA 57.051 26.923 10.02 0.00 0.00 3.25
213 214 1.967319 ACCGCATCAACTGTTCAACT 58.033 45.000 0.00 0.00 0.00 3.16
305 306 6.647067 CCTAGTTTATCTCCTAAATTGGCTCG 59.353 42.308 0.00 0.00 32.12 5.03
308 309 5.179555 CGCCTAGTTTATCTCCTAAATTGGC 59.820 44.000 0.00 0.00 37.83 4.52
311 312 7.598759 TCTCGCCTAGTTTATCTCCTAAATT 57.401 36.000 0.00 0.00 32.12 1.82
328 329 1.334869 CTTTGTGTGCTTTTCTCGCCT 59.665 47.619 0.00 0.00 0.00 5.52
331 332 3.184379 TCGATCTTTGTGTGCTTTTCTCG 59.816 43.478 0.00 0.00 0.00 4.04
346 347 4.590647 TCCTCCTTCTAATGCATCGATCTT 59.409 41.667 0.00 0.00 0.00 2.40
347 348 4.155709 TCCTCCTTCTAATGCATCGATCT 58.844 43.478 0.00 0.00 0.00 2.75
348 349 4.527509 TCCTCCTTCTAATGCATCGATC 57.472 45.455 0.00 0.00 0.00 3.69
354 355 9.693739 TTATTTTATGTTCCTCCTTCTAATGCA 57.306 29.630 0.00 0.00 0.00 3.96
367 368 8.073467 TCCCCACTCATTTTATTTTATGTTCC 57.927 34.615 0.00 0.00 0.00 3.62
368 369 8.197439 CCTCCCCACTCATTTTATTTTATGTTC 58.803 37.037 0.00 0.00 0.00 3.18
369 370 7.898636 TCCTCCCCACTCATTTTATTTTATGTT 59.101 33.333 0.00 0.00 0.00 2.71
370 371 7.418378 TCCTCCCCACTCATTTTATTTTATGT 58.582 34.615 0.00 0.00 0.00 2.29
371 372 7.896383 TCCTCCCCACTCATTTTATTTTATG 57.104 36.000 0.00 0.00 0.00 1.90
422 423 2.675844 TGTTGTTGTGTCTCGGAGTTTG 59.324 45.455 4.69 0.00 0.00 2.93
424 425 2.277084 GTGTTGTTGTGTCTCGGAGTT 58.723 47.619 4.69 0.00 0.00 3.01
427 428 2.209273 CATGTGTTGTTGTGTCTCGGA 58.791 47.619 0.00 0.00 0.00 4.55
440 441 0.458543 CTAGCTCGTCCGCATGTGTT 60.459 55.000 5.38 0.00 0.00 3.32
460 461 5.827756 TCTAGTATCACATCGTGGGGATAT 58.172 41.667 4.76 0.00 33.87 1.63
472 473 7.239763 TGATTGTGTTTCCTCTAGTATCACA 57.760 36.000 0.00 0.00 33.53 3.58
485 486 4.530094 TGACACTCGTTGATTGTGTTTC 57.470 40.909 0.00 0.00 43.81 2.78
499 500 4.151867 GGAGTTTTACGGTCAATGACACTC 59.848 45.833 15.86 16.11 33.68 3.51
508 509 0.947180 GCTGCGGAGTTTTACGGTCA 60.947 55.000 5.62 0.00 0.00 4.02
523 524 0.179163 GTATCACGCCCTTTTGCTGC 60.179 55.000 0.00 0.00 0.00 5.25
525 526 1.453155 CAGTATCACGCCCTTTTGCT 58.547 50.000 0.00 0.00 0.00 3.91
531 532 1.134401 CATTGTCCAGTATCACGCCCT 60.134 52.381 0.00 0.00 0.00 5.19
535 536 2.621338 ACTGCATTGTCCAGTATCACG 58.379 47.619 0.00 0.00 41.47 4.35
543 544 0.735978 CTCGCGTACTGCATTGTCCA 60.736 55.000 5.77 0.00 46.97 4.02
559 560 1.153449 TGGCTTATTGGCGGTCTCG 60.153 57.895 0.00 0.00 45.14 4.04
612 613 2.655090 TGCCATTGAGTTGGACTTCA 57.345 45.000 0.00 0.00 39.25 3.02
644 645 5.419239 TTGACACAGTACATGGATGATGA 57.581 39.130 0.00 0.00 35.80 2.92
658 659 2.160615 TGTCGTTGGTTGTTTGACACAG 59.839 45.455 0.00 0.00 36.48 3.66
663 664 5.301555 TGAGATATGTCGTTGGTTGTTTGA 58.698 37.500 0.00 0.00 0.00 2.69
673 674 8.668510 AAGAATTAGCAATGAGATATGTCGTT 57.331 30.769 1.54 1.54 0.00 3.85
734 739 5.859495 TGTTGTGTTTTCTCCTTTTGGTTT 58.141 33.333 0.00 0.00 41.38 3.27
747 752 5.491982 TGTTTTAAGGCCATGTTGTGTTTT 58.508 33.333 5.01 0.00 0.00 2.43
751 756 4.511082 CCTTTGTTTTAAGGCCATGTTGTG 59.489 41.667 5.01 0.00 38.39 3.33
752 757 4.444164 CCCTTTGTTTTAAGGCCATGTTGT 60.444 41.667 5.01 0.00 42.79 3.32
753 758 4.064388 CCCTTTGTTTTAAGGCCATGTTG 58.936 43.478 5.01 0.00 42.79 3.33
755 760 3.313791 ACCCTTTGTTTTAAGGCCATGT 58.686 40.909 5.01 0.00 42.79 3.21
756 761 4.314961 GAACCCTTTGTTTTAAGGCCATG 58.685 43.478 5.01 0.00 42.79 3.66
757 762 3.006430 CGAACCCTTTGTTTTAAGGCCAT 59.994 43.478 5.01 0.00 42.79 4.40
758 763 2.362717 CGAACCCTTTGTTTTAAGGCCA 59.637 45.455 5.01 0.00 42.79 5.36
759 764 2.864882 GCGAACCCTTTGTTTTAAGGCC 60.865 50.000 0.00 0.00 42.79 5.19
785 790 3.058651 CGAACGCTCGGTAGTAAGTTTTC 59.941 47.826 0.00 0.00 41.57 2.29
801 806 0.921347 ACGATGTTGATAGCGAACGC 59.079 50.000 11.31 11.31 42.33 4.84
802 807 1.517276 GGACGATGTTGATAGCGAACG 59.483 52.381 0.00 0.00 33.07 3.95
803 808 1.859080 GGGACGATGTTGATAGCGAAC 59.141 52.381 0.00 0.00 33.07 3.95
804 809 1.478916 TGGGACGATGTTGATAGCGAA 59.521 47.619 0.00 0.00 33.07 4.70
805 810 1.107945 TGGGACGATGTTGATAGCGA 58.892 50.000 0.00 0.00 33.07 4.93
806 811 1.860950 CTTGGGACGATGTTGATAGCG 59.139 52.381 0.00 0.00 35.27 4.26
807 812 3.179443 TCTTGGGACGATGTTGATAGC 57.821 47.619 0.00 0.00 0.00 2.97
808 813 6.494893 TTTTTCTTGGGACGATGTTGATAG 57.505 37.500 0.00 0.00 0.00 2.08
833 838 7.557719 CCACATAAGATATGAGGAGGTGTTTTT 59.442 37.037 7.76 0.00 32.53 1.94
834 839 7.056635 CCACATAAGATATGAGGAGGTGTTTT 58.943 38.462 7.76 0.00 32.53 2.43
840 845 3.054802 GGCCCACATAAGATATGAGGAGG 60.055 52.174 13.34 5.75 32.53 4.30
841 846 3.368843 CGGCCCACATAAGATATGAGGAG 60.369 52.174 13.34 6.66 32.53 3.69
924 1125 1.296715 CTCCCCTTCAGGTGTTCGG 59.703 63.158 0.00 0.00 0.00 4.30
932 1133 0.547712 TCCACTTCCCTCCCCTTCAG 60.548 60.000 0.00 0.00 0.00 3.02
1152 1364 2.234908 CTCTGGTCTCTTGGTTACCTGG 59.765 54.545 2.07 0.00 34.14 4.45
1162 1374 3.394836 GGCGGGCTCTGGTCTCTT 61.395 66.667 0.00 0.00 0.00 2.85
1166 1378 4.344865 TTTGGGCGGGCTCTGGTC 62.345 66.667 0.26 0.00 0.00 4.02
1198 1410 1.636769 GCAGGGAAGGTAAGAGGGGG 61.637 65.000 0.00 0.00 0.00 5.40
1199 1411 1.915983 GCAGGGAAGGTAAGAGGGG 59.084 63.158 0.00 0.00 0.00 4.79
1200 1412 1.522569 CGCAGGGAAGGTAAGAGGG 59.477 63.158 0.00 0.00 0.00 4.30
1201 1413 1.153349 GCGCAGGGAAGGTAAGAGG 60.153 63.158 0.30 0.00 0.00 3.69
1202 1414 0.250513 AAGCGCAGGGAAGGTAAGAG 59.749 55.000 11.47 0.00 0.00 2.85
1215 1438 2.740826 GTGAGCCGGTAAAGCGCA 60.741 61.111 11.47 0.00 37.73 6.09
1248 1640 1.301637 TAGCTTTGCTGCGCAGACA 60.302 52.632 40.21 31.20 40.61 3.41
1273 1665 2.667536 AGGTCGTGCAGCTGCTTG 60.668 61.111 36.61 27.92 42.66 4.01
1359 1751 2.614229 GGCAAAACAACAAACAGGTGGT 60.614 45.455 0.00 0.00 40.07 4.16
1393 1785 4.803426 CCAGAGCGCGGTCAGGAC 62.803 72.222 37.24 14.55 0.00 3.85
1411 1803 1.083657 CTGCACGACGAACAAACGG 60.084 57.895 0.00 0.00 37.61 4.44
1412 1804 0.650476 CACTGCACGACGAACAAACG 60.650 55.000 0.00 0.00 39.31 3.60
1418 1810 3.776659 TTCGGCACTGCACGACGAA 62.777 57.895 16.16 16.16 40.69 3.85
1458 1850 3.969250 GACTTTCCATCCCGCGCCA 62.969 63.158 0.00 0.00 0.00 5.69
1531 1923 6.305638 GTCTTCGATTTCACAATGCTTTAACC 59.694 38.462 0.00 0.00 0.00 2.85
1535 1927 5.239306 TCTGTCTTCGATTTCACAATGCTTT 59.761 36.000 0.00 0.00 0.00 3.51
1537 1929 4.318332 TCTGTCTTCGATTTCACAATGCT 58.682 39.130 0.00 0.00 0.00 3.79
1548 1953 1.401670 GCACACGACTCTGTCTTCGAT 60.402 52.381 0.00 0.00 38.63 3.59
1551 1956 2.141535 AAGCACACGACTCTGTCTTC 57.858 50.000 0.00 0.00 0.00 2.87
1552 1957 2.623889 ACTAAGCACACGACTCTGTCTT 59.376 45.455 0.00 0.00 0.00 3.01
1557 1962 4.547532 CAGTTTACTAAGCACACGACTCT 58.452 43.478 0.00 0.00 0.00 3.24
1563 1968 3.746492 CCACTCCAGTTTACTAAGCACAC 59.254 47.826 0.00 0.00 0.00 3.82
1571 1976 1.000955 CACGAGCCACTCCAGTTTACT 59.999 52.381 0.00 0.00 0.00 2.24
1574 1979 0.249911 GTCACGAGCCACTCCAGTTT 60.250 55.000 0.00 0.00 0.00 2.66
1576 1981 0.251209 TAGTCACGAGCCACTCCAGT 60.251 55.000 0.00 0.00 0.00 4.00
1577 1982 1.066303 GATAGTCACGAGCCACTCCAG 59.934 57.143 0.00 0.00 0.00 3.86
1583 1988 2.094182 GGACAAAGATAGTCACGAGCCA 60.094 50.000 0.00 0.00 37.74 4.75
1597 2009 1.355720 AGGAAGGACCATGGGACAAAG 59.644 52.381 18.09 0.00 42.04 2.77
1600 2012 0.698238 CAAGGAAGGACCATGGGACA 59.302 55.000 18.09 0.00 42.04 4.02
1605 2017 2.431954 ATCTGCAAGGAAGGACCATG 57.568 50.000 0.00 0.00 42.04 3.66
1615 2027 3.622163 CAGCTTGAGAAGTATCTGCAAGG 59.378 47.826 0.00 0.00 39.10 3.61
1616 2028 3.622163 CCAGCTTGAGAAGTATCTGCAAG 59.378 47.826 0.00 0.00 40.25 4.01
1617 2029 3.261643 TCCAGCTTGAGAAGTATCTGCAA 59.738 43.478 0.00 0.00 35.54 4.08
1618 2030 2.833943 TCCAGCTTGAGAAGTATCTGCA 59.166 45.455 0.00 0.00 35.54 4.41
1635 2047 1.051812 ACCAGTCTGTTGTCCTCCAG 58.948 55.000 0.00 0.00 0.00 3.86
1673 2085 2.110213 GTGCCCCTGTCGTCAACA 59.890 61.111 0.00 0.00 36.18 3.33
1700 2112 2.241880 CGACGAAACACAGGCGGTT 61.242 57.895 0.00 0.00 0.00 4.44
1732 2144 2.173758 TAGCATCAAACGGCACCGGA 62.174 55.000 9.46 1.32 44.69 5.14
1761 2173 2.726760 GTCAACAACACTGAGCTAGTCG 59.273 50.000 0.00 0.00 37.60 4.18
1964 2376 1.263217 CCGGAACAGAAAAGAACACGG 59.737 52.381 0.00 0.00 0.00 4.94
1984 2396 1.334960 CGCCAGAACACCAATTCACAC 60.335 52.381 0.00 0.00 0.00 3.82
2088 2500 1.271054 GCCTCCAGAACTGCTTTGAGA 60.271 52.381 7.16 0.00 0.00 3.27
2151 2563 1.813513 CTCAAGGGAACGCATGACTT 58.186 50.000 0.00 0.00 0.00 3.01
2156 2568 0.392193 CTGAGCTCAAGGGAACGCAT 60.392 55.000 18.85 0.00 0.00 4.73
2159 2571 2.743636 TAACTGAGCTCAAGGGAACG 57.256 50.000 18.85 6.60 0.00 3.95
2406 2818 8.439971 TGTCTATTATTGATGCTAAGAACCCAT 58.560 33.333 0.00 0.00 0.00 4.00
2460 2872 2.290705 ACAGTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2461 2873 3.007635 GACAGTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2462 2874 2.671396 CGACAGTTATTTTGGGACGGAG 59.329 50.000 0.00 0.00 0.00 4.63
2463 2875 2.690786 CGACAGTTATTTTGGGACGGA 58.309 47.619 0.00 0.00 0.00 4.69
2464 2876 1.129811 GCGACAGTTATTTTGGGACGG 59.870 52.381 0.00 0.00 0.00 4.79
2465 2877 2.073816 AGCGACAGTTATTTTGGGACG 58.926 47.619 0.00 0.00 0.00 4.79
2466 2878 3.071479 TCAGCGACAGTTATTTTGGGAC 58.929 45.455 0.00 0.00 0.00 4.46
2467 2879 3.410631 TCAGCGACAGTTATTTTGGGA 57.589 42.857 0.00 0.00 0.00 4.37
2468 2880 4.701956 AATCAGCGACAGTTATTTTGGG 57.298 40.909 0.00 0.00 0.00 4.12
2469 2881 6.842163 ACTAAATCAGCGACAGTTATTTTGG 58.158 36.000 0.00 0.00 0.00 3.28
2470 2882 8.440059 TGTACTAAATCAGCGACAGTTATTTTG 58.560 33.333 0.00 0.00 0.00 2.44
2471 2883 8.542497 TGTACTAAATCAGCGACAGTTATTTT 57.458 30.769 0.00 0.00 0.00 1.82
2472 2884 8.542497 TTGTACTAAATCAGCGACAGTTATTT 57.458 30.769 0.00 0.00 0.00 1.40
2473 2885 8.542497 TTTGTACTAAATCAGCGACAGTTATT 57.458 30.769 0.00 0.00 0.00 1.40
2474 2886 7.201530 GCTTTGTACTAAATCAGCGACAGTTAT 60.202 37.037 0.00 0.00 0.00 1.89
2475 2887 6.090358 GCTTTGTACTAAATCAGCGACAGTTA 59.910 38.462 0.00 0.00 0.00 2.24
2476 2888 5.107065 GCTTTGTACTAAATCAGCGACAGTT 60.107 40.000 0.00 0.00 0.00 3.16
2477 2889 4.389077 GCTTTGTACTAAATCAGCGACAGT 59.611 41.667 0.00 0.00 0.00 3.55
2478 2890 4.627467 AGCTTTGTACTAAATCAGCGACAG 59.373 41.667 0.00 0.00 0.00 3.51
2479 2891 4.566004 AGCTTTGTACTAAATCAGCGACA 58.434 39.130 0.00 0.00 0.00 4.35
2480 2892 5.805994 ACTAGCTTTGTACTAAATCAGCGAC 59.194 40.000 0.00 0.00 0.00 5.19
2481 2893 5.962433 ACTAGCTTTGTACTAAATCAGCGA 58.038 37.500 0.00 0.00 0.00 4.93
2482 2894 6.750501 TGTACTAGCTTTGTACTAAATCAGCG 59.249 38.462 21.94 0.00 40.44 5.18
2483 2895 8.381387 GTTGTACTAGCTTTGTACTAAATCAGC 58.619 37.037 21.94 0.00 40.44 4.26
2484 2896 9.640963 AGTTGTACTAGCTTTGTACTAAATCAG 57.359 33.333 21.94 1.56 40.44 2.90
2485 2897 9.991906 AAGTTGTACTAGCTTTGTACTAAATCA 57.008 29.630 21.94 6.36 40.44 2.57
2514 2926 9.566530 CGTCCAAAAATAAATGTCATTGATGTA 57.433 29.630 0.00 0.00 0.00 2.29
2515 2927 7.545265 CCGTCCAAAAATAAATGTCATTGATGT 59.455 33.333 0.00 0.00 0.00 3.06
2516 2928 7.758980 TCCGTCCAAAAATAAATGTCATTGATG 59.241 33.333 0.00 0.00 0.00 3.07
2517 2929 7.835822 TCCGTCCAAAAATAAATGTCATTGAT 58.164 30.769 0.00 0.00 0.00 2.57
2518 2930 7.040062 ACTCCGTCCAAAAATAAATGTCATTGA 60.040 33.333 0.00 0.00 0.00 2.57
2519 2931 7.062138 CACTCCGTCCAAAAATAAATGTCATTG 59.938 37.037 0.00 0.00 0.00 2.82
2520 2932 7.040062 TCACTCCGTCCAAAAATAAATGTCATT 60.040 33.333 0.00 0.00 0.00 2.57
2521 2933 6.432783 TCACTCCGTCCAAAAATAAATGTCAT 59.567 34.615 0.00 0.00 0.00 3.06
2522 2934 5.765677 TCACTCCGTCCAAAAATAAATGTCA 59.234 36.000 0.00 0.00 0.00 3.58
2523 2935 6.072673 ACTCACTCCGTCCAAAAATAAATGTC 60.073 38.462 0.00 0.00 0.00 3.06
2524 2936 5.768164 ACTCACTCCGTCCAAAAATAAATGT 59.232 36.000 0.00 0.00 0.00 2.71
2525 2937 6.254281 ACTCACTCCGTCCAAAAATAAATG 57.746 37.500 0.00 0.00 0.00 2.32
2526 2938 7.166167 AGTACTCACTCCGTCCAAAAATAAAT 58.834 34.615 0.00 0.00 0.00 1.40
2527 2939 6.527423 AGTACTCACTCCGTCCAAAAATAAA 58.473 36.000 0.00 0.00 0.00 1.40
2528 2940 6.105397 AGTACTCACTCCGTCCAAAAATAA 57.895 37.500 0.00 0.00 0.00 1.40
2529 2941 5.733620 AGTACTCACTCCGTCCAAAAATA 57.266 39.130 0.00 0.00 0.00 1.40
2530 2942 4.618920 AGTACTCACTCCGTCCAAAAAT 57.381 40.909 0.00 0.00 0.00 1.82
2531 2943 4.411256 AAGTACTCACTCCGTCCAAAAA 57.589 40.909 0.00 0.00 32.29 1.94
2532 2944 4.341806 TGTAAGTACTCACTCCGTCCAAAA 59.658 41.667 0.00 0.00 32.29 2.44
2533 2945 3.890756 TGTAAGTACTCACTCCGTCCAAA 59.109 43.478 0.00 0.00 32.29 3.28
2534 2946 3.489355 TGTAAGTACTCACTCCGTCCAA 58.511 45.455 0.00 0.00 32.29 3.53
2535 2947 3.144657 TGTAAGTACTCACTCCGTCCA 57.855 47.619 0.00 0.00 32.29 4.02
2536 2948 4.510038 TTTGTAAGTACTCACTCCGTCC 57.490 45.455 0.00 0.00 32.29 4.79
2537 2949 5.527033 AGTTTTGTAAGTACTCACTCCGTC 58.473 41.667 0.00 0.00 32.29 4.79
2538 2950 5.068198 TGAGTTTTGTAAGTACTCACTCCGT 59.932 40.000 0.00 0.00 42.31 4.69
2539 2951 5.526115 TGAGTTTTGTAAGTACTCACTCCG 58.474 41.667 0.00 0.00 42.31 4.63
2651 3063 6.207691 ACAAATTATAGAAGCAAATGCCGT 57.792 33.333 0.94 0.00 43.38 5.68
2653 3065 9.154847 AGAAAACAAATTATAGAAGCAAATGCC 57.845 29.630 0.94 0.00 43.38 4.40
2693 3105 1.338105 GCATGCAGGCTGATACGGATA 60.338 52.381 20.86 0.00 0.00 2.59
2696 3108 2.256591 GGCATGCAGGCTGATACGG 61.257 63.158 24.04 3.18 40.24 4.02
2801 3213 1.289066 CCTGCGTCCAGTTTCGAGA 59.711 57.895 0.00 0.00 37.38 4.04
2822 3234 3.002038 AGTAGGGTGTACTCGAAGGAG 57.998 52.381 0.00 0.00 46.13 3.69
2837 3249 7.948034 AAGCATAGCTAGATTACCTAGTAGG 57.052 40.000 15.09 15.09 45.26 3.18
2840 3252 7.287927 TGTGAAAGCATAGCTAGATTACCTAGT 59.712 37.037 0.00 0.00 45.26 2.57
2851 3264 5.733676 TCATTCAGTGTGAAAGCATAGCTA 58.266 37.500 0.00 0.00 40.12 3.32
2853 3266 4.952262 TCATTCAGTGTGAAAGCATAGC 57.048 40.909 0.00 0.00 40.12 2.97
2859 3272 7.498239 ACATAGATGGATCATTCAGTGTGAAAG 59.502 37.037 0.00 0.00 40.12 2.62
2860 3273 7.281549 CACATAGATGGATCATTCAGTGTGAAA 59.718 37.037 17.46 0.00 40.12 2.69
2884 3297 3.582998 TTGAAGATCCATCCCCATCAC 57.417 47.619 0.00 0.00 0.00 3.06
2888 3301 3.451902 GCAATTTTGAAGATCCATCCCCA 59.548 43.478 0.00 0.00 0.00 4.96
2889 3302 3.451902 TGCAATTTTGAAGATCCATCCCC 59.548 43.478 0.00 0.00 0.00 4.81
2891 3304 8.145767 TCATAATGCAATTTTGAAGATCCATCC 58.854 33.333 0.00 0.00 40.49 3.51
2899 3312 8.120465 GGCTGAAATCATAATGCAATTTTGAAG 58.880 33.333 0.00 0.00 45.09 3.02
2902 3315 7.310072 TGGCTGAAATCATAATGCAATTTTG 57.690 32.000 0.00 0.00 37.87 2.44
2906 3319 6.588204 ACAATGGCTGAAATCATAATGCAAT 58.412 32.000 0.00 0.00 0.00 3.56
2907 3320 5.979993 ACAATGGCTGAAATCATAATGCAA 58.020 33.333 0.00 0.00 0.00 4.08
2917 3330 2.821969 GTCAGGTGACAATGGCTGAAAT 59.178 45.455 5.21 0.00 44.18 2.17
2931 3344 4.083110 GGAACAGTTCAATCATGTCAGGTG 60.083 45.833 15.36 0.00 0.00 4.00
2960 3373 4.362470 TCATCATTAATCCCAGCTGAGG 57.638 45.455 17.39 15.01 0.00 3.86
2976 3390 0.592637 CAGCGTGTGCCTTTTCATCA 59.407 50.000 0.00 0.00 44.31 3.07
3030 3444 3.973206 ATCAGGTTCACGTGATAACCA 57.027 42.857 31.23 18.06 46.03 3.67
3112 3526 5.163652 GGCATTGTGACTAAAACTGGGATAC 60.164 44.000 0.00 0.00 0.00 2.24
3331 3745 2.121963 TTGGGCTCAGAGGGTGGT 60.122 61.111 0.00 0.00 0.00 4.16
3376 3790 1.077625 AGGAACGAGGCTGGACTCT 59.922 57.895 2.65 0.00 35.33 3.24
3452 3867 3.440522 GGGCCTGTGTGAACTTTAGAATC 59.559 47.826 0.84 0.00 0.00 2.52
3548 3963 1.216710 GGAGCCTCTCACACCGAAG 59.783 63.158 0.00 0.00 31.08 3.79
3690 4121 5.422970 TGGAATAAGATTTGGCAGCTTCAAT 59.577 36.000 0.00 0.00 0.00 2.57
3718 4150 9.872684 AGGATGGTTATATTGAAATTCAGACAT 57.127 29.630 0.00 0.00 0.00 3.06
3929 4361 1.147817 GTTGATAATGGGGGCCTGGAT 59.852 52.381 0.84 0.00 0.00 3.41
3961 4393 4.955925 TTGCTTCGTCTTCTGAAAAACA 57.044 36.364 0.00 0.00 0.00 2.83
3964 4396 6.612247 TGTTATTGCTTCGTCTTCTGAAAA 57.388 33.333 0.00 0.00 0.00 2.29
3968 4400 5.784750 TGATGTTATTGCTTCGTCTTCTG 57.215 39.130 0.00 0.00 0.00 3.02
3969 4401 7.307632 GCATATGATGTTATTGCTTCGTCTTCT 60.308 37.037 6.97 0.00 0.00 2.85
3970 4402 6.794158 GCATATGATGTTATTGCTTCGTCTTC 59.206 38.462 6.97 0.00 0.00 2.87
3993 4428 0.623723 GGAAGTATGTCTTGGGGGCA 59.376 55.000 0.00 0.00 36.40 5.36
3994 4429 0.919710 AGGAAGTATGTCTTGGGGGC 59.080 55.000 0.00 0.00 36.40 5.80
4022 4457 5.539955 TCTTTCTTTTTGCTTAGCATCCCTT 59.460 36.000 8.05 0.00 38.76 3.95
4027 4462 7.720442 AGTTTCTCTTTCTTTTTGCTTAGCAT 58.280 30.769 8.05 0.00 38.76 3.79
4038 4473 8.500238 TCCCCTAGTTAAAGTTTCTCTTTCTTT 58.500 33.333 0.00 0.00 44.18 2.52
4118 4553 4.098044 TCTCTTATCGCAGTTTAGTCCAGG 59.902 45.833 0.00 0.00 0.00 4.45
4162 4597 7.424803 TGATTTCACTGTTTCCTGTTTACATG 58.575 34.615 0.00 0.00 0.00 3.21
4170 4605 5.181811 TGCTACATGATTTCACTGTTTCCTG 59.818 40.000 0.00 0.00 0.00 3.86
4199 4634 4.072131 GCCTACCAGTGAAGTGATTTTGA 58.928 43.478 0.00 0.00 0.00 2.69
4286 4721 3.779759 CTGCTCATGGTGTCTAGAAGAC 58.220 50.000 0.00 0.01 45.26 3.01
4337 4772 1.066858 TCTGCTGGATTCGTGGACTTC 60.067 52.381 0.00 0.00 0.00 3.01
4345 4780 5.111989 TCTTTATGTTCTCTGCTGGATTCG 58.888 41.667 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.