Multiple sequence alignment - TraesCS2D01G404100

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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 TraesCS2D01G404100 chr2D 100.000 3365 0 0 1 3365 518609785 518606421 0.000000e+00 6215.0
1 TraesCS2D01G404100 chr2B 92.593 2214 111 32 464 2651 610917836 610915650 0.000000e+00 3131.0
2 TraesCS2D01G404100 chr2B 89.097 587 38 12 2653 3223 610915199 610914623 0.000000e+00 706.0
3 TraesCS2D01G404100 chr2A 90.882 1338 76 23 1344 2651 662893734 662892413 0.000000e+00 1753.0
4 TraesCS2D01G404100 chr2A 89.932 884 55 20 466 1325 662894589 662893716 0.000000e+00 1109.0
5 TraesCS2D01G404100 chr2A 92.807 570 29 6 2653 3216 662892046 662891483 0.000000e+00 815.0
6 TraesCS2D01G404100 chr7B 96.471 85 3 0 3222 3306 213252051 213251967 1.260000e-29 141.0
7 TraesCS2D01G404100 chr7B 91.753 97 8 0 3221 3317 315581229 315581325 5.860000e-28 135.0
8 TraesCS2D01G404100 chr7B 86.726 113 14 1 3221 3332 672601985 672602097 1.270000e-24 124.0
9 TraesCS2D01G404100 chr7A 92.553 94 7 0 3222 3315 657720221 657720314 5.860000e-28 135.0
10 TraesCS2D01G404100 chr5B 94.444 90 2 3 3221 3308 442754472 442754384 5.860000e-28 135.0
11 TraesCS2D01G404100 chr5B 91.753 97 6 2 3221 3315 556628709 556628613 2.110000e-27 134.0
12 TraesCS2D01G404100 chr1D 92.553 94 6 1 3222 3314 407351179 407351086 2.110000e-27 134.0
13 TraesCS2D01G404100 chr4D 87.611 113 13 1 3221 3332 71301685 71301573 2.720000e-26 130.0
14 TraesCS2D01G404100 chr4D 93.182 88 6 0 3221 3308 230661477 230661390 2.720000e-26 130.0
15 TraesCS2D01G404100 chrUn 85.185 54 6 1 2978 3031 178188126 178188177 2.000000e-03 54.7


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 TraesCS2D01G404100 chr2D 518606421 518609785 3364 True 6215.000000 6215 100.000 1 3365 1 chr2D.!!$R1 3364
1 TraesCS2D01G404100 chr2B 610914623 610917836 3213 True 1918.500000 3131 90.845 464 3223 2 chr2B.!!$R1 2759
2 TraesCS2D01G404100 chr2A 662891483 662894589 3106 True 1225.666667 1753 91.207 466 3216 3 chr2A.!!$R1 2750

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
692 701 0.027979 CTTGTGTGACGCCACTTGTG 59.972 55.0 2.85 0.0 43.55 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2414 2476 0.178992 ACCACACACCAATCACCAGG 60.179 55.0 0.0 0.0 0.0 4.45 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
33 34 8.981647 ACACATTTGACATTTCTTTTCTAATGC 58.018 29.630 0.00 0.00 36.52 3.56
34 35 9.199982 CACATTTGACATTTCTTTTCTAATGCT 57.800 29.630 0.00 0.00 36.52 3.79
35 36 9.768662 ACATTTGACATTTCTTTTCTAATGCTT 57.231 25.926 0.00 0.00 36.52 3.91
37 38 9.985730 ATTTGACATTTCTTTTCTAATGCTTGA 57.014 25.926 0.00 0.00 35.63 3.02
38 39 9.985730 TTTGACATTTCTTTTCTAATGCTTGAT 57.014 25.926 0.00 0.00 35.63 2.57
39 40 9.985730 TTGACATTTCTTTTCTAATGCTTGATT 57.014 25.926 0.00 0.00 35.63 2.57
395 396 4.473477 AAAACTAGAATAGCGAGGCTGT 57.527 40.909 0.00 0.00 44.39 4.40
396 397 3.444703 AACTAGAATAGCGAGGCTGTG 57.555 47.619 0.00 0.00 44.39 3.66
397 398 1.683917 ACTAGAATAGCGAGGCTGTGG 59.316 52.381 0.00 0.00 44.39 4.17
398 399 0.389391 TAGAATAGCGAGGCTGTGGC 59.611 55.000 0.00 0.00 40.10 5.01
432 433 4.962836 CCGGCCCATCTCATGCCC 62.963 72.222 0.00 0.00 42.29 5.36
436 437 4.193893 CCCATCTCATGCCCGCCA 62.194 66.667 0.00 0.00 0.00 5.69
437 438 2.593725 CCATCTCATGCCCGCCAG 60.594 66.667 0.00 0.00 0.00 4.85
438 439 2.507452 CATCTCATGCCCGCCAGA 59.493 61.111 0.00 0.00 0.00 3.86
439 440 1.153107 CATCTCATGCCCGCCAGAA 60.153 57.895 0.00 0.00 0.00 3.02
440 441 1.147824 ATCTCATGCCCGCCAGAAG 59.852 57.895 0.00 0.00 0.00 2.85
441 442 2.955022 ATCTCATGCCCGCCAGAAGC 62.955 60.000 0.00 0.00 38.52 3.86
451 452 3.202923 GCCAGAAGCGAGGTATAGC 57.797 57.895 0.00 0.00 0.00 2.97
452 453 0.319986 GCCAGAAGCGAGGTATAGCC 60.320 60.000 0.00 0.00 37.58 3.93
453 454 0.039074 CCAGAAGCGAGGTATAGCCG 60.039 60.000 0.00 3.58 43.70 5.52
458 459 2.338984 CGAGGTATAGCCGCACCC 59.661 66.667 0.00 0.00 43.70 4.61
459 460 2.741747 GAGGTATAGCCGCACCCC 59.258 66.667 0.00 0.00 43.70 4.95
460 461 2.847715 AGGTATAGCCGCACCCCC 60.848 66.667 0.00 0.00 43.70 5.40
461 462 3.165685 GGTATAGCCGCACCCCCA 61.166 66.667 0.00 0.00 0.00 4.96
462 463 2.110420 GTATAGCCGCACCCCCAC 59.890 66.667 0.00 0.00 0.00 4.61
536 540 4.039245 CACCAAAGAGAGAGACACCAGTTA 59.961 45.833 0.00 0.00 0.00 2.24
537 541 4.841246 ACCAAAGAGAGAGACACCAGTTAT 59.159 41.667 0.00 0.00 0.00 1.89
644 653 0.033796 AGAAGGGGCATGTGATGTGG 60.034 55.000 0.00 0.00 0.00 4.17
692 701 0.027979 CTTGTGTGACGCCACTTGTG 59.972 55.000 2.85 0.00 43.55 3.33
735 744 7.039644 TCCATTTAACCAATTACAAATGACGGT 60.040 33.333 7.31 0.00 39.59 4.83
797 806 1.032014 TTCTTTGCCACAAGCCTCAC 58.968 50.000 0.00 0.00 42.71 3.51
798 807 0.106769 TCTTTGCCACAAGCCTCACA 60.107 50.000 0.00 0.00 42.71 3.58
804 813 1.537202 GCCACAAGCCTCACAAAGTAG 59.463 52.381 0.00 0.00 34.35 2.57
812 821 4.518249 AGCCTCACAAAGTAGCTTTATCC 58.482 43.478 0.00 0.00 31.96 2.59
817 826 4.534500 TCACAAAGTAGCTTTATCCTCCCA 59.466 41.667 0.00 0.00 31.96 4.37
850 859 6.092748 CACATTAGTTTACAAGGCATTGACC 58.907 40.000 19.41 2.25 38.83 4.02
942 956 4.178169 ACGCAACGGGACCCAACA 62.178 61.111 12.15 0.00 0.00 3.33
943 957 3.353836 CGCAACGGGACCCAACAG 61.354 66.667 12.15 0.00 0.00 3.16
945 959 2.983592 CAACGGGACCCAACAGCC 60.984 66.667 12.15 0.00 0.00 4.85
946 960 4.280019 AACGGGACCCAACAGCCC 62.280 66.667 12.15 0.00 38.53 5.19
948 962 4.722700 CGGGACCCAACAGCCCAG 62.723 72.222 12.15 0.00 42.14 4.45
950 964 3.971702 GGACCCAACAGCCCAGCT 61.972 66.667 0.00 0.00 40.77 4.24
1020 1035 0.693049 AGACTAGGTTTGCCCCAGTG 59.307 55.000 0.00 0.00 32.55 3.66
1109 1124 0.319641 GTCGTCTCAACACTCCACCC 60.320 60.000 0.00 0.00 0.00 4.61
1264 1294 1.377994 CAGAGCCAAGGCCAAGACT 59.622 57.895 5.01 0.00 43.17 3.24
1363 1393 3.674528 TCTCCTTGTCAGCTGAAGAAG 57.325 47.619 20.19 21.35 0.00 2.85
1379 1409 4.752101 TGAAGAAGACTACAAAAGCTCTGC 59.248 41.667 0.00 0.00 0.00 4.26
1392 1422 5.370875 AAAGCTCTGCTATCTCATTTCCT 57.629 39.130 0.00 0.00 38.25 3.36
1418 1452 2.359900 ACGATCATGAAACTTCTGGCC 58.640 47.619 0.00 0.00 0.00 5.36
1433 1467 5.010415 ACTTCTGGCCTTGATTTTGAAAGAG 59.990 40.000 3.32 0.00 0.00 2.85
1435 1469 4.520492 TCTGGCCTTGATTTTGAAAGAGAC 59.480 41.667 3.32 0.00 0.00 3.36
1437 1471 4.895297 TGGCCTTGATTTTGAAAGAGACTT 59.105 37.500 3.32 0.00 0.00 3.01
1440 1474 7.069331 TGGCCTTGATTTTGAAAGAGACTTTAA 59.931 33.333 3.32 0.00 0.00 1.52
1449 1483 8.776680 TTTGAAAGAGACTTTAATTAACACGC 57.223 30.769 0.00 0.00 0.00 5.34
1466 1500 2.549754 CACGCTTTTGGAGTGACTGATT 59.450 45.455 0.00 0.00 46.30 2.57
1525 1559 5.178996 CGAGCAAATGATAAGGGAGATTCTG 59.821 44.000 0.00 0.00 0.00 3.02
1540 1574 0.614979 TTCTGGAGGAGGGGAACGAG 60.615 60.000 0.00 0.00 0.00 4.18
1543 1577 2.363361 GAGGAGGGGAACGAGGGA 59.637 66.667 0.00 0.00 0.00 4.20
1557 1591 0.107459 GAGGGAGACAAGGGCATCAC 60.107 60.000 0.00 0.00 0.00 3.06
1559 1593 1.685224 GGAGACAAGGGCATCACCA 59.315 57.895 0.00 0.00 42.05 4.17
1561 1595 1.457346 GAGACAAGGGCATCACCAAG 58.543 55.000 0.00 0.00 42.05 3.61
1565 1599 0.890683 CAAGGGCATCACCAAGAACC 59.109 55.000 0.00 0.00 42.05 3.62
1572 1606 2.159517 GCATCACCAAGAACCGAATGAC 60.160 50.000 0.00 0.00 0.00 3.06
1629 1663 1.338674 TGGGATCAAGCACTGGTAACG 60.339 52.381 0.00 0.00 42.51 3.18
1641 1680 3.736252 CACTGGTAACGTCTTCTCACAAG 59.264 47.826 0.00 0.00 42.51 3.16
1642 1681 3.635373 ACTGGTAACGTCTTCTCACAAGA 59.365 43.478 0.00 0.00 42.51 3.02
1643 1682 4.230657 CTGGTAACGTCTTCTCACAAGAG 58.769 47.826 0.00 0.00 41.27 2.85
1644 1683 3.887110 TGGTAACGTCTTCTCACAAGAGA 59.113 43.478 0.00 0.00 45.19 3.10
1705 1747 8.893727 TCCTTTTTCTCTTCTGAAAAGTACTTG 58.106 33.333 9.34 0.00 43.79 3.16
1712 1754 3.754965 TCTGAAAAGTACTTGCAGCCAT 58.245 40.909 23.82 1.75 0.00 4.40
1713 1755 4.144297 TCTGAAAAGTACTTGCAGCCATT 58.856 39.130 23.82 9.26 0.00 3.16
1814 1860 0.478072 AGTTGGATGCCCTGTCACAA 59.522 50.000 0.00 0.00 0.00 3.33
1865 1914 0.727398 GGCCAAGAAGCATACGACAC 59.273 55.000 0.00 0.00 0.00 3.67
1894 1943 5.336929 GGTGGAAAATAAAAGGCATTACGGT 60.337 40.000 0.00 0.00 0.00 4.83
1905 1954 3.067106 GGCATTACGGTCCATACTCATG 58.933 50.000 0.00 0.00 0.00 3.07
2004 2056 5.451520 GGAGAAGCTTCTTAGTGCCGTATTA 60.452 44.000 29.02 0.00 37.73 0.98
2005 2057 5.974108 AGAAGCTTCTTAGTGCCGTATTAA 58.026 37.500 23.49 0.00 32.55 1.40
2006 2058 6.403878 AGAAGCTTCTTAGTGCCGTATTAAA 58.596 36.000 23.49 0.00 32.55 1.52
2007 2059 7.048512 AGAAGCTTCTTAGTGCCGTATTAAAT 58.951 34.615 23.49 0.00 32.55 1.40
2008 2060 7.553044 AGAAGCTTCTTAGTGCCGTATTAAATT 59.447 33.333 23.49 0.00 32.55 1.82
2148 2204 1.339055 TGGATGACAAGGGAAGAAGCG 60.339 52.381 0.00 0.00 0.00 4.68
2201 2257 1.289066 CCTCAAAGTCCGCTCGTCA 59.711 57.895 0.00 0.00 0.00 4.35
2318 2376 6.183360 TGTGACAAGGACGGAATAATTTATGC 60.183 38.462 0.00 0.00 0.00 3.14
2349 2407 5.679734 AGTTTGTCTGAATGCTGTACTTG 57.320 39.130 0.00 0.00 0.00 3.16
2414 2476 7.949962 GCGTCAATTTTTATCTTACTTTTTGGC 59.050 33.333 0.00 0.00 0.00 4.52
2569 2640 9.791801 ATAAAATTAAATATCCAACAATGCCCC 57.208 29.630 0.00 0.00 0.00 5.80
2596 2668 5.236263 GCAACAAGGTTTCCACTTAATTTGG 59.764 40.000 0.00 0.00 35.18 3.28
2663 3184 1.535462 GCGCATGAGTTTTGGTGTACT 59.465 47.619 0.30 0.00 0.00 2.73
2664 3185 2.739913 GCGCATGAGTTTTGGTGTACTA 59.260 45.455 0.30 0.00 0.00 1.82
2749 3270 4.715792 AGGATAGATATGATGTCCAGCCAG 59.284 45.833 0.00 0.00 0.00 4.85
2823 3348 0.179000 CTCAATCTCAACCTCCCCGG 59.821 60.000 0.00 0.00 39.35 5.73
2830 3355 1.217244 CAACCTCCCCGGACTTACG 59.783 63.158 0.73 0.00 36.31 3.18
2852 3378 6.273071 ACGGAAATGCTGCCTTAATTTATTC 58.727 36.000 0.00 0.00 0.00 1.75
2894 3420 2.152016 GCACCTTAAGTCCAACCTGAC 58.848 52.381 0.97 0.00 35.43 3.51
2919 3445 5.413833 ACTGCATCCAATGAAACAGAGTAAG 59.586 40.000 0.00 0.00 33.77 2.34
2936 3470 7.015682 ACAGAGTAAGTTCTTGGAGATTGAAGA 59.984 37.037 0.00 0.00 0.00 2.87
3054 3594 8.543774 GCACACAGTATATCATCTAAACAAGAC 58.456 37.037 0.00 0.00 36.93 3.01
3065 3605 5.888691 TCTAAACAAGACACAAACAAGCA 57.111 34.783 0.00 0.00 0.00 3.91
3085 3625 6.336842 AGCAAAAAGTCTGAAATGCATAGT 57.663 33.333 0.00 0.00 36.30 2.12
3134 3676 3.618690 ACTCAGTGCTCCTAACCAATC 57.381 47.619 0.00 0.00 0.00 2.67
3136 3678 3.327757 ACTCAGTGCTCCTAACCAATCAA 59.672 43.478 0.00 0.00 0.00 2.57
3223 3765 7.488187 TTAGTCAGTATCAGGTATCACGTAC 57.512 40.000 0.00 0.00 0.00 3.67
3224 3766 5.682659 AGTCAGTATCAGGTATCACGTACT 58.317 41.667 0.00 0.00 33.64 2.73
3225 3767 5.759273 AGTCAGTATCAGGTATCACGTACTC 59.241 44.000 0.00 0.00 33.64 2.59
3226 3768 5.049543 GTCAGTATCAGGTATCACGTACTCC 60.050 48.000 0.00 0.00 33.64 3.85
3227 3769 4.215827 CAGTATCAGGTATCACGTACTCCC 59.784 50.000 0.00 0.00 33.64 4.30
3228 3770 3.596940 ATCAGGTATCACGTACTCCCT 57.403 47.619 0.00 0.00 33.64 4.20
3229 3771 2.928334 TCAGGTATCACGTACTCCCTC 58.072 52.381 0.00 0.00 33.64 4.30
3230 3772 1.955080 CAGGTATCACGTACTCCCTCC 59.045 57.143 0.00 0.00 33.64 4.30
3231 3773 0.950116 GGTATCACGTACTCCCTCCG 59.050 60.000 0.00 0.00 33.64 4.63
3232 3774 1.673168 GTATCACGTACTCCCTCCGT 58.327 55.000 0.00 0.00 34.71 4.69
3233 3775 2.019984 GTATCACGTACTCCCTCCGTT 58.980 52.381 0.00 0.00 31.46 4.44
3234 3776 1.101331 ATCACGTACTCCCTCCGTTC 58.899 55.000 0.00 0.00 31.46 3.95
3235 3777 0.962356 TCACGTACTCCCTCCGTTCC 60.962 60.000 0.00 0.00 31.46 3.62
3236 3778 1.075482 ACGTACTCCCTCCGTTCCA 59.925 57.895 0.00 0.00 0.00 3.53
3237 3779 0.540365 ACGTACTCCCTCCGTTCCAA 60.540 55.000 0.00 0.00 0.00 3.53
3238 3780 0.604578 CGTACTCCCTCCGTTCCAAA 59.395 55.000 0.00 0.00 0.00 3.28
3239 3781 1.001181 CGTACTCCCTCCGTTCCAAAA 59.999 52.381 0.00 0.00 0.00 2.44
3240 3782 2.354403 CGTACTCCCTCCGTTCCAAAAT 60.354 50.000 0.00 0.00 0.00 1.82
3241 3783 3.119029 CGTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
3242 3784 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3243 3785 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3244 3786 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3245 3787 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3246 3788 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
3247 3789 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3248 3790 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
3249 3791 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
3250 3792 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
3251 3793 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
3252 3794 6.414732 TCCGTTCCAAAATAGATGACTCAAT 58.585 36.000 0.00 0.00 0.00 2.57
3253 3795 6.884295 TCCGTTCCAAAATAGATGACTCAATT 59.116 34.615 0.00 0.00 0.00 2.32
3254 3796 7.393234 TCCGTTCCAAAATAGATGACTCAATTT 59.607 33.333 0.00 0.00 0.00 1.82
3255 3797 8.028938 CCGTTCCAAAATAGATGACTCAATTTT 58.971 33.333 0.00 0.00 33.07 1.82
3256 3798 8.853345 CGTTCCAAAATAGATGACTCAATTTTG 58.147 33.333 15.00 15.00 43.77 2.44
3257 3799 9.696917 GTTCCAAAATAGATGACTCAATTTTGT 57.303 29.630 18.01 0.00 43.14 2.83
3279 3821 7.894376 TGTACAAAGTTAGATTAAAGTCGGG 57.106 36.000 0.00 0.00 0.00 5.14
3280 3822 7.444299 TGTACAAAGTTAGATTAAAGTCGGGT 58.556 34.615 0.00 0.00 0.00 5.28
3281 3823 7.599998 TGTACAAAGTTAGATTAAAGTCGGGTC 59.400 37.037 0.00 0.00 0.00 4.46
3282 3824 6.527423 ACAAAGTTAGATTAAAGTCGGGTCA 58.473 36.000 0.00 0.00 0.00 4.02
3283 3825 7.166167 ACAAAGTTAGATTAAAGTCGGGTCAT 58.834 34.615 0.00 0.00 0.00 3.06
3284 3826 7.333672 ACAAAGTTAGATTAAAGTCGGGTCATC 59.666 37.037 0.00 0.00 0.00 2.92
3285 3827 6.793505 AGTTAGATTAAAGTCGGGTCATCT 57.206 37.500 0.00 0.00 0.00 2.90
3286 3828 7.893124 AGTTAGATTAAAGTCGGGTCATCTA 57.107 36.000 0.00 0.00 0.00 1.98
3287 3829 8.480133 AGTTAGATTAAAGTCGGGTCATCTAT 57.520 34.615 0.00 0.00 0.00 1.98
3288 3830 8.925338 AGTTAGATTAAAGTCGGGTCATCTATT 58.075 33.333 0.00 0.00 0.00 1.73
3289 3831 9.543783 GTTAGATTAAAGTCGGGTCATCTATTT 57.456 33.333 0.00 0.00 0.00 1.40
3291 3833 8.438676 AGATTAAAGTCGGGTCATCTATTTTG 57.561 34.615 0.00 0.00 0.00 2.44
3292 3834 6.995511 TTAAAGTCGGGTCATCTATTTTGG 57.004 37.500 0.00 0.00 0.00 3.28
3293 3835 4.837093 AAGTCGGGTCATCTATTTTGGA 57.163 40.909 0.00 0.00 0.00 3.53
3294 3836 4.837093 AGTCGGGTCATCTATTTTGGAA 57.163 40.909 0.00 0.00 0.00 3.53
3295 3837 4.514401 AGTCGGGTCATCTATTTTGGAAC 58.486 43.478 0.00 0.00 0.00 3.62
3296 3838 3.308866 GTCGGGTCATCTATTTTGGAACG 59.691 47.826 0.00 0.00 0.00 3.95
3297 3839 2.612212 CGGGTCATCTATTTTGGAACGG 59.388 50.000 0.00 0.00 0.00 4.44
3298 3840 3.680475 CGGGTCATCTATTTTGGAACGGA 60.680 47.826 0.00 0.00 0.00 4.69
3299 3841 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
3300 3842 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
3301 3843 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3302 3844 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
3303 3845 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
3304 3846 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
3305 3847 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
3306 3848 4.778958 TCTATTTTGGAACGGAGGGAGTAA 59.221 41.667 0.00 0.00 0.00 2.24
3307 3849 4.586306 ATTTTGGAACGGAGGGAGTAAT 57.414 40.909 0.00 0.00 0.00 1.89
3308 3850 5.703730 ATTTTGGAACGGAGGGAGTAATA 57.296 39.130 0.00 0.00 0.00 0.98
3309 3851 5.502089 TTTTGGAACGGAGGGAGTAATAA 57.498 39.130 0.00 0.00 0.00 1.40
3310 3852 5.703730 TTTGGAACGGAGGGAGTAATAAT 57.296 39.130 0.00 0.00 0.00 1.28
3311 3853 5.703730 TTGGAACGGAGGGAGTAATAATT 57.296 39.130 0.00 0.00 0.00 1.40
3312 3854 6.811634 TTGGAACGGAGGGAGTAATAATTA 57.188 37.500 0.00 0.00 0.00 1.40
3313 3855 6.165700 TGGAACGGAGGGAGTAATAATTAC 57.834 41.667 0.00 0.00 36.38 1.89
3314 3856 5.070847 TGGAACGGAGGGAGTAATAATTACC 59.929 44.000 0.00 0.00 36.81 2.85
3315 3857 5.306419 GGAACGGAGGGAGTAATAATTACCT 59.694 44.000 0.00 0.00 36.81 3.08
3316 3858 5.803237 ACGGAGGGAGTAATAATTACCTG 57.197 43.478 0.00 0.00 36.81 4.00
3317 3859 4.040095 ACGGAGGGAGTAATAATTACCTGC 59.960 45.833 0.00 0.00 36.81 4.85
3318 3860 4.039973 CGGAGGGAGTAATAATTACCTGCA 59.960 45.833 8.95 0.00 36.40 4.41
3319 3861 5.552178 GGAGGGAGTAATAATTACCTGCAG 58.448 45.833 6.78 6.78 36.59 4.41
3320 3862 5.513267 GGAGGGAGTAATAATTACCTGCAGG 60.513 48.000 31.60 31.60 36.59 4.85
3321 3863 5.224441 AGGGAGTAATAATTACCTGCAGGA 58.776 41.667 39.19 18.86 36.81 3.86
3322 3864 5.852250 AGGGAGTAATAATTACCTGCAGGAT 59.148 40.000 39.19 24.04 36.81 3.24
3323 3865 6.332901 AGGGAGTAATAATTACCTGCAGGATT 59.667 38.462 39.19 28.35 36.81 3.01
3324 3866 6.431234 GGGAGTAATAATTACCTGCAGGATTG 59.569 42.308 39.19 13.22 36.81 2.67
3325 3867 6.072452 GGAGTAATAATTACCTGCAGGATTGC 60.072 42.308 39.19 27.06 42.64 3.56
3326 3868 6.605119 AGTAATAATTACCTGCAGGATTGCT 58.395 36.000 39.19 28.65 42.71 3.91
3327 3869 6.488006 AGTAATAATTACCTGCAGGATTGCTG 59.512 38.462 39.19 11.20 45.65 4.41
3336 3878 3.760580 GCAGGATTGCTGGAGTATACT 57.239 47.619 4.68 4.68 46.95 2.12
3337 3879 4.873746 GCAGGATTGCTGGAGTATACTA 57.126 45.455 5.09 0.00 46.95 1.82
3338 3880 4.561105 GCAGGATTGCTGGAGTATACTAC 58.439 47.826 8.29 8.29 46.95 2.73
3339 3881 4.282195 GCAGGATTGCTGGAGTATACTACT 59.718 45.833 16.20 0.00 46.95 2.57
3340 3882 5.477291 GCAGGATTGCTGGAGTATACTACTA 59.523 44.000 16.20 2.32 46.95 1.82
3341 3883 6.349777 GCAGGATTGCTGGAGTATACTACTAG 60.350 46.154 16.20 12.15 46.95 2.57
3342 3884 6.717540 CAGGATTGCTGGAGTATACTACTAGT 59.282 42.308 16.20 0.00 39.59 2.57
3343 3885 7.231722 CAGGATTGCTGGAGTATACTACTAGTT 59.768 40.741 16.20 0.00 39.59 2.24
3344 3886 7.231722 AGGATTGCTGGAGTATACTACTAGTTG 59.768 40.741 16.20 0.59 39.59 3.16
3345 3887 6.710597 TTGCTGGAGTATACTACTAGTTGG 57.289 41.667 16.20 0.00 39.59 3.77
3346 3888 6.009908 TGCTGGAGTATACTACTAGTTGGA 57.990 41.667 16.20 0.00 39.59 3.53
3347 3889 6.062749 TGCTGGAGTATACTACTAGTTGGAG 58.937 44.000 16.20 4.54 39.59 3.86
3348 3890 6.126565 TGCTGGAGTATACTACTAGTTGGAGA 60.127 42.308 16.20 0.00 39.59 3.71
3349 3891 6.943718 GCTGGAGTATACTACTAGTTGGAGAT 59.056 42.308 16.20 0.00 39.59 2.75
3350 3892 8.102047 GCTGGAGTATACTACTAGTTGGAGATA 58.898 40.741 16.20 0.00 39.59 1.98
3351 3893 9.439500 CTGGAGTATACTACTAGTTGGAGATAC 57.561 40.741 16.20 8.99 39.59 2.24
3352 3894 9.168553 TGGAGTATACTACTAGTTGGAGATACT 57.831 37.037 16.20 19.08 39.59 2.12
3359 3901 8.508883 ACTACTAGTTGGAGATACTACAAGTG 57.491 38.462 12.60 6.80 38.32 3.16
3360 3902 6.210287 ACTAGTTGGAGATACTACAAGTGC 57.790 41.667 12.60 0.00 38.32 4.40
3361 3903 5.715279 ACTAGTTGGAGATACTACAAGTGCA 59.285 40.000 12.60 0.00 38.32 4.57
3362 3904 5.078411 AGTTGGAGATACTACAAGTGCAG 57.922 43.478 3.61 0.00 36.68 4.41
3363 3905 4.528596 AGTTGGAGATACTACAAGTGCAGT 59.471 41.667 3.61 0.00 36.68 4.40
3364 3906 5.715279 AGTTGGAGATACTACAAGTGCAGTA 59.285 40.000 0.00 0.00 36.68 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.981647 GCATTAGAAAAGAAATGTCAAATGTGT 58.018 29.630 0.00 0.00 35.86 3.72
8 9 9.199982 AGCATTAGAAAAGAAATGTCAAATGTG 57.800 29.630 0.00 0.00 35.86 3.21
9 10 9.768662 AAGCATTAGAAAAGAAATGTCAAATGT 57.231 25.926 0.00 0.00 35.86 2.71
11 12 9.985730 TCAAGCATTAGAAAAGAAATGTCAAAT 57.014 25.926 0.00 0.00 35.86 2.32
12 13 9.985730 ATCAAGCATTAGAAAAGAAATGTCAAA 57.014 25.926 0.00 0.00 35.86 2.69
13 14 9.985730 AATCAAGCATTAGAAAAGAAATGTCAA 57.014 25.926 0.00 0.00 35.86 3.18
373 374 4.631813 CACAGCCTCGCTATTCTAGTTTTT 59.368 41.667 0.00 0.00 36.40 1.94
374 375 4.184629 CACAGCCTCGCTATTCTAGTTTT 58.815 43.478 0.00 0.00 36.40 2.43
375 376 3.430929 CCACAGCCTCGCTATTCTAGTTT 60.431 47.826 0.00 0.00 36.40 2.66
376 377 2.101582 CCACAGCCTCGCTATTCTAGTT 59.898 50.000 0.00 0.00 36.40 2.24
377 378 1.683917 CCACAGCCTCGCTATTCTAGT 59.316 52.381 0.00 0.00 36.40 2.57
378 379 1.604185 GCCACAGCCTCGCTATTCTAG 60.604 57.143 0.00 0.00 36.40 2.43
379 380 0.389391 GCCACAGCCTCGCTATTCTA 59.611 55.000 0.00 0.00 36.40 2.10
380 381 1.144936 GCCACAGCCTCGCTATTCT 59.855 57.895 0.00 0.00 36.40 2.40
381 382 3.724494 GCCACAGCCTCGCTATTC 58.276 61.111 0.00 0.00 36.40 1.75
419 420 4.193893 TGGCGGGCATGAGATGGG 62.194 66.667 0.00 0.00 0.00 4.00
420 421 2.593725 CTGGCGGGCATGAGATGG 60.594 66.667 4.16 0.00 0.00 3.51
421 422 1.153107 TTCTGGCGGGCATGAGATG 60.153 57.895 4.16 0.00 0.00 2.90
422 423 1.147824 CTTCTGGCGGGCATGAGAT 59.852 57.895 4.16 0.00 0.00 2.75
423 424 2.586245 CTTCTGGCGGGCATGAGA 59.414 61.111 4.16 0.00 0.00 3.27
424 425 3.207669 GCTTCTGGCGGGCATGAG 61.208 66.667 4.16 7.29 0.00 2.90
433 434 0.319986 GGCTATACCTCGCTTCTGGC 60.320 60.000 0.00 0.00 34.51 4.85
434 435 0.039074 CGGCTATACCTCGCTTCTGG 60.039 60.000 0.00 0.00 35.61 3.86
435 436 0.664767 GCGGCTATACCTCGCTTCTG 60.665 60.000 0.00 0.00 45.16 3.02
436 437 1.660917 GCGGCTATACCTCGCTTCT 59.339 57.895 0.00 0.00 45.16 2.85
437 438 4.246727 GCGGCTATACCTCGCTTC 57.753 61.111 0.00 0.00 45.16 3.86
441 442 2.338984 GGGTGCGGCTATACCTCG 59.661 66.667 7.76 0.00 37.15 4.63
442 443 2.741747 GGGGTGCGGCTATACCTC 59.258 66.667 7.76 0.18 37.15 3.85
443 444 2.847715 GGGGGTGCGGCTATACCT 60.848 66.667 7.76 0.00 37.15 3.08
444 445 3.165685 TGGGGGTGCGGCTATACC 61.166 66.667 0.00 0.00 36.21 2.73
445 446 2.110420 GTGGGGGTGCGGCTATAC 59.890 66.667 0.00 0.00 0.00 1.47
446 447 1.563577 TTTGTGGGGGTGCGGCTATA 61.564 55.000 0.00 0.00 0.00 1.31
447 448 2.433646 TTTTGTGGGGGTGCGGCTAT 62.434 55.000 0.00 0.00 0.00 2.97
448 449 3.134703 TTTTGTGGGGGTGCGGCTA 62.135 57.895 0.00 0.00 0.00 3.93
449 450 4.531426 TTTTGTGGGGGTGCGGCT 62.531 61.111 0.00 0.00 0.00 5.52
450 451 4.293648 GTTTTGTGGGGGTGCGGC 62.294 66.667 0.00 0.00 0.00 6.53
451 452 2.520741 AGTTTTGTGGGGGTGCGG 60.521 61.111 0.00 0.00 0.00 5.69
452 453 2.561037 GGAGTTTTGTGGGGGTGCG 61.561 63.158 0.00 0.00 0.00 5.34
453 454 2.207229 GGGAGTTTTGTGGGGGTGC 61.207 63.158 0.00 0.00 0.00 5.01
454 455 1.533033 GGGGAGTTTTGTGGGGGTG 60.533 63.158 0.00 0.00 0.00 4.61
455 456 1.301160 AAGGGGAGTTTTGTGGGGGT 61.301 55.000 0.00 0.00 0.00 4.95
456 457 0.541998 GAAGGGGAGTTTTGTGGGGG 60.542 60.000 0.00 0.00 0.00 5.40
457 458 0.541998 GGAAGGGGAGTTTTGTGGGG 60.542 60.000 0.00 0.00 0.00 4.96
458 459 0.541998 GGGAAGGGGAGTTTTGTGGG 60.542 60.000 0.00 0.00 0.00 4.61
459 460 0.482887 AGGGAAGGGGAGTTTTGTGG 59.517 55.000 0.00 0.00 0.00 4.17
460 461 3.518992 TTAGGGAAGGGGAGTTTTGTG 57.481 47.619 0.00 0.00 0.00 3.33
461 462 4.546224 TTTTAGGGAAGGGGAGTTTTGT 57.454 40.909 0.00 0.00 0.00 2.83
487 490 1.040646 AGACTTGCAGGAGTTCGTCA 58.959 50.000 1.40 0.00 0.00 4.35
488 491 1.795286 CAAGACTTGCAGGAGTTCGTC 59.205 52.381 1.40 0.00 0.00 4.20
622 631 0.458669 CATCACATGCCCCTTCTTGC 59.541 55.000 0.00 0.00 0.00 4.01
692 701 8.560374 GTTAAATGGAGCTGGTAATCTTGATAC 58.440 37.037 0.00 0.00 0.00 2.24
735 744 2.229543 GTGCCAACAAGCAAGATGATCA 59.770 45.455 0.00 0.00 46.19 2.92
797 806 5.501156 AGTTGGGAGGATAAAGCTACTTTG 58.499 41.667 2.88 0.00 35.21 2.77
798 807 5.780958 AGTTGGGAGGATAAAGCTACTTT 57.219 39.130 0.00 0.00 37.46 2.66
817 826 6.462347 CCTTGTAAACTAATGTGGCCAAAGTT 60.462 38.462 7.24 12.51 34.25 2.66
942 956 1.308216 ATAGGTTGGGAGCTGGGCT 60.308 57.895 0.00 0.00 43.88 5.19
943 957 1.149401 GATAGGTTGGGAGCTGGGC 59.851 63.158 0.00 0.00 34.88 5.36
945 959 2.441001 AGAATGATAGGTTGGGAGCTGG 59.559 50.000 0.00 0.00 34.88 4.85
946 960 3.135348 TGAGAATGATAGGTTGGGAGCTG 59.865 47.826 0.00 0.00 34.88 4.24
947 961 3.135530 GTGAGAATGATAGGTTGGGAGCT 59.864 47.826 0.00 0.00 37.40 4.09
948 962 3.118261 TGTGAGAATGATAGGTTGGGAGC 60.118 47.826 0.00 0.00 0.00 4.70
949 963 4.760530 TGTGAGAATGATAGGTTGGGAG 57.239 45.455 0.00 0.00 0.00 4.30
950 964 4.103153 GGATGTGAGAATGATAGGTTGGGA 59.897 45.833 0.00 0.00 0.00 4.37
1084 1099 1.609555 GAGTGTTGAGACGACTGAGGT 59.390 52.381 0.00 0.00 0.00 3.85
1109 1124 3.068873 CGTCCCTCCTATTCTTCTTCCTG 59.931 52.174 0.00 0.00 0.00 3.86
1121 1136 2.037144 GATTTGGTAGCGTCCCTCCTA 58.963 52.381 0.00 0.00 0.00 2.94
1255 1285 0.687354 TGACCTTGAGAGTCTTGGCC 59.313 55.000 0.00 0.00 35.21 5.36
1264 1294 1.194781 GCAGGGGTCTGACCTTGAGA 61.195 60.000 25.01 0.00 43.49 3.27
1363 1393 5.655488 TGAGATAGCAGAGCTTTTGTAGTC 58.345 41.667 0.00 0.00 40.44 2.59
1379 1409 7.652727 TGATCGTAACAGAGGAAATGAGATAG 58.347 38.462 0.00 0.00 0.00 2.08
1392 1422 5.869344 CCAGAAGTTTCATGATCGTAACAGA 59.131 40.000 9.94 0.00 0.00 3.41
1433 1467 7.112984 CACTCCAAAAGCGTGTTAATTAAAGTC 59.887 37.037 0.00 0.00 0.00 3.01
1435 1469 7.112984 GTCACTCCAAAAGCGTGTTAATTAAAG 59.887 37.037 0.00 0.00 32.79 1.85
1437 1471 6.261381 AGTCACTCCAAAAGCGTGTTAATTAA 59.739 34.615 0.00 0.00 32.79 1.40
1440 1474 4.024048 CAGTCACTCCAAAAGCGTGTTAAT 60.024 41.667 0.00 0.00 32.79 1.40
1525 1559 2.764547 CCCTCGTTCCCCTCCTCC 60.765 72.222 0.00 0.00 0.00 4.30
1540 1574 1.077429 GGTGATGCCCTTGTCTCCC 60.077 63.158 0.00 0.00 0.00 4.30
1543 1577 1.067295 TCTTGGTGATGCCCTTGTCT 58.933 50.000 0.00 0.00 36.04 3.41
1565 1599 1.068474 GAAGGTGTCACCGTCATTCG 58.932 55.000 27.13 0.00 44.59 3.34
1572 1606 1.669115 CTGCTGGAAGGTGTCACCG 60.669 63.158 16.44 2.97 44.90 4.94
1577 1611 2.883828 CGACCCTGCTGGAAGGTGT 61.884 63.158 11.88 0.00 35.34 4.16
1580 1614 4.785453 GGCGACCCTGCTGGAAGG 62.785 72.222 11.88 0.00 38.00 3.46
1600 1634 1.230324 GCTTGATCCCAATCCGTAGC 58.770 55.000 0.00 0.00 0.00 3.58
1601 1635 2.158900 AGTGCTTGATCCCAATCCGTAG 60.159 50.000 0.00 0.00 0.00 3.51
1641 1680 6.036626 GCTAGAATTGCTACAGGAAAGTTCTC 59.963 42.308 0.00 0.00 0.00 2.87
1642 1681 5.877564 GCTAGAATTGCTACAGGAAAGTTCT 59.122 40.000 0.00 5.17 0.00 3.01
1643 1682 5.643777 TGCTAGAATTGCTACAGGAAAGTTC 59.356 40.000 0.00 0.00 0.00 3.01
1644 1683 5.412904 GTGCTAGAATTGCTACAGGAAAGTT 59.587 40.000 0.00 0.00 0.00 2.66
1645 1684 4.938226 GTGCTAGAATTGCTACAGGAAAGT 59.062 41.667 0.00 0.00 0.00 2.66
1814 1860 3.532896 CTGGTACGGCATTGTGAGT 57.467 52.632 0.00 0.00 0.00 3.41
1865 1914 3.323403 TGCCTTTTATTTTCCACCACCTG 59.677 43.478 0.00 0.00 0.00 4.00
1917 1966 8.575454 CAGAAATAAATTTTTGCTAGCGTGTAC 58.425 33.333 10.77 0.00 0.00 2.90
2004 2056 8.617809 CACATGTACTACCGCCTAATTAAATTT 58.382 33.333 0.00 0.00 0.00 1.82
2005 2057 7.227910 CCACATGTACTACCGCCTAATTAAATT 59.772 37.037 0.00 0.00 0.00 1.82
2006 2058 6.708949 CCACATGTACTACCGCCTAATTAAAT 59.291 38.462 0.00 0.00 0.00 1.40
2007 2059 6.050432 CCACATGTACTACCGCCTAATTAAA 58.950 40.000 0.00 0.00 0.00 1.52
2008 2060 5.363292 TCCACATGTACTACCGCCTAATTAA 59.637 40.000 0.00 0.00 0.00 1.40
2162 2218 3.681897 GGCATCTGTCTTGCGGAATATAG 59.318 47.826 0.00 0.00 41.07 1.31
2201 2257 6.600882 AAGATGACAAATGAAGCAGGAATT 57.399 33.333 0.00 0.00 0.00 2.17
2318 2376 7.095060 ACAGCATTCAGACAAACTTATACACAG 60.095 37.037 0.00 0.00 0.00 3.66
2349 2407 6.370718 ACACGGTCTTCCACTTAATTTGATAC 59.629 38.462 0.00 0.00 0.00 2.24
2414 2476 0.178992 ACCACACACCAATCACCAGG 60.179 55.000 0.00 0.00 0.00 4.45
2452 2523 4.279169 ACTGTCAGCACATGCAATACTTTT 59.721 37.500 6.64 0.00 45.16 2.27
2569 2640 1.308998 AGTGGAAACCTTGTTGCTCG 58.691 50.000 0.00 0.00 0.00 5.03
2596 2668 2.033194 GCACCGCCACTCCACTTAC 61.033 63.158 0.00 0.00 0.00 2.34
2644 2716 3.994392 ACTAGTACACCAAAACTCATGCG 59.006 43.478 0.00 0.00 0.00 4.73
2651 2723 5.178809 CACCTTGCTACTAGTACACCAAAAC 59.821 44.000 0.00 0.00 0.00 2.43
2708 3229 3.941629 TCCTAAGTAGATCATGCCCCTT 58.058 45.455 0.00 0.00 0.00 3.95
2709 3230 3.637821 TCCTAAGTAGATCATGCCCCT 57.362 47.619 0.00 0.00 0.00 4.79
2749 3270 6.496338 AAACAATCTAATGTTCTTCCGGTC 57.504 37.500 0.00 0.00 42.49 4.79
2823 3348 1.739067 AGGCAGCATTTCCGTAAGTC 58.261 50.000 0.00 0.00 0.00 3.01
2830 3355 5.991606 GGGAATAAATTAAGGCAGCATTTCC 59.008 40.000 0.00 0.00 0.00 3.13
2894 3420 3.504906 ACTCTGTTTCATTGGATGCAGTG 59.495 43.478 3.15 3.15 31.32 3.66
2919 3445 6.867662 TCTGTTTCTTCAATCTCCAAGAAC 57.132 37.500 0.00 0.00 38.16 3.01
2936 3470 9.974980 TTAGTTTCTTCTTTGTTTGTTCTGTTT 57.025 25.926 0.00 0.00 0.00 2.83
2968 3502 0.965439 GGCTGCTCAGACGATCCTAT 59.035 55.000 0.00 0.00 0.00 2.57
2976 3510 2.977772 AACTATCTGGCTGCTCAGAC 57.022 50.000 18.65 0.00 45.27 3.51
3054 3594 6.464895 TTTCAGACTTTTTGCTTGTTTGTG 57.535 33.333 0.00 0.00 0.00 3.33
3065 3605 8.624776 GGCTATACTATGCATTTCAGACTTTTT 58.375 33.333 3.54 0.00 0.00 1.94
3104 3646 5.746990 AGGAGCACTGAGTATTTAACTGT 57.253 39.130 0.00 0.00 39.07 3.55
3134 3676 9.547753 AACACCTACTAAGAGTAATATGCATTG 57.452 33.333 3.54 0.00 29.00 2.82
3136 3678 8.368668 GGAACACCTACTAAGAGTAATATGCAT 58.631 37.037 3.79 3.79 29.00 3.96
3152 3694 5.300792 TCACCATTTCTTTTGGAACACCTAC 59.699 40.000 0.00 0.00 39.29 3.18
3156 3698 4.502645 CGTTCACCATTTCTTTTGGAACAC 59.497 41.667 0.00 0.00 39.29 3.32
3209 3751 2.422519 GGAGGGAGTACGTGATACCTGA 60.423 54.545 10.16 0.00 33.85 3.86
3223 3765 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
3224 3766 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
3225 3767 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3226 3768 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
3227 3769 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
3228 3770 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
3229 3771 6.683974 ATTGAGTCATCTATTTTGGAACGG 57.316 37.500 0.00 0.00 0.00 4.44
3230 3772 8.970691 AAAATTGAGTCATCTATTTTGGAACG 57.029 30.769 11.47 0.00 44.08 3.95
3253 3795 8.776470 CCCGACTTTAATCTAACTTTGTACAAA 58.224 33.333 19.53 19.53 0.00 2.83
3254 3796 7.933033 ACCCGACTTTAATCTAACTTTGTACAA 59.067 33.333 3.59 3.59 0.00 2.41
3255 3797 7.444299 ACCCGACTTTAATCTAACTTTGTACA 58.556 34.615 0.00 0.00 0.00 2.90
3256 3798 7.599998 TGACCCGACTTTAATCTAACTTTGTAC 59.400 37.037 0.00 0.00 0.00 2.90
3257 3799 7.669427 TGACCCGACTTTAATCTAACTTTGTA 58.331 34.615 0.00 0.00 0.00 2.41
3258 3800 6.527423 TGACCCGACTTTAATCTAACTTTGT 58.473 36.000 0.00 0.00 0.00 2.83
3259 3801 7.549488 AGATGACCCGACTTTAATCTAACTTTG 59.451 37.037 0.00 0.00 0.00 2.77
3260 3802 7.621796 AGATGACCCGACTTTAATCTAACTTT 58.378 34.615 0.00 0.00 0.00 2.66
3261 3803 7.184067 AGATGACCCGACTTTAATCTAACTT 57.816 36.000 0.00 0.00 0.00 2.66
3262 3804 6.793505 AGATGACCCGACTTTAATCTAACT 57.206 37.500 0.00 0.00 0.00 2.24
3263 3805 9.543783 AAATAGATGACCCGACTTTAATCTAAC 57.456 33.333 0.00 0.00 32.15 2.34
3265 3807 9.542462 CAAAATAGATGACCCGACTTTAATCTA 57.458 33.333 0.00 0.00 32.74 1.98
3266 3808 7.499232 CCAAAATAGATGACCCGACTTTAATCT 59.501 37.037 0.00 0.00 0.00 2.40
3267 3809 7.497909 TCCAAAATAGATGACCCGACTTTAATC 59.502 37.037 0.00 0.00 0.00 1.75
3268 3810 7.343357 TCCAAAATAGATGACCCGACTTTAAT 58.657 34.615 0.00 0.00 0.00 1.40
3269 3811 6.713276 TCCAAAATAGATGACCCGACTTTAA 58.287 36.000 0.00 0.00 0.00 1.52
3270 3812 6.302535 TCCAAAATAGATGACCCGACTTTA 57.697 37.500 0.00 0.00 0.00 1.85
3271 3813 5.174037 TCCAAAATAGATGACCCGACTTT 57.826 39.130 0.00 0.00 0.00 2.66
3272 3814 4.837093 TCCAAAATAGATGACCCGACTT 57.163 40.909 0.00 0.00 0.00 3.01
3273 3815 4.514401 GTTCCAAAATAGATGACCCGACT 58.486 43.478 0.00 0.00 0.00 4.18
3274 3816 3.308866 CGTTCCAAAATAGATGACCCGAC 59.691 47.826 0.00 0.00 0.00 4.79
3275 3817 3.527533 CGTTCCAAAATAGATGACCCGA 58.472 45.455 0.00 0.00 0.00 5.14
3276 3818 2.612212 CCGTTCCAAAATAGATGACCCG 59.388 50.000 0.00 0.00 0.00 5.28
3277 3819 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
3278 3820 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
3279 3821 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3280 3822 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
3281 3823 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3282 3824 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3283 3825 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3284 3826 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3285 3827 5.703730 ATTACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
3286 3828 4.586306 ATTACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
3287 3829 5.502089 TTATTACTCCCTCCGTTCCAAAA 57.498 39.130 0.00 0.00 0.00 2.44
3288 3830 5.703730 ATTATTACTCCCTCCGTTCCAAA 57.296 39.130 0.00 0.00 0.00 3.28
3289 3831 5.703730 AATTATTACTCCCTCCGTTCCAA 57.296 39.130 0.00 0.00 0.00 3.53
3290 3832 5.070847 GGTAATTATTACTCCCTCCGTTCCA 59.929 44.000 13.86 0.00 36.39 3.53
3291 3833 5.306419 AGGTAATTATTACTCCCTCCGTTCC 59.694 44.000 13.86 0.00 36.39 3.62
3292 3834 6.221659 CAGGTAATTATTACTCCCTCCGTTC 58.778 44.000 13.86 0.00 36.39 3.95
3293 3835 5.454329 GCAGGTAATTATTACTCCCTCCGTT 60.454 44.000 13.86 0.00 36.39 4.44
3294 3836 4.040095 GCAGGTAATTATTACTCCCTCCGT 59.960 45.833 13.86 0.00 36.39 4.69
3295 3837 4.039973 TGCAGGTAATTATTACTCCCTCCG 59.960 45.833 13.86 0.00 36.39 4.63
3296 3838 5.513267 CCTGCAGGTAATTATTACTCCCTCC 60.513 48.000 25.53 0.00 36.39 4.30
3297 3839 5.307196 TCCTGCAGGTAATTATTACTCCCTC 59.693 44.000 31.58 0.00 36.39 4.30
3298 3840 5.224441 TCCTGCAGGTAATTATTACTCCCT 58.776 41.667 31.58 1.56 36.39 4.20
3299 3841 5.562298 TCCTGCAGGTAATTATTACTCCC 57.438 43.478 31.58 0.00 36.39 4.30
3300 3842 7.440523 CAATCCTGCAGGTAATTATTACTCC 57.559 40.000 31.58 0.00 36.39 3.85
3314 3856 5.795139 GTAGTATACTCCAGCAATCCTGCAG 60.795 48.000 9.12 6.78 44.44 4.41
3315 3857 4.039245 GTAGTATACTCCAGCAATCCTGCA 59.961 45.833 9.12 0.00 44.44 4.41
3316 3858 4.561105 GTAGTATACTCCAGCAATCCTGC 58.439 47.826 9.12 0.00 43.24 4.85
3333 3875 9.610705 CACTTGTAGTATCTCCAACTAGTAGTA 57.389 37.037 2.50 0.00 30.26 1.82
3334 3876 7.067251 GCACTTGTAGTATCTCCAACTAGTAGT 59.933 40.741 0.00 0.00 30.26 2.73
3335 3877 7.067129 TGCACTTGTAGTATCTCCAACTAGTAG 59.933 40.741 0.00 0.00 30.26 2.57
3336 3878 6.888088 TGCACTTGTAGTATCTCCAACTAGTA 59.112 38.462 0.00 0.00 30.26 1.82
3337 3879 5.715279 TGCACTTGTAGTATCTCCAACTAGT 59.285 40.000 0.00 0.00 30.26 2.57
3338 3880 6.127591 ACTGCACTTGTAGTATCTCCAACTAG 60.128 42.308 0.00 0.00 39.21 2.57
3339 3881 5.715279 ACTGCACTTGTAGTATCTCCAACTA 59.285 40.000 0.00 0.00 39.21 2.24
3340 3882 4.528596 ACTGCACTTGTAGTATCTCCAACT 59.471 41.667 0.00 0.00 39.21 3.16
3341 3883 4.822026 ACTGCACTTGTAGTATCTCCAAC 58.178 43.478 0.00 0.00 39.21 3.77


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

AutoCloner maintained by Alex Coulton.