Multiple sequence alignment - TraesCS5B01G442100

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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 TraesCS5B01G442100 chr5B 100.000 4708 0 0 1 4708 615202408 615197701 0.000000e+00 8695.0
1 TraesCS5B01G442100 chr5B 99.405 168 1 0 4116 4283 656461942 656461775 5.920000e-79 305.0
2 TraesCS5B01G442100 chr5B 100.000 41 0 0 4553 4593 615197780 615197740 5.050000e-10 76.8
3 TraesCS5B01G442100 chr5B 100.000 41 0 0 4629 4669 615197856 615197816 5.050000e-10 76.8
4 TraesCS5B01G442100 chr5D 94.055 2254 67 28 936 3182 496589739 496587546 0.000000e+00 3358.0
5 TraesCS5B01G442100 chr5D 96.645 924 30 1 3181 4104 496587452 496586530 0.000000e+00 1533.0
6 TraesCS5B01G442100 chr5D 93.242 873 50 7 1 869 496590745 496589878 0.000000e+00 1277.0
7 TraesCS5B01G442100 chr5D 84.581 227 13 9 4481 4706 496585639 496585434 6.180000e-49 206.0
8 TraesCS5B01G442100 chr5D 85.792 183 4 2 4288 4448 496586512 496586330 1.740000e-39 174.0
9 TraesCS5B01G442100 chr5D 97.561 41 1 0 4629 4669 496585580 496585540 2.350000e-08 71.3
10 TraesCS5B01G442100 chr1A 94.846 1494 62 7 1073 2563 537356828 537355347 0.000000e+00 2318.0
11 TraesCS5B01G442100 chr1A 90.785 293 20 3 3420 3712 537354583 537354298 7.390000e-103 385.0
12 TraesCS5B01G442100 chr1A 97.727 176 2 2 4111 4285 494815408 494815582 7.660000e-78 302.0
13 TraesCS5B01G442100 chr1A 98.182 165 3 0 4118 4282 33392702 33392538 5.960000e-74 289.0
14 TraesCS5B01G442100 chr1A 90.452 199 17 2 3265 3462 537354780 537354583 1.300000e-65 261.0
15 TraesCS5B01G442100 chr1A 97.436 39 1 0 4591 4629 504241638 504241676 3.040000e-07 67.6
16 TraesCS5B01G442100 chr1D 94.054 1480 60 14 1011 2474 360093335 360094802 0.000000e+00 2220.0
17 TraesCS5B01G442100 chr1D 87.805 492 39 9 3244 3723 360095324 360095806 1.480000e-154 556.0
18 TraesCS5B01G442100 chr1D 81.056 322 36 15 2819 3131 360094935 360095240 2.830000e-57 233.0
19 TraesCS5B01G442100 chr1D 82.143 112 10 8 4597 4706 408072094 408072197 2.330000e-13 87.9
20 TraesCS5B01G442100 chr1D 93.103 58 3 1 4284 4340 408239019 408239076 3.020000e-12 84.2
21 TraesCS5B01G442100 chr1D 91.667 60 4 1 2414 2473 360094814 360094872 1.090000e-11 82.4
22 TraesCS5B01G442100 chr1D 97.619 42 1 0 4588 4629 408240460 408240501 6.540000e-09 73.1
23 TraesCS5B01G442100 chr1B 95.106 1410 57 5 1067 2474 482164026 482165425 0.000000e+00 2211.0
24 TraesCS5B01G442100 chr1B 86.775 431 40 10 3244 3671 482165948 482166364 9.230000e-127 464.0
25 TraesCS5B01G442100 chr1B 100.000 36 0 0 4671 4706 548621925 548621960 3.040000e-07 67.6
26 TraesCS5B01G442100 chr1B 95.238 42 2 0 4588 4629 548965462 548965503 3.040000e-07 67.6
27 TraesCS5B01G442100 chr5A 96.187 1259 44 2 1067 2325 620563126 620561872 0.000000e+00 2056.0
28 TraesCS5B01G442100 chr5A 92.185 1446 79 14 2479 3917 620561877 620560459 0.000000e+00 2013.0
29 TraesCS5B01G442100 chr5A 89.381 226 13 8 4481 4705 620559388 620559173 1.670000e-69 274.0
30 TraesCS5B01G442100 chr5A 94.737 114 6 0 2422 2535 620561877 620561764 1.350000e-40 178.0
31 TraesCS5B01G442100 chr5A 81.683 202 17 8 4288 4486 620560259 620560075 2.930000e-32 150.0
32 TraesCS5B01G442100 chr5A 100.000 41 0 0 4629 4669 620559318 620559278 5.050000e-10 76.8
33 TraesCS5B01G442100 chr2A 86.942 919 97 15 1 907 472359029 472359936 0.000000e+00 1011.0
34 TraesCS5B01G442100 chr2A 93.467 199 8 5 4118 4312 769550988 769551185 1.660000e-74 291.0
35 TraesCS5B01G442100 chr2A 91.026 78 7 0 937 1014 472360123 472360200 6.440000e-19 106.0
36 TraesCS5B01G442100 chr2A 97.436 39 0 1 4592 4629 40647029 40647067 1.090000e-06 65.8
37 TraesCS5B01G442100 chr7B 91.924 681 41 5 2113 2790 421501186 421500517 0.000000e+00 941.0
38 TraesCS5B01G442100 chr7B 91.189 681 46 6 2113 2790 632609559 632610228 0.000000e+00 913.0
39 TraesCS5B01G442100 chr2D 90.956 387 33 2 541 926 597804760 597805145 1.940000e-143 520.0
40 TraesCS5B01G442100 chr2D 90.956 387 33 2 541 926 597806167 597806552 1.940000e-143 520.0
41 TraesCS5B01G442100 chr2D 90.956 387 33 2 541 926 597808333 597808718 1.940000e-143 520.0
42 TraesCS5B01G442100 chr2D 90.956 387 33 2 541 926 597810461 597810846 1.940000e-143 520.0
43 TraesCS5B01G442100 chr2D 90.956 387 33 2 541 926 597811148 597811533 1.940000e-143 520.0
44 TraesCS5B01G442100 chr2D 90.956 387 33 2 541 926 597812555 597812940 1.940000e-143 520.0
45 TraesCS5B01G442100 chr2D 90.956 387 33 2 541 926 597817938 597818323 1.940000e-143 520.0
46 TraesCS5B01G442100 chr3D 95.868 242 10 0 4105 4346 489166308 489166067 4.420000e-105 392.0
47 TraesCS5B01G442100 chr3D 94.074 135 5 2 3799 3930 489176431 489176297 7.990000e-48 202.0
48 TraesCS5B01G442100 chr3D 85.256 156 9 4 4338 4486 489166024 489165876 1.060000e-31 148.0
49 TraesCS5B01G442100 chr3D 97.403 77 0 1 3965 4039 489176184 489176108 3.820000e-26 130.0
50 TraesCS5B01G442100 chr3D 80.925 173 9 12 4523 4690 489165043 489164890 1.070000e-21 115.0
51 TraesCS5B01G442100 chr3D 100.000 32 0 0 4638 4669 489165003 489164972 5.090000e-05 60.2
52 TraesCS5B01G442100 chr3A 97.268 183 4 1 4112 4293 602023229 602023047 4.580000e-80 309.0
53 TraesCS5B01G442100 chr3A 85.526 228 18 12 4481 4706 632549487 632549273 1.700000e-54 224.0
54 TraesCS5B01G442100 chr3A 90.511 137 8 2 3799 3930 632554564 632554428 4.840000e-40 176.0
55 TraesCS5B01G442100 chr3A 89.474 95 6 3 3955 4045 632554321 632554227 2.980000e-22 117.0
56 TraesCS5B01G442100 chr2B 100.000 167 0 0 4116 4282 357152327 357152493 4.580000e-80 309.0
57 TraesCS5B01G442100 chr4A 99.405 168 1 0 4116 4283 583979524 583979357 5.920000e-79 305.0
58 TraesCS5B01G442100 chr4A 92.667 150 9 2 4481 4630 27666809 27666956 1.030000e-51 215.0
59 TraesCS5B01G442100 chr7A 98.824 170 2 0 4113 4282 226849932 226849763 2.130000e-78 303.0
60 TraesCS5B01G442100 chr4B 84.211 228 21 9 4481 4706 541920781 541920995 1.720000e-49 207.0
61 TraesCS5B01G442100 chr6B 85.906 149 7 5 4338 4486 136933891 136933757 3.800000e-31 147.0
62 TraesCS5B01G442100 chr6B 97.436 39 1 0 4668 4706 136932358 136932320 3.040000e-07 67.6


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 TraesCS5B01G442100 chr5B 615197701 615202408 4707 True 8695.000000 8695 100.000000 1 4708 1 chr5B.!!$R1 4707
1 TraesCS5B01G442100 chr5D 496585434 496590745 5311 True 1103.216667 3358 91.979333 1 4706 6 chr5D.!!$R1 4705
2 TraesCS5B01G442100 chr1A 537354298 537356828 2530 True 988.000000 2318 92.027667 1073 3712 3 chr1A.!!$R2 2639
3 TraesCS5B01G442100 chr1D 360093335 360095806 2471 False 772.850000 2220 88.645500 1011 3723 4 chr1D.!!$F2 2712
4 TraesCS5B01G442100 chr1B 482164026 482166364 2338 False 1337.500000 2211 90.940500 1067 3671 2 chr1B.!!$F3 2604
5 TraesCS5B01G442100 chr5A 620559173 620563126 3953 True 791.300000 2056 92.362167 1067 4705 6 chr5A.!!$R1 3638
6 TraesCS5B01G442100 chr2A 472359029 472360200 1171 False 558.500000 1011 88.984000 1 1014 2 chr2A.!!$F3 1013
7 TraesCS5B01G442100 chr7B 421500517 421501186 669 True 941.000000 941 91.924000 2113 2790 1 chr7B.!!$R1 677
8 TraesCS5B01G442100 chr7B 632609559 632610228 669 False 913.000000 913 91.189000 2113 2790 1 chr7B.!!$F1 677
9 TraesCS5B01G442100 chr2D 597804760 597812940 8180 False 520.000000 520 90.956000 541 926 6 chr2D.!!$F2 385

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
933 7366 0.661020 AAACACGTGCACCACTAAGC 59.339 50.0 17.22 0.0 31.34 3.09 F
996 7568 0.882927 CGAAACCCCAGCAACTCGAA 60.883 55.0 0.00 0.0 0.00 3.71 F
2150 8735 0.110486 GTGTCAAGGCCAGGAAGGAA 59.890 55.0 5.01 0.0 41.22 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 8735 3.652869 TGGTCCTCTTGGAGTTGATCTTT 59.347 43.478 0.00 0.00 44.16 2.52 R
2895 9703 4.998672 CCATCAAAGAAATTGCACATGGTT 59.001 37.500 0.00 0.00 36.70 3.67 R
3739 10747 1.164411 TCATAACAAGCCGTGCAAGG 58.836 50.000 15.06 15.06 0.00 3.61 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
57 58 4.792528 AAAACGTGCACCATTGAATTTG 57.207 36.364 12.15 0.00 0.00 2.32
61 62 2.472115 CGTGCACCATTGAATTTGTGTG 59.528 45.455 12.15 0.00 0.00 3.82
111 112 9.910511 GAATTTCACATTGCAAATATGTTCATC 57.089 29.630 1.71 0.00 34.11 2.92
148 149 8.308931 AGCATGTTTTAGAAATGTGTTCATGAT 58.691 29.630 0.00 0.00 34.14 2.45
150 151 7.872163 TGTTTTAGAAATGTGTTCATGATGC 57.128 32.000 0.00 0.00 34.19 3.91
445 457 2.350192 TGCGGCTTATTGTTGATACACG 59.650 45.455 0.00 0.00 32.98 4.49
446 458 2.350498 GCGGCTTATTGTTGATACACGT 59.650 45.455 0.00 0.00 32.98 4.49
498 510 1.320344 AAGATGGTGGCTAGCGACGA 61.320 55.000 21.58 19.02 0.00 4.20
504 516 1.226575 TGGCTAGCGACGATGTTCG 60.227 57.895 9.00 0.00 46.93 3.95
532 544 2.405191 GGCCTCGAATTTGCGCTC 59.595 61.111 9.73 0.00 0.00 5.03
554 566 2.287970 CCGGGTGTTTAAGTTTTGCCTC 60.288 50.000 0.00 0.00 0.00 4.70
555 567 2.603652 CGGGTGTTTAAGTTTTGCCTCG 60.604 50.000 0.00 0.00 0.00 4.63
556 568 2.619646 GGGTGTTTAAGTTTTGCCTCGA 59.380 45.455 0.00 0.00 0.00 4.04
559 571 4.148891 GTGTTTAAGTTTTGCCTCGATCG 58.851 43.478 9.36 9.36 0.00 3.69
608 7007 2.491675 TCGGAGACTAGAACTCTGCA 57.508 50.000 18.51 0.00 39.69 4.41
650 7049 2.342279 CAACCCGCTTCGAGGTCA 59.658 61.111 0.00 0.00 34.45 4.02
665 7064 1.076332 GGTCACTTGTTCGAATCCCG 58.924 55.000 0.00 0.00 40.25 5.14
669 7068 3.742369 GTCACTTGTTCGAATCCCGTTTA 59.258 43.478 0.00 0.00 39.75 2.01
691 7091 1.154395 GCGCGCTCCTTTTTCAGTC 60.154 57.895 26.67 0.00 0.00 3.51
741 7141 2.431782 AGGTTTCTTTTGCACTGCACAT 59.568 40.909 2.26 0.00 38.71 3.21
816 7217 5.871539 TCGTGAAAGAAACAGTTTTACACC 58.128 37.500 0.00 0.00 0.00 4.16
875 7276 6.976088 TCTCCTTTAGATTATCTCGCTCAAG 58.024 40.000 0.00 0.00 0.00 3.02
931 7364 2.025589 TCAAACACGTGCACCACTAA 57.974 45.000 17.22 0.00 31.34 2.24
932 7365 1.937223 TCAAACACGTGCACCACTAAG 59.063 47.619 17.22 0.00 31.34 2.18
933 7366 0.661020 AAACACGTGCACCACTAAGC 59.339 50.000 17.22 0.00 31.34 3.09
934 7367 1.164041 AACACGTGCACCACTAAGCC 61.164 55.000 17.22 0.00 31.34 4.35
996 7568 0.882927 CGAAACCCCAGCAACTCGAA 60.883 55.000 0.00 0.00 0.00 3.71
1221 7806 2.266055 CCTTCGTCCACAGGCTCC 59.734 66.667 0.00 0.00 0.00 4.70
2150 8735 0.110486 GTGTCAAGGCCAGGAAGGAA 59.890 55.000 5.01 0.00 41.22 3.36
2193 8778 1.661821 CTCAGCGCGGTATGCTACC 60.662 63.158 11.92 3.11 41.72 3.18
2226 8811 6.460676 CCCTTTGCCATCTGTTTCATATCTTC 60.461 42.308 0.00 0.00 0.00 2.87
2255 8840 9.650539 ACACATGATGACAGATAGCTTATAATC 57.349 33.333 0.00 0.00 0.00 1.75
2286 8873 8.440833 AGTATTTGTTGAATGTTCGTACTAAGC 58.559 33.333 0.00 0.00 0.00 3.09
2663 9268 1.164041 AGTGCCTTGTGGTTGTACGC 61.164 55.000 0.00 0.00 35.27 4.42
2950 9765 6.690194 ACTGAATTCTGAAGTATCCAATGC 57.310 37.500 18.13 0.00 0.00 3.56
2951 9766 5.591877 ACTGAATTCTGAAGTATCCAATGCC 59.408 40.000 18.13 0.00 0.00 4.40
3096 9913 4.825422 CTGTACTGAAAATCTGAGGCAGA 58.175 43.478 0.00 0.00 44.99 4.26
3213 10155 1.066716 CATGTTTGGGTGCTTGGGATG 60.067 52.381 0.00 0.00 0.00 3.51
3284 10226 7.560991 TGTTTAAATTCCACATCCTGCATCTAT 59.439 33.333 0.00 0.00 0.00 1.98
3322 10267 2.936498 ACTGACGAAGGAACACTTGTTG 59.064 45.455 0.00 0.00 40.21 3.33
3355 10300 2.569059 GCATCTAAGATCAAGGCTGCA 58.431 47.619 0.50 0.00 0.00 4.41
3502 10489 8.252624 ACCTTAAGAGACCCTAAAGTATGATC 57.747 38.462 3.36 0.00 0.00 2.92
3555 10560 4.156556 TGAGACATCTTATGCTGTTTTGGC 59.843 41.667 0.00 0.00 0.00 4.52
3596 10601 6.472163 GTGTTTTATCTATGGACGCATTTTGG 59.528 38.462 0.00 0.00 0.00 3.28
3739 10747 2.790433 TGGCATACCCACAGTTTCTTC 58.210 47.619 0.00 0.00 39.18 2.87
3772 10780 6.202570 GGCTTGTTATGAATTTCTTTGCAACA 59.797 34.615 0.00 0.00 0.00 3.33
3831 10839 8.767085 ACTGCTTTATCATTGTTGATTTTGTTG 58.233 29.630 0.00 0.00 42.61 3.33
3898 10906 2.159226 ACCTGATCGTGTTGCTACTAGC 60.159 50.000 0.61 0.61 42.82 3.42
4012 11712 6.381133 TGATAGCTTGTTCTGAGGATTGAGTA 59.619 38.462 0.00 0.00 0.00 2.59
4092 11792 6.325919 TGATCCAACATGAACTTAAACACC 57.674 37.500 0.00 0.00 0.00 4.16
4093 11793 6.068010 TGATCCAACATGAACTTAAACACCT 58.932 36.000 0.00 0.00 0.00 4.00
4097 11797 6.708949 TCCAACATGAACTTAAACACCTAGTC 59.291 38.462 0.00 0.00 0.00 2.59
4098 11798 6.485313 CCAACATGAACTTAAACACCTAGTCA 59.515 38.462 0.00 0.00 0.00 3.41
4100 11800 7.672983 ACATGAACTTAAACACCTAGTCATG 57.327 36.000 0.00 8.38 35.70 3.07
4101 11801 7.224297 ACATGAACTTAAACACCTAGTCATGT 58.776 34.615 9.52 9.52 36.71 3.21
4102 11802 7.387948 ACATGAACTTAAACACCTAGTCATGTC 59.612 37.037 9.52 0.00 36.77 3.06
4104 11804 7.152645 TGAACTTAAACACCTAGTCATGTCTC 58.847 38.462 0.00 0.00 0.00 3.36
4106 11806 3.983044 AAACACCTAGTCATGTCTCCC 57.017 47.619 0.00 0.00 0.00 4.30
4107 11807 2.930109 ACACCTAGTCATGTCTCCCT 57.070 50.000 0.00 0.00 0.00 4.20
4108 11808 4.332683 AACACCTAGTCATGTCTCCCTA 57.667 45.455 0.00 0.00 0.00 3.53
4109 11809 3.904717 ACACCTAGTCATGTCTCCCTAG 58.095 50.000 0.00 0.00 0.00 3.02
4111 11811 4.477581 ACACCTAGTCATGTCTCCCTAGTA 59.522 45.833 0.00 0.00 0.00 1.82
4112 11812 5.067273 CACCTAGTCATGTCTCCCTAGTAG 58.933 50.000 0.00 0.00 0.00 2.57
4113 11813 4.727841 ACCTAGTCATGTCTCCCTAGTAGT 59.272 45.833 0.00 0.00 0.00 2.73
4114 11814 5.194132 ACCTAGTCATGTCTCCCTAGTAGTT 59.806 44.000 0.00 0.00 0.00 2.24
4115 11815 6.130569 CCTAGTCATGTCTCCCTAGTAGTTT 58.869 44.000 0.00 0.00 0.00 2.66
4116 11816 7.092083 ACCTAGTCATGTCTCCCTAGTAGTTTA 60.092 40.741 0.00 0.00 0.00 2.01
4117 11817 7.229106 CCTAGTCATGTCTCCCTAGTAGTTTAC 59.771 44.444 0.00 0.00 0.00 2.01
4118 11818 6.733509 AGTCATGTCTCCCTAGTAGTTTACT 58.266 40.000 0.00 0.00 42.68 2.24
4119 11819 7.870027 AGTCATGTCTCCCTAGTAGTTTACTA 58.130 38.462 0.00 0.00 40.14 1.82
4120 11820 7.774625 AGTCATGTCTCCCTAGTAGTTTACTAC 59.225 40.741 11.25 11.25 46.93 2.73
4131 11831 5.242069 GTAGTTTACTACTCCCTCCGTTC 57.758 47.826 11.80 0.00 44.06 3.95
4132 11832 3.095332 AGTTTACTACTCCCTCCGTTCC 58.905 50.000 0.00 0.00 28.23 3.62
4133 11833 3.095332 GTTTACTACTCCCTCCGTTCCT 58.905 50.000 0.00 0.00 0.00 3.36
4134 11834 4.018050 AGTTTACTACTCCCTCCGTTCCTA 60.018 45.833 0.00 0.00 28.23 2.94
4135 11835 4.591321 TTACTACTCCCTCCGTTCCTAA 57.409 45.455 0.00 0.00 0.00 2.69
4136 11836 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
4137 11837 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
4138 11838 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
4139 11839 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
4140 11840 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
4141 11841 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
4142 11842 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
4143 11843 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
4144 11844 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
4145 11845 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
4146 11846 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
4147 11847 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
4148 11848 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
4149 11849 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
4150 11850 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
4151 11851 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
4152 11852 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
4153 11853 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
4154 11854 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
4155 11855 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
4156 11856 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
4157 11857 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
4159 11859 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
4160 11860 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
4161 11861 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
4162 11862 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
4163 11863 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
4164 11864 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
4165 11865 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
4166 11866 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
4167 11867 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
4168 11868 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
4169 11869 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
4170 11870 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
4171 11871 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
4172 11872 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
4173 11873 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
4174 11874 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
4175 11875 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
4176 11876 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
4177 11877 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
4178 11878 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
4179 11879 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
4180 11880 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
4181 11881 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
4182 11882 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
4183 11883 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
4184 11884 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
4185 11885 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
4186 11886 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
4187 11887 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
4188 11888 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
4189 11889 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
4190 11890 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
4191 11891 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4192 11892 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
4193 11893 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4194 11894 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
4195 11895 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
4196 11896 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
4197 11897 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
4198 11898 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
4199 11899 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
4273 11973 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
4274 11974 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
4275 11975 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
4276 11976 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
4277 11977 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4278 11978 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4279 11979 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4280 11980 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
4281 11981 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
4282 11982 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
4283 11983 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
4284 11984 2.905415 TAGGAACGGAGGGAGTACAA 57.095 50.000 0.00 0.00 0.00 2.41
4285 11985 1.264295 AGGAACGGAGGGAGTACAAC 58.736 55.000 0.00 0.00 0.00 3.32
4286 11986 1.203149 AGGAACGGAGGGAGTACAACT 60.203 52.381 0.00 0.00 0.00 3.16
4420 12142 0.672401 ATTGTTGTACACGAGGCCCG 60.672 55.000 11.48 11.48 45.44 6.13
4447 12169 3.929610 GCAGATCTGTACACTCACTTTCC 59.070 47.826 23.38 0.00 0.00 3.13
4448 12170 4.169508 CAGATCTGTACACTCACTTTCCG 58.830 47.826 14.95 0.00 0.00 4.30
4449 12171 3.193691 AGATCTGTACACTCACTTTCCGG 59.806 47.826 0.00 0.00 0.00 5.14
4450 12172 2.313317 TCTGTACACTCACTTTCCGGT 58.687 47.619 0.00 0.00 0.00 5.28
4451 12173 2.035449 TCTGTACACTCACTTTCCGGTG 59.965 50.000 0.00 0.00 38.44 4.94
4452 12174 2.033372 TGTACACTCACTTTCCGGTGA 58.967 47.619 0.00 0.00 42.96 4.02
4462 12184 2.308866 ACTTTCCGGTGAGAATTGGGAT 59.691 45.455 12.64 0.00 0.00 3.85
4521 12951 8.819643 ATTAGCCATTAGAAGACGTTAAGATC 57.180 34.615 0.00 0.00 0.00 2.75
4541 12971 5.758296 AGATCTGTGAACGCTTTTTGTCTTA 59.242 36.000 0.00 0.00 0.00 2.10
4542 12972 6.428159 AGATCTGTGAACGCTTTTTGTCTTAT 59.572 34.615 0.00 0.00 0.00 1.73
4543 12973 7.602644 AGATCTGTGAACGCTTTTTGTCTTATA 59.397 33.333 0.00 0.00 0.00 0.98
4631 13061 7.255104 CCAGACTGTTTTGCTAGTTGTCAAATA 60.255 37.037 0.93 0.00 32.92 1.40
4632 13062 8.292448 CAGACTGTTTTGCTAGTTGTCAAATAT 58.708 33.333 0.00 0.00 32.92 1.28
4633 13063 8.292448 AGACTGTTTTGCTAGTTGTCAAATATG 58.708 33.333 0.00 0.00 32.92 1.78
4635 13065 8.292448 ACTGTTTTGCTAGTTGTCAAATATGAG 58.708 33.333 0.00 0.00 35.88 2.90
4637 13067 7.040478 TGTTTTGCTAGTTGTCAAATATGAGCT 60.040 33.333 7.54 0.00 35.88 4.09
4639 13069 7.539712 TTGCTAGTTGTCAAATATGAGCTAC 57.460 36.000 7.54 0.00 35.88 3.58
4640 13070 6.878317 TGCTAGTTGTCAAATATGAGCTACT 58.122 36.000 7.54 0.00 35.88 2.57
4641 13071 7.331026 TGCTAGTTGTCAAATATGAGCTACTT 58.669 34.615 7.54 0.00 35.88 2.24
4643 13073 7.492669 GCTAGTTGTCAAATATGAGCTACTTGA 59.507 37.037 0.00 0.00 35.88 3.02
4644 13074 7.840342 AGTTGTCAAATATGAGCTACTTGAG 57.160 36.000 0.00 0.00 35.88 3.02
4645 13075 7.390027 AGTTGTCAAATATGAGCTACTTGAGT 58.610 34.615 0.00 0.00 35.88 3.41
4647 13077 9.151471 GTTGTCAAATATGAGCTACTTGAGTTA 57.849 33.333 0.00 0.00 35.88 2.24
4648 13078 9.719355 TTGTCAAATATGAGCTACTTGAGTTAA 57.281 29.630 0.00 0.00 35.88 2.01
4659 13089 8.904099 AGCTACTTGAGTTAAAAGTACACAAT 57.096 30.769 0.00 0.00 38.73 2.71
4660 13090 8.989980 AGCTACTTGAGTTAAAAGTACACAATC 58.010 33.333 0.00 0.00 38.73 2.67
4661 13091 8.770828 GCTACTTGAGTTAAAAGTACACAATCA 58.229 33.333 0.00 0.00 38.73 2.57
4663 13093 7.639945 ACTTGAGTTAAAAGTACACAATCAGC 58.360 34.615 0.00 0.00 36.11 4.26
4664 13094 7.282224 ACTTGAGTTAAAAGTACACAATCAGCA 59.718 33.333 0.00 0.00 36.11 4.41
4665 13095 7.189693 TGAGTTAAAAGTACACAATCAGCAG 57.810 36.000 0.00 0.00 0.00 4.24
4706 13136 6.013379 TGAAGATATGTAATCCAGATCCCACC 60.013 42.308 0.00 0.00 41.73 4.61
4707 13137 5.415065 AGATATGTAATCCAGATCCCACCA 58.585 41.667 0.00 0.00 41.73 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.644685 CCCCGGAACATTTATTGATTCTGT 59.355 41.667 0.73 0.00 0.00 3.41
9 10 5.770162 AGATCCCCGGAACATTTATTGATTC 59.230 40.000 0.73 0.00 0.00 2.52
45 46 3.815856 TGTGCACACAAATTCAATGGT 57.184 38.095 17.42 0.00 38.56 3.55
57 58 7.649306 AGAAACATTCTCTAAATTTGTGCACAC 59.351 33.333 21.56 0.80 34.07 3.82
61 62 7.370383 TCCAGAAACATTCTCTAAATTTGTGC 58.630 34.615 0.00 0.00 38.11 4.57
72 73 7.148689 GCAATGTGAAATTCCAGAAACATTCTC 60.149 37.037 5.88 3.62 38.11 2.87
119 120 8.715191 TGAACACATTTCTAAAACATGCTTTT 57.285 26.923 0.00 5.51 0.00 2.27
133 134 8.332464 CAATATTTGGCATCATGAACACATTTC 58.668 33.333 0.00 0.00 0.00 2.17
148 149 6.213195 AGAAATTCCCTGAACAATATTTGGCA 59.787 34.615 0.00 0.00 34.12 4.92
417 429 2.979813 CAACAATAAGCCGCAAACAGAC 59.020 45.455 0.00 0.00 0.00 3.51
469 481 1.369625 CCACCATCTTTACTGCGACC 58.630 55.000 0.00 0.00 0.00 4.79
498 510 1.413077 GGCCCTCTTACTAGCGAACAT 59.587 52.381 0.00 0.00 0.00 2.71
504 516 1.400737 TTCGAGGCCCTCTTACTAGC 58.599 55.000 9.52 0.00 0.00 3.42
532 544 1.269883 GGCAAAACTTAAACACCCGGG 60.270 52.381 22.25 22.25 0.00 5.73
554 566 5.840250 ACGCTTAAAAGAAGTAAACGATCG 58.160 37.500 14.88 14.88 0.00 3.69
555 567 5.944697 CGACGCTTAAAAGAAGTAAACGATC 59.055 40.000 0.00 0.00 0.00 3.69
556 568 5.403466 ACGACGCTTAAAAGAAGTAAACGAT 59.597 36.000 0.00 0.00 0.00 3.73
559 571 4.606004 GCACGACGCTTAAAAGAAGTAAAC 59.394 41.667 0.00 0.00 37.77 2.01
608 7007 1.142748 GAGCTAGCCACTGCGACAT 59.857 57.895 12.13 0.00 44.33 3.06
650 7049 3.069289 GGTAAACGGGATTCGAACAAGT 58.931 45.455 0.00 0.00 42.43 3.16
691 7091 4.858935 TCAGAAAGACCAAATTCTTTGCG 58.141 39.130 2.90 0.00 44.27 4.85
741 7141 9.886132 AAACTTAGACTAGACTGTTTTGAGAAA 57.114 29.630 4.90 0.00 0.00 2.52
769 7169 7.323656 CGAATAACACAAAATTGGACAGTCTTC 59.676 37.037 0.00 0.00 0.00 2.87
816 7217 0.307760 GCACTGTTTCGTCAGGTTGG 59.692 55.000 9.02 0.00 39.48 3.77
871 7272 1.222300 ATGCGTGCACGTTAACTTGA 58.778 45.000 36.80 13.52 42.22 3.02
875 7276 0.247537 GGCTATGCGTGCACGTTAAC 60.248 55.000 36.80 23.40 42.22 2.01
968 7540 1.369625 CTGGGGTTTCGCATACAGAC 58.630 55.000 0.00 0.00 35.25 3.51
972 7544 0.170339 GTTGCTGGGGTTTCGCATAC 59.830 55.000 0.00 0.00 35.25 2.39
996 7568 2.863401 TATATGTGACGCGTTCTGCT 57.137 45.000 15.53 0.00 43.27 4.24
1221 7806 3.123620 GCGGCTGTTGCAGGAGAG 61.124 66.667 0.00 0.00 41.91 3.20
1259 7844 2.047179 GTCTGGTGACCGGCCTTC 60.047 66.667 5.33 0.00 37.24 3.46
1709 8294 2.728817 CCGTAGACGATGAGGGGC 59.271 66.667 3.07 0.00 43.02 5.80
2150 8735 3.652869 TGGTCCTCTTGGAGTTGATCTTT 59.347 43.478 0.00 0.00 44.16 2.52
2255 8840 6.668323 ACGAACATTCAACAAATACTGAAGG 58.332 36.000 0.00 0.00 38.84 3.46
2264 8851 6.854496 AGCTTAGTACGAACATTCAACAAA 57.146 33.333 0.00 0.00 0.00 2.83
2663 9268 6.201806 GCTTGCTCCATATAGAACAGTACAAG 59.798 42.308 0.00 0.00 34.29 3.16
2895 9703 4.998672 CCATCAAAGAAATTGCACATGGTT 59.001 37.500 0.00 0.00 36.70 3.67
2976 9791 8.401490 AGCTTCAAGACAAACTGAGATAAATT 57.599 30.769 0.00 0.00 0.00 1.82
3015 9830 6.989759 TCAGTGCTAATGAAACAAGACAAGTA 59.010 34.615 0.00 0.00 0.00 2.24
3030 9846 5.190528 TCCTTCAGGAAGATTCAGTGCTAAT 59.809 40.000 10.52 0.00 42.18 1.73
3096 9913 9.926158 TGCAGTCATGATTAATGTTAAACAATT 57.074 25.926 0.00 0.00 37.56 2.32
3213 10155 1.477105 GGCAACAGAAAAACGACAGC 58.523 50.000 0.00 0.00 0.00 4.40
3322 10267 3.961408 TCTTAGATGCCTCCTCCTACAAC 59.039 47.826 0.00 0.00 0.00 3.32
3502 10489 6.410845 CGGATAAACGATAACATGACACAAG 58.589 40.000 0.00 0.00 35.47 3.16
3555 10560 5.597813 AAAACACTCGAGATAAACAGCTG 57.402 39.130 21.68 13.48 0.00 4.24
3596 10601 4.330250 AGCATGCCATATAACATGTCTCC 58.670 43.478 15.66 3.19 44.43 3.71
3739 10747 1.164411 TCATAACAAGCCGTGCAAGG 58.836 50.000 15.06 15.06 0.00 3.61
3831 10839 2.867429 GCAAGTGGCACATTATCACAC 58.133 47.619 21.41 0.00 44.52 3.82
4092 11792 7.994334 AGTAAACTACTAGGGAGACATGACTAG 59.006 40.741 0.00 5.77 37.23 2.57
4093 11793 7.870027 AGTAAACTACTAGGGAGACATGACTA 58.130 38.462 0.00 0.00 37.23 2.59
4109 11809 4.097135 GGAACGGAGGGAGTAGTAAACTAC 59.903 50.000 11.54 11.54 46.93 2.73
4111 11811 3.095332 GGAACGGAGGGAGTAGTAAACT 58.905 50.000 0.00 0.00 42.80 2.66
4112 11812 3.095332 AGGAACGGAGGGAGTAGTAAAC 58.905 50.000 0.00 0.00 0.00 2.01
4113 11813 3.463048 AGGAACGGAGGGAGTAGTAAA 57.537 47.619 0.00 0.00 0.00 2.01
4114 11814 4.591321 TTAGGAACGGAGGGAGTAGTAA 57.409 45.455 0.00 0.00 0.00 2.24
4115 11815 4.591321 TTTAGGAACGGAGGGAGTAGTA 57.409 45.455 0.00 0.00 0.00 1.82
4116 11816 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
4117 11817 5.139001 AGTATTTAGGAACGGAGGGAGTAG 58.861 45.833 0.00 0.00 0.00 2.57
4118 11818 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
4119 11819 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
4120 11820 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
4121 11821 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
4122 11822 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
4123 11823 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
4124 11824 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
4125 11825 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
4126 11826 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
4127 11827 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
4128 11828 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
4129 11829 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
4130 11830 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
4131 11831 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
4133 11833 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
4134 11834 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
4135 11835 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
4136 11836 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
4137 11837 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
4138 11838 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
4139 11839 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
4140 11840 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
4141 11841 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
4142 11842 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
4143 11843 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
4144 11844 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
4145 11845 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
4146 11846 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
4147 11847 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
4148 11848 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
4149 11849 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
4150 11850 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
4151 11851 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
4152 11852 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
4153 11853 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
4154 11854 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
4155 11855 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
4156 11856 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
4157 11857 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
4158 11858 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
4159 11859 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
4160 11860 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
4161 11861 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
4162 11862 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
4163 11863 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
4164 11864 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
4165 11865 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
4166 11866 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
4167 11867 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
4168 11868 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
4169 11869 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
4170 11870 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4171 11871 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4172 11872 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
4173 11873 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
4174 11874 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
4175 11875 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
4176 11876 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
4177 11877 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4247 11947 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
4248 11948 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
4249 11949 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4250 11950 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4251 11951 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4252 11952 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4253 11953 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4254 11954 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4255 11955 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4256 11956 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4257 11957 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4258 11958 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4259 11959 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
4260 11960 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
4261 11961 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
4262 11962 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
4263 11963 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
4264 11964 2.827921 GTTGTACTCCCTCCGTTCCTAA 59.172 50.000 0.00 0.00 0.00 2.69
4265 11965 2.042162 AGTTGTACTCCCTCCGTTCCTA 59.958 50.000 0.00 0.00 0.00 2.94
4266 11966 1.203149 AGTTGTACTCCCTCCGTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
4267 11967 1.067071 CAGTTGTACTCCCTCCGTTCC 60.067 57.143 0.00 0.00 0.00 3.62
4268 11968 1.891150 TCAGTTGTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
4269 11969 2.005370 TCAGTTGTACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
4270 11970 2.005370 TTCAGTTGTACTCCCTCCGT 57.995 50.000 0.00 0.00 0.00 4.69
4271 11971 3.611766 ATTTCAGTTGTACTCCCTCCG 57.388 47.619 0.00 0.00 0.00 4.63
4272 11972 5.183969 GGTAATTTCAGTTGTACTCCCTCC 58.816 45.833 0.00 0.00 0.00 4.30
4273 11973 5.801380 TGGTAATTTCAGTTGTACTCCCTC 58.199 41.667 0.00 0.00 0.00 4.30
4274 11974 5.803470 GCTGGTAATTTCAGTTGTACTCCCT 60.803 44.000 9.32 0.00 34.89 4.20
4275 11975 4.395231 GCTGGTAATTTCAGTTGTACTCCC 59.605 45.833 9.32 0.00 34.89 4.30
4276 11976 4.092968 CGCTGGTAATTTCAGTTGTACTCC 59.907 45.833 9.32 0.00 34.89 3.85
4277 11977 4.927425 TCGCTGGTAATTTCAGTTGTACTC 59.073 41.667 9.32 0.00 34.89 2.59
4278 11978 4.890088 TCGCTGGTAATTTCAGTTGTACT 58.110 39.130 9.32 0.00 34.89 2.73
4279 11979 5.178809 AGTTCGCTGGTAATTTCAGTTGTAC 59.821 40.000 9.32 0.00 34.89 2.90
4280 11980 5.302360 AGTTCGCTGGTAATTTCAGTTGTA 58.698 37.500 9.32 0.00 34.89 2.41
4281 11981 4.134563 AGTTCGCTGGTAATTTCAGTTGT 58.865 39.130 9.32 0.00 34.89 3.32
4282 11982 4.213270 TGAGTTCGCTGGTAATTTCAGTTG 59.787 41.667 9.32 4.46 34.89 3.16
4283 11983 4.385825 TGAGTTCGCTGGTAATTTCAGTT 58.614 39.130 9.32 0.00 34.89 3.16
4284 11984 4.002906 TGAGTTCGCTGGTAATTTCAGT 57.997 40.909 9.32 0.00 34.89 3.41
4285 11985 4.631377 TCATGAGTTCGCTGGTAATTTCAG 59.369 41.667 0.00 4.66 35.49 3.02
4286 11986 4.574892 TCATGAGTTCGCTGGTAATTTCA 58.425 39.130 0.00 0.00 0.00 2.69
4420 12142 3.862267 GTGAGTGTACAGATCTGCATGAC 59.138 47.826 22.83 15.06 0.00 3.06
4447 12169 2.882927 TACGATCCCAATTCTCACCG 57.117 50.000 0.00 0.00 0.00 4.94
4448 12170 4.402056 TCTTACGATCCCAATTCTCACC 57.598 45.455 0.00 0.00 0.00 4.02
4449 12171 6.737254 TTTTCTTACGATCCCAATTCTCAC 57.263 37.500 0.00 0.00 0.00 3.51
4450 12172 6.712998 TGTTTTTCTTACGATCCCAATTCTCA 59.287 34.615 0.00 0.00 0.00 3.27
4451 12173 7.021790 GTGTTTTTCTTACGATCCCAATTCTC 58.978 38.462 0.00 0.00 0.00 2.87
4452 12174 6.072119 GGTGTTTTTCTTACGATCCCAATTCT 60.072 38.462 0.00 0.00 0.00 2.40
4453 12175 6.090783 GGTGTTTTTCTTACGATCCCAATTC 58.909 40.000 0.00 0.00 0.00 2.17
4454 12176 5.335348 CGGTGTTTTTCTTACGATCCCAATT 60.335 40.000 0.00 0.00 0.00 2.32
4455 12177 4.155280 CGGTGTTTTTCTTACGATCCCAAT 59.845 41.667 0.00 0.00 0.00 3.16
4462 12184 3.176552 TGGTCGGTGTTTTTCTTACGA 57.823 42.857 0.00 0.00 0.00 3.43
4521 12951 8.728088 ATTTATAAGACAAAAAGCGTTCACAG 57.272 30.769 0.00 0.00 0.00 3.66
4541 12971 8.884323 TCAAGTAGCTCATATTCCTGGATTTAT 58.116 33.333 0.00 0.00 0.00 1.40
4542 12972 8.262601 TCAAGTAGCTCATATTCCTGGATTTA 57.737 34.615 0.00 0.00 0.00 1.40
4543 12973 7.141758 TCAAGTAGCTCATATTCCTGGATTT 57.858 36.000 0.00 0.00 0.00 2.17
4631 13061 8.148351 TGTGTACTTTTAACTCAAGTAGCTCAT 58.852 33.333 0.00 0.00 37.39 2.90
4632 13062 7.494211 TGTGTACTTTTAACTCAAGTAGCTCA 58.506 34.615 0.00 1.31 37.39 4.26
4633 13063 7.941795 TGTGTACTTTTAACTCAAGTAGCTC 57.058 36.000 0.00 0.00 37.39 4.09
4635 13065 8.770828 TGATTGTGTACTTTTAACTCAAGTAGC 58.229 33.333 0.00 0.00 37.39 3.58
4637 13067 8.770828 GCTGATTGTGTACTTTTAACTCAAGTA 58.229 33.333 0.00 0.00 35.95 2.24
4639 13069 7.639039 TGCTGATTGTGTACTTTTAACTCAAG 58.361 34.615 0.00 0.00 34.81 3.02
4640 13070 7.255104 CCTGCTGATTGTGTACTTTTAACTCAA 60.255 37.037 0.00 0.00 35.52 3.02
4641 13071 6.204688 CCTGCTGATTGTGTACTTTTAACTCA 59.795 38.462 0.00 0.00 0.00 3.41
4643 13073 6.296026 TCCTGCTGATTGTGTACTTTTAACT 58.704 36.000 0.00 0.00 0.00 2.24
4644 13074 6.554334 TCCTGCTGATTGTGTACTTTTAAC 57.446 37.500 0.00 0.00 0.00 2.01
4645 13075 6.995686 TCTTCCTGCTGATTGTGTACTTTTAA 59.004 34.615 0.00 0.00 0.00 1.52
4647 13077 5.376625 TCTTCCTGCTGATTGTGTACTTTT 58.623 37.500 0.00 0.00 0.00 2.27
4648 13078 4.973168 TCTTCCTGCTGATTGTGTACTTT 58.027 39.130 0.00 0.00 0.00 2.66
4650 13080 4.511527 CATCTTCCTGCTGATTGTGTACT 58.488 43.478 0.00 0.00 0.00 2.73
4651 13081 3.064545 GCATCTTCCTGCTGATTGTGTAC 59.935 47.826 0.00 0.00 39.12 2.90
4652 13082 3.273434 GCATCTTCCTGCTGATTGTGTA 58.727 45.455 0.00 0.00 39.12 2.90
4654 13084 2.089201 TGCATCTTCCTGCTGATTGTG 58.911 47.619 0.00 0.00 42.75 3.33
4655 13085 2.502142 TGCATCTTCCTGCTGATTGT 57.498 45.000 0.00 0.00 42.75 2.71
4659 13089 2.793288 TCAATGCATCTTCCTGCTGA 57.207 45.000 0.00 0.00 42.75 4.26
4660 13090 4.112634 CAATTCAATGCATCTTCCTGCTG 58.887 43.478 0.00 0.00 42.75 4.41
4661 13091 4.021229 TCAATTCAATGCATCTTCCTGCT 58.979 39.130 0.00 0.00 42.75 4.24
4662 13092 4.380841 TCAATTCAATGCATCTTCCTGC 57.619 40.909 0.00 0.00 42.62 4.85
4663 13093 6.203808 TCTTCAATTCAATGCATCTTCCTG 57.796 37.500 0.00 0.00 0.00 3.86
4664 13094 8.577296 CATATCTTCAATTCAATGCATCTTCCT 58.423 33.333 0.00 0.00 0.00 3.36
4665 13095 8.358148 ACATATCTTCAATTCAATGCATCTTCC 58.642 33.333 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.