Multiple sequence alignment - TraesCS7A01G226500

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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 TraesCS7A01G226500 chr7A 100.000 5231 0 0 1 5231 195832726 195827496 0.000000e+00 9660
1 TraesCS7A01G226500 chr7A 78.252 938 174 22 2250 3174 18980261 18981181 4.540000e-160 575
2 TraesCS7A01G226500 chr7D 95.205 3045 130 11 305 3348 188288388 188291417 0.000000e+00 4800
3 TraesCS7A01G226500 chr7D 95.516 959 43 0 3359 4317 188291401 188292359 0.000000e+00 1533
4 TraesCS7A01G226500 chr7D 93.333 540 24 4 4346 4883 188292346 188292875 0.000000e+00 787
5 TraesCS7A01G226500 chr7D 92.131 305 10 4 4937 5231 188293014 188293314 8.100000e-113 418
6 TraesCS7A01G226500 chr7D 94.466 253 13 1 1 252 188190084 188190336 6.350000e-104 388
7 TraesCS7A01G226500 chr7B 92.906 1889 94 24 1 1875 332127895 332129757 0.000000e+00 2710
8 TraesCS7A01G226500 chr7B 93.708 747 35 7 1965 2706 332129902 332130641 0.000000e+00 1109
9 TraesCS7A01G226500 chr5A 78.560 1292 233 36 2047 3315 687280350 687279080 0.000000e+00 811
10 TraesCS7A01G226500 chr6A 77.488 1075 199 34 2129 3177 7006315 7005258 5.790000e-169 604
11 TraesCS7A01G226500 chr6A 76.510 745 137 28 998 1729 6976864 6976145 6.400000e-99 372
12 TraesCS7A01G226500 chr6A 72.853 722 170 24 1015 1724 611338373 611337666 1.900000e-54 224
13 TraesCS7A01G226500 chr6D 77.801 964 170 29 2244 3177 7283414 7282465 5.920000e-154 555
14 TraesCS7A01G226500 chr6D 77.694 928 185 20 2255 3174 21706903 21705990 9.900000e-152 547
15 TraesCS7A01G226500 chr6D 77.094 812 154 24 998 1790 7292498 7291700 1.730000e-119 440
16 TraesCS7A01G226500 chr4D 77.947 789 155 16 1010 1790 502762017 502761240 4.740000e-130 475
17 TraesCS7A01G226500 chr6B 73.710 601 142 16 1010 1602 708730902 708730310 2.450000e-53 220
18 TraesCS7A01G226500 chr6B 73.920 602 122 29 1014 1602 708723886 708723307 5.310000e-50 209
19 TraesCS7A01G226500 chr4A 81.061 132 24 1 2485 2616 647381192 647381062 2.580000e-18 104


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 TraesCS7A01G226500 chr7A 195827496 195832726 5230 True 9660.0 9660 100.00000 1 5231 1 chr7A.!!$R1 5230
1 TraesCS7A01G226500 chr7A 18980261 18981181 920 False 575.0 575 78.25200 2250 3174 1 chr7A.!!$F1 924
2 TraesCS7A01G226500 chr7D 188288388 188293314 4926 False 1884.5 4800 94.04625 305 5231 4 chr7D.!!$F2 4926
3 TraesCS7A01G226500 chr7B 332127895 332130641 2746 False 1909.5 2710 93.30700 1 2706 2 chr7B.!!$F1 2705
4 TraesCS7A01G226500 chr5A 687279080 687280350 1270 True 811.0 811 78.56000 2047 3315 1 chr5A.!!$R1 1268
5 TraesCS7A01G226500 chr6A 7005258 7006315 1057 True 604.0 604 77.48800 2129 3177 1 chr6A.!!$R2 1048
6 TraesCS7A01G226500 chr6A 6976145 6976864 719 True 372.0 372 76.51000 998 1729 1 chr6A.!!$R1 731
7 TraesCS7A01G226500 chr6A 611337666 611338373 707 True 224.0 224 72.85300 1015 1724 1 chr6A.!!$R3 709
8 TraesCS7A01G226500 chr6D 7282465 7283414 949 True 555.0 555 77.80100 2244 3177 1 chr6D.!!$R1 933
9 TraesCS7A01G226500 chr6D 21705990 21706903 913 True 547.0 547 77.69400 2255 3174 1 chr6D.!!$R3 919
10 TraesCS7A01G226500 chr6D 7291700 7292498 798 True 440.0 440 77.09400 998 1790 1 chr6D.!!$R2 792
11 TraesCS7A01G226500 chr4D 502761240 502762017 777 True 475.0 475 77.94700 1010 1790 1 chr4D.!!$R1 780
12 TraesCS7A01G226500 chr6B 708730310 708730902 592 True 220.0 220 73.71000 1010 1602 1 chr6B.!!$R2 592
13 TraesCS7A01G226500 chr6B 708723307 708723886 579 True 209.0 209 73.92000 1014 1602 1 chr6B.!!$R1 588

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
534 548 0.796312 CCTTATTTCGCACGTGCAGT 59.204 50.000 37.03 21.99 42.21 4.40 F
715 729 1.055849 TGCCAACCTGAGCTTCAGTA 58.944 50.000 10.86 0.00 42.80 2.74 F
1462 1485 1.150536 ATTGACCCACGTGTTGCCT 59.849 52.632 15.65 0.00 0.00 4.75 F
3177 3303 0.892063 AGCTCCTCCGAGTTCTGTTC 59.108 55.000 0.00 0.00 38.49 3.18 F
3903 4029 0.180171 TTGTCATATGTGCGGGGAGG 59.820 55.000 1.90 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1485 0.999406 GCTGCGTTTTCATAGAGCGA 59.001 50.000 0.00 0.00 0.00 4.93 R
2639 2762 4.086706 ACTCCTTCCAACGTGAGATTTT 57.913 40.909 5.44 0.00 0.00 1.82 R
3185 3311 0.685097 ATCAACTGTAGCACGGTGGT 59.315 50.000 17.69 17.69 37.84 4.16 R
4113 4239 0.034896 TGCTTCTCTTCGTGGGTTCC 59.965 55.000 0.00 0.00 0.00 3.62 R
4988 5201 0.916086 ACGGGATACATCAGGGCAAA 59.084 50.000 0.00 0.00 39.74 3.68 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
121 122 1.201181 ACGCTGTGAGTCTGAGATGAC 59.799 52.381 0.00 0.00 37.23 3.06
126 127 3.347216 TGTGAGTCTGAGATGACGATCA 58.653 45.455 0.00 0.00 41.47 2.92
139 140 1.412710 GACGATCAAGGTCAGCCCATA 59.587 52.381 0.00 0.00 34.56 2.74
140 141 2.037772 GACGATCAAGGTCAGCCCATAT 59.962 50.000 0.00 0.00 34.56 1.78
141 142 2.224378 ACGATCAAGGTCAGCCCATATG 60.224 50.000 0.00 0.00 34.66 1.78
142 143 2.037641 CGATCAAGGTCAGCCCATATGA 59.962 50.000 3.65 0.00 34.66 2.15
143 144 3.307269 CGATCAAGGTCAGCCCATATGAT 60.307 47.826 3.65 0.00 36.54 2.45
144 145 3.777106 TCAAGGTCAGCCCATATGATC 57.223 47.619 3.65 0.00 34.66 2.92
146 147 2.107031 CAAGGTCAGCCCATATGATCCA 59.893 50.000 3.65 0.00 34.66 3.41
147 148 2.640651 AGGTCAGCCCATATGATCCAT 58.359 47.619 3.65 0.00 34.66 3.41
148 149 3.806975 AGGTCAGCCCATATGATCCATA 58.193 45.455 3.65 0.00 34.66 2.74
149 150 4.378047 AGGTCAGCCCATATGATCCATAT 58.622 43.478 3.65 0.00 37.51 1.78
166 168 5.693961 TCCATATAGCTCAAAATTGGCAGA 58.306 37.500 0.00 0.00 0.00 4.26
185 187 7.265673 TGGCAGACAATACTAATACTGAACTC 58.734 38.462 0.00 0.00 0.00 3.01
188 190 8.596380 GCAGACAATACTAATACTGAACTCAAC 58.404 37.037 0.00 0.00 0.00 3.18
191 193 9.856488 GACAATACTAATACTGAACTCAACAGA 57.144 33.333 0.00 0.00 38.55 3.41
215 217 8.055181 AGACATATATGATGGGAAAACACAACT 58.945 33.333 19.63 0.00 0.00 3.16
218 220 4.853924 ATGATGGGAAAACACAACTGAC 57.146 40.909 0.00 0.00 0.00 3.51
223 225 5.215252 TGGGAAAACACAACTGACAAAAA 57.785 34.783 0.00 0.00 0.00 1.94
265 267 1.555075 GACAGTTACATCCAGAGGGCA 59.445 52.381 0.00 0.00 0.00 5.36
276 278 2.103094 TCCAGAGGGCAACTAATCATCG 59.897 50.000 0.00 0.00 0.00 3.84
284 286 4.578928 GGGCAACTAATCATCGTGGTTTAT 59.421 41.667 0.00 0.00 0.00 1.40
300 302 3.181510 GGTTTATCTGCACATTGTCGACC 60.182 47.826 14.12 0.00 0.00 4.79
301 303 3.326836 TTATCTGCACATTGTCGACCA 57.673 42.857 14.12 1.38 0.00 4.02
302 304 2.183478 ATCTGCACATTGTCGACCAA 57.817 45.000 14.12 7.96 37.49 3.67
303 305 1.960417 TCTGCACATTGTCGACCAAA 58.040 45.000 14.12 1.35 36.44 3.28
333 335 6.553857 TGTAATGTTTATACCCCTTGTTGGT 58.446 36.000 0.00 0.00 39.97 3.67
420 423 2.887733 GTGCGAAGTACGAAAACACAG 58.112 47.619 0.00 0.00 45.77 3.66
428 439 3.746492 AGTACGAAAACACAGCCTCAATC 59.254 43.478 0.00 0.00 0.00 2.67
429 440 2.571212 ACGAAAACACAGCCTCAATCA 58.429 42.857 0.00 0.00 0.00 2.57
434 445 6.037172 ACGAAAACACAGCCTCAATCATATAC 59.963 38.462 0.00 0.00 0.00 1.47
438 449 5.773575 ACACAGCCTCAATCATATACGTAG 58.226 41.667 0.08 0.00 0.00 3.51
456 470 2.240493 AGGTGGACTTGACTTGTTCG 57.760 50.000 0.00 0.00 0.00 3.95
459 473 2.287103 GGTGGACTTGACTTGTTCGTTC 59.713 50.000 0.00 0.00 0.00 3.95
480 494 1.073199 CCAACCACTCCCACCAGAC 59.927 63.158 0.00 0.00 0.00 3.51
511 525 2.032302 CGCATACTACTCTGCTCGTTCT 59.968 50.000 0.00 0.00 36.23 3.01
534 548 0.796312 CCTTATTTCGCACGTGCAGT 59.204 50.000 37.03 21.99 42.21 4.40
535 549 1.996898 CCTTATTTCGCACGTGCAGTA 59.003 47.619 37.03 22.28 42.21 2.74
537 551 2.640346 TATTTCGCACGTGCAGTAGA 57.360 45.000 37.03 24.17 42.21 2.59
563 577 2.257691 TCTCCTCCGACTCCGATAAG 57.742 55.000 0.00 0.00 38.22 1.73
673 687 8.423906 ACTTTCAGAGGTTATTAACTCTCTCA 57.576 34.615 17.55 8.58 41.90 3.27
674 688 8.527810 ACTTTCAGAGGTTATTAACTCTCTCAG 58.472 37.037 17.55 15.88 41.90 3.35
715 729 1.055849 TGCCAACCTGAGCTTCAGTA 58.944 50.000 10.86 0.00 42.80 2.74
742 756 6.092955 TGTGAATTAGTAGGAACTCAACGT 57.907 37.500 0.00 0.00 41.75 3.99
783 797 7.767198 ACAGCTACAAAGTTGTACTAAAGTTGA 59.233 33.333 12.06 0.00 44.39 3.18
877 891 7.393551 AGTTTTCGTTTCAATTAACATGCTG 57.606 32.000 0.00 0.00 0.00 4.41
884 898 8.722394 TCGTTTCAATTAACATGCTGTTACATA 58.278 29.630 7.87 0.00 41.97 2.29
885 899 9.502145 CGTTTCAATTAACATGCTGTTACATAT 57.498 29.630 7.87 0.00 41.97 1.78
956 970 4.679639 CGAACCAACTCGGAAATCCTGATA 60.680 45.833 0.00 0.00 38.63 2.15
998 1012 2.304761 AGGAGCCAAGATAAACGGTTGA 59.695 45.455 0.00 0.00 0.00 3.18
1365 1388 3.629398 GGATTGCTCGACAAATTGAGGAT 59.371 43.478 0.00 0.00 42.86 3.24
1462 1485 1.150536 ATTGACCCACGTGTTGCCT 59.849 52.632 15.65 0.00 0.00 4.75
1633 1656 2.859165 TGGTAAGCTCAAGGGTGAAG 57.141 50.000 0.00 0.00 31.88 3.02
2211 2306 8.610248 TTTGGTTCGATGTCTTAATTACTTGA 57.390 30.769 0.00 0.00 0.00 3.02
2639 2762 7.940137 TGTAAGGAGTTGTTTAGGCTCATTAAA 59.060 33.333 0.00 0.00 37.29 1.52
2808 2934 2.755103 GGAAGGATTTGTCGGCAAAGAT 59.245 45.455 21.05 4.67 46.30 2.40
2809 2935 3.193479 GGAAGGATTTGTCGGCAAAGATT 59.807 43.478 21.05 14.21 46.30 2.40
2821 2947 5.066505 GTCGGCAAAGATTATGGACAAGATT 59.933 40.000 0.00 0.00 0.00 2.40
2901 3027 3.745799 TGTAAAATTTGACGGCAGAGGA 58.254 40.909 0.00 0.00 0.00 3.71
2910 3036 1.142748 CGGCAGAGGATCAGTGACC 59.857 63.158 0.00 0.00 37.82 4.02
3045 3171 1.335597 CGTCGGCTGTCTGTTCACTTA 60.336 52.381 0.00 0.00 0.00 2.24
3054 3180 6.262601 GCTGTCTGTTCACTTAGATAGTCTC 58.737 44.000 0.00 0.00 35.40 3.36
3060 3186 8.948145 TCTGTTCACTTAGATAGTCTCAGTAAC 58.052 37.037 0.00 2.16 29.82 2.50
3061 3187 8.631480 TGTTCACTTAGATAGTCTCAGTAACA 57.369 34.615 0.00 9.58 29.82 2.41
3148 3274 4.515191 GCTCTGAGAGTACACCTGATCTAG 59.485 50.000 11.64 0.00 31.39 2.43
3160 3286 5.126384 ACACCTGATCTAGTAGAGTTCAAGC 59.874 44.000 5.98 0.00 34.23 4.01
3177 3303 0.892063 AGCTCCTCCGAGTTCTGTTC 59.108 55.000 0.00 0.00 38.49 3.18
3185 3311 4.562757 CCTCCGAGTTCTGTTCATTAACCA 60.563 45.833 0.00 0.00 34.49 3.67
3189 3315 4.084013 CGAGTTCTGTTCATTAACCACCAC 60.084 45.833 0.00 0.00 34.49 4.16
3256 3382 4.581824 TGAGGTATTTACGGATTAGTCGCT 59.418 41.667 0.00 0.00 0.00 4.93
3316 3442 5.574891 ACAACACTTGCAAACACTTGATA 57.425 34.783 0.00 0.00 34.14 2.15
3318 3444 5.978919 ACAACACTTGCAAACACTTGATATG 59.021 36.000 0.00 0.00 34.14 1.78
3326 3452 4.947388 GCAAACACTTGATATGGGAAGGTA 59.053 41.667 0.00 0.00 34.14 3.08
3347 3473 8.940012 AGGTATTCCAATATTCCCTCAGATAT 57.060 34.615 0.00 0.00 35.89 1.63
3348 3474 9.356649 AGGTATTCCAATATTCCCTCAGATATT 57.643 33.333 0.00 0.00 35.89 1.28
3349 3475 9.981460 GGTATTCCAATATTCCCTCAGATATTT 57.019 33.333 0.00 0.00 0.00 1.40
3352 3478 9.887862 ATTCCAATATTCCCTCAGATATTTTGT 57.112 29.630 0.00 0.00 0.00 2.83
3353 3479 8.924511 TCCAATATTCCCTCAGATATTTTGTC 57.075 34.615 0.00 0.00 0.00 3.18
3354 3480 7.661437 TCCAATATTCCCTCAGATATTTTGTCG 59.339 37.037 0.00 0.00 0.00 4.35
3355 3481 7.661437 CCAATATTCCCTCAGATATTTTGTCGA 59.339 37.037 0.00 0.00 0.00 4.20
3356 3482 9.056005 CAATATTCCCTCAGATATTTTGTCGAA 57.944 33.333 0.00 0.00 0.00 3.71
3357 3483 9.627123 AATATTCCCTCAGATATTTTGTCGAAA 57.373 29.630 0.00 0.00 0.00 3.46
3358 3484 7.938140 ATTCCCTCAGATATTTTGTCGAAAA 57.062 32.000 0.00 0.00 35.52 2.29
3359 3485 7.753309 TTCCCTCAGATATTTTGTCGAAAAA 57.247 32.000 0.00 0.00 34.72 1.94
3388 3514 6.019748 CCCTCAGATATAGTTCACCTACCAT 58.980 44.000 0.00 0.00 0.00 3.55
3397 3523 4.770795 AGTTCACCTACCATACTTGATGC 58.229 43.478 0.00 0.00 33.79 3.91
3414 3540 5.678132 TGATGCATCTAAATGTTGGATCG 57.322 39.130 26.32 0.00 42.44 3.69
3418 3544 3.058639 GCATCTAAATGTTGGATCGGAGC 60.059 47.826 0.00 0.00 35.18 4.70
3432 3558 3.924114 TCGGAGCTTTTTGATGGGATA 57.076 42.857 0.00 0.00 0.00 2.59
3452 3578 1.482593 AGGCAAGATGAAGTCCCTACG 59.517 52.381 0.00 0.00 0.00 3.51
3516 3642 7.092716 ACAATATCAAAAACATTGGTGAGCTC 58.907 34.615 6.82 6.82 34.63 4.09
3555 3681 3.281727 TTTATCTCATGTGGCCCTCAC 57.718 47.619 0.00 0.00 46.23 3.51
3557 3683 0.622738 ATCTCATGTGGCCCTCACCT 60.623 55.000 0.00 0.00 45.48 4.00
3561 3687 2.606587 ATGTGGCCCTCACCTGGAC 61.607 63.158 0.00 0.00 45.48 4.02
3576 3702 0.812811 TGGACGATACGGAGAGACGG 60.813 60.000 0.00 0.00 38.39 4.79
3577 3703 0.531532 GGACGATACGGAGAGACGGA 60.532 60.000 0.00 0.00 38.39 4.69
3603 3729 3.628008 TGTATTACGCTCTTCTCTGGGA 58.372 45.455 0.00 0.00 0.00 4.37
3612 3738 2.739379 CTCTTCTCTGGGAAAACTTCGC 59.261 50.000 0.00 0.00 42.39 4.70
3621 3747 2.287608 GGGAAAACTTCGCAACCTTGAG 60.288 50.000 0.00 0.00 41.74 3.02
3622 3748 2.287608 GGAAAACTTCGCAACCTTGAGG 60.288 50.000 0.00 0.00 42.17 3.86
3628 3754 1.118965 TCGCAACCTTGAGGACCTGA 61.119 55.000 0.00 0.00 38.94 3.86
3651 3777 2.101640 TCAGTATGAGGGGCTGCATA 57.898 50.000 0.50 0.00 42.56 3.14
3692 3818 0.549169 CCTCCCCCAACTCCTTACCA 60.549 60.000 0.00 0.00 0.00 3.25
3744 3870 1.564348 TGGTTTTCCAGGATCCCTAGC 59.436 52.381 8.55 0.00 46.22 3.42
3761 3887 0.760945 AGCTGGATAGGGGAACTCCG 60.761 60.000 0.00 0.00 36.71 4.63
3779 3905 1.466360 CCGTAACCTCGGTGAACTACG 60.466 57.143 9.83 9.83 44.77 3.51
3804 3930 3.318839 TGCAAGTTTGTGAGCTGCTAAAT 59.681 39.130 0.15 0.00 0.00 1.40
3828 3954 4.286297 TGGTGTTGGTATCCTTTCAGAG 57.714 45.455 0.00 0.00 0.00 3.35
3834 3960 1.488393 GGTATCCTTTCAGAGCTGCCT 59.512 52.381 0.00 0.00 0.00 4.75
3887 4013 6.201044 CGAAGAGCCGTAGATAAAATGATTGT 59.799 38.462 0.00 0.00 0.00 2.71
3903 4029 0.180171 TTGTCATATGTGCGGGGAGG 59.820 55.000 1.90 0.00 0.00 4.30
4019 4145 7.896811 AGACTCGAGGTAATGCATAATATGAA 58.103 34.615 18.41 0.00 0.00 2.57
4042 4168 2.107901 GGATCAGATCAGAATGGGGCTT 59.892 50.000 12.66 0.00 36.16 4.35
4080 4206 2.412065 GCACTTGTTAGCGCTTGAAGAG 60.412 50.000 18.68 14.55 0.00 2.85
4113 4239 2.094659 CGGCTGTGAAGGTGCTACG 61.095 63.158 0.00 0.00 0.00 3.51
4131 4257 1.014564 CGGAACCCACGAAGAGAAGC 61.015 60.000 0.00 0.00 0.00 3.86
4276 4402 5.523916 AGCAACATCTCGTATGTACAAATCC 59.476 40.000 0.00 0.00 0.00 3.01
4302 4428 3.462021 CTTCATTCTCCCCGTCTCAATC 58.538 50.000 0.00 0.00 0.00 2.67
4317 4443 5.452496 CGTCTCAATCTCTCTCTCTCTCTCT 60.452 48.000 0.00 0.00 0.00 3.10
4318 4444 5.988561 GTCTCAATCTCTCTCTCTCTCTCTC 59.011 48.000 0.00 0.00 0.00 3.20
4319 4445 5.901853 TCTCAATCTCTCTCTCTCTCTCTCT 59.098 44.000 0.00 0.00 0.00 3.10
4320 4446 6.041409 TCTCAATCTCTCTCTCTCTCTCTCTC 59.959 46.154 0.00 0.00 0.00 3.20
4321 4447 5.901853 TCAATCTCTCTCTCTCTCTCTCTCT 59.098 44.000 0.00 0.00 0.00 3.10
4322 4448 6.041409 TCAATCTCTCTCTCTCTCTCTCTCTC 59.959 46.154 0.00 0.00 0.00 3.20
4323 4449 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
4324 4450 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4325 4451 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4326 4452 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4327 4453 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4328 4454 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4329 4455 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4330 4456 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4331 4457 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4332 4458 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4333 4459 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4334 4460 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4335 4461 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4336 4462 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4337 4463 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4338 4464 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4339 4465 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4340 4466 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4341 4467 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4342 4468 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4343 4469 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4344 4470 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4345 4471 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4346 4472 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4347 4473 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4348 4474 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4349 4475 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4350 4476 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4351 4477 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4352 4478 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4353 4479 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4354 4480 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4355 4481 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4356 4482 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4357 4483 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4358 4484 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4359 4485 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
4360 4486 5.462240 TCTCTCTCTCTCTCTCTCTCTCAT 58.538 45.833 0.00 0.00 0.00 2.90
4408 4534 4.336433 CCATGAAATGTACATCCACCTCAC 59.664 45.833 9.23 0.00 44.81 3.51
4418 4544 0.473694 TCCACCTCACCAGTCACCAT 60.474 55.000 0.00 0.00 0.00 3.55
4457 4583 9.741647 GCTTTGCTAGCTATGATTTTCTTTTAT 57.258 29.630 17.23 0.00 46.77 1.40
4477 4603 8.834749 TTTTATTTTGGTATGGCAAGGTTTAC 57.165 30.769 0.00 0.00 0.00 2.01
4489 4615 7.116075 TGGCAAGGTTTACGTAAGATATACT 57.884 36.000 8.23 0.00 43.62 2.12
4634 4760 9.716507 GTGAAATATGTTTGCTAATACGACATT 57.283 29.630 0.00 0.00 33.42 2.71
4658 4784 9.672673 ATTTAGACTTTGTATGCTGTGTCTTAT 57.327 29.630 0.00 0.00 36.39 1.73
4679 4805 8.256605 TCTTATGTTCCTCTCTTCAATCTTCTG 58.743 37.037 0.00 0.00 0.00 3.02
4713 4839 6.981722 TCTTTATTTTCTTGAGGAAACTGCC 58.018 36.000 0.00 0.00 44.43 4.85
4717 4843 2.450609 TCTTGAGGAAACTGCCGTAC 57.549 50.000 0.00 0.00 44.43 3.67
4753 4879 6.713762 TGGGCAATAAATTGTAGAAGATGG 57.286 37.500 4.71 0.00 39.88 3.51
4801 4928 7.381408 GCCTGAGTTTTTACAAAATTACTGACC 59.619 37.037 0.00 0.00 0.00 4.02
4802 4929 8.410141 CCTGAGTTTTTACAAAATTACTGACCA 58.590 33.333 0.00 0.00 0.00 4.02
4845 4973 3.119814 GGAAAGGAGCGGATTTCAGTTTC 60.120 47.826 11.09 0.00 37.19 2.78
4878 5006 1.932156 AACAGGCCAGGGTCACAACA 61.932 55.000 5.01 0.00 0.00 3.33
4905 5087 5.207354 AGGAAGATGTCTCTGCTGAAGATA 58.793 41.667 0.00 0.00 33.29 1.98
4925 5107 6.555315 AGATAAAGCTATTGGTTTTTGCTCG 58.445 36.000 9.50 0.00 42.84 5.03
4980 5193 3.191371 GCTTGTAACAGGATTGTTGGAGG 59.809 47.826 3.33 0.00 46.63 4.30
4988 5201 1.342374 GGATTGTTGGAGGGCAGGAAT 60.342 52.381 0.00 0.00 0.00 3.01
5060 5280 2.358582 TGTTGTTCTGGTGTGCTGAATG 59.641 45.455 0.00 0.00 0.00 2.67
5064 5284 3.070878 TGTTCTGGTGTGCTGAATGACTA 59.929 43.478 0.00 0.00 0.00 2.59
5065 5285 4.256920 GTTCTGGTGTGCTGAATGACTAT 58.743 43.478 0.00 0.00 0.00 2.12
5066 5286 3.865446 TCTGGTGTGCTGAATGACTATG 58.135 45.455 0.00 0.00 0.00 2.23
5067 5287 2.941064 CTGGTGTGCTGAATGACTATGG 59.059 50.000 0.00 0.00 0.00 2.74
5068 5288 2.305635 TGGTGTGCTGAATGACTATGGT 59.694 45.455 0.00 0.00 0.00 3.55
5121 5341 5.684704 CCCTGATGCTCCTACTTTGATAAA 58.315 41.667 0.00 0.00 0.00 1.40
5127 5347 8.514594 TGATGCTCCTACTTTGATAAAAACTTG 58.485 33.333 0.00 0.00 0.00 3.16
5180 5403 9.494271 AATACAAGTAGATGCGTTTGATATGAT 57.506 29.630 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.542005 TCTGCAGACAAGAAACATTCAGTTAA 59.458 34.615 13.74 0.00 40.26 2.01
70 71 7.140705 TGAACTTGCATTGAAATTGACAGTAG 58.859 34.615 0.00 0.00 0.00 2.57
121 122 2.037641 TCATATGGGCTGACCTTGATCG 59.962 50.000 0.00 0.00 41.11 3.69
126 127 2.421725 TGGATCATATGGGCTGACCTT 58.578 47.619 0.00 0.00 41.11 3.50
139 140 6.722590 TGCCAATTTTGAGCTATATGGATCAT 59.277 34.615 7.91 0.00 31.57 2.45
140 141 6.069994 TGCCAATTTTGAGCTATATGGATCA 58.930 36.000 2.54 2.54 0.00 2.92
141 142 6.432162 TCTGCCAATTTTGAGCTATATGGATC 59.568 38.462 0.00 0.00 0.00 3.36
142 143 6.208204 GTCTGCCAATTTTGAGCTATATGGAT 59.792 38.462 0.00 0.00 0.00 3.41
143 144 5.532406 GTCTGCCAATTTTGAGCTATATGGA 59.468 40.000 0.00 0.00 0.00 3.41
144 145 5.300034 TGTCTGCCAATTTTGAGCTATATGG 59.700 40.000 0.00 0.00 0.00 2.74
146 147 7.592885 ATTGTCTGCCAATTTTGAGCTATAT 57.407 32.000 0.00 0.00 41.01 0.86
147 148 7.775093 AGTATTGTCTGCCAATTTTGAGCTATA 59.225 33.333 0.00 0.00 41.01 1.31
148 149 5.927281 ATTGTCTGCCAATTTTGAGCTAT 57.073 34.783 0.00 0.00 41.01 2.97
149 150 5.945784 AGTATTGTCTGCCAATTTTGAGCTA 59.054 36.000 0.00 0.00 41.01 3.32
166 168 9.640963 GTCTGTTGAGTTCAGTATTAGTATTGT 57.359 33.333 0.00 0.00 34.86 2.71
185 187 8.131100 GTGTTTTCCCATCATATATGTCTGTTG 58.869 37.037 12.42 4.57 0.00 3.33
188 190 7.806409 TGTGTTTTCCCATCATATATGTCTG 57.194 36.000 12.42 10.79 0.00 3.51
191 193 7.833682 TCAGTTGTGTTTTCCCATCATATATGT 59.166 33.333 12.42 0.00 0.00 2.29
198 200 3.625853 TGTCAGTTGTGTTTTCCCATCA 58.374 40.909 0.00 0.00 0.00 3.07
223 225 8.862325 TGTCAGTCTGAATGTTATTACCAAAT 57.138 30.769 3.51 0.00 0.00 2.32
265 267 6.037172 GTGCAGATAAACCACGATGATTAGTT 59.963 38.462 0.00 0.00 0.00 2.24
276 278 3.435327 TCGACAATGTGCAGATAAACCAC 59.565 43.478 0.00 0.00 0.00 4.16
284 286 1.960417 TTTGGTCGACAATGTGCAGA 58.040 45.000 18.91 0.00 39.21 4.26
300 302 7.998964 AGGGGTATAAACATTACAGGAGATTTG 59.001 37.037 0.00 0.00 0.00 2.32
301 303 8.114301 AGGGGTATAAACATTACAGGAGATTT 57.886 34.615 0.00 0.00 0.00 2.17
302 304 7.707467 AGGGGTATAAACATTACAGGAGATT 57.293 36.000 0.00 0.00 0.00 2.40
303 305 7.128883 ACAAGGGGTATAAACATTACAGGAGAT 59.871 37.037 0.00 0.00 0.00 2.75
333 335 0.994247 AGCATGACATGGGAGGTGAA 59.006 50.000 17.03 0.00 0.00 3.18
414 417 5.023533 ACGTATATGATTGAGGCTGTGTT 57.976 39.130 0.00 0.00 0.00 3.32
420 423 4.219944 TCCACCTACGTATATGATTGAGGC 59.780 45.833 0.00 0.00 0.00 4.70
428 439 5.769484 AGTCAAGTCCACCTACGTATATG 57.231 43.478 0.00 0.00 0.00 1.78
429 440 5.655532 ACAAGTCAAGTCCACCTACGTATAT 59.344 40.000 0.00 0.00 0.00 0.86
434 445 2.814280 ACAAGTCAAGTCCACCTACG 57.186 50.000 0.00 0.00 0.00 3.51
438 449 1.949465 ACGAACAAGTCAAGTCCACC 58.051 50.000 0.00 0.00 0.00 4.61
456 470 2.439245 GGGAGTGGTTGGGGGAAC 59.561 66.667 0.00 0.00 0.00 3.62
459 473 3.979497 GGTGGGAGTGGTTGGGGG 61.979 72.222 0.00 0.00 0.00 5.40
480 494 5.586339 CAGAGTAGTATGCGATGATATGGG 58.414 45.833 0.00 0.00 0.00 4.00
511 525 1.730064 GCACGTGCGAAATAAGGAGAA 59.270 47.619 26.77 0.00 0.00 2.87
534 548 4.585162 GGAGTCGGAGGAGATGAAATTCTA 59.415 45.833 0.00 0.00 0.00 2.10
535 549 3.386402 GGAGTCGGAGGAGATGAAATTCT 59.614 47.826 0.00 0.00 0.00 2.40
537 551 2.101582 CGGAGTCGGAGGAGATGAAATT 59.898 50.000 0.00 0.00 0.00 1.82
673 687 2.291741 CGAAAAGCAAAGCAGAGTTCCT 59.708 45.455 0.00 0.00 0.00 3.36
674 688 2.033424 ACGAAAAGCAAAGCAGAGTTCC 59.967 45.455 0.00 0.00 0.00 3.62
715 729 6.299805 TGAGTTCCTACTAATTCACAGCAT 57.700 37.500 0.00 0.00 33.84 3.79
742 756 3.695830 AGCTGTTTACCCAATCGAAGA 57.304 42.857 0.00 0.00 45.75 2.87
783 797 7.316393 TCCCTTCGATCCATATTAATTGTCT 57.684 36.000 0.00 0.00 0.00 3.41
933 947 1.732259 CAGGATTTCCGAGTTGGTTCG 59.268 52.381 0.00 0.00 42.08 3.95
998 1012 4.102210 CACTCACCAATATCCTGTCCATCT 59.898 45.833 0.00 0.00 0.00 2.90
1227 1244 5.842907 TCAATGATTTCCTCGATGTCGTAT 58.157 37.500 2.04 0.00 40.80 3.06
1365 1388 6.334989 TGTCTCGAGAACAAGTTTCTTTACA 58.665 36.000 18.55 3.08 0.00 2.41
1462 1485 0.999406 GCTGCGTTTTCATAGAGCGA 59.001 50.000 0.00 0.00 0.00 4.93
2031 2115 7.825331 TTGTTTAAGACCAATATTGTCACCA 57.175 32.000 14.25 3.98 0.00 4.17
2271 2373 6.014755 AGGCTGATACATCCCATATATCATCG 60.015 42.308 0.00 0.00 35.37 3.84
2639 2762 4.086706 ACTCCTTCCAACGTGAGATTTT 57.913 40.909 5.44 0.00 0.00 1.82
2808 2934 5.630121 ACCTTCACACAATCTTGTCCATAA 58.370 37.500 0.00 0.00 39.91 1.90
2809 2935 5.241403 ACCTTCACACAATCTTGTCCATA 57.759 39.130 0.00 0.00 39.91 2.74
2821 2947 2.605837 TTACTTGCGACCTTCACACA 57.394 45.000 0.00 0.00 0.00 3.72
2901 3027 5.255687 TGTATCTTGCATTTGGTCACTGAT 58.744 37.500 0.00 0.00 0.00 2.90
2910 3036 8.244113 AGCATCATATCATGTATCTTGCATTTG 58.756 33.333 14.42 0.00 0.00 2.32
2998 3124 5.487488 TCTTGTAATCCAGTCCTGTAATGGT 59.513 40.000 0.00 0.00 35.51 3.55
3045 3171 5.712446 TGCTTGACTGTTACTGAGACTATCT 59.288 40.000 0.00 0.00 0.00 1.98
3054 3180 6.533723 TCGGTAATATTGCTTGACTGTTACTG 59.466 38.462 3.46 0.00 0.00 2.74
3060 3186 4.693283 TCCTCGGTAATATTGCTTGACTG 58.307 43.478 3.46 0.00 0.00 3.51
3061 3187 5.116882 GTTCCTCGGTAATATTGCTTGACT 58.883 41.667 3.46 0.00 0.00 3.41
3148 3274 2.093106 TCGGAGGAGCTTGAACTCTAC 58.907 52.381 0.00 0.00 36.87 2.59
3160 3286 3.601443 AATGAACAGAACTCGGAGGAG 57.399 47.619 10.23 0.00 46.13 3.69
3185 3311 0.685097 ATCAACTGTAGCACGGTGGT 59.315 50.000 17.69 17.69 37.84 4.16
3189 3315 2.094494 ACTGAGATCAACTGTAGCACGG 60.094 50.000 0.00 0.00 0.00 4.94
3326 3452 9.887862 ACAAAATATCTGAGGGAATATTGGAAT 57.112 29.630 0.00 0.00 0.00 3.01
3357 3483 8.560903 AGGTGAACTATATCTGAGGGAATTTTT 58.439 33.333 0.00 0.00 0.00 1.94
3358 3484 8.107196 AGGTGAACTATATCTGAGGGAATTTT 57.893 34.615 0.00 0.00 0.00 1.82
3359 3485 7.698163 AGGTGAACTATATCTGAGGGAATTT 57.302 36.000 0.00 0.00 0.00 1.82
3360 3486 7.235812 GGTAGGTGAACTATATCTGAGGGAATT 59.764 40.741 0.00 0.00 33.43 2.17
3361 3487 6.726764 GGTAGGTGAACTATATCTGAGGGAAT 59.273 42.308 0.00 0.00 33.43 3.01
3362 3488 6.075984 GGTAGGTGAACTATATCTGAGGGAA 58.924 44.000 0.00 0.00 33.43 3.97
3363 3489 5.135533 TGGTAGGTGAACTATATCTGAGGGA 59.864 44.000 0.00 0.00 33.43 4.20
3364 3490 5.394738 TGGTAGGTGAACTATATCTGAGGG 58.605 45.833 0.00 0.00 33.43 4.30
3365 3491 7.891183 AGTATGGTAGGTGAACTATATCTGAGG 59.109 40.741 0.00 0.00 33.43 3.86
3366 3492 8.871629 AGTATGGTAGGTGAACTATATCTGAG 57.128 38.462 0.00 0.00 33.43 3.35
3367 3493 9.078990 CAAGTATGGTAGGTGAACTATATCTGA 57.921 37.037 0.00 0.00 33.43 3.27
3368 3494 9.078990 TCAAGTATGGTAGGTGAACTATATCTG 57.921 37.037 0.00 0.00 33.43 2.90
3369 3495 9.830186 ATCAAGTATGGTAGGTGAACTATATCT 57.170 33.333 0.00 0.00 33.43 1.98
3370 3496 9.862371 CATCAAGTATGGTAGGTGAACTATATC 57.138 37.037 0.00 0.00 33.43 1.63
3371 3497 8.314751 GCATCAAGTATGGTAGGTGAACTATAT 58.685 37.037 0.00 0.00 35.99 0.86
3372 3498 7.289084 TGCATCAAGTATGGTAGGTGAACTATA 59.711 37.037 0.00 0.00 35.99 1.31
3373 3499 6.099701 TGCATCAAGTATGGTAGGTGAACTAT 59.900 38.462 0.00 0.00 35.99 2.12
3381 3507 7.663081 ACATTTAGATGCATCAAGTATGGTAGG 59.337 37.037 27.81 8.07 36.72 3.18
3388 3514 7.041848 CGATCCAACATTTAGATGCATCAAGTA 60.042 37.037 27.81 9.62 36.72 2.24
3397 3523 4.384056 AGCTCCGATCCAACATTTAGATG 58.616 43.478 0.00 0.00 39.25 2.90
3414 3540 2.625314 GCCTATCCCATCAAAAAGCTCC 59.375 50.000 0.00 0.00 0.00 4.70
3418 3544 5.595542 TCATCTTGCCTATCCCATCAAAAAG 59.404 40.000 0.00 0.00 0.00 2.27
3432 3558 1.482593 CGTAGGGACTTCATCTTGCCT 59.517 52.381 0.00 0.00 41.75 4.75
3452 3578 5.461078 GCCAAATCAAATGCACATAGATGTC 59.539 40.000 0.00 0.00 39.39 3.06
3489 3615 6.311200 GCTCACCAATGTTTTTGATATTGTCC 59.689 38.462 0.00 0.00 35.69 4.02
3492 3618 7.062605 GTGAGCTCACCAATGTTTTTGATATTG 59.937 37.037 32.55 0.00 40.85 1.90
3555 3681 0.945813 GTCTCTCCGTATCGTCCAGG 59.054 60.000 0.00 0.00 0.00 4.45
3557 3683 0.812811 CCGTCTCTCCGTATCGTCCA 60.813 60.000 0.00 0.00 0.00 4.02
3561 3687 0.517755 CCATCCGTCTCTCCGTATCG 59.482 60.000 0.00 0.00 0.00 2.92
3576 3702 5.861251 CAGAGAAGAGCGTAATACATCCATC 59.139 44.000 0.00 0.00 0.00 3.51
3577 3703 5.279206 CCAGAGAAGAGCGTAATACATCCAT 60.279 44.000 0.00 0.00 0.00 3.41
3603 3729 2.357952 GTCCTCAAGGTTGCGAAGTTTT 59.642 45.455 0.00 0.00 36.34 2.43
3612 3738 3.077359 GACAATCAGGTCCTCAAGGTTG 58.923 50.000 0.00 0.00 36.34 3.77
3628 3754 1.133976 GCAGCCCCTCATACTGACAAT 60.134 52.381 0.00 0.00 33.10 2.71
3692 3818 4.932200 GGAACATGACGAATCTCTCAAGTT 59.068 41.667 0.00 0.00 32.47 2.66
3744 3870 2.364647 GTTACGGAGTTCCCCTATCCAG 59.635 54.545 0.00 0.00 37.78 3.86
3761 3887 1.541588 ACCGTAGTTCACCGAGGTTAC 59.458 52.381 0.00 0.00 0.00 2.50
3779 3905 1.843992 CAGCTCACAAACTTGCAACC 58.156 50.000 0.00 0.00 0.00 3.77
3804 3930 4.288366 TCTGAAAGGATACCAACACCATCA 59.712 41.667 0.00 0.00 37.17 3.07
3828 3954 2.029844 GTGAACGAGGACAGGCAGC 61.030 63.158 0.00 0.00 0.00 5.25
3834 3960 3.118775 CCATATCAAGGTGAACGAGGACA 60.119 47.826 0.00 0.00 0.00 4.02
3887 4013 2.146724 CCCCTCCCCGCACATATGA 61.147 63.158 10.38 0.00 0.00 2.15
3930 4056 4.034975 GTCATGCTGCTTATTTGGAGAGAC 59.965 45.833 0.00 0.00 0.00 3.36
3984 4110 1.889829 ACCTCGAGTCTCTGGAGTTTG 59.110 52.381 12.31 0.00 35.12 2.93
4019 4145 2.041350 GCCCCATTCTGATCTGATCCAT 59.959 50.000 14.71 2.28 0.00 3.41
4042 4168 4.147449 CTCGATGCCGGCTGGTGA 62.147 66.667 29.70 18.29 37.67 4.02
4080 4206 3.833706 GCCGATTGCTGCAGATAAC 57.166 52.632 20.43 0.00 36.87 1.89
4113 4239 0.034896 TGCTTCTCTTCGTGGGTTCC 59.965 55.000 0.00 0.00 0.00 3.62
4131 4257 0.972134 TCCTCAAGGCAGACTCTGTG 59.028 55.000 7.89 0.00 33.43 3.66
4221 4347 4.289672 AGCCAAAGGAGAAATTACTCTGGA 59.710 41.667 0.00 0.00 34.05 3.86
4224 4350 5.495640 CTGAGCCAAAGGAGAAATTACTCT 58.504 41.667 0.00 0.00 37.13 3.24
4276 4402 1.815421 CGGGGAGAATGAAGGTGCG 60.815 63.158 0.00 0.00 0.00 5.34
4302 4428 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4317 4443 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4318 4444 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4319 4445 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4320 4446 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4321 4447 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4322 4448 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4323 4449 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4324 4450 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4325 4451 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4326 4452 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4327 4453 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4328 4454 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4329 4455 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4330 4456 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4331 4457 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4332 4458 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4333 4459 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4334 4460 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4335 4461 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
4336 4462 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
4337 4463 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
4338 4464 5.804944 ATGAGAGAGAGAGAGAGAGAGAG 57.195 47.826 0.00 0.00 0.00 3.20
4339 4465 6.566079 AAATGAGAGAGAGAGAGAGAGAGA 57.434 41.667 0.00 0.00 0.00 3.10
4340 4466 7.636150 AAAAATGAGAGAGAGAGAGAGAGAG 57.364 40.000 0.00 0.00 0.00 3.20
4398 4524 0.473694 TGGTGACTGGTGAGGTGGAT 60.474 55.000 0.00 0.00 0.00 3.41
4401 4527 0.321919 CCATGGTGACTGGTGAGGTG 60.322 60.000 2.57 0.00 0.00 4.00
4408 4534 5.048504 GCAATAATGATACCATGGTGACTGG 60.049 44.000 28.17 8.68 39.80 4.00
4457 4583 3.890147 ACGTAAACCTTGCCATACCAAAA 59.110 39.130 0.00 0.00 0.00 2.44
4462 4588 7.958053 ATATCTTACGTAAACCTTGCCATAC 57.042 36.000 9.68 0.00 0.00 2.39
4614 4740 9.811995 AGTCTAAATGTCGTATTAGCAAACATA 57.188 29.630 0.00 0.00 30.71 2.29
4615 4741 8.718102 AGTCTAAATGTCGTATTAGCAAACAT 57.282 30.769 0.00 0.00 32.15 2.71
4616 4742 8.542497 AAGTCTAAATGTCGTATTAGCAAACA 57.458 30.769 0.00 0.00 0.00 2.83
4617 4743 9.262472 CAAAGTCTAAATGTCGTATTAGCAAAC 57.738 33.333 0.00 0.00 0.00 2.93
4618 4744 8.995220 ACAAAGTCTAAATGTCGTATTAGCAAA 58.005 29.630 0.00 0.00 0.00 3.68
4634 4760 8.094548 ACATAAGACACAGCATACAAAGTCTAA 58.905 33.333 0.00 0.00 35.47 2.10
4648 4774 6.030548 TGAAGAGAGGAACATAAGACACAG 57.969 41.667 0.00 0.00 0.00 3.66
4658 4784 4.285517 AGCAGAAGATTGAAGAGAGGAACA 59.714 41.667 0.00 0.00 0.00 3.18
4679 4805 5.011635 TCAAGAAAATAAAGAAACCCCCAGC 59.988 40.000 0.00 0.00 0.00 4.85
4713 4839 4.377021 TGCCCATTTAATCTAGCAGTACG 58.623 43.478 0.00 0.00 0.00 3.67
4717 4843 9.199982 CAATTTATTGCCCATTTAATCTAGCAG 57.800 33.333 0.00 0.00 0.00 4.24
4746 4872 6.710744 TGTAGGAGTTCAGAAAAACCATCTTC 59.289 38.462 0.00 0.00 0.00 2.87
4749 4875 5.106515 GCTGTAGGAGTTCAGAAAAACCATC 60.107 44.000 0.00 0.00 34.02 3.51
4753 4879 4.319839 GCAGCTGTAGGAGTTCAGAAAAAC 60.320 45.833 16.64 0.00 34.02 2.43
4801 4928 6.338146 TCCTGAAAACCAATATAGTCGAGTG 58.662 40.000 2.10 0.00 0.00 3.51
4802 4929 6.540438 TCCTGAAAACCAATATAGTCGAGT 57.460 37.500 0.00 0.00 0.00 4.18
4845 4973 1.334869 GCCTGTTGTTCCAAGTGACAG 59.665 52.381 0.00 0.00 37.92 3.51
4878 5006 3.326006 TCAGCAGAGACATCTTCCTTGTT 59.674 43.478 0.00 0.00 31.64 2.83
4905 5087 4.037446 TCACGAGCAAAAACCAATAGCTTT 59.963 37.500 0.00 0.00 35.36 3.51
4925 5107 8.492673 TGGAACAACAGATGAAATAGTATCAC 57.507 34.615 0.00 0.00 31.92 3.06
4988 5201 0.916086 ACGGGATACATCAGGGCAAA 59.084 50.000 0.00 0.00 39.74 3.68
5060 5280 6.932947 ACAGTACAAAGTAGGAACCATAGTC 58.067 40.000 0.00 0.00 0.00 2.59
5064 5284 6.495872 TCAGTACAGTACAAAGTAGGAACCAT 59.504 38.462 13.37 0.00 0.00 3.55
5065 5285 5.834742 TCAGTACAGTACAAAGTAGGAACCA 59.165 40.000 13.37 0.00 0.00 3.67
5066 5286 6.336842 TCAGTACAGTACAAAGTAGGAACC 57.663 41.667 13.37 0.00 0.00 3.62
5067 5287 9.918630 TTATTCAGTACAGTACAAAGTAGGAAC 57.081 33.333 13.37 0.00 0.00 3.62
5143 5363 7.307042 CGCATCTACTTGTATTGAAATCCAGAG 60.307 40.741 0.00 0.00 0.00 3.35
5144 5364 6.479990 CGCATCTACTTGTATTGAAATCCAGA 59.520 38.462 0.00 0.00 0.00 3.86
5180 5403 2.244000 GCAGCTTGCAAGTCGGTTA 58.756 52.632 26.55 0.00 44.26 2.85


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

AutoCloner maintained by Alex Coulton.