Multiple sequence alignment - TraesCS2B01G177600

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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 TraesCS2B01G177600 chr2B 100.000 4348 0 0 1 4348 152611784 152607437 0.000000e+00 8030
1 TraesCS2B01G177600 chr2B 87.447 1171 129 11 2033 3194 152472991 152474152 0.000000e+00 1332
2 TraesCS2B01G177600 chr2B 87.469 806 101 0 2389 3194 152569896 152569091 0.000000e+00 929
3 TraesCS2B01G177600 chr2B 92.624 583 41 2 1109 1691 152472322 152472902 0.000000e+00 837
4 TraesCS2B01G177600 chr2B 86.184 608 56 15 1109 1691 152570846 152570242 2.210000e-177 632
5 TraesCS2B01G177600 chr2B 90.040 251 25 0 2033 2283 152570140 152569890 4.190000e-85 326
6 TraesCS2B01G177600 chr2D 97.209 1684 36 8 1841 3519 101379232 101377555 0.000000e+00 2839
7 TraesCS2B01G177600 chr2D 90.442 1109 58 15 760 1842 101380555 101379469 0.000000e+00 1417
8 TraesCS2B01G177600 chr2D 87.083 1169 137 7 2033 3194 100421021 100422182 0.000000e+00 1310
9 TraesCS2B01G177600 chr2D 86.621 1166 145 6 2033 3194 101364446 101363288 0.000000e+00 1279
10 TraesCS2B01G177600 chr2D 85.848 1173 156 9 2029 3194 100954306 100953137 0.000000e+00 1238
11 TraesCS2B01G177600 chr2D 92.909 691 26 2 3680 4348 101377556 101376867 0.000000e+00 983
12 TraesCS2B01G177600 chr2D 83.847 941 97 35 782 1691 101365443 101364527 0.000000e+00 845
13 TraesCS2B01G177600 chr2D 91.537 579 47 2 1108 1686 100420385 100420961 0.000000e+00 797
14 TraesCS2B01G177600 chr2D 87.167 600 53 14 1109 1686 100784270 100783673 0.000000e+00 660
15 TraesCS2B01G177600 chr2D 87.617 533 32 16 193 708 101382992 101382477 4.840000e-164 588
16 TraesCS2B01G177600 chr2D 95.266 169 7 1 3515 3682 560959652 560959484 2.580000e-67 267
17 TraesCS2B01G177600 chr2D 94.737 171 8 1 3513 3682 580013762 580013932 9.270000e-67 265
18 TraesCS2B01G177600 chr2D 93.785 177 9 2 3515 3690 647970090 647970265 9.270000e-67 265
19 TraesCS2B01G177600 chr2A 92.040 1583 96 16 1954 3519 100651240 100649671 0.000000e+00 2198
20 TraesCS2B01G177600 chr2A 92.574 983 52 8 930 1895 100657162 100656184 0.000000e+00 1391
21 TraesCS2B01G177600 chr2A 87.210 1165 137 8 2033 3193 100539039 100540195 0.000000e+00 1315
22 TraesCS2B01G177600 chr2A 85.739 1171 137 17 2029 3194 100632458 100631313 0.000000e+00 1210
23 TraesCS2B01G177600 chr2A 91.500 600 29 1 3680 4257 100649672 100649073 0.000000e+00 806
24 TraesCS2B01G177600 chr2A 86.310 767 67 28 936 1689 100538208 100538949 0.000000e+00 800
25 TraesCS2B01G177600 chr2A 87.562 603 53 15 1109 1691 100633158 100632558 0.000000e+00 678
26 TraesCS2B01G177600 chr2A 85.851 523 42 19 209 708 100667869 100667356 1.070000e-145 527
27 TraesCS2B01G177600 chr2A 92.547 161 8 1 760 916 100659137 100658977 1.220000e-55 228
28 TraesCS2B01G177600 chr1D 93.478 184 8 4 3510 3691 178466477 178466296 1.990000e-68 270
29 TraesCS2B01G177600 chr5A 95.266 169 7 1 3515 3682 290391694 290391862 2.580000e-67 267
30 TraesCS2B01G177600 chr5A 87.919 149 11 2 4 146 69544726 69544579 7.480000e-38 169
31 TraesCS2B01G177600 chr4D 95.266 169 7 1 3514 3681 75782221 75782053 2.580000e-67 267
32 TraesCS2B01G177600 chr4D 93.785 177 8 3 3510 3685 403412903 403413077 3.330000e-66 263
33 TraesCS2B01G177600 chr4D 84.768 151 12 2 6 145 507721821 507721671 1.630000e-29 141
34 TraesCS2B01G177600 chr4D 92.632 95 7 0 4 98 323597305 323597211 2.110000e-28 137
35 TraesCS2B01G177600 chr3D 94.737 171 7 2 3514 3682 7607563 7607393 9.270000e-67 265
36 TraesCS2B01G177600 chr6D 93.750 176 9 2 3507 3681 392896965 392897139 3.330000e-66 263
37 TraesCS2B01G177600 chr1B 86.986 146 12 4 4 144 597430664 597430521 1.620000e-34 158
38 TraesCS2B01G177600 chr1A 85.430 151 13 4 2 144 437724136 437723987 9.740000e-32 148
39 TraesCS2B01G177600 chr5D 85.135 148 12 5 4 141 374393309 374393162 4.530000e-30 143
40 TraesCS2B01G177600 chr5D 92.222 90 5 2 632 720 385126925 385126837 4.560000e-25 126
41 TraesCS2B01G177600 chr4A 93.684 95 6 0 4 98 607282104 607282010 4.530000e-30 143
42 TraesCS2B01G177600 chr4A 83.803 142 23 0 4 145 4001298 4001439 7.580000e-28 135
43 TraesCS2B01G177600 chr6A 84.028 144 19 3 2 141 559439497 559439640 7.580000e-28 135


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 TraesCS2B01G177600 chr2B 152607437 152611784 4347 True 8030.00 8030 100.000000 1 4348 1 chr2B.!!$R1 4347
1 TraesCS2B01G177600 chr2B 152472322 152474152 1830 False 1084.50 1332 90.035500 1109 3194 2 chr2B.!!$F1 2085
2 TraesCS2B01G177600 chr2B 152569091 152570846 1755 True 629.00 929 87.897667 1109 3194 3 chr2B.!!$R2 2085
3 TraesCS2B01G177600 chr2D 101376867 101382992 6125 True 1456.75 2839 92.044250 193 4348 4 chr2D.!!$R5 4155
4 TraesCS2B01G177600 chr2D 100953137 100954306 1169 True 1238.00 1238 85.848000 2029 3194 1 chr2D.!!$R2 1165
5 TraesCS2B01G177600 chr2D 101363288 101365443 2155 True 1062.00 1279 85.234000 782 3194 2 chr2D.!!$R4 2412
6 TraesCS2B01G177600 chr2D 100420385 100422182 1797 False 1053.50 1310 89.310000 1108 3194 2 chr2D.!!$F3 2086
7 TraesCS2B01G177600 chr2D 100783673 100784270 597 True 660.00 660 87.167000 1109 1686 1 chr2D.!!$R1 577
8 TraesCS2B01G177600 chr2A 100649073 100651240 2167 True 1502.00 2198 91.770000 1954 4257 2 chr2A.!!$R3 2303
9 TraesCS2B01G177600 chr2A 100538208 100540195 1987 False 1057.50 1315 86.760000 936 3193 2 chr2A.!!$F1 2257
10 TraesCS2B01G177600 chr2A 100631313 100633158 1845 True 944.00 1210 86.650500 1109 3194 2 chr2A.!!$R2 2085
11 TraesCS2B01G177600 chr2A 100656184 100659137 2953 True 809.50 1391 92.560500 760 1895 2 chr2A.!!$R4 1135
12 TraesCS2B01G177600 chr2A 100667356 100667869 513 True 527.00 527 85.851000 209 708 1 chr2A.!!$R1 499

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
692 741 0.034896 TTGGCGAGGAAGACAAGTCC 59.965 55.0 0.0 0.0 33.56 3.85 F
733 2578 0.321298 ATGTTGCCGCTAGAACCGTT 60.321 50.0 0.0 0.0 0.00 4.44 F
1706 5525 0.374063 CGTGGCGTGTGTGTTTTGTA 59.626 50.0 0.0 0.0 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 6517 0.179092 TCATGAGCATGCTCCTGACG 60.179 55.0 36.92 24.15 40.82 4.35 R
2443 6520 1.746470 TGTTCATGAGCATGCTCCTG 58.254 50.0 37.92 36.02 42.09 3.86 R
3669 7758 0.113776 TCACAACCTACTCCCTCCGT 59.886 55.0 0.00 0.00 0.00 4.69 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
50 51 8.904099 ATACTAGTGCAAAAGTAAGTCAAGTT 57.096 30.769 5.39 0.00 32.24 2.66
51 52 7.625828 ACTAGTGCAAAAGTAAGTCAAGTTT 57.374 32.000 0.00 0.00 0.00 2.66
52 53 8.726870 ACTAGTGCAAAAGTAAGTCAAGTTTA 57.273 30.769 0.00 0.00 0.00 2.01
53 54 9.338622 ACTAGTGCAAAAGTAAGTCAAGTTTAT 57.661 29.630 0.00 0.00 0.00 1.40
56 57 8.903820 AGTGCAAAAGTAAGTCAAGTTTATTCT 58.096 29.630 0.00 0.00 0.00 2.40
120 121 8.719560 TTTTTCCACATAGCGTGTATATACAA 57.280 30.769 17.07 2.33 44.78 2.41
121 122 7.703298 TTTCCACATAGCGTGTATATACAAC 57.297 36.000 17.07 12.20 44.78 3.32
122 123 6.644248 TCCACATAGCGTGTATATACAACT 57.356 37.500 17.07 18.01 44.78 3.16
123 124 7.748691 TCCACATAGCGTGTATATACAACTA 57.251 36.000 17.07 19.36 44.78 2.24
124 125 7.813645 TCCACATAGCGTGTATATACAACTAG 58.186 38.462 17.07 15.16 44.78 2.57
125 126 7.662669 TCCACATAGCGTGTATATACAACTAGA 59.337 37.037 17.07 11.54 44.78 2.43
126 127 8.294577 CCACATAGCGTGTATATACAACTAGAA 58.705 37.037 17.07 4.32 44.78 2.10
127 128 9.673454 CACATAGCGTGTATATACAACTAGAAA 57.327 33.333 17.07 4.00 39.62 2.52
128 129 9.674824 ACATAGCGTGTATATACAACTAGAAAC 57.325 33.333 17.07 1.91 39.91 2.78
129 130 9.125906 CATAGCGTGTATATACAACTAGAAACC 57.874 37.037 17.07 1.23 38.04 3.27
130 131 7.104043 AGCGTGTATATACAACTAGAAACCA 57.896 36.000 17.07 0.00 38.04 3.67
131 132 7.549839 AGCGTGTATATACAACTAGAAACCAA 58.450 34.615 17.07 0.00 38.04 3.67
132 133 8.036575 AGCGTGTATATACAACTAGAAACCAAA 58.963 33.333 17.07 0.00 38.04 3.28
133 134 8.658609 GCGTGTATATACAACTAGAAACCAAAA 58.341 33.333 17.07 0.00 38.04 2.44
143 144 9.758651 ACAACTAGAAACCAAAATGTATTTTCC 57.241 29.630 0.00 0.00 37.86 3.13
144 145 9.757227 CAACTAGAAACCAAAATGTATTTTCCA 57.243 29.630 0.00 0.00 37.86 3.53
146 147 9.927668 ACTAGAAACCAAAATGTATTTTCCATG 57.072 29.630 0.00 0.00 37.86 3.66
147 148 9.927668 CTAGAAACCAAAATGTATTTTCCATGT 57.072 29.630 0.00 0.00 37.86 3.21
152 153 9.705290 AACCAAAATGTATTTTCCATGTTAGTC 57.295 29.630 0.00 0.00 37.86 2.59
153 154 8.311109 ACCAAAATGTATTTTCCATGTTAGTCC 58.689 33.333 0.00 0.00 37.86 3.85
154 155 8.531146 CCAAAATGTATTTTCCATGTTAGTCCT 58.469 33.333 0.00 0.00 37.86 3.85
155 156 9.357652 CAAAATGTATTTTCCATGTTAGTCCTG 57.642 33.333 0.00 0.00 37.86 3.86
156 157 8.650143 AAATGTATTTTCCATGTTAGTCCTGT 57.350 30.769 0.00 0.00 0.00 4.00
157 158 8.650143 AATGTATTTTCCATGTTAGTCCTGTT 57.350 30.769 0.00 0.00 0.00 3.16
158 159 9.747898 AATGTATTTTCCATGTTAGTCCTGTTA 57.252 29.630 0.00 0.00 0.00 2.41
159 160 9.920946 ATGTATTTTCCATGTTAGTCCTGTTAT 57.079 29.630 0.00 0.00 0.00 1.89
163 164 8.556213 TTTTCCATGTTAGTCCTGTTATACAC 57.444 34.615 0.00 0.00 0.00 2.90
164 165 5.898174 TCCATGTTAGTCCTGTTATACACG 58.102 41.667 0.00 0.00 0.00 4.49
165 166 5.419788 TCCATGTTAGTCCTGTTATACACGT 59.580 40.000 0.00 0.00 0.00 4.49
166 167 5.518847 CCATGTTAGTCCTGTTATACACGTG 59.481 44.000 15.48 15.48 0.00 4.49
167 168 4.487948 TGTTAGTCCTGTTATACACGTGC 58.512 43.478 17.22 0.00 0.00 5.34
168 169 4.022155 TGTTAGTCCTGTTATACACGTGCA 60.022 41.667 17.22 2.06 0.00 4.57
169 170 2.955614 AGTCCTGTTATACACGTGCAC 58.044 47.619 17.22 6.82 0.00 4.57
170 171 2.561419 AGTCCTGTTATACACGTGCACT 59.439 45.455 17.22 2.65 0.00 4.40
171 172 2.666508 GTCCTGTTATACACGTGCACTG 59.333 50.000 17.22 14.19 0.00 3.66
172 173 1.393539 CCTGTTATACACGTGCACTGC 59.606 52.381 17.22 4.24 0.00 4.40
173 174 2.065512 CTGTTATACACGTGCACTGCA 58.934 47.619 17.22 8.88 35.60 4.41
174 175 2.065512 TGTTATACACGTGCACTGCAG 58.934 47.619 17.22 13.48 40.08 4.41
175 176 1.075542 TTATACACGTGCACTGCAGC 58.924 50.000 17.22 1.39 40.08 5.25
176 177 0.246360 TATACACGTGCACTGCAGCT 59.754 50.000 17.22 0.00 40.08 4.24
177 178 0.246360 ATACACGTGCACTGCAGCTA 59.754 50.000 17.22 0.00 40.08 3.32
178 179 0.246360 TACACGTGCACTGCAGCTAT 59.754 50.000 17.22 0.00 40.08 2.97
179 180 0.246360 ACACGTGCACTGCAGCTATA 59.754 50.000 17.22 0.00 40.08 1.31
180 181 0.647410 CACGTGCACTGCAGCTATAC 59.353 55.000 15.27 7.26 40.08 1.47
181 182 0.246360 ACGTGCACTGCAGCTATACA 59.754 50.000 15.27 1.87 40.08 2.29
182 183 1.134699 ACGTGCACTGCAGCTATACAT 60.135 47.619 15.27 0.00 40.08 2.29
183 184 1.935873 CGTGCACTGCAGCTATACATT 59.064 47.619 15.27 0.00 40.08 2.71
184 185 2.286008 CGTGCACTGCAGCTATACATTG 60.286 50.000 15.27 2.68 40.08 2.82
185 186 2.938451 GTGCACTGCAGCTATACATTGA 59.062 45.455 15.27 0.00 40.08 2.57
186 187 2.938451 TGCACTGCAGCTATACATTGAC 59.062 45.455 15.27 0.00 33.32 3.18
187 188 3.201290 GCACTGCAGCTATACATTGACT 58.799 45.455 15.27 0.00 0.00 3.41
188 189 3.002042 GCACTGCAGCTATACATTGACTG 59.998 47.826 15.27 0.25 0.00 3.51
201 202 3.565482 ACATTGACTGCTGTCGTTTCAAT 59.435 39.130 17.59 9.79 45.70 2.57
278 279 2.718993 GATCGGCGGCGAGTGACTAG 62.719 65.000 36.74 4.17 0.00 2.57
340 342 1.841302 CTCACAGGGCCTTGGCACTA 61.841 60.000 20.34 0.05 0.00 2.74
341 343 1.377725 CACAGGGCCTTGGCACTAG 60.378 63.158 20.34 12.92 0.00 2.57
346 348 1.153147 GGCCTTGGCACTAGGTAGC 60.153 63.158 14.04 0.00 35.13 3.58
350 352 2.633488 CCTTGGCACTAGGTAGCTTTC 58.367 52.381 0.00 0.00 0.00 2.62
355 357 4.324267 TGGCACTAGGTAGCTTTCTTTTC 58.676 43.478 0.00 0.00 0.00 2.29
357 359 4.632251 GGCACTAGGTAGCTTTCTTTTCTC 59.368 45.833 0.00 0.00 0.00 2.87
358 360 5.483811 GCACTAGGTAGCTTTCTTTTCTCT 58.516 41.667 0.00 0.00 0.00 3.10
359 361 5.579119 GCACTAGGTAGCTTTCTTTTCTCTC 59.421 44.000 0.00 0.00 0.00 3.20
414 422 2.984471 TCGAAGGAAATCGTTGAAGTCG 59.016 45.455 0.00 0.00 43.19 4.18
415 423 2.729882 CGAAGGAAATCGTTGAAGTCGT 59.270 45.455 0.00 0.00 38.01 4.34
423 431 0.935831 CGTTGAAGTCGTGTACCGCA 60.936 55.000 0.00 0.00 36.19 5.69
447 455 4.127171 GTGTGGTGCCCATGTTACTATAG 58.873 47.826 0.00 0.00 35.28 1.31
481 489 4.109050 CGCATTTTTGTGTAGGTTGTTGT 58.891 39.130 0.00 0.00 0.00 3.32
502 510 3.109044 TGCTCTAATCATCAGCTCTGC 57.891 47.619 0.00 0.00 34.03 4.26
547 584 1.132453 TCGACGCTCCTGTGAGTATTG 59.868 52.381 0.00 0.00 40.95 1.90
554 591 4.393062 CGCTCCTGTGAGTATTGAAATGTT 59.607 41.667 0.00 0.00 40.95 2.71
557 594 6.183360 GCTCCTGTGAGTATTGAAATGTTCTC 60.183 42.308 0.00 0.00 40.95 2.87
559 596 7.453393 TCCTGTGAGTATTGAAATGTTCTCTT 58.547 34.615 0.00 0.00 0.00 2.85
692 741 0.034896 TTGGCGAGGAAGACAAGTCC 59.965 55.000 0.00 0.00 33.56 3.85
710 759 3.593442 TCCAGTGGGACAAATCAAAGT 57.407 42.857 9.92 0.00 44.16 2.66
711 760 3.221771 TCCAGTGGGACAAATCAAAGTG 58.778 45.455 9.92 0.00 44.16 3.16
712 761 2.958355 CCAGTGGGACAAATCAAAGTGT 59.042 45.455 0.00 0.00 44.16 3.55
717 2562 4.037923 GTGGGACAAATCAAAGTGTCATGT 59.962 41.667 6.18 0.00 44.89 3.21
727 2572 0.608130 AGTGTCATGTTGCCGCTAGA 59.392 50.000 0.00 0.00 0.00 2.43
728 2573 1.001974 AGTGTCATGTTGCCGCTAGAA 59.998 47.619 0.00 0.00 0.00 2.10
733 2578 0.321298 ATGTTGCCGCTAGAACCGTT 60.321 50.000 0.00 0.00 0.00 4.44
738 2583 1.888018 CCGCTAGAACCGTTGGAGA 59.112 57.895 0.00 0.00 0.00 3.71
741 2586 1.336517 CGCTAGAACCGTTGGAGAACA 60.337 52.381 0.00 0.00 31.78 3.18
746 2591 1.812571 GAACCGTTGGAGAACATGCAT 59.187 47.619 0.00 0.00 31.78 3.96
755 2600 6.317857 GTTGGAGAACATGCATTTTCTCTAC 58.682 40.000 36.41 31.08 44.86 2.59
775 2696 1.194781 AAGTCGACCTGCAGGACCAT 61.195 55.000 39.19 17.35 38.94 3.55
793 2714 1.107114 ATGCCAAACCACACGTTTCA 58.893 45.000 0.00 0.00 42.98 2.69
814 2735 3.505773 GAGCTGGGGGCCATCCAT 61.506 66.667 16.16 4.11 43.05 3.41
816 2737 4.610526 GCTGGGGGCCATCCATCC 62.611 72.222 16.16 8.07 37.22 3.51
1023 4751 2.224621 ACAGAAACACACATCTCCCAGG 60.225 50.000 0.00 0.00 0.00 4.45
1258 5002 2.443416 GGGCCGGAATACAAGTTCTTT 58.557 47.619 5.05 0.00 0.00 2.52
1291 5035 1.591059 CGAGATCAAGCGGCTCCTG 60.591 63.158 1.45 0.00 0.00 3.86
1294 5038 3.687321 GATCAAGCGGCTCCTGGCA 62.687 63.158 1.45 0.00 44.01 4.92
1691 5478 1.429463 GACAAGCTCAAGGTACGTGG 58.571 55.000 0.00 0.00 38.64 4.94
1706 5525 0.374063 CGTGGCGTGTGTGTTTTGTA 59.626 50.000 0.00 0.00 0.00 2.41
1759 5578 1.750193 ATCCAGTTAATGCACCGTGG 58.250 50.000 0.00 0.00 0.00 4.94
1776 5596 4.828387 ACCGTGGCATAAAAAGGAAACTAA 59.172 37.500 0.00 0.00 42.68 2.24
1783 5603 9.868277 TGGCATAAAAAGGAAACTAATAATGTG 57.132 29.630 0.00 0.00 42.68 3.21
1896 5956 5.823353 TGTAATCGGTGTCTTTCCAAAAAC 58.177 37.500 0.00 0.00 0.00 2.43
1899 5959 3.207778 TCGGTGTCTTTCCAAAAACGAT 58.792 40.909 0.00 0.00 0.00 3.73
1902 5962 5.470777 TCGGTGTCTTTCCAAAAACGATAAT 59.529 36.000 0.00 0.00 0.00 1.28
1904 5964 6.959311 CGGTGTCTTTCCAAAAACGATAATAG 59.041 38.462 0.00 0.00 0.00 1.73
1932 5992 5.989168 TGCCTATTTCATAATCGTACCACTG 59.011 40.000 0.00 0.00 0.00 3.66
1933 5993 5.408604 GCCTATTTCATAATCGTACCACTGG 59.591 44.000 0.00 0.00 0.00 4.00
1934 5994 5.932303 CCTATTTCATAATCGTACCACTGGG 59.068 44.000 0.00 0.00 41.29 4.45
1935 5995 3.830744 TTCATAATCGTACCACTGGGG 57.169 47.619 0.00 0.00 44.81 4.96
1950 6010 4.290942 CACTGGGGTAGAAGGTAAGAGAT 58.709 47.826 0.00 0.00 0.00 2.75
1956 6016 6.044754 TGGGGTAGAAGGTAAGAGATCGTATA 59.955 42.308 0.00 0.00 0.00 1.47
2199 6261 1.605058 GGAGCAGCTACGAACAGGGA 61.605 60.000 0.00 0.00 0.00 4.20
2440 6517 4.775236 AGATATGGAAGCTTGACAAGGAC 58.225 43.478 16.80 1.18 0.00 3.85
2443 6520 1.149148 GGAAGCTTGACAAGGACGTC 58.851 55.000 16.80 7.13 36.40 4.34
2803 6880 2.557869 ACTCTTAGGTTGTATGGCCCA 58.442 47.619 0.00 0.00 0.00 5.36
2846 6923 2.095461 CAGGTTCAGATCTCGAGGTCA 58.905 52.381 26.87 4.96 0.00 4.02
3194 7271 5.048294 GTCCTTAAGAGCCTAGAGATGTAGC 60.048 48.000 3.36 0.00 0.00 3.58
3196 7273 1.243902 AGAGCCTAGAGATGTAGCGC 58.756 55.000 0.00 0.00 0.00 5.92
3287 7366 7.004555 TGCTGGACTTTATTGAGAACTAGAA 57.995 36.000 0.00 0.00 0.00 2.10
3462 7550 5.032846 AGGAATTAGGTGAGATGGACTTCA 58.967 41.667 0.00 0.00 0.00 3.02
3500 7589 9.136952 GAAGTTAAGCTCGTGTTTATTTCTAGA 57.863 33.333 0.00 0.00 0.00 2.43
3517 7606 6.406692 TTCTAGAACGAAGCCTAAGCATAT 57.593 37.500 0.00 0.00 43.56 1.78
3518 7607 7.520451 TTCTAGAACGAAGCCTAAGCATATA 57.480 36.000 0.00 0.00 43.56 0.86
3519 7608 6.910995 TCTAGAACGAAGCCTAAGCATATAC 58.089 40.000 0.00 0.00 43.56 1.47
3520 7609 5.793030 AGAACGAAGCCTAAGCATATACT 57.207 39.130 0.00 0.00 43.56 2.12
3521 7610 5.774630 AGAACGAAGCCTAAGCATATACTC 58.225 41.667 0.00 0.00 43.56 2.59
3522 7611 4.522722 ACGAAGCCTAAGCATATACTCC 57.477 45.455 0.00 0.00 43.56 3.85
3523 7612 3.258622 ACGAAGCCTAAGCATATACTCCC 59.741 47.826 0.00 0.00 43.56 4.30
3524 7613 3.511934 CGAAGCCTAAGCATATACTCCCT 59.488 47.826 0.00 0.00 43.56 4.20
3525 7614 4.381079 CGAAGCCTAAGCATATACTCCCTC 60.381 50.000 0.00 0.00 43.56 4.30
3526 7615 3.445987 AGCCTAAGCATATACTCCCTCC 58.554 50.000 0.00 0.00 43.56 4.30
3527 7616 2.166664 GCCTAAGCATATACTCCCTCCG 59.833 54.545 0.00 0.00 39.53 4.63
3528 7617 3.432378 CCTAAGCATATACTCCCTCCGT 58.568 50.000 0.00 0.00 0.00 4.69
3529 7618 3.833070 CCTAAGCATATACTCCCTCCGTT 59.167 47.826 0.00 0.00 0.00 4.44
3530 7619 4.082136 CCTAAGCATATACTCCCTCCGTTC 60.082 50.000 0.00 0.00 0.00 3.95
3531 7620 2.249139 AGCATATACTCCCTCCGTTCC 58.751 52.381 0.00 0.00 0.00 3.62
3532 7621 2.158295 AGCATATACTCCCTCCGTTCCT 60.158 50.000 0.00 0.00 0.00 3.36
3533 7622 3.075582 AGCATATACTCCCTCCGTTCCTA 59.924 47.826 0.00 0.00 0.00 2.94
3534 7623 3.830755 GCATATACTCCCTCCGTTCCTAA 59.169 47.826 0.00 0.00 0.00 2.69
3535 7624 4.282703 GCATATACTCCCTCCGTTCCTAAA 59.717 45.833 0.00 0.00 0.00 1.85
3536 7625 5.046520 GCATATACTCCCTCCGTTCCTAAAT 60.047 44.000 0.00 0.00 0.00 1.40
3537 7626 4.957684 ATACTCCCTCCGTTCCTAAATG 57.042 45.455 0.00 0.00 0.00 2.32
3538 7627 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
3539 7628 2.910977 ACTCCCTCCGTTCCTAAATGTT 59.089 45.455 0.00 0.00 0.00 2.71
3540 7629 3.329814 ACTCCCTCCGTTCCTAAATGTTT 59.670 43.478 0.00 0.00 0.00 2.83
3541 7630 3.681593 TCCCTCCGTTCCTAAATGTTTG 58.318 45.455 0.00 0.00 0.00 2.93
3542 7631 3.073356 TCCCTCCGTTCCTAAATGTTTGT 59.927 43.478 0.00 0.00 0.00 2.83
3543 7632 3.439129 CCCTCCGTTCCTAAATGTTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
3544 7633 4.324267 CCTCCGTTCCTAAATGTTTGTCT 58.676 43.478 0.00 0.00 0.00 3.41
3545 7634 4.760204 CCTCCGTTCCTAAATGTTTGTCTT 59.240 41.667 0.00 0.00 0.00 3.01
3546 7635 5.240844 CCTCCGTTCCTAAATGTTTGTCTTT 59.759 40.000 0.00 0.00 0.00 2.52
3547 7636 6.308371 TCCGTTCCTAAATGTTTGTCTTTC 57.692 37.500 0.00 0.00 0.00 2.62
3548 7637 6.059484 TCCGTTCCTAAATGTTTGTCTTTCT 58.941 36.000 0.00 0.00 0.00 2.52
3549 7638 7.218614 TCCGTTCCTAAATGTTTGTCTTTCTA 58.781 34.615 0.00 0.00 0.00 2.10
3550 7639 7.386848 TCCGTTCCTAAATGTTTGTCTTTCTAG 59.613 37.037 0.00 0.00 0.00 2.43
3551 7640 7.386848 CCGTTCCTAAATGTTTGTCTTTCTAGA 59.613 37.037 0.00 0.00 0.00 2.43
3552 7641 8.436200 CGTTCCTAAATGTTTGTCTTTCTAGAG 58.564 37.037 0.00 0.00 0.00 2.43
3553 7642 9.490379 GTTCCTAAATGTTTGTCTTTCTAGAGA 57.510 33.333 0.00 0.00 0.00 3.10
3561 7650 8.731275 TGTTTGTCTTTCTAGAGATTTCAACA 57.269 30.769 0.00 0.00 0.00 3.33
3562 7651 9.173021 TGTTTGTCTTTCTAGAGATTTCAACAA 57.827 29.630 0.00 0.00 0.00 2.83
3563 7652 9.657121 GTTTGTCTTTCTAGAGATTTCAACAAG 57.343 33.333 0.00 0.00 0.00 3.16
3564 7653 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
3565 7654 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
3566 7655 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
3567 7656 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3568 7657 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
3569 7658 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
3570 7659 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
3571 7660 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
3572 7661 8.082852 TCTAGAGATTTCAACAAGTGACTACAC 58.917 37.037 0.00 0.00 46.24 2.90
3576 7665 5.749596 TTTCAACAAGTGACTACACATGG 57.250 39.130 9.64 0.00 45.96 3.66
3577 7666 4.681074 TCAACAAGTGACTACACATGGA 57.319 40.909 9.64 0.00 45.96 3.41
3578 7667 4.631131 TCAACAAGTGACTACACATGGAG 58.369 43.478 9.64 0.00 45.96 3.86
3579 7668 3.045601 ACAAGTGACTACACATGGAGC 57.954 47.619 9.64 0.00 45.96 4.70
3580 7669 2.368548 ACAAGTGACTACACATGGAGCA 59.631 45.455 9.64 0.00 45.96 4.26
3581 7670 3.181455 ACAAGTGACTACACATGGAGCAA 60.181 43.478 9.64 0.00 45.96 3.91
3582 7671 4.685848 ACAAGTGACTACACATGGAGCAAA 60.686 41.667 9.64 0.00 45.96 3.68
3583 7672 5.978457 ACAAGTGACTACACATGGAGCAAAT 60.978 40.000 9.64 0.00 45.96 2.32
3584 7673 4.346734 GTGACTACACATGGAGCAAATG 57.653 45.455 0.00 0.00 45.32 2.32
3585 7674 4.002982 GTGACTACACATGGAGCAAATGA 58.997 43.478 0.00 0.00 45.32 2.57
3586 7675 4.093998 GTGACTACACATGGAGCAAATGAG 59.906 45.833 0.00 0.00 45.32 2.90
3587 7676 4.256920 GACTACACATGGAGCAAATGAGT 58.743 43.478 0.00 1.99 34.04 3.41
3588 7677 4.005650 ACTACACATGGAGCAAATGAGTG 58.994 43.478 0.00 0.00 32.25 3.51
3589 7678 3.144657 ACACATGGAGCAAATGAGTGA 57.855 42.857 0.00 0.00 29.29 3.41
3590 7679 3.693807 ACACATGGAGCAAATGAGTGAT 58.306 40.909 0.00 0.00 29.29 3.06
3591 7680 4.084287 ACACATGGAGCAAATGAGTGATT 58.916 39.130 0.00 0.00 29.29 2.57
3592 7681 4.157289 ACACATGGAGCAAATGAGTGATTC 59.843 41.667 0.00 0.00 29.29 2.52
3593 7682 4.398358 CACATGGAGCAAATGAGTGATTCT 59.602 41.667 0.00 0.00 0.00 2.40
3594 7683 5.587443 CACATGGAGCAAATGAGTGATTCTA 59.413 40.000 0.00 0.00 0.00 2.10
3595 7684 5.587844 ACATGGAGCAAATGAGTGATTCTAC 59.412 40.000 0.00 0.00 0.00 2.59
3596 7685 5.164620 TGGAGCAAATGAGTGATTCTACA 57.835 39.130 0.00 0.00 0.00 2.74
3597 7686 4.937620 TGGAGCAAATGAGTGATTCTACAC 59.062 41.667 0.00 0.00 40.60 2.90
3653 7742 9.231297 TGGTAGTCCATTTGAAATCTCTAAAAG 57.769 33.333 0.00 0.00 39.03 2.27
3654 7743 8.678199 GGTAGTCCATTTGAAATCTCTAAAAGG 58.322 37.037 0.00 0.00 0.00 3.11
3655 7744 9.449719 GTAGTCCATTTGAAATCTCTAAAAGGA 57.550 33.333 0.00 0.00 0.00 3.36
3656 7745 8.341892 AGTCCATTTGAAATCTCTAAAAGGAC 57.658 34.615 12.72 12.72 41.02 3.85
3657 7746 7.944554 AGTCCATTTGAAATCTCTAAAAGGACA 59.055 33.333 19.19 0.00 41.93 4.02
3658 7747 8.576442 GTCCATTTGAAATCTCTAAAAGGACAA 58.424 33.333 14.70 0.00 40.75 3.18
3659 7748 9.142014 TCCATTTGAAATCTCTAAAAGGACAAA 57.858 29.630 0.00 0.00 0.00 2.83
3660 7749 9.933723 CCATTTGAAATCTCTAAAAGGACAAAT 57.066 29.630 0.00 0.00 36.38 2.32
3672 7761 9.169592 TCTAAAAGGACAAATATTTAGGAACGG 57.830 33.333 0.00 0.00 36.48 4.44
3673 7762 9.169592 CTAAAAGGACAAATATTTAGGAACGGA 57.830 33.333 0.00 0.00 33.69 4.69
3674 7763 7.625828 AAAGGACAAATATTTAGGAACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
3675 7764 5.681639 AGGACAAATATTTAGGAACGGAGG 58.318 41.667 0.00 0.00 0.00 4.30
3676 7765 4.820173 GGACAAATATTTAGGAACGGAGGG 59.180 45.833 0.00 0.00 0.00 4.30
3677 7766 5.397109 GGACAAATATTTAGGAACGGAGGGA 60.397 44.000 0.00 0.00 0.00 4.20
3678 7767 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3687 7776 0.974383 AACGGAGGGAGTAGGTTGTG 59.026 55.000 0.00 0.00 0.00 3.33
3710 7799 6.038271 GTGAAACCATTGACTCACTGTACTTT 59.962 38.462 0.00 0.00 36.18 2.66
3853 7942 8.153550 GGATTTGGTTCTATCACTCATGTATCT 58.846 37.037 0.00 0.00 0.00 1.98
4077 8188 9.213799 GTTTTCCAAAGGATTGCATATGTTTTA 57.786 29.630 4.29 0.00 35.10 1.52
4164 8275 2.733956 TGGTGCTCCTGAAAGTGTTTT 58.266 42.857 6.34 0.00 34.23 2.43
4228 8339 1.595311 TGGCTATGGTGGTGGAGAAT 58.405 50.000 0.00 0.00 0.00 2.40
4267 8378 4.927267 TTGGAGCTATCTTTTGGGAGAA 57.073 40.909 0.00 0.00 0.00 2.87
4274 8385 7.558081 GGAGCTATCTTTTGGGAGAAACTATTT 59.442 37.037 0.00 0.00 0.00 1.40
4281 8392 5.659440 TTGGGAGAAACTATTTTGGATGC 57.341 39.130 0.00 0.00 0.00 3.91
4282 8393 4.023291 TGGGAGAAACTATTTTGGATGCC 58.977 43.478 0.00 0.00 0.00 4.40
4318 8429 8.810427 CACATCAACACTATTTCATTAATTGCC 58.190 33.333 0.00 0.00 0.00 4.52
4335 8446 3.391506 TGCCGGAGATGTATGATTCTG 57.608 47.619 5.05 0.00 0.00 3.02
4343 8454 7.198390 CGGAGATGTATGATTCTGCAAAAATT 58.802 34.615 0.00 0.00 31.34 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.991906 AACTTGACTTACTTTTGCACTAGTATA 57.008 29.630 7.69 0.00 0.00 1.47
25 26 8.904099 AACTTGACTTACTTTTGCACTAGTAT 57.096 30.769 7.69 0.00 0.00 2.12
26 27 8.726870 AAACTTGACTTACTTTTGCACTAGTA 57.273 30.769 0.00 3.57 0.00 1.82
27 28 7.625828 AAACTTGACTTACTTTTGCACTAGT 57.374 32.000 5.34 5.34 0.00 2.57
30 31 8.903820 AGAATAAACTTGACTTACTTTTGCACT 58.096 29.630 0.00 0.00 0.00 4.40
102 103 9.674824 GTTTCTAGTTGTATATACACGCTATGT 57.325 33.333 15.20 0.00 46.06 2.29
103 104 9.125906 GGTTTCTAGTTGTATATACACGCTATG 57.874 37.037 15.20 12.78 35.64 2.23
104 105 8.853126 TGGTTTCTAGTTGTATATACACGCTAT 58.147 33.333 15.20 3.01 35.64 2.97
105 106 8.224389 TGGTTTCTAGTTGTATATACACGCTA 57.776 34.615 15.20 17.05 35.64 4.26
106 107 7.104043 TGGTTTCTAGTTGTATATACACGCT 57.896 36.000 15.20 16.86 35.64 5.07
107 108 7.760131 TTGGTTTCTAGTTGTATATACACGC 57.240 36.000 15.20 11.02 35.64 5.34
117 118 9.758651 GGAAAATACATTTTGGTTTCTAGTTGT 57.241 29.630 4.70 0.00 39.86 3.32
118 119 9.757227 TGGAAAATACATTTTGGTTTCTAGTTG 57.243 29.630 4.70 0.00 39.86 3.16
120 121 9.927668 CATGGAAAATACATTTTGGTTTCTAGT 57.072 29.630 4.70 0.00 39.86 2.57
121 122 9.927668 ACATGGAAAATACATTTTGGTTTCTAG 57.072 29.630 4.70 0.00 39.86 2.43
126 127 9.705290 GACTAACATGGAAAATACATTTTGGTT 57.295 29.630 4.70 6.62 39.86 3.67
127 128 8.311109 GGACTAACATGGAAAATACATTTTGGT 58.689 33.333 4.70 0.00 39.86 3.67
128 129 8.531146 AGGACTAACATGGAAAATACATTTTGG 58.469 33.333 4.70 0.00 39.86 3.28
129 130 9.357652 CAGGACTAACATGGAAAATACATTTTG 57.642 33.333 4.70 0.00 39.86 2.44
130 131 9.088987 ACAGGACTAACATGGAAAATACATTTT 57.911 29.630 0.00 0.00 36.94 1.82
131 132 8.650143 ACAGGACTAACATGGAAAATACATTT 57.350 30.769 0.00 0.00 34.35 2.32
132 133 8.650143 AACAGGACTAACATGGAAAATACATT 57.350 30.769 0.00 0.00 34.35 2.71
133 134 9.920946 ATAACAGGACTAACATGGAAAATACAT 57.079 29.630 0.00 0.00 34.35 2.29
137 138 9.174166 GTGTATAACAGGACTAACATGGAAAAT 57.826 33.333 0.00 0.00 34.35 1.82
138 139 7.332430 CGTGTATAACAGGACTAACATGGAAAA 59.668 37.037 0.00 0.00 36.17 2.29
139 140 6.814644 CGTGTATAACAGGACTAACATGGAAA 59.185 38.462 0.00 0.00 36.17 3.13
140 141 6.071221 ACGTGTATAACAGGACTAACATGGAA 60.071 38.462 6.74 0.00 37.42 3.53
141 142 5.419788 ACGTGTATAACAGGACTAACATGGA 59.580 40.000 6.74 0.00 37.42 3.41
142 143 5.518847 CACGTGTATAACAGGACTAACATGG 59.481 44.000 7.58 0.00 37.42 3.66
143 144 5.005394 GCACGTGTATAACAGGACTAACATG 59.995 44.000 18.38 0.00 37.42 3.21
144 145 5.107133 GCACGTGTATAACAGGACTAACAT 58.893 41.667 18.38 0.00 37.42 2.71
145 146 4.022155 TGCACGTGTATAACAGGACTAACA 60.022 41.667 18.38 0.00 37.42 2.41
146 147 4.325472 GTGCACGTGTATAACAGGACTAAC 59.675 45.833 18.38 0.00 37.42 2.34
147 148 4.219070 AGTGCACGTGTATAACAGGACTAA 59.781 41.667 18.38 0.00 37.42 2.24
148 149 3.760151 AGTGCACGTGTATAACAGGACTA 59.240 43.478 18.38 0.00 37.42 2.59
149 150 2.561419 AGTGCACGTGTATAACAGGACT 59.439 45.455 18.38 1.75 37.42 3.85
150 151 2.666508 CAGTGCACGTGTATAACAGGAC 59.333 50.000 18.38 0.00 37.42 3.85
151 152 2.929161 GCAGTGCACGTGTATAACAGGA 60.929 50.000 18.38 0.00 37.42 3.86
152 153 1.393539 GCAGTGCACGTGTATAACAGG 59.606 52.381 18.38 8.33 39.65 4.00
153 154 2.065512 TGCAGTGCACGTGTATAACAG 58.934 47.619 15.37 8.78 31.71 3.16
154 155 2.065512 CTGCAGTGCACGTGTATAACA 58.934 47.619 15.37 10.82 33.79 2.41
155 156 1.201921 GCTGCAGTGCACGTGTATAAC 60.202 52.381 15.37 10.63 33.79 1.89
156 157 1.075542 GCTGCAGTGCACGTGTATAA 58.924 50.000 15.37 0.00 33.79 0.98
157 158 0.246360 AGCTGCAGTGCACGTGTATA 59.754 50.000 15.37 1.01 33.79 1.47
158 159 0.246360 TAGCTGCAGTGCACGTGTAT 59.754 50.000 15.37 0.00 33.79 2.29
159 160 0.246360 ATAGCTGCAGTGCACGTGTA 59.754 50.000 15.37 10.46 33.79 2.90
160 161 0.246360 TATAGCTGCAGTGCACGTGT 59.754 50.000 15.37 5.08 33.79 4.49
161 162 0.647410 GTATAGCTGCAGTGCACGTG 59.353 55.000 15.37 12.28 33.79 4.49
162 163 0.246360 TGTATAGCTGCAGTGCACGT 59.754 50.000 15.37 6.71 33.79 4.49
163 164 1.575244 ATGTATAGCTGCAGTGCACG 58.425 50.000 15.37 11.72 33.79 5.34
164 165 2.938451 TCAATGTATAGCTGCAGTGCAC 59.062 45.455 15.37 9.40 33.78 4.57
165 166 2.938451 GTCAATGTATAGCTGCAGTGCA 59.062 45.455 18.58 18.58 33.78 4.57
166 167 3.002042 CAGTCAATGTATAGCTGCAGTGC 59.998 47.826 16.64 8.58 33.78 4.40
167 168 4.790810 CAGTCAATGTATAGCTGCAGTG 57.209 45.455 16.64 2.78 34.86 3.66
173 174 3.131223 ACGACAGCAGTCAATGTATAGCT 59.869 43.478 10.09 0.00 45.23 3.32
174 175 3.448686 ACGACAGCAGTCAATGTATAGC 58.551 45.455 10.09 0.00 45.23 2.97
175 176 5.576774 TGAAACGACAGCAGTCAATGTATAG 59.423 40.000 10.09 0.00 45.23 1.31
176 177 5.474825 TGAAACGACAGCAGTCAATGTATA 58.525 37.500 10.09 0.00 45.23 1.47
177 178 4.314961 TGAAACGACAGCAGTCAATGTAT 58.685 39.130 10.09 0.00 45.23 2.29
178 179 3.723260 TGAAACGACAGCAGTCAATGTA 58.277 40.909 10.09 0.00 45.23 2.29
179 180 2.560504 TGAAACGACAGCAGTCAATGT 58.439 42.857 10.09 0.00 45.23 2.71
180 181 3.607422 TTGAAACGACAGCAGTCAATG 57.393 42.857 10.09 0.00 45.23 2.82
181 182 4.142816 GCTATTGAAACGACAGCAGTCAAT 60.143 41.667 10.09 4.48 45.23 2.57
182 183 3.186409 GCTATTGAAACGACAGCAGTCAA 59.814 43.478 10.09 0.00 45.23 3.18
183 184 2.736721 GCTATTGAAACGACAGCAGTCA 59.263 45.455 10.09 0.00 45.23 3.41
184 185 2.736721 TGCTATTGAAACGACAGCAGTC 59.263 45.455 0.00 0.00 37.32 3.51
185 186 2.766313 TGCTATTGAAACGACAGCAGT 58.234 42.857 0.00 0.00 37.32 4.40
186 187 3.811722 TTGCTATTGAAACGACAGCAG 57.188 42.857 0.00 0.00 42.68 4.24
187 188 4.560136 TTTTGCTATTGAAACGACAGCA 57.440 36.364 0.00 0.00 40.31 4.41
188 189 4.324402 CCATTTTGCTATTGAAACGACAGC 59.676 41.667 0.00 0.00 0.00 4.40
189 190 4.324402 GCCATTTTGCTATTGAAACGACAG 59.676 41.667 0.00 0.00 0.00 3.51
190 191 4.233789 GCCATTTTGCTATTGAAACGACA 58.766 39.130 0.00 0.00 0.00 4.35
191 192 4.233789 TGCCATTTTGCTATTGAAACGAC 58.766 39.130 0.00 0.00 0.00 4.34
201 202 4.557097 CGACATGCATATGCCATTTTGCTA 60.557 41.667 24.54 3.07 41.18 3.49
306 308 4.025145 CCCTGTGAGTTCTCGTTAAACAAC 60.025 45.833 0.00 0.00 0.00 3.32
340 342 4.767928 TCGAGAGAGAAAAGAAAGCTACCT 59.232 41.667 0.00 0.00 34.84 3.08
341 343 5.061920 TCGAGAGAGAAAAGAAAGCTACC 57.938 43.478 0.00 0.00 34.84 3.18
357 359 1.270826 TCAGTGCCACTTTCTCGAGAG 59.729 52.381 15.94 7.70 0.00 3.20
358 360 1.270826 CTCAGTGCCACTTTCTCGAGA 59.729 52.381 12.08 12.08 0.00 4.04
359 361 1.000283 ACTCAGTGCCACTTTCTCGAG 60.000 52.381 5.93 5.93 0.00 4.04
414 422 1.866237 CACCACACATGCGGTACAC 59.134 57.895 2.00 0.00 32.98 2.90
415 423 1.963855 GCACCACACATGCGGTACA 60.964 57.895 2.00 0.00 32.98 2.90
447 455 6.757162 ACACAAAAATGCGTTCTTAAACAAC 58.243 32.000 0.00 0.00 34.93 3.32
481 489 3.464907 GCAGAGCTGATGATTAGAGCAA 58.535 45.455 0.85 0.00 35.03 3.91
502 510 2.103941 GGACATAAAGAGCTCCCAGAGG 59.896 54.545 10.93 0.00 0.00 3.69
547 584 2.096218 AGCGAACGCAAGAGAACATTTC 60.096 45.455 20.66 0.00 44.88 2.17
554 591 1.999735 CCATTAAGCGAACGCAAGAGA 59.000 47.619 20.66 3.11 44.88 3.10
557 594 2.892373 TTCCATTAAGCGAACGCAAG 57.108 45.000 20.66 5.83 44.88 4.01
559 596 4.185394 TCTAATTCCATTAAGCGAACGCA 58.815 39.130 20.66 1.07 44.88 5.24
692 741 3.631686 TGACACTTTGATTTGTCCCACTG 59.368 43.478 0.00 0.00 41.31 3.66
708 757 0.608130 TCTAGCGGCAACATGACACT 59.392 50.000 0.00 0.00 0.00 3.55
709 758 1.128692 GTTCTAGCGGCAACATGACAC 59.871 52.381 0.00 0.00 0.00 3.67
710 759 1.438651 GTTCTAGCGGCAACATGACA 58.561 50.000 0.00 0.00 0.00 3.58
711 760 0.727398 GGTTCTAGCGGCAACATGAC 59.273 55.000 0.00 0.00 0.00 3.06
712 761 0.739462 CGGTTCTAGCGGCAACATGA 60.739 55.000 0.00 0.00 35.16 3.07
717 2562 1.669760 CCAACGGTTCTAGCGGCAA 60.670 57.895 1.45 0.00 44.33 4.52
727 2572 1.909700 ATGCATGTTCTCCAACGGTT 58.090 45.000 0.00 0.00 34.95 4.44
728 2573 1.909700 AATGCATGTTCTCCAACGGT 58.090 45.000 0.00 0.00 34.95 4.83
738 2583 5.700832 TCGACTTGTAGAGAAAATGCATGTT 59.299 36.000 0.40 0.40 0.00 2.71
741 2586 4.631813 GGTCGACTTGTAGAGAAAATGCAT 59.368 41.667 16.46 0.00 0.00 3.96
746 2591 3.069016 TGCAGGTCGACTTGTAGAGAAAA 59.931 43.478 26.07 2.80 0.00 2.29
755 2600 1.374758 GGTCCTGCAGGTCGACTTG 60.375 63.158 31.58 22.26 36.34 3.16
814 2735 2.359850 GCGCACCAACTGGATGGA 60.360 61.111 0.30 0.00 43.54 3.41
816 2737 3.027170 GACGCGCACCAACTGGATG 62.027 63.158 5.73 0.00 38.94 3.51
911 2836 3.003113 GCCAGGTCGCCGAGTTACT 62.003 63.158 0.00 0.00 0.00 2.24
955 4681 3.123621 CGGATGATTTATAGCAGGTTCGC 59.876 47.826 0.00 0.00 0.00 4.70
1023 4751 3.206150 TGTTTGAGTTGGTTGAGAGAGC 58.794 45.455 0.00 0.00 0.00 4.09
1245 4989 2.235016 TGCCGGCAAAGAACTTGTATT 58.765 42.857 30.74 0.00 37.36 1.89
1246 4990 1.904287 TGCCGGCAAAGAACTTGTAT 58.096 45.000 30.74 0.00 37.36 2.29
1466 5253 2.168496 CTCCGAACCAGTAGAGGAACA 58.832 52.381 0.00 0.00 0.00 3.18
1691 5478 5.137403 CAGTAGAATACAAAACACACACGC 58.863 41.667 0.00 0.00 46.26 5.34
1706 5525 8.307483 AGCGCAATGAATATAGTACAGTAGAAT 58.693 33.333 11.47 0.00 0.00 2.40
1902 5962 9.865321 GGTACGATTATGAAATAGGCAATACTA 57.135 33.333 0.00 0.00 0.00 1.82
1904 5964 8.440833 GTGGTACGATTATGAAATAGGCAATAC 58.559 37.037 0.00 0.00 0.00 1.89
1932 5992 3.564264 ACGATCTCTTACCTTCTACCCC 58.436 50.000 0.00 0.00 0.00 4.95
1933 5993 7.282901 GGATATACGATCTCTTACCTTCTACCC 59.717 44.444 0.00 0.00 0.00 3.69
1934 5994 7.282901 GGGATATACGATCTCTTACCTTCTACC 59.717 44.444 0.00 0.00 0.00 3.18
1935 5995 8.048514 AGGGATATACGATCTCTTACCTTCTAC 58.951 40.741 0.00 0.00 0.00 2.59
1950 6010 6.099125 TGTTCTTTGATCCAAGGGATATACGA 59.901 38.462 6.70 0.00 43.27 3.43
1956 6016 6.069440 TGTCTATGTTCTTTGATCCAAGGGAT 60.069 38.462 6.70 0.00 46.28 3.85
2024 6086 1.890979 GTCATCATCTGGCCGGCAG 60.891 63.158 30.85 22.72 0.00 4.85
2363 6432 2.627863 TTCACAAACATACATGGCGC 57.372 45.000 0.00 0.00 0.00 6.53
2440 6517 0.179092 TCATGAGCATGCTCCTGACG 60.179 55.000 36.92 24.15 40.82 4.35
2443 6520 1.746470 TGTTCATGAGCATGCTCCTG 58.254 50.000 37.92 36.02 42.09 3.86
2736 6813 2.689471 TGCAGTTTGTTGAGCATGTCTT 59.311 40.909 0.00 0.00 31.05 3.01
2803 6880 4.622695 GCCTTTCTCTGAATGACAGCTACT 60.623 45.833 0.00 0.00 45.38 2.57
3462 7550 5.687706 CGAGCTTAACTTCTGGGGGAAATAT 60.688 44.000 0.00 0.00 33.07 1.28
3500 7589 4.262506 GGGAGTATATGCTTAGGCTTCGTT 60.263 45.833 0.00 0.00 39.59 3.85
3517 7606 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
3518 7607 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
3519 7608 3.629142 AACATTTAGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
3520 7609 3.073356 ACAAACATTTAGGAACGGAGGGA 59.927 43.478 0.00 0.00 0.00 4.20
3521 7610 3.418047 ACAAACATTTAGGAACGGAGGG 58.582 45.455 0.00 0.00 0.00 4.30
3522 7611 4.324267 AGACAAACATTTAGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
3523 7612 5.941948 AAGACAAACATTTAGGAACGGAG 57.058 39.130 0.00 0.00 0.00 4.63
3524 7613 6.059484 AGAAAGACAAACATTTAGGAACGGA 58.941 36.000 0.00 0.00 0.00 4.69
3525 7614 6.313744 AGAAAGACAAACATTTAGGAACGG 57.686 37.500 0.00 0.00 0.00 4.44
3526 7615 8.306680 TCTAGAAAGACAAACATTTAGGAACG 57.693 34.615 0.00 0.00 0.00 3.95
3527 7616 9.490379 TCTCTAGAAAGACAAACATTTAGGAAC 57.510 33.333 0.00 0.00 0.00 3.62
3535 7624 9.342308 TGTTGAAATCTCTAGAAAGACAAACAT 57.658 29.630 0.00 0.00 0.00 2.71
3536 7625 8.731275 TGTTGAAATCTCTAGAAAGACAAACA 57.269 30.769 0.00 0.00 0.00 2.83
3537 7626 9.657121 CTTGTTGAAATCTCTAGAAAGACAAAC 57.343 33.333 0.00 0.00 0.00 2.93
3538 7627 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
3539 7628 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
3540 7629 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
3541 7630 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3542 7631 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3543 7632 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3544 7633 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
3545 7634 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
3546 7635 8.082852 GTGTAGTCACTTGTTGAAATCTCTAGA 58.917 37.037 0.00 0.00 40.98 2.43
3547 7636 7.867909 TGTGTAGTCACTTGTTGAAATCTCTAG 59.132 37.037 0.00 0.00 44.14 2.43
3548 7637 7.722363 TGTGTAGTCACTTGTTGAAATCTCTA 58.278 34.615 0.00 0.00 44.14 2.43
3549 7638 6.582636 TGTGTAGTCACTTGTTGAAATCTCT 58.417 36.000 0.00 0.00 44.14 3.10
3550 7639 6.844696 TGTGTAGTCACTTGTTGAAATCTC 57.155 37.500 0.00 0.00 44.14 2.75
3551 7640 6.205464 CCATGTGTAGTCACTTGTTGAAATCT 59.795 38.462 11.31 0.00 43.58 2.40
3552 7641 6.204688 TCCATGTGTAGTCACTTGTTGAAATC 59.795 38.462 11.31 0.00 43.58 2.17
3553 7642 6.061441 TCCATGTGTAGTCACTTGTTGAAAT 58.939 36.000 11.31 0.00 43.58 2.17
3554 7643 5.432645 TCCATGTGTAGTCACTTGTTGAAA 58.567 37.500 11.31 0.00 43.58 2.69
3555 7644 5.029807 TCCATGTGTAGTCACTTGTTGAA 57.970 39.130 11.31 0.00 43.58 2.69
3556 7645 4.631131 CTCCATGTGTAGTCACTTGTTGA 58.369 43.478 11.31 4.41 43.58 3.18
3557 7646 3.187227 GCTCCATGTGTAGTCACTTGTTG 59.813 47.826 11.31 6.49 43.58 3.33
3558 7647 3.181455 TGCTCCATGTGTAGTCACTTGTT 60.181 43.478 11.31 0.00 43.58 2.83
3559 7648 2.368548 TGCTCCATGTGTAGTCACTTGT 59.631 45.455 11.31 0.00 43.58 3.16
3560 7649 3.044235 TGCTCCATGTGTAGTCACTTG 57.956 47.619 7.09 7.09 44.22 3.16
3561 7650 3.769739 TTGCTCCATGTGTAGTCACTT 57.230 42.857 0.00 0.00 44.14 3.16
3562 7651 3.769739 TTTGCTCCATGTGTAGTCACT 57.230 42.857 0.00 0.00 44.14 3.41
3563 7652 4.002982 TCATTTGCTCCATGTGTAGTCAC 58.997 43.478 0.00 0.00 44.08 3.67
3564 7653 4.256110 CTCATTTGCTCCATGTGTAGTCA 58.744 43.478 0.00 0.00 0.00 3.41
3565 7654 4.093998 CACTCATTTGCTCCATGTGTAGTC 59.906 45.833 0.00 0.00 29.39 2.59
3566 7655 4.005650 CACTCATTTGCTCCATGTGTAGT 58.994 43.478 0.00 0.00 29.39 2.73
3567 7656 4.256110 TCACTCATTTGCTCCATGTGTAG 58.744 43.478 0.00 0.00 29.39 2.74
3568 7657 4.284829 TCACTCATTTGCTCCATGTGTA 57.715 40.909 0.00 0.00 29.39 2.90
3569 7658 3.144657 TCACTCATTTGCTCCATGTGT 57.855 42.857 0.00 0.00 0.00 3.72
3570 7659 4.398358 AGAATCACTCATTTGCTCCATGTG 59.602 41.667 0.00 0.00 0.00 3.21
3571 7660 4.597004 AGAATCACTCATTTGCTCCATGT 58.403 39.130 0.00 0.00 0.00 3.21
3572 7661 5.587443 TGTAGAATCACTCATTTGCTCCATG 59.413 40.000 0.00 0.00 0.00 3.66
3573 7662 5.587844 GTGTAGAATCACTCATTTGCTCCAT 59.412 40.000 0.00 0.00 35.68 3.41
3574 7663 4.937620 GTGTAGAATCACTCATTTGCTCCA 59.062 41.667 0.00 0.00 35.68 3.86
3575 7664 5.181748 AGTGTAGAATCACTCATTTGCTCC 58.818 41.667 0.00 0.00 44.07 4.70
3628 7717 8.678199 CCTTTTAGAGATTTCAAATGGACTACC 58.322 37.037 0.00 0.00 31.44 3.18
3629 7718 9.449719 TCCTTTTAGAGATTTCAAATGGACTAC 57.550 33.333 0.00 0.00 33.17 2.73
3630 7719 9.449719 GTCCTTTTAGAGATTTCAAATGGACTA 57.550 33.333 21.88 0.00 44.76 2.59
3631 7720 7.944554 TGTCCTTTTAGAGATTTCAAATGGACT 59.055 33.333 25.02 1.39 46.43 3.85
3632 7721 8.110860 TGTCCTTTTAGAGATTTCAAATGGAC 57.889 34.615 22.10 22.10 46.45 4.02
3633 7722 8.704849 TTGTCCTTTTAGAGATTTCAAATGGA 57.295 30.769 0.00 9.53 34.75 3.41
3634 7723 9.933723 ATTTGTCCTTTTAGAGATTTCAAATGG 57.066 29.630 0.00 0.00 33.66 3.16
3646 7735 9.169592 CCGTTCCTAAATATTTGTCCTTTTAGA 57.830 33.333 11.05 0.00 34.90 2.10
3647 7736 9.169592 TCCGTTCCTAAATATTTGTCCTTTTAG 57.830 33.333 11.05 0.00 33.47 1.85
3648 7737 9.169592 CTCCGTTCCTAAATATTTGTCCTTTTA 57.830 33.333 11.05 0.00 0.00 1.52
3649 7738 7.122204 CCTCCGTTCCTAAATATTTGTCCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
3650 7739 6.602009 CCTCCGTTCCTAAATATTTGTCCTTT 59.398 38.462 11.05 0.00 0.00 3.11
3651 7740 6.120220 CCTCCGTTCCTAAATATTTGTCCTT 58.880 40.000 11.05 0.00 0.00 3.36
3652 7741 5.397559 CCCTCCGTTCCTAAATATTTGTCCT 60.398 44.000 11.05 0.00 0.00 3.85
3653 7742 4.820173 CCCTCCGTTCCTAAATATTTGTCC 59.180 45.833 11.05 0.00 0.00 4.02
3654 7743 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3655 7744 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3656 7745 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3657 7746 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3658 7747 5.543020 CCTACTCCCTCCGTTCCTAAATATT 59.457 44.000 0.00 0.00 0.00 1.28
3659 7748 5.085219 CCTACTCCCTCCGTTCCTAAATAT 58.915 45.833 0.00 0.00 0.00 1.28
3660 7749 4.078980 ACCTACTCCCTCCGTTCCTAAATA 60.079 45.833 0.00 0.00 0.00 1.40
3661 7750 3.306613 CCTACTCCCTCCGTTCCTAAAT 58.693 50.000 0.00 0.00 0.00 1.40
3662 7751 2.043526 ACCTACTCCCTCCGTTCCTAAA 59.956 50.000 0.00 0.00 0.00 1.85
3663 7752 1.642762 ACCTACTCCCTCCGTTCCTAA 59.357 52.381 0.00 0.00 0.00 2.69
3664 7753 1.302907 ACCTACTCCCTCCGTTCCTA 58.697 55.000 0.00 0.00 0.00 2.94
3665 7754 0.412640 AACCTACTCCCTCCGTTCCT 59.587 55.000 0.00 0.00 0.00 3.36
3666 7755 0.535797 CAACCTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
3667 7756 1.067071 CACAACCTACTCCCTCCGTTC 60.067 57.143 0.00 0.00 0.00 3.95
3668 7757 0.974383 CACAACCTACTCCCTCCGTT 59.026 55.000 0.00 0.00 0.00 4.44
3669 7758 0.113776 TCACAACCTACTCCCTCCGT 59.886 55.000 0.00 0.00 0.00 4.69
3670 7759 1.263356 TTCACAACCTACTCCCTCCG 58.737 55.000 0.00 0.00 0.00 4.63
3671 7760 3.055209 GTTTCACAACCTACTCCCTCC 57.945 52.381 0.00 0.00 0.00 4.30
3687 7776 6.619801 AAAGTACAGTGAGTCAATGGTTTC 57.380 37.500 23.28 10.86 33.50 2.78
3943 8032 7.780064 TGGTTGCACATATGTATGCTATTTTT 58.220 30.769 16.59 0.00 42.55 1.94
3947 8036 6.944290 AGATTGGTTGCACATATGTATGCTAT 59.056 34.615 16.59 3.29 42.55 2.97
4267 8378 7.068103 TGTCATATTTCGGCATCCAAAATAGTT 59.932 33.333 0.00 0.00 30.71 2.24
4274 8385 3.615155 TGTGTCATATTTCGGCATCCAA 58.385 40.909 0.00 0.00 0.00 3.53
4281 8392 5.801350 AGTGTTGATGTGTCATATTTCGG 57.199 39.130 0.00 0.00 33.56 4.30
4282 8393 9.425893 GAAATAGTGTTGATGTGTCATATTTCG 57.574 33.333 0.00 0.00 35.30 3.46
4318 8429 5.739752 TTTTGCAGAATCATACATCTCCG 57.260 39.130 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.