Multiple sequence alignment - TraesCS4D01G053700

Loading Multiple Alignment...

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 TraesCS4D01G053700 chr4D 100.000 4151 0 0 1 4151 29826189 29830339 0.000000e+00 7666.0
1 TraesCS4D01G053700 chr4D 87.543 289 35 1 1 289 312589619 312589906 2.390000e-87 333.0
2 TraesCS4D01G053700 chr4D 71.569 408 86 26 2142 2528 384670477 384670875 2.660000e-12 84.2
3 TraesCS4D01G053700 chr4B 96.173 1437 52 2 1836 3270 42394958 42396393 0.000000e+00 2346.0
4 TraesCS4D01G053700 chr4B 88.434 1513 55 38 406 1834 42393442 42394918 0.000000e+00 1714.0
5 TraesCS4D01G053700 chr4B 90.122 658 28 20 3531 4151 42396470 42397127 0.000000e+00 821.0
6 TraesCS4D01G053700 chr4B 81.600 125 13 5 3282 3404 165299105 165298989 1.230000e-15 95.3
7 TraesCS4D01G053700 chr4B 71.569 408 86 26 2142 2528 471652817 471653215 2.660000e-12 84.2
8 TraesCS4D01G053700 chr4A 95.594 1430 55 4 1841 3270 573327490 573326069 0.000000e+00 2285.0
9 TraesCS4D01G053700 chr4A 96.792 530 12 3 3627 4151 573325802 573325273 0.000000e+00 880.0
10 TraesCS4D01G053700 chr4A 89.170 711 70 3 9 719 573329274 573328571 0.000000e+00 880.0
11 TraesCS4D01G053700 chr4A 85.833 600 40 26 784 1366 573328561 573327990 2.760000e-166 595.0
12 TraesCS4D01G053700 chr4A 89.623 424 34 4 1407 1820 573327983 573327560 7.900000e-147 531.0
13 TraesCS4D01G053700 chr4A 72.696 293 63 16 2142 2421 66338591 66338879 9.560000e-12 82.4
14 TraesCS4D01G053700 chr1D 85.556 360 45 5 1 356 47844209 47844565 1.820000e-98 370.0
15 TraesCS4D01G053700 chr1D 82.258 124 14 3 3282 3404 108103281 108103165 2.640000e-17 100.0
16 TraesCS4D01G053700 chr2B 84.397 282 36 7 6 284 712964427 712964151 1.900000e-68 270.0
17 TraesCS4D01G053700 chr2B 79.695 197 33 6 151 347 583787590 583787779 7.240000e-28 135.0
18 TraesCS4D01G053700 chr2B 82.171 129 17 3 3282 3409 653689818 653689695 5.680000e-19 106.0
19 TraesCS4D01G053700 chr2A 82.594 293 45 5 1 290 591612518 591612229 1.920000e-63 254.0
20 TraesCS4D01G053700 chr2A 79.457 258 37 11 11 256 562646321 562646068 7.140000e-38 169.0
21 TraesCS4D01G053700 chrUn 76.846 298 49 15 2342 2626 194663653 194663943 2.590000e-32 150.0
22 TraesCS4D01G053700 chr3D 81.921 177 22 7 169 345 121390679 121390845 1.560000e-29 141.0
23 TraesCS4D01G053700 chr3D 84.496 129 12 3 3282 3409 251316017 251316138 2.030000e-23 121.0
24 TraesCS4D01G053700 chr7A 76.000 300 48 21 2342 2626 35628575 35628865 2.600000e-27 134.0
25 TraesCS4D01G053700 chr7A 80.153 131 16 5 3282 3410 28588298 28588176 5.720000e-14 89.8
26 TraesCS4D01G053700 chr2D 86.047 129 12 3 3282 3409 547203604 547203481 2.600000e-27 134.0
27 TraesCS4D01G053700 chr5A 86.154 130 6 6 3282 3409 367133286 367133167 3.370000e-26 130.0
28 TraesCS4D01G053700 chr3A 84.496 129 12 3 3282 3409 332556287 332556166 2.030000e-23 121.0
29 TraesCS4D01G053700 chr6B 84.127 126 15 4 168 291 450642594 450642716 2.620000e-22 117.0
30 TraesCS4D01G053700 chr6D 80.488 123 18 4 3293 3415 433035602 433035718 5.720000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G053700 chr4D 29826189 29830339 4150 False 7666.0 7666 100.000000 1 4151 1 chr4D.!!$F1 4150
1 TraesCS4D01G053700 chr4B 42393442 42397127 3685 False 1627.0 2346 91.576333 406 4151 3 chr4B.!!$F2 3745
2 TraesCS4D01G053700 chr4A 573325273 573329274 4001 True 1034.2 2285 91.402400 9 4151 5 chr4A.!!$R1 4142

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
385 386 0.035439 TTGAGAGGTCGGATTTGCCC 60.035 55.0 0.00 0.00 0.00 5.36 F
849 880 0.249615 ACTCACATCATCGCATCCGG 60.250 55.0 0.00 0.00 34.56 5.14 F
1551 1634 0.393808 TAGCCCGGGAAAGAATGTGC 60.394 55.0 29.31 3.85 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 1921 0.179097 ACGGCATTTTGGCAAAACGT 60.179 45.0 26.23 25.46 43.94 3.99 R
2652 2797 0.175989 GGTGGGAGACGAGATTGGAC 59.824 60.0 0.00 0.00 0.00 4.02 R
3480 3627 0.249120 CTGTCGGTGTATTCCCTGCA 59.751 55.0 0.00 0.00 0.00 4.41 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
26 27 3.816054 GGAAGGGGAAAGGTCCGA 58.184 61.111 0.00 0.00 46.04 4.55
30 31 0.908180 AAGGGGAAAGGTCCGACGAT 60.908 55.000 0.00 0.00 46.04 3.73
41 42 0.526211 TCCGACGATGAAGTGGTGAG 59.474 55.000 0.00 0.00 0.00 3.51
59 60 1.757699 GAGGAAGCTCCCTCGTATGTT 59.242 52.381 2.02 0.00 42.80 2.71
62 63 3.385111 AGGAAGCTCCCTCGTATGTTTAG 59.615 47.826 0.00 0.00 37.19 1.85
114 115 2.029728 CGATGAACTGCGGTGATCTTTC 59.970 50.000 0.00 0.00 0.00 2.62
135 136 6.503589 TTCGGATAATGTAAAGTGGGTTTG 57.496 37.500 0.00 0.00 0.00 2.93
141 142 4.953940 ATGTAAAGTGGGTTTGTGCATT 57.046 36.364 0.00 0.00 0.00 3.56
149 150 3.248125 GTGGGTTTGTGCATTTCATTGTG 59.752 43.478 0.00 0.00 0.00 3.33
150 151 2.223845 GGGTTTGTGCATTTCATTGTGC 59.776 45.455 0.00 0.00 41.61 4.57
164 165 2.592796 TTGTGCGTTTGATGTCGATG 57.407 45.000 0.00 0.00 0.00 3.84
166 167 1.194322 TGTGCGTTTGATGTCGATGTG 59.806 47.619 0.00 0.00 0.00 3.21
172 173 3.900116 CGTTTGATGTCGATGTGTTTGTC 59.100 43.478 0.00 0.00 0.00 3.18
183 184 3.479505 TGTGTTTGTCCGTTGTTTGAG 57.520 42.857 0.00 0.00 0.00 3.02
188 189 1.368850 GTCCGTTGTTTGAGCACGC 60.369 57.895 0.00 0.00 0.00 5.34
192 193 0.522286 CGTTGTTTGAGCACGCACAA 60.522 50.000 0.00 0.00 0.00 3.33
194 195 1.518102 GTTGTTTGAGCACGCACAATG 59.482 47.619 2.74 0.00 32.00 2.82
200 201 1.608109 TGAGCACGCACAATGTTTCAT 59.392 42.857 0.00 0.00 0.00 2.57
202 203 1.608109 AGCACGCACAATGTTTCATCA 59.392 42.857 0.00 0.00 0.00 3.07
212 213 3.921119 ATGTTTCATCACGTTGCATGT 57.079 38.095 0.00 0.00 0.00 3.21
213 214 5.152804 CAATGTTTCATCACGTTGCATGTA 58.847 37.500 0.00 0.00 36.97 2.29
217 218 5.641636 TGTTTCATCACGTTGCATGTATAGT 59.358 36.000 0.00 0.00 0.00 2.12
227 228 9.237846 CACGTTGCATGTATAGTATGGATATAG 57.762 37.037 0.00 0.00 0.00 1.31
247 248 2.690497 AGGATGCCGGATATGAGATACG 59.310 50.000 5.05 0.00 0.00 3.06
255 256 3.439293 GGATATGAGATACGCGGATGTG 58.561 50.000 9.57 0.00 0.00 3.21
256 257 3.128764 GGATATGAGATACGCGGATGTGA 59.871 47.826 9.57 0.00 0.00 3.58
258 259 2.492019 TGAGATACGCGGATGTGAAG 57.508 50.000 9.57 0.00 0.00 3.02
260 261 2.033424 TGAGATACGCGGATGTGAAGAG 59.967 50.000 9.57 0.00 0.00 2.85
265 266 2.456000 GCGGATGTGAAGAGCGAAA 58.544 52.632 0.00 0.00 0.00 3.46
268 269 2.033662 GCGGATGTGAAGAGCGAAATAC 60.034 50.000 0.00 0.00 0.00 1.89
278 279 2.128128 CGAAATACGATGCGCGCC 60.128 61.111 30.77 13.55 46.04 6.53
279 280 2.585869 CGAAATACGATGCGCGCCT 61.586 57.895 30.77 20.77 46.04 5.52
281 282 2.430080 GAAATACGATGCGCGCCTGG 62.430 60.000 30.77 22.82 46.04 4.45
298 299 4.295119 GTCAGTGCCCGTGTCCGT 62.295 66.667 0.00 0.00 0.00 4.69
316 317 2.434359 GGACGTTTGAGAGGCCGG 60.434 66.667 0.00 0.00 0.00 6.13
349 350 2.282820 GCAGTTGTAGATGCTCTAACGC 59.717 50.000 0.00 0.00 39.38 4.84
352 353 2.860735 GTTGTAGATGCTCTAACGCAGG 59.139 50.000 0.00 0.00 44.10 4.85
356 357 1.550524 AGATGCTCTAACGCAGGACAA 59.449 47.619 0.00 0.00 44.10 3.18
357 358 2.028112 AGATGCTCTAACGCAGGACAAA 60.028 45.455 0.00 0.00 44.10 2.83
374 375 3.214328 ACAAAATGAGCGTTTGAGAGGT 58.786 40.909 10.74 0.00 38.05 3.85
385 386 0.035439 TTGAGAGGTCGGATTTGCCC 60.035 55.000 0.00 0.00 0.00 5.36
448 449 3.324846 GCATCCAGGTAGATACATCACCA 59.675 47.826 11.11 0.00 33.36 4.17
449 450 4.562347 GCATCCAGGTAGATACATCACCAG 60.562 50.000 11.11 5.51 33.36 4.00
488 489 2.502492 CGCCCACCTCGATCCTGAT 61.502 63.158 0.00 0.00 0.00 2.90
494 495 1.612950 CACCTCGATCCTGATCCTGAG 59.387 57.143 1.69 3.93 34.40 3.35
498 499 1.670590 GATCCTGATCCTGAGCCGG 59.329 63.158 0.00 0.00 31.76 6.13
708 731 2.674380 CCGCTTTGCTTGCTCCCT 60.674 61.111 0.00 0.00 0.00 4.20
711 734 1.239968 CGCTTTGCTTGCTCCCTCTT 61.240 55.000 0.00 0.00 0.00 2.85
737 760 7.861629 TCTCTCTTTCCAGCCTTATTATTGAA 58.138 34.615 0.00 0.00 0.00 2.69
738 761 7.989741 TCTCTCTTTCCAGCCTTATTATTGAAG 59.010 37.037 0.00 0.00 0.00 3.02
739 762 7.861629 TCTCTTTCCAGCCTTATTATTGAAGA 58.138 34.615 0.00 0.00 0.00 2.87
740 763 7.989741 TCTCTTTCCAGCCTTATTATTGAAGAG 59.010 37.037 0.00 0.00 38.32 2.85
741 764 6.543831 TCTTTCCAGCCTTATTATTGAAGAGC 59.456 38.462 0.00 0.00 0.00 4.09
743 766 3.058639 CCAGCCTTATTATTGAAGAGCGC 60.059 47.826 0.00 0.00 0.00 5.92
795 826 2.184579 CCGCGTCTCCCTTCCTTC 59.815 66.667 4.92 0.00 0.00 3.46
796 827 2.184579 CGCGTCTCCCTTCCTTCC 59.815 66.667 0.00 0.00 0.00 3.46
797 828 2.352032 CGCGTCTCCCTTCCTTCCT 61.352 63.158 0.00 0.00 0.00 3.36
798 829 1.889530 CGCGTCTCCCTTCCTTCCTT 61.890 60.000 0.00 0.00 0.00 3.36
842 873 2.884827 TCAGCTCAACTCACATCATCG 58.115 47.619 0.00 0.00 0.00 3.84
843 874 1.326852 CAGCTCAACTCACATCATCGC 59.673 52.381 0.00 0.00 0.00 4.58
849 880 0.249615 ACTCACATCATCGCATCCGG 60.250 55.000 0.00 0.00 34.56 5.14
853 884 1.118965 ACATCATCGCATCCGGGGTA 61.119 55.000 0.00 0.00 34.56 3.69
859 911 4.910585 GCATCCGGGGTAGTGCCG 62.911 72.222 0.00 0.00 38.44 5.69
880 932 2.882137 GCACCAGCACTAGTTAAACCAA 59.118 45.455 0.00 0.00 41.58 3.67
982 1051 1.202087 ACAAGAAGAGCTCGATCGACG 60.202 52.381 15.15 11.63 44.09 5.12
1054 1123 3.114390 CTCTCCTCCTCCTGGGGT 58.886 66.667 0.00 0.00 35.33 4.95
1066 1135 1.073722 CTGGGGTTCTTGCTGCTCA 59.926 57.895 0.00 0.00 0.00 4.26
1077 1146 1.276859 TGCTGCTCATCCATGTCCCT 61.277 55.000 0.00 0.00 0.00 4.20
1156 1225 6.227298 TCTTCTTCGGCTAATCTGAATTCT 57.773 37.500 7.05 0.00 39.22 2.40
1159 1228 5.352284 TCTTCGGCTAATCTGAATTCTGTC 58.648 41.667 7.05 0.00 39.22 3.51
1161 1230 3.134458 CGGCTAATCTGAATTCTGTCCC 58.866 50.000 7.05 3.92 0.00 4.46
1210 1287 2.037772 TGGAAGCTTCTTCTCGCTTTCT 59.962 45.455 25.05 0.00 45.70 2.52
1455 1538 4.637977 ACTAAGTACTAGTAACTGGCGTCC 59.362 45.833 3.61 0.00 39.20 4.79
1483 1566 2.095718 CGTAGGTTCTTCAGCCAAAAGC 60.096 50.000 0.00 0.00 44.25 3.51
1551 1634 0.393808 TAGCCCGGGAAAGAATGTGC 60.394 55.000 29.31 3.85 0.00 4.57
1573 1656 4.083537 GCGTGACAATGAAATGAACCTACA 60.084 41.667 0.00 0.00 0.00 2.74
1575 1658 6.611381 CGTGACAATGAAATGAACCTACATT 58.389 36.000 0.00 0.00 41.43 2.71
1595 1681 4.742438 TTCATCTGTAGAAAACAACGGC 57.258 40.909 0.00 0.00 37.74 5.68
1602 1688 1.092921 AGAAAACAACGGCGTCTGCA 61.093 50.000 15.17 0.00 45.35 4.41
1623 1709 1.394917 CTCTCAACCGTGCAACATAGC 59.605 52.381 0.00 0.00 35.74 2.97
1696 1792 2.028484 TCGTGTCGTTGTGAGGGC 59.972 61.111 0.00 0.00 0.00 5.19
1721 1817 0.729116 GTACTAGCGCTGTACCGACA 59.271 55.000 26.31 5.66 35.52 4.35
1768 1864 9.428097 GTCTAGCCATTTGAAATTTTGAATTCT 57.572 29.630 7.05 0.00 0.00 2.40
1774 1870 3.324993 TGAAATTTTGAATTCTGCGGGC 58.675 40.909 7.05 0.00 0.00 6.13
1834 1933 5.821995 AGTAACCTTACTACGTTTTGCCAAA 59.178 36.000 0.00 0.00 41.92 3.28
2067 2212 2.506472 GACATCCCCTCCTTCGCC 59.494 66.667 0.00 0.00 0.00 5.54
2658 2803 3.118454 CGCGCCTTCGTGTCCAAT 61.118 61.111 0.00 0.00 40.97 3.16
2757 2902 2.636412 CGACGAGGACCTCAAGCCA 61.636 63.158 21.49 0.00 0.00 4.75
2781 2926 1.186267 AGGCGTCGGAGAAGTCCTTT 61.186 55.000 0.00 0.00 42.76 3.11
2971 3118 4.964555 GCTTTCGAAGTTTCTTGTGAACTC 59.035 41.667 0.00 0.00 31.02 3.01
2997 3144 1.292061 GAGCTCTCGTCTCGCTTCTA 58.708 55.000 6.43 0.00 33.47 2.10
3081 3228 1.428448 GTCATGTTCGTAGTGCTGCA 58.572 50.000 0.00 0.00 0.00 4.41
3086 3233 2.766313 TGTTCGTAGTGCTGCAGAATT 58.234 42.857 20.43 6.38 0.00 2.17
3097 3244 2.334946 GCAGAATTGCCTCGCACCA 61.335 57.895 0.00 0.00 44.74 4.17
3099 3246 0.379669 CAGAATTGCCTCGCACCATC 59.620 55.000 0.00 0.00 38.71 3.51
3100 3247 0.254178 AGAATTGCCTCGCACCATCT 59.746 50.000 0.00 0.00 38.71 2.90
3102 3249 0.749454 AATTGCCTCGCACCATCTCC 60.749 55.000 0.00 0.00 38.71 3.71
3116 3263 2.635229 ATCTCCGCGCTCCATGTGTC 62.635 60.000 5.56 0.00 0.00 3.67
3144 3291 5.610398 TGTTTCTTGTTCATGTCTCTGCTA 58.390 37.500 0.00 0.00 0.00 3.49
3232 3379 4.563976 GCTCATATGTGGTTTTGCATTGTC 59.436 41.667 1.90 0.00 0.00 3.18
3275 3422 9.871238 ATACGATGTGAACAAATATATACTCCC 57.129 33.333 0.00 0.00 0.00 4.30
3276 3423 7.963532 ACGATGTGAACAAATATATACTCCCT 58.036 34.615 0.00 0.00 0.00 4.20
3277 3424 8.088981 ACGATGTGAACAAATATATACTCCCTC 58.911 37.037 0.00 0.00 0.00 4.30
3278 3425 7.545965 CGATGTGAACAAATATATACTCCCTCC 59.454 40.741 0.00 0.00 0.00 4.30
3279 3426 6.755206 TGTGAACAAATATATACTCCCTCCG 58.245 40.000 0.00 0.00 0.00 4.63
3280 3427 6.325545 TGTGAACAAATATATACTCCCTCCGT 59.674 38.462 0.00 0.00 0.00 4.69
3281 3428 6.867293 GTGAACAAATATATACTCCCTCCGTC 59.133 42.308 0.00 0.00 0.00 4.79
3282 3429 5.997384 ACAAATATATACTCCCTCCGTCC 57.003 43.478 0.00 0.00 0.00 4.79
3283 3430 5.652324 ACAAATATATACTCCCTCCGTCCT 58.348 41.667 0.00 0.00 0.00 3.85
3284 3431 5.715753 ACAAATATATACTCCCTCCGTCCTC 59.284 44.000 0.00 0.00 0.00 3.71
3285 3432 5.531753 AATATATACTCCCTCCGTCCTCA 57.468 43.478 0.00 0.00 0.00 3.86
3286 3433 2.953284 TATACTCCCTCCGTCCTCAG 57.047 55.000 0.00 0.00 0.00 3.35
3287 3434 0.927767 ATACTCCCTCCGTCCTCAGT 59.072 55.000 0.00 0.00 0.00 3.41
3288 3435 0.255318 TACTCCCTCCGTCCTCAGTC 59.745 60.000 0.00 0.00 0.00 3.51
3289 3436 1.755008 CTCCCTCCGTCCTCAGTCC 60.755 68.421 0.00 0.00 0.00 3.85
3290 3437 2.760385 CCCTCCGTCCTCAGTCCC 60.760 72.222 0.00 0.00 0.00 4.46
3291 3438 3.141488 CCTCCGTCCTCAGTCCCG 61.141 72.222 0.00 0.00 0.00 5.14
3292 3439 2.045242 CTCCGTCCTCAGTCCCGA 60.045 66.667 0.00 0.00 0.00 5.14
3293 3440 1.677966 CTCCGTCCTCAGTCCCGAA 60.678 63.158 0.00 0.00 0.00 4.30
3294 3441 1.000019 TCCGTCCTCAGTCCCGAAT 60.000 57.895 0.00 0.00 0.00 3.34
3295 3442 0.613853 TCCGTCCTCAGTCCCGAATT 60.614 55.000 0.00 0.00 0.00 2.17
3296 3443 1.108776 CCGTCCTCAGTCCCGAATTA 58.891 55.000 0.00 0.00 0.00 1.40
3297 3444 1.067212 CCGTCCTCAGTCCCGAATTAG 59.933 57.143 0.00 0.00 0.00 1.73
3298 3445 1.749634 CGTCCTCAGTCCCGAATTAGT 59.250 52.381 0.00 0.00 0.00 2.24
3299 3446 2.165845 CGTCCTCAGTCCCGAATTAGTT 59.834 50.000 0.00 0.00 0.00 2.24
3300 3447 3.522553 GTCCTCAGTCCCGAATTAGTTG 58.477 50.000 0.00 0.00 0.00 3.16
3301 3448 3.056035 GTCCTCAGTCCCGAATTAGTTGT 60.056 47.826 0.00 0.00 0.00 3.32
3302 3449 3.194968 TCCTCAGTCCCGAATTAGTTGTC 59.805 47.826 0.00 0.00 0.00 3.18
3303 3450 3.522553 CTCAGTCCCGAATTAGTTGTCC 58.477 50.000 0.00 0.00 0.00 4.02
3304 3451 3.170717 TCAGTCCCGAATTAGTTGTCCT 58.829 45.455 0.00 0.00 0.00 3.85
3305 3452 4.346730 TCAGTCCCGAATTAGTTGTCCTA 58.653 43.478 0.00 0.00 0.00 2.94
3306 3453 4.401519 TCAGTCCCGAATTAGTTGTCCTAG 59.598 45.833 0.00 0.00 0.00 3.02
3307 3454 4.401519 CAGTCCCGAATTAGTTGTCCTAGA 59.598 45.833 0.00 0.00 0.00 2.43
3308 3455 5.069251 CAGTCCCGAATTAGTTGTCCTAGAT 59.931 44.000 0.00 0.00 0.00 1.98
3309 3456 5.661759 AGTCCCGAATTAGTTGTCCTAGATT 59.338 40.000 0.00 0.00 0.00 2.40
3310 3457 6.156429 AGTCCCGAATTAGTTGTCCTAGATTT 59.844 38.462 0.00 0.00 0.00 2.17
3311 3458 6.258068 GTCCCGAATTAGTTGTCCTAGATTTG 59.742 42.308 0.00 0.00 0.00 2.32
3312 3459 6.070424 TCCCGAATTAGTTGTCCTAGATTTGT 60.070 38.462 0.00 0.00 0.00 2.83
3313 3460 6.258068 CCCGAATTAGTTGTCCTAGATTTGTC 59.742 42.308 0.00 0.00 0.00 3.18
3314 3461 7.042335 CCGAATTAGTTGTCCTAGATTTGTCT 58.958 38.462 0.00 0.00 0.00 3.41
3315 3462 8.195436 CCGAATTAGTTGTCCTAGATTTGTCTA 58.805 37.037 0.00 0.00 0.00 2.59
3316 3463 9.239002 CGAATTAGTTGTCCTAGATTTGTCTAG 57.761 37.037 5.66 5.66 39.40 2.43
3321 3468 7.932335 AGTTGTCCTAGATTTGTCTAGATACG 58.068 38.462 12.74 0.00 41.56 3.06
3322 3469 6.879276 TGTCCTAGATTTGTCTAGATACGG 57.121 41.667 12.74 0.00 41.56 4.02
3323 3470 6.598503 TGTCCTAGATTTGTCTAGATACGGA 58.401 40.000 12.74 1.34 41.56 4.69
3324 3471 7.232188 TGTCCTAGATTTGTCTAGATACGGAT 58.768 38.462 12.74 0.00 41.56 4.18
3325 3472 8.380867 TGTCCTAGATTTGTCTAGATACGGATA 58.619 37.037 12.74 0.25 41.56 2.59
3326 3473 9.398538 GTCCTAGATTTGTCTAGATACGGATAT 57.601 37.037 12.74 0.00 41.56 1.63
3340 3487 8.789825 AGATACGGATATATCTAGACACGTTT 57.210 34.615 14.69 9.16 39.63 3.60
3341 3488 9.228949 AGATACGGATATATCTAGACACGTTTT 57.771 33.333 14.69 6.38 39.63 2.43
3344 3491 8.388484 ACGGATATATCTAGACACGTTTTAGT 57.612 34.615 12.42 0.00 0.00 2.24
3345 3492 8.502387 ACGGATATATCTAGACACGTTTTAGTC 58.498 37.037 12.42 0.00 35.02 2.59
3346 3493 8.719648 CGGATATATCTAGACACGTTTTAGTCT 58.280 37.037 12.42 10.66 46.19 3.24
3350 3497 5.624344 TCTAGACACGTTTTAGTCTCAGG 57.376 43.478 9.32 3.27 43.59 3.86
3351 3498 5.068636 TCTAGACACGTTTTAGTCTCAGGT 58.931 41.667 9.32 0.00 43.59 4.00
3352 3499 6.233434 TCTAGACACGTTTTAGTCTCAGGTA 58.767 40.000 9.32 0.00 43.59 3.08
3353 3500 5.979288 AGACACGTTTTAGTCTCAGGTAT 57.021 39.130 0.68 0.00 40.96 2.73
3354 3501 6.342338 AGACACGTTTTAGTCTCAGGTATT 57.658 37.500 0.68 0.00 40.96 1.89
3355 3502 7.458409 AGACACGTTTTAGTCTCAGGTATTA 57.542 36.000 0.68 0.00 40.96 0.98
3356 3503 7.536855 AGACACGTTTTAGTCTCAGGTATTAG 58.463 38.462 0.68 0.00 40.96 1.73
3357 3504 7.392673 AGACACGTTTTAGTCTCAGGTATTAGA 59.607 37.037 0.68 0.00 40.96 2.10
3358 3505 8.064336 ACACGTTTTAGTCTCAGGTATTAGAT 57.936 34.615 0.00 0.00 0.00 1.98
3359 3506 9.182214 ACACGTTTTAGTCTCAGGTATTAGATA 57.818 33.333 0.00 0.00 0.00 1.98
3360 3507 9.448294 CACGTTTTAGTCTCAGGTATTAGATAC 57.552 37.037 0.00 0.00 35.00 2.24
3361 3508 9.182214 ACGTTTTAGTCTCAGGTATTAGATACA 57.818 33.333 1.06 0.00 37.48 2.29
3365 3512 9.877222 TTTAGTCTCAGGTATTAGATACATCCA 57.123 33.333 1.06 0.00 37.48 3.41
3368 3515 9.469097 AGTCTCAGGTATTAGATACATCCATAC 57.531 37.037 1.06 2.52 37.48 2.39
3369 3516 9.469097 GTCTCAGGTATTAGATACATCCATACT 57.531 37.037 1.06 0.00 37.48 2.12
3384 3531 8.451908 ACATCCATACTAAACAAATCTAAGGC 57.548 34.615 0.00 0.00 0.00 4.35
3385 3532 8.052748 ACATCCATACTAAACAAATCTAAGGCA 58.947 33.333 0.00 0.00 0.00 4.75
3386 3533 8.902806 CATCCATACTAAACAAATCTAAGGCAA 58.097 33.333 0.00 0.00 0.00 4.52
3387 3534 9.646522 ATCCATACTAAACAAATCTAAGGCAAT 57.353 29.630 0.00 0.00 0.00 3.56
3388 3535 9.474313 TCCATACTAAACAAATCTAAGGCAATT 57.526 29.630 0.00 0.00 0.00 2.32
3396 3543 8.791327 AACAAATCTAAGGCAATTAATTTGGG 57.209 30.769 18.82 0.00 36.88 4.12
3397 3544 8.144862 ACAAATCTAAGGCAATTAATTTGGGA 57.855 30.769 18.82 0.00 36.88 4.37
3398 3545 8.040727 ACAAATCTAAGGCAATTAATTTGGGAC 58.959 33.333 18.82 0.00 36.88 4.46
3399 3546 5.828299 TCTAAGGCAATTAATTTGGGACG 57.172 39.130 0.00 0.00 35.75 4.79
3400 3547 3.885724 AAGGCAATTAATTTGGGACGG 57.114 42.857 0.00 0.00 35.75 4.79
3401 3548 3.094484 AGGCAATTAATTTGGGACGGA 57.906 42.857 0.00 0.00 35.75 4.69
3402 3549 3.023832 AGGCAATTAATTTGGGACGGAG 58.976 45.455 0.00 0.00 35.75 4.63
3403 3550 2.100749 GGCAATTAATTTGGGACGGAGG 59.899 50.000 0.00 0.00 35.75 4.30
3404 3551 2.758423 GCAATTAATTTGGGACGGAGGT 59.242 45.455 0.00 0.00 35.75 3.85
3405 3552 3.949113 GCAATTAATTTGGGACGGAGGTA 59.051 43.478 0.00 0.00 35.75 3.08
3406 3553 4.399934 GCAATTAATTTGGGACGGAGGTAA 59.600 41.667 0.00 0.00 35.75 2.85
3407 3554 5.068591 GCAATTAATTTGGGACGGAGGTAAT 59.931 40.000 0.00 0.00 35.75 1.89
3408 3555 6.263617 GCAATTAATTTGGGACGGAGGTAATA 59.736 38.462 0.00 0.00 35.75 0.98
3409 3556 7.645402 CAATTAATTTGGGACGGAGGTAATAC 58.355 38.462 0.00 0.00 0.00 1.89
3410 3557 3.851458 ATTTGGGACGGAGGTAATACC 57.149 47.619 0.07 0.07 38.99 2.73
3411 3558 2.250921 TTGGGACGGAGGTAATACCA 57.749 50.000 12.54 0.00 41.95 3.25
3413 3560 2.322658 TGGGACGGAGGTAATACCATC 58.677 52.381 12.54 6.32 41.95 3.51
3419 3566 5.277857 ACGGAGGTAATACCATCTTTCAG 57.722 43.478 12.54 3.51 41.95 3.02
3426 3573 8.324191 AGGTAATACCATCTTTCAGAATCAGA 57.676 34.615 12.54 0.00 41.95 3.27
3428 3575 9.213799 GGTAATACCATCTTTCAGAATCAGATC 57.786 37.037 4.24 0.00 38.42 2.75
3430 3577 4.125703 ACCATCTTTCAGAATCAGATCGC 58.874 43.478 0.00 0.00 0.00 4.58
3432 3579 4.211584 CCATCTTTCAGAATCAGATCGCAG 59.788 45.833 0.00 0.00 0.00 5.18
3433 3580 3.790091 TCTTTCAGAATCAGATCGCAGG 58.210 45.455 0.00 0.00 0.00 4.85
3435 3582 1.117994 TCAGAATCAGATCGCAGGCT 58.882 50.000 0.00 0.00 0.00 4.58
3436 3583 1.068281 TCAGAATCAGATCGCAGGCTC 59.932 52.381 0.00 0.00 0.00 4.70
3445 3592 0.320771 ATCGCAGGCTCAGTTCGTTT 60.321 50.000 0.00 0.00 0.00 3.60
3446 3593 0.315886 TCGCAGGCTCAGTTCGTTTA 59.684 50.000 0.00 0.00 0.00 2.01
3447 3594 1.144969 CGCAGGCTCAGTTCGTTTAA 58.855 50.000 0.00 0.00 0.00 1.52
3448 3595 1.529438 CGCAGGCTCAGTTCGTTTAAA 59.471 47.619 0.00 0.00 0.00 1.52
3449 3596 2.411547 CGCAGGCTCAGTTCGTTTAAAG 60.412 50.000 0.00 0.00 0.00 1.85
3460 3607 8.259049 TCAGTTCGTTTAAAGAAAGAAACAGA 57.741 30.769 0.00 0.00 35.67 3.41
3461 3608 8.723311 TCAGTTCGTTTAAAGAAAGAAACAGAA 58.277 29.630 0.00 0.00 35.67 3.02
3462 3609 8.786028 CAGTTCGTTTAAAGAAAGAAACAGAAC 58.214 33.333 17.44 17.44 42.01 3.01
3463 3610 7.691050 AGTTCGTTTAAAGAAAGAAACAGAACG 59.309 33.333 18.20 0.00 43.69 3.95
3474 3621 3.380004 AGAAACAGAACGCCAACATCAAA 59.620 39.130 0.00 0.00 0.00 2.69
3480 3627 3.569701 AGAACGCCAACATCAAAGACAAT 59.430 39.130 0.00 0.00 0.00 2.71
3482 3629 1.987770 CGCCAACATCAAAGACAATGC 59.012 47.619 0.00 0.00 0.00 3.56
3488 3635 3.499338 ACATCAAAGACAATGCAGGGAA 58.501 40.909 0.00 0.00 0.00 3.97
3489 3636 4.091549 ACATCAAAGACAATGCAGGGAAT 58.908 39.130 0.00 0.00 0.00 3.01
3490 3637 5.263599 ACATCAAAGACAATGCAGGGAATA 58.736 37.500 0.00 0.00 0.00 1.75
3491 3638 5.126061 ACATCAAAGACAATGCAGGGAATAC 59.874 40.000 0.00 0.00 0.00 1.89
3492 3639 4.661222 TCAAAGACAATGCAGGGAATACA 58.339 39.130 0.00 0.00 0.00 2.29
3494 3641 3.004752 AGACAATGCAGGGAATACACC 57.995 47.619 0.00 0.00 0.00 4.16
3495 3642 1.670811 GACAATGCAGGGAATACACCG 59.329 52.381 0.00 0.00 0.00 4.94
3496 3643 1.280710 ACAATGCAGGGAATACACCGA 59.719 47.619 0.00 0.00 0.00 4.69
3497 3644 1.670811 CAATGCAGGGAATACACCGAC 59.329 52.381 0.00 0.00 0.00 4.79
3498 3645 0.908910 ATGCAGGGAATACACCGACA 59.091 50.000 0.00 0.00 0.00 4.35
3499 3646 0.249120 TGCAGGGAATACACCGACAG 59.751 55.000 0.00 0.00 0.00 3.51
3504 3655 2.838202 AGGGAATACACCGACAGTCATT 59.162 45.455 0.41 0.00 0.00 2.57
3505 3656 2.936498 GGGAATACACCGACAGTCATTG 59.064 50.000 0.41 0.00 0.00 2.82
3522 3673 9.793252 ACAGTCATTGCATAAAAAGAATCATAC 57.207 29.630 0.00 0.00 0.00 2.39
3523 3674 9.791820 CAGTCATTGCATAAAAAGAATCATACA 57.208 29.630 0.00 0.00 0.00 2.29
3553 3721 7.204496 TGTAGTTTGTTGGCGTACAAATAAT 57.796 32.000 17.13 10.96 46.29 1.28
3607 3776 2.047274 CAGGCCGTACACACTGGG 60.047 66.667 0.00 0.00 0.00 4.45
3717 3936 2.229062 TCGAACAAACAAACAGCCACAA 59.771 40.909 0.00 0.00 0.00 3.33
3927 4152 5.808366 AGTACAGAAGAGGAATTCACACA 57.192 39.130 7.93 0.00 0.00 3.72
3943 4168 7.935338 ATTCACACAGTGCAAAAATAAAGAG 57.065 32.000 0.00 0.00 32.98 2.85
3944 4169 6.449635 TCACACAGTGCAAAAATAAAGAGT 57.550 33.333 0.00 0.00 32.98 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.830704 CTTTCCCCTTCCGGTCGTCG 62.831 65.000 0.00 0.00 38.88 5.12
2 3 1.079336 CTTTCCCCTTCCGGTCGTC 60.079 63.158 0.00 0.00 0.00 4.20
3 4 2.590114 CCTTTCCCCTTCCGGTCGT 61.590 63.158 0.00 0.00 0.00 4.34
4 5 2.267961 CCTTTCCCCTTCCGGTCG 59.732 66.667 0.00 0.00 0.00 4.79
5 6 1.298993 GACCTTTCCCCTTCCGGTC 59.701 63.158 0.00 0.00 37.57 4.79
6 7 2.229203 GGACCTTTCCCCTTCCGGT 61.229 63.158 0.00 0.00 35.57 5.28
7 8 2.675371 GGACCTTTCCCCTTCCGG 59.325 66.667 0.00 0.00 35.57 5.14
22 23 0.526211 CTCACCACTTCATCGTCGGA 59.474 55.000 0.00 0.00 0.00 4.55
26 27 1.338200 GCTTCCTCACCACTTCATCGT 60.338 52.381 0.00 0.00 0.00 3.73
30 31 0.687354 GGAGCTTCCTCACCACTTCA 59.313 55.000 0.00 0.00 39.96 3.02
41 42 2.693267 AAACATACGAGGGAGCTTCC 57.307 50.000 1.27 1.27 35.23 3.46
114 115 5.636837 CACAAACCCACTTTACATTATCCG 58.363 41.667 0.00 0.00 0.00 4.18
135 136 2.793790 TCAAACGCACAATGAAATGCAC 59.206 40.909 0.00 0.00 42.17 4.57
141 142 2.545946 TCGACATCAAACGCACAATGAA 59.454 40.909 0.00 0.00 0.00 2.57
149 150 2.594529 AACACATCGACATCAAACGC 57.405 45.000 0.00 0.00 0.00 4.84
150 151 3.872354 ACAAACACATCGACATCAAACG 58.128 40.909 0.00 0.00 0.00 3.60
164 165 2.182014 GCTCAAACAACGGACAAACAC 58.818 47.619 0.00 0.00 0.00 3.32
166 167 2.182014 GTGCTCAAACAACGGACAAAC 58.818 47.619 0.00 0.00 0.00 2.93
172 173 1.654137 GTGCGTGCTCAAACAACGG 60.654 57.895 0.00 0.00 0.00 4.44
183 184 1.715519 GTGATGAAACATTGTGCGTGC 59.284 47.619 0.00 0.00 0.00 5.34
188 189 3.370276 TGCAACGTGATGAAACATTGTG 58.630 40.909 0.00 0.00 0.00 3.33
192 193 3.921119 ACATGCAACGTGATGAAACAT 57.079 38.095 8.92 0.00 0.00 2.71
194 195 6.106877 ACTATACATGCAACGTGATGAAAC 57.893 37.500 8.92 0.00 0.00 2.78
200 201 5.523438 TCCATACTATACATGCAACGTGA 57.477 39.130 0.00 0.00 0.00 4.35
202 203 8.414003 CCTATATCCATACTATACATGCAACGT 58.586 37.037 0.00 0.00 0.00 3.99
212 213 7.098845 TCCGGCATCCTATATCCATACTATA 57.901 40.000 0.00 0.00 0.00 1.31
213 214 5.965486 TCCGGCATCCTATATCCATACTAT 58.035 41.667 0.00 0.00 0.00 2.12
217 218 6.561294 TCATATCCGGCATCCTATATCCATA 58.439 40.000 0.00 0.00 0.00 2.74
227 228 2.799917 GCGTATCTCATATCCGGCATCC 60.800 54.545 0.00 0.00 0.00 3.51
247 248 1.009829 ATTTCGCTCTTCACATCCGC 58.990 50.000 0.00 0.00 0.00 5.54
255 256 1.396068 GCGCATCGTATTTCGCTCTTC 60.396 52.381 0.30 0.00 43.70 2.87
256 257 0.577269 GCGCATCGTATTTCGCTCTT 59.423 50.000 0.30 0.00 43.70 2.85
258 259 1.155016 CGCGCATCGTATTTCGCTC 60.155 57.895 8.75 0.00 44.72 5.03
260 261 2.787326 GCGCGCATCGTATTTCGC 60.787 61.111 29.10 0.00 43.62 4.70
265 266 4.221422 ACCAGGCGCGCATCGTAT 62.221 61.111 34.42 9.86 41.07 3.06
278 279 2.357517 GACACGGGCACTGACCAG 60.358 66.667 0.64 0.00 38.67 4.00
279 280 3.936203 GGACACGGGCACTGACCA 61.936 66.667 0.64 0.00 38.67 4.02
281 282 4.295119 ACGGACACGGGCACTGAC 62.295 66.667 0.00 0.00 46.48 3.51
288 289 3.795499 AAACGTCCACGGACACGGG 62.795 63.158 16.23 2.50 44.77 5.28
298 299 2.342279 CGGCCTCTCAAACGTCCA 59.658 61.111 0.00 0.00 0.00 4.02
301 302 0.036306 AAATCCGGCCTCTCAAACGT 59.964 50.000 0.00 0.00 0.00 3.99
349 350 3.250762 TCTCAAACGCTCATTTTGTCCTG 59.749 43.478 0.00 0.00 35.75 3.86
352 353 3.251004 ACCTCTCAAACGCTCATTTTGTC 59.749 43.478 0.00 0.00 35.75 3.18
356 357 2.069273 CGACCTCTCAAACGCTCATTT 58.931 47.619 0.00 0.00 0.00 2.32
357 358 1.673033 CCGACCTCTCAAACGCTCATT 60.673 52.381 0.00 0.00 0.00 2.57
385 386 1.607713 CTCTGTGTTAGAGCACGACG 58.392 55.000 0.00 0.00 45.94 5.12
404 405 1.592223 CAACTCCTCGTCCTGTCCC 59.408 63.158 0.00 0.00 0.00 4.46
448 449 2.341176 GCCCGTACGTGGTGAACT 59.659 61.111 15.21 0.00 0.00 3.01
449 450 2.029369 TGCCCGTACGTGGTGAAC 59.971 61.111 15.21 3.32 0.00 3.18
488 489 2.317992 ATCAGGGATCCGGCTCAGGA 62.318 60.000 7.74 1.61 45.54 3.86
498 499 1.839894 GTGGGTGGGATCAGGGATC 59.160 63.158 0.00 0.00 38.25 3.36
577 578 1.339631 CCGCCTGATTTGAACTACCCA 60.340 52.381 0.00 0.00 0.00 4.51
708 731 6.380079 AATAAGGCTGGAAAGAGAGAAAGA 57.620 37.500 0.00 0.00 0.00 2.52
711 734 7.861629 TCAATAATAAGGCTGGAAAGAGAGAA 58.138 34.615 0.00 0.00 0.00 2.87
741 764 3.602317 CTCTCTTTCTCGCGCGCG 61.602 66.667 44.84 44.84 41.35 6.86
743 766 2.220887 GCTCTCTCTTTCTCGCGCG 61.221 63.158 26.76 26.76 0.00 6.86
795 826 1.202475 GCTTAGCGAGGAGGAGAAAGG 60.202 57.143 0.00 0.00 0.00 3.11
796 827 1.478510 TGCTTAGCGAGGAGGAGAAAG 59.521 52.381 0.00 0.00 0.00 2.62
797 828 1.557099 TGCTTAGCGAGGAGGAGAAA 58.443 50.000 0.00 0.00 0.00 2.52
798 829 1.204941 GTTGCTTAGCGAGGAGGAGAA 59.795 52.381 0.00 0.00 0.00 2.87
842 873 4.910585 CGGCACTACCCCGGATGC 62.911 72.222 0.73 4.42 41.99 3.91
843 874 4.910585 GCGGCACTACCCCGGATG 62.911 72.222 0.73 0.00 45.66 3.51
859 911 2.500229 TGGTTTAACTAGTGCTGGTGC 58.500 47.619 0.00 0.00 40.20 5.01
865 917 3.146847 AGGCTGTTGGTTTAACTAGTGC 58.853 45.455 0.00 0.00 40.05 4.40
934 998 1.381928 CCCGCTTCCTCGTACTGCTA 61.382 60.000 0.00 0.00 0.00 3.49
1054 1123 2.362736 GACATGGATGAGCAGCAAGAA 58.637 47.619 0.00 0.00 0.00 2.52
1066 1135 2.138542 ACCAGCATAAGGGACATGGAT 58.861 47.619 0.00 0.00 0.00 3.41
1077 1146 2.484770 GCCGAAGACCATACCAGCATAA 60.485 50.000 0.00 0.00 0.00 1.90
1156 1225 2.920912 AACGGCGAGAAGGGGACA 60.921 61.111 16.62 0.00 0.00 4.02
1159 1228 2.125512 CTCAACGGCGAGAAGGGG 60.126 66.667 16.62 0.00 34.79 4.79
1161 1230 1.738099 CACCTCAACGGCGAGAAGG 60.738 63.158 16.62 18.36 34.79 3.46
1210 1287 9.865321 AAGAGCGTACAGTACTAATGATAAAAA 57.135 29.630 9.10 0.00 0.00 1.94
1390 1470 6.231211 TCTACTCCAGGATTCTGTTTCAAAC 58.769 40.000 0.00 0.00 39.31 2.93
1455 1538 2.737252 GCTGAAGAACCTACGTGAAAGG 59.263 50.000 0.00 0.00 40.20 3.11
1551 1634 5.605564 TGTAGGTTCATTTCATTGTCACG 57.394 39.130 0.00 0.00 0.00 4.35
1573 1656 4.142902 CGCCGTTGTTTTCTACAGATGAAT 60.143 41.667 0.00 0.00 38.19 2.57
1575 1658 2.734606 CGCCGTTGTTTTCTACAGATGA 59.265 45.455 0.00 0.00 38.19 2.92
1595 1681 1.007271 ACGGTTGAGAGTGCAGACG 60.007 57.895 0.00 0.00 0.00 4.18
1602 1688 2.688507 CTATGTTGCACGGTTGAGAGT 58.311 47.619 0.00 0.00 0.00 3.24
1696 1792 2.438583 GTACAGCGCTAGTACAAGTCG 58.561 52.381 29.15 12.18 41.08 4.18
1721 1817 5.418840 AGACTTGGAAAACAAACTGTGTCAT 59.581 36.000 0.00 0.00 40.60 3.06
1768 1864 1.865788 GAGCACAAGAAATGCCCGCA 61.866 55.000 0.00 0.00 44.53 5.69
1808 1904 4.751600 GGCAAAACGTAGTAAGGTTACTGT 59.248 41.667 11.88 0.77 45.00 3.55
1822 1921 0.179097 ACGGCATTTTGGCAAAACGT 60.179 45.000 26.23 25.46 43.94 3.99
1824 1923 3.602718 CGTTAACGGCATTTTGGCAAAAC 60.603 43.478 26.23 14.99 43.94 2.43
1869 2014 1.194218 TGATGCCGATGAAGGACTGA 58.806 50.000 0.00 0.00 0.00 3.41
2652 2797 0.175989 GGTGGGAGACGAGATTGGAC 59.824 60.000 0.00 0.00 0.00 4.02
2658 2803 2.045242 CGGAGGTGGGAGACGAGA 60.045 66.667 0.00 0.00 0.00 4.04
2757 2902 2.283676 TTCTCCGACGCCTTCCCT 60.284 61.111 0.00 0.00 0.00 4.20
2917 3062 1.211212 CAAGGGCAGAGTGATGGATGA 59.789 52.381 0.00 0.00 0.00 2.92
2971 3118 2.179517 GACGAGAGCTCCACCGTG 59.820 66.667 24.57 6.95 35.22 4.94
2997 3144 2.672996 GGCGTCACCTGCACCAAT 60.673 61.111 0.00 0.00 34.51 3.16
3081 3228 0.254178 AGATGGTGCGAGGCAATTCT 59.746 50.000 0.00 0.00 41.47 2.40
3086 3233 4.147449 CGGAGATGGTGCGAGGCA 62.147 66.667 0.00 0.00 44.08 4.75
3097 3244 2.107750 CACATGGAGCGCGGAGAT 59.892 61.111 8.83 0.00 0.00 2.75
3099 3246 2.887568 GACACATGGAGCGCGGAG 60.888 66.667 8.83 0.00 0.00 4.63
3100 3247 3.381983 AGACACATGGAGCGCGGA 61.382 61.111 8.83 0.00 0.00 5.54
3102 3249 3.857854 GCAGACACATGGAGCGCG 61.858 66.667 0.00 0.00 0.00 6.86
3116 3263 5.008415 AGAGACATGAACAAGAAACAAGCAG 59.992 40.000 0.00 0.00 0.00 4.24
3144 3291 3.906846 AGACAGAAATGGAAGGTCAGACT 59.093 43.478 0.00 0.00 0.00 3.24
3232 3379 2.352651 CGTATCTGAGTTGCACCATTGG 59.647 50.000 0.00 0.00 0.00 3.16
3237 3384 2.604914 CACATCGTATCTGAGTTGCACC 59.395 50.000 0.00 0.00 0.00 5.01
3270 3417 1.000646 GACTGAGGACGGAGGGAGT 60.001 63.158 0.00 0.00 0.00 3.85
3271 3418 1.755008 GGACTGAGGACGGAGGGAG 60.755 68.421 0.00 0.00 0.00 4.30
3272 3419 2.359404 GGACTGAGGACGGAGGGA 59.641 66.667 0.00 0.00 0.00 4.20
3273 3420 2.760385 GGGACTGAGGACGGAGGG 60.760 72.222 0.00 0.00 0.00 4.30
3274 3421 3.141488 CGGGACTGAGGACGGAGG 61.141 72.222 0.00 0.00 0.00 4.30
3275 3422 1.038130 ATTCGGGACTGAGGACGGAG 61.038 60.000 0.00 0.00 0.00 4.63
3276 3423 0.613853 AATTCGGGACTGAGGACGGA 60.614 55.000 0.00 0.00 0.00 4.69
3277 3424 1.067212 CTAATTCGGGACTGAGGACGG 59.933 57.143 0.00 0.00 0.00 4.79
3278 3425 1.749634 ACTAATTCGGGACTGAGGACG 59.250 52.381 0.00 0.00 0.00 4.79
3279 3426 3.056035 ACAACTAATTCGGGACTGAGGAC 60.056 47.826 0.00 0.00 0.00 3.85
3280 3427 3.170717 ACAACTAATTCGGGACTGAGGA 58.829 45.455 0.00 0.00 0.00 3.71
3281 3428 3.522553 GACAACTAATTCGGGACTGAGG 58.477 50.000 0.00 0.00 0.00 3.86
3282 3429 3.195825 AGGACAACTAATTCGGGACTGAG 59.804 47.826 0.00 0.00 0.00 3.35
3283 3430 3.170717 AGGACAACTAATTCGGGACTGA 58.829 45.455 0.00 0.00 0.00 3.41
3284 3431 3.611766 AGGACAACTAATTCGGGACTG 57.388 47.619 0.00 0.00 0.00 3.51
3285 3432 4.607239 TCTAGGACAACTAATTCGGGACT 58.393 43.478 0.00 0.00 0.00 3.85
3286 3433 4.996788 TCTAGGACAACTAATTCGGGAC 57.003 45.455 0.00 0.00 0.00 4.46
3287 3434 6.070424 ACAAATCTAGGACAACTAATTCGGGA 60.070 38.462 0.00 0.00 0.00 5.14
3288 3435 6.113411 ACAAATCTAGGACAACTAATTCGGG 58.887 40.000 0.00 0.00 0.00 5.14
3289 3436 7.042335 AGACAAATCTAGGACAACTAATTCGG 58.958 38.462 0.00 0.00 31.46 4.30
3314 3461 9.881649 AAACGTGTCTAGATATATCCGTATCTA 57.118 33.333 9.18 4.21 40.79 1.98
3315 3462 8.789825 AAACGTGTCTAGATATATCCGTATCT 57.210 34.615 9.18 2.43 42.50 1.98
3318 3465 9.494271 ACTAAAACGTGTCTAGATATATCCGTA 57.506 33.333 9.18 0.00 0.00 4.02
3319 3466 8.388484 ACTAAAACGTGTCTAGATATATCCGT 57.612 34.615 9.18 7.72 0.00 4.69
3320 3467 8.719648 AGACTAAAACGTGTCTAGATATATCCG 58.280 37.037 9.18 7.11 41.19 4.18
3324 3471 9.053840 CCTGAGACTAAAACGTGTCTAGATATA 57.946 37.037 6.28 0.00 42.79 0.86
3325 3472 7.556996 ACCTGAGACTAAAACGTGTCTAGATAT 59.443 37.037 6.28 0.00 42.79 1.63
3326 3473 6.883217 ACCTGAGACTAAAACGTGTCTAGATA 59.117 38.462 6.28 0.00 42.79 1.98
3327 3474 5.711036 ACCTGAGACTAAAACGTGTCTAGAT 59.289 40.000 6.28 0.00 42.79 1.98
3328 3475 5.068636 ACCTGAGACTAAAACGTGTCTAGA 58.931 41.667 6.28 0.00 42.79 2.43
3329 3476 5.373981 ACCTGAGACTAAAACGTGTCTAG 57.626 43.478 6.28 2.38 42.79 2.43
3330 3477 7.458409 AATACCTGAGACTAAAACGTGTCTA 57.542 36.000 6.28 0.00 42.79 2.59
3331 3478 5.979288 ATACCTGAGACTAAAACGTGTCT 57.021 39.130 6.01 6.01 45.06 3.41
3332 3479 7.533426 TCTAATACCTGAGACTAAAACGTGTC 58.467 38.462 0.00 0.00 0.00 3.67
3333 3480 7.458409 TCTAATACCTGAGACTAAAACGTGT 57.542 36.000 0.00 0.00 0.00 4.49
3334 3481 9.448294 GTATCTAATACCTGAGACTAAAACGTG 57.552 37.037 0.00 0.00 0.00 4.49
3335 3482 9.182214 TGTATCTAATACCTGAGACTAAAACGT 57.818 33.333 0.00 0.00 34.86 3.99
3339 3486 9.877222 TGGATGTATCTAATACCTGAGACTAAA 57.123 33.333 0.00 0.00 34.86 1.85
3342 3489 9.469097 GTATGGATGTATCTAATACCTGAGACT 57.531 37.037 0.00 0.00 34.86 3.24
3343 3490 9.469097 AGTATGGATGTATCTAATACCTGAGAC 57.531 37.037 11.31 0.00 34.86 3.36
3358 3505 9.555727 GCCTTAGATTTGTTTAGTATGGATGTA 57.444 33.333 0.00 0.00 0.00 2.29
3359 3506 8.052748 TGCCTTAGATTTGTTTAGTATGGATGT 58.947 33.333 0.00 0.00 0.00 3.06
3360 3507 8.450578 TGCCTTAGATTTGTTTAGTATGGATG 57.549 34.615 0.00 0.00 0.00 3.51
3361 3508 9.646522 ATTGCCTTAGATTTGTTTAGTATGGAT 57.353 29.630 0.00 0.00 0.00 3.41
3362 3509 9.474313 AATTGCCTTAGATTTGTTTAGTATGGA 57.526 29.630 0.00 0.00 0.00 3.41
3370 3517 9.230122 CCCAAATTAATTGCCTTAGATTTGTTT 57.770 29.630 0.39 0.00 37.73 2.83
3371 3518 8.601546 TCCCAAATTAATTGCCTTAGATTTGTT 58.398 29.630 0.39 0.00 37.73 2.83
3372 3519 8.040727 GTCCCAAATTAATTGCCTTAGATTTGT 58.959 33.333 0.39 0.00 37.73 2.83
3373 3520 7.222611 CGTCCCAAATTAATTGCCTTAGATTTG 59.777 37.037 0.39 0.00 37.73 2.32
3374 3521 7.264947 CGTCCCAAATTAATTGCCTTAGATTT 58.735 34.615 0.39 0.00 37.73 2.17
3375 3522 6.183360 CCGTCCCAAATTAATTGCCTTAGATT 60.183 38.462 0.39 0.00 37.73 2.40
3376 3523 5.301805 CCGTCCCAAATTAATTGCCTTAGAT 59.698 40.000 0.39 0.00 37.73 1.98
3377 3524 4.642885 CCGTCCCAAATTAATTGCCTTAGA 59.357 41.667 0.39 0.00 37.73 2.10
3378 3525 4.642885 TCCGTCCCAAATTAATTGCCTTAG 59.357 41.667 0.39 0.00 37.73 2.18
3379 3526 4.601084 TCCGTCCCAAATTAATTGCCTTA 58.399 39.130 0.39 0.00 37.73 2.69
3380 3527 3.436243 TCCGTCCCAAATTAATTGCCTT 58.564 40.909 0.39 0.00 37.73 4.35
3381 3528 3.023832 CTCCGTCCCAAATTAATTGCCT 58.976 45.455 0.39 0.00 37.73 4.75
3382 3529 2.100749 CCTCCGTCCCAAATTAATTGCC 59.899 50.000 0.39 0.00 37.73 4.52
3383 3530 2.758423 ACCTCCGTCCCAAATTAATTGC 59.242 45.455 0.39 0.00 37.73 3.56
3384 3531 6.709018 ATTACCTCCGTCCCAAATTAATTG 57.291 37.500 0.39 0.00 38.84 2.32
3385 3532 6.774170 GGTATTACCTCCGTCCCAAATTAATT 59.226 38.462 5.56 0.00 34.73 1.40
3386 3533 6.126420 TGGTATTACCTCCGTCCCAAATTAAT 60.126 38.462 13.90 0.00 39.58 1.40
3387 3534 5.191323 TGGTATTACCTCCGTCCCAAATTAA 59.809 40.000 13.90 0.00 39.58 1.40
3388 3535 4.720773 TGGTATTACCTCCGTCCCAAATTA 59.279 41.667 13.90 0.00 39.58 1.40
3389 3536 3.524380 TGGTATTACCTCCGTCCCAAATT 59.476 43.478 13.90 0.00 39.58 1.82
3390 3537 3.116959 TGGTATTACCTCCGTCCCAAAT 58.883 45.455 13.90 0.00 39.58 2.32
3391 3538 2.549082 TGGTATTACCTCCGTCCCAAA 58.451 47.619 13.90 0.00 39.58 3.28
3392 3539 2.250921 TGGTATTACCTCCGTCCCAA 57.749 50.000 13.90 0.00 39.58 4.12
3393 3540 2.090943 AGATGGTATTACCTCCGTCCCA 60.091 50.000 13.90 0.00 39.58 4.37
3394 3541 2.606378 AGATGGTATTACCTCCGTCCC 58.394 52.381 13.90 0.00 39.58 4.46
3395 3542 4.100498 TGAAAGATGGTATTACCTCCGTCC 59.900 45.833 13.90 1.28 39.58 4.79
3396 3543 5.068723 TCTGAAAGATGGTATTACCTCCGTC 59.931 44.000 13.90 7.09 38.67 4.79
3397 3544 4.960469 TCTGAAAGATGGTATTACCTCCGT 59.040 41.667 13.90 1.86 38.67 4.69
3398 3545 5.531122 TCTGAAAGATGGTATTACCTCCG 57.469 43.478 13.90 0.28 38.67 4.63
3399 3546 7.509546 TGATTCTGAAAGATGGTATTACCTCC 58.490 38.462 13.90 5.82 46.36 4.30
3400 3547 8.424918 TCTGATTCTGAAAGATGGTATTACCTC 58.575 37.037 13.90 8.80 46.36 3.85
3401 3548 8.324191 TCTGATTCTGAAAGATGGTATTACCT 57.676 34.615 13.90 0.00 46.36 3.08
3402 3549 9.213799 GATCTGATTCTGAAAGATGGTATTACC 57.786 37.037 8.85 5.87 46.36 2.85
3403 3550 8.920665 CGATCTGATTCTGAAAGATGGTATTAC 58.079 37.037 8.85 0.00 46.36 1.89
3404 3551 7.600375 GCGATCTGATTCTGAAAGATGGTATTA 59.400 37.037 8.85 0.00 46.36 0.98
3405 3552 6.426328 GCGATCTGATTCTGAAAGATGGTATT 59.574 38.462 8.85 0.00 46.36 1.89
3406 3553 5.931146 GCGATCTGATTCTGAAAGATGGTAT 59.069 40.000 8.85 0.00 46.36 2.73
3407 3554 5.163416 TGCGATCTGATTCTGAAAGATGGTA 60.163 40.000 8.85 5.42 46.36 3.25
3408 3555 4.125703 GCGATCTGATTCTGAAAGATGGT 58.874 43.478 8.85 0.00 46.36 3.55
3409 3556 4.124970 TGCGATCTGATTCTGAAAGATGG 58.875 43.478 8.85 8.80 46.36 3.51
3410 3557 4.211584 CCTGCGATCTGATTCTGAAAGATG 59.788 45.833 8.85 4.26 46.36 2.90
3411 3558 4.378774 CCTGCGATCTGATTCTGAAAGAT 58.621 43.478 4.65 4.65 46.36 2.40
3413 3560 2.287373 GCCTGCGATCTGATTCTGAAAG 59.713 50.000 0.00 0.00 0.00 2.62
3419 3566 1.202510 ACTGAGCCTGCGATCTGATTC 60.203 52.381 0.00 0.00 0.00 2.52
3426 3573 0.320771 AAACGAACTGAGCCTGCGAT 60.321 50.000 0.00 0.00 0.00 4.58
3428 3575 1.144969 TTAAACGAACTGAGCCTGCG 58.855 50.000 0.00 0.00 0.00 5.18
3430 3577 5.236478 TCTTTCTTTAAACGAACTGAGCCTG 59.764 40.000 0.00 0.00 0.00 4.85
3432 3579 5.668558 TCTTTCTTTAAACGAACTGAGCC 57.331 39.130 0.00 0.00 0.00 4.70
3433 3580 6.964934 TGTTTCTTTCTTTAAACGAACTGAGC 59.035 34.615 0.00 0.00 38.21 4.26
3435 3582 8.259049 TCTGTTTCTTTCTTTAAACGAACTGA 57.741 30.769 0.00 0.00 38.21 3.41
3436 3583 8.786028 GTTCTGTTTCTTTCTTTAAACGAACTG 58.214 33.333 17.80 0.00 40.65 3.16
3445 3592 5.124138 TGTTGGCGTTCTGTTTCTTTCTTTA 59.876 36.000 0.00 0.00 0.00 1.85
3446 3593 4.082463 TGTTGGCGTTCTGTTTCTTTCTTT 60.082 37.500 0.00 0.00 0.00 2.52
3447 3594 3.442273 TGTTGGCGTTCTGTTTCTTTCTT 59.558 39.130 0.00 0.00 0.00 2.52
3448 3595 3.013921 TGTTGGCGTTCTGTTTCTTTCT 58.986 40.909 0.00 0.00 0.00 2.52
3449 3596 3.414549 TGTTGGCGTTCTGTTTCTTTC 57.585 42.857 0.00 0.00 0.00 2.62
3460 3607 3.641648 CATTGTCTTTGATGTTGGCGTT 58.358 40.909 0.00 0.00 0.00 4.84
3461 3608 2.607771 GCATTGTCTTTGATGTTGGCGT 60.608 45.455 0.00 0.00 0.00 5.68
3462 3609 1.987770 GCATTGTCTTTGATGTTGGCG 59.012 47.619 0.00 0.00 0.00 5.69
3463 3610 2.991190 CTGCATTGTCTTTGATGTTGGC 59.009 45.455 0.00 0.00 0.00 4.52
3474 3621 2.680805 CGGTGTATTCCCTGCATTGTCT 60.681 50.000 0.00 0.00 0.00 3.41
3480 3627 0.249120 CTGTCGGTGTATTCCCTGCA 59.751 55.000 0.00 0.00 0.00 4.41
3482 3629 1.548719 TGACTGTCGGTGTATTCCCTG 59.451 52.381 2.98 0.00 0.00 4.45
3488 3635 2.760634 TGCAATGACTGTCGGTGTAT 57.239 45.000 2.98 0.00 0.00 2.29
3489 3636 2.760634 ATGCAATGACTGTCGGTGTA 57.239 45.000 2.98 3.77 0.00 2.90
3490 3637 2.760634 TATGCAATGACTGTCGGTGT 57.239 45.000 2.98 0.00 0.00 4.16
3491 3638 4.418013 TTTTATGCAATGACTGTCGGTG 57.582 40.909 2.98 4.87 0.00 4.94
3492 3639 4.759693 TCTTTTTATGCAATGACTGTCGGT 59.240 37.500 2.98 0.00 0.00 4.69
3494 3641 7.022979 TGATTCTTTTTATGCAATGACTGTCG 58.977 34.615 2.98 0.00 0.00 4.35
3495 3642 8.922058 ATGATTCTTTTTATGCAATGACTGTC 57.078 30.769 0.00 0.00 0.00 3.51
3496 3643 9.793252 GTATGATTCTTTTTATGCAATGACTGT 57.207 29.630 0.00 0.00 0.00 3.55
3497 3644 9.791820 TGTATGATTCTTTTTATGCAATGACTG 57.208 29.630 0.00 0.00 0.00 3.51
3504 3655 9.844790 CAACTTCTGTATGATTCTTTTTATGCA 57.155 29.630 0.00 0.00 0.00 3.96
3505 3656 9.846248 ACAACTTCTGTATGATTCTTTTTATGC 57.154 29.630 0.00 0.00 36.10 3.14
3521 3672 3.064820 CGCCAACAAACTACAACTTCTGT 59.935 43.478 0.00 0.00 42.47 3.41
3522 3673 3.064820 ACGCCAACAAACTACAACTTCTG 59.935 43.478 0.00 0.00 0.00 3.02
3523 3674 3.275999 ACGCCAACAAACTACAACTTCT 58.724 40.909 0.00 0.00 0.00 2.85
3524 3675 3.685836 ACGCCAACAAACTACAACTTC 57.314 42.857 0.00 0.00 0.00 3.01
3525 3676 3.940221 TGTACGCCAACAAACTACAACTT 59.060 39.130 0.00 0.00 0.00 2.66
3526 3677 3.533547 TGTACGCCAACAAACTACAACT 58.466 40.909 0.00 0.00 0.00 3.16
3527 3678 3.948196 TGTACGCCAACAAACTACAAC 57.052 42.857 0.00 0.00 0.00 3.32
3565 3734 2.890311 TGTATGTTTTCCTTGCACCTGG 59.110 45.455 0.00 0.00 0.00 4.45
3568 3737 2.352715 GCCTGTATGTTTTCCTTGCACC 60.353 50.000 0.00 0.00 0.00 5.01
3596 3765 3.367292 CCATTCATTTGCCCAGTGTGTAC 60.367 47.826 0.00 0.00 0.00 2.90
3607 3776 4.309099 TGTTTCTCTTGCCATTCATTTGC 58.691 39.130 0.00 0.00 0.00 3.68
3685 3902 2.881513 TGTTTGTTCGATGCTGCCTTTA 59.118 40.909 0.00 0.00 0.00 1.85
3858 4083 2.973694 TAAGCTACAGGCCTAAACCG 57.026 50.000 3.98 0.00 43.05 4.44
3927 4152 6.336842 AGATGCACTCTTTATTTTTGCACT 57.663 33.333 0.00 0.00 45.45 4.40
3943 4168 1.090052 GGCGACTGGGTAAGATGCAC 61.090 60.000 0.00 0.00 33.19 4.57
3944 4169 1.220749 GGCGACTGGGTAAGATGCA 59.779 57.895 0.00 0.00 33.19 3.96


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

AutoCloner maintained by Alex Coulton.