Multiple sequence alignment - TraesCS5D01G025200

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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 TraesCS5D01G025200 chr5D 100.000 4363 0 0 1 4363 22436782 22432420 0.000000e+00 8058.0
1 TraesCS5D01G025200 chr5D 88.830 1316 114 15 1694 2998 22401355 22400062 0.000000e+00 1585.0
2 TraesCS5D01G025200 chr5D 80.000 1040 95 49 680 1654 22402419 22401428 0.000000e+00 664.0
3 TraesCS5D01G025200 chr5D 89.884 346 29 2 3071 3415 22400046 22399706 1.440000e-119 440.0
4 TraesCS5D01G025200 chr5D 79.476 458 66 13 3496 3943 22399647 22399208 2.550000e-77 300.0
5 TraesCS5D01G025200 chr5D 84.774 243 23 8 423 659 22403030 22402796 9.440000e-57 231.0
6 TraesCS5D01G025200 chr5B 93.361 2696 103 28 808 3456 16004397 16001731 0.000000e+00 3917.0
7 TraesCS5D01G025200 chr5B 88.619 1318 117 13 1702 3007 15560091 15558795 0.000000e+00 1572.0
8 TraesCS5D01G025200 chr5B 96.456 395 9 1 3969 4363 16001261 16000872 0.000000e+00 647.0
9 TraesCS5D01G025200 chr5B 90.065 463 29 7 3458 3918 16001701 16001254 6.290000e-163 584.0
10 TraesCS5D01G025200 chr5B 80.732 820 73 29 882 1654 15561091 15560310 1.060000e-155 560.0
11 TraesCS5D01G025200 chr5B 81.170 701 60 30 1 666 16005165 16004502 8.430000e-137 497.0
12 TraesCS5D01G025200 chr5B 89.337 347 30 3 3071 3415 15558796 15558455 3.120000e-116 429.0
13 TraesCS5D01G025200 chr5B 82.781 302 17 14 254 533 15935016 15934728 2.030000e-58 237.0
14 TraesCS5D01G025200 chr5B 82.166 314 20 16 242 533 15998867 15998568 2.030000e-58 237.0
15 TraesCS5D01G025200 chr5B 81.962 316 21 12 241 533 15919330 15919028 7.290000e-58 235.0
16 TraesCS5D01G025200 chr5B 82.178 303 19 15 253 533 15988044 15987755 1.220000e-55 228.0
17 TraesCS5D01G025200 chr5B 83.471 242 22 8 436 666 15562051 15561817 4.420000e-50 209.0
18 TraesCS5D01G025200 chr5B 82.716 243 33 6 3475 3710 15558426 15558186 1.590000e-49 207.0
19 TraesCS5D01G025200 chr5B 92.500 40 1 1 1 38 15903671 15903632 6.100000e-04 56.5
20 TraesCS5D01G025200 chr5A 88.906 1325 114 15 1694 3007 15866766 15865464 0.000000e+00 1602.0
21 TraesCS5D01G025200 chr5A 78.412 1033 118 52 683 1654 15867827 15866839 3.780000e-160 575.0
22 TraesCS5D01G025200 chr5A 88.728 346 35 3 3071 3415 15865465 15865123 1.880000e-113 420.0
23 TraesCS5D01G025200 chr5A 79.050 463 70 20 3496 3943 15865064 15864614 4.270000e-75 292.0
24 TraesCS5D01G025200 chr5A 83.399 253 25 10 423 666 15868436 15868192 7.350000e-53 219.0
25 TraesCS5D01G025200 chr2B 91.677 793 37 8 1138 1915 178773945 178773167 0.000000e+00 1072.0


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 TraesCS5D01G025200 chr5D 22432420 22436782 4362 True 8058.0 8058 100.0000 1 4363 1 chr5D.!!$R1 4362
1 TraesCS5D01G025200 chr5D 22399208 22403030 3822 True 644.0 1585 84.5928 423 3943 5 chr5D.!!$R2 3520
2 TraesCS5D01G025200 chr5B 15998568 16005165 6597 True 1176.4 3917 88.6436 1 4363 5 chr5B.!!$R6 4362
3 TraesCS5D01G025200 chr5B 15558186 15562051 3865 True 595.4 1572 84.9750 436 3710 5 chr5B.!!$R5 3274
4 TraesCS5D01G025200 chr5A 15864614 15868436 3822 True 621.6 1602 83.6990 423 3943 5 chr5A.!!$R1 3520
5 TraesCS5D01G025200 chr2B 178773167 178773945 778 True 1072.0 1072 91.6770 1138 1915 1 chr2B.!!$R1 777

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
557 606 0.037790 GGCTGGTCATCGCTATCCTC 60.038 60.0 0.0 0.0 0.00 3.71 F
960 1558 0.322322 TCGGTTGGTTGGCGTTATCT 59.678 50.0 0.0 0.0 0.00 1.98 F
2408 3245 0.395312 ACTGGTTTCCGGTGTCGAAT 59.605 50.0 0.0 0.0 42.23 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 2314 0.393132 TTGTTGGCACGGACTGAACA 60.393 50.000 0.00 0.0 0.00 3.18 R
2681 3519 2.665185 GCGGACTCTGCACGGTTT 60.665 61.111 4.87 0.0 0.00 3.27 R
3912 4831 0.389296 CCCATGCAATGCACACACAG 60.389 55.000 11.23 0.0 44.97 3.66 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
43 44 3.712881 GACTGCCACAACGCGACC 61.713 66.667 15.93 0.00 0.00 4.79
87 94 1.424493 CGAATCTCTCGGTTGCTGCC 61.424 60.000 0.00 0.00 44.20 4.85
88 95 0.107945 GAATCTCTCGGTTGCTGCCT 60.108 55.000 0.00 0.00 0.00 4.75
89 96 0.392193 AATCTCTCGGTTGCTGCCTG 60.392 55.000 0.00 0.00 0.00 4.85
90 97 1.260538 ATCTCTCGGTTGCTGCCTGA 61.261 55.000 0.00 0.00 0.00 3.86
91 98 1.739562 CTCTCGGTTGCTGCCTGAC 60.740 63.158 0.00 0.00 0.00 3.51
92 99 2.743928 CTCGGTTGCTGCCTGACC 60.744 66.667 0.00 1.97 0.00 4.02
155 179 4.736165 GCAACCCTGCTGTTGTTG 57.264 55.556 14.80 14.80 45.80 3.33
161 185 1.007734 CCTGCTGTTGTTGCTGCTG 60.008 57.895 0.00 0.00 34.93 4.41
186 210 1.531259 TGCCAGTGCAAGGTCTTGA 59.469 52.632 14.20 0.00 46.66 3.02
187 211 0.535780 TGCCAGTGCAAGGTCTTGAG 60.536 55.000 14.20 1.57 46.66 3.02
188 212 0.250467 GCCAGTGCAAGGTCTTGAGA 60.250 55.000 14.20 0.00 42.93 3.27
189 213 1.815408 GCCAGTGCAAGGTCTTGAGAA 60.815 52.381 14.20 0.00 42.93 2.87
190 214 2.575532 CCAGTGCAAGGTCTTGAGAAA 58.424 47.619 14.20 0.00 42.93 2.52
191 215 2.291741 CCAGTGCAAGGTCTTGAGAAAC 59.708 50.000 14.20 6.55 42.93 2.78
192 216 3.209410 CAGTGCAAGGTCTTGAGAAACT 58.791 45.455 14.20 8.37 42.93 2.66
193 217 3.003068 CAGTGCAAGGTCTTGAGAAACTG 59.997 47.826 14.20 14.76 42.93 3.16
194 218 2.291741 GTGCAAGGTCTTGAGAAACTGG 59.708 50.000 14.20 0.00 42.93 4.00
195 219 2.172505 TGCAAGGTCTTGAGAAACTGGA 59.827 45.455 14.20 0.00 42.93 3.86
196 220 2.810852 GCAAGGTCTTGAGAAACTGGAG 59.189 50.000 14.20 0.00 42.93 3.86
197 221 2.810852 CAAGGTCTTGAGAAACTGGAGC 59.189 50.000 4.82 0.00 42.93 4.70
198 222 1.349357 AGGTCTTGAGAAACTGGAGCC 59.651 52.381 0.00 0.00 0.00 4.70
268 295 2.373224 CCCCCTTTTGAGATCTTGAGC 58.627 52.381 0.00 0.00 0.00 4.26
269 296 2.025510 CCCCCTTTTGAGATCTTGAGCT 60.026 50.000 0.00 0.00 0.00 4.09
270 297 3.563043 CCCCCTTTTGAGATCTTGAGCTT 60.563 47.826 0.00 0.00 0.00 3.74
271 298 3.693578 CCCCTTTTGAGATCTTGAGCTTC 59.306 47.826 0.00 0.00 0.00 3.86
272 299 4.330250 CCCTTTTGAGATCTTGAGCTTCA 58.670 43.478 0.00 0.00 0.00 3.02
273 300 4.948621 CCCTTTTGAGATCTTGAGCTTCAT 59.051 41.667 0.00 0.00 0.00 2.57
274 301 5.066246 CCCTTTTGAGATCTTGAGCTTCATC 59.934 44.000 0.00 0.00 0.00 2.92
276 303 5.432680 TTTGAGATCTTGAGCTTCATCCT 57.567 39.130 0.00 0.00 0.00 3.24
277 304 4.669206 TGAGATCTTGAGCTTCATCCTC 57.331 45.455 0.00 0.00 0.00 3.71
278 305 4.028825 TGAGATCTTGAGCTTCATCCTCA 58.971 43.478 0.00 0.00 37.54 3.86
279 306 4.468868 TGAGATCTTGAGCTTCATCCTCAA 59.531 41.667 0.00 4.08 44.54 3.02
280 307 5.130643 TGAGATCTTGAGCTTCATCCTCAAT 59.869 40.000 0.00 0.00 45.30 2.57
281 308 5.613329 AGATCTTGAGCTTCATCCTCAATC 58.387 41.667 4.52 1.63 45.30 2.67
282 309 4.148128 TCTTGAGCTTCATCCTCAATCC 57.852 45.455 4.52 0.00 45.30 3.01
283 310 2.609427 TGAGCTTCATCCTCAATCCG 57.391 50.000 0.00 0.00 36.46 4.18
284 311 1.139654 TGAGCTTCATCCTCAATCCGG 59.860 52.381 0.00 0.00 36.46 5.14
285 312 0.179034 AGCTTCATCCTCAATCCGGC 60.179 55.000 0.00 0.00 0.00 6.13
286 313 1.502163 GCTTCATCCTCAATCCGGCG 61.502 60.000 0.00 0.00 0.00 6.46
287 314 0.882042 CTTCATCCTCAATCCGGCGG 60.882 60.000 22.51 22.51 0.00 6.13
288 315 1.334384 TTCATCCTCAATCCGGCGGA 61.334 55.000 33.10 33.10 35.55 5.54
289 316 1.146041 CATCCTCAATCCGGCGGAA 59.854 57.895 34.58 16.22 34.34 4.30
290 317 1.146263 ATCCTCAATCCGGCGGAAC 59.854 57.895 34.58 0.00 34.34 3.62
291 318 1.338136 ATCCTCAATCCGGCGGAACT 61.338 55.000 34.58 20.44 34.34 3.01
292 319 1.815421 CCTCAATCCGGCGGAACTG 60.815 63.158 34.58 29.89 34.34 3.16
293 320 1.079127 CTCAATCCGGCGGAACTGT 60.079 57.895 34.58 14.21 34.34 3.55
294 321 0.174845 CTCAATCCGGCGGAACTGTA 59.825 55.000 34.58 19.22 34.34 2.74
295 322 0.828022 TCAATCCGGCGGAACTGTAT 59.172 50.000 34.58 12.88 34.34 2.29
296 323 1.202486 TCAATCCGGCGGAACTGTATC 60.202 52.381 34.58 0.00 34.34 2.24
297 324 1.120530 AATCCGGCGGAACTGTATCT 58.879 50.000 34.58 11.13 34.34 1.98
298 325 1.120530 ATCCGGCGGAACTGTATCTT 58.879 50.000 34.58 10.27 34.34 2.40
299 326 0.458669 TCCGGCGGAACTGTATCTTC 59.541 55.000 29.11 0.00 0.00 2.87
300 327 0.174845 CCGGCGGAACTGTATCTTCA 59.825 55.000 24.41 0.00 0.00 3.02
301 328 1.404986 CCGGCGGAACTGTATCTTCAA 60.405 52.381 24.41 0.00 0.00 2.69
302 329 2.550978 CGGCGGAACTGTATCTTCAAT 58.449 47.619 0.00 0.00 0.00 2.57
303 330 2.936498 CGGCGGAACTGTATCTTCAATT 59.064 45.455 0.00 0.00 0.00 2.32
304 331 4.116961 CGGCGGAACTGTATCTTCAATTA 58.883 43.478 0.00 0.00 0.00 1.40
323 350 7.251281 TCAATTATTCATACGAGATAGGCGAG 58.749 38.462 0.00 0.00 0.00 5.03
326 353 5.804692 ATTCATACGAGATAGGCGAGTAG 57.195 43.478 0.00 0.00 0.00 2.57
327 354 4.268797 TCATACGAGATAGGCGAGTAGT 57.731 45.455 0.00 0.00 0.00 2.73
329 356 5.167121 TCATACGAGATAGGCGAGTAGTAC 58.833 45.833 0.00 0.00 0.00 2.73
331 358 3.391965 ACGAGATAGGCGAGTAGTACTG 58.608 50.000 7.76 1.62 0.00 2.74
332 359 3.181467 ACGAGATAGGCGAGTAGTACTGT 60.181 47.826 7.76 0.00 0.00 3.55
333 360 4.038522 ACGAGATAGGCGAGTAGTACTGTA 59.961 45.833 7.76 0.00 0.00 2.74
334 361 4.622313 CGAGATAGGCGAGTAGTACTGTAG 59.378 50.000 7.76 0.20 0.00 2.74
335 362 5.564455 CGAGATAGGCGAGTAGTACTGTAGA 60.564 48.000 7.76 0.00 0.00 2.59
336 363 6.172136 AGATAGGCGAGTAGTACTGTAGAA 57.828 41.667 7.76 0.00 0.00 2.10
337 364 6.771573 AGATAGGCGAGTAGTACTGTAGAAT 58.228 40.000 7.76 0.00 0.00 2.40
339 366 7.720515 AGATAGGCGAGTAGTACTGTAGAATTT 59.279 37.037 7.76 0.00 0.00 1.82
399 443 5.202765 AGATACATCCATGGTGAAATTGCA 58.797 37.500 12.58 0.00 0.00 4.08
405 449 4.148079 TCCATGGTGAAATTGCACTTGTA 58.852 39.130 16.28 0.00 38.78 2.41
415 459 6.922957 TGAAATTGCACTTGTATTCAACTTCC 59.077 34.615 0.00 0.00 0.00 3.46
421 465 4.274950 CACTTGTATTCAACTTCCACGGTT 59.725 41.667 0.00 0.00 0.00 4.44
504 552 6.365247 TCGTTTTCACATCTTTAGCTAGTGAC 59.635 38.462 11.19 2.59 38.77 3.67
506 554 5.738619 TTCACATCTTTAGCTAGTGACCA 57.261 39.130 11.19 0.00 38.77 4.02
507 555 5.073311 TCACATCTTTAGCTAGTGACCAC 57.927 43.478 8.30 0.00 34.59 4.16
508 556 4.526650 TCACATCTTTAGCTAGTGACCACA 59.473 41.667 8.30 0.00 34.59 4.17
510 558 5.521735 CACATCTTTAGCTAGTGACCACATC 59.478 44.000 4.48 0.00 32.14 3.06
544 593 1.336755 GTGAACAAAATCGTGGCTGGT 59.663 47.619 0.00 0.00 0.00 4.00
557 606 0.037790 GGCTGGTCATCGCTATCCTC 60.038 60.000 0.00 0.00 0.00 3.71
586 635 4.907875 AGGATGGTAGGTAGTGCACATATT 59.092 41.667 21.04 0.00 0.00 1.28
611 666 3.312146 GCCACCAAAAGAACAAAATGTGG 59.688 43.478 0.00 0.00 43.73 4.17
660 727 5.766150 AGTTTGTTGCTGCTACACAATTA 57.234 34.783 16.15 0.00 0.00 1.40
666 733 8.741101 TTGTTGCTGCTACACAATTAATTAAG 57.259 30.769 16.15 0.00 0.00 1.85
693 1126 9.677567 GACTAATTAATGTTGCTTTCTTTGTGA 57.322 29.630 0.00 0.00 0.00 3.58
702 1135 6.423042 GTTGCTTTCTTTGTGAGAGAGTAAC 58.577 40.000 10.19 10.19 46.70 2.50
704 1137 5.163301 TGCTTTCTTTGTGAGAGAGTAACCT 60.163 40.000 0.00 0.00 38.53 3.50
706 1139 4.258702 TCTTTGTGAGAGAGTAACCTGC 57.741 45.455 0.00 0.00 0.00 4.85
733 1166 4.454728 TCTTTGGCATGCCATTCTTTAC 57.545 40.909 38.78 9.10 46.64 2.01
735 1168 4.282957 TCTTTGGCATGCCATTCTTTACAA 59.717 37.500 38.78 25.05 46.64 2.41
736 1169 3.872511 TGGCATGCCATTCTTTACAAG 57.127 42.857 35.59 0.00 41.89 3.16
737 1170 3.164268 TGGCATGCCATTCTTTACAAGT 58.836 40.909 35.59 0.00 41.89 3.16
793 1226 2.311701 CCAAACGCGCACGGTCTTA 61.312 57.895 5.73 0.00 39.25 2.10
800 1233 1.484356 GCGCACGGTCTTATTCGTAT 58.516 50.000 0.30 0.00 37.88 3.06
801 1234 2.653890 GCGCACGGTCTTATTCGTATA 58.346 47.619 0.30 0.00 37.88 1.47
803 1236 3.851105 GCGCACGGTCTTATTCGTATACT 60.851 47.826 0.30 0.00 37.88 2.12
804 1237 4.611355 GCGCACGGTCTTATTCGTATACTA 60.611 45.833 0.30 0.00 37.88 1.82
805 1238 5.443261 CGCACGGTCTTATTCGTATACTAA 58.557 41.667 0.56 0.00 37.88 2.24
806 1239 5.909054 CGCACGGTCTTATTCGTATACTAAA 59.091 40.000 0.56 0.00 37.88 1.85
807 1240 6.580041 CGCACGGTCTTATTCGTATACTAAAT 59.420 38.462 0.56 3.81 37.88 1.40
808 1241 7.746034 CGCACGGTCTTATTCGTATACTAAATA 59.254 37.037 0.56 2.90 37.88 1.40
908 1503 5.540337 CCCAACAACTCCAGCTCTATATCTA 59.460 44.000 0.00 0.00 0.00 1.98
960 1558 0.322322 TCGGTTGGTTGGCGTTATCT 59.678 50.000 0.00 0.00 0.00 1.98
961 1559 0.446222 CGGTTGGTTGGCGTTATCTG 59.554 55.000 0.00 0.00 0.00 2.90
992 1592 7.558444 TGTTCCTCTTCTCCTCTTTCTCTATAC 59.442 40.741 0.00 0.00 0.00 1.47
1082 1703 3.012518 CCAGTGTAAGATTCCAGCAAGG 58.987 50.000 0.00 0.00 39.47 3.61
1098 1719 2.606725 GCAAGGACTGTGATCAGATTCG 59.393 50.000 0.00 0.00 43.76 3.34
1158 1795 1.134367 TCTGAATTCAGGTAGGCGACG 59.866 52.381 30.33 6.64 43.91 5.12
1358 2009 9.219603 CTGTGTCATAGAAGGAATAAGAACAAA 57.780 33.333 0.00 0.00 0.00 2.83
1428 2079 4.591321 AATTCTTGGTTGGCCAGATCTA 57.409 40.909 5.11 0.00 46.91 1.98
1519 2172 2.198827 TCAGTCCATGCCGACAAAAT 57.801 45.000 5.12 0.00 35.07 1.82
1638 2297 3.279917 TGGCAGGGCGTTATGGCATAT 62.280 52.381 8.24 0.00 45.82 1.78
1649 2308 5.278957 GCGTTATGGCATATTTTTCTCCCAT 60.279 40.000 8.24 0.00 36.98 4.00
1655 2314 8.731591 ATGGCATATTTTTCTCCCATAATCTT 57.268 30.769 0.00 0.00 31.70 2.40
1658 2317 8.424133 GGCATATTTTTCTCCCATAATCTTGTT 58.576 33.333 0.00 0.00 0.00 2.83
1659 2318 9.468532 GCATATTTTTCTCCCATAATCTTGTTC 57.531 33.333 0.00 0.00 0.00 3.18
1663 2322 7.687941 TTTTCTCCCATAATCTTGTTCAGTC 57.312 36.000 0.00 0.00 0.00 3.51
1664 2323 5.359194 TCTCCCATAATCTTGTTCAGTCC 57.641 43.478 0.00 0.00 0.00 3.85
1665 2324 4.122776 CTCCCATAATCTTGTTCAGTCCG 58.877 47.826 0.00 0.00 0.00 4.79
1968 2798 5.749109 GGATACAGTCACCGATCAGTTAAAG 59.251 44.000 0.00 0.00 0.00 1.85
2001 2831 7.066887 TCTGTGTCATCTGATAAGACTCTTCTC 59.933 40.741 8.89 0.00 33.56 2.87
2016 2846 6.719370 AGACTCTTCTCTTGTTCTACATGTCT 59.281 38.462 0.00 0.00 0.00 3.41
2042 2872 7.943413 ATCTTATGAACATCACTTCTCATCG 57.057 36.000 0.00 0.00 31.20 3.84
2107 2937 5.789521 TCGACACATATGACTTCAAAGGAA 58.210 37.500 10.38 0.00 0.00 3.36
2214 3047 7.377398 CCTCATATCCACATAGAGTTTCAGAG 58.623 42.308 0.00 0.00 0.00 3.35
2309 3146 5.718130 TCTTTCTGCCAATCCATCTGAAATT 59.282 36.000 0.00 0.00 30.91 1.82
2408 3245 0.395312 ACTGGTTTCCGGTGTCGAAT 59.605 50.000 0.00 0.00 42.23 3.34
2418 3255 1.330521 CGGTGTCGAATATGCCAAAGG 59.669 52.381 0.00 0.00 39.00 3.11
2546 3383 5.186409 CCAGTGGAATTTCATGGTTGAGAAT 59.814 40.000 1.68 0.00 32.27 2.40
2681 3519 0.612453 TGGATGCTGGCAAATGCTCA 60.612 50.000 5.25 1.31 41.70 4.26
2879 3717 7.549488 GCAGTTGATTACTACAAGGTACTGAAT 59.451 37.037 0.00 0.00 34.52 2.57
2884 3722 9.470399 TGATTACTACAAGGTACTGAATACAGA 57.530 33.333 0.00 0.00 46.03 3.41
2890 3728 9.653287 CTACAAGGTACTGAATACAGAAATCAA 57.347 33.333 0.00 0.00 46.03 2.57
3018 3868 4.938080 ACCTATTAACTCTCGATGCAGTG 58.062 43.478 0.00 0.00 0.00 3.66
3102 3952 9.029243 TGTTACACAAAATCATTGATGTTTGTC 57.971 29.630 22.77 16.89 0.00 3.18
3251 4102 7.864882 GCAAGATATAATTTCTTCCTCCTTTGC 59.135 37.037 0.00 0.00 31.11 3.68
3271 4122 2.871022 GCTGTGCATCTATGTCTCTTGG 59.129 50.000 0.00 0.00 0.00 3.61
3282 4133 8.824781 CATCTATGTCTCTTGGTATCTTTGTTG 58.175 37.037 0.00 0.00 0.00 3.33
3294 4145 6.375174 TGGTATCTTTGTTGTCTGAATCATGG 59.625 38.462 0.00 0.00 0.00 3.66
3344 4200 3.385577 CCTTTTGTAGCGAGGATCTAGC 58.614 50.000 0.00 0.00 32.11 3.42
3357 4213 5.421277 GAGGATCTAGCGTAGTATGCTCTA 58.579 45.833 20.11 10.16 40.15 2.43
3367 4223 4.519350 CGTAGTATGCTCTACCTGAATCCA 59.481 45.833 0.00 0.00 37.56 3.41
3430 4293 6.901300 ACAAGGTATGACAGGATAGGACTTTA 59.099 38.462 0.00 0.00 0.00 1.85
3449 4312 7.254421 GGACTTTAACTTTCTGGCAAACAAATG 60.254 37.037 0.00 0.00 0.00 2.32
3456 4319 7.327214 ACTTTCTGGCAAACAAATGAAAAGTA 58.673 30.769 0.00 0.00 0.00 2.24
3480 4372 2.309162 AGGGGAGCTTCTTAGGGTTTTC 59.691 50.000 0.00 0.00 0.00 2.29
3490 4382 1.448185 TAGGGTTTTCCGGGTCCTTT 58.552 50.000 0.00 0.00 41.82 3.11
3491 4383 0.559205 AGGGTTTTCCGGGTCCTTTT 59.441 50.000 0.00 0.00 41.82 2.27
3617 4515 6.668133 TTCTTTCTGGGTAGGGGAAATATT 57.332 37.500 0.00 0.00 0.00 1.28
3644 4542 7.168905 ACTTAGGATTCAGATTTTCCGAAACT 58.831 34.615 0.00 0.00 34.61 2.66
3668 4567 7.169158 TGAAAGTTGAAAATGACTGGTTTCT 57.831 32.000 0.00 0.00 35.26 2.52
3707 4606 6.017605 GGTGAAGATGTTGGATAGTGCATTAG 60.018 42.308 0.00 0.00 0.00 1.73
3710 4609 7.828717 TGAAGATGTTGGATAGTGCATTAGAAA 59.171 33.333 0.00 0.00 0.00 2.52
3782 4688 2.435437 GCCTGGTGGAATATTTGGCATT 59.565 45.455 0.00 0.00 38.79 3.56
3783 4689 3.640967 GCCTGGTGGAATATTTGGCATTA 59.359 43.478 0.00 0.00 38.79 1.90
3784 4690 4.284234 GCCTGGTGGAATATTTGGCATTAT 59.716 41.667 0.00 0.00 38.79 1.28
3785 4691 5.786311 CCTGGTGGAATATTTGGCATTATG 58.214 41.667 0.00 0.00 34.57 1.90
3787 4693 5.215069 TGGTGGAATATTTGGCATTATGGT 58.785 37.500 0.00 0.00 0.00 3.55
3788 4694 5.664908 TGGTGGAATATTTGGCATTATGGTT 59.335 36.000 0.00 0.00 0.00 3.67
3789 4695 6.841229 TGGTGGAATATTTGGCATTATGGTTA 59.159 34.615 0.00 0.00 0.00 2.85
3790 4696 7.512058 TGGTGGAATATTTGGCATTATGGTTAT 59.488 33.333 0.00 0.00 0.00 1.89
3791 4697 8.374743 GGTGGAATATTTGGCATTATGGTTATT 58.625 33.333 0.00 0.00 0.00 1.40
3792 4698 9.777297 GTGGAATATTTGGCATTATGGTTATTT 57.223 29.630 0.00 0.00 0.00 1.40
3793 4699 9.995003 TGGAATATTTGGCATTATGGTTATTTC 57.005 29.630 0.00 0.00 0.00 2.17
3802 4708 9.194972 TGGCATTATGGTTATTTCTTTCATACA 57.805 29.630 0.00 0.00 0.00 2.29
3912 4831 4.670896 ATTTGCCCACATTATTGGCTAC 57.329 40.909 0.00 0.00 45.56 3.58
3915 4834 2.025416 TGCCCACATTATTGGCTACTGT 60.025 45.455 0.00 0.00 45.56 3.55
3916 4835 2.358898 GCCCACATTATTGGCTACTGTG 59.641 50.000 0.00 0.00 42.01 3.66
3938 4857 1.866483 TGCATTGCATGGGAGGGACT 61.866 55.000 7.38 0.00 35.09 3.85
3959 4878 2.669364 GCAAATGGCAGAGAAACACTG 58.331 47.619 0.00 0.00 43.97 3.66
3960 4879 2.608752 GCAAATGGCAGAGAAACACTGG 60.609 50.000 0.00 0.00 43.97 4.00
3961 4880 2.624838 CAAATGGCAGAGAAACACTGGT 59.375 45.455 0.00 0.00 36.09 4.00
3962 4881 2.664402 ATGGCAGAGAAACACTGGTT 57.336 45.000 0.00 0.00 39.43 3.67
3963 4882 1.967319 TGGCAGAGAAACACTGGTTC 58.033 50.000 0.00 0.00 35.82 3.62
3964 4883 1.490490 TGGCAGAGAAACACTGGTTCT 59.510 47.619 9.20 9.20 35.82 3.01
3965 4884 2.092429 TGGCAGAGAAACACTGGTTCTT 60.092 45.455 10.75 0.00 35.82 2.52
3966 4885 2.952310 GGCAGAGAAACACTGGTTCTTT 59.048 45.455 10.75 2.37 35.82 2.52
3967 4886 3.243201 GGCAGAGAAACACTGGTTCTTTG 60.243 47.826 18.80 18.80 35.82 2.77
4025 4944 6.479095 AAATTTGGTGAATTACGGCAAATG 57.521 33.333 0.00 0.00 36.96 2.32
4116 5035 7.284034 CCTTGCATATTCCATGACTTCTTAACT 59.716 37.037 0.00 0.00 0.00 2.24
4117 5036 9.330063 CTTGCATATTCCATGACTTCTTAACTA 57.670 33.333 0.00 0.00 0.00 2.24
4118 5037 8.662781 TGCATATTCCATGACTTCTTAACTAC 57.337 34.615 0.00 0.00 0.00 2.73
4119 5038 8.486210 TGCATATTCCATGACTTCTTAACTACT 58.514 33.333 0.00 0.00 0.00 2.57
4120 5039 9.982651 GCATATTCCATGACTTCTTAACTACTA 57.017 33.333 0.00 0.00 0.00 1.82
4158 5077 4.607239 TGGGTCTATCTTACTTTCGAGGT 58.393 43.478 0.00 0.00 0.00 3.85
4208 5127 8.581057 ACTCATAATAAACTGCTACAGAATCG 57.419 34.615 0.78 0.00 35.18 3.34
4214 5133 2.544685 ACTGCTACAGAATCGCATGAC 58.455 47.619 0.00 0.00 35.18 3.06
4272 5191 3.023832 ACATAATAACACAGGGCCAAGC 58.976 45.455 6.18 0.00 0.00 4.01
4309 5228 9.864034 GTAACTTGATTCAATATTGATGTACCG 57.136 33.333 18.61 8.75 37.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.719369 GCTCTCCGGTCGCGTTGT 62.719 66.667 5.77 0.00 0.00 3.32
101 108 2.793317 AAATGGGCCAGTCCAGCAGG 62.793 60.000 13.78 0.00 40.56 4.85
176 200 2.810852 GCTCCAGTTTCTCAAGACCTTG 59.189 50.000 3.47 3.47 41.71 3.61
177 201 2.224646 GGCTCCAGTTTCTCAAGACCTT 60.225 50.000 0.00 0.00 0.00 3.50
180 204 2.421619 CAGGCTCCAGTTTCTCAAGAC 58.578 52.381 0.00 0.00 0.00 3.01
182 206 1.163554 GCAGGCTCCAGTTTCTCAAG 58.836 55.000 0.00 0.00 0.00 3.02
183 207 0.473755 TGCAGGCTCCAGTTTCTCAA 59.526 50.000 0.00 0.00 0.00 3.02
184 208 0.694771 ATGCAGGCTCCAGTTTCTCA 59.305 50.000 0.00 0.00 0.00 3.27
186 210 0.990374 AGATGCAGGCTCCAGTTTCT 59.010 50.000 0.00 0.00 0.00 2.52
187 211 1.339438 TGAGATGCAGGCTCCAGTTTC 60.339 52.381 14.63 0.00 0.00 2.78
188 212 0.694771 TGAGATGCAGGCTCCAGTTT 59.305 50.000 14.63 0.00 0.00 2.66
189 213 0.252479 CTGAGATGCAGGCTCCAGTT 59.748 55.000 14.63 0.00 41.07 3.16
190 214 1.906253 CTGAGATGCAGGCTCCAGT 59.094 57.895 14.63 0.00 41.07 4.00
191 215 1.524165 GCTGAGATGCAGGCTCCAG 60.524 63.158 14.63 12.66 45.03 3.86
192 216 0.688749 TAGCTGAGATGCAGGCTCCA 60.689 55.000 14.63 0.00 45.03 3.86
193 217 0.249826 GTAGCTGAGATGCAGGCTCC 60.250 60.000 14.63 3.17 45.03 4.70
194 218 0.463204 TGTAGCTGAGATGCAGGCTC 59.537 55.000 11.37 11.37 45.03 4.70
195 219 0.464870 CTGTAGCTGAGATGCAGGCT 59.535 55.000 7.96 0.00 45.03 4.58
196 220 0.532417 CCTGTAGCTGAGATGCAGGC 60.532 60.000 21.21 0.00 42.47 4.85
197 221 3.682766 CCTGTAGCTGAGATGCAGG 57.317 57.895 19.83 19.83 45.03 4.85
249 273 3.362870 AGCTCAAGATCTCAAAAGGGG 57.637 47.619 0.00 0.00 0.00 4.79
250 274 4.330250 TGAAGCTCAAGATCTCAAAAGGG 58.670 43.478 0.00 0.00 0.00 3.95
251 275 5.066246 GGATGAAGCTCAAGATCTCAAAAGG 59.934 44.000 0.00 0.00 0.00 3.11
252 276 5.881443 AGGATGAAGCTCAAGATCTCAAAAG 59.119 40.000 0.00 0.00 0.00 2.27
265 292 1.876322 CCGGATTGAGGATGAAGCTC 58.124 55.000 0.00 0.00 0.00 4.09
266 293 0.179034 GCCGGATTGAGGATGAAGCT 60.179 55.000 5.05 0.00 0.00 3.74
267 294 1.502163 CGCCGGATTGAGGATGAAGC 61.502 60.000 5.05 0.00 0.00 3.86
268 295 0.882042 CCGCCGGATTGAGGATGAAG 60.882 60.000 5.05 0.00 0.00 3.02
269 296 1.146041 CCGCCGGATTGAGGATGAA 59.854 57.895 5.05 0.00 0.00 2.57
270 297 1.334384 TTCCGCCGGATTGAGGATGA 61.334 55.000 6.69 0.00 32.19 2.92
271 298 1.146041 TTCCGCCGGATTGAGGATG 59.854 57.895 6.69 0.00 32.19 3.51
272 299 1.146263 GTTCCGCCGGATTGAGGAT 59.854 57.895 6.69 0.00 32.19 3.24
273 300 1.987855 AGTTCCGCCGGATTGAGGA 60.988 57.895 6.69 1.77 0.00 3.71
274 301 1.815421 CAGTTCCGCCGGATTGAGG 60.815 63.158 6.69 0.00 0.00 3.86
276 303 0.828022 ATACAGTTCCGCCGGATTGA 59.172 50.000 20.72 0.00 0.00 2.57
277 304 1.202533 AGATACAGTTCCGCCGGATTG 60.203 52.381 6.69 11.67 0.00 2.67
278 305 1.120530 AGATACAGTTCCGCCGGATT 58.879 50.000 6.69 0.00 0.00 3.01
279 306 1.068741 GAAGATACAGTTCCGCCGGAT 59.931 52.381 6.69 0.00 0.00 4.18
280 307 0.458669 GAAGATACAGTTCCGCCGGA 59.541 55.000 5.05 0.00 0.00 5.14
281 308 0.174845 TGAAGATACAGTTCCGCCGG 59.825 55.000 0.00 0.00 0.00 6.13
282 309 2.004583 TTGAAGATACAGTTCCGCCG 57.995 50.000 0.00 0.00 0.00 6.46
283 310 6.260050 TGAATAATTGAAGATACAGTTCCGCC 59.740 38.462 0.00 0.00 0.00 6.13
284 311 7.246674 TGAATAATTGAAGATACAGTTCCGC 57.753 36.000 0.00 0.00 0.00 5.54
294 321 9.593134 GCCTATCTCGTATGAATAATTGAAGAT 57.407 33.333 0.00 0.00 0.00 2.40
295 322 7.755373 CGCCTATCTCGTATGAATAATTGAAGA 59.245 37.037 0.00 0.00 0.00 2.87
296 323 7.755373 TCGCCTATCTCGTATGAATAATTGAAG 59.245 37.037 0.00 0.00 0.00 3.02
297 324 7.599171 TCGCCTATCTCGTATGAATAATTGAA 58.401 34.615 0.00 0.00 0.00 2.69
298 325 7.094334 ACTCGCCTATCTCGTATGAATAATTGA 60.094 37.037 0.00 0.00 0.00 2.57
299 326 7.030165 ACTCGCCTATCTCGTATGAATAATTG 58.970 38.462 0.00 0.00 0.00 2.32
300 327 7.159322 ACTCGCCTATCTCGTATGAATAATT 57.841 36.000 0.00 0.00 0.00 1.40
301 328 6.761099 ACTCGCCTATCTCGTATGAATAAT 57.239 37.500 0.00 0.00 0.00 1.28
302 329 6.877855 ACTACTCGCCTATCTCGTATGAATAA 59.122 38.462 0.00 0.00 0.00 1.40
303 330 6.404708 ACTACTCGCCTATCTCGTATGAATA 58.595 40.000 0.00 0.00 0.00 1.75
304 331 5.247084 ACTACTCGCCTATCTCGTATGAAT 58.753 41.667 0.00 0.00 0.00 2.57
370 414 9.479549 AATTTCACCATGGATGTATCTAAAACT 57.520 29.630 21.47 0.00 0.00 2.66
374 418 6.832900 TGCAATTTCACCATGGATGTATCTAA 59.167 34.615 21.47 0.43 0.00 2.10
386 430 6.343716 TGAATACAAGTGCAATTTCACCAT 57.656 33.333 4.51 0.00 37.68 3.55
399 443 4.081322 ACCGTGGAAGTTGAATACAAGT 57.919 40.909 0.00 0.00 40.84 3.16
405 449 5.699458 CACTAAGTAACCGTGGAAGTTGAAT 59.301 40.000 0.00 0.00 0.00 2.57
504 552 4.400567 TCACTAGTGAGATGTGAGATGTGG 59.599 45.833 21.74 0.00 36.03 4.17
506 554 5.478332 TGTTCACTAGTGAGATGTGAGATGT 59.522 40.000 23.97 0.00 41.01 3.06
507 555 5.958955 TGTTCACTAGTGAGATGTGAGATG 58.041 41.667 23.97 0.00 41.01 2.90
508 556 6.596309 TTGTTCACTAGTGAGATGTGAGAT 57.404 37.500 23.97 0.00 41.01 2.75
510 558 7.411264 CGATTTTGTTCACTAGTGAGATGTGAG 60.411 40.741 23.97 10.95 41.01 3.51
544 593 4.470602 TCCTTAACAGAGGATAGCGATGA 58.529 43.478 0.00 0.00 40.87 2.92
557 606 4.161565 TGCACTACCTACCATCCTTAACAG 59.838 45.833 0.00 0.00 0.00 3.16
586 635 4.407296 ACATTTTGTTCTTTTGGTGGCCTA 59.593 37.500 3.32 0.00 0.00 3.93
641 696 7.812191 CCTTAATTAATTGTGTAGCAGCAACAA 59.188 33.333 11.05 9.87 0.00 2.83
666 733 8.915654 CACAAAGAAAGCAACATTAATTAGTCC 58.084 33.333 0.00 0.00 0.00 3.85
673 744 7.283127 ACTCTCTCACAAAGAAAGCAACATTAA 59.717 33.333 0.00 0.00 32.23 1.40
674 745 6.767902 ACTCTCTCACAAAGAAAGCAACATTA 59.232 34.615 0.00 0.00 32.23 1.90
675 746 5.591877 ACTCTCTCACAAAGAAAGCAACATT 59.408 36.000 0.00 0.00 32.23 2.71
676 747 5.128919 ACTCTCTCACAAAGAAAGCAACAT 58.871 37.500 0.00 0.00 32.23 2.71
677 748 4.517285 ACTCTCTCACAAAGAAAGCAACA 58.483 39.130 0.00 0.00 32.23 3.33
678 749 6.423042 GTTACTCTCTCACAAAGAAAGCAAC 58.577 40.000 0.00 0.00 32.23 4.17
679 750 5.527582 GGTTACTCTCTCACAAAGAAAGCAA 59.472 40.000 0.00 0.00 32.23 3.91
680 751 5.057149 GGTTACTCTCTCACAAAGAAAGCA 58.943 41.667 0.00 0.00 32.23 3.91
681 752 5.178438 CAGGTTACTCTCTCACAAAGAAAGC 59.822 44.000 0.00 0.00 32.23 3.51
683 754 5.057149 GCAGGTTACTCTCTCACAAAGAAA 58.943 41.667 0.00 0.00 32.23 2.52
685 756 3.898123 AGCAGGTTACTCTCTCACAAAGA 59.102 43.478 0.00 0.00 0.00 2.52
686 757 3.993081 CAGCAGGTTACTCTCTCACAAAG 59.007 47.826 0.00 0.00 0.00 2.77
693 1126 2.903135 AGAAAGCAGCAGGTTACTCTCT 59.097 45.455 0.00 0.00 34.49 3.10
702 1135 0.606604 ATGCCAAAGAAAGCAGCAGG 59.393 50.000 0.00 0.00 43.38 4.85
704 1137 0.320073 GCATGCCAAAGAAAGCAGCA 60.320 50.000 6.36 0.00 43.38 4.41
706 1139 0.319083 TGGCATGCCAAAGAAAGCAG 59.681 50.000 36.95 0.00 44.12 4.24
733 1166 7.316640 AGAGTGCAGTATTGAACTACTACTTG 58.683 38.462 0.00 0.00 43.56 3.16
735 1168 7.469537 AAGAGTGCAGTATTGAACTACTACT 57.530 36.000 0.00 0.00 43.56 2.57
736 1169 9.453325 GATAAGAGTGCAGTATTGAACTACTAC 57.547 37.037 11.66 0.00 43.56 2.73
737 1170 9.409918 AGATAAGAGTGCAGTATTGAACTACTA 57.590 33.333 11.66 0.00 43.56 1.82
782 1215 3.881795 AGTATACGAATAAGACCGTGCG 58.118 45.455 0.00 0.00 39.54 5.34
793 1226 8.877195 ACCTTGTCCCATATTTAGTATACGAAT 58.123 33.333 10.86 10.86 0.00 3.34
800 1233 7.504926 ACTTGACCTTGTCCCATATTTAGTA 57.495 36.000 0.00 0.00 0.00 1.82
801 1234 6.388619 ACTTGACCTTGTCCCATATTTAGT 57.611 37.500 0.00 0.00 0.00 2.24
803 1236 7.743116 TCTACTTGACCTTGTCCCATATTTA 57.257 36.000 0.00 0.00 0.00 1.40
804 1237 6.636454 TCTACTTGACCTTGTCCCATATTT 57.364 37.500 0.00 0.00 0.00 1.40
805 1238 6.617371 AGATCTACTTGACCTTGTCCCATATT 59.383 38.462 0.00 0.00 0.00 1.28
806 1239 6.146760 AGATCTACTTGACCTTGTCCCATAT 58.853 40.000 0.00 0.00 0.00 1.78
807 1240 5.529289 AGATCTACTTGACCTTGTCCCATA 58.471 41.667 0.00 0.00 0.00 2.74
808 1241 4.366267 AGATCTACTTGACCTTGTCCCAT 58.634 43.478 0.00 0.00 0.00 4.00
810 1243 4.957327 ACTAGATCTACTTGACCTTGTCCC 59.043 45.833 0.00 0.00 0.00 4.46
811 1244 7.826918 ATACTAGATCTACTTGACCTTGTCC 57.173 40.000 0.00 0.00 27.66 4.02
853 1433 5.003160 TGCAGACTTGTAGTGCATTAATGT 58.997 37.500 16.61 0.00 42.20 2.71
854 1434 5.550232 TGCAGACTTGTAGTGCATTAATG 57.450 39.130 11.27 11.27 42.20 1.90
855 1435 5.106157 GGTTGCAGACTTGTAGTGCATTAAT 60.106 40.000 9.98 0.00 46.18 1.40
856 1436 4.215399 GGTTGCAGACTTGTAGTGCATTAA 59.785 41.667 9.98 0.00 46.18 1.40
857 1437 3.751175 GGTTGCAGACTTGTAGTGCATTA 59.249 43.478 9.98 0.00 46.18 1.90
863 1443 1.202770 GGGTGGTTGCAGACTTGTAGT 60.203 52.381 0.00 0.00 0.00 2.73
960 1558 4.227197 AGAGGAGAAGAGGAACAGAAACA 58.773 43.478 0.00 0.00 0.00 2.83
961 1559 4.882842 AGAGGAGAAGAGGAACAGAAAC 57.117 45.455 0.00 0.00 0.00 2.78
992 1592 1.755783 GCTGCCCCCATCTGAAAGG 60.756 63.158 0.00 0.00 0.00 3.11
1082 1703 2.299993 TGGCGAATCTGATCACAGTC 57.700 50.000 0.00 0.00 43.81 3.51
1098 1719 5.789643 TTTTAGCAGGGAATCATTATGGC 57.210 39.130 0.00 0.00 0.00 4.40
1171 1808 3.767230 CGCAGCCAACACTCGTCG 61.767 66.667 0.00 0.00 0.00 5.12
1172 1809 3.414700 CCGCAGCCAACACTCGTC 61.415 66.667 0.00 0.00 0.00 4.20
1173 1810 4.235762 ACCGCAGCCAACACTCGT 62.236 61.111 0.00 0.00 0.00 4.18
1174 1811 3.716006 CACCGCAGCCAACACTCG 61.716 66.667 0.00 0.00 0.00 4.18
1175 1812 4.030452 GCACCGCAGCCAACACTC 62.030 66.667 0.00 0.00 0.00 3.51
1326 1977 3.099905 TCCTTCTATGACACAGGACAGG 58.900 50.000 0.00 0.00 29.97 4.00
1327 1978 4.808414 TTCCTTCTATGACACAGGACAG 57.192 45.455 0.00 0.00 35.04 3.51
1329 1980 7.113658 TCTTATTCCTTCTATGACACAGGAC 57.886 40.000 0.00 0.00 35.04 3.85
1450 2101 4.343231 ACAATCTGCCCATGACATAAACA 58.657 39.130 0.00 0.00 0.00 2.83
1638 2297 7.176690 GGACTGAACAAGATTATGGGAGAAAAA 59.823 37.037 0.00 0.00 0.00 1.94
1649 2308 2.037902 TGGCACGGACTGAACAAGATTA 59.962 45.455 0.00 0.00 0.00 1.75
1655 2314 0.393132 TTGTTGGCACGGACTGAACA 60.393 50.000 0.00 0.00 0.00 3.18
1658 2317 1.464734 TTTTTGTTGGCACGGACTGA 58.535 45.000 0.00 0.00 0.00 3.41
1968 2798 3.876274 TCAGATGACACAGAAGCTACC 57.124 47.619 0.00 0.00 0.00 3.18
2016 2846 9.468532 CGATGAGAAGTGATGTTCATAAGATAA 57.531 33.333 0.00 0.00 30.85 1.75
2297 3134 6.093495 GGATCAACGTAACAATTTCAGATGGA 59.907 38.462 0.00 0.00 0.00 3.41
2309 3146 3.576982 AGTCTTCCAGGATCAACGTAACA 59.423 43.478 0.00 0.00 0.00 2.41
2418 3255 3.732938 AGGCCACTCCTGACCATC 58.267 61.111 5.01 0.00 45.54 3.51
2546 3383 5.778241 TGGAGGAACTAGTGTCTCACAATTA 59.222 40.000 20.48 4.32 41.55 1.40
2681 3519 2.665185 GCGGACTCTGCACGGTTT 60.665 61.111 4.87 0.00 0.00 3.27
3044 3894 3.382227 TGTTGTACTCGACCAGAACTTGA 59.618 43.478 0.00 0.00 0.00 3.02
3046 3896 4.369182 CTTGTTGTACTCGACCAGAACTT 58.631 43.478 0.00 0.00 0.00 2.66
3102 3952 9.695526 TGAATTTAGTTCATTTCAGAAACATGG 57.304 29.630 0.00 0.00 41.79 3.66
3251 4102 4.134379 ACCAAGAGACATAGATGCACAG 57.866 45.455 0.00 0.00 0.00 3.66
3271 4122 6.127925 TGCCATGATTCAGACAACAAAGATAC 60.128 38.462 0.00 0.00 0.00 2.24
3282 4133 5.278660 GGTTAATCCATGCCATGATTCAGAC 60.279 44.000 6.18 4.93 35.97 3.51
3316 4169 1.206578 CGCTACAAAAGGCCACACG 59.793 57.895 5.01 0.00 0.00 4.49
3344 4200 4.519350 TGGATTCAGGTAGAGCATACTACG 59.481 45.833 0.00 0.00 42.30 3.51
3367 4223 2.035632 GCTACATGTCCTAGCTGTCCT 58.964 52.381 0.00 0.00 34.82 3.85
3371 4227 3.193263 CAGTTGCTACATGTCCTAGCTG 58.807 50.000 17.64 11.46 37.98 4.24
3430 4293 6.654582 ACTTTTCATTTGTTTGCCAGAAAGTT 59.345 30.769 0.00 0.00 0.00 2.66
3449 4312 4.495690 AGAAGCTCCCCTGATACTTTTC 57.504 45.455 0.00 0.00 0.00 2.29
3456 4319 1.010170 ACCCTAAGAAGCTCCCCTGAT 59.990 52.381 0.00 0.00 0.00 2.90
3600 4498 7.294008 TCCTAAGTAAATATTTCCCCTACCCAG 59.706 40.741 3.39 0.00 0.00 4.45
3617 4515 8.943002 GTTTCGGAAAATCTGAATCCTAAGTAA 58.057 33.333 4.46 0.00 41.02 2.24
3636 4534 6.094881 AGTCATTTTCAACTTTCAGTTTCGGA 59.905 34.615 0.00 0.00 36.03 4.55
3644 4542 7.035004 CAGAAACCAGTCATTTTCAACTTTCA 58.965 34.615 0.00 0.00 34.68 2.69
3668 4567 2.690497 TCTTCACCATTTTTCCGTTGCA 59.310 40.909 0.00 0.00 0.00 4.08
3792 4698 9.142515 GCATTTGATGTGAAAATGTATGAAAGA 57.857 29.630 9.80 0.00 43.72 2.52
3793 4699 9.146984 AGCATTTGATGTGAAAATGTATGAAAG 57.853 29.630 9.80 0.00 43.72 2.62
3794 4700 8.927721 CAGCATTTGATGTGAAAATGTATGAAA 58.072 29.630 9.80 0.00 43.72 2.69
3795 4701 8.089597 ACAGCATTTGATGTGAAAATGTATGAA 58.910 29.630 16.22 0.00 43.73 2.57
3796 4702 7.604549 ACAGCATTTGATGTGAAAATGTATGA 58.395 30.769 16.22 0.00 43.73 2.15
3797 4703 7.821595 ACAGCATTTGATGTGAAAATGTATG 57.178 32.000 0.00 10.69 43.73 2.39
3798 4704 7.148540 GCAACAGCATTTGATGTGAAAATGTAT 60.149 33.333 1.73 0.00 44.74 2.29
3799 4705 6.145858 GCAACAGCATTTGATGTGAAAATGTA 59.854 34.615 1.73 0.00 44.74 2.29
3800 4706 5.049954 GCAACAGCATTTGATGTGAAAATGT 60.050 36.000 1.73 0.00 44.74 2.71
3801 4707 5.178623 AGCAACAGCATTTGATGTGAAAATG 59.821 36.000 1.73 4.84 44.74 2.32
3802 4708 5.302360 AGCAACAGCATTTGATGTGAAAAT 58.698 33.333 1.73 0.00 44.74 1.82
3803 4709 4.695396 AGCAACAGCATTTGATGTGAAAA 58.305 34.783 1.73 0.00 44.74 2.29
3806 4712 6.319405 ACATATAGCAACAGCATTTGATGTGA 59.681 34.615 1.73 0.00 44.74 3.58
3859 4765 7.489113 GGCCACAGTAAATGTATGAAAGAAATG 59.511 37.037 0.00 0.00 41.41 2.32
3912 4831 0.389296 CCCATGCAATGCACACACAG 60.389 55.000 11.23 0.00 44.97 3.66
3915 4834 1.252215 CCTCCCATGCAATGCACACA 61.252 55.000 11.23 0.00 44.97 3.72
3916 4835 1.514087 CCTCCCATGCAATGCACAC 59.486 57.895 11.23 0.00 44.97 3.82
3943 4862 2.107204 AGAACCAGTGTTTCTCTGCCAT 59.893 45.455 0.00 0.00 33.97 4.40
3944 4863 1.490490 AGAACCAGTGTTTCTCTGCCA 59.510 47.619 0.00 0.00 33.97 4.92
3945 4864 2.262423 AGAACCAGTGTTTCTCTGCC 57.738 50.000 0.00 0.00 33.97 4.85
3946 4865 3.378427 ACAAAGAACCAGTGTTTCTCTGC 59.622 43.478 3.11 0.00 33.97 4.26
3947 4866 5.584649 TGTACAAAGAACCAGTGTTTCTCTG 59.415 40.000 3.11 2.75 33.97 3.35
3948 4867 5.741011 TGTACAAAGAACCAGTGTTTCTCT 58.259 37.500 3.11 0.00 33.97 3.10
3949 4868 5.585047 ACTGTACAAAGAACCAGTGTTTCTC 59.415 40.000 3.11 0.00 36.82 2.87
3950 4869 5.354234 CACTGTACAAAGAACCAGTGTTTCT 59.646 40.000 9.80 0.00 46.05 2.52
3951 4870 5.569413 CACTGTACAAAGAACCAGTGTTTC 58.431 41.667 9.80 0.00 46.05 2.78
3952 4871 5.560966 CACTGTACAAAGAACCAGTGTTT 57.439 39.130 9.80 0.00 46.05 2.83
3956 4875 4.481368 TGACACTGTACAAAGAACCAGT 57.519 40.909 0.00 0.00 38.64 4.00
3957 4876 4.816385 ACATGACACTGTACAAAGAACCAG 59.184 41.667 0.00 0.00 0.00 4.00
3958 4877 4.776349 ACATGACACTGTACAAAGAACCA 58.224 39.130 0.00 0.00 0.00 3.67
3959 4878 7.435068 AATACATGACACTGTACAAAGAACC 57.565 36.000 0.00 0.00 34.59 3.62
3961 4880 8.717821 GCTAAATACATGACACTGTACAAAGAA 58.282 33.333 0.00 0.00 34.59 2.52
3962 4881 7.333423 GGCTAAATACATGACACTGTACAAAGA 59.667 37.037 0.00 0.00 34.59 2.52
3963 4882 7.414098 GGGCTAAATACATGACACTGTACAAAG 60.414 40.741 0.00 0.00 34.59 2.77
3964 4883 6.373216 GGGCTAAATACATGACACTGTACAAA 59.627 38.462 0.00 0.00 34.59 2.83
3965 4884 5.878116 GGGCTAAATACATGACACTGTACAA 59.122 40.000 0.00 0.00 34.59 2.41
3966 4885 5.188948 AGGGCTAAATACATGACACTGTACA 59.811 40.000 0.00 0.00 34.59 2.90
3967 4886 5.671493 AGGGCTAAATACATGACACTGTAC 58.329 41.667 0.00 0.00 34.59 2.90
4025 4944 6.830873 ATTTTATAATCCTGAGCAGATGCC 57.169 37.500 0.14 0.00 43.38 4.40
4116 5035 7.901322 AGACCCATCTATTTGCCTGATATAGTA 59.099 37.037 0.00 0.00 31.46 1.82
4117 5036 6.732862 AGACCCATCTATTTGCCTGATATAGT 59.267 38.462 0.00 0.00 31.46 2.12
4118 5037 7.192852 AGACCCATCTATTTGCCTGATATAG 57.807 40.000 0.00 0.00 31.46 1.31
4119 5038 8.860517 ATAGACCCATCTATTTGCCTGATATA 57.139 34.615 0.00 0.00 44.39 0.86
4120 5039 7.626890 AGATAGACCCATCTATTTGCCTGATAT 59.373 37.037 0.00 0.00 46.34 1.63
4208 5127 3.199880 ACTGCATAGGGTTAGTCATGC 57.800 47.619 0.00 0.00 43.22 4.06
4239 5158 7.371126 TGTGTTATTATGTCGATGCAGAAAA 57.629 32.000 0.00 0.00 0.00 2.29
4272 5191 5.830912 TGAATCAAGTTACAGGCACAAAAG 58.169 37.500 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.