Multiple sequence alignment - TraesCS7A01G117600

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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 TraesCS7A01G117600 chr7A 100.000 4771 0 0 1 4771 76122509 76117739 0.000000e+00 8811.0
1 TraesCS7A01G117600 chr7A 94.982 1136 40 7 2945 4067 75668630 75667499 0.000000e+00 1766.0
2 TraesCS7A01G117600 chr7A 79.890 905 136 28 3295 4170 75572985 75572098 5.240000e-174 621.0
3 TraesCS7A01G117600 chr7A 79.282 975 126 40 3324 4233 75869051 75868088 3.160000e-171 612.0
4 TraesCS7A01G117600 chr7A 86.527 334 36 9 1957 2284 75616475 75616145 4.540000e-95 359.0
5 TraesCS7A01G117600 chr7A 91.071 56 5 0 4167 4222 75572075 75572020 5.120000e-10 76.8
6 TraesCS7A01G117600 chr7D 91.689 1468 101 13 1782 3235 69592355 69590895 0.000000e+00 2015.0
7 TraesCS7A01G117600 chr7D 92.296 1350 64 8 3337 4650 69590882 69589537 0.000000e+00 1881.0
8 TraesCS7A01G117600 chr7D 85.780 1737 174 40 2449 4151 69488681 69486984 0.000000e+00 1772.0
9 TraesCS7A01G117600 chr7D 85.229 1442 108 43 1 1417 69594256 69592895 0.000000e+00 1386.0
10 TraesCS7A01G117600 chr7D 89.239 762 74 6 3414 4172 69532436 69531680 0.000000e+00 946.0
11 TraesCS7A01G117600 chr7D 80.165 1215 162 50 3067 4222 69484071 69482877 0.000000e+00 835.0
12 TraesCS7A01G117600 chr7D 83.207 661 83 21 1797 2438 69581030 69580379 8.900000e-162 580.0
13 TraesCS7A01G117600 chr7D 90.373 322 29 1 4452 4771 69493147 69492826 5.710000e-114 422.0
14 TraesCS7A01G117600 chr7D 95.522 67 2 1 4385 4450 69493241 69493175 6.530000e-19 106.0
15 TraesCS7A01G117600 chr7D 100.000 36 0 0 4354 4389 69531684 69531649 3.080000e-07 67.6
16 TraesCS7A01G117600 chr7B 85.238 1741 171 52 3101 4771 11958104 11956380 0.000000e+00 1712.0
17 TraesCS7A01G117600 chr7B 85.531 1244 128 26 396 1616 11960533 11959319 0.000000e+00 1253.0
18 TraesCS7A01G117600 chr7B 84.756 820 82 22 3412 4212 11925869 11925074 0.000000e+00 782.0
19 TraesCS7A01G117600 chr7B 82.947 862 114 26 1796 2638 11959156 11958309 0.000000e+00 747.0
20 TraesCS7A01G117600 chr7B 80.667 869 132 27 1795 2646 11921811 11920962 4.030000e-180 641.0
21 TraesCS7A01G117600 chr7B 78.645 974 130 41 3324 4233 11896164 11895205 4.140000e-160 575.0
22 TraesCS7A01G117600 chr7B 84.141 454 54 13 1156 1598 11929269 11928823 1.590000e-114 424.0
23 TraesCS7A01G117600 chr7B 90.878 296 26 1 4477 4771 11918140 11917845 3.460000e-106 396.0
24 TraesCS7A01G117600 chr7B 79.690 581 92 18 2069 2638 11926882 11926317 3.460000e-106 396.0
25 TraesCS7A01G117600 chr7B 84.359 390 45 10 3 379 11960992 11960606 7.540000e-98 368.0
26 TraesCS7A01G117600 chr7B 87.458 295 25 7 4166 4450 11918487 11918195 3.560000e-86 329.0
27 TraesCS7A01G117600 chr1B 80.741 270 26 12 1904 2169 623941080 623940833 2.270000e-43 187.0


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 TraesCS7A01G117600 chr7A 76117739 76122509 4770 True 8811.000000 8811 100.000000 1 4771 1 chr7A.!!$R4 4770
1 TraesCS7A01G117600 chr7A 75667499 75668630 1131 True 1766.000000 1766 94.982000 2945 4067 1 chr7A.!!$R2 1122
2 TraesCS7A01G117600 chr7A 75868088 75869051 963 True 612.000000 612 79.282000 3324 4233 1 chr7A.!!$R3 909
3 TraesCS7A01G117600 chr7A 75572020 75572985 965 True 348.900000 621 85.480500 3295 4222 2 chr7A.!!$R5 927
4 TraesCS7A01G117600 chr7D 69589537 69594256 4719 True 1760.666667 2015 89.738000 1 4650 3 chr7D.!!$R5 4649
5 TraesCS7A01G117600 chr7D 69482877 69488681 5804 True 1303.500000 1772 82.972500 2449 4222 2 chr7D.!!$R2 1773
6 TraesCS7A01G117600 chr7D 69580379 69581030 651 True 580.000000 580 83.207000 1797 2438 1 chr7D.!!$R1 641
7 TraesCS7A01G117600 chr7D 69531649 69532436 787 True 506.800000 946 94.619500 3414 4389 2 chr7D.!!$R4 975
8 TraesCS7A01G117600 chr7B 11956380 11960992 4612 True 1020.000000 1712 84.518750 3 4771 4 chr7B.!!$R3 4768
9 TraesCS7A01G117600 chr7B 11895205 11896164 959 True 575.000000 575 78.645000 3324 4233 1 chr7B.!!$R1 909
10 TraesCS7A01G117600 chr7B 11917845 11929269 11424 True 494.666667 782 84.598333 1156 4771 6 chr7B.!!$R2 3615

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
287 303 0.038343 TACTCCGTGTTGGGCGTTAC 60.038 55.000 0.00 0.0 38.76 2.50 F
518 591 0.100861 GGACCGACGATTCCTCAGTC 59.899 60.000 0.00 0.0 0.00 3.51 F
1466 1598 0.037160 TTTTAGACACCGGAAGCCCC 59.963 55.000 9.46 0.0 0.00 5.80 F
1717 2236 0.107897 TTGCTTGTGTCACGTCCTGT 60.108 50.000 0.00 0.0 0.00 4.00 F
1744 2263 0.904649 ATCCATGCTTCGGTGTGAGA 59.095 50.000 0.00 0.0 0.00 3.27 F
2071 3903 2.162681 CTTTCCTGACAAATTCGGCCT 58.837 47.619 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 1552 0.032540 CCAAAAGACAGCAGGCCAAC 59.967 55.0 5.01 0.00 0.00 3.77 R
1489 1621 0.244994 AGCTCTGGCGAACACTACAG 59.755 55.0 0.00 0.00 44.37 2.74 R
2783 4657 0.407528 TTGGCTAGCCCATGGTTGAA 59.592 50.0 30.81 12.89 44.89 2.69 R
2784 4658 0.407528 TTTGGCTAGCCCATGGTTGA 59.592 50.0 30.81 6.69 44.89 3.18 R
2881 4755 0.887933 CCAATATTATGGTGCGCCCC 59.112 55.0 15.15 2.15 35.65 5.80 R
3834 5795 0.458543 ATTCAGCACGGCAGTACTCG 60.459 55.0 0.00 0.00 0.00 4.18 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
77 78 6.914757 CAGACCACAAGAGAAAAGAAATTGTC 59.085 38.462 0.00 0.00 32.01 3.18
83 84 7.646922 CACAAGAGAAAAGAAATTGTCAGGAAG 59.353 37.037 0.00 0.00 32.01 3.46
113 115 1.203262 TCAACCCTACCAGTGGCTAGT 60.203 52.381 9.78 0.00 0.00 2.57
118 120 2.457598 CCTACCAGTGGCTAGTGAAGA 58.542 52.381 9.78 0.00 0.00 2.87
120 122 3.452627 CCTACCAGTGGCTAGTGAAGAAT 59.547 47.826 9.78 0.00 0.00 2.40
121 123 4.080863 CCTACCAGTGGCTAGTGAAGAATT 60.081 45.833 9.78 0.00 0.00 2.17
202 206 5.307196 AGCCTTTGTTGTAAGGAGAAGACTA 59.693 40.000 6.59 0.00 46.28 2.59
208 215 6.166279 TGTTGTAAGGAGAAGACTAGCAATG 58.834 40.000 0.00 0.00 0.00 2.82
214 221 5.729510 AGGAGAAGACTAGCAATGAGAAAC 58.270 41.667 0.00 0.00 0.00 2.78
270 286 8.491152 CAGTGCAGTAATGCAGATTTATACTAC 58.509 37.037 19.62 1.89 46.32 2.73
272 288 8.704234 GTGCAGTAATGCAGATTTATACTACTC 58.296 37.037 19.62 0.00 46.32 2.59
273 289 7.872993 TGCAGTAATGCAGATTTATACTACTCC 59.127 37.037 14.87 0.00 40.23 3.85
274 290 7.062371 GCAGTAATGCAGATTTATACTACTCCG 59.938 40.741 10.86 0.00 34.41 4.63
275 291 8.082852 CAGTAATGCAGATTTATACTACTCCGT 58.917 37.037 0.00 0.00 0.00 4.69
276 292 8.082852 AGTAATGCAGATTTATACTACTCCGTG 58.917 37.037 0.00 0.00 0.00 4.94
277 293 5.847111 TGCAGATTTATACTACTCCGTGT 57.153 39.130 0.00 0.00 0.00 4.49
279 295 6.040247 TGCAGATTTATACTACTCCGTGTTG 58.960 40.000 0.00 0.00 0.00 3.33
280 296 5.462398 GCAGATTTATACTACTCCGTGTTGG 59.538 44.000 0.00 0.00 40.09 3.77
281 297 5.983720 CAGATTTATACTACTCCGTGTTGGG 59.016 44.000 0.00 0.00 38.76 4.12
282 298 3.806625 TTATACTACTCCGTGTTGGGC 57.193 47.619 0.00 0.00 38.76 5.36
283 299 0.458669 ATACTACTCCGTGTTGGGCG 59.541 55.000 0.00 0.00 38.76 6.13
284 300 0.895100 TACTACTCCGTGTTGGGCGT 60.895 55.000 0.00 0.00 38.76 5.68
285 301 1.005394 CTACTCCGTGTTGGGCGTT 60.005 57.895 0.00 0.00 38.76 4.84
286 302 0.244450 CTACTCCGTGTTGGGCGTTA 59.756 55.000 0.00 0.00 38.76 3.18
287 303 0.038343 TACTCCGTGTTGGGCGTTAC 60.038 55.000 0.00 0.00 38.76 2.50
288 304 1.301087 CTCCGTGTTGGGCGTTACA 60.301 57.895 0.00 0.00 38.76 2.41
289 305 0.881159 CTCCGTGTTGGGCGTTACAA 60.881 55.000 0.00 0.00 38.76 2.41
290 306 0.881159 TCCGTGTTGGGCGTTACAAG 60.881 55.000 0.00 0.00 38.76 3.16
291 307 0.881159 CCGTGTTGGGCGTTACAAGA 60.881 55.000 0.00 0.00 0.00 3.02
292 308 0.938713 CGTGTTGGGCGTTACAAGAA 59.061 50.000 0.00 0.00 0.00 2.52
293 309 1.333435 CGTGTTGGGCGTTACAAGAAC 60.333 52.381 0.00 0.00 0.00 3.01
294 310 1.944709 GTGTTGGGCGTTACAAGAACT 59.055 47.619 0.00 0.00 0.00 3.01
295 311 3.132925 GTGTTGGGCGTTACAAGAACTA 58.867 45.455 0.00 0.00 0.00 2.24
316 332 9.638239 GAACTAGCAAATTCATTCAACCAAATA 57.362 29.630 0.00 0.00 0.00 1.40
346 362 4.650734 TCACATCATTGCTACCAAGAACA 58.349 39.130 0.00 0.00 33.80 3.18
394 467 9.573166 TTTCTCTGAAATCTAACAATTCCAAGA 57.427 29.630 0.00 0.00 0.00 3.02
399 472 9.565213 CTGAAATCTAACAATTCCAAGATCAAC 57.435 33.333 0.00 0.00 0.00 3.18
414 487 6.810182 CCAAGATCAACTTCAAATCAACCATC 59.190 38.462 0.00 0.00 36.61 3.51
438 511 6.816140 TCGAGCAACAGATAATCACACAATTA 59.184 34.615 0.00 0.00 0.00 1.40
440 513 7.962373 CGAGCAACAGATAATCACACAATTAAA 59.038 33.333 0.00 0.00 0.00 1.52
457 530 8.450180 CACAATTAAAAAGTAATGGAATTGGGC 58.550 33.333 9.28 0.00 36.99 5.36
459 532 8.667463 CAATTAAAAAGTAATGGAATTGGGCAG 58.333 33.333 0.00 0.00 36.99 4.85
460 533 5.823861 AAAAAGTAATGGAATTGGGCAGT 57.176 34.783 0.00 0.00 36.99 4.40
463 536 5.914898 AAGTAATGGAATTGGGCAGTAAC 57.085 39.130 0.00 0.00 36.99 2.50
518 591 0.100861 GGACCGACGATTCCTCAGTC 59.899 60.000 0.00 0.00 0.00 3.51
576 649 4.838486 GCCGAGACCGTCAGAGCG 62.838 72.222 0.40 0.00 0.00 5.03
617 690 3.256960 GGGCACACCTCCCTTCCA 61.257 66.667 0.00 0.00 40.66 3.53
745 840 0.248215 GAACATCGCGGAATGGCTTG 60.248 55.000 6.13 0.00 0.00 4.01
746 841 1.656818 AACATCGCGGAATGGCTTGG 61.657 55.000 6.13 0.00 0.00 3.61
748 843 1.524621 ATCGCGGAATGGCTTGGAG 60.525 57.895 6.13 0.00 0.00 3.86
750 845 3.521796 GCGGAATGGCTTGGAGGC 61.522 66.667 0.00 0.00 41.77 4.70
780 875 0.171903 GCATGGGCAATGACTGACAC 59.828 55.000 5.91 0.00 38.72 3.67
812 920 2.361737 GCCCAAGAGTTCAGGCCC 60.362 66.667 0.00 0.00 39.60 5.80
813 921 2.045926 CCCAAGAGTTCAGGCCCG 60.046 66.667 0.00 0.00 0.00 6.13
814 922 2.045926 CCAAGAGTTCAGGCCCGG 60.046 66.667 0.00 0.00 0.00 5.73
815 923 2.592993 CCAAGAGTTCAGGCCCGGA 61.593 63.158 0.73 0.00 0.00 5.14
816 924 1.078848 CAAGAGTTCAGGCCCGGAG 60.079 63.158 0.73 0.00 0.00 4.63
841 949 2.219458 CCAGTTAGACGCCGATAGAGA 58.781 52.381 0.00 0.00 39.76 3.10
844 953 3.185594 CAGTTAGACGCCGATAGAGAGAG 59.814 52.174 0.00 0.00 39.76 3.20
845 954 3.069872 AGTTAGACGCCGATAGAGAGAGA 59.930 47.826 0.00 0.00 39.76 3.10
846 955 2.163818 AGACGCCGATAGAGAGAGAG 57.836 55.000 0.00 0.00 39.76 3.20
847 956 1.689813 AGACGCCGATAGAGAGAGAGA 59.310 52.381 0.00 0.00 39.76 3.10
848 957 2.066262 GACGCCGATAGAGAGAGAGAG 58.934 57.143 0.00 0.00 39.76 3.20
849 958 1.689813 ACGCCGATAGAGAGAGAGAGA 59.310 52.381 0.00 0.00 39.76 3.10
989 1105 4.189188 CGGTGGTAGGGCGTCGAG 62.189 72.222 0.00 0.00 0.00 4.04
1069 1185 3.272574 TCATCAGCAAGAAGACCATCC 57.727 47.619 0.00 0.00 0.00 3.51
1082 1199 0.898320 ACCATCCAGAAGTGAGTCCG 59.102 55.000 0.00 0.00 0.00 4.79
1095 1212 1.891722 GAGTCCGCCGTTCCCCTTTA 61.892 60.000 0.00 0.00 0.00 1.85
1129 1246 1.135199 GTGGTTTCGTATGCTCGGAGA 60.135 52.381 9.69 0.00 0.00 3.71
1130 1247 1.546923 TGGTTTCGTATGCTCGGAGAA 59.453 47.619 9.69 0.00 34.09 2.87
1171 1294 3.370209 GCCGGTTTAGGTACAAGGAAGAT 60.370 47.826 1.90 0.00 0.00 2.40
1234 1357 2.390599 CCGGAATGTGTGAGTGCCG 61.391 63.158 0.00 0.00 38.54 5.69
1235 1358 2.870372 GGAATGTGTGAGTGCCGC 59.130 61.111 0.00 0.00 0.00 6.53
1236 1359 2.690778 GGAATGTGTGAGTGCCGCC 61.691 63.158 0.00 0.00 0.00 6.13
1256 1379 0.109597 CTGCTCGCGCTTGGATTTTT 60.110 50.000 5.56 0.00 36.97 1.94
1261 1384 1.671166 GCGCTTGGATTTTTGGGGT 59.329 52.632 0.00 0.00 0.00 4.95
1262 1385 0.892063 GCGCTTGGATTTTTGGGGTA 59.108 50.000 0.00 0.00 0.00 3.69
1264 1387 1.135517 CGCTTGGATTTTTGGGGTACG 60.136 52.381 0.00 0.00 0.00 3.67
1266 1389 3.083293 GCTTGGATTTTTGGGGTACGTA 58.917 45.455 0.00 0.00 0.00 3.57
1286 1409 1.701031 TTTGGGGGTGCTCGTCTTGA 61.701 55.000 0.00 0.00 0.00 3.02
1287 1410 1.488705 TTGGGGGTGCTCGTCTTGAT 61.489 55.000 0.00 0.00 0.00 2.57
1288 1411 1.153349 GGGGGTGCTCGTCTTGATC 60.153 63.158 0.00 0.00 0.00 2.92
1289 1412 1.617947 GGGGGTGCTCGTCTTGATCT 61.618 60.000 0.00 0.00 0.00 2.75
1290 1413 1.112113 GGGGTGCTCGTCTTGATCTA 58.888 55.000 0.00 0.00 0.00 1.98
1427 1552 2.805353 CAAGGTCCGTGCGTCGAG 60.805 66.667 0.00 0.00 42.86 4.04
1430 1555 3.103911 GGTCCGTGCGTCGAGTTG 61.104 66.667 0.00 0.00 42.86 3.16
1440 1565 2.029844 GTCGAGTTGGCCTGCTGTC 61.030 63.158 3.32 0.00 0.00 3.51
1452 1577 3.552890 GGCCTGCTGTCTTTTGGTTTTAG 60.553 47.826 0.00 0.00 0.00 1.85
1453 1578 3.317993 GCCTGCTGTCTTTTGGTTTTAGA 59.682 43.478 0.00 0.00 0.00 2.10
1454 1579 4.793028 GCCTGCTGTCTTTTGGTTTTAGAC 60.793 45.833 0.00 0.00 38.96 2.59
1456 1581 5.243426 TGCTGTCTTTTGGTTTTAGACAC 57.757 39.130 0.00 0.00 42.31 3.67
1458 1583 4.788521 GCTGTCTTTTGGTTTTAGACACCG 60.789 45.833 0.00 0.00 42.31 4.94
1459 1584 3.628487 TGTCTTTTGGTTTTAGACACCGG 59.372 43.478 0.00 0.00 42.31 5.28
1461 1586 4.336153 GTCTTTTGGTTTTAGACACCGGAA 59.664 41.667 9.46 0.00 38.49 4.30
1462 1587 4.577283 TCTTTTGGTTTTAGACACCGGAAG 59.423 41.667 9.46 1.96 37.07 3.46
1466 1598 0.037160 TTTTAGACACCGGAAGCCCC 59.963 55.000 9.46 0.00 0.00 5.80
1472 1604 1.376812 CACCGGAAGCCCCTGTAAC 60.377 63.158 9.46 0.00 30.67 2.50
1481 1613 0.690762 GCCCCTGTAACCTCAACTGA 59.309 55.000 0.00 0.00 0.00 3.41
1483 1615 2.290960 GCCCCTGTAACCTCAACTGAAT 60.291 50.000 0.00 0.00 0.00 2.57
1484 1616 3.610911 CCCCTGTAACCTCAACTGAATC 58.389 50.000 0.00 0.00 0.00 2.52
1489 1621 5.409826 CCTGTAACCTCAACTGAATCAAGTC 59.590 44.000 0.00 0.00 0.00 3.01
1491 1787 5.991606 TGTAACCTCAACTGAATCAAGTCTG 59.008 40.000 0.00 0.00 0.00 3.51
1493 1789 5.808366 ACCTCAACTGAATCAAGTCTGTA 57.192 39.130 0.00 0.00 0.00 2.74
1500 1796 5.223382 ACTGAATCAAGTCTGTAGTGTTCG 58.777 41.667 0.00 0.00 0.00 3.95
1506 1802 1.542030 AGTCTGTAGTGTTCGCCAGAG 59.458 52.381 0.00 0.00 34.80 3.35
1516 1812 1.996191 GTTCGCCAGAGCTTGTCTTAG 59.004 52.381 0.00 0.00 36.60 2.18
1522 1818 3.594134 CCAGAGCTTGTCTTAGAACTGG 58.406 50.000 0.00 0.00 35.43 4.00
1541 1842 0.601311 GCTCGTTTGGACAGCAGACT 60.601 55.000 0.00 0.00 33.19 3.24
1577 1878 2.610433 TCAGCAACACTCGAAGCATAG 58.390 47.619 0.00 0.00 0.00 2.23
1578 1879 2.029020 TCAGCAACACTCGAAGCATAGT 60.029 45.455 0.00 0.00 0.00 2.12
1589 1890 8.033038 ACACTCGAAGCATAGTATGAAGTTTAA 58.967 33.333 14.52 0.00 0.00 1.52
1611 2129 9.691362 TTTAATTTTCTTATTGACAGGTTGAGC 57.309 29.630 0.00 0.00 0.00 4.26
1613 2131 5.947228 TTTCTTATTGACAGGTTGAGCTG 57.053 39.130 8.54 8.54 0.00 4.24
1614 2132 4.623932 TCTTATTGACAGGTTGAGCTGT 57.376 40.909 15.01 15.01 36.40 4.40
1615 2133 5.738619 TCTTATTGACAGGTTGAGCTGTA 57.261 39.130 15.06 2.41 33.50 2.74
1617 2135 6.711277 TCTTATTGACAGGTTGAGCTGTAAT 58.289 36.000 15.06 15.30 33.50 1.89
1618 2136 6.595326 TCTTATTGACAGGTTGAGCTGTAATG 59.405 38.462 15.06 5.38 33.50 1.90
1619 2137 3.769739 TGACAGGTTGAGCTGTAATGT 57.230 42.857 15.06 0.00 33.50 2.71
1621 2139 5.222079 TGACAGGTTGAGCTGTAATGTTA 57.778 39.130 15.06 0.00 33.50 2.41
1622 2140 4.994852 TGACAGGTTGAGCTGTAATGTTAC 59.005 41.667 15.06 3.06 33.50 2.50
1623 2141 4.968259 ACAGGTTGAGCTGTAATGTTACA 58.032 39.130 13.65 5.57 41.06 2.41
1624 2142 4.755123 ACAGGTTGAGCTGTAATGTTACAC 59.245 41.667 13.65 0.87 38.64 2.90
1625 2143 4.997395 CAGGTTGAGCTGTAATGTTACACT 59.003 41.667 0.00 5.04 38.64 3.55
1626 2144 4.997395 AGGTTGAGCTGTAATGTTACACTG 59.003 41.667 0.00 0.00 38.64 3.66
1627 2145 4.755123 GGTTGAGCTGTAATGTTACACTGT 59.245 41.667 0.00 0.00 38.64 3.55
1628 2146 5.238650 GGTTGAGCTGTAATGTTACACTGTT 59.761 40.000 0.00 0.00 38.64 3.16
1629 2147 6.425721 GGTTGAGCTGTAATGTTACACTGTTA 59.574 38.462 0.00 0.00 38.64 2.41
1630 2148 7.119262 GGTTGAGCTGTAATGTTACACTGTTAT 59.881 37.037 0.00 0.00 38.64 1.89
1631 2149 9.146984 GTTGAGCTGTAATGTTACACTGTTATA 57.853 33.333 0.00 0.00 38.64 0.98
1632 2150 8.697846 TGAGCTGTAATGTTACACTGTTATAC 57.302 34.615 0.00 0.00 38.64 1.47
1633 2151 8.528643 TGAGCTGTAATGTTACACTGTTATACT 58.471 33.333 0.00 0.00 38.64 2.12
1634 2152 8.703604 AGCTGTAATGTTACACTGTTATACTG 57.296 34.615 1.62 0.00 38.64 2.74
1635 2153 8.311836 AGCTGTAATGTTACACTGTTATACTGT 58.688 33.333 1.62 0.00 38.64 3.55
1636 2154 8.932791 GCTGTAATGTTACACTGTTATACTGTT 58.067 33.333 1.62 0.00 38.64 3.16
1674 2193 2.469826 TGTGTGCTAGTTCACGTGAAG 58.530 47.619 30.38 20.00 39.73 3.02
1677 2196 1.721926 GTGCTAGTTCACGTGAAGAGC 59.278 52.381 36.11 36.11 41.25 4.09
1693 2212 9.197694 ACGTGAAGAGCTAATGTATTCATAATC 57.802 33.333 0.00 0.00 32.93 1.75
1710 2229 6.845302 TCATAATCTCATTTGCTTGTGTCAC 58.155 36.000 0.00 0.00 0.00 3.67
1712 2231 2.560504 TCTCATTTGCTTGTGTCACGT 58.439 42.857 0.00 0.00 0.00 4.49
1713 2232 2.543848 TCTCATTTGCTTGTGTCACGTC 59.456 45.455 0.00 0.00 0.00 4.34
1714 2233 1.601903 TCATTTGCTTGTGTCACGTCC 59.398 47.619 0.00 0.00 0.00 4.79
1715 2234 1.603802 CATTTGCTTGTGTCACGTCCT 59.396 47.619 0.00 0.00 0.00 3.85
1716 2235 1.013596 TTTGCTTGTGTCACGTCCTG 58.986 50.000 0.00 0.00 0.00 3.86
1717 2236 0.107897 TTGCTTGTGTCACGTCCTGT 60.108 50.000 0.00 0.00 0.00 4.00
1744 2263 0.904649 ATCCATGCTTCGGTGTGAGA 59.095 50.000 0.00 0.00 0.00 3.27
1750 2280 3.129792 CTTCGGTGTGAGAAGCCTC 57.870 57.895 0.00 0.00 38.65 4.70
1762 2292 5.078411 TGAGAAGCCTCAACTAAAGCTAG 57.922 43.478 0.00 0.00 45.74 3.42
1763 2293 4.772624 TGAGAAGCCTCAACTAAAGCTAGA 59.227 41.667 0.00 0.00 45.74 2.43
1785 2353 4.957759 AATTATTACCAGACAACGTGGC 57.042 40.909 0.00 0.00 38.83 5.01
1792 2363 3.793559 ACCAGACAACGTGGCTATATTC 58.206 45.455 0.00 0.00 29.42 1.75
1793 2364 3.196901 ACCAGACAACGTGGCTATATTCA 59.803 43.478 0.00 0.00 29.42 2.57
1803 2374 8.651588 CAACGTGGCTATATTCAGATTAGATTC 58.348 37.037 0.00 0.00 0.00 2.52
1834 2405 2.480759 GCCTTGGTCATATGCTTTGCTG 60.481 50.000 0.00 0.00 0.00 4.41
1849 2420 4.659088 CTTTGCTGATGCTAGTGATGTTG 58.341 43.478 0.00 0.00 40.48 3.33
1850 2422 3.339253 TGCTGATGCTAGTGATGTTGT 57.661 42.857 0.00 0.00 40.48 3.32
1859 2432 8.257306 TGATGCTAGTGATGTTGTATTCAAGTA 58.743 33.333 0.00 0.00 33.97 2.24
1884 2457 3.372206 ACTCGTCTTCATGCATACAAAGC 59.628 43.478 0.00 0.49 0.00 3.51
1891 2464 6.259608 GTCTTCATGCATACAAAGCTATCTGT 59.740 38.462 0.00 0.00 0.00 3.41
1892 2465 5.996669 TCATGCATACAAAGCTATCTGTG 57.003 39.130 0.00 0.00 33.65 3.66
1894 2467 5.525012 TCATGCATACAAAGCTATCTGTGTC 59.475 40.000 0.00 0.00 39.91 3.67
1898 2471 5.220548 GCATACAAAGCTATCTGTGTCACTG 60.221 44.000 4.27 3.89 39.91 3.66
1899 2472 4.607293 ACAAAGCTATCTGTGTCACTGA 57.393 40.909 14.13 14.13 35.96 3.41
1911 2485 5.008019 TCTGTGTCACTGAATGCTTCTTTTC 59.992 40.000 9.88 0.00 0.00 2.29
1948 2522 5.837438 GGATTTGGAGAAAGGAATGATGGAT 59.163 40.000 0.00 0.00 0.00 3.41
1975 2549 9.717942 TGCCTTTATGCAAAATGTAAGTTTTAT 57.282 25.926 0.00 0.00 38.56 1.40
1981 2555 7.789341 TGCAAAATGTAAGTTTTATAGCACG 57.211 32.000 0.00 0.00 27.89 5.34
1982 2556 7.585867 TGCAAAATGTAAGTTTTATAGCACGA 58.414 30.769 0.00 0.00 27.89 4.35
1984 2558 9.072294 GCAAAATGTAAGTTTTATAGCACGATT 57.928 29.630 0.00 0.00 27.89 3.34
1986 2560 9.072294 AAAATGTAAGTTTTATAGCACGATTGC 57.928 29.630 0.00 0.00 39.21 3.56
2008 2582 8.970691 TTGCTTGCTTTCAGTTATCTTATTTC 57.029 30.769 0.00 0.00 0.00 2.17
2012 2586 9.994432 CTTGCTTTCAGTTATCTTATTTCGATT 57.006 29.630 0.00 0.00 0.00 3.34
2022 2596 9.813080 GTTATCTTATTTCGATTTGTGCTATCC 57.187 33.333 0.00 0.00 0.00 2.59
2027 2601 8.909708 TTATTTCGATTTGTGCTATCCTTTTG 57.090 30.769 0.00 0.00 0.00 2.44
2028 2602 4.963276 TCGATTTGTGCTATCCTTTTGG 57.037 40.909 0.00 0.00 42.21 3.28
2031 2605 5.242838 TCGATTTGTGCTATCCTTTTGGTTT 59.757 36.000 0.00 0.00 41.38 3.27
2032 2606 5.345741 CGATTTGTGCTATCCTTTTGGTTTG 59.654 40.000 0.00 0.00 41.38 2.93
2033 2607 5.606348 TTTGTGCTATCCTTTTGGTTTGT 57.394 34.783 0.00 0.00 41.38 2.83
2034 2608 6.716934 TTTGTGCTATCCTTTTGGTTTGTA 57.283 33.333 0.00 0.00 41.38 2.41
2035 2609 6.909550 TTGTGCTATCCTTTTGGTTTGTAT 57.090 33.333 0.00 0.00 41.38 2.29
2037 2613 6.686630 TGTGCTATCCTTTTGGTTTGTATTG 58.313 36.000 0.00 0.00 41.38 1.90
2048 2624 3.894427 TGGTTTGTATTGGAACTGCACAT 59.106 39.130 0.00 0.00 0.00 3.21
2049 2625 4.022416 TGGTTTGTATTGGAACTGCACATC 60.022 41.667 0.00 0.00 0.00 3.06
2055 2631 5.412594 TGTATTGGAACTGCACATCTCTTTC 59.587 40.000 0.00 0.00 0.00 2.62
2064 2640 4.401022 TGCACATCTCTTTCCTGACAAAT 58.599 39.130 0.00 0.00 0.00 2.32
2065 2641 4.828939 TGCACATCTCTTTCCTGACAAATT 59.171 37.500 0.00 0.00 0.00 1.82
2071 3903 2.162681 CTTTCCTGACAAATTCGGCCT 58.837 47.619 0.00 0.00 0.00 5.19
2090 3922 3.308904 GCCTTTGTTATGAAGGTACCCCT 60.309 47.826 8.74 0.00 44.44 4.79
2197 4030 9.772973 ATAATTACTGTAATATTTGCCGAGTCA 57.227 29.630 13.07 0.00 0.00 3.41
2423 4271 6.512297 TGCTTCCTTGAATTACCTTTTGTTC 58.488 36.000 0.00 0.00 0.00 3.18
2439 4287 5.367945 TTTGTTCTGTTAGAGTGGAGGTT 57.632 39.130 0.00 0.00 0.00 3.50
2441 4289 4.223953 TGTTCTGTTAGAGTGGAGGTTCT 58.776 43.478 0.00 0.00 0.00 3.01
2508 4360 2.560542 CTGGATCCCTGTAGAATCTCCG 59.439 54.545 9.90 0.00 0.00 4.63
2830 4704 3.117738 TGGAAAATGTTTTTGCCACCCAT 60.118 39.130 0.00 0.00 44.33 4.00
2866 4740 3.701205 TGGCAGAGATTTGAACTAGCA 57.299 42.857 0.00 0.00 0.00 3.49
2881 4755 0.755079 TAGCATGCTGTAGAGGGCTG 59.245 55.000 30.42 0.00 33.10 4.85
3000 4876 2.231235 GCCCCAAAATGTCCTGTACAAG 59.769 50.000 0.00 0.00 42.70 3.16
3095 4987 4.488770 TCATGGCATGTACTACCTCCATA 58.511 43.478 25.62 0.00 33.42 2.74
3096 4988 4.904853 TCATGGCATGTACTACCTCCATAA 59.095 41.667 25.62 0.00 33.42 1.90
3236 5143 7.559590 AGAATGGCTTCACAGTATAATGTTC 57.440 36.000 2.43 0.00 33.56 3.18
3580 5524 0.540365 ATTGGCAGGTTCCTGGTGTG 60.540 55.000 18.81 0.00 34.85 3.82
3780 5740 3.782523 ACCAAGAATCTGATTAGCCCTGA 59.217 43.478 2.28 0.00 0.00 3.86
3834 5795 6.712547 CAGGTTCCTTGATTTAGGATGGATAC 59.287 42.308 0.00 0.00 43.66 2.24
3960 5925 5.767816 AAGTGTATGGTTGTCCTTTGTTC 57.232 39.130 0.00 0.00 34.23 3.18
3995 5960 1.043022 CCAACTTCCCAGCTTGCTTT 58.957 50.000 0.00 0.00 0.00 3.51
4008 5974 5.042593 CAGCTTGCTTTGTGTTGTTAATGA 58.957 37.500 0.00 0.00 0.00 2.57
4015 5999 5.344128 GCTTTGTGTTGTTAATGATGCAGAG 59.656 40.000 0.00 0.00 0.00 3.35
4069 6053 6.646240 GTGTTGTCATATGGTTCAATGCTTTT 59.354 34.615 2.13 0.00 0.00 2.27
4110 6102 0.031178 CTCAGTTGCCAAGCCAACAC 59.969 55.000 7.65 0.00 45.73 3.32
4117 6110 1.005867 CCAAGCCAACACATGTGCC 60.006 57.895 25.68 11.45 0.00 5.01
4122 10129 2.427245 CAACACATGTGCCGCGTG 60.427 61.111 25.68 11.88 39.90 5.34
4141 10151 6.402334 CCGCGTGTTGGATTTTGTAAACTATA 60.402 38.462 4.92 0.00 0.00 1.31
4175 16830 2.929531 ATGAGCTCAGTGTACTCGTG 57.070 50.000 22.96 0.00 32.98 4.35
4470 17161 1.472376 CGAATGGAGGAGACAGGAAGC 60.472 57.143 0.00 0.00 0.00 3.86
4474 17165 1.671901 GGAGGAGACAGGAAGCGAGG 61.672 65.000 0.00 0.00 0.00 4.63
4493 17186 2.240667 AGGCAGAGTTTATCACCATGCT 59.759 45.455 0.00 0.00 37.46 3.79
4497 17190 4.509600 GCAGAGTTTATCACCATGCTCTAC 59.490 45.833 0.00 0.00 35.41 2.59
4572 17265 1.827399 CGGTTCACCTGGGTGCTAGT 61.827 60.000 14.35 0.00 45.04 2.57
4593 17286 5.815581 AGTTTGTAGTAGCATGATGGGAAA 58.184 37.500 0.00 0.00 0.00 3.13
4611 17304 4.463891 GGGAAATGTTGACTCACATTGGAT 59.536 41.667 0.00 0.00 44.95 3.41
4638 17331 7.817962 CCACATAGAATAATTTAGGAGGGTACG 59.182 40.741 0.00 0.00 0.00 3.67
4660 17353 2.575735 TGCTGGGGAATGTGAGATAACA 59.424 45.455 0.00 0.00 0.00 2.41
4665 17358 6.078456 TGGGGAATGTGAGATAACAATCTT 57.922 37.500 0.00 0.00 31.80 2.40
4676 17369 9.003658 GTGAGATAACAATCTTCCTCAAAAGAA 57.996 33.333 0.00 0.00 38.69 2.52
4680 17373 3.821033 ACAATCTTCCTCAAAAGAACCCG 59.179 43.478 0.00 0.00 38.69 5.28
4685 17378 1.142060 TCCTCAAAAGAACCCGCTTGA 59.858 47.619 0.00 0.00 0.00 3.02
4713 17406 9.614792 GTTGTATAAGTAGAATCATCAAGGGTT 57.385 33.333 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 4.010349 CTGGTAGGGTTGAAATGAAGGAC 58.990 47.826 0.00 0.00 0.00 3.85
126 128 1.455849 CACCTGTGGCCTCCTTTGA 59.544 57.895 3.32 0.00 0.00 2.69
180 184 5.639931 GCTAGTCTTCTCCTTACAACAAAGG 59.360 44.000 0.00 0.00 46.35 3.11
189 193 7.179338 AGTTTCTCATTGCTAGTCTTCTCCTTA 59.821 37.037 0.00 0.00 0.00 2.69
208 215 2.333014 CCTCACAGCGAGAAGTTTCTC 58.667 52.381 11.06 11.06 45.45 2.87
214 221 1.406898 TGATAGCCTCACAGCGAGAAG 59.593 52.381 0.00 0.00 45.45 2.85
219 226 1.593750 GCCTGATAGCCTCACAGCG 60.594 63.158 0.00 0.00 38.01 5.18
270 286 0.881159 TTGTAACGCCCAACACGGAG 60.881 55.000 0.00 0.00 36.56 4.63
272 288 0.881159 TCTTGTAACGCCCAACACGG 60.881 55.000 0.00 0.00 34.00 4.94
273 289 0.938713 TTCTTGTAACGCCCAACACG 59.061 50.000 0.00 0.00 0.00 4.49
274 290 1.944709 AGTTCTTGTAACGCCCAACAC 59.055 47.619 0.00 0.00 0.00 3.32
275 291 2.335316 AGTTCTTGTAACGCCCAACA 57.665 45.000 0.00 0.00 0.00 3.33
276 292 2.159037 GCTAGTTCTTGTAACGCCCAAC 59.841 50.000 0.00 0.00 0.00 3.77
277 293 2.224329 TGCTAGTTCTTGTAACGCCCAA 60.224 45.455 0.00 0.00 0.00 4.12
279 295 2.088950 TGCTAGTTCTTGTAACGCCC 57.911 50.000 0.00 0.00 0.00 6.13
280 296 4.680171 ATTTGCTAGTTCTTGTAACGCC 57.320 40.909 0.00 0.00 0.00 5.68
281 297 5.685841 TGAATTTGCTAGTTCTTGTAACGC 58.314 37.500 5.15 0.00 0.00 4.84
282 298 8.015087 TGAATGAATTTGCTAGTTCTTGTAACG 58.985 33.333 5.15 0.00 0.00 3.18
283 299 9.677567 TTGAATGAATTTGCTAGTTCTTGTAAC 57.322 29.630 5.15 0.00 0.00 2.50
284 300 9.677567 GTTGAATGAATTTGCTAGTTCTTGTAA 57.322 29.630 5.15 0.00 0.00 2.41
285 301 8.296713 GGTTGAATGAATTTGCTAGTTCTTGTA 58.703 33.333 5.15 0.00 0.00 2.41
286 302 7.147976 GGTTGAATGAATTTGCTAGTTCTTGT 58.852 34.615 5.15 0.00 0.00 3.16
287 303 7.147312 TGGTTGAATGAATTTGCTAGTTCTTG 58.853 34.615 5.15 0.00 0.00 3.02
288 304 7.288810 TGGTTGAATGAATTTGCTAGTTCTT 57.711 32.000 5.15 0.00 0.00 2.52
289 305 6.899393 TGGTTGAATGAATTTGCTAGTTCT 57.101 33.333 5.15 0.00 0.00 3.01
290 306 7.945033 TTTGGTTGAATGAATTTGCTAGTTC 57.055 32.000 0.00 0.00 0.00 3.01
291 307 9.995003 TTATTTGGTTGAATGAATTTGCTAGTT 57.005 25.926 0.00 0.00 0.00 2.24
292 308 9.423061 GTTATTTGGTTGAATGAATTTGCTAGT 57.577 29.630 0.00 0.00 0.00 2.57
293 309 8.872845 GGTTATTTGGTTGAATGAATTTGCTAG 58.127 33.333 0.00 0.00 0.00 3.42
294 310 7.821846 GGGTTATTTGGTTGAATGAATTTGCTA 59.178 33.333 0.00 0.00 0.00 3.49
295 311 6.654582 GGGTTATTTGGTTGAATGAATTTGCT 59.345 34.615 0.00 0.00 0.00 3.91
316 332 5.072741 GGTAGCAATGATGTGATATGGGTT 58.927 41.667 0.00 0.00 0.00 4.11
346 362 7.679881 AGAAAGGGGAGGTTTTCATTTTATCAT 59.320 33.333 0.56 0.00 36.11 2.45
394 467 5.392380 GCTCGATGGTTGATTTGAAGTTGAT 60.392 40.000 0.00 0.00 0.00 2.57
399 472 4.161333 GTTGCTCGATGGTTGATTTGAAG 58.839 43.478 0.00 0.00 0.00 3.02
414 487 4.926860 TTGTGTGATTATCTGTTGCTCG 57.073 40.909 0.00 0.00 0.00 5.03
438 511 5.823861 ACTGCCCAATTCCATTACTTTTT 57.176 34.783 0.00 0.00 0.00 1.94
440 513 5.186992 GGTTACTGCCCAATTCCATTACTTT 59.813 40.000 0.00 0.00 0.00 2.66
446 519 2.917713 TGGTTACTGCCCAATTCCAT 57.082 45.000 0.00 0.00 0.00 3.41
450 523 1.895131 CTGCTTGGTTACTGCCCAATT 59.105 47.619 0.00 0.00 41.00 2.32
454 527 1.603455 TGCTGCTTGGTTACTGCCC 60.603 57.895 0.00 0.00 0.00 5.36
457 530 3.045601 ACTAGTGCTGCTTGGTTACTG 57.954 47.619 0.00 0.00 0.00 2.74
459 532 4.082136 ACTCTACTAGTGCTGCTTGGTTAC 60.082 45.833 5.39 0.00 36.93 2.50
460 533 4.087182 ACTCTACTAGTGCTGCTTGGTTA 58.913 43.478 5.39 0.00 36.93 2.85
463 536 3.697045 ACTACTCTACTAGTGCTGCTTGG 59.303 47.826 5.39 0.00 39.39 3.61
467 540 6.047870 TGTAGTACTACTCTACTAGTGCTGC 58.952 44.000 28.56 6.46 39.30 5.25
468 541 7.765360 AGTTGTAGTACTACTCTACTAGTGCTG 59.235 40.741 28.56 0.00 39.30 4.41
518 591 0.969894 CGGCTAGGGTAAGATGAGGG 59.030 60.000 0.00 0.00 0.00 4.30
604 677 2.526873 AGCGTGGAAGGGAGGTGT 60.527 61.111 0.00 0.00 0.00 4.16
606 679 3.382832 CGAGCGTGGAAGGGAGGT 61.383 66.667 0.00 0.00 0.00 3.85
617 690 2.202623 GCAATCTCCGTCGAGCGT 60.203 61.111 0.00 0.00 39.32 5.07
750 845 4.517934 CCCATGCTCCCAGCCCAG 62.518 72.222 0.00 0.00 41.51 4.45
812 920 3.458163 TCTAACTGGGCCGCTCCG 61.458 66.667 0.00 0.00 34.94 4.63
813 921 2.187163 GTCTAACTGGGCCGCTCC 59.813 66.667 0.00 0.00 0.00 4.70
814 922 2.202756 CGTCTAACTGGGCCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
815 923 4.452733 GCGTCTAACTGGGCCGCT 62.453 66.667 0.00 0.00 41.06 5.52
826 934 2.892215 TCTCTCTCTCTATCGGCGTCTA 59.108 50.000 6.85 0.00 0.00 2.59
841 949 1.688884 GCCAAGCCCCTCTCTCTCT 60.689 63.158 0.00 0.00 0.00 3.10
892 1005 1.152943 ATAGCTCTCGAGGTCGGCA 60.153 57.895 13.56 4.43 40.09 5.69
977 1093 2.708255 CTCGACTCGACGCCCTAC 59.292 66.667 0.00 0.00 0.00 3.18
984 1100 1.448922 CCATCCTCCCTCGACTCGAC 61.449 65.000 0.00 0.00 0.00 4.20
989 1105 1.382695 TTCCCCATCCTCCCTCGAC 60.383 63.158 0.00 0.00 0.00 4.20
1069 1185 1.006102 AACGGCGGACTCACTTCTG 60.006 57.895 13.24 0.00 0.00 3.02
1082 1199 1.456296 AAATCGTAAAGGGGAACGGC 58.544 50.000 0.00 0.00 39.52 5.68
1105 1222 2.224549 CCGAGCATACGAAACCACAAAA 59.775 45.455 0.00 0.00 35.09 2.44
1106 1223 1.801771 CCGAGCATACGAAACCACAAA 59.198 47.619 0.00 0.00 35.09 2.83
1107 1224 1.001068 TCCGAGCATACGAAACCACAA 59.999 47.619 0.00 0.00 35.09 3.33
1108 1225 0.604073 TCCGAGCATACGAAACCACA 59.396 50.000 0.00 0.00 35.09 4.17
1122 1239 1.680735 CTCATCTCAGGGTTCTCCGAG 59.319 57.143 0.00 0.00 41.52 4.63
1123 1240 1.285078 TCTCATCTCAGGGTTCTCCGA 59.715 52.381 0.00 0.00 41.52 4.55
1129 1246 2.636830 CGCAAATCTCATCTCAGGGTT 58.363 47.619 0.00 0.00 0.00 4.11
1130 1247 1.745141 GCGCAAATCTCATCTCAGGGT 60.745 52.381 0.30 0.00 0.00 4.34
1256 1379 0.549658 ACCCCCAAATACGTACCCCA 60.550 55.000 0.00 0.00 0.00 4.96
1261 1384 0.176219 CGAGCACCCCCAAATACGTA 59.824 55.000 0.00 0.00 0.00 3.57
1262 1385 1.078708 CGAGCACCCCCAAATACGT 60.079 57.895 0.00 0.00 0.00 3.57
1264 1387 0.252197 AGACGAGCACCCCCAAATAC 59.748 55.000 0.00 0.00 0.00 1.89
1266 1389 0.609131 CAAGACGAGCACCCCCAAAT 60.609 55.000 0.00 0.00 0.00 2.32
1286 1409 0.736325 GCGAGCACACACCGTTAGAT 60.736 55.000 0.00 0.00 0.00 1.98
1287 1410 1.372499 GCGAGCACACACCGTTAGA 60.372 57.895 0.00 0.00 0.00 2.10
1288 1411 1.617755 CTGCGAGCACACACCGTTAG 61.618 60.000 0.00 0.00 0.00 2.34
1289 1412 1.663388 CTGCGAGCACACACCGTTA 60.663 57.895 0.00 0.00 0.00 3.18
1290 1413 2.967076 CTGCGAGCACACACCGTT 60.967 61.111 0.00 0.00 0.00 4.44
1427 1552 0.032540 CCAAAAGACAGCAGGCCAAC 59.967 55.000 5.01 0.00 0.00 3.77
1430 1555 0.752658 AAACCAAAAGACAGCAGGCC 59.247 50.000 0.00 0.00 0.00 5.19
1440 1565 4.791734 GCTTCCGGTGTCTAAAACCAAAAG 60.792 45.833 0.00 0.00 37.57 2.27
1452 1577 1.833787 TTACAGGGGCTTCCGGTGTC 61.834 60.000 0.00 0.00 43.74 3.67
1453 1578 1.844289 TTACAGGGGCTTCCGGTGT 60.844 57.895 0.00 0.00 43.74 4.16
1454 1579 1.376812 GTTACAGGGGCTTCCGGTG 60.377 63.158 0.00 0.00 43.74 4.94
1456 1581 2.253403 GAGGTTACAGGGGCTTCCGG 62.253 65.000 0.00 0.00 41.52 5.14
1458 1583 0.696501 TTGAGGTTACAGGGGCTTCC 59.303 55.000 0.00 0.00 0.00 3.46
1459 1584 1.351350 AGTTGAGGTTACAGGGGCTTC 59.649 52.381 0.00 0.00 0.00 3.86
1461 1586 0.693049 CAGTTGAGGTTACAGGGGCT 59.307 55.000 0.00 0.00 0.00 5.19
1462 1587 0.690762 TCAGTTGAGGTTACAGGGGC 59.309 55.000 0.00 0.00 0.00 5.80
1466 1598 6.146837 CAGACTTGATTCAGTTGAGGTTACAG 59.853 42.308 0.00 0.00 0.00 2.74
1472 1604 5.636965 CACTACAGACTTGATTCAGTTGAGG 59.363 44.000 0.00 0.00 0.00 3.86
1481 1613 3.244078 TGGCGAACACTACAGACTTGATT 60.244 43.478 0.00 0.00 0.00 2.57
1483 1615 1.684450 TGGCGAACACTACAGACTTGA 59.316 47.619 0.00 0.00 0.00 3.02
1484 1616 2.061773 CTGGCGAACACTACAGACTTG 58.938 52.381 0.00 0.00 32.86 3.16
1489 1621 0.244994 AGCTCTGGCGAACACTACAG 59.755 55.000 0.00 0.00 44.37 2.74
1491 1787 1.071605 CAAGCTCTGGCGAACACTAC 58.928 55.000 0.00 0.00 44.37 2.73
1493 1789 0.601311 GACAAGCTCTGGCGAACACT 60.601 55.000 0.00 0.00 44.37 3.55
1500 1796 2.999355 CAGTTCTAAGACAAGCTCTGGC 59.001 50.000 0.00 0.00 39.06 4.85
1506 1802 1.996191 CGAGCCAGTTCTAAGACAAGC 59.004 52.381 0.00 0.00 0.00 4.01
1516 1812 0.868406 CTGTCCAAACGAGCCAGTTC 59.132 55.000 0.00 0.00 32.43 3.01
1522 1818 0.601311 AGTCTGCTGTCCAAACGAGC 60.601 55.000 0.00 0.00 33.11 5.03
1563 1864 5.584253 ACTTCATACTATGCTTCGAGTGT 57.416 39.130 0.00 0.00 0.00 3.55
1565 1866 9.601217 AATTAAACTTCATACTATGCTTCGAGT 57.399 29.630 0.00 0.00 0.00 4.18
1589 1890 6.491403 ACAGCTCAACCTGTCAATAAGAAAAT 59.509 34.615 0.00 0.00 42.10 1.82
1604 2122 4.755123 ACAGTGTAACATTACAGCTCAACC 59.245 41.667 4.71 0.00 43.67 3.77
1608 2126 8.808529 CAGTATAACAGTGTAACATTACAGCTC 58.191 37.037 4.71 0.00 43.67 4.09
1609 2127 8.311836 ACAGTATAACAGTGTAACATTACAGCT 58.688 33.333 4.71 3.58 43.67 4.24
1642 2160 2.256391 GCACACATGCCTGTTAGCA 58.744 52.632 9.67 0.00 46.97 3.49
1668 2186 9.416794 AGATTATGAATACATTAGCTCTTCACG 57.583 33.333 0.00 0.00 37.87 4.35
1693 2212 2.349817 GGACGTGACACAAGCAAATGAG 60.350 50.000 6.37 0.00 0.00 2.90
1710 2229 3.711086 CATGGATCTAGAACACAGGACG 58.289 50.000 0.00 0.00 0.00 4.79
1712 2231 3.378512 AGCATGGATCTAGAACACAGGA 58.621 45.455 0.00 0.00 0.00 3.86
1713 2232 3.834489 AGCATGGATCTAGAACACAGG 57.166 47.619 0.00 0.00 0.00 4.00
1714 2233 3.801050 CGAAGCATGGATCTAGAACACAG 59.199 47.826 0.00 0.00 0.00 3.66
1715 2234 3.430790 CCGAAGCATGGATCTAGAACACA 60.431 47.826 0.00 0.00 0.00 3.72
1716 2235 3.126831 CCGAAGCATGGATCTAGAACAC 58.873 50.000 0.00 0.00 0.00 3.32
1717 2236 2.766263 ACCGAAGCATGGATCTAGAACA 59.234 45.455 0.00 0.00 0.00 3.18
1718 2237 3.126831 CACCGAAGCATGGATCTAGAAC 58.873 50.000 0.00 0.00 0.00 3.01
1719 2238 2.766263 ACACCGAAGCATGGATCTAGAA 59.234 45.455 0.00 0.00 0.00 2.10
1720 2239 2.101415 CACACCGAAGCATGGATCTAGA 59.899 50.000 0.00 0.00 0.00 2.43
1721 2240 2.101415 TCACACCGAAGCATGGATCTAG 59.899 50.000 0.00 0.00 0.00 2.43
1722 2241 2.101415 CTCACACCGAAGCATGGATCTA 59.899 50.000 0.00 0.00 0.00 1.98
1723 2242 0.904649 TCACACCGAAGCATGGATCT 59.095 50.000 0.00 0.00 0.00 2.75
1724 2243 1.134699 TCTCACACCGAAGCATGGATC 60.135 52.381 0.00 0.00 0.00 3.36
1725 2244 0.904649 TCTCACACCGAAGCATGGAT 59.095 50.000 0.00 0.00 0.00 3.41
1726 2245 0.684535 TTCTCACACCGAAGCATGGA 59.315 50.000 0.00 0.00 0.00 3.41
1727 2246 1.081892 CTTCTCACACCGAAGCATGG 58.918 55.000 0.00 0.00 32.40 3.66
1744 2263 9.467796 AATAATTTCTAGCTTTAGTTGAGGCTT 57.532 29.630 0.00 0.00 36.40 4.35
1755 2285 8.665685 CGTTGTCTGGTAATAATTTCTAGCTTT 58.334 33.333 0.00 0.00 0.00 3.51
1762 2292 5.123344 AGCCACGTTGTCTGGTAATAATTTC 59.877 40.000 0.00 0.00 0.00 2.17
1763 2293 5.007682 AGCCACGTTGTCTGGTAATAATTT 58.992 37.500 0.00 0.00 0.00 1.82
1777 2307 8.539770 AATCTAATCTGAATATAGCCACGTTG 57.460 34.615 0.00 0.00 0.00 4.10
1792 2363 5.304101 AGGCTAGTGGACTGAATCTAATCTG 59.696 44.000 0.00 0.00 0.00 2.90
1793 2364 5.463154 AGGCTAGTGGACTGAATCTAATCT 58.537 41.667 0.00 0.00 0.00 2.40
1803 2374 0.976641 TGACCAAGGCTAGTGGACTG 59.023 55.000 12.14 0.00 39.62 3.51
1834 2405 7.545362 ACTTGAATACAACATCACTAGCATC 57.455 36.000 0.00 0.00 32.27 3.91
1884 2457 5.715429 GAAGCATTCAGTGACACAGATAG 57.285 43.478 8.59 2.46 46.62 2.08
1899 2472 3.703052 CTGCATAGGGGAAAAGAAGCATT 59.297 43.478 0.00 0.00 0.00 3.56
1911 2485 2.034124 CCAAATCCAACTGCATAGGGG 58.966 52.381 0.00 0.00 0.00 4.79
1977 2551 1.335324 ACTGAAAGCAAGCAATCGTGC 60.335 47.619 0.00 0.00 45.71 5.34
1978 2552 2.693797 ACTGAAAGCAAGCAATCGTG 57.306 45.000 0.00 0.00 37.60 4.35
1979 2553 4.697352 AGATAACTGAAAGCAAGCAATCGT 59.303 37.500 0.00 0.00 37.60 3.73
1981 2555 9.578439 AAATAAGATAACTGAAAGCAAGCAATC 57.422 29.630 0.00 0.00 37.60 2.67
1982 2556 9.578439 GAAATAAGATAACTGAAAGCAAGCAAT 57.422 29.630 0.00 0.00 37.60 3.56
1984 2558 7.119116 TCGAAATAAGATAACTGAAAGCAAGCA 59.881 33.333 0.00 0.00 37.60 3.91
1985 2559 7.464358 TCGAAATAAGATAACTGAAAGCAAGC 58.536 34.615 0.00 0.00 37.60 4.01
1986 2560 9.994432 AATCGAAATAAGATAACTGAAAGCAAG 57.006 29.630 0.00 0.00 37.60 4.01
1992 2566 8.946085 AGCACAAATCGAAATAAGATAACTGAA 58.054 29.630 0.00 0.00 0.00 3.02
2008 2582 4.701956 ACCAAAAGGATAGCACAAATCG 57.298 40.909 0.00 0.00 0.00 3.34
2012 2586 6.909550 ATACAAACCAAAAGGATAGCACAA 57.090 33.333 0.00 0.00 0.00 3.33
2022 2596 5.234116 GTGCAGTTCCAATACAAACCAAAAG 59.766 40.000 0.00 0.00 0.00 2.27
2027 2601 4.218417 AGATGTGCAGTTCCAATACAAACC 59.782 41.667 0.00 0.00 0.00 3.27
2028 2602 5.182001 AGAGATGTGCAGTTCCAATACAAAC 59.818 40.000 0.00 0.00 0.00 2.93
2031 2605 4.558226 AGAGATGTGCAGTTCCAATACA 57.442 40.909 0.00 0.00 0.00 2.29
2032 2606 5.163713 GGAAAGAGATGTGCAGTTCCAATAC 60.164 44.000 0.00 0.00 35.61 1.89
2033 2607 4.943705 GGAAAGAGATGTGCAGTTCCAATA 59.056 41.667 0.00 0.00 35.61 1.90
2034 2608 3.760684 GGAAAGAGATGTGCAGTTCCAAT 59.239 43.478 0.00 0.00 35.61 3.16
2035 2609 3.149196 GGAAAGAGATGTGCAGTTCCAA 58.851 45.455 0.00 0.00 35.61 3.53
2037 2613 2.746362 CAGGAAAGAGATGTGCAGTTCC 59.254 50.000 0.00 0.00 35.74 3.62
2048 2624 3.074412 GCCGAATTTGTCAGGAAAGAGA 58.926 45.455 0.00 0.00 0.00 3.10
2049 2625 2.162408 GGCCGAATTTGTCAGGAAAGAG 59.838 50.000 0.00 0.00 0.00 2.85
2055 2631 1.613437 ACAAAGGCCGAATTTGTCAGG 59.387 47.619 14.17 0.00 45.33 3.86
2064 2640 3.149005 ACCTTCATAACAAAGGCCGAA 57.851 42.857 0.00 0.00 46.03 4.30
2065 2641 2.871096 ACCTTCATAACAAAGGCCGA 57.129 45.000 0.00 0.00 46.03 5.54
2392 4238 7.814264 AGGTAATTCAAGGAAGCAGAATATG 57.186 36.000 0.00 0.00 32.11 1.78
2423 4271 2.354203 GCCAGAACCTCCACTCTAACAG 60.354 54.545 0.00 0.00 0.00 3.16
2508 4360 9.778741 TGGTCTTGATATAAATGTCATCCTTAC 57.221 33.333 0.00 0.00 0.00 2.34
2721 4593 3.055530 CGCCCTGGAAGATATTAGATGCT 60.056 47.826 0.00 0.00 34.07 3.79
2780 4654 0.457443 GCTAGCCCATGGTTGAAAGC 59.543 55.000 11.73 5.60 0.00 3.51
2783 4657 0.407528 TTGGCTAGCCCATGGTTGAA 59.592 50.000 30.81 12.89 44.89 2.69
2784 4658 0.407528 TTTGGCTAGCCCATGGTTGA 59.592 50.000 30.81 6.69 44.89 3.18
2811 4685 3.117738 TCCATGGGTGGCAAAAACATTTT 60.118 39.130 13.02 0.00 45.63 1.82
2844 4718 4.592942 TGCTAGTTCAAATCTCTGCCAAT 58.407 39.130 0.00 0.00 0.00 3.16
2866 4740 2.074948 CCCCAGCCCTCTACAGCAT 61.075 63.158 0.00 0.00 0.00 3.79
2881 4755 0.887933 CCAATATTATGGTGCGCCCC 59.112 55.000 15.15 2.15 35.65 5.80
2892 4766 8.392631 ACTCATATGGATGGCTACCAATATTA 57.607 34.615 2.13 0.00 40.93 0.98
3000 4876 3.978718 GGAAGCATCCATAAAGAGTGC 57.021 47.619 2.32 0.00 45.79 4.40
3069 4961 4.283467 GGAGGTAGTACATGCCATGATACA 59.717 45.833 12.53 0.11 35.79 2.29
3236 5143 6.416750 TGATTTTCGTATGAGTATGTGCGTAG 59.583 38.462 0.00 0.00 0.00 3.51
3580 5524 4.826733 TGTTGGGTGATATACATGATTGGC 59.173 41.667 0.00 0.00 0.00 4.52
3834 5795 0.458543 ATTCAGCACGGCAGTACTCG 60.459 55.000 0.00 0.00 0.00 4.18
3960 5925 5.582665 GGAAGTTGGCTATAGTTCAGTTCAG 59.417 44.000 0.84 0.00 0.00 3.02
3995 5960 5.062528 TGACTCTGCATCATTAACAACACA 58.937 37.500 0.00 0.00 0.00 3.72
4069 6053 1.067425 GCAATGAACCAGAAGCATGCA 60.067 47.619 21.98 0.00 0.00 3.96
4110 6102 2.198906 AATCCAACACGCGGCACATG 62.199 55.000 12.47 0.56 0.00 3.21
4117 6110 3.623863 AGTTTACAAAATCCAACACGCG 58.376 40.909 3.53 3.53 0.00 6.01
4141 10151 5.319453 TGAGCTCATTTCCTTTCAGAACAT 58.681 37.500 13.74 0.00 0.00 2.71
4470 17161 2.672961 TGGTGATAAACTCTGCCTCG 57.327 50.000 0.00 0.00 0.00 4.63
4474 17165 3.539604 AGAGCATGGTGATAAACTCTGC 58.460 45.455 0.00 0.00 36.80 4.26
4572 17265 6.186957 ACATTTCCCATCATGCTACTACAAA 58.813 36.000 0.00 0.00 0.00 2.83
4587 17280 3.573538 CCAATGTGAGTCAACATTTCCCA 59.426 43.478 14.45 0.00 46.19 4.37
4590 17283 5.183713 TGGATCCAATGTGAGTCAACATTTC 59.816 40.000 13.46 11.22 46.19 2.17
4593 17286 4.012374 GTGGATCCAATGTGAGTCAACAT 58.988 43.478 18.20 0.00 42.62 2.71
4611 17304 7.947782 ACCCTCCTAAATTATTCTATGTGGA 57.052 36.000 0.00 0.00 0.00 4.02
4638 17331 2.945668 GTTATCTCACATTCCCCAGCAC 59.054 50.000 0.00 0.00 0.00 4.40
4660 17353 2.820197 GCGGGTTCTTTTGAGGAAGATT 59.180 45.455 0.00 0.00 35.70 2.40
4665 17358 1.142060 TCAAGCGGGTTCTTTTGAGGA 59.858 47.619 0.00 0.00 0.00 3.71
4676 17369 4.216411 ACTTATACAACATCAAGCGGGT 57.784 40.909 0.00 0.00 0.00 5.28
4685 17378 9.784531 CCCTTGATGATTCTACTTATACAACAT 57.215 33.333 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.