Multiple sequence alignment - TraesCS2A01G582500

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 TraesCS2A01G582500 chr2A 100.000 7742 0 0 1 7742 774848332 774856073 0.000000e+00 14297
1 TraesCS2A01G582500 chr2A 91.463 82 6 1 3345 3426 350778847 350778927 2.280000e-20 111
2 TraesCS2A01G582500 chr2D 96.166 3730 87 20 3967 7683 650063364 650059678 0.000000e+00 6045
3 TraesCS2A01G582500 chr2D 92.506 3109 122 61 432 3476 650067226 650064165 0.000000e+00 4348
4 TraesCS2A01G582500 chr2D 96.903 452 11 1 3477 3925 650063811 650063360 0.000000e+00 754
5 TraesCS2A01G582500 chr2D 86.550 342 18 12 1 335 650068623 650068303 1.240000e-92 351
6 TraesCS2A01G582500 chr2D 91.463 82 6 1 3345 3426 271501900 271501820 2.280000e-20 111
7 TraesCS2A01G582500 chr2B 88.473 2455 133 47 442 2785 786040342 786037927 0.000000e+00 2828
8 TraesCS2A01G582500 chr2B 90.057 1760 108 27 2585 4322 786037936 786036222 0.000000e+00 2218
9 TraesCS2A01G582500 chr2B 89.294 1644 79 36 6070 7681 786034423 786032845 0.000000e+00 1971
10 TraesCS2A01G582500 chr2B 90.940 1159 65 22 4321 5471 786036128 786035002 0.000000e+00 1522
11 TraesCS2A01G582500 chr2B 90.669 493 34 7 7254 7742 786027810 786027326 0.000000e+00 645
12 TraesCS2A01G582500 chr2B 85.481 489 54 11 5596 6072 786034967 786034484 1.940000e-135 494
13 TraesCS2A01G582500 chr2B 86.264 182 19 3 2357 2532 189767765 189767584 7.930000e-45 193
14 TraesCS2A01G582500 chrUn 100.000 414 0 0 2926 3339 477385026 477384613 0.000000e+00 765
15 TraesCS2A01G582500 chr7A 79.832 357 59 11 2989 3339 477025448 477025099 1.670000e-61 248
16 TraesCS2A01G582500 chr7A 86.286 175 16 4 2358 2532 323417086 323416920 4.770000e-42 183
17 TraesCS2A01G582500 chr7A 87.654 162 15 3 3331 3487 350571400 350571239 4.770000e-42 183
18 TraesCS2A01G582500 chr7D 79.609 358 58 12 2989 3339 414520216 414519867 7.760000e-60 243
19 TraesCS2A01G582500 chr7D 86.076 158 19 3 3332 3488 166465593 166465748 4.810000e-37 167
20 TraesCS2A01G582500 chr1B 89.840 187 17 2 2348 2532 356985259 356985445 1.000000e-58 239
21 TraesCS2A01G582500 chr7B 79.272 357 61 11 2989 3339 428966556 428966207 3.610000e-58 237
22 TraesCS2A01G582500 chr7B 88.608 158 18 0 2358 2515 642208406 642208563 7.930000e-45 193
23 TraesCS2A01G582500 chr3D 78.116 329 34 20 3833 4137 611796467 611796153 2.870000e-39 174
24 TraesCS2A01G582500 chr3D 92.708 96 7 0 3707 3802 611796557 611796462 1.050000e-28 139
25 TraesCS2A01G582500 chr3B 86.164 159 17 5 3332 3488 610228556 610228711 4.810000e-37 167
26 TraesCS2A01G582500 chr3A 88.372 129 13 2 3899 4027 746543788 746543662 3.740000e-33 154
27 TraesCS2A01G582500 chr3A 94.595 74 2 2 4091 4164 746538599 746538528 6.350000e-21 113


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 TraesCS2A01G582500 chr2A 774848332 774856073 7741 False 14297.0 14297 100.00000 1 7742 1 chr2A.!!$F2 7741
1 TraesCS2A01G582500 chr2D 650059678 650068623 8945 True 2874.5 6045 93.03125 1 7683 4 chr2D.!!$R2 7682
2 TraesCS2A01G582500 chr2B 786032845 786040342 7497 True 1806.6 2828 88.84900 442 7681 5 chr2B.!!$R3 7239

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
65 67 0.030908 CTATCTCGTCCGTGCCTTCC 59.969 60.000 0.00 0.00 0.00 3.46 F
704 1735 0.033601 TGGTGAGAGAGGAGAGAGCC 60.034 60.000 0.00 0.00 0.00 4.70 F
1227 2308 0.179163 CTTCCGCGATTTTTGCTCCC 60.179 55.000 8.23 0.00 0.00 4.30 F
2296 3441 0.891373 TCTGTCTGTAGCAGGACAGC 59.109 55.000 15.54 10.21 45.44 4.40 F
4052 5751 1.202417 CGCCTCTAACATCACCGTGAT 60.202 52.381 8.28 8.28 37.65 3.06 F
4377 6174 2.103094 TGAAGATATTGACCTGCCCTCG 59.897 50.000 0.00 0.00 0.00 4.63 F
5631 7431 3.876309 AAACAGGCCTCTTTCCTAACA 57.124 42.857 0.00 0.00 31.52 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1135 2211 0.464870 TCTCGAGAGCTAGTAGCCGT 59.535 55.000 18.65 6.04 43.77 5.68 R
1968 3109 0.541392 TGCTGTCTCACACTGGTTGT 59.459 50.000 0.00 0.00 39.97 3.32 R
2551 3697 1.540363 GGCGACTCACAGTGGAAAAGA 60.540 52.381 0.00 0.00 0.00 2.52 R
4218 5917 1.551430 TGATGCCAATTGCCAAGGAAG 59.449 47.619 0.00 0.00 40.16 3.46 R
5889 7700 2.030363 TGGCTGTTCTTAAAACATGCCG 60.030 45.455 21.30 9.12 42.24 5.69 R
6113 7988 1.538687 GCTGCAGCAAGGGGACAAAT 61.539 55.000 33.36 0.00 41.59 2.32 R
7325 9228 0.526662 GAGGGACGACGTTGTCTCAT 59.473 55.000 32.40 20.97 42.01 2.90 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
46 48 0.533755 CGATGATGGAGCTGGTTCCC 60.534 60.000 0.00 0.00 36.35 3.97
63 65 1.392710 CCCTATCTCGTCCGTGCCTT 61.393 60.000 0.00 0.00 0.00 4.35
65 67 0.030908 CTATCTCGTCCGTGCCTTCC 59.969 60.000 0.00 0.00 0.00 3.46
145 152 2.222445 ACGTGCAACCAGTTTAATCGTC 59.778 45.455 0.00 0.00 0.00 4.20
206 213 3.693245 CGATCACCGCTTTCGAGG 58.307 61.111 0.00 0.00 38.10 4.63
207 214 1.138883 CGATCACCGCTTTCGAGGA 59.861 57.895 0.00 0.00 38.10 3.71
208 215 0.457853 CGATCACCGCTTTCGAGGAA 60.458 55.000 0.00 0.00 38.10 3.36
209 216 1.802880 CGATCACCGCTTTCGAGGAAT 60.803 52.381 0.00 0.00 38.10 3.01
210 217 1.594862 GATCACCGCTTTCGAGGAATG 59.405 52.381 0.00 0.00 38.10 2.67
211 218 0.606096 TCACCGCTTTCGAGGAATGA 59.394 50.000 0.00 0.00 38.10 2.57
221 228 5.399596 GCTTTCGAGGAATGAAAAAGTGAAC 59.600 40.000 0.00 0.00 35.11 3.18
255 262 2.443958 TCGGTCCATCTCATCTCAGT 57.556 50.000 0.00 0.00 0.00 3.41
256 263 2.739943 TCGGTCCATCTCATCTCAGTT 58.260 47.619 0.00 0.00 0.00 3.16
257 264 3.099905 TCGGTCCATCTCATCTCAGTTT 58.900 45.455 0.00 0.00 0.00 2.66
258 265 3.118992 TCGGTCCATCTCATCTCAGTTTG 60.119 47.826 0.00 0.00 0.00 2.93
259 266 2.941720 GGTCCATCTCATCTCAGTTTGC 59.058 50.000 0.00 0.00 0.00 3.68
260 267 2.606725 GTCCATCTCATCTCAGTTTGCG 59.393 50.000 0.00 0.00 0.00 4.85
261 268 2.234661 TCCATCTCATCTCAGTTTGCGT 59.765 45.455 0.00 0.00 0.00 5.24
273 280 2.981805 CAGTTTGCGTTTGTCATCATGG 59.018 45.455 0.00 0.00 0.00 3.66
275 282 0.243365 TTGCGTTTGTCATCATGGCC 59.757 50.000 0.00 0.00 0.00 5.36
295 302 2.813908 CGTACGCACCCAAGAGCC 60.814 66.667 0.52 0.00 0.00 4.70
297 304 1.078426 GTACGCACCCAAGAGCCAT 60.078 57.895 0.00 0.00 0.00 4.40
299 306 1.264749 TACGCACCCAAGAGCCATCT 61.265 55.000 0.00 0.00 37.39 2.90
301 308 0.107703 CGCACCCAAGAGCCATCTTA 60.108 55.000 0.00 0.00 44.15 2.10
302 309 1.475751 CGCACCCAAGAGCCATCTTAT 60.476 52.381 0.00 0.00 44.15 1.73
303 310 2.225467 GCACCCAAGAGCCATCTTATC 58.775 52.381 0.00 0.00 44.15 1.75
306 313 3.135348 CACCCAAGAGCCATCTTATCTCA 59.865 47.826 0.00 0.00 44.15 3.27
323 330 9.553064 TCTTATCTCAGATAAAGATGGAAAAGC 57.447 33.333 8.50 0.00 35.20 3.51
324 331 9.558396 CTTATCTCAGATAAAGATGGAAAAGCT 57.442 33.333 8.50 0.00 35.20 3.74
335 342 5.006386 AGATGGAAAAGCTAGTGAAAGTGG 58.994 41.667 0.00 0.00 0.00 4.00
347 967 2.554462 GTGAAAGTGGGCCTTCTTTCTC 59.446 50.000 32.49 28.72 45.36 2.87
348 968 2.163509 GAAAGTGGGCCTTCTTTCTCC 58.836 52.381 29.29 15.80 43.26 3.71
349 969 0.036875 AAGTGGGCCTTCTTTCTCCG 59.963 55.000 4.53 0.00 0.00 4.63
350 970 1.128188 AGTGGGCCTTCTTTCTCCGT 61.128 55.000 4.53 0.00 0.00 4.69
351 971 0.673956 GTGGGCCTTCTTTCTCCGTC 60.674 60.000 4.53 0.00 0.00 4.79
353 973 0.108089 GGGCCTTCTTTCTCCGTCTC 60.108 60.000 0.84 0.00 0.00 3.36
355 975 1.079317 GCCTTCTTTCTCCGTCTCGC 61.079 60.000 0.00 0.00 0.00 5.03
356 976 0.798771 CCTTCTTTCTCCGTCTCGCG 60.799 60.000 0.00 0.00 40.95 5.87
357 977 1.406970 CTTCTTTCTCCGTCTCGCGC 61.407 60.000 0.00 0.00 39.71 6.86
358 978 2.814183 TTCTTTCTCCGTCTCGCGCC 62.814 60.000 0.00 0.00 39.71 6.53
359 979 3.626680 CTTTCTCCGTCTCGCGCCA 62.627 63.158 0.00 0.00 39.71 5.69
372 992 2.049248 CGCCACGCCATTTTGCTT 60.049 55.556 0.00 0.00 0.00 3.91
373 993 2.374226 CGCCACGCCATTTTGCTTG 61.374 57.895 0.00 0.00 0.00 4.01
375 995 1.300775 CCACGCCATTTTGCTTGCA 60.301 52.632 0.00 0.00 0.00 4.08
376 996 0.879400 CCACGCCATTTTGCTTGCAA 60.879 50.000 3.70 3.70 0.00 4.08
377 997 0.509499 CACGCCATTTTGCTTGCAAG 59.491 50.000 22.44 22.44 0.00 4.01
387 1340 1.580942 GCTTGCAAGCCGTGATTCA 59.419 52.632 36.21 0.00 46.20 2.57
391 1344 0.597568 TGCAAGCCGTGATTCAAAGG 59.402 50.000 5.35 5.35 0.00 3.11
413 1366 3.707102 GGACCCTCTTTGACTAGCAGTAT 59.293 47.826 0.00 0.00 0.00 2.12
420 1373 7.310113 CCCTCTTTGACTAGCAGTATTATAGGG 60.310 44.444 0.00 0.00 31.83 3.53
421 1374 7.233757 CCTCTTTGACTAGCAGTATTATAGGGT 59.766 40.741 0.00 0.00 0.00 4.34
422 1375 9.298250 CTCTTTGACTAGCAGTATTATAGGGTA 57.702 37.037 0.00 0.00 0.00 3.69
423 1376 9.298250 TCTTTGACTAGCAGTATTATAGGGTAG 57.702 37.037 7.88 7.88 37.37 3.18
424 1377 8.418597 TTTGACTAGCAGTATTATAGGGTAGG 57.581 38.462 11.90 0.00 36.07 3.18
429 1382 8.110908 ACTAGCAGTATTATAGGGTAGGAAGAG 58.889 40.741 11.90 0.00 36.07 2.85
434 1387 5.986501 ATTATAGGGTAGGAAGAGAAGCG 57.013 43.478 0.00 0.00 0.00 4.68
440 1393 1.248785 TAGGAAGAGAAGCGGCGTGT 61.249 55.000 9.37 0.00 0.00 4.49
471 1462 4.973663 CGTTTTAGGCGGGCATTTATTTAG 59.026 41.667 3.78 0.00 0.00 1.85
473 1464 6.334989 GTTTTAGGCGGGCATTTATTTAGTT 58.665 36.000 3.78 0.00 0.00 2.24
474 1465 7.482474 GTTTTAGGCGGGCATTTATTTAGTTA 58.518 34.615 3.78 0.00 0.00 2.24
475 1466 6.870971 TTAGGCGGGCATTTATTTAGTTAG 57.129 37.500 3.78 0.00 0.00 2.34
476 1467 3.568430 AGGCGGGCATTTATTTAGTTAGC 59.432 43.478 3.78 0.00 0.00 3.09
477 1468 3.551551 GCGGGCATTTATTTAGTTAGCG 58.448 45.455 0.00 0.00 0.00 4.26
519 1516 2.093106 CGAGTAGTGGAGCAAGTACCT 58.907 52.381 0.00 0.00 0.00 3.08
520 1517 2.159366 CGAGTAGTGGAGCAAGTACCTG 60.159 54.545 0.00 0.00 0.00 4.00
538 1555 2.285756 CCTGAAATTACCGCGCGATTAA 59.714 45.455 34.63 26.40 0.00 1.40
543 1560 0.108233 TTACCGCGCGATTAAACCCT 60.108 50.000 34.63 3.85 0.00 4.34
544 1561 0.743688 TACCGCGCGATTAAACCCTA 59.256 50.000 34.63 0.00 0.00 3.53
545 1562 0.807275 ACCGCGCGATTAAACCCTAC 60.807 55.000 34.63 0.00 0.00 3.18
546 1563 0.529119 CCGCGCGATTAAACCCTACT 60.529 55.000 34.63 0.00 0.00 2.57
547 1564 1.269206 CCGCGCGATTAAACCCTACTA 60.269 52.381 34.63 0.00 0.00 1.82
548 1565 2.049228 CGCGCGATTAAACCCTACTAG 58.951 52.381 28.94 0.00 0.00 2.57
549 1566 2.401351 GCGCGATTAAACCCTACTAGG 58.599 52.381 12.10 0.00 34.30 3.02
550 1567 2.401351 CGCGATTAAACCCTACTAGGC 58.599 52.381 0.00 0.00 32.73 3.93
552 1569 2.549563 GCGATTAAACCCTACTAGGCCC 60.550 54.545 0.00 0.00 32.73 5.80
553 1570 2.701951 CGATTAAACCCTACTAGGCCCA 59.298 50.000 0.00 0.00 32.73 5.36
554 1571 3.493873 CGATTAAACCCTACTAGGCCCAC 60.494 52.174 0.00 0.00 32.73 4.61
555 1572 2.645951 TAAACCCTACTAGGCCCACA 57.354 50.000 0.00 0.00 32.73 4.17
556 1573 1.286248 AAACCCTACTAGGCCCACAG 58.714 55.000 0.00 0.00 32.73 3.66
596 1613 5.114081 ACAGGCATGTCGGTATAAAACTAC 58.886 41.667 0.00 0.00 32.99 2.73
635 1665 1.597663 ACAGCGGCATTAGCGAATAAC 59.402 47.619 1.45 0.00 43.41 1.89
701 1732 1.076438 TGGTGGTGAGAGAGGAGAGA 58.924 55.000 0.00 0.00 0.00 3.10
702 1733 1.005332 TGGTGGTGAGAGAGGAGAGAG 59.995 57.143 0.00 0.00 0.00 3.20
703 1734 1.102978 GTGGTGAGAGAGGAGAGAGC 58.897 60.000 0.00 0.00 0.00 4.09
704 1735 0.033601 TGGTGAGAGAGGAGAGAGCC 60.034 60.000 0.00 0.00 0.00 4.70
707 1738 0.843309 TGAGAGAGGAGAGAGCCGAT 59.157 55.000 0.00 0.00 0.00 4.18
712 1743 2.038557 GAGAGGAGAGAGCCGATAGAGT 59.961 54.545 0.00 0.00 39.76 3.24
745 1776 3.591835 GGCGAGAGAGAGCCGAGG 61.592 72.222 0.00 0.00 44.22 4.63
982 2058 4.144727 GGCGAGGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1009 2085 4.562425 GGATCGGAATGGGCGCCA 62.562 66.667 30.85 15.30 38.19 5.69
1103 2179 4.742201 CGGTGCGTGCCTACTGCT 62.742 66.667 0.00 0.00 42.00 4.24
1104 2180 2.815647 GGTGCGTGCCTACTGCTC 60.816 66.667 0.00 0.00 42.00 4.26
1131 2207 2.821688 GCTCCATGCTCGCTTGCTC 61.822 63.158 0.00 0.00 38.95 4.26
1132 2208 2.510012 TCCATGCTCGCTTGCTCG 60.510 61.111 0.00 0.00 0.00 5.03
1133 2209 4.233635 CCATGCTCGCTTGCTCGC 62.234 66.667 0.00 0.00 0.00 5.03
1135 2211 4.765449 ATGCTCGCTTGCTCGCCA 62.765 61.111 0.00 0.00 0.00 5.69
1227 2308 0.179163 CTTCCGCGATTTTTGCTCCC 60.179 55.000 8.23 0.00 0.00 4.30
1231 2312 1.701545 CGCGATTTTTGCTCCCGCTA 61.702 55.000 0.00 0.00 43.19 4.26
1245 2327 2.797278 CGCTAGCCCCCGAGATTGT 61.797 63.158 9.66 0.00 0.00 2.71
1314 2413 2.283604 ATTTGGGGGCGGTTGACC 60.284 61.111 0.00 0.00 45.75 4.02
1346 2445 3.562182 CCCAAGGGTTATTATTCGCCTT 58.438 45.455 0.00 0.00 0.00 4.35
1709 2831 3.250744 TCTAGTAACAATGTGCGTCTGC 58.749 45.455 0.00 0.00 43.20 4.26
1711 2833 2.069273 AGTAACAATGTGCGTCTGCTC 58.931 47.619 0.00 0.00 43.34 4.26
1746 2871 3.857052 CCTTGATGCCACTAGTTCGTTA 58.143 45.455 0.00 0.00 0.00 3.18
1876 3017 4.486125 ACTTGTTTTGCTTTTGGATGGT 57.514 36.364 0.00 0.00 0.00 3.55
2074 3215 5.445010 GGCAAATCAACGATTCAGCATTTTC 60.445 40.000 12.94 0.00 35.87 2.29
2107 3248 6.639632 ATTGCGTTGCTATCATAATTTCCT 57.360 33.333 0.00 0.00 0.00 3.36
2211 3354 5.510520 CCCTTCTGCTATCAGTTATCTCACC 60.511 48.000 0.00 0.00 41.10 4.02
2215 3358 5.767665 TCTGCTATCAGTTATCTCACCTCTC 59.232 44.000 0.00 0.00 41.10 3.20
2296 3441 0.891373 TCTGTCTGTAGCAGGACAGC 59.109 55.000 15.54 10.21 45.44 4.40
2378 3524 4.384208 GCTTGACCCATACAGTTCCAGTAT 60.384 45.833 0.00 0.00 32.62 2.12
2551 3697 4.451096 CCTAACGACACACTAGCAAAACAT 59.549 41.667 0.00 0.00 0.00 2.71
2712 3858 7.502226 TGGTCTCTGTTCATGTCTAAATTTTGT 59.498 33.333 0.00 0.00 0.00 2.83
2924 4246 2.638363 GACCTTTAAGTGGACTGGGACT 59.362 50.000 3.95 0.00 0.00 3.85
3382 4704 7.559897 TGCTAAAACCCTATAGCTTGCTTTTAT 59.440 33.333 0.00 0.00 43.85 1.40
3457 4779 4.627035 GCACTGAACTTTCTTGCAAAGTTT 59.373 37.500 14.51 0.00 46.81 2.66
3591 5285 8.424274 TGTCATAGTATAGCACTGTTTTCATG 57.576 34.615 0.00 0.00 38.24 3.07
3610 5304 6.174720 TCATGACACCCTACATTAGATTCC 57.825 41.667 0.00 0.00 0.00 3.01
3710 5405 6.288294 TGGCTTACAATATGATCTGTACCAC 58.712 40.000 0.00 0.00 0.00 4.16
3734 5429 5.289675 CGAATGTACCTTGAGATCTTCACAC 59.710 44.000 0.00 0.00 34.94 3.82
3735 5430 5.745312 ATGTACCTTGAGATCTTCACACA 57.255 39.130 0.00 0.00 34.94 3.72
3845 5543 4.721776 AGAGGATATTGACAGTTTGCCCTA 59.278 41.667 0.00 0.00 0.00 3.53
3897 5596 5.587289 TCACAACCAAGCATGTTAACTTTC 58.413 37.500 7.22 0.00 0.00 2.62
4013 5712 6.656632 TGCTCCCAAAAATAACACATTGTA 57.343 33.333 0.00 0.00 0.00 2.41
4052 5751 1.202417 CGCCTCTAACATCACCGTGAT 60.202 52.381 8.28 8.28 37.65 3.06
4327 6027 3.579709 ACTGCTATAGTATGTCATGCGC 58.420 45.455 0.00 0.00 38.04 6.09
4377 6174 2.103094 TGAAGATATTGACCTGCCCTCG 59.897 50.000 0.00 0.00 0.00 4.63
4991 6789 9.817809 TTTTCTTAGCCTGACAGTATAATACAG 57.182 33.333 0.93 0.00 0.00 2.74
4992 6790 8.534954 TTCTTAGCCTGACAGTATAATACAGT 57.465 34.615 0.93 0.00 0.00 3.55
4993 6791 9.636789 TTCTTAGCCTGACAGTATAATACAGTA 57.363 33.333 0.93 0.00 0.00 2.74
4994 6792 9.064706 TCTTAGCCTGACAGTATAATACAGTAC 57.935 37.037 0.93 0.00 0.00 2.73
4995 6793 8.756486 TTAGCCTGACAGTATAATACAGTACA 57.244 34.615 0.93 0.00 0.00 2.90
5458 7258 7.148590 GCATTTTGGTTGATTGGATTGAAGTAC 60.149 37.037 0.00 0.00 0.00 2.73
5481 7281 5.706369 ACGTATATCACATACTCCCTCTGTC 59.294 44.000 0.00 0.00 0.00 3.51
5503 7303 9.529325 CTGTCCATCAATATAAGACGTTTTAGA 57.471 33.333 4.75 0.06 0.00 2.10
5504 7304 9.529325 TGTCCATCAATATAAGACGTTTTAGAG 57.471 33.333 4.75 0.00 0.00 2.43
5505 7305 9.745880 GTCCATCAATATAAGACGTTTTAGAGA 57.254 33.333 4.75 0.94 0.00 3.10
5506 7306 9.745880 TCCATCAATATAAGACGTTTTAGAGAC 57.254 33.333 4.75 0.00 0.00 3.36
5507 7307 9.751542 CCATCAATATAAGACGTTTTAGAGACT 57.248 33.333 4.75 0.00 0.00 3.24
5513 7313 7.870588 ATAAGACGTTTTAGAGACTTGTGAC 57.129 36.000 4.75 0.00 0.00 3.67
5514 7314 5.258456 AGACGTTTTAGAGACTTGTGACA 57.742 39.130 0.00 0.00 0.00 3.58
5517 7317 5.416947 ACGTTTTAGAGACTTGTGACAAGT 58.583 37.500 29.08 29.08 0.00 3.16
5527 7327 5.964070 GACTTGTGACAAGTCTCTAAAACG 58.036 41.667 37.66 10.48 42.44 3.60
5550 7350 6.127168 ACGTTGTATATTGATGAACAGAGGGA 60.127 38.462 0.00 0.00 0.00 4.20
5580 7380 9.136952 TCTTTTAGCGAGAAGTTATAGTGTTTC 57.863 33.333 0.00 0.00 0.00 2.78
5631 7431 3.876309 AAACAGGCCTCTTTCCTAACA 57.124 42.857 0.00 0.00 31.52 2.41
5866 7674 4.757149 AGAAGAGGAATGTCAAAACCTTCG 59.243 41.667 0.00 0.00 35.33 3.79
5979 7791 8.045176 ACATTCTCTTGCCTAATCTTGTAAAC 57.955 34.615 0.00 0.00 0.00 2.01
5983 7795 6.810182 TCTCTTGCCTAATCTTGTAAACGTAC 59.190 38.462 0.00 0.00 0.00 3.67
6033 7845 5.670361 TCCTTTCCTTAAGCCCTATGTACAT 59.330 40.000 13.93 13.93 32.19 2.29
6113 7988 9.920133 TTAAAATTGCTTTGCTGTTACATGATA 57.080 25.926 0.00 0.00 0.00 2.15
6365 8247 5.105997 CCATTGGCTCTCCTAAAGTTCAAAG 60.106 44.000 0.00 0.00 0.00 2.77
6806 8690 8.028938 CCAGGTATTGTCTTTTACCAAATCTTG 58.971 37.037 2.29 0.00 40.33 3.02
7069 8964 6.020984 TGAAGCGTTTCGAATATCATTGTTG 58.979 36.000 7.53 0.00 36.04 3.33
7271 9171 1.537202 GAATGGACGAAGCAGCTGTTT 59.463 47.619 16.33 16.33 0.00 2.83
7325 9228 2.749076 AGCTTCTTATGATTTGCGTGCA 59.251 40.909 0.00 0.00 0.00 4.57
7326 9229 3.379372 AGCTTCTTATGATTTGCGTGCAT 59.621 39.130 0.00 0.00 0.00 3.96
7329 9232 4.541085 TCTTATGATTTGCGTGCATGAG 57.459 40.909 10.93 0.00 0.00 2.90
7332 9235 1.521580 TGATTTGCGTGCATGAGACA 58.478 45.000 10.93 0.00 0.00 3.41
7345 9248 1.212229 GAGACAACGTCGTCCCTCC 59.788 63.158 2.29 0.00 37.67 4.30
7420 9324 7.230510 TGCCATATACATTGAAGGGTGAATAAC 59.769 37.037 0.00 0.00 0.00 1.89
7436 9340 2.323999 TAACCCCCGTAGACAGGAAA 57.676 50.000 0.00 0.00 0.00 3.13
7464 9369 2.073816 TGGAAGCGAAAAATCCGTCTC 58.926 47.619 0.00 0.00 35.96 3.36
7484 9389 0.399075 GGTTCCTCCCACCGAAGAAA 59.601 55.000 0.00 0.00 0.00 2.52
7487 9392 1.198759 TCCTCCCACCGAAGAAAGGG 61.199 60.000 0.00 0.00 42.86 3.95
7488 9393 1.377333 CTCCCACCGAAGAAAGGGC 60.377 63.158 0.00 0.00 41.22 5.19
7489 9394 2.746277 CCCACCGAAGAAAGGGCG 60.746 66.667 0.00 0.00 33.91 6.13
7494 9399 1.069227 CACCGAAGAAAGGGCGAAAAG 60.069 52.381 0.00 0.00 0.00 2.27
7495 9400 1.202722 ACCGAAGAAAGGGCGAAAAGA 60.203 47.619 0.00 0.00 0.00 2.52
7496 9401 1.877443 CCGAAGAAAGGGCGAAAAGAA 59.123 47.619 0.00 0.00 0.00 2.52
7497 9402 2.095718 CCGAAGAAAGGGCGAAAAGAAG 60.096 50.000 0.00 0.00 0.00 2.85
7560 9469 0.108138 CCTTTTCGGAGCAGGATCGT 60.108 55.000 0.00 0.00 33.16 3.73
7564 9473 0.895530 TTCGGAGCAGGATCGTCTTT 59.104 50.000 0.00 0.00 0.00 2.52
7590 9500 5.287674 TGAATGGTTGCCAAAAATTCTCA 57.712 34.783 12.15 0.00 36.95 3.27
7610 9520 9.666626 ATTCTCAGTTTCTATTACTACGATTCG 57.333 33.333 4.14 4.14 0.00 3.34
7611 9521 8.429493 TCTCAGTTTCTATTACTACGATTCGA 57.571 34.615 13.95 0.00 0.00 3.71
7612 9522 8.333908 TCTCAGTTTCTATTACTACGATTCGAC 58.666 37.037 13.95 0.00 0.00 4.20
7613 9523 8.206325 TCAGTTTCTATTACTACGATTCGACT 57.794 34.615 13.95 0.00 0.00 4.18
7625 9535 4.433615 ACGATTCGACTCTGTTGCAATAT 58.566 39.130 13.95 0.00 0.00 1.28
7626 9536 4.268644 ACGATTCGACTCTGTTGCAATATG 59.731 41.667 13.95 0.00 0.00 1.78
7630 9540 5.940192 TCGACTCTGTTGCAATATGTTTT 57.060 34.783 0.59 0.00 0.00 2.43
7633 9543 5.334802 CGACTCTGTTGCAATATGTTTTGGA 60.335 40.000 0.59 0.00 0.00 3.53
7639 9549 6.908825 TGTTGCAATATGTTTTGGAGAGTAC 58.091 36.000 0.59 0.00 0.00 2.73
7641 9551 7.230510 TGTTGCAATATGTTTTGGAGAGTACTT 59.769 33.333 0.59 0.00 0.00 2.24
7643 9553 6.030228 GCAATATGTTTTGGAGAGTACTTGC 58.970 40.000 0.00 0.00 0.00 4.01
7647 9557 0.685097 TTTGGAGAGTACTTGCCGCT 59.315 50.000 0.00 0.00 0.00 5.52
7650 9560 1.079503 GGAGAGTACTTGCCGCTTTG 58.920 55.000 0.00 0.00 0.00 2.77
7651 9561 0.444260 GAGAGTACTTGCCGCTTTGC 59.556 55.000 0.00 0.00 0.00 3.68
7652 9562 0.250295 AGAGTACTTGCCGCTTTGCA 60.250 50.000 0.00 0.00 40.07 4.08
7664 9576 2.476854 CCGCTTTGCAAGTTATCAGCTC 60.477 50.000 14.69 0.00 0.00 4.09
7665 9577 2.160219 CGCTTTGCAAGTTATCAGCTCA 59.840 45.455 14.69 0.00 0.00 4.26
7683 9595 8.044060 TCAGCTCATGATTTTATTTTCTCGTT 57.956 30.769 0.00 0.00 31.12 3.85
7684 9596 8.177663 TCAGCTCATGATTTTATTTTCTCGTTC 58.822 33.333 0.00 0.00 31.12 3.95
7685 9597 7.964559 CAGCTCATGATTTTATTTTCTCGTTCA 59.035 33.333 0.00 0.00 0.00 3.18
7686 9598 8.180267 AGCTCATGATTTTATTTTCTCGTTCAG 58.820 33.333 0.00 0.00 0.00 3.02
7687 9599 8.177663 GCTCATGATTTTATTTTCTCGTTCAGA 58.822 33.333 0.00 0.00 0.00 3.27
7692 9604 9.988350 TGATTTTATTTTCTCGTTCAGATTAGC 57.012 29.630 0.00 0.00 0.00 3.09
7693 9605 9.988350 GATTTTATTTTCTCGTTCAGATTAGCA 57.012 29.630 0.00 0.00 0.00 3.49
7695 9607 9.607285 TTTTATTTTCTCGTTCAGATTAGCAAC 57.393 29.630 0.00 0.00 0.00 4.17
7696 9608 5.607119 TTTTCTCGTTCAGATTAGCAACC 57.393 39.130 0.00 0.00 0.00 3.77
7697 9609 2.876091 TCTCGTTCAGATTAGCAACCG 58.124 47.619 0.00 0.00 0.00 4.44
7698 9610 1.324736 CTCGTTCAGATTAGCAACCGC 59.675 52.381 0.00 0.00 38.99 5.68
7708 9620 2.202479 GCAACCGCTGCCGATTTC 60.202 61.111 0.00 0.00 46.13 2.17
7709 9621 2.690778 GCAACCGCTGCCGATTTCT 61.691 57.895 0.00 0.00 46.13 2.52
7710 9622 1.875963 CAACCGCTGCCGATTTCTT 59.124 52.632 0.00 0.00 36.29 2.52
7711 9623 0.240945 CAACCGCTGCCGATTTCTTT 59.759 50.000 0.00 0.00 36.29 2.52
7712 9624 0.521735 AACCGCTGCCGATTTCTTTC 59.478 50.000 0.00 0.00 36.29 2.62
7713 9625 0.605319 ACCGCTGCCGATTTCTTTCA 60.605 50.000 0.00 0.00 36.29 2.69
7714 9626 0.097674 CCGCTGCCGATTTCTTTCAG 59.902 55.000 0.00 0.00 36.29 3.02
7715 9627 0.798776 CGCTGCCGATTTCTTTCAGT 59.201 50.000 0.00 0.00 36.29 3.41
7716 9628 1.197721 CGCTGCCGATTTCTTTCAGTT 59.802 47.619 0.00 0.00 36.29 3.16
7717 9629 2.726066 CGCTGCCGATTTCTTTCAGTTC 60.726 50.000 0.00 0.00 36.29 3.01
7718 9630 2.485814 GCTGCCGATTTCTTTCAGTTCT 59.514 45.455 0.00 0.00 0.00 3.01
7719 9631 3.669023 GCTGCCGATTTCTTTCAGTTCTG 60.669 47.826 0.00 0.00 0.00 3.02
7720 9632 3.476552 TGCCGATTTCTTTCAGTTCTGT 58.523 40.909 0.00 0.00 0.00 3.41
7721 9633 3.882888 TGCCGATTTCTTTCAGTTCTGTT 59.117 39.130 0.00 0.00 0.00 3.16
7722 9634 4.024048 TGCCGATTTCTTTCAGTTCTGTTC 60.024 41.667 0.00 0.00 0.00 3.18
7723 9635 4.702392 CCGATTTCTTTCAGTTCTGTTCG 58.298 43.478 0.00 0.00 0.00 3.95
7724 9636 4.211374 CCGATTTCTTTCAGTTCTGTTCGT 59.789 41.667 0.00 0.00 0.00 3.85
7725 9637 5.277345 CCGATTTCTTTCAGTTCTGTTCGTT 60.277 40.000 0.00 0.00 0.00 3.85
7726 9638 6.192360 CGATTTCTTTCAGTTCTGTTCGTTT 58.808 36.000 0.00 0.00 0.00 3.60
7727 9639 6.687105 CGATTTCTTTCAGTTCTGTTCGTTTT 59.313 34.615 0.00 0.00 0.00 2.43
7728 9640 7.304849 CGATTTCTTTCAGTTCTGTTCGTTTTG 60.305 37.037 0.00 0.00 0.00 2.44
7729 9641 5.873179 TCTTTCAGTTCTGTTCGTTTTGT 57.127 34.783 0.00 0.00 0.00 2.83
7730 9642 5.627172 TCTTTCAGTTCTGTTCGTTTTGTG 58.373 37.500 0.00 0.00 0.00 3.33
7731 9643 3.398954 TCAGTTCTGTTCGTTTTGTGC 57.601 42.857 0.00 0.00 0.00 4.57
7732 9644 3.006940 TCAGTTCTGTTCGTTTTGTGCT 58.993 40.909 0.00 0.00 0.00 4.40
7733 9645 3.100817 CAGTTCTGTTCGTTTTGTGCTG 58.899 45.455 0.00 0.00 0.00 4.41
7734 9646 2.747446 AGTTCTGTTCGTTTTGTGCTGT 59.253 40.909 0.00 0.00 0.00 4.40
7735 9647 3.936453 AGTTCTGTTCGTTTTGTGCTGTA 59.064 39.130 0.00 0.00 0.00 2.74
7736 9648 4.034048 AGTTCTGTTCGTTTTGTGCTGTAG 59.966 41.667 0.00 0.00 0.00 2.74
7737 9649 2.286833 TCTGTTCGTTTTGTGCTGTAGC 59.713 45.455 0.00 0.00 42.50 3.58
7738 9650 2.285083 TGTTCGTTTTGTGCTGTAGCT 58.715 42.857 5.38 0.00 42.66 3.32
7739 9651 2.031560 TGTTCGTTTTGTGCTGTAGCTG 59.968 45.455 5.38 0.00 42.66 4.24
7740 9652 1.948104 TCGTTTTGTGCTGTAGCTGT 58.052 45.000 5.38 0.00 42.66 4.40
7741 9653 1.597195 TCGTTTTGTGCTGTAGCTGTG 59.403 47.619 5.38 0.00 42.66 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 0.030908 GGAAGGCACGGACGAGATAG 59.969 60.000 0.00 0.00 0.00 2.08
63 65 3.702048 GTACAGCGTGGCAGGGGA 61.702 66.667 9.49 0.00 0.00 4.81
105 112 3.762992 CAGTACGTGCGTGCGTGG 61.763 66.667 14.68 0.00 45.33 4.94
131 138 3.309682 CGCATGATGACGATTAAACTGGT 59.690 43.478 0.00 0.00 0.00 4.00
198 205 5.915196 GGTTCACTTTTTCATTCCTCGAAAG 59.085 40.000 0.00 0.00 34.07 2.62
199 206 5.592688 AGGTTCACTTTTTCATTCCTCGAAA 59.407 36.000 0.00 0.00 0.00 3.46
201 208 4.714632 AGGTTCACTTTTTCATTCCTCGA 58.285 39.130 0.00 0.00 0.00 4.04
202 209 5.438761 AAGGTTCACTTTTTCATTCCTCG 57.561 39.130 0.00 0.00 35.35 4.63
221 228 1.594862 GACCGATTCGCTGATGAAAGG 59.405 52.381 0.00 0.00 36.44 3.11
255 262 1.336702 GGCCATGATGACAAACGCAAA 60.337 47.619 0.00 0.00 0.00 3.68
256 263 0.243365 GGCCATGATGACAAACGCAA 59.757 50.000 0.00 0.00 0.00 4.85
257 264 1.594194 GGGCCATGATGACAAACGCA 61.594 55.000 4.39 0.00 0.00 5.24
258 265 1.139520 GGGCCATGATGACAAACGC 59.860 57.895 4.39 0.00 0.00 4.84
259 266 0.171007 GTGGGCCATGATGACAAACG 59.829 55.000 10.70 0.00 0.00 3.60
260 267 0.171007 CGTGGGCCATGATGACAAAC 59.829 55.000 21.47 0.00 0.00 2.93
261 268 0.251121 ACGTGGGCCATGATGACAAA 60.251 50.000 31.76 0.00 0.00 2.83
273 280 4.992511 TTGGGTGCGTACGTGGGC 62.993 66.667 17.90 1.29 0.00 5.36
275 282 1.736645 CTCTTGGGTGCGTACGTGG 60.737 63.158 17.90 0.00 0.00 4.94
297 304 9.553064 GCTTTTCCATCTTTATCTGAGATAAGA 57.447 33.333 13.96 13.45 32.75 2.10
301 308 8.713036 ACTAGCTTTTCCATCTTTATCTGAGAT 58.287 33.333 0.00 0.00 34.26 2.75
302 309 7.984050 CACTAGCTTTTCCATCTTTATCTGAGA 59.016 37.037 0.00 0.00 0.00 3.27
303 310 7.984050 TCACTAGCTTTTCCATCTTTATCTGAG 59.016 37.037 0.00 0.00 0.00 3.35
306 313 9.171877 CTTTCACTAGCTTTTCCATCTTTATCT 57.828 33.333 0.00 0.00 0.00 1.98
318 325 2.158460 AGGCCCACTTTCACTAGCTTTT 60.158 45.455 0.00 0.00 0.00 2.27
320 327 1.068121 AGGCCCACTTTCACTAGCTT 58.932 50.000 0.00 0.00 0.00 3.74
321 328 1.003696 GAAGGCCCACTTTCACTAGCT 59.996 52.381 0.00 0.00 40.21 3.32
323 330 3.425162 AAGAAGGCCCACTTTCACTAG 57.575 47.619 0.00 0.00 40.21 2.57
324 331 3.751518 GAAAGAAGGCCCACTTTCACTA 58.248 45.455 30.48 0.00 46.16 2.74
335 342 0.458716 CGAGACGGAGAAAGAAGGCC 60.459 60.000 0.00 0.00 0.00 5.19
355 975 2.049248 AAGCAAAATGGCGTGGCG 60.049 55.556 0.00 0.00 39.27 5.69
356 976 2.670210 GCAAGCAAAATGGCGTGGC 61.670 57.895 3.51 0.00 42.42 5.01
357 977 0.879400 TTGCAAGCAAAATGGCGTGG 60.879 50.000 4.79 0.00 42.42 4.94
358 978 0.509499 CTTGCAAGCAAAATGGCGTG 59.491 50.000 14.65 0.00 44.51 5.34
359 979 2.903284 CTTGCAAGCAAAATGGCGT 58.097 47.368 14.65 0.00 39.27 5.68
370 990 2.322161 CTTTGAATCACGGCTTGCAAG 58.678 47.619 22.44 22.44 0.00 4.01
371 991 1.000385 CCTTTGAATCACGGCTTGCAA 60.000 47.619 0.00 0.00 0.00 4.08
372 992 0.597568 CCTTTGAATCACGGCTTGCA 59.402 50.000 0.00 0.00 0.00 4.08
373 993 0.109132 CCCTTTGAATCACGGCTTGC 60.109 55.000 0.00 0.00 0.00 4.01
375 995 1.534729 GTCCCTTTGAATCACGGCTT 58.465 50.000 0.00 0.00 0.00 4.35
376 996 0.322546 GGTCCCTTTGAATCACGGCT 60.323 55.000 0.00 0.00 0.00 5.52
377 997 1.313091 GGGTCCCTTTGAATCACGGC 61.313 60.000 0.00 0.00 0.00 5.68
379 999 1.279271 AGAGGGTCCCTTTGAATCACG 59.721 52.381 13.13 0.00 31.76 4.35
380 1000 3.441500 AAGAGGGTCCCTTTGAATCAC 57.558 47.619 13.13 0.00 31.76 3.06
387 1340 2.306219 GCTAGTCAAAGAGGGTCCCTTT 59.694 50.000 13.13 2.68 31.76 3.11
391 1344 1.903183 ACTGCTAGTCAAAGAGGGTCC 59.097 52.381 0.00 0.00 0.00 4.46
403 1356 7.997915 TCTTCCTACCCTATAATACTGCTAGT 58.002 38.462 0.00 0.00 0.00 2.57
413 1366 4.150359 CCGCTTCTCTTCCTACCCTATAA 58.850 47.826 0.00 0.00 0.00 0.98
420 1373 0.802607 CACGCCGCTTCTCTTCCTAC 60.803 60.000 0.00 0.00 0.00 3.18
421 1374 1.248785 ACACGCCGCTTCTCTTCCTA 61.249 55.000 0.00 0.00 0.00 2.94
422 1375 2.262915 CACGCCGCTTCTCTTCCT 59.737 61.111 0.00 0.00 0.00 3.36
423 1376 2.048127 ACACGCCGCTTCTCTTCC 60.048 61.111 0.00 0.00 0.00 3.46
424 1377 3.016474 GCACACGCCGCTTCTCTTC 62.016 63.158 0.00 0.00 0.00 2.87
500 1497 3.090037 TCAGGTACTTGCTCCACTACTC 58.910 50.000 0.00 0.00 34.60 2.59
519 1516 3.485546 GGTTTAATCGCGCGGTAATTTCA 60.486 43.478 31.69 8.20 0.00 2.69
520 1517 3.031126 GGTTTAATCGCGCGGTAATTTC 58.969 45.455 31.69 18.40 0.00 2.17
538 1555 1.272554 GCTGTGGGCCTAGTAGGGTT 61.273 60.000 18.13 0.00 35.37 4.11
560 1577 2.742372 CCTGTACTGTGTGCCGCC 60.742 66.667 0.00 0.00 0.00 6.13
568 1585 1.552578 TACCGACATGCCTGTACTGT 58.447 50.000 0.00 0.00 35.14 3.55
612 1642 0.878416 TTCGCTAATGCCGCTGTTTT 59.122 45.000 0.00 0.00 35.36 2.43
617 1647 1.597663 GTGTTATTCGCTAATGCCGCT 59.402 47.619 0.00 0.00 35.36 5.52
620 1650 2.032924 GGTGGTGTTATTCGCTAATGCC 59.967 50.000 0.00 0.00 35.36 4.40
666 1696 1.825191 CCACCTTGCTGTGCTGTGT 60.825 57.895 0.00 0.00 34.85 3.72
668 1698 1.825191 CACCACCTTGCTGTGCTGT 60.825 57.895 0.00 0.00 34.85 4.40
689 1720 2.301870 TCTATCGGCTCTCTCCTCTCTC 59.698 54.545 0.00 0.00 0.00 3.20
690 1721 2.303022 CTCTATCGGCTCTCTCCTCTCT 59.697 54.545 0.00 0.00 0.00 3.10
707 1738 1.146485 CTCTCGCCCCTCGACTCTA 59.854 63.158 0.00 0.00 43.16 2.43
728 1759 3.591835 CCTCGGCTCTCTCTCGCC 61.592 72.222 0.00 0.00 42.86 5.54
734 1765 1.152830 GGATCTCCCTCGGCTCTCT 59.847 63.158 0.00 0.00 0.00 3.10
745 1776 2.512705 GCTGGATTGGATTGGATCTCC 58.487 52.381 0.00 0.00 0.00 3.71
887 1932 2.586245 CGGATCTGAGCAAGGCCA 59.414 61.111 5.01 0.00 0.00 5.36
922 1993 2.817396 GCAGCCTGAGAACGGAGC 60.817 66.667 0.00 0.00 0.00 4.70
924 1995 2.973899 GAGCAGCCTGAGAACGGA 59.026 61.111 0.00 0.00 0.00 4.69
926 1997 3.184683 GCGAGCAGCCTGAGAACG 61.185 66.667 0.00 0.00 40.81 3.95
971 2047 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
972 2048 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
973 2049 2.018086 CCCTCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
974 2050 2.612251 CCCTCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
975 2051 2.612251 CCCCTCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
976 2052 2.929738 ATCCCCCTCCTCCTCCTCCT 62.930 65.000 0.00 0.00 0.00 3.69
977 2053 2.395180 GATCCCCCTCCTCCTCCTCC 62.395 70.000 0.00 0.00 0.00 4.30
978 2054 1.157513 GATCCCCCTCCTCCTCCTC 59.842 68.421 0.00 0.00 0.00 3.71
979 2055 2.784654 CGATCCCCCTCCTCCTCCT 61.785 68.421 0.00 0.00 0.00 3.69
980 2056 2.203714 CGATCCCCCTCCTCCTCC 60.204 72.222 0.00 0.00 0.00 4.30
981 2057 2.203714 CCGATCCCCCTCCTCCTC 60.204 72.222 0.00 0.00 0.00 3.71
982 2058 1.679969 ATTCCGATCCCCCTCCTCCT 61.680 60.000 0.00 0.00 0.00 3.69
1008 2084 2.282462 GTGGCCTTGGACACCCTG 60.282 66.667 14.46 0.00 0.00 4.45
1103 2179 1.820906 GCATGGAGCATTGCGAGGA 60.821 57.895 2.38 0.00 44.79 3.71
1104 2180 2.719979 GCATGGAGCATTGCGAGG 59.280 61.111 2.38 0.00 44.79 4.63
1131 2207 2.026301 GAGCTAGTAGCCGTGGCG 59.974 66.667 18.65 0.00 43.77 5.69
1132 2208 1.360911 GAGAGCTAGTAGCCGTGGC 59.639 63.158 18.65 1.67 43.77 5.01
1133 2209 0.814410 TCGAGAGCTAGTAGCCGTGG 60.814 60.000 18.65 7.67 43.77 4.94
1135 2211 0.464870 TCTCGAGAGCTAGTAGCCGT 59.535 55.000 18.65 6.04 43.77 5.68
1137 2213 4.542735 GAAAATCTCGAGAGCTAGTAGCC 58.457 47.826 21.52 10.17 43.77 3.93
1195 2276 2.046217 GGAAGCCGACAAGGTCCC 60.046 66.667 0.00 0.00 43.70 4.46
1227 2308 2.029666 CAATCTCGGGGGCTAGCG 59.970 66.667 9.00 0.00 0.00 4.26
1255 2337 4.863539 GCGCGATCGGAAAACCGC 62.864 66.667 18.30 17.65 43.68 5.68
1256 2338 4.553101 CGCGCGATCGGAAAACCG 62.553 66.667 28.94 11.56 35.95 4.44
1309 2408 4.841441 GGCTCAACCCATGGTCAA 57.159 55.556 11.73 0.00 33.12 3.18
1346 2445 3.623960 CCGCGGACCTAATAACAAATCAA 59.376 43.478 24.07 0.00 0.00 2.57
1709 2831 3.857052 TCAAGGCATTAGTAACACCGAG 58.143 45.455 0.00 0.00 0.00 4.63
1711 2833 3.242739 GCATCAAGGCATTAGTAACACCG 60.243 47.826 0.00 0.00 0.00 4.94
1746 2871 2.081462 GCGGCACAATAACTAACCAGT 58.919 47.619 0.00 0.00 36.19 4.00
1876 3017 3.650281 TCTGCCAGCCATCATAAGAAA 57.350 42.857 0.00 0.00 0.00 2.52
1968 3109 0.541392 TGCTGTCTCACACTGGTTGT 59.459 50.000 0.00 0.00 39.97 3.32
2107 3248 9.023962 ACCTTGTCAAATAGATTAGCATTTGAA 57.976 29.630 10.39 0.00 46.91 2.69
2309 3455 8.286097 GGAATTTTGTTTTGACTTTTGACACAA 58.714 29.630 0.00 0.00 0.00 3.33
2551 3697 1.540363 GGCGACTCACAGTGGAAAAGA 60.540 52.381 0.00 0.00 0.00 2.52
2649 3795 3.739810 CGACATCATGAACCTATGAGCAG 59.260 47.826 0.00 0.00 40.16 4.24
2924 4246 8.570488 CAAGGCATTAAAGATAATGTGCAGATA 58.430 33.333 0.00 0.00 46.68 1.98
3591 5285 4.654262 TCTGGGAATCTAATGTAGGGTGTC 59.346 45.833 0.00 0.00 0.00 3.67
3710 5405 5.289675 GTGTGAAGATCTCAAGGTACATTCG 59.710 44.000 0.00 0.00 35.22 3.34
3734 5429 8.206867 TCCTCTCCTCTTACAATTATCACAATG 58.793 37.037 0.00 0.00 0.00 2.82
3735 5430 8.324191 TCCTCTCCTCTTACAATTATCACAAT 57.676 34.615 0.00 0.00 0.00 2.71
3929 5628 4.270834 TCACCTAGACTGCCTAGTACAAG 58.729 47.826 0.00 0.00 42.63 3.16
3989 5688 5.923204 ACAATGTGTTATTTTTGGGAGCAA 58.077 33.333 0.00 0.00 0.00 3.91
4013 5712 5.497474 AGGCGAACTATGGTGTAAGAAATT 58.503 37.500 0.00 0.00 0.00 1.82
4027 5726 2.098607 CGGTGATGTTAGAGGCGAACTA 59.901 50.000 0.00 0.00 0.00 2.24
4052 5751 8.833493 GCAAGTAAAAGAGTAAACAGGAAAGTA 58.167 33.333 0.00 0.00 0.00 2.24
4218 5917 1.551430 TGATGCCAATTGCCAAGGAAG 59.449 47.619 0.00 0.00 40.16 3.46
4220 5919 1.868713 ATGATGCCAATTGCCAAGGA 58.131 45.000 0.00 0.00 40.16 3.36
4221 5920 2.702592 AATGATGCCAATTGCCAAGG 57.297 45.000 0.00 0.00 40.16 3.61
4251 5950 8.660373 CGAAGAAGCTCAAAGTATAAGAAATGT 58.340 33.333 0.00 0.00 0.00 2.71
4252 5951 8.119226 CCGAAGAAGCTCAAAGTATAAGAAATG 58.881 37.037 0.00 0.00 0.00 2.32
4253 5952 7.201652 GCCGAAGAAGCTCAAAGTATAAGAAAT 60.202 37.037 0.00 0.00 0.00 2.17
4254 5953 6.092259 GCCGAAGAAGCTCAAAGTATAAGAAA 59.908 38.462 0.00 0.00 0.00 2.52
4255 5954 5.581085 GCCGAAGAAGCTCAAAGTATAAGAA 59.419 40.000 0.00 0.00 0.00 2.52
4256 5955 5.109903 GCCGAAGAAGCTCAAAGTATAAGA 58.890 41.667 0.00 0.00 0.00 2.10
4257 5956 4.870426 TGCCGAAGAAGCTCAAAGTATAAG 59.130 41.667 0.00 0.00 0.00 1.73
4258 5957 4.630069 GTGCCGAAGAAGCTCAAAGTATAA 59.370 41.667 0.00 0.00 0.00 0.98
4327 6027 2.873170 TAGTTTCGCATTGCTTCACG 57.127 45.000 7.12 0.00 0.00 4.35
4377 6174 4.507710 TCACATTGTTCAGTGGAGATAGC 58.492 43.478 0.00 0.00 36.43 2.97
5387 7187 5.605488 AGGTCTTACACTAAAACTTCTCCCA 59.395 40.000 0.00 0.00 0.00 4.37
5458 7258 5.124138 GGACAGAGGGAGTATGTGATATACG 59.876 48.000 0.00 0.00 27.90 3.06
5481 7281 9.751542 AGTCTCTAAAACGTCTTATATTGATGG 57.248 33.333 0.00 0.00 0.00 3.51
5504 7304 5.519206 ACGTTTTAGAGACTTGTCACAAGTC 59.481 40.000 34.58 34.58 45.21 3.01
5505 7305 5.416947 ACGTTTTAGAGACTTGTCACAAGT 58.583 37.500 23.53 23.53 0.00 3.16
5506 7306 5.968387 ACGTTTTAGAGACTTGTCACAAG 57.032 39.130 16.42 16.42 0.00 3.16
5507 7307 5.640357 ACAACGTTTTAGAGACTTGTCACAA 59.360 36.000 0.00 0.00 0.00 3.33
5508 7308 5.172934 ACAACGTTTTAGAGACTTGTCACA 58.827 37.500 0.00 0.00 0.00 3.58
5509 7309 5.713822 ACAACGTTTTAGAGACTTGTCAC 57.286 39.130 0.00 0.00 0.00 3.67
5510 7310 9.701098 AATATACAACGTTTTAGAGACTTGTCA 57.299 29.630 0.00 0.00 0.00 3.58
5511 7311 9.953825 CAATATACAACGTTTTAGAGACTTGTC 57.046 33.333 0.00 0.00 0.00 3.18
5512 7312 9.701098 TCAATATACAACGTTTTAGAGACTTGT 57.299 29.630 0.00 0.00 0.00 3.16
5527 7327 7.275920 ACTCCCTCTGTTCATCAATATACAAC 58.724 38.462 0.00 0.00 0.00 3.32
5550 7350 9.953697 CACTATAACTTCTCGCTAAAAGATACT 57.046 33.333 0.00 0.00 0.00 2.12
5580 7380 7.886970 AGGAATATATGGTCATGGAAAGATGTG 59.113 37.037 0.00 0.00 0.00 3.21
5878 7686 7.136119 TCTTAAAACATGCCGTACAAGAAAAG 58.864 34.615 0.00 0.00 0.00 2.27
5889 7700 2.030363 TGGCTGTTCTTAAAACATGCCG 60.030 45.455 21.30 9.12 42.24 5.69
6033 7845 9.730705 AAGTACAAGAGTATATATACAGGCGTA 57.269 33.333 22.00 14.88 35.74 4.42
6113 7988 1.538687 GCTGCAGCAAGGGGACAAAT 61.539 55.000 33.36 0.00 41.59 2.32
6340 8222 3.282885 GAACTTTAGGAGAGCCAATGGG 58.717 50.000 0.00 0.00 36.29 4.00
6365 8247 6.073222 CCGGAATTGATGTTACTATTAGTGCC 60.073 42.308 6.60 0.00 0.00 5.01
6423 8305 5.048713 AGCCTTTTAGAAAAGTCAACGGATG 60.049 40.000 12.51 0.00 42.92 3.51
6519 8403 1.692411 GAGCATAAATGGTGGGGGAC 58.308 55.000 0.00 0.00 38.85 4.46
7056 8951 7.820648 ACTTCCAAGTGACAACAATGATATTC 58.179 34.615 0.00 0.00 37.98 1.75
7069 8964 5.890334 TCATTGTTTCAACTTCCAAGTGAC 58.110 37.500 0.00 0.00 39.66 3.67
7258 9158 3.549299 AGATGAAAAACAGCTGCTTCG 57.451 42.857 15.27 0.00 43.96 3.79
7271 9171 3.295093 TGGCCAAAGTTGACAGATGAAA 58.705 40.909 0.61 0.00 0.00 2.69
7325 9228 0.526662 GAGGGACGACGTTGTCTCAT 59.473 55.000 32.40 20.97 42.01 2.90
7326 9229 1.521450 GGAGGGACGACGTTGTCTCA 61.521 60.000 32.40 0.00 42.01 3.27
7329 9232 1.212229 GAGGAGGGACGACGTTGTC 59.788 63.158 25.13 25.13 38.17 3.18
7332 9235 2.469465 TACGGAGGAGGGACGACGTT 62.469 60.000 0.13 0.00 35.97 3.99
7345 9248 7.352739 GCTTTGTTCCATATTTACATACGGAG 58.647 38.462 0.00 0.00 28.87 4.63
7420 9324 2.801077 AAATTTCCTGTCTACGGGGG 57.199 50.000 8.11 0.00 42.72 5.40
7484 9389 3.008485 ACAATCTCTCTTCTTTTCGCCCT 59.992 43.478 0.00 0.00 0.00 5.19
7487 9392 5.597813 TCAACAATCTCTCTTCTTTTCGC 57.402 39.130 0.00 0.00 0.00 4.70
7488 9393 7.126726 ACATCAACAATCTCTCTTCTTTTCG 57.873 36.000 0.00 0.00 0.00 3.46
7489 9394 8.993121 TGTACATCAACAATCTCTCTTCTTTTC 58.007 33.333 0.00 0.00 0.00 2.29
7590 9500 8.336806 CAGAGTCGAATCGTAGTAATAGAAACT 58.663 37.037 7.29 0.00 0.00 2.66
7609 9519 4.853196 CCAAAACATATTGCAACAGAGTCG 59.147 41.667 0.00 0.00 0.00 4.18
7610 9520 6.012658 TCCAAAACATATTGCAACAGAGTC 57.987 37.500 0.00 0.00 0.00 3.36
7611 9521 5.769662 TCTCCAAAACATATTGCAACAGAGT 59.230 36.000 0.00 0.00 0.00 3.24
7612 9522 6.072286 ACTCTCCAAAACATATTGCAACAGAG 60.072 38.462 0.00 2.82 31.50 3.35
7613 9523 5.769662 ACTCTCCAAAACATATTGCAACAGA 59.230 36.000 0.00 0.00 0.00 3.41
7625 9535 2.489971 CGGCAAGTACTCTCCAAAACA 58.510 47.619 12.25 0.00 0.00 2.83
7626 9536 1.197036 GCGGCAAGTACTCTCCAAAAC 59.803 52.381 12.25 0.00 0.00 2.43
7630 9540 0.685097 AAAGCGGCAAGTACTCTCCA 59.315 50.000 1.45 0.00 0.00 3.86
7633 9543 0.250295 TGCAAAGCGGCAAGTACTCT 60.250 50.000 1.45 0.00 41.65 3.24
7647 9557 6.519679 AATCATGAGCTGATAACTTGCAAA 57.480 33.333 0.00 0.00 44.03 3.68
7650 9560 9.525409 AAATAAAATCATGAGCTGATAACTTGC 57.475 29.630 0.09 0.00 44.03 4.01
7692 9604 0.240945 AAAGAAATCGGCAGCGGTTG 59.759 50.000 0.00 0.00 0.00 3.77
7693 9605 0.521735 GAAAGAAATCGGCAGCGGTT 59.478 50.000 0.00 0.00 0.00 4.44
7694 9606 0.605319 TGAAAGAAATCGGCAGCGGT 60.605 50.000 0.00 0.00 0.00 5.68
7695 9607 0.097674 CTGAAAGAAATCGGCAGCGG 59.902 55.000 0.00 0.00 34.07 5.52
7696 9608 0.798776 ACTGAAAGAAATCGGCAGCG 59.201 50.000 0.00 0.00 37.43 5.18
7697 9609 2.485814 AGAACTGAAAGAAATCGGCAGC 59.514 45.455 0.00 0.00 37.43 5.25
7698 9610 3.499918 ACAGAACTGAAAGAAATCGGCAG 59.500 43.478 8.87 0.00 37.43 4.85
7699 9611 3.476552 ACAGAACTGAAAGAAATCGGCA 58.523 40.909 8.87 0.00 37.43 5.69
7700 9612 4.467735 GAACAGAACTGAAAGAAATCGGC 58.532 43.478 8.87 0.00 37.43 5.54
7701 9613 4.211374 ACGAACAGAACTGAAAGAAATCGG 59.789 41.667 8.87 0.00 37.43 4.18
7702 9614 5.330271 ACGAACAGAACTGAAAGAAATCG 57.670 39.130 8.87 8.45 37.43 3.34
7703 9615 7.484959 ACAAAACGAACAGAACTGAAAGAAATC 59.515 33.333 8.87 0.00 37.43 2.17
7704 9616 7.273381 CACAAAACGAACAGAACTGAAAGAAAT 59.727 33.333 8.87 0.00 37.43 2.17
7705 9617 6.580791 CACAAAACGAACAGAACTGAAAGAAA 59.419 34.615 8.87 0.00 37.43 2.52
7706 9618 6.083630 CACAAAACGAACAGAACTGAAAGAA 58.916 36.000 8.87 0.00 37.43 2.52
7707 9619 5.627172 CACAAAACGAACAGAACTGAAAGA 58.373 37.500 8.87 0.00 37.43 2.52
7708 9620 4.262976 GCACAAAACGAACAGAACTGAAAG 59.737 41.667 8.87 2.07 42.29 2.62
7709 9621 4.083003 AGCACAAAACGAACAGAACTGAAA 60.083 37.500 8.87 0.00 0.00 2.69
7710 9622 3.438781 AGCACAAAACGAACAGAACTGAA 59.561 39.130 8.87 0.00 0.00 3.02
7711 9623 3.006940 AGCACAAAACGAACAGAACTGA 58.993 40.909 8.87 0.00 0.00 3.41
7712 9624 3.100817 CAGCACAAAACGAACAGAACTG 58.899 45.455 0.00 0.00 0.00 3.16
7713 9625 2.747446 ACAGCACAAAACGAACAGAACT 59.253 40.909 0.00 0.00 0.00 3.01
7714 9626 3.131240 ACAGCACAAAACGAACAGAAC 57.869 42.857 0.00 0.00 0.00 3.01
7715 9627 3.242608 GCTACAGCACAAAACGAACAGAA 60.243 43.478 0.00 0.00 41.59 3.02
7716 9628 2.286833 GCTACAGCACAAAACGAACAGA 59.713 45.455 0.00 0.00 41.59 3.41
7717 9629 2.287915 AGCTACAGCACAAAACGAACAG 59.712 45.455 3.70 0.00 45.16 3.16
7718 9630 2.031560 CAGCTACAGCACAAAACGAACA 59.968 45.455 3.70 0.00 45.16 3.18
7719 9631 2.031683 ACAGCTACAGCACAAAACGAAC 59.968 45.455 3.70 0.00 45.16 3.95
7720 9632 2.031560 CACAGCTACAGCACAAAACGAA 59.968 45.455 3.70 0.00 45.16 3.85
7721 9633 1.597195 CACAGCTACAGCACAAAACGA 59.403 47.619 3.70 0.00 45.16 3.85
7722 9634 2.022808 CACAGCTACAGCACAAAACG 57.977 50.000 3.70 0.00 45.16 3.60


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

AutoCloner maintained by Alex Coulton.