Multiple sequence alignment - TraesCS3B01G389500

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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 TraesCS3B01G389500 chr3B 100.000 4379 0 0 1 4379 612810456 612806078 0.000000e+00 8087
1 TraesCS3B01G389500 chr3A 88.347 2214 124 56 694 2838 604346030 604343882 0.000000e+00 2536
2 TraesCS3B01G389500 chr3A 82.901 655 45 28 2996 3632 604343798 604343193 1.080000e-145 527
3 TraesCS3B01G389500 chr3A 84.000 375 20 17 260 605 604346417 604346054 1.520000e-84 324
4 TraesCS3B01G389500 chr3A 93.377 151 6 3 109 255 604346605 604346455 2.050000e-53 220
5 TraesCS3B01G389500 chr3D 93.707 1303 44 12 1541 2820 461957164 461955877 0.000000e+00 1917
6 TraesCS3B01G389500 chr3D 88.789 1222 71 32 260 1443 461958411 461957218 0.000000e+00 1437
7 TraesCS3B01G389500 chr3D 91.413 722 37 11 2933 3632 461955629 461954911 0.000000e+00 966
8 TraesCS3B01G389500 chr3D 93.289 149 7 3 109 255 461958599 461958452 2.650000e-52 217
9 TraesCS3B01G389500 chr6B 97.721 746 16 1 3635 4379 687091010 687090265 0.000000e+00 1282
10 TraesCS3B01G389500 chr1B 96.644 745 24 1 3635 4379 172423967 172423224 0.000000e+00 1236
11 TraesCS3B01G389500 chr1B 95.559 743 33 0 3637 4379 282045245 282044503 0.000000e+00 1190
12 TraesCS3B01G389500 chr6A 96.107 745 29 0 3635 4379 559445164 559445908 0.000000e+00 1216
13 TraesCS3B01G389500 chr4B 96.107 745 27 2 3635 4379 204162657 204163399 0.000000e+00 1214
14 TraesCS3B01G389500 chr2D 95.839 745 31 0 3635 4379 431530436 431529692 0.000000e+00 1205
15 TraesCS3B01G389500 chr1A 95.839 745 31 0 3635 4379 558983408 558982664 0.000000e+00 1205
16 TraesCS3B01G389500 chr6D 95.710 746 30 2 3635 4379 401187953 401188697 0.000000e+00 1199
17 TraesCS3B01G389500 chr5A 95.448 747 32 1 3635 4379 40815798 40816544 0.000000e+00 1190


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 TraesCS3B01G389500 chr3B 612806078 612810456 4378 True 8087.00 8087 100.00000 1 4379 1 chr3B.!!$R1 4378
1 TraesCS3B01G389500 chr3A 604343193 604346605 3412 True 901.75 2536 87.15625 109 3632 4 chr3A.!!$R1 3523
2 TraesCS3B01G389500 chr3D 461954911 461958599 3688 True 1134.25 1917 91.79950 109 3632 4 chr3D.!!$R1 3523
3 TraesCS3B01G389500 chr6B 687090265 687091010 745 True 1282.00 1282 97.72100 3635 4379 1 chr6B.!!$R1 744
4 TraesCS3B01G389500 chr1B 172423224 172423967 743 True 1236.00 1236 96.64400 3635 4379 1 chr1B.!!$R1 744
5 TraesCS3B01G389500 chr1B 282044503 282045245 742 True 1190.00 1190 95.55900 3637 4379 1 chr1B.!!$R2 742
6 TraesCS3B01G389500 chr6A 559445164 559445908 744 False 1216.00 1216 96.10700 3635 4379 1 chr6A.!!$F1 744
7 TraesCS3B01G389500 chr4B 204162657 204163399 742 False 1214.00 1214 96.10700 3635 4379 1 chr4B.!!$F1 744
8 TraesCS3B01G389500 chr2D 431529692 431530436 744 True 1205.00 1205 95.83900 3635 4379 1 chr2D.!!$R1 744
9 TraesCS3B01G389500 chr1A 558982664 558983408 744 True 1205.00 1205 95.83900 3635 4379 1 chr1A.!!$R1 744
10 TraesCS3B01G389500 chr6D 401187953 401188697 744 False 1199.00 1199 95.71000 3635 4379 1 chr6D.!!$F1 744
11 TraesCS3B01G389500 chr5A 40815798 40816544 746 False 1190.00 1190 95.44800 3635 4379 1 chr5A.!!$F1 744

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
303 344 0.467474 TCCACCGACTGACTGACACT 60.467 55.0 0.0 0.0 0.0 3.55 F
638 713 0.523072 CAACCAGACCCATGCTTTCG 59.477 55.0 0.0 0.0 0.0 3.46 F
1525 1635 0.027716 GCGCTCTGTCATGCATTCTG 59.972 55.0 0.0 0.0 0.0 3.02 F
3042 3411 0.034896 TTGAACTCCTCCGGCTCAAC 59.965 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1415 0.603065 TAGCACATGACGCTCAGTGT 59.397 50.0 15.92 0.00 40.96 3.55 R
2451 2599 0.458260 AACGACGGCCAAAAAGCTTT 59.542 45.0 5.69 5.69 0.00 3.51 R
3303 3693 0.035458 CGTCCTTCTTGCTCTTGGGT 59.965 55.0 0.00 0.00 0.00 4.51 R
4176 4572 0.819582 CATTGCCCAAGGTGATGACC 59.180 55.0 0.00 0.00 43.52 4.02 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
17 18 2.642129 TTCCCACGCACGCAAATG 59.358 55.556 0.00 0.00 0.00 2.32
18 19 3.550339 TTCCCACGCACGCAAATGC 62.550 57.895 0.00 0.00 42.48 3.56
19 20 4.041917 CCCACGCACGCAAATGCT 62.042 61.111 3.63 0.00 43.80 3.79
20 21 2.050168 CCACGCACGCAAATGCTT 60.050 55.556 3.63 0.00 43.80 3.91
21 22 2.082366 CCACGCACGCAAATGCTTC 61.082 57.895 3.63 0.00 43.80 3.86
22 23 2.082366 CACGCACGCAAATGCTTCC 61.082 57.895 3.63 0.00 43.80 3.46
23 24 2.254951 CGCACGCAAATGCTTCCA 59.745 55.556 3.63 0.00 43.80 3.53
24 25 1.371512 CGCACGCAAATGCTTCCAA 60.372 52.632 3.63 0.00 43.80 3.53
25 26 0.938637 CGCACGCAAATGCTTCCAAA 60.939 50.000 3.63 0.00 43.80 3.28
26 27 1.431496 GCACGCAAATGCTTCCAAAT 58.569 45.000 3.63 0.00 42.62 2.32
27 28 2.605030 GCACGCAAATGCTTCCAAATA 58.395 42.857 3.63 0.00 42.62 1.40
28 29 3.189285 GCACGCAAATGCTTCCAAATAT 58.811 40.909 3.63 0.00 42.62 1.28
29 30 3.618150 GCACGCAAATGCTTCCAAATATT 59.382 39.130 3.63 0.00 42.62 1.28
30 31 4.093261 GCACGCAAATGCTTCCAAATATTT 59.907 37.500 3.63 0.00 42.62 1.40
31 32 5.390779 GCACGCAAATGCTTCCAAATATTTT 60.391 36.000 0.00 0.00 42.62 1.82
32 33 6.601264 CACGCAAATGCTTCCAAATATTTTT 58.399 32.000 0.00 0.00 39.32 1.94
33 34 7.623089 GCACGCAAATGCTTCCAAATATTTTTA 60.623 33.333 0.00 0.00 42.62 1.52
34 35 7.687757 CACGCAAATGCTTCCAAATATTTTTAC 59.312 33.333 0.00 0.00 39.32 2.01
35 36 7.602265 ACGCAAATGCTTCCAAATATTTTTACT 59.398 29.630 0.00 0.00 39.32 2.24
36 37 9.081997 CGCAAATGCTTCCAAATATTTTTACTA 57.918 29.630 0.00 0.00 39.32 1.82
46 47 9.377312 TCCAAATATTTTTACTAGCAATTTGCC 57.623 29.630 17.51 0.52 46.52 4.52
47 48 9.160496 CCAAATATTTTTACTAGCAATTTGCCA 57.840 29.630 17.51 3.38 46.52 4.92
79 80 9.986833 ACAAATCAGAAAGTTTTATTGTTTTGC 57.013 25.926 19.24 0.00 33.48 3.68
80 81 9.146270 CAAATCAGAAAGTTTTATTGTTTTGCG 57.854 29.630 13.37 0.00 0.00 4.85
81 82 8.419076 AATCAGAAAGTTTTATTGTTTTGCGT 57.581 26.923 0.00 0.00 0.00 5.24
82 83 7.820044 TCAGAAAGTTTTATTGTTTTGCGTT 57.180 28.000 0.00 0.00 0.00 4.84
83 84 7.890763 TCAGAAAGTTTTATTGTTTTGCGTTC 58.109 30.769 0.00 0.00 0.00 3.95
84 85 7.542477 TCAGAAAGTTTTATTGTTTTGCGTTCA 59.458 29.630 0.00 0.00 0.00 3.18
85 86 8.165428 CAGAAAGTTTTATTGTTTTGCGTTCAA 58.835 29.630 0.00 0.00 0.00 2.69
86 87 8.166066 AGAAAGTTTTATTGTTTTGCGTTCAAC 58.834 29.630 0.00 0.00 30.75 3.18
87 88 6.952935 AGTTTTATTGTTTTGCGTTCAACA 57.047 29.167 0.00 0.00 30.75 3.33
88 89 7.352719 AGTTTTATTGTTTTGCGTTCAACAA 57.647 28.000 9.58 9.58 44.78 2.83
89 90 7.797819 AGTTTTATTGTTTTGCGTTCAACAAA 58.202 26.923 10.75 0.00 44.08 2.83
90 91 7.742525 AGTTTTATTGTTTTGCGTTCAACAAAC 59.257 29.630 10.75 6.26 44.08 2.93
91 92 6.706055 TTATTGTTTTGCGTTCAACAAACA 57.294 29.167 10.75 1.50 44.08 2.83
92 93 5.597813 ATTGTTTTGCGTTCAACAAACAA 57.402 30.435 15.79 15.79 44.08 2.83
93 94 5.403897 TTGTTTTGCGTTCAACAAACAAA 57.596 30.435 12.60 5.82 38.72 2.83
94 95 5.597813 TGTTTTGCGTTCAACAAACAAAT 57.402 30.435 2.91 0.00 36.77 2.32
95 96 5.612865 TGTTTTGCGTTCAACAAACAAATC 58.387 33.333 2.91 3.22 36.77 2.17
96 97 5.177511 TGTTTTGCGTTCAACAAACAAATCA 59.822 32.000 2.91 5.26 36.77 2.57
97 98 5.447478 TTTGCGTTCAACAAACAAATCAG 57.553 34.783 0.00 0.00 37.77 2.90
98 99 4.362932 TGCGTTCAACAAACAAATCAGA 57.637 36.364 0.00 0.00 37.77 3.27
99 100 4.930963 TGCGTTCAACAAACAAATCAGAT 58.069 34.783 0.00 0.00 37.77 2.90
100 101 5.347342 TGCGTTCAACAAACAAATCAGATT 58.653 33.333 0.00 0.00 37.77 2.40
101 102 5.809562 TGCGTTCAACAAACAAATCAGATTT 59.190 32.000 2.20 2.20 37.77 2.17
102 103 6.312426 TGCGTTCAACAAACAAATCAGATTTT 59.688 30.769 5.58 0.00 37.77 1.82
103 104 7.489435 TGCGTTCAACAAACAAATCAGATTTTA 59.511 29.630 5.58 0.00 37.77 1.52
104 105 7.787480 GCGTTCAACAAACAAATCAGATTTTAC 59.213 33.333 5.58 0.00 37.77 2.01
105 106 8.265998 CGTTCAACAAACAAATCAGATTTTACC 58.734 33.333 5.58 0.00 37.77 2.85
106 107 9.092876 GTTCAACAAACAAATCAGATTTTACCA 57.907 29.630 5.58 0.00 37.82 3.25
107 108 8.870160 TCAACAAACAAATCAGATTTTACCAG 57.130 30.769 5.58 0.00 0.00 4.00
127 128 2.009774 GTAGCATCATCAACGGCAACT 58.990 47.619 0.00 0.00 0.00 3.16
129 130 0.523072 GCATCATCAACGGCAACTGT 59.477 50.000 0.00 0.00 0.00 3.55
136 137 2.746269 TCAACGGCAACTGTAGTGTAC 58.254 47.619 0.00 0.00 0.00 2.90
248 252 6.039829 TCAGACATGAAGTGACGCTAATCTAT 59.960 38.462 0.00 0.00 30.61 1.98
249 253 7.228706 TCAGACATGAAGTGACGCTAATCTATA 59.771 37.037 0.00 0.00 30.61 1.31
251 255 8.580720 AGACATGAAGTGACGCTAATCTATAAT 58.419 33.333 0.00 0.00 0.00 1.28
252 256 8.749841 ACATGAAGTGACGCTAATCTATAATC 57.250 34.615 0.00 0.00 0.00 1.75
253 257 8.360390 ACATGAAGTGACGCTAATCTATAATCA 58.640 33.333 0.00 0.00 0.00 2.57
255 259 8.803201 TGAAGTGACGCTAATCTATAATCAAG 57.197 34.615 0.00 0.00 0.00 3.02
258 299 6.015010 AGTGACGCTAATCTATAATCAAGCCT 60.015 38.462 0.00 0.00 0.00 4.58
262 303 7.667557 ACGCTAATCTATAATCAAGCCTTACA 58.332 34.615 0.00 0.00 0.00 2.41
277 318 2.157668 CCTTACACTACGCTTTGCACAG 59.842 50.000 0.00 0.00 0.00 3.66
296 337 2.022129 CGTGCTTCCACCGACTGAC 61.022 63.158 0.00 0.00 38.79 3.51
297 338 1.367840 GTGCTTCCACCGACTGACT 59.632 57.895 0.00 0.00 35.92 3.41
298 339 0.946221 GTGCTTCCACCGACTGACTG 60.946 60.000 0.00 0.00 35.92 3.51
299 340 1.112916 TGCTTCCACCGACTGACTGA 61.113 55.000 0.00 0.00 0.00 3.41
303 344 0.467474 TCCACCGACTGACTGACACT 60.467 55.000 0.00 0.00 0.00 3.55
305 346 1.491670 CACCGACTGACTGACACTTG 58.508 55.000 0.00 0.00 0.00 3.16
374 419 0.831307 GGCCTCGATAGTCAAACCCT 59.169 55.000 0.00 0.00 37.40 4.34
450 496 1.140772 AGAAACCAGTCCCCTTCCCC 61.141 60.000 0.00 0.00 0.00 4.81
465 532 2.049767 CCCCACATTAACACCCGCC 61.050 63.158 0.00 0.00 0.00 6.13
481 548 1.376037 GCCCTCAAAGTCACCTCCG 60.376 63.158 0.00 0.00 0.00 4.63
483 550 0.685097 CCCTCAAAGTCACCTCCGAA 59.315 55.000 0.00 0.00 0.00 4.30
526 593 5.941948 AGTCAACAGTGCCACTAATTAAC 57.058 39.130 0.00 0.00 0.00 2.01
531 598 1.064979 AGTGCCACTAATTAACCCCCG 60.065 52.381 0.00 0.00 0.00 5.73
537 607 1.762370 ACTAATTAACCCCCGGTACCG 59.238 52.381 27.68 27.68 33.12 4.02
573 643 5.070001 TCCTCCATACAAAGTGGAAACAAG 58.930 41.667 0.00 0.00 44.69 3.16
574 644 5.070001 CCTCCATACAAAGTGGAAACAAGA 58.930 41.667 0.00 0.00 44.69 3.02
575 645 5.048713 CCTCCATACAAAGTGGAAACAAGAC 60.049 44.000 0.00 0.00 44.69 3.01
576 646 4.825085 TCCATACAAAGTGGAAACAAGACC 59.175 41.667 0.00 0.00 46.06 3.85
577 647 4.022329 CCATACAAAGTGGAAACAAGACCC 60.022 45.833 0.00 0.00 46.06 4.46
578 648 2.384828 ACAAAGTGGAAACAAGACCCC 58.615 47.619 0.00 0.00 46.06 4.95
579 649 2.024369 ACAAAGTGGAAACAAGACCCCT 60.024 45.455 0.00 0.00 46.06 4.79
631 706 3.636764 GAGAAACAAACAACCAGACCCAT 59.363 43.478 0.00 0.00 0.00 4.00
638 713 0.523072 CAACCAGACCCATGCTTTCG 59.477 55.000 0.00 0.00 0.00 3.46
647 722 1.604378 CATGCTTTCGTCCCCTCCT 59.396 57.895 0.00 0.00 0.00 3.69
653 728 1.125093 TTTCGTCCCCTCCTTGCTCA 61.125 55.000 0.00 0.00 0.00 4.26
721 803 3.259425 CTGCACCAAACCGCTCTGC 62.259 63.158 0.00 0.00 0.00 4.26
722 804 3.286751 GCACCAAACCGCTCTGCA 61.287 61.111 0.00 0.00 0.00 4.41
840 925 2.030562 ACCTTCCCTTGTGTCGCG 59.969 61.111 0.00 0.00 0.00 5.87
958 1051 4.898320 ACGAGATTGCAGCATATCCATTA 58.102 39.130 0.00 0.00 0.00 1.90
972 1065 0.813610 CCATTATCCAAGCACGGCGA 60.814 55.000 16.62 0.00 0.00 5.54
974 1067 2.412870 CATTATCCAAGCACGGCGATA 58.587 47.619 16.62 0.00 0.00 2.92
1299 1397 3.788766 ATGGCGCGTGCGTCTTTC 61.789 61.111 20.13 0.00 45.16 2.62
1317 1415 5.006358 GTCTTTCTTGTTTCGTTCTGCACTA 59.994 40.000 0.00 0.00 0.00 2.74
1318 1416 4.789095 TTCTTGTTTCGTTCTGCACTAC 57.211 40.909 0.00 0.00 0.00 2.73
1319 1417 3.787785 TCTTGTTTCGTTCTGCACTACA 58.212 40.909 0.00 0.00 0.00 2.74
1320 1418 3.554324 TCTTGTTTCGTTCTGCACTACAC 59.446 43.478 0.00 0.00 0.00 2.90
1321 1419 3.173668 TGTTTCGTTCTGCACTACACT 57.826 42.857 0.00 0.00 0.00 3.55
1329 1427 0.039165 CTGCACTACACTGAGCGTCA 60.039 55.000 0.00 0.00 0.00 4.35
1334 1432 0.994995 CTACACTGAGCGTCATGTGC 59.005 55.000 4.80 4.80 32.55 4.57
1345 1454 2.414559 GCGTCATGTGCTATTGTTGCTT 60.415 45.455 5.60 0.00 0.00 3.91
1346 1455 3.165890 CGTCATGTGCTATTGTTGCTTG 58.834 45.455 0.00 0.00 0.00 4.01
1347 1456 2.919229 GTCATGTGCTATTGTTGCTTGC 59.081 45.455 0.00 0.00 0.00 4.01
1348 1457 2.821378 TCATGTGCTATTGTTGCTTGCT 59.179 40.909 0.00 0.00 0.00 3.91
1349 1458 2.710220 TGTGCTATTGTTGCTTGCTG 57.290 45.000 0.00 0.00 0.00 4.41
1350 1459 1.955778 TGTGCTATTGTTGCTTGCTGT 59.044 42.857 0.00 0.00 0.00 4.40
1351 1460 3.145286 TGTGCTATTGTTGCTTGCTGTA 58.855 40.909 0.00 0.00 0.00 2.74
1352 1461 3.758023 TGTGCTATTGTTGCTTGCTGTAT 59.242 39.130 0.00 0.00 0.00 2.29
1353 1462 4.100529 GTGCTATTGTTGCTTGCTGTATG 58.899 43.478 0.00 0.00 0.00 2.39
1354 1463 3.758023 TGCTATTGTTGCTTGCTGTATGT 59.242 39.130 0.00 0.00 0.00 2.29
1355 1464 4.940654 TGCTATTGTTGCTTGCTGTATGTA 59.059 37.500 0.00 0.00 0.00 2.29
1356 1465 5.589855 TGCTATTGTTGCTTGCTGTATGTAT 59.410 36.000 0.00 0.00 0.00 2.29
1357 1466 5.911280 GCTATTGTTGCTTGCTGTATGTATG 59.089 40.000 0.00 0.00 0.00 2.39
1358 1467 5.902613 ATTGTTGCTTGCTGTATGTATGT 57.097 34.783 0.00 0.00 0.00 2.29
1359 1468 7.254761 GCTATTGTTGCTTGCTGTATGTATGTA 60.255 37.037 0.00 0.00 0.00 2.29
1360 1469 7.572523 ATTGTTGCTTGCTGTATGTATGTAT 57.427 32.000 0.00 0.00 0.00 2.29
1361 1470 6.362210 TGTTGCTTGCTGTATGTATGTATG 57.638 37.500 0.00 0.00 0.00 2.39
1362 1471 5.879777 TGTTGCTTGCTGTATGTATGTATGT 59.120 36.000 0.00 0.00 0.00 2.29
1363 1472 7.044798 TGTTGCTTGCTGTATGTATGTATGTA 58.955 34.615 0.00 0.00 0.00 2.29
1364 1473 7.011016 TGTTGCTTGCTGTATGTATGTATGTAC 59.989 37.037 0.00 0.00 0.00 2.90
1425 1534 1.882625 GATGGCGCGCATGTACTCA 60.883 57.895 34.42 19.87 0.00 3.41
1459 1568 2.890945 AGGTTTGCAGTTCGGCTTAAAT 59.109 40.909 0.00 0.00 34.04 1.40
1462 1572 4.509970 GGTTTGCAGTTCGGCTTAAATTTT 59.490 37.500 0.00 0.00 34.04 1.82
1514 1624 3.768922 GAGGCTCTGGCGCTCTGT 61.769 66.667 7.64 0.00 39.81 3.41
1516 1626 4.074526 GGCTCTGGCGCTCTGTCA 62.075 66.667 7.64 0.00 39.81 3.58
1520 1630 2.435410 CTGGCGCTCTGTCATGCA 60.435 61.111 7.64 0.00 0.00 3.96
1525 1635 0.027716 GCGCTCTGTCATGCATTCTG 59.972 55.000 0.00 0.00 0.00 3.02
1526 1636 0.027716 CGCTCTGTCATGCATTCTGC 59.972 55.000 0.00 0.00 45.29 4.26
1527 1637 0.381089 GCTCTGTCATGCATTCTGCC 59.619 55.000 0.00 0.00 44.23 4.85
1528 1638 1.746470 CTCTGTCATGCATTCTGCCA 58.254 50.000 0.00 0.00 44.23 4.92
1529 1639 2.298610 CTCTGTCATGCATTCTGCCAT 58.701 47.619 0.00 0.00 44.23 4.40
1530 1640 2.688446 CTCTGTCATGCATTCTGCCATT 59.312 45.455 0.00 0.00 44.23 3.16
1531 1641 2.425668 TCTGTCATGCATTCTGCCATTG 59.574 45.455 0.00 0.00 44.23 2.82
1532 1642 2.165641 CTGTCATGCATTCTGCCATTGT 59.834 45.455 0.00 0.00 44.23 2.71
1533 1643 2.563620 TGTCATGCATTCTGCCATTGTT 59.436 40.909 0.00 0.00 44.23 2.83
2268 2385 4.008933 GCCTGGTGGAGACGCAGT 62.009 66.667 0.00 0.00 44.70 4.40
2387 2516 1.743623 CCGATAAGCACGCACCCAA 60.744 57.895 0.00 0.00 0.00 4.12
2442 2587 2.900546 AGTTAGTGACTACCAGCAGCTT 59.099 45.455 0.00 0.00 36.65 3.74
2451 2599 0.111061 ACCAGCAGCTTGTCATTCCA 59.889 50.000 0.00 0.00 0.00 3.53
2459 2607 4.374399 CAGCTTGTCATTCCAAAGCTTTT 58.626 39.130 9.53 0.00 31.18 2.27
2517 2669 0.892755 TTGATTCGTCCTGCCGTAGT 59.107 50.000 0.00 0.00 0.00 2.73
2551 2703 0.598065 GGCACTGCGAAAATTCCACT 59.402 50.000 0.00 0.00 0.00 4.00
2552 2704 1.401539 GGCACTGCGAAAATTCCACTC 60.402 52.381 0.00 0.00 0.00 3.51
2574 2732 2.419159 GGGGTACTTGATCGGTGGTTAC 60.419 54.545 0.00 0.00 0.00 2.50
2575 2733 2.234414 GGGTACTTGATCGGTGGTTACA 59.766 50.000 0.00 0.00 0.00 2.41
2737 2907 0.179234 TGGAAGTGTTCTTGGCGTGA 59.821 50.000 0.00 0.00 33.64 4.35
2825 2998 2.165845 GACTCCGGTACAAGTGCATAGT 59.834 50.000 0.00 0.00 0.00 2.12
2827 3000 3.129988 ACTCCGGTACAAGTGCATAGTAC 59.870 47.826 0.00 14.33 37.87 2.73
2828 3001 2.097954 TCCGGTACAAGTGCATAGTACG 59.902 50.000 0.00 12.05 39.12 3.67
2829 3002 2.159338 CCGGTACAAGTGCATAGTACGT 60.159 50.000 15.49 0.00 39.12 3.57
2830 3003 3.065233 CCGGTACAAGTGCATAGTACGTA 59.935 47.826 15.49 0.00 39.12 3.57
2833 3006 5.006649 CGGTACAAGTGCATAGTACGTAGTA 59.993 44.000 12.39 12.39 45.11 1.82
2843 3016 2.780595 TACGTAGTAGCACCCGGTC 58.219 57.895 0.00 0.00 45.11 4.79
2844 3017 0.035534 TACGTAGTAGCACCCGGTCA 60.036 55.000 0.00 0.00 45.11 4.02
2845 3018 1.138247 CGTAGTAGCACCCGGTCAC 59.862 63.158 0.00 0.00 0.00 3.67
2846 3019 1.310933 CGTAGTAGCACCCGGTCACT 61.311 60.000 0.00 0.00 0.00 3.41
2847 3020 0.172803 GTAGTAGCACCCGGTCACTG 59.827 60.000 0.00 0.00 0.00 3.66
2848 3021 1.601419 TAGTAGCACCCGGTCACTGC 61.601 60.000 0.00 1.26 0.00 4.40
2849 3022 4.063967 TAGCACCCGGTCACTGCG 62.064 66.667 0.00 0.00 35.98 5.18
2854 3027 4.063967 CCCGGTCACTGCGCAGTA 62.064 66.667 40.17 25.43 40.20 2.74
2864 3037 2.539346 CTGCGCAGTAGTAAGTACGT 57.461 50.000 29.24 0.00 36.66 3.57
2865 3038 3.663464 CTGCGCAGTAGTAAGTACGTA 57.337 47.619 29.24 0.00 36.66 3.57
2866 3039 3.605406 CTGCGCAGTAGTAAGTACGTAG 58.395 50.000 29.24 0.00 36.66 3.51
2867 3040 3.063180 CTGCGCAGTAGTAAGTACGTAGT 59.937 47.826 29.24 0.00 39.36 2.73
2868 3041 4.180817 TGCGCAGTAGTAAGTACGTAGTA 58.819 43.478 5.66 0.00 45.11 1.82
2869 3042 5.556006 CTGCGCAGTAGTAAGTACGTAGTAG 60.556 48.000 29.24 0.00 38.66 2.57
2870 3043 8.869365 CTGCGCAGTAGTAAGTACGTAGTAGC 62.869 50.000 29.24 5.11 38.66 3.58
2884 3057 6.081872 ACGTAGTAGCACTGGTAATAATCC 57.918 41.667 0.00 0.00 41.94 3.01
2907 3080 1.135460 GGGACCGAGTAAGACGTGAAG 60.135 57.143 0.00 0.00 0.00 3.02
2923 3096 6.767902 AGACGTGAAGCCATCAATACATTATT 59.232 34.615 0.00 0.00 40.50 1.40
2928 3101 8.507249 GTGAAGCCATCAATACATTATTAGGAC 58.493 37.037 0.00 0.00 40.50 3.85
2929 3102 8.439971 TGAAGCCATCAATACATTATTAGGACT 58.560 33.333 0.00 0.00 34.30 3.85
2930 3103 9.944376 GAAGCCATCAATACATTATTAGGACTA 57.056 33.333 0.00 0.00 0.00 2.59
2931 3104 9.726438 AAGCCATCAATACATTATTAGGACTAC 57.274 33.333 0.00 0.00 0.00 2.73
2932 3105 9.105844 AGCCATCAATACATTATTAGGACTACT 57.894 33.333 0.00 0.00 0.00 2.57
2962 3331 6.410243 GCTTTAAGCAGGAGTAGTAAGTTG 57.590 41.667 12.54 0.00 41.89 3.16
3042 3411 0.034896 TTGAACTCCTCCGGCTCAAC 59.965 55.000 0.00 0.00 0.00 3.18
3104 3477 1.126846 CGGCGCTCTTGTACAAAGAAG 59.873 52.381 10.03 8.56 0.00 2.85
3169 3544 0.826715 AGTCGTGATGATGGAGGGTG 59.173 55.000 0.00 0.00 0.00 4.61
3202 3577 3.964347 CGATGCGAAATGATAACTGCTTG 59.036 43.478 0.00 0.00 0.00 4.01
3218 3593 4.158025 ACTGCTTGCGACTTACTGTACTAT 59.842 41.667 0.00 0.00 0.00 2.12
3375 3768 3.797353 GGCAAGAGGATCGGGGCA 61.797 66.667 0.00 0.00 42.67 5.36
3380 3773 0.692419 AAGAGGATCGGGGCATGAGT 60.692 55.000 0.00 0.00 42.67 3.41
3382 3775 1.383109 AGGATCGGGGCATGAGTGA 60.383 57.895 0.00 0.00 0.00 3.41
3383 3776 1.070445 GGATCGGGGCATGAGTGAG 59.930 63.158 0.00 0.00 0.00 3.51
3402 3795 0.316689 GCGAGTTTGGTTTGACCGTG 60.317 55.000 0.00 0.00 42.58 4.94
3405 3798 1.602377 GAGTTTGGTTTGACCGTGGAG 59.398 52.381 0.00 0.00 42.58 3.86
3407 3800 1.104577 TTTGGTTTGACCGTGGAGGC 61.105 55.000 0.00 0.00 46.52 4.70
3408 3801 2.671963 GGTTTGACCGTGGAGGCC 60.672 66.667 0.00 0.00 46.52 5.19
3409 3802 3.047877 GTTTGACCGTGGAGGCCG 61.048 66.667 0.00 0.00 46.52 6.13
3410 3803 3.552384 TTTGACCGTGGAGGCCGT 61.552 61.111 0.00 0.00 46.52 5.68
3411 3804 3.524648 TTTGACCGTGGAGGCCGTC 62.525 63.158 0.00 0.00 46.52 4.79
3426 3821 3.624305 CGTCGTCGGTTCATCATCT 57.376 52.632 0.00 0.00 0.00 2.90
3429 3824 0.525455 TCGTCGGTTCATCATCTGCG 60.525 55.000 0.00 0.00 0.00 5.18
3432 3827 1.102978 TCGGTTCATCATCTGCGAGA 58.897 50.000 0.00 0.00 0.00 4.04
3433 3828 1.683385 TCGGTTCATCATCTGCGAGAT 59.317 47.619 0.00 0.00 34.74 2.75
3440 3835 2.097680 TCATCTGCGAGATTGCAACA 57.902 45.000 0.00 0.00 45.74 3.33
3441 3836 2.635714 TCATCTGCGAGATTGCAACAT 58.364 42.857 0.00 0.00 45.74 2.71
3442 3837 3.795877 TCATCTGCGAGATTGCAACATA 58.204 40.909 0.00 0.00 45.74 2.29
3443 3838 4.383173 TCATCTGCGAGATTGCAACATAT 58.617 39.130 0.00 0.00 45.74 1.78
3444 3839 5.540911 TCATCTGCGAGATTGCAACATATA 58.459 37.500 0.00 0.00 45.74 0.86
3445 3840 6.168389 TCATCTGCGAGATTGCAACATATAT 58.832 36.000 0.00 0.00 45.74 0.86
3446 3841 5.851047 TCTGCGAGATTGCAACATATATG 57.149 39.130 11.29 11.29 45.74 1.78
3451 3846 5.869344 GCGAGATTGCAACATATATGTCCTA 59.131 40.000 18.52 10.14 40.80 2.94
3454 3849 7.761249 CGAGATTGCAACATATATGTCCTATGA 59.239 37.037 18.52 4.34 40.80 2.15
3528 3923 1.078759 GAGTGTGATTCGGTCGGCTG 61.079 60.000 0.00 0.00 0.00 4.85
3632 4027 2.631418 TTCGCTGTGCTCAGTAGTAC 57.369 50.000 16.59 0.00 43.05 2.73
3633 4028 1.530323 TCGCTGTGCTCAGTAGTACA 58.470 50.000 16.59 0.00 44.82 2.90
3733 4128 1.065418 CGATGAAGTACCTGGGCCTTT 60.065 52.381 4.53 0.00 0.00 3.11
3747 4142 1.065418 GGCCTTTCCCTTTCGATCTGA 60.065 52.381 0.00 0.00 0.00 3.27
3970 4365 0.734253 GTGGTCAGCTAGCGACACAG 60.734 60.000 28.30 11.21 34.97 3.66
3976 4371 0.888619 AGCTAGCGACACAGCTACAA 59.111 50.000 9.55 0.00 46.14 2.41
4050 4445 1.211949 GGGCTTGGCATACTCCACTTA 59.788 52.381 0.00 0.00 35.50 2.24
4102 4497 1.925120 CCCTGGATGGCATGGAAGA 59.075 57.895 3.81 0.00 0.00 2.87
4133 4528 4.702274 GTGGGTTGGCCTGGGCAT 62.702 66.667 24.56 0.00 44.11 4.40
4176 4572 1.722011 ACCTTTTCTACGCATCCACG 58.278 50.000 0.00 0.00 39.50 4.94
4275 4671 1.664873 CCCACTCATTTTTGCGGCA 59.335 52.632 0.00 0.00 0.00 5.69
4346 4744 2.897326 GGGTGCACAAGATTAACCCTTT 59.103 45.455 20.43 0.00 45.93 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.642129 CATTTGCGTGCGTGGGAA 59.358 55.556 0.00 0.00 0.00 3.97
1 2 4.036804 GCATTTGCGTGCGTGGGA 62.037 61.111 0.00 0.00 35.10 4.37
20 21 9.377312 GGCAAATTGCTAGTAAAAATATTTGGA 57.623 29.630 18.04 0.00 44.28 3.53
21 22 9.160496 TGGCAAATTGCTAGTAAAAATATTTGG 57.840 29.630 18.04 0.00 44.28 3.28
53 54 9.986833 GCAAAACAATAAAACTTTCTGATTTGT 57.013 25.926 14.49 0.00 33.45 2.83
54 55 9.146270 CGCAAAACAATAAAACTTTCTGATTTG 57.854 29.630 11.54 11.54 33.71 2.32
55 56 8.878769 ACGCAAAACAATAAAACTTTCTGATTT 58.121 25.926 0.00 0.00 0.00 2.17
56 57 8.419076 ACGCAAAACAATAAAACTTTCTGATT 57.581 26.923 0.00 0.00 0.00 2.57
57 58 8.419076 AACGCAAAACAATAAAACTTTCTGAT 57.581 26.923 0.00 0.00 0.00 2.90
58 59 7.542477 TGAACGCAAAACAATAAAACTTTCTGA 59.458 29.630 0.00 0.00 0.00 3.27
59 60 7.670916 TGAACGCAAAACAATAAAACTTTCTG 58.329 30.769 0.00 0.00 0.00 3.02
60 61 7.820044 TGAACGCAAAACAATAAAACTTTCT 57.180 28.000 0.00 0.00 0.00 2.52
61 62 7.952637 TGTTGAACGCAAAACAATAAAACTTTC 59.047 29.630 0.00 0.00 35.42 2.62
62 63 7.797819 TGTTGAACGCAAAACAATAAAACTTT 58.202 26.923 0.00 0.00 35.42 2.66
63 64 7.352719 TGTTGAACGCAAAACAATAAAACTT 57.647 28.000 0.00 0.00 35.42 2.66
64 65 6.952935 TGTTGAACGCAAAACAATAAAACT 57.047 29.167 0.00 0.00 35.42 2.66
65 66 7.530861 TGTTTGTTGAACGCAAAACAATAAAAC 59.469 29.630 9.19 0.00 43.66 2.43
66 67 7.572759 TGTTTGTTGAACGCAAAACAATAAAA 58.427 26.923 9.19 0.00 43.66 1.52
67 68 7.117241 TGTTTGTTGAACGCAAAACAATAAA 57.883 28.000 9.19 0.00 43.66 1.40
68 69 6.706055 TGTTTGTTGAACGCAAAACAATAA 57.294 29.167 9.19 0.00 43.66 1.40
69 70 6.706055 TTGTTTGTTGAACGCAAAACAATA 57.294 29.167 16.34 2.21 43.66 1.90
70 71 5.597813 TTGTTTGTTGAACGCAAAACAAT 57.402 30.435 16.34 0.00 43.66 2.71
71 72 5.403897 TTTGTTTGTTGAACGCAAAACAA 57.596 30.435 16.34 16.34 42.82 2.83
72 73 5.177511 TGATTTGTTTGTTGAACGCAAAACA 59.822 32.000 13.40 13.63 41.29 2.83
73 74 5.612865 TGATTTGTTTGTTGAACGCAAAAC 58.387 33.333 13.40 11.90 41.29 2.43
74 75 5.635280 TCTGATTTGTTTGTTGAACGCAAAA 59.365 32.000 13.40 3.29 41.29 2.44
75 76 5.164233 TCTGATTTGTTTGTTGAACGCAAA 58.836 33.333 12.33 12.33 41.29 3.68
76 77 4.738124 TCTGATTTGTTTGTTGAACGCAA 58.262 34.783 0.00 0.00 41.29 4.85
77 78 4.362932 TCTGATTTGTTTGTTGAACGCA 57.637 36.364 0.00 0.00 41.29 5.24
78 79 5.888412 AATCTGATTTGTTTGTTGAACGC 57.112 34.783 0.00 0.00 41.29 4.84
79 80 8.265998 GGTAAAATCTGATTTGTTTGTTGAACG 58.734 33.333 15.80 0.00 41.29 3.95
80 81 9.092876 TGGTAAAATCTGATTTGTTTGTTGAAC 57.907 29.630 15.80 0.00 38.78 3.18
81 82 9.311916 CTGGTAAAATCTGATTTGTTTGTTGAA 57.688 29.630 15.80 0.00 31.77 2.69
82 83 8.474025 ACTGGTAAAATCTGATTTGTTTGTTGA 58.526 29.630 15.80 0.00 31.77 3.18
83 84 8.647143 ACTGGTAAAATCTGATTTGTTTGTTG 57.353 30.769 15.80 6.77 31.77 3.33
84 85 9.965824 CTACTGGTAAAATCTGATTTGTTTGTT 57.034 29.630 15.80 2.65 31.77 2.83
85 86 8.082242 GCTACTGGTAAAATCTGATTTGTTTGT 58.918 33.333 15.80 12.88 31.77 2.83
86 87 8.081633 TGCTACTGGTAAAATCTGATTTGTTTG 58.918 33.333 15.80 8.53 31.77 2.93
87 88 8.177119 TGCTACTGGTAAAATCTGATTTGTTT 57.823 30.769 15.80 4.00 31.77 2.83
88 89 7.759489 TGCTACTGGTAAAATCTGATTTGTT 57.241 32.000 15.80 4.68 31.77 2.83
89 90 7.611467 TGATGCTACTGGTAAAATCTGATTTGT 59.389 33.333 15.80 11.22 31.77 2.83
90 91 7.988737 TGATGCTACTGGTAAAATCTGATTTG 58.011 34.615 15.80 6.19 31.77 2.32
91 92 8.757982 ATGATGCTACTGGTAAAATCTGATTT 57.242 30.769 9.76 9.76 0.00 2.17
92 93 7.994911 TGATGATGCTACTGGTAAAATCTGATT 59.005 33.333 0.00 0.00 0.00 2.57
93 94 7.512130 TGATGATGCTACTGGTAAAATCTGAT 58.488 34.615 0.00 0.00 0.00 2.90
94 95 6.888105 TGATGATGCTACTGGTAAAATCTGA 58.112 36.000 0.00 0.00 0.00 3.27
95 96 7.412853 GTTGATGATGCTACTGGTAAAATCTG 58.587 38.462 0.00 0.00 0.00 2.90
96 97 6.258727 CGTTGATGATGCTACTGGTAAAATCT 59.741 38.462 0.00 0.00 0.00 2.40
97 98 6.422223 CGTTGATGATGCTACTGGTAAAATC 58.578 40.000 0.00 0.00 0.00 2.17
98 99 5.296780 CCGTTGATGATGCTACTGGTAAAAT 59.703 40.000 0.00 0.00 0.00 1.82
99 100 4.634004 CCGTTGATGATGCTACTGGTAAAA 59.366 41.667 0.00 0.00 0.00 1.52
100 101 4.188462 CCGTTGATGATGCTACTGGTAAA 58.812 43.478 0.00 0.00 0.00 2.01
101 102 3.792401 CCGTTGATGATGCTACTGGTAA 58.208 45.455 0.00 0.00 0.00 2.85
102 103 2.483013 GCCGTTGATGATGCTACTGGTA 60.483 50.000 0.00 0.00 0.00 3.25
103 104 1.743772 GCCGTTGATGATGCTACTGGT 60.744 52.381 0.00 0.00 0.00 4.00
104 105 0.940126 GCCGTTGATGATGCTACTGG 59.060 55.000 0.00 0.00 0.00 4.00
105 106 1.655484 TGCCGTTGATGATGCTACTG 58.345 50.000 0.00 0.00 0.00 2.74
106 107 2.009774 GTTGCCGTTGATGATGCTACT 58.990 47.619 0.00 0.00 0.00 2.57
107 108 2.009774 AGTTGCCGTTGATGATGCTAC 58.990 47.619 0.00 0.00 0.00 3.58
127 128 7.778382 ACTATGATGGTATGACTGTACACTACA 59.222 37.037 0.00 0.00 37.13 2.74
129 130 9.281371 GTACTATGATGGTATGACTGTACACTA 57.719 37.037 0.00 0.00 0.00 2.74
136 137 5.564848 CGGGTGTACTATGATGGTATGACTG 60.565 48.000 0.00 0.00 0.00 3.51
139 143 4.279922 CACGGGTGTACTATGATGGTATGA 59.720 45.833 0.00 0.00 0.00 2.15
143 147 1.138266 GCACGGGTGTACTATGATGGT 59.862 52.381 0.25 0.00 0.00 3.55
230 234 7.382488 GCTTGATTATAGATTAGCGTCACTTCA 59.618 37.037 0.00 0.00 0.00 3.02
248 252 4.730949 AGCGTAGTGTAAGGCTTGATTA 57.269 40.909 10.69 0.00 37.30 1.75
249 253 3.611766 AGCGTAGTGTAAGGCTTGATT 57.388 42.857 10.69 0.00 37.30 2.57
251 255 3.064207 CAAAGCGTAGTGTAAGGCTTGA 58.936 45.455 10.69 0.00 46.69 3.02
252 256 2.412847 GCAAAGCGTAGTGTAAGGCTTG 60.413 50.000 10.69 0.00 46.69 4.01
255 259 1.136057 GTGCAAAGCGTAGTGTAAGGC 60.136 52.381 0.00 0.00 0.00 4.35
258 299 1.529438 GCTGTGCAAAGCGTAGTGTAA 59.471 47.619 14.36 0.00 32.56 2.41
277 318 3.414700 CAGTCGGTGGAAGCACGC 61.415 66.667 0.00 0.00 0.00 5.34
286 327 1.491670 CAAGTGTCAGTCAGTCGGTG 58.508 55.000 0.00 0.00 0.00 4.94
374 419 0.739561 ACCGGTTGTTTTAAGCGCAA 59.260 45.000 11.47 0.00 39.52 4.85
450 496 0.322098 TGAGGGCGGGTGTTAATGTG 60.322 55.000 0.00 0.00 0.00 3.21
465 532 1.608283 GGTTCGGAGGTGACTTTGAGG 60.608 57.143 0.00 0.00 44.43 3.86
481 548 1.883021 CAGTGGGGATTTGCGGTTC 59.117 57.895 0.00 0.00 0.00 3.62
483 550 2.676471 GCAGTGGGGATTTGCGGT 60.676 61.111 0.00 0.00 0.00 5.68
531 598 0.322187 ATTGTCCTGTTGGCGGTACC 60.322 55.000 0.16 0.16 39.84 3.34
573 643 2.041405 CAGAGGAGGGGAGGGGTC 60.041 72.222 0.00 0.00 0.00 4.46
574 644 3.700350 CCAGAGGAGGGGAGGGGT 61.700 72.222 0.00 0.00 0.00 4.95
575 645 3.700350 ACCAGAGGAGGGGAGGGG 61.700 72.222 0.00 0.00 0.00 4.79
576 646 2.041405 GACCAGAGGAGGGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
577 647 0.327000 AATGACCAGAGGAGGGGAGG 60.327 60.000 0.00 0.00 0.00 4.30
578 648 0.835941 CAATGACCAGAGGAGGGGAG 59.164 60.000 0.00 0.00 0.00 4.30
579 649 0.119155 ACAATGACCAGAGGAGGGGA 59.881 55.000 0.00 0.00 0.00 4.81
606 676 3.315470 GGTCTGGTTGTTTGTTTCTCCTC 59.685 47.826 0.00 0.00 0.00 3.71
631 706 1.374947 CAAGGAGGGGACGAAAGCA 59.625 57.895 0.00 0.00 0.00 3.91
638 713 0.106967 GGATTGAGCAAGGAGGGGAC 60.107 60.000 0.00 0.00 0.00 4.46
647 722 0.608035 GACCGGGTTGGATTGAGCAA 60.608 55.000 6.32 0.00 42.00 3.91
653 728 2.349755 CGGTGACCGGGTTGGATT 59.650 61.111 17.80 0.00 44.15 3.01
721 803 3.260483 CTAGCGGCGCAGAAGCTG 61.260 66.667 35.02 11.13 45.82 4.24
958 1051 0.032678 CTCTATCGCCGTGCTTGGAT 59.967 55.000 0.00 0.00 0.00 3.41
981 1074 5.527951 GCCATCTATATATCTCCAAGCTCG 58.472 45.833 0.00 0.00 0.00 5.03
1230 1323 4.828296 TAGAGGCCGTCGGGGGAC 62.828 72.222 14.38 0.00 35.78 4.46
1292 1390 3.242284 TGCAGAACGAAACAAGAAAGACG 60.242 43.478 0.00 0.00 0.00 4.18
1293 1391 4.029043 GTGCAGAACGAAACAAGAAAGAC 58.971 43.478 0.00 0.00 0.00 3.01
1294 1392 3.938963 AGTGCAGAACGAAACAAGAAAGA 59.061 39.130 0.00 0.00 0.00 2.52
1299 1397 3.555956 AGTGTAGTGCAGAACGAAACAAG 59.444 43.478 0.00 0.00 0.00 3.16
1317 1415 0.603065 TAGCACATGACGCTCAGTGT 59.397 50.000 15.92 0.00 40.96 3.55
1318 1416 1.931906 ATAGCACATGACGCTCAGTG 58.068 50.000 15.92 0.00 40.96 3.66
1319 1417 2.274437 CAATAGCACATGACGCTCAGT 58.726 47.619 15.92 3.89 40.96 3.41
1320 1418 2.274437 ACAATAGCACATGACGCTCAG 58.726 47.619 15.92 10.55 40.96 3.35
1321 1419 2.385013 ACAATAGCACATGACGCTCA 57.615 45.000 15.92 5.85 40.96 4.26
1329 1427 2.559668 ACAGCAAGCAACAATAGCACAT 59.440 40.909 0.00 0.00 0.00 3.21
1334 1432 7.019774 ACATACATACAGCAAGCAACAATAG 57.980 36.000 0.00 0.00 0.00 1.73
1345 1454 8.685838 TCTACAGTACATACATACATACAGCA 57.314 34.615 0.00 0.00 0.00 4.41
1346 1455 9.561270 CATCTACAGTACATACATACATACAGC 57.439 37.037 0.00 0.00 0.00 4.40
1352 1461 8.504005 CGATCACATCTACAGTACATACATACA 58.496 37.037 0.00 0.00 0.00 2.29
1353 1462 8.718734 TCGATCACATCTACAGTACATACATAC 58.281 37.037 0.00 0.00 0.00 2.39
1354 1463 8.842358 TCGATCACATCTACAGTACATACATA 57.158 34.615 0.00 0.00 0.00 2.29
1355 1464 7.745620 TCGATCACATCTACAGTACATACAT 57.254 36.000 0.00 0.00 0.00 2.29
1356 1465 7.360101 CGATCGATCACATCTACAGTACATACA 60.360 40.741 24.40 0.00 0.00 2.29
1357 1466 6.956520 CGATCGATCACATCTACAGTACATAC 59.043 42.308 24.40 0.00 0.00 2.39
1358 1467 6.092259 CCGATCGATCACATCTACAGTACATA 59.908 42.308 24.40 0.00 0.00 2.29
1359 1468 5.106515 CCGATCGATCACATCTACAGTACAT 60.107 44.000 24.40 0.00 0.00 2.29
1360 1469 4.213482 CCGATCGATCACATCTACAGTACA 59.787 45.833 24.40 0.00 0.00 2.90
1361 1470 4.713806 CCGATCGATCACATCTACAGTAC 58.286 47.826 24.40 0.00 0.00 2.73
1362 1471 3.188667 GCCGATCGATCACATCTACAGTA 59.811 47.826 24.40 0.00 0.00 2.74
1363 1472 2.030717 GCCGATCGATCACATCTACAGT 60.031 50.000 24.40 0.00 0.00 3.55
1364 1473 2.227626 AGCCGATCGATCACATCTACAG 59.772 50.000 24.40 5.32 0.00 2.74
1392 1501 3.011517 ATCCCCTTGCCTCGCAGT 61.012 61.111 0.00 0.00 40.61 4.40
1459 1568 4.495679 GCATCGCCGATGAACTAATCAAAA 60.496 41.667 29.82 0.00 42.09 2.44
1462 1572 2.135139 GCATCGCCGATGAACTAATCA 58.865 47.619 29.82 0.00 42.09 2.57
1490 1600 4.891037 GCCAGAGCCTCCATGCCC 62.891 72.222 0.00 0.00 0.00 5.36
1498 1608 3.768922 GACAGAGCGCCAGAGCCT 61.769 66.667 2.29 0.00 38.01 4.58
1520 1630 4.546829 AATCAGCAAACAATGGCAGAAT 57.453 36.364 0.00 0.00 0.00 2.40
1525 1635 1.127213 CGCAAATCAGCAAACAATGGC 59.873 47.619 0.00 0.00 0.00 4.40
1526 1636 1.727880 CCGCAAATCAGCAAACAATGG 59.272 47.619 0.00 0.00 0.00 3.16
1527 1637 2.156117 CACCGCAAATCAGCAAACAATG 59.844 45.455 0.00 0.00 0.00 2.82
1528 1638 2.224018 ACACCGCAAATCAGCAAACAAT 60.224 40.909 0.00 0.00 0.00 2.71
1529 1639 1.135915 ACACCGCAAATCAGCAAACAA 59.864 42.857 0.00 0.00 0.00 2.83
1530 1640 0.743688 ACACCGCAAATCAGCAAACA 59.256 45.000 0.00 0.00 0.00 2.83
1531 1641 1.522258 CAACACCGCAAATCAGCAAAC 59.478 47.619 0.00 0.00 0.00 2.93
1532 1642 1.135915 ACAACACCGCAAATCAGCAAA 59.864 42.857 0.00 0.00 0.00 3.68
1533 1643 0.743688 ACAACACCGCAAATCAGCAA 59.256 45.000 0.00 0.00 0.00 3.91
1706 1823 4.500116 GAGGAGCAGGACGACGCC 62.500 72.222 0.00 0.00 0.00 5.68
1807 1924 1.226435 CTGTACTCGCCGAGCTCAC 60.226 63.158 15.20 10.36 32.04 3.51
1808 1925 2.407428 CCTGTACTCGCCGAGCTCA 61.407 63.158 15.20 12.34 32.04 4.26
1988 2105 3.267860 GCCTTGATCAGCGCCTCG 61.268 66.667 2.29 0.00 0.00 4.63
2354 2479 2.607411 ATCGGCATTGATGGTCGGCA 62.607 55.000 0.00 0.00 0.00 5.69
2387 2516 1.341852 GGTGGTGCCGGTTTAATTTGT 59.658 47.619 1.90 0.00 0.00 2.83
2451 2599 0.458260 AACGACGGCCAAAAAGCTTT 59.542 45.000 5.69 5.69 0.00 3.51
2459 2607 2.392181 CGCCATTAACGACGGCCAA 61.392 57.895 2.24 0.00 43.17 4.52
2517 2669 3.146066 CAGTGCCTTTAACTAACTGCCA 58.854 45.455 0.00 0.00 32.61 4.92
2525 2677 4.546570 GAATTTTCGCAGTGCCTTTAACT 58.453 39.130 10.11 0.00 0.00 2.24
2551 2703 1.324740 CCACCGATCAAGTACCCCGA 61.325 60.000 0.00 0.00 0.00 5.14
2552 2704 1.143183 CCACCGATCAAGTACCCCG 59.857 63.158 0.00 0.00 0.00 5.73
2574 2732 9.144747 CGTGAGACCTATTCCTATTTATGAATG 57.855 37.037 0.00 0.00 33.46 2.67
2575 2733 8.314751 CCGTGAGACCTATTCCTATTTATGAAT 58.685 37.037 0.00 0.00 35.48 2.57
2697 2865 3.899981 ATTTGGTGCTGGCTCGCGA 62.900 57.895 9.26 9.26 0.00 5.87
2765 2935 6.605594 TCTGAACCAAGTGTAAATCCAAAACT 59.394 34.615 0.00 0.00 0.00 2.66
2825 2998 0.035534 TGACCGGGTGCTACTACGTA 60.036 55.000 3.30 0.00 0.00 3.57
2827 3000 1.138247 GTGACCGGGTGCTACTACG 59.862 63.158 3.30 0.00 0.00 3.51
2828 3001 0.172803 CAGTGACCGGGTGCTACTAC 59.827 60.000 3.30 0.00 0.00 2.73
2829 3002 1.601419 GCAGTGACCGGGTGCTACTA 61.601 60.000 3.30 0.00 34.23 1.82
2830 3003 2.943978 GCAGTGACCGGGTGCTACT 61.944 63.158 3.30 3.29 34.23 2.57
2832 3005 4.063967 CGCAGTGACCGGGTGCTA 62.064 66.667 3.30 0.00 34.92 3.49
2837 3010 3.989698 CTACTGCGCAGTGACCGGG 62.990 68.421 44.69 25.34 42.52 5.73
2838 3011 1.929806 TACTACTGCGCAGTGACCGG 61.930 60.000 44.69 30.31 42.52 5.28
2839 3012 0.109458 TTACTACTGCGCAGTGACCG 60.109 55.000 44.69 31.67 42.52 4.79
2840 3013 1.067776 ACTTACTACTGCGCAGTGACC 60.068 52.381 44.69 0.00 42.52 4.02
2841 3014 2.349297 ACTTACTACTGCGCAGTGAC 57.651 50.000 44.69 0.06 42.52 3.67
2842 3015 2.159612 CGTACTTACTACTGCGCAGTGA 60.160 50.000 44.69 29.64 42.52 3.41
2843 3016 2.174764 CGTACTTACTACTGCGCAGTG 58.825 52.381 44.69 35.03 42.52 3.66
2844 3017 1.808945 ACGTACTTACTACTGCGCAGT 59.191 47.619 41.46 41.46 45.02 4.40
2845 3018 2.539346 ACGTACTTACTACTGCGCAG 57.461 50.000 34.89 34.89 0.00 5.18
2846 3019 3.002791 ACTACGTACTTACTACTGCGCA 58.997 45.455 10.98 10.98 0.00 6.09
2847 3020 3.665173 ACTACGTACTTACTACTGCGC 57.335 47.619 0.00 0.00 0.00 6.09
2848 3021 4.268644 TGCTACTACGTACTTACTACTGCG 59.731 45.833 0.00 0.00 0.00 5.18
2849 3022 5.293079 AGTGCTACTACGTACTTACTACTGC 59.707 44.000 0.00 0.00 0.00 4.40
2850 3023 6.238049 CCAGTGCTACTACGTACTTACTACTG 60.238 46.154 0.00 3.06 0.00 2.74
2851 3024 5.814705 CCAGTGCTACTACGTACTTACTACT 59.185 44.000 0.00 0.00 0.00 2.57
2852 3025 5.582665 ACCAGTGCTACTACGTACTTACTAC 59.417 44.000 0.00 0.00 0.00 2.73
2853 3026 5.734720 ACCAGTGCTACTACGTACTTACTA 58.265 41.667 0.00 0.00 0.00 1.82
2854 3027 4.583871 ACCAGTGCTACTACGTACTTACT 58.416 43.478 0.00 0.00 0.00 2.24
2855 3028 4.954092 ACCAGTGCTACTACGTACTTAC 57.046 45.455 0.00 0.00 0.00 2.34
2856 3029 8.731275 TTATTACCAGTGCTACTACGTACTTA 57.269 34.615 0.00 0.00 0.00 2.24
2857 3030 7.630242 TTATTACCAGTGCTACTACGTACTT 57.370 36.000 0.00 0.00 0.00 2.24
2858 3031 7.040823 GGATTATTACCAGTGCTACTACGTACT 60.041 40.741 0.00 0.00 0.00 2.73
2859 3032 7.080724 GGATTATTACCAGTGCTACTACGTAC 58.919 42.308 0.00 0.00 0.00 3.67
2860 3033 6.073058 CGGATTATTACCAGTGCTACTACGTA 60.073 42.308 0.00 0.00 0.00 3.57
2861 3034 5.278169 CGGATTATTACCAGTGCTACTACGT 60.278 44.000 0.00 0.00 0.00 3.57
2862 3035 5.049198 TCGGATTATTACCAGTGCTACTACG 60.049 44.000 0.00 0.00 0.00 3.51
2863 3036 6.323203 TCGGATTATTACCAGTGCTACTAC 57.677 41.667 0.00 0.00 0.00 2.73
2864 3037 5.475909 CCTCGGATTATTACCAGTGCTACTA 59.524 44.000 0.00 0.00 0.00 1.82
2865 3038 4.281182 CCTCGGATTATTACCAGTGCTACT 59.719 45.833 0.00 0.00 0.00 2.57
2866 3039 4.557205 CCTCGGATTATTACCAGTGCTAC 58.443 47.826 0.00 0.00 0.00 3.58
2867 3040 3.576982 CCCTCGGATTATTACCAGTGCTA 59.423 47.826 0.00 0.00 0.00 3.49
2868 3041 2.368875 CCCTCGGATTATTACCAGTGCT 59.631 50.000 0.00 0.00 0.00 4.40
2869 3042 2.367567 TCCCTCGGATTATTACCAGTGC 59.632 50.000 0.00 0.00 0.00 4.40
2870 3043 3.244112 GGTCCCTCGGATTATTACCAGTG 60.244 52.174 0.00 0.00 32.73 3.66
2871 3044 2.970640 GGTCCCTCGGATTATTACCAGT 59.029 50.000 0.00 0.00 32.73 4.00
2872 3045 2.029290 CGGTCCCTCGGATTATTACCAG 60.029 54.545 0.00 0.00 32.73 4.00
2873 3046 1.965643 CGGTCCCTCGGATTATTACCA 59.034 52.381 0.00 0.00 32.73 3.25
2874 3047 2.230750 CTCGGTCCCTCGGATTATTACC 59.769 54.545 0.00 0.00 32.73 2.85
2875 3048 2.889678 ACTCGGTCCCTCGGATTATTAC 59.110 50.000 0.00 0.00 32.73 1.89
2884 3057 1.023513 ACGTCTTACTCGGTCCCTCG 61.024 60.000 0.00 0.00 0.00 4.63
2923 3096 5.163540 GCTTAAAGCAGCAGTAGTAGTCCTA 60.164 44.000 0.00 0.00 41.89 2.94
2953 3322 7.809331 CACGTTGTAGATTGTACCAACTTACTA 59.191 37.037 8.23 0.00 0.00 1.82
2957 3326 5.603596 TCACGTTGTAGATTGTACCAACTT 58.396 37.500 8.23 0.00 0.00 2.66
2958 3327 5.204409 TCACGTTGTAGATTGTACCAACT 57.796 39.130 8.23 0.00 0.00 3.16
2962 3331 3.846360 AGCTCACGTTGTAGATTGTACC 58.154 45.455 0.00 0.00 0.00 3.34
2969 3338 5.128992 TCATTACAAGCTCACGTTGTAGA 57.871 39.130 0.00 0.00 40.55 2.59
2976 3345 4.486090 ACAGTACTCATTACAAGCTCACG 58.514 43.478 0.00 0.00 32.41 4.35
3202 3577 9.512435 TTCAGAATAAATAGTACAGTAAGTCGC 57.488 33.333 0.00 0.00 0.00 5.19
3218 3593 9.070179 CATCCACCATCACATATTCAGAATAAA 57.930 33.333 6.96 0.00 0.00 1.40
3303 3693 0.035458 CGTCCTTCTTGCTCTTGGGT 59.965 55.000 0.00 0.00 0.00 4.51
3375 3768 2.549754 CAAACCAAACTCGCTCACTCAT 59.450 45.455 0.00 0.00 0.00 2.90
3380 3773 1.305201 GGTCAAACCAAACTCGCTCA 58.695 50.000 0.00 0.00 38.42 4.26
3382 3775 0.463116 ACGGTCAAACCAAACTCGCT 60.463 50.000 0.00 0.00 38.47 4.93
3383 3776 0.316689 CACGGTCAAACCAAACTCGC 60.317 55.000 0.00 0.00 38.47 5.03
3408 3801 1.191944 CAGATGATGAACCGACGACG 58.808 55.000 0.00 0.00 39.43 5.12
3409 3802 0.924090 GCAGATGATGAACCGACGAC 59.076 55.000 0.00 0.00 0.00 4.34
3410 3803 0.525455 CGCAGATGATGAACCGACGA 60.525 55.000 0.00 0.00 0.00 4.20
3411 3804 0.525455 TCGCAGATGATGAACCGACG 60.525 55.000 0.00 0.00 0.00 5.12
3412 3805 1.202302 TCTCGCAGATGATGAACCGAC 60.202 52.381 0.00 0.00 33.89 4.79
3413 3806 1.102978 TCTCGCAGATGATGAACCGA 58.897 50.000 0.00 0.00 33.89 4.69
3414 3807 2.145958 ATCTCGCAGATGATGAACCG 57.854 50.000 0.00 0.00 32.80 4.44
3426 3821 4.452114 GGACATATATGTTGCAATCTCGCA 59.548 41.667 19.19 0.00 41.95 5.10
3429 3824 9.610705 ATCATAGGACATATATGTTGCAATCTC 57.389 33.333 19.19 4.34 41.95 2.75
3432 3827 9.524496 AACATCATAGGACATATATGTTGCAAT 57.476 29.630 19.19 8.51 41.95 3.56
3433 3828 8.922931 AACATCATAGGACATATATGTTGCAA 57.077 30.769 19.19 0.00 41.95 4.08
3441 3836 9.958180 CACCCAAATAACATCATAGGACATATA 57.042 33.333 0.00 0.00 0.00 0.86
3442 3837 7.890127 CCACCCAAATAACATCATAGGACATAT 59.110 37.037 0.00 0.00 0.00 1.78
3443 3838 7.230747 CCACCCAAATAACATCATAGGACATA 58.769 38.462 0.00 0.00 0.00 2.29
3444 3839 6.070656 CCACCCAAATAACATCATAGGACAT 58.929 40.000 0.00 0.00 0.00 3.06
3445 3840 5.445069 CCACCCAAATAACATCATAGGACA 58.555 41.667 0.00 0.00 0.00 4.02
3446 3841 4.278419 GCCACCCAAATAACATCATAGGAC 59.722 45.833 0.00 0.00 0.00 3.85
3451 3846 2.031120 CGGCCACCCAAATAACATCAT 58.969 47.619 2.24 0.00 0.00 2.45
3454 3849 1.181786 CACGGCCACCCAAATAACAT 58.818 50.000 2.24 0.00 0.00 2.71
3479 3874 1.268539 CCAGACAAACCACAAACGAGC 60.269 52.381 0.00 0.00 0.00 5.03
3528 3923 0.951040 CCAGCTGAACAGAACCGGAC 60.951 60.000 17.39 0.99 0.00 4.79
3632 4027 4.268644 CACACCGAATAGCAACTACAGATG 59.731 45.833 0.00 0.00 0.00 2.90
3633 4028 4.433615 CACACCGAATAGCAACTACAGAT 58.566 43.478 0.00 0.00 0.00 2.90
3733 4128 1.478510 GAGCTGTCAGATCGAAAGGGA 59.521 52.381 3.32 0.00 28.39 4.20
3747 4142 2.736670 AGTCAACCCTTTTGAGCTGT 57.263 45.000 0.00 0.00 0.00 4.40
3819 4214 1.470890 CGCCCAATCGTGGTAATGTTT 59.529 47.619 0.00 0.00 44.30 2.83
3930 4325 3.509575 ACAAAAATGCCCGCTCAATCTTA 59.490 39.130 0.00 0.00 0.00 2.10
3976 4371 4.312443 CAATTGACCTTGCATTTTGCTCT 58.688 39.130 0.00 0.00 45.31 4.09
4050 4445 1.280421 AGAGCTCTCGCAAATTTCCCT 59.720 47.619 11.45 0.00 39.10 4.20
4074 4469 1.351080 CCATCCAGGGCCATCTCAGT 61.351 60.000 6.18 0.00 0.00 3.41
4133 4528 3.083349 CCACCTCGGAGCATGGGA 61.083 66.667 15.34 0.00 36.56 4.37
4176 4572 0.819582 CATTGCCCAAGGTGATGACC 59.180 55.000 0.00 0.00 43.52 4.02


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

AutoCloner maintained by Alex Coulton.