Multiple sequence alignment - TraesCS3A01G487700

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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 TraesCS3A01G487700 chr3A 100.000 2808 0 0 1 2808 715595866 715593059 0.000000e+00 5186
1 TraesCS3A01G487700 chr3A 93.564 606 18 6 2224 2808 709209074 709209679 0.000000e+00 883
2 TraesCS3A01G487700 chr3A 86.344 703 64 23 2116 2808 740871500 740870820 0.000000e+00 737
3 TraesCS3A01G487700 chr3A 89.444 540 34 10 2269 2808 93319888 93320404 0.000000e+00 660
4 TraesCS3A01G487700 chr3A 84.815 270 30 6 490 749 582944882 582944614 7.710000e-66 261
5 TraesCS3A01G487700 chr3B 93.984 1147 63 3 738 1882 775563103 775561961 0.000000e+00 1731
6 TraesCS3A01G487700 chr3B 90.190 683 30 10 1433 2115 775445354 775444709 0.000000e+00 856
7 TraesCS3A01G487700 chr3B 89.626 588 51 4 745 1322 775446020 775445433 0.000000e+00 739
8 TraesCS3A01G487700 chr3B 84.538 692 61 15 2117 2808 800828241 800827596 0.000000e+00 643
9 TraesCS3A01G487700 chr3B 80.952 273 49 2 1053 1322 802921504 802921232 2.190000e-51 213
10 TraesCS3A01G487700 chr3B 80.586 273 50 2 1053 1322 802902580 802902308 1.020000e-49 207
11 TraesCS3A01G487700 chr3D 89.372 1402 92 27 739 2120 580318842 580317478 0.000000e+00 1711
12 TraesCS3A01G487700 chr3D 89.069 494 32 11 1 492 580319312 580318839 6.700000e-166 593
13 TraesCS3A01G487700 chr3D 78.626 262 53 2 1064 1322 596886486 596886225 1.340000e-38 171
14 TraesCS3A01G487700 chr7A 90.909 704 24 20 2117 2808 66986995 66987670 0.000000e+00 909
15 TraesCS3A01G487700 chr7A 90.922 705 23 22 2117 2808 67002793 67003469 0.000000e+00 909
16 TraesCS3A01G487700 chr7A 90.483 704 27 20 2117 2808 67018367 67019042 0.000000e+00 893
17 TraesCS3A01G487700 chr7A 100.000 77 0 0 2117 2193 67266209 67266285 2.920000e-30 143
18 TraesCS3A01G487700 chr7A 97.403 77 2 0 2117 2193 67281835 67281911 6.310000e-27 132
19 TraesCS3A01G487700 chr4A 93.624 596 25 7 2224 2808 596078818 596079411 0.000000e+00 878
20 TraesCS3A01G487700 chr4A 85.328 259 29 4 487 736 743449603 743449861 2.770000e-65 259
21 TraesCS3A01G487700 chr6A 93.234 606 18 5 2224 2808 37779532 37780135 0.000000e+00 870
22 TraesCS3A01G487700 chr1A 93.081 607 20 8 2224 2808 21550870 21551476 0.000000e+00 869
23 TraesCS3A01G487700 chr6D 86.154 715 45 26 2117 2808 428955265 428954582 0.000000e+00 723
24 TraesCS3A01G487700 chr6D 85.659 258 26 6 495 743 52294567 52294312 7.710000e-66 261
25 TraesCS3A01G487700 chr5A 85.735 701 58 20 2117 2806 631682172 631682841 0.000000e+00 702
26 TraesCS3A01G487700 chr5A 85.227 264 25 8 493 747 427372326 427372584 2.770000e-65 259
27 TraesCS3A01G487700 chr6B 85.356 717 50 15 2115 2808 696372018 696371334 0.000000e+00 691
28 TraesCS3A01G487700 chr6B 85.115 262 29 5 491 743 536831173 536831433 2.770000e-65 259
29 TraesCS3A01G487700 chr2A 85.159 694 54 19 2117 2808 707296012 707295366 0.000000e+00 665
30 TraesCS3A01G487700 chr1B 88.506 261 21 4 491 742 442201637 442201897 9.770000e-80 307
31 TraesCS3A01G487700 chr5D 85.551 263 29 4 490 743 279293132 279292870 1.660000e-67 267
32 TraesCS3A01G487700 chr5D 86.939 245 23 4 502 737 538762619 538762375 1.660000e-67 267
33 TraesCS3A01G487700 chr2D 85.551 263 29 3 490 743 558801358 558801620 1.660000e-67 267
34 TraesCS3A01G487700 chr7D 76.176 340 73 8 1435 1770 46523858 46524193 3.720000e-39 172


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 TraesCS3A01G487700 chr3A 715593059 715595866 2807 True 5186.0 5186 100.0000 1 2808 1 chr3A.!!$R2 2807
1 TraesCS3A01G487700 chr3A 709209074 709209679 605 False 883.0 883 93.5640 2224 2808 1 chr3A.!!$F2 584
2 TraesCS3A01G487700 chr3A 740870820 740871500 680 True 737.0 737 86.3440 2116 2808 1 chr3A.!!$R3 692
3 TraesCS3A01G487700 chr3A 93319888 93320404 516 False 660.0 660 89.4440 2269 2808 1 chr3A.!!$F1 539
4 TraesCS3A01G487700 chr3B 775561961 775563103 1142 True 1731.0 1731 93.9840 738 1882 1 chr3B.!!$R1 1144
5 TraesCS3A01G487700 chr3B 775444709 775446020 1311 True 797.5 856 89.9080 745 2115 2 chr3B.!!$R5 1370
6 TraesCS3A01G487700 chr3B 800827596 800828241 645 True 643.0 643 84.5380 2117 2808 1 chr3B.!!$R2 691
7 TraesCS3A01G487700 chr3D 580317478 580319312 1834 True 1152.0 1711 89.2205 1 2120 2 chr3D.!!$R2 2119
8 TraesCS3A01G487700 chr7A 66986995 66987670 675 False 909.0 909 90.9090 2117 2808 1 chr7A.!!$F1 691
9 TraesCS3A01G487700 chr7A 67002793 67003469 676 False 909.0 909 90.9220 2117 2808 1 chr7A.!!$F2 691
10 TraesCS3A01G487700 chr7A 67018367 67019042 675 False 893.0 893 90.4830 2117 2808 1 chr7A.!!$F3 691
11 TraesCS3A01G487700 chr4A 596078818 596079411 593 False 878.0 878 93.6240 2224 2808 1 chr4A.!!$F1 584
12 TraesCS3A01G487700 chr6A 37779532 37780135 603 False 870.0 870 93.2340 2224 2808 1 chr6A.!!$F1 584
13 TraesCS3A01G487700 chr1A 21550870 21551476 606 False 869.0 869 93.0810 2224 2808 1 chr1A.!!$F1 584
14 TraesCS3A01G487700 chr6D 428954582 428955265 683 True 723.0 723 86.1540 2117 2808 1 chr6D.!!$R2 691
15 TraesCS3A01G487700 chr5A 631682172 631682841 669 False 702.0 702 85.7350 2117 2806 1 chr5A.!!$F2 689
16 TraesCS3A01G487700 chr6B 696371334 696372018 684 True 691.0 691 85.3560 2115 2808 1 chr6B.!!$R1 693
17 TraesCS3A01G487700 chr2A 707295366 707296012 646 True 665.0 665 85.1590 2117 2808 1 chr2A.!!$R1 691

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
949 951 0.741927 AGTAACCGGCCATTACGCAC 60.742 55.0 17.15 1.49 37.56 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2437 0.245266 TAGATTTGACGGCGTCAGCA 59.755 50.0 36.94 28.84 43.69 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.553904 GCTAATGGATGGATGGTGGAGG 60.554 54.545 0.00 0.00 0.00 4.30
104 105 3.804873 GGTTGATGAGCCGATAGAGAAAC 59.195 47.826 0.00 0.00 39.76 2.78
105 106 4.433615 GTTGATGAGCCGATAGAGAAACA 58.566 43.478 0.00 0.00 39.76 2.83
114 115 4.034510 GCCGATAGAGAAACAAATGAGGTG 59.965 45.833 0.00 0.00 39.76 4.00
118 119 2.887152 AGAGAAACAAATGAGGTGGCAC 59.113 45.455 9.70 9.70 0.00 5.01
120 121 3.030291 AGAAACAAATGAGGTGGCACAA 58.970 40.909 20.82 4.57 44.16 3.33
129 130 1.760480 GGTGGCACAAACCAACCCT 60.760 57.895 20.82 0.00 41.96 4.34
134 135 1.201414 GGCACAAACCAACCCTTATCG 59.799 52.381 0.00 0.00 0.00 2.92
140 141 2.467566 ACCAACCCTTATCGTGTCAC 57.532 50.000 0.00 0.00 0.00 3.67
145 146 1.968493 ACCCTTATCGTGTCACTGTGT 59.032 47.619 7.79 0.00 0.00 3.72
146 147 2.288825 ACCCTTATCGTGTCACTGTGTG 60.289 50.000 7.79 0.00 34.45 3.82
147 148 2.337583 CCTTATCGTGTCACTGTGTGG 58.662 52.381 7.79 0.00 33.87 4.17
148 149 2.288825 CCTTATCGTGTCACTGTGTGGT 60.289 50.000 7.79 0.00 33.87 4.16
149 150 3.390135 CTTATCGTGTCACTGTGTGGTT 58.610 45.455 7.79 0.00 33.87 3.67
150 151 4.552355 CTTATCGTGTCACTGTGTGGTTA 58.448 43.478 7.79 0.00 33.87 2.85
151 152 2.212869 TCGTGTCACTGTGTGGTTAC 57.787 50.000 7.79 0.00 33.87 2.50
153 154 1.534385 CGTGTCACTGTGTGGTTACGA 60.534 52.381 7.79 0.00 37.02 3.43
154 155 2.124903 GTGTCACTGTGTGGTTACGAG 58.875 52.381 7.79 0.00 33.87 4.18
155 156 1.067974 TGTCACTGTGTGGTTACGAGG 59.932 52.381 7.79 0.00 33.87 4.63
156 157 1.068127 GTCACTGTGTGGTTACGAGGT 59.932 52.381 7.79 0.00 33.87 3.85
157 158 1.758280 TCACTGTGTGGTTACGAGGTT 59.242 47.619 7.79 0.00 33.87 3.50
158 159 1.864711 CACTGTGTGGTTACGAGGTTG 59.135 52.381 0.00 0.00 0.00 3.77
159 160 1.758280 ACTGTGTGGTTACGAGGTTGA 59.242 47.619 0.00 0.00 0.00 3.18
160 161 2.132762 CTGTGTGGTTACGAGGTTGAC 58.867 52.381 0.00 0.00 0.00 3.18
161 162 1.202557 TGTGTGGTTACGAGGTTGACC 60.203 52.381 0.00 0.00 0.00 4.02
176 177 6.620877 AGGTTGACCTAATGACAGACATTA 57.379 37.500 0.00 5.39 46.48 1.90
185 186 8.321353 ACCTAATGACAGACATTATTGAAGTCA 58.679 33.333 5.88 0.00 46.22 3.41
206 207 3.868077 CAGAGGAGGAGTTTTAGAATGCG 59.132 47.826 0.00 0.00 0.00 4.73
231 232 2.481449 GCAACCGGAGATGTGGTAGTAG 60.481 54.545 9.46 0.00 37.54 2.57
234 235 1.955080 CCGGAGATGTGGTAGTAGGAC 59.045 57.143 0.00 0.00 0.00 3.85
238 239 2.694109 GAGATGTGGTAGTAGGACACCC 59.306 54.545 0.00 0.00 34.33 4.61
260 261 1.974236 CTAGAGATCGGGGCAAAGGAT 59.026 52.381 0.00 0.00 0.00 3.24
281 282 3.411446 TGGTGAAGATGGTAACTGCTTG 58.589 45.455 0.00 0.00 32.20 4.01
285 286 5.183904 GGTGAAGATGGTAACTGCTTGATTT 59.816 40.000 0.00 0.00 32.20 2.17
288 289 8.125448 GTGAAGATGGTAACTGCTTGATTTATC 58.875 37.037 0.00 0.00 32.20 1.75
289 290 8.049117 TGAAGATGGTAACTGCTTGATTTATCT 58.951 33.333 0.00 0.00 32.20 1.98
427 429 2.837498 TGTATCAGACGCCCATTCATG 58.163 47.619 0.00 0.00 0.00 3.07
441 443 2.512485 TTCATGTTGGCTTGCTGTTG 57.488 45.000 0.00 0.00 0.00 3.33
454 456 3.266510 TGCTGTTGCTATAACTCCCTG 57.733 47.619 0.00 0.00 40.48 4.45
497 499 1.723288 GGCCTGGCCTAGTATTCTCT 58.277 55.000 30.42 0.00 46.69 3.10
498 500 1.621317 GGCCTGGCCTAGTATTCTCTC 59.379 57.143 30.42 0.00 46.69 3.20
499 501 2.604139 GCCTGGCCTAGTATTCTCTCT 58.396 52.381 7.66 0.00 0.00 3.10
500 502 2.298729 GCCTGGCCTAGTATTCTCTCTG 59.701 54.545 7.66 0.00 0.00 3.35
501 503 3.571590 CCTGGCCTAGTATTCTCTCTGT 58.428 50.000 3.32 0.00 0.00 3.41
502 504 3.964031 CCTGGCCTAGTATTCTCTCTGTT 59.036 47.826 3.32 0.00 0.00 3.16
503 505 4.407296 CCTGGCCTAGTATTCTCTCTGTTT 59.593 45.833 3.32 0.00 0.00 2.83
504 506 5.104735 CCTGGCCTAGTATTCTCTCTGTTTT 60.105 44.000 3.32 0.00 0.00 2.43
505 507 6.374417 TGGCCTAGTATTCTCTCTGTTTTT 57.626 37.500 3.32 0.00 0.00 1.94
506 508 7.364762 CCTGGCCTAGTATTCTCTCTGTTTTTA 60.365 40.741 3.32 0.00 0.00 1.52
507 509 8.090788 TGGCCTAGTATTCTCTCTGTTTTTAT 57.909 34.615 3.32 0.00 0.00 1.40
508 510 8.548877 TGGCCTAGTATTCTCTCTGTTTTTATT 58.451 33.333 3.32 0.00 0.00 1.40
509 511 9.397280 GGCCTAGTATTCTCTCTGTTTTTATTT 57.603 33.333 0.00 0.00 0.00 1.40
517 519 8.902540 TTCTCTCTGTTTTTATTTACTCTGCA 57.097 30.769 0.00 0.00 0.00 4.41
518 520 9.507329 TTCTCTCTGTTTTTATTTACTCTGCAT 57.493 29.630 0.00 0.00 0.00 3.96
535 537 7.244166 CTCTGCATATTAGAGTTGGTTGAAG 57.756 40.000 5.84 0.00 37.48 3.02
536 538 6.711277 TCTGCATATTAGAGTTGGTTGAAGT 58.289 36.000 0.00 0.00 0.00 3.01
537 539 6.818644 TCTGCATATTAGAGTTGGTTGAAGTC 59.181 38.462 0.00 0.00 34.56 3.01
538 540 6.472016 TGCATATTAGAGTTGGTTGAAGTCA 58.528 36.000 0.00 0.00 36.57 3.41
539 541 6.939730 TGCATATTAGAGTTGGTTGAAGTCAA 59.060 34.615 0.00 0.00 36.57 3.18
540 542 7.446931 TGCATATTAGAGTTGGTTGAAGTCAAA 59.553 33.333 0.00 0.00 36.57 2.69
541 543 7.750903 GCATATTAGAGTTGGTTGAAGTCAAAC 59.249 37.037 1.98 1.98 43.57 2.93
542 544 9.003658 CATATTAGAGTTGGTTGAAGTCAAACT 57.996 33.333 10.29 3.94 43.65 2.66
543 545 7.881775 ATTAGAGTTGGTTGAAGTCAAACTT 57.118 32.000 10.29 0.00 43.65 2.66
544 546 7.696992 TTAGAGTTGGTTGAAGTCAAACTTT 57.303 32.000 10.29 2.55 43.65 2.66
545 547 5.954335 AGAGTTGGTTGAAGTCAAACTTTG 58.046 37.500 10.29 0.00 43.65 2.77
546 548 5.476945 AGAGTTGGTTGAAGTCAAACTTTGT 59.523 36.000 10.29 0.00 43.65 2.83
547 549 6.657541 AGAGTTGGTTGAAGTCAAACTTTGTA 59.342 34.615 10.29 0.00 43.65 2.41
548 550 7.175990 AGAGTTGGTTGAAGTCAAACTTTGTAA 59.824 33.333 10.29 0.00 43.65 2.41
549 551 7.662897 AGTTGGTTGAAGTCAAACTTTGTAAA 58.337 30.769 10.29 0.00 43.65 2.01
550 552 8.311109 AGTTGGTTGAAGTCAAACTTTGTAAAT 58.689 29.630 10.29 0.00 43.65 1.40
551 553 8.931775 GTTGGTTGAAGTCAAACTTTGTAAATT 58.068 29.630 10.29 0.00 43.65 1.82
552 554 8.472683 TGGTTGAAGTCAAACTTTGTAAATTG 57.527 30.769 10.29 0.00 43.65 2.32
553 555 8.307483 TGGTTGAAGTCAAACTTTGTAAATTGA 58.693 29.630 10.29 0.00 43.65 2.57
554 556 9.313118 GGTTGAAGTCAAACTTTGTAAATTGAT 57.687 29.630 1.72 0.00 38.80 2.57
593 595 9.953697 AAAAATACAAACGCTGACTATAACAAA 57.046 25.926 0.00 0.00 0.00 2.83
595 597 9.769093 AAATACAAACGCTGACTATAACAAATC 57.231 29.630 0.00 0.00 0.00 2.17
596 598 8.718102 ATACAAACGCTGACTATAACAAATCT 57.282 30.769 0.00 0.00 0.00 2.40
597 599 9.811995 ATACAAACGCTGACTATAACAAATCTA 57.188 29.630 0.00 0.00 0.00 1.98
598 600 8.718102 ACAAACGCTGACTATAACAAATCTAT 57.282 30.769 0.00 0.00 0.00 1.98
599 601 9.811995 ACAAACGCTGACTATAACAAATCTATA 57.188 29.630 0.00 0.00 0.00 1.31
717 719 7.953710 ACAAAACTTAACTAAAGCTAATACGCG 59.046 33.333 3.53 3.53 38.93 6.01
718 720 6.579491 AACTTAACTAAAGCTAATACGCGG 57.421 37.500 12.47 0.00 38.93 6.46
719 721 5.894807 ACTTAACTAAAGCTAATACGCGGA 58.105 37.500 12.47 0.00 38.93 5.54
720 722 6.510536 ACTTAACTAAAGCTAATACGCGGAT 58.489 36.000 12.47 3.58 38.93 4.18
721 723 6.982724 ACTTAACTAAAGCTAATACGCGGATT 59.017 34.615 22.18 22.18 38.93 3.01
722 724 5.652744 AACTAAAGCTAATACGCGGATTG 57.347 39.130 26.70 16.51 34.40 2.67
723 725 4.940463 ACTAAAGCTAATACGCGGATTGA 58.060 39.130 26.70 9.61 34.40 2.57
724 726 5.353938 ACTAAAGCTAATACGCGGATTGAA 58.646 37.500 26.70 6.58 34.40 2.69
725 727 5.989777 ACTAAAGCTAATACGCGGATTGAAT 59.010 36.000 26.70 8.78 34.40 2.57
726 728 4.732285 AAGCTAATACGCGGATTGAATG 57.268 40.909 26.70 13.99 34.40 2.67
727 729 3.990092 AGCTAATACGCGGATTGAATGA 58.010 40.909 26.70 4.98 34.40 2.57
728 730 4.377021 AGCTAATACGCGGATTGAATGAA 58.623 39.130 26.70 4.18 34.40 2.57
729 731 4.814234 AGCTAATACGCGGATTGAATGAAA 59.186 37.500 26.70 3.40 34.40 2.69
730 732 5.295787 AGCTAATACGCGGATTGAATGAAAA 59.704 36.000 26.70 2.60 34.40 2.29
731 733 5.395486 GCTAATACGCGGATTGAATGAAAAC 59.605 40.000 26.70 0.00 0.00 2.43
732 734 4.955925 ATACGCGGATTGAATGAAAACA 57.044 36.364 12.47 0.00 0.00 2.83
733 735 3.201726 ACGCGGATTGAATGAAAACAG 57.798 42.857 12.47 0.00 0.00 3.16
734 736 2.811431 ACGCGGATTGAATGAAAACAGA 59.189 40.909 12.47 0.00 0.00 3.41
735 737 3.120199 ACGCGGATTGAATGAAAACAGAG 60.120 43.478 12.47 0.00 0.00 3.35
736 738 3.728864 CGCGGATTGAATGAAAACAGAGG 60.729 47.826 0.00 0.00 0.00 3.69
737 739 3.762779 CGGATTGAATGAAAACAGAGGC 58.237 45.455 0.00 0.00 0.00 4.70
738 740 3.191162 CGGATTGAATGAAAACAGAGGCA 59.809 43.478 0.00 0.00 0.00 4.75
739 741 4.673580 CGGATTGAATGAAAACAGAGGCAG 60.674 45.833 0.00 0.00 0.00 4.85
740 742 4.219288 GGATTGAATGAAAACAGAGGCAGT 59.781 41.667 0.00 0.00 0.00 4.40
743 745 3.745975 TGAATGAAAACAGAGGCAGTACG 59.254 43.478 0.00 0.00 0.00 3.67
765 767 9.655769 GTACGTTATTTTATCGATCACTCTGTA 57.344 33.333 0.00 0.00 0.00 2.74
822 824 2.689471 AGCAACATTTGACTTGTGCTCA 59.311 40.909 0.00 0.00 30.79 4.26
933 935 7.201661 CCAAGCGCTATAAAATACCACAAAGTA 60.202 37.037 12.05 0.00 0.00 2.24
949 951 0.741927 AGTAACCGGCCATTACGCAC 60.742 55.000 17.15 1.49 37.56 5.34
1080 1092 2.125106 GAGGTTACCCTGCGCCTG 60.125 66.667 4.18 0.00 42.86 4.85
1107 1119 1.757699 GTTCCCTACGAGCTCATCCTT 59.242 52.381 15.40 0.00 0.00 3.36
1185 1197 3.402681 CCCGTGCTCCTCCATGGT 61.403 66.667 12.58 0.00 39.72 3.55
1225 1237 1.003866 CGCTCATCATCGTCGAGTACA 60.004 52.381 0.00 0.00 0.00 2.90
1269 1281 3.823330 CTTCTCCCGACCGACCCG 61.823 72.222 0.00 0.00 0.00 5.28
1351 1367 0.373370 CTCTCGTCTCACTCTGCTCG 59.627 60.000 0.00 0.00 0.00 5.03
1373 1389 5.521735 TCGTACTTTCTCTAGTAGTTAGCGG 59.478 44.000 0.00 0.00 31.56 5.52
1384 1408 2.180432 AGTTAGCGGTCTTGTTTCCC 57.820 50.000 0.00 0.00 0.00 3.97
1391 1415 2.031420 GCGGTCTTGTTTCCCTGTAAAC 60.031 50.000 0.00 0.00 39.35 2.01
1392 1416 3.473625 CGGTCTTGTTTCCCTGTAAACT 58.526 45.455 0.00 0.00 39.57 2.66
1393 1417 3.497262 CGGTCTTGTTTCCCTGTAAACTC 59.503 47.826 0.00 0.00 39.57 3.01
1588 1614 3.221222 GGCCTCGTGGACATAGCT 58.779 61.111 7.92 0.00 42.34 3.32
1721 1747 1.589113 GAGAAGGTCAGAGCGTGCT 59.411 57.895 0.00 0.00 0.00 4.40
1883 1909 2.970639 CCCACGGTCGTCATGTCT 59.029 61.111 0.00 0.00 0.00 3.41
1884 1910 1.940883 GCCCACGGTCGTCATGTCTA 61.941 60.000 0.00 0.00 0.00 2.59
1885 1911 0.179145 CCCACGGTCGTCATGTCTAC 60.179 60.000 0.00 0.00 0.00 2.59
1886 1912 0.809385 CCACGGTCGTCATGTCTACT 59.191 55.000 0.00 0.00 0.00 2.57
1887 1913 1.201647 CCACGGTCGTCATGTCTACTT 59.798 52.381 0.00 0.00 0.00 2.24
1888 1914 2.251040 CACGGTCGTCATGTCTACTTG 58.749 52.381 0.00 0.00 0.00 3.16
1890 1916 2.095364 ACGGTCGTCATGTCTACTTGTC 60.095 50.000 0.00 0.00 0.00 3.18
1891 1917 2.161808 CGGTCGTCATGTCTACTTGTCT 59.838 50.000 0.00 0.00 0.00 3.41
1892 1918 3.373130 CGGTCGTCATGTCTACTTGTCTA 59.627 47.826 0.00 0.00 0.00 2.59
1893 1919 4.494362 CGGTCGTCATGTCTACTTGTCTAG 60.494 50.000 0.00 0.00 0.00 2.43
1894 1920 4.201930 GGTCGTCATGTCTACTTGTCTAGG 60.202 50.000 0.00 0.00 0.00 3.02
1895 1921 4.634883 GTCGTCATGTCTACTTGTCTAGGA 59.365 45.833 0.00 0.00 0.00 2.94
1896 1922 5.123502 GTCGTCATGTCTACTTGTCTAGGAA 59.876 44.000 0.00 0.00 0.00 3.36
1897 1923 5.886474 TCGTCATGTCTACTTGTCTAGGAAT 59.114 40.000 0.00 0.00 0.00 3.01
1898 1924 7.012138 GTCGTCATGTCTACTTGTCTAGGAATA 59.988 40.741 0.00 0.00 0.00 1.75
1899 1925 7.555195 TCGTCATGTCTACTTGTCTAGGAATAA 59.445 37.037 0.00 0.00 0.00 1.40
1900 1926 7.858382 CGTCATGTCTACTTGTCTAGGAATAAG 59.142 40.741 0.00 0.00 0.00 1.73
1907 1933 9.654663 TCTACTTGTCTAGGAATAAGAAAAAGC 57.345 33.333 0.00 0.00 0.00 3.51
1920 1946 3.227614 AGAAAAAGCCCACGTTTACCAT 58.772 40.909 0.00 0.00 0.00 3.55
1936 1962 7.719633 ACGTTTACCATTATTAATCAGCCATCT 59.280 33.333 0.00 0.00 0.00 2.90
1937 1963 8.230486 CGTTTACCATTATTAATCAGCCATCTC 58.770 37.037 0.00 0.00 0.00 2.75
2000 2026 2.560981 TCACATTACTCCTCTCGCAACA 59.439 45.455 0.00 0.00 0.00 3.33
2001 2027 2.926200 CACATTACTCCTCTCGCAACAG 59.074 50.000 0.00 0.00 0.00 3.16
2002 2028 2.563179 ACATTACTCCTCTCGCAACAGT 59.437 45.455 0.00 0.00 0.00 3.55
2003 2029 3.006967 ACATTACTCCTCTCGCAACAGTT 59.993 43.478 0.00 0.00 0.00 3.16
2004 2030 3.299340 TTACTCCTCTCGCAACAGTTC 57.701 47.619 0.00 0.00 0.00 3.01
2005 2031 1.040646 ACTCCTCTCGCAACAGTTCA 58.959 50.000 0.00 0.00 0.00 3.18
2006 2032 1.412710 ACTCCTCTCGCAACAGTTCAA 59.587 47.619 0.00 0.00 0.00 2.69
2007 2033 1.795286 CTCCTCTCGCAACAGTTCAAC 59.205 52.381 0.00 0.00 0.00 3.18
2197 2236 5.008619 CATAGATGGAGCTATGCCTACAG 57.991 47.826 0.00 0.00 40.71 2.74
2198 2237 1.622811 AGATGGAGCTATGCCTACAGC 59.377 52.381 0.00 0.00 44.14 4.40
2212 2251 3.275400 CTACAGCAGTCGTAGGCATAG 57.725 52.381 0.00 0.00 34.03 2.23
2213 2252 0.103208 ACAGCAGTCGTAGGCATAGC 59.897 55.000 0.00 0.00 0.00 2.97
2214 2253 0.387202 CAGCAGTCGTAGGCATAGCT 59.613 55.000 0.00 0.00 37.48 3.32
2215 2254 0.671251 AGCAGTCGTAGGCATAGCTC 59.329 55.000 0.00 0.00 32.05 4.09
2216 2255 0.319125 GCAGTCGTAGGCATAGCTCC 60.319 60.000 0.00 0.00 0.00 4.70
2217 2256 1.032794 CAGTCGTAGGCATAGCTCCA 58.967 55.000 0.00 0.00 0.00 3.86
2218 2257 1.615883 CAGTCGTAGGCATAGCTCCAT 59.384 52.381 0.00 0.00 0.00 3.41
2219 2258 1.889829 AGTCGTAGGCATAGCTCCATC 59.110 52.381 0.00 0.00 0.00 3.51
2220 2259 1.889829 GTCGTAGGCATAGCTCCATCT 59.110 52.381 0.00 0.00 0.00 2.90
2221 2260 3.082548 GTCGTAGGCATAGCTCCATCTA 58.917 50.000 0.00 0.00 0.00 1.98
2222 2261 3.697045 GTCGTAGGCATAGCTCCATCTAT 59.303 47.826 0.00 0.00 0.00 1.98
2240 2279 0.988832 ATGCCTAGGGAAAACCGTCA 59.011 50.000 7.22 0.00 46.96 4.35
2347 2386 0.103208 ACAGCAGTCGTAGGCATAGC 59.897 55.000 0.00 0.00 0.00 2.97
2498 2543 0.601558 ACGTGGTATAGCTATGCCGG 59.398 55.000 28.90 25.20 40.81 6.13
2518 2563 1.378531 CGGCAAAGCTGTAGGCATAA 58.621 50.000 7.47 0.00 44.79 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.553904 CCTCCACCATCCATCCATTAGC 60.554 54.545 0.00 0.00 0.00 3.09
104 105 1.411977 TGGTTTGTGCCACCTCATTTG 59.588 47.619 0.00 0.00 35.07 2.32
105 106 1.786937 TGGTTTGTGCCACCTCATTT 58.213 45.000 0.00 0.00 35.07 2.32
114 115 1.201414 CGATAAGGGTTGGTTTGTGCC 59.799 52.381 0.00 0.00 0.00 5.01
118 119 3.058501 GTGACACGATAAGGGTTGGTTTG 60.059 47.826 0.00 0.00 35.98 2.93
120 121 2.370849 AGTGACACGATAAGGGTTGGTT 59.629 45.455 0.00 0.00 35.98 3.67
126 127 2.337583 CACACAGTGACACGATAAGGG 58.662 52.381 7.81 0.00 35.23 3.95
129 130 3.462483 AACCACACAGTGACACGATAA 57.538 42.857 7.81 0.00 35.23 1.75
134 135 2.124903 CTCGTAACCACACAGTGACAC 58.875 52.381 7.81 0.00 35.23 3.67
140 141 2.132762 GTCAACCTCGTAACCACACAG 58.867 52.381 0.00 0.00 0.00 3.66
145 146 3.833650 TCATTAGGTCAACCTCGTAACCA 59.166 43.478 4.63 0.00 44.77 3.67
146 147 4.179298 GTCATTAGGTCAACCTCGTAACC 58.821 47.826 4.63 0.00 44.77 2.85
147 148 4.813027 TGTCATTAGGTCAACCTCGTAAC 58.187 43.478 4.63 1.90 44.77 2.50
148 149 4.768448 TCTGTCATTAGGTCAACCTCGTAA 59.232 41.667 4.63 0.00 44.77 3.18
149 150 4.157289 GTCTGTCATTAGGTCAACCTCGTA 59.843 45.833 4.63 0.00 44.77 3.43
150 151 3.056749 GTCTGTCATTAGGTCAACCTCGT 60.057 47.826 4.63 0.00 44.77 4.18
151 152 3.056821 TGTCTGTCATTAGGTCAACCTCG 60.057 47.826 4.63 0.00 44.77 4.63
153 154 5.505181 AATGTCTGTCATTAGGTCAACCT 57.495 39.130 6.95 6.95 43.93 3.50
163 164 7.551974 CCTCTGACTTCAATAATGTCTGTCATT 59.448 37.037 5.52 5.52 46.82 2.57
164 165 7.046652 CCTCTGACTTCAATAATGTCTGTCAT 58.953 38.462 0.00 0.00 38.57 3.06
165 166 6.211384 TCCTCTGACTTCAATAATGTCTGTCA 59.789 38.462 0.00 0.00 33.68 3.58
166 167 6.634805 TCCTCTGACTTCAATAATGTCTGTC 58.365 40.000 0.00 0.00 33.43 3.51
167 168 6.351711 CCTCCTCTGACTTCAATAATGTCTGT 60.352 42.308 0.00 0.00 33.43 3.41
176 177 5.574970 AAAACTCCTCCTCTGACTTCAAT 57.425 39.130 0.00 0.00 0.00 2.57
185 186 3.118592 CCGCATTCTAAAACTCCTCCTCT 60.119 47.826 0.00 0.00 0.00 3.69
206 207 2.040544 CACATCTCCGGTTGCCACC 61.041 63.158 0.00 0.00 40.16 4.61
231 232 1.033574 CCGATCTCTAGTGGGTGTCC 58.966 60.000 0.00 0.00 0.00 4.02
234 235 1.749334 GCCCCGATCTCTAGTGGGTG 61.749 65.000 0.00 0.00 40.20 4.61
238 239 1.202580 CCTTTGCCCCGATCTCTAGTG 60.203 57.143 0.00 0.00 0.00 2.74
260 261 3.072330 TCAAGCAGTTACCATCTTCACCA 59.928 43.478 0.00 0.00 0.00 4.17
321 323 6.128742 CCGTGAAAATTGTTACTTAGCGTAGT 60.129 38.462 0.00 0.00 0.00 2.73
409 411 3.205338 CAACATGAATGGGCGTCTGATA 58.795 45.455 0.00 0.00 0.00 2.15
427 429 3.191371 AGTTATAGCAACAGCAAGCCAAC 59.809 43.478 0.00 0.00 0.00 3.77
441 443 2.808543 CCAAATCGCAGGGAGTTATAGC 59.191 50.000 0.00 0.00 30.54 2.97
454 456 0.170116 TGTTTCCATCGCCAAATCGC 59.830 50.000 0.00 0.00 0.00 4.58
491 493 9.507329 TGCAGAGTAAATAAAAACAGAGAGAAT 57.493 29.630 0.00 0.00 0.00 2.40
492 494 8.902540 TGCAGAGTAAATAAAAACAGAGAGAA 57.097 30.769 0.00 0.00 0.00 2.87
511 513 6.820656 ACTTCAACCAACTCTAATATGCAGAG 59.179 38.462 11.37 11.37 44.28 3.35
512 514 6.711277 ACTTCAACCAACTCTAATATGCAGA 58.289 36.000 0.00 0.00 0.00 4.26
513 515 6.595326 TGACTTCAACCAACTCTAATATGCAG 59.405 38.462 0.00 0.00 0.00 4.41
514 516 6.472016 TGACTTCAACCAACTCTAATATGCA 58.528 36.000 0.00 0.00 0.00 3.96
515 517 6.985188 TGACTTCAACCAACTCTAATATGC 57.015 37.500 0.00 0.00 0.00 3.14
516 518 9.003658 AGTTTGACTTCAACCAACTCTAATATG 57.996 33.333 0.00 0.00 35.28 1.78
517 519 9.574516 AAGTTTGACTTCAACCAACTCTAATAT 57.425 29.630 0.00 0.00 31.77 1.28
518 520 8.974060 AAGTTTGACTTCAACCAACTCTAATA 57.026 30.769 0.00 0.00 31.77 0.98
519 521 7.881775 AAGTTTGACTTCAACCAACTCTAAT 57.118 32.000 0.00 0.00 31.77 1.73
520 522 7.175990 ACAAAGTTTGACTTCAACCAACTCTAA 59.824 33.333 22.23 0.00 37.47 2.10
521 523 6.657541 ACAAAGTTTGACTTCAACCAACTCTA 59.342 34.615 22.23 0.00 37.47 2.43
522 524 5.476945 ACAAAGTTTGACTTCAACCAACTCT 59.523 36.000 22.23 0.00 37.47 3.24
523 525 5.709966 ACAAAGTTTGACTTCAACCAACTC 58.290 37.500 22.23 0.00 37.47 3.01
524 526 5.722021 ACAAAGTTTGACTTCAACCAACT 57.278 34.783 22.23 0.00 37.47 3.16
525 527 7.876896 TTTACAAAGTTTGACTTCAACCAAC 57.123 32.000 22.23 0.00 37.47 3.77
526 528 8.930760 CAATTTACAAAGTTTGACTTCAACCAA 58.069 29.630 22.23 2.15 37.47 3.67
527 529 8.307483 TCAATTTACAAAGTTTGACTTCAACCA 58.693 29.630 22.23 0.00 37.47 3.67
528 530 8.696410 TCAATTTACAAAGTTTGACTTCAACC 57.304 30.769 22.23 0.00 37.47 3.77
567 569 9.953697 TTTGTTATAGTCAGCGTTTGTATTTTT 57.046 25.926 0.00 0.00 0.00 1.94
569 571 9.769093 GATTTGTTATAGTCAGCGTTTGTATTT 57.231 29.630 0.00 0.00 0.00 1.40
570 572 9.162764 AGATTTGTTATAGTCAGCGTTTGTATT 57.837 29.630 0.00 0.00 0.00 1.89
571 573 8.718102 AGATTTGTTATAGTCAGCGTTTGTAT 57.282 30.769 0.00 0.00 0.00 2.29
572 574 9.811995 ATAGATTTGTTATAGTCAGCGTTTGTA 57.188 29.630 0.00 0.00 0.00 2.41
573 575 8.718102 ATAGATTTGTTATAGTCAGCGTTTGT 57.282 30.769 0.00 0.00 0.00 2.83
691 693 7.953710 CGCGTATTAGCTTTAGTTAAGTTTTGT 59.046 33.333 0.00 0.00 36.19 2.83
692 694 7.424452 CCGCGTATTAGCTTTAGTTAAGTTTTG 59.576 37.037 4.92 0.00 36.19 2.44
693 695 7.331687 TCCGCGTATTAGCTTTAGTTAAGTTTT 59.668 33.333 4.92 0.00 36.19 2.43
694 696 6.813152 TCCGCGTATTAGCTTTAGTTAAGTTT 59.187 34.615 4.92 0.00 36.19 2.66
695 697 6.332630 TCCGCGTATTAGCTTTAGTTAAGTT 58.667 36.000 4.92 0.00 36.19 2.66
696 698 5.894807 TCCGCGTATTAGCTTTAGTTAAGT 58.105 37.500 4.92 0.00 36.19 2.24
697 699 7.168637 TCAATCCGCGTATTAGCTTTAGTTAAG 59.831 37.037 4.92 0.00 36.90 1.85
698 700 6.979817 TCAATCCGCGTATTAGCTTTAGTTAA 59.020 34.615 4.92 0.00 34.40 2.01
699 701 6.506147 TCAATCCGCGTATTAGCTTTAGTTA 58.494 36.000 4.92 0.00 34.40 2.24
700 702 5.353938 TCAATCCGCGTATTAGCTTTAGTT 58.646 37.500 4.92 0.00 34.40 2.24
701 703 4.940463 TCAATCCGCGTATTAGCTTTAGT 58.060 39.130 4.92 0.00 34.40 2.24
702 704 5.900339 TTCAATCCGCGTATTAGCTTTAG 57.100 39.130 4.92 0.00 34.40 1.85
703 705 5.986741 TCATTCAATCCGCGTATTAGCTTTA 59.013 36.000 4.92 0.00 34.40 1.85
704 706 4.814234 TCATTCAATCCGCGTATTAGCTTT 59.186 37.500 4.92 0.00 34.40 3.51
705 707 4.377021 TCATTCAATCCGCGTATTAGCTT 58.623 39.130 4.92 0.00 34.40 3.74
706 708 3.990092 TCATTCAATCCGCGTATTAGCT 58.010 40.909 4.92 0.00 34.40 3.32
707 709 4.725556 TTCATTCAATCCGCGTATTAGC 57.274 40.909 4.92 0.00 0.00 3.09
708 710 6.482835 TGTTTTCATTCAATCCGCGTATTAG 58.517 36.000 4.92 0.00 0.00 1.73
709 711 6.314152 TCTGTTTTCATTCAATCCGCGTATTA 59.686 34.615 4.92 0.00 0.00 0.98
710 712 5.123186 TCTGTTTTCATTCAATCCGCGTATT 59.877 36.000 4.92 0.00 0.00 1.89
711 713 4.634004 TCTGTTTTCATTCAATCCGCGTAT 59.366 37.500 4.92 0.00 0.00 3.06
712 714 3.997681 TCTGTTTTCATTCAATCCGCGTA 59.002 39.130 4.92 0.00 0.00 4.42
713 715 2.811431 TCTGTTTTCATTCAATCCGCGT 59.189 40.909 4.92 0.00 0.00 6.01
714 716 3.419915 CTCTGTTTTCATTCAATCCGCG 58.580 45.455 0.00 0.00 0.00 6.46
715 717 3.762779 CCTCTGTTTTCATTCAATCCGC 58.237 45.455 0.00 0.00 0.00 5.54
716 718 3.191162 TGCCTCTGTTTTCATTCAATCCG 59.809 43.478 0.00 0.00 0.00 4.18
717 719 4.219288 ACTGCCTCTGTTTTCATTCAATCC 59.781 41.667 0.00 0.00 0.00 3.01
718 720 5.382618 ACTGCCTCTGTTTTCATTCAATC 57.617 39.130 0.00 0.00 0.00 2.67
719 721 5.106555 CGTACTGCCTCTGTTTTCATTCAAT 60.107 40.000 0.00 0.00 0.00 2.57
720 722 4.213270 CGTACTGCCTCTGTTTTCATTCAA 59.787 41.667 0.00 0.00 0.00 2.69
721 723 3.745975 CGTACTGCCTCTGTTTTCATTCA 59.254 43.478 0.00 0.00 0.00 2.57
722 724 3.746492 ACGTACTGCCTCTGTTTTCATTC 59.254 43.478 0.00 0.00 0.00 2.67
723 725 3.740115 ACGTACTGCCTCTGTTTTCATT 58.260 40.909 0.00 0.00 0.00 2.57
724 726 3.402628 ACGTACTGCCTCTGTTTTCAT 57.597 42.857 0.00 0.00 0.00 2.57
725 727 2.902705 ACGTACTGCCTCTGTTTTCA 57.097 45.000 0.00 0.00 0.00 2.69
726 728 5.857822 AATAACGTACTGCCTCTGTTTTC 57.142 39.130 0.00 0.00 0.00 2.29
727 729 6.628919 AAAATAACGTACTGCCTCTGTTTT 57.371 33.333 0.00 0.00 0.00 2.43
728 730 7.201496 CGATAAAATAACGTACTGCCTCTGTTT 60.201 37.037 0.00 0.00 0.00 2.83
729 731 6.255020 CGATAAAATAACGTACTGCCTCTGTT 59.745 38.462 0.00 0.00 0.00 3.16
730 732 5.747197 CGATAAAATAACGTACTGCCTCTGT 59.253 40.000 0.00 0.00 0.00 3.41
731 733 5.975344 TCGATAAAATAACGTACTGCCTCTG 59.025 40.000 0.00 0.00 0.00 3.35
732 734 6.140303 TCGATAAAATAACGTACTGCCTCT 57.860 37.500 0.00 0.00 0.00 3.69
733 735 6.639686 TGATCGATAAAATAACGTACTGCCTC 59.360 38.462 0.00 0.00 0.00 4.70
734 736 6.420008 GTGATCGATAAAATAACGTACTGCCT 59.580 38.462 0.00 0.00 0.00 4.75
735 737 6.420008 AGTGATCGATAAAATAACGTACTGCC 59.580 38.462 0.00 0.00 0.00 4.85
736 738 7.378995 AGAGTGATCGATAAAATAACGTACTGC 59.621 37.037 0.00 0.00 0.00 4.40
737 739 8.682895 CAGAGTGATCGATAAAATAACGTACTG 58.317 37.037 0.00 0.00 0.00 2.74
738 740 8.404000 ACAGAGTGATCGATAAAATAACGTACT 58.596 33.333 0.00 0.00 0.00 2.73
739 741 8.557869 ACAGAGTGATCGATAAAATAACGTAC 57.442 34.615 0.00 0.00 0.00 3.67
743 745 9.692749 TCCATACAGAGTGATCGATAAAATAAC 57.307 33.333 0.00 0.00 0.00 1.89
765 767 0.036732 TCCTTGTTGCTTCGCTCCAT 59.963 50.000 0.00 0.00 0.00 3.41
822 824 7.041721 GGAAGAACAGATTGTTTTTGTTTCCT 58.958 34.615 2.91 0.00 41.28 3.36
861 863 6.477688 CGAGGCTATTTTAATCGAGTTGGTAA 59.522 38.462 0.00 0.00 35.47 2.85
933 935 2.032834 TGTGCGTAATGGCCGGTT 59.967 55.556 1.90 0.00 0.00 4.44
949 951 6.427853 TCAAATGTAGATTGTTGTGAGGTCTG 59.572 38.462 0.00 0.00 0.00 3.51
1107 1119 1.345741 CTCTTGTTGTGGAGCTCCTCA 59.654 52.381 32.28 30.68 37.70 3.86
1142 1154 1.002624 TTGTGGACGGGATTGCTCC 60.003 57.895 0.00 0.00 41.26 4.70
1149 1161 1.752198 CACCTTCTTGTGGACGGGA 59.248 57.895 0.00 0.00 37.64 5.14
1251 1263 3.459063 GGGTCGGTCGGGAGAAGG 61.459 72.222 0.00 0.00 42.89 3.46
1351 1367 6.538381 AGACCGCTAACTACTAGAGAAAGTAC 59.462 42.308 0.00 0.00 29.30 2.73
1373 1389 4.715713 AGGAGTTTACAGGGAAACAAGAC 58.284 43.478 9.62 0.00 41.00 3.01
1384 1408 2.159226 CGTAGCCAGGAGGAGTTTACAG 60.159 54.545 0.00 0.00 36.89 2.74
1391 1415 0.395311 TGGTACGTAGCCAGGAGGAG 60.395 60.000 21.20 0.00 36.89 3.69
1392 1416 1.693034 TGGTACGTAGCCAGGAGGA 59.307 57.895 21.20 0.00 36.89 3.71
1393 1417 4.349682 TGGTACGTAGCCAGGAGG 57.650 61.111 21.20 0.00 38.23 4.30
1579 1605 2.590007 CCGCAGGCAGCTATGTCC 60.590 66.667 0.00 0.00 46.14 4.02
1883 1909 7.827729 GGGCTTTTTCTTATTCCTAGACAAGTA 59.172 37.037 0.00 0.00 0.00 2.24
1884 1910 6.659668 GGGCTTTTTCTTATTCCTAGACAAGT 59.340 38.462 0.00 0.00 0.00 3.16
1885 1911 6.659242 TGGGCTTTTTCTTATTCCTAGACAAG 59.341 38.462 0.00 0.00 0.00 3.16
1886 1912 6.433093 GTGGGCTTTTTCTTATTCCTAGACAA 59.567 38.462 0.00 0.00 0.00 3.18
1887 1913 5.944007 GTGGGCTTTTTCTTATTCCTAGACA 59.056 40.000 0.00 0.00 0.00 3.41
1888 1914 5.064834 CGTGGGCTTTTTCTTATTCCTAGAC 59.935 44.000 0.00 0.00 0.00 2.59
1890 1916 4.941873 ACGTGGGCTTTTTCTTATTCCTAG 59.058 41.667 0.00 0.00 0.00 3.02
1891 1917 4.913784 ACGTGGGCTTTTTCTTATTCCTA 58.086 39.130 0.00 0.00 0.00 2.94
1892 1918 3.763057 ACGTGGGCTTTTTCTTATTCCT 58.237 40.909 0.00 0.00 0.00 3.36
1893 1919 4.514781 AACGTGGGCTTTTTCTTATTCC 57.485 40.909 0.00 0.00 0.00 3.01
1894 1920 5.860182 GGTAAACGTGGGCTTTTTCTTATTC 59.140 40.000 0.00 0.00 0.00 1.75
1895 1921 5.302313 TGGTAAACGTGGGCTTTTTCTTATT 59.698 36.000 0.00 0.00 0.00 1.40
1896 1922 4.828387 TGGTAAACGTGGGCTTTTTCTTAT 59.172 37.500 0.00 0.00 0.00 1.73
1897 1923 4.205587 TGGTAAACGTGGGCTTTTTCTTA 58.794 39.130 0.00 0.00 0.00 2.10
1898 1924 3.025262 TGGTAAACGTGGGCTTTTTCTT 58.975 40.909 0.00 0.00 0.00 2.52
1899 1925 2.657143 TGGTAAACGTGGGCTTTTTCT 58.343 42.857 0.00 0.00 0.00 2.52
1900 1926 3.653539 ATGGTAAACGTGGGCTTTTTC 57.346 42.857 0.00 0.00 0.00 2.29
1906 1932 6.380095 TGATTAATAATGGTAAACGTGGGC 57.620 37.500 0.00 0.00 0.00 5.36
1907 1933 6.435428 GCTGATTAATAATGGTAAACGTGGG 58.565 40.000 0.00 0.00 0.00 4.61
1920 1946 6.358974 TCATCCGAGATGGCTGATTAATAA 57.641 37.500 12.17 0.00 37.95 1.40
1936 1962 5.185454 AGCAAAGTTGATACATTCATCCGA 58.815 37.500 0.00 0.00 33.34 4.55
1937 1963 5.490139 AGCAAAGTTGATACATTCATCCG 57.510 39.130 0.00 0.00 33.34 4.18
2000 2026 4.330074 CGAAGTTCTGTCAAGTGTTGAACT 59.670 41.667 0.56 0.00 46.04 3.01
2001 2027 4.092968 ACGAAGTTCTGTCAAGTGTTGAAC 59.907 41.667 0.56 0.00 37.78 3.18
2002 2028 4.250464 ACGAAGTTCTGTCAAGTGTTGAA 58.750 39.130 0.56 0.00 37.78 2.69
2003 2029 3.857052 ACGAAGTTCTGTCAAGTGTTGA 58.143 40.909 0.56 0.00 37.78 3.18
2193 2232 1.337071 GCTATGCCTACGACTGCTGTA 59.663 52.381 0.00 0.00 0.00 2.74
2196 2235 0.671251 GAGCTATGCCTACGACTGCT 59.329 55.000 0.00 0.00 0.00 4.24
2197 2236 0.319125 GGAGCTATGCCTACGACTGC 60.319 60.000 0.00 0.00 0.00 4.40
2198 2237 1.032794 TGGAGCTATGCCTACGACTG 58.967 55.000 0.00 0.00 0.00 3.51
2199 2238 1.889829 GATGGAGCTATGCCTACGACT 59.110 52.381 0.00 0.00 0.00 4.18
2200 2239 1.889829 AGATGGAGCTATGCCTACGAC 59.110 52.381 0.00 0.00 0.00 4.34
2201 2240 2.294449 AGATGGAGCTATGCCTACGA 57.706 50.000 0.00 0.00 0.00 3.43
2202 2241 4.039151 CATAGATGGAGCTATGCCTACG 57.961 50.000 0.00 0.00 40.71 3.51
2208 2247 3.387374 CCCTAGGCATAGATGGAGCTATG 59.613 52.174 7.04 7.43 46.66 2.23
2209 2248 3.273351 TCCCTAGGCATAGATGGAGCTAT 59.727 47.826 7.04 0.00 0.00 2.97
2210 2249 2.654896 TCCCTAGGCATAGATGGAGCTA 59.345 50.000 7.04 0.00 0.00 3.32
2211 2250 1.434773 TCCCTAGGCATAGATGGAGCT 59.565 52.381 7.04 0.00 0.00 4.09
2212 2251 1.944177 TCCCTAGGCATAGATGGAGC 58.056 55.000 7.04 0.00 0.00 4.70
2213 2252 4.505742 GGTTTTCCCTAGGCATAGATGGAG 60.506 50.000 7.04 0.00 0.00 3.86
2214 2253 3.394606 GGTTTTCCCTAGGCATAGATGGA 59.605 47.826 7.04 3.01 0.00 3.41
2215 2254 3.756117 GGTTTTCCCTAGGCATAGATGG 58.244 50.000 7.04 0.31 0.00 3.51
2216 2255 3.181454 ACGGTTTTCCCTAGGCATAGATG 60.181 47.826 7.04 0.00 36.42 2.90
2217 2256 3.046374 ACGGTTTTCCCTAGGCATAGAT 58.954 45.455 7.04 0.00 36.42 1.98
2218 2257 2.433239 GACGGTTTTCCCTAGGCATAGA 59.567 50.000 7.04 0.00 36.42 1.98
2219 2258 2.169769 TGACGGTTTTCCCTAGGCATAG 59.830 50.000 2.05 0.00 36.42 2.23
2220 2259 2.189676 TGACGGTTTTCCCTAGGCATA 58.810 47.619 2.05 0.00 36.42 3.14
2221 2260 0.988832 TGACGGTTTTCCCTAGGCAT 59.011 50.000 2.05 0.00 36.42 4.40
2222 2261 0.766131 TTGACGGTTTTCCCTAGGCA 59.234 50.000 2.05 0.00 36.42 4.75
2240 2279 1.084289 GCCGACGGCTTTTCTATGTT 58.916 50.000 31.30 0.00 46.69 2.71
2347 2386 0.875728 CCTCTATGTCGACGGCCTAG 59.124 60.000 11.62 5.52 0.00 3.02
2382 2422 3.626924 AGCACACCGTCTGTCCCC 61.627 66.667 0.00 0.00 0.00 4.81
2394 2435 1.565156 GATTTGACGGCGTCAGCACA 61.565 55.000 36.94 23.35 43.69 4.57
2396 2437 0.245266 TAGATTTGACGGCGTCAGCA 59.755 50.000 36.94 28.84 43.69 4.41
2498 2543 1.095228 TATGCCTACAGCTTTGCCGC 61.095 55.000 0.00 0.00 44.23 6.53


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

AutoCloner maintained by Alex Coulton.