Multiple sequence alignment - TraesCS2D01G462300

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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 TraesCS2D01G462300 chr2D 100.000 5386 0 0 1 5386 568253532 568248147 0.000000e+00 9947
1 TraesCS2D01G462300 chr2B 94.383 3062 107 37 1386 4409 680806489 680803455 0.000000e+00 4641
2 TraesCS2D01G462300 chr2B 86.703 737 60 26 685 1391 680812276 680811548 0.000000e+00 784
3 TraesCS2D01G462300 chr2B 87.706 667 69 10 1 660 680812994 680812334 0.000000e+00 765
4 TraesCS2D01G462300 chr4D 96.805 939 24 3 4453 5386 313885089 313884152 0.000000e+00 1563
5 TraesCS2D01G462300 chr4D 96.802 938 21 5 4454 5386 355818481 355817548 0.000000e+00 1557
6 TraesCS2D01G462300 chr4D 97.126 835 17 4 4557 5386 368858976 368859808 0.000000e+00 1402
7 TraesCS2D01G462300 chr3A 96.692 937 26 2 4455 5386 33139895 33140831 0.000000e+00 1554
8 TraesCS2D01G462300 chr7A 96.398 944 28 3 4448 5386 211723904 211722962 0.000000e+00 1550
9 TraesCS2D01G462300 chr7A 92.267 944 59 8 4455 5386 547149930 547148989 0.000000e+00 1327
10 TraesCS2D01G462300 chr7B 96.296 945 28 4 4448 5386 697093257 697092314 0.000000e+00 1544
11 TraesCS2D01G462300 chr7B 91.983 948 62 9 4451 5386 124130190 124131135 0.000000e+00 1317
12 TraesCS2D01G462300 chr6D 95.765 921 24 6 4455 5369 451770619 451769708 0.000000e+00 1471
13 TraesCS2D01G462300 chr6D 79.307 1010 186 18 1459 2452 433940041 433939039 0.000000e+00 686
14 TraesCS2D01G462300 chr6D 83.863 409 66 0 3225 3633 433938279 433937871 1.820000e-104 390
15 TraesCS2D01G462300 chr6D 83.819 309 49 1 2856 3163 433938693 433938385 5.280000e-75 292
16 TraesCS2D01G462300 chr6D 83.946 299 47 1 2858 3156 433710309 433710012 8.830000e-73 285
17 TraesCS2D01G462300 chr6D 77.778 198 38 4 2507 2701 433938957 433938763 3.410000e-22 117
18 TraesCS2D01G462300 chr6B 79.782 1009 183 17 1459 2452 656284005 656283003 0.000000e+00 713
19 TraesCS2D01G462300 chr6B 77.767 1021 202 16 1456 2456 655889446 655890461 5.970000e-169 604
20 TraesCS2D01G462300 chr6B 80.682 792 135 15 2858 3633 656282654 656281865 2.780000e-167 599
21 TraesCS2D01G462300 chr6B 79.208 808 144 17 2847 3633 655890791 655891595 1.710000e-149 540
22 TraesCS2D01G462300 chr6B 79.032 806 145 18 2847 3633 655763980 655764780 1.030000e-146 531
23 TraesCS2D01G462300 chr6B 83.660 306 47 2 2851 3156 655313083 655313385 8.830000e-73 285
24 TraesCS2D01G462300 chr6B 79.293 198 35 4 2507 2701 656282921 656282727 3.380000e-27 134
25 TraesCS2D01G462300 chr6A 78.803 1019 194 18 1459 2460 580206286 580205273 0.000000e+00 665
26 TraesCS2D01G462300 chr6A 80.025 796 135 17 2856 3633 580204935 580204146 7.830000e-158 568
27 TraesCS2D01G462300 chr6A 76.847 1015 212 18 1461 2456 579842030 579843040 7.880000e-153 551
28 TraesCS2D01G462300 chr6A 79.524 757 129 21 2847 3582 579843367 579844118 2.880000e-142 516


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 TraesCS2D01G462300 chr2D 568248147 568253532 5385 True 9947.00 9947 100.00000 1 5386 1 chr2D.!!$R1 5385
1 TraesCS2D01G462300 chr2B 680803455 680806489 3034 True 4641.00 4641 94.38300 1386 4409 1 chr2B.!!$R1 3023
2 TraesCS2D01G462300 chr2B 680811548 680812994 1446 True 774.50 784 87.20450 1 1391 2 chr2B.!!$R2 1390
3 TraesCS2D01G462300 chr4D 313884152 313885089 937 True 1563.00 1563 96.80500 4453 5386 1 chr4D.!!$R1 933
4 TraesCS2D01G462300 chr4D 355817548 355818481 933 True 1557.00 1557 96.80200 4454 5386 1 chr4D.!!$R2 932
5 TraesCS2D01G462300 chr4D 368858976 368859808 832 False 1402.00 1402 97.12600 4557 5386 1 chr4D.!!$F1 829
6 TraesCS2D01G462300 chr3A 33139895 33140831 936 False 1554.00 1554 96.69200 4455 5386 1 chr3A.!!$F1 931
7 TraesCS2D01G462300 chr7A 211722962 211723904 942 True 1550.00 1550 96.39800 4448 5386 1 chr7A.!!$R1 938
8 TraesCS2D01G462300 chr7A 547148989 547149930 941 True 1327.00 1327 92.26700 4455 5386 1 chr7A.!!$R2 931
9 TraesCS2D01G462300 chr7B 697092314 697093257 943 True 1544.00 1544 96.29600 4448 5386 1 chr7B.!!$R1 938
10 TraesCS2D01G462300 chr7B 124130190 124131135 945 False 1317.00 1317 91.98300 4451 5386 1 chr7B.!!$F1 935
11 TraesCS2D01G462300 chr6D 451769708 451770619 911 True 1471.00 1471 95.76500 4455 5369 1 chr6D.!!$R2 914
12 TraesCS2D01G462300 chr6D 433937871 433940041 2170 True 371.25 686 81.19175 1459 3633 4 chr6D.!!$R3 2174
13 TraesCS2D01G462300 chr6B 655889446 655891595 2149 False 572.00 604 78.48750 1456 3633 2 chr6B.!!$F3 2177
14 TraesCS2D01G462300 chr6B 655763980 655764780 800 False 531.00 531 79.03200 2847 3633 1 chr6B.!!$F2 786
15 TraesCS2D01G462300 chr6B 656281865 656284005 2140 True 482.00 713 79.91900 1459 3633 3 chr6B.!!$R1 2174
16 TraesCS2D01G462300 chr6A 580204146 580206286 2140 True 616.50 665 79.41400 1459 3633 2 chr6A.!!$R1 2174
17 TraesCS2D01G462300 chr6A 579842030 579844118 2088 False 533.50 551 78.18550 1461 3582 2 chr6A.!!$F1 2121

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
256 257 0.108662 TGGCTGAGTGTGTCGCATAG 60.109 55.0 0.00 0.0 0.00 2.23 F
1212 1292 0.105453 AGATGGCGGTGGAGGACTAT 60.105 55.0 0.00 0.0 0.00 2.12 F
1400 1481 0.102663 TGTTAGTTGTGCACCGTCGA 59.897 50.0 15.69 0.0 0.00 4.20 F
2459 2566 0.108804 GAGTTCGGGATCACGCAAGA 60.109 55.0 13.88 0.0 43.62 3.02 F
3639 3849 0.036952 CAAGACTGTCGGCCTGTCAT 60.037 55.0 11.78 0.0 42.68 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 1383 0.104855 AGCGCCGATGATTGAGCTTA 59.895 50.0 2.29 0.0 0.00 3.09 R
2460 2567 0.036388 GCTGTTGGGGTTCAGATCGA 60.036 55.0 0.00 0.0 34.02 3.59 R
2561 2699 0.512952 CTGCTTGAACCCGTTCTTCG 59.487 55.0 8.91 0.0 40.14 3.79 R
3654 3864 0.171679 TCGTATGTGTAGTGGCGTGG 59.828 55.0 0.00 0.0 0.00 4.94 R
4441 4668 0.619543 GCCCCTGGTTAGGTCTGGTA 60.620 60.0 0.00 0.0 42.96 3.25 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
31 32 9.640974 CATGTAATGTTTTGAAAAAGAAAGCTG 57.359 29.630 0.00 0.00 40.20 4.24
33 34 8.655092 TGTAATGTTTTGAAAAAGAAAGCTGTG 58.345 29.630 0.00 0.00 0.00 3.66
34 35 5.529014 TGTTTTGAAAAAGAAAGCTGTGC 57.471 34.783 0.00 0.00 0.00 4.57
35 36 5.237048 TGTTTTGAAAAAGAAAGCTGTGCT 58.763 33.333 0.00 0.00 42.56 4.40
36 37 5.348451 TGTTTTGAAAAAGAAAGCTGTGCTC 59.652 36.000 0.00 0.00 38.25 4.26
37 38 3.715628 TGAAAAAGAAAGCTGTGCTCC 57.284 42.857 0.00 0.00 38.25 4.70
60 61 5.336451 CCGAAAAGCCTTTTGCCTATTTAGT 60.336 40.000 7.25 0.00 42.71 2.24
67 68 6.211384 AGCCTTTTGCCTATTTAGTTGTCATT 59.789 34.615 0.00 0.00 42.71 2.57
110 111 0.394762 AATCTGCCATCACCGCATGT 60.395 50.000 0.00 0.00 35.25 3.21
116 117 1.091771 CCATCACCGCATGTCTGGTC 61.092 60.000 3.78 0.00 35.96 4.02
118 119 2.578163 ATCACCGCATGTCTGGTCCG 62.578 60.000 3.78 0.00 35.96 4.79
124 125 1.819229 CATGTCTGGTCCGCTAGCT 59.181 57.895 13.93 0.00 0.00 3.32
131 132 1.464997 CTGGTCCGCTAGCTTTTTCAC 59.535 52.381 13.93 0.00 0.00 3.18
140 141 3.368236 GCTAGCTTTTTCACGACGATTCT 59.632 43.478 7.70 0.00 0.00 2.40
141 142 4.143094 GCTAGCTTTTTCACGACGATTCTT 60.143 41.667 7.70 0.00 0.00 2.52
183 184 2.806244 ACTTCGATCAAAGGAACCAACG 59.194 45.455 0.00 0.00 0.00 4.10
198 199 2.223618 ACCAACGGTTCAAAACAATCGG 60.224 45.455 0.00 0.00 27.29 4.18
203 204 2.657184 GGTTCAAAACAATCGGGTTCG 58.343 47.619 0.00 0.00 37.82 3.95
256 257 0.108662 TGGCTGAGTGTGTCGCATAG 60.109 55.000 0.00 0.00 0.00 2.23
266 267 4.520874 AGTGTGTCGCATAGTCTATAGCAT 59.479 41.667 12.05 0.00 0.00 3.79
282 283 8.322091 GTCTATAGCATGGATTGTAACCCTAAT 58.678 37.037 0.00 0.00 0.00 1.73
288 289 6.572519 CATGGATTGTAACCCTAATGTTTGG 58.427 40.000 0.00 0.00 0.00 3.28
293 294 8.755028 GGATTGTAACCCTAATGTTTGGTTAAT 58.245 33.333 2.18 0.00 44.01 1.40
318 319 7.772332 ACATAAAGGTTTGTCTATGATCGAC 57.228 36.000 0.00 0.00 0.00 4.20
324 325 4.804139 GGTTTGTCTATGATCGACGAATGT 59.196 41.667 0.00 0.00 37.19 2.71
351 352 6.377327 TTCGGCATGGAATAAAATCTCTTC 57.623 37.500 0.00 0.00 0.00 2.87
358 359 4.142026 TGGAATAAAATCTCTTCGGCTCGA 60.142 41.667 0.00 0.00 0.00 4.04
367 368 3.318539 TTCGGCTCGACCTCGTTCG 62.319 63.158 0.00 0.00 40.80 3.95
383 384 4.462280 CGGGTGGGGCTTCGTACC 62.462 72.222 0.00 0.00 0.00 3.34
389 390 1.004679 GGGGCTTCGTACCGTTCAA 60.005 57.895 0.00 0.00 0.00 2.69
399 400 1.003652 GTACCGTTCAAAACCGTGTGG 60.004 52.381 0.00 0.00 42.84 4.17
404 405 1.064952 GTTCAAAACCGTGTGGAGGTG 59.935 52.381 0.00 0.00 41.95 4.00
453 455 1.278985 TGCTCCATTGTCGAGATGGTT 59.721 47.619 21.16 0.00 43.64 3.67
488 490 7.608376 TCTGTATAGATTCCTATTGTCTCCTCG 59.392 40.741 0.00 0.00 36.93 4.63
489 491 6.659668 TGTATAGATTCCTATTGTCTCCTCGG 59.340 42.308 0.00 0.00 36.93 4.63
491 493 2.840640 TTCCTATTGTCTCCTCGGGA 57.159 50.000 0.00 0.00 0.00 5.14
513 515 0.940833 GCGAGGCTAGGATTTCTTGC 59.059 55.000 0.00 0.00 42.21 4.01
525 527 1.109609 TTTCTTGCCATGTGTGCACA 58.890 45.000 17.42 17.42 46.44 4.57
526 528 0.385029 TTCTTGCCATGTGTGCACAC 59.615 50.000 37.28 37.28 45.05 3.82
528 530 1.736365 CTTGCCATGTGTGCACACCA 61.736 55.000 39.34 28.88 45.88 4.17
538 540 2.287915 GTGTGCACACCAGTAAGTTCTG 59.712 50.000 34.94 0.00 40.85 3.02
545 547 4.634004 CACACCAGTAAGTTCTGTTGTCAA 59.366 41.667 3.65 0.00 38.62 3.18
565 567 5.048504 GTCAAGTGCTTCAGATTGATTTGGA 60.049 40.000 0.00 0.00 34.45 3.53
568 570 4.699257 AGTGCTTCAGATTGATTTGGAGTC 59.301 41.667 0.00 0.00 0.00 3.36
572 574 5.126707 GCTTCAGATTGATTTGGAGTCCAAT 59.873 40.000 25.12 14.84 43.55 3.16
575 577 5.649395 TCAGATTGATTTGGAGTCCAATGAC 59.351 40.000 25.12 18.01 43.55 3.06
579 581 1.522668 TTTGGAGTCCAATGACAGCG 58.477 50.000 25.12 0.00 43.55 5.18
582 584 0.247736 GGAGTCCAATGACAGCGACT 59.752 55.000 3.60 2.42 44.33 4.18
592 594 1.934220 GACAGCGACTGTGGATCCGA 61.934 60.000 15.61 0.00 45.44 4.55
594 596 2.105128 GCGACTGTGGATCCGAGG 59.895 66.667 7.39 1.64 0.00 4.63
611 613 0.563173 AGGTGCTAGCCTCTATGGGA 59.437 55.000 13.29 0.00 32.39 4.37
614 616 5.817212 AGGTGCTAGCCTCTATGGGAACA 62.817 52.174 13.29 0.00 38.81 3.18
630 637 3.154710 GGAACAAAGGATTTCCCGACTT 58.845 45.455 0.00 0.00 35.03 3.01
642 649 0.721718 CCCGACTTTCATCGACAAGC 59.278 55.000 0.00 0.00 45.13 4.01
646 653 2.343843 CGACTTTCATCGACAAGCTCAG 59.656 50.000 0.00 0.00 45.13 3.35
647 654 3.579709 GACTTTCATCGACAAGCTCAGA 58.420 45.455 0.00 0.00 0.00 3.27
650 657 1.982612 TCATCGACAAGCTCAGAACG 58.017 50.000 0.00 0.00 0.00 3.95
656 663 2.159824 CGACAAGCTCAGAACGACTCTA 59.840 50.000 0.00 0.00 31.12 2.43
660 667 4.393680 ACAAGCTCAGAACGACTCTAGTAG 59.606 45.833 0.00 0.00 31.12 2.57
661 668 4.475051 AGCTCAGAACGACTCTAGTAGA 57.525 45.455 0.00 0.00 31.12 2.59
664 671 4.871557 GCTCAGAACGACTCTAGTAGAGAA 59.128 45.833 29.87 7.01 45.07 2.87
668 675 2.553086 ACGACTCTAGTAGAGAAGCCG 58.447 52.381 29.87 24.96 45.07 5.52
669 676 1.262151 CGACTCTAGTAGAGAAGCCGC 59.738 57.143 29.87 12.36 45.07 6.53
670 677 1.262151 GACTCTAGTAGAGAAGCCGCG 59.738 57.143 29.87 0.00 45.07 6.46
676 683 2.022195 AGTAGAGAAGCCGCGATAACA 58.978 47.619 8.23 0.00 0.00 2.41
679 686 1.204941 AGAGAAGCCGCGATAACAACT 59.795 47.619 8.23 0.00 0.00 3.16
681 688 1.732259 AGAAGCCGCGATAACAACTTG 59.268 47.619 8.23 0.00 0.00 3.16
682 689 1.730064 GAAGCCGCGATAACAACTTGA 59.270 47.619 8.23 0.00 0.00 3.02
683 690 1.803334 AGCCGCGATAACAACTTGAA 58.197 45.000 8.23 0.00 0.00 2.69
695 735 8.755941 CGATAACAACTTGAATAGGTGATACAG 58.244 37.037 0.00 0.00 44.86 2.74
711 751 6.295349 GGTGATACAGGGATCTCGATGTAATT 60.295 42.308 0.00 0.00 32.31 1.40
712 752 7.155328 GTGATACAGGGATCTCGATGTAATTT 58.845 38.462 0.00 0.00 32.31 1.82
715 755 9.706691 GATACAGGGATCTCGATGTAATTTTTA 57.293 33.333 0.00 0.00 32.31 1.52
720 760 9.204570 AGGGATCTCGATGTAATTTTTATTACG 57.795 33.333 0.00 0.00 39.27 3.18
754 800 5.565592 TTCCGTAGTACAGCTTTCGAATA 57.434 39.130 0.00 0.00 0.00 1.75
776 822 2.159234 ACTAGTCGACACGTAGCTTCAC 59.841 50.000 19.50 0.00 0.00 3.18
793 839 2.771089 TCACTGCATGTCTTTGGTCTC 58.229 47.619 0.00 0.00 0.00 3.36
875 924 3.845178 CTTGTCATACACCAGCTAACGA 58.155 45.455 0.00 0.00 0.00 3.85
882 931 0.584396 CACCAGCTAACGACGCAAAA 59.416 50.000 0.00 0.00 0.00 2.44
886 935 2.474526 CCAGCTAACGACGCAAAATCAG 60.475 50.000 0.00 0.00 0.00 2.90
914 963 0.884704 ACACGCAATCTCGCCAAGTT 60.885 50.000 0.00 0.00 0.00 2.66
931 980 4.234574 CAAGTTGCCATGCTGCATATATG 58.765 43.478 15.78 8.45 41.70 1.78
932 981 2.823747 AGTTGCCATGCTGCATATATGG 59.176 45.455 15.78 14.87 41.70 2.74
963 1012 4.892345 AGACACAGAGAGAGCATTATAGCA 59.108 41.667 0.00 0.00 36.85 3.49
964 1013 5.362143 AGACACAGAGAGAGCATTATAGCAA 59.638 40.000 0.00 0.00 36.85 3.91
967 1022 3.995705 CAGAGAGAGCATTATAGCAAGCC 59.004 47.826 0.00 0.00 36.85 4.35
975 1030 0.179020 TTATAGCAAGCCGCAGCCAT 60.179 50.000 4.42 0.01 46.13 4.40
983 1038 2.182842 GCCGCAGCCATCTTGTAGG 61.183 63.158 0.00 0.00 0.00 3.18
986 1041 0.176680 CGCAGCCATCTTGTAGGAGT 59.823 55.000 0.00 0.00 0.00 3.85
987 1042 1.409064 CGCAGCCATCTTGTAGGAGTA 59.591 52.381 0.00 0.00 0.00 2.59
989 1044 2.695666 GCAGCCATCTTGTAGGAGTAGA 59.304 50.000 0.00 0.00 0.00 2.59
992 1047 3.386402 AGCCATCTTGTAGGAGTAGAAGC 59.614 47.826 0.00 0.00 31.02 3.86
993 1048 3.386402 GCCATCTTGTAGGAGTAGAAGCT 59.614 47.826 0.00 0.00 31.02 3.74
994 1049 4.585162 GCCATCTTGTAGGAGTAGAAGCTA 59.415 45.833 0.00 0.00 31.02 3.32
995 1050 5.278758 GCCATCTTGTAGGAGTAGAAGCTAG 60.279 48.000 0.00 0.00 31.02 3.42
996 1051 6.065374 CCATCTTGTAGGAGTAGAAGCTAGA 58.935 44.000 0.00 0.00 31.02 2.43
997 1052 6.206634 CCATCTTGTAGGAGTAGAAGCTAGAG 59.793 46.154 0.00 0.00 31.02 2.43
998 1053 6.563037 TCTTGTAGGAGTAGAAGCTAGAGA 57.437 41.667 0.00 0.00 31.02 3.10
1035 1115 0.614979 TACTGGTGCAGTCTCCCTCC 60.615 60.000 0.00 0.00 41.21 4.30
1036 1116 1.611851 CTGGTGCAGTCTCCCTCCT 60.612 63.158 0.00 0.00 0.00 3.69
1037 1117 1.610673 TGGTGCAGTCTCCCTCCTC 60.611 63.158 0.00 0.00 0.00 3.71
1038 1118 1.305718 GGTGCAGTCTCCCTCCTCT 60.306 63.158 0.00 0.00 0.00 3.69
1039 1119 0.907230 GGTGCAGTCTCCCTCCTCTT 60.907 60.000 0.00 0.00 0.00 2.85
1040 1120 0.980423 GTGCAGTCTCCCTCCTCTTT 59.020 55.000 0.00 0.00 0.00 2.52
1048 1128 3.196901 GTCTCCCTCCTCTTTCTTCTTCC 59.803 52.174 0.00 0.00 0.00 3.46
1065 1145 1.215647 CCCCTTCGTTCTCCTGTCG 59.784 63.158 0.00 0.00 0.00 4.35
1208 1288 2.896677 ATCCAGATGGCGGTGGAGGA 62.897 60.000 8.11 0.00 46.09 3.71
1212 1292 0.105453 AGATGGCGGTGGAGGACTAT 60.105 55.000 0.00 0.00 0.00 2.12
1226 1306 3.335534 CTATTACGCCGCGCACCC 61.336 66.667 13.88 0.00 0.00 4.61
1267 1347 0.462759 GCTCCATTTCAGGGACTCCG 60.463 60.000 0.00 0.00 34.60 4.63
1302 1382 1.815421 CGCCGCTTCTGCTGGTAAT 60.815 57.895 0.00 0.00 36.03 1.89
1303 1383 1.369091 CGCCGCTTCTGCTGGTAATT 61.369 55.000 0.00 0.00 36.03 1.40
1304 1384 1.663695 GCCGCTTCTGCTGGTAATTA 58.336 50.000 0.00 0.00 36.03 1.40
1305 1385 2.014128 GCCGCTTCTGCTGGTAATTAA 58.986 47.619 0.00 0.00 36.03 1.40
1315 1395 6.359804 TCTGCTGGTAATTAAGCTCAATCAT 58.640 36.000 9.88 0.00 40.21 2.45
1317 1397 5.237127 TGCTGGTAATTAAGCTCAATCATCG 59.763 40.000 9.88 0.00 40.21 3.84
1318 1398 5.334414 GCTGGTAATTAAGCTCAATCATCGG 60.334 44.000 2.47 0.00 36.47 4.18
1335 1415 2.510238 GCGCTCGCTTCACCATCT 60.510 61.111 0.00 0.00 38.26 2.90
1342 1422 0.463295 CGCTTCACCATCTGGCATCT 60.463 55.000 0.00 0.00 39.32 2.90
1359 1439 8.609176 TCTGGCATCTTTACGTTTACATAATTC 58.391 33.333 0.00 0.00 0.00 2.17
1398 1479 2.350388 CCAATGTTAGTTGTGCACCGTC 60.350 50.000 15.69 4.64 0.00 4.79
1400 1481 0.102663 TGTTAGTTGTGCACCGTCGA 59.897 50.000 15.69 0.00 0.00 4.20
1401 1482 1.269883 TGTTAGTTGTGCACCGTCGAT 60.270 47.619 15.69 0.00 0.00 3.59
1402 1483 1.389106 GTTAGTTGTGCACCGTCGATC 59.611 52.381 15.69 0.00 0.00 3.69
1403 1484 0.455464 TAGTTGTGCACCGTCGATCG 60.455 55.000 15.69 9.36 39.52 3.69
1435 1516 0.736325 GCTGAGCGTGGTACATCGTT 60.736 55.000 9.84 4.78 44.52 3.85
1692 1774 4.070552 GTCCTCGGCGCCTTCAGT 62.071 66.667 26.68 0.00 0.00 3.41
1893 1984 1.130613 GTTCGTCGTGCACATGCTC 59.869 57.895 18.64 0.32 42.66 4.26
2136 2227 4.047125 CCGGCAGATGGGGGTGTT 62.047 66.667 0.00 0.00 0.00 3.32
2138 2229 3.070576 GGCAGATGGGGGTGTTGC 61.071 66.667 0.00 0.00 0.00 4.17
2331 2438 2.427905 CTCGCCACGACGTTCGAA 60.428 61.111 18.62 0.00 43.74 3.71
2353 2460 2.419574 GGTATAGCCGGCAAGTTCAAGA 60.420 50.000 31.54 1.67 0.00 3.02
2459 2566 0.108804 GAGTTCGGGATCACGCAAGA 60.109 55.000 13.88 0.00 43.62 3.02
2460 2567 0.537188 AGTTCGGGATCACGCAAGAT 59.463 50.000 13.88 0.00 43.62 2.40
2461 2568 0.931005 GTTCGGGATCACGCAAGATC 59.069 55.000 13.88 6.80 42.89 2.75
2497 2613 2.437359 GCCAAGGCGCTGAGACAT 60.437 61.111 7.64 0.00 0.00 3.06
2545 2683 2.974698 CGAATGGGCGGATGCTCC 60.975 66.667 0.00 0.00 42.67 4.70
2546 2684 2.512896 GAATGGGCGGATGCTCCT 59.487 61.111 0.00 0.00 42.67 3.69
2550 2688 4.864334 GGGCGGATGCTCCTGGTG 62.864 72.222 0.00 0.00 42.25 4.17
2615 2753 1.003118 CCAGAATTCCACAACCGGAGA 59.997 52.381 9.46 0.00 36.12 3.71
2778 2916 5.065988 GGTTAGTACCATAACGACCGAACTA 59.934 44.000 0.00 0.00 44.36 2.24
2793 2934 2.741878 CGAACTATCGGCATTGGGTTCT 60.742 50.000 0.00 0.00 45.32 3.01
2800 2941 3.691575 TCGGCATTGGGTTCTCATTTTA 58.308 40.909 0.00 0.00 0.00 1.52
2807 2948 6.976925 GCATTGGGTTCTCATTTTAGAAGATG 59.023 38.462 0.00 0.00 36.19 2.90
2808 2949 7.363268 GCATTGGGTTCTCATTTTAGAAGATGT 60.363 37.037 0.00 0.00 36.19 3.06
2809 2950 9.177608 CATTGGGTTCTCATTTTAGAAGATGTA 57.822 33.333 0.00 0.00 36.19 2.29
2810 2951 8.561738 TTGGGTTCTCATTTTAGAAGATGTAC 57.438 34.615 0.00 0.00 36.19 2.90
2811 2952 6.816640 TGGGTTCTCATTTTAGAAGATGTACG 59.183 38.462 0.00 0.00 36.19 3.67
2812 2953 6.817140 GGGTTCTCATTTTAGAAGATGTACGT 59.183 38.462 0.00 0.00 36.19 3.57
2813 2954 7.977853 GGGTTCTCATTTTAGAAGATGTACGTA 59.022 37.037 0.00 0.00 36.19 3.57
2814 2955 8.805688 GGTTCTCATTTTAGAAGATGTACGTAC 58.194 37.037 18.90 18.90 36.19 3.67
2815 2956 8.521860 GTTCTCATTTTAGAAGATGTACGTACG 58.478 37.037 20.18 15.01 36.19 3.67
2817 2958 7.907045 TCTCATTTTAGAAGATGTACGTACGTC 59.093 37.037 31.66 31.66 41.41 4.34
2917 3058 1.398390 GACTTCACGATGCCATTCACC 59.602 52.381 0.00 0.00 0.00 4.02
2938 3079 3.072468 TCGGGGTGGTCGATGGTC 61.072 66.667 0.00 0.00 0.00 4.02
2975 3116 1.603455 ACGGGCTCAAACATGTGGG 60.603 57.895 0.00 0.00 0.00 4.61
3136 3279 2.110901 TCTACTTCGCCTTCTCGACT 57.889 50.000 0.00 0.00 38.30 4.18
3142 3285 0.321741 TCGCCTTCTCGACTCTCACT 60.322 55.000 0.00 0.00 33.02 3.41
3323 3520 2.745100 TCGAGCTACACGGCGAGT 60.745 61.111 16.62 15.91 37.29 4.18
3488 3693 3.771798 GATGAGGAAGTACAACTCGTCC 58.228 50.000 16.59 5.48 39.96 4.79
3527 3732 1.456196 TATCCAGAGGCTCGGCGAAG 61.456 60.000 12.13 6.52 0.00 3.79
3608 3818 3.201290 CTGCAAGGACTACATGATGGTC 58.799 50.000 0.00 4.38 38.07 4.02
3634 3844 1.478510 CATCTACAAGACTGTCGGCCT 59.521 52.381 0.00 0.00 36.96 5.19
3635 3845 0.888619 TCTACAAGACTGTCGGCCTG 59.111 55.000 0.00 0.00 36.96 4.85
3638 3848 1.367471 CAAGACTGTCGGCCTGTCA 59.633 57.895 11.78 0.00 42.68 3.58
3639 3849 0.036952 CAAGACTGTCGGCCTGTCAT 60.037 55.000 11.78 0.00 42.68 3.06
3640 3850 0.687354 AAGACTGTCGGCCTGTCATT 59.313 50.000 11.78 0.00 42.68 2.57
3641 3851 0.687354 AGACTGTCGGCCTGTCATTT 59.313 50.000 11.78 0.00 42.68 2.32
3642 3852 0.798776 GACTGTCGGCCTGTCATTTG 59.201 55.000 0.00 0.00 40.63 2.32
3643 3853 0.108585 ACTGTCGGCCTGTCATTTGT 59.891 50.000 0.00 0.00 0.00 2.83
3645 3855 2.224426 ACTGTCGGCCTGTCATTTGTAA 60.224 45.455 0.00 0.00 0.00 2.41
3646 3856 2.416547 CTGTCGGCCTGTCATTTGTAAG 59.583 50.000 0.00 0.00 0.00 2.34
3647 3857 1.130561 GTCGGCCTGTCATTTGTAAGC 59.869 52.381 0.00 0.00 0.00 3.09
3650 3860 2.436417 GGCCTGTCATTTGTAAGCTCA 58.564 47.619 0.00 0.00 0.00 4.26
3652 3862 2.159462 GCCTGTCATTTGTAAGCTCAGC 60.159 50.000 0.00 0.00 0.00 4.26
3653 3863 2.094894 CCTGTCATTTGTAAGCTCAGCG 59.905 50.000 0.00 0.00 0.00 5.18
3654 3864 1.464608 TGTCATTTGTAAGCTCAGCGC 59.535 47.619 0.00 0.00 39.57 5.92
3655 3865 1.086696 TCATTTGTAAGCTCAGCGCC 58.913 50.000 2.29 0.00 40.39 6.53
3656 3866 0.804364 CATTTGTAAGCTCAGCGCCA 59.196 50.000 2.29 0.00 40.39 5.69
3657 3867 0.804989 ATTTGTAAGCTCAGCGCCAC 59.195 50.000 2.29 0.00 40.39 5.01
3684 3894 3.410631 ACACATACGATGTTGGGTTCA 57.589 42.857 0.00 0.00 42.70 3.18
3831 4045 0.384309 TATACTGACGCTGGCGGAAG 59.616 55.000 18.99 16.38 44.69 3.46
3934 4148 1.134907 GTCGTCCGGCCTAAGATTCAA 60.135 52.381 0.00 0.00 0.00 2.69
3944 4158 3.430929 GCCTAAGATTCAAGAGCTTCGGA 60.431 47.826 0.00 0.00 28.85 4.55
4248 4472 3.326981 CGTTCAGCGTGCGTGTCA 61.327 61.111 0.00 0.00 35.54 3.58
4268 4492 1.068753 CTCGGAGATGAATGCCGCT 59.931 57.895 0.00 0.00 44.45 5.52
4366 4593 0.320771 GAGATGGCCACGTCAACAGT 60.321 55.000 8.16 0.00 35.00 3.55
4373 4600 0.813610 CCACGTCAACAGTGCCTCAA 60.814 55.000 0.00 0.00 38.22 3.02
4391 4618 1.933853 CAACTGCACCGCTAGATTACC 59.066 52.381 0.00 0.00 0.00 2.85
4392 4619 1.191535 ACTGCACCGCTAGATTACCA 58.808 50.000 0.00 0.00 0.00 3.25
4398 4625 3.714391 CACCGCTAGATTACCAGTTACC 58.286 50.000 0.00 0.00 0.00 2.85
4402 4629 3.314635 CGCTAGATTACCAGTTACCGTCT 59.685 47.826 0.00 0.00 0.00 4.18
4406 4633 5.326200 AGATTACCAGTTACCGTCTCTTG 57.674 43.478 0.00 0.00 0.00 3.02
4409 4636 2.595238 ACCAGTTACCGTCTCTTGACT 58.405 47.619 0.00 0.00 40.86 3.41
4410 4637 3.759581 ACCAGTTACCGTCTCTTGACTA 58.240 45.455 0.00 0.00 40.86 2.59
4411 4638 3.757493 ACCAGTTACCGTCTCTTGACTAG 59.243 47.826 0.00 0.00 40.86 2.57
4412 4639 4.008330 CCAGTTACCGTCTCTTGACTAGA 58.992 47.826 0.00 0.00 40.86 2.43
4413 4640 4.142643 CCAGTTACCGTCTCTTGACTAGAC 60.143 50.000 0.00 0.00 40.86 2.59
4414 4641 4.696402 CAGTTACCGTCTCTTGACTAGACT 59.304 45.833 0.00 0.00 41.02 3.24
4415 4642 5.181622 CAGTTACCGTCTCTTGACTAGACTT 59.818 44.000 0.00 0.00 41.02 3.01
4416 4643 6.370994 CAGTTACCGTCTCTTGACTAGACTTA 59.629 42.308 0.00 0.00 41.02 2.24
4417 4644 7.066043 CAGTTACCGTCTCTTGACTAGACTTAT 59.934 40.741 0.00 0.00 41.02 1.73
4418 4645 7.611079 AGTTACCGTCTCTTGACTAGACTTATT 59.389 37.037 0.00 0.00 41.02 1.40
4419 4646 6.837471 ACCGTCTCTTGACTAGACTTATTT 57.163 37.500 0.00 0.00 41.02 1.40
4420 4647 6.854778 ACCGTCTCTTGACTAGACTTATTTC 58.145 40.000 0.00 0.00 41.02 2.17
4421 4648 6.660094 ACCGTCTCTTGACTAGACTTATTTCT 59.340 38.462 0.00 0.00 41.02 2.52
4422 4649 7.177041 ACCGTCTCTTGACTAGACTTATTTCTT 59.823 37.037 0.00 0.00 41.02 2.52
4423 4650 8.030106 CCGTCTCTTGACTAGACTTATTTCTTT 58.970 37.037 0.00 0.00 41.02 2.52
4424 4651 9.068008 CGTCTCTTGACTAGACTTATTTCTTTC 57.932 37.037 0.00 0.00 41.02 2.62
4425 4652 9.915629 GTCTCTTGACTAGACTTATTTCTTTCA 57.084 33.333 0.00 0.00 40.21 2.69
4428 4655 9.658799 TCTTGACTAGACTTATTTCTTTCATGG 57.341 33.333 0.00 0.00 0.00 3.66
4429 4656 9.442047 CTTGACTAGACTTATTTCTTTCATGGT 57.558 33.333 0.00 0.00 0.00 3.55
4433 4660 9.384764 ACTAGACTTATTTCTTTCATGGTAAGC 57.615 33.333 0.00 0.00 0.00 3.09
4434 4661 7.631717 AGACTTATTTCTTTCATGGTAAGCC 57.368 36.000 0.00 0.00 0.00 4.35
4914 5148 5.350365 GCTCGGACACAACAATGTAAAGATA 59.650 40.000 0.00 0.00 37.82 1.98
4936 5170 2.753247 AGGTGATGTCTAAGGTCCCTC 58.247 52.381 0.00 0.00 0.00 4.30
5336 5578 0.112025 TTGTCCATGTGGTGATGGCA 59.888 50.000 0.00 0.00 42.52 4.92
5364 5607 1.956477 ACATTAATCCCTTCATGCGGC 59.044 47.619 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.033299 CGGAGCACAGCTTTCTTTTTCA 59.967 45.455 0.00 0.00 39.88 2.69
18 19 2.290641 TCGGAGCACAGCTTTCTTTTTC 59.709 45.455 0.00 0.00 39.88 2.29
24 25 1.664302 GCTTTTCGGAGCACAGCTTTC 60.664 52.381 0.00 0.00 39.88 2.62
26 27 1.518903 GGCTTTTCGGAGCACAGCTT 61.519 55.000 8.26 0.00 44.49 3.74
28 29 1.518903 AAGGCTTTTCGGAGCACAGC 61.519 55.000 0.00 0.00 44.49 4.40
29 30 0.954452 AAAGGCTTTTCGGAGCACAG 59.046 50.000 6.68 0.00 44.49 3.66
30 31 1.066908 CAAAAGGCTTTTCGGAGCACA 59.933 47.619 21.77 0.00 44.49 4.57
31 32 1.770957 CAAAAGGCTTTTCGGAGCAC 58.229 50.000 21.77 0.00 44.49 4.40
33 34 0.667487 GGCAAAAGGCTTTTCGGAGC 60.667 55.000 21.77 20.18 44.01 4.70
34 35 0.961753 AGGCAAAAGGCTTTTCGGAG 59.038 50.000 21.77 12.11 44.01 4.63
35 36 2.279935 TAGGCAAAAGGCTTTTCGGA 57.720 45.000 21.77 5.74 44.01 4.55
36 37 3.592898 AATAGGCAAAAGGCTTTTCGG 57.407 42.857 21.77 13.13 44.01 4.30
37 38 5.709966 ACTAAATAGGCAAAAGGCTTTTCG 58.290 37.500 21.77 17.19 44.01 3.46
60 61 7.517614 TTTTGGAGCATACAACTAATGACAA 57.482 32.000 0.00 0.00 0.00 3.18
77 78 6.994496 TGATGGCAGATTAGTAGATTTTGGAG 59.006 38.462 0.00 0.00 0.00 3.86
110 111 1.346395 TGAAAAAGCTAGCGGACCAGA 59.654 47.619 9.55 0.00 0.00 3.86
116 117 0.093026 CGTCGTGAAAAAGCTAGCGG 59.907 55.000 9.55 0.00 0.00 5.52
118 119 3.368236 AGAATCGTCGTGAAAAAGCTAGC 59.632 43.478 6.62 6.62 0.00 3.42
124 125 5.751509 TCTTCTCAAGAATCGTCGTGAAAAA 59.248 36.000 0.00 0.00 41.00 1.94
131 132 4.728534 ACTCTTCTTCTCAAGAATCGTCG 58.271 43.478 0.00 0.00 45.75 5.12
163 164 2.159627 CCGTTGGTTCCTTTGATCGAAG 59.840 50.000 14.94 14.94 0.00 3.79
183 184 2.033675 ACGAACCCGATTGTTTTGAACC 59.966 45.455 0.00 0.00 39.50 3.62
193 194 4.569564 GCTGTAAAATAGACGAACCCGATT 59.430 41.667 0.00 0.00 39.50 3.34
203 204 6.482308 ACATATCCAACGGCTGTAAAATAGAC 59.518 38.462 0.00 0.00 0.00 2.59
239 240 1.135257 AGACTATGCGACACACTCAGC 60.135 52.381 0.00 0.00 0.00 4.26
242 243 4.023963 TGCTATAGACTATGCGACACACTC 60.024 45.833 3.21 0.00 0.00 3.51
256 257 6.115448 AGGGTTACAATCCATGCTATAGAC 57.885 41.667 3.21 0.00 0.00 2.59
266 267 5.646215 ACCAAACATTAGGGTTACAATCCA 58.354 37.500 0.00 0.00 0.00 3.41
282 283 9.968870 GACAAACCTTTATGTATTAACCAAACA 57.031 29.630 0.00 0.00 0.00 2.83
293 294 7.646526 CGTCGATCATAGACAAACCTTTATGTA 59.353 37.037 0.00 0.00 38.46 2.29
310 311 2.205074 GAAGGCACATTCGTCGATCAT 58.795 47.619 0.00 0.00 0.00 2.45
314 315 4.162640 CGAAGGCACATTCGTCGA 57.837 55.556 9.11 0.00 45.37 4.20
337 338 4.209495 GGTCGAGCCGAAGAGATTTTATTC 59.791 45.833 2.39 0.00 37.72 1.75
346 347 1.924320 AACGAGGTCGAGCCGAAGAG 61.924 60.000 25.01 9.03 43.70 2.85
351 352 4.831307 CCGAACGAGGTCGAGCCG 62.831 72.222 19.23 19.23 43.86 5.52
383 384 0.306533 CCTCCACACGGTTTTGAACG 59.693 55.000 0.00 0.00 0.00 3.95
389 390 1.153046 CACCACCTCCACACGGTTT 60.153 57.895 0.00 0.00 30.82 3.27
399 400 2.657237 CGAGGACCACACCACCTC 59.343 66.667 0.00 0.00 44.50 3.85
404 405 2.262915 CTCTGCGAGGACCACACC 59.737 66.667 0.00 0.00 0.00 4.16
429 431 1.079819 CTCGACAATGGAGCACCGT 60.080 57.895 0.00 0.00 39.42 4.83
453 455 6.327386 AGGAATCTATACAGAGCCCAAAAA 57.673 37.500 0.00 0.00 33.22 1.94
459 461 7.363443 GGAGACAATAGGAATCTATACAGAGCC 60.363 44.444 0.00 0.00 35.28 4.70
463 465 7.148154 CCGAGGAGACAATAGGAATCTATACAG 60.148 44.444 0.00 0.00 35.28 2.74
464 466 6.659668 CCGAGGAGACAATAGGAATCTATACA 59.340 42.308 0.00 0.00 35.28 2.29
466 468 6.011893 TCCCGAGGAGACAATAGGAATCTATA 60.012 42.308 0.00 0.00 35.28 1.31
470 472 3.231818 TCCCGAGGAGACAATAGGAATC 58.768 50.000 0.00 0.00 0.00 2.52
488 490 1.484444 AATCCTAGCCTCGCCATCCC 61.484 60.000 0.00 0.00 0.00 3.85
489 491 0.398318 AAATCCTAGCCTCGCCATCC 59.602 55.000 0.00 0.00 0.00 3.51
491 493 1.428869 AGAAATCCTAGCCTCGCCAT 58.571 50.000 0.00 0.00 0.00 4.40
500 502 3.181493 GCACACATGGCAAGAAATCCTAG 60.181 47.826 0.00 0.00 0.00 3.02
525 527 4.876107 CACTTGACAACAGAACTTACTGGT 59.124 41.667 0.00 0.00 41.59 4.00
526 528 4.260784 GCACTTGACAACAGAACTTACTGG 60.261 45.833 0.00 0.00 41.59 4.00
528 530 4.770795 AGCACTTGACAACAGAACTTACT 58.229 39.130 0.00 0.00 0.00 2.24
538 540 4.818534 TCAATCTGAAGCACTTGACAAC 57.181 40.909 0.00 0.00 0.00 3.32
545 547 4.660168 ACTCCAAATCAATCTGAAGCACT 58.340 39.130 0.00 0.00 0.00 4.40
565 567 0.681733 ACAGTCGCTGTCATTGGACT 59.318 50.000 6.67 0.00 41.21 3.85
568 570 0.320683 TCCACAGTCGCTGTCATTGG 60.321 55.000 9.15 8.19 43.43 3.16
572 574 1.591703 GGATCCACAGTCGCTGTCA 59.408 57.895 6.95 1.32 43.43 3.58
575 577 1.226802 CTCGGATCCACAGTCGCTG 60.227 63.158 13.41 5.47 37.52 5.18
579 581 1.153549 GCACCTCGGATCCACAGTC 60.154 63.158 13.41 0.00 0.00 3.51
582 584 1.676678 GCTAGCACCTCGGATCCACA 61.677 60.000 13.41 0.00 0.00 4.17
592 594 0.563173 TCCCATAGAGGCTAGCACCT 59.437 55.000 18.24 14.56 45.04 4.00
594 596 1.762957 TGTTCCCATAGAGGCTAGCAC 59.237 52.381 18.24 10.01 35.39 4.40
611 613 4.211920 TGAAAGTCGGGAAATCCTTTGTT 58.788 39.130 0.00 0.00 35.95 2.83
614 616 3.689649 CGATGAAAGTCGGGAAATCCTTT 59.310 43.478 0.00 0.00 37.94 3.11
615 617 3.055385 TCGATGAAAGTCGGGAAATCCTT 60.055 43.478 0.00 0.00 41.74 3.36
616 618 2.500098 TCGATGAAAGTCGGGAAATCCT 59.500 45.455 0.00 0.00 41.74 3.24
617 619 2.608090 GTCGATGAAAGTCGGGAAATCC 59.392 50.000 0.00 0.00 41.74 3.01
625 632 2.328473 TGAGCTTGTCGATGAAAGTCG 58.672 47.619 0.00 0.00 42.74 4.18
630 637 2.030274 TCGTTCTGAGCTTGTCGATGAA 60.030 45.455 0.00 0.00 0.00 2.57
642 649 5.006358 GCTTCTCTACTAGAGTCGTTCTGAG 59.994 48.000 12.06 0.00 42.83 3.35
646 653 3.001533 CGGCTTCTCTACTAGAGTCGTTC 59.998 52.174 12.06 1.38 42.83 3.95
647 654 2.937799 CGGCTTCTCTACTAGAGTCGTT 59.062 50.000 12.06 0.00 42.83 3.85
650 657 1.262151 CGCGGCTTCTCTACTAGAGTC 59.738 57.143 12.06 4.32 42.83 3.36
656 663 2.022195 TGTTATCGCGGCTTCTCTACT 58.978 47.619 6.13 0.00 0.00 2.57
660 667 1.641577 AGTTGTTATCGCGGCTTCTC 58.358 50.000 6.13 0.00 0.00 2.87
661 668 1.732259 CAAGTTGTTATCGCGGCTTCT 59.268 47.619 6.13 0.00 0.00 2.85
662 669 1.730064 TCAAGTTGTTATCGCGGCTTC 59.270 47.619 6.13 0.00 0.00 3.86
664 671 1.803334 TTCAAGTTGTTATCGCGGCT 58.197 45.000 6.13 0.00 0.00 5.52
668 675 6.604735 ATCACCTATTCAAGTTGTTATCGC 57.395 37.500 2.11 0.00 0.00 4.58
669 676 8.642908 TGTATCACCTATTCAAGTTGTTATCG 57.357 34.615 2.11 0.00 0.00 2.92
670 677 9.046296 CCTGTATCACCTATTCAAGTTGTTATC 57.954 37.037 2.11 0.00 0.00 1.75
676 683 6.617371 AGATCCCTGTATCACCTATTCAAGTT 59.383 38.462 0.00 0.00 0.00 2.66
679 686 5.243954 CGAGATCCCTGTATCACCTATTCAA 59.756 44.000 0.00 0.00 0.00 2.69
681 688 5.010933 TCGAGATCCCTGTATCACCTATTC 58.989 45.833 0.00 0.00 0.00 1.75
682 689 4.999310 TCGAGATCCCTGTATCACCTATT 58.001 43.478 0.00 0.00 0.00 1.73
683 690 4.659529 TCGAGATCCCTGTATCACCTAT 57.340 45.455 0.00 0.00 0.00 2.57
695 735 9.199982 TCGTAATAAAAATTACATCGAGATCCC 57.800 33.333 8.52 0.00 36.96 3.85
711 751 3.162202 TGGCGTCCGATCGTAATAAAA 57.838 42.857 15.09 0.00 0.00 1.52
712 752 2.867287 TGGCGTCCGATCGTAATAAA 57.133 45.000 15.09 0.00 0.00 1.40
715 755 1.604693 GGAATGGCGTCCGATCGTAAT 60.605 52.381 15.09 0.00 0.00 1.89
738 778 6.093219 TCGACTAGTTATTCGAAAGCTGTACT 59.907 38.462 0.00 2.55 41.16 2.73
739 779 6.194325 GTCGACTAGTTATTCGAAAGCTGTAC 59.806 42.308 8.70 0.00 45.35 2.90
740 780 6.128200 TGTCGACTAGTTATTCGAAAGCTGTA 60.128 38.462 17.92 0.00 45.35 2.74
754 800 2.810274 TGAAGCTACGTGTCGACTAGTT 59.190 45.455 17.92 5.52 0.00 2.24
767 813 3.120060 CCAAAGACATGCAGTGAAGCTAC 60.120 47.826 0.00 0.00 34.99 3.58
858 907 1.468565 GCGTCGTTAGCTGGTGTATGA 60.469 52.381 0.00 0.00 0.00 2.15
875 924 3.880490 TGTGGACTTTACTGATTTTGCGT 59.120 39.130 0.00 0.00 0.00 5.24
882 931 2.831685 TGCGTGTGGACTTTACTGAT 57.168 45.000 0.00 0.00 0.00 2.90
886 935 2.092211 CGAGATTGCGTGTGGACTTTAC 59.908 50.000 0.00 0.00 0.00 2.01
931 980 1.466950 CTCTCTGTGTCTCGTGTCTCC 59.533 57.143 0.00 0.00 0.00 3.71
932 981 2.415168 CTCTCTCTGTGTCTCGTGTCTC 59.585 54.545 0.00 0.00 0.00 3.36
944 993 4.502950 GGCTTGCTATAATGCTCTCTCTGT 60.503 45.833 0.00 0.00 0.00 3.41
945 994 3.995705 GGCTTGCTATAATGCTCTCTCTG 59.004 47.826 0.00 0.00 0.00 3.35
946 995 3.305950 CGGCTTGCTATAATGCTCTCTCT 60.306 47.826 0.00 0.00 0.00 3.10
947 996 2.992543 CGGCTTGCTATAATGCTCTCTC 59.007 50.000 0.00 0.00 0.00 3.20
963 1012 0.745845 CTACAAGATGGCTGCGGCTT 60.746 55.000 18.85 5.23 38.73 4.35
964 1013 1.153289 CTACAAGATGGCTGCGGCT 60.153 57.895 18.85 0.00 38.73 5.52
967 1022 0.176680 ACTCCTACAAGATGGCTGCG 59.823 55.000 0.00 0.00 0.00 5.18
975 1030 6.384595 TCTCTCTAGCTTCTACTCCTACAAGA 59.615 42.308 0.00 0.00 0.00 3.02
983 1038 4.141287 TGCCATCTCTCTAGCTTCTACTC 58.859 47.826 0.00 0.00 0.00 2.59
986 1041 6.286758 CAATTTGCCATCTCTCTAGCTTCTA 58.713 40.000 0.00 0.00 0.00 2.10
987 1042 5.124645 CAATTTGCCATCTCTCTAGCTTCT 58.875 41.667 0.00 0.00 0.00 2.85
989 1044 3.631227 GCAATTTGCCATCTCTCTAGCTT 59.369 43.478 10.34 0.00 37.42 3.74
1018 1098 1.611851 AGGAGGGAGACTGCACCAG 60.612 63.158 10.83 0.00 40.51 4.00
1019 1099 1.610673 GAGGAGGGAGACTGCACCA 60.611 63.158 10.83 0.00 40.51 4.17
1020 1100 0.907230 AAGAGGAGGGAGACTGCACC 60.907 60.000 0.00 0.00 40.51 5.01
1021 1101 0.980423 AAAGAGGAGGGAGACTGCAC 59.020 55.000 0.00 0.00 40.51 4.57
1022 1102 1.203237 AGAAAGAGGAGGGAGACTGCA 60.203 52.381 0.00 0.00 40.51 4.41
1025 1105 3.845109 AGAAGAAAGAGGAGGGAGACT 57.155 47.619 0.00 0.00 0.00 3.24
1035 1115 3.686916 ACGAAGGGGAAGAAGAAAGAG 57.313 47.619 0.00 0.00 0.00 2.85
1036 1116 3.646637 AGAACGAAGGGGAAGAAGAAAGA 59.353 43.478 0.00 0.00 0.00 2.52
1037 1117 3.997681 GAGAACGAAGGGGAAGAAGAAAG 59.002 47.826 0.00 0.00 0.00 2.62
1038 1118 3.244457 GGAGAACGAAGGGGAAGAAGAAA 60.244 47.826 0.00 0.00 0.00 2.52
1039 1119 2.302157 GGAGAACGAAGGGGAAGAAGAA 59.698 50.000 0.00 0.00 0.00 2.52
1040 1120 1.900486 GGAGAACGAAGGGGAAGAAGA 59.100 52.381 0.00 0.00 0.00 2.87
1048 1128 1.215647 CCGACAGGAGAACGAAGGG 59.784 63.158 0.00 0.00 41.02 3.95
1084 1164 2.753043 GGCCACCATGCTCACCTG 60.753 66.667 0.00 0.00 0.00 4.00
1140 1220 2.673893 CGTCGTCAAATCCAGGATGACA 60.674 50.000 19.22 7.34 45.81 3.58
1143 1223 0.652592 GCGTCGTCAAATCCAGGATG 59.347 55.000 1.44 0.00 0.00 3.51
1185 1265 4.552365 ACCGCCATCTGGATGCCG 62.552 66.667 6.92 6.92 39.10 5.69
1208 1288 2.584143 GGTGCGCGGCGTAATAGT 60.584 61.111 24.46 0.00 0.00 2.12
1302 1382 0.937304 GCGCCGATGATTGAGCTTAA 59.063 50.000 0.00 0.00 0.00 1.85
1303 1383 0.104855 AGCGCCGATGATTGAGCTTA 59.895 50.000 2.29 0.00 0.00 3.09
1304 1384 1.153289 AGCGCCGATGATTGAGCTT 60.153 52.632 2.29 0.00 0.00 3.74
1305 1385 1.593750 GAGCGCCGATGATTGAGCT 60.594 57.895 2.29 2.97 37.69 4.09
1317 1397 3.567797 GATGGTGAAGCGAGCGCC 61.568 66.667 11.66 0.00 43.17 6.53
1318 1398 2.510238 AGATGGTGAAGCGAGCGC 60.510 61.111 6.78 6.78 42.33 5.92
1332 1412 8.677148 ATTATGTAAACGTAAAGATGCCAGAT 57.323 30.769 0.00 0.00 31.83 2.90
1335 1415 8.270080 TGAATTATGTAAACGTAAAGATGCCA 57.730 30.769 0.00 0.00 31.83 4.92
1342 1422 9.275398 AGTTGACCTGAATTATGTAAACGTAAA 57.725 29.630 0.00 0.00 30.18 2.01
1359 1439 1.274167 TGGTTAGCCGTAGTTGACCTG 59.726 52.381 0.00 0.00 37.67 4.00
1398 1479 5.657470 TCAGCAAATAGAAAATCCGATCG 57.343 39.130 8.51 8.51 0.00 3.69
1400 1481 4.024556 CGCTCAGCAAATAGAAAATCCGAT 60.025 41.667 0.00 0.00 0.00 4.18
1401 1482 3.309682 CGCTCAGCAAATAGAAAATCCGA 59.690 43.478 0.00 0.00 0.00 4.55
1402 1483 3.063997 ACGCTCAGCAAATAGAAAATCCG 59.936 43.478 0.00 0.00 0.00 4.18
1403 1484 4.346129 CACGCTCAGCAAATAGAAAATCC 58.654 43.478 0.00 0.00 0.00 3.01
1404 1485 4.142600 ACCACGCTCAGCAAATAGAAAATC 60.143 41.667 0.00 0.00 0.00 2.17
1405 1486 3.758554 ACCACGCTCAGCAAATAGAAAAT 59.241 39.130 0.00 0.00 0.00 1.82
1406 1487 3.146066 ACCACGCTCAGCAAATAGAAAA 58.854 40.909 0.00 0.00 0.00 2.29
1435 1516 4.400884 ACCATTACACAAACAGCAAAGTCA 59.599 37.500 0.00 0.00 0.00 3.41
1597 1679 4.619227 CTGCACGGGGGTCAACGT 62.619 66.667 0.00 0.00 45.25 3.99
1780 1865 0.392998 GTGCGGTCCATGATCTTGGT 60.393 55.000 23.12 0.00 38.01 3.67
1839 1930 1.078709 CCATGAAGTGGTACAGCACG 58.921 55.000 5.95 0.00 43.44 5.34
1977 2068 2.109126 GTCCATGAAGCTGCCGACC 61.109 63.158 0.00 0.00 0.00 4.79
2136 2227 0.684535 TCATCAAGGTTGAGTCGGCA 59.315 50.000 0.00 0.00 41.08 5.69
2138 2229 2.015736 CCTCATCAAGGTTGAGTCGG 57.984 55.000 0.00 0.00 41.08 4.79
2331 2438 1.200519 TGAACTTGCCGGCTATACCT 58.799 50.000 29.70 7.04 35.61 3.08
2353 2460 2.903357 CAGCTGCCCGTCTACCAT 59.097 61.111 0.00 0.00 0.00 3.55
2458 2565 2.555199 CTGTTGGGGTTCAGATCGATC 58.445 52.381 17.91 17.91 34.02 3.69
2459 2566 1.407437 GCTGTTGGGGTTCAGATCGAT 60.407 52.381 0.00 0.00 34.02 3.59
2460 2567 0.036388 GCTGTTGGGGTTCAGATCGA 60.036 55.000 0.00 0.00 34.02 3.59
2461 2568 1.361668 CGCTGTTGGGGTTCAGATCG 61.362 60.000 0.00 0.00 34.02 3.69
2497 2613 4.388499 GCCTTTCGGAGCGGACCA 62.388 66.667 0.00 0.00 0.00 4.02
2539 2677 4.415150 CACGGCCACCAGGAGCAT 62.415 66.667 2.24 0.00 36.89 3.79
2561 2699 0.512952 CTGCTTGAACCCGTTCTTCG 59.487 55.000 8.91 0.00 40.14 3.79
2615 2753 3.181456 GCAATAGCCTGTGATCTTCTCCT 60.181 47.826 0.00 0.00 33.58 3.69
2706 2844 7.665559 AGTTTGTCATAAGAATCCAAGCTAACA 59.334 33.333 0.00 0.00 0.00 2.41
2773 2911 2.872858 GAGAACCCAATGCCGATAGTTC 59.127 50.000 0.00 0.00 35.08 3.01
2778 2916 2.442236 AATGAGAACCCAATGCCGAT 57.558 45.000 0.00 0.00 0.00 4.18
2782 2920 6.515272 TCTTCTAAAATGAGAACCCAATGC 57.485 37.500 0.00 0.00 32.05 3.56
2784 2922 9.178758 GTACATCTTCTAAAATGAGAACCCAAT 57.821 33.333 0.00 0.00 32.05 3.16
2785 2923 7.333423 CGTACATCTTCTAAAATGAGAACCCAA 59.667 37.037 0.00 0.00 32.05 4.12
2786 2924 6.816640 CGTACATCTTCTAAAATGAGAACCCA 59.183 38.462 0.00 0.00 32.05 4.51
2787 2925 6.817140 ACGTACATCTTCTAAAATGAGAACCC 59.183 38.462 0.00 0.00 32.05 4.11
2793 2934 6.684131 CGACGTACGTACATCTTCTAAAATGA 59.316 38.462 22.87 0.00 37.22 2.57
2817 2958 3.420691 GCATGTGCAACCGTCACTACG 62.421 57.143 0.00 0.00 44.06 3.51
2917 3058 3.138798 ATCGACCACCCCGACTCG 61.139 66.667 0.00 0.00 38.97 4.18
3136 3279 3.005897 GCCTACTGTGTGAGAAAGTGAGA 59.994 47.826 0.00 0.00 0.00 3.27
3142 3285 2.965831 AGAGTGCCTACTGTGTGAGAAA 59.034 45.455 0.00 0.00 37.25 2.52
3183 3365 1.138036 CACAATCACGCCCATGCAG 59.862 57.895 0.00 0.00 37.32 4.41
3323 3520 1.506718 GGTCAGCATCGACGTCAGA 59.493 57.895 17.16 13.90 36.73 3.27
3488 3693 2.813908 GCGTCTGCGTACCCCTTG 60.814 66.667 0.00 0.00 40.81 3.61
3608 3818 0.179073 CAGTCTTGTAGATGGGCCCG 60.179 60.000 19.37 0.00 0.00 6.13
3634 3844 1.464608 GCGCTGAGCTTACAAATGACA 59.535 47.619 1.78 0.00 44.04 3.58
3635 3845 2.165282 GCGCTGAGCTTACAAATGAC 57.835 50.000 1.78 0.00 44.04 3.06
3652 3862 1.153726 TATGTGTAGTGGCGTGGCG 60.154 57.895 0.00 0.00 0.00 5.69
3653 3863 1.418342 CGTATGTGTAGTGGCGTGGC 61.418 60.000 0.00 0.00 0.00 5.01
3654 3864 0.171679 TCGTATGTGTAGTGGCGTGG 59.828 55.000 0.00 0.00 0.00 4.94
3655 3865 1.852280 CATCGTATGTGTAGTGGCGTG 59.148 52.381 0.00 0.00 0.00 5.34
3656 3866 1.475280 ACATCGTATGTGTAGTGGCGT 59.525 47.619 0.56 0.00 43.01 5.68
3657 3867 2.203800 ACATCGTATGTGTAGTGGCG 57.796 50.000 0.56 0.00 43.01 5.69
3660 3870 3.857052 ACCCAACATCGTATGTGTAGTG 58.143 45.455 2.00 0.00 44.07 2.74
3662 3872 4.500127 TGAACCCAACATCGTATGTGTAG 58.500 43.478 2.00 0.00 44.07 2.74
3663 3873 4.538746 TGAACCCAACATCGTATGTGTA 57.461 40.909 2.00 0.00 44.07 2.90
3684 3894 5.047660 GCAGAGTATAATCCGAGTTCCTGAT 60.048 44.000 0.00 0.00 0.00 2.90
3812 4026 0.384309 CTTCCGCCAGCGTCAGTATA 59.616 55.000 11.55 0.00 37.81 1.47
3831 4045 3.634448 TCGATCTTGGACATCTTCTCTCC 59.366 47.826 0.00 0.00 0.00 3.71
3934 4148 2.158234 AGGAATATCCCTCCGAAGCTCT 60.158 50.000 0.00 0.00 37.19 4.09
3944 4158 2.903926 CCGGTTAGGAGGAATATCCCT 58.096 52.381 0.00 0.00 45.00 4.20
4095 4310 0.674581 GTGTCATAGTGCTGCAGCCA 60.675 55.000 34.64 20.59 41.18 4.75
4178 4402 3.430862 CATGTGGGCGTCCGGTTG 61.431 66.667 0.00 0.00 35.24 3.77
4248 4472 0.811616 GCGGCATTCATCTCCGAGTT 60.812 55.000 3.91 0.00 45.53 3.01
4268 4492 1.000955 GGCGTGTTCTCCAGAGAAGAA 59.999 52.381 10.33 0.01 46.93 2.52
4345 4569 2.100631 GTTGACGTGGCCATCTCCG 61.101 63.158 9.72 10.86 0.00 4.63
4366 4593 2.786539 CTAGCGGTGCAGTTGAGGCA 62.787 60.000 0.00 0.00 39.32 4.75
4373 4600 1.137086 CTGGTAATCTAGCGGTGCAGT 59.863 52.381 0.00 0.00 0.00 4.40
4402 4629 9.658799 CCATGAAAGAAATAAGTCTAGTCAAGA 57.341 33.333 0.00 0.00 30.05 3.02
4409 4636 8.325787 TGGCTTACCATGAAAGAAATAAGTCTA 58.674 33.333 10.83 0.00 42.67 2.59
4410 4637 7.175104 TGGCTTACCATGAAAGAAATAAGTCT 58.825 34.615 10.83 0.00 42.67 3.24
4411 4638 7.391148 TGGCTTACCATGAAAGAAATAAGTC 57.609 36.000 10.83 0.00 42.67 3.01
4427 4654 4.593634 AGGTCTGGTAATATCTGGCTTACC 59.406 45.833 5.84 5.84 44.70 2.85
4428 4655 5.810080 AGGTCTGGTAATATCTGGCTTAC 57.190 43.478 0.00 0.00 0.00 2.34
4429 4656 6.269307 GGTTAGGTCTGGTAATATCTGGCTTA 59.731 42.308 0.00 0.00 0.00 3.09
4430 4657 5.071923 GGTTAGGTCTGGTAATATCTGGCTT 59.928 44.000 0.00 0.00 0.00 4.35
4431 4658 4.593634 GGTTAGGTCTGGTAATATCTGGCT 59.406 45.833 0.00 0.00 0.00 4.75
4432 4659 4.347000 TGGTTAGGTCTGGTAATATCTGGC 59.653 45.833 0.00 0.00 0.00 4.85
4433 4660 5.012148 CCTGGTTAGGTCTGGTAATATCTGG 59.988 48.000 0.00 0.00 39.39 3.86
4434 4661 5.012148 CCCTGGTTAGGTCTGGTAATATCTG 59.988 48.000 0.00 0.00 42.96 2.90
4435 4662 5.155905 CCCTGGTTAGGTCTGGTAATATCT 58.844 45.833 0.00 0.00 42.96 1.98
4436 4663 4.286291 CCCCTGGTTAGGTCTGGTAATATC 59.714 50.000 0.00 0.00 42.96 1.63
4437 4664 4.240323 CCCCTGGTTAGGTCTGGTAATAT 58.760 47.826 0.00 0.00 42.96 1.28
4438 4665 3.660959 CCCCTGGTTAGGTCTGGTAATA 58.339 50.000 0.00 0.00 42.96 0.98
4439 4666 2.488836 CCCCTGGTTAGGTCTGGTAAT 58.511 52.381 0.00 0.00 42.96 1.89
4440 4667 1.961133 CCCCTGGTTAGGTCTGGTAA 58.039 55.000 0.00 0.00 42.96 2.85
4441 4668 0.619543 GCCCCTGGTTAGGTCTGGTA 60.620 60.000 0.00 0.00 42.96 3.25
4442 4669 1.923909 GCCCCTGGTTAGGTCTGGT 60.924 63.158 0.00 0.00 42.96 4.00
4443 4670 2.998949 GCCCCTGGTTAGGTCTGG 59.001 66.667 0.00 0.00 42.96 3.86
4444 4671 2.584608 CGCCCCTGGTTAGGTCTG 59.415 66.667 0.00 0.00 42.96 3.51
4445 4672 2.547123 ATCCGCCCCTGGTTAGGTCT 62.547 60.000 0.00 0.00 42.96 3.85
4446 4673 2.041206 GATCCGCCCCTGGTTAGGTC 62.041 65.000 0.00 0.00 42.96 3.85
4872 5105 2.556189 GAGCAAGATGATCGCTCCTCTA 59.444 50.000 10.15 0.00 45.14 2.43
4914 5148 3.519913 GAGGGACCTTAGACATCACCTTT 59.480 47.826 0.00 0.00 0.00 3.11
5364 5607 3.535561 AGATGGACAAAGTAATGCCTCG 58.464 45.455 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.