Multiple sequence alignment - TraesCS4B01G196000

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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 TraesCS4B01G196000 chr4B 100.000 4857 0 0 1 4857 422526088 422521232 0.000000e+00 8970
1 TraesCS4B01G196000 chr4A 93.178 2668 108 30 579 3213 126419050 126421676 0.000000e+00 3851
2 TraesCS4B01G196000 chr4A 92.828 739 38 12 3453 4183 126422090 126422821 0.000000e+00 1057
3 TraesCS4B01G196000 chr4A 86.386 404 49 5 1 403 126418650 126419048 2.080000e-118 436
4 TraesCS4B01G196000 chr4A 82.388 335 27 15 4187 4492 126422860 126423191 3.730000e-66 263
5 TraesCS4B01G196000 chr4A 84.647 241 19 8 3240 3471 126421837 126422068 1.760000e-54 224
6 TraesCS4B01G196000 chr4D 94.792 2477 101 15 574 3038 341032508 341030048 0.000000e+00 3834
7 TraesCS4B01G196000 chr4D 97.360 985 19 5 3330 4310 341029741 341028760 0.000000e+00 1668
8 TraesCS4B01G196000 chr4D 90.544 349 16 6 4296 4630 341028706 341028361 3.450000e-121 446
9 TraesCS4B01G196000 chr4D 94.248 226 7 2 3087 3312 341030053 341029834 1.670000e-89 340
10 TraesCS4B01G196000 chr4D 89.286 224 24 0 128 351 341033001 341032778 1.030000e-71 281
11 TraesCS4B01G196000 chr4D 90.476 210 8 1 4608 4817 341028346 341028149 2.880000e-67 267
12 TraesCS4B01G196000 chr2D 78.920 389 75 5 13 398 388057281 388057665 1.730000e-64 257
13 TraesCS4B01G196000 chr2D 85.567 194 19 7 392 580 623514850 623515039 1.380000e-45 195
14 TraesCS4B01G196000 chr3B 78.649 370 73 6 20 385 812616181 812615814 1.750000e-59 241
15 TraesCS4B01G196000 chr3B 80.719 306 55 4 86 389 172725065 172724762 8.130000e-58 235
16 TraesCS4B01G196000 chrUn 80.921 304 56 2 86 388 68800937 68801239 6.280000e-59 239
17 TraesCS4B01G196000 chrUn 87.898 157 18 1 396 551 369790578 369790734 2.990000e-42 183
18 TraesCS4B01G196000 chrUn 87.898 157 18 1 396 551 434534497 434534653 2.990000e-42 183
19 TraesCS4B01G196000 chr3D 80.247 324 58 5 81 401 463681835 463681515 6.280000e-59 239
20 TraesCS4B01G196000 chr3D 90.850 153 10 3 403 551 137021026 137020874 8.240000e-48 202
21 TraesCS4B01G196000 chr3D 90.604 149 12 2 405 551 614910477 614910329 3.840000e-46 196
22 TraesCS4B01G196000 chr6D 77.363 402 86 4 1 399 471072609 471072210 2.920000e-57 233
23 TraesCS4B01G196000 chr5D 79.331 329 61 7 75 401 334240618 334240941 1.760000e-54 224
24 TraesCS4B01G196000 chr7B 90.278 144 12 2 403 544 97361711 97361568 2.310000e-43 187
25 TraesCS4B01G196000 chr5B 88.462 156 11 7 402 551 35248026 35248180 1.070000e-41 182
26 TraesCS4B01G196000 chr2B 88.079 151 16 2 402 551 203854774 203854625 1.390000e-40 178
27 TraesCS4B01G196000 chr1A 85.465 172 16 7 399 570 527787461 527787299 2.320000e-38 171


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 TraesCS4B01G196000 chr4B 422521232 422526088 4856 True 8970.000000 8970 100.000000 1 4857 1 chr4B.!!$R1 4856
1 TraesCS4B01G196000 chr4A 126418650 126423191 4541 False 1166.200000 3851 87.885400 1 4492 5 chr4A.!!$F1 4491
2 TraesCS4B01G196000 chr4D 341028149 341033001 4852 True 1139.333333 3834 92.784333 128 4817 6 chr4D.!!$R1 4689

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
93 94 0.324368 TGGGTCTGCGTGGATCTAGT 60.324 55.0 0.00 0.00 0.00 2.57 F
1281 1526 0.100682 CGCTGCGGCTCTAGAGTTTA 59.899 55.0 20.75 5.03 36.09 2.01 F
2926 3186 0.745845 AAGCGGATGTCATCTGGTGC 60.746 55.0 23.63 16.13 45.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1999 0.318441 CAGCAGAGTCTTCGGTGGAA 59.682 55.0 0.00 0.0 0.00 3.53 R
3259 3655 0.249489 ACTGACGTCTCCACACTTGC 60.249 55.0 17.92 0.0 0.00 4.01 R
4597 5268 0.039035 ACGGAGCCAGAGAGAGTCTT 59.961 55.0 0.00 0.0 30.64 3.01 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 2.147387 GGAGGGTGTGTGGAGGTGT 61.147 63.158 0.00 0.00 0.00 4.16
32 33 1.371558 GAGGGTGTGTGGAGGTGTC 59.628 63.158 0.00 0.00 0.00 3.67
33 34 1.074471 AGGGTGTGTGGAGGTGTCT 60.074 57.895 0.00 0.00 0.00 3.41
34 35 0.694444 AGGGTGTGTGGAGGTGTCTT 60.694 55.000 0.00 0.00 0.00 3.01
47 48 1.002087 GGTGTCTTCGGTGGATCTTGT 59.998 52.381 0.00 0.00 0.00 3.16
48 49 2.232941 GGTGTCTTCGGTGGATCTTGTA 59.767 50.000 0.00 0.00 0.00 2.41
70 71 2.614481 GGATTTGGTCCGTGCTTGTCTA 60.614 50.000 0.00 0.00 37.23 2.59
78 79 1.610624 CCGTGCTTGTCTATGTTGGGT 60.611 52.381 0.00 0.00 0.00 4.51
93 94 0.324368 TGGGTCTGCGTGGATCTAGT 60.324 55.000 0.00 0.00 0.00 2.57
106 107 6.625300 GCGTGGATCTAGTCTTTGTTCTTCTA 60.625 42.308 0.00 0.00 0.00 2.10
111 112 7.485595 GGATCTAGTCTTTGTTCTTCTACGTTC 59.514 40.741 0.00 0.00 0.00 3.95
112 113 7.268199 TCTAGTCTTTGTTCTTCTACGTTCA 57.732 36.000 0.00 0.00 0.00 3.18
114 115 8.021973 TCTAGTCTTTGTTCTTCTACGTTCATC 58.978 37.037 0.00 0.00 0.00 2.92
119 120 4.806330 TGTTCTTCTACGTTCATCTGTCC 58.194 43.478 0.00 0.00 0.00 4.02
131 132 6.098409 ACGTTCATCTGTCCATAGGTTAGATT 59.902 38.462 0.00 0.00 29.42 2.40
135 136 8.324191 TCATCTGTCCATAGGTTAGATTCTTT 57.676 34.615 0.00 0.00 29.42 2.52
140 141 8.473358 TGTCCATAGGTTAGATTCTTTCGATA 57.527 34.615 0.00 0.00 0.00 2.92
144 145 9.765795 CCATAGGTTAGATTCTTTCGATAAACT 57.234 33.333 0.00 0.00 0.00 2.66
213 214 2.562738 GGGCCTTAGCATGACAACTTTT 59.437 45.455 0.84 0.00 42.56 2.27
215 216 3.255642 GGCCTTAGCATGACAACTTTTCA 59.744 43.478 0.00 0.00 42.56 2.69
293 294 2.314647 CGTTTTCGGCTCGCTCCAA 61.315 57.895 0.00 0.00 39.94 3.53
315 316 1.731424 GCTTGTAGTCGTCGCTTGCTA 60.731 52.381 0.00 0.00 0.00 3.49
321 322 2.290464 AGTCGTCGCTTGCTAGTCTAT 58.710 47.619 0.00 0.00 0.00 1.98
325 326 3.315470 TCGTCGCTTGCTAGTCTATGAAT 59.685 43.478 0.00 0.00 0.00 2.57
326 327 4.514066 TCGTCGCTTGCTAGTCTATGAATA 59.486 41.667 0.00 0.00 0.00 1.75
385 611 7.027760 GCACTGCCATGATATTTGATGAATAG 58.972 38.462 0.00 0.00 33.87 1.73
389 615 9.174166 CTGCCATGATATTTGATGAATAGATCA 57.826 33.333 0.00 0.00 43.67 2.92
429 655 9.591792 TCAGTTTGTCTAATTCACATCTAGATG 57.408 33.333 27.63 27.63 44.15 2.90
454 680 9.547753 TGTTTTCTAAGGATATCACATCTAAGC 57.452 33.333 4.83 0.00 0.00 3.09
455 681 9.771534 GTTTTCTAAGGATATCACATCTAAGCT 57.228 33.333 4.83 0.00 0.00 3.74
457 683 9.988815 TTTCTAAGGATATCACATCTAAGCTTC 57.011 33.333 0.00 0.00 0.00 3.86
458 684 8.128322 TCTAAGGATATCACATCTAAGCTTCC 57.872 38.462 0.00 0.00 0.00 3.46
459 685 6.753913 AAGGATATCACATCTAAGCTTCCA 57.246 37.500 0.00 0.00 0.00 3.53
460 686 6.107901 AGGATATCACATCTAAGCTTCCAC 57.892 41.667 0.00 0.00 0.00 4.02
461 687 5.604231 AGGATATCACATCTAAGCTTCCACA 59.396 40.000 0.00 0.00 0.00 4.17
462 688 6.100279 AGGATATCACATCTAAGCTTCCACAA 59.900 38.462 0.00 0.00 0.00 3.33
463 689 6.767902 GGATATCACATCTAAGCTTCCACAAA 59.232 38.462 0.00 0.00 0.00 2.83
464 690 7.446625 GGATATCACATCTAAGCTTCCACAAAT 59.553 37.037 0.00 0.00 0.00 2.32
465 691 9.494271 GATATCACATCTAAGCTTCCACAAATA 57.506 33.333 0.00 0.00 0.00 1.40
466 692 9.851686 ATATCACATCTAAGCTTCCACAAATAA 57.148 29.630 0.00 0.00 0.00 1.40
467 693 7.377766 TCACATCTAAGCTTCCACAAATAAC 57.622 36.000 0.00 0.00 0.00 1.89
468 694 6.092122 TCACATCTAAGCTTCCACAAATAACG 59.908 38.462 0.00 0.00 0.00 3.18
469 695 4.939509 TCTAAGCTTCCACAAATAACGC 57.060 40.909 0.00 0.00 0.00 4.84
470 696 4.320023 TCTAAGCTTCCACAAATAACGCA 58.680 39.130 0.00 0.00 0.00 5.24
471 697 4.941263 TCTAAGCTTCCACAAATAACGCAT 59.059 37.500 0.00 0.00 0.00 4.73
472 698 3.764885 AGCTTCCACAAATAACGCATC 57.235 42.857 0.00 0.00 0.00 3.91
473 699 3.081061 AGCTTCCACAAATAACGCATCA 58.919 40.909 0.00 0.00 0.00 3.07
474 700 3.505680 AGCTTCCACAAATAACGCATCAA 59.494 39.130 0.00 0.00 0.00 2.57
475 701 4.158394 AGCTTCCACAAATAACGCATCAAT 59.842 37.500 0.00 0.00 0.00 2.57
476 702 5.356751 AGCTTCCACAAATAACGCATCAATA 59.643 36.000 0.00 0.00 0.00 1.90
477 703 6.033341 GCTTCCACAAATAACGCATCAATAA 58.967 36.000 0.00 0.00 0.00 1.40
478 704 6.697019 GCTTCCACAAATAACGCATCAATAAT 59.303 34.615 0.00 0.00 0.00 1.28
479 705 7.860373 GCTTCCACAAATAACGCATCAATAATA 59.140 33.333 0.00 0.00 0.00 0.98
480 706 9.729023 CTTCCACAAATAACGCATCAATAATAA 57.271 29.630 0.00 0.00 0.00 1.40
524 750 8.458573 AAAATAGACCACAAACATAGTTGACA 57.541 30.769 0.00 0.00 32.59 3.58
525 751 7.435068 AATAGACCACAAACATAGTTGACAC 57.565 36.000 0.00 0.00 32.59 3.67
526 752 4.776349 AGACCACAAACATAGTTGACACA 58.224 39.130 0.00 0.00 32.59 3.72
527 753 5.189928 AGACCACAAACATAGTTGACACAA 58.810 37.500 0.00 0.00 32.59 3.33
528 754 5.296780 AGACCACAAACATAGTTGACACAAG 59.703 40.000 0.00 0.00 32.59 3.16
529 755 4.338118 ACCACAAACATAGTTGACACAAGG 59.662 41.667 0.00 0.00 32.59 3.61
530 756 4.261572 CCACAAACATAGTTGACACAAGGG 60.262 45.833 0.00 0.00 32.59 3.95
531 757 4.338118 CACAAACATAGTTGACACAAGGGT 59.662 41.667 0.00 0.00 32.59 4.34
532 758 5.529430 CACAAACATAGTTGACACAAGGGTA 59.471 40.000 0.00 0.00 32.59 3.69
533 759 5.763204 ACAAACATAGTTGACACAAGGGTAG 59.237 40.000 0.00 0.00 32.59 3.18
534 760 5.818678 AACATAGTTGACACAAGGGTAGA 57.181 39.130 0.00 0.00 0.00 2.59
535 761 6.374417 AACATAGTTGACACAAGGGTAGAT 57.626 37.500 0.00 0.00 0.00 1.98
536 762 5.734720 ACATAGTTGACACAAGGGTAGATG 58.265 41.667 0.00 0.00 0.00 2.90
537 763 5.248477 ACATAGTTGACACAAGGGTAGATGT 59.752 40.000 0.00 0.00 0.00 3.06
548 774 7.676683 ACAAGGGTAGATGTGACATAGTTAT 57.323 36.000 0.00 0.00 0.00 1.89
549 775 7.500992 ACAAGGGTAGATGTGACATAGTTATG 58.499 38.462 0.00 0.00 39.55 1.90
551 777 8.638873 CAAGGGTAGATGTGACATAGTTATGTA 58.361 37.037 0.00 0.00 46.20 2.29
552 778 8.958060 AGGGTAGATGTGACATAGTTATGTAT 57.042 34.615 0.00 0.00 46.20 2.29
553 779 8.807118 AGGGTAGATGTGACATAGTTATGTATG 58.193 37.037 0.00 0.00 46.20 2.39
554 780 8.585881 GGGTAGATGTGACATAGTTATGTATGT 58.414 37.037 0.00 0.00 46.20 2.29
555 781 9.411801 GGTAGATGTGACATAGTTATGTATGTG 57.588 37.037 0.00 0.00 46.20 3.21
556 782 9.967346 GTAGATGTGACATAGTTATGTATGTGT 57.033 33.333 0.00 0.00 46.20 3.72
558 784 8.144478 AGATGTGACATAGTTATGTATGTGTCC 58.856 37.037 0.00 0.00 46.20 4.02
559 785 7.418337 TGTGACATAGTTATGTATGTGTCCT 57.582 36.000 4.84 0.00 46.20 3.85
560 786 8.528044 TGTGACATAGTTATGTATGTGTCCTA 57.472 34.615 4.84 0.00 46.20 2.94
561 787 8.630037 TGTGACATAGTTATGTATGTGTCCTAG 58.370 37.037 4.84 0.00 46.20 3.02
562 788 8.847196 GTGACATAGTTATGTATGTGTCCTAGA 58.153 37.037 4.84 0.00 46.20 2.43
563 789 8.847196 TGACATAGTTATGTATGTGTCCTAGAC 58.153 37.037 4.84 0.00 46.20 2.59
564 790 7.872881 ACATAGTTATGTATGTGTCCTAGACG 58.127 38.462 3.03 0.00 44.54 4.18
565 791 5.769484 AGTTATGTATGTGTCCTAGACGG 57.231 43.478 0.00 0.00 34.95 4.79
566 792 5.443283 AGTTATGTATGTGTCCTAGACGGA 58.557 41.667 0.00 0.00 40.30 4.69
737 968 1.244019 CGGCCTCACCCAAAAGGAAG 61.244 60.000 0.00 0.00 39.89 3.46
815 1048 9.019764 CAGTTCAAAATATTTCAAACTCAACGT 57.980 29.630 18.34 0.00 0.00 3.99
877 1110 2.294078 CCCCCACTCTCTCCACACC 61.294 68.421 0.00 0.00 0.00 4.16
880 1114 1.536418 CCACTCTCTCCACACCCCA 60.536 63.158 0.00 0.00 0.00 4.96
943 1177 1.097547 CCGCATCTTCCGCCATTTCT 61.098 55.000 0.00 0.00 0.00 2.52
1014 1253 4.586235 GCCATGGATCCCCACCCG 62.586 72.222 18.40 0.00 46.98 5.28
1054 1293 0.251341 AAGAAACCAGCGCCATTCCT 60.251 50.000 2.29 0.00 0.00 3.36
1085 1324 1.524482 GAGCCCTGCCTCTCGATTT 59.476 57.895 0.00 0.00 0.00 2.17
1087 1326 1.221840 GCCCTGCCTCTCGATTTCA 59.778 57.895 0.00 0.00 0.00 2.69
1279 1524 1.388065 ATCGCTGCGGCTCTAGAGTT 61.388 55.000 23.03 0.00 36.09 3.01
1281 1526 0.100682 CGCTGCGGCTCTAGAGTTTA 59.899 55.000 20.75 5.03 36.09 2.01
1282 1527 1.846541 GCTGCGGCTCTAGAGTTTAG 58.153 55.000 20.75 14.22 35.22 1.85
1284 1529 2.035321 GCTGCGGCTCTAGAGTTTAGAT 59.965 50.000 20.75 0.00 35.22 1.98
1285 1530 3.491792 GCTGCGGCTCTAGAGTTTAGATT 60.492 47.826 20.75 0.00 35.22 2.40
1286 1531 4.295051 CTGCGGCTCTAGAGTTTAGATTC 58.705 47.826 20.75 1.64 0.00 2.52
1287 1532 3.243101 TGCGGCTCTAGAGTTTAGATTCG 60.243 47.826 20.75 12.11 0.00 3.34
1288 1533 3.003482 GCGGCTCTAGAGTTTAGATTCGA 59.997 47.826 20.75 0.00 0.00 3.71
1289 1534 4.320641 GCGGCTCTAGAGTTTAGATTCGAT 60.321 45.833 20.75 0.00 0.00 3.59
1291 1536 5.627367 CGGCTCTAGAGTTTAGATTCGATTG 59.373 44.000 20.75 0.00 0.00 2.67
1292 1537 6.508777 GGCTCTAGAGTTTAGATTCGATTGT 58.491 40.000 20.75 0.00 0.00 2.71
1293 1538 6.419413 GGCTCTAGAGTTTAGATTCGATTGTG 59.581 42.308 20.75 0.00 0.00 3.33
1294 1539 6.975772 GCTCTAGAGTTTAGATTCGATTGTGT 59.024 38.462 20.75 0.00 0.00 3.72
1295 1540 7.489757 GCTCTAGAGTTTAGATTCGATTGTGTT 59.510 37.037 20.75 0.00 0.00 3.32
1339 1584 2.029623 CTTGCTTACCGAGGCTAGGTA 58.970 52.381 20.90 20.90 42.81 3.08
1493 1738 3.049674 CCGCCGAAGCTGCAGAAA 61.050 61.111 20.43 0.00 36.60 2.52
1511 1756 1.227102 ACCTGCTGCAAAGGTGTCA 59.773 52.632 17.81 0.00 46.51 3.58
1514 1759 2.121564 CTGCTGCAAAGGTGTCACCG 62.122 60.000 16.44 3.72 44.90 4.94
1535 1780 2.752358 CCTCCACAGAAGCCTGCA 59.248 61.111 0.00 0.00 44.16 4.41
1622 1867 2.492090 CCTTCTCGTCCCGCAGAG 59.508 66.667 0.00 0.00 35.91 3.35
1719 1964 4.457496 AGGATGACGTGGCAGCGG 62.457 66.667 12.66 0.00 35.98 5.52
1754 1999 1.679898 CGGGGAGAAGGTCAAAGCT 59.320 57.895 0.00 0.00 0.00 3.74
1778 2023 2.659610 GAAGACTCTGCTGGGCGT 59.340 61.111 0.00 0.00 0.00 5.68
1850 2095 1.004918 CGCAGAGACCCCGTTCTTT 60.005 57.895 0.00 0.00 0.00 2.52
1871 2116 1.919956 GCGCTCAGAATTGCAGCAGT 61.920 55.000 0.00 0.00 32.27 4.40
1908 2153 1.380112 GAGTCCGCCTCCTACTGGT 60.380 63.158 0.00 0.00 33.79 4.00
2021 2266 2.544267 AGTTCAAAGCACACTTACGAGC 59.456 45.455 0.00 0.00 34.05 5.03
2044 2289 7.072030 AGCGAACGATTTGATATATTTTCTGC 58.928 34.615 0.00 0.00 0.00 4.26
2140 2385 2.289002 GTGGCTGCATGATTAGTACTGC 59.711 50.000 5.39 0.04 35.21 4.40
2273 2530 1.142748 GCGCCATGAGAGTGCTAGT 59.857 57.895 0.00 0.00 37.75 2.57
2453 2710 1.263217 GAACGTGATTGTGGTGGTGAC 59.737 52.381 0.00 0.00 0.00 3.67
2513 2770 2.192263 GAGGAAGAGATGGACCAACCT 58.808 52.381 0.00 0.00 39.86 3.50
2660 2917 3.064545 GTGAAATAGTCCAGTCAGCATGC 59.935 47.826 10.51 10.51 34.76 4.06
2825 3085 1.494721 AGCCCTTTCAACAACTCTCCA 59.505 47.619 0.00 0.00 0.00 3.86
2926 3186 0.745845 AAGCGGATGTCATCTGGTGC 60.746 55.000 23.63 16.13 45.00 5.01
3044 3307 2.590821 ACATGTGCAGAGCTTTTCCTT 58.409 42.857 0.00 0.00 0.00 3.36
3058 3321 5.833131 AGCTTTTCCTTTGACTTGGTCATTA 59.167 36.000 1.10 0.00 42.40 1.90
3060 3323 6.983890 GCTTTTCCTTTGACTTGGTCATTAAA 59.016 34.615 1.10 0.00 42.40 1.52
3062 3325 8.940768 TTTTCCTTTGACTTGGTCATTAAAAG 57.059 30.769 1.10 2.84 42.40 2.27
3063 3326 7.889873 TTCCTTTGACTTGGTCATTAAAAGA 57.110 32.000 9.85 0.00 42.40 2.52
3064 3327 8.477419 TTCCTTTGACTTGGTCATTAAAAGAT 57.523 30.769 9.85 0.00 42.40 2.40
3065 3328 8.477419 TCCTTTGACTTGGTCATTAAAAGATT 57.523 30.769 9.85 0.00 42.40 2.40
3066 3329 9.581289 TCCTTTGACTTGGTCATTAAAAGATTA 57.419 29.630 9.85 0.00 42.40 1.75
3148 3411 2.149578 GGAGTATGATGATGCTGCCAC 58.850 52.381 0.00 0.00 28.02 5.01
3220 3483 9.665719 TTCTGTTGTATCAAAGCTAATGACATA 57.334 29.630 4.40 0.00 0.00 2.29
3221 3484 9.317936 TCTGTTGTATCAAAGCTAATGACATAG 57.682 33.333 4.40 3.40 0.00 2.23
3279 3678 1.806623 GCAAGTGTGGAGACGTCAGTT 60.807 52.381 19.50 3.28 33.06 3.16
3280 3679 2.545113 GCAAGTGTGGAGACGTCAGTTA 60.545 50.000 19.50 0.00 32.12 2.24
3281 3680 3.309388 CAAGTGTGGAGACGTCAGTTAG 58.691 50.000 19.50 0.00 32.12 2.34
3312 3711 6.819146 CAGAAAATCTTGTACTCCCTCCTTAC 59.181 42.308 0.00 0.00 0.00 2.34
3321 3720 6.884832 TGTACTCCCTCCTTACATTTATGTG 58.115 40.000 5.64 0.00 41.89 3.21
3324 3723 7.504926 ACTCCCTCCTTACATTTATGTGTTA 57.495 36.000 5.64 0.00 41.89 2.41
3448 3922 0.104855 AGTTGCAGACTCGCAGAACA 59.895 50.000 0.00 0.00 44.14 3.18
3452 3926 4.112634 GTTGCAGACTCGCAGAACATATA 58.887 43.478 0.00 0.00 44.14 0.86
3454 3928 4.550422 TGCAGACTCGCAGAACATATATC 58.450 43.478 0.00 0.00 36.86 1.63
3455 3929 3.923461 GCAGACTCGCAGAACATATATCC 59.077 47.826 0.00 0.00 34.09 2.59
3577 4100 0.317160 CTGTTGCCACTCGTCTACCA 59.683 55.000 0.00 0.00 0.00 3.25
3616 4139 9.750125 ATCTTTGGAAAAGATTTTACAGTGTTC 57.250 29.630 0.00 0.00 41.64 3.18
3663 4187 0.833287 TCTGCTCTTATGGCCCAGTC 59.167 55.000 0.00 0.00 0.00 3.51
3836 4366 2.357075 GTGGAGCTAACTTACCCTTGC 58.643 52.381 0.00 0.00 0.00 4.01
3952 4482 3.534524 TGATTATGCGTGTGTTGTGTG 57.465 42.857 0.00 0.00 0.00 3.82
4037 4567 4.397481 TCACGCTCTGATGATCTTTGAT 57.603 40.909 0.00 0.00 0.00 2.57
4057 4587 1.502190 GGCTTGACAGGTTTAGCGC 59.498 57.895 0.00 0.00 34.50 5.92
4105 4635 2.162408 GTGCTTGCTCTTGGTTGATACC 59.838 50.000 0.00 0.00 45.26 2.73
4207 4775 4.006319 ACTATGCTTTGCCTTCTTCTCAC 58.994 43.478 0.00 0.00 0.00 3.51
4213 4781 4.517075 GCTTTGCCTTCTTCTCACTTAGTT 59.483 41.667 0.00 0.00 0.00 2.24
4302 4870 9.273016 TCTTGACCTACTTTTTAGTCAGAAATG 57.727 33.333 0.00 0.00 40.14 2.32
4307 4875 7.881751 ACCTACTTTTTAGTCAGAAATGGGTAC 59.118 37.037 0.00 0.00 0.00 3.34
4308 4876 8.101419 CCTACTTTTTAGTCAGAAATGGGTACT 58.899 37.037 0.00 0.00 0.00 2.73
4319 4956 8.255905 GTCAGAAATGGGTACTAGCTAGTTTTA 58.744 37.037 30.40 11.22 37.73 1.52
4406 5077 0.722799 GCAGAAAGACTTGCGTTCGC 60.723 55.000 10.34 10.34 39.55 4.70
4465 5136 5.175673 GCAAGAAGCAAGGAAAACAACATAC 59.824 40.000 0.00 0.00 44.79 2.39
4470 5141 4.578928 AGCAAGGAAAACAACATACGAGTT 59.421 37.500 0.00 0.00 0.00 3.01
4471 5142 5.067283 AGCAAGGAAAACAACATACGAGTTT 59.933 36.000 0.00 0.00 37.08 2.66
4525 5196 3.250323 CGAGGCGACGCTCATGTG 61.250 66.667 20.77 0.35 0.00 3.21
4597 5268 1.142097 TCGACACGGCACAAGTTGA 59.858 52.632 10.54 0.00 0.00 3.18
4598 5269 0.460459 TCGACACGGCACAAGTTGAA 60.460 50.000 10.54 0.00 0.00 2.69
4644 5351 3.790437 CCGTGGCCCAGCTGATCT 61.790 66.667 17.39 0.00 0.00 2.75
4654 5361 1.202463 CCAGCTGATCTAAGTCCACCG 60.202 57.143 17.39 0.00 0.00 4.94
4673 5380 4.406173 CGACACCGAGAGCTGCGT 62.406 66.667 0.00 0.00 38.22 5.24
4674 5381 2.049063 GACACCGAGAGCTGCGTT 60.049 61.111 0.00 0.00 0.00 4.84
4685 5392 2.743718 CTGCGTTGGTCAGACCCT 59.256 61.111 17.59 0.00 37.50 4.34
4686 5393 1.972198 CTGCGTTGGTCAGACCCTA 59.028 57.895 17.59 2.10 37.50 3.53
4687 5394 0.108615 CTGCGTTGGTCAGACCCTAG 60.109 60.000 17.59 8.83 37.50 3.02
4688 5395 0.541063 TGCGTTGGTCAGACCCTAGA 60.541 55.000 17.59 0.00 37.50 2.43
4689 5396 0.824759 GCGTTGGTCAGACCCTAGAT 59.175 55.000 17.59 0.00 37.50 1.98
4690 5397 1.207329 GCGTTGGTCAGACCCTAGATT 59.793 52.381 17.59 0.00 37.50 2.40
4691 5398 2.738964 GCGTTGGTCAGACCCTAGATTC 60.739 54.545 17.59 0.00 37.50 2.52
4692 5399 2.761208 CGTTGGTCAGACCCTAGATTCT 59.239 50.000 17.59 0.00 37.50 2.40
4693 5400 3.952323 CGTTGGTCAGACCCTAGATTCTA 59.048 47.826 17.59 0.00 37.50 2.10
4694 5401 4.036971 CGTTGGTCAGACCCTAGATTCTAG 59.963 50.000 17.59 12.94 37.50 2.43
4695 5402 4.186077 TGGTCAGACCCTAGATTCTAGG 57.814 50.000 26.73 26.73 37.50 3.02
4696 5403 2.894765 GGTCAGACCCTAGATTCTAGGC 59.105 54.545 27.84 17.97 33.41 3.93
4780 5487 3.001026 CGTAGCATGCATTGAGTTGAGAG 59.999 47.826 21.98 0.00 0.00 3.20
4785 5492 2.407090 TGCATTGAGTTGAGAGTGACG 58.593 47.619 0.00 0.00 0.00 4.35
4820 5527 4.435436 CAGCTCGTGCGTGGGCTA 62.435 66.667 1.62 0.00 45.42 3.93
4821 5528 4.135153 AGCTCGTGCGTGGGCTAG 62.135 66.667 0.00 0.00 45.42 3.42
4822 5529 4.129737 GCTCGTGCGTGGGCTAGA 62.130 66.667 0.00 0.00 40.82 2.43
4823 5530 2.571757 CTCGTGCGTGGGCTAGAA 59.428 61.111 0.00 0.00 40.82 2.10
4824 5531 1.805945 CTCGTGCGTGGGCTAGAAC 60.806 63.158 0.00 0.00 40.82 3.01
4825 5532 2.813908 CGTGCGTGGGCTAGAACC 60.814 66.667 0.00 0.00 40.82 3.62
4826 5533 2.813908 GTGCGTGGGCTAGAACCG 60.814 66.667 0.00 0.00 40.82 4.44
4827 5534 3.307906 TGCGTGGGCTAGAACCGT 61.308 61.111 0.00 0.00 40.82 4.83
4828 5535 2.508663 GCGTGGGCTAGAACCGTC 60.509 66.667 0.00 0.00 35.83 4.79
4829 5536 2.202570 CGTGGGCTAGAACCGTCG 60.203 66.667 0.00 0.77 0.00 5.12
4830 5537 2.508663 GTGGGCTAGAACCGTCGC 60.509 66.667 0.00 0.00 0.00 5.19
4831 5538 2.678934 TGGGCTAGAACCGTCGCT 60.679 61.111 0.00 0.00 0.00 4.93
4832 5539 2.202756 GGGCTAGAACCGTCGCTG 60.203 66.667 0.00 0.00 0.00 5.18
4833 5540 2.202756 GGCTAGAACCGTCGCTGG 60.203 66.667 0.00 0.00 0.00 4.85
4834 5541 2.886124 GCTAGAACCGTCGCTGGC 60.886 66.667 0.00 0.00 0.00 4.85
4835 5542 2.571757 CTAGAACCGTCGCTGGCA 59.428 61.111 0.00 0.00 0.00 4.92
4836 5543 1.141881 CTAGAACCGTCGCTGGCAT 59.858 57.895 0.00 0.00 0.00 4.40
4837 5544 1.148157 CTAGAACCGTCGCTGGCATG 61.148 60.000 0.00 0.00 0.00 4.06
4838 5545 4.166011 GAACCGTCGCTGGCATGC 62.166 66.667 9.90 9.90 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.611200 CACACACCCTCCGGACAATA 59.389 55.000 0.00 0.00 0.00 1.90
9 10 2.920912 TCCACACACCCTCCGGAC 60.921 66.667 0.00 0.00 0.00 4.79
10 11 2.603473 CTCCACACACCCTCCGGA 60.603 66.667 2.93 2.93 0.00 5.14
11 12 3.706373 CCTCCACACACCCTCCGG 61.706 72.222 0.00 0.00 0.00 5.14
19 20 1.046472 ACCGAAGACACCTCCACACA 61.046 55.000 0.00 0.00 0.00 3.72
31 32 3.095912 TCCTACAAGATCCACCGAAGA 57.904 47.619 0.00 0.00 0.00 2.87
32 33 4.408182 AATCCTACAAGATCCACCGAAG 57.592 45.455 0.00 0.00 0.00 3.79
33 34 4.513442 CAAATCCTACAAGATCCACCGAA 58.487 43.478 0.00 0.00 0.00 4.30
34 35 3.118408 CCAAATCCTACAAGATCCACCGA 60.118 47.826 0.00 0.00 0.00 4.69
47 48 1.349688 ACAAGCACGGACCAAATCCTA 59.650 47.619 0.00 0.00 46.69 2.94
48 49 0.110486 ACAAGCACGGACCAAATCCT 59.890 50.000 0.00 0.00 46.69 3.24
59 60 1.732259 GACCCAACATAGACAAGCACG 59.268 52.381 0.00 0.00 0.00 5.34
61 62 2.875672 GCAGACCCAACATAGACAAGCA 60.876 50.000 0.00 0.00 0.00 3.91
70 71 0.392998 GATCCACGCAGACCCAACAT 60.393 55.000 0.00 0.00 0.00 2.71
78 79 2.826128 ACAAAGACTAGATCCACGCAGA 59.174 45.455 0.00 0.00 0.00 4.26
93 94 6.513180 ACAGATGAACGTAGAAGAACAAAGA 58.487 36.000 0.00 0.00 0.00 2.52
106 107 4.954202 TCTAACCTATGGACAGATGAACGT 59.046 41.667 0.00 0.00 0.00 3.99
111 112 7.383572 CGAAAGAATCTAACCTATGGACAGATG 59.616 40.741 0.00 0.00 31.21 2.90
112 113 7.287927 TCGAAAGAATCTAACCTATGGACAGAT 59.712 37.037 0.00 0.00 37.03 2.90
114 115 6.806751 TCGAAAGAATCTAACCTATGGACAG 58.193 40.000 0.00 0.00 37.03 3.51
213 214 5.864418 ACCTTGTTGTAGTAGACAGTTGA 57.136 39.130 0.00 0.00 39.88 3.18
215 216 5.296035 GCAAACCTTGTTGTAGTAGACAGTT 59.704 40.000 0.00 0.00 39.88 3.16
293 294 1.350193 CAAGCGACGACTACAAGCAT 58.650 50.000 0.00 0.00 0.00 3.79
348 349 3.921119 TGGCAGTGCAAAGAACATTAG 57.079 42.857 18.61 0.00 0.00 1.73
361 587 8.331730 TCTATTCATCAAATATCATGGCAGTG 57.668 34.615 0.00 0.00 0.00 3.66
428 654 9.547753 GCTTAGATGTGATATCCTTAGAAAACA 57.452 33.333 0.00 0.00 0.00 2.83
429 655 9.771534 AGCTTAGATGTGATATCCTTAGAAAAC 57.228 33.333 0.00 0.00 0.00 2.43
431 657 9.988815 GAAGCTTAGATGTGATATCCTTAGAAA 57.011 33.333 0.00 0.00 0.00 2.52
432 658 8.589338 GGAAGCTTAGATGTGATATCCTTAGAA 58.411 37.037 0.00 0.00 0.00 2.10
433 659 7.730332 TGGAAGCTTAGATGTGATATCCTTAGA 59.270 37.037 0.00 0.00 0.00 2.10
434 660 7.816995 GTGGAAGCTTAGATGTGATATCCTTAG 59.183 40.741 0.00 0.00 0.00 2.18
435 661 7.290014 TGTGGAAGCTTAGATGTGATATCCTTA 59.710 37.037 0.00 0.00 0.00 2.69
436 662 6.100279 TGTGGAAGCTTAGATGTGATATCCTT 59.900 38.462 0.00 0.00 0.00 3.36
437 663 5.604231 TGTGGAAGCTTAGATGTGATATCCT 59.396 40.000 0.00 0.00 0.00 3.24
438 664 5.858381 TGTGGAAGCTTAGATGTGATATCC 58.142 41.667 0.00 0.00 0.00 2.59
439 665 7.792374 TTTGTGGAAGCTTAGATGTGATATC 57.208 36.000 0.00 0.00 0.00 1.63
440 666 9.851686 TTATTTGTGGAAGCTTAGATGTGATAT 57.148 29.630 0.00 0.00 0.00 1.63
441 667 9.109393 GTTATTTGTGGAAGCTTAGATGTGATA 57.891 33.333 0.00 0.00 0.00 2.15
442 668 7.201644 CGTTATTTGTGGAAGCTTAGATGTGAT 60.202 37.037 0.00 0.00 0.00 3.06
443 669 6.092122 CGTTATTTGTGGAAGCTTAGATGTGA 59.908 38.462 0.00 0.00 0.00 3.58
444 670 6.250819 CGTTATTTGTGGAAGCTTAGATGTG 58.749 40.000 0.00 0.00 0.00 3.21
445 671 5.163754 GCGTTATTTGTGGAAGCTTAGATGT 60.164 40.000 0.00 0.00 0.00 3.06
446 672 5.163764 TGCGTTATTTGTGGAAGCTTAGATG 60.164 40.000 0.00 0.00 0.00 2.90
447 673 4.941263 TGCGTTATTTGTGGAAGCTTAGAT 59.059 37.500 0.00 0.00 0.00 1.98
448 674 4.320023 TGCGTTATTTGTGGAAGCTTAGA 58.680 39.130 0.00 0.00 0.00 2.10
449 675 4.678509 TGCGTTATTTGTGGAAGCTTAG 57.321 40.909 0.00 0.00 0.00 2.18
450 676 4.697828 TGATGCGTTATTTGTGGAAGCTTA 59.302 37.500 0.00 0.00 0.00 3.09
451 677 3.505680 TGATGCGTTATTTGTGGAAGCTT 59.494 39.130 0.00 0.00 0.00 3.74
452 678 3.081061 TGATGCGTTATTTGTGGAAGCT 58.919 40.909 0.00 0.00 0.00 3.74
453 679 3.485947 TGATGCGTTATTTGTGGAAGC 57.514 42.857 0.00 0.00 0.00 3.86
454 680 9.729023 TTATTATTGATGCGTTATTTGTGGAAG 57.271 29.630 0.00 0.00 0.00 3.46
498 724 8.908903 TGTCAACTATGTTTGTGGTCTATTTTT 58.091 29.630 0.00 0.00 0.00 1.94
499 725 8.349983 GTGTCAACTATGTTTGTGGTCTATTTT 58.650 33.333 0.00 0.00 0.00 1.82
500 726 7.500892 TGTGTCAACTATGTTTGTGGTCTATTT 59.499 33.333 0.00 0.00 0.00 1.40
501 727 6.995686 TGTGTCAACTATGTTTGTGGTCTATT 59.004 34.615 0.00 0.00 0.00 1.73
502 728 6.530120 TGTGTCAACTATGTTTGTGGTCTAT 58.470 36.000 0.00 0.00 0.00 1.98
503 729 5.919755 TGTGTCAACTATGTTTGTGGTCTA 58.080 37.500 0.00 0.00 0.00 2.59
504 730 4.776349 TGTGTCAACTATGTTTGTGGTCT 58.224 39.130 0.00 0.00 0.00 3.85
505 731 5.493133 TTGTGTCAACTATGTTTGTGGTC 57.507 39.130 0.00 0.00 0.00 4.02
506 732 4.338118 CCTTGTGTCAACTATGTTTGTGGT 59.662 41.667 0.00 0.00 0.00 4.16
507 733 4.261572 CCCTTGTGTCAACTATGTTTGTGG 60.262 45.833 0.00 0.00 0.00 4.17
508 734 4.338118 ACCCTTGTGTCAACTATGTTTGTG 59.662 41.667 0.00 0.00 0.00 3.33
509 735 4.532834 ACCCTTGTGTCAACTATGTTTGT 58.467 39.130 0.00 0.00 0.00 2.83
510 736 5.995282 TCTACCCTTGTGTCAACTATGTTTG 59.005 40.000 0.00 0.00 0.00 2.93
511 737 6.182507 TCTACCCTTGTGTCAACTATGTTT 57.817 37.500 0.00 0.00 0.00 2.83
512 738 5.818678 TCTACCCTTGTGTCAACTATGTT 57.181 39.130 0.00 0.00 0.00 2.71
513 739 5.248477 ACATCTACCCTTGTGTCAACTATGT 59.752 40.000 0.00 0.00 0.00 2.29
514 740 5.582269 CACATCTACCCTTGTGTCAACTATG 59.418 44.000 0.00 0.00 38.69 2.23
515 741 5.483937 TCACATCTACCCTTGTGTCAACTAT 59.516 40.000 3.30 0.00 42.95 2.12
516 742 4.836175 TCACATCTACCCTTGTGTCAACTA 59.164 41.667 3.30 0.00 42.95 2.24
517 743 3.646162 TCACATCTACCCTTGTGTCAACT 59.354 43.478 3.30 0.00 42.95 3.16
518 744 3.746492 GTCACATCTACCCTTGTGTCAAC 59.254 47.826 3.30 0.00 42.95 3.18
519 745 3.389656 TGTCACATCTACCCTTGTGTCAA 59.610 43.478 3.30 0.00 42.95 3.18
520 746 2.969262 TGTCACATCTACCCTTGTGTCA 59.031 45.455 3.30 1.65 42.95 3.58
521 747 3.678056 TGTCACATCTACCCTTGTGTC 57.322 47.619 3.30 0.00 42.95 3.67
522 748 4.777896 ACTATGTCACATCTACCCTTGTGT 59.222 41.667 0.00 0.00 42.95 3.72
523 749 5.344743 ACTATGTCACATCTACCCTTGTG 57.655 43.478 0.00 0.00 43.61 3.33
524 750 7.125811 ACATAACTATGTCACATCTACCCTTGT 59.874 37.037 0.00 0.00 42.96 3.16
525 751 7.500992 ACATAACTATGTCACATCTACCCTTG 58.499 38.462 0.00 0.00 42.96 3.61
526 752 7.676683 ACATAACTATGTCACATCTACCCTT 57.323 36.000 0.00 0.00 42.96 3.95
527 753 8.807118 CATACATAACTATGTCACATCTACCCT 58.193 37.037 5.64 0.00 45.11 4.34
528 754 8.585881 ACATACATAACTATGTCACATCTACCC 58.414 37.037 5.64 0.00 45.11 3.69
529 755 9.411801 CACATACATAACTATGTCACATCTACC 57.588 37.037 5.64 0.00 45.11 3.18
530 756 9.967346 ACACATACATAACTATGTCACATCTAC 57.033 33.333 5.64 0.00 45.11 2.59
532 758 8.144478 GGACACATACATAACTATGTCACATCT 58.856 37.037 5.64 0.00 45.11 2.90
533 759 8.144478 AGGACACATACATAACTATGTCACATC 58.856 37.037 5.64 0.69 45.11 3.06
534 760 8.023021 AGGACACATACATAACTATGTCACAT 57.977 34.615 5.64 0.00 45.11 3.21
535 761 7.418337 AGGACACATACATAACTATGTCACA 57.582 36.000 5.64 0.00 45.11 3.58
536 762 8.847196 TCTAGGACACATACATAACTATGTCAC 58.153 37.037 5.64 0.00 45.11 3.67
537 763 8.847196 GTCTAGGACACATACATAACTATGTCA 58.153 37.037 5.64 0.00 38.84 3.58
538 764 8.016229 CGTCTAGGACACATACATAACTATGTC 58.984 40.741 5.64 0.00 38.84 3.06
539 765 7.040617 CCGTCTAGGACACATACATAACTATGT 60.041 40.741 7.48 7.48 45.33 2.29
540 766 7.174426 TCCGTCTAGGACACATACATAACTATG 59.826 40.741 0.00 0.00 45.98 2.23
541 767 7.229308 TCCGTCTAGGACACATACATAACTAT 58.771 38.462 0.00 0.00 45.98 2.12
542 768 6.594744 TCCGTCTAGGACACATACATAACTA 58.405 40.000 0.00 0.00 45.98 2.24
543 769 5.443283 TCCGTCTAGGACACATACATAACT 58.557 41.667 0.00 0.00 45.98 2.24
544 770 5.762825 TCCGTCTAGGACACATACATAAC 57.237 43.478 0.00 0.00 45.98 1.89
557 783 1.481363 GAAAAGGAGGGTCCGTCTAGG 59.519 57.143 11.28 0.00 42.75 3.02
558 784 2.458620 AGAAAAGGAGGGTCCGTCTAG 58.541 52.381 11.28 0.00 42.75 2.43
559 785 2.617840 AGAAAAGGAGGGTCCGTCTA 57.382 50.000 11.28 0.00 42.75 2.59
560 786 2.617840 TAGAAAAGGAGGGTCCGTCT 57.382 50.000 11.28 1.23 42.75 4.18
561 787 3.908643 AATAGAAAAGGAGGGTCCGTC 57.091 47.619 2.75 2.75 42.75 4.79
562 788 5.970501 AATAATAGAAAAGGAGGGTCCGT 57.029 39.130 0.00 0.00 42.75 4.69
563 789 7.640597 AAAAATAATAGAAAAGGAGGGTCCG 57.359 36.000 0.00 0.00 42.75 4.79
737 968 2.178235 GTTTCGCTGGGCCCGATAC 61.178 63.158 19.37 12.17 34.35 2.24
845 1078 3.658422 GGGGAGGTGGTGGGGAAC 61.658 72.222 0.00 0.00 0.00 3.62
877 1110 4.518211 GGAAACTGCTGATATGAGATTGGG 59.482 45.833 0.00 0.00 0.00 4.12
880 1114 6.656902 TCAAGGAAACTGCTGATATGAGATT 58.343 36.000 0.00 0.00 42.68 2.40
943 1177 1.231221 CGGACGGTGTTTGGATGAAA 58.769 50.000 0.00 0.00 0.00 2.69
1054 1293 0.324738 AGGGCTCGGATGTTGAGAGA 60.325 55.000 0.00 0.00 35.43 3.10
1082 1321 6.663523 ACCACGAAGAAATTAATCCCTGAAAT 59.336 34.615 0.00 0.00 0.00 2.17
1085 1324 5.174037 ACCACGAAGAAATTAATCCCTGA 57.826 39.130 0.00 0.00 0.00 3.86
1087 1326 6.943718 TGTAAACCACGAAGAAATTAATCCCT 59.056 34.615 0.00 0.00 0.00 4.20
1188 1433 2.511600 GTGGTCATCTTCCCGCGG 60.512 66.667 21.04 21.04 0.00 6.46
1197 1442 2.125106 GTGGCGGAGGTGGTCATC 60.125 66.667 0.00 0.00 0.00 2.92
1279 1524 6.612247 ACACACAAACACAATCGAATCTAA 57.388 33.333 0.00 0.00 0.00 2.10
1281 1526 6.204688 ACATACACACAAACACAATCGAATCT 59.795 34.615 0.00 0.00 0.00 2.40
1282 1527 6.370593 ACATACACACAAACACAATCGAATC 58.629 36.000 0.00 0.00 0.00 2.52
1284 1529 5.743026 ACATACACACAAACACAATCGAA 57.257 34.783 0.00 0.00 0.00 3.71
1285 1530 6.846325 TTACATACACACAAACACAATCGA 57.154 33.333 0.00 0.00 0.00 3.59
1286 1531 6.740905 GGATTACATACACACAAACACAATCG 59.259 38.462 0.00 0.00 0.00 3.34
1287 1532 7.750458 CAGGATTACATACACACAAACACAATC 59.250 37.037 0.00 0.00 0.00 2.67
1288 1533 7.230510 ACAGGATTACATACACACAAACACAAT 59.769 33.333 0.00 0.00 0.00 2.71
1289 1534 6.544197 ACAGGATTACATACACACAAACACAA 59.456 34.615 0.00 0.00 0.00 3.33
1291 1536 6.554334 ACAGGATTACATACACACAAACAC 57.446 37.500 0.00 0.00 0.00 3.32
1292 1537 6.073494 CGAACAGGATTACATACACACAAACA 60.073 38.462 0.00 0.00 0.00 2.83
1293 1538 6.073440 ACGAACAGGATTACATACACACAAAC 60.073 38.462 0.00 0.00 0.00 2.93
1294 1539 5.992829 ACGAACAGGATTACATACACACAAA 59.007 36.000 0.00 0.00 0.00 2.83
1295 1540 5.543714 ACGAACAGGATTACATACACACAA 58.456 37.500 0.00 0.00 0.00 3.33
1339 1584 0.537143 TCGTGGCCTGAAAACAGCAT 60.537 50.000 3.32 0.00 0.00 3.79
1493 1738 1.103398 GTGACACCTTTGCAGCAGGT 61.103 55.000 12.84 12.84 46.35 4.00
1499 1744 2.904866 GGCGGTGACACCTTTGCA 60.905 61.111 22.14 0.00 35.66 4.08
1523 1768 1.683385 GAAACCTTTGCAGGCTTCTGT 59.317 47.619 1.82 0.00 45.56 3.41
1535 1780 3.292159 GGTGGCGGCGAAACCTTT 61.292 61.111 20.18 0.00 35.61 3.11
1622 1867 2.606551 GCAAGCTTTCTTCAGTGGCTTC 60.607 50.000 0.00 0.00 40.60 3.86
1754 1999 0.318441 CAGCAGAGTCTTCGGTGGAA 59.682 55.000 0.00 0.00 0.00 3.53
1778 2023 0.973496 TGACAGGCACCATAGGCGTA 60.973 55.000 0.00 0.00 39.37 4.42
1831 2076 1.469335 AAAGAACGGGGTCTCTGCGA 61.469 55.000 0.00 0.00 0.00 5.10
1850 2095 0.391528 TGCTGCAATTCTGAGCGCTA 60.392 50.000 11.50 0.00 35.36 4.26
2021 2266 7.063456 ACGCAGAAAATATATCAAATCGTTCG 58.937 34.615 0.00 0.00 0.00 3.95
2140 2385 5.104900 AGCCTACTTGGATTGGTACTAAGTG 60.105 44.000 0.00 0.00 38.92 3.16
2204 2449 0.385029 TGTGAAATGGCTGCACACAC 59.615 50.000 0.50 5.03 37.60 3.82
2209 2466 1.466856 GATCCTGTGAAATGGCTGCA 58.533 50.000 0.50 0.00 0.00 4.41
2273 2530 6.395780 TCATGGAATAAAGGGGTCAAAGTA 57.604 37.500 0.00 0.00 0.00 2.24
2323 2580 3.374058 AGTGTCAAACTTCAGTTGGTTCG 59.626 43.478 0.00 0.00 38.44 3.95
2453 2710 1.203050 ACTTCCCCCACATCAACAAGG 60.203 52.381 0.00 0.00 0.00 3.61
2513 2770 3.769739 TCCAGTTTCTGCTCAAAGCTA 57.230 42.857 0.11 0.00 42.97 3.32
2660 2917 1.227089 CCTGTCGATGGAAGAGCGG 60.227 63.158 1.68 0.00 0.00 5.52
2825 3085 1.565759 TGTAATGAGCCCCTGCAGAAT 59.434 47.619 17.39 0.00 41.13 2.40
2885 3145 2.046314 GACAGGCCGCCTTTAGCA 60.046 61.111 9.99 0.00 44.04 3.49
3066 3329 9.280174 GAGCTCTAGTCAGAACATAACTAGTAT 57.720 37.037 6.43 0.00 41.97 2.12
3067 3330 7.716123 GGAGCTCTAGTCAGAACATAACTAGTA 59.284 40.741 14.64 0.00 41.97 1.82
3068 3331 6.544564 GGAGCTCTAGTCAGAACATAACTAGT 59.455 42.308 14.64 0.00 41.97 2.57
3069 3332 6.544197 TGGAGCTCTAGTCAGAACATAACTAG 59.456 42.308 14.64 3.01 42.43 2.57
3148 3411 3.935203 AGTTCATAAACGCACCTCATCAG 59.065 43.478 0.00 0.00 40.48 2.90
3220 3483 5.401531 TCAAATGTAAGGACGAAGCTACT 57.598 39.130 0.00 0.00 0.00 2.57
3221 3484 5.581085 ACATCAAATGTAAGGACGAAGCTAC 59.419 40.000 0.00 0.00 42.78 3.58
3259 3655 0.249489 ACTGACGTCTCCACACTTGC 60.249 55.000 17.92 0.00 0.00 4.01
3279 3678 7.362401 GGGAGTACAAGATTTTCTGTCGTACTA 60.362 40.741 11.53 0.00 38.47 1.82
3280 3679 6.388278 GGAGTACAAGATTTTCTGTCGTACT 58.612 40.000 11.44 11.44 40.42 2.73
3281 3680 5.575995 GGGAGTACAAGATTTTCTGTCGTAC 59.424 44.000 0.00 0.00 0.00 3.67
3321 3720 4.092675 GCAGCACTCAAGAGTCAAGATAAC 59.907 45.833 0.00 0.00 40.20 1.89
3324 3723 2.614987 GGCAGCACTCAAGAGTCAAGAT 60.615 50.000 0.00 0.00 40.20 2.40
3452 3926 8.958060 AATACATGGAGTATACTAGTGTGGAT 57.042 34.615 19.61 11.04 42.56 3.41
3454 3928 7.040617 ACGAATACATGGAGTATACTAGTGTGG 60.041 40.741 19.61 12.20 42.56 4.17
3455 3929 7.872881 ACGAATACATGGAGTATACTAGTGTG 58.127 38.462 19.61 13.12 42.56 3.82
3577 4100 8.157476 TCTTTTCCAAAGATGCTAGAAACTAGT 58.843 33.333 0.00 0.00 0.00 2.57
3616 4139 6.346096 TGTAAATATCTCCGTCCTTTGGAAG 58.654 40.000 0.00 0.00 34.44 3.46
3709 4239 3.612423 TCACGATTGCATAAGAGAACACG 59.388 43.478 0.00 0.00 0.00 4.49
3836 4366 4.872691 CAGCTACTGGGTCTGTAAAGAATG 59.127 45.833 0.00 0.00 0.00 2.67
3919 4449 7.649705 CACACGCATAATCAAACTAGACTAGAT 59.350 37.037 16.55 0.98 0.00 1.98
3952 4482 3.363178 GTTGCAAACTAACTCACAGCAC 58.637 45.455 0.00 0.00 45.32 4.40
4037 4567 0.605319 CGCTAAACCTGTCAAGCCCA 60.605 55.000 0.00 0.00 0.00 5.36
4105 4635 7.656707 AATCCAAAAGGTTTGATTGATTTCG 57.343 32.000 2.30 0.00 30.11 3.46
4114 4644 7.123355 ACAATCTGAAATCCAAAAGGTTTGA 57.877 32.000 2.30 0.00 0.00 2.69
4167 4697 8.307582 AGCATAGTACTAGTATTCACAAGGTT 57.692 34.615 5.75 0.00 0.00 3.50
4302 4870 8.016301 ACCAGTATTAAAACTAGCTAGTACCC 57.984 38.462 26.29 10.35 34.99 3.69
4406 5077 1.006102 AGACCTTCCACGTCGCAAG 60.006 57.895 0.00 0.00 35.33 4.01
4465 5136 8.231837 TCTTCCGTCCAAATATTTTTAAACTCG 58.768 33.333 0.00 0.00 0.00 4.18
4470 5141 7.455641 TGCTCTTCCGTCCAAATATTTTTAA 57.544 32.000 0.00 0.00 0.00 1.52
4471 5142 6.404293 GCTGCTCTTCCGTCCAAATATTTTTA 60.404 38.462 0.00 0.00 0.00 1.52
4545 5216 2.109181 GGCGAGGACCATGTAGCC 59.891 66.667 0.00 0.00 37.61 3.93
4597 5268 0.039035 ACGGAGCCAGAGAGAGTCTT 59.961 55.000 0.00 0.00 30.64 3.01
4598 5269 0.679640 CACGGAGCCAGAGAGAGTCT 60.680 60.000 0.00 0.00 35.00 3.24
4628 5335 0.531532 CTTAGATCAGCTGGGCCACG 60.532 60.000 15.13 0.00 0.00 4.94
4644 5351 1.855213 CGGTGTCGACGGTGGACTTA 61.855 60.000 21.28 2.47 39.00 2.24
4654 5361 2.505118 GCAGCTCTCGGTGTCGAC 60.505 66.667 9.11 9.11 40.88 4.20
4673 5380 4.547671 CCTAGAATCTAGGGTCTGACCAA 58.452 47.826 25.07 14.04 41.02 3.67
4674 5381 3.691603 GCCTAGAATCTAGGGTCTGACCA 60.692 52.174 31.10 8.09 41.02 4.02
4687 5394 4.490743 GCCGATTCTTCTAGCCTAGAATC 58.509 47.826 14.33 20.65 46.83 2.52
4688 5395 3.057174 CGCCGATTCTTCTAGCCTAGAAT 60.057 47.826 14.33 1.30 43.32 2.40
4689 5396 2.293677 CGCCGATTCTTCTAGCCTAGAA 59.706 50.000 13.35 13.35 42.19 2.10
4690 5397 1.880675 CGCCGATTCTTCTAGCCTAGA 59.119 52.381 0.00 0.00 0.00 2.43
4691 5398 1.068194 CCGCCGATTCTTCTAGCCTAG 60.068 57.143 0.00 0.00 0.00 3.02
4692 5399 0.959553 CCGCCGATTCTTCTAGCCTA 59.040 55.000 0.00 0.00 0.00 3.93
4693 5400 0.755698 TCCGCCGATTCTTCTAGCCT 60.756 55.000 0.00 0.00 0.00 4.58
4694 5401 0.597898 GTCCGCCGATTCTTCTAGCC 60.598 60.000 0.00 0.00 0.00 3.93
4695 5402 0.935366 CGTCCGCCGATTCTTCTAGC 60.935 60.000 0.00 0.00 39.56 3.42
4696 5403 0.935366 GCGTCCGCCGATTCTTCTAG 60.935 60.000 0.00 0.00 39.56 2.43
4755 5462 1.656652 ACTCAATGCATGCTACGTCC 58.343 50.000 20.33 0.00 0.00 4.79
4780 5487 1.269444 GATAGATGCGGCGTCGTCAC 61.269 60.000 12.58 2.25 38.89 3.67
4785 5492 2.649257 GCGTGATAGATGCGGCGTC 61.649 63.158 14.27 14.27 0.00 5.19
4817 5524 2.886124 GCCAGCGACGGTTCTAGC 60.886 66.667 0.00 0.00 0.00 3.42
4818 5525 1.141881 ATGCCAGCGACGGTTCTAG 59.858 57.895 0.00 0.00 0.00 2.43
4819 5526 1.153647 CATGCCAGCGACGGTTCTA 60.154 57.895 0.00 0.00 0.00 2.10
4820 5527 2.434884 CATGCCAGCGACGGTTCT 60.435 61.111 0.00 0.00 0.00 3.01
4821 5528 4.166011 GCATGCCAGCGACGGTTC 62.166 66.667 6.36 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.