Multiple sequence alignment - TraesCS3D01G291700

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G291700 chr3D 100.000 5607 0 0 1 5607 401869533 401875139 0.000000e+00 10355.0
1 TraesCS3D01G291700 chr3D 80.747 509 75 13 1 494 382980371 382980871 5.300000e-100 375.0
2 TraesCS3D01G291700 chr3B 95.676 2035 71 12 573 2599 527293097 527295122 0.000000e+00 3254.0
3 TraesCS3D01G291700 chr3B 95.847 1517 52 5 2652 4157 527295124 527296640 0.000000e+00 2442.0
4 TraesCS3D01G291700 chr3B 92.319 664 39 4 4953 5607 527297344 527298004 0.000000e+00 933.0
5 TraesCS3D01G291700 chr3B 91.948 534 28 10 4357 4888 527296804 527297324 0.000000e+00 734.0
6 TraesCS3D01G291700 chr3B 92.632 95 1 1 4264 4352 527296634 527296728 1.270000e-26 132.0
7 TraesCS3D01G291700 chr3A 93.831 2075 84 20 573 2619 522172607 522174665 0.000000e+00 3083.0
8 TraesCS3D01G291700 chr3A 89.576 1746 128 29 2616 4347 522174789 522176494 0.000000e+00 2167.0
9 TraesCS3D01G291700 chr3A 93.412 1275 43 19 4353 5607 522176780 522178033 0.000000e+00 1851.0
10 TraesCS3D01G291700 chr4A 85.889 900 72 30 4724 5603 225583502 225582638 0.000000e+00 907.0
11 TraesCS3D01G291700 chr4A 84.449 926 69 28 4721 5603 195312098 195312991 0.000000e+00 843.0
12 TraesCS3D01G291700 chr4A 80.396 556 81 14 2 541 515560298 515560841 1.130000e-106 398.0
13 TraesCS3D01G291700 chr5D 85.574 915 67 22 4721 5603 437570663 437571544 0.000000e+00 898.0
14 TraesCS3D01G291700 chr5D 85.520 221 19 6 3 212 497834881 497834663 9.460000e-53 219.0
15 TraesCS3D01G291700 chr5B 84.233 945 74 34 4638 5553 261373911 261374809 0.000000e+00 850.0
16 TraesCS3D01G291700 chr5B 97.500 40 0 1 5565 5603 261374804 261374843 3.630000e-07 67.6
17 TraesCS3D01G291700 chr1D 80.810 568 91 9 1 552 365301011 365301576 4.010000e-116 429.0
18 TraesCS3D01G291700 chr1D 80.819 537 74 16 2 522 361982253 361982776 1.460000e-105 394.0
19 TraesCS3D01G291700 chr6A 80.470 553 85 15 1 536 65791893 65792439 8.750000e-108 401.0
20 TraesCS3D01G291700 chr4D 80.403 546 85 12 1 528 499735635 499735094 4.070000e-106 396.0
21 TraesCS3D01G291700 chr1B 81.837 479 73 5 4 469 595471401 595470924 1.890000e-104 390.0
22 TraesCS3D01G291700 chr2D 81.796 412 59 10 30 427 6970452 6970861 1.160000e-86 331.0
23 TraesCS3D01G291700 chr7A 81.176 425 64 7 36 446 579017905 579018327 1.510000e-85 327.0
24 TraesCS3D01G291700 chr7A 81.579 380 48 16 1 363 127373215 127372841 1.530000e-75 294.0
25 TraesCS3D01G291700 chr1A 78.148 540 87 12 1 529 144774624 144775143 1.170000e-81 315.0
26 TraesCS3D01G291700 chr2A 80.383 418 66 15 86 495 44075147 44074738 2.540000e-78 303.0
27 TraesCS3D01G291700 chr5A 79.075 411 70 11 2 400 649252768 649253174 9.260000e-68 268.0
28 TraesCS3D01G291700 chr5A 83.140 172 27 2 3 173 621865069 621864899 7.520000e-34 156.0
29 TraesCS3D01G291700 chr4B 79.302 401 59 12 1 388 561008261 561008650 5.570000e-65 259.0
30 TraesCS3D01G291700 chr6D 73.857 547 113 15 9 534 438820475 438821012 2.060000e-44 191.0


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 TraesCS3D01G291700 chr3D 401869533 401875139 5606 False 10355.0 10355 100.0000 1 5607 1 chr3D.!!$F2 5606
1 TraesCS3D01G291700 chr3D 382980371 382980871 500 False 375.0 375 80.7470 1 494 1 chr3D.!!$F1 493
2 TraesCS3D01G291700 chr3B 527293097 527298004 4907 False 1499.0 3254 93.6844 573 5607 5 chr3B.!!$F1 5034
3 TraesCS3D01G291700 chr3A 522172607 522178033 5426 False 2367.0 3083 92.2730 573 5607 3 chr3A.!!$F1 5034
4 TraesCS3D01G291700 chr4A 225582638 225583502 864 True 907.0 907 85.8890 4724 5603 1 chr4A.!!$R1 879
5 TraesCS3D01G291700 chr4A 195312098 195312991 893 False 843.0 843 84.4490 4721 5603 1 chr4A.!!$F1 882
6 TraesCS3D01G291700 chr4A 515560298 515560841 543 False 398.0 398 80.3960 2 541 1 chr4A.!!$F2 539
7 TraesCS3D01G291700 chr5D 437570663 437571544 881 False 898.0 898 85.5740 4721 5603 1 chr5D.!!$F1 882
8 TraesCS3D01G291700 chr5B 261373911 261374843 932 False 458.8 850 90.8665 4638 5603 2 chr5B.!!$F1 965
9 TraesCS3D01G291700 chr1D 365301011 365301576 565 False 429.0 429 80.8100 1 552 1 chr1D.!!$F2 551
10 TraesCS3D01G291700 chr1D 361982253 361982776 523 False 394.0 394 80.8190 2 522 1 chr1D.!!$F1 520
11 TraesCS3D01G291700 chr6A 65791893 65792439 546 False 401.0 401 80.4700 1 536 1 chr6A.!!$F1 535
12 TraesCS3D01G291700 chr4D 499735094 499735635 541 True 396.0 396 80.4030 1 528 1 chr4D.!!$R1 527
13 TraesCS3D01G291700 chr1A 144774624 144775143 519 False 315.0 315 78.1480 1 529 1 chr1A.!!$F1 528

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
556 579 0.036388 ACGGGTGCTGAAGGTATGTG 60.036 55.000 0.00 0.00 0.00 3.21 F
1325 1358 0.394216 TTTCTGATGACATGCGGGGG 60.394 55.000 0.00 0.00 0.00 5.40 F
1428 1462 0.950555 TTGCGGTGCTTGCTACTGAG 60.951 55.000 7.73 0.00 0.00 3.35 F
2181 2236 1.035139 AGTTTGGTTGCCTGCTTGAG 58.965 50.000 0.00 0.00 0.00 3.02 F
3475 3668 1.064952 GTTGCAAAACTGCAGTACGGT 59.935 47.619 22.01 0.19 46.21 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 2554 1.066002 CTGCTGAATACGCAAATGGGG 59.934 52.381 2.43 0.0 36.88 4.96 R
2979 3164 1.141657 AGGTCAAGAGACTTTGCTGCA 59.858 47.619 0.00 0.0 44.36 4.41 R
2980 3165 1.889545 AGGTCAAGAGACTTTGCTGC 58.110 50.000 0.00 0.0 44.36 5.25 R
3535 3728 0.603707 ACATGGAGTTGCACGACTGG 60.604 55.000 0.00 0.0 0.00 4.00 R
5174 5811 1.538047 TTGGTCTGAATTGGAGCTGC 58.462 50.000 0.00 0.0 33.06 5.25 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
33 34 0.389426 GTGAATACGGCCAGTCACGT 60.389 55.000 7.77 0.00 46.17 4.49
154 156 3.687102 CACCTGTCGGGCGTGGTA 61.687 66.667 0.00 0.00 39.10 3.25
158 160 2.363276 TGTCGGGCGTGGTATCCT 60.363 61.111 0.00 0.00 0.00 3.24
159 161 1.956629 CTGTCGGGCGTGGTATCCTT 61.957 60.000 0.00 0.00 0.00 3.36
184 198 2.875094 AGGTAGTCGAGTGTACCTGT 57.125 50.000 16.68 0.00 46.10 4.00
297 312 2.322161 CCGAAGACGTACAACAACGAT 58.678 47.619 3.10 0.00 45.68 3.73
307 322 1.375523 AACAACGATGGCGGAGGTC 60.376 57.895 0.00 0.00 43.17 3.85
332 348 2.554344 GGTGTGGATGCAAAGTAAGGGA 60.554 50.000 0.00 0.00 0.00 4.20
335 351 3.073798 TGTGGATGCAAAGTAAGGGAAGA 59.926 43.478 0.00 0.00 0.00 2.87
349 365 1.671742 GAAGAAGGGTGCGGAGTGA 59.328 57.895 0.00 0.00 0.00 3.41
413 432 1.672145 GGAGTCCTACGTTTCAGGTGC 60.672 57.143 0.41 0.00 34.56 5.01
417 436 1.290955 CTACGTTTCAGGTGCCCGA 59.709 57.895 0.00 0.00 0.00 5.14
420 439 2.613506 CGTTTCAGGTGCCCGAACC 61.614 63.158 0.00 0.00 40.85 3.62
438 458 2.938798 TCCGCAAACCTCCCCCAT 60.939 61.111 0.00 0.00 0.00 4.00
446 467 2.299867 CAAACCTCCCCCATTTTGTCTG 59.700 50.000 0.00 0.00 0.00 3.51
486 508 0.179134 GTTCAGATCGTCCCGTGGAG 60.179 60.000 0.00 0.00 29.39 3.86
503 525 2.654404 GCGATACAGACCCGCGTC 60.654 66.667 4.92 0.00 39.54 5.19
547 570 3.311110 GGTCCAGACGGGTGCTGA 61.311 66.667 0.00 0.00 38.11 4.26
552 575 1.541310 CCAGACGGGTGCTGAAGGTA 61.541 60.000 0.00 0.00 35.39 3.08
553 576 0.537188 CAGACGGGTGCTGAAGGTAT 59.463 55.000 0.00 0.00 35.39 2.73
554 577 0.537188 AGACGGGTGCTGAAGGTATG 59.463 55.000 0.00 0.00 0.00 2.39
555 578 0.249398 GACGGGTGCTGAAGGTATGT 59.751 55.000 0.00 0.00 0.00 2.29
556 579 0.036388 ACGGGTGCTGAAGGTATGTG 60.036 55.000 0.00 0.00 0.00 3.21
557 580 0.744414 CGGGTGCTGAAGGTATGTGG 60.744 60.000 0.00 0.00 0.00 4.17
558 581 0.618458 GGGTGCTGAAGGTATGTGGA 59.382 55.000 0.00 0.00 0.00 4.02
559 582 1.212935 GGGTGCTGAAGGTATGTGGAT 59.787 52.381 0.00 0.00 0.00 3.41
560 583 2.565841 GGTGCTGAAGGTATGTGGATC 58.434 52.381 0.00 0.00 0.00 3.36
561 584 2.171448 GGTGCTGAAGGTATGTGGATCT 59.829 50.000 0.00 0.00 0.00 2.75
562 585 3.201290 GTGCTGAAGGTATGTGGATCTG 58.799 50.000 0.00 0.00 0.00 2.90
563 586 2.216898 GCTGAAGGTATGTGGATCTGC 58.783 52.381 0.00 0.00 0.00 4.26
564 587 2.843701 CTGAAGGTATGTGGATCTGCC 58.156 52.381 0.00 0.00 37.10 4.85
565 588 2.171237 CTGAAGGTATGTGGATCTGCCA 59.829 50.000 0.00 0.00 46.96 4.92
582 605 1.195448 GCCATGAGCATATGTGTACGC 59.805 52.381 4.29 0.00 42.97 4.42
583 606 1.456923 CCATGAGCATATGTGTACGCG 59.543 52.381 3.53 3.53 0.00 6.01
610 633 6.691388 GCTGAATTTATGGAAAATCACCGTAC 59.309 38.462 0.00 0.00 32.31 3.67
666 689 0.810426 CGGACGGACGAGATCTCTCA 60.810 60.000 20.26 0.00 43.00 3.27
853 878 4.918583 GCTCGATTATTCTTAACCCTCTCG 59.081 45.833 0.00 0.00 0.00 4.04
1167 1196 4.918201 CCCGATCTGAAGCCCGGC 62.918 72.222 0.00 0.00 40.56 6.13
1213 1242 0.978146 CTCCATCAACCCCCTCGACT 60.978 60.000 0.00 0.00 0.00 4.18
1246 1276 3.693411 CCCCCATTTTGGACACCG 58.307 61.111 0.00 0.00 40.96 4.94
1247 1277 2.645192 CCCCCATTTTGGACACCGC 61.645 63.158 0.00 0.00 40.96 5.68
1248 1278 2.645192 CCCCATTTTGGACACCGCC 61.645 63.158 0.00 0.00 40.96 6.13
1249 1279 2.645192 CCCATTTTGGACACCGCCC 61.645 63.158 0.00 0.00 40.96 6.13
1250 1280 1.905843 CCATTTTGGACACCGCCCA 60.906 57.895 0.00 0.00 40.96 5.36
1325 1358 0.394216 TTTCTGATGACATGCGGGGG 60.394 55.000 0.00 0.00 0.00 5.40
1414 1448 2.668279 GCCACTCACTAATTTGTTGCGG 60.668 50.000 0.00 0.00 0.00 5.69
1428 1462 0.950555 TTGCGGTGCTTGCTACTGAG 60.951 55.000 7.73 0.00 0.00 3.35
1538 1572 9.889128 TGATGTGTGTTATCAGAATATGAGAAA 57.111 29.630 0.00 0.00 40.66 2.52
1615 1649 7.448777 TGGTGCTAATTGTTGGAGTGTTTATAA 59.551 33.333 0.00 0.00 0.00 0.98
1883 1917 3.291584 CTCATGTGGTAGGAGCTCACTA 58.708 50.000 17.19 11.58 29.51 2.74
1895 1929 4.595350 AGGAGCTCACTAAAATCCTATCCC 59.405 45.833 17.19 0.00 38.62 3.85
1953 1987 4.825085 GGATTACTTTCAGTTTGTCCACCA 59.175 41.667 0.00 0.00 0.00 4.17
2181 2236 1.035139 AGTTTGGTTGCCTGCTTGAG 58.965 50.000 0.00 0.00 0.00 3.02
2247 2302 2.054453 GGAGGCCAGTGCAATTCCC 61.054 63.158 5.01 0.00 40.13 3.97
2437 2492 7.789202 ACTGCTATGTTCATGATCTAGGTAT 57.211 36.000 0.00 0.00 0.00 2.73
2498 2554 2.162681 AGCAGTTATGTTTGTGCTCCC 58.837 47.619 0.00 0.00 42.67 4.30
2551 2607 6.002062 AGCATGCTACTGTCAAAAGTTAAC 57.998 37.500 21.21 0.00 0.00 2.01
2600 2657 1.519408 TTTTGCGCTACAGTTCCTCC 58.481 50.000 9.73 0.00 0.00 4.30
2602 2659 2.202756 GCGCTACAGTTCCTCCCG 60.203 66.667 0.00 0.00 0.00 5.14
2679 2863 6.037062 CCCTTTTGATTGTTCTGAAAACCAAC 59.963 38.462 0.00 0.00 0.00 3.77
2737 2922 8.539674 GCCAGCATATTAAAGTTTATTTTTCCG 58.460 33.333 0.00 0.00 0.00 4.30
2945 3130 3.262405 ACGCCACTGAGGTAAAAATCCTA 59.738 43.478 0.00 0.00 40.61 2.94
2946 3131 4.258543 CGCCACTGAGGTAAAAATCCTAA 58.741 43.478 0.00 0.00 40.61 2.69
2965 3150 7.125792 TCCTAAAGAAGTCAGAACTCTTGTT 57.874 36.000 0.00 0.00 39.42 2.83
2970 3155 7.541122 AAGAAGTCAGAACTCTTGTTGTTAC 57.459 36.000 0.00 0.00 36.39 2.50
2976 3161 6.879458 GTCAGAACTCTTGTTGTTACCCATAT 59.121 38.462 0.00 0.00 36.39 1.78
2977 3162 6.878923 TCAGAACTCTTGTTGTTACCCATATG 59.121 38.462 0.00 0.00 36.39 1.78
2978 3163 6.878923 CAGAACTCTTGTTGTTACCCATATGA 59.121 38.462 3.65 0.00 36.39 2.15
2979 3164 7.554118 CAGAACTCTTGTTGTTACCCATATGAT 59.446 37.037 3.65 0.00 36.39 2.45
2980 3165 7.554118 AGAACTCTTGTTGTTACCCATATGATG 59.446 37.037 3.65 0.00 36.39 3.07
2981 3166 5.590259 ACTCTTGTTGTTACCCATATGATGC 59.410 40.000 3.65 0.00 0.00 3.91
2982 3167 5.504853 TCTTGTTGTTACCCATATGATGCA 58.495 37.500 3.65 0.00 0.00 3.96
2983 3168 5.589855 TCTTGTTGTTACCCATATGATGCAG 59.410 40.000 3.65 0.00 0.00 4.41
2984 3169 3.631686 TGTTGTTACCCATATGATGCAGC 59.368 43.478 3.65 0.00 0.00 5.25
3053 3245 3.689649 GTCATGTATGTCCCTGGTTTGTC 59.310 47.826 0.00 0.00 0.00 3.18
3227 3419 7.658575 GCTGGTAAATTCATGCATAAATGGAAT 59.341 33.333 0.00 0.71 0.00 3.01
3261 3453 6.833933 ACCTAGAATCACCACTTTTTCAACTT 59.166 34.615 0.00 0.00 0.00 2.66
3314 3506 4.437239 ACTGCTAGCTGTTGTGTATCATC 58.563 43.478 20.37 0.00 0.00 2.92
3355 3548 4.521146 GCTGAATCTCCCATTTCTCTTCA 58.479 43.478 0.00 0.00 0.00 3.02
3356 3549 5.131784 GCTGAATCTCCCATTTCTCTTCAT 58.868 41.667 0.00 0.00 0.00 2.57
3409 3602 2.261729 TGGCAGGATGTGGTTAGTACA 58.738 47.619 0.00 0.00 39.31 2.90
3410 3603 2.027561 TGGCAGGATGTGGTTAGTACAC 60.028 50.000 0.00 0.00 39.31 2.90
3439 3632 8.417884 AGAGTGGCTTTACTTAGATCTATTGTC 58.582 37.037 2.58 0.00 0.00 3.18
3475 3668 1.064952 GTTGCAAAACTGCAGTACGGT 59.935 47.619 22.01 0.19 46.21 4.83
3535 3728 5.574830 CAGTAGTTCTGTATGTGAGCTTGAC 59.425 44.000 0.00 0.00 39.17 3.18
3615 3810 8.442632 TCTGAAATTGCTAGTTATTCTCCATG 57.557 34.615 0.00 0.00 0.00 3.66
3637 3832 5.125356 TGTCTGAGAAAGCATGAAAGAACA 58.875 37.500 0.00 0.00 0.00 3.18
3647 3842 3.671928 GCATGAAAGAACATTGTGTCAGC 59.328 43.478 0.00 0.00 0.00 4.26
3694 3891 4.475051 TGAAATAGTTAAGCCGCTACCA 57.525 40.909 0.00 0.00 0.00 3.25
3736 3933 7.918076 TCTCTTTTCAAGAAATTCCTAGCCTA 58.082 34.615 0.00 0.00 37.02 3.93
3749 3946 6.824958 TTCCTAGCCTAGAATACCATTTGT 57.175 37.500 0.00 0.00 0.00 2.83
3864 4061 6.064717 AGTAGCTGAAACTGAAAGAATTGGT 58.935 36.000 0.00 0.00 37.43 3.67
3921 4118 4.467769 CCCTTCAGGTAATCAATCTGCAT 58.532 43.478 0.00 0.00 0.00 3.96
3929 4126 8.407832 TCAGGTAATCAATCTGCATGTTTAATG 58.592 33.333 0.00 0.00 0.00 1.90
4092 4290 2.609459 GCAGTATCGTTGTTCTCATGGG 59.391 50.000 0.00 0.00 0.00 4.00
4157 4473 7.424227 TCGTATAATTCGTTTTGGAACTTGT 57.576 32.000 0.00 0.00 33.51 3.16
4158 4474 7.863666 TCGTATAATTCGTTTTGGAACTTGTT 58.136 30.769 0.00 0.00 33.51 2.83
4159 4475 8.986847 TCGTATAATTCGTTTTGGAACTTGTTA 58.013 29.630 0.00 0.00 33.51 2.41
4160 4476 9.763465 CGTATAATTCGTTTTGGAACTTGTTAT 57.237 29.630 0.00 0.00 33.51 1.89
4163 4479 7.924103 AATTCGTTTTGGAACTTGTTATGTC 57.076 32.000 0.00 0.00 33.51 3.06
4164 4480 5.427036 TCGTTTTGGAACTTGTTATGTCC 57.573 39.130 0.00 0.00 33.51 4.02
4165 4481 4.024725 TCGTTTTGGAACTTGTTATGTCCG 60.025 41.667 0.00 0.00 33.51 4.79
4166 4482 4.024725 CGTTTTGGAACTTGTTATGTCCGA 60.025 41.667 0.00 0.00 33.51 4.55
4167 4483 5.449304 GTTTTGGAACTTGTTATGTCCGAG 58.551 41.667 0.00 0.00 32.91 4.63
4168 4484 4.345859 TTGGAACTTGTTATGTCCGAGT 57.654 40.909 0.00 0.00 0.00 4.18
4169 4485 3.921677 TGGAACTTGTTATGTCCGAGTC 58.078 45.455 0.00 0.00 0.00 3.36
4170 4486 3.576982 TGGAACTTGTTATGTCCGAGTCT 59.423 43.478 0.00 0.00 0.00 3.24
4171 4487 3.927142 GGAACTTGTTATGTCCGAGTCTG 59.073 47.826 0.00 0.00 0.00 3.51
4172 4488 4.321750 GGAACTTGTTATGTCCGAGTCTGA 60.322 45.833 0.00 0.00 0.00 3.27
4173 4489 4.442375 ACTTGTTATGTCCGAGTCTGAG 57.558 45.455 0.00 0.00 0.00 3.35
4174 4490 3.193691 ACTTGTTATGTCCGAGTCTGAGG 59.806 47.826 0.00 0.00 0.00 3.86
4175 4491 3.081710 TGTTATGTCCGAGTCTGAGGA 57.918 47.619 0.00 0.00 0.00 3.71
4176 4492 3.427573 TGTTATGTCCGAGTCTGAGGAA 58.572 45.455 0.00 0.00 38.41 3.36
4177 4493 3.830178 TGTTATGTCCGAGTCTGAGGAAA 59.170 43.478 0.00 0.00 38.41 3.13
4178 4494 4.174762 GTTATGTCCGAGTCTGAGGAAAC 58.825 47.826 0.00 0.00 38.41 2.78
4179 4495 0.966920 TGTCCGAGTCTGAGGAAACC 59.033 55.000 0.00 0.00 38.41 3.27
4180 4496 1.258676 GTCCGAGTCTGAGGAAACCT 58.741 55.000 0.00 0.00 38.41 3.50
4181 4497 2.224942 TGTCCGAGTCTGAGGAAACCTA 60.225 50.000 0.00 0.00 38.41 3.08
4182 4498 3.025262 GTCCGAGTCTGAGGAAACCTAT 58.975 50.000 0.00 0.00 38.41 2.57
4183 4499 3.447944 GTCCGAGTCTGAGGAAACCTATT 59.552 47.826 0.00 0.00 38.41 1.73
4184 4500 4.081586 GTCCGAGTCTGAGGAAACCTATTT 60.082 45.833 0.00 0.00 38.41 1.40
4185 4501 5.126707 GTCCGAGTCTGAGGAAACCTATTTA 59.873 44.000 0.00 0.00 38.41 1.40
4186 4502 5.718130 TCCGAGTCTGAGGAAACCTATTTAA 59.282 40.000 0.00 0.00 31.76 1.52
4187 4503 6.383147 TCCGAGTCTGAGGAAACCTATTTAAT 59.617 38.462 0.00 0.00 31.76 1.40
4188 4504 6.702282 CCGAGTCTGAGGAAACCTATTTAATC 59.298 42.308 0.00 0.00 31.76 1.75
4189 4505 7.265673 CGAGTCTGAGGAAACCTATTTAATCA 58.734 38.462 0.00 0.00 31.76 2.57
4190 4506 7.222999 CGAGTCTGAGGAAACCTATTTAATCAC 59.777 40.741 0.00 0.00 31.76 3.06
4191 4507 8.152023 AGTCTGAGGAAACCTATTTAATCACT 57.848 34.615 0.00 0.00 31.76 3.41
4192 4508 9.268282 AGTCTGAGGAAACCTATTTAATCACTA 57.732 33.333 0.00 0.00 31.76 2.74
4222 4538 7.821595 TGTGGTAACTGTTTATAATCTGTCG 57.178 36.000 0.00 0.00 37.61 4.35
4223 4539 7.604549 TGTGGTAACTGTTTATAATCTGTCGA 58.395 34.615 0.00 0.00 37.61 4.20
4224 4540 7.758076 TGTGGTAACTGTTTATAATCTGTCGAG 59.242 37.037 0.00 0.00 37.61 4.04
4225 4541 7.222224 GTGGTAACTGTTTATAATCTGTCGAGG 59.778 40.741 0.00 0.00 37.61 4.63
4226 4542 6.200475 GGTAACTGTTTATAATCTGTCGAGGC 59.800 42.308 0.00 0.00 0.00 4.70
4227 4543 4.694339 ACTGTTTATAATCTGTCGAGGCC 58.306 43.478 0.00 0.00 0.00 5.19
4228 4544 4.058817 CTGTTTATAATCTGTCGAGGCCC 58.941 47.826 0.00 0.00 0.00 5.80
4229 4545 3.452990 TGTTTATAATCTGTCGAGGCCCA 59.547 43.478 0.00 0.00 0.00 5.36
4230 4546 3.746045 TTATAATCTGTCGAGGCCCAC 57.254 47.619 0.00 0.00 0.00 4.61
4231 4547 1.496060 ATAATCTGTCGAGGCCCACA 58.504 50.000 0.00 0.00 0.00 4.17
4232 4548 0.535335 TAATCTGTCGAGGCCCACAC 59.465 55.000 0.00 0.00 0.00 3.82
4233 4549 1.194781 AATCTGTCGAGGCCCACACT 61.195 55.000 0.00 0.00 0.00 3.55
4234 4550 1.194781 ATCTGTCGAGGCCCACACTT 61.195 55.000 0.00 0.00 0.00 3.16
4235 4551 1.374758 CTGTCGAGGCCCACACTTC 60.375 63.158 0.00 0.00 0.00 3.01
4236 4552 2.047179 GTCGAGGCCCACACTTCC 60.047 66.667 0.00 0.00 0.00 3.46
4237 4553 2.525629 TCGAGGCCCACACTTCCA 60.526 61.111 0.00 0.00 0.00 3.53
4238 4554 2.046892 CGAGGCCCACACTTCCAG 60.047 66.667 0.00 0.00 0.00 3.86
4239 4555 2.583441 CGAGGCCCACACTTCCAGA 61.583 63.158 0.00 0.00 0.00 3.86
4240 4556 1.003233 GAGGCCCACACTTCCAGAC 60.003 63.158 0.00 0.00 0.00 3.51
4241 4557 1.768684 GAGGCCCACACTTCCAGACA 61.769 60.000 0.00 0.00 0.00 3.41
4242 4558 1.600916 GGCCCACACTTCCAGACAC 60.601 63.158 0.00 0.00 0.00 3.67
4243 4559 1.148273 GCCCACACTTCCAGACACA 59.852 57.895 0.00 0.00 0.00 3.72
4244 4560 0.465460 GCCCACACTTCCAGACACAA 60.465 55.000 0.00 0.00 0.00 3.33
4245 4561 1.597742 CCCACACTTCCAGACACAAG 58.402 55.000 0.00 0.00 0.00 3.16
4246 4562 0.947244 CCACACTTCCAGACACAAGC 59.053 55.000 0.00 0.00 0.00 4.01
4247 4563 1.475751 CCACACTTCCAGACACAAGCT 60.476 52.381 0.00 0.00 0.00 3.74
4248 4564 1.600957 CACACTTCCAGACACAAGCTG 59.399 52.381 0.00 0.00 0.00 4.24
4249 4565 1.486310 ACACTTCCAGACACAAGCTGA 59.514 47.619 0.00 0.00 35.39 4.26
4250 4566 2.105477 ACACTTCCAGACACAAGCTGAT 59.895 45.455 0.00 0.00 35.39 2.90
4251 4567 3.144506 CACTTCCAGACACAAGCTGATT 58.855 45.455 0.00 0.00 35.39 2.57
4252 4568 3.058432 CACTTCCAGACACAAGCTGATTG 60.058 47.826 3.77 3.77 45.01 2.67
4253 4569 1.527034 TCCAGACACAAGCTGATTGC 58.473 50.000 5.42 0.00 43.15 3.56
4264 4580 2.251409 GCTGATTGCTGCCATCTAGA 57.749 50.000 13.95 0.00 38.95 2.43
4265 4581 2.569059 GCTGATTGCTGCCATCTAGAA 58.431 47.619 13.95 0.00 38.95 2.10
4266 4582 2.290093 GCTGATTGCTGCCATCTAGAAC 59.710 50.000 13.95 0.00 38.95 3.01
4267 4583 3.806380 CTGATTGCTGCCATCTAGAACT 58.194 45.455 13.95 0.00 0.00 3.01
4268 4584 4.197750 CTGATTGCTGCCATCTAGAACTT 58.802 43.478 13.95 0.00 0.00 2.66
4269 4585 3.943381 TGATTGCTGCCATCTAGAACTTG 59.057 43.478 13.95 0.00 0.00 3.16
4352 4674 8.911247 ACAAAGTGCTTTCTTTAGTTTAGTTG 57.089 30.769 0.00 0.00 36.12 3.16
4353 4675 8.736244 ACAAAGTGCTTTCTTTAGTTTAGTTGA 58.264 29.630 0.00 0.00 36.12 3.18
4354 4676 9.226345 CAAAGTGCTTTCTTTAGTTTAGTTGAG 57.774 33.333 0.00 0.00 36.12 3.02
4355 4677 8.507524 AAGTGCTTTCTTTAGTTTAGTTGAGT 57.492 30.769 0.00 0.00 0.00 3.41
4905 5524 4.030134 ACGTAGTCTCATCCATCGTTTC 57.970 45.455 0.00 0.00 29.74 2.78
4906 5525 3.036633 CGTAGTCTCATCCATCGTTTCG 58.963 50.000 0.00 0.00 0.00 3.46
4907 5526 3.487042 CGTAGTCTCATCCATCGTTTCGT 60.487 47.826 0.00 0.00 0.00 3.85
4908 5527 2.881074 AGTCTCATCCATCGTTTCGTG 58.119 47.619 0.00 0.00 0.00 4.35
4909 5528 1.927174 GTCTCATCCATCGTTTCGTGG 59.073 52.381 0.00 0.00 36.82 4.94
4910 5529 1.548719 TCTCATCCATCGTTTCGTGGT 59.451 47.619 9.24 0.00 36.84 4.16
4911 5530 2.028476 TCTCATCCATCGTTTCGTGGTT 60.028 45.455 9.24 1.90 36.84 3.67
4912 5531 2.343101 TCATCCATCGTTTCGTGGTTC 58.657 47.619 9.24 0.00 36.84 3.62
4913 5532 2.073056 CATCCATCGTTTCGTGGTTCA 58.927 47.619 9.24 0.00 36.84 3.18
4914 5533 2.465860 TCCATCGTTTCGTGGTTCAT 57.534 45.000 9.24 0.00 36.84 2.57
4915 5534 3.596310 TCCATCGTTTCGTGGTTCATA 57.404 42.857 9.24 0.00 36.84 2.15
4916 5535 3.255725 TCCATCGTTTCGTGGTTCATAC 58.744 45.455 9.24 0.00 36.84 2.39
4917 5536 3.056393 TCCATCGTTTCGTGGTTCATACT 60.056 43.478 9.24 0.00 36.84 2.12
4918 5537 3.306166 CCATCGTTTCGTGGTTCATACTC 59.694 47.826 0.00 0.00 0.00 2.59
4931 5550 4.381079 GGTTCATACTCACTCTTCGCTTCT 60.381 45.833 0.00 0.00 0.00 2.85
4951 5570 7.904461 CGCTTCTTGACAAAATTTTTCAATGTT 59.096 29.630 19.54 0.00 0.00 2.71
5137 5762 6.146760 ACTACCAGGAACATATCATCCTCTT 58.853 40.000 0.00 0.00 44.26 2.85
5174 5811 8.263640 AGAAAAGAATATATCATCCTCCATCGG 58.736 37.037 0.00 0.00 0.00 4.18
5235 5872 0.383002 CACAACACGCGCTACACAAG 60.383 55.000 5.73 0.00 0.00 3.16
5283 5925 2.098117 GGAATCATTCAAGGAACTGCCG 59.902 50.000 0.00 0.00 40.86 5.69
5433 6082 4.083862 GTCACCCGCTCCACCTCC 62.084 72.222 0.00 0.00 0.00 4.30
5472 6121 1.633774 TCTGCTTTTCCCTCTCGAGT 58.366 50.000 13.13 0.00 0.00 4.18
5484 6133 2.763448 CCTCTCGAGTTCCTCCATCTTT 59.237 50.000 13.13 0.00 0.00 2.52
5488 6137 2.236395 TCGAGTTCCTCCATCTTTTCCC 59.764 50.000 0.00 0.00 0.00 3.97
5518 6169 5.759273 TCCTGCCATTTTCAAACATGAAAAG 59.241 36.000 18.22 9.64 46.64 2.27
5539 6191 3.118702 AGGAGTTGATCATCTCTGCACAG 60.119 47.826 25.67 0.00 0.00 3.66
5600 6263 3.243068 ACTGTCAGCGATTTGTTTTGTCC 60.243 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.268896 CGATACGTGACTGGCCGTATT 60.269 52.381 15.07 3.62 46.82 1.89
28 29 2.055838 GAGTTGTTGTGCGATACGTGA 58.944 47.619 0.00 0.00 0.00 4.35
33 34 3.932710 GGAGAATGAGTTGTTGTGCGATA 59.067 43.478 0.00 0.00 0.00 2.92
111 113 7.087409 TCGATCAAATGTCATTGTGCTTATT 57.913 32.000 0.00 0.00 0.00 1.40
118 120 4.761739 AGGTGTTCGATCAAATGTCATTGT 59.238 37.500 0.00 0.00 0.00 2.71
158 160 2.803956 ACACTCGACTACCTCCATGAA 58.196 47.619 0.00 0.00 0.00 2.57
159 161 2.509166 ACACTCGACTACCTCCATGA 57.491 50.000 0.00 0.00 0.00 3.07
184 198 1.373435 CCCTGGAGCCGTTTGTACA 59.627 57.895 0.00 0.00 0.00 2.90
280 295 1.796459 GCCATCGTTGTTGTACGTCTT 59.204 47.619 0.00 0.00 42.01 3.01
307 322 0.606401 ACTTTGCATCCACACCCTCG 60.606 55.000 0.00 0.00 0.00 4.63
332 348 0.472471 TTTCACTCCGCACCCTTCTT 59.528 50.000 0.00 0.00 0.00 2.52
335 351 3.505835 TTTTTCACTCCGCACCCTT 57.494 47.368 0.00 0.00 0.00 3.95
363 381 1.308216 CCCACCCAATCCCTCCTCT 60.308 63.158 0.00 0.00 0.00 3.69
391 410 0.172803 CCTGAAACGTAGGACTCCGG 59.827 60.000 0.00 0.00 37.52 5.14
413 432 3.053896 GGTTTGCGGAGGTTCGGG 61.054 66.667 0.00 0.00 0.00 5.14
417 436 2.434774 GGGAGGTTTGCGGAGGTT 59.565 61.111 0.00 0.00 0.00 3.50
420 439 2.499303 AATGGGGGAGGTTTGCGGAG 62.499 60.000 0.00 0.00 0.00 4.63
421 440 2.087857 AAATGGGGGAGGTTTGCGGA 62.088 55.000 0.00 0.00 0.00 5.54
438 458 4.428209 TCTTTCGCAAATTGCAGACAAAA 58.572 34.783 18.65 8.56 45.36 2.44
458 480 2.186076 GACGATCTGAACGCGATTTCT 58.814 47.619 15.93 0.00 0.00 2.52
486 508 2.654404 GACGCGGGTCTGTATCGC 60.654 66.667 23.96 0.00 45.15 4.58
541 564 3.201290 CAGATCCACATACCTTCAGCAC 58.799 50.000 0.00 0.00 0.00 4.40
545 568 2.195727 TGGCAGATCCACATACCTTCA 58.804 47.619 0.00 0.00 40.72 3.02
562 585 1.195448 GCGTACACATATGCTCATGGC 59.805 52.381 1.58 0.00 39.81 4.40
563 586 1.456923 CGCGTACACATATGCTCATGG 59.543 52.381 1.58 0.00 40.63 3.66
564 587 2.097250 CACGCGTACACATATGCTCATG 60.097 50.000 13.44 0.00 40.63 3.07
565 588 2.127251 CACGCGTACACATATGCTCAT 58.873 47.619 13.44 0.00 40.63 2.90
566 589 1.555477 CACGCGTACACATATGCTCA 58.445 50.000 13.44 0.00 40.63 4.26
567 590 0.229753 GCACGCGTACACATATGCTC 59.770 55.000 13.44 0.00 40.63 4.26
568 591 0.179111 AGCACGCGTACACATATGCT 60.179 50.000 13.44 11.55 40.63 3.79
569 592 0.043053 CAGCACGCGTACACATATGC 60.043 55.000 13.44 8.96 39.58 3.14
570 593 1.555477 TCAGCACGCGTACACATATG 58.445 50.000 13.44 0.00 0.00 1.78
571 594 2.287393 TTCAGCACGCGTACACATAT 57.713 45.000 13.44 0.00 0.00 1.78
572 595 2.287393 ATTCAGCACGCGTACACATA 57.713 45.000 13.44 0.00 0.00 2.29
573 596 1.438651 AATTCAGCACGCGTACACAT 58.561 45.000 13.44 0.00 0.00 3.21
574 597 1.222300 AAATTCAGCACGCGTACACA 58.778 45.000 13.44 0.00 0.00 3.72
575 598 3.342269 CATAAATTCAGCACGCGTACAC 58.658 45.455 13.44 4.42 0.00 2.90
576 599 2.350192 CCATAAATTCAGCACGCGTACA 59.650 45.455 13.44 0.00 0.00 2.90
577 600 2.605818 TCCATAAATTCAGCACGCGTAC 59.394 45.455 13.44 6.32 0.00 3.67
578 601 2.894902 TCCATAAATTCAGCACGCGTA 58.105 42.857 13.44 0.00 0.00 4.42
579 602 1.732941 TCCATAAATTCAGCACGCGT 58.267 45.000 5.58 5.58 0.00 6.01
580 603 2.823196 TTCCATAAATTCAGCACGCG 57.177 45.000 3.53 3.53 0.00 6.01
581 604 5.004726 GTGATTTTCCATAAATTCAGCACGC 59.995 40.000 0.00 0.00 36.28 5.34
582 605 5.516339 GGTGATTTTCCATAAATTCAGCACG 59.484 40.000 14.88 0.00 44.74 5.34
583 606 5.516339 CGGTGATTTTCCATAAATTCAGCAC 59.484 40.000 17.69 0.00 45.17 4.40
610 633 0.656785 GTACGGCTCTAGACTCGTGG 59.343 60.000 19.77 0.00 37.10 4.94
941 970 2.181021 CGTGGCCTAGTGACGGAC 59.819 66.667 3.32 0.00 0.00 4.79
1246 1276 4.366684 CAAGGTGGGGAGGTGGGC 62.367 72.222 0.00 0.00 0.00 5.36
1247 1277 3.661648 CCAAGGTGGGGAGGTGGG 61.662 72.222 0.00 0.00 32.67 4.61
1270 1300 3.476552 TGTTTCACCAGACAGTTCCATC 58.523 45.455 0.00 0.00 0.00 3.51
1271 1301 3.480470 CTGTTTCACCAGACAGTTCCAT 58.520 45.455 0.00 0.00 38.70 3.41
1272 1302 2.917933 CTGTTTCACCAGACAGTTCCA 58.082 47.619 0.00 0.00 38.70 3.53
1325 1358 2.103263 ACGACCCAAGCTAATCCTGATC 59.897 50.000 0.00 0.00 0.00 2.92
1414 1448 2.989840 CACACTACTCAGTAGCAAGCAC 59.010 50.000 12.11 0.00 39.51 4.40
1428 1462 3.887621 TGGCAGTAATCCTCACACTAC 57.112 47.619 0.00 0.00 0.00 2.73
1615 1649 6.096695 GCCGACAAACAATACATTTACCAAT 58.903 36.000 0.00 0.00 0.00 3.16
1883 1917 6.915786 AGTAGAATGCAAGGGATAGGATTTT 58.084 36.000 0.00 0.00 0.00 1.82
1981 2015 8.232913 GGTATATGCCCAAAACTAGATCAAAA 57.767 34.615 0.00 0.00 0.00 2.44
2247 2302 1.723542 CGCAGTCAACGCAGCAAAG 60.724 57.895 0.00 0.00 0.00 2.77
2437 2492 8.523915 AATTCAGAAACCATCTAATGCATACA 57.476 30.769 0.00 0.00 36.32 2.29
2478 2534 2.162681 GGGAGCACAAACATAACTGCT 58.837 47.619 0.00 0.00 42.73 4.24
2498 2554 1.066002 CTGCTGAATACGCAAATGGGG 59.934 52.381 2.43 0.00 36.88 4.96
2602 2659 2.005560 GCCAAGTACACGGTAGAAGCC 61.006 57.143 0.00 0.00 0.00 4.35
2646 2830 4.405358 AGAACAATCAAAAGGGAAGTGCAA 59.595 37.500 0.00 0.00 0.00 4.08
2945 3130 7.065923 GGTAACAACAAGAGTTCTGACTTCTTT 59.934 37.037 1.29 0.00 35.88 2.52
2946 3131 6.539103 GGTAACAACAAGAGTTCTGACTTCTT 59.461 38.462 0.00 0.00 35.88 2.52
2965 3150 3.574354 TGCTGCATCATATGGGTAACA 57.426 42.857 0.00 0.00 39.74 2.41
2970 3155 3.220110 AGACTTTGCTGCATCATATGGG 58.780 45.455 1.84 0.00 0.00 4.00
2976 3161 2.810274 GTCAAGAGACTTTGCTGCATCA 59.190 45.455 1.84 0.00 41.64 3.07
2977 3162 2.161211 GGTCAAGAGACTTTGCTGCATC 59.839 50.000 1.84 0.00 44.36 3.91
2978 3163 2.157738 GGTCAAGAGACTTTGCTGCAT 58.842 47.619 1.84 0.00 44.36 3.96
2979 3164 1.141657 AGGTCAAGAGACTTTGCTGCA 59.858 47.619 0.00 0.00 44.36 4.41
2980 3165 1.889545 AGGTCAAGAGACTTTGCTGC 58.110 50.000 0.00 0.00 44.36 5.25
2981 3166 3.737850 AGAAGGTCAAGAGACTTTGCTG 58.262 45.455 0.00 0.00 43.23 4.41
2982 3167 5.552870 TTAGAAGGTCAAGAGACTTTGCT 57.447 39.130 0.00 0.00 43.23 3.91
2983 3168 8.499403 AATATTAGAAGGTCAAGAGACTTTGC 57.501 34.615 0.00 0.00 43.23 3.68
3227 3419 4.226620 GTGGTGATTCTAGGTTCCCCTTTA 59.773 45.833 0.00 0.00 42.66 1.85
3314 3506 6.182039 TCAGCGAAAACATAAAAGGAGATG 57.818 37.500 0.00 0.00 0.00 2.90
3332 3525 3.191078 AGAGAAATGGGAGATTCAGCG 57.809 47.619 0.00 0.00 0.00 5.18
3409 3602 5.482175 AGATCTAAGTAAAGCCACTCTGTGT 59.518 40.000 0.00 0.00 0.00 3.72
3410 3603 5.971763 AGATCTAAGTAAAGCCACTCTGTG 58.028 41.667 0.00 0.00 0.00 3.66
3439 3632 9.301153 AGTTTTGCAACAAAAGAAATAGTAGTG 57.699 29.630 0.00 0.00 35.05 2.74
3475 3668 8.352201 GCATGGTTGATAAATCTGCAAGTATTA 58.648 33.333 0.00 0.00 33.76 0.98
3535 3728 0.603707 ACATGGAGTTGCACGACTGG 60.604 55.000 0.00 0.00 0.00 4.00
3615 3810 5.679734 TGTTCTTTCATGCTTTCTCAGAC 57.320 39.130 0.00 0.00 0.00 3.51
3637 3832 2.851263 TTCCTTACCGCTGACACAAT 57.149 45.000 0.00 0.00 0.00 2.71
3647 3842 3.600388 ACTGCAGAAAGATTCCTTACCG 58.400 45.455 23.35 0.00 31.15 4.02
3801 3998 5.009010 CACAGCATCAAACTTTCCTGTAACT 59.991 40.000 0.00 0.00 32.76 2.24
3864 4061 5.833667 TCCGCCTCTTCTCAGAAGATTAATA 59.166 40.000 17.75 1.60 0.00 0.98
3921 4118 8.535690 AAAGAAAAACACGGAAACATTAAACA 57.464 26.923 0.00 0.00 0.00 2.83
3929 4126 7.112528 AGAAACAAAAGAAAAACACGGAAAC 57.887 32.000 0.00 0.00 0.00 2.78
4092 4290 4.142227 TGTCAACGGAGCTCTTTACCTATC 60.142 45.833 14.64 0.00 0.00 2.08
4157 4473 3.194968 GGTTTCCTCAGACTCGGACATAA 59.805 47.826 0.00 0.00 0.00 1.90
4158 4474 2.758979 GGTTTCCTCAGACTCGGACATA 59.241 50.000 0.00 0.00 0.00 2.29
4159 4475 1.550976 GGTTTCCTCAGACTCGGACAT 59.449 52.381 0.00 0.00 0.00 3.06
4160 4476 0.966920 GGTTTCCTCAGACTCGGACA 59.033 55.000 0.00 0.00 0.00 4.02
4161 4477 1.258676 AGGTTTCCTCAGACTCGGAC 58.741 55.000 0.00 0.00 0.00 4.79
4162 4478 2.893215 TAGGTTTCCTCAGACTCGGA 57.107 50.000 0.00 0.00 34.61 4.55
4163 4479 4.473477 AAATAGGTTTCCTCAGACTCGG 57.527 45.455 0.00 0.00 34.61 4.63
4164 4480 7.222999 GTGATTAAATAGGTTTCCTCAGACTCG 59.777 40.741 0.00 0.00 34.61 4.18
4165 4481 8.261522 AGTGATTAAATAGGTTTCCTCAGACTC 58.738 37.037 0.00 0.00 34.61 3.36
4166 4482 8.152023 AGTGATTAAATAGGTTTCCTCAGACT 57.848 34.615 0.00 0.00 34.61 3.24
4196 4512 9.524106 CGACAGATTATAAACAGTTACCACATA 57.476 33.333 0.00 0.00 0.00 2.29
4197 4513 8.255206 TCGACAGATTATAAACAGTTACCACAT 58.745 33.333 0.00 0.00 0.00 3.21
4198 4514 7.604549 TCGACAGATTATAAACAGTTACCACA 58.395 34.615 0.00 0.00 0.00 4.17
4199 4515 7.222224 CCTCGACAGATTATAAACAGTTACCAC 59.778 40.741 0.00 0.00 0.00 4.16
4200 4516 7.262772 CCTCGACAGATTATAAACAGTTACCA 58.737 38.462 0.00 0.00 0.00 3.25
4201 4517 6.200475 GCCTCGACAGATTATAAACAGTTACC 59.800 42.308 0.00 0.00 0.00 2.85
4202 4518 6.200475 GGCCTCGACAGATTATAAACAGTTAC 59.800 42.308 0.00 0.00 0.00 2.50
4203 4519 6.278363 GGCCTCGACAGATTATAAACAGTTA 58.722 40.000 0.00 0.00 0.00 2.24
4204 4520 5.116882 GGCCTCGACAGATTATAAACAGTT 58.883 41.667 0.00 0.00 0.00 3.16
4205 4521 4.443034 GGGCCTCGACAGATTATAAACAGT 60.443 45.833 0.84 0.00 0.00 3.55
4206 4522 4.058817 GGGCCTCGACAGATTATAAACAG 58.941 47.826 0.84 0.00 0.00 3.16
4207 4523 3.452990 TGGGCCTCGACAGATTATAAACA 59.547 43.478 4.53 0.00 0.00 2.83
4208 4524 3.808174 GTGGGCCTCGACAGATTATAAAC 59.192 47.826 4.53 0.00 0.00 2.01
4209 4525 3.452990 TGTGGGCCTCGACAGATTATAAA 59.547 43.478 4.53 0.00 0.00 1.40
4210 4526 3.035363 TGTGGGCCTCGACAGATTATAA 58.965 45.455 4.53 0.00 0.00 0.98
4211 4527 2.364324 GTGTGGGCCTCGACAGATTATA 59.636 50.000 4.53 0.00 32.36 0.98
4212 4528 1.139058 GTGTGGGCCTCGACAGATTAT 59.861 52.381 4.53 0.00 32.36 1.28
4213 4529 0.535335 GTGTGGGCCTCGACAGATTA 59.465 55.000 4.53 0.00 32.36 1.75
4214 4530 1.194781 AGTGTGGGCCTCGACAGATT 61.195 55.000 4.53 0.00 32.36 2.40
4215 4531 1.194781 AAGTGTGGGCCTCGACAGAT 61.195 55.000 4.53 0.00 32.36 2.90
4216 4532 1.816863 GAAGTGTGGGCCTCGACAGA 61.817 60.000 4.53 0.00 32.36 3.41
4217 4533 1.374758 GAAGTGTGGGCCTCGACAG 60.375 63.158 4.53 0.00 32.36 3.51
4218 4534 2.741092 GAAGTGTGGGCCTCGACA 59.259 61.111 4.53 0.00 0.00 4.35
4219 4535 2.047179 GGAAGTGTGGGCCTCGAC 60.047 66.667 4.53 2.62 0.00 4.20
4220 4536 2.525629 TGGAAGTGTGGGCCTCGA 60.526 61.111 4.53 0.00 0.00 4.04
4221 4537 2.046892 CTGGAAGTGTGGGCCTCG 60.047 66.667 4.53 0.00 0.00 4.63
4222 4538 1.003233 GTCTGGAAGTGTGGGCCTC 60.003 63.158 4.53 0.49 33.76 4.70
4223 4539 1.770110 TGTCTGGAAGTGTGGGCCT 60.770 57.895 4.53 0.00 33.76 5.19
4224 4540 1.600916 GTGTCTGGAAGTGTGGGCC 60.601 63.158 0.00 0.00 33.76 5.80
4225 4541 0.465460 TTGTGTCTGGAAGTGTGGGC 60.465 55.000 0.00 0.00 33.76 5.36
4226 4542 1.597742 CTTGTGTCTGGAAGTGTGGG 58.402 55.000 0.00 0.00 33.76 4.61
4227 4543 0.947244 GCTTGTGTCTGGAAGTGTGG 59.053 55.000 0.00 0.00 33.76 4.17
4228 4544 1.600957 CAGCTTGTGTCTGGAAGTGTG 59.399 52.381 0.00 0.00 33.76 3.82
4229 4545 1.486310 TCAGCTTGTGTCTGGAAGTGT 59.514 47.619 0.00 0.00 33.76 3.55
4230 4546 2.245159 TCAGCTTGTGTCTGGAAGTG 57.755 50.000 0.00 0.00 33.76 3.16
4231 4547 3.144506 CAATCAGCTTGTGTCTGGAAGT 58.855 45.455 0.00 0.00 33.76 3.01
4232 4548 2.095364 GCAATCAGCTTGTGTCTGGAAG 60.095 50.000 0.00 0.00 41.15 3.46
4233 4549 1.881973 GCAATCAGCTTGTGTCTGGAA 59.118 47.619 0.00 0.00 41.15 3.53
4234 4550 1.527034 GCAATCAGCTTGTGTCTGGA 58.473 50.000 0.00 0.00 41.15 3.86
4245 4561 2.251409 TCTAGATGGCAGCAATCAGC 57.749 50.000 12.62 0.00 46.19 4.26
4246 4562 3.806380 AGTTCTAGATGGCAGCAATCAG 58.194 45.455 12.62 7.56 0.00 2.90
4247 4563 3.920231 AGTTCTAGATGGCAGCAATCA 57.080 42.857 12.62 0.00 0.00 2.57
4248 4564 3.314635 CCAAGTTCTAGATGGCAGCAATC 59.685 47.826 5.19 0.78 0.00 2.67
4249 4565 3.285484 CCAAGTTCTAGATGGCAGCAAT 58.715 45.455 5.19 0.00 0.00 3.56
4250 4566 2.040278 ACCAAGTTCTAGATGGCAGCAA 59.960 45.455 5.19 0.00 37.77 3.91
4251 4567 1.630369 ACCAAGTTCTAGATGGCAGCA 59.370 47.619 5.19 0.00 37.77 4.41
4252 4568 2.284190 GACCAAGTTCTAGATGGCAGC 58.716 52.381 10.26 0.00 37.77 5.25
4253 4569 3.055530 ACTGACCAAGTTCTAGATGGCAG 60.056 47.826 21.35 21.35 40.76 4.85
4254 4570 2.906389 ACTGACCAAGTTCTAGATGGCA 59.094 45.455 10.26 8.59 34.57 4.92
4255 4571 3.618690 ACTGACCAAGTTCTAGATGGC 57.381 47.619 10.26 5.01 34.57 4.40
4256 4572 6.102663 CAGTTACTGACCAAGTTCTAGATGG 58.897 44.000 6.50 8.99 40.56 3.51
4257 4573 6.102663 CCAGTTACTGACCAAGTTCTAGATG 58.897 44.000 14.66 0.00 40.56 2.90
4258 4574 5.337652 GCCAGTTACTGACCAAGTTCTAGAT 60.338 44.000 14.66 0.00 40.56 1.98
4259 4575 4.021368 GCCAGTTACTGACCAAGTTCTAGA 60.021 45.833 14.66 0.00 40.56 2.43
4260 4576 4.246458 GCCAGTTACTGACCAAGTTCTAG 58.754 47.826 14.66 0.00 40.56 2.43
4261 4577 3.644265 TGCCAGTTACTGACCAAGTTCTA 59.356 43.478 14.66 0.00 40.56 2.10
4262 4578 2.438021 TGCCAGTTACTGACCAAGTTCT 59.562 45.455 14.66 0.00 40.56 3.01
4263 4579 2.846193 TGCCAGTTACTGACCAAGTTC 58.154 47.619 14.66 0.00 40.56 3.01
4264 4580 3.290948 TTGCCAGTTACTGACCAAGTT 57.709 42.857 14.66 0.00 40.56 2.66
4265 4581 3.118038 TCTTTGCCAGTTACTGACCAAGT 60.118 43.478 14.66 0.00 43.40 3.16
4266 4582 3.476552 TCTTTGCCAGTTACTGACCAAG 58.523 45.455 14.66 9.88 32.44 3.61
4267 4583 3.569194 TCTTTGCCAGTTACTGACCAA 57.431 42.857 14.66 13.09 32.44 3.67
4268 4584 3.569194 TTCTTTGCCAGTTACTGACCA 57.431 42.857 14.66 7.69 32.44 4.02
4269 4585 4.911514 TTTTCTTTGCCAGTTACTGACC 57.088 40.909 14.66 5.07 32.44 4.02
4894 5513 2.465860 TGAACCACGAAACGATGGAT 57.534 45.000 15.26 7.23 39.46 3.41
4896 5515 3.259064 AGTATGAACCACGAAACGATGG 58.741 45.455 0.00 0.00 42.13 3.51
4897 5516 3.924073 TGAGTATGAACCACGAAACGATG 59.076 43.478 0.00 0.00 0.00 3.84
4900 5519 3.314553 AGTGAGTATGAACCACGAAACG 58.685 45.455 0.00 0.00 34.13 3.60
4901 5520 4.557205 AGAGTGAGTATGAACCACGAAAC 58.443 43.478 0.00 0.00 34.13 2.78
4902 5521 4.866508 AGAGTGAGTATGAACCACGAAA 57.133 40.909 0.00 0.00 34.13 3.46
4903 5522 4.615223 CGAAGAGTGAGTATGAACCACGAA 60.615 45.833 0.00 0.00 34.13 3.85
4904 5523 3.119955 CGAAGAGTGAGTATGAACCACGA 60.120 47.826 0.00 0.00 34.13 4.35
4905 5524 3.172050 CGAAGAGTGAGTATGAACCACG 58.828 50.000 0.00 0.00 34.13 4.94
4906 5525 2.924290 GCGAAGAGTGAGTATGAACCAC 59.076 50.000 0.00 0.00 0.00 4.16
4907 5526 2.826128 AGCGAAGAGTGAGTATGAACCA 59.174 45.455 0.00 0.00 0.00 3.67
4908 5527 3.512033 AGCGAAGAGTGAGTATGAACC 57.488 47.619 0.00 0.00 0.00 3.62
4909 5528 4.739195 AGAAGCGAAGAGTGAGTATGAAC 58.261 43.478 0.00 0.00 0.00 3.18
4910 5529 5.048013 TCAAGAAGCGAAGAGTGAGTATGAA 60.048 40.000 0.00 0.00 0.00 2.57
4911 5530 4.459337 TCAAGAAGCGAAGAGTGAGTATGA 59.541 41.667 0.00 0.00 0.00 2.15
4912 5531 4.560819 GTCAAGAAGCGAAGAGTGAGTATG 59.439 45.833 0.00 0.00 0.00 2.39
4913 5532 4.218635 TGTCAAGAAGCGAAGAGTGAGTAT 59.781 41.667 0.00 0.00 0.00 2.12
4914 5533 3.568430 TGTCAAGAAGCGAAGAGTGAGTA 59.432 43.478 0.00 0.00 0.00 2.59
4915 5534 2.362397 TGTCAAGAAGCGAAGAGTGAGT 59.638 45.455 0.00 0.00 0.00 3.41
4916 5535 3.018598 TGTCAAGAAGCGAAGAGTGAG 57.981 47.619 0.00 0.00 0.00 3.51
4917 5536 3.452755 TTGTCAAGAAGCGAAGAGTGA 57.547 42.857 0.00 0.00 0.00 3.41
4918 5537 4.536364 TTTTGTCAAGAAGCGAAGAGTG 57.464 40.909 0.00 0.00 0.00 3.51
4931 5550 9.617975 GGAACAAACATTGAAAAATTTTGTCAA 57.382 25.926 15.34 15.34 35.83 3.18
4951 5570 2.088423 AGCAGAACAAACACGGAACAA 58.912 42.857 0.00 0.00 0.00 2.83
5088 5707 3.421844 GAGGTGCCTGGAATTGTAGTTT 58.578 45.455 0.00 0.00 0.00 2.66
5153 5790 4.964897 TGCCGATGGAGGATGATATATTCT 59.035 41.667 0.00 0.00 0.00 2.40
5174 5811 1.538047 TTGGTCTGAATTGGAGCTGC 58.462 50.000 0.00 0.00 33.06 5.25
5235 5872 2.035442 GGAAACCCAGCGCTGAGAC 61.035 63.158 38.06 21.68 0.00 3.36
5364 6013 2.154074 AAGGGCCTTCACTTCCGGT 61.154 57.895 14.48 0.00 0.00 5.28
5433 6082 1.817099 GATGAAGCTGAGGGTGGCG 60.817 63.158 0.00 0.00 0.00 5.69
5472 6121 6.010739 AGGAAATAAGGGAAAAGATGGAGGAA 60.011 38.462 0.00 0.00 0.00 3.36
5484 6133 5.090139 TGAAAATGGCAGGAAATAAGGGAA 58.910 37.500 0.00 0.00 0.00 3.97
5488 6137 7.603404 TCATGTTTGAAAATGGCAGGAAATAAG 59.397 33.333 0.00 0.00 0.00 1.73
5518 6169 3.196463 CTGTGCAGAGATGATCAACTCC 58.804 50.000 24.71 13.79 34.13 3.85
5539 6191 5.525378 CCCTACATACAATCTTGTCAAGAGC 59.475 44.000 19.64 0.00 41.61 4.09


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

AutoCloner maintained by Alex Coulton.