Multiple sequence alignment - TraesCS4B01G158100

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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 TraesCS4B01G158100 chr4B 100.000 5172 0 0 1 5172 304065652 304070823 0.000000e+00 9551.0
1 TraesCS4B01G158100 chr4B 93.004 486 20 4 4545 5017 130614253 130613769 0.000000e+00 697.0
2 TraesCS4B01G158100 chr4B 93.220 118 6 1 5057 5172 130613770 130613653 6.890000e-39 172.0
3 TraesCS4B01G158100 chr4D 93.823 3691 161 34 1 3669 261257185 261253540 0.000000e+00 5491.0
4 TraesCS4B01G158100 chr4D 97.467 829 19 2 3666 4492 261253578 261252750 0.000000e+00 1413.0
5 TraesCS4B01G158100 chr4D 84.211 304 46 2 322 623 76602502 76602199 1.410000e-75 294.0
6 TraesCS4B01G158100 chr4D 85.586 111 13 3 2170 2279 260726175 260726067 4.230000e-21 113.0
7 TraesCS4B01G158100 chr4D 100.000 27 0 0 4522 4548 261252740 261252714 3.400000e-02 51.0
8 TraesCS4B01G158100 chr4A 95.451 1341 45 12 912 2249 326134419 326135746 0.000000e+00 2124.0
9 TraesCS4B01G158100 chr4A 93.263 1425 50 25 2267 3669 326135809 326137209 0.000000e+00 2058.0
10 TraesCS4B01G158100 chr4A 95.821 670 22 4 3799 4466 326137390 326138055 0.000000e+00 1077.0
11 TraesCS4B01G158100 chr4A 88.485 660 36 16 4547 5169 432984471 432985127 0.000000e+00 761.0
12 TraesCS4B01G158100 chr4A 95.000 140 4 1 3666 3802 326137171 326137310 3.140000e-52 217.0
13 TraesCS4B01G158100 chr4A 81.633 147 19 8 2133 2276 255308294 255308153 1.180000e-21 115.0
14 TraesCS4B01G158100 chr4A 96.552 58 2 0 705 762 326134351 326134408 4.260000e-16 97.1
15 TraesCS4B01G158100 chr1B 92.116 761 49 8 2917 3669 2118780 2118023 0.000000e+00 1062.0
16 TraesCS4B01G158100 chr1B 90.557 413 16 12 3907 4296 2117863 2117451 4.590000e-145 525.0
17 TraesCS4B01G158100 chr1B 93.443 183 8 2 3669 3847 2118058 2117876 8.540000e-68 268.0
18 TraesCS4B01G158100 chr2B 93.802 484 16 4 4547 5017 482748577 482748095 0.000000e+00 715.0
19 TraesCS4B01G158100 chr2B 84.211 304 45 3 324 625 72827601 72827903 5.070000e-75 292.0
20 TraesCS4B01G158100 chr2B 94.872 117 5 1 5057 5172 482748096 482747980 1.140000e-41 182.0
21 TraesCS4B01G158100 chr2B 92.500 40 2 1 2155 2194 134480421 134480383 7.230000e-04 56.5
22 TraesCS4B01G158100 chr6B 85.583 652 63 15 4546 5172 704665639 704666284 0.000000e+00 654.0
23 TraesCS4B01G158100 chr6B 91.518 224 17 2 68 289 639977008 639977231 1.810000e-79 307.0
24 TraesCS4B01G158100 chr6B 82.026 306 46 5 3097 3401 25811181 25810884 8.600000e-63 252.0
25 TraesCS4B01G158100 chr1A 90.688 494 21 7 4538 5017 7054094 7054576 7.310000e-178 634.0
26 TraesCS4B01G158100 chr1A 90.852 481 19 6 4547 5014 575747028 575747496 5.690000e-174 621.0
27 TraesCS4B01G158100 chr1A 93.220 118 6 1 5057 5172 7054575 7054692 6.890000e-39 172.0
28 TraesCS4B01G158100 chr1A 92.437 119 7 1 5056 5172 575747497 575747615 8.910000e-38 169.0
29 TraesCS4B01G158100 chr1A 80.412 194 23 5 4546 4724 530159843 530159650 3.250000e-27 134.0
30 TraesCS4B01G158100 chr1A 80.124 161 24 8 2103 2259 14135360 14135204 4.230000e-21 113.0
31 TraesCS4B01G158100 chr5A 84.769 650 67 16 4548 5172 493354898 493355540 1.580000e-174 623.0
32 TraesCS4B01G158100 chr5A 78.894 199 36 6 2178 2372 241288771 241288967 4.200000e-26 130.0
33 TraesCS4B01G158100 chr5A 93.220 59 3 1 4548 4606 56369039 56369096 9.230000e-13 86.1
34 TraesCS4B01G158100 chr6D 90.805 261 20 4 68 324 150788313 150788053 3.830000e-91 346.0
35 TraesCS4B01G158100 chr6D 88.710 62 7 0 6 67 239042117 239042056 5.550000e-10 76.8
36 TraesCS4B01G158100 chr2D 90.805 261 20 3 68 324 424680836 424681096 3.830000e-91 346.0
37 TraesCS4B01G158100 chr5D 89.655 261 22 4 69 324 458765289 458765029 1.390000e-85 327.0
38 TraesCS4B01G158100 chr5D 80.000 170 19 7 4547 4702 540010483 540010651 1.520000e-20 111.0
39 TraesCS4B01G158100 chr2A 85.667 300 43 0 324 623 459017005 459017304 3.010000e-82 316.0
40 TraesCS4B01G158100 chr1D 85.862 290 41 0 322 611 8279646 8279357 5.030000e-80 309.0
41 TraesCS4B01G158100 chrUn 87.778 270 20 8 68 324 311355885 311356154 2.340000e-78 303.0
42 TraesCS4B01G158100 chr3B 84.488 303 45 1 321 621 666193298 666193600 1.090000e-76 298.0
43 TraesCS4B01G158100 chr3B 83.758 314 48 3 312 623 820355085 820354773 1.410000e-75 294.0
44 TraesCS4B01G158100 chr7D 84.281 299 47 0 325 623 595688187 595687889 5.070000e-75 292.0
45 TraesCS4B01G158100 chr3A 83.125 320 50 4 322 638 60170338 60170656 6.550000e-74 289.0
46 TraesCS4B01G158100 chr7B 83.755 277 27 11 4548 4807 487987653 487987928 4.000000e-61 246.0
47 TraesCS4B01G158100 chr7A 83.333 258 25 10 4573 4813 575286054 575285798 6.740000e-54 222.0
48 TraesCS4B01G158100 chr7A 81.250 192 21 5 4548 4724 593697310 593697119 1.940000e-29 141.0
49 TraesCS4B01G158100 chr5B 93.333 45 1 2 11 54 372238753 372238796 1.200000e-06 65.8


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 TraesCS4B01G158100 chr4B 304065652 304070823 5171 False 9551.000000 9551 100.000000 1 5172 1 chr4B.!!$F1 5171
1 TraesCS4B01G158100 chr4B 130613653 130614253 600 True 434.500000 697 93.112000 4545 5172 2 chr4B.!!$R1 627
2 TraesCS4B01G158100 chr4D 261252714 261257185 4471 True 2318.333333 5491 97.096667 1 4548 3 chr4D.!!$R3 4547
3 TraesCS4B01G158100 chr4A 326134351 326138055 3704 False 1114.620000 2124 95.217400 705 4466 5 chr4A.!!$F2 3761
4 TraesCS4B01G158100 chr4A 432984471 432985127 656 False 761.000000 761 88.485000 4547 5169 1 chr4A.!!$F1 622
5 TraesCS4B01G158100 chr1B 2117451 2118780 1329 True 618.333333 1062 92.038667 2917 4296 3 chr1B.!!$R1 1379
6 TraesCS4B01G158100 chr2B 482747980 482748577 597 True 448.500000 715 94.337000 4547 5172 2 chr2B.!!$R2 625
7 TraesCS4B01G158100 chr6B 704665639 704666284 645 False 654.000000 654 85.583000 4546 5172 1 chr6B.!!$F2 626
8 TraesCS4B01G158100 chr1A 7054094 7054692 598 False 403.000000 634 91.954000 4538 5172 2 chr1A.!!$F1 634
9 TraesCS4B01G158100 chr1A 575747028 575747615 587 False 395.000000 621 91.644500 4547 5172 2 chr1A.!!$F2 625
10 TraesCS4B01G158100 chr5A 493354898 493355540 642 False 623.000000 623 84.769000 4548 5172 1 chr5A.!!$F3 624

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
400 406 0.031585 TGAGCTCACACACGTACACC 59.968 55.000 13.74 0.0 0.0 4.16 F
504 510 0.038159 GAGAACGTCACCTCCCAGTG 60.038 60.000 0.00 0.0 39.2 3.66 F
847 861 0.105709 CCACCAAACTTCCACCCCTT 60.106 55.000 0.00 0.0 0.0 3.95 F
849 863 0.187606 ACCAAACTTCCACCCCTTCC 59.812 55.000 0.00 0.0 0.0 3.46 F
850 864 0.482887 CCAAACTTCCACCCCTTCCT 59.517 55.000 0.00 0.0 0.0 3.36 F
1661 1679 1.075212 TCATTGGTGCCAGGACATTGA 59.925 47.619 0.00 0.0 0.0 2.57 F
2152 2171 1.895131 TGCCCCATCTGCTTTTCTTTC 59.105 47.619 0.00 0.0 0.0 2.62 F
3538 3633 2.439507 ACTTCGTGAATGGATAGGGCAT 59.560 45.455 0.00 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 2126 0.539438 CCACTGTAGCCCTTTTGCCA 60.539 55.000 0.00 0.00 0.00 4.92 R
2108 2127 1.877576 GCCACTGTAGCCCTTTTGCC 61.878 60.000 0.00 0.00 0.00 4.52 R
2440 2506 3.492313 GGAATGCAAGTCGATGTTTGAC 58.508 45.455 10.32 4.19 36.60 3.18 R
2802 2886 8.079211 TCTCTACCTTAAATATCACTTGCAGT 57.921 34.615 0.00 0.00 0.00 4.40 R
2882 2966 2.345876 TGGCTTACACATCATGTCACG 58.654 47.619 0.00 0.00 42.09 4.35 R
3669 3764 1.112950 TGTACGATGCCCGATAACCA 58.887 50.000 2.54 0.00 41.76 3.67 R
3670 3765 2.228138 TTGTACGATGCCCGATAACC 57.772 50.000 2.54 0.00 41.76 2.85 R
4485 4695 0.108945 GCAGCTGCCCACTGAAAATC 60.109 55.000 28.76 0.00 37.32 2.17 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
23 24 4.347876 TGTGAGTTCATCTCTTTTCCTCCA 59.652 41.667 0.00 0.00 43.13 3.86
25 26 5.584251 GTGAGTTCATCTCTTTTCCTCCATC 59.416 44.000 0.00 0.00 43.13 3.51
33 34 4.844085 TCTCTTTTCCTCCATCCAAGTGTA 59.156 41.667 0.00 0.00 0.00 2.90
80 81 5.105837 ACCGTATAACAGACCTTGTCTCTTC 60.106 44.000 0.00 0.00 41.37 2.87
85 86 2.224161 ACAGACCTTGTCTCTTCTGCAC 60.224 50.000 0.00 0.00 41.37 4.57
115 116 1.066071 TGGGAAATATGGTGCGAACGA 60.066 47.619 0.00 0.00 0.00 3.85
116 117 2.011222 GGGAAATATGGTGCGAACGAA 58.989 47.619 0.00 0.00 0.00 3.85
117 118 2.420722 GGGAAATATGGTGCGAACGAAA 59.579 45.455 0.00 0.00 0.00 3.46
118 119 3.066203 GGGAAATATGGTGCGAACGAAAT 59.934 43.478 0.00 0.00 0.00 2.17
119 120 4.273969 GGGAAATATGGTGCGAACGAAATA 59.726 41.667 0.00 0.00 0.00 1.40
120 121 5.440685 GGAAATATGGTGCGAACGAAATAG 58.559 41.667 0.00 0.00 0.00 1.73
121 122 5.235616 GGAAATATGGTGCGAACGAAATAGA 59.764 40.000 0.00 0.00 0.00 1.98
122 123 5.652744 AATATGGTGCGAACGAAATAGAC 57.347 39.130 0.00 0.00 0.00 2.59
123 124 2.442212 TGGTGCGAACGAAATAGACA 57.558 45.000 0.00 0.00 0.00 3.41
124 125 2.333926 TGGTGCGAACGAAATAGACAG 58.666 47.619 0.00 0.00 0.00 3.51
125 126 1.060698 GGTGCGAACGAAATAGACAGC 59.939 52.381 0.00 0.00 0.00 4.40
126 127 1.993370 GTGCGAACGAAATAGACAGCT 59.007 47.619 0.00 0.00 0.00 4.24
127 128 1.992667 TGCGAACGAAATAGACAGCTG 59.007 47.619 13.48 13.48 0.00 4.24
135 136 4.997395 ACGAAATAGACAGCTGTTGACAAT 59.003 37.500 22.65 6.26 0.00 2.71
139 140 7.689812 CGAAATAGACAGCTGTTGACAATAAAG 59.310 37.037 22.65 3.28 0.00 1.85
145 146 5.413833 ACAGCTGTTGACAATAAAGAGATGG 59.586 40.000 15.25 0.00 38.30 3.51
153 154 7.437713 TGACAATAAAGAGATGGATACTGGT 57.562 36.000 0.00 0.00 37.61 4.00
154 155 8.547481 TGACAATAAAGAGATGGATACTGGTA 57.453 34.615 0.00 0.00 37.61 3.25
155 156 8.421784 TGACAATAAAGAGATGGATACTGGTAC 58.578 37.037 0.00 0.00 37.61 3.34
156 157 7.434492 ACAATAAAGAGATGGATACTGGTACG 58.566 38.462 0.00 0.00 37.61 3.67
199 200 8.910944 AGGATGAAATTAGAATCTGAAACATGG 58.089 33.333 0.00 0.00 0.00 3.66
200 201 8.689972 GGATGAAATTAGAATCTGAAACATGGT 58.310 33.333 0.00 0.00 0.00 3.55
248 251 3.627123 GGCTGATTTGTTGCCTTGTTTTT 59.373 39.130 0.00 0.00 43.05 1.94
306 311 1.989706 TTTTTGGCACCCCTCTGTAC 58.010 50.000 0.00 0.00 0.00 2.90
307 312 1.145571 TTTTGGCACCCCTCTGTACT 58.854 50.000 0.00 0.00 0.00 2.73
322 327 5.927115 CCTCTGTACTGTTTTCACTCCTTAC 59.073 44.000 0.00 0.00 0.00 2.34
365 371 2.845764 GCAAACGCTCATACATACACGC 60.846 50.000 0.00 0.00 0.00 5.34
369 375 4.174411 ACGCTCATACATACACGCATAT 57.826 40.909 0.00 0.00 0.00 1.78
373 379 5.452623 CGCTCATACATACACGCATATACTC 59.547 44.000 0.00 0.00 0.00 2.59
376 382 7.489435 GCTCATACATACACGCATATACTCATT 59.511 37.037 0.00 0.00 0.00 2.57
394 400 2.654749 TTCCTATGAGCTCACACACG 57.345 50.000 20.97 5.18 0.00 4.49
396 402 2.718563 TCCTATGAGCTCACACACGTA 58.281 47.619 20.97 5.37 0.00 3.57
400 406 0.031585 TGAGCTCACACACGTACACC 59.968 55.000 13.74 0.00 0.00 4.16
409 415 2.895404 ACACACGTACACCCTACATCTT 59.105 45.455 0.00 0.00 0.00 2.40
411 417 3.678072 CACACGTACACCCTACATCTTTG 59.322 47.826 0.00 0.00 0.00 2.77
413 419 4.174009 CACGTACACCCTACATCTTTGAG 58.826 47.826 0.00 0.00 0.00 3.02
414 420 3.194968 ACGTACACCCTACATCTTTGAGG 59.805 47.826 0.00 0.00 0.00 3.86
416 422 3.983044 ACACCCTACATCTTTGAGGAC 57.017 47.619 0.00 0.00 31.45 3.85
420 426 4.469945 CACCCTACATCTTTGAGGACCTTA 59.530 45.833 0.00 0.00 31.45 2.69
456 462 5.062683 CCGGCATATCATCTTGAGATTTACG 59.937 44.000 0.00 0.00 31.21 3.18
459 465 7.411264 CGGCATATCATCTTGAGATTTACGAAG 60.411 40.741 0.00 0.00 31.21 3.79
465 471 6.808704 TCATCTTGAGATTTACGAAGTCACTG 59.191 38.462 0.00 0.00 35.39 3.66
478 484 2.202623 CACTGTAGGCGCCTCGTC 60.203 66.667 36.73 24.11 0.00 4.20
479 485 3.450115 ACTGTAGGCGCCTCGTCC 61.450 66.667 36.73 19.71 28.67 4.79
502 508 1.213013 CGAGAACGTCACCTCCCAG 59.787 63.158 0.00 0.00 34.56 4.45
503 509 1.524863 CGAGAACGTCACCTCCCAGT 61.525 60.000 0.00 0.00 34.56 4.00
504 510 0.038159 GAGAACGTCACCTCCCAGTG 60.038 60.000 0.00 0.00 39.20 3.66
514 520 1.271597 ACCTCCCAGTGAAAGTGCATC 60.272 52.381 0.00 0.00 35.41 3.91
517 523 1.503542 CCAGTGAAAGTGCATCGCC 59.496 57.895 0.00 0.00 35.41 5.54
519 525 2.034879 AGTGAAAGTGCATCGCCGG 61.035 57.895 0.00 0.00 0.00 6.13
523 529 0.454452 GAAAGTGCATCGCCGGAAAC 60.454 55.000 5.05 0.00 0.00 2.78
536 542 3.119280 CGCCGGAAACCCTGAAATAAATT 60.119 43.478 5.05 0.00 0.00 1.82
537 543 4.619628 CGCCGGAAACCCTGAAATAAATTT 60.620 41.667 5.05 0.00 0.00 1.82
539 545 6.399743 GCCGGAAACCCTGAAATAAATTTAA 58.600 36.000 5.05 0.00 0.00 1.52
569 575 2.618045 CGAGCACCAGGATTTAAACCCT 60.618 50.000 0.00 0.00 0.00 4.34
579 585 6.441088 AGGATTTAAACCCTGATAGGCTAG 57.559 41.667 0.00 0.00 32.73 3.42
580 586 6.151049 AGGATTTAAACCCTGATAGGCTAGA 58.849 40.000 0.00 0.00 32.73 2.43
581 587 6.619852 AGGATTTAAACCCTGATAGGCTAGAA 59.380 38.462 0.00 0.00 32.73 2.10
586 592 5.827326 AACCCTGATAGGCTAGAAATACC 57.173 43.478 0.00 0.00 32.73 2.73
588 594 5.415961 ACCCTGATAGGCTAGAAATACCAT 58.584 41.667 0.00 0.00 32.73 3.55
596 602 4.103311 AGGCTAGAAATACCATTGTCCCTC 59.897 45.833 0.00 0.00 0.00 4.30
600 606 7.454225 GCTAGAAATACCATTGTCCCTCTAAT 58.546 38.462 0.00 0.00 0.00 1.73
611 617 5.715439 TGTCCCTCTAATCATCCAACAAT 57.285 39.130 0.00 0.00 0.00 2.71
614 620 6.183361 TGTCCCTCTAATCATCCAACAATAGG 60.183 42.308 0.00 0.00 0.00 2.57
616 622 6.389869 TCCCTCTAATCATCCAACAATAGGTT 59.610 38.462 0.00 0.00 41.47 3.50
628 634 5.585820 AACAATAGGTTGGTTCGTGTTTT 57.414 34.783 0.00 0.00 38.60 2.43
629 635 5.177725 ACAATAGGTTGGTTCGTGTTTTC 57.822 39.130 0.00 0.00 39.70 2.29
630 636 4.641094 ACAATAGGTTGGTTCGTGTTTTCA 59.359 37.500 0.00 0.00 39.70 2.69
633 639 9.272098 ACAATAGGTTGGTTCGTGTTTTCACTC 62.272 40.741 0.00 0.00 42.60 3.51
673 679 4.986054 TGGTACAACTCCTACCAACATT 57.014 40.909 0.00 0.00 40.63 2.71
676 682 6.839454 TGGTACAACTCCTACCAACATTAAA 58.161 36.000 0.00 0.00 40.63 1.52
677 683 7.288560 TGGTACAACTCCTACCAACATTAAAA 58.711 34.615 0.00 0.00 40.63 1.52
678 684 7.778853 TGGTACAACTCCTACCAACATTAAAAA 59.221 33.333 0.00 0.00 40.63 1.94
762 776 7.411486 TCTCTTTCCTCTCGTCATAAATTCT 57.589 36.000 0.00 0.00 0.00 2.40
763 777 7.484975 TCTCTTTCCTCTCGTCATAAATTCTC 58.515 38.462 0.00 0.00 0.00 2.87
766 780 5.776173 TCCTCTCGTCATAAATTCTCTCC 57.224 43.478 0.00 0.00 0.00 3.71
803 817 0.996583 AACCTCTCTCCGAGTCTCCT 59.003 55.000 0.00 0.00 38.11 3.69
820 834 4.454161 GTCTCCTCTCTTTTCCAGCTTTTC 59.546 45.833 0.00 0.00 0.00 2.29
843 857 1.533033 CCCCCACCAAACTTCCACC 60.533 63.158 0.00 0.00 0.00 4.61
844 858 1.533033 CCCCACCAAACTTCCACCC 60.533 63.158 0.00 0.00 0.00 4.61
845 859 1.533033 CCCACCAAACTTCCACCCC 60.533 63.158 0.00 0.00 0.00 4.95
846 860 1.541672 CCACCAAACTTCCACCCCT 59.458 57.895 0.00 0.00 0.00 4.79
847 861 0.105709 CCACCAAACTTCCACCCCTT 60.106 55.000 0.00 0.00 0.00 3.95
848 862 1.328279 CACCAAACTTCCACCCCTTC 58.672 55.000 0.00 0.00 0.00 3.46
849 863 0.187606 ACCAAACTTCCACCCCTTCC 59.812 55.000 0.00 0.00 0.00 3.46
850 864 0.482887 CCAAACTTCCACCCCTTCCT 59.517 55.000 0.00 0.00 0.00 3.36
851 865 1.547901 CCAAACTTCCACCCCTTCCTC 60.548 57.143 0.00 0.00 0.00 3.71
978 992 4.965858 GAGAGCGCGATCCGTCCG 62.966 72.222 22.41 0.00 39.71 4.79
1046 1060 4.129737 CGTCGTCGCCACCTCCAT 62.130 66.667 0.00 0.00 0.00 3.41
1277 1292 1.798283 CCCACACGATTAAACGGACA 58.202 50.000 10.03 0.00 37.61 4.02
1299 1314 6.879400 ACATTCTTGGACTAACTAGGTGATC 58.121 40.000 0.00 0.00 0.00 2.92
1304 1319 3.053842 TGGACTAACTAGGTGATCTCCGT 60.054 47.826 8.14 0.00 0.00 4.69
1489 1504 9.699410 AATATTAACTTCCATGAGAAACCATCA 57.301 29.630 0.00 0.00 32.88 3.07
1661 1679 1.075212 TCATTGGTGCCAGGACATTGA 59.925 47.619 0.00 0.00 0.00 2.57
1818 1836 3.066291 ACCACTGTCAGTTTTGTGTCA 57.934 42.857 1.67 0.00 0.00 3.58
2082 2101 2.683933 ATCGGACGGCTGGAAGGT 60.684 61.111 0.00 0.00 0.00 3.50
2107 2126 4.458989 TCAGAGTGTTGTTGTTTGCTTTCT 59.541 37.500 0.00 0.00 0.00 2.52
2108 2127 4.560035 CAGAGTGTTGTTGTTTGCTTTCTG 59.440 41.667 0.00 0.00 0.00 3.02
2152 2171 1.895131 TGCCCCATCTGCTTTTCTTTC 59.105 47.619 0.00 0.00 0.00 2.62
2391 2457 5.650266 TGACAATGTCACAAGTTGGTTAACT 59.350 36.000 12.63 0.00 42.08 2.24
2440 2506 3.062639 CCAGTCAACGAGAAATTCCATCG 59.937 47.826 3.56 3.56 42.04 3.84
2705 2771 3.500680 TGCCATAACGTTGGTTCTCTTTC 59.499 43.478 11.99 0.00 39.11 2.62
2754 2821 8.621532 TTTTGGTGGTGCATATTCTATATCTC 57.378 34.615 0.00 0.00 0.00 2.75
2755 2822 5.965922 TGGTGGTGCATATTCTATATCTCG 58.034 41.667 0.00 0.00 0.00 4.04
2882 2966 5.188327 AGCCAAAAGAAACTGAAGCTAAC 57.812 39.130 0.00 0.00 0.00 2.34
2892 2976 4.193826 ACTGAAGCTAACGTGACATGAT 57.806 40.909 0.00 0.00 0.00 2.45
2895 2979 3.679502 TGAAGCTAACGTGACATGATGTG 59.320 43.478 1.23 0.00 0.00 3.21
2937 3021 8.324163 ACAAGTATAGAAACCAAGTCATGTTC 57.676 34.615 0.00 0.00 0.00 3.18
3016 3104 9.930693 ATCTTCTTCTTGTACTTGTAAACTAGG 57.069 33.333 0.00 0.00 0.00 3.02
3077 3165 6.128472 CCTGCAAATAAGAAAAGCACATTTCC 60.128 38.462 6.16 0.00 39.59 3.13
3181 3269 6.610830 TGCACATATTCCAGGATTTTGGTAAT 59.389 34.615 0.00 0.00 39.35 1.89
3286 3381 4.612943 GACCGGAGATACTTGATCTTCAC 58.387 47.826 9.46 0.00 45.48 3.18
3538 3633 2.439507 ACTTCGTGAATGGATAGGGCAT 59.560 45.455 0.00 0.00 0.00 4.40
3598 3693 8.641498 AAGAATCATCAAGGTAAACATGTTCT 57.359 30.769 12.39 1.67 0.00 3.01
3646 3741 9.857957 GAATTTTGTTATTTTGGTTATCGGGTA 57.142 29.630 0.00 0.00 0.00 3.69
3649 3744 9.640963 TTTTGTTATTTTGGTTATCGGGTATTG 57.359 29.630 0.00 0.00 0.00 1.90
3650 3745 7.941431 TGTTATTTTGGTTATCGGGTATTGT 57.059 32.000 0.00 0.00 0.00 2.71
3651 3746 9.458727 TTGTTATTTTGGTTATCGGGTATTGTA 57.541 29.630 0.00 0.00 0.00 2.41
3652 3747 8.891720 TGTTATTTTGGTTATCGGGTATTGTAC 58.108 33.333 0.00 0.00 0.00 2.90
3653 3748 8.891720 GTTATTTTGGTTATCGGGTATTGTACA 58.108 33.333 0.00 0.00 0.00 2.90
3654 3749 7.941431 ATTTTGGTTATCGGGTATTGTACAA 57.059 32.000 11.41 11.41 0.00 2.41
3655 3750 7.941431 TTTTGGTTATCGGGTATTGTACAAT 57.059 32.000 23.80 23.80 34.93 2.71
3656 3751 6.928979 TTGGTTATCGGGTATTGTACAATG 57.071 37.500 27.62 13.21 32.50 2.82
3657 3752 5.991861 TGGTTATCGGGTATTGTACAATGT 58.008 37.500 27.62 9.01 32.50 2.71
3658 3753 7.122138 TGGTTATCGGGTATTGTACAATGTA 57.878 36.000 27.62 9.01 32.50 2.29
3659 3754 7.737869 TGGTTATCGGGTATTGTACAATGTAT 58.262 34.615 27.62 16.01 32.50 2.29
3660 3755 7.658167 TGGTTATCGGGTATTGTACAATGTATG 59.342 37.037 27.62 16.01 32.50 2.39
3661 3756 7.874016 GGTTATCGGGTATTGTACAATGTATGA 59.126 37.037 27.62 19.87 32.50 2.15
3662 3757 9.431887 GTTATCGGGTATTGTACAATGTATGAT 57.568 33.333 27.62 23.81 32.50 2.45
3663 3758 9.647797 TTATCGGGTATTGTACAATGTATGATC 57.352 33.333 27.62 10.19 32.50 2.92
3664 3759 6.460781 TCGGGTATTGTACAATGTATGATCC 58.539 40.000 27.62 17.06 32.50 3.36
3665 3760 6.042208 TCGGGTATTGTACAATGTATGATCCA 59.958 38.462 27.62 4.73 32.50 3.41
3666 3761 6.878923 CGGGTATTGTACAATGTATGATCCAT 59.121 38.462 27.62 3.50 32.50 3.41
3667 3762 7.390440 CGGGTATTGTACAATGTATGATCCATT 59.610 37.037 27.62 3.30 32.88 3.16
3668 3763 9.077885 GGGTATTGTACAATGTATGATCCATTT 57.922 33.333 27.62 2.88 30.28 2.32
3672 3767 7.953005 TGTACAATGTATGATCCATTTTGGT 57.047 32.000 0.00 0.00 39.03 3.67
3673 3768 8.359875 TGTACAATGTATGATCCATTTTGGTT 57.640 30.769 0.00 0.00 39.03 3.67
3674 3769 9.467796 TGTACAATGTATGATCCATTTTGGTTA 57.532 29.630 0.00 0.00 39.03 2.85
3677 3772 8.352201 ACAATGTATGATCCATTTTGGTTATCG 58.648 33.333 0.00 0.00 39.03 2.92
3678 3773 6.875948 TGTATGATCCATTTTGGTTATCGG 57.124 37.500 0.00 0.00 39.03 4.18
3679 3774 5.767665 TGTATGATCCATTTTGGTTATCGGG 59.232 40.000 0.00 0.00 39.03 5.14
3680 3775 2.955660 TGATCCATTTTGGTTATCGGGC 59.044 45.455 0.00 0.00 39.03 6.13
3829 4014 7.696981 TCCTAGACGGATCCTTACATACTTAT 58.303 38.462 10.75 0.00 36.69 1.73
4197 4385 1.268899 GCAGCCATGGACTTCATATGC 59.731 52.381 18.40 7.87 34.12 3.14
4419 4629 6.293698 GTCCTTTTTCAGTTGGACCTTACTA 58.706 40.000 0.00 0.00 42.11 1.82
4437 4647 2.766828 ACTAGGTGGACTTGGCATAGAC 59.233 50.000 0.00 0.00 0.00 2.59
4464 4674 1.674322 GCCATGTTGGTACTGCCGT 60.674 57.895 0.00 0.00 40.46 5.68
4465 4675 1.241315 GCCATGTTGGTACTGCCGTT 61.241 55.000 0.00 0.00 40.46 4.44
4466 4676 1.243902 CCATGTTGGTACTGCCGTTT 58.756 50.000 0.00 0.00 41.21 3.60
4467 4677 1.199097 CCATGTTGGTACTGCCGTTTC 59.801 52.381 0.00 0.00 41.21 2.78
4468 4678 1.876799 CATGTTGGTACTGCCGTTTCA 59.123 47.619 0.00 0.00 41.21 2.69
4469 4679 1.588674 TGTTGGTACTGCCGTTTCAG 58.411 50.000 0.00 0.00 41.21 3.02
4471 4681 1.263217 GTTGGTACTGCCGTTTCAGTG 59.737 52.381 11.07 0.00 45.95 3.66
4472 4682 0.250124 TGGTACTGCCGTTTCAGTGG 60.250 55.000 11.07 0.00 45.95 4.00
4473 4683 0.953960 GGTACTGCCGTTTCAGTGGG 60.954 60.000 11.07 0.00 45.95 4.61
4474 4684 1.302192 TACTGCCGTTTCAGTGGGC 60.302 57.895 11.07 1.47 45.95 5.36
4477 4687 4.043200 GCCGTTTCAGTGGGCAGC 62.043 66.667 3.50 0.00 46.13 5.25
4478 4688 2.281761 CCGTTTCAGTGGGCAGCT 60.282 61.111 0.00 0.00 0.00 4.24
4479 4689 2.620112 CCGTTTCAGTGGGCAGCTG 61.620 63.158 10.11 10.11 35.43 4.24
4480 4690 2.647297 GTTTCAGTGGGCAGCTGC 59.353 61.111 30.88 30.88 41.14 5.25
4481 4691 1.900498 GTTTCAGTGGGCAGCTGCT 60.900 57.895 35.82 15.73 41.70 4.24
4482 4692 1.601759 TTTCAGTGGGCAGCTGCTC 60.602 57.895 35.82 34.09 43.24 4.26
4764 5025 5.308497 TCACCTTACATAAGACTGTTTCCCA 59.692 40.000 0.00 0.00 35.33 4.37
4797 5058 5.709594 TCTCATGACTCTCCCATATTGAGA 58.290 41.667 0.00 0.00 37.33 3.27
4855 5116 8.537049 TTCAAGGATTCAACAATGCTAATTTG 57.463 30.769 0.00 0.00 39.65 2.32
4874 5135 9.502091 CTAATTTGGTGCTAGTATATTAGGCAA 57.498 33.333 4.61 0.00 34.65 4.52
4915 5176 7.433425 GTGAAGAAAAATGGCAGCAATAGATAC 59.567 37.037 0.00 0.00 0.00 2.24
4954 5215 7.776107 AGCAGTACATAATATATCGTGAGCAT 58.224 34.615 0.00 0.00 0.00 3.79
5031 5292 2.029838 AATACTTGGGCTCTCGCTTG 57.970 50.000 0.00 0.00 36.09 4.01
5053 5314 5.396484 TGTATCTTCTCACCTAAAACGACG 58.604 41.667 0.00 0.00 0.00 5.12
5137 5400 0.896940 AGGCATTTCACCCACTGCAG 60.897 55.000 13.48 13.48 36.34 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.639310 CACTTGGATGGAGGAAAAGAGATG 59.361 45.833 0.00 0.00 0.00 2.90
23 24 6.394345 AGAGGGATCTTTTTACACTTGGAT 57.606 37.500 0.00 0.00 0.00 3.41
25 26 6.599638 CCTAAGAGGGATCTTTTTACACTTGG 59.400 42.308 0.00 0.00 0.00 3.61
59 60 5.808030 GCAGAAGAGACAAGGTCTGTTATAC 59.192 44.000 8.51 0.00 44.30 1.47
62 63 3.641436 TGCAGAAGAGACAAGGTCTGTTA 59.359 43.478 8.51 0.00 44.30 2.41
80 81 3.634397 TTCCCAAGAGATTAGGTGCAG 57.366 47.619 0.00 0.00 0.00 4.41
85 86 5.474876 GCACCATATTTCCCAAGAGATTAGG 59.525 44.000 0.00 0.00 0.00 2.69
115 116 8.621532 TCTTTATTGTCAACAGCTGTCTATTT 57.378 30.769 21.95 0.00 0.00 1.40
116 117 8.097038 TCTCTTTATTGTCAACAGCTGTCTATT 58.903 33.333 21.95 0.24 0.00 1.73
117 118 7.615403 TCTCTTTATTGTCAACAGCTGTCTAT 58.385 34.615 21.95 12.44 0.00 1.98
118 119 6.993079 TCTCTTTATTGTCAACAGCTGTCTA 58.007 36.000 21.95 8.52 0.00 2.59
119 120 5.858381 TCTCTTTATTGTCAACAGCTGTCT 58.142 37.500 21.95 7.79 0.00 3.41
120 121 6.402983 CCATCTCTTTATTGTCAACAGCTGTC 60.403 42.308 21.95 8.58 0.00 3.51
121 122 5.413833 CCATCTCTTTATTGTCAACAGCTGT 59.586 40.000 15.25 15.25 0.00 4.40
122 123 5.645067 TCCATCTCTTTATTGTCAACAGCTG 59.355 40.000 13.48 13.48 0.00 4.24
123 124 5.809001 TCCATCTCTTTATTGTCAACAGCT 58.191 37.500 0.00 0.00 0.00 4.24
124 125 6.690194 ATCCATCTCTTTATTGTCAACAGC 57.310 37.500 0.00 0.00 0.00 4.40
125 126 8.824781 CAGTATCCATCTCTTTATTGTCAACAG 58.175 37.037 0.00 0.00 0.00 3.16
126 127 7.770433 CCAGTATCCATCTCTTTATTGTCAACA 59.230 37.037 0.00 0.00 0.00 3.33
127 128 7.770897 ACCAGTATCCATCTCTTTATTGTCAAC 59.229 37.037 0.00 0.00 0.00 3.18
135 136 5.009710 CAGCGTACCAGTATCCATCTCTTTA 59.990 44.000 0.00 0.00 0.00 1.85
139 140 2.608261 GCAGCGTACCAGTATCCATCTC 60.608 54.545 0.00 0.00 0.00 2.75
145 146 1.269309 CCTCAGCAGCGTACCAGTATC 60.269 57.143 0.00 0.00 0.00 2.24
153 154 3.181475 CCTTAATTCTCCTCAGCAGCGTA 60.181 47.826 0.00 0.00 0.00 4.42
154 155 2.419297 CCTTAATTCTCCTCAGCAGCGT 60.419 50.000 0.00 0.00 0.00 5.07
155 156 2.159043 TCCTTAATTCTCCTCAGCAGCG 60.159 50.000 0.00 0.00 0.00 5.18
156 157 3.550437 TCCTTAATTCTCCTCAGCAGC 57.450 47.619 0.00 0.00 0.00 5.25
189 190 2.636830 CCTGCTCCTACCATGTTTCAG 58.363 52.381 0.00 0.00 0.00 3.02
191 192 1.559682 TCCCTGCTCCTACCATGTTTC 59.440 52.381 0.00 0.00 0.00 2.78
199 200 3.893324 GGGGATCCCTGCTCCTAC 58.107 66.667 30.08 7.21 41.34 3.18
218 219 0.400213 AACAAATCAGCCTGGGTCGA 59.600 50.000 0.00 0.00 0.00 4.20
248 251 3.895704 AAAAGGGTGCTAAAGGAGGAA 57.104 42.857 0.00 0.00 0.00 3.36
249 252 3.895704 AAAAAGGGTGCTAAAGGAGGA 57.104 42.857 0.00 0.00 0.00 3.71
298 303 4.608948 AGGAGTGAAAACAGTACAGAGG 57.391 45.455 0.00 0.00 0.00 3.69
301 306 7.787725 AAAGTAAGGAGTGAAAACAGTACAG 57.212 36.000 0.00 0.00 0.00 2.74
373 379 2.862536 CGTGTGTGAGCTCATAGGAATG 59.137 50.000 21.47 7.53 0.00 2.67
376 382 1.545841 ACGTGTGTGAGCTCATAGGA 58.454 50.000 21.47 3.73 0.00 2.94
384 390 0.599558 TAGGGTGTACGTGTGTGAGC 59.400 55.000 0.00 0.00 0.00 4.26
385 391 1.610038 TGTAGGGTGTACGTGTGTGAG 59.390 52.381 0.00 0.00 0.00 3.51
386 392 1.689984 TGTAGGGTGTACGTGTGTGA 58.310 50.000 0.00 0.00 0.00 3.58
394 400 4.382793 GGTCCTCAAAGATGTAGGGTGTAC 60.383 50.000 0.00 0.00 0.00 2.90
396 402 2.572104 GGTCCTCAAAGATGTAGGGTGT 59.428 50.000 0.00 0.00 0.00 4.16
400 406 7.726291 TCTCTATAAGGTCCTCAAAGATGTAGG 59.274 40.741 0.00 0.00 0.00 3.18
409 415 4.890581 GCTCAGTCTCTATAAGGTCCTCAA 59.109 45.833 0.00 0.00 0.00 3.02
411 417 3.824443 GGCTCAGTCTCTATAAGGTCCTC 59.176 52.174 0.00 0.00 0.00 3.71
413 419 2.554893 CGGCTCAGTCTCTATAAGGTCC 59.445 54.545 0.00 0.00 0.00 4.46
414 420 2.554893 CCGGCTCAGTCTCTATAAGGTC 59.445 54.545 0.00 0.00 0.00 3.85
416 422 1.271102 GCCGGCTCAGTCTCTATAAGG 59.729 57.143 22.15 0.00 0.00 2.69
420 426 2.294449 TATGCCGGCTCAGTCTCTAT 57.706 50.000 29.70 11.78 0.00 1.98
456 462 1.592223 AGGCGCCTACAGTGACTTC 59.408 57.895 31.86 0.00 44.04 3.01
459 465 2.202623 CGAGGCGCCTACAGTGAC 60.203 66.667 32.97 14.51 0.00 3.67
465 471 4.253257 CGAGGACGAGGCGCCTAC 62.253 72.222 32.97 22.82 42.66 3.18
494 500 0.773644 ATGCACTTTCACTGGGAGGT 59.226 50.000 0.00 0.00 0.00 3.85
499 505 1.503542 GGCGATGCACTTTCACTGG 59.496 57.895 0.00 0.00 0.00 4.00
500 506 1.133253 CGGCGATGCACTTTCACTG 59.867 57.895 0.00 0.00 0.00 3.66
502 508 1.573829 TTCCGGCGATGCACTTTCAC 61.574 55.000 9.30 0.00 0.00 3.18
503 509 0.886938 TTTCCGGCGATGCACTTTCA 60.887 50.000 9.30 0.00 0.00 2.69
504 510 0.454452 GTTTCCGGCGATGCACTTTC 60.454 55.000 9.30 0.00 0.00 2.62
508 514 3.810896 GGGTTTCCGGCGATGCAC 61.811 66.667 9.30 0.00 0.00 4.57
514 520 1.455248 TTATTTCAGGGTTTCCGGCG 58.545 50.000 0.00 0.00 38.33 6.46
536 542 3.438781 CCTGGTGCTCGCACTATTTTTAA 59.561 43.478 20.05 0.00 45.52 1.52
537 543 3.006940 CCTGGTGCTCGCACTATTTTTA 58.993 45.455 20.05 0.52 45.52 1.52
539 545 1.003118 TCCTGGTGCTCGCACTATTTT 59.997 47.619 20.05 0.00 45.52 1.82
545 551 1.448985 TTAAATCCTGGTGCTCGCAC 58.551 50.000 13.37 13.37 45.49 5.34
546 552 1.810151 GTTTAAATCCTGGTGCTCGCA 59.190 47.619 0.00 0.00 0.00 5.10
548 554 1.743394 GGGTTTAAATCCTGGTGCTCG 59.257 52.381 10.45 0.00 0.00 5.03
569 575 6.239887 GGGACAATGGTATTTCTAGCCTATCA 60.240 42.308 0.00 0.00 0.00 2.15
579 585 7.391833 GGATGATTAGAGGGACAATGGTATTTC 59.608 40.741 0.00 0.00 0.00 2.17
580 586 7.147141 TGGATGATTAGAGGGACAATGGTATTT 60.147 37.037 0.00 0.00 0.00 1.40
581 587 6.332635 TGGATGATTAGAGGGACAATGGTATT 59.667 38.462 0.00 0.00 0.00 1.89
586 592 5.439721 TGTTGGATGATTAGAGGGACAATG 58.560 41.667 0.00 0.00 0.00 2.82
588 594 5.512942 TTGTTGGATGATTAGAGGGACAA 57.487 39.130 0.00 0.00 0.00 3.18
611 617 3.872771 GAGTGAAAACACGAACCAACCTA 59.127 43.478 0.00 0.00 0.00 3.08
614 620 2.681344 AGGAGTGAAAACACGAACCAAC 59.319 45.455 0.00 0.00 0.00 3.77
616 622 2.702592 AGGAGTGAAAACACGAACCA 57.297 45.000 0.00 0.00 0.00 3.67
620 626 6.751157 TGATTAGTAAGGAGTGAAAACACGA 58.249 36.000 0.00 0.00 0.00 4.35
621 627 7.416154 TTGATTAGTAAGGAGTGAAAACACG 57.584 36.000 0.00 0.00 0.00 4.49
622 628 8.999431 TCATTGATTAGTAAGGAGTGAAAACAC 58.001 33.333 0.00 0.00 0.00 3.32
623 629 9.567776 TTCATTGATTAGTAAGGAGTGAAAACA 57.432 29.630 0.00 0.00 0.00 2.83
628 634 9.177608 CCAAATTCATTGATTAGTAAGGAGTGA 57.822 33.333 0.00 0.00 41.85 3.41
629 635 8.960591 ACCAAATTCATTGATTAGTAAGGAGTG 58.039 33.333 0.00 0.00 41.85 3.51
640 646 7.781324 AGGAGTTGTACCAAATTCATTGATT 57.219 32.000 0.00 0.00 41.85 2.57
644 650 6.548321 TGGTAGGAGTTGTACCAAATTCATT 58.452 36.000 0.00 0.00 45.67 2.57
676 682 7.646130 CGTGGCACGGTATGATTTATTTATTTT 59.354 33.333 31.19 0.00 38.08 1.82
677 683 7.136119 CGTGGCACGGTATGATTTATTTATTT 58.864 34.615 31.19 0.00 38.08 1.40
678 684 6.664515 CGTGGCACGGTATGATTTATTTATT 58.335 36.000 31.19 0.00 38.08 1.40
679 685 5.334569 GCGTGGCACGGTATGATTTATTTAT 60.335 40.000 37.33 0.00 42.82 1.40
684 691 1.292061 GCGTGGCACGGTATGATTTA 58.708 50.000 37.33 0.00 42.82 1.40
762 776 0.981277 GTGATCCGGGAAAGGGGAGA 60.981 60.000 0.00 0.00 35.40 3.71
763 777 1.271840 TGTGATCCGGGAAAGGGGAG 61.272 60.000 0.00 0.00 35.40 4.30
766 780 0.037590 TTGTGTGATCCGGGAAAGGG 59.962 55.000 0.00 0.00 0.00 3.95
803 817 3.498661 GGAGGGAAAAGCTGGAAAAGAGA 60.499 47.826 0.00 0.00 0.00 3.10
843 857 2.122167 CGGAGGTCTCGAGGAAGGG 61.122 68.421 13.56 0.00 0.00 3.95
844 858 3.515611 CGGAGGTCTCGAGGAAGG 58.484 66.667 13.56 0.00 0.00 3.46
978 992 4.452733 CTCGTCTTGGGGCCGGAC 62.453 72.222 5.05 0.00 0.00 4.79
1046 1060 4.641645 CCAACCAGTGGGCGCAGA 62.642 66.667 15.21 0.00 44.64 4.26
1131 1146 4.169696 TAATCGCCCTGGCACCGG 62.170 66.667 9.17 0.00 42.06 5.28
1136 1151 1.337823 ACGATATGTAATCGCCCTGGC 60.338 52.381 7.27 0.00 44.60 4.85
1277 1292 6.325286 GGAGATCACCTAGTTAGTCCAAGAAT 59.675 42.308 1.33 0.00 0.00 2.40
1299 1314 4.270325 GGCTTATAACTAGCAAACACGGAG 59.730 45.833 0.00 0.00 40.42 4.63
1304 1319 2.940410 GCCGGCTTATAACTAGCAAACA 59.060 45.455 22.15 0.00 40.42 2.83
1422 1437 1.112113 GCGGGACAAGATGGTCTAGA 58.888 55.000 0.00 0.00 37.91 2.43
1489 1504 2.136026 ACTTTCCCCTCCACTCAGTTT 58.864 47.619 0.00 0.00 0.00 2.66
1631 1649 2.164017 TGGCACCAATGATCACGAATTG 59.836 45.455 0.00 0.00 34.26 2.32
1830 1848 3.269178 GTGAAGAGCTTGATTGAGAGGG 58.731 50.000 0.00 0.00 0.00 4.30
1831 1849 3.933955 CTGTGAAGAGCTTGATTGAGAGG 59.066 47.826 0.00 0.00 0.00 3.69
2045 2064 1.802365 TGAAGAATCGACGTCGTCTCA 59.198 47.619 34.40 25.08 40.80 3.27
2082 2101 3.081061 AGCAAACAACAACACTCTGACA 58.919 40.909 0.00 0.00 0.00 3.58
2107 2126 0.539438 CCACTGTAGCCCTTTTGCCA 60.539 55.000 0.00 0.00 0.00 4.92
2108 2127 1.877576 GCCACTGTAGCCCTTTTGCC 61.878 60.000 0.00 0.00 0.00 4.52
2152 2171 4.935808 AGCCTTACAAGATTGTAGGAAACG 59.064 41.667 14.41 1.85 43.77 3.60
2286 2350 5.603596 AGCAAAAGTTGAGATTGATTGCAA 58.396 33.333 0.00 0.00 42.95 4.08
2287 2351 5.204409 AGCAAAAGTTGAGATTGATTGCA 57.796 34.783 9.83 0.00 42.95 4.08
2440 2506 3.492313 GGAATGCAAGTCGATGTTTGAC 58.508 45.455 10.32 4.19 36.60 3.18
2802 2886 8.079211 TCTCTACCTTAAATATCACTTGCAGT 57.921 34.615 0.00 0.00 0.00 4.40
2882 2966 2.345876 TGGCTTACACATCATGTCACG 58.654 47.619 0.00 0.00 42.09 4.35
2956 3040 8.843262 CATCATGTGCTGGAAGAAGAATAATTA 58.157 33.333 0.00 0.00 34.07 1.40
2957 3041 7.201884 CCATCATGTGCTGGAAGAAGAATAATT 60.202 37.037 0.00 0.00 33.33 1.40
2959 3043 5.591472 CCATCATGTGCTGGAAGAAGAATAA 59.409 40.000 0.00 0.00 33.33 1.40
3014 3100 1.577736 AGCTAAGGAGATGTGTGCCT 58.422 50.000 0.00 0.00 0.00 4.75
3016 3104 4.210120 CGAATAAGCTAAGGAGATGTGTGC 59.790 45.833 0.00 0.00 0.00 4.57
3286 3381 3.119884 TCTGTGTGCACTGTTCACTTTTG 60.120 43.478 19.41 0.70 35.58 2.44
3414 3509 8.017373 AGAACAAATCGACATGTATCAAACAAG 58.983 33.333 0.00 0.00 42.70 3.16
3538 3633 1.535028 CTAACGTGGCACTGCATTTCA 59.465 47.619 16.72 0.00 0.00 2.69
3598 3693 1.774254 ACAACTCCTTGGGACATGTGA 59.226 47.619 1.15 0.00 39.30 3.58
3646 3741 8.980596 ACCAAAATGGATCATACATTGTACAAT 58.019 29.630 15.47 15.47 40.96 2.71
3647 3742 8.359875 ACCAAAATGGATCATACATTGTACAA 57.640 30.769 11.41 11.41 40.96 2.41
3648 3743 7.953005 ACCAAAATGGATCATACATTGTACA 57.047 32.000 0.00 0.00 40.96 2.90
3651 3746 8.352201 CGATAACCAAAATGGATCATACATTGT 58.648 33.333 0.00 0.00 40.96 2.71
3652 3747 7.809331 CCGATAACCAAAATGGATCATACATTG 59.191 37.037 0.00 0.00 40.96 2.82
3653 3748 7.039784 CCCGATAACCAAAATGGATCATACATT 60.040 37.037 2.85 0.00 40.96 2.71
3654 3749 6.434028 CCCGATAACCAAAATGGATCATACAT 59.566 38.462 2.85 0.00 40.96 2.29
3655 3750 5.767665 CCCGATAACCAAAATGGATCATACA 59.232 40.000 2.85 0.00 40.96 2.29
3656 3751 5.335661 GCCCGATAACCAAAATGGATCATAC 60.336 44.000 2.85 0.00 40.96 2.39
3657 3752 4.764823 GCCCGATAACCAAAATGGATCATA 59.235 41.667 2.85 0.00 40.96 2.15
3658 3753 3.573967 GCCCGATAACCAAAATGGATCAT 59.426 43.478 2.85 0.00 40.96 2.45
3659 3754 2.955660 GCCCGATAACCAAAATGGATCA 59.044 45.455 2.85 0.00 40.96 2.92
3660 3755 2.955660 TGCCCGATAACCAAAATGGATC 59.044 45.455 2.85 0.00 40.96 3.36
3661 3756 3.025322 TGCCCGATAACCAAAATGGAT 57.975 42.857 2.85 0.00 40.96 3.41
3662 3757 2.516227 TGCCCGATAACCAAAATGGA 57.484 45.000 2.85 0.00 40.96 3.41
3663 3758 2.287547 CGATGCCCGATAACCAAAATGG 60.288 50.000 0.00 0.00 41.77 3.16
3664 3759 2.357637 ACGATGCCCGATAACCAAAATG 59.642 45.455 2.54 0.00 41.76 2.32
3665 3760 2.650322 ACGATGCCCGATAACCAAAAT 58.350 42.857 2.54 0.00 41.76 1.82
3666 3761 2.116827 ACGATGCCCGATAACCAAAA 57.883 45.000 2.54 0.00 41.76 2.44
3667 3762 2.093606 TGTACGATGCCCGATAACCAAA 60.094 45.455 2.54 0.00 41.76 3.28
3668 3763 1.481363 TGTACGATGCCCGATAACCAA 59.519 47.619 2.54 0.00 41.76 3.67
3669 3764 1.112950 TGTACGATGCCCGATAACCA 58.887 50.000 2.54 0.00 41.76 3.67
3670 3765 2.228138 TTGTACGATGCCCGATAACC 57.772 50.000 2.54 0.00 41.76 2.85
3671 3766 3.128349 ACATTGTACGATGCCCGATAAC 58.872 45.455 21.02 0.00 41.76 1.89
3672 3767 3.462483 ACATTGTACGATGCCCGATAA 57.538 42.857 21.02 0.00 41.76 1.75
3673 3768 4.218852 TCATACATTGTACGATGCCCGATA 59.781 41.667 21.02 7.72 41.76 2.92
3674 3769 3.006430 TCATACATTGTACGATGCCCGAT 59.994 43.478 21.02 8.36 41.76 4.18
3675 3770 2.362717 TCATACATTGTACGATGCCCGA 59.637 45.455 21.02 12.45 41.76 5.14
3676 3771 2.749776 TCATACATTGTACGATGCCCG 58.250 47.619 21.02 10.55 45.44 6.13
3677 3772 3.684788 GGATCATACATTGTACGATGCCC 59.315 47.826 21.02 10.10 0.00 5.36
3678 3773 4.314961 TGGATCATACATTGTACGATGCC 58.685 43.478 21.02 13.75 0.00 4.40
3679 3774 6.486253 AATGGATCATACATTGTACGATGC 57.514 37.500 21.02 14.94 37.18 3.91
4419 4629 0.537188 CGTCTATGCCAAGTCCACCT 59.463 55.000 0.00 0.00 0.00 4.00
4437 4647 0.955428 ACCAACATGGCAGCAGTACG 60.955 55.000 0.00 0.00 42.67 3.67
4464 4674 1.601759 GAGCAGCTGCCCACTGAAA 60.602 57.895 34.39 0.00 43.38 2.69
4465 4675 2.033141 GAGCAGCTGCCCACTGAA 59.967 61.111 34.39 0.00 43.38 3.02
4466 4676 2.599757 ATGAGCAGCTGCCCACTGA 61.600 57.895 34.39 11.46 43.38 3.41
4467 4677 2.045242 ATGAGCAGCTGCCCACTG 60.045 61.111 34.39 0.00 43.38 3.66
4468 4678 1.923006 ATCATGAGCAGCTGCCCACT 61.923 55.000 34.39 17.05 43.38 4.00
4469 4679 1.035932 AATCATGAGCAGCTGCCCAC 61.036 55.000 34.39 24.69 43.38 4.61
4470 4680 0.323999 AAATCATGAGCAGCTGCCCA 60.324 50.000 34.39 30.26 43.38 5.36
4471 4681 0.822164 AAAATCATGAGCAGCTGCCC 59.178 50.000 34.39 25.00 43.38 5.36
4472 4682 1.475280 TGAAAATCATGAGCAGCTGCC 59.525 47.619 34.39 24.89 43.38 4.85
4473 4683 2.163815 ACTGAAAATCATGAGCAGCTGC 59.836 45.455 31.53 31.53 42.49 5.25
4474 4684 3.427638 CCACTGAAAATCATGAGCAGCTG 60.428 47.826 10.11 10.11 0.00 4.24
4475 4685 2.753452 CCACTGAAAATCATGAGCAGCT 59.247 45.455 14.07 0.00 0.00 4.24
4476 4686 2.159282 CCCACTGAAAATCATGAGCAGC 60.159 50.000 14.07 0.00 0.00 5.25
4477 4687 2.159282 GCCCACTGAAAATCATGAGCAG 60.159 50.000 0.09 8.59 0.00 4.24
4478 4688 1.820519 GCCCACTGAAAATCATGAGCA 59.179 47.619 0.09 0.00 0.00 4.26
4479 4689 1.820519 TGCCCACTGAAAATCATGAGC 59.179 47.619 0.09 0.00 0.00 4.26
4480 4690 2.159282 GCTGCCCACTGAAAATCATGAG 60.159 50.000 0.09 0.00 0.00 2.90
4481 4691 1.820519 GCTGCCCACTGAAAATCATGA 59.179 47.619 0.00 0.00 0.00 3.07
4482 4692 1.822990 AGCTGCCCACTGAAAATCATG 59.177 47.619 0.00 0.00 0.00 3.07
4483 4693 1.822990 CAGCTGCCCACTGAAAATCAT 59.177 47.619 0.00 0.00 37.32 2.45
4484 4694 1.250328 CAGCTGCCCACTGAAAATCA 58.750 50.000 0.00 0.00 37.32 2.57
4485 4695 0.108945 GCAGCTGCCCACTGAAAATC 60.109 55.000 28.76 0.00 37.32 2.17
4486 4696 0.541296 AGCAGCTGCCCACTGAAAAT 60.541 50.000 34.39 9.65 43.38 1.82
4487 4697 1.152694 AGCAGCTGCCCACTGAAAA 60.153 52.632 34.39 0.00 43.38 2.29
4653 4903 9.546428 CTCAATGTGTACCTATCAACAATATGA 57.454 33.333 0.00 0.00 0.00 2.15
4729 4988 9.178758 GTCTTATGTAAGGTGAAAATGGAGATT 57.821 33.333 0.32 0.00 34.14 2.40
4764 5025 5.012893 GGAGAGTCATGAGAAAATTGGGTT 58.987 41.667 0.00 0.00 0.00 4.11
4797 5058 7.823745 AACAACATATCTTGTTCTTTGTCCT 57.176 32.000 3.51 0.00 45.55 3.85
4855 5116 6.059484 TGGTTTTGCCTAATATACTAGCACC 58.941 40.000 0.00 0.00 38.35 5.01
4947 5208 8.076178 GTGGACCATTTATAATTGTATGCTCAC 58.924 37.037 0.00 3.63 0.00 3.51
5031 5292 5.397326 ACGTCGTTTTAGGTGAGAAGATAC 58.603 41.667 0.00 0.00 0.00 2.24
5053 5314 2.240493 ACTGTAGGTGCTTGTGTGAC 57.760 50.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.