Multiple sequence alignment - TraesCS3D01G328300

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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 TraesCS3D01G328300 chr3D 100.000 6293 0 0 1 6293 441144021 441150313 0.000000e+00 11622.0
1 TraesCS3D01G328300 chr3D 88.684 433 43 4 2400 2827 441145984 441146415 2.010000e-144 523.0
2 TraesCS3D01G328300 chr3D 88.684 433 43 4 1964 2395 441146420 441146847 2.010000e-144 523.0
3 TraesCS3D01G328300 chr3D 84.422 199 26 5 5759 5952 441181458 441181656 2.320000e-44 191.0
4 TraesCS3D01G328300 chr3D 100.000 32 0 0 5719 5750 441181432 441181463 6.810000e-05 60.2
5 TraesCS3D01G328300 chr3A 90.374 2701 136 55 2996 5639 581273634 581276267 0.000000e+00 3434.0
6 TraesCS3D01G328300 chr3A 89.644 898 66 13 1513 2395 581272389 581273274 0.000000e+00 1118.0
7 TraesCS3D01G328300 chr3A 84.295 1178 100 41 373 1514 581271225 581272353 0.000000e+00 1072.0
8 TraesCS3D01G328300 chr3A 96.322 435 16 0 2400 2834 581272847 581273281 0.000000e+00 715.0
9 TraesCS3D01G328300 chr3A 90.349 487 25 16 5709 6175 581369792 581370276 2.490000e-173 619.0
10 TraesCS3D01G328300 chr3A 96.491 171 5 1 2830 2999 581273307 581273477 1.340000e-71 281.0
11 TraesCS3D01G328300 chr3A 80.617 227 38 5 6040 6264 581612224 581612446 3.020000e-38 171.0
12 TraesCS3D01G328300 chr3A 78.800 250 31 15 5709 5952 581611893 581612126 1.410000e-31 148.0
13 TraesCS3D01G328300 chr3A 91.358 81 7 0 998 1078 215482212 215482132 1.850000e-20 111.0
14 TraesCS3D01G328300 chr3A 98.077 52 1 0 2 53 581270751 581270802 2.420000e-14 91.6
15 TraesCS3D01G328300 chr3A 96.774 31 1 0 309 339 581271069 581271099 1.100000e-02 52.8
16 TraesCS3D01G328300 chr3B 89.805 1491 69 26 2957 4433 578401014 578402435 0.000000e+00 1834.0
17 TraesCS3D01G328300 chr3B 88.444 1073 71 22 4469 5507 578402435 578403488 0.000000e+00 1245.0
18 TraesCS3D01G328300 chr3B 90.086 817 36 11 1515 2314 578399709 578400497 0.000000e+00 1018.0
19 TraesCS3D01G328300 chr3B 86.241 814 55 28 727 1514 578398889 578399671 0.000000e+00 830.0
20 TraesCS3D01G328300 chr3B 88.042 577 43 12 5693 6253 578586913 578587479 0.000000e+00 660.0
21 TraesCS3D01G328300 chr3B 91.243 354 28 3 343 694 578396790 578397142 4.410000e-131 479.0
22 TraesCS3D01G328300 chr3B 86.740 362 27 13 2 344 578395754 578396113 3.560000e-102 383.0
23 TraesCS3D01G328300 chr3B 84.857 350 27 8 2400 2746 578400171 578400497 4.700000e-86 329.0
24 TraesCS3D01G328300 chr3B 92.562 121 7 2 2830 2949 578400856 578400975 8.390000e-39 172.0
25 TraesCS3D01G328300 chr3B 95.455 88 4 0 2747 2834 578400743 578400830 2.370000e-29 141.0
26 TraesCS3D01G328300 chr3B 95.122 82 4 0 2315 2396 578400743 578400824 5.120000e-26 130.0
27 TraesCS3D01G328300 chr3B 92.308 91 4 2 5620 5707 578586803 578586893 6.620000e-25 126.0
28 TraesCS3D01G328300 chr3B 91.358 81 7 0 998 1078 254779962 254779882 1.850000e-20 111.0
29 TraesCS3D01G328300 chr1B 91.990 387 29 2 3368 3752 543498127 543497741 5.550000e-150 542.0
30 TraesCS3D01G328300 chr1B 91.250 80 7 0 1000 1079 543500052 543499973 6.670000e-20 110.0
31 TraesCS3D01G328300 chr1A 92.348 379 29 0 3374 3752 499785376 499784998 2.000000e-149 540.0
32 TraesCS3D01G328300 chr1D 91.731 387 30 2 3368 3752 404138652 404138266 2.580000e-148 536.0
33 TraesCS3D01G328300 chr1D 92.593 81 6 0 999 1079 404139954 404139874 3.990000e-22 117.0
34 TraesCS3D01G328300 chr4D 89.125 377 41 0 3374 3750 312800700 312800324 2.660000e-128 470.0
35 TraesCS3D01G328300 chr2B 87.696 382 46 1 3371 3751 77170290 77170671 1.610000e-120 444.0
36 TraesCS3D01G328300 chr2B 91.139 79 7 0 1000 1078 77168977 77169055 2.400000e-19 108.0
37 TraesCS3D01G328300 chr2D 87.566 378 47 0 3374 3751 49877341 49877718 7.490000e-119 438.0
38 TraesCS3D01G328300 chr2D 85.294 306 41 3 4845 5148 641975872 641976175 4.740000e-81 313.0
39 TraesCS3D01G328300 chr2D 85.321 109 14 2 1000 1107 49875921 49876028 1.850000e-20 111.0
40 TraesCS3D01G328300 chr2A 87.302 378 48 0 3374 3751 51583544 51583921 3.480000e-117 433.0
41 TraesCS3D01G328300 chr2A 85.849 106 12 3 1000 1104 51582360 51582463 6.670000e-20 110.0
42 TraesCS3D01G328300 chr6A 93.478 46 2 1 5952 5996 4678178 4678223 4.070000e-07 67.6


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 TraesCS3D01G328300 chr3D 441144021 441150313 6292 False 11622.000000 11622 100.000000 1 6293 1 chr3D.!!$F1 6292
1 TraesCS3D01G328300 chr3D 441145984 441146847 863 False 523.000000 523 88.684000 1964 2827 2 chr3D.!!$F2 863
2 TraesCS3D01G328300 chr3A 581270751 581276267 5516 False 966.342857 3434 93.139571 2 5639 7 chr3A.!!$F2 5637
3 TraesCS3D01G328300 chr3B 578395754 578403488 7734 False 656.100000 1834 90.055500 2 5507 10 chr3B.!!$F1 5505
4 TraesCS3D01G328300 chr3B 578586803 578587479 676 False 393.000000 660 90.175000 5620 6253 2 chr3B.!!$F2 633
5 TraesCS3D01G328300 chr1B 543497741 543500052 2311 True 326.000000 542 91.620000 1000 3752 2 chr1B.!!$R1 2752
6 TraesCS3D01G328300 chr1D 404138266 404139954 1688 True 326.500000 536 92.162000 999 3752 2 chr1D.!!$R1 2753
7 TraesCS3D01G328300 chr2B 77168977 77170671 1694 False 276.000000 444 89.417500 1000 3751 2 chr2B.!!$F1 2751
8 TraesCS3D01G328300 chr2D 49875921 49877718 1797 False 274.500000 438 86.443500 1000 3751 2 chr2D.!!$F2 2751
9 TraesCS3D01G328300 chr2A 51582360 51583921 1561 False 271.500000 433 86.575500 1000 3751 2 chr2A.!!$F1 2751

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
166 179 0.176910 GGCTTACACCTCTCTGCCTC 59.823 60.000 0.00 0.0 37.58 4.70 F
1280 3884 0.179004 TTGGTTGTCTCGGCATGGTT 60.179 50.000 0.00 0.0 0.00 3.67 F
1441 4052 0.478072 AGGCCTGTGGTGATTTGACA 59.522 50.000 3.11 0.0 0.00 3.58 F
1591 4240 0.643822 ATTTGGGGGAAGGGCATCAT 59.356 50.000 0.00 0.0 0.00 2.45 F
1735 4400 1.545582 GCTTGCTTACCATGCTTCCAA 59.454 47.619 0.00 0.0 40.42 3.53 F
3545 8364 2.223803 AGATGAAGGACACCGACTCT 57.776 50.000 0.00 0.0 0.00 3.24 F
3755 8574 0.038166 TGATGGCCAAGTGAGGAACC 59.962 55.000 10.96 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 4037 0.238289 GCCGTGTCAAATCACCACAG 59.762 55.000 0.00 0.00 35.18 3.66 R
2954 7575 6.237648 GCATAAAGCATTCAACGGATTTTGAG 60.238 38.462 0.00 0.00 44.79 3.02 R
3342 8161 3.118629 TGCCACCTCATGATAAGACAGAC 60.119 47.826 0.00 0.00 0.00 3.51 R
3545 8364 0.325110 CCTCCTTGAGCTCCTCCTCA 60.325 60.000 12.15 0.00 39.94 3.86 R
3755 8574 1.923148 AGGGTTATTTCAGAGGGGGTG 59.077 52.381 0.00 0.00 0.00 4.61 R
5122 9998 0.175760 TCCAATTTCGCTCTCGGGAG 59.824 55.000 8.32 8.32 42.18 4.30 R
6012 10941 0.388907 GTACGCGAGTTGGCACCTAA 60.389 55.000 15.93 0.00 46.40 2.69 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
43 44 4.458295 CAGAAATGACCTCTTTGTGCAGAT 59.542 41.667 0.00 0.00 0.00 2.90
62 63 5.007332 GCAGATGAATTGCAAAATCATTCCC 59.993 40.000 23.86 15.32 41.17 3.97
80 81 7.792032 TCATTCCCGATTCTTCACTATACTTT 58.208 34.615 0.00 0.00 0.00 2.66
104 105 0.470766 AGTGAAACAGGGCCACGTAA 59.529 50.000 6.18 0.00 41.43 3.18
105 106 1.134037 AGTGAAACAGGGCCACGTAAA 60.134 47.619 6.18 0.00 41.43 2.01
129 130 1.605457 GGACACGTTGATGTGCTCTCA 60.605 52.381 3.34 0.00 43.74 3.27
164 177 0.324943 TTGGCTTACACCTCTCTGCC 59.675 55.000 0.00 0.00 40.62 4.85
166 179 0.176910 GGCTTACACCTCTCTGCCTC 59.823 60.000 0.00 0.00 37.58 4.70
167 180 1.190643 GCTTACACCTCTCTGCCTCT 58.809 55.000 0.00 0.00 0.00 3.69
168 181 1.136110 GCTTACACCTCTCTGCCTCTC 59.864 57.143 0.00 0.00 0.00 3.20
169 182 1.754226 CTTACACCTCTCTGCCTCTCC 59.246 57.143 0.00 0.00 0.00 3.71
189 202 5.190925 TCTCCTCTCTTCTCTACTGTTAGCT 59.809 44.000 0.00 0.00 0.00 3.32
223 236 2.248835 CGGCAAGTCGGGTTCGTTT 61.249 57.895 0.00 0.00 37.69 3.60
309 335 9.347240 CAAGATGAGTGAGATATTTTAACCCAT 57.653 33.333 0.00 0.00 0.00 4.00
310 336 8.915057 AGATGAGTGAGATATTTTAACCCATG 57.085 34.615 0.00 0.00 0.00 3.66
344 395 9.994432 CAACTTCATCCAAAAAGATACTGATAC 57.006 33.333 0.00 0.00 0.00 2.24
407 1137 5.317733 TGGTTATTTGATTTTAGGCGTGG 57.682 39.130 0.00 0.00 0.00 4.94
426 1156 1.564348 GGGGTGCTCCTCAATCCTTTA 59.436 52.381 4.53 0.00 33.58 1.85
464 1194 4.201881 GGTTTTGTATGTATGAGGCGAACC 60.202 45.833 0.00 0.00 0.00 3.62
511 1241 9.461312 AAGAATGCAACACAAATTCTATACCTA 57.539 29.630 0.00 0.00 39.22 3.08
586 1317 3.375782 AGACAAGCAAGCCAATGAAAC 57.624 42.857 0.00 0.00 0.00 2.78
613 1344 7.201688 GGAGAGAAAAAGATCAAATACAGAGGC 60.202 40.741 0.00 0.00 0.00 4.70
625 1356 0.595588 ACAGAGGCAGATATCTCGCG 59.404 55.000 1.03 0.00 35.34 5.87
627 1358 0.893270 AGAGGCAGATATCTCGCGCT 60.893 55.000 5.56 9.32 35.34 5.92
630 1361 1.583986 GCAGATATCTCGCGCTCCT 59.416 57.895 5.56 0.00 0.00 3.69
639 1370 2.656651 CGCGCTCCTGAATCCTCG 60.657 66.667 5.56 0.00 0.00 4.63
642 1373 1.880340 CGCTCCTGAATCCTCGCAC 60.880 63.158 0.00 0.00 0.00 5.34
643 1374 1.522580 GCTCCTGAATCCTCGCACC 60.523 63.158 0.00 0.00 0.00 5.01
713 3169 8.359060 AGAAAATATTCTCAGACAATACTCGC 57.641 34.615 0.00 0.00 42.26 5.03
715 3171 8.492673 AAAATATTCTCAGACAATACTCGCAA 57.507 30.769 0.00 0.00 0.00 4.85
716 3172 8.492673 AAATATTCTCAGACAATACTCGCAAA 57.507 30.769 0.00 0.00 0.00 3.68
717 3173 8.492673 AATATTCTCAGACAATACTCGCAAAA 57.507 30.769 0.00 0.00 0.00 2.44
718 3174 6.801539 ATTCTCAGACAATACTCGCAAAAA 57.198 33.333 0.00 0.00 0.00 1.94
1110 3619 1.309102 CCCTTCCCTTCCCCCATCT 60.309 63.158 0.00 0.00 0.00 2.90
1235 3839 4.552365 ATCTGATGGCGTGCCGGG 62.552 66.667 2.18 0.00 39.42 5.73
1275 3879 1.573829 GCGATTTGGTTGTCTCGGCA 61.574 55.000 0.00 0.00 0.00 5.69
1276 3880 1.086696 CGATTTGGTTGTCTCGGCAT 58.913 50.000 0.00 0.00 0.00 4.40
1278 3882 1.133025 GATTTGGTTGTCTCGGCATGG 59.867 52.381 0.00 0.00 0.00 3.66
1280 3884 0.179004 TTGGTTGTCTCGGCATGGTT 60.179 50.000 0.00 0.00 0.00 3.67
1282 3886 0.521735 GGTTGTCTCGGCATGGTTTC 59.478 55.000 0.00 0.00 0.00 2.78
1284 3888 1.880027 GTTGTCTCGGCATGGTTTCTT 59.120 47.619 0.00 0.00 0.00 2.52
1286 3890 3.627395 TGTCTCGGCATGGTTTCTTAT 57.373 42.857 0.00 0.00 0.00 1.73
1338 3949 3.334691 TCATCAATCTGTTCCGTGGTTC 58.665 45.455 0.00 0.00 0.00 3.62
1346 3957 1.156736 GTTCCGTGGTTCAGGTCATG 58.843 55.000 0.00 0.00 0.00 3.07
1418 4029 1.202200 GGTGTGCGTTTTGTGCTTGTA 60.202 47.619 0.00 0.00 0.00 2.41
1419 4030 2.542824 GGTGTGCGTTTTGTGCTTGTAT 60.543 45.455 0.00 0.00 0.00 2.29
1420 4031 2.467305 GTGTGCGTTTTGTGCTTGTATG 59.533 45.455 0.00 0.00 0.00 2.39
1421 4032 2.098280 TGTGCGTTTTGTGCTTGTATGT 59.902 40.909 0.00 0.00 0.00 2.29
1426 4037 3.669557 CGTTTTGTGCTTGTATGTAGGCC 60.670 47.826 0.00 0.00 0.00 5.19
1430 4041 2.009774 GTGCTTGTATGTAGGCCTGTG 58.990 52.381 17.99 0.00 0.00 3.66
1441 4052 0.478072 AGGCCTGTGGTGATTTGACA 59.522 50.000 3.11 0.00 0.00 3.58
1498 4110 4.045334 TCAGGAACAAGGATGGGGTAAATT 59.955 41.667 0.00 0.00 0.00 1.82
1591 4240 0.643822 ATTTGGGGGAAGGGCATCAT 59.356 50.000 0.00 0.00 0.00 2.45
1735 4400 1.545582 GCTTGCTTACCATGCTTCCAA 59.454 47.619 0.00 0.00 40.42 3.53
1738 4403 4.824289 CTTGCTTACCATGCTTCCAATTT 58.176 39.130 0.00 0.00 0.00 1.82
1763 4428 4.625028 TCGCATCAGATTCCTTAGATGTG 58.375 43.478 8.14 8.14 45.50 3.21
1773 4438 6.609212 AGATTCCTTAGATGTGTCTGCTTCTA 59.391 38.462 0.00 0.00 35.87 2.10
1779 4444 7.147983 CCTTAGATGTGTCTGCTTCTAGTTACT 60.148 40.741 0.00 0.00 35.87 2.24
1780 4445 6.202516 AGATGTGTCTGCTTCTAGTTACTC 57.797 41.667 0.00 0.00 32.13 2.59
1834 4499 2.360165 CCTGGCCATTCAGTTTAGCATC 59.640 50.000 5.51 0.00 33.14 3.91
1841 4506 4.326205 CATTCAGTTTAGCATCGACAACG 58.674 43.478 0.00 0.00 41.26 4.10
2954 7575 5.507315 CCATTTGTGTTTGGAAGGTGTAGAC 60.507 44.000 0.00 0.00 34.81 2.59
3284 8102 3.947834 ACCTTCTGCTGTATATTTGTGGC 59.052 43.478 0.00 0.00 0.00 5.01
3342 8161 7.076362 GCACATTGCACATATTCTCTCTTATG 58.924 38.462 0.00 0.00 44.26 1.90
3363 8182 3.118629 TGTCTGTCTTATCATGAGGTGGC 60.119 47.826 0.09 0.00 0.00 5.01
3364 8183 3.106827 TCTGTCTTATCATGAGGTGGCA 58.893 45.455 0.09 0.22 0.00 4.92
3366 8185 3.812262 TGTCTTATCATGAGGTGGCATG 58.188 45.455 0.09 0.00 45.41 4.06
3545 8364 2.223803 AGATGAAGGACACCGACTCT 57.776 50.000 0.00 0.00 0.00 3.24
3755 8574 0.038166 TGATGGCCAAGTGAGGAACC 59.962 55.000 10.96 0.00 0.00 3.62
3784 8605 7.285629 CCCCTCTGAAATAACCCTTTCTATTTC 59.714 40.741 7.35 7.35 41.67 2.17
3900 8724 2.378886 TGTAGTCACTGAGGGGAGAAGA 59.621 50.000 0.00 0.00 0.00 2.87
3902 8726 1.190643 GTCACTGAGGGGAGAAGAGG 58.809 60.000 0.00 0.00 0.00 3.69
3904 8728 1.306568 ACTGAGGGGAGAAGAGGCC 60.307 63.158 0.00 0.00 0.00 5.19
3905 8729 1.306482 CTGAGGGGAGAAGAGGCCA 60.306 63.158 5.01 0.00 0.00 5.36
3906 8730 1.306482 TGAGGGGAGAAGAGGCCAG 60.306 63.158 5.01 0.00 0.00 4.85
3907 8731 1.002274 GAGGGGAGAAGAGGCCAGA 59.998 63.158 5.01 0.00 0.00 3.86
3908 8732 0.399806 GAGGGGAGAAGAGGCCAGAT 60.400 60.000 5.01 0.00 0.00 2.90
3909 8733 0.693767 AGGGGAGAAGAGGCCAGATG 60.694 60.000 5.01 0.00 0.00 2.90
3910 8734 0.985490 GGGGAGAAGAGGCCAGATGT 60.985 60.000 5.01 0.00 0.00 3.06
3951 8775 2.162008 GTCACGGACTTCTCCTGTACTC 59.838 54.545 0.00 0.00 33.79 2.59
3990 8819 0.463620 TTGGTTGGGTTGCTTCTTGC 59.536 50.000 0.00 0.00 43.25 4.01
4014 8843 1.088306 TGCTTGTCGTTCGGTTTGTT 58.912 45.000 0.00 0.00 0.00 2.83
4015 8844 1.202087 TGCTTGTCGTTCGGTTTGTTG 60.202 47.619 0.00 0.00 0.00 3.33
4016 8845 1.062880 GCTTGTCGTTCGGTTTGTTGA 59.937 47.619 0.00 0.00 0.00 3.18
4189 9020 1.004044 CAATCACCTGTGGAGCCTCTT 59.996 52.381 0.00 0.00 0.00 2.85
4190 9021 0.908198 ATCACCTGTGGAGCCTCTTC 59.092 55.000 0.00 0.00 0.00 2.87
4236 9067 4.700365 TCGAGTCGTGCGTGCCAG 62.700 66.667 13.12 0.00 0.00 4.85
4245 9076 1.302752 TGCGTGCCAGAGAATTGCT 60.303 52.632 0.00 0.00 0.00 3.91
4265 9099 2.084681 CGTAGGCCGTTGTCACGTC 61.085 63.158 0.00 0.00 45.62 4.34
4313 9147 1.099879 GCCAGGCAGCTCGATTTGAT 61.100 55.000 6.55 0.00 0.00 2.57
4317 9151 0.659957 GGCAGCTCGATTTGATGTCC 59.340 55.000 0.00 0.00 0.00 4.02
4320 9154 0.811616 AGCTCGATTTGATGTCCGGC 60.812 55.000 0.00 0.00 0.00 6.13
4321 9155 1.089481 GCTCGATTTGATGTCCGGCA 61.089 55.000 0.00 0.00 0.00 5.69
4322 9156 1.368641 CTCGATTTGATGTCCGGCAA 58.631 50.000 0.00 0.00 0.00 4.52
4323 9157 1.062587 CTCGATTTGATGTCCGGCAAC 59.937 52.381 0.00 0.00 0.00 4.17
4336 9170 4.077188 GCAACGTGGCTGCGACTC 62.077 66.667 7.95 0.00 35.59 3.36
4337 9171 3.414700 CAACGTGGCTGCGACTCC 61.415 66.667 12.88 0.00 35.59 3.85
4338 9172 3.616721 AACGTGGCTGCGACTCCT 61.617 61.111 12.88 0.00 35.59 3.69
4339 9173 3.865929 AACGTGGCTGCGACTCCTG 62.866 63.158 12.88 0.00 35.59 3.86
4340 9174 4.363990 CGTGGCTGCGACTCCTGT 62.364 66.667 12.88 0.00 0.00 4.00
4341 9175 2.740055 GTGGCTGCGACTCCTGTG 60.740 66.667 7.59 0.00 0.00 3.66
4342 9176 4.007644 TGGCTGCGACTCCTGTGG 62.008 66.667 0.00 0.00 0.00 4.17
4388 9222 1.301423 CTTCTCGAGACGGTCCCTAG 58.699 60.000 16.36 3.14 0.00 3.02
4432 9268 2.279937 GAACGCGACGCCATTGTCTC 62.280 60.000 15.93 3.68 36.71 3.36
4433 9269 2.507102 CGCGACGCCATTGTCTCT 60.507 61.111 15.34 0.00 36.71 3.10
4436 9272 1.687494 GCGACGCCATTGTCTCTGTC 61.687 60.000 9.14 0.00 36.71 3.51
4442 9278 1.406069 GCCATTGTCTCTGTCGATGGT 60.406 52.381 12.06 0.00 44.45 3.55
4470 9306 3.937079 TCGTGCGGAGATATATCATACGT 59.063 43.478 15.08 0.00 0.00 3.57
4496 9332 1.586154 GGCCAGTGGACATGGTTTCG 61.586 60.000 15.20 0.00 40.17 3.46
4499 9335 0.238289 CAGTGGACATGGTTTCGTGC 59.762 55.000 0.00 0.00 33.32 5.34
4500 9336 0.179032 AGTGGACATGGTTTCGTGCA 60.179 50.000 0.00 0.00 33.32 4.57
4509 9345 3.134574 TGGTTTCGTGCAGGAATAACT 57.865 42.857 21.46 0.00 0.00 2.24
4558 9395 6.670695 ATATATGCCATCCAAACCCTTTTC 57.329 37.500 0.00 0.00 0.00 2.29
4630 9467 6.017770 TGTTGTGTTCGTATAAAGTGAAAGGG 60.018 38.462 0.00 0.00 0.00 3.95
4671 9508 6.683110 GCTCAAGAGAGGGATTTATTCGTACA 60.683 42.308 0.32 0.00 42.33 2.90
4734 9572 0.038166 TGCAGACCCCCTCAATGAAC 59.962 55.000 0.00 0.00 0.00 3.18
4736 9574 0.392998 CAGACCCCCTCAATGAACGG 60.393 60.000 0.00 0.00 0.00 4.44
4752 9590 1.173444 ACGGACACGAGCTCTTCTGT 61.173 55.000 12.85 12.95 44.60 3.41
4753 9591 0.455295 CGGACACGAGCTCTTCTGTC 60.455 60.000 20.05 20.05 44.60 3.51
4754 9592 0.598562 GGACACGAGCTCTTCTGTCA 59.401 55.000 25.36 0.00 36.50 3.58
4755 9593 1.402194 GGACACGAGCTCTTCTGTCAG 60.402 57.143 25.36 8.37 36.50 3.51
4756 9594 1.537638 GACACGAGCTCTTCTGTCAGA 59.462 52.381 21.94 0.00 35.66 3.27
4768 9609 7.041235 AGCTCTTCTGTCAGATTCTTTGAAAAG 60.041 37.037 2.68 0.00 37.36 2.27
4832 9674 1.027357 GCATTCACTCCCGCATGAAT 58.973 50.000 0.00 0.00 44.52 2.57
4833 9675 2.158769 AGCATTCACTCCCGCATGAATA 60.159 45.455 0.00 0.00 42.35 1.75
4834 9676 2.225019 GCATTCACTCCCGCATGAATAG 59.775 50.000 0.00 0.00 42.35 1.73
4835 9677 3.470709 CATTCACTCCCGCATGAATAGT 58.529 45.455 0.00 0.00 42.35 2.12
4836 9678 4.631131 CATTCACTCCCGCATGAATAGTA 58.369 43.478 0.00 0.00 42.35 1.82
4837 9679 3.728076 TCACTCCCGCATGAATAGTAC 57.272 47.619 0.00 0.00 0.00 2.73
4839 9681 2.365617 CACTCCCGCATGAATAGTACCT 59.634 50.000 0.00 0.00 0.00 3.08
4840 9682 2.628657 ACTCCCGCATGAATAGTACCTC 59.371 50.000 0.00 0.00 0.00 3.85
4842 9684 1.971357 CCCGCATGAATAGTACCTCCT 59.029 52.381 0.00 0.00 0.00 3.69
4843 9685 2.289072 CCCGCATGAATAGTACCTCCTG 60.289 54.545 0.00 0.00 0.00 3.86
4844 9686 2.289072 CCGCATGAATAGTACCTCCTGG 60.289 54.545 0.00 0.00 39.83 4.45
4892 9755 3.752747 TCATGTTAGTGTCACAAGCATGG 59.247 43.478 22.08 11.53 34.68 3.66
4930 9796 3.071479 GGAACGGAGCAATAGTGTTTCA 58.929 45.455 0.00 0.00 0.00 2.69
4967 9833 6.375945 AACAAATTTGAGGTGGCATTTTTC 57.624 33.333 24.64 0.00 0.00 2.29
4968 9834 4.821260 ACAAATTTGAGGTGGCATTTTTCC 59.179 37.500 24.64 0.00 0.00 3.13
5040 9908 3.688673 CCTTTTTGCCTGAAACTTTGCAA 59.311 39.130 0.00 0.00 41.57 4.08
5045 9913 3.287222 TGCCTGAAACTTTGCAAGTAGT 58.713 40.909 0.00 0.00 41.91 2.73
5120 9996 8.663911 ACATTTCAAAAATCATTTTTCACACGT 58.336 25.926 5.04 0.00 40.65 4.49
5121 9997 8.935941 CATTTCAAAAATCATTTTTCACACGTG 58.064 29.630 15.48 15.48 40.65 4.49
5122 9998 6.030379 TCAAAAATCATTTTTCACACGTGC 57.970 33.333 17.22 0.00 40.65 5.34
5123 9999 5.809562 TCAAAAATCATTTTTCACACGTGCT 59.190 32.000 17.22 0.00 40.65 4.40
5124 10000 5.888412 AAAATCATTTTTCACACGTGCTC 57.112 34.783 17.22 0.00 28.82 4.26
5125 10001 3.559238 ATCATTTTTCACACGTGCTCC 57.441 42.857 17.22 0.00 0.00 4.70
5126 10002 1.606668 TCATTTTTCACACGTGCTCCC 59.393 47.619 17.22 0.00 0.00 4.30
5127 10003 0.591170 ATTTTTCACACGTGCTCCCG 59.409 50.000 17.22 0.00 0.00 5.14
5128 10004 0.462225 TTTTTCACACGTGCTCCCGA 60.462 50.000 17.22 1.61 0.00 5.14
5148 10024 2.678336 GAGAGCGAAATTGGATTTCCGT 59.322 45.455 7.58 0.00 44.40 4.69
5172 10048 5.534654 TGAAGGCTTATGCATATGTAAACCC 59.465 40.000 17.98 11.48 41.91 4.11
5173 10049 5.324832 AGGCTTATGCATATGTAAACCCT 57.675 39.130 17.98 13.14 41.91 4.34
5174 10050 5.072741 AGGCTTATGCATATGTAAACCCTG 58.927 41.667 17.98 0.00 41.91 4.45
5175 10051 4.827284 GGCTTATGCATATGTAAACCCTGT 59.173 41.667 17.98 0.00 41.91 4.00
5176 10052 5.301805 GGCTTATGCATATGTAAACCCTGTT 59.698 40.000 17.98 0.00 41.91 3.16
5177 10053 6.183360 GGCTTATGCATATGTAAACCCTGTTT 60.183 38.462 17.98 0.00 41.91 2.83
5311 10187 1.144969 GCTGAAACCATCGAACGTGA 58.855 50.000 0.00 0.00 0.00 4.35
5483 10375 7.251704 TGCAGAAAAAGAAGAAAGTGTAGAG 57.748 36.000 0.00 0.00 0.00 2.43
5492 10384 1.727335 GAAAGTGTAGAGACAAGGCGC 59.273 52.381 0.00 0.00 37.31 6.53
5514 10406 1.989430 CGGAGCTTGAGAGTTGAGAC 58.011 55.000 0.00 0.00 0.00 3.36
5515 10407 1.730772 CGGAGCTTGAGAGTTGAGACG 60.731 57.143 0.00 0.00 0.00 4.18
5516 10408 1.271102 GGAGCTTGAGAGTTGAGACGT 59.729 52.381 0.00 0.00 0.00 4.34
5538 10430 0.970937 ACCATCACGGACAGGTCGAT 60.971 55.000 0.00 0.00 38.63 3.59
5587 10479 0.872881 AAAACACGGACAGGTCGACG 60.873 55.000 9.92 0.00 0.00 5.12
5691 10583 2.165301 CGCCTACGCTGCTGTAACC 61.165 63.158 0.00 0.00 0.00 2.85
5697 10626 0.105964 ACGCTGCTGTAACCACTTGA 59.894 50.000 0.00 0.00 0.00 3.02
5776 10705 4.243008 TTGCCGCCCACTTCGACA 62.243 61.111 0.00 0.00 0.00 4.35
5782 10711 2.251642 GCCCACTTCGACACCACAC 61.252 63.158 0.00 0.00 0.00 3.82
5786 10715 0.104120 CACTTCGACACCACACCAGA 59.896 55.000 0.00 0.00 0.00 3.86
5791 10720 1.598130 GACACCACACCAGAGCACC 60.598 63.158 0.00 0.00 0.00 5.01
5812 10741 2.796193 CCCACGGCCATCGATCTGA 61.796 63.158 2.24 0.00 42.43 3.27
5836 10765 2.176055 CTTTGCTCTGCTGCAGCG 59.824 61.111 32.11 25.46 44.27 5.18
5855 10784 1.875576 CGATGTGCTGCCCTAATCTCC 60.876 57.143 0.00 0.00 0.00 3.71
5856 10785 0.475906 ATGTGCTGCCCTAATCTCCC 59.524 55.000 0.00 0.00 0.00 4.30
5980 10909 0.384669 GCGGCGAGAGTTAGGTATGT 59.615 55.000 12.98 0.00 0.00 2.29
5997 10926 5.068198 AGGTATGTCATGTGATTGCATTTCC 59.932 40.000 0.00 0.00 0.00 3.13
5999 10928 3.080319 TGTCATGTGATTGCATTTCCGA 58.920 40.909 0.00 0.00 0.00 4.55
6045 10974 0.378257 GCGTACCATGGACATGCTTG 59.622 55.000 21.47 0.00 37.49 4.01
6049 10978 1.771565 ACCATGGACATGCTTGGATG 58.228 50.000 21.47 0.59 37.49 3.51
6050 10979 1.285667 ACCATGGACATGCTTGGATGA 59.714 47.619 21.47 0.00 37.49 2.92
6051 10980 2.091499 ACCATGGACATGCTTGGATGAT 60.091 45.455 21.47 0.00 37.49 2.45
6069 10998 6.071952 TGGATGATTTGGTAGAAGAAACAAGC 60.072 38.462 0.00 0.00 0.00 4.01
6074 11003 4.150897 TGGTAGAAGAAACAAGCACTGT 57.849 40.909 0.00 0.00 41.27 3.55
6125 11054 2.661718 TGGGGAATAAAAGGCGGAATC 58.338 47.619 0.00 0.00 0.00 2.52
6140 11072 2.779506 GGAATCCTTAGGCGGTAATGG 58.220 52.381 0.00 0.00 0.00 3.16
6152 11088 2.822764 CGGTAATGGGTAAGCAGTCTC 58.177 52.381 0.00 0.00 0.00 3.36
6182 11118 4.181578 GTGTGGACTTAATGTACGAGCAT 58.818 43.478 0.00 0.00 30.20 3.79
6188 11124 6.923508 TGGACTTAATGTACGAGCATCAATAG 59.076 38.462 0.00 0.00 33.17 1.73
6190 11126 8.080417 GGACTTAATGTACGAGCATCAATAGTA 58.920 37.037 0.00 0.00 33.17 1.82
6191 11127 9.119329 GACTTAATGTACGAGCATCAATAGTAG 57.881 37.037 0.00 0.00 33.17 2.57
6192 11128 8.082852 ACTTAATGTACGAGCATCAATAGTAGG 58.917 37.037 0.00 0.00 33.17 3.18
6193 11129 4.848562 TGTACGAGCATCAATAGTAGGG 57.151 45.455 0.00 0.00 33.17 3.53
6194 11130 4.212716 TGTACGAGCATCAATAGTAGGGT 58.787 43.478 0.00 0.00 33.17 4.34
6221 11157 1.651737 TCTCAAATGGAAGGGGACGA 58.348 50.000 0.00 0.00 0.00 4.20
6226 11162 1.584724 AATGGAAGGGGACGAGTCAT 58.415 50.000 5.55 0.00 0.00 3.06
6229 11165 1.617947 GGAAGGGGACGAGTCATGCT 61.618 60.000 5.55 0.00 0.00 3.79
6231 11167 0.036010 AAGGGGACGAGTCATGCTTG 60.036 55.000 5.55 0.00 34.71 4.01
6241 11186 3.673338 CGAGTCATGCTTGAAAACTCGTA 59.327 43.478 23.16 0.00 39.38 3.43
6245 11190 4.211374 GTCATGCTTGAAAACTCGTACAGT 59.789 41.667 3.51 0.00 32.40 3.55
6253 11198 7.168804 GCTTGAAAACTCGTACAGTTAGTAAGT 59.831 37.037 9.98 0.00 45.32 2.24
6254 11199 7.919313 TGAAAACTCGTACAGTTAGTAAGTG 57.081 36.000 14.93 14.93 45.32 3.16
6255 11200 7.706159 TGAAAACTCGTACAGTTAGTAAGTGA 58.294 34.615 21.92 5.49 45.32 3.41
6256 11201 7.859377 TGAAAACTCGTACAGTTAGTAAGTGAG 59.141 37.037 21.92 12.14 45.32 3.51
6257 11202 5.294050 ACTCGTACAGTTAGTAAGTGAGC 57.706 43.478 21.92 13.13 34.54 4.26
6258 11203 4.758674 ACTCGTACAGTTAGTAAGTGAGCA 59.241 41.667 21.92 6.15 34.54 4.26
6259 11204 5.240183 ACTCGTACAGTTAGTAAGTGAGCAA 59.760 40.000 21.92 6.22 34.54 3.91
6260 11205 6.072064 ACTCGTACAGTTAGTAAGTGAGCAAT 60.072 38.462 21.92 4.27 34.54 3.56
6261 11206 7.120285 ACTCGTACAGTTAGTAAGTGAGCAATA 59.880 37.037 21.92 3.38 34.54 1.90
6262 11207 7.993101 TCGTACAGTTAGTAAGTGAGCAATAT 58.007 34.615 21.92 2.98 35.76 1.28
6263 11208 8.464404 TCGTACAGTTAGTAAGTGAGCAATATT 58.536 33.333 21.92 2.34 35.76 1.28
6264 11209 9.084164 CGTACAGTTAGTAAGTGAGCAATATTT 57.916 33.333 21.92 1.70 35.76 1.40
6267 11212 9.502091 ACAGTTAGTAAGTGAGCAATATTTGAA 57.498 29.630 21.92 0.00 35.76 2.69
6273 11218 9.107177 AGTAAGTGAGCAATATTTGAATCTGAG 57.893 33.333 0.00 0.00 0.00 3.35
6274 11219 9.102757 GTAAGTGAGCAATATTTGAATCTGAGA 57.897 33.333 0.00 0.00 0.00 3.27
6275 11220 7.789273 AGTGAGCAATATTTGAATCTGAGAG 57.211 36.000 0.00 0.00 0.00 3.20
6276 11221 7.337167 AGTGAGCAATATTTGAATCTGAGAGT 58.663 34.615 0.00 0.00 0.00 3.24
6277 11222 7.828223 AGTGAGCAATATTTGAATCTGAGAGTT 59.172 33.333 0.00 0.00 0.00 3.01
6278 11223 9.102757 GTGAGCAATATTTGAATCTGAGAGTTA 57.897 33.333 0.00 0.00 0.00 2.24
6279 11224 9.842775 TGAGCAATATTTGAATCTGAGAGTTAT 57.157 29.630 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.797800 TCGGGAATGATTTTGCAATTCA 57.202 36.364 13.19 13.19 0.00 2.57
80 81 2.289195 CGTGGCCCTGTTTCACTAAGTA 60.289 50.000 0.00 0.00 0.00 2.24
104 105 1.593196 CACATCAACGTGTCCTGGTT 58.407 50.000 0.00 0.00 32.00 3.67
105 106 0.884704 GCACATCAACGTGTCCTGGT 60.885 55.000 0.00 0.00 39.19 4.00
129 130 1.615392 GCCAAATCACAGACCAAGCTT 59.385 47.619 0.00 0.00 0.00 3.74
164 177 5.527582 GCTAACAGTAGAGAAGAGAGGAGAG 59.472 48.000 0.00 0.00 0.00 3.20
166 179 5.437060 AGCTAACAGTAGAGAAGAGAGGAG 58.563 45.833 0.00 0.00 0.00 3.69
167 180 5.444744 AGCTAACAGTAGAGAAGAGAGGA 57.555 43.478 0.00 0.00 0.00 3.71
168 181 6.995686 TGATAGCTAACAGTAGAGAAGAGAGG 59.004 42.308 0.00 0.00 0.00 3.69
169 182 8.342634 GTTGATAGCTAACAGTAGAGAAGAGAG 58.657 40.741 3.75 0.00 0.00 3.20
189 202 3.658757 TGCCGATCGATGATGTTGATA 57.341 42.857 18.66 0.00 30.77 2.15
223 236 1.890041 CGCAAGAACCGTGTGGGAA 60.890 57.895 0.00 0.00 39.08 3.97
309 335 8.112822 TCTTTTTGGATGAAGTTGTATATCCCA 58.887 33.333 0.00 0.00 38.62 4.37
310 336 8.519799 TCTTTTTGGATGAAGTTGTATATCCC 57.480 34.615 0.00 0.00 38.62 3.85
396 1126 1.302993 GAGCACCCCACGCCTAAAA 60.303 57.895 0.00 0.00 0.00 1.52
407 1137 3.054361 TCTTAAAGGATTGAGGAGCACCC 60.054 47.826 0.00 0.00 36.73 4.61
437 1167 4.272504 CGCCTCATACATACAAAACCGATT 59.727 41.667 0.00 0.00 0.00 3.34
464 1194 6.602179 TCTTCACACAATTGATTTTCTAGCG 58.398 36.000 13.59 0.00 0.00 4.26
511 1241 6.049149 CCACCATCGTATTTGTATTCTCTGT 58.951 40.000 0.00 0.00 0.00 3.41
543 1274 2.736347 TCCTCCACTAGACTACAAGCC 58.264 52.381 0.00 0.00 0.00 4.35
586 1317 7.010923 CCTCTGTATTTGATCTTTTTCTCTCCG 59.989 40.741 0.00 0.00 0.00 4.63
613 1344 0.877743 TCAGGAGCGCGAGATATCTG 59.122 55.000 12.10 8.10 33.88 2.90
625 1356 1.522580 GGTGCGAGGATTCAGGAGC 60.523 63.158 0.00 0.00 0.00 4.70
627 1358 0.614697 TCAGGTGCGAGGATTCAGGA 60.615 55.000 0.00 0.00 0.00 3.86
630 1361 1.688735 CCTATCAGGTGCGAGGATTCA 59.311 52.381 0.00 0.00 0.00 2.57
639 1370 3.406595 AAGCGGGCCTATCAGGTGC 62.407 63.158 0.84 0.00 37.80 5.01
642 1373 1.227674 GTGAAGCGGGCCTATCAGG 60.228 63.158 0.84 0.00 38.80 3.86
643 1374 0.107456 ATGTGAAGCGGGCCTATCAG 59.893 55.000 0.84 0.00 0.00 2.90
792 3248 3.408853 CCGGTTCCCCTTCCCCTC 61.409 72.222 0.00 0.00 0.00 4.30
833 3299 1.134189 CGTGGGGAACTAGGGATTTCC 60.134 57.143 0.00 0.00 40.67 3.13
834 3300 1.746171 GCGTGGGGAACTAGGGATTTC 60.746 57.143 0.00 0.00 0.00 2.17
835 3301 0.255033 GCGTGGGGAACTAGGGATTT 59.745 55.000 0.00 0.00 0.00 2.17
983 3452 0.243636 CATGGCAAACCGAAACCTCC 59.756 55.000 0.00 0.00 39.70 4.30
1110 3619 0.459899 ACGCGAGATCACCTAATGCA 59.540 50.000 15.93 0.00 0.00 3.96
1186 3777 1.584483 GCATGGCGCAGATCAAACG 60.584 57.895 10.83 0.00 41.79 3.60
1212 3803 0.390860 GCACGCCATCAGATCTAGGT 59.609 55.000 0.00 0.00 0.00 3.08
1275 3879 5.063880 GCCTCGATTACCATAAGAAACCAT 58.936 41.667 0.00 0.00 0.00 3.55
1276 3880 4.448210 GCCTCGATTACCATAAGAAACCA 58.552 43.478 0.00 0.00 0.00 3.67
1278 3882 3.059800 GCGCCTCGATTACCATAAGAAAC 60.060 47.826 0.00 0.00 0.00 2.78
1280 3884 2.547218 GGCGCCTCGATTACCATAAGAA 60.547 50.000 22.15 0.00 0.00 2.52
1282 3886 1.000955 AGGCGCCTCGATTACCATAAG 59.999 52.381 27.08 0.00 0.00 1.73
1284 3888 0.317160 CAGGCGCCTCGATTACCATA 59.683 55.000 30.29 0.00 0.00 2.74
1286 3890 2.499205 CAGGCGCCTCGATTACCA 59.501 61.111 30.29 0.00 0.00 3.25
1338 3949 3.775202 CCTCTAACGAGAACATGACCTG 58.225 50.000 0.00 0.00 39.74 4.00
1346 3957 0.388134 TGCACGCCTCTAACGAGAAC 60.388 55.000 0.00 0.00 39.74 3.01
1418 4029 2.308570 TCAAATCACCACAGGCCTACAT 59.691 45.455 3.98 0.00 0.00 2.29
1419 4030 1.702401 TCAAATCACCACAGGCCTACA 59.298 47.619 3.98 0.00 0.00 2.74
1420 4031 2.084546 GTCAAATCACCACAGGCCTAC 58.915 52.381 3.98 0.00 0.00 3.18
1421 4032 1.702401 TGTCAAATCACCACAGGCCTA 59.298 47.619 3.98 0.00 0.00 3.93
1426 4037 0.238289 GCCGTGTCAAATCACCACAG 59.762 55.000 0.00 0.00 35.18 3.66
1430 4041 1.130561 GCTAAGCCGTGTCAAATCACC 59.869 52.381 0.00 0.00 35.18 4.02
1441 4052 1.964373 CACCCAAACGCTAAGCCGT 60.964 57.895 0.00 0.00 44.41 5.68
1563 4212 4.297768 CCCTTCCCCCAAATAACATTGAT 58.702 43.478 0.00 0.00 31.84 2.57
1735 4400 8.944029 CATCTAAGGAATCTGATGCGAATAAAT 58.056 33.333 0.00 0.00 31.51 1.40
1738 4403 6.870439 CACATCTAAGGAATCTGATGCGAATA 59.130 38.462 0.00 0.00 39.68 1.75
1779 4444 4.956700 AGATATTTCTTGGTCTCAGACGGA 59.043 41.667 0.00 0.00 32.65 4.69
1780 4445 5.046529 CAGATATTTCTTGGTCTCAGACGG 58.953 45.833 0.00 0.00 32.65 4.79
1788 4453 5.468409 GGCTTAGAGCAGATATTTCTTGGTC 59.532 44.000 2.04 6.67 44.75 4.02
1834 4499 1.193650 CACATTACACCCACGTTGTCG 59.806 52.381 0.00 0.00 43.34 4.35
1841 4506 0.251165 ACAGCCCACATTACACCCAC 60.251 55.000 0.00 0.00 0.00 4.61
1961 4628 4.166539 CCTAGATTCTCCTCCATGACCAT 58.833 47.826 0.00 0.00 0.00 3.55
2954 7575 6.237648 GCATAAAGCATTCAACGGATTTTGAG 60.238 38.462 0.00 0.00 44.79 3.02
3080 7893 6.727824 AATCTCCGATTAGACAAAACAGTG 57.272 37.500 0.00 0.00 0.00 3.66
3275 8093 8.184304 ACTTAAAAATGTAGTGGCCACAAATA 57.816 30.769 36.39 22.30 0.00 1.40
3333 8151 8.298854 CCTCATGATAAGACAGACATAAGAGAG 58.701 40.741 0.00 0.00 0.00 3.20
3342 8161 3.118629 TGCCACCTCATGATAAGACAGAC 60.119 47.826 0.00 0.00 0.00 3.51
3363 8182 4.514441 GGTGATGCTACCTGAGAAATCATG 59.486 45.833 0.00 0.00 37.74 3.07
3364 8183 4.164796 TGGTGATGCTACCTGAGAAATCAT 59.835 41.667 6.86 0.00 41.43 2.45
3366 8185 3.873952 GTGGTGATGCTACCTGAGAAATC 59.126 47.826 6.86 0.00 41.43 2.17
3545 8364 0.325110 CCTCCTTGAGCTCCTCCTCA 60.325 60.000 12.15 0.00 39.94 3.86
3755 8574 1.923148 AGGGTTATTTCAGAGGGGGTG 59.077 52.381 0.00 0.00 0.00 4.61
3784 8605 1.745768 GACGGTTCGTTATTCGGCGG 61.746 60.000 7.21 0.00 41.37 6.13
3921 8745 2.297597 AGAAGTCCGTGACCAAGAGAAG 59.702 50.000 1.06 0.00 32.18 2.85
3951 8775 3.369546 AGAAAAACACCAAATCCAGCG 57.630 42.857 0.00 0.00 0.00 5.18
3990 8819 1.148310 ACCGAACGACAAGCATGAAG 58.852 50.000 0.00 0.00 0.00 3.02
4014 8843 9.767684 CGCAAAATTAGTGTATAACTTTCATCA 57.232 29.630 0.00 0.00 40.56 3.07
4015 8844 8.734030 GCGCAAAATTAGTGTATAACTTTCATC 58.266 33.333 0.30 0.00 40.56 2.92
4016 8845 7.700656 GGCGCAAAATTAGTGTATAACTTTCAT 59.299 33.333 10.83 0.00 40.56 2.57
4236 9067 1.766143 CGGCCTACGCAGCAATTCTC 61.766 60.000 0.00 0.00 36.38 2.87
4265 9099 1.431488 CGACCAGGCATCACATTCGG 61.431 60.000 0.00 0.00 0.00 4.30
4320 9154 3.414700 GGAGTCGCAGCCACGTTG 61.415 66.667 0.00 0.00 0.00 4.10
4321 9155 3.616721 AGGAGTCGCAGCCACGTT 61.617 61.111 0.00 0.00 0.00 3.99
4322 9156 4.363990 CAGGAGTCGCAGCCACGT 62.364 66.667 0.00 0.00 0.00 4.49
4323 9157 4.363990 ACAGGAGTCGCAGCCACG 62.364 66.667 0.00 0.00 0.00 4.94
4324 9158 2.740055 CACAGGAGTCGCAGCCAC 60.740 66.667 0.00 0.00 0.00 5.01
4325 9159 4.007644 CCACAGGAGTCGCAGCCA 62.008 66.667 0.00 0.00 0.00 4.75
4326 9160 3.655810 CTCCACAGGAGTCGCAGCC 62.656 68.421 4.89 0.00 44.25 4.85
4327 9161 2.125753 CTCCACAGGAGTCGCAGC 60.126 66.667 4.89 0.00 44.25 5.25
4336 9170 4.641645 TTGGCACGGCTCCACAGG 62.642 66.667 0.00 0.00 32.45 4.00
4337 9171 1.973281 ATTTGGCACGGCTCCACAG 60.973 57.895 0.00 0.00 32.45 3.66
4338 9172 2.115052 ATTTGGCACGGCTCCACA 59.885 55.556 0.00 0.00 32.45 4.17
4339 9173 2.568090 CATTTGGCACGGCTCCAC 59.432 61.111 0.00 0.00 32.45 4.02
4340 9174 3.372730 GCATTTGGCACGGCTCCA 61.373 61.111 0.00 0.00 43.97 3.86
4341 9175 4.481112 CGCATTTGGCACGGCTCC 62.481 66.667 0.00 0.00 45.17 4.70
4342 9176 4.481112 CCGCATTTGGCACGGCTC 62.481 66.667 1.10 0.00 45.17 4.70
4360 9194 3.764466 CTCGAGAAGCCGCCACCT 61.764 66.667 6.58 0.00 0.00 4.00
4388 9222 4.526262 TCCATCTTCATCTTCTAGCTAGCC 59.474 45.833 16.35 0.00 0.00 3.93
4432 9268 0.667487 ACGACTGCAACCATCGACAG 60.667 55.000 14.12 0.00 39.16 3.51
4433 9269 0.943835 CACGACTGCAACCATCGACA 60.944 55.000 14.12 0.00 39.16 4.35
4436 9272 2.476051 GCACGACTGCAACCATCG 59.524 61.111 7.54 7.54 43.62 3.84
4442 9278 0.459899 ATATCTCCGCACGACTGCAA 59.540 50.000 0.00 0.00 44.50 4.08
4453 9289 5.713822 TGTCGACGTATGATATATCTCCG 57.286 43.478 11.62 13.81 0.00 4.63
4454 9290 6.431278 CCATGTCGACGTATGATATATCTCC 58.569 44.000 10.54 1.39 0.00 3.71
4470 9306 1.552799 ATGTCCACTGGCCATGTCGA 61.553 55.000 5.51 1.89 0.00 4.20
4496 9332 1.369625 CCGACCAGTTATTCCTGCAC 58.630 55.000 0.00 0.00 0.00 4.57
4499 9335 1.139058 CCTCCCGACCAGTTATTCCTG 59.861 57.143 0.00 0.00 0.00 3.86
4500 9336 1.273666 ACCTCCCGACCAGTTATTCCT 60.274 52.381 0.00 0.00 0.00 3.36
4671 9508 6.402226 GCAAACCGAGAAAACGAATAAGATCT 60.402 38.462 0.00 0.00 35.09 2.75
4720 9558 1.131303 TGTCCGTTCATTGAGGGGGT 61.131 55.000 6.13 0.00 0.00 4.95
4734 9572 0.455295 GACAGAAGAGCTCGTGTCCG 60.455 60.000 24.99 13.36 34.45 4.79
4736 9574 1.537638 TCTGACAGAAGAGCTCGTGTC 59.462 52.381 27.02 27.02 39.85 3.67
4768 9609 5.250982 TCCCCCTTCGTCTATTTTCTTTTC 58.749 41.667 0.00 0.00 0.00 2.29
4772 9613 2.772515 CCTCCCCCTTCGTCTATTTTCT 59.227 50.000 0.00 0.00 0.00 2.52
4778 9619 2.441532 CGCCTCCCCCTTCGTCTA 60.442 66.667 0.00 0.00 0.00 2.59
4832 9674 6.945636 TCAGAATTTTTCCAGGAGGTACTA 57.054 37.500 0.00 0.00 41.55 1.82
4833 9675 7.241628 AAATCAGAATTTTTCCAGGAGGTACT 58.758 34.615 0.00 0.00 33.91 2.73
4834 9676 7.468141 AAATCAGAATTTTTCCAGGAGGTAC 57.532 36.000 0.00 0.00 30.79 3.34
4860 9723 7.766283 TGTGACACTAACATGAACATTCAAAA 58.234 30.769 7.20 0.00 41.13 2.44
4861 9724 7.326968 TGTGACACTAACATGAACATTCAAA 57.673 32.000 7.20 0.00 41.13 2.69
4865 9728 5.299028 TGCTTGTGACACTAACATGAACATT 59.701 36.000 7.20 0.00 0.00 2.71
4872 9735 3.754965 ACCATGCTTGTGACACTAACAT 58.245 40.909 7.20 3.66 0.00 2.71
4892 9755 2.077413 TCCGCATGAAAATTGGCAAC 57.923 45.000 0.00 0.00 0.00 4.17
4896 9759 1.201181 TCCGTTCCGCATGAAAATTGG 59.799 47.619 0.00 0.00 33.94 3.16
4946 9812 4.083908 CGGAAAAATGCCACCTCAAATTTG 60.084 41.667 12.15 12.15 0.00 2.32
4948 9814 3.070878 ACGGAAAAATGCCACCTCAAATT 59.929 39.130 0.00 0.00 0.00 1.82
4949 9815 2.632512 ACGGAAAAATGCCACCTCAAAT 59.367 40.909 0.00 0.00 0.00 2.32
4951 9817 1.698506 ACGGAAAAATGCCACCTCAA 58.301 45.000 0.00 0.00 0.00 3.02
4952 9818 2.554893 GTTACGGAAAAATGCCACCTCA 59.445 45.455 0.00 0.00 0.00 3.86
4955 9821 3.586100 ATGTTACGGAAAAATGCCACC 57.414 42.857 0.00 0.00 0.00 4.61
4956 9822 4.151512 CCAAATGTTACGGAAAAATGCCAC 59.848 41.667 0.00 0.00 0.00 5.01
4959 9825 7.329717 TGAATACCAAATGTTACGGAAAAATGC 59.670 33.333 0.00 0.00 0.00 3.56
4967 9833 8.980143 AAGAAATTGAATACCAAATGTTACGG 57.020 30.769 0.00 0.00 38.43 4.02
5122 9998 0.175760 TCCAATTTCGCTCTCGGGAG 59.824 55.000 8.32 8.32 42.18 4.30
5123 9999 0.830648 ATCCAATTTCGCTCTCGGGA 59.169 50.000 0.00 0.00 36.13 5.14
5124 10000 1.668419 AATCCAATTTCGCTCTCGGG 58.332 50.000 0.00 0.00 36.13 5.14
5125 10001 3.325230 GAAATCCAATTTCGCTCTCGG 57.675 47.619 0.00 0.00 39.23 4.63
5148 10024 5.534654 GGGTTTACATATGCATAAGCCTTCA 59.465 40.000 11.13 0.00 41.13 3.02
5172 10048 2.945008 TCTCCTGCACAAACAGAAACAG 59.055 45.455 0.00 0.00 40.25 3.16
5173 10049 2.997980 TCTCCTGCACAAACAGAAACA 58.002 42.857 0.00 0.00 40.25 2.83
5174 10050 3.243201 CCTTCTCCTGCACAAACAGAAAC 60.243 47.826 0.00 0.00 40.25 2.78
5175 10051 2.951642 CCTTCTCCTGCACAAACAGAAA 59.048 45.455 0.00 0.00 40.25 2.52
5176 10052 2.575532 CCTTCTCCTGCACAAACAGAA 58.424 47.619 0.00 0.00 40.25 3.02
5177 10053 1.202806 CCCTTCTCCTGCACAAACAGA 60.203 52.381 0.00 0.00 40.25 3.41
5311 10187 0.250295 AGCGCACCACACACACTATT 60.250 50.000 11.47 0.00 0.00 1.73
5339 10226 2.584418 CAGCTCAGATGCGTCGGG 60.584 66.667 6.22 0.37 38.13 5.14
5492 10384 2.097038 CAACTCTCAAGCTCCGCCG 61.097 63.158 0.00 0.00 0.00 6.46
5507 10399 2.410730 CCGTGATGGTTAACGTCTCAAC 59.589 50.000 0.00 0.00 38.11 3.18
5510 10402 2.257034 GTCCGTGATGGTTAACGTCTC 58.743 52.381 0.00 1.28 38.11 3.36
5512 10404 1.990563 CTGTCCGTGATGGTTAACGTC 59.009 52.381 0.00 1.29 38.11 4.34
5513 10405 1.337447 CCTGTCCGTGATGGTTAACGT 60.337 52.381 0.00 0.00 38.11 3.99
5514 10406 1.337447 ACCTGTCCGTGATGGTTAACG 60.337 52.381 0.00 0.00 39.52 3.18
5515 10407 2.344025 GACCTGTCCGTGATGGTTAAC 58.656 52.381 0.00 0.00 39.52 2.01
5516 10408 1.067425 CGACCTGTCCGTGATGGTTAA 60.067 52.381 0.00 0.00 39.52 2.01
5551 10443 9.640963 TCCGTGTTTTTCTTTTTCTTTTTGATA 57.359 25.926 0.00 0.00 0.00 2.15
5552 10444 8.440059 GTCCGTGTTTTTCTTTTTCTTTTTGAT 58.560 29.630 0.00 0.00 0.00 2.57
5553 10445 7.438459 TGTCCGTGTTTTTCTTTTTCTTTTTGA 59.562 29.630 0.00 0.00 0.00 2.69
5554 10446 7.568433 TGTCCGTGTTTTTCTTTTTCTTTTTG 58.432 30.769 0.00 0.00 0.00 2.44
5555 10447 7.095397 CCTGTCCGTGTTTTTCTTTTTCTTTTT 60.095 33.333 0.00 0.00 0.00 1.94
5556 10448 6.367695 CCTGTCCGTGTTTTTCTTTTTCTTTT 59.632 34.615 0.00 0.00 0.00 2.27
5557 10449 5.867174 CCTGTCCGTGTTTTTCTTTTTCTTT 59.133 36.000 0.00 0.00 0.00 2.52
5558 10450 5.047590 ACCTGTCCGTGTTTTTCTTTTTCTT 60.048 36.000 0.00 0.00 0.00 2.52
5559 10451 4.461431 ACCTGTCCGTGTTTTTCTTTTTCT 59.539 37.500 0.00 0.00 0.00 2.52
5560 10452 4.740268 ACCTGTCCGTGTTTTTCTTTTTC 58.260 39.130 0.00 0.00 0.00 2.29
5566 10458 1.259770 GTCGACCTGTCCGTGTTTTTC 59.740 52.381 3.51 0.00 0.00 2.29
5587 10479 2.674177 CGCCATATCTAACGGTGGATCC 60.674 54.545 1.16 4.20 33.53 3.36
5676 10568 1.726791 CAAGTGGTTACAGCAGCGTAG 59.273 52.381 0.00 0.00 0.00 3.51
5691 10583 3.551496 TTCCGGGCCAGCTCAAGTG 62.551 63.158 4.39 0.00 0.00 3.16
5758 10687 3.723348 GTCGAAGTGGGCGGCAAC 61.723 66.667 8.80 8.80 32.84 4.17
5759 10688 4.243008 TGTCGAAGTGGGCGGCAA 62.243 61.111 12.47 0.00 40.74 4.52
5760 10689 4.980805 GTGTCGAAGTGGGCGGCA 62.981 66.667 12.47 0.00 41.50 5.69
5773 10702 1.598130 GGTGCTCTGGTGTGGTGTC 60.598 63.158 0.00 0.00 0.00 3.67
5776 10705 4.626081 GCGGTGCTCTGGTGTGGT 62.626 66.667 0.00 0.00 0.00 4.16
5812 10741 3.106738 AGCAGAGCAAAGCTGTTGT 57.893 47.368 0.00 0.00 39.88 3.32
5836 10765 1.544314 GGGAGATTAGGGCAGCACATC 60.544 57.143 0.00 0.00 0.00 3.06
5848 10777 1.315690 CCGAGCTGTACGGGAGATTA 58.684 55.000 3.34 0.00 45.65 1.75
5963 10892 3.068307 ACATGACATACCTAACTCTCGCC 59.932 47.826 0.00 0.00 0.00 5.54
5970 10899 6.624352 ATGCAATCACATGACATACCTAAC 57.376 37.500 0.00 0.00 0.00 2.34
5980 10909 3.346315 AGTCGGAAATGCAATCACATGA 58.654 40.909 0.00 0.00 0.00 3.07
5997 10926 6.183072 GGCACCTAAGCTACGAAAAAGTCG 62.183 50.000 0.00 0.00 44.37 4.18
5999 10928 3.072211 GGCACCTAAGCTACGAAAAAGT 58.928 45.455 0.00 0.00 34.17 2.66
6007 10936 1.641577 CGAGTTGGCACCTAAGCTAC 58.358 55.000 0.00 0.00 34.17 3.58
6012 10941 0.388907 GTACGCGAGTTGGCACCTAA 60.389 55.000 15.93 0.00 46.40 2.69
6045 10974 6.071952 TGCTTGTTTCTTCTACCAAATCATCC 60.072 38.462 0.00 0.00 0.00 3.51
6049 10978 6.145535 CAGTGCTTGTTTCTTCTACCAAATC 58.854 40.000 0.00 0.00 0.00 2.17
6050 10979 5.594317 ACAGTGCTTGTTTCTTCTACCAAAT 59.406 36.000 0.00 0.00 36.31 2.32
6051 10980 4.947388 ACAGTGCTTGTTTCTTCTACCAAA 59.053 37.500 0.00 0.00 36.31 3.28
6069 10998 4.460382 AGGCTGTGGATTCAAATTACAGTG 59.540 41.667 15.99 0.00 40.52 3.66
6074 11003 3.831333 TGCAAGGCTGTGGATTCAAATTA 59.169 39.130 0.00 0.00 0.00 1.40
6125 11054 2.809299 GCTTACCCATTACCGCCTAAGG 60.809 54.545 0.00 0.00 37.30 2.69
6140 11072 2.224548 ACAAACCCTGAGACTGCTTACC 60.225 50.000 0.00 0.00 0.00 2.85
6152 11088 3.888930 ACATTAAGTCCACACAAACCCTG 59.111 43.478 0.00 0.00 0.00 4.45
6182 11118 5.121380 AGAACTCGGTACCCTACTATTGA 57.879 43.478 6.25 0.00 0.00 2.57
6188 11124 4.430908 CATTTGAGAACTCGGTACCCTAC 58.569 47.826 6.25 0.00 0.00 3.18
6190 11126 2.236395 CCATTTGAGAACTCGGTACCCT 59.764 50.000 6.25 0.00 0.00 4.34
6191 11127 2.235402 TCCATTTGAGAACTCGGTACCC 59.765 50.000 6.25 0.00 0.00 3.69
6192 11128 3.604875 TCCATTTGAGAACTCGGTACC 57.395 47.619 0.16 0.16 0.00 3.34
6193 11129 3.933332 CCTTCCATTTGAGAACTCGGTAC 59.067 47.826 0.00 0.00 0.00 3.34
6194 11130 3.055385 CCCTTCCATTTGAGAACTCGGTA 60.055 47.826 0.00 0.00 0.00 4.02
6221 11157 4.377021 TGTACGAGTTTTCAAGCATGACT 58.623 39.130 0.00 0.00 34.61 3.41
6226 11162 5.353938 ACTAACTGTACGAGTTTTCAAGCA 58.646 37.500 13.48 0.00 42.70 3.91
6229 11165 8.190122 TCACTTACTAACTGTACGAGTTTTCAA 58.810 33.333 13.48 6.82 42.70 2.69
6231 11167 7.148999 GCTCACTTACTAACTGTACGAGTTTTC 60.149 40.741 13.48 0.00 42.70 2.29
6241 11186 9.502091 TTCAAATATTGCTCACTTACTAACTGT 57.498 29.630 0.00 0.00 0.00 3.55
6253 11198 9.842775 ATAACTCTCAGATTCAAATATTGCTCA 57.157 29.630 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.