Multiple sequence alignment - TraesCS1D01G309300

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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 TraesCS1D01G309300 chr1D 100.000 4251 0 0 1 4251 405163259 405167509 0.000000e+00 7851.0
1 TraesCS1D01G309300 chr1D 85.597 1708 128 54 1126 2734 405281044 405282732 0.000000e+00 1683.0
2 TraesCS1D01G309300 chr1D 86.356 579 54 14 2804 3361 405282820 405283394 3.630000e-170 608.0
3 TraesCS1D01G309300 chr1D 81.731 104 7 7 3436 3527 405283509 405283612 4.560000e-10 76.8
4 TraesCS1D01G309300 chr1D 100.000 29 0 0 3705 3733 405166927 405166955 2.000000e-03 54.7
5 TraesCS1D01G309300 chr1D 100.000 29 0 0 3669 3697 405166963 405166991 2.000000e-03 54.7
6 TraesCS1D01G309300 chr1B 90.076 3164 151 71 486 3542 545071767 545074874 0.000000e+00 3952.0
7 TraesCS1D01G309300 chr1B 82.593 1689 169 54 1126 2729 545162304 545163952 0.000000e+00 1375.0
8 TraesCS1D01G309300 chr1B 80.745 779 80 36 2804 3530 545164046 545164806 1.040000e-150 544.0
9 TraesCS1D01G309300 chr1B 90.625 224 11 8 198 411 545071492 545071715 5.380000e-74 289.0
10 TraesCS1D01G309300 chr1A 94.212 1987 64 23 1646 3589 500663923 500665901 0.000000e+00 2985.0
11 TraesCS1D01G309300 chr1A 82.639 2425 204 103 1126 3419 500818726 500821064 0.000000e+00 1945.0
12 TraesCS1D01G309300 chr1A 84.398 1064 84 38 2 1033 500662078 500663091 0.000000e+00 970.0
13 TraesCS1D01G309300 chr1A 95.298 553 25 1 1098 1650 500663328 500663879 0.000000e+00 876.0
14 TraesCS1D01G309300 chr1A 83.163 196 3 6 3824 4008 500666029 500666205 7.360000e-33 152.0
15 TraesCS1D01G309300 chr1A 97.468 79 1 1 4161 4238 500666346 500666424 2.670000e-27 134.0
16 TraesCS1D01G309300 chr1A 89.320 103 3 1 4005 4099 500666238 500666340 5.770000e-24 122.0
17 TraesCS1D01G309300 chr1A 81.081 111 9 7 3429 3527 500821095 500821205 1.270000e-10 78.7
18 TraesCS1D01G309300 chr3B 80.952 420 49 12 2917 3307 10488021 10487604 1.920000e-78 303.0
19 TraesCS1D01G309300 chr3B 79.130 115 11 8 3429 3530 10487456 10487342 2.740000e-07 67.6
20 TraesCS1D01G309300 chr5A 76.183 634 89 31 1197 1786 400508881 400508266 1.160000e-70 278.0
21 TraesCS1D01G309300 chr5A 73.745 518 84 32 1197 1678 644924425 644924926 5.690000e-34 156.0
22 TraesCS1D01G309300 chr7A 76.025 634 90 33 1197 1786 588281828 588282443 5.420000e-69 272.0
23 TraesCS1D01G309300 chr7B 75.868 634 91 33 1197 1786 581398459 581399074 2.520000e-67 267.0
24 TraesCS1D01G309300 chr3D 73.019 530 110 27 2196 2706 438608679 438608164 5.690000e-34 156.0
25 TraesCS1D01G309300 chr5B 100.000 29 0 0 1040 1068 185183827 185183799 2.000000e-03 54.7


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 TraesCS1D01G309300 chr1D 405163259 405167509 4250 False 2653.466667 7851 100.000000 1 4251 3 chr1D.!!$F1 4250
1 TraesCS1D01G309300 chr1D 405281044 405283612 2568 False 789.266667 1683 84.561333 1126 3527 3 chr1D.!!$F2 2401
2 TraesCS1D01G309300 chr1B 545071492 545074874 3382 False 2120.500000 3952 90.350500 198 3542 2 chr1B.!!$F1 3344
3 TraesCS1D01G309300 chr1B 545162304 545164806 2502 False 959.500000 1375 81.669000 1126 3530 2 chr1B.!!$F2 2404
4 TraesCS1D01G309300 chr1A 500818726 500821205 2479 False 1011.850000 1945 81.860000 1126 3527 2 chr1A.!!$F2 2401
5 TraesCS1D01G309300 chr1A 500662078 500666424 4346 False 873.166667 2985 90.643167 2 4238 6 chr1A.!!$F1 4236
6 TraesCS1D01G309300 chr5A 400508266 400508881 615 True 278.000000 278 76.183000 1197 1786 1 chr5A.!!$R1 589
7 TraesCS1D01G309300 chr7A 588281828 588282443 615 False 272.000000 272 76.025000 1197 1786 1 chr7A.!!$F1 589
8 TraesCS1D01G309300 chr7B 581398459 581399074 615 False 267.000000 267 75.868000 1197 1786 1 chr7B.!!$F1 589

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
321 331 0.037734 GGACACCCACAAACCCCTAG 59.962 60.0 0.0 0.0 0.0 3.02 F
1161 1375 0.028770 CTTGCGGCTTGTTTCGTTCA 59.971 50.0 0.0 0.0 0.0 3.18 F
1857 2198 0.107312 CCAGGAAGCCATCAGAGGTG 60.107 60.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2535 1.512926 ACATCGTCAGAACAGTTGCC 58.487 50.0 0.00 0.00 0.0 4.52 R
2779 3238 0.244450 ACGCAAATTCCATGGCACTG 59.756 50.0 6.96 2.72 0.0 3.66 R
3600 4211 0.106769 TTCCAACAGGTGCAGCAGAA 60.107 50.0 19.63 9.58 0.0 3.02 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
18 19 2.584608 GCAGTGGAGTGCGGGTAT 59.415 61.111 0.00 0.00 32.74 2.73
23 24 0.179108 GTGGAGTGCGGGTATGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
64 65 3.403968 GCCAGAGCCCTAGTTAAATAGC 58.596 50.000 4.40 0.00 0.00 2.97
72 73 2.550208 CCTAGTTAAATAGCCGGGGCAG 60.550 54.545 12.97 0.00 44.88 4.85
73 74 1.209621 AGTTAAATAGCCGGGGCAGA 58.790 50.000 12.97 0.00 44.88 4.26
74 75 1.774856 AGTTAAATAGCCGGGGCAGAT 59.225 47.619 12.97 1.81 44.88 2.90
80 81 4.864334 GCCGGGGCAGATGGACAG 62.864 72.222 2.18 0.00 41.49 3.51
87 88 2.887568 CAGATGGACAGACGCCGC 60.888 66.667 0.00 0.00 0.00 6.53
88 89 3.071206 AGATGGACAGACGCCGCT 61.071 61.111 0.00 0.00 0.00 5.52
89 90 2.125512 GATGGACAGACGCCGCTT 60.126 61.111 0.00 0.00 0.00 4.68
92 93 2.357034 GGACAGACGCCGCTTCAA 60.357 61.111 0.00 0.00 0.00 2.69
93 94 1.741770 GGACAGACGCCGCTTCAAT 60.742 57.895 0.00 0.00 0.00 2.57
94 95 1.421485 GACAGACGCCGCTTCAATG 59.579 57.895 0.00 0.00 0.00 2.82
103 104 3.741058 GCTTCAATGCGACGCAAC 58.259 55.556 28.24 8.47 43.62 4.17
104 105 1.207593 GCTTCAATGCGACGCAACT 59.792 52.632 28.24 14.38 43.62 3.16
105 106 0.385974 GCTTCAATGCGACGCAACTT 60.386 50.000 28.24 15.00 43.62 2.66
106 107 1.321016 CTTCAATGCGACGCAACTTG 58.679 50.000 28.24 25.51 43.62 3.16
119 120 2.785679 GCAACTTGCGTAATAGGCTTG 58.214 47.619 6.51 4.20 31.71 4.01
122 123 3.328382 ACTTGCGTAATAGGCTTGTCA 57.672 42.857 6.51 0.00 0.00 3.58
130 131 1.972660 ATAGGCTTGTCAGTCCCCGC 61.973 60.000 0.00 0.00 0.00 6.13
135 136 3.234630 TTGTCAGTCCCCGCTTCCG 62.235 63.158 0.00 0.00 0.00 4.30
139 140 3.717294 AGTCCCCGCTTCCGCATT 61.717 61.111 0.00 0.00 35.30 3.56
144 145 2.040544 CCCGCTTCCGCATTGAAGT 61.041 57.895 8.79 0.00 42.98 3.01
145 146 4.751539 CGCTTCCGCATTGAAGTG 57.248 55.556 8.79 7.78 43.89 3.16
146 147 1.135315 CGCTTCCGCATTGAAGTGG 59.865 57.895 11.39 0.00 45.01 4.00
147 148 1.153958 GCTTCCGCATTGAAGTGGC 60.154 57.895 8.79 0.00 42.98 5.01
170 171 2.179517 CCTCTCGTCCAGTCACGC 59.820 66.667 0.00 0.00 39.74 5.34
319 329 2.931921 GGACACCCACAAACCCCT 59.068 61.111 0.00 0.00 0.00 4.79
320 330 1.770749 CGGACACCCACAAACCCCTA 61.771 60.000 0.00 0.00 0.00 3.53
321 331 0.037734 GGACACCCACAAACCCCTAG 59.962 60.000 0.00 0.00 0.00 3.02
322 332 1.061546 GACACCCACAAACCCCTAGA 58.938 55.000 0.00 0.00 0.00 2.43
323 333 1.633945 GACACCCACAAACCCCTAGAT 59.366 52.381 0.00 0.00 0.00 1.98
348 359 0.040514 TGCCAGTTTGCACGAATTCG 60.041 50.000 25.64 25.64 46.33 3.34
355 375 1.588674 TTGCACGAATTCGGACAGTT 58.411 45.000 29.79 6.69 44.95 3.16
362 382 3.254060 CGAATTCGGACAGTTGACAGAT 58.746 45.455 20.16 0.00 35.37 2.90
392 412 5.049405 CGGCATTAGATGGTGAAAATAGTCC 60.049 44.000 0.00 0.00 0.00 3.85
445 480 2.611224 GCCTTGGAGAGCAAATTTGGTG 60.611 50.000 26.47 11.68 39.30 4.17
450 485 2.819608 GGAGAGCAAATTTGGTGCACTA 59.180 45.455 26.47 8.10 42.04 2.74
492 527 1.202940 AGGACAGGGAAGAAAACCAGC 60.203 52.381 0.00 0.00 0.00 4.85
495 530 0.600057 CAGGGAAGAAAACCAGCAGC 59.400 55.000 0.00 0.00 0.00 5.25
602 637 4.250305 GCCGCCACCGATACCCAT 62.250 66.667 0.00 0.00 36.29 4.00
603 638 2.874664 GCCGCCACCGATACCCATA 61.875 63.158 0.00 0.00 36.29 2.74
604 639 1.005394 CCGCCACCGATACCCATAC 60.005 63.158 0.00 0.00 36.29 2.39
605 640 1.372499 CGCCACCGATACCCATACG 60.372 63.158 0.00 0.00 36.29 3.06
606 641 1.798234 CGCCACCGATACCCATACGA 61.798 60.000 0.00 0.00 36.29 3.43
613 648 2.223548 CCGATACCCATACGAACGAACA 60.224 50.000 0.14 0.00 0.00 3.18
616 651 2.074547 ACCCATACGAACGAACACAG 57.925 50.000 0.14 0.00 0.00 3.66
648 683 0.108396 TGCCATGCTACGTATGCCAT 59.892 50.000 12.45 6.24 0.00 4.40
813 848 4.394712 CCGTCCTCCACACCAGCC 62.395 72.222 0.00 0.00 0.00 4.85
814 849 4.394712 CGTCCTCCACACCAGCCC 62.395 72.222 0.00 0.00 0.00 5.19
815 850 4.035102 GTCCTCCACACCAGCCCC 62.035 72.222 0.00 0.00 0.00 5.80
866 906 0.260523 AATACAATCCCCCAACCCCG 59.739 55.000 0.00 0.00 0.00 5.73
905 946 2.722201 GCAGGGACGAATCGGAGGT 61.722 63.158 7.80 0.00 0.00 3.85
966 1008 3.379445 GCACCTCCCGGTTCTCGA 61.379 66.667 0.00 0.00 42.13 4.04
1068 1110 2.431683 GCCAACAGAGGTGAGCCA 59.568 61.111 0.00 0.00 37.19 4.75
1069 1111 1.001641 GCCAACAGAGGTGAGCCAT 60.002 57.895 0.00 0.00 37.19 4.40
1073 1115 2.202987 CAGAGGTGAGCCATCCGC 60.203 66.667 0.00 0.00 37.19 5.54
1161 1375 0.028770 CTTGCGGCTTGTTTCGTTCA 59.971 50.000 0.00 0.00 0.00 3.18
1296 1512 4.691860 ACAAGCGATTCCTTGATCTTTG 57.308 40.909 16.78 2.46 43.79 2.77
1305 1521 6.238049 CGATTCCTTGATCTTTGACTCATGTC 60.238 42.308 0.00 0.00 43.20 3.06
1453 1700 3.134458 GGGTAAGAAGATCAATCAGCGG 58.866 50.000 0.00 0.00 0.00 5.52
1456 1703 5.059833 GGTAAGAAGATCAATCAGCGGAAT 58.940 41.667 0.00 0.00 0.00 3.01
1466 1717 2.888834 TCAGCGGAATGATCGAATCA 57.111 45.000 0.00 0.00 44.55 2.57
1467 1718 3.177997 TCAGCGGAATGATCGAATCAA 57.822 42.857 0.00 0.00 43.50 2.57
1483 1735 5.299279 TCGAATCAAGTCCTGCTTTTCTTTT 59.701 36.000 0.00 0.00 34.69 2.27
1508 1778 4.127171 CCGTTCTTTCTCCTGAACTGAAA 58.873 43.478 0.00 0.00 40.04 2.69
1518 1788 2.287009 CCTGAACTGAAACCGTTCTTGC 60.287 50.000 0.00 0.00 40.95 4.01
1679 2005 9.193133 GCAATTTCTTGATGATGGATTCTAATG 57.807 33.333 0.00 0.00 34.04 1.90
1716 2042 2.251371 GGTTTGCAGAACGGCGTC 59.749 61.111 15.17 7.22 36.28 5.19
1857 2198 0.107312 CCAGGAAGCCATCAGAGGTG 60.107 60.000 0.00 0.00 0.00 4.00
2168 2535 1.380524 CCTCTTCAGGATTGCTGCAG 58.619 55.000 10.11 10.11 43.65 4.41
2452 2829 4.292178 GAGGAGATCTGGGCGCCG 62.292 72.222 22.54 7.85 0.00 6.46
2523 2968 2.028658 TGCCTCAGTCTGTTCATGTCTC 60.029 50.000 0.00 0.00 0.00 3.36
2568 3024 4.202357 TGAAGTGTCTGTCTGCAGGTAAAT 60.202 41.667 15.13 0.00 42.78 1.40
2688 3144 1.509923 CCCGTACGTCTTCCTGGTC 59.490 63.158 15.21 0.00 0.00 4.02
2733 3192 4.455877 AGCGACAAGGAGGTAAAAAGATTG 59.544 41.667 0.00 0.00 0.00 2.67
2739 3198 8.533569 ACAAGGAGGTAAAAAGATTGAAAGAA 57.466 30.769 0.00 0.00 0.00 2.52
2777 3236 5.874895 TTCTGAATCTCTGAAGTTGCATG 57.125 39.130 0.00 0.00 31.94 4.06
2778 3237 4.903054 TCTGAATCTCTGAAGTTGCATGT 58.097 39.130 0.00 0.00 0.00 3.21
2779 3238 4.934001 TCTGAATCTCTGAAGTTGCATGTC 59.066 41.667 0.00 0.00 0.00 3.06
2780 3239 4.644498 TGAATCTCTGAAGTTGCATGTCA 58.356 39.130 0.00 0.00 0.00 3.58
2822 3317 4.330074 CGTATGCTGAATTTCGTTTCCTCT 59.670 41.667 0.00 0.00 0.00 3.69
3006 3501 0.606401 CAAGCACCACACCGGATTCT 60.606 55.000 9.46 0.00 38.63 2.40
3008 3503 1.745489 GCACCACACCGGATTCTCC 60.745 63.158 9.46 0.00 38.63 3.71
3085 3613 5.540911 TCAACTTTGCTGAATGGAAATTCC 58.459 37.500 4.79 4.79 35.49 3.01
3253 3781 4.880537 CAGCGCCAGGCCTAGTCG 62.881 72.222 3.98 10.70 45.17 4.18
3378 3947 9.502145 TTCATTCATTTCATATGTTTTAGCGAC 57.498 29.630 1.90 0.00 0.00 5.19
3589 4200 6.662414 TGCCTGATTTTGTACTTAATCTCG 57.338 37.500 16.29 10.15 33.08 4.04
3590 4201 6.170506 TGCCTGATTTTGTACTTAATCTCGT 58.829 36.000 16.29 0.00 33.08 4.18
3591 4202 6.653320 TGCCTGATTTTGTACTTAATCTCGTT 59.347 34.615 16.29 0.00 33.08 3.85
3594 4205 7.360861 CCTGATTTTGTACTTAATCTCGTTGCA 60.361 37.037 16.29 0.00 33.08 4.08
3595 4206 7.866729 TGATTTTGTACTTAATCTCGTTGCAA 58.133 30.769 16.29 0.00 33.08 4.08
3597 4208 6.854496 TTTGTACTTAATCTCGTTGCAAGT 57.146 33.333 0.00 0.00 34.10 3.16
3598 4209 5.839262 TGTACTTAATCTCGTTGCAAGTG 57.161 39.130 0.00 0.00 32.09 3.16
3599 4210 5.534407 TGTACTTAATCTCGTTGCAAGTGA 58.466 37.500 0.00 0.00 32.09 3.41
3600 4211 6.163476 TGTACTTAATCTCGTTGCAAGTGAT 58.837 36.000 0.00 0.90 32.09 3.06
3601 4212 6.649141 TGTACTTAATCTCGTTGCAAGTGATT 59.351 34.615 18.90 18.90 36.31 2.57
3602 4213 6.170675 ACTTAATCTCGTTGCAAGTGATTC 57.829 37.500 18.63 0.00 34.77 2.52
3603 4214 5.934625 ACTTAATCTCGTTGCAAGTGATTCT 59.065 36.000 18.63 5.66 34.77 2.40
3604 4215 4.675190 AATCTCGTTGCAAGTGATTCTG 57.325 40.909 0.00 0.00 29.17 3.02
3605 4216 1.800586 TCTCGTTGCAAGTGATTCTGC 59.199 47.619 0.00 0.00 0.00 4.26
3606 4217 1.802960 CTCGTTGCAAGTGATTCTGCT 59.197 47.619 0.00 0.00 0.00 4.24
3607 4218 1.532437 TCGTTGCAAGTGATTCTGCTG 59.468 47.619 0.00 0.00 0.00 4.41
3608 4219 1.694639 GTTGCAAGTGATTCTGCTGC 58.305 50.000 0.00 0.00 32.37 5.25
3609 4220 1.001048 GTTGCAAGTGATTCTGCTGCA 60.001 47.619 0.00 0.88 37.90 4.41
3610 4221 0.594602 TGCAAGTGATTCTGCTGCAC 59.405 50.000 0.00 0.00 35.70 4.57
3611 4222 0.109412 GCAAGTGATTCTGCTGCACC 60.109 55.000 0.00 0.00 32.12 5.01
3612 4223 1.531423 CAAGTGATTCTGCTGCACCT 58.469 50.000 0.00 0.00 33.14 4.00
3613 4224 1.199327 CAAGTGATTCTGCTGCACCTG 59.801 52.381 0.00 0.00 33.14 4.00
3614 4225 0.399454 AGTGATTCTGCTGCACCTGT 59.601 50.000 0.00 0.00 33.14 4.00
3615 4226 1.202855 AGTGATTCTGCTGCACCTGTT 60.203 47.619 0.00 0.00 33.14 3.16
3616 4227 1.068748 GTGATTCTGCTGCACCTGTTG 60.069 52.381 0.00 0.00 0.00 3.33
3617 4228 0.524862 GATTCTGCTGCACCTGTTGG 59.475 55.000 0.00 0.00 39.83 3.77
3618 4229 0.111061 ATTCTGCTGCACCTGTTGGA 59.889 50.000 0.00 0.00 37.04 3.53
3619 4230 0.106769 TTCTGCTGCACCTGTTGGAA 60.107 50.000 0.00 0.00 37.04 3.53
3620 4231 0.535780 TCTGCTGCACCTGTTGGAAG 60.536 55.000 0.00 0.00 37.04 3.46
3621 4232 0.535780 CTGCTGCACCTGTTGGAAGA 60.536 55.000 0.00 0.00 37.04 2.87
3622 4233 0.819259 TGCTGCACCTGTTGGAAGAC 60.819 55.000 0.00 0.00 37.04 3.01
3623 4234 0.819259 GCTGCACCTGTTGGAAGACA 60.819 55.000 0.00 0.00 37.04 3.41
3624 4235 1.901591 CTGCACCTGTTGGAAGACAT 58.098 50.000 0.00 0.00 37.04 3.06
3625 4236 1.538512 CTGCACCTGTTGGAAGACATG 59.461 52.381 0.00 0.00 37.04 3.21
3626 4237 1.142667 TGCACCTGTTGGAAGACATGA 59.857 47.619 0.00 0.00 37.04 3.07
3627 4238 2.224843 TGCACCTGTTGGAAGACATGAT 60.225 45.455 0.00 0.00 37.04 2.45
3628 4239 2.821969 GCACCTGTTGGAAGACATGATT 59.178 45.455 0.00 0.00 37.04 2.57
3629 4240 3.256631 GCACCTGTTGGAAGACATGATTT 59.743 43.478 0.00 0.00 37.04 2.17
3630 4241 4.262164 GCACCTGTTGGAAGACATGATTTT 60.262 41.667 0.00 0.00 37.04 1.82
3635 4246 4.455533 TGTTGGAAGACATGATTTTCCTCG 59.544 41.667 20.23 0.00 40.77 4.63
3638 4249 4.253685 GGAAGACATGATTTTCCTCGTCA 58.746 43.478 15.55 0.00 37.86 4.35
3689 4300 6.790232 AAAACTGTTTTCCCAATCTCAAGA 57.210 33.333 12.50 0.00 0.00 3.02
3690 4301 6.396829 AAACTGTTTTCCCAATCTCAAGAG 57.603 37.500 0.00 0.00 0.00 2.85
3691 4302 5.053978 ACTGTTTTCCCAATCTCAAGAGT 57.946 39.130 0.00 0.00 0.00 3.24
3692 4303 4.823989 ACTGTTTTCCCAATCTCAAGAGTG 59.176 41.667 0.58 0.58 39.59 3.51
3693 4304 5.047566 TGTTTTCCCAATCTCAAGAGTGA 57.952 39.130 8.92 0.00 42.16 3.41
3694 4305 5.445069 TGTTTTCCCAATCTCAAGAGTGAA 58.555 37.500 8.92 0.00 42.16 3.18
3695 4306 5.299279 TGTTTTCCCAATCTCAAGAGTGAAC 59.701 40.000 8.92 6.06 42.16 3.18
3696 4307 4.705110 TTCCCAATCTCAAGAGTGAACA 57.295 40.909 8.92 0.00 42.16 3.18
3697 4308 4.277515 TCCCAATCTCAAGAGTGAACAG 57.722 45.455 8.92 0.00 42.16 3.16
3698 4309 3.903714 TCCCAATCTCAAGAGTGAACAGA 59.096 43.478 8.92 0.00 42.16 3.41
3699 4310 4.347876 TCCCAATCTCAAGAGTGAACAGAA 59.652 41.667 8.92 0.00 42.16 3.02
3700 4311 5.065914 CCCAATCTCAAGAGTGAACAGAAA 58.934 41.667 8.92 0.00 42.16 2.52
3701 4312 5.709164 CCCAATCTCAAGAGTGAACAGAAAT 59.291 40.000 8.92 0.00 42.16 2.17
3702 4313 6.208204 CCCAATCTCAAGAGTGAACAGAAATT 59.792 38.462 8.92 0.00 42.16 1.82
3703 4314 7.082602 CCAATCTCAAGAGTGAACAGAAATTG 58.917 38.462 8.92 1.25 42.16 2.32
3704 4315 7.040892 CCAATCTCAAGAGTGAACAGAAATTGA 60.041 37.037 8.92 0.00 42.16 2.57
3705 4316 8.347771 CAATCTCAAGAGTGAACAGAAATTGAA 58.652 33.333 1.31 0.00 42.16 2.69
3706 4317 7.251704 TCTCAAGAGTGAACAGAAATTGAAC 57.748 36.000 0.00 0.00 31.88 3.18
3707 4318 7.050377 TCTCAAGAGTGAACAGAAATTGAACT 58.950 34.615 0.00 0.00 31.88 3.01
3708 4319 7.011763 TCTCAAGAGTGAACAGAAATTGAACTG 59.988 37.037 0.00 0.00 39.65 3.16
3716 4327 5.930837 ACAGAAATTGAACTGTTTTCCCA 57.069 34.783 0.00 0.00 43.52 4.37
3727 4338 5.053978 ACTGTTTTCCCAATCTCAAGAGT 57.946 39.130 0.00 0.00 0.00 3.24
3733 4344 4.705110 TCCCAATCTCAAGAGTGAACAA 57.295 40.909 8.92 0.00 42.16 2.83
3734 4345 5.047566 TCCCAATCTCAAGAGTGAACAAA 57.952 39.130 8.92 0.00 42.16 2.83
3737 4348 6.016024 TCCCAATCTCAAGAGTGAACAAATTG 60.016 38.462 8.92 0.00 42.16 2.32
3740 4351 4.464008 TCTCAAGAGTGAACAAATTGCCT 58.536 39.130 0.00 0.00 31.88 4.75
3741 4352 4.516698 TCTCAAGAGTGAACAAATTGCCTC 59.483 41.667 0.00 0.00 31.88 4.70
3742 4353 3.569701 TCAAGAGTGAACAAATTGCCTCC 59.430 43.478 0.00 0.00 0.00 4.30
3743 4354 3.228188 AGAGTGAACAAATTGCCTCCA 57.772 42.857 0.00 0.00 0.00 3.86
3744 4355 3.771216 AGAGTGAACAAATTGCCTCCAT 58.229 40.909 0.00 0.00 0.00 3.41
3745 4356 3.508793 AGAGTGAACAAATTGCCTCCATG 59.491 43.478 0.00 0.00 0.00 3.66
3746 4357 2.564062 AGTGAACAAATTGCCTCCATGG 59.436 45.455 4.97 4.97 39.35 3.66
3774 4385 4.570930 GCCTGTAGCTAGAAGAAAACTGT 58.429 43.478 0.00 0.00 38.99 3.55
3775 4386 4.627900 GCCTGTAGCTAGAAGAAAACTGTC 59.372 45.833 0.00 0.00 38.99 3.51
3776 4387 5.567823 GCCTGTAGCTAGAAGAAAACTGTCT 60.568 44.000 0.00 0.00 38.99 3.41
3777 4388 6.096695 CCTGTAGCTAGAAGAAAACTGTCTC 58.903 44.000 0.00 0.00 0.00 3.36
3778 4389 6.026947 TGTAGCTAGAAGAAAACTGTCTCC 57.973 41.667 0.00 0.00 0.00 3.71
3779 4390 5.538813 TGTAGCTAGAAGAAAACTGTCTCCA 59.461 40.000 0.00 0.00 0.00 3.86
3780 4391 5.753721 AGCTAGAAGAAAACTGTCTCCAT 57.246 39.130 0.00 0.00 0.00 3.41
3781 4392 5.486526 AGCTAGAAGAAAACTGTCTCCATG 58.513 41.667 0.00 0.00 0.00 3.66
3782 4393 4.633565 GCTAGAAGAAAACTGTCTCCATGG 59.366 45.833 4.97 4.97 0.00 3.66
3787 4398 3.815401 AGAAAACTGTCTCCATGGAAACG 59.185 43.478 17.00 11.68 0.00 3.60
3797 4408 1.203052 CCATGGAAACGCAGCTCAAAT 59.797 47.619 5.56 0.00 0.00 2.32
3799 4410 3.319755 CATGGAAACGCAGCTCAAATTT 58.680 40.909 0.00 0.00 0.00 1.82
3800 4411 3.451141 TGGAAACGCAGCTCAAATTTT 57.549 38.095 0.00 0.00 0.00 1.82
3802 4413 3.068024 TGGAAACGCAGCTCAAATTTTCT 59.932 39.130 0.00 0.00 0.00 2.52
3804 4415 3.988379 AACGCAGCTCAAATTTTCTCA 57.012 38.095 0.00 0.00 0.00 3.27
3805 4416 4.510038 AACGCAGCTCAAATTTTCTCAT 57.490 36.364 0.00 0.00 0.00 2.90
3806 4417 4.510038 ACGCAGCTCAAATTTTCTCATT 57.490 36.364 0.00 0.00 0.00 2.57
3807 4418 4.232221 ACGCAGCTCAAATTTTCTCATTG 58.768 39.130 0.00 0.00 0.00 2.82
3808 4419 3.611113 CGCAGCTCAAATTTTCTCATTGG 59.389 43.478 0.00 0.00 0.00 3.16
3809 4420 4.616604 CGCAGCTCAAATTTTCTCATTGGA 60.617 41.667 0.00 0.00 0.00 3.53
3810 4421 5.416947 GCAGCTCAAATTTTCTCATTGGAT 58.583 37.500 0.00 0.00 0.00 3.41
3811 4422 5.519206 GCAGCTCAAATTTTCTCATTGGATC 59.481 40.000 0.00 0.00 0.00 3.36
3812 4423 6.627243 CAGCTCAAATTTTCTCATTGGATCA 58.373 36.000 0.00 0.00 0.00 2.92
3813 4424 6.752351 CAGCTCAAATTTTCTCATTGGATCAG 59.248 38.462 0.00 0.00 0.00 2.90
3814 4425 6.436532 AGCTCAAATTTTCTCATTGGATCAGT 59.563 34.615 0.00 0.00 0.00 3.41
3815 4426 6.750963 GCTCAAATTTTCTCATTGGATCAGTC 59.249 38.462 0.00 0.00 0.00 3.51
3816 4427 7.362747 GCTCAAATTTTCTCATTGGATCAGTCT 60.363 37.037 0.00 0.00 0.00 3.24
3817 4428 9.170734 CTCAAATTTTCTCATTGGATCAGTCTA 57.829 33.333 0.00 0.00 0.00 2.59
3818 4429 8.950210 TCAAATTTTCTCATTGGATCAGTCTAC 58.050 33.333 0.00 0.00 0.00 2.59
3819 4430 7.872113 AATTTTCTCATTGGATCAGTCTACC 57.128 36.000 0.00 0.00 0.00 3.18
3820 4431 6.373005 TTTTCTCATTGGATCAGTCTACCA 57.627 37.500 0.00 0.00 0.00 3.25
3821 4432 5.604758 TTCTCATTGGATCAGTCTACCAG 57.395 43.478 0.00 0.00 35.08 4.00
3822 4433 3.963374 TCTCATTGGATCAGTCTACCAGG 59.037 47.826 0.00 0.00 35.08 4.45
3917 4539 5.180680 AGTTTATTTCGCAGTCCCTTAACAC 59.819 40.000 0.00 0.00 0.00 3.32
3918 4540 2.623878 TTTCGCAGTCCCTTAACACA 57.376 45.000 0.00 0.00 0.00 3.72
3919 4541 2.851263 TTCGCAGTCCCTTAACACAT 57.149 45.000 0.00 0.00 0.00 3.21
3920 4542 2.851263 TCGCAGTCCCTTAACACATT 57.149 45.000 0.00 0.00 0.00 2.71
3921 4543 3.134574 TCGCAGTCCCTTAACACATTT 57.865 42.857 0.00 0.00 0.00 2.32
3922 4544 4.274602 TCGCAGTCCCTTAACACATTTA 57.725 40.909 0.00 0.00 0.00 1.40
3923 4545 4.250464 TCGCAGTCCCTTAACACATTTAG 58.750 43.478 0.00 0.00 0.00 1.85
3924 4546 4.000988 CGCAGTCCCTTAACACATTTAGT 58.999 43.478 0.00 0.00 0.00 2.24
3925 4547 4.454504 CGCAGTCCCTTAACACATTTAGTT 59.545 41.667 0.00 0.00 0.00 2.24
3926 4548 5.640357 CGCAGTCCCTTAACACATTTAGTTA 59.360 40.000 0.00 0.00 0.00 2.24
3953 4575 4.141892 TGACCTGACTCGAACCAACTAAAA 60.142 41.667 0.00 0.00 0.00 1.52
3970 4592 0.544697 AAATATCGGGGCCAACGAGT 59.455 50.000 23.21 13.72 44.24 4.18
3971 4593 0.544697 AATATCGGGGCCAACGAGTT 59.455 50.000 23.21 17.75 44.24 3.01
3972 4594 0.179056 ATATCGGGGCCAACGAGTTG 60.179 55.000 23.21 8.87 44.24 3.16
3973 4595 1.546589 TATCGGGGCCAACGAGTTGT 61.547 55.000 23.21 11.67 44.24 3.32
3974 4596 3.353836 CGGGGCCAACGAGTTGTG 61.354 66.667 13.19 7.44 38.85 3.33
3975 4597 3.670377 GGGGCCAACGAGTTGTGC 61.670 66.667 4.39 15.08 38.85 4.57
3976 4598 2.904866 GGGCCAACGAGTTGTGCA 60.905 61.111 21.62 0.00 38.85 4.57
3977 4599 2.639286 GGCCAACGAGTTGTGCAG 59.361 61.111 21.62 8.07 38.85 4.41
3978 4600 2.050985 GCCAACGAGTTGTGCAGC 60.051 61.111 17.94 10.32 38.85 5.25
3993 4615 0.595095 GCAGCTGTTTTGACCTCCTG 59.405 55.000 16.64 0.00 0.00 3.86
4038 4704 2.673200 GGATGAGCACTCTGGGGCA 61.673 63.158 0.00 0.00 0.00 5.36
4054 4720 2.823829 GCATGCAACCCGGACGATC 61.824 63.158 14.21 0.00 0.00 3.69
4063 4729 2.877866 ACCCGGACGATCTAGATGATT 58.122 47.619 10.74 0.00 35.14 2.57
4122 4788 6.003234 GATGATCTTAATCGACGAGGAAGA 57.997 41.667 20.32 20.32 34.39 2.87
4123 4789 5.171147 TGATCTTAATCGACGAGGAAGAC 57.829 43.478 20.41 15.77 34.39 3.01
4124 4790 4.036498 TGATCTTAATCGACGAGGAAGACC 59.964 45.833 20.41 14.59 34.39 3.85
4125 4791 2.353889 TCTTAATCGACGAGGAAGACCG 59.646 50.000 16.27 0.00 41.83 4.79
4126 4792 2.028420 TAATCGACGAGGAAGACCGA 57.972 50.000 3.01 0.00 41.83 4.69
4127 4793 0.733729 AATCGACGAGGAAGACCGAG 59.266 55.000 3.01 0.00 41.83 4.63
4128 4794 1.716826 ATCGACGAGGAAGACCGAGC 61.717 60.000 3.01 0.00 41.83 5.03
4129 4795 2.400158 CGACGAGGAAGACCGAGCT 61.400 63.158 0.00 0.00 41.83 4.09
4130 4796 1.430228 GACGAGGAAGACCGAGCTC 59.570 63.158 2.73 2.73 41.83 4.09
4131 4797 1.303398 ACGAGGAAGACCGAGCTCA 60.303 57.895 15.40 0.00 41.83 4.26
4132 4798 0.894184 ACGAGGAAGACCGAGCTCAA 60.894 55.000 15.40 0.00 41.83 3.02
4133 4799 0.457851 CGAGGAAGACCGAGCTCAAT 59.542 55.000 15.40 0.00 41.83 2.57
4134 4800 1.800655 CGAGGAAGACCGAGCTCAATG 60.801 57.143 15.40 3.86 41.83 2.82
4135 4801 1.478510 GAGGAAGACCGAGCTCAATGA 59.521 52.381 15.40 0.00 41.83 2.57
4136 4802 1.480137 AGGAAGACCGAGCTCAATGAG 59.520 52.381 15.40 5.78 41.83 2.90
4146 4812 1.719600 GCTCAATGAGCGAGTGTTCT 58.280 50.000 20.11 0.00 45.85 3.01
4147 4813 2.072298 GCTCAATGAGCGAGTGTTCTT 58.928 47.619 20.11 0.00 45.85 2.52
4148 4814 2.093467 GCTCAATGAGCGAGTGTTCTTC 59.907 50.000 20.11 0.00 45.85 2.87
4149 4815 2.670414 CTCAATGAGCGAGTGTTCTTCC 59.330 50.000 0.00 0.00 0.00 3.46
4150 4816 1.391485 CAATGAGCGAGTGTTCTTCCG 59.609 52.381 0.00 0.00 0.00 4.30
4151 4817 0.737715 ATGAGCGAGTGTTCTTCCGC 60.738 55.000 0.00 0.00 47.00 5.54
4153 4819 3.637714 GCGAGTGTTCTTCCGCAA 58.362 55.556 0.00 0.00 46.04 4.85
4154 4820 1.493311 GCGAGTGTTCTTCCGCAAG 59.507 57.895 0.00 0.00 46.04 4.01
4155 4821 0.944311 GCGAGTGTTCTTCCGCAAGA 60.944 55.000 0.00 0.00 46.04 3.02
4156 4822 1.714794 CGAGTGTTCTTCCGCAAGAT 58.285 50.000 0.00 0.00 38.50 2.40
4157 4823 1.391485 CGAGTGTTCTTCCGCAAGATG 59.609 52.381 0.00 0.00 38.50 2.90
4158 4824 2.688507 GAGTGTTCTTCCGCAAGATGA 58.311 47.619 0.00 0.00 38.50 2.92
4159 4825 2.670414 GAGTGTTCTTCCGCAAGATGAG 59.330 50.000 0.00 0.00 38.50 2.90
4245 4912 1.613437 CCACCAGGCTACAAACAAAGG 59.387 52.381 0.00 0.00 0.00 3.11
4246 4913 2.306847 CACCAGGCTACAAACAAAGGT 58.693 47.619 0.00 0.00 0.00 3.50
4247 4914 2.693074 CACCAGGCTACAAACAAAGGTT 59.307 45.455 0.00 0.00 39.43 3.50
4248 4915 2.956333 ACCAGGCTACAAACAAAGGTTC 59.044 45.455 0.00 0.00 35.82 3.62
4249 4916 2.955660 CCAGGCTACAAACAAAGGTTCA 59.044 45.455 0.00 0.00 35.82 3.18
4250 4917 3.383185 CCAGGCTACAAACAAAGGTTCAA 59.617 43.478 0.00 0.00 35.82 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.031417 ATACCCGCACTCCACTGCC 62.031 63.158 0.00 0.00 33.18 4.85
12 13 0.386100 CGCATCTCGTCTCATACCCG 60.386 60.000 0.00 0.00 0.00 5.28
23 24 2.098298 CGGCCAAAACGCATCTCG 59.902 61.111 2.24 0.00 45.38 4.04
43 44 3.403968 GCTATTTAACTAGGGCTCTGGC 58.596 50.000 0.00 0.00 37.82 4.85
46 47 2.633481 CCGGCTATTTAACTAGGGCTCT 59.367 50.000 0.00 0.00 0.00 4.09
51 52 1.418637 TGCCCCGGCTATTTAACTAGG 59.581 52.381 7.35 0.00 42.51 3.02
55 56 1.880027 CATCTGCCCCGGCTATTTAAC 59.120 52.381 7.35 0.00 42.51 2.01
64 65 3.083349 TCTGTCCATCTGCCCCGG 61.083 66.667 0.00 0.00 0.00 5.73
72 73 2.125512 AAGCGGCGTCTGTCCATC 60.126 61.111 9.37 0.00 0.00 3.51
73 74 2.125512 GAAGCGGCGTCTGTCCAT 60.126 61.111 9.37 0.00 0.00 3.41
74 75 2.449031 ATTGAAGCGGCGTCTGTCCA 62.449 55.000 16.51 3.41 0.00 4.02
87 88 1.321016 CAAGTTGCGTCGCATTGAAG 58.679 50.000 22.96 9.55 38.76 3.02
88 89 0.660005 GCAAGTTGCGTCGCATTGAA 60.660 50.000 28.70 10.99 38.76 2.69
89 90 1.082169 GCAAGTTGCGTCGCATTGA 60.082 52.632 28.70 11.34 38.76 2.57
104 105 3.259064 GACTGACAAGCCTATTACGCAA 58.741 45.455 0.00 0.00 0.00 4.85
105 106 2.418197 GGACTGACAAGCCTATTACGCA 60.418 50.000 0.00 0.00 0.00 5.24
106 107 2.202566 GGACTGACAAGCCTATTACGC 58.797 52.381 0.00 0.00 0.00 4.42
109 110 1.760613 CGGGGACTGACAAGCCTATTA 59.239 52.381 0.00 0.00 36.31 0.98
149 150 3.827898 GACTGGACGAGAGGGCGG 61.828 72.222 0.00 0.00 35.12 6.13
155 156 3.733960 CGGCGTGACTGGACGAGA 61.734 66.667 0.00 0.00 42.10 4.04
256 257 3.561313 GCCCCATCCAATATTATCACCGT 60.561 47.826 0.00 0.00 0.00 4.83
348 359 3.990469 CCGCATATATCTGTCAACTGTCC 59.010 47.826 0.00 0.00 0.00 4.02
355 375 5.659440 TCTAATGCCGCATATATCTGTCA 57.341 39.130 6.22 0.00 0.00 3.58
362 382 4.817318 TCACCATCTAATGCCGCATATA 57.183 40.909 6.22 1.22 0.00 0.86
392 412 0.390340 CGTCTGGACCATGGTGTCTG 60.390 60.000 25.52 17.26 35.54 3.51
445 480 3.427503 ACACTTTTGTTGTGCACTAGTGC 60.428 43.478 35.76 35.76 44.94 4.40
450 485 2.094752 GGTGACACTTTTGTTGTGCACT 60.095 45.455 19.41 0.00 39.70 4.40
495 530 3.476552 TGTGGAAGCCTAAAACAGAGTG 58.523 45.455 0.00 0.00 0.00 3.51
602 637 1.937278 TTTGGCTGTGTTCGTTCGTA 58.063 45.000 0.00 0.00 0.00 3.43
603 638 1.088306 TTTTGGCTGTGTTCGTTCGT 58.912 45.000 0.00 0.00 0.00 3.85
604 639 2.181426 TTTTTGGCTGTGTTCGTTCG 57.819 45.000 0.00 0.00 0.00 3.95
633 668 1.067565 CGAGGATGGCATACGTAGCAT 60.068 52.381 3.56 9.17 0.00 3.79
648 683 2.365105 GGTGGGTGGATCCGAGGA 60.365 66.667 7.39 0.00 37.00 3.71
850 885 2.533232 TCGGGGTTGGGGGATTGT 60.533 61.111 0.00 0.00 0.00 2.71
892 933 2.278661 GGCGACCTCCGATTCGTC 60.279 66.667 5.20 0.00 41.76 4.20
911 952 4.162690 GAGCGGAACAGGGCGGAT 62.163 66.667 0.00 0.00 0.00 4.18
966 1008 1.004918 CGGCTCCGTTCAAAGACCT 60.005 57.895 0.00 0.00 34.35 3.85
1085 1127 1.509703 GGCGAGAAAGAAAGGTTCGT 58.490 50.000 0.00 0.00 34.05 3.85
1090 1132 2.778679 CGCGGCGAGAAAGAAAGG 59.221 61.111 19.16 0.00 0.00 3.11
1161 1375 4.230657 CGAGACGAACAGATCAAGAACTT 58.769 43.478 0.00 0.00 0.00 2.66
1296 1512 4.427096 TCACGAAAGAGAGACATGAGTC 57.573 45.455 0.00 0.00 45.31 3.36
1305 1521 2.232452 ACCTGGACATCACGAAAGAGAG 59.768 50.000 0.00 0.00 33.27 3.20
1441 1688 3.320626 TCGATCATTCCGCTGATTGATC 58.679 45.455 22.80 22.80 45.89 2.92
1453 1700 4.125703 AGCAGGACTTGATTCGATCATTC 58.874 43.478 0.00 0.00 39.39 2.67
1456 1703 3.616956 AAGCAGGACTTGATTCGATCA 57.383 42.857 0.00 0.00 37.17 2.92
1483 1735 4.127171 CAGTTCAGGAGAAAGAACGGAAA 58.873 43.478 0.00 0.00 46.54 3.13
1508 1778 3.044305 GCAGCGAGCAAGAACGGT 61.044 61.111 0.00 0.00 44.79 4.83
1679 2005 5.622770 ACCACCACAAGAAATCGATTTAC 57.377 39.130 22.78 15.63 0.00 2.01
1806 2135 3.195698 GTGACGATCTTGGCGGCC 61.196 66.667 13.32 13.32 35.47 6.13
1857 2198 2.671682 GAGGTCTTGGGGGCAGAC 59.328 66.667 0.00 0.00 40.12 3.51
2168 2535 1.512926 ACATCGTCAGAACAGTTGCC 58.487 50.000 0.00 0.00 0.00 4.52
2452 2829 0.912486 AAGTGTCTGGCCATACCTCC 59.088 55.000 17.87 6.68 40.22 4.30
2465 2847 1.353091 AGGGGGTGAGAGAAAGTGTC 58.647 55.000 0.00 0.00 0.00 3.67
2523 2968 4.620609 CAGATTCAGAGTTCGTTCACAGAG 59.379 45.833 0.00 0.00 0.00 3.35
2568 3024 1.960689 TCGGCGATGGATATGAAGTCA 59.039 47.619 4.99 0.00 0.00 3.41
2733 3192 6.849588 AATCAAAATGCAGTTGGTTCTTTC 57.150 33.333 0.00 0.00 0.00 2.62
2739 3198 5.534207 TTCAGAATCAAAATGCAGTTGGT 57.466 34.783 0.00 0.00 0.00 3.67
2777 3236 1.733389 CGCAAATTCCATGGCACTGAC 60.733 52.381 6.96 0.00 0.00 3.51
2778 3237 0.527113 CGCAAATTCCATGGCACTGA 59.473 50.000 6.96 0.00 0.00 3.41
2779 3238 0.244450 ACGCAAATTCCATGGCACTG 59.756 50.000 6.96 2.72 0.00 3.66
2780 3239 0.527565 GACGCAAATTCCATGGCACT 59.472 50.000 6.96 0.00 0.00 4.40
2822 3317 3.791789 GCTGCGTTCATTCACAAGAACAA 60.792 43.478 0.00 0.00 43.20 2.83
3006 3501 4.069232 CAGGAGCTGCGGTTCGGA 62.069 66.667 0.00 0.00 0.00 4.55
3008 3503 3.114616 CACAGGAGCTGCGGTTCG 61.115 66.667 8.55 0.00 34.37 3.95
3085 3613 4.099266 TCCCTGAAAACCAACAAACAGATG 59.901 41.667 0.00 0.00 0.00 2.90
3253 3781 1.090728 GAGCAGCAGTTCCTAAAGCC 58.909 55.000 0.00 0.00 0.00 4.35
3264 3792 2.433145 TCGAAAGCCGAGCAGCAG 60.433 61.111 0.00 0.00 43.23 4.24
3378 3947 2.549754 TCTCTTTCGAAAGCCAAGCAAG 59.450 45.455 29.10 19.89 35.99 4.01
3475 4074 1.337260 CCAAGACCACCGAGAGAACTG 60.337 57.143 0.00 0.00 0.00 3.16
3476 4075 0.969894 CCAAGACCACCGAGAGAACT 59.030 55.000 0.00 0.00 0.00 3.01
3530 4141 2.831526 ACAGTGGAAGGCAAACAAAAGT 59.168 40.909 0.00 0.00 0.00 2.66
3561 4172 3.923017 AGTACAAAATCAGGCAAGTGC 57.077 42.857 0.00 0.00 41.14 4.40
3562 4173 7.820648 AGATTAAGTACAAAATCAGGCAAGTG 58.179 34.615 17.49 0.00 35.07 3.16
3589 4200 1.001048 TGCAGCAGAATCACTTGCAAC 60.001 47.619 0.00 0.00 38.77 4.17
3590 4201 1.001048 GTGCAGCAGAATCACTTGCAA 60.001 47.619 0.00 0.00 41.85 4.08
3591 4202 0.594602 GTGCAGCAGAATCACTTGCA 59.405 50.000 0.00 2.33 39.21 4.08
3594 4205 1.202855 ACAGGTGCAGCAGAATCACTT 60.203 47.619 19.63 0.00 0.00 3.16
3595 4206 0.399454 ACAGGTGCAGCAGAATCACT 59.601 50.000 19.63 0.00 0.00 3.41
3597 4208 1.241165 CAACAGGTGCAGCAGAATCA 58.759 50.000 19.63 0.00 0.00 2.57
3598 4209 0.524862 CCAACAGGTGCAGCAGAATC 59.475 55.000 19.63 0.00 0.00 2.52
3599 4210 0.111061 TCCAACAGGTGCAGCAGAAT 59.889 50.000 19.63 2.12 0.00 2.40
3600 4211 0.106769 TTCCAACAGGTGCAGCAGAA 60.107 50.000 19.63 9.58 0.00 3.02
3601 4212 0.535780 CTTCCAACAGGTGCAGCAGA 60.536 55.000 19.63 3.68 0.00 4.26
3602 4213 0.535780 TCTTCCAACAGGTGCAGCAG 60.536 55.000 19.63 13.21 0.00 4.24
3603 4214 0.819259 GTCTTCCAACAGGTGCAGCA 60.819 55.000 19.63 0.00 0.00 4.41
3604 4215 0.819259 TGTCTTCCAACAGGTGCAGC 60.819 55.000 8.11 8.11 0.00 5.25
3605 4216 1.538512 CATGTCTTCCAACAGGTGCAG 59.461 52.381 0.00 0.00 31.50 4.41
3606 4217 1.142667 TCATGTCTTCCAACAGGTGCA 59.857 47.619 0.00 0.00 32.93 4.57
3607 4218 1.896220 TCATGTCTTCCAACAGGTGC 58.104 50.000 0.00 0.00 32.93 5.01
3608 4219 5.458041 AAAATCATGTCTTCCAACAGGTG 57.542 39.130 0.00 0.00 32.93 4.00
3609 4220 4.524328 GGAAAATCATGTCTTCCAACAGGT 59.476 41.667 14.42 0.00 38.80 4.00
3610 4221 4.768968 AGGAAAATCATGTCTTCCAACAGG 59.231 41.667 18.82 0.00 41.00 4.00
3611 4222 5.391310 CGAGGAAAATCATGTCTTCCAACAG 60.391 44.000 18.82 8.31 41.00 3.16
3612 4223 4.455533 CGAGGAAAATCATGTCTTCCAACA 59.544 41.667 18.82 0.00 41.00 3.33
3613 4224 4.455877 ACGAGGAAAATCATGTCTTCCAAC 59.544 41.667 18.82 13.35 41.00 3.77
3614 4225 4.651778 ACGAGGAAAATCATGTCTTCCAA 58.348 39.130 18.82 0.00 41.00 3.53
3615 4226 4.253685 GACGAGGAAAATCATGTCTTCCA 58.746 43.478 18.82 0.00 41.00 3.53
3616 4227 4.253685 TGACGAGGAAAATCATGTCTTCC 58.746 43.478 12.48 12.48 39.18 3.46
3617 4228 5.862924 TTGACGAGGAAAATCATGTCTTC 57.137 39.130 0.00 0.00 0.00 2.87
3618 4229 6.633500 TTTTGACGAGGAAAATCATGTCTT 57.367 33.333 0.00 0.00 0.00 3.01
3619 4230 6.633500 TTTTTGACGAGGAAAATCATGTCT 57.367 33.333 0.00 0.00 0.00 3.41
3645 4256 5.699097 TTTTGTACCTAATGTTCCTGCAC 57.301 39.130 0.00 0.00 0.00 4.57
3671 4282 5.047566 TCACTCTTGAGATTGGGAAAACA 57.952 39.130 4.49 0.00 0.00 2.83
3672 4283 5.299279 TGTTCACTCTTGAGATTGGGAAAAC 59.701 40.000 4.49 0.00 31.71 2.43
3673 4284 5.445069 TGTTCACTCTTGAGATTGGGAAAA 58.555 37.500 4.49 0.00 31.71 2.29
3674 4285 5.047566 TGTTCACTCTTGAGATTGGGAAA 57.952 39.130 4.49 0.00 31.71 3.13
3675 4286 4.347876 TCTGTTCACTCTTGAGATTGGGAA 59.652 41.667 4.49 0.00 31.71 3.97
3676 4287 3.903714 TCTGTTCACTCTTGAGATTGGGA 59.096 43.478 4.49 0.00 31.71 4.37
3677 4288 4.277515 TCTGTTCACTCTTGAGATTGGG 57.722 45.455 4.49 0.00 31.71 4.12
3678 4289 6.814506 ATTTCTGTTCACTCTTGAGATTGG 57.185 37.500 4.49 0.00 31.71 3.16
3679 4290 7.868775 TCAATTTCTGTTCACTCTTGAGATTG 58.131 34.615 4.49 0.00 31.71 2.67
3680 4291 8.348507 GTTCAATTTCTGTTCACTCTTGAGATT 58.651 33.333 4.49 0.00 31.71 2.40
3681 4292 7.718753 AGTTCAATTTCTGTTCACTCTTGAGAT 59.281 33.333 4.49 0.00 31.71 2.75
3682 4293 7.011763 CAGTTCAATTTCTGTTCACTCTTGAGA 59.988 37.037 4.49 0.00 31.71 3.27
3683 4294 7.130917 CAGTTCAATTTCTGTTCACTCTTGAG 58.869 38.462 0.00 0.00 31.71 3.02
3684 4295 6.599244 ACAGTTCAATTTCTGTTCACTCTTGA 59.401 34.615 0.00 0.00 41.33 3.02
3685 4296 6.789262 ACAGTTCAATTTCTGTTCACTCTTG 58.211 36.000 0.00 0.00 41.33 3.02
3694 4305 5.930837 TGGGAAAACAGTTCAATTTCTGT 57.069 34.783 0.00 0.00 45.21 3.41
3695 4306 7.212274 AGATTGGGAAAACAGTTCAATTTCTG 58.788 34.615 0.76 0.00 34.34 3.02
3696 4307 7.069826 TGAGATTGGGAAAACAGTTCAATTTCT 59.930 33.333 13.07 4.15 33.16 2.52
3697 4308 7.209475 TGAGATTGGGAAAACAGTTCAATTTC 58.791 34.615 8.15 8.15 32.83 2.17
3698 4309 7.123355 TGAGATTGGGAAAACAGTTCAATTT 57.877 32.000 0.76 0.00 0.00 1.82
3699 4310 6.729690 TGAGATTGGGAAAACAGTTCAATT 57.270 33.333 0.76 0.00 0.00 2.32
3700 4311 6.550854 TCTTGAGATTGGGAAAACAGTTCAAT 59.449 34.615 0.00 0.00 0.00 2.57
3701 4312 5.890985 TCTTGAGATTGGGAAAACAGTTCAA 59.109 36.000 0.00 0.00 0.00 2.69
3702 4313 5.445069 TCTTGAGATTGGGAAAACAGTTCA 58.555 37.500 0.00 0.00 0.00 3.18
3703 4314 5.532779 ACTCTTGAGATTGGGAAAACAGTTC 59.467 40.000 4.49 0.00 0.00 3.01
3704 4315 5.300286 CACTCTTGAGATTGGGAAAACAGTT 59.700 40.000 4.49 0.00 0.00 3.16
3705 4316 4.823989 CACTCTTGAGATTGGGAAAACAGT 59.176 41.667 4.49 0.00 0.00 3.55
3706 4317 5.065914 TCACTCTTGAGATTGGGAAAACAG 58.934 41.667 4.49 0.00 0.00 3.16
3707 4318 5.047566 TCACTCTTGAGATTGGGAAAACA 57.952 39.130 4.49 0.00 0.00 2.83
3708 4319 5.299279 TGTTCACTCTTGAGATTGGGAAAAC 59.701 40.000 4.49 0.00 31.71 2.43
3713 4324 5.972107 ATTTGTTCACTCTTGAGATTGGG 57.028 39.130 4.49 0.00 31.71 4.12
3716 4327 5.537674 AGGCAATTTGTTCACTCTTGAGATT 59.462 36.000 4.49 0.00 31.71 2.40
3752 4363 4.570930 ACAGTTTTCTTCTAGCTACAGGC 58.429 43.478 0.00 0.00 42.19 4.85
3753 4364 6.031751 AGACAGTTTTCTTCTAGCTACAGG 57.968 41.667 0.00 0.00 0.00 4.00
3754 4365 6.096695 GGAGACAGTTTTCTTCTAGCTACAG 58.903 44.000 0.00 0.00 0.00 2.74
3755 4366 5.538813 TGGAGACAGTTTTCTTCTAGCTACA 59.461 40.000 0.00 0.00 35.01 2.74
3756 4367 6.026947 TGGAGACAGTTTTCTTCTAGCTAC 57.973 41.667 0.00 0.00 35.01 3.58
3773 4384 0.674895 AGCTGCGTTTCCATGGAGAC 60.675 55.000 22.60 22.60 28.62 3.36
3774 4385 0.391661 GAGCTGCGTTTCCATGGAGA 60.392 55.000 15.53 7.90 28.62 3.71
3775 4386 0.674581 TGAGCTGCGTTTCCATGGAG 60.675 55.000 15.53 4.71 0.00 3.86
3776 4387 0.250684 TTGAGCTGCGTTTCCATGGA 60.251 50.000 11.44 11.44 0.00 3.41
3777 4388 0.597568 TTTGAGCTGCGTTTCCATGG 59.402 50.000 4.97 4.97 0.00 3.66
3778 4389 2.642139 ATTTGAGCTGCGTTTCCATG 57.358 45.000 0.00 0.00 0.00 3.66
3779 4390 3.665745 AAATTTGAGCTGCGTTTCCAT 57.334 38.095 0.00 0.00 0.00 3.41
3780 4391 3.068024 AGAAAATTTGAGCTGCGTTTCCA 59.932 39.130 0.00 0.00 0.00 3.53
3781 4392 3.642705 AGAAAATTTGAGCTGCGTTTCC 58.357 40.909 0.00 0.00 0.00 3.13
3782 4393 4.290155 TGAGAAAATTTGAGCTGCGTTTC 58.710 39.130 0.00 0.00 0.00 2.78
3787 4398 4.813027 TCCAATGAGAAAATTTGAGCTGC 58.187 39.130 0.00 0.00 0.00 5.25
3797 4408 6.373005 TGGTAGACTGATCCAATGAGAAAA 57.627 37.500 0.00 0.00 0.00 2.29
3799 4410 4.406972 CCTGGTAGACTGATCCAATGAGAA 59.593 45.833 0.00 0.00 0.00 2.87
3800 4411 3.963374 CCTGGTAGACTGATCCAATGAGA 59.037 47.826 0.00 0.00 0.00 3.27
3802 4413 3.706594 GACCTGGTAGACTGATCCAATGA 59.293 47.826 0.00 0.00 0.00 2.57
3804 4415 3.708631 CTGACCTGGTAGACTGATCCAAT 59.291 47.826 0.00 0.00 0.00 3.16
3805 4416 3.099905 CTGACCTGGTAGACTGATCCAA 58.900 50.000 0.00 0.00 0.00 3.53
3806 4417 2.624293 CCTGACCTGGTAGACTGATCCA 60.624 54.545 0.00 0.00 0.00 3.41
3807 4418 2.035632 CCTGACCTGGTAGACTGATCC 58.964 57.143 0.00 0.00 0.00 3.36
3808 4419 3.019799 TCCTGACCTGGTAGACTGATC 57.980 52.381 0.00 0.00 0.00 2.92
3809 4420 3.474798 TTCCTGACCTGGTAGACTGAT 57.525 47.619 0.00 0.00 0.00 2.90
3810 4421 2.992847 TTCCTGACCTGGTAGACTGA 57.007 50.000 0.00 0.00 0.00 3.41
3811 4422 4.351874 TTTTTCCTGACCTGGTAGACTG 57.648 45.455 0.00 0.00 0.00 3.51
3835 4446 4.470334 AGAATCTGTCCTCTTTGCTCTC 57.530 45.455 0.00 0.00 0.00 3.20
3917 4539 9.529325 TTCGAGTCAGGTCATAATAACTAAATG 57.471 33.333 0.00 0.00 0.00 2.32
3918 4540 9.530633 GTTCGAGTCAGGTCATAATAACTAAAT 57.469 33.333 0.00 0.00 0.00 1.40
3919 4541 7.977853 GGTTCGAGTCAGGTCATAATAACTAAA 59.022 37.037 0.00 0.00 0.00 1.85
3920 4542 7.123098 TGGTTCGAGTCAGGTCATAATAACTAA 59.877 37.037 0.00 0.00 0.00 2.24
3921 4543 6.604396 TGGTTCGAGTCAGGTCATAATAACTA 59.396 38.462 0.00 0.00 0.00 2.24
3922 4544 5.421056 TGGTTCGAGTCAGGTCATAATAACT 59.579 40.000 0.00 0.00 0.00 2.24
3923 4545 5.657474 TGGTTCGAGTCAGGTCATAATAAC 58.343 41.667 0.00 0.00 0.00 1.89
3924 4546 5.925506 TGGTTCGAGTCAGGTCATAATAA 57.074 39.130 0.00 0.00 0.00 1.40
3925 4547 5.421056 AGTTGGTTCGAGTCAGGTCATAATA 59.579 40.000 0.00 0.00 0.00 0.98
3926 4548 4.223032 AGTTGGTTCGAGTCAGGTCATAAT 59.777 41.667 0.00 0.00 0.00 1.28
3953 4575 0.179056 CAACTCGTTGGCCCCGATAT 60.179 55.000 14.18 4.44 36.95 1.63
3970 4592 1.405105 GAGGTCAAAACAGCTGCACAA 59.595 47.619 15.27 0.00 0.00 3.33
3971 4593 1.024271 GAGGTCAAAACAGCTGCACA 58.976 50.000 15.27 0.00 0.00 4.57
3972 4594 0.312102 GGAGGTCAAAACAGCTGCAC 59.688 55.000 15.27 2.70 32.81 4.57
3973 4595 0.183492 AGGAGGTCAAAACAGCTGCA 59.817 50.000 15.27 0.00 34.86 4.41
3974 4596 0.595095 CAGGAGGTCAAAACAGCTGC 59.405 55.000 15.27 0.00 32.72 5.25
3975 4597 1.876156 GACAGGAGGTCAAAACAGCTG 59.124 52.381 13.48 13.48 46.19 4.24
3976 4598 2.262423 GACAGGAGGTCAAAACAGCT 57.738 50.000 0.00 0.00 46.19 4.24
3993 4615 1.189403 CCATAGCGAGTTTCGTCGAC 58.811 55.000 5.18 5.18 42.85 4.20
3998 4620 0.103208 AGGAGCCATAGCGAGTTTCG 59.897 55.000 0.00 0.00 46.67 3.46
4038 4704 0.389391 CTAGATCGTCCGGGTTGCAT 59.611 55.000 0.00 0.00 0.00 3.96
4099 4765 5.854338 GTCTTCCTCGTCGATTAAGATCATC 59.146 44.000 17.45 6.20 32.33 2.92
4100 4766 5.278561 GGTCTTCCTCGTCGATTAAGATCAT 60.279 44.000 18.24 0.00 29.58 2.45
4101 4767 4.036498 GGTCTTCCTCGTCGATTAAGATCA 59.964 45.833 18.24 1.10 29.58 2.92
4102 4768 4.538917 GGTCTTCCTCGTCGATTAAGATC 58.461 47.826 17.45 14.68 0.00 2.75
4103 4769 3.003482 CGGTCTTCCTCGTCGATTAAGAT 59.997 47.826 17.45 0.00 0.00 2.40
4104 4770 2.353889 CGGTCTTCCTCGTCGATTAAGA 59.646 50.000 12.81 12.81 0.00 2.10
4105 4771 2.353889 TCGGTCTTCCTCGTCGATTAAG 59.646 50.000 0.00 2.96 0.00 1.85
4106 4772 2.353889 CTCGGTCTTCCTCGTCGATTAA 59.646 50.000 0.00 0.00 0.00 1.40
4107 4773 1.938577 CTCGGTCTTCCTCGTCGATTA 59.061 52.381 0.00 0.00 0.00 1.75
4108 4774 0.733729 CTCGGTCTTCCTCGTCGATT 59.266 55.000 0.00 0.00 0.00 3.34
4109 4775 1.716826 GCTCGGTCTTCCTCGTCGAT 61.717 60.000 0.00 0.00 0.00 3.59
4110 4776 2.396955 GCTCGGTCTTCCTCGTCGA 61.397 63.158 0.00 0.00 0.00 4.20
4111 4777 2.100603 GCTCGGTCTTCCTCGTCG 59.899 66.667 0.00 0.00 0.00 5.12
4112 4778 1.306642 TGAGCTCGGTCTTCCTCGTC 61.307 60.000 9.64 0.00 0.00 4.20
4113 4779 0.894184 TTGAGCTCGGTCTTCCTCGT 60.894 55.000 9.64 0.00 0.00 4.18
4114 4780 0.457851 ATTGAGCTCGGTCTTCCTCG 59.542 55.000 9.64 0.00 0.00 4.63
4115 4781 1.478510 TCATTGAGCTCGGTCTTCCTC 59.521 52.381 9.64 0.00 0.00 3.71
4116 4782 1.480137 CTCATTGAGCTCGGTCTTCCT 59.520 52.381 9.64 0.00 0.00 3.36
4117 4783 1.933247 CTCATTGAGCTCGGTCTTCC 58.067 55.000 9.64 0.00 0.00 3.46
4128 4794 2.670414 GGAAGAACACTCGCTCATTGAG 59.330 50.000 9.40 9.40 39.40 3.02
4129 4795 2.688507 GGAAGAACACTCGCTCATTGA 58.311 47.619 0.00 0.00 0.00 2.57
4130 4796 1.391485 CGGAAGAACACTCGCTCATTG 59.609 52.381 0.00 0.00 0.00 2.82
4131 4797 1.714794 CGGAAGAACACTCGCTCATT 58.285 50.000 0.00 0.00 0.00 2.57
4132 4798 0.737715 GCGGAAGAACACTCGCTCAT 60.738 55.000 0.00 0.00 44.10 2.90
4133 4799 1.372997 GCGGAAGAACACTCGCTCA 60.373 57.895 0.00 0.00 44.10 4.26
4134 4800 3.464628 GCGGAAGAACACTCGCTC 58.535 61.111 0.00 0.00 44.10 5.03
4136 4802 2.268302 ATCTTGCGGAAGAACACTCGC 61.268 52.381 23.62 0.00 41.64 5.03
4137 4803 1.391485 CATCTTGCGGAAGAACACTCG 59.609 52.381 23.62 4.58 41.64 4.18
4138 4804 2.670414 CTCATCTTGCGGAAGAACACTC 59.330 50.000 23.62 0.00 41.64 3.51
4139 4805 2.613977 CCTCATCTTGCGGAAGAACACT 60.614 50.000 23.62 3.92 41.64 3.55
4140 4806 1.734465 CCTCATCTTGCGGAAGAACAC 59.266 52.381 23.62 0.00 41.64 3.32
4141 4807 1.339055 CCCTCATCTTGCGGAAGAACA 60.339 52.381 23.62 11.61 41.64 3.18
4142 4808 1.066143 TCCCTCATCTTGCGGAAGAAC 60.066 52.381 23.62 0.00 41.64 3.01
4143 4809 1.066143 GTCCCTCATCTTGCGGAAGAA 60.066 52.381 23.62 7.18 41.64 2.52
4144 4810 0.537188 GTCCCTCATCTTGCGGAAGA 59.463 55.000 22.12 22.12 42.53 2.87
4145 4811 0.807667 CGTCCCTCATCTTGCGGAAG 60.808 60.000 10.87 10.87 0.00 3.46
4146 4812 1.218047 CGTCCCTCATCTTGCGGAA 59.782 57.895 0.00 0.00 0.00 4.30
4147 4813 1.945354 GACGTCCCTCATCTTGCGGA 61.945 60.000 3.51 0.00 0.00 5.54
4148 4814 1.519455 GACGTCCCTCATCTTGCGG 60.519 63.158 3.51 0.00 0.00 5.69
4149 4815 0.803768 CAGACGTCCCTCATCTTGCG 60.804 60.000 13.01 0.00 0.00 4.85
4150 4816 0.460987 CCAGACGTCCCTCATCTTGC 60.461 60.000 13.01 0.00 0.00 4.01
4151 4817 1.186200 TCCAGACGTCCCTCATCTTG 58.814 55.000 13.01 0.70 0.00 3.02
4152 4818 1.938585 TTCCAGACGTCCCTCATCTT 58.061 50.000 13.01 0.00 0.00 2.40
4153 4819 2.035632 GATTCCAGACGTCCCTCATCT 58.964 52.381 13.01 0.00 0.00 2.90
4154 4820 1.069358 GGATTCCAGACGTCCCTCATC 59.931 57.143 13.01 9.17 0.00 2.92
4155 4821 1.123928 GGATTCCAGACGTCCCTCAT 58.876 55.000 13.01 0.00 0.00 2.90
4156 4822 0.976073 GGGATTCCAGACGTCCCTCA 60.976 60.000 13.01 0.00 46.59 3.86
4157 4823 1.823976 GGGATTCCAGACGTCCCTC 59.176 63.158 13.01 2.06 46.59 4.30
4158 4824 4.051932 GGGATTCCAGACGTCCCT 57.948 61.111 13.01 0.00 46.59 4.20


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

AutoCloner maintained by Alex Coulton.