Multiple sequence alignment - TraesCS3A01G362300

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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 TraesCS3A01G362300 chr3A 100.000 6021 0 0 1 6021 610410544 610416564 0.000000e+00 11119.0
1 TraesCS3A01G362300 chr3A 75.258 776 145 30 2272 3014 610523688 610524449 5.820000e-85 326.0
2 TraesCS3A01G362300 chr3A 80.214 374 56 13 2273 2632 610424695 610425064 1.290000e-66 265.0
3 TraesCS3A01G362300 chr3A 84.375 96 14 1 5906 6000 37309423 37309518 6.430000e-15 93.5
4 TraesCS3A01G362300 chr3D 92.950 4525 193 41 1551 6010 467767731 467772194 0.000000e+00 6473.0
5 TraesCS3A01G362300 chr3D 93.497 1261 56 15 298 1554 467766457 467767695 0.000000e+00 1851.0
6 TraesCS3A01G362300 chr3D 80.407 393 63 10 2272 2652 468654506 468654896 2.750000e-73 287.0
7 TraesCS3A01G362300 chr3D 79.697 330 55 10 2314 2632 467777825 467778153 1.690000e-55 228.0
8 TraesCS3A01G362300 chr3D 83.406 229 8 8 1 228 467766180 467766379 1.030000e-42 185.0
9 TraesCS3A01G362300 chr3D 80.000 100 16 3 5907 6003 85223317 85223415 3.010000e-08 71.3
10 TraesCS3A01G362300 chr3B 95.673 1710 55 15 1551 3251 622079120 622080819 0.000000e+00 2730.0
11 TraesCS3A01G362300 chr3B 94.839 1705 83 2 3620 5319 622080819 622082523 0.000000e+00 2656.0
12 TraesCS3A01G362300 chr3B 87.211 1556 117 51 1 1508 622077318 622078839 0.000000e+00 1696.0
13 TraesCS3A01G362300 chr3B 79.144 374 60 13 2273 2632 622085598 622085967 6.030000e-60 243.0
14 TraesCS3A01G362300 chr3B 76.963 191 33 9 5532 5714 82835582 82835769 1.380000e-16 99.0
15 TraesCS3A01G362300 chr3B 100.000 45 0 0 1506 1550 622079035 622079079 3.870000e-12 84.2
16 TraesCS3A01G362300 chr5A 79.255 188 29 9 5532 5714 565246206 565246388 8.200000e-24 122.0
17 TraesCS3A01G362300 chr5A 78.351 194 24 14 5537 5720 446615021 446614836 6.380000e-20 110.0
18 TraesCS3A01G362300 chr5A 77.041 196 35 9 5533 5720 467736348 467736155 2.970000e-18 104.0
19 TraesCS3A01G362300 chr4A 78.061 196 31 10 5533 5720 665472675 665472484 4.930000e-21 113.0
20 TraesCS3A01G362300 chr5D 95.385 65 3 0 1 65 543752939 543752875 2.970000e-18 104.0
21 TraesCS3A01G362300 chr1B 77.273 198 31 12 5527 5712 46832297 46832102 2.970000e-18 104.0
22 TraesCS3A01G362300 chr1A 77.083 192 33 9 5537 5720 250488475 250488287 3.840000e-17 100.0
23 TraesCS3A01G362300 chr1A 77.876 113 16 7 5907 6015 522187394 522187501 1.810000e-05 62.1
24 TraesCS3A01G362300 chr1A 76.699 103 20 3 5907 6006 119040856 119040755 3.000000e-03 54.7
25 TraesCS3A01G362300 chr2B 76.056 213 36 11 5514 5714 495440438 495440647 4.970000e-16 97.1
26 TraesCS3A01G362300 chr2B 77.000 100 21 2 5907 6004 815559 815658 8.430000e-04 56.5
27 TraesCS3A01G362300 chr7B 81.188 101 15 4 5907 6005 80513158 80513060 1.800000e-10 78.7
28 TraesCS3A01G362300 chr4D 86.765 68 6 2 3360 3424 22039508 22039441 8.370000e-09 73.1
29 TraesCS3A01G362300 chr4B 86.765 68 6 2 3360 3424 34056369 34056302 8.370000e-09 73.1
30 TraesCS3A01G362300 chr1D 78.431 102 20 2 5907 6006 306222564 306222463 1.400000e-06 65.8
31 TraesCS3A01G362300 chr1D 90.244 41 4 0 5968 6008 299586860 299586820 3.000000e-03 54.7
32 TraesCS3A01G362300 chr7A 78.431 102 19 3 5907 6006 726649506 726649606 5.040000e-06 63.9
33 TraesCS3A01G362300 chr6D 100.000 29 0 0 5907 5935 7532024 7531996 3.000000e-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 TraesCS3A01G362300 chr3A 610410544 610416564 6020 False 11119.000000 11119 100.0000 1 6021 1 chr3A.!!$F2 6020
1 TraesCS3A01G362300 chr3A 610523688 610524449 761 False 326.000000 326 75.2580 2272 3014 1 chr3A.!!$F4 742
2 TraesCS3A01G362300 chr3D 467766180 467772194 6014 False 2836.333333 6473 89.9510 1 6010 3 chr3D.!!$F4 6009
3 TraesCS3A01G362300 chr3B 622077318 622085967 8649 False 1481.840000 2730 91.3734 1 5319 5 chr3B.!!$F2 5318

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
392 454 0.674895 AGGCAGAAATCACTCACGGC 60.675 55.000 0.00 0.00 0.00 5.68 F
1041 1104 0.671781 ACGATGTGCTGGAGAAGTGC 60.672 55.000 0.00 0.00 0.00 4.40 F
1559 1876 1.271325 TGACCTATGGCGGCAATATGG 60.271 52.381 18.31 17.38 0.00 2.74 F
1916 2238 3.854784 GCAGTAAGGACAGCTTTGCAAAG 60.855 47.826 30.70 30.70 35.32 2.77 F
3442 3796 0.321034 TCACACAGCATCAGCCAGTC 60.321 55.000 0.00 0.00 43.56 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1573 1.347707 GGACCTGTCAATGAGTCACCA 59.652 52.381 0.00 0.0 0.00 4.17 R
2733 3076 1.992557 TCCAAAGGTGGTAGGATTGCT 59.007 47.619 0.00 0.0 46.11 3.91 R
3031 3380 2.093288 CAGAGAGATGGTTGGCTTAGCA 60.093 50.000 6.53 0.0 0.00 3.49 R
3582 3938 1.985684 GCTAAACGTGCTTTCATTGGC 59.014 47.619 0.00 0.0 0.00 4.52 R
5274 5662 0.174162 GCACAAGGGGAATGCATGTC 59.826 55.000 0.00 0.0 39.23 3.06 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 2.014857 GTAAAAATCCCCTCGCCACTC 58.985 52.381 0.00 0.00 0.00 3.51
68 75 2.484928 GGCTAGTCCGTACGACCCC 61.485 68.421 18.76 9.70 43.08 4.95
69 76 2.484928 GCTAGTCCGTACGACCCCC 61.485 68.421 18.76 0.00 43.08 5.40
98 105 3.711190 GCATGAAATTTTGGGATAGGGGT 59.289 43.478 0.00 0.00 0.00 4.95
99 106 4.202253 GCATGAAATTTTGGGATAGGGGTC 60.202 45.833 0.00 0.00 0.00 4.46
100 107 4.965283 TGAAATTTTGGGATAGGGGTCT 57.035 40.909 0.00 0.00 0.00 3.85
102 109 5.660533 TGAAATTTTGGGATAGGGGTCTTT 58.339 37.500 0.00 0.00 0.00 2.52
103 110 5.719563 TGAAATTTTGGGATAGGGGTCTTTC 59.280 40.000 0.00 0.00 0.00 2.62
105 112 2.257391 TTGGGATAGGGGTCTTTCGA 57.743 50.000 0.00 0.00 0.00 3.71
106 113 2.489528 TGGGATAGGGGTCTTTCGAT 57.510 50.000 0.00 0.00 0.00 3.59
159 183 1.160329 CCCCGCCGCTCTGATTAAAG 61.160 60.000 0.00 0.00 0.00 1.85
165 190 2.600792 GCCGCTCTGATTAAAGAATGCG 60.601 50.000 0.00 0.00 39.34 4.73
199 224 2.548707 GGCTGATACTCGATGCATGGAA 60.549 50.000 12.74 0.00 0.00 3.53
228 253 4.470462 CATGTCAGTGCTTTGCTTTCTAC 58.530 43.478 0.00 0.00 0.00 2.59
229 254 3.808728 TGTCAGTGCTTTGCTTTCTACT 58.191 40.909 0.00 0.00 0.00 2.57
230 255 4.956085 TGTCAGTGCTTTGCTTTCTACTA 58.044 39.130 0.00 0.00 0.00 1.82
231 256 4.750098 TGTCAGTGCTTTGCTTTCTACTAC 59.250 41.667 0.00 0.00 0.00 2.73
232 257 4.991687 GTCAGTGCTTTGCTTTCTACTACT 59.008 41.667 0.00 0.00 0.00 2.57
234 259 6.309251 GTCAGTGCTTTGCTTTCTACTACTAG 59.691 42.308 0.00 0.00 0.00 2.57
235 260 5.062809 CAGTGCTTTGCTTTCTACTACTAGC 59.937 44.000 0.00 0.00 0.00 3.42
237 262 4.223032 TGCTTTGCTTTCTACTACTAGCCT 59.777 41.667 0.00 0.00 32.73 4.58
238 263 5.421056 TGCTTTGCTTTCTACTACTAGCCTA 59.579 40.000 0.00 0.00 32.73 3.93
239 264 5.980715 GCTTTGCTTTCTACTACTAGCCTAG 59.019 44.000 0.00 0.00 32.73 3.02
240 265 5.517322 TTGCTTTCTACTACTAGCCTAGC 57.483 43.478 0.00 0.00 32.73 3.42
241 266 3.564644 TGCTTTCTACTACTAGCCTAGCG 59.435 47.826 0.00 0.00 32.73 4.26
242 267 3.609879 GCTTTCTACTACTAGCCTAGCGC 60.610 52.174 0.00 0.00 37.98 5.92
259 284 4.320456 CTCACGGTGGGCAGCACT 62.320 66.667 8.50 0.00 0.00 4.40
260 285 2.920384 TCACGGTGGGCAGCACTA 60.920 61.111 8.50 0.00 0.00 2.74
261 286 2.434884 CACGGTGGGCAGCACTAG 60.435 66.667 0.00 0.00 0.00 2.57
262 287 2.923035 ACGGTGGGCAGCACTAGT 60.923 61.111 0.00 0.00 0.00 2.57
263 288 2.347490 CGGTGGGCAGCACTAGTT 59.653 61.111 0.00 0.00 0.00 2.24
264 289 2.034879 CGGTGGGCAGCACTAGTTG 61.035 63.158 0.00 0.00 0.00 3.16
278 303 0.692476 TAGTTGTGGTGCATCAGCCT 59.308 50.000 0.00 0.00 41.13 4.58
377 439 2.500509 AAAATTTCGCGTTTGAGGCA 57.499 40.000 5.77 0.00 0.00 4.75
378 440 2.050477 AAATTTCGCGTTTGAGGCAG 57.950 45.000 5.77 0.00 0.00 4.85
379 441 1.234821 AATTTCGCGTTTGAGGCAGA 58.765 45.000 5.77 0.00 0.00 4.26
388 450 2.807967 CGTTTGAGGCAGAAATCACTCA 59.192 45.455 0.00 0.00 38.12 3.41
389 451 3.364366 CGTTTGAGGCAGAAATCACTCAC 60.364 47.826 0.00 0.00 39.47 3.51
390 452 2.084610 TGAGGCAGAAATCACTCACG 57.915 50.000 0.00 0.00 35.24 4.35
391 453 1.338105 TGAGGCAGAAATCACTCACGG 60.338 52.381 0.00 0.00 35.24 4.94
392 454 0.674895 AGGCAGAAATCACTCACGGC 60.675 55.000 0.00 0.00 0.00 5.68
393 455 0.955428 GGCAGAAATCACTCACGGCA 60.955 55.000 0.00 0.00 0.00 5.69
394 456 1.089920 GCAGAAATCACTCACGGCAT 58.910 50.000 0.00 0.00 0.00 4.40
425 487 4.984785 GGAGCTTTTTCTGTGGATTGTTTC 59.015 41.667 0.00 0.00 0.00 2.78
451 513 6.431543 CCATGTTGTGTGTTAATGGTAGGTAA 59.568 38.462 0.00 0.00 34.35 2.85
496 558 3.467374 TGCACAAAAAGGTTCCATTCC 57.533 42.857 0.00 0.00 0.00 3.01
526 588 1.141657 GCAGTGATGCTTCCCCTCATA 59.858 52.381 0.00 0.00 0.00 2.15
590 652 1.207089 TCCGAGTTGCATTGAGGGTAG 59.793 52.381 0.00 0.00 0.00 3.18
607 669 1.279271 GTAGTCCACTCCATGTGCCTT 59.721 52.381 0.00 0.00 44.92 4.35
640 702 6.046762 TCAAGATCCTAGGGGAGTCACATATA 59.953 42.308 9.46 0.00 45.86 0.86
641 703 6.682622 AGATCCTAGGGGAGTCACATATAT 57.317 41.667 9.46 0.00 45.86 0.86
642 704 7.789128 AGATCCTAGGGGAGTCACATATATA 57.211 40.000 9.46 0.00 45.86 0.86
643 705 8.370028 AGATCCTAGGGGAGTCACATATATAT 57.630 38.462 9.46 0.00 45.86 0.86
684 746 1.524008 AAAACTTGGTAGCGCTGCCC 61.524 55.000 36.94 27.31 34.17 5.36
693 755 1.341913 TAGCGCTGCCCCTAAATCCA 61.342 55.000 22.90 0.00 0.00 3.41
694 756 1.529244 GCGCTGCCCCTAAATCCAT 60.529 57.895 0.00 0.00 0.00 3.41
699 761 2.508526 CTGCCCCTAAATCCATACTGC 58.491 52.381 0.00 0.00 0.00 4.40
704 766 3.395941 CCCCTAAATCCATACTGCCTTCT 59.604 47.826 0.00 0.00 0.00 2.85
716 778 7.016957 TCCATACTGCCTTCTCATTATGAAGAT 59.983 37.037 5.21 0.00 42.37 2.40
816 879 3.187432 GCAGTGCTCCACTAAGTTCTTTC 59.813 47.826 8.18 0.00 43.43 2.62
824 887 7.012044 TGCTCCACTAAGTTCTTTCTTTGTTAC 59.988 37.037 0.00 0.00 32.92 2.50
909 972 5.415701 AGGGCAATCATTGTACTTGTAACTG 59.584 40.000 0.00 0.00 0.00 3.16
981 1044 4.464008 TGCTTTGGTCTCATGTTTCTTCT 58.536 39.130 0.00 0.00 0.00 2.85
1041 1104 0.671781 ACGATGTGCTGGAGAAGTGC 60.672 55.000 0.00 0.00 0.00 4.40
1077 1140 4.843728 TCTCTCAAATAAAACCGGCAGAT 58.156 39.130 0.00 0.00 0.00 2.90
1364 1443 4.965283 ATCCCCAAAGGTTTTCCATAGA 57.035 40.909 0.00 0.00 43.73 1.98
1365 1444 4.316025 TCCCCAAAGGTTTTCCATAGAG 57.684 45.455 0.00 0.00 43.73 2.43
1367 1446 4.017126 CCCCAAAGGTTTTCCATAGAGTC 58.983 47.826 0.00 0.00 43.73 3.36
1369 1448 5.045140 CCCCAAAGGTTTTCCATAGAGTCTA 60.045 44.000 1.45 1.45 43.73 2.59
1370 1449 6.353951 CCCCAAAGGTTTTCCATAGAGTCTAT 60.354 42.308 6.86 6.86 43.73 1.98
1371 1450 6.768381 CCCAAAGGTTTTCCATAGAGTCTATC 59.232 42.308 9.84 0.00 43.73 2.08
1372 1451 7.338710 CCAAAGGTTTTCCATAGAGTCTATCA 58.661 38.462 9.84 0.00 43.73 2.15
1494 1573 8.579850 TTCATTTGGAGACTAAGTATTGCAAT 57.420 30.769 17.56 17.56 0.00 3.56
1559 1876 1.271325 TGACCTATGGCGGCAATATGG 60.271 52.381 18.31 17.38 0.00 2.74
1916 2238 3.854784 GCAGTAAGGACAGCTTTGCAAAG 60.855 47.826 30.70 30.70 35.32 2.77
1942 2264 9.322769 GGGGAGGTAATTCTATCTATTCTACAA 57.677 37.037 0.00 0.00 0.00 2.41
2025 2347 8.877779 CAGAATGATGAATTTCTAGTTTCGACT 58.122 33.333 0.00 0.00 39.69 4.18
2062 2384 5.831997 AGCTTTTGTGGTAAAACAGTCATC 58.168 37.500 0.00 0.00 0.00 2.92
2104 2427 5.978814 AGTAGTACAAATCATGTGAGGGAC 58.021 41.667 2.52 0.00 43.77 4.46
2125 2448 6.483640 GGGACCATCATTCTAACTTATGTGTC 59.516 42.308 0.00 0.00 0.00 3.67
2168 2491 9.480053 AAGAATTTCATTATTGTTCTGTGGTTG 57.520 29.630 0.00 0.00 0.00 3.77
2466 2796 7.284489 GTGATATGGTTTTATTGGTAAGCTCCA 59.716 37.037 0.00 0.00 35.49 3.86
2733 3076 5.335897 GCTAAATTTTGAGACATGTGAGCCA 60.336 40.000 1.15 0.00 0.00 4.75
2902 3251 7.011482 ACGCTTTATAATGAGGAACATCTTGAC 59.989 37.037 2.66 0.00 38.38 3.18
3031 3380 3.019564 GCATTGTGCCCTCACTATCTTT 58.980 45.455 0.00 0.00 43.49 2.52
3257 3611 8.928448 TGATACTTCAACTAATTGATAGGAGCT 58.072 33.333 0.00 0.00 44.36 4.09
3273 3627 3.840666 AGGAGCTTTCAGGACAGTGATAA 59.159 43.478 0.00 0.00 0.00 1.75
3314 3668 8.918202 AGAATTTGTCATACAACTTACAAGGA 57.082 30.769 0.00 0.00 37.90 3.36
3318 3672 3.617263 GTCATACAACTTACAAGGAGGCG 59.383 47.826 0.00 0.00 0.00 5.52
3333 3687 4.973168 AGGAGGCGAAATGCTAATTGATA 58.027 39.130 0.00 0.00 45.43 2.15
3438 3792 0.604780 AGTGTCACACAGCATCAGCC 60.605 55.000 11.40 0.00 36.74 4.85
3442 3796 0.321034 TCACACAGCATCAGCCAGTC 60.321 55.000 0.00 0.00 43.56 3.51
3558 3914 5.807011 GGTTTCATGGATTAGTTCATGTTGC 59.193 40.000 6.41 0.00 40.94 4.17
3574 3930 7.270757 TCATGTTGCTAGCTTAAGTTTTTGA 57.729 32.000 17.23 4.22 0.00 2.69
3575 3931 7.711846 TCATGTTGCTAGCTTAAGTTTTTGAA 58.288 30.769 17.23 0.00 0.00 2.69
3576 3932 7.862372 TCATGTTGCTAGCTTAAGTTTTTGAAG 59.138 33.333 17.23 0.00 0.00 3.02
3577 3933 7.095695 TGTTGCTAGCTTAAGTTTTTGAAGT 57.904 32.000 17.23 0.00 0.00 3.01
3578 3934 7.543756 TGTTGCTAGCTTAAGTTTTTGAAGTT 58.456 30.769 17.23 0.00 0.00 2.66
3579 3935 8.032451 TGTTGCTAGCTTAAGTTTTTGAAGTTT 58.968 29.630 17.23 0.00 0.00 2.66
3580 3936 8.869897 GTTGCTAGCTTAAGTTTTTGAAGTTTT 58.130 29.630 17.23 0.00 0.00 2.43
3581 3937 8.996024 TGCTAGCTTAAGTTTTTGAAGTTTTT 57.004 26.923 17.23 0.00 0.00 1.94
3582 3938 8.868916 TGCTAGCTTAAGTTTTTGAAGTTTTTG 58.131 29.630 17.23 0.00 0.00 2.44
3587 3943 7.967854 GCTTAAGTTTTTGAAGTTTTTGCCAAT 59.032 29.630 4.02 0.00 0.00 3.16
3595 3951 4.332268 TGAAGTTTTTGCCAATGAAAGCAC 59.668 37.500 0.00 0.00 39.10 4.40
3601 3957 3.281341 TGCCAATGAAAGCACGTTTAG 57.719 42.857 0.00 0.00 33.08 1.85
3613 3969 2.031683 GCACGTTTAGCATTTATCCGCT 59.968 45.455 0.00 0.00 42.34 5.52
3617 3973 6.347079 GCACGTTTAGCATTTATCCGCTATTA 60.347 38.462 0.00 0.00 40.28 0.98
3759 4115 3.679389 ACAAGCCTAACTGGTGATCTTG 58.321 45.455 0.00 0.00 37.84 3.02
3828 4184 2.440409 TCTACCTACACGGGTCAGTTC 58.560 52.381 0.00 0.00 40.48 3.01
3853 4209 7.452501 TCAAGAAGATTCAGGACATTCCAATTT 59.547 33.333 0.00 0.00 39.61 1.82
3854 4210 7.787623 AGAAGATTCAGGACATTCCAATTTT 57.212 32.000 0.00 0.00 39.61 1.82
3919 4275 6.210796 TGTGCATTTTGCTGCTGATATAATC 58.789 36.000 0.00 0.00 45.31 1.75
3920 4276 6.183360 TGTGCATTTTGCTGCTGATATAATCA 60.183 34.615 0.00 0.00 45.31 2.57
4045 4401 1.271108 GGGCTCCTCCTAATTGCTAGC 60.271 57.143 8.10 8.10 34.39 3.42
4198 4554 1.301401 CCCGCAAAGGACTCGACAA 60.301 57.895 0.00 0.00 45.00 3.18
4239 4595 8.041919 GGGAGCTAAGGTATCTAATAATCAACC 58.958 40.741 0.00 0.00 0.00 3.77
4245 4601 5.780793 AGGTATCTAATAATCAACCTCGCCT 59.219 40.000 0.00 0.00 31.78 5.52
4399 4782 6.716620 CCTCCTCAGGTTTATGCTAACGCA 62.717 50.000 0.00 0.00 42.13 5.24
4451 4834 5.457633 GGGCTATACACAAACCATTATCCCT 60.458 44.000 0.00 0.00 0.00 4.20
4466 4849 6.408548 CCATTATCCCTCATCGGCATATACTT 60.409 42.308 0.00 0.00 0.00 2.24
4494 4877 3.356290 GCCAAACAACAGGATCATACCT 58.644 45.455 0.00 0.00 41.43 3.08
4598 4981 0.957395 CCCAGTGTACCAAGCAGCAG 60.957 60.000 0.00 0.00 0.00 4.24
4667 5050 3.054434 CCAAACACCAGGATCATACCAGA 60.054 47.826 0.00 0.00 0.00 3.86
4700 5083 2.299013 AGTCAGTCGCCTGTTCATACAA 59.701 45.455 0.00 0.00 39.82 2.41
4765 5148 1.354368 CAGGGTCATACAACTGGGGTT 59.646 52.381 0.00 0.00 35.86 4.11
4866 5249 3.505184 GGCGCAATACACACCCGG 61.505 66.667 10.83 0.00 0.00 5.73
4874 5257 1.983119 ATACACACCCGGCCATCAGG 61.983 60.000 2.24 0.00 38.23 3.86
5023 5409 0.036732 GCCAACATCAGACCTGACCA 59.963 55.000 1.31 0.00 43.11 4.02
5036 5422 2.296471 ACCTGACCAGAACTGTTAGTCG 59.704 50.000 11.08 7.48 0.00 4.18
5085 5471 4.096231 CCATTGGCTGACAAAATGTATCGA 59.904 41.667 0.00 0.00 43.46 3.59
5124 5510 8.839310 ATGTATGTCATCCTTCATACTTTAGC 57.161 34.615 13.74 0.00 43.63 3.09
5133 5519 3.497297 TCATACTTTAGCTTGTCGCGA 57.503 42.857 3.71 3.71 45.59 5.87
5140 5526 0.391130 TAGCTTGTCGCGAAGGCAAT 60.391 50.000 23.88 11.86 44.32 3.56
5186 5574 0.874390 GCAGAATGTTTCGCTGGTGA 59.126 50.000 0.00 0.00 39.31 4.02
5214 5602 1.614903 CTTGAGATGCCAAACCTTGCA 59.385 47.619 0.00 0.00 42.52 4.08
5271 5659 4.724399 TGCCTTTATCCACTGAACTTTGA 58.276 39.130 0.00 0.00 0.00 2.69
5274 5662 5.393461 GCCTTTATCCACTGAACTTTGATGG 60.393 44.000 0.00 0.00 0.00 3.51
5280 5668 3.366679 CCACTGAACTTTGATGGACATGC 60.367 47.826 0.00 0.00 31.69 4.06
5330 5718 1.623811 GAGCAGTGACTAGGGGTTTCA 59.376 52.381 0.00 0.00 0.00 2.69
5332 5720 2.644798 AGCAGTGACTAGGGGTTTCAAT 59.355 45.455 0.00 0.00 0.00 2.57
5333 5721 2.749621 GCAGTGACTAGGGGTTTCAATG 59.250 50.000 0.00 4.01 38.16 2.82
5334 5722 2.749621 CAGTGACTAGGGGTTTCAATGC 59.250 50.000 0.00 0.00 29.61 3.56
5362 5751 6.015772 AGTGTACCCGTAAATGCAATTTTCTT 60.016 34.615 0.00 0.00 46.10 2.52
5391 5783 7.395190 AAATGCTACATATCACTGCTTTTGA 57.605 32.000 0.00 0.00 32.48 2.69
5426 5818 3.148279 CGGTCCTCCTTCCCTCGG 61.148 72.222 0.00 0.00 0.00 4.63
5439 5831 2.742348 TCCCTCGGCTATTGTACTGAA 58.258 47.619 0.00 0.00 0.00 3.02
5450 5844 6.297353 GCTATTGTACTGAACGTGTTCTTTC 58.703 40.000 13.40 3.50 40.14 2.62
5649 8215 1.127951 GCGACGACTACAACCATTTGG 59.872 52.381 0.00 0.00 37.00 3.28
5662 8228 0.253044 CATTTGGAGGGAGCCGAAGA 59.747 55.000 0.00 0.00 34.86 2.87
5683 8249 1.302431 CGTCACTGTCATTGCCCCA 60.302 57.895 0.00 0.00 0.00 4.96
5694 8260 0.482446 ATTGCCCCACTTCACTGGAA 59.518 50.000 0.00 0.00 32.30 3.53
5708 8274 2.033801 CACTGGAACTGAGCAAACCTTG 59.966 50.000 0.00 0.00 0.00 3.61
5712 8278 2.427095 GGAACTGAGCAAACCTTGTTGT 59.573 45.455 0.00 0.00 0.00 3.32
5714 8280 4.097286 GGAACTGAGCAAACCTTGTTGTAA 59.903 41.667 0.00 0.00 0.00 2.41
5717 8283 6.952773 ACTGAGCAAACCTTGTTGTAATAA 57.047 33.333 0.00 0.00 0.00 1.40
5720 8286 6.202937 TGAGCAAACCTTGTTGTAATAAACG 58.797 36.000 0.00 0.00 32.47 3.60
5721 8287 4.979815 AGCAAACCTTGTTGTAATAAACGC 59.020 37.500 0.00 0.00 32.47 4.84
5722 8288 4.740695 GCAAACCTTGTTGTAATAAACGCA 59.259 37.500 0.00 0.00 32.47 5.24
5725 8291 6.815672 AACCTTGTTGTAATAAACGCAAAC 57.184 33.333 0.00 0.00 32.47 2.93
5728 8294 5.980715 CCTTGTTGTAATAAACGCAAACCTT 59.019 36.000 0.00 0.00 32.47 3.50
5729 8295 6.074569 CCTTGTTGTAATAAACGCAAACCTTG 60.075 38.462 0.00 0.00 32.47 3.61
5730 8296 5.892568 TGTTGTAATAAACGCAAACCTTGT 58.107 33.333 0.00 0.00 32.47 3.16
5731 8297 6.331061 TGTTGTAATAAACGCAAACCTTGTT 58.669 32.000 0.00 0.00 32.47 2.83
5732 8298 6.253727 TGTTGTAATAAACGCAAACCTTGTTG 59.746 34.615 0.00 0.00 32.47 3.33
5733 8299 5.892568 TGTAATAAACGCAAACCTTGTTGT 58.107 33.333 0.00 0.00 0.00 3.32
5736 8302 5.761165 ATAAACGCAAACCTTGTTGTAGT 57.239 34.783 0.00 0.00 0.00 2.73
5737 8303 6.864360 ATAAACGCAAACCTTGTTGTAGTA 57.136 33.333 0.00 0.00 0.00 1.82
5738 8304 4.806342 AACGCAAACCTTGTTGTAGTAG 57.194 40.909 0.00 0.00 0.00 2.57
5739 8305 4.062677 ACGCAAACCTTGTTGTAGTAGA 57.937 40.909 0.00 0.00 0.00 2.59
5740 8306 3.805971 ACGCAAACCTTGTTGTAGTAGAC 59.194 43.478 0.00 0.00 0.00 2.59
5741 8307 3.805422 CGCAAACCTTGTTGTAGTAGACA 59.195 43.478 0.00 0.00 35.78 3.41
5742 8308 4.271533 CGCAAACCTTGTTGTAGTAGACAA 59.728 41.667 0.00 0.00 46.03 3.18
5771 8337 9.556030 GTAAATCATTGTGTTAAGGCTTAAGAC 57.444 33.333 30.04 30.04 39.19 3.01
5782 8348 3.527937 AGGCTTAAGACCCTAAAGGACA 58.472 45.455 4.17 0.00 39.89 4.02
5791 8357 3.949113 GACCCTAAAGGACAAACACACAA 59.051 43.478 0.00 0.00 39.89 3.33
5792 8358 3.697542 ACCCTAAAGGACAAACACACAAC 59.302 43.478 0.00 0.00 39.89 3.32
5799 8365 2.659279 GGACAAACACACAACAACAACG 59.341 45.455 0.00 0.00 0.00 4.10
5800 8366 2.055100 ACAAACACACAACAACAACGC 58.945 42.857 0.00 0.00 0.00 4.84
5842 8411 9.036980 GTACAAGGATCCAACCTATAGACATAT 57.963 37.037 15.82 0.00 39.62 1.78
5846 8415 8.923838 AGGATCCAACCTATAGACATATGAAT 57.076 34.615 15.82 2.71 38.65 2.57
5847 8416 8.766476 AGGATCCAACCTATAGACATATGAATG 58.234 37.037 15.82 0.00 38.65 2.67
5853 8422 7.425224 ACCTATAGACATATGAATGTAGCCC 57.575 40.000 10.38 0.00 46.49 5.19
5856 8425 4.955811 AGACATATGAATGTAGCCCGAA 57.044 40.909 10.38 0.00 46.49 4.30
5857 8426 4.632153 AGACATATGAATGTAGCCCGAAC 58.368 43.478 10.38 0.00 46.49 3.95
5862 8431 0.651031 GAATGTAGCCCGAACGAAGC 59.349 55.000 0.00 0.00 0.00 3.86
5867 8436 0.108804 TAGCCCGAACGAAGCTTGAG 60.109 55.000 2.10 0.00 38.06 3.02
5882 8550 3.070734 AGCTTGAGTCTTCGCATATCCAT 59.929 43.478 0.00 0.00 0.00 3.41
5884 8552 4.625028 CTTGAGTCTTCGCATATCCATCA 58.375 43.478 0.00 0.00 0.00 3.07
5895 8563 5.030295 CGCATATCCATCAAAGACAAACAC 58.970 41.667 0.00 0.00 0.00 3.32
5903 8576 4.300189 TCAAAGACAAACACCAATTCCG 57.700 40.909 0.00 0.00 0.00 4.30
5915 8588 1.227263 AATTCCGTGAGATCCGCCG 60.227 57.895 0.00 0.00 0.00 6.46
5923 8596 3.471244 GAGATCCGCCGGAGACACG 62.471 68.421 13.12 0.00 34.05 4.49
5938 8611 4.664677 ACGCCTCCACACGCAGTC 62.665 66.667 0.00 0.00 41.61 3.51
5945 8618 3.097728 CACACGCAGTCCGACGAC 61.098 66.667 0.00 0.00 41.61 4.34
5960 8633 2.235016 CGACGCGAAACACACCACT 61.235 57.895 15.93 0.00 0.00 4.00
5966 8639 1.732259 GCGAAACACACCACTAGGATG 59.268 52.381 0.00 0.00 38.69 3.51
5980 8655 0.031111 AGGATGGGCTAGGCAGTACA 60.031 55.000 19.14 7.03 0.00 2.90
6011 8686 1.617947 ATCTTCAGGGAGCCACGGTC 61.618 60.000 0.00 0.00 0.00 4.79
6012 8687 3.649277 CTTCAGGGAGCCACGGTCG 62.649 68.421 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.466819 GGGATTTTTACCTGGAGAAAAACG 58.533 41.667 19.07 0.00 37.35 3.60
70 77 1.134729 CCCAAAATTTCATGCCGGGAG 60.135 52.381 2.18 0.00 33.83 4.30
71 78 0.901124 CCCAAAATTTCATGCCGGGA 59.099 50.000 2.18 0.00 33.83 5.14
142 166 1.651987 TTCTTTAATCAGAGCGGCGG 58.348 50.000 9.78 0.00 0.00 6.13
147 171 5.261661 CAAGACGCATTCTTTAATCAGAGC 58.738 41.667 0.00 0.00 42.37 4.09
159 183 0.371645 CCTCGAAGCAAGACGCATTC 59.628 55.000 0.00 0.00 46.13 2.67
165 190 0.107945 ATCAGCCCTCGAAGCAAGAC 60.108 55.000 9.54 0.00 0.00 3.01
235 260 4.514577 CCCACCGTGAGCGCTAGG 62.515 72.222 11.50 17.34 36.67 3.02
242 267 2.842394 CTAGTGCTGCCCACCGTGAG 62.842 65.000 0.00 0.00 45.83 3.51
243 268 2.920384 TAGTGCTGCCCACCGTGA 60.920 61.111 0.00 0.00 45.83 4.35
244 269 2.434884 CTAGTGCTGCCCACCGTG 60.435 66.667 0.00 0.00 45.83 4.94
245 270 2.516888 AACTAGTGCTGCCCACCGT 61.517 57.895 0.00 0.00 45.83 4.83
246 271 2.034879 CAACTAGTGCTGCCCACCG 61.035 63.158 0.00 0.00 45.83 4.94
247 272 1.073199 ACAACTAGTGCTGCCCACC 59.927 57.895 0.00 0.00 45.83 4.61
248 273 2.247790 CACAACTAGTGCTGCCCAC 58.752 57.895 0.00 0.00 42.15 4.61
249 274 4.798433 CACAACTAGTGCTGCCCA 57.202 55.556 0.00 0.00 42.15 5.36
256 281 1.466167 GCTGATGCACCACAACTAGTG 59.534 52.381 0.00 0.00 42.60 2.74
257 282 1.611673 GGCTGATGCACCACAACTAGT 60.612 52.381 0.00 0.00 41.91 2.57
258 283 1.089920 GGCTGATGCACCACAACTAG 58.910 55.000 0.00 0.00 41.91 2.57
259 284 0.692476 AGGCTGATGCACCACAACTA 59.308 50.000 0.00 0.00 41.91 2.24
260 285 0.692476 TAGGCTGATGCACCACAACT 59.308 50.000 0.00 0.00 41.91 3.16
261 286 1.533625 TTAGGCTGATGCACCACAAC 58.466 50.000 0.00 0.00 41.91 3.32
262 287 2.512692 ATTAGGCTGATGCACCACAA 57.487 45.000 0.00 0.00 41.91 3.33
263 288 2.512692 AATTAGGCTGATGCACCACA 57.487 45.000 0.00 0.00 41.91 4.17
264 289 3.243201 GCTTAATTAGGCTGATGCACCAC 60.243 47.826 12.04 0.00 41.91 4.16
274 299 9.602568 GAGTCTTAAAAGTAGCTTAATTAGGCT 57.397 33.333 23.60 23.60 41.75 4.58
327 389 9.880157 ATCAAATTTTCTGTATATTGCAGCTTT 57.120 25.926 0.00 0.00 34.21 3.51
329 391 8.689061 TCATCAAATTTTCTGTATATTGCAGCT 58.311 29.630 0.00 0.00 34.21 4.24
361 423 1.234821 TTCTGCCTCAAACGCGAAAT 58.765 45.000 15.93 0.00 0.00 2.17
362 424 1.018148 TTTCTGCCTCAAACGCGAAA 58.982 45.000 15.93 0.00 31.33 3.46
377 439 1.645034 CGATGCCGTGAGTGATTTCT 58.355 50.000 0.00 0.00 0.00 2.52
378 440 0.652592 CCGATGCCGTGAGTGATTTC 59.347 55.000 0.00 0.00 0.00 2.17
379 441 1.369091 GCCGATGCCGTGAGTGATTT 61.369 55.000 0.00 0.00 0.00 2.17
388 450 4.552365 CTCCCATGCCGATGCCGT 62.552 66.667 0.00 0.00 36.33 5.68
390 452 4.575973 AGCTCCCATGCCGATGCC 62.576 66.667 0.00 0.00 36.33 4.40
391 453 1.669999 AAAAGCTCCCATGCCGATGC 61.670 55.000 0.00 0.00 38.26 3.91
392 454 0.819582 AAAAAGCTCCCATGCCGATG 59.180 50.000 0.00 0.00 0.00 3.84
393 455 1.106285 GAAAAAGCTCCCATGCCGAT 58.894 50.000 0.00 0.00 0.00 4.18
394 456 0.038166 AGAAAAAGCTCCCATGCCGA 59.962 50.000 0.00 0.00 0.00 5.54
425 487 4.157656 CCTACCATTAACACACAACATGGG 59.842 45.833 0.00 0.00 39.06 4.00
451 513 6.597562 TGTCCTATCTTGTTTGTGTTTACCT 58.402 36.000 0.00 0.00 0.00 3.08
496 558 0.524862 GCATCACTGCCCAAGTCAAG 59.475 55.000 0.00 0.00 42.88 3.02
607 669 5.285401 TCCCCTAGGATCTTGATGTAAACA 58.715 41.667 11.48 0.00 37.19 2.83
641 703 9.902684 TTTAACGTAATGGGGATTTTGAGTATA 57.097 29.630 0.00 0.00 0.00 1.47
642 704 8.810990 TTTAACGTAATGGGGATTTTGAGTAT 57.189 30.769 0.00 0.00 0.00 2.12
643 705 8.513774 GTTTTAACGTAATGGGGATTTTGAGTA 58.486 33.333 0.00 0.00 0.00 2.59
684 746 5.296151 TGAGAAGGCAGTATGGATTTAGG 57.704 43.478 0.00 0.00 35.86 2.69
693 755 8.658619 AGAATCTTCATAATGAGAAGGCAGTAT 58.341 33.333 0.00 0.00 42.09 2.12
694 756 8.027524 AGAATCTTCATAATGAGAAGGCAGTA 57.972 34.615 0.00 0.00 42.09 2.74
699 761 9.844257 AAACCTAGAATCTTCATAATGAGAAGG 57.156 33.333 0.00 0.00 42.09 3.46
716 778 6.126710 TGGAGACCACAAACTAAAACCTAGAA 60.127 38.462 0.00 0.00 0.00 2.10
816 879 7.253950 CCATGTTTTCAAAGAACCGTAACAAAG 60.254 37.037 0.00 0.00 0.00 2.77
824 887 3.308530 GAGCCATGTTTTCAAAGAACCG 58.691 45.455 0.00 0.00 0.00 4.44
964 1027 3.149196 GCCAAGAAGAAACATGAGACCA 58.851 45.455 0.00 0.00 0.00 4.02
965 1028 3.416156 AGCCAAGAAGAAACATGAGACC 58.584 45.455 0.00 0.00 0.00 3.85
966 1029 4.516698 TGAAGCCAAGAAGAAACATGAGAC 59.483 41.667 0.00 0.00 0.00 3.36
970 1033 4.843220 ACTGAAGCCAAGAAGAAACATG 57.157 40.909 0.00 0.00 0.00 3.21
981 1044 4.334552 TCATGCTGAAATACTGAAGCCAA 58.665 39.130 0.00 0.00 34.70 4.52
1013 1076 1.603455 AGCACATCGTTGTTGGGGG 60.603 57.895 0.00 0.00 32.34 5.40
1077 1140 7.279536 GCAGATAGTCTTTTGTTCAGATCATCA 59.720 37.037 0.00 0.00 0.00 3.07
1166 1232 2.339769 GGATAAGGCTCCCATGGTAGT 58.660 52.381 11.73 0.00 0.00 2.73
1195 1262 5.819379 TCACTGTCAATATCAGGCTCATTTC 59.181 40.000 0.00 0.00 37.25 2.17
1370 1449 9.589461 CTACTCTAGGGTTCTTTAGGAATATGA 57.411 37.037 0.00 0.00 36.24 2.15
1371 1450 9.369672 ACTACTCTAGGGTTCTTTAGGAATATG 57.630 37.037 0.00 0.00 36.24 1.78
1372 1451 9.954992 AACTACTCTAGGGTTCTTTAGGAATAT 57.045 33.333 0.00 0.00 36.24 1.28
1494 1573 1.347707 GGACCTGTCAATGAGTCACCA 59.652 52.381 0.00 0.00 0.00 4.17
1559 1876 3.251972 GCAGCTCATAACCTAGCAAATCC 59.748 47.826 0.00 0.00 41.32 3.01
1779 2101 9.796120 GAGTATAGATTTGATAGAAAGGATCCG 57.204 37.037 5.98 0.00 0.00 4.18
1916 2238 8.896722 TGTAGAATAGATAGAATTACCTCCCC 57.103 38.462 0.00 0.00 0.00 4.81
1942 2264 6.128282 GCAACGCATTATGTAGGCTTATGTAT 60.128 38.462 0.00 0.00 0.00 2.29
1952 2274 3.809279 TGATCAGGCAACGCATTATGTAG 59.191 43.478 0.00 0.00 46.39 2.74
1961 2283 2.131183 GATAGAGTGATCAGGCAACGC 58.869 52.381 0.00 0.00 46.39 4.84
2019 2341 6.208988 AGCTATGAGTATTCACAAGTCGAA 57.791 37.500 0.00 0.00 35.83 3.71
2025 2347 6.714810 ACCACAAAAGCTATGAGTATTCACAA 59.285 34.615 6.45 0.00 35.83 3.33
2062 2384 4.241590 ACTTGGTGCACACAAACATATG 57.758 40.909 20.43 0.00 0.00 1.78
2104 2427 6.017605 GCCAGACACATAAGTTAGAATGATGG 60.018 42.308 11.33 11.33 0.00 3.51
2125 2448 8.030692 TGAAATTCTTGAATAAATCACAGCCAG 58.969 33.333 0.00 0.00 37.92 4.85
2168 2491 4.202111 ACAAAGTGCCACAGTAAATTCACC 60.202 41.667 0.00 0.00 0.00 4.02
2466 2796 5.416952 CCCATCAGCAAAAGACTATCACTTT 59.583 40.000 0.00 0.00 38.91 2.66
2655 2990 9.226606 TGAAACGATAAACAAGATAATTGGACT 57.773 29.630 0.00 0.00 0.00 3.85
2733 3076 1.992557 TCCAAAGGTGGTAGGATTGCT 59.007 47.619 0.00 0.00 46.11 3.91
3031 3380 2.093288 CAGAGAGATGGTTGGCTTAGCA 60.093 50.000 6.53 0.00 0.00 3.49
3130 3479 5.838531 AATGACCGTAACCAAGACAAAAA 57.161 34.783 0.00 0.00 0.00 1.94
3255 3609 4.569943 TCTGTTATCACTGTCCTGAAAGC 58.430 43.478 0.00 0.00 0.00 3.51
3257 3611 9.739276 AATATTTCTGTTATCACTGTCCTGAAA 57.261 29.630 0.00 0.00 0.00 2.69
3314 3668 7.281774 CCTATCATATCAATTAGCATTTCGCCT 59.718 37.037 0.00 0.00 44.04 5.52
3558 3914 8.328146 GGCAAAAACTTCAAAAACTTAAGCTAG 58.672 33.333 1.29 0.00 0.00 3.42
3574 3930 3.309410 CGTGCTTTCATTGGCAAAAACTT 59.691 39.130 3.01 0.00 40.26 2.66
3575 3931 2.865551 CGTGCTTTCATTGGCAAAAACT 59.134 40.909 3.01 0.00 40.26 2.66
3576 3932 2.607180 ACGTGCTTTCATTGGCAAAAAC 59.393 40.909 3.01 0.00 40.26 2.43
3577 3933 2.898705 ACGTGCTTTCATTGGCAAAAA 58.101 38.095 3.01 0.00 40.26 1.94
3578 3934 2.593346 ACGTGCTTTCATTGGCAAAA 57.407 40.000 3.01 0.00 40.26 2.44
3579 3935 2.593346 AACGTGCTTTCATTGGCAAA 57.407 40.000 3.01 0.00 40.26 3.68
3580 3936 2.593346 AAACGTGCTTTCATTGGCAA 57.407 40.000 0.68 0.68 40.26 4.52
3581 3937 2.606795 GCTAAACGTGCTTTCATTGGCA 60.607 45.455 0.00 0.00 36.01 4.92
3582 3938 1.985684 GCTAAACGTGCTTTCATTGGC 59.014 47.619 0.00 0.00 0.00 4.52
3587 3943 5.636837 GGATAAATGCTAAACGTGCTTTCA 58.363 37.500 0.00 0.00 0.00 2.69
3595 3951 7.115805 TGAGTAATAGCGGATAAATGCTAAACG 59.884 37.037 0.00 0.00 45.92 3.60
3601 3957 6.524586 GCAAATGAGTAATAGCGGATAAATGC 59.475 38.462 0.00 0.00 0.00 3.56
3759 4115 6.826893 ATGTGACAAAACTGCAAACAATAC 57.173 33.333 0.00 0.00 0.00 1.89
3828 4184 6.770746 ATTGGAATGTCCTGAATCTTCTTG 57.229 37.500 0.00 0.00 37.46 3.02
3853 4209 5.250774 ACAAGCTATAGGGTTTCTTCCTCAA 59.749 40.000 1.04 0.00 35.92 3.02
3854 4210 4.783227 ACAAGCTATAGGGTTTCTTCCTCA 59.217 41.667 1.04 0.00 35.92 3.86
3919 4275 8.830580 CATGTCAGTATGTAGGGTAAATTCTTG 58.169 37.037 0.00 0.00 37.40 3.02
3920 4276 8.768397 TCATGTCAGTATGTAGGGTAAATTCTT 58.232 33.333 0.00 0.00 37.40 2.52
4045 4401 2.299993 TCTTAGCATCACTGAAGGCG 57.700 50.000 0.00 0.00 0.00 5.52
4147 4503 3.953712 TTGTTAGCGATGACTCTTCCA 57.046 42.857 0.00 0.00 0.00 3.53
4198 4554 2.027192 AGCTCCCACGTTGATTACATGT 60.027 45.455 2.69 2.69 0.00 3.21
4239 4595 1.449246 CCTTTGGCTCTGAGGCGAG 60.449 63.158 23.82 21.87 44.78 5.03
4245 4601 3.587061 TCCTGTAAATCCTTTGGCTCTGA 59.413 43.478 0.00 0.00 0.00 3.27
4399 4782 2.026542 TCTTGATGGCTGATGAACTGCT 60.027 45.455 0.00 0.00 41.95 4.24
4451 4834 1.067142 GCCCGAAGTATATGCCGATGA 60.067 52.381 0.00 0.00 0.00 2.92
4466 4849 4.877619 TGTTGTTTGGCGGCCCGA 62.878 61.111 17.97 1.76 0.00 5.14
4494 4877 0.900421 CTGTGGATGGCTCTGACTCA 59.100 55.000 0.00 0.00 0.00 3.41
4598 4981 1.163554 CTCGGATAGTAGTACGGCCC 58.836 60.000 0.00 0.00 0.00 5.80
4667 5050 2.096174 GCGACTGACTCTGATACTCGTT 59.904 50.000 0.00 0.00 0.00 3.85
4700 5083 3.338250 TGGCCTTTGGATCCCGCT 61.338 61.111 9.90 0.00 0.00 5.52
4765 5148 1.632920 TGGTATTGTCCTGGCATGTGA 59.367 47.619 0.00 0.00 0.00 3.58
4794 5177 4.209288 CAGTATACGCCAGCTGATTGTAAC 59.791 45.833 17.39 13.61 0.00 2.50
4806 5189 2.504032 GGCCTGCAGTATACGCCA 59.496 61.111 21.72 6.20 39.50 5.69
4846 5229 2.360600 GGTGTGTATTGCGCCCCA 60.361 61.111 4.18 0.00 0.00 4.96
4874 5257 3.518303 ACCCCATTCCTATAATACCTCGC 59.482 47.826 0.00 0.00 0.00 5.03
4876 5259 5.785940 AGTCACCCCATTCCTATAATACCTC 59.214 44.000 0.00 0.00 0.00 3.85
4882 5268 5.368523 CCTTGTAGTCACCCCATTCCTATAA 59.631 44.000 0.00 0.00 0.00 0.98
4883 5269 4.905456 CCTTGTAGTCACCCCATTCCTATA 59.095 45.833 0.00 0.00 0.00 1.31
5023 5409 2.526304 TTGCTGCGACTAACAGTTCT 57.474 45.000 0.00 0.00 37.47 3.01
5121 5507 0.391130 ATTGCCTTCGCGACAAGCTA 60.391 50.000 20.70 15.48 45.59 3.32
5124 5510 1.075542 TACATTGCCTTCGCGACAAG 58.924 50.000 9.15 4.12 38.08 3.16
5133 5519 4.079253 AGTGGAAATCGTTACATTGCCTT 58.921 39.130 6.25 0.00 32.91 4.35
5140 5526 8.842280 ACAAAATCTTTAGTGGAAATCGTTACA 58.158 29.630 0.00 0.00 0.00 2.41
5186 5574 4.262164 GGTTTGGCATCTCAAGTGACATTT 60.262 41.667 0.00 0.00 33.92 2.32
5214 5602 4.050037 TCATCATCAGGGAAGAGGGAAAT 58.950 43.478 0.00 0.00 0.00 2.17
5271 5659 1.007479 ACAAGGGGAATGCATGTCCAT 59.993 47.619 21.73 12.95 36.83 3.41
5274 5662 0.174162 GCACAAGGGGAATGCATGTC 59.826 55.000 0.00 0.00 39.23 3.06
5280 5668 0.458669 GATGCAGCACAAGGGGAATG 59.541 55.000 0.00 0.00 0.00 2.67
5330 5718 4.334481 GCATTTACGGGTACACTAAGCATT 59.666 41.667 0.00 0.00 0.00 3.56
5332 5720 3.264104 GCATTTACGGGTACACTAAGCA 58.736 45.455 0.00 0.00 0.00 3.91
5333 5721 3.264104 TGCATTTACGGGTACACTAAGC 58.736 45.455 0.00 0.00 0.00 3.09
5334 5722 6.431198 AATTGCATTTACGGGTACACTAAG 57.569 37.500 0.00 0.00 0.00 2.18
5362 5751 8.737168 AAGCAGTGATATGTAGCATTTTTCTA 57.263 30.769 0.00 0.00 0.00 2.10
5426 5818 5.840940 AAGAACACGTTCAGTACAATAGC 57.159 39.130 12.21 0.00 41.84 2.97
5439 5831 0.752054 TACCACCCGAAAGAACACGT 59.248 50.000 0.00 0.00 0.00 4.49
5450 5844 1.153706 GACCATCACGTACCACCCG 60.154 63.158 0.00 0.00 0.00 5.28
5477 5898 8.316946 TCTATTTCTTCTCTCTTTCATTGCTCA 58.683 33.333 0.00 0.00 0.00 4.26
5561 5983 3.021695 CTGCCATGATGTTTGATGGAGT 58.978 45.455 0.00 0.00 41.63 3.85
5562 5984 3.021695 ACTGCCATGATGTTTGATGGAG 58.978 45.455 0.00 0.00 41.63 3.86
5564 5986 6.487668 TCTTATACTGCCATGATGTTTGATGG 59.512 38.462 0.00 0.00 41.95 3.51
5649 8215 4.856607 CGCGTCTTCGGCTCCCTC 62.857 72.222 0.00 0.00 37.56 4.30
5662 8228 2.317609 GGCAATGACAGTGACGCGT 61.318 57.895 13.85 13.85 0.00 6.01
5683 8249 2.945668 GTTTGCTCAGTTCCAGTGAAGT 59.054 45.455 0.00 0.00 34.39 3.01
5694 8260 6.952773 TTATTACAACAAGGTTTGCTCAGT 57.047 33.333 0.00 0.00 0.00 3.41
5708 8274 6.253942 ACAACAAGGTTTGCGTTTATTACAAC 59.746 34.615 0.00 0.00 0.00 3.32
5712 8278 7.261829 ACTACAACAAGGTTTGCGTTTATTA 57.738 32.000 0.00 0.00 0.00 0.98
5714 8280 5.761165 ACTACAACAAGGTTTGCGTTTAT 57.239 34.783 0.00 0.00 0.00 1.40
5717 8283 4.271776 GTCTACTACAACAAGGTTTGCGTT 59.728 41.667 0.00 0.00 0.00 4.84
5720 8286 5.744666 TTGTCTACTACAACAAGGTTTGC 57.255 39.130 0.00 0.00 43.22 3.68
5738 8304 9.503427 GCCTTAACACAATGATTTACTATTGTC 57.497 33.333 0.00 0.00 43.53 3.18
5739 8305 9.243105 AGCCTTAACACAATGATTTACTATTGT 57.757 29.630 0.00 0.00 45.56 2.71
5744 8310 9.515226 TCTTAAGCCTTAACACAATGATTTACT 57.485 29.630 0.00 0.00 0.00 2.24
5745 8311 9.556030 GTCTTAAGCCTTAACACAATGATTTAC 57.444 33.333 0.00 0.00 0.00 2.01
5762 8328 3.994931 TGTCCTTTAGGGTCTTAAGCC 57.005 47.619 0.00 2.49 43.79 4.35
5763 8329 5.048921 GTGTTTGTCCTTTAGGGTCTTAAGC 60.049 44.000 0.00 0.00 36.25 3.09
5769 8335 3.547746 TGTGTGTTTGTCCTTTAGGGTC 58.452 45.455 0.00 0.00 36.25 4.46
5771 8337 3.697045 TGTTGTGTGTTTGTCCTTTAGGG 59.303 43.478 0.00 0.00 35.41 3.53
5782 8348 1.704070 GGCGTTGTTGTTGTGTGTTT 58.296 45.000 0.00 0.00 0.00 2.83
5791 8357 1.729470 TTGATTGGCGGCGTTGTTGT 61.729 50.000 9.37 0.00 0.00 3.32
5792 8358 1.003262 CTTGATTGGCGGCGTTGTTG 61.003 55.000 9.37 0.00 0.00 3.33
5799 8365 1.666189 GTACTTCTCTTGATTGGCGGC 59.334 52.381 0.00 0.00 0.00 6.53
5800 8366 2.972625 TGTACTTCTCTTGATTGGCGG 58.027 47.619 0.00 0.00 0.00 6.13
5842 8411 2.004583 CTTCGTTCGGGCTACATTCA 57.995 50.000 0.00 0.00 0.00 2.57
5846 8415 0.669318 CAAGCTTCGTTCGGGCTACA 60.669 55.000 0.00 0.00 35.06 2.74
5847 8416 0.389426 TCAAGCTTCGTTCGGGCTAC 60.389 55.000 0.00 0.00 35.06 3.58
5862 8431 4.625028 TGATGGATATGCGAAGACTCAAG 58.375 43.478 0.00 0.00 0.00 3.02
5867 8436 4.811024 TGTCTTTGATGGATATGCGAAGAC 59.189 41.667 17.55 17.55 40.95 3.01
5873 8442 5.105797 TGGTGTTTGTCTTTGATGGATATGC 60.106 40.000 0.00 0.00 0.00 3.14
5882 8550 3.697045 ACGGAATTGGTGTTTGTCTTTGA 59.303 39.130 0.00 0.00 0.00 2.69
5884 8552 3.697045 TCACGGAATTGGTGTTTGTCTTT 59.303 39.130 6.22 0.00 36.76 2.52
5895 8563 1.160329 GGCGGATCTCACGGAATTGG 61.160 60.000 0.00 0.00 0.00 3.16
5903 8576 2.413765 GTCTCCGGCGGATCTCAC 59.586 66.667 31.23 18.97 0.00 3.51
5938 8611 3.025743 TGTGTTTCGCGTCGTCGG 61.026 61.111 5.77 0.00 37.56 4.79
5939 8612 2.164673 GTGTGTTTCGCGTCGTCG 59.835 61.111 5.77 0.00 40.37 5.12
5945 8618 0.319211 TCCTAGTGGTGTGTTTCGCG 60.319 55.000 0.00 0.00 34.23 5.87
5960 8633 1.219469 TGTACTGCCTAGCCCATCCTA 59.781 52.381 0.00 0.00 0.00 2.94
5966 8639 0.618981 AGGTTTGTACTGCCTAGCCC 59.381 55.000 0.00 0.00 0.00 5.19
5980 8655 5.654209 GCTCCCTGAAGATGAAATAAGGTTT 59.346 40.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.