Multiple sequence alignment - TraesCS2B01G263900

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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 TraesCS2B01G263900 chr2B 100.000 4857 0 0 1 4857 356315098 356319954 0.000000e+00 8970.0
1 TraesCS2B01G263900 chr2B 97.143 35 1 0 3352 3386 385194529 385194495 5.250000e-05 60.2
2 TraesCS2B01G263900 chr2D 94.694 2337 72 17 68 2376 298943699 298941387 0.000000e+00 3581.0
3 TraesCS2B01G263900 chr2D 89.804 1324 80 32 3556 4857 298938786 298937496 0.000000e+00 1646.0
4 TraesCS2B01G263900 chr2D 85.078 831 29 26 2522 3316 298941126 298940355 0.000000e+00 760.0
5 TraesCS2B01G263900 chr2D 89.600 125 6 2 2387 2504 298941234 298941110 8.420000e-33 152.0
6 TraesCS2B01G263900 chr2D 88.421 95 9 1 3467 3559 298939366 298939272 3.970000e-21 113.0
7 TraesCS2B01G263900 chr2D 100.000 32 0 0 3314 3345 298939408 298939377 5.250000e-05 60.2
8 TraesCS2B01G263900 chr2D 92.500 40 2 1 3350 3388 157795930 157795891 6.790000e-04 56.5
9 TraesCS2B01G263900 chr2D 92.500 40 2 1 3350 3388 157802430 157802391 6.790000e-04 56.5
10 TraesCS2B01G263900 chr2A 94.579 1697 43 14 829 2504 372737548 372735880 0.000000e+00 2579.0
11 TraesCS2B01G263900 chr2A 89.296 1037 53 33 3637 4632 372735079 372734060 0.000000e+00 1247.0
12 TraesCS2B01G263900 chr2A 89.432 634 32 18 2522 3132 372735896 372735275 0.000000e+00 767.0
13 TraesCS2B01G263900 chr2A 93.646 362 19 3 68 428 372760730 372760372 5.530000e-149 538.0
14 TraesCS2B01G263900 chr2A 86.735 392 20 15 420 787 372759881 372759498 1.630000e-109 407.0
15 TraesCS2B01G263900 chr2A 89.928 278 24 2 4584 4857 372734058 372733781 5.980000e-94 355.0
16 TraesCS2B01G263900 chr2A 90.426 188 13 3 3468 3653 372735277 372735093 4.860000e-60 243.0
17 TraesCS2B01G263900 chr2A 97.778 45 1 0 4 48 372761985 372761941 1.450000e-10 78.7
18 TraesCS2B01G263900 chr5B 85.155 1226 155 19 1110 2323 604143990 604142780 0.000000e+00 1230.0
19 TraesCS2B01G263900 chr5D 84.967 1224 158 18 1110 2323 490006699 490005492 0.000000e+00 1218.0
20 TraesCS2B01G263900 chr5D 95.122 41 2 0 4499 4539 10503234 10503194 1.130000e-06 65.8
21 TraesCS2B01G263900 chr5D 97.143 35 1 0 3352 3386 118664706 118664672 5.250000e-05 60.2
22 TraesCS2B01G263900 chr5A 84.791 1223 162 16 1110 2323 611632741 611631534 0.000000e+00 1206.0
23 TraesCS2B01G263900 chr5A 89.167 240 26 0 1936 2175 645413292 645413053 2.840000e-77 300.0
24 TraesCS2B01G263900 chr5A 89.773 88 6 3 4390 4475 8065283 8065369 5.140000e-20 110.0
25 TraesCS2B01G263900 chr3D 85.992 257 32 4 1110 1364 7969831 7969577 6.190000e-69 272.0
26 TraesCS2B01G263900 chr3D 90.805 87 5 3 4403 4487 454156497 454156412 3.970000e-21 113.0
27 TraesCS2B01G263900 chr3B 86.364 242 29 4 1125 1364 10172041 10171802 1.340000e-65 261.0
28 TraesCS2B01G263900 chr3B 100.000 35 0 0 3352 3386 432957257 432957291 1.130000e-06 65.8
29 TraesCS2B01G263900 chr3B 97.368 38 0 1 3349 3386 664053039 664053075 4.060000e-06 63.9
30 TraesCS2B01G263900 chr3A 78.082 438 76 15 1111 1544 12562523 12562944 4.820000e-65 259.0
31 TraesCS2B01G263900 chr3A 88.889 90 6 4 4392 4478 20743628 20743716 1.850000e-19 108.0
32 TraesCS2B01G263900 chr7A 94.118 102 6 0 1940 2041 83536090 83536191 6.510000e-34 156.0
33 TraesCS2B01G263900 chr7A 86.139 101 9 5 4390 4487 524701269 524701367 2.390000e-18 104.0
34 TraesCS2B01G263900 chr7A 83.036 112 15 4 4391 4499 14307824 14307934 1.110000e-16 99.0
35 TraesCS2B01G263900 chr7A 97.059 34 1 0 3353 3386 712703993 712703960 1.890000e-04 58.4
36 TraesCS2B01G263900 chr6A 82.237 152 15 6 4390 4539 577699143 577699284 2.370000e-23 121.0
37 TraesCS2B01G263900 chr6B 88.889 90 8 2 4391 4478 183753444 183753533 5.140000e-20 110.0
38 TraesCS2B01G263900 chr6B 100.000 29 0 0 4539 4567 480375965 480375993 2.000000e-03 54.7
39 TraesCS2B01G263900 chr6D 88.043 92 7 4 4390 4478 29378190 29378280 6.650000e-19 106.0
40 TraesCS2B01G263900 chr6D 91.489 47 2 2 4494 4539 472279206 472279251 4.060000e-06 63.9
41 TraesCS2B01G263900 chr6D 94.737 38 2 0 4502 4539 338511088 338511051 5.250000e-05 60.2
42 TraesCS2B01G263900 chr6D 100.000 28 0 0 4539 4566 458975418 458975445 9.000000e-03 52.8
43 TraesCS2B01G263900 chr1D 88.506 87 7 2 4403 4487 437855351 437855266 8.600000e-18 102.0
44 TraesCS2B01G263900 chr1D 95.122 41 2 0 4499 4539 384151872 384151912 1.130000e-06 65.8
45 TraesCS2B01G263900 chr7B 100.000 37 0 0 3349 3385 132399584 132399620 8.720000e-08 69.4
46 TraesCS2B01G263900 chr4D 95.122 41 2 0 4499 4539 163791110 163791070 1.130000e-06 65.8
47 TraesCS2B01G263900 chr4D 97.143 35 1 0 3352 3386 267594186 267594220 5.250000e-05 60.2
48 TraesCS2B01G263900 chr4D 94.286 35 2 0 4539 4573 70234554 70234520 2.000000e-03 54.7
49 TraesCS2B01G263900 chr4D 100.000 29 0 0 4539 4567 502014089 502014061 2.000000e-03 54.7
50 TraesCS2B01G263900 chr4A 95.122 41 2 0 4499 4539 621187638 621187678 1.130000e-06 65.8
51 TraesCS2B01G263900 chr4A 94.286 35 2 0 4539 4573 522917002 522916968 2.000000e-03 54.7
52 TraesCS2B01G263900 chr7D 92.308 39 3 0 4501 4539 169559226 169559188 6.790000e-04 56.5
53 TraesCS2B01G263900 chr1A 92.500 40 1 2 4501 4539 16854000 16854038 6.790000e-04 56.5
54 TraesCS2B01G263900 chrUn 100.000 29 0 0 4539 4567 97741855 97741827 2.000000e-03 54.7
55 TraesCS2B01G263900 chr1B 100.000 29 0 0 4539 4567 609304909 609304881 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 TraesCS2B01G263900 chr2B 356315098 356319954 4856 False 8970.000000 8970 100.000000 1 4857 1 chr2B.!!$F1 4856
1 TraesCS2B01G263900 chr2D 298937496 298943699 6203 True 1052.033333 3581 91.266167 68 4857 6 chr2D.!!$R3 4789
2 TraesCS2B01G263900 chr2A 372733781 372737548 3767 True 1038.200000 2579 90.732200 829 4857 5 chr2A.!!$R1 4028
3 TraesCS2B01G263900 chr2A 372759498 372761985 2487 True 341.233333 538 92.719667 4 787 3 chr2A.!!$R2 783
4 TraesCS2B01G263900 chr5B 604142780 604143990 1210 True 1230.000000 1230 85.155000 1110 2323 1 chr5B.!!$R1 1213
5 TraesCS2B01G263900 chr5D 490005492 490006699 1207 True 1218.000000 1218 84.967000 1110 2323 1 chr5D.!!$R3 1213
6 TraesCS2B01G263900 chr5A 611631534 611632741 1207 True 1206.000000 1206 84.791000 1110 2323 1 chr5A.!!$R1 1213

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
867 2583 0.519586 CGACGCGTTCTCTCTCTCAC 60.520 60.0 15.53 0.0 0.00 3.51 F
2329 4052 0.242017 ACGCGGTCAGTACAGTAACC 59.758 55.0 12.47 0.0 0.00 2.85 F
3417 6298 0.102481 CGCCTGCTCCATACGTAGTT 59.898 55.0 0.08 0.0 37.78 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2831 4725 0.034089 CCCCACCCAGAATCTGAACC 60.034 60.0 12.53 0.0 32.44 3.62 R
3452 6333 0.039911 ACTCTACTGCTCCCTCGGTT 59.960 55.0 0.00 0.0 0.00 4.44 R
4835 8342 0.827507 GTGCCAAAGAAGCCCAGGAA 60.828 55.0 0.00 0.0 0.00 3.36 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
45 46 6.380995 TGATGATATAATTGGCGCATTTGTC 58.619 36.000 10.83 1.68 0.00 3.18
48 49 5.299028 TGATATAATTGGCGCATTTGTCAGT 59.701 36.000 10.83 0.00 0.00 3.41
49 50 6.484977 TGATATAATTGGCGCATTTGTCAGTA 59.515 34.615 10.83 0.00 0.00 2.74
50 51 5.772825 ATAATTGGCGCATTTGTCAGTAT 57.227 34.783 10.83 0.00 0.00 2.12
51 52 2.917701 TTGGCGCATTTGTCAGTATG 57.082 45.000 10.83 0.00 37.54 2.39
52 53 1.819928 TGGCGCATTTGTCAGTATGT 58.180 45.000 10.83 0.00 37.40 2.29
53 54 2.158559 TGGCGCATTTGTCAGTATGTT 58.841 42.857 10.83 0.00 37.40 2.71
55 56 3.005261 TGGCGCATTTGTCAGTATGTTTT 59.995 39.130 10.83 0.00 37.40 2.43
56 57 3.987220 GGCGCATTTGTCAGTATGTTTTT 59.013 39.130 10.83 0.00 37.40 1.94
57 58 4.089923 GGCGCATTTGTCAGTATGTTTTTC 59.910 41.667 10.83 0.00 37.40 2.29
58 59 4.089923 GCGCATTTGTCAGTATGTTTTTCC 59.910 41.667 0.30 0.00 37.40 3.13
60 61 5.920273 CGCATTTGTCAGTATGTTTTTCCTT 59.080 36.000 0.00 0.00 37.40 3.36
61 62 6.088085 CGCATTTGTCAGTATGTTTTTCCTTC 59.912 38.462 0.00 0.00 37.40 3.46
62 63 7.147976 GCATTTGTCAGTATGTTTTTCCTTCT 58.852 34.615 0.00 0.00 37.40 2.85
65 66 5.376625 TGTCAGTATGTTTTTCCTTCTGCT 58.623 37.500 0.00 0.00 37.40 4.24
66 67 5.239306 TGTCAGTATGTTTTTCCTTCTGCTG 59.761 40.000 0.00 0.00 37.40 4.41
71 1263 2.951642 TGTTTTTCCTTCTGCTGTCCAG 59.048 45.455 0.00 0.00 43.17 3.86
133 1325 4.100529 CGCTTGTTGATCATGGATTTGAC 58.899 43.478 0.00 0.00 0.00 3.18
152 1344 6.838198 TTGACGAGGGAAATTCAATATACG 57.162 37.500 0.00 0.00 0.00 3.06
164 1356 1.219522 AATATACGGCAGGTTCGCGC 61.220 55.000 0.00 0.00 0.00 6.86
177 1369 1.257936 GTTCGCGCGTGATAATCATGT 59.742 47.619 30.98 0.00 35.86 3.21
188 1380 3.987220 TGATAATCATGTGCCGATGTACG 59.013 43.478 0.00 0.00 42.18 3.67
247 1439 1.600916 GACTTATGCGGATGCCCCC 60.601 63.158 0.00 0.00 41.78 5.40
285 1477 1.800805 CTCGGCTGTCAACATCTTGT 58.199 50.000 0.00 0.00 0.00 3.16
376 1568 6.773638 AGCATATATTCCACCTTTCACCTAG 58.226 40.000 0.00 0.00 0.00 3.02
385 1578 4.514066 CCACCTTTCACCTAGTGTTTACAC 59.486 45.833 4.87 4.87 46.77 2.90
416 1610 2.554032 CGCTCAAATGACCCAAAAGTCT 59.446 45.455 0.00 0.00 37.66 3.24
469 2162 4.986034 CACTTTCTGAAGAAATGCAATGCA 59.014 37.500 11.44 11.44 42.44 3.96
476 2169 6.146510 TCTGAAGAAATGCAATGCAAATTGTC 59.853 34.615 13.45 8.23 43.62 3.18
537 2231 1.507141 CCAGCTTTTCACCGCGTCTT 61.507 55.000 4.92 0.00 0.00 3.01
581 2287 1.205893 GAGTGCAGTGTAGAGAAGGGG 59.794 57.143 0.00 0.00 0.00 4.79
669 2382 1.026584 GCAACAACCACCCGTAAAGT 58.973 50.000 0.00 0.00 0.00 2.66
679 2392 5.683681 ACCACCCGTAAAGTAAAGAAAAGA 58.316 37.500 0.00 0.00 0.00 2.52
681 2394 6.602803 ACCACCCGTAAAGTAAAGAAAAGAAA 59.397 34.615 0.00 0.00 0.00 2.52
682 2395 7.122501 ACCACCCGTAAAGTAAAGAAAAGAAAA 59.877 33.333 0.00 0.00 0.00 2.29
685 2398 7.148035 ACCCGTAAAGTAAAGAAAAGAAAAGCA 60.148 33.333 0.00 0.00 0.00 3.91
687 2400 7.166970 CCGTAAAGTAAAGAAAAGAAAAGCACC 59.833 37.037 0.00 0.00 0.00 5.01
751 2467 8.487313 AATACAAAACTCAAAAACAAAGGGAC 57.513 30.769 0.00 0.00 0.00 4.46
783 2499 1.365368 GAGGAAGGAAAGCTCTGCGC 61.365 60.000 0.00 0.00 39.57 6.09
866 2582 0.949588 ACGACGCGTTCTCTCTCTCA 60.950 55.000 15.53 0.00 36.35 3.27
867 2583 0.519586 CGACGCGTTCTCTCTCTCAC 60.520 60.000 15.53 0.00 0.00 3.51
868 2584 0.800012 GACGCGTTCTCTCTCTCACT 59.200 55.000 15.53 0.00 0.00 3.41
869 2585 0.800012 ACGCGTTCTCTCTCTCACTC 59.200 55.000 5.58 0.00 0.00 3.51
870 2586 1.083489 CGCGTTCTCTCTCTCACTCT 58.917 55.000 0.00 0.00 0.00 3.24
871 2587 1.062002 CGCGTTCTCTCTCTCACTCTC 59.938 57.143 0.00 0.00 0.00 3.20
872 2588 2.356135 GCGTTCTCTCTCTCACTCTCT 58.644 52.381 0.00 0.00 0.00 3.10
873 2589 2.351726 GCGTTCTCTCTCTCACTCTCTC 59.648 54.545 0.00 0.00 0.00 3.20
1098 2818 4.521062 CCCTCCTCTTCAGCGGCG 62.521 72.222 0.51 0.51 0.00 6.46
1818 3541 3.352338 GACGCTGGTCCTGTACGGG 62.352 68.421 15.21 15.21 37.19 5.28
1836 3559 2.572284 GGGTACAACGAGCTCGCT 59.428 61.111 34.83 22.04 44.43 4.93
2025 3748 2.864114 CGAGTACCAGACGGAGGAA 58.136 57.895 0.00 0.00 35.59 3.36
2329 4052 0.242017 ACGCGGTCAGTACAGTAACC 59.758 55.000 12.47 0.00 0.00 2.85
2332 4055 1.992170 CGGTCAGTACAGTAACCTGC 58.008 55.000 0.00 0.00 42.81 4.85
2333 4056 1.403780 CGGTCAGTACAGTAACCTGCC 60.404 57.143 0.00 1.82 42.81 4.85
2334 4057 1.621814 GGTCAGTACAGTAACCTGCCA 59.378 52.381 0.00 0.00 42.81 4.92
2336 4059 3.522553 GTCAGTACAGTAACCTGCCATC 58.477 50.000 0.00 0.00 42.81 3.51
2343 4069 2.744202 CAGTAACCTGCCATCTTCACAC 59.256 50.000 0.00 0.00 0.00 3.82
2355 4081 6.145535 GCCATCTTCACACTACTTCTTTTTG 58.854 40.000 0.00 0.00 0.00 2.44
2356 4082 6.672147 CCATCTTCACACTACTTCTTTTTGG 58.328 40.000 0.00 0.00 0.00 3.28
2357 4083 6.263168 CCATCTTCACACTACTTCTTTTTGGT 59.737 38.462 0.00 0.00 0.00 3.67
2401 4269 2.950309 ACGCGGTAGATGTAGAGATTGT 59.050 45.455 12.47 0.00 0.00 2.71
2414 4282 4.025040 AGAGATTGTGCAAGAATGGTCA 57.975 40.909 0.00 0.00 25.38 4.02
2418 4286 4.525487 AGATTGTGCAAGAATGGTCATGTT 59.475 37.500 0.00 0.00 25.38 2.71
2504 4387 0.810648 TCACATTCGCCATTGCCTTC 59.189 50.000 0.00 0.00 0.00 3.46
2505 4388 0.813184 CACATTCGCCATTGCCTTCT 59.187 50.000 0.00 0.00 0.00 2.85
2506 4389 1.098050 ACATTCGCCATTGCCTTCTC 58.902 50.000 0.00 0.00 0.00 2.87
2507 4390 1.340405 ACATTCGCCATTGCCTTCTCT 60.340 47.619 0.00 0.00 0.00 3.10
2508 4391 1.332997 CATTCGCCATTGCCTTCTCTC 59.667 52.381 0.00 0.00 0.00 3.20
2509 4392 0.740868 TTCGCCATTGCCTTCTCTCG 60.741 55.000 0.00 0.00 0.00 4.04
2510 4393 2.817423 CGCCATTGCCTTCTCTCGC 61.817 63.158 0.00 0.00 0.00 5.03
2511 4394 1.746615 GCCATTGCCTTCTCTCGCA 60.747 57.895 0.00 0.00 0.00 5.10
2536 4419 2.837532 AAAAACATTCGCCATTGCCT 57.162 40.000 0.00 0.00 0.00 4.75
2537 4420 2.837532 AAAACATTCGCCATTGCCTT 57.162 40.000 0.00 0.00 0.00 4.35
2640 4532 5.068460 GTCTAGCTTAGATGTGTCACCTCAT 59.932 44.000 10.42 0.00 37.13 2.90
2666 4558 3.241701 GACAGAGAGACAGAAGCTTTCG 58.758 50.000 0.00 0.00 34.02 3.46
2674 4566 2.034221 GAAGCTTTCGGTGGGCCT 59.966 61.111 4.53 0.00 0.00 5.19
2729 4621 8.410000 AGGGTGAAATTAATTAAGGGGTACTA 57.590 34.615 0.01 0.00 0.00 1.82
2730 4622 8.500238 AGGGTGAAATTAATTAAGGGGTACTAG 58.500 37.037 0.01 0.00 0.00 2.57
2731 4623 8.277197 GGGTGAAATTAATTAAGGGGTACTAGT 58.723 37.037 0.01 0.00 0.00 2.57
2805 4699 1.036707 CGGTGAAAATGGTTGGTGGT 58.963 50.000 0.00 0.00 0.00 4.16
2827 4721 1.149148 GTTCTCGTTCTGGTTCTGGC 58.851 55.000 0.00 0.00 0.00 4.85
2828 4722 1.048601 TTCTCGTTCTGGTTCTGGCT 58.951 50.000 0.00 0.00 0.00 4.75
2829 4723 0.603569 TCTCGTTCTGGTTCTGGCTC 59.396 55.000 0.00 0.00 0.00 4.70
2830 4724 0.605589 CTCGTTCTGGTTCTGGCTCT 59.394 55.000 0.00 0.00 0.00 4.09
2831 4725 0.318441 TCGTTCTGGTTCTGGCTCTG 59.682 55.000 0.00 0.00 0.00 3.35
2832 4726 0.671781 CGTTCTGGTTCTGGCTCTGG 60.672 60.000 0.00 0.00 0.00 3.86
2833 4727 0.398318 GTTCTGGTTCTGGCTCTGGT 59.602 55.000 0.00 0.00 0.00 4.00
2834 4728 1.140312 TTCTGGTTCTGGCTCTGGTT 58.860 50.000 0.00 0.00 0.00 3.67
2835 4729 0.687354 TCTGGTTCTGGCTCTGGTTC 59.313 55.000 0.00 0.00 0.00 3.62
2836 4730 0.397941 CTGGTTCTGGCTCTGGTTCA 59.602 55.000 0.00 0.00 0.00 3.18
2837 4731 0.397941 TGGTTCTGGCTCTGGTTCAG 59.602 55.000 0.00 0.00 0.00 3.02
2838 4732 0.687354 GGTTCTGGCTCTGGTTCAGA 59.313 55.000 0.00 0.00 38.25 3.27
2989 4890 2.756042 AAGTGGTGGTGAGCTGGCA 61.756 57.895 0.00 0.00 0.00 4.92
3143 5060 5.487433 TCTTGATGAAGAAAGCCGTGATAA 58.513 37.500 0.00 0.00 35.14 1.75
3153 5070 3.194005 AGCCGTGATAATGGAACGAAT 57.806 42.857 0.00 0.00 39.64 3.34
3160 5077 6.073058 CCGTGATAATGGAACGAATGATCATT 60.073 38.462 20.85 20.85 39.64 2.57
3165 5082 9.338291 GATAATGGAACGAATGATCATTCAATG 57.662 33.333 35.71 25.86 45.60 2.82
3167 5084 6.367686 TGGAACGAATGATCATTCAATGAG 57.632 37.500 35.71 25.30 45.60 2.90
3251 5183 7.330900 TGGAGTACTATAGTTACAGTTCAGC 57.669 40.000 11.40 0.00 0.00 4.26
3252 5184 6.037940 TGGAGTACTATAGTTACAGTTCAGCG 59.962 42.308 11.40 0.00 0.00 5.18
3253 5185 6.374565 AGTACTATAGTTACAGTTCAGCGG 57.625 41.667 11.40 0.00 0.00 5.52
3254 5186 4.043037 ACTATAGTTACAGTTCAGCGGC 57.957 45.455 0.00 0.00 0.00 6.53
3255 5187 3.446161 ACTATAGTTACAGTTCAGCGGCA 59.554 43.478 1.45 0.00 0.00 5.69
3256 5188 2.823924 TAGTTACAGTTCAGCGGCAA 57.176 45.000 1.45 0.00 0.00 4.52
3257 5189 1.961793 AGTTACAGTTCAGCGGCAAA 58.038 45.000 1.45 0.00 0.00 3.68
3258 5190 2.294074 AGTTACAGTTCAGCGGCAAAA 58.706 42.857 1.45 0.00 0.00 2.44
3259 5191 2.685897 AGTTACAGTTCAGCGGCAAAAA 59.314 40.909 1.45 0.00 0.00 1.94
3285 5217 2.846039 AATCCTCAGTACACGTAGCG 57.154 50.000 0.00 0.00 0.00 4.26
3345 6226 8.041919 TGTCGGTAATTACCATCTTTATTGTGA 58.958 33.333 29.56 13.94 46.80 3.58
3347 6228 8.262227 TCGGTAATTACCATCTTTATTGTGAGT 58.738 33.333 29.56 0.00 46.80 3.41
3365 6246 4.940905 GAGTAACTACTCCCTCCATTCC 57.059 50.000 5.70 0.00 45.33 3.01
3366 6247 4.548669 GAGTAACTACTCCCTCCATTCCT 58.451 47.826 5.70 0.00 45.33 3.36
3367 6248 5.703310 GAGTAACTACTCCCTCCATTCCTA 58.297 45.833 5.70 0.00 45.33 2.94
3368 6249 6.101274 AGTAACTACTCCCTCCATTCCTAA 57.899 41.667 0.00 0.00 0.00 2.69
3369 6250 6.509386 AGTAACTACTCCCTCCATTCCTAAA 58.491 40.000 0.00 0.00 0.00 1.85
3370 6251 5.695424 AACTACTCCCTCCATTCCTAAAC 57.305 43.478 0.00 0.00 0.00 2.01
3371 6252 4.695606 ACTACTCCCTCCATTCCTAAACA 58.304 43.478 0.00 0.00 0.00 2.83
3372 6253 5.289510 ACTACTCCCTCCATTCCTAAACAT 58.710 41.667 0.00 0.00 0.00 2.71
3373 6254 6.449956 ACTACTCCCTCCATTCCTAAACATA 58.550 40.000 0.00 0.00 0.00 2.29
3374 6255 6.906901 ACTACTCCCTCCATTCCTAAACATAA 59.093 38.462 0.00 0.00 0.00 1.90
3375 6256 6.253946 ACTCCCTCCATTCCTAAACATAAG 57.746 41.667 0.00 0.00 0.00 1.73
3376 6257 5.731678 ACTCCCTCCATTCCTAAACATAAGT 59.268 40.000 0.00 0.00 0.00 2.24
3377 6258 6.126739 ACTCCCTCCATTCCTAAACATAAGTC 60.127 42.308 0.00 0.00 0.00 3.01
3378 6259 5.970640 TCCCTCCATTCCTAAACATAAGTCT 59.029 40.000 0.00 0.00 0.00 3.24
3379 6260 6.447084 TCCCTCCATTCCTAAACATAAGTCTT 59.553 38.462 0.00 0.00 0.00 3.01
3380 6261 7.036863 TCCCTCCATTCCTAAACATAAGTCTTT 60.037 37.037 0.00 0.00 0.00 2.52
3381 6262 7.283354 CCCTCCATTCCTAAACATAAGTCTTTC 59.717 40.741 0.00 0.00 0.00 2.62
3382 6263 8.049721 CCTCCATTCCTAAACATAAGTCTTTCT 58.950 37.037 0.00 0.00 0.00 2.52
3412 6293 1.647346 TTTTACGCCTGCTCCATACG 58.353 50.000 0.00 0.00 0.00 3.06
3413 6294 0.533491 TTTACGCCTGCTCCATACGT 59.467 50.000 0.00 0.00 40.53 3.57
3414 6295 1.391577 TTACGCCTGCTCCATACGTA 58.608 50.000 0.00 0.00 38.12 3.57
3415 6296 0.949397 TACGCCTGCTCCATACGTAG 59.051 55.000 0.08 0.00 38.12 3.51
3417 6298 0.102481 CGCCTGCTCCATACGTAGTT 59.898 55.000 0.08 0.00 37.78 2.24
3418 6299 1.854227 GCCTGCTCCATACGTAGTTC 58.146 55.000 0.08 0.00 37.78 3.01
3419 6300 1.136305 GCCTGCTCCATACGTAGTTCA 59.864 52.381 0.08 0.00 37.78 3.18
3420 6301 2.224066 GCCTGCTCCATACGTAGTTCAT 60.224 50.000 0.08 0.00 37.78 2.57
3421 6302 3.005472 GCCTGCTCCATACGTAGTTCATA 59.995 47.826 0.08 0.00 37.78 2.15
3422 6303 4.547532 CCTGCTCCATACGTAGTTCATAC 58.452 47.826 0.08 0.00 37.78 2.39
3423 6304 4.278669 CCTGCTCCATACGTAGTTCATACT 59.721 45.833 0.08 0.00 37.78 2.12
3424 6305 5.472478 CCTGCTCCATACGTAGTTCATACTA 59.528 44.000 0.08 0.00 37.78 1.82
3425 6306 6.016527 CCTGCTCCATACGTAGTTCATACTAA 60.017 42.308 0.08 0.00 37.78 2.24
3426 6307 7.337480 TGCTCCATACGTAGTTCATACTAAA 57.663 36.000 0.08 0.00 37.78 1.85
3427 6308 7.774134 TGCTCCATACGTAGTTCATACTAAAA 58.226 34.615 0.08 0.00 37.78 1.52
3428 6309 8.418662 TGCTCCATACGTAGTTCATACTAAAAT 58.581 33.333 0.08 0.00 37.78 1.82
3429 6310 8.913656 GCTCCATACGTAGTTCATACTAAAATC 58.086 37.037 0.08 0.00 37.78 2.17
3459 6340 8.808092 AGAAAGAGATATATTTAGGAACCGAGG 58.192 37.037 0.00 0.00 0.00 4.63
3460 6341 7.483580 AAGAGATATATTTAGGAACCGAGGG 57.516 40.000 0.00 0.00 0.00 4.30
3461 6342 6.801953 AGAGATATATTTAGGAACCGAGGGA 58.198 40.000 0.00 0.00 0.00 4.20
3462 6343 6.893005 AGAGATATATTTAGGAACCGAGGGAG 59.107 42.308 0.00 0.00 0.00 4.30
3463 6344 5.422650 AGATATATTTAGGAACCGAGGGAGC 59.577 44.000 0.00 0.00 0.00 4.70
3464 6345 1.580059 ATTTAGGAACCGAGGGAGCA 58.420 50.000 0.00 0.00 0.00 4.26
3465 6346 0.902531 TTTAGGAACCGAGGGAGCAG 59.097 55.000 0.00 0.00 0.00 4.24
3513 6394 0.244994 GGCGTCGAGATGGAGCATAT 59.755 55.000 0.00 0.00 0.00 1.78
3515 6396 1.988063 CGTCGAGATGGAGCATATGG 58.012 55.000 4.56 0.00 0.00 2.74
3516 6397 1.403382 CGTCGAGATGGAGCATATGGG 60.403 57.143 4.56 0.00 0.00 4.00
3563 6935 1.806542 CAGCACCACATCAGTAACCAC 59.193 52.381 0.00 0.00 0.00 4.16
3586 6958 0.815213 TGAAGTGACAGTGCACCTGC 60.815 55.000 14.63 1.79 45.68 4.85
3597 6969 1.588082 GCACCTGCAAATGGGACAG 59.412 57.895 0.00 0.00 41.60 3.51
3618 6990 2.124693 CACCCAACACCAACGCCTT 61.125 57.895 0.00 0.00 0.00 4.35
3626 6998 3.915437 ACACCAACGCCTTAAAATGAG 57.085 42.857 0.00 0.00 0.00 2.90
3627 6999 2.556622 ACACCAACGCCTTAAAATGAGG 59.443 45.455 0.00 0.00 37.35 3.86
3673 7072 4.767578 TGCAGCTCATTAATCCTCTTCT 57.232 40.909 0.00 0.00 0.00 2.85
3811 7218 3.443045 GAAGGGGCGTGCCATGTG 61.443 66.667 13.76 0.00 37.98 3.21
3835 7242 2.582498 GTCTTCGGTGGGCGATCG 60.582 66.667 11.69 11.69 0.00 3.69
3937 7344 3.426695 GGCTCAAAGATGAACATGAACCG 60.427 47.826 0.00 0.00 34.49 4.44
4035 7444 4.095036 GCCGTCAGGAAATTAGGAGAAAAG 59.905 45.833 0.00 0.00 41.02 2.27
4071 7480 7.255139 GGAAATTTGTTTATACGGGAGATCAGG 60.255 40.741 0.00 0.00 0.00 3.86
4090 7499 2.290916 AGGTCGACATCAGTGTATAGCG 59.709 50.000 18.91 0.00 39.09 4.26
4140 7551 9.237187 TGATTTGTGGTTTAAGATGCTACATAA 57.763 29.630 0.00 0.00 0.00 1.90
4250 7662 4.683781 GCCTTCTACTCTATCAAATCAGCG 59.316 45.833 0.00 0.00 0.00 5.18
4251 7663 5.226396 CCTTCTACTCTATCAAATCAGCGG 58.774 45.833 0.00 0.00 0.00 5.52
4254 7666 3.266510 ACTCTATCAAATCAGCGGCAA 57.733 42.857 1.45 0.00 0.00 4.52
4260 7672 6.902341 TCTATCAAATCAGCGGCAATTATTC 58.098 36.000 1.45 0.00 0.00 1.75
4277 7689 8.234546 GCAATTATTCTTTTAAGACGGAGACAA 58.765 33.333 0.00 0.00 34.13 3.18
4375 7817 1.620822 ACAAACCAGGTTCAGGCATC 58.379 50.000 4.93 0.00 0.00 3.91
4396 7838 7.323420 GCATCAAGGCTAAAAACCTCTAAATT 58.677 34.615 0.00 0.00 36.14 1.82
4397 7839 8.466798 GCATCAAGGCTAAAAACCTCTAAATTA 58.533 33.333 0.00 0.00 36.14 1.40
4497 7941 9.944376 TTTGCTCTAGTCTGTATTGAAATTAGT 57.056 29.630 0.00 0.00 0.00 2.24
4499 7943 9.587772 TGCTCTAGTCTGTATTGAAATTAGTTC 57.412 33.333 0.00 0.00 36.70 3.01
4500 7944 9.036671 GCTCTAGTCTGTATTGAAATTAGTTCC 57.963 37.037 0.00 0.00 35.12 3.62
4522 7969 7.919313 TCCGTATGTAGTTCGTATTGAAATC 57.081 36.000 0.00 0.00 38.60 2.17
4616 8066 6.375455 ACAACCAGTTGAGGCTTATTATTGAG 59.625 38.462 17.06 0.00 42.93 3.02
4692 8196 0.842635 GGAGATCAGGGATTGGCAGT 59.157 55.000 0.00 0.00 0.00 4.40
4786 8293 0.248825 CCTCTTCGGAGCAGATGTCG 60.249 60.000 0.00 0.00 40.56 4.35
4821 8328 0.036010 CCTCCGTTGCCAGATGACTT 60.036 55.000 0.00 0.00 0.00 3.01
4823 8330 0.396435 TCCGTTGCCAGATGACTTGT 59.604 50.000 0.00 0.00 0.00 3.16
4824 8331 0.518636 CCGTTGCCAGATGACTTGTG 59.481 55.000 0.00 0.00 0.00 3.33
4835 8342 1.145377 GACTTGTGGTCGTGGGTGT 59.855 57.895 0.00 0.00 35.07 4.16
4849 8356 0.178961 GGGTGTTCCTGGGCTTCTTT 60.179 55.000 0.00 0.00 0.00 2.52
4851 8358 0.961753 GTGTTCCTGGGCTTCTTTGG 59.038 55.000 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.428083 TCATTAGGTACCTGTGTTTCTCAA 57.572 37.500 25.33 7.56 0.00 3.02
1 2 6.212589 TCATCATTAGGTACCTGTGTTTCTCA 59.787 38.462 25.33 6.55 0.00 3.27
2 3 6.640518 TCATCATTAGGTACCTGTGTTTCTC 58.359 40.000 25.33 0.00 0.00 2.87
45 46 5.335191 GGACAGCAGAAGGAAAAACATACTG 60.335 44.000 0.00 0.00 0.00 2.74
48 49 4.724399 TGGACAGCAGAAGGAAAAACATA 58.276 39.130 0.00 0.00 0.00 2.29
49 50 3.565307 TGGACAGCAGAAGGAAAAACAT 58.435 40.909 0.00 0.00 0.00 2.71
50 51 2.951642 CTGGACAGCAGAAGGAAAAACA 59.048 45.455 0.00 0.00 0.00 2.83
51 52 3.632855 CTGGACAGCAGAAGGAAAAAC 57.367 47.619 0.00 0.00 0.00 2.43
133 1325 4.062293 TGCCGTATATTGAATTTCCCTCG 58.938 43.478 0.00 0.00 0.00 4.63
164 1356 2.802247 ACATCGGCACATGATTATCACG 59.198 45.455 0.00 0.00 0.00 4.35
167 1359 3.181530 GCGTACATCGGCACATGATTATC 60.182 47.826 0.00 0.00 40.26 1.75
168 1360 2.736721 GCGTACATCGGCACATGATTAT 59.263 45.455 0.00 0.00 40.26 1.28
247 1439 1.156645 GCGGATCTTGCTACAGCCTG 61.157 60.000 0.00 0.00 41.18 4.85
285 1477 3.240134 GAACTGCCGAGTGCCAGGA 62.240 63.158 0.00 0.00 40.16 3.86
376 1568 0.945743 GTCCCGTCCCGTGTAAACAC 60.946 60.000 3.08 3.08 43.15 3.32
385 1578 3.659089 ATTTGAGCGTCCCGTCCCG 62.659 63.158 0.00 0.00 0.00 5.14
394 1587 2.293399 GACTTTTGGGTCATTTGAGCGT 59.707 45.455 3.88 0.00 43.03 5.07
416 1610 3.011818 TGTATCCGACGCTCTCAACTTA 58.988 45.455 0.00 0.00 0.00 2.24
469 2162 8.627208 TTCTTGCTCTCAGAATAAGACAATTT 57.373 30.769 0.78 0.00 0.00 1.82
537 2231 2.886523 CTCTTTCTTGCACCATGACCAA 59.113 45.455 0.00 0.00 0.00 3.67
581 2287 0.175760 TACGCAGGCATCTCACCTTC 59.824 55.000 0.00 0.00 34.42 3.46
669 2382 4.712337 TGGGTGGTGCTTTTCTTTTCTTTA 59.288 37.500 0.00 0.00 0.00 1.85
679 2392 4.410555 TCCTTTTATTTGGGTGGTGCTTTT 59.589 37.500 0.00 0.00 0.00 2.27
681 2394 3.578282 CTCCTTTTATTTGGGTGGTGCTT 59.422 43.478 0.00 0.00 0.00 3.91
682 2395 3.165071 CTCCTTTTATTTGGGTGGTGCT 58.835 45.455 0.00 0.00 0.00 4.40
685 2398 4.140782 AGGAACTCCTTTTATTTGGGTGGT 60.141 41.667 0.00 0.00 46.09 4.16
764 2480 1.365368 GCGCAGAGCTTTCCTTCCTC 61.365 60.000 0.30 0.00 44.04 3.71
866 2582 4.458989 CACTGCTACTTGAAGAGAGAGAGT 59.541 45.833 0.00 0.00 0.00 3.24
867 2583 4.699735 TCACTGCTACTTGAAGAGAGAGAG 59.300 45.833 0.00 0.00 0.00 3.20
868 2584 4.657013 TCACTGCTACTTGAAGAGAGAGA 58.343 43.478 0.00 0.00 0.00 3.10
869 2585 5.160641 GTTCACTGCTACTTGAAGAGAGAG 58.839 45.833 0.00 0.00 32.40 3.20
870 2586 4.021894 GGTTCACTGCTACTTGAAGAGAGA 60.022 45.833 0.00 0.00 32.40 3.10
871 2587 4.241681 GGTTCACTGCTACTTGAAGAGAG 58.758 47.826 0.00 0.00 32.40 3.20
872 2588 3.006967 GGGTTCACTGCTACTTGAAGAGA 59.993 47.826 0.00 0.00 32.40 3.10
873 2589 3.330267 GGGTTCACTGCTACTTGAAGAG 58.670 50.000 0.00 0.00 32.40 2.85
899 2615 5.221461 GGAAGAAGGCGGAGTGAGAAATATA 60.221 44.000 0.00 0.00 0.00 0.86
902 2618 2.355209 GGAAGAAGGCGGAGTGAGAAAT 60.355 50.000 0.00 0.00 0.00 2.17
1098 2818 3.637273 ACCCCCGTGGAGCTGTTC 61.637 66.667 0.00 0.00 38.00 3.18
1143 2863 1.583495 CCGTGTAGTGCGAGTCCAGA 61.583 60.000 0.00 0.00 0.00 3.86
1542 3265 3.753797 GGTTGAAATCCTCCTGAACTGAC 59.246 47.826 0.00 0.00 0.00 3.51
1818 3541 2.508663 GCGAGCTCGTTGTACCCC 60.509 66.667 34.46 13.69 42.22 4.95
1836 3559 2.430694 CGTCAGGTTCACCAGGATATCA 59.569 50.000 4.83 0.00 38.89 2.15
1890 3613 1.198713 CTGTGAGCACATACCCCTCT 58.801 55.000 3.49 0.00 41.01 3.69
2025 3748 1.866237 CACGGCGTTGTACATGCTT 59.134 52.632 11.19 5.40 37.58 3.91
2313 4036 1.403780 GGCAGGTTACTGTACTGACCG 60.404 57.143 6.77 3.29 46.62 4.79
2329 4052 4.199432 AGAAGTAGTGTGAAGATGGCAG 57.801 45.455 0.00 0.00 0.00 4.85
2332 4055 6.263168 ACCAAAAAGAAGTAGTGTGAAGATGG 59.737 38.462 0.00 0.00 0.00 3.51
2333 4056 7.264373 ACCAAAAAGAAGTAGTGTGAAGATG 57.736 36.000 0.00 0.00 0.00 2.90
2378 4104 4.213694 ACAATCTCTACATCTACCGCGTAG 59.786 45.833 4.92 7.37 37.47 3.51
2380 4106 2.950309 ACAATCTCTACATCTACCGCGT 59.050 45.455 4.92 0.00 0.00 6.01
2381 4107 3.300857 CACAATCTCTACATCTACCGCG 58.699 50.000 0.00 0.00 0.00 6.46
2382 4108 3.053455 GCACAATCTCTACATCTACCGC 58.947 50.000 0.00 0.00 0.00 5.68
2383 4109 4.307443 TGCACAATCTCTACATCTACCG 57.693 45.455 0.00 0.00 0.00 4.02
2384 4110 5.907207 TCTTGCACAATCTCTACATCTACC 58.093 41.667 0.00 0.00 0.00 3.18
2401 4269 3.193903 CCATCAACATGACCATTCTTGCA 59.806 43.478 0.00 0.00 31.41 4.08
2414 4282 1.351017 ACAACCCTCGACCATCAACAT 59.649 47.619 0.00 0.00 0.00 2.71
2418 4286 1.003839 GCACAACCCTCGACCATCA 60.004 57.895 0.00 0.00 0.00 3.07
2517 4400 2.807392 CAAGGCAATGGCGAATGTTTTT 59.193 40.909 0.00 0.00 42.47 1.94
2518 4401 2.415776 CAAGGCAATGGCGAATGTTTT 58.584 42.857 0.00 0.00 42.47 2.43
2519 4402 1.940752 GCAAGGCAATGGCGAATGTTT 60.941 47.619 0.00 0.00 42.47 2.83
2520 4403 0.390209 GCAAGGCAATGGCGAATGTT 60.390 50.000 0.00 0.00 42.47 2.71
2521 4404 1.216178 GCAAGGCAATGGCGAATGT 59.784 52.632 0.00 0.00 42.47 2.71
2522 4405 1.519898 GGCAAGGCAATGGCGAATG 60.520 57.895 0.00 3.66 42.47 2.67
2523 4406 2.894919 GGCAAGGCAATGGCGAAT 59.105 55.556 0.00 0.00 42.47 3.34
2534 4417 3.142838 CTTGGATGCCCGGCAAGG 61.143 66.667 18.00 0.00 43.62 3.61
2535 4418 3.830192 GCTTGGATGCCCGGCAAG 61.830 66.667 18.00 10.43 43.62 4.01
2536 4419 4.675161 TGCTTGGATGCCCGGCAA 62.675 61.111 18.00 0.00 43.62 4.52
2537 4420 4.675161 TTGCTTGGATGCCCGGCA 62.675 61.111 16.17 16.17 44.86 5.69
2610 4502 6.766944 GTGACACATCTAAGCTAGACCTAGTA 59.233 42.308 0.00 0.00 37.69 1.82
2611 4503 5.591067 GTGACACATCTAAGCTAGACCTAGT 59.409 44.000 0.00 0.00 37.69 2.57
2612 4504 5.009210 GGTGACACATCTAAGCTAGACCTAG 59.991 48.000 8.08 0.00 37.69 3.02
2640 4532 1.891811 CTTCTGTCTCTCTGTCCTGCA 59.108 52.381 0.00 0.00 0.00 4.41
2674 4566 4.077184 CGCCTACCCAACTCGCCA 62.077 66.667 0.00 0.00 0.00 5.69
2729 4621 3.890147 CGGCATTTACTCCTACTCCTACT 59.110 47.826 0.00 0.00 0.00 2.57
2730 4622 3.552478 GCGGCATTTACTCCTACTCCTAC 60.552 52.174 0.00 0.00 0.00 3.18
2731 4623 2.626743 GCGGCATTTACTCCTACTCCTA 59.373 50.000 0.00 0.00 0.00 2.94
2732 4624 1.413077 GCGGCATTTACTCCTACTCCT 59.587 52.381 0.00 0.00 0.00 3.69
2733 4625 1.138266 TGCGGCATTTACTCCTACTCC 59.862 52.381 0.00 0.00 0.00 3.85
2734 4626 2.474816 CTGCGGCATTTACTCCTACTC 58.525 52.381 1.75 0.00 0.00 2.59
2827 4721 2.355513 CCACCCAGAATCTGAACCAGAG 60.356 54.545 12.53 0.00 44.08 3.35
2828 4722 1.630369 CCACCCAGAATCTGAACCAGA 59.370 52.381 12.53 0.00 44.99 3.86
2829 4723 1.340405 CCCACCCAGAATCTGAACCAG 60.340 57.143 12.53 0.00 32.44 4.00
2830 4724 0.698238 CCCACCCAGAATCTGAACCA 59.302 55.000 12.53 0.00 32.44 3.67
2831 4725 0.034089 CCCCACCCAGAATCTGAACC 60.034 60.000 12.53 0.00 32.44 3.62
2832 4726 0.991920 TCCCCACCCAGAATCTGAAC 59.008 55.000 12.53 0.00 32.44 3.18
2833 4727 1.289160 CTCCCCACCCAGAATCTGAA 58.711 55.000 12.53 0.00 32.44 3.02
2834 4728 0.621571 CCTCCCCACCCAGAATCTGA 60.622 60.000 12.53 0.00 32.44 3.27
2835 4729 1.639635 CCCTCCCCACCCAGAATCTG 61.640 65.000 2.68 2.68 0.00 2.90
2836 4730 1.308216 CCCTCCCCACCCAGAATCT 60.308 63.158 0.00 0.00 0.00 2.40
2837 4731 2.386935 CCCCTCCCCACCCAGAATC 61.387 68.421 0.00 0.00 0.00 2.52
2838 4732 2.287194 CCCCTCCCCACCCAGAAT 60.287 66.667 0.00 0.00 0.00 2.40
2989 4890 1.881252 GTGACACTGACAACGCGGT 60.881 57.895 12.47 0.00 0.00 5.68
3123 5040 4.576053 CCATTATCACGGCTTTCTTCATCA 59.424 41.667 0.00 0.00 0.00 3.07
3153 5070 4.393990 GTCACTGTGCTCATTGAATGATCA 59.606 41.667 8.50 7.98 38.85 2.92
3160 5077 0.249826 TGCGTCACTGTGCTCATTGA 60.250 50.000 2.12 4.86 32.26 2.57
3165 5082 1.642037 ATGCATGCGTCACTGTGCTC 61.642 55.000 14.09 0.00 38.37 4.26
3167 5084 1.513373 CATGCATGCGTCACTGTGC 60.513 57.895 14.93 0.00 38.05 4.57
3228 5160 6.428799 CGCTGAACTGTAACTATAGTACTCC 58.571 44.000 5.65 0.00 0.00 3.85
3233 5165 3.446161 TGCCGCTGAACTGTAACTATAGT 59.554 43.478 0.00 0.00 0.00 2.12
3234 5166 4.041740 TGCCGCTGAACTGTAACTATAG 57.958 45.455 0.00 0.00 0.00 1.31
3235 5167 4.459390 TTGCCGCTGAACTGTAACTATA 57.541 40.909 0.00 0.00 0.00 1.31
3237 5169 2.823924 TTGCCGCTGAACTGTAACTA 57.176 45.000 0.00 0.00 0.00 2.24
3238 5170 1.961793 TTTGCCGCTGAACTGTAACT 58.038 45.000 0.00 0.00 0.00 2.24
3239 5171 2.766970 TTTTGCCGCTGAACTGTAAC 57.233 45.000 0.00 0.00 0.00 2.50
3274 5206 0.447011 AGCTGTCTCGCTACGTGTAC 59.553 55.000 0.00 0.00 38.76 2.90
3345 6226 4.628661 AGGAATGGAGGGAGTAGTTACT 57.371 45.455 0.00 0.00 39.71 2.24
3347 6228 6.266080 TGTTTAGGAATGGAGGGAGTAGTTA 58.734 40.000 0.00 0.00 0.00 2.24
3350 6231 5.896073 ATGTTTAGGAATGGAGGGAGTAG 57.104 43.478 0.00 0.00 0.00 2.57
3351 6232 6.906901 ACTTATGTTTAGGAATGGAGGGAGTA 59.093 38.462 0.00 0.00 0.00 2.59
3353 6234 6.100424 AGACTTATGTTTAGGAATGGAGGGAG 59.900 42.308 0.00 0.00 0.00 4.30
3354 6235 5.970640 AGACTTATGTTTAGGAATGGAGGGA 59.029 40.000 0.00 0.00 0.00 4.20
3355 6236 6.253946 AGACTTATGTTTAGGAATGGAGGG 57.746 41.667 0.00 0.00 0.00 4.30
3356 6237 8.049721 AGAAAGACTTATGTTTAGGAATGGAGG 58.950 37.037 0.00 0.00 0.00 4.30
3392 6273 2.004017 CGTATGGAGCAGGCGTAAAAA 58.996 47.619 0.00 0.00 0.00 1.94
3393 6274 1.066716 ACGTATGGAGCAGGCGTAAAA 60.067 47.619 0.00 0.00 33.85 1.52
3394 6275 0.533491 ACGTATGGAGCAGGCGTAAA 59.467 50.000 0.00 0.00 33.85 2.01
3395 6276 1.335810 CTACGTATGGAGCAGGCGTAA 59.664 52.381 0.00 0.00 37.54 3.18
3396 6277 0.949397 CTACGTATGGAGCAGGCGTA 59.051 55.000 0.00 0.00 37.05 4.42
3397 6278 1.035932 ACTACGTATGGAGCAGGCGT 61.036 55.000 0.00 0.00 39.23 5.68
3398 6279 0.102481 AACTACGTATGGAGCAGGCG 59.898 55.000 0.00 0.00 0.00 5.52
3399 6280 1.136305 TGAACTACGTATGGAGCAGGC 59.864 52.381 0.00 0.00 0.00 4.85
3400 6281 3.735237 ATGAACTACGTATGGAGCAGG 57.265 47.619 0.00 0.00 0.00 4.85
3401 6282 5.440234 AGTATGAACTACGTATGGAGCAG 57.560 43.478 0.00 0.00 35.35 4.24
3402 6283 6.947644 TTAGTATGAACTACGTATGGAGCA 57.052 37.500 0.00 0.00 37.94 4.26
3403 6284 8.813643 ATTTTAGTATGAACTACGTATGGAGC 57.186 34.615 0.00 0.00 37.94 4.70
3433 6314 8.808092 CCTCGGTTCCTAAATATATCTCTTTCT 58.192 37.037 0.00 0.00 0.00 2.52
3434 6315 8.035984 CCCTCGGTTCCTAAATATATCTCTTTC 58.964 40.741 0.00 0.00 0.00 2.62
3435 6316 7.733501 TCCCTCGGTTCCTAAATATATCTCTTT 59.266 37.037 0.00 0.00 0.00 2.52
3436 6317 7.246763 TCCCTCGGTTCCTAAATATATCTCTT 58.753 38.462 0.00 0.00 0.00 2.85
3437 6318 6.801953 TCCCTCGGTTCCTAAATATATCTCT 58.198 40.000 0.00 0.00 0.00 3.10
3438 6319 6.406065 GCTCCCTCGGTTCCTAAATATATCTC 60.406 46.154 0.00 0.00 0.00 2.75
3439 6320 5.422650 GCTCCCTCGGTTCCTAAATATATCT 59.577 44.000 0.00 0.00 0.00 1.98
3440 6321 5.187186 TGCTCCCTCGGTTCCTAAATATATC 59.813 44.000 0.00 0.00 0.00 1.63
3441 6322 5.091552 TGCTCCCTCGGTTCCTAAATATAT 58.908 41.667 0.00 0.00 0.00 0.86
3442 6323 4.485875 TGCTCCCTCGGTTCCTAAATATA 58.514 43.478 0.00 0.00 0.00 0.86
3443 6324 3.314693 TGCTCCCTCGGTTCCTAAATAT 58.685 45.455 0.00 0.00 0.00 1.28
3444 6325 2.698797 CTGCTCCCTCGGTTCCTAAATA 59.301 50.000 0.00 0.00 0.00 1.40
3445 6326 1.486726 CTGCTCCCTCGGTTCCTAAAT 59.513 52.381 0.00 0.00 0.00 1.40
3446 6327 0.902531 CTGCTCCCTCGGTTCCTAAA 59.097 55.000 0.00 0.00 0.00 1.85
3447 6328 0.252103 ACTGCTCCCTCGGTTCCTAA 60.252 55.000 0.00 0.00 0.00 2.69
3448 6329 0.627451 TACTGCTCCCTCGGTTCCTA 59.373 55.000 0.00 0.00 0.00 2.94
3449 6330 0.684805 CTACTGCTCCCTCGGTTCCT 60.685 60.000 0.00 0.00 0.00 3.36
3450 6331 0.683504 TCTACTGCTCCCTCGGTTCC 60.684 60.000 0.00 0.00 0.00 3.62
3451 6332 0.741915 CTCTACTGCTCCCTCGGTTC 59.258 60.000 0.00 0.00 0.00 3.62
3452 6333 0.039911 ACTCTACTGCTCCCTCGGTT 59.960 55.000 0.00 0.00 0.00 4.44
3453 6334 0.917533 TACTCTACTGCTCCCTCGGT 59.082 55.000 0.00 0.00 0.00 4.69
3454 6335 2.054232 TTACTCTACTGCTCCCTCGG 57.946 55.000 0.00 0.00 0.00 4.63
3455 6336 2.287909 GCATTACTCTACTGCTCCCTCG 60.288 54.545 0.00 0.00 33.15 4.63
3456 6337 2.287909 CGCATTACTCTACTGCTCCCTC 60.288 54.545 0.00 0.00 33.75 4.30
3457 6338 1.683917 CGCATTACTCTACTGCTCCCT 59.316 52.381 0.00 0.00 33.75 4.20
3458 6339 1.870167 GCGCATTACTCTACTGCTCCC 60.870 57.143 0.30 0.00 33.75 4.30
3459 6340 1.492720 GCGCATTACTCTACTGCTCC 58.507 55.000 0.30 0.00 33.75 4.70
3460 6341 1.202417 TGGCGCATTACTCTACTGCTC 60.202 52.381 10.83 0.00 33.75 4.26
3461 6342 0.824109 TGGCGCATTACTCTACTGCT 59.176 50.000 10.83 0.00 33.75 4.24
3462 6343 1.327764 GTTGGCGCATTACTCTACTGC 59.672 52.381 10.83 0.00 0.00 4.40
3463 6344 2.616960 TGTTGGCGCATTACTCTACTG 58.383 47.619 10.83 0.00 0.00 2.74
3464 6345 3.328382 TTGTTGGCGCATTACTCTACT 57.672 42.857 10.83 0.00 0.00 2.57
3465 6346 3.181510 CCTTTGTTGGCGCATTACTCTAC 60.182 47.826 10.83 0.00 0.00 2.59
3513 6394 0.401395 AGGAGAGGACACCAAACCCA 60.401 55.000 0.00 0.00 0.00 4.51
3515 6396 1.143073 ACAAGGAGAGGACACCAAACC 59.857 52.381 0.00 0.00 0.00 3.27
3516 6397 2.158813 TGACAAGGAGAGGACACCAAAC 60.159 50.000 0.00 0.00 0.00 2.93
3563 6935 0.585357 GTGCACTGTCACTTCAGCAG 59.415 55.000 10.32 0.00 38.84 4.24
3586 6958 2.961424 GGGTGGTCTGTCCCATTTG 58.039 57.895 0.00 0.00 42.95 2.32
3597 6969 2.841160 GCGTTGGTGTTGGGTGGTC 61.841 63.158 0.00 0.00 0.00 4.02
3641 7040 2.232756 TGAGCTGCAAAGTTACGTCA 57.767 45.000 1.02 0.00 0.00 4.35
3689 7090 2.104111 AGGAGTGTCACCGACAATTGAA 59.896 45.455 13.59 0.00 44.49 2.69
3731 7137 4.646945 TGGTAAGATGAGAGAGTCCATGAC 59.353 45.833 0.00 0.00 0.00 3.06
3835 7242 2.666190 TGGCAGCTCGTGAAGTGC 60.666 61.111 0.00 0.00 39.48 4.40
3994 7403 0.177836 GCCCAACAAGCAAAACCAGT 59.822 50.000 0.00 0.00 0.00 4.00
3995 7404 0.532640 GGCCCAACAAGCAAAACCAG 60.533 55.000 0.00 0.00 0.00 4.00
4035 7444 7.700656 CGTATAAACAAATTTCCATCCACCTTC 59.299 37.037 0.00 0.00 0.00 3.46
4071 7480 3.604065 TCGCTATACACTGATGTCGAC 57.396 47.619 9.11 9.11 40.48 4.20
4140 7551 6.481976 GGAATTCCCTTTGTTTCGTCAAAAAT 59.518 34.615 14.03 0.00 36.96 1.82
4184 7596 2.910688 ACAAACTGATGAGTGGTCGT 57.089 45.000 0.00 0.00 30.61 4.34
4250 7662 7.148306 TGTCTCCGTCTTAAAAGAATAATTGCC 60.148 37.037 0.00 0.00 36.68 4.52
4251 7663 7.748847 TGTCTCCGTCTTAAAAGAATAATTGC 58.251 34.615 0.00 0.00 36.68 3.56
4301 7718 4.908601 GGAAACCCCTTTCATCCAAAAT 57.091 40.909 0.00 0.00 38.04 1.82
4320 7737 3.116939 TGAAAAAGATGGAACCAAGGGGA 60.117 43.478 0.00 0.00 38.05 4.81
4375 7817 9.419297 GGTTTAATTTAGAGGTTTTTAGCCTTG 57.581 33.333 0.00 0.00 36.29 3.61
4497 7941 8.192774 AGATTTCAATACGAACTACATACGGAA 58.807 33.333 0.00 0.00 31.73 4.30
4499 7943 7.925703 AGATTTCAATACGAACTACATACGG 57.074 36.000 0.00 0.00 31.73 4.02
4559 8006 2.116125 GCTGGTTTGCCACCCTCT 59.884 61.111 0.00 0.00 46.68 3.69
4576 8023 3.750371 TGGTTGTTAGACTTGATGGTGG 58.250 45.455 0.00 0.00 0.00 4.61
4616 8066 5.866335 TTGTCGGTTTATGTATGTTGTCC 57.134 39.130 0.00 0.00 0.00 4.02
4692 8196 2.135139 GAGTGCGACAGACAATGAACA 58.865 47.619 0.00 0.00 0.00 3.18
4730 8234 1.279271 GGAGCTTCTTCAGGTTGCCTA 59.721 52.381 0.00 0.00 31.44 3.93
4738 8242 1.743252 GCGTGGGGAGCTTCTTCAG 60.743 63.158 0.00 0.00 0.00 3.02
4771 8275 1.135489 GTGTACGACATCTGCTCCGAA 60.135 52.381 0.00 0.00 0.00 4.30
4821 8328 2.067605 AGGAACACCCACGACCACA 61.068 57.895 0.00 0.00 37.41 4.17
4823 8330 2.813726 CCAGGAACACCCACGACCA 61.814 63.158 0.00 0.00 37.41 4.02
4824 8331 2.032071 CCAGGAACACCCACGACC 59.968 66.667 0.00 0.00 37.41 4.79
4835 8342 0.827507 GTGCCAAAGAAGCCCAGGAA 60.828 55.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.