Multiple sequence alignment - TraesCS5A01G060800

Loading Multiple Alignment...

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 TraesCS5A01G060800 chr5A 100.000 7318 0 0 1 7318 64387534 64380217 0.000000e+00 13514.0
1 TraesCS5A01G060800 chr5B 96.321 3398 101 12 1954 5345 82458530 82461909 0.000000e+00 5561.0
2 TraesCS5A01G060800 chr5B 91.150 1435 55 30 567 1970 82457028 82458421 0.000000e+00 1881.0
3 TraesCS5A01G060800 chr5B 91.605 1346 76 24 5432 6749 82461913 82463249 0.000000e+00 1825.0
4 TraesCS5A01G060800 chr5B 95.695 302 13 0 7017 7318 82464314 82464615 3.070000e-133 486.0
5 TraesCS5A01G060800 chr5B 87.755 196 12 5 6730 6923 82463262 82463447 1.240000e-52 219.0
6 TraesCS5A01G060800 chr5B 93.578 109 3 3 13 121 82456115 82456219 7.600000e-35 159.0
7 TraesCS5A01G060800 chr5B 94.318 88 5 0 1953 2040 82458440 82458527 1.280000e-27 135.0
8 TraesCS5A01G060800 chr5B 91.000 100 7 1 6916 7013 82464175 82464274 4.610000e-27 134.0
9 TraesCS5A01G060800 chr5B 89.474 57 3 2 6440 6496 82462860 82462913 1.320000e-07 69.4
10 TraesCS5A01G060800 chr5D 94.208 2659 90 30 581 3213 71906096 71903476 0.000000e+00 3999.0
11 TraesCS5A01G060800 chr5D 95.738 2182 64 7 3172 5349 71903435 71901279 0.000000e+00 3487.0
12 TraesCS5A01G060800 chr5D 96.281 995 30 5 5430 6417 71901281 71900287 0.000000e+00 1626.0
13 TraesCS5A01G060800 chr5D 93.818 275 16 1 7045 7318 71899485 71899211 5.280000e-111 412.0
14 TraesCS5A01G060800 chr5D 85.924 341 34 9 4586 4923 17232531 17232202 1.170000e-92 351.0
15 TraesCS5A01G060800 chr5D 90.608 181 8 2 6836 7016 71899724 71899553 1.590000e-56 231.0
16 TraesCS5A01G060800 chr5D 86.857 175 18 2 6433 6607 71900328 71900159 2.690000e-44 191.0
17 TraesCS5A01G060800 chr5D 94.624 93 2 1 6734 6826 71899883 71899794 2.750000e-29 141.0
18 TraesCS5A01G060800 chr5D 81.152 191 18 11 6574 6749 71900086 71899899 3.560000e-28 137.0
19 TraesCS5A01G060800 chr5D 95.833 48 2 0 6521 6568 491432613 491432660 2.190000e-10 78.7
20 TraesCS5A01G060800 chr5D 97.619 42 1 0 3172 3213 71903476 71903435 1.020000e-08 73.1
21 TraesCS5A01G060800 chr5D 100.000 34 0 0 6574 6607 71900139 71900106 6.130000e-06 63.9
22 TraesCS5A01G060800 chr1A 86.129 757 88 12 4586 5338 157886782 157887525 0.000000e+00 800.0
23 TraesCS5A01G060800 chr1A 87.234 329 39 2 4860 5185 157886007 157886335 8.970000e-99 372.0
24 TraesCS5A01G060800 chr2B 89.294 439 44 2 4903 5338 691253229 691253667 1.390000e-151 547.0
25 TraesCS5A01G060800 chr2B 90.415 313 24 6 4597 4906 691251002 691251311 2.460000e-109 407.0
26 TraesCS5A01G060800 chr2D 84.281 299 33 8 4628 4923 507440527 507440240 5.590000e-71 279.0
27 TraesCS5A01G060800 chr2D 93.939 99 4 2 5341 5438 647402204 647402107 1.640000e-31 148.0
28 TraesCS5A01G060800 chr7D 97.895 95 1 1 5337 5431 633397713 633397806 5.870000e-36 163.0
29 TraesCS5A01G060800 chr6D 95.960 99 3 1 5340 5437 65497176 65497078 7.600000e-35 159.0
30 TraesCS5A01G060800 chr6D 98.837 86 1 0 5345 5430 434443288 434443373 3.540000e-33 154.0
31 TraesCS5A01G060800 chr3B 98.864 88 1 0 5343 5430 752120277 752120190 2.730000e-34 158.0
32 TraesCS5A01G060800 chr6B 94.059 101 4 2 5334 5433 503547523 503547622 1.270000e-32 152.0
33 TraesCS5A01G060800 chr2A 94.845 97 3 2 5345 5441 7521968 7522062 4.570000e-32 150.0
34 TraesCS5A01G060800 chr2A 96.154 52 2 0 6521 6572 745788408 745788459 1.310000e-12 86.1
35 TraesCS5A01G060800 chr7B 93.939 99 4 1 5337 5433 476201221 476201123 1.640000e-31 148.0
36 TraesCS5A01G060800 chr7B 93.939 99 5 1 5333 5431 627534547 627534450 1.640000e-31 148.0
37 TraesCS5A01G060800 chr7B 95.918 49 2 0 6520 6568 612304321 612304369 6.090000e-11 80.5
38 TraesCS5A01G060800 chr7A 97.917 48 1 0 6521 6568 97912716 97912669 4.700000e-12 84.2
39 TraesCS5A01G060800 chr4B 97.917 48 1 0 6521 6568 139763291 139763338 4.700000e-12 84.2
40 TraesCS5A01G060800 chr4D 95.833 48 2 0 6521 6568 98451630 98451677 2.190000e-10 78.7
41 TraesCS5A01G060800 chr4A 95.833 48 2 0 6521 6568 477880072 477880025 2.190000e-10 78.7


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 TraesCS5A01G060800 chr5A 64380217 64387534 7317 True 13514.000000 13514 100.000000 1 7318 1 chr5A.!!$R1 7317
1 TraesCS5A01G060800 chr5B 82456115 82464615 8500 False 1163.266667 5561 92.321778 13 7318 9 chr5B.!!$F1 7305
2 TraesCS5A01G060800 chr5D 71899211 71906096 6885 True 1036.100000 3999 93.090500 581 7318 10 chr5D.!!$R2 6737
3 TraesCS5A01G060800 chr1A 157886007 157887525 1518 False 586.000000 800 86.681500 4586 5338 2 chr1A.!!$F1 752
4 TraesCS5A01G060800 chr2B 691251002 691253667 2665 False 477.000000 547 89.854500 4597 5338 2 chr2B.!!$F1 741

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
652 1027 0.102300 AAAACAAGTCAACCAGCGGC 59.898 50.000 0.00 0.00 0.00 6.53 F
1392 1797 0.721718 CGAATTGCCCTCTGTTCGTC 59.278 55.000 0.00 0.00 38.77 4.20 F
1857 2268 0.107459 GATCTGGGTTGGCCTCACTC 60.107 60.000 3.32 0.57 34.45 3.51 F
1981 2428 1.003349 AGAGTTGCTCTGCTGCATTCT 59.997 47.619 1.31 5.10 42.96 2.40 F
3037 3575 1.208052 GAGCCACATCAGCCTGTCTTA 59.792 52.381 0.00 0.00 0.00 2.10 F
4130 4754 1.697432 AGACCAATTCGTCCAGGTTGA 59.303 47.619 0.00 0.00 33.77 3.18 F
5361 7915 0.264955 ACATACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 2099 3.554934 TCAGACAAAAAGACAGGTGCAT 58.445 40.909 0.00 0.0 0.00 3.96 R
3296 3918 0.531200 GTACCAAGGACTGACCCTCG 59.469 60.000 0.00 0.0 40.05 4.63 R
3743 4367 1.368641 TCATGCATGGCGAACTACAC 58.631 50.000 25.97 0.0 0.00 2.90 R
3929 4553 3.115554 GCAATAACCACGATTCAATGCC 58.884 45.455 0.00 0.0 0.00 4.40 R
4755 5383 0.036010 AGCACAGTTTCCTCCCATCG 60.036 55.000 0.00 0.0 0.00 3.84 R
5785 8339 0.674895 GATGCCGAACTGGAAGCAGT 60.675 55.000 0.00 0.0 42.00 4.40 R
6431 8999 0.657840 ATAGCGCGCAAAATCCACTC 59.342 50.000 35.10 0.0 0.00 3.51 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
78 79 8.693542 ATATTTGTTCAAGCTTGCAAGAATAC 57.306 30.769 30.39 17.83 0.00 1.89
81 82 4.022935 TGTTCAAGCTTGCAAGAATACCAG 60.023 41.667 30.39 11.16 0.00 4.00
84 85 2.731572 AGCTTGCAAGAATACCAGCAT 58.268 42.857 30.39 0.15 36.80 3.79
95 96 7.629222 GCAAGAATACCAGCATTGTATTTGTCT 60.629 37.037 6.89 0.00 38.63 3.41
175 176 9.753674 AAAAATCACATATTAGGGAGAACAAGA 57.246 29.630 0.00 0.00 0.00 3.02
176 177 9.753674 AAAATCACATATTAGGGAGAACAAGAA 57.246 29.630 0.00 0.00 0.00 2.52
177 178 9.753674 AAATCACATATTAGGGAGAACAAGAAA 57.246 29.630 0.00 0.00 0.00 2.52
178 179 9.927081 AATCACATATTAGGGAGAACAAGAAAT 57.073 29.630 0.00 0.00 0.00 2.17
179 180 9.927081 ATCACATATTAGGGAGAACAAGAAATT 57.073 29.630 0.00 0.00 0.00 1.82
190 191 8.451748 GGGAGAACAAGAAATTACATTAGTGAC 58.548 37.037 0.00 0.00 0.00 3.67
191 192 8.999431 GGAGAACAAGAAATTACATTAGTGACA 58.001 33.333 0.00 0.00 0.00 3.58
213 214 9.549509 TGACATTTACAAACTAAACATATTCGC 57.450 29.630 0.00 0.00 0.00 4.70
261 452 7.044052 GCACGCCTTATATTTTGAGACATTTTC 60.044 37.037 0.00 0.00 0.00 2.29
301 492 9.097257 AGTCGTGTTATTTAGTACTACTCTCTC 57.903 37.037 0.91 0.00 0.00 3.20
303 494 9.096160 TCGTGTTATTTAGTACTACTCTCTCTG 57.904 37.037 0.91 0.00 0.00 3.35
304 495 8.881743 CGTGTTATTTAGTACTACTCTCTCTGT 58.118 37.037 0.91 0.00 0.00 3.41
366 557 5.668558 ACTTCATTACGTTTGACCAAGTC 57.331 39.130 0.00 0.00 0.00 3.01
373 564 9.961265 TCATTACGTTTGACCAAGTCTATATAG 57.039 33.333 3.10 3.10 33.15 1.31
408 599 5.634859 GCATCTACAACACCAAATTTTCCTG 59.365 40.000 0.00 0.00 0.00 3.86
418 609 6.054295 CACCAAATTTTCCTGAACCAATTCA 58.946 36.000 0.00 0.00 42.73 2.57
499 690 8.532977 TTTTTCAGTCTTGGTCAAAAAGAAAG 57.467 30.769 0.00 0.00 35.50 2.62
550 903 9.685828 TTGAATTATTTTTAAAACGAGGGAGTG 57.314 29.630 0.00 0.00 0.00 3.51
551 904 8.301002 TGAATTATTTTTAAAACGAGGGAGTGG 58.699 33.333 0.00 0.00 0.00 4.00
555 908 1.886886 TAAAACGAGGGAGTGGTTGC 58.113 50.000 0.00 0.00 0.00 4.17
574 947 3.766545 TGCCTTTGCTTTCTATTGGTCT 58.233 40.909 0.00 0.00 38.71 3.85
579 952 6.612306 CCTTTGCTTTCTATTGGTCTTGTAC 58.388 40.000 0.00 0.00 0.00 2.90
581 954 7.255451 CCTTTGCTTTCTATTGGTCTTGTACAA 60.255 37.037 8.28 8.28 0.00 2.41
652 1027 0.102300 AAAACAAGTCAACCAGCGGC 59.898 50.000 0.00 0.00 0.00 6.53
710 1085 4.475444 TCCGGGCGGATTCCCTCT 62.475 66.667 0.00 0.00 44.30 3.69
716 1091 1.458588 GCGGATTCCCTCTCCCTCT 60.459 63.158 0.00 0.00 0.00 3.69
717 1092 1.468506 GCGGATTCCCTCTCCCTCTC 61.469 65.000 0.00 0.00 0.00 3.20
718 1093 1.175983 CGGATTCCCTCTCCCTCTCG 61.176 65.000 0.00 0.00 0.00 4.04
952 1331 4.394712 CTCCACCACCACCTCCGC 62.395 72.222 0.00 0.00 0.00 5.54
953 1332 4.954118 TCCACCACCACCTCCGCT 62.954 66.667 0.00 0.00 0.00 5.52
954 1333 4.394712 CCACCACCACCTCCGCTC 62.395 72.222 0.00 0.00 0.00 5.03
955 1334 4.394712 CACCACCACCTCCGCTCC 62.395 72.222 0.00 0.00 0.00 4.70
1253 1654 4.448537 TGAACTGTTCAGGTTTTTGTGG 57.551 40.909 18.69 0.00 34.08 4.17
1254 1655 2.959507 ACTGTTCAGGTTTTTGTGGC 57.040 45.000 4.82 0.00 0.00 5.01
1260 1661 2.200337 AGGTTTTTGTGGCTCCGGC 61.200 57.895 0.00 0.00 37.82 6.13
1316 1721 6.814506 ATGTTGGTCTTCTTCTTTGATCTG 57.185 37.500 0.00 0.00 0.00 2.90
1320 1725 4.103153 TGGTCTTCTTCTTTGATCTGGTGT 59.897 41.667 0.00 0.00 0.00 4.16
1328 1733 0.976641 TTGATCTGGTGTCCGAGCTT 59.023 50.000 0.00 0.00 0.00 3.74
1392 1797 0.721718 CGAATTGCCCTCTGTTCGTC 59.278 55.000 0.00 0.00 38.77 4.20
1400 1805 1.889829 CCCTCTGTTCGTCTCAGAAGT 59.110 52.381 7.88 0.00 40.68 3.01
1423 1828 1.698532 TGCTTCCAATTTGGGCATGTT 59.301 42.857 15.37 0.00 38.32 2.71
1424 1829 2.106166 TGCTTCCAATTTGGGCATGTTT 59.894 40.909 15.37 0.00 38.32 2.83
1425 1830 2.743664 GCTTCCAATTTGGGCATGTTTC 59.256 45.455 15.37 0.00 38.32 2.78
1426 1831 3.557686 GCTTCCAATTTGGGCATGTTTCT 60.558 43.478 15.37 0.00 38.32 2.52
1436 1841 2.169352 GGGCATGTTTCTCTCTGCTAGA 59.831 50.000 0.00 0.00 35.03 2.43
1437 1842 3.369892 GGGCATGTTTCTCTCTGCTAGAA 60.370 47.826 0.00 0.00 35.03 2.10
1438 1843 4.450053 GGCATGTTTCTCTCTGCTAGAAT 58.550 43.478 0.00 0.00 33.17 2.40
1439 1844 4.880696 GGCATGTTTCTCTCTGCTAGAATT 59.119 41.667 0.00 0.00 33.17 2.17
1440 1845 5.356470 GGCATGTTTCTCTCTGCTAGAATTT 59.644 40.000 0.00 0.00 33.17 1.82
1484 1890 5.235186 GGATTCGATCGAATTGACAAGTGAT 59.765 40.000 36.28 16.65 43.98 3.06
1488 1894 5.232202 TCGATCGAATTGACAAGTGATAAGC 59.768 40.000 16.99 0.00 0.00 3.09
1505 1911 7.395489 AGTGATAAGCAAAATCCAGTTGATTCT 59.605 33.333 0.00 0.00 42.97 2.40
1857 2268 0.107459 GATCTGGGTTGGCCTCACTC 60.107 60.000 3.32 0.57 34.45 3.51
1886 2297 5.946377 CCAAGGAGTCTAAATAGCTGGTTTT 59.054 40.000 0.00 0.00 0.00 2.43
1981 2428 1.003349 AGAGTTGCTCTGCTGCATTCT 59.997 47.619 1.31 5.10 42.96 2.40
1992 2439 5.463286 TCTGCTGCATTCTGTTTGTTATTG 58.537 37.500 1.31 0.00 0.00 1.90
2042 2489 3.058224 GTGGGAATTCAGACCGAAACTTG 60.058 47.826 7.93 0.00 37.12 3.16
2043 2490 3.146847 GGGAATTCAGACCGAAACTTGT 58.853 45.455 7.93 0.00 37.12 3.16
2045 2492 4.758165 GGGAATTCAGACCGAAACTTGTTA 59.242 41.667 7.93 0.00 37.12 2.41
2046 2493 5.414765 GGGAATTCAGACCGAAACTTGTTAT 59.585 40.000 7.93 0.00 37.12 1.89
2048 2495 6.801862 GGAATTCAGACCGAAACTTGTTATTG 59.198 38.462 7.93 0.00 37.12 1.90
2049 2496 7.308348 GGAATTCAGACCGAAACTTGTTATTGA 60.308 37.037 7.93 0.00 37.12 2.57
2111 2648 5.170748 TGTGGCTCGTATCATAATGCATAG 58.829 41.667 0.00 0.00 0.00 2.23
2168 2705 2.730928 ACTGCAACGCAAATTAATGCAC 59.269 40.909 3.20 0.00 46.76 4.57
2173 2710 3.485947 ACGCAAATTAATGCACGTCAT 57.514 38.095 3.20 0.00 46.76 3.06
2726 3264 5.444176 CCATTCTTATCCTCTTGCCTCTTT 58.556 41.667 0.00 0.00 0.00 2.52
2847 3385 7.494952 AGTCAGTTACTGAGTAAAAGTTGTTCC 59.505 37.037 19.88 1.81 41.70 3.62
3037 3575 1.208052 GAGCCACATCAGCCTGTCTTA 59.792 52.381 0.00 0.00 0.00 2.10
3202 3742 7.179516 TGGTATGTAGTATGTTTCTTCACCTGA 59.820 37.037 0.00 0.00 0.00 3.86
3249 3871 3.225104 TGGAAGCTCAAAAGTGCTGATT 58.775 40.909 0.00 0.00 39.71 2.57
3296 3918 7.739498 TGGTGAAAGGAAAGTAAGTCATAAC 57.261 36.000 0.00 0.00 0.00 1.89
3381 4005 5.931146 AGCTCTACACATATGCTAGCATTTC 59.069 40.000 33.74 12.30 37.82 2.17
3431 4055 6.656270 CCATAGTATGCAAATTGGCTATCTCA 59.344 38.462 6.34 0.00 34.04 3.27
3445 4069 6.240894 TGGCTATCTCATCTTTTTGACTTGT 58.759 36.000 0.00 0.00 0.00 3.16
3465 4089 4.709250 TGTTACAAGCACCATCACACTAA 58.291 39.130 0.00 0.00 0.00 2.24
3482 4106 3.370978 CACTAACAGTAGTTTGGATGCCG 59.629 47.826 0.00 0.00 38.58 5.69
3696 4320 8.566260 GGTATATAAGCCTACTATATCACCACG 58.434 40.741 0.00 0.00 0.00 4.94
3929 4553 7.050377 TGGCTAGAGTTAAATTCTTGATCTGG 58.950 38.462 0.00 0.00 0.00 3.86
4130 4754 1.697432 AGACCAATTCGTCCAGGTTGA 59.303 47.619 0.00 0.00 33.77 3.18
4401 5027 4.269183 TGTTCTTGGTGCCAGTATAATGG 58.731 43.478 14.95 14.95 43.72 3.16
4490 5116 7.680442 TTATCATTTCGGTTCTGAACATTGA 57.320 32.000 21.01 14.79 0.00 2.57
4497 5123 2.143122 GTTCTGAACATTGACCTGCGA 58.857 47.619 15.34 0.00 0.00 5.10
4809 5437 1.980765 TCTGCAACAATGGACTCTCCT 59.019 47.619 0.00 0.00 37.46 3.69
4839 5467 5.010516 CCAACACCTTTACATGGACATTCAA 59.989 40.000 0.00 0.00 32.82 2.69
5055 7607 2.501723 TCCTGAAACCAGAGGTCTATGC 59.498 50.000 0.00 0.00 33.12 3.14
5105 7657 6.194796 TGTAAGTTTCTAAATGCTGCCATC 57.805 37.500 0.00 0.00 0.00 3.51
5345 7899 3.737559 TTCCCCTTGCTATGAACACAT 57.262 42.857 0.00 0.00 0.00 3.21
5346 7900 4.853468 TTCCCCTTGCTATGAACACATA 57.147 40.909 0.00 0.00 0.00 2.29
5347 7901 4.150897 TCCCCTTGCTATGAACACATAC 57.849 45.455 0.00 0.00 0.00 2.39
5348 7902 3.780294 TCCCCTTGCTATGAACACATACT 59.220 43.478 0.00 0.00 0.00 2.12
5349 7903 4.130118 CCCCTTGCTATGAACACATACTC 58.870 47.826 0.00 0.00 0.00 2.59
5350 7904 4.130118 CCCTTGCTATGAACACATACTCC 58.870 47.826 0.00 0.00 0.00 3.85
5351 7905 4.130118 CCTTGCTATGAACACATACTCCC 58.870 47.826 0.00 0.00 0.00 4.30
5352 7906 4.141620 CCTTGCTATGAACACATACTCCCT 60.142 45.833 0.00 0.00 0.00 4.20
5353 7907 4.672587 TGCTATGAACACATACTCCCTC 57.327 45.455 0.00 0.00 0.00 4.30
5354 7908 3.388024 TGCTATGAACACATACTCCCTCC 59.612 47.826 0.00 0.00 0.00 4.30
5355 7909 3.553096 GCTATGAACACATACTCCCTCCG 60.553 52.174 0.00 0.00 0.00 4.63
5356 7910 1.933021 TGAACACATACTCCCTCCGT 58.067 50.000 0.00 0.00 0.00 4.69
5357 7911 1.822990 TGAACACATACTCCCTCCGTC 59.177 52.381 0.00 0.00 0.00 4.79
5358 7912 1.136500 GAACACATACTCCCTCCGTCC 59.864 57.143 0.00 0.00 0.00 4.79
5359 7913 0.686769 ACACATACTCCCTCCGTCCC 60.687 60.000 0.00 0.00 0.00 4.46
5360 7914 0.686441 CACATACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
5361 7915 0.264955 ACATACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
5362 7916 1.502039 ACATACTCCCTCCGTCCCATA 59.498 52.381 0.00 0.00 0.00 2.74
5363 7917 2.090943 ACATACTCCCTCCGTCCCATAA 60.091 50.000 0.00 0.00 0.00 1.90
5364 7918 3.173965 CATACTCCCTCCGTCCCATAAT 58.826 50.000 0.00 0.00 0.00 1.28
5365 7919 4.202749 ACATACTCCCTCCGTCCCATAATA 60.203 45.833 0.00 0.00 0.00 0.98
5366 7920 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
5367 7921 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
5368 7922 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5369 7923 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
5370 7924 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5371 7925 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
5372 7926 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
5373 7927 5.247564 CCCTCCGTCCCATAATATAAGAACA 59.752 44.000 0.00 0.00 0.00 3.18
5374 7928 6.070194 CCCTCCGTCCCATAATATAAGAACAT 60.070 42.308 0.00 0.00 0.00 2.71
5375 7929 7.394816 CCTCCGTCCCATAATATAAGAACATT 58.605 38.462 0.00 0.00 0.00 2.71
5376 7930 7.883311 CCTCCGTCCCATAATATAAGAACATTT 59.117 37.037 0.00 0.00 0.00 2.32
5377 7931 9.284968 CTCCGTCCCATAATATAAGAACATTTT 57.715 33.333 0.00 0.00 0.00 1.82
5378 7932 9.635404 TCCGTCCCATAATATAAGAACATTTTT 57.365 29.630 0.00 0.00 0.00 1.94
5379 7933 9.677567 CCGTCCCATAATATAAGAACATTTTTG 57.322 33.333 0.00 0.00 0.00 2.44
5392 7946 8.732746 AAGAACATTTTTGACACTACACTAGT 57.267 30.769 0.00 0.00 40.28 2.57
5405 7959 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
5406 7960 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
5407 7961 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
5408 7962 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
5409 7963 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
5410 7964 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
5411 7965 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
5417 7971 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
5418 7972 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
5419 7973 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
5627 8181 6.864560 CATGTAGTCATGCTCACAAATTTG 57.135 37.500 16.67 16.67 43.66 2.32
5647 8201 5.627499 TTGTAGTTGGATTCACTTGCATC 57.373 39.130 0.00 0.00 0.00 3.91
5648 8202 4.910195 TGTAGTTGGATTCACTTGCATCT 58.090 39.130 0.00 0.00 0.00 2.90
5649 8203 4.696877 TGTAGTTGGATTCACTTGCATCTG 59.303 41.667 0.00 0.00 0.00 2.90
5692 8246 5.248640 CCTTCTTTCTTTCTGCAGGATACA 58.751 41.667 15.13 0.00 41.41 2.29
5697 8251 5.946942 TTCTTTCTGCAGGATACAGATCT 57.053 39.130 15.13 0.00 43.40 2.75
5743 8297 2.467880 TCTGTCAAGTCCTATCCCACC 58.532 52.381 0.00 0.00 0.00 4.61
5949 8503 0.109132 GTTTTCGGGCAGGCATTCAG 60.109 55.000 0.00 0.00 0.00 3.02
6006 8560 2.045524 CATATGAGGCTGACAGGGTCT 58.954 52.381 4.26 0.00 33.15 3.85
6041 8601 8.728337 TGATGATCATTCAAGTAAAGAGAAGG 57.272 34.615 10.14 0.00 34.96 3.46
6062 8622 6.575162 AGGACATTACTCCAATTTGTGAAC 57.425 37.500 0.00 0.00 31.94 3.18
6264 8828 4.470334 AGTTGTTTTTCACATTGCCAGT 57.530 36.364 0.00 0.00 34.43 4.00
6322 8886 8.830580 CATACAGGAGTACAACATTTGGATAAG 58.169 37.037 0.00 0.00 31.96 1.73
6331 8895 4.396357 ACATTTGGATAAGTTGTGGGGA 57.604 40.909 0.00 0.00 0.00 4.81
6354 8919 3.747099 ATGTTCTTATCAACTGCGTGC 57.253 42.857 0.00 0.00 0.00 5.34
6375 8940 6.303970 CGTGCTCATTTTTGTTTCACTATGAG 59.696 38.462 0.00 0.00 41.03 2.90
6382 8950 4.488126 TTGTTTCACTATGAGCAAGTGC 57.512 40.909 0.00 0.00 43.30 4.40
6425 8993 2.106332 GGGCACCGAGATACACCG 59.894 66.667 0.00 0.00 40.86 4.94
6431 8999 0.729116 ACCGAGATACACCGTACACG 59.271 55.000 0.00 0.00 39.44 4.49
6437 9005 1.739466 GATACACCGTACACGAGTGGA 59.261 52.381 19.95 15.25 41.46 4.02
6446 9014 1.509787 CACGAGTGGATTTTGCGCG 60.510 57.895 0.00 0.00 0.00 6.86
6449 9017 1.692148 CGAGTGGATTTTGCGCGCTA 61.692 55.000 33.29 23.57 0.00 4.26
6492 9061 2.979151 CGACGAACGTACCATACACAAA 59.021 45.455 0.00 0.00 37.22 2.83
6497 9066 4.209703 CGAACGTACCATACACAAAGTGTT 59.790 41.667 8.20 0.00 45.08 3.32
6516 9085 3.517901 TGTTCGTTCCATCATACTCCCTT 59.482 43.478 0.00 0.00 0.00 3.95
6517 9086 3.819564 TCGTTCCATCATACTCCCTTG 57.180 47.619 0.00 0.00 0.00 3.61
6529 9098 8.748412 CATCATACTCCCTTGGTTTCAAATTTA 58.252 33.333 0.00 0.00 31.77 1.40
6555 9124 7.556733 ACTAAAACCACGACAAGTATTTTGA 57.443 32.000 0.00 0.00 34.30 2.69
6564 9133 4.378046 CGACAAGTATTTTGAAACGGAGGG 60.378 45.833 0.00 0.00 0.00 4.30
6568 9137 4.576879 AGTATTTTGAAACGGAGGGAGTC 58.423 43.478 0.00 0.00 0.00 3.36
6569 9138 1.873698 TTTTGAAACGGAGGGAGTCG 58.126 50.000 0.00 0.00 0.00 4.18
6570 9139 0.601841 TTTGAAACGGAGGGAGTCGC 60.602 55.000 0.00 0.00 0.00 5.19
6571 9140 2.125633 GAAACGGAGGGAGTCGCC 60.126 66.667 3.13 0.00 0.00 5.54
6644 9319 8.324191 ACAAGATCTTTATATCCCTTGTCTGA 57.676 34.615 4.86 0.00 39.72 3.27
6647 9322 8.733092 AGATCTTTATATCCCTTGTCTGATCA 57.267 34.615 0.00 0.00 31.85 2.92
6648 9323 9.163894 AGATCTTTATATCCCTTGTCTGATCAA 57.836 33.333 0.00 0.00 31.85 2.57
6652 9327 8.696043 TTTATATCCCTTGTCTGATCAAATGG 57.304 34.615 0.00 0.00 0.00 3.16
6653 9328 4.598036 ATCCCTTGTCTGATCAAATGGT 57.402 40.909 0.00 0.00 0.00 3.55
6657 9332 4.768968 CCCTTGTCTGATCAAATGGTTCTT 59.231 41.667 0.00 0.00 0.00 2.52
6658 9333 5.105997 CCCTTGTCTGATCAAATGGTTCTTC 60.106 44.000 0.00 0.00 0.00 2.87
6659 9334 5.391310 CCTTGTCTGATCAAATGGTTCTTCG 60.391 44.000 0.00 0.00 0.00 3.79
6661 9336 5.789521 TGTCTGATCAAATGGTTCTTCGTA 58.210 37.500 0.00 0.00 0.00 3.43
6662 9337 5.869344 TGTCTGATCAAATGGTTCTTCGTAG 59.131 40.000 0.00 0.00 0.00 3.51
6667 9357 6.485313 TGATCAAATGGTTCTTCGTAGTTTGT 59.515 34.615 0.00 0.00 0.00 2.83
6673 9363 6.092955 TGGTTCTTCGTAGTTTGTAGTGAT 57.907 37.500 0.00 0.00 0.00 3.06
6686 9376 8.918202 AGTTTGTAGTGATTTAGAAATGGTCA 57.082 30.769 0.00 0.00 0.00 4.02
6698 9388 8.519799 TTTAGAAATGGTCATCTGGGAAATAC 57.480 34.615 0.00 0.00 0.00 1.89
6724 9415 9.566624 CTAATATTTTTGTTTTCAAGCGTGTTG 57.433 29.630 0.00 0.00 41.09 3.33
6725 9416 4.653806 TTTTTGTTTTCAAGCGTGTTGG 57.346 36.364 0.00 0.00 41.09 3.77
6762 9485 3.721087 ACGGAATGGAGAAGACCAAAT 57.279 42.857 0.00 0.00 43.47 2.32
6797 9520 6.663093 TGATGGTTTGTAATTAAGCTGGTGAT 59.337 34.615 0.00 0.00 0.00 3.06
6798 9521 6.266168 TGGTTTGTAATTAAGCTGGTGATG 57.734 37.500 0.00 0.00 0.00 3.07
6799 9522 6.007076 TGGTTTGTAATTAAGCTGGTGATGA 58.993 36.000 0.00 0.00 0.00 2.92
6804 9527 6.341316 TGTAATTAAGCTGGTGATGACTCTC 58.659 40.000 0.00 0.00 0.00 3.20
6834 9617 8.693625 TCATGTATGCAAAATTCCATCATACAA 58.306 29.630 18.22 7.80 46.81 2.41
6953 10473 0.178891 AGGGAGAAGGAAGAGGCACA 60.179 55.000 0.00 0.00 0.00 4.57
6955 10475 0.390472 GGAGAAGGAAGAGGCACACG 60.390 60.000 0.00 0.00 0.00 4.49
6956 10476 1.004440 AGAAGGAAGAGGCACACGC 60.004 57.895 0.00 0.00 37.44 5.34
6987 10507 2.290323 CCTCCACAGAAGAAAATCCGGT 60.290 50.000 0.00 0.00 0.00 5.28
7060 10630 2.985456 CCGCTTCTGGCTCCTCTT 59.015 61.111 0.00 0.00 39.13 2.85
7072 10642 1.843206 GCTCCTCTTCCATTCTTCCCT 59.157 52.381 0.00 0.00 0.00 4.20
7186 10757 3.292159 GTGCGTGGGGGTTGGAAC 61.292 66.667 0.00 0.00 0.00 3.62
7256 10827 2.435938 GCGGAATCTGCAACCCGA 60.436 61.111 9.52 0.00 44.29 5.14
7260 10831 0.608035 GGAATCTGCAACCCGACCAA 60.608 55.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.259829 GTGCCAAAGTTTTAAATGGTCAACAT 59.740 34.615 7.27 0.00 43.07 2.71
18 19 5.582665 GTGCCAAAGTTTTAAATGGTCAACA 59.417 36.000 7.27 0.00 35.34 3.33
78 79 8.761575 AAATACAAAGACAAATACAATGCTGG 57.238 30.769 0.00 0.00 0.00 4.85
150 151 9.753674 TTCTTGTTCTCCCTAATATGTGATTTT 57.246 29.630 0.00 0.00 0.00 1.82
151 152 9.753674 TTTCTTGTTCTCCCTAATATGTGATTT 57.246 29.630 0.00 0.00 0.00 2.17
152 153 9.927081 ATTTCTTGTTCTCCCTAATATGTGATT 57.073 29.630 0.00 0.00 0.00 2.57
153 154 9.927081 AATTTCTTGTTCTCCCTAATATGTGAT 57.073 29.630 0.00 0.00 0.00 3.06
163 164 8.383175 TCACTAATGTAATTTCTTGTTCTCCCT 58.617 33.333 0.00 0.00 37.87 4.20
164 165 8.451748 GTCACTAATGTAATTTCTTGTTCTCCC 58.548 37.037 0.00 0.00 37.87 4.30
187 188 9.549509 GCGAATATGTTTAGTTTGTAAATGTCA 57.450 29.630 0.00 0.00 0.00 3.58
235 425 4.875544 TGTCTCAAAATATAAGGCGTGC 57.124 40.909 0.00 0.00 0.00 5.34
238 428 8.909708 TTGAAAATGTCTCAAAATATAAGGCG 57.090 30.769 0.00 0.00 29.93 5.52
324 515 8.915871 TGAAGTTTGACTTTGAAGAAAATCTG 57.084 30.769 0.00 0.00 38.80 2.90
332 523 8.614994 AAACGTAATGAAGTTTGACTTTGAAG 57.385 30.769 0.00 0.00 38.80 3.02
373 564 6.017440 TGGTGTTGTAGATGCTAACTTGTTTC 60.017 38.462 0.00 0.00 0.00 2.78
384 575 5.634859 CAGGAAAATTTGGTGTTGTAGATGC 59.365 40.000 0.00 0.00 0.00 3.91
478 669 6.834168 AACTTTCTTTTTGACCAAGACTGA 57.166 33.333 0.00 0.00 29.70 3.41
479 670 7.090173 TCAAACTTTCTTTTTGACCAAGACTG 58.910 34.615 0.00 0.00 37.91 3.51
485 676 6.093357 GCCAAATCAAACTTTCTTTTTGACCA 59.907 34.615 0.00 0.00 43.84 4.02
486 677 6.093357 TGCCAAATCAAACTTTCTTTTTGACC 59.907 34.615 0.00 0.00 43.84 4.02
488 679 6.652481 TGTGCCAAATCAAACTTTCTTTTTGA 59.348 30.769 0.31 0.31 44.84 2.69
489 680 6.840075 TGTGCCAAATCAAACTTTCTTTTTG 58.160 32.000 0.00 0.00 35.61 2.44
492 683 6.260714 GGATTGTGCCAAATCAAACTTTCTTT 59.739 34.615 9.82 0.00 38.14 2.52
493 684 5.759763 GGATTGTGCCAAATCAAACTTTCTT 59.240 36.000 9.82 0.00 38.14 2.52
494 685 5.070847 AGGATTGTGCCAAATCAAACTTTCT 59.929 36.000 9.82 0.00 38.14 2.52
495 686 5.299949 AGGATTGTGCCAAATCAAACTTTC 58.700 37.500 9.82 0.00 38.14 2.62
499 690 7.489574 TTTTTAGGATTGTGCCAAATCAAAC 57.510 32.000 9.82 0.00 38.14 2.93
536 729 1.543871 GGCAACCACTCCCTCGTTTTA 60.544 52.381 0.00 0.00 0.00 1.52
537 730 0.822121 GGCAACCACTCCCTCGTTTT 60.822 55.000 0.00 0.00 0.00 2.43
539 732 1.705997 AAGGCAACCACTCCCTCGTT 61.706 55.000 0.00 0.00 37.17 3.85
550 903 3.006859 ACCAATAGAAAGCAAAGGCAACC 59.993 43.478 0.00 0.00 44.61 3.77
551 904 4.021981 AGACCAATAGAAAGCAAAGGCAAC 60.022 41.667 0.00 0.00 44.61 4.17
555 908 5.712152 ACAAGACCAATAGAAAGCAAAGG 57.288 39.130 0.00 0.00 0.00 3.11
589 964 5.805994 ACGCTTGAGCAGTTTATTACTACTC 59.194 40.000 3.65 0.00 44.41 2.59
652 1027 4.767255 GGCGGAGTGGCAGAGTGG 62.767 72.222 0.00 0.00 44.08 4.00
952 1331 1.264749 TGACATGGACGGGAAGGGAG 61.265 60.000 0.00 0.00 0.00 4.30
953 1332 1.229368 TGACATGGACGGGAAGGGA 60.229 57.895 0.00 0.00 0.00 4.20
954 1333 1.078426 GTGACATGGACGGGAAGGG 60.078 63.158 0.00 0.00 0.00 3.95
955 1334 1.447838 CGTGACATGGACGGGAAGG 60.448 63.158 10.76 0.00 33.08 3.46
1241 1642 1.659794 CCGGAGCCACAAAAACCTG 59.340 57.895 0.00 0.00 0.00 4.00
1244 1645 2.050442 CGCCGGAGCCACAAAAAC 60.050 61.111 5.05 0.00 34.57 2.43
1245 1646 3.972276 GCGCCGGAGCCACAAAAA 61.972 61.111 20.74 0.00 34.57 1.94
1268 1669 0.532862 AATCAGTAAGCCCCATCGCG 60.533 55.000 0.00 0.00 0.00 5.87
1316 1721 1.066858 TGAGATCAAAGCTCGGACACC 60.067 52.381 0.00 0.00 35.15 4.16
1320 1725 2.300152 ACAACTGAGATCAAAGCTCGGA 59.700 45.455 7.96 0.00 40.43 4.55
1328 1733 8.455903 AGAAAATCAAGAACAACTGAGATCAA 57.544 30.769 0.00 0.00 0.00 2.57
1400 1805 3.147629 CATGCCCAAATTGGAAGCAAAA 58.852 40.909 17.42 0.00 40.96 2.44
1409 1814 4.491676 CAGAGAGAAACATGCCCAAATTG 58.508 43.478 0.00 0.00 0.00 2.32
1410 1815 3.056322 GCAGAGAGAAACATGCCCAAATT 60.056 43.478 0.00 0.00 32.49 1.82
1411 1816 2.494870 GCAGAGAGAAACATGCCCAAAT 59.505 45.455 0.00 0.00 32.49 2.32
1423 1828 7.067494 GGCCAAATTAAATTCTAGCAGAGAGAA 59.933 37.037 0.00 0.00 37.34 2.87
1424 1829 6.543831 GGCCAAATTAAATTCTAGCAGAGAGA 59.456 38.462 0.00 0.00 34.93 3.10
1425 1830 6.545298 AGGCCAAATTAAATTCTAGCAGAGAG 59.455 38.462 5.01 0.00 34.93 3.20
1426 1831 6.426587 AGGCCAAATTAAATTCTAGCAGAGA 58.573 36.000 5.01 0.00 0.00 3.10
1484 1890 7.707624 ATCAGAATCAACTGGATTTTGCTTA 57.292 32.000 0.00 0.00 46.17 3.09
1488 1894 7.253422 GTGGTATCAGAATCAACTGGATTTTG 58.747 38.462 0.00 0.00 46.17 2.44
1505 1911 5.211201 TCAGATCATCAGAAGGTGGTATCA 58.789 41.667 0.00 0.00 0.00 2.15
1688 2099 3.554934 TCAGACAAAAAGACAGGTGCAT 58.445 40.909 0.00 0.00 0.00 3.96
1828 2239 3.813443 CCAACCCAGATCATACTCCAAG 58.187 50.000 0.00 0.00 0.00 3.61
1857 2268 3.873952 GCTATTTAGACTCCTTGGCAGTG 59.126 47.826 0.00 0.00 0.00 3.66
1992 2439 9.366216 AGGAAACAAGAACAAAATAACAAGAAC 57.634 29.630 0.00 0.00 0.00 3.01
2111 2648 4.392921 TCAGTAAGACAAGGCTAGCATC 57.607 45.455 18.24 8.16 0.00 3.91
2168 2705 5.639506 ACTTGTTGAGACCTTCATAATGACG 59.360 40.000 0.00 0.00 35.27 4.35
2173 2710 6.591935 ACAGAACTTGTTGAGACCTTCATAA 58.408 36.000 0.00 0.00 36.31 1.90
2404 2941 8.511748 AGGATAAATGACTGGGAAGTATATGT 57.488 34.615 0.00 0.00 0.00 2.29
2555 3093 5.717119 AGCAACTTGAATAGCCATTCTTTG 58.283 37.500 6.43 7.86 41.09 2.77
3037 3575 1.352352 CACCTGAATCCACTTGAGGGT 59.648 52.381 0.00 0.00 42.15 4.34
3131 3669 4.617645 CGTGTTGAGAAAACAAACGGAAAA 59.382 37.500 0.00 0.00 34.36 2.29
3202 3742 2.237392 GAGAAAGGGGCTCACAGTGTAT 59.763 50.000 0.00 0.00 32.67 2.29
3249 3871 7.093988 ACCATTTATGTTCGATTCAATCACCAA 60.094 33.333 0.00 0.00 0.00 3.67
3296 3918 0.531200 GTACCAAGGACTGACCCTCG 59.469 60.000 0.00 0.00 40.05 4.63
3381 4005 5.238868 AGCTAATCATGCTGTGCTTTATGAG 59.761 40.000 0.00 0.00 39.56 2.90
3431 4055 6.127479 TGGTGCTTGTAACAAGTCAAAAAGAT 60.127 34.615 0.00 0.00 0.00 2.40
3445 4069 4.709250 TGTTAGTGTGATGGTGCTTGTAA 58.291 39.130 0.00 0.00 0.00 2.41
3465 4089 2.501723 AGATCGGCATCCAAACTACTGT 59.498 45.455 0.00 0.00 0.00 3.55
3482 4106 9.308318 GTAGGTTCTTCTGATCAAGTTAAGATC 57.692 37.037 0.00 3.71 41.72 2.75
3696 4320 9.748708 TTATTTAATCTAATTGAAGCATGGCAC 57.251 29.630 0.00 0.00 0.00 5.01
3743 4367 1.368641 TCATGCATGGCGAACTACAC 58.631 50.000 25.97 0.00 0.00 2.90
3929 4553 3.115554 GCAATAACCACGATTCAATGCC 58.884 45.455 0.00 0.00 0.00 4.40
4130 4754 3.046374 ACTTCCAGTAACAGGAACCAGT 58.954 45.455 0.00 0.00 40.11 4.00
4207 4831 1.462670 GCTTTTGCGTCTTCTCAGAGG 59.537 52.381 0.00 0.00 37.88 3.69
4234 4860 5.357878 TGGTCCTTTCTATCAATGCATCAAC 59.642 40.000 0.00 0.00 0.00 3.18
4236 4862 5.114764 TGGTCCTTTCTATCAATGCATCA 57.885 39.130 0.00 0.00 0.00 3.07
4401 5027 5.822519 TCACCCATTAACACTGATAATGAGC 59.177 40.000 16.72 0.00 41.25 4.26
4490 5116 2.166254 CCTGGCAATAAAAATCGCAGGT 59.834 45.455 0.00 0.00 0.00 4.00
4497 5123 7.910584 AGTTTCAAGATCCTGGCAATAAAAAT 58.089 30.769 0.00 0.00 0.00 1.82
4755 5383 0.036010 AGCACAGTTTCCTCCCATCG 60.036 55.000 0.00 0.00 0.00 3.84
4809 5437 3.257873 CCATGTAAAGGTGTTGGCATTCA 59.742 43.478 0.00 0.00 0.00 2.57
5055 7607 7.031226 TCTGACAATTTGTTCTTCAGAAAGG 57.969 36.000 13.36 0.00 35.58 3.11
5105 7657 9.100554 TGCCTGCAATCAAATAAATTCAATAAG 57.899 29.630 0.00 0.00 0.00 1.73
5125 7677 2.094597 TGTAAAATCTGCACATGCCTGC 60.095 45.455 0.49 1.45 41.18 4.85
5333 7887 3.553096 CGGAGGGAGTATGTGTTCATAGC 60.553 52.174 0.00 0.00 37.23 2.97
5345 7899 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
5346 7900 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
5347 7901 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
5348 7902 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
5349 7903 5.247564 TGTTCTTATATTATGGGACGGAGGG 59.752 44.000 0.00 0.00 0.00 4.30
5350 7904 6.354794 TGTTCTTATATTATGGGACGGAGG 57.645 41.667 0.00 0.00 0.00 4.30
5351 7905 8.848474 AAATGTTCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
5352 7906 9.635404 AAAAATGTTCTTATATTATGGGACGGA 57.365 29.630 0.00 0.00 0.00 4.69
5353 7907 9.677567 CAAAAATGTTCTTATATTATGGGACGG 57.322 33.333 0.00 0.00 0.00 4.79
5366 7920 9.826574 ACTAGTGTAGTGTCAAAAATGTTCTTA 57.173 29.630 0.00 0.00 37.69 2.10
5367 7921 8.732746 ACTAGTGTAGTGTCAAAAATGTTCTT 57.267 30.769 0.00 0.00 37.69 2.52
5382 7936 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
5383 7937 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
5384 7938 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
5391 7945 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
5392 7946 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
5393 7947 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
5394 7948 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
5395 7949 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
5396 7950 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
5397 7951 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
5398 7952 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
5399 7953 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
5400 7954 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
5401 7955 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
5402 7956 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
5403 7957 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
5404 7958 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
5405 7959 7.896496 AGTACTCCCTCTGTCCCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
5406 7960 7.776745 AGTACTCCCTCTGTCCCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
5407 7961 7.358255 AGTACTCCCTCTGTCCCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
5408 7962 6.234404 AGTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
5409 7963 5.681494 AGTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
5410 7964 4.561254 AGTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
5411 7965 4.730392 TCTAGTACTCCCTCTGTCCCATAA 59.270 45.833 0.00 0.00 0.00 1.90
5412 7966 4.313362 TCTAGTACTCCCTCTGTCCCATA 58.687 47.826 0.00 0.00 0.00 2.74
5413 7967 3.132056 TCTAGTACTCCCTCTGTCCCAT 58.868 50.000 0.00 0.00 0.00 4.00
5414 7968 2.570098 TCTAGTACTCCCTCTGTCCCA 58.430 52.381 0.00 0.00 0.00 4.37
5415 7969 3.887916 ATCTAGTACTCCCTCTGTCCC 57.112 52.381 0.00 0.00 0.00 4.46
5416 7970 4.538738 ACAATCTAGTACTCCCTCTGTCC 58.461 47.826 0.00 0.00 0.00 4.02
5417 7971 5.419471 ACAACAATCTAGTACTCCCTCTGTC 59.581 44.000 0.00 0.00 0.00 3.51
5418 7972 5.334421 ACAACAATCTAGTACTCCCTCTGT 58.666 41.667 0.00 0.00 0.00 3.41
5419 7973 5.923733 ACAACAATCTAGTACTCCCTCTG 57.076 43.478 0.00 0.00 0.00 3.35
5420 7974 6.257586 AGAACAACAATCTAGTACTCCCTCT 58.742 40.000 0.00 0.00 0.00 3.69
5421 7975 6.532988 AGAACAACAATCTAGTACTCCCTC 57.467 41.667 0.00 0.00 0.00 4.30
5422 7976 6.936968 AAGAACAACAATCTAGTACTCCCT 57.063 37.500 0.00 0.00 0.00 4.20
5423 7977 7.764901 CCTTAAGAACAACAATCTAGTACTCCC 59.235 40.741 3.36 0.00 0.00 4.30
5424 7978 8.529476 TCCTTAAGAACAACAATCTAGTACTCC 58.471 37.037 3.36 0.00 0.00 3.85
5425 7979 9.356433 GTCCTTAAGAACAACAATCTAGTACTC 57.644 37.037 3.36 0.00 0.00 2.59
5426 7980 8.312564 GGTCCTTAAGAACAACAATCTAGTACT 58.687 37.037 3.36 0.00 29.87 2.73
5427 7981 8.312564 AGGTCCTTAAGAACAACAATCTAGTAC 58.687 37.037 3.36 0.00 33.03 2.73
5428 7982 8.431910 AGGTCCTTAAGAACAACAATCTAGTA 57.568 34.615 3.36 0.00 33.03 1.82
5620 8174 6.700960 TGCAAGTGAATCCAACTACAAATTTG 59.299 34.615 16.67 16.67 0.00 2.32
5627 8181 4.437930 GCAGATGCAAGTGAATCCAACTAC 60.438 45.833 0.00 0.00 41.59 2.73
5647 8201 2.402305 GACGCTGAGAATAGGATGCAG 58.598 52.381 0.00 0.00 0.00 4.41
5648 8202 1.269257 CGACGCTGAGAATAGGATGCA 60.269 52.381 0.00 0.00 0.00 3.96
5649 8203 1.413382 CGACGCTGAGAATAGGATGC 58.587 55.000 0.00 0.00 0.00 3.91
5692 8246 3.037549 CAACCTGAGGGCTAAGAGATCT 58.962 50.000 2.38 0.00 35.63 2.75
5697 8251 2.902608 TCTTCAACCTGAGGGCTAAGA 58.097 47.619 2.38 5.53 35.63 2.10
5743 8297 3.405831 TGATTTCAGACTCAAGCCACAG 58.594 45.455 0.00 0.00 0.00 3.66
5785 8339 0.674895 GATGCCGAACTGGAAGCAGT 60.675 55.000 0.00 0.00 42.00 4.40
5949 8503 3.193267 TCAAGCCATATTGTTCAACTGCC 59.807 43.478 0.00 0.00 0.00 4.85
5952 8506 6.506500 CTTCTCAAGCCATATTGTTCAACT 57.493 37.500 0.00 0.00 0.00 3.16
5976 8530 3.784511 AGCCTCATATGATCAAGGGTG 57.215 47.619 13.75 4.76 38.17 4.61
6029 8589 7.554959 TTGGAGTAATGTCCTTCTCTTTACT 57.445 36.000 0.00 0.00 37.97 2.24
6030 8590 8.794335 AATTGGAGTAATGTCCTTCTCTTTAC 57.206 34.615 0.00 0.00 37.52 2.01
6031 8591 9.231297 CAAATTGGAGTAATGTCCTTCTCTTTA 57.769 33.333 0.00 0.00 37.52 1.85
6034 8594 6.656693 CACAAATTGGAGTAATGTCCTTCTCT 59.343 38.462 0.00 0.00 37.52 3.10
6035 8595 6.655003 TCACAAATTGGAGTAATGTCCTTCTC 59.345 38.462 0.00 0.00 37.52 2.87
6036 8596 6.542821 TCACAAATTGGAGTAATGTCCTTCT 58.457 36.000 0.00 0.00 37.52 2.85
6037 8597 6.817765 TCACAAATTGGAGTAATGTCCTTC 57.182 37.500 0.00 0.00 37.52 3.46
6038 8598 6.549364 TGTTCACAAATTGGAGTAATGTCCTT 59.451 34.615 0.00 0.00 37.52 3.36
6039 8599 6.068010 TGTTCACAAATTGGAGTAATGTCCT 58.932 36.000 0.00 0.00 37.52 3.85
6040 8600 6.325919 TGTTCACAAATTGGAGTAATGTCC 57.674 37.500 0.00 0.00 37.10 4.02
6041 8601 6.808212 CCATGTTCACAAATTGGAGTAATGTC 59.192 38.462 0.00 0.00 0.00 3.06
6062 8622 2.696707 ACCTCCAAAATATGCAGCCATG 59.303 45.455 0.00 0.00 32.85 3.66
6322 8886 6.339587 TGATAAGAACATTTTCCCCACAAC 57.660 37.500 0.00 0.00 31.28 3.32
6331 8895 4.917415 GCACGCAGTTGATAAGAACATTTT 59.083 37.500 0.00 0.00 41.61 1.82
6354 8919 7.864379 ACTTGCTCATAGTGAAACAAAAATGAG 59.136 33.333 5.90 5.90 41.19 2.90
6382 8950 4.130118 AGAACTTATGAATAGGGCGCAAG 58.870 43.478 10.83 2.95 43.44 4.01
6389 8957 5.529060 GTGCCCTTGAGAACTTATGAATAGG 59.471 44.000 0.00 0.00 0.00 2.57
6417 8985 1.739466 TCCACTCGTGTACGGTGTATC 59.261 52.381 17.96 0.00 38.19 2.24
6421 8989 2.074547 AAATCCACTCGTGTACGGTG 57.925 50.000 14.72 14.72 40.29 4.94
6425 8993 1.463528 GCGCAAAATCCACTCGTGTAC 60.464 52.381 0.30 0.00 0.00 2.90
6431 8999 0.657840 ATAGCGCGCAAAATCCACTC 59.342 50.000 35.10 0.00 0.00 3.51
6437 9005 4.552166 ACTTATGAATAGCGCGCAAAAT 57.448 36.364 35.10 20.32 0.00 1.82
6446 9014 5.008118 GTGCCCTTGAGAACTTATGAATAGC 59.992 44.000 0.00 0.00 0.00 2.97
6449 9017 4.273318 GGTGCCCTTGAGAACTTATGAAT 58.727 43.478 0.00 0.00 0.00 2.57
6492 9061 3.118738 GGGAGTATGATGGAACGAACACT 60.119 47.826 0.00 0.00 0.00 3.55
6497 9066 2.434336 CCAAGGGAGTATGATGGAACGA 59.566 50.000 0.00 0.00 32.82 3.85
6517 9086 9.085250 TCGTGGTTTTAGTTTAAATTTGAAACC 57.915 29.630 22.02 22.02 42.85 3.27
6529 9098 8.460428 TCAAAATACTTGTCGTGGTTTTAGTTT 58.540 29.630 0.00 0.00 0.00 2.66
6553 9122 2.654877 GCGACTCCCTCCGTTTCA 59.345 61.111 0.00 0.00 0.00 2.69
6564 9133 1.400737 ACCTACACTATGGGCGACTC 58.599 55.000 0.00 0.00 29.87 3.36
6568 9137 5.699458 CCTAATTTAACCTACACTATGGGCG 59.301 44.000 0.00 0.00 29.87 6.13
6569 9138 6.834107 TCCTAATTTAACCTACACTATGGGC 58.166 40.000 0.00 0.00 29.87 5.36
6570 9139 8.269317 TGTTCCTAATTTAACCTACACTATGGG 58.731 37.037 0.00 0.00 34.27 4.00
6571 9140 9.847224 ATGTTCCTAATTTAACCTACACTATGG 57.153 33.333 0.00 0.00 0.00 2.74
6641 9316 6.727824 AACTACGAAGAACCATTTGATCAG 57.272 37.500 0.00 0.00 0.00 2.90
6644 9319 6.877611 ACAAACTACGAAGAACCATTTGAT 57.122 33.333 0.00 0.00 31.59 2.57
6647 9322 6.987992 TCACTACAAACTACGAAGAACCATTT 59.012 34.615 0.00 0.00 0.00 2.32
6648 9323 6.518493 TCACTACAAACTACGAAGAACCATT 58.482 36.000 0.00 0.00 0.00 3.16
6652 9327 9.403110 TCTAAATCACTACAAACTACGAAGAAC 57.597 33.333 0.00 0.00 0.00 3.01
6653 9328 9.970395 TTCTAAATCACTACAAACTACGAAGAA 57.030 29.630 0.00 0.00 0.00 2.52
6657 9332 9.146984 CCATTTCTAAATCACTACAAACTACGA 57.853 33.333 0.00 0.00 0.00 3.43
6658 9333 8.932791 ACCATTTCTAAATCACTACAAACTACG 58.067 33.333 0.00 0.00 0.00 3.51
6661 9336 8.918202 TGACCATTTCTAAATCACTACAAACT 57.082 30.769 0.00 0.00 0.00 2.66
6662 9337 9.774742 GATGACCATTTCTAAATCACTACAAAC 57.225 33.333 0.00 0.00 0.00 2.93
6667 9357 7.127186 TCCCAGATGACCATTTCTAAATCACTA 59.873 37.037 0.00 0.00 0.00 2.74
6673 9363 8.336235 AGTATTTCCCAGATGACCATTTCTAAA 58.664 33.333 0.00 0.00 0.00 1.85
6698 9388 9.566624 CAACACGCTTGAAAACAAAAATATTAG 57.433 29.630 0.00 0.00 0.00 1.73
6724 9415 2.412847 CCGTTTTTCATCTCGTTGAGCC 60.413 50.000 0.00 0.00 0.00 4.70
6725 9416 2.478894 TCCGTTTTTCATCTCGTTGAGC 59.521 45.455 0.00 0.00 0.00 4.26
6797 9520 5.603170 TTGCATACATGATCAGAGAGTCA 57.397 39.130 0.00 0.00 0.00 3.41
6798 9521 6.915544 TTTTGCATACATGATCAGAGAGTC 57.084 37.500 0.00 0.00 0.00 3.36
6799 9522 7.013083 GGAATTTTGCATACATGATCAGAGAGT 59.987 37.037 0.00 0.00 0.00 3.24
6804 9527 7.430441 TGATGGAATTTTGCATACATGATCAG 58.570 34.615 0.00 0.00 39.44 2.90
6834 9617 4.471386 ACAAACTAGTCCCTATGAGCATGT 59.529 41.667 0.00 0.00 0.00 3.21
6917 9702 1.710809 CCCTTCCCCTTCTTTCTTCCA 59.289 52.381 0.00 0.00 0.00 3.53
6955 10475 4.554036 GTGGAGGCGATCTGGGGC 62.554 72.222 0.00 0.00 0.00 5.80
6956 10476 3.083349 TGTGGAGGCGATCTGGGG 61.083 66.667 0.00 0.00 0.00 4.96
6999 10519 4.673298 TGTGGGTGCGTACGGCTG 62.673 66.667 18.39 0.00 44.05 4.85
7050 10620 1.561542 GGAAGAATGGAAGAGGAGCCA 59.438 52.381 0.00 0.00 38.78 4.75
7060 10630 2.780010 GGAGATGGAAGGGAAGAATGGA 59.220 50.000 0.00 0.00 0.00 3.41
7186 10757 3.031417 AAGGGTCCAGGCGAATCCG 62.031 63.158 0.00 0.00 40.77 4.18


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

AutoCloner maintained by Alex Coulton.