Multiple sequence alignment - TraesCS5B01G471600

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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 TraesCS5B01G471600 chr5B 100.000 5172 0 0 1 5172 644884488 644889659 0.000000e+00 9551.0
1 TraesCS5B01G471600 chr5B 79.749 479 44 17 4144 4580 644865850 644865383 1.090000e-76 298.0
2 TraesCS5B01G471600 chr5B 83.688 141 5 8 4954 5094 644864429 644864307 3.270000e-22 117.0
3 TraesCS5B01G471600 chr5B 84.615 91 8 4 4858 4948 644864589 644864505 9.230000e-13 86.1
4 TraesCS5B01G471600 chr5A 91.473 2791 143 27 1960 4709 641729721 641732457 0.000000e+00 3747.0
5 TraesCS5B01G471600 chr5A 88.420 1304 71 25 671 1909 641728427 641729715 0.000000e+00 1498.0
6 TraesCS5B01G471600 chr5A 84.694 686 77 16 3906 4581 641684664 641683997 0.000000e+00 660.0
7 TraesCS5B01G471600 chr5A 87.931 406 41 6 3907 4309 641682780 641682380 6.060000e-129 472.0
8 TraesCS5B01G471600 chr5A 89.954 219 9 3 4954 5172 641732856 641733061 2.370000e-68 270.0
9 TraesCS5B01G471600 chr5A 85.938 128 12 5 4456 4579 641684849 641684724 1.170000e-26 132.0
10 TraesCS5B01G471600 chr5D 93.461 1988 89 22 3043 5014 513975145 513977107 0.000000e+00 2913.0
11 TraesCS5B01G471600 chr5D 89.746 1258 77 15 671 1909 513972804 513974028 0.000000e+00 1561.0
12 TraesCS5B01G471600 chr5D 97.074 752 19 2 2294 3045 513974316 513975064 0.000000e+00 1264.0
13 TraesCS5B01G471600 chr5D 92.226 283 19 1 1960 2242 513974034 513974313 1.040000e-106 398.0
14 TraesCS5B01G471600 chr5D 78.598 542 81 18 1 535 92170945 92170432 4.990000e-85 326.0
15 TraesCS5B01G471600 chr5D 93.333 150 10 0 5023 5172 513977985 513978134 6.740000e-54 222.0
16 TraesCS5B01G471600 chr5D 82.463 268 28 8 4324 4581 513908166 513907908 3.140000e-52 217.0
17 TraesCS5B01G471600 chr5D 84.868 152 4 9 4950 5100 513907013 513906880 9.030000e-28 135.0
18 TraesCS5B01G471600 chr5D 93.333 75 1 1 4954 5028 513977192 513977262 1.970000e-19 108.0
19 TraesCS5B01G471600 chr5D 90.411 73 7 0 4801 4873 513907263 513907191 4.260000e-16 97.1
20 TraesCS5B01G471600 chr5D 95.745 47 2 0 4287 4333 513977143 513977189 5.550000e-10 76.8
21 TraesCS5B01G471600 chrUn 97.943 389 8 0 2366 2754 480189589 480189201 0.000000e+00 675.0
22 TraesCS5B01G471600 chr7D 83.281 640 66 19 1 614 83753996 83754620 7.570000e-153 551.0
23 TraesCS5B01G471600 chr2D 77.541 797 155 16 3342 4121 402307534 402306745 4.720000e-125 459.0
24 TraesCS5B01G471600 chr2D 85.000 80 9 3 570 647 143923050 143923128 1.540000e-10 78.7
25 TraesCS5B01G471600 chr2B 77.284 810 163 14 3324 4121 476400022 476400822 1.700000e-124 457.0
26 TraesCS5B01G471600 chr2A 76.638 809 173 12 3323 4121 539394318 539393516 2.860000e-117 433.0
27 TraesCS5B01G471600 chr2A 82.014 278 32 12 381 653 561856555 561856291 2.420000e-53 220.0
28 TraesCS5B01G471600 chr1A 76.368 804 163 20 3323 4116 303854569 303853783 1.730000e-109 407.0
29 TraesCS5B01G471600 chr1D 76.051 785 171 13 3342 4121 239806955 239806183 4.850000e-105 392.0
30 TraesCS5B01G471600 chr3B 78.201 289 45 12 6 293 766800299 766800028 8.910000e-38 169.0
31 TraesCS5B01G471600 chr3B 73.585 371 55 32 4167 4521 718350638 718350981 9.160000e-18 102.0
32 TraesCS5B01G471600 chr3B 91.489 47 1 1 4538 4581 718350980 718351026 1.560000e-05 62.1
33 TraesCS5B01G471600 chr3D 80.769 156 13 9 485 636 419462301 419462159 7.080000e-19 106.0


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 TraesCS5B01G471600 chr5B 644884488 644889659 5171 False 9551.000000 9551 100.000000 1 5172 1 chr5B.!!$F1 5171
1 TraesCS5B01G471600 chr5A 641728427 641733061 4634 False 1838.333333 3747 89.949000 671 5172 3 chr5A.!!$F1 4501
2 TraesCS5B01G471600 chr5A 641682380 641684849 2469 True 421.333333 660 86.187667 3906 4581 3 chr5A.!!$R1 675
3 TraesCS5B01G471600 chr5D 513972804 513978134 5330 False 934.685714 2913 93.559714 671 5172 7 chr5D.!!$F1 4501
4 TraesCS5B01G471600 chr5D 92170432 92170945 513 True 326.000000 326 78.598000 1 535 1 chr5D.!!$R1 534
5 TraesCS5B01G471600 chr7D 83753996 83754620 624 False 551.000000 551 83.281000 1 614 1 chr7D.!!$F1 613
6 TraesCS5B01G471600 chr2D 402306745 402307534 789 True 459.000000 459 77.541000 3342 4121 1 chr2D.!!$R1 779
7 TraesCS5B01G471600 chr2B 476400022 476400822 800 False 457.000000 457 77.284000 3324 4121 1 chr2B.!!$F1 797
8 TraesCS5B01G471600 chr2A 539393516 539394318 802 True 433.000000 433 76.638000 3323 4121 1 chr2A.!!$R1 798
9 TraesCS5B01G471600 chr1A 303853783 303854569 786 True 407.000000 407 76.368000 3323 4116 1 chr1A.!!$R1 793
10 TraesCS5B01G471600 chr1D 239806183 239806955 772 True 392.000000 392 76.051000 3342 4121 1 chr1D.!!$R1 779

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
953 1012 0.191314 GGATCTACCAGCCTACCCCT 59.809 60.0 0.00 0.00 38.79 4.79 F
956 1015 0.559699 TCTACCAGCCTACCCCTACC 59.440 60.0 0.00 0.00 0.00 3.18 F
1259 1325 0.678395 ATCAGGCTCTGTATCCGCTG 59.322 55.0 2.68 0.00 32.61 5.18 F
2572 2684 0.679640 CCGCCCCACTATTCTTGCAA 60.680 55.0 0.00 0.00 0.00 4.08 F
3985 4208 0.109597 AGGTCTACGGTTACAACGCG 60.110 55.0 3.53 3.53 34.00 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2572 2684 0.250513 GCCCAGAAGACAGTTCCGAT 59.749 55.000 0.00 0.0 0.0 4.18 R
2664 2776 1.670811 GGTATGACAATGGCAAGTCCG 59.329 52.381 17.35 0.0 37.8 4.79 R
2931 3043 3.328237 GTGTCGTCGTCACCAAAATTT 57.672 42.857 10.95 0.0 0.0 1.82 R
4066 4289 0.178981 ACAGGCAGCACAGACCAAAT 60.179 50.000 0.00 0.0 0.0 2.32 R
4866 5631 0.040058 TGGTCCTGCATGCCTTCAAT 59.960 50.000 16.68 0.0 0.0 2.57 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
64 65 2.390599 CCATGGTCGCCGACAACTG 61.391 63.158 20.08 12.07 33.68 3.16
86 87 0.806884 AAACGACTGTCGAAACCGCA 60.807 50.000 33.99 0.00 43.74 5.69
122 123 4.397832 GCCGGCCGACCTTGGTTA 62.398 66.667 30.73 0.00 0.00 2.85
211 216 4.803426 GCGGCCTCCAGAGTGACG 62.803 72.222 0.00 6.94 34.63 4.35
300 305 2.203015 CGCGTTGGGGATAGGTGG 60.203 66.667 0.00 0.00 0.00 4.61
301 306 2.995547 GCGTTGGGGATAGGTGGT 59.004 61.111 0.00 0.00 0.00 4.16
426 465 4.832608 GGTCGCGCGAAAGGGGAT 62.833 66.667 36.57 0.00 45.27 3.85
500 539 5.183904 GGAGTTGGAGATGTAAATTTGCACT 59.816 40.000 11.35 10.39 0.00 4.40
524 563 6.636705 TGCGAAGTGGTATAGTTTACATCTT 58.363 36.000 0.00 0.00 0.00 2.40
539 578 1.182385 ATCTTCGGGAGGCGGAGATC 61.182 60.000 0.00 0.00 0.00 2.75
540 579 2.838225 TTCGGGAGGCGGAGATCC 60.838 66.667 0.00 0.00 34.66 3.36
544 583 2.123251 GGAGGCGGAGATCCCAGA 60.123 66.667 0.00 0.00 34.14 3.86
545 584 2.206536 GGAGGCGGAGATCCCAGAG 61.207 68.421 0.00 0.00 34.14 3.35
546 585 1.152652 GAGGCGGAGATCCCAGAGA 60.153 63.158 0.00 0.00 34.14 3.10
547 586 0.541764 GAGGCGGAGATCCCAGAGAT 60.542 60.000 0.00 0.00 38.17 2.75
548 587 0.831288 AGGCGGAGATCCCAGAGATG 60.831 60.000 0.00 0.00 34.42 2.90
549 588 1.118356 GGCGGAGATCCCAGAGATGT 61.118 60.000 0.00 0.00 34.42 3.06
550 589 1.621992 GCGGAGATCCCAGAGATGTA 58.378 55.000 0.00 0.00 34.42 2.29
551 590 2.175202 GCGGAGATCCCAGAGATGTAT 58.825 52.381 0.00 0.00 34.42 2.29
552 591 2.165437 GCGGAGATCCCAGAGATGTATC 59.835 54.545 0.00 0.00 34.42 2.24
553 592 3.696045 CGGAGATCCCAGAGATGTATCT 58.304 50.000 0.00 0.00 34.42 1.98
554 593 4.085733 CGGAGATCCCAGAGATGTATCTT 58.914 47.826 0.00 0.00 34.42 2.40
555 594 4.526262 CGGAGATCCCAGAGATGTATCTTT 59.474 45.833 0.00 0.00 34.42 2.52
556 595 5.011533 CGGAGATCCCAGAGATGTATCTTTT 59.988 44.000 0.00 0.00 34.42 2.27
584 623 5.946942 ACATCTACATCATCTGTTGGAGT 57.053 39.130 1.44 0.00 39.39 3.85
586 625 7.609097 ACATCTACATCATCTGTTGGAGTAT 57.391 36.000 1.44 0.00 39.39 2.12
601 640 5.249780 TGGAGTATTGTTTTTGGCCTCTA 57.750 39.130 3.32 0.00 0.00 2.43
602 641 5.636123 TGGAGTATTGTTTTTGGCCTCTAA 58.364 37.500 3.32 0.00 0.00 2.10
614 653 3.766545 TGGCCTCTAAAGATGCAAAAGT 58.233 40.909 3.32 0.00 37.41 2.66
615 654 4.151883 TGGCCTCTAAAGATGCAAAAGTT 58.848 39.130 3.32 0.00 37.41 2.66
616 655 5.321102 TGGCCTCTAAAGATGCAAAAGTTA 58.679 37.500 3.32 0.00 37.41 2.24
617 656 5.772672 TGGCCTCTAAAGATGCAAAAGTTAA 59.227 36.000 3.32 0.00 37.41 2.01
618 657 6.437162 TGGCCTCTAAAGATGCAAAAGTTAAT 59.563 34.615 3.32 0.00 37.41 1.40
619 658 7.039082 TGGCCTCTAAAGATGCAAAAGTTAATT 60.039 33.333 3.32 0.00 37.41 1.40
620 659 8.466798 GGCCTCTAAAGATGCAAAAGTTAATTA 58.533 33.333 9.08 0.00 37.41 1.40
651 690 6.737720 TCTACATCACTTATTGGAGATGCT 57.262 37.500 0.00 0.00 41.08 3.79
652 691 6.753180 TCTACATCACTTATTGGAGATGCTC 58.247 40.000 0.00 0.00 41.08 4.26
667 706 5.240013 AGATGCTCCAAGAAGATTATCCC 57.760 43.478 0.00 0.00 0.00 3.85
668 707 3.864789 TGCTCCAAGAAGATTATCCCC 57.135 47.619 0.00 0.00 0.00 4.81
669 708 2.443255 TGCTCCAAGAAGATTATCCCCC 59.557 50.000 0.00 0.00 0.00 5.40
675 714 5.734140 TCCAAGAAGATTATCCCCCAAACTA 59.266 40.000 0.00 0.00 0.00 2.24
680 719 7.119387 AGAAGATTATCCCCCAAACTAAACTG 58.881 38.462 0.00 0.00 0.00 3.16
682 721 6.187682 AGATTATCCCCCAAACTAAACTGTG 58.812 40.000 0.00 0.00 0.00 3.66
692 731 6.147821 CCCAAACTAAACTGTGTAGACATCTG 59.852 42.308 11.91 2.04 0.00 2.90
951 1010 1.817911 GCGGATCTACCAGCCTACCC 61.818 65.000 0.00 0.00 38.90 3.69
952 1011 1.186267 CGGATCTACCAGCCTACCCC 61.186 65.000 0.00 0.00 38.90 4.95
953 1012 0.191314 GGATCTACCAGCCTACCCCT 59.809 60.000 0.00 0.00 38.79 4.79
954 1013 1.432024 GGATCTACCAGCCTACCCCTA 59.568 57.143 0.00 0.00 38.79 3.53
955 1014 2.527497 GATCTACCAGCCTACCCCTAC 58.473 57.143 0.00 0.00 0.00 3.18
956 1015 0.559699 TCTACCAGCCTACCCCTACC 59.440 60.000 0.00 0.00 0.00 3.18
1043 1104 3.151022 CGGTGGCTCCTCTCCTCC 61.151 72.222 3.83 0.00 34.70 4.30
1101 1165 1.134729 CAGGCCAATGGGGAATTTTCG 60.135 52.381 5.01 0.00 40.01 3.46
1104 1168 2.498078 GGCCAATGGGGAATTTTCGTTA 59.502 45.455 0.00 0.00 40.01 3.18
1140 1206 2.620585 TGCGTGAATGGTGTTCATTTGA 59.379 40.909 0.00 0.00 45.36 2.69
1142 1208 3.549827 GCGTGAATGGTGTTCATTTGACA 60.550 43.478 0.00 0.00 45.36 3.58
1153 1219 2.972625 TCATTTGACACCCATCTCGAC 58.027 47.619 0.00 0.00 0.00 4.20
1215 1281 0.974010 TTACCCGGTCGAATGAGGCT 60.974 55.000 0.00 0.00 0.00 4.58
1259 1325 0.678395 ATCAGGCTCTGTATCCGCTG 59.322 55.000 2.68 0.00 32.61 5.18
1309 1375 2.825836 GCATTCAGGTGCCCGAGG 60.826 66.667 0.00 0.00 39.18 4.63
1416 1490 2.388232 CCGTTGACCTTAGCCGTGC 61.388 63.158 0.00 0.00 0.00 5.34
1462 1553 1.943968 GCAAGCCACACGAATCTGGTA 60.944 52.381 0.00 0.00 0.00 3.25
1465 1556 1.066858 AGCCACACGAATCTGGTAGTG 60.067 52.381 0.00 0.00 40.17 2.74
1527 1624 5.929058 ATGCTAGAGATTCAAGTGAGACA 57.071 39.130 0.00 0.00 0.00 3.41
1604 1710 7.337942 GGATATTCTTGTTCTTCCATTGTCACT 59.662 37.037 0.00 0.00 0.00 3.41
1605 1711 5.756195 TTCTTGTTCTTCCATTGTCACTG 57.244 39.130 0.00 0.00 0.00 3.66
1606 1712 3.565482 TCTTGTTCTTCCATTGTCACTGC 59.435 43.478 0.00 0.00 0.00 4.40
1663 1769 2.026822 AGGATCTCATGACAACCACCAC 60.027 50.000 0.27 0.00 0.00 4.16
1664 1770 2.359900 GATCTCATGACAACCACCACC 58.640 52.381 0.00 0.00 0.00 4.61
1665 1771 1.135960 TCTCATGACAACCACCACCA 58.864 50.000 0.00 0.00 0.00 4.17
1670 1776 3.767630 GACAACCACCACCACGGCT 62.768 63.158 0.00 0.00 39.03 5.52
1710 1816 3.262420 GAGATCACGTTAAGCACCATGT 58.738 45.455 0.00 0.00 0.00 3.21
1735 1841 8.076178 GTGATCGGCATATATAGCTTTGTTTTT 58.924 33.333 0.00 0.00 0.00 1.94
1772 1878 8.848182 CCTGTTAACTAATAGTACTAGGTCCTG 58.152 40.741 8.85 0.00 0.00 3.86
1872 1981 7.536895 TTTGTGTGGAAATCTTTGAATGTTG 57.463 32.000 0.00 0.00 0.00 3.33
1888 1997 0.883833 GTTGCCTCATCACACCCTTG 59.116 55.000 0.00 0.00 0.00 3.61
1891 2000 1.310933 GCCTCATCACACCCTTGCAG 61.311 60.000 0.00 0.00 0.00 4.41
1909 2021 2.851195 CAGTTAGTGGCAAACTCACCT 58.149 47.619 1.63 0.00 40.56 4.00
1910 2022 2.549754 CAGTTAGTGGCAAACTCACCTG 59.450 50.000 1.63 0.00 40.56 4.00
1914 2026 5.045578 AGTTAGTGGCAAACTCACCTGATAT 60.046 40.000 0.00 0.00 40.56 1.63
1915 2027 6.156256 AGTTAGTGGCAAACTCACCTGATATA 59.844 38.462 0.00 0.00 40.56 0.86
1916 2028 5.636903 AGTGGCAAACTCACCTGATATAT 57.363 39.130 0.00 0.00 31.64 0.86
1917 2029 6.006275 AGTGGCAAACTCACCTGATATATT 57.994 37.500 0.00 0.00 31.64 1.28
1918 2030 6.426587 AGTGGCAAACTCACCTGATATATTT 58.573 36.000 0.00 0.00 31.64 1.40
1919 2031 6.319658 AGTGGCAAACTCACCTGATATATTTG 59.680 38.462 0.00 0.00 31.64 2.32
1920 2032 6.095440 GTGGCAAACTCACCTGATATATTTGT 59.905 38.462 0.00 0.00 0.00 2.83
1921 2033 7.282224 GTGGCAAACTCACCTGATATATTTGTA 59.718 37.037 0.00 0.00 0.00 2.41
1922 2034 7.998383 TGGCAAACTCACCTGATATATTTGTAT 59.002 33.333 0.00 0.00 0.00 2.29
1923 2035 9.502091 GGCAAACTCACCTGATATATTTGTATA 57.498 33.333 0.00 0.00 0.00 1.47
1955 2067 9.314321 AGTTCTGTTTTACATATGTATTCCTCG 57.686 33.333 16.16 4.74 0.00 4.63
1956 2068 8.548721 GTTCTGTTTTACATATGTATTCCTCGG 58.451 37.037 16.16 10.20 0.00 4.63
1957 2069 7.788026 TCTGTTTTACATATGTATTCCTCGGT 58.212 34.615 16.16 0.00 0.00 4.69
1958 2070 8.262227 TCTGTTTTACATATGTATTCCTCGGTT 58.738 33.333 16.16 0.00 0.00 4.44
1994 2106 4.320608 TGAAGCATGAAAAACAGGAACC 57.679 40.909 0.00 0.00 31.40 3.62
2021 2133 9.930693 CTTCTAGGTATTATGTCTACAATTCCC 57.069 37.037 0.00 0.00 0.00 3.97
2047 2159 5.982516 TGTGGTGTGAATGCAATTAACTTTC 59.017 36.000 0.00 0.00 38.57 2.62
2089 2201 7.865875 TTCATTCATTACAACCGTTTCATTG 57.134 32.000 0.00 0.00 0.00 2.82
2108 2220 5.357878 TCATTGTAGATCTTTTGCACCCATC 59.642 40.000 0.00 0.00 0.00 3.51
2109 2221 4.574674 TGTAGATCTTTTGCACCCATCT 57.425 40.909 0.00 0.00 0.00 2.90
2144 2256 4.212143 ACATACTGTGCACATGTGAGAT 57.788 40.909 29.80 11.29 31.83 2.75
2228 2340 7.144722 TGTGAATAGTGGATTGAAACATGTC 57.855 36.000 0.00 0.00 0.00 3.06
2231 2343 9.113838 GTGAATAGTGGATTGAAACATGTCTAT 57.886 33.333 0.00 0.00 0.00 1.98
2269 2381 6.939163 CAGAAATATCCCCAGGATTCTGTTAG 59.061 42.308 13.68 0.00 39.79 2.34
2287 2399 2.048444 AGTGTCATGTGGCATCCATC 57.952 50.000 0.00 0.00 35.28 3.51
2466 2578 2.514824 GCCTTCGATGCTGGTCCC 60.515 66.667 0.52 0.00 0.00 4.46
2571 2683 1.077787 CCGCCCCACTATTCTTGCA 60.078 57.895 0.00 0.00 0.00 4.08
2572 2684 0.679640 CCGCCCCACTATTCTTGCAA 60.680 55.000 0.00 0.00 0.00 4.08
2625 2737 0.949105 CCGTTGGTGTCAGCCAGTAC 60.949 60.000 0.00 0.00 40.01 2.73
2662 2774 5.629133 GCATTCTGGAGAGGTGTAAATGGTA 60.629 44.000 0.00 0.00 0.00 3.25
2664 2776 5.871396 TCTGGAGAGGTGTAAATGGTATC 57.129 43.478 0.00 0.00 0.00 2.24
2931 3043 5.726308 TGATCCTAGAAAAACATCTCCAGGA 59.274 40.000 0.00 0.00 38.14 3.86
2975 3087 5.945784 CCAATGAGAGGTATGGTTTTCTTCA 59.054 40.000 0.00 0.00 0.00 3.02
3076 3275 3.890756 TGGTGATCAAGTGCTGACATTTT 59.109 39.130 0.00 0.00 36.69 1.82
3146 3345 5.140747 TCAACTTCCTCTCAGCTCTAAAC 57.859 43.478 0.00 0.00 0.00 2.01
3182 3381 4.403734 TGGAATTTTGAGGAAGTGTACCC 58.596 43.478 0.00 0.00 0.00 3.69
3859 4082 2.240230 GAACAACCCGATGTTCGCA 58.760 52.632 11.20 0.00 46.74 5.10
3985 4208 0.109597 AGGTCTACGGTTACAACGCG 60.110 55.000 3.53 3.53 34.00 6.01
4030 4253 4.794648 GTGGCAGGGGCATACGCA 62.795 66.667 0.00 0.00 43.71 5.24
4066 4289 3.270027 GTTGACCATGATGATCGTTCCA 58.730 45.455 0.00 0.00 0.00 3.53
4093 4316 0.758734 TGTGCTGCCTGTTCTACACT 59.241 50.000 0.00 0.00 0.00 3.55
4105 4328 3.057736 TGTTCTACACTCCGCTGTACTTC 60.058 47.826 0.00 0.00 0.00 3.01
4181 4404 1.135139 AGCTAATGTGATGCTCGACGT 59.865 47.619 0.00 0.00 30.41 4.34
4214 4437 5.398169 CAGTTTGTTGTTTCAGTTGCAGTA 58.602 37.500 0.00 0.00 0.00 2.74
4333 4565 7.017645 CCTTCAGACACATGAAAAGAAATACG 58.982 38.462 0.00 0.00 38.66 3.06
4395 4628 7.755373 GGGTAGAGACAGTGATTTTAATTTTGC 59.245 37.037 0.00 0.00 0.00 3.68
4498 4742 8.244113 CGCCTAGGATTTATTTTTCTTTTGTCT 58.756 33.333 14.75 0.00 0.00 3.41
4536 4780 5.355350 ACTGAATTTTTAGATGAAGAGGGCG 59.645 40.000 0.00 0.00 0.00 6.13
4581 4830 5.241728 GTGAACTTGGTTAAGCAAGAGGAAT 59.758 40.000 39.86 24.64 37.43 3.01
4598 4857 3.641439 GAATGAACATTCAGTCGGACG 57.359 47.619 18.73 0.00 44.89 4.79
4721 5036 8.425577 AGTATGGTTTCTCTTGATACAAATCG 57.574 34.615 0.00 0.00 34.60 3.34
4792 5541 1.698506 TTGCGTGGGAAAAAGGATGT 58.301 45.000 0.00 0.00 0.00 3.06
4794 5543 2.156098 TGCGTGGGAAAAAGGATGTAC 58.844 47.619 0.00 0.00 0.00 2.90
4795 5544 2.156098 GCGTGGGAAAAAGGATGTACA 58.844 47.619 0.00 0.00 0.00 2.90
4796 5545 2.554893 GCGTGGGAAAAAGGATGTACAA 59.445 45.455 0.00 0.00 0.00 2.41
4797 5546 3.610821 GCGTGGGAAAAAGGATGTACAAC 60.611 47.826 0.00 0.00 0.00 3.32
4805 5568 5.934935 AAAAGGATGTACAACTGTTACGG 57.065 39.130 0.00 0.00 0.00 4.02
4826 5589 4.154195 CGGCTATAACAAATGTAGGATGCC 59.846 45.833 0.00 0.00 0.00 4.40
4846 5611 3.118519 GCCCATGCTTTCAAATGGAGAAT 60.119 43.478 3.24 0.00 45.29 2.40
4847 5612 4.099881 GCCCATGCTTTCAAATGGAGAATA 59.900 41.667 3.24 0.00 45.29 1.75
4855 5620 5.393068 TTCAAATGGAGAATATCAGGCCT 57.607 39.130 0.00 0.00 0.00 5.19
4864 5629 5.994668 GGAGAATATCAGGCCTTGAACTAAG 59.005 44.000 0.00 0.00 39.77 2.18
4866 5631 7.202011 GGAGAATATCAGGCCTTGAACTAAGTA 60.202 40.741 0.00 0.00 39.77 2.24
4943 5742 7.389053 TGGACAACTTTAAAACATGTTTTGCTT 59.611 29.630 35.69 21.67 42.18 3.91
4950 5749 9.853921 CTTTAAAACATGTTTTGCTTCATTCTC 57.146 29.630 35.69 0.00 42.18 2.87
4984 6552 7.928908 CAGATGAACTGTAGAATTAGAGAGC 57.071 40.000 0.00 0.00 41.30 4.09
4988 6556 9.973450 GATGAACTGTAGAATTAGAGAGCATAA 57.027 33.333 0.00 0.00 0.00 1.90
5038 7344 5.373854 ACCATCTCCTTTTATTATCCTGCCT 59.626 40.000 0.00 0.00 0.00 4.75
5039 7345 6.562608 ACCATCTCCTTTTATTATCCTGCCTA 59.437 38.462 0.00 0.00 0.00 3.93
5040 7346 7.073725 ACCATCTCCTTTTATTATCCTGCCTAA 59.926 37.037 0.00 0.00 0.00 2.69
5041 7347 7.944554 CCATCTCCTTTTATTATCCTGCCTAAA 59.055 37.037 0.00 0.00 0.00 1.85
5042 7348 8.787852 CATCTCCTTTTATTATCCTGCCTAAAC 58.212 37.037 0.00 0.00 0.00 2.01
5043 7349 7.287810 TCTCCTTTTATTATCCTGCCTAAACC 58.712 38.462 0.00 0.00 0.00 3.27
5044 7350 7.128883 TCTCCTTTTATTATCCTGCCTAAACCT 59.871 37.037 0.00 0.00 0.00 3.50
5045 7351 7.060421 TCCTTTTATTATCCTGCCTAAACCTG 58.940 38.462 0.00 0.00 0.00 4.00
5046 7352 6.239036 CCTTTTATTATCCTGCCTAAACCTGC 60.239 42.308 0.00 0.00 0.00 4.85
5047 7353 5.646692 TTATTATCCTGCCTAAACCTGCT 57.353 39.130 0.00 0.00 0.00 4.24
5112 7418 9.810545 TTTTGGTAAAAATACAACCTCTGAAAG 57.189 29.630 0.00 0.00 34.23 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.647346 TTCGACAGTCGTTTTGCAGT 58.353 45.000 22.16 0.00 41.35 4.40
64 65 1.738432 GGTTTCGACAGTCGTTTTGC 58.262 50.000 22.16 9.41 41.35 3.68
316 321 4.742201 CTGACCCACCTCGCCGTG 62.742 72.222 0.00 0.00 0.00 4.94
418 457 2.279173 ACTGCCACTTCTATCCCCTTT 58.721 47.619 0.00 0.00 0.00 3.11
426 465 1.003839 CGCCCAACTGCCACTTCTA 60.004 57.895 0.00 0.00 0.00 2.10
454 493 2.167693 AGGAGATGTAAAATCGCGTCCA 59.832 45.455 5.77 0.00 0.00 4.02
462 501 5.779241 TCCAACTCCAGGAGATGTAAAAT 57.221 39.130 24.45 0.00 31.83 1.82
500 539 6.216801 AGATGTAAACTATACCACTTCGCA 57.783 37.500 0.00 0.00 0.00 5.10
524 563 4.916314 GGGATCTCCGCCTCCCGA 62.916 72.222 0.00 0.00 41.74 5.14
556 595 9.513906 TCCAACAGATGATGTAGATGTTAAAAA 57.486 29.630 0.00 0.00 43.00 1.94
561 600 6.305272 ACTCCAACAGATGATGTAGATGTT 57.695 37.500 0.00 0.00 43.00 2.71
577 616 4.280929 AGAGGCCAAAAACAATACTCCAAC 59.719 41.667 5.01 0.00 0.00 3.77
584 623 6.630071 GCATCTTTAGAGGCCAAAAACAATA 58.370 36.000 5.01 0.00 45.12 1.90
586 625 4.881920 GCATCTTTAGAGGCCAAAAACAA 58.118 39.130 5.01 0.00 45.12 2.83
623 662 9.987272 CATCTCCAATAAGTGATGTAGATGTAA 57.013 33.333 0.00 0.00 36.14 2.41
624 663 8.090831 GCATCTCCAATAAGTGATGTAGATGTA 58.909 37.037 0.00 0.00 40.62 2.29
625 664 6.933521 GCATCTCCAATAAGTGATGTAGATGT 59.066 38.462 0.00 0.00 40.62 3.06
626 665 7.160049 AGCATCTCCAATAAGTGATGTAGATG 58.840 38.462 0.00 0.00 41.16 2.90
627 666 7.313740 AGCATCTCCAATAAGTGATGTAGAT 57.686 36.000 0.00 0.00 38.68 1.98
628 667 6.737720 AGCATCTCCAATAAGTGATGTAGA 57.262 37.500 0.00 0.00 38.68 2.59
644 683 5.244755 GGGATAATCTTCTTGGAGCATCTC 58.755 45.833 0.00 0.00 33.73 2.75
645 684 4.042684 GGGGATAATCTTCTTGGAGCATCT 59.957 45.833 0.00 0.00 33.73 2.90
646 685 4.331108 GGGGATAATCTTCTTGGAGCATC 58.669 47.826 0.00 0.00 0.00 3.91
647 686 3.075134 GGGGGATAATCTTCTTGGAGCAT 59.925 47.826 0.00 0.00 0.00 3.79
648 687 2.443255 GGGGGATAATCTTCTTGGAGCA 59.557 50.000 0.00 0.00 0.00 4.26
649 688 2.443255 TGGGGGATAATCTTCTTGGAGC 59.557 50.000 0.00 0.00 0.00 4.70
650 689 4.796110 TTGGGGGATAATCTTCTTGGAG 57.204 45.455 0.00 0.00 0.00 3.86
651 690 4.544152 AGTTTGGGGGATAATCTTCTTGGA 59.456 41.667 0.00 0.00 0.00 3.53
652 691 4.871822 AGTTTGGGGGATAATCTTCTTGG 58.128 43.478 0.00 0.00 0.00 3.61
653 692 7.615757 AGTTTAGTTTGGGGGATAATCTTCTTG 59.384 37.037 0.00 0.00 0.00 3.02
654 693 7.615757 CAGTTTAGTTTGGGGGATAATCTTCTT 59.384 37.037 0.00 0.00 0.00 2.52
655 694 7.119387 CAGTTTAGTTTGGGGGATAATCTTCT 58.881 38.462 0.00 0.00 0.00 2.85
656 695 6.890268 ACAGTTTAGTTTGGGGGATAATCTTC 59.110 38.462 0.00 0.00 0.00 2.87
657 696 6.663523 CACAGTTTAGTTTGGGGGATAATCTT 59.336 38.462 0.00 0.00 0.00 2.40
658 697 6.187682 CACAGTTTAGTTTGGGGGATAATCT 58.812 40.000 0.00 0.00 0.00 2.40
659 698 5.949952 ACACAGTTTAGTTTGGGGGATAATC 59.050 40.000 0.00 0.00 0.00 1.75
660 699 5.899278 ACACAGTTTAGTTTGGGGGATAAT 58.101 37.500 0.00 0.00 0.00 1.28
661 700 5.327737 ACACAGTTTAGTTTGGGGGATAA 57.672 39.130 0.00 0.00 0.00 1.75
662 701 5.786457 TCTACACAGTTTAGTTTGGGGGATA 59.214 40.000 0.00 0.00 0.00 2.59
663 702 3.895704 ACACAGTTTAGTTTGGGGGAT 57.104 42.857 0.00 0.00 0.00 3.85
664 703 3.975312 TCTACACAGTTTAGTTTGGGGGA 59.025 43.478 0.00 0.00 0.00 4.81
665 704 4.070009 GTCTACACAGTTTAGTTTGGGGG 58.930 47.826 0.00 0.00 0.00 5.40
666 705 4.710324 TGTCTACACAGTTTAGTTTGGGG 58.290 43.478 0.00 0.00 0.00 4.96
667 706 6.147821 CAGATGTCTACACAGTTTAGTTTGGG 59.852 42.308 0.00 0.00 35.41 4.12
668 707 6.147821 CCAGATGTCTACACAGTTTAGTTTGG 59.852 42.308 0.00 0.00 35.41 3.28
669 708 6.929049 TCCAGATGTCTACACAGTTTAGTTTG 59.071 38.462 0.00 0.00 35.41 2.93
675 714 3.615110 CGCTCCAGATGTCTACACAGTTT 60.615 47.826 0.00 0.00 35.41 2.66
680 719 2.943690 TCTACGCTCCAGATGTCTACAC 59.056 50.000 0.00 0.00 0.00 2.90
682 721 2.943690 TGTCTACGCTCCAGATGTCTAC 59.056 50.000 0.00 0.00 0.00 2.59
831 886 2.823147 CGACTAGCGACGAGGGGT 60.823 66.667 0.00 0.00 44.57 4.95
882 941 2.989253 GCTCCCCGGGTGTTTTGG 60.989 66.667 21.85 1.24 0.00 3.28
1028 1089 2.766229 GGGGAGGAGAGGAGCCAC 60.766 72.222 0.00 0.00 0.00 5.01
1032 1093 1.456705 CGAAGGGGGAGGAGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
1043 1104 0.745845 CAGTGCTGGAATCGAAGGGG 60.746 60.000 0.00 0.00 0.00 4.79
1101 1165 9.790389 ATTCACGCATAGAGCTAGTATATTAAC 57.210 33.333 0.00 0.00 42.61 2.01
1104 1168 7.093727 ACCATTCACGCATAGAGCTAGTATATT 60.094 37.037 0.00 0.00 42.61 1.28
1140 1206 4.443034 GCCTAATTAAGTCGAGATGGGTGT 60.443 45.833 0.00 0.00 0.00 4.16
1142 1208 3.071167 GGCCTAATTAAGTCGAGATGGGT 59.929 47.826 0.00 0.00 0.00 4.51
1153 1219 5.843019 TCCCCTATCTTGGCCTAATTAAG 57.157 43.478 3.32 0.00 0.00 1.85
1215 1281 5.456619 CCACTAATTAATCCTGCTCCATCCA 60.457 44.000 0.00 0.00 0.00 3.41
1259 1325 1.329906 CACATCTCCGCATCTGCTTTC 59.670 52.381 0.09 0.00 39.32 2.62
1272 1338 4.124970 TGCATTGCTCAGATACACATCTC 58.875 43.478 10.49 0.00 39.62 2.75
1309 1375 2.583593 GCACATCCGAGTCGCTCC 60.584 66.667 7.12 0.00 0.00 4.70
1416 1490 2.743928 GAGCAGGCAACCAGACCG 60.744 66.667 0.00 0.00 37.17 4.79
1462 1553 0.539051 GCAGCCTCACAGATACCACT 59.461 55.000 0.00 0.00 0.00 4.00
1465 1556 4.427394 CGCAGCCTCACAGATACC 57.573 61.111 0.00 0.00 0.00 2.73
1548 1645 2.697751 CTCAAGGATCTGAGAACCGGAT 59.302 50.000 9.46 0.00 44.82 4.18
1604 1710 1.354368 AGAATCCGAAAAGGGAAGGCA 59.646 47.619 0.00 0.00 40.09 4.75
1605 1711 1.745653 CAGAATCCGAAAAGGGAAGGC 59.254 52.381 0.00 0.00 40.09 4.35
1606 1712 3.350219 TCAGAATCCGAAAAGGGAAGG 57.650 47.619 0.00 0.00 40.09 3.46
1663 1769 0.389948 GTACCAAGAGTCAGCCGTGG 60.390 60.000 0.00 0.00 38.77 4.94
1664 1770 0.389948 GGTACCAAGAGTCAGCCGTG 60.390 60.000 7.15 0.00 0.00 4.94
1665 1771 1.972978 GGTACCAAGAGTCAGCCGT 59.027 57.895 7.15 0.00 0.00 5.68
1705 1811 4.953667 AGCTATATATGCCGATCACATGG 58.046 43.478 8.18 0.00 0.00 3.66
1710 1816 7.744087 AAAACAAAGCTATATATGCCGATCA 57.256 32.000 0.00 0.00 0.00 2.92
1735 1841 3.737559 AGTTAACAGGCCAATCCATCA 57.262 42.857 5.01 0.00 37.29 3.07
1772 1878 1.978580 TCTCCCCTGGAACTGAAACTC 59.021 52.381 0.00 0.00 0.00 3.01
1799 1905 8.243289 TGCTATACTAGTTGGTTTAAACGAAC 57.757 34.615 28.61 28.61 44.66 3.95
1872 1981 1.303561 TGCAAGGGTGTGATGAGGC 60.304 57.895 0.00 0.00 0.00 4.70
1888 1997 1.266989 GGTGAGTTTGCCACTAACTGC 59.733 52.381 0.00 0.00 37.07 4.40
1891 2000 2.846193 TCAGGTGAGTTTGCCACTAAC 58.154 47.619 0.00 0.00 36.18 2.34
1929 2041 9.314321 CGAGGAATACATATGTAAAACAGAACT 57.686 33.333 19.11 9.08 33.76 3.01
1930 2042 8.548721 CCGAGGAATACATATGTAAAACAGAAC 58.451 37.037 19.11 5.01 33.76 3.01
1931 2043 8.262227 ACCGAGGAATACATATGTAAAACAGAA 58.738 33.333 19.11 0.00 33.76 3.02
1932 2044 7.788026 ACCGAGGAATACATATGTAAAACAGA 58.212 34.615 19.11 0.00 33.76 3.41
1933 2045 8.433421 AACCGAGGAATACATATGTAAAACAG 57.567 34.615 19.11 9.41 33.76 3.16
1934 2046 8.795842 AAACCGAGGAATACATATGTAAAACA 57.204 30.769 19.11 0.00 33.76 2.83
1939 2051 9.844790 CGTATAAAACCGAGGAATACATATGTA 57.155 33.333 17.65 17.65 34.67 2.29
1940 2052 8.362639 ACGTATAAAACCGAGGAATACATATGT 58.637 33.333 13.93 13.93 0.00 2.29
1941 2053 8.752766 ACGTATAAAACCGAGGAATACATATG 57.247 34.615 0.00 0.00 0.00 1.78
1945 2057 9.066892 ACTATACGTATAAAACCGAGGAATACA 57.933 33.333 15.80 0.00 0.00 2.29
1946 2058 9.899226 AACTATACGTATAAAACCGAGGAATAC 57.101 33.333 15.80 0.00 0.00 1.89
1948 2060 9.252962 CAAACTATACGTATAAAACCGAGGAAT 57.747 33.333 15.80 0.00 0.00 3.01
1949 2061 8.465999 TCAAACTATACGTATAAAACCGAGGAA 58.534 33.333 15.80 0.00 0.00 3.36
1950 2062 7.995289 TCAAACTATACGTATAAAACCGAGGA 58.005 34.615 15.80 4.23 0.00 3.71
1951 2063 8.633075 TTCAAACTATACGTATAAAACCGAGG 57.367 34.615 15.80 4.98 0.00 4.63
1952 2064 8.264632 GCTTCAAACTATACGTATAAAACCGAG 58.735 37.037 15.80 7.15 0.00 4.63
1953 2065 7.758980 TGCTTCAAACTATACGTATAAAACCGA 59.241 33.333 15.80 6.93 0.00 4.69
1954 2066 7.897920 TGCTTCAAACTATACGTATAAAACCG 58.102 34.615 15.80 6.94 0.00 4.44
1955 2067 9.646336 CATGCTTCAAACTATACGTATAAAACC 57.354 33.333 15.80 3.17 0.00 3.27
1963 2075 7.644490 TGTTTTTCATGCTTCAAACTATACGT 58.356 30.769 0.00 0.00 31.59 3.57
1968 2080 6.707440 TCCTGTTTTTCATGCTTCAAACTA 57.293 33.333 0.00 0.00 31.59 2.24
1994 2106 9.930693 GGAATTGTAGACATAATACCTAGAAGG 57.069 37.037 0.00 0.00 42.49 3.46
2021 2133 5.472148 AGTTAATTGCATTCACACCACATG 58.528 37.500 0.00 0.00 0.00 3.21
2047 2159 6.988580 TGAATGAATACTGAACTATGCTCCAG 59.011 38.462 0.00 0.00 0.00 3.86
2089 2201 3.065925 GCAGATGGGTGCAAAAGATCTAC 59.934 47.826 0.00 0.00 43.41 2.59
2108 2220 0.739462 TATGTTTCGAGGCGTGGCAG 60.739 55.000 0.00 0.00 0.00 4.85
2109 2221 1.017177 GTATGTTTCGAGGCGTGGCA 61.017 55.000 0.00 0.00 0.00 4.92
2269 2381 0.659427 CGATGGATGCCACATGACAC 59.341 55.000 0.00 0.00 35.80 3.67
2287 2399 5.237236 AGGTAAACATTCCATATACCCCG 57.763 43.478 0.00 0.00 37.35 5.73
2320 2432 2.292828 TTTCCCCTGAAAGAAGGCAG 57.707 50.000 0.00 0.00 35.58 4.85
2466 2578 2.100916 CGTAAGGTACCCCAGATCAGTG 59.899 54.545 8.74 0.00 0.00 3.66
2553 2665 0.679640 TTGCAAGAATAGTGGGGCGG 60.680 55.000 0.00 0.00 0.00 6.13
2571 2683 1.339151 GCCCAGAAGACAGTTCCGATT 60.339 52.381 0.00 0.00 0.00 3.34
2572 2684 0.250513 GCCCAGAAGACAGTTCCGAT 59.749 55.000 0.00 0.00 0.00 4.18
2625 2737 2.352421 CCAGAATGCAACCTGCTGAAAG 60.352 50.000 11.84 0.00 45.31 2.62
2662 2774 2.425143 ATGACAATGGCAAGTCCGAT 57.575 45.000 17.35 5.94 37.80 4.18
2664 2776 1.670811 GGTATGACAATGGCAAGTCCG 59.329 52.381 17.35 0.00 37.80 4.79
2931 3043 3.328237 GTGTCGTCGTCACCAAAATTT 57.672 42.857 10.95 0.00 0.00 1.82
2953 3065 7.020827 TCTGAAGAAAACCATACCTCTCATT 57.979 36.000 0.00 0.00 0.00 2.57
3086 3285 8.871862 TGCAAGCATAATGTTTGATATGAAAAC 58.128 29.630 0.00 0.00 40.38 2.43
3088 3287 8.871862 GTTGCAAGCATAATGTTTGATATGAAA 58.128 29.630 0.00 0.00 40.38 2.69
3089 3288 8.252417 AGTTGCAAGCATAATGTTTGATATGAA 58.748 29.630 0.00 0.00 40.38 2.57
3090 3289 7.774134 AGTTGCAAGCATAATGTTTGATATGA 58.226 30.769 0.00 0.00 40.38 2.15
3091 3290 7.997107 AGTTGCAAGCATAATGTTTGATATG 57.003 32.000 0.00 0.00 40.38 1.78
3182 3381 7.917505 ACACATCAGCTTAGAAAAAGAAAACAG 59.082 33.333 0.00 0.00 0.00 3.16
3349 3548 5.699915 AGATCTTGCTGTTATCCATGAATCG 59.300 40.000 0.00 0.00 0.00 3.34
3787 4010 1.595109 CAGGAACAGCGTGACAGCA 60.595 57.895 2.68 0.00 40.15 4.41
3970 4193 1.645751 GTCTTCGCGTTGTAACCGTAG 59.354 52.381 5.77 0.00 0.00 3.51
3976 4199 2.495409 TCACAGTCTTCGCGTTGTAA 57.505 45.000 5.77 0.00 0.00 2.41
3985 4208 0.951040 CCGCCAGGTTCACAGTCTTC 60.951 60.000 0.00 0.00 0.00 2.87
4024 4247 0.461961 GCCCTCTTGAGAGTGCGTAT 59.538 55.000 7.21 0.00 40.48 3.06
4030 4253 1.346068 GTCAACAGCCCTCTTGAGAGT 59.654 52.381 7.21 0.00 40.48 3.24
4066 4289 0.178981 ACAGGCAGCACAGACCAAAT 60.179 50.000 0.00 0.00 0.00 2.32
4093 4316 0.669619 TGAACACGAAGTACAGCGGA 59.330 50.000 11.26 0.00 41.61 5.54
4105 4328 2.544359 CGGTCACGCTTGAACACG 59.456 61.111 9.13 4.16 39.75 4.49
4199 4422 6.606234 TTAACGAATACTGCAACTGAAACA 57.394 33.333 0.00 0.00 0.00 2.83
4214 4437 6.092944 TGAATCAACTAACCGCATTAACGAAT 59.907 34.615 0.00 0.00 34.06 3.34
4289 4517 5.652994 AAGGTGTACTTCTCATCTGTCTC 57.347 43.478 0.00 0.00 32.85 3.36
4333 4565 4.218635 TCATCTGTCTGAAGGTGTACTCAC 59.781 45.833 0.00 0.00 43.19 3.51
4424 4661 8.128322 TGCCATTTATTTACCTACACAATGTT 57.872 30.769 0.00 0.00 0.00 2.71
4498 4742 9.231297 CTAAAAATTCAGTTCAGGATTACAGGA 57.769 33.333 0.00 0.00 0.00 3.86
4536 4780 0.329596 AGTTCAGGATCAGGGGCAAC 59.670 55.000 0.00 0.00 0.00 4.17
4581 4830 2.060326 GTCGTCCGACTGAATGTTCA 57.940 50.000 12.31 0.00 41.57 3.18
4594 4843 3.181500 GGCAAATACAAATCCAGTCGTCC 60.181 47.826 0.00 0.00 0.00 4.79
4598 4857 3.065371 CGGAGGCAAATACAAATCCAGTC 59.935 47.826 0.00 0.00 0.00 3.51
4652 4967 6.279513 TGTTTTGGTTGTCTGAACTCAAAT 57.720 33.333 0.00 0.00 0.00 2.32
4778 5527 4.798882 ACAGTTGTACATCCTTTTTCCCA 58.201 39.130 0.00 0.00 0.00 4.37
4779 5528 5.784578 AACAGTTGTACATCCTTTTTCCC 57.215 39.130 0.00 0.00 0.00 3.97
4781 5530 6.368213 CCGTAACAGTTGTACATCCTTTTTC 58.632 40.000 0.00 0.00 0.00 2.29
4792 5541 7.603404 ACATTTGTTATAGCCGTAACAGTTGTA 59.397 33.333 17.51 3.29 43.27 2.41
4794 5543 6.837992 ACATTTGTTATAGCCGTAACAGTTG 58.162 36.000 10.33 12.82 43.27 3.16
4795 5544 7.279313 CCTACATTTGTTATAGCCGTAACAGTT 59.721 37.037 10.33 0.00 43.27 3.16
4796 5545 6.759827 CCTACATTTGTTATAGCCGTAACAGT 59.240 38.462 10.33 8.58 43.27 3.55
4797 5546 6.982141 TCCTACATTTGTTATAGCCGTAACAG 59.018 38.462 10.33 4.28 43.27 3.16
4805 5568 5.070001 TGGGCATCCTACATTTGTTATAGC 58.930 41.667 0.00 0.00 0.00 2.97
4826 5589 7.046292 TGATATTCTCCATTTGAAAGCATGG 57.954 36.000 0.00 0.00 41.39 3.66
4846 5611 7.432148 TCAATACTTAGTTCAAGGCCTGATA 57.568 36.000 5.69 0.00 38.70 2.15
4847 5612 6.313519 TCAATACTTAGTTCAAGGCCTGAT 57.686 37.500 5.69 0.00 38.70 2.90
4855 5620 5.709631 TGCATGCCTTCAATACTTAGTTCAA 59.290 36.000 16.68 0.00 0.00 2.69
4864 5629 1.678101 GGTCCTGCATGCCTTCAATAC 59.322 52.381 16.68 3.71 0.00 1.89
4866 5631 0.040058 TGGTCCTGCATGCCTTCAAT 59.960 50.000 16.68 0.00 0.00 2.57
4943 5742 4.958581 TCATCTGCCTGAAGTAGAGAATGA 59.041 41.667 0.00 0.00 40.87 2.57
4988 6556 8.593945 TGCCATTTCTTCATCTACCTAAAATT 57.406 30.769 0.00 0.00 0.00 1.82
4990 6558 7.093945 GGTTGCCATTTCTTCATCTACCTAAAA 60.094 37.037 0.00 0.00 0.00 1.52
4991 6559 6.377146 GGTTGCCATTTCTTCATCTACCTAAA 59.623 38.462 0.00 0.00 0.00 1.85
4994 6562 4.263905 TGGTTGCCATTTCTTCATCTACCT 60.264 41.667 0.00 0.00 0.00 3.08
4995 6563 4.016444 TGGTTGCCATTTCTTCATCTACC 58.984 43.478 0.00 0.00 0.00 3.18
5038 7344 5.720041 ACTACACTGATCCTAAGCAGGTTTA 59.280 40.000 0.00 0.00 43.33 2.01
5039 7345 4.532521 ACTACACTGATCCTAAGCAGGTTT 59.467 41.667 0.00 0.00 43.33 3.27
5040 7346 4.097418 ACTACACTGATCCTAAGCAGGTT 58.903 43.478 0.00 0.00 43.33 3.50
5041 7347 3.714144 ACTACACTGATCCTAAGCAGGT 58.286 45.455 0.00 0.00 43.33 4.00
5042 7348 4.744795 AACTACACTGATCCTAAGCAGG 57.255 45.455 0.00 0.00 43.33 4.85
5043 7349 5.349817 CACAAACTACACTGATCCTAAGCAG 59.650 44.000 0.00 0.00 44.61 4.24
5044 7350 5.237815 CACAAACTACACTGATCCTAAGCA 58.762 41.667 0.00 0.00 0.00 3.91
5045 7351 4.631813 CCACAAACTACACTGATCCTAAGC 59.368 45.833 0.00 0.00 0.00 3.09
5046 7352 5.178797 CCCACAAACTACACTGATCCTAAG 58.821 45.833 0.00 0.00 0.00 2.18
5047 7353 4.019681 CCCCACAAACTACACTGATCCTAA 60.020 45.833 0.00 0.00 0.00 2.69
5117 7423 8.820153 AGCTCTGAAAAGAAATGATTATCCTT 57.180 30.769 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.