Multiple sequence alignment - TraesCS6B01G181100

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 TraesCS6B01G181100 chr6B 100.000 3159 0 0 1 3159 202508588 202511746 0.000000e+00 5834.0
1 TraesCS6B01G181100 chr6B 84.375 96 13 2 2893 2987 169482054 169481960 3.350000e-15 93.5
2 TraesCS6B01G181100 chr6D 91.701 964 43 10 1291 2244 112953957 112954893 0.000000e+00 1303.0
3 TraesCS6B01G181100 chr6D 95.079 569 17 6 727 1288 112952984 112953548 0.000000e+00 885.0
4 TraesCS6B01G181100 chr6D 93.092 579 11 8 2240 2792 112954924 112955499 0.000000e+00 821.0
5 TraesCS6B01G181100 chr6D 87.857 280 32 2 452 731 464990267 464990544 8.450000e-86 327.0
6 TraesCS6B01G181100 chr6D 88.889 261 23 6 73 330 464989952 464990209 1.830000e-82 316.0
7 TraesCS6B01G181100 chr6D 91.667 108 2 3 2976 3078 112958817 112958922 3.280000e-30 143.0
8 TraesCS6B01G181100 chr6D 94.118 51 1 1 2810 2860 112955568 112955616 3.380000e-10 76.8
9 TraesCS6B01G181100 chr6D 97.222 36 0 1 2893 2927 138401510 138401475 3.400000e-05 60.2
10 TraesCS6B01G181100 chr6A 92.308 832 34 4 1419 2244 140723985 140724792 0.000000e+00 1155.0
11 TraesCS6B01G181100 chr6A 94.853 680 31 3 747 1422 140723279 140723958 0.000000e+00 1059.0
12 TraesCS6B01G181100 chr6A 92.486 346 16 6 2240 2581 140724823 140725162 1.320000e-133 486.0
13 TraesCS6B01G181100 chr6A 89.916 119 10 1 2573 2691 140730253 140730369 5.460000e-33 152.0
14 TraesCS6B01G181100 chr6A 90.566 53 1 4 2893 2942 35922049 35921998 2.030000e-07 67.6
15 TraesCS6B01G181100 chr3B 94.895 666 25 2 67 732 630296236 630295580 0.000000e+00 1033.0
16 TraesCS6B01G181100 chr3B 83.660 153 19 6 582 731 657370535 657370386 4.250000e-29 139.0
17 TraesCS6B01G181100 chr3B 88.506 87 8 2 2893 2978 270949126 270949041 1.550000e-18 104.0
18 TraesCS6B01G181100 chr5A 91.031 669 42 2 67 735 559063376 559062726 0.000000e+00 887.0
19 TraesCS6B01G181100 chr5A 89.763 674 52 4 67 732 24190475 24191139 0.000000e+00 846.0
20 TraesCS6B01G181100 chr5A 83.030 495 63 8 239 732 527924227 527923753 2.250000e-116 429.0
21 TraesCS6B01G181100 chr2B 87.275 668 50 10 67 731 652819506 652820141 0.000000e+00 730.0
22 TraesCS6B01G181100 chr2B 85.057 87 11 2 2893 2978 725613433 725613348 1.560000e-13 87.9
23 TraesCS6B01G181100 chr3A 82.414 671 95 13 73 739 672072254 672071603 5.920000e-157 564.0
24 TraesCS6B01G181100 chr3A 87.143 70 5 4 2896 2963 490779170 490779103 3.380000e-10 76.8
25 TraesCS6B01G181100 chr7D 92.857 322 16 1 67 381 269033846 269034167 7.980000e-126 460.0
26 TraesCS6B01G181100 chr7D 85.644 202 26 1 997 1195 590429089 590429290 3.190000e-50 209.0
27 TraesCS6B01G181100 chr7D 81.690 142 25 1 2021 2161 590430153 590430294 1.990000e-22 117.0
28 TraesCS6B01G181100 chr4A 82.051 273 44 5 164 433 576569739 576569469 8.810000e-56 228.0
29 TraesCS6B01G181100 chr4A 83.721 172 23 5 575 744 576570002 576570170 1.170000e-34 158.0
30 TraesCS6B01G181100 chr7B 86.598 194 22 2 991 1180 665413896 665414089 8.880000e-51 211.0
31 TraesCS6B01G181100 chr7B 84.848 99 12 1 997 1092 665410687 665410785 2.590000e-16 97.1
32 TraesCS6B01G181100 chr2D 93.913 115 6 1 67 181 314042352 314042465 4.190000e-39 172.0
33 TraesCS6B01G181100 chr3D 87.500 72 7 2 2893 2963 75961193 75961123 7.260000e-12 82.4
34 TraesCS6B01G181100 chr5D 86.567 67 9 0 2897 2963 113381075 113381009 1.220000e-09 75.0
35 TraesCS6B01G181100 chr5B 97.368 38 1 0 2897 2934 234087943 234087906 7.310000e-07 65.8


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 TraesCS6B01G181100 chr6B 202508588 202511746 3158 False 5834.00 5834 100.000000 1 3159 1 chr6B.!!$F1 3158
1 TraesCS6B01G181100 chr6D 112952984 112958922 5938 False 645.76 1303 93.131400 727 3078 5 chr6D.!!$F1 2351
2 TraesCS6B01G181100 chr6D 464989952 464990544 592 False 321.50 327 88.373000 73 731 2 chr6D.!!$F2 658
3 TraesCS6B01G181100 chr6A 140723279 140725162 1883 False 900.00 1155 93.215667 747 2581 3 chr6A.!!$F2 1834
4 TraesCS6B01G181100 chr3B 630295580 630296236 656 True 1033.00 1033 94.895000 67 732 1 chr3B.!!$R2 665
5 TraesCS6B01G181100 chr5A 559062726 559063376 650 True 887.00 887 91.031000 67 735 1 chr5A.!!$R2 668
6 TraesCS6B01G181100 chr5A 24190475 24191139 664 False 846.00 846 89.763000 67 732 1 chr5A.!!$F1 665
7 TraesCS6B01G181100 chr2B 652819506 652820141 635 False 730.00 730 87.275000 67 731 1 chr2B.!!$F1 664
8 TraesCS6B01G181100 chr3A 672071603 672072254 651 True 564.00 564 82.414000 73 739 1 chr3A.!!$R2 666

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
28 29 0.097325 GTCGCTCTAGTCTGTGACCG 59.903 60.0 12.37 0.00 37.63 4.79 F
61 62 0.248907 CATCCTCGTCGTGCGGTTAT 60.249 55.0 0.00 0.00 41.72 1.89 F
62 63 0.458669 ATCCTCGTCGTGCGGTTATT 59.541 50.0 0.00 0.00 41.72 1.40 F
801 816 0.531974 GGAATTGTAGCCCATCGCGA 60.532 55.0 13.09 13.09 44.76 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 1236 0.541863 GAAAATGGAGGCGGAGAGGA 59.458 55.000 0.0 0.0 0.00 3.71 R
1674 2141 1.208052 TCCATAGTTCTCACTGCTGGC 59.792 52.381 0.0 0.0 37.20 4.85 R
1929 2402 2.696506 TCATGAGTGCTGCTGAAAGAG 58.303 47.619 0.0 0.0 34.07 2.85 R
2724 3238 0.176680 GAGTGGTGATGTGCTCGGAT 59.823 55.000 0.0 0.0 0.00 4.18 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
17 18 3.449227 CCACCGGCTGTCGCTCTA 61.449 66.667 0.00 0.00 37.59 2.43
18 19 2.103143 CACCGGCTGTCGCTCTAG 59.897 66.667 0.00 0.00 37.59 2.43
19 20 2.361357 ACCGGCTGTCGCTCTAGT 60.361 61.111 0.00 0.00 37.59 2.57
20 21 2.408241 ACCGGCTGTCGCTCTAGTC 61.408 63.158 0.00 0.00 37.59 2.59
21 22 2.115911 CCGGCTGTCGCTCTAGTCT 61.116 63.158 0.00 0.00 37.59 3.24
22 23 1.063327 CGGCTGTCGCTCTAGTCTG 59.937 63.158 0.00 0.00 36.09 3.51
23 24 1.649390 CGGCTGTCGCTCTAGTCTGT 61.649 60.000 0.00 0.00 36.09 3.41
24 25 0.179150 GGCTGTCGCTCTAGTCTGTG 60.179 60.000 0.00 0.00 36.09 3.66
25 26 0.805614 GCTGTCGCTCTAGTCTGTGA 59.194 55.000 0.00 0.00 0.00 3.58
26 27 1.466697 GCTGTCGCTCTAGTCTGTGAC 60.467 57.143 14.85 14.85 42.16 3.67
27 28 1.131504 CTGTCGCTCTAGTCTGTGACC 59.868 57.143 17.22 6.76 41.42 4.02
28 29 0.097325 GTCGCTCTAGTCTGTGACCG 59.903 60.000 12.37 0.00 37.63 4.79
29 30 1.226435 CGCTCTAGTCTGTGACCGC 60.226 63.158 0.00 0.00 32.18 5.68
30 31 1.226435 GCTCTAGTCTGTGACCGCG 60.226 63.158 0.00 0.00 32.18 6.46
31 32 1.429825 CTCTAGTCTGTGACCGCGG 59.570 63.158 26.86 26.86 32.18 6.46
32 33 1.994507 CTCTAGTCTGTGACCGCGGG 61.995 65.000 31.76 11.50 32.18 6.13
33 34 2.282674 TAGTCTGTGACCGCGGGT 60.283 61.111 31.76 15.52 39.44 5.28
34 35 1.002257 TAGTCTGTGACCGCGGGTA 60.002 57.895 31.76 15.42 35.25 3.69
35 36 1.028330 TAGTCTGTGACCGCGGGTAG 61.028 60.000 31.76 20.39 35.25 3.18
36 37 3.066190 TCTGTGACCGCGGGTAGG 61.066 66.667 31.76 15.06 35.25 3.18
37 38 4.814294 CTGTGACCGCGGGTAGGC 62.814 72.222 31.76 14.77 35.25 3.93
45 46 4.971125 GCGGGTAGGCGGCTCATC 62.971 72.222 17.67 7.51 0.00 2.92
46 47 4.301027 CGGGTAGGCGGCTCATCC 62.301 72.222 17.67 16.46 0.00 3.51
47 48 2.844839 GGGTAGGCGGCTCATCCT 60.845 66.667 17.67 0.00 36.51 3.24
48 49 2.737830 GGTAGGCGGCTCATCCTC 59.262 66.667 17.67 0.17 34.02 3.71
49 50 2.336809 GTAGGCGGCTCATCCTCG 59.663 66.667 17.67 0.00 34.02 4.63
50 51 2.123854 TAGGCGGCTCATCCTCGT 60.124 61.111 17.67 0.00 34.02 4.18
51 52 2.194212 TAGGCGGCTCATCCTCGTC 61.194 63.158 17.67 0.00 34.02 4.20
52 53 4.933064 GGCGGCTCATCCTCGTCG 62.933 72.222 0.00 0.00 0.00 5.12
53 54 4.194720 GCGGCTCATCCTCGTCGT 62.195 66.667 0.00 0.00 0.00 4.34
54 55 2.278206 CGGCTCATCCTCGTCGTG 60.278 66.667 0.00 0.00 0.00 4.35
55 56 2.583593 GGCTCATCCTCGTCGTGC 60.584 66.667 0.00 0.00 0.00 5.34
56 57 2.951745 GCTCATCCTCGTCGTGCG 60.952 66.667 0.00 0.00 43.01 5.34
57 58 2.278206 CTCATCCTCGTCGTGCGG 60.278 66.667 0.00 0.00 41.72 5.69
58 59 3.052620 CTCATCCTCGTCGTGCGGT 62.053 63.158 0.00 0.00 41.72 5.68
59 60 2.126071 CATCCTCGTCGTGCGGTT 60.126 61.111 0.00 0.00 41.72 4.44
60 61 1.138036 CATCCTCGTCGTGCGGTTA 59.862 57.895 0.00 0.00 41.72 2.85
61 62 0.248907 CATCCTCGTCGTGCGGTTAT 60.249 55.000 0.00 0.00 41.72 1.89
62 63 0.458669 ATCCTCGTCGTGCGGTTATT 59.541 50.000 0.00 0.00 41.72 1.40
63 64 1.093972 TCCTCGTCGTGCGGTTATTA 58.906 50.000 0.00 0.00 41.72 0.98
64 65 1.472082 TCCTCGTCGTGCGGTTATTAA 59.528 47.619 0.00 0.00 41.72 1.40
65 66 2.094803 TCCTCGTCGTGCGGTTATTAAA 60.095 45.455 0.00 0.00 41.72 1.52
288 294 2.902484 GACTCGCACAAATTACTTTGCG 59.098 45.455 8.46 8.46 44.63 4.85
347 353 1.451504 CAGTGTGGCTCAAGGTGGA 59.548 57.895 0.00 0.00 0.00 4.02
444 451 0.838122 AGAGGGTGTCAGAAGGGTGG 60.838 60.000 0.00 0.00 0.00 4.61
445 452 1.842381 GAGGGTGTCAGAAGGGTGGG 61.842 65.000 0.00 0.00 0.00 4.61
446 453 2.757077 GGTGTCAGAAGGGTGGGG 59.243 66.667 0.00 0.00 0.00 4.96
447 454 2.757077 GTGTCAGAAGGGTGGGGG 59.243 66.667 0.00 0.00 0.00 5.40
448 455 3.256960 TGTCAGAAGGGTGGGGGC 61.257 66.667 0.00 0.00 0.00 5.80
449 456 4.048470 GTCAGAAGGGTGGGGGCC 62.048 72.222 0.00 0.00 0.00 5.80
450 457 4.285790 TCAGAAGGGTGGGGGCCT 62.286 66.667 0.84 0.00 0.00 5.19
451 458 4.052518 CAGAAGGGTGGGGGCCTG 62.053 72.222 0.84 0.00 0.00 4.85
622 629 8.747538 AATTATAACAAAATCGCTCTAGGGTT 57.252 30.769 0.00 0.00 0.00 4.11
664 672 9.753674 TGAGAATTTCAGGGTTAAAATCATACT 57.246 29.630 0.00 0.00 0.00 2.12
732 747 7.043961 AGGGTGAAAAATGAACTTCTTTCTC 57.956 36.000 0.00 0.00 34.97 2.87
735 750 7.230712 GGGTGAAAAATGAACTTCTTTCTCCTA 59.769 37.037 15.63 0.00 39.60 2.94
736 751 8.797438 GGTGAAAAATGAACTTCTTTCTCCTAT 58.203 33.333 11.94 0.00 37.96 2.57
801 816 0.531974 GGAATTGTAGCCCATCGCGA 60.532 55.000 13.09 13.09 44.76 5.87
849 864 4.467084 GCGCTCCCGTCCAATCCA 62.467 66.667 0.00 0.00 36.67 3.41
898 919 2.031120 CCAAGCCGATCTCTCTTCTCT 58.969 52.381 0.00 0.00 0.00 3.10
901 924 0.591170 GCCGATCTCTCTTCTCTCCG 59.409 60.000 0.00 0.00 0.00 4.63
907 930 1.662438 CTCTCTTCTCTCCGGCGCTT 61.662 60.000 7.64 0.00 0.00 4.68
916 939 2.125147 CCGGCGCTTCATCTTCCA 60.125 61.111 7.64 0.00 0.00 3.53
917 940 2.176273 CCGGCGCTTCATCTTCCAG 61.176 63.158 7.64 0.00 0.00 3.86
1250 1274 7.255730 CCATTTTCTTCTTTCCCTATATGCCTG 60.256 40.741 0.00 0.00 0.00 4.85
1306 1736 7.885297 TGAAGTTGCTGCAATTTTCTAACTAT 58.115 30.769 27.41 7.90 0.00 2.12
1329 1759 9.352784 CTATTGCTGTATGAGTATCTTAAGAGC 57.647 37.037 11.53 6.53 35.12 4.09
1330 1760 6.968263 TGCTGTATGAGTATCTTAAGAGCT 57.032 37.500 11.53 11.17 35.36 4.09
1331 1761 8.465273 TTGCTGTATGAGTATCTTAAGAGCTA 57.535 34.615 11.53 0.00 35.36 3.32
1451 1918 1.807142 GTAGCAGTTGTTTGGGAGCTC 59.193 52.381 4.71 4.71 33.83 4.09
1466 1933 3.191791 GGGAGCTCGATAGGTGACTTATC 59.808 52.174 7.83 4.78 43.67 1.75
1470 1937 6.461788 GGAGCTCGATAGGTGACTTATCTTTT 60.462 42.308 7.83 0.00 43.67 2.27
1537 2004 5.598416 GCATTTGTAAGGCCTTAGGAAAT 57.402 39.130 25.83 25.04 30.71 2.17
1538 2005 5.977635 GCATTTGTAAGGCCTTAGGAAATT 58.022 37.500 25.83 13.11 30.71 1.82
1541 2008 8.038351 GCATTTGTAAGGCCTTAGGAAATTTTA 58.962 33.333 25.83 6.71 30.71 1.52
1579 2046 2.479560 GCTTGCGTTTTGTGAGGTTTCT 60.480 45.455 0.00 0.00 0.00 2.52
1580 2047 3.242936 GCTTGCGTTTTGTGAGGTTTCTA 60.243 43.478 0.00 0.00 0.00 2.10
1581 2048 4.527564 CTTGCGTTTTGTGAGGTTTCTAG 58.472 43.478 0.00 0.00 0.00 2.43
1582 2049 3.537580 TGCGTTTTGTGAGGTTTCTAGT 58.462 40.909 0.00 0.00 0.00 2.57
1583 2050 3.942748 TGCGTTTTGTGAGGTTTCTAGTT 59.057 39.130 0.00 0.00 0.00 2.24
1584 2051 4.201871 TGCGTTTTGTGAGGTTTCTAGTTG 60.202 41.667 0.00 0.00 0.00 3.16
1585 2052 4.279659 CGTTTTGTGAGGTTTCTAGTTGC 58.720 43.478 0.00 0.00 0.00 4.17
1586 2053 4.279659 GTTTTGTGAGGTTTCTAGTTGCG 58.720 43.478 0.00 0.00 0.00 4.85
1587 2054 2.902705 TGTGAGGTTTCTAGTTGCGT 57.097 45.000 0.00 0.00 0.00 5.24
1588 2055 3.188159 TGTGAGGTTTCTAGTTGCGTT 57.812 42.857 0.00 0.00 0.00 4.84
1589 2056 3.537580 TGTGAGGTTTCTAGTTGCGTTT 58.462 40.909 0.00 0.00 0.00 3.60
1590 2057 3.942748 TGTGAGGTTTCTAGTTGCGTTTT 59.057 39.130 0.00 0.00 0.00 2.43
1591 2058 4.201871 TGTGAGGTTTCTAGTTGCGTTTTG 60.202 41.667 0.00 0.00 0.00 2.44
1592 2059 3.942748 TGAGGTTTCTAGTTGCGTTTTGT 59.057 39.130 0.00 0.00 0.00 2.83
1593 2060 4.201871 TGAGGTTTCTAGTTGCGTTTTGTG 60.202 41.667 0.00 0.00 0.00 3.33
1594 2061 3.942748 AGGTTTCTAGTTGCGTTTTGTGA 59.057 39.130 0.00 0.00 0.00 3.58
1595 2062 4.035208 AGGTTTCTAGTTGCGTTTTGTGAG 59.965 41.667 0.00 0.00 0.00 3.51
1596 2063 4.279659 GTTTCTAGTTGCGTTTTGTGAGG 58.720 43.478 0.00 0.00 0.00 3.86
1597 2064 3.188159 TCTAGTTGCGTTTTGTGAGGT 57.812 42.857 0.00 0.00 0.00 3.85
1598 2065 3.537580 TCTAGTTGCGTTTTGTGAGGTT 58.462 40.909 0.00 0.00 0.00 3.50
1599 2066 3.942748 TCTAGTTGCGTTTTGTGAGGTTT 59.057 39.130 0.00 0.00 0.00 3.27
1600 2067 3.586100 AGTTGCGTTTTGTGAGGTTTT 57.414 38.095 0.00 0.00 0.00 2.43
1614 2081 4.581409 GTGAGGTTTTTAGTACTTTGGGCA 59.419 41.667 0.00 0.00 0.00 5.36
1664 2131 4.083855 CGCACAATGTTCATAGTGAAGTGT 60.084 41.667 0.00 5.34 37.00 3.55
1670 2137 5.290493 TGTTCATAGTGAAGTGTTCCAGT 57.710 39.130 0.00 0.00 37.00 4.00
1674 2141 7.441157 TGTTCATAGTGAAGTGTTCCAGTAAAG 59.559 37.037 0.00 0.00 37.00 1.85
1691 2158 3.710209 AAAGCCAGCAGTGAGAACTAT 57.290 42.857 0.00 0.00 0.00 2.12
1908 2381 3.633525 TGCTTGCACTTTGACTCTCATTT 59.366 39.130 0.00 0.00 0.00 2.32
1938 2411 5.450137 ATTGATGCAATACAGCTCTTTCAGC 60.450 40.000 0.00 0.00 39.29 4.26
1951 2424 3.682696 TCTTTCAGCAGCACTCATGAAT 58.317 40.909 0.00 0.00 32.13 2.57
2027 2501 9.121517 CTTACTCAAACATCTGCAACTATTTTG 57.878 33.333 0.00 0.00 0.00 2.44
2193 2667 1.046204 AAACTCGTTCGGGTCCTTCT 58.954 50.000 0.00 0.00 0.00 2.85
2469 2983 6.886459 TCTCTTTAGCAATCTATGTGCCTTTT 59.114 34.615 0.00 0.00 43.27 2.27
2490 3004 5.459536 TTCATCTCATCCGAGTAAGATGG 57.540 43.478 10.38 1.59 43.36 3.51
2600 3114 1.785041 TTTGCTCAGCTCAACACCGC 61.785 55.000 0.00 0.00 0.00 5.68
2638 3152 8.527810 GTGTTATTCCATTCATTTTTGTCCCTA 58.472 33.333 0.00 0.00 0.00 3.53
2642 3156 6.985653 TCCATTCATTTTTGTCCCTAAACA 57.014 33.333 0.00 0.00 0.00 2.83
2643 3157 7.366847 TCCATTCATTTTTGTCCCTAAACAA 57.633 32.000 0.00 0.00 37.37 2.83
2647 3161 8.764287 CATTCATTTTTGTCCCTAAACAAAGTC 58.236 33.333 2.85 0.00 46.56 3.01
2653 3167 5.033589 TGTCCCTAAACAAAGTCGGTTAA 57.966 39.130 0.00 0.00 0.00 2.01
2660 3174 4.640789 AACAAAGTCGGTTAATGCACAA 57.359 36.364 0.00 0.00 0.00 3.33
2669 3183 4.094294 TCGGTTAATGCACAATTAGAGCAC 59.906 41.667 0.00 0.00 46.51 4.40
2713 3227 4.005650 TCTTCAGCCTTTGATGCTACAAG 58.994 43.478 0.00 0.00 36.81 3.16
2716 3230 3.054139 TCAGCCTTTGATGCTACAAGGAT 60.054 43.478 1.21 0.00 36.81 3.24
2719 3233 5.357878 CAGCCTTTGATGCTACAAGGATTTA 59.642 40.000 1.21 0.00 36.81 1.40
2720 3234 6.040166 CAGCCTTTGATGCTACAAGGATTTAT 59.960 38.462 1.21 0.00 36.81 1.40
2721 3235 6.264067 AGCCTTTGATGCTACAAGGATTTATC 59.736 38.462 1.21 0.00 37.28 1.75
2722 3236 6.264067 GCCTTTGATGCTACAAGGATTTATCT 59.736 38.462 1.21 0.00 0.00 1.98
2723 3237 7.201857 GCCTTTGATGCTACAAGGATTTATCTT 60.202 37.037 1.21 0.00 0.00 2.40
2724 3238 9.342308 CCTTTGATGCTACAAGGATTTATCTTA 57.658 33.333 7.01 0.00 0.00 2.10
2838 3429 4.408921 TCTGTGGGTTCAAAAAGAGAGAGA 59.591 41.667 0.00 0.00 0.00 3.10
2839 3430 4.708177 TGTGGGTTCAAAAAGAGAGAGAG 58.292 43.478 0.00 0.00 0.00 3.20
2913 4262 9.921637 TTACATCCCAAAATAAATGTCTCAAAC 57.078 29.630 0.00 0.00 34.39 2.93
2967 5165 8.141909 ACAAAGTTAAGACATTTCTTTTAGGGC 58.858 33.333 0.00 0.00 39.17 5.19
2970 5168 3.713826 AGACATTTCTTTTAGGGCGGA 57.286 42.857 0.00 0.00 0.00 5.54
2972 5170 2.683362 GACATTTCTTTTAGGGCGGAGG 59.317 50.000 0.00 0.00 0.00 4.30
2974 5172 1.364269 TTTCTTTTAGGGCGGAGGGA 58.636 50.000 0.00 0.00 0.00 4.20
3001 6682 9.635520 GTAGTACTAAAACTGTCAAGCTATTGA 57.364 33.333 3.61 0.00 43.20 2.57
3031 6712 9.640952 ACACCATTAGCCTTATTGTAACAATAT 57.359 29.630 0.00 0.00 0.00 1.28
3049 6730 6.697395 ACAATATTTTAAACAGCACCTTCCC 58.303 36.000 0.00 0.00 0.00 3.97
3073 6754 5.572511 CGATCATAGTAGATTGCTTCTGCTC 59.427 44.000 10.21 0.00 43.11 4.26
3077 6758 7.105588 TCATAGTAGATTGCTTCTGCTCAAAA 58.894 34.615 10.21 0.00 43.11 2.44
3078 6759 7.607607 TCATAGTAGATTGCTTCTGCTCAAAAA 59.392 33.333 10.21 0.00 43.11 1.94
3079 6760 6.830873 AGTAGATTGCTTCTGCTCAAAAAT 57.169 33.333 2.82 0.00 43.11 1.82
3080 6761 7.928307 AGTAGATTGCTTCTGCTCAAAAATA 57.072 32.000 2.82 0.00 43.11 1.40
3081 6762 8.340618 AGTAGATTGCTTCTGCTCAAAAATAA 57.659 30.769 2.82 0.00 43.11 1.40
3082 6763 8.239998 AGTAGATTGCTTCTGCTCAAAAATAAC 58.760 33.333 2.82 0.00 43.11 1.89
3083 6764 6.985117 AGATTGCTTCTGCTCAAAAATAACA 58.015 32.000 0.00 0.00 40.48 2.41
3084 6765 6.865205 AGATTGCTTCTGCTCAAAAATAACAC 59.135 34.615 0.00 0.00 40.48 3.32
3085 6766 5.772825 TGCTTCTGCTCAAAAATAACACT 57.227 34.783 0.00 0.00 40.48 3.55
3086 6767 5.522456 TGCTTCTGCTCAAAAATAACACTG 58.478 37.500 0.00 0.00 40.48 3.66
3087 6768 4.383948 GCTTCTGCTCAAAAATAACACTGC 59.616 41.667 0.00 0.00 36.03 4.40
3088 6769 4.503741 TCTGCTCAAAAATAACACTGCC 57.496 40.909 0.00 0.00 0.00 4.85
3089 6770 3.255642 TCTGCTCAAAAATAACACTGCCC 59.744 43.478 0.00 0.00 0.00 5.36
3090 6771 2.961741 TGCTCAAAAATAACACTGCCCA 59.038 40.909 0.00 0.00 0.00 5.36
3091 6772 3.005684 TGCTCAAAAATAACACTGCCCAG 59.994 43.478 0.00 0.00 0.00 4.45
3092 6773 3.614870 GCTCAAAAATAACACTGCCCAGG 60.615 47.826 0.00 0.00 0.00 4.45
3093 6774 3.571590 TCAAAAATAACACTGCCCAGGT 58.428 40.909 0.00 0.00 0.00 4.00
3094 6775 3.320541 TCAAAAATAACACTGCCCAGGTG 59.679 43.478 0.00 0.00 40.19 4.00
3095 6776 1.256812 AAATAACACTGCCCAGGTGC 58.743 50.000 0.00 0.00 38.14 5.01
3096 6777 0.405585 AATAACACTGCCCAGGTGCT 59.594 50.000 0.00 0.00 38.14 4.40
3097 6778 0.405585 ATAACACTGCCCAGGTGCTT 59.594 50.000 0.00 0.00 38.14 3.91
3098 6779 0.184933 TAACACTGCCCAGGTGCTTT 59.815 50.000 0.00 0.00 38.14 3.51
3099 6780 1.109323 AACACTGCCCAGGTGCTTTC 61.109 55.000 0.00 0.00 38.14 2.62
3100 6781 2.281761 ACTGCCCAGGTGCTTTCG 60.282 61.111 0.00 0.00 0.00 3.46
3101 6782 3.058160 CTGCCCAGGTGCTTTCGG 61.058 66.667 2.06 0.00 0.00 4.30
3102 6783 3.850098 CTGCCCAGGTGCTTTCGGT 62.850 63.158 2.06 0.00 0.00 4.69
3103 6784 3.365265 GCCCAGGTGCTTTCGGTG 61.365 66.667 0.00 0.00 0.00 4.94
3104 6785 2.113139 CCCAGGTGCTTTCGGTGT 59.887 61.111 0.00 0.00 0.00 4.16
3105 6786 1.528309 CCCAGGTGCTTTCGGTGTT 60.528 57.895 0.00 0.00 0.00 3.32
3106 6787 1.515521 CCCAGGTGCTTTCGGTGTTC 61.516 60.000 0.00 0.00 0.00 3.18
3107 6788 1.515521 CCAGGTGCTTTCGGTGTTCC 61.516 60.000 0.00 0.00 0.00 3.62
3108 6789 0.817634 CAGGTGCTTTCGGTGTTCCA 60.818 55.000 0.00 0.00 0.00 3.53
3109 6790 0.110486 AGGTGCTTTCGGTGTTCCAT 59.890 50.000 0.00 0.00 0.00 3.41
3110 6791 0.240945 GGTGCTTTCGGTGTTCCATG 59.759 55.000 0.00 0.00 0.00 3.66
3111 6792 0.240945 GTGCTTTCGGTGTTCCATGG 59.759 55.000 4.97 4.97 0.00 3.66
3112 6793 0.179004 TGCTTTCGGTGTTCCATGGT 60.179 50.000 12.58 0.00 0.00 3.55
3113 6794 0.958822 GCTTTCGGTGTTCCATGGTT 59.041 50.000 12.58 0.00 0.00 3.67
3114 6795 1.335872 GCTTTCGGTGTTCCATGGTTG 60.336 52.381 12.58 0.00 0.00 3.77
3115 6796 2.226330 CTTTCGGTGTTCCATGGTTGA 58.774 47.619 12.58 0.00 0.00 3.18
3116 6797 2.350057 TTCGGTGTTCCATGGTTGAA 57.650 45.000 12.58 5.44 0.00 2.69
3117 6798 1.600023 TCGGTGTTCCATGGTTGAAC 58.400 50.000 12.58 9.71 41.91 3.18
3118 6799 1.142060 TCGGTGTTCCATGGTTGAACT 59.858 47.619 12.58 0.00 42.04 3.01
3119 6800 1.953686 CGGTGTTCCATGGTTGAACTT 59.046 47.619 12.58 0.00 42.04 2.66
3120 6801 2.031157 CGGTGTTCCATGGTTGAACTTC 60.031 50.000 12.58 6.79 42.04 3.01
3121 6802 2.296190 GGTGTTCCATGGTTGAACTTCC 59.704 50.000 12.58 11.51 42.04 3.46
3122 6803 2.296190 GTGTTCCATGGTTGAACTTCCC 59.704 50.000 12.58 0.00 42.04 3.97
3123 6804 2.176798 TGTTCCATGGTTGAACTTCCCT 59.823 45.455 12.58 0.00 42.04 4.20
3124 6805 2.558359 GTTCCATGGTTGAACTTCCCTG 59.442 50.000 12.58 0.00 39.18 4.45
3125 6806 0.890683 CCATGGTTGAACTTCCCTGC 59.109 55.000 2.57 0.00 0.00 4.85
3126 6807 1.548582 CCATGGTTGAACTTCCCTGCT 60.549 52.381 2.57 0.00 0.00 4.24
3127 6808 2.290896 CCATGGTTGAACTTCCCTGCTA 60.291 50.000 2.57 0.00 0.00 3.49
3128 6809 2.561478 TGGTTGAACTTCCCTGCTAC 57.439 50.000 0.00 0.00 0.00 3.58
3129 6810 1.073284 TGGTTGAACTTCCCTGCTACC 59.927 52.381 0.00 0.00 0.00 3.18
3130 6811 1.439679 GTTGAACTTCCCTGCTACCG 58.560 55.000 0.00 0.00 0.00 4.02
3131 6812 0.323629 TTGAACTTCCCTGCTACCGG 59.676 55.000 0.00 0.00 0.00 5.28
3132 6813 0.543410 TGAACTTCCCTGCTACCGGA 60.543 55.000 9.46 0.00 0.00 5.14
3133 6814 0.831307 GAACTTCCCTGCTACCGGAT 59.169 55.000 9.46 0.00 0.00 4.18
3134 6815 0.541863 AACTTCCCTGCTACCGGATG 59.458 55.000 9.46 0.23 0.00 3.51
3135 6816 0.325296 ACTTCCCTGCTACCGGATGA 60.325 55.000 9.46 0.00 0.00 2.92
3136 6817 1.051812 CTTCCCTGCTACCGGATGAT 58.948 55.000 9.46 0.00 0.00 2.45
3137 6818 1.001406 CTTCCCTGCTACCGGATGATC 59.999 57.143 9.46 0.00 0.00 2.92
3138 6819 0.105709 TCCCTGCTACCGGATGATCA 60.106 55.000 9.46 0.00 0.00 2.92
3139 6820 0.319728 CCCTGCTACCGGATGATCAG 59.680 60.000 9.46 7.68 0.00 2.90
3140 6821 1.332195 CCTGCTACCGGATGATCAGA 58.668 55.000 9.46 0.00 0.00 3.27
3141 6822 1.000283 CCTGCTACCGGATGATCAGAC 60.000 57.143 9.46 0.00 0.00 3.51
3142 6823 0.668535 TGCTACCGGATGATCAGACG 59.331 55.000 9.46 13.19 0.00 4.18
3143 6824 0.952280 GCTACCGGATGATCAGACGA 59.048 55.000 19.67 3.91 0.00 4.20
3144 6825 1.542030 GCTACCGGATGATCAGACGAT 59.458 52.381 19.67 8.39 33.31 3.73
3145 6826 2.029828 GCTACCGGATGATCAGACGATT 60.030 50.000 19.67 10.69 29.66 3.34
3146 6827 2.515926 ACCGGATGATCAGACGATTG 57.484 50.000 19.67 8.56 29.66 2.67
3147 6828 1.143305 CCGGATGATCAGACGATTGC 58.857 55.000 19.67 0.00 29.66 3.56
3148 6829 1.538849 CCGGATGATCAGACGATTGCA 60.539 52.381 19.67 0.00 29.66 4.08
3149 6830 2.410939 CGGATGATCAGACGATTGCAT 58.589 47.619 14.56 0.00 29.66 3.96
3150 6831 2.157085 CGGATGATCAGACGATTGCATG 59.843 50.000 14.56 0.00 29.66 4.06
3151 6832 3.396560 GGATGATCAGACGATTGCATGA 58.603 45.455 0.09 0.00 29.66 3.07
3152 6833 3.811497 GGATGATCAGACGATTGCATGAA 59.189 43.478 0.09 0.00 29.66 2.57
3153 6834 4.274214 GGATGATCAGACGATTGCATGAAA 59.726 41.667 0.09 0.00 29.66 2.69
3154 6835 5.048921 GGATGATCAGACGATTGCATGAAAT 60.049 40.000 0.00 0.00 29.66 2.17
3155 6836 5.823209 TGATCAGACGATTGCATGAAATT 57.177 34.783 0.00 0.00 29.66 1.82
3156 6837 5.813717 TGATCAGACGATTGCATGAAATTC 58.186 37.500 0.00 0.00 29.66 2.17
3157 6838 5.354792 TGATCAGACGATTGCATGAAATTCA 59.645 36.000 0.00 0.00 29.66 2.57
3158 6839 5.225899 TCAGACGATTGCATGAAATTCAG 57.774 39.130 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.115911 AGACTAGAGCGACAGCCGG 61.116 63.158 0.00 0.00 46.67 6.13
5 6 0.179150 CACAGACTAGAGCGACAGCC 60.179 60.000 0.00 0.00 46.67 4.85
6 7 0.805614 TCACAGACTAGAGCGACAGC 59.194 55.000 0.00 0.00 45.58 4.40
12 13 1.226435 CGCGGTCACAGACTAGAGC 60.226 63.158 0.00 0.00 32.47 4.09
13 14 1.429825 CCGCGGTCACAGACTAGAG 59.570 63.158 19.50 0.00 32.47 2.43
14 15 2.044555 CCCGCGGTCACAGACTAGA 61.045 63.158 26.12 0.00 32.47 2.43
15 16 1.028330 TACCCGCGGTCACAGACTAG 61.028 60.000 26.12 6.79 37.09 2.57
16 17 1.002257 TACCCGCGGTCACAGACTA 60.002 57.895 26.12 0.00 37.09 2.59
17 18 2.282674 TACCCGCGGTCACAGACT 60.283 61.111 26.12 0.00 37.09 3.24
18 19 2.181021 CTACCCGCGGTCACAGAC 59.819 66.667 26.12 0.00 37.09 3.51
19 20 3.066190 CCTACCCGCGGTCACAGA 61.066 66.667 26.12 0.86 37.09 3.41
20 21 4.814294 GCCTACCCGCGGTCACAG 62.814 72.222 26.12 14.38 37.09 3.66
28 29 4.971125 GATGAGCCGCCTACCCGC 62.971 72.222 0.00 0.00 0.00 6.13
29 30 4.301027 GGATGAGCCGCCTACCCG 62.301 72.222 0.00 0.00 0.00 5.28
30 31 2.844839 AGGATGAGCCGCCTACCC 60.845 66.667 0.00 0.00 43.43 3.69
31 32 2.737830 GAGGATGAGCCGCCTACC 59.262 66.667 0.00 0.00 43.43 3.18
32 33 2.336809 CGAGGATGAGCCGCCTAC 59.663 66.667 0.00 0.00 43.43 3.18
33 34 2.123854 ACGAGGATGAGCCGCCTA 60.124 61.111 0.00 0.00 43.43 3.93
34 35 3.532155 GACGAGGATGAGCCGCCT 61.532 66.667 0.00 0.00 43.43 5.52
35 36 4.933064 CGACGAGGATGAGCCGCC 62.933 72.222 0.00 0.00 43.43 6.13
36 37 4.194720 ACGACGAGGATGAGCCGC 62.195 66.667 0.00 0.00 43.43 6.53
37 38 2.278206 CACGACGAGGATGAGCCG 60.278 66.667 0.00 0.00 43.43 5.52
38 39 2.583593 GCACGACGAGGATGAGCC 60.584 66.667 0.00 0.00 0.00 4.70
48 49 2.761326 GGTTTTAATAACCGCACGACG 58.239 47.619 0.00 0.00 43.15 5.12
56 57 3.763097 CCGGTTCCGGTTTTAATAACC 57.237 47.619 20.65 5.01 43.86 2.85
288 294 1.144276 GCCTCCCTCGCCTACTTTC 59.856 63.158 0.00 0.00 0.00 2.62
312 318 1.281287 ACTGCCATGTCAAGCATCTCT 59.719 47.619 1.72 0.00 38.56 3.10
610 617 4.458295 CGGATAAATCTAACCCTAGAGCGA 59.542 45.833 0.00 0.00 37.58 4.93
622 629 9.456147 TGAAATTCTCAAAACCGGATAAATCTA 57.544 29.630 9.46 0.00 0.00 1.98
664 672 7.951245 ACAAATACCACCCCAAAGTCTATTTTA 59.049 33.333 0.00 0.00 0.00 1.52
732 747 6.759497 GGCAAAGCCCAGTTATTATATAGG 57.241 41.667 0.00 0.00 44.06 2.57
759 774 1.866925 CGAGTCTTTTGGAACCGGC 59.133 57.895 0.00 0.00 0.00 6.13
898 919 2.186903 GGAAGATGAAGCGCCGGA 59.813 61.111 5.05 0.00 0.00 5.14
901 924 2.476320 GGCTGGAAGATGAAGCGCC 61.476 63.158 2.29 0.00 37.83 6.53
907 930 1.691219 GTTGGGGGCTGGAAGATGA 59.309 57.895 0.00 0.00 34.07 2.92
916 939 3.580319 GTGGTCTGGTTGGGGGCT 61.580 66.667 0.00 0.00 0.00 5.19
917 940 4.678743 GGTGGTCTGGTTGGGGGC 62.679 72.222 0.00 0.00 0.00 5.80
1210 1234 0.618968 AAATGGAGGCGGAGAGGAGT 60.619 55.000 0.00 0.00 0.00 3.85
1212 1236 0.541863 GAAAATGGAGGCGGAGAGGA 59.458 55.000 0.00 0.00 0.00 3.71
1250 1274 8.821894 CCTAGATGCAGTAACAATTCTTCTTAC 58.178 37.037 0.00 0.00 0.00 2.34
1306 1736 7.353414 AGCTCTTAAGATACTCATACAGCAA 57.647 36.000 5.44 0.00 0.00 3.91
1330 1760 9.863650 ACTTCTAGCCATGAATTACTAGTAGTA 57.136 33.333 5.90 5.90 39.84 1.82
1331 1761 8.770010 ACTTCTAGCCATGAATTACTAGTAGT 57.230 34.615 8.14 8.14 38.06 2.73
1451 1918 8.888579 ATACCAAAAAGATAAGTCACCTATCG 57.111 34.615 0.00 0.00 0.00 2.92
1470 1937 7.953493 TCACCTGGTCATACTCATATATACCAA 59.047 37.037 0.00 0.00 36.38 3.67
1579 2046 4.705337 AAAACCTCACAAAACGCAACTA 57.295 36.364 0.00 0.00 0.00 2.24
1580 2047 3.586100 AAAACCTCACAAAACGCAACT 57.414 38.095 0.00 0.00 0.00 3.16
1581 2048 4.860352 ACTAAAAACCTCACAAAACGCAAC 59.140 37.500 0.00 0.00 0.00 4.17
1582 2049 5.061920 ACTAAAAACCTCACAAAACGCAA 57.938 34.783 0.00 0.00 0.00 4.85
1583 2050 4.705337 ACTAAAAACCTCACAAAACGCA 57.295 36.364 0.00 0.00 0.00 5.24
1584 2051 5.813717 AGTACTAAAAACCTCACAAAACGC 58.186 37.500 0.00 0.00 0.00 4.84
1585 2052 7.219344 CCAAAGTACTAAAAACCTCACAAAACG 59.781 37.037 0.00 0.00 0.00 3.60
1586 2053 7.490079 CCCAAAGTACTAAAAACCTCACAAAAC 59.510 37.037 0.00 0.00 0.00 2.43
1587 2054 7.548967 CCCAAAGTACTAAAAACCTCACAAAA 58.451 34.615 0.00 0.00 0.00 2.44
1588 2055 6.406065 GCCCAAAGTACTAAAAACCTCACAAA 60.406 38.462 0.00 0.00 0.00 2.83
1589 2056 5.068067 GCCCAAAGTACTAAAAACCTCACAA 59.932 40.000 0.00 0.00 0.00 3.33
1590 2057 4.581409 GCCCAAAGTACTAAAAACCTCACA 59.419 41.667 0.00 0.00 0.00 3.58
1591 2058 4.581409 TGCCCAAAGTACTAAAAACCTCAC 59.419 41.667 0.00 0.00 0.00 3.51
1592 2059 4.581409 GTGCCCAAAGTACTAAAAACCTCA 59.419 41.667 0.00 0.00 0.00 3.86
1593 2060 4.581409 TGTGCCCAAAGTACTAAAAACCTC 59.419 41.667 0.00 0.00 31.32 3.85
1594 2061 4.538738 TGTGCCCAAAGTACTAAAAACCT 58.461 39.130 0.00 0.00 31.32 3.50
1595 2062 4.922471 TGTGCCCAAAGTACTAAAAACC 57.078 40.909 0.00 0.00 31.32 3.27
1596 2063 7.780008 AATTTGTGCCCAAAGTACTAAAAAC 57.220 32.000 0.00 0.00 43.45 2.43
1597 2064 8.145122 CCTAATTTGTGCCCAAAGTACTAAAAA 58.855 33.333 0.00 0.00 43.45 1.94
1598 2065 7.256012 CCCTAATTTGTGCCCAAAGTACTAAAA 60.256 37.037 0.00 0.00 43.45 1.52
1599 2066 6.209788 CCCTAATTTGTGCCCAAAGTACTAAA 59.790 38.462 0.00 0.00 43.45 1.85
1600 2067 5.712917 CCCTAATTTGTGCCCAAAGTACTAA 59.287 40.000 0.00 0.00 43.45 2.24
1614 2081 2.957474 ACACAAGCACCCCTAATTTGT 58.043 42.857 0.00 0.00 32.60 2.83
1664 2131 1.419762 TCACTGCTGGCTTTACTGGAA 59.580 47.619 0.00 0.00 0.00 3.53
1670 2137 4.507710 CATAGTTCTCACTGCTGGCTTTA 58.492 43.478 0.00 0.00 34.06 1.85
1674 2141 1.208052 TCCATAGTTCTCACTGCTGGC 59.792 52.381 0.00 0.00 37.20 4.85
1691 2158 3.995636 AGCTCTTAGTACCCAATCTCCA 58.004 45.455 0.00 0.00 0.00 3.86
1800 2273 4.130118 GACATCCTACCATAAAGCCACAG 58.870 47.826 0.00 0.00 0.00 3.66
1868 2341 5.676837 GCAAGCAAAATTTCCAAGCTTTTGT 60.677 36.000 13.87 0.00 43.06 2.83
1929 2402 2.696506 TCATGAGTGCTGCTGAAAGAG 58.303 47.619 0.00 0.00 34.07 2.85
1931 2404 5.752892 ATATTCATGAGTGCTGCTGAAAG 57.247 39.130 0.13 0.00 31.92 2.62
1938 2411 6.649557 TCAAGCAGATATATTCATGAGTGCTG 59.350 38.462 0.13 4.79 39.86 4.41
2027 2501 5.105997 CCATGAAGAAGATTCCTGTTCCAAC 60.106 44.000 0.00 0.00 0.00 3.77
2193 2667 5.674525 CTTTATCAGTAGAGCCATTGGACA 58.325 41.667 6.95 0.00 0.00 4.02
2469 2983 3.256879 GCCATCTTACTCGGATGAGATGA 59.743 47.826 17.47 0.00 45.17 2.92
2490 3004 6.846350 AGAAACATTTACTATGCAGTTGAGC 58.154 36.000 0.00 0.00 36.14 4.26
2632 3146 5.618418 GCATTAACCGACTTTGTTTAGGGAC 60.618 44.000 0.00 0.00 0.00 4.46
2638 3152 4.640789 TGTGCATTAACCGACTTTGTTT 57.359 36.364 0.00 0.00 0.00 2.83
2642 3156 6.622896 GCTCTAATTGTGCATTAACCGACTTT 60.623 38.462 0.00 0.00 35.45 2.66
2643 3157 5.163754 GCTCTAATTGTGCATTAACCGACTT 60.164 40.000 0.00 0.00 35.45 3.01
2647 3161 4.094887 AGTGCTCTAATTGTGCATTAACCG 59.905 41.667 0.00 0.00 45.23 4.44
2653 3167 6.769341 TCATCATTAGTGCTCTAATTGTGCAT 59.231 34.615 16.45 4.02 45.23 3.96
2660 3174 9.650539 GTGATACATCATCATTAGTGCTCTAAT 57.349 33.333 13.92 13.92 45.37 1.73
2669 3183 8.604640 AAGAAGCTGTGATACATCATCATTAG 57.395 34.615 0.00 0.00 45.37 1.73
2713 3227 6.091441 GTGATGTGCTCGGATAAGATAAATCC 59.909 42.308 0.00 0.00 39.71 3.01
2716 3230 5.163353 TGGTGATGTGCTCGGATAAGATAAA 60.163 40.000 0.00 0.00 0.00 1.40
2719 3233 2.700371 TGGTGATGTGCTCGGATAAGAT 59.300 45.455 0.00 0.00 0.00 2.40
2720 3234 2.107366 TGGTGATGTGCTCGGATAAGA 58.893 47.619 0.00 0.00 0.00 2.10
2721 3235 2.159043 AGTGGTGATGTGCTCGGATAAG 60.159 50.000 0.00 0.00 0.00 1.73
2722 3236 1.831106 AGTGGTGATGTGCTCGGATAA 59.169 47.619 0.00 0.00 0.00 1.75
2723 3237 1.409064 GAGTGGTGATGTGCTCGGATA 59.591 52.381 0.00 0.00 0.00 2.59
2724 3238 0.176680 GAGTGGTGATGTGCTCGGAT 59.823 55.000 0.00 0.00 0.00 4.18
2941 5139 8.141909 GCCCTAAAAGAAATGTCTTAACTTTGT 58.858 33.333 0.00 0.00 43.59 2.83
2945 5143 5.414765 CCGCCCTAAAAGAAATGTCTTAACT 59.585 40.000 0.00 0.00 43.59 2.24
2946 5144 5.413523 TCCGCCCTAAAAGAAATGTCTTAAC 59.586 40.000 0.00 0.00 43.59 2.01
2949 5147 4.010349 CTCCGCCCTAAAAGAAATGTCTT 58.990 43.478 0.00 0.00 46.47 3.01
2953 5151 2.024414 CCCTCCGCCCTAAAAGAAATG 58.976 52.381 0.00 0.00 0.00 2.32
2954 5152 1.920351 TCCCTCCGCCCTAAAAGAAAT 59.080 47.619 0.00 0.00 0.00 2.17
2955 5153 1.280998 CTCCCTCCGCCCTAAAAGAAA 59.719 52.381 0.00 0.00 0.00 2.52
2956 5154 0.909623 CTCCCTCCGCCCTAAAAGAA 59.090 55.000 0.00 0.00 0.00 2.52
2957 5155 0.252558 ACTCCCTCCGCCCTAAAAGA 60.253 55.000 0.00 0.00 0.00 2.52
2958 5156 1.413077 CTACTCCCTCCGCCCTAAAAG 59.587 57.143 0.00 0.00 0.00 2.27
2959 5157 1.273438 ACTACTCCCTCCGCCCTAAAA 60.273 52.381 0.00 0.00 0.00 1.52
2960 5158 0.337428 ACTACTCCCTCCGCCCTAAA 59.663 55.000 0.00 0.00 0.00 1.85
2962 5160 0.475906 GTACTACTCCCTCCGCCCTA 59.524 60.000 0.00 0.00 0.00 3.53
2963 5161 1.229643 GTACTACTCCCTCCGCCCT 59.770 63.158 0.00 0.00 0.00 5.19
2964 5162 0.475906 TAGTACTACTCCCTCCGCCC 59.524 60.000 0.00 0.00 0.00 6.13
2965 5163 2.355010 TTAGTACTACTCCCTCCGCC 57.645 55.000 0.91 0.00 0.00 6.13
2966 5164 3.698539 AGTTTTAGTACTACTCCCTCCGC 59.301 47.826 0.91 0.00 0.00 5.54
2967 5165 4.704057 ACAGTTTTAGTACTACTCCCTCCG 59.296 45.833 0.91 0.00 0.00 4.63
2970 5168 6.295180 GCTTGACAGTTTTAGTACTACTCCCT 60.295 42.308 0.91 0.00 0.00 4.20
2972 5170 6.689554 AGCTTGACAGTTTTAGTACTACTCC 58.310 40.000 0.91 0.00 0.00 3.85
2974 5172 9.640963 CAATAGCTTGACAGTTTTAGTACTACT 57.359 33.333 0.91 0.00 34.04 2.57
3001 6682 3.290710 CAATAAGGCTAATGGTGTGGCT 58.709 45.455 0.00 0.00 38.25 4.75
3031 6712 2.933573 TCGGGAAGGTGCTGTTTAAAA 58.066 42.857 0.00 0.00 0.00 1.52
3049 6730 5.468592 AGCAGAAGCAATCTACTATGATCG 58.531 41.667 0.00 0.00 45.49 3.69
3073 6754 3.652274 CACCTGGGCAGTGTTATTTTTG 58.348 45.455 0.00 0.00 0.00 2.44
3077 6758 0.405585 AGCACCTGGGCAGTGTTATT 59.594 50.000 9.36 0.00 35.83 1.40
3078 6759 0.405585 AAGCACCTGGGCAGTGTTAT 59.594 50.000 9.36 0.00 35.83 1.89
3079 6760 0.184933 AAAGCACCTGGGCAGTGTTA 59.815 50.000 9.36 0.00 35.83 2.41
3080 6761 1.076044 AAAGCACCTGGGCAGTGTT 60.076 52.632 9.36 0.00 35.83 3.32
3081 6762 1.529244 GAAAGCACCTGGGCAGTGT 60.529 57.895 9.36 0.00 35.83 3.55
3082 6763 2.620112 CGAAAGCACCTGGGCAGTG 61.620 63.158 9.36 0.00 35.83 3.66
3083 6764 2.281761 CGAAAGCACCTGGGCAGT 60.282 61.111 9.36 0.00 35.83 4.40
3084 6765 3.058160 CCGAAAGCACCTGGGCAG 61.058 66.667 9.36 0.00 35.83 4.85
3085 6766 3.884774 ACCGAAAGCACCTGGGCA 61.885 61.111 9.36 0.00 35.83 5.36
3086 6767 3.365265 CACCGAAAGCACCTGGGC 61.365 66.667 0.00 0.00 0.00 5.36
3087 6768 1.515521 GAACACCGAAAGCACCTGGG 61.516 60.000 0.00 0.00 0.00 4.45
3088 6769 1.515521 GGAACACCGAAAGCACCTGG 61.516 60.000 0.00 0.00 0.00 4.45
3089 6770 0.817634 TGGAACACCGAAAGCACCTG 60.818 55.000 0.00 0.00 0.00 4.00
3090 6771 1.529796 TGGAACACCGAAAGCACCT 59.470 52.632 0.00 0.00 0.00 4.00
3091 6772 4.150994 TGGAACACCGAAAGCACC 57.849 55.556 0.00 0.00 0.00 5.01
3102 6783 2.176798 AGGGAAGTTCAACCATGGAACA 59.823 45.455 21.47 0.00 45.45 3.18
3103 6784 2.558359 CAGGGAAGTTCAACCATGGAAC 59.442 50.000 21.47 12.84 43.82 3.62
3104 6785 2.875296 CAGGGAAGTTCAACCATGGAA 58.125 47.619 21.47 0.00 34.84 3.53
3105 6786 1.547675 GCAGGGAAGTTCAACCATGGA 60.548 52.381 21.47 0.00 38.23 3.41
3106 6787 0.890683 GCAGGGAAGTTCAACCATGG 59.109 55.000 11.19 11.19 38.23 3.66
3107 6788 1.915141 AGCAGGGAAGTTCAACCATG 58.085 50.000 5.01 0.00 40.33 3.66
3108 6789 2.290960 GGTAGCAGGGAAGTTCAACCAT 60.291 50.000 5.01 0.00 0.00 3.55
3109 6790 1.073284 GGTAGCAGGGAAGTTCAACCA 59.927 52.381 5.01 0.00 0.00 3.67
3110 6791 1.822506 GGTAGCAGGGAAGTTCAACC 58.177 55.000 5.01 0.00 0.00 3.77
3111 6792 1.439679 CGGTAGCAGGGAAGTTCAAC 58.560 55.000 5.01 0.00 0.00 3.18
3112 6793 0.323629 CCGGTAGCAGGGAAGTTCAA 59.676 55.000 5.01 0.00 0.00 2.69
3113 6794 0.543410 TCCGGTAGCAGGGAAGTTCA 60.543 55.000 0.00 0.00 0.00 3.18
3114 6795 0.831307 ATCCGGTAGCAGGGAAGTTC 59.169 55.000 0.00 0.00 35.60 3.01
3115 6796 0.541863 CATCCGGTAGCAGGGAAGTT 59.458 55.000 0.00 0.00 35.60 2.66
3116 6797 0.325296 TCATCCGGTAGCAGGGAAGT 60.325 55.000 0.00 0.00 35.60 3.01
3117 6798 1.001406 GATCATCCGGTAGCAGGGAAG 59.999 57.143 0.00 0.00 35.60 3.46
3118 6799 1.048601 GATCATCCGGTAGCAGGGAA 58.951 55.000 0.00 0.00 35.60 3.97
3119 6800 0.105709 TGATCATCCGGTAGCAGGGA 60.106 55.000 0.00 0.00 36.61 4.20
3120 6801 0.319728 CTGATCATCCGGTAGCAGGG 59.680 60.000 0.00 0.00 0.00 4.45
3121 6802 1.000283 GTCTGATCATCCGGTAGCAGG 60.000 57.143 15.75 0.00 0.00 4.85
3122 6803 1.335415 CGTCTGATCATCCGGTAGCAG 60.335 57.143 0.00 7.24 0.00 4.24
3123 6804 0.668535 CGTCTGATCATCCGGTAGCA 59.331 55.000 0.00 0.00 0.00 3.49
3124 6805 0.952280 TCGTCTGATCATCCGGTAGC 59.048 55.000 0.00 0.00 0.00 3.58
3125 6806 3.569548 CAATCGTCTGATCATCCGGTAG 58.430 50.000 0.00 0.00 32.24 3.18
3126 6807 2.288213 GCAATCGTCTGATCATCCGGTA 60.288 50.000 0.00 0.00 32.24 4.02
3127 6808 1.539065 GCAATCGTCTGATCATCCGGT 60.539 52.381 0.00 4.57 32.24 5.28
3128 6809 1.143305 GCAATCGTCTGATCATCCGG 58.857 55.000 12.52 0.00 32.24 5.14
3129 6810 1.856802 TGCAATCGTCTGATCATCCG 58.143 50.000 0.00 1.49 32.24 4.18
3130 6811 3.396560 TCATGCAATCGTCTGATCATCC 58.603 45.455 0.00 0.00 32.24 3.51
3131 6812 5.413969 TTTCATGCAATCGTCTGATCATC 57.586 39.130 0.00 0.00 32.24 2.92
3132 6813 6.038936 TGAATTTCATGCAATCGTCTGATCAT 59.961 34.615 0.00 0.00 32.24 2.45
3133 6814 5.354792 TGAATTTCATGCAATCGTCTGATCA 59.645 36.000 0.00 0.00 32.24 2.92
3134 6815 5.813717 TGAATTTCATGCAATCGTCTGATC 58.186 37.500 0.00 0.00 32.24 2.92
3135 6816 5.817988 CTGAATTTCATGCAATCGTCTGAT 58.182 37.500 0.00 0.00 35.98 2.90
3136 6817 5.225899 CTGAATTTCATGCAATCGTCTGA 57.774 39.130 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.