Multiple sequence alignment - TraesCS3D01G259700

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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 TraesCS3D01G259700 chr3D 100.000 5822 0 0 1 5822 361382852 361388673 0.000000e+00 10752.0
1 TraesCS3D01G259700 chr3D 95.708 233 8 2 3523 3753 146189145 146188913 1.980000e-99 374.0
2 TraesCS3D01G259700 chr3A 94.611 1336 50 10 1411 2728 481889462 481890793 0.000000e+00 2049.0
3 TraesCS3D01G259700 chr3A 90.690 1289 60 16 3751 5034 481890791 481892024 0.000000e+00 1661.0
4 TraesCS3D01G259700 chr3A 93.524 664 17 4 805 1448 481888807 481889464 0.000000e+00 965.0
5 TraesCS3D01G259700 chr3A 91.948 534 35 7 5291 5822 481892217 481892744 0.000000e+00 741.0
6 TraesCS3D01G259700 chr3A 94.305 439 13 3 3 441 481888031 481888457 0.000000e+00 662.0
7 TraesCS3D01G259700 chr3A 88.919 370 14 12 426 789 481888472 481888820 1.160000e-116 431.0
8 TraesCS3D01G259700 chr3A 89.011 91 6 2 1671 1758 658653499 658653410 6.170000e-20 110.0
9 TraesCS3D01G259700 chr3A 97.059 34 1 0 5031 5064 117319654 117319687 2.270000e-04 58.4
10 TraesCS3D01G259700 chr3B 93.280 1369 63 15 3758 5117 471249080 471250428 0.000000e+00 1991.0
11 TraesCS3D01G259700 chr3B 95.618 1027 37 5 1708 2728 471247853 471248877 0.000000e+00 1640.0
12 TraesCS3D01G259700 chr3B 96.386 830 23 3 835 1658 471247023 471247851 0.000000e+00 1360.0
13 TraesCS3D01G259700 chr3B 90.695 806 61 9 2726 3525 22177117 22177914 0.000000e+00 1061.0
14 TraesCS3D01G259700 chr3B 92.188 512 33 6 1 507 471245696 471246205 0.000000e+00 717.0
15 TraesCS3D01G259700 chr3B 91.897 506 29 4 5321 5822 471251235 471251732 0.000000e+00 697.0
16 TraesCS3D01G259700 chr3B 85.204 588 59 13 2726 3303 92666366 92666935 3.910000e-161 579.0
17 TraesCS3D01G259700 chr3B 86.650 397 25 17 453 837 471246200 471246580 1.170000e-111 414.0
18 TraesCS3D01G259700 chr3B 92.040 201 15 1 1 201 11604219 11604418 1.240000e-71 281.0
19 TraesCS3D01G259700 chr3B 81.362 279 25 12 2726 2999 384308697 384308441 9.890000e-48 202.0
20 TraesCS3D01G259700 chr3B 94.872 78 3 1 5238 5314 471250530 471250607 2.850000e-23 121.0
21 TraesCS3D01G259700 chr6D 94.553 1028 36 9 2728 3751 60514264 60515275 0.000000e+00 1570.0
22 TraesCS3D01G259700 chr6D 91.542 201 17 0 1 201 26597001 26596801 1.600000e-70 278.0
23 TraesCS3D01G259700 chr6D 91.045 201 18 0 1 201 12480131 12480331 7.430000e-69 272.0
24 TraesCS3D01G259700 chr6D 91.045 201 18 0 1 201 68353813 68353613 7.430000e-69 272.0
25 TraesCS3D01G259700 chr6D 91.045 201 18 0 1 201 429960188 429959988 7.430000e-69 272.0
26 TraesCS3D01G259700 chr6D 91.045 201 18 0 1 201 454868682 454868482 7.430000e-69 272.0
27 TraesCS3D01G259700 chr6D 90.547 201 19 0 1 201 90435255 90435055 3.460000e-67 267.0
28 TraesCS3D01G259700 chr6D 90.547 201 19 0 1 201 436523994 436524194 3.460000e-67 267.0
29 TraesCS3D01G259700 chr6D 90.050 201 20 0 1 201 35516240 35516040 1.610000e-65 261.0
30 TraesCS3D01G259700 chr6D 90.476 84 4 1 1680 1759 470575013 470575096 2.220000e-19 108.0
31 TraesCS3D01G259700 chr6D 90.909 77 3 1 1680 1752 91072607 91072531 3.710000e-17 100.0
32 TraesCS3D01G259700 chr6D 89.024 82 5 1 1680 1757 470575088 470575007 1.340000e-16 99.0
33 TraesCS3D01G259700 chr6D 90.411 73 3 1 1688 1756 91072540 91072612 6.210000e-15 93.5
34 TraesCS3D01G259700 chr6D 90.411 73 3 2 1680 1751 382614463 382614394 6.210000e-15 93.5
35 TraesCS3D01G259700 chr6D 88.312 77 4 1 1680 1756 136473274 136473345 2.890000e-13 87.9
36 TraesCS3D01G259700 chr6D 87.500 80 4 5 1685 1760 246972531 246972454 2.890000e-13 87.9
37 TraesCS3D01G259700 chr7D 89.839 1053 37 23 2728 3751 16804219 16805230 0.000000e+00 1288.0
38 TraesCS3D01G259700 chr7D 93.609 798 32 6 2728 3525 472735063 472734285 0.000000e+00 1173.0
39 TraesCS3D01G259700 chr7D 94.606 241 11 2 3523 3762 628443435 628443196 7.120000e-99 372.0
40 TraesCS3D01G259700 chr4D 94.625 800 32 7 2726 3525 472211779 472212567 0.000000e+00 1229.0
41 TraesCS3D01G259700 chr4D 93.655 788 30 6 2739 3525 506032751 506031983 0.000000e+00 1160.0
42 TraesCS3D01G259700 chr4D 91.045 201 18 0 1 201 82749392 82749592 7.430000e-69 272.0
43 TraesCS3D01G259700 chr4D 89.157 83 6 1 1680 1759 303843548 303843466 3.710000e-17 100.0
44 TraesCS3D01G259700 chr4D 88.506 87 5 5 1674 1756 303843468 303843553 3.710000e-17 100.0
45 TraesCS3D01G259700 chr4D 83.838 99 6 8 1674 1763 401206822 401206919 1.040000e-12 86.1
46 TraesCS3D01G259700 chr4D 94.545 55 2 1 5108 5162 57876673 57876726 3.740000e-12 84.2
47 TraesCS3D01G259700 chr5D 94.493 799 35 7 2728 3525 428699520 428698730 0.000000e+00 1223.0
48 TraesCS3D01G259700 chr5D 94.486 798 25 5 2728 3525 13914723 13915501 0.000000e+00 1212.0
49 TraesCS3D01G259700 chr5D 96.070 229 9 0 3523 3751 399963340 399963568 1.980000e-99 374.0
50 TraesCS3D01G259700 chr5D 91.045 201 18 0 1 201 168652678 168652878 7.430000e-69 272.0
51 TraesCS3D01G259700 chr5D 87.356 87 9 2 1672 1756 393754275 393754361 1.340000e-16 99.0
52 TraesCS3D01G259700 chr5D 87.640 89 4 7 1680 1763 428386503 428386589 4.800000e-16 97.1
53 TraesCS3D01G259700 chr5D 94.444 54 2 1 5110 5163 289423540 289423592 1.340000e-11 82.4
54 TraesCS3D01G259700 chr2D 91.990 799 39 8 2728 3525 524268510 524267736 0.000000e+00 1098.0
55 TraesCS3D01G259700 chr2D 95.238 84 3 1 1680 1762 473096444 473096361 1.320000e-26 132.0
56 TraesCS3D01G259700 chr2D 93.750 80 2 1 1675 1751 622916665 622916744 3.690000e-22 117.0
57 TraesCS3D01G259700 chr2D 90.698 86 2 5 1680 1760 24451828 24451744 6.170000e-20 110.0
58 TraesCS3D01G259700 chr2D 90.588 85 3 5 1680 1760 622916744 622916661 2.220000e-19 108.0
59 TraesCS3D01G259700 chr2B 91.447 795 57 5 2726 3519 748058917 748059701 0.000000e+00 1081.0
60 TraesCS3D01G259700 chr2B 92.040 201 16 0 1 201 698093369 698093569 3.430000e-72 283.0
61 TraesCS3D01G259700 chr2B 100.000 33 0 0 5040 5072 95093916 95093884 1.750000e-05 62.1
62 TraesCS3D01G259700 chrUn 96.552 232 7 1 3523 3753 46246838 46246607 3.290000e-102 383.0
63 TraesCS3D01G259700 chrUn 96.121 232 8 1 3523 3753 154744850 154744619 1.530000e-100 377.0
64 TraesCS3D01G259700 chrUn 90.050 201 20 0 1 201 96949372 96949172 1.610000e-65 261.0
65 TraesCS3D01G259700 chrUn 90.840 131 12 0 1 131 153250280 153250150 6.000000e-40 176.0
66 TraesCS3D01G259700 chrUn 86.047 86 3 3 1673 1757 110336348 110336271 3.740000e-12 84.2
67 TraesCS3D01G259700 chrUn 94.340 53 3 0 1708 1760 71312905 71312957 1.340000e-11 82.4
68 TraesCS3D01G259700 chrUn 84.706 85 5 2 1680 1763 215727704 215727627 1.740000e-10 78.7
69 TraesCS3D01G259700 chrUn 88.060 67 4 1 1689 1751 43172758 43172692 6.260000e-10 76.8
70 TraesCS3D01G259700 chrUn 88.060 67 4 1 1689 1751 178595823 178595757 6.260000e-10 76.8
71 TraesCS3D01G259700 chrUn 88.060 67 4 1 1689 1751 377641091 377641025 6.260000e-10 76.8
72 TraesCS3D01G259700 chrUn 88.060 67 4 1 1689 1751 396425051 396424985 6.260000e-10 76.8
73 TraesCS3D01G259700 chrUn 92.593 54 1 3 1708 1759 71312906 71312854 2.250000e-09 75.0
74 TraesCS3D01G259700 chrUn 95.556 45 2 0 1707 1751 102818974 102818930 8.090000e-09 73.1
75 TraesCS3D01G259700 chrUn 92.308 52 1 3 1712 1761 45996720 45996770 2.910000e-08 71.3
76 TraesCS3D01G259700 chrUn 97.500 40 1 0 1721 1760 371149063 371149024 1.050000e-07 69.4
77 TraesCS3D01G259700 chrUn 91.667 48 3 1 1717 1764 314370611 314370565 1.350000e-06 65.8
78 TraesCS3D01G259700 chrUn 97.059 34 1 0 1675 1708 45996764 45996731 2.270000e-04 58.4
79 TraesCS3D01G259700 chrUn 94.444 36 2 0 1673 1708 8484341 8484376 8.150000e-04 56.5
80 TraesCS3D01G259700 chrUn 100.000 29 0 0 1680 1708 34213236 34213264 3.000000e-03 54.7
81 TraesCS3D01G259700 chrUn 100.000 28 0 0 1681 1708 86686262 86686235 1.100000e-02 52.8
82 TraesCS3D01G259700 chr5B 96.522 230 7 1 3523 3751 461608920 461609149 4.260000e-101 379.0
83 TraesCS3D01G259700 chr5B 86.170 94 9 2 1667 1757 51843389 51843297 1.340000e-16 99.0
84 TraesCS3D01G259700 chr5B 94.340 53 3 0 5111 5163 261673050 261673102 1.340000e-11 82.4
85 TraesCS3D01G259700 chr1D 96.087 230 7 2 3523 3751 464850465 464850237 1.980000e-99 374.0
86 TraesCS3D01G259700 chr1D 91.045 201 18 0 1 201 416602864 416603064 7.430000e-69 272.0
87 TraesCS3D01G259700 chr1D 91.045 201 18 0 1 201 480003816 480003616 7.430000e-69 272.0
88 TraesCS3D01G259700 chr1D 77.404 208 33 10 2144 2341 454568002 454567799 1.710000e-20 111.0
89 TraesCS3D01G259700 chr1D 86.735 98 6 5 1668 1761 199068363 199068269 1.030000e-17 102.0
90 TraesCS3D01G259700 chr1D 86.667 90 6 4 1668 1756 89127676 89127760 1.730000e-15 95.3
91 TraesCS3D01G259700 chr1D 88.750 80 6 3 1680 1757 199068278 199068356 1.730000e-15 95.3
92 TraesCS3D01G259700 chr1D 96.078 51 2 0 5113 5163 296167757 296167807 3.740000e-12 84.2
93 TraesCS3D01G259700 chr1D 84.211 95 6 7 1664 1751 407873430 407873338 3.740000e-12 84.2
94 TraesCS3D01G259700 chr4A 94.561 239 11 2 3523 3759 673023913 673024151 9.220000e-98 368.0
95 TraesCS3D01G259700 chr4A 91.542 201 17 0 1 201 652023486 652023286 1.600000e-70 278.0
96 TraesCS3D01G259700 chr4A 91.954 87 2 5 1673 1757 625758308 625758225 3.690000e-22 117.0
97 TraesCS3D01G259700 chr4A 86.170 94 10 3 1675 1768 469243356 469243446 1.340000e-16 99.0
98 TraesCS3D01G259700 chr4A 96.078 51 2 0 5111 5161 517406466 517406516 3.740000e-12 84.2
99 TraesCS3D01G259700 chr4A 96.875 32 1 0 5033 5064 76939847 76939816 3.000000e-03 54.7
100 TraesCS3D01G259700 chr1A 92.537 201 15 0 1 201 386399345 386399545 7.380000e-74 289.0
101 TraesCS3D01G259700 chr1A 77.778 207 32 10 2145 2341 548672348 548672550 1.330000e-21 115.0
102 TraesCS3D01G259700 chr1A 96.970 33 0 1 5034 5065 572014773 572014741 3.000000e-03 54.7
103 TraesCS3D01G259700 chr6B 92.040 201 16 0 1 201 620974577 620974377 3.430000e-72 283.0
104 TraesCS3D01G259700 chr6B 91.626 203 15 1 1 201 127029068 127029270 4.440000e-71 279.0
105 TraesCS3D01G259700 chr6B 91.542 201 17 0 1 201 189634387 189634187 1.600000e-70 278.0
106 TraesCS3D01G259700 chr6B 91.542 201 17 0 1 201 286729219 286729019 1.600000e-70 278.0
107 TraesCS3D01G259700 chr6B 90.588 85 3 2 1680 1759 163967854 163967938 2.220000e-19 108.0
108 TraesCS3D01G259700 chr6B 90.476 84 4 1 1680 1759 545839647 545839564 2.220000e-19 108.0
109 TraesCS3D01G259700 chr4B 91.542 201 17 0 1 201 66186134 66185934 1.600000e-70 278.0
110 TraesCS3D01G259700 chr4B 91.542 201 17 0 1 201 484758114 484758314 1.600000e-70 278.0
111 TraesCS3D01G259700 chr4B 96.296 54 2 0 5112 5165 93739215 93739268 8.040000e-14 89.8
112 TraesCS3D01G259700 chr4B 96.296 54 2 0 5112 5165 664170756 664170809 8.040000e-14 89.8
113 TraesCS3D01G259700 chr2A 93.590 78 5 0 1680 1757 522505489 522505412 3.690000e-22 117.0
114 TraesCS3D01G259700 chr7A 91.667 84 3 2 1680 1759 475977264 475977181 4.770000e-21 113.0
115 TraesCS3D01G259700 chr7A 97.959 49 1 0 5113 5161 115779135 115779183 1.040000e-12 86.1
116 TraesCS3D01G259700 chr5A 89.888 89 3 3 1680 1763 55158984 55159071 6.170000e-20 110.0
117 TraesCS3D01G259700 chr5A 85.714 105 9 3 1669 1768 55159071 55158968 7.980000e-19 106.0
118 TraesCS3D01G259700 chr5A 91.139 79 3 2 1686 1760 452111576 452111498 2.870000e-18 104.0
119 TraesCS3D01G259700 chr5A 87.912 91 3 6 1673 1757 700362828 700362916 3.710000e-17 100.0
120 TraesCS3D01G259700 chr1B 76.636 214 36 10 2138 2341 624882638 624882847 7.980000e-19 106.0
121 TraesCS3D01G259700 chr1B 88.235 85 8 2 1680 1763 131503016 131502933 3.710000e-17 100.0
122 TraesCS3D01G259700 chr1B 100.000 30 0 0 5043 5072 18090260 18090231 8.150000e-04 56.5
123 TraesCS3D01G259700 chr7B 90.476 63 4 2 5101 5161 324138728 324138666 1.340000e-11 82.4


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 TraesCS3D01G259700 chr3D 361382852 361388673 5821 False 10752.000000 10752 100.000000 1 5822 1 chr3D.!!$F1 5821
1 TraesCS3D01G259700 chr3A 481888031 481892744 4713 False 1084.833333 2049 92.332833 3 5822 6 chr3A.!!$F2 5819
2 TraesCS3D01G259700 chr3B 22177117 22177914 797 False 1061.000000 1061 90.695000 2726 3525 1 chr3B.!!$F2 799
3 TraesCS3D01G259700 chr3B 471245696 471251732 6036 False 991.428571 1991 92.984429 1 5822 7 chr3B.!!$F4 5821
4 TraesCS3D01G259700 chr3B 92666366 92666935 569 False 579.000000 579 85.204000 2726 3303 1 chr3B.!!$F3 577
5 TraesCS3D01G259700 chr6D 60514264 60515275 1011 False 1570.000000 1570 94.553000 2728 3751 1 chr6D.!!$F2 1023
6 TraesCS3D01G259700 chr7D 16804219 16805230 1011 False 1288.000000 1288 89.839000 2728 3751 1 chr7D.!!$F1 1023
7 TraesCS3D01G259700 chr7D 472734285 472735063 778 True 1173.000000 1173 93.609000 2728 3525 1 chr7D.!!$R1 797
8 TraesCS3D01G259700 chr4D 472211779 472212567 788 False 1229.000000 1229 94.625000 2726 3525 1 chr4D.!!$F5 799
9 TraesCS3D01G259700 chr4D 506031983 506032751 768 True 1160.000000 1160 93.655000 2739 3525 1 chr4D.!!$R2 786
10 TraesCS3D01G259700 chr5D 428698730 428699520 790 True 1223.000000 1223 94.493000 2728 3525 1 chr5D.!!$R1 797
11 TraesCS3D01G259700 chr5D 13914723 13915501 778 False 1212.000000 1212 94.486000 2728 3525 1 chr5D.!!$F1 797
12 TraesCS3D01G259700 chr2D 524267736 524268510 774 True 1098.000000 1098 91.990000 2728 3525 1 chr2D.!!$R3 797
13 TraesCS3D01G259700 chr2B 748058917 748059701 784 False 1081.000000 1081 91.447000 2726 3519 1 chr2B.!!$F2 793

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
973 1516 0.322187 AATCACTACCGGTGCCCAAC 60.322 55.000 19.93 0.00 44.98 3.77 F
1226 1781 0.097674 GTAAGCTTCCGTGCATGCTG 59.902 55.000 20.33 11.33 35.79 4.41 F
1751 2358 2.374170 ACACTTATTTTGGGACGGAGGT 59.626 45.455 0.00 0.00 0.00 3.85 F
3047 3677 1.208293 GTCGGCCTTCTTCTCCTTGAT 59.792 52.381 0.00 0.00 0.00 2.57 F
3752 4449 1.443407 GCGGCTGGAGATGCTCTAA 59.557 57.895 0.00 0.00 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 2885 1.304282 CCAGCTGCCCAACCTGTAT 59.696 57.895 8.66 0.0 0.0 2.29 R
3038 3668 2.186903 GCGCCCGAATCAAGGAGA 59.813 61.111 0.00 0.0 0.0 3.71 R
3320 4000 2.756283 CCTCGTCGGCTCCTCCTT 60.756 66.667 0.00 0.0 0.0 3.36 R
4068 4965 0.459759 GCTAGTTAAGTTCGCCCGCT 60.460 55.000 0.00 0.0 0.0 5.52 R
5168 6072 1.209504 TGGCAGCAACAGTATACTCCC 59.790 52.381 1.26 0.0 0.0 4.30 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
202 203 7.390027 AGATTGTCACAAGACTTAGTATGCTT 58.610 34.615 0.00 0.00 45.20 3.91
247 248 5.648092 AGTTTTGATAAGTTTGCCTCGCTAT 59.352 36.000 0.00 0.00 0.00 2.97
499 580 7.981789 ACTATCGATGTAGTGATTGTTGATTGT 59.018 33.333 8.54 0.00 33.78 2.71
534 620 6.200114 ACCACATACTATACACCTGGTAACT 58.800 40.000 0.00 0.00 35.14 2.24
539 625 7.783119 ACATACTATACACCTGGTAACTGATGA 59.217 37.037 0.00 0.00 35.14 2.92
543 629 4.908601 ACACCTGGTAACTGATGATCAA 57.091 40.909 0.00 0.00 37.83 2.57
589 676 5.305386 CACATATGAATCCCTAGTCCAGACA 59.695 44.000 10.38 0.00 0.00 3.41
598 685 3.244112 CCCTAGTCCAGACAAAAACGACT 60.244 47.826 0.00 0.00 37.54 4.18
637 724 6.749118 GCTAATTGGATTAACTGCTTGTGAAG 59.251 38.462 0.00 0.00 0.00 3.02
653 740 9.386010 TGCTTGTGAAGTAAGTAGTTTTCTTTA 57.614 29.630 0.00 0.00 0.00 1.85
858 1395 1.750193 ATGTGTGGTTAGATTGGGCG 58.250 50.000 0.00 0.00 0.00 6.13
873 1410 3.676091 GGCGAAACGACCAATTCAG 57.324 52.632 0.00 0.00 0.00 3.02
973 1516 0.322187 AATCACTACCGGTGCCCAAC 60.322 55.000 19.93 0.00 44.98 3.77
1219 1774 0.511221 CCACAACGTAAGCTTCCGTG 59.489 55.000 18.21 13.74 45.62 4.94
1226 1781 0.097674 GTAAGCTTCCGTGCATGCTG 59.902 55.000 20.33 11.33 35.79 4.41
1241 1796 6.324819 GTGCATGCTGTATTCACTGTAAAAT 58.675 36.000 20.33 0.00 31.32 1.82
1306 1861 3.563808 TCGTGGGTTGAAATGTTGAGAAG 59.436 43.478 0.00 0.00 0.00 2.85
1476 2072 5.994054 CGATTGAAGATATTGTCTGATGGGT 59.006 40.000 0.00 0.00 37.23 4.51
1503 2099 8.132362 TGTTAACCTGTTGTTGATAAACACATC 58.868 33.333 2.48 0.00 37.83 3.06
1677 2274 8.495949 CCAAGGTCATTATGCTATAAAAGTACG 58.504 37.037 0.00 0.00 0.00 3.67
1678 2275 9.042008 CAAGGTCATTATGCTATAAAAGTACGT 57.958 33.333 0.00 0.00 0.00 3.57
1708 2305 6.425721 CGTCCCAAAATAAGTGTCTCAACTTA 59.574 38.462 0.00 0.00 44.52 2.24
1751 2358 2.374170 ACACTTATTTTGGGACGGAGGT 59.626 45.455 0.00 0.00 0.00 3.85
1874 2481 8.914328 TGTTGTATAGAATTGAATTGCACATG 57.086 30.769 0.00 0.00 0.00 3.21
2106 2713 4.155280 TCCTTTAAAATTCTGTAGGCGCAC 59.845 41.667 10.83 0.00 0.00 5.34
2278 2885 2.817258 CCTTGTTTGACGCCCTGAATTA 59.183 45.455 0.00 0.00 0.00 1.40
2342 2949 7.651704 ACTTAATCAAGTTGTTGTGGTAAATGC 59.348 33.333 2.11 0.00 42.51 3.56
2365 2972 7.153985 TGCTAATCTTGATTTGGTTCCTTTTG 58.846 34.615 0.95 0.00 0.00 2.44
2375 2982 4.163441 TGGTTCCTTTTGTCACAGATCA 57.837 40.909 0.00 0.00 0.00 2.92
2410 3017 7.106239 GGTTCCAACATCATTCTTCTCTTCTA 58.894 38.462 0.00 0.00 0.00 2.10
2568 3178 6.824704 CCTATTGTCCCGTCCTTTATTTTACA 59.175 38.462 0.00 0.00 0.00 2.41
2628 3238 6.395629 TGTAATCGCTAAGCACTCTTAAGTT 58.604 36.000 1.63 0.00 34.62 2.66
2776 3386 4.293626 CGCCTAAAATCGCCGCCG 62.294 66.667 0.00 0.00 0.00 6.46
2935 3563 3.380004 CGGCAAACTTGGGCTTATATTCA 59.620 43.478 0.00 0.00 0.00 2.57
3047 3677 1.208293 GTCGGCCTTCTTCTCCTTGAT 59.792 52.381 0.00 0.00 0.00 2.57
3144 3792 4.815489 ACGACTCCTCCTTCGTCA 57.185 55.556 0.00 0.00 45.10 4.35
3624 4320 4.324991 GTTCGGGTTGGGTCCGCT 62.325 66.667 0.00 0.00 46.43 5.52
3636 4332 1.665442 GTCCGCTGGCACCAATTTT 59.335 52.632 0.00 0.00 0.00 1.82
3751 4448 2.849964 CGCGGCTGGAGATGCTCTA 61.850 63.158 0.00 0.00 0.00 2.43
3752 4449 1.443407 GCGGCTGGAGATGCTCTAA 59.557 57.895 0.00 0.00 0.00 2.10
3796 4691 5.927115 TGTTGATGTTATGTACGCACAGTAA 59.073 36.000 0.00 0.00 38.30 2.24
3803 4698 3.671008 TGTACGCACAGTAAATGGTCT 57.329 42.857 0.00 0.00 37.02 3.85
3805 4700 5.333299 TGTACGCACAGTAAATGGTCTAT 57.667 39.130 0.00 0.00 37.02 1.98
3858 4753 7.275999 CCGTGATCTCTTAGTTAGGAAGTTTTC 59.724 40.741 0.00 0.00 0.00 2.29
4066 4963 4.156008 GCCTAGTACCCAACAGACAAAATG 59.844 45.833 0.00 0.00 0.00 2.32
4067 4964 4.156008 CCTAGTACCCAACAGACAAAATGC 59.844 45.833 0.00 0.00 0.00 3.56
4068 4965 3.561143 AGTACCCAACAGACAAAATGCA 58.439 40.909 0.00 0.00 0.00 3.96
4069 4966 3.569701 AGTACCCAACAGACAAAATGCAG 59.430 43.478 0.00 0.00 0.00 4.41
4070 4967 1.069049 ACCCAACAGACAAAATGCAGC 59.931 47.619 0.00 0.00 0.00 5.25
4071 4968 1.411394 CCAACAGACAAAATGCAGCG 58.589 50.000 0.00 0.00 0.00 5.18
4072 4969 1.411394 CAACAGACAAAATGCAGCGG 58.589 50.000 0.00 0.00 0.00 5.52
4073 4970 0.314935 AACAGACAAAATGCAGCGGG 59.685 50.000 0.00 0.00 0.00 6.13
4074 4971 1.444895 CAGACAAAATGCAGCGGGC 60.445 57.895 0.00 0.00 45.13 6.13
4083 4980 2.479198 GCAGCGGGCGAACTTAAC 59.521 61.111 0.00 0.00 0.00 2.01
4102 4999 4.430137 AACTAGCATGCTGACATTTGTG 57.570 40.909 30.42 10.37 32.87 3.33
4119 5016 4.963276 TTGTGCATTTATTTCTCCCTCG 57.037 40.909 0.00 0.00 0.00 4.63
4188 5085 9.638239 AACGCAATAACTTTTATCATTGTGAAT 57.362 25.926 12.21 0.75 39.91 2.57
4222 5119 1.434188 TGTTCTGGGAAGAGCTTGGA 58.566 50.000 0.00 0.00 0.00 3.53
4232 5129 4.324641 GGGAAGAGCTTGGAAGAACCTAAT 60.325 45.833 0.00 0.00 39.86 1.73
4305 5202 6.448207 AAGAGCTATTTTTCTCTTGGCATC 57.552 37.500 3.96 0.00 45.09 3.91
4306 5203 5.753716 AGAGCTATTTTTCTCTTGGCATCT 58.246 37.500 0.00 0.00 36.33 2.90
4307 5204 5.589452 AGAGCTATTTTTCTCTTGGCATCTG 59.411 40.000 0.00 0.00 36.33 2.90
4318 5215 1.878211 TGGCATCTGTCCACCATCTA 58.122 50.000 0.00 0.00 0.00 1.98
4349 5246 6.541278 TGAGAAGCATTATCAACCATCTCAAG 59.459 38.462 0.00 0.00 44.25 3.02
4354 5251 5.277876 GCATTATCAACCATCTCAAGCAGAG 60.278 44.000 0.09 0.09 46.14 3.35
4514 5411 0.593128 CCAACTTTGTTCTCAGGCCG 59.407 55.000 0.00 0.00 0.00 6.13
4665 5563 8.837788 ATGATCTTTATATCGATTCAAGTGCA 57.162 30.769 1.71 6.98 0.00 4.57
4698 5596 7.429340 CCGAACAATAATGCAAGTAATCTGTTC 59.571 37.037 15.26 15.26 34.29 3.18
4803 5701 2.440409 GTGAACACTGCCCAATCATCT 58.560 47.619 0.00 0.00 0.00 2.90
4826 5724 8.515695 TCTGAAATGCTGAATAGATGACAAAT 57.484 30.769 0.00 0.00 0.00 2.32
4967 5869 6.642540 CACCCTGAAAACTGAAGCTTTATTTC 59.357 38.462 0.00 9.80 0.00 2.17
4991 5894 6.823182 TCTTCATATACGGCAATATTGGATGG 59.177 38.462 17.02 0.00 0.00 3.51
5041 5944 6.146347 GTGAAACATTGTGAACTACTCTCTCC 59.854 42.308 0.00 0.00 36.32 3.71
5121 6025 9.391006 TCATAACATTTGAGTTTATGTACTCCC 57.609 33.333 0.00 0.00 43.11 4.30
5122 6026 9.396022 CATAACATTTGAGTTTATGTACTCCCT 57.604 33.333 0.00 0.00 43.11 4.20
5123 6027 7.923414 AACATTTGAGTTTATGTACTCCCTC 57.077 36.000 0.00 0.00 43.11 4.30
5124 6028 6.415573 ACATTTGAGTTTATGTACTCCCTCC 58.584 40.000 0.00 0.00 43.11 4.30
5125 6029 4.730949 TTGAGTTTATGTACTCCCTCCG 57.269 45.455 0.00 0.00 43.11 4.63
5126 6030 3.705051 TGAGTTTATGTACTCCCTCCGT 58.295 45.455 0.00 0.00 43.11 4.69
5127 6031 4.091549 TGAGTTTATGTACTCCCTCCGTT 58.908 43.478 0.00 0.00 43.11 4.44
5128 6032 4.159135 TGAGTTTATGTACTCCCTCCGTTC 59.841 45.833 0.00 0.00 43.11 3.95
5129 6033 3.450096 AGTTTATGTACTCCCTCCGTTCC 59.550 47.826 0.00 0.00 0.00 3.62
5130 6034 2.832643 TATGTACTCCCTCCGTTCCA 57.167 50.000 0.00 0.00 0.00 3.53
5131 6035 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
5132 6036 1.946984 TGTACTCCCTCCGTTCCAAT 58.053 50.000 0.00 0.00 0.00 3.16
5133 6037 3.104519 TGTACTCCCTCCGTTCCAATA 57.895 47.619 0.00 0.00 0.00 1.90
5134 6038 3.649843 TGTACTCCCTCCGTTCCAATAT 58.350 45.455 0.00 0.00 0.00 1.28
5135 6039 4.806892 TGTACTCCCTCCGTTCCAATATA 58.193 43.478 0.00 0.00 0.00 0.86
5136 6040 5.399991 TGTACTCCCTCCGTTCCAATATAT 58.600 41.667 0.00 0.00 0.00 0.86
5137 6041 6.554784 TGTACTCCCTCCGTTCCAATATATA 58.445 40.000 0.00 0.00 0.00 0.86
5138 6042 7.011994 TGTACTCCCTCCGTTCCAATATATAA 58.988 38.462 0.00 0.00 0.00 0.98
5139 6043 6.607004 ACTCCCTCCGTTCCAATATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
5140 6044 6.082707 ACTCCCTCCGTTCCAATATATAAGT 58.917 40.000 0.00 0.00 0.00 2.24
5141 6045 6.210984 ACTCCCTCCGTTCCAATATATAAGTC 59.789 42.308 0.00 0.00 0.00 3.01
5142 6046 6.320518 TCCCTCCGTTCCAATATATAAGTCT 58.679 40.000 0.00 0.00 0.00 3.24
5143 6047 6.785963 TCCCTCCGTTCCAATATATAAGTCTT 59.214 38.462 0.00 0.00 0.00 3.01
5144 6048 7.291651 TCCCTCCGTTCCAATATATAAGTCTTT 59.708 37.037 0.00 0.00 0.00 2.52
5145 6049 7.937394 CCCTCCGTTCCAATATATAAGTCTTTT 59.063 37.037 0.00 0.00 0.00 2.27
5146 6050 9.338622 CCTCCGTTCCAATATATAAGTCTTTTT 57.661 33.333 0.00 0.00 0.00 1.94
5165 6069 9.453325 GTCTTTTTAGAGATTCCACTATAGTCG 57.547 37.037 1.26 0.00 0.00 4.18
5166 6070 8.630917 TCTTTTTAGAGATTCCACTATAGTCGG 58.369 37.037 1.26 8.54 0.00 4.79
5167 6071 8.529424 TTTTTAGAGATTCCACTATAGTCGGA 57.471 34.615 15.83 15.83 0.00 4.55
5168 6072 7.747155 TTTAGAGATTCCACTATAGTCGGAG 57.253 40.000 17.83 3.42 30.79 4.63
5169 6073 4.658063 AGAGATTCCACTATAGTCGGAGG 58.342 47.826 17.83 10.90 30.79 4.30
5170 6074 3.759618 GAGATTCCACTATAGTCGGAGGG 59.240 52.174 17.83 10.61 30.79 4.30
5171 6075 3.398292 AGATTCCACTATAGTCGGAGGGA 59.602 47.826 17.83 12.35 30.79 4.20
5172 6076 2.953284 TCCACTATAGTCGGAGGGAG 57.047 55.000 15.83 0.00 0.00 4.30
5173 6077 2.133520 TCCACTATAGTCGGAGGGAGT 58.866 52.381 15.83 0.00 0.00 3.85
5174 6078 3.321039 TCCACTATAGTCGGAGGGAGTA 58.679 50.000 15.83 0.00 35.10 2.59
5204 6109 4.141413 TGCTGCCATGTTCATTAGGAGTAT 60.141 41.667 0.00 0.00 0.00 2.12
5257 6200 6.382869 AGCATATTAGTCTGCAAATTGACC 57.617 37.500 0.00 0.00 40.88 4.02
5322 6323 7.272978 AGTTTTCGTTGTATATACTCATGCCT 58.727 34.615 13.89 0.00 0.00 4.75
5324 6325 8.485591 GTTTTCGTTGTATATACTCATGCCTAC 58.514 37.037 13.89 1.20 0.00 3.18
5329 6330 7.094762 CGTTGTATATACTCATGCCTACTGAGA 60.095 40.741 13.89 0.00 42.22 3.27
5330 6331 7.929941 TGTATATACTCATGCCTACTGAGAG 57.070 40.000 13.89 0.00 42.22 3.20
5362 6982 2.705658 TGTTGACCTCCACTCACTGAAT 59.294 45.455 0.00 0.00 0.00 2.57
5363 6983 3.136443 TGTTGACCTCCACTCACTGAATT 59.864 43.478 0.00 0.00 0.00 2.17
5423 7050 8.270080 AGAAAAGAAGAGAAAAGAAAACGAGT 57.730 30.769 0.00 0.00 0.00 4.18
5440 7067 2.523168 TCCAGCACTCGGTGTCCA 60.523 61.111 6.02 0.00 39.05 4.02
5445 7072 0.670546 AGCACTCGGTGTCCATTTCG 60.671 55.000 6.02 0.00 35.75 3.46
5482 7109 2.743752 CGAGCAACGGCATGTCTGG 61.744 63.158 0.00 0.00 44.61 3.86
5488 7115 1.237285 AACGGCATGTCTGGCTGAAC 61.237 55.000 0.00 0.00 45.42 3.18
5561 7188 0.386476 AACGTCGTTGGCACTGTAGA 59.614 50.000 10.39 0.00 0.00 2.59
5648 7279 0.611896 CCCTCCAGCCGTCCAAAATT 60.612 55.000 0.00 0.00 0.00 1.82
5695 7326 6.001460 TCCATTCTCCACGTTCTAAATGTTT 58.999 36.000 0.00 0.00 0.00 2.83
5697 7328 6.072728 CCATTCTCCACGTTCTAAATGTTTGA 60.073 38.462 0.00 0.00 0.00 2.69
5749 7380 2.481449 CGTTCCGGAGAGGGATAAGTTG 60.481 54.545 3.34 0.00 41.52 3.16
5815 7446 2.806856 CGTCCAGCTCAAGCATCGC 61.807 63.158 4.59 0.00 45.16 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 248 5.815581 AGTGGCATAACTCTTGTTTATCCA 58.184 37.500 0.00 0.00 37.59 3.41
373 375 5.676532 TGTCACCAACAAGTAAAATACGG 57.323 39.130 0.00 0.00 34.03 4.02
374 376 7.858382 TCAAATGTCACCAACAAGTAAAATACG 59.142 33.333 0.00 0.00 42.37 3.06
402 404 9.038072 TGTTATGTACAAATAGGGAAGTGAGTA 57.962 33.333 0.00 0.00 32.64 2.59
507 588 4.781087 ACCAGGTGTATAGTATGTGGTTGT 59.219 41.667 0.00 0.00 32.87 3.32
509 590 6.670902 AGTTACCAGGTGTATAGTATGTGGTT 59.329 38.462 0.76 0.00 37.90 3.67
510 591 6.097839 CAGTTACCAGGTGTATAGTATGTGGT 59.902 42.308 0.76 0.00 40.02 4.16
511 592 6.322969 TCAGTTACCAGGTGTATAGTATGTGG 59.677 42.308 0.76 0.00 0.00 4.17
512 593 7.342769 TCAGTTACCAGGTGTATAGTATGTG 57.657 40.000 0.76 0.00 0.00 3.21
513 594 7.783119 TCATCAGTTACCAGGTGTATAGTATGT 59.217 37.037 0.76 0.00 0.00 2.29
514 595 8.178313 TCATCAGTTACCAGGTGTATAGTATG 57.822 38.462 0.76 0.00 0.00 2.39
515 596 8.958060 ATCATCAGTTACCAGGTGTATAGTAT 57.042 34.615 0.76 0.00 0.00 2.12
550 636 2.183478 ATGTGGCATGTTCTCGACAA 57.817 45.000 0.00 0.00 42.62 3.18
551 637 3.118811 TCATATGTGGCATGTTCTCGACA 60.119 43.478 1.90 0.00 43.71 4.35
557 643 4.147321 AGGGATTCATATGTGGCATGTTC 58.853 43.478 1.90 0.00 0.00 3.18
589 676 4.271776 CGGTCCTTCTTTACAGTCGTTTTT 59.728 41.667 0.00 0.00 0.00 1.94
598 685 4.020039 TCCAATTAGCGGTCCTTCTTTACA 60.020 41.667 0.00 0.00 0.00 2.41
792 884 5.535783 TCTCATTGCTCAATCACCTCAAAAA 59.464 36.000 0.00 0.00 0.00 1.94
793 885 5.072055 TCTCATTGCTCAATCACCTCAAAA 58.928 37.500 0.00 0.00 0.00 2.44
795 887 4.290711 TCTCATTGCTCAATCACCTCAA 57.709 40.909 0.00 0.00 0.00 3.02
797 889 5.831702 ATTTCTCATTGCTCAATCACCTC 57.168 39.130 0.00 0.00 0.00 3.85
798 890 6.888632 ACTTATTTCTCATTGCTCAATCACCT 59.111 34.615 0.00 0.00 0.00 4.00
799 891 7.066766 AGACTTATTTCTCATTGCTCAATCACC 59.933 37.037 0.00 0.00 0.00 4.02
800 892 7.983307 AGACTTATTTCTCATTGCTCAATCAC 58.017 34.615 0.00 0.00 0.00 3.06
802 894 8.457261 ACAAGACTTATTTCTCATTGCTCAATC 58.543 33.333 0.00 0.00 0.00 2.67
804 896 7.229306 ACACAAGACTTATTTCTCATTGCTCAA 59.771 33.333 0.00 0.00 0.00 3.02
806 898 7.020010 CACACAAGACTTATTTCTCATTGCTC 58.980 38.462 0.00 0.00 0.00 4.26
807 899 6.488006 ACACACAAGACTTATTTCTCATTGCT 59.512 34.615 0.00 0.00 0.00 3.91
858 1395 5.163884 GGTAGTTAGCTGAATTGGTCGTTTC 60.164 44.000 0.00 0.00 0.00 2.78
1153 1708 2.281208 CCCGAGCCCAACGAACAA 60.281 61.111 0.00 0.00 0.00 2.83
1219 1774 5.973565 GGATTTTACAGTGAATACAGCATGC 59.026 40.000 10.51 10.51 42.53 4.06
1226 1781 9.941664 CAGAATGATGGATTTTACAGTGAATAC 57.058 33.333 0.00 0.00 39.69 1.89
1241 1796 0.178767 CCACCGAGCAGAATGATGGA 59.821 55.000 0.00 0.00 39.69 3.41
1306 1861 3.869246 CGTCCAACTCCAATATGTACCAC 59.131 47.826 0.00 0.00 0.00 4.16
1476 2072 7.827701 TGTGTTTATCAACAACAGGTTAACAA 58.172 30.769 8.10 0.00 44.72 2.83
1503 2099 7.864108 TTCTGATAACCACCATGATTACAAG 57.136 36.000 0.00 0.00 0.00 3.16
1677 2274 3.007635 CACTTATTTTGGGACGGAGGAC 58.992 50.000 0.00 0.00 0.00 3.85
1678 2275 2.640826 ACACTTATTTTGGGACGGAGGA 59.359 45.455 0.00 0.00 0.00 3.71
1708 2305 7.822822 AGTGTCTCAACTTTAGTACAACTTTGT 59.177 33.333 0.00 0.00 44.86 2.83
1925 2532 4.162131 TCAATCATCTCGAATCCAACCTGA 59.838 41.667 0.00 0.00 0.00 3.86
2080 2687 5.673818 GCGCCTACAGAATTTTAAAGGAGTG 60.674 44.000 0.00 0.00 0.00 3.51
2278 2885 1.304282 CCAGCTGCCCAACCTGTAT 59.696 57.895 8.66 0.00 0.00 2.29
2328 2935 7.701539 ATCAAGATTAGCATTTACCACAACA 57.298 32.000 0.00 0.00 0.00 3.33
2342 2949 8.359642 TGACAAAAGGAACCAAATCAAGATTAG 58.640 33.333 0.00 0.00 0.00 1.73
2365 2972 8.902806 TGGAACCAAATTATATTGATCTGTGAC 58.097 33.333 0.00 0.00 31.84 3.67
2410 3017 3.575687 TCCAGATCATCGTACATCTGCAT 59.424 43.478 13.07 0.00 43.27 3.96
2568 3178 6.995091 GTCATGAGGCTTTCATCCTATAGTTT 59.005 38.462 0.00 0.00 44.76 2.66
2605 3215 6.889019 AACTTAAGAGTGCTTAGCGATTAC 57.111 37.500 10.09 0.00 37.84 1.89
2664 3274 5.888161 ACTGAGTTCAAAGAACAGTTCCAAT 59.112 36.000 9.85 0.00 38.41 3.16
2710 3320 9.548208 GAGATGCTCTTACAATCAGTTTTTAAC 57.452 33.333 0.00 0.00 0.00 2.01
2754 3364 2.826738 GCGATTTTAGGCGCCCCA 60.827 61.111 26.15 8.93 46.93 4.96
2935 3563 3.486542 GCGACTACTCGACTTAAATCCGT 60.487 47.826 0.00 0.00 43.06 4.69
3038 3668 2.186903 GCGCCCGAATCAAGGAGA 59.813 61.111 0.00 0.00 0.00 3.71
3320 4000 2.756283 CCTCGTCGGCTCCTCCTT 60.756 66.667 0.00 0.00 0.00 3.36
3751 4448 2.174854 ACAGCCTGGAACCTTACAAGTT 59.825 45.455 0.00 0.00 0.00 2.66
3752 4449 1.774856 ACAGCCTGGAACCTTACAAGT 59.225 47.619 0.00 0.00 0.00 3.16
3803 4698 8.303780 TCATTTCACTAAATTGGCATTGGATA 57.696 30.769 0.00 0.00 32.87 2.59
3805 4700 6.602410 TCATTTCACTAAATTGGCATTGGA 57.398 33.333 0.00 0.00 32.87 3.53
3858 4753 7.651808 ACCGCAAAATGATATCTTCCTAATTG 58.348 34.615 3.98 1.92 0.00 2.32
3918 4815 4.822350 GGCCTAACAATCCAATCTAAGGAC 59.178 45.833 0.00 0.00 38.13 3.85
3952 4849 7.120726 GCTTGCTTTATTCTACAAAGGGTCTTA 59.879 37.037 0.00 0.00 34.28 2.10
4066 4963 0.738412 TAGTTAAGTTCGCCCGCTGC 60.738 55.000 0.00 0.00 0.00 5.25
4067 4964 1.278238 CTAGTTAAGTTCGCCCGCTG 58.722 55.000 0.00 0.00 0.00 5.18
4068 4965 0.459759 GCTAGTTAAGTTCGCCCGCT 60.460 55.000 0.00 0.00 0.00 5.52
4069 4966 0.738412 TGCTAGTTAAGTTCGCCCGC 60.738 55.000 0.00 0.00 0.00 6.13
4070 4967 1.593006 CATGCTAGTTAAGTTCGCCCG 59.407 52.381 0.00 0.00 0.00 6.13
4071 4968 1.330829 GCATGCTAGTTAAGTTCGCCC 59.669 52.381 11.37 0.00 0.00 6.13
4072 4969 2.030946 CAGCATGCTAGTTAAGTTCGCC 59.969 50.000 22.19 0.00 0.00 5.54
4073 4970 2.930040 TCAGCATGCTAGTTAAGTTCGC 59.070 45.455 22.19 0.00 34.76 4.70
4074 4971 3.926527 TGTCAGCATGCTAGTTAAGTTCG 59.073 43.478 22.19 3.76 34.76 3.95
4075 4972 6.428385 AATGTCAGCATGCTAGTTAAGTTC 57.572 37.500 22.19 5.81 35.15 3.01
4076 4973 6.207417 ACAAATGTCAGCATGCTAGTTAAGTT 59.793 34.615 22.19 7.35 35.15 2.66
4077 4974 5.707298 ACAAATGTCAGCATGCTAGTTAAGT 59.293 36.000 22.19 11.08 35.15 2.24
4078 4975 6.025896 CACAAATGTCAGCATGCTAGTTAAG 58.974 40.000 22.19 7.04 35.15 1.85
4079 4976 5.619757 GCACAAATGTCAGCATGCTAGTTAA 60.620 40.000 22.19 5.02 35.15 2.01
4080 4977 4.142622 GCACAAATGTCAGCATGCTAGTTA 60.143 41.667 22.19 7.73 35.15 2.24
4081 4978 3.366679 GCACAAATGTCAGCATGCTAGTT 60.367 43.478 22.19 7.95 35.15 2.24
4082 4979 2.163010 GCACAAATGTCAGCATGCTAGT 59.837 45.455 22.19 0.49 35.15 2.57
4083 4980 2.162809 TGCACAAATGTCAGCATGCTAG 59.837 45.455 22.19 14.88 35.15 3.42
4102 4999 6.315393 TGAGTAAACGAGGGAGAAATAAATGC 59.685 38.462 0.00 0.00 0.00 3.56
4164 5061 9.507280 AGATTCACAATGATAAAAGTTATTGCG 57.493 29.630 0.00 0.00 34.69 4.85
4188 5085 6.369629 TCCCAGAACAATAACAAAGGAAAGA 58.630 36.000 0.00 0.00 0.00 2.52
4232 5129 5.260424 TCCCAGCTCATTGCAACTATTTTA 58.740 37.500 0.00 0.00 45.94 1.52
4318 5215 6.189859 TGGTTGATAATGCTTCTCATCCTTT 58.810 36.000 10.81 0.00 33.40 3.11
4349 5246 2.882742 GTGGAAAATCACGACTCTGC 57.117 50.000 0.00 0.00 0.00 4.26
4653 5551 1.664016 GGTTGTGCTGCACTTGAATCG 60.664 52.381 30.43 0.00 35.11 3.34
4665 5563 2.556189 TGCATTATTGTTCGGTTGTGCT 59.444 40.909 0.00 0.00 32.87 4.40
4698 5596 3.508762 GAATGTGAAATCAAGCTGCAGG 58.491 45.455 17.12 0.00 0.00 4.85
4803 5701 8.283699 TGATTTGTCATCTATTCAGCATTTCA 57.716 30.769 0.00 0.00 0.00 2.69
4967 5869 6.599244 ACCATCCAATATTGCCGTATATGAAG 59.401 38.462 10.11 0.00 0.00 3.02
5117 6021 6.437793 AGACTTATATATTGGAACGGAGGGAG 59.562 42.308 0.00 0.00 0.00 4.30
5118 6022 6.320518 AGACTTATATATTGGAACGGAGGGA 58.679 40.000 0.00 0.00 0.00 4.20
5119 6023 6.607004 AGACTTATATATTGGAACGGAGGG 57.393 41.667 0.00 0.00 0.00 4.30
5120 6024 8.904099 AAAAGACTTATATATTGGAACGGAGG 57.096 34.615 0.00 0.00 0.00 4.30
5139 6043 9.453325 CGACTATAGTGGAATCTCTAAAAAGAC 57.547 37.037 10.90 0.00 0.00 3.01
5140 6044 8.630917 CCGACTATAGTGGAATCTCTAAAAAGA 58.369 37.037 15.77 0.00 0.00 2.52
5141 6045 8.630917 TCCGACTATAGTGGAATCTCTAAAAAG 58.369 37.037 15.77 0.00 0.00 2.27
5142 6046 8.529424 TCCGACTATAGTGGAATCTCTAAAAA 57.471 34.615 15.77 0.00 0.00 1.94
5143 6047 7.230913 CCTCCGACTATAGTGGAATCTCTAAAA 59.769 40.741 15.77 0.00 0.00 1.52
5144 6048 6.715718 CCTCCGACTATAGTGGAATCTCTAAA 59.284 42.308 15.77 0.00 0.00 1.85
5145 6049 6.239396 CCTCCGACTATAGTGGAATCTCTAA 58.761 44.000 15.77 0.00 0.00 2.10
5146 6050 5.280573 CCCTCCGACTATAGTGGAATCTCTA 60.281 48.000 15.77 0.00 0.00 2.43
5147 6051 4.507691 CCCTCCGACTATAGTGGAATCTCT 60.508 50.000 15.77 0.00 0.00 3.10
5148 6052 3.759618 CCCTCCGACTATAGTGGAATCTC 59.240 52.174 15.77 0.00 0.00 2.75
5149 6053 3.398292 TCCCTCCGACTATAGTGGAATCT 59.602 47.826 15.77 0.00 0.00 2.40
5150 6054 3.759618 CTCCCTCCGACTATAGTGGAATC 59.240 52.174 15.77 0.00 0.00 2.52
5151 6055 3.140519 ACTCCCTCCGACTATAGTGGAAT 59.859 47.826 15.77 0.69 0.00 3.01
5152 6056 2.512896 ACTCCCTCCGACTATAGTGGAA 59.487 50.000 15.77 0.00 0.00 3.53
5153 6057 2.133520 ACTCCCTCCGACTATAGTGGA 58.866 52.381 15.77 16.91 0.00 4.02
5154 6058 2.660670 ACTCCCTCCGACTATAGTGG 57.339 55.000 10.90 9.20 0.00 4.00
5155 6059 5.875910 CAGTATACTCCCTCCGACTATAGTG 59.124 48.000 10.90 2.85 0.00 2.74
5156 6060 5.547276 ACAGTATACTCCCTCCGACTATAGT 59.453 44.000 4.68 4.68 0.00 2.12
5157 6061 6.052405 ACAGTATACTCCCTCCGACTATAG 57.948 45.833 1.26 0.00 0.00 1.31
5158 6062 6.236409 CAACAGTATACTCCCTCCGACTATA 58.764 44.000 1.26 0.00 0.00 1.31
5159 6063 4.997545 ACAGTATACTCCCTCCGACTAT 57.002 45.455 1.26 0.00 0.00 2.12
5160 6064 4.458397 CAACAGTATACTCCCTCCGACTA 58.542 47.826 1.26 0.00 0.00 2.59
5161 6065 3.288964 CAACAGTATACTCCCTCCGACT 58.711 50.000 1.26 0.00 0.00 4.18
5162 6066 2.223758 GCAACAGTATACTCCCTCCGAC 60.224 54.545 1.26 0.00 0.00 4.79
5163 6067 2.029623 GCAACAGTATACTCCCTCCGA 58.970 52.381 1.26 0.00 0.00 4.55
5164 6068 2.032620 AGCAACAGTATACTCCCTCCG 58.967 52.381 1.26 0.00 0.00 4.63
5165 6069 2.483889 GCAGCAACAGTATACTCCCTCC 60.484 54.545 1.26 0.00 0.00 4.30
5166 6070 2.483889 GGCAGCAACAGTATACTCCCTC 60.484 54.545 1.26 0.00 0.00 4.30
5167 6071 1.486726 GGCAGCAACAGTATACTCCCT 59.513 52.381 1.26 0.00 0.00 4.20
5168 6072 1.209504 TGGCAGCAACAGTATACTCCC 59.790 52.381 1.26 0.00 0.00 4.30
5169 6073 2.691409 TGGCAGCAACAGTATACTCC 57.309 50.000 1.26 0.00 0.00 3.85
5170 6074 3.535561 ACATGGCAGCAACAGTATACTC 58.464 45.455 1.26 0.00 0.00 2.59
5171 6075 3.634397 ACATGGCAGCAACAGTATACT 57.366 42.857 0.00 0.00 0.00 2.12
5172 6076 3.689161 TGAACATGGCAGCAACAGTATAC 59.311 43.478 0.00 0.00 0.00 1.47
5173 6077 3.949132 TGAACATGGCAGCAACAGTATA 58.051 40.909 0.00 0.00 0.00 1.47
5174 6078 2.794103 TGAACATGGCAGCAACAGTAT 58.206 42.857 0.00 0.00 0.00 2.12
5223 6128 8.131100 TGCAGACTAATATGCTTCTTAATTTGC 58.869 33.333 0.00 0.00 43.75 3.68
5229 6134 9.394767 TCAATTTGCAGACTAATATGCTTCTTA 57.605 29.630 0.00 0.00 43.75 2.10
5329 6330 2.625790 GAGGTCAACATCCGAGATAGCT 59.374 50.000 0.00 0.00 0.00 3.32
5330 6331 2.288518 GGAGGTCAACATCCGAGATAGC 60.289 54.545 0.00 0.00 37.06 2.97
5340 6960 2.329267 TCAGTGAGTGGAGGTCAACAT 58.671 47.619 0.00 0.00 0.00 2.71
5404 7024 5.559225 GCTGGACTCGTTTTCTTTTCTCTTC 60.559 44.000 0.00 0.00 0.00 2.87
5405 7025 4.273724 GCTGGACTCGTTTTCTTTTCTCTT 59.726 41.667 0.00 0.00 0.00 2.85
5406 7026 3.810386 GCTGGACTCGTTTTCTTTTCTCT 59.190 43.478 0.00 0.00 0.00 3.10
5407 7027 3.560068 TGCTGGACTCGTTTTCTTTTCTC 59.440 43.478 0.00 0.00 0.00 2.87
5408 7028 3.312697 GTGCTGGACTCGTTTTCTTTTCT 59.687 43.478 0.00 0.00 0.00 2.52
5423 7050 1.480212 AATGGACACCGAGTGCTGGA 61.480 55.000 4.23 0.00 39.64 3.86
5440 7067 2.035449 TGTCACGACAGGAGAACGAAAT 59.965 45.455 0.00 0.00 36.21 2.17
5445 7072 1.488527 GTGTGTCACGACAGGAGAAC 58.511 55.000 0.00 0.00 42.74 3.01
5488 7115 6.777091 TGGAAATACAAATATCCCCTGATGTG 59.223 38.462 0.00 0.00 32.18 3.21
5626 7257 1.710996 TTTGGACGGCTGGAGGGAAA 61.711 55.000 0.00 0.00 0.00 3.13
5648 7279 2.202797 GAGCGCCGCTGAAGATCA 60.203 61.111 20.07 0.00 39.88 2.92
5697 7328 5.877031 TCGAACGAAAACGAGAGATTATCT 58.123 37.500 0.00 0.00 42.61 1.98


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

AutoCloner maintained by Alex Coulton.