Multiple sequence alignment - TraesCS2B01G269300

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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 TraesCS2B01G269300 chr2B 100.000 3071 0 0 577 3647 364950157 364947087 0.000000e+00 5672.0
1 TraesCS2B01G269300 chr2B 87.356 522 49 13 2772 3284 228887064 228886551 1.890000e-162 582.0
2 TraesCS2B01G269300 chr2B 100.000 260 0 0 1 260 364950733 364950474 7.080000e-132 481.0
3 TraesCS2B01G269300 chr2B 83.529 170 16 10 600 766 72808070 72808230 8.160000e-32 148.0
4 TraesCS2B01G269300 chr2D 89.269 1053 64 20 594 1608 296708568 296709609 0.000000e+00 1273.0
5 TraesCS2B01G269300 chr2D 89.481 732 59 11 2780 3503 647764699 647765420 0.000000e+00 909.0
6 TraesCS2B01G269300 chr2D 88.139 548 29 13 949 1460 63554210 63554757 1.440000e-173 619.0
7 TraesCS2B01G269300 chr2D 95.479 376 17 0 2370 2745 63555556 63555931 5.210000e-168 601.0
8 TraesCS2B01G269300 chr2D 95.763 354 14 1 2025 2378 296710112 296710464 1.470000e-158 569.0
9 TraesCS2B01G269300 chr2D 94.857 350 16 2 1692 2041 296709609 296709956 2.480000e-151 545.0
10 TraesCS2B01G269300 chr2D 97.569 288 7 0 2370 2657 296710519 296710806 9.100000e-136 494.0
11 TraesCS2B01G269300 chr2D 88.162 321 23 7 1705 2016 63554905 63555219 5.750000e-98 368.0
12 TraesCS2B01G269300 chr2D 85.223 291 30 10 2095 2378 63555217 63555501 1.660000e-73 287.0
13 TraesCS2B01G269300 chr2D 85.145 276 17 7 1 253 296708048 296708322 1.000000e-65 261.0
14 TraesCS2B01G269300 chr2D 84.536 194 22 3 612 803 644056068 644056255 6.220000e-43 185.0
15 TraesCS2B01G269300 chr2D 91.803 61 5 0 1551 1611 243120618 243120558 6.490000e-13 86.1
16 TraesCS2B01G269300 chr2A 93.134 670 43 2 1711 2378 369215006 369215674 0.000000e+00 979.0
17 TraesCS2B01G269300 chr2A 90.375 613 30 8 876 1460 65173478 65174089 0.000000e+00 778.0
18 TraesCS2B01G269300 chr2A 92.944 411 27 2 2370 2779 369215729 369216138 6.740000e-167 597.0
19 TraesCS2B01G269300 chr2A 95.213 376 18 0 2370 2745 65174834 65175209 2.420000e-166 595.0
20 TraesCS2B01G269300 chr2A 86.988 415 35 9 1713 2122 65174178 65174578 2.000000e-122 449.0
21 TraesCS2B01G269300 chr2A 91.667 264 14 2 808 1067 369201634 369201375 3.460000e-95 359.0
22 TraesCS2B01G269300 chr2A 84.469 367 38 14 1251 1611 369214637 369214990 9.700000e-91 344.0
23 TraesCS2B01G269300 chr2A 91.795 195 11 2 1073 1265 369204547 369204738 2.160000e-67 267.0
24 TraesCS2B01G269300 chr2A 93.642 173 11 0 2206 2378 65174607 65174779 3.610000e-65 259.0
25 TraesCS2B01G269300 chr2A 96.040 101 4 0 1595 1695 159582129 159582029 8.100000e-37 165.0
26 TraesCS2B01G269300 chr2A 81.068 206 27 9 600 803 176051325 176051520 1.750000e-33 154.0
27 TraesCS2B01G269300 chr2A 93.182 44 3 0 2397 2440 65176505 65176548 8.450000e-07 65.8
28 TraesCS2B01G269300 chr6B 85.383 732 84 16 2780 3503 189357860 189357144 0.000000e+00 737.0
29 TraesCS2B01G269300 chr6B 97.938 97 2 0 1603 1699 63750275 63750179 6.260000e-38 169.0
30 TraesCS2B01G269300 chr6B 96.117 103 3 1 1602 1703 28914251 28914353 2.250000e-37 167.0
31 TraesCS2B01G269300 chr6B 98.913 92 1 0 1609 1700 506874009 506874100 8.100000e-37 165.0
32 TraesCS2B01G269300 chr6B 86.486 111 6 7 645 754 450312 450414 2.980000e-21 113.0
33 TraesCS2B01G269300 chr1A 90.310 516 37 10 2779 3284 302919230 302919742 0.000000e+00 664.0
34 TraesCS2B01G269300 chr1A 86.634 202 20 3 603 803 33136328 33136523 2.210000e-52 217.0
35 TraesCS2B01G269300 chr1A 84.906 159 16 3 645 803 489352232 489352082 1.750000e-33 154.0
36 TraesCS2B01G269300 chr1A 82.014 139 21 4 676 812 507890445 507890309 8.280000e-22 115.0
37 TraesCS2B01G269300 chr5B 87.961 515 48 13 2780 3284 280983229 280983739 2.420000e-166 595.0
38 TraesCS2B01G269300 chr1B 86.219 566 56 17 2779 3333 31225261 31225815 8.720000e-166 593.0
39 TraesCS2B01G269300 chr1B 81.604 212 27 7 602 809 108847093 108846890 8.100000e-37 165.0
40 TraesCS2B01G269300 chr1B 97.895 95 2 0 1601 1695 660748386 660748480 8.100000e-37 165.0
41 TraesCS2B01G269300 chr1B 97.849 93 2 0 1604 1696 102141162 102141254 1.050000e-35 161.0
42 TraesCS2B01G269300 chr1B 97.872 94 1 1 1607 1699 149606481 149606574 1.050000e-35 161.0
43 TraesCS2B01G269300 chr1B 98.889 90 1 0 1609 1698 301949518 301949429 1.050000e-35 161.0
44 TraesCS2B01G269300 chr1B 94.118 102 5 1 1594 1695 563409900 563409800 1.750000e-33 154.0
45 TraesCS2B01G269300 chr1B 90.991 111 8 2 1586 1696 301949410 301949518 8.160000e-32 148.0
46 TraesCS2B01G269300 chr4B 87.938 514 46 12 2779 3284 512736382 512736887 3.140000e-165 592.0
47 TraesCS2B01G269300 chr4B 100.000 91 0 0 1605 1695 23323108 23323018 6.260000e-38 169.0
48 TraesCS2B01G269300 chr4B 95.960 99 2 2 1609 1705 40169983 40170081 3.770000e-35 159.0
49 TraesCS2B01G269300 chr4B 95.833 96 4 0 1602 1697 323791057 323790962 4.880000e-34 156.0
50 TraesCS2B01G269300 chr4B 96.774 93 3 0 1603 1695 631442106 631442198 4.880000e-34 156.0
51 TraesCS2B01G269300 chr7B 87.743 514 50 13 2780 3284 651305691 651306200 4.060000e-164 588.0
52 TraesCS2B01G269300 chr7B 96.078 153 4 2 3495 3647 463158519 463158369 7.820000e-62 248.0
53 TraesCS2B01G269300 chr7B 82.988 241 27 10 577 810 453288364 453288597 4.770000e-49 206.0
54 TraesCS2B01G269300 chr7B 95.192 104 2 2 1597 1698 697607626 697607728 1.050000e-35 161.0
55 TraesCS2B01G269300 chr7A 81.465 669 88 25 2780 3437 379023647 379024290 1.940000e-142 516.0
56 TraesCS2B01G269300 chr7A 86.038 265 36 1 3240 3503 628952139 628952403 2.140000e-72 283.0
57 TraesCS2B01G269300 chr7A 100.000 91 0 0 1607 1697 556574278 556574368 6.260000e-38 169.0
58 TraesCS2B01G269300 chr7A 82.036 167 16 12 645 809 18671657 18671811 2.960000e-26 130.0
59 TraesCS2B01G269300 chr6D 98.611 144 2 0 3504 3647 148179382 148179525 4.670000e-64 255.0
60 TraesCS2B01G269300 chr6D 93.373 166 7 4 3484 3647 85807584 85807421 3.640000e-60 243.0
61 TraesCS2B01G269300 chr6D 83.824 204 22 7 602 803 388144110 388144304 2.240000e-42 183.0
62 TraesCS2B01G269300 chr6D 86.667 165 15 3 645 809 81153161 81153004 3.740000e-40 176.0
63 TraesCS2B01G269300 chr6D 100.000 86 0 0 1610 1695 379808968 379809053 3.770000e-35 159.0
64 TraesCS2B01G269300 chr6D 98.864 88 1 0 1609 1696 155146866 155146779 1.360000e-34 158.0
65 TraesCS2B01G269300 chr6D 97.802 91 2 0 1605 1695 194007125 194007035 1.360000e-34 158.0
66 TraesCS2B01G269300 chr6D 97.753 89 2 0 1608 1696 216847365 216847277 1.750000e-33 154.0
67 TraesCS2B01G269300 chr6D 93.204 103 5 2 1603 1705 277256766 277256666 2.270000e-32 150.0
68 TraesCS2B01G269300 chr6D 84.466 103 15 1 701 803 283547833 283547934 2.320000e-17 100.0
69 TraesCS2B01G269300 chr1D 98.611 144 2 0 3504 3647 10693576 10693719 4.670000e-64 255.0
70 TraesCS2B01G269300 chr1D 85.321 218 25 3 594 810 247368850 247369061 6.130000e-53 219.0
71 TraesCS2B01G269300 chr1D 83.163 196 22 7 609 802 60942300 60942114 6.260000e-38 169.0
72 TraesCS2B01G269300 chr1D 98.876 89 1 0 1610 1698 107173677 107173589 3.770000e-35 159.0
73 TraesCS2B01G269300 chr1D 97.802 91 2 0 1609 1699 464771375 464771285 1.360000e-34 158.0
74 TraesCS2B01G269300 chr1D 95.833 96 4 0 1600 1695 21548178 21548083 4.880000e-34 156.0
75 TraesCS2B01G269300 chr1D 95.833 96 4 0 1609 1704 27855873 27855778 4.880000e-34 156.0
76 TraesCS2B01G269300 chr3D 96.711 152 4 1 3497 3647 188313486 188313637 6.050000e-63 252.0
77 TraesCS2B01G269300 chr3D 94.904 157 7 1 3491 3647 402725155 402725000 1.010000e-60 244.0
78 TraesCS2B01G269300 chr3D 83.019 212 27 5 596 806 579962978 579962775 2.240000e-42 183.0
79 TraesCS2B01G269300 chr7D 95.541 157 4 3 3493 3647 119876874 119876719 7.820000e-62 248.0
80 TraesCS2B01G269300 chr7D 95.513 156 5 2 3492 3647 425528230 425528077 7.820000e-62 248.0
81 TraesCS2B01G269300 chr7D 93.636 110 6 1 1602 1710 264138554 264138445 2.910000e-36 163.0
82 TraesCS2B01G269300 chr7D 91.071 112 9 1 1585 1696 264138437 264138547 2.270000e-32 150.0
83 TraesCS2B01G269300 chr7D 82.486 177 22 6 634 810 371827419 371827586 2.930000e-31 147.0
84 TraesCS2B01G269300 chr7D 82.222 135 16 6 596 729 565962092 565961965 3.850000e-20 110.0
85 TraesCS2B01G269300 chr4D 94.937 158 7 1 3490 3647 80104026 80104182 2.810000e-61 246.0
86 TraesCS2B01G269300 chr4D 98.913 92 1 0 1607 1698 9296464 9296555 8.100000e-37 165.0
87 TraesCS2B01G269300 chr4D 98.913 92 0 1 1609 1699 164649455 164649546 2.910000e-36 163.0
88 TraesCS2B01G269300 chr4D 90.179 112 11 0 1605 1716 9296557 9296446 2.930000e-31 147.0
89 TraesCS2B01G269300 chr4D 85.507 69 10 0 7 75 19414663 19414595 5.050000e-09 73.1
90 TraesCS2B01G269300 chr3A 84.615 195 23 5 609 803 730676315 730676502 1.730000e-43 187.0
91 TraesCS2B01G269300 chr3A 83.085 201 27 4 609 809 375488597 375488404 3.740000e-40 176.0
92 TraesCS2B01G269300 chr3A 87.500 136 17 0 1555 1690 647888520 647888385 1.360000e-34 158.0
93 TraesCS2B01G269300 chr3A 82.635 167 22 4 644 810 102688880 102688721 1.370000e-29 141.0
94 TraesCS2B01G269300 chr6A 83.254 209 23 7 597 802 99374918 99374719 8.040000e-42 182.0
95 TraesCS2B01G269300 chr6A 95.098 102 4 1 1603 1703 224620494 224620595 3.770000e-35 159.0
96 TraesCS2B01G269300 chrUn 98.851 87 1 0 1609 1695 35713342 35713256 4.880000e-34 156.0
97 TraesCS2B01G269300 chrUn 98.851 87 1 0 1609 1695 37289164 37289250 4.880000e-34 156.0
98 TraesCS2B01G269300 chrUn 98.851 87 1 0 1609 1695 37292340 37292426 4.880000e-34 156.0
99 TraesCS2B01G269300 chrUn 96.809 94 2 1 1610 1702 94636343 94636250 4.880000e-34 156.0
100 TraesCS2B01G269300 chrUn 97.753 89 2 0 1609 1697 48472395 48472307 1.750000e-33 154.0
101 TraesCS2B01G269300 chrUn 96.739 92 3 0 1605 1696 65676763 65676672 1.750000e-33 154.0
102 TraesCS2B01G269300 chrUn 96.739 92 3 0 1604 1695 122302095 122302186 1.750000e-33 154.0
103 TraesCS2B01G269300 chrUn 97.753 89 2 0 1609 1697 235114496 235114408 1.750000e-33 154.0
104 TraesCS2B01G269300 chrUn 98.837 86 1 0 1610 1695 263385879 263385964 1.750000e-33 154.0
105 TraesCS2B01G269300 chrUn 96.739 92 3 0 1606 1697 433967105 433967196 1.750000e-33 154.0
106 TraesCS2B01G269300 chrUn 97.753 89 1 1 1608 1695 82709976 82710064 6.310000e-33 152.0
107 TraesCS2B01G269300 chrUn 93.137 102 5 2 1597 1696 37336849 37336950 8.160000e-32 148.0
108 TraesCS2B01G269300 chrUn 79.275 193 17 16 580 765 34348225 34348401 2.980000e-21 113.0
109 TraesCS2B01G269300 chr5D 88.636 88 10 0 7 94 542495804 542495717 1.380000e-19 108.0
110 TraesCS2B01G269300 chr5D 89.130 46 5 0 1 46 446307257 446307302 1.410000e-04 58.4
111 TraesCS2B01G269300 chr5A 95.349 43 2 0 1555 1597 139894254 139894212 6.530000e-08 69.4


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 TraesCS2B01G269300 chr2B 364947087 364950733 3646 True 3076.50 5672 100.000000 1 3647 2 chr2B.!!$R2 3646
1 TraesCS2B01G269300 chr2B 228886551 228887064 513 True 582.00 582 87.356000 2772 3284 1 chr2B.!!$R1 512
2 TraesCS2B01G269300 chr2D 647764699 647765420 721 False 909.00 909 89.481000 2780 3503 1 chr2D.!!$F2 723
3 TraesCS2B01G269300 chr2D 296708048 296710806 2758 False 628.40 1273 92.520600 1 2657 5 chr2D.!!$F4 2656
4 TraesCS2B01G269300 chr2D 63554210 63555931 1721 False 468.75 619 89.250750 949 2745 4 chr2D.!!$F3 1796
5 TraesCS2B01G269300 chr2A 369214637 369216138 1501 False 640.00 979 90.182333 1251 2779 3 chr2A.!!$F4 1528
6 TraesCS2B01G269300 chr2A 65173478 65176548 3070 False 429.36 778 91.880000 876 2745 5 chr2A.!!$F3 1869
7 TraesCS2B01G269300 chr6B 189357144 189357860 716 True 737.00 737 85.383000 2780 3503 1 chr6B.!!$R2 723
8 TraesCS2B01G269300 chr1A 302919230 302919742 512 False 664.00 664 90.310000 2779 3284 1 chr1A.!!$F2 505
9 TraesCS2B01G269300 chr5B 280983229 280983739 510 False 595.00 595 87.961000 2780 3284 1 chr5B.!!$F1 504
10 TraesCS2B01G269300 chr1B 31225261 31225815 554 False 593.00 593 86.219000 2779 3333 1 chr1B.!!$F1 554
11 TraesCS2B01G269300 chr4B 512736382 512736887 505 False 592.00 592 87.938000 2779 3284 1 chr4B.!!$F2 505
12 TraesCS2B01G269300 chr7B 651305691 651306200 509 False 588.00 588 87.743000 2780 3284 1 chr7B.!!$F2 504
13 TraesCS2B01G269300 chr7A 379023647 379024290 643 False 516.00 516 81.465000 2780 3437 1 chr7A.!!$F2 657

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
750 786 0.459078 GGGCTACGGACCTCAACTAC 59.541 60.0 0.0 0.0 37.73 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2647 3060 0.456653 GCAACCAATTAGCTGGCACG 60.457 55.0 0.0 0.0 40.45 5.34 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
42 43 1.151450 GACATGGCGGGAATGGGAT 59.849 57.895 0.00 0.00 0.00 3.85
46 47 4.521292 GGCGGGAATGGGATGGCA 62.521 66.667 0.00 0.00 0.00 4.92
60 61 4.148825 GGCACGGGCGACTCAGAT 62.149 66.667 2.17 0.00 42.47 2.90
61 62 2.887568 GCACGGGCGACTCAGATG 60.888 66.667 0.00 0.00 0.00 2.90
144 145 3.200593 CTGCGGCTCAGGCACATC 61.201 66.667 0.00 0.00 39.15 3.06
147 148 4.147449 CGGCTCAGGCACATCCGA 62.147 66.667 0.00 0.00 42.43 4.55
253 276 1.135083 GCGTATGGATGGATCGGGTAG 60.135 57.143 0.00 0.00 0.00 3.18
254 277 1.135083 CGTATGGATGGATCGGGTAGC 60.135 57.143 0.00 0.00 0.00 3.58
255 278 1.135083 GTATGGATGGATCGGGTAGCG 60.135 57.143 0.00 0.00 0.00 4.26
256 279 1.544825 ATGGATGGATCGGGTAGCGG 61.545 60.000 0.00 0.00 0.00 5.52
257 280 2.657237 GATGGATCGGGTAGCGGG 59.343 66.667 0.00 0.00 0.00 6.13
258 281 3.591254 GATGGATCGGGTAGCGGGC 62.591 68.421 0.00 0.00 0.00 6.13
636 672 0.798771 CCGACGGAAGCGAGAAAGAG 60.799 60.000 8.64 0.00 33.58 2.85
643 679 3.018149 GGAAGCGAGAAAGAGACCTAGA 58.982 50.000 0.00 0.00 0.00 2.43
656 692 7.741554 AAGAGACCTAGAAAACTGATACCAT 57.258 36.000 0.00 0.00 0.00 3.55
657 693 7.118496 AGAGACCTAGAAAACTGATACCATG 57.882 40.000 0.00 0.00 0.00 3.66
676 712 9.916360 ATACCATGTATGAGATTATGATTGCAT 57.084 29.630 0.00 0.00 38.54 3.96
677 713 8.051901 ACCATGTATGAGATTATGATTGCATG 57.948 34.615 0.00 0.00 35.94 4.06
678 714 7.886446 ACCATGTATGAGATTATGATTGCATGA 59.114 33.333 0.00 0.00 35.94 3.07
679 715 8.903820 CCATGTATGAGATTATGATTGCATGAT 58.096 33.333 0.00 0.00 35.94 2.45
680 716 9.722056 CATGTATGAGATTATGATTGCATGATG 57.278 33.333 0.00 0.00 35.94 3.07
681 717 7.758495 TGTATGAGATTATGATTGCATGATGC 58.242 34.615 11.12 11.12 45.29 3.91
698 734 3.805971 TGATGCAGATGTATTGCTCTTCG 59.194 43.478 0.00 0.00 42.02 3.79
701 737 2.286067 GCAGATGTATTGCTCTTCGTGC 60.286 50.000 0.00 0.00 38.51 5.34
709 745 2.967599 TGCTCTTCGTGCATAGACAT 57.032 45.000 0.00 0.00 35.31 3.06
742 778 3.322828 TGTATAAAGATGGGCTACGGACC 59.677 47.826 0.00 0.00 42.24 4.46
750 786 0.459078 GGGCTACGGACCTCAACTAC 59.541 60.000 0.00 0.00 37.73 2.73
756 792 3.547054 ACGGACCTCAACTACACAAAA 57.453 42.857 0.00 0.00 0.00 2.44
778 814 6.819397 AAAACTAAGAGACAAGCCCAATAC 57.181 37.500 0.00 0.00 0.00 1.89
788 824 6.658849 AGACAAGCCCAATACACAATATACA 58.341 36.000 0.00 0.00 0.00 2.29
789 825 6.542370 AGACAAGCCCAATACACAATATACAC 59.458 38.462 0.00 0.00 0.00 2.90
819 867 7.766219 ACATATACACATCACGTCTTTTACC 57.234 36.000 0.00 0.00 0.00 2.85
820 868 7.324935 ACATATACACATCACGTCTTTTACCA 58.675 34.615 0.00 0.00 0.00 3.25
821 869 7.277098 ACATATACACATCACGTCTTTTACCAC 59.723 37.037 0.00 0.00 0.00 4.16
822 870 3.799366 ACACATCACGTCTTTTACCACA 58.201 40.909 0.00 0.00 0.00 4.17
823 871 4.385825 ACACATCACGTCTTTTACCACAT 58.614 39.130 0.00 0.00 0.00 3.21
824 872 4.451096 ACACATCACGTCTTTTACCACATC 59.549 41.667 0.00 0.00 0.00 3.06
825 873 3.678072 ACATCACGTCTTTTACCACATCG 59.322 43.478 0.00 0.00 0.00 3.84
827 875 1.730064 CACGTCTTTTACCACATCGGG 59.270 52.381 0.00 0.00 40.22 5.14
828 876 1.338389 ACGTCTTTTACCACATCGGGG 60.338 52.381 0.00 0.00 40.22 5.73
848 896 4.948004 GGGGAAATGACCAAAGTAGTAAGG 59.052 45.833 0.00 0.00 0.00 2.69
959 1011 4.649954 GCGTGTGCGTGTGCTGTC 62.650 66.667 0.00 0.00 43.34 3.51
1136 1218 1.098869 GTCGAGAGAGAGATGTGGCA 58.901 55.000 0.00 0.00 43.49 4.92
1188 1270 1.154016 CTTCGTGACGGCGATGTCT 60.154 57.895 16.62 0.00 40.76 3.41
1237 1319 3.456365 GCCTCTCTGAGCTCCGCA 61.456 66.667 12.15 0.00 0.00 5.69
1474 1594 3.813166 CGAGGTAAAGGTCTTGCTTCAAA 59.187 43.478 0.00 0.00 0.00 2.69
1486 1606 7.493645 AGGTCTTGCTTCAAAAATTCTTTCTTG 59.506 33.333 0.00 0.00 0.00 3.02
1538 1669 4.282496 ACTCTCTGTCCCGAAATACTCAT 58.718 43.478 0.00 0.00 0.00 2.90
1539 1670 4.339814 ACTCTCTGTCCCGAAATACTCATC 59.660 45.833 0.00 0.00 0.00 2.92
1617 1755 8.575649 TCCATTTCTTTAACAAATACTCCCTC 57.424 34.615 0.00 0.00 0.00 4.30
1618 1756 7.614192 TCCATTTCTTTAACAAATACTCCCTCC 59.386 37.037 0.00 0.00 0.00 4.30
1619 1757 7.415206 CCATTTCTTTAACAAATACTCCCTCCG 60.415 40.741 0.00 0.00 0.00 4.63
1620 1758 5.750352 TCTTTAACAAATACTCCCTCCGT 57.250 39.130 0.00 0.00 0.00 4.69
1621 1759 6.117975 TCTTTAACAAATACTCCCTCCGTT 57.882 37.500 0.00 0.00 0.00 4.44
1622 1760 6.168389 TCTTTAACAAATACTCCCTCCGTTC 58.832 40.000 0.00 0.00 0.00 3.95
1623 1761 3.345508 AACAAATACTCCCTCCGTTCC 57.654 47.619 0.00 0.00 0.00 3.62
1624 1762 2.262637 ACAAATACTCCCTCCGTTCCA 58.737 47.619 0.00 0.00 0.00 3.53
1625 1763 2.640826 ACAAATACTCCCTCCGTTCCAA 59.359 45.455 0.00 0.00 0.00 3.53
1626 1764 3.073356 ACAAATACTCCCTCCGTTCCAAA 59.927 43.478 0.00 0.00 0.00 3.28
1627 1765 4.076394 CAAATACTCCCTCCGTTCCAAAA 58.924 43.478 0.00 0.00 0.00 2.44
1628 1766 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
1629 1767 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
1630 1768 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1631 1769 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1632 1770 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1633 1771 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1634 1772 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1635 1773 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1636 1774 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1637 1775 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1638 1776 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1639 1777 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1640 1778 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1641 1779 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1642 1780 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1643 1781 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1644 1782 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1645 1783 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1646 1784 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1647 1785 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1648 1786 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1671 1809 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
1672 1810 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
1673 1811 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
1674 1812 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
1675 1813 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
1676 1814 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
1677 1815 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
1678 1816 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
1679 1817 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
1680 1818 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
1681 1819 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
1682 1820 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
1683 1821 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
1684 1822 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
1685 1823 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
1686 1824 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
1687 1825 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
1688 1826 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1689 1827 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1690 1828 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1691 1829 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1698 1836 4.376225 TTTGGAACGGAGGGAGTATTTT 57.624 40.909 0.00 0.00 0.00 1.82
1703 1841 4.948004 GGAACGGAGGGAGTATTTTCAAAT 59.052 41.667 0.00 0.00 0.00 2.32
1730 1868 7.235812 AGAGGAAGTACTAATGAAGAACTGGTT 59.764 37.037 0.00 0.00 0.00 3.67
1834 1981 4.764679 TCACATCTTGGACGAAAATTGG 57.235 40.909 0.00 0.00 0.00 3.16
2066 2400 6.546034 CCTGAAAGAAAAACCTGAGGACTAAA 59.454 38.462 4.99 0.00 34.07 1.85
2150 2484 6.100279 TCCAGTAGAGGCATGAATATTGTTCT 59.900 38.462 0.00 0.00 0.00 3.01
2247 2597 7.918076 TCTTTTACAAGGTACTCTTCATCCAT 58.082 34.615 0.00 0.00 38.49 3.41
2253 2603 4.742012 AGGTACTCTTCATCCATCGGTAT 58.258 43.478 0.00 0.00 0.00 2.73
2505 2918 1.065764 CGGGTTCGCGATGATCTCA 59.934 57.895 10.88 0.00 0.00 3.27
2611 3024 1.066430 CCAAGTTCGAGGAATTCCCGA 60.066 52.381 25.05 25.05 40.87 5.14
2647 3060 3.578716 TCTGGTGCCCTATATCTTGTAGC 59.421 47.826 0.00 0.00 0.00 3.58
2649 3062 2.299297 GGTGCCCTATATCTTGTAGCGT 59.701 50.000 0.00 0.00 0.00 5.07
2666 3079 0.456653 CGTGCCAGCTAATTGGTTGC 60.457 55.000 0.00 0.00 40.49 4.17
2690 3103 4.553330 ACCGGATTGTCTATTCACAAGT 57.447 40.909 9.46 0.00 39.63 3.16
2771 3200 7.363705 CCCTAATCTCATCTCACTCCATACATC 60.364 44.444 0.00 0.00 0.00 3.06
2903 3337 5.147162 CGAGGCTCAAACAATACAAAGAAC 58.853 41.667 15.95 0.00 0.00 3.01
2915 3353 8.650143 ACAATACAAAGAACCAACTATTCCAT 57.350 30.769 0.00 0.00 0.00 3.41
3104 3555 3.517500 CTGCCCTAGAGAGTCTTTTTCCT 59.482 47.826 0.00 0.00 0.00 3.36
3133 3588 5.832539 TTGATCTGGGTTTTTCTCTCTCT 57.167 39.130 0.00 0.00 0.00 3.10
3135 3590 3.944055 TCTGGGTTTTTCTCTCTCTCG 57.056 47.619 0.00 0.00 0.00 4.04
3137 3592 1.002087 TGGGTTTTTCTCTCTCTCGCC 59.998 52.381 0.00 0.00 0.00 5.54
3241 4523 0.896226 GCCTCTACTCCGACTTTGGT 59.104 55.000 0.00 0.00 0.00 3.67
3266 4548 1.303888 TACACCGGCGTCTTCTCCT 60.304 57.895 6.01 0.00 0.00 3.69
3302 4611 2.034066 CACGTGGTGGCCTGGAAT 59.966 61.111 7.95 0.00 0.00 3.01
3305 4614 2.440599 GTGGTGGCCTGGAATGGT 59.559 61.111 3.32 0.00 0.00 3.55
3307 4616 2.043953 GGTGGCCTGGAATGGTCC 60.044 66.667 3.32 0.00 45.21 4.46
3309 4618 1.384191 GTGGCCTGGAATGGTCCTT 59.616 57.895 3.32 0.00 45.22 3.36
3452 4830 0.877071 CAAGCCTCACGATGCAAGTT 59.123 50.000 0.00 0.00 0.00 2.66
3503 4881 2.673114 CCAAACCATGCGTACGCGT 61.673 57.895 32.65 30.65 45.51 6.01
3509 4887 2.569657 ATGCGTACGCGTGAAGGA 59.430 55.556 32.57 15.28 45.51 3.36
3510 4888 1.080366 ATGCGTACGCGTGAAGGAA 60.080 52.632 32.57 14.50 45.51 3.36
3511 4889 0.668096 ATGCGTACGCGTGAAGGAAA 60.668 50.000 32.57 13.73 45.51 3.13
3512 4890 0.668096 TGCGTACGCGTGAAGGAAAT 60.668 50.000 32.65 0.00 45.51 2.17
3513 4891 1.270971 GCGTACGCGTGAAGGAAATA 58.729 50.000 26.17 0.00 40.81 1.40
3514 4892 1.856597 GCGTACGCGTGAAGGAAATAT 59.143 47.619 26.17 0.00 40.81 1.28
3515 4893 2.347292 GCGTACGCGTGAAGGAAATATG 60.347 50.000 26.17 4.74 40.81 1.78
3516 4894 2.347292 CGTACGCGTGAAGGAAATATGC 60.347 50.000 24.59 0.00 0.00 3.14
3517 4895 1.014352 ACGCGTGAAGGAAATATGCC 58.986 50.000 12.93 0.00 0.00 4.40
3518 4896 0.307760 CGCGTGAAGGAAATATGCCC 59.692 55.000 0.00 0.00 0.00 5.36
3519 4897 1.680338 GCGTGAAGGAAATATGCCCT 58.320 50.000 0.00 0.00 0.00 5.19
3520 4898 2.805295 CGCGTGAAGGAAATATGCCCTA 60.805 50.000 0.00 0.00 31.36 3.53
3521 4899 2.808543 GCGTGAAGGAAATATGCCCTAG 59.191 50.000 0.00 0.00 31.36 3.02
3522 4900 3.494398 GCGTGAAGGAAATATGCCCTAGA 60.494 47.826 0.00 0.00 31.36 2.43
3523 4901 4.310769 CGTGAAGGAAATATGCCCTAGAG 58.689 47.826 0.00 0.00 31.36 2.43
3524 4902 4.646572 GTGAAGGAAATATGCCCTAGAGG 58.353 47.826 0.00 0.00 39.47 3.69
3540 4918 7.881775 CCCTAGAGGCAATAATAAAGTTGTT 57.118 36.000 0.00 0.00 0.00 2.83
3541 4919 8.974060 CCCTAGAGGCAATAATAAAGTTGTTA 57.026 34.615 0.00 0.00 0.00 2.41
3542 4920 9.574516 CCCTAGAGGCAATAATAAAGTTGTTAT 57.425 33.333 0.00 0.00 0.00 1.89
3602 4980 9.851686 ATTCATGCTAGAATTGTATTAACTGGA 57.148 29.630 0.00 0.00 34.70 3.86
3603 4981 9.679661 TTCATGCTAGAATTGTATTAACTGGAA 57.320 29.630 0.00 0.00 0.00 3.53
3604 4982 9.679661 TCATGCTAGAATTGTATTAACTGGAAA 57.320 29.630 0.00 0.00 0.00 3.13
3605 4983 9.722056 CATGCTAGAATTGTATTAACTGGAAAC 57.278 33.333 0.00 0.00 0.00 2.78
3606 4984 9.686683 ATGCTAGAATTGTATTAACTGGAAACT 57.313 29.630 0.00 0.00 0.00 2.66
3607 4985 9.515226 TGCTAGAATTGTATTAACTGGAAACTT 57.485 29.630 0.00 0.00 0.00 2.66
3612 4990 9.556030 GAATTGTATTAACTGGAAACTTAGTGC 57.444 33.333 0.00 0.00 0.00 4.40
3613 4991 8.630054 ATTGTATTAACTGGAAACTTAGTGCA 57.370 30.769 0.00 0.00 0.00 4.57
3614 4992 8.630054 TTGTATTAACTGGAAACTTAGTGCAT 57.370 30.769 0.00 0.00 0.00 3.96
3615 4993 8.039603 TGTATTAACTGGAAACTTAGTGCATG 57.960 34.615 0.00 0.00 0.00 4.06
3616 4994 7.663905 TGTATTAACTGGAAACTTAGTGCATGT 59.336 33.333 0.00 0.00 0.00 3.21
3617 4995 4.836125 AACTGGAAACTTAGTGCATGTG 57.164 40.909 0.00 0.00 0.00 3.21
3618 4996 3.820557 ACTGGAAACTTAGTGCATGTGT 58.179 40.909 0.00 0.00 0.00 3.72
3619 4997 3.565482 ACTGGAAACTTAGTGCATGTGTG 59.435 43.478 0.00 0.00 0.00 3.82
3620 4998 3.814625 TGGAAACTTAGTGCATGTGTGA 58.185 40.909 0.00 0.00 0.00 3.58
3621 4999 4.203226 TGGAAACTTAGTGCATGTGTGAA 58.797 39.130 0.00 0.00 0.00 3.18
3622 5000 4.826733 TGGAAACTTAGTGCATGTGTGAAT 59.173 37.500 0.00 0.00 0.00 2.57
3623 5001 6.000840 TGGAAACTTAGTGCATGTGTGAATA 58.999 36.000 0.00 0.00 0.00 1.75
3624 5002 6.072728 TGGAAACTTAGTGCATGTGTGAATAC 60.073 38.462 0.00 0.00 0.00 1.89
3625 5003 6.072728 GGAAACTTAGTGCATGTGTGAATACA 60.073 38.462 0.00 0.00 34.63 2.29
3626 5004 7.362056 GGAAACTTAGTGCATGTGTGAATACAT 60.362 37.037 0.00 0.00 41.77 2.29
3627 5005 8.560355 AAACTTAGTGCATGTGTGAATACATA 57.440 30.769 0.00 0.00 39.17 2.29
3628 5006 7.776933 ACTTAGTGCATGTGTGAATACATAG 57.223 36.000 0.00 0.00 39.17 2.23
3629 5007 7.555965 ACTTAGTGCATGTGTGAATACATAGA 58.444 34.615 0.00 0.00 39.17 1.98
3630 5008 7.492669 ACTTAGTGCATGTGTGAATACATAGAC 59.507 37.037 0.00 0.00 39.17 2.59
3631 5009 5.733676 AGTGCATGTGTGAATACATAGACA 58.266 37.500 0.00 0.00 39.17 3.41
3632 5010 6.172630 AGTGCATGTGTGAATACATAGACAA 58.827 36.000 0.00 0.00 39.17 3.18
3633 5011 6.654582 AGTGCATGTGTGAATACATAGACAAA 59.345 34.615 0.00 0.00 39.17 2.83
3634 5012 6.742718 GTGCATGTGTGAATACATAGACAAAC 59.257 38.462 0.00 0.00 39.17 2.93
3635 5013 6.429385 TGCATGTGTGAATACATAGACAAACA 59.571 34.615 0.00 0.00 39.17 2.83
3636 5014 6.963242 GCATGTGTGAATACATAGACAAACAG 59.037 38.462 0.00 0.00 39.17 3.16
3637 5015 7.148423 GCATGTGTGAATACATAGACAAACAGA 60.148 37.037 0.00 0.00 39.17 3.41
3638 5016 7.889589 TGTGTGAATACATAGACAAACAGAG 57.110 36.000 0.00 0.00 39.39 3.35
3639 5017 6.873605 TGTGTGAATACATAGACAAACAGAGG 59.126 38.462 0.00 0.00 39.39 3.69
3640 5018 6.313905 GTGTGAATACATAGACAAACAGAGGG 59.686 42.308 0.00 0.00 39.39 4.30
3641 5019 6.013725 TGTGAATACATAGACAAACAGAGGGT 60.014 38.462 0.00 0.00 0.00 4.34
3642 5020 6.535508 GTGAATACATAGACAAACAGAGGGTC 59.464 42.308 0.00 0.00 0.00 4.46
3643 5021 6.212589 TGAATACATAGACAAACAGAGGGTCA 59.787 38.462 0.00 0.00 34.04 4.02
3644 5022 4.273148 ACATAGACAAACAGAGGGTCAC 57.727 45.455 0.00 0.00 34.04 3.67
3645 5023 3.904339 ACATAGACAAACAGAGGGTCACT 59.096 43.478 0.00 0.00 34.04 3.41
3646 5024 5.084519 ACATAGACAAACAGAGGGTCACTA 58.915 41.667 0.00 0.00 34.04 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.671590 TCCGTCACCTCCTCCGCA 62.672 66.667 0.00 0.00 0.00 5.69
46 47 4.148825 GCCATCTGAGTCGCCCGT 62.149 66.667 0.00 0.00 0.00 5.28
75 76 1.581402 CGAGTCGTCTGCTGCTACG 60.581 63.158 17.85 17.85 40.40 3.51
78 79 4.767841 CGCGAGTCGTCTGCTGCT 62.768 66.667 15.08 0.00 0.00 4.24
128 129 4.783621 GGATGTGCCTGAGCCGCA 62.784 66.667 0.00 0.00 38.69 5.69
136 137 4.457496 CAGCCGTCGGATGTGCCT 62.457 66.667 21.30 0.88 34.00 4.75
172 195 4.082523 TCCTTCGCCCGAGCAAGG 62.083 66.667 11.94 11.94 43.22 3.61
174 197 4.735132 CGTCCTTCGCCCGAGCAA 62.735 66.667 0.00 0.00 39.83 3.91
236 259 1.182667 CGCTACCCGATCCATCCATA 58.817 55.000 0.00 0.00 40.02 2.74
616 639 2.431942 TTTCTCGCTTCCGTCGGC 60.432 61.111 6.34 0.00 35.54 5.54
617 640 0.798771 CTCTTTCTCGCTTCCGTCGG 60.799 60.000 4.39 4.39 35.54 4.79
620 643 0.244178 GGTCTCTTTCTCGCTTCCGT 59.756 55.000 0.00 0.00 35.54 4.69
621 644 0.528470 AGGTCTCTTTCTCGCTTCCG 59.472 55.000 0.00 0.00 0.00 4.30
636 672 8.421784 TCATACATGGTATCAGTTTTCTAGGTC 58.578 37.037 0.00 0.00 0.00 3.85
656 692 7.758495 GCATCATGCAATCATAATCTCATACA 58.242 34.615 4.20 0.00 44.26 2.29
676 712 3.805971 CGAAGAGCAATACATCTGCATCA 59.194 43.478 0.00 0.00 42.48 3.07
677 713 3.806521 ACGAAGAGCAATACATCTGCATC 59.193 43.478 0.00 0.00 42.48 3.91
678 714 3.558829 CACGAAGAGCAATACATCTGCAT 59.441 43.478 0.00 0.00 42.48 3.96
679 715 2.931969 CACGAAGAGCAATACATCTGCA 59.068 45.455 0.00 0.00 42.48 4.41
680 716 2.286067 GCACGAAGAGCAATACATCTGC 60.286 50.000 0.00 0.00 45.32 4.26
681 717 3.582444 GCACGAAGAGCAATACATCTG 57.418 47.619 0.00 0.00 45.32 2.90
691 727 2.544685 ACATGTCTATGCACGAAGAGC 58.455 47.619 0.00 0.00 46.44 4.09
718 754 5.512576 GGTCCGTAGCCCATCTTTATACATT 60.513 44.000 0.00 0.00 0.00 2.71
722 758 3.830755 GAGGTCCGTAGCCCATCTTTATA 59.169 47.826 0.00 0.00 0.00 0.98
723 759 2.633481 GAGGTCCGTAGCCCATCTTTAT 59.367 50.000 0.00 0.00 0.00 1.40
732 768 1.135170 GTGTAGTTGAGGTCCGTAGCC 60.135 57.143 0.00 0.00 0.00 3.93
756 792 5.705905 GTGTATTGGGCTTGTCTCTTAGTTT 59.294 40.000 0.00 0.00 0.00 2.66
759 795 4.832248 TGTGTATTGGGCTTGTCTCTTAG 58.168 43.478 0.00 0.00 0.00 2.18
760 796 4.901197 TGTGTATTGGGCTTGTCTCTTA 57.099 40.909 0.00 0.00 0.00 2.10
762 798 3.788227 TTGTGTATTGGGCTTGTCTCT 57.212 42.857 0.00 0.00 0.00 3.10
766 802 6.184068 TGTGTATATTGTGTATTGGGCTTGT 58.816 36.000 0.00 0.00 0.00 3.16
803 839 3.678072 CGATGTGGTAAAAGACGTGATGT 59.322 43.478 0.00 0.00 0.00 3.06
806 842 2.610976 CCCGATGTGGTAAAAGACGTGA 60.611 50.000 0.00 0.00 35.15 4.35
817 865 0.034477 GGTCATTTCCCCGATGTGGT 60.034 55.000 0.00 0.00 35.15 4.16
819 867 1.832883 TTGGTCATTTCCCCGATGTG 58.167 50.000 0.00 0.00 0.00 3.21
820 868 2.225017 ACTTTGGTCATTTCCCCGATGT 60.225 45.455 0.00 0.00 0.00 3.06
821 869 2.446435 ACTTTGGTCATTTCCCCGATG 58.554 47.619 0.00 0.00 0.00 3.84
822 870 2.899303 ACTTTGGTCATTTCCCCGAT 57.101 45.000 0.00 0.00 0.00 4.18
823 871 2.640826 ACTACTTTGGTCATTTCCCCGA 59.359 45.455 0.00 0.00 0.00 5.14
824 872 3.067684 ACTACTTTGGTCATTTCCCCG 57.932 47.619 0.00 0.00 0.00 5.73
825 873 4.948004 CCTTACTACTTTGGTCATTTCCCC 59.052 45.833 0.00 0.00 0.00 4.81
827 875 4.094442 CGCCTTACTACTTTGGTCATTTCC 59.906 45.833 0.00 0.00 0.00 3.13
828 876 4.436986 GCGCCTTACTACTTTGGTCATTTC 60.437 45.833 0.00 0.00 0.00 2.17
848 896 1.324718 CGTCCTATACATACACGCGC 58.675 55.000 5.73 0.00 0.00 6.86
1117 1188 1.065401 CTGCCACATCTCTCTCTCGAC 59.935 57.143 0.00 0.00 0.00 4.20
1136 1218 2.567049 GGTACAGCAGCGACGACT 59.433 61.111 0.00 0.00 0.00 4.18
1188 1270 2.656007 GACGCGAACGACACCACA 60.656 61.111 15.93 0.00 43.93 4.17
1242 1324 1.362224 ACTTGGAGTAGGCCATGTGT 58.638 50.000 5.01 0.00 42.63 3.72
1474 1594 9.794685 GAAAAGAGTGTCTTCAAGAAAGAATTT 57.205 29.630 0.00 0.00 45.50 1.82
1513 1644 5.892119 TGAGTATTTCGGGACAGAGAGTATT 59.108 40.000 0.00 0.00 0.00 1.89
1515 1646 4.851843 TGAGTATTTCGGGACAGAGAGTA 58.148 43.478 0.00 0.00 0.00 2.59
1516 1647 3.698289 TGAGTATTTCGGGACAGAGAGT 58.302 45.455 0.00 0.00 0.00 3.24
1522 1653 4.278310 TCTCTGATGAGTATTTCGGGACA 58.722 43.478 0.00 0.00 40.98 4.02
1538 1669 7.453393 ACATCCATTTTTGTCTAGTTCTCTGA 58.547 34.615 0.00 0.00 0.00 3.27
1539 1670 7.678947 ACATCCATTTTTGTCTAGTTCTCTG 57.321 36.000 0.00 0.00 0.00 3.35
1601 1739 4.286549 TGGAACGGAGGGAGTATTTGTTAA 59.713 41.667 0.00 0.00 0.00 2.01
1611 1749 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1612 1750 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1613 1751 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1614 1752 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1615 1753 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1616 1754 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1617 1755 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1618 1756 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1619 1757 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1620 1758 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1621 1759 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1622 1760 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1645 1783 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
1646 1784 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
1647 1785 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
1648 1786 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
1650 1788 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
1651 1789 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
1652 1790 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
1653 1791 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
1654 1792 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
1655 1793 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
1656 1794 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
1657 1795 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
1658 1796 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
1659 1797 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
1660 1798 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
1661 1799 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
1662 1800 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
1663 1801 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1664 1802 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1665 1803 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1666 1804 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1667 1805 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1668 1806 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1669 1807 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1670 1808 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1671 1809 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1672 1810 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1673 1811 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1674 1812 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
1675 1813 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
1676 1814 4.376225 AAATACTCCCTCCGTTCCAAAA 57.624 40.909 0.00 0.00 0.00 2.44
1677 1815 4.202482 TGAAAATACTCCCTCCGTTCCAAA 60.202 41.667 0.00 0.00 0.00 3.28
1678 1816 3.328343 TGAAAATACTCCCTCCGTTCCAA 59.672 43.478 0.00 0.00 0.00 3.53
1679 1817 2.907696 TGAAAATACTCCCTCCGTTCCA 59.092 45.455 0.00 0.00 0.00 3.53
1680 1818 3.622166 TGAAAATACTCCCTCCGTTCC 57.378 47.619 0.00 0.00 0.00 3.62
1681 1819 7.046033 TCTATTTGAAAATACTCCCTCCGTTC 58.954 38.462 0.00 0.00 0.00 3.95
1682 1820 6.954232 TCTATTTGAAAATACTCCCTCCGTT 58.046 36.000 0.00 0.00 0.00 4.44
1683 1821 6.408206 CCTCTATTTGAAAATACTCCCTCCGT 60.408 42.308 0.00 0.00 0.00 4.69
1684 1822 5.992217 CCTCTATTTGAAAATACTCCCTCCG 59.008 44.000 0.00 0.00 0.00 4.63
1685 1823 7.138054 TCCTCTATTTGAAAATACTCCCTCC 57.862 40.000 0.00 0.00 0.00 4.30
1686 1824 8.268605 ACTTCCTCTATTTGAAAATACTCCCTC 58.731 37.037 0.00 0.00 0.00 4.30
1687 1825 8.164057 ACTTCCTCTATTTGAAAATACTCCCT 57.836 34.615 0.00 0.00 0.00 4.20
1688 1826 9.327628 GTACTTCCTCTATTTGAAAATACTCCC 57.672 37.037 0.00 0.00 0.00 4.30
1703 1841 7.894364 ACCAGTTCTTCATTAGTACTTCCTCTA 59.106 37.037 0.00 0.00 32.75 2.43
1718 1856 5.009610 GTGGCATCTAAAAACCAGTTCTTCA 59.990 40.000 0.00 0.00 31.46 3.02
1730 1868 6.162777 GCAATACTTTTGGTGGCATCTAAAA 58.837 36.000 8.62 9.18 0.00 1.52
1790 1937 3.134081 ACCCCACTTCTATAACATGTCCG 59.866 47.826 0.00 0.00 0.00 4.79
1791 1938 4.772886 ACCCCACTTCTATAACATGTCC 57.227 45.455 0.00 0.00 0.00 4.02
1834 1981 7.096551 TGCACTAAAATTCCTAATTTTCCTGC 58.903 34.615 20.09 20.09 45.32 4.85
2114 2448 3.616560 GCCTCTACTGGAACACGATTTGA 60.617 47.826 0.00 0.00 0.00 2.69
2171 2521 9.898152 AAAACCAGGAAACTTATTTTGAAATGA 57.102 25.926 0.00 0.00 40.21 2.57
2247 2597 1.414919 GGCATGTTCCCACTATACCGA 59.585 52.381 0.00 0.00 0.00 4.69
2505 2918 1.076533 CGAGCGCATAAACCGTCTGT 61.077 55.000 11.47 0.00 0.00 3.41
2647 3060 0.456653 GCAACCAATTAGCTGGCACG 60.457 55.000 0.00 0.00 40.45 5.34
2649 3062 0.541530 TGGCAACCAATTAGCTGGCA 60.542 50.000 0.00 0.00 40.45 4.92
2666 3079 3.605634 TGTGAATAGACAATCCGGTTGG 58.394 45.455 17.36 3.76 42.28 3.77
2690 3103 8.182227 CGCCGATGTTAGATAAATATGAGACTA 58.818 37.037 0.00 0.00 0.00 2.59
2812 3244 5.471456 ACAAGCCAGAACAAATTCTAGTCTG 59.529 40.000 0.00 0.00 43.69 3.51
2890 3324 8.650143 ATGGAATAGTTGGTTCTTTGTATTGT 57.350 30.769 0.00 0.00 0.00 2.71
2903 3337 7.521669 AGAGAGGGATTTAATGGAATAGTTGG 58.478 38.462 0.00 0.00 0.00 3.77
2915 3353 6.269194 TGTTAGAAGGGAGAGAGGGATTTAA 58.731 40.000 0.00 0.00 0.00 1.52
3043 3492 1.755783 CGAACCCTAGGTACGGGCT 60.756 63.158 8.29 0.00 46.04 5.19
3133 3588 1.882625 CCGATCAAAGCGATGGCGA 60.883 57.895 0.00 0.00 46.35 5.54
3135 3590 2.329339 GCCGATCAAAGCGATGGC 59.671 61.111 0.00 0.00 39.50 4.40
3220 4193 0.526662 CAAAGTCGGAGTAGAGGCGT 59.473 55.000 0.00 0.00 0.00 5.68
3241 4523 0.462581 AGACGCCGGTGTAGTCGATA 60.463 55.000 23.00 0.00 39.65 2.92
3284 4591 2.829384 ATTCCAGGCCACCACGTGT 61.829 57.895 15.65 0.00 0.00 4.49
3289 4596 2.763215 GACCATTCCAGGCCACCA 59.237 61.111 5.01 0.00 0.00 4.17
3302 4611 3.876589 GAGGCGCGAACAAGGACCA 62.877 63.158 12.10 0.00 0.00 4.02
3305 4614 2.048222 CTGAGGCGCGAACAAGGA 60.048 61.111 12.10 0.00 0.00 3.36
3307 4616 2.383527 GGACTGAGGCGCGAACAAG 61.384 63.158 12.10 3.74 0.00 3.16
3309 4618 4.717629 CGGACTGAGGCGCGAACA 62.718 66.667 12.10 5.10 0.00 3.18
3452 4830 4.561530 GCCTCATACGAGATGGCTGATTTA 60.562 45.833 0.00 0.00 42.34 1.40
3503 4881 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
3516 4894 7.881775 AACAACTTTATTATTGCCTCTAGGG 57.118 36.000 0.00 0.00 35.18 3.53
3576 4954 9.851686 TCCAGTTAATACAATTCTAGCATGAAT 57.148 29.630 0.00 0.00 38.19 2.57
3577 4955 9.679661 TTCCAGTTAATACAATTCTAGCATGAA 57.320 29.630 0.00 0.00 0.00 2.57
3578 4956 9.679661 TTTCCAGTTAATACAATTCTAGCATGA 57.320 29.630 0.00 0.00 0.00 3.07
3579 4957 9.722056 GTTTCCAGTTAATACAATTCTAGCATG 57.278 33.333 0.00 0.00 0.00 4.06
3580 4958 9.686683 AGTTTCCAGTTAATACAATTCTAGCAT 57.313 29.630 0.00 0.00 0.00 3.79
3581 4959 9.515226 AAGTTTCCAGTTAATACAATTCTAGCA 57.485 29.630 0.00 0.00 0.00 3.49
3586 4964 9.556030 GCACTAAGTTTCCAGTTAATACAATTC 57.444 33.333 0.00 0.00 0.00 2.17
3587 4965 9.073475 TGCACTAAGTTTCCAGTTAATACAATT 57.927 29.630 0.00 0.00 0.00 2.32
3588 4966 8.630054 TGCACTAAGTTTCCAGTTAATACAAT 57.370 30.769 0.00 0.00 0.00 2.71
3589 4967 8.511321 CATGCACTAAGTTTCCAGTTAATACAA 58.489 33.333 0.00 0.00 0.00 2.41
3590 4968 7.663905 ACATGCACTAAGTTTCCAGTTAATACA 59.336 33.333 0.00 0.00 0.00 2.29
3591 4969 7.962918 CACATGCACTAAGTTTCCAGTTAATAC 59.037 37.037 0.00 0.00 0.00 1.89
3592 4970 7.663905 ACACATGCACTAAGTTTCCAGTTAATA 59.336 33.333 0.00 0.00 0.00 0.98
3593 4971 6.490040 ACACATGCACTAAGTTTCCAGTTAAT 59.510 34.615 0.00 0.00 0.00 1.40
3594 4972 5.825679 ACACATGCACTAAGTTTCCAGTTAA 59.174 36.000 0.00 0.00 0.00 2.01
3595 4973 5.238432 CACACATGCACTAAGTTTCCAGTTA 59.762 40.000 0.00 0.00 0.00 2.24
3596 4974 4.036734 CACACATGCACTAAGTTTCCAGTT 59.963 41.667 0.00 0.00 0.00 3.16
3597 4975 3.565482 CACACATGCACTAAGTTTCCAGT 59.435 43.478 0.00 0.00 0.00 4.00
3598 4976 3.814842 TCACACATGCACTAAGTTTCCAG 59.185 43.478 0.00 0.00 0.00 3.86
3599 4977 3.814625 TCACACATGCACTAAGTTTCCA 58.185 40.909 0.00 0.00 0.00 3.53
3600 4978 4.829064 TTCACACATGCACTAAGTTTCC 57.171 40.909 0.00 0.00 0.00 3.13
3601 4979 6.898041 TGTATTCACACATGCACTAAGTTTC 58.102 36.000 0.00 0.00 0.00 2.78
3602 4980 6.875948 TGTATTCACACATGCACTAAGTTT 57.124 33.333 0.00 0.00 0.00 2.66
3603 4981 8.040727 TCTATGTATTCACACATGCACTAAGTT 58.959 33.333 0.00 0.00 39.46 2.66
3604 4982 7.492669 GTCTATGTATTCACACATGCACTAAGT 59.507 37.037 0.00 0.00 39.46 2.24
3605 4983 7.492344 TGTCTATGTATTCACACATGCACTAAG 59.508 37.037 0.00 0.00 39.46 2.18
3606 4984 7.327214 TGTCTATGTATTCACACATGCACTAA 58.673 34.615 0.00 0.00 39.46 2.24
3607 4985 6.872920 TGTCTATGTATTCACACATGCACTA 58.127 36.000 0.00 0.00 39.46 2.74
3608 4986 5.733676 TGTCTATGTATTCACACATGCACT 58.266 37.500 0.00 0.00 39.46 4.40
3609 4987 6.421377 TTGTCTATGTATTCACACATGCAC 57.579 37.500 0.00 0.00 39.46 4.57
3610 4988 6.429385 TGTTTGTCTATGTATTCACACATGCA 59.571 34.615 0.00 0.00 39.46 3.96
3611 4989 6.841119 TGTTTGTCTATGTATTCACACATGC 58.159 36.000 0.00 0.00 39.46 4.06
3612 4990 8.255394 TCTGTTTGTCTATGTATTCACACATG 57.745 34.615 0.00 0.00 39.46 3.21
3613 4991 7.550551 CCTCTGTTTGTCTATGTATTCACACAT 59.449 37.037 0.00 0.00 41.88 3.21
3614 4992 6.873605 CCTCTGTTTGTCTATGTATTCACACA 59.126 38.462 0.00 0.00 37.54 3.72
3615 4993 6.313905 CCCTCTGTTTGTCTATGTATTCACAC 59.686 42.308 0.00 0.00 37.54 3.82
3616 4994 6.013725 ACCCTCTGTTTGTCTATGTATTCACA 60.014 38.462 0.00 0.00 39.52 3.58
3617 4995 6.407202 ACCCTCTGTTTGTCTATGTATTCAC 58.593 40.000 0.00 0.00 0.00 3.18
3618 4996 6.212589 TGACCCTCTGTTTGTCTATGTATTCA 59.787 38.462 0.00 0.00 0.00 2.57
3619 4997 6.535508 GTGACCCTCTGTTTGTCTATGTATTC 59.464 42.308 0.00 0.00 0.00 1.75
3620 4998 6.213600 AGTGACCCTCTGTTTGTCTATGTATT 59.786 38.462 0.00 0.00 0.00 1.89
3621 4999 5.721960 AGTGACCCTCTGTTTGTCTATGTAT 59.278 40.000 0.00 0.00 0.00 2.29
3622 5000 5.084519 AGTGACCCTCTGTTTGTCTATGTA 58.915 41.667 0.00 0.00 0.00 2.29
3623 5001 3.904339 AGTGACCCTCTGTTTGTCTATGT 59.096 43.478 0.00 0.00 0.00 2.29
3624 5002 4.543590 AGTGACCCTCTGTTTGTCTATG 57.456 45.455 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.