Multiple sequence alignment - TraesCS3B01G402700

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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 TraesCS3B01G402700 chr3B 100.000 7432 0 0 1448 8879 637056712 637064143 0.000000e+00 13725.0
1 TraesCS3B01G402700 chr3B 100.000 1115 0 0 1 1115 637055265 637056379 0.000000e+00 2060.0
2 TraesCS3B01G402700 chr3B 87.324 142 10 3 5487 5627 791284286 791284152 1.190000e-33 156.0
3 TraesCS3B01G402700 chr3B 85.714 147 13 5 5487 5627 368095323 368095179 2.000000e-31 148.0
4 TraesCS3B01G402700 chr3B 90.741 108 10 0 5628 5735 417730201 417730094 2.580000e-30 145.0
5 TraesCS3B01G402700 chr3A 93.041 4009 190 39 4267 8247 621211532 621215479 0.000000e+00 5775.0
6 TraesCS3B01G402700 chr3A 94.330 2822 129 14 1448 4254 621208742 621211547 0.000000e+00 4296.0
7 TraesCS3B01G402700 chr3A 87.111 450 24 14 691 1115 621208286 621208726 6.240000e-131 479.0
8 TraesCS3B01G402700 chr3A 94.884 215 11 0 8352 8566 621215483 621215697 3.970000e-88 337.0
9 TraesCS3B01G402700 chr3A 82.875 327 27 13 8560 8872 621217854 621218165 5.280000e-67 267.0
10 TraesCS3B01G402700 chr3A 84.167 240 38 0 6049 6288 627652349 627652110 5.360000e-57 233.0
11 TraesCS3B01G402700 chr3A 85.167 209 31 0 6079 6287 157433363 157433155 1.940000e-51 215.0
12 TraesCS3B01G402700 chr3A 76.276 392 60 16 5899 6286 299718867 299719229 2.550000e-40 178.0
13 TraesCS3B01G402700 chr3A 84.466 103 9 2 5688 5790 340284781 340284686 2.640000e-15 95.3
14 TraesCS3B01G402700 chr3D 96.840 2658 73 7 1485 4135 477874212 477876865 0.000000e+00 4433.0
15 TraesCS3B01G402700 chr3D 92.051 2126 120 25 6079 8183 477878795 477880892 0.000000e+00 2944.0
16 TraesCS3B01G402700 chr3D 95.450 1824 63 10 4267 6075 477876935 477878753 0.000000e+00 2891.0
17 TraesCS3B01G402700 chr3D 86.076 553 41 18 8335 8879 477881034 477881558 6.020000e-156 562.0
18 TraesCS3B01G402700 chr3D 88.961 462 22 16 672 1115 477873256 477873706 2.180000e-150 544.0
19 TraesCS3B01G402700 chr3D 83.036 224 37 1 6080 6303 489901126 489900904 1.510000e-47 202.0
20 TraesCS3B01G402700 chr3D 84.242 165 17 3 5683 5847 541192777 541192932 1.540000e-32 152.0
21 TraesCS3B01G402700 chr3D 81.595 163 23 4 5628 5790 303580916 303581071 2.600000e-25 128.0
22 TraesCS3B01G402700 chr3D 92.857 84 6 0 4171 4254 477876867 477876950 1.210000e-23 122.0
23 TraesCS3B01G402700 chr3D 93.443 61 4 0 5787 5847 67244523 67244583 3.410000e-14 91.6
24 TraesCS3B01G402700 chr3D 89.362 47 4 1 5850 5896 439545825 439545870 3.460000e-04 58.4
25 TraesCS3B01G402700 chr6B 96.880 673 19 2 1 672 474198709 474199380 0.000000e+00 1125.0
26 TraesCS3B01G402700 chr6B 96.731 673 20 2 1 672 474195431 474196102 0.000000e+00 1120.0
27 TraesCS3B01G402700 chr6B 83.534 498 71 8 6618 7107 352079413 352079907 1.050000e-123 455.0
28 TraesCS3B01G402700 chr6B 81.061 396 41 11 5900 6293 446847772 446847409 1.460000e-72 285.0
29 TraesCS3B01G402700 chr5B 96.588 674 18 5 1 670 428460198 428460870 0.000000e+00 1112.0
30 TraesCS3B01G402700 chr5B 79.250 400 51 13 5902 6291 174876717 174876340 5.320000e-62 250.0
31 TraesCS3B01G402700 chr5B 86.290 124 12 4 6490 6610 300382054 300382175 7.230000e-26 130.0
32 TraesCS3B01G402700 chr5B 91.379 58 5 0 5790 5847 192284445 192284388 7.390000e-11 80.5
33 TraesCS3B01G402700 chr7B 96.577 672 20 3 1 670 219661112 219660442 0.000000e+00 1110.0
34 TraesCS3B01G402700 chr7B 78.899 327 50 13 5899 6221 110225999 110226310 4.200000e-48 204.0
35 TraesCS3B01G402700 chr1B 96.577 672 20 3 1 670 638773259 638773929 0.000000e+00 1110.0
36 TraesCS3B01G402700 chr1B 95.710 676 24 5 1 672 554014010 554014684 0.000000e+00 1083.0
37 TraesCS3B01G402700 chr1B 95.710 676 21 7 1 672 503621880 503622551 0.000000e+00 1081.0
38 TraesCS3B01G402700 chr1B 90.000 50 4 1 5850 5899 297233161 297233209 7.440000e-06 63.9
39 TraesCS3B01G402700 chr4B 95.994 674 22 5 1 670 566241758 566242430 0.000000e+00 1090.0
40 TraesCS3B01G402700 chr4B 95.982 672 24 3 1 670 10430246 10429576 0.000000e+00 1088.0
41 TraesCS3B01G402700 chr4B 81.873 502 79 11 6618 7111 96646168 96646665 6.410000e-111 412.0
42 TraesCS3B01G402700 chr4B 87.234 141 11 2 5487 5627 400685059 400684926 4.290000e-33 154.0
43 TraesCS3B01G402700 chr4B 88.000 100 10 2 4112 4209 650697278 650697377 5.630000e-22 117.0
44 TraesCS3B01G402700 chr4B 86.486 111 8 2 5680 5790 455361990 455361887 2.030000e-21 115.0
45 TraesCS3B01G402700 chr2D 85.230 501 58 9 6618 7105 380417026 380416529 1.330000e-137 501.0
46 TraesCS3B01G402700 chr2D 86.620 142 19 0 7392 7533 37486861 37486720 3.320000e-34 158.0
47 TraesCS3B01G402700 chr2D 87.200 125 14 2 6496 6618 445732971 445732847 3.340000e-29 141.0
48 TraesCS3B01G402700 chr2D 84.173 139 14 5 5653 5790 233384030 233384161 2.600000e-25 128.0
49 TraesCS3B01G402700 chr2D 88.889 63 7 0 5787 5849 207247020 207247082 2.660000e-10 78.7
50 TraesCS3B01G402700 chr5A 84.813 507 63 10 6618 7111 366235322 366234817 1.720000e-136 497.0
51 TraesCS3B01G402700 chr5A 88.235 119 11 3 6490 6607 353857281 353857165 1.200000e-28 139.0
52 TraesCS3B01G402700 chr5A 92.000 50 3 1 5850 5899 100435724 100435676 1.600000e-07 69.4
53 TraesCS3B01G402700 chr5A 88.000 50 5 1 5850 5899 48910451 48910403 3.460000e-04 58.4
54 TraesCS3B01G402700 chr5D 84.921 504 61 8 6617 7106 360542358 360541856 6.190000e-136 496.0
55 TraesCS3B01G402700 chr5D 88.618 123 11 3 6490 6610 266753198 266753319 7.180000e-31 147.0
56 TraesCS3B01G402700 chr5D 82.390 159 22 4 6958 7111 322379390 322379233 5.590000e-27 134.0
57 TraesCS3B01G402700 chr5D 89.720 107 4 2 5684 5790 281028757 281028658 7.230000e-26 130.0
58 TraesCS3B01G402700 chr5D 91.860 86 6 1 4127 4211 539963271 539963186 1.570000e-22 119.0
59 TraesCS3B01G402700 chr5D 93.103 58 2 2 5790 5847 488778348 488778293 5.710000e-12 84.2
60 TraesCS3B01G402700 chr5D 91.379 58 5 0 5790 5847 176098262 176098205 7.390000e-11 80.5
61 TraesCS3B01G402700 chr5D 90.000 50 5 0 5850 5899 344537335 344537286 2.070000e-06 65.8
62 TraesCS3B01G402700 chr2A 84.692 503 60 11 6618 7106 515952140 515951641 3.730000e-133 486.0
63 TraesCS3B01G402700 chr2A 80.928 582 68 22 7520 8067 42334296 42333724 3.830000e-113 420.0
64 TraesCS3B01G402700 chr2A 83.402 241 38 2 6045 6285 185968157 185967919 1.160000e-53 222.0
65 TraesCS3B01G402700 chr2A 78.061 392 56 12 5899 6287 675903486 675903122 4.170000e-53 220.0
66 TraesCS3B01G402700 chr2A 88.393 112 13 0 7392 7503 42361343 42361232 1.550000e-27 135.0
67 TraesCS3B01G402700 chr2A 84.286 140 16 6 6942 7077 115418468 115418605 2.010000e-26 132.0
68 TraesCS3B01G402700 chr2A 89.474 95 6 2 4123 4213 115452898 115452804 5.630000e-22 117.0
69 TraesCS3B01G402700 chr2A 82.203 118 7 8 5680 5790 216538289 216538179 1.230000e-13 89.8
70 TraesCS3B01G402700 chr4D 84.387 506 64 11 6618 7110 47532662 47533165 4.820000e-132 483.0
71 TraesCS3B01G402700 chr4D 90.909 44 4 0 5850 5893 21683558 21683515 9.630000e-05 60.2
72 TraesCS3B01G402700 chr6A 81.955 399 36 14 5900 6298 407096879 407096517 1.120000e-78 305.0
73 TraesCS3B01G402700 chr6A 84.000 150 15 3 5627 5776 407097175 407097035 1.550000e-27 135.0
74 TraesCS3B01G402700 chr6A 89.583 96 4 4 4124 4218 88767672 88767582 5.630000e-22 117.0
75 TraesCS3B01G402700 chr6D 79.353 402 49 15 5899 6298 285881443 285881074 1.480000e-62 252.0
76 TraesCS3B01G402700 chr6D 84.434 212 33 0 6080 6291 275508186 275507975 9.030000e-50 209.0
77 TraesCS3B01G402700 chr6D 87.500 144 8 6 5487 5627 255024384 255024248 3.320000e-34 158.0
78 TraesCS3B01G402700 chr6D 83.537 164 20 2 5627 5790 285881743 285881587 7.180000e-31 147.0
79 TraesCS3B01G402700 chr6D 91.304 92 3 3 4124 4214 72021813 72021726 4.350000e-23 121.0
80 TraesCS3B01G402700 chr6D 87.255 102 12 1 4114 4214 63328298 63328197 2.030000e-21 115.0
81 TraesCS3B01G402700 chrUn 86.385 213 25 3 6080 6291 67792143 67791934 6.930000e-56 230.0
82 TraesCS3B01G402700 chr1D 78.406 389 52 13 5902 6286 319656107 319656467 3.230000e-54 224.0
83 TraesCS3B01G402700 chr1D 87.234 141 11 2 5487 5627 493217407 493217540 4.290000e-33 154.0
84 TraesCS3B01G402700 chr1D 92.708 96 7 0 5642 5737 331307499 331307594 1.200000e-28 139.0
85 TraesCS3B01G402700 chr1D 88.000 50 5 1 5850 5899 439100922 439100874 3.460000e-04 58.4
86 TraesCS3B01G402700 chr4A 85.714 154 11 5 5477 5627 266953790 266953935 1.540000e-32 152.0
87 TraesCS3B01G402700 chr4A 86.525 141 12 3 5487 5627 143248286 143248153 2.000000e-31 148.0
88 TraesCS3B01G402700 chr1A 82.716 162 21 2 5625 5786 428579680 428579834 4.320000e-28 137.0
89 TraesCS3B01G402700 chr1A 91.954 87 6 1 4127 4212 568396162 568396076 4.350000e-23 121.0
90 TraesCS3B01G402700 chr1A 91.765 85 6 1 4128 4211 58933899 58933983 5.630000e-22 117.0
91 TraesCS3B01G402700 chr1A 90.164 61 6 0 5787 5847 209356465 209356405 7.390000e-11 80.5
92 TraesCS3B01G402700 chr2B 83.969 131 19 1 6490 6618 630765365 630765235 3.370000e-24 124.0
93 TraesCS3B01G402700 chr7A 84.112 107 10 2 5684 5790 638576922 638577021 7.340000e-16 97.1
94 TraesCS3B01G402700 chr7D 78.906 128 18 6 6488 6615 513203759 513203641 2.660000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G402700 chr3B 637055265 637064143 8878 False 7892.5 13725 100.000000 1 8879 2 chr3B.!!$F1 8878
1 TraesCS3B01G402700 chr3A 621208286 621218165 9879 False 2230.8 5775 90.448200 691 8872 5 chr3A.!!$F2 8181
2 TraesCS3B01G402700 chr3D 477873256 477881558 8302 False 1916.0 4433 92.039167 672 8879 6 chr3D.!!$F5 8207
3 TraesCS3B01G402700 chr6B 474195431 474199380 3949 False 1122.5 1125 96.805500 1 672 2 chr6B.!!$F2 671
4 TraesCS3B01G402700 chr5B 428460198 428460870 672 False 1112.0 1112 96.588000 1 670 1 chr5B.!!$F2 669
5 TraesCS3B01G402700 chr7B 219660442 219661112 670 True 1110.0 1110 96.577000 1 670 1 chr7B.!!$R1 669
6 TraesCS3B01G402700 chr1B 638773259 638773929 670 False 1110.0 1110 96.577000 1 670 1 chr1B.!!$F4 669
7 TraesCS3B01G402700 chr1B 554014010 554014684 674 False 1083.0 1083 95.710000 1 672 1 chr1B.!!$F3 671
8 TraesCS3B01G402700 chr1B 503621880 503622551 671 False 1081.0 1081 95.710000 1 672 1 chr1B.!!$F2 671
9 TraesCS3B01G402700 chr4B 566241758 566242430 672 False 1090.0 1090 95.994000 1 670 1 chr4B.!!$F2 669
10 TraesCS3B01G402700 chr4B 10429576 10430246 670 True 1088.0 1088 95.982000 1 670 1 chr4B.!!$R1 669
11 TraesCS3B01G402700 chr5A 366234817 366235322 505 True 497.0 497 84.813000 6618 7111 1 chr5A.!!$R4 493
12 TraesCS3B01G402700 chr5D 360541856 360542358 502 True 496.0 496 84.921000 6617 7106 1 chr5D.!!$R5 489
13 TraesCS3B01G402700 chr2A 42333724 42334296 572 True 420.0 420 80.928000 7520 8067 1 chr2A.!!$R1 547
14 TraesCS3B01G402700 chr4D 47532662 47533165 503 False 483.0 483 84.387000 6618 7110 1 chr4D.!!$F1 492
15 TraesCS3B01G402700 chr6A 407096517 407097175 658 True 220.0 305 82.977500 5627 6298 2 chr6A.!!$R2 671

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
634 3919 0.182299 TTTTACCCCAAACGGACGGT 59.818 50.000 0.00 0.00 0.00 4.83 F
823 4115 0.459411 CACACACAGTCACGGTCACA 60.459 55.000 0.00 0.00 0.00 3.58 F
2031 5814 0.464735 CCGAAACACCCACAGTTCCA 60.465 55.000 0.00 0.00 0.00 3.53 F
2324 6110 0.240145 CGACGGTGTTGCTAGTCTCA 59.760 55.000 0.00 0.00 0.00 3.27 F
3407 7204 0.249155 TTGTCGTCTCACCAACGGTC 60.249 55.000 0.00 0.00 40.45 4.79 F
3856 7653 1.002576 TGCGATGCAAATATTCCTGCG 60.003 47.619 7.45 1.75 41.63 5.18 F
3968 7765 1.865340 GGTTCAGATTTCCGTATCCGC 59.135 52.381 0.00 0.00 0.00 5.54 F
5638 9441 0.393267 GGCGTAACTGTAATGCCCCA 60.393 55.000 5.97 0.00 39.83 4.96 F
5819 9650 0.695347 CTCCCAGAAAGGAAGGTGCT 59.305 55.000 0.00 0.00 41.22 4.40 F
7077 11032 0.317160 GCCTACCCCAACTTGTTTGC 59.683 55.000 0.00 0.00 33.34 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 5779 0.252558 TCGGCTTTCCTCCTTAGGGT 60.253 55.000 0.00 0.00 43.84 4.34 R
2046 5829 1.619654 TGCACACATTAGCAAGCCTT 58.380 45.000 0.00 0.00 37.90 4.35 R
3407 7204 1.205064 CGAAAGTCCAACAGCTGCG 59.795 57.895 15.27 5.03 0.00 5.18 R
3968 7765 2.036098 TGGAGTGCCCCATTGCAG 59.964 61.111 0.00 0.00 43.02 4.41 R
4399 8197 1.234821 TGAGCGTTCAATGGTTCCAC 58.765 50.000 0.00 0.00 0.00 4.02 R
5447 9250 1.796459 GTGGCTTTGAGCAGCAAATTG 59.204 47.619 5.40 0.00 44.90 2.32 R
5877 9724 2.032681 GCTGGGCCAACGAGAACT 59.967 61.111 8.04 0.00 0.00 3.01 R
6454 10381 0.172803 ACTACACCCGAGCGTCAATC 59.827 55.000 0.00 0.00 0.00 2.67 R
7741 11706 0.539901 ACACTCGGTACCTCTGCTGT 60.540 55.000 10.90 1.28 0.00 4.40 R
8350 12356 0.250234 CAGTCTCCCATCGCTGGAAA 59.750 55.000 6.92 0.00 46.37 3.13 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
53 54 8.314021 ACAAAGGAAGTGATGAAAGAAAAACTT 58.686 29.630 0.00 0.00 40.98 2.66
153 156 2.360350 CGCAGCAGGGATGGTTGT 60.360 61.111 0.00 0.00 0.00 3.32
433 3717 3.119096 GAAGCGTTGGGAGCGGAC 61.119 66.667 0.00 0.00 40.04 4.79
451 3735 3.310652 GGACTGCTAGTGTCCCCC 58.689 66.667 19.74 3.29 46.01 5.40
593 3878 4.287781 TCCGTTTGAGACCGCGCA 62.288 61.111 8.75 0.00 0.00 6.09
634 3919 0.182299 TTTTACCCCAAACGGACGGT 59.818 50.000 0.00 0.00 0.00 4.83
682 3968 4.141869 GGAGTTGGCCTTAGTAATTCCGTA 60.142 45.833 3.32 0.00 0.00 4.02
751 4042 2.033194 GGCCTCACGTAAGGTGCAC 61.033 63.158 8.80 8.80 46.56 4.57
817 4109 0.778223 CGATCACACACACAGTCACG 59.222 55.000 0.00 0.00 0.00 4.35
823 4115 0.459411 CACACACAGTCACGGTCACA 60.459 55.000 0.00 0.00 0.00 3.58
900 4203 4.368543 GACCGAAACCCTCGCCGT 62.369 66.667 0.00 0.00 46.71 5.68
901 4204 4.368543 ACCGAAACCCTCGCCGTC 62.369 66.667 0.00 0.00 46.71 4.79
902 4205 4.367023 CCGAAACCCTCGCCGTCA 62.367 66.667 0.00 0.00 46.71 4.35
904 4207 3.110178 GAAACCCTCGCCGTCACG 61.110 66.667 0.00 0.00 0.00 4.35
1005 4314 2.606587 GGCCAGTCAGTCACCCCAT 61.607 63.158 0.00 0.00 0.00 4.00
1021 4330 1.375853 CCATCGCAAAATCTCCGCCA 61.376 55.000 0.00 0.00 0.00 5.69
1660 5434 4.020617 CACCGCCTCTGCTCCCAA 62.021 66.667 0.00 0.00 34.43 4.12
1871 5654 2.419198 CGCAGGAGGGATTCGGAG 59.581 66.667 0.00 0.00 0.00 4.63
1883 5666 2.840203 ATTCGGAGGGAGGAAGGCCA 62.840 60.000 5.01 0.00 36.29 5.36
1886 5669 1.926426 CGGAGGGAGGAAGGCCAAAT 61.926 60.000 5.01 0.00 36.29 2.32
1996 5779 6.262496 CGTGACTCTCCTGGAATATGTAAGTA 59.738 42.308 0.00 0.00 0.00 2.24
2000 5783 6.039415 TCTCCTGGAATATGTAAGTACCCT 57.961 41.667 0.00 0.00 0.00 4.34
2020 5803 1.605753 AAGGAGGAAAGCCGAAACAC 58.394 50.000 0.00 0.00 39.96 3.32
2025 5808 1.104577 GGAAAGCCGAAACACCCACA 61.105 55.000 0.00 0.00 0.00 4.17
2031 5814 0.464735 CCGAAACACCCACAGTTCCA 60.465 55.000 0.00 0.00 0.00 3.53
2044 5827 6.012858 ACCCACAGTTCCAATGAGAGTTATAA 60.013 38.462 0.00 0.00 0.00 0.98
2045 5828 7.056635 CCCACAGTTCCAATGAGAGTTATAAT 58.943 38.462 0.00 0.00 0.00 1.28
2046 5829 8.210946 CCCACAGTTCCAATGAGAGTTATAATA 58.789 37.037 0.00 0.00 0.00 0.98
2047 5830 9.613428 CCACAGTTCCAATGAGAGTTATAATAA 57.387 33.333 0.00 0.00 0.00 1.40
2064 5847 4.376340 AATAAGGCTTGCTAATGTGTGC 57.624 40.909 10.69 0.00 0.00 4.57
2093 5876 1.882912 CTGTGCTGCAGTTCCAGTAA 58.117 50.000 16.64 0.00 40.27 2.24
2179 5962 3.136123 CCTGCAATGGGTGGCTCG 61.136 66.667 0.00 0.00 0.00 5.03
2207 5990 7.273381 CCGTGAGTTCATCATTGAATTTTTACC 59.727 37.037 0.00 0.00 43.49 2.85
2210 5996 9.859427 TGAGTTCATCATTGAATTTTTACCATC 57.141 29.630 0.00 0.00 43.49 3.51
2324 6110 0.240145 CGACGGTGTTGCTAGTCTCA 59.760 55.000 0.00 0.00 0.00 3.27
2799 6585 1.204146 TGGACCTGATTGACCTAGGC 58.796 55.000 9.30 2.11 34.93 3.93
3054 6849 6.044512 ACTTTGTTTACAACTACTGAAGCG 57.955 37.500 0.00 0.00 35.28 4.68
3064 6859 3.894759 ACTACTGAAGCGTGGGTATAGA 58.105 45.455 0.00 0.00 0.00 1.98
3217 7012 4.342951 TCTGTAACCCAATATAGTCCACGG 59.657 45.833 0.00 0.00 0.00 4.94
3273 7070 6.037610 CCAGTATCCTAAACATCTTTCTGTGC 59.962 42.308 0.00 0.00 0.00 4.57
3288 7085 2.751259 TCTGTGCTGAATTCATTGGCTC 59.249 45.455 8.96 10.42 0.00 4.70
3332 7129 2.271800 GTGACCATCGACCAAGCTAAG 58.728 52.381 0.00 0.00 0.00 2.18
3407 7204 0.249155 TTGTCGTCTCACCAACGGTC 60.249 55.000 0.00 0.00 40.45 4.79
3711 7508 1.083489 TGCTGCATTACGGTTACTGC 58.917 50.000 0.00 0.00 35.06 4.40
3856 7653 1.002576 TGCGATGCAAATATTCCTGCG 60.003 47.619 7.45 1.75 41.63 5.18
3968 7765 1.865340 GGTTCAGATTTCCGTATCCGC 59.135 52.381 0.00 0.00 0.00 5.54
4216 8014 7.786046 TTTGTCTACAGAGGGAGTATTACAA 57.214 36.000 0.00 0.00 31.25 2.41
4721 8519 5.464168 TCTCTTGTTGGTAAGTAACTACGC 58.536 41.667 0.00 0.00 0.00 4.42
4746 8547 5.050363 GCATTTGTCTTGAGTCTTGACGTAA 60.050 40.000 0.00 7.99 33.81 3.18
4747 8548 6.511121 GCATTTGTCTTGAGTCTTGACGTAAA 60.511 38.462 0.00 0.00 33.81 2.01
4748 8549 6.971527 TTTGTCTTGAGTCTTGACGTAAAA 57.028 33.333 0.00 0.00 33.81 1.52
4793 8594 5.246203 AGAGCAAACATCACTTAGTCAGGTA 59.754 40.000 0.00 0.00 0.00 3.08
4889 8690 3.289836 CATCCCTGATGTTATGGTTGCA 58.710 45.455 0.00 0.00 35.54 4.08
5036 8837 7.038302 TCAGTTCCTTCATACTTCCAACAGTAT 60.038 37.037 0.00 0.00 40.08 2.12
5368 9169 2.224548 GGTACTGGGATTGTCCTATGGC 60.225 54.545 0.00 0.00 36.57 4.40
5426 9227 8.458573 ACTACTACCATTTTGACAAACAATCA 57.541 30.769 0.00 0.00 38.36 2.57
5464 9267 0.794473 GGCAATTTGCTGCTCAAAGC 59.206 50.000 20.06 8.45 46.68 3.51
5490 9293 4.378356 CGCTTCAACTGAAAATTGATCCGA 60.378 41.667 0.00 0.00 36.02 4.55
5632 9435 1.910671 TCCTTGGGGCGTAACTGTAAT 59.089 47.619 0.00 0.00 0.00 1.89
5638 9441 0.393267 GGCGTAACTGTAATGCCCCA 60.393 55.000 5.97 0.00 39.83 4.96
5640 9443 1.406341 GCGTAACTGTAATGCCCCAGA 60.406 52.381 0.00 0.00 32.93 3.86
5737 9540 1.679139 TTCCTGTGCACTTTGTCCTG 58.321 50.000 19.41 0.00 0.00 3.86
5819 9650 0.695347 CTCCCAGAAAGGAAGGTGCT 59.305 55.000 0.00 0.00 41.22 4.40
5877 9724 1.412361 CCCCCACTCAAAGGAACCAAA 60.412 52.381 0.00 0.00 0.00 3.28
5880 9727 3.031013 CCCACTCAAAGGAACCAAAGTT 58.969 45.455 0.00 0.00 39.54 2.66
5974 9858 1.150536 ACAAACCTGACCCGCACAT 59.849 52.632 0.00 0.00 0.00 3.21
6119 10041 6.164176 CACCGACCAATACTAGTCTTTTCTT 58.836 40.000 0.00 0.00 0.00 2.52
6248 10170 1.777272 AGCTCCTGGAAAAGAAGGTGT 59.223 47.619 0.00 0.00 34.94 4.16
6270 10192 6.308282 GTGTACCTTCTTGATTTGAGTAGTCG 59.692 42.308 0.00 0.00 0.00 4.18
6359 10281 1.272985 TGGTCTTAAATGGGCAAGGGG 60.273 52.381 0.00 0.00 0.00 4.79
6433 10360 1.556911 AGTGAGCAAGGATCGGTCATT 59.443 47.619 0.00 0.00 42.35 2.57
6447 10374 2.680805 CGGTCATTGCATCCTTAGTGGT 60.681 50.000 0.00 0.00 37.07 4.16
6454 10381 1.858091 CATCCTTAGTGGTGCGCTAG 58.142 55.000 9.73 0.00 37.07 3.42
6563 10494 5.046159 ACGGGAGTTAGTTGATACAATGGAA 60.046 40.000 0.00 0.00 43.33 3.53
6711 10643 2.427453 CAGTTAGGTGTAGCGGAGATGT 59.573 50.000 0.00 0.00 0.00 3.06
6756 10688 5.529060 GGTCACACAAGAAAGAATCAAGTCT 59.471 40.000 0.00 0.00 0.00 3.24
6790 10722 2.601905 ACGTGTTAGAGTTGGGGTAGT 58.398 47.619 0.00 0.00 0.00 2.73
6834 10766 3.119849 CCAACATCGTTTGAGATGGTTCC 60.120 47.826 11.06 0.00 45.46 3.62
6861 10797 1.676635 GCACATGCCTCCAGAAGCA 60.677 57.895 0.00 0.00 44.45 3.91
6902 10840 8.023128 ACAGTTAAATGTGCTGATAATGTCAAC 58.977 33.333 7.92 0.00 31.71 3.18
6950 10889 3.493334 TGTGAGGAGTCCGTAAAGAGAA 58.507 45.455 2.76 0.00 0.00 2.87
6988 10927 6.547510 GGAATATCACCAAAGAACTAGCCATT 59.452 38.462 0.00 0.00 0.00 3.16
7014 10953 0.528684 GGTGCGTGGAAGCTAGCTAG 60.529 60.000 19.70 16.84 38.13 3.42
7029 10982 3.878160 AGCTAGCCAGAACTGTAACTC 57.122 47.619 12.13 0.00 0.00 3.01
7077 11032 0.317160 GCCTACCCCAACTTGTTTGC 59.683 55.000 0.00 0.00 33.34 3.68
7214 11170 5.546621 AGTGTAGTTTGTGACCTGTATGT 57.453 39.130 0.00 0.00 0.00 2.29
7443 11402 4.217118 TCTCAGGTAAACTACGTCCTCAAC 59.783 45.833 0.00 0.00 0.00 3.18
7446 11405 3.638160 AGGTAAACTACGTCCTCAACACA 59.362 43.478 0.00 0.00 0.00 3.72
7447 11406 4.099881 AGGTAAACTACGTCCTCAACACAA 59.900 41.667 0.00 0.00 0.00 3.33
7494 11453 4.635765 GCATTTCTGGTTGCTGTCATACTA 59.364 41.667 0.00 0.00 35.95 1.82
7500 11459 4.566004 TGGTTGCTGTCATACTAGACAAC 58.434 43.478 0.00 0.00 46.90 3.32
7515 11474 1.898574 CAACACTGTCCCTGGTGGC 60.899 63.158 0.00 0.00 37.72 5.01
7516 11475 2.078665 AACACTGTCCCTGGTGGCT 61.079 57.895 0.00 0.00 37.72 4.75
7592 11552 5.189180 ACCATCCTTCTTGAAAGACTATGC 58.811 41.667 0.00 0.00 34.13 3.14
7593 11553 4.272018 CCATCCTTCTTGAAAGACTATGCG 59.728 45.833 0.00 0.00 34.13 4.73
7616 11576 0.546598 CCTTTCAAGATAGGGCGGGT 59.453 55.000 0.00 0.00 0.00 5.28
7735 11700 0.980423 TCATGTTCCATGACGGACCA 59.020 50.000 2.88 0.00 46.36 4.02
7741 11706 0.988063 TCCATGACGGACCATTTCCA 59.012 50.000 0.00 0.00 46.29 3.53
7779 11753 4.750098 AGTGTATATTCCGAAGAATTGCCG 59.250 41.667 0.00 0.00 39.83 5.69
7831 11805 2.933928 GCGTGGGACGAATTTTCCTAGT 60.934 50.000 0.00 0.00 46.05 2.57
7832 11806 3.676873 GCGTGGGACGAATTTTCCTAGTA 60.677 47.826 0.00 0.00 46.05 1.82
7833 11807 4.690122 CGTGGGACGAATTTTCCTAGTAT 58.310 43.478 6.92 0.00 46.05 2.12
7953 11949 0.253327 GGTCTGAACTAAGCCTGGGG 59.747 60.000 0.00 0.00 0.00 4.96
7954 11950 1.276622 GTCTGAACTAAGCCTGGGGA 58.723 55.000 0.00 0.00 0.00 4.81
7961 11957 1.677637 CTAAGCCTGGGGACTCCGAC 61.678 65.000 0.00 0.00 38.76 4.79
8021 12017 4.531854 TGACTTCCAACTTGGTCAAATCA 58.468 39.130 7.72 0.00 39.03 2.57
8022 12018 4.580167 TGACTTCCAACTTGGTCAAATCAG 59.420 41.667 7.72 0.00 39.03 2.90
8059 12065 9.571810 TTGCATACAATATTCTGTGTTGAATTC 57.428 29.630 0.00 0.00 37.73 2.17
8132 12138 4.163078 CCTTTTCCAATCTCTCAGCTAGGA 59.837 45.833 0.00 0.00 0.00 2.94
8135 12141 7.419518 CCTTTTCCAATCTCTCAGCTAGGAATA 60.420 40.741 0.00 0.00 34.06 1.75
8202 12208 6.696411 TCAAAAGTTGTGTGACTTTGGAAAT 58.304 32.000 5.37 0.00 46.23 2.17
8243 12249 3.532542 CCAAAGAGGTTCGGAGAATACC 58.467 50.000 0.00 0.00 45.90 2.73
8244 12250 3.532542 CAAAGAGGTTCGGAGAATACCC 58.467 50.000 0.00 0.00 45.90 3.69
8245 12251 2.850695 AGAGGTTCGGAGAATACCCT 57.149 50.000 0.00 0.00 45.90 4.34
8246 12252 3.967467 AGAGGTTCGGAGAATACCCTA 57.033 47.619 0.00 0.00 45.90 3.53
8247 12253 3.834938 AGAGGTTCGGAGAATACCCTAG 58.165 50.000 0.00 0.00 45.90 3.02
8248 12254 3.462579 AGAGGTTCGGAGAATACCCTAGA 59.537 47.826 0.00 0.00 45.90 2.43
8249 12255 3.822167 GAGGTTCGGAGAATACCCTAGAG 59.178 52.174 0.00 0.00 45.90 2.43
8250 12256 2.892215 GGTTCGGAGAATACCCTAGAGG 59.108 54.545 0.00 0.00 45.90 3.69
8251 12257 2.289592 TCGGAGAATACCCTAGAGGC 57.710 55.000 0.00 0.00 40.58 4.70
8252 12258 1.497716 TCGGAGAATACCCTAGAGGCA 59.502 52.381 0.00 0.00 40.58 4.75
8253 12259 1.889829 CGGAGAATACCCTAGAGGCAG 59.110 57.143 0.00 0.00 40.58 4.85
8254 12260 2.753507 CGGAGAATACCCTAGAGGCAGT 60.754 54.545 0.00 0.00 40.58 4.40
8255 12261 2.630580 GGAGAATACCCTAGAGGCAGTG 59.369 54.545 0.00 0.00 40.58 3.66
8256 12262 2.630580 GAGAATACCCTAGAGGCAGTGG 59.369 54.545 0.00 0.00 40.58 4.00
8257 12263 1.694696 GAATACCCTAGAGGCAGTGGG 59.305 57.143 0.00 0.00 44.89 4.61
8260 12266 2.517609 CCCTAGAGGCAGTGGGTAC 58.482 63.158 0.00 0.00 35.13 3.34
8280 12286 5.221244 GGTACCACCATTTGCATCCTTAATC 60.221 44.000 7.15 0.00 38.42 1.75
8281 12287 4.613437 ACCACCATTTGCATCCTTAATCT 58.387 39.130 0.00 0.00 0.00 2.40
8282 12288 4.646492 ACCACCATTTGCATCCTTAATCTC 59.354 41.667 0.00 0.00 0.00 2.75
8283 12289 4.646040 CCACCATTTGCATCCTTAATCTCA 59.354 41.667 0.00 0.00 0.00 3.27
8292 12298 1.765314 TCCTTAATCTCAGCAGGCTCC 59.235 52.381 0.00 0.00 0.00 4.70
8308 12314 1.965754 CTCCTGTCTGGTAGGCTGCC 61.966 65.000 15.45 15.45 35.23 4.85
8313 12319 1.075226 TCTGGTAGGCTGCCTAGGG 60.075 63.158 28.02 19.29 36.71 3.53
8334 12340 4.735132 CGTCGCCGAGCTTGGGAA 62.735 66.667 22.06 0.00 35.63 3.97
8335 12341 2.815647 GTCGCCGAGCTTGGGAAG 60.816 66.667 22.06 8.00 0.00 3.46
8336 12342 2.994995 TCGCCGAGCTTGGGAAGA 60.995 61.111 22.06 10.06 0.00 2.87
8337 12343 2.510238 CGCCGAGCTTGGGAAGAG 60.510 66.667 22.06 0.00 0.00 2.85
8338 12344 2.665603 GCCGAGCTTGGGAAGAGT 59.334 61.111 22.06 0.00 0.00 3.24
8339 12345 1.003233 GCCGAGCTTGGGAAGAGTT 60.003 57.895 22.06 0.00 0.00 3.01
8341 12347 1.897560 CCGAGCTTGGGAAGAGTTTT 58.102 50.000 12.81 0.00 0.00 2.43
8343 12349 1.068954 CGAGCTTGGGAAGAGTTTTGC 60.069 52.381 0.00 0.00 0.00 3.68
8344 12350 1.956477 GAGCTTGGGAAGAGTTTTGCA 59.044 47.619 0.00 0.00 0.00 4.08
8345 12351 2.362077 GAGCTTGGGAAGAGTTTTGCAA 59.638 45.455 0.00 0.00 0.00 4.08
8346 12352 2.765699 AGCTTGGGAAGAGTTTTGCAAA 59.234 40.909 8.05 8.05 0.00 3.68
8348 12354 3.557185 GCTTGGGAAGAGTTTTGCAAAAG 59.443 43.478 24.46 10.00 0.00 2.27
8349 12355 4.758688 CTTGGGAAGAGTTTTGCAAAAGT 58.241 39.130 28.01 28.01 34.41 2.66
8350 12356 4.817318 TGGGAAGAGTTTTGCAAAAGTT 57.183 36.364 28.22 19.69 32.00 2.66
8360 12397 3.451141 TTGCAAAAGTTTTCCAGCGAT 57.549 38.095 0.00 0.00 0.00 4.58
8363 12400 2.676076 CAAAAGTTTTCCAGCGATGGG 58.324 47.619 21.53 0.72 0.00 4.00
8535 12576 2.633657 GTCACGCACTTGGCTGTG 59.366 61.111 6.80 6.80 43.54 3.66
8536 12577 2.591429 TCACGCACTTGGCTGTGG 60.591 61.111 11.75 6.00 42.90 4.17
8557 12598 2.485426 GTGTCATCATGAGTGTTGTGGG 59.515 50.000 0.09 0.00 0.00 4.61
8584 14787 0.108615 ACAAACGCCGAGAGAGGATG 60.109 55.000 0.00 0.00 0.00 3.51
8585 14788 0.807667 CAAACGCCGAGAGAGGATGG 60.808 60.000 0.00 0.00 0.00 3.51
8586 14789 1.961180 AAACGCCGAGAGAGGATGGG 61.961 60.000 0.00 0.00 0.00 4.00
8587 14790 4.292178 CGCCGAGAGAGGATGGGC 62.292 72.222 0.00 0.00 38.11 5.36
8588 14791 3.934962 GCCGAGAGAGGATGGGCC 61.935 72.222 0.00 0.00 35.68 5.80
8589 14792 2.444706 CCGAGAGAGGATGGGCCA 60.445 66.667 9.61 9.61 40.02 5.36
8590 14793 2.066393 CCGAGAGAGGATGGGCCAA 61.066 63.158 11.89 0.00 40.02 4.52
8591 14794 1.144936 CGAGAGAGGATGGGCCAAC 59.855 63.158 11.89 8.12 40.02 3.77
8592 14795 1.529309 GAGAGAGGATGGGCCAACC 59.471 63.158 24.37 24.37 40.02 3.77
8638 14847 4.980805 GCCGCACAGACCGTCCAA 62.981 66.667 0.00 0.00 0.00 3.53
8639 14848 2.280524 CCGCACAGACCGTCCAAA 60.281 61.111 0.00 0.00 0.00 3.28
8679 14891 0.032678 CCAGACGACAGCACTCAACT 59.967 55.000 0.00 0.00 0.00 3.16
8727 14943 1.450312 GCTGCAGGGTCGCACTAAT 60.450 57.895 17.12 0.00 36.86 1.73
8771 14987 1.408702 TGCAACTTTTCCTGTCTTGCC 59.591 47.619 0.00 0.00 37.09 4.52
8772 14988 1.683385 GCAACTTTTCCTGTCTTGCCT 59.317 47.619 0.00 0.00 32.71 4.75
8773 14989 2.101415 GCAACTTTTCCTGTCTTGCCTT 59.899 45.455 0.00 0.00 32.71 4.35
8774 14990 3.709987 CAACTTTTCCTGTCTTGCCTTG 58.290 45.455 0.00 0.00 0.00 3.61
8775 14991 2.310538 ACTTTTCCTGTCTTGCCTTGG 58.689 47.619 0.00 0.00 0.00 3.61
8776 14992 1.615392 CTTTTCCTGTCTTGCCTTGGG 59.385 52.381 0.00 0.00 0.00 4.12
8790 15006 3.444818 TTGGGCTTGGGCGAGGTTT 62.445 57.895 0.00 0.00 39.81 3.27
8800 15016 1.702491 GGCGAGGTTTGCACGGATAC 61.702 60.000 0.00 0.00 0.00 2.24
8804 15020 2.156098 GAGGTTTGCACGGATACCAAA 58.844 47.619 1.42 0.00 33.02 3.28
8820 15036 4.058721 ACCAAACAAACAAAGGCATCTC 57.941 40.909 0.00 0.00 0.00 2.75
8845 15062 2.678786 ACTGCCGGTGATTCCTGTA 58.321 52.632 1.90 0.00 0.00 2.74
8856 15073 4.583073 GGTGATTCCTGTAAACAAACTGGT 59.417 41.667 0.00 0.00 39.01 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.623418 AGGTATGGACAGTGGAGACA 57.377 50.000 0.00 0.00 38.70 3.41
593 3878 2.282462 CAAAAGAGGCGGCCCAGT 60.282 61.111 17.02 0.00 0.00 4.00
682 3968 4.719369 GGTTCTCGTGCGTCCGCT 62.719 66.667 13.31 0.00 42.51 5.52
720 4008 2.417651 CGTGAGGCCGTGGAAGTTATTA 60.418 50.000 0.00 0.00 0.00 0.98
721 4009 1.674817 CGTGAGGCCGTGGAAGTTATT 60.675 52.381 0.00 0.00 0.00 1.40
722 4010 0.108329 CGTGAGGCCGTGGAAGTTAT 60.108 55.000 0.00 0.00 0.00 1.89
751 4042 1.635663 CCTTTTGTCACTAGCGGCGG 61.636 60.000 9.78 0.00 0.00 6.13
817 4109 1.660575 CGTGACGGTGACTGTGACC 60.661 63.158 8.53 6.34 0.00 4.02
853 4151 3.633116 CGGTTTGGTCCCGGTCCT 61.633 66.667 12.98 0.00 41.78 3.85
907 4210 0.599060 TTTGAAATTTCGGGGGACGC 59.401 50.000 13.34 0.00 43.86 5.19
996 4305 1.401905 GAGATTTTGCGATGGGGTGAC 59.598 52.381 0.00 0.00 0.00 3.67
1005 4314 2.038269 GGTGGCGGAGATTTTGCGA 61.038 57.895 0.00 0.00 44.18 5.10
1055 4364 1.226435 GAGCTGGAGACGCGTACTG 60.226 63.158 13.97 11.03 35.50 2.74
1090 4405 2.757980 TTTTAGGCGAGGGGTGGTGC 62.758 60.000 0.00 0.00 0.00 5.01
1658 5432 4.785453 GGAGCCTGCCCGGAGTTG 62.785 72.222 0.73 0.00 33.16 3.16
1871 5654 1.381735 CCCATTTGGCCTTCCTCCC 60.382 63.158 3.32 0.00 0.00 4.30
1996 5779 0.252558 TCGGCTTTCCTCCTTAGGGT 60.253 55.000 0.00 0.00 43.84 4.34
2000 5783 2.551504 GGTGTTTCGGCTTTCCTCCTTA 60.552 50.000 0.00 0.00 0.00 2.69
2020 5803 2.867109 ACTCTCATTGGAACTGTGGG 57.133 50.000 0.00 0.00 0.00 4.61
2025 5808 8.718656 AGCCTTATTATAACTCTCATTGGAACT 58.281 33.333 0.00 0.00 0.00 3.01
2044 5827 3.355378 TGCACACATTAGCAAGCCTTAT 58.645 40.909 0.00 0.00 37.90 1.73
2045 5828 2.789213 TGCACACATTAGCAAGCCTTA 58.211 42.857 0.00 0.00 37.90 2.69
2046 5829 1.619654 TGCACACATTAGCAAGCCTT 58.380 45.000 0.00 0.00 37.90 4.35
2047 5830 1.843368 ATGCACACATTAGCAAGCCT 58.157 45.000 0.00 0.00 44.88 4.58
2093 5876 6.946340 TGTAATGCTGGAATCCGTATATCAT 58.054 36.000 0.00 0.00 0.00 2.45
2179 5962 1.737838 TCAATGATGAACTCACGGCC 58.262 50.000 0.00 0.00 36.48 6.13
2207 5990 7.094334 ACAGCCATGCTATATGAAAATGAGATG 60.094 37.037 0.00 0.00 36.40 2.90
2210 5996 6.570672 ACAGCCATGCTATATGAAAATGAG 57.429 37.500 0.00 0.00 36.40 2.90
2324 6110 4.519540 GTGCAACAATGTGGTTAATCCT 57.480 40.909 0.00 0.00 36.32 3.24
2799 6585 7.675478 TCGTTCAAATCTCGATTTATTCACTG 58.325 34.615 4.70 0.00 38.84 3.66
2965 6760 7.591426 GCGGGAAATGATCATTAAGATGTTTAC 59.409 37.037 21.00 4.72 37.00 2.01
3054 6849 4.103311 AGGAAAGGCTGATTCTATACCCAC 59.897 45.833 0.00 0.00 0.00 4.61
3064 6859 6.830838 CCTAAGTTGATAAGGAAAGGCTGATT 59.169 38.462 0.00 0.00 31.64 2.57
3217 7012 2.448542 TCCCCCTCAGGCCTATGC 60.449 66.667 3.98 0.00 0.00 3.14
3273 7070 1.469703 TGCACGAGCCAATGAATTCAG 59.530 47.619 14.54 1.48 41.13 3.02
3288 7085 1.534595 GCCAAGCCAATCTATTGCACG 60.535 52.381 0.00 0.00 36.48 5.34
3332 7129 9.736023 ATTGAATTGTAGAACAGAAGAACAAAC 57.264 29.630 0.00 0.00 34.08 2.93
3407 7204 1.205064 CGAAAGTCCAACAGCTGCG 59.795 57.895 15.27 5.03 0.00 5.18
3711 7508 4.576216 AGGTTAGTATCTCATGCAGTCG 57.424 45.455 0.00 0.00 0.00 4.18
3856 7653 6.476706 GGCAAAAGGCTGATATATTGTTTGAC 59.523 38.462 6.68 0.58 44.01 3.18
3897 7694 4.184629 GTCTACACGGCAAGATTTCATCT 58.815 43.478 0.00 0.00 42.61 2.90
3968 7765 2.036098 TGGAGTGCCCCATTGCAG 59.964 61.111 0.00 0.00 43.02 4.41
4166 7963 9.865321 ATATAAGACGTTTTAGCTCACTAAACA 57.135 29.630 4.75 0.00 45.74 2.83
4399 8197 1.234821 TGAGCGTTCAATGGTTCCAC 58.765 50.000 0.00 0.00 0.00 4.02
4721 8519 3.662713 CGTCAAGACTCAAGACAAATGCG 60.663 47.826 0.00 0.00 32.68 4.73
4746 8547 8.579850 TCTTCCAATATTGTGTAAGAGCATTT 57.420 30.769 14.25 0.00 0.00 2.32
4747 8548 8.218338 CTCTTCCAATATTGTGTAAGAGCATT 57.782 34.615 24.53 0.00 35.14 3.56
4748 8549 7.798596 CTCTTCCAATATTGTGTAAGAGCAT 57.201 36.000 24.53 0.00 35.14 3.79
4793 8594 3.028850 AGCAAGAACCATGCATGCTATT 58.971 40.909 21.69 14.16 44.92 1.73
4889 8690 3.152341 CCACATGAAACAAAGGAGAGCT 58.848 45.455 0.00 0.00 0.00 4.09
5057 8858 5.935945 TGAAAGTAGGTTGGAACTGATGAA 58.064 37.500 0.00 0.00 0.00 2.57
5368 9169 7.338800 AGCAATTCCAAATATACCAAGTGAG 57.661 36.000 0.00 0.00 0.00 3.51
5447 9250 1.796459 GTGGCTTTGAGCAGCAAATTG 59.204 47.619 5.40 0.00 44.90 2.32
5464 9267 3.963665 TCAATTTTCAGTTGAAGCGTGG 58.036 40.909 0.00 0.00 35.21 4.94
5632 9435 2.197324 GTGGGTTTGTCTGGGGCA 59.803 61.111 0.00 0.00 0.00 5.36
5819 9650 8.996651 TGATAGACTACTCATATCAACAAGGA 57.003 34.615 0.00 0.00 33.99 3.36
5877 9724 2.032681 GCTGGGCCAACGAGAACT 59.967 61.111 8.04 0.00 0.00 3.01
5880 9727 4.020617 CCTGCTGGGCCAACGAGA 62.021 66.667 8.04 0.00 0.00 4.04
5974 9858 2.429571 GTCGCGGTTACACGAGCA 60.430 61.111 6.13 0.00 39.30 4.26
5991 9875 0.469917 ATTGGTATCAGAGCCACCCG 59.530 55.000 0.00 0.00 34.02 5.28
6077 9999 2.778270 GGTGGGGCTAGTCTAAATCCTT 59.222 50.000 0.00 0.00 0.00 3.36
6119 10041 0.318699 CGAGTGAGGACAAAGTGCGA 60.319 55.000 0.00 0.00 0.00 5.10
6226 10148 1.002544 ACCTTCTTTTCCAGGAGCTCG 59.997 52.381 7.83 0.00 33.90 5.03
6248 10170 6.829229 TCGACTACTCAAATCAAGAAGGTA 57.171 37.500 0.00 0.00 0.00 3.08
6260 10182 8.082852 GCTTAATAGGAATGATCGACTACTCAA 58.917 37.037 0.00 0.00 0.00 3.02
6270 10192 4.553330 TCCCGGCTTAATAGGAATGATC 57.447 45.455 0.00 0.00 0.00 2.92
6407 10334 3.197766 ACCGATCCTTGCTCACTTATCAA 59.802 43.478 0.00 0.00 0.00 2.57
6433 10360 1.745115 GCGCACCACTAAGGATGCA 60.745 57.895 0.30 0.00 41.22 3.96
6454 10381 0.172803 ACTACACCCGAGCGTCAATC 59.827 55.000 0.00 0.00 0.00 2.67
6503 10434 2.468915 GACCCTACTTTCCAGCTACCT 58.531 52.381 0.00 0.00 0.00 3.08
6563 10494 3.194542 GCATAGGATATCAACGCCTCTCT 59.805 47.826 4.83 0.00 33.28 3.10
6711 10643 4.139038 CCACATATCCATCTCAACATGCA 58.861 43.478 0.00 0.00 0.00 3.96
6756 10688 8.178313 ACTCTAACACGTATATCATCATTCCA 57.822 34.615 0.00 0.00 0.00 3.53
6790 10722 5.003804 GGACAAGCTTCTCTTCAATTGGTA 58.996 41.667 5.42 0.00 31.27 3.25
6861 10797 1.219124 CTGTCCGCTATGCACTGGT 59.781 57.895 0.00 0.00 0.00 4.00
6950 10889 4.080299 GGTGATATTCCAGTCCTTCAGGTT 60.080 45.833 0.00 0.00 36.34 3.50
6988 10927 3.164977 TTCCACGCACCCCTGTCA 61.165 61.111 0.00 0.00 0.00 3.58
7014 10953 2.165319 AACCGAGTTACAGTTCTGGC 57.835 50.000 4.82 0.00 0.00 4.85
7029 10982 6.973474 AGTTAACTCATAAGATCTCGAAACCG 59.027 38.462 1.12 0.00 0.00 4.44
7047 11000 2.067386 TGGGGTAGGCCAAAGTTAACT 58.933 47.619 5.01 1.12 36.17 2.24
7107 11062 6.259167 TCGCTACAAAGTAAAACACACTCAAT 59.741 34.615 0.00 0.00 0.00 2.57
7326 11282 4.207019 CACTTTTCAGAATTTTTCGCGCTT 59.793 37.500 5.56 0.00 34.02 4.68
7332 11289 8.006027 GCTTATGCACACTTTTCAGAATTTTTC 58.994 33.333 0.00 0.00 39.41 2.29
7384 11343 9.838339 ACAGAGAATGACGATTAAATTTCCTAT 57.162 29.630 0.00 0.00 0.00 2.57
7391 11350 7.827236 TGGGTAAACAGAGAATGACGATTAAAT 59.173 33.333 0.00 0.00 0.00 1.40
7401 11360 5.491070 TGAGATGTGGGTAAACAGAGAATG 58.509 41.667 0.00 0.00 32.52 2.67
7443 11402 6.818142 TCACCATATTGAGTGACAGTATTGTG 59.182 38.462 0.00 0.00 41.55 3.33
7446 11405 7.012704 GCAATCACCATATTGAGTGACAGTATT 59.987 37.037 8.62 0.00 45.24 1.89
7447 11406 6.484643 GCAATCACCATATTGAGTGACAGTAT 59.515 38.462 8.62 0.00 45.24 2.12
7500 11459 2.033141 CAGCCACCAGGGACAGTG 59.967 66.667 0.00 0.00 40.01 3.66
7592 11552 1.943340 GCCCTATCTTGAAAGGAAGCG 59.057 52.381 0.00 0.00 34.58 4.68
7593 11553 1.943340 CGCCCTATCTTGAAAGGAAGC 59.057 52.381 0.00 0.00 34.58 3.86
7616 11576 1.327303 GCATTTGACCCACCTGAACA 58.673 50.000 0.00 0.00 0.00 3.18
7735 11700 1.066143 CGGTACCTCTGCTGTGGAAAT 60.066 52.381 17.40 0.00 0.00 2.17
7741 11706 0.539901 ACACTCGGTACCTCTGCTGT 60.540 55.000 10.90 1.28 0.00 4.40
7779 11753 5.619533 CGTCAGGACAAGAGAACTAACCTAC 60.620 48.000 0.00 0.00 0.00 3.18
7864 11850 5.659849 ATAGGAAGAGCAAAATCCCTCAT 57.340 39.130 0.00 0.00 33.55 2.90
7953 11949 0.450983 CTAACAGGTCGGTCGGAGTC 59.549 60.000 0.00 0.00 0.00 3.36
7954 11950 0.964358 CCTAACAGGTCGGTCGGAGT 60.964 60.000 0.00 0.00 0.00 3.85
7961 11957 6.518493 TGTAAATATAAGCCTAACAGGTCGG 58.482 40.000 0.00 0.00 37.80 4.79
8022 12018 7.930865 AGAATATTGTATGCAAAGAGACCTCTC 59.069 37.037 0.00 0.00 39.39 3.20
8059 12065 2.376109 AGACCATACACCTACACTCCG 58.624 52.381 0.00 0.00 0.00 4.63
8132 12138 3.257127 CGTGGGGGTCACAAATTTGTATT 59.743 43.478 22.87 0.00 46.36 1.89
8135 12141 1.036707 CGTGGGGGTCACAAATTTGT 58.963 50.000 18.13 18.13 46.36 2.83
8187 12193 8.871686 ATGAACTAAAATTTCCAAAGTCACAC 57.128 30.769 0.00 0.00 0.00 3.82
8223 12229 3.197983 AGGGTATTCTCCGAACCTCTTTG 59.802 47.826 0.00 0.00 33.59 2.77
8243 12249 0.325296 TGGTACCCACTGCCTCTAGG 60.325 60.000 10.07 0.00 38.53 3.02
8244 12250 3.300032 TGGTACCCACTGCCTCTAG 57.700 57.895 10.07 0.00 0.00 2.43
8254 12260 1.618345 GGATGCAAATGGTGGTACCCA 60.618 52.381 10.07 0.63 37.50 4.51
8255 12261 1.111277 GGATGCAAATGGTGGTACCC 58.889 55.000 10.07 0.11 37.50 3.69
8256 12262 2.143876 AGGATGCAAATGGTGGTACC 57.856 50.000 4.43 4.43 39.22 3.34
8257 12263 5.594317 AGATTAAGGATGCAAATGGTGGTAC 59.406 40.000 0.00 0.00 0.00 3.34
8258 12264 5.765510 AGATTAAGGATGCAAATGGTGGTA 58.234 37.500 0.00 0.00 0.00 3.25
8259 12265 4.613437 AGATTAAGGATGCAAATGGTGGT 58.387 39.130 0.00 0.00 0.00 4.16
8260 12266 4.646040 TGAGATTAAGGATGCAAATGGTGG 59.354 41.667 0.00 0.00 0.00 4.61
8261 12267 5.735354 GCTGAGATTAAGGATGCAAATGGTG 60.735 44.000 0.00 0.00 0.00 4.17
8262 12268 4.340381 GCTGAGATTAAGGATGCAAATGGT 59.660 41.667 0.00 0.00 0.00 3.55
8292 12298 0.749649 CTAGGCAGCCTACCAGACAG 59.250 60.000 18.06 3.72 34.61 3.51
8330 12336 5.064707 GGAAAACTTTTGCAAAACTCTTCCC 59.935 40.000 26.21 18.04 0.00 3.97
8334 12340 4.631377 GCTGGAAAACTTTTGCAAAACTCT 59.369 37.500 20.46 5.72 0.00 3.24
8335 12341 4.492409 CGCTGGAAAACTTTTGCAAAACTC 60.492 41.667 20.46 13.45 0.00 3.01
8336 12342 3.370672 CGCTGGAAAACTTTTGCAAAACT 59.629 39.130 20.46 9.26 0.00 2.66
8337 12343 3.369451 TCGCTGGAAAACTTTTGCAAAAC 59.631 39.130 20.46 10.35 0.00 2.43
8338 12344 3.589988 TCGCTGGAAAACTTTTGCAAAA 58.410 36.364 22.61 22.61 0.00 2.44
8339 12345 3.238108 TCGCTGGAAAACTTTTGCAAA 57.762 38.095 8.05 8.05 0.00 3.68
8341 12347 2.545532 CCATCGCTGGAAAACTTTTGCA 60.546 45.455 0.00 8.05 46.37 4.08
8343 12349 2.295909 TCCCATCGCTGGAAAACTTTTG 59.704 45.455 6.92 0.00 46.37 2.44
8344 12350 2.558359 CTCCCATCGCTGGAAAACTTTT 59.442 45.455 6.92 0.00 46.37 2.27
8345 12351 2.162681 CTCCCATCGCTGGAAAACTTT 58.837 47.619 6.92 0.00 46.37 2.66
8346 12352 1.351017 TCTCCCATCGCTGGAAAACTT 59.649 47.619 6.92 0.00 46.37 2.66
8348 12354 1.087501 GTCTCCCATCGCTGGAAAAC 58.912 55.000 6.92 0.00 46.37 2.43
8349 12355 0.984230 AGTCTCCCATCGCTGGAAAA 59.016 50.000 6.92 0.00 46.37 2.29
8350 12356 0.250234 CAGTCTCCCATCGCTGGAAA 59.750 55.000 6.92 0.00 46.37 3.13
8360 12397 1.920325 CTGCCCTTCCAGTCTCCCA 60.920 63.158 0.00 0.00 0.00 4.37
8363 12400 1.078567 CAGCTGCCCTTCCAGTCTC 60.079 63.158 0.00 0.00 35.28 3.36
8431 12472 1.102809 TGTGTTGCCTCCAGTTGCAG 61.103 55.000 0.00 0.00 38.95 4.41
8535 12576 2.485426 CCACAACACTCATGATGACACC 59.515 50.000 0.00 0.00 33.05 4.16
8536 12577 2.485426 CCCACAACACTCATGATGACAC 59.515 50.000 0.00 0.00 33.05 3.67
8587 14790 4.740822 CCTCCGGCCCTTGGTTGG 62.741 72.222 0.00 0.00 0.00 3.77
8588 14791 3.966543 ACCTCCGGCCCTTGGTTG 61.967 66.667 0.00 0.00 0.00 3.77
8589 14792 3.966543 CACCTCCGGCCCTTGGTT 61.967 66.667 0.00 0.00 0.00 3.67
8592 14795 4.101448 CTCCACCTCCGGCCCTTG 62.101 72.222 0.00 0.00 0.00 3.61
8622 14831 2.280524 TTTGGACGGTCTGTGCGG 60.281 61.111 8.23 0.00 42.78 5.69
8623 14832 1.831389 CTGTTTGGACGGTCTGTGCG 61.831 60.000 8.23 0.00 42.78 5.34
8624 14833 1.507141 CCTGTTTGGACGGTCTGTGC 61.507 60.000 8.23 0.00 39.78 4.57
8625 14834 1.507141 GCCTGTTTGGACGGTCTGTG 61.507 60.000 8.23 0.00 38.35 3.66
8627 14836 1.966451 GGCCTGTTTGGACGGTCTG 60.966 63.158 8.23 0.00 38.35 3.51
8628 14837 2.430367 GGCCTGTTTGGACGGTCT 59.570 61.111 8.23 0.00 38.35 3.85
8633 14842 2.904866 TGTGCGGCCTGTTTGGAC 60.905 61.111 0.00 0.00 41.70 4.02
8634 14843 2.594303 CTGTGCGGCCTGTTTGGA 60.594 61.111 0.00 0.00 38.35 3.53
8637 14846 1.148273 TCTTCTGTGCGGCCTGTTT 59.852 52.632 0.00 0.00 0.00 2.83
8638 14847 1.598130 GTCTTCTGTGCGGCCTGTT 60.598 57.895 0.00 0.00 0.00 3.16
8639 14848 2.031163 GTCTTCTGTGCGGCCTGT 59.969 61.111 0.00 0.00 0.00 4.00
8679 14891 3.206150 GACTGAAACTCAAACAGCTCCA 58.794 45.455 0.00 0.00 35.38 3.86
8749 14965 3.054878 GCAAGACAGGAAAAGTTGCATG 58.945 45.455 0.00 0.00 42.48 4.06
8751 14967 1.408702 GGCAAGACAGGAAAAGTTGCA 59.591 47.619 7.58 0.00 44.29 4.08
8771 14987 3.868200 AACCTCGCCCAAGCCCAAG 62.868 63.158 0.00 0.00 34.57 3.61
8772 14988 3.444818 AAACCTCGCCCAAGCCCAA 62.445 57.895 0.00 0.00 34.57 4.12
8773 14989 3.897122 AAACCTCGCCCAAGCCCA 61.897 61.111 0.00 0.00 34.57 5.36
8774 14990 3.373565 CAAACCTCGCCCAAGCCC 61.374 66.667 0.00 0.00 34.57 5.19
8775 14991 4.056125 GCAAACCTCGCCCAAGCC 62.056 66.667 0.00 0.00 34.57 4.35
8776 14992 3.294493 TGCAAACCTCGCCCAAGC 61.294 61.111 0.00 0.00 0.00 4.01
8790 15006 2.298610 TGTTTGTTTGGTATCCGTGCA 58.701 42.857 0.00 0.00 0.00 4.57
8800 15016 4.057406 TGAGATGCCTTTGTTTGTTTGG 57.943 40.909 0.00 0.00 0.00 3.28
8804 15020 3.760684 GGAGATGAGATGCCTTTGTTTGT 59.239 43.478 0.00 0.00 0.00 2.83
8856 15073 2.712539 CGGCGTTGTCAAGCACAA 59.287 55.556 0.00 0.00 43.12 3.33


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

AutoCloner maintained by Alex Coulton.