Multiple sequence alignment - TraesCS1A01G261300

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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 TraesCS1A01G261300 chr1A 100.000 5400 0 0 1 5400 455611778 455606379 0.000000e+00 9973.0
1 TraesCS1A01G261300 chr1A 83.041 342 39 8 4803 5127 532264173 532264512 5.290000e-75 292.0
2 TraesCS1A01G261300 chr1A 94.505 91 4 1 345 434 507880714 507880804 7.290000e-29 139.0
3 TraesCS1A01G261300 chr1B 93.287 5035 231 49 428 5395 478060094 478055100 0.000000e+00 7326.0
4 TraesCS1A01G261300 chr1B 89.822 1179 72 18 1069 2216 477943673 477944834 0.000000e+00 1469.0
5 TraesCS1A01G261300 chr1B 92.028 991 63 7 3493 4467 477946777 477947767 0.000000e+00 1378.0
6 TraesCS1A01G261300 chr1B 85.323 1206 130 23 3344 4527 477947871 477949051 0.000000e+00 1203.0
7 TraesCS1A01G261300 chr1B 89.855 483 47 2 1736 2216 477945138 477945620 2.140000e-173 619.0
8 TraesCS1A01G261300 chr1B 89.504 343 31 3 7 349 478060427 478060090 3.860000e-116 429.0
9 TraesCS1A01G261300 chr1B 85.894 397 45 6 2290 2686 477945748 477946133 3.890000e-111 412.0
10 TraesCS1A01G261300 chr1B 82.783 424 57 7 4975 5392 587526516 587526929 1.110000e-96 364.0
11 TraesCS1A01G261300 chr1B 82.195 410 47 12 4527 4919 477949005 477949405 4.030000e-86 329.0
12 TraesCS1A01G261300 chr1B 87.838 148 18 0 3344 3491 477946581 477946728 2.000000e-39 174.0
13 TraesCS1A01G261300 chr1B 96.552 87 3 0 345 431 129095889 129095803 1.570000e-30 145.0
14 TraesCS1A01G261300 chr1D 93.654 4775 188 38 709 5400 355435516 355430774 0.000000e+00 7033.0
15 TraesCS1A01G261300 chr1D 92.020 990 64 6 3493 4467 355319634 355320623 0.000000e+00 1376.0
16 TraesCS1A01G261300 chr1D 85.750 1207 121 26 3344 4527 355320727 355321905 0.000000e+00 1229.0
17 TraesCS1A01G261300 chr1D 90.083 484 45 3 1736 2216 355317979 355318462 4.590000e-175 625.0
18 TraesCS1A01G261300 chr1D 81.129 620 67 25 4803 5392 434034251 434034850 8.250000e-123 451.0
19 TraesCS1A01G261300 chr1D 87.433 374 24 9 1853 2216 355317314 355317674 5.030000e-110 409.0
20 TraesCS1A01G261300 chr1D 83.834 433 45 13 4965 5392 433979452 433979864 6.560000e-104 388.0
21 TraesCS1A01G261300 chr1D 82.927 410 45 11 4527 4919 355321859 355322260 4.000000e-91 346.0
22 TraesCS1A01G261300 chr1D 79.947 379 52 12 4906 5270 209738954 209739322 1.930000e-64 257.0
23 TraesCS1A01G261300 chr1D 85.556 180 25 1 2291 2470 355317799 355317977 2.570000e-43 187.0
24 TraesCS1A01G261300 chr1D 88.514 148 17 0 3344 3491 355319438 355319585 4.300000e-41 180.0
25 TraesCS1A01G261300 chr1D 89.000 100 10 1 335 433 216026970 216027069 7.350000e-24 122.0
26 TraesCS1A01G261300 chr1D 87.736 106 12 1 242 347 483976336 483976232 7.350000e-24 122.0
27 TraesCS1A01G261300 chr1D 88.372 86 9 1 1 85 355435611 355435526 9.570000e-18 102.0
28 TraesCS1A01G261300 chr1D 82.569 109 8 9 429 528 467808789 467808895 9.640000e-13 86.1
29 TraesCS1A01G261300 chr7A 93.750 208 11 2 1115 1320 20685095 20684888 1.460000e-80 311.0
30 TraesCS1A01G261300 chr7A 91.237 194 14 1 1467 1657 20684889 20684696 1.490000e-65 261.0
31 TraesCS1A01G261300 chr7A 90.863 197 15 2 1464 1657 454493555 454493751 1.490000e-65 261.0
32 TraesCS1A01G261300 chr7A 91.813 171 14 0 3808 3978 1837471 1837301 6.990000e-59 239.0
33 TraesCS1A01G261300 chr7A 92.617 149 11 0 3808 3956 1793359 1793211 1.180000e-51 215.0
34 TraesCS1A01G261300 chr7A 84.298 121 12 7 560 673 116190054 116189934 1.590000e-20 111.0
35 TraesCS1A01G261300 chr4A 92.788 208 13 2 1115 1320 603348254 603348461 3.160000e-77 300.0
36 TraesCS1A01G261300 chr4A 92.308 208 14 2 1115 1320 728411708 728411915 1.470000e-75 294.0
37 TraesCS1A01G261300 chr4A 91.878 197 13 1 1464 1657 603348457 603348653 6.890000e-69 272.0
38 TraesCS1A01G261300 chr4A 91.371 197 14 1 1464 1657 728411911 728412107 3.210000e-67 267.0
39 TraesCS1A01G261300 chr4A 86.667 225 24 3 3808 4026 67514492 67514716 1.500000e-60 244.0
40 TraesCS1A01G261300 chr4D 81.551 374 50 9 4909 5270 319546521 319546155 1.900000e-74 291.0
41 TraesCS1A01G261300 chr4D 88.073 109 6 6 242 349 473832679 473832577 7.350000e-24 122.0
42 TraesCS1A01G261300 chr2A 91.827 208 15 2 1115 1320 680893919 680893712 6.840000e-74 289.0
43 TraesCS1A01G261300 chr2A 92.784 97 7 0 338 434 15846405 15846309 2.030000e-29 141.0
44 TraesCS1A01G261300 chr6A 91.469 211 15 3 1115 1323 60063020 60062811 2.460000e-73 287.0
45 TraesCS1A01G261300 chr6A 91.000 100 9 0 342 441 25637759 25637660 9.430000e-28 135.0
46 TraesCS1A01G261300 chr6A 86.957 115 11 4 238 349 461649839 461649952 5.680000e-25 126.0
47 TraesCS1A01G261300 chr6A 95.238 63 3 0 1469 1531 60062812 60062750 3.440000e-17 100.0
48 TraesCS1A01G261300 chr4B 92.784 194 14 0 1118 1311 84651528 84651721 1.150000e-71 281.0
49 TraesCS1A01G261300 chr4B 91.623 191 13 1 1470 1657 84651733 84651923 1.490000e-65 261.0
50 TraesCS1A01G261300 chr4B 88.696 115 12 1 238 351 99595495 99595609 7.290000e-29 139.0
51 TraesCS1A01G261300 chr4B 83.636 110 10 6 428 537 117108330 117108431 4.450000e-16 97.1
52 TraesCS1A01G261300 chr4B 80.531 113 13 8 428 536 91116390 91116283 1.610000e-10 78.7
53 TraesCS1A01G261300 chr3A 91.667 204 16 1 1118 1320 459525845 459525642 1.150000e-71 281.0
54 TraesCS1A01G261300 chr6B 91.176 204 17 1 1118 1320 104567901 104568104 5.330000e-70 276.0
55 TraesCS1A01G261300 chr6B 90.863 197 15 1 1464 1657 104568100 104568296 1.490000e-65 261.0
56 TraesCS1A01G261300 chr6B 83.065 124 11 8 560 673 68386030 68386153 2.660000e-18 104.0
57 TraesCS1A01G261300 chr5B 80.697 373 54 11 4909 5270 665948989 665948624 1.920000e-69 274.0
58 TraesCS1A01G261300 chr5B 86.620 142 16 3 4952 5092 202952676 202952537 2.600000e-33 154.0
59 TraesCS1A01G261300 chr5B 90.625 96 9 0 336 431 429030598 429030693 1.580000e-25 128.0
60 TraesCS1A01G261300 chr5B 100.000 34 0 0 3291 3324 64309942 64309909 4.520000e-06 63.9
61 TraesCS1A01G261300 chr5A 91.579 190 13 2 1471 1657 102199154 102198965 5.370000e-65 259.0
62 TraesCS1A01G261300 chr5A 89.908 109 8 2 1552 1657 517847533 517847641 2.620000e-28 137.0
63 TraesCS1A01G261300 chr5A 89.691 97 9 1 338 433 230818124 230818220 7.350000e-24 122.0
64 TraesCS1A01G261300 chr5A 89.691 97 9 1 338 433 230848705 230848801 7.350000e-24 122.0
65 TraesCS1A01G261300 chr5A 84.483 116 10 7 428 537 510011536 510011423 2.060000e-19 108.0
66 TraesCS1A01G261300 chr7B 87.111 225 23 3 3808 4026 52983548 52983772 3.230000e-62 250.0
67 TraesCS1A01G261300 chr7B 87.558 217 23 1 3808 4020 52956882 52956666 1.160000e-61 248.0
68 TraesCS1A01G261300 chr7B 92.553 94 7 0 346 439 661996393 661996486 9.430000e-28 135.0
69 TraesCS1A01G261300 chr7B 88.776 98 9 2 337 433 324308194 324308098 9.500000e-23 119.0
70 TraesCS1A01G261300 chr7B 87.037 108 11 3 242 349 631322086 631321982 9.500000e-23 119.0
71 TraesCS1A01G261300 chr7B 84.615 117 14 4 341 454 242162537 242162422 4.420000e-21 113.0
72 TraesCS1A01G261300 chr7B 77.586 116 22 3 561 673 489129634 489129748 3.490000e-07 67.6
73 TraesCS1A01G261300 chrUn 93.000 100 7 0 342 441 94824234 94824135 4.360000e-31 147.0
74 TraesCS1A01G261300 chrUn 93.617 94 6 0 345 438 17148598 17148691 2.030000e-29 141.0
75 TraesCS1A01G261300 chrUn 83.036 112 15 4 432 540 37381426 37381536 1.240000e-16 99.0
76 TraesCS1A01G261300 chr3B 93.548 93 6 0 346 438 552477311 552477403 7.290000e-29 139.0
77 TraesCS1A01G261300 chr3B 86.239 109 15 0 242 350 166171450 166171342 9.500000e-23 119.0
78 TraesCS1A01G261300 chr3B 87.500 104 11 2 329 430 450380286 450380183 9.500000e-23 119.0
79 TraesCS1A01G261300 chr7D 89.720 107 9 2 242 347 572686925 572686820 9.430000e-28 135.0
80 TraesCS1A01G261300 chr5D 92.553 94 7 0 343 436 60072264 60072171 9.430000e-28 135.0
81 TraesCS1A01G261300 chr5D 81.034 116 12 7 560 673 336052847 336052954 3.470000e-12 84.2
82 TraesCS1A01G261300 chr2D 88.182 110 11 2 242 349 578682288 578682179 4.390000e-26 130.0
83 TraesCS1A01G261300 chr2D 82.787 122 13 8 560 673 21664172 21664051 9.570000e-18 102.0
84 TraesCS1A01G261300 chr2D 82.787 122 13 8 560 673 21680587 21680466 9.570000e-18 102.0
85 TraesCS1A01G261300 chr2D 82.645 121 14 7 560 673 21641772 21641652 3.440000e-17 100.0
86 TraesCS1A01G261300 chr6D 89.796 98 10 0 334 431 13561130 13561227 5.680000e-25 126.0
87 TraesCS1A01G261300 chr6D 80.159 126 13 8 452 568 378169266 378169144 3.470000e-12 84.2
88 TraesCS1A01G261300 chr2B 83.471 121 13 6 560 673 34952338 34952458 7.400000e-19 106.0
89 TraesCS1A01G261300 chr2B 83.333 102 10 6 560 654 34865192 34865293 2.680000e-13 87.9
90 TraesCS1A01G261300 chr2B 97.297 37 1 0 501 537 695921367 695921331 4.520000e-06 63.9
91 TraesCS1A01G261300 chr2B 97.297 37 1 0 501 537 695957834 695957798 4.520000e-06 63.9
92 TraesCS1A01G261300 chr2B 97.297 37 1 0 501 537 695988609 695988573 4.520000e-06 63.9


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 TraesCS1A01G261300 chr1A 455606379 455611778 5399 True 9973.000000 9973 100.0000 1 5400 1 chr1A.!!$R1 5399
1 TraesCS1A01G261300 chr1B 478055100 478060427 5327 True 3877.500000 7326 91.3955 7 5395 2 chr1B.!!$R2 5388
2 TraesCS1A01G261300 chr1B 477943673 477949405 5732 False 797.714286 1469 87.5650 1069 4919 7 chr1B.!!$F2 3850
3 TraesCS1A01G261300 chr1D 355430774 355435611 4837 True 3567.500000 7033 91.0130 1 5400 2 chr1D.!!$R2 5399
4 TraesCS1A01G261300 chr1D 355317314 355322260 4946 False 621.714286 1376 87.4690 1736 4919 7 chr1D.!!$F6 3183
5 TraesCS1A01G261300 chr1D 434034251 434034850 599 False 451.000000 451 81.1290 4803 5392 1 chr1D.!!$F4 589

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
432 434 0.338814 ATGGGACGGAGGGAGTACTT 59.661 55.0 0.00 0.0 0.00 2.24 F
435 437 0.531200 GGACGGAGGGAGTACTTGTG 59.469 60.0 0.00 0.0 0.00 3.33 F
863 868 0.614697 AACCCTAGCCCACCAAATGC 60.615 55.0 0.00 0.0 0.00 3.56 F
1777 1809 0.723981 GCCAACTCTGCGTCAATCTC 59.276 55.0 0.00 0.0 0.00 2.75 F
2208 3040 0.953727 TTTGATCACCAGTGTGCTGC 59.046 50.0 0.00 0.0 42.46 5.25 F
3170 4240 0.465287 TCTGGCGCTCATGCTTGATA 59.535 50.0 7.64 0.0 36.97 2.15 F
4231 5368 0.607489 ATGGCGGGCTATTCATCTGC 60.607 55.0 2.38 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 1594 0.317160 TCTCCGCTGTGGTACAACAG 59.683 55.000 23.89 23.89 44.16 3.16 R
1899 1937 1.020861 GTCAGCGACACATGCATCCA 61.021 55.000 0.00 0.00 32.09 3.41 R
2208 3040 4.481930 TCTCCACAAGTAAAACAATGCG 57.518 40.909 0.00 0.00 0.00 4.73 R
3170 4240 1.800805 CAGGCAGATCAAACACGACT 58.199 50.000 0.00 0.00 0.00 4.18 R
3959 5090 0.535335 GGTACTGGCGGATGAACTCA 59.465 55.000 0.00 0.00 0.00 3.41 R
4327 5464 1.146041 GTGCTCACCAGACCACACA 59.854 57.895 0.00 0.00 31.92 3.72 R
5259 7678 0.961019 TGGTGCTTGCAATCCTGAAC 59.039 50.000 0.00 0.00 0.00 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.194201 TTTCGGCCAGTTTCCCTTAG 57.806 50.000 2.24 0.00 0.00 2.18
66 67 4.666512 TCTCTTCTTCTTTTTGATGGGGG 58.333 43.478 0.00 0.00 0.00 5.40
101 103 1.243902 TCCTGCCGGTTGCTAAAAAG 58.756 50.000 1.90 0.00 42.00 2.27
103 105 1.611491 CCTGCCGGTTGCTAAAAAGAA 59.389 47.619 1.90 0.00 42.00 2.52
104 106 2.035321 CCTGCCGGTTGCTAAAAAGAAA 59.965 45.455 1.90 0.00 42.00 2.52
105 107 3.306019 CCTGCCGGTTGCTAAAAAGAAAT 60.306 43.478 1.90 0.00 42.00 2.17
106 108 4.306600 CTGCCGGTTGCTAAAAAGAAATT 58.693 39.130 1.90 0.00 42.00 1.82
107 109 4.054671 TGCCGGTTGCTAAAAAGAAATTG 58.945 39.130 1.90 0.00 42.00 2.32
108 110 4.202161 TGCCGGTTGCTAAAAAGAAATTGA 60.202 37.500 1.90 0.00 42.00 2.57
109 111 4.149922 GCCGGTTGCTAAAAAGAAATTGAC 59.850 41.667 1.90 0.00 36.87 3.18
110 112 4.684242 CCGGTTGCTAAAAAGAAATTGACC 59.316 41.667 0.00 0.00 0.00 4.02
114 116 7.042119 CGGTTGCTAAAAAGAAATTGACCAATT 60.042 33.333 2.38 2.38 42.35 2.32
134 136 8.863086 ACCAATTCTCTTCTTGATGATGAAAAA 58.137 29.630 0.00 0.00 0.00 1.94
135 137 9.355215 CCAATTCTCTTCTTGATGATGAAAAAG 57.645 33.333 0.00 0.00 0.00 2.27
148 150 4.287067 TGATGAAAAAGGTAGAGCTCCTGT 59.713 41.667 10.93 0.00 35.27 4.00
150 152 3.646162 TGAAAAAGGTAGAGCTCCTGTCA 59.354 43.478 10.93 3.90 35.27 3.58
228 230 8.948401 AAAGCTCAGTATCTATGAATCCTAGA 57.052 34.615 0.00 0.00 0.00 2.43
229 231 7.938140 AGCTCAGTATCTATGAATCCTAGAC 57.062 40.000 0.00 0.00 0.00 2.59
232 234 6.238648 TCAGTATCTATGAATCCTAGACGCA 58.761 40.000 0.00 0.00 0.00 5.24
235 237 5.791336 ATCTATGAATCCTAGACGCACAA 57.209 39.130 0.00 0.00 0.00 3.33
247 249 0.806241 ACGCACAAAGACGTTTGGTT 59.194 45.000 5.07 0.00 46.42 3.67
349 351 7.923414 ATAAACTTGACCTTCCATTGTACTC 57.077 36.000 0.00 0.00 0.00 2.59
350 352 4.287766 ACTTGACCTTCCATTGTACTCC 57.712 45.455 0.00 0.00 0.00 3.85
351 353 3.009143 ACTTGACCTTCCATTGTACTCCC 59.991 47.826 0.00 0.00 0.00 4.30
352 354 2.915869 TGACCTTCCATTGTACTCCCT 58.084 47.619 0.00 0.00 0.00 4.20
353 355 2.838202 TGACCTTCCATTGTACTCCCTC 59.162 50.000 0.00 0.00 0.00 4.30
354 356 3.108376 GACCTTCCATTGTACTCCCTCT 58.892 50.000 0.00 0.00 0.00 3.69
355 357 4.264668 TGACCTTCCATTGTACTCCCTCTA 60.265 45.833 0.00 0.00 0.00 2.43
356 358 4.897051 ACCTTCCATTGTACTCCCTCTAT 58.103 43.478 0.00 0.00 0.00 1.98
357 359 4.902448 ACCTTCCATTGTACTCCCTCTATC 59.098 45.833 0.00 0.00 0.00 2.08
358 360 4.284746 CCTTCCATTGTACTCCCTCTATCC 59.715 50.000 0.00 0.00 0.00 2.59
359 361 3.858135 TCCATTGTACTCCCTCTATCCC 58.142 50.000 0.00 0.00 0.00 3.85
360 362 3.208922 TCCATTGTACTCCCTCTATCCCA 59.791 47.826 0.00 0.00 0.00 4.37
361 363 4.140447 TCCATTGTACTCCCTCTATCCCAT 60.140 45.833 0.00 0.00 0.00 4.00
362 364 5.077300 TCCATTGTACTCCCTCTATCCCATA 59.923 44.000 0.00 0.00 0.00 2.74
363 365 5.785423 CCATTGTACTCCCTCTATCCCATAA 59.215 44.000 0.00 0.00 0.00 1.90
364 366 6.445139 CCATTGTACTCCCTCTATCCCATAAT 59.555 42.308 0.00 0.00 0.00 1.28
365 367 6.935240 TTGTACTCCCTCTATCCCATAATG 57.065 41.667 0.00 0.00 0.00 1.90
366 368 5.977533 TGTACTCCCTCTATCCCATAATGT 58.022 41.667 0.00 0.00 0.00 2.71
367 369 7.111136 TGTACTCCCTCTATCCCATAATGTA 57.889 40.000 0.00 0.00 0.00 2.29
368 370 7.541074 TGTACTCCCTCTATCCCATAATGTAA 58.459 38.462 0.00 0.00 0.00 2.41
369 371 7.674348 TGTACTCCCTCTATCCCATAATGTAAG 59.326 40.741 0.00 0.00 0.00 2.34
370 372 6.026186 ACTCCCTCTATCCCATAATGTAAGG 58.974 44.000 0.00 0.00 0.00 2.69
371 373 4.783227 TCCCTCTATCCCATAATGTAAGGC 59.217 45.833 0.00 0.00 0.00 4.35
372 374 4.536090 CCCTCTATCCCATAATGTAAGGCA 59.464 45.833 0.00 0.00 0.00 4.75
373 375 5.192522 CCCTCTATCCCATAATGTAAGGCAT 59.807 44.000 0.00 0.00 40.03 4.40
375 377 7.177878 CCTCTATCCCATAATGTAAGGCATTT 58.822 38.462 0.00 0.00 44.82 2.32
376 378 7.671398 CCTCTATCCCATAATGTAAGGCATTTT 59.329 37.037 0.00 0.00 44.82 1.82
377 379 9.082313 CTCTATCCCATAATGTAAGGCATTTTT 57.918 33.333 0.00 0.00 44.82 1.94
396 398 5.617528 TTTTTGACCCTAGTGTAGTGTCA 57.382 39.130 0.00 0.00 40.59 3.58
397 399 5.617528 TTTTGACCCTAGTGTAGTGTCAA 57.382 39.130 7.62 7.62 46.48 3.18
399 401 5.617528 TTGACCCTAGTGTAGTGTCAAAA 57.382 39.130 8.88 0.00 45.64 2.44
400 402 5.617528 TGACCCTAGTGTAGTGTCAAAAA 57.382 39.130 0.00 0.00 39.63 1.94
422 424 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
423 425 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
424 426 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
425 427 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
426 428 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
427 429 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
428 430 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
429 431 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
430 432 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
431 433 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
432 434 0.338814 ATGGGACGGAGGGAGTACTT 59.661 55.000 0.00 0.00 0.00 2.24
433 435 0.613853 TGGGACGGAGGGAGTACTTG 60.614 60.000 0.00 0.00 0.00 3.16
434 436 0.614134 GGGACGGAGGGAGTACTTGT 60.614 60.000 0.00 0.00 0.00 3.16
435 437 0.531200 GGACGGAGGGAGTACTTGTG 59.469 60.000 0.00 0.00 0.00 3.33
441 443 4.202430 ACGGAGGGAGTACTTGTGAAAAAT 60.202 41.667 0.00 0.00 0.00 1.82
474 476 4.342378 AGAAAAAGGCCCTTTGACTTCTTC 59.658 41.667 10.04 8.58 33.64 2.87
488 490 7.883229 TTGACTTCTTCAAAAAGACAAAACC 57.117 32.000 0.00 0.00 41.51 3.27
489 491 7.227049 TGACTTCTTCAAAAAGACAAAACCT 57.773 32.000 0.00 0.00 41.23 3.50
490 492 7.312899 TGACTTCTTCAAAAAGACAAAACCTC 58.687 34.615 0.00 0.00 41.23 3.85
491 493 7.176690 TGACTTCTTCAAAAAGACAAAACCTCT 59.823 33.333 0.00 0.00 41.23 3.69
492 494 7.315890 ACTTCTTCAAAAAGACAAAACCTCTG 58.684 34.615 0.00 0.00 41.23 3.35
494 496 4.385358 TCAAAAAGACAAAACCTCTGCC 57.615 40.909 0.00 0.00 0.00 4.85
506 509 1.812571 ACCTCTGCCAAAAATAGTGCG 59.187 47.619 0.00 0.00 0.00 5.34
509 512 3.129287 CCTCTGCCAAAAATAGTGCGAAT 59.871 43.478 0.00 0.00 0.00 3.34
518 521 6.537301 CCAAAAATAGTGCGAATAGTGACCTA 59.463 38.462 0.00 0.00 0.00 3.08
520 523 9.256477 CAAAAATAGTGCGAATAGTGACCTATA 57.744 33.333 0.00 0.00 32.57 1.31
550 553 7.598869 GCAAATAACTTTTTCCCCTAAAGTCAG 59.401 37.037 0.00 0.00 43.14 3.51
551 554 8.638873 CAAATAACTTTTTCCCCTAAAGTCAGT 58.361 33.333 0.00 0.00 43.14 3.41
553 556 3.889538 ACTTTTTCCCCTAAAGTCAGTGC 59.110 43.478 0.00 0.00 40.78 4.40
575 578 4.740205 GCTGGTTTAGTGCAAAAGAAAGTC 59.260 41.667 0.00 0.00 0.00 3.01
797 802 3.566853 CGCGCATCAATCGGCTGT 61.567 61.111 8.75 0.00 0.00 4.40
816 821 4.777854 AAGGGGCCCATTTCCGGC 62.778 66.667 27.72 2.59 46.29 6.13
829 834 3.058160 CCGGCCCTGTTTGCTGAG 61.058 66.667 0.00 0.00 37.27 3.35
845 850 2.289072 GCTGAGTTGCTCTAGTCCACAA 60.289 50.000 0.00 0.00 0.00 3.33
863 868 0.614697 AACCCTAGCCCACCAAATGC 60.615 55.000 0.00 0.00 0.00 3.56
926 935 1.227089 CGGCGAGTCCATCCTCTTG 60.227 63.158 0.00 0.00 34.01 3.02
1150 1162 2.202610 CCGCGCTCTTCGTCATCA 60.203 61.111 5.56 0.00 41.07 3.07
1233 1248 3.331293 CCCTATGGCCGGGACTTT 58.669 61.111 8.48 0.00 44.90 2.66
1337 1361 3.107601 TCTCTCGGTTTCTCCATGGATT 58.892 45.455 16.63 0.00 35.57 3.01
1338 1362 3.118629 TCTCTCGGTTTCTCCATGGATTG 60.119 47.826 16.63 4.55 35.57 2.67
1341 1365 1.745087 CGGTTTCTCCATGGATTGGTG 59.255 52.381 16.63 2.86 46.52 4.17
1342 1366 1.478105 GGTTTCTCCATGGATTGGTGC 59.522 52.381 16.63 3.90 46.52 5.01
1343 1367 1.133025 GTTTCTCCATGGATTGGTGCG 59.867 52.381 16.63 1.19 46.52 5.34
1369 1393 2.415168 CGCTGCTGGTTTCTCGATTTTA 59.585 45.455 0.00 0.00 0.00 1.52
1383 1407 2.505866 GATTTTACGCGTCCTTGCTTG 58.494 47.619 18.63 0.00 0.00 4.01
1389 1413 1.083806 CGCGTCCTTGCTTGCAGATA 61.084 55.000 0.00 0.00 0.00 1.98
1431 1455 2.158900 GGTCTCCATGGTTCATCGTGAT 60.159 50.000 12.58 0.00 0.00 3.06
1448 1472 4.028383 CGTGATTACGGATGATTGTTTGC 58.972 43.478 1.39 0.00 46.23 3.68
1529 1558 4.720902 TGGCAGCCCCATGTGACG 62.721 66.667 9.64 0.00 39.18 4.35
1565 1594 4.559862 TCTCTTGATTTCTGACCCCTTC 57.440 45.455 0.00 0.00 0.00 3.46
1777 1809 0.723981 GCCAACTCTGCGTCAATCTC 59.276 55.000 0.00 0.00 0.00 2.75
1786 1822 2.535984 CTGCGTCAATCTCATAACGTCC 59.464 50.000 0.00 0.00 37.45 4.79
1841 1877 2.227388 CTGCTGTCAATCTGTGGTTTCC 59.773 50.000 0.00 0.00 0.00 3.13
1867 1903 3.798337 CACCAAATTTGATGCTAATCGGC 59.202 43.478 19.86 0.00 35.37 5.54
2195 3027 1.453155 TGCTCGCCTCCTTTTTGATC 58.547 50.000 0.00 0.00 0.00 2.92
2208 3040 0.953727 TTTGATCACCAGTGTGCTGC 59.046 50.000 0.00 0.00 42.46 5.25
2504 3407 8.549548 TGCGGCATTTTGATAAAATATGAAATG 58.450 29.630 0.00 0.00 38.97 2.32
2560 3463 7.940137 ACAATGAGGTGTAATGGTGTTTAGTTA 59.060 33.333 0.00 0.00 0.00 2.24
2605 3508 5.826643 TGGTAGCCAAAAACTTATCTCCAT 58.173 37.500 0.00 0.00 0.00 3.41
2606 3509 6.252995 TGGTAGCCAAAAACTTATCTCCATT 58.747 36.000 0.00 0.00 0.00 3.16
2607 3510 6.723977 TGGTAGCCAAAAACTTATCTCCATTT 59.276 34.615 0.00 0.00 0.00 2.32
2608 3511 7.234577 TGGTAGCCAAAAACTTATCTCCATTTT 59.765 33.333 0.00 0.00 0.00 1.82
2825 3744 7.880713 TGTGTTGTTGTATATTAGAAGAAGGCA 59.119 33.333 0.00 0.00 0.00 4.75
2881 3949 5.602561 ACCCTGAAAAGCAAAAGTCCTAAAT 59.397 36.000 0.00 0.00 0.00 1.40
2955 4025 2.166907 AGGTGCTACTCATGCTACCT 57.833 50.000 0.00 0.00 37.23 3.08
2989 4059 7.239166 CACAGCATACTATCTTAAACTGTGG 57.761 40.000 11.04 0.00 46.18 4.17
3071 4141 8.880750 GTTCAAGTTAAGTCTGTTGTACTTTCT 58.119 33.333 0.00 0.00 38.18 2.52
3114 4184 4.927425 TCGTTCTAGGATGCAGTGTTTTAC 59.073 41.667 0.00 0.00 0.00 2.01
3156 4226 3.674997 TCACTGGTCTGTAATTTCTGGC 58.325 45.455 0.00 0.00 0.00 4.85
3170 4240 0.465287 TCTGGCGCTCATGCTTGATA 59.535 50.000 7.64 0.00 36.97 2.15
3231 4301 3.191371 AGTTGCTTTACCTGTATGCTTGC 59.809 43.478 0.00 0.00 0.00 4.01
3254 4324 3.068165 AGGTTTAGCTTCCTGTTTTGTGC 59.932 43.478 0.00 0.00 32.29 4.57
3259 4329 2.501316 AGCTTCCTGTTTTGTGCCTTTT 59.499 40.909 0.00 0.00 0.00 2.27
3279 4349 8.604890 GCCTTTTATGTTTCTCATACTCTGTAC 58.395 37.037 0.00 0.00 38.55 2.90
3284 4354 9.639601 TTATGTTTCTCATACTCTGTACAACTG 57.360 33.333 0.00 0.00 38.55 3.16
3289 4359 3.576550 TCATACTCTGTACAACTGTGCCA 59.423 43.478 0.00 0.00 0.00 4.92
3339 4409 3.487207 GCTCGTTGCCTCAAAAGAAAAAG 59.513 43.478 0.00 0.00 35.15 2.27
3343 4415 6.159988 TCGTTGCCTCAAAAGAAAAAGAAAA 58.840 32.000 0.00 0.00 0.00 2.29
3347 4419 8.931775 GTTGCCTCAAAAGAAAAAGAAAAAGTA 58.068 29.630 0.00 0.00 0.00 2.24
3428 4500 4.263639 ACTGTTCATGATCTGACCATGGTT 60.264 41.667 20.85 1.76 41.16 3.67
3434 4506 2.040145 TGATCTGACCATGGTTCAAGCA 59.960 45.455 20.85 13.08 0.00 3.91
3882 5013 0.801067 CTTCCTTTCGGACTACGGCG 60.801 60.000 4.80 4.80 44.45 6.46
3941 5072 3.692593 TCGTGATCGAGTTCAACTATGGA 59.307 43.478 0.00 0.00 41.35 3.41
4231 5368 0.607489 ATGGCGGGCTATTCATCTGC 60.607 55.000 2.38 0.00 0.00 4.26
4311 5448 1.374125 CGACCGATGCTGTGAACCA 60.374 57.895 0.00 0.00 0.00 3.67
4454 5591 6.873076 TGCTCAACTTCTGTGTTTTCATTTTT 59.127 30.769 0.00 0.00 0.00 1.94
4475 6839 2.866156 TGACAAAGAACTTCTGCGAGTG 59.134 45.455 0.00 0.00 0.00 3.51
4499 6864 6.097696 TGGGACAGTGAAATGTATATCGAGAA 59.902 38.462 0.00 0.00 32.25 2.87
4503 6868 8.581057 ACAGTGAAATGTATATCGAGAATCAC 57.419 34.615 0.00 0.00 35.95 3.06
4512 6877 2.921634 TCGAGAATCACGGAGTTCAG 57.078 50.000 0.00 0.00 41.61 3.02
4546 6911 8.996024 TTTTGAGTGAAATGTATATCGAGTCA 57.004 30.769 0.00 0.00 0.00 3.41
4548 6913 6.199393 TGAGTGAAATGTATATCGAGTCACG 58.801 40.000 0.00 0.00 39.06 4.35
4597 6964 8.181573 CAGTTCAGGTTAAATGCACGTATATTT 58.818 33.333 12.15 12.15 0.00 1.40
4602 6969 5.912955 GGTTAAATGCACGTATATTTGCCTC 59.087 40.000 15.52 6.58 38.00 4.70
4630 6997 6.971726 TGTACCGTGAAGAATCTATATGGT 57.028 37.500 12.97 12.97 0.00 3.55
4632 6999 5.122512 ACCGTGAAGAATCTATATGGTCG 57.877 43.478 5.15 0.00 0.00 4.79
4634 7001 5.048643 ACCGTGAAGAATCTATATGGTCGAG 60.049 44.000 5.15 0.00 0.00 4.04
4803 7174 5.406175 CCAAAAATTTGTACTGTGAGCATGG 59.594 40.000 5.27 0.00 36.45 3.66
4935 7337 2.684881 GGTTATGTCCCTGCATCACAAG 59.315 50.000 0.00 0.00 0.00 3.16
4959 7361 2.674954 CTCAGCTGTCAGTCAAGAGTG 58.325 52.381 14.67 0.00 0.00 3.51
5128 7546 1.198637 GCCTGCTTGAATGTCTGTCAC 59.801 52.381 0.00 0.00 0.00 3.67
5173 7592 2.421424 GCAGAGTGGTAATGCTTCTTGG 59.579 50.000 0.00 0.00 37.00 3.61
5192 7611 1.636988 GGCAGCAACATTTCATCTGC 58.363 50.000 4.14 4.14 46.68 4.26
5259 7678 4.106197 CAGAAAGAAGTAGGTCCGATTCG 58.894 47.826 0.00 0.00 0.00 3.34
5320 7739 1.461127 GCCAGTTTCAGTAAGTGCTCG 59.539 52.381 0.00 0.00 36.11 5.03
5344 7763 8.143193 TCGAACTGTCAAATTGTAAAGGTAGTA 58.857 33.333 0.00 0.00 0.00 1.82
5347 7767 9.569122 AACTGTCAAATTGTAAAGGTAGTATGT 57.431 29.630 0.00 0.00 0.00 2.29
5356 7776 9.982651 ATTGTAAAGGTAGTATGTGTGCTATAG 57.017 33.333 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.106857 TCTAAGGGAAACTGGCCGAAAA 59.893 45.455 0.00 0.00 0.00 2.29
31 32 7.503521 AAGAAGAAGAGAATTGGTCAGTTTC 57.496 36.000 0.00 0.00 0.00 2.78
66 67 4.379918 CGGCAGGAAATTCTCTTCTTTTCC 60.380 45.833 5.69 5.69 45.69 3.13
67 68 4.379918 CCGGCAGGAAATTCTCTTCTTTTC 60.380 45.833 0.00 0.00 41.02 2.29
87 89 4.684242 GGTCAATTTCTTTTTAGCAACCGG 59.316 41.667 0.00 0.00 0.00 5.28
101 103 8.517878 TCATCAAGAAGAGAATTGGTCAATTTC 58.482 33.333 9.88 9.29 40.77 2.17
103 105 8.467598 CATCATCAAGAAGAGAATTGGTCAATT 58.532 33.333 8.48 8.48 43.14 2.32
104 106 7.832685 TCATCATCAAGAAGAGAATTGGTCAAT 59.167 33.333 0.00 0.00 0.00 2.57
105 107 7.170277 TCATCATCAAGAAGAGAATTGGTCAA 58.830 34.615 0.00 0.00 0.00 3.18
106 108 6.714278 TCATCATCAAGAAGAGAATTGGTCA 58.286 36.000 0.00 0.00 0.00 4.02
107 109 7.621428 TTCATCATCAAGAAGAGAATTGGTC 57.379 36.000 0.00 0.00 0.00 4.02
108 110 8.413309 TTTTCATCATCAAGAAGAGAATTGGT 57.587 30.769 0.00 0.00 0.00 3.67
109 111 9.355215 CTTTTTCATCATCAAGAAGAGAATTGG 57.645 33.333 0.00 0.00 0.00 3.16
110 112 9.355215 CCTTTTTCATCATCAAGAAGAGAATTG 57.645 33.333 0.00 0.00 0.00 2.32
114 116 8.597167 TCTACCTTTTTCATCATCAAGAAGAGA 58.403 33.333 0.00 0.00 0.00 3.10
134 136 2.175202 CAACTGACAGGAGCTCTACCT 58.825 52.381 14.64 0.00 38.40 3.08
135 137 1.404851 GCAACTGACAGGAGCTCTACC 60.405 57.143 14.64 0.00 0.00 3.18
174 176 0.023732 CTATGCTCACGCGTCAAACG 59.976 55.000 9.86 0.00 45.88 3.60
179 181 1.154205 ATTGGCTATGCTCACGCGTC 61.154 55.000 9.86 0.00 39.65 5.19
198 200 9.988815 GGATTCATAGATACTGAGCTTTTCTAA 57.011 33.333 0.00 0.00 0.00 2.10
228 230 0.806241 AACCAAACGTCTTTGTGCGT 59.194 45.000 0.00 0.00 43.64 5.24
229 231 1.902840 AAACCAAACGTCTTTGTGCG 58.097 45.000 0.00 0.00 35.84 5.34
232 234 3.955551 ACCCATAAACCAAACGTCTTTGT 59.044 39.130 0.00 0.00 35.84 2.83
235 237 3.558033 ACACCCATAAACCAAACGTCTT 58.442 40.909 0.00 0.00 0.00 3.01
315 317 9.323985 TGGAAGGTCAAGTTTATTTCAAAAATG 57.676 29.630 0.00 0.00 0.00 2.32
339 341 3.587498 TGGGATAGAGGGAGTACAATGG 58.413 50.000 0.00 0.00 0.00 3.16
349 351 4.536090 TGCCTTACATTATGGGATAGAGGG 59.464 45.833 0.00 0.00 0.00 4.30
350 352 5.762179 TGCCTTACATTATGGGATAGAGG 57.238 43.478 0.00 0.00 0.00 3.69
397 399 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
398 400 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
399 401 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
400 402 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
401 403 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
403 405 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
404 406 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
405 407 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
406 408 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
407 409 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
408 410 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
409 411 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
410 412 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
411 413 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
412 414 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
413 415 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
414 416 0.613853 CAAGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
415 417 0.614134 ACAAGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
416 418 0.531200 CACAAGTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
417 419 1.542492 TCACAAGTACTCCCTCCGTC 58.458 55.000 0.00 0.00 0.00 4.79
418 420 2.005370 TTCACAAGTACTCCCTCCGT 57.995 50.000 0.00 0.00 0.00 4.69
419 421 3.396260 TTTTCACAAGTACTCCCTCCG 57.604 47.619 0.00 0.00 0.00 4.63
420 422 6.264518 TGAAATTTTTCACAAGTACTCCCTCC 59.735 38.462 0.00 0.00 41.88 4.30
421 423 7.272037 TGAAATTTTTCACAAGTACTCCCTC 57.728 36.000 0.00 0.00 41.88 4.30
441 443 8.049721 TCAAAGGGCCTTTTTCTTTTTATGAAA 58.950 29.630 28.54 0.00 30.60 2.69
446 448 6.553953 AGTCAAAGGGCCTTTTTCTTTTTA 57.446 33.333 28.54 4.65 30.60 1.52
452 454 4.099419 TGAAGAAGTCAAAGGGCCTTTTTC 59.901 41.667 28.54 26.24 30.60 2.29
455 457 3.312736 TGAAGAAGTCAAAGGGCCTTT 57.687 42.857 25.68 25.68 33.58 3.11
474 476 4.122143 TGGCAGAGGTTTTGTCTTTTTG 57.878 40.909 0.00 0.00 0.00 2.44
480 482 5.691754 CACTATTTTTGGCAGAGGTTTTGTC 59.308 40.000 0.00 0.00 0.00 3.18
481 483 5.600696 CACTATTTTTGGCAGAGGTTTTGT 58.399 37.500 0.00 0.00 0.00 2.83
482 484 4.448732 GCACTATTTTTGGCAGAGGTTTTG 59.551 41.667 0.00 0.00 0.00 2.44
486 488 1.812571 CGCACTATTTTTGGCAGAGGT 59.187 47.619 0.00 0.00 0.00 3.85
487 489 2.083774 TCGCACTATTTTTGGCAGAGG 58.916 47.619 0.00 0.00 0.00 3.69
488 490 3.829886 TTCGCACTATTTTTGGCAGAG 57.170 42.857 0.00 0.00 0.00 3.35
489 491 4.941263 ACTATTCGCACTATTTTTGGCAGA 59.059 37.500 0.00 0.00 0.00 4.26
490 492 5.030295 CACTATTCGCACTATTTTTGGCAG 58.970 41.667 0.00 0.00 0.00 4.85
491 493 4.697828 TCACTATTCGCACTATTTTTGGCA 59.302 37.500 0.00 0.00 0.00 4.92
492 494 5.028375 GTCACTATTCGCACTATTTTTGGC 58.972 41.667 0.00 0.00 0.00 4.52
494 496 6.422776 AGGTCACTATTCGCACTATTTTTG 57.577 37.500 0.00 0.00 0.00 2.44
524 527 7.438564 TGACTTTAGGGGAAAAAGTTATTTGC 58.561 34.615 3.02 0.00 44.94 3.68
534 537 3.486383 CAGCACTGACTTTAGGGGAAAA 58.514 45.455 0.00 0.00 0.00 2.29
550 553 3.708563 TCTTTTGCACTAAACCAGCAC 57.291 42.857 0.00 0.00 38.11 4.40
551 554 4.159506 ACTTTCTTTTGCACTAAACCAGCA 59.840 37.500 0.00 0.00 36.32 4.41
553 556 5.890334 TGACTTTCTTTTGCACTAAACCAG 58.110 37.500 0.00 0.00 0.00 4.00
648 651 4.530553 GGAAATACCCATTGGTTTCTGGTT 59.469 41.667 13.80 0.00 44.75 3.67
649 652 4.093743 GGAAATACCCATTGGTTTCTGGT 58.906 43.478 13.80 2.36 44.75 4.00
650 653 4.736126 GGAAATACCCATTGGTTTCTGG 57.264 45.455 13.80 0.00 44.75 3.86
668 671 7.423443 AGAATAGGAGGTCTAAGATAGGGAA 57.577 40.000 0.00 0.00 0.00 3.97
754 759 3.382546 CCTTGGCCTGTTTGATATCCTTG 59.617 47.826 3.32 0.00 0.00 3.61
782 787 0.027194 CTTCACAGCCGATTGATGCG 59.973 55.000 0.00 0.00 0.00 4.73
797 802 2.358619 CGGAAATGGGCCCCTTCA 59.641 61.111 26.85 8.88 0.00 3.02
816 821 0.595095 GAGCAACTCAGCAAACAGGG 59.405 55.000 0.00 0.00 36.85 4.45
817 822 1.602311 AGAGCAACTCAGCAAACAGG 58.398 50.000 0.00 0.00 36.85 4.00
829 834 1.348036 AGGGTTGTGGACTAGAGCAAC 59.652 52.381 0.00 5.92 40.08 4.17
845 850 1.000359 GCATTTGGTGGGCTAGGGT 60.000 57.895 0.00 0.00 0.00 4.34
863 868 0.627986 AGGATGGAGGAAAAGGCCTG 59.372 55.000 5.69 0.00 38.73 4.85
945 954 2.167037 TTGGGAAAGGTGGGGGAGG 61.167 63.158 0.00 0.00 0.00 4.30
1008 1018 2.752238 ACGAGGTGAGCGAGGGAG 60.752 66.667 0.00 0.00 0.00 4.30
1343 1367 4.043200 GAAACCAGCAGCGCACCC 62.043 66.667 11.47 0.00 0.00 4.61
1350 1374 3.725010 GCGTAAAATCGAGAAACCAGCAG 60.725 47.826 0.00 0.00 0.00 4.24
1369 1393 3.349006 CTGCAAGCAAGGACGCGT 61.349 61.111 13.85 13.85 36.85 6.01
1383 1407 1.129326 CCGAAACGATCCGTATCTGC 58.871 55.000 0.00 0.00 39.99 4.26
1389 1413 4.114794 CCTAATAAACCGAAACGATCCGT 58.885 43.478 0.00 0.00 43.97 4.69
1431 1455 5.705441 AGAAGAAGCAAACAATCATCCGTAA 59.295 36.000 0.00 0.00 0.00 3.18
1435 1459 4.704057 AGGAGAAGAAGCAAACAATCATCC 59.296 41.667 0.00 0.00 0.00 3.51
1445 1469 4.520492 GGAACAATCAAGGAGAAGAAGCAA 59.480 41.667 0.00 0.00 0.00 3.91
1446 1470 4.074970 GGAACAATCAAGGAGAAGAAGCA 58.925 43.478 0.00 0.00 0.00 3.91
1447 1471 3.126000 CGGAACAATCAAGGAGAAGAAGC 59.874 47.826 0.00 0.00 0.00 3.86
1448 1472 4.153117 CACGGAACAATCAAGGAGAAGAAG 59.847 45.833 0.00 0.00 0.00 2.85
1529 1558 8.840833 AAATCAAGAGAAGAGAAACTAGGAAC 57.159 34.615 0.00 0.00 0.00 3.62
1565 1594 0.317160 TCTCCGCTGTGGTACAACAG 59.683 55.000 23.89 23.89 44.16 3.16
1595 1627 3.072468 TACGGAGGCACGAAGGGG 61.072 66.667 8.58 0.00 37.61 4.79
1648 1680 2.110967 CCGATGTTGCTGAGGCCAG 61.111 63.158 5.01 0.00 43.22 4.85
1759 1791 2.084610 TGAGATTGACGCAGAGTTGG 57.915 50.000 0.00 0.00 0.00 3.77
1760 1792 4.259570 CGTTATGAGATTGACGCAGAGTTG 60.260 45.833 0.00 0.00 0.00 3.16
1777 1809 1.359848 GACAGCACCAGGACGTTATG 58.640 55.000 0.00 0.00 0.00 1.90
1786 1822 1.102154 AGATCTCTCGACAGCACCAG 58.898 55.000 0.00 0.00 0.00 4.00
1841 1877 5.740569 CGATTAGCATCAAATTTGGTGTGAG 59.259 40.000 27.67 12.88 41.32 3.51
1867 1903 1.069978 ACCAAATCGCAAAAACCCCAG 59.930 47.619 0.00 0.00 0.00 4.45
1899 1937 1.020861 GTCAGCGACACATGCATCCA 61.021 55.000 0.00 0.00 32.09 3.41
2208 3040 4.481930 TCTCCACAAGTAAAACAATGCG 57.518 40.909 0.00 0.00 0.00 4.73
2527 3430 6.823182 CACCATTACACCTCATTGTAGAATCA 59.177 38.462 0.00 0.00 33.50 2.57
2560 3463 6.159751 ACCATCCAAACATACCCTTACATACT 59.840 38.462 0.00 0.00 0.00 2.12
2624 3527 7.159322 TGAACTAGAGTTGGTAAAGAGCTAG 57.841 40.000 0.00 0.00 38.56 3.42
2825 3744 5.674569 GCTTTGTACTTTGCGTCATCATGAT 60.675 40.000 1.18 1.18 0.00 2.45
2881 3949 7.115663 GCCTTTGTATTGCTTCGTTTTCAATAA 59.884 33.333 0.00 0.00 35.31 1.40
2955 4025 2.179427 AGTATGCTGTGGTGTAGCTCA 58.821 47.619 0.00 0.00 41.66 4.26
3024 4094 4.980573 ACCTAAAACAGATGGTAGCACAA 58.019 39.130 0.00 0.00 0.00 3.33
3025 4095 4.634012 ACCTAAAACAGATGGTAGCACA 57.366 40.909 0.00 0.00 0.00 4.57
3043 4113 6.885922 AGTACAACAGACTTAACTTGAACCT 58.114 36.000 0.00 0.00 0.00 3.50
3071 4141 2.239654 GAGGGTTCCATCCATGAACTCA 59.760 50.000 5.87 0.00 32.12 3.41
3114 4184 6.207417 AGTGAAAATACATCAAGTTCCACAGG 59.793 38.462 0.00 0.00 0.00 4.00
3170 4240 1.800805 CAGGCAGATCAAACACGACT 58.199 50.000 0.00 0.00 0.00 4.18
3254 4324 9.653287 TGTACAGAGTATGAGAAACATAAAAGG 57.347 33.333 0.00 0.00 42.19 3.11
3259 4329 8.803235 ACAGTTGTACAGAGTATGAGAAACATA 58.197 33.333 0.00 0.00 40.07 2.29
3284 4354 5.572896 CGATTTCCATTAAAGAAACTGGCAC 59.427 40.000 6.26 0.00 36.13 5.01
3289 4359 7.829211 TCCTCATCGATTTCCATTAAAGAAACT 59.171 33.333 0.00 0.00 36.13 2.66
3428 4500 3.130280 TGAACTGAGAAGCATGCTTGA 57.870 42.857 36.48 18.58 36.26 3.02
3434 4506 4.011966 TGACACATGAACTGAGAAGCAT 57.988 40.909 0.00 0.00 0.00 3.79
3882 5013 0.547553 ATGCATTCCCCATTTTGGCC 59.452 50.000 0.00 0.00 35.79 5.36
3941 5072 3.386078 ACTCACTTGACATGTGTCTCAGT 59.614 43.478 18.05 12.42 44.99 3.41
3956 5087 0.687354 ACTGGCGGATGAACTCACTT 59.313 50.000 0.00 0.00 0.00 3.16
3959 5090 0.535335 GGTACTGGCGGATGAACTCA 59.465 55.000 0.00 0.00 0.00 3.41
4311 5448 3.087031 CACACATTTTCTGCCAGGATCT 58.913 45.455 0.00 0.00 0.00 2.75
4327 5464 1.146041 GTGCTCACCAGACCACACA 59.854 57.895 0.00 0.00 31.92 3.72
4454 5591 2.866156 CACTCGCAGAAGTTCTTTGTCA 59.134 45.455 1.56 0.00 34.09 3.58
4475 6839 6.085555 TCTCGATATACATTTCACTGTCCC 57.914 41.667 0.00 0.00 0.00 4.46
4499 6864 4.866508 TTTGACTACTGAACTCCGTGAT 57.133 40.909 0.00 0.00 0.00 3.06
4503 6868 6.202954 ACTCAAAATTTGACTACTGAACTCCG 59.797 38.462 4.03 0.00 35.46 4.63
4544 6909 5.707242 AATCTGACTACTGAACTTCGTGA 57.293 39.130 0.00 0.00 0.00 4.35
4545 6910 6.420903 TCAAAATCTGACTACTGAACTTCGTG 59.579 38.462 0.00 0.00 0.00 4.35
4546 6911 6.513180 TCAAAATCTGACTACTGAACTTCGT 58.487 36.000 0.00 0.00 0.00 3.85
4597 6964 3.512329 TCTTCACGGTACATTTAGAGGCA 59.488 43.478 0.00 0.00 0.00 4.75
4630 6997 5.817296 ACATTTGCAATATCTAACAGCTCGA 59.183 36.000 0.00 0.00 0.00 4.04
4632 6999 9.956720 ATTTACATTTGCAATATCTAACAGCTC 57.043 29.630 0.00 0.00 0.00 4.09
4719 7090 3.754850 CAGAATGTGCAGTGAGAAATGGA 59.245 43.478 0.00 0.00 0.00 3.41
4935 7337 2.001159 CTTGACTGACAGCTGAGCATC 58.999 52.381 23.35 12.74 0.00 3.91
4959 7361 4.022068 TGGAAAACAATGCCTGAGAACATC 60.022 41.667 0.00 0.00 0.00 3.06
5155 7574 1.745653 GCCCAAGAAGCATTACCACTC 59.254 52.381 0.00 0.00 0.00 3.51
5160 7579 1.176527 TGCTGCCCAAGAAGCATTAC 58.823 50.000 0.00 0.00 44.26 1.89
5173 7592 1.636988 GCAGATGAAATGTTGCTGCC 58.363 50.000 0.00 0.00 44.50 4.85
5192 7611 5.282055 AGATCAGGTACATACACCACATG 57.718 43.478 0.00 0.00 41.40 3.21
5259 7678 0.961019 TGGTGCTTGCAATCCTGAAC 59.039 50.000 0.00 0.00 0.00 3.18
5344 7763 3.348647 TGCACCAACTATAGCACACAT 57.651 42.857 0.00 0.00 31.05 3.21
5347 7767 6.654582 CCATTATATGCACCAACTATAGCACA 59.345 38.462 0.00 0.00 40.14 4.57
5356 7776 5.580297 CACAAAACCCATTATATGCACCAAC 59.420 40.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.