Multiple sequence alignment - TraesCS2B01G100400

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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 TraesCS2B01G100400 chr2B 100.000 5747 0 0 1 5747 59761959 59756213 0.000000e+00 10613.0
1 TraesCS2B01G100400 chr2B 82.199 1601 192 45 2990 4532 695581030 695582595 0.000000e+00 1291.0
2 TraesCS2B01G100400 chr2B 80.193 1141 125 53 2538 3635 60144325 60143243 0.000000e+00 761.0
3 TraesCS2B01G100400 chr2B 88.590 631 42 12 4696 5322 59708579 59707975 0.000000e+00 739.0
4 TraesCS2B01G100400 chr2B 90.985 477 28 10 1027 1488 695579388 695579864 3.780000e-176 628.0
5 TraesCS2B01G100400 chr2B 88.367 490 46 6 2430 2909 695580513 695581001 3.860000e-161 579.0
6 TraesCS2B01G100400 chr2B 90.390 385 24 8 5376 5747 59707955 59707571 1.440000e-135 494.0
7 TraesCS2B01G100400 chr2B 81.239 565 65 20 1972 2525 59772610 59772076 8.910000e-113 418.0
8 TraesCS2B01G100400 chr2B 83.297 461 60 12 4463 4912 314669134 314669588 5.360000e-110 409.0
9 TraesCS2B01G100400 chr2D 93.731 4291 154 41 1481 5737 36280623 36284832 0.000000e+00 6327.0
10 TraesCS2B01G100400 chr2D 82.510 2390 266 74 2226 4538 578601193 578603507 0.000000e+00 1958.0
11 TraesCS2B01G100400 chr2D 91.550 1290 73 19 798 2072 36279311 36280579 0.000000e+00 1746.0
12 TraesCS2B01G100400 chr2D 81.514 1136 121 45 2538 3632 36271074 36272161 0.000000e+00 852.0
13 TraesCS2B01G100400 chr2D 92.453 477 21 9 1027 1488 578600040 578600516 0.000000e+00 667.0
14 TraesCS2B01G100400 chr2D 82.770 296 38 12 338 631 36278927 36279211 9.560000e-63 252.0
15 TraesCS2B01G100400 chr2D 86.784 227 24 5 87 308 36278644 36278869 1.240000e-61 248.0
16 TraesCS2B01G100400 chr2D 95.312 64 3 0 1328 1391 342054287 342054350 1.020000e-17 102.0
17 TraesCS2B01G100400 chr2A 94.590 3549 104 33 1800 5322 39707346 39703860 0.000000e+00 5409.0
18 TraesCS2B01G100400 chr2A 85.706 1630 168 30 2310 3908 716177470 716179065 0.000000e+00 1659.0
19 TraesCS2B01G100400 chr2A 94.290 683 32 5 1146 1823 39708733 39708053 0.000000e+00 1038.0
20 TraesCS2B01G100400 chr2A 80.600 1134 121 45 2538 3635 39717530 39716460 0.000000e+00 784.0
21 TraesCS2B01G100400 chr2A 95.980 398 16 0 1091 1488 716176288 716176685 0.000000e+00 647.0
22 TraesCS2B01G100400 chr2A 93.182 352 17 4 807 1153 39709453 39709104 1.430000e-140 510.0
23 TraesCS2B01G100400 chr2A 81.738 564 63 19 1972 2525 39718042 39717509 8.840000e-118 435.0
24 TraesCS2B01G100400 chr2A 89.855 345 21 9 5381 5715 39703835 39703495 1.140000e-116 431.0
25 TraesCS2B01G100400 chr2A 83.432 338 42 10 4571 4903 3353937 3354265 9.360000e-78 302.0
26 TraesCS2B01G100400 chr2A 77.577 553 76 20 3941 4461 716179174 716179710 2.030000e-74 291.0
27 TraesCS2B01G100400 chr2A 91.765 170 13 1 4583 4751 716179833 716180002 9.630000e-58 235.0
28 TraesCS2B01G100400 chr2A 96.403 139 5 0 1800 1938 39707474 39707336 4.480000e-56 230.0
29 TraesCS2B01G100400 chr2A 97.479 119 3 0 1820 1938 39707582 39707464 2.710000e-48 204.0
30 TraesCS2B01G100400 chr2A 91.406 128 5 2 5447 5568 39950010 39950137 2.750000e-38 171.0
31 TraesCS2B01G100400 chr2A 88.060 134 13 3 4141 4274 3351488 3351618 7.710000e-34 156.0
32 TraesCS2B01G100400 chr2A 91.304 115 7 2 5590 5703 39969753 39969865 2.770000e-33 154.0
33 TraesCS2B01G100400 chr2A 93.684 95 4 2 1 93 16815449 16815355 2.160000e-29 141.0
34 TraesCS2B01G100400 chr1D 83.053 950 96 37 2931 3845 467859845 467860764 0.000000e+00 802.0
35 TraesCS2B01G100400 chr1D 87.598 508 42 12 2224 2722 467859204 467859699 2.320000e-158 569.0
36 TraesCS2B01G100400 chr1D 91.000 300 19 4 1197 1488 467857602 467857901 1.160000e-106 398.0
37 TraesCS2B01G100400 chr1D 82.222 450 60 15 4471 4907 404479670 404479228 2.530000e-98 370.0
38 TraesCS2B01G100400 chr1D 83.957 187 21 4 4231 4408 467860927 467861113 2.750000e-38 171.0
39 TraesCS2B01G100400 chr1D 95.556 90 2 2 1 89 9310090 9310002 6.000000e-30 143.0
40 TraesCS2B01G100400 chr1D 93.333 90 5 1 4233 4322 404480093 404480005 1.300000e-26 132.0
41 TraesCS2B01G100400 chrUn 80.600 1134 121 45 2538 3635 12899467 12898397 0.000000e+00 784.0
42 TraesCS2B01G100400 chrUn 81.738 564 63 19 1972 2525 12899979 12899446 8.840000e-118 435.0
43 TraesCS2B01G100400 chrUn 80.859 256 23 14 2006 2257 268348320 268348087 1.650000e-40 178.0
44 TraesCS2B01G100400 chrUn 80.859 256 23 14 2006 2257 460924643 460924410 1.650000e-40 178.0
45 TraesCS2B01G100400 chrUn 80.078 256 25 11 2006 2257 34119887 34120120 3.560000e-37 167.0
46 TraesCS2B01G100400 chr1A 82.421 950 87 39 2931 3830 560876820 560877739 0.000000e+00 756.0
47 TraesCS2B01G100400 chr1A 86.268 284 19 5 2533 2813 560876482 560876748 2.030000e-74 291.0
48 TraesCS2B01G100400 chr1A 89.529 191 17 3 4592 4779 560878227 560878417 7.440000e-59 239.0
49 TraesCS2B01G100400 chr1A 78.607 402 43 25 4022 4410 560877803 560878174 5.790000e-55 226.0
50 TraesCS2B01G100400 chr5D 83.033 666 81 19 4266 4916 403569882 403570530 4.990000e-160 575.0
51 TraesCS2B01G100400 chr5D 94.624 93 3 2 1 92 13914809 13914718 6.000000e-30 143.0
52 TraesCS2B01G100400 chr5D 95.556 90 2 2 1 89 123600944 123600856 6.000000e-30 143.0
53 TraesCS2B01G100400 chr5D 96.774 62 2 0 1328 1389 78436517 78436456 2.830000e-18 104.0
54 TraesCS2B01G100400 chr5D 95.312 64 3 0 1328 1391 8377598 8377535 1.020000e-17 102.0
55 TraesCS2B01G100400 chr5D 83.333 72 6 5 592 657 410485680 410485751 1.730000e-05 62.1
56 TraesCS2B01G100400 chr5B 82.609 460 62 12 4465 4912 441132580 441133033 1.940000e-104 390.0
57 TraesCS2B01G100400 chr1B 92.857 168 10 1 3678 3845 645931330 645931495 5.750000e-60 243.0
58 TraesCS2B01G100400 chr4B 89.011 182 15 5 4141 4322 314340480 314340304 2.700000e-53 220.0
59 TraesCS2B01G100400 chr4B 80.460 261 24 14 2002 2257 260902861 260902623 2.130000e-39 174.0
60 TraesCS2B01G100400 chr4B 80.077 261 25 12 2002 2257 260745802 260745564 9.900000e-38 169.0
61 TraesCS2B01G100400 chr4B 80.077 261 25 12 2002 2257 261072832 261072594 9.900000e-38 169.0
62 TraesCS2B01G100400 chr6B 97.753 89 2 0 1 89 685003254 685003166 2.770000e-33 154.0
63 TraesCS2B01G100400 chr4D 95.699 93 2 2 1 93 366315588 366315498 1.290000e-31 148.0
64 TraesCS2B01G100400 chr4D 92.135 89 6 1 4234 4322 374469079 374468992 2.170000e-24 124.0
65 TraesCS2B01G100400 chr7B 96.591 88 2 1 1 87 644538172 644538085 1.670000e-30 145.0
66 TraesCS2B01G100400 chr3B 96.591 88 1 2 1 87 19206078 19206164 1.670000e-30 145.0
67 TraesCS2B01G100400 chr6D 95.556 90 2 2 1 89 240728493 240728405 6.000000e-30 143.0
68 TraesCS2B01G100400 chr6D 91.667 48 2 2 589 636 451766254 451766209 1.340000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G100400 chr2B 59756213 59761959 5746 True 10613.000000 10613 100.000000 1 5747 1 chr2B.!!$R1 5746
1 TraesCS2B01G100400 chr2B 695579388 695582595 3207 False 832.666667 1291 87.183667 1027 4532 3 chr2B.!!$F2 3505
2 TraesCS2B01G100400 chr2B 60143243 60144325 1082 True 761.000000 761 80.193000 2538 3635 1 chr2B.!!$R3 1097
3 TraesCS2B01G100400 chr2B 59707571 59708579 1008 True 616.500000 739 89.490000 4696 5747 2 chr2B.!!$R4 1051
4 TraesCS2B01G100400 chr2B 59772076 59772610 534 True 418.000000 418 81.239000 1972 2525 1 chr2B.!!$R2 553
5 TraesCS2B01G100400 chr2D 36278644 36284832 6188 False 2143.250000 6327 88.708750 87 5737 4 chr2D.!!$F3 5650
6 TraesCS2B01G100400 chr2D 578600040 578603507 3467 False 1312.500000 1958 87.481500 1027 4538 2 chr2D.!!$F4 3511
7 TraesCS2B01G100400 chr2D 36271074 36272161 1087 False 852.000000 852 81.514000 2538 3632 1 chr2D.!!$F1 1094
8 TraesCS2B01G100400 chr2A 39703495 39709453 5958 True 1303.666667 5409 94.299833 807 5715 6 chr2A.!!$R2 4908
9 TraesCS2B01G100400 chr2A 716176288 716180002 3714 False 708.000000 1659 87.757000 1091 4751 4 chr2A.!!$F4 3660
10 TraesCS2B01G100400 chr2A 39716460 39718042 1582 True 609.500000 784 81.169000 1972 3635 2 chr2A.!!$R3 1663
11 TraesCS2B01G100400 chr2A 3351488 3354265 2777 False 229.000000 302 85.746000 4141 4903 2 chr2A.!!$F3 762
12 TraesCS2B01G100400 chr1D 467857602 467861113 3511 False 485.000000 802 86.402000 1197 4408 4 chr1D.!!$F1 3211
13 TraesCS2B01G100400 chr1D 404479228 404480093 865 True 251.000000 370 87.777500 4233 4907 2 chr1D.!!$R2 674
14 TraesCS2B01G100400 chrUn 12898397 12899979 1582 True 609.500000 784 81.169000 1972 3635 2 chrUn.!!$R3 1663
15 TraesCS2B01G100400 chr1A 560876482 560878417 1935 False 378.000000 756 84.206250 2533 4779 4 chr1A.!!$F1 2246
16 TraesCS2B01G100400 chr5D 403569882 403570530 648 False 575.000000 575 83.033000 4266 4916 1 chr5D.!!$F1 650

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
61 62 0.028110 GCGATTTTAGGCGCCTTCTG 59.972 55.000 37.74 21.01 46.93 3.02 F
237 238 0.107831 TACGACTTGGGCAAGCAACT 59.892 50.000 0.00 0.00 41.99 3.16 F
543 578 0.452950 CGGTCGACTGAGACTTGACG 60.453 60.000 20.01 3.74 40.76 4.35 F
982 1040 2.045340 CCACCAAACCCTAGCCCG 60.045 66.667 0.00 0.00 0.00 6.13 F
1495 1964 2.100418 GTCCTGTACTCGGTATGGGTTC 59.900 54.545 0.00 0.00 0.00 3.62 F
1789 3321 2.101249 CTGTGGCCTGTGTTCAATTTGT 59.899 45.455 3.32 0.00 0.00 2.83 F
1793 3325 2.548493 GGCCTGTGTTCAATTTGTGCAT 60.548 45.455 0.00 0.00 0.00 3.96 F
1916 4262 4.095410 CAAGTGTGCTTCAGTTGTTTCA 57.905 40.909 16.30 0.00 46.52 2.69 F
2951 5710 4.943705 AGTGTGAACATCTGACACAACTTT 59.056 37.500 13.09 2.75 44.21 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 2011 1.035923 TTGGCAAATCGAAGGCAACA 58.964 45.000 16.93 1.56 44.04 3.33 R
1545 2015 1.215382 GGGTTGGCAAATCGAAGGC 59.785 57.895 0.00 0.00 0.00 4.35 R
2286 4808 0.110486 AGTGTTCAATCTTGGCCGGT 59.890 50.000 1.90 0.00 0.00 5.28 R
2424 5123 6.540189 GTCCTGAACATAACAGAACATAGCAT 59.460 38.462 0.00 0.00 37.54 3.79 R
3125 5918 5.689383 TTCAGGTAGCAAATTCTTGTGTC 57.311 39.130 0.00 0.00 34.79 3.67 R
3534 6352 7.016661 AGTCACAGATATTATTCCTAAGGGTGG 59.983 40.741 0.00 0.00 0.00 4.61 R
3941 6894 7.280876 GCAAGAACTATGAATACAAGACCATCA 59.719 37.037 0.00 0.00 0.00 3.07 R
3944 6897 6.371548 GTGCAAGAACTATGAATACAAGACCA 59.628 38.462 0.00 0.00 0.00 4.02 R
4851 9924 0.111266 GTGCAAACTACACGAGCACG 60.111 55.000 0.76 0.76 44.84 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
33 34 3.597728 TTTTTGCGCCGGGTCACC 61.598 61.111 4.18 0.00 0.00 4.02
50 51 2.124487 CCCCAGGCGGCGATTTTA 60.124 61.111 12.98 0.00 0.00 1.52
51 52 2.186826 CCCCAGGCGGCGATTTTAG 61.187 63.158 12.98 0.00 0.00 1.85
52 53 2.186826 CCCAGGCGGCGATTTTAGG 61.187 63.158 12.98 2.42 0.00 2.69
53 54 2.715624 CAGGCGGCGATTTTAGGC 59.284 61.111 12.98 0.00 0.00 3.93
59 60 4.998294 GCGATTTTAGGCGCCTTC 57.002 55.556 37.74 24.80 46.93 3.46
60 61 2.394604 GCGATTTTAGGCGCCTTCT 58.605 52.632 37.74 16.96 46.93 2.85
61 62 0.028110 GCGATTTTAGGCGCCTTCTG 59.972 55.000 37.74 21.01 46.93 3.02
62 63 0.657840 CGATTTTAGGCGCCTTCTGG 59.342 55.000 37.74 15.60 0.00 3.86
63 64 1.025041 GATTTTAGGCGCCTTCTGGG 58.975 55.000 37.74 0.00 38.36 4.45
85 86 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
86 87 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
87 88 0.461548 CAACGGCTGGAGATGCTCTA 59.538 55.000 0.00 0.00 0.00 2.43
88 89 1.134699 CAACGGCTGGAGATGCTCTAA 60.135 52.381 0.00 0.00 0.00 2.10
103 104 7.633789 AGATGCTCTAAACTTAGGAAAATGGA 58.366 34.615 0.00 0.00 0.00 3.41
145 146 5.801350 AATGAGATGATGGTGTAACAACG 57.199 39.130 0.00 0.00 39.98 4.10
149 150 1.057471 TGATGGTGTAACAACGGGGA 58.943 50.000 0.00 0.00 39.98 4.81
150 151 1.631388 TGATGGTGTAACAACGGGGAT 59.369 47.619 0.00 0.00 39.98 3.85
151 152 2.040545 TGATGGTGTAACAACGGGGATT 59.959 45.455 0.00 0.00 39.98 3.01
154 155 1.542472 GGTGTAACAACGGGGATTTGG 59.458 52.381 0.00 0.00 39.98 3.28
172 173 1.073125 TGGTCATCACATTGGTCCGTT 59.927 47.619 0.00 0.00 0.00 4.44
173 174 2.159382 GGTCATCACATTGGTCCGTTT 58.841 47.619 0.00 0.00 0.00 3.60
183 184 1.314730 TGGTCCGTTTGCCTCTTTTC 58.685 50.000 0.00 0.00 0.00 2.29
197 198 9.474920 TTTGCCTCTTTTCAAACATATAAACAG 57.525 29.630 0.00 0.00 0.00 3.16
211 212 9.498176 AACATATAAACAGACCTTAACTCGTTT 57.502 29.630 0.00 0.00 0.00 3.60
212 213 8.932791 ACATATAAACAGACCTTAACTCGTTTG 58.067 33.333 0.00 0.00 0.00 2.93
220 221 7.386025 ACAGACCTTAACTCGTTTGGTTAATAC 59.614 37.037 8.02 0.00 38.12 1.89
221 222 6.587608 AGACCTTAACTCGTTTGGTTAATACG 59.412 38.462 8.02 0.00 38.12 3.06
222 223 6.454795 ACCTTAACTCGTTTGGTTAATACGA 58.545 36.000 0.00 0.00 41.47 3.43
237 238 0.107831 TACGACTTGGGCAAGCAACT 59.892 50.000 0.00 0.00 41.99 3.16
240 241 1.606668 CGACTTGGGCAAGCAACTTTA 59.393 47.619 0.00 0.00 41.99 1.85
248 249 4.277423 TGGGCAAGCAACTTTAAGTTCTAC 59.723 41.667 7.45 1.06 36.03 2.59
254 255 6.487689 AGCAACTTTAAGTTCTACTCATGC 57.512 37.500 7.45 6.70 36.03 4.06
257 258 7.175641 AGCAACTTTAAGTTCTACTCATGCATT 59.824 33.333 7.45 0.00 36.03 3.56
259 260 9.334693 CAACTTTAAGTTCTACTCATGCATTTC 57.665 33.333 7.45 0.00 36.03 2.17
260 261 8.045176 ACTTTAAGTTCTACTCATGCATTTCC 57.955 34.615 0.00 0.00 0.00 3.13
262 263 4.574674 AGTTCTACTCATGCATTTCCCA 57.425 40.909 0.00 0.00 0.00 4.37
263 264 5.121380 AGTTCTACTCATGCATTTCCCAT 57.879 39.130 0.00 0.00 0.00 4.00
265 266 4.776435 TCTACTCATGCATTTCCCATCA 57.224 40.909 0.00 0.00 0.00 3.07
266 267 5.314718 TCTACTCATGCATTTCCCATCAT 57.685 39.130 0.00 0.00 0.00 2.45
267 268 6.438186 TCTACTCATGCATTTCCCATCATA 57.562 37.500 0.00 0.00 0.00 2.15
268 269 6.840527 TCTACTCATGCATTTCCCATCATAA 58.159 36.000 0.00 0.00 0.00 1.90
269 270 5.779529 ACTCATGCATTTCCCATCATAAC 57.220 39.130 0.00 0.00 0.00 1.89
271 272 5.301045 ACTCATGCATTTCCCATCATAACTG 59.699 40.000 0.00 0.00 0.00 3.16
293 298 6.722129 ACTGACACAAAGGTCTCTCTAACTAT 59.278 38.462 0.00 0.00 38.61 2.12
301 306 3.707102 GGTCTCTCTAACTATTGCCTGGT 59.293 47.826 0.00 0.00 0.00 4.00
308 313 0.912486 ACTATTGCCTGGTCCCTCAC 59.088 55.000 0.00 0.00 0.00 3.51
310 315 1.279025 TATTGCCTGGTCCCTCACCC 61.279 60.000 0.00 0.00 46.18 4.61
372 405 6.653740 CACCCCTTTCGTTTTCTTAGTTCTAT 59.346 38.462 0.00 0.00 0.00 1.98
374 407 8.039538 ACCCCTTTCGTTTTCTTAGTTCTATAG 58.960 37.037 0.00 0.00 0.00 1.31
375 408 8.039538 CCCCTTTCGTTTTCTTAGTTCTATAGT 58.960 37.037 0.00 0.00 0.00 2.12
411 444 8.850454 TTTTCTTAATTTTTGGTTCTCAGACG 57.150 30.769 0.00 0.00 0.00 4.18
439 472 3.195610 TGTGAGATGGTACTGGTGATGAC 59.804 47.826 0.00 0.00 0.00 3.06
463 496 5.615544 CGCATCAACCTAAACAAAGAGACTG 60.616 44.000 0.00 0.00 0.00 3.51
469 502 4.202367 ACCTAAACAAAGAGACTGTGAGGG 60.202 45.833 0.00 0.00 36.04 4.30
470 503 3.933861 AAACAAAGAGACTGTGAGGGT 57.066 42.857 0.00 0.00 0.00 4.34
472 505 5.568620 AAACAAAGAGACTGTGAGGGTAT 57.431 39.130 0.00 0.00 0.00 2.73
478 511 4.290093 AGAGACTGTGAGGGTATGCATAA 58.710 43.478 8.28 0.00 0.00 1.90
479 512 4.904251 AGAGACTGTGAGGGTATGCATAAT 59.096 41.667 8.28 0.00 0.00 1.28
480 513 5.011533 AGAGACTGTGAGGGTATGCATAATC 59.988 44.000 8.28 7.82 0.00 1.75
481 514 4.655649 AGACTGTGAGGGTATGCATAATCA 59.344 41.667 8.28 10.32 0.00 2.57
493 528 6.687105 GGTATGCATAATCAAACGAAGAACAC 59.313 38.462 8.28 0.00 0.00 3.32
497 532 7.144661 TGCATAATCAAACGAAGAACACAAAT 58.855 30.769 0.00 0.00 0.00 2.32
507 542 9.620660 AAACGAAGAACACAAATATTATGGTTC 57.379 29.630 13.82 13.82 35.95 3.62
508 543 7.758495 ACGAAGAACACAAATATTATGGTTCC 58.242 34.615 16.29 7.04 36.25 3.62
509 544 7.392113 ACGAAGAACACAAATATTATGGTTCCA 59.608 33.333 16.29 0.00 36.25 3.53
512 547 7.182060 AGAACACAAATATTATGGTTCCAGGT 58.818 34.615 16.29 3.02 36.25 4.00
517 552 6.440328 ACAAATATTATGGTTCCAGGTTTGCT 59.560 34.615 0.00 0.00 0.00 3.91
518 553 7.617723 ACAAATATTATGGTTCCAGGTTTGCTA 59.382 33.333 0.00 0.00 0.00 3.49
525 560 3.127030 GGTTCCAGGTTTGCTAAATCTCG 59.873 47.826 0.00 0.00 26.66 4.04
526 561 2.985896 TCCAGGTTTGCTAAATCTCGG 58.014 47.619 0.00 0.00 26.66 4.63
527 562 2.304761 TCCAGGTTTGCTAAATCTCGGT 59.695 45.455 0.00 0.00 26.66 4.69
528 563 2.678336 CCAGGTTTGCTAAATCTCGGTC 59.322 50.000 0.00 0.00 26.66 4.79
529 564 2.348666 CAGGTTTGCTAAATCTCGGTCG 59.651 50.000 0.00 0.00 26.66 4.79
530 565 2.232941 AGGTTTGCTAAATCTCGGTCGA 59.767 45.455 0.00 0.00 0.00 4.20
531 566 2.347755 GGTTTGCTAAATCTCGGTCGAC 59.652 50.000 7.13 7.13 0.00 4.20
532 567 3.251571 GTTTGCTAAATCTCGGTCGACT 58.748 45.455 16.46 0.00 0.00 4.18
533 568 2.561733 TGCTAAATCTCGGTCGACTG 57.438 50.000 18.66 18.66 0.00 3.51
534 569 2.089201 TGCTAAATCTCGGTCGACTGA 58.911 47.619 25.02 25.02 0.00 3.41
541 576 3.317449 TCGGTCGACTGAGACTTGA 57.683 52.632 23.11 0.00 40.76 3.02
542 577 0.873054 TCGGTCGACTGAGACTTGAC 59.127 55.000 23.11 0.00 40.76 3.18
543 578 0.452950 CGGTCGACTGAGACTTGACG 60.453 60.000 20.01 3.74 40.76 4.35
550 585 6.256686 GTCGACTGAGACTTGACGTATATTT 58.743 40.000 8.70 0.00 38.09 1.40
551 586 6.194876 GTCGACTGAGACTTGACGTATATTTG 59.805 42.308 8.70 0.00 38.09 2.32
556 591 6.330278 TGAGACTTGACGTATATTTGTGAGG 58.670 40.000 0.00 0.00 0.00 3.86
560 595 7.338703 AGACTTGACGTATATTTGTGAGGTCTA 59.661 37.037 8.61 0.00 0.00 2.59
587 622 9.725019 ACATGAAGATCTGTGTAAAAAGATACA 57.275 29.630 0.00 0.00 33.26 2.29
635 670 8.354711 TCTGTCACTTGACTGAGACTTATATT 57.645 34.615 13.26 0.00 44.43 1.28
636 671 8.807118 TCTGTCACTTGACTGAGACTTATATTT 58.193 33.333 13.26 0.00 44.43 1.40
637 672 9.429359 CTGTCACTTGACTGAGACTTATATTTT 57.571 33.333 10.63 0.00 44.99 1.82
638 673 9.208022 TGTCACTTGACTGAGACTTATATTTTG 57.792 33.333 10.63 0.00 44.99 2.44
639 674 9.209175 GTCACTTGACTGAGACTTATATTTTGT 57.791 33.333 1.92 0.00 41.65 2.83
641 676 9.817365 CACTTGACTGAGACTTATATTTTGTTG 57.183 33.333 0.00 0.00 0.00 3.33
642 677 9.778741 ACTTGACTGAGACTTATATTTTGTTGA 57.221 29.630 0.00 0.00 0.00 3.18
645 680 9.208022 TGACTGAGACTTATATTTTGTTGAGTG 57.792 33.333 0.00 0.00 0.00 3.51
646 681 9.424319 GACTGAGACTTATATTTTGTTGAGTGA 57.576 33.333 0.00 0.00 0.00 3.41
647 682 9.429359 ACTGAGACTTATATTTTGTTGAGTGAG 57.571 33.333 0.00 0.00 0.00 3.51
655 690 9.547753 TTATATTTTGTTGAGTGAGATCTAGCC 57.452 33.333 0.00 0.00 0.00 3.93
656 691 4.890158 TTTGTTGAGTGAGATCTAGCCA 57.110 40.909 0.00 0.00 0.00 4.75
657 692 3.876274 TGTTGAGTGAGATCTAGCCAC 57.124 47.619 0.00 0.00 0.00 5.01
658 693 3.165071 TGTTGAGTGAGATCTAGCCACA 58.835 45.455 13.72 2.75 33.53 4.17
659 694 3.056536 TGTTGAGTGAGATCTAGCCACAC 60.057 47.826 13.72 9.05 33.53 3.82
660 695 2.103373 TGAGTGAGATCTAGCCACACC 58.897 52.381 13.72 7.00 33.53 4.16
661 696 2.291865 TGAGTGAGATCTAGCCACACCT 60.292 50.000 13.72 1.16 33.53 4.00
662 697 2.763448 GAGTGAGATCTAGCCACACCTT 59.237 50.000 13.72 0.00 33.53 3.50
663 698 3.177228 AGTGAGATCTAGCCACACCTTT 58.823 45.455 13.72 0.00 33.53 3.11
664 699 4.353777 AGTGAGATCTAGCCACACCTTTA 58.646 43.478 13.72 0.00 33.53 1.85
665 700 4.965532 AGTGAGATCTAGCCACACCTTTAT 59.034 41.667 13.72 0.00 33.53 1.40
666 701 5.053145 GTGAGATCTAGCCACACCTTTATG 58.947 45.833 7.89 0.00 0.00 1.90
667 702 4.101585 TGAGATCTAGCCACACCTTTATGG 59.898 45.833 0.00 0.00 42.93 2.74
713 748 9.667107 TTCCGATCTTTTTATATCTTGTTGTCT 57.333 29.630 0.00 0.00 0.00 3.41
714 749 9.667107 TCCGATCTTTTTATATCTTGTTGTCTT 57.333 29.630 0.00 0.00 0.00 3.01
728 763 8.958119 TCTTGTTGTCTTTCTAATACTGTGTT 57.042 30.769 0.00 0.00 0.00 3.32
731 766 9.826574 TTGTTGTCTTTCTAATACTGTGTTACT 57.173 29.630 0.00 0.00 0.00 2.24
732 767 9.826574 TGTTGTCTTTCTAATACTGTGTTACTT 57.173 29.630 0.00 0.00 0.00 2.24
862 915 4.516092 GCAAACAGTGGCTATTACTACG 57.484 45.455 0.00 0.00 0.00 3.51
863 916 4.178540 GCAAACAGTGGCTATTACTACGA 58.821 43.478 0.00 0.00 0.00 3.43
921 978 2.358737 CAGGTTCCTCCGCACACC 60.359 66.667 0.00 0.00 41.99 4.16
922 979 4.003788 AGGTTCCTCCGCACACCG 62.004 66.667 0.00 0.00 41.99 4.94
982 1040 2.045340 CCACCAAACCCTAGCCCG 60.045 66.667 0.00 0.00 0.00 6.13
1495 1964 2.100418 GTCCTGTACTCGGTATGGGTTC 59.900 54.545 0.00 0.00 0.00 3.62
1552 2022 5.941058 TGTTTATTAGGATTGTTGCCTTCGA 59.059 36.000 0.00 0.00 36.96 3.71
1589 2099 7.830099 AGATACATTTGGGATCCTGAATTTC 57.170 36.000 12.58 8.62 0.00 2.17
1619 2754 3.543680 TTAGGATTCACACTAGCTGGC 57.456 47.619 0.00 0.00 0.00 4.85
1663 3051 7.149569 TCTGCTTCAATTCTCAGTTATTTGG 57.850 36.000 0.00 0.00 0.00 3.28
1703 3097 9.902684 AGTAGTAGCAGTAGAGTCATAGTTTAA 57.097 33.333 0.00 0.00 0.00 1.52
1708 3102 7.852263 AGCAGTAGAGTCATAGTTTAATGGTT 58.148 34.615 0.00 0.00 0.00 3.67
1709 3103 7.766278 AGCAGTAGAGTCATAGTTTAATGGTTG 59.234 37.037 0.00 0.00 0.00 3.77
1729 3259 6.718912 TGGTTGATAATTGTTCAATGGACAGA 59.281 34.615 0.00 0.00 35.68 3.41
1770 3302 2.354003 GGTGGAATGTTGGATTTGCCTG 60.354 50.000 0.00 0.00 37.63 4.85
1789 3321 2.101249 CTGTGGCCTGTGTTCAATTTGT 59.899 45.455 3.32 0.00 0.00 2.83
1793 3325 2.548493 GGCCTGTGTTCAATTTGTGCAT 60.548 45.455 0.00 0.00 0.00 3.96
1916 4262 4.095410 CAAGTGTGCTTCAGTTGTTTCA 57.905 40.909 16.30 0.00 46.52 2.69
2825 5572 8.637986 TGTTAGGTTTTCTTGTTTATGCTCAAT 58.362 29.630 0.00 0.00 0.00 2.57
2951 5710 4.943705 AGTGTGAACATCTGACACAACTTT 59.056 37.500 13.09 2.75 44.21 2.66
3125 5918 6.876789 TGGTAGTGGTTCATACATTACACTTG 59.123 38.462 0.00 0.00 39.59 3.16
3499 6313 9.529325 AAAGAAAAACACTTAGATTGTAAAGCC 57.471 29.630 0.00 0.00 27.83 4.35
3534 6352 6.701400 AGTTCTGATTTTACAAAATGTGTGCC 59.299 34.615 4.70 0.00 41.89 5.01
3938 6891 8.648557 TTCAGTGTAGTAGATTGTATTGATGC 57.351 34.615 0.00 0.00 0.00 3.91
3939 6892 7.210174 TCAGTGTAGTAGATTGTATTGATGCC 58.790 38.462 0.00 0.00 0.00 4.40
3940 6893 7.069950 TCAGTGTAGTAGATTGTATTGATGCCT 59.930 37.037 0.00 0.00 0.00 4.75
3941 6894 7.712639 CAGTGTAGTAGATTGTATTGATGCCTT 59.287 37.037 0.00 0.00 0.00 4.35
3942 6895 7.712639 AGTGTAGTAGATTGTATTGATGCCTTG 59.287 37.037 0.00 0.00 0.00 3.61
3943 6896 7.710907 GTGTAGTAGATTGTATTGATGCCTTGA 59.289 37.037 0.00 0.00 0.00 3.02
3944 6897 8.432013 TGTAGTAGATTGTATTGATGCCTTGAT 58.568 33.333 0.00 0.00 0.00 2.57
3945 6898 7.741027 AGTAGATTGTATTGATGCCTTGATG 57.259 36.000 0.00 0.00 0.00 3.07
3996 6949 6.369890 TGCAGTCATTTTCTTTAGAGCAGTAG 59.630 38.462 0.00 0.00 0.00 2.57
4013 6966 4.397417 GCAGTAGATGGCTCTCAAACATTT 59.603 41.667 0.00 0.00 32.66 2.32
4014 6967 5.105997 GCAGTAGATGGCTCTCAAACATTTT 60.106 40.000 0.00 0.00 32.66 1.82
4107 7074 4.525024 TGACCTAGAGCTCCAACTAGTAC 58.475 47.826 10.93 2.92 35.65 2.73
4175 7143 8.841300 ACTGAAAATCTTAGTTTCTTGAACCTC 58.159 33.333 2.13 0.00 39.13 3.85
4366 7457 5.302059 AGTCTCTTCACTTGTACTACTGCAA 59.698 40.000 0.00 0.00 0.00 4.08
4369 7460 5.047847 TCTTCACTTGTACTACTGCAACAC 58.952 41.667 0.00 0.00 0.00 3.32
4397 7490 7.650903 GGAAATTCATTGCCTCAGATCAATTAC 59.349 37.037 0.00 0.00 32.35 1.89
4723 9790 1.541233 CCAACGTCAAGAAGCCTGAGT 60.541 52.381 0.00 0.00 0.00 3.41
4758 9825 4.144297 TCTACAAATGAGGCAGCAAACTT 58.856 39.130 0.00 0.00 0.00 2.66
4761 9828 5.275067 ACAAATGAGGCAGCAAACTTTTA 57.725 34.783 0.00 0.00 0.00 1.52
4784 9854 9.747898 TTTAAAGAGGATGCTTTATTTCCTACA 57.252 29.630 0.00 0.00 39.98 2.74
4833 9906 3.728076 TTGTGGATAGTCGCCTGATAC 57.272 47.619 0.00 0.00 0.00 2.24
4841 9914 6.260271 TGGATAGTCGCCTGATACTAATATCG 59.740 42.308 0.00 0.00 40.26 2.92
4849 9922 6.691818 CGCCTGATACTAATATCGTTGTATCC 59.308 42.308 0.00 0.00 40.26 2.59
4851 9924 7.490000 CCTGATACTAATATCGTTGTATCCCC 58.510 42.308 0.00 0.00 40.26 4.81
4858 9931 1.876714 CGTTGTATCCCCGTGCTCG 60.877 63.158 0.14 0.14 0.00 5.03
4938 10014 4.015872 TCCTAAAGTTTCGCTTGACCAT 57.984 40.909 0.00 0.00 37.52 3.55
4948 10024 1.501169 GCTTGACCATTTTGCGCTTT 58.499 45.000 9.73 0.00 0.00 3.51
5006 10082 5.311265 AGTACCCCCTTTTCGTTCTTAAAG 58.689 41.667 0.00 0.00 0.00 1.85
5173 10250 7.229306 GGAGATGTTGATATTTCTGTATGCCAA 59.771 37.037 0.00 0.00 0.00 4.52
5174 10251 8.701908 AGATGTTGATATTTCTGTATGCCAAT 57.298 30.769 0.00 0.00 0.00 3.16
5175 10252 9.797642 AGATGTTGATATTTCTGTATGCCAATA 57.202 29.630 0.00 0.00 0.00 1.90
5305 10382 1.675310 CATGGCGATGGTGGTGTGT 60.675 57.895 0.00 0.00 0.00 3.72
5327 10404 2.638480 TCCCATCGGAGGCTTATTTG 57.362 50.000 0.00 0.00 32.86 2.32
5328 10405 1.843851 TCCCATCGGAGGCTTATTTGT 59.156 47.619 0.00 0.00 32.86 2.83
5344 10430 6.599638 GCTTATTTGTAAGTCAGATTCCCTGT 59.400 38.462 0.00 0.00 43.38 4.00
5358 10444 3.768632 CTGTAAGGCGTCGCAGTC 58.231 61.111 20.50 1.18 0.00 3.51
5359 10445 1.805945 CTGTAAGGCGTCGCAGTCC 60.806 63.158 20.50 0.77 0.00 3.85
5360 10446 2.260434 GTAAGGCGTCGCAGTCCA 59.740 61.111 20.50 0.00 0.00 4.02
5361 10447 2.092882 GTAAGGCGTCGCAGTCCAC 61.093 63.158 20.50 5.31 0.00 4.02
5362 10448 2.566570 TAAGGCGTCGCAGTCCACA 61.567 57.895 20.50 0.00 0.00 4.17
5363 10449 2.089887 TAAGGCGTCGCAGTCCACAA 62.090 55.000 20.50 0.00 0.00 3.33
5364 10450 2.731691 AAGGCGTCGCAGTCCACAAT 62.732 55.000 20.50 0.00 0.00 2.71
5365 10451 2.325082 GGCGTCGCAGTCCACAATT 61.325 57.895 20.50 0.00 0.00 2.32
5388 10474 4.478206 TTTTGACTTCAATTTGGCACCA 57.522 36.364 0.00 0.00 35.55 4.17
5389 10475 4.478206 TTTGACTTCAATTTGGCACCAA 57.522 36.364 0.00 0.00 35.55 3.67
5390 10476 4.686191 TTGACTTCAATTTGGCACCAAT 57.314 36.364 2.31 0.00 35.70 3.16
5425 10513 4.916983 TTCCATTGTCACAAACTCCAAG 57.083 40.909 0.00 0.00 0.00 3.61
5428 10516 4.338118 TCCATTGTCACAAACTCCAAGTTC 59.662 41.667 0.00 0.00 37.47 3.01
5492 10583 9.906660 CTGCATTACACAAGGAAATAACTAAAA 57.093 29.630 0.00 0.00 0.00 1.52
5493 10584 9.685828 TGCATTACACAAGGAAATAACTAAAAC 57.314 29.630 0.00 0.00 0.00 2.43
5494 10585 9.685828 GCATTACACAAGGAAATAACTAAAACA 57.314 29.630 0.00 0.00 0.00 2.83
5527 10619 7.762588 TCCACATTTTTATTCTACGGGAAAA 57.237 32.000 0.00 0.00 37.49 2.29
5568 10667 5.083533 TCAAAATTTTGAAGCGGCCATAT 57.916 34.783 27.22 0.00 43.62 1.78
5569 10668 4.869297 TCAAAATTTTGAAGCGGCCATATG 59.131 37.500 27.22 0.00 43.62 1.78
5575 10674 2.929641 TGAAGCGGCCATATGATTTCA 58.070 42.857 2.24 4.13 0.00 2.69
5580 10679 5.280654 AGCGGCCATATGATTTCAAATTT 57.719 34.783 2.24 0.00 0.00 1.82
5581 10680 5.051816 AGCGGCCATATGATTTCAAATTTG 58.948 37.500 12.15 12.15 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.597728 GGTGACCCGGCGCAAAAA 61.598 61.111 10.83 0.00 0.00 1.94
34 35 2.186826 CCTAAAATCGCCGCCTGGG 61.187 63.158 0.00 0.00 39.58 4.45
35 36 2.834618 GCCTAAAATCGCCGCCTGG 61.835 63.158 0.00 0.00 38.77 4.45
36 37 2.715624 GCCTAAAATCGCCGCCTG 59.284 61.111 0.00 0.00 0.00 4.85
37 38 2.895372 CGCCTAAAATCGCCGCCT 60.895 61.111 0.00 0.00 0.00 5.52
38 39 4.607606 GCGCCTAAAATCGCCGCC 62.608 66.667 0.00 0.00 45.01 6.13
43 44 0.657840 CCAGAAGGCGCCTAAAATCG 59.342 55.000 33.07 18.06 0.00 3.34
44 45 1.025041 CCCAGAAGGCGCCTAAAATC 58.975 55.000 33.07 23.73 0.00 2.17
45 46 0.395724 CCCCAGAAGGCGCCTAAAAT 60.396 55.000 33.07 15.20 0.00 1.82
46 47 1.001393 CCCCAGAAGGCGCCTAAAA 60.001 57.895 33.07 0.00 0.00 1.52
47 48 2.674754 CCCCAGAAGGCGCCTAAA 59.325 61.111 33.07 0.00 0.00 1.85
48 49 3.407967 CCCCCAGAAGGCGCCTAA 61.408 66.667 33.07 0.00 0.00 2.69
68 69 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
79 80 7.770897 TCTCCATTTTCCTAAGTTTAGAGCATC 59.229 37.037 0.51 0.00 32.47 3.91
80 81 7.633789 TCTCCATTTTCCTAAGTTTAGAGCAT 58.366 34.615 0.51 0.00 32.47 3.79
81 82 7.016153 TCTCCATTTTCCTAAGTTTAGAGCA 57.984 36.000 0.51 0.00 32.47 4.26
82 83 6.540551 CCTCTCCATTTTCCTAAGTTTAGAGC 59.459 42.308 0.51 0.00 32.47 4.09
83 84 7.625469 ACCTCTCCATTTTCCTAAGTTTAGAG 58.375 38.462 0.51 0.00 32.47 2.43
84 85 7.569599 ACCTCTCCATTTTCCTAAGTTTAGA 57.430 36.000 0.51 0.00 32.47 2.10
85 86 8.759782 TCTACCTCTCCATTTTCCTAAGTTTAG 58.240 37.037 0.00 0.00 0.00 1.85
86 87 8.674925 TCTACCTCTCCATTTTCCTAAGTTTA 57.325 34.615 0.00 0.00 0.00 2.01
87 88 7.569599 TCTACCTCTCCATTTTCCTAAGTTT 57.430 36.000 0.00 0.00 0.00 2.66
88 89 7.395617 GTTCTACCTCTCCATTTTCCTAAGTT 58.604 38.462 0.00 0.00 0.00 2.66
103 104 7.069578 TCTCATTATTAAAGCCGTTCTACCTCT 59.930 37.037 0.00 0.00 0.00 3.69
145 146 2.431782 CCAATGTGATGACCAAATCCCC 59.568 50.000 0.00 0.00 0.00 4.81
149 150 2.754552 CGGACCAATGTGATGACCAAAT 59.245 45.455 0.00 0.00 0.00 2.32
150 151 2.158559 CGGACCAATGTGATGACCAAA 58.841 47.619 0.00 0.00 0.00 3.28
151 152 1.073125 ACGGACCAATGTGATGACCAA 59.927 47.619 0.00 0.00 0.00 3.67
154 155 2.668279 GCAAACGGACCAATGTGATGAC 60.668 50.000 0.00 0.00 0.00 3.06
172 173 8.855110 TCTGTTTATATGTTTGAAAAGAGGCAA 58.145 29.630 0.00 0.00 0.00 4.52
173 174 8.296713 GTCTGTTTATATGTTTGAAAAGAGGCA 58.703 33.333 0.00 0.00 29.94 4.75
183 184 8.932791 ACGAGTTAAGGTCTGTTTATATGTTTG 58.067 33.333 0.00 0.00 0.00 2.93
188 189 8.098912 ACCAAACGAGTTAAGGTCTGTTTATAT 58.901 33.333 7.06 0.00 0.00 0.86
197 198 6.586082 TCGTATTAACCAAACGAGTTAAGGTC 59.414 38.462 11.64 1.85 41.57 3.85
211 212 3.340034 CTTGCCCAAGTCGTATTAACCA 58.660 45.455 0.00 0.00 33.87 3.67
212 213 2.096980 GCTTGCCCAAGTCGTATTAACC 59.903 50.000 9.53 0.00 40.45 2.85
220 221 0.385390 AAAGTTGCTTGCCCAAGTCG 59.615 50.000 9.53 0.00 40.45 4.18
221 222 3.068165 ACTTAAAGTTGCTTGCCCAAGTC 59.932 43.478 9.53 3.42 40.45 3.01
222 223 3.031013 ACTTAAAGTTGCTTGCCCAAGT 58.969 40.909 9.53 0.00 40.45 3.16
237 238 6.945435 TGGGAAATGCATGAGTAGAACTTAAA 59.055 34.615 0.00 0.00 0.00 1.52
240 241 4.922206 TGGGAAATGCATGAGTAGAACTT 58.078 39.130 0.00 0.00 0.00 2.66
248 249 5.533528 TCAGTTATGATGGGAAATGCATGAG 59.466 40.000 0.00 0.00 0.00 2.90
254 255 6.513806 TTGTGTCAGTTATGATGGGAAATG 57.486 37.500 0.00 0.00 37.87 2.32
257 258 5.009631 CCTTTGTGTCAGTTATGATGGGAA 58.990 41.667 0.00 0.00 37.87 3.97
259 260 4.335416 ACCTTTGTGTCAGTTATGATGGG 58.665 43.478 0.00 0.00 37.87 4.00
260 261 5.248640 AGACCTTTGTGTCAGTTATGATGG 58.751 41.667 0.00 0.00 37.87 3.51
262 263 6.212388 AGAGAGACCTTTGTGTCAGTTATGAT 59.788 38.462 0.00 0.00 37.24 2.45
263 264 5.540337 AGAGAGACCTTTGTGTCAGTTATGA 59.460 40.000 0.00 0.00 37.24 2.15
265 266 7.233757 AGTTAGAGAGACCTTTGTGTCAGTTAT 59.766 37.037 0.00 0.00 37.24 1.89
266 267 6.550108 AGTTAGAGAGACCTTTGTGTCAGTTA 59.450 38.462 0.00 0.00 37.24 2.24
267 268 5.364157 AGTTAGAGAGACCTTTGTGTCAGTT 59.636 40.000 0.00 0.00 37.24 3.16
268 269 4.896482 AGTTAGAGAGACCTTTGTGTCAGT 59.104 41.667 0.00 0.00 37.24 3.41
269 270 5.461032 AGTTAGAGAGACCTTTGTGTCAG 57.539 43.478 0.00 0.00 37.24 3.51
271 272 6.311690 GCAATAGTTAGAGAGACCTTTGTGTC 59.688 42.308 0.00 0.00 35.07 3.67
333 338 3.194719 GGTGAGTCCCGACTACCG 58.805 66.667 0.00 0.00 42.66 4.02
346 379 4.426736 ACTAAGAAAACGAAAGGGGTGA 57.573 40.909 0.00 0.00 0.00 4.02
423 456 0.901827 TGCGTCATCACCAGTACCAT 59.098 50.000 0.00 0.00 0.00 3.55
439 472 4.452455 AGTCTCTTTGTTTAGGTTGATGCG 59.548 41.667 0.00 0.00 0.00 4.73
450 483 3.933861 ACCCTCACAGTCTCTTTGTTT 57.066 42.857 0.00 0.00 0.00 2.83
451 484 4.804261 GCATACCCTCACAGTCTCTTTGTT 60.804 45.833 0.00 0.00 0.00 2.83
463 496 4.814234 TCGTTTGATTATGCATACCCTCAC 59.186 41.667 5.74 0.52 0.00 3.51
469 502 7.240674 TGTGTTCTTCGTTTGATTATGCATAC 58.759 34.615 5.74 0.00 0.00 2.39
470 503 7.371126 TGTGTTCTTCGTTTGATTATGCATA 57.629 32.000 1.16 1.16 0.00 3.14
472 505 5.681337 TGTGTTCTTCGTTTGATTATGCA 57.319 34.783 0.00 0.00 0.00 3.96
478 511 9.787532 CCATAATATTTGTGTTCTTCGTTTGAT 57.212 29.630 0.00 0.00 0.00 2.57
479 512 8.788806 ACCATAATATTTGTGTTCTTCGTTTGA 58.211 29.630 0.00 0.00 0.00 2.69
480 513 8.964420 ACCATAATATTTGTGTTCTTCGTTTG 57.036 30.769 0.00 0.00 0.00 2.93
481 514 9.620660 GAACCATAATATTTGTGTTCTTCGTTT 57.379 29.630 12.66 0.00 0.00 3.60
493 528 6.877236 AGCAAACCTGGAACCATAATATTTG 58.123 36.000 0.00 0.00 0.00 2.32
497 532 8.058847 AGATTTAGCAAACCTGGAACCATAATA 58.941 33.333 0.00 0.00 0.00 0.98
507 542 2.678336 GACCGAGATTTAGCAAACCTGG 59.322 50.000 0.00 0.00 0.00 4.45
508 543 2.348666 CGACCGAGATTTAGCAAACCTG 59.651 50.000 0.00 0.00 0.00 4.00
509 544 2.232941 TCGACCGAGATTTAGCAAACCT 59.767 45.455 0.00 0.00 0.00 3.50
512 547 3.057104 TCAGTCGACCGAGATTTAGCAAA 60.057 43.478 13.01 0.00 0.00 3.68
517 552 3.607741 AGTCTCAGTCGACCGAGATTTA 58.392 45.455 29.03 8.97 40.27 1.40
518 553 2.438411 AGTCTCAGTCGACCGAGATTT 58.562 47.619 29.03 19.45 40.27 2.17
525 560 0.592148 ACGTCAAGTCTCAGTCGACC 59.408 55.000 13.01 0.00 34.46 4.79
526 561 3.743567 ATACGTCAAGTCTCAGTCGAC 57.256 47.619 7.70 7.70 0.00 4.20
527 562 6.128090 ACAAATATACGTCAAGTCTCAGTCGA 60.128 38.462 0.00 0.00 0.00 4.20
528 563 6.021390 CACAAATATACGTCAAGTCTCAGTCG 60.021 42.308 0.00 0.00 0.00 4.18
529 564 7.027760 TCACAAATATACGTCAAGTCTCAGTC 58.972 38.462 0.00 0.00 0.00 3.51
530 565 6.920817 TCACAAATATACGTCAAGTCTCAGT 58.079 36.000 0.00 0.00 0.00 3.41
531 566 6.473778 CCTCACAAATATACGTCAAGTCTCAG 59.526 42.308 0.00 0.00 0.00 3.35
532 567 6.071560 ACCTCACAAATATACGTCAAGTCTCA 60.072 38.462 0.00 0.00 0.00 3.27
533 568 6.331061 ACCTCACAAATATACGTCAAGTCTC 58.669 40.000 0.00 0.00 0.00 3.36
534 569 6.153000 AGACCTCACAAATATACGTCAAGTCT 59.847 38.462 0.00 0.00 0.00 3.24
535 570 6.331061 AGACCTCACAAATATACGTCAAGTC 58.669 40.000 0.00 0.00 0.00 3.01
536 571 6.282199 AGACCTCACAAATATACGTCAAGT 57.718 37.500 0.00 0.00 0.00 3.16
537 572 7.758076 TGTTAGACCTCACAAATATACGTCAAG 59.242 37.037 0.00 0.00 0.00 3.02
538 573 7.604549 TGTTAGACCTCACAAATATACGTCAA 58.395 34.615 0.00 0.00 0.00 3.18
539 574 7.160547 TGTTAGACCTCACAAATATACGTCA 57.839 36.000 0.00 0.00 0.00 4.35
540 575 7.919091 TCATGTTAGACCTCACAAATATACGTC 59.081 37.037 0.00 0.00 0.00 4.34
541 576 7.778083 TCATGTTAGACCTCACAAATATACGT 58.222 34.615 0.00 0.00 0.00 3.57
542 577 8.642908 TTCATGTTAGACCTCACAAATATACG 57.357 34.615 0.00 0.00 0.00 3.06
543 578 9.817809 TCTTCATGTTAGACCTCACAAATATAC 57.182 33.333 0.00 0.00 0.00 1.47
550 585 5.481824 ACAGATCTTCATGTTAGACCTCACA 59.518 40.000 0.00 0.00 0.00 3.58
551 586 5.809562 CACAGATCTTCATGTTAGACCTCAC 59.190 44.000 0.00 0.00 0.00 3.51
614 649 9.778741 AACAAAATATAAGTCTCAGTCAAGTGA 57.221 29.630 0.00 0.00 0.00 3.41
631 666 7.497249 GTGGCTAGATCTCACTCAACAAAATAT 59.503 37.037 0.00 0.00 0.00 1.28
632 667 6.818644 GTGGCTAGATCTCACTCAACAAAATA 59.181 38.462 0.00 0.00 0.00 1.40
633 668 5.645497 GTGGCTAGATCTCACTCAACAAAAT 59.355 40.000 0.00 0.00 0.00 1.82
635 670 4.040339 TGTGGCTAGATCTCACTCAACAAA 59.960 41.667 12.69 0.00 33.04 2.83
636 671 3.578282 TGTGGCTAGATCTCACTCAACAA 59.422 43.478 12.69 0.00 33.04 2.83
637 672 3.056536 GTGTGGCTAGATCTCACTCAACA 60.057 47.826 12.69 3.93 33.04 3.33
638 673 3.516615 GTGTGGCTAGATCTCACTCAAC 58.483 50.000 12.69 1.86 33.04 3.18
639 674 2.497675 GGTGTGGCTAGATCTCACTCAA 59.502 50.000 12.69 0.00 33.04 3.02
641 676 2.383855 AGGTGTGGCTAGATCTCACTC 58.616 52.381 12.69 9.56 33.04 3.51
642 677 2.541233 AGGTGTGGCTAGATCTCACT 57.459 50.000 12.69 0.00 33.04 3.41
645 680 4.636249 CCATAAAGGTGTGGCTAGATCTC 58.364 47.826 0.00 0.00 0.00 2.75
646 681 4.696479 CCATAAAGGTGTGGCTAGATCT 57.304 45.455 0.00 0.00 0.00 2.75
687 722 9.667107 AGACAACAAGATATAAAAAGATCGGAA 57.333 29.630 0.00 0.00 0.00 4.30
688 723 9.667107 AAGACAACAAGATATAAAAAGATCGGA 57.333 29.630 0.00 0.00 0.00 4.55
702 737 9.561069 AACACAGTATTAGAAAGACAACAAGAT 57.439 29.630 0.00 0.00 0.00 2.40
703 738 8.958119 AACACAGTATTAGAAAGACAACAAGA 57.042 30.769 0.00 0.00 0.00 3.02
705 740 9.826574 AGTAACACAGTATTAGAAAGACAACAA 57.173 29.630 0.00 0.00 0.00 2.83
706 741 9.826574 AAGTAACACAGTATTAGAAAGACAACA 57.173 29.630 0.00 0.00 0.00 3.33
788 824 5.752650 TCCAAGAATACTCGACTCTCCTAA 58.247 41.667 0.00 0.00 0.00 2.69
789 825 5.130643 TCTCCAAGAATACTCGACTCTCCTA 59.869 44.000 0.00 0.00 0.00 2.94
791 827 4.200874 TCTCCAAGAATACTCGACTCTCC 58.799 47.826 0.00 0.00 0.00 3.71
794 830 4.512198 TCGATCTCCAAGAATACTCGACTC 59.488 45.833 0.00 0.00 30.08 3.36
796 849 4.815040 TCGATCTCCAAGAATACTCGAC 57.185 45.455 0.00 0.00 30.08 4.20
801 854 4.681942 CACGGATTCGATCTCCAAGAATAC 59.318 45.833 0.00 0.00 40.11 1.89
853 906 4.284178 AGGGAAAGGCAGTCGTAGTAATA 58.716 43.478 0.00 0.00 0.00 0.98
854 907 3.105283 AGGGAAAGGCAGTCGTAGTAAT 58.895 45.455 0.00 0.00 0.00 1.89
855 908 2.532843 AGGGAAAGGCAGTCGTAGTAA 58.467 47.619 0.00 0.00 0.00 2.24
856 909 2.226962 AGGGAAAGGCAGTCGTAGTA 57.773 50.000 0.00 0.00 0.00 1.82
857 910 1.275573 GAAGGGAAAGGCAGTCGTAGT 59.724 52.381 0.00 0.00 0.00 2.73
858 911 1.550976 AGAAGGGAAAGGCAGTCGTAG 59.449 52.381 0.00 0.00 0.00 3.51
859 912 1.640917 AGAAGGGAAAGGCAGTCGTA 58.359 50.000 0.00 0.00 0.00 3.43
860 913 0.765510 AAGAAGGGAAAGGCAGTCGT 59.234 50.000 0.00 0.00 0.00 4.34
861 914 1.443802 GAAGAAGGGAAAGGCAGTCG 58.556 55.000 0.00 0.00 0.00 4.18
862 915 1.073923 TGGAAGAAGGGAAAGGCAGTC 59.926 52.381 0.00 0.00 0.00 3.51
863 916 1.149101 TGGAAGAAGGGAAAGGCAGT 58.851 50.000 0.00 0.00 0.00 4.40
1495 1964 2.887568 GCGCACACGGATCTGAGG 60.888 66.667 9.00 2.40 40.57 3.86
1541 2011 1.035923 TTGGCAAATCGAAGGCAACA 58.964 45.000 16.93 1.56 44.04 3.33
1542 2012 3.883997 TTGGCAAATCGAAGGCAAC 57.116 47.368 16.93 0.01 44.04 4.17
1544 2014 1.531739 GGGTTGGCAAATCGAAGGCA 61.532 55.000 0.00 7.82 38.64 4.75
1545 2015 1.215382 GGGTTGGCAAATCGAAGGC 59.785 57.895 0.00 0.00 0.00 4.35
1546 2016 2.017049 CTAGGGTTGGCAAATCGAAGG 58.983 52.381 0.00 0.00 0.00 3.46
1549 2019 3.452990 TGTATCTAGGGTTGGCAAATCGA 59.547 43.478 0.00 0.00 0.00 3.59
1552 2022 5.363580 CCAAATGTATCTAGGGTTGGCAAAT 59.636 40.000 0.00 0.00 29.99 2.32
1589 2099 5.308825 AGTGTGAATCCTAAAGTGGTCAAG 58.691 41.667 0.00 0.00 0.00 3.02
1702 3096 7.905265 TGTCCATTGAACAATTATCAACCATT 58.095 30.769 7.73 0.00 39.43 3.16
1703 3097 7.396907 TCTGTCCATTGAACAATTATCAACCAT 59.603 33.333 7.73 0.00 39.43 3.55
1705 3099 7.156876 TCTGTCCATTGAACAATTATCAACC 57.843 36.000 7.73 0.23 39.43 3.77
1708 3102 8.812513 ATCTTCTGTCCATTGAACAATTATCA 57.187 30.769 0.00 0.00 0.00 2.15
1724 3254 7.333921 CCAATCTATCTGCCAATATCTTCTGTC 59.666 40.741 0.00 0.00 0.00 3.51
1729 3259 6.044754 TCCACCAATCTATCTGCCAATATCTT 59.955 38.462 0.00 0.00 0.00 2.40
1770 3302 2.472816 CACAAATTGAACACAGGCCAC 58.527 47.619 5.01 0.00 0.00 5.01
1789 3321 6.532826 TGCCATAATCTACATGAAGTATGCA 58.467 36.000 0.00 0.00 40.59 3.96
1793 3325 7.559335 AGGATGCCATAATCTACATGAAGTA 57.441 36.000 0.00 0.00 0.00 2.24
2003 4349 4.734398 AAAATGTGGAAGCAAGTCAACA 57.266 36.364 0.00 0.00 35.90 3.33
2031 4379 5.772672 TCCCAGCATTTTAAAGAGTAGCAAA 59.227 36.000 0.00 0.00 0.00 3.68
2249 4765 5.766150 AAAACGACACAGGATCAAATCAA 57.234 34.783 0.00 0.00 0.00 2.57
2286 4808 0.110486 AGTGTTCAATCTTGGCCGGT 59.890 50.000 1.90 0.00 0.00 5.28
2424 5123 6.540189 GTCCTGAACATAACAGAACATAGCAT 59.460 38.462 0.00 0.00 37.54 3.79
3125 5918 5.689383 TTCAGGTAGCAAATTCTTGTGTC 57.311 39.130 0.00 0.00 34.79 3.67
3499 6313 9.796120 TTTGTAAAATCAGAACTAAACAACTGG 57.204 29.630 0.00 0.00 0.00 4.00
3534 6352 7.016661 AGTCACAGATATTATTCCTAAGGGTGG 59.983 40.741 0.00 0.00 0.00 4.61
3938 6891 7.989741 AGAACTATGAATACAAGACCATCAAGG 59.010 37.037 0.00 0.00 45.67 3.61
3939 6892 8.954950 AGAACTATGAATACAAGACCATCAAG 57.045 34.615 0.00 0.00 0.00 3.02
3940 6893 9.166173 CAAGAACTATGAATACAAGACCATCAA 57.834 33.333 0.00 0.00 0.00 2.57
3941 6894 7.280876 GCAAGAACTATGAATACAAGACCATCA 59.719 37.037 0.00 0.00 0.00 3.07
3942 6895 7.280876 TGCAAGAACTATGAATACAAGACCATC 59.719 37.037 0.00 0.00 0.00 3.51
3943 6896 7.066284 GTGCAAGAACTATGAATACAAGACCAT 59.934 37.037 0.00 0.00 0.00 3.55
3944 6897 6.371548 GTGCAAGAACTATGAATACAAGACCA 59.628 38.462 0.00 0.00 0.00 4.02
3945 6898 6.595716 AGTGCAAGAACTATGAATACAAGACC 59.404 38.462 0.00 0.00 0.00 3.85
3996 6949 7.719778 AAAAGAAAAATGTTTGAGAGCCATC 57.280 32.000 0.00 0.00 0.00 3.51
4175 7143 9.173939 GATGCAAACGAAATATAATCCAAGAAG 57.826 33.333 0.00 0.00 0.00 2.85
4366 7457 3.499338 TGAGGCAATGAATTTCCTGTGT 58.501 40.909 0.00 0.00 0.00 3.72
4369 7460 4.643334 TGATCTGAGGCAATGAATTTCCTG 59.357 41.667 0.00 0.00 0.00 3.86
4723 9790 6.931281 CCTCATTTGTAGAAGTCAAAGTCTGA 59.069 38.462 0.00 0.00 38.02 3.27
4758 9825 9.747898 TGTAGGAAATAAAGCATCCTCTTTAAA 57.252 29.630 0.00 0.00 42.53 1.52
4761 9828 6.830838 CCTGTAGGAAATAAAGCATCCTCTTT 59.169 38.462 0.00 0.00 42.53 2.52
4784 9854 3.895232 AGAGTGTTAATCATGTCGCCT 57.105 42.857 0.00 0.00 0.00 5.52
4833 9906 3.924686 GCACGGGGATACAACGATATTAG 59.075 47.826 0.00 0.00 40.39 1.73
4841 9914 1.082117 CACGAGCACGGGGATACAAC 61.082 60.000 8.74 0.00 44.46 3.32
4851 9924 0.111266 GTGCAAACTACACGAGCACG 60.111 55.000 0.76 0.76 44.84 5.34
4858 9931 2.864343 AGACTGAACGTGCAAACTACAC 59.136 45.455 0.00 0.00 34.62 2.90
4938 10014 0.249405 CAGCCTCCAAAAGCGCAAAA 60.249 50.000 11.47 0.00 0.00 2.44
4948 10024 2.957402 AGACAAATCACAGCCTCCAA 57.043 45.000 0.00 0.00 0.00 3.53
5023 10100 9.720667 GGGAAAGTTTGAAATTCAATCAAAAAG 57.279 29.630 16.29 0.00 45.43 2.27
5039 10116 9.492973 AAAGTTCATCAAATATGGGAAAGTTTG 57.507 29.630 0.00 0.00 33.91 2.93
5184 10261 5.006552 GCTCAAATCAGATCTAGTTGTGCTC 59.993 44.000 20.74 0.00 36.36 4.26
5203 10280 7.552687 ACATCATCTTTATTTTAGACGGCTCAA 59.447 33.333 0.00 0.00 0.00 3.02
5264 10341 3.055094 TGGGATAGACCAAGAGCTGAAAC 60.055 47.826 0.00 0.00 41.20 2.78
5305 10382 9.735432 CTTACAAATAAGCCTCCGATGGGAGAA 62.735 44.444 24.24 7.77 45.23 2.87
5322 10399 8.265055 CCTTACAGGGAATCTGACTTACAAATA 58.735 37.037 0.00 0.00 46.18 1.40
5324 10401 6.472887 CCTTACAGGGAATCTGACTTACAAA 58.527 40.000 0.00 0.00 46.18 2.83
5325 10402 5.570844 GCCTTACAGGGAATCTGACTTACAA 60.571 44.000 0.00 0.00 46.18 2.41
5326 10403 4.081087 GCCTTACAGGGAATCTGACTTACA 60.081 45.833 0.00 0.00 46.18 2.41
5327 10404 4.443621 GCCTTACAGGGAATCTGACTTAC 58.556 47.826 0.00 0.00 46.18 2.34
5328 10405 3.132289 CGCCTTACAGGGAATCTGACTTA 59.868 47.826 0.00 0.00 46.18 2.24
5344 10430 2.089887 TTGTGGACTGCGACGCCTTA 62.090 55.000 18.69 0.00 0.00 2.69
5352 10438 5.046910 AGTCAAAATAATTGTGGACTGCG 57.953 39.130 0.00 0.00 34.57 5.18
5353 10439 6.446318 TGAAGTCAAAATAATTGTGGACTGC 58.554 36.000 0.00 0.00 35.90 4.40
5354 10440 9.480053 AATTGAAGTCAAAATAATTGTGGACTG 57.520 29.630 0.00 0.00 39.55 3.51
5357 10443 9.270640 CCAAATTGAAGTCAAAATAATTGTGGA 57.729 29.630 0.00 0.00 39.55 4.02
5358 10444 8.016801 GCCAAATTGAAGTCAAAATAATTGTGG 58.983 33.333 0.00 0.00 39.55 4.17
5359 10445 8.557864 TGCCAAATTGAAGTCAAAATAATTGTG 58.442 29.630 0.00 0.00 39.55 3.33
5360 10446 8.558700 GTGCCAAATTGAAGTCAAAATAATTGT 58.441 29.630 0.00 0.00 39.55 2.71
5361 10447 8.016801 GGTGCCAAATTGAAGTCAAAATAATTG 58.983 33.333 0.00 0.44 39.55 2.32
5362 10448 7.718753 TGGTGCCAAATTGAAGTCAAAATAATT 59.281 29.630 0.00 0.00 39.55 1.40
5363 10449 7.222872 TGGTGCCAAATTGAAGTCAAAATAAT 58.777 30.769 0.00 0.00 39.55 1.28
5364 10450 6.586344 TGGTGCCAAATTGAAGTCAAAATAA 58.414 32.000 0.00 0.00 39.55 1.40
5365 10451 6.166984 TGGTGCCAAATTGAAGTCAAAATA 57.833 33.333 0.00 0.00 39.55 1.40
5468 10558 9.685828 TGTTTTAGTTATTTCCTTGTGTAATGC 57.314 29.630 0.00 0.00 0.00 3.56
5503 10594 7.762588 TTTTCCCGTAGAATAAAAATGTGGA 57.237 32.000 0.00 0.00 33.44 4.02
5527 10619 6.478512 TTTGAAGATAGGTTTTGTGGCTTT 57.521 33.333 0.00 0.00 0.00 3.51
5575 10674 7.846644 TGCACAATTTTCTGAAGTCAAATTT 57.153 28.000 0.00 0.00 29.49 1.82
5580 10679 5.068855 TGGATTGCACAATTTTCTGAAGTCA 59.931 36.000 0.00 0.00 0.00 3.41
5581 10680 5.531634 TGGATTGCACAATTTTCTGAAGTC 58.468 37.500 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.