Multiple sequence alignment - TraesCS7D01G266300

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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 TraesCS7D01G266300 chr7D 100.000 6075 0 0 1001 7075 249368711 249374785 0.000000e+00 11219
1 TraesCS7D01G266300 chr7D 100.000 595 0 0 1 595 249367711 249368305 0.000000e+00 1099
2 TraesCS7D01G266300 chr7D 86.217 341 36 8 3000 3337 249370328 249370660 6.750000e-95 359
3 TraesCS7D01G266300 chr7D 86.217 341 36 8 2618 2950 249370710 249371047 6.750000e-95 359
4 TraesCS7D01G266300 chr7D 89.308 159 13 4 6614 6770 140786367 140786211 5.600000e-46 196
5 TraesCS7D01G266300 chr7D 89.172 157 11 3 6615 6767 135151732 135151886 2.600000e-44 191
6 TraesCS7D01G266300 chr7A 95.200 3375 72 12 1001 4319 271799864 271796524 0.000000e+00 5252
7 TraesCS7D01G266300 chr7A 95.307 2088 45 17 4317 6374 271796497 271794433 0.000000e+00 3264
8 TraesCS7D01G266300 chr7A 91.422 408 19 9 202 595 271800398 271799993 4.830000e-151 545
9 TraesCS7D01G266300 chr7A 86.047 344 38 7 2999 3337 271798204 271797866 1.880000e-95 361
10 TraesCS7D01G266300 chr7A 85.561 187 19 5 6774 6960 271794061 271793883 9.370000e-44 189
11 TraesCS7D01G266300 chr7A 89.011 91 0 1 6995 7075 271793884 271793794 3.490000e-18 104
12 TraesCS7D01G266300 chr7B 93.718 1958 79 13 4451 6377 226330401 226332345 0.000000e+00 2894
13 TraesCS7D01G266300 chr7B 91.232 1015 39 11 3314 4319 226328547 226329520 0.000000e+00 1336
14 TraesCS7D01G266300 chr7B 88.089 1125 78 20 1001 2106 226326810 226327897 0.000000e+00 1284
15 TraesCS7D01G266300 chr7B 94.337 671 29 6 2618 3281 226327884 226328552 0.000000e+00 1020
16 TraesCS7D01G266300 chr7B 92.066 605 23 8 1 590 226326094 226326688 0.000000e+00 828
17 TraesCS7D01G266300 chr7B 84.039 307 21 12 6774 7075 226332721 226333004 3.250000e-68 270
18 TraesCS7D01G266300 chr7B 89.677 155 11 3 6615 6765 463039140 463038987 7.240000e-45 193
19 TraesCS7D01G266300 chr3B 91.075 493 43 1 2125 2616 335110355 335110847 0.000000e+00 665
20 TraesCS7D01G266300 chr4A 88.330 497 57 1 2125 2620 352271993 352272489 4.720000e-166 595
21 TraesCS7D01G266300 chr4A 88.438 493 56 1 2128 2619 255311413 255310921 1.700000e-165 593
22 TraesCS7D01G266300 chr4A 85.325 477 65 3 2121 2592 352512571 352513047 8.250000e-134 488
23 TraesCS7D01G266300 chr3D 88.330 497 56 2 2124 2619 104804505 104804010 4.720000e-166 595
24 TraesCS7D01G266300 chr3D 86.869 198 25 1 1 197 431454070 431453873 3.320000e-53 220
25 TraesCS7D01G266300 chr2D 91.467 375 29 2 2246 2619 463876198 463875826 4.890000e-141 512
26 TraesCS7D01G266300 chr2D 88.384 198 22 1 1 197 245594230 245594033 3.300000e-58 237
27 TraesCS7D01G266300 chr2D 87.374 198 24 1 1 197 352185690 352185493 7.140000e-55 226
28 TraesCS7D01G266300 chr2D 87.374 198 23 2 1 197 376828047 376828243 7.140000e-55 226
29 TraesCS7D01G266300 chr4D 85.535 477 64 5 2121 2592 208420868 208421344 1.770000e-135 494
30 TraesCS7D01G266300 chr4D 87.310 197 24 1 2 197 473420144 473419948 2.570000e-54 224
31 TraesCS7D01G266300 chr4B 85.000 480 65 7 2121 2595 240211054 240211531 1.380000e-131 481
32 TraesCS7D01G266300 chr2B 88.000 200 19 3 1 197 302036807 302036610 1.530000e-56 231
33 TraesCS7D01G266300 chr5D 87.374 198 24 1 1 197 364407020 364406823 7.140000e-55 226
34 TraesCS7D01G266300 chr5D 87.310 197 23 2 2 197 366099953 366099758 2.570000e-54 224
35 TraesCS7D01G266300 chr1D 87.374 198 24 1 1 197 367923937 367923740 7.140000e-55 226
36 TraesCS7D01G266300 chr6B 91.667 156 10 3 6615 6767 41607152 41606997 5.560000e-51 213
37 TraesCS7D01G266300 chr1B 90.850 153 12 2 6616 6767 31175537 31175688 3.350000e-48 204
38 TraesCS7D01G266300 chr1B 88.961 154 16 1 6615 6767 12095807 12095960 9.370000e-44 189
39 TraesCS7D01G266300 chrUn 88.961 154 16 1 6615 6767 391378856 391379009 9.370000e-44 189
40 TraesCS7D01G266300 chrUn 88.961 154 16 1 6615 6767 391465443 391465596 9.370000e-44 189
41 TraesCS7D01G266300 chr2A 88.235 153 17 1 6615 6766 722814484 722814332 1.570000e-41 182


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 TraesCS7D01G266300 chr7D 249367711 249374785 7074 False 6159.000000 11219 100.000000 1 7075 2 chr7D.!!$F2 7074
1 TraesCS7D01G266300 chr7D 249370328 249371047 719 False 359.000000 359 86.217000 2618 3337 2 chr7D.!!$F3 719
2 TraesCS7D01G266300 chr7A 271793794 271800398 6604 True 1619.166667 5252 90.424667 202 7075 6 chr7A.!!$R1 6873
3 TraesCS7D01G266300 chr7B 226326094 226333004 6910 False 1272.000000 2894 90.580167 1 7075 6 chr7B.!!$F1 7074


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
190 191 0.106619 TTAGGAGAGTCTCGAGGGGC 60.107 60.000 13.56 3.54 0.00 5.80 F
1212 1231 0.250124 TTTCAACCGGATCTGTGCGT 60.250 50.000 9.46 0.00 37.49 5.24 F
1682 1721 0.321298 GCTGTACACGGGTTGGATGT 60.321 55.000 0.00 0.00 0.00 3.06 F
2529 2606 0.107703 GTCCACTGATCGGCCAATGA 60.108 55.000 2.24 0.00 0.00 2.57 F
3688 3770 1.544246 GCCTCGTGCCTTATGGTTTTT 59.456 47.619 0.00 0.00 35.27 1.94 F
4338 5216 1.406860 GCCCTTTCCTTGGTTTGCCA 61.407 55.000 0.00 0.00 44.38 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1704 0.035598 CCACATCCAACCCGTGTACA 59.964 55.0 0.00 0.00 0.00 2.90 R
2511 2588 0.107703 GTCATTGGCCGATCAGTGGA 60.108 55.0 1.06 0.00 0.00 4.02 R
2589 2666 0.668535 AAAACGCAAAGGACCTCTGC 59.331 50.0 9.98 9.98 0.00 4.26 R
3693 3775 1.457346 ACTGTAAGGATGCAAGCAGC 58.543 50.0 0.94 0.94 41.23 5.25 R
5274 6160 0.323360 GGGCCTGCAGTATTTGGACA 60.323 55.0 13.81 0.00 0.00 4.02 R
6294 7208 0.107703 ATGCGGGGATATGGCGTATG 60.108 55.0 3.45 0.00 0.00 2.39 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
21 22 0.857675 AAGGTTGGTGTAAAGGCCCT 59.142 50.000 0.00 0.00 0.00 5.19
24 25 0.958876 GTTGGTGTAAAGGCCCTCCG 60.959 60.000 0.00 0.00 37.47 4.63
30 31 0.539986 GTAAAGGCCCTCCGTGATCA 59.460 55.000 0.00 0.00 37.47 2.92
35 36 0.181350 GGCCCTCCGTGATCAAATCT 59.819 55.000 0.00 0.00 0.00 2.40
44 45 0.469917 TGATCAAATCTCCCTCCGGC 59.530 55.000 0.00 0.00 0.00 6.13
71 72 0.611896 CGGAAAAGGCCCCAAGATGT 60.612 55.000 0.00 0.00 0.00 3.06
108 109 1.008995 GCTTGCGGCGAAAGAAACA 60.009 52.632 31.06 4.21 0.00 2.83
127 128 3.247162 ACATATTTTTGGTGTGCCCCTT 58.753 40.909 0.00 0.00 0.00 3.95
128 129 3.007831 ACATATTTTTGGTGTGCCCCTTG 59.992 43.478 0.00 0.00 0.00 3.61
130 131 0.618968 TTTTTGGTGTGCCCCTTGGT 60.619 50.000 0.00 0.00 0.00 3.67
134 135 0.621609 TGGTGTGCCCCTTGGTATAC 59.378 55.000 0.00 0.00 37.58 1.47
135 136 0.463116 GGTGTGCCCCTTGGTATACG 60.463 60.000 0.00 0.00 38.89 3.06
136 137 0.463116 GTGTGCCCCTTGGTATACGG 60.463 60.000 0.00 0.00 29.42 4.02
137 138 1.147600 GTGCCCCTTGGTATACGGG 59.852 63.158 8.75 8.75 38.70 5.28
156 157 4.651962 ACGGGGAATTTTTGGGTATTATGG 59.348 41.667 0.00 0.00 0.00 2.74
190 191 0.106619 TTAGGAGAGTCTCGAGGGGC 60.107 60.000 13.56 3.54 0.00 5.80
194 195 3.462678 GAGTCTCGAGGGGCCCAC 61.463 72.222 27.72 19.04 0.00 4.61
211 212 4.379652 GCCCACAAACATTTTTCTCACAT 58.620 39.130 0.00 0.00 0.00 3.21
314 318 6.580788 CAGAGAAGAAGAAGAATATGCTCCA 58.419 40.000 0.00 0.00 0.00 3.86
315 319 7.046652 CAGAGAAGAAGAAGAATATGCTCCAA 58.953 38.462 0.00 0.00 0.00 3.53
1212 1231 0.250124 TTTCAACCGGATCTGTGCGT 60.250 50.000 9.46 0.00 37.49 5.24
1299 1332 2.265073 AAAAATGGGCGATCGGCGTG 62.265 55.000 31.80 0.00 44.92 5.34
1310 1343 0.521291 ATCGGCGTGGTTGAATTGTG 59.479 50.000 6.85 0.00 0.00 3.33
1483 1516 1.385743 CCGATTCGAACAGTGTTCGTC 59.614 52.381 41.51 33.89 42.09 4.20
1492 1525 1.068055 ACAGTGTTCGTCGATGGTACC 60.068 52.381 4.43 4.43 0.00 3.34
1582 1621 6.761714 ACATCGTTTTAGGCTTCTAGTTATGG 59.238 38.462 0.00 0.00 0.00 2.74
1583 1622 5.114081 TCGTTTTAGGCTTCTAGTTATGGC 58.886 41.667 0.00 0.00 0.00 4.40
1665 1704 2.766828 GGCTATATAATCCCTGGTCGCT 59.233 50.000 0.00 0.00 0.00 4.93
1682 1721 0.321298 GCTGTACACGGGTTGGATGT 60.321 55.000 0.00 0.00 0.00 3.06
1695 1734 0.888736 TGGATGTGGTGCTTCGGTTG 60.889 55.000 0.00 0.00 0.00 3.77
1697 1736 2.513065 GATGTGGTGCTTCGGTTGCG 62.513 60.000 0.00 0.00 0.00 4.85
1768 1813 1.199097 GTGGTGGTTGCCTGAATTACG 59.801 52.381 0.00 0.00 0.00 3.18
1781 1826 5.049680 GCCTGAATTACGAGTGTTCTTTGAA 60.050 40.000 0.00 0.00 0.00 2.69
1802 1847 0.663153 GTTTTGTCGCTGCTTGGTCT 59.337 50.000 0.00 0.00 0.00 3.85
1903 1948 8.938801 TTATGATGTATTAACCTTGGCATGAT 57.061 30.769 0.00 0.00 0.00 2.45
2188 2257 1.963515 AGAAACAATCCAACACCTGCC 59.036 47.619 0.00 0.00 0.00 4.85
2192 2261 1.077265 AATCCAACACCTGCCCCTG 59.923 57.895 0.00 0.00 0.00 4.45
2208 2277 3.249189 TGACCTGCCCCTTCGCTT 61.249 61.111 0.00 0.00 0.00 4.68
2243 2312 1.376424 CATCCTGTCTTGGCTGCGT 60.376 57.895 0.00 0.00 0.00 5.24
2311 2380 1.845266 CTGCGAGTGAACGAGCATAT 58.155 50.000 6.39 0.00 39.02 1.78
2314 2383 0.855349 CGAGTGAACGAGCATATGCC 59.145 55.000 23.96 14.15 43.38 4.40
2317 2386 1.069204 AGTGAACGAGCATATGCCGAT 59.931 47.619 31.64 24.62 43.38 4.18
2407 2476 3.258498 CGTCTTTGACAATGCGACG 57.742 52.632 15.79 15.79 40.92 5.12
2501 2578 4.519610 GGGTTGTTCTGCCCACAT 57.480 55.556 0.00 0.00 44.23 3.21
2529 2606 0.107703 GTCCACTGATCGGCCAATGA 60.108 55.000 2.24 0.00 0.00 2.57
2576 2653 5.440610 AGGCTTGTTCTCTCTTTCTTTTCA 58.559 37.500 0.00 0.00 0.00 2.69
2589 2666 9.236691 TCTCTTTCTTTTCAATGAAATGAAACG 57.763 29.630 29.61 25.53 46.06 3.60
2616 2693 3.289076 GTCCTTTGCGTTTTCTCGAAAG 58.711 45.455 0.00 0.00 32.99 2.62
3567 3649 6.737254 ATACACATCTAAGGGTTCAAAACG 57.263 37.500 0.00 0.00 0.00 3.60
3681 3763 2.899900 TCATATGAGCCTCGTGCCTTAT 59.100 45.455 0.00 0.00 42.71 1.73
3688 3770 1.544246 GCCTCGTGCCTTATGGTTTTT 59.456 47.619 0.00 0.00 35.27 1.94
3689 3771 2.750712 GCCTCGTGCCTTATGGTTTTTA 59.249 45.455 0.00 0.00 35.27 1.52
3690 3772 3.380320 GCCTCGTGCCTTATGGTTTTTAT 59.620 43.478 0.00 0.00 35.27 1.40
3691 3773 4.733523 GCCTCGTGCCTTATGGTTTTTATG 60.734 45.833 0.00 0.00 35.27 1.90
3692 3774 4.398044 CCTCGTGCCTTATGGTTTTTATGT 59.602 41.667 0.00 0.00 35.27 2.29
3693 3775 5.303747 TCGTGCCTTATGGTTTTTATGTG 57.696 39.130 0.00 0.00 35.27 3.21
3694 3776 3.857093 CGTGCCTTATGGTTTTTATGTGC 59.143 43.478 0.00 0.00 35.27 4.57
3695 3777 4.380444 CGTGCCTTATGGTTTTTATGTGCT 60.380 41.667 0.00 0.00 35.27 4.40
3696 3778 4.864247 GTGCCTTATGGTTTTTATGTGCTG 59.136 41.667 0.00 0.00 35.27 4.41
3697 3779 3.865164 GCCTTATGGTTTTTATGTGCTGC 59.135 43.478 0.00 0.00 35.27 5.25
3698 3780 4.381932 GCCTTATGGTTTTTATGTGCTGCT 60.382 41.667 0.00 0.00 35.27 4.24
3699 3781 5.723295 CCTTATGGTTTTTATGTGCTGCTT 58.277 37.500 0.00 0.00 0.00 3.91
3700 3782 5.577945 CCTTATGGTTTTTATGTGCTGCTTG 59.422 40.000 0.00 0.00 0.00 4.01
3701 3783 2.753296 TGGTTTTTATGTGCTGCTTGC 58.247 42.857 0.00 0.00 43.25 4.01
3712 3794 1.457346 GCTGCTTGCATCCTTACAGT 58.543 50.000 0.00 0.00 42.31 3.55
3713 3795 1.815003 GCTGCTTGCATCCTTACAGTT 59.185 47.619 0.00 0.00 42.31 3.16
3714 3796 2.229784 GCTGCTTGCATCCTTACAGTTT 59.770 45.455 0.00 0.00 42.31 2.66
3715 3797 3.305608 GCTGCTTGCATCCTTACAGTTTT 60.306 43.478 0.00 0.00 42.31 2.43
3772 3854 4.067192 AGGCATTTTCAGTTTTGGAATGC 58.933 39.130 10.05 10.05 44.41 3.56
3774 3856 3.814283 GCATTTTCAGTTTTGGAATGCCA 59.186 39.130 7.86 0.00 42.20 4.92
3976 4059 9.780413 GGTTAATGATCTAAAAGCAAGAAAGAG 57.220 33.333 0.00 0.00 0.00 2.85
4334 5212 3.582164 TGTATTGCCCTTTCCTTGGTTT 58.418 40.909 0.00 0.00 0.00 3.27
4338 5216 1.406860 GCCCTTTCCTTGGTTTGCCA 61.407 55.000 0.00 0.00 44.38 4.92
4436 5314 6.261826 ACACTTCATCAGGTTCTTCAAAGAAG 59.738 38.462 5.45 0.39 45.01 2.85
5526 6412 2.753029 GGCTGAGGTTGGAGTGCT 59.247 61.111 0.00 0.00 0.00 4.40
5754 6640 3.811807 CTCCCGGGGAGCGGATACT 62.812 68.421 29.32 0.00 43.29 2.12
6083 6981 1.269206 ACTCATTGCCGCAGTTGTTTG 60.269 47.619 0.00 0.00 0.00 2.93
6104 7002 1.686587 TCTCAAGTCGTGCTTTCCTGA 59.313 47.619 0.00 0.00 34.69 3.86
6134 7038 0.318360 GGTTTTGCTACCGGTTGTGC 60.318 55.000 15.04 16.09 0.00 4.57
6188 7092 0.836400 ATCACCGGACACAGGAGGTT 60.836 55.000 9.46 0.00 34.25 3.50
6206 7120 0.461870 TTGATCGGGACTTGATGGCG 60.462 55.000 0.00 0.00 0.00 5.69
6223 7137 3.244582 TGGCGACTAATATGGGGTACAT 58.755 45.455 0.00 0.00 43.68 2.29
6240 7154 5.279809 GGGTACATGACTCCTCAAACTGTAA 60.280 44.000 0.00 0.00 0.00 2.41
6243 7157 6.808008 ACATGACTCCTCAAACTGTAATTG 57.192 37.500 0.00 0.00 0.00 2.32
6289 7203 8.884124 TGATTGGATGAACTCTCCTTAAAAAT 57.116 30.769 0.00 0.00 33.69 1.82
6290 7204 8.742777 TGATTGGATGAACTCTCCTTAAAAATG 58.257 33.333 0.00 0.00 33.69 2.32
6291 7205 6.515272 TGGATGAACTCTCCTTAAAAATGC 57.485 37.500 0.00 0.00 33.69 3.56
6292 7206 5.418840 TGGATGAACTCTCCTTAAAAATGCC 59.581 40.000 0.00 0.00 33.69 4.40
6293 7207 5.163509 GGATGAACTCTCCTTAAAAATGCCC 60.164 44.000 0.00 0.00 0.00 5.36
6294 7208 4.086457 TGAACTCTCCTTAAAAATGCCCC 58.914 43.478 0.00 0.00 0.00 5.80
6295 7209 3.825908 ACTCTCCTTAAAAATGCCCCA 57.174 42.857 0.00 0.00 0.00 4.96
6296 7210 4.337264 ACTCTCCTTAAAAATGCCCCAT 57.663 40.909 0.00 0.00 0.00 4.00
6299 7213 4.204012 TCTCCTTAAAAATGCCCCATACG 58.796 43.478 0.00 0.00 0.00 3.06
6305 7219 2.603075 AAATGCCCCATACGCCATAT 57.397 45.000 0.00 0.00 0.00 1.78
6321 7235 3.071602 GCCATATCCCCGCATATAGATGT 59.928 47.826 0.00 0.00 35.30 3.06
6334 7248 2.904697 TAGATGTGGAGATGCAGCTG 57.095 50.000 10.40 10.11 33.18 4.24
6354 7271 4.286032 GCTGTACCTATAATCCCATCACCA 59.714 45.833 0.00 0.00 0.00 4.17
6378 7295 4.115199 GAGCCAACCGCCTGGGAT 62.115 66.667 0.00 0.00 40.75 3.85
6379 7296 3.645268 GAGCCAACCGCCTGGGATT 62.645 63.158 0.00 0.00 40.75 3.01
6380 7297 2.679996 GCCAACCGCCTGGGATTT 60.680 61.111 0.00 0.00 40.75 2.17
6381 7298 2.710902 GCCAACCGCCTGGGATTTC 61.711 63.158 0.00 0.00 40.75 2.17
6382 7299 1.304052 CCAACCGCCTGGGATTTCA 60.304 57.895 0.00 0.00 40.75 2.69
6384 7301 1.674322 AACCGCCTGGGATTTCACG 60.674 57.895 0.00 0.00 40.75 4.35
6385 7302 2.824041 CCGCCTGGGATTTCACGG 60.824 66.667 0.00 0.00 38.47 4.94
6386 7303 2.046314 CGCCTGGGATTTCACGGT 60.046 61.111 0.00 0.00 0.00 4.83
6387 7304 2.106683 CGCCTGGGATTTCACGGTC 61.107 63.158 0.00 0.00 0.00 4.79
6388 7305 1.299976 GCCTGGGATTTCACGGTCT 59.700 57.895 0.00 0.00 0.00 3.85
6389 7306 0.539986 GCCTGGGATTTCACGGTCTA 59.460 55.000 0.00 0.00 0.00 2.59
6390 7307 1.473434 GCCTGGGATTTCACGGTCTAG 60.473 57.143 0.00 0.00 0.00 2.43
6391 7308 1.473434 CCTGGGATTTCACGGTCTAGC 60.473 57.143 0.00 0.00 0.00 3.42
6392 7309 0.174845 TGGGATTTCACGGTCTAGCG 59.825 55.000 0.00 0.00 0.00 4.26
6393 7310 1.152383 GGGATTTCACGGTCTAGCGC 61.152 60.000 0.00 0.00 0.00 5.92
6394 7311 1.480219 GGATTTCACGGTCTAGCGCG 61.480 60.000 0.00 0.00 0.00 6.86
6395 7312 2.078958 GATTTCACGGTCTAGCGCGC 62.079 60.000 26.66 26.66 0.00 6.86
6396 7313 4.789075 TTCACGGTCTAGCGCGCC 62.789 66.667 30.33 12.61 0.00 6.53
6418 7335 4.473520 CCATGACGGGCCGAAGCT 62.474 66.667 35.78 10.44 39.73 3.74
6419 7336 2.892425 CATGACGGGCCGAAGCTC 60.892 66.667 35.78 20.32 39.73 4.09
6448 7365 3.095911 CGATCACGCTGCTGCATT 58.904 55.556 16.29 0.00 39.64 3.56
6451 7368 0.169672 GATCACGCTGCTGCATTGTT 59.830 50.000 16.29 6.89 39.64 2.83
6454 7371 2.195567 ACGCTGCTGCATTGTTGGT 61.196 52.632 16.29 0.37 39.64 3.67
6460 7377 1.005867 CTGCATTGTTGGTGGCCAC 60.006 57.895 28.57 28.57 30.78 5.01
6462 7379 2.855514 GCATTGTTGGTGGCCACGT 61.856 57.895 29.08 8.13 30.78 4.49
6463 7380 1.007502 CATTGTTGGTGGCCACGTG 60.008 57.895 29.08 15.80 30.78 4.49
6522 7439 1.064758 TCCATTGATACCACACTGCCC 60.065 52.381 0.00 0.00 0.00 5.36
6543 7460 2.284190 GCCTTCTAGAGCAACACATCC 58.716 52.381 0.00 0.00 0.00 3.51
6544 7461 2.093235 GCCTTCTAGAGCAACACATCCT 60.093 50.000 0.00 0.00 0.00 3.24
6584 7501 5.615925 ATTAAGAGAGACCCTAAACGCAT 57.384 39.130 0.00 0.00 0.00 4.73
6616 7696 3.685435 GGGAACCGGTCGTCTGTA 58.315 61.111 8.04 0.00 40.86 2.74
6617 7697 1.509923 GGGAACCGGTCGTCTGTAG 59.490 63.158 8.04 0.00 40.86 2.74
6619 7699 1.593296 GGAACCGGTCGTCTGTAGCT 61.593 60.000 8.04 0.00 0.00 3.32
6621 7701 1.063764 GAACCGGTCGTCTGTAGCTAG 59.936 57.143 8.04 0.00 0.00 3.42
6623 7703 1.445716 CCGGTCGTCTGTAGCTAGGG 61.446 65.000 0.00 0.00 0.00 3.53
6624 7704 1.445716 CGGTCGTCTGTAGCTAGGGG 61.446 65.000 0.00 0.00 0.00 4.79
6626 7706 0.395448 GTCGTCTGTAGCTAGGGGGT 60.395 60.000 0.00 0.00 0.00 4.95
6627 7707 0.395311 TCGTCTGTAGCTAGGGGGTG 60.395 60.000 0.00 0.00 0.00 4.61
6629 7709 0.032416 GTCTGTAGCTAGGGGGTGGA 60.032 60.000 0.00 0.00 0.00 4.02
6631 7711 0.325296 CTGTAGCTAGGGGGTGGACA 60.325 60.000 0.00 0.00 0.00 4.02
6632 7712 0.325296 TGTAGCTAGGGGGTGGACAG 60.325 60.000 0.00 0.00 0.00 3.51
6634 7714 2.252012 TAGCTAGGGGGTGGACAGGG 62.252 65.000 0.00 0.00 0.00 4.45
6635 7715 2.454941 CTAGGGGGTGGACAGGGT 59.545 66.667 0.00 0.00 0.00 4.34
6636 7716 1.995626 CTAGGGGGTGGACAGGGTG 60.996 68.421 0.00 0.00 0.00 4.61
6637 7717 3.572715 TAGGGGGTGGACAGGGTGG 62.573 68.421 0.00 0.00 0.00 4.61
6639 7719 3.647771 GGGGTGGACAGGGTGGTC 61.648 72.222 0.00 0.00 37.06 4.02
6656 7736 2.806945 GTCCATGGACCATCCTGAAA 57.193 50.000 31.37 0.00 39.08 2.69
6657 7737 3.085952 GTCCATGGACCATCCTGAAAA 57.914 47.619 31.37 0.00 39.08 2.29
6658 7738 3.635591 GTCCATGGACCATCCTGAAAAT 58.364 45.455 31.37 0.00 39.08 1.82
6659 7739 4.026052 GTCCATGGACCATCCTGAAAATT 58.974 43.478 31.37 0.00 39.08 1.82
6660 7740 4.098501 GTCCATGGACCATCCTGAAAATTC 59.901 45.833 31.37 2.86 39.08 2.17
6661 7741 3.385755 CCATGGACCATCCTGAAAATTCC 59.614 47.826 5.56 0.00 37.46 3.01
6662 7742 3.100207 TGGACCATCCTGAAAATTCCC 57.900 47.619 0.00 0.00 37.46 3.97
6663 7743 2.292192 TGGACCATCCTGAAAATTCCCC 60.292 50.000 0.00 0.00 37.46 4.81
6664 7744 2.388735 GACCATCCTGAAAATTCCCCC 58.611 52.381 0.00 0.00 0.00 5.40
6665 7745 1.721691 ACCATCCTGAAAATTCCCCCA 59.278 47.619 0.00 0.00 0.00 4.96
6666 7746 2.318822 ACCATCCTGAAAATTCCCCCAT 59.681 45.455 0.00 0.00 0.00 4.00
6667 7747 3.535590 ACCATCCTGAAAATTCCCCCATA 59.464 43.478 0.00 0.00 0.00 2.74
6668 7748 4.154942 CCATCCTGAAAATTCCCCCATAG 58.845 47.826 0.00 0.00 0.00 2.23
6669 7749 3.312736 TCCTGAAAATTCCCCCATAGC 57.687 47.619 0.00 0.00 0.00 2.97
6670 7750 2.091333 TCCTGAAAATTCCCCCATAGCC 60.091 50.000 0.00 0.00 0.00 3.93
6671 7751 2.359143 CCTGAAAATTCCCCCATAGCCA 60.359 50.000 0.00 0.00 0.00 4.75
6672 7752 3.373830 CTGAAAATTCCCCCATAGCCAA 58.626 45.455 0.00 0.00 0.00 4.52
6673 7753 3.969312 CTGAAAATTCCCCCATAGCCAAT 59.031 43.478 0.00 0.00 0.00 3.16
6674 7754 5.147032 CTGAAAATTCCCCCATAGCCAATA 58.853 41.667 0.00 0.00 0.00 1.90
6675 7755 5.725490 TGAAAATTCCCCCATAGCCAATAT 58.275 37.500 0.00 0.00 0.00 1.28
6676 7756 6.868826 TGAAAATTCCCCCATAGCCAATATA 58.131 36.000 0.00 0.00 0.00 0.86
6677 7757 7.486473 TGAAAATTCCCCCATAGCCAATATAT 58.514 34.615 0.00 0.00 0.00 0.86
6678 7758 8.628281 TGAAAATTCCCCCATAGCCAATATATA 58.372 33.333 0.00 0.00 0.00 0.86
6679 7759 9.136323 GAAAATTCCCCCATAGCCAATATATAG 57.864 37.037 0.00 0.00 0.00 1.31
6680 7760 6.786843 ATTCCCCCATAGCCAATATATAGG 57.213 41.667 0.00 0.00 0.00 2.57
6681 7761 5.249301 TCCCCCATAGCCAATATATAGGT 57.751 43.478 0.00 0.00 0.00 3.08
6682 7762 5.619926 TCCCCCATAGCCAATATATAGGTT 58.380 41.667 0.00 0.00 0.00 3.50
6683 7763 6.768914 TCCCCCATAGCCAATATATAGGTTA 58.231 40.000 0.00 0.00 0.00 2.85
6684 7764 6.849697 TCCCCCATAGCCAATATATAGGTTAG 59.150 42.308 0.00 0.00 0.00 2.34
6685 7765 6.849697 CCCCCATAGCCAATATATAGGTTAGA 59.150 42.308 0.00 0.00 0.00 2.10
6686 7766 7.349859 CCCCCATAGCCAATATATAGGTTAGAA 59.650 40.741 0.00 0.00 0.00 2.10
6687 7767 8.778059 CCCCATAGCCAATATATAGGTTAGAAA 58.222 37.037 0.00 0.00 0.00 2.52
6738 7818 9.332301 GAATTACATGCAAATTTTCATTGTTGG 57.668 29.630 0.17 0.00 0.00 3.77
6739 7819 8.618702 ATTACATGCAAATTTTCATTGTTGGA 57.381 26.923 0.17 0.00 0.00 3.53
6740 7820 6.303021 ACATGCAAATTTTCATTGTTGGAC 57.697 33.333 0.17 0.00 0.00 4.02
6741 7821 5.239087 ACATGCAAATTTTCATTGTTGGACC 59.761 36.000 0.17 0.00 0.00 4.46
6742 7822 4.774124 TGCAAATTTTCATTGTTGGACCA 58.226 34.783 0.00 0.00 0.00 4.02
6743 7823 4.574013 TGCAAATTTTCATTGTTGGACCAC 59.426 37.500 0.00 0.00 0.00 4.16
6744 7824 4.024133 GCAAATTTTCATTGTTGGACCACC 60.024 41.667 0.00 0.00 0.00 4.61
6745 7825 4.350368 AATTTTCATTGTTGGACCACCC 57.650 40.909 0.00 0.00 34.81 4.61
6746 7826 2.765689 TTTCATTGTTGGACCACCCT 57.234 45.000 0.00 0.00 35.38 4.34
6747 7827 1.993956 TTCATTGTTGGACCACCCTG 58.006 50.000 0.00 0.00 35.38 4.45
6748 7828 0.112218 TCATTGTTGGACCACCCTGG 59.888 55.000 0.00 0.00 45.02 4.45
6749 7829 1.228862 ATTGTTGGACCACCCTGGC 60.229 57.895 0.00 0.00 42.67 4.85
6750 7830 1.729267 ATTGTTGGACCACCCTGGCT 61.729 55.000 0.00 0.00 42.67 4.75
6751 7831 2.034221 GTTGGACCACCCTGGCTC 59.966 66.667 0.00 0.00 42.67 4.70
6752 7832 2.449518 TTGGACCACCCTGGCTCA 60.450 61.111 0.00 0.00 42.67 4.26
6753 7833 2.829384 TTGGACCACCCTGGCTCAC 61.829 63.158 0.00 0.00 42.67 3.51
6754 7834 4.035102 GGACCACCCTGGCTCACC 62.035 72.222 0.00 0.00 42.67 4.02
6755 7835 4.394712 GACCACCCTGGCTCACCG 62.395 72.222 0.00 0.00 42.67 4.94
6756 7836 4.954118 ACCACCCTGGCTCACCGA 62.954 66.667 0.00 0.00 42.67 4.69
6757 7837 4.087892 CCACCCTGGCTCACCGAG 62.088 72.222 0.00 0.00 39.70 4.63
6766 7846 2.103143 CTCACCGAGCTGGCTACG 59.897 66.667 0.00 1.74 43.94 3.51
6767 7847 2.675423 TCACCGAGCTGGCTACGT 60.675 61.111 0.00 0.00 43.94 3.57
6768 7848 2.202623 CACCGAGCTGGCTACGTC 60.203 66.667 0.00 0.00 43.94 4.34
6769 7849 2.675423 ACCGAGCTGGCTACGTCA 60.675 61.111 0.00 0.00 43.94 4.35
6770 7850 2.052690 ACCGAGCTGGCTACGTCAT 61.053 57.895 0.00 0.00 43.94 3.06
6771 7851 1.141881 CCGAGCTGGCTACGTCATT 59.858 57.895 0.00 0.00 0.00 2.57
6772 7852 0.460284 CCGAGCTGGCTACGTCATTT 60.460 55.000 0.00 0.00 0.00 2.32
6779 7859 4.700213 AGCTGGCTACGTCATTTACATTTT 59.300 37.500 0.00 0.00 0.00 1.82
6783 7863 6.607689 TGGCTACGTCATTTACATTTTCAAG 58.392 36.000 0.00 0.00 0.00 3.02
6952 8033 3.620488 TGCTTTCTCAGTGTGAACCTTT 58.380 40.909 7.12 0.00 0.00 3.11
6956 8037 5.731686 GCTTTCTCAGTGTGAACCTTTCTTG 60.732 44.000 7.12 0.00 0.00 3.02
6958 8039 2.945008 CTCAGTGTGAACCTTTCTTGCA 59.055 45.455 0.00 0.00 0.00 4.08
6959 8040 3.351740 TCAGTGTGAACCTTTCTTGCAA 58.648 40.909 0.00 0.00 0.00 4.08
6960 8041 3.128589 TCAGTGTGAACCTTTCTTGCAAC 59.871 43.478 0.00 0.00 0.00 4.17
6963 8044 0.383949 TGAACCTTTCTTGCAACGCC 59.616 50.000 0.00 0.00 0.00 5.68
6964 8045 0.660300 GAACCTTTCTTGCAACGCCG 60.660 55.000 0.00 0.00 0.00 6.46
6965 8046 2.070654 AACCTTTCTTGCAACGCCGG 62.071 55.000 0.00 0.00 0.00 6.13
6966 8047 2.429069 CTTTCTTGCAACGCCGGC 60.429 61.111 19.07 19.07 0.00 6.13
6967 8048 3.896863 CTTTCTTGCAACGCCGGCC 62.897 63.158 23.46 7.25 0.00 6.13
6978 8059 4.434354 GCCGGCCCACCAATGGTA 62.434 66.667 18.11 0.00 45.66 3.25
6979 8060 2.600731 CCGGCCCACCAATGGTAT 59.399 61.111 3.85 0.00 45.66 2.73
6980 8061 1.528309 CCGGCCCACCAATGGTATC 60.528 63.158 3.85 0.00 45.66 2.24
6993 8074 1.078988 GGTATCCGCGTGAAACCCA 60.079 57.895 4.92 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.252197 ATCACGGAGGGCCTTTACAC 59.748 55.000 7.89 0.00 0.00 2.90
14 15 0.625849 ATTTGATCACGGAGGGCCTT 59.374 50.000 7.89 0.00 0.00 4.35
21 22 1.762957 GGAGGGAGATTTGATCACGGA 59.237 52.381 0.00 0.00 0.00 4.69
44 45 0.955919 GGGCCTTTTCCGACACTCTG 60.956 60.000 0.84 0.00 0.00 3.35
71 72 2.822561 AGCTTCTGTTCTCGTGAGATCA 59.177 45.455 9.59 9.59 40.84 2.92
100 101 5.762711 GGGCACACCAAAAATATGTTTCTTT 59.237 36.000 0.00 0.00 39.85 2.52
101 102 5.304778 GGGCACACCAAAAATATGTTTCTT 58.695 37.500 0.00 0.00 39.85 2.52
102 103 4.262851 GGGGCACACCAAAAATATGTTTCT 60.263 41.667 0.00 0.00 42.91 2.52
108 109 2.571202 CCAAGGGGCACACCAAAAATAT 59.429 45.455 0.00 0.00 42.91 1.28
127 128 3.011482 ACCCAAAAATTCCCCGTATACCA 59.989 43.478 0.00 0.00 0.00 3.25
128 129 3.634504 ACCCAAAAATTCCCCGTATACC 58.365 45.455 0.00 0.00 0.00 2.73
130 131 7.670559 CCATAATACCCAAAAATTCCCCGTATA 59.329 37.037 0.00 0.00 0.00 1.47
134 135 4.896482 TCCATAATACCCAAAAATTCCCCG 59.104 41.667 0.00 0.00 0.00 5.73
135 136 5.221641 GCTCCATAATACCCAAAAATTCCCC 60.222 44.000 0.00 0.00 0.00 4.81
136 137 5.602561 AGCTCCATAATACCCAAAAATTCCC 59.397 40.000 0.00 0.00 0.00 3.97
137 138 6.323739 TCAGCTCCATAATACCCAAAAATTCC 59.676 38.462 0.00 0.00 0.00 3.01
138 139 7.285401 TCTCAGCTCCATAATACCCAAAAATTC 59.715 37.037 0.00 0.00 0.00 2.17
139 140 7.125391 TCTCAGCTCCATAATACCCAAAAATT 58.875 34.615 0.00 0.00 0.00 1.82
140 141 6.672593 TCTCAGCTCCATAATACCCAAAAAT 58.327 36.000 0.00 0.00 0.00 1.82
141 142 6.073447 TCTCAGCTCCATAATACCCAAAAA 57.927 37.500 0.00 0.00 0.00 1.94
142 143 5.708736 TCTCAGCTCCATAATACCCAAAA 57.291 39.130 0.00 0.00 0.00 2.44
156 157 6.010219 ACTCTCCTAATCCTAATCTCAGCTC 58.990 44.000 0.00 0.00 0.00 4.09
190 191 5.846203 AGATGTGAGAAAAATGTTTGTGGG 58.154 37.500 0.00 0.00 0.00 4.61
219 220 3.311596 GTCTGCTTCGGTTGTTTGTAAGT 59.688 43.478 0.00 0.00 0.00 2.24
237 241 2.575805 AGAGGGCTGGAAAAAGTCTG 57.424 50.000 0.00 0.00 0.00 3.51
314 318 0.655733 CACGTGTTCCGAGTTTGCTT 59.344 50.000 7.58 0.00 40.70 3.91
315 319 0.461339 ACACGTGTTCCGAGTTTGCT 60.461 50.000 17.22 0.00 37.02 3.91
1212 1231 5.592054 GTCGAATTACATGTCCATCTCTCA 58.408 41.667 0.00 0.00 0.00 3.27
1259 1290 5.499004 TTACAGTCCACAGCCTAAAATCT 57.501 39.130 0.00 0.00 0.00 2.40
1299 1332 1.199097 CCACGGTAGCACAATTCAACC 59.801 52.381 0.00 0.00 0.00 3.77
1310 1343 0.947180 TGCGAACTTTCCACGGTAGC 60.947 55.000 0.00 0.00 0.00 3.58
1483 1516 9.151471 CACCATAAATAAATCTAGGTACCATCG 57.849 37.037 15.94 1.47 0.00 3.84
1582 1621 1.005630 ACCAAGAGCTCAGTGTCGC 60.006 57.895 17.77 0.00 0.00 5.19
1583 1622 1.287730 GCACCAAGAGCTCAGTGTCG 61.288 60.000 23.96 13.06 32.75 4.35
1665 1704 0.035598 CCACATCCAACCCGTGTACA 59.964 55.000 0.00 0.00 0.00 2.90
1682 1721 4.555709 ACCGCAACCGAAGCACCA 62.556 61.111 0.00 0.00 36.29 4.17
1695 1734 2.038387 ACACCCTGATAAATGACCGC 57.962 50.000 0.00 0.00 0.00 5.68
1697 1736 3.963129 TGGAACACCCTGATAAATGACC 58.037 45.455 0.00 0.00 35.38 4.02
1768 1813 5.028375 CGACAAAACCTTCAAAGAACACTC 58.972 41.667 0.00 0.00 0.00 3.51
1781 1826 0.751643 ACCAAGCAGCGACAAAACCT 60.752 50.000 0.00 0.00 0.00 3.50
1802 1847 7.987649 ACTAACAAAGAAACGGACAAATAACA 58.012 30.769 0.00 0.00 0.00 2.41
1831 1876 4.744631 CCCAAAACAAACAGCAGATACAAC 59.255 41.667 0.00 0.00 0.00 3.32
1903 1948 4.711846 ACACTCATAGAGCATTCACCTACA 59.288 41.667 0.00 0.00 32.04 2.74
2188 2257 4.101448 CGAAGGGGCAGGTCAGGG 62.101 72.222 0.00 0.00 0.00 4.45
2192 2261 2.747855 CAAGCGAAGGGGCAGGTC 60.748 66.667 0.00 0.00 34.64 3.85
2243 2312 2.751436 GGCGCCTGGATCAGCAAA 60.751 61.111 22.15 0.00 0.00 3.68
2299 2368 1.068434 TCATCGGCATATGCTCGTTCA 59.932 47.619 26.12 12.76 41.70 3.18
2317 2386 2.829914 GGGCCTTGCGATGCATCA 60.830 61.111 25.70 5.71 38.76 3.07
2407 2476 0.876342 CTAGCAAATCGACCGAGGGC 60.876 60.000 0.00 1.96 0.00 5.19
2511 2588 0.107703 GTCATTGGCCGATCAGTGGA 60.108 55.000 1.06 0.00 0.00 4.02
2529 2606 5.546499 TCCTAGGAGGTGAGTTTTACAATGT 59.454 40.000 7.62 0.00 36.53 2.71
2576 2653 3.191371 GGACCTCTGCGTTTCATTTCATT 59.809 43.478 0.00 0.00 0.00 2.57
2589 2666 0.668535 AAAACGCAAAGGACCTCTGC 59.331 50.000 9.98 9.98 0.00 4.26
2616 2693 5.690409 CCACTATTTCTTGCATGCATGATTC 59.310 40.000 30.13 13.12 31.64 2.52
3681 3763 2.753296 GCAAGCAGCACATAAAAACCA 58.247 42.857 0.00 0.00 44.79 3.67
3693 3775 1.457346 ACTGTAAGGATGCAAGCAGC 58.543 50.000 0.94 0.94 41.23 5.25
3694 3776 4.510038 AAAACTGTAAGGATGCAAGCAG 57.490 40.909 0.00 0.00 39.30 4.24
3695 3777 4.935352 AAAAACTGTAAGGATGCAAGCA 57.065 36.364 0.00 0.00 39.30 3.91
3696 3778 6.308766 CACATAAAAACTGTAAGGATGCAAGC 59.691 38.462 0.00 0.00 39.30 4.01
3697 3779 6.308766 GCACATAAAAACTGTAAGGATGCAAG 59.691 38.462 0.00 0.00 39.30 4.01
3698 3780 6.015519 AGCACATAAAAACTGTAAGGATGCAA 60.016 34.615 0.00 0.00 39.30 4.08
3699 3781 5.476599 AGCACATAAAAACTGTAAGGATGCA 59.523 36.000 0.00 0.00 39.30 3.96
3700 3782 5.801947 CAGCACATAAAAACTGTAAGGATGC 59.198 40.000 0.00 0.00 39.30 3.91
3701 3783 5.801947 GCAGCACATAAAAACTGTAAGGATG 59.198 40.000 0.00 0.00 39.30 3.51
3702 3784 5.711976 AGCAGCACATAAAAACTGTAAGGAT 59.288 36.000 0.00 0.00 39.30 3.24
3703 3785 5.070001 AGCAGCACATAAAAACTGTAAGGA 58.930 37.500 0.00 0.00 39.30 3.36
3704 3786 5.376854 AGCAGCACATAAAAACTGTAAGG 57.623 39.130 0.00 0.00 39.30 2.69
3705 3787 5.117592 GCAAGCAGCACATAAAAACTGTAAG 59.882 40.000 0.00 0.00 44.79 2.34
3706 3788 4.981674 GCAAGCAGCACATAAAAACTGTAA 59.018 37.500 0.00 0.00 44.79 2.41
3707 3789 4.545610 GCAAGCAGCACATAAAAACTGTA 58.454 39.130 0.00 0.00 44.79 2.74
3708 3790 3.383761 GCAAGCAGCACATAAAAACTGT 58.616 40.909 0.00 0.00 44.79 3.55
3772 3854 2.180432 ATGATGTCAGATGCCGATGG 57.820 50.000 0.00 0.00 0.00 3.51
3774 3856 3.562973 GTGAAATGATGTCAGATGCCGAT 59.437 43.478 0.00 0.00 0.00 4.18
4362 5240 6.923508 GCTAAGGTTTTGCAATACAGAAGTTT 59.076 34.615 19.60 7.85 0.00 2.66
4574 5452 9.722056 GCGACTGTATGATCTTCATAAAAATTT 57.278 29.630 0.00 0.00 40.64 1.82
4575 5453 8.892723 TGCGACTGTATGATCTTCATAAAAATT 58.107 29.630 0.00 0.00 40.64 1.82
4577 5455 7.763985 TCTGCGACTGTATGATCTTCATAAAAA 59.236 33.333 0.00 0.00 40.64 1.94
4856 5734 4.212847 CCAAATGGAGCTACAGAATGATCG 59.787 45.833 4.19 0.00 37.05 3.69
5017 5895 5.738619 AGTTTTGAAGTTTTGAACAGGGT 57.261 34.783 0.00 0.00 0.00 4.34
5272 6158 2.102578 GGCCTGCAGTATTTGGACATT 58.897 47.619 13.81 0.00 0.00 2.71
5273 6159 1.686115 GGGCCTGCAGTATTTGGACAT 60.686 52.381 13.81 0.00 0.00 3.06
5274 6160 0.323360 GGGCCTGCAGTATTTGGACA 60.323 55.000 13.81 0.00 0.00 4.02
5647 6533 3.075005 CCGTCGACAGGGACCCAT 61.075 66.667 17.16 0.00 33.30 4.00
5725 6611 4.148825 CCGGGAGCAGGTCTTCGG 62.149 72.222 16.33 16.33 36.27 4.30
6083 6981 1.795286 CAGGAAAGCACGACTTGAGAC 59.205 52.381 0.00 0.00 39.09 3.36
6104 7002 3.055891 GGTAGCAAAACCCATGCAAGATT 60.056 43.478 0.00 0.00 46.22 2.40
6134 7038 3.035942 CCACGCAAGAAAAGAAGAAACG 58.964 45.455 0.00 0.00 43.62 3.60
6188 7092 1.143838 CGCCATCAAGTCCCGATCA 59.856 57.895 0.00 0.00 0.00 2.92
6206 7120 5.780793 AGGAGTCATGTACCCCATATTAGTC 59.219 44.000 0.00 0.00 30.71 2.59
6223 7137 9.739276 ATATTTCAATTACAGTTTGAGGAGTCA 57.261 29.630 0.00 0.00 34.76 3.41
6240 7154 8.240682 TCAAACGTTCGATGGAAATATTTCAAT 58.759 29.630 25.55 21.30 38.92 2.57
6243 7157 8.523464 CAATCAAACGTTCGATGGAAATATTTC 58.477 33.333 18.22 18.22 33.05 2.17
6260 7174 4.256920 AGGAGAGTTCATCCAATCAAACG 58.743 43.478 0.00 0.00 39.47 3.60
6290 7204 1.077716 GGGATATGGCGTATGGGGC 60.078 63.158 3.45 0.00 0.00 5.80
6291 7205 1.607612 GGGGATATGGCGTATGGGG 59.392 63.158 3.45 0.00 0.00 4.96
6292 7206 1.220749 CGGGGATATGGCGTATGGG 59.779 63.158 3.45 0.00 0.00 4.00
6293 7207 1.449601 GCGGGGATATGGCGTATGG 60.450 63.158 3.45 0.00 0.00 2.74
6294 7208 0.107703 ATGCGGGGATATGGCGTATG 60.108 55.000 3.45 0.00 0.00 2.39
6295 7209 1.491668 TATGCGGGGATATGGCGTAT 58.508 50.000 0.00 0.00 0.00 3.06
6296 7210 1.491668 ATATGCGGGGATATGGCGTA 58.508 50.000 0.00 0.00 33.18 4.42
6299 7213 3.071602 ACATCTATATGCGGGGATATGGC 59.928 47.826 3.29 0.00 36.50 4.40
6305 7219 2.179427 CTCCACATCTATATGCGGGGA 58.821 52.381 0.00 0.00 37.93 4.81
6321 7235 2.159179 TAGGTACAGCTGCATCTCCA 57.841 50.000 15.27 0.00 0.00 3.86
6334 7248 5.745227 CCATGGTGATGGGATTATAGGTAC 58.255 45.833 2.57 0.00 45.11 3.34
6371 7288 1.473434 GCTAGACCGTGAAATCCCAGG 60.473 57.143 0.00 0.00 0.00 4.45
6377 7294 2.165301 GCGCGCTAGACCGTGAAAT 61.165 57.895 26.67 0.00 40.91 2.17
6378 7295 2.807895 GCGCGCTAGACCGTGAAA 60.808 61.111 26.67 0.00 40.91 2.69
6379 7296 4.789075 GGCGCGCTAGACCGTGAA 62.789 66.667 32.29 0.00 40.91 3.18
6401 7318 4.473520 AGCTTCGGCCCGTCATGG 62.474 66.667 1.63 0.00 43.01 3.66
6402 7319 2.892425 GAGCTTCGGCCCGTCATG 60.892 66.667 1.63 0.00 43.01 3.07
6403 7320 4.514577 CGAGCTTCGGCCCGTCAT 62.515 66.667 1.63 0.00 43.01 3.06
6434 7351 1.283487 CAACAATGCAGCAGCGTGA 59.717 52.632 10.89 0.00 46.23 4.35
6440 7357 2.735883 GCCACCAACAATGCAGCA 59.264 55.556 0.00 0.00 0.00 4.41
6492 7409 3.244422 TGGTATCAATGGAGGCGGTAATC 60.244 47.826 0.00 0.00 0.00 1.75
6495 7412 1.414919 GTGGTATCAATGGAGGCGGTA 59.585 52.381 0.00 0.00 0.00 4.02
6496 7413 0.180406 GTGGTATCAATGGAGGCGGT 59.820 55.000 0.00 0.00 0.00 5.68
6497 7414 0.180171 TGTGGTATCAATGGAGGCGG 59.820 55.000 0.00 0.00 0.00 6.13
6498 7415 1.134401 AGTGTGGTATCAATGGAGGCG 60.134 52.381 0.00 0.00 0.00 5.52
6499 7416 2.292267 CAGTGTGGTATCAATGGAGGC 58.708 52.381 0.00 0.00 31.10 4.70
6500 7417 2.292267 GCAGTGTGGTATCAATGGAGG 58.708 52.381 0.00 0.00 34.58 4.30
6506 7423 1.376683 GCGGGCAGTGTGGTATCAA 60.377 57.895 0.00 0.00 0.00 2.57
6507 7424 2.267642 GCGGGCAGTGTGGTATCA 59.732 61.111 0.00 0.00 0.00 2.15
6522 7439 1.929836 GATGTGTTGCTCTAGAAGGCG 59.070 52.381 0.00 0.00 0.00 5.52
6565 7482 3.676324 CGAATGCGTTTAGGGTCTCTCTT 60.676 47.826 0.00 0.00 0.00 2.85
6566 7483 2.159226 CGAATGCGTTTAGGGTCTCTCT 60.159 50.000 0.00 0.00 0.00 3.10
6572 7489 0.107848 CCTCCGAATGCGTTTAGGGT 60.108 55.000 12.38 0.00 35.23 4.34
6581 7498 1.202348 CCCTCAAAAACCTCCGAATGC 59.798 52.381 0.00 0.00 0.00 3.56
6584 7501 2.578786 GTTCCCTCAAAAACCTCCGAA 58.421 47.619 0.00 0.00 0.00 4.30
6609 7689 1.392710 CCACCCCCTAGCTACAGACG 61.393 65.000 0.00 0.00 0.00 4.18
6611 7691 0.032416 GTCCACCCCCTAGCTACAGA 60.032 60.000 0.00 0.00 0.00 3.41
6612 7692 0.325296 TGTCCACCCCCTAGCTACAG 60.325 60.000 0.00 0.00 0.00 2.74
6613 7693 0.325296 CTGTCCACCCCCTAGCTACA 60.325 60.000 0.00 0.00 0.00 2.74
6614 7694 1.049289 CCTGTCCACCCCCTAGCTAC 61.049 65.000 0.00 0.00 0.00 3.58
6615 7695 1.313475 CCTGTCCACCCCCTAGCTA 59.687 63.158 0.00 0.00 0.00 3.32
6616 7696 2.041265 CCTGTCCACCCCCTAGCT 59.959 66.667 0.00 0.00 0.00 3.32
6617 7697 3.090532 CCCTGTCCACCCCCTAGC 61.091 72.222 0.00 0.00 0.00 3.42
6619 7699 2.124085 CACCCTGTCCACCCCCTA 59.876 66.667 0.00 0.00 0.00 3.53
6629 7709 3.495729 GTCCATGGACCACCCTGT 58.504 61.111 31.37 0.00 39.08 4.00
6637 7717 2.806945 TTTCAGGATGGTCCATGGAC 57.193 50.000 33.14 33.14 39.61 4.02
6638 7718 4.280819 GAATTTTCAGGATGGTCCATGGA 58.719 43.478 11.44 11.44 39.61 3.41
6639 7719 3.385755 GGAATTTTCAGGATGGTCCATGG 59.614 47.826 9.76 4.97 39.61 3.66
6640 7720 3.385755 GGGAATTTTCAGGATGGTCCATG 59.614 47.826 9.76 0.00 39.61 3.66
6641 7721 3.630828 GGGGAATTTTCAGGATGGTCCAT 60.631 47.826 3.26 3.26 39.61 3.41
6642 7722 2.292192 GGGGAATTTTCAGGATGGTCCA 60.292 50.000 0.00 0.00 39.61 4.02
6643 7723 2.388735 GGGGAATTTTCAGGATGGTCC 58.611 52.381 0.00 0.00 36.16 4.46
6644 7724 2.292192 TGGGGGAATTTTCAGGATGGTC 60.292 50.000 0.00 0.00 36.16 4.02
6645 7725 1.721691 TGGGGGAATTTTCAGGATGGT 59.278 47.619 0.00 0.00 36.16 3.55
6646 7726 2.548464 TGGGGGAATTTTCAGGATGG 57.452 50.000 0.00 0.00 36.16 3.51
6647 7727 3.575687 GCTATGGGGGAATTTTCAGGATG 59.424 47.826 0.00 0.00 37.54 3.51
6648 7728 3.438520 GGCTATGGGGGAATTTTCAGGAT 60.439 47.826 0.00 0.00 0.00 3.24
6649 7729 2.091333 GGCTATGGGGGAATTTTCAGGA 60.091 50.000 0.00 0.00 0.00 3.86
6650 7730 2.319844 GGCTATGGGGGAATTTTCAGG 58.680 52.381 0.00 0.00 0.00 3.86
6651 7731 3.030873 TGGCTATGGGGGAATTTTCAG 57.969 47.619 0.00 0.00 0.00 3.02
6652 7732 3.481559 TTGGCTATGGGGGAATTTTCA 57.518 42.857 0.00 0.00 0.00 2.69
6653 7733 7.978099 ATATATTGGCTATGGGGGAATTTTC 57.022 36.000 0.00 0.00 0.00 2.29
6654 7734 8.067488 CCTATATATTGGCTATGGGGGAATTTT 58.933 37.037 0.00 0.00 0.00 1.82
6655 7735 7.188267 ACCTATATATTGGCTATGGGGGAATTT 59.812 37.037 12.51 0.00 32.93 1.82
6656 7736 6.687415 ACCTATATATTGGCTATGGGGGAATT 59.313 38.462 12.51 0.00 32.93 2.17
6657 7737 6.227966 ACCTATATATTGGCTATGGGGGAAT 58.772 40.000 12.51 0.00 32.93 3.01
6658 7738 5.619926 ACCTATATATTGGCTATGGGGGAA 58.380 41.667 12.51 0.00 32.93 3.97
6659 7739 5.249301 ACCTATATATTGGCTATGGGGGA 57.751 43.478 12.51 0.00 32.93 4.81
6660 7740 5.994416 AACCTATATATTGGCTATGGGGG 57.006 43.478 12.51 0.00 32.93 5.40
6661 7741 7.931015 TCTAACCTATATATTGGCTATGGGG 57.069 40.000 12.51 0.00 32.93 4.96
6712 7792 9.332301 CCAACAATGAAAATTTGCATGTAATTC 57.668 29.630 12.58 0.00 0.00 2.17
6713 7793 9.064706 TCCAACAATGAAAATTTGCATGTAATT 57.935 25.926 12.58 2.64 0.00 1.40
6714 7794 8.505625 GTCCAACAATGAAAATTTGCATGTAAT 58.494 29.630 12.58 0.00 0.00 1.89
6715 7795 7.041508 GGTCCAACAATGAAAATTTGCATGTAA 60.042 33.333 12.58 0.00 0.00 2.41
6716 7796 6.426328 GGTCCAACAATGAAAATTTGCATGTA 59.574 34.615 12.58 0.00 0.00 2.29
6717 7797 5.239087 GGTCCAACAATGAAAATTTGCATGT 59.761 36.000 12.58 9.78 0.00 3.21
6718 7798 5.238868 TGGTCCAACAATGAAAATTTGCATG 59.761 36.000 12.58 9.20 0.00 4.06
6719 7799 5.239087 GTGGTCCAACAATGAAAATTTGCAT 59.761 36.000 5.77 5.77 0.00 3.96
6720 7800 4.574013 GTGGTCCAACAATGAAAATTTGCA 59.426 37.500 0.07 0.07 0.00 4.08
6721 7801 4.024133 GGTGGTCCAACAATGAAAATTTGC 60.024 41.667 0.61 0.00 0.00 3.68
6722 7802 4.514816 GGGTGGTCCAACAATGAAAATTTG 59.485 41.667 9.70 0.00 35.00 2.32
6723 7803 4.411869 AGGGTGGTCCAACAATGAAAATTT 59.588 37.500 9.70 0.00 38.24 1.82
6724 7804 3.973305 AGGGTGGTCCAACAATGAAAATT 59.027 39.130 9.70 0.00 38.24 1.82
6725 7805 3.324556 CAGGGTGGTCCAACAATGAAAAT 59.675 43.478 9.70 0.00 38.24 1.82
6726 7806 2.697751 CAGGGTGGTCCAACAATGAAAA 59.302 45.455 9.70 0.00 38.24 2.29
6727 7807 2.315176 CAGGGTGGTCCAACAATGAAA 58.685 47.619 9.70 0.00 38.24 2.69
6728 7808 1.480312 CCAGGGTGGTCCAACAATGAA 60.480 52.381 9.70 0.00 38.24 2.57
6729 7809 0.112218 CCAGGGTGGTCCAACAATGA 59.888 55.000 9.70 0.00 38.24 2.57
6730 7810 1.535204 GCCAGGGTGGTCCAACAATG 61.535 60.000 9.70 6.81 40.46 2.82
6731 7811 1.228862 GCCAGGGTGGTCCAACAAT 60.229 57.895 9.70 0.00 40.46 2.71
6732 7812 2.197324 GCCAGGGTGGTCCAACAA 59.803 61.111 9.70 0.00 40.46 2.83
6733 7813 2.776526 AGCCAGGGTGGTCCAACA 60.777 61.111 9.70 0.00 40.46 3.33
6734 7814 2.034221 GAGCCAGGGTGGTCCAAC 59.966 66.667 0.00 0.00 40.46 3.77
6735 7815 2.449518 TGAGCCAGGGTGGTCCAA 60.450 61.111 0.00 0.00 40.46 3.53
6736 7816 3.249189 GTGAGCCAGGGTGGTCCA 61.249 66.667 0.00 0.00 40.46 4.02
6737 7817 4.035102 GGTGAGCCAGGGTGGTCC 62.035 72.222 0.00 0.00 40.46 4.46
6738 7818 4.394712 CGGTGAGCCAGGGTGGTC 62.395 72.222 0.00 0.00 40.46 4.02
6739 7819 4.954118 TCGGTGAGCCAGGGTGGT 62.954 66.667 0.00 0.00 40.46 4.16
6740 7820 4.087892 CTCGGTGAGCCAGGGTGG 62.088 72.222 0.00 0.00 41.55 4.61
6749 7829 2.103143 CGTAGCCAGCTCGGTGAG 59.897 66.667 0.00 0.00 36.97 3.51
6750 7830 2.675423 ACGTAGCCAGCTCGGTGA 60.675 61.111 13.37 0.00 36.97 4.02
6751 7831 2.202623 GACGTAGCCAGCTCGGTG 60.203 66.667 13.37 0.00 36.97 4.94
6752 7832 1.605058 AATGACGTAGCCAGCTCGGT 61.605 55.000 13.37 5.99 36.97 4.69
6753 7833 0.460284 AAATGACGTAGCCAGCTCGG 60.460 55.000 13.37 0.00 38.11 4.63
6754 7834 1.852895 GTAAATGACGTAGCCAGCTCG 59.147 52.381 0.00 2.73 0.00 5.03
6755 7835 2.888594 TGTAAATGACGTAGCCAGCTC 58.111 47.619 0.00 0.00 0.00 4.09
6756 7836 3.543680 ATGTAAATGACGTAGCCAGCT 57.456 42.857 0.00 0.00 0.00 4.24
6757 7837 4.616181 AAATGTAAATGACGTAGCCAGC 57.384 40.909 0.00 0.00 0.00 4.85
6758 7838 6.176975 TGAAAATGTAAATGACGTAGCCAG 57.823 37.500 0.00 0.00 0.00 4.85
6759 7839 6.348950 CCTTGAAAATGTAAATGACGTAGCCA 60.349 38.462 0.00 0.00 0.00 4.75
6760 7840 6.027749 CCTTGAAAATGTAAATGACGTAGCC 58.972 40.000 0.00 0.00 0.00 3.93
6761 7841 6.608610 ACCTTGAAAATGTAAATGACGTAGC 58.391 36.000 0.00 0.00 0.00 3.58
6762 7842 8.932791 AGTACCTTGAAAATGTAAATGACGTAG 58.067 33.333 0.00 0.00 28.79 3.51
6763 7843 8.836268 AGTACCTTGAAAATGTAAATGACGTA 57.164 30.769 0.00 0.00 28.79 3.57
6764 7844 7.442969 TGAGTACCTTGAAAATGTAAATGACGT 59.557 33.333 0.00 0.00 28.79 4.34
6765 7845 7.802738 TGAGTACCTTGAAAATGTAAATGACG 58.197 34.615 0.00 0.00 28.79 4.35
6876 7956 8.783093 CGATTCCATGTTAATATTAGGCAAGAA 58.217 33.333 13.69 13.69 0.00 2.52
6916 7996 2.777832 AAGCAGCTACCCTTCTTCTG 57.222 50.000 0.00 0.00 0.00 3.02
6922 8003 1.981495 ACTGAGAAAGCAGCTACCCTT 59.019 47.619 0.00 0.00 39.51 3.95
6925 8006 2.072298 CACACTGAGAAAGCAGCTACC 58.928 52.381 0.00 0.00 39.51 3.18
6968 8049 0.461163 TCACGCGGATACCATTGGTG 60.461 55.000 18.83 2.51 36.19 4.17
6969 8050 0.250793 TTCACGCGGATACCATTGGT 59.749 50.000 13.94 13.94 40.16 3.67
6970 8051 1.063469 GTTTCACGCGGATACCATTGG 59.937 52.381 12.47 0.00 0.00 3.16
6971 8052 1.063469 GGTTTCACGCGGATACCATTG 59.937 52.381 22.53 7.36 44.40 2.82
6972 8053 1.375551 GGTTTCACGCGGATACCATT 58.624 50.000 22.53 0.00 44.40 3.16
6973 8054 0.463116 GGGTTTCACGCGGATACCAT 60.463 55.000 25.89 0.00 46.15 3.55
6974 8055 1.078988 GGGTTTCACGCGGATACCA 60.079 57.895 25.89 1.35 46.15 3.25
6975 8056 0.674269 TTGGGTTTCACGCGGATACC 60.674 55.000 20.67 20.67 44.30 2.73
6976 8057 1.158434 TTTGGGTTTCACGCGGATAC 58.842 50.000 12.47 10.08 33.25 2.24
6977 8058 1.893544 TTTTGGGTTTCACGCGGATA 58.106 45.000 12.47 0.00 33.25 2.59
6978 8059 1.033574 TTTTTGGGTTTCACGCGGAT 58.966 45.000 12.47 0.00 33.25 4.18
6979 8060 0.100861 GTTTTTGGGTTTCACGCGGA 59.899 50.000 12.47 1.33 33.25 5.54
6980 8061 0.101579 AGTTTTTGGGTTTCACGCGG 59.898 50.000 12.47 0.00 33.25 6.46
6993 8074 6.293900 CCTGTTTGGTTTGCTTTTGAGTTTTT 60.294 34.615 0.00 0.00 0.00 1.94



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

AutoCloner maintained by Alex Coulton.