Multiple sequence alignment - TraesCS3A01G144600

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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 TraesCS3A01G144600 chr3A 100.000 4462 0 0 1 4462 127091787 127087326 0.000000e+00 8240.0
1 TraesCS3A01G144600 chr3A 90.937 651 45 5 3814 4462 64084220 64084858 0.000000e+00 863.0
2 TraesCS3A01G144600 chr3A 91.304 253 21 1 4211 4462 359361457 359361709 1.190000e-90 344.0
3 TraesCS3A01G144600 chr3A 92.254 142 10 1 3808 3948 359360972 359361113 2.720000e-47 200.0
4 TraesCS3A01G144600 chr3A 100.000 28 0 0 563 590 78188037 78188010 8.000000e-03 52.8
5 TraesCS3A01G144600 chr3D 92.617 3508 180 36 318 3769 120149578 120146094 0.000000e+00 4970.0
6 TraesCS3A01G144600 chr3D 89.781 274 25 1 1 274 120150026 120149756 9.190000e-92 348.0
7 TraesCS3A01G144600 chr3D 80.000 155 26 4 3806 3959 459486964 459487114 4.720000e-20 110.0
8 TraesCS3A01G144600 chr5B 87.445 1139 84 21 2570 3673 507795338 507796452 0.000000e+00 1256.0
9 TraesCS3A01G144600 chr5B 92.373 118 6 3 3696 3810 507796742 507796859 9.930000e-37 165.0
10 TraesCS3A01G144600 chr1B 77.273 792 145 23 2114 2899 642060894 642061656 2.470000e-117 433.0
11 TraesCS3A01G144600 chr2A 86.269 335 37 7 3808 4140 723649501 723649174 5.490000e-94 355.0
12 TraesCS3A01G144600 chr2A 90.146 274 21 2 4189 4462 723643101 723642834 7.100000e-93 351.0
13 TraesCS3A01G144600 chr2A 93.443 61 2 2 4137 4195 723643329 723643269 6.150000e-14 89.8
14 TraesCS3A01G144600 chr5D 89.916 238 21 3 4196 4431 66297894 66297658 2.020000e-78 303.0
15 TraesCS3A01G144600 chr1D 80.685 321 58 4 2581 2899 465100393 465100711 3.450000e-61 246.0
16 TraesCS3A01G144600 chr1D 92.308 39 3 0 620 658 51933923 51933885 6.240000e-04 56.5
17 TraesCS3A01G144600 chr6A 89.617 183 16 2 3808 3990 384874351 384874530 3.470000e-56 230.0
18 TraesCS3A01G144600 chr6A 84.536 194 26 4 1333 1524 549045374 549045183 5.890000e-44 189.0
19 TraesCS3A01G144600 chr6A 100.000 32 0 0 2125 2156 529019664 529019695 4.820000e-05 60.2
20 TraesCS3A01G144600 chr1A 79.154 331 65 4 2571 2899 557425828 557426156 4.490000e-55 226.0
21 TraesCS3A01G144600 chr6D 86.154 195 21 6 1333 1524 402353130 402352939 5.850000e-49 206.0
22 TraesCS3A01G144600 chr6D 100.000 32 0 0 2125 2156 384439725 384439756 4.820000e-05 60.2
23 TraesCS3A01G144600 chr7A 85.787 197 22 6 1333 1526 96051658 96051465 2.100000e-48 204.0
24 TraesCS3A01G144600 chr7A 84.264 197 25 6 1333 1526 95230431 95230238 2.120000e-43 187.0
25 TraesCS3A01G144600 chr7D 85.354 198 21 8 1333 1526 93033667 93033474 9.790000e-47 198.0
26 TraesCS3A01G144600 chr7D 80.255 157 19 10 3808 3959 49821618 49821469 1.700000e-19 108.0
27 TraesCS3A01G144600 chr7D 90.000 80 8 0 582 661 261818604 261818683 2.200000e-18 104.0
28 TraesCS3A01G144600 chr7B 85.279 197 23 6 1333 1526 45641846 45641653 9.790000e-47 198.0
29 TraesCS3A01G144600 chr7B 89.831 118 9 1 3813 3930 698890964 698890850 1.000000e-31 148.0
30 TraesCS3A01G144600 chr6B 87.006 177 19 4 1333 1507 603147732 603147558 3.520000e-46 196.0
31 TraesCS3A01G144600 chr6B 100.000 32 0 0 2125 2156 574715899 574715930 4.820000e-05 60.2
32 TraesCS3A01G144600 chrUn 84.264 197 25 6 1333 1526 82676770 82676963 2.120000e-43 187.0
33 TraesCS3A01G144600 chrUn 90.678 118 8 1 3813 3930 87693053 87692939 2.150000e-33 154.0
34 TraesCS3A01G144600 chr5A 78.613 173 23 11 3798 3965 651545792 651545629 7.900000e-18 102.0
35 TraesCS3A01G144600 chr4D 88.095 84 10 0 568 651 89538562 89538645 2.840000e-17 100.0
36 TraesCS3A01G144600 chr4D 79.091 110 10 8 566 664 384268344 384268237 3.730000e-06 63.9
37 TraesCS3A01G144600 chr2B 82.474 97 13 3 566 660 202180233 202180139 1.030000e-11 82.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G144600 chr3A 127087326 127091787 4461 True 8240.0 8240 100.000 1 4462 1 chr3A.!!$R2 4461
1 TraesCS3A01G144600 chr3A 64084220 64084858 638 False 863.0 863 90.937 3814 4462 1 chr3A.!!$F1 648
2 TraesCS3A01G144600 chr3A 359360972 359361709 737 False 272.0 344 91.779 3808 4462 2 chr3A.!!$F2 654
3 TraesCS3A01G144600 chr3D 120146094 120150026 3932 True 2659.0 4970 91.199 1 3769 2 chr3D.!!$R1 3768
4 TraesCS3A01G144600 chr5B 507795338 507796859 1521 False 710.5 1256 89.909 2570 3810 2 chr5B.!!$F1 1240
5 TraesCS3A01G144600 chr1B 642060894 642061656 762 False 433.0 433 77.273 2114 2899 1 chr1B.!!$F1 785

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
966 1126 0.034670 GAGCTCCCATCCAAAGCACT 60.035 55.0 0.87 0.0 38.51 4.40 F
1209 1369 0.245813 GGTCCAACTCCGGTCTACAC 59.754 60.0 0.00 0.0 0.00 2.90 F
2062 2226 0.249657 GATCAGATGGACACTCCGCC 60.250 60.0 0.00 0.0 40.17 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 2086 0.033796 CTGAGCCATCCACCAATGGT 60.034 55.0 0.00 0.0 46.69 3.55 R
2434 2598 0.109342 CTGGAGGTTGTTCCACTGCT 59.891 55.0 0.00 0.0 42.24 4.24 R
4039 4519 0.173481 AGTGCTAGCGATTTCAGCGA 59.827 50.0 10.77 0.0 38.15 4.93 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.924356 TGAACTGTGTCTTCAATTACCAGA 58.076 37.500 0.00 0.00 0.00 3.86
44 45 4.642429 ACTGTGTCTTCAATTACCAGACC 58.358 43.478 7.88 2.48 36.83 3.85
49 50 4.935205 TGTCTTCAATTACCAGACCATTCG 59.065 41.667 7.88 0.00 36.83 3.34
99 100 5.301551 TCTCTTGCTCCTCTTATTAGCTCTG 59.698 44.000 0.00 0.00 37.16 3.35
117 118 7.840342 AGCTCTGTAATGAAAGAAGTACATG 57.160 36.000 0.00 0.00 0.00 3.21
128 129 8.106247 TGAAAGAAGTACATGTTTTATCACCC 57.894 34.615 2.30 0.00 0.00 4.61
143 144 3.992943 TCACCCGTTCATAACCATTCT 57.007 42.857 0.00 0.00 0.00 2.40
144 145 4.295141 TCACCCGTTCATAACCATTCTT 57.705 40.909 0.00 0.00 0.00 2.52
164 165 1.109920 TGCGAGCTCCCTATCTCCAC 61.110 60.000 8.47 0.00 0.00 4.02
170 171 3.172339 AGCTCCCTATCTCCACATGATC 58.828 50.000 0.00 0.00 0.00 2.92
171 172 3.172339 GCTCCCTATCTCCACATGATCT 58.828 50.000 0.00 0.00 0.00 2.75
172 173 3.195396 GCTCCCTATCTCCACATGATCTC 59.805 52.174 0.00 0.00 0.00 2.75
178 179 3.341318 TCTCCACATGATCTCCTCCAT 57.659 47.619 0.00 0.00 0.00 3.41
191 192 5.762179 TCTCCTCCATGTGTTTGAGTTAT 57.238 39.130 0.00 0.00 0.00 1.89
193 194 7.437713 TCTCCTCCATGTGTTTGAGTTATAT 57.562 36.000 0.00 0.00 0.00 0.86
231 232 9.753674 TGATCTTTAATTCTAGGTGGTCAAAAT 57.246 29.630 0.00 0.00 0.00 1.82
245 246 3.257375 GGTCAAAATCAACCCTACCAACC 59.743 47.826 0.00 0.00 0.00 3.77
248 249 4.354387 TCAAAATCAACCCTACCAACCCTA 59.646 41.667 0.00 0.00 0.00 3.53
278 279 3.170362 TCCAGCTTGGAACCAGGG 58.830 61.111 5.20 1.85 45.00 4.45
294 295 3.717294 GGACGGACCTGCACCCAT 61.717 66.667 0.00 0.00 35.41 4.00
295 296 2.436646 GACGGACCTGCACCCATG 60.437 66.667 0.00 0.00 0.00 3.66
297 298 4.033776 CGGACCTGCACCCATGGT 62.034 66.667 11.73 0.00 35.62 3.55
298 299 2.665089 CGGACCTGCACCCATGGTA 61.665 63.158 11.73 0.00 32.11 3.25
300 301 1.452108 GACCTGCACCCATGGTAGC 60.452 63.158 11.73 14.51 32.11 3.58
301 302 2.124151 CCTGCACCCATGGTAGCC 60.124 66.667 19.45 3.18 32.11 3.93
302 303 2.683465 CCTGCACCCATGGTAGCCT 61.683 63.158 19.45 0.00 32.11 4.58
303 304 1.452651 CTGCACCCATGGTAGCCTG 60.453 63.158 19.45 10.78 32.11 4.85
304 305 2.124151 GCACCCATGGTAGCCTGG 60.124 66.667 11.73 9.10 32.11 4.45
394 536 9.557061 TCTATAGAGTAATATAGCCCACATACG 57.443 37.037 0.00 0.00 36.22 3.06
399 541 3.955650 ATATAGCCCACATACGTGACC 57.044 47.619 0.00 0.00 46.80 4.02
406 548 0.740868 CACATACGTGACCCAGCCTG 60.741 60.000 0.00 0.00 46.80 4.85
407 549 0.902984 ACATACGTGACCCAGCCTGA 60.903 55.000 0.00 0.00 0.00 3.86
436 578 0.877213 CAAACCGAACGTCCGAACCT 60.877 55.000 0.00 0.00 0.00 3.50
442 584 3.216944 AACGTCCGAACCTGGGTCG 62.217 63.158 26.70 26.70 34.66 4.79
461 603 3.624410 GTCGGTCCATTTATGTAACACCC 59.376 47.826 0.00 0.00 0.00 4.61
465 607 4.959839 GGTCCATTTATGTAACACCCCAAT 59.040 41.667 0.00 0.00 0.00 3.16
497 639 8.064336 ACTTTAGATGACCTACAACTTCGTAT 57.936 34.615 0.00 0.00 33.74 3.06
498 640 8.529476 ACTTTAGATGACCTACAACTTCGTATT 58.471 33.333 0.00 0.00 33.74 1.89
530 673 8.307483 CGAGATCTGGTACCACATATCTATTTT 58.693 37.037 21.44 7.28 35.30 1.82
591 735 7.589993 ACTCCCTCAGATCCAAATTAATTGAT 58.410 34.615 0.39 1.14 41.85 2.57
592 736 7.504911 ACTCCCTCAGATCCAAATTAATTGATG 59.495 37.037 0.39 0.00 41.85 3.07
635 779 8.709386 AAAATAGACATTATATAGAGGCTGCG 57.291 34.615 0.00 0.00 0.00 5.18
649 793 3.609853 AGGCTGCGTCAATTAATTCAGA 58.390 40.909 15.29 2.33 0.00 3.27
653 797 5.449041 GGCTGCGTCAATTAATTCAGATTGA 60.449 40.000 15.29 7.39 39.30 2.57
701 845 8.007405 TGAAATCATGAAACTCGGATACTCTA 57.993 34.615 0.00 0.00 0.00 2.43
705 849 9.482627 AATCATGAAACTCGGATACTCTATTTC 57.517 33.333 0.00 0.00 0.00 2.17
730 874 3.697166 ACCGAAGAAATTAGGGTGCATT 58.303 40.909 0.00 0.00 0.00 3.56
780 924 4.256110 TGATTTTGAGATGTGCACGATCT 58.744 39.130 23.25 23.25 32.63 2.75
782 926 2.749280 TTGAGATGTGCACGATCTGT 57.251 45.000 26.21 11.51 29.97 3.41
794 938 3.120060 GCACGATCTGTCTCATTTGCTTT 60.120 43.478 0.00 0.00 0.00 3.51
796 940 4.152938 CACGATCTGTCTCATTTGCTTTCA 59.847 41.667 0.00 0.00 0.00 2.69
812 956 4.856487 TGCTTTCAAATATTTAGTGTGCGC 59.144 37.500 0.00 0.00 0.00 6.09
813 957 5.095490 GCTTTCAAATATTTAGTGTGCGCT 58.905 37.500 9.73 0.00 0.00 5.92
829 977 1.860326 GCGCTTTTTCATTTGTGCAGT 59.140 42.857 0.00 0.00 36.16 4.40
854 1002 7.715249 GTCACCATTTAGATAGCCAACAGATTA 59.285 37.037 0.00 0.00 0.00 1.75
855 1003 8.271458 TCACCATTTAGATAGCCAACAGATTAA 58.729 33.333 0.00 0.00 0.00 1.40
891 1051 3.121030 CCTTTGAGCGCCGTCCTG 61.121 66.667 2.29 0.00 0.00 3.86
905 1065 1.682684 TCCTGGCGTCCTCTTCCTC 60.683 63.158 0.00 0.00 0.00 3.71
937 1097 3.812609 CACGCTATAAATACACATGCCCA 59.187 43.478 0.00 0.00 0.00 5.36
938 1098 3.813166 ACGCTATAAATACACATGCCCAC 59.187 43.478 0.00 0.00 0.00 4.61
966 1126 0.034670 GAGCTCCCATCCAAAGCACT 60.035 55.000 0.87 0.00 38.51 4.40
968 1128 1.065126 AGCTCCCATCCAAAGCACTAC 60.065 52.381 0.00 0.00 38.51 2.73
1041 1201 0.325296 TAGCCATGGGTCTCCTCGTT 60.325 55.000 22.15 0.00 0.00 3.85
1043 1203 1.221840 CCATGGGTCTCCTCGTTGG 59.778 63.158 2.85 0.00 37.10 3.77
1050 1210 0.670854 GTCTCCTCGTTGGCTTGGTC 60.671 60.000 0.00 0.00 35.26 4.02
1054 1214 0.537371 CCTCGTTGGCTTGGTCCTTT 60.537 55.000 0.00 0.00 0.00 3.11
1206 1366 0.324091 GGAGGTCCAACTCCGGTCTA 60.324 60.000 0.00 0.00 46.81 2.59
1209 1369 0.245813 GGTCCAACTCCGGTCTACAC 59.754 60.000 0.00 0.00 0.00 2.90
1235 1395 2.828549 GGCCAACGGGGTATGCAG 60.829 66.667 0.00 0.00 39.65 4.41
1237 1397 2.272146 CCAACGGGGTATGCAGCT 59.728 61.111 0.00 0.00 0.00 4.24
1243 1403 1.227973 GGGGTATGCAGCTGCCTAC 60.228 63.158 33.54 33.54 40.09 3.18
1246 1406 0.533755 GGTATGCAGCTGCCTACTGG 60.534 60.000 36.76 6.58 40.47 4.00
1259 1419 5.435291 CTGCCTACTGGAAATCTCAAATCT 58.565 41.667 0.00 0.00 34.57 2.40
1283 1443 6.477253 TGGGTGCAACTAATTAATCTGTGTA 58.523 36.000 0.00 0.00 36.74 2.90
1317 1477 6.223120 ACATTAACTTCTGCATTTTCCAACC 58.777 36.000 0.00 0.00 0.00 3.77
1329 1489 1.455822 TTCCAACCCAGGTGGATCTT 58.544 50.000 1.43 0.00 37.39 2.40
1426 1586 3.807538 GCGTCCTCGAGTACGGCA 61.808 66.667 28.28 0.00 39.46 5.69
1588 1748 1.009903 CATGCACGTCGGGTTTACGA 61.010 55.000 2.27 0.00 42.90 3.43
1612 1776 1.794701 CATACGCGTAGTCGGTAGCTA 59.205 52.381 24.78 0.00 37.56 3.32
1628 1792 3.053831 AGCTAACCAAGTGTACGCATT 57.946 42.857 9.48 0.28 0.00 3.56
1634 1798 2.222445 ACCAAGTGTACGCATTTCGAAC 59.778 45.455 9.48 0.00 41.67 3.95
1641 1805 1.434555 ACGCATTTCGAACGGATTCA 58.565 45.000 10.80 0.00 41.67 2.57
1664 1828 1.908793 CAGGTGGGAGACGGTGACT 60.909 63.158 0.00 0.00 0.00 3.41
1828 1992 2.279252 CCGGGATACGCGAACCTG 60.279 66.667 15.93 17.06 42.31 4.00
1857 2021 0.954452 CACTCCAAGCAGGTTTGTCC 59.046 55.000 0.00 0.00 39.02 4.02
1861 2025 0.310854 CCAAGCAGGTTTGTCCGTTC 59.689 55.000 0.00 0.00 41.99 3.95
1865 2029 3.202829 AGCAGGTTTGTCCGTTCTAAA 57.797 42.857 0.00 0.00 41.99 1.85
1866 2030 2.876550 AGCAGGTTTGTCCGTTCTAAAC 59.123 45.455 0.00 0.00 41.99 2.01
1867 2031 2.876550 GCAGGTTTGTCCGTTCTAAACT 59.123 45.455 0.00 0.00 41.99 2.66
1868 2032 4.060205 GCAGGTTTGTCCGTTCTAAACTA 58.940 43.478 0.00 0.00 41.99 2.24
1869 2033 4.084171 GCAGGTTTGTCCGTTCTAAACTAC 60.084 45.833 0.00 0.00 41.99 2.73
1882 2046 7.039882 CGTTCTAAACTACACTAACCATCCAT 58.960 38.462 0.00 0.00 0.00 3.41
1884 2048 6.346096 TCTAAACTACACTAACCATCCATGC 58.654 40.000 0.00 0.00 0.00 4.06
1896 2060 3.227614 CCATCCATGCTGAAATGATCCA 58.772 45.455 0.00 0.00 0.00 3.41
1901 2065 5.698104 TCCATGCTGAAATGATCCAATAGT 58.302 37.500 0.00 0.00 0.00 2.12
1904 2068 6.040054 CCATGCTGAAATGATCCAATAGTTGA 59.960 38.462 0.00 0.00 0.00 3.18
1909 2073 7.521748 GCTGAAATGATCCAATAGTTGATCCTG 60.522 40.741 2.22 0.00 0.00 3.86
1922 2086 3.438216 TGATCCTGATGTTTCTTGGCA 57.562 42.857 0.00 0.00 0.00 4.92
1950 2114 0.807496 GGATGGCTCAGCTGTTTGAC 59.193 55.000 14.67 8.25 0.00 3.18
1964 2128 2.129607 GTTTGACTTCGCCGACAAGTA 58.870 47.619 0.00 0.00 34.10 2.24
1993 2157 2.355986 TACGACGCCAGCATCCCTT 61.356 57.895 0.00 0.00 0.00 3.95
2004 2168 1.657751 GCATCCCTTTGGCGAGGAAC 61.658 60.000 8.19 0.00 39.25 3.62
2052 2216 4.986875 CGTAAGCAATCAGATCAGATGG 57.013 45.455 0.79 0.00 0.00 3.51
2053 2217 4.625028 CGTAAGCAATCAGATCAGATGGA 58.375 43.478 6.67 0.00 0.00 3.41
2054 2218 4.447054 CGTAAGCAATCAGATCAGATGGAC 59.553 45.833 6.67 0.00 0.00 4.02
2055 2219 4.498894 AAGCAATCAGATCAGATGGACA 57.501 40.909 6.67 0.00 0.00 4.02
2056 2220 3.806380 AGCAATCAGATCAGATGGACAC 58.194 45.455 6.67 0.00 0.00 3.67
2057 2221 3.455177 AGCAATCAGATCAGATGGACACT 59.545 43.478 6.67 0.00 0.00 3.55
2058 2222 3.808726 GCAATCAGATCAGATGGACACTC 59.191 47.826 6.67 0.00 0.00 3.51
2059 2223 4.378774 CAATCAGATCAGATGGACACTCC 58.621 47.826 0.79 0.00 36.96 3.85
2060 2224 2.027385 TCAGATCAGATGGACACTCCG 58.973 52.381 0.00 0.00 40.17 4.63
2061 2225 0.749649 AGATCAGATGGACACTCCGC 59.250 55.000 0.00 0.00 40.17 5.54
2062 2226 0.249657 GATCAGATGGACACTCCGCC 60.250 60.000 0.00 0.00 40.17 6.13
2066 2230 2.124570 ATGGACACTCCGCCATGC 60.125 61.111 0.00 0.00 43.04 4.06
2101 2265 1.412710 GCATCCCGTCTTGATCTGGTA 59.587 52.381 0.00 0.00 0.00 3.25
2102 2266 2.158957 GCATCCCGTCTTGATCTGGTAA 60.159 50.000 0.00 0.00 0.00 2.85
2111 2275 6.213677 CGTCTTGATCTGGTAATTAATCCGA 58.786 40.000 0.00 0.00 0.00 4.55
2246 2410 1.603455 CTGGTCCACCGCCATGTTT 60.603 57.895 0.00 0.00 39.43 2.83
2270 2434 1.217244 GGACATCAAGTACGCCGGT 59.783 57.895 1.90 0.00 0.00 5.28
2297 2461 2.498941 CCTCGCCGCCAAGATCCTA 61.499 63.158 0.00 0.00 0.00 2.94
2373 2537 2.014554 GACTTCTTCGTGTGCGCGA 61.015 57.895 12.10 3.58 39.28 5.87
2433 2597 1.523938 GGCGGCCTCTTGTATCACC 60.524 63.158 12.87 0.00 0.00 4.02
2434 2598 1.220749 GCGGCCTCTTGTATCACCA 59.779 57.895 0.00 0.00 0.00 4.17
2492 2656 2.759973 CTCCTGGCCGCCTACTCA 60.760 66.667 11.61 0.00 0.00 3.41
2751 2915 0.759346 GATCTGGTATCCCCGCAAGT 59.241 55.000 0.00 0.00 35.15 3.16
2774 2939 1.738099 CAACCCGAACCTGCTCGAG 60.738 63.158 8.45 8.45 41.44 4.04
2835 3000 1.948834 TCGACGACAGGAACAACTACA 59.051 47.619 0.00 0.00 0.00 2.74
2939 3104 4.804139 CAGTCAATTCCAGATGGTACGTAC 59.196 45.833 17.56 17.56 36.34 3.67
2970 3141 7.849804 TTTCAGAAGTTATTATCTCAGGCAC 57.150 36.000 0.00 0.00 0.00 5.01
2971 3142 5.918608 TCAGAAGTTATTATCTCAGGCACC 58.081 41.667 0.00 0.00 0.00 5.01
2991 3167 5.690409 GCACCAAGCATCATTTGATATTCTG 59.310 40.000 0.00 0.00 44.79 3.02
3025 3201 2.958818 TGACAACCAGACCTCAGTAGT 58.041 47.619 0.00 0.00 0.00 2.73
3056 3232 7.565398 TCTCTTTCTGCTGGTAATAATCTACCT 59.435 37.037 1.76 0.00 41.78 3.08
3086 3262 5.745312 TGGCTTTCTAGATTCAGTTCAGA 57.255 39.130 0.00 0.00 0.00 3.27
3087 3263 5.728471 TGGCTTTCTAGATTCAGTTCAGAG 58.272 41.667 0.00 0.00 0.00 3.35
3092 3268 6.522625 TTCTAGATTCAGTTCAGAGACAGG 57.477 41.667 0.00 0.00 0.00 4.00
3093 3269 3.608316 AGATTCAGTTCAGAGACAGGC 57.392 47.619 0.00 0.00 0.00 4.85
3096 3272 2.827800 TCAGTTCAGAGACAGGCTTG 57.172 50.000 0.00 0.00 0.00 4.01
3098 3274 2.141517 CAGTTCAGAGACAGGCTTGTG 58.858 52.381 6.05 0.00 37.76 3.33
3106 3286 4.335315 CAGAGACAGGCTTGTGTTTTTACA 59.665 41.667 6.05 0.00 37.76 2.41
3115 3295 5.112686 GCTTGTGTTTTTACAACCCAATCA 58.887 37.500 0.00 0.00 35.75 2.57
3119 3299 5.654650 TGTGTTTTTACAACCCAATCAGAGT 59.345 36.000 0.00 0.00 0.00 3.24
3173 3365 2.434658 ATCAAGGTGAGCACGCGTCA 62.435 55.000 9.86 0.55 0.00 4.35
3338 3530 1.218316 GACGGGGCTCGACAAGAAT 59.782 57.895 16.65 0.00 42.43 2.40
3351 3543 1.308998 CAAGAATCGGTATGGCCACC 58.691 55.000 8.16 4.52 36.97 4.61
3410 3602 2.474920 CGTCACGTTCGAGTACGCG 61.475 63.158 13.19 13.19 45.06 6.01
3475 3667 2.548057 TCGTCTGAACTGAAACCAATGC 59.452 45.455 0.00 0.00 0.00 3.56
3479 3671 3.753272 TCTGAACTGAAACCAATGCTAGC 59.247 43.478 8.10 8.10 0.00 3.42
3542 3734 4.047627 TGGGTCTAGTGACAATCTCTCA 57.952 45.455 0.00 0.00 44.61 3.27
3557 3749 6.558014 ACAATCTCTCAGTCATCCTCCATATT 59.442 38.462 0.00 0.00 0.00 1.28
3568 3760 8.260818 AGTCATCCTCCATATTCCGTTATAATG 58.739 37.037 0.00 0.00 0.00 1.90
3575 3767 9.653287 CTCCATATTCCGTTATAATGAGCTAAA 57.347 33.333 6.24 0.00 0.00 1.85
3660 3869 7.161418 GTGTTGTTGCGCTATAAAGTATAAACG 59.839 37.037 9.73 0.00 0.00 3.60
3791 4270 0.319900 AGACACTGCTACTGCCGTTG 60.320 55.000 0.00 0.00 34.44 4.10
3810 4289 5.221048 CCGTTGTGGAAAGGATTGGATATTC 60.221 44.000 0.00 0.00 42.00 1.75
3848 4327 3.288092 GGCCAGGTTTAGTTTATCAGGG 58.712 50.000 0.00 0.00 0.00 4.45
3922 4402 2.306512 ACGTTAATTTGTGGGGGAGCTA 59.693 45.455 0.00 0.00 0.00 3.32
3950 4430 0.026803 CGCTTCTGGATGCGTTTAGC 59.973 55.000 18.34 1.53 45.88 3.09
3990 4470 3.030291 TGGTCAAAGTTTGGCTGTTGAT 58.970 40.909 19.07 0.00 35.12 2.57
3997 4477 8.462016 GTCAAAGTTTGGCTGTTGATTATAGAT 58.538 33.333 12.99 0.00 32.93 1.98
4004 4484 7.350744 TGGCTGTTGATTATAGATTGCAATT 57.649 32.000 14.33 6.39 0.00 2.32
4016 4496 5.280654 AGATTGCAATTGACTGGTTTGTT 57.719 34.783 14.33 0.00 0.00 2.83
4017 4497 6.403866 AGATTGCAATTGACTGGTTTGTTA 57.596 33.333 14.33 0.00 0.00 2.41
4018 4498 6.449698 AGATTGCAATTGACTGGTTTGTTAG 58.550 36.000 14.33 0.00 0.00 2.34
4037 4517 5.005394 TGTTAGTACGTTCGTATAGTCGGTC 59.995 44.000 8.26 0.00 0.00 4.79
4039 4519 1.359848 ACGTTCGTATAGTCGGTCGT 58.640 50.000 0.00 0.00 36.51 4.34
4049 4529 0.456312 AGTCGGTCGTCGCTGAAATC 60.456 55.000 0.68 0.00 39.05 2.17
4056 4536 1.139816 CGTCGCTGAAATCGCTAGCA 61.140 55.000 16.45 2.17 37.29 3.49
4063 4543 3.243434 GCTGAAATCGCTAGCACTAGGTA 60.243 47.826 16.45 0.00 37.40 3.08
4075 4555 2.614983 GCACTAGGTACTTCGAGAGAGG 59.385 54.545 0.00 0.00 43.69 3.69
4140 4620 6.983984 ACTATAAATAGACTTCCTTCGCTCC 58.016 40.000 4.02 0.00 34.50 4.70
4176 4656 3.073735 CTCCACAGCCGAGCTCCT 61.074 66.667 8.47 0.00 36.40 3.69
4193 4828 1.452108 CTGTTCCCTTCATCCGCCC 60.452 63.158 0.00 0.00 0.00 6.13
4198 4833 4.883354 CCTTCATCCGCCCTGGCC 62.883 72.222 1.86 0.00 37.80 5.36
4231 4866 1.919816 TGAGGAGCTGCCATGACCA 60.920 57.895 0.00 0.00 40.02 4.02
4289 4925 0.639943 TACCCCTCCCTGATGTGCTA 59.360 55.000 0.00 0.00 0.00 3.49
4425 5061 1.337387 GTACGTGCCTAGATCACTCCC 59.663 57.143 0.00 0.00 32.54 4.30
4429 5065 2.667470 GTGCCTAGATCACTCCCTGTA 58.333 52.381 0.00 0.00 0.00 2.74
4432 5068 2.599677 CCTAGATCACTCCCTGTACCC 58.400 57.143 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.101585 ACACAGTTCAGATGGAAGTTCTGA 59.898 41.667 2.25 0.00 45.93 3.27
20 21 5.179555 GGTCTGGTAATTGAAGACACAGTTC 59.820 44.000 14.94 0.00 41.73 3.01
23 24 4.641396 TGGTCTGGTAATTGAAGACACAG 58.359 43.478 14.94 0.00 41.73 3.66
42 43 1.660560 GCCTTGCTGATGCGAATGGT 61.661 55.000 0.00 0.00 43.34 3.55
44 45 0.454600 AAGCCTTGCTGATGCGAATG 59.545 50.000 0.00 0.00 39.62 2.67
81 82 6.987386 TCATTACAGAGCTAATAAGAGGAGC 58.013 40.000 0.00 0.00 36.42 4.70
114 115 6.127869 TGGTTATGAACGGGTGATAAAACATG 60.128 38.462 0.00 0.00 0.00 3.21
115 116 5.946972 TGGTTATGAACGGGTGATAAAACAT 59.053 36.000 0.00 0.00 0.00 2.71
117 118 5.883503 TGGTTATGAACGGGTGATAAAAC 57.116 39.130 0.00 0.00 0.00 2.43
128 129 4.334443 CTCGCAAAGAATGGTTATGAACG 58.666 43.478 0.00 0.00 0.00 3.95
143 144 0.753262 GGAGATAGGGAGCTCGCAAA 59.247 55.000 29.95 18.87 39.11 3.68
144 145 0.397114 TGGAGATAGGGAGCTCGCAA 60.397 55.000 29.95 8.20 39.11 4.85
164 165 4.520179 TCAAACACATGGAGGAGATCATG 58.480 43.478 0.00 0.00 44.42 3.07
170 171 7.275183 TGATATAACTCAAACACATGGAGGAG 58.725 38.462 0.00 0.00 32.98 3.69
171 172 7.194112 TGATATAACTCAAACACATGGAGGA 57.806 36.000 0.00 0.00 32.98 3.71
172 173 6.484643 CCTGATATAACTCAAACACATGGAGG 59.515 42.308 0.00 0.00 32.98 4.30
178 179 8.684386 TGAAAACCTGATATAACTCAAACACA 57.316 30.769 0.00 0.00 0.00 3.72
231 232 2.848071 GGAATAGGGTTGGTAGGGTTGA 59.152 50.000 0.00 0.00 0.00 3.18
245 246 1.344763 CTGGACCGGCTAAGGAATAGG 59.655 57.143 0.00 0.00 34.73 2.57
248 249 0.983378 AGCTGGACCGGCTAAGGAAT 60.983 55.000 26.96 0.00 45.07 3.01
277 278 3.717294 ATGGGTGCAGGTCCGTCC 61.717 66.667 0.00 0.00 0.00 4.79
278 279 2.436646 CATGGGTGCAGGTCCGTC 60.437 66.667 0.00 0.00 0.00 4.79
311 312 0.251165 TTTGGACCTAAGCACCAGGC 60.251 55.000 0.00 0.00 45.30 4.85
313 314 2.863809 AGTTTTGGACCTAAGCACCAG 58.136 47.619 5.42 0.00 35.08 4.00
314 315 3.136809 TGTAGTTTTGGACCTAAGCACCA 59.863 43.478 5.42 0.00 0.00 4.17
315 316 3.746940 TGTAGTTTTGGACCTAAGCACC 58.253 45.455 5.42 0.00 0.00 5.01
316 317 5.959618 ATTGTAGTTTTGGACCTAAGCAC 57.040 39.130 5.42 2.87 0.00 4.40
382 524 0.615261 TGGGTCACGTATGTGGGCTA 60.615 55.000 15.02 0.00 46.42 3.93
436 578 3.263681 TGTTACATAAATGGACCGACCCA 59.736 43.478 0.00 0.00 41.05 4.51
442 584 3.970842 TGGGGTGTTACATAAATGGACC 58.029 45.455 0.00 0.00 0.00 4.46
556 700 8.618240 TTGGATCTGAGGGAGTATTAAAACTA 57.382 34.615 0.00 0.00 0.00 2.24
568 712 6.266103 GCATCAATTAATTTGGATCTGAGGGA 59.734 38.462 0.00 0.00 35.92 4.20
573 717 9.193133 GAGATTGCATCAATTAATTTGGATCTG 57.807 33.333 0.00 0.00 33.90 2.90
635 779 9.565213 CACTTCCTTCAATCTGAATTAATTGAC 57.435 33.333 5.17 0.00 40.58 3.18
649 793 5.473504 ACATAAAACGAGCACTTCCTTCAAT 59.526 36.000 0.00 0.00 0.00 2.57
653 797 4.385825 TGACATAAAACGAGCACTTCCTT 58.614 39.130 0.00 0.00 0.00 3.36
701 845 7.151976 CACCCTAATTTCTTCGGTTTTGAAAT 58.848 34.615 0.00 0.00 40.71 2.17
705 849 4.234574 GCACCCTAATTTCTTCGGTTTTG 58.765 43.478 0.00 0.00 0.00 2.44
764 908 1.821136 AGACAGATCGTGCACATCTCA 59.179 47.619 21.49 1.39 0.00 3.27
794 938 7.142021 TGAAAAAGCGCACACTAAATATTTGA 58.858 30.769 11.47 0.00 0.00 2.69
796 940 8.532977 AATGAAAAAGCGCACACTAAATATTT 57.467 26.923 11.47 5.89 0.00 1.40
810 954 3.061006 GTGACTGCACAAATGAAAAAGCG 60.061 43.478 0.00 0.00 44.51 4.68
812 956 4.431809 TGGTGACTGCACAAATGAAAAAG 58.568 39.130 0.00 0.00 46.96 2.27
813 957 4.462508 TGGTGACTGCACAAATGAAAAA 57.537 36.364 0.00 0.00 46.96 1.94
829 977 5.692115 TCTGTTGGCTATCTAAATGGTGA 57.308 39.130 0.00 0.00 0.00 4.02
855 1003 0.822121 GTGGCGGAGGTCTGGTTTTT 60.822 55.000 0.00 0.00 0.00 1.94
891 1051 3.839432 CGGGAGGAAGAGGACGCC 61.839 72.222 0.00 0.00 0.00 5.68
905 1065 1.727511 TTATAGCGTGTCCCGTCGGG 61.728 60.000 25.31 25.31 46.11 5.14
966 1126 1.003118 GAGGGAATGCCACACTGTGTA 59.997 52.381 13.89 0.00 35.15 2.90
968 1128 0.037303 AGAGGGAATGCCACACTGTG 59.963 55.000 6.19 6.19 35.15 3.66
1008 1168 0.611618 TGGCTATGGCTGGTTGGTTG 60.612 55.000 0.00 0.00 38.73 3.77
1041 1201 2.282180 GCGGAAAGGACCAAGCCA 60.282 61.111 0.00 0.00 0.00 4.75
1043 1203 1.678970 ATGGCGGAAAGGACCAAGC 60.679 57.895 0.00 0.00 36.94 4.01
1050 1210 2.676121 TGTGCCATGGCGGAAAGG 60.676 61.111 30.87 0.00 45.51 3.11
1054 1214 4.720902 CACCTGTGCCATGGCGGA 62.721 66.667 29.44 19.21 45.51 5.54
1089 1249 1.375523 GTAGTTCTGGGTGGTGCGG 60.376 63.158 0.00 0.00 0.00 5.69
1090 1250 1.375523 GGTAGTTCTGGGTGGTGCG 60.376 63.158 0.00 0.00 0.00 5.34
1203 1363 2.345760 GGCCTTCCCGTCGTGTAGA 61.346 63.158 0.00 0.00 0.00 2.59
1206 1366 3.552384 TTGGCCTTCCCGTCGTGT 61.552 61.111 3.32 0.00 35.87 4.49
1235 1395 2.698855 TGAGATTTCCAGTAGGCAGC 57.301 50.000 0.00 0.00 33.74 5.25
1237 1397 5.188434 CAGATTTGAGATTTCCAGTAGGCA 58.812 41.667 0.00 0.00 33.74 4.75
1243 1403 3.129988 GCACCCAGATTTGAGATTTCCAG 59.870 47.826 0.00 0.00 0.00 3.86
1246 1406 4.219288 AGTTGCACCCAGATTTGAGATTTC 59.781 41.667 0.00 0.00 0.00 2.17
1259 1419 5.321102 ACACAGATTAATTAGTTGCACCCA 58.679 37.500 0.00 0.00 0.00 4.51
1283 1443 6.237901 TGCAGAAGTTAATGTTGATACTGGT 58.762 36.000 0.00 0.00 0.00 4.00
1291 1451 7.307337 GGTTGGAAAATGCAGAAGTTAATGTTG 60.307 37.037 0.00 0.00 0.00 3.33
1292 1452 6.705825 GGTTGGAAAATGCAGAAGTTAATGTT 59.294 34.615 0.00 0.00 0.00 2.71
1317 1477 1.146263 GCCCGTAAGATCCACCTGG 59.854 63.158 0.00 0.00 43.02 4.45
1329 1489 2.180204 GTCGTAGTAGCCGCCCGTA 61.180 63.158 0.00 0.00 0.00 4.02
1588 1748 0.745845 ACCGACTACGCGTATGACCT 60.746 55.000 20.91 0.00 38.29 3.85
1612 1776 2.485903 TCGAAATGCGTACACTTGGTT 58.514 42.857 0.00 0.00 41.80 3.67
1628 1792 1.731709 CTGCACATGAATCCGTTCGAA 59.268 47.619 0.00 0.00 37.15 3.71
1634 1798 1.378882 CCCACCTGCACATGAATCCG 61.379 60.000 0.00 0.00 0.00 4.18
1641 1805 2.665000 CGTCTCCCACCTGCACAT 59.335 61.111 0.00 0.00 0.00 3.21
1664 1828 3.059982 CCAGCAGAAGTGGTCGGA 58.940 61.111 0.00 0.00 29.64 4.55
1828 1992 1.860484 GCTTGGAGTGTTGCAGGAGC 61.860 60.000 0.00 0.00 42.57 4.70
1857 2021 6.392354 TGGATGGTTAGTGTAGTTTAGAACG 58.608 40.000 0.00 0.00 36.23 3.95
1861 2025 6.258727 CAGCATGGATGGTTAGTGTAGTTTAG 59.741 42.308 0.00 0.00 36.17 1.85
1865 2029 3.774766 TCAGCATGGATGGTTAGTGTAGT 59.225 43.478 0.00 0.00 36.17 2.73
1866 2030 4.406648 TCAGCATGGATGGTTAGTGTAG 57.593 45.455 0.00 0.00 36.17 2.74
1867 2031 4.835284 TTCAGCATGGATGGTTAGTGTA 57.165 40.909 0.00 0.00 36.17 2.90
1868 2032 3.719268 TTCAGCATGGATGGTTAGTGT 57.281 42.857 0.00 0.00 36.17 3.55
1869 2033 4.641541 TCATTTCAGCATGGATGGTTAGTG 59.358 41.667 0.00 0.00 36.17 2.74
1882 2046 6.263842 GGATCAACTATTGGATCATTTCAGCA 59.736 38.462 0.00 0.00 41.30 4.41
1884 2048 7.718314 TCAGGATCAACTATTGGATCATTTCAG 59.282 37.037 0.00 0.00 41.30 3.02
1896 2060 6.096001 GCCAAGAAACATCAGGATCAACTATT 59.904 38.462 0.00 0.00 0.00 1.73
1901 2065 3.507233 GTGCCAAGAAACATCAGGATCAA 59.493 43.478 0.00 0.00 0.00 2.57
1904 2068 2.225091 TGGTGCCAAGAAACATCAGGAT 60.225 45.455 0.00 0.00 0.00 3.24
1909 2073 2.299867 ACCAATGGTGCCAAGAAACATC 59.700 45.455 3.09 0.00 32.98 3.06
1922 2086 0.033796 CTGAGCCATCCACCAATGGT 60.034 55.000 0.00 0.00 46.69 3.55
1932 2096 1.818642 AGTCAAACAGCTGAGCCATC 58.181 50.000 23.35 6.12 0.00 3.51
1936 2100 0.110464 GCGAAGTCAAACAGCTGAGC 60.110 55.000 23.35 0.00 0.00 4.26
1950 2114 1.804326 CCGGTACTTGTCGGCGAAG 60.804 63.158 12.92 9.44 39.78 3.79
1964 2128 3.064324 CGTCGTACCTTCCCCGGT 61.064 66.667 0.00 0.00 41.10 5.28
1993 2157 2.835764 ACTGGTAATAGTTCCTCGCCAA 59.164 45.455 0.00 0.00 0.00 4.52
2004 2168 2.688446 TCCGCTGACTGACTGGTAATAG 59.312 50.000 0.00 0.00 0.00 1.73
2038 2202 3.069300 CGGAGTGTCCATCTGATCTGATT 59.931 47.826 12.05 0.00 35.91 2.57
2039 2203 2.627221 CGGAGTGTCCATCTGATCTGAT 59.373 50.000 9.15 9.15 35.91 2.90
2041 2205 1.537776 GCGGAGTGTCCATCTGATCTG 60.538 57.143 0.00 0.00 35.91 2.90
2043 2207 0.249657 GGCGGAGTGTCCATCTGATC 60.250 60.000 0.00 0.00 35.91 2.92
2045 2209 0.977627 ATGGCGGAGTGTCCATCTGA 60.978 55.000 0.00 0.00 38.65 3.27
2046 2210 0.812811 CATGGCGGAGTGTCCATCTG 60.813 60.000 0.00 0.00 40.88 2.90
2047 2211 1.524002 CATGGCGGAGTGTCCATCT 59.476 57.895 0.00 0.00 40.88 2.90
2048 2212 2.182842 GCATGGCGGAGTGTCCATC 61.183 63.158 0.00 0.00 40.88 3.51
2049 2213 2.124570 GCATGGCGGAGTGTCCAT 60.125 61.111 0.00 0.00 43.45 3.41
2050 2214 2.970379 ATGCATGGCGGAGTGTCCA 61.970 57.895 0.00 0.00 35.91 4.02
2051 2215 2.124570 ATGCATGGCGGAGTGTCC 60.125 61.111 0.00 0.00 0.00 4.02
2052 2216 1.308069 AACATGCATGGCGGAGTGTC 61.308 55.000 29.41 0.00 0.00 3.67
2053 2217 1.303561 AACATGCATGGCGGAGTGT 60.304 52.632 29.41 5.52 0.00 3.55
2054 2218 1.307355 TGAACATGCATGGCGGAGTG 61.307 55.000 29.41 4.81 0.00 3.51
2055 2219 0.608856 TTGAACATGCATGGCGGAGT 60.609 50.000 29.41 5.49 0.00 3.85
2056 2220 0.179156 GTTGAACATGCATGGCGGAG 60.179 55.000 29.41 4.72 0.00 4.63
2057 2221 0.892814 TGTTGAACATGCATGGCGGA 60.893 50.000 29.41 10.86 0.00 5.54
2058 2222 0.173935 ATGTTGAACATGCATGGCGG 59.826 50.000 29.41 5.90 37.45 6.13
2059 2223 1.999048 AATGTTGAACATGCATGGCG 58.001 45.000 29.41 6.29 37.97 5.69
2060 2224 2.417239 CCAAATGTTGAACATGCATGGC 59.583 45.455 29.41 20.69 37.97 4.40
2061 2225 2.417239 GCCAAATGTTGAACATGCATGG 59.583 45.455 29.41 23.10 37.97 3.66
2062 2226 3.067833 TGCCAAATGTTGAACATGCATG 58.932 40.909 25.09 25.09 37.97 4.06
2066 2230 3.264104 GGGATGCCAAATGTTGAACATG 58.736 45.455 12.09 1.55 37.97 3.21
2111 2275 1.227853 GTCCTGAAACCGCACCACT 60.228 57.895 0.00 0.00 0.00 4.00
2156 2320 3.066190 TCGTCGGTCGCCTGGAAT 61.066 61.111 0.00 0.00 39.67 3.01
2246 2410 1.136305 GCGTACTTGATGTCCCAGCTA 59.864 52.381 0.00 0.00 0.00 3.32
2433 2597 0.179020 TGGAGGTTGTTCCACTGCTG 60.179 55.000 0.00 0.00 42.24 4.41
2434 2598 0.109342 CTGGAGGTTGTTCCACTGCT 59.891 55.000 0.00 0.00 42.24 4.24
2751 2915 2.429930 CAGGTTCGGGTTGCTGGA 59.570 61.111 0.00 0.00 0.00 3.86
2904 3069 2.539003 TTGACTGATCAAACCGGCG 58.461 52.632 0.00 0.00 41.99 6.46
2917 3082 4.142004 GGTACGTACCATCTGGAATTGACT 60.142 45.833 34.65 0.00 45.73 3.41
2968 3139 6.802608 ACAGAATATCAAATGATGCTTGGTG 58.197 36.000 6.17 3.35 36.05 4.17
2970 3141 7.713750 AGAACAGAATATCAAATGATGCTTGG 58.286 34.615 6.17 0.00 36.05 3.61
2971 3142 9.020813 CAAGAACAGAATATCAAATGATGCTTG 57.979 33.333 6.17 0.00 36.05 4.01
2986 3157 1.891150 CAAGCCCTGCAAGAACAGAAT 59.109 47.619 0.00 0.00 40.25 2.40
2987 3158 1.133823 TCAAGCCCTGCAAGAACAGAA 60.134 47.619 0.00 0.00 40.25 3.02
2991 3167 1.032014 TTGTCAAGCCCTGCAAGAAC 58.968 50.000 0.00 0.00 34.07 3.01
3025 3201 0.694771 ACCAGCAGAAAGAGATGGCA 59.305 50.000 0.00 0.00 34.24 4.92
3056 3232 7.568349 ACTGAATCTAGAAAGCCATGATGTTA 58.432 34.615 0.00 0.00 0.00 2.41
3086 3262 4.142249 GGTTGTAAAAACACAAGCCTGTCT 60.142 41.667 6.87 0.00 46.32 3.41
3087 3263 4.109766 GGTTGTAAAAACACAAGCCTGTC 58.890 43.478 6.87 0.00 46.32 3.51
3093 3269 6.568869 TCTGATTGGGTTGTAAAAACACAAG 58.431 36.000 11.17 0.00 45.45 3.16
3096 3272 6.144078 ACTCTGATTGGGTTGTAAAAACAC 57.856 37.500 0.00 0.00 0.00 3.32
3098 3274 7.262048 TCAAACTCTGATTGGGTTGTAAAAAC 58.738 34.615 0.00 0.00 0.00 2.43
3115 3295 4.217118 GCACATGGTGAAGAATCAAACTCT 59.783 41.667 0.00 0.00 37.30 3.24
3119 3299 2.351641 GCGCACATGGTGAAGAATCAAA 60.352 45.455 0.30 0.00 37.30 2.69
3149 3341 2.109126 GTGCTCACCTTGATCGGCC 61.109 63.158 0.00 0.00 0.00 6.13
3151 3343 2.456119 GCGTGCTCACCTTGATCGG 61.456 63.158 0.00 0.00 0.00 4.18
3264 3456 1.149361 TCGTGCACCGTCTTGTTCAC 61.149 55.000 12.15 0.00 37.94 3.18
3338 3530 2.687200 AGCAGGTGGCCATACCGA 60.687 61.111 9.72 0.00 45.56 4.69
3428 3620 2.424302 CCGGTGACCCAGACGTTT 59.576 61.111 0.00 0.00 0.00 3.60
3475 3667 4.002906 TGTAACCTGACAAACTGGCTAG 57.997 45.455 0.00 0.00 40.59 3.42
3479 3671 6.627395 TGTAATTGTAACCTGACAAACTGG 57.373 37.500 0.00 0.00 42.39 4.00
3542 3734 7.792364 TTATAACGGAATATGGAGGATGACT 57.208 36.000 0.00 0.00 0.00 3.41
3557 3749 7.667557 AGCATAGTTTAGCTCATTATAACGGA 58.332 34.615 0.00 0.00 36.00 4.69
3568 3760 7.279750 AGTTACTCCTAGCATAGTTTAGCTC 57.720 40.000 0.00 0.00 42.05 4.09
3575 3767 4.828387 GCCACTAGTTACTCCTAGCATAGT 59.172 45.833 0.00 0.00 38.39 2.12
3763 4242 4.452455 GCAGTAGCAGTGTCTTTGTTGTAT 59.548 41.667 0.00 0.00 41.58 2.29
3770 4249 3.217242 CGGCAGTAGCAGTGTCTTT 57.783 52.632 0.00 0.00 44.61 2.52
3871 4351 4.166531 ACCCTATTGGCCCGATTTTTACTA 59.833 41.667 0.00 0.00 37.83 1.82
3948 4428 1.134521 TCTATCCACGGCAAAATCGCT 60.135 47.619 0.00 0.00 0.00 4.93
3950 4430 2.224079 CCATCTATCCACGGCAAAATCG 59.776 50.000 0.00 0.00 0.00 3.34
3959 4439 4.094887 CCAAACTTTGACCATCTATCCACG 59.905 45.833 2.87 0.00 0.00 4.94
3990 4470 8.121305 ACAAACCAGTCAATTGCAATCTATAA 57.879 30.769 13.38 0.00 0.00 0.98
3997 4477 5.590530 ACTAACAAACCAGTCAATTGCAA 57.409 34.783 0.00 0.00 0.00 4.08
4004 4484 4.043750 CGAACGTACTAACAAACCAGTCA 58.956 43.478 0.00 0.00 0.00 3.41
4016 4496 3.729217 CGACCGACTATACGAACGTACTA 59.271 47.826 9.19 3.64 33.01 1.82
4017 4497 2.535984 CGACCGACTATACGAACGTACT 59.464 50.000 9.19 2.75 33.01 2.73
4018 4498 2.281762 ACGACCGACTATACGAACGTAC 59.718 50.000 9.19 0.00 40.28 3.67
4037 4517 1.139816 TGCTAGCGATTTCAGCGACG 61.140 55.000 10.77 0.00 38.15 5.12
4039 4519 0.173481 AGTGCTAGCGATTTCAGCGA 59.827 50.000 10.77 0.00 38.15 4.93
4049 4529 1.938577 TCGAAGTACCTAGTGCTAGCG 59.061 52.381 10.77 0.00 31.66 4.26
4056 4536 2.421811 GGCCTCTCTCGAAGTACCTAGT 60.422 54.545 0.00 0.00 0.00 2.57
4075 4555 4.094684 CCTTGACATCGACGAGGC 57.905 61.111 9.79 3.31 32.98 4.70
4140 4620 3.787001 GGGGAGGAAGGTGAGGCG 61.787 72.222 0.00 0.00 0.00 5.52
4176 4656 1.923395 AGGGCGGATGAAGGGAACA 60.923 57.895 0.00 0.00 0.00 3.18
4198 4833 1.669115 CTCACCTTGGCACACTCCG 60.669 63.158 0.00 0.00 39.29 4.63
4231 4866 0.699231 GAGGAGGTTGGGGGATCCAT 60.699 60.000 15.23 0.00 46.52 3.41
4392 5028 1.073722 ACGTACAGGAGACACCGGA 59.926 57.895 9.46 0.00 44.74 5.14
4425 5061 1.380785 TAGCGGGGACAGGGTACAG 60.381 63.158 0.00 0.00 0.00 2.74
4429 5065 2.683933 CTGTAGCGGGGACAGGGT 60.684 66.667 3.92 0.00 40.58 4.34
4432 5068 4.514577 CGGCTGTAGCGGGGACAG 62.515 72.222 3.75 6.71 45.90 3.51


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

AutoCloner maintained by Alex Coulton.