Multiple sequence alignment - TraesCS4A01G338600

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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 TraesCS4A01G338600 chr4A 100.000 3773 0 0 683 4455 620555966 620559738 0.000000e+00 6968.0
1 TraesCS4A01G338600 chr4A 100.000 458 0 0 1 458 620555284 620555741 0.000000e+00 846.0
2 TraesCS4A01G338600 chr4A 81.512 860 124 21 2634 3464 609942577 609943430 0.000000e+00 675.0
3 TraesCS4A01G338600 chr4A 77.291 982 174 33 1157 2116 609941223 609942177 2.360000e-147 532.0
4 TraesCS4A01G338600 chr4A 94.624 93 5 0 890 982 621812568 621812476 1.290000e-30 145.0
5 TraesCS4A01G338600 chr5B 97.054 2478 62 5 995 3465 700743555 700741082 0.000000e+00 4161.0
6 TraesCS4A01G338600 chr5B 85.172 843 110 8 2635 3464 705071823 705070983 0.000000e+00 850.0
7 TraesCS4A01G338600 chr5B 78.467 1305 210 38 2185 3464 705082276 705081018 0.000000e+00 787.0
8 TraesCS4A01G338600 chr5B 84.165 461 42 10 7 458 700744215 700743777 6.890000e-113 418.0
9 TraesCS4A01G338600 chr5B 78.584 551 91 16 1612 2147 705072899 705072361 5.520000e-89 339.0
10 TraesCS4A01G338600 chr5D 85.842 2020 208 39 1489 3464 558056746 558054761 0.000000e+00 2074.0
11 TraesCS4A01G338600 chr5D 76.609 1103 213 30 1117 2183 558067474 558066381 2.330000e-157 566.0
12 TraesCS4A01G338600 chr5D 83.232 328 40 8 2203 2530 558066325 558066013 2.030000e-73 287.0
13 TraesCS4A01G338600 chr5D 96.629 89 3 0 897 985 57225962 57226050 9.980000e-32 148.0
14 TraesCS4A01G338600 chr5D 78.512 121 25 1 2205 2325 393767648 393767767 1.330000e-10 78.7
15 TraesCS4A01G338600 chr7D 92.843 978 51 13 3495 4455 609899538 609898563 0.000000e+00 1400.0
16 TraesCS4A01G338600 chr7D 91.862 983 57 14 3494 4455 205947706 205948686 0.000000e+00 1351.0
17 TraesCS4A01G338600 chr7D 91.291 999 50 24 3494 4455 2215396 2216394 0.000000e+00 1328.0
18 TraesCS4A01G338600 chr3D 92.716 961 58 8 3495 4455 452628123 452627175 0.000000e+00 1376.0
19 TraesCS4A01G338600 chr3D 92.054 969 66 6 3495 4455 327464738 327465703 0.000000e+00 1352.0
20 TraesCS4A01G338600 chr3D 91.268 962 61 16 3495 4455 48164509 48165448 0.000000e+00 1290.0
21 TraesCS4A01G338600 chr2D 91.903 988 49 13 3495 4454 636041976 636040992 0.000000e+00 1352.0
22 TraesCS4A01G338600 chr2D 91.491 999 46 17 3495 4455 54603457 54602460 0.000000e+00 1338.0
23 TraesCS4A01G338600 chr2D 81.424 323 46 11 1821 2139 586330695 586331007 7.400000e-63 252.0
24 TraesCS4A01G338600 chr6A 91.828 979 60 8 3497 4455 572809669 572810647 0.000000e+00 1347.0
25 TraesCS4A01G338600 chr6A 90.476 105 10 0 885 989 447873699 447873595 6.010000e-29 139.0
26 TraesCS4A01G338600 chr2A 91.291 999 48 15 3495 4455 86268337 86269334 0.000000e+00 1327.0
27 TraesCS4A01G338600 chr2A 89.834 964 84 10 3497 4455 749591359 749590405 0.000000e+00 1225.0
28 TraesCS4A01G338600 chr1A 91.937 955 65 9 3511 4455 84792110 84791158 0.000000e+00 1327.0
29 TraesCS4A01G338600 chr1D 91.002 978 58 18 3494 4455 41769059 41770022 0.000000e+00 1291.0
30 TraesCS4A01G338600 chr1D 95.695 604 25 1 3852 4455 354530334 354529732 0.000000e+00 970.0
31 TraesCS4A01G338600 chr1D 76.056 497 94 18 1648 2134 342140148 342140629 7.450000e-58 235.0
32 TraesCS4A01G338600 chr1D 92.857 98 7 0 891 988 447863811 447863714 4.650000e-30 143.0
33 TraesCS4A01G338600 chr1D 92.079 101 7 1 883 982 247300187 247300087 1.670000e-29 141.0
34 TraesCS4A01G338600 chr1B 90.192 989 68 15 3495 4455 633142664 633143651 0.000000e+00 1262.0
35 TraesCS4A01G338600 chr2B 89.970 987 70 11 3495 4455 28735103 28734120 0.000000e+00 1247.0
36 TraesCS4A01G338600 chr2B 77.654 537 89 21 1651 2176 754554801 754554285 9.370000e-77 298.0
37 TraesCS4A01G338600 chr2B 73.806 691 136 32 1671 2334 105414303 105413631 9.640000e-57 231.0
38 TraesCS4A01G338600 chr2B 97.727 88 2 0 895 982 799071320 799071233 7.720000e-33 152.0
39 TraesCS4A01G338600 chr4B 74.596 433 93 12 2938 3363 2015176 2015598 1.650000e-39 174.0
40 TraesCS4A01G338600 chr3B 93.878 98 5 1 897 993 807575427 807575524 3.590000e-31 147.0
41 TraesCS4A01G338600 chr7A 94.681 94 4 1 890 982 80994073 80994166 1.290000e-30 145.0
42 TraesCS4A01G338600 chr3A 92.233 103 7 1 890 991 709065592 709065490 1.290000e-30 145.0


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 TraesCS4A01G338600 chr4A 620555284 620559738 4454 False 3907.0 6968 100.0000 1 4455 2 chr4A.!!$F2 4454
1 TraesCS4A01G338600 chr4A 609941223 609943430 2207 False 603.5 675 79.4015 1157 3464 2 chr4A.!!$F1 2307
2 TraesCS4A01G338600 chr5B 700741082 700744215 3133 True 2289.5 4161 90.6095 7 3465 2 chr5B.!!$R2 3458
3 TraesCS4A01G338600 chr5B 705081018 705082276 1258 True 787.0 787 78.4670 2185 3464 1 chr5B.!!$R1 1279
4 TraesCS4A01G338600 chr5B 705070983 705072899 1916 True 594.5 850 81.8780 1612 3464 2 chr5B.!!$R3 1852
5 TraesCS4A01G338600 chr5D 558054761 558056746 1985 True 2074.0 2074 85.8420 1489 3464 1 chr5D.!!$R1 1975
6 TraesCS4A01G338600 chr5D 558066013 558067474 1461 True 426.5 566 79.9205 1117 2530 2 chr5D.!!$R2 1413
7 TraesCS4A01G338600 chr7D 609898563 609899538 975 True 1400.0 1400 92.8430 3495 4455 1 chr7D.!!$R1 960
8 TraesCS4A01G338600 chr7D 205947706 205948686 980 False 1351.0 1351 91.8620 3494 4455 1 chr7D.!!$F2 961
9 TraesCS4A01G338600 chr7D 2215396 2216394 998 False 1328.0 1328 91.2910 3494 4455 1 chr7D.!!$F1 961
10 TraesCS4A01G338600 chr3D 452627175 452628123 948 True 1376.0 1376 92.7160 3495 4455 1 chr3D.!!$R1 960
11 TraesCS4A01G338600 chr3D 327464738 327465703 965 False 1352.0 1352 92.0540 3495 4455 1 chr3D.!!$F2 960
12 TraesCS4A01G338600 chr3D 48164509 48165448 939 False 1290.0 1290 91.2680 3495 4455 1 chr3D.!!$F1 960
13 TraesCS4A01G338600 chr2D 636040992 636041976 984 True 1352.0 1352 91.9030 3495 4454 1 chr2D.!!$R2 959
14 TraesCS4A01G338600 chr2D 54602460 54603457 997 True 1338.0 1338 91.4910 3495 4455 1 chr2D.!!$R1 960
15 TraesCS4A01G338600 chr6A 572809669 572810647 978 False 1347.0 1347 91.8280 3497 4455 1 chr6A.!!$F1 958
16 TraesCS4A01G338600 chr2A 86268337 86269334 997 False 1327.0 1327 91.2910 3495 4455 1 chr2A.!!$F1 960
17 TraesCS4A01G338600 chr2A 749590405 749591359 954 True 1225.0 1225 89.8340 3497 4455 1 chr2A.!!$R1 958
18 TraesCS4A01G338600 chr1A 84791158 84792110 952 True 1327.0 1327 91.9370 3511 4455 1 chr1A.!!$R1 944
19 TraesCS4A01G338600 chr1D 41769059 41770022 963 False 1291.0 1291 91.0020 3494 4455 1 chr1D.!!$F1 961
20 TraesCS4A01G338600 chr1D 354529732 354530334 602 True 970.0 970 95.6950 3852 4455 1 chr1D.!!$R2 603
21 TraesCS4A01G338600 chr1B 633142664 633143651 987 False 1262.0 1262 90.1920 3495 4455 1 chr1B.!!$F1 960
22 TraesCS4A01G338600 chr2B 28734120 28735103 983 True 1247.0 1247 89.9700 3495 4455 1 chr2B.!!$R1 960
23 TraesCS4A01G338600 chr2B 754554285 754554801 516 True 298.0 298 77.6540 1651 2176 1 chr2B.!!$R3 525
24 TraesCS4A01G338600 chr2B 105413631 105414303 672 True 231.0 231 73.8060 1671 2334 1 chr2B.!!$R2 663

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
836 847 0.105964 GCACATAGCGGGTATCACCA 59.894 55.0 0.00 0.00 41.02 4.17 F
848 859 0.685131 TATCACCATGGTCGGACGGT 60.685 55.0 16.53 1.69 0.00 4.83 F
1964 2041 1.522668 TTGCCTGTGACGAATCCAAG 58.477 50.0 0.00 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2041 0.109132 CAAAATTGCGTGCCCTCTCC 60.109 55.0 0.0 0.0 0.00 3.71 R
2031 2114 0.179018 AGCACCTTGAACACCCTGTC 60.179 55.0 0.0 0.0 0.00 3.51 R
3475 3698 0.249911 GCCGTGGTCTCCCATATCAC 60.250 60.0 0.0 0.0 44.35 3.06 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 1.597663 GTGCGTGTGTTTCTGTTAGCT 59.402 47.619 0.00 0.00 0.00 3.32
58 59 1.879575 AGCTGTGGGCATCCTAACTA 58.120 50.000 0.00 0.00 44.79 2.24
74 75 4.220821 CCTAACTATGCAGATACCGGACAT 59.779 45.833 9.46 0.00 0.00 3.06
78 79 0.901827 TGCAGATACCGGACATGTGT 59.098 50.000 9.46 0.00 0.00 3.72
84 85 4.034394 CAGATACCGGACATGTGTTCATTG 59.966 45.833 9.46 0.00 31.15 2.82
91 92 5.106357 CCGGACATGTGTTCATTGTGATTTA 60.106 40.000 1.15 0.00 31.15 1.40
109 110 6.716628 GTGATTTATATCCTTTGGATGCTCCA 59.283 38.462 9.17 1.25 46.61 3.86
173 175 2.067766 GAGCTCTGCACTTGAACTCAG 58.932 52.381 6.43 0.00 29.82 3.35
183 185 7.761704 TCTGCACTTGAACTCAGTAGAAATATC 59.238 37.037 0.00 0.00 0.00 1.63
230 232 9.520515 ACAAATATTCAGTGGAAATTAGTGAGT 57.479 29.630 0.00 0.00 36.43 3.41
231 233 9.994432 CAAATATTCAGTGGAAATTAGTGAGTC 57.006 33.333 0.00 0.00 36.43 3.36
232 234 9.739276 AAATATTCAGTGGAAATTAGTGAGTCA 57.261 29.630 0.00 0.00 36.43 3.41
233 235 9.739276 AATATTCAGTGGAAATTAGTGAGTCAA 57.261 29.630 0.00 0.00 36.43 3.18
234 236 7.678947 ATTCAGTGGAAATTAGTGAGTCAAG 57.321 36.000 0.00 0.00 36.43 3.02
235 237 6.174720 TCAGTGGAAATTAGTGAGTCAAGT 57.825 37.500 0.00 0.00 0.00 3.16
237 239 6.706270 TCAGTGGAAATTAGTGAGTCAAGTTC 59.294 38.462 0.00 0.00 0.00 3.01
238 240 5.696724 AGTGGAAATTAGTGAGTCAAGTTCG 59.303 40.000 0.00 0.00 31.34 3.95
239 241 5.465724 GTGGAAATTAGTGAGTCAAGTTCGT 59.534 40.000 0.00 0.00 31.34 3.85
240 242 5.694910 TGGAAATTAGTGAGTCAAGTTCGTC 59.305 40.000 0.00 0.00 31.34 4.20
241 243 5.927115 GGAAATTAGTGAGTCAAGTTCGTCT 59.073 40.000 0.00 0.00 31.34 4.18
242 244 6.424207 GGAAATTAGTGAGTCAAGTTCGTCTT 59.576 38.462 0.00 0.00 36.75 3.01
251 253 1.499049 AAGTTCGTCTTGAAGACCGC 58.501 50.000 18.78 9.49 42.12 5.68
252 254 0.663568 AGTTCGTCTTGAAGACCGCG 60.664 55.000 18.78 8.41 42.12 6.46
253 255 0.938168 GTTCGTCTTGAAGACCGCGT 60.938 55.000 18.78 0.00 42.12 6.01
254 256 0.662374 TTCGTCTTGAAGACCGCGTC 60.662 55.000 18.78 2.66 42.12 5.19
255 257 1.371267 CGTCTTGAAGACCGCGTCA 60.371 57.895 18.78 0.00 42.12 4.35
256 258 0.937699 CGTCTTGAAGACCGCGTCAA 60.938 55.000 18.78 7.57 42.12 3.18
257 259 1.429463 GTCTTGAAGACCGCGTCAAT 58.571 50.000 14.23 0.00 40.74 2.57
258 260 1.798813 GTCTTGAAGACCGCGTCAATT 59.201 47.619 14.23 0.00 40.74 2.32
259 261 2.223377 GTCTTGAAGACCGCGTCAATTT 59.777 45.455 14.23 0.00 40.74 1.82
260 262 2.223144 TCTTGAAGACCGCGTCAATTTG 59.777 45.455 4.92 0.00 40.74 2.32
261 263 0.237235 TGAAGACCGCGTCAATTTGC 59.763 50.000 4.92 0.00 34.60 3.68
275 277 3.493877 TCAATTTGCTTGTTTTGCGATGG 59.506 39.130 0.00 0.00 36.20 3.51
292 294 5.627503 TGCGATGGCATAGAGCATGTATATT 60.628 40.000 17.14 0.00 46.21 1.28
305 307 8.319881 AGAGCATGTATATTCACTGATATTGCT 58.680 33.333 4.60 4.60 36.78 3.91
324 326 4.809815 GCTTTAGGCATTTGTTTTTGCA 57.190 36.364 0.00 0.00 40.66 4.08
338 340 9.791801 ATTTGTTTTTGCAAATTATTAGTCCCT 57.208 25.926 13.65 0.00 43.97 4.20
340 342 9.620259 TTGTTTTTGCAAATTATTAGTCCCTTT 57.380 25.926 13.65 0.00 0.00 3.11
357 366 7.862675 AGTCCCTTTTACATACTGCTATTCTT 58.137 34.615 0.00 0.00 0.00 2.52
711 720 7.399245 TGGTCTTTTGCCAAAATAGTATACC 57.601 36.000 2.58 5.66 32.29 2.73
755 766 2.027625 CCGAACGCCTGTCCACTTC 61.028 63.158 0.00 0.00 0.00 3.01
761 772 2.425592 CCTGTCCACTTCGCCACA 59.574 61.111 0.00 0.00 0.00 4.17
765 776 3.542676 TCCACTTCGCCACACGGT 61.543 61.111 0.00 0.00 43.89 4.83
788 799 1.667724 GACATCACCTGCTGCATGTAC 59.332 52.381 10.22 0.00 29.43 2.90
789 800 0.654160 CATCACCTGCTGCATGTACG 59.346 55.000 10.22 0.11 0.00 3.67
790 801 0.462581 ATCACCTGCTGCATGTACGG 60.463 55.000 10.22 6.78 0.00 4.02
791 802 1.079197 CACCTGCTGCATGTACGGA 60.079 57.895 10.22 0.00 0.00 4.69
792 803 1.079127 ACCTGCTGCATGTACGGAC 60.079 57.895 8.86 0.00 0.00 4.79
793 804 1.079197 CCTGCTGCATGTACGGACA 60.079 57.895 1.10 1.10 40.72 4.02
794 805 1.086067 CCTGCTGCATGTACGGACAG 61.086 60.000 6.62 0.00 39.50 3.51
796 807 4.919653 CTGCATGTACGGACAGCT 57.080 55.556 18.77 0.00 39.50 4.24
797 808 2.377004 CTGCATGTACGGACAGCTG 58.623 57.895 13.48 13.48 39.50 4.24
798 809 1.079197 TGCATGTACGGACAGCTGG 60.079 57.895 19.93 2.38 39.50 4.85
799 810 1.815421 GCATGTACGGACAGCTGGG 60.815 63.158 19.93 9.39 39.50 4.45
800 811 1.815421 CATGTACGGACAGCTGGGC 60.815 63.158 19.93 9.55 39.50 5.36
801 812 3.371097 ATGTACGGACAGCTGGGCG 62.371 63.158 19.93 8.56 39.50 6.13
802 813 4.065281 GTACGGACAGCTGGGCGT 62.065 66.667 19.93 13.38 0.00 5.68
803 814 4.063967 TACGGACAGCTGGGCGTG 62.064 66.667 19.93 8.21 0.00 5.34
807 818 4.735132 GACAGCTGGGCGTGCGTA 62.735 66.667 19.93 0.00 35.28 4.42
836 847 0.105964 GCACATAGCGGGTATCACCA 59.894 55.000 0.00 0.00 41.02 4.17
838 849 2.416747 CACATAGCGGGTATCACCATG 58.583 52.381 0.00 0.00 41.02 3.66
848 859 0.685131 TATCACCATGGTCGGACGGT 60.685 55.000 16.53 1.69 0.00 4.83
849 860 2.434185 CACCATGGTCGGACGGTG 60.434 66.667 16.53 15.96 42.72 4.94
877 889 5.773176 ACTTTTCAAAATAAGACCATCCCGT 59.227 36.000 0.00 0.00 0.00 5.28
893 905 6.041069 ACCATCCCGTCTTTTGTTATGAAAAA 59.959 34.615 0.00 0.00 0.00 1.94
913 925 6.511017 AAAAAGGTACTCCCTCTGTAAACT 57.489 37.500 0.00 0.00 45.47 2.66
914 926 7.622502 AAAAAGGTACTCCCTCTGTAAACTA 57.377 36.000 0.00 0.00 45.47 2.24
915 927 7.622502 AAAAGGTACTCCCTCTGTAAACTAA 57.377 36.000 0.00 0.00 45.47 2.24
916 928 7.809880 AAAGGTACTCCCTCTGTAAACTAAT 57.190 36.000 0.00 0.00 45.47 1.73
917 929 8.906238 AAAGGTACTCCCTCTGTAAACTAATA 57.094 34.615 0.00 0.00 45.47 0.98
918 930 9.503369 AAAGGTACTCCCTCTGTAAACTAATAT 57.497 33.333 0.00 0.00 45.47 1.28
924 936 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
925 937 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
926 938 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
927 939 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
928 940 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
957 969 6.990546 CACTAAAATAGTGTCCTAAACGCTC 58.009 40.000 8.94 0.00 45.69 5.03
958 970 6.812160 CACTAAAATAGTGTCCTAAACGCTCT 59.188 38.462 8.94 0.00 45.69 4.09
959 971 7.331193 CACTAAAATAGTGTCCTAAACGCTCTT 59.669 37.037 8.94 0.00 45.69 2.85
960 972 8.526147 ACTAAAATAGTGTCCTAAACGCTCTTA 58.474 33.333 0.00 0.00 45.69 2.10
961 973 9.530633 CTAAAATAGTGTCCTAAACGCTCTTAT 57.469 33.333 0.00 0.00 45.69 1.73
967 979 8.235359 AGTGTCCTAAACGCTCTTATATTAGT 57.765 34.615 0.00 0.00 45.69 2.24
968 980 8.693625 AGTGTCCTAAACGCTCTTATATTAGTT 58.306 33.333 0.00 0.00 45.69 2.24
969 981 8.966194 GTGTCCTAAACGCTCTTATATTAGTTC 58.034 37.037 0.00 0.00 35.42 3.01
970 982 8.689061 TGTCCTAAACGCTCTTATATTAGTTCA 58.311 33.333 0.00 0.00 0.00 3.18
971 983 8.966194 GTCCTAAACGCTCTTATATTAGTTCAC 58.034 37.037 0.00 0.00 0.00 3.18
972 984 7.859377 TCCTAAACGCTCTTATATTAGTTCACG 59.141 37.037 0.00 0.00 0.00 4.35
973 985 6.823678 AAACGCTCTTATATTAGTTCACGG 57.176 37.500 0.00 0.00 0.00 4.94
974 986 5.762825 ACGCTCTTATATTAGTTCACGGA 57.237 39.130 0.00 0.00 0.00 4.69
975 987 5.759963 ACGCTCTTATATTAGTTCACGGAG 58.240 41.667 0.00 0.00 0.00 4.63
976 988 5.154932 CGCTCTTATATTAGTTCACGGAGG 58.845 45.833 0.00 0.00 0.00 4.30
977 989 5.471257 GCTCTTATATTAGTTCACGGAGGG 58.529 45.833 0.00 0.00 0.00 4.30
978 990 5.243283 GCTCTTATATTAGTTCACGGAGGGA 59.757 44.000 0.00 0.00 0.00 4.20
979 991 6.570764 GCTCTTATATTAGTTCACGGAGGGAG 60.571 46.154 0.00 0.00 0.00 4.30
980 992 6.371278 TCTTATATTAGTTCACGGAGGGAGT 58.629 40.000 0.00 0.00 0.00 3.85
981 993 7.520798 TCTTATATTAGTTCACGGAGGGAGTA 58.479 38.462 0.00 0.00 0.00 2.59
982 994 8.168725 TCTTATATTAGTTCACGGAGGGAGTAT 58.831 37.037 0.00 0.00 0.00 2.12
983 995 9.458727 CTTATATTAGTTCACGGAGGGAGTATA 57.541 37.037 0.00 0.00 0.00 1.47
984 996 9.986157 TTATATTAGTTCACGGAGGGAGTATAT 57.014 33.333 0.00 0.00 0.00 0.86
985 997 6.591750 ATTAGTTCACGGAGGGAGTATATG 57.408 41.667 0.00 0.00 0.00 1.78
986 998 2.628657 AGTTCACGGAGGGAGTATATGC 59.371 50.000 0.00 0.00 0.00 3.14
987 999 2.628657 GTTCACGGAGGGAGTATATGCT 59.371 50.000 0.00 0.00 0.00 3.79
988 1000 3.801307 TCACGGAGGGAGTATATGCTA 57.199 47.619 0.00 0.00 0.00 3.49
989 1001 4.108501 TCACGGAGGGAGTATATGCTAA 57.891 45.455 0.00 0.00 0.00 3.09
990 1002 4.673968 TCACGGAGGGAGTATATGCTAAT 58.326 43.478 0.00 0.00 0.00 1.73
991 1003 4.705507 TCACGGAGGGAGTATATGCTAATC 59.294 45.833 0.00 0.00 0.00 1.75
992 1004 4.707448 CACGGAGGGAGTATATGCTAATCT 59.293 45.833 0.00 0.00 0.00 2.40
993 1005 4.951094 ACGGAGGGAGTATATGCTAATCTC 59.049 45.833 0.00 1.78 0.00 2.75
1006 1018 3.132111 TGCTAATCTCAGCCATCAACGTA 59.868 43.478 0.00 0.00 41.04 3.57
1015 1027 3.938963 CAGCCATCAACGTATTTAGTGGT 59.061 43.478 0.00 0.00 0.00 4.16
1074 1089 3.006940 TCTCGTCAAACAAAGTTGTGCT 58.993 40.909 0.00 0.00 41.31 4.40
1075 1090 3.100817 CTCGTCAAACAAAGTTGTGCTG 58.899 45.455 0.00 0.00 41.31 4.41
1081 1096 4.081752 TCAAACAAAGTTGTGCTGGTCATT 60.082 37.500 0.00 0.00 41.31 2.57
1086 1101 5.984926 ACAAAGTTGTGCTGGTCATTTATTG 59.015 36.000 0.00 0.00 40.49 1.90
1089 1104 1.824230 TGTGCTGGTCATTTATTGCCC 59.176 47.619 0.00 0.00 0.00 5.36
1095 1110 3.157881 TGGTCATTTATTGCCCGTCAAA 58.842 40.909 0.00 0.00 38.34 2.69
1096 1111 3.574396 TGGTCATTTATTGCCCGTCAAAA 59.426 39.130 0.00 0.00 38.34 2.44
1097 1112 4.039245 TGGTCATTTATTGCCCGTCAAAAA 59.961 37.500 0.00 0.00 38.34 1.94
1129 1148 5.473504 AGTTGTGCTGGTCATTTAAGGTTAG 59.526 40.000 0.00 0.00 0.00 2.34
1155 1174 2.044946 GTGATGGTGGGCAGGGAC 60.045 66.667 0.00 0.00 0.00 4.46
1382 1411 2.163613 GGTGGCAACTTACATACTTGGC 59.836 50.000 0.00 0.00 40.08 4.52
1726 1773 3.290948 AGCTAAGGGTGTGTTTGTCAA 57.709 42.857 0.00 0.00 0.00 3.18
1869 1946 2.928334 AGATATGGCAGTGCAAGGAAG 58.072 47.619 18.61 0.00 0.00 3.46
1964 2041 1.522668 TTGCCTGTGACGAATCCAAG 58.477 50.000 0.00 0.00 0.00 3.61
1967 2044 2.009042 GCCTGTGACGAATCCAAGGAG 61.009 57.143 0.00 0.00 0.00 3.69
2031 2114 0.465705 AGATGGTGCCATGGACTACG 59.534 55.000 18.40 0.00 36.70 3.51
2148 2231 3.288092 ACAGTTTGGTCCCTGTTTTCTC 58.712 45.455 0.00 0.00 38.76 2.87
2384 2554 6.266786 GGGGATTAAAGGAGTTTCTTGACAAA 59.733 38.462 0.00 0.00 0.00 2.83
2565 2745 5.410746 AGATCTGCATGCAGGTTATTATTCG 59.589 40.000 39.72 16.89 43.75 3.34
2728 2914 6.289064 CGGTTATCTGCTCCCTTAAAAGTAT 58.711 40.000 0.00 0.00 0.00 2.12
2732 2918 5.359194 TCTGCTCCCTTAAAAGTATGGAG 57.641 43.478 8.39 8.39 44.38 3.86
3107 3315 4.181578 CCATGAAGAGTTTACCAGTACCG 58.818 47.826 0.00 0.00 0.00 4.02
3218 3426 3.999663 CTGATTTCTGGGCCGAGATAATC 59.000 47.826 26.92 26.92 0.00 1.75
3245 3453 2.667318 CGCGCCGTCAGACAATGTT 61.667 57.895 0.00 0.00 0.00 2.71
3353 3561 2.188817 GACCAGGAGTATCAAGGTGGT 58.811 52.381 0.00 0.00 42.72 4.16
3410 3633 5.987777 TGCATTGTTTTCAATTTCTGTGG 57.012 34.783 0.00 0.00 46.94 4.17
3465 3688 1.301423 TGTACCGCTGTTTGTGTTCC 58.699 50.000 0.00 0.00 0.00 3.62
3466 3689 1.134340 TGTACCGCTGTTTGTGTTCCT 60.134 47.619 0.00 0.00 0.00 3.36
3467 3690 1.263217 GTACCGCTGTTTGTGTTCCTG 59.737 52.381 0.00 0.00 0.00 3.86
3468 3691 0.393808 ACCGCTGTTTGTGTTCCTGT 60.394 50.000 0.00 0.00 0.00 4.00
3469 3692 1.134340 ACCGCTGTTTGTGTTCCTGTA 60.134 47.619 0.00 0.00 0.00 2.74
3470 3693 1.531149 CCGCTGTTTGTGTTCCTGTAG 59.469 52.381 0.00 0.00 0.00 2.74
3471 3694 2.479837 CGCTGTTTGTGTTCCTGTAGA 58.520 47.619 0.00 0.00 0.00 2.59
3472 3695 2.221055 CGCTGTTTGTGTTCCTGTAGAC 59.779 50.000 0.00 0.00 0.00 2.59
3473 3696 3.202906 GCTGTTTGTGTTCCTGTAGACA 58.797 45.455 0.00 0.00 0.00 3.41
3474 3697 3.248602 GCTGTTTGTGTTCCTGTAGACAG 59.751 47.826 2.50 2.50 43.40 3.51
3486 3709 4.862902 CTGTAGACAGGTGATATGGGAG 57.137 50.000 1.47 0.00 40.20 4.30
3487 3710 4.474394 CTGTAGACAGGTGATATGGGAGA 58.526 47.826 1.47 0.00 40.20 3.71
3488 3711 4.215908 TGTAGACAGGTGATATGGGAGAC 58.784 47.826 0.00 0.00 0.00 3.36
3489 3712 6.731540 CTGTAGACAGGTGATATGGGAGACC 61.732 52.000 1.47 0.00 45.36 3.85
3631 3882 2.920384 GCGGGGGATCTCCTCTCC 60.920 72.222 12.53 0.00 44.83 3.71
3643 3894 4.116328 CTCTCCCGCGCGTCTTCA 62.116 66.667 29.95 7.30 0.00 3.02
3842 4165 4.858680 TTGGTTGCGGTGGCGTGA 62.859 61.111 0.00 0.00 44.10 4.35
3851 4174 2.177531 GTGGCGTGATTGCTGCTG 59.822 61.111 0.00 0.00 34.52 4.41
3852 4175 3.057548 TGGCGTGATTGCTGCTGG 61.058 61.111 0.00 0.00 34.52 4.85
3854 4177 4.824166 GCGTGATTGCTGCTGGCG 62.824 66.667 0.00 0.03 45.43 5.69
4114 4453 0.609957 TGTGACTACCGTCGACCCAT 60.610 55.000 10.58 0.00 43.21 4.00
4338 4677 2.920384 TGGTCGGCAGGTGCTACA 60.920 61.111 1.26 0.00 41.70 2.74
4354 4693 1.064208 CTACACACGACAGATCCTCCG 59.936 57.143 0.00 0.00 0.00 4.63
4391 4733 1.228429 GGCTGGTGGTACTTGGCAA 60.228 57.895 0.00 0.00 0.00 4.52
4410 4752 1.119684 ACATGGCGCTGAGGTGTATA 58.880 50.000 7.64 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.741145 ACCCGATCTCTAGCAGTTCTT 58.259 47.619 0.00 0.00 0.00 2.52
1 2 2.428890 CAACCCGATCTCTAGCAGTTCT 59.571 50.000 0.00 0.00 0.00 3.01
2 3 2.166664 ACAACCCGATCTCTAGCAGTTC 59.833 50.000 0.00 0.00 0.00 3.01
3 4 2.093973 CACAACCCGATCTCTAGCAGTT 60.094 50.000 0.00 0.00 0.00 3.16
6 7 0.175760 GCACAACCCGATCTCTAGCA 59.824 55.000 0.00 0.00 0.00 3.49
8 9 0.456221 ACGCACAACCCGATCTCTAG 59.544 55.000 0.00 0.00 0.00 2.43
10 11 1.079819 CACGCACAACCCGATCTCT 60.080 57.895 0.00 0.00 0.00 3.10
11 12 1.374252 ACACGCACAACCCGATCTC 60.374 57.895 0.00 0.00 0.00 2.75
12 13 1.667830 CACACGCACAACCCGATCT 60.668 57.895 0.00 0.00 0.00 2.75
14 15 1.098712 AAACACACGCACAACCCGAT 61.099 50.000 0.00 0.00 0.00 4.18
15 16 1.707239 GAAACACACGCACAACCCGA 61.707 55.000 0.00 0.00 0.00 5.14
16 17 1.298041 GAAACACACGCACAACCCG 60.298 57.895 0.00 0.00 0.00 5.28
17 18 0.248458 CAGAAACACACGCACAACCC 60.248 55.000 0.00 0.00 0.00 4.11
18 19 0.450184 ACAGAAACACACGCACAACC 59.550 50.000 0.00 0.00 0.00 3.77
19 20 2.256445 AACAGAAACACACGCACAAC 57.744 45.000 0.00 0.00 0.00 3.32
42 43 2.638480 GCATAGTTAGGATGCCCACA 57.362 50.000 0.00 0.00 43.24 4.17
58 59 1.486310 ACACATGTCCGGTATCTGCAT 59.514 47.619 0.00 0.00 0.00 3.96
65 66 3.070748 CACAATGAACACATGTCCGGTA 58.929 45.455 0.00 0.00 0.00 4.02
67 68 2.150390 TCACAATGAACACATGTCCGG 58.850 47.619 0.00 0.00 0.00 5.14
151 153 2.067766 GAGTTCAAGTGCAGAGCTCAG 58.932 52.381 17.77 9.50 41.32 3.35
158 160 7.547019 TGATATTTCTACTGAGTTCAAGTGCAG 59.453 37.037 0.00 0.00 34.65 4.41
217 219 5.927115 AGACGAACTTGACTCACTAATTTCC 59.073 40.000 0.00 0.00 0.00 3.13
232 234 1.499049 GCGGTCTTCAAGACGAACTT 58.501 50.000 11.52 0.00 45.96 2.66
233 235 0.663568 CGCGGTCTTCAAGACGAACT 60.664 55.000 11.52 0.00 45.96 3.01
234 236 0.938168 ACGCGGTCTTCAAGACGAAC 60.938 55.000 12.47 2.56 45.96 3.95
235 237 0.662374 GACGCGGTCTTCAAGACGAA 60.662 55.000 12.47 0.00 45.96 3.85
237 239 0.937699 TTGACGCGGTCTTCAAGACG 60.938 55.000 12.47 8.06 45.96 4.18
238 240 1.429463 ATTGACGCGGTCTTCAAGAC 58.571 50.000 12.47 9.27 44.32 3.01
239 241 2.163818 AATTGACGCGGTCTTCAAGA 57.836 45.000 12.47 0.00 34.57 3.02
240 242 2.574322 CAAATTGACGCGGTCTTCAAG 58.426 47.619 12.47 0.00 34.57 3.02
241 243 1.334599 GCAAATTGACGCGGTCTTCAA 60.335 47.619 12.47 11.95 35.38 2.69
242 244 0.237235 GCAAATTGACGCGGTCTTCA 59.763 50.000 12.47 1.07 33.15 3.02
243 245 0.517316 AGCAAATTGACGCGGTCTTC 59.483 50.000 12.47 0.00 33.15 2.87
244 246 0.951558 AAGCAAATTGACGCGGTCTT 59.048 45.000 12.47 0.00 33.15 3.01
245 247 0.238289 CAAGCAAATTGACGCGGTCT 59.762 50.000 12.47 0.00 41.83 3.85
246 248 0.040425 ACAAGCAAATTGACGCGGTC 60.040 50.000 12.47 6.39 41.83 4.79
247 249 0.383949 AACAAGCAAATTGACGCGGT 59.616 45.000 12.47 0.00 41.83 5.68
248 250 1.486439 AAACAAGCAAATTGACGCGG 58.514 45.000 12.47 0.00 41.83 6.46
249 251 2.878042 CAAAACAAGCAAATTGACGCG 58.122 42.857 3.53 3.53 41.83 6.01
250 252 2.627956 GCAAAACAAGCAAATTGACGC 58.372 42.857 0.00 0.00 41.83 5.19
251 253 2.533535 TCGCAAAACAAGCAAATTGACG 59.466 40.909 0.00 0.00 41.83 4.35
252 254 4.448005 CATCGCAAAACAAGCAAATTGAC 58.552 39.130 0.00 0.00 41.83 3.18
253 255 3.493877 CCATCGCAAAACAAGCAAATTGA 59.506 39.130 0.00 0.00 41.83 2.57
254 256 3.801293 CCATCGCAAAACAAGCAAATTG 58.199 40.909 0.00 0.00 45.01 2.32
255 257 2.223845 GCCATCGCAAAACAAGCAAATT 59.776 40.909 0.00 0.00 34.03 1.82
256 258 1.799994 GCCATCGCAAAACAAGCAAAT 59.200 42.857 0.00 0.00 34.03 2.32
257 259 1.216122 GCCATCGCAAAACAAGCAAA 58.784 45.000 0.00 0.00 34.03 3.68
258 260 0.103755 TGCCATCGCAAAACAAGCAA 59.896 45.000 0.00 0.00 43.74 3.91
259 261 1.738432 TGCCATCGCAAAACAAGCA 59.262 47.368 0.00 0.00 43.74 3.91
260 262 4.651585 TGCCATCGCAAAACAAGC 57.348 50.000 0.00 0.00 43.74 4.01
275 277 9.761504 ATATCAGTGAATATACATGCTCTATGC 57.238 33.333 0.00 0.00 40.59 3.14
309 311 9.328721 GACTAATAATTTGCAAAAACAAATGCC 57.671 29.630 17.19 0.00 46.80 4.40
310 312 9.328721 GGACTAATAATTTGCAAAAACAAATGC 57.671 29.630 17.19 3.63 46.80 3.56
340 342 8.428852 TGGAATAGCAAGAATAGCAGTATGTAA 58.571 33.333 0.00 0.00 39.31 2.41
350 359 7.615582 TTGTGAACTGGAATAGCAAGAATAG 57.384 36.000 0.00 0.00 0.00 1.73
357 366 8.177119 ACTTTTATTTGTGAACTGGAATAGCA 57.823 30.769 0.00 0.00 0.00 3.49
691 700 6.379988 AGGTGGGTATACTATTTTGGCAAAAG 59.620 38.462 27.21 18.43 33.22 2.27
725 736 2.889578 CGTTCGGACGTCTCCAAAA 58.110 52.632 16.46 0.33 44.08 2.44
726 737 4.639824 CGTTCGGACGTCTCCAAA 57.360 55.556 16.46 2.12 44.08 3.28
745 756 2.310233 CGTGTGGCGAAGTGGACAG 61.310 63.158 0.00 0.00 44.77 3.51
773 784 1.079197 TCCGTACATGCAGCAGGTG 60.079 57.895 22.83 8.76 29.18 4.00
779 790 1.086067 CCAGCTGTCCGTACATGCAG 61.086 60.000 13.81 0.00 34.37 4.41
790 801 4.735132 TACGCACGCCCAGCTGTC 62.735 66.667 13.81 2.93 0.00 3.51
791 802 3.605749 AATACGCACGCCCAGCTGT 62.606 57.895 13.81 0.00 0.00 4.40
792 803 1.922135 AAAATACGCACGCCCAGCTG 61.922 55.000 6.78 6.78 0.00 4.24
793 804 1.241315 AAAAATACGCACGCCCAGCT 61.241 50.000 0.00 0.00 0.00 4.24
794 805 1.070471 CAAAAATACGCACGCCCAGC 61.070 55.000 0.00 0.00 0.00 4.85
795 806 0.239879 ACAAAAATACGCACGCCCAG 59.760 50.000 0.00 0.00 0.00 4.45
796 807 1.197264 GTACAAAAATACGCACGCCCA 59.803 47.619 0.00 0.00 0.00 5.36
797 808 1.787635 CGTACAAAAATACGCACGCCC 60.788 52.381 0.00 0.00 41.28 6.13
798 809 1.516208 CGTACAAAAATACGCACGCC 58.484 50.000 0.00 0.00 41.28 5.68
818 829 2.416747 CATGGTGATACCCGCTATGTG 58.583 52.381 0.00 0.00 38.81 3.21
826 837 0.106149 GTCCGACCATGGTGATACCC 59.894 60.000 25.52 5.40 37.50 3.69
834 845 2.125673 GTCACCGTCCGACCATGG 60.126 66.667 11.19 11.19 0.00 3.66
836 847 2.674033 TCGTCACCGTCCGACCAT 60.674 61.111 0.00 0.00 35.01 3.55
848 859 6.928979 TGGTCTTATTTTGAAAAGTCGTCA 57.071 33.333 0.00 0.00 0.00 4.35
849 860 7.021790 GGATGGTCTTATTTTGAAAAGTCGTC 58.978 38.462 0.00 0.00 0.00 4.20
857 869 5.174037 AGACGGGATGGTCTTATTTTGAA 57.826 39.130 0.00 0.00 44.65 2.69
898 910 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
899 911 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
900 912 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
901 913 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
902 914 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
934 946 6.932947 AGAGCGTTTAGGACACTATTTTAGT 58.067 36.000 0.00 0.00 40.28 2.24
935 947 7.829378 AAGAGCGTTTAGGACACTATTTTAG 57.171 36.000 0.00 0.00 0.00 1.85
941 953 9.347240 ACTAATATAAGAGCGTTTAGGACACTA 57.653 33.333 0.00 0.00 0.00 2.74
942 954 8.235359 ACTAATATAAGAGCGTTTAGGACACT 57.765 34.615 0.00 0.00 0.00 3.55
943 955 8.868635 AACTAATATAAGAGCGTTTAGGACAC 57.131 34.615 0.00 0.00 0.00 3.67
944 956 8.689061 TGAACTAATATAAGAGCGTTTAGGACA 58.311 33.333 0.00 0.00 0.00 4.02
945 957 8.966194 GTGAACTAATATAAGAGCGTTTAGGAC 58.034 37.037 0.00 0.00 0.00 3.85
946 958 7.859377 CGTGAACTAATATAAGAGCGTTTAGGA 59.141 37.037 0.00 0.00 0.00 2.94
947 959 7.114529 CCGTGAACTAATATAAGAGCGTTTAGG 59.885 40.741 0.00 0.00 0.00 2.69
948 960 7.859377 TCCGTGAACTAATATAAGAGCGTTTAG 59.141 37.037 0.00 0.00 0.00 1.85
949 961 7.706159 TCCGTGAACTAATATAAGAGCGTTTA 58.294 34.615 0.00 0.00 0.00 2.01
950 962 6.567050 TCCGTGAACTAATATAAGAGCGTTT 58.433 36.000 0.00 0.00 0.00 3.60
951 963 6.140303 TCCGTGAACTAATATAAGAGCGTT 57.860 37.500 0.00 0.00 0.00 4.84
952 964 5.278364 CCTCCGTGAACTAATATAAGAGCGT 60.278 44.000 0.00 0.00 0.00 5.07
953 965 5.154932 CCTCCGTGAACTAATATAAGAGCG 58.845 45.833 0.00 0.00 0.00 5.03
954 966 5.243283 TCCCTCCGTGAACTAATATAAGAGC 59.757 44.000 0.00 0.00 0.00 4.09
955 967 6.490721 ACTCCCTCCGTGAACTAATATAAGAG 59.509 42.308 0.00 0.00 0.00 2.85
956 968 6.371278 ACTCCCTCCGTGAACTAATATAAGA 58.629 40.000 0.00 0.00 0.00 2.10
957 969 6.651975 ACTCCCTCCGTGAACTAATATAAG 57.348 41.667 0.00 0.00 0.00 1.73
958 970 9.986157 ATATACTCCCTCCGTGAACTAATATAA 57.014 33.333 0.00 0.00 0.00 0.98
959 971 9.404848 CATATACTCCCTCCGTGAACTAATATA 57.595 37.037 0.00 0.00 0.00 0.86
960 972 7.147880 GCATATACTCCCTCCGTGAACTAATAT 60.148 40.741 0.00 0.00 0.00 1.28
961 973 6.152323 GCATATACTCCCTCCGTGAACTAATA 59.848 42.308 0.00 0.00 0.00 0.98
962 974 5.047235 GCATATACTCCCTCCGTGAACTAAT 60.047 44.000 0.00 0.00 0.00 1.73
963 975 4.280174 GCATATACTCCCTCCGTGAACTAA 59.720 45.833 0.00 0.00 0.00 2.24
964 976 3.825014 GCATATACTCCCTCCGTGAACTA 59.175 47.826 0.00 0.00 0.00 2.24
965 977 2.628657 GCATATACTCCCTCCGTGAACT 59.371 50.000 0.00 0.00 0.00 3.01
966 978 2.628657 AGCATATACTCCCTCCGTGAAC 59.371 50.000 0.00 0.00 0.00 3.18
967 979 2.958818 AGCATATACTCCCTCCGTGAA 58.041 47.619 0.00 0.00 0.00 3.18
968 980 2.677542 AGCATATACTCCCTCCGTGA 57.322 50.000 0.00 0.00 0.00 4.35
969 981 4.707448 AGATTAGCATATACTCCCTCCGTG 59.293 45.833 0.00 0.00 0.00 4.94
970 982 4.936802 AGATTAGCATATACTCCCTCCGT 58.063 43.478 0.00 0.00 0.00 4.69
971 983 4.950475 TGAGATTAGCATATACTCCCTCCG 59.050 45.833 0.00 0.00 0.00 4.63
972 984 5.163457 GCTGAGATTAGCATATACTCCCTCC 60.163 48.000 0.00 0.00 43.17 4.30
973 985 5.163457 GGCTGAGATTAGCATATACTCCCTC 60.163 48.000 0.00 0.00 45.46 4.30
974 986 4.714308 GGCTGAGATTAGCATATACTCCCT 59.286 45.833 0.00 0.00 45.46 4.20
975 987 4.467795 TGGCTGAGATTAGCATATACTCCC 59.532 45.833 0.00 0.00 45.46 4.30
976 988 5.667539 TGGCTGAGATTAGCATATACTCC 57.332 43.478 0.00 0.00 45.46 3.85
977 989 6.871844 TGATGGCTGAGATTAGCATATACTC 58.128 40.000 0.00 0.00 45.46 2.59
978 990 6.864151 TGATGGCTGAGATTAGCATATACT 57.136 37.500 0.00 0.00 45.46 2.12
979 991 6.035435 CGTTGATGGCTGAGATTAGCATATAC 59.965 42.308 0.00 0.00 45.46 1.47
980 992 6.101997 CGTTGATGGCTGAGATTAGCATATA 58.898 40.000 0.00 0.00 45.46 0.86
981 993 4.934001 CGTTGATGGCTGAGATTAGCATAT 59.066 41.667 0.00 0.00 45.46 1.78
982 994 4.202253 ACGTTGATGGCTGAGATTAGCATA 60.202 41.667 0.00 0.00 45.46 3.14
983 995 3.136763 CGTTGATGGCTGAGATTAGCAT 58.863 45.455 0.00 0.00 45.46 3.79
984 996 2.093500 ACGTTGATGGCTGAGATTAGCA 60.093 45.455 0.00 0.00 45.46 3.49
985 997 2.555199 ACGTTGATGGCTGAGATTAGC 58.445 47.619 0.00 0.00 42.94 3.09
986 998 6.851222 AAATACGTTGATGGCTGAGATTAG 57.149 37.500 0.00 0.00 0.00 1.73
987 999 7.438160 CACTAAATACGTTGATGGCTGAGATTA 59.562 37.037 0.00 0.00 0.00 1.75
988 1000 6.258727 CACTAAATACGTTGATGGCTGAGATT 59.741 38.462 0.00 0.00 0.00 2.40
989 1001 5.755375 CACTAAATACGTTGATGGCTGAGAT 59.245 40.000 0.00 0.00 0.00 2.75
990 1002 5.109210 CACTAAATACGTTGATGGCTGAGA 58.891 41.667 0.00 0.00 0.00 3.27
991 1003 4.271049 CCACTAAATACGTTGATGGCTGAG 59.729 45.833 0.00 0.00 0.00 3.35
992 1004 4.188462 CCACTAAATACGTTGATGGCTGA 58.812 43.478 0.00 0.00 0.00 4.26
993 1005 3.938963 ACCACTAAATACGTTGATGGCTG 59.061 43.478 0.00 0.00 31.60 4.85
1015 1027 4.039973 AGAATTCACTTCTTCGGTACACCA 59.960 41.667 8.44 0.00 41.60 4.17
1051 1066 4.814234 AGCACAACTTTGTTTGACGAGATA 59.186 37.500 0.00 0.00 39.91 1.98
1057 1072 3.179048 GACCAGCACAACTTTGTTTGAC 58.821 45.455 0.00 0.00 39.91 3.18
1095 1110 4.462483 TGACCAGCACAACTCTTTTCTTTT 59.538 37.500 0.00 0.00 0.00 2.27
1096 1111 4.016444 TGACCAGCACAACTCTTTTCTTT 58.984 39.130 0.00 0.00 0.00 2.52
1097 1112 3.620488 TGACCAGCACAACTCTTTTCTT 58.380 40.909 0.00 0.00 0.00 2.52
1098 1113 3.281727 TGACCAGCACAACTCTTTTCT 57.718 42.857 0.00 0.00 0.00 2.52
1099 1114 4.574599 AATGACCAGCACAACTCTTTTC 57.425 40.909 0.00 0.00 0.00 2.29
1104 1119 3.821033 ACCTTAAATGACCAGCACAACTC 59.179 43.478 0.00 0.00 0.00 3.01
1129 1148 2.475466 CCACCATCACCATGAGCGC 61.475 63.158 0.00 0.00 30.57 5.92
1382 1411 4.502016 TCAGCAAAGAAGACTGCATAGAG 58.498 43.478 0.00 0.00 41.17 2.43
1726 1773 1.611673 GGTAACTGCAGTGCTCCATGT 60.612 52.381 22.49 4.17 0.00 3.21
1869 1946 2.159028 CCTTTAGCTCTGGGACTAGTGC 60.159 54.545 5.70 5.70 37.43 4.40
1964 2041 0.109132 CAAAATTGCGTGCCCTCTCC 60.109 55.000 0.00 0.00 0.00 3.71
1967 2044 0.598065 AGACAAAATTGCGTGCCCTC 59.402 50.000 0.00 0.00 0.00 4.30
2031 2114 0.179018 AGCACCTTGAACACCCTGTC 60.179 55.000 0.00 0.00 0.00 3.51
2148 2231 3.763902 CCGTGATAGATAAGCCGATGAG 58.236 50.000 0.00 0.00 0.00 2.90
2195 2314 9.911788 AAGGTGATAACAACATCATCTCTAAAT 57.088 29.630 0.00 0.00 43.99 1.40
2384 2554 1.949525 GATGCAAGACACACACCAACT 59.050 47.619 0.00 0.00 0.00 3.16
2565 2745 2.749621 CTGTCCCCATTAAGCAACTGAC 59.250 50.000 0.00 0.00 0.00 3.51
2613 2796 7.774625 AACATTTGTTTGATGGAAGAACCAAAT 59.225 29.630 0.00 0.00 43.23 2.32
2728 2914 3.308832 CCCATTGCTTAGTTTACCCTCCA 60.309 47.826 0.00 0.00 0.00 3.86
2732 2918 1.404035 CGCCCATTGCTTAGTTTACCC 59.596 52.381 0.00 0.00 38.05 3.69
3041 3249 3.334583 TGTAGGAATGTGACTGCTTCC 57.665 47.619 4.65 4.65 38.99 3.46
3107 3315 3.732471 CGAAGATCTTCTCCGTCTTGTCC 60.732 52.174 28.28 3.33 37.44 4.02
3218 3426 4.253257 GACGGCGCGAGGTAGAGG 62.253 72.222 12.10 0.00 0.00 3.69
3245 3453 1.514553 CTGCTCGATGTGCTCCTCA 59.485 57.895 0.00 0.00 0.00 3.86
3410 3633 5.350091 ACAACAAGCACAAATTAAACACACC 59.650 36.000 0.00 0.00 0.00 4.16
3465 3688 4.279671 GTCTCCCATATCACCTGTCTACAG 59.720 50.000 3.02 3.02 43.40 2.74
3466 3689 4.215908 GTCTCCCATATCACCTGTCTACA 58.784 47.826 0.00 0.00 0.00 2.74
3467 3690 3.574826 GGTCTCCCATATCACCTGTCTAC 59.425 52.174 0.00 0.00 0.00 2.59
3468 3691 3.206639 TGGTCTCCCATATCACCTGTCTA 59.793 47.826 0.00 0.00 35.17 2.59
3469 3692 2.023015 TGGTCTCCCATATCACCTGTCT 60.023 50.000 0.00 0.00 35.17 3.41
3470 3693 2.103263 GTGGTCTCCCATATCACCTGTC 59.897 54.545 0.00 0.00 44.35 3.51
3471 3694 2.119495 GTGGTCTCCCATATCACCTGT 58.881 52.381 0.00 0.00 44.35 4.00
3472 3695 1.069204 CGTGGTCTCCCATATCACCTG 59.931 57.143 0.00 0.00 44.35 4.00
3473 3696 1.414158 CGTGGTCTCCCATATCACCT 58.586 55.000 0.00 0.00 44.35 4.00
3474 3697 0.393077 CCGTGGTCTCCCATATCACC 59.607 60.000 0.00 0.00 44.35 4.02
3475 3698 0.249911 GCCGTGGTCTCCCATATCAC 60.250 60.000 0.00 0.00 44.35 3.06
3476 3699 1.407656 GGCCGTGGTCTCCCATATCA 61.408 60.000 0.00 0.00 44.35 2.15
3477 3700 1.371558 GGCCGTGGTCTCCCATATC 59.628 63.158 0.00 0.00 44.35 1.63
3478 3701 2.147387 GGGCCGTGGTCTCCCATAT 61.147 63.158 0.00 0.00 44.35 1.78
3479 3702 2.766651 GGGCCGTGGTCTCCCATA 60.767 66.667 0.00 0.00 44.35 2.74
3829 4135 4.036804 GCAATCACGCCACCGCAA 62.037 61.111 0.00 0.00 38.22 4.85
3842 4165 4.349503 TCCACCGCCAGCAGCAAT 62.350 61.111 0.00 0.00 44.04 3.56
3925 4264 2.095461 TCTGACGGAAGAGATGACCAG 58.905 52.381 0.00 0.00 0.00 4.00
4028 4367 2.758497 CCGTCGGCTCGGTTTTTAT 58.242 52.632 0.00 0.00 44.77 1.40
4114 4453 1.187974 TTCCCTCGGAGCAATACGAA 58.812 50.000 0.00 0.00 38.79 3.85
4338 4677 1.032657 CCTCGGAGGATCTGTCGTGT 61.033 60.000 19.57 0.00 43.66 4.49
4354 4693 1.294659 CGACACAGCTTGAAGCCCTC 61.295 60.000 14.45 2.49 43.77 4.30
4391 4733 1.119684 TATACACCTCAGCGCCATGT 58.880 50.000 2.29 4.20 0.00 3.21
4410 4752 4.373116 ATGTCGCGGTCGCCACTT 62.373 61.111 6.13 5.35 37.98 3.16


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

AutoCloner maintained by Alex Coulton.