Multiple sequence alignment - TraesCS3D01G515800

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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 TraesCS3D01G515800 chr3D 100.000 4325 0 0 1 4325 599175188 599179512 0.000000e+00 7987.0
1 TraesCS3D01G515800 chr3D 90.067 1188 93 11 2512 3690 599268092 599266921 0.000000e+00 1517.0
2 TraesCS3D01G515800 chr3D 86.447 1033 69 23 810 1815 599269372 599268384 0.000000e+00 1066.0
3 TraesCS3D01G515800 chr3D 84.666 613 68 23 41 646 599270735 599270142 4.820000e-164 588.0
4 TraesCS3D01G515800 chr3D 87.442 430 33 14 3560 3977 599266912 599266492 3.910000e-130 475.0
5 TraesCS3D01G515800 chr3D 94.636 261 13 1 2141 2401 509752920 509753179 1.870000e-108 403.0
6 TraesCS3D01G515800 chr3D 92.910 268 19 0 2138 2405 91831890 91831623 1.460000e-104 390.0
7 TraesCS3D01G515800 chr3D 77.154 267 29 14 1815 2078 599268330 599268093 4.540000e-25 126.0
8 TraesCS3D01G515800 chr3A 93.736 1804 94 8 2503 4297 729392587 729394380 0.000000e+00 2687.0
9 TraesCS3D01G515800 chr3A 96.750 1077 16 3 632 1708 729391314 729392371 0.000000e+00 1777.0
10 TraesCS3D01G515800 chr3A 89.899 1188 96 12 2512 3690 729315914 729314742 0.000000e+00 1507.0
11 TraesCS3D01G515800 chr3A 85.904 1057 69 36 810 1816 729317207 729316181 0.000000e+00 1053.0
12 TraesCS3D01G515800 chr3A 96.552 377 11 2 1 375 729390403 729390779 1.320000e-174 623.0
13 TraesCS3D01G515800 chr3A 87.822 427 31 11 3560 3977 729314733 729314319 8.410000e-132 481.0
14 TraesCS3D01G515800 chr3A 76.834 259 31 10 1815 2072 729316145 729315915 7.600000e-23 119.0
15 TraesCS3D01G515800 chr3A 89.552 67 4 2 2079 2142 735552810 735552876 9.970000e-12 82.4
16 TraesCS3D01G515800 chr6D 96.617 266 9 0 2139 2404 341080830 341080565 3.970000e-120 442.0
17 TraesCS3D01G515800 chr6D 96.935 261 7 1 2141 2401 206587460 206587719 1.850000e-118 436.0
18 TraesCS3D01G515800 chr6D 95.802 262 11 0 2140 2401 421886354 421886093 1.440000e-114 424.0
19 TraesCS3D01G515800 chr6D 87.419 310 34 5 3993 4297 113909027 113909336 6.880000e-93 351.0
20 TraesCS3D01G515800 chr6D 87.266 267 29 5 4036 4297 283808270 283808004 2.530000e-77 300.0
21 TraesCS3D01G515800 chr6D 93.333 105 6 1 2396 2499 338408461 338408565 2.080000e-33 154.0
22 TraesCS3D01G515800 chr6D 90.625 64 2 3 2082 2142 147691136 147691198 9.970000e-12 82.4
23 TraesCS3D01G515800 chr6D 87.500 72 6 1 2074 2142 25764313 25764384 3.590000e-11 80.5
24 TraesCS3D01G515800 chr6D 91.667 60 2 1 2078 2134 428647292 428647351 3.590000e-11 80.5
25 TraesCS3D01G515800 chr6D 89.394 66 4 2 2081 2143 460745088 460745023 3.590000e-11 80.5
26 TraesCS3D01G515800 chr6D 88.235 68 3 3 2079 2142 149462242 149462308 4.640000e-10 76.8
27 TraesCS3D01G515800 chr6D 89.231 65 2 4 2082 2142 454259301 454259364 4.640000e-10 76.8
28 TraesCS3D01G515800 chr7A 94.424 269 14 1 2141 2408 16122698 16122430 3.110000e-111 412.0
29 TraesCS3D01G515800 chr7A 94.424 269 14 1 2138 2405 578444491 578444759 3.110000e-111 412.0
30 TraesCS3D01G515800 chr7A 93.536 263 17 0 2141 2403 79196486 79196748 4.050000e-105 392.0
31 TraesCS3D01G515800 chr5A 93.284 268 16 2 2140 2405 3711300 3711033 1.130000e-105 394.0
32 TraesCS3D01G515800 chr2D 87.616 323 35 5 3980 4297 609655869 609656191 1.900000e-98 370.0
33 TraesCS3D01G515800 chr2D 80.508 118 19 4 378 492 505843669 505843553 2.140000e-13 87.9
34 TraesCS3D01G515800 chr2D 89.552 67 4 2 2079 2142 593512485 593512551 9.970000e-12 82.4
35 TraesCS3D01G515800 chr2D 85.000 60 7 2 378 436 102661554 102661612 4.670000e-05 60.2
36 TraesCS3D01G515800 chr5D 86.111 324 40 5 3979 4297 456573398 456573075 1.150000e-90 344.0
37 TraesCS3D01G515800 chr5D 89.394 66 4 2 2080 2142 314422153 314422088 3.590000e-11 80.5
38 TraesCS3D01G515800 chr5D 86.301 73 7 2 2073 2142 464065874 464065946 4.640000e-10 76.8
39 TraesCS3D01G515800 chr5D 100.000 28 0 0 161 188 95289667 95289640 8.000000e-03 52.8
40 TraesCS3D01G515800 chr6A 92.857 112 5 3 2391 2499 478925009 478925120 4.480000e-35 159.0
41 TraesCS3D01G515800 chr4D 94.175 103 6 0 2399 2501 36603108 36603210 1.610000e-34 158.0
42 TraesCS3D01G515800 chr4D 93.396 106 6 1 2396 2500 64390528 64390633 5.790000e-34 156.0
43 TraesCS3D01G515800 chr4D 92.381 105 7 1 2396 2499 89423956 89424060 9.690000e-32 148.0
44 TraesCS3D01G515800 chr4D 90.909 66 3 2 2080 2142 83140418 83140483 7.710000e-13 86.1
45 TraesCS3D01G515800 chr4D 89.062 64 4 2 2082 2142 106682054 106682117 4.640000e-10 76.8
46 TraesCS3D01G515800 chr4D 87.879 66 4 3 2080 2142 416761694 416761758 1.670000e-09 75.0
47 TraesCS3D01G515800 chr4D 86.765 68 5 3 2078 2142 21147729 21147795 6.000000e-09 73.1
48 TraesCS3D01G515800 chr4D 85.938 64 6 2 2082 2142 463336495 463336432 1.000000e-06 65.8
49 TraesCS3D01G515800 chr7D 93.333 105 6 1 2396 2499 525768025 525768129 2.080000e-33 154.0
50 TraesCS3D01G515800 chr7D 93.333 105 6 1 2396 2499 619400730 619400834 2.080000e-33 154.0
51 TraesCS3D01G515800 chr5B 93.333 105 6 1 2396 2499 70793438 70793542 2.080000e-33 154.0
52 TraesCS3D01G515800 chr4A 93.333 105 6 1 2396 2499 37306970 37306866 2.080000e-33 154.0
53 TraesCS3D01G515800 chr4A 91.045 67 3 1 2079 2142 139870769 139870703 2.140000e-13 87.9
54 TraesCS3D01G515800 chr4A 89.552 67 4 2 2079 2142 450788269 450788335 9.970000e-12 82.4
55 TraesCS3D01G515800 chr4A 89.394 66 3 4 2077 2138 564157178 564157113 3.590000e-11 80.5
56 TraesCS3D01G515800 chr1A 92.188 64 2 1 2082 2142 368368352 368368415 2.140000e-13 87.9
57 TraesCS3D01G515800 chr1A 90.625 64 3 1 2082 2142 532768397 532768334 9.970000e-12 82.4
58 TraesCS3D01G515800 chr4B 91.935 62 4 1 2081 2142 628656003 628655943 7.710000e-13 86.1
59 TraesCS3D01G515800 chr1D 90.625 64 3 1 2082 2142 415974909 415974846 9.970000e-12 82.4
60 TraesCS3D01G515800 chr2A 100.000 29 0 0 378 406 101832662 101832690 2.000000e-03 54.7


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 TraesCS3D01G515800 chr3D 599175188 599179512 4324 False 7987.000000 7987 100.000000 1 4325 1 chr3D.!!$F2 4324
1 TraesCS3D01G515800 chr3D 599266492 599270735 4243 True 754.400000 1517 85.155200 41 3977 5 chr3D.!!$R2 3936
2 TraesCS3D01G515800 chr3A 729390403 729394380 3977 False 1695.666667 2687 95.679333 1 4297 3 chr3A.!!$F2 4296
3 TraesCS3D01G515800 chr3A 729314319 729317207 2888 True 790.000000 1507 85.114750 810 3977 4 chr3A.!!$R1 3167

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
857 1840 0.322975 AGAAGAAGCGCAGACCATGT 59.677 50.0 11.47 0.0 0.0 3.21 F
1923 3009 0.251341 AGGCAAAGTTCCAGCGGATT 60.251 50.0 0.00 0.0 0.0 3.01 F
3070 4162 0.445436 CGTCCAAATCTCACTGCTGC 59.555 55.0 0.00 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2484 3571 0.528470 ACTGCTACTCGCTCTGTTCC 59.472 55.0 0.0 0.0 40.11 3.62 R
3193 4285 0.530870 GCTATCGCTCGGCCTTCTTT 60.531 55.0 0.0 0.0 0.00 2.52 R
4223 5589 0.107165 GCCAACCCCTTCGAATAGCT 60.107 55.0 0.0 0.0 0.00 3.32 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
122 123 8.617290 TTTCATAACAAAGGGTTTCTAGACTC 57.383 34.615 0.00 0.00 40.96 3.36
127 128 4.846940 ACAAAGGGTTTCTAGACTCTGGAT 59.153 41.667 0.00 0.00 28.77 3.41
825 1808 1.439679 CTAGTGGGTCGGTTCTTTGC 58.560 55.000 0.00 0.00 0.00 3.68
843 1826 4.584638 TTGCTAGGCCCATAAAAGAAGA 57.415 40.909 0.00 0.00 0.00 2.87
844 1827 4.584638 TGCTAGGCCCATAAAAGAAGAA 57.415 40.909 0.00 0.00 0.00 2.52
845 1828 4.526970 TGCTAGGCCCATAAAAGAAGAAG 58.473 43.478 0.00 0.00 0.00 2.85
846 1829 3.316588 GCTAGGCCCATAAAAGAAGAAGC 59.683 47.826 0.00 0.00 0.00 3.86
849 1832 1.472480 GCCCATAAAAGAAGAAGCGCA 59.528 47.619 11.47 0.00 0.00 6.09
850 1833 2.478539 GCCCATAAAAGAAGAAGCGCAG 60.479 50.000 11.47 0.00 0.00 5.18
852 1835 3.181506 CCCATAAAAGAAGAAGCGCAGAC 60.182 47.826 11.47 0.00 0.00 3.51
853 1836 3.181506 CCATAAAAGAAGAAGCGCAGACC 60.182 47.826 11.47 0.00 0.00 3.85
854 1837 1.967319 AAAAGAAGAAGCGCAGACCA 58.033 45.000 11.47 0.00 0.00 4.02
855 1838 2.191128 AAAGAAGAAGCGCAGACCAT 57.809 45.000 11.47 0.00 0.00 3.55
856 1839 1.446907 AAGAAGAAGCGCAGACCATG 58.553 50.000 11.47 0.00 0.00 3.66
857 1840 0.322975 AGAAGAAGCGCAGACCATGT 59.677 50.000 11.47 0.00 0.00 3.21
858 1841 0.445436 GAAGAAGCGCAGACCATGTG 59.555 55.000 11.47 0.00 42.62 3.21
859 1842 0.957395 AAGAAGCGCAGACCATGTGG 60.957 55.000 11.47 0.00 39.94 4.17
883 1866 2.536066 GGTTTGGCCCTGGAGTATTTT 58.464 47.619 0.00 0.00 0.00 1.82
887 1870 5.503002 GTTTGGCCCTGGAGTATTTTACTA 58.497 41.667 0.00 0.00 39.59 1.82
1284 2284 2.046411 TGGTCGCACGGCATGATT 60.046 55.556 0.00 0.00 0.00 2.57
1362 2367 0.329261 CCAGGATCCTTGGTTGCTCA 59.671 55.000 13.00 0.00 0.00 4.26
1519 2547 3.034924 CCTTACTGGTGGCTTGCAA 57.965 52.632 0.00 0.00 0.00 4.08
1615 2643 1.172812 AAAGGGACGACTGCCAAAGC 61.173 55.000 0.00 0.00 40.48 3.51
1726 2754 5.592282 TCACTATCTTTTTGTGCTTCACCAA 59.408 36.000 0.00 0.00 32.73 3.67
1796 2828 8.858003 TCTAGAATCAAGTCATAAGCTTTACG 57.142 34.615 3.20 0.00 0.00 3.18
1798 2830 7.527084 AGAATCAAGTCATAAGCTTTACGAC 57.473 36.000 3.20 9.29 0.00 4.34
1877 2963 5.584649 TGCCTAATGGTTTCGAAGATAACAG 59.415 40.000 0.00 0.00 38.80 3.16
1884 2970 4.026475 GGTTTCGAAGATAACAGCATCTCG 60.026 45.833 0.00 0.00 34.08 4.04
1918 3004 2.185004 TCAGTAGGCAAAGTTCCAGC 57.815 50.000 0.00 0.00 0.00 4.85
1921 3007 0.321298 GTAGGCAAAGTTCCAGCGGA 60.321 55.000 0.00 0.00 0.00 5.54
1922 3008 0.618458 TAGGCAAAGTTCCAGCGGAT 59.382 50.000 0.00 0.00 0.00 4.18
1923 3009 0.251341 AGGCAAAGTTCCAGCGGATT 60.251 50.000 0.00 0.00 0.00 3.01
2021 3108 2.408368 GCGCATTTGCAGGTCTTTAAAC 59.592 45.455 0.30 0.00 42.21 2.01
2023 3110 3.670055 CGCATTTGCAGGTCTTTAAACTG 59.330 43.478 3.13 1.00 42.21 3.16
2058 3145 6.070824 TCCTGTGCTTGAGTATACAGATTTCA 60.071 38.462 5.50 0.00 42.28 2.69
2061 3148 8.648557 TGTGCTTGAGTATACAGATTTCATAC 57.351 34.615 5.50 1.50 0.00 2.39
2090 3177 7.939784 ATTCTTGTTATTTTGTACTCCCTCC 57.060 36.000 0.00 0.00 0.00 4.30
2091 3178 6.442541 TCTTGTTATTTTGTACTCCCTCCA 57.557 37.500 0.00 0.00 0.00 3.86
2092 3179 7.027874 TCTTGTTATTTTGTACTCCCTCCAT 57.972 36.000 0.00 0.00 0.00 3.41
2093 3180 7.466804 TCTTGTTATTTTGTACTCCCTCCATT 58.533 34.615 0.00 0.00 0.00 3.16
2094 3181 7.610305 TCTTGTTATTTTGTACTCCCTCCATTC 59.390 37.037 0.00 0.00 0.00 2.67
2095 3182 6.785076 TGTTATTTTGTACTCCCTCCATTCA 58.215 36.000 0.00 0.00 0.00 2.57
2096 3183 7.235079 TGTTATTTTGTACTCCCTCCATTCAA 58.765 34.615 0.00 0.00 0.00 2.69
2097 3184 7.893302 TGTTATTTTGTACTCCCTCCATTCAAT 59.107 33.333 0.00 0.00 0.00 2.57
2098 3185 9.403583 GTTATTTTGTACTCCCTCCATTCAATA 57.596 33.333 0.00 0.00 0.00 1.90
2102 3189 9.627123 TTTTGTACTCCCTCCATTCAATATAAG 57.373 33.333 0.00 0.00 0.00 1.73
2103 3190 7.931015 TGTACTCCCTCCATTCAATATAAGT 57.069 36.000 0.00 0.00 0.00 2.24
2104 3191 7.963532 TGTACTCCCTCCATTCAATATAAGTC 58.036 38.462 0.00 0.00 0.00 3.01
2105 3192 7.567250 TGTACTCCCTCCATTCAATATAAGTCA 59.433 37.037 0.00 0.00 0.00 3.41
2106 3193 7.639062 ACTCCCTCCATTCAATATAAGTCAT 57.361 36.000 0.00 0.00 0.00 3.06
2107 3194 8.050316 ACTCCCTCCATTCAATATAAGTCATT 57.950 34.615 0.00 0.00 0.00 2.57
2108 3195 8.506083 ACTCCCTCCATTCAATATAAGTCATTT 58.494 33.333 0.00 0.00 0.00 2.32
2109 3196 9.359653 CTCCCTCCATTCAATATAAGTCATTTT 57.640 33.333 0.00 0.00 0.00 1.82
2126 3213 9.667107 AAGTCATTTTAGAGATTTCAATACGGA 57.333 29.630 0.00 0.00 0.00 4.69
2127 3214 9.099454 AGTCATTTTAGAGATTTCAATACGGAC 57.901 33.333 0.00 0.00 0.00 4.79
2128 3215 9.099454 GTCATTTTAGAGATTTCAATACGGACT 57.901 33.333 0.00 0.00 0.00 3.85
2135 3222 8.234136 AGAGATTTCAATACGGACTACATACA 57.766 34.615 0.00 0.00 0.00 2.29
2136 3223 8.353684 AGAGATTTCAATACGGACTACATACAG 58.646 37.037 0.00 0.00 0.00 2.74
2137 3224 8.234136 AGATTTCAATACGGACTACATACAGA 57.766 34.615 0.00 0.00 0.00 3.41
2138 3225 8.861086 AGATTTCAATACGGACTACATACAGAT 58.139 33.333 0.00 0.00 0.00 2.90
2139 3226 8.818141 ATTTCAATACGGACTACATACAGATG 57.182 34.615 0.00 0.00 39.16 2.90
2141 3228 8.454570 TTCAATACGGACTACATACAGATGTA 57.545 34.615 0.00 0.00 44.77 2.29
2142 3229 7.868775 TCAATACGGACTACATACAGATGTAC 58.131 38.462 0.00 0.00 44.77 2.90
2143 3230 7.718314 TCAATACGGACTACATACAGATGTACT 59.282 37.037 0.00 0.00 44.77 2.73
2144 3231 8.350722 CAATACGGACTACATACAGATGTACTT 58.649 37.037 0.00 0.00 44.77 2.24
2145 3232 6.374565 ACGGACTACATACAGATGTACTTC 57.625 41.667 0.50 0.50 44.77 3.01
2146 3233 5.298777 ACGGACTACATACAGATGTACTTCC 59.701 44.000 5.19 9.25 44.77 3.46
2147 3234 5.531659 CGGACTACATACAGATGTACTTCCT 59.468 44.000 5.19 0.00 44.77 3.36
2148 3235 6.293516 CGGACTACATACAGATGTACTTCCTC 60.294 46.154 5.19 0.00 44.77 3.71
2149 3236 6.016108 GGACTACATACAGATGTACTTCCTCC 60.016 46.154 5.19 0.00 44.77 4.30
2150 3237 4.920640 ACATACAGATGTACTTCCTCCG 57.079 45.455 5.19 0.00 44.77 4.63
2151 3238 3.637229 ACATACAGATGTACTTCCTCCGG 59.363 47.826 0.00 0.00 44.77 5.14
2152 3239 2.233305 ACAGATGTACTTCCTCCGGT 57.767 50.000 0.00 0.00 0.00 5.28
2153 3240 2.100989 ACAGATGTACTTCCTCCGGTC 58.899 52.381 0.00 0.00 0.00 4.79
2154 3241 2.291670 ACAGATGTACTTCCTCCGGTCT 60.292 50.000 0.00 0.00 0.00 3.85
2155 3242 2.761208 CAGATGTACTTCCTCCGGTCTT 59.239 50.000 0.00 0.00 0.00 3.01
2156 3243 3.195825 CAGATGTACTTCCTCCGGTCTTT 59.804 47.826 0.00 0.00 0.00 2.52
2157 3244 3.838903 AGATGTACTTCCTCCGGTCTTTT 59.161 43.478 0.00 0.00 0.00 2.27
2158 3245 4.286291 AGATGTACTTCCTCCGGTCTTTTT 59.714 41.667 0.00 0.00 0.00 1.94
2186 3273 9.236006 AGTTTGCATATAAGATTTGTCTGAAGT 57.764 29.630 0.00 0.00 0.00 3.01
2187 3274 9.495754 GTTTGCATATAAGATTTGTCTGAAGTC 57.504 33.333 0.00 0.00 0.00 3.01
2188 3275 8.791327 TTGCATATAAGATTTGTCTGAAGTCA 57.209 30.769 0.00 0.00 0.00 3.41
2189 3276 8.791327 TGCATATAAGATTTGTCTGAAGTCAA 57.209 30.769 0.00 0.00 0.00 3.18
2190 3277 9.230122 TGCATATAAGATTTGTCTGAAGTCAAA 57.770 29.630 5.43 5.43 37.44 2.69
2191 3278 9.495754 GCATATAAGATTTGTCTGAAGTCAAAC 57.504 33.333 5.13 1.59 36.30 2.93
2192 3279 9.994432 CATATAAGATTTGTCTGAAGTCAAACC 57.006 33.333 5.13 0.00 36.30 3.27
2193 3280 9.965902 ATATAAGATTTGTCTGAAGTCAAACCT 57.034 29.630 5.13 0.00 36.30 3.50
2194 3281 6.625873 AAGATTTGTCTGAAGTCAAACCTC 57.374 37.500 5.13 1.70 36.30 3.85
2195 3282 4.752101 AGATTTGTCTGAAGTCAAACCTCG 59.248 41.667 5.13 0.00 36.30 4.63
2196 3283 3.536956 TTGTCTGAAGTCAAACCTCGT 57.463 42.857 0.00 0.00 0.00 4.18
2197 3284 4.659111 TTGTCTGAAGTCAAACCTCGTA 57.341 40.909 0.00 0.00 0.00 3.43
2198 3285 4.659111 TGTCTGAAGTCAAACCTCGTAA 57.341 40.909 0.00 0.00 0.00 3.18
2199 3286 5.013568 TGTCTGAAGTCAAACCTCGTAAA 57.986 39.130 0.00 0.00 0.00 2.01
2200 3287 4.807304 TGTCTGAAGTCAAACCTCGTAAAC 59.193 41.667 0.00 0.00 0.00 2.01
2201 3288 5.048507 GTCTGAAGTCAAACCTCGTAAACT 58.951 41.667 0.00 0.00 0.00 2.66
2202 3289 5.522824 GTCTGAAGTCAAACCTCGTAAACTT 59.477 40.000 0.00 0.00 0.00 2.66
2203 3290 6.036844 GTCTGAAGTCAAACCTCGTAAACTTT 59.963 38.462 0.00 0.00 0.00 2.66
2204 3291 6.036735 TCTGAAGTCAAACCTCGTAAACTTTG 59.963 38.462 0.00 0.00 0.00 2.77
2205 3292 5.875910 TGAAGTCAAACCTCGTAAACTTTGA 59.124 36.000 0.00 0.00 31.68 2.69
2206 3293 5.729974 AGTCAAACCTCGTAAACTTTGAC 57.270 39.130 12.19 12.19 46.84 3.18
2207 3294 4.840911 GTCAAACCTCGTAAACTTTGACC 58.159 43.478 9.86 0.00 43.35 4.02
2208 3295 4.333372 GTCAAACCTCGTAAACTTTGACCA 59.667 41.667 9.86 0.00 43.35 4.02
2209 3296 4.942483 TCAAACCTCGTAAACTTTGACCAA 59.058 37.500 0.00 0.00 29.66 3.67
2210 3297 5.065474 TCAAACCTCGTAAACTTTGACCAAG 59.935 40.000 0.00 0.00 38.64 3.61
2264 3351 7.103159 TGTGAAATCAACAACATTAAATGCG 57.897 32.000 0.00 0.00 0.00 4.73
2265 3352 6.699204 TGTGAAATCAACAACATTAAATGCGT 59.301 30.769 0.00 0.00 0.00 5.24
2266 3353 7.096271 TGTGAAATCAACAACATTAAATGCGTC 60.096 33.333 0.00 0.00 0.00 5.19
2267 3354 6.920210 TGAAATCAACAACATTAAATGCGTCA 59.080 30.769 0.00 0.00 0.00 4.35
2268 3355 7.598118 TGAAATCAACAACATTAAATGCGTCAT 59.402 29.630 0.00 0.00 0.00 3.06
2269 3356 6.874297 ATCAACAACATTAAATGCGTCATG 57.126 33.333 0.00 0.00 0.00 3.07
2270 3357 6.006759 TCAACAACATTAAATGCGTCATGA 57.993 33.333 0.00 0.00 0.00 3.07
2271 3358 5.855925 TCAACAACATTAAATGCGTCATGAC 59.144 36.000 16.21 16.21 0.00 3.06
2272 3359 5.627499 ACAACATTAAATGCGTCATGACT 57.373 34.783 22.95 7.01 0.00 3.41
2273 3360 6.012658 ACAACATTAAATGCGTCATGACTT 57.987 33.333 22.95 12.92 0.00 3.01
2274 3361 6.446318 ACAACATTAAATGCGTCATGACTTT 58.554 32.000 22.95 17.91 0.00 2.66
2275 3362 7.589395 ACAACATTAAATGCGTCATGACTTTA 58.411 30.769 22.95 16.98 0.00 1.85
2276 3363 8.079203 ACAACATTAAATGCGTCATGACTTTAA 58.921 29.630 23.10 23.10 0.00 1.52
2277 3364 9.075519 CAACATTAAATGCGTCATGACTTTAAT 57.924 29.630 24.59 24.59 33.37 1.40
2278 3365 9.638239 AACATTAAATGCGTCATGACTTTAATT 57.362 25.926 26.22 17.96 32.06 1.40
2279 3366 9.638239 ACATTAAATGCGTCATGACTTTAATTT 57.362 25.926 26.22 21.52 32.06 1.82
2282 3369 9.684448 TTAAATGCGTCATGACTTTAATTTTCA 57.316 25.926 22.95 10.37 0.00 2.69
2283 3370 8.761575 AAATGCGTCATGACTTTAATTTTCAT 57.238 26.923 22.95 9.11 0.00 2.57
2284 3371 9.853555 AAATGCGTCATGACTTTAATTTTCATA 57.146 25.926 22.95 0.00 0.00 2.15
2375 3462 9.495754 GTTTGACTTCAGACAATTCTTATATGC 57.504 33.333 0.00 0.00 31.96 3.14
2376 3463 8.791327 TTGACTTCAGACAATTCTTATATGCA 57.209 30.769 0.00 0.00 0.00 3.96
2377 3464 8.429493 TGACTTCAGACAATTCTTATATGCAG 57.571 34.615 0.00 0.00 0.00 4.41
2378 3465 8.260114 TGACTTCAGACAATTCTTATATGCAGA 58.740 33.333 0.00 0.00 0.00 4.26
2379 3466 8.659925 ACTTCAGACAATTCTTATATGCAGAG 57.340 34.615 0.00 0.00 0.00 3.35
2380 3467 8.263640 ACTTCAGACAATTCTTATATGCAGAGT 58.736 33.333 0.00 0.00 0.00 3.24
2381 3468 9.755804 CTTCAGACAATTCTTATATGCAGAGTA 57.244 33.333 0.00 0.00 0.00 2.59
2390 3477 8.732746 TTCTTATATGCAGAGTAAAAAGGACC 57.267 34.615 0.00 0.00 0.00 4.46
2391 3478 6.984474 TCTTATATGCAGAGTAAAAAGGACCG 59.016 38.462 0.00 0.00 0.00 4.79
2392 3479 2.178912 TGCAGAGTAAAAAGGACCGG 57.821 50.000 0.00 0.00 0.00 5.28
2393 3480 1.695242 TGCAGAGTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14
2394 3481 2.289444 TGCAGAGTAAAAAGGACCGGAG 60.289 50.000 9.46 0.00 0.00 4.63
2413 3500 6.998968 CGGAGGGAGTATATAGACGTAATT 57.001 41.667 0.00 0.00 0.00 1.40
2414 3501 7.388460 CGGAGGGAGTATATAGACGTAATTT 57.612 40.000 0.00 0.00 0.00 1.82
2415 3502 8.498054 CGGAGGGAGTATATAGACGTAATTTA 57.502 38.462 0.00 0.00 0.00 1.40
2416 3503 8.950210 CGGAGGGAGTATATAGACGTAATTTAA 58.050 37.037 0.00 0.00 0.00 1.52
2440 3527 8.976986 AAAGTGTAGATTCATTCATTTTGCTC 57.023 30.769 0.00 0.00 0.00 4.26
2441 3528 7.093322 AGTGTAGATTCATTCATTTTGCTCC 57.907 36.000 0.00 0.00 0.00 4.70
2442 3529 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
2443 3530 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
2444 3531 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
2445 3532 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
2446 3533 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
2447 3534 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
2448 3535 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
2449 3536 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
2450 3537 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
2451 3538 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
2452 3539 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
2453 3540 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
2454 3541 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
2455 3542 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
2456 3543 5.801531 TTTGCTCCGTATGTAGTCCATAT 57.198 39.130 0.00 0.00 38.29 1.78
2457 3544 5.801531 TTGCTCCGTATGTAGTCCATATT 57.198 39.130 0.00 0.00 38.29 1.28
2458 3545 5.134202 TGCTCCGTATGTAGTCCATATTG 57.866 43.478 0.00 0.00 38.29 1.90
2459 3546 4.021456 TGCTCCGTATGTAGTCCATATTGG 60.021 45.833 0.00 0.00 38.29 3.16
2460 3547 4.219944 GCTCCGTATGTAGTCCATATTGGA 59.780 45.833 0.00 0.00 45.98 3.53
2494 3581 8.594881 AATGACTTATATTTAGGAACAGAGCG 57.405 34.615 0.00 0.00 0.00 5.03
2495 3582 7.342769 TGACTTATATTTAGGAACAGAGCGA 57.657 36.000 0.00 0.00 0.00 4.93
2496 3583 7.426410 TGACTTATATTTAGGAACAGAGCGAG 58.574 38.462 0.00 0.00 0.00 5.03
2497 3584 7.068348 TGACTTATATTTAGGAACAGAGCGAGT 59.932 37.037 0.00 0.00 0.00 4.18
2498 3585 8.461249 ACTTATATTTAGGAACAGAGCGAGTA 57.539 34.615 0.00 0.00 0.00 2.59
2499 3586 8.569641 ACTTATATTTAGGAACAGAGCGAGTAG 58.430 37.037 0.00 0.00 0.00 2.57
2565 3652 4.154015 TGCGGTCTTATTGTTGATGAACAG 59.846 41.667 0.00 0.00 43.03 3.16
2578 3665 8.682128 TGTTGATGAACAGAACTTTTTGTTAC 57.318 30.769 0.00 0.00 36.74 2.50
2661 3748 9.868277 TTTATCAACATTTGGTGGATTGAATAC 57.132 29.630 0.00 0.00 36.76 1.89
2662 3749 7.722949 ATCAACATTTGGTGGATTGAATACT 57.277 32.000 0.00 0.00 36.76 2.12
2741 3833 8.394971 TGATTAGTTAATTGATGCATACAGGG 57.605 34.615 0.00 0.00 0.00 4.45
2821 3913 5.538053 TCACATTTGGAGGTTATGCTCAAAA 59.462 36.000 0.00 0.00 32.23 2.44
2840 3932 7.769044 GCTCAAAATGAAGGGTACTACTGAATA 59.231 37.037 0.00 0.00 0.00 1.75
2917 4009 6.127310 CCTTCCTATTGAGTACACTAGCAAGT 60.127 42.308 0.00 0.00 30.24 3.16
2940 4032 3.286329 TGCACAGTGGAGATGCAATAT 57.714 42.857 1.84 0.00 45.96 1.28
3043 4135 5.074584 ACTAACTGCTAGTACCTTGAAGC 57.925 43.478 0.00 0.00 39.20 3.86
3070 4162 0.445436 CGTCCAAATCTCACTGCTGC 59.555 55.000 0.00 0.00 0.00 5.25
3114 4206 4.523943 TCTGTTAATGCTGATGGCTTTGTT 59.476 37.500 0.00 0.00 42.39 2.83
3185 4277 3.515502 CTGTCTATCTTCCAACAGGGTGA 59.484 47.826 0.00 0.00 36.36 4.02
3193 4285 1.767036 CAACAGGGTGATGGTGGGA 59.233 57.895 0.00 0.00 34.09 4.37
3403 4495 3.838244 AACTGTAGACAAGTGGCTTGA 57.162 42.857 14.81 0.00 43.42 3.02
3448 4540 6.088616 CGTGCTTTGTGTAGTAACTAGTAACC 59.911 42.308 0.00 0.00 0.00 2.85
3536 4628 8.997621 TCTAATTCTGCTAAGTAACGTGAAAT 57.002 30.769 0.00 0.00 0.00 2.17
3558 4650 5.947228 TGCCTCTTGTTCTGATTTTAGTG 57.053 39.130 0.00 0.00 0.00 2.74
3568 4660 9.730420 TTGTTCTGATTTTAGTGTTTTAGAAGC 57.270 29.630 0.00 0.00 0.00 3.86
3569 4661 9.120538 TGTTCTGATTTTAGTGTTTTAGAAGCT 57.879 29.630 0.00 0.00 0.00 3.74
3711 5067 3.119352 GGTTCAAAGCCATCAGAATCACC 60.119 47.826 0.00 0.00 0.00 4.02
3712 5068 2.358957 TCAAAGCCATCAGAATCACCG 58.641 47.619 0.00 0.00 0.00 4.94
3789 5146 1.656652 GCCATATTCAGCACTCGTGT 58.343 50.000 0.00 0.00 0.00 4.49
3872 5238 9.897744 TTGTGATTTTCATTGATTAAGTGAGTC 57.102 29.630 0.00 0.00 0.00 3.36
4003 5369 4.329545 TTCCTGCCCTGGCGACAC 62.330 66.667 3.32 0.00 45.51 3.67
4027 5393 4.572571 AAGACCCAAACCGCGCCA 62.573 61.111 0.00 0.00 0.00 5.69
4060 5426 2.835895 GTCGCTCTCCCTCCCCTC 60.836 72.222 0.00 0.00 0.00 4.30
4101 5467 1.154016 GAGCTAAGCTCGCACGACA 60.154 57.895 10.18 0.00 45.85 4.35
4104 5470 0.526524 GCTAAGCTCGCACGACAGAT 60.527 55.000 3.31 0.00 0.00 2.90
4107 5473 2.125912 GCTCGCACGACAGATGGT 60.126 61.111 0.00 0.00 0.00 3.55
4109 5475 1.807165 CTCGCACGACAGATGGTGG 60.807 63.158 0.00 0.00 35.24 4.61
4111 5477 2.358615 GCACGACAGATGGTGGCA 60.359 61.111 0.00 0.00 35.24 4.92
4179 5545 2.577593 GGTCCACCTCGGCTACAC 59.422 66.667 0.00 0.00 33.14 2.90
4180 5546 2.577593 GTCCACCTCGGCTACACC 59.422 66.667 0.00 0.00 33.14 4.16
4209 5575 4.101790 CCGGCAATTTCGCGCAGT 62.102 61.111 8.75 0.00 0.00 4.40
4223 5589 2.580815 CAGTGGCGCTCATCTCCA 59.419 61.111 7.64 0.00 0.00 3.86
4226 5592 3.079478 TGGCGCTCATCTCCAGCT 61.079 61.111 7.64 0.00 34.45 4.24
4231 5597 1.695813 CGCTCATCTCCAGCTATTCG 58.304 55.000 0.00 0.00 34.45 3.34
4292 5658 2.412112 GGATCGGACCTTCGACGG 59.588 66.667 6.37 6.37 42.21 4.79
4313 5679 2.753043 CCAGGGTGTGATGGCAGC 60.753 66.667 0.00 0.00 36.26 5.25
4314 5680 2.353958 CAGGGTGTGATGGCAGCT 59.646 61.111 3.69 0.00 37.09 4.24
4315 5681 1.748122 CAGGGTGTGATGGCAGCTC 60.748 63.158 3.69 0.00 37.09 4.09
4316 5682 2.439156 GGGTGTGATGGCAGCTCC 60.439 66.667 3.69 4.03 37.09 4.70
4317 5683 2.439156 GGTGTGATGGCAGCTCCC 60.439 66.667 3.69 0.45 34.39 4.30
4318 5684 2.439156 GTGTGATGGCAGCTCCCC 60.439 66.667 3.69 0.00 0.00 4.81
4319 5685 2.611800 TGTGATGGCAGCTCCCCT 60.612 61.111 3.69 0.00 0.00 4.79
4320 5686 2.233566 TGTGATGGCAGCTCCCCTT 61.234 57.895 3.69 0.00 0.00 3.95
4321 5687 1.452833 GTGATGGCAGCTCCCCTTC 60.453 63.158 3.69 0.04 0.00 3.46
4322 5688 1.617536 TGATGGCAGCTCCCCTTCT 60.618 57.895 3.69 0.00 0.00 2.85
4323 5689 1.153005 GATGGCAGCTCCCCTTCTG 60.153 63.158 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 1.415659 CCTACTCCTGCCTCAATCCAG 59.584 57.143 0.00 0.00 0.00 3.86
127 128 1.063942 TCGATCCTACTCCTGCCTCAA 60.064 52.381 0.00 0.00 0.00 3.02
825 1808 3.561725 CGCTTCTTCTTTTATGGGCCTAG 59.438 47.826 4.53 0.00 0.00 3.02
843 1826 2.360350 CCCACATGGTCTGCGCTT 60.360 61.111 9.73 0.00 0.00 4.68
852 1835 2.582493 GCCAAACCCACCCACATGG 61.582 63.158 0.00 0.00 39.71 3.66
853 1836 2.582493 GGCCAAACCCACCCACATG 61.582 63.158 0.00 0.00 0.00 3.21
854 1837 2.203773 GGCCAAACCCACCCACAT 60.204 61.111 0.00 0.00 0.00 3.21
866 1849 5.987019 ATAGTAAAATACTCCAGGGCCAA 57.013 39.130 6.18 0.00 40.14 4.52
883 1866 3.181487 GGGGTCGCGTTGTCTAAATAGTA 60.181 47.826 5.77 0.00 0.00 1.82
887 1870 0.322322 TGGGGTCGCGTTGTCTAAAT 59.678 50.000 5.77 0.00 0.00 1.40
1284 2284 3.744719 CTGACGGCGTCGAAGGGA 61.745 66.667 31.90 14.71 40.11 4.20
1519 2547 1.464376 CGTAGACATCGAGGGGCCAT 61.464 60.000 4.39 0.00 0.00 4.40
1615 2643 2.349590 TCACGAACCTGCTCATTGATG 58.650 47.619 0.00 0.00 0.00 3.07
1698 2726 8.296713 GGTGAAGCACAAAAAGATAGTGAATTA 58.703 33.333 0.00 0.00 35.86 1.40
1796 2828 4.377431 CGAGTTTGTTTGTAGGCATGAGTC 60.377 45.833 0.00 0.00 0.00 3.36
1798 2830 3.745975 TCGAGTTTGTTTGTAGGCATGAG 59.254 43.478 0.00 0.00 0.00 2.90
1856 2942 6.662414 TGCTGTTATCTTCGAAACCATTAG 57.338 37.500 0.00 0.00 0.00 1.73
1877 2963 1.802960 CCATGTATGGCTTCGAGATGC 59.197 52.381 0.00 2.77 41.75 3.91
1900 2986 0.798776 CGCTGGAACTTTGCCTACTG 59.201 55.000 0.00 0.00 0.00 2.74
1929 3016 7.482474 CAAAAACTGGACATATGCATCATGTA 58.518 34.615 16.66 6.65 36.76 2.29
2021 3108 1.845809 GCACAGGAAAGCACGTCCAG 61.846 60.000 3.50 0.00 37.65 3.86
2023 3110 1.166531 AAGCACAGGAAAGCACGTCC 61.167 55.000 0.00 0.00 35.17 4.79
2072 3159 7.696992 TTGAATGGAGGGAGTACAAAATAAC 57.303 36.000 0.00 0.00 0.00 1.89
2080 3167 7.963532 TGACTTATATTGAATGGAGGGAGTAC 58.036 38.462 0.00 0.00 0.00 2.73
2081 3168 8.742125 ATGACTTATATTGAATGGAGGGAGTA 57.258 34.615 0.00 0.00 0.00 2.59
2082 3169 7.639062 ATGACTTATATTGAATGGAGGGAGT 57.361 36.000 0.00 0.00 0.00 3.85
2083 3170 8.930846 AAATGACTTATATTGAATGGAGGGAG 57.069 34.615 0.00 0.00 0.00 4.30
2100 3187 9.667107 TCCGTATTGAAATCTCTAAAATGACTT 57.333 29.630 0.00 0.00 0.00 3.01
2101 3188 9.099454 GTCCGTATTGAAATCTCTAAAATGACT 57.901 33.333 0.00 0.00 0.00 3.41
2102 3189 9.099454 AGTCCGTATTGAAATCTCTAAAATGAC 57.901 33.333 0.00 0.00 0.00 3.06
2109 3196 9.346005 TGTATGTAGTCCGTATTGAAATCTCTA 57.654 33.333 0.00 0.00 0.00 2.43
2110 3197 8.234136 TGTATGTAGTCCGTATTGAAATCTCT 57.766 34.615 0.00 0.00 0.00 3.10
2111 3198 8.350722 TCTGTATGTAGTCCGTATTGAAATCTC 58.649 37.037 0.00 0.00 0.00 2.75
2112 3199 8.234136 TCTGTATGTAGTCCGTATTGAAATCT 57.766 34.615 0.00 0.00 0.00 2.40
2113 3200 8.916654 CATCTGTATGTAGTCCGTATTGAAATC 58.083 37.037 0.00 0.00 0.00 2.17
2114 3201 8.421784 ACATCTGTATGTAGTCCGTATTGAAAT 58.578 33.333 0.00 0.00 44.66 2.17
2115 3202 7.778083 ACATCTGTATGTAGTCCGTATTGAAA 58.222 34.615 0.00 0.00 44.66 2.69
2116 3203 7.342769 ACATCTGTATGTAGTCCGTATTGAA 57.657 36.000 0.00 0.00 44.66 2.69
2117 3204 6.954487 ACATCTGTATGTAGTCCGTATTGA 57.046 37.500 0.00 0.00 44.66 2.57
2118 3205 7.872881 AGTACATCTGTATGTAGTCCGTATTG 58.127 38.462 0.00 0.00 45.22 1.90
2119 3206 8.461249 AAGTACATCTGTATGTAGTCCGTATT 57.539 34.615 6.38 0.00 46.83 1.89
2120 3207 7.174599 GGAAGTACATCTGTATGTAGTCCGTAT 59.825 40.741 6.38 0.00 46.83 3.06
2121 3208 6.484643 GGAAGTACATCTGTATGTAGTCCGTA 59.515 42.308 6.38 0.00 46.83 4.02
2122 3209 5.298777 GGAAGTACATCTGTATGTAGTCCGT 59.701 44.000 6.38 0.00 46.83 4.69
2123 3210 5.531659 AGGAAGTACATCTGTATGTAGTCCG 59.468 44.000 15.69 0.00 46.83 4.79
2124 3211 6.016108 GGAGGAAGTACATCTGTATGTAGTCC 60.016 46.154 14.69 14.69 46.83 3.85
2125 3212 6.293516 CGGAGGAAGTACATCTGTATGTAGTC 60.294 46.154 6.38 4.30 46.83 2.59
2127 3214 6.003234 CGGAGGAAGTACATCTGTATGTAG 57.997 45.833 0.00 0.00 46.68 2.74
2160 3247 9.236006 ACTTCAGACAAATCTTATATGCAAACT 57.764 29.630 0.00 0.00 30.42 2.66
2161 3248 9.495754 GACTTCAGACAAATCTTATATGCAAAC 57.504 33.333 0.00 0.00 30.42 2.93
2162 3249 9.230122 TGACTTCAGACAAATCTTATATGCAAA 57.770 29.630 0.00 0.00 30.42 3.68
2163 3250 8.791327 TGACTTCAGACAAATCTTATATGCAA 57.209 30.769 0.00 0.00 30.42 4.08
2164 3251 8.791327 TTGACTTCAGACAAATCTTATATGCA 57.209 30.769 0.00 0.00 30.42 3.96
2165 3252 9.495754 GTTTGACTTCAGACAAATCTTATATGC 57.504 33.333 7.54 0.00 40.50 3.14
2166 3253 9.994432 GGTTTGACTTCAGACAAATCTTATATG 57.006 33.333 7.54 0.00 40.50 1.78
2167 3254 9.965902 AGGTTTGACTTCAGACAAATCTTATAT 57.034 29.630 10.55 0.00 44.38 0.86
2168 3255 9.436957 GAGGTTTGACTTCAGACAAATCTTATA 57.563 33.333 15.60 0.00 45.82 0.98
2169 3256 7.118390 CGAGGTTTGACTTCAGACAAATCTTAT 59.882 37.037 15.60 0.00 45.82 1.73
2170 3257 6.423905 CGAGGTTTGACTTCAGACAAATCTTA 59.576 38.462 15.60 0.00 45.82 2.10
2171 3258 5.237344 CGAGGTTTGACTTCAGACAAATCTT 59.763 40.000 15.60 3.91 45.82 2.40
2173 3260 4.511826 ACGAGGTTTGACTTCAGACAAATC 59.488 41.667 7.54 7.19 40.50 2.17
2174 3261 4.451900 ACGAGGTTTGACTTCAGACAAAT 58.548 39.130 7.54 0.00 40.50 2.32
2175 3262 3.869065 ACGAGGTTTGACTTCAGACAAA 58.131 40.909 2.66 1.04 37.36 2.83
2176 3263 3.536956 ACGAGGTTTGACTTCAGACAA 57.463 42.857 2.66 0.00 33.14 3.18
2177 3264 4.659111 TTACGAGGTTTGACTTCAGACA 57.341 40.909 2.66 0.00 33.14 3.41
2178 3265 5.048507 AGTTTACGAGGTTTGACTTCAGAC 58.951 41.667 0.00 0.00 0.00 3.51
2179 3266 5.272283 AGTTTACGAGGTTTGACTTCAGA 57.728 39.130 0.00 0.00 0.00 3.27
2180 3267 5.986004 AAGTTTACGAGGTTTGACTTCAG 57.014 39.130 0.00 0.00 0.00 3.02
2181 3268 5.875910 TCAAAGTTTACGAGGTTTGACTTCA 59.124 36.000 0.00 0.00 34.72 3.02
2182 3269 6.354039 TCAAAGTTTACGAGGTTTGACTTC 57.646 37.500 0.00 0.00 34.72 3.01
2186 3273 4.515361 TGGTCAAAGTTTACGAGGTTTGA 58.485 39.130 0.00 0.00 36.74 2.69
2187 3274 4.886247 TGGTCAAAGTTTACGAGGTTTG 57.114 40.909 0.00 0.00 0.00 2.93
2188 3275 5.494632 CTTGGTCAAAGTTTACGAGGTTT 57.505 39.130 0.00 0.00 0.00 3.27
2226 3313 8.959548 TGTTGATTTCACATTATGAATGCTAGT 58.040 29.630 0.00 0.00 46.80 2.57
2227 3314 9.791820 TTGTTGATTTCACATTATGAATGCTAG 57.208 29.630 0.00 0.00 46.80 3.42
2228 3315 9.571810 GTTGTTGATTTCACATTATGAATGCTA 57.428 29.630 0.00 0.00 46.80 3.49
2229 3316 8.089597 TGTTGTTGATTTCACATTATGAATGCT 58.910 29.630 0.00 0.00 46.80 3.79
2230 3317 8.242085 TGTTGTTGATTTCACATTATGAATGC 57.758 30.769 0.00 0.00 46.80 3.56
2238 3325 8.222433 CGCATTTAATGTTGTTGATTTCACATT 58.778 29.630 6.81 0.00 0.00 2.71
2239 3326 7.384660 ACGCATTTAATGTTGTTGATTTCACAT 59.615 29.630 6.81 0.00 0.00 3.21
2240 3327 6.699204 ACGCATTTAATGTTGTTGATTTCACA 59.301 30.769 6.81 0.00 0.00 3.58
2241 3328 7.096271 TGACGCATTTAATGTTGTTGATTTCAC 60.096 33.333 6.81 0.00 0.00 3.18
2242 3329 6.920210 TGACGCATTTAATGTTGTTGATTTCA 59.080 30.769 6.81 0.00 0.00 2.69
2243 3330 7.332003 TGACGCATTTAATGTTGTTGATTTC 57.668 32.000 6.81 0.00 0.00 2.17
2244 3331 7.598118 TCATGACGCATTTAATGTTGTTGATTT 59.402 29.630 6.81 0.00 0.00 2.17
2245 3332 7.062138 GTCATGACGCATTTAATGTTGTTGATT 59.938 33.333 10.69 0.00 0.00 2.57
2246 3333 6.527722 GTCATGACGCATTTAATGTTGTTGAT 59.472 34.615 10.69 1.09 0.00 2.57
2247 3334 5.855925 GTCATGACGCATTTAATGTTGTTGA 59.144 36.000 10.69 5.18 0.00 3.18
2248 3335 5.858049 AGTCATGACGCATTTAATGTTGTTG 59.142 36.000 19.85 3.20 36.20 3.33
2249 3336 6.012658 AGTCATGACGCATTTAATGTTGTT 57.987 33.333 19.85 0.00 36.20 2.83
2250 3337 5.627499 AGTCATGACGCATTTAATGTTGT 57.373 34.783 19.85 5.83 36.20 3.32
2251 3338 6.932901 AAAGTCATGACGCATTTAATGTTG 57.067 33.333 19.85 2.71 36.20 3.33
2252 3339 9.638239 AATTAAAGTCATGACGCATTTAATGTT 57.362 25.926 27.72 18.82 36.60 2.71
2253 3340 9.638239 AAATTAAAGTCATGACGCATTTAATGT 57.362 25.926 27.72 23.62 36.60 2.71
2256 3343 9.684448 TGAAAATTAAAGTCATGACGCATTTAA 57.316 25.926 23.10 23.10 36.20 1.52
2257 3344 9.853555 ATGAAAATTAAAGTCATGACGCATTTA 57.146 25.926 19.85 15.53 36.20 1.40
2258 3345 8.761575 ATGAAAATTAAAGTCATGACGCATTT 57.238 26.923 19.85 16.47 36.20 2.32
2331 3418 9.520515 AAGTCAAACTTCATAAAGTATGACCAT 57.479 29.630 0.00 0.00 45.07 3.55
2332 3419 8.918202 AAGTCAAACTTCATAAAGTATGACCA 57.082 30.769 0.00 0.00 45.07 4.02
2349 3436 9.495754 GCATATAAGAATTGTCTGAAGTCAAAC 57.504 33.333 0.00 0.00 33.05 2.93
2350 3437 9.230122 TGCATATAAGAATTGTCTGAAGTCAAA 57.770 29.630 0.00 0.00 33.05 2.69
2351 3438 8.791327 TGCATATAAGAATTGTCTGAAGTCAA 57.209 30.769 0.00 0.00 33.05 3.18
2352 3439 8.260114 TCTGCATATAAGAATTGTCTGAAGTCA 58.740 33.333 0.00 0.00 33.05 3.41
2353 3440 8.654230 TCTGCATATAAGAATTGTCTGAAGTC 57.346 34.615 0.00 0.00 33.05 3.01
2354 3441 8.263640 ACTCTGCATATAAGAATTGTCTGAAGT 58.736 33.333 0.00 0.00 33.05 3.01
2355 3442 8.659925 ACTCTGCATATAAGAATTGTCTGAAG 57.340 34.615 0.00 0.00 33.05 3.02
2364 3451 9.343539 GGTCCTTTTTACTCTGCATATAAGAAT 57.656 33.333 0.00 0.00 0.00 2.40
2365 3452 7.494625 CGGTCCTTTTTACTCTGCATATAAGAA 59.505 37.037 0.00 0.00 0.00 2.52
2366 3453 6.984474 CGGTCCTTTTTACTCTGCATATAAGA 59.016 38.462 0.00 0.00 0.00 2.10
2367 3454 6.202954 CCGGTCCTTTTTACTCTGCATATAAG 59.797 42.308 0.00 0.00 0.00 1.73
2368 3455 6.053005 CCGGTCCTTTTTACTCTGCATATAA 58.947 40.000 0.00 0.00 0.00 0.98
2369 3456 5.364446 TCCGGTCCTTTTTACTCTGCATATA 59.636 40.000 0.00 0.00 0.00 0.86
2370 3457 4.163458 TCCGGTCCTTTTTACTCTGCATAT 59.837 41.667 0.00 0.00 0.00 1.78
2371 3458 3.516300 TCCGGTCCTTTTTACTCTGCATA 59.484 43.478 0.00 0.00 0.00 3.14
2372 3459 2.304761 TCCGGTCCTTTTTACTCTGCAT 59.695 45.455 0.00 0.00 0.00 3.96
2373 3460 1.695242 TCCGGTCCTTTTTACTCTGCA 59.305 47.619 0.00 0.00 0.00 4.41
2374 3461 2.347731 CTCCGGTCCTTTTTACTCTGC 58.652 52.381 0.00 0.00 0.00 4.26
2375 3462 2.354805 CCCTCCGGTCCTTTTTACTCTG 60.355 54.545 0.00 0.00 0.00 3.35
2376 3463 1.907255 CCCTCCGGTCCTTTTTACTCT 59.093 52.381 0.00 0.00 0.00 3.24
2377 3464 1.904537 TCCCTCCGGTCCTTTTTACTC 59.095 52.381 0.00 0.00 0.00 2.59
2378 3465 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
2379 3466 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
2380 3467 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
2381 3468 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
2382 3469 2.265526 ATACTCCCTCCGGTCCTTTT 57.734 50.000 0.00 0.00 0.00 2.27
2383 3470 3.632420 ATATACTCCCTCCGGTCCTTT 57.368 47.619 0.00 0.00 0.00 3.11
2384 3471 3.921486 TCTATATACTCCCTCCGGTCCTT 59.079 47.826 0.00 0.00 0.00 3.36
2385 3472 3.266513 GTCTATATACTCCCTCCGGTCCT 59.733 52.174 0.00 0.00 0.00 3.85
2386 3473 3.619419 GTCTATATACTCCCTCCGGTCC 58.381 54.545 0.00 0.00 0.00 4.46
2387 3474 3.269178 CGTCTATATACTCCCTCCGGTC 58.731 54.545 0.00 0.00 0.00 4.79
2388 3475 2.641815 ACGTCTATATACTCCCTCCGGT 59.358 50.000 0.00 0.00 0.00 5.28
2389 3476 3.347077 ACGTCTATATACTCCCTCCGG 57.653 52.381 0.00 0.00 0.00 5.14
2390 3477 6.998968 AATTACGTCTATATACTCCCTCCG 57.001 41.667 0.00 0.00 0.00 4.63
2415 3502 8.031277 GGAGCAAAATGAATGAATCTACACTTT 58.969 33.333 0.00 0.00 0.00 2.66
2416 3503 7.542025 GGAGCAAAATGAATGAATCTACACTT 58.458 34.615 0.00 0.00 0.00 3.16
2417 3504 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
2418 3505 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
2419 3506 5.647658 ACGGAGCAAAATGAATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
2420 3507 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
2421 3508 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
2422 3509 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
2423 3510 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
2424 3511 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
2425 3512 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
2426 3513 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
2427 3514 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
2428 3515 5.527582 GGACTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
2429 3516 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
2430 3517 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
2431 3518 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
2432 3519 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
2433 3520 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
2434 3521 5.801531 ATATGGACTACATACGGAGCAAA 57.198 39.130 0.00 0.00 44.41 3.68
2435 3522 5.510690 CCAATATGGACTACATACGGAGCAA 60.511 44.000 0.00 0.00 44.41 3.91
2436 3523 4.021456 CCAATATGGACTACATACGGAGCA 60.021 45.833 0.00 0.00 44.41 4.26
2437 3524 4.219944 TCCAATATGGACTACATACGGAGC 59.780 45.833 0.00 0.00 42.67 4.70
2438 3525 5.977489 TCCAATATGGACTACATACGGAG 57.023 43.478 0.00 0.00 42.67 4.63
2468 3555 9.046296 CGCTCTGTTCCTAAATATAAGTCATTT 57.954 33.333 0.00 0.00 0.00 2.32
2469 3556 8.421784 TCGCTCTGTTCCTAAATATAAGTCATT 58.578 33.333 0.00 0.00 0.00 2.57
2470 3557 7.952671 TCGCTCTGTTCCTAAATATAAGTCAT 58.047 34.615 0.00 0.00 0.00 3.06
2471 3558 7.068348 ACTCGCTCTGTTCCTAAATATAAGTCA 59.932 37.037 0.00 0.00 0.00 3.41
2472 3559 7.427214 ACTCGCTCTGTTCCTAAATATAAGTC 58.573 38.462 0.00 0.00 0.00 3.01
2473 3560 7.349412 ACTCGCTCTGTTCCTAAATATAAGT 57.651 36.000 0.00 0.00 0.00 2.24
2474 3561 7.539366 GCTACTCGCTCTGTTCCTAAATATAAG 59.461 40.741 0.00 0.00 35.14 1.73
2475 3562 7.013942 TGCTACTCGCTCTGTTCCTAAATATAA 59.986 37.037 0.00 0.00 40.11 0.98
2476 3563 6.489022 TGCTACTCGCTCTGTTCCTAAATATA 59.511 38.462 0.00 0.00 40.11 0.86
2477 3564 5.302059 TGCTACTCGCTCTGTTCCTAAATAT 59.698 40.000 0.00 0.00 40.11 1.28
2478 3565 4.643334 TGCTACTCGCTCTGTTCCTAAATA 59.357 41.667 0.00 0.00 40.11 1.40
2479 3566 3.447586 TGCTACTCGCTCTGTTCCTAAAT 59.552 43.478 0.00 0.00 40.11 1.40
2480 3567 2.823747 TGCTACTCGCTCTGTTCCTAAA 59.176 45.455 0.00 0.00 40.11 1.85
2481 3568 2.423892 CTGCTACTCGCTCTGTTCCTAA 59.576 50.000 0.00 0.00 40.11 2.69
2482 3569 2.017782 CTGCTACTCGCTCTGTTCCTA 58.982 52.381 0.00 0.00 40.11 2.94
2483 3570 0.814457 CTGCTACTCGCTCTGTTCCT 59.186 55.000 0.00 0.00 40.11 3.36
2484 3571 0.528470 ACTGCTACTCGCTCTGTTCC 59.472 55.000 0.00 0.00 40.11 3.62
2485 3572 3.701532 ATACTGCTACTCGCTCTGTTC 57.298 47.619 0.00 0.00 40.11 3.18
2486 3573 5.278561 GGATTATACTGCTACTCGCTCTGTT 60.279 44.000 0.00 0.00 40.11 3.16
2487 3574 4.216687 GGATTATACTGCTACTCGCTCTGT 59.783 45.833 0.00 0.00 40.11 3.41
2488 3575 4.216472 TGGATTATACTGCTACTCGCTCTG 59.784 45.833 0.00 0.00 40.11 3.35
2489 3576 4.399219 TGGATTATACTGCTACTCGCTCT 58.601 43.478 0.00 0.00 40.11 4.09
2490 3577 4.768130 TGGATTATACTGCTACTCGCTC 57.232 45.455 0.00 0.00 40.11 5.03
2491 3578 4.767409 TGATGGATTATACTGCTACTCGCT 59.233 41.667 0.00 0.00 40.11 4.93
2492 3579 5.060662 TGATGGATTATACTGCTACTCGC 57.939 43.478 0.00 0.00 39.77 5.03
2493 3580 7.093354 ACAATGATGGATTATACTGCTACTCG 58.907 38.462 0.00 0.00 0.00 4.18
2494 3581 8.839310 AACAATGATGGATTATACTGCTACTC 57.161 34.615 0.00 0.00 0.00 2.59
2495 3582 9.060347 CAAACAATGATGGATTATACTGCTACT 57.940 33.333 0.00 0.00 0.00 2.57
2496 3583 9.056005 TCAAACAATGATGGATTATACTGCTAC 57.944 33.333 0.00 0.00 31.50 3.58
2610 3697 6.668541 AATGAGAATGTATTCACTGGAACG 57.331 37.500 7.30 0.00 39.23 3.95
2639 3726 7.537596 AAGTATTCAATCCACCAAATGTTGA 57.462 32.000 0.00 0.00 0.00 3.18
2647 3734 5.421693 CCAATGGAAAGTATTCAATCCACCA 59.578 40.000 0.00 0.00 44.25 4.17
2649 3736 6.378280 ACTCCAATGGAAAGTATTCAATCCAC 59.622 38.462 2.61 0.00 44.25 4.02
2717 3809 8.396272 ACCCTGTATGCATCAATTAACTAATC 57.604 34.615 0.19 0.00 0.00 1.75
2741 3833 5.148651 ACCTGTCAGTGTTAGGTATGAAC 57.851 43.478 16.12 0.00 42.78 3.18
2821 3913 8.783660 TCTTCATATTCAGTAGTACCCTTCAT 57.216 34.615 0.00 0.00 0.00 2.57
2871 3963 1.077501 GCAGCCCAGCCTGTATGAA 60.078 57.895 0.00 0.00 35.28 2.57
2917 4009 1.689984 TGCATCTCCACTGTGCAAAA 58.310 45.000 1.29 0.00 44.99 2.44
2940 4032 3.810941 CCACGGAACTAAAAGCAGTGTAA 59.189 43.478 0.00 0.00 0.00 2.41
3043 4135 4.151335 CAGTGAGATTTGGACGTCTCTTTG 59.849 45.833 16.46 6.83 41.10 2.77
3070 4162 9.850628 AACAGACAATTCATCATCATTAAGTTG 57.149 29.630 0.00 0.00 0.00 3.16
3097 4189 3.512724 AGCTTAACAAAGCCATCAGCATT 59.487 39.130 6.50 0.00 46.61 3.56
3114 4206 7.601130 ACACAAATAACACGTCTTGATAGCTTA 59.399 33.333 0.00 0.00 0.00 3.09
3185 4277 1.000896 CGGCCTTCTTTCCCACCAT 60.001 57.895 0.00 0.00 0.00 3.55
3193 4285 0.530870 GCTATCGCTCGGCCTTCTTT 60.531 55.000 0.00 0.00 0.00 2.52
3227 4319 1.815003 CTTTTCCGGCATCTTCAGCTT 59.185 47.619 0.00 0.00 0.00 3.74
3403 4495 2.548057 CGCACCAGTTCACACTAATTGT 59.452 45.455 0.00 0.00 39.97 2.71
3448 4540 3.181497 CCATACAAAAGCACCAATCTCCG 60.181 47.826 0.00 0.00 0.00 4.63
3536 4628 5.376625 ACACTAAAATCAGAACAAGAGGCA 58.623 37.500 0.00 0.00 0.00 4.75
3558 4650 7.665561 AAATCTCTGTGAGAGCTTCTAAAAC 57.334 36.000 3.64 0.00 42.26 2.43
3683 5039 3.258872 TCTGATGGCTTTGAACCCAAATG 59.741 43.478 0.00 0.00 41.03 2.32
3711 5067 7.008628 GCCTCATATTTTCACAAAAACAGATCG 59.991 37.037 0.00 0.00 37.20 3.69
3712 5068 7.276438 GGCCTCATATTTTCACAAAAACAGATC 59.724 37.037 0.00 0.00 37.20 2.75
3789 5146 2.806434 ACATCAGCTTGCCATGGTTAA 58.194 42.857 14.67 8.43 0.00 2.01
3867 5233 7.789831 ACCTTATGGGATTATGTCTAAGACTCA 59.210 37.037 0.00 0.00 38.76 3.41
3983 5349 4.329545 TCGCCAGGGCAGGAACAC 62.330 66.667 11.42 0.00 42.06 3.32
3984 5350 4.329545 GTCGCCAGGGCAGGAACA 62.330 66.667 11.42 0.00 42.06 3.18
3985 5351 4.329545 TGTCGCCAGGGCAGGAAC 62.330 66.667 11.42 3.46 42.06 3.62
3986 5352 4.329545 GTGTCGCCAGGGCAGGAA 62.330 66.667 11.42 0.00 42.06 3.36
3994 5360 4.680237 TTCCGCCTGTGTCGCCAG 62.680 66.667 0.00 0.00 0.00 4.85
4003 5369 1.971695 GGTTTGGGTCTTCCGCCTG 60.972 63.158 0.00 0.00 38.76 4.85
4027 5393 1.077858 GACGAGGAGGGTAGTCGGT 60.078 63.158 0.00 0.00 38.03 4.69
4031 5397 1.451747 GAGCGACGAGGAGGGTAGT 60.452 63.158 0.00 0.00 0.00 2.73
4096 5462 2.046892 GCTGCCACCATCTGTCGT 60.047 61.111 0.00 0.00 0.00 4.34
4099 5465 4.415150 CCCGCTGCCACCATCTGT 62.415 66.667 0.00 0.00 0.00 3.41
4137 5503 4.227134 CCCCACCGAGATCTGCCG 62.227 72.222 0.00 0.00 0.00 5.69
4162 5528 2.577593 GTGTAGCCGAGGTGGACC 59.422 66.667 0.00 0.00 42.00 4.46
4185 5551 0.787787 GCGAAATTGCCGGAAAAACC 59.212 50.000 5.05 0.00 0.00 3.27
4189 5555 2.126657 GCGCGAAATTGCCGGAAA 60.127 55.556 12.10 0.00 0.00 3.13
4194 5560 2.504681 CCACTGCGCGAAATTGCC 60.505 61.111 12.10 0.00 0.00 4.52
4195 5561 3.174573 GCCACTGCGCGAAATTGC 61.175 61.111 12.10 1.73 0.00 3.56
4209 5575 1.117749 ATAGCTGGAGATGAGCGCCA 61.118 55.000 2.29 1.52 44.78 5.69
4219 5585 1.123928 ACCCCTTCGAATAGCTGGAG 58.876 55.000 0.00 0.00 0.00 3.86
4223 5589 0.107165 GCCAACCCCTTCGAATAGCT 60.107 55.000 0.00 0.00 0.00 3.32
4226 5592 0.996583 AAGGCCAACCCCTTCGAATA 59.003 50.000 5.01 0.00 41.28 1.75
4276 5642 2.278661 GCCGTCGAAGGTCCGATC 60.279 66.667 18.88 0.00 40.91 3.69
4297 5663 1.748122 GAGCTGCCATCACACCCTG 60.748 63.158 0.00 0.00 0.00 4.45
4298 5664 2.673523 GAGCTGCCATCACACCCT 59.326 61.111 0.00 0.00 0.00 4.34
4299 5665 2.439156 GGAGCTGCCATCACACCC 60.439 66.667 0.00 0.00 36.34 4.61
4300 5666 2.439156 GGGAGCTGCCATCACACC 60.439 66.667 20.97 0.00 38.95 4.16
4301 5667 2.439156 GGGGAGCTGCCATCACAC 60.439 66.667 26.95 3.10 38.95 3.82
4302 5668 2.202236 GAAGGGGAGCTGCCATCACA 62.202 60.000 26.95 0.00 38.95 3.58
4303 5669 1.452833 GAAGGGGAGCTGCCATCAC 60.453 63.158 26.95 13.04 38.95 3.06
4304 5670 1.617536 AGAAGGGGAGCTGCCATCA 60.618 57.895 26.95 0.00 38.95 3.07
4305 5671 1.153005 CAGAAGGGGAGCTGCCATC 60.153 63.158 26.95 21.90 38.95 3.51
4306 5672 3.004951 CAGAAGGGGAGCTGCCAT 58.995 61.111 26.95 17.65 38.95 4.40


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

AutoCloner maintained by Alex Coulton.