Multiple sequence alignment - TraesCS4A01G196000

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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 TraesCS4A01G196000 chr4A 100.000 3825 0 0 1 3825 478220705 478216881 0.000000e+00 7064.0
1 TraesCS4A01G196000 chr4A 85.615 1008 69 39 706 1673 478340331 478339360 0.000000e+00 989.0
2 TraesCS4A01G196000 chr4A 84.676 1018 82 34 706 1680 478303035 478302049 0.000000e+00 948.0
3 TraesCS4A01G196000 chr4A 89.151 424 44 2 2426 2849 478300959 478300538 9.410000e-146 527.0
4 TraesCS4A01G196000 chr4A 89.027 401 42 2 2428 2827 478338760 478338361 2.650000e-136 496.0
5 TraesCS4A01G196000 chr4A 86.395 147 10 6 508 654 478303186 478303050 6.620000e-33 152.0
6 TraesCS4A01G196000 chr4A 86.066 122 11 6 1942 2062 478339108 478338992 4.010000e-25 126.0
7 TraesCS4A01G196000 chr4A 93.750 48 3 0 1978 2025 478301796 478301749 5.300000e-09 73.1
8 TraesCS4A01G196000 chr4D 92.648 1877 97 21 1 1854 97956920 97958778 0.000000e+00 2663.0
9 TraesCS4A01G196000 chr4D 91.089 1212 65 30 2290 3487 97959126 97960308 0.000000e+00 1600.0
10 TraesCS4A01G196000 chr4D 87.054 896 61 28 822 1684 97508442 97509315 0.000000e+00 961.0
11 TraesCS4A01G196000 chr4D 88.671 715 47 16 996 1684 97605247 97605953 0.000000e+00 841.0
12 TraesCS4A01G196000 chr4D 87.429 700 50 16 996 1676 97720620 97721300 0.000000e+00 771.0
13 TraesCS4A01G196000 chr4D 86.974 499 41 9 1186 1676 97766056 97765574 1.210000e-149 540.0
14 TraesCS4A01G196000 chr4D 89.303 402 43 0 2426 2827 97760666 97760265 4.410000e-139 505.0
15 TraesCS4A01G196000 chr4D 89.055 402 44 0 2426 2827 97510009 97510410 2.050000e-137 499.0
16 TraesCS4A01G196000 chr4D 88.557 402 46 0 2426 2827 97606663 97607064 4.440000e-134 488.0
17 TraesCS4A01G196000 chr4D 94.774 287 12 3 3540 3825 97960290 97960574 9.750000e-121 444.0
18 TraesCS4A01G196000 chr4D 83.619 409 34 17 19 419 97604372 97604755 1.690000e-93 353.0
19 TraesCS4A01G196000 chr4D 83.619 409 34 17 19 419 97717801 97718184 1.690000e-93 353.0
20 TraesCS4A01G196000 chr4D 93.333 225 10 2 1838 2062 97958793 97959012 1.020000e-85 327.0
21 TraesCS4A01G196000 chr4D 84.553 246 15 7 706 934 97604994 97605233 4.970000e-54 222.0
22 TraesCS4A01G196000 chr4D 83.254 209 20 4 706 900 97718423 97718630 1.090000e-40 178.0
23 TraesCS4A01G196000 chr4D 86.486 148 19 1 2061 2207 3329203 3329056 1.100000e-35 161.0
24 TraesCS4A01G196000 chr4D 79.781 183 33 4 1208 1388 394361889 394362069 3.100000e-26 130.0
25 TraesCS4A01G196000 chr4B 91.647 1293 58 14 2222 3505 139545737 139546988 0.000000e+00 1744.0
26 TraesCS4A01G196000 chr4B 89.278 914 48 15 1 901 139544366 139545242 0.000000e+00 1099.0
27 TraesCS4A01G196000 chr4B 85.629 1009 69 37 706 1680 139398827 139399793 0.000000e+00 990.0
28 TraesCS4A01G196000 chr4B 85.473 1005 69 39 708 1680 139471978 139472937 0.000000e+00 976.0
29 TraesCS4A01G196000 chr4B 85.473 1005 69 39 708 1680 139510426 139511385 0.000000e+00 976.0
30 TraesCS4A01G196000 chr4B 87.928 497 34 9 1181 1676 139511506 139511977 2.580000e-156 562.0
31 TraesCS4A01G196000 chr4B 95.266 338 15 1 3489 3825 139547001 139547338 5.620000e-148 534.0
32 TraesCS4A01G196000 chr4B 89.851 404 37 4 2426 2827 139473540 139473941 2.040000e-142 516.0
33 TraesCS4A01G196000 chr4B 89.109 404 40 4 2426 2827 139400396 139400797 2.050000e-137 499.0
34 TraesCS4A01G196000 chr4B 81.276 486 47 25 1568 2028 139545245 139545711 1.690000e-93 353.0
35 TraesCS4A01G196000 chr4B 82.667 150 18 6 505 654 139471820 139471961 4.010000e-25 126.0
36 TraesCS4A01G196000 chr4B 83.636 110 14 2 1953 2062 139532005 139532110 2.430000e-17 100.0
37 TraesCS4A01G196000 chr4B 97.368 38 1 0 505 542 139529083 139529120 8.870000e-07 65.8
38 TraesCS4A01G196000 chr5D 81.375 349 63 2 1052 1399 230505193 230505540 2.250000e-72 283.0
39 TraesCS4A01G196000 chr5A 81.375 349 63 2 1052 1399 326058237 326057890 2.250000e-72 283.0
40 TraesCS4A01G196000 chr7D 88.024 167 5 4 2059 2210 246035002 246034836 2.350000e-42 183.0
41 TraesCS4A01G196000 chr7D 80.465 215 36 6 1176 1387 535967297 535967508 3.960000e-35 159.0
42 TraesCS4A01G196000 chr7D 80.982 163 27 4 2555 2715 478328493 478328653 4.010000e-25 126.0
43 TraesCS4A01G196000 chr7D 82.418 91 10 5 1120 1207 478327703 478327790 1.470000e-09 75.0
44 TraesCS4A01G196000 chr7D 82.022 89 14 2 1120 1207 478370406 478370493 1.470000e-09 75.0
45 TraesCS4A01G196000 chr1B 87.117 163 14 5 2056 2211 426854632 426854794 1.090000e-40 178.0
46 TraesCS4A01G196000 chr2B 87.417 151 13 2 2058 2207 356544664 356544809 6.570000e-38 169.0
47 TraesCS4A01G196000 chr7B 75.543 368 68 19 2466 2822 643295529 643295173 1.100000e-35 161.0
48 TraesCS4A01G196000 chr7B 74.658 146 35 2 1067 1211 504439447 504439591 3.190000e-06 63.9
49 TraesCS4A01G196000 chr6B 85.806 155 18 3 2057 2207 136827219 136827065 1.100000e-35 161.0
50 TraesCS4A01G196000 chr6B 75.329 304 65 10 2477 2775 42004908 42004610 1.850000e-28 137.0
51 TraesCS4A01G196000 chr6B 77.174 184 24 14 2042 2209 217165523 217165704 1.460000e-14 91.6
52 TraesCS4A01G196000 chr3B 87.413 143 15 3 2058 2197 236121517 236121659 1.100000e-35 161.0
53 TraesCS4A01G196000 chr3B 84.967 153 22 1 2058 2209 385480510 385480662 1.840000e-33 154.0
54 TraesCS4A01G196000 chr7A 75.419 358 68 16 2466 2813 670946427 670946080 5.120000e-34 156.0
55 TraesCS4A01G196000 chr2D 87.500 136 12 3 2062 2196 235074601 235074470 6.620000e-33 152.0
56 TraesCS4A01G196000 chr1D 80.095 211 34 7 1181 1387 467611838 467611632 2.380000e-32 150.0
57 TraesCS4A01G196000 chr1D 78.302 212 40 6 1179 1387 81726194 81726402 8.620000e-27 132.0
58 TraesCS4A01G196000 chr1D 77.130 223 46 5 1176 1397 288546062 288546280 1.440000e-24 124.0
59 TraesCS4A01G196000 chr1D 97.297 37 0 1 1176 1212 62858101 62858136 1.150000e-05 62.1
60 TraesCS4A01G196000 chr1D 73.272 217 39 15 1189 1400 413213002 413213204 1.150000e-05 62.1
61 TraesCS4A01G196000 chr6D 75.817 306 60 12 2477 2775 25804238 25803940 3.980000e-30 143.0
62 TraesCS4A01G196000 chr6D 71.552 348 87 11 2484 2825 90924171 90924512 2.450000e-12 84.2
63 TraesCS4A01G196000 chr6D 92.727 55 4 0 1153 1207 90922791 90922845 3.170000e-11 80.5
64 TraesCS4A01G196000 chr6D 74.242 198 46 4 1203 1396 72405848 72406044 1.140000e-10 78.7
65 TraesCS4A01G196000 chr6D 95.238 42 2 0 1166 1207 72405740 72405781 2.470000e-07 67.6
66 TraesCS4A01G196000 chr1A 83.871 155 19 4 2059 2207 584472134 584471980 3.980000e-30 143.0
67 TraesCS4A01G196000 chr3D 93.878 49 3 0 1159 1207 95840241 95840193 1.470000e-09 75.0
68 TraesCS4A01G196000 chrUn 96.774 31 1 0 1176 1206 17365005 17365035 7.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G196000 chr4A 478216881 478220705 3824 True 7064.000000 7064 100.000000 1 3825 1 chr4A.!!$R1 3824
1 TraesCS4A01G196000 chr4A 478338361 478340331 1970 True 537.000000 989 86.902667 706 2827 3 chr4A.!!$R3 2121
2 TraesCS4A01G196000 chr4A 478300538 478303186 2648 True 425.025000 948 88.493000 508 2849 4 chr4A.!!$R2 2341
3 TraesCS4A01G196000 chr4D 97956920 97960574 3654 False 1258.500000 2663 92.961000 1 3825 4 chr4D.!!$F5 3824
4 TraesCS4A01G196000 chr4D 97508442 97510410 1968 False 730.000000 961 88.054500 822 2827 2 chr4D.!!$F2 2005
5 TraesCS4A01G196000 chr4D 97604372 97607064 2692 False 476.000000 841 86.350000 19 2827 4 chr4D.!!$F3 2808
6 TraesCS4A01G196000 chr4D 97717801 97721300 3499 False 434.000000 771 84.767333 19 1676 3 chr4D.!!$F4 1657
7 TraesCS4A01G196000 chr4B 139544366 139547338 2972 False 932.500000 1744 89.366750 1 3825 4 chr4B.!!$F5 3824
8 TraesCS4A01G196000 chr4B 139510426 139511977 1551 False 769.000000 976 86.700500 708 1680 2 chr4B.!!$F3 972
9 TraesCS4A01G196000 chr4B 139398827 139400797 1970 False 744.500000 990 87.369000 706 2827 2 chr4B.!!$F1 2121
10 TraesCS4A01G196000 chr4B 139471820 139473941 2121 False 539.333333 976 85.997000 505 2827 3 chr4B.!!$F2 2322

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
112 121 1.021202 TTTTGACCGTGACCAAGCAG 58.979 50.000 0.0 0.0 0.00 4.24 F
924 2960 1.067516 GCAAACAAGCTCTCAAGGCAA 59.932 47.619 0.0 0.0 0.00 4.52 F
1661 3738 1.361668 CCCAGAAAGACATGGTCGCG 61.362 60.000 0.0 0.0 37.67 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1287 3344 0.401395 TGACCTCAAACCCCCTGACT 60.401 55.0 0.00 0.0 0.00 3.41 R
1976 4278 0.727398 GTGGCTATCAGTTCCGTTGC 59.273 55.0 0.00 0.0 0.00 4.17 R
3352 6343 0.690192 TGGCCAATCTGGTTCTTCGA 59.310 50.0 0.61 0.0 40.46 3.71 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
108 117 3.283751 AGAATGTTTTGACCGTGACCAA 58.716 40.909 0.00 0.00 0.00 3.67
112 121 1.021202 TTTTGACCGTGACCAAGCAG 58.979 50.000 0.00 0.00 0.00 4.24
135 144 4.437930 GCATGCATGTCTCCAGTTTCTAAC 60.438 45.833 26.79 1.51 0.00 2.34
146 155 3.935203 CCAGTTTCTAACGATGAGCATGT 59.065 43.478 0.00 0.00 36.23 3.21
149 163 4.860916 AGTTTCTAACGATGAGCATGTGCT 60.861 41.667 7.31 7.31 45.44 4.40
180 197 2.273449 GGAGACCCGGTCCGTCTA 59.727 66.667 14.32 0.00 40.67 2.59
273 294 1.108776 TCATGTACCGGTAGGCAGTC 58.891 55.000 16.41 2.24 42.76 3.51
311 335 3.660865 ACGTGGACTAACCTTGACATTC 58.339 45.455 0.00 0.00 39.86 2.67
333 357 3.614630 CGTTGGGTAGTGAAACGGTGATA 60.615 47.826 0.00 0.00 45.86 2.15
412 441 1.398390 CGCCTCAAAGTCCATGTAAGC 59.602 52.381 0.00 0.00 0.00 3.09
452 496 9.539825 GATCTAAATTTGACTCAGAGATGCTAA 57.460 33.333 3.79 0.00 0.00 3.09
454 498 6.434018 AAATTTGACTCAGAGATGCTAAGC 57.566 37.500 3.79 0.00 0.00 3.09
474 518 2.670414 GCAGAGTAGCTAGCAAACACAG 59.330 50.000 18.83 10.91 0.00 3.66
669 723 4.112634 AGCTACGACGTTACGTATACTCA 58.887 43.478 11.32 0.00 45.37 3.41
749 804 2.760159 CGCGCCCGTTTGGATCAAT 61.760 57.895 0.00 0.00 37.49 2.57
810 893 7.884354 TGCAATCTAATAATATGTGATGGCAGA 59.116 33.333 11.30 0.00 38.64 4.26
811 894 8.180267 GCAATCTAATAATATGTGATGGCAGAC 58.820 37.037 9.01 0.00 35.01 3.51
812 895 9.445878 CAATCTAATAATATGTGATGGCAGACT 57.554 33.333 0.00 0.00 0.00 3.24
813 896 9.445878 AATCTAATAATATGTGATGGCAGACTG 57.554 33.333 0.00 0.00 0.00 3.51
814 897 7.389232 TCTAATAATATGTGATGGCAGACTGG 58.611 38.462 4.26 0.00 0.00 4.00
815 898 3.939740 AATATGTGATGGCAGACTGGT 57.060 42.857 4.26 0.00 0.00 4.00
819 902 1.550524 TGTGATGGCAGACTGGTACTC 59.449 52.381 4.26 0.00 0.00 2.59
820 903 1.134670 GTGATGGCAGACTGGTACTCC 60.135 57.143 4.26 0.00 0.00 3.85
924 2960 1.067516 GCAAACAAGCTCTCAAGGCAA 59.932 47.619 0.00 0.00 0.00 4.52
939 2975 6.151985 TCTCAAGGCAATATCTAGCTAGCTAC 59.848 42.308 20.67 8.87 0.00 3.58
940 2976 6.013379 TCAAGGCAATATCTAGCTAGCTACT 58.987 40.000 20.67 12.94 0.00 2.57
941 2977 6.151985 TCAAGGCAATATCTAGCTAGCTACTC 59.848 42.308 20.67 4.82 0.00 2.59
942 2978 4.953579 AGGCAATATCTAGCTAGCTACTCC 59.046 45.833 20.67 12.51 0.00 3.85
943 2979 4.953579 GGCAATATCTAGCTAGCTACTCCT 59.046 45.833 20.67 7.90 0.00 3.69
945 2981 6.262273 GGCAATATCTAGCTAGCTACTCCTAG 59.738 46.154 20.67 11.75 38.24 3.02
946 2982 7.051623 GCAATATCTAGCTAGCTACTCCTAGA 58.948 42.308 20.67 16.74 40.16 2.43
947 2983 7.719633 GCAATATCTAGCTAGCTACTCCTAGAT 59.280 40.741 20.67 21.86 45.02 1.98
959 3000 5.242838 GCTACTCCTAGATAGCACACTTGAT 59.757 44.000 12.94 0.00 42.82 2.57
993 3035 4.034048 GTCAGCAACGTAAACCCATAGATG 59.966 45.833 0.00 0.00 0.00 2.90
994 3036 3.938963 CAGCAACGTAAACCCATAGATGT 59.061 43.478 0.00 0.00 0.00 3.06
998 3040 4.037858 ACGTAAACCCATAGATGTCGAC 57.962 45.455 9.11 9.11 0.00 4.20
1287 3344 1.691196 CCAAGCCCAACAAGAACTCA 58.309 50.000 0.00 0.00 0.00 3.41
1299 3356 1.821088 AGAACTCAGTCAGGGGGTTT 58.179 50.000 0.00 0.00 0.00 3.27
1411 3468 3.015327 AGCGTCGTCTTGGTAAGTATCT 58.985 45.455 0.00 0.00 0.00 1.98
1461 3527 7.323046 GCTATAGCTTGTACGTATTCTTCAC 57.677 40.000 17.75 0.00 38.21 3.18
1564 3641 2.430921 AACGACGGCGAGCTTCAG 60.431 61.111 22.49 0.00 41.64 3.02
1592 3669 4.344865 AACAACATCCCGCCGCCT 62.345 61.111 0.00 0.00 0.00 5.52
1661 3738 1.361668 CCCAGAAAGACATGGTCGCG 61.362 60.000 0.00 0.00 37.67 5.87
1682 3765 3.878103 CGCTCTCAGGTAGTACTACACAT 59.122 47.826 29.38 15.04 37.78 3.21
1683 3766 4.260825 CGCTCTCAGGTAGTACTACACATG 60.261 50.000 29.38 23.52 37.78 3.21
1723 3837 4.036616 ACGTTAACCGCCAAATAAACAACT 59.963 37.500 0.00 0.00 41.42 3.16
1770 3885 8.850156 TCTTTTTACTGGGATTTTCAGAAGAAG 58.150 33.333 0.00 0.00 34.71 2.85
1775 3893 7.660030 ACTGGGATTTTCAGAAGAAGAAAAA 57.340 32.000 5.35 0.00 45.02 1.94
1849 4073 9.278978 TGAAATACTGTTGCAGTCTTAATAACA 57.721 29.630 4.95 0.00 41.21 2.41
1872 4127 7.404203 ACAAACAAAAGTAGTGATCACGTAAC 58.596 34.615 19.85 17.93 36.20 2.50
1891 4151 8.342634 CACGTAACATATATTTTCCTTTCCTGG 58.657 37.037 0.00 0.00 0.00 4.45
1900 4163 2.038863 TCCTTTCCTGGAGCAAGGTA 57.961 50.000 21.17 9.79 38.62 3.08
1901 4164 2.344592 TCCTTTCCTGGAGCAAGGTAA 58.655 47.619 21.17 5.95 38.62 2.85
1976 4278 1.614903 TGCAAAACAGCTGGGATCAAG 59.385 47.619 19.93 2.12 34.99 3.02
2022 4330 6.920569 TTGACTCGAAAGCTAAAAACTTCT 57.079 33.333 0.00 0.00 0.00 2.85
2023 4331 8.428186 TTTGACTCGAAAGCTAAAAACTTCTA 57.572 30.769 0.00 0.00 0.00 2.10
2024 4332 7.404139 TGACTCGAAAGCTAAAAACTTCTAC 57.596 36.000 0.00 0.00 0.00 2.59
2052 4360 8.383175 ACATAAGACCTTTTCTCAGGATTAACA 58.617 33.333 0.00 0.00 37.39 2.41
2064 4378 9.847224 TTCTCAGGATTAACAAAATATACTCCC 57.153 33.333 0.00 0.00 0.00 4.30
2066 4380 9.495572 CTCAGGATTAACAAAATATACTCCCTC 57.504 37.037 0.00 0.00 0.00 4.30
2067 4381 8.437575 TCAGGATTAACAAAATATACTCCCTCC 58.562 37.037 0.00 0.00 0.00 4.30
2070 4384 7.718314 GGATTAACAAAATATACTCCCTCCGTT 59.282 37.037 0.00 0.00 0.00 4.44
2071 4385 8.672823 ATTAACAAAATATACTCCCTCCGTTC 57.327 34.615 0.00 0.00 0.00 3.95
2072 4386 5.032327 ACAAAATATACTCCCTCCGTTCC 57.968 43.478 0.00 0.00 0.00 3.62
2073 4387 4.720273 ACAAAATATACTCCCTCCGTTCCT 59.280 41.667 0.00 0.00 0.00 3.36
2075 4389 6.384886 ACAAAATATACTCCCTCCGTTCCTAA 59.615 38.462 0.00 0.00 0.00 2.69
2076 4390 7.092757 ACAAAATATACTCCCTCCGTTCCTAAA 60.093 37.037 0.00 0.00 0.00 1.85
2077 4391 7.628501 AAATATACTCCCTCCGTTCCTAAAT 57.371 36.000 0.00 0.00 0.00 1.40
2078 4392 8.731591 AAATATACTCCCTCCGTTCCTAAATA 57.268 34.615 0.00 0.00 0.00 1.40
2079 4393 8.912614 AATATACTCCCTCCGTTCCTAAATAT 57.087 34.615 0.00 0.00 0.00 1.28
2080 4394 8.912614 ATATACTCCCTCCGTTCCTAAATATT 57.087 34.615 0.00 0.00 0.00 1.28
2081 4395 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2082 4396 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2083 4397 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2084 4398 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2085 4399 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2086 4400 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2087 4401 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2088 4402 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2089 4403 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2106 4420 9.810545 TTGTCTTTTTAGAGGTTTTAAATGGTG 57.189 29.630 0.00 0.00 0.00 4.17
2107 4421 9.191479 TGTCTTTTTAGAGGTTTTAAATGGTGA 57.809 29.630 0.00 0.00 0.00 4.02
2114 4428 7.839680 AGAGGTTTTAAATGGTGAAATGAGT 57.160 32.000 0.00 0.00 0.00 3.41
2115 4429 7.661040 AGAGGTTTTAAATGGTGAAATGAGTG 58.339 34.615 0.00 0.00 0.00 3.51
2116 4430 7.505585 AGAGGTTTTAAATGGTGAAATGAGTGA 59.494 33.333 0.00 0.00 0.00 3.41
2117 4431 8.017418 AGGTTTTAAATGGTGAAATGAGTGAA 57.983 30.769 0.00 0.00 0.00 3.18
2118 4432 8.650490 AGGTTTTAAATGGTGAAATGAGTGAAT 58.350 29.630 0.00 0.00 0.00 2.57
2119 4433 8.925700 GGTTTTAAATGGTGAAATGAGTGAATC 58.074 33.333 0.00 0.00 0.00 2.52
2120 4434 9.696917 GTTTTAAATGGTGAAATGAGTGAATCT 57.303 29.630 0.00 0.00 0.00 2.40
2123 4437 9.513906 TTAAATGGTGAAATGAGTGAATCTACA 57.486 29.630 0.00 0.00 0.00 2.74
2124 4438 6.992063 ATGGTGAAATGAGTGAATCTACAC 57.008 37.500 0.00 0.00 40.60 2.90
2157 4471 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2158 4472 7.153217 TGTCTATATACATCCGTATGTGGTG 57.847 40.000 3.56 0.00 45.99 4.17
2159 4473 6.943718 TGTCTATATACATCCGTATGTGGTGA 59.056 38.462 3.56 0.00 45.99 4.02
2160 4474 7.094506 TGTCTATATACATCCGTATGTGGTGAC 60.095 40.741 3.56 5.93 45.99 3.67
2161 4475 3.746045 ATACATCCGTATGTGGTGACC 57.254 47.619 3.56 0.00 45.99 4.02
2162 4476 1.271856 ACATCCGTATGTGGTGACCA 58.728 50.000 0.00 0.00 44.79 4.02
2163 4477 1.837439 ACATCCGTATGTGGTGACCAT 59.163 47.619 7.94 0.00 44.79 3.55
2164 4478 2.238646 ACATCCGTATGTGGTGACCATT 59.761 45.455 7.94 0.86 44.79 3.16
2165 4479 3.278574 CATCCGTATGTGGTGACCATTT 58.721 45.455 7.94 0.45 35.28 2.32
2166 4480 4.080807 ACATCCGTATGTGGTGACCATTTA 60.081 41.667 7.94 0.00 44.79 1.40
2167 4481 4.554960 TCCGTATGTGGTGACCATTTAA 57.445 40.909 7.94 0.00 35.28 1.52
2168 4482 4.907809 TCCGTATGTGGTGACCATTTAAA 58.092 39.130 7.94 0.00 35.28 1.52
2169 4483 5.314529 TCCGTATGTGGTGACCATTTAAAA 58.685 37.500 7.94 0.00 35.28 1.52
2170 4484 5.946972 TCCGTATGTGGTGACCATTTAAAAT 59.053 36.000 7.94 0.00 35.28 1.82
2171 4485 6.094325 TCCGTATGTGGTGACCATTTAAAATC 59.906 38.462 7.94 0.00 35.28 2.17
2172 4486 6.094881 CCGTATGTGGTGACCATTTAAAATCT 59.905 38.462 7.94 0.00 35.28 2.40
2173 4487 7.186804 CGTATGTGGTGACCATTTAAAATCTC 58.813 38.462 7.94 0.00 35.28 2.75
2174 4488 7.065803 CGTATGTGGTGACCATTTAAAATCTCT 59.934 37.037 7.94 0.00 35.28 3.10
2175 4489 9.391006 GTATGTGGTGACCATTTAAAATCTCTA 57.609 33.333 7.94 0.00 35.28 2.43
2176 4490 7.921786 TGTGGTGACCATTTAAAATCTCTAG 57.078 36.000 7.94 0.00 35.28 2.43
2177 4491 7.685481 TGTGGTGACCATTTAAAATCTCTAGA 58.315 34.615 7.94 0.00 35.28 2.43
2178 4492 8.160765 TGTGGTGACCATTTAAAATCTCTAGAA 58.839 33.333 7.94 0.00 35.28 2.10
2179 4493 9.010029 GTGGTGACCATTTAAAATCTCTAGAAA 57.990 33.333 7.94 0.00 35.28 2.52
2180 4494 9.231297 TGGTGACCATTTAAAATCTCTAGAAAG 57.769 33.333 0.00 0.00 0.00 2.62
2181 4495 9.449719 GGTGACCATTTAAAATCTCTAGAAAGA 57.550 33.333 0.00 0.00 0.00 2.52
2201 4515 9.025041 AGAAAGACAAATATTTAGAAACAGGGG 57.975 33.333 0.00 0.00 0.00 4.79
2202 4516 7.718334 AAGACAAATATTTAGAAACAGGGGG 57.282 36.000 0.00 0.00 0.00 5.40
2203 4517 7.039722 AGACAAATATTTAGAAACAGGGGGA 57.960 36.000 0.00 0.00 0.00 4.81
2204 4518 7.119387 AGACAAATATTTAGAAACAGGGGGAG 58.881 38.462 0.00 0.00 0.00 4.30
2205 4519 6.800890 ACAAATATTTAGAAACAGGGGGAGT 58.199 36.000 0.00 0.00 0.00 3.85
2206 4520 7.935405 ACAAATATTTAGAAACAGGGGGAGTA 58.065 34.615 0.00 0.00 0.00 2.59
2207 4521 8.395605 ACAAATATTTAGAAACAGGGGGAGTAA 58.604 33.333 0.00 0.00 0.00 2.24
2208 4522 9.421399 CAAATATTTAGAAACAGGGGGAGTAAT 57.579 33.333 0.00 0.00 0.00 1.89
2212 4526 8.818622 ATTTAGAAACAGGGGGAGTAATTAAC 57.181 34.615 0.00 0.00 0.00 2.01
2213 4527 5.853572 AGAAACAGGGGGAGTAATTAACA 57.146 39.130 0.00 0.00 0.00 2.41
2214 4528 6.208840 AGAAACAGGGGGAGTAATTAACAA 57.791 37.500 0.00 0.00 0.00 2.83
2215 4529 6.616577 AGAAACAGGGGGAGTAATTAACAAA 58.383 36.000 0.00 0.00 0.00 2.83
2216 4530 7.070629 AGAAACAGGGGGAGTAATTAACAAAA 58.929 34.615 0.00 0.00 0.00 2.44
2217 4531 6.911250 AACAGGGGGAGTAATTAACAAAAG 57.089 37.500 0.00 0.00 0.00 2.27
2218 4532 5.330233 ACAGGGGGAGTAATTAACAAAAGG 58.670 41.667 0.00 0.00 0.00 3.11
2219 4533 5.162914 ACAGGGGGAGTAATTAACAAAAGGT 60.163 40.000 0.00 0.00 0.00 3.50
2220 4534 5.185056 CAGGGGGAGTAATTAACAAAAGGTG 59.815 44.000 0.00 0.00 0.00 4.00
2226 4540 8.683615 GGGAGTAATTAACAAAAGGTGATTAGG 58.316 37.037 0.00 0.00 0.00 2.69
2234 4552 4.280929 ACAAAAGGTGATTAGGAAGTTGGC 59.719 41.667 0.00 0.00 0.00 4.52
2249 4570 7.179269 AGGAAGTTGGCAACTAATTACCATTA 58.821 34.615 31.34 0.00 41.91 1.90
2256 4577 6.601613 TGGCAACTAATTACCATTAACCTGAG 59.398 38.462 0.00 0.00 37.61 3.35
2300 4650 9.687210 TGTAAGACTACTATACAACAACAACAG 57.313 33.333 0.00 0.00 0.00 3.16
2327 4678 3.676291 TTGATCTGTTCCGTGATCACA 57.324 42.857 24.93 4.12 45.72 3.58
2353 5241 2.373540 ACGTAGAAGCGCCAATTACA 57.626 45.000 2.29 0.00 34.88 2.41
2357 5245 4.023878 ACGTAGAAGCGCCAATTACAAAAA 60.024 37.500 2.29 0.00 34.88 1.94
2444 5352 3.636231 TTCCAGGAGCCCACACGG 61.636 66.667 0.00 0.00 0.00 4.94
2595 5503 3.775654 GGACCTGCAGACCCCGAG 61.776 72.222 17.39 0.00 0.00 4.63
2632 5609 4.147321 ACTACTACAAGAACCTCGTCCAA 58.853 43.478 0.00 0.00 0.00 3.53
2779 5756 2.125912 GACATCACGCCGCTGACT 60.126 61.111 0.00 0.00 0.00 3.41
3008 5986 6.459923 GTTGTGCCTGGTGGATTAATAAAAA 58.540 36.000 0.00 0.00 34.57 1.94
3027 6005 2.660670 AGGTCTACCCCGTCTCTATG 57.339 55.000 0.00 0.00 36.42 2.23
3031 6009 1.202734 TCTACCCCGTCTCTATGGTCG 60.203 57.143 0.00 0.00 32.27 4.79
3041 6019 5.989777 CCGTCTCTATGGTCGGAAATTATTT 59.010 40.000 0.00 0.00 44.86 1.40
3078 6056 1.848608 CTACAGCACGACGACATGATG 59.151 52.381 0.00 0.60 38.20 3.07
3102 6080 6.002062 ACCTTATTTTTCGCAACTGAAGAG 57.998 37.500 0.00 0.00 0.00 2.85
3133 6117 2.082231 CATGAAGAAGCTGTGACCCTG 58.918 52.381 0.00 0.00 0.00 4.45
3159 6143 8.349983 GTGGAACAACAACTACTTTATCATTGT 58.650 33.333 0.00 0.00 44.16 2.71
3188 6172 8.099537 GCAGAAGATCATAGAATAAATGGAGGA 58.900 37.037 0.00 0.00 0.00 3.71
3189 6173 9.656040 CAGAAGATCATAGAATAAATGGAGGAG 57.344 37.037 0.00 0.00 0.00 3.69
3190 6174 8.824783 AGAAGATCATAGAATAAATGGAGGAGG 58.175 37.037 0.00 0.00 0.00 4.30
3191 6175 6.956497 AGATCATAGAATAAATGGAGGAGGC 58.044 40.000 0.00 0.00 0.00 4.70
3192 6176 6.734755 AGATCATAGAATAAATGGAGGAGGCT 59.265 38.462 0.00 0.00 0.00 4.58
3198 6182 0.182299 AAATGGAGGAGGCTAGCAGC 59.818 55.000 18.24 7.31 41.46 5.25
3199 6183 0.984961 AATGGAGGAGGCTAGCAGCA 60.985 55.000 18.24 0.00 44.75 4.41
3200 6184 0.984961 ATGGAGGAGGCTAGCAGCAA 60.985 55.000 18.24 0.00 44.75 3.91
3201 6185 1.200760 TGGAGGAGGCTAGCAGCAAA 61.201 55.000 18.24 0.00 44.75 3.68
3202 6186 0.463474 GGAGGAGGCTAGCAGCAAAG 60.463 60.000 18.24 0.00 44.75 2.77
3203 6187 0.539051 GAGGAGGCTAGCAGCAAAGA 59.461 55.000 18.24 0.00 44.75 2.52
3204 6188 0.540923 AGGAGGCTAGCAGCAAAGAG 59.459 55.000 18.24 0.00 44.75 2.85
3205 6189 0.251634 GGAGGCTAGCAGCAAAGAGT 59.748 55.000 18.24 0.00 44.75 3.24
3206 6190 1.482593 GGAGGCTAGCAGCAAAGAGTA 59.517 52.381 18.24 0.00 44.75 2.59
3207 6191 2.093447 GGAGGCTAGCAGCAAAGAGTAA 60.093 50.000 18.24 0.00 44.75 2.24
3208 6192 2.933260 GAGGCTAGCAGCAAAGAGTAAC 59.067 50.000 18.24 0.00 44.75 2.50
3209 6193 2.569404 AGGCTAGCAGCAAAGAGTAACT 59.431 45.455 18.24 0.00 44.75 2.24
3210 6194 2.675348 GGCTAGCAGCAAAGAGTAACTG 59.325 50.000 18.24 0.00 44.75 3.16
3225 6209 2.522836 AACTGATCTAGGATGCTGCG 57.477 50.000 0.00 0.00 0.00 5.18
3244 6228 1.808512 CGTATCATAGTTTGGCCGCCA 60.809 52.381 8.43 8.43 0.00 5.69
3264 6252 3.448686 CAGGACACACTATTCTTAGGCG 58.551 50.000 0.00 0.00 0.00 5.52
3301 6292 7.161773 TCAAGTTACTATTACCTTAGCACGT 57.838 36.000 0.00 0.00 0.00 4.49
3336 6327 2.188062 AATTGGCTTGCAAATGGTGG 57.812 45.000 0.00 0.00 0.00 4.61
3366 6357 2.972625 TCGCAATCGAAGAACCAGATT 58.027 42.857 0.00 0.00 43.58 2.40
3383 6374 3.057033 CAGATTGGCCATAAATAGCTGCC 60.057 47.826 6.09 0.00 42.49 4.85
3399 6390 2.739609 GCTGCCCCAATAATTGACTTGC 60.740 50.000 0.00 0.00 0.00 4.01
3401 6392 1.202405 GCCCCAATAATTGACTTGCCG 60.202 52.381 0.00 0.00 0.00 5.69
3464 6455 7.313646 CACAATCTGAGAGCATCAAAATCTTT 58.686 34.615 0.00 0.00 37.52 2.52
3559 6579 4.079385 TCTCAGCTGTTACTACTATCCCCA 60.079 45.833 14.67 0.00 0.00 4.96
3595 6616 4.700692 AGCCTCATATGAATAGCAGCAATG 59.299 41.667 18.89 0.53 0.00 2.82
3711 6732 2.028748 ACAGCATTTCCAACAGAATGGC 60.029 45.455 0.00 0.00 43.62 4.40
3771 6792 1.581934 CAGAAACAAGAGTCCGTGCA 58.418 50.000 0.00 0.00 0.00 4.57
3815 6836 2.268762 TAGTGCATGTCCAAACTGCA 57.731 45.000 0.00 0.00 43.20 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.921515 AGGCAGCATATAAATACGTACGTG 59.078 41.667 30.25 12.21 0.00 4.49
87 89 2.925724 TGGTCACGGTCAAAACATTCT 58.074 42.857 0.00 0.00 0.00 2.40
101 103 0.457853 CATGCATGCTGCTTGGTCAC 60.458 55.000 20.33 1.63 45.31 3.67
108 117 0.748367 CTGGAGACATGCATGCTGCT 60.748 55.000 28.51 22.67 39.34 4.24
112 121 2.089980 AGAAACTGGAGACATGCATGC 58.910 47.619 26.53 18.25 41.51 4.06
121 130 3.509967 TGCTCATCGTTAGAAACTGGAGA 59.490 43.478 0.00 0.00 0.00 3.71
146 155 3.382546 GTCTCCGGTGGTACTATTTAGCA 59.617 47.826 0.00 0.00 0.00 3.49
149 163 3.299503 GGGTCTCCGGTGGTACTATTTA 58.700 50.000 0.00 0.00 0.00 1.40
207 224 4.036498 CCATCCTGCTGCTTTTTCTCATAG 59.964 45.833 0.00 0.00 0.00 2.23
219 236 1.596477 GATCCGACCATCCTGCTGC 60.596 63.158 0.00 0.00 0.00 5.25
311 335 0.863144 CACCGTTTCACTACCCAACG 59.137 55.000 0.00 0.00 42.33 4.10
452 496 2.300152 TGTGTTTGCTAGCTACTCTGCT 59.700 45.455 17.23 0.00 46.11 4.24
454 498 4.172505 CTCTGTGTTTGCTAGCTACTCTG 58.827 47.826 17.23 16.44 0.00 3.35
474 518 2.104530 GCCTTCCGCTACCGACTC 59.895 66.667 0.00 0.00 36.29 3.36
564 618 5.250200 ACGGTTAAGTAAAGAATCATGGCA 58.750 37.500 0.00 0.00 0.00 4.92
565 619 5.585047 AGACGGTTAAGTAAAGAATCATGGC 59.415 40.000 0.00 0.00 0.00 4.40
567 621 6.750501 TCGAGACGGTTAAGTAAAGAATCATG 59.249 38.462 0.00 0.00 0.00 3.07
568 622 6.860080 TCGAGACGGTTAAGTAAAGAATCAT 58.140 36.000 0.00 0.00 0.00 2.45
632 686 3.120616 TCGTAGCTCGTGAAAAATGAACG 59.879 43.478 0.00 0.00 40.80 3.95
749 804 1.420430 ACTCCGGTGGACTTTGAGAA 58.580 50.000 8.63 0.00 0.00 2.87
810 893 7.986704 TGATTATACTAGCTAGGAGTACCAGT 58.013 38.462 24.35 5.49 38.94 4.00
811 894 8.898761 CATGATTATACTAGCTAGGAGTACCAG 58.101 40.741 24.35 0.00 38.94 4.00
812 895 7.834681 CCATGATTATACTAGCTAGGAGTACCA 59.165 40.741 24.35 13.23 38.94 3.25
813 896 7.201839 GCCATGATTATACTAGCTAGGAGTACC 60.202 44.444 24.35 8.24 32.34 3.34
814 897 7.201839 GGCCATGATTATACTAGCTAGGAGTAC 60.202 44.444 24.35 9.87 32.34 2.73
815 898 6.834451 GGCCATGATTATACTAGCTAGGAGTA 59.166 42.308 24.35 11.30 34.01 2.59
819 902 4.202161 CCGGCCATGATTATACTAGCTAGG 60.202 50.000 24.35 7.13 0.00 3.02
820 903 4.737946 GCCGGCCATGATTATACTAGCTAG 60.738 50.000 18.11 19.44 0.00 3.42
924 2960 8.594550 GCTATCTAGGAGTAGCTAGCTAGATAT 58.405 40.741 24.78 13.50 43.36 1.63
939 2975 5.009110 TCGAATCAAGTGTGCTATCTAGGAG 59.991 44.000 0.00 0.00 0.00 3.69
940 2976 4.887655 TCGAATCAAGTGTGCTATCTAGGA 59.112 41.667 0.00 0.00 0.00 2.94
941 2977 5.188327 TCGAATCAAGTGTGCTATCTAGG 57.812 43.478 0.00 0.00 0.00 3.02
942 2978 5.567154 CGATCGAATCAAGTGTGCTATCTAG 59.433 44.000 10.26 0.00 0.00 2.43
943 2979 5.238650 TCGATCGAATCAAGTGTGCTATCTA 59.761 40.000 16.99 0.00 0.00 1.98
945 2981 4.290969 TCGATCGAATCAAGTGTGCTATC 58.709 43.478 16.99 0.00 0.00 2.08
946 2982 4.307443 TCGATCGAATCAAGTGTGCTAT 57.693 40.909 16.99 0.00 0.00 2.97
947 2983 3.775661 TCGATCGAATCAAGTGTGCTA 57.224 42.857 16.99 0.00 0.00 3.49
948 2984 2.654749 TCGATCGAATCAAGTGTGCT 57.345 45.000 16.99 0.00 0.00 4.40
949 2985 3.495894 GATCGATCGAATCAAGTGTGC 57.504 47.619 23.50 0.00 0.00 4.57
1017 3063 3.384014 GAGCGAGACCAGGACGACG 62.384 68.421 0.00 0.02 0.00 5.12
1287 3344 0.401395 TGACCTCAAACCCCCTGACT 60.401 55.000 0.00 0.00 0.00 3.41
1299 3356 1.319614 TGATGGCGTCGATGACCTCA 61.320 55.000 13.78 13.78 0.00 3.86
1411 3468 7.447374 AAGCACGCCTTTAATTATATGCATA 57.553 32.000 9.27 9.27 34.27 3.14
1422 3479 4.056050 GCTATAGCTAAGCACGCCTTTAA 58.944 43.478 17.75 0.00 39.83 1.52
1423 3480 3.650139 GCTATAGCTAAGCACGCCTTTA 58.350 45.455 17.75 0.00 39.83 1.85
1425 3482 2.156343 GCTATAGCTAAGCACGCCTT 57.844 50.000 17.75 0.00 39.83 4.35
1461 3527 5.597806 TGTCACAGTAGTGTTAGACTTTGG 58.402 41.667 17.43 0.00 46.01 3.28
1547 3624 2.430921 CTGAAGCTCGCCGTCGTT 60.431 61.111 0.00 0.00 36.96 3.85
1592 3669 3.682885 TTTGCGAGCCCCGACGTA 61.683 61.111 0.00 0.00 41.76 3.57
1661 3738 4.641094 ACATGTGTAGTACTACCTGAGAGC 59.359 45.833 26.41 10.77 35.26 4.09
1740 3854 6.715264 TCTGAAAATCCCAGTAAAAAGAGGTC 59.285 38.462 0.00 0.00 33.57 3.85
1849 4073 7.542534 TGTTACGTGATCACTACTTTTGTTT 57.457 32.000 22.95 0.00 0.00 2.83
1872 4127 7.587037 TTGCTCCAGGAAAGGAAAATATATG 57.413 36.000 0.00 0.00 37.20 1.78
1922 4186 6.651225 AGCTACCTTGAGAAATTAACAGTGTC 59.349 38.462 0.00 0.00 0.00 3.67
1976 4278 0.727398 GTGGCTATCAGTTCCGTTGC 59.273 55.000 0.00 0.00 0.00 4.17
2022 4330 8.840200 ATCCTGAGAAAAGGTCTTATGTAGTA 57.160 34.615 0.00 0.00 36.41 1.82
2023 4331 7.741554 ATCCTGAGAAAAGGTCTTATGTAGT 57.258 36.000 0.00 0.00 36.41 2.73
2052 4360 7.441903 TTTAGGAACGGAGGGAGTATATTTT 57.558 36.000 0.00 0.00 0.00 1.82
2062 4376 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2063 4377 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2080 4394 9.810545 CACCATTTAAAACCTCTAAAAAGACAA 57.189 29.630 0.00 0.00 0.00 3.18
2081 4395 9.191479 TCACCATTTAAAACCTCTAAAAAGACA 57.809 29.630 0.00 0.00 0.00 3.41
2088 4402 9.362151 ACTCATTTCACCATTTAAAACCTCTAA 57.638 29.630 0.00 0.00 0.00 2.10
2089 4403 8.792633 CACTCATTTCACCATTTAAAACCTCTA 58.207 33.333 0.00 0.00 0.00 2.43
2090 4404 7.505585 TCACTCATTTCACCATTTAAAACCTCT 59.494 33.333 0.00 0.00 0.00 3.69
2091 4405 7.657336 TCACTCATTTCACCATTTAAAACCTC 58.343 34.615 0.00 0.00 0.00 3.85
2092 4406 7.595819 TCACTCATTTCACCATTTAAAACCT 57.404 32.000 0.00 0.00 0.00 3.50
2093 4407 8.831715 ATTCACTCATTTCACCATTTAAAACC 57.168 30.769 0.00 0.00 0.00 3.27
2094 4408 9.696917 AGATTCACTCATTTCACCATTTAAAAC 57.303 29.630 0.00 0.00 0.00 2.43
2097 4411 9.513906 TGTAGATTCACTCATTTCACCATTTAA 57.486 29.630 0.00 0.00 0.00 1.52
2098 4412 8.946085 GTGTAGATTCACTCATTTCACCATTTA 58.054 33.333 0.00 0.00 35.68 1.40
2099 4413 7.667219 AGTGTAGATTCACTCATTTCACCATTT 59.333 33.333 0.00 0.00 44.07 2.32
2100 4414 7.170965 AGTGTAGATTCACTCATTTCACCATT 58.829 34.615 0.00 0.00 44.07 3.16
2101 4415 6.715280 AGTGTAGATTCACTCATTTCACCAT 58.285 36.000 0.00 0.00 44.07 3.55
2102 4416 6.114187 AGTGTAGATTCACTCATTTCACCA 57.886 37.500 0.00 0.00 44.07 4.17
2103 4417 7.440523 AAAGTGTAGATTCACTCATTTCACC 57.559 36.000 0.00 0.00 46.25 4.02
2131 4445 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
2132 4446 8.899771 CACCACATACGGATGTATATAGACATA 58.100 37.037 14.23 0.00 44.82 2.29
2133 4447 7.614192 TCACCACATACGGATGTATATAGACAT 59.386 37.037 14.23 12.70 44.82 3.06
2134 4448 6.943718 TCACCACATACGGATGTATATAGACA 59.056 38.462 14.23 2.07 44.82 3.41
2135 4449 7.249147 GTCACCACATACGGATGTATATAGAC 58.751 42.308 14.23 12.97 44.82 2.59
2136 4450 6.376299 GGTCACCACATACGGATGTATATAGA 59.624 42.308 14.23 4.80 44.82 1.98
2137 4451 6.152154 TGGTCACCACATACGGATGTATATAG 59.848 42.308 14.23 0.00 44.82 1.31
2138 4452 6.011481 TGGTCACCACATACGGATGTATATA 58.989 40.000 14.23 0.00 44.82 0.86
2139 4453 4.836175 TGGTCACCACATACGGATGTATAT 59.164 41.667 14.23 0.00 44.82 0.86
2140 4454 4.216708 TGGTCACCACATACGGATGTATA 58.783 43.478 14.23 0.00 44.82 1.47
2141 4455 3.035363 TGGTCACCACATACGGATGTAT 58.965 45.455 14.23 1.38 44.82 2.29
2142 4456 2.458620 TGGTCACCACATACGGATGTA 58.541 47.619 14.23 0.00 44.82 2.29
2144 4458 2.620251 ATGGTCACCACATACGGATG 57.380 50.000 5.94 5.94 35.80 3.51
2145 4459 3.644966 AAATGGTCACCACATACGGAT 57.355 42.857 0.00 0.00 35.80 4.18
2146 4460 4.554960 TTAAATGGTCACCACATACGGA 57.445 40.909 0.00 0.00 35.80 4.69
2147 4461 5.630661 TTTTAAATGGTCACCACATACGG 57.369 39.130 0.00 0.00 35.80 4.02
2148 4462 7.065803 AGAGATTTTAAATGGTCACCACATACG 59.934 37.037 0.00 0.00 35.80 3.06
2149 4463 8.281212 AGAGATTTTAAATGGTCACCACATAC 57.719 34.615 0.00 0.00 35.80 2.39
2150 4464 9.613428 CTAGAGATTTTAAATGGTCACCACATA 57.387 33.333 0.00 0.00 35.80 2.29
2151 4465 8.328758 TCTAGAGATTTTAAATGGTCACCACAT 58.671 33.333 0.00 0.00 35.80 3.21
2152 4466 7.685481 TCTAGAGATTTTAAATGGTCACCACA 58.315 34.615 0.00 0.00 35.80 4.17
2153 4467 8.561738 TTCTAGAGATTTTAAATGGTCACCAC 57.438 34.615 0.00 0.00 35.80 4.16
2154 4468 9.231297 CTTTCTAGAGATTTTAAATGGTCACCA 57.769 33.333 0.00 0.00 38.19 4.17
2155 4469 9.449719 TCTTTCTAGAGATTTTAAATGGTCACC 57.550 33.333 0.00 0.00 0.00 4.02
2175 4489 9.025041 CCCCTGTTTCTAAATATTTGTCTTTCT 57.975 33.333 11.05 0.00 0.00 2.52
2176 4490 8.251026 CCCCCTGTTTCTAAATATTTGTCTTTC 58.749 37.037 11.05 0.00 0.00 2.62
2177 4491 7.953493 TCCCCCTGTTTCTAAATATTTGTCTTT 59.047 33.333 11.05 0.00 0.00 2.52
2178 4492 7.475299 TCCCCCTGTTTCTAAATATTTGTCTT 58.525 34.615 11.05 0.00 0.00 3.01
2179 4493 7.039722 TCCCCCTGTTTCTAAATATTTGTCT 57.960 36.000 11.05 0.00 0.00 3.41
2180 4494 6.890268 ACTCCCCCTGTTTCTAAATATTTGTC 59.110 38.462 11.05 0.00 0.00 3.18
2181 4495 6.800890 ACTCCCCCTGTTTCTAAATATTTGT 58.199 36.000 11.05 0.00 0.00 2.83
2182 4496 8.817092 TTACTCCCCCTGTTTCTAAATATTTG 57.183 34.615 11.05 1.65 0.00 2.32
2186 4500 9.910267 GTTAATTACTCCCCCTGTTTCTAAATA 57.090 33.333 0.00 0.00 0.00 1.40
2187 4501 8.395605 TGTTAATTACTCCCCCTGTTTCTAAAT 58.604 33.333 0.00 0.00 0.00 1.40
2188 4502 7.757611 TGTTAATTACTCCCCCTGTTTCTAAA 58.242 34.615 0.00 0.00 0.00 1.85
2189 4503 7.332433 TGTTAATTACTCCCCCTGTTTCTAA 57.668 36.000 0.00 0.00 0.00 2.10
2190 4504 6.956102 TGTTAATTACTCCCCCTGTTTCTA 57.044 37.500 0.00 0.00 0.00 2.10
2191 4505 5.853572 TGTTAATTACTCCCCCTGTTTCT 57.146 39.130 0.00 0.00 0.00 2.52
2192 4506 6.904463 TTTGTTAATTACTCCCCCTGTTTC 57.096 37.500 0.00 0.00 0.00 2.78
2193 4507 6.269077 CCTTTTGTTAATTACTCCCCCTGTTT 59.731 38.462 0.00 0.00 0.00 2.83
2194 4508 5.778241 CCTTTTGTTAATTACTCCCCCTGTT 59.222 40.000 0.00 0.00 0.00 3.16
2195 4509 5.162914 ACCTTTTGTTAATTACTCCCCCTGT 60.163 40.000 0.00 0.00 0.00 4.00
2196 4510 5.185056 CACCTTTTGTTAATTACTCCCCCTG 59.815 44.000 0.00 0.00 0.00 4.45
2197 4511 5.075344 TCACCTTTTGTTAATTACTCCCCCT 59.925 40.000 0.00 0.00 0.00 4.79
2198 4512 5.326900 TCACCTTTTGTTAATTACTCCCCC 58.673 41.667 0.00 0.00 0.00 5.40
2199 4513 7.476540 AATCACCTTTTGTTAATTACTCCCC 57.523 36.000 0.00 0.00 0.00 4.81
2200 4514 8.683615 CCTAATCACCTTTTGTTAATTACTCCC 58.316 37.037 0.00 0.00 0.00 4.30
2201 4515 9.457436 TCCTAATCACCTTTTGTTAATTACTCC 57.543 33.333 0.00 0.00 0.00 3.85
2206 4520 9.981114 CAACTTCCTAATCACCTTTTGTTAATT 57.019 29.630 0.00 0.00 0.00 1.40
2207 4521 8.585018 CCAACTTCCTAATCACCTTTTGTTAAT 58.415 33.333 0.00 0.00 0.00 1.40
2208 4522 7.470841 GCCAACTTCCTAATCACCTTTTGTTAA 60.471 37.037 0.00 0.00 0.00 2.01
2209 4523 6.015772 GCCAACTTCCTAATCACCTTTTGTTA 60.016 38.462 0.00 0.00 0.00 2.41
2210 4524 5.221441 GCCAACTTCCTAATCACCTTTTGTT 60.221 40.000 0.00 0.00 0.00 2.83
2211 4525 4.280929 GCCAACTTCCTAATCACCTTTTGT 59.719 41.667 0.00 0.00 0.00 2.83
2212 4526 4.280677 TGCCAACTTCCTAATCACCTTTTG 59.719 41.667 0.00 0.00 0.00 2.44
2213 4527 4.479158 TGCCAACTTCCTAATCACCTTTT 58.521 39.130 0.00 0.00 0.00 2.27
2214 4528 4.112634 TGCCAACTTCCTAATCACCTTT 57.887 40.909 0.00 0.00 0.00 3.11
2215 4529 3.806949 TGCCAACTTCCTAATCACCTT 57.193 42.857 0.00 0.00 0.00 3.50
2216 4530 3.074538 AGTTGCCAACTTCCTAATCACCT 59.925 43.478 3.74 0.00 39.04 4.00
2217 4531 3.421844 AGTTGCCAACTTCCTAATCACC 58.578 45.455 3.74 0.00 39.04 4.02
2218 4532 6.759497 ATTAGTTGCCAACTTCCTAATCAC 57.241 37.500 16.40 0.00 42.81 3.06
2219 4533 7.338449 GGTAATTAGTTGCCAACTTCCTAATCA 59.662 37.037 16.40 0.00 42.81 2.57
2220 4534 7.338449 TGGTAATTAGTTGCCAACTTCCTAATC 59.662 37.037 16.40 0.00 45.50 1.75
2234 4552 6.828785 AGGCTCAGGTTAATGGTAATTAGTTG 59.171 38.462 0.00 0.00 30.00 3.16
2249 4570 3.160269 CAAATTTCCAGAGGCTCAGGTT 58.840 45.455 23.39 9.75 0.00 3.50
2256 4577 2.165998 ACAGAGCAAATTTCCAGAGGC 58.834 47.619 0.00 0.00 0.00 4.70
2300 4650 4.545610 TCACGGAACAGATCAATTTTTGC 58.454 39.130 0.00 0.00 0.00 3.68
2327 4678 6.613755 AATTGGCGCTTCTACGTATTTTAT 57.386 33.333 7.64 0.00 34.88 1.40
2353 5241 7.437748 TCGGTAACAATCATTCACCAATTTTT 58.562 30.769 0.00 0.00 0.00 1.94
2357 5245 5.067674 CCATCGGTAACAATCATTCACCAAT 59.932 40.000 0.00 0.00 0.00 3.16
2697 5674 2.187946 GGCTGCCGATGTACTGCT 59.812 61.111 1.35 0.00 0.00 4.24
3008 5986 1.145325 CCATAGAGACGGGGTAGACCT 59.855 57.143 0.00 0.00 40.03 3.85
3027 6005 7.142680 TCAGTTTTCACAAATAATTTCCGACC 58.857 34.615 0.00 0.00 0.00 4.79
3031 6009 9.650371 GCTTTTCAGTTTTCACAAATAATTTCC 57.350 29.630 0.00 0.00 0.00 3.13
3041 6019 4.202010 GCTGTAGGCTTTTCAGTTTTCACA 60.202 41.667 0.00 0.00 38.06 3.58
3078 6056 5.997385 TCTTCAGTTGCGAAAAATAAGGTC 58.003 37.500 0.00 0.00 0.00 3.85
3133 6117 8.349983 ACAATGATAAAGTAGTTGTTGTTCCAC 58.650 33.333 0.00 0.00 29.38 4.02
3140 6124 7.228507 TCTGCACACAATGATAAAGTAGTTGTT 59.771 33.333 0.00 0.00 31.19 2.83
3159 6143 8.212995 TCCATTTATTCTATGATCTTCTGCACA 58.787 33.333 0.00 0.00 0.00 4.57
3188 6172 2.569404 AGTTACTCTTTGCTGCTAGCCT 59.431 45.455 13.29 0.00 41.51 4.58
3189 6173 2.675348 CAGTTACTCTTTGCTGCTAGCC 59.325 50.000 13.29 0.00 41.51 3.93
3190 6174 3.589988 TCAGTTACTCTTTGCTGCTAGC 58.410 45.455 8.10 8.10 42.82 3.42
3191 6175 5.659463 AGATCAGTTACTCTTTGCTGCTAG 58.341 41.667 0.00 0.00 0.00 3.42
3192 6176 5.667539 AGATCAGTTACTCTTTGCTGCTA 57.332 39.130 0.00 0.00 0.00 3.49
3198 6182 6.700960 CAGCATCCTAGATCAGTTACTCTTTG 59.299 42.308 0.00 0.00 0.00 2.77
3199 6183 6.685116 GCAGCATCCTAGATCAGTTACTCTTT 60.685 42.308 0.00 0.00 0.00 2.52
3200 6184 5.221422 GCAGCATCCTAGATCAGTTACTCTT 60.221 44.000 0.00 0.00 0.00 2.85
3201 6185 4.280677 GCAGCATCCTAGATCAGTTACTCT 59.719 45.833 0.00 0.00 0.00 3.24
3202 6186 4.555262 GCAGCATCCTAGATCAGTTACTC 58.445 47.826 0.00 0.00 0.00 2.59
3203 6187 3.005261 CGCAGCATCCTAGATCAGTTACT 59.995 47.826 0.00 0.00 0.00 2.24
3204 6188 3.243569 ACGCAGCATCCTAGATCAGTTAC 60.244 47.826 0.00 0.00 0.00 2.50
3205 6189 2.959030 ACGCAGCATCCTAGATCAGTTA 59.041 45.455 0.00 0.00 0.00 2.24
3206 6190 1.759445 ACGCAGCATCCTAGATCAGTT 59.241 47.619 0.00 0.00 0.00 3.16
3207 6191 1.407936 ACGCAGCATCCTAGATCAGT 58.592 50.000 0.00 0.00 0.00 3.41
3208 6192 3.192212 TGATACGCAGCATCCTAGATCAG 59.808 47.826 0.00 0.00 0.00 2.90
3209 6193 3.157087 TGATACGCAGCATCCTAGATCA 58.843 45.455 0.00 0.00 0.00 2.92
3210 6194 3.857549 TGATACGCAGCATCCTAGATC 57.142 47.619 0.00 0.00 0.00 2.75
3225 6209 1.873591 CTGGCGGCCAAACTATGATAC 59.126 52.381 23.94 0.00 30.80 2.24
3244 6228 3.097614 ACGCCTAAGAATAGTGTGTCCT 58.902 45.455 0.00 0.00 0.00 3.85
3301 6292 5.059833 AGCCAATTTGGTTATTTTCGCAAA 58.940 33.333 16.62 0.00 40.46 3.68
3352 6343 0.690192 TGGCCAATCTGGTTCTTCGA 59.310 50.000 0.61 0.00 40.46 3.71
3353 6344 1.755179 ATGGCCAATCTGGTTCTTCG 58.245 50.000 10.96 0.00 40.46 3.79
3383 6374 1.476085 TGCGGCAAGTCAATTATTGGG 59.524 47.619 0.00 0.00 0.00 4.12
3464 6455 2.760092 GGATATTTGTTCCAGCTGGCAA 59.240 45.455 28.91 23.05 33.21 4.52
3521 6541 5.948162 ACAGCTGAGATAATCCATGTTTTGT 59.052 36.000 23.35 0.00 0.00 2.83
3559 6579 1.384191 GAGGCTTGATGTTGGGGGT 59.616 57.895 0.00 0.00 0.00 4.95
3595 6616 6.845302 TCTGATGAGAATTACATTGCACAAC 58.155 36.000 0.00 0.00 0.00 3.32
3701 6722 2.629137 TGCAAATGACTGCCATTCTGTT 59.371 40.909 0.00 0.00 44.28 3.16
3711 6732 4.153986 GTCTTCGTTGATGCAAATGACTG 58.846 43.478 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.