Multiple sequence alignment - TraesCS2A01G041200

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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 TraesCS2A01G041200 chr2A 100.000 4474 0 0 1 4474 16715477 16719950 0.000000e+00 8263.0
1 TraesCS2A01G041200 chr2A 92.972 1309 30 13 2173 3457 21193921 21195191 0.000000e+00 1851.0
2 TraesCS2A01G041200 chr2A 98.020 606 10 1 686 1291 21193324 21193927 0.000000e+00 1051.0
3 TraesCS2A01G041200 chr2A 94.903 569 7 7 2908 3457 20621681 20621116 0.000000e+00 870.0
4 TraesCS2A01G041200 chr2A 82.573 987 114 28 686 1630 780781781 780782751 0.000000e+00 817.0
5 TraesCS2A01G041200 chr2A 84.257 343 42 6 3908 4242 16729239 16729577 1.550000e-84 324.0
6 TraesCS2A01G041200 chr2A 76.565 687 75 38 2517 3193 688204945 688204335 9.410000e-77 298.0
7 TraesCS2A01G041200 chr2A 99.301 143 1 0 2772 2914 20622086 20621944 4.440000e-65 259.0
8 TraesCS2A01G041200 chr2A 88.158 152 16 1 3310 3459 17409324 17409475 3.560000e-41 180.0
9 TraesCS2A01G041200 chr2A 84.868 152 17 5 3310 3457 738370397 738370546 1.000000e-31 148.0
10 TraesCS2A01G041200 chr2B 85.058 2590 231 77 684 3191 477578863 477576348 0.000000e+00 2495.0
11 TraesCS2A01G041200 chr2B 86.593 2163 216 37 688 2812 63805326 63807452 0.000000e+00 2320.0
12 TraesCS2A01G041200 chr2B 87.789 1990 154 40 788 2741 110755163 110757099 0.000000e+00 2246.0
13 TraesCS2A01G041200 chr2B 88.724 1818 121 40 1021 2812 461252580 461254339 0.000000e+00 2145.0
14 TraesCS2A01G041200 chr2B 84.493 2270 247 63 684 2903 794224893 794227107 0.000000e+00 2145.0
15 TraesCS2A01G041200 chr2B 81.184 2636 331 106 923 3454 625250583 625253157 0.000000e+00 1967.0
16 TraesCS2A01G041200 chr2B 86.515 1053 79 31 3455 4466 26309480 26310510 0.000000e+00 1099.0
17 TraesCS2A01G041200 chr2B 92.697 178 13 0 3908 4085 26322070 26322247 1.600000e-64 257.0
18 TraesCS2A01G041200 chr2B 74.144 584 90 40 2899 3460 788662855 788662311 7.640000e-43 185.0
19 TraesCS2A01G041200 chr2B 82.581 155 19 7 3310 3459 166857301 166857452 3.630000e-26 130.0
20 TraesCS2A01G041200 chr2B 72.517 604 89 50 2899 3461 794227073 794227640 1.690000e-24 124.0
21 TraesCS2A01G041200 chr2B 89.888 89 7 2 4154 4241 26322344 26322431 3.660000e-21 113.0
22 TraesCS2A01G041200 chr1B 85.215 2489 255 55 684 3115 540153789 540151357 0.000000e+00 2453.0
23 TraesCS2A01G041200 chr1B 85.780 2173 223 43 688 2811 1744644 1742509 0.000000e+00 2222.0
24 TraesCS2A01G041200 chr1B 85.271 2193 231 55 688 2849 217559954 217557823 0.000000e+00 2176.0
25 TraesCS2A01G041200 chr1B 81.961 2550 293 91 1016 3457 672154495 672156985 0.000000e+00 2006.0
26 TraesCS2A01G041200 chr1B 83.607 122 14 4 2899 3020 673998291 673998406 4.730000e-20 110.0
27 TraesCS2A01G041200 chr6B 88.053 2101 173 41 688 2741 474182890 474180821 0.000000e+00 2418.0
28 TraesCS2A01G041200 chr6B 88.021 2087 182 35 686 2741 646705069 646703020 0.000000e+00 2407.0
29 TraesCS2A01G041200 chr6B 84.480 2442 232 81 1073 3454 56064882 56062528 0.000000e+00 2274.0
30 TraesCS2A01G041200 chr6B 86.178 2156 213 52 688 2812 544639936 544642037 0.000000e+00 2252.0
31 TraesCS2A01G041200 chr6B 90.187 1549 98 24 1214 2741 47872197 47870682 0.000000e+00 1969.0
32 TraesCS2A01G041200 chr6B 81.871 342 36 8 2689 3020 551981664 551981339 9.540000e-67 265.0
33 TraesCS2A01G041200 chr6B 85.526 152 18 3 3310 3458 31585314 31585464 5.990000e-34 156.0
34 TraesCS2A01G041200 chr6B 84.354 147 17 6 3316 3458 140095093 140094949 6.030000e-29 139.0
35 TraesCS2A01G041200 chr6B 94.595 74 4 0 4012 4085 463559459 463559532 1.020000e-21 115.0
36 TraesCS2A01G041200 chr6B 78.022 91 16 4 571 659 438957012 438957100 2.000000e-03 54.7
37 TraesCS2A01G041200 chr5B 82.363 2852 305 103 688 3457 9057519 9054784 0.000000e+00 2298.0
38 TraesCS2A01G041200 chr5B 86.745 2052 207 32 686 2695 549630528 549632556 0.000000e+00 2222.0
39 TraesCS2A01G041200 chr5B 91.298 1356 71 13 1405 2741 659750969 659749642 0.000000e+00 1807.0
40 TraesCS2A01G041200 chr7A 85.945 2170 226 37 681 2812 515741559 515739431 0.000000e+00 2244.0
41 TraesCS2A01G041200 chr7A 90.909 55 3 2 3140 3193 430274586 430274533 6.210000e-09 73.1
42 TraesCS2A01G041200 chr7A 90.000 50 5 0 536 585 108860853 108860902 1.040000e-06 65.8
43 TraesCS2A01G041200 chr7B 88.167 1817 143 31 1030 2812 24069134 24070912 0.000000e+00 2098.0
44 TraesCS2A01G041200 chr7B 84.354 147 17 4 3316 3459 686000009 685999866 6.030000e-29 139.0
45 TraesCS2A01G041200 chr4B 90.704 1592 105 18 1191 2741 562345952 562344363 0.000000e+00 2080.0
46 TraesCS2A01G041200 chr4B 86.578 1572 157 28 688 2223 39732514 39734067 0.000000e+00 1685.0
47 TraesCS2A01G041200 chr4B 91.892 74 6 0 4012 4085 434190721 434190648 2.200000e-18 104.0
48 TraesCS2A01G041200 chr4B 78.400 125 25 2 536 659 574424712 574424835 3.710000e-11 80.5
49 TraesCS2A01G041200 chr4A 88.040 1781 149 22 1094 2812 701267194 701265416 0.000000e+00 2050.0
50 TraesCS2A01G041200 chr4A 83.794 2135 239 50 1140 3193 690138720 690140828 0.000000e+00 1927.0
51 TraesCS2A01G041200 chr4A 84.990 1912 184 44 1275 3115 659244904 659246783 0.000000e+00 1845.0
52 TraesCS2A01G041200 chr4A 83.740 123 12 6 2899 3020 631941475 631941590 4.730000e-20 110.0
53 TraesCS2A01G041200 chr4A 91.892 74 6 0 4012 4085 604668255 604668182 2.200000e-18 104.0
54 TraesCS2A01G041200 chr3B 82.497 2251 255 78 1300 3456 671138395 671136190 0.000000e+00 1845.0
55 TraesCS2A01G041200 chr3B 74.314 911 128 65 2601 3454 159572675 159571814 5.660000e-74 289.0
56 TraesCS2A01G041200 chr3B 75.000 692 94 48 2792 3459 596851347 596851983 3.460000e-61 246.0
57 TraesCS2A01G041200 chr3B 81.349 252 35 11 2601 2849 771352056 771351814 1.270000e-45 195.0
58 TraesCS2A01G041200 chr3B 96.875 32 1 0 553 584 800208060 800208029 2.000000e-03 54.7
59 TraesCS2A01G041200 chr2D 93.702 1032 41 12 3454 4471 14411959 14412980 0.000000e+00 1524.0
60 TraesCS2A01G041200 chr2D 92.526 388 24 4 2 386 14411442 14411827 6.540000e-153 551.0
61 TraesCS2A01G041200 chr2D 84.012 344 41 8 3908 4242 14422784 14423122 7.220000e-83 318.0
62 TraesCS2A01G041200 chr2D 82.799 343 44 9 3908 4241 14628375 14628711 4.380000e-75 292.0
63 TraesCS2A01G041200 chr2D 74.615 780 110 52 2719 3453 30081178 30080442 3.430000e-66 263.0
64 TraesCS2A01G041200 chr2D 91.429 140 8 2 551 690 14411828 14411963 5.910000e-44 189.0
65 TraesCS2A01G041200 chr7D 73.856 765 118 51 2722 3449 621229214 621228495 3.480000e-56 230.0
66 TraesCS2A01G041200 chr7D 76.087 230 41 8 4012 4228 55192906 55193134 1.700000e-19 108.0
67 TraesCS2A01G041200 chr5D 78.421 380 51 18 2723 3092 332784102 332784460 7.540000e-53 219.0
68 TraesCS2A01G041200 chr4D 91.892 74 6 0 4012 4085 165072476 165072549 2.200000e-18 104.0
69 TraesCS2A01G041200 chr3A 91.892 74 6 0 4012 4085 12991545 12991472 2.200000e-18 104.0
70 TraesCS2A01G041200 chr6A 90.541 74 7 0 4012 4085 529569790 529569863 1.020000e-16 99.0
71 TraesCS2A01G041200 chr1A 90.541 74 7 0 4012 4085 296331612 296331539 1.020000e-16 99.0


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 TraesCS2A01G041200 chr2A 16715477 16719950 4473 False 8263.000000 8263 100.000000 1 4474 1 chr2A.!!$F1 4473
1 TraesCS2A01G041200 chr2A 21193324 21195191 1867 False 1451.000000 1851 95.496000 686 3457 2 chr2A.!!$F6 2771
2 TraesCS2A01G041200 chr2A 780781781 780782751 970 False 817.000000 817 82.573000 686 1630 1 chr2A.!!$F5 944
3 TraesCS2A01G041200 chr2A 20621116 20622086 970 True 564.500000 870 97.102000 2772 3457 2 chr2A.!!$R2 685
4 TraesCS2A01G041200 chr2A 688204335 688204945 610 True 298.000000 298 76.565000 2517 3193 1 chr2A.!!$R1 676
5 TraesCS2A01G041200 chr2B 477576348 477578863 2515 True 2495.000000 2495 85.058000 684 3191 1 chr2B.!!$R1 2507
6 TraesCS2A01G041200 chr2B 63805326 63807452 2126 False 2320.000000 2320 86.593000 688 2812 1 chr2B.!!$F2 2124
7 TraesCS2A01G041200 chr2B 110755163 110757099 1936 False 2246.000000 2246 87.789000 788 2741 1 chr2B.!!$F3 1953
8 TraesCS2A01G041200 chr2B 461252580 461254339 1759 False 2145.000000 2145 88.724000 1021 2812 1 chr2B.!!$F5 1791
9 TraesCS2A01G041200 chr2B 625250583 625253157 2574 False 1967.000000 1967 81.184000 923 3454 1 chr2B.!!$F6 2531
10 TraesCS2A01G041200 chr2B 794224893 794227640 2747 False 1134.500000 2145 78.505000 684 3461 2 chr2B.!!$F8 2777
11 TraesCS2A01G041200 chr2B 26309480 26310510 1030 False 1099.000000 1099 86.515000 3455 4466 1 chr2B.!!$F1 1011
12 TraesCS2A01G041200 chr1B 540151357 540153789 2432 True 2453.000000 2453 85.215000 684 3115 1 chr1B.!!$R3 2431
13 TraesCS2A01G041200 chr1B 1742509 1744644 2135 True 2222.000000 2222 85.780000 688 2811 1 chr1B.!!$R1 2123
14 TraesCS2A01G041200 chr1B 217557823 217559954 2131 True 2176.000000 2176 85.271000 688 2849 1 chr1B.!!$R2 2161
15 TraesCS2A01G041200 chr1B 672154495 672156985 2490 False 2006.000000 2006 81.961000 1016 3457 1 chr1B.!!$F1 2441
16 TraesCS2A01G041200 chr6B 474180821 474182890 2069 True 2418.000000 2418 88.053000 688 2741 1 chr6B.!!$R4 2053
17 TraesCS2A01G041200 chr6B 646703020 646705069 2049 True 2407.000000 2407 88.021000 686 2741 1 chr6B.!!$R6 2055
18 TraesCS2A01G041200 chr6B 56062528 56064882 2354 True 2274.000000 2274 84.480000 1073 3454 1 chr6B.!!$R2 2381
19 TraesCS2A01G041200 chr6B 544639936 544642037 2101 False 2252.000000 2252 86.178000 688 2812 1 chr6B.!!$F4 2124
20 TraesCS2A01G041200 chr6B 47870682 47872197 1515 True 1969.000000 1969 90.187000 1214 2741 1 chr6B.!!$R1 1527
21 TraesCS2A01G041200 chr5B 9054784 9057519 2735 True 2298.000000 2298 82.363000 688 3457 1 chr5B.!!$R1 2769
22 TraesCS2A01G041200 chr5B 549630528 549632556 2028 False 2222.000000 2222 86.745000 686 2695 1 chr5B.!!$F1 2009
23 TraesCS2A01G041200 chr5B 659749642 659750969 1327 True 1807.000000 1807 91.298000 1405 2741 1 chr5B.!!$R2 1336
24 TraesCS2A01G041200 chr7A 515739431 515741559 2128 True 2244.000000 2244 85.945000 681 2812 1 chr7A.!!$R2 2131
25 TraesCS2A01G041200 chr7B 24069134 24070912 1778 False 2098.000000 2098 88.167000 1030 2812 1 chr7B.!!$F1 1782
26 TraesCS2A01G041200 chr4B 562344363 562345952 1589 True 2080.000000 2080 90.704000 1191 2741 1 chr4B.!!$R2 1550
27 TraesCS2A01G041200 chr4B 39732514 39734067 1553 False 1685.000000 1685 86.578000 688 2223 1 chr4B.!!$F1 1535
28 TraesCS2A01G041200 chr4A 701265416 701267194 1778 True 2050.000000 2050 88.040000 1094 2812 1 chr4A.!!$R2 1718
29 TraesCS2A01G041200 chr4A 690138720 690140828 2108 False 1927.000000 1927 83.794000 1140 3193 1 chr4A.!!$F3 2053
30 TraesCS2A01G041200 chr4A 659244904 659246783 1879 False 1845.000000 1845 84.990000 1275 3115 1 chr4A.!!$F2 1840
31 TraesCS2A01G041200 chr3B 671136190 671138395 2205 True 1845.000000 1845 82.497000 1300 3456 1 chr3B.!!$R2 2156
32 TraesCS2A01G041200 chr3B 159571814 159572675 861 True 289.000000 289 74.314000 2601 3454 1 chr3B.!!$R1 853
33 TraesCS2A01G041200 chr3B 596851347 596851983 636 False 246.000000 246 75.000000 2792 3459 1 chr3B.!!$F1 667
34 TraesCS2A01G041200 chr2D 14411442 14412980 1538 False 754.666667 1524 92.552333 2 4471 3 chr2D.!!$F3 4469
35 TraesCS2A01G041200 chr2D 30080442 30081178 736 True 263.000000 263 74.615000 2719 3453 1 chr2D.!!$R1 734
36 TraesCS2A01G041200 chr7D 621228495 621229214 719 True 230.000000 230 73.856000 2722 3449 1 chr7D.!!$R1 727

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
537 540 0.031716 AGCCTAGCTCAGATGGTCCA 60.032 55.0 0.00 0.00 30.62 4.02 F
543 546 0.108207 GCTCAGATGGTCCATCAGGG 59.892 60.0 29.57 23.79 42.72 4.45 F
544 547 0.108207 CTCAGATGGTCCATCAGGGC 59.892 60.0 29.57 6.98 42.72 5.19 F
546 549 0.108207 CAGATGGTCCATCAGGGCTC 59.892 60.0 29.57 6.46 42.72 4.70 F
1617 1717 0.255890 AGAGCGGGCAATTACACCAT 59.744 50.0 0.00 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2289 0.318441 TCTTGCCGTCCTCACTTGAG 59.682 55.000 0.00 0.00 41.71 3.02 R
2450 2576 0.390860 CCTAGTTCGCTCCTCCATGG 59.609 60.000 4.97 4.97 37.10 3.66 R
2500 2626 5.437289 TCATTGAACAAAGATGTGTCCAC 57.563 39.130 0.00 0.00 40.46 4.02 R
2662 2857 1.529948 CAATGATGCCGAGGCCCAT 60.530 57.895 12.05 11.75 41.09 4.00 R
3728 4595 1.225403 TGGGGTTTTATGGGGGAGGG 61.225 60.000 0.00 0.00 0.00 4.30 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
38 39 1.651240 GGAGCGCACATTGTCATGCT 61.651 55.000 11.47 6.64 39.79 3.79
56 57 7.147742 TGTCATGCTCTATAGATGTTGGTGTTA 60.148 37.037 2.11 0.00 0.00 2.41
62 63 8.713271 GCTCTATAGATGTTGGTGTTAATTAGC 58.287 37.037 2.11 0.00 0.00 3.09
82 83 8.732746 ATTAGCGAATAACTTTGGTAGAACAT 57.267 30.769 0.00 0.00 31.92 2.71
89 90 2.916934 ACTTTGGTAGAACATAGGGCCA 59.083 45.455 6.18 0.00 0.00 5.36
110 111 4.451900 CAAACCATGGTGTATCTAGGGTC 58.548 47.826 20.60 0.00 40.64 4.46
113 114 3.052109 ACCATGGTGTATCTAGGGTCTGA 60.052 47.826 18.99 0.00 37.08 3.27
116 117 3.845860 TGGTGTATCTAGGGTCTGATCC 58.154 50.000 0.00 0.00 0.00 3.36
215 216 6.777213 AATTCTTTCTACTCTAAGGCGAGA 57.223 37.500 0.00 0.00 35.06 4.04
226 227 4.459089 GGCGAGACTGGAGTGGCC 62.459 72.222 0.00 0.00 37.10 5.36
227 228 4.459089 GCGAGACTGGAGTGGCCC 62.459 72.222 0.00 0.00 34.97 5.80
228 229 2.681778 CGAGACTGGAGTGGCCCT 60.682 66.667 0.00 0.00 34.97 5.19
231 232 0.033011 GAGACTGGAGTGGCCCTCTA 60.033 60.000 17.51 12.43 40.30 2.43
233 234 3.225235 CTGGAGTGGCCCTCTAGC 58.775 66.667 17.44 5.68 41.25 3.42
273 275 2.106857 ACCGAAACTCACCCAATGGTTA 59.893 45.455 0.00 0.00 44.75 2.85
275 277 3.558321 CCGAAACTCACCCAATGGTTAGA 60.558 47.826 0.00 0.00 44.75 2.10
290 292 3.591527 TGGTTAGATGGTGAGAATTGGGT 59.408 43.478 0.00 0.00 0.00 4.51
295 297 1.071314 TGGTGAGAATTGGGTGGGGT 61.071 55.000 0.00 0.00 0.00 4.95
304 306 3.344176 GGGTGGGGTAAGGGGGTG 61.344 72.222 0.00 0.00 0.00 4.61
321 324 0.389948 GTGTGAGCGGGGTTGTAGAG 60.390 60.000 0.00 0.00 0.00 2.43
323 326 0.606604 GTGAGCGGGGTTGTAGAGAA 59.393 55.000 0.00 0.00 0.00 2.87
332 335 4.434520 GGGGTTGTAGAGAAGAAAGATCG 58.565 47.826 0.00 0.00 0.00 3.69
382 385 2.128535 TGAGGGTGGACCAACAAAGTA 58.871 47.619 12.67 0.00 43.89 2.24
386 389 2.158726 GGGTGGACCAACAAAGTAGACA 60.159 50.000 12.67 0.00 39.85 3.41
387 390 3.497942 GGGTGGACCAACAAAGTAGACAT 60.498 47.826 12.67 0.00 39.85 3.06
388 391 4.142038 GGTGGACCAACAAAGTAGACATT 58.858 43.478 4.08 0.00 35.64 2.71
389 392 4.023193 GGTGGACCAACAAAGTAGACATTG 60.023 45.833 4.08 0.00 35.64 2.82
390 393 4.578928 GTGGACCAACAAAGTAGACATTGT 59.421 41.667 0.00 0.00 39.15 2.71
391 394 5.067283 GTGGACCAACAAAGTAGACATTGTT 59.933 40.000 9.56 9.56 45.15 2.83
397 400 6.639632 AACAAAGTAGACATTGTTGAGCAT 57.360 33.333 13.52 0.00 43.41 3.79
398 401 6.005583 ACAAAGTAGACATTGTTGAGCATG 57.994 37.500 0.00 0.00 34.57 4.06
399 402 5.048504 ACAAAGTAGACATTGTTGAGCATGG 60.049 40.000 0.00 0.00 34.57 3.66
400 403 3.012518 AGTAGACATTGTTGAGCATGGC 58.987 45.455 0.00 0.00 0.00 4.40
401 404 0.806868 AGACATTGTTGAGCATGGCG 59.193 50.000 0.00 0.00 0.00 5.69
402 405 0.804364 GACATTGTTGAGCATGGCGA 59.196 50.000 0.00 0.00 0.00 5.54
403 406 0.806868 ACATTGTTGAGCATGGCGAG 59.193 50.000 0.00 0.00 0.00 5.03
404 407 0.099968 CATTGTTGAGCATGGCGAGG 59.900 55.000 0.00 0.00 0.00 4.63
405 408 1.033746 ATTGTTGAGCATGGCGAGGG 61.034 55.000 0.00 0.00 0.00 4.30
406 409 2.123248 TTGTTGAGCATGGCGAGGGA 62.123 55.000 0.00 0.00 0.00 4.20
407 410 1.377202 GTTGAGCATGGCGAGGGAA 60.377 57.895 0.00 0.00 0.00 3.97
408 411 0.960364 GTTGAGCATGGCGAGGGAAA 60.960 55.000 0.00 0.00 0.00 3.13
409 412 0.960364 TTGAGCATGGCGAGGGAAAC 60.960 55.000 0.00 0.00 0.00 2.78
410 413 1.377202 GAGCATGGCGAGGGAAACA 60.377 57.895 0.00 0.00 0.00 2.83
411 414 1.648467 GAGCATGGCGAGGGAAACAC 61.648 60.000 0.00 0.00 0.00 3.32
412 415 3.039202 GCATGGCGAGGGAAACACG 62.039 63.158 0.00 0.00 35.40 4.49
413 416 1.375396 CATGGCGAGGGAAACACGA 60.375 57.895 0.00 0.00 34.50 4.35
414 417 1.375523 ATGGCGAGGGAAACACGAC 60.376 57.895 0.00 0.00 39.50 4.34
415 418 1.827399 ATGGCGAGGGAAACACGACT 61.827 55.000 0.00 0.00 39.71 4.18
416 419 1.737008 GGCGAGGGAAACACGACTC 60.737 63.158 0.00 0.00 36.88 3.36
417 420 1.289380 GCGAGGGAAACACGACTCT 59.711 57.895 0.00 0.00 34.50 3.24
418 421 0.524862 GCGAGGGAAACACGACTCTA 59.475 55.000 0.00 0.00 34.50 2.43
419 422 1.731750 GCGAGGGAAACACGACTCTAC 60.732 57.143 0.00 0.00 34.50 2.59
420 423 1.538512 CGAGGGAAACACGACTCTACA 59.461 52.381 0.00 0.00 34.50 2.74
421 424 2.163815 CGAGGGAAACACGACTCTACAT 59.836 50.000 0.00 0.00 34.50 2.29
422 425 3.731264 CGAGGGAAACACGACTCTACATC 60.731 52.174 0.00 0.00 34.50 3.06
423 426 3.162666 AGGGAAACACGACTCTACATCA 58.837 45.455 0.00 0.00 0.00 3.07
424 427 3.769844 AGGGAAACACGACTCTACATCAT 59.230 43.478 0.00 0.00 0.00 2.45
425 428 4.113354 GGGAAACACGACTCTACATCATC 58.887 47.826 0.00 0.00 0.00 2.92
426 429 3.791887 GGAAACACGACTCTACATCATCG 59.208 47.826 0.00 0.00 40.39 3.84
427 430 4.438336 GGAAACACGACTCTACATCATCGA 60.438 45.833 0.00 0.00 37.97 3.59
428 431 4.902443 AACACGACTCTACATCATCGAT 57.098 40.909 0.00 0.00 37.97 3.59
429 432 4.216366 ACACGACTCTACATCATCGATG 57.784 45.455 19.61 19.61 44.71 3.84
439 442 3.070429 CATCATCGATGTCACTCACGA 57.930 47.619 24.09 2.70 35.54 4.35
440 443 3.636381 CATCATCGATGTCACTCACGAT 58.364 45.455 24.09 5.05 39.16 3.73
441 444 3.340337 TCATCGATGTCACTCACGATC 57.660 47.619 24.09 0.00 37.80 3.69
442 445 2.039804 CATCGATGTCACTCACGATCG 58.960 52.381 17.50 14.88 37.80 3.69
443 446 1.365699 TCGATGTCACTCACGATCGA 58.634 50.000 24.34 0.00 40.06 3.59
444 447 1.940613 TCGATGTCACTCACGATCGAT 59.059 47.619 24.34 0.00 38.75 3.59
445 448 2.039804 CGATGTCACTCACGATCGATG 58.960 52.381 24.34 15.96 37.82 3.84
446 449 2.389059 GATGTCACTCACGATCGATGG 58.611 52.381 24.34 3.61 0.00 3.51
447 450 0.179137 TGTCACTCACGATCGATGGC 60.179 55.000 24.34 15.41 0.00 4.40
448 451 0.179137 GTCACTCACGATCGATGGCA 60.179 55.000 24.34 0.00 0.00 4.92
449 452 0.530288 TCACTCACGATCGATGGCAA 59.470 50.000 24.34 0.00 0.00 4.52
450 453 0.926155 CACTCACGATCGATGGCAAG 59.074 55.000 24.34 11.64 0.00 4.01
451 454 0.532573 ACTCACGATCGATGGCAAGT 59.467 50.000 24.34 12.22 0.00 3.16
452 455 1.203928 CTCACGATCGATGGCAAGTC 58.796 55.000 24.34 0.00 0.00 3.01
453 456 0.525455 TCACGATCGATGGCAAGTCG 60.525 55.000 24.34 0.87 40.30 4.18
454 457 1.878522 ACGATCGATGGCAAGTCGC 60.879 57.895 24.34 0.00 38.88 5.19
471 474 4.308458 CCTGGCGACGGTGACCAA 62.308 66.667 1.11 0.00 31.81 3.67
472 475 2.280524 CTGGCGACGGTGACCAAA 60.281 61.111 1.11 0.00 31.81 3.28
473 476 1.671054 CTGGCGACGGTGACCAAAT 60.671 57.895 1.11 0.00 31.81 2.32
474 477 1.635663 CTGGCGACGGTGACCAAATC 61.636 60.000 1.11 0.00 31.81 2.17
475 478 1.375523 GGCGACGGTGACCAAATCT 60.376 57.895 1.11 0.00 0.00 2.40
476 479 1.359459 GGCGACGGTGACCAAATCTC 61.359 60.000 1.11 0.00 0.00 2.75
477 480 0.669318 GCGACGGTGACCAAATCTCA 60.669 55.000 1.11 0.00 0.00 3.27
478 481 1.068474 CGACGGTGACCAAATCTCAC 58.932 55.000 1.11 0.00 37.84 3.51
482 485 3.266240 GTGACCAAATCTCACCCCC 57.734 57.895 0.00 0.00 33.23 5.40
483 486 0.404040 GTGACCAAATCTCACCCCCA 59.596 55.000 0.00 0.00 33.23 4.96
484 487 0.404040 TGACCAAATCTCACCCCCAC 59.596 55.000 0.00 0.00 0.00 4.61
485 488 0.323451 GACCAAATCTCACCCCCACC 60.323 60.000 0.00 0.00 0.00 4.61
486 489 1.378514 CCAAATCTCACCCCCACCG 60.379 63.158 0.00 0.00 0.00 4.94
487 490 2.046285 CAAATCTCACCCCCACCGC 61.046 63.158 0.00 0.00 0.00 5.68
488 491 3.622060 AAATCTCACCCCCACCGCG 62.622 63.158 0.00 0.00 0.00 6.46
498 501 3.728636 CCACCGCGCCGCTAAAAA 61.729 61.111 7.78 0.00 0.00 1.94
518 521 5.365403 AAAAATCCGTAATTGCGAACAGA 57.635 34.783 17.96 6.30 0.00 3.41
519 522 4.600012 AAATCCGTAATTGCGAACAGAG 57.400 40.909 17.96 0.00 0.00 3.35
520 523 1.355971 TCCGTAATTGCGAACAGAGC 58.644 50.000 17.96 0.00 0.00 4.09
521 524 0.373716 CCGTAATTGCGAACAGAGCC 59.626 55.000 17.96 0.00 0.00 4.70
522 525 1.359848 CGTAATTGCGAACAGAGCCT 58.640 50.000 10.69 0.00 0.00 4.58
523 526 2.536365 CGTAATTGCGAACAGAGCCTA 58.464 47.619 10.69 0.00 0.00 3.93
524 527 2.535984 CGTAATTGCGAACAGAGCCTAG 59.464 50.000 10.69 0.00 0.00 3.02
525 528 1.373570 AATTGCGAACAGAGCCTAGC 58.626 50.000 0.00 0.00 0.00 3.42
526 529 0.539051 ATTGCGAACAGAGCCTAGCT 59.461 50.000 0.00 0.00 43.88 3.32
536 539 2.833244 AGCCTAGCTCAGATGGTCC 58.167 57.895 0.00 0.00 30.62 4.46
537 540 0.031716 AGCCTAGCTCAGATGGTCCA 60.032 55.000 0.00 0.00 30.62 4.02
538 541 1.055040 GCCTAGCTCAGATGGTCCAT 58.945 55.000 3.26 3.26 0.00 3.41
539 542 1.001860 GCCTAGCTCAGATGGTCCATC 59.998 57.143 22.47 22.47 40.80 3.51
540 543 2.323599 CCTAGCTCAGATGGTCCATCA 58.676 52.381 29.57 12.33 42.72 3.07
541 544 2.299582 CCTAGCTCAGATGGTCCATCAG 59.700 54.545 29.57 23.10 42.72 2.90
542 545 1.129917 AGCTCAGATGGTCCATCAGG 58.870 55.000 29.57 21.57 42.72 3.86
543 546 0.108207 GCTCAGATGGTCCATCAGGG 59.892 60.000 29.57 23.79 42.72 4.45
544 547 0.108207 CTCAGATGGTCCATCAGGGC 59.892 60.000 29.57 6.98 42.72 5.19
545 548 0.326904 TCAGATGGTCCATCAGGGCT 60.327 55.000 29.57 9.41 42.72 5.19
546 549 0.108207 CAGATGGTCCATCAGGGCTC 59.892 60.000 29.57 6.46 42.72 4.70
547 550 0.326904 AGATGGTCCATCAGGGCTCA 60.327 55.000 29.57 0.00 42.72 4.26
548 551 0.548031 GATGGTCCATCAGGGCTCAA 59.452 55.000 24.55 0.00 40.28 3.02
549 552 0.549950 ATGGTCCATCAGGGCTCAAG 59.450 55.000 0.00 0.00 40.27 3.02
587 590 1.308069 TGCTCGCATTTTCCTGGCTC 61.308 55.000 0.00 0.00 0.00 4.70
594 597 2.498885 GCATTTTCCTGGCTCCATTTCT 59.501 45.455 0.00 0.00 0.00 2.52
595 598 3.677976 GCATTTTCCTGGCTCCATTTCTG 60.678 47.826 0.00 0.00 0.00 3.02
602 605 0.323725 GGCTCCATTTCTGGCTTCCA 60.324 55.000 0.00 0.00 42.80 3.53
604 607 2.105766 GCTCCATTTCTGGCTTCCATT 58.894 47.619 0.00 0.00 42.80 3.16
615 618 2.964464 TGGCTTCCATTGATGTTTGTGT 59.036 40.909 0.00 0.00 0.00 3.72
655 658 2.108514 TCGAATACGAGACGCCCGT 61.109 57.895 0.00 0.00 43.81 5.28
656 659 1.937846 CGAATACGAGACGCCCGTG 60.938 63.158 0.00 0.00 40.76 4.94
657 660 1.588139 GAATACGAGACGCCCGTGG 60.588 63.158 0.00 0.00 40.76 4.94
658 661 2.275547 GAATACGAGACGCCCGTGGT 62.276 60.000 0.00 0.00 40.76 4.16
669 672 1.301716 CCCGTGGTTGGTGACTCTG 60.302 63.158 0.00 0.00 0.00 3.35
1336 1416 4.513519 TCAATAGTTGAGCCGGCG 57.486 55.556 23.20 0.00 34.08 6.46
1370 1450 3.068064 TGCTCGACGAGATGCCCA 61.068 61.111 28.43 13.08 0.00 5.36
1377 1457 1.003355 ACGAGATGCCCACAAGGTG 60.003 57.895 0.00 0.00 38.26 4.00
1540 1640 4.350368 AACCAATGAAACCCATTTGGAC 57.650 40.909 7.49 0.00 42.55 4.02
1617 1717 0.255890 AGAGCGGGCAATTACACCAT 59.744 50.000 0.00 0.00 0.00 3.55
1621 1721 1.408702 GCGGGCAATTACACCATCAAT 59.591 47.619 0.00 0.00 0.00 2.57
1630 1730 6.812656 GCAATTACACCATCAATGATGACAAA 59.187 34.615 23.55 12.29 42.09 2.83
1672 1772 1.759445 CAAGTGTCGAGGGATCCATCT 59.241 52.381 23.17 7.56 0.00 2.90
1735 1835 5.428496 TGAAAGAACACTTTGATGCTCAG 57.572 39.130 0.00 0.00 34.54 3.35
1801 1901 1.341852 TGGTCGACAATCAACTCGGAA 59.658 47.619 18.91 0.00 0.00 4.30
1841 1941 2.195922 CACAAAAGGCAGTTGACAAGC 58.804 47.619 7.12 0.00 0.00 4.01
1907 2015 8.781196 GCATCTCATACATGTTCATCATACTTT 58.219 33.333 2.30 0.00 34.67 2.66
1976 2084 5.120519 ACAACATTGCACAAAACTTGTTCAG 59.879 36.000 0.00 0.00 43.23 3.02
1992 2100 1.728068 TCAGAGAAGAGACGAGGACG 58.272 55.000 0.00 0.00 45.75 4.79
2021 2129 5.075067 AGAAGGGGAAGATCAAGAAAGGAAA 59.925 40.000 0.00 0.00 0.00 3.13
2075 2183 5.884232 TGTTGAAGGATGATGAGAAATGGAG 59.116 40.000 0.00 0.00 0.00 3.86
2124 2232 2.639000 GAGCAACAAACGCAAGCGC 61.639 57.895 15.09 0.00 44.19 5.92
2163 2289 2.305052 TGATGATGAGGAGGATGATGCC 59.695 50.000 0.00 0.00 0.00 4.40
2283 2409 6.616548 AGAAGAAGAGGAAAGGAGATGATGAT 59.383 38.462 0.00 0.00 0.00 2.45
2330 2456 3.057946 GTGAAGGCAAGAAAAGAAGCGAT 60.058 43.478 0.00 0.00 0.00 4.58
2343 2469 0.457851 AAGCGATCGAGGTGAGGAAG 59.542 55.000 21.57 0.00 0.00 3.46
2448 2574 1.283321 GCATTGGAGGAGAGGAAGGTT 59.717 52.381 0.00 0.00 0.00 3.50
2450 2576 0.693049 TTGGAGGAGAGGAAGGTTGC 59.307 55.000 0.00 0.00 0.00 4.17
2500 2626 6.806739 GGAATGGGAAAAATACTTGTTCTTCG 59.193 38.462 0.00 0.00 0.00 3.79
2599 2749 3.023119 GCCATGATCAACACAATGGGTA 58.977 45.455 11.73 0.00 0.00 3.69
2894 3264 4.033776 CATGGGTGCACCTCCGGT 62.034 66.667 33.91 13.62 41.11 5.28
3239 4032 9.453325 GTTCATTGCATTTTGATTGAACATTTT 57.547 25.926 8.32 0.00 41.44 1.82
3461 4309 5.163774 GCTGTTGGAGATGCTCTAAGAAAAG 60.164 44.000 0.00 0.00 31.92 2.27
3462 4310 6.114187 TGTTGGAGATGCTCTAAGAAAAGA 57.886 37.500 0.00 0.00 31.92 2.52
3463 4311 6.169094 TGTTGGAGATGCTCTAAGAAAAGAG 58.831 40.000 0.00 0.00 44.92 2.85
3464 4312 6.169800 GTTGGAGATGCTCTAAGAAAAGAGT 58.830 40.000 3.08 0.00 44.13 3.24
3465 4313 5.971763 TGGAGATGCTCTAAGAAAAGAGTC 58.028 41.667 3.08 0.00 44.13 3.36
3466 4314 5.719085 TGGAGATGCTCTAAGAAAAGAGTCT 59.281 40.000 3.08 0.00 44.13 3.24
3467 4315 6.042143 GGAGATGCTCTAAGAAAAGAGTCTG 58.958 44.000 0.00 0.00 44.13 3.51
3468 4316 6.350949 GGAGATGCTCTAAGAAAAGAGTCTGT 60.351 42.308 0.00 0.00 44.13 3.41
3469 4317 7.147983 GGAGATGCTCTAAGAAAAGAGTCTGTA 60.148 40.741 0.00 0.00 44.13 2.74
3521 4369 2.715763 ACTTTGGTGGTCCTAGAGGA 57.284 50.000 0.00 0.00 43.08 3.71
3580 4428 3.665190 TGGTACATTTACATGTGCGTGA 58.335 40.909 9.11 0.00 44.68 4.35
3581 4429 3.682377 TGGTACATTTACATGTGCGTGAG 59.318 43.478 9.11 0.00 44.68 3.51
3727 4594 2.435693 CCCCGGTCATCCTCTCCAC 61.436 68.421 0.00 0.00 0.00 4.02
3728 4595 2.435693 CCCGGTCATCCTCTCCACC 61.436 68.421 0.00 0.00 0.00 4.61
3756 4623 3.905437 TAAAACCCCACTCGCCGGC 62.905 63.158 19.07 19.07 0.00 6.13
4272 5162 2.520120 TGATCCTATCCCCTGTCTCTGT 59.480 50.000 0.00 0.00 0.00 3.41
4330 5225 1.311859 CACAAGCAAGGAAGCAGACA 58.688 50.000 0.00 0.00 36.85 3.41
4340 5235 2.952310 AGGAAGCAGACAGGACAAAAAC 59.048 45.455 0.00 0.00 0.00 2.43
4454 5360 2.346766 TTCTGCTGCTGGAACTGAAA 57.653 45.000 6.69 0.00 0.00 2.69
4467 5373 4.112634 GGAACTGAAAAAGGCACAGAAAC 58.887 43.478 0.00 0.00 35.85 2.78
4471 5377 6.463995 ACTGAAAAAGGCACAGAAACATAA 57.536 33.333 0.00 0.00 35.85 1.90
4472 5378 6.872920 ACTGAAAAAGGCACAGAAACATAAA 58.127 32.000 0.00 0.00 35.85 1.40
4473 5379 7.500141 ACTGAAAAAGGCACAGAAACATAAAT 58.500 30.769 0.00 0.00 35.85 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 8.635328 TCGCTAATTAACACCAACATCTATAGA 58.365 33.333 4.57 4.57 0.00 1.98
56 57 8.556213 TGTTCTACCAAAGTTATTCGCTAATT 57.444 30.769 0.00 0.00 0.00 1.40
62 63 6.018180 GCCCTATGTTCTACCAAAGTTATTCG 60.018 42.308 0.00 0.00 0.00 3.34
89 90 4.164221 CAGACCCTAGATACACCATGGTTT 59.836 45.833 16.84 12.51 0.00 3.27
107 108 2.392662 TGACCTCATCTGGATCAGACC 58.607 52.381 0.00 0.00 43.63 3.85
110 111 4.141779 TGTTCATGACCTCATCTGGATCAG 60.142 45.833 0.00 0.00 33.61 2.90
113 114 5.131067 CAATGTTCATGACCTCATCTGGAT 58.869 41.667 0.00 0.00 33.61 3.41
116 117 4.939439 TGACAATGTTCATGACCTCATCTG 59.061 41.667 0.00 5.47 33.61 2.90
195 196 4.636648 CAGTCTCGCCTTAGAGTAGAAAGA 59.363 45.833 0.00 0.00 39.21 2.52
226 227 2.501223 TTTGTCGGTGCCGCTAGAGG 62.501 60.000 8.37 8.37 39.59 3.69
227 228 0.460284 ATTTGTCGGTGCCGCTAGAG 60.460 55.000 5.64 0.00 39.59 2.43
228 229 0.739462 CATTTGTCGGTGCCGCTAGA 60.739 55.000 5.64 0.00 39.59 2.43
231 232 0.604243 TTACATTTGTCGGTGCCGCT 60.604 50.000 5.64 0.00 39.59 5.52
232 233 0.179200 CTTACATTTGTCGGTGCCGC 60.179 55.000 5.64 2.16 39.59 6.53
233 234 1.127951 GTCTTACATTTGTCGGTGCCG 59.872 52.381 3.94 3.94 41.35 5.69
273 275 1.285962 CCCACCCAATTCTCACCATCT 59.714 52.381 0.00 0.00 0.00 2.90
275 277 0.336048 CCCCACCCAATTCTCACCAT 59.664 55.000 0.00 0.00 0.00 3.55
290 292 1.540367 CTCACACCCCCTTACCCCA 60.540 63.158 0.00 0.00 0.00 4.96
295 297 3.006728 CCCGCTCACACCCCCTTA 61.007 66.667 0.00 0.00 0.00 2.69
304 306 0.606604 TTCTCTACAACCCCGCTCAC 59.393 55.000 0.00 0.00 0.00 3.51
321 324 2.202295 AGAGCGCTCGATCTTTCTTC 57.798 50.000 30.39 4.16 37.65 2.87
323 326 1.003331 CGTAGAGCGCTCGATCTTTCT 60.003 52.381 30.39 13.88 41.46 2.52
351 354 0.329261 CCACCCTCATCTTGCCTTCA 59.671 55.000 0.00 0.00 0.00 3.02
382 385 0.806868 CGCCATGCTCAACAATGTCT 59.193 50.000 0.00 0.00 0.00 3.41
386 389 1.033746 CCCTCGCCATGCTCAACAAT 61.034 55.000 0.00 0.00 0.00 2.71
387 390 1.675310 CCCTCGCCATGCTCAACAA 60.675 57.895 0.00 0.00 0.00 2.83
388 391 2.046023 CCCTCGCCATGCTCAACA 60.046 61.111 0.00 0.00 0.00 3.33
389 392 0.960364 TTTCCCTCGCCATGCTCAAC 60.960 55.000 0.00 0.00 0.00 3.18
390 393 0.960364 GTTTCCCTCGCCATGCTCAA 60.960 55.000 0.00 0.00 0.00 3.02
391 394 1.377202 GTTTCCCTCGCCATGCTCA 60.377 57.895 0.00 0.00 0.00 4.26
392 395 1.377202 TGTTTCCCTCGCCATGCTC 60.377 57.895 0.00 0.00 0.00 4.26
393 396 1.675641 GTGTTTCCCTCGCCATGCT 60.676 57.895 0.00 0.00 0.00 3.79
394 397 2.877691 GTGTTTCCCTCGCCATGC 59.122 61.111 0.00 0.00 0.00 4.06
395 398 1.375396 TCGTGTTTCCCTCGCCATG 60.375 57.895 0.00 0.00 0.00 3.66
396 399 1.375523 GTCGTGTTTCCCTCGCCAT 60.376 57.895 0.00 0.00 0.00 4.40
397 400 2.029964 GTCGTGTTTCCCTCGCCA 59.970 61.111 0.00 0.00 0.00 5.69
398 401 1.737008 GAGTCGTGTTTCCCTCGCC 60.737 63.158 0.00 0.00 0.00 5.54
399 402 0.524862 TAGAGTCGTGTTTCCCTCGC 59.475 55.000 0.00 0.00 0.00 5.03
400 403 1.538512 TGTAGAGTCGTGTTTCCCTCG 59.461 52.381 0.00 0.00 0.00 4.63
401 404 3.192844 TGATGTAGAGTCGTGTTTCCCTC 59.807 47.826 0.00 0.00 0.00 4.30
402 405 3.162666 TGATGTAGAGTCGTGTTTCCCT 58.837 45.455 0.00 0.00 0.00 4.20
403 406 3.587797 TGATGTAGAGTCGTGTTTCCC 57.412 47.619 0.00 0.00 0.00 3.97
404 407 3.791887 CGATGATGTAGAGTCGTGTTTCC 59.208 47.826 0.00 0.00 0.00 3.13
405 408 4.659088 TCGATGATGTAGAGTCGTGTTTC 58.341 43.478 0.00 0.00 35.71 2.78
406 409 4.696899 TCGATGATGTAGAGTCGTGTTT 57.303 40.909 0.00 0.00 35.71 2.83
407 410 4.602006 CATCGATGATGTAGAGTCGTGTT 58.398 43.478 21.02 0.00 35.54 3.32
408 411 4.216366 CATCGATGATGTAGAGTCGTGT 57.784 45.455 21.02 0.00 35.54 4.49
419 422 3.070429 TCGTGAGTGACATCGATGATG 57.930 47.619 31.33 13.18 44.71 3.07
420 423 3.608008 CGATCGTGAGTGACATCGATGAT 60.608 47.826 31.33 15.55 40.14 2.45
421 424 2.286418 CGATCGTGAGTGACATCGATGA 60.286 50.000 31.33 7.62 40.14 2.92
422 425 2.039804 CGATCGTGAGTGACATCGATG 58.960 52.381 23.68 23.68 40.14 3.84
423 426 1.940613 TCGATCGTGAGTGACATCGAT 59.059 47.619 15.94 8.66 41.46 3.59
424 427 1.365699 TCGATCGTGAGTGACATCGA 58.634 50.000 15.94 11.12 39.82 3.59
425 428 2.039804 CATCGATCGTGAGTGACATCG 58.960 52.381 15.94 7.76 37.14 3.84
426 429 2.389059 CCATCGATCGTGAGTGACATC 58.611 52.381 15.94 0.00 0.00 3.06
427 430 1.536922 GCCATCGATCGTGAGTGACAT 60.537 52.381 15.94 0.00 0.00 3.06
428 431 0.179137 GCCATCGATCGTGAGTGACA 60.179 55.000 15.94 0.00 0.00 3.58
429 432 0.179137 TGCCATCGATCGTGAGTGAC 60.179 55.000 15.94 3.78 0.00 3.67
430 433 0.530288 TTGCCATCGATCGTGAGTGA 59.470 50.000 15.94 0.00 0.00 3.41
431 434 0.926155 CTTGCCATCGATCGTGAGTG 59.074 55.000 15.94 9.81 0.00 3.51
432 435 0.532573 ACTTGCCATCGATCGTGAGT 59.467 50.000 15.94 9.26 0.00 3.41
433 436 1.203928 GACTTGCCATCGATCGTGAG 58.796 55.000 15.94 8.69 0.00 3.51
434 437 0.525455 CGACTTGCCATCGATCGTGA 60.525 55.000 15.94 0.00 42.25 4.35
435 438 1.920051 CGACTTGCCATCGATCGTG 59.080 57.895 15.94 12.28 42.25 4.35
436 439 1.878522 GCGACTTGCCATCGATCGT 60.879 57.895 15.94 0.00 42.25 3.73
437 440 2.923854 GCGACTTGCCATCGATCG 59.076 61.111 9.36 9.36 42.25 3.69
454 457 3.818121 TTTGGTCACCGTCGCCAGG 62.818 63.158 0.00 0.00 33.41 4.45
455 458 1.635663 GATTTGGTCACCGTCGCCAG 61.636 60.000 0.00 0.00 33.41 4.85
456 459 1.669760 GATTTGGTCACCGTCGCCA 60.670 57.895 0.00 0.00 0.00 5.69
457 460 1.359459 GAGATTTGGTCACCGTCGCC 61.359 60.000 0.00 0.00 0.00 5.54
458 461 0.669318 TGAGATTTGGTCACCGTCGC 60.669 55.000 0.00 0.00 0.00 5.19
459 462 1.068474 GTGAGATTTGGTCACCGTCG 58.932 55.000 0.00 0.00 38.75 5.12
464 467 0.404040 TGGGGGTGAGATTTGGTCAC 59.596 55.000 0.00 0.00 43.12 3.67
465 468 0.404040 GTGGGGGTGAGATTTGGTCA 59.596 55.000 0.00 0.00 0.00 4.02
466 469 0.323451 GGTGGGGGTGAGATTTGGTC 60.323 60.000 0.00 0.00 0.00 4.02
467 470 1.774300 GGTGGGGGTGAGATTTGGT 59.226 57.895 0.00 0.00 0.00 3.67
468 471 1.378514 CGGTGGGGGTGAGATTTGG 60.379 63.158 0.00 0.00 0.00 3.28
469 472 2.046285 GCGGTGGGGGTGAGATTTG 61.046 63.158 0.00 0.00 0.00 2.32
470 473 2.355115 GCGGTGGGGGTGAGATTT 59.645 61.111 0.00 0.00 0.00 2.17
471 474 4.096003 CGCGGTGGGGGTGAGATT 62.096 66.667 0.00 0.00 0.00 2.40
481 484 3.728636 TTTTTAGCGGCGCGGTGG 61.729 61.111 27.59 0.00 38.30 4.61
496 499 5.365403 TCTGTTCGCAATTACGGATTTTT 57.635 34.783 0.00 0.00 0.00 1.94
497 500 4.671766 GCTCTGTTCGCAATTACGGATTTT 60.672 41.667 0.00 0.00 0.00 1.82
498 501 3.181510 GCTCTGTTCGCAATTACGGATTT 60.182 43.478 0.00 0.00 0.00 2.17
499 502 2.351726 GCTCTGTTCGCAATTACGGATT 59.648 45.455 0.00 0.00 0.00 3.01
500 503 1.933853 GCTCTGTTCGCAATTACGGAT 59.066 47.619 0.00 0.00 0.00 4.18
501 504 1.355971 GCTCTGTTCGCAATTACGGA 58.644 50.000 0.00 0.00 0.00 4.69
502 505 0.373716 GGCTCTGTTCGCAATTACGG 59.626 55.000 0.00 0.00 0.00 4.02
503 506 1.359848 AGGCTCTGTTCGCAATTACG 58.640 50.000 0.00 0.00 0.00 3.18
504 507 2.285488 GCTAGGCTCTGTTCGCAATTAC 59.715 50.000 0.00 0.00 0.00 1.89
505 508 2.168521 AGCTAGGCTCTGTTCGCAATTA 59.831 45.455 0.00 0.00 30.62 1.40
506 509 1.065854 AGCTAGGCTCTGTTCGCAATT 60.066 47.619 0.00 0.00 30.62 2.32
507 510 0.539051 AGCTAGGCTCTGTTCGCAAT 59.461 50.000 0.00 0.00 30.62 3.56
508 511 1.975327 AGCTAGGCTCTGTTCGCAA 59.025 52.632 0.00 0.00 30.62 4.85
509 512 3.700109 AGCTAGGCTCTGTTCGCA 58.300 55.556 0.00 0.00 30.62 5.10
517 520 5.180837 GATGGACCATCTGAGCTAGGCTC 62.181 56.522 24.77 12.01 41.99 4.70
518 521 0.031716 TGGACCATCTGAGCTAGGCT 60.032 55.000 0.00 0.00 43.88 4.58
519 522 1.001860 GATGGACCATCTGAGCTAGGC 59.998 57.143 24.77 0.00 37.82 3.93
520 523 2.299582 CTGATGGACCATCTGAGCTAGG 59.700 54.545 30.11 10.12 40.60 3.02
521 524 2.299582 CCTGATGGACCATCTGAGCTAG 59.700 54.545 32.17 21.08 40.60 3.42
522 525 2.323599 CCTGATGGACCATCTGAGCTA 58.676 52.381 32.17 14.33 40.60 3.32
523 526 1.129917 CCTGATGGACCATCTGAGCT 58.870 55.000 32.17 2.07 40.60 4.09
524 527 0.108207 CCCTGATGGACCATCTGAGC 59.892 60.000 32.17 12.00 40.60 4.26
525 528 0.108207 GCCCTGATGGACCATCTGAG 59.892 60.000 32.17 24.40 40.60 3.35
526 529 0.326904 AGCCCTGATGGACCATCTGA 60.327 55.000 32.17 16.20 40.60 3.27
527 530 0.108207 GAGCCCTGATGGACCATCTG 59.892 60.000 30.11 28.28 41.06 2.90
528 531 0.326904 TGAGCCCTGATGGACCATCT 60.327 55.000 30.11 13.58 41.06 2.90
529 532 0.548031 TTGAGCCCTGATGGACCATC 59.452 55.000 25.21 25.21 40.88 3.51
530 533 0.549950 CTTGAGCCCTGATGGACCAT 59.450 55.000 6.71 6.71 35.39 3.55
531 534 0.842030 ACTTGAGCCCTGATGGACCA 60.842 55.000 0.00 0.00 35.39 4.02
532 535 0.107459 GACTTGAGCCCTGATGGACC 60.107 60.000 0.00 0.00 35.39 4.46
533 536 0.908198 AGACTTGAGCCCTGATGGAC 59.092 55.000 0.00 0.00 35.39 4.02
534 537 1.661463 AAGACTTGAGCCCTGATGGA 58.339 50.000 0.00 0.00 35.39 3.41
535 538 3.634397 TTAAGACTTGAGCCCTGATGG 57.366 47.619 0.00 0.00 37.09 3.51
536 539 4.583871 AGTTTAAGACTTGAGCCCTGATG 58.416 43.478 0.00 0.00 33.92 3.07
537 540 4.917906 AGTTTAAGACTTGAGCCCTGAT 57.082 40.909 0.00 0.00 33.92 2.90
538 541 4.706842 AAGTTTAAGACTTGAGCCCTGA 57.293 40.909 0.00 0.00 46.66 3.86
547 550 4.501400 GCACCAATGCCAAGTTTAAGACTT 60.501 41.667 0.00 0.00 46.97 3.01
548 551 3.005791 GCACCAATGCCAAGTTTAAGACT 59.994 43.478 0.00 0.00 46.97 3.24
549 552 3.317150 GCACCAATGCCAAGTTTAAGAC 58.683 45.455 0.00 0.00 46.97 3.01
587 590 3.449737 ACATCAATGGAAGCCAGAAATGG 59.550 43.478 0.00 0.00 36.75 3.16
594 597 2.964464 ACACAAACATCAATGGAAGCCA 59.036 40.909 0.00 0.00 38.19 4.75
595 598 3.665745 ACACAAACATCAATGGAAGCC 57.334 42.857 0.00 0.00 0.00 4.35
602 605 4.314961 TCTCACGCTACACAAACATCAAT 58.685 39.130 0.00 0.00 0.00 2.57
604 607 3.378911 TCTCACGCTACACAAACATCA 57.621 42.857 0.00 0.00 0.00 3.07
615 618 3.243636 ACGGAAAAAGTCTTCTCACGCTA 60.244 43.478 0.00 0.00 0.00 4.26
653 656 2.519377 TTACAGAGTCACCAACCACG 57.481 50.000 0.00 0.00 0.00 4.94
655 658 4.431416 ACAATTACAGAGTCACCAACCA 57.569 40.909 0.00 0.00 0.00 3.67
656 659 6.430000 ACAATACAATTACAGAGTCACCAACC 59.570 38.462 0.00 0.00 0.00 3.77
657 660 7.041372 ACACAATACAATTACAGAGTCACCAAC 60.041 37.037 0.00 0.00 0.00 3.77
658 661 6.995686 ACACAATACAATTACAGAGTCACCAA 59.004 34.615 0.00 0.00 0.00 3.67
669 672 8.883731 AGATGCTCTTACACACAATACAATTAC 58.116 33.333 0.00 0.00 0.00 1.89
1355 1435 0.803768 CTTGTGGGCATCTCGTCGAG 60.804 60.000 16.33 16.33 0.00 4.04
1442 1530 5.940192 TCGTTGAGACTACAAATGCAAAT 57.060 34.783 0.00 0.00 0.00 2.32
1446 1534 5.496387 CATCATCGTTGAGACTACAAATGC 58.504 41.667 2.21 0.00 34.73 3.56
1447 1535 5.063817 TGCATCATCGTTGAGACTACAAATG 59.936 40.000 2.21 0.00 34.73 2.32
1540 1640 1.001974 TCCACCTCAAACTCATGGTCG 59.998 52.381 0.00 0.00 0.00 4.79
1672 1772 4.838423 TCTCTACTTTGATCACCTCCAACA 59.162 41.667 0.00 0.00 0.00 3.33
1735 1835 2.159517 GCGGTCAATTCCACTCATGTTC 60.160 50.000 0.00 0.00 0.00 3.18
1801 1901 2.275380 GGCCGCCCACTTTTGACAT 61.275 57.895 0.00 0.00 0.00 3.06
1855 1955 7.655328 CCACTTACTCTATCATCCTCATTTGTC 59.345 40.741 0.00 0.00 0.00 3.18
1976 2084 0.728542 GGTCGTCCTCGTCTCTTCTC 59.271 60.000 0.00 0.00 38.33 2.87
1992 2100 3.264450 TCTTGATCTTCCCCTTCTTGGTC 59.736 47.826 0.00 0.00 0.00 4.02
2021 2129 3.950395 GCAATGAGGCAAGGTAAAGATCT 59.050 43.478 0.00 0.00 0.00 2.75
2075 2183 3.009723 TCATCCAAATCTTCACGCTTCC 58.990 45.455 0.00 0.00 0.00 3.46
2124 2232 8.188139 TCATCATCATCATTCAACTCAATTGTG 58.812 33.333 5.13 5.59 39.54 3.33
2163 2289 0.318441 TCTTGCCGTCCTCACTTGAG 59.682 55.000 0.00 0.00 41.71 3.02
2330 2456 0.614697 TGCCATCTTCCTCACCTCGA 60.615 55.000 0.00 0.00 0.00 4.04
2343 2469 1.135721 GCATCTTGGTTCCTTGCCATC 59.864 52.381 0.00 0.00 35.71 3.51
2448 2574 0.975556 TAGTTCGCTCCTCCATGGCA 60.976 55.000 6.96 0.00 35.26 4.92
2450 2576 0.390860 CCTAGTTCGCTCCTCCATGG 59.609 60.000 4.97 4.97 37.10 3.66
2500 2626 5.437289 TCATTGAACAAAGATGTGTCCAC 57.563 39.130 0.00 0.00 40.46 4.02
2662 2857 1.529948 CAATGATGCCGAGGCCCAT 60.530 57.895 12.05 11.75 41.09 4.00
2675 2936 1.383799 CCACCCAAGCCTCCAATGA 59.616 57.895 0.00 0.00 0.00 2.57
3521 4369 2.002586 CACGACAAGGCGATCAATTCT 58.997 47.619 0.66 0.00 34.83 2.40
3720 4587 1.973346 TATGGGGGAGGGGTGGAGAG 61.973 65.000 0.00 0.00 0.00 3.20
3727 4594 1.624188 GGGTTTTATGGGGGAGGGG 59.376 63.158 0.00 0.00 0.00 4.79
3728 4595 1.225403 TGGGGTTTTATGGGGGAGGG 61.225 60.000 0.00 0.00 0.00 4.30
3835 4702 1.599797 CGGGTCGGTTTCTTTGCCT 60.600 57.895 0.00 0.00 0.00 4.75
3839 4706 0.035725 GATCCCGGGTCGGTTTCTTT 60.036 55.000 22.86 0.00 46.80 2.52
4090 4957 0.871024 AAAATTGGGGAAGGGGGTGA 59.129 50.000 0.00 0.00 0.00 4.02
4092 4959 0.252057 CGAAAATTGGGGAAGGGGGT 60.252 55.000 0.00 0.00 0.00 4.95
4095 4965 3.762407 AAAACGAAAATTGGGGAAGGG 57.238 42.857 0.00 0.00 0.00 3.95
4231 5110 2.820787 CAGAGAAGAGAACGTACCCTGT 59.179 50.000 0.00 0.00 0.00 4.00
4272 5162 3.882888 AGCGACAATTTCAAAGGAACAGA 59.117 39.130 0.00 0.00 31.35 3.41
4330 5225 8.716909 CAATTAGTGTTTGTTTGTTTTTGTCCT 58.283 29.630 0.00 0.00 0.00 3.85
4374 5269 9.561069 ACTGAATCAAAACAAGTACTAGAACAT 57.439 29.630 0.00 0.00 0.00 2.71
4375 5270 8.958119 ACTGAATCAAAACAAGTACTAGAACA 57.042 30.769 0.00 0.00 0.00 3.18
4376 5271 9.042008 TGACTGAATCAAAACAAGTACTAGAAC 57.958 33.333 0.00 0.00 33.02 3.01
4378 5273 9.261180 CTTGACTGAATCAAAACAAGTACTAGA 57.739 33.333 0.00 0.00 46.80 2.43
4379 5274 9.046296 ACTTGACTGAATCAAAACAAGTACTAG 57.954 33.333 19.52 0.00 46.80 2.57
4380 5275 8.958119 ACTTGACTGAATCAAAACAAGTACTA 57.042 30.769 19.52 0.00 46.80 1.82
4382 5277 8.181573 TGAACTTGACTGAATCAAAACAAGTAC 58.818 33.333 20.49 0.00 46.80 2.73
4430 5336 4.592942 TCAGTTCCAGCAGCAGAATTTAT 58.407 39.130 0.00 0.00 0.00 1.40
4434 5340 2.574006 TTCAGTTCCAGCAGCAGAAT 57.426 45.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.