Multiple sequence alignment - TraesCS5A01G408200

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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 TraesCS5A01G408200 chr5A 100.000 3689 0 0 1 3689 598631827 598635515 0.000000e+00 6813.0
1 TraesCS5A01G408200 chr5A 78.484 976 153 48 12 951 317122674 317123628 1.480000e-163 586.0
2 TraesCS5A01G408200 chr5A 91.029 379 28 5 2371 2743 78905122 78905500 1.180000e-139 507.0
3 TraesCS5A01G408200 chr5A 84.298 242 35 2 2799 3038 480804913 480805153 2.220000e-57 233.0
4 TraesCS5A01G408200 chr5A 100.000 33 0 0 2384 2416 125215727 125215759 1.110000e-05 62.1
5 TraesCS5A01G408200 chr6B 86.733 1304 137 11 1 1272 256498342 256497043 0.000000e+00 1417.0
6 TraesCS5A01G408200 chr6B 80.645 217 35 3 1925 2140 233778658 233778868 1.060000e-35 161.0
7 TraesCS5A01G408200 chr6B 89.344 122 13 0 3079 3200 708785302 708785423 1.770000e-33 154.0
8 TraesCS5A01G408200 chr7D 95.503 845 34 4 1 842 141388820 141389663 0.000000e+00 1347.0
9 TraesCS5A01G408200 chr7D 95.131 842 40 1 1 842 537625437 537624597 0.000000e+00 1327.0
10 TraesCS5A01G408200 chr7D 87.131 474 55 6 832 1300 202394394 202394866 1.950000e-147 532.0
11 TraesCS5A01G408200 chr7D 85.950 121 16 1 3083 3203 555049532 555049413 1.080000e-25 128.0
12 TraesCS5A01G408200 chr7D 95.000 40 1 1 2384 2422 60544398 60544359 1.110000e-05 62.1
13 TraesCS5A01G408200 chr3A 95.482 841 37 1 1 841 51973058 51972219 0.000000e+00 1341.0
14 TraesCS5A01G408200 chr3A 95.833 216 8 1 2528 2743 733287797 733287583 7.580000e-92 348.0
15 TraesCS5A01G408200 chr3A 94.118 187 11 0 2557 2743 79458657 79458471 6.030000e-73 285.0
16 TraesCS5A01G408200 chr3A 90.811 185 10 2 2392 2570 79460106 79459923 1.320000e-59 241.0
17 TraesCS5A01G408200 chr3A 89.610 154 10 1 2372 2519 733318017 733317864 1.350000e-44 191.0
18 TraesCS5A01G408200 chr3A 98.000 50 1 0 2752 2801 733281901 733281852 1.830000e-13 87.9
19 TraesCS5A01G408200 chr5D 95.368 842 38 1 1 842 509495919 509496759 0.000000e+00 1338.0
20 TraesCS5A01G408200 chr5D 88.058 762 82 8 1300 2058 480142747 480143502 0.000000e+00 894.0
21 TraesCS5A01G408200 chr5D 90.968 465 39 2 836 1300 135281598 135281137 1.130000e-174 623.0
22 TraesCS5A01G408200 chr5D 80.784 255 34 7 1933 2177 206887865 206887616 6.290000e-43 185.0
23 TraesCS5A01G408200 chr5D 94.286 70 4 0 2319 2388 480154854 480154923 1.400000e-19 108.0
24 TraesCS5A01G408200 chr5D 97.436 39 1 0 3087 3125 311311804 311311842 2.380000e-07 67.6
25 TraesCS5A01G408200 chr5D 95.000 40 1 1 2384 2422 445085941 445085902 1.110000e-05 62.1
26 TraesCS5A01G408200 chr4D 95.255 843 38 2 1 842 349942538 349941697 0.000000e+00 1334.0
27 TraesCS5A01G408200 chr4D 89.103 468 46 4 836 1300 228564086 228563621 8.880000e-161 577.0
28 TraesCS5A01G408200 chr4D 91.289 287 15 4 2802 3088 6774093 6773817 2.080000e-102 383.0
29 TraesCS5A01G408200 chr4D 82.898 421 42 13 3202 3608 6773818 6773414 5.860000e-93 351.0
30 TraesCS5A01G408200 chr4D 77.573 379 46 17 1933 2277 63110045 63109672 3.760000e-45 193.0
31 TraesCS5A01G408200 chr2D 95.142 844 39 2 1 844 593243372 593242531 0.000000e+00 1330.0
32 TraesCS5A01G408200 chr2D 87.475 495 54 5 3202 3689 181260029 181259536 6.920000e-157 564.0
33 TraesCS5A01G408200 chr2D 87.071 495 50 4 3202 3689 375576182 375576669 6.970000e-152 547.0
34 TraesCS5A01G408200 chr2D 89.769 303 15 2 2802 3088 181260330 181260028 1.250000e-99 374.0
35 TraesCS5A01G408200 chr2D 94.421 233 12 1 2800 3031 375575880 375576112 1.260000e-94 357.0
36 TraesCS5A01G408200 chr2D 85.408 233 25 5 2801 3031 181258534 181258759 2.220000e-57 233.0
37 TraesCS5A01G408200 chr2D 85.106 235 26 4 2802 3034 375577482 375577255 7.970000e-57 231.0
38 TraesCS5A01G408200 chr2D 87.179 117 15 0 3087 3203 122863517 122863401 2.310000e-27 134.0
39 TraesCS5A01G408200 chr2D 86.726 113 15 0 3092 3204 302261457 302261345 3.870000e-25 126.0
40 TraesCS5A01G408200 chr2D 88.350 103 11 1 2534 2635 481176109 481176007 5.000000e-24 122.0
41 TraesCS5A01G408200 chr1D 95.232 839 39 1 3 841 203546324 203545487 0.000000e+00 1327.0
42 TraesCS5A01G408200 chr1D 94.503 855 44 3 1 854 267621745 267620893 0.000000e+00 1315.0
43 TraesCS5A01G408200 chr1D 89.495 495 43 5 3202 3689 246101433 246100941 5.230000e-173 617.0
44 TraesCS5A01G408200 chr1D 88.936 470 44 3 836 1299 121113361 121113828 1.150000e-159 573.0
45 TraesCS5A01G408200 chr1D 93.004 243 13 2 2505 2743 366165320 366165078 5.860000e-93 351.0
46 TraesCS5A01G408200 chr1D 88.973 263 13 2 2842 3088 246101694 246101432 9.950000e-81 311.0
47 TraesCS5A01G408200 chr1D 84.615 208 27 1 1933 2140 299209228 299209026 6.250000e-48 202.0
48 TraesCS5A01G408200 chr1D 100.000 50 0 0 2752 2801 366163319 366163270 3.920000e-15 93.5
49 TraesCS5A01G408200 chr1D 91.304 46 4 0 3080 3125 205500195 205500240 3.080000e-06 63.9
50 TraesCS5A01G408200 chr3D 95.125 841 40 1 1 841 307991216 307990377 0.000000e+00 1325.0
51 TraesCS5A01G408200 chr3D 88.627 466 50 2 836 1299 336269965 336270429 6.920000e-157 564.0
52 TraesCS5A01G408200 chr3D 87.905 463 50 5 842 1299 194930543 194931004 1.170000e-149 540.0
53 TraesCS5A01G408200 chr3D 88.608 79 3 1 2383 2455 340695123 340695045 1.410000e-14 91.6
54 TraesCS5A01G408200 chr1A 96.307 704 24 2 2800 3501 452279061 452278358 0.000000e+00 1155.0
55 TraesCS5A01G408200 chr1A 90.302 464 44 1 836 1299 444469798 444470260 1.130000e-169 606.0
56 TraesCS5A01G408200 chr1A 75.592 422 60 16 1890 2277 50817019 50816607 6.340000e-38 169.0
57 TraesCS5A01G408200 chr5B 85.149 1037 121 18 1300 2321 588154493 588155511 0.000000e+00 1031.0
58 TraesCS5A01G408200 chr5B 76.596 376 47 19 1935 2275 190282359 190281990 6.340000e-38 169.0
59 TraesCS5A01G408200 chr5B 85.827 127 17 1 3081 3206 359484467 359484341 2.310000e-27 134.0
60 TraesCS5A01G408200 chr5B 74.745 392 49 22 1919 2270 343207794 343207413 2.990000e-26 130.0
61 TraesCS5A01G408200 chr5B 100.000 31 0 0 2384 2414 669952148 669952178 1.430000e-04 58.4
62 TraesCS5A01G408200 chr6A 79.665 954 142 39 12 934 445158037 445158969 1.120000e-179 640.0
63 TraesCS5A01G408200 chr6A 84.746 354 36 4 3342 3689 467598396 467598055 4.560000e-89 339.0
64 TraesCS5A01G408200 chr6A 85.526 228 23 4 2807 3031 467597249 467597469 2.870000e-56 230.0
65 TraesCS5A01G408200 chr6A 84.874 238 23 5 2801 3034 467598974 467598746 1.030000e-55 228.0
66 TraesCS5A01G408200 chr6A 86.066 122 17 0 3079 3200 611414365 611414486 8.310000e-27 132.0
67 TraesCS5A01G408200 chr6A 100.000 32 0 0 2384 2415 23587268 23587237 3.980000e-05 60.2
68 TraesCS5A01G408200 chr6A 96.875 32 1 0 3202 3233 467597542 467597573 2.000000e-03 54.7
69 TraesCS5A01G408200 chr1B 86.869 495 56 7 3202 3689 499653982 499654474 2.510000e-151 545.0
70 TraesCS5A01G408200 chr1B 90.759 303 12 1 2802 3088 499653681 499653983 1.240000e-104 390.0
71 TraesCS5A01G408200 chr1B 85.345 232 32 2 2803 3034 566102320 566102091 4.760000e-59 239.0
72 TraesCS5A01G408200 chr1B 84.746 118 17 1 3084 3200 117290343 117290460 2.330000e-22 117.0
73 TraesCS5A01G408200 chr1B 82.857 105 18 0 3087 3191 426111252 426111148 1.090000e-15 95.3
74 TraesCS5A01G408200 chr1B 81.739 115 14 3 2027 2140 189091140 189091032 5.070000e-14 89.8
75 TraesCS5A01G408200 chr1B 86.792 53 6 1 3202 3254 499654972 499654921 1.430000e-04 58.4
76 TraesCS5A01G408200 chr2A 87.339 466 55 2 836 1299 359426765 359427228 7.010000e-147 531.0
77 TraesCS5A01G408200 chr2A 87.179 117 15 0 3087 3203 62368571 62368687 2.310000e-27 134.0
78 TraesCS5A01G408200 chr2A 100.000 33 0 0 2384 2416 591730604 591730636 1.110000e-05 62.1
79 TraesCS5A01G408200 chr7A 85.455 495 57 6 3202 3689 230483924 230484410 5.500000e-138 501.0
80 TraesCS5A01G408200 chr7A 83.010 206 30 1 1935 2140 490645194 490644994 8.140000e-42 182.0
81 TraesCS5A01G408200 chr4B 84.444 495 60 10 3202 3689 12140643 12140159 4.310000e-129 472.0
82 TraesCS5A01G408200 chr4B 81.481 189 25 5 2845 3031 12139434 12139614 2.970000e-31 147.0
83 TraesCS5A01G408200 chr4B 80.000 120 13 4 3086 3204 394641156 394641265 1.100000e-10 78.7
84 TraesCS5A01G408200 chr2B 85.408 233 31 1 2802 3031 757233095 757233327 4.760000e-59 239.0
85 TraesCS5A01G408200 chr2B 76.000 400 45 23 1919 2277 704001136 704001525 3.810000e-35 159.0
86 TraesCS5A01G408200 chr2B 84.706 85 7 3 2373 2451 49317242 49317326 3.050000e-11 80.5
87 TraesCS5A01G408200 chr3B 76.842 380 47 17 1933 2277 554269188 554268815 3.790000e-40 176.0
88 TraesCS5A01G408200 chr3B 81.776 214 35 3 1930 2140 706902449 706902661 3.790000e-40 176.0
89 TraesCS5A01G408200 chr3B 91.304 46 4 0 2371 2416 62001419 62001464 3.080000e-06 63.9
90 TraesCS5A01G408200 chr4A 81.333 225 31 5 1927 2140 173682038 173681814 4.900000e-39 172.0
91 TraesCS5A01G408200 chr4A 86.667 120 15 1 3086 3204 157206948 157206829 8.310000e-27 132.0
92 TraesCS5A01G408200 chrUn 76.000 400 45 23 1919 2277 273290581 273290970 3.810000e-35 159.0
93 TraesCS5A01G408200 chrUn 76.000 400 45 23 1919 2277 318784981 318784592 3.810000e-35 159.0
94 TraesCS5A01G408200 chr6D 87.705 122 15 0 3079 3200 464836682 464836803 3.840000e-30 143.0
95 TraesCS5A01G408200 chr6D 87.288 118 15 0 3087 3204 452541972 452541855 6.430000e-28 135.0
96 TraesCS5A01G408200 chr6D 86.607 112 12 3 2169 2277 11479824 11479713 1.800000e-23 121.0
97 TraesCS5A01G408200 chr6D 84.211 114 18 0 3087 3200 86863393 86863506 1.080000e-20 111.0
98 TraesCS5A01G408200 chr6D 93.750 48 3 0 3087 3134 426990808 426990761 5.110000e-09 73.1
99 TraesCS5A01G408200 chr7B 85.600 125 16 2 3080 3203 320319262 320319139 2.990000e-26 130.0
100 TraesCS5A01G408200 chr7B 100.000 30 0 0 2384 2413 623672985 623672956 5.150000e-04 56.5


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 TraesCS5A01G408200 chr5A 598631827 598635515 3688 False 6813.00 6813 100.0000 1 3689 1 chr5A.!!$F5 3688
1 TraesCS5A01G408200 chr5A 317122674 317123628 954 False 586.00 586 78.4840 12 951 1 chr5A.!!$F3 939
2 TraesCS5A01G408200 chr6B 256497043 256498342 1299 True 1417.00 1417 86.7330 1 1272 1 chr6B.!!$R1 1271
3 TraesCS5A01G408200 chr7D 141388820 141389663 843 False 1347.00 1347 95.5030 1 842 1 chr7D.!!$F1 841
4 TraesCS5A01G408200 chr7D 537624597 537625437 840 True 1327.00 1327 95.1310 1 842 1 chr7D.!!$R2 841
5 TraesCS5A01G408200 chr3A 51972219 51973058 839 True 1341.00 1341 95.4820 1 841 1 chr3A.!!$R1 840
6 TraesCS5A01G408200 chr3A 79458471 79460106 1635 True 263.00 285 92.4645 2392 2743 2 chr3A.!!$R5 351
7 TraesCS5A01G408200 chr5D 509495919 509496759 840 False 1338.00 1338 95.3680 1 842 1 chr5D.!!$F4 841
8 TraesCS5A01G408200 chr5D 480142747 480143502 755 False 894.00 894 88.0580 1300 2058 1 chr5D.!!$F2 758
9 TraesCS5A01G408200 chr4D 349941697 349942538 841 True 1334.00 1334 95.2550 1 842 1 chr4D.!!$R3 841
10 TraesCS5A01G408200 chr4D 6773414 6774093 679 True 367.00 383 87.0935 2802 3608 2 chr4D.!!$R4 806
11 TraesCS5A01G408200 chr2D 593242531 593243372 841 True 1330.00 1330 95.1420 1 844 1 chr2D.!!$R5 843
12 TraesCS5A01G408200 chr2D 181259536 181260330 794 True 469.00 564 88.6220 2802 3689 2 chr2D.!!$R6 887
13 TraesCS5A01G408200 chr2D 375575880 375576669 789 False 452.00 547 90.7460 2800 3689 2 chr2D.!!$F2 889
14 TraesCS5A01G408200 chr1D 203545487 203546324 837 True 1327.00 1327 95.2320 3 841 1 chr1D.!!$R1 838
15 TraesCS5A01G408200 chr1D 267620893 267621745 852 True 1315.00 1315 94.5030 1 854 1 chr1D.!!$R2 853
16 TraesCS5A01G408200 chr1D 246100941 246101694 753 True 464.00 617 89.2340 2842 3689 2 chr1D.!!$R4 847
17 TraesCS5A01G408200 chr1D 366163270 366165320 2050 True 222.25 351 96.5020 2505 2801 2 chr1D.!!$R5 296
18 TraesCS5A01G408200 chr3D 307990377 307991216 839 True 1325.00 1325 95.1250 1 841 1 chr3D.!!$R1 840
19 TraesCS5A01G408200 chr1A 452278358 452279061 703 True 1155.00 1155 96.3070 2800 3501 1 chr1A.!!$R2 701
20 TraesCS5A01G408200 chr5B 588154493 588155511 1018 False 1031.00 1031 85.1490 1300 2321 1 chr5B.!!$F1 1021
21 TraesCS5A01G408200 chr6A 445158037 445158969 932 False 640.00 640 79.6650 12 934 1 chr6A.!!$F1 922
22 TraesCS5A01G408200 chr6A 467598055 467598974 919 True 283.50 339 84.8100 2801 3689 2 chr6A.!!$R2 888
23 TraesCS5A01G408200 chr1B 499653681 499654474 793 False 467.50 545 88.8140 2802 3689 2 chr1B.!!$F2 887

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
198 215 0.179084 TGCCCAAGATTCGATCGTCC 60.179 55.0 15.94 5.58 0.00 4.79 F
1081 1138 0.976073 CCCTCCCACGAAGCCTCTAA 60.976 60.0 0.00 0.00 0.00 2.10 F
1914 1973 0.034896 ATGACGAAGGCGAAAGTGGT 59.965 50.0 0.00 0.00 41.64 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 1348 0.036164 TTGGCAGGCACTTGATACGT 59.964 50.0 0.0 0.00 34.60 3.57 R
2217 2286 0.683504 AATCGCTACTCGGGGTGACT 60.684 55.0 0.0 0.00 39.05 3.41 R
3504 6819 0.234625 TGAATTTGCACGACGACAGC 59.765 50.0 0.0 3.14 0.00 4.40 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
110 111 6.013466 TGCTCATATTGGCTCCTACATATTCA 60.013 38.462 0.00 0.00 0.00 2.57
113 114 7.744733 TCATATTGGCTCCTACATATTCAACA 58.255 34.615 0.00 0.00 0.00 3.33
178 195 4.223255 TCCCTTTGTCATCGGTATGTTACA 59.777 41.667 0.00 0.00 34.50 2.41
184 201 2.436173 TCATCGGTATGTTACATGCCCA 59.564 45.455 23.14 13.76 34.50 5.36
198 215 0.179084 TGCCCAAGATTCGATCGTCC 60.179 55.000 15.94 5.58 0.00 4.79
221 238 8.737175 GTCCGTATCATCATACCTAGTTCAATA 58.263 37.037 0.00 0.00 32.42 1.90
234 251 3.454375 AGTTCAATATCGTTACCGGCAG 58.546 45.455 0.00 0.00 33.95 4.85
260 277 6.312918 GTCTCTTTACTCGTTCCATAATGCAA 59.687 38.462 0.00 0.00 0.00 4.08
303 320 3.047796 GTCACATTGCTTGCAAGTCTTG 58.952 45.455 26.55 21.26 0.00 3.02
305 322 3.047796 CACATTGCTTGCAAGTCTTGTC 58.952 45.455 26.55 10.14 0.00 3.18
618 639 5.539955 TCATTCTCTAATGATGTGATCCCGA 59.460 40.000 0.00 0.00 45.17 5.14
909 964 4.807039 GCGGCGGCGGAACTTCTA 62.807 66.667 33.02 0.00 0.00 2.10
928 983 8.035448 ACTTCTAATCTAGGGTTATTTCTGGG 57.965 38.462 0.00 0.00 0.00 4.45
965 1022 8.682936 ATAGGATTTTTCAGCGTTAGAATCAT 57.317 30.769 0.00 0.00 0.00 2.45
966 1023 6.789262 AGGATTTTTCAGCGTTAGAATCATG 58.211 36.000 0.00 0.00 0.00 3.07
999 1056 1.765255 GAGGGGCCCACTAGGTACC 60.765 68.421 27.72 2.73 38.26 3.34
1001 1058 1.385489 GGGGCCCACTAGGTACCAT 60.385 63.158 26.86 1.66 36.73 3.55
1081 1138 0.976073 CCCTCCCACGAAGCCTCTAA 60.976 60.000 0.00 0.00 0.00 2.10
1095 1152 4.928263 AGCCTCTAATGCCTCTTTTCTTT 58.072 39.130 0.00 0.00 0.00 2.52
1147 1204 4.488126 TTGGAGAACTTTGATTTCTGCG 57.512 40.909 0.00 0.00 42.63 5.18
1182 1239 4.137543 CCAAGGTAGTTCTGCTGAAAACT 58.862 43.478 7.68 5.46 39.07 2.66
1183 1240 4.023707 CCAAGGTAGTTCTGCTGAAAACTG 60.024 45.833 7.68 5.35 36.44 3.16
1184 1241 4.423625 AGGTAGTTCTGCTGAAAACTGT 57.576 40.909 7.68 0.16 36.44 3.55
1185 1242 4.130118 AGGTAGTTCTGCTGAAAACTGTG 58.870 43.478 7.68 0.00 36.44 3.66
1195 1252 4.141937 TGCTGAAAACTGTGTCAGTCTAGT 60.142 41.667 17.93 0.00 44.62 2.57
1248 1305 6.652900 ACACCCAAACCATATAAAATTGTTGC 59.347 34.615 0.00 0.00 0.00 4.17
1288 1345 9.745880 ATACTTCATAAATTATAGATACGCCGG 57.254 33.333 0.00 0.00 0.00 6.13
1289 1346 7.833786 ACTTCATAAATTATAGATACGCCGGA 58.166 34.615 5.05 0.00 0.00 5.14
1290 1347 7.758528 ACTTCATAAATTATAGATACGCCGGAC 59.241 37.037 5.05 0.00 0.00 4.79
1291 1348 7.160547 TCATAAATTATAGATACGCCGGACA 57.839 36.000 5.05 0.00 0.00 4.02
1292 1349 7.031372 TCATAAATTATAGATACGCCGGACAC 58.969 38.462 5.05 0.00 0.00 3.67
1293 1350 2.975410 TTATAGATACGCCGGACACG 57.025 50.000 5.05 0.74 40.55 4.49
1298 1355 3.902318 TACGCCGGACACGTATCA 58.098 55.556 5.05 0.00 44.55 2.15
1342 1400 2.112928 ACGAAGCACATGCCACCA 59.887 55.556 0.00 0.00 43.38 4.17
1349 1407 1.252904 GCACATGCCACCATCCAACT 61.253 55.000 0.00 0.00 34.31 3.16
1381 1439 0.590195 GATGATGAACATCGGCCTGC 59.410 55.000 0.00 0.00 44.46 4.85
1383 1441 0.035152 TGATGAACATCGGCCTGCTT 60.035 50.000 0.00 0.00 40.63 3.91
1384 1442 1.209261 TGATGAACATCGGCCTGCTTA 59.791 47.619 0.00 0.00 40.63 3.09
1385 1443 2.158769 TGATGAACATCGGCCTGCTTAT 60.159 45.455 0.00 0.00 40.63 1.73
1397 1456 6.058833 TCGGCCTGCTTATAAAATCACATTA 58.941 36.000 0.00 0.00 0.00 1.90
1416 1475 8.593679 TCACATTATGATCCATTAACGATAGGT 58.406 33.333 0.00 0.00 33.49 3.08
1422 1481 5.129650 TGATCCATTAACGATAGGTTCACCA 59.870 40.000 0.00 0.00 40.09 4.17
1457 1516 1.001268 CCCACTCCGTCGTAGATCATG 60.001 57.143 0.00 0.00 40.67 3.07
1458 1517 1.001268 CCACTCCGTCGTAGATCATGG 60.001 57.143 0.00 0.00 40.67 3.66
1501 1560 2.348411 CCTTCAAGGTGGTGACTGTT 57.652 50.000 0.00 0.00 0.00 3.16
1505 1564 1.525995 AAGGTGGTGACTGTTGGCG 60.526 57.895 0.00 0.00 0.00 5.69
1525 1584 3.318017 CGTCTTCAAGGTGATCGTCTTT 58.682 45.455 0.00 0.00 0.00 2.52
1551 1610 3.782523 ACCAATGACATAGAGGTGATGGT 59.217 43.478 6.39 3.04 0.00 3.55
1631 1690 5.238006 TGTTGCGTGCTAGTTTACTTTTT 57.762 34.783 0.00 0.00 0.00 1.94
1652 1711 6.782298 TTTCGTTCGATTGTTAATGTACCA 57.218 33.333 0.00 0.00 0.00 3.25
1667 1726 6.721571 AATGTACCACATTTAAGACTGTCG 57.278 37.500 1.52 0.00 45.80 4.35
1733 1792 9.155975 CCTATGGTAATGTTCTGCATATAAGAC 57.844 37.037 0.00 0.00 36.67 3.01
1734 1793 9.935241 CTATGGTAATGTTCTGCATATAAGACT 57.065 33.333 0.00 0.00 36.67 3.24
1740 1799 5.595885 TGTTCTGCATATAAGACTCTCTGC 58.404 41.667 0.00 0.00 0.00 4.26
1772 1831 1.971357 ACCTCACCACTCGAACAAGAT 59.029 47.619 0.00 0.00 0.00 2.40
1787 1846 3.914312 ACAAGATGTTACGAGACCACAG 58.086 45.455 0.00 0.00 0.00 3.66
1804 1863 4.253685 CCACAGGTCTTGTATGTTACCAG 58.746 47.826 0.00 0.00 38.16 4.00
1834 1893 4.923871 ACACTTTGCATCTACGTAGAACAG 59.076 41.667 27.90 20.44 35.69 3.16
1835 1894 4.923871 CACTTTGCATCTACGTAGAACAGT 59.076 41.667 27.90 20.00 35.69 3.55
1837 1896 4.776795 TTGCATCTACGTAGAACAGTCA 57.223 40.909 27.90 17.25 35.69 3.41
1853 1912 5.947228 ACAGTCATACAACCAAACATCAG 57.053 39.130 0.00 0.00 0.00 2.90
1854 1913 4.216257 ACAGTCATACAACCAAACATCAGC 59.784 41.667 0.00 0.00 0.00 4.26
1860 1919 2.558359 ACAACCAAACATCAGCTTAGGC 59.442 45.455 0.00 0.00 39.06 3.93
1872 1931 3.119459 TCAGCTTAGGCGTTTCTACTCAG 60.119 47.826 0.00 0.00 44.37 3.35
1898 1957 2.622470 CTGCGAAGAGATGGAGAGATGA 59.378 50.000 0.00 0.00 0.00 2.92
1902 1961 3.313803 CGAAGAGATGGAGAGATGACGAA 59.686 47.826 0.00 0.00 0.00 3.85
1907 1966 0.679960 TGGAGAGATGACGAAGGCGA 60.680 55.000 0.00 0.00 41.64 5.54
1909 1968 1.135083 GGAGAGATGACGAAGGCGAAA 60.135 52.381 0.00 0.00 41.64 3.46
1914 1973 0.034896 ATGACGAAGGCGAAAGTGGT 59.965 50.000 0.00 0.00 41.64 4.16
1954 2013 1.745264 GAGAAGATCCAGAGGGCGG 59.255 63.158 0.00 0.00 0.00 6.13
1958 2017 4.247380 GATCCAGAGGGCGGGCAG 62.247 72.222 3.27 0.00 0.00 4.85
2034 2093 0.532862 GATCGGGAACATGGCGATGT 60.533 55.000 8.73 8.73 45.24 3.06
2060 2119 1.153086 GATCAGGAACATGGCGGCT 60.153 57.895 11.43 0.00 0.00 5.52
2086 2145 1.639108 GACAGGACCCCAAACCCTATT 59.361 52.381 0.00 0.00 0.00 1.73
2090 2149 1.063942 GGACCCCAAACCCTATTGAGG 60.064 57.143 0.00 0.00 43.33 3.86
2105 2164 6.356556 CCTATTGAGGGACAACATTATGTGA 58.643 40.000 0.00 0.00 41.52 3.58
2115 2174 0.953727 CATTATGTGATGTGCGGGGG 59.046 55.000 0.00 0.00 0.00 5.40
2140 2199 1.202348 GAGGCCCATTTTGAGGTTTCG 59.798 52.381 0.00 0.00 0.00 3.46
2141 2200 0.966179 GGCCCATTTTGAGGTTTCGT 59.034 50.000 0.00 0.00 0.00 3.85
2142 2201 1.336795 GGCCCATTTTGAGGTTTCGTG 60.337 52.381 0.00 0.00 0.00 4.35
2143 2202 1.934849 GCCCATTTTGAGGTTTCGTGC 60.935 52.381 0.00 0.00 0.00 5.34
2144 2203 1.339610 CCCATTTTGAGGTTTCGTGCA 59.660 47.619 0.00 0.00 0.00 4.57
2156 2225 3.917985 GGTTTCGTGCAACCACATTAATC 59.082 43.478 0.21 0.00 45.12 1.75
2165 2234 7.219917 CGTGCAACCACATTAATCGAAATATTT 59.780 33.333 0.00 0.00 42.17 1.40
2166 2235 8.320295 GTGCAACCACATTAATCGAAATATTTG 58.680 33.333 5.17 0.00 41.67 2.32
2217 2286 6.467677 GTGAAGATATGGCCTAATCTTAGCA 58.532 40.000 24.42 18.57 41.40 3.49
2233 2303 2.490217 CAGTCACCCCGAGTAGCG 59.510 66.667 0.00 0.00 40.47 4.26
2240 2310 2.295349 TCACCCCGAGTAGCGATTAATC 59.705 50.000 5.30 5.30 44.57 1.75
2266 2336 1.847818 TAAATCGCTGAATCGGTCGG 58.152 50.000 6.18 0.00 35.48 4.79
2279 2349 2.562635 TCGGTCGGTTTTTGAACATCA 58.437 42.857 0.00 0.00 0.00 3.07
2283 2353 4.024725 CGGTCGGTTTTTGAACATCAGTTA 60.025 41.667 0.00 0.00 38.30 2.24
2286 2356 7.019418 GGTCGGTTTTTGAACATCAGTTATAC 58.981 38.462 0.00 0.00 38.30 1.47
2287 2357 6.735063 GTCGGTTTTTGAACATCAGTTATACG 59.265 38.462 0.00 0.00 38.30 3.06
2298 2369 1.134907 CAGTTATACGTGGCGGAGGTT 60.135 52.381 0.00 0.00 0.00 3.50
2300 2371 1.662122 GTTATACGTGGCGGAGGTTTG 59.338 52.381 0.00 0.00 0.00 2.93
2306 2377 1.012486 GTGGCGGAGGTTTGTACTCG 61.012 60.000 0.00 0.00 35.82 4.18
2307 2378 1.291272 GGCGGAGGTTTGTACTCGT 59.709 57.895 0.00 0.00 35.82 4.18
2342 2413 4.129148 GCCCCCACCTCCATCCAC 62.129 72.222 0.00 0.00 0.00 4.02
2343 2414 2.613696 CCCCCACCTCCATCCACA 60.614 66.667 0.00 0.00 0.00 4.17
2344 2415 2.677228 CCCCACCTCCATCCACAC 59.323 66.667 0.00 0.00 0.00 3.82
2345 2416 2.268920 CCCACCTCCATCCACACG 59.731 66.667 0.00 0.00 0.00 4.49
2346 2417 2.592993 CCCACCTCCATCCACACGT 61.593 63.158 0.00 0.00 0.00 4.49
2347 2418 1.079127 CCACCTCCATCCACACGTC 60.079 63.158 0.00 0.00 0.00 4.34
2348 2419 1.079127 CACCTCCATCCACACGTCC 60.079 63.158 0.00 0.00 0.00 4.79
2349 2420 1.535444 ACCTCCATCCACACGTCCA 60.535 57.895 0.00 0.00 0.00 4.02
2350 2421 1.079127 CCTCCATCCACACGTCCAC 60.079 63.158 0.00 0.00 0.00 4.02
2351 2422 1.079127 CTCCATCCACACGTCCACC 60.079 63.158 0.00 0.00 0.00 4.61
2352 2423 1.826340 CTCCATCCACACGTCCACCA 61.826 60.000 0.00 0.00 0.00 4.17
2353 2424 1.198094 TCCATCCACACGTCCACCAT 61.198 55.000 0.00 0.00 0.00 3.55
2354 2425 0.744414 CCATCCACACGTCCACCATC 60.744 60.000 0.00 0.00 0.00 3.51
2355 2426 1.083806 CATCCACACGTCCACCATCG 61.084 60.000 0.00 0.00 0.00 3.84
2356 2427 2.852495 ATCCACACGTCCACCATCGC 62.852 60.000 0.00 0.00 0.00 4.58
2357 2428 3.118454 CACACGTCCACCATCGCC 61.118 66.667 0.00 0.00 0.00 5.54
2358 2429 4.735132 ACACGTCCACCATCGCCG 62.735 66.667 0.00 0.00 0.00 6.46
2365 2436 4.899239 CACCATCGCCGCCTCCTC 62.899 72.222 0.00 0.00 0.00 3.71
2383 2454 4.516195 GGCTCCGCCGTTCTCTCC 62.516 72.222 0.00 0.00 39.62 3.71
2384 2455 4.516195 GCTCCGCCGTTCTCTCCC 62.516 72.222 0.00 0.00 0.00 4.30
2385 2456 3.068691 CTCCGCCGTTCTCTCCCA 61.069 66.667 0.00 0.00 0.00 4.37
2386 2457 3.068691 TCCGCCGTTCTCTCCCAG 61.069 66.667 0.00 0.00 0.00 4.45
2387 2458 4.821589 CCGCCGTTCTCTCCCAGC 62.822 72.222 0.00 0.00 0.00 4.85
2389 2460 3.760035 GCCGTTCTCTCCCAGCGA 61.760 66.667 0.00 0.00 0.00 4.93
2390 2461 2.182030 CCGTTCTCTCCCAGCGAC 59.818 66.667 0.00 0.00 0.00 5.19
2410 2481 3.535962 GAGGAGAGGAGCAGCCGG 61.536 72.222 0.00 0.00 43.43 6.13
2431 2508 2.016961 CGGCCATCCATTGAAGACG 58.983 57.895 2.24 0.00 0.00 4.18
2465 2542 1.795286 GATCGAGACCGCATCAATTCC 59.205 52.381 0.00 0.00 35.37 3.01
2493 2570 4.642429 GATTTATACACTCGCCCAATCCT 58.358 43.478 0.00 0.00 0.00 3.24
2511 2588 1.964608 CTGATCGAGCCTTCCCAGCA 61.965 60.000 0.00 0.00 0.00 4.41
2526 2606 2.217038 AGCAACCGGAGAGGAGCAA 61.217 57.895 9.46 0.00 45.00 3.91
2530 2610 3.382832 CCGGAGAGGAGCAACCGT 61.383 66.667 0.00 0.00 45.00 4.83
2647 4006 2.169789 CGCGTGCCAGATTCAGGAG 61.170 63.158 0.00 0.00 0.00 3.69
2705 4064 1.144503 CTAGCAATCATGGCCCTCCTT 59.855 52.381 0.00 0.00 0.00 3.36
2743 4102 2.089980 CCCTCCTTGAAGCTCACAATG 58.910 52.381 6.73 5.10 0.00 2.82
2744 4103 2.553904 CCCTCCTTGAAGCTCACAATGT 60.554 50.000 6.73 0.00 0.00 2.71
2745 4104 3.307691 CCCTCCTTGAAGCTCACAATGTA 60.308 47.826 6.73 0.00 0.00 2.29
2746 4105 4.521146 CCTCCTTGAAGCTCACAATGTAT 58.479 43.478 6.73 0.00 0.00 2.29
2747 4106 5.396772 CCCTCCTTGAAGCTCACAATGTATA 60.397 44.000 6.73 0.00 0.00 1.47
2748 4107 6.115446 CCTCCTTGAAGCTCACAATGTATAA 58.885 40.000 6.73 0.00 0.00 0.98
2749 4108 6.599244 CCTCCTTGAAGCTCACAATGTATAAA 59.401 38.462 6.73 0.00 0.00 1.40
2805 5914 1.689813 TCTGCCACTTTCTTACGGACA 59.310 47.619 0.00 0.00 0.00 4.02
3110 6242 1.479323 TCCTCCGTCCGGAATTACTTG 59.521 52.381 5.23 0.00 44.66 3.16
3122 6254 4.436852 CGGAATTACTTGTCACGGAAATGG 60.437 45.833 0.00 0.00 0.00 3.16
3142 6274 5.068234 TGGATAAAAGTGGACGTGTCTAG 57.932 43.478 0.00 0.00 0.00 2.43
3174 6306 5.305585 TGCGTCTAGATAAATCCATTTCCC 58.694 41.667 0.00 0.00 0.00 3.97
3188 6320 4.703093 TCCATTTCCCCGACAAGTATTTTC 59.297 41.667 0.00 0.00 0.00 2.29
3193 6325 3.869866 CGACAAGTATTTTCGGGCG 57.130 52.632 0.00 0.00 0.00 6.13
3395 6699 3.795041 CAGCAGGGAGGGAGGCTG 61.795 72.222 0.00 0.00 46.47 4.85
3504 6819 0.674534 GGTACCAGACGGATAGCCAG 59.325 60.000 7.15 0.00 35.59 4.85
3524 6839 1.135972 GCTGTCGTCGTGCAAATTCAT 60.136 47.619 0.00 0.00 0.00 2.57
3561 6876 3.300032 TGGGTCTCCAACGATAGCT 57.700 52.632 0.00 0.00 40.73 3.32
3638 6953 3.036577 GTCAGACCGACGTGACCA 58.963 61.111 0.00 0.00 37.67 4.02
3652 6967 3.642848 ACGTGACCAAGAACCCTACTTTA 59.357 43.478 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 7.368059 GGTTTGACCGATAAAGATCTTTTGTT 58.632 34.615 25.02 11.19 34.23 2.83
178 195 1.541233 GGACGATCGAATCTTGGGCAT 60.541 52.381 24.34 0.00 0.00 4.40
184 201 4.215613 TGATGATACGGACGATCGAATCTT 59.784 41.667 24.34 12.99 0.00 2.40
198 215 9.439537 CGATATTGAACTAGGTATGATGATACG 57.560 37.037 0.00 0.00 36.08 3.06
234 251 5.234543 GCATTATGGAACGAGTAAAGAGACC 59.765 44.000 0.00 0.00 0.00 3.85
260 277 3.350219 AATGAGTTAGTTGCGGGATGT 57.650 42.857 0.00 0.00 0.00 3.06
303 320 1.588404 CTCGGTAATGCACATCACGAC 59.412 52.381 0.00 0.00 0.00 4.34
305 322 1.854743 CTCTCGGTAATGCACATCACG 59.145 52.381 0.00 0.00 0.00 4.35
738 765 9.528018 CATGCTAAAATTGTATTAACCGGAAAT 57.472 29.630 9.46 10.35 0.00 2.17
909 964 4.390008 ACCCCCAGAAATAACCCTAGATT 58.610 43.478 0.00 0.00 0.00 2.40
954 1011 3.185188 CCCATCTTCGCATGATTCTAACG 59.815 47.826 0.00 0.00 0.00 3.18
958 1015 1.602311 GCCCATCTTCGCATGATTCT 58.398 50.000 0.00 0.00 0.00 2.40
959 1016 0.595095 GGCCCATCTTCGCATGATTC 59.405 55.000 0.00 0.00 0.00 2.52
965 1022 3.664025 CTCGTGGCCCATCTTCGCA 62.664 63.158 0.00 0.00 0.00 5.10
966 1023 2.892425 CTCGTGGCCCATCTTCGC 60.892 66.667 0.00 0.00 0.00 4.70
992 1049 1.382009 TGGCTCGCCATGGTACCTA 60.382 57.895 14.67 0.00 41.89 3.08
1043 1100 1.001641 CCAGAAGAGCCACAAGGGG 60.002 63.158 0.00 0.00 37.04 4.79
1103 1160 4.241590 TGCAGCGAAACTTTTTGATGAT 57.758 36.364 10.71 0.00 39.67 2.45
1104 1161 3.706802 TGCAGCGAAACTTTTTGATGA 57.293 38.095 10.71 0.00 39.67 2.92
1105 1162 4.977741 AATGCAGCGAAACTTTTTGATG 57.022 36.364 3.27 3.27 40.13 3.07
1106 1163 4.211794 CCAAATGCAGCGAAACTTTTTGAT 59.788 37.500 5.44 0.00 0.00 2.57
1118 1175 2.030893 TCAAAGTTCTCCAAATGCAGCG 60.031 45.455 0.00 0.00 0.00 5.18
1158 1215 2.839486 TCAGCAGAACTACCTTGGTG 57.161 50.000 2.03 0.00 0.00 4.17
1163 1220 4.130118 CACAGTTTTCAGCAGAACTACCT 58.870 43.478 0.00 0.00 34.52 3.08
1182 1239 6.665992 ATGGAACTAAACTAGACTGACACA 57.334 37.500 0.00 0.00 0.00 3.72
1183 1240 7.964604 AAATGGAACTAAACTAGACTGACAC 57.035 36.000 0.00 0.00 0.00 3.67
1222 1279 7.174080 GCAACAATTTTATATGGTTTGGGTGTT 59.826 33.333 0.00 0.00 0.00 3.32
1223 1280 6.652900 GCAACAATTTTATATGGTTTGGGTGT 59.347 34.615 0.00 0.00 0.00 4.16
1272 1329 3.254166 ACGTGTCCGGCGTATCTATAATT 59.746 43.478 6.01 0.00 41.06 1.40
1273 1330 2.816087 ACGTGTCCGGCGTATCTATAAT 59.184 45.455 6.01 0.00 41.06 1.28
1274 1331 2.221169 ACGTGTCCGGCGTATCTATAA 58.779 47.619 6.01 0.00 41.06 0.98
1275 1332 1.882912 ACGTGTCCGGCGTATCTATA 58.117 50.000 6.01 0.00 41.06 1.31
1276 1333 1.882912 TACGTGTCCGGCGTATCTAT 58.117 50.000 6.01 0.00 42.85 1.98
1277 1334 3.377933 TACGTGTCCGGCGTATCTA 57.622 52.632 6.01 0.00 42.85 1.98
1278 1335 4.223800 TACGTGTCCGGCGTATCT 57.776 55.556 6.01 0.00 42.85 1.98
1281 1338 0.099259 CTTGATACGTGTCCGGCGTA 59.901 55.000 13.93 13.93 46.63 4.42
1282 1339 1.153901 CTTGATACGTGTCCGGCGT 60.154 57.895 10.00 10.44 45.11 5.68
1283 1340 1.153901 ACTTGATACGTGTCCGGCG 60.154 57.895 10.00 0.00 38.78 6.46
1284 1341 1.693083 GCACTTGATACGTGTCCGGC 61.693 60.000 10.00 4.58 38.78 6.13
1285 1342 1.082117 GGCACTTGATACGTGTCCGG 61.082 60.000 10.00 0.00 38.78 5.14
1286 1343 0.108804 AGGCACTTGATACGTGTCCG 60.109 55.000 10.00 3.70 37.70 4.79
1287 1344 1.359848 CAGGCACTTGATACGTGTCC 58.640 55.000 10.00 0.00 37.70 4.02
1288 1345 0.721718 GCAGGCACTTGATACGTGTC 59.278 55.000 5.21 5.21 34.60 3.67
1289 1346 0.673644 GGCAGGCACTTGATACGTGT 60.674 55.000 0.00 0.00 34.60 4.49
1290 1347 0.673333 TGGCAGGCACTTGATACGTG 60.673 55.000 0.00 0.00 34.60 4.49
1291 1348 0.036164 TTGGCAGGCACTTGATACGT 59.964 50.000 0.00 0.00 34.60 3.57
1292 1349 1.064505 CATTGGCAGGCACTTGATACG 59.935 52.381 0.00 0.00 34.60 3.06
1293 1350 1.202336 GCATTGGCAGGCACTTGATAC 60.202 52.381 9.65 0.00 40.72 2.24
1294 1351 1.105457 GCATTGGCAGGCACTTGATA 58.895 50.000 9.65 0.00 40.72 2.15
1295 1352 1.610554 GGCATTGGCAGGCACTTGAT 61.611 55.000 13.99 0.00 43.71 2.57
1296 1353 2.277591 GGCATTGGCAGGCACTTGA 61.278 57.895 13.99 0.00 43.71 3.02
1297 1354 2.263540 GGCATTGGCAGGCACTTG 59.736 61.111 13.99 0.00 43.71 3.16
1298 1355 2.999063 GGGCATTGGCAGGCACTT 60.999 61.111 12.70 0.00 43.71 3.16
1327 1384 0.966875 TGGATGGTGGCATGTGCTTC 60.967 55.000 4.84 0.00 41.70 3.86
1342 1400 1.208052 CATCACGACCTCCAGTTGGAT 59.792 52.381 0.48 0.00 44.46 3.41
1349 1407 2.387757 TCATCATCATCACGACCTCCA 58.612 47.619 0.00 0.00 0.00 3.86
1397 1456 6.183361 TGGTGAACCTATCGTTAATGGATCAT 60.183 38.462 0.37 0.00 34.70 2.45
1406 1465 7.713507 CCTTTATCAATGGTGAACCTATCGTTA 59.286 37.037 0.37 0.00 37.30 3.18
1412 1471 5.505780 CACCCTTTATCAATGGTGAACCTA 58.494 41.667 8.03 0.00 46.56 3.08
1416 1475 3.096092 GGCACCCTTTATCAATGGTGAA 58.904 45.455 15.79 0.00 46.56 3.18
1443 1502 0.319040 CAGGCCATGATCTACGACGG 60.319 60.000 5.01 0.00 0.00 4.79
1448 1507 4.567971 CTGATCTTCAGGCCATGATCTAC 58.432 47.826 20.14 9.24 40.71 2.59
1501 1560 0.389817 CGATCACCTTGAAGACGCCA 60.390 55.000 0.00 0.00 0.00 5.69
1505 1564 4.150804 GTCAAAGACGATCACCTTGAAGAC 59.849 45.833 0.00 2.19 0.00 3.01
1525 1584 3.837731 TCACCTCTATGTCATTGGTGTCA 59.162 43.478 21.35 9.28 45.82 3.58
1631 1690 5.228665 TGTGGTACATTAACAATCGAACGA 58.771 37.500 0.00 0.00 44.52 3.85
1652 1711 6.688578 AGTCATACACGACAGTCTTAAATGT 58.311 36.000 0.00 0.00 38.43 2.71
1701 1760 4.261322 GCAGAACATTACCATAGGTGCATG 60.261 45.833 0.00 4.12 36.19 4.06
1733 1792 1.258982 GTTGTCAACACACGCAGAGAG 59.741 52.381 10.93 0.00 29.76 3.20
1734 1793 1.286501 GTTGTCAACACACGCAGAGA 58.713 50.000 10.93 0.00 29.76 3.10
1740 1799 0.655733 GGTGAGGTTGTCAACACACG 59.344 55.000 24.85 0.00 43.18 4.49
1804 1863 4.211389 CGTAGATGCAAAGTGTTGTTGTC 58.789 43.478 0.00 0.00 37.06 3.18
1834 1893 5.376854 AAGCTGATGTTTGGTTGTATGAC 57.623 39.130 0.00 0.00 0.00 3.06
1835 1894 5.647658 CCTAAGCTGATGTTTGGTTGTATGA 59.352 40.000 0.00 0.00 0.00 2.15
1837 1896 4.399303 GCCTAAGCTGATGTTTGGTTGTAT 59.601 41.667 0.00 0.00 35.50 2.29
1853 1912 1.927838 GCTGAGTAGAAACGCCTAAGC 59.072 52.381 0.00 0.00 0.00 3.09
1854 1913 2.541556 GGCTGAGTAGAAACGCCTAAG 58.458 52.381 0.00 0.00 37.76 2.18
1860 1919 1.354040 CAGCAGGCTGAGTAGAAACG 58.646 55.000 20.86 0.00 46.30 3.60
1872 1931 2.178890 CCATCTCTTCGCAGCAGGC 61.179 63.158 0.00 0.00 39.90 4.85
1881 1940 4.261572 CCTTCGTCATCTCTCCATCTCTTC 60.262 50.000 0.00 0.00 0.00 2.87
1898 1957 1.164041 CCAACCACTTTCGCCTTCGT 61.164 55.000 0.00 0.00 36.96 3.85
1902 1961 1.774894 TAGCCCAACCACTTTCGCCT 61.775 55.000 0.00 0.00 0.00 5.52
1907 1966 2.923629 TCCCTAATAGCCCAACCACTTT 59.076 45.455 0.00 0.00 0.00 2.66
1909 1968 2.280308 TCCCTAATAGCCCAACCACT 57.720 50.000 0.00 0.00 0.00 4.00
1914 1973 3.318313 CTCCTCTTCCCTAATAGCCCAA 58.682 50.000 0.00 0.00 0.00 4.12
1954 2013 3.605749 TAGCACCACCGAAGCTGCC 62.606 63.158 0.00 0.00 39.30 4.85
1958 2017 1.448013 GACCTAGCACCACCGAAGC 60.448 63.158 0.00 0.00 0.00 3.86
1961 2020 3.066190 CGGACCTAGCACCACCGA 61.066 66.667 0.00 0.00 45.31 4.69
2034 2093 3.622206 GCCATGTTCCTGATCCACACTAA 60.622 47.826 0.00 0.00 0.00 2.24
2035 2094 2.092968 GCCATGTTCCTGATCCACACTA 60.093 50.000 0.00 0.00 0.00 2.74
2060 2119 1.282653 TTTGGGGTCCTGTCCACACA 61.283 55.000 0.00 0.00 40.96 3.72
2086 2145 4.943093 CACATCACATAATGTTGTCCCTCA 59.057 41.667 0.00 0.00 38.88 3.86
2090 2149 3.487376 CCGCACATCACATAATGTTGTCC 60.487 47.826 0.00 0.00 38.88 4.02
2105 2164 3.411517 CTCCCTTCCCCCGCACAT 61.412 66.667 0.00 0.00 0.00 3.21
2115 2174 1.478631 CTCAAAATGGGCCTCCCTTC 58.521 55.000 4.53 0.00 45.70 3.46
2140 2199 7.985634 AATATTTCGATTAATGTGGTTGCAC 57.014 32.000 0.00 0.00 0.00 4.57
2141 2200 8.031864 ACAAATATTTCGATTAATGTGGTTGCA 58.968 29.630 0.00 0.00 0.00 4.08
2142 2201 8.320295 CACAAATATTTCGATTAATGTGGTTGC 58.680 33.333 0.00 0.00 34.73 4.17
2143 2202 9.566530 TCACAAATATTTCGATTAATGTGGTTG 57.433 29.630 10.98 7.09 37.94 3.77
2175 2244 3.696045 TCACCATTAATCTGTTGGGGTG 58.304 45.455 10.99 10.99 44.28 4.61
2176 2245 4.044065 TCTTCACCATTAATCTGTTGGGGT 59.956 41.667 0.00 0.00 35.36 4.95
2177 2246 4.599041 TCTTCACCATTAATCTGTTGGGG 58.401 43.478 0.00 0.00 35.13 4.96
2217 2286 0.683504 AATCGCTACTCGGGGTGACT 60.684 55.000 0.00 0.00 39.05 3.41
2258 2328 3.142951 TGATGTTCAAAAACCGACCGAT 58.857 40.909 0.00 0.00 34.28 4.18
2261 2331 3.982576 ACTGATGTTCAAAAACCGACC 57.017 42.857 0.00 0.00 34.28 4.79
2263 2333 6.424509 ACGTATAACTGATGTTCAAAAACCGA 59.575 34.615 0.00 0.00 37.59 4.69
2266 2336 6.304683 GCCACGTATAACTGATGTTCAAAAAC 59.695 38.462 0.00 0.00 37.59 2.43
2279 2349 1.188863 AACCTCCGCCACGTATAACT 58.811 50.000 0.00 0.00 0.00 2.24
2283 2353 0.896923 TACAAACCTCCGCCACGTAT 59.103 50.000 0.00 0.00 0.00 3.06
2286 2356 1.005394 AGTACAAACCTCCGCCACG 60.005 57.895 0.00 0.00 0.00 4.94
2287 2357 1.012486 CGAGTACAAACCTCCGCCAC 61.012 60.000 0.00 0.00 0.00 5.01
2298 2369 0.887387 GGGGCTTTGCACGAGTACAA 60.887 55.000 0.00 0.00 29.41 2.41
2300 2371 2.038837 GGGGGCTTTGCACGAGTAC 61.039 63.158 0.00 0.00 29.41 2.73
2325 2396 4.129148 GTGGATGGAGGTGGGGGC 62.129 72.222 0.00 0.00 0.00 5.80
2326 2397 2.613696 TGTGGATGGAGGTGGGGG 60.614 66.667 0.00 0.00 0.00 5.40
2327 2398 2.677228 GTGTGGATGGAGGTGGGG 59.323 66.667 0.00 0.00 0.00 4.96
2328 2399 2.268920 CGTGTGGATGGAGGTGGG 59.731 66.667 0.00 0.00 0.00 4.61
2329 2400 1.079127 GACGTGTGGATGGAGGTGG 60.079 63.158 0.00 0.00 0.00 4.61
2330 2401 1.079127 GGACGTGTGGATGGAGGTG 60.079 63.158 0.00 0.00 0.00 4.00
2331 2402 1.535444 TGGACGTGTGGATGGAGGT 60.535 57.895 0.00 0.00 0.00 3.85
2332 2403 1.079127 GTGGACGTGTGGATGGAGG 60.079 63.158 0.00 0.00 0.00 4.30
2333 2404 1.079127 GGTGGACGTGTGGATGGAG 60.079 63.158 0.00 0.00 0.00 3.86
2334 2405 1.198094 ATGGTGGACGTGTGGATGGA 61.198 55.000 0.00 0.00 0.00 3.41
2335 2406 0.744414 GATGGTGGACGTGTGGATGG 60.744 60.000 0.00 0.00 0.00 3.51
2336 2407 1.083806 CGATGGTGGACGTGTGGATG 61.084 60.000 0.00 0.00 0.00 3.51
2337 2408 1.218047 CGATGGTGGACGTGTGGAT 59.782 57.895 0.00 0.00 0.00 3.41
2338 2409 2.654289 CGATGGTGGACGTGTGGA 59.346 61.111 0.00 0.00 0.00 4.02
2339 2410 3.118454 GCGATGGTGGACGTGTGG 61.118 66.667 0.00 0.00 0.00 4.17
2340 2411 3.118454 GGCGATGGTGGACGTGTG 61.118 66.667 0.00 0.00 0.00 3.82
2341 2412 4.735132 CGGCGATGGTGGACGTGT 62.735 66.667 0.00 0.00 0.00 4.49
2348 2419 4.899239 GAGGAGGCGGCGATGGTG 62.899 72.222 12.98 0.00 0.00 4.17
2368 2439 3.068691 TGGGAGAGAACGGCGGAG 61.069 66.667 13.24 0.00 0.00 4.63
2369 2440 3.068691 CTGGGAGAGAACGGCGGA 61.069 66.667 13.24 0.00 0.00 5.54
2370 2441 4.821589 GCTGGGAGAGAACGGCGG 62.822 72.222 13.24 0.00 0.00 6.13
2372 2443 3.760035 TCGCTGGGAGAGAACGGC 61.760 66.667 0.00 0.00 35.67 5.68
2373 2444 2.182030 GTCGCTGGGAGAGAACGG 59.818 66.667 0.00 0.00 0.00 4.44
2374 2445 2.182030 GGTCGCTGGGAGAGAACG 59.818 66.667 0.00 0.00 0.00 3.95
2375 2446 2.182030 CGGTCGCTGGGAGAGAAC 59.818 66.667 0.00 0.00 0.00 3.01
2376 2447 3.068691 CCGGTCGCTGGGAGAGAA 61.069 66.667 0.00 0.00 0.00 2.87
2377 2448 4.043100 TCCGGTCGCTGGGAGAGA 62.043 66.667 0.00 0.00 0.00 3.10
2383 2454 3.522731 CTCTCCTCCGGTCGCTGG 61.523 72.222 0.00 0.00 0.00 4.85
2384 2455 3.522731 CCTCTCCTCCGGTCGCTG 61.523 72.222 0.00 0.00 0.00 5.18
2385 2456 3.707640 CTCCTCTCCTCCGGTCGCT 62.708 68.421 0.00 0.00 0.00 4.93
2386 2457 3.213402 CTCCTCTCCTCCGGTCGC 61.213 72.222 0.00 0.00 0.00 5.19
2387 2458 3.213402 GCTCCTCTCCTCCGGTCG 61.213 72.222 0.00 0.00 0.00 4.79
2388 2459 2.043852 TGCTCCTCTCCTCCGGTC 60.044 66.667 0.00 0.00 0.00 4.79
2389 2460 2.043450 CTGCTCCTCTCCTCCGGT 60.043 66.667 0.00 0.00 0.00 5.28
2390 2461 3.535962 GCTGCTCCTCTCCTCCGG 61.536 72.222 0.00 0.00 0.00 5.14
2410 2481 1.031571 TCTTCAATGGATGGCCGCAC 61.032 55.000 0.00 0.00 36.79 5.34
2431 2508 3.641454 GATCCCATCCCTCGCCCC 61.641 72.222 0.00 0.00 0.00 5.80
2465 2542 3.050619 GGCGAGTGTATAAATCGGACTG 58.949 50.000 0.00 0.00 36.96 3.51
2493 2570 1.552799 TTGCTGGGAAGGCTCGATCA 61.553 55.000 0.00 0.00 0.00 2.92
2511 2588 2.943978 CGGTTGCTCCTCTCCGGTT 61.944 63.158 0.00 0.00 39.41 4.44
2526 2606 3.081804 GTCTTCAATGGATGGAAACGGT 58.918 45.455 0.00 0.00 0.00 4.83
2530 2610 2.620367 CCCCGTCTTCAATGGATGGAAA 60.620 50.000 3.80 0.00 41.11 3.13
2613 3972 2.123428 GCGCTGGATTGGATTGCCT 61.123 57.895 0.00 0.00 34.31 4.75
2705 4064 1.271379 GGGCAGAGCAGTTTCCAGTAA 60.271 52.381 0.00 0.00 0.00 2.24
2805 5914 1.566298 GGGCAAGTCACCTGATCCCT 61.566 60.000 0.00 0.00 0.00 4.20
3090 6222 1.479323 CAAGTAATTCCGGACGGAGGA 59.521 52.381 13.64 0.22 46.06 3.71
3094 6226 1.997606 GTGACAAGTAATTCCGGACGG 59.002 52.381 1.83 3.96 0.00 4.79
3095 6227 1.652124 CGTGACAAGTAATTCCGGACG 59.348 52.381 1.83 0.00 0.00 4.79
3110 6242 4.698304 TCCACTTTTATCCATTTCCGTGAC 59.302 41.667 0.00 0.00 0.00 3.67
3122 6254 6.388278 AGTTCTAGACACGTCCACTTTTATC 58.612 40.000 0.00 0.00 0.00 1.75
3142 6274 9.042008 TGGATTTATCTAGACGCATTTTAGTTC 57.958 33.333 0.00 0.00 0.00 3.01
3188 6320 2.012051 GCAATATATTCCCTCCGCCCG 61.012 57.143 0.00 0.00 0.00 6.13
3294 6590 2.677875 GGTCGACGGGGTGGTAGT 60.678 66.667 9.92 0.00 0.00 2.73
3504 6819 0.234625 TGAATTTGCACGACGACAGC 59.765 50.000 0.00 3.14 0.00 4.40
3524 6839 9.444600 GAGACCCATATTTTTGTACTTCTTGTA 57.555 33.333 0.00 0.00 0.00 2.41
3652 6967 3.282157 CACTGCAGCGCAACACCT 61.282 61.111 15.27 0.00 38.41 4.00


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

AutoCloner maintained by Alex Coulton.