Multiple sequence alignment - TraesCS2A01G271200

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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 TraesCS2A01G271200 chr2A 100.000 3767 0 0 1 3767 442765329 442769095 0.000000e+00 6957.0
1 TraesCS2A01G271200 chr2A 92.253 3111 151 29 1 3056 442808829 442811904 0.000000e+00 4327.0
2 TraesCS2A01G271200 chr2A 87.790 3448 280 67 1 3355 422857259 422853860 0.000000e+00 3904.0
3 TraesCS2A01G271200 chr2A 85.577 1352 133 40 1 1304 343430103 343428766 0.000000e+00 1360.0
4 TraesCS2A01G271200 chr2A 82.375 1583 163 52 1 1505 706106412 706107956 0.000000e+00 1271.0
5 TraesCS2A01G271200 chr2A 86.157 1033 96 31 1 999 145740039 145739020 0.000000e+00 1072.0
6 TraesCS2A01G271200 chr2A 88.914 875 65 19 2406 3268 159902325 159903179 0.000000e+00 1050.0
7 TraesCS2A01G271200 chr2A 83.446 1033 112 42 2364 3355 204955491 204956505 0.000000e+00 905.0
8 TraesCS2A01G271200 chr2A 87.451 773 78 9 1385 2144 27244328 27243562 0.000000e+00 872.0
9 TraesCS2A01G271200 chr2A 86.859 799 78 19 2570 3352 345053745 345054532 0.000000e+00 869.0
10 TraesCS2A01G271200 chr2A 85.856 806 81 21 2563 3355 344747597 344748382 0.000000e+00 826.0
11 TraesCS2A01G271200 chr2A 89.339 666 46 14 2406 3058 159910556 159911209 0.000000e+00 813.0
12 TraesCS2A01G271200 chr2A 80.053 752 83 42 2552 3266 381315041 381314320 2.610000e-136 496.0
13 TraesCS2A01G271200 chr2A 86.364 440 45 10 3333 3767 68784417 68783988 2.050000e-127 466.0
14 TraesCS2A01G271200 chr2A 86.136 440 50 8 3333 3767 56027966 56028399 7.370000e-127 464.0
15 TraesCS2A01G271200 chr2A 91.698 265 19 1 2159 2420 233930582 233930846 7.690000e-97 364.0
16 TraesCS2A01G271200 chr3A 93.540 1223 65 6 1848 3057 353893087 353894308 0.000000e+00 1808.0
17 TraesCS2A01G271200 chr3A 85.736 1332 131 36 1 1296 353633371 353634679 0.000000e+00 1352.0
18 TraesCS2A01G271200 chr3A 85.165 910 107 17 2838 3740 553234195 553235083 0.000000e+00 907.0
19 TraesCS2A01G271200 chr3A 77.910 756 90 54 2356 3058 521149433 521148702 2.110000e-107 399.0
20 TraesCS2A01G271200 chr3A 77.532 543 58 38 2552 3058 188732264 188731750 6.200000e-68 268.0
21 TraesCS2A01G271200 chr3A 76.923 468 66 20 2527 2961 246877348 246876890 1.050000e-55 228.0
22 TraesCS2A01G271200 chr3A 92.308 52 2 2 2366 2415 210119091 210119040 5.220000e-09 73.1
23 TraesCS2A01G271200 chr7A 86.534 1359 132 25 1 1330 110122016 110120680 0.000000e+00 1448.0
24 TraesCS2A01G271200 chr7A 85.154 1300 130 44 1 1250 330402559 330403845 0.000000e+00 1273.0
25 TraesCS2A01G271200 chr7A 87.738 1101 97 25 1 1071 330394469 330395561 0.000000e+00 1251.0
26 TraesCS2A01G271200 chr7A 83.370 1377 150 57 1 1324 281820434 281819084 0.000000e+00 1201.0
27 TraesCS2A01G271200 chr7A 84.112 1284 147 36 1 1250 458353420 458352160 0.000000e+00 1188.0
28 TraesCS2A01G271200 chr7A 83.749 1323 142 52 1 1270 281880711 281879409 0.000000e+00 1184.0
29 TraesCS2A01G271200 chr7A 89.016 965 85 13 1 949 609601876 609602835 0.000000e+00 1175.0
30 TraesCS2A01G271200 chr7A 85.360 888 84 24 2503 3355 445551824 445552700 0.000000e+00 878.0
31 TraesCS2A01G271200 chr7A 94.286 105 5 1 2077 2180 315997848 315997952 3.890000e-35 159.0
32 TraesCS2A01G271200 chr7A 82.569 109 10 9 2302 2404 216157470 216157365 1.860000e-13 87.9
33 TraesCS2A01G271200 chr7A 100.000 33 0 0 2406 2438 549638350 549638318 1.130000e-05 62.1
34 TraesCS2A01G271200 chr1A 86.436 1327 136 28 1 1296 128731605 128730292 0.000000e+00 1413.0
35 TraesCS2A01G271200 chr1A 85.890 1304 130 38 1 1273 173782494 173781214 0.000000e+00 1339.0
36 TraesCS2A01G271200 chr1A 80.780 1717 191 82 1 1615 441201033 441202712 0.000000e+00 1214.0
37 TraesCS2A01G271200 chr1A 83.453 834 109 24 2949 3767 455803127 455802308 0.000000e+00 749.0
38 TraesCS2A01G271200 chr1A 82.614 834 115 25 2949 3767 455753193 455752375 0.000000e+00 710.0
39 TraesCS2A01G271200 chr1A 90.979 521 24 4 1923 2420 338350607 338350087 0.000000e+00 680.0
40 TraesCS2A01G271200 chr1A 89.556 450 29 9 1385 1821 538212453 538212009 4.250000e-154 555.0
41 TraesCS2A01G271200 chr1A 95.652 69 3 0 2182 2250 507856562 507856494 1.110000e-20 111.0
42 TraesCS2A01G271200 chr1A 97.500 40 1 0 2376 2415 334398688 334398649 6.750000e-08 69.4
43 TraesCS2A01G271200 chr1A 95.000 40 2 0 2376 2415 334391649 334391610 3.140000e-06 63.9
44 TraesCS2A01G271200 chr4A 82.810 1530 170 43 1 1457 426266979 426265470 0.000000e+00 1282.0
45 TraesCS2A01G271200 chr4A 85.128 1291 138 39 1 1249 359958268 359959546 0.000000e+00 1271.0
46 TraesCS2A01G271200 chr4A 89.233 873 67 16 2406 3268 247383930 247383075 0.000000e+00 1066.0
47 TraesCS2A01G271200 chr4A 78.286 1750 212 88 1 1612 257886885 257885166 0.000000e+00 972.0
48 TraesCS2A01G271200 chr4A 81.720 1209 152 42 2579 3767 384880876 384882035 0.000000e+00 944.0
49 TraesCS2A01G271200 chr4A 85.931 725 87 12 3047 3767 322294693 322295406 0.000000e+00 760.0
50 TraesCS2A01G271200 chr4A 87.783 663 41 19 2406 3057 247376738 247376105 0.000000e+00 739.0
51 TraesCS2A01G271200 chr4A 85.359 724 89 13 3047 3767 322245220 322245929 0.000000e+00 734.0
52 TraesCS2A01G271200 chr4A 81.135 705 81 28 2406 3066 277465878 277466574 5.580000e-143 518.0
53 TraesCS2A01G271200 chr4A 88.739 222 21 3 1924 2144 354730234 354730452 6.200000e-68 268.0
54 TraesCS2A01G271200 chr4A 88.739 222 22 3 1924 2144 354738138 354738357 6.200000e-68 268.0
55 TraesCS2A01G271200 chr4A 88.667 150 15 2 1385 1533 393021343 393021195 8.310000e-42 182.0
56 TraesCS2A01G271200 chr4A 88.571 105 12 0 1924 2028 79608785 79608889 1.100000e-25 128.0
57 TraesCS2A01G271200 chr5A 85.200 1277 146 30 1 1249 192760844 192759583 0.000000e+00 1271.0
58 TraesCS2A01G271200 chr5A 84.897 1311 124 50 1 1258 81390334 81391623 0.000000e+00 1256.0
59 TraesCS2A01G271200 chr5A 93.382 544 33 3 2805 3347 450712773 450713314 0.000000e+00 802.0
60 TraesCS2A01G271200 chr5A 93.382 544 33 3 2805 3347 450728997 450729538 0.000000e+00 802.0
61 TraesCS2A01G271200 chr5A 82.494 834 116 23 2949 3765 297233893 297233073 0.000000e+00 704.0
62 TraesCS2A01G271200 chr5A 93.077 390 21 6 1552 1939 398147706 398148091 1.960000e-157 566.0
63 TraesCS2A01G271200 chr5A 93.005 386 25 2 1554 1939 128701213 128701596 2.540000e-156 562.0
64 TraesCS2A01G271200 chr5A 92.746 386 26 2 1554 1939 128685240 128685623 1.180000e-154 556.0
65 TraesCS2A01G271200 chr5A 91.753 388 30 2 1552 1939 398163627 398164012 4.280000e-149 538.0
66 TraesCS2A01G271200 chr5A 97.826 46 0 1 2376 2420 179422156 179422111 1.120000e-10 78.7
67 TraesCS2A01G271200 chr5A 97.500 40 1 0 2376 2415 271543599 271543560 6.750000e-08 69.4
68 TraesCS2A01G271200 chr5A 97.436 39 1 0 2377 2415 271540653 271540615 2.430000e-07 67.6
69 TraesCS2A01G271200 chr5A 95.000 40 2 0 2376 2415 347184601 347184562 3.140000e-06 63.9
70 TraesCS2A01G271200 chr4D 83.501 1291 152 47 1 1250 248746950 248748220 0.000000e+00 1147.0
71 TraesCS2A01G271200 chr4D 94.667 75 4 0 2244 2318 193971578 193971504 2.380000e-22 117.0
72 TraesCS2A01G271200 chr4D 94.667 75 3 1 2244 2318 193979642 193979569 8.550000e-22 115.0
73 TraesCS2A01G271200 chr6A 87.450 749 76 14 1397 2140 542819941 542820676 0.000000e+00 846.0
74 TraesCS2A01G271200 chr6A 82.150 986 124 37 2805 3765 121366426 121365468 0.000000e+00 798.0
75 TraesCS2A01G271200 chr6A 89.111 450 32 6 1385 1821 250239034 250238589 9.200000e-151 544.0
76 TraesCS2A01G271200 chr6A 88.739 222 22 3 1924 2144 131214139 131213920 6.200000e-68 268.0
77 TraesCS2A01G271200 chr6A 88.128 219 24 2 1927 2144 131206020 131205803 3.730000e-65 259.0
78 TraesCS2A01G271200 chr6A 94.286 105 5 1 2077 2180 535656855 535656751 3.890000e-35 159.0
79 TraesCS2A01G271200 chr6A 97.778 45 0 1 2376 2419 242026598 242026554 4.030000e-10 76.8
80 TraesCS2A01G271200 chr6A 97.778 45 0 1 2376 2419 242046176 242046132 4.030000e-10 76.8
81 TraesCS2A01G271200 chr6D 95.181 83 4 0 2244 2326 232956610 232956528 8.490000e-27 132.0
82 TraesCS2A01G271200 chr6D 89.796 98 10 0 2229 2326 308904201 308904104 3.950000e-25 126.0
83 TraesCS2A01G271200 chr6D 96.000 75 3 0 2244 2318 121005089 121005015 5.110000e-24 122.0
84 TraesCS2A01G271200 chr6D 92.771 83 6 0 2244 2326 232927826 232927744 1.840000e-23 121.0
85 TraesCS2A01G271200 chr6D 95.833 72 3 0 2244 2315 334164718 334164789 2.380000e-22 117.0
86 TraesCS2A01G271200 chr6D 95.833 72 3 0 2244 2315 410854147 410854076 2.380000e-22 117.0
87 TraesCS2A01G271200 chr6D 95.652 69 3 0 2244 2312 251033210 251033278 1.110000e-20 111.0
88 TraesCS2A01G271200 chr6D 94.444 72 4 0 2244 2315 251045412 251045483 1.110000e-20 111.0
89 TraesCS2A01G271200 chr6D 94.872 39 2 0 2277 2315 179756778 179756740 1.130000e-05 62.1
90 TraesCS2A01G271200 chr6D 86.441 59 3 5 2259 2315 202158729 202158674 4.060000e-05 60.2
91 TraesCS2A01G271200 chr7D 93.976 83 5 0 2244 2326 189448577 189448495 3.950000e-25 126.0
92 TraesCS2A01G271200 chr7D 93.827 81 5 0 2244 2324 363315637 363315557 5.110000e-24 122.0
93 TraesCS2A01G271200 chr7D 87.879 99 12 0 2229 2327 146130123 146130221 2.380000e-22 117.0
94 TraesCS2A01G271200 chr2D 93.976 83 5 0 2244 2326 306133319 306133401 3.950000e-25 126.0
95 TraesCS2A01G271200 chr3D 92.941 85 6 0 2242 2326 265604398 265604482 1.420000e-24 124.0
96 TraesCS2A01G271200 chr5D 91.765 85 7 0 2242 2326 311018059 311018143 6.610000e-23 119.0
97 TraesCS2A01G271200 chr5D 89.247 93 10 0 2229 2321 153778589 153778681 2.380000e-22 117.0
98 TraesCS2A01G271200 chr5D 87.755 98 11 1 2229 2326 11597762 11597858 3.080000e-21 113.0
99 TraesCS2A01G271200 chr5D 87.500 96 12 0 2229 2324 11605505 11605600 1.110000e-20 111.0


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 TraesCS2A01G271200 chr2A 442765329 442769095 3766 False 6957 6957 100.000 1 3767 1 chr2A.!!$F8 3766
1 TraesCS2A01G271200 chr2A 442808829 442811904 3075 False 4327 4327 92.253 1 3056 1 chr2A.!!$F9 3055
2 TraesCS2A01G271200 chr2A 422853860 422857259 3399 True 3904 3904 87.790 1 3355 1 chr2A.!!$R6 3354
3 TraesCS2A01G271200 chr2A 343428766 343430103 1337 True 1360 1360 85.577 1 1304 1 chr2A.!!$R4 1303
4 TraesCS2A01G271200 chr2A 706106412 706107956 1544 False 1271 1271 82.375 1 1505 1 chr2A.!!$F10 1504
5 TraesCS2A01G271200 chr2A 145739020 145740039 1019 True 1072 1072 86.157 1 999 1 chr2A.!!$R3 998
6 TraesCS2A01G271200 chr2A 159902325 159903179 854 False 1050 1050 88.914 2406 3268 1 chr2A.!!$F2 862
7 TraesCS2A01G271200 chr2A 204955491 204956505 1014 False 905 905 83.446 2364 3355 1 chr2A.!!$F4 991
8 TraesCS2A01G271200 chr2A 27243562 27244328 766 True 872 872 87.451 1385 2144 1 chr2A.!!$R1 759
9 TraesCS2A01G271200 chr2A 345053745 345054532 787 False 869 869 86.859 2570 3352 1 chr2A.!!$F7 782
10 TraesCS2A01G271200 chr2A 344747597 344748382 785 False 826 826 85.856 2563 3355 1 chr2A.!!$F6 792
11 TraesCS2A01G271200 chr2A 159910556 159911209 653 False 813 813 89.339 2406 3058 1 chr2A.!!$F3 652
12 TraesCS2A01G271200 chr2A 381314320 381315041 721 True 496 496 80.053 2552 3266 1 chr2A.!!$R5 714
13 TraesCS2A01G271200 chr3A 353893087 353894308 1221 False 1808 1808 93.540 1848 3057 1 chr3A.!!$F2 1209
14 TraesCS2A01G271200 chr3A 353633371 353634679 1308 False 1352 1352 85.736 1 1296 1 chr3A.!!$F1 1295
15 TraesCS2A01G271200 chr3A 553234195 553235083 888 False 907 907 85.165 2838 3740 1 chr3A.!!$F3 902
16 TraesCS2A01G271200 chr3A 521148702 521149433 731 True 399 399 77.910 2356 3058 1 chr3A.!!$R4 702
17 TraesCS2A01G271200 chr3A 188731750 188732264 514 True 268 268 77.532 2552 3058 1 chr3A.!!$R1 506
18 TraesCS2A01G271200 chr7A 110120680 110122016 1336 True 1448 1448 86.534 1 1330 1 chr7A.!!$R1 1329
19 TraesCS2A01G271200 chr7A 330402559 330403845 1286 False 1273 1273 85.154 1 1250 1 chr7A.!!$F3 1249
20 TraesCS2A01G271200 chr7A 330394469 330395561 1092 False 1251 1251 87.738 1 1071 1 chr7A.!!$F2 1070
21 TraesCS2A01G271200 chr7A 281819084 281820434 1350 True 1201 1201 83.370 1 1324 1 chr7A.!!$R3 1323
22 TraesCS2A01G271200 chr7A 458352160 458353420 1260 True 1188 1188 84.112 1 1250 1 chr7A.!!$R5 1249
23 TraesCS2A01G271200 chr7A 281879409 281880711 1302 True 1184 1184 83.749 1 1270 1 chr7A.!!$R4 1269
24 TraesCS2A01G271200 chr7A 609601876 609602835 959 False 1175 1175 89.016 1 949 1 chr7A.!!$F5 948
25 TraesCS2A01G271200 chr7A 445551824 445552700 876 False 878 878 85.360 2503 3355 1 chr7A.!!$F4 852
26 TraesCS2A01G271200 chr1A 128730292 128731605 1313 True 1413 1413 86.436 1 1296 1 chr1A.!!$R1 1295
27 TraesCS2A01G271200 chr1A 173781214 173782494 1280 True 1339 1339 85.890 1 1273 1 chr1A.!!$R2 1272
28 TraesCS2A01G271200 chr1A 441201033 441202712 1679 False 1214 1214 80.780 1 1615 1 chr1A.!!$F1 1614
29 TraesCS2A01G271200 chr1A 455802308 455803127 819 True 749 749 83.453 2949 3767 1 chr1A.!!$R7 818
30 TraesCS2A01G271200 chr1A 455752375 455753193 818 True 710 710 82.614 2949 3767 1 chr1A.!!$R6 818
31 TraesCS2A01G271200 chr1A 338350087 338350607 520 True 680 680 90.979 1923 2420 1 chr1A.!!$R5 497
32 TraesCS2A01G271200 chr4A 426265470 426266979 1509 True 1282 1282 82.810 1 1457 1 chr4A.!!$R5 1456
33 TraesCS2A01G271200 chr4A 359958268 359959546 1278 False 1271 1271 85.128 1 1249 1 chr4A.!!$F7 1248
34 TraesCS2A01G271200 chr4A 247383075 247383930 855 True 1066 1066 89.233 2406 3268 1 chr4A.!!$R2 862
35 TraesCS2A01G271200 chr4A 257885166 257886885 1719 True 972 972 78.286 1 1612 1 chr4A.!!$R3 1611
36 TraesCS2A01G271200 chr4A 384880876 384882035 1159 False 944 944 81.720 2579 3767 1 chr4A.!!$F8 1188
37 TraesCS2A01G271200 chr4A 322294693 322295406 713 False 760 760 85.931 3047 3767 1 chr4A.!!$F4 720
38 TraesCS2A01G271200 chr4A 247376105 247376738 633 True 739 739 87.783 2406 3057 1 chr4A.!!$R1 651
39 TraesCS2A01G271200 chr4A 322245220 322245929 709 False 734 734 85.359 3047 3767 1 chr4A.!!$F3 720
40 TraesCS2A01G271200 chr4A 277465878 277466574 696 False 518 518 81.135 2406 3066 1 chr4A.!!$F2 660
41 TraesCS2A01G271200 chr5A 192759583 192760844 1261 True 1271 1271 85.200 1 1249 1 chr5A.!!$R2 1248
42 TraesCS2A01G271200 chr5A 81390334 81391623 1289 False 1256 1256 84.897 1 1258 1 chr5A.!!$F1 1257
43 TraesCS2A01G271200 chr5A 450712773 450713314 541 False 802 802 93.382 2805 3347 1 chr5A.!!$F6 542
44 TraesCS2A01G271200 chr5A 450728997 450729538 541 False 802 802 93.382 2805 3347 1 chr5A.!!$F7 542
45 TraesCS2A01G271200 chr5A 297233073 297233893 820 True 704 704 82.494 2949 3765 1 chr5A.!!$R3 816
46 TraesCS2A01G271200 chr4D 248746950 248748220 1270 False 1147 1147 83.501 1 1250 1 chr4D.!!$F1 1249
47 TraesCS2A01G271200 chr6A 542819941 542820676 735 False 846 846 87.450 1397 2140 1 chr6A.!!$F1 743
48 TraesCS2A01G271200 chr6A 121365468 121366426 958 True 798 798 82.150 2805 3765 1 chr6A.!!$R1 960

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
391 439 1.068264 CGGCATAGCAATAGAGCGAGA 60.068 52.381 0.00 0.00 40.15 4.04 F
1723 1983 0.754217 ACAGGCCATGGCATTAGCAG 60.754 55.000 36.56 20.47 44.61 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 2634 0.927029 TCTCCTCTCGATCCCTCCAA 59.073 55.000 0.0 0.0 0.0 3.53 R
3239 3639 1.549170 TCCTCTTTCCTAACGGAGTGC 59.451 52.381 0.0 0.0 45.0 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
69 70 3.791245 AGCAACGCAAAAATCAAGGAAA 58.209 36.364 0.00 0.00 0.00 3.13
77 78 6.074569 ACGCAAAAATCAAGGAAAATAACACG 60.075 34.615 0.00 0.00 0.00 4.49
99 100 1.406539 GTATGACGGAAACTAGGGCGA 59.593 52.381 0.00 0.00 0.00 5.54
120 122 2.422127 ACAAGAGTGGAACAAAACACCG 59.578 45.455 0.00 0.00 44.16 4.94
340 382 3.054139 AGAGGCTTGACTTGGCAATATGA 60.054 43.478 0.00 0.00 0.00 2.15
391 439 1.068264 CGGCATAGCAATAGAGCGAGA 60.068 52.381 0.00 0.00 40.15 4.04
487 537 2.350522 GTCCATGCAGAAGACGAACAT 58.649 47.619 0.00 0.00 0.00 2.71
559 615 2.067365 AAAGCAACCCGGAAAGAAGT 57.933 45.000 0.73 0.00 0.00 3.01
1017 1149 4.142182 ACGGCGATGAATCCAAAAATGATT 60.142 37.500 16.62 0.00 35.21 2.57
1297 1499 6.679843 CAAAGTAGAGGAAGTAGACGTTCTT 58.320 40.000 0.00 0.00 0.00 2.52
1417 1652 1.026584 TCACGAGACGGAACTTGACA 58.973 50.000 0.00 0.00 0.00 3.58
1431 1666 0.768622 TTGACATCCACGGGGTCTTT 59.231 50.000 2.12 0.00 34.93 2.52
1514 1761 3.685865 AGGTACTTGCCGAGGTACT 57.314 52.632 0.00 0.00 36.38 2.73
1515 1762 1.934410 AGGTACTTGCCGAGGTACTT 58.066 50.000 0.00 0.00 31.69 2.24
1529 1776 2.555757 AGGTACTTGTCGTTCTTAGCGT 59.444 45.455 0.00 0.00 27.25 5.07
1723 1983 0.754217 ACAGGCCATGGCATTAGCAG 60.754 55.000 36.56 20.47 44.61 4.24
1762 2022 1.654954 GCAGCAAGCATAGCAGCAGT 61.655 55.000 7.38 0.00 43.05 4.40
1830 2090 2.510238 GCGGCGCTTGTCTGATCT 60.510 61.111 26.86 0.00 0.00 2.75
2083 2362 2.124983 GCGCAAGAGAGGCCATGA 60.125 61.111 5.01 0.00 43.02 3.07
2095 2374 1.445095 GCCATGACGAGGAGCTCAT 59.555 57.895 17.19 8.81 0.00 2.90
2458 2742 2.853430 TGGGCTTAGAGGTAAATGGGA 58.147 47.619 0.00 0.00 0.00 4.37
2459 2743 3.403322 TGGGCTTAGAGGTAAATGGGAT 58.597 45.455 0.00 0.00 0.00 3.85
2460 2744 3.394606 TGGGCTTAGAGGTAAATGGGATC 59.605 47.826 0.00 0.00 0.00 3.36
2461 2745 3.653352 GGGCTTAGAGGTAAATGGGATCT 59.347 47.826 0.00 0.00 0.00 2.75
2462 2746 4.844655 GGGCTTAGAGGTAAATGGGATCTA 59.155 45.833 0.00 0.00 0.00 1.98
2463 2747 5.489278 GGGCTTAGAGGTAAATGGGATCTAT 59.511 44.000 0.00 0.00 0.00 1.98
2464 2748 6.410540 GGCTTAGAGGTAAATGGGATCTATG 58.589 44.000 0.00 0.00 0.00 2.23
2465 2749 5.877564 GCTTAGAGGTAAATGGGATCTATGC 59.122 44.000 0.00 0.00 36.85 3.14
2466 2750 6.520742 GCTTAGAGGTAAATGGGATCTATGCA 60.521 42.308 11.35 0.00 40.55 3.96
2468 2752 8.679344 TTAGAGGTAAATGGGATCTATGCATA 57.321 34.615 6.20 6.20 0.00 3.14
2471 2755 5.792712 AGGTAAATGGGATCTATGCATAGGT 59.207 40.000 29.02 24.82 0.00 3.08
2472 2756 5.882557 GGTAAATGGGATCTATGCATAGGTG 59.117 44.000 29.02 9.25 0.00 4.00
2684 3005 5.534207 TTGAACTAGGACTTGGTTAACGA 57.466 39.130 0.00 0.00 0.00 3.85
3169 3560 3.876914 TGCTTCTTTGACAAACGAGTGAT 59.123 39.130 0.00 0.00 0.00 3.06
3219 3619 7.061905 GTCATCTTCGAGAAAAGAATACAACGA 59.938 37.037 0.00 0.00 38.69 3.85
3239 3639 9.072294 ACAACGAAAGATGAACAAAGTTAAAAG 57.928 29.630 0.00 0.00 37.33 2.27
3270 3672 3.821748 AGGAAAGAGGAACAAGGAACAC 58.178 45.455 0.00 0.00 0.00 3.32
3318 3721 1.969923 TGAGAAAAGGGTTGCAATGGG 59.030 47.619 0.59 0.00 0.00 4.00
3319 3722 2.247358 GAGAAAAGGGTTGCAATGGGA 58.753 47.619 0.59 0.00 0.00 4.37
3355 3758 1.801178 GCACTCCGGTTGAAAAGAGAG 59.199 52.381 0.00 0.00 0.00 3.20
3360 3763 1.953686 CCGGTTGAAAAGAGAGGCAAA 59.046 47.619 0.00 0.00 0.00 3.68
3389 3793 9.956640 AACTTGATGAGATAAGAGAACTTGAAT 57.043 29.630 0.00 0.00 37.53 2.57
3390 3794 9.381033 ACTTGATGAGATAAGAGAACTTGAATG 57.619 33.333 0.00 0.00 37.53 2.67
3394 3798 9.814899 GATGAGATAAGAGAACTTGAATGAAGA 57.185 33.333 0.00 0.00 37.53 2.87
3401 3805 6.049149 AGAGAACTTGAATGAAGAACACGAA 58.951 36.000 0.00 0.00 35.42 3.85
3414 3818 5.729974 AGAACACGAAACTCCAGTTAAAC 57.270 39.130 0.00 0.00 37.25 2.01
3420 3824 5.061808 CACGAAACTCCAGTTAAACGGATAG 59.938 44.000 13.84 0.00 37.25 2.08
3529 3943 2.846193 TGGAAAGAACAGAGGGAAACG 58.154 47.619 0.00 0.00 0.00 3.60
3544 3977 3.445805 GGGAAACGAGATCTTGAGAGAGT 59.554 47.826 17.27 0.00 34.85 3.24
3646 4083 5.757850 ACATCTCAAAACTGAGGTGAAAC 57.242 39.130 19.56 0.00 46.92 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 7.582319 GTGTTATTTTCCTTGATTTTTGCGTTG 59.418 33.333 0.00 0.00 0.00 4.10
60 61 6.317893 GTCATACCCGTGTTATTTTCCTTGAT 59.682 38.462 0.00 0.00 0.00 2.57
69 70 3.891422 TTCCGTCATACCCGTGTTATT 57.109 42.857 0.00 0.00 0.00 1.40
77 78 1.202615 GCCCTAGTTTCCGTCATACCC 60.203 57.143 0.00 0.00 0.00 3.69
99 100 2.422127 CGGTGTTTTGTTCCACTCTTGT 59.578 45.455 0.00 0.00 0.00 3.16
302 344 1.279271 CCTCTAACCCACCTTGTCCTG 59.721 57.143 0.00 0.00 0.00 3.86
340 382 3.649981 ACCACTTGCTATATCATGCCTCT 59.350 43.478 0.00 0.00 0.00 3.69
391 439 6.936900 TCACTTCTATCTTTGCTTGCTAGTTT 59.063 34.615 0.00 0.00 0.00 2.66
487 537 2.205074 GAGGATCCGTTCGACTACGTA 58.795 52.381 5.98 0.00 39.81 3.57
559 615 6.975772 GTGATGGTTGTTTACTTTGTTGCTTA 59.024 34.615 0.00 0.00 0.00 3.09
803 887 2.938838 TGTTATATCCGGGCCCTTTTG 58.061 47.619 22.43 3.31 0.00 2.44
807 891 1.847737 TGTTTGTTATATCCGGGCCCT 59.152 47.619 22.43 3.09 0.00 5.19
811 895 6.270064 GGATTTGTTGTTTGTTATATCCGGG 58.730 40.000 0.00 0.00 0.00 5.73
983 1112 1.901464 ATCGCCGTGGCACCTTTTT 60.901 52.632 12.86 0.00 42.06 1.94
1017 1149 0.250793 AACCGATATGTTGCCGTGGA 59.749 50.000 0.00 0.00 0.00 4.02
1052 1189 5.477291 TCATTTTTCCTTTTGCACCGGTATA 59.523 36.000 6.87 0.00 0.00 1.47
1297 1499 1.246056 CCTCCACTACGAACGTCCCA 61.246 60.000 2.45 0.00 0.00 4.37
1333 1550 1.999648 AGACCCGTGTACAACTACCA 58.000 50.000 0.00 0.00 0.00 3.25
1368 1585 5.108517 ACCTCTACAAAAACGTTGTACGAA 58.891 37.500 0.00 0.00 46.05 3.85
1383 1618 1.246056 CGTGACCCCGAACCTCTACA 61.246 60.000 0.00 0.00 0.00 2.74
1417 1652 1.562672 CCCTCAAAGACCCCGTGGAT 61.563 60.000 0.00 0.00 34.81 3.41
1431 1666 1.676635 CCACTACCGTCGACCCTCA 60.677 63.158 10.58 0.00 0.00 3.86
1505 1752 2.719426 AAGAACGACAAGTACCTCGG 57.281 50.000 9.31 0.00 34.07 4.63
1511 1758 4.863491 AGAAACGCTAAGAACGACAAGTA 58.137 39.130 0.00 0.00 0.00 2.24
1512 1759 3.714391 AGAAACGCTAAGAACGACAAGT 58.286 40.909 0.00 0.00 0.00 3.16
1514 1761 5.112220 TCTAGAAACGCTAAGAACGACAA 57.888 39.130 0.00 0.00 0.00 3.18
1515 1762 4.754372 TCTAGAAACGCTAAGAACGACA 57.246 40.909 0.00 0.00 0.00 4.35
1529 1776 4.562789 CGACGCATCTTGTTCATCTAGAAA 59.437 41.667 0.00 0.00 38.13 2.52
1669 1929 2.669569 CCAGCCCGACCACTTGTG 60.670 66.667 0.00 0.00 0.00 3.33
1817 2077 1.703438 GCTGCCAGATCAGACAAGCG 61.703 60.000 0.00 0.00 36.19 4.68
1830 2090 2.766229 TATGTAGCCCGGCTGCCA 60.766 61.111 22.95 17.86 40.45 4.92
1909 2169 1.761784 CCCTGCTGTAGATGCTCTTCT 59.238 52.381 0.00 0.00 0.00 2.85
1921 2181 3.790437 CCTCCATCGCCCTGCTGT 61.790 66.667 0.00 0.00 0.00 4.40
2083 2362 3.842923 CGCCCATGAGCTCCTCGT 61.843 66.667 12.15 0.00 32.35 4.18
2124 2403 3.080121 CTCCTCGAAGCTGGCCCT 61.080 66.667 0.00 0.00 0.00 5.19
2320 2602 3.311110 ACACACGCCCGATCCACT 61.311 61.111 0.00 0.00 0.00 4.00
2352 2634 0.927029 TCTCCTCTCGATCCCTCCAA 59.073 55.000 0.00 0.00 0.00 3.53
2458 2742 2.836981 GAGAGCCCACCTATGCATAGAT 59.163 50.000 31.14 15.47 32.05 1.98
2459 2743 2.158249 AGAGAGCCCACCTATGCATAGA 60.158 50.000 31.14 1.78 32.05 1.98
2460 2744 2.233431 GAGAGAGCCCACCTATGCATAG 59.767 54.545 24.33 24.33 0.00 2.23
2461 2745 2.158249 AGAGAGAGCCCACCTATGCATA 60.158 50.000 6.20 6.20 0.00 3.14
2462 2746 1.055040 GAGAGAGCCCACCTATGCAT 58.945 55.000 3.79 3.79 0.00 3.96
2463 2747 0.031716 AGAGAGAGCCCACCTATGCA 60.032 55.000 0.00 0.00 0.00 3.96
2464 2748 1.069978 GAAGAGAGAGCCCACCTATGC 59.930 57.143 0.00 0.00 0.00 3.14
2465 2749 2.627699 GAGAAGAGAGAGCCCACCTATG 59.372 54.545 0.00 0.00 0.00 2.23
2466 2750 2.246067 TGAGAAGAGAGAGCCCACCTAT 59.754 50.000 0.00 0.00 0.00 2.57
2468 2752 0.411452 TGAGAAGAGAGAGCCCACCT 59.589 55.000 0.00 0.00 0.00 4.00
2471 2755 0.411452 AGGTGAGAAGAGAGAGCCCA 59.589 55.000 0.00 0.00 0.00 5.36
2472 2756 1.567357 AAGGTGAGAAGAGAGAGCCC 58.433 55.000 0.00 0.00 0.00 5.19
2860 3216 6.423182 TCCATTTAAATCGAGGGAATTCACT 58.577 36.000 10.80 10.80 0.00 3.41
3194 3587 7.088272 TCGTTGTATTCTTTTCTCGAAGATGA 58.912 34.615 0.00 0.00 35.70 2.92
3198 3591 7.784176 TCTTTCGTTGTATTCTTTTCTCGAAG 58.216 34.615 0.00 0.00 37.37 3.79
3219 3619 7.706607 GGAGTGCTTTTAACTTTGTTCATCTTT 59.293 33.333 0.00 0.00 0.00 2.52
3239 3639 1.549170 TCCTCTTTCCTAACGGAGTGC 59.451 52.381 0.00 0.00 45.00 4.40
3318 3721 4.378874 GGAGTGCTTGCATGTACTTCTTTC 60.379 45.833 21.26 10.48 33.21 2.62
3319 3722 3.503748 GGAGTGCTTGCATGTACTTCTTT 59.496 43.478 21.26 2.55 33.21 2.52
3371 3774 9.429359 TGTTCTTCATTCAAGTTCTCTTATCTC 57.571 33.333 0.00 0.00 33.27 2.75
3389 3793 3.536956 ACTGGAGTTTCGTGTTCTTCA 57.463 42.857 0.00 0.00 0.00 3.02
3390 3794 5.978934 TTAACTGGAGTTTCGTGTTCTTC 57.021 39.130 0.00 0.00 39.31 2.87
3394 3798 3.310501 CCGTTTAACTGGAGTTTCGTGTT 59.689 43.478 0.00 0.00 39.31 3.32
3401 3805 3.262405 TGCCTATCCGTTTAACTGGAGTT 59.738 43.478 12.42 0.00 37.76 3.01
3414 3818 2.343101 TGTTCTTTTCGTGCCTATCCG 58.657 47.619 0.00 0.00 0.00 4.18
3420 3824 2.749621 AGGATCATGTTCTTTTCGTGCC 59.250 45.455 3.86 0.00 0.00 5.01
3529 3943 7.270757 TGTAAGCATACTCTCTCAAGATCTC 57.729 40.000 0.00 0.00 32.98 2.75
3544 3977 6.183360 CCGTTCTAGCATTTGTTGTAAGCATA 60.183 38.462 0.00 0.00 0.00 3.14
3602 4036 4.650972 TTTCCATAAGCCCACTACAAGT 57.349 40.909 0.00 0.00 0.00 3.16
3646 4083 4.545823 TTGTTTTTCGTTAGTGGCAGAG 57.454 40.909 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.