Multiple sequence alignment - TraesCS7A01G174300

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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 TraesCS7A01G174300 chr7A 100.000 4864 0 0 1 4864 128298090 128302953 0.000000e+00 8983.0
1 TraesCS7A01G174300 chr7A 90.646 1347 85 13 1746 3055 79626031 79627373 0.000000e+00 1751.0
2 TraesCS7A01G174300 chr7A 100.000 59 0 0 3394 3452 128301560 128301618 5.150000e-20 110.0
3 TraesCS7A01G174300 chr1A 90.003 3321 189 68 1 3223 38346918 38343643 0.000000e+00 4161.0
4 TraesCS7A01G174300 chr1A 92.186 883 62 6 3450 4329 38343261 38342383 0.000000e+00 1242.0
5 TraesCS7A01G174300 chr1A 82.812 192 13 5 3224 3395 38343464 38343273 2.340000e-33 154.0
6 TraesCS7A01G174300 chr1A 87.826 115 13 1 3281 3395 33835234 33835347 3.050000e-27 134.0
7 TraesCS7A01G174300 chr1A 94.643 56 1 1 3394 3449 38343239 38343186 8.670000e-13 86.1
8 TraesCS7A01G174300 chr1A 96.078 51 2 0 3232 3282 576693280 576693230 3.120000e-12 84.2
9 TraesCS7A01G174300 chr1A 94.231 52 2 1 3400 3450 576693091 576693040 1.450000e-10 78.7
10 TraesCS7A01G174300 chr1A 91.228 57 2 2 3394 3450 475637415 475637468 1.880000e-09 75.0
11 TraesCS7A01G174300 chr5D 93.850 2260 92 9 1182 3395 4661345 4663603 0.000000e+00 3360.0
12 TraesCS7A01G174300 chr5D 91.782 1010 46 10 907 1879 4661035 4662044 0.000000e+00 1371.0
13 TraesCS7A01G174300 chr5D 92.061 781 37 8 1 757 4659976 4660755 0.000000e+00 1075.0
14 TraesCS7A01G174300 chr5D 90.435 115 11 0 3281 3395 26559080 26558966 8.430000e-33 152.0
15 TraesCS7A01G174300 chr5D 93.333 60 1 2 3394 3450 4663637 4663696 8.670000e-13 86.1
16 TraesCS7A01G174300 chr2A 92.867 2257 110 23 1189 3395 547851605 547853860 0.000000e+00 3229.0
17 TraesCS7A01G174300 chr2A 89.278 1940 116 35 1 1879 671215688 671217596 0.000000e+00 2346.0
18 TraesCS7A01G174300 chr2A 93.073 895 51 7 3448 4333 547853870 547854762 0.000000e+00 1299.0
19 TraesCS7A01G174300 chr2A 89.906 852 58 13 1 830 547850441 547851286 0.000000e+00 1072.0
20 TraesCS7A01G174300 chr2A 94.216 536 30 1 4330 4864 659789308 659788773 0.000000e+00 817.0
21 TraesCS7A01G174300 chr2A 94.019 535 32 0 4330 4864 408996174 408996708 0.000000e+00 811.0
22 TraesCS7A01G174300 chr2A 93.458 535 33 2 4330 4864 632378499 632379031 0.000000e+00 793.0
23 TraesCS7A01G174300 chr2A 82.294 401 38 23 35 432 34173558 34173928 2.830000e-82 316.0
24 TraesCS7A01G174300 chr2D 92.396 2262 108 18 1192 3395 16920688 16918433 0.000000e+00 3166.0
25 TraesCS7A01G174300 chr2D 92.567 2166 112 14 1278 3395 221291612 221293776 0.000000e+00 3062.0
26 TraesCS7A01G174300 chr2D 88.000 1200 87 31 35 1189 16921933 16920746 0.000000e+00 1365.0
27 TraesCS7A01G174300 chr2D 93.236 887 49 6 3450 4329 16918421 16917539 0.000000e+00 1295.0
28 TraesCS7A01G174300 chr2D 92.404 882 63 3 3450 4329 221293788 221294667 0.000000e+00 1254.0
29 TraesCS7A01G174300 chr2D 96.552 58 0 2 3393 3450 619155591 619155536 1.440000e-15 95.3
30 TraesCS7A01G174300 chr3A 93.780 2090 98 7 1182 3240 101775640 101777728 0.000000e+00 3110.0
31 TraesCS7A01G174300 chr3A 92.679 1926 105 15 1350 3240 297824491 297822567 0.000000e+00 2743.0
32 TraesCS7A01G174300 chr3A 90.041 1938 102 36 1 1879 732954900 732952995 0.000000e+00 2425.0
33 TraesCS7A01G174300 chr3A 89.427 1343 82 21 576 1879 101775018 101776339 0.000000e+00 1639.0
34 TraesCS7A01G174300 chr3A 87.856 807 59 17 586 1354 297837478 297836673 0.000000e+00 911.0
35 TraesCS7A01G174300 chr3A 93.470 536 34 1 4330 4864 595499416 595499951 0.000000e+00 795.0
36 TraesCS7A01G174300 chr3A 93.284 536 35 1 4330 4864 391362952 391362417 0.000000e+00 789.0
37 TraesCS7A01G174300 chr3A 90.232 604 36 10 1 585 101774176 101774775 0.000000e+00 767.0
38 TraesCS7A01G174300 chr3A 89.706 612 38 12 1 591 297838338 297837731 0.000000e+00 758.0
39 TraesCS7A01G174300 chr3A 98.246 57 0 1 3394 3450 101777964 101778019 1.110000e-16 99.0
40 TraesCS7A01G174300 chr3A 94.915 59 3 0 3224 3282 732951445 732951387 5.180000e-15 93.5
41 TraesCS7A01G174300 chr4A 90.768 1614 89 18 1655 3223 605879069 605880667 0.000000e+00 2100.0
42 TraesCS7A01G174300 chr4A 92.978 883 55 3 3448 4329 294601669 294602545 0.000000e+00 1280.0
43 TraesCS7A01G174300 chr4A 94.216 536 29 2 4330 4864 557617317 557617851 0.000000e+00 817.0
44 TraesCS7A01G174300 chr4A 93.458 535 35 0 4330 4864 383412160 383412694 0.000000e+00 795.0
45 TraesCS7A01G174300 chr4A 87.179 429 35 9 26 435 294551827 294552254 2.050000e-128 470.0
46 TraesCS7A01G174300 chr4A 81.383 188 19 3 3224 3395 294601472 294601659 6.560000e-29 139.0
47 TraesCS7A01G174300 chr4A 94.737 57 0 2 3394 3450 395300289 395300236 8.670000e-13 86.1
48 TraesCS7A01G174300 chr7D 91.679 1358 66 14 1746 3067 75332846 75334192 0.000000e+00 1838.0
49 TraesCS7A01G174300 chr7D 86.255 1215 105 32 26 1189 52491018 52492221 0.000000e+00 1262.0
50 TraesCS7A01G174300 chr7D 92.063 882 62 5 3450 4329 529361548 529360673 0.000000e+00 1234.0
51 TraesCS7A01G174300 chr7D 93.043 690 45 3 1192 1879 52492279 52492967 0.000000e+00 1005.0
52 TraesCS7A01G174300 chr7D 80.978 184 12 5 3228 3395 529361736 529361560 1.840000e-24 124.0
53 TraesCS7A01G174300 chr7D 96.552 58 0 2 3393 3450 531608293 531608348 1.440000e-15 95.3
54 TraesCS7A01G174300 chr7B 91.240 1347 74 15 1746 3053 21654525 21655866 0.000000e+00 1794.0
55 TraesCS7A01G174300 chr7B 86.111 180 9 4 3232 3395 710107489 710107310 3.870000e-41 180.0
56 TraesCS7A01G174300 chr7B 86.111 180 8 5 3232 3395 710047540 710047362 1.390000e-40 178.0
57 TraesCS7A01G174300 chr7B 86.111 180 8 5 3232 3395 710119176 710118998 1.390000e-40 178.0
58 TraesCS7A01G174300 chr7B 89.916 119 11 1 3281 3399 672816650 672816767 8.430000e-33 152.0
59 TraesCS7A01G174300 chr7B 96.491 57 1 1 3394 3450 710047328 710047273 5.180000e-15 93.5
60 TraesCS7A01G174300 chr7B 96.491 57 1 1 3394 3450 710107276 710107221 5.180000e-15 93.5
61 TraesCS7A01G174300 chr7B 96.491 57 1 1 3394 3450 710129983 710129928 5.180000e-15 93.5
62 TraesCS7A01G174300 chr7B 94.737 57 1 1 3394 3450 710118964 710118910 2.410000e-13 87.9
63 TraesCS7A01G174300 chr3B 88.489 1138 91 20 3224 4331 342732655 342731528 0.000000e+00 1339.0
64 TraesCS7A01G174300 chr3B 88.360 1134 96 22 3224 4329 30963841 30962716 0.000000e+00 1330.0
65 TraesCS7A01G174300 chr3B 86.128 483 36 10 35 489 824975874 824975395 4.370000e-135 492.0
66 TraesCS7A01G174300 chr3B 84.932 146 13 4 1052 1189 30966109 30965965 6.560000e-29 139.0
67 TraesCS7A01G174300 chr6B 88.261 1133 98 19 3224 4329 447557719 447558843 0.000000e+00 1323.0
68 TraesCS7A01G174300 chr2B 86.935 1194 115 22 26 1183 51802260 51801072 0.000000e+00 1303.0
69 TraesCS7A01G174300 chr2B 86.029 1181 104 32 26 1166 723977256 723978415 0.000000e+00 1210.0
70 TraesCS7A01G174300 chr2B 92.806 695 45 3 1190 1879 723978465 723979159 0.000000e+00 1002.0
71 TraesCS7A01G174300 chr1D 92.203 885 59 6 3450 4329 369303553 369304432 0.000000e+00 1243.0
72 TraesCS7A01G174300 chr1D 90.909 110 9 1 3286 3395 438031132 438031024 3.920000e-31 147.0
73 TraesCS7A01G174300 chr1D 92.982 57 2 1 3394 3450 16289979 16289925 1.120000e-11 82.4
74 TraesCS7A01G174300 chr1D 92.982 57 2 1 3394 3450 448804204 448804258 1.120000e-11 82.4
75 TraesCS7A01G174300 chr1D 94.231 52 2 1 3400 3450 369303575 369303626 1.450000e-10 78.7
76 TraesCS7A01G174300 chr1D 89.655 58 1 3 3393 3450 416879720 416879668 8.740000e-08 69.4
77 TraesCS7A01G174300 chr5B 92.919 692 43 3 1190 1879 669731711 669732398 0.000000e+00 1002.0
78 TraesCS7A01G174300 chr5B 83.511 188 15 5 3224 3395 669733879 669734066 1.400000e-35 161.0
79 TraesCS7A01G174300 chr5A 93.470 536 34 1 4330 4864 229798640 229798105 0.000000e+00 795.0
80 TraesCS7A01G174300 chr5A 93.458 535 35 0 4330 4864 429766040 429765506 0.000000e+00 795.0
81 TraesCS7A01G174300 chr5A 84.483 174 23 4 26 197 575817776 575817947 8.370000e-38 169.0
82 TraesCS7A01G174300 chrUn 87.414 437 35 9 35 453 158031682 158031248 7.320000e-133 484.0
83 TraesCS7A01G174300 chrUn 86.111 180 8 5 3232 3395 275274910 275274732 1.390000e-40 178.0
84 TraesCS7A01G174300 chrUn 92.982 57 0 1 3394 3450 392499626 392499574 4.040000e-11 80.5
85 TraesCS7A01G174300 chrUn 92.982 57 0 1 3394 3450 392501247 392501195 4.040000e-11 80.5
86 TraesCS7A01G174300 chrUn 92.982 57 0 1 3394 3450 470982384 470982332 4.040000e-11 80.5
87 TraesCS7A01G174300 chrUn 97.368 38 0 1 3407 3444 68844582 68844618 4.060000e-06 63.9
88 TraesCS7A01G174300 chr6D 89.565 115 12 0 3281 3395 54819654 54819768 3.920000e-31 147.0
89 TraesCS7A01G174300 chr6D 92.308 52 3 1 3400 3450 19368993 19368942 6.750000e-09 73.1
90 TraesCS7A01G174300 chr6D 91.071 56 1 3 3394 3449 62077256 62077205 6.750000e-09 73.1
91 TraesCS7A01G174300 chr6D 95.349 43 1 1 3408 3450 54819812 54819853 3.140000e-07 67.6
92 TraesCS7A01G174300 chr6D 95.349 43 1 1 3408 3450 156013785 156013744 3.140000e-07 67.6
93 TraesCS7A01G174300 chr6D 95.238 42 1 1 3408 3449 232274580 232274540 1.130000e-06 65.8
94 TraesCS7A01G174300 chr1B 81.915 188 17 4 3224 3395 17944333 17944519 5.070000e-30 143.0
95 TraesCS7A01G174300 chr1B 87.826 115 14 0 3281 3395 426934176 426934290 8.490000e-28 135.0
96 TraesCS7A01G174300 chr6A 84.615 117 2 3 3232 3332 418102251 418102367 8.610000e-18 102.0
97 TraesCS7A01G174300 chr6A 98.246 57 1 0 3394 3450 441294193 441294137 3.100000e-17 100.0
98 TraesCS7A01G174300 chr6A 98.246 57 1 0 3394 3450 510233978 510233922 3.100000e-17 100.0
99 TraesCS7A01G174300 chr6A 98.246 57 0 1 3394 3450 418102440 418102495 1.110000e-16 99.0
100 TraesCS7A01G174300 chr4D 94.118 51 2 1 3400 3449 90750761 90750811 5.220000e-10 76.8
101 TraesCS7A01G174300 chr4D 90.385 52 4 1 3400 3450 267713919 267713868 3.140000e-07 67.6
102 TraesCS7A01G174300 chr4D 90.385 52 4 1 3400 3450 498072590 498072539 3.140000e-07 67.6


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 TraesCS7A01G174300 chr7A 128298090 128302953 4863 False 4546.500000 8983 100.000000 1 4864 2 chr7A.!!$F2 4863
1 TraesCS7A01G174300 chr7A 79626031 79627373 1342 False 1751.000000 1751 90.646000 1746 3055 1 chr7A.!!$F1 1309
2 TraesCS7A01G174300 chr1A 38342383 38346918 4535 True 1410.775000 4161 89.911000 1 4329 4 chr1A.!!$R1 4328
3 TraesCS7A01G174300 chr5D 4659976 4663696 3720 False 1473.025000 3360 92.756500 1 3450 4 chr5D.!!$F1 3449
4 TraesCS7A01G174300 chr2A 671215688 671217596 1908 False 2346.000000 2346 89.278000 1 1879 1 chr2A.!!$F4 1878
5 TraesCS7A01G174300 chr2A 547850441 547854762 4321 False 1866.666667 3229 91.948667 1 4333 3 chr2A.!!$F5 4332
6 TraesCS7A01G174300 chr2A 659788773 659789308 535 True 817.000000 817 94.216000 4330 4864 1 chr2A.!!$R1 534
7 TraesCS7A01G174300 chr2A 408996174 408996708 534 False 811.000000 811 94.019000 4330 4864 1 chr2A.!!$F2 534
8 TraesCS7A01G174300 chr2A 632378499 632379031 532 False 793.000000 793 93.458000 4330 4864 1 chr2A.!!$F3 534
9 TraesCS7A01G174300 chr2D 221291612 221294667 3055 False 2158.000000 3062 92.485500 1278 4329 2 chr2D.!!$F1 3051
10 TraesCS7A01G174300 chr2D 16917539 16921933 4394 True 1942.000000 3166 91.210667 35 4329 3 chr2D.!!$R2 4294
11 TraesCS7A01G174300 chr3A 297822567 297824491 1924 True 2743.000000 2743 92.679000 1350 3240 1 chr3A.!!$R1 1890
12 TraesCS7A01G174300 chr3A 101774176 101778019 3843 False 1403.750000 3110 92.921250 1 3450 4 chr3A.!!$F2 3449
13 TraesCS7A01G174300 chr3A 732951387 732954900 3513 True 1259.250000 2425 92.478000 1 3282 2 chr3A.!!$R4 3281
14 TraesCS7A01G174300 chr3A 297836673 297838338 1665 True 834.500000 911 88.781000 1 1354 2 chr3A.!!$R3 1353
15 TraesCS7A01G174300 chr3A 595499416 595499951 535 False 795.000000 795 93.470000 4330 4864 1 chr3A.!!$F1 534
16 TraesCS7A01G174300 chr3A 391362417 391362952 535 True 789.000000 789 93.284000 4330 4864 1 chr3A.!!$R2 534
17 TraesCS7A01G174300 chr4A 605879069 605880667 1598 False 2100.000000 2100 90.768000 1655 3223 1 chr4A.!!$F4 1568
18 TraesCS7A01G174300 chr4A 557617317 557617851 534 False 817.000000 817 94.216000 4330 4864 1 chr4A.!!$F3 534
19 TraesCS7A01G174300 chr4A 383412160 383412694 534 False 795.000000 795 93.458000 4330 4864 1 chr4A.!!$F2 534
20 TraesCS7A01G174300 chr4A 294601472 294602545 1073 False 709.500000 1280 87.180500 3224 4329 2 chr4A.!!$F5 1105
21 TraesCS7A01G174300 chr7D 75332846 75334192 1346 False 1838.000000 1838 91.679000 1746 3067 1 chr7D.!!$F1 1321
22 TraesCS7A01G174300 chr7D 52491018 52492967 1949 False 1133.500000 1262 89.649000 26 1879 2 chr7D.!!$F3 1853
23 TraesCS7A01G174300 chr7D 529360673 529361736 1063 True 679.000000 1234 86.520500 3228 4329 2 chr7D.!!$R1 1101
24 TraesCS7A01G174300 chr7B 21654525 21655866 1341 False 1794.000000 1794 91.240000 1746 3053 1 chr7B.!!$F1 1307
25 TraesCS7A01G174300 chr3B 342731528 342732655 1127 True 1339.000000 1339 88.489000 3224 4331 1 chr3B.!!$R1 1107
26 TraesCS7A01G174300 chr3B 30962716 30966109 3393 True 734.500000 1330 86.646000 1052 4329 2 chr3B.!!$R3 3277
27 TraesCS7A01G174300 chr6B 447557719 447558843 1124 False 1323.000000 1323 88.261000 3224 4329 1 chr6B.!!$F1 1105
28 TraesCS7A01G174300 chr2B 51801072 51802260 1188 True 1303.000000 1303 86.935000 26 1183 1 chr2B.!!$R1 1157
29 TraesCS7A01G174300 chr2B 723977256 723979159 1903 False 1106.000000 1210 89.417500 26 1879 2 chr2B.!!$F1 1853
30 TraesCS7A01G174300 chr1D 369303553 369304432 879 False 660.850000 1243 93.217000 3400 4329 2 chr1D.!!$F2 929
31 TraesCS7A01G174300 chr5B 669731711 669734066 2355 False 581.500000 1002 88.215000 1190 3395 2 chr5B.!!$F1 2205
32 TraesCS7A01G174300 chr5A 229798105 229798640 535 True 795.000000 795 93.470000 4330 4864 1 chr5A.!!$R1 534
33 TraesCS7A01G174300 chr5A 429765506 429766040 534 True 795.000000 795 93.458000 4330 4864 1 chr5A.!!$R2 534

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
879 1426 0.104120 CCGCATATCCGTGTCCTTGA 59.896 55.000 0.0 0.0 0.00 3.02 F
887 1434 1.003355 CGTGTCCTTGACCATGCCT 60.003 57.895 0.0 0.0 0.00 4.75 F
2472 3683 1.743958 CCTGGAGAAGCAAGCAATGAG 59.256 52.381 0.0 0.0 0.00 2.90 F
2958 4482 1.222936 CAGGTGCTGATGACCCTCC 59.777 63.158 0.0 0.0 33.51 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 3446 1.347707 CCTGTAGCCACCACAAAGAGA 59.652 52.381 0.00 0.0 0.0 3.10 R
2849 4372 2.223377 GGTTAACAACAGTTCTGGCTCG 59.777 50.000 8.10 0.0 0.0 5.03 R
3702 5518 0.405585 AGTGGGTTGTGGCAATAGCT 59.594 50.000 0.00 0.0 41.7 3.32 R
4241 6067 0.738389 ACCTGTTGCCGTGAAACAAG 59.262 50.000 0.07 0.0 37.1 3.16 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
30 31 5.945784 AGTAGCCAAGTTTTTGCTGATGATA 59.054 36.000 0.00 0.00 32.79 2.15
44 45 6.805713 TGCTGATGATACTCGAAATTGTAGA 58.194 36.000 0.00 0.00 0.00 2.59
247 266 0.898320 CTCCATCCTCGGTGTTGACT 59.102 55.000 0.00 0.00 0.00 3.41
360 379 1.694696 GCCGGACTTAGGGAAGATGAT 59.305 52.381 5.05 0.00 36.45 2.45
364 383 3.006323 CGGACTTAGGGAAGATGATGGAG 59.994 52.174 0.00 0.00 36.45 3.86
512 535 9.807649 CATTATTCTAAACATTCCCTCCAAAAG 57.192 33.333 0.00 0.00 0.00 2.27
539 563 9.719355 GAATTACTTTCCCACCACATAATTTTT 57.281 29.630 0.00 0.00 0.00 1.94
662 1208 2.533266 AATCACACAGCGTCTTCACT 57.467 45.000 0.00 0.00 0.00 3.41
757 1304 0.745468 AGAAATCCTAGCGTCGTCCC 59.255 55.000 0.00 0.00 0.00 4.46
877 1424 1.227556 GCCGCATATCCGTGTCCTT 60.228 57.895 0.00 0.00 0.00 3.36
879 1426 0.104120 CCGCATATCCGTGTCCTTGA 59.896 55.000 0.00 0.00 0.00 3.02
887 1434 1.003355 CGTGTCCTTGACCATGCCT 60.003 57.895 0.00 0.00 0.00 4.75
974 1682 1.974875 TCCTACCGCTCGCTGTCAA 60.975 57.895 0.00 0.00 0.00 3.18
1157 1893 2.301738 GCTAGTGCCCTCCCTTGGT 61.302 63.158 0.00 0.00 0.00 3.67
1221 2020 5.012046 AGCCATGCACTGCTAATGTAGTATA 59.988 40.000 9.92 0.00 37.02 1.47
1262 2061 7.552458 TTCGCATAATGTTGTTCATGACTAT 57.448 32.000 0.00 0.00 36.81 2.12
1299 2098 7.819415 ACTCTGATTTTATTGTGAAGATGTCGA 59.181 33.333 0.00 0.00 0.00 4.20
1387 2186 9.388506 CAATATGAGATGTTAGTATTCCCATCC 57.611 37.037 0.00 0.00 35.42 3.51
1511 2316 4.094294 GCTATTGTCGGCATGTTGTCTTTA 59.906 41.667 0.00 0.00 0.00 1.85
1535 2343 3.262915 AGCAGCTCATTGAGAAGTTAGGT 59.737 43.478 17.87 2.78 0.00 3.08
1666 2474 7.308649 GGTGATATCTTGACGAGTTATAGAGCA 60.309 40.741 3.98 0.00 0.00 4.26
1717 2525 5.343307 ACAAGGGATTGCATTGGAATTAC 57.657 39.130 7.46 2.09 0.00 1.89
1730 2538 9.023962 TGCATTGGAATTACTTCTGATTAAGTT 57.976 29.630 0.00 0.00 40.20 2.66
1811 2649 3.956199 CACTATCTGGGTTGGCATTTCAT 59.044 43.478 0.00 0.00 0.00 2.57
1814 2652 3.959535 TCTGGGTTGGCATTTCATTTC 57.040 42.857 0.00 0.00 0.00 2.17
1879 2717 5.661056 TGTCTTCTACTGTATGACTTGGG 57.339 43.478 13.11 0.00 0.00 4.12
1880 2718 4.081642 TGTCTTCTACTGTATGACTTGGGC 60.082 45.833 13.11 0.00 0.00 5.36
1881 2719 3.451178 TCTTCTACTGTATGACTTGGGCC 59.549 47.826 0.00 0.00 0.00 5.80
1882 2720 3.116096 TCTACTGTATGACTTGGGCCT 57.884 47.619 4.53 0.00 0.00 5.19
1883 2721 4.259933 TCTACTGTATGACTTGGGCCTA 57.740 45.455 4.53 0.00 0.00 3.93
1939 2805 4.072131 GTGTGGGACTTGATAAAGCTTGA 58.928 43.478 0.00 0.00 0.00 3.02
2109 3293 3.881688 GAGCTGAATACAGGAATGCATGT 59.118 43.478 0.00 0.00 43.62 3.21
2133 3321 3.196463 TGTTTGCTGCTTTTTGTGGATG 58.804 40.909 0.00 0.00 0.00 3.51
2193 3383 8.542497 TCAGGTACACACATCAGTAATTTTAC 57.458 34.615 0.00 0.00 0.00 2.01
2244 3446 6.909550 TTGTCCCATGTAAGTAAAGCAATT 57.090 33.333 0.00 0.00 0.00 2.32
2456 3667 8.511604 AGTATATGTCATTTTGTCTTTCCTGG 57.488 34.615 0.00 0.00 0.00 4.45
2466 3677 1.809547 GTCTTTCCTGGAGAAGCAAGC 59.190 52.381 11.45 0.00 35.40 4.01
2468 3679 2.158623 TCTTTCCTGGAGAAGCAAGCAA 60.159 45.455 11.45 0.00 35.40 3.91
2472 3683 1.743958 CCTGGAGAAGCAAGCAATGAG 59.256 52.381 0.00 0.00 0.00 2.90
2478 3689 2.039480 AGAAGCAAGCAATGAGTCAGGA 59.961 45.455 0.00 0.00 0.00 3.86
2516 3859 3.130340 GCAGAGGTTGTGAAAAAGGTGAA 59.870 43.478 0.00 0.00 0.00 3.18
2635 4000 3.009033 ACCTGCTATGGCTTCACAGTTTA 59.991 43.478 1.68 0.00 39.59 2.01
2958 4482 1.222936 CAGGTGCTGATGACCCTCC 59.777 63.158 0.00 0.00 33.51 4.30
3035 4559 2.706339 AGCTGGTTCTGCAGATAAGG 57.294 50.000 19.04 9.78 0.00 2.69
3078 4602 5.163141 TGCTCCCTCCGATCCAAATTAATTA 60.163 40.000 0.01 0.00 0.00 1.40
3102 4626 7.636150 AACGCTCCTCTAGTACAACTTTATA 57.364 36.000 0.00 0.00 0.00 0.98
3133 4658 6.806249 ACATGCAATATGTTTACTTTTCACCG 59.194 34.615 0.00 0.00 0.00 4.94
3334 5091 4.944619 CTGATCCCTCAGTTACATGCTA 57.055 45.455 0.00 0.00 43.35 3.49
3395 5160 5.616270 TCTTTTTAAAAATGGGGCTGGAAC 58.384 37.500 13.55 0.00 0.00 3.62
3396 5161 5.368230 TCTTTTTAAAAATGGGGCTGGAACT 59.632 36.000 13.55 0.00 0.00 3.01
3398 5163 5.993748 TTTAAAAATGGGGCTGGAACTAG 57.006 39.130 0.00 0.00 0.00 2.57
3399 5164 3.825908 AAAAATGGGGCTGGAACTAGA 57.174 42.857 0.00 0.00 0.00 2.43
3400 5165 3.825908 AAAATGGGGCTGGAACTAGAA 57.174 42.857 0.00 0.00 0.00 2.10
3401 5166 2.808906 AATGGGGCTGGAACTAGAAC 57.191 50.000 0.00 0.00 0.00 3.01
3402 5167 1.972588 ATGGGGCTGGAACTAGAACT 58.027 50.000 0.00 0.00 0.00 3.01
3403 5168 2.634639 TGGGGCTGGAACTAGAACTA 57.365 50.000 0.00 0.00 0.00 2.24
3404 5169 3.130734 TGGGGCTGGAACTAGAACTAT 57.869 47.619 0.00 0.00 0.00 2.12
3407 5172 5.224441 TGGGGCTGGAACTAGAACTATATT 58.776 41.667 0.00 0.00 0.00 1.28
3409 5174 6.159751 TGGGGCTGGAACTAGAACTATATTTT 59.840 38.462 0.00 0.00 0.00 1.82
3432 5197 7.894376 TTTTTGATTTCTTGATTGCAGGATC 57.106 32.000 0.00 0.00 29.57 3.36
3433 5198 5.587388 TTGATTTCTTGATTGCAGGATCC 57.413 39.130 2.48 2.48 29.57 3.36
3434 5199 4.602107 TGATTTCTTGATTGCAGGATCCA 58.398 39.130 15.82 0.00 29.57 3.41
3435 5200 5.018149 TGATTTCTTGATTGCAGGATCCAA 58.982 37.500 15.82 0.00 29.57 3.53
3436 5201 5.481122 TGATTTCTTGATTGCAGGATCCAAA 59.519 36.000 15.82 5.74 29.57 3.28
3437 5202 5.395682 TTTCTTGATTGCAGGATCCAAAG 57.604 39.130 15.82 4.42 29.57 2.77
3438 5203 4.305539 TCTTGATTGCAGGATCCAAAGA 57.694 40.909 15.82 8.07 0.00 2.52
3439 5204 4.665451 TCTTGATTGCAGGATCCAAAGAA 58.335 39.130 15.82 1.10 0.00 2.52
3440 5205 4.460382 TCTTGATTGCAGGATCCAAAGAAC 59.540 41.667 15.82 1.86 0.00 3.01
3441 5206 4.038271 TGATTGCAGGATCCAAAGAACT 57.962 40.909 15.82 0.00 0.00 3.01
3442 5207 5.178096 TGATTGCAGGATCCAAAGAACTA 57.822 39.130 15.82 0.00 0.00 2.24
3443 5208 5.188434 TGATTGCAGGATCCAAAGAACTAG 58.812 41.667 15.82 0.00 0.00 2.57
3444 5209 2.991250 TGCAGGATCCAAAGAACTAGC 58.009 47.619 15.82 4.13 0.00 3.42
3445 5210 2.573462 TGCAGGATCCAAAGAACTAGCT 59.427 45.455 15.82 0.00 0.00 3.32
3446 5211 3.202097 GCAGGATCCAAAGAACTAGCTC 58.798 50.000 15.82 0.00 0.00 4.09
3447 5212 3.452474 CAGGATCCAAAGAACTAGCTCG 58.548 50.000 15.82 0.00 0.00 5.03
3448 5213 3.131223 CAGGATCCAAAGAACTAGCTCGA 59.869 47.826 15.82 0.00 0.00 4.04
3449 5214 3.131400 AGGATCCAAAGAACTAGCTCGAC 59.869 47.826 15.82 0.00 0.00 4.20
3450 5215 2.631418 TCCAAAGAACTAGCTCGACG 57.369 50.000 0.00 0.00 0.00 5.12
3451 5216 1.884579 TCCAAAGAACTAGCTCGACGT 59.115 47.619 0.00 0.00 0.00 4.34
3452 5217 3.076621 TCCAAAGAACTAGCTCGACGTA 58.923 45.455 0.00 0.00 0.00 3.57
3453 5218 3.693085 TCCAAAGAACTAGCTCGACGTAT 59.307 43.478 0.00 0.00 0.00 3.06
3454 5219 3.791887 CCAAAGAACTAGCTCGACGTATG 59.208 47.826 0.00 0.00 0.00 2.39
3455 5220 4.413087 CAAAGAACTAGCTCGACGTATGT 58.587 43.478 0.00 0.00 0.00 2.29
3456 5221 4.698583 AAGAACTAGCTCGACGTATGTT 57.301 40.909 0.00 0.00 0.00 2.71
3457 5222 5.808042 AAGAACTAGCTCGACGTATGTTA 57.192 39.130 0.00 0.00 0.00 2.41
3458 5223 6.374565 AAGAACTAGCTCGACGTATGTTAT 57.625 37.500 0.00 0.00 0.00 1.89
3459 5224 5.749620 AGAACTAGCTCGACGTATGTTATG 58.250 41.667 0.00 0.00 0.00 1.90
3527 5340 2.631418 TCCAAAGAACTAGCTCGACG 57.369 50.000 0.00 0.00 0.00 5.12
3528 5341 1.884579 TCCAAAGAACTAGCTCGACGT 59.115 47.619 0.00 0.00 0.00 4.34
3836 5658 3.426159 CCGCCAAAACTAGTATGTTGCAG 60.426 47.826 0.00 0.00 0.00 4.41
3893 5718 6.374333 CCATAACTTAATGCCACAAGTGTAGT 59.626 38.462 0.00 0.00 35.23 2.73
4077 5902 8.858186 CATGATTCGTTACATGTTGCATTAAAA 58.142 29.630 2.30 0.00 38.98 1.52
4157 5983 2.582052 GACTTCCCACATGGTTGTTGA 58.418 47.619 0.00 0.00 32.34 3.18
4241 6067 1.268032 CGCAATGGCTACCAACGAATC 60.268 52.381 0.00 0.00 36.95 2.52
4250 6076 4.464112 GCTACCAACGAATCTTGTTTCAC 58.536 43.478 0.00 0.00 0.00 3.18
4256 6082 2.286772 ACGAATCTTGTTTCACGGCAAC 60.287 45.455 0.00 0.00 0.00 4.17
4281 6107 3.585748 ATTTATCGCCACAAATCGACG 57.414 42.857 0.00 0.00 37.55 5.12
4527 6355 5.664457 CTGTGTTCTCAGTGCCAGATATTA 58.336 41.667 0.00 0.00 0.00 0.98
4720 6551 6.889301 TTCTAAATTCATCCATCTCATGCC 57.111 37.500 0.00 0.00 0.00 4.40
4729 6560 3.025978 TCCATCTCATGCCCATCAAAAC 58.974 45.455 0.00 0.00 0.00 2.43
4801 6632 7.201661 CGAATAACATGGAACCGGAGAATTTTA 60.202 37.037 9.46 0.53 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.452455 CAGGTTTGCTCTACAATTTCGAGT 59.548 41.667 0.00 0.00 38.31 4.18
44 45 2.440253 TGTAGGTACAACCAGGTTTGCT 59.560 45.455 0.44 0.00 41.95 3.91
198 217 3.083997 GGGAGCCATGGTCGACCT 61.084 66.667 33.39 17.38 36.82 3.85
247 266 1.001633 GAGGGACAACGGAACTGCTTA 59.998 52.381 0.00 0.00 0.00 3.09
360 379 1.209504 GATGAAATCGTCCCACCTCCA 59.790 52.381 0.00 0.00 31.13 3.86
391 410 5.596361 GTCATCTTCCCTCTGAACTAGATCA 59.404 44.000 2.41 2.41 34.21 2.92
539 563 2.562635 TGGCGCAAACTACAGTAAACA 58.437 42.857 10.83 0.00 0.00 2.83
651 1197 0.530744 TAATCGCCAGTGAAGACGCT 59.469 50.000 0.00 0.00 37.34 5.07
662 1208 1.615883 GAGCTCCAGATCTAATCGCCA 59.384 52.381 0.87 0.00 0.00 5.69
857 1404 2.421739 GACACGGATATGCGGCCT 59.578 61.111 21.09 2.14 0.00 5.19
864 1411 2.485479 GCATGGTCAAGGACACGGATAT 60.485 50.000 0.00 0.00 33.68 1.63
866 1413 0.392998 GCATGGTCAAGGACACGGAT 60.393 55.000 0.00 0.00 33.68 4.18
954 1632 3.412879 GACAGCGAGCGGTAGGACC 62.413 68.421 0.11 0.00 34.05 4.46
965 1643 2.110213 AACGGCCTTTGACAGCGA 59.890 55.556 0.00 0.00 0.00 4.93
1075 1809 3.529341 ATGTCGCCCTGTGACGCAA 62.529 57.895 3.63 0.00 44.86 4.85
1299 2098 4.577693 CGATCACCCATTGTCTTCATCATT 59.422 41.667 0.00 0.00 0.00 2.57
1382 2181 5.139435 TCAGAATTATGTAGAGCGGATGG 57.861 43.478 0.00 0.00 0.00 3.51
1387 2186 7.649705 ACATACAGTTCAGAATTATGTAGAGCG 59.350 37.037 10.96 0.00 32.77 5.03
1471 2276 9.416794 CGACAATAGCAGATATTCTTCATACTT 57.583 33.333 0.00 0.00 31.40 2.24
1472 2277 8.031864 CCGACAATAGCAGATATTCTTCATACT 58.968 37.037 0.00 0.00 31.40 2.12
1495 2300 3.867857 TGCTATAAAGACAACATGCCGA 58.132 40.909 0.00 0.00 0.00 5.54
1511 2316 5.130145 ACCTAACTTCTCAATGAGCTGCTAT 59.870 40.000 5.18 0.00 0.00 2.97
1535 2343 9.461312 ACTGGCTTATGAGTCACATTATTAAAA 57.539 29.630 0.00 0.00 40.07 1.52
1674 2482 1.430369 AACCTTCCCAAGCTGCCTCT 61.430 55.000 0.00 0.00 0.00 3.69
1717 2525 8.729805 ATCCAGAGCTAAAACTTAATCAGAAG 57.270 34.615 0.00 0.00 0.00 2.85
1730 2538 5.221843 ACAACAGTGGTAATCCAGAGCTAAA 60.222 40.000 0.00 0.00 45.24 1.85
1814 2652 9.362539 CAGACCAAAAGAATAAATCCAGAATTG 57.637 33.333 0.00 0.00 0.00 2.32
1939 2805 8.875168 CATCCTCCCTTACACTAAGATAATCTT 58.125 37.037 0.00 0.00 40.35 2.40
1985 2851 4.383118 CCTCCGAGTGATTCACCAGTAATT 60.383 45.833 13.14 0.00 34.49 1.40
2109 3293 5.016051 TCCACAAAAAGCAGCAAACAATA 57.984 34.783 0.00 0.00 0.00 1.90
2133 3321 2.766970 ACAACAACATTGTACCGTGC 57.233 45.000 0.00 0.00 41.31 5.34
2193 3383 2.839486 ACTATGTGCACCCATATCGG 57.161 50.000 15.69 0.90 0.00 4.18
2244 3446 1.347707 CCTGTAGCCACCACAAAGAGA 59.652 52.381 0.00 0.00 0.00 3.10
2456 3667 2.419324 CCTGACTCATTGCTTGCTTCTC 59.581 50.000 0.00 0.00 0.00 2.87
2466 3677 6.814506 ATTTCACTCTTTCCTGACTCATTG 57.185 37.500 0.00 0.00 0.00 2.82
2468 3679 7.487822 TCTATTTCACTCTTTCCTGACTCAT 57.512 36.000 0.00 0.00 0.00 2.90
2472 3683 5.877012 TGCATCTATTTCACTCTTTCCTGAC 59.123 40.000 0.00 0.00 0.00 3.51
2478 3689 6.059787 ACCTCTGCATCTATTTCACTCTTT 57.940 37.500 0.00 0.00 0.00 2.52
2635 4000 2.769095 GAGGAACTGAGTAGGGAGCATT 59.231 50.000 0.00 0.00 41.55 3.56
2675 4043 6.362248 TGATAGGTTTTACCATTTAGGAGGC 58.638 40.000 0.00 0.00 41.95 4.70
2849 4372 2.223377 GGTTAACAACAGTTCTGGCTCG 59.777 50.000 8.10 0.00 0.00 5.03
3028 4552 8.552296 AGATTGAATGTTACCTTGACCTTATCT 58.448 33.333 0.00 0.00 0.00 1.98
3035 4559 5.163713 GGAGCAGATTGAATGTTACCTTGAC 60.164 44.000 0.00 0.00 0.00 3.18
3078 4602 4.868314 AAAGTTGTACTAGAGGAGCGTT 57.132 40.909 0.00 0.00 0.00 4.84
3133 4658 4.261447 GGAAAACATACAACCACACCTCAC 60.261 45.833 0.00 0.00 0.00 3.51
3334 5091 6.537453 AACTAGAGTAATGATGTGTCAGCT 57.463 37.500 0.00 0.00 37.87 4.24
3381 5142 2.649816 AGTTCTAGTTCCAGCCCCATTT 59.350 45.455 0.00 0.00 0.00 2.32
3409 5174 6.014413 TGGATCCTGCAATCAAGAAATCAAAA 60.014 34.615 14.23 0.00 0.00 2.44
3411 5176 5.018149 TGGATCCTGCAATCAAGAAATCAA 58.982 37.500 14.23 0.00 0.00 2.57
3413 5178 5.587388 TTGGATCCTGCAATCAAGAAATC 57.413 39.130 14.23 0.00 0.00 2.17
3418 5183 4.461781 AGTTCTTTGGATCCTGCAATCAAG 59.538 41.667 14.23 4.16 0.00 3.02
3419 5184 4.410099 AGTTCTTTGGATCCTGCAATCAA 58.590 39.130 14.23 0.00 0.00 2.57
3420 5185 4.038271 AGTTCTTTGGATCCTGCAATCA 57.962 40.909 14.23 0.00 0.00 2.57
3421 5186 4.036144 GCTAGTTCTTTGGATCCTGCAATC 59.964 45.833 14.23 0.08 0.00 2.67
3422 5187 3.950395 GCTAGTTCTTTGGATCCTGCAAT 59.050 43.478 14.23 0.00 0.00 3.56
3423 5188 3.009473 AGCTAGTTCTTTGGATCCTGCAA 59.991 43.478 14.23 2.43 0.00 4.08
3424 5189 2.573462 AGCTAGTTCTTTGGATCCTGCA 59.427 45.455 14.23 0.00 0.00 4.41
3425 5190 3.202097 GAGCTAGTTCTTTGGATCCTGC 58.798 50.000 14.23 3.68 0.00 4.85
3426 5191 3.131223 TCGAGCTAGTTCTTTGGATCCTG 59.869 47.826 14.23 3.49 0.00 3.86
3427 5192 3.131400 GTCGAGCTAGTTCTTTGGATCCT 59.869 47.826 14.23 0.00 0.00 3.24
3428 5193 3.449632 GTCGAGCTAGTTCTTTGGATCC 58.550 50.000 4.20 4.20 0.00 3.36
3429 5194 3.109619 CGTCGAGCTAGTTCTTTGGATC 58.890 50.000 4.99 0.00 0.00 3.36
3430 5195 2.492484 ACGTCGAGCTAGTTCTTTGGAT 59.508 45.455 0.00 0.00 0.00 3.41
3431 5196 1.884579 ACGTCGAGCTAGTTCTTTGGA 59.115 47.619 0.00 0.00 0.00 3.53
3432 5197 2.349297 ACGTCGAGCTAGTTCTTTGG 57.651 50.000 0.00 0.00 0.00 3.28
3433 5198 4.413087 ACATACGTCGAGCTAGTTCTTTG 58.587 43.478 0.00 0.00 0.00 2.77
3434 5199 4.698583 ACATACGTCGAGCTAGTTCTTT 57.301 40.909 0.00 0.00 0.00 2.52
3435 5200 4.698583 AACATACGTCGAGCTAGTTCTT 57.301 40.909 0.00 0.00 0.00 2.52
3436 5201 5.296283 ACATAACATACGTCGAGCTAGTTCT 59.704 40.000 0.00 0.00 0.00 3.01
3437 5202 5.508872 ACATAACATACGTCGAGCTAGTTC 58.491 41.667 0.00 0.00 0.00 3.01
3438 5203 5.496133 ACATAACATACGTCGAGCTAGTT 57.504 39.130 0.00 0.00 0.00 2.24
3439 5204 5.093169 GACATAACATACGTCGAGCTAGT 57.907 43.478 0.00 0.00 0.00 2.57
3447 5212 7.642978 AGTTAATGAGTCGACATAACATACGTC 59.357 37.037 19.50 2.69 0.00 4.34
3448 5213 7.478322 AGTTAATGAGTCGACATAACATACGT 58.522 34.615 19.50 0.00 0.00 3.57
3449 5214 7.909777 AGTTAATGAGTCGACATAACATACG 57.090 36.000 19.50 0.00 0.00 3.06
3452 5217 9.517609 GTTCTAGTTAATGAGTCGACATAACAT 57.482 33.333 19.50 13.83 0.00 2.71
3453 5218 8.737175 AGTTCTAGTTAATGAGTCGACATAACA 58.263 33.333 19.50 12.17 0.00 2.41
3527 5340 4.640789 ATTGTCCGTGATCTAGAGTCAC 57.359 45.455 18.09 18.09 41.91 3.67
3528 5341 5.661056 AAATTGTCCGTGATCTAGAGTCA 57.339 39.130 0.00 0.00 0.00 3.41
3702 5518 0.405585 AGTGGGTTGTGGCAATAGCT 59.594 50.000 0.00 0.00 41.70 3.32
3836 5658 4.361451 TCCAGTCGTCGTAATAGGAAAC 57.639 45.455 0.00 0.00 0.00 2.78
3893 5718 1.698506 AGGCATTTTTCCACGAACCA 58.301 45.000 0.00 0.00 0.00 3.67
3944 5769 8.550376 GTGGCAATATTAAATTGTGGCAATAAG 58.450 33.333 8.83 0.00 44.98 1.73
4157 5983 5.720371 TGTGGCAATAAAGTGTGCTATTT 57.280 34.783 0.00 0.00 40.70 1.40
4202 6028 3.133901 TGCGACTGGACACATGGTAATAT 59.866 43.478 0.00 0.00 0.00 1.28
4241 6067 0.738389 ACCTGTTGCCGTGAAACAAG 59.262 50.000 0.07 0.00 37.10 3.16
4250 6076 1.263217 GGCGATAAATACCTGTTGCCG 59.737 52.381 0.00 0.00 31.90 5.69
4256 6082 4.509970 TCGATTTGTGGCGATAAATACCTG 59.490 41.667 3.50 0.00 0.00 4.00
4281 6107 4.673311 ACAAAATTGTTCGTCGCAATACAC 59.327 37.500 0.00 0.00 38.47 2.90
4473 6301 2.113139 CACTTGGCCACGAGGGTT 59.887 61.111 17.43 0.00 39.65 4.11
4676 6507 6.415573 AGAAAACACAACTCTCTGTACCTTT 58.584 36.000 0.00 0.00 0.00 3.11
4720 6551 5.621197 TGTTAGTGGATTCGTTTTGATGG 57.379 39.130 0.00 0.00 0.00 3.51
4729 6560 4.935205 TGATCAACCTTGTTAGTGGATTCG 59.065 41.667 0.00 0.00 0.00 3.34
4801 6632 8.881262 CCCATTGAGGTAACCTAGTATTATTCT 58.119 37.037 0.00 0.00 31.76 2.40


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

AutoCloner maintained by Alex Coulton.