Multiple sequence alignment - TraesCS2B01G259000

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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 TraesCS2B01G259000 chr2B 100.000 6025 0 0 641 6665 320341077 320347101 0.000000e+00 11127.0
1 TraesCS2B01G259000 chr2B 100.000 322 0 0 1 322 320340437 320340758 4.450000e-166 595.0
2 TraesCS2B01G259000 chr2B 95.263 190 7 2 29 216 134306033 134305844 3.910000e-77 300.0
3 TraesCS2B01G259000 chr2B 96.032 126 4 1 4629 4753 49128606 49128731 3.150000e-48 204.0
4 TraesCS2B01G259000 chr2B 95.946 74 0 3 27 98 460563990 460564062 4.220000e-22 117.0
5 TraesCS2B01G259000 chr2B 93.421 76 3 2 23 97 49123645 49123719 1.960000e-20 111.0
6 TraesCS2B01G259000 chr2B 92.424 66 2 2 3495 3557 546204114 546204049 2.560000e-14 91.6
7 TraesCS2B01G259000 chr3B 96.956 4303 104 15 641 4922 328467090 328471386 0.000000e+00 7195.0
8 TraesCS2B01G259000 chr3B 95.633 4305 162 14 645 4928 632785826 632790125 0.000000e+00 6885.0
9 TraesCS2B01G259000 chr3B 95.255 4278 159 22 641 4897 322354772 322359026 0.000000e+00 6735.0
10 TraesCS2B01G259000 chr3B 96.761 1760 35 2 4927 6665 328471434 328473192 0.000000e+00 2915.0
11 TraesCS2B01G259000 chr3B 95.398 1760 54 11 4926 6662 632790163 632791918 0.000000e+00 2776.0
12 TraesCS2B01G259000 chr3B 92.984 955 45 3 3080 4033 347920102 347919169 0.000000e+00 1373.0
13 TraesCS2B01G259000 chr3B 93.078 679 35 5 5987 6665 628846900 628847566 0.000000e+00 983.0
14 TraesCS2B01G259000 chr3B 92.718 618 22 3 5366 5962 85699885 85700500 0.000000e+00 870.0
15 TraesCS2B01G259000 chr3B 86.752 702 44 19 2368 3034 456613157 456612470 0.000000e+00 736.0
16 TraesCS2B01G259000 chr3B 96.622 296 9 1 27 322 328466781 328467075 2.160000e-134 490.0
17 TraesCS2B01G259000 chr3B 95.817 263 9 2 27 288 322354106 322354367 2.220000e-114 424.0
18 TraesCS2B01G259000 chr3B 96.774 217 5 2 5366 5582 327810018 327810232 1.770000e-95 361.0
19 TraesCS2B01G259000 chr4D 97.010 2575 56 10 2367 4922 249168074 249165502 0.000000e+00 4309.0
20 TraesCS2B01G259000 chr4D 95.516 1628 66 5 699 2323 249193623 249192000 0.000000e+00 2595.0
21 TraesCS2B01G259000 chr4D 96.536 433 9 2 4926 5357 249165456 249165029 0.000000e+00 712.0
22 TraesCS2B01G259000 chr4D 94.700 434 14 4 4926 5357 266761034 266760608 0.000000e+00 665.0
23 TraesCS2B01G259000 chr4D 96.907 194 4 1 6474 6665 192252468 192252275 2.320000e-84 324.0
24 TraesCS2B01G259000 chr4D 96.512 172 6 0 4751 4922 266761251 266761080 1.090000e-72 285.0
25 TraesCS2B01G259000 chr4D 92.670 191 10 3 4294 4480 106660881 106661071 8.520000e-69 272.0
26 TraesCS2B01G259000 chr4D 83.333 192 17 7 4746 4922 157233873 157234064 5.350000e-36 163.0
27 TraesCS2B01G259000 chr4D 90.678 118 11 0 4805 4922 448359092 448358975 2.490000e-34 158.0
28 TraesCS2B01G259000 chr4D 88.764 89 6 4 27 113 130359959 130359873 9.140000e-19 106.0
29 TraesCS2B01G259000 chr4D 78.977 176 22 12 29 200 249194325 249194161 9.140000e-19 106.0
30 TraesCS2B01G259000 chr4D 95.312 64 3 0 5899 5962 249136493 249136556 1.180000e-17 102.0
31 TraesCS2B01G259000 chr6B 96.272 2173 63 5 2767 4922 462293657 462295828 0.000000e+00 3548.0
32 TraesCS2B01G259000 chr6B 96.447 1942 62 6 831 2771 462282982 462284917 0.000000e+00 3197.0
33 TraesCS2B01G259000 chr6B 96.141 1762 44 4 4926 6665 462295874 462297633 0.000000e+00 2856.0
34 TraesCS2B01G259000 chr6B 85.965 456 43 6 5987 6441 123579693 123580128 1.010000e-127 468.0
35 TraesCS2B01G259000 chr6B 96.815 157 3 2 641 797 462282831 462282985 1.840000e-65 261.0
36 TraesCS2B01G259000 chr6B 85.792 183 19 4 4746 4921 129868607 129868425 3.170000e-43 187.0
37 TraesCS2B01G259000 chr2A 92.293 1557 78 13 3080 4616 645828503 645826969 0.000000e+00 2172.0
38 TraesCS2B01G259000 chr2A 90.909 1034 56 9 3214 4242 356885359 356884359 0.000000e+00 1354.0
39 TraesCS2B01G259000 chr2A 89.409 491 25 4 5434 5902 279780089 279780574 1.600000e-165 593.0
40 TraesCS2B01G259000 chr2A 91.455 433 18 8 4926 5357 380539477 380539891 1.610000e-160 577.0
41 TraesCS2B01G259000 chr2A 92.973 370 20 4 4249 4616 356875632 356875267 9.840000e-148 534.0
42 TraesCS2B01G259000 chr2A 96.552 174 5 1 4749 4922 380539259 380539431 3.040000e-73 287.0
43 TraesCS2B01G259000 chr2D 94.196 1344 51 5 1750 3072 298537645 298538982 0.000000e+00 2025.0
44 TraesCS2B01G259000 chr2D 91.538 130 9 2 4629 4756 292660366 292660237 1.910000e-40 178.0
45 TraesCS2B01G259000 chr2D 84.293 191 15 3 4746 4922 358942163 358942352 8.890000e-39 172.0
46 TraesCS2B01G259000 chr5A 93.650 1244 61 11 999 2241 122832925 122834151 0.000000e+00 1844.0
47 TraesCS2B01G259000 chr5A 86.469 1722 176 25 678 2372 274965255 274966946 0.000000e+00 1836.0
48 TraesCS2B01G259000 chr5A 89.698 796 40 12 3080 3871 122835067 122835824 0.000000e+00 977.0
49 TraesCS2B01G259000 chr5A 93.088 217 5 2 5366 5582 456529220 456529426 6.490000e-80 309.0
50 TraesCS2B01G259000 chr5A 82.402 358 40 18 2368 2705 80929827 80930181 2.350000e-74 291.0
51 TraesCS2B01G259000 chr5A 92.025 163 11 2 141 303 274964720 274964880 1.870000e-55 228.0
52 TraesCS2B01G259000 chr5A 95.935 123 5 0 4629 4751 205457798 205457920 4.080000e-47 200.0
53 TraesCS2B01G259000 chr4B 91.019 1325 99 14 641 1962 442238367 442237060 0.000000e+00 1770.0
54 TraesCS2B01G259000 chr4B 92.761 967 59 10 999 1962 167719133 167718175 0.000000e+00 1387.0
55 TraesCS2B01G259000 chr4B 92.078 972 66 10 994 1962 427399140 427398177 0.000000e+00 1358.0
56 TraesCS2B01G259000 chr4B 95.238 672 29 3 5994 6665 287898086 287897418 0.000000e+00 1061.0
57 TraesCS2B01G259000 chr4B 93.769 337 15 1 5366 5696 465832701 465833037 9.980000e-138 501.0
58 TraesCS2B01G259000 chr4B 93.182 176 11 1 4748 4922 340780859 340781034 2.380000e-64 257.0
59 TraesCS2B01G259000 chr4B 96.800 125 4 0 4629 4753 47121639 47121515 6.770000e-50 209.0
60 TraesCS2B01G259000 chr4B 96.825 126 3 1 4629 4753 241686415 241686540 6.770000e-50 209.0
61 TraesCS2B01G259000 chr4B 95.200 125 5 1 4629 4752 283152771 283152647 5.270000e-46 196.0
62 TraesCS2B01G259000 chr4B 94.444 126 6 1 4629 4753 138849015 138848890 6.820000e-45 193.0
63 TraesCS2B01G259000 chr4B 85.864 191 13 6 4746 4922 527928500 527928310 2.450000e-44 191.0
64 TraesCS2B01G259000 chr4B 92.174 115 8 1 27 140 413716773 413716887 1.920000e-35 161.0
65 TraesCS2B01G259000 chr4B 83.243 185 18 2 4751 4922 465831445 465831629 2.490000e-34 158.0
66 TraesCS2B01G259000 chr4B 95.312 64 3 0 5899 5962 240639650 240639587 1.180000e-17 102.0
67 TraesCS2B01G259000 chr6A 89.929 1122 66 9 3133 4246 587377950 587376868 0.000000e+00 1402.0
68 TraesCS2B01G259000 chr6A 91.434 537 28 7 2531 3065 11893610 11894130 0.000000e+00 721.0
69 TraesCS2B01G259000 chr6A 91.917 433 15 7 4926 5357 121236392 121236805 7.450000e-164 588.0
70 TraesCS2B01G259000 chr6A 96.354 192 7 0 6474 6665 409741156 409741347 3.880000e-82 316.0
71 TraesCS2B01G259000 chr6A 89.831 236 24 0 2129 2364 301682702 301682467 3.020000e-78 303.0
72 TraesCS2B01G259000 chr6A 96.512 172 5 1 4751 4922 121236176 121236346 3.930000e-72 283.0
73 TraesCS2B01G259000 chr6A 94.118 170 10 0 2368 2537 11893417 11893586 6.630000e-65 259.0
74 TraesCS2B01G259000 chr6A 96.032 126 4 1 4629 4753 356107068 356106943 3.150000e-48 204.0
75 TraesCS2B01G259000 chr6A 95.238 126 5 1 4629 4753 318625677 318625802 1.470000e-46 198.0
76 TraesCS2B01G259000 chr6A 80.000 135 18 6 4629 4756 269911717 269911849 2.560000e-14 91.6
77 TraesCS2B01G259000 chr6A 96.078 51 1 1 4249 4299 587376846 587376797 1.540000e-11 82.4
78 TraesCS2B01G259000 chr3D 91.040 904 48 14 3080 3952 288639393 288640294 0.000000e+00 1190.0
79 TraesCS2B01G259000 chr3D 92.537 67 5 0 4270 4336 564762712 564762646 5.500000e-16 97.1
80 TraesCS2B01G259000 chr1B 95.441 680 29 2 5987 6665 327716091 327716769 0.000000e+00 1083.0
81 TraesCS2B01G259000 chr1B 94.857 175 9 0 4748 4922 303012908 303013082 2.370000e-69 274.0
82 TraesCS2B01G259000 chr1B 85.641 195 26 2 5710 5902 220393084 220393278 3.150000e-48 204.0
83 TraesCS2B01G259000 chr1B 96.000 125 5 0 4629 4753 529120468 529120344 3.150000e-48 204.0
84 TraesCS2B01G259000 chr3A 92.489 679 31 8 5987 6665 301064864 301064206 0.000000e+00 953.0
85 TraesCS2B01G259000 chr3A 90.835 491 22 7 5434 5902 596167131 596166642 2.620000e-178 636.0
86 TraesCS2B01G259000 chr3A 91.026 390 34 1 5987 6376 39916341 39916729 5.920000e-145 525.0
87 TraesCS2B01G259000 chr6D 91.376 603 45 4 671 1273 366992757 366992162 0.000000e+00 819.0
88 TraesCS2B01G259000 chr6D 91.993 537 25 7 2531 3065 10401067 10401587 0.000000e+00 737.0
89 TraesCS2B01G259000 chr6D 83.200 250 27 12 28 274 366993354 366993117 1.460000e-51 215.0
90 TraesCS2B01G259000 chr6D 95.238 63 3 0 5899 5961 428045707 428045645 4.250000e-17 100.0
91 TraesCS2B01G259000 chr5B 88.496 565 31 11 5366 5902 430299647 430300205 0.000000e+00 652.0
92 TraesCS2B01G259000 chr5B 88.957 489 31 7 4147 4616 88875677 88875193 3.460000e-162 582.0
93 TraesCS2B01G259000 chr5B 89.723 253 12 5 4926 5177 235762979 235762740 1.800000e-80 311.0
94 TraesCS2B01G259000 chr5B 94.286 175 10 0 4748 4922 235763199 235763025 1.100000e-67 268.0
95 TraesCS2B01G259000 chr5B 89.655 87 5 3 27 110 197370436 197370521 2.540000e-19 108.0
96 TraesCS2B01G259000 chr5D 90.531 433 22 7 4926 5357 53010090 53009676 7.550000e-154 555.0
97 TraesCS2B01G259000 chr7D 89.572 374 19 9 2536 2890 176344491 176344863 2.190000e-124 457.0
98 TraesCS2B01G259000 chr7D 100.000 64 0 0 5899 5962 289566011 289566074 1.170000e-22 119.0
99 TraesCS2B01G259000 chr7D 100.000 64 0 0 5899 5962 291384186 291384123 1.170000e-22 119.0
100 TraesCS2B01G259000 chr7B 94.218 294 16 1 4629 4922 90425860 90426152 1.320000e-121 448.0
101 TraesCS2B01G259000 chr7B 95.434 219 3 2 5139 5357 666894866 666894655 6.400000e-90 342.0
102 TraesCS2B01G259000 chr7B 92.593 81 3 3 29 107 428791699 428791620 5.460000e-21 113.0
103 TraesCS2B01G259000 chr4A 88.770 374 22 9 2536 2890 242661014 242660642 2.210000e-119 440.0
104 TraesCS2B01G259000 chr7A 88.235 289 21 10 3959 4246 327389210 327389486 3.850000e-87 333.0
105 TraesCS2B01G259000 chr7A 81.053 190 23 5 4746 4922 404983847 404984036 9.010000e-29 139.0
106 TraesCS2B01G259000 chr1A 95.902 122 5 0 4632 4753 239943635 239943514 1.470000e-46 198.0
107 TraesCS2B01G259000 chr1A 95.238 126 5 1 4629 4753 352917192 352917317 1.470000e-46 198.0
108 TraesCS2B01G259000 chrUn 84.545 110 5 9 6414 6511 77287320 77287211 1.530000e-16 99.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G259000 chr2B 320340437 320347101 6664 False 5861.000000 11127 100.000000 1 6665 2 chr2B.!!$F4 6664
1 TraesCS2B01G259000 chr3B 632785826 632791918 6092 False 4830.500000 6885 95.515500 645 6662 2 chr3B.!!$F6 6017
2 TraesCS2B01G259000 chr3B 322354106 322359026 4920 False 3579.500000 6735 95.536000 27 4897 2 chr3B.!!$F4 4870
3 TraesCS2B01G259000 chr3B 328466781 328473192 6411 False 3533.333333 7195 96.779667 27 6665 3 chr3B.!!$F5 6638
4 TraesCS2B01G259000 chr3B 347919169 347920102 933 True 1373.000000 1373 92.984000 3080 4033 1 chr3B.!!$R1 953
5 TraesCS2B01G259000 chr3B 628846900 628847566 666 False 983.000000 983 93.078000 5987 6665 1 chr3B.!!$F3 678
6 TraesCS2B01G259000 chr3B 85699885 85700500 615 False 870.000000 870 92.718000 5366 5962 1 chr3B.!!$F1 596
7 TraesCS2B01G259000 chr3B 456612470 456613157 687 True 736.000000 736 86.752000 2368 3034 1 chr3B.!!$R2 666
8 TraesCS2B01G259000 chr4D 249165029 249168074 3045 True 2510.500000 4309 96.773000 2367 5357 2 chr4D.!!$R4 2990
9 TraesCS2B01G259000 chr4D 249192000 249194325 2325 True 1350.500000 2595 87.246500 29 2323 2 chr4D.!!$R5 2294
10 TraesCS2B01G259000 chr4D 266760608 266761251 643 True 475.000000 665 95.606000 4751 5357 2 chr4D.!!$R6 606
11 TraesCS2B01G259000 chr6B 462293657 462297633 3976 False 3202.000000 3548 96.206500 2767 6665 2 chr6B.!!$F3 3898
12 TraesCS2B01G259000 chr6B 462282831 462284917 2086 False 1729.000000 3197 96.631000 641 2771 2 chr6B.!!$F2 2130
13 TraesCS2B01G259000 chr2A 645826969 645828503 1534 True 2172.000000 2172 92.293000 3080 4616 1 chr2A.!!$R3 1536
14 TraesCS2B01G259000 chr2A 356884359 356885359 1000 True 1354.000000 1354 90.909000 3214 4242 1 chr2A.!!$R2 1028
15 TraesCS2B01G259000 chr2A 380539259 380539891 632 False 432.000000 577 94.003500 4749 5357 2 chr2A.!!$F2 608
16 TraesCS2B01G259000 chr2D 298537645 298538982 1337 False 2025.000000 2025 94.196000 1750 3072 1 chr2D.!!$F1 1322
17 TraesCS2B01G259000 chr5A 122832925 122835824 2899 False 1410.500000 1844 91.674000 999 3871 2 chr5A.!!$F4 2872
18 TraesCS2B01G259000 chr5A 274964720 274966946 2226 False 1032.000000 1836 89.247000 141 2372 2 chr5A.!!$F5 2231
19 TraesCS2B01G259000 chr4B 442237060 442238367 1307 True 1770.000000 1770 91.019000 641 1962 1 chr4B.!!$R8 1321
20 TraesCS2B01G259000 chr4B 167718175 167719133 958 True 1387.000000 1387 92.761000 999 1962 1 chr4B.!!$R3 963
21 TraesCS2B01G259000 chr4B 427398177 427399140 963 True 1358.000000 1358 92.078000 994 1962 1 chr4B.!!$R7 968
22 TraesCS2B01G259000 chr4B 287897418 287898086 668 True 1061.000000 1061 95.238000 5994 6665 1 chr4B.!!$R6 671
23 TraesCS2B01G259000 chr4B 465831445 465833037 1592 False 329.500000 501 88.506000 4751 5696 2 chr4B.!!$F4 945
24 TraesCS2B01G259000 chr6A 587376797 587377950 1153 True 742.200000 1402 93.003500 3133 4299 2 chr6A.!!$R3 1166
25 TraesCS2B01G259000 chr6A 11893417 11894130 713 False 490.000000 721 92.776000 2368 3065 2 chr6A.!!$F4 697
26 TraesCS2B01G259000 chr6A 121236176 121236805 629 False 435.500000 588 94.214500 4751 5357 2 chr6A.!!$F5 606
27 TraesCS2B01G259000 chr3D 288639393 288640294 901 False 1190.000000 1190 91.040000 3080 3952 1 chr3D.!!$F1 872
28 TraesCS2B01G259000 chr1B 327716091 327716769 678 False 1083.000000 1083 95.441000 5987 6665 1 chr1B.!!$F3 678
29 TraesCS2B01G259000 chr3A 301064206 301064864 658 True 953.000000 953 92.489000 5987 6665 1 chr3A.!!$R1 678
30 TraesCS2B01G259000 chr6D 10401067 10401587 520 False 737.000000 737 91.993000 2531 3065 1 chr6D.!!$F1 534
31 TraesCS2B01G259000 chr6D 366992162 366993354 1192 True 517.000000 819 87.288000 28 1273 2 chr6D.!!$R2 1245
32 TraesCS2B01G259000 chr5B 430299647 430300205 558 False 652.000000 652 88.496000 5366 5902 1 chr5B.!!$F2 536

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
25 26 0.677731 ATGATTGTGTCCCCTGTGCG 60.678 55.000 0.00 0.0 0.00 5.34 F
860 1243 2.211619 ATTTTCCGCGGTCGTCGGTA 62.212 55.000 27.15 0.0 46.49 4.02 F
2130 2553 3.536917 TCCGGCGGCGAGATGAAT 61.537 61.111 34.49 0.0 0.00 2.57 F
2331 2755 0.251341 GGCCACCATCTTCACCAACT 60.251 55.000 0.00 0.0 0.00 3.16 F
4247 5408 0.322975 AATGGCGTCTTCAGCTCAGT 59.677 50.000 0.00 0.0 34.52 3.41 F
4924 6122 0.253044 GATGCCTCTGTGCCTAACCA 59.747 55.000 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 1973 2.037772 ACCAGTCAGTCAGTCATGTTCC 59.962 50.000 0.00 0.0 0.00 3.62 R
2156 2580 0.172578 CACACGAGGCGGAAGTGATA 59.827 55.000 10.55 0.0 39.04 2.15 R
3861 5019 2.105128 CCTGGCTCGTCATCGTCC 59.895 66.667 0.00 0.0 38.33 4.79 R
4522 5703 6.183361 CCTTTCTCCTATAGAGGGCATTTTCT 60.183 42.308 2.96 0.0 43.94 2.52 R
5068 6977 3.561310 CAGCAATATAGCGAACATGTGGT 59.439 43.478 0.00 0.0 40.15 4.16 R
6205 8186 7.108841 ACAGGAAATATACTAGCGAGAACAA 57.891 36.000 0.00 0.0 0.00 2.83 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
23 24 5.894807 GAAAATATGATTGTGTCCCCTGTG 58.105 41.667 0.00 0.00 0.00 3.66
24 25 2.418368 TATGATTGTGTCCCCTGTGC 57.582 50.000 0.00 0.00 0.00 4.57
25 26 0.677731 ATGATTGTGTCCCCTGTGCG 60.678 55.000 0.00 0.00 0.00 5.34
87 88 7.653767 CAGAATATTATTCTGTTACCCCGTC 57.346 40.000 27.48 0.00 40.63 4.79
88 89 7.442656 CAGAATATTATTCTGTTACCCCGTCT 58.557 38.462 27.48 0.52 40.63 4.18
90 91 6.989155 ATATTATTCTGTTACCCCGTCTCA 57.011 37.500 0.00 0.00 0.00 3.27
236 239 2.931649 ACCCCCACACTAACCGGG 60.932 66.667 6.32 0.00 39.92 5.73
860 1243 2.211619 ATTTTCCGCGGTCGTCGGTA 62.212 55.000 27.15 0.00 46.49 4.02
1123 1510 7.639113 AACCTGACAAAAGAATACTGAACAA 57.361 32.000 0.00 0.00 0.00 2.83
1351 1764 6.153851 TCCGGTACACAGAGAAGAAAATATCA 59.846 38.462 0.00 0.00 0.00 2.15
2069 2492 4.717233 TTTCAGCAGTGTCATGTTTTGT 57.283 36.364 0.00 0.00 0.00 2.83
2130 2553 3.536917 TCCGGCGGCGAGATGAAT 61.537 61.111 34.49 0.00 0.00 2.57
2156 2580 1.299976 GTGATCCCTGCTTCCCGTT 59.700 57.895 0.00 0.00 0.00 4.44
2166 2590 1.287425 GCTTCCCGTTATCACTTCCG 58.713 55.000 0.00 0.00 0.00 4.30
2330 2754 1.586154 CGGCCACCATCTTCACCAAC 61.586 60.000 2.24 0.00 0.00 3.77
2331 2755 0.251341 GGCCACCATCTTCACCAACT 60.251 55.000 0.00 0.00 0.00 3.16
3163 4282 1.266989 GTGTTTCTGTTAGTGCCTGCC 59.733 52.381 0.00 0.00 0.00 4.85
3212 4331 3.182772 GTGGGCATTTTTCCGTAAAAACG 59.817 43.478 0.34 0.00 44.95 3.60
3452 4577 6.658816 ACACTGGAATGCATATGTGTTTCTTA 59.341 34.615 16.09 0.17 35.47 2.10
3613 4762 3.327757 AGTCCATCTTGCAAACCAGTAGA 59.672 43.478 0.00 0.00 0.00 2.59
3670 4825 1.734465 CCGATCCAGACTTGAAGCAAC 59.266 52.381 0.00 0.00 0.00 4.17
3715 4870 8.664211 TTCGTAGCTCATCGATACTCATATAT 57.336 34.615 0.00 0.00 36.01 0.86
3861 5019 2.983592 GGGTGCGGGGTTCAGTTG 60.984 66.667 0.00 0.00 0.00 3.16
3955 5113 2.437651 TCCCTGATGTTGAGTGTGTCAA 59.562 45.455 0.00 0.00 43.26 3.18
4046 5204 4.804108 TGTTCACTTTCCTGTGTTTTGTG 58.196 39.130 0.00 0.00 38.90 3.33
4060 5218 7.040478 CCTGTGTTTTGTGGAATAATTCTCAGA 60.040 37.037 0.00 0.00 0.00 3.27
4247 5408 0.322975 AATGGCGTCTTCAGCTCAGT 59.677 50.000 0.00 0.00 34.52 3.41
4522 5703 5.988310 ATGAATGTCAAGGAAAAGCATGA 57.012 34.783 0.00 0.00 0.00 3.07
4564 5745 6.316640 GGAGAAAGGCTTCTACAGAAAATACC 59.683 42.308 0.00 0.00 41.62 2.73
4883 6081 1.001633 ACGCCGAGTTCAGGTACATTT 59.998 47.619 0.00 0.00 0.00 2.32
4922 6120 0.464554 GGGATGCCTCTGTGCCTAAC 60.465 60.000 0.00 0.00 0.00 2.34
4923 6121 0.464554 GGATGCCTCTGTGCCTAACC 60.465 60.000 0.00 0.00 0.00 2.85
4924 6122 0.253044 GATGCCTCTGTGCCTAACCA 59.747 55.000 0.00 0.00 0.00 3.67
5024 6816 2.832129 TCTTCTAGGATTTGTCGCCACT 59.168 45.455 0.00 0.00 0.00 4.00
5068 6977 1.832366 AGCACATAAAATGCATGCCCA 59.168 42.857 16.68 0.00 45.92 5.36
5659 7618 1.804151 GACTGTACCGATTTGCAGCAA 59.196 47.619 2.83 2.83 32.65 3.91
6088 8069 3.003173 AAGGTAGCGCTCTGGGCA 61.003 61.111 16.34 0.00 44.06 5.36
6097 8078 3.013932 CTCTGGGCAGCCCTCCTT 61.014 66.667 31.51 0.00 45.70 3.36
6205 8186 3.737172 GCGCCGCCACACATCTTT 61.737 61.111 0.00 0.00 0.00 2.52
6453 8434 4.041464 TGGGTTAGGGTAATGCATGTCTA 58.959 43.478 0.00 0.00 0.00 2.59
6555 8538 7.970614 GGATGTCTGACCAAAGAAATTATTGTC 59.029 37.037 5.17 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.160252 GCACAGGGGACACAATCATATTTT 59.840 41.667 0.00 0.00 0.00 1.82
2 3 3.701040 GCACAGGGGACACAATCATATTT 59.299 43.478 0.00 0.00 0.00 1.40
3 4 3.290710 GCACAGGGGACACAATCATATT 58.709 45.455 0.00 0.00 0.00 1.28
4 5 2.746142 CGCACAGGGGACACAATCATAT 60.746 50.000 0.00 0.00 0.00 1.78
5 6 1.406751 CGCACAGGGGACACAATCATA 60.407 52.381 0.00 0.00 0.00 2.15
6 7 0.677731 CGCACAGGGGACACAATCAT 60.678 55.000 0.00 0.00 0.00 2.45
7 8 1.302431 CGCACAGGGGACACAATCA 60.302 57.895 0.00 0.00 0.00 2.57
8 9 0.392998 ATCGCACAGGGGACACAATC 60.393 55.000 0.00 0.00 38.96 2.67
9 10 0.908910 TATCGCACAGGGGACACAAT 59.091 50.000 0.00 0.00 38.96 2.71
10 11 0.908910 ATATCGCACAGGGGACACAA 59.091 50.000 0.00 0.00 38.96 3.33
11 12 1.783071 TATATCGCACAGGGGACACA 58.217 50.000 0.00 0.00 38.96 3.72
12 13 4.737855 ATATATATCGCACAGGGGACAC 57.262 45.455 0.00 0.00 38.96 3.67
13 14 6.719829 CCTATATATATATCGCACAGGGGACA 59.280 42.308 8.55 0.00 38.96 4.02
14 15 6.153000 CCCTATATATATATCGCACAGGGGAC 59.847 46.154 20.98 0.00 38.96 4.46
15 16 6.253758 CCCTATATATATATCGCACAGGGGA 58.746 44.000 20.98 0.00 40.57 4.81
16 17 5.105310 GCCCTATATATATATCGCACAGGGG 60.105 48.000 25.82 15.89 32.68 4.79
17 18 5.717178 AGCCCTATATATATATCGCACAGGG 59.283 44.000 22.95 22.95 34.99 4.45
18 19 6.350528 CCAGCCCTATATATATATCGCACAGG 60.351 46.154 8.55 9.42 0.00 4.00
19 20 6.434340 TCCAGCCCTATATATATATCGCACAG 59.566 42.308 8.55 1.16 0.00 3.66
20 21 6.208797 GTCCAGCCCTATATATATATCGCACA 59.791 42.308 8.55 0.00 0.00 4.57
21 22 6.434652 AGTCCAGCCCTATATATATATCGCAC 59.565 42.308 8.55 10.41 0.00 5.34
22 23 6.552932 AGTCCAGCCCTATATATATATCGCA 58.447 40.000 8.55 0.00 0.00 5.10
23 24 8.754991 ATAGTCCAGCCCTATATATATATCGC 57.245 38.462 8.55 9.24 0.00 4.58
85 86 2.974536 GCGTCGTGCTCTATATTGAGAC 59.025 50.000 17.01 10.98 41.73 3.36
87 88 2.287608 TGGCGTCGTGCTCTATATTGAG 60.288 50.000 9.53 9.53 45.43 3.02
88 89 1.679153 TGGCGTCGTGCTCTATATTGA 59.321 47.619 0.00 0.00 45.43 2.57
90 91 1.599667 CGTGGCGTCGTGCTCTATATT 60.600 52.381 0.00 0.00 45.43 1.28
1123 1510 3.750130 CACTTCTTCAGCTTAGTGCACAT 59.250 43.478 21.04 6.83 45.94 3.21
1351 1764 5.956563 AGAAATTCTCTTTTCATGCCCTGAT 59.043 36.000 0.00 0.00 37.93 2.90
1556 1973 2.037772 ACCAGTCAGTCAGTCATGTTCC 59.962 50.000 0.00 0.00 0.00 3.62
2008 2431 6.827586 ACAAAACAGGACACTAGTGAAAAA 57.172 33.333 29.30 0.00 0.00 1.94
2069 2492 3.367743 CGAGGACGGGACCGACAA 61.368 66.667 18.80 0.00 42.83 3.18
2130 2553 3.080641 CAGGGATCACAGGTGGCA 58.919 61.111 0.00 0.00 0.00 4.92
2156 2580 0.172578 CACACGAGGCGGAAGTGATA 59.827 55.000 10.55 0.00 39.04 2.15
2166 2590 2.049063 AGCGAACTCACACGAGGC 60.049 61.111 0.00 0.00 44.17 4.70
2435 2880 4.082845 TGATGCACGGGGAATTTTAGAAA 58.917 39.130 0.00 0.00 0.00 2.52
2578 3052 1.768275 TCCAGAGAACCAGAACTGCAA 59.232 47.619 0.00 0.00 0.00 4.08
2687 3331 3.195396 TGAGCTATACTGCATCACACACA 59.805 43.478 0.00 0.00 34.99 3.72
3015 3670 4.592942 AGTGTAGTAACCGTACCATGAGA 58.407 43.478 0.00 0.00 0.00 3.27
3163 4282 4.843220 AGTTCCACAGCTCTTTCAATTG 57.157 40.909 0.00 0.00 0.00 2.32
3290 4415 4.128925 TGCTCACATCTCCATCTACAAC 57.871 45.455 0.00 0.00 0.00 3.32
3452 4577 4.051661 ACTCCCAAAATCATCACCACAT 57.948 40.909 0.00 0.00 0.00 3.21
3861 5019 2.105128 CCTGGCTCGTCATCGTCC 59.895 66.667 0.00 0.00 38.33 4.79
4522 5703 6.183361 CCTTTCTCCTATAGAGGGCATTTTCT 60.183 42.308 2.96 0.00 43.94 2.52
4564 5745 2.092524 GCATGCCTAAAATGTTGCAACG 59.907 45.455 23.79 9.32 37.27 4.10
4883 6081 1.595929 GAACTTGGCCGTCCACGAA 60.596 57.895 0.00 0.00 43.33 3.85
4922 6120 4.631377 TGCTGTACAAGATCGAAGAATTGG 59.369 41.667 0.00 0.00 43.58 3.16
4923 6121 5.784750 TGCTGTACAAGATCGAAGAATTG 57.215 39.130 0.00 0.00 43.58 2.32
5024 6816 1.543802 CACCGCCCAAGCTTAAATCAA 59.456 47.619 0.00 0.00 36.60 2.57
5068 6977 3.561310 CAGCAATATAGCGAACATGTGGT 59.439 43.478 0.00 0.00 40.15 4.16
5426 7385 8.198778 TCACGTCTAAGGCATTTAACACATATA 58.801 33.333 0.00 0.00 0.00 0.86
5659 7618 9.696917 CTGAATTTTAAAGGAAGCAAACTACAT 57.303 29.630 0.00 0.00 0.00 2.29
6205 8186 7.108841 ACAGGAAATATACTAGCGAGAACAA 57.891 36.000 0.00 0.00 0.00 2.83
6384 8365 7.715657 AGTTTCAGAATTTTTGCACTACATCA 58.284 30.769 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.