Multiple sequence alignment - TraesCS7A01G028000

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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 TraesCS7A01G028000 chr7A 100.000 4860 0 0 1 4860 11231467 11226608 0.000000e+00 8975.0
1 TraesCS7A01G028000 chr7A 94.794 826 40 2 1806 2629 11345646 11344822 0.000000e+00 1284.0
2 TraesCS7A01G028000 chr7A 94.685 715 32 6 2623 3335 11344735 11344025 0.000000e+00 1105.0
3 TraesCS7A01G028000 chr7A 95.933 418 13 3 1 415 5439932 5440348 0.000000e+00 675.0
4 TraesCS7A01G028000 chr7A 94.272 419 20 2 1 415 696841831 696841413 5.300000e-179 638.0
5 TraesCS7A01G028000 chr7A 81.806 753 107 14 3592 4333 11287754 11287021 5.380000e-169 604.0
6 TraesCS7A01G028000 chr7A 93.893 393 24 0 1414 1806 11346222 11345830 1.160000e-165 593.0
7 TraesCS7A01G028000 chr7A 95.455 374 14 2 417 788 696841350 696840978 1.160000e-165 593.0
8 TraesCS7A01G028000 chr7A 92.548 416 15 9 376 788 5440433 5440835 2.520000e-162 582.0
9 TraesCS7A01G028000 chr7A 77.887 1013 170 26 1551 2526 11311827 11310832 9.070000e-162 580.0
10 TraesCS7A01G028000 chr7A 83.767 653 64 16 3337 3962 11343859 11343222 9.070000e-162 580.0
11 TraesCS7A01G028000 chr7A 96.532 346 11 1 1 345 104811294 104811639 5.460000e-159 571.0
12 TraesCS7A01G028000 chr7A 92.704 233 17 0 1187 1419 11346966 11346734 2.170000e-88 337.0
13 TraesCS7A01G028000 chr7A 88.809 277 22 4 790 1066 11347245 11346978 1.010000e-86 331.0
14 TraesCS7A01G028000 chr7A 81.250 384 41 14 2822 3202 11310664 11310309 1.030000e-71 281.0
15 TraesCS7A01G028000 chr7A 88.710 186 17 3 4328 4512 11342989 11342807 1.760000e-54 224.0
16 TraesCS7A01G028000 chr7A 88.136 59 7 0 4383 4441 11435414 11435472 2.430000e-08 71.3
17 TraesCS7A01G028000 chr7D 96.776 1427 22 5 3456 4860 11684388 11682964 0.000000e+00 2359.0
18 TraesCS7A01G028000 chr7D 94.789 1017 48 4 1616 2629 11726764 11725750 0.000000e+00 1580.0
19 TraesCS7A01G028000 chr7D 97.616 839 17 3 2623 3459 23653925 23654762 0.000000e+00 1435.0
20 TraesCS7A01G028000 chr7D 97.628 801 17 2 2623 3422 11693801 11693002 0.000000e+00 1373.0
21 TraesCS7A01G028000 chr7D 95.664 715 26 5 2623 3335 11725663 11724952 0.000000e+00 1144.0
22 TraesCS7A01G028000 chr7D 90.647 834 47 13 795 1626 11727823 11727019 0.000000e+00 1079.0
23 TraesCS7A01G028000 chr7D 79.874 1267 210 26 1110 2363 11928922 11927688 0.000000e+00 885.0
24 TraesCS7A01G028000 chr7D 83.308 653 67 12 3337 3962 11724786 11724149 9.130000e-157 564.0
25 TraesCS7A01G028000 chr7D 86.792 318 38 3 2772 3089 49175650 49175337 7.740000e-93 351.0
26 TraesCS7A01G028000 chr7D 82.078 385 35 16 2822 3202 11705263 11704909 1.020000e-76 298.0
27 TraesCS7A01G028000 chr7D 83.178 321 54 0 1173 1493 27228326 27228646 1.320000e-75 294.0
28 TraesCS7A01G028000 chr7D 83.172 309 27 14 2237 2526 11705731 11705429 4.830000e-65 259.0
29 TraesCS7A01G028000 chr7D 81.714 350 28 17 4532 4854 11755473 11755813 4.830000e-65 259.0
30 TraesCS7A01G028000 chr7D 81.429 350 27 18 4532 4854 11731345 11731683 8.080000e-63 252.0
31 TraesCS7A01G028000 chr7D 89.247 186 16 3 4328 4512 11723916 11723734 3.780000e-56 230.0
32 TraesCS7A01G028000 chr7D 85.068 221 31 2 3766 3985 11730998 11731217 1.760000e-54 224.0
33 TraesCS7A01G028000 chr7D 85.068 221 31 2 3766 3985 11755126 11755345 1.760000e-54 224.0
34 TraesCS7A01G028000 chr7D 95.798 119 5 0 2511 2629 11693997 11693879 4.960000e-45 193.0
35 TraesCS7A01G028000 chr7D 94.958 119 6 0 2511 2629 23653729 23653847 2.310000e-43 187.0
36 TraesCS7A01G028000 chr7D 100.000 42 0 0 3418 3459 11684450 11684409 1.450000e-10 78.7
37 TraesCS7A01G028000 chr7D 92.857 56 1 2 3109 3161 49175339 49175284 1.450000e-10 78.7
38 TraesCS7A01G028000 chr4A 93.478 1012 64 2 1123 2133 726027582 726028592 0.000000e+00 1502.0
39 TraesCS7A01G028000 chr4A 92.157 714 30 5 2623 3335 726065277 726065965 0.000000e+00 985.0
40 TraesCS7A01G028000 chr4A 94.212 501 26 2 2131 2629 726064691 726065190 0.000000e+00 761.0
41 TraesCS7A01G028000 chr4A 76.488 1327 224 58 1145 2425 726107574 726108858 4.100000e-180 641.0
42 TraesCS7A01G028000 chr4A 96.812 345 10 1 1 345 30761035 30761378 4.220000e-160 575.0
43 TraesCS7A01G028000 chr4A 77.909 1014 162 25 1551 2526 726073342 726074331 4.220000e-160 575.0
44 TraesCS7A01G028000 chr4A 83.002 653 68 13 3337 3962 726066130 726066766 7.110000e-153 551.0
45 TraesCS7A01G028000 chr4A 78.636 660 121 18 1178 1829 703668131 703668778 2.090000e-113 420.0
46 TraesCS7A01G028000 chr4A 88.218 348 25 6 788 1127 726014128 726014467 7.580000e-108 401.0
47 TraesCS7A01G028000 chr4A 78.660 567 99 12 1177 1734 710786618 710786065 1.660000e-94 357.0
48 TraesCS7A01G028000 chr4A 83.871 372 32 5 4498 4845 726101672 726102039 3.630000e-86 329.0
49 TraesCS7A01G028000 chr4A 79.770 435 72 13 1178 1606 703554018 703554442 7.910000e-78 302.0
50 TraesCS7A01G028000 chr4A 85.520 221 30 2 3766 3985 726012292 726012073 3.780000e-56 230.0
51 TraesCS7A01G028000 chr4A 87.634 186 19 3 4328 4512 726066999 726067181 3.810000e-51 213.0
52 TraesCS7A01G028000 chr4A 90.476 63 6 0 2464 2526 703572407 703572469 3.120000e-12 84.2
53 TraesCS7A01G028000 chr4A 90.476 63 6 0 2464 2526 703627020 703627082 3.120000e-12 84.2
54 TraesCS7A01G028000 chr4A 90.476 63 6 0 2464 2526 703678040 703678102 3.120000e-12 84.2
55 TraesCS7A01G028000 chr4A 88.136 59 6 1 4383 4441 725933209 725933152 8.730000e-08 69.4
56 TraesCS7A01G028000 chr7B 80.031 1307 234 23 1144 2441 750116612 750115324 0.000000e+00 942.0
57 TraesCS7A01G028000 chr7B 89.595 346 19 5 446 788 551949580 551949249 1.620000e-114 424.0
58 TraesCS7A01G028000 chr3D 78.723 1316 228 34 1139 2441 602261534 602260258 0.000000e+00 832.0
59 TraesCS7A01G028000 chr3A 78.356 1326 226 37 1139 2441 731894362 731893075 0.000000e+00 802.0
60 TraesCS7A01G028000 chr3A 89.049 347 21 5 446 789 686142971 686142639 9.730000e-112 414.0
61 TraesCS7A01G028000 chr5A 92.100 481 21 13 1 472 282591273 282590801 0.000000e+00 662.0
62 TraesCS7A01G028000 chr5A 97.878 377 7 1 1 376 547390965 547391341 0.000000e+00 651.0
63 TraesCS7A01G028000 chr5A 93.810 420 16 6 376 791 282590833 282590420 1.490000e-174 623.0
64 TraesCS7A01G028000 chr5A 95.954 346 13 1 1 345 549184537 549184882 1.180000e-155 560.0
65 TraesCS7A01G028000 chr5A 87.835 411 28 10 383 788 549185033 549185426 3.430000e-126 462.0
66 TraesCS7A01G028000 chrUn 92.328 378 19 8 1 373 430960473 430960101 3.330000e-146 529.0
67 TraesCS7A01G028000 chrUn 84.639 319 40 5 2772 3090 333781102 333780793 4.720000e-80 309.0
68 TraesCS7A01G028000 chrUn 85.068 221 31 2 3766 3985 89601530 89601749 1.760000e-54 224.0
69 TraesCS7A01G028000 chrUn 88.136 59 7 0 4383 4441 405165802 405165860 2.430000e-08 71.3
70 TraesCS7A01G028000 chr2B 92.328 378 19 8 1 373 399344562 399344190 3.330000e-146 529.0
71 TraesCS7A01G028000 chr4B 94.671 319 13 2 470 788 322646399 322646085 4.370000e-135 492.0
72 TraesCS7A01G028000 chr1D 93.750 304 12 5 486 788 80297119 80296822 2.670000e-122 449.0
73 TraesCS7A01G028000 chr4D 92.698 315 16 5 475 788 339059620 339059928 9.600000e-122 448.0
74 TraesCS7A01G028000 chr3B 81.058 586 87 15 1177 1753 809237369 809236799 3.450000e-121 446.0
75 TraesCS7A01G028000 chr3B 89.625 347 19 5 446 789 177085472 177085804 4.500000e-115 425.0
76 TraesCS7A01G028000 chr5B 89.459 351 19 6 446 792 588934805 588934469 1.250000e-115 427.0
77 TraesCS7A01G028000 chr5B 89.899 99 7 2 468 564 646469139 646469236 1.840000e-24 124.0
78 TraesCS7A01G028000 chr5D 91.857 307 17 6 483 788 527195433 527195732 5.820000e-114 422.0
79 TraesCS7A01G028000 chr6A 89.017 346 21 7 446 788 59571729 59571398 3.500000e-111 412.0


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 TraesCS7A01G028000 chr7A 11226608 11231467 4859 True 8975.000000 8975 100.000000 1 4860 1 chr7A.!!$R1 4859
1 TraesCS7A01G028000 chr7A 11342807 11347245 4438 True 636.285714 1284 91.051714 790 4512 7 chr7A.!!$R4 3722
2 TraesCS7A01G028000 chr7A 5439932 5440835 903 False 628.500000 675 94.240500 1 788 2 chr7A.!!$F3 787
3 TraesCS7A01G028000 chr7A 696840978 696841831 853 True 615.500000 638 94.863500 1 788 2 chr7A.!!$R5 787
4 TraesCS7A01G028000 chr7A 11287021 11287754 733 True 604.000000 604 81.806000 3592 4333 1 chr7A.!!$R2 741
5 TraesCS7A01G028000 chr7A 11310309 11311827 1518 True 430.500000 580 79.568500 1551 3202 2 chr7A.!!$R3 1651
6 TraesCS7A01G028000 chr7D 11682964 11684450 1486 True 1218.850000 2359 98.388000 3418 4860 2 chr7D.!!$R2 1442
7 TraesCS7A01G028000 chr7D 11723734 11727823 4089 True 919.400000 1580 90.731000 795 4512 5 chr7D.!!$R5 3717
8 TraesCS7A01G028000 chr7D 11927688 11928922 1234 True 885.000000 885 79.874000 1110 2363 1 chr7D.!!$R1 1253
9 TraesCS7A01G028000 chr7D 23653729 23654762 1033 False 811.000000 1435 96.287000 2511 3459 2 chr7D.!!$F4 948
10 TraesCS7A01G028000 chr7D 11693002 11693997 995 True 783.000000 1373 96.713000 2511 3422 2 chr7D.!!$R3 911
11 TraesCS7A01G028000 chr7D 11704909 11705731 822 True 278.500000 298 82.625000 2237 3202 2 chr7D.!!$R4 965
12 TraesCS7A01G028000 chr7D 11755126 11755813 687 False 241.500000 259 83.391000 3766 4854 2 chr7D.!!$F3 1088
13 TraesCS7A01G028000 chr7D 11730998 11731683 685 False 238.000000 252 83.248500 3766 4854 2 chr7D.!!$F2 1088
14 TraesCS7A01G028000 chr4A 726027582 726028592 1010 False 1502.000000 1502 93.478000 1123 2133 1 chr4A.!!$F8 1010
15 TraesCS7A01G028000 chr4A 726107574 726108858 1284 False 641.000000 641 76.488000 1145 2425 1 chr4A.!!$F11 1280
16 TraesCS7A01G028000 chr4A 726064691 726067181 2490 False 627.500000 985 89.251250 2131 4512 4 chr4A.!!$F12 2381
17 TraesCS7A01G028000 chr4A 726073342 726074331 989 False 575.000000 575 77.909000 1551 2526 1 chr4A.!!$F9 975
18 TraesCS7A01G028000 chr4A 703668131 703668778 647 False 420.000000 420 78.636000 1178 1829 1 chr4A.!!$F5 651
19 TraesCS7A01G028000 chr4A 710786065 710786618 553 True 357.000000 357 78.660000 1177 1734 1 chr4A.!!$R1 557
20 TraesCS7A01G028000 chr7B 750115324 750116612 1288 True 942.000000 942 80.031000 1144 2441 1 chr7B.!!$R2 1297
21 TraesCS7A01G028000 chr3D 602260258 602261534 1276 True 832.000000 832 78.723000 1139 2441 1 chr3D.!!$R1 1302
22 TraesCS7A01G028000 chr3A 731893075 731894362 1287 True 802.000000 802 78.356000 1139 2441 1 chr3A.!!$R2 1302
23 TraesCS7A01G028000 chr5A 282590420 282591273 853 True 642.500000 662 92.955000 1 791 2 chr5A.!!$R1 790
24 TraesCS7A01G028000 chr5A 549184537 549185426 889 False 511.000000 560 91.894500 1 788 2 chr5A.!!$F2 787
25 TraesCS7A01G028000 chr3B 809236799 809237369 570 True 446.000000 446 81.058000 1177 1753 1 chr3B.!!$R1 576

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
989 1250 0.188342 AATCCCCAATTCCCCATCCG 59.812 55.0 0.00 0.00 0.00 4.18 F
1669 2732 0.629596 TAGACCGGACCTCCTCATGT 59.370 55.0 9.46 0.00 0.00 3.21 F
2268 3568 0.103390 TCAAGACGTTGCAGGTCGAA 59.897 50.0 12.56 2.51 37.99 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 3542 0.249699 TGCAACGTCTTGACGTCCAT 60.250 50.000 25.59 10.61 46.41 3.41 R
2679 4116 1.069049 GCATGCTGGTCAAAACAAGGT 59.931 47.619 11.37 0.00 0.00 3.50 R
3955 5780 1.448013 GGAGTACAGGACCAAGCGC 60.448 63.158 0.00 0.00 0.00 5.92 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
43 44 4.502087 CCCTCTCATCATAAGCACGATCAA 60.502 45.833 0.00 0.00 0.00 2.57
157 158 3.991051 CTGGACGTGGCGGACAGT 61.991 66.667 0.00 0.00 32.87 3.55
263 264 0.684535 TCAAAGATCACCGGACAGCA 59.315 50.000 9.46 0.00 0.00 4.41
732 991 4.406456 TGTGGAACATATGCAGAAAACCT 58.594 39.130 1.58 0.00 45.67 3.50
759 1018 9.333724 CTTATACAACGGGATAAATACAAAGGT 57.666 33.333 0.00 0.00 0.00 3.50
833 1094 2.930826 AGTTGGACAATCTTGGTCGT 57.069 45.000 0.00 0.00 36.12 4.34
879 1140 4.286297 TGGAATGTTTAGACAGAGGTGG 57.714 45.455 0.00 0.00 39.58 4.61
880 1141 3.650942 TGGAATGTTTAGACAGAGGTGGT 59.349 43.478 0.00 0.00 39.58 4.16
881 1142 4.104102 TGGAATGTTTAGACAGAGGTGGTT 59.896 41.667 0.00 0.00 39.58 3.67
888 1149 6.885376 TGTTTAGACAGAGGTGGTTTTGTTTA 59.115 34.615 0.00 0.00 0.00 2.01
951 1212 0.321653 ATTGGCACTCGTTCCTCACC 60.322 55.000 0.00 0.00 0.00 4.02
952 1213 2.432628 GGCACTCGTTCCTCACCG 60.433 66.667 0.00 0.00 0.00 4.94
953 1214 2.432628 GCACTCGTTCCTCACCGG 60.433 66.667 0.00 0.00 0.00 5.28
964 1225 1.450211 CTCACCGGTCACCAAACCT 59.550 57.895 2.59 0.00 37.15 3.50
984 1245 1.965414 ACCAAAATCCCCAATTCCCC 58.035 50.000 0.00 0.00 0.00 4.81
989 1250 0.188342 AATCCCCAATTCCCCATCCG 59.812 55.000 0.00 0.00 0.00 4.18
991 1252 2.391130 CCCCAATTCCCCATCCGGA 61.391 63.158 6.61 6.61 0.00 5.14
1028 1289 2.520968 GCCAACCTCCAACCCAGT 59.479 61.111 0.00 0.00 0.00 4.00
1062 1323 2.939261 GCCGTCCCTTCGAGTCCAA 61.939 63.158 0.00 0.00 0.00 3.53
1068 1329 1.215647 CCTTCGAGTCCAAGACGGG 59.784 63.158 0.00 0.00 37.67 5.28
1097 1358 1.407025 GGAAATCTTCCTCCCGTCCAC 60.407 57.143 0.00 0.00 46.57 4.02
1142 1403 2.673200 GCCCTCAGCAGATCCCACA 61.673 63.158 0.00 0.00 42.97 4.17
1467 2259 4.275936 AGTGAAATTGACTTCTTTGACGGG 59.724 41.667 0.00 0.00 0.00 5.28
1504 2296 0.676782 CGCCCCGGTCAAAGAAGAAT 60.677 55.000 0.00 0.00 0.00 2.40
1518 2310 3.880846 GAATCCGGCAGCCGCTTG 61.881 66.667 29.55 15.42 46.86 4.01
1669 2732 0.629596 TAGACCGGACCTCCTCATGT 59.370 55.000 9.46 0.00 0.00 3.21
1704 2767 3.917760 CCCGGCGAGGATGAGGAC 61.918 72.222 9.30 0.00 45.00 3.85
1766 2837 4.142790 AGAATAAATCTGCTGATGCTGGG 58.857 43.478 6.88 0.00 36.88 4.45
1868 3150 1.376942 CTGAGCCTTGGCTGTCCTG 60.377 63.158 19.84 5.23 0.00 3.86
2233 3533 4.739716 CACAACACATGCTTAAGTTTGGAC 59.260 41.667 4.02 0.00 0.00 4.02
2242 3542 7.232534 ACATGCTTAAGTTTGGACTATTTTCCA 59.767 33.333 4.02 0.00 44.39 3.53
2268 3568 0.103390 TCAAGACGTTGCAGGTCGAA 59.897 50.000 12.56 2.51 37.99 3.71
2306 3606 2.560542 GCAAACCCAACATGTATGGTCA 59.439 45.455 17.01 0.00 36.14 4.02
2354 3654 4.566545 TTGTGTGCACCAACTATTTGAG 57.433 40.909 15.69 0.00 34.24 3.02
2405 3715 9.692749 TGCTTACTATTATTTAATCTGGTCTCG 57.307 33.333 0.00 0.00 0.00 4.04
2420 3736 5.046878 TCTGGTCTCGGTGTTATACAACAAT 60.047 40.000 0.00 0.00 45.99 2.71
2603 3937 5.940192 TTTTGTGCTAATGTACTGTCCAG 57.060 39.130 0.00 0.00 0.00 3.86
2605 3939 5.731957 TTGTGCTAATGTACTGTCCAGTA 57.268 39.130 3.06 3.06 42.54 2.74
2670 4106 2.106511 AGTTGGCATCGGGCTTGTATAT 59.893 45.455 0.00 0.00 44.01 0.86
2679 4116 3.452990 TCGGGCTTGTATATTTGACTGGA 59.547 43.478 0.00 0.00 0.00 3.86
2887 4371 5.480422 CCACTGGCTCTTTTATAAACCCTTT 59.520 40.000 0.00 0.00 0.00 3.11
3212 4723 3.311106 AGCGATGTTGCAATTGAGTTTG 58.689 40.909 10.34 0.00 37.31 2.93
3217 4730 5.332506 CGATGTTGCAATTGAGTTTGTTTCC 60.333 40.000 10.34 0.00 0.00 3.13
3329 4843 3.001939 GGTGTACTGTTTGTTTCCTCACG 59.998 47.826 0.00 0.00 0.00 4.35
3506 5235 6.952773 AAATTTCCGGCTGCATAGTTTATA 57.047 33.333 0.50 0.00 0.00 0.98
3821 5573 7.905604 TTCATGTGCTTCCTATTATATTCCG 57.094 36.000 0.00 0.00 0.00 4.30
3936 5689 4.553330 AGACAAAGTGATACCGGAATGT 57.447 40.909 9.46 0.40 0.00 2.71
3955 5780 8.755941 CGGAATGTGACATATTTACTAGTTCAG 58.244 37.037 0.00 0.00 0.00 3.02
3960 5785 6.255887 GTGACATATTTACTAGTTCAGCGCTT 59.744 38.462 7.50 0.00 0.00 4.68
3961 5786 6.255670 TGACATATTTACTAGTTCAGCGCTTG 59.744 38.462 7.50 3.43 0.00 4.01
3962 5787 5.523916 ACATATTTACTAGTTCAGCGCTTGG 59.476 40.000 7.50 0.00 0.00 3.61
3963 5788 3.396260 TTTACTAGTTCAGCGCTTGGT 57.604 42.857 7.50 3.69 0.00 3.67
3964 5789 2.649331 TACTAGTTCAGCGCTTGGTC 57.351 50.000 7.50 0.00 0.00 4.02
3965 5790 0.037232 ACTAGTTCAGCGCTTGGTCC 60.037 55.000 7.50 0.00 0.00 4.46
3966 5791 0.247736 CTAGTTCAGCGCTTGGTCCT 59.752 55.000 7.50 1.78 0.00 3.85
3967 5792 0.037326 TAGTTCAGCGCTTGGTCCTG 60.037 55.000 7.50 0.00 0.00 3.86
3968 5793 1.598130 GTTCAGCGCTTGGTCCTGT 60.598 57.895 7.50 0.00 0.00 4.00
3969 5794 0.320421 GTTCAGCGCTTGGTCCTGTA 60.320 55.000 7.50 0.00 0.00 2.74
3970 5795 0.320421 TTCAGCGCTTGGTCCTGTAC 60.320 55.000 7.50 0.00 0.00 2.90
3971 5796 1.185618 TCAGCGCTTGGTCCTGTACT 61.186 55.000 7.50 0.00 0.00 2.73
3972 5797 0.737715 CAGCGCTTGGTCCTGTACTC 60.738 60.000 7.50 0.00 0.00 2.59
3973 5798 1.448013 GCGCTTGGTCCTGTACTCC 60.448 63.158 0.00 0.00 0.00 3.85
3974 5799 1.972198 CGCTTGGTCCTGTACTCCA 59.028 57.895 0.00 0.00 0.00 3.86
3975 5800 0.108615 CGCTTGGTCCTGTACTCCAG 60.109 60.000 0.00 0.00 41.15 3.86
3976 5801 0.977395 GCTTGGTCCTGTACTCCAGT 59.023 55.000 0.00 0.00 39.74 4.00
3977 5802 1.338200 GCTTGGTCCTGTACTCCAGTG 60.338 57.143 0.00 0.00 39.74 3.66
3978 5803 2.248248 CTTGGTCCTGTACTCCAGTGA 58.752 52.381 0.00 0.00 39.74 3.41
3979 5804 2.623418 TGGTCCTGTACTCCAGTGAT 57.377 50.000 0.00 0.00 39.74 3.06
3980 5805 2.179427 TGGTCCTGTACTCCAGTGATG 58.821 52.381 0.00 0.00 39.74 3.07
3981 5806 2.180276 GGTCCTGTACTCCAGTGATGT 58.820 52.381 0.00 0.00 39.74 3.06
3982 5807 2.567615 GGTCCTGTACTCCAGTGATGTT 59.432 50.000 0.00 0.00 39.74 2.71
3983 5808 3.589988 GTCCTGTACTCCAGTGATGTTG 58.410 50.000 0.00 0.00 39.74 3.33
3984 5809 3.006967 GTCCTGTACTCCAGTGATGTTGT 59.993 47.826 0.00 0.00 39.74 3.32
3985 5810 4.219944 GTCCTGTACTCCAGTGATGTTGTA 59.780 45.833 0.00 0.00 39.74 2.41
3986 5811 5.023452 TCCTGTACTCCAGTGATGTTGTAT 58.977 41.667 0.00 0.00 39.74 2.29
3987 5812 5.127194 TCCTGTACTCCAGTGATGTTGTATC 59.873 44.000 0.00 0.00 39.74 2.24
3988 5813 4.993905 TGTACTCCAGTGATGTTGTATCG 58.006 43.478 0.00 0.00 0.00 2.92
3989 5814 4.461431 TGTACTCCAGTGATGTTGTATCGT 59.539 41.667 0.00 0.00 0.00 3.73
3990 5815 4.111375 ACTCCAGTGATGTTGTATCGTC 57.889 45.455 0.00 0.00 0.00 4.20
3991 5816 3.764434 ACTCCAGTGATGTTGTATCGTCT 59.236 43.478 0.00 0.00 0.00 4.18
3992 5817 4.220821 ACTCCAGTGATGTTGTATCGTCTT 59.779 41.667 0.00 0.00 0.00 3.01
3993 5818 5.147330 TCCAGTGATGTTGTATCGTCTTT 57.853 39.130 0.00 0.00 0.00 2.52
3994 5819 4.929211 TCCAGTGATGTTGTATCGTCTTTG 59.071 41.667 0.00 0.00 0.00 2.77
3995 5820 4.929211 CCAGTGATGTTGTATCGTCTTTGA 59.071 41.667 0.00 0.00 0.00 2.69
3996 5821 5.408299 CCAGTGATGTTGTATCGTCTTTGAA 59.592 40.000 0.00 0.00 0.00 2.69
3997 5822 6.092670 CCAGTGATGTTGTATCGTCTTTGAAT 59.907 38.462 0.00 0.00 0.00 2.57
3998 5823 7.361201 CCAGTGATGTTGTATCGTCTTTGAATT 60.361 37.037 0.00 0.00 0.00 2.17
3999 5824 7.479603 CAGTGATGTTGTATCGTCTTTGAATTG 59.520 37.037 0.00 0.00 0.00 2.32
4000 5825 6.249260 GTGATGTTGTATCGTCTTTGAATTGC 59.751 38.462 0.00 0.00 0.00 3.56
4001 5826 5.940192 TGTTGTATCGTCTTTGAATTGCT 57.060 34.783 0.00 0.00 0.00 3.91
4002 5827 7.333174 TGATGTTGTATCGTCTTTGAATTGCTA 59.667 33.333 0.00 0.00 0.00 3.49
4003 5828 7.428282 TGTTGTATCGTCTTTGAATTGCTAA 57.572 32.000 0.00 0.00 0.00 3.09
4004 5829 7.518161 TGTTGTATCGTCTTTGAATTGCTAAG 58.482 34.615 0.00 0.00 0.00 2.18
4005 5830 7.172532 TGTTGTATCGTCTTTGAATTGCTAAGT 59.827 33.333 0.00 0.00 32.25 2.24
4006 5831 8.653338 GTTGTATCGTCTTTGAATTGCTAAGTA 58.347 33.333 0.00 0.00 32.25 2.24
4007 5832 8.407457 TGTATCGTCTTTGAATTGCTAAGTAG 57.593 34.615 0.00 0.00 32.25 2.57
4079 5905 8.132995 TGAAGATATTGCTTGCTATTGATGTTG 58.867 33.333 0.00 0.00 0.00 3.33
4131 5958 7.445402 AGTTCTTTGCTCAAGTGTAACATATGT 59.555 33.333 1.41 1.41 41.43 2.29
4143 5970 8.856153 AGTGTAACATATGTTGTCCAATAACA 57.144 30.769 27.62 18.64 41.43 2.41
4243 6077 8.856153 ATTTGAGGTGTGTTTGTATGTATGTA 57.144 30.769 0.00 0.00 0.00 2.29
4244 6078 7.661127 TTGAGGTGTGTTTGTATGTATGTAC 57.339 36.000 0.00 0.00 0.00 2.90
4245 6079 5.865013 TGAGGTGTGTTTGTATGTATGTACG 59.135 40.000 0.00 0.00 0.00 3.67
4246 6080 5.786311 AGGTGTGTTTGTATGTATGTACGT 58.214 37.500 0.00 0.00 0.00 3.57
4396 6234 5.728637 TGTGACTACATCTCAATGACTGT 57.271 39.130 0.33 0.33 36.67 3.55
4397 6235 6.834168 TGTGACTACATCTCAATGACTGTA 57.166 37.500 2.26 2.26 36.67 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 0.037877 AAGCTTGCTGATGAGGCTGT 59.962 50.000 0.00 0.00 33.30 4.40
157 158 2.029290 GTGTTCTTTCTGGCGAGGTCTA 60.029 50.000 0.00 0.00 0.00 2.59
263 264 0.034089 GGGCTATGTTGCTGTCCCTT 60.034 55.000 0.00 0.00 0.00 3.95
732 991 9.550406 CCTTTGTATTTATCCCGTTGTATAAGA 57.450 33.333 0.00 0.00 0.00 2.10
822 1083 5.997746 TCTCTTGATTTTGACGACCAAGATT 59.002 36.000 0.00 0.00 41.31 2.40
855 1116 6.158695 ACCACCTCTGTCTAAACATTCCATAT 59.841 38.462 0.00 0.00 34.13 1.78
888 1149 9.872684 AGATGGTCAACATAATCCATTCTAAAT 57.127 29.630 0.00 0.00 40.72 1.40
951 1212 1.970092 TTTGGTAGGTTTGGTGACCG 58.030 50.000 0.00 0.00 44.62 4.79
952 1213 3.257375 GGATTTTGGTAGGTTTGGTGACC 59.743 47.826 0.00 0.00 40.11 4.02
953 1214 3.257375 GGGATTTTGGTAGGTTTGGTGAC 59.743 47.826 0.00 0.00 0.00 3.67
964 1225 2.387160 TGGGGAATTGGGGATTTTGGTA 59.613 45.455 0.00 0.00 0.00 3.25
1055 1316 2.435059 GCAGCCCGTCTTGGACTC 60.435 66.667 0.00 0.00 42.00 3.36
1062 1323 4.704103 TCCTGGAGCAGCCCGTCT 62.704 66.667 0.00 0.00 34.97 4.18
1068 1329 1.387539 GGAAGATTTCCTGGAGCAGC 58.612 55.000 0.00 0.00 46.57 5.25
1253 1514 4.148825 GGCCGGAGATGACGCTGT 62.149 66.667 5.05 0.00 0.00 4.40
1704 2767 4.122776 CCACTCTGAATGATAAAGGGTCG 58.877 47.826 0.00 0.00 0.00 4.79
1802 2883 4.196971 CTGAGCACTCCATTGATCATGAA 58.803 43.478 0.00 0.00 40.95 2.57
2233 3533 4.032900 CGTCTTGACGTCCATGGAAAATAG 59.967 45.833 18.20 10.55 0.00 1.73
2242 3542 0.249699 TGCAACGTCTTGACGTCCAT 60.250 50.000 25.59 10.61 46.41 3.41
2268 3568 2.099141 TGCTAAGCTCAGCGAACAAT 57.901 45.000 3.93 0.00 44.88 2.71
2306 3606 3.931907 TGGCAAACCAGCATATAGTCT 57.068 42.857 0.00 0.00 42.67 3.24
2354 3654 4.463186 AGAGTAGATAACACACTCACCACC 59.537 45.833 4.01 0.00 40.94 4.61
2420 3736 5.999205 ACAAATCCCTGCAACATATTGAA 57.001 34.783 7.84 0.00 38.15 2.69
2564 3898 6.542574 CACAAAATGCACCAACAATACATT 57.457 33.333 0.00 0.00 32.53 2.71
2603 3937 8.818057 CAGTAAAGCTTCCAGTTACATGTATAC 58.182 37.037 6.36 8.04 31.47 1.47
2605 3939 7.394816 ACAGTAAAGCTTCCAGTTACATGTAT 58.605 34.615 6.36 0.00 31.47 2.29
2670 4106 3.445805 GGTCAAAACAAGGTCCAGTCAAA 59.554 43.478 0.00 0.00 0.00 2.69
2679 4116 1.069049 GCATGCTGGTCAAAACAAGGT 59.931 47.619 11.37 0.00 0.00 3.50
2887 4371 8.288689 GGGCAAACCTATTCTTTTAGACATTA 57.711 34.615 0.00 0.00 35.85 1.90
3212 4723 5.063564 CCTAGCTGTTTATCAGTTCGGAAAC 59.936 44.000 0.00 0.00 45.23 2.78
3217 4730 6.910536 ATTTCCTAGCTGTTTATCAGTTCG 57.089 37.500 0.00 0.00 45.23 3.95
3239 4752 7.226441 TGATAACTTCCACTATATGCAGCAAT 58.774 34.615 0.00 0.00 0.00 3.56
3576 5306 9.541143 GAAATCAATTTAGTTTGTTTCCTTGGA 57.459 29.630 0.00 0.00 0.00 3.53
3821 5573 6.575162 AACAAGATGAATTTACCACACCTC 57.425 37.500 0.00 0.00 0.00 3.85
3936 5689 5.902681 AGCGCTGAACTAGTAAATATGTCA 58.097 37.500 10.39 0.00 0.00 3.58
3955 5780 1.448013 GGAGTACAGGACCAAGCGC 60.448 63.158 0.00 0.00 0.00 5.92
3966 5791 4.461431 ACGATACAACATCACTGGAGTACA 59.539 41.667 0.00 0.00 0.00 2.90
3967 5792 4.995124 ACGATACAACATCACTGGAGTAC 58.005 43.478 0.00 0.00 0.00 2.73
3968 5793 4.948004 AGACGATACAACATCACTGGAGTA 59.052 41.667 0.00 0.00 0.00 2.59
3969 5794 3.764434 AGACGATACAACATCACTGGAGT 59.236 43.478 0.00 0.00 0.00 3.85
3970 5795 4.377839 AGACGATACAACATCACTGGAG 57.622 45.455 0.00 0.00 0.00 3.86
3971 5796 4.801330 AAGACGATACAACATCACTGGA 57.199 40.909 0.00 0.00 0.00 3.86
3972 5797 4.929211 TCAAAGACGATACAACATCACTGG 59.071 41.667 0.00 0.00 0.00 4.00
3973 5798 6.466308 TTCAAAGACGATACAACATCACTG 57.534 37.500 0.00 0.00 0.00 3.66
3974 5799 7.521529 CAATTCAAAGACGATACAACATCACT 58.478 34.615 0.00 0.00 0.00 3.41
3975 5800 6.249260 GCAATTCAAAGACGATACAACATCAC 59.751 38.462 0.00 0.00 0.00 3.06
3976 5801 6.149308 AGCAATTCAAAGACGATACAACATCA 59.851 34.615 0.00 0.00 0.00 3.07
3977 5802 6.546395 AGCAATTCAAAGACGATACAACATC 58.454 36.000 0.00 0.00 0.00 3.06
3978 5803 6.500684 AGCAATTCAAAGACGATACAACAT 57.499 33.333 0.00 0.00 0.00 2.71
3979 5804 5.940192 AGCAATTCAAAGACGATACAACA 57.060 34.783 0.00 0.00 0.00 3.33
3980 5805 7.519002 ACTTAGCAATTCAAAGACGATACAAC 58.481 34.615 0.00 0.00 0.00 3.32
3981 5806 7.667043 ACTTAGCAATTCAAAGACGATACAA 57.333 32.000 0.00 0.00 0.00 2.41
3982 5807 8.407457 CTACTTAGCAATTCAAAGACGATACA 57.593 34.615 0.00 0.00 0.00 2.29
4006 5831 9.454859 AAGCTTTATATAAGTTCAGAAAGTGCT 57.545 29.630 0.00 0.00 0.00 4.40
4007 5832 9.495754 CAAGCTTTATATAAGTTCAGAAAGTGC 57.504 33.333 0.00 0.00 0.00 4.40
4015 5840 9.944376 AGTTGACTCAAGCTTTATATAAGTTCA 57.056 29.630 0.00 0.00 0.00 3.18
4018 5843 9.593134 CAGAGTTGACTCAAGCTTTATATAAGT 57.407 33.333 13.20 0.00 45.21 2.24
4019 5844 9.809096 TCAGAGTTGACTCAAGCTTTATATAAG 57.191 33.333 13.20 0.00 45.21 1.73
4021 5846 9.809096 CTTCAGAGTTGACTCAAGCTTTATATA 57.191 33.333 13.20 0.00 45.21 0.86
4022 5847 7.279758 GCTTCAGAGTTGACTCAAGCTTTATAT 59.720 37.037 20.33 0.00 43.22 0.86
4023 5848 6.591834 GCTTCAGAGTTGACTCAAGCTTTATA 59.408 38.462 20.33 0.00 43.22 0.98
4024 5849 5.411053 GCTTCAGAGTTGACTCAAGCTTTAT 59.589 40.000 20.33 0.00 43.22 1.40
4025 5850 4.752101 GCTTCAGAGTTGACTCAAGCTTTA 59.248 41.667 20.33 0.00 43.22 1.85
4026 5851 3.563390 GCTTCAGAGTTGACTCAAGCTTT 59.437 43.478 20.33 0.00 43.22 3.51
4027 5852 3.137533 GCTTCAGAGTTGACTCAAGCTT 58.862 45.455 20.33 0.00 43.22 3.74
4028 5853 2.103771 TGCTTCAGAGTTGACTCAAGCT 59.896 45.455 24.46 3.66 45.07 3.74
4029 5854 2.479656 CTGCTTCAGAGTTGACTCAAGC 59.520 50.000 20.61 20.61 45.06 4.01
4030 5855 3.065655 CCTGCTTCAGAGTTGACTCAAG 58.934 50.000 13.20 9.61 45.21 3.02
4031 5856 2.808202 GCCTGCTTCAGAGTTGACTCAA 60.808 50.000 13.20 0.00 45.21 3.02
4079 5905 4.215349 GCACCTCATCTCTGCCAC 57.785 61.111 0.00 0.00 0.00 5.01
4131 5958 5.329399 ACTAGGGCATTTGTTATTGGACAA 58.671 37.500 0.00 0.00 37.73 3.18
4143 5970 3.362706 TCTACTGTCGACTAGGGCATTT 58.637 45.455 17.92 0.00 0.00 2.32
4243 6077 3.797039 CATGTAATCAGGTGGATGACGT 58.203 45.455 0.00 0.00 39.90 4.34
4244 6078 2.545526 GCATGTAATCAGGTGGATGACG 59.454 50.000 0.00 0.00 39.90 4.35
4245 6079 3.813443 AGCATGTAATCAGGTGGATGAC 58.187 45.455 0.00 0.00 37.81 3.06
4246 6080 4.080413 TCAAGCATGTAATCAGGTGGATGA 60.080 41.667 0.00 0.00 36.02 2.92
4512 6350 8.812329 CAACTATTTCTAGAGTGCTTACATGTC 58.188 37.037 0.00 0.00 0.00 3.06
4804 6728 7.047891 ACATCGTCACTATGAATGTGGTAAAT 58.952 34.615 0.00 0.00 36.21 1.40


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

AutoCloner maintained by Alex Coulton.