Multiple sequence alignment - TraesCS6D01G064800

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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 TraesCS6D01G064800 chr6D 100.000 6592 0 0 1 6592 31468888 31475479 0.000000e+00 12174.0
1 TraesCS6D01G064800 chr6D 93.201 1456 67 20 2833 4262 31269928 31268479 0.000000e+00 2111.0
2 TraesCS6D01G064800 chr6D 92.032 1255 71 15 4347 5595 31268399 31267168 0.000000e+00 1736.0
3 TraesCS6D01G064800 chr6D 88.971 1360 80 26 2940 4262 30097791 30096465 0.000000e+00 1616.0
4 TraesCS6D01G064800 chr6D 82.715 1267 167 31 4347 5595 29926518 29927750 0.000000e+00 1079.0
5 TraesCS6D01G064800 chr6D 86.961 974 61 21 1764 2690 31270879 31269925 0.000000e+00 1035.0
6 TraesCS6D01G064800 chr6D 80.469 1408 209 41 4347 5734 29852360 29853721 0.000000e+00 1016.0
7 TraesCS6D01G064800 chr6D 82.508 1292 97 45 1684 2908 30099023 30097794 0.000000e+00 1014.0
8 TraesCS6D01G064800 chr6D 90.846 721 57 7 1 718 31272731 31272017 0.000000e+00 957.0
9 TraesCS6D01G064800 chr6D 85.097 463 38 15 812 1267 29848972 29849410 1.690000e-120 444.0
10 TraesCS6D01G064800 chr6D 91.185 329 17 1 5467 5783 31267251 31266923 2.820000e-118 436.0
11 TraesCS6D01G064800 chr6D 85.446 426 31 8 789 1214 31271670 31271276 1.320000e-111 414.0
12 TraesCS6D01G064800 chr6D 82.816 419 38 22 813 1214 29922324 29922725 1.760000e-90 344.0
13 TraesCS6D01G064800 chr6D 82.410 415 34 19 815 1214 30099820 30099430 6.370000e-85 326.0
14 TraesCS6D01G064800 chr6D 94.118 102 6 0 5960 6061 221219409 221219308 8.850000e-34 156.0
15 TraesCS6D01G064800 chr6D 96.739 92 3 0 1257 1348 31470063 31470154 3.180000e-33 154.0
16 TraesCS6D01G064800 chr6D 96.739 92 3 0 1176 1267 31470144 31470235 3.180000e-33 154.0
17 TraesCS6D01G064800 chr6D 91.176 102 9 0 5879 5980 31266549 31266650 8.910000e-29 139.0
18 TraesCS6D01G064800 chr6D 95.000 60 3 0 4284 4343 31268487 31268428 1.960000e-15 95.3
19 TraesCS6D01G064800 chr6D 97.561 41 1 0 6421 6461 60481498 60481458 3.300000e-08 71.3
20 TraesCS6D01G064800 chr6A 96.398 3137 81 14 2473 5595 31753732 31750614 0.000000e+00 5138.0
21 TraesCS6D01G064800 chr6A 85.482 3010 308 60 2653 5602 46699569 46696629 0.000000e+00 3018.0
22 TraesCS6D01G064800 chr6A 88.821 1789 109 34 663 2435 31755441 31753728 0.000000e+00 2111.0
23 TraesCS6D01G064800 chr6A 89.068 1363 86 28 2940 4262 32741303 32742642 0.000000e+00 1633.0
24 TraesCS6D01G064800 chr6A 85.999 1457 119 41 4348 5783 32742720 32744112 0.000000e+00 1482.0
25 TraesCS6D01G064800 chr6A 83.281 1268 162 28 4347 5595 32811227 32809991 0.000000e+00 1122.0
26 TraesCS6D01G064800 chr6A 80.922 1389 204 39 4347 5717 32884590 32883245 0.000000e+00 1040.0
27 TraesCS6D01G064800 chr6A 83.932 1002 88 31 1684 2646 32740080 32741047 0.000000e+00 891.0
28 TraesCS6D01G064800 chr6A 95.804 429 18 0 5467 5895 31750697 31750269 0.000000e+00 693.0
29 TraesCS6D01G064800 chr6A 87.751 498 46 8 2754 3239 45353753 45354247 9.590000e-158 568.0
30 TraesCS6D01G064800 chr6A 87.366 467 48 8 1 459 31755904 31755441 5.860000e-145 525.0
31 TraesCS6D01G064800 chr6A 87.500 432 42 8 1 423 31796704 31796276 7.680000e-134 488.0
32 TraesCS6D01G064800 chr6A 79.140 791 67 55 1685 2426 46700632 46699891 2.170000e-124 457.0
33 TraesCS6D01G064800 chr6A 93.080 289 15 3 785 1073 31756781 31756498 1.020000e-112 418.0
34 TraesCS6D01G064800 chr6A 86.216 399 37 11 818 1214 32739288 32739670 3.680000e-112 416.0
35 TraesCS6D01G064800 chr6A 83.090 479 41 15 810 1267 32887970 32887511 3.700000e-107 399.0
36 TraesCS6D01G064800 chr6A 79.458 443 52 20 858 1282 46701065 46700644 1.810000e-70 278.0
37 TraesCS6D01G064800 chr6A 77.338 556 64 29 683 1214 32814463 32813946 8.420000e-69 272.0
38 TraesCS6D01G064800 chr6A 91.099 191 16 1 5939 6129 31750275 31750086 2.360000e-64 257.0
39 TraesCS6D01G064800 chr6A 96.190 105 4 0 5966 6070 463805433 463805329 8.790000e-39 172.0
40 TraesCS6D01G064800 chr6A 94.118 102 6 0 5960 6061 262052143 262052042 8.850000e-34 156.0
41 TraesCS6D01G064800 chr6A 88.333 120 14 0 663 782 31760450 31760331 1.920000e-30 145.0
42 TraesCS6D01G064800 chr6A 94.505 91 5 0 1257 1347 31754947 31754857 2.480000e-29 141.0
43 TraesCS6D01G064800 chr6A 90.000 50 5 0 5805 5854 46696019 46695970 1.530000e-06 65.8
44 TraesCS6D01G064800 chr6B 93.208 3416 135 31 2106 5469 56398309 56394939 0.000000e+00 4933.0
45 TraesCS6D01G064800 chr6B 96.010 2005 55 10 3597 5595 56378585 56376600 0.000000e+00 3236.0
46 TraesCS6D01G064800 chr6B 85.183 3010 314 61 2654 5595 79877174 79880119 0.000000e+00 2966.0
47 TraesCS6D01G064800 chr6B 97.224 1621 41 3 1982 3600 56380283 56378665 0.000000e+00 2741.0
48 TraesCS6D01G064800 chr6B 89.257 1359 88 22 2940 4262 57417260 57418596 0.000000e+00 1648.0
49 TraesCS6D01G064800 chr6B 86.259 1470 126 33 4347 5783 57418673 57420099 0.000000e+00 1526.0
50 TraesCS6D01G064800 chr6B 89.710 1137 80 16 244 1372 56382124 56381017 0.000000e+00 1417.0
51 TraesCS6D01G064800 chr6B 86.907 1222 103 22 1 1214 56400279 56399107 0.000000e+00 1317.0
52 TraesCS6D01G064800 chr6B 83.346 1267 164 27 4347 5595 57732753 57731516 0.000000e+00 1127.0
53 TraesCS6D01G064800 chr6B 90.793 858 48 12 3322 4157 50409585 50408737 0.000000e+00 1118.0
54 TraesCS6D01G064800 chr6B 82.855 1289 95 50 1685 2908 57416030 57417257 0.000000e+00 1040.0
55 TraesCS6D01G064800 chr6B 96.846 539 16 1 6055 6592 56376173 56375635 0.000000e+00 900.0
56 TraesCS6D01G064800 chr6B 92.599 581 27 9 1369 1944 56380845 56380276 0.000000e+00 821.0
57 TraesCS6D01G064800 chr6B 95.712 513 14 1 5467 5971 56376683 56376171 0.000000e+00 819.0
58 TraesCS6D01G064800 chr6B 91.597 357 21 3 1637 1990 56398690 56398340 9.940000e-133 484.0
59 TraesCS6D01G064800 chr6B 80.694 663 51 22 1946 2562 79876382 79877013 1.690000e-120 444.0
60 TraesCS6D01G064800 chr6B 84.048 420 41 17 813 1214 57737013 57736602 1.340000e-101 381.0
61 TraesCS6D01G064800 chr6B 82.725 411 49 12 811 1214 57415227 57415622 4.890000e-91 346.0
62 TraesCS6D01G064800 chr6B 83.920 199 17 11 6150 6341 56394236 56394046 6.790000e-40 176.0
63 TraesCS6D01G064800 chr6B 85.093 161 18 3 666 826 56382283 56382129 6.840000e-35 159.0
64 TraesCS6D01G064800 chr6B 96.703 91 3 0 1257 1347 56381216 56381126 1.140000e-32 152.0
65 TraesCS6D01G064800 chr6B 91.579 95 5 1 1176 1267 56381135 56381041 1.930000e-25 128.0
66 TraesCS6D01G064800 chr6B 90.000 50 5 0 5805 5854 79880685 79880734 1.530000e-06 65.8
67 TraesCS6D01G064800 chrUn 84.677 2493 229 65 3322 5734 137913395 137910976 0.000000e+00 2346.0
68 TraesCS6D01G064800 chrUn 88.160 1647 137 22 2653 4262 27472851 27474476 0.000000e+00 1908.0
69 TraesCS6D01G064800 chrUn 84.712 1269 147 25 4347 5595 27474556 27475797 0.000000e+00 1225.0
70 TraesCS6D01G064800 chrUn 87.174 499 48 8 2754 3239 137913906 137913411 2.690000e-153 553.0
71 TraesCS6D01G064800 chrUn 80.867 669 50 31 1946 2562 27472050 27472692 7.790000e-124 455.0
72 TraesCS6D01G064800 chrUn 82.778 540 58 14 1668 2188 68355763 68356286 3.630000e-122 449.0
73 TraesCS6D01G064800 chrUn 82.674 531 58 17 1668 2188 268239291 268239797 2.180000e-119 440.0
74 TraesCS6D01G064800 chrUn 82.674 531 58 17 1668 2188 312454620 312454114 2.180000e-119 440.0
75 TraesCS6D01G064800 chrUn 86.740 181 24 0 5467 5647 27475714 27475894 1.120000e-47 202.0
76 TraesCS6D01G064800 chrUn 85.047 107 11 4 6470 6575 95262297 95262195 3.250000e-18 104.0
77 TraesCS6D01G064800 chr2D 79.917 1454 195 59 4347 5734 48566433 48567855 0.000000e+00 977.0
78 TraesCS6D01G064800 chr2D 82.584 1068 104 32 1659 2661 48562867 48563917 0.000000e+00 867.0
79 TraesCS6D01G064800 chr2D 86.837 471 31 12 812 1267 48562243 48562697 1.280000e-136 497.0
80 TraesCS6D01G064800 chr2D 82.667 150 12 4 1257 1405 48562615 48562751 3.230000e-23 121.0
81 TraesCS6D01G064800 chr2B 87.171 608 55 12 4360 4947 96277722 96278326 0.000000e+00 669.0
82 TraesCS6D01G064800 chr4B 87.007 608 56 14 4360 4947 614205250 614204646 0.000000e+00 664.0
83 TraesCS6D01G064800 chr4B 93.396 106 6 1 5951 6056 403270795 403270691 8.850000e-34 156.0
84 TraesCS6D01G064800 chr4B 97.500 40 1 0 6422 6461 564902382 564902343 1.190000e-07 69.4
85 TraesCS6D01G064800 chr4B 88.889 54 4 2 6410 6461 167355495 167355548 1.530000e-06 65.8
86 TraesCS6D01G064800 chr3B 86.184 608 61 13 4360 4947 701122710 701122106 2.590000e-178 636.0
87 TraesCS6D01G064800 chr5A 84.259 432 42 14 1780 2190 655642348 655642774 1.330000e-106 398.0
88 TraesCS6D01G064800 chr5A 88.889 243 26 1 1946 2188 655640983 655641224 1.390000e-76 298.0
89 TraesCS6D01G064800 chr5A 89.744 117 9 2 5954 6070 9507996 9508109 5.330000e-31 147.0
90 TraesCS6D01G064800 chr5A 84.058 69 7 3 6391 6456 368561817 368561884 5.520000e-06 63.9
91 TraesCS6D01G064800 chr5B 81.391 532 58 19 1668 2188 664893064 664893565 4.790000e-106 396.0
92 TraesCS6D01G064800 chr5B 97.561 41 1 0 6422 6462 82475840 82475880 3.300000e-08 71.3
93 TraesCS6D01G064800 chr1A 98.901 91 1 0 5966 6056 498811735 498811645 5.290000e-36 163.0
94 TraesCS6D01G064800 chr1A 95.098 102 2 3 5965 6063 327008617 327008718 2.460000e-34 158.0
95 TraesCS6D01G064800 chr4D 92.453 106 7 1 5966 6070 436376804 436376699 4.120000e-32 150.0
96 TraesCS6D01G064800 chr4D 84.722 72 8 3 6494 6563 47500188 47500118 1.190000e-07 69.4
97 TraesCS6D01G064800 chr4D 97.500 40 1 0 6422 6461 486185382 486185343 1.190000e-07 69.4
98 TraesCS6D01G064800 chr2A 100.000 38 0 0 6422 6459 706204949 706204986 3.300000e-08 71.3
99 TraesCS6D01G064800 chr5D 97.500 40 1 0 6422 6461 533641527 533641488 1.190000e-07 69.4


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 TraesCS6D01G064800 chr6D 31468888 31475479 6591 False 12174.000000 12174 100.000000 1 6592 1 chr6D.!!$F2 6591
1 TraesCS6D01G064800 chr6D 30096465 30099820 3355 True 985.333333 1616 84.629667 815 4262 3 chr6D.!!$R3 3447
2 TraesCS6D01G064800 chr6D 31266923 31272731 5808 True 969.185714 2111 90.667286 1 5783 7 chr6D.!!$R4 5782
3 TraesCS6D01G064800 chr6D 29848972 29853721 4749 False 730.000000 1016 82.783000 812 5734 2 chr6D.!!$F3 4922
4 TraesCS6D01G064800 chr6D 29922324 29927750 5426 False 711.500000 1079 82.765500 813 5595 2 chr6D.!!$F4 4782
5 TraesCS6D01G064800 chr6A 31750086 31760450 10364 True 1178.500000 5138 91.925750 1 6129 8 chr6A.!!$R4 6128
6 TraesCS6D01G064800 chr6A 32739288 32744112 4824 False 1105.500000 1633 86.303750 818 5783 4 chr6A.!!$F2 4965
7 TraesCS6D01G064800 chr6A 46695970 46701065 5095 True 954.700000 3018 83.520000 858 5854 4 chr6A.!!$R7 4996
8 TraesCS6D01G064800 chr6A 32883245 32887970 4725 True 719.500000 1040 82.006000 810 5717 2 chr6A.!!$R6 4907
9 TraesCS6D01G064800 chr6A 32809991 32814463 4472 True 697.000000 1122 80.309500 683 5595 2 chr6A.!!$R5 4912
10 TraesCS6D01G064800 chr6B 56394046 56400279 6233 True 1727.500000 4933 88.908000 1 6341 4 chr6B.!!$R3 6340
11 TraesCS6D01G064800 chr6B 79876382 79880734 4352 False 1158.600000 2966 85.292333 1946 5854 3 chr6B.!!$F2 3908
12 TraesCS6D01G064800 chr6B 56375635 56382283 6648 True 1152.555556 3236 93.497333 244 6592 9 chr6B.!!$R2 6348
13 TraesCS6D01G064800 chr6B 57415227 57420099 4872 False 1140.000000 1648 85.274000 811 5783 4 chr6B.!!$F1 4972
14 TraesCS6D01G064800 chr6B 50408737 50409585 848 True 1118.000000 1118 90.793000 3322 4157 1 chr6B.!!$R1 835
15 TraesCS6D01G064800 chr6B 57731516 57737013 5497 True 754.000000 1127 83.697000 813 5595 2 chr6B.!!$R4 4782
16 TraesCS6D01G064800 chrUn 137910976 137913906 2930 True 1449.500000 2346 85.925500 2754 5734 2 chrUn.!!$R3 2980
17 TraesCS6D01G064800 chrUn 27472050 27475894 3844 False 947.500000 1908 85.119750 1946 5647 4 chrUn.!!$F3 3701
18 TraesCS6D01G064800 chrUn 68355763 68356286 523 False 449.000000 449 82.778000 1668 2188 1 chrUn.!!$F1 520
19 TraesCS6D01G064800 chrUn 268239291 268239797 506 False 440.000000 440 82.674000 1668 2188 1 chrUn.!!$F2 520
20 TraesCS6D01G064800 chrUn 312454114 312454620 506 True 440.000000 440 82.674000 1668 2188 1 chrUn.!!$R2 520
21 TraesCS6D01G064800 chr2D 48562243 48567855 5612 False 615.500000 977 83.001250 812 5734 4 chr2D.!!$F1 4922
22 TraesCS6D01G064800 chr2B 96277722 96278326 604 False 669.000000 669 87.171000 4360 4947 1 chr2B.!!$F1 587
23 TraesCS6D01G064800 chr4B 614204646 614205250 604 True 664.000000 664 87.007000 4360 4947 1 chr4B.!!$R3 587
24 TraesCS6D01G064800 chr3B 701122106 701122710 604 True 636.000000 636 86.184000 4360 4947 1 chr3B.!!$R1 587
25 TraesCS6D01G064800 chr5A 655640983 655642774 1791 False 348.000000 398 86.574000 1780 2190 2 chr5A.!!$F3 410
26 TraesCS6D01G064800 chr5B 664893064 664893565 501 False 396.000000 396 81.391000 1668 2188 1 chr5B.!!$F2 520

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
326 4886 0.554865 TGGGTGGAAGGATGGGGATT 60.555 55.000 0.00 0.00 0.0 3.01 F
446 5006 1.841302 ATCCTTGGCGGCTCTGTTGA 61.841 55.000 11.43 0.00 0.0 3.18 F
695 5258 2.033448 GGCGGTGGATTGGTCACA 59.967 61.111 0.00 0.00 36.9 3.58 F
2619 9083 2.005451 CCTGAATCTTGTCCGCTCTTG 58.995 52.381 0.00 0.00 0.0 3.02 F
2631 9103 1.728971 CCGCTCTTGTCACTTGTGATC 59.271 52.381 6.74 2.34 0.0 2.92 F
4414 13700 3.806625 ATGCCATCACAGTTTTATGCC 57.193 42.857 0.00 0.00 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 7010 1.002134 CAACCAGCTTGGGGTCGAT 60.002 57.895 7.06 0.0 43.37 3.59 R
1942 7578 1.565759 ACTGCTAAATCATCCCCAGCA 59.434 47.619 0.00 0.0 39.79 4.41 R
2631 9103 0.178068 CCAGTTCATACCACCCGAGG 59.822 60.000 0.00 0.0 0.00 4.63 R
4414 13700 4.326504 AATTTGAGTTTCTGCCAACAGG 57.673 40.909 0.00 0.0 44.59 4.00 R
4814 14151 4.440112 GCAAGTCAAAAACCTGCTAGTTGT 60.440 41.667 0.00 0.0 41.33 3.32 R
5933 15807 0.883833 CCAGCCAGGTTGTTGTGATC 59.116 55.000 2.14 0.0 0.00 2.92 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
237 4797 2.691011 GAGGCTACTCTCTAGTGTTGGG 59.309 54.545 0.00 0.00 40.68 4.12
238 4798 2.312140 AGGCTACTCTCTAGTGTTGGGA 59.688 50.000 0.00 0.00 36.36 4.37
239 4799 3.052490 AGGCTACTCTCTAGTGTTGGGAT 60.052 47.826 0.00 0.00 36.36 3.85
240 4800 3.707102 GGCTACTCTCTAGTGTTGGGATT 59.293 47.826 0.00 0.00 36.36 3.01
241 4801 4.162509 GGCTACTCTCTAGTGTTGGGATTT 59.837 45.833 0.00 0.00 36.36 2.17
242 4802 5.112686 GCTACTCTCTAGTGTTGGGATTTG 58.887 45.833 0.00 0.00 36.36 2.32
281 4841 5.934402 AGCCTCTTCTACTTCCGATTTTA 57.066 39.130 0.00 0.00 0.00 1.52
326 4886 0.554865 TGGGTGGAAGGATGGGGATT 60.555 55.000 0.00 0.00 0.00 3.01
331 4891 2.175499 GTGGAAGGATGGGGATTCATGA 59.825 50.000 0.00 0.00 0.00 3.07
344 4904 3.058432 GGATTCATGATGCCATTGAGTCG 60.058 47.826 0.00 0.00 0.00 4.18
348 4908 3.118445 TCATGATGCCATTGAGTCGGTTA 60.118 43.478 0.00 0.00 0.00 2.85
363 4923 5.957798 AGTCGGTTATCTCATCGTTTGTTA 58.042 37.500 0.00 0.00 0.00 2.41
365 4925 7.039882 AGTCGGTTATCTCATCGTTTGTTATT 58.960 34.615 0.00 0.00 0.00 1.40
380 4940 7.982354 TCGTTTGTTATTTTCCAAGGATTGTTT 59.018 29.630 0.00 0.00 46.99 2.83
406 4966 2.036733 CTGACCCGAGTTTACCAAGACA 59.963 50.000 0.00 0.00 0.00 3.41
419 4979 8.806146 AGTTTACCAAGACAATGCTTTATTCAT 58.194 29.630 0.00 0.00 0.00 2.57
446 5006 1.841302 ATCCTTGGCGGCTCTGTTGA 61.841 55.000 11.43 0.00 0.00 3.18
504 5064 4.405358 TCTCATTTTTCTTGGTTTGTGCCT 59.595 37.500 0.00 0.00 0.00 4.75
588 5151 9.561069 ACTAGTGACAGATTGAATTTTGTTAGT 57.439 29.630 0.00 1.31 0.00 2.24
597 5160 5.856126 TGAATTTTGTTAGTAGAGGCGTG 57.144 39.130 0.00 0.00 0.00 5.34
652 5215 6.795053 CACGAATGCAACCTATATTTTGTG 57.205 37.500 0.00 0.00 0.00 3.33
695 5258 2.033448 GGCGGTGGATTGGTCACA 59.967 61.111 0.00 0.00 36.90 3.58
897 5757 5.163733 GGGTTTTCGAAATAAATAGCCGTCA 60.164 40.000 12.12 0.00 0.00 4.35
1071 5967 2.434359 GTCGAAGAACCGGCCCAG 60.434 66.667 0.00 0.00 39.69 4.45
1222 6151 2.198304 GAAGGGCAAGGATCCGGTGT 62.198 60.000 16.92 0.00 0.00 4.16
1872 7401 2.093658 GGAAGAGGCGATGTACAGGAAA 60.094 50.000 0.33 0.00 0.00 3.13
1937 7573 2.872245 TGCTTGCTGTAGTCTGTGAAAC 59.128 45.455 0.00 0.00 37.35 2.78
1940 7576 3.013276 TGCTGTAGTCTGTGAAACTCG 57.987 47.619 0.00 0.00 38.04 4.18
1942 7578 3.181479 TGCTGTAGTCTGTGAAACTCGTT 60.181 43.478 0.00 0.00 38.04 3.85
1944 7580 3.120792 TGTAGTCTGTGAAACTCGTTGC 58.879 45.455 0.00 0.00 38.04 4.17
2050 7722 2.668457 AGTTCTTCTTGCGATGCGTTAG 59.332 45.455 0.00 0.00 0.00 2.34
2193 7878 7.373966 CACTTTTGCTACAATTGAAAATTGTGC 59.626 33.333 22.43 21.48 41.73 4.57
2288 7980 8.977412 TGTATCAGTTTCCAGTGTAGATGAATA 58.023 33.333 0.00 0.00 0.00 1.75
2290 7982 8.899427 ATCAGTTTCCAGTGTAGATGAATATG 57.101 34.615 0.00 0.00 0.00 1.78
2291 7983 7.275183 TCAGTTTCCAGTGTAGATGAATATGG 58.725 38.462 0.00 0.00 0.00 2.74
2292 7984 7.050377 CAGTTTCCAGTGTAGATGAATATGGT 58.950 38.462 0.00 0.00 0.00 3.55
2293 7985 7.011763 CAGTTTCCAGTGTAGATGAATATGGTG 59.988 40.741 0.00 0.00 0.00 4.17
2294 7986 6.560003 TTCCAGTGTAGATGAATATGGTGT 57.440 37.500 0.00 0.00 0.00 4.16
2295 7987 6.560003 TCCAGTGTAGATGAATATGGTGTT 57.440 37.500 0.00 0.00 0.00 3.32
2296 7988 7.669089 TCCAGTGTAGATGAATATGGTGTTA 57.331 36.000 0.00 0.00 0.00 2.41
2297 7989 8.084985 TCCAGTGTAGATGAATATGGTGTTAA 57.915 34.615 0.00 0.00 0.00 2.01
2482 8892 5.122869 CCTTGCTAATCCGGAATATGTGATG 59.877 44.000 9.01 0.00 0.00 3.07
2619 9083 2.005451 CCTGAATCTTGTCCGCTCTTG 58.995 52.381 0.00 0.00 0.00 3.02
2631 9103 1.728971 CCGCTCTTGTCACTTGTGATC 59.271 52.381 6.74 2.34 0.00 2.92
2719 10190 8.474025 TCTTTGGTTTCTGTTTGTTCATGTTAT 58.526 29.630 0.00 0.00 0.00 1.89
3063 11227 7.446625 AGACTGCATAATTGGACATAATTCCTC 59.553 37.037 0.00 0.00 36.51 3.71
3364 11544 8.251026 ACTCGATCTTGTTGATTCTGTACAATA 58.749 33.333 0.00 0.00 35.14 1.90
4052 13264 4.381411 GTCCTCCCCTCTTTTCATTATCG 58.619 47.826 0.00 0.00 0.00 2.92
4069 13281 7.600065 TCATTATCGTAGGATGTAGGTTTAGC 58.400 38.462 8.18 0.00 34.00 3.09
4414 13700 3.806625 ATGCCATCACAGTTTTATGCC 57.193 42.857 0.00 0.00 0.00 4.40
4814 14151 2.151202 GACGGAAACATGGCAGAGAAA 58.849 47.619 0.00 0.00 0.00 2.52
4845 14182 2.601314 GGTTTTTGACTTGCGTGGTTTC 59.399 45.455 0.00 0.00 0.00 2.78
4894 14232 3.928005 ATGCATTCCATCTCACTGACT 57.072 42.857 0.00 0.00 0.00 3.41
5445 14810 0.727398 GCTGTACTCGGCAAATCACC 59.273 55.000 0.00 0.00 44.61 4.02
5531 14971 3.009584 AGACTTCCCAGAGAAAACATCCC 59.990 47.826 0.00 0.00 32.88 3.85
5800 15666 8.121305 TGGTATACTTGTGCATTCTTTGAAAT 57.879 30.769 2.25 0.00 0.00 2.17
5869 15743 3.940209 TTGATTGATCAGTTTGGTGCC 57.060 42.857 0.00 0.00 38.19 5.01
5888 15762 3.069443 TGCCAAGGATGAAACTGTTTTCC 59.931 43.478 13.65 13.65 40.55 3.13
5891 15765 5.049828 CCAAGGATGAAACTGTTTTCCAAC 58.950 41.667 20.44 9.24 40.55 3.77
6056 15930 6.951062 ATTAGTTTACGGAGGGAGTACTAC 57.049 41.667 0.00 0.00 0.00 2.73
6146 16539 5.930135 ACATCAGTGGAAGTTGTAGAAACT 58.070 37.500 0.00 0.00 0.00 2.66
6176 16569 1.456296 CACATGTGGTGTCATCCAGG 58.544 55.000 18.51 0.00 42.75 4.45
6179 16572 1.075601 ATGTGGTGTCATCCAGGGTT 58.924 50.000 0.00 0.00 38.23 4.11
6210 16603 4.154918 GCTCTGGAATAAGGTTCAACACAG 59.845 45.833 0.00 0.00 0.00 3.66
6415 16808 5.602978 AGATACTCCATCCGTCCTAAAATGT 59.397 40.000 0.00 0.00 33.75 2.71
6457 16850 6.793478 TGATCTTATATTTTGGGATGGAGGG 58.207 40.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 4797 6.144563 GGCTAACAGAAAAAGAGCAACAAATC 59.855 38.462 0.00 0.00 34.76 2.17
238 4798 5.985530 GGCTAACAGAAAAAGAGCAACAAAT 59.014 36.000 0.00 0.00 34.76 2.32
239 4799 5.127031 AGGCTAACAGAAAAAGAGCAACAAA 59.873 36.000 0.00 0.00 34.76 2.83
240 4800 4.644685 AGGCTAACAGAAAAAGAGCAACAA 59.355 37.500 0.00 0.00 34.76 2.83
241 4801 4.207165 AGGCTAACAGAAAAAGAGCAACA 58.793 39.130 0.00 0.00 34.76 3.33
242 4802 4.517075 AGAGGCTAACAGAAAAAGAGCAAC 59.483 41.667 0.00 0.00 34.76 4.17
326 4886 1.210234 ACCGACTCAATGGCATCATGA 59.790 47.619 0.00 0.00 33.18 3.07
331 4891 3.134623 TGAGATAACCGACTCAATGGCAT 59.865 43.478 0.00 0.00 39.68 4.40
344 4904 8.455682 TGGAAAATAACAAACGATGAGATAACC 58.544 33.333 0.00 0.00 0.00 2.85
348 4908 7.393234 TCCTTGGAAAATAACAAACGATGAGAT 59.607 33.333 0.00 0.00 0.00 2.75
363 4923 8.306761 GTCAGATGTAAACAATCCTTGGAAAAT 58.693 33.333 0.00 0.00 34.12 1.82
365 4925 6.208599 GGTCAGATGTAAACAATCCTTGGAAA 59.791 38.462 0.00 0.00 34.12 3.13
380 4940 3.433343 TGGTAAACTCGGGTCAGATGTA 58.567 45.455 0.00 0.00 0.00 2.29
406 4966 6.041637 AGGATGCACATGATGAATAAAGCATT 59.958 34.615 0.00 0.00 41.07 3.56
419 4979 1.750018 CCGCCAAGGATGCACATGA 60.750 57.895 0.00 0.00 45.00 3.07
585 5148 0.182061 ATCGGACCACGCCTCTACTA 59.818 55.000 0.00 0.00 43.86 1.82
588 5151 2.125326 CCATCGGACCACGCCTCTA 61.125 63.158 0.00 0.00 43.86 2.43
589 5152 3.461773 CCATCGGACCACGCCTCT 61.462 66.667 0.00 0.00 43.86 3.69
597 5160 3.925090 CGGGGTAGCCATCGGACC 61.925 72.222 14.06 0.00 0.00 4.46
645 5208 1.668751 ACGTGTCAAGTCGCACAAAAT 59.331 42.857 0.00 0.00 35.51 1.82
652 5215 1.269166 CAGGATACGTGTCAAGTCGC 58.731 55.000 14.58 0.00 46.39 5.19
695 5258 0.625849 AGAAAGGCATTCGGGGACAT 59.374 50.000 0.00 0.00 43.15 3.06
741 5332 3.264193 ACAGGTCCATTTGCAGATACAGA 59.736 43.478 0.00 0.00 0.00 3.41
835 5682 5.359860 GTCCTTGGGAGTTTTCTTTTCTTCA 59.640 40.000 0.00 0.00 29.39 3.02
836 5683 5.221263 GGTCCTTGGGAGTTTTCTTTTCTTC 60.221 44.000 0.00 0.00 29.39 2.87
837 5684 4.649674 GGTCCTTGGGAGTTTTCTTTTCTT 59.350 41.667 0.00 0.00 29.39 2.52
897 5757 4.223700 GGATGGAAAATGGGAGAAGCTTTT 59.776 41.667 0.00 0.00 0.00 2.27
1266 6195 4.729856 CGGGGGTCGAACACCGTC 62.730 72.222 35.79 0.76 44.60 4.79
1633 7010 1.002134 CAACCAGCTTGGGGTCGAT 60.002 57.895 7.06 0.00 43.37 3.59
1872 7401 5.190528 ACCAGATTCATGTCATACCTGTTCT 59.809 40.000 0.00 0.00 0.00 3.01
1937 7573 1.755179 AAATCATCCCCAGCAACGAG 58.245 50.000 0.00 0.00 0.00 4.18
1940 7576 2.360165 CTGCTAAATCATCCCCAGCAAC 59.640 50.000 0.00 0.00 41.38 4.17
1942 7578 1.565759 ACTGCTAAATCATCCCCAGCA 59.434 47.619 0.00 0.00 39.79 4.41
1944 7580 3.889815 TCAACTGCTAAATCATCCCCAG 58.110 45.455 0.00 0.00 0.00 4.45
2050 7722 3.967987 TCCTTGCCTACCTCTAAATCTCC 59.032 47.826 0.00 0.00 0.00 3.71
2177 7862 4.582701 TCTCCGCACAATTTTCAATTGT 57.417 36.364 8.71 8.71 42.38 2.71
2181 7866 5.066375 CCTCATATCTCCGCACAATTTTCAA 59.934 40.000 0.00 0.00 0.00 2.69
2188 7873 2.965147 TGATCCTCATATCTCCGCACAA 59.035 45.455 0.00 0.00 0.00 3.33
2193 7878 5.409211 CAAGACATGATCCTCATATCTCCG 58.591 45.833 0.00 0.00 39.52 4.63
2288 7980 7.220890 ACTTCCCCTATAACATTAACACCAT 57.779 36.000 0.00 0.00 0.00 3.55
2290 7982 8.270030 ACTAACTTCCCCTATAACATTAACACC 58.730 37.037 0.00 0.00 0.00 4.16
2291 7983 9.322773 GACTAACTTCCCCTATAACATTAACAC 57.677 37.037 0.00 0.00 0.00 3.32
2292 7984 9.275572 AGACTAACTTCCCCTATAACATTAACA 57.724 33.333 0.00 0.00 0.00 2.41
2293 7985 9.543783 CAGACTAACTTCCCCTATAACATTAAC 57.456 37.037 0.00 0.00 0.00 2.01
2294 7986 9.496710 TCAGACTAACTTCCCCTATAACATTAA 57.503 33.333 0.00 0.00 0.00 1.40
2295 7987 9.496710 TTCAGACTAACTTCCCCTATAACATTA 57.503 33.333 0.00 0.00 0.00 1.90
2296 7988 7.989947 TCAGACTAACTTCCCCTATAACATT 57.010 36.000 0.00 0.00 0.00 2.71
2297 7989 7.989947 TTCAGACTAACTTCCCCTATAACAT 57.010 36.000 0.00 0.00 0.00 2.71
2482 8892 3.691118 TGCTCCACAGAATTAGCATCAAC 59.309 43.478 0.00 0.00 39.92 3.18
2619 9083 0.608640 ACCCGAGGATCACAAGTGAC 59.391 55.000 4.84 0.24 43.11 3.67
2631 9103 0.178068 CCAGTTCATACCACCCGAGG 59.822 60.000 0.00 0.00 0.00 4.63
2719 10190 8.141298 TGATTACACTAACAGGTCCAAGAATA 57.859 34.615 0.00 0.00 0.00 1.75
3063 11227 5.639757 TCATGTGAATGGCAAACGATTTAG 58.360 37.500 0.00 0.00 0.00 1.85
3364 11544 1.279496 TACATCCTGCCAGTCTTGCT 58.721 50.000 0.00 0.00 0.00 3.91
3690 12896 9.187455 GTTGTTGTTCAGTAAGAAAACAAGAAA 57.813 29.630 10.18 2.69 43.36 2.52
4414 13700 4.326504 AATTTGAGTTTCTGCCAACAGG 57.673 40.909 0.00 0.00 44.59 4.00
4814 14151 4.440112 GCAAGTCAAAAACCTGCTAGTTGT 60.440 41.667 0.00 0.00 41.33 3.32
4838 14175 2.562298 TGATGGAATTGCAGGAAACCAC 59.438 45.455 5.69 3.07 30.34 4.16
4845 14182 6.294342 CCACAATACTATGATGGAATTGCAGG 60.294 42.308 5.69 0.00 32.10 4.85
5231 14590 5.447624 ACAACAACAATAACAGGTTAGGC 57.552 39.130 0.00 0.00 0.00 3.93
5445 14810 2.603110 CACGTGGGTAGATGATTTCGTG 59.397 50.000 7.95 0.00 40.50 4.35
5531 14971 2.951726 TGACTTGAACTCTGATCAGCG 58.048 47.619 18.36 14.69 0.00 5.18
5819 15685 5.114780 GGCATCAGCAGTATGTATATCTGG 58.885 45.833 0.00 0.00 44.61 3.86
5824 15690 4.262592 CCAGTGGCATCAGCAGTATGTATA 60.263 45.833 0.00 0.00 44.61 1.47
5869 15743 5.659463 TGTTGGAAAACAGTTTCATCCTTG 58.341 37.500 15.10 0.00 44.29 3.61
5888 15762 7.285401 AGGCAGGGTAATATGAGTAAATTGTTG 59.715 37.037 0.00 0.00 0.00 3.33
5891 15765 6.294176 GCAGGCAGGGTAATATGAGTAAATTG 60.294 42.308 0.00 0.00 0.00 2.32
5933 15807 0.883833 CCAGCCAGGTTGTTGTGATC 59.116 55.000 2.14 0.00 0.00 2.92
6025 15899 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
6034 15908 5.193679 GGTAGTACTCCCTCCGTAAACTAA 58.806 45.833 0.00 0.00 0.00 2.24
6035 15909 4.227300 TGGTAGTACTCCCTCCGTAAACTA 59.773 45.833 6.02 0.00 0.00 2.24
6043 15917 2.093606 GCAGTTTGGTAGTACTCCCTCC 60.094 54.545 6.02 3.17 0.00 4.30
6056 15930 2.970576 CCACGTTTTGGCAGTTTGG 58.029 52.632 0.00 0.00 39.07 3.28
6080 16413 6.908825 TGAATCAATAGGTACAACAAGTTGC 58.091 36.000 12.54 0.00 44.03 4.17
6210 16603 7.391148 TTTCCCTTCTTGTAGATTGTATTGC 57.609 36.000 0.00 0.00 0.00 3.56
6388 16781 5.786264 TTAGGACGGATGGAGTATCTTTC 57.214 43.478 0.00 0.00 36.03 2.62


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

AutoCloner maintained by Alex Coulton.