Multiple sequence alignment - TraesCS2D01G135700

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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 TraesCS2D01G135700 chr2D 100.000 6402 0 0 1 6402 79872731 79879132 0.000000e+00 11823.0
1 TraesCS2D01G135700 chr2D 88.231 2634 188 61 3830 6402 42888721 42886149 0.000000e+00 3035.0
2 TraesCS2D01G135700 chr2D 89.524 1890 115 33 626 2472 42934933 42933084 0.000000e+00 2316.0
3 TraesCS2D01G135700 chr2D 95.574 949 42 0 2645 3593 630617935 630616987 0.000000e+00 1520.0
4 TraesCS2D01G135700 chr2D 89.312 683 48 13 1226 1897 79686171 79686839 0.000000e+00 833.0
5 TraesCS2D01G135700 chr2D 82.353 272 39 6 1996 2267 79686913 79687175 1.800000e-55 228.0
6 TraesCS2D01G135700 chr2D 85.366 164 13 4 3611 3771 42899872 42899717 6.640000e-35 159.0
7 TraesCS2D01G135700 chr2D 81.250 128 22 2 2415 2541 79688209 79688335 1.140000e-17 102.0
8 TraesCS2D01G135700 chr2D 94.000 50 2 1 4764 4812 648111237 648111286 2.480000e-09 75.0
9 TraesCS2D01G135700 chr2A 89.925 2263 131 37 4208 6402 80478209 80480442 0.000000e+00 2826.0
10 TraesCS2D01G135700 chr2A 89.249 1665 88 34 750 2372 80475358 80476973 0.000000e+00 1999.0
11 TraesCS2D01G135700 chr2A 88.415 751 60 13 1156 1897 80264102 80264834 0.000000e+00 880.0
12 TraesCS2D01G135700 chr2A 93.095 391 16 5 114 498 80461359 80461744 4.330000e-156 562.0
13 TraesCS2D01G135700 chr2A 91.155 407 20 5 3772 4169 80477692 80478091 7.300000e-149 538.0
14 TraesCS2D01G135700 chr2A 93.750 224 8 4 2355 2574 80476987 80477208 1.330000e-86 331.0
15 TraesCS2D01G135700 chr2A 93.678 174 9 1 3604 3777 80477398 80477569 6.370000e-65 259.0
16 TraesCS2D01G135700 chr2A 82.353 272 39 6 1996 2267 80264928 80265190 1.800000e-55 228.0
17 TraesCS2D01G135700 chr2A 86.449 214 20 7 543 754 80474869 80475075 6.460000e-55 226.0
18 TraesCS2D01G135700 chr2A 98.936 94 1 0 22 115 80460920 80461013 1.100000e-37 169.0
19 TraesCS2D01G135700 chr2A 97.826 46 1 0 4764 4809 295069669 295069624 5.320000e-11 80.5
20 TraesCS2D01G135700 chr2A 91.228 57 4 1 4752 4807 680546342 680546398 6.880000e-10 76.8
21 TraesCS2D01G135700 chr2B 94.785 1745 74 6 542 2279 131285652 131287386 0.000000e+00 2702.0
22 TraesCS2D01G135700 chr2B 88.896 1540 102 48 4404 5908 131289283 131290788 0.000000e+00 1832.0
23 TraesCS2D01G135700 chr2B 87.302 756 71 16 1156 1897 131180161 131180905 0.000000e+00 841.0
24 TraesCS2D01G135700 chr2B 95.382 498 21 2 5905 6402 131290890 131291385 0.000000e+00 791.0
25 TraesCS2D01G135700 chr2B 90.203 541 31 13 22 549 131285054 131285585 0.000000e+00 686.0
26 TraesCS2D01G135700 chr2B 94.017 234 10 4 2355 2585 131287523 131287755 1.020000e-92 351.0
27 TraesCS2D01G135700 chr2B 82.143 420 40 18 3756 4167 131288697 131289089 1.720000e-85 327.0
28 TraesCS2D01G135700 chr2B 80.515 272 44 6 1996 2267 131180991 131181253 3.910000e-47 200.0
29 TraesCS2D01G135700 chr2B 83.902 205 24 7 4905 5104 132706296 132706496 3.050000e-43 187.0
30 TraesCS2D01G135700 chr2B 92.208 77 6 0 5153 5229 63555630 63555554 6.790000e-20 110.0
31 TraesCS2D01G135700 chr2B 90.361 83 8 0 5144 5226 137138878 137138960 6.790000e-20 110.0
32 TraesCS2D01G135700 chr2B 98.039 51 1 0 2583 2633 131287828 131287878 8.840000e-14 89.8
33 TraesCS2D01G135700 chr7D 96.101 949 36 1 2645 3593 604993505 604992558 0.000000e+00 1546.0
34 TraesCS2D01G135700 chr7D 83.929 112 16 2 1733 1843 602847922 602847812 8.780000e-19 106.0
35 TraesCS2D01G135700 chr4D 95.532 940 39 1 2652 3591 3499751 3498815 0.000000e+00 1500.0
36 TraesCS2D01G135700 chr1B 95.047 949 46 1 2645 3593 543087373 543088320 0.000000e+00 1491.0
37 TraesCS2D01G135700 chr1B 84.586 266 29 8 4847 5104 587582864 587583125 2.960000e-63 254.0
38 TraesCS2D01G135700 chr5B 94.837 949 49 0 2645 3593 19112154 19113102 0.000000e+00 1482.0
39 TraesCS2D01G135700 chr5B 85.714 266 26 8 4847 5104 546457330 546457591 2.940000e-68 270.0
40 TraesCS2D01G135700 chr5B 78.723 329 41 18 4905 5230 534882036 534881734 6.550000e-45 193.0
41 TraesCS2D01G135700 chr5B 90.780 141 11 2 4905 5044 534873761 534873622 3.050000e-43 187.0
42 TraesCS2D01G135700 chr5B 79.724 217 42 2 1627 1842 421834121 421833906 8.590000e-34 156.0
43 TraesCS2D01G135700 chr5B 87.037 108 14 0 1405 1512 421861409 421861302 8.720000e-24 122.0
44 TraesCS2D01G135700 chr5B 91.358 81 7 0 5144 5224 546457604 546457684 1.890000e-20 111.0
45 TraesCS2D01G135700 chr1D 94.931 947 45 1 2645 3591 75907636 75906693 0.000000e+00 1480.0
46 TraesCS2D01G135700 chr3B 94.831 948 48 1 2646 3593 257316211 257317157 0.000000e+00 1478.0
47 TraesCS2D01G135700 chr3B 90.452 199 17 2 4847 5044 35683258 35683455 1.770000e-65 261.0
48 TraesCS2D01G135700 chr3B 84.804 204 25 4 4906 5104 403866072 403866274 3.910000e-47 200.0
49 TraesCS2D01G135700 chr3B 87.879 66 7 1 4700 4765 35683133 35683197 6.880000e-10 76.8
50 TraesCS2D01G135700 chr6A 94.731 949 50 0 2645 3593 2366526 2365578 0.000000e+00 1476.0
51 TraesCS2D01G135700 chr7A 94.521 949 51 1 2645 3593 27256487 27257434 0.000000e+00 1463.0
52 TraesCS2D01G135700 chr7A 82.787 122 16 3 1398 1519 720912008 720912124 3.160000e-18 104.0
53 TraesCS2D01G135700 chrUn 84.791 263 28 8 4850 5104 205346072 205345814 2.960000e-63 254.0
54 TraesCS2D01G135700 chrUn 84.586 266 29 8 4847 5104 349933671 349933932 2.960000e-63 254.0
55 TraesCS2D01G135700 chrUn 84.030 263 30 8 4850 5104 168660020 168659762 6.410000e-60 243.0
56 TraesCS2D01G135700 chr7B 84.211 266 30 8 4847 5104 690176721 690176982 1.380000e-61 248.0
57 TraesCS2D01G135700 chr7B 92.593 81 6 0 5144 5224 690176995 690177075 4.060000e-22 117.0
58 TraesCS2D01G135700 chr7B 88.506 87 10 0 5144 5230 612587941 612588027 8.780000e-19 106.0
59 TraesCS2D01G135700 chr7B 87.879 66 7 1 4700 4765 690176596 690176660 6.880000e-10 76.8
60 TraesCS2D01G135700 chr5D 79.747 237 46 2 1626 1861 357061773 357061538 3.070000e-38 171.0
61 TraesCS2D01G135700 chr5D 89.474 114 10 2 1731 1843 357079934 357079822 6.690000e-30 143.0
62 TraesCS2D01G135700 chr5A 79.358 218 43 2 1626 1842 458316632 458316416 1.110000e-32 152.0
63 TraesCS2D01G135700 chr5A 89.474 114 10 2 1731 1843 458330747 458330635 6.690000e-30 143.0
64 TraesCS2D01G135700 chr5A 88.333 60 5 2 4747 4806 311673966 311673909 3.200000e-08 71.3
65 TraesCS2D01G135700 chr4A 77.350 234 43 8 1624 1852 27297908 27297680 5.210000e-26 130.0
66 TraesCS2D01G135700 chr4A 85.938 64 7 2 4764 4825 504216586 504216523 4.140000e-07 67.6
67 TraesCS2D01G135700 chr3A 97.727 44 1 0 4764 4807 163801529 163801486 6.880000e-10 76.8
68 TraesCS2D01G135700 chr6B 92.308 52 3 1 4764 4814 48981472 48981421 8.900000e-09 73.1
69 TraesCS2D01G135700 chr3D 84.286 70 9 2 4764 4833 66523423 66523490 4.140000e-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 TraesCS2D01G135700 chr2D 79872731 79879132 6401 False 11823.000000 11823 100.000000 1 6402 1 chr2D.!!$F1 6401
1 TraesCS2D01G135700 chr2D 42886149 42888721 2572 True 3035.000000 3035 88.231000 3830 6402 1 chr2D.!!$R1 2572
2 TraesCS2D01G135700 chr2D 42933084 42934933 1849 True 2316.000000 2316 89.524000 626 2472 1 chr2D.!!$R3 1846
3 TraesCS2D01G135700 chr2D 630616987 630617935 948 True 1520.000000 1520 95.574000 2645 3593 1 chr2D.!!$R4 948
4 TraesCS2D01G135700 chr2D 79686171 79688335 2164 False 387.666667 833 84.305000 1226 2541 3 chr2D.!!$F3 1315
5 TraesCS2D01G135700 chr2A 80474869 80480442 5573 False 1029.833333 2826 90.701000 543 6402 6 chr2A.!!$F4 5859
6 TraesCS2D01G135700 chr2A 80264102 80265190 1088 False 554.000000 880 85.384000 1156 2267 2 chr2A.!!$F2 1111
7 TraesCS2D01G135700 chr2A 80460920 80461744 824 False 365.500000 562 96.015500 22 498 2 chr2A.!!$F3 476
8 TraesCS2D01G135700 chr2B 131285054 131291385 6331 False 968.400000 2702 91.923571 22 6402 7 chr2B.!!$F4 6380
9 TraesCS2D01G135700 chr2B 131180161 131181253 1092 False 520.500000 841 83.908500 1156 2267 2 chr2B.!!$F3 1111
10 TraesCS2D01G135700 chr7D 604992558 604993505 947 True 1546.000000 1546 96.101000 2645 3593 1 chr7D.!!$R2 948
11 TraesCS2D01G135700 chr4D 3498815 3499751 936 True 1500.000000 1500 95.532000 2652 3591 1 chr4D.!!$R1 939
12 TraesCS2D01G135700 chr1B 543087373 543088320 947 False 1491.000000 1491 95.047000 2645 3593 1 chr1B.!!$F1 948
13 TraesCS2D01G135700 chr5B 19112154 19113102 948 False 1482.000000 1482 94.837000 2645 3593 1 chr5B.!!$F1 948
14 TraesCS2D01G135700 chr1D 75906693 75907636 943 True 1480.000000 1480 94.931000 2645 3591 1 chr1D.!!$R1 946
15 TraesCS2D01G135700 chr3B 257316211 257317157 946 False 1478.000000 1478 94.831000 2646 3593 1 chr3B.!!$F1 947
16 TraesCS2D01G135700 chr6A 2365578 2366526 948 True 1476.000000 1476 94.731000 2645 3593 1 chr6A.!!$R1 948
17 TraesCS2D01G135700 chr7A 27256487 27257434 947 False 1463.000000 1463 94.521000 2645 3593 1 chr7A.!!$F1 948

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
341 696 1.000060 TCCTAACCCAACGAACGAGTG 60.000 52.381 0.14 0.00 0.00 3.51 F
468 827 1.078709 ATCGACGACATGCAAAGTGG 58.921 50.000 0.00 1.76 0.00 4.00 F
518 880 1.208358 CTGCGACAAGGCACACATG 59.792 57.895 0.00 0.00 38.17 3.21 F
1767 2558 1.227674 GGCTAACTGGATGGAGCGG 60.228 63.158 0.00 0.00 35.71 5.52 F
2547 4294 0.109342 AGCCTGCAGGTATGTATGCC 59.891 55.000 32.81 13.48 41.85 4.40 F
3380 5212 0.038618 TCTGACACGTCGACAATGGG 60.039 55.000 17.16 2.70 0.00 4.00 F
4527 7241 1.026182 TCTTGCTAGTTGCCCATGCG 61.026 55.000 0.00 0.00 41.78 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 2558 1.078637 GCCCTTGTACTCCGGGAAC 60.079 63.158 15.89 0.0 40.55 3.62 R
1978 2804 1.647346 TCTGTTTCACACCACACGTC 58.353 50.000 0.00 0.0 0.00 4.34 R
1980 2806 2.286950 CCAATCTGTTTCACACCACACG 60.287 50.000 0.00 0.0 0.00 4.49 R
2578 4335 0.322726 TGTGTGAGATGCATGGTGGG 60.323 55.000 2.46 0.0 0.00 4.61 R
3690 6143 0.395724 ATTGGGTTTCCTCCATCGGC 60.396 55.000 0.00 0.0 33.82 5.54 R
4678 7424 1.149288 TCCCGGATAATAGGCAGGACT 59.851 52.381 0.73 0.0 0.00 3.85 R
5927 8846 2.624838 AGTTTGGCAATCACTGTTCAGG 59.375 45.455 10.67 0.0 0.00 3.86 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
121 473 2.427453 GAGGCTGACCGATTAAGACTCA 59.573 50.000 0.00 0.00 44.21 3.41
341 696 1.000060 TCCTAACCCAACGAACGAGTG 60.000 52.381 0.14 0.00 0.00 3.51
415 771 5.648960 TGGTTTAACTAAATCGATGGGTTCC 59.351 40.000 0.00 3.71 0.00 3.62
457 816 4.669318 TCAACCTTTATCTCATCGACGAC 58.331 43.478 0.00 0.00 0.00 4.34
459 818 4.920640 ACCTTTATCTCATCGACGACAT 57.079 40.909 0.00 0.00 0.00 3.06
468 827 1.078709 ATCGACGACATGCAAAGTGG 58.921 50.000 0.00 1.76 0.00 4.00
517 879 2.620112 GCTGCGACAAGGCACACAT 61.620 57.895 0.00 0.00 38.17 3.21
518 880 1.208358 CTGCGACAAGGCACACATG 59.792 57.895 0.00 0.00 38.17 3.21
523 888 2.808244 CGACAAGGCACACATGTTTTT 58.192 42.857 0.00 0.00 0.00 1.94
554 993 9.846248 CGATTTATCAAAGAAAAGATGGTTCTT 57.154 29.630 0.00 0.00 45.14 2.52
563 1002 9.817809 AAAGAAAAGATGGTTCTTAAGGAAAAC 57.182 29.630 1.85 0.00 43.00 2.43
603 1042 6.413018 GATAAAATCGAAAACGTAGGTGGT 57.587 37.500 0.00 0.00 0.00 4.16
608 1047 1.538634 CGAAAACGTAGGTGGTGTGGA 60.539 52.381 0.00 0.00 0.00 4.02
616 1055 2.838637 AGGTGGTGTGGAAGGAAAAA 57.161 45.000 0.00 0.00 0.00 1.94
712 1152 2.672478 CGAGGACCAGACTAACAGCAAG 60.672 54.545 0.00 0.00 0.00 4.01
728 1168 3.622060 AAGTGGCCGGGGATCAACG 62.622 63.158 2.18 0.00 0.00 4.10
781 1508 2.280186 GGACGCATGGACGGATCC 60.280 66.667 0.00 0.00 46.48 3.36
850 1581 2.504175 GGCTCCTACCTGTCACCATTTA 59.496 50.000 0.00 0.00 0.00 1.40
1297 2038 4.421479 CGAGCGGCGTGGACTTCT 62.421 66.667 9.37 0.00 34.64 2.85
1485 2238 4.083862 GAGGAGCTCGGCCCGTTT 62.084 66.667 7.83 0.00 0.00 3.60
1620 2403 3.070446 AGTGATCGACCGGGCAATTAATA 59.930 43.478 8.76 0.00 0.00 0.98
1621 2404 4.000988 GTGATCGACCGGGCAATTAATAT 58.999 43.478 8.76 0.00 0.00 1.28
1767 2558 1.227674 GGCTAACTGGATGGAGCGG 60.228 63.158 0.00 0.00 35.71 5.52
2050 2882 1.165270 GCAAGGGCATGTACGACTTT 58.835 50.000 0.00 0.00 40.72 2.66
2245 3077 0.889638 AGTCGGAGAAGCTCGTCACA 60.890 55.000 0.00 0.00 39.69 3.58
2328 3189 0.604780 ACTGCCAGTGCTAAGTGCTG 60.605 55.000 0.00 0.00 43.37 4.41
2349 3210 4.876125 TGAATGATCGATGAGGCTAGTTC 58.124 43.478 0.54 0.00 0.00 3.01
2432 4179 1.464997 GGCCAGATCGACAACTTTGAC 59.535 52.381 0.00 0.00 0.00 3.18
2542 4289 1.200760 TGGTCAGCCTGCAGGTATGT 61.201 55.000 32.81 13.43 37.57 2.29
2543 4290 0.830648 GGTCAGCCTGCAGGTATGTA 59.169 55.000 32.81 17.81 37.57 2.29
2544 4291 1.417890 GGTCAGCCTGCAGGTATGTAT 59.582 52.381 32.81 10.37 37.57 2.29
2545 4292 2.487934 GTCAGCCTGCAGGTATGTATG 58.512 52.381 32.81 20.40 37.57 2.39
2547 4294 0.109342 AGCCTGCAGGTATGTATGCC 59.891 55.000 32.81 13.48 41.85 4.40
2551 4298 1.141657 CTGCAGGTATGTATGCCACCT 59.858 52.381 5.57 0.00 43.56 4.00
2552 4299 2.368548 CTGCAGGTATGTATGCCACCTA 59.631 50.000 5.57 0.00 40.77 3.08
2553 4300 2.104111 TGCAGGTATGTATGCCACCTAC 59.896 50.000 4.24 0.63 40.77 3.18
2554 4301 2.104111 GCAGGTATGTATGCCACCTACA 59.896 50.000 4.24 0.00 40.77 2.74
2578 4335 0.674534 CTACACCCATCCTACTCGCC 59.325 60.000 0.00 0.00 0.00 5.54
2602 4434 2.302733 ACCATGCATCTCACACAGTACA 59.697 45.455 0.00 0.00 0.00 2.90
2633 4465 3.245948 ACCTGGAGACTCCTCTCTGATTT 60.246 47.826 22.14 0.00 42.55 2.17
2635 4467 5.147032 CCTGGAGACTCCTCTCTGATTTAT 58.853 45.833 22.14 0.00 42.55 1.40
2636 4468 5.602145 CCTGGAGACTCCTCTCTGATTTATT 59.398 44.000 22.14 0.00 42.55 1.40
2639 4471 8.012957 TGGAGACTCCTCTCTGATTTATTTAC 57.987 38.462 22.14 0.00 42.55 2.01
2640 4472 7.142680 GGAGACTCCTCTCTGATTTATTTACG 58.857 42.308 14.72 0.00 42.55 3.18
2641 4473 7.201839 GGAGACTCCTCTCTGATTTATTTACGT 60.202 40.741 14.72 0.00 42.55 3.57
2643 4475 9.186837 AGACTCCTCTCTGATTTATTTACGTAA 57.813 33.333 3.29 3.29 0.00 3.18
2817 4649 2.430921 CCGGAGTATCGCATCGGC 60.431 66.667 0.00 0.00 34.37 5.54
3051 4883 4.954118 TCCGGTGGTGGTGAGCCT 62.954 66.667 0.00 0.00 35.27 4.58
3380 5212 0.038618 TCTGACACGTCGACAATGGG 60.039 55.000 17.16 2.70 0.00 4.00
3411 5243 3.011517 ATGGAGCAGCGGGGTCTT 61.012 61.111 9.83 0.00 43.58 3.01
3422 5254 4.666253 GGGTCTTGCTGCTGGGCA 62.666 66.667 0.00 0.00 40.74 5.36
3516 5348 3.599343 CAAGGTAGATGCAGCAGTACAA 58.401 45.455 16.14 0.00 0.00 2.41
3690 6143 1.081892 CACAATCAAGCTGAGACCGG 58.918 55.000 0.00 0.00 0.00 5.28
3694 6147 4.069232 CAAGCTGAGACCGGCCGA 62.069 66.667 30.73 4.63 45.76 5.54
3696 6149 3.376935 AAGCTGAGACCGGCCGATG 62.377 63.158 30.73 14.21 45.76 3.84
3703 6156 3.006728 ACCGGCCGATGGAGGAAA 61.007 61.111 30.73 0.00 0.00 3.13
3729 6182 2.125106 GGGGTCGACATGGCACTC 60.125 66.667 18.91 0.00 0.00 3.51
3893 6489 4.876107 CACACCACACTAATCAATACCCTC 59.124 45.833 0.00 0.00 0.00 4.30
3946 6550 8.122952 CAGTTTAGAGTTTAGACCAACACTTTG 58.877 37.037 0.00 0.00 31.09 2.77
3971 6575 2.236766 ACCAATATCCTACGCTACGCT 58.763 47.619 0.00 0.00 0.00 5.07
4038 6645 2.433491 GCGTGCATGGACGGTGTA 60.433 61.111 35.56 0.00 39.81 2.90
4229 6923 3.124297 GTGAGGCAATTCTCTTCGAGTTG 59.876 47.826 0.00 0.00 40.98 3.16
4230 6924 3.244215 TGAGGCAATTCTCTTCGAGTTGT 60.244 43.478 0.00 0.00 40.38 3.32
4237 6931 9.042008 GGCAATTCTCTTCGAGTTGTAATAATA 57.958 33.333 0.00 0.00 40.38 0.98
4269 6967 4.769063 TGGGGCATGCGTGGTACG 62.769 66.667 12.44 0.00 45.88 3.67
4277 6975 1.676678 ATGCGTGGTACGAGCTCCAT 61.677 55.000 8.47 0.00 46.05 3.41
4282 6980 1.066303 GTGGTACGAGCTCCATCTGAG 59.934 57.143 8.47 0.00 44.47 3.35
4285 6983 3.150767 GGTACGAGCTCCATCTGAGTAT 58.849 50.000 8.47 0.00 43.48 2.12
4320 7018 2.853003 GCGTGTTCTCGAGGAAAGATAC 59.147 50.000 13.56 2.19 35.51 2.24
4332 7030 4.694339 AGGAAAGATACGCTCATACCAAC 58.306 43.478 0.00 0.00 0.00 3.77
4339 7045 2.893637 ACGCTCATACCAACATCTGAC 58.106 47.619 0.00 0.00 0.00 3.51
4465 7174 3.743521 TCTTTAAGTCTGTGCACATGCT 58.256 40.909 22.00 17.82 42.66 3.79
4527 7241 1.026182 TCTTGCTAGTTGCCCATGCG 61.026 55.000 0.00 0.00 41.78 4.73
4540 7254 1.078214 CATGCGGATGACTGGGTGT 60.078 57.895 12.09 0.00 0.00 4.16
4570 7284 7.035840 GTGCAATCACATCCTTTCAATCTAT 57.964 36.000 0.00 0.00 42.66 1.98
4678 7424 2.539338 GGTCGACAGCGCCAAAACA 61.539 57.895 18.91 0.00 37.46 2.83
4762 7508 4.966366 GCATCACGAGCATTTTCAGATTAC 59.034 41.667 0.00 0.00 0.00 1.89
4767 7513 7.097192 TCACGAGCATTTTCAGATTACTAGTT 58.903 34.615 0.00 0.00 0.00 2.24
5026 7807 1.836802 CTCTCCTCTTCCCTTCCCAAG 59.163 57.143 0.00 0.00 0.00 3.61
5045 7826 1.672881 AGTCTGTTCACTGCAACAAGC 59.327 47.619 0.00 0.00 45.96 4.01
5056 7844 4.266029 CACTGCAACAAGCTAACAAACAAG 59.734 41.667 0.00 0.00 45.94 3.16
5060 7848 5.129901 CAACAAGCTAACAAACAAGTTGC 57.870 39.130 1.81 0.00 41.31 4.17
5076 7864 4.483476 AGTTGCGGTGAACTTTCATAAC 57.517 40.909 0.00 0.51 39.73 1.89
5104 7892 3.058293 TGCTAAAGAAGTGCACGGAAATG 60.058 43.478 12.01 1.94 0.00 2.32
5357 8150 3.149196 GTGCTTGTCCAGAATTTCCTCA 58.851 45.455 0.00 0.00 0.00 3.86
5597 8406 7.736893 AGATAGGAAACTGTATGGTGTAATCC 58.263 38.462 0.00 0.00 43.88 3.01
6010 8929 7.159372 TGACTAACCAGGAGAATGAAACTTAC 58.841 38.462 0.00 0.00 0.00 2.34
6058 8977 8.946085 CACTACAAAGTCTGAATATTTGCCTTA 58.054 33.333 9.76 0.00 37.42 2.69
6114 9033 1.281899 GCAATCTGACTACGCCTCAC 58.718 55.000 0.00 0.00 0.00 3.51
6167 9086 8.547967 TTTTTGCAGAAACAGTAGATACCTAG 57.452 34.615 0.00 0.00 0.00 3.02
6201 9120 9.209175 GAACATACCACATGAATATACTCCTTC 57.791 37.037 0.00 0.00 0.00 3.46
6204 9123 8.993121 CATACCACATGAATATACTCCTTCAAC 58.007 37.037 0.00 0.00 35.20 3.18
6252 9171 6.237942 CCACGCAAACAAAAATACAATCAACA 60.238 34.615 0.00 0.00 0.00 3.33
6272 9192 8.321650 TCAACAAATAATGGCAATTTCTTTCC 57.678 30.769 0.00 0.00 0.00 3.13
6285 9205 6.375455 GCAATTTCTTTCCTATTCCACAGAGA 59.625 38.462 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.060421 GGGGAAACATATTCTTAGTCCAATCA 58.940 38.462 0.00 0.00 0.00 2.57
1 2 7.290813 AGGGGAAACATATTCTTAGTCCAATC 58.709 38.462 0.00 0.00 0.00 2.67
2 3 7.226059 AGGGGAAACATATTCTTAGTCCAAT 57.774 36.000 0.00 0.00 0.00 3.16
3 4 6.652205 AGGGGAAACATATTCTTAGTCCAA 57.348 37.500 0.00 0.00 0.00 3.53
4 5 6.011981 ACAAGGGGAAACATATTCTTAGTCCA 60.012 38.462 0.00 0.00 0.00 4.02
5 6 6.424032 ACAAGGGGAAACATATTCTTAGTCC 58.576 40.000 0.00 0.00 0.00 3.85
6 7 7.110155 TGACAAGGGGAAACATATTCTTAGTC 58.890 38.462 0.00 0.00 0.00 2.59
7 8 7.027874 TGACAAGGGGAAACATATTCTTAGT 57.972 36.000 0.00 0.00 0.00 2.24
8 9 8.525290 AATGACAAGGGGAAACATATTCTTAG 57.475 34.615 0.00 0.00 0.00 2.18
10 11 9.492730 AATAATGACAAGGGGAAACATATTCTT 57.507 29.630 0.00 0.00 0.00 2.52
16 17 8.485392 CCAAATAATAATGACAAGGGGAAACAT 58.515 33.333 0.00 0.00 0.00 2.71
17 18 7.580495 GCCAAATAATAATGACAAGGGGAAACA 60.580 37.037 0.00 0.00 0.00 2.83
18 19 6.761242 GCCAAATAATAATGACAAGGGGAAAC 59.239 38.462 0.00 0.00 0.00 2.78
19 20 6.671779 AGCCAAATAATAATGACAAGGGGAAA 59.328 34.615 0.00 0.00 0.00 3.13
20 21 6.098124 CAGCCAAATAATAATGACAAGGGGAA 59.902 38.462 0.00 0.00 0.00 3.97
121 473 4.897509 ATCACACACGGATGATATGGAT 57.102 40.909 0.00 0.00 33.73 3.41
341 696 4.728021 GCCGCTGTCAAGAAACTAATAAGC 60.728 45.833 0.00 0.00 0.00 3.09
374 730 7.593644 AGTTAAACCAATCGTGCACTTAATTTC 59.406 33.333 16.19 0.38 0.00 2.17
415 771 4.002982 TGAGGTTGATGGTTTCTTCATCG 58.997 43.478 0.00 0.00 42.73 3.84
468 827 7.328493 GGCCAATTATAGTGTTTTGTCAAAGAC 59.672 37.037 0.00 0.42 36.59 3.01
554 993 1.769006 CCCCCACCGGTTTTCCTTA 59.231 57.895 2.97 0.00 37.95 2.69
603 1042 1.679153 GCGGTTCTTTTTCCTTCCACA 59.321 47.619 0.00 0.00 0.00 4.17
608 1047 4.149598 AGGTTATGCGGTTCTTTTTCCTT 58.850 39.130 0.00 0.00 0.00 3.36
781 1508 7.550712 TCCGATACAAGATAGATCATCCATTG 58.449 38.462 0.00 1.52 33.75 2.82
788 1515 7.094162 GGTTCTCATCCGATACAAGATAGATCA 60.094 40.741 0.00 0.00 0.00 2.92
850 1581 4.454728 CAATTGAATTTGGACGTGGGAT 57.545 40.909 0.00 0.00 0.00 3.85
941 1679 1.226831 GAGCTAGAGCACGCTGGAC 60.227 63.158 4.01 0.00 45.16 4.02
1145 1883 2.997315 CCAGCGACTCCCAGGACA 60.997 66.667 0.00 0.00 0.00 4.02
1297 2038 2.689785 CGTACCCGGCGTACTGTGA 61.690 63.158 22.69 0.00 44.52 3.58
1620 2403 2.180204 GTTCGCCGCTGCACCATAT 61.180 57.895 0.00 0.00 37.32 1.78
1621 2404 2.817834 GTTCGCCGCTGCACCATA 60.818 61.111 0.00 0.00 37.32 2.74
1767 2558 1.078637 GCCCTTGTACTCCGGGAAC 60.079 63.158 15.89 0.00 40.55 3.62
1978 2804 1.647346 TCTGTTTCACACCACACGTC 58.353 50.000 0.00 0.00 0.00 4.34
1979 2805 2.325583 ATCTGTTTCACACCACACGT 57.674 45.000 0.00 0.00 0.00 4.49
1980 2806 2.286950 CCAATCTGTTTCACACCACACG 60.287 50.000 0.00 0.00 0.00 4.49
2274 3106 4.602259 CCGGCTGTGGTGTCACGT 62.602 66.667 0.00 0.00 46.42 4.49
2328 3189 3.917380 CGAACTAGCCTCATCGATCATTC 59.083 47.826 0.00 0.00 37.48 2.67
2542 4289 4.342951 GGTGTAGTGTATGTAGGTGGCATA 59.657 45.833 0.00 0.00 0.00 3.14
2543 4290 3.134081 GGTGTAGTGTATGTAGGTGGCAT 59.866 47.826 0.00 0.00 0.00 4.40
2544 4291 2.498481 GGTGTAGTGTATGTAGGTGGCA 59.502 50.000 0.00 0.00 0.00 4.92
2545 4292 2.159000 GGGTGTAGTGTATGTAGGTGGC 60.159 54.545 0.00 0.00 0.00 5.01
2547 4294 4.202223 GGATGGGTGTAGTGTATGTAGGTG 60.202 50.000 0.00 0.00 0.00 4.00
2551 4298 6.022107 AGTAGGATGGGTGTAGTGTATGTA 57.978 41.667 0.00 0.00 0.00 2.29
2552 4299 4.880164 AGTAGGATGGGTGTAGTGTATGT 58.120 43.478 0.00 0.00 0.00 2.29
2553 4300 4.023107 CGAGTAGGATGGGTGTAGTGTATG 60.023 50.000 0.00 0.00 0.00 2.39
2554 4301 4.142790 CGAGTAGGATGGGTGTAGTGTAT 58.857 47.826 0.00 0.00 0.00 2.29
2578 4335 0.322726 TGTGTGAGATGCATGGTGGG 60.323 55.000 2.46 0.00 0.00 4.61
2602 4434 3.103742 GGAGTCTCCAGGTCTCTGAATT 58.896 50.000 14.46 0.00 43.49 2.17
2633 4465 2.481104 CGCCCCCGAGTTTACGTAAATA 60.481 50.000 22.65 0.00 36.29 1.40
2635 4467 0.389687 CGCCCCCGAGTTTACGTAAA 60.390 55.000 16.59 16.59 36.29 2.01
2636 4468 1.215117 CGCCCCCGAGTTTACGTAA 59.785 57.895 3.29 3.29 36.29 3.18
2680 4512 2.506472 GACGGAAGGGGGATGAGC 59.494 66.667 0.00 0.00 0.00 4.26
2841 4673 3.227276 CCGCCTCGCTGATAGGGT 61.227 66.667 0.00 0.00 34.46 4.34
2867 4699 3.069980 GCAGACGTCTCCAGCCGAT 62.070 63.158 16.96 0.00 0.00 4.18
3051 4883 1.133730 GGACCCAAAGTACACCACCAA 60.134 52.381 0.00 0.00 0.00 3.67
3380 5212 4.864334 CCATGCCGCTGAGACCCC 62.864 72.222 0.00 0.00 0.00 4.95
3422 5254 1.361668 GCGCTCGTCCATCAACACAT 61.362 55.000 0.00 0.00 0.00 3.21
3476 5308 2.772691 CCCGGTCTAGCTGTCGTCC 61.773 68.421 0.00 0.00 0.00 4.79
3516 5348 3.201487 TGCCATCAATCCATCTTCAGAGT 59.799 43.478 0.00 0.00 0.00 3.24
3690 6143 0.395724 ATTGGGTTTCCTCCATCGGC 60.396 55.000 0.00 0.00 33.82 5.54
3694 6147 2.834638 CCTGATTGGGTTTCCTCCAT 57.165 50.000 0.00 0.00 33.82 3.41
3912 6509 3.857157 AAACTCTAAACTGGTCTGGCA 57.143 42.857 0.00 0.00 0.00 4.92
3946 6550 4.142730 CGTAGCGTAGGATATTGGTAGGAC 60.143 50.000 0.00 0.00 0.00 3.85
4035 6642 4.079615 TGATGCACCTACCTACCTACTACA 60.080 45.833 0.00 0.00 0.00 2.74
4036 6643 4.277921 GTGATGCACCTACCTACCTACTAC 59.722 50.000 0.00 0.00 0.00 2.73
4037 6644 4.079615 TGTGATGCACCTACCTACCTACTA 60.080 45.833 0.00 0.00 32.73 1.82
4038 6645 3.297736 GTGATGCACCTACCTACCTACT 58.702 50.000 0.00 0.00 0.00 2.57
4230 6924 9.627123 CCCCATCTTCTCACTTGTTTATTATTA 57.373 33.333 0.00 0.00 0.00 0.98
4237 6931 2.158475 TGCCCCATCTTCTCACTTGTTT 60.158 45.455 0.00 0.00 0.00 2.83
4243 6937 1.442526 CGCATGCCCCATCTTCTCAC 61.443 60.000 13.15 0.00 0.00 3.51
4253 6947 4.460683 TCGTACCACGCATGCCCC 62.461 66.667 13.15 0.00 42.21 5.80
4277 6975 9.678941 CACGCAATATTAACTAGAATACTCAGA 57.321 33.333 0.00 0.00 0.00 3.27
4285 6983 7.252708 TCGAGAACACGCAATATTAACTAGAA 58.747 34.615 0.00 0.00 0.00 2.10
4320 7018 1.854743 CGTCAGATGTTGGTATGAGCG 59.145 52.381 0.00 0.00 0.00 5.03
4620 7366 7.308435 GTCACTGAAAACAAAATAGGATGGAG 58.692 38.462 0.00 0.00 0.00 3.86
4626 7372 6.300354 AGACGTCACTGAAAACAAAATAGG 57.700 37.500 19.50 0.00 0.00 2.57
4678 7424 1.149288 TCCCGGATAATAGGCAGGACT 59.851 52.381 0.73 0.00 0.00 3.85
4795 7541 9.059260 CAGACTCTAATTAAGTAGTACTCCCTC 57.941 40.741 9.60 0.00 0.00 4.30
5026 7807 1.672881 AGCTTGTTGCAGTGAACAGAC 59.327 47.619 0.00 0.00 45.94 3.51
5045 7826 3.684103 TCACCGCAACTTGTTTGTTAG 57.316 42.857 0.00 0.00 37.54 2.34
5056 7844 4.024387 TGAGTTATGAAAGTTCACCGCAAC 60.024 41.667 0.00 0.00 40.49 4.17
5060 7848 5.679906 CAACTGAGTTATGAAAGTTCACCG 58.320 41.667 0.00 0.00 40.49 4.94
5076 7864 3.363378 CGTGCACTTCTTTAGCAACTGAG 60.363 47.826 16.19 0.00 40.35 3.35
5357 8150 3.913107 AGGGAGAGCTTTGCCTGT 58.087 55.556 17.05 0.00 37.53 4.00
5597 8406 5.592054 TGGCATAGATCTTCAGACTTAACG 58.408 41.667 0.00 0.00 0.00 3.18
5927 8846 2.624838 AGTTTGGCAATCACTGTTCAGG 59.375 45.455 10.67 0.00 0.00 3.86
6010 8929 6.147821 AGTGTCGATTCTTTGTTACCAAGATG 59.852 38.462 0.00 0.00 0.00 2.90
6029 8948 6.955963 GCAAATATTCAGACTTTGTAGTGTCG 59.044 38.462 0.00 0.00 38.16 4.35
6032 8951 7.383102 AGGCAAATATTCAGACTTTGTAGTG 57.617 36.000 0.00 0.00 33.84 2.74
6087 9006 2.738846 CGTAGTCAGATTGCAAGTTGCT 59.261 45.455 27.17 9.42 45.31 3.91
6100 9019 3.565902 TGAGATATGTGAGGCGTAGTCAG 59.434 47.826 0.00 0.00 0.00 3.51
6159 9078 6.099269 TGGTATGTTCTGGGTTTCTAGGTATC 59.901 42.308 0.00 0.00 0.00 2.24
6167 9086 4.331968 TCATGTGGTATGTTCTGGGTTTC 58.668 43.478 0.00 0.00 0.00 2.78
6222 9141 6.132791 TGTATTTTTGTTTGCGTGGAAGTA 57.867 33.333 0.00 0.00 0.00 2.24
6252 9171 9.836864 GGAATAGGAAAGAAATTGCCATTATTT 57.163 29.630 0.00 0.00 0.00 1.40
6272 9192 5.587844 CCCAGTTTCATTCTCTGTGGAATAG 59.412 44.000 0.00 0.00 34.59 1.73
6285 9205 6.462909 GGAACAGAATTTGTCCCAGTTTCATT 60.463 38.462 0.00 0.00 39.73 2.57


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

AutoCloner maintained by Alex Coulton.