Multiple sequence alignment - TraesCS7D01G057000

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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 TraesCS7D01G057000 chr7D 100.000 4474 0 0 1 4474 30498469 30502942 0.000000e+00 8263.0
1 TraesCS7D01G057000 chr7D 79.377 1508 224 53 2511 3971 111277769 111279236 0.000000e+00 981.0
2 TraesCS7D01G057000 chr7D 81.879 1054 135 25 99 1123 30485216 30486242 0.000000e+00 837.0
3 TraesCS7D01G057000 chr7D 77.778 1278 185 55 217 1474 30477294 30478492 0.000000e+00 695.0
4 TraesCS7D01G057000 chr7D 77.452 1091 165 48 2702 3744 111403653 111404710 1.080000e-160 577.0
5 TraesCS7D01G057000 chr7D 79.051 864 136 27 218 1068 30488522 30489353 6.540000e-153 551.0
6 TraesCS7D01G057000 chr7D 85.895 475 52 10 1864 2329 30469681 30470149 4.020000e-135 492.0
7 TraesCS7D01G057000 chr7D 86.064 409 43 6 3146 3540 30470196 30470604 1.150000e-115 427.0
8 TraesCS7D01G057000 chr7D 81.333 375 46 12 2960 3312 111221092 111221464 2.630000e-72 283.0
9 TraesCS7D01G057000 chr7D 90.052 191 18 1 1007 1196 30467619 30467809 3.460000e-61 246.0
10 TraesCS7D01G057000 chr7D 80.755 265 36 9 4151 4402 111399797 111400059 4.570000e-45 193.0
11 TraesCS7D01G057000 chr7D 83.673 196 29 2 1925 2119 30410825 30411018 9.890000e-42 182.0
12 TraesCS7D01G057000 chr7D 77.667 300 58 7 3355 3652 111221471 111221763 1.650000e-39 174.0
13 TraesCS7D01G057000 chr7D 80.925 173 16 7 4276 4444 111406595 111406754 2.190000e-23 121.0
14 TraesCS7D01G057000 chr7D 93.333 45 3 0 4311 4355 111313605 111313649 2.890000e-07 67.6
15 TraesCS7D01G057000 chr7A 93.945 2923 108 35 1590 4474 31073503 31076394 0.000000e+00 4353.0
16 TraesCS7D01G057000 chr7A 86.724 1386 132 27 117 1462 31072094 31073467 0.000000e+00 1493.0
17 TraesCS7D01G057000 chr7A 80.395 760 98 16 135 880 31065205 31065927 8.520000e-147 531.0
18 TraesCS7D01G057000 chr7A 79.098 665 85 28 2511 3146 116527252 116527891 4.170000e-110 409.0
19 TraesCS7D01G057000 chr7A 79.412 476 56 22 4037 4474 40099088 40099559 9.410000e-77 298.0
20 TraesCS7D01G057000 chr7A 82.370 346 37 11 2628 2963 40098391 40098722 3.410000e-71 279.0
21 TraesCS7D01G057000 chr7A 79.692 389 57 12 2080 2466 40097971 40098339 1.230000e-65 261.0
22 TraesCS7D01G057000 chr7A 78.319 452 62 23 2625 3071 116585702 116586122 4.440000e-65 259.0
23 TraesCS7D01G057000 chr7A 84.158 202 18 5 1026 1220 31065979 31066173 2.750000e-42 183.0
24 TraesCS7D01G057000 chr4A 92.370 1979 112 15 2514 4474 698054488 698052531 0.000000e+00 2782.0
25 TraesCS7D01G057000 chr4A 89.931 1748 91 28 637 2350 698056179 698054483 0.000000e+00 2174.0
26 TraesCS7D01G057000 chr4A 80.231 1730 254 55 2080 3745 646324422 646326127 0.000000e+00 1219.0
27 TraesCS7D01G057000 chr4A 86.902 481 54 4 104 579 698056812 698056336 8.520000e-147 531.0
28 TraesCS7D01G057000 chr4A 81.901 547 81 9 136 679 698090961 698090430 3.180000e-121 446.0
29 TraesCS7D01G057000 chr4A 82.543 464 59 13 1439 1885 698362343 698362801 5.430000e-104 388.0
30 TraesCS7D01G057000 chr4A 81.381 478 75 8 2736 3206 646481968 646482438 1.170000e-100 377.0
31 TraesCS7D01G057000 chr4A 82.447 376 36 16 1024 1392 698361983 698362335 7.270000e-78 302.0
32 TraesCS7D01G057000 chr4A 88.000 225 27 0 1032 1256 646586522 646586746 2.650000e-67 267.0
33 TraesCS7D01G057000 chr4A 84.133 271 41 1 135 403 698368112 698368382 1.230000e-65 261.0
34 TraesCS7D01G057000 chr4A 80.899 267 36 7 465 728 698368402 698368656 3.530000e-46 196.0
35 TraesCS7D01G057000 chr4A 88.554 166 9 5 1309 1474 698369113 698369268 4.570000e-45 193.0
36 TraesCS7D01G057000 chr4A 81.944 216 22 9 1873 2078 698362821 698363029 2.770000e-37 167.0
37 TraesCS7D01G057000 chr4A 86.364 132 8 5 1349 1480 698088561 698088440 7.810000e-28 135.0
38 TraesCS7D01G057000 chr4A 92.593 81 6 0 2124 2204 646514557 646514637 2.830000e-22 117.0
39 TraesCS7D01G057000 chr7B 78.669 1022 147 44 2513 3499 70871244 70872229 8.230000e-172 614.0
40 TraesCS7D01G057000 chr7B 79.851 268 33 15 4151 4398 70866225 70866491 4.600000e-40 176.0


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 TraesCS7D01G057000 chr7D 30498469 30502942 4473 False 8263.000000 8263 100.000000 1 4474 1 chr7D.!!$F3 4473
1 TraesCS7D01G057000 chr7D 111277769 111279236 1467 False 981.000000 981 79.377000 2511 3971 1 chr7D.!!$F4 1460
2 TraesCS7D01G057000 chr7D 30477294 30478492 1198 False 695.000000 695 77.778000 217 1474 1 chr7D.!!$F2 1257
3 TraesCS7D01G057000 chr7D 30485216 30489353 4137 False 694.000000 837 80.465000 99 1123 2 chr7D.!!$F7 1024
4 TraesCS7D01G057000 chr7D 30467619 30470604 2985 False 388.333333 492 87.337000 1007 3540 3 chr7D.!!$F6 2533
5 TraesCS7D01G057000 chr7D 111399797 111406754 6957 False 297.000000 577 79.710667 2702 4444 3 chr7D.!!$F9 1742
6 TraesCS7D01G057000 chr7D 111221092 111221763 671 False 228.500000 283 79.500000 2960 3652 2 chr7D.!!$F8 692
7 TraesCS7D01G057000 chr7A 31072094 31076394 4300 False 2923.000000 4353 90.334500 117 4474 2 chr7A.!!$F4 4357
8 TraesCS7D01G057000 chr7A 116527252 116527891 639 False 409.000000 409 79.098000 2511 3146 1 chr7A.!!$F1 635
9 TraesCS7D01G057000 chr7A 31065205 31066173 968 False 357.000000 531 82.276500 135 1220 2 chr7A.!!$F3 1085
10 TraesCS7D01G057000 chr7A 40097971 40099559 1588 False 279.333333 298 80.491333 2080 4474 3 chr7A.!!$F5 2394
11 TraesCS7D01G057000 chr4A 698052531 698056812 4281 True 1829.000000 2782 89.734333 104 4474 3 chr4A.!!$R1 4370
12 TraesCS7D01G057000 chr4A 646324422 646326127 1705 False 1219.000000 1219 80.231000 2080 3745 1 chr4A.!!$F1 1665
13 TraesCS7D01G057000 chr4A 698088440 698090961 2521 True 290.500000 446 84.132500 136 1480 2 chr4A.!!$R2 1344
14 TraesCS7D01G057000 chr4A 698361983 698363029 1046 False 285.666667 388 82.311333 1024 2078 3 chr4A.!!$F5 1054
15 TraesCS7D01G057000 chr4A 698368112 698369268 1156 False 216.666667 261 84.528667 135 1474 3 chr4A.!!$F6 1339
16 TraesCS7D01G057000 chr7B 70871244 70872229 985 False 614.000000 614 78.669000 2513 3499 1 chr7B.!!$F2 986

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
24 25 0.109532 TTCCTGCATTCCGAACACCA 59.890 50.000 0.0 0.0 0.00 4.17 F
25 26 0.321564 TCCTGCATTCCGAACACCAG 60.322 55.000 0.0 0.0 0.00 4.00 F
73 74 0.524414 TTCCTTCGAGATTCGTGCGA 59.476 50.000 0.0 0.0 41.35 5.10 F
74 75 0.524414 TCCTTCGAGATTCGTGCGAA 59.476 50.000 9.5 9.5 41.35 4.70 F
96 97 0.600782 TCCTACAAACCGAACGCACC 60.601 55.000 0.0 0.0 0.00 5.01 F
1057 2825 1.004080 GTCCTGCTGCTCTGCTTGA 60.004 57.895 0.0 0.0 0.00 3.02 F
1368 3149 2.079158 TGTTATCAGACAGCAAGCAGC 58.921 47.619 0.0 0.0 46.19 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 5163 0.324943 ATGTGAAACCTCCGTCCTGG 59.675 55.000 0.00 0.00 34.36 4.45 R
1963 5225 1.198408 GGTTTTAGTACCCTGCGTTGC 59.802 52.381 0.00 0.00 31.71 4.17 R
2057 5327 7.867752 TGTTGTTTACTGCCTACAAGTATTTC 58.132 34.615 0.00 0.00 32.89 2.17 R
2178 5451 1.069636 AGACACGGTAAAGACGTCGAC 60.070 52.381 10.46 5.18 43.58 4.20 R
2315 5590 9.529325 GAAATGGGGAATTAAAGCTAATTACAC 57.471 33.333 6.53 3.46 40.81 2.90 R
2927 6265 1.339631 TGCATTAGCCCGTACTTGCTT 60.340 47.619 10.71 0.00 41.13 3.91 R
3489 9020 2.700783 TCCTGCTCCATGGACATGT 58.299 52.632 11.44 0.00 37.11 3.21 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
19 20 2.332063 GGAGATTCCTGCATTCCGAA 57.668 50.000 0.00 0.00 32.53 4.30
21 22 2.632377 GAGATTCCTGCATTCCGAACA 58.368 47.619 0.00 0.00 0.00 3.18
23 24 1.401905 GATTCCTGCATTCCGAACACC 59.598 52.381 0.00 0.00 0.00 4.16
24 25 0.109532 TTCCTGCATTCCGAACACCA 59.890 50.000 0.00 0.00 0.00 4.17
25 26 0.321564 TCCTGCATTCCGAACACCAG 60.322 55.000 0.00 0.00 0.00 4.00
26 27 0.321564 CCTGCATTCCGAACACCAGA 60.322 55.000 0.00 0.00 0.00 3.86
29 30 1.879380 TGCATTCCGAACACCAGAAAG 59.121 47.619 0.00 0.00 0.00 2.62
30 31 1.401539 GCATTCCGAACACCAGAAAGC 60.402 52.381 0.00 0.00 0.00 3.51
31 32 1.879380 CATTCCGAACACCAGAAAGCA 59.121 47.619 0.00 0.00 0.00 3.91
32 33 2.045561 TTCCGAACACCAGAAAGCAA 57.954 45.000 0.00 0.00 0.00 3.91
34 35 1.021202 CCGAACACCAGAAAGCAACA 58.979 50.000 0.00 0.00 0.00 3.33
35 36 1.608590 CCGAACACCAGAAAGCAACAT 59.391 47.619 0.00 0.00 0.00 2.71
36 37 2.811431 CCGAACACCAGAAAGCAACATA 59.189 45.455 0.00 0.00 0.00 2.29
39 40 4.675114 CGAACACCAGAAAGCAACATAAAC 59.325 41.667 0.00 0.00 0.00 2.01
40 41 4.584327 ACACCAGAAAGCAACATAAACC 57.416 40.909 0.00 0.00 0.00 3.27
41 42 4.215109 ACACCAGAAAGCAACATAAACCT 58.785 39.130 0.00 0.00 0.00 3.50
42 43 4.649218 ACACCAGAAAGCAACATAAACCTT 59.351 37.500 0.00 0.00 0.00 3.50
44 45 4.023193 ACCAGAAAGCAACATAAACCTTCG 60.023 41.667 0.00 0.00 0.00 3.79
46 47 4.911610 CAGAAAGCAACATAAACCTTCGTG 59.088 41.667 0.00 0.00 0.00 4.35
48 49 5.298276 AGAAAGCAACATAAACCTTCGTGAA 59.702 36.000 0.00 0.00 0.00 3.18
49 50 4.483476 AGCAACATAAACCTTCGTGAAC 57.517 40.909 0.00 0.00 0.00 3.18
50 51 3.880490 AGCAACATAAACCTTCGTGAACA 59.120 39.130 0.00 0.00 0.00 3.18
51 52 4.024048 AGCAACATAAACCTTCGTGAACAG 60.024 41.667 0.00 0.00 0.00 3.16
53 54 5.049954 GCAACATAAACCTTCGTGAACAGTA 60.050 40.000 0.00 0.00 0.00 2.74
58 59 4.618920 AACCTTCGTGAACAGTATTCCT 57.381 40.909 0.00 0.00 0.00 3.36
59 60 4.618920 ACCTTCGTGAACAGTATTCCTT 57.381 40.909 0.00 0.00 0.00 3.36
60 61 4.566987 ACCTTCGTGAACAGTATTCCTTC 58.433 43.478 0.00 0.00 0.00 3.46
61 62 3.612860 CCTTCGTGAACAGTATTCCTTCG 59.387 47.826 0.00 0.00 0.00 3.79
62 63 4.482386 CTTCGTGAACAGTATTCCTTCGA 58.518 43.478 0.00 0.00 0.00 3.71
63 64 4.092771 TCGTGAACAGTATTCCTTCGAG 57.907 45.455 0.00 0.00 0.00 4.04
64 65 3.754850 TCGTGAACAGTATTCCTTCGAGA 59.245 43.478 0.00 0.00 0.00 4.04
66 67 5.103000 CGTGAACAGTATTCCTTCGAGATT 58.897 41.667 0.00 0.00 0.00 2.40
67 68 5.230306 CGTGAACAGTATTCCTTCGAGATTC 59.770 44.000 0.00 0.00 0.00 2.52
70 71 4.673441 ACAGTATTCCTTCGAGATTCGTG 58.327 43.478 0.00 0.00 41.35 4.35
72 73 1.560923 ATTCCTTCGAGATTCGTGCG 58.439 50.000 0.00 0.00 41.35 5.34
73 74 0.524414 TTCCTTCGAGATTCGTGCGA 59.476 50.000 0.00 0.00 41.35 5.10
74 75 0.524414 TCCTTCGAGATTCGTGCGAA 59.476 50.000 9.50 9.50 41.35 4.70
75 76 1.068125 TCCTTCGAGATTCGTGCGAAA 60.068 47.619 11.09 0.00 42.54 3.46
76 77 1.724623 CCTTCGAGATTCGTGCGAAAA 59.275 47.619 11.09 0.35 42.54 2.29
77 78 2.348666 CCTTCGAGATTCGTGCGAAAAT 59.651 45.455 11.09 3.04 42.54 1.82
78 79 3.542291 CCTTCGAGATTCGTGCGAAAATC 60.542 47.826 11.09 10.58 42.54 2.17
79 80 1.924524 TCGAGATTCGTGCGAAAATCC 59.075 47.619 11.09 2.10 41.35 3.01
80 81 1.927174 CGAGATTCGTGCGAAAATCCT 59.073 47.619 11.09 6.41 37.69 3.24
81 82 3.113322 CGAGATTCGTGCGAAAATCCTA 58.887 45.455 11.09 0.00 37.69 2.94
82 83 3.061139 CGAGATTCGTGCGAAAATCCTAC 60.061 47.826 11.09 0.96 37.69 3.18
84 85 4.250464 AGATTCGTGCGAAAATCCTACAA 58.750 39.130 11.09 0.00 37.69 2.41
86 87 3.799137 TCGTGCGAAAATCCTACAAAC 57.201 42.857 0.00 0.00 0.00 2.93
87 88 2.481185 TCGTGCGAAAATCCTACAAACC 59.519 45.455 0.00 0.00 0.00 3.27
88 89 2.723618 CGTGCGAAAATCCTACAAACCG 60.724 50.000 0.00 0.00 0.00 4.44
89 90 2.481185 GTGCGAAAATCCTACAAACCGA 59.519 45.455 0.00 0.00 0.00 4.69
90 91 3.058777 GTGCGAAAATCCTACAAACCGAA 60.059 43.478 0.00 0.00 0.00 4.30
92 93 3.728600 CGAAAATCCTACAAACCGAACG 58.271 45.455 0.00 0.00 0.00 3.95
93 94 3.485633 GAAAATCCTACAAACCGAACGC 58.514 45.455 0.00 0.00 0.00 4.84
94 95 2.172851 AATCCTACAAACCGAACGCA 57.827 45.000 0.00 0.00 0.00 5.24
96 97 0.600782 TCCTACAAACCGAACGCACC 60.601 55.000 0.00 0.00 0.00 5.01
97 98 1.571215 CCTACAAACCGAACGCACCC 61.571 60.000 0.00 0.00 0.00 4.61
138 139 1.745653 GGTTAGGAGCTGCCATGTTTC 59.254 52.381 0.00 0.00 40.02 2.78
155 156 6.183360 CCATGTTTCCAGTCCAACTATCAATC 60.183 42.308 0.00 0.00 0.00 2.67
158 159 4.655762 TCCAGTCCAACTATCAATCGAG 57.344 45.455 0.00 0.00 0.00 4.04
285 288 4.697514 ACATCCTCTTGATTATGTGTCCG 58.302 43.478 0.00 0.00 31.56 4.79
348 351 9.709495 TTATTGAATGAAAATGGTGAAAAGAGG 57.291 29.630 0.00 0.00 0.00 3.69
349 352 5.540911 TGAATGAAAATGGTGAAAAGAGGC 58.459 37.500 0.00 0.00 0.00 4.70
350 353 5.070180 TGAATGAAAATGGTGAAAAGAGGCA 59.930 36.000 0.00 0.00 0.00 4.75
351 354 4.589216 TGAAAATGGTGAAAAGAGGCAG 57.411 40.909 0.00 0.00 0.00 4.85
382 397 7.635423 CAAATGTAAAATGCATGGATGAATGG 58.365 34.615 0.00 0.00 0.00 3.16
464 482 5.394443 CGGGTAAGTGTAGTTTAGGCATGTA 60.394 44.000 0.00 0.00 0.00 2.29
465 483 6.589135 GGGTAAGTGTAGTTTAGGCATGTAT 58.411 40.000 0.00 0.00 0.00 2.29
466 484 6.482308 GGGTAAGTGTAGTTTAGGCATGTATG 59.518 42.308 0.00 0.00 0.00 2.39
595 635 5.133221 TGAAGTCTGAGATATGATGTCGGA 58.867 41.667 0.00 0.00 35.79 4.55
698 2271 7.925993 TCCACTAACAGAAATAAACAGTGTTG 58.074 34.615 9.79 0.00 33.50 3.33
747 2366 6.616237 AAAAGAACGAATAACCCTCCTCTA 57.384 37.500 0.00 0.00 0.00 2.43
839 2467 1.484653 ACATCCCGAATCACATCCGAA 59.515 47.619 0.00 0.00 0.00 4.30
951 2719 2.373335 ACTGCTCCATCCTCTCGTAT 57.627 50.000 0.00 0.00 0.00 3.06
994 2762 1.845627 TAGCTGGCTTGCTTGCTCCT 61.846 55.000 10.43 0.06 43.74 3.69
1057 2825 1.004080 GTCCTGCTGCTCTGCTTGA 60.004 57.895 0.00 0.00 0.00 3.02
1362 3143 5.359576 ACTTTTTGGTTGTTATCAGACAGCA 59.640 36.000 0.00 0.00 33.06 4.41
1368 3149 2.079158 TGTTATCAGACAGCAAGCAGC 58.921 47.619 0.00 0.00 46.19 5.25
1612 3406 3.449737 CCTGAATGCAGATTGACCCATTT 59.550 43.478 0.74 0.00 45.17 2.32
1826 3695 3.204526 CTCTCATTCAAGCTCCATGACC 58.795 50.000 0.00 0.00 0.00 4.02
1885 5111 5.815233 TCTTCCTATGGCCTGAAGAATAG 57.185 43.478 18.76 10.51 40.98 1.73
1886 5112 5.219739 TCTTCCTATGGCCTGAAGAATAGT 58.780 41.667 18.76 0.00 40.98 2.12
1887 5113 5.305644 TCTTCCTATGGCCTGAAGAATAGTC 59.694 44.000 18.76 0.00 40.98 2.59
1890 5116 6.382087 TCCTATGGCCTGAAGAATAGTCTAA 58.618 40.000 3.32 0.00 32.16 2.10
1891 5117 6.267928 TCCTATGGCCTGAAGAATAGTCTAAC 59.732 42.308 3.32 0.00 32.16 2.34
1893 5119 4.362677 TGGCCTGAAGAATAGTCTAACCT 58.637 43.478 3.32 0.00 32.16 3.50
1898 5160 7.051000 GCCTGAAGAATAGTCTAACCTCATTT 58.949 38.462 0.00 0.00 32.16 2.32
1963 5225 6.426633 TGAATGTTATATACGCATTGACAGGG 59.573 38.462 13.43 0.00 33.56 4.45
2178 5451 2.726760 GCTGTCACTGTACAAACTCTCG 59.273 50.000 0.00 0.00 0.00 4.04
2315 5590 2.966516 GACATGGAAGGTACCCTCCTAG 59.033 54.545 26.62 20.81 36.74 3.02
2927 6265 9.015367 GTGAGAGATACCACTATATTTCAGCTA 57.985 37.037 0.00 0.00 0.00 3.32
2937 6281 7.096023 CCACTATATTTCAGCTAAGCAAGTACG 60.096 40.741 0.00 0.00 0.00 3.67
2942 6286 1.136305 CAGCTAAGCAAGTACGGGCTA 59.864 52.381 13.54 3.77 40.01 3.93
2970 6317 6.199719 GCATAGAATCACAGCCTAAAATTTGC 59.800 38.462 0.00 0.00 0.00 3.68
2976 6323 4.217550 TCACAGCCTAAAATTTGCACTACC 59.782 41.667 0.00 0.00 0.00 3.18
3443 8970 0.099968 CAATTGGCAGGCAGATGTCG 59.900 55.000 0.00 0.00 0.00 4.35
3451 8978 0.615331 AGGCAGATGTCGACACCATT 59.385 50.000 22.71 4.38 0.00 3.16
3489 9020 4.679373 AACTGAGACAAAAGAGAGCTGA 57.321 40.909 0.00 0.00 0.00 4.26
3506 9037 0.253894 TGACATGTCCATGGAGCAGG 59.746 55.000 22.85 19.09 42.91 4.85
3540 9071 5.983540 AGTTTTAAACAGCAATTGGGAACA 58.016 33.333 10.60 0.00 39.83 3.18
3586 9117 6.183360 CCCTTAGCTTCAAAGTACACAAAACA 60.183 38.462 0.00 0.00 0.00 2.83
3683 9216 2.374184 TGGGATAATGCGGGAACAAAG 58.626 47.619 0.00 0.00 0.00 2.77
3785 9472 4.082571 ACAGTCTCAAGTATGCAAAATGGC 60.083 41.667 0.00 0.00 0.00 4.40
3852 10805 7.107639 TGTACATCATCTAATTCCAGACGAA 57.892 36.000 0.00 0.00 34.14 3.85
4184 11190 6.091986 ACAAAGTGTGCCACAAATAAAACTTG 59.908 34.615 0.00 0.00 36.74 3.16
4316 11343 3.498774 AGACTGCCTTCAACACTTCAT 57.501 42.857 0.00 0.00 0.00 2.57
4325 11352 5.472137 GCCTTCAACACTTCATTACCAGTAA 59.528 40.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.352960 GTGTTCGGAATGCAGGAATCTC 59.647 50.000 0.00 0.00 0.00 2.75
3 4 1.401905 GGTGTTCGGAATGCAGGAATC 59.598 52.381 0.00 0.00 0.00 2.52
4 5 1.271871 TGGTGTTCGGAATGCAGGAAT 60.272 47.619 0.00 0.00 0.00 3.01
6 7 0.321564 CTGGTGTTCGGAATGCAGGA 60.322 55.000 0.00 0.00 0.00 3.86
9 10 1.879380 CTTTCTGGTGTTCGGAATGCA 59.121 47.619 0.00 0.00 40.17 3.96
10 11 2.619013 CTTTCTGGTGTTCGGAATGC 57.381 50.000 0.00 0.00 40.17 3.56
11 12 1.879380 TGCTTTCTGGTGTTCGGAATG 59.121 47.619 0.00 0.00 40.17 2.67
14 15 1.305201 GTTGCTTTCTGGTGTTCGGA 58.695 50.000 0.00 0.00 0.00 4.55
15 16 1.021202 TGTTGCTTTCTGGTGTTCGG 58.979 50.000 0.00 0.00 0.00 4.30
16 17 4.481930 TTATGTTGCTTTCTGGTGTTCG 57.518 40.909 0.00 0.00 0.00 3.95
17 18 4.982295 GGTTTATGTTGCTTTCTGGTGTTC 59.018 41.667 0.00 0.00 0.00 3.18
18 19 4.649218 AGGTTTATGTTGCTTTCTGGTGTT 59.351 37.500 0.00 0.00 0.00 3.32
19 20 4.215109 AGGTTTATGTTGCTTTCTGGTGT 58.785 39.130 0.00 0.00 0.00 4.16
21 22 4.023193 CGAAGGTTTATGTTGCTTTCTGGT 60.023 41.667 0.00 0.00 0.00 4.00
23 24 4.911610 CACGAAGGTTTATGTTGCTTTCTG 59.088 41.667 0.00 0.00 0.00 3.02
24 25 4.819630 TCACGAAGGTTTATGTTGCTTTCT 59.180 37.500 0.00 0.00 0.00 2.52
25 26 5.103290 TCACGAAGGTTTATGTTGCTTTC 57.897 39.130 0.00 0.00 0.00 2.62
26 27 5.163602 TGTTCACGAAGGTTTATGTTGCTTT 60.164 36.000 0.00 0.00 0.00 3.51
29 30 4.217754 TGTTCACGAAGGTTTATGTTGC 57.782 40.909 0.00 0.00 0.00 4.17
30 31 5.418310 ACTGTTCACGAAGGTTTATGTTG 57.582 39.130 0.00 0.00 0.00 3.33
31 32 7.094933 GGAATACTGTTCACGAAGGTTTATGTT 60.095 37.037 0.00 0.00 0.00 2.71
32 33 6.370718 GGAATACTGTTCACGAAGGTTTATGT 59.629 38.462 0.00 0.00 0.00 2.29
34 35 6.708285 AGGAATACTGTTCACGAAGGTTTAT 58.292 36.000 0.00 0.00 0.00 1.40
35 36 6.105397 AGGAATACTGTTCACGAAGGTTTA 57.895 37.500 0.00 0.00 0.00 2.01
36 37 4.969484 AGGAATACTGTTCACGAAGGTTT 58.031 39.130 0.00 0.00 0.00 3.27
39 40 3.612860 CGAAGGAATACTGTTCACGAAGG 59.387 47.826 0.00 0.00 0.00 3.46
40 41 4.482386 TCGAAGGAATACTGTTCACGAAG 58.518 43.478 0.00 0.00 0.00 3.79
41 42 4.216902 TCTCGAAGGAATACTGTTCACGAA 59.783 41.667 0.00 0.00 0.00 3.85
42 43 3.754850 TCTCGAAGGAATACTGTTCACGA 59.245 43.478 0.00 0.00 0.00 4.35
44 45 5.230306 CGAATCTCGAAGGAATACTGTTCAC 59.770 44.000 0.00 0.00 43.74 3.18
46 47 5.230306 CACGAATCTCGAAGGAATACTGTTC 59.770 44.000 2.59 0.00 43.74 3.18
48 49 4.673441 CACGAATCTCGAAGGAATACTGT 58.327 43.478 2.59 0.00 43.74 3.55
49 50 3.487574 GCACGAATCTCGAAGGAATACTG 59.512 47.826 2.59 0.00 43.74 2.74
50 51 3.707793 GCACGAATCTCGAAGGAATACT 58.292 45.455 2.59 0.00 43.74 2.12
51 52 2.468040 CGCACGAATCTCGAAGGAATAC 59.532 50.000 2.59 0.00 43.74 1.89
53 54 1.134367 TCGCACGAATCTCGAAGGAAT 59.866 47.619 2.59 0.00 43.74 3.01
58 59 2.347452 GGATTTTCGCACGAATCTCGAA 59.653 45.455 6.28 0.00 43.74 3.71
59 60 1.924524 GGATTTTCGCACGAATCTCGA 59.075 47.619 6.28 0.00 43.74 4.04
60 61 1.927174 AGGATTTTCGCACGAATCTCG 59.073 47.619 6.28 0.00 46.93 4.04
61 62 3.863424 TGTAGGATTTTCGCACGAATCTC 59.137 43.478 6.28 6.46 33.75 2.75
62 63 3.857052 TGTAGGATTTTCGCACGAATCT 58.143 40.909 6.28 5.30 33.75 2.40
63 64 4.593597 TTGTAGGATTTTCGCACGAATC 57.406 40.909 6.28 2.24 33.79 2.52
64 65 4.379082 GGTTTGTAGGATTTTCGCACGAAT 60.379 41.667 6.28 0.00 33.79 3.34
66 67 2.481185 GGTTTGTAGGATTTTCGCACGA 59.519 45.455 0.00 0.00 0.00 4.35
67 68 2.723618 CGGTTTGTAGGATTTTCGCACG 60.724 50.000 0.00 0.00 0.00 5.34
70 71 3.485633 GTTCGGTTTGTAGGATTTTCGC 58.514 45.455 0.00 0.00 0.00 4.70
72 73 3.058777 TGCGTTCGGTTTGTAGGATTTTC 60.059 43.478 0.00 0.00 0.00 2.29
73 74 2.879646 TGCGTTCGGTTTGTAGGATTTT 59.120 40.909 0.00 0.00 0.00 1.82
74 75 2.224784 GTGCGTTCGGTTTGTAGGATTT 59.775 45.455 0.00 0.00 0.00 2.17
75 76 1.802365 GTGCGTTCGGTTTGTAGGATT 59.198 47.619 0.00 0.00 0.00 3.01
76 77 1.435577 GTGCGTTCGGTTTGTAGGAT 58.564 50.000 0.00 0.00 0.00 3.24
77 78 0.600782 GGTGCGTTCGGTTTGTAGGA 60.601 55.000 0.00 0.00 0.00 2.94
78 79 1.571215 GGGTGCGTTCGGTTTGTAGG 61.571 60.000 0.00 0.00 0.00 3.18
79 80 0.601841 AGGGTGCGTTCGGTTTGTAG 60.602 55.000 0.00 0.00 0.00 2.74
80 81 0.678395 TAGGGTGCGTTCGGTTTGTA 59.322 50.000 0.00 0.00 0.00 2.41
81 82 0.179051 TTAGGGTGCGTTCGGTTTGT 60.179 50.000 0.00 0.00 0.00 2.83
82 83 0.236449 GTTAGGGTGCGTTCGGTTTG 59.764 55.000 0.00 0.00 0.00 2.93
84 85 1.301953 GGTTAGGGTGCGTTCGGTT 60.302 57.895 0.00 0.00 0.00 4.44
86 87 2.812178 CGGTTAGGGTGCGTTCGG 60.812 66.667 0.00 0.00 0.00 4.30
87 88 2.812178 CCGGTTAGGGTGCGTTCG 60.812 66.667 0.00 0.00 35.97 3.95
88 89 2.344872 ACCGGTTAGGGTGCGTTC 59.655 61.111 0.00 0.00 46.96 3.95
94 95 0.616891 CCTTTAGCACCGGTTAGGGT 59.383 55.000 2.97 1.43 46.96 4.34
97 98 0.746923 GCCCCTTTAGCACCGGTTAG 60.747 60.000 2.97 0.00 0.00 2.34
138 139 3.384789 TCCTCGATTGATAGTTGGACTGG 59.615 47.826 0.00 0.00 0.00 4.00
195 196 2.675844 TGAATTTATCGTTCCGCACCAG 59.324 45.455 0.00 0.00 0.00 4.00
236 237 1.077212 ATGCATGACTGGGAGGCAC 60.077 57.895 0.00 0.00 35.04 5.01
268 271 2.905075 TGGCGGACACATAATCAAGAG 58.095 47.619 0.00 0.00 0.00 2.85
285 288 5.532406 ACACATAAACATAGGACATGATGGC 59.468 40.000 0.00 0.00 0.00 4.40
348 351 4.389382 TGCATTTTACATTTGCACATCTGC 59.611 37.500 0.00 0.00 41.18 4.26
382 397 1.139853 AGGAAAGCCCATCATCTCGTC 59.860 52.381 0.00 0.00 37.41 4.20
464 482 2.420547 CCCATCGACCTTCATGTGACAT 60.421 50.000 0.00 0.00 0.00 3.06
465 483 1.066215 CCCATCGACCTTCATGTGACA 60.066 52.381 0.00 0.00 0.00 3.58
466 484 1.656652 CCCATCGACCTTCATGTGAC 58.343 55.000 0.00 0.00 0.00 3.67
479 499 5.457473 GTGCGTTTTATTAATTTCCCCATCG 59.543 40.000 0.00 0.00 0.00 3.84
595 635 4.956075 AGTTGGTTTTCTGGATCACAAAGT 59.044 37.500 0.00 0.00 0.00 2.66
728 2334 6.238402 GCAAAATAGAGGAGGGTTATTCGTTC 60.238 42.308 0.00 0.00 0.00 3.95
747 2366 4.436113 ACTGGGAAAAACATGGCAAAAT 57.564 36.364 0.00 0.00 0.00 1.82
951 2719 3.202906 AGCAAACTTAGAAGCACAACGA 58.797 40.909 0.00 0.00 0.00 3.85
994 2762 2.672651 CGTGGCTGGCATGGACAA 60.673 61.111 15.06 0.00 0.00 3.18
1368 3149 0.389037 TAGCAGCAGTTCAGCACTCG 60.389 55.000 0.00 0.00 36.85 4.18
1612 3406 7.722363 TCCATAGCTGTTATCGAAAATGAGTA 58.278 34.615 0.00 0.00 0.00 2.59
1885 5111 4.392138 CGTCCTGGAAAAATGAGGTTAGAC 59.608 45.833 0.00 0.00 0.00 2.59
1886 5112 4.564821 CCGTCCTGGAAAAATGAGGTTAGA 60.565 45.833 0.00 0.00 42.00 2.10
1887 5113 3.689649 CCGTCCTGGAAAAATGAGGTTAG 59.310 47.826 0.00 0.00 42.00 2.34
1890 5116 1.702957 TCCGTCCTGGAAAAATGAGGT 59.297 47.619 0.00 0.00 46.38 3.85
1891 5117 2.489938 TCCGTCCTGGAAAAATGAGG 57.510 50.000 0.00 0.00 46.38 3.86
1898 5160 3.813263 TGTGAAACCTCCGTCCTGGAAA 61.813 50.000 0.00 0.00 39.54 3.13
1901 5163 0.324943 ATGTGAAACCTCCGTCCTGG 59.675 55.000 0.00 0.00 34.36 4.45
1963 5225 1.198408 GGTTTTAGTACCCTGCGTTGC 59.802 52.381 0.00 0.00 31.71 4.17
2057 5327 7.867752 TGTTGTTTACTGCCTACAAGTATTTC 58.132 34.615 0.00 0.00 32.89 2.17
2178 5451 1.069636 AGACACGGTAAAGACGTCGAC 60.070 52.381 10.46 5.18 43.58 4.20
2315 5590 9.529325 GAAATGGGGAATTAAAGCTAATTACAC 57.471 33.333 6.53 3.46 40.81 2.90
2372 5649 7.775561 ACCAGATTCCAGTTTTTATCTGTATCC 59.224 37.037 0.00 0.00 41.39 2.59
2927 6265 1.339631 TGCATTAGCCCGTACTTGCTT 60.340 47.619 10.71 0.00 41.13 3.91
2937 6281 3.190118 GCTGTGATTCTATGCATTAGCCC 59.810 47.826 3.54 0.00 41.13 5.19
2942 6286 7.592885 ATTTTAGGCTGTGATTCTATGCATT 57.407 32.000 3.54 0.00 0.00 3.56
2970 6317 7.876068 TGACCTACAGAAATTTTACAGGTAGTG 59.124 37.037 12.14 7.80 35.11 2.74
2976 6323 7.745620 AGGTTGACCTACAGAAATTTTACAG 57.254 36.000 0.00 0.00 46.48 2.74
3443 8970 4.829064 TGAACTTTGTGCTAATGGTGTC 57.171 40.909 0.00 0.00 0.00 3.67
3489 9020 2.700783 TCCTGCTCCATGGACATGT 58.299 52.632 11.44 0.00 37.11 3.21
3540 9071 6.784031 AGGGTCACTTATCACTCTGAATTTT 58.216 36.000 0.00 0.00 0.00 1.82
3554 9085 5.562298 ACTTTGAAGCTAAGGGTCACTTA 57.438 39.130 0.00 0.00 40.64 2.24
3628 9160 4.556942 AACGGATTGACATATGCATGTG 57.443 40.909 20.59 20.59 45.58 3.21
3683 9216 7.875971 AGAACATTCTGTCTTTTATTCACCAC 58.124 34.615 0.00 0.00 35.89 4.16
3852 10805 8.421002 ACCACAGAAAACACTGCTATTTTATTT 58.579 29.630 0.00 0.00 41.06 1.40
4232 11242 5.099042 ACAAGTAAGCCTATGAATTCGGT 57.901 39.130 0.04 0.00 0.00 4.69
4316 11343 6.367374 TGTTCATGTGGAGATTACTGGTAA 57.633 37.500 0.00 0.00 0.00 2.85
4325 11352 4.843728 ACGGTAAATGTTCATGTGGAGAT 58.156 39.130 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.