Multiple sequence alignment - TraesCS6A01G290700

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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 TraesCS6A01G290700 chr6A 100.000 2408 0 0 1 2408 522207558 522209965 0.000000e+00 4447.0
1 TraesCS6A01G290700 chr6A 85.837 233 24 9 574 806 29611310 29611087 3.090000e-59 239.0
2 TraesCS6A01G290700 chr6A 77.582 397 57 21 2030 2408 522410109 522409727 6.740000e-51 211.0
3 TraesCS6A01G290700 chr6A 97.959 49 1 0 273 321 522207763 522207811 4.270000e-13 86.1
4 TraesCS6A01G290700 chr6A 97.959 49 1 0 206 254 522207830 522207878 4.270000e-13 86.1
5 TraesCS6A01G290700 chr6B 91.220 877 57 6 747 1622 9468979 9469836 0.000000e+00 1175.0
6 TraesCS6A01G290700 chr6B 87.155 724 39 19 1711 2408 568195144 568195839 0.000000e+00 773.0
7 TraesCS6A01G290700 chr6B 91.262 412 34 2 320 731 9461712 9462121 5.810000e-156 560.0
8 TraesCS6A01G290700 chr6B 79.270 685 64 36 1783 2408 568069686 568070351 8.010000e-110 407.0
9 TraesCS6A01G290700 chr6B 85.065 154 3 6 120 273 568194871 568195004 3.230000e-29 139.0
10 TraesCS6A01G290700 chr7B 89.694 883 76 15 751 1628 613876155 613877027 0.000000e+00 1112.0
11 TraesCS6A01G290700 chr7B 87.291 598 39 14 331 895 613875617 613876210 0.000000e+00 649.0
12 TraesCS6A01G290700 chr4B 93.065 721 45 4 753 1470 665177962 665177244 0.000000e+00 1050.0
13 TraesCS6A01G290700 chr4B 90.018 571 37 17 320 886 665178445 665177891 0.000000e+00 721.0
14 TraesCS6A01G290700 chr4B 91.765 255 18 3 315 568 583771980 583771728 3.810000e-93 351.0
15 TraesCS6A01G290700 chr4B 88.660 291 27 4 1332 1621 583770807 583770522 1.370000e-92 350.0
16 TraesCS6A01G290700 chr4A 88.409 509 42 14 320 823 539144268 539143772 4.430000e-167 597.0
17 TraesCS6A01G290700 chr4A 93.151 73 5 0 895 967 539143551 539143479 9.100000e-20 108.0
18 TraesCS6A01G290700 chr6D 92.150 293 20 3 1332 1623 270594228 270593938 6.200000e-111 411.0
19 TraesCS6A01G290700 chr6D 79.717 636 55 34 1783 2359 380729807 380730427 2.240000e-105 392.0
20 TraesCS6A01G290700 chr6D 85.372 376 23 12 1710 2054 380791540 380791914 6.330000e-96 361.0
21 TraesCS6A01G290700 chr6D 86.337 344 29 6 2078 2408 380792692 380793030 2.280000e-95 359.0
22 TraesCS6A01G290700 chr4D 90.753 292 23 4 1332 1622 454985398 454985110 1.040000e-103 387.0
23 TraesCS6A01G290700 chr3D 92.910 268 16 3 1358 1623 268095906 268096172 1.040000e-103 387.0
24 TraesCS6A01G290700 chr3D 93.200 250 15 2 320 568 268071131 268071379 1.360000e-97 366.0
25 TraesCS6A01G290700 chr3B 90.411 292 24 4 1332 1621 62979415 62979704 4.860000e-102 381.0
26 TraesCS6A01G290700 chr3B 90.800 250 23 0 319 568 62978134 62978383 3.840000e-88 335.0
27 TraesCS6A01G290700 chr7A 90.345 290 22 6 1337 1623 75201982 75202268 2.260000e-100 375.0
28 TraesCS6A01G290700 chr7A 93.333 120 3 2 1 120 676058966 676058852 3.180000e-39 172.0
29 TraesCS6A01G290700 chr1D 90.068 292 25 4 1332 1621 220881473 220881762 2.260000e-100 375.0
30 TraesCS6A01G290700 chr1D 90.837 251 20 3 320 568 220880211 220880460 1.380000e-87 333.0
31 TraesCS6A01G290700 chr1A 87.797 295 34 2 1004 1298 438737633 438737925 6.370000e-91 344.0
32 TraesCS6A01G290700 chr5D 89.723 253 24 2 320 571 511252226 511251975 2.990000e-84 322.0
33 TraesCS6A01G290700 chr5A 80.539 334 44 8 1004 1331 87180399 87180717 1.110000e-58 237.0
34 TraesCS6A01G290700 chr5A 83.981 206 13 13 762 967 446608718 446608903 1.900000e-41 180.0
35 TraesCS6A01G290700 chr5A 91.597 119 5 2 1 119 576611703 576611590 2.480000e-35 159.0
36 TraesCS6A01G290700 chr5A 85.366 123 11 5 701 823 446608110 446608225 1.170000e-23 121.0
37 TraesCS6A01G290700 chr3A 98.333 120 2 0 1 120 17439530 17439649 6.740000e-51 211.0
38 TraesCS6A01G290700 chr3A 91.736 121 5 2 1 121 988255 988140 1.920000e-36 163.0
39 TraesCS6A01G290700 chr3A 91.597 119 5 2 1 119 33137126 33137239 2.480000e-35 159.0
40 TraesCS6A01G290700 chr2A 96.639 119 4 0 1 119 36413581 36413463 5.250000e-47 198.0
41 TraesCS6A01G290700 chr2A 79.661 295 36 8 1004 1298 316872830 316873100 8.790000e-45 191.0
42 TraesCS6A01G290700 chr2A 94.118 119 7 0 1 119 757463749 757463631 5.290000e-42 182.0
43 TraesCS6A01G290700 chr2A 90.517 116 6 2 1 116 734598956 734598846 5.360000e-32 148.0
44 TraesCS6A01G290700 chr2A 89.167 120 8 2 1 120 726366040 726366154 6.940000e-31 145.0


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 TraesCS6A01G290700 chr6A 522207558 522209965 2407 False 1539.733333 4447 98.639333 1 2408 3 chr6A.!!$F1 2407
1 TraesCS6A01G290700 chr6B 9468979 9469836 857 False 1175.000000 1175 91.220000 747 1622 1 chr6B.!!$F2 875
2 TraesCS6A01G290700 chr6B 568194871 568195839 968 False 456.000000 773 86.110000 120 2408 2 chr6B.!!$F4 2288
3 TraesCS6A01G290700 chr6B 568069686 568070351 665 False 407.000000 407 79.270000 1783 2408 1 chr6B.!!$F3 625
4 TraesCS6A01G290700 chr7B 613875617 613877027 1410 False 880.500000 1112 88.492500 331 1628 2 chr7B.!!$F1 1297
5 TraesCS6A01G290700 chr4B 665177244 665178445 1201 True 885.500000 1050 91.541500 320 1470 2 chr4B.!!$R2 1150
6 TraesCS6A01G290700 chr4B 583770522 583771980 1458 True 350.500000 351 90.212500 315 1621 2 chr4B.!!$R1 1306
7 TraesCS6A01G290700 chr4A 539143479 539144268 789 True 352.500000 597 90.780000 320 967 2 chr4A.!!$R1 647
8 TraesCS6A01G290700 chr6D 380729807 380730427 620 False 392.000000 392 79.717000 1783 2359 1 chr6D.!!$F1 576
9 TraesCS6A01G290700 chr6D 380791540 380793030 1490 False 360.000000 361 85.854500 1710 2408 2 chr6D.!!$F2 698
10 TraesCS6A01G290700 chr3B 62978134 62979704 1570 False 358.000000 381 90.605500 319 1621 2 chr3B.!!$F1 1302
11 TraesCS6A01G290700 chr1D 220880211 220881762 1551 False 354.000000 375 90.452500 320 1621 2 chr1D.!!$F1 1301

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
314 315 0.034477 GATTGGGGGACACGGAACAT 60.034 55.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 2620 0.032952 GTATGGAACGGGCGCATCTA 59.967 55.0 10.83 0.0 0.0 1.98 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
17 18 4.090057 GAACGGACTTGCGGCTGC 62.090 66.667 11.65 11.65 43.20 5.25
33 34 3.478394 GCGACGTGCATCAGCGAA 61.478 61.111 0.00 0.00 46.23 4.70
34 35 2.691522 CGACGTGCATCAGCGAAG 59.308 61.111 0.00 0.00 46.23 3.79
48 49 1.991430 CGAAGCGAACATGGAGACG 59.009 57.895 0.00 0.00 0.00 4.18
49 50 0.732880 CGAAGCGAACATGGAGACGT 60.733 55.000 0.00 0.00 0.00 4.34
50 51 1.466866 CGAAGCGAACATGGAGACGTA 60.467 52.381 0.00 0.00 0.00 3.57
51 52 2.602878 GAAGCGAACATGGAGACGTAA 58.397 47.619 0.00 0.00 0.00 3.18
53 54 1.135083 AGCGAACATGGAGACGTAAGG 60.135 52.381 0.00 0.00 46.39 2.69
54 55 1.403780 GCGAACATGGAGACGTAAGGT 60.404 52.381 0.00 0.00 46.39 3.50
55 56 2.259618 CGAACATGGAGACGTAAGGTG 58.740 52.381 0.00 0.00 46.39 4.00
56 57 2.352421 CGAACATGGAGACGTAAGGTGT 60.352 50.000 0.00 0.00 46.39 4.16
57 58 2.743636 ACATGGAGACGTAAGGTGTG 57.256 50.000 0.00 0.00 46.39 3.82
58 59 2.244695 ACATGGAGACGTAAGGTGTGA 58.755 47.619 0.00 0.00 46.39 3.58
59 60 2.029290 ACATGGAGACGTAAGGTGTGAC 60.029 50.000 0.00 0.00 46.39 3.67
60 61 1.991121 TGGAGACGTAAGGTGTGACT 58.009 50.000 0.00 0.00 46.39 3.41
61 62 1.611977 TGGAGACGTAAGGTGTGACTG 59.388 52.381 0.00 0.00 46.39 3.51
62 63 1.612463 GGAGACGTAAGGTGTGACTGT 59.388 52.381 0.00 0.00 46.39 3.55
63 64 2.816087 GGAGACGTAAGGTGTGACTGTA 59.184 50.000 0.00 0.00 46.39 2.74
64 65 3.119919 GGAGACGTAAGGTGTGACTGTAG 60.120 52.174 0.00 0.00 46.39 2.74
65 66 2.818432 AGACGTAAGGTGTGACTGTAGG 59.182 50.000 0.00 0.00 46.39 3.18
66 67 1.891150 ACGTAAGGTGTGACTGTAGGG 59.109 52.381 0.00 0.00 46.39 3.53
67 68 1.403780 CGTAAGGTGTGACTGTAGGGC 60.404 57.143 0.00 0.00 0.00 5.19
68 69 1.066358 GTAAGGTGTGACTGTAGGGCC 60.066 57.143 0.00 0.00 0.00 5.80
69 70 1.489560 AAGGTGTGACTGTAGGGCCC 61.490 60.000 16.46 16.46 0.00 5.80
70 71 2.221299 GGTGTGACTGTAGGGCCCA 61.221 63.158 27.56 7.27 0.00 5.36
71 72 1.562672 GGTGTGACTGTAGGGCCCAT 61.563 60.000 27.56 12.06 0.00 4.00
72 73 0.328258 GTGTGACTGTAGGGCCCATT 59.672 55.000 27.56 6.67 0.00 3.16
73 74 0.327924 TGTGACTGTAGGGCCCATTG 59.672 55.000 27.56 13.53 0.00 2.82
74 75 0.328258 GTGACTGTAGGGCCCATTGT 59.672 55.000 27.56 16.93 0.00 2.71
75 76 1.557832 GTGACTGTAGGGCCCATTGTA 59.442 52.381 27.56 4.01 0.00 2.41
76 77 1.557832 TGACTGTAGGGCCCATTGTAC 59.442 52.381 27.56 18.14 0.00 2.90
77 78 0.916809 ACTGTAGGGCCCATTGTACC 59.083 55.000 27.56 3.36 0.00 3.34
78 79 0.916086 CTGTAGGGCCCATTGTACCA 59.084 55.000 27.56 8.13 0.00 3.25
79 80 1.494721 CTGTAGGGCCCATTGTACCAT 59.505 52.381 27.56 1.16 0.00 3.55
80 81 1.493022 TGTAGGGCCCATTGTACCATC 59.507 52.381 27.56 1.84 0.00 3.51
81 82 1.774856 GTAGGGCCCATTGTACCATCT 59.225 52.381 27.56 0.00 0.00 2.90
82 83 1.308877 AGGGCCCATTGTACCATCTT 58.691 50.000 27.56 0.00 0.00 2.40
83 84 1.215423 AGGGCCCATTGTACCATCTTC 59.785 52.381 27.56 0.00 0.00 2.87
84 85 1.308998 GGCCCATTGTACCATCTTCG 58.691 55.000 0.00 0.00 0.00 3.79
85 86 0.663153 GCCCATTGTACCATCTTCGC 59.337 55.000 0.00 0.00 0.00 4.70
86 87 2.016604 GCCCATTGTACCATCTTCGCA 61.017 52.381 0.00 0.00 0.00 5.10
87 88 1.670811 CCCATTGTACCATCTTCGCAC 59.329 52.381 0.00 0.00 0.00 5.34
88 89 2.632377 CCATTGTACCATCTTCGCACT 58.368 47.619 0.00 0.00 0.00 4.40
89 90 3.431626 CCCATTGTACCATCTTCGCACTA 60.432 47.826 0.00 0.00 0.00 2.74
90 91 3.804325 CCATTGTACCATCTTCGCACTAG 59.196 47.826 0.00 0.00 0.00 2.57
91 92 3.520290 TTGTACCATCTTCGCACTAGG 57.480 47.619 0.00 0.00 0.00 3.02
92 93 1.754803 TGTACCATCTTCGCACTAGGG 59.245 52.381 0.00 0.00 0.00 3.53
93 94 0.750850 TACCATCTTCGCACTAGGGC 59.249 55.000 6.99 6.99 0.00 5.19
94 95 1.227674 CCATCTTCGCACTAGGGCC 60.228 63.158 12.39 0.00 0.00 5.80
95 96 1.690219 CCATCTTCGCACTAGGGCCT 61.690 60.000 12.39 12.58 0.00 5.19
96 97 0.249657 CATCTTCGCACTAGGGCCTC 60.250 60.000 10.74 0.00 0.00 4.70
97 98 1.403687 ATCTTCGCACTAGGGCCTCC 61.404 60.000 10.74 0.00 0.00 4.30
98 99 3.432051 CTTCGCACTAGGGCCTCCG 62.432 68.421 10.74 9.49 38.33 4.63
99 100 3.949885 TTCGCACTAGGGCCTCCGA 62.950 63.158 10.74 11.92 38.33 4.55
100 101 3.905678 CGCACTAGGGCCTCCGAG 61.906 72.222 10.74 4.38 40.96 4.63
101 102 2.442272 GCACTAGGGCCTCCGAGA 60.442 66.667 10.74 0.00 37.92 4.04
102 103 1.834822 GCACTAGGGCCTCCGAGAT 60.835 63.158 10.74 0.00 37.92 2.75
103 104 2.045280 CACTAGGGCCTCCGAGATG 58.955 63.158 10.74 0.00 37.92 2.90
104 105 1.834822 ACTAGGGCCTCCGAGATGC 60.835 63.158 10.74 0.00 37.92 3.91
105 106 1.532794 CTAGGGCCTCCGAGATGCT 60.533 63.158 10.74 0.00 37.92 3.79
106 107 0.251386 CTAGGGCCTCCGAGATGCTA 60.251 60.000 10.74 0.00 37.92 3.49
107 108 0.251386 TAGGGCCTCCGAGATGCTAG 60.251 60.000 10.74 0.00 38.33 3.42
108 109 2.578714 GGGCCTCCGAGATGCTAGG 61.579 68.421 0.84 0.00 0.00 3.02
109 110 2.578714 GGCCTCCGAGATGCTAGGG 61.579 68.421 0.00 0.00 0.00 3.53
110 111 3.055580 CCTCCGAGATGCTAGGGC 58.944 66.667 0.00 0.00 39.26 5.19
111 112 2.578714 CCTCCGAGATGCTAGGGCC 61.579 68.421 0.00 0.00 37.74 5.80
112 113 2.912542 TCCGAGATGCTAGGGCCG 60.913 66.667 0.00 0.00 37.74 6.13
113 114 3.996124 CCGAGATGCTAGGGCCGG 61.996 72.222 0.00 0.00 37.74 6.13
114 115 4.671569 CGAGATGCTAGGGCCGGC 62.672 72.222 21.18 21.18 37.74 6.13
115 116 4.321966 GAGATGCTAGGGCCGGCC 62.322 72.222 38.57 38.57 37.74 6.13
168 169 3.406361 CGGCCAGCGATGCGATAC 61.406 66.667 2.24 0.00 0.00 2.24
221 222 2.578713 CTACGTAGGTGCGTGCGG 60.579 66.667 15.07 0.00 45.33 5.69
222 223 4.118995 TACGTAGGTGCGTGCGGG 62.119 66.667 3.18 0.00 45.33 6.13
254 255 2.869503 GGACACGGAACATGGCCGAT 62.870 60.000 28.67 18.64 43.14 4.18
262 263 2.515290 CATGGCCGATGCAGCAGA 60.515 61.111 1.53 0.00 40.13 4.26
280 281 4.060038 CAGAATGCCAGAATACGTAGGT 57.940 45.455 0.08 0.00 0.00 3.08
281 282 3.804325 CAGAATGCCAGAATACGTAGGTG 59.196 47.826 0.08 0.00 0.00 4.00
282 283 2.240493 ATGCCAGAATACGTAGGTGC 57.760 50.000 0.08 0.14 0.00 5.01
283 284 0.179121 TGCCAGAATACGTAGGTGCG 60.179 55.000 0.08 0.00 37.94 5.34
285 286 1.556564 CCAGAATACGTAGGTGCGTG 58.443 55.000 0.08 0.00 45.33 5.34
286 287 0.921347 CAGAATACGTAGGTGCGTGC 59.079 55.000 0.08 0.00 45.33 5.34
287 288 0.524816 AGAATACGTAGGTGCGTGCG 60.525 55.000 0.08 1.29 45.33 5.34
288 289 1.477030 GAATACGTAGGTGCGTGCGG 61.477 60.000 0.08 0.00 45.33 5.69
289 290 2.894240 AATACGTAGGTGCGTGCGGG 62.894 60.000 0.08 0.00 45.33 6.13
305 306 4.851179 GGCGTCGGATTGGGGGAC 62.851 72.222 0.00 0.00 0.00 4.46
306 307 4.090588 GCGTCGGATTGGGGGACA 62.091 66.667 0.00 0.00 0.00 4.02
307 308 2.125269 CGTCGGATTGGGGGACAC 60.125 66.667 0.00 0.00 0.00 3.67
308 309 2.125269 GTCGGATTGGGGGACACG 60.125 66.667 0.00 0.00 0.00 4.49
309 310 3.395702 TCGGATTGGGGGACACGG 61.396 66.667 0.00 0.00 0.00 4.94
310 311 3.395702 CGGATTGGGGGACACGGA 61.396 66.667 0.00 0.00 0.00 4.69
311 312 2.961893 CGGATTGGGGGACACGGAA 61.962 63.158 0.00 0.00 0.00 4.30
312 313 1.378119 GGATTGGGGGACACGGAAC 60.378 63.158 0.00 0.00 0.00 3.62
313 314 1.377229 GATTGGGGGACACGGAACA 59.623 57.895 0.00 0.00 0.00 3.18
314 315 0.034477 GATTGGGGGACACGGAACAT 60.034 55.000 0.00 0.00 0.00 2.71
315 316 0.323360 ATTGGGGGACACGGAACATG 60.323 55.000 0.00 0.00 0.00 3.21
316 317 2.045340 GGGGGACACGGAACATGG 60.045 66.667 0.00 0.00 0.00 3.66
317 318 2.598787 GGGGGACACGGAACATGGA 61.599 63.158 0.00 0.00 0.00 3.41
329 330 3.074412 GGAACATGGACGAGTGAATTGT 58.926 45.455 0.00 0.00 0.00 2.71
355 357 1.344438 ACATCGACACTTCAGGCAAGA 59.656 47.619 0.00 0.00 35.82 3.02
469 473 6.876804 ACCGTTTTAAGTACGTTTATGACAC 58.123 36.000 0.00 0.00 37.30 3.67
471 475 6.129221 CCGTTTTAAGTACGTTTATGACACGA 60.129 38.462 0.00 0.00 40.20 4.35
556 561 4.193240 ACCAAAAGCTCCCTCCTTTTTA 57.807 40.909 0.00 0.00 39.70 1.52
604 612 1.185618 TCCTCTCCCACCGTTGACTG 61.186 60.000 0.00 0.00 0.00 3.51
868 1132 4.135153 CTGCTGCTCCCGTACGCT 62.135 66.667 10.49 0.00 0.00 5.07
1096 1380 2.030412 TCAACGCAGTGGACGCAT 59.970 55.556 0.00 0.00 45.00 4.73
1099 1383 1.596752 AACGCAGTGGACGCATCAA 60.597 52.632 0.00 0.00 45.00 2.57
1208 1492 2.406616 CGCTTGGGTCCAAATCCGG 61.407 63.158 0.00 0.00 35.33 5.14
1221 1505 4.316823 TCCGGTGTGGAGGGCTCT 62.317 66.667 0.00 0.00 43.74 4.09
1347 2320 2.307686 AGGAAAAGGACCCGATTGCTTA 59.692 45.455 0.00 0.00 0.00 3.09
1423 2396 4.370917 GGTGTAAAACCGTCTGTCTAACA 58.629 43.478 0.00 0.00 39.81 2.41
1463 2436 1.580942 GCCACATCAGCAAAAGCGA 59.419 52.632 0.00 0.00 0.00 4.93
1503 2477 5.123027 ACGTACTTAAAACGGTCCAAACAAA 59.877 36.000 12.92 0.00 44.48 2.83
1575 2551 6.588373 GGCATAATTTCGTAAATGTGTGGTTT 59.412 34.615 0.00 0.00 0.00 3.27
1576 2552 7.411372 GGCATAATTTCGTAAATGTGTGGTTTG 60.411 37.037 0.00 0.00 0.00 2.93
1583 2559 4.505922 CGTAAATGTGTGGTTTGTGCAAAT 59.494 37.500 0.46 0.00 32.36 2.32
1637 2613 2.480419 CACTCTGAAAACACCGATGGAC 59.520 50.000 0.00 0.00 0.00 4.02
1644 2620 1.640917 AACACCGATGGACTAGTGGT 58.359 50.000 0.00 0.00 34.50 4.16
1658 2634 2.171725 GTGGTAGATGCGCCCGTTC 61.172 63.158 4.18 0.00 0.00 3.95
1660 2636 2.185867 GTAGATGCGCCCGTTCCA 59.814 61.111 4.18 0.00 0.00 3.53
1699 2675 4.854784 TCCGCTCGCTCGCACATC 62.855 66.667 0.00 0.00 0.00 3.06
1714 2726 3.005539 ATCACCAGCGCCCAGTCT 61.006 61.111 2.29 0.00 0.00 3.24
1721 2733 2.281484 GCGCCCAGTCTTTCACCA 60.281 61.111 0.00 0.00 0.00 4.17
1726 2738 1.609208 CCCAGTCTTTCACCAGGTTG 58.391 55.000 0.00 0.00 0.00 3.77
1766 2788 3.790437 CTGGATGCCCACCGAGCT 61.790 66.667 0.00 0.00 37.58 4.09
1767 2789 4.100084 TGGATGCCCACCGAGCTG 62.100 66.667 0.00 0.00 37.58 4.24
1768 2790 3.785859 GGATGCCCACCGAGCTGA 61.786 66.667 0.00 0.00 0.00 4.26
1769 2791 2.507944 GATGCCCACCGAGCTGAT 59.492 61.111 0.00 0.00 0.00 2.90
1908 2949 0.385390 CAAAACCACACTGCTGGGAC 59.615 55.000 0.00 0.00 35.34 4.46
1923 2964 2.036733 CTGGGACTACGACTTGGAAACA 59.963 50.000 0.00 0.00 39.83 2.83
2054 3122 4.744570 TCACGTAATCAAGAGATCGCTTT 58.255 39.130 9.19 0.00 31.90 3.51
2071 3890 0.774276 TTTATCACCCACCACAGCCA 59.226 50.000 0.00 0.00 0.00 4.75
2123 3946 2.089427 CGCTTCAATTTTCATGCACACG 59.911 45.455 0.00 0.00 0.00 4.49
2142 3973 3.574074 AATCACTGCGCTTGGCCCT 62.574 57.895 9.73 0.00 42.61 5.19
2155 3986 3.611674 GCCCTCCTCCTCGCTAGC 61.612 72.222 4.06 4.06 0.00 3.42
2159 3990 2.123683 TCCTCCTCGCTAGCCTGG 60.124 66.667 9.66 11.60 0.00 4.45
2194 4035 2.480419 ACGTTTGAGCTAGCACATGTTC 59.520 45.455 18.83 4.90 0.00 3.18
2316 4166 1.502163 GGCAGATGCTTTCGGATCGG 61.502 60.000 4.59 0.00 42.21 4.18
2377 4233 5.362556 TTCTTTTTCTTCAAGAGCGATGG 57.637 39.130 0.00 0.00 31.84 3.51
2384 4240 2.299993 TCAAGAGCGATGGTTAGCAG 57.700 50.000 0.00 0.00 35.48 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.090057 GCAGCCGCAAGTCCGTTC 62.090 66.667 0.00 0.00 38.36 3.95
16 17 3.411703 CTTCGCTGATGCACGTCGC 62.412 63.158 0.00 3.44 39.64 5.19
17 18 2.691522 CTTCGCTGATGCACGTCG 59.308 61.111 0.00 0.00 39.64 5.12
18 19 2.397252 GCTTCGCTGATGCACGTC 59.603 61.111 0.00 0.00 39.64 4.34
19 20 3.481903 CGCTTCGCTGATGCACGT 61.482 61.111 13.66 0.00 39.64 4.49
20 21 2.729675 TTCGCTTCGCTGATGCACG 61.730 57.895 13.66 0.00 39.64 5.34
21 22 1.225854 GTTCGCTTCGCTGATGCAC 60.226 57.895 13.66 4.99 39.64 4.57
22 23 1.020861 ATGTTCGCTTCGCTGATGCA 61.021 50.000 13.66 0.00 39.64 3.96
23 24 0.588233 CATGTTCGCTTCGCTGATGC 60.588 55.000 6.42 6.42 0.00 3.91
24 25 0.027194 CCATGTTCGCTTCGCTGATG 59.973 55.000 0.00 0.00 0.00 3.07
25 26 0.108186 TCCATGTTCGCTTCGCTGAT 60.108 50.000 0.00 0.00 0.00 2.90
26 27 0.737367 CTCCATGTTCGCTTCGCTGA 60.737 55.000 0.00 0.00 0.00 4.26
27 28 0.737367 TCTCCATGTTCGCTTCGCTG 60.737 55.000 0.00 0.00 0.00 5.18
28 29 0.737715 GTCTCCATGTTCGCTTCGCT 60.738 55.000 0.00 0.00 0.00 4.93
29 30 1.710339 GTCTCCATGTTCGCTTCGC 59.290 57.895 0.00 0.00 0.00 4.70
30 31 0.732880 ACGTCTCCATGTTCGCTTCG 60.733 55.000 0.00 0.00 0.00 3.79
31 32 2.273370 TACGTCTCCATGTTCGCTTC 57.727 50.000 0.00 0.00 0.00 3.86
32 33 2.607187 CTTACGTCTCCATGTTCGCTT 58.393 47.619 0.00 0.00 0.00 4.68
33 34 1.135083 CCTTACGTCTCCATGTTCGCT 60.135 52.381 0.00 0.00 0.00 4.93
34 35 1.278238 CCTTACGTCTCCATGTTCGC 58.722 55.000 0.00 0.00 0.00 4.70
35 36 2.259618 CACCTTACGTCTCCATGTTCG 58.740 52.381 0.00 0.00 0.00 3.95
36 37 2.993899 CACACCTTACGTCTCCATGTTC 59.006 50.000 0.00 0.00 0.00 3.18
37 38 2.631062 TCACACCTTACGTCTCCATGTT 59.369 45.455 0.00 0.00 0.00 2.71
38 39 2.029290 GTCACACCTTACGTCTCCATGT 60.029 50.000 0.00 0.00 0.00 3.21
39 40 2.231478 AGTCACACCTTACGTCTCCATG 59.769 50.000 0.00 0.00 0.00 3.66
40 41 2.231478 CAGTCACACCTTACGTCTCCAT 59.769 50.000 0.00 0.00 0.00 3.41
41 42 1.611977 CAGTCACACCTTACGTCTCCA 59.388 52.381 0.00 0.00 0.00 3.86
42 43 1.612463 ACAGTCACACCTTACGTCTCC 59.388 52.381 0.00 0.00 0.00 3.71
43 44 3.119919 CCTACAGTCACACCTTACGTCTC 60.120 52.174 0.00 0.00 0.00 3.36
44 45 2.818432 CCTACAGTCACACCTTACGTCT 59.182 50.000 0.00 0.00 0.00 4.18
45 46 2.094854 CCCTACAGTCACACCTTACGTC 60.095 54.545 0.00 0.00 0.00 4.34
46 47 1.891150 CCCTACAGTCACACCTTACGT 59.109 52.381 0.00 0.00 0.00 3.57
47 48 1.403780 GCCCTACAGTCACACCTTACG 60.404 57.143 0.00 0.00 0.00 3.18
48 49 1.066358 GGCCCTACAGTCACACCTTAC 60.066 57.143 0.00 0.00 0.00 2.34
49 50 1.272807 GGCCCTACAGTCACACCTTA 58.727 55.000 0.00 0.00 0.00 2.69
50 51 1.489560 GGGCCCTACAGTCACACCTT 61.490 60.000 17.04 0.00 0.00 3.50
51 52 1.918800 GGGCCCTACAGTCACACCT 60.919 63.158 17.04 0.00 0.00 4.00
52 53 1.562672 ATGGGCCCTACAGTCACACC 61.563 60.000 25.70 0.00 0.00 4.16
53 54 0.328258 AATGGGCCCTACAGTCACAC 59.672 55.000 25.70 0.00 0.00 3.82
54 55 0.327924 CAATGGGCCCTACAGTCACA 59.672 55.000 25.70 0.00 0.00 3.58
55 56 0.328258 ACAATGGGCCCTACAGTCAC 59.672 55.000 25.70 0.00 0.00 3.67
56 57 1.557832 GTACAATGGGCCCTACAGTCA 59.442 52.381 25.70 0.00 0.00 3.41
57 58 1.134189 GGTACAATGGGCCCTACAGTC 60.134 57.143 25.70 9.56 0.00 3.51
58 59 0.916809 GGTACAATGGGCCCTACAGT 59.083 55.000 25.70 18.08 0.00 3.55
59 60 0.916086 TGGTACAATGGGCCCTACAG 59.084 55.000 25.70 12.86 31.92 2.74
60 61 3.106441 TGGTACAATGGGCCCTACA 57.894 52.632 25.70 2.00 31.92 2.74
73 74 1.538419 GCCCTAGTGCGAAGATGGTAC 60.538 57.143 0.00 0.00 0.00 3.34
74 75 0.750850 GCCCTAGTGCGAAGATGGTA 59.249 55.000 0.00 0.00 0.00 3.25
75 76 1.522569 GCCCTAGTGCGAAGATGGT 59.477 57.895 0.00 0.00 0.00 3.55
76 77 1.227674 GGCCCTAGTGCGAAGATGG 60.228 63.158 0.00 0.00 0.00 3.51
77 78 0.249657 GAGGCCCTAGTGCGAAGATG 60.250 60.000 0.00 0.00 0.00 2.90
78 79 1.403687 GGAGGCCCTAGTGCGAAGAT 61.404 60.000 0.00 0.00 0.00 2.40
79 80 2.058595 GGAGGCCCTAGTGCGAAGA 61.059 63.158 0.00 0.00 0.00 2.87
80 81 2.501610 GGAGGCCCTAGTGCGAAG 59.498 66.667 0.00 0.00 0.00 3.79
81 82 3.458163 CGGAGGCCCTAGTGCGAA 61.458 66.667 0.00 0.00 0.00 4.70
82 83 4.435970 TCGGAGGCCCTAGTGCGA 62.436 66.667 0.00 0.00 33.83 5.10
83 84 3.905678 CTCGGAGGCCCTAGTGCG 61.906 72.222 0.00 0.00 0.00 5.34
84 85 1.834822 ATCTCGGAGGCCCTAGTGC 60.835 63.158 0.00 0.00 0.00 4.40
85 86 2.045280 CATCTCGGAGGCCCTAGTG 58.955 63.158 0.00 0.00 0.00 2.74
86 87 1.834822 GCATCTCGGAGGCCCTAGT 60.835 63.158 0.00 0.00 32.93 2.57
87 88 0.251386 TAGCATCTCGGAGGCCCTAG 60.251 60.000 0.00 0.00 40.43 3.02
88 89 0.251386 CTAGCATCTCGGAGGCCCTA 60.251 60.000 0.00 2.84 40.43 3.53
89 90 1.532794 CTAGCATCTCGGAGGCCCT 60.533 63.158 0.00 0.00 40.43 5.19
90 91 2.578714 CCTAGCATCTCGGAGGCCC 61.579 68.421 0.00 0.00 40.43 5.80
91 92 2.578714 CCCTAGCATCTCGGAGGCC 61.579 68.421 4.96 0.00 40.43 5.19
92 93 3.055580 CCCTAGCATCTCGGAGGC 58.944 66.667 4.96 1.51 39.81 4.70
93 94 2.578714 GGCCCTAGCATCTCGGAGG 61.579 68.421 4.96 0.00 42.56 4.30
94 95 2.925262 CGGCCCTAGCATCTCGGAG 61.925 68.421 0.00 0.00 42.56 4.63
95 96 2.912542 CGGCCCTAGCATCTCGGA 60.913 66.667 0.00 0.00 42.56 4.55
96 97 3.996124 CCGGCCCTAGCATCTCGG 61.996 72.222 0.00 0.00 42.56 4.63
97 98 4.671569 GCCGGCCCTAGCATCTCG 62.672 72.222 18.11 0.00 42.56 4.04
98 99 4.321966 GGCCGGCCCTAGCATCTC 62.322 72.222 36.64 5.01 42.56 2.75
180 181 3.707189 TCTCCCCCTTCCTCCCCC 61.707 72.222 0.00 0.00 0.00 5.40
181 182 2.367107 GTCTCCCCCTTCCTCCCC 60.367 72.222 0.00 0.00 0.00 4.81
182 183 2.764547 CGTCTCCCCCTTCCTCCC 60.765 72.222 0.00 0.00 0.00 4.30
183 184 2.764547 CCGTCTCCCCCTTCCTCC 60.765 72.222 0.00 0.00 0.00 4.30
184 185 2.039137 ACCGTCTCCCCCTTCCTC 59.961 66.667 0.00 0.00 0.00 3.71
185 186 2.039137 GACCGTCTCCCCCTTCCT 59.961 66.667 0.00 0.00 0.00 3.36
186 187 3.082055 GGACCGTCTCCCCCTTCC 61.082 72.222 0.00 0.00 31.83 3.46
221 222 4.851179 GTCCCCCAATCCGACGCC 62.851 72.222 0.00 0.00 0.00 5.68
222 223 4.090588 TGTCCCCCAATCCGACGC 62.091 66.667 0.00 0.00 0.00 5.19
223 224 2.125269 GTGTCCCCCAATCCGACG 60.125 66.667 0.00 0.00 0.00 5.12
225 226 3.395702 CCGTGTCCCCCAATCCGA 61.396 66.667 0.00 0.00 0.00 4.55
226 227 2.961893 TTCCGTGTCCCCCAATCCG 61.962 63.158 0.00 0.00 0.00 4.18
227 228 1.378119 GTTCCGTGTCCCCCAATCC 60.378 63.158 0.00 0.00 0.00 3.01
228 229 0.034477 ATGTTCCGTGTCCCCCAATC 60.034 55.000 0.00 0.00 0.00 2.67
229 230 0.323360 CATGTTCCGTGTCCCCCAAT 60.323 55.000 0.00 0.00 0.00 3.16
230 231 1.074072 CATGTTCCGTGTCCCCCAA 59.926 57.895 0.00 0.00 0.00 4.12
254 255 2.019249 GTATTCTGGCATTCTGCTGCA 58.981 47.619 0.88 0.88 44.28 4.41
262 263 2.561569 GCACCTACGTATTCTGGCATT 58.438 47.619 0.00 0.00 0.00 3.56
288 289 4.851179 GTCCCCCAATCCGACGCC 62.851 72.222 0.00 0.00 0.00 5.68
289 290 4.090588 TGTCCCCCAATCCGACGC 62.091 66.667 0.00 0.00 0.00 5.19
290 291 2.125269 GTGTCCCCCAATCCGACG 60.125 66.667 0.00 0.00 0.00 5.12
291 292 2.125269 CGTGTCCCCCAATCCGAC 60.125 66.667 0.00 0.00 0.00 4.79
292 293 3.395702 CCGTGTCCCCCAATCCGA 61.396 66.667 0.00 0.00 0.00 4.55
293 294 2.961893 TTCCGTGTCCCCCAATCCG 61.962 63.158 0.00 0.00 0.00 4.18
294 295 1.378119 GTTCCGTGTCCCCCAATCC 60.378 63.158 0.00 0.00 0.00 3.01
295 296 0.034477 ATGTTCCGTGTCCCCCAATC 60.034 55.000 0.00 0.00 0.00 2.67
296 297 0.323360 CATGTTCCGTGTCCCCCAAT 60.323 55.000 0.00 0.00 0.00 3.16
297 298 1.074072 CATGTTCCGTGTCCCCCAA 59.926 57.895 0.00 0.00 0.00 4.12
298 299 2.753701 CATGTTCCGTGTCCCCCA 59.246 61.111 0.00 0.00 0.00 4.96
299 300 2.045340 CCATGTTCCGTGTCCCCC 60.045 66.667 0.00 0.00 0.00 5.40
300 301 1.376812 GTCCATGTTCCGTGTCCCC 60.377 63.158 0.00 0.00 0.00 4.81
301 302 1.740296 CGTCCATGTTCCGTGTCCC 60.740 63.158 0.00 0.00 0.00 4.46
302 303 0.736325 CTCGTCCATGTTCCGTGTCC 60.736 60.000 0.00 0.00 0.00 4.02
303 304 0.038526 ACTCGTCCATGTTCCGTGTC 60.039 55.000 0.00 0.00 0.00 3.67
304 305 0.319555 CACTCGTCCATGTTCCGTGT 60.320 55.000 0.00 0.00 0.00 4.49
305 306 0.038618 TCACTCGTCCATGTTCCGTG 60.039 55.000 0.00 0.00 0.00 4.94
306 307 0.677288 TTCACTCGTCCATGTTCCGT 59.323 50.000 0.00 0.00 0.00 4.69
307 308 2.010145 ATTCACTCGTCCATGTTCCG 57.990 50.000 0.00 0.00 0.00 4.30
308 309 3.074412 ACAATTCACTCGTCCATGTTCC 58.926 45.455 0.00 0.00 0.00 3.62
309 310 5.856126 TTACAATTCACTCGTCCATGTTC 57.144 39.130 0.00 0.00 0.00 3.18
310 311 6.627395 TTTTACAATTCACTCGTCCATGTT 57.373 33.333 0.00 0.00 0.00 2.71
311 312 6.627395 TTTTTACAATTCACTCGTCCATGT 57.373 33.333 0.00 0.00 0.00 3.21
366 368 4.292327 GCACAATTTCGTAAATGTGTGC 57.708 40.909 19.85 22.09 46.00 4.57
418 421 3.498397 ACGAGCAACCAGTGTTTATTGAG 59.502 43.478 0.00 0.00 30.42 3.02
419 423 3.472652 ACGAGCAACCAGTGTTTATTGA 58.527 40.909 0.00 0.00 30.42 2.57
423 427 2.356382 CCAAACGAGCAACCAGTGTTTA 59.644 45.455 0.00 0.00 32.00 2.01
469 473 3.403038 GTCATCATTTATGGGACCCTCG 58.597 50.000 13.00 0.00 36.15 4.63
471 475 2.777692 ACGTCATCATTTATGGGACCCT 59.222 45.455 13.00 0.00 36.15 4.34
556 561 3.816994 ACTTACCGTTGGCTCTTTTCTT 58.183 40.909 0.00 0.00 0.00 2.52
572 579 3.775316 TGGGAGAGGAGATGGAAACTTAC 59.225 47.826 0.00 0.00 0.00 2.34
604 612 4.416738 GGGAGGCCCAGCTGACAC 62.417 72.222 17.39 4.21 44.65 3.67
992 1276 3.860605 CCGCATCCATCGACCCCA 61.861 66.667 0.00 0.00 0.00 4.96
1081 1365 0.955428 ATTGATGCGTCCACTGCGTT 60.955 50.000 2.83 0.00 34.24 4.84
1096 1380 0.895100 GCTTCCACCTGCACCATTGA 60.895 55.000 0.00 0.00 0.00 2.57
1099 1383 1.303888 CTGCTTCCACCTGCACCAT 60.304 57.895 0.00 0.00 35.20 3.55
1208 1492 3.196207 TTGCCAGAGCCCTCCACAC 62.196 63.158 0.00 0.00 38.69 3.82
1220 1504 1.569493 CGAACCAAGTCGTTGCCAG 59.431 57.895 0.00 0.00 36.26 4.85
1221 1505 2.539338 GCGAACCAAGTCGTTGCCA 61.539 57.895 0.00 0.00 43.06 4.92
1347 2320 1.411074 GGTCCTTGGCCCGGAAAATAT 60.411 52.381 12.10 0.00 31.13 1.28
1450 2423 0.678048 GGGGTCTCGCTTTTGCTGAT 60.678 55.000 0.00 0.00 44.80 2.90
1554 2530 6.418226 GCACAAACCACACATTTACGAAATTA 59.582 34.615 0.00 0.00 0.00 1.40
1583 2559 2.224281 ACATCGAACACTTCAGGCAAGA 60.224 45.455 0.00 0.00 35.82 3.02
1610 2586 4.196193 TCGGTGTTTTCAGAGTGAATTGT 58.804 39.130 0.00 0.00 36.11 2.71
1628 2604 3.223435 CATCTACCACTAGTCCATCGGT 58.777 50.000 7.00 7.00 0.00 4.69
1637 2613 1.007271 CGGGCGCATCTACCACTAG 60.007 63.158 10.83 0.00 0.00 2.57
1644 2620 0.032952 GTATGGAACGGGCGCATCTA 59.967 55.000 10.83 0.00 0.00 1.98
1682 2658 4.854784 GATGTGCGAGCGAGCGGA 62.855 66.667 0.00 0.00 40.67 5.54
1685 2661 3.558411 GGTGATGTGCGAGCGAGC 61.558 66.667 0.00 0.00 37.71 5.03
1688 2664 3.857854 GCTGGTGATGTGCGAGCG 61.858 66.667 0.00 0.00 0.00 5.03
1694 2670 3.129502 CTGGGCGCTGGTGATGTG 61.130 66.667 7.64 0.00 0.00 3.21
1695 2671 3.612247 GACTGGGCGCTGGTGATGT 62.612 63.158 7.64 0.00 0.00 3.06
1697 2673 2.129555 AAAGACTGGGCGCTGGTGAT 62.130 55.000 7.64 0.00 0.00 3.06
1698 2674 2.731691 GAAAGACTGGGCGCTGGTGA 62.732 60.000 7.64 0.00 0.00 4.02
1699 2675 2.281761 AAAGACTGGGCGCTGGTG 60.282 61.111 7.64 0.00 0.00 4.17
1700 2676 2.032681 GAAAGACTGGGCGCTGGT 59.967 61.111 7.64 3.48 0.00 4.00
1707 2719 1.142870 TCAACCTGGTGAAAGACTGGG 59.857 52.381 0.00 0.00 0.00 4.45
1708 2720 2.638480 TCAACCTGGTGAAAGACTGG 57.362 50.000 0.00 0.00 0.00 4.00
1714 2726 1.790755 CGTCGATCAACCTGGTGAAA 58.209 50.000 0.00 0.00 0.00 2.69
1721 2733 1.153745 GCTCTGCGTCGATCAACCT 60.154 57.895 0.00 0.00 0.00 3.50
1747 2759 2.503061 CTCGGTGGGCATCCAGAG 59.497 66.667 0.00 0.00 45.05 3.35
1908 2949 3.318017 CTGTCCTGTTTCCAAGTCGTAG 58.682 50.000 0.00 0.00 0.00 3.51
1923 2964 1.614525 TGCATCCTCAGGCTGTCCT 60.615 57.895 15.27 0.00 45.66 3.85
2026 3094 6.032985 GCGATCTCTTGATTACGTGATGTATC 59.967 42.308 0.00 0.00 32.19 2.24
2054 3122 1.488812 GTATGGCTGTGGTGGGTGATA 59.511 52.381 0.00 0.00 0.00 2.15
2071 3890 3.932459 GACGGACGTCGATTGGTAT 57.068 52.632 9.92 0.00 42.43 2.73
2123 3946 2.486966 GGCCAAGCGCAGTGATTC 59.513 61.111 11.47 0.16 40.31 2.52
2142 3973 2.012824 ATCCAGGCTAGCGAGGAGGA 62.013 60.000 25.05 18.92 32.91 3.71
2155 3986 1.860950 CGTGCGTATCAGAAATCCAGG 59.139 52.381 0.00 0.00 0.00 4.45
2159 3990 4.569029 CTCAAACGTGCGTATCAGAAATC 58.431 43.478 0.00 0.00 0.00 2.17
2194 4035 2.324014 TATAGCAGGGCGGCAAGTGG 62.324 60.000 12.47 0.00 35.83 4.00
2254 4103 1.270839 TGTCGCTGAAAGAAGGGAAGG 60.271 52.381 0.00 0.00 40.41 3.46
2334 4184 1.403687 AATCTAGCTCGGCTGGGGAC 61.404 60.000 8.44 0.00 40.10 4.46
2377 4233 2.541762 CTGCCGCTCTATTTCTGCTAAC 59.458 50.000 0.00 0.00 0.00 2.34
2384 4240 0.806102 TCGTGCTGCCGCTCTATTTC 60.806 55.000 0.70 0.00 36.97 2.17


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

AutoCloner maintained by Alex Coulton.