Multiple sequence alignment - TraesCS2A01G453500

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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 TraesCS2A01G453500 chr2A 100.000 2291 0 0 1 2291 702950018 702952308 0.000000e+00 4231
1 TraesCS2A01G453500 chr2A 95.563 293 13 0 1004 1296 702956876 702957168 9.580000e-129 470
2 TraesCS2A01G453500 chr2A 82.303 469 54 22 987 1436 702940260 702940718 1.660000e-101 379
3 TraesCS2A01G453500 chr6A 96.266 616 17 1 312 921 381551848 381551233 0.000000e+00 1005
4 TraesCS2A01G453500 chr6A 95.617 616 21 1 312 921 779677 779062 0.000000e+00 983
5 TraesCS2A01G453500 chrUn 95.974 621 19 1 307 921 12271184 12270564 0.000000e+00 1003
6 TraesCS2A01G453500 chrUn 90.000 730 41 17 1592 2291 124553272 124552545 0.000000e+00 915
7 TraesCS2A01G453500 chrUn 89.899 99 10 0 1590 1688 460825476 460825574 6.640000e-26 128
8 TraesCS2A01G453500 chrUn 89.899 99 10 0 1590 1688 469770655 469770753 6.640000e-26 128
9 TraesCS2A01G453500 chr5A 95.942 616 19 1 312 921 110511613 110510998 0.000000e+00 994
10 TraesCS2A01G453500 chr5A 95.659 622 20 2 307 922 606038934 606039554 0.000000e+00 992
11 TraesCS2A01G453500 chr5A 95.617 616 20 2 312 921 456428700 456429314 0.000000e+00 981
12 TraesCS2A01G453500 chr7A 95.779 616 20 1 312 921 57602744 57603359 0.000000e+00 989
13 TraesCS2A01G453500 chr7A 95.624 617 21 1 311 921 726103802 726104418 0.000000e+00 985
14 TraesCS2A01G453500 chr7A 94.941 593 29 1 1700 2291 85594077 85593485 0.000000e+00 928
15 TraesCS2A01G453500 chr4A 95.477 619 22 1 309 921 504096461 504097079 0.000000e+00 983
16 TraesCS2A01G453500 chr4A 96.459 593 19 2 1699 2291 538891154 538891744 0.000000e+00 977
17 TraesCS2A01G453500 chr4A 91.613 155 12 1 1 154 620935838 620935684 1.780000e-51 213
18 TraesCS2A01G453500 chr4A 88.961 154 16 1 3 155 42254028 42254181 3.000000e-44 189
19 TraesCS2A01G453500 chr5D 95.953 593 23 1 1700 2291 388606992 388606400 0.000000e+00 961
20 TraesCS2A01G453500 chr5D 82.463 747 69 29 1590 2278 24780394 24779652 4.210000e-167 597
21 TraesCS2A01G453500 chr5D 90.260 154 14 1 1 153 52324229 52324076 1.390000e-47 200
22 TraesCS2A01G453500 chr2B 95.777 592 23 1 1700 2291 744092199 744092788 0.000000e+00 953
23 TraesCS2A01G453500 chr2B 85.352 512 42 16 922 1424 672023148 672023635 1.220000e-137 499
24 TraesCS2A01G453500 chr2B 88.976 381 29 7 924 1295 671910136 671910512 2.070000e-125 459
25 TraesCS2A01G453500 chr2B 86.184 456 25 12 1004 1427 672059551 672060000 2.070000e-125 459
26 TraesCS2A01G453500 chr2B 94.839 155 7 1 1 154 797637584 797637430 8.180000e-60 241
27 TraesCS2A01G453500 chr2B 77.950 322 26 16 1295 1590 671910542 671910844 2.360000e-35 159
28 TraesCS2A01G453500 chr2B 93.204 103 7 0 1590 1692 744092060 744092162 3.940000e-33 152
29 TraesCS2A01G453500 chr6D 94.435 593 31 2 1700 2291 78784174 78783583 0.000000e+00 911
30 TraesCS2A01G453500 chr6D 88.889 153 16 1 3 154 176916476 176916628 1.080000e-43 187
31 TraesCS2A01G453500 chr4D 94.098 593 34 1 1700 2291 94370700 94371292 0.000000e+00 900
32 TraesCS2A01G453500 chr4D 94.000 100 5 1 1589 1687 94370559 94370658 1.420000e-32 150
33 TraesCS2A01G453500 chr1B 86.842 722 59 12 1591 2278 1492159 1492878 0.000000e+00 774
34 TraesCS2A01G453500 chr1B 89.216 102 11 0 1590 1691 576932058 576931957 6.640000e-26 128
35 TraesCS2A01G453500 chr3D 89.097 587 49 10 1700 2278 366432648 366432069 0.000000e+00 715
36 TraesCS2A01G453500 chr2D 85.900 617 41 17 1004 1589 562353665 562354266 1.160000e-172 616
37 TraesCS2A01G453500 chr2D 79.944 713 51 36 922 1590 562267958 562268622 7.510000e-120 440
38 TraesCS2A01G453500 chr2D 79.343 731 63 47 922 1591 562235200 562235903 1.260000e-117 433
39 TraesCS2A01G453500 chr2D 87.173 382 28 11 923 1295 562340882 562341251 4.550000e-112 414
40 TraesCS2A01G453500 chr2D 86.721 369 40 6 922 1290 562308061 562308420 3.550000e-108 401
41 TraesCS2A01G453500 chr2D 94.416 197 11 0 1002 1198 562449274 562449470 1.030000e-78 303
42 TraesCS2A01G453500 chr2D 87.730 163 12 6 156 311 562340727 562340888 1.400000e-42 183
43 TraesCS2A01G453500 chr5B 82.250 631 58 20 1595 2192 505568045 505568654 1.580000e-136 496
44 TraesCS2A01G453500 chr3A 98.065 155 3 0 1 155 729707318 729707164 1.040000e-68 270
45 TraesCS2A01G453500 chr3A 97.436 156 3 1 1 155 720147437 720147592 4.850000e-67 265
46 TraesCS2A01G453500 chr3A 96.154 156 5 1 1 155 720176412 720176567 1.050000e-63 254
47 TraesCS2A01G453500 chr3B 96.129 155 5 1 1 154 816797562 816797716 3.780000e-63 252
48 TraesCS2A01G453500 chr4B 90.909 99 9 0 1590 1688 627016443 627016541 1.430000e-27 134


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 TraesCS2A01G453500 chr2A 702950018 702952308 2290 False 4231.0 4231 100.0000 1 2291 1 chr2A.!!$F2 2290
1 TraesCS2A01G453500 chr6A 381551233 381551848 615 True 1005.0 1005 96.2660 312 921 1 chr6A.!!$R2 609
2 TraesCS2A01G453500 chr6A 779062 779677 615 True 983.0 983 95.6170 312 921 1 chr6A.!!$R1 609
3 TraesCS2A01G453500 chrUn 12270564 12271184 620 True 1003.0 1003 95.9740 307 921 1 chrUn.!!$R1 614
4 TraesCS2A01G453500 chrUn 124552545 124553272 727 True 915.0 915 90.0000 1592 2291 1 chrUn.!!$R2 699
5 TraesCS2A01G453500 chr5A 110510998 110511613 615 True 994.0 994 95.9420 312 921 1 chr5A.!!$R1 609
6 TraesCS2A01G453500 chr5A 606038934 606039554 620 False 992.0 992 95.6590 307 922 1 chr5A.!!$F2 615
7 TraesCS2A01G453500 chr5A 456428700 456429314 614 False 981.0 981 95.6170 312 921 1 chr5A.!!$F1 609
8 TraesCS2A01G453500 chr7A 57602744 57603359 615 False 989.0 989 95.7790 312 921 1 chr7A.!!$F1 609
9 TraesCS2A01G453500 chr7A 726103802 726104418 616 False 985.0 985 95.6240 311 921 1 chr7A.!!$F2 610
10 TraesCS2A01G453500 chr7A 85593485 85594077 592 True 928.0 928 94.9410 1700 2291 1 chr7A.!!$R1 591
11 TraesCS2A01G453500 chr4A 504096461 504097079 618 False 983.0 983 95.4770 309 921 1 chr4A.!!$F2 612
12 TraesCS2A01G453500 chr4A 538891154 538891744 590 False 977.0 977 96.4590 1699 2291 1 chr4A.!!$F3 592
13 TraesCS2A01G453500 chr5D 388606400 388606992 592 True 961.0 961 95.9530 1700 2291 1 chr5D.!!$R3 591
14 TraesCS2A01G453500 chr5D 24779652 24780394 742 True 597.0 597 82.4630 1590 2278 1 chr5D.!!$R1 688
15 TraesCS2A01G453500 chr2B 744092060 744092788 728 False 552.5 953 94.4905 1590 2291 2 chr2B.!!$F4 701
16 TraesCS2A01G453500 chr2B 671910136 671910844 708 False 309.0 459 83.4630 924 1590 2 chr2B.!!$F3 666
17 TraesCS2A01G453500 chr6D 78783583 78784174 591 True 911.0 911 94.4350 1700 2291 1 chr6D.!!$R1 591
18 TraesCS2A01G453500 chr4D 94370559 94371292 733 False 525.0 900 94.0490 1589 2291 2 chr4D.!!$F1 702
19 TraesCS2A01G453500 chr1B 1492159 1492878 719 False 774.0 774 86.8420 1591 2278 1 chr1B.!!$F1 687
20 TraesCS2A01G453500 chr3D 366432069 366432648 579 True 715.0 715 89.0970 1700 2278 1 chr3D.!!$R1 578
21 TraesCS2A01G453500 chr2D 562353665 562354266 601 False 616.0 616 85.9000 1004 1589 1 chr2D.!!$F4 585
22 TraesCS2A01G453500 chr2D 562267958 562268622 664 False 440.0 440 79.9440 922 1590 1 chr2D.!!$F2 668
23 TraesCS2A01G453500 chr2D 562235200 562235903 703 False 433.0 433 79.3430 922 1591 1 chr2D.!!$F1 669
24 TraesCS2A01G453500 chr2D 562340727 562341251 524 False 298.5 414 87.4515 156 1295 2 chr2D.!!$F6 1139
25 TraesCS2A01G453500 chr5B 505568045 505568654 609 False 496.0 496 82.2500 1595 2192 1 chr5B.!!$F1 597

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
84 85 0.037139 TAACACACGCCGGTATGCTT 60.037 50.0 1.9 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 1615 0.035915 AAAGAAAGGAGAGCCGAGGC 60.036 55.0 5.89 5.89 39.96 4.7 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
24 25 6.658188 AAATTTTCCCTCGTGGTAAAATGA 57.342 33.333 17.21 0.00 37.01 2.57
25 26 6.658188 AATTTTCCCTCGTGGTAAAATGAA 57.342 33.333 17.21 4.09 37.01 2.57
26 27 6.850752 ATTTTCCCTCGTGGTAAAATGAAT 57.149 33.333 16.16 0.00 37.01 2.57
27 28 6.658188 TTTTCCCTCGTGGTAAAATGAATT 57.342 33.333 3.21 0.00 31.19 2.17
28 29 6.658188 TTTCCCTCGTGGTAAAATGAATTT 57.342 33.333 2.33 0.00 34.77 1.82
29 30 7.762588 TTTCCCTCGTGGTAAAATGAATTTA 57.237 32.000 2.33 0.00 34.77 1.40
30 31 7.948034 TTCCCTCGTGGTAAAATGAATTTAT 57.052 32.000 2.33 0.00 35.98 1.40
31 32 9.463902 TTTCCCTCGTGGTAAAATGAATTTATA 57.536 29.630 2.33 0.00 35.98 0.98
32 33 9.635404 TTCCCTCGTGGTAAAATGAATTTATAT 57.365 29.630 2.33 0.00 35.98 0.86
33 34 9.635404 TCCCTCGTGGTAAAATGAATTTATATT 57.365 29.630 2.33 0.00 35.98 1.28
70 71 9.944663 TGTGAATTTTTGACATACTTCTAACAC 57.055 29.630 0.00 0.00 0.00 3.32
71 72 9.944663 GTGAATTTTTGACATACTTCTAACACA 57.055 29.630 0.00 0.00 0.00 3.72
72 73 9.944663 TGAATTTTTGACATACTTCTAACACAC 57.055 29.630 0.00 0.00 0.00 3.82
73 74 9.103048 GAATTTTTGACATACTTCTAACACACG 57.897 33.333 0.00 0.00 0.00 4.49
74 75 5.585500 TTTGACATACTTCTAACACACGC 57.415 39.130 0.00 0.00 0.00 5.34
75 76 3.581755 TGACATACTTCTAACACACGCC 58.418 45.455 0.00 0.00 0.00 5.68
76 77 2.597305 GACATACTTCTAACACACGCCG 59.403 50.000 0.00 0.00 0.00 6.46
77 78 1.924524 CATACTTCTAACACACGCCGG 59.075 52.381 0.00 0.00 0.00 6.13
78 79 0.961019 TACTTCTAACACACGCCGGT 59.039 50.000 1.90 0.00 0.00 5.28
79 80 0.961019 ACTTCTAACACACGCCGGTA 59.039 50.000 1.90 0.00 0.00 4.02
80 81 1.547372 ACTTCTAACACACGCCGGTAT 59.453 47.619 1.90 0.00 0.00 2.73
81 82 1.924524 CTTCTAACACACGCCGGTATG 59.075 52.381 1.90 4.17 0.00 2.39
82 83 0.458889 TCTAACACACGCCGGTATGC 60.459 55.000 1.90 0.00 0.00 3.14
83 84 0.459585 CTAACACACGCCGGTATGCT 60.460 55.000 1.90 0.00 0.00 3.79
84 85 0.037139 TAACACACGCCGGTATGCTT 60.037 50.000 1.90 0.00 0.00 3.91
85 86 1.573829 AACACACGCCGGTATGCTTG 61.574 55.000 1.90 0.00 36.64 4.01
86 87 2.435938 ACACGCCGGTATGCTTGG 60.436 61.111 1.90 0.00 35.03 3.61
87 88 2.435938 CACGCCGGTATGCTTGGT 60.436 61.111 1.90 0.00 0.00 3.67
88 89 1.153529 CACGCCGGTATGCTTGGTA 60.154 57.895 1.90 0.00 0.00 3.25
89 90 0.531974 CACGCCGGTATGCTTGGTAT 60.532 55.000 1.90 0.00 0.00 2.73
90 91 0.179468 ACGCCGGTATGCTTGGTATT 59.821 50.000 1.90 0.00 0.00 1.89
91 92 1.305201 CGCCGGTATGCTTGGTATTT 58.695 50.000 1.90 0.00 0.00 1.40
92 93 1.002900 CGCCGGTATGCTTGGTATTTG 60.003 52.381 1.90 0.00 0.00 2.32
93 94 2.294074 GCCGGTATGCTTGGTATTTGA 58.706 47.619 1.90 0.00 0.00 2.69
94 95 2.032924 GCCGGTATGCTTGGTATTTGAC 59.967 50.000 1.90 0.00 0.00 3.18
95 96 2.286833 CCGGTATGCTTGGTATTTGACG 59.713 50.000 0.00 0.00 0.00 4.35
96 97 2.933906 CGGTATGCTTGGTATTTGACGT 59.066 45.455 0.00 0.00 0.00 4.34
97 98 3.372822 CGGTATGCTTGGTATTTGACGTT 59.627 43.478 0.00 0.00 0.00 3.99
98 99 4.567558 CGGTATGCTTGGTATTTGACGTTA 59.432 41.667 0.00 0.00 0.00 3.18
99 100 5.235616 CGGTATGCTTGGTATTTGACGTTAT 59.764 40.000 0.00 0.00 0.00 1.89
100 101 6.238266 CGGTATGCTTGGTATTTGACGTTATT 60.238 38.462 0.00 0.00 0.00 1.40
101 102 7.477494 GGTATGCTTGGTATTTGACGTTATTT 58.523 34.615 0.00 0.00 0.00 1.40
102 103 7.971722 GGTATGCTTGGTATTTGACGTTATTTT 59.028 33.333 0.00 0.00 0.00 1.82
103 104 9.349145 GTATGCTTGGTATTTGACGTTATTTTT 57.651 29.630 0.00 0.00 0.00 1.94
105 106 8.958175 TGCTTGGTATTTGACGTTATTTTTAG 57.042 30.769 0.00 0.00 0.00 1.85
106 107 8.569641 TGCTTGGTATTTGACGTTATTTTTAGT 58.430 29.630 0.00 0.00 0.00 2.24
107 108 9.058424 GCTTGGTATTTGACGTTATTTTTAGTC 57.942 33.333 0.00 0.00 0.00 2.59
109 110 9.881529 TTGGTATTTGACGTTATTTTTAGTCAC 57.118 29.630 0.00 0.00 42.44 3.67
110 111 9.275398 TGGTATTTGACGTTATTTTTAGTCACT 57.725 29.630 0.00 0.00 42.44 3.41
123 124 8.935614 ATTTTTAGTCACTTAGTTTTAGCCCT 57.064 30.769 0.00 0.00 0.00 5.19
125 126 9.498176 TTTTTAGTCACTTAGTTTTAGCCCTAG 57.502 33.333 0.00 0.00 0.00 3.02
126 127 5.678955 AGTCACTTAGTTTTAGCCCTAGG 57.321 43.478 0.06 0.06 0.00 3.02
139 140 2.302260 GCCCTAGGCTTTGAGAAATCC 58.698 52.381 2.05 0.00 46.69 3.01
140 141 2.092158 GCCCTAGGCTTTGAGAAATCCT 60.092 50.000 2.05 0.00 46.69 3.24
141 142 3.136626 GCCCTAGGCTTTGAGAAATCCTA 59.863 47.826 2.05 0.00 46.69 2.94
146 147 4.849518 AGGCTTTGAGAAATCCTAGTTCC 58.150 43.478 0.00 0.00 35.35 3.62
147 148 3.623510 GGCTTTGAGAAATCCTAGTTCCG 59.376 47.826 0.00 0.00 0.00 4.30
148 149 3.064134 GCTTTGAGAAATCCTAGTTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
149 150 2.981859 TGAGAAATCCTAGTTCCGCC 57.018 50.000 0.00 0.00 0.00 6.13
150 151 2.467880 TGAGAAATCCTAGTTCCGCCT 58.532 47.619 0.00 0.00 0.00 5.52
151 152 2.431057 TGAGAAATCCTAGTTCCGCCTC 59.569 50.000 0.00 0.00 0.00 4.70
152 153 2.696187 GAGAAATCCTAGTTCCGCCTCT 59.304 50.000 0.00 0.00 0.00 3.69
153 154 2.432510 AGAAATCCTAGTTCCGCCTCTG 59.567 50.000 0.00 0.00 0.00 3.35
154 155 1.123928 AATCCTAGTTCCGCCTCTGG 58.876 55.000 0.00 0.00 0.00 3.86
187 188 1.848652 CTCCCTCGTCCTTGGTTAGA 58.151 55.000 0.00 0.00 0.00 2.10
193 194 1.808945 TCGTCCTTGGTTAGACTCGTC 59.191 52.381 0.00 0.00 0.00 4.20
241 242 3.491652 GTGCTCGCTCGCCTTTCC 61.492 66.667 0.00 0.00 0.00 3.13
253 254 3.646715 CTTTCCCCCAGCGGACCA 61.647 66.667 0.00 0.00 0.00 4.02
260 261 2.030562 CCAGCGGACCAGTTTCGT 59.969 61.111 0.00 0.00 0.00 3.85
263 264 2.207924 AGCGGACCAGTTTCGTCCT 61.208 57.895 5.52 0.00 46.48 3.85
264 265 1.737008 GCGGACCAGTTTCGTCCTC 60.737 63.158 5.52 0.00 46.48 3.71
265 266 1.443872 CGGACCAGTTTCGTCCTCG 60.444 63.158 5.52 0.00 46.48 4.63
270 271 3.300765 AGTTTCGTCCTCGCCCGT 61.301 61.111 0.00 0.00 36.96 5.28
271 272 2.808321 GTTTCGTCCTCGCCCGTC 60.808 66.667 0.00 0.00 36.96 4.79
288 293 2.426024 CCGTCCCATATATACCCAGACG 59.574 54.545 14.69 14.69 43.76 4.18
305 311 0.605589 ACGCCCTAGTTTGGTTCAGC 60.606 55.000 0.00 0.00 0.00 4.26
713 719 9.807649 CTAGAAATTTGAAAATTACCTCCCATG 57.192 33.333 0.00 0.00 37.62 3.66
749 755 8.871125 GGATACGGATATATCCAGTTCCATATT 58.129 37.037 27.55 7.95 46.94 1.28
842 848 5.890424 TCTATTTCCATTTTGGTTCGGAC 57.110 39.130 0.00 0.00 39.03 4.79
858 864 1.636340 GACGCGGATGTTTCGGATG 59.364 57.895 12.47 0.00 0.00 3.51
915 927 8.109634 AGATATTTATCCGCTACCAATTTCCAT 58.890 33.333 0.00 0.00 33.17 3.41
937 951 1.195448 CCTAAGCACAGCAAACACTCG 59.805 52.381 0.00 0.00 0.00 4.18
945 959 1.197721 CAGCAAACACTCGATCAACCC 59.802 52.381 0.00 0.00 0.00 4.11
977 991 1.396316 CGTACCAAAAGCAACGACGTC 60.396 52.381 5.18 5.18 37.53 4.34
978 992 1.862827 GTACCAAAAGCAACGACGTCT 59.137 47.619 14.70 0.00 0.00 4.18
979 993 2.228138 ACCAAAAGCAACGACGTCTA 57.772 45.000 14.70 0.00 0.00 2.59
980 994 1.862827 ACCAAAAGCAACGACGTCTAC 59.137 47.619 14.70 0.00 0.00 2.59
981 995 1.862201 CCAAAAGCAACGACGTCTACA 59.138 47.619 14.70 0.00 0.00 2.74
982 996 2.285756 CCAAAAGCAACGACGTCTACAA 59.714 45.455 14.70 0.00 0.00 2.41
983 997 3.531982 CAAAAGCAACGACGTCTACAAG 58.468 45.455 14.70 0.00 0.00 3.16
984 998 1.779569 AAGCAACGACGTCTACAAGG 58.220 50.000 14.70 0.00 0.00 3.61
985 999 0.666577 AGCAACGACGTCTACAAGGC 60.667 55.000 14.70 8.48 0.00 4.35
997 1020 0.533308 TACAAGGCCACACGAACACC 60.533 55.000 5.01 0.00 0.00 4.16
998 1021 1.821759 CAAGGCCACACGAACACCA 60.822 57.895 5.01 0.00 0.00 4.17
1167 1190 3.857854 CGCCACGAGCAGATGCAC 61.858 66.667 7.68 0.00 45.16 4.57
1296 1323 4.789075 GTCGCGAGCTAACCGGCA 62.789 66.667 10.24 0.00 34.17 5.69
1378 1435 3.326836 GGAGACTCTCCTTGGTTGAAG 57.673 52.381 16.91 0.00 46.41 3.02
1404 1461 4.143333 AAGACGCGGGTCATCGGG 62.143 66.667 31.03 0.00 45.92 5.14
1448 1528 0.821517 CATGGGCATCAATGTGCAGT 59.178 50.000 9.30 0.00 46.81 4.40
1451 1531 0.966875 GGGCATCAATGTGCAGTGGA 60.967 55.000 9.30 0.00 46.81 4.02
1462 1542 0.473755 TGCAGTGGAAAAGGAGCTGA 59.526 50.000 0.00 0.00 0.00 4.26
1487 1570 6.243900 ACTGGATCTGAAGTCAATCAAACAT 58.756 36.000 0.00 0.00 0.00 2.71
1491 1574 8.048514 TGGATCTGAAGTCAATCAAACATGATA 58.951 33.333 0.00 0.00 0.00 2.15
1502 1585 0.908910 AACATGATACTCCACGGCCA 59.091 50.000 2.24 0.00 0.00 5.36
1548 1634 2.188207 GGCCTCGGCTCTCCTTTC 59.812 66.667 8.00 0.00 41.60 2.62
1553 1644 1.276421 CCTCGGCTCTCCTTTCTTTCA 59.724 52.381 0.00 0.00 0.00 2.69
1623 1714 2.172717 ACCAGTGGTGCTAGAACTTGTT 59.827 45.455 15.86 0.00 32.98 2.83
1660 1751 6.588719 TTAGTGCCTGAACTTGCAAAATAT 57.411 33.333 0.00 0.00 39.57 1.28
1688 1779 6.663093 TGAACTGGTTTCATAACTTGGCATAT 59.337 34.615 0.00 0.00 39.45 1.78
1692 1783 7.283127 ACTGGTTTCATAACTTGGCATATACAG 59.717 37.037 0.00 0.00 34.59 2.74
1693 1784 7.116075 TGGTTTCATAACTTGGCATATACAGT 58.884 34.615 0.00 0.00 34.59 3.55
1695 1786 8.129211 GGTTTCATAACTTGGCATATACAGTTC 58.871 37.037 4.87 0.00 34.59 3.01
1696 1787 8.673711 GTTTCATAACTTGGCATATACAGTTCA 58.326 33.333 4.87 0.00 0.00 3.18
1712 1832 2.365617 AGTTCAAACGAAGCTGAGGAGA 59.634 45.455 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.658188 AAATTCATTTTACCACGAGGGAAA 57.342 33.333 5.02 5.02 46.18 3.13
6 7 7.948034 ATAAATTCATTTTACCACGAGGGAA 57.052 32.000 3.29 0.00 41.15 3.97
7 8 9.635404 AATATAAATTCATTTTACCACGAGGGA 57.365 29.630 3.29 0.00 41.15 4.20
44 45 9.944663 GTGTTAGAAGTATGTCAAAAATTCACA 57.055 29.630 2.77 0.00 0.00 3.58
45 46 9.944663 TGTGTTAGAAGTATGTCAAAAATTCAC 57.055 29.630 2.77 0.00 0.00 3.18
46 47 9.944663 GTGTGTTAGAAGTATGTCAAAAATTCA 57.055 29.630 2.77 0.00 0.00 2.57
47 48 9.103048 CGTGTGTTAGAAGTATGTCAAAAATTC 57.897 33.333 0.00 0.00 0.00 2.17
48 49 7.589954 GCGTGTGTTAGAAGTATGTCAAAAATT 59.410 33.333 0.00 0.00 0.00 1.82
49 50 7.075741 GCGTGTGTTAGAAGTATGTCAAAAAT 58.924 34.615 0.00 0.00 0.00 1.82
50 51 6.423862 GCGTGTGTTAGAAGTATGTCAAAAA 58.576 36.000 0.00 0.00 0.00 1.94
51 52 5.049954 GGCGTGTGTTAGAAGTATGTCAAAA 60.050 40.000 0.00 0.00 0.00 2.44
52 53 4.449743 GGCGTGTGTTAGAAGTATGTCAAA 59.550 41.667 0.00 0.00 0.00 2.69
53 54 3.991773 GGCGTGTGTTAGAAGTATGTCAA 59.008 43.478 0.00 0.00 0.00 3.18
54 55 3.581755 GGCGTGTGTTAGAAGTATGTCA 58.418 45.455 0.00 0.00 0.00 3.58
55 56 2.597305 CGGCGTGTGTTAGAAGTATGTC 59.403 50.000 0.00 0.00 0.00 3.06
56 57 2.602878 CGGCGTGTGTTAGAAGTATGT 58.397 47.619 0.00 0.00 0.00 2.29
57 58 1.924524 CCGGCGTGTGTTAGAAGTATG 59.075 52.381 6.01 0.00 0.00 2.39
58 59 1.547372 ACCGGCGTGTGTTAGAAGTAT 59.453 47.619 6.01 0.00 0.00 2.12
59 60 0.961019 ACCGGCGTGTGTTAGAAGTA 59.039 50.000 6.01 0.00 0.00 2.24
60 61 0.961019 TACCGGCGTGTGTTAGAAGT 59.039 50.000 6.01 0.00 0.00 3.01
61 62 1.924524 CATACCGGCGTGTGTTAGAAG 59.075 52.381 6.01 0.00 0.00 2.85
62 63 1.999048 CATACCGGCGTGTGTTAGAA 58.001 50.000 6.01 0.00 0.00 2.10
63 64 0.458889 GCATACCGGCGTGTGTTAGA 60.459 55.000 6.01 0.00 33.85 2.10
64 65 0.459585 AGCATACCGGCGTGTGTTAG 60.460 55.000 6.01 0.00 39.27 2.34
65 66 0.037139 AAGCATACCGGCGTGTGTTA 60.037 50.000 6.01 0.00 39.27 2.41
66 67 1.302192 AAGCATACCGGCGTGTGTT 60.302 52.632 6.01 0.00 39.27 3.32
67 68 2.032634 CAAGCATACCGGCGTGTGT 61.033 57.895 6.01 0.00 38.27 3.72
68 69 2.749865 CCAAGCATACCGGCGTGTG 61.750 63.158 6.01 4.04 40.91 3.82
69 70 1.890625 TACCAAGCATACCGGCGTGT 61.891 55.000 6.01 6.18 40.91 4.49
70 71 0.531974 ATACCAAGCATACCGGCGTG 60.532 55.000 6.01 0.81 41.93 5.34
71 72 0.179468 AATACCAAGCATACCGGCGT 59.821 50.000 6.01 0.00 39.27 5.68
72 73 1.002900 CAAATACCAAGCATACCGGCG 60.003 52.381 0.00 0.00 39.27 6.46
73 74 2.032924 GTCAAATACCAAGCATACCGGC 59.967 50.000 0.00 0.00 0.00 6.13
74 75 2.286833 CGTCAAATACCAAGCATACCGG 59.713 50.000 0.00 0.00 0.00 5.28
75 76 2.933906 ACGTCAAATACCAAGCATACCG 59.066 45.455 0.00 0.00 0.00 4.02
76 77 4.957759 AACGTCAAATACCAAGCATACC 57.042 40.909 0.00 0.00 0.00 2.73
77 78 8.905103 AAAATAACGTCAAATACCAAGCATAC 57.095 30.769 0.00 0.00 0.00 2.39
79 80 9.567848 CTAAAAATAACGTCAAATACCAAGCAT 57.432 29.630 0.00 0.00 0.00 3.79
80 81 8.569641 ACTAAAAATAACGTCAAATACCAAGCA 58.430 29.630 0.00 0.00 0.00 3.91
81 82 8.959734 ACTAAAAATAACGTCAAATACCAAGC 57.040 30.769 0.00 0.00 0.00 4.01
83 84 9.881529 GTGACTAAAAATAACGTCAAATACCAA 57.118 29.630 0.00 0.00 38.04 3.67
84 85 9.275398 AGTGACTAAAAATAACGTCAAATACCA 57.725 29.630 0.00 0.00 38.04 3.25
98 99 8.935614 AGGGCTAAAACTAAGTGACTAAAAAT 57.064 30.769 0.00 0.00 0.00 1.82
99 100 9.498176 CTAGGGCTAAAACTAAGTGACTAAAAA 57.502 33.333 0.00 0.00 0.00 1.94
100 101 8.098912 CCTAGGGCTAAAACTAAGTGACTAAAA 58.901 37.037 0.00 0.00 0.00 1.52
101 102 7.618137 CCTAGGGCTAAAACTAAGTGACTAAA 58.382 38.462 0.00 0.00 0.00 1.85
102 103 6.351626 GCCTAGGGCTAAAACTAAGTGACTAA 60.352 42.308 11.72 0.00 46.69 2.24
103 104 5.128335 GCCTAGGGCTAAAACTAAGTGACTA 59.872 44.000 11.72 0.00 46.69 2.59
104 105 4.081031 GCCTAGGGCTAAAACTAAGTGACT 60.081 45.833 11.72 0.00 46.69 3.41
105 106 4.190001 GCCTAGGGCTAAAACTAAGTGAC 58.810 47.826 11.72 0.00 46.69 3.67
106 107 4.482952 GCCTAGGGCTAAAACTAAGTGA 57.517 45.455 11.72 0.00 46.69 3.41
126 127 3.064134 GCGGAACTAGGATTTCTCAAAGC 59.936 47.826 0.00 0.00 0.00 3.51
127 128 3.623510 GGCGGAACTAGGATTTCTCAAAG 59.376 47.826 0.00 0.00 0.00 2.77
128 129 3.263425 AGGCGGAACTAGGATTTCTCAAA 59.737 43.478 0.00 0.00 0.00 2.69
129 130 2.838202 AGGCGGAACTAGGATTTCTCAA 59.162 45.455 0.00 0.00 0.00 3.02
130 131 2.431057 GAGGCGGAACTAGGATTTCTCA 59.569 50.000 0.00 0.00 0.00 3.27
131 132 2.696187 AGAGGCGGAACTAGGATTTCTC 59.304 50.000 0.00 0.00 0.00 2.87
132 133 2.432510 CAGAGGCGGAACTAGGATTTCT 59.567 50.000 0.00 0.00 0.00 2.52
133 134 2.483889 CCAGAGGCGGAACTAGGATTTC 60.484 54.545 0.00 0.00 0.00 2.17
134 135 1.486726 CCAGAGGCGGAACTAGGATTT 59.513 52.381 0.00 0.00 0.00 2.17
135 136 1.123928 CCAGAGGCGGAACTAGGATT 58.876 55.000 0.00 0.00 0.00 3.01
136 137 0.261991 TCCAGAGGCGGAACTAGGAT 59.738 55.000 0.00 0.00 29.93 3.24
137 138 0.395862 CTCCAGAGGCGGAACTAGGA 60.396 60.000 0.00 0.00 33.65 2.94
138 139 0.395862 TCTCCAGAGGCGGAACTAGG 60.396 60.000 0.00 0.00 33.65 3.02
139 140 1.475403 TTCTCCAGAGGCGGAACTAG 58.525 55.000 0.00 0.00 33.65 2.57
140 141 1.549170 GTTTCTCCAGAGGCGGAACTA 59.451 52.381 0.00 0.00 33.65 2.24
141 142 0.321996 GTTTCTCCAGAGGCGGAACT 59.678 55.000 0.00 0.00 33.65 3.01
142 143 0.673956 GGTTTCTCCAGAGGCGGAAC 60.674 60.000 0.00 0.00 33.65 3.62
143 144 1.677552 GGTTTCTCCAGAGGCGGAA 59.322 57.895 0.00 0.00 33.65 4.30
144 145 2.646175 CGGTTTCTCCAGAGGCGGA 61.646 63.158 0.00 0.00 35.57 5.54
145 146 2.125512 CGGTTTCTCCAGAGGCGG 60.126 66.667 0.00 0.00 35.57 6.13
146 147 1.014564 GTTCGGTTTCTCCAGAGGCG 61.015 60.000 0.00 0.00 35.57 5.52
147 148 0.673956 GGTTCGGTTTCTCCAGAGGC 60.674 60.000 0.00 0.00 35.57 4.70
148 149 0.389948 CGGTTCGGTTTCTCCAGAGG 60.390 60.000 0.00 0.00 35.57 3.69
149 150 1.014564 GCGGTTCGGTTTCTCCAGAG 61.015 60.000 0.00 0.00 35.57 3.35
150 151 1.005394 GCGGTTCGGTTTCTCCAGA 60.005 57.895 0.00 0.00 35.57 3.86
151 152 1.004918 AGCGGTTCGGTTTCTCCAG 60.005 57.895 0.00 0.00 32.22 3.86
152 153 1.005394 GAGCGGTTCGGTTTCTCCA 60.005 57.895 0.00 0.00 37.83 3.86
153 154 1.740664 GGAGCGGTTCGGTTTCTCC 60.741 63.158 0.00 0.00 37.83 3.71
154 155 1.740664 GGGAGCGGTTCGGTTTCTC 60.741 63.158 0.00 0.00 37.83 2.87
193 194 3.114825 AATACCATGGGCCGTCCGG 62.115 63.158 18.09 0.24 38.76 5.14
202 203 2.489275 GGGCCACGCAATACCATGG 61.489 63.158 11.19 11.19 35.17 3.66
235 236 4.426313 GGTCCGCTGGGGGAAAGG 62.426 72.222 11.17 0.00 37.96 3.11
241 242 2.359975 GAAACTGGTCCGCTGGGG 60.360 66.667 4.03 4.03 37.02 4.96
243 244 2.027625 GACGAAACTGGTCCGCTGG 61.028 63.158 0.00 0.00 0.00 4.85
250 251 2.342648 GGCGAGGACGAAACTGGT 59.657 61.111 0.00 0.00 42.66 4.00
253 254 3.278592 GACGGGCGAGGACGAAACT 62.279 63.158 0.00 0.00 42.66 2.66
260 261 0.040646 ATATATGGGACGGGCGAGGA 59.959 55.000 0.00 0.00 0.00 3.71
263 264 1.477553 GGTATATATGGGACGGGCGA 58.522 55.000 0.00 0.00 0.00 5.54
264 265 0.462789 GGGTATATATGGGACGGGCG 59.537 60.000 0.00 0.00 0.00 6.13
265 266 1.485066 CTGGGTATATATGGGACGGGC 59.515 57.143 0.00 0.00 0.00 6.13
270 271 2.463752 GGCGTCTGGGTATATATGGGA 58.536 52.381 0.00 0.00 0.00 4.37
271 272 1.485066 GGGCGTCTGGGTATATATGGG 59.515 57.143 0.00 0.00 0.00 4.00
288 293 0.881796 GTGCTGAACCAAACTAGGGC 59.118 55.000 0.00 0.00 0.00 5.19
305 311 0.673644 CGTTTCCACCCCTAGCTGTG 60.674 60.000 0.00 0.00 0.00 3.66
842 848 2.324477 GCATCCGAAACATCCGCG 59.676 61.111 0.00 0.00 0.00 6.46
889 895 7.458397 TGGAAATTGGTAGCGGATAAATATCT 58.542 34.615 0.81 0.00 33.28 1.98
915 927 1.142870 AGTGTTTGCTGTGCTTAGGGA 59.857 47.619 0.00 0.00 0.00 4.20
959 973 2.228138 AGACGTCGTTGCTTTTGGTA 57.772 45.000 10.46 0.00 0.00 3.25
977 991 0.865769 GTGTTCGTGTGGCCTTGTAG 59.134 55.000 3.32 0.00 0.00 2.74
978 992 0.533308 GGTGTTCGTGTGGCCTTGTA 60.533 55.000 3.32 0.00 0.00 2.41
979 993 1.822186 GGTGTTCGTGTGGCCTTGT 60.822 57.895 3.32 0.00 0.00 3.16
980 994 1.785041 CTGGTGTTCGTGTGGCCTTG 61.785 60.000 3.32 0.00 0.00 3.61
981 995 1.525995 CTGGTGTTCGTGTGGCCTT 60.526 57.895 3.32 0.00 0.00 4.35
982 996 1.768684 ATCTGGTGTTCGTGTGGCCT 61.769 55.000 3.32 0.00 0.00 5.19
983 997 1.302511 ATCTGGTGTTCGTGTGGCC 60.303 57.895 0.00 0.00 0.00 5.36
984 998 1.577328 CCATCTGGTGTTCGTGTGGC 61.577 60.000 0.00 0.00 0.00 5.01
985 999 1.577328 GCCATCTGGTGTTCGTGTGG 61.577 60.000 0.00 0.00 37.57 4.17
1099 1122 3.429410 CCTCTGTACATGAAGATGTCGCA 60.429 47.826 0.00 0.00 42.14 5.10
1296 1323 0.235665 CGTGCACGCAGATCTTGTTT 59.764 50.000 28.16 0.00 0.00 2.83
1340 1397 2.907407 TCGATCCCGCGCTGATCT 60.907 61.111 24.95 3.18 37.15 2.75
1378 1435 2.815647 CCGCGTCTTGCTTCCTCC 60.816 66.667 4.92 0.00 43.27 4.30
1379 1436 2.815647 CCCGCGTCTTGCTTCCTC 60.816 66.667 4.92 0.00 43.27 3.71
1380 1437 3.591254 GACCCGCGTCTTGCTTCCT 62.591 63.158 4.92 0.00 43.27 3.36
1381 1438 3.119096 GACCCGCGTCTTGCTTCC 61.119 66.667 4.92 0.00 43.27 3.46
1436 1497 3.499338 TCCTTTTCCACTGCACATTGAT 58.501 40.909 0.00 0.00 0.00 2.57
1437 1498 2.886523 CTCCTTTTCCACTGCACATTGA 59.113 45.455 0.00 0.00 0.00 2.57
1439 1500 1.615392 GCTCCTTTTCCACTGCACATT 59.385 47.619 0.00 0.00 0.00 2.71
1440 1501 1.202976 AGCTCCTTTTCCACTGCACAT 60.203 47.619 0.00 0.00 0.00 3.21
1441 1502 0.183492 AGCTCCTTTTCCACTGCACA 59.817 50.000 0.00 0.00 0.00 4.57
1442 1503 0.595095 CAGCTCCTTTTCCACTGCAC 59.405 55.000 0.00 0.00 0.00 4.57
1443 1504 0.473755 TCAGCTCCTTTTCCACTGCA 59.526 50.000 0.00 0.00 0.00 4.41
1444 1505 1.268079 GTTCAGCTCCTTTTCCACTGC 59.732 52.381 0.00 0.00 0.00 4.40
1448 1528 1.774254 TCCAGTTCAGCTCCTTTTCCA 59.226 47.619 0.00 0.00 0.00 3.53
1451 1531 3.328931 TCAGATCCAGTTCAGCTCCTTTT 59.671 43.478 0.00 0.00 0.00 2.27
1462 1542 6.064060 TGTTTGATTGACTTCAGATCCAGTT 58.936 36.000 0.00 0.00 0.00 3.16
1487 1570 0.679505 GCTATGGCCGTGGAGTATCA 59.320 55.000 13.37 0.00 36.25 2.15
1532 1615 0.035915 AAAGAAAGGAGAGCCGAGGC 60.036 55.000 5.89 5.89 39.96 4.70
1548 1634 5.050091 ACAGAACTGACATTAACGCTGAAAG 60.050 40.000 8.87 0.00 0.00 2.62
1553 1644 5.720202 TCATACAGAACTGACATTAACGCT 58.280 37.500 8.87 0.00 0.00 5.07
1688 1779 3.069016 TCCTCAGCTTCGTTTGAACTGTA 59.931 43.478 0.00 0.00 36.01 2.74
1692 1783 2.476997 GTCTCCTCAGCTTCGTTTGAAC 59.523 50.000 0.00 0.00 0.00 3.18
1693 1784 2.755650 GTCTCCTCAGCTTCGTTTGAA 58.244 47.619 0.00 0.00 0.00 2.69
1695 1786 1.063806 CGTCTCCTCAGCTTCGTTTG 58.936 55.000 0.00 0.00 0.00 2.93
1696 1787 0.667792 GCGTCTCCTCAGCTTCGTTT 60.668 55.000 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.