Multiple sequence alignment - TraesCS2D01G444800

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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 TraesCS2D01G444800 chr2D 100.000 2541 0 0 1 2541 555910930 555913470 0.000000e+00 4693
1 TraesCS2D01G444800 chr2B 96.863 797 22 3 1745 2541 662684544 662685337 0.000000e+00 1330
2 TraesCS2D01G444800 chr2B 87.500 1048 73 21 736 1749 662683469 662684492 0.000000e+00 1157
3 TraesCS2D01G444800 chr2B 94.153 496 27 2 169 662 662682931 662683426 0.000000e+00 754
4 TraesCS2D01G444800 chr2A 92.881 590 25 7 1167 1749 695312854 695313433 0.000000e+00 841
5 TraesCS2D01G444800 chr2A 93.305 478 24 4 227 703 695305478 695305948 0.000000e+00 699
6 TraesCS2D01G444800 chr2A 93.363 452 19 4 734 1174 695307458 695307909 0.000000e+00 658
7 TraesCS2D01G444800 chr2A 97.802 364 7 1 2178 2541 695313982 695314344 5.970000e-176 627
8 TraesCS2D01G444800 chr2A 91.743 436 22 9 1745 2177 695313484 695313908 6.050000e-166 593
9 TraesCS2D01G444800 chr5D 97.179 319 8 1 268 585 472384549 472384867 2.880000e-149 538
10 TraesCS2D01G444800 chr4B 85.965 399 49 5 185 581 525267979 525267586 1.090000e-113 420
11 TraesCS2D01G444800 chr4B 88.629 299 33 1 284 581 525305094 525305392 1.860000e-96 363
12 TraesCS2D01G444800 chr4B 87.500 296 33 2 287 581 525389586 525389294 3.130000e-89 339
13 TraesCS2D01G444800 chr7D 100.000 91 0 0 82 172 342585473 342585383 4.350000e-38 169
14 TraesCS2D01G444800 chr3A 96.907 97 3 0 75 171 739385356 739385260 2.020000e-36 163
15 TraesCS2D01G444800 chr1D 95.098 102 5 0 80 181 379468010 379467909 7.280000e-36 161
16 TraesCS2D01G444800 chr6B 96.875 96 2 1 86 181 342268394 342268488 2.620000e-35 159
17 TraesCS2D01G444800 chr6B 96.842 95 2 1 85 179 79369125 79369218 9.410000e-35 158
18 TraesCS2D01G444800 chr6D 92.857 112 3 3 85 195 291718568 291718675 9.410000e-35 158
19 TraesCS2D01G444800 chr6D 91.964 112 4 3 85 195 429317715 429317608 4.380000e-33 152
20 TraesCS2D01G444800 chr4D 92.857 112 3 3 85 195 215187790 215187683 9.410000e-35 158
21 TraesCS2D01G444800 chr3B 93.458 107 6 1 85 191 553867901 553867796 9.410000e-35 158


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 TraesCS2D01G444800 chr2D 555910930 555913470 2540 False 4693.000000 4693 100.000000 1 2541 1 chr2D.!!$F1 2540
1 TraesCS2D01G444800 chr2B 662682931 662685337 2406 False 1080.333333 1330 92.838667 169 2541 3 chr2B.!!$F1 2372
2 TraesCS2D01G444800 chr2A 695312854 695314344 1490 False 687.000000 841 94.142000 1167 2541 3 chr2A.!!$F2 1374
3 TraesCS2D01G444800 chr2A 695305478 695307909 2431 False 678.500000 699 93.334000 227 1174 2 chr2A.!!$F1 947

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
19 20 0.107654 GGAGTTGGCGGTATTGCTCT 60.108 55.0 0.0 0.0 34.52 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 3520 0.106149 ACACTGTTGACCCCGACTTC 59.894 55.0 0.0 0.0 0.0 3.01 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 4.637771 GGAGTTGGCGGTATTGCT 57.362 55.556 0.00 0.00 34.52 3.91
18 19 2.394604 GGAGTTGGCGGTATTGCTC 58.605 57.895 0.00 0.00 34.52 4.26
19 20 0.107654 GGAGTTGGCGGTATTGCTCT 60.108 55.000 0.00 0.00 34.52 4.09
20 21 1.009829 GAGTTGGCGGTATTGCTCTG 58.990 55.000 0.00 0.00 34.52 3.35
21 22 0.613260 AGTTGGCGGTATTGCTCTGA 59.387 50.000 0.00 0.00 34.52 3.27
22 23 1.210478 AGTTGGCGGTATTGCTCTGAT 59.790 47.619 0.00 0.00 34.52 2.90
23 24 2.017049 GTTGGCGGTATTGCTCTGATT 58.983 47.619 0.00 0.00 34.52 2.57
24 25 3.118408 AGTTGGCGGTATTGCTCTGATTA 60.118 43.478 0.00 0.00 34.52 1.75
25 26 3.552132 TGGCGGTATTGCTCTGATTAA 57.448 42.857 0.00 0.00 34.52 1.40
26 27 3.466836 TGGCGGTATTGCTCTGATTAAG 58.533 45.455 0.00 0.00 34.52 1.85
27 28 2.224314 GGCGGTATTGCTCTGATTAAGC 59.776 50.000 0.00 0.00 40.26 3.09
36 37 5.362556 TGCTCTGATTAAGCAAGAACAAC 57.637 39.130 0.00 0.00 46.29 3.32
37 38 5.065914 TGCTCTGATTAAGCAAGAACAACT 58.934 37.500 0.00 0.00 46.29 3.16
38 39 5.532406 TGCTCTGATTAAGCAAGAACAACTT 59.468 36.000 0.00 0.00 46.29 2.66
39 40 6.039717 TGCTCTGATTAAGCAAGAACAACTTT 59.960 34.615 0.00 0.00 46.29 2.66
40 41 6.920210 GCTCTGATTAAGCAAGAACAACTTTT 59.080 34.615 0.00 0.00 39.61 2.27
41 42 7.096312 GCTCTGATTAAGCAAGAACAACTTTTG 60.096 37.037 0.00 0.00 39.61 2.44
42 43 7.995289 TCTGATTAAGCAAGAACAACTTTTGA 58.005 30.769 0.00 0.00 36.61 2.69
43 44 8.465999 TCTGATTAAGCAAGAACAACTTTTGAA 58.534 29.630 0.00 0.00 36.61 2.69
44 45 8.406172 TGATTAAGCAAGAACAACTTTTGAAC 57.594 30.769 0.00 0.00 36.61 3.18
45 46 7.491048 TGATTAAGCAAGAACAACTTTTGAACC 59.509 33.333 0.00 0.00 36.61 3.62
46 47 4.799564 AGCAAGAACAACTTTTGAACCA 57.200 36.364 0.00 0.00 36.61 3.67
47 48 4.494484 AGCAAGAACAACTTTTGAACCAC 58.506 39.130 0.00 0.00 36.61 4.16
48 49 4.021544 AGCAAGAACAACTTTTGAACCACA 60.022 37.500 0.00 0.00 36.61 4.17
49 50 4.688413 GCAAGAACAACTTTTGAACCACAA 59.312 37.500 0.00 0.00 36.61 3.33
50 51 5.178438 GCAAGAACAACTTTTGAACCACAAA 59.822 36.000 0.00 0.00 45.22 2.83
51 52 6.618379 GCAAGAACAACTTTTGAACCACAAAG 60.618 38.462 0.00 0.00 46.93 2.77
52 53 4.929211 AGAACAACTTTTGAACCACAAAGC 59.071 37.500 0.00 0.00 46.93 3.51
53 54 4.535526 ACAACTTTTGAACCACAAAGCT 57.464 36.364 0.00 0.00 46.93 3.74
54 55 4.893608 ACAACTTTTGAACCACAAAGCTT 58.106 34.783 0.00 0.00 46.93 3.74
55 56 5.304778 ACAACTTTTGAACCACAAAGCTTT 58.695 33.333 5.69 5.69 46.93 3.51
56 57 6.459923 ACAACTTTTGAACCACAAAGCTTTA 58.540 32.000 12.25 0.00 46.93 1.85
57 58 6.367695 ACAACTTTTGAACCACAAAGCTTTAC 59.632 34.615 12.25 0.73 46.93 2.01
58 59 6.031751 ACTTTTGAACCACAAAGCTTTACA 57.968 33.333 12.25 3.25 46.93 2.41
59 60 6.639563 ACTTTTGAACCACAAAGCTTTACAT 58.360 32.000 12.25 0.00 46.93 2.29
60 61 6.534793 ACTTTTGAACCACAAAGCTTTACATG 59.465 34.615 12.25 10.44 46.93 3.21
61 62 5.590530 TTGAACCACAAAGCTTTACATGT 57.409 34.783 12.25 2.69 35.39 3.21
62 63 5.181690 TGAACCACAAAGCTTTACATGTC 57.818 39.130 12.25 7.76 0.00 3.06
63 64 4.887071 TGAACCACAAAGCTTTACATGTCT 59.113 37.500 12.25 0.00 0.00 3.41
64 65 5.008613 TGAACCACAAAGCTTTACATGTCTC 59.991 40.000 12.25 9.31 0.00 3.36
65 66 3.821033 ACCACAAAGCTTTACATGTCTCC 59.179 43.478 12.25 0.00 0.00 3.71
66 67 3.120199 CCACAAAGCTTTACATGTCTCCG 60.120 47.826 12.25 0.00 0.00 4.63
67 68 3.745975 CACAAAGCTTTACATGTCTCCGA 59.254 43.478 12.25 0.00 0.00 4.55
68 69 4.393062 CACAAAGCTTTACATGTCTCCGAT 59.607 41.667 12.25 0.00 0.00 4.18
69 70 4.393062 ACAAAGCTTTACATGTCTCCGATG 59.607 41.667 12.25 0.00 0.00 3.84
70 71 3.895232 AGCTTTACATGTCTCCGATGT 57.105 42.857 0.00 0.00 37.75 3.06
71 72 3.786635 AGCTTTACATGTCTCCGATGTC 58.213 45.455 0.00 0.00 35.62 3.06
72 73 3.449018 AGCTTTACATGTCTCCGATGTCT 59.551 43.478 0.00 0.00 35.62 3.41
73 74 3.553511 GCTTTACATGTCTCCGATGTCTG 59.446 47.826 0.00 0.00 35.62 3.51
74 75 4.678044 GCTTTACATGTCTCCGATGTCTGA 60.678 45.833 0.00 0.00 35.62 3.27
75 76 4.639135 TTACATGTCTCCGATGTCTGAG 57.361 45.455 0.00 0.00 35.62 3.35
76 77 1.135915 ACATGTCTCCGATGTCTGAGC 59.864 52.381 0.00 0.00 27.16 4.26
77 78 1.408340 CATGTCTCCGATGTCTGAGCT 59.592 52.381 0.00 0.00 0.00 4.09
78 79 2.420058 TGTCTCCGATGTCTGAGCTA 57.580 50.000 0.00 0.00 0.00 3.32
79 80 2.293170 TGTCTCCGATGTCTGAGCTAG 58.707 52.381 0.00 0.00 0.00 3.42
80 81 2.294074 GTCTCCGATGTCTGAGCTAGT 58.706 52.381 0.00 0.00 0.00 2.57
81 82 2.685897 GTCTCCGATGTCTGAGCTAGTT 59.314 50.000 0.00 0.00 0.00 2.24
82 83 3.129638 GTCTCCGATGTCTGAGCTAGTTT 59.870 47.826 0.00 0.00 0.00 2.66
83 84 3.764434 TCTCCGATGTCTGAGCTAGTTTT 59.236 43.478 0.00 0.00 0.00 2.43
84 85 4.109050 CTCCGATGTCTGAGCTAGTTTTC 58.891 47.826 0.00 0.00 0.00 2.29
85 86 3.764434 TCCGATGTCTGAGCTAGTTTTCT 59.236 43.478 0.00 0.00 0.00 2.52
86 87 4.948004 TCCGATGTCTGAGCTAGTTTTCTA 59.052 41.667 0.00 0.00 0.00 2.10
87 88 5.038033 CCGATGTCTGAGCTAGTTTTCTAC 58.962 45.833 0.00 0.00 0.00 2.59
88 89 5.163602 CCGATGTCTGAGCTAGTTTTCTACT 60.164 44.000 0.00 0.00 41.04 2.57
89 90 5.968848 CGATGTCTGAGCTAGTTTTCTACTC 59.031 44.000 0.00 0.00 38.33 2.59
90 91 5.646577 TGTCTGAGCTAGTTTTCTACTCC 57.353 43.478 0.00 0.00 38.33 3.85
91 92 4.463186 TGTCTGAGCTAGTTTTCTACTCCC 59.537 45.833 0.00 0.00 38.33 4.30
92 93 4.707934 GTCTGAGCTAGTTTTCTACTCCCT 59.292 45.833 0.00 0.00 38.33 4.20
93 94 4.951094 TCTGAGCTAGTTTTCTACTCCCTC 59.049 45.833 0.00 0.00 38.33 4.30
94 95 4.024670 TGAGCTAGTTTTCTACTCCCTCC 58.975 47.826 0.00 0.00 38.33 4.30
95 96 3.025262 AGCTAGTTTTCTACTCCCTCCG 58.975 50.000 0.00 0.00 38.33 4.63
96 97 2.759535 GCTAGTTTTCTACTCCCTCCGT 59.240 50.000 0.00 0.00 38.33 4.69
97 98 3.950395 GCTAGTTTTCTACTCCCTCCGTA 59.050 47.826 0.00 0.00 38.33 4.02
98 99 4.400567 GCTAGTTTTCTACTCCCTCCGTAA 59.599 45.833 0.00 0.00 38.33 3.18
99 100 5.105595 GCTAGTTTTCTACTCCCTCCGTAAA 60.106 44.000 0.00 0.00 38.33 2.01
100 101 5.144692 AGTTTTCTACTCCCTCCGTAAAC 57.855 43.478 0.00 0.00 28.23 2.01
101 102 4.837298 AGTTTTCTACTCCCTCCGTAAACT 59.163 41.667 0.00 0.00 28.23 2.66
102 103 6.012745 AGTTTTCTACTCCCTCCGTAAACTA 58.987 40.000 0.00 0.00 28.23 2.24
103 104 6.494835 AGTTTTCTACTCCCTCCGTAAACTAA 59.505 38.462 0.00 0.00 28.23 2.24
104 105 7.179872 AGTTTTCTACTCCCTCCGTAAACTAAT 59.820 37.037 0.00 0.00 28.23 1.73
105 106 8.470002 GTTTTCTACTCCCTCCGTAAACTAATA 58.530 37.037 0.00 0.00 0.00 0.98
106 107 8.773033 TTTCTACTCCCTCCGTAAACTAATAT 57.227 34.615 0.00 0.00 0.00 1.28
107 108 9.866655 TTTCTACTCCCTCCGTAAACTAATATA 57.133 33.333 0.00 0.00 0.00 0.86
108 109 9.866655 TTCTACTCCCTCCGTAAACTAATATAA 57.133 33.333 0.00 0.00 0.00 0.98
109 110 9.512588 TCTACTCCCTCCGTAAACTAATATAAG 57.487 37.037 0.00 0.00 0.00 1.73
110 111 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
111 112 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
112 113 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
113 114 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
114 115 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
115 116 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
116 117 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
117 118 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
118 119 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
119 120 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
164 165 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
165 166 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
166 167 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
167 168 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
184 185 4.793201 AGGGAGTACTTCATTAATTGCCC 58.207 43.478 2.92 2.15 0.00 5.36
188 189 6.183360 GGGAGTACTTCATTAATTGCCCTTTC 60.183 42.308 2.92 0.00 0.00 2.62
191 192 9.174166 GAGTACTTCATTAATTGCCCTTTCTTA 57.826 33.333 0.00 0.00 0.00 2.10
192 193 9.528489 AGTACTTCATTAATTGCCCTTTCTTAA 57.472 29.630 0.00 0.00 0.00 1.85
221 222 6.540189 TCAGAGAGGTGCTTTTATGAAATAGC 59.460 38.462 0.00 0.00 0.00 2.97
223 224 5.428253 AGAGGTGCTTTTATGAAATAGCGA 58.572 37.500 0.00 0.00 0.00 4.93
224 225 6.058183 AGAGGTGCTTTTATGAAATAGCGAT 58.942 36.000 0.00 0.00 0.00 4.58
225 226 6.543831 AGAGGTGCTTTTATGAAATAGCGATT 59.456 34.615 0.00 0.00 0.00 3.34
239 241 7.972832 TGAAATAGCGATTGATTAATTGTTGCA 59.027 29.630 0.00 0.00 31.44 4.08
253 255 6.415798 AATTGTTGCACTGGTTTTGTTTAC 57.584 33.333 0.00 0.00 0.00 2.01
266 268 9.906660 CTGGTTTTGTTTACTGCTTTGATAATA 57.093 29.630 0.00 0.00 0.00 0.98
612 615 6.018425 CCTGACTTTTCTGGAACATGATATCG 60.018 42.308 0.00 0.00 42.26 2.92
658 661 8.321005 GCAAATGTTTTCTGTTAAGAAGTTCAC 58.679 33.333 5.50 0.00 43.27 3.18
667 679 5.182487 TGTTAAGAAGTTCACAAGCACAGA 58.818 37.500 5.50 0.00 0.00 3.41
693 705 0.383949 CCACACCACCCTGAAAAACG 59.616 55.000 0.00 0.00 0.00 3.60
703 715 0.667993 CTGAAAAACGGCCAGCTGAA 59.332 50.000 17.39 0.00 0.00 3.02
704 716 1.270550 CTGAAAAACGGCCAGCTGAAT 59.729 47.619 17.39 0.00 0.00 2.57
705 717 1.269448 TGAAAAACGGCCAGCTGAATC 59.731 47.619 17.39 3.53 0.00 2.52
706 718 1.541588 GAAAAACGGCCAGCTGAATCT 59.458 47.619 17.39 0.00 0.00 2.40
707 719 2.489938 AAAACGGCCAGCTGAATCTA 57.510 45.000 17.39 0.00 0.00 1.98
708 720 2.717639 AAACGGCCAGCTGAATCTAT 57.282 45.000 17.39 0.00 0.00 1.98
710 722 0.833287 ACGGCCAGCTGAATCTATGT 59.167 50.000 17.39 0.50 0.00 2.29
713 725 2.802816 CGGCCAGCTGAATCTATGTAAC 59.197 50.000 17.39 0.00 0.00 2.50
714 726 3.493350 CGGCCAGCTGAATCTATGTAACT 60.493 47.826 17.39 0.00 0.00 2.24
715 727 4.455606 GGCCAGCTGAATCTATGTAACTT 58.544 43.478 17.39 0.00 0.00 2.66
836 2337 2.251371 GGCACCGAAAACGTCAGC 59.749 61.111 0.00 0.00 0.00 4.26
935 2440 0.395312 TCCCAGTTCACGTCCCTTTC 59.605 55.000 0.00 0.00 0.00 2.62
980 2485 4.274147 ACCGATCTCTTTCTCTTCAGCTA 58.726 43.478 0.00 0.00 0.00 3.32
1138 2649 3.851845 TTCCAGGTGACGGTTCGCG 62.852 63.158 0.00 0.00 32.51 5.87
1281 2802 5.355596 CCATTTTCTGACGCTTCTCTATCT 58.644 41.667 0.00 0.00 0.00 1.98
1332 2853 3.361977 GCACGGGGCGTCATGTTT 61.362 61.111 0.00 0.00 38.32 2.83
1548 3080 1.709147 GCCAAGCACTGATACCGCAG 61.709 60.000 0.00 0.00 41.63 5.18
1564 3096 2.959516 CGCAGGTGATTAACAGAGACA 58.040 47.619 0.00 0.00 0.00 3.41
1647 3185 0.039527 GCCGCGGCCTTAATATTTGG 60.040 55.000 39.89 1.15 34.56 3.28
1648 3186 1.600023 CCGCGGCCTTAATATTTGGA 58.400 50.000 14.67 0.00 0.00 3.53
1649 3187 1.950909 CCGCGGCCTTAATATTTGGAA 59.049 47.619 14.67 0.00 0.00 3.53
1650 3188 2.359531 CCGCGGCCTTAATATTTGGAAA 59.640 45.455 14.67 0.00 0.00 3.13
1651 3189 3.368495 CGCGGCCTTAATATTTGGAAAC 58.632 45.455 0.00 1.34 0.00 2.78
1652 3190 3.368495 GCGGCCTTAATATTTGGAAACG 58.632 45.455 0.00 10.86 0.00 3.60
1653 3191 3.181494 GCGGCCTTAATATTTGGAAACGT 60.181 43.478 0.00 0.00 0.00 3.99
1654 3192 4.675933 GCGGCCTTAATATTTGGAAACGTT 60.676 41.667 0.00 0.00 0.00 3.99
1655 3193 4.796312 CGGCCTTAATATTTGGAAACGTTG 59.204 41.667 0.00 0.00 0.00 4.10
1656 3194 5.620429 CGGCCTTAATATTTGGAAACGTTGT 60.620 40.000 0.00 0.00 0.00 3.32
1657 3195 5.575218 GGCCTTAATATTTGGAAACGTTGTG 59.425 40.000 0.00 0.00 0.00 3.33
1658 3196 5.061684 GCCTTAATATTTGGAAACGTTGTGC 59.938 40.000 0.00 0.00 0.00 4.57
1740 3279 8.474831 TCCTCGATGTAAAAACAAGATGATCTA 58.525 33.333 0.00 0.00 0.00 1.98
1744 3283 7.010183 CGATGTAAAAACAAGATGATCTACGGT 59.990 37.037 0.00 0.00 0.00 4.83
1794 3389 7.468141 AAGTGTGACTGTCAATACTATCTGA 57.532 36.000 21.77 0.00 29.52 3.27
1827 3422 2.430694 GGCAGAGGACAAAAACCTGTTT 59.569 45.455 0.00 0.00 37.93 2.83
1832 3427 4.956075 AGAGGACAAAAACCTGTTTGACAT 59.044 37.500 4.76 0.00 40.29 3.06
1833 3428 5.422012 AGAGGACAAAAACCTGTTTGACATT 59.578 36.000 4.76 0.00 40.29 2.71
1868 3463 1.072678 CGCCCTGGCATCATCTCAT 59.927 57.895 9.17 0.00 42.06 2.90
1922 3520 0.394488 TGGTCCAGCCTCTCTAGACG 60.394 60.000 0.00 0.00 34.78 4.18
2102 3700 4.718276 TCATCCACCAGAATCATCAAGAGA 59.282 41.667 0.00 0.00 0.00 3.10
2285 3957 3.251729 GCTCTTTCTGCATGTTTCTGACA 59.748 43.478 0.00 0.00 43.71 3.58
2300 3972 6.543465 TGTTTCTGACAACATCATTCACTTCT 59.457 34.615 2.66 0.00 36.48 2.85
2312 3984 6.672266 TCATTCACTTCTACCTTCACTCTT 57.328 37.500 0.00 0.00 0.00 2.85
2442 4114 3.814504 AACAAGGGGACATCACAAGAT 57.185 42.857 0.00 0.00 33.87 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.107654 AGAGCAATACCGCCAACTCC 60.108 55.000 0.00 0.00 0.00 3.85
1 2 1.009829 CAGAGCAATACCGCCAACTC 58.990 55.000 0.00 0.00 0.00 3.01
2 3 0.613260 TCAGAGCAATACCGCCAACT 59.387 50.000 0.00 0.00 0.00 3.16
3 4 1.668419 ATCAGAGCAATACCGCCAAC 58.332 50.000 0.00 0.00 0.00 3.77
4 5 2.418368 AATCAGAGCAATACCGCCAA 57.582 45.000 0.00 0.00 0.00 4.52
5 6 3.466836 CTTAATCAGAGCAATACCGCCA 58.533 45.455 0.00 0.00 0.00 5.69
6 7 2.224314 GCTTAATCAGAGCAATACCGCC 59.776 50.000 0.00 0.00 39.89 6.13
7 8 2.872245 TGCTTAATCAGAGCAATACCGC 59.128 45.455 0.00 0.00 46.35 5.68
15 16 5.619625 AGTTGTTCTTGCTTAATCAGAGC 57.380 39.130 0.00 0.00 40.53 4.09
16 17 8.131100 TCAAAAGTTGTTCTTGCTTAATCAGAG 58.869 33.333 0.00 0.00 36.40 3.35
17 18 7.995289 TCAAAAGTTGTTCTTGCTTAATCAGA 58.005 30.769 0.00 0.00 36.40 3.27
18 19 8.534778 GTTCAAAAGTTGTTCTTGCTTAATCAG 58.465 33.333 0.00 0.00 36.40 2.90
19 20 7.491048 GGTTCAAAAGTTGTTCTTGCTTAATCA 59.509 33.333 0.00 0.00 36.40 2.57
20 21 7.491048 TGGTTCAAAAGTTGTTCTTGCTTAATC 59.509 33.333 0.00 0.00 36.40 1.75
21 22 7.277760 GTGGTTCAAAAGTTGTTCTTGCTTAAT 59.722 33.333 0.00 0.00 36.40 1.40
22 23 6.588373 GTGGTTCAAAAGTTGTTCTTGCTTAA 59.412 34.615 0.00 0.00 36.40 1.85
23 24 6.096695 GTGGTTCAAAAGTTGTTCTTGCTTA 58.903 36.000 0.00 0.00 36.40 3.09
24 25 4.929211 GTGGTTCAAAAGTTGTTCTTGCTT 59.071 37.500 0.00 0.00 36.40 3.91
25 26 4.021544 TGTGGTTCAAAAGTTGTTCTTGCT 60.022 37.500 0.00 0.00 36.40 3.91
26 27 4.241681 TGTGGTTCAAAAGTTGTTCTTGC 58.758 39.130 0.00 0.00 36.40 4.01
27 28 6.618379 GCTTTGTGGTTCAAAAGTTGTTCTTG 60.618 38.462 0.00 0.00 44.08 3.02
28 29 5.408299 GCTTTGTGGTTCAAAAGTTGTTCTT 59.592 36.000 0.00 0.00 44.08 2.52
29 30 4.929211 GCTTTGTGGTTCAAAAGTTGTTCT 59.071 37.500 0.00 0.00 44.08 3.01
30 31 4.929211 AGCTTTGTGGTTCAAAAGTTGTTC 59.071 37.500 0.00 0.00 44.08 3.18
31 32 4.893608 AGCTTTGTGGTTCAAAAGTTGTT 58.106 34.783 0.00 0.00 44.08 2.83
32 33 4.535526 AGCTTTGTGGTTCAAAAGTTGT 57.464 36.364 0.00 0.00 44.08 3.32
33 34 5.861222 AAAGCTTTGTGGTTCAAAAGTTG 57.139 34.783 11.80 0.00 44.08 3.16
34 35 6.459923 TGTAAAGCTTTGTGGTTCAAAAGTT 58.540 32.000 22.02 0.00 44.08 2.66
35 36 6.031751 TGTAAAGCTTTGTGGTTCAAAAGT 57.968 33.333 22.02 0.00 44.08 2.66
36 37 6.534793 ACATGTAAAGCTTTGTGGTTCAAAAG 59.465 34.615 22.02 7.97 44.08 2.27
37 38 6.402222 ACATGTAAAGCTTTGTGGTTCAAAA 58.598 32.000 22.02 0.00 44.08 2.44
38 39 5.971763 ACATGTAAAGCTTTGTGGTTCAAA 58.028 33.333 22.02 0.00 42.79 2.69
39 40 5.359576 AGACATGTAAAGCTTTGTGGTTCAA 59.640 36.000 22.02 0.00 35.02 2.69
40 41 4.887071 AGACATGTAAAGCTTTGTGGTTCA 59.113 37.500 22.02 10.70 35.02 3.18
41 42 5.438761 AGACATGTAAAGCTTTGTGGTTC 57.561 39.130 22.02 11.91 35.02 3.62
42 43 4.278419 GGAGACATGTAAAGCTTTGTGGTT 59.722 41.667 22.02 9.73 38.10 3.67
43 44 3.821033 GGAGACATGTAAAGCTTTGTGGT 59.179 43.478 22.02 13.56 0.00 4.16
44 45 3.120199 CGGAGACATGTAAAGCTTTGTGG 60.120 47.826 22.02 10.59 0.00 4.17
45 46 3.745975 TCGGAGACATGTAAAGCTTTGTG 59.254 43.478 22.02 17.99 0.00 3.33
46 47 4.002906 TCGGAGACATGTAAAGCTTTGT 57.997 40.909 22.02 11.63 0.00 2.83
47 48 4.393062 ACATCGGAGACATGTAAAGCTTTG 59.607 41.667 22.02 8.16 42.51 2.77
48 49 4.579869 ACATCGGAGACATGTAAAGCTTT 58.420 39.130 17.30 17.30 42.51 3.51
49 50 4.081420 AGACATCGGAGACATGTAAAGCTT 60.081 41.667 0.00 0.00 42.51 3.74
50 51 3.449018 AGACATCGGAGACATGTAAAGCT 59.551 43.478 0.00 0.00 42.51 3.74
51 52 3.553511 CAGACATCGGAGACATGTAAAGC 59.446 47.826 0.00 0.00 42.51 3.51
52 53 4.998788 TCAGACATCGGAGACATGTAAAG 58.001 43.478 0.00 0.00 42.51 1.85
53 54 4.678044 GCTCAGACATCGGAGACATGTAAA 60.678 45.833 12.51 0.00 42.51 2.01
54 55 3.181486 GCTCAGACATCGGAGACATGTAA 60.181 47.826 12.51 0.00 42.51 2.41
55 56 2.359214 GCTCAGACATCGGAGACATGTA 59.641 50.000 12.51 0.00 42.51 2.29
56 57 1.135915 GCTCAGACATCGGAGACATGT 59.864 52.381 12.51 0.00 42.51 3.21
57 58 1.408340 AGCTCAGACATCGGAGACATG 59.592 52.381 12.51 0.00 42.51 3.21
58 59 1.774110 AGCTCAGACATCGGAGACAT 58.226 50.000 12.51 0.00 42.51 3.06
59 60 2.293170 CTAGCTCAGACATCGGAGACA 58.707 52.381 12.51 0.00 42.51 3.41
60 61 2.294074 ACTAGCTCAGACATCGGAGAC 58.706 52.381 12.51 4.75 42.51 3.36
61 62 2.719531 ACTAGCTCAGACATCGGAGA 57.280 50.000 12.51 0.00 39.97 3.71
62 63 3.791973 AAACTAGCTCAGACATCGGAG 57.208 47.619 4.83 4.83 40.42 4.63
63 64 3.764434 AGAAAACTAGCTCAGACATCGGA 59.236 43.478 0.00 0.00 0.00 4.55
64 65 4.116747 AGAAAACTAGCTCAGACATCGG 57.883 45.455 0.00 0.00 0.00 4.18
65 66 5.885881 AGTAGAAAACTAGCTCAGACATCG 58.114 41.667 0.00 0.00 36.36 3.84
66 67 6.270064 GGAGTAGAAAACTAGCTCAGACATC 58.730 44.000 0.00 0.00 39.07 3.06
67 68 5.128008 GGGAGTAGAAAACTAGCTCAGACAT 59.872 44.000 0.00 0.00 39.07 3.06
68 69 4.463186 GGGAGTAGAAAACTAGCTCAGACA 59.537 45.833 0.00 0.00 39.07 3.41
69 70 4.707934 AGGGAGTAGAAAACTAGCTCAGAC 59.292 45.833 0.00 0.00 39.07 3.51
70 71 4.936802 AGGGAGTAGAAAACTAGCTCAGA 58.063 43.478 0.00 0.00 39.07 3.27
71 72 4.098807 GGAGGGAGTAGAAAACTAGCTCAG 59.901 50.000 0.00 0.00 39.07 3.35
72 73 4.024670 GGAGGGAGTAGAAAACTAGCTCA 58.975 47.826 0.00 0.00 39.07 4.26
73 74 3.067040 CGGAGGGAGTAGAAAACTAGCTC 59.933 52.174 0.00 0.00 39.07 4.09
74 75 3.025262 CGGAGGGAGTAGAAAACTAGCT 58.975 50.000 0.00 0.00 39.07 3.32
75 76 2.759535 ACGGAGGGAGTAGAAAACTAGC 59.240 50.000 0.00 0.00 39.07 3.42
76 77 6.152492 AGTTTACGGAGGGAGTAGAAAACTAG 59.848 42.308 0.00 0.00 39.07 2.57
77 78 6.012745 AGTTTACGGAGGGAGTAGAAAACTA 58.987 40.000 0.00 0.00 39.07 2.24
78 79 4.837298 AGTTTACGGAGGGAGTAGAAAACT 59.163 41.667 0.00 0.00 42.80 2.66
79 80 5.144692 AGTTTACGGAGGGAGTAGAAAAC 57.855 43.478 0.00 0.00 0.00 2.43
80 81 6.916360 TTAGTTTACGGAGGGAGTAGAAAA 57.084 37.500 0.00 0.00 0.00 2.29
81 82 8.773033 ATATTAGTTTACGGAGGGAGTAGAAA 57.227 34.615 0.00 0.00 0.00 2.52
82 83 9.866655 TTATATTAGTTTACGGAGGGAGTAGAA 57.133 33.333 0.00 0.00 0.00 2.10
83 84 9.512588 CTTATATTAGTTTACGGAGGGAGTAGA 57.487 37.037 0.00 0.00 0.00 2.59
84 85 9.512588 TCTTATATTAGTTTACGGAGGGAGTAG 57.487 37.037 0.00 0.00 0.00 2.57
85 86 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
86 87 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
87 88 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
88 89 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
89 90 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
90 91 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
91 92 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
92 93 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
93 94 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
138 139 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
139 140 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
140 141 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
141 142 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
142 143 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
148 149 9.710818 TGAAGTACTCCCTCTGTAAACTAATAT 57.289 33.333 0.00 0.00 0.00 1.28
149 150 9.710818 ATGAAGTACTCCCTCTGTAAACTAATA 57.289 33.333 0.00 0.00 0.00 0.98
150 151 8.611051 ATGAAGTACTCCCTCTGTAAACTAAT 57.389 34.615 0.00 0.00 0.00 1.73
151 152 8.431910 AATGAAGTACTCCCTCTGTAAACTAA 57.568 34.615 0.00 0.00 0.00 2.24
152 153 9.537852 TTAATGAAGTACTCCCTCTGTAAACTA 57.462 33.333 0.00 0.00 0.00 2.24
153 154 6.936968 AATGAAGTACTCCCTCTGTAAACT 57.063 37.500 0.00 0.00 0.00 2.66
154 155 9.668497 AATTAATGAAGTACTCCCTCTGTAAAC 57.332 33.333 0.00 0.00 0.00 2.01
155 156 9.667107 CAATTAATGAAGTACTCCCTCTGTAAA 57.333 33.333 0.00 0.00 0.00 2.01
156 157 7.769044 GCAATTAATGAAGTACTCCCTCTGTAA 59.231 37.037 0.00 0.00 0.00 2.41
157 158 7.272978 GCAATTAATGAAGTACTCCCTCTGTA 58.727 38.462 0.00 0.00 0.00 2.74
158 159 6.116126 GCAATTAATGAAGTACTCCCTCTGT 58.884 40.000 0.00 0.00 0.00 3.41
159 160 5.529060 GGCAATTAATGAAGTACTCCCTCTG 59.471 44.000 0.00 0.00 0.00 3.35
160 161 5.398012 GGGCAATTAATGAAGTACTCCCTCT 60.398 44.000 0.00 0.00 0.00 3.69
161 162 4.822350 GGGCAATTAATGAAGTACTCCCTC 59.178 45.833 0.00 0.00 0.00 4.30
162 163 4.478686 AGGGCAATTAATGAAGTACTCCCT 59.521 41.667 5.80 5.80 35.67 4.20
163 164 4.793201 AGGGCAATTAATGAAGTACTCCC 58.207 43.478 0.00 0.00 0.00 4.30
164 165 6.603599 AGAAAGGGCAATTAATGAAGTACTCC 59.396 38.462 0.00 0.00 0.00 3.85
165 166 7.631717 AGAAAGGGCAATTAATGAAGTACTC 57.368 36.000 0.00 0.00 0.00 2.59
166 167 9.528489 TTAAGAAAGGGCAATTAATGAAGTACT 57.472 29.630 0.00 0.00 0.00 2.73
184 185 7.446001 AGCACCTCTCTGAAAATTAAGAAAG 57.554 36.000 0.00 0.00 0.00 2.62
188 189 9.565213 CATAAAAGCACCTCTCTGAAAATTAAG 57.435 33.333 0.00 0.00 0.00 1.85
191 192 7.765695 TCATAAAAGCACCTCTCTGAAAATT 57.234 32.000 0.00 0.00 0.00 1.82
192 193 7.765695 TTCATAAAAGCACCTCTCTGAAAAT 57.234 32.000 0.00 0.00 0.00 1.82
196 197 6.540189 GCTATTTCATAAAAGCACCTCTCTGA 59.460 38.462 0.00 0.00 0.00 3.27
221 222 5.401550 ACCAGTGCAACAATTAATCAATCG 58.598 37.500 0.00 0.00 41.43 3.34
223 224 7.498570 ACAAAACCAGTGCAACAATTAATCAAT 59.501 29.630 0.00 0.00 41.43 2.57
224 225 6.820656 ACAAAACCAGTGCAACAATTAATCAA 59.179 30.769 0.00 0.00 41.43 2.57
225 226 6.344500 ACAAAACCAGTGCAACAATTAATCA 58.656 32.000 0.00 0.00 41.43 2.57
233 235 4.489810 CAGTAAACAAAACCAGTGCAACA 58.510 39.130 0.00 0.00 41.43 3.33
239 241 5.652994 TCAAAGCAGTAAACAAAACCAGT 57.347 34.783 0.00 0.00 0.00 4.00
253 255 6.600350 CATAGCAGCTGTATTATCAAAGCAG 58.400 40.000 16.64 0.00 38.14 4.24
266 268 1.222936 GACTGGGCATAGCAGCTGT 59.777 57.895 16.64 4.79 34.17 4.40
296 298 1.822990 TCCTCTATCCGCTTCAACGTT 59.177 47.619 0.00 0.00 0.00 3.99
612 615 4.520078 TGCGAATTTTACAAACGAGTCAC 58.480 39.130 0.00 0.00 0.00 3.67
658 661 3.504863 GTGTGGCAATTATCTGTGCTTG 58.495 45.455 0.00 0.00 40.70 4.01
667 679 1.357420 TCAGGGTGGTGTGGCAATTAT 59.643 47.619 0.00 0.00 0.00 1.28
693 705 4.078639 AGTTACATAGATTCAGCTGGCC 57.921 45.455 15.13 0.00 0.00 5.36
726 2125 0.321122 CATAGATTCAGCTCCCCCGC 60.321 60.000 0.00 0.00 0.00 6.13
728 2127 3.648545 AGTTACATAGATTCAGCTCCCCC 59.351 47.826 0.00 0.00 0.00 5.40
729 2128 4.345257 TCAGTTACATAGATTCAGCTCCCC 59.655 45.833 0.00 0.00 0.00 4.81
730 2129 5.069781 AGTCAGTTACATAGATTCAGCTCCC 59.930 44.000 0.00 0.00 0.00 4.30
731 2130 5.982516 CAGTCAGTTACATAGATTCAGCTCC 59.017 44.000 0.00 0.00 0.00 4.70
787 2287 4.267214 CGAGATCTAAGACATGCACAACTG 59.733 45.833 0.00 0.00 0.00 3.16
836 2337 4.199310 AGATGGTTCAATGGTCATTACGG 58.801 43.478 0.00 0.00 0.00 4.02
935 2440 0.967380 GCTGTTGGTGATCTTGGGGG 60.967 60.000 0.00 0.00 0.00 5.40
1154 2665 4.261741 GGTTGTAGTTGTAGTCGTCTTCCA 60.262 45.833 0.00 0.00 0.00 3.53
1332 2853 2.363018 CTCAGGGGCTCGGTCTCA 60.363 66.667 0.00 0.00 0.00 3.27
1386 2907 5.064452 CAGGAATGTTCACTCACTTGATAGC 59.936 44.000 0.00 0.00 0.00 2.97
1459 2985 3.093814 TCCTGCTCAACCAGAACGTATA 58.906 45.455 0.00 0.00 34.77 1.47
1548 3080 4.507710 TGCTCATGTCTCTGTTAATCACC 58.492 43.478 0.00 0.00 0.00 4.02
1564 3096 2.025605 TCCTTCCTTTGATGCTGCTCAT 60.026 45.455 0.00 0.00 38.32 2.90
1647 3185 6.128391 TGGATTTCAGTATAGCACAACGTTTC 60.128 38.462 0.00 0.00 0.00 2.78
1648 3186 5.703592 TGGATTTCAGTATAGCACAACGTTT 59.296 36.000 0.00 0.00 0.00 3.60
1649 3187 5.242434 TGGATTTCAGTATAGCACAACGTT 58.758 37.500 0.00 0.00 0.00 3.99
1650 3188 4.827692 TGGATTTCAGTATAGCACAACGT 58.172 39.130 0.00 0.00 0.00 3.99
1651 3189 4.260375 GCTGGATTTCAGTATAGCACAACG 60.260 45.833 0.00 0.00 45.08 4.10
1652 3190 4.635765 TGCTGGATTTCAGTATAGCACAAC 59.364 41.667 0.00 0.00 45.08 3.32
1653 3191 4.842574 TGCTGGATTTCAGTATAGCACAA 58.157 39.130 0.00 0.00 45.08 3.33
1654 3192 4.486125 TGCTGGATTTCAGTATAGCACA 57.514 40.909 0.00 0.00 45.08 4.57
1655 3193 4.260948 GCTTGCTGGATTTCAGTATAGCAC 60.261 45.833 0.00 0.00 45.08 4.40
1656 3194 3.879295 GCTTGCTGGATTTCAGTATAGCA 59.121 43.478 10.24 0.00 45.08 3.49
1657 3195 4.133078 AGCTTGCTGGATTTCAGTATAGC 58.867 43.478 0.00 8.25 45.08 2.97
1658 3196 6.493116 CAAAGCTTGCTGGATTTCAGTATAG 58.507 40.000 0.00 0.00 45.08 1.31
1686 3224 5.637810 TCAGTTTTGTGCGAGAGGTTTATAG 59.362 40.000 0.00 0.00 0.00 1.31
1794 3389 2.876550 GTCCTCTGCCGTTTAACAGTTT 59.123 45.455 0.00 0.00 35.37 2.66
1827 3422 2.295909 GCACTGGTTTTGGCTAATGTCA 59.704 45.455 0.00 0.00 0.00 3.58
1832 3427 1.234821 CGAGCACTGGTTTTGGCTAA 58.765 50.000 0.00 0.00 36.59 3.09
1833 3428 1.234615 GCGAGCACTGGTTTTGGCTA 61.235 55.000 0.00 0.00 36.59 3.93
1876 3471 2.723658 GAGCGACGATCATGAATCAGAC 59.276 50.000 8.48 0.00 33.65 3.51
1922 3520 0.106149 ACACTGTTGACCCCGACTTC 59.894 55.000 0.00 0.00 0.00 3.01
2285 3957 6.773638 AGTGAAGGTAGAAGTGAATGATGTT 58.226 36.000 0.00 0.00 0.00 2.71
2300 3972 4.024670 GGGAGAAGCTAAGAGTGAAGGTA 58.975 47.826 0.00 0.00 0.00 3.08
2312 3984 4.100963 TGCAAAATCGATAGGGAGAAGCTA 59.899 41.667 0.00 0.00 0.00 3.32
2442 4114 9.209048 AGTCAAGGTCATACAAGGTACATATTA 57.791 33.333 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.