Multiple sequence alignment - TraesCS5B01G468900

Loading Multiple Alignment...

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 TraesCS5B01G468900 chr5B 100.000 3260 0 0 1 3260 642280802 642284061 0.000000e+00 6021.0
1 TraesCS5B01G468900 chr5B 82.731 1135 185 9 1115 2242 642142269 642141139 0.000000e+00 1000.0
2 TraesCS5B01G468900 chr5B 81.057 1135 192 13 1112 2239 642306726 642307844 0.000000e+00 883.0
3 TraesCS5B01G468900 chr5B 81.016 669 110 14 2578 3239 166606864 166606206 1.730000e-142 516.0
4 TraesCS5B01G468900 chr5A 89.937 2524 174 41 121 2582 639302580 639300075 0.000000e+00 3181.0
5 TraesCS5B01G468900 chr5A 82.363 1134 188 10 1115 2242 639293240 639292113 0.000000e+00 976.0
6 TraesCS5B01G468900 chr5A 85.129 659 89 8 2585 3240 309042532 309041880 0.000000e+00 665.0
7 TraesCS5B01G468900 chr5A 78.098 589 110 9 1089 1668 639220806 639221384 4.000000e-94 355.0
8 TraesCS5B01G468900 chr5D 92.050 2000 116 25 589 2582 510967196 510965234 0.000000e+00 2772.0
9 TraesCS5B01G468900 chr5D 82.540 1134 189 8 1115 2242 510959327 510958197 0.000000e+00 989.0
10 TraesCS5B01G468900 chr5D 84.965 705 48 34 129 807 510967644 510966972 0.000000e+00 662.0
11 TraesCS5B01G468900 chr5D 81.250 464 65 11 1658 2112 510964971 510964521 4.000000e-94 355.0
12 TraesCS5B01G468900 chr2B 95.710 676 28 1 2585 3260 146633749 146633075 0.000000e+00 1086.0
13 TraesCS5B01G468900 chr3B 93.205 677 44 2 2585 3260 309373002 309372327 0.000000e+00 994.0
14 TraesCS5B01G468900 chr7B 87.969 640 71 6 2615 3252 591691584 591692219 0.000000e+00 750.0
15 TraesCS5B01G468900 chr3A 85.757 667 86 7 2582 3242 303540714 303541377 0.000000e+00 697.0
16 TraesCS5B01G468900 chr3A 85.113 665 88 10 2582 3240 441088984 441089643 0.000000e+00 669.0
17 TraesCS5B01G468900 chr7D 82.994 688 97 13 2585 3260 165725857 165725178 3.600000e-169 604.0
18 TraesCS5B01G468900 chr2A 81.166 669 111 13 2585 3242 89999989 89999325 1.040000e-144 523.0
19 TraesCS5B01G468900 chr4A 90.476 42 4 0 1626 1667 538840139 538840098 4.540000e-04 56.5


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 TraesCS5B01G468900 chr5B 642280802 642284061 3259 False 6021 6021 100.000000 1 3260 1 chr5B.!!$F1 3259
1 TraesCS5B01G468900 chr5B 642141139 642142269 1130 True 1000 1000 82.731000 1115 2242 1 chr5B.!!$R2 1127
2 TraesCS5B01G468900 chr5B 642306726 642307844 1118 False 883 883 81.057000 1112 2239 1 chr5B.!!$F2 1127
3 TraesCS5B01G468900 chr5B 166606206 166606864 658 True 516 516 81.016000 2578 3239 1 chr5B.!!$R1 661
4 TraesCS5B01G468900 chr5A 639300075 639302580 2505 True 3181 3181 89.937000 121 2582 1 chr5A.!!$R3 2461
5 TraesCS5B01G468900 chr5A 639292113 639293240 1127 True 976 976 82.363000 1115 2242 1 chr5A.!!$R2 1127
6 TraesCS5B01G468900 chr5A 309041880 309042532 652 True 665 665 85.129000 2585 3240 1 chr5A.!!$R1 655
7 TraesCS5B01G468900 chr5A 639220806 639221384 578 False 355 355 78.098000 1089 1668 1 chr5A.!!$F1 579
8 TraesCS5B01G468900 chr5D 510964521 510967644 3123 True 1263 2772 86.088333 129 2582 3 chr5D.!!$R2 2453
9 TraesCS5B01G468900 chr5D 510958197 510959327 1130 True 989 989 82.540000 1115 2242 1 chr5D.!!$R1 1127
10 TraesCS5B01G468900 chr2B 146633075 146633749 674 True 1086 1086 95.710000 2585 3260 1 chr2B.!!$R1 675
11 TraesCS5B01G468900 chr3B 309372327 309373002 675 True 994 994 93.205000 2585 3260 1 chr3B.!!$R1 675
12 TraesCS5B01G468900 chr7B 591691584 591692219 635 False 750 750 87.969000 2615 3252 1 chr7B.!!$F1 637
13 TraesCS5B01G468900 chr3A 303540714 303541377 663 False 697 697 85.757000 2582 3242 1 chr3A.!!$F1 660
14 TraesCS5B01G468900 chr3A 441088984 441089643 659 False 669 669 85.113000 2582 3240 1 chr3A.!!$F2 658
15 TraesCS5B01G468900 chr7D 165725178 165725857 679 True 604 604 82.994000 2585 3260 1 chr7D.!!$R1 675
16 TraesCS5B01G468900 chr2A 89999325 89999989 664 True 523 523 81.166000 2585 3242 1 chr2A.!!$R1 657

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
808 856 0.034670 ATGCCCAACTTCAGAGCCTC 60.035 55.0 0.0 0.0 0.00 4.70 F
1008 1071 0.035439 TCTCTCCCAAAATGGCGTCC 60.035 55.0 0.0 0.0 35.79 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2088 0.178068 TACCGCTGAATTCTGGCTCC 59.822 55.0 13.50 0.0 0.0 4.70 R
2916 3231 1.169661 ATGGTTTTTGCTCGGCGACA 61.170 50.0 4.99 6.8 0.0 4.35 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
20 21 3.528597 TTTTGTTTGCAGGTAACCCAC 57.471 42.857 0.00 0.00 37.17 4.61
21 22 1.025812 TTGTTTGCAGGTAACCCACG 58.974 50.000 0.00 0.00 37.17 4.94
22 23 0.820074 TGTTTGCAGGTAACCCACGG 60.820 55.000 0.00 0.00 37.17 4.94
23 24 0.820482 GTTTGCAGGTAACCCACGGT 60.820 55.000 0.00 0.00 37.65 4.83
24 25 0.820074 TTTGCAGGTAACCCACGGTG 60.820 55.000 0.00 0.00 35.34 4.94
25 26 1.697082 TTGCAGGTAACCCACGGTGA 61.697 55.000 10.28 0.00 35.34 4.02
26 27 1.298667 GCAGGTAACCCACGGTGAT 59.701 57.895 10.28 0.00 35.34 3.06
27 28 1.024579 GCAGGTAACCCACGGTGATG 61.025 60.000 10.28 2.85 35.34 3.07
28 29 0.611200 CAGGTAACCCACGGTGATGA 59.389 55.000 10.28 0.00 35.34 2.92
29 30 1.209504 CAGGTAACCCACGGTGATGAT 59.790 52.381 10.28 0.00 35.34 2.45
30 31 1.209504 AGGTAACCCACGGTGATGATG 59.790 52.381 10.28 0.00 35.34 3.07
31 32 1.014352 GTAACCCACGGTGATGATGC 58.986 55.000 10.28 0.00 35.34 3.91
32 33 0.908910 TAACCCACGGTGATGATGCT 59.091 50.000 10.28 0.00 35.34 3.79
33 34 0.038166 AACCCACGGTGATGATGCTT 59.962 50.000 10.28 0.00 35.34 3.91
34 35 0.908910 ACCCACGGTGATGATGCTTA 59.091 50.000 10.28 0.00 32.98 3.09
35 36 1.299541 CCCACGGTGATGATGCTTAC 58.700 55.000 10.28 0.00 0.00 2.34
36 37 1.299541 CCACGGTGATGATGCTTACC 58.700 55.000 10.28 0.00 0.00 2.85
49 50 3.328382 TGCTTACCGCACTGATTTACT 57.672 42.857 0.00 0.00 45.47 2.24
50 51 4.459390 TGCTTACCGCACTGATTTACTA 57.541 40.909 0.00 0.00 45.47 1.82
51 52 4.178540 TGCTTACCGCACTGATTTACTAC 58.821 43.478 0.00 0.00 45.47 2.73
52 53 3.242248 GCTTACCGCACTGATTTACTACG 59.758 47.826 0.00 0.00 38.92 3.51
53 54 4.665212 CTTACCGCACTGATTTACTACGA 58.335 43.478 0.00 0.00 0.00 3.43
54 55 2.872370 ACCGCACTGATTTACTACGAC 58.128 47.619 0.00 0.00 0.00 4.34
55 56 2.190981 CCGCACTGATTTACTACGACC 58.809 52.381 0.00 0.00 0.00 4.79
56 57 2.416296 CCGCACTGATTTACTACGACCA 60.416 50.000 0.00 0.00 0.00 4.02
57 58 3.444916 CGCACTGATTTACTACGACCAT 58.555 45.455 0.00 0.00 0.00 3.55
58 59 3.863424 CGCACTGATTTACTACGACCATT 59.137 43.478 0.00 0.00 0.00 3.16
59 60 4.328983 CGCACTGATTTACTACGACCATTT 59.671 41.667 0.00 0.00 0.00 2.32
60 61 5.560148 GCACTGATTTACTACGACCATTTG 58.440 41.667 0.00 0.00 0.00 2.32
61 62 5.350365 GCACTGATTTACTACGACCATTTGA 59.650 40.000 0.00 0.00 0.00 2.69
62 63 6.128391 GCACTGATTTACTACGACCATTTGAA 60.128 38.462 0.00 0.00 0.00 2.69
63 64 7.572353 GCACTGATTTACTACGACCATTTGAAA 60.572 37.037 0.00 0.00 0.00 2.69
64 65 8.450964 CACTGATTTACTACGACCATTTGAAAT 58.549 33.333 0.00 0.00 0.00 2.17
65 66 9.010029 ACTGATTTACTACGACCATTTGAAATT 57.990 29.630 0.00 0.00 0.00 1.82
66 67 9.840427 CTGATTTACTACGACCATTTGAAATTT 57.160 29.630 0.00 0.00 0.00 1.82
70 71 9.562583 TTTACTACGACCATTTGAAATTTATGC 57.437 29.630 0.00 0.00 0.00 3.14
71 72 7.151999 ACTACGACCATTTGAAATTTATGCA 57.848 32.000 0.00 0.00 0.00 3.96
72 73 7.771183 ACTACGACCATTTGAAATTTATGCAT 58.229 30.769 3.79 3.79 0.00 3.96
73 74 8.898761 ACTACGACCATTTGAAATTTATGCATA 58.101 29.630 1.16 1.16 0.00 3.14
74 75 7.985634 ACGACCATTTGAAATTTATGCATAC 57.014 32.000 5.74 0.00 0.00 2.39
75 76 7.542890 ACGACCATTTGAAATTTATGCATACA 58.457 30.769 5.74 0.00 0.00 2.29
76 77 7.487829 ACGACCATTTGAAATTTATGCATACAC 59.512 33.333 5.74 0.00 0.00 2.90
77 78 7.487509 CGACCATTTGAAATTTATGCATACACA 59.512 33.333 5.74 0.13 0.00 3.72
78 79 9.149225 GACCATTTGAAATTTATGCATACACAA 57.851 29.630 5.74 6.10 0.00 3.33
79 80 9.669887 ACCATTTGAAATTTATGCATACACAAT 57.330 25.926 5.74 0.92 0.00 2.71
85 86 9.823098 TGAAATTTATGCATACACAATTTTTGC 57.177 25.926 20.60 12.95 34.43 3.68
87 88 9.828852 AAATTTATGCATACACAATTTTTGCTG 57.171 25.926 16.58 0.00 32.07 4.41
88 89 7.959689 TTTATGCATACACAATTTTTGCTGT 57.040 28.000 5.74 0.00 34.47 4.40
89 90 7.959689 TTATGCATACACAATTTTTGCTGTT 57.040 28.000 5.74 0.00 34.47 3.16
90 91 5.654317 TGCATACACAATTTTTGCTGTTG 57.346 34.783 0.00 0.00 34.47 3.33
91 92 4.025061 TGCATACACAATTTTTGCTGTTGC 60.025 37.500 0.00 14.08 40.20 4.17
105 106 5.893897 TGCTGTTGCATGTATATGTTTGA 57.106 34.783 1.14 0.00 45.31 2.69
106 107 5.882553 TGCTGTTGCATGTATATGTTTGAG 58.117 37.500 1.14 0.00 45.31 3.02
107 108 5.647225 TGCTGTTGCATGTATATGTTTGAGA 59.353 36.000 1.14 0.00 45.31 3.27
108 109 6.319405 TGCTGTTGCATGTATATGTTTGAGAT 59.681 34.615 1.14 0.00 45.31 2.75
109 110 6.635641 GCTGTTGCATGTATATGTTTGAGATG 59.364 38.462 1.14 0.00 39.41 2.90
110 111 7.628769 TGTTGCATGTATATGTTTGAGATGT 57.371 32.000 1.14 0.00 36.65 3.06
111 112 8.054152 TGTTGCATGTATATGTTTGAGATGTT 57.946 30.769 1.14 0.00 36.65 2.71
112 113 7.969508 TGTTGCATGTATATGTTTGAGATGTTG 59.030 33.333 1.14 0.00 36.65 3.33
113 114 6.497437 TGCATGTATATGTTTGAGATGTTGC 58.503 36.000 1.14 0.00 36.65 4.17
114 115 6.095160 TGCATGTATATGTTTGAGATGTTGCA 59.905 34.615 1.14 0.00 36.65 4.08
115 116 6.974048 GCATGTATATGTTTGAGATGTTGCAA 59.026 34.615 0.00 0.00 36.65 4.08
116 117 7.043854 GCATGTATATGTTTGAGATGTTGCAAC 60.044 37.037 22.83 22.83 36.65 4.17
117 118 6.851609 TGTATATGTTTGAGATGTTGCAACC 58.148 36.000 26.14 12.17 0.00 3.77
118 119 6.658816 TGTATATGTTTGAGATGTTGCAACCT 59.341 34.615 26.14 17.24 0.00 3.50
119 120 3.988379 TGTTTGAGATGTTGCAACCTC 57.012 42.857 26.14 24.32 0.00 3.85
145 146 2.415512 CGTTGAACTCCCGAATTTCTCC 59.584 50.000 0.00 0.00 0.00 3.71
149 150 1.558233 ACTCCCGAATTTCTCCGAGT 58.442 50.000 0.00 0.43 0.00 4.18
178 179 5.786311 ACACAATTTCAAGGGTTGATCATG 58.214 37.500 0.00 0.00 39.84 3.07
261 262 1.721487 GGTACATGCATGCACGGAC 59.279 57.895 25.37 22.90 0.00 4.79
272 273 3.411351 CACGGACCGAACGGCTTG 61.411 66.667 23.38 1.91 39.32 4.01
276 277 1.814169 GGACCGAACGGCTTGGATC 60.814 63.158 13.32 2.24 39.32 3.36
283 284 2.540101 CGAACGGCTTGGATCAGTTATC 59.460 50.000 0.00 0.00 0.00 1.75
351 358 2.606308 CGCTTAATCATGGCTCCATTGC 60.606 50.000 0.00 0.00 33.90 3.56
363 380 1.779157 CTCCATTGCATACGTACGTCG 59.221 52.381 26.53 18.19 46.00 5.12
434 451 2.722487 CAGGGACGGCGCTACTAG 59.278 66.667 7.86 0.00 35.26 2.57
472 489 1.358759 CGGCTGCCTTTTCGTGTTT 59.641 52.632 17.92 0.00 0.00 2.83
489 506 4.446385 CGTGTTTTCGAAGGAGTCATGTTA 59.554 41.667 0.00 0.00 0.00 2.41
490 507 5.388475 CGTGTTTTCGAAGGAGTCATGTTAG 60.388 44.000 0.00 0.00 0.00 2.34
491 508 5.465724 GTGTTTTCGAAGGAGTCATGTTAGT 59.534 40.000 0.00 0.00 0.00 2.24
492 509 5.465390 TGTTTTCGAAGGAGTCATGTTAGTG 59.535 40.000 0.00 0.00 0.00 2.74
515 536 5.580691 TGTTAGTGCCGATCATCAAAACTAG 59.419 40.000 0.00 0.00 0.00 2.57
556 578 2.238521 GGTGCCATTGAAGAACCAAGA 58.761 47.619 0.00 0.00 0.00 3.02
566 588 2.590575 AACCAAGACCCGTGCACG 60.591 61.111 31.77 31.77 39.44 5.34
567 589 3.394635 AACCAAGACCCGTGCACGT 62.395 57.895 34.81 20.11 37.74 4.49
570 592 2.029073 AAGACCCGTGCACGTCTG 59.971 61.111 34.81 24.78 39.29 3.51
614 644 0.871722 TACAAACACGTCTGCATGGC 59.128 50.000 0.00 0.00 0.00 4.40
638 668 3.546724 TGGAGTTGGATTTTTGTCGTGA 58.453 40.909 0.00 0.00 0.00 4.35
653 683 1.197492 TCGTGAGAAACATGCATGCAC 59.803 47.619 25.37 21.99 37.03 4.57
676 708 1.002868 AACAATGCCTGCTCTCGCT 60.003 52.632 0.00 0.00 36.97 4.93
679 711 2.365586 AATGCCTGCTCTCGCTCCT 61.366 57.895 0.00 0.00 36.97 3.69
680 712 2.590391 AATGCCTGCTCTCGCTCCTG 62.590 60.000 0.00 0.00 36.97 3.86
687 719 0.459411 GCTCTCGCTCCTGTTTCTCC 60.459 60.000 0.00 0.00 0.00 3.71
693 725 1.294659 GCTCCTGTTTCTCCTGCACG 61.295 60.000 0.00 0.00 0.00 5.34
731 768 4.107363 TGTATGCAATGTACGTTCGGTA 57.893 40.909 0.00 0.00 0.00 4.02
754 791 2.355718 GCTAGCTAGCTCGCCTGC 60.356 66.667 33.71 17.25 45.62 4.85
755 792 3.123768 CTAGCTAGCTCGCCTGCA 58.876 61.111 23.26 0.00 34.99 4.41
756 793 1.664873 CTAGCTAGCTCGCCTGCAT 59.335 57.895 23.26 0.00 34.99 3.96
807 855 0.323178 CATGCCCAACTTCAGAGCCT 60.323 55.000 0.00 0.00 0.00 4.58
808 856 0.034670 ATGCCCAACTTCAGAGCCTC 60.035 55.000 0.00 0.00 0.00 4.70
814 862 1.830477 CAACTTCAGAGCCTCTAGCCT 59.170 52.381 0.00 0.00 45.47 4.58
817 865 0.539051 TTCAGAGCCTCTAGCCTTGC 59.461 55.000 0.00 0.00 45.47 4.01
828 876 1.344114 CTAGCCTTGCCTCTCTCCATC 59.656 57.143 0.00 0.00 0.00 3.51
829 877 0.619832 AGCCTTGCCTCTCTCCATCA 60.620 55.000 0.00 0.00 0.00 3.07
830 878 0.463474 GCCTTGCCTCTCTCCATCAC 60.463 60.000 0.00 0.00 0.00 3.06
831 879 0.907486 CCTTGCCTCTCTCCATCACA 59.093 55.000 0.00 0.00 0.00 3.58
832 880 1.280133 CCTTGCCTCTCTCCATCACAA 59.720 52.381 0.00 0.00 0.00 3.33
833 881 2.630158 CTTGCCTCTCTCCATCACAAG 58.370 52.381 0.00 0.00 0.00 3.16
835 883 0.463474 GCCTCTCTCCATCACAAGCC 60.463 60.000 0.00 0.00 0.00 4.35
858 909 3.985008 ACACCGCATCTATAAATACGCA 58.015 40.909 0.00 0.00 0.00 5.24
867 918 1.877637 ATAAATACGCATCGCCAGCA 58.122 45.000 0.00 0.00 0.00 4.41
882 933 1.664965 AGCACCGCTTCGTCTTCAC 60.665 57.895 0.00 0.00 33.89 3.18
885 936 2.809601 CCGCTTCGTCTTCACCCG 60.810 66.667 0.00 0.00 0.00 5.28
965 1027 3.072038 CCTTCATCTATCCATCCAGCACA 59.928 47.826 0.00 0.00 0.00 4.57
966 1028 3.758755 TCATCTATCCATCCAGCACAC 57.241 47.619 0.00 0.00 0.00 3.82
978 1040 2.094700 TCCAGCACACTCATACTTCGAC 60.095 50.000 0.00 0.00 0.00 4.20
1008 1071 0.035439 TCTCTCCCAAAATGGCGTCC 60.035 55.000 0.00 0.00 35.79 4.79
1080 1143 1.227853 GTCCACGGCCAACTCAGTT 60.228 57.895 2.24 0.00 0.00 3.16
1086 1149 0.868406 CGGCCAACTCAGTTCAAGAC 59.132 55.000 2.24 0.00 0.00 3.01
1103 1166 2.433838 CACCGGCAGCTCACTCAG 60.434 66.667 0.00 0.00 0.00 3.35
1284 1353 0.415429 ACTCCATCACCCTCTCTGGT 59.585 55.000 0.00 0.00 39.96 4.00
1302 1371 0.745845 GTCCGTGCAGATCCAGCATT 60.746 55.000 12.88 0.00 44.79 3.56
1563 1639 5.589050 GGAGAACCTGAAACTTGTAAACAGT 59.411 40.000 0.00 0.00 0.00 3.55
1768 1844 8.219546 TCACAATCTTCATGTCACAAAAGTTA 57.780 30.769 3.85 0.00 0.00 2.24
1809 1885 3.285484 CATCAGCATTGGAAGCTTAGGT 58.715 45.455 0.00 0.00 41.14 3.08
1838 1914 1.457643 CCAGAGCCGAGGTATCCCA 60.458 63.158 0.00 0.00 0.00 4.37
2012 2088 3.515286 CTCCGCCAAGCCATGCAG 61.515 66.667 0.00 0.00 0.00 4.41
2040 2119 1.760192 ATTCAGCGGTAGAGGTACGT 58.240 50.000 0.00 0.00 0.00 3.57
2199 2278 0.388649 AGAGTACTTGCCAGAACGCG 60.389 55.000 3.53 3.53 0.00 6.01
2247 2327 3.420893 TCCACTACCATGCAAAGGAAAG 58.579 45.455 14.81 12.76 0.00 2.62
2369 2450 2.787035 TGTAGTTCCTTTTGGGGGTCTT 59.213 45.455 0.00 0.00 40.87 3.01
2425 2506 9.838975 GGTGTTTTCTTTTTGAAATGAACAATT 57.161 25.926 4.79 0.00 43.34 2.32
2468 2549 7.330208 AGCTTCAAATGCTCATTGACAATTAAC 59.670 33.333 0.00 0.00 35.67 2.01
2498 2579 8.708742 CAATCACGTAGTAAAGTCAATTCTTCA 58.291 33.333 0.00 0.00 41.61 3.02
2547 2628 7.653767 ACATCTAGGAAGAGTAAACGTTTTG 57.346 36.000 20.19 8.76 34.49 2.44
2558 2639 7.867752 AGAGTAAACGTTTTGCAAAGCTATTA 58.132 30.769 20.19 16.61 0.00 0.98
2706 2787 2.228343 ACGCTTCGCTACATATACTCCC 59.772 50.000 0.00 0.00 0.00 4.30
2897 3212 2.678580 CCGGCCAATTTTCCCCGT 60.679 61.111 2.24 0.00 39.12 5.28
3244 3660 2.049802 GAGCGGTGGTTCGAACGA 60.050 61.111 21.34 15.63 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.159226 CGTGGGTTACCTGCAAACAAAA 60.159 45.455 0.00 0.00 37.76 2.44
1 2 1.405821 CGTGGGTTACCTGCAAACAAA 59.594 47.619 0.00 0.00 37.76 2.83
2 3 1.025812 CGTGGGTTACCTGCAAACAA 58.974 50.000 0.00 0.00 37.76 2.83
3 4 0.820074 CCGTGGGTTACCTGCAAACA 60.820 55.000 0.00 0.00 37.76 2.83
4 5 0.820482 ACCGTGGGTTACCTGCAAAC 60.820 55.000 0.00 0.00 37.76 2.93
5 6 0.820074 CACCGTGGGTTACCTGCAAA 60.820 55.000 0.00 0.00 37.76 3.68
6 7 1.228003 CACCGTGGGTTACCTGCAA 60.228 57.895 0.00 0.00 37.76 4.08
7 8 1.485294 ATCACCGTGGGTTACCTGCA 61.485 55.000 0.00 0.00 37.76 4.41
8 9 1.024579 CATCACCGTGGGTTACCTGC 61.025 60.000 0.00 0.00 37.76 4.85
9 10 0.611200 TCATCACCGTGGGTTACCTG 59.389 55.000 0.00 0.00 37.76 4.00
10 11 1.209504 CATCATCACCGTGGGTTACCT 59.790 52.381 0.00 0.00 37.76 3.08
11 12 1.663695 CATCATCACCGTGGGTTACC 58.336 55.000 0.00 0.00 31.02 2.85
12 13 1.014352 GCATCATCACCGTGGGTTAC 58.986 55.000 0.00 0.00 31.02 2.50
13 14 0.908910 AGCATCATCACCGTGGGTTA 59.091 50.000 0.00 0.00 31.02 2.85
14 15 0.038166 AAGCATCATCACCGTGGGTT 59.962 50.000 0.00 0.00 31.02 4.11
15 16 0.908910 TAAGCATCATCACCGTGGGT 59.091 50.000 0.00 0.00 35.62 4.51
16 17 1.299541 GTAAGCATCATCACCGTGGG 58.700 55.000 0.00 0.00 0.00 4.61
17 18 1.299541 GGTAAGCATCATCACCGTGG 58.700 55.000 0.00 0.00 0.00 4.94
18 19 0.930310 CGGTAAGCATCATCACCGTG 59.070 55.000 3.92 0.00 46.81 4.94
19 20 3.362581 CGGTAAGCATCATCACCGT 57.637 52.632 3.92 0.00 46.81 4.83
31 32 4.498323 GTCGTAGTAAATCAGTGCGGTAAG 59.502 45.833 0.00 0.00 36.45 2.34
32 33 4.414852 GTCGTAGTAAATCAGTGCGGTAA 58.585 43.478 0.00 0.00 36.45 2.85
33 34 3.181497 GGTCGTAGTAAATCAGTGCGGTA 60.181 47.826 0.00 0.00 36.45 4.02
34 35 2.416431 GGTCGTAGTAAATCAGTGCGGT 60.416 50.000 0.00 0.00 36.45 5.68
35 36 2.190981 GGTCGTAGTAAATCAGTGCGG 58.809 52.381 0.00 0.00 36.45 5.69
36 37 2.871133 TGGTCGTAGTAAATCAGTGCG 58.129 47.619 0.00 0.00 37.06 5.34
37 38 5.350365 TCAAATGGTCGTAGTAAATCAGTGC 59.650 40.000 0.00 0.00 0.00 4.40
38 39 6.961359 TCAAATGGTCGTAGTAAATCAGTG 57.039 37.500 0.00 0.00 0.00 3.66
39 40 7.972832 TTTCAAATGGTCGTAGTAAATCAGT 57.027 32.000 0.00 0.00 0.00 3.41
40 41 9.840427 AAATTTCAAATGGTCGTAGTAAATCAG 57.160 29.630 0.00 0.00 0.00 2.90
44 45 9.562583 GCATAAATTTCAAATGGTCGTAGTAAA 57.437 29.630 0.00 0.00 0.00 2.01
45 46 8.731605 TGCATAAATTTCAAATGGTCGTAGTAA 58.268 29.630 0.00 0.00 0.00 2.24
46 47 8.270080 TGCATAAATTTCAAATGGTCGTAGTA 57.730 30.769 0.00 0.00 0.00 1.82
47 48 7.151999 TGCATAAATTTCAAATGGTCGTAGT 57.848 32.000 0.00 0.00 0.00 2.73
48 49 9.169468 GTATGCATAAATTTCAAATGGTCGTAG 57.831 33.333 8.28 0.00 0.00 3.51
49 50 8.678199 TGTATGCATAAATTTCAAATGGTCGTA 58.322 29.630 8.28 0.00 0.00 3.43
50 51 7.487829 GTGTATGCATAAATTTCAAATGGTCGT 59.512 33.333 8.28 0.00 0.00 4.34
51 52 7.487509 TGTGTATGCATAAATTTCAAATGGTCG 59.512 33.333 8.28 0.00 0.00 4.79
52 53 8.700722 TGTGTATGCATAAATTTCAAATGGTC 57.299 30.769 8.28 0.00 0.00 4.02
53 54 9.669887 ATTGTGTATGCATAAATTTCAAATGGT 57.330 25.926 8.28 0.00 29.75 3.55
59 60 9.823098 GCAAAAATTGTGTATGCATAAATTTCA 57.177 25.926 20.18 8.42 35.03 2.69
61 62 9.828852 CAGCAAAAATTGTGTATGCATAAATTT 57.171 25.926 16.58 16.58 39.42 1.82
62 63 9.001542 ACAGCAAAAATTGTGTATGCATAAATT 57.998 25.926 8.28 8.37 39.42 1.82
63 64 8.550710 ACAGCAAAAATTGTGTATGCATAAAT 57.449 26.923 8.28 2.05 39.42 1.40
64 65 7.959689 ACAGCAAAAATTGTGTATGCATAAA 57.040 28.000 8.28 0.00 39.42 1.40
65 66 7.570875 GCAACAGCAAAAATTGTGTATGCATAA 60.571 33.333 8.28 0.00 39.42 1.90
66 67 6.128607 GCAACAGCAAAAATTGTGTATGCATA 60.129 34.615 1.16 1.16 39.42 3.14
67 68 5.334260 GCAACAGCAAAAATTGTGTATGCAT 60.334 36.000 3.79 3.79 39.42 3.96
68 69 4.025061 GCAACAGCAAAAATTGTGTATGCA 60.025 37.500 0.00 0.00 39.42 3.96
69 70 4.025061 TGCAACAGCAAAAATTGTGTATGC 60.025 37.500 0.00 15.33 34.85 3.14
70 71 5.654317 TGCAACAGCAAAAATTGTGTATG 57.346 34.783 0.00 0.00 34.85 2.39
71 72 5.759273 ACATGCAACAGCAAAAATTGTGTAT 59.241 32.000 0.00 0.00 42.37 2.29
72 73 5.114780 ACATGCAACAGCAAAAATTGTGTA 58.885 33.333 0.00 0.00 42.37 2.90
73 74 3.940221 ACATGCAACAGCAAAAATTGTGT 59.060 34.783 0.00 0.00 42.37 3.72
74 75 4.539509 ACATGCAACAGCAAAAATTGTG 57.460 36.364 0.00 0.00 42.37 3.33
75 76 7.603404 ACATATACATGCAACAGCAAAAATTGT 59.397 29.630 0.00 0.00 42.37 2.71
76 77 7.966111 ACATATACATGCAACAGCAAAAATTG 58.034 30.769 0.00 0.00 42.37 2.32
77 78 8.550710 AACATATACATGCAACAGCAAAAATT 57.449 26.923 0.00 0.00 42.37 1.82
78 79 8.444715 CAAACATATACATGCAACAGCAAAAAT 58.555 29.630 0.00 0.00 42.37 1.82
79 80 7.654923 TCAAACATATACATGCAACAGCAAAAA 59.345 29.630 0.00 0.00 42.37 1.94
80 81 7.150640 TCAAACATATACATGCAACAGCAAAA 58.849 30.769 0.00 0.00 42.37 2.44
81 82 6.685657 TCAAACATATACATGCAACAGCAAA 58.314 32.000 0.00 0.00 42.37 3.68
82 83 6.150809 TCTCAAACATATACATGCAACAGCAA 59.849 34.615 0.00 0.00 42.37 3.91
83 84 5.647225 TCTCAAACATATACATGCAACAGCA 59.353 36.000 0.00 0.00 43.41 4.41
84 85 6.122850 TCTCAAACATATACATGCAACAGC 57.877 37.500 0.00 0.00 35.39 4.40
85 86 7.700505 ACATCTCAAACATATACATGCAACAG 58.299 34.615 0.00 0.00 35.39 3.16
86 87 7.628769 ACATCTCAAACATATACATGCAACA 57.371 32.000 0.00 0.00 35.39 3.33
87 88 7.043854 GCAACATCTCAAACATATACATGCAAC 60.044 37.037 0.00 0.00 35.39 4.17
88 89 6.974048 GCAACATCTCAAACATATACATGCAA 59.026 34.615 0.00 0.00 35.39 4.08
89 90 6.095160 TGCAACATCTCAAACATATACATGCA 59.905 34.615 0.00 0.00 35.39 3.96
90 91 6.497437 TGCAACATCTCAAACATATACATGC 58.503 36.000 0.00 0.00 35.39 4.06
91 92 7.433131 GGTTGCAACATCTCAAACATATACATG 59.567 37.037 29.55 0.00 38.21 3.21
92 93 7.340232 AGGTTGCAACATCTCAAACATATACAT 59.660 33.333 29.55 0.00 32.60 2.29
93 94 6.658816 AGGTTGCAACATCTCAAACATATACA 59.341 34.615 29.55 0.00 32.60 2.29
94 95 7.088589 AGGTTGCAACATCTCAAACATATAC 57.911 36.000 29.55 7.48 32.60 1.47
95 96 6.883756 TGAGGTTGCAACATCTCAAACATATA 59.116 34.615 35.57 15.55 40.17 0.86
96 97 5.711506 TGAGGTTGCAACATCTCAAACATAT 59.288 36.000 35.57 2.95 40.17 1.78
97 98 5.069318 TGAGGTTGCAACATCTCAAACATA 58.931 37.500 35.57 16.83 40.17 2.29
98 99 3.890756 TGAGGTTGCAACATCTCAAACAT 59.109 39.130 35.57 6.03 40.17 2.71
99 100 3.286353 TGAGGTTGCAACATCTCAAACA 58.714 40.909 35.57 18.66 40.17 2.83
100 101 3.854784 GCTGAGGTTGCAACATCTCAAAC 60.855 47.826 35.57 24.59 40.17 2.93
101 102 2.294233 GCTGAGGTTGCAACATCTCAAA 59.706 45.455 35.57 20.11 40.17 2.69
102 103 1.881973 GCTGAGGTTGCAACATCTCAA 59.118 47.619 35.57 20.42 40.17 3.02
103 104 1.202794 TGCTGAGGTTGCAACATCTCA 60.203 47.619 35.57 30.78 40.17 3.27
104 105 1.198637 GTGCTGAGGTTGCAACATCTC 59.801 52.381 35.57 28.54 42.41 2.75
105 106 1.242076 GTGCTGAGGTTGCAACATCT 58.758 50.000 35.57 23.21 42.41 2.90
106 107 0.110056 CGTGCTGAGGTTGCAACATC 60.110 55.000 31.63 31.63 42.41 3.06
107 108 0.819259 ACGTGCTGAGGTTGCAACAT 60.819 50.000 29.55 24.42 42.41 2.71
108 109 1.029408 AACGTGCTGAGGTTGCAACA 61.029 50.000 29.55 9.89 42.41 3.33
109 110 0.592247 CAACGTGCTGAGGTTGCAAC 60.592 55.000 21.59 21.59 42.41 4.17
110 111 0.746204 TCAACGTGCTGAGGTTGCAA 60.746 50.000 0.00 0.00 44.25 4.08
111 112 0.746204 TTCAACGTGCTGAGGTTGCA 60.746 50.000 5.08 0.00 44.25 4.08
112 113 0.317020 GTTCAACGTGCTGAGGTTGC 60.317 55.000 5.08 0.00 44.25 4.17
113 114 1.261619 GAGTTCAACGTGCTGAGGTTG 59.738 52.381 0.00 3.84 45.40 3.77
114 115 1.583054 GAGTTCAACGTGCTGAGGTT 58.417 50.000 0.00 0.00 0.00 3.50
115 116 0.249911 GGAGTTCAACGTGCTGAGGT 60.250 55.000 0.00 0.00 0.00 3.85
116 117 0.951040 GGGAGTTCAACGTGCTGAGG 60.951 60.000 0.00 0.00 0.00 3.86
117 118 1.284982 CGGGAGTTCAACGTGCTGAG 61.285 60.000 0.00 0.00 0.00 3.35
118 119 1.300620 CGGGAGTTCAACGTGCTGA 60.301 57.895 0.00 0.00 0.00 4.26
119 120 0.878523 TTCGGGAGTTCAACGTGCTG 60.879 55.000 0.00 0.00 0.00 4.41
145 146 5.445939 CCCTTGAAATTGTGTAATCGACTCG 60.446 44.000 0.00 0.00 0.00 4.18
149 150 5.765677 TCAACCCTTGAAATTGTGTAATCGA 59.234 36.000 0.00 0.00 36.59 3.59
197 198 7.335924 CCAGTCCTTCTTCATTATTCCGTTAAA 59.664 37.037 0.00 0.00 0.00 1.52
237 238 1.735018 GTGCATGCATGTACCGTTACA 59.265 47.619 30.83 14.57 42.53 2.41
261 262 0.673644 AACTGATCCAAGCCGTTCGG 60.674 55.000 6.90 6.90 0.00 4.30
272 273 2.610727 GCGCCTACCTGATAACTGATCC 60.611 54.545 0.00 0.00 33.07 3.36
276 277 0.597637 CGGCGCCTACCTGATAACTG 60.598 60.000 26.68 0.00 0.00 3.16
351 358 1.226101 ACGCACCGACGTACGTATG 60.226 57.895 22.87 19.78 46.19 2.39
434 451 4.380550 GCCGCTTAATAATAATGGAAGGGC 60.381 45.833 0.00 0.00 0.00 5.19
437 454 5.393962 GCAGCCGCTTAATAATAATGGAAG 58.606 41.667 0.00 0.00 34.30 3.46
472 489 4.866508 ACACTAACATGACTCCTTCGAA 57.133 40.909 0.00 0.00 0.00 3.71
489 506 3.610040 TTGATGATCGGCACTAACACT 57.390 42.857 0.00 0.00 0.00 3.55
490 507 4.154195 AGTTTTGATGATCGGCACTAACAC 59.846 41.667 11.19 0.00 0.00 3.32
491 508 4.323417 AGTTTTGATGATCGGCACTAACA 58.677 39.130 11.19 0.00 0.00 2.41
492 509 4.946784 AGTTTTGATGATCGGCACTAAC 57.053 40.909 0.00 0.00 0.00 2.34
515 536 2.287427 CGCAATCATCATTGGCCTTCTC 60.287 50.000 3.32 0.00 40.03 2.87
576 598 0.596083 ACGTCTCTATGCGAGCATGC 60.596 55.000 19.64 10.51 39.70 4.06
577 599 2.287009 TGTACGTCTCTATGCGAGCATG 60.287 50.000 19.64 10.21 39.70 4.06
579 601 1.375551 TGTACGTCTCTATGCGAGCA 58.624 50.000 0.00 0.00 39.70 4.26
580 602 2.470196 TTGTACGTCTCTATGCGAGC 57.530 50.000 0.00 0.00 39.70 5.03
581 603 3.542704 GTGTTTGTACGTCTCTATGCGAG 59.457 47.826 0.00 0.00 41.30 5.03
582 604 3.495193 GTGTTTGTACGTCTCTATGCGA 58.505 45.455 0.00 0.00 0.00 5.10
583 605 2.275510 CGTGTTTGTACGTCTCTATGCG 59.724 50.000 0.00 0.00 39.13 4.73
584 606 3.883441 CGTGTTTGTACGTCTCTATGC 57.117 47.619 0.00 0.00 39.13 3.14
595 625 0.871722 GCCATGCAGACGTGTTTGTA 59.128 50.000 0.00 0.00 0.00 2.41
597 627 1.081242 GGCCATGCAGACGTGTTTG 60.081 57.895 0.00 0.00 0.00 2.93
605 635 0.681887 CAACTCCATGGCCATGCAGA 60.682 55.000 37.88 28.18 37.49 4.26
614 644 3.255642 ACGACAAAAATCCAACTCCATGG 59.744 43.478 4.97 4.97 42.12 3.66
676 708 1.000506 GTACGTGCAGGAGAAACAGGA 59.999 52.381 14.38 0.00 0.00 3.86
679 711 0.386476 ACGTACGTGCAGGAGAAACA 59.614 50.000 22.14 0.00 0.00 2.83
680 712 2.336554 TACGTACGTGCAGGAGAAAC 57.663 50.000 30.25 4.86 0.00 2.78
693 725 4.143115 GCATACATCACCATGCATACGTAC 60.143 45.833 0.00 0.00 45.51 3.67
753 790 2.997621 TTTGGTCGTGTGCGCAATGC 62.998 55.000 14.00 0.00 46.70 3.56
754 791 1.009108 TTTGGTCGTGTGCGCAATG 60.009 52.632 14.00 8.60 38.14 2.82
755 792 1.008995 GTTTGGTCGTGTGCGCAAT 60.009 52.632 14.00 0.00 38.14 3.56
756 793 2.405594 GTTTGGTCGTGTGCGCAA 59.594 55.556 14.00 0.00 38.14 4.85
766 810 0.942252 GTTCGGTGAGTGGTTTGGTC 59.058 55.000 0.00 0.00 0.00 4.02
807 855 0.336392 TGGAGAGAGGCAAGGCTAGA 59.664 55.000 0.00 0.00 0.00 2.43
808 856 1.344114 GATGGAGAGAGGCAAGGCTAG 59.656 57.143 0.00 0.00 0.00 3.42
814 862 1.339438 GCTTGTGATGGAGAGAGGCAA 60.339 52.381 0.00 0.00 0.00 4.52
817 865 0.907486 TGGCTTGTGATGGAGAGAGG 59.093 55.000 0.00 0.00 0.00 3.69
828 876 1.081242 GATGCGGTGTTGGCTTGTG 60.081 57.895 0.00 0.00 0.00 3.33
829 877 0.036164 TAGATGCGGTGTTGGCTTGT 59.964 50.000 0.00 0.00 0.00 3.16
830 878 1.382522 ATAGATGCGGTGTTGGCTTG 58.617 50.000 0.00 0.00 0.00 4.01
831 879 3.275617 TTATAGATGCGGTGTTGGCTT 57.724 42.857 0.00 0.00 0.00 4.35
832 880 3.275617 TTTATAGATGCGGTGTTGGCT 57.724 42.857 0.00 0.00 0.00 4.75
833 881 4.377022 CGTATTTATAGATGCGGTGTTGGC 60.377 45.833 5.94 0.00 32.53 4.52
835 883 4.210328 TGCGTATTTATAGATGCGGTGTTG 59.790 41.667 14.03 0.00 35.96 3.33
867 918 2.342648 GGGTGAAGACGAAGCGGT 59.657 61.111 0.00 0.00 0.00 5.68
870 921 1.737008 GGACGGGTGAAGACGAAGC 60.737 63.158 0.00 0.00 0.00 3.86
882 933 1.528161 GTTGTTTGAGTAACGGACGGG 59.472 52.381 0.00 0.00 39.72 5.28
885 936 5.048507 AGAAGAGTTGTTTGAGTAACGGAC 58.951 41.667 0.00 0.00 39.72 4.79
965 1027 5.010933 TCTCAAAGGAGTCGAAGTATGAGT 58.989 41.667 11.51 0.00 42.05 3.41
966 1028 5.568685 TCTCAAAGGAGTCGAAGTATGAG 57.431 43.478 0.00 0.00 42.05 2.90
978 1040 4.833478 TTTGGGAGAGATCTCAAAGGAG 57.167 45.455 24.39 0.00 44.60 3.69
1080 1143 2.343758 GAGCTGCCGGTGTCTTGA 59.656 61.111 1.90 0.00 0.00 3.02
1086 1149 2.433838 CTGAGTGAGCTGCCGGTG 60.434 66.667 1.90 0.00 0.00 4.94
1103 1166 2.290577 ACATTCTTCTGGGTGGAGCTTC 60.291 50.000 0.00 0.00 0.00 3.86
1284 1353 0.745486 CAATGCTGGATCTGCACGGA 60.745 55.000 14.21 0.00 40.77 4.69
1347 1416 3.362797 TCGTTCTCGCTCCACGCT 61.363 61.111 0.00 0.00 43.23 5.07
1422 1491 1.964373 ACCGTTGCCGTTGATGGTC 60.964 57.895 0.00 0.00 29.16 4.02
1563 1639 1.271325 ACCGACACATGGATTTGCTGA 60.271 47.619 0.00 0.00 0.00 4.26
1702 1778 1.078759 CAGTCATCGCCGGTCTTGAC 61.079 60.000 19.00 19.00 38.97 3.18
1768 1844 1.682005 CATGTCCCGGGCCACAAAT 60.682 57.895 18.49 0.00 0.00 2.32
1838 1914 9.701098 ACAATCGTACGGTATCAATGTAAATAT 57.299 29.630 16.52 0.00 0.00 1.28
2012 2088 0.178068 TACCGCTGAATTCTGGCTCC 59.822 55.000 13.50 0.00 0.00 4.70
2040 2119 4.033932 CGAATATTCTTGAACGCCACATCA 59.966 41.667 13.45 0.00 0.00 3.07
2199 2278 5.012893 ACATTTCCTGACTTCCTCCATTTC 58.987 41.667 0.00 0.00 0.00 2.17
2247 2327 7.617041 AGCTCATTTCCACTACAACTTAATC 57.383 36.000 0.00 0.00 0.00 1.75
2369 2450 7.540400 CGGTAACACATTTCATATTCTTTGCAA 59.460 33.333 0.00 0.00 0.00 4.08
2439 2520 6.330004 TGTCAATGAGCATTTGAAGCTAAA 57.670 33.333 0.00 0.00 43.58 1.85
2468 2549 9.530129 GAATTGACTTTACTACGTGATTGAAAG 57.470 33.333 0.00 3.69 0.00 2.62
2547 2628 9.304731 TCATTCAAAACATCATAATAGCTTTGC 57.695 29.630 0.00 0.00 0.00 3.68
2558 2639 4.022068 ACAACGCCTCATTCAAAACATCAT 60.022 37.500 0.00 0.00 0.00 2.45
2916 3231 1.169661 ATGGTTTTTGCTCGGCGACA 61.170 50.000 4.99 6.80 0.00 4.35
3095 3410 1.375908 GCCGATGGTGAGCTTGACA 60.376 57.895 0.00 0.00 0.00 3.58
3183 3498 0.978146 CCAGGTTCCCTCGGTGAGAT 60.978 60.000 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.