Multiple sequence alignment - TraesCS2B01G121800

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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 TraesCS2B01G121800 chr2B 100.000 4023 0 0 1 4023 89325445 89329467 0.000000e+00 7430.0
1 TraesCS2B01G121800 chr2B 83.538 650 89 9 2116 2761 89432554 89433189 3.460000e-165 592.0
2 TraesCS2B01G121800 chr2B 80.217 460 69 14 3578 4018 89433875 89434331 3.880000e-85 326.0
3 TraesCS2B01G121800 chr2B 85.156 128 17 2 3884 4009 89316290 89316417 3.260000e-26 130.0
4 TraesCS2B01G121800 chr2D 89.103 1450 67 22 1780 3149 56254908 56256346 0.000000e+00 1718.0
5 TraesCS2B01G121800 chr2D 92.308 676 45 4 2090 2762 56321365 56322036 0.000000e+00 953.0
6 TraesCS2B01G121800 chr2D 94.352 602 21 5 3423 4023 56257216 56257805 0.000000e+00 911.0
7 TraesCS2B01G121800 chr2D 94.253 522 15 6 113 633 56310972 56311479 0.000000e+00 784.0
8 TraesCS2B01G121800 chr2D 85.544 754 49 14 722 1420 56253475 56254223 0.000000e+00 734.0
9 TraesCS2B01G121800 chr2D 88.449 606 48 10 3423 4023 56322990 56323578 0.000000e+00 712.0
10 TraesCS2B01G121800 chr2D 91.274 424 31 4 2829 3249 56322148 56322568 1.250000e-159 573.0
11 TraesCS2B01G121800 chr2D 93.247 385 21 4 630 1013 56311536 56311916 2.710000e-156 562.0
12 TraesCS2B01G121800 chr2D 91.270 378 22 8 1605 1974 56320715 56321089 4.640000e-139 505.0
13 TraesCS2B01G121800 chr2D 88.034 351 23 12 1445 1784 56254332 56254674 8.100000e-107 398.0
14 TraesCS2B01G121800 chr2D 78.618 608 65 32 3429 4009 56260510 56261079 3.850000e-90 342.0
15 TraesCS2B01G121800 chr2D 87.500 312 18 10 397 706 56253197 56253489 1.380000e-89 340.0
16 TraesCS2B01G121800 chr2D 80.645 465 62 17 3578 4017 56302128 56302589 6.440000e-88 335.0
17 TraesCS2B01G121800 chr2D 76.605 483 61 24 3561 4018 56300370 56300825 6.770000e-53 219.0
18 TraesCS2B01G121800 chr2D 83.264 239 20 12 3164 3387 56256642 56256875 6.820000e-48 202.0
19 TraesCS2B01G121800 chr2D 89.610 154 15 1 3578 3731 56450593 56450745 1.140000e-45 195.0
20 TraesCS2B01G121800 chr2D 75.881 369 50 22 1445 1782 56298379 56298739 6.960000e-33 152.0
21 TraesCS2B01G121800 chr2D 86.232 138 13 5 3884 4017 56251748 56251883 1.170000e-30 145.0
22 TraesCS2B01G121800 chr2D 95.122 82 4 0 1480 1561 56320553 56320634 3.260000e-26 130.0
23 TraesCS2B01G121800 chr2D 95.161 62 2 1 2024 2084 56321240 56321301 3.310000e-16 97.1
24 TraesCS2B01G121800 chr2D 100.000 41 0 0 1 41 56310940 56310980 4.310000e-10 76.8
25 TraesCS2B01G121800 chr2D 100.000 31 0 0 3271 3301 56256719 56256749 1.560000e-04 58.4
26 TraesCS2B01G121800 chr2A 88.061 846 56 24 593 1420 57863710 57864528 0.000000e+00 961.0
27 TraesCS2B01G121800 chr2A 88.663 688 69 6 2079 2762 57865495 57866177 0.000000e+00 830.0
28 TraesCS2B01G121800 chr2A 82.669 652 80 16 2116 2761 57890187 57890811 7.600000e-152 547.0
29 TraesCS2B01G121800 chr2A 93.651 189 11 1 1658 1846 57864909 57865096 8.510000e-72 281.0
30 TraesCS2B01G121800 chr2A 79.795 391 58 14 3647 4019 57891647 57892034 8.570000e-67 265.0
31 TraesCS2B01G121800 chr2A 88.940 217 14 4 3807 4023 57868804 57869010 3.990000e-65 259.0
32 TraesCS2B01G121800 chr2A 84.322 236 11 11 1848 2081 57865181 57865392 1.470000e-49 207.0
33 TraesCS2B01G121800 chr7D 77.647 255 46 8 113 362 75949161 75949409 1.170000e-30 145.0
34 TraesCS2B01G121800 chr7B 77.519 258 42 10 167 412 22437477 22437730 1.510000e-29 141.0
35 TraesCS2B01G121800 chr7B 100.000 39 0 0 190 228 686651572 686651610 5.580000e-09 73.1
36 TraesCS2B01G121800 chr5A 92.958 71 5 0 42 112 566090240 566090170 1.980000e-18 104.0


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 TraesCS2B01G121800 chr2B 89325445 89329467 4022 False 7430.000000 7430 100.000000 1 4023 1 chr2B.!!$F2 4022
1 TraesCS2B01G121800 chr2B 89432554 89434331 1777 False 459.000000 592 81.877500 2116 4018 2 chr2B.!!$F3 1902
2 TraesCS2B01G121800 chr2D 56251748 56261079 9331 False 538.711111 1718 88.071889 397 4023 9 chr2D.!!$F2 3626
3 TraesCS2B01G121800 chr2D 56320553 56323578 3025 False 495.016667 953 92.264000 1480 4023 6 chr2D.!!$F5 2543
4 TraesCS2B01G121800 chr2D 56310940 56311916 976 False 474.266667 784 95.833333 1 1013 3 chr2D.!!$F4 1012
5 TraesCS2B01G121800 chr2D 56298379 56302589 4210 False 235.333333 335 77.710333 1445 4018 3 chr2D.!!$F3 2573
6 TraesCS2B01G121800 chr2A 57863710 57869010 5300 False 507.600000 961 88.727400 593 4023 5 chr2A.!!$F1 3430
7 TraesCS2B01G121800 chr2A 57890187 57892034 1847 False 406.000000 547 81.232000 2116 4019 2 chr2A.!!$F2 1903

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
52 53 0.029834 CCGCATAACAATCAGCTGGC 59.970 55.0 15.13 5.53 0.00 4.85 F
58 59 0.034670 AACAATCAGCTGGCTCTCCC 60.035 55.0 15.13 0.00 0.00 4.30 F
60 61 0.179051 CAATCAGCTGGCTCTCCCTC 60.179 60.0 15.13 0.00 0.00 4.30 F
523 1576 0.179070 GGAAGATGCTCCGTTCCTCC 60.179 60.0 0.00 0.00 37.38 4.30 F
1615 3094 0.684153 ACTTGGGCATGCATGGGTAC 60.684 55.0 27.34 10.91 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 3070 0.032316 ATGTACCCATGCATGCCCAA 60.032 50.0 21.69 5.53 28.78 4.12 R
1599 3071 0.467844 GATGTACCCATGCATGCCCA 60.468 55.0 21.69 13.59 30.29 5.36 R
1662 3148 1.595466 GCTCTTCATCCTGCCATGAG 58.405 55.0 0.00 0.00 34.22 2.90 R
2117 4249 0.179097 GCACCTGTAGTAGCTCCTGC 60.179 60.0 0.00 0.00 40.05 4.85 R
3336 7897 0.309612 GGGGTTTTAGTGTGTGCGTG 59.690 55.0 0.00 0.00 0.00 5.34 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
46 47 3.256281 TGCACCCGCATAACAATCA 57.744 47.368 0.00 0.00 45.36 2.57
47 48 1.093972 TGCACCCGCATAACAATCAG 58.906 50.000 0.00 0.00 45.36 2.90
48 49 0.248621 GCACCCGCATAACAATCAGC 60.249 55.000 0.00 0.00 38.36 4.26
49 50 1.382522 CACCCGCATAACAATCAGCT 58.617 50.000 0.00 0.00 0.00 4.24
50 51 1.064505 CACCCGCATAACAATCAGCTG 59.935 52.381 7.63 7.63 0.00 4.24
51 52 0.664761 CCCGCATAACAATCAGCTGG 59.335 55.000 15.13 0.00 0.00 4.85
52 53 0.029834 CCGCATAACAATCAGCTGGC 59.970 55.000 15.13 5.53 0.00 4.85
53 54 1.019673 CGCATAACAATCAGCTGGCT 58.980 50.000 15.13 0.00 0.00 4.75
54 55 1.003116 CGCATAACAATCAGCTGGCTC 60.003 52.381 15.13 0.00 0.00 4.70
55 56 2.295885 GCATAACAATCAGCTGGCTCT 58.704 47.619 15.13 0.00 0.00 4.09
56 57 2.290093 GCATAACAATCAGCTGGCTCTC 59.710 50.000 15.13 0.00 0.00 3.20
57 58 2.698855 TAACAATCAGCTGGCTCTCC 57.301 50.000 15.13 0.00 0.00 3.71
58 59 0.034670 AACAATCAGCTGGCTCTCCC 60.035 55.000 15.13 0.00 0.00 4.30
60 61 0.179051 CAATCAGCTGGCTCTCCCTC 60.179 60.000 15.13 0.00 0.00 4.30
62 63 3.847602 CAGCTGGCTCTCCCTCCG 61.848 72.222 5.57 0.00 0.00 4.63
69 70 3.955101 CTCTCCCTCCGCGCGTAG 61.955 72.222 29.95 23.22 0.00 3.51
70 71 4.790962 TCTCCCTCCGCGCGTAGT 62.791 66.667 29.95 0.00 0.00 2.73
72 73 4.124351 TCCCTCCGCGCGTAGTTG 62.124 66.667 29.95 15.48 0.00 3.16
73 74 4.430765 CCCTCCGCGCGTAGTTGT 62.431 66.667 29.95 0.00 0.00 3.32
75 76 2.025418 CCTCCGCGCGTAGTTGTTT 61.025 57.895 29.95 0.00 0.00 2.83
76 77 1.562575 CCTCCGCGCGTAGTTGTTTT 61.563 55.000 29.95 0.00 0.00 2.43
77 78 0.179258 CTCCGCGCGTAGTTGTTTTC 60.179 55.000 29.95 0.00 0.00 2.29
78 79 1.154543 CCGCGCGTAGTTGTTTTCC 60.155 57.895 29.95 0.00 0.00 3.13
79 80 1.506277 CGCGCGTAGTTGTTTTCCG 60.506 57.895 24.19 0.00 0.00 4.30
83 84 0.236449 GCGTAGTTGTTTTCCGTGGG 59.764 55.000 0.00 0.00 0.00 4.61
84 85 0.236449 CGTAGTTGTTTTCCGTGGGC 59.764 55.000 0.00 0.00 0.00 5.36
85 86 1.601166 GTAGTTGTTTTCCGTGGGCT 58.399 50.000 0.00 0.00 0.00 5.19
87 88 1.892209 AGTTGTTTTCCGTGGGCTAG 58.108 50.000 0.00 0.00 0.00 3.42
90 91 2.046700 TTTTCCGTGGGCTAGCCG 60.047 61.111 27.24 15.73 36.85 5.52
91 92 2.886134 TTTTCCGTGGGCTAGCCGT 61.886 57.895 27.24 0.00 36.85 5.68
92 93 2.791501 TTTTCCGTGGGCTAGCCGTC 62.792 60.000 27.24 20.02 36.85 4.79
96 97 3.142838 GTGGGCTAGCCGTCCGTA 61.143 66.667 27.24 6.52 41.63 4.02
98 99 2.416260 GGGCTAGCCGTCCGTAAG 59.584 66.667 27.24 0.00 36.85 2.34
99 100 2.421399 GGGCTAGCCGTCCGTAAGT 61.421 63.158 27.24 0.00 36.85 2.24
100 101 1.226888 GGCTAGCCGTCCGTAAGTG 60.227 63.158 20.16 0.00 0.00 3.16
101 102 1.509923 GCTAGCCGTCCGTAAGTGT 59.490 57.895 2.29 0.00 0.00 3.55
102 103 0.734889 GCTAGCCGTCCGTAAGTGTA 59.265 55.000 2.29 0.00 0.00 2.90
103 104 1.268437 GCTAGCCGTCCGTAAGTGTAG 60.268 57.143 2.29 0.00 0.00 2.74
104 105 0.734889 TAGCCGTCCGTAAGTGTAGC 59.265 55.000 0.00 0.00 0.00 3.58
105 106 1.213537 GCCGTCCGTAAGTGTAGCA 59.786 57.895 0.00 0.00 0.00 3.49
106 107 0.179119 GCCGTCCGTAAGTGTAGCAT 60.179 55.000 0.00 0.00 0.00 3.79
107 108 1.836383 CCGTCCGTAAGTGTAGCATC 58.164 55.000 0.00 0.00 0.00 3.91
108 109 1.463805 CGTCCGTAAGTGTAGCATCG 58.536 55.000 0.00 0.00 0.00 3.84
109 110 1.202110 CGTCCGTAAGTGTAGCATCGT 60.202 52.381 0.00 0.00 0.00 3.73
110 111 2.730090 CGTCCGTAAGTGTAGCATCGTT 60.730 50.000 0.00 0.00 0.00 3.85
111 112 2.597305 GTCCGTAAGTGTAGCATCGTTG 59.403 50.000 0.00 0.00 0.00 4.10
278 280 1.137675 GGGGATTCTGCATTTTGGAGC 59.862 52.381 0.00 0.00 35.65 4.70
290 292 4.612033 GCATTTTGGAGCACTCATTTTTGC 60.612 41.667 0.00 0.01 39.16 3.68
358 360 8.850454 TTTTGTAGCATGTTAGAAAACTTGTC 57.150 30.769 17.07 0.00 40.88 3.18
484 1536 2.089600 AGGTACTCCCCTGCTGATAC 57.910 55.000 0.00 0.00 32.11 2.24
516 1569 1.081892 CTGTGTTGGAAGATGCTCCG 58.918 55.000 0.00 0.00 38.44 4.63
517 1570 0.396435 TGTGTTGGAAGATGCTCCGT 59.604 50.000 0.00 0.00 38.44 4.69
518 1571 1.202758 TGTGTTGGAAGATGCTCCGTT 60.203 47.619 0.00 0.00 38.44 4.44
519 1572 1.464997 GTGTTGGAAGATGCTCCGTTC 59.535 52.381 0.00 0.00 38.44 3.95
520 1573 1.087501 GTTGGAAGATGCTCCGTTCC 58.912 55.000 0.00 0.00 40.29 3.62
521 1574 0.984230 TTGGAAGATGCTCCGTTCCT 59.016 50.000 2.26 0.00 40.49 3.36
522 1575 0.537188 TGGAAGATGCTCCGTTCCTC 59.463 55.000 2.26 0.00 40.49 3.71
523 1576 0.179070 GGAAGATGCTCCGTTCCTCC 60.179 60.000 0.00 0.00 37.38 4.30
622 1675 5.107133 TCAGTTTGCTAGTTATAGGCGTTC 58.893 41.667 0.00 0.00 0.00 3.95
699 1814 1.049855 TGGCATCCATCAATTGGCCC 61.050 55.000 15.72 3.78 46.01 5.80
735 1884 2.500098 GGAGGAAAATTGGCCCTTTACC 59.500 50.000 0.00 1.83 0.00 2.85
740 1889 4.021280 GGAAAATTGGCCCTTTACCGTAAA 60.021 41.667 0.00 3.73 0.00 2.01
859 2011 3.416253 ATGCATGCATGAGAGGGAC 57.584 52.632 31.74 10.88 35.03 4.46
1040 2222 2.433662 AACCCTACCGACTCTACTCC 57.566 55.000 0.00 0.00 0.00 3.85
1047 2229 1.226435 CGACTCTACTCCGCAGCAC 60.226 63.158 0.00 0.00 0.00 4.40
1074 2277 2.511145 CAGCTTCGCCTGCTCTCC 60.511 66.667 0.00 0.00 38.92 3.71
1077 2286 2.186384 CTTCGCCTGCTCTCCCTG 59.814 66.667 0.00 0.00 0.00 4.45
1081 2290 3.325753 GCCTGCTCTCCCTGTGGT 61.326 66.667 0.00 0.00 0.00 4.16
1084 2293 1.757306 CTGCTCTCCCTGTGGTTGT 59.243 57.895 0.00 0.00 0.00 3.32
1094 2303 1.577328 CTGTGGTTGTCATGGCGTCC 61.577 60.000 3.99 3.99 0.00 4.79
1283 2495 4.082523 CTCGGCACCGGTGATGGT 62.083 66.667 38.30 0.00 45.21 3.55
1295 2510 4.760047 GATGGTGGCGTGGCGTCT 62.760 66.667 0.00 0.00 30.55 4.18
1337 2552 3.157949 GGCGGGAGGAGGAAGAGG 61.158 72.222 0.00 0.00 0.00 3.69
1340 2555 2.122167 CGGGAGGAGGAAGAGGTCG 61.122 68.421 0.00 0.00 0.00 4.79
1346 2561 1.985116 GAGGAAGAGGTCGGGCACT 60.985 63.158 0.00 0.00 0.00 4.40
1395 2610 1.134175 GCTCGAGGAGAAGGTGAAGAG 59.866 57.143 15.58 0.00 0.00 2.85
1402 2617 4.855340 AGGAGAAGGTGAAGAGACTCTAG 58.145 47.826 5.14 0.00 0.00 2.43
1413 2629 7.093245 GGTGAAGAGACTCTAGAACCCTTTATT 60.093 40.741 5.14 0.00 0.00 1.40
1415 2631 9.191479 TGAAGAGACTCTAGAACCCTTTATTAG 57.809 37.037 5.14 0.00 0.00 1.73
1420 2636 6.131961 ACTCTAGAACCCTTTATTAGCCGTA 58.868 40.000 0.00 0.00 0.00 4.02
1421 2637 6.781507 ACTCTAGAACCCTTTATTAGCCGTAT 59.218 38.462 0.00 0.00 0.00 3.06
1423 2639 8.890410 TCTAGAACCCTTTATTAGCCGTATAT 57.110 34.615 0.00 0.00 0.00 0.86
1426 2642 7.845037 AGAACCCTTTATTAGCCGTATATACC 58.155 38.462 7.30 0.00 0.00 2.73
1441 2657 5.942872 GTATATACCGGTATACGTGCAACT 58.057 41.667 31.71 17.99 42.24 3.16
1442 2658 7.072177 GTATATACCGGTATACGTGCAACTA 57.928 40.000 31.71 17.08 42.24 2.24
1443 2659 2.857592 ACCGGTATACGTGCAACTAG 57.142 50.000 4.49 0.00 42.24 2.57
1564 2877 9.132521 CAATTCCTGTGTTATCAGATTGAAAAC 57.867 33.333 0.00 0.00 34.47 2.43
1615 3094 0.684153 ACTTGGGCATGCATGGGTAC 60.684 55.000 27.34 10.91 0.00 3.34
1625 3104 4.441773 GCATGCATGGGTACATCAAATCAA 60.442 41.667 27.34 0.00 34.35 2.57
1629 3108 6.804677 TGCATGGGTACATCAAATCAAATAC 58.195 36.000 0.00 0.00 34.35 1.89
1630 3109 6.606796 TGCATGGGTACATCAAATCAAATACT 59.393 34.615 0.00 0.00 34.35 2.12
1632 3111 7.013655 GCATGGGTACATCAAATCAAATACTCT 59.986 37.037 0.00 0.00 34.35 3.24
1633 3112 9.559732 CATGGGTACATCAAATCAAATACTCTA 57.440 33.333 0.00 0.00 34.35 2.43
1692 3178 3.903090 AGGATGAAGAGCCCTCTAATCAG 59.097 47.826 16.46 0.00 39.39 2.90
1797 3521 5.236478 CGAGGTACACCATTTCAATATGTCC 59.764 44.000 0.38 0.00 38.89 4.02
1809 3533 4.900684 TCAATATGTCCGAACTGTCCAAA 58.099 39.130 0.00 0.00 0.00 3.28
1879 3688 1.360192 GCACACTTGCCAACTGGTC 59.640 57.895 0.00 0.00 43.66 4.02
2001 3817 4.401519 GCATATGGTACTTATCGCTCCCTA 59.598 45.833 4.56 0.00 0.00 3.53
2002 3818 5.105473 GCATATGGTACTTATCGCTCCCTAA 60.105 44.000 4.56 0.00 0.00 2.69
2003 3819 6.565234 CATATGGTACTTATCGCTCCCTAAG 58.435 44.000 0.00 0.00 0.00 2.18
2049 4000 7.057894 TGTTGTATTGGGGTATTATTGGAGAC 58.942 38.462 0.00 0.00 0.00 3.36
2088 4162 8.006298 AGCTAGCTCACATATGTAGGATTATC 57.994 38.462 12.68 0.00 0.00 1.75
2152 4284 0.451383 GTGCACGCATTTGCCAGATA 59.549 50.000 0.00 0.00 42.25 1.98
2154 4286 1.132834 TGCACGCATTTGCCAGATAAG 59.867 47.619 0.00 0.00 42.25 1.73
2446 4578 0.391793 CTTCTCCCGCTTCTCCAACC 60.392 60.000 0.00 0.00 0.00 3.77
2457 4589 0.178921 TCTCCAACCACAGCTCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
2463 4595 3.385384 CACAGCTCCTCTCCGCCA 61.385 66.667 0.00 0.00 0.00 5.69
2557 4689 2.805671 CAGTTCATCAACGTTACTGGCA 59.194 45.455 16.83 0.00 37.61 4.92
2667 4808 1.201429 TGGACAGCTTCCCTTCCTCC 61.201 60.000 11.06 0.00 45.17 4.30
2702 4849 1.822114 TTCATGTCGGGCTCGTTGGA 61.822 55.000 5.57 0.00 37.69 3.53
2778 4989 0.179156 CATAACAAGGGCTTGCGCAG 60.179 55.000 11.31 6.32 44.03 5.18
2797 5014 1.962306 TTTGCACGGGCCGAGTAAC 60.962 57.895 35.78 16.46 40.13 2.50
2820 5037 5.913637 CGATAGTACGGTGTACTGTCTATG 58.086 45.833 22.77 10.53 34.73 2.23
2822 5039 6.642540 CGATAGTACGGTGTACTGTCTATGTA 59.357 42.308 22.77 4.17 34.73 2.29
2824 5041 6.615264 AGTACGGTGTACTGTCTATGTATG 57.385 41.667 8.72 0.00 36.70 2.39
2825 5042 6.351711 AGTACGGTGTACTGTCTATGTATGA 58.648 40.000 8.72 0.00 36.70 2.15
2874 5120 8.874156 TGTGGATATGAACAGAAAGATAGCTAT 58.126 33.333 5.76 5.76 0.00 2.97
3015 7149 4.640771 AGAAGCTTTCATTACCTGACCA 57.359 40.909 0.00 0.00 32.17 4.02
3149 7284 2.094675 CCCCTCAGCTATTTGTTGTGG 58.905 52.381 0.00 0.00 39.31 4.17
3150 7285 2.555227 CCCCTCAGCTATTTGTTGTGGT 60.555 50.000 0.00 0.00 38.37 4.16
3153 7288 5.397447 CCCCTCAGCTATTTGTTGTGGTATA 60.397 44.000 0.00 0.00 38.37 1.47
3154 7289 5.760253 CCCTCAGCTATTTGTTGTGGTATAG 59.240 44.000 0.00 0.00 38.37 1.31
3155 7290 6.408092 CCCTCAGCTATTTGTTGTGGTATAGA 60.408 42.308 0.00 0.00 38.37 1.98
3156 7291 6.703607 CCTCAGCTATTTGTTGTGGTATAGAG 59.296 42.308 0.00 0.00 36.31 2.43
3157 7292 6.049149 TCAGCTATTTGTTGTGGTATAGAGC 58.951 40.000 0.00 0.00 0.00 4.09
3198 7733 5.181245 ACAACCAACTAATGCACATGAGTAC 59.819 40.000 0.00 0.00 31.26 2.73
3240 7775 8.664211 TGAACCTTTTGTGTTGTAAAAACTTT 57.336 26.923 0.00 0.00 34.29 2.66
3241 7776 9.760077 TGAACCTTTTGTGTTGTAAAAACTTTA 57.240 25.926 0.00 0.00 34.29 1.85
3330 7891 5.705609 ATCATTACAACCAACTCAACACC 57.294 39.130 0.00 0.00 0.00 4.16
3334 7895 1.822371 ACAACCAACTCAACACCCAAC 59.178 47.619 0.00 0.00 0.00 3.77
3335 7896 1.099689 AACCAACTCAACACCCAACG 58.900 50.000 0.00 0.00 0.00 4.10
3336 7897 1.358759 CCAACTCAACACCCAACGC 59.641 57.895 0.00 0.00 0.00 4.84
3337 7898 1.380403 CCAACTCAACACCCAACGCA 61.380 55.000 0.00 0.00 0.00 5.24
3338 7899 0.248458 CAACTCAACACCCAACGCAC 60.248 55.000 0.00 0.00 0.00 5.34
3339 7900 1.711060 AACTCAACACCCAACGCACG 61.711 55.000 0.00 0.00 0.00 5.34
3340 7901 3.521308 CTCAACACCCAACGCACGC 62.521 63.158 0.00 0.00 0.00 5.34
3341 7902 3.882013 CAACACCCAACGCACGCA 61.882 61.111 0.00 0.00 0.00 5.24
3483 8401 1.849116 CTATGCTGGGGGAAGCCAT 59.151 57.895 0.00 0.00 42.83 4.40
3529 8448 1.335145 AAGCAGGAGCAGTGCAATTT 58.665 45.000 19.20 0.00 43.82 1.82
3767 8989 6.712179 TGTTTATTAGATGATGCATGCCAA 57.288 33.333 16.68 0.00 0.00 4.52
3845 9068 3.372566 GGTTGGACCAATGGATATCCACA 60.373 47.826 26.82 15.65 43.22 4.17
3856 9079 3.915711 TGGATATCCACATTGGCCATAGA 59.084 43.478 20.98 0.00 42.01 1.98
3857 9080 4.263462 TGGATATCCACATTGGCCATAGAC 60.263 45.833 20.98 0.00 42.01 2.59
3858 9081 2.664402 ATCCACATTGGCCATAGACC 57.336 50.000 6.09 0.00 37.47 3.85
3859 9082 1.294041 TCCACATTGGCCATAGACCA 58.706 50.000 6.09 0.00 37.47 4.02
3860 9083 1.852309 TCCACATTGGCCATAGACCAT 59.148 47.619 6.09 0.00 37.47 3.55
3861 9084 3.052329 TCCACATTGGCCATAGACCATA 58.948 45.455 6.09 0.00 37.47 2.74
3862 9085 3.072915 TCCACATTGGCCATAGACCATAG 59.927 47.826 6.09 0.00 37.47 2.23
3874 9097 5.872617 CCATAGACCATAGTGACAACGAAAA 59.127 40.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.913451 AGGGAGAGCCAGCTGATTGT 60.913 55.000 17.39 0.33 35.15 2.71
41 42 0.179051 GAGGGAGAGCCAGCTGATTG 60.179 60.000 17.39 0.00 35.15 2.67
42 43 1.344191 GGAGGGAGAGCCAGCTGATT 61.344 60.000 17.39 1.79 35.15 2.57
43 44 1.765657 GGAGGGAGAGCCAGCTGAT 60.766 63.158 17.39 2.58 35.15 2.90
44 45 2.364842 GGAGGGAGAGCCAGCTGA 60.365 66.667 17.39 0.00 35.15 4.26
45 46 3.847602 CGGAGGGAGAGCCAGCTG 61.848 72.222 6.78 6.78 35.15 4.24
52 53 3.955101 CTACGCGCGGAGGGAGAG 61.955 72.222 34.28 8.45 46.37 3.20
53 54 4.790962 ACTACGCGCGGAGGGAGA 62.791 66.667 42.03 13.95 46.37 3.71
54 55 3.823330 AACTACGCGCGGAGGGAG 61.823 66.667 42.03 26.61 46.37 4.30
55 56 4.124351 CAACTACGCGCGGAGGGA 62.124 66.667 42.03 17.46 46.37 4.20
56 57 3.927163 AACAACTACGCGCGGAGGG 62.927 63.158 42.03 34.28 46.11 4.30
57 58 1.562575 AAAACAACTACGCGCGGAGG 61.563 55.000 42.03 28.86 0.00 4.30
58 59 0.179258 GAAAACAACTACGCGCGGAG 60.179 55.000 39.03 39.03 0.00 4.63
60 61 1.154543 GGAAAACAACTACGCGCGG 60.155 57.895 35.22 19.92 0.00 6.46
62 63 0.720173 CACGGAAAACAACTACGCGC 60.720 55.000 5.73 0.00 0.00 6.86
63 64 0.111001 CCACGGAAAACAACTACGCG 60.111 55.000 3.53 3.53 0.00 6.01
64 65 0.236449 CCCACGGAAAACAACTACGC 59.764 55.000 0.00 0.00 0.00 4.42
65 66 0.236449 GCCCACGGAAAACAACTACG 59.764 55.000 0.00 0.00 0.00 3.51
66 67 1.601166 AGCCCACGGAAAACAACTAC 58.399 50.000 0.00 0.00 0.00 2.73
67 68 2.872842 GCTAGCCCACGGAAAACAACTA 60.873 50.000 2.29 0.00 0.00 2.24
69 70 0.240145 GCTAGCCCACGGAAAACAAC 59.760 55.000 2.29 0.00 0.00 3.32
70 71 0.891904 GGCTAGCCCACGGAAAACAA 60.892 55.000 24.19 0.00 0.00 2.83
72 73 2.396157 CGGCTAGCCCACGGAAAAC 61.396 63.158 28.09 0.00 0.00 2.43
73 74 2.046700 CGGCTAGCCCACGGAAAA 60.047 61.111 28.09 0.00 0.00 2.29
75 76 3.766691 GACGGCTAGCCCACGGAA 61.767 66.667 28.09 0.00 0.00 4.30
79 80 2.624437 CTTACGGACGGCTAGCCCAC 62.624 65.000 28.09 20.35 0.00 4.61
83 84 0.734889 TACACTTACGGACGGCTAGC 59.265 55.000 6.04 6.04 0.00 3.42
84 85 1.268437 GCTACACTTACGGACGGCTAG 60.268 57.143 0.00 0.00 0.00 3.42
85 86 0.734889 GCTACACTTACGGACGGCTA 59.265 55.000 0.00 0.00 0.00 3.93
87 88 0.179119 ATGCTACACTTACGGACGGC 60.179 55.000 0.00 0.00 0.00 5.68
90 91 2.556534 ACGATGCTACACTTACGGAC 57.443 50.000 0.00 0.00 0.00 4.79
91 92 2.871133 CAACGATGCTACACTTACGGA 58.129 47.619 0.00 0.00 0.00 4.69
108 109 2.486592 AGTTACTGTTTATGCGGGCAAC 59.513 45.455 0.00 0.00 0.00 4.17
109 110 2.745281 GAGTTACTGTTTATGCGGGCAA 59.255 45.455 0.00 0.00 0.00 4.52
110 111 2.352388 GAGTTACTGTTTATGCGGGCA 58.648 47.619 0.00 0.00 0.00 5.36
111 112 1.669265 GGAGTTACTGTTTATGCGGGC 59.331 52.381 0.00 0.00 0.00 6.13
112 113 2.936498 CAGGAGTTACTGTTTATGCGGG 59.064 50.000 0.00 0.00 33.81 6.13
113 114 3.857052 TCAGGAGTTACTGTTTATGCGG 58.143 45.455 0.00 0.00 39.48 5.69
114 115 5.178623 TGTTTCAGGAGTTACTGTTTATGCG 59.821 40.000 0.00 0.00 39.48 4.73
115 116 6.554334 TGTTTCAGGAGTTACTGTTTATGC 57.446 37.500 0.00 0.00 39.48 3.14
299 301 6.367149 CGAATAATCATCCATAGAGGTGTGTG 59.633 42.308 0.00 0.00 39.02 3.82
311 313 1.052617 TCGCCCCGAATAATCATCCA 58.947 50.000 0.00 0.00 31.06 3.41
416 1468 9.274065 CCGCAAAAATACTACAAGTAAATTCTC 57.726 33.333 0.00 0.00 33.89 2.87
417 1469 8.241367 CCCGCAAAAATACTACAAGTAAATTCT 58.759 33.333 0.00 0.00 33.89 2.40
521 1574 1.923395 AGCAATCGTCCAAGGGGGA 60.923 57.895 0.00 0.00 45.89 4.81
522 1575 1.750399 CAGCAATCGTCCAAGGGGG 60.750 63.158 0.00 0.00 38.37 5.40
523 1576 1.750399 CCAGCAATCGTCCAAGGGG 60.750 63.158 0.00 0.00 0.00 4.79
622 1675 7.066525 TCACCAAGGAAAATATAGTAAAAGCGG 59.933 37.037 0.00 0.00 0.00 5.52
626 1679 8.871629 TGCTCACCAAGGAAAATATAGTAAAA 57.128 30.769 0.00 0.00 0.00 1.52
627 1680 9.474313 AATGCTCACCAAGGAAAATATAGTAAA 57.526 29.630 0.00 0.00 0.00 2.01
990 2172 0.247537 GTTTTTATCGGCGTGCTCGG 60.248 55.000 6.85 0.00 37.56 4.63
1074 2277 1.577328 GACGCCATGACAACCACAGG 61.577 60.000 0.00 0.00 0.00 4.00
1077 2286 1.298859 GAGGACGCCATGACAACCAC 61.299 60.000 0.00 0.00 0.00 4.16
1081 2290 2.264480 CGGAGGACGCCATGACAA 59.736 61.111 0.00 0.00 34.82 3.18
1115 2324 2.992689 TCTAAGACCACCGCCGCA 60.993 61.111 0.00 0.00 0.00 5.69
1257 2466 2.432628 GGTGCCGAGAACCGACAG 60.433 66.667 0.00 0.00 41.76 3.51
1379 2594 3.697166 AGAGTCTCTTCACCTTCTCCTC 58.303 50.000 0.00 0.00 0.00 3.71
1395 2610 5.068855 ACGGCTAATAAAGGGTTCTAGAGTC 59.931 44.000 0.00 0.00 0.00 3.36
1402 2617 6.753744 CGGTATATACGGCTAATAAAGGGTTC 59.246 42.308 6.79 0.00 0.00 3.62
1420 2636 5.392380 GCTAGTTGCACGTATACCGGTATAT 60.392 44.000 31.66 17.74 42.24 0.86
1421 2637 4.083324 GCTAGTTGCACGTATACCGGTATA 60.083 45.833 27.01 27.01 42.24 1.47
1423 2639 2.033299 GCTAGTTGCACGTATACCGGTA 59.967 50.000 18.46 18.46 42.24 4.02
1425 2641 1.066605 AGCTAGTTGCACGTATACCGG 59.933 52.381 0.00 0.00 45.94 5.28
1426 2642 2.486951 AGCTAGTTGCACGTATACCG 57.513 50.000 0.00 0.00 45.94 4.02
1428 2644 4.624024 TGTTGAAGCTAGTTGCACGTATAC 59.376 41.667 0.00 0.00 45.94 1.47
1429 2645 4.811908 TGTTGAAGCTAGTTGCACGTATA 58.188 39.130 0.00 0.00 45.94 1.47
1430 2646 3.659786 TGTTGAAGCTAGTTGCACGTAT 58.340 40.909 0.00 0.00 45.94 3.06
1435 2651 2.813754 GTGGATGTTGAAGCTAGTTGCA 59.186 45.455 0.00 0.00 45.94 4.08
1436 2652 3.077359 AGTGGATGTTGAAGCTAGTTGC 58.923 45.455 0.00 0.00 43.29 4.17
1437 2653 5.695851 AAAGTGGATGTTGAAGCTAGTTG 57.304 39.130 0.00 0.00 0.00 3.16
1438 2654 5.507985 GCAAAAGTGGATGTTGAAGCTAGTT 60.508 40.000 0.00 0.00 0.00 2.24
1441 2657 3.888323 TGCAAAAGTGGATGTTGAAGCTA 59.112 39.130 0.00 0.00 0.00 3.32
1442 2658 2.694628 TGCAAAAGTGGATGTTGAAGCT 59.305 40.909 0.00 0.00 0.00 3.74
1443 2659 3.096489 TGCAAAAGTGGATGTTGAAGC 57.904 42.857 0.00 0.00 0.00 3.86
1478 2791 2.034999 CCCACTAGGCCGCCAAAA 59.965 61.111 13.15 0.00 0.00 2.44
1595 3067 0.922626 TACCCATGCATGCCCAAGTA 59.077 50.000 21.69 12.99 0.00 2.24
1597 3069 0.683828 TGTACCCATGCATGCCCAAG 60.684 55.000 21.69 7.04 0.00 3.61
1598 3070 0.032316 ATGTACCCATGCATGCCCAA 60.032 50.000 21.69 5.53 28.78 4.12
1599 3071 0.467844 GATGTACCCATGCATGCCCA 60.468 55.000 21.69 13.59 30.29 5.36
1651 3137 5.172687 TCCTGCCATGAGTAACAAACATA 57.827 39.130 0.00 0.00 0.00 2.29
1656 3142 3.998913 TCATCCTGCCATGAGTAACAA 57.001 42.857 0.00 0.00 0.00 2.83
1662 3148 1.595466 GCTCTTCATCCTGCCATGAG 58.405 55.000 0.00 0.00 34.22 2.90
1797 3521 9.367444 ACTCTTTACTTATATTTGGACAGTTCG 57.633 33.333 0.00 0.00 0.00 3.95
1987 3803 2.091222 AGGGACTTAGGGAGCGATAAGT 60.091 50.000 5.86 5.86 43.23 2.24
2001 3817 6.787957 ACAACTGGTGCTATATATAGGGACTT 59.212 38.462 19.19 2.91 41.75 3.01
2002 3818 6.323737 ACAACTGGTGCTATATATAGGGACT 58.676 40.000 19.19 0.00 46.37 3.85
2003 3819 6.607004 ACAACTGGTGCTATATATAGGGAC 57.393 41.667 19.19 11.74 0.00 4.46
2049 4000 5.237779 GTGAGCTAGCTACAAGTCTACTAGG 59.762 48.000 19.38 0.00 32.69 3.02
2108 4240 6.272822 TGTAGTAGCTCCTGCATACATATG 57.727 41.667 0.00 0.00 42.74 1.78
2110 4242 4.767409 CCTGTAGTAGCTCCTGCATACATA 59.233 45.833 0.00 0.00 42.74 2.29
2111 4243 3.576118 CCTGTAGTAGCTCCTGCATACAT 59.424 47.826 0.00 0.00 42.74 2.29
2112 4244 2.959030 CCTGTAGTAGCTCCTGCATACA 59.041 50.000 0.00 0.00 42.74 2.29
2113 4245 2.959707 ACCTGTAGTAGCTCCTGCATAC 59.040 50.000 0.00 0.00 42.74 2.39
2117 4249 0.179097 GCACCTGTAGTAGCTCCTGC 60.179 60.000 0.00 0.00 40.05 4.85
2307 4439 1.159285 CGAAGCTGATGAGGTTTGCA 58.841 50.000 0.00 0.00 40.07 4.08
2446 4578 3.368190 CTGGCGGAGAGGAGCTGTG 62.368 68.421 0.00 0.00 0.00 3.66
2463 4595 3.386237 GACACGCCCTCCTGAGCT 61.386 66.667 0.00 0.00 0.00 4.09
2557 4689 1.480954 AGTCAACGGCGATGTCCTTAT 59.519 47.619 16.62 0.00 0.00 1.73
2639 4774 3.258228 AAGCTGTCCATGCCTGCGA 62.258 57.895 0.00 0.00 32.68 5.10
2702 4849 3.631250 ACGTTATTGCCAAATGATCCCT 58.369 40.909 0.00 0.00 0.00 4.20
2778 4989 1.962306 TTACTCGGCCCGTGCAAAC 60.962 57.895 1.63 0.00 40.13 2.93
2789 5004 2.609459 ACACCGTACTATCGTTACTCGG 59.391 50.000 0.00 0.00 41.77 4.63
2790 5005 3.933155 ACACCGTACTATCGTTACTCG 57.067 47.619 0.00 0.00 41.41 4.18
2791 5006 5.292101 ACAGTACACCGTACTATCGTTACTC 59.708 44.000 6.49 0.00 0.00 2.59
2797 5014 5.464722 ACATAGACAGTACACCGTACTATCG 59.535 44.000 6.49 0.00 0.00 2.92
2805 5022 5.752892 ACTCATACATAGACAGTACACCG 57.247 43.478 0.00 0.00 0.00 4.94
2820 5037 5.412594 CCACACATGCCCAATATACTCATAC 59.587 44.000 0.00 0.00 0.00 2.39
2822 5039 4.104579 TCCACACATGCCCAATATACTCAT 59.895 41.667 0.00 0.00 0.00 2.90
2824 5041 4.085357 TCCACACATGCCCAATATACTC 57.915 45.455 0.00 0.00 0.00 2.59
2825 5042 4.079787 AGTTCCACACATGCCCAATATACT 60.080 41.667 0.00 0.00 0.00 2.12
3149 7284 5.667539 TCATGGGCTCTAATGCTCTATAC 57.332 43.478 0.00 0.00 33.90 1.47
3150 7285 5.960202 TGATCATGGGCTCTAATGCTCTATA 59.040 40.000 0.00 0.00 33.90 1.31
3153 7288 2.977580 TGATCATGGGCTCTAATGCTCT 59.022 45.455 0.00 0.00 33.90 4.09
3154 7289 3.072944 GTGATCATGGGCTCTAATGCTC 58.927 50.000 0.00 0.00 0.00 4.26
3155 7290 2.440627 TGTGATCATGGGCTCTAATGCT 59.559 45.455 0.00 0.00 0.00 3.79
3156 7291 2.854963 TGTGATCATGGGCTCTAATGC 58.145 47.619 0.00 0.00 0.00 3.56
3157 7292 3.567164 GGTTGTGATCATGGGCTCTAATG 59.433 47.826 0.00 0.00 0.00 1.90
3198 7733 3.689649 GGTTCAACCTTACATGCAGGTAG 59.310 47.826 15.90 3.83 44.48 3.18
3309 7870 3.886505 GGGTGTTGAGTTGGTTGTAATGA 59.113 43.478 0.00 0.00 0.00 2.57
3330 7891 1.767127 TTAGTGTGTGCGTGCGTTGG 61.767 55.000 0.00 0.00 0.00 3.77
3334 7895 0.656205 GGTTTTAGTGTGTGCGTGCG 60.656 55.000 0.00 0.00 0.00 5.34
3335 7896 0.317519 GGGTTTTAGTGTGTGCGTGC 60.318 55.000 0.00 0.00 0.00 5.34
3336 7897 0.309612 GGGGTTTTAGTGTGTGCGTG 59.690 55.000 0.00 0.00 0.00 5.34
3337 7898 0.820482 GGGGGTTTTAGTGTGTGCGT 60.820 55.000 0.00 0.00 0.00 5.24
3338 7899 0.820074 TGGGGGTTTTAGTGTGTGCG 60.820 55.000 0.00 0.00 0.00 5.34
3339 7900 1.627864 ATGGGGGTTTTAGTGTGTGC 58.372 50.000 0.00 0.00 0.00 4.57
3340 7901 5.793030 TTTTATGGGGGTTTTAGTGTGTG 57.207 39.130 0.00 0.00 0.00 3.82
3341 7902 8.493787 TTATTTTTATGGGGGTTTTAGTGTGT 57.506 30.769 0.00 0.00 0.00 3.72
3483 8401 5.188948 TCAGGTTCCTCGGAAATAATCTTGA 59.811 40.000 0.00 0.00 35.75 3.02
3529 8448 8.045507 ACATGCTCATTCTCTTCTTCTTGATAA 58.954 33.333 0.00 0.00 0.00 1.75
3845 9068 3.716353 TGTCACTATGGTCTATGGCCAAT 59.284 43.478 10.96 0.00 39.72 3.16
3852 9075 7.065803 CCAATTTTCGTTGTCACTATGGTCTAT 59.934 37.037 0.00 0.00 0.00 1.98
3856 9079 5.067273 TCCAATTTTCGTTGTCACTATGGT 58.933 37.500 0.00 0.00 0.00 3.55
3857 9080 5.621197 TCCAATTTTCGTTGTCACTATGG 57.379 39.130 0.00 0.00 0.00 2.74
3858 9081 7.922505 TTTTCCAATTTTCGTTGTCACTATG 57.077 32.000 0.00 0.00 0.00 2.23
3859 9082 8.141268 ACATTTTCCAATTTTCGTTGTCACTAT 58.859 29.630 0.00 0.00 0.00 2.12
3860 9083 7.484975 ACATTTTCCAATTTTCGTTGTCACTA 58.515 30.769 0.00 0.00 0.00 2.74
3861 9084 6.337356 ACATTTTCCAATTTTCGTTGTCACT 58.663 32.000 0.00 0.00 0.00 3.41
3862 9085 6.254589 TGACATTTTCCAATTTTCGTTGTCAC 59.745 34.615 0.00 0.00 36.85 3.67
3874 9097 2.627699 ACTTGGCGTGACATTTTCCAAT 59.372 40.909 0.00 0.00 36.37 3.16


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

AutoCloner maintained by Alex Coulton.