Multiple sequence alignment - TraesCS6B01G110400

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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 TraesCS6B01G110400 chr6B 100.000 3165 0 0 1 3165 92696277 92699441 0.000000e+00 5845.0
1 TraesCS6B01G110400 chr6B 84.000 275 19 7 104 354 134106650 134106923 1.130000e-59 241.0
2 TraesCS6B01G110400 chr6B 85.938 192 27 0 1475 1666 527043570 527043761 4.140000e-49 206.0
3 TraesCS6B01G110400 chr6B 93.333 135 7 1 3031 3165 482755443 482755311 6.920000e-47 198.0
4 TraesCS6B01G110400 chr6A 90.374 2836 156 55 32 2812 56133150 56135923 0.000000e+00 3616.0
5 TraesCS6B01G110400 chr6A 89.627 241 20 3 2925 3165 56136730 56136965 5.130000e-78 302.0
6 TraesCS6B01G110400 chr6A 84.739 249 36 2 104 351 615728882 615729129 6.780000e-62 248.0
7 TraesCS6B01G110400 chr6A 86.458 192 26 0 1475 1666 491027848 491028039 8.890000e-51 211.0
8 TraesCS6B01G110400 chr6A 92.063 63 4 1 2958 3020 212682618 212682679 1.560000e-13 87.9
9 TraesCS6B01G110400 chr6A 92.063 63 4 1 2962 3024 212763668 212763729 1.560000e-13 87.9
10 TraesCS6B01G110400 chr6A 96.078 51 2 0 2872 2922 56135925 56135975 2.020000e-12 84.2
11 TraesCS6B01G110400 chr6A 100.000 37 0 0 1 37 310189095 310189059 5.660000e-08 69.4
12 TraesCS6B01G110400 chrUn 91.007 2402 98 51 554 2922 20366386 20368702 0.000000e+00 3131.0
13 TraesCS6B01G110400 chr1D 87.149 249 29 3 104 350 268943878 268943631 2.400000e-71 279.0
14 TraesCS6B01G110400 chr1D 86.000 250 32 3 104 351 457970263 457970015 6.730000e-67 265.0
15 TraesCS6B01G110400 chr1D 90.110 182 10 6 190 367 439031610 439031787 2.460000e-56 230.0
16 TraesCS6B01G110400 chr1D 94.074 135 7 1 3031 3165 85642338 85642205 1.490000e-48 204.0
17 TraesCS6B01G110400 chr1D 100.000 38 0 0 1 38 259254092 259254055 1.570000e-08 71.3
18 TraesCS6B01G110400 chr4A 86.747 249 25 6 104 351 681652500 681652259 1.450000e-68 270.0
19 TraesCS6B01G110400 chr4A 94.074 135 6 1 3031 3165 165178754 165178886 1.490000e-48 204.0
20 TraesCS6B01G110400 chr4A 82.292 192 30 4 1475 1664 72294418 72294607 2.530000e-36 163.0
21 TraesCS6B01G110400 chr2D 85.283 265 24 6 104 354 120561229 120561492 3.130000e-65 259.0
22 TraesCS6B01G110400 chr2D 93.333 135 6 2 3031 3165 442218731 442218862 2.490000e-46 196.0
23 TraesCS6B01G110400 chr2D 82.443 131 16 4 2484 2610 198728541 198728668 1.200000e-19 108.0
24 TraesCS6B01G110400 chr2D 81.250 128 23 1 2484 2610 630131589 630131462 5.590000e-18 102.0
25 TraesCS6B01G110400 chr2D 92.063 63 4 1 2962 3024 337962552 337962491 1.560000e-13 87.9
26 TraesCS6B01G110400 chr3D 84.047 257 34 6 101 354 157096304 157096556 1.130000e-59 241.0
27 TraesCS6B01G110400 chr4D 83.691 233 36 2 120 351 378301626 378301395 5.320000e-53 219.0
28 TraesCS6B01G110400 chr4D 94.074 135 6 1 3031 3165 30578785 30578917 1.490000e-48 204.0
29 TraesCS6B01G110400 chr4D 93.651 63 4 0 2960 3022 33511607 33511669 9.350000e-16 95.3
30 TraesCS6B01G110400 chr4D 89.231 65 6 1 2960 3024 373451781 373451718 2.620000e-11 80.5
31 TraesCS6B01G110400 chr7D 94.815 135 6 1 3031 3165 596854381 596854514 3.200000e-50 209.0
32 TraesCS6B01G110400 chr7D 93.333 135 6 1 3031 3165 209621151 209621020 2.490000e-46 196.0
33 TraesCS6B01G110400 chr1B 81.818 275 24 6 104 354 317201053 317200781 1.150000e-49 207.0
34 TraesCS6B01G110400 chr3A 81.429 280 24 9 104 357 423678833 423678556 1.490000e-48 204.0
35 TraesCS6B01G110400 chr3A 85.246 122 13 5 2484 2603 563387760 563387642 1.540000e-23 121.0
36 TraesCS6B01G110400 chr3A 100.000 37 0 0 1 37 532318126 532318162 5.660000e-08 69.4
37 TraesCS6B01G110400 chr2A 93.333 135 7 1 3031 3165 473121584 473121452 6.920000e-47 198.0
38 TraesCS6B01G110400 chr2A 81.538 130 18 4 2484 2610 216837721 216837847 5.590000e-18 102.0
39 TraesCS6B01G110400 chr5D 85.799 169 22 2 1497 1664 317453008 317452841 9.020000e-41 178.0
40 TraesCS6B01G110400 chr5B 85.799 169 22 2 1497 1664 367212607 367212440 9.020000e-41 178.0
41 TraesCS6B01G110400 chr5B 83.200 125 18 3 2481 2603 427286553 427286676 9.280000e-21 111.0
42 TraesCS6B01G110400 chr5B 100.000 37 0 0 1 37 111623763 111623799 5.660000e-08 69.4
43 TraesCS6B01G110400 chr5A 85.799 169 22 2 1497 1664 412104171 412104004 9.020000e-41 178.0
44 TraesCS6B01G110400 chr5A 88.288 111 9 4 2484 2592 488022054 488022162 2.560000e-26 130.0
45 TraesCS6B01G110400 chr5A 100.000 37 0 0 1 37 581935310 581935346 5.660000e-08 69.4
46 TraesCS6B01G110400 chr4B 82.292 192 30 4 1475 1664 480590895 480591084 2.530000e-36 163.0
47 TraesCS6B01G110400 chr4B 92.188 64 4 1 2962 3025 49732469 49732407 4.350000e-14 89.8
48 TraesCS6B01G110400 chr7A 82.645 121 18 3 2484 2602 130093175 130093294 1.550000e-18 104.0
49 TraesCS6B01G110400 chr7A 100.000 38 0 0 1 38 77531792 77531755 1.570000e-08 71.3
50 TraesCS6B01G110400 chr7A 100.000 37 0 0 1 37 2609329 2609293 5.660000e-08 69.4
51 TraesCS6B01G110400 chr3B 92.063 63 5 0 2960 3022 455134015 455133953 4.350000e-14 89.8
52 TraesCS6B01G110400 chr3B 91.045 67 5 1 2958 3024 660688193 660688128 4.350000e-14 89.8
53 TraesCS6B01G110400 chr1A 100.000 37 0 0 1 37 64215954 64215990 5.660000e-08 69.4
54 TraesCS6B01G110400 chr1A 100.000 37 0 0 1 37 365450008 365450044 5.660000e-08 69.4


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 TraesCS6B01G110400 chr6B 92696277 92699441 3164 False 5845.000000 5845 100.000000 1 3165 1 chr6B.!!$F1 3164
1 TraesCS6B01G110400 chr6A 56133150 56136965 3815 False 1334.066667 3616 92.026333 32 3165 3 chr6A.!!$F5 3133
2 TraesCS6B01G110400 chrUn 20366386 20368702 2316 False 3131.000000 3131 91.007000 554 2922 1 chrUn.!!$F1 2368

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
363 386 0.107214 ACATGCCTTACATCACCCCG 60.107 55.0 0.00 0.0 36.64 5.73 F
387 410 0.250295 CCTTCTCCCGTGTCTGCAAA 60.250 55.0 0.00 0.0 0.00 3.68 F
1429 1479 0.320334 TCTTCAGCGCGTCCATCAAA 60.320 50.0 8.43 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 1418 0.754217 CGAGATGAACCCCGACCCTA 60.754 60.000 0.00 0.00 0.00 3.53 R
1483 1533 1.068417 CGTCTTGGGGAACACGTCA 59.932 57.895 0.00 0.00 0.00 4.35 R
2396 2460 0.108615 CCTGAAACGGAGCTCATCGT 60.109 55.000 17.19 14.08 41.71 3.73 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
27 28 9.770097 AGACTATCTTATCAACCATTGTACATG 57.230 33.333 0.00 0.00 0.00 3.21
28 29 8.383318 ACTATCTTATCAACCATTGTACATGC 57.617 34.615 0.00 0.00 0.00 4.06
29 30 6.639632 ATCTTATCAACCATTGTACATGCC 57.360 37.500 0.00 0.00 0.00 4.40
30 31 4.887071 TCTTATCAACCATTGTACATGCCC 59.113 41.667 0.00 0.00 0.00 5.36
38 39 4.705023 ACCATTGTACATGCCCTTAGTTTC 59.295 41.667 0.00 0.00 0.00 2.78
39 40 4.201910 CCATTGTACATGCCCTTAGTTTCG 60.202 45.833 0.00 0.00 0.00 3.46
43 44 1.076995 ATGCCCTTAGTTTCGGCCC 60.077 57.895 0.00 0.00 42.29 5.80
74 75 0.897621 CCCTGGTTCAGCAATTTCCC 59.102 55.000 0.00 0.00 0.00 3.97
75 76 1.631405 CCTGGTTCAGCAATTTCCCA 58.369 50.000 0.00 0.00 0.00 4.37
76 77 1.547372 CCTGGTTCAGCAATTTCCCAG 59.453 52.381 0.00 0.00 39.32 4.45
77 78 0.968405 TGGTTCAGCAATTTCCCAGC 59.032 50.000 0.00 0.00 0.00 4.85
78 79 0.968405 GGTTCAGCAATTTCCCAGCA 59.032 50.000 0.00 0.00 0.00 4.41
79 80 1.067354 GGTTCAGCAATTTCCCAGCAG 60.067 52.381 0.00 0.00 0.00 4.24
80 81 0.604578 TTCAGCAATTTCCCAGCAGC 59.395 50.000 0.00 0.00 0.00 5.25
81 82 0.540133 TCAGCAATTTCCCAGCAGCA 60.540 50.000 0.00 0.00 0.00 4.41
90 91 1.898574 CCCAGCAGCAAACGACCTT 60.899 57.895 0.00 0.00 0.00 3.50
103 104 1.883021 GACCTTGCCGTTCCCATTG 59.117 57.895 0.00 0.00 0.00 2.82
106 107 2.994417 TTGCCGTTCCCATTGGGC 60.994 61.111 17.60 5.40 43.94 5.36
108 109 2.759560 GCCGTTCCCATTGGGCAT 60.760 61.111 17.60 0.00 43.94 4.40
109 110 1.454847 GCCGTTCCCATTGGGCATA 60.455 57.895 17.60 1.90 43.94 3.14
110 111 0.827507 GCCGTTCCCATTGGGCATAT 60.828 55.000 17.60 0.00 43.94 1.78
111 112 1.546773 GCCGTTCCCATTGGGCATATA 60.547 52.381 17.60 0.00 43.94 0.86
112 113 2.883888 GCCGTTCCCATTGGGCATATAT 60.884 50.000 17.60 0.00 43.94 0.86
113 114 3.623703 GCCGTTCCCATTGGGCATATATA 60.624 47.826 17.60 0.00 43.94 0.86
124 125 7.040201 CCATTGGGCATATATAATGGTGCTATC 60.040 40.741 13.58 0.00 42.78 2.08
157 167 5.248477 GCCACCTAGGATAAATGATGAGGTA 59.752 44.000 17.98 0.00 41.22 3.08
160 170 7.093552 CCACCTAGGATAAATGATGAGGTAGAG 60.094 44.444 17.98 0.00 41.22 2.43
161 171 6.957020 ACCTAGGATAAATGATGAGGTAGAGG 59.043 42.308 17.98 0.00 34.08 3.69
162 172 7.185565 CCTAGGATAAATGATGAGGTAGAGGA 58.814 42.308 1.05 0.00 0.00 3.71
166 176 6.154363 GGATAAATGATGAGGTAGAGGAGAGG 59.846 46.154 0.00 0.00 0.00 3.69
167 177 4.823364 AATGATGAGGTAGAGGAGAGGA 57.177 45.455 0.00 0.00 0.00 3.71
170 180 4.541705 TGATGAGGTAGAGGAGAGGAAAG 58.458 47.826 0.00 0.00 0.00 2.62
173 183 4.090090 TGAGGTAGAGGAGAGGAAAGTTG 58.910 47.826 0.00 0.00 0.00 3.16
174 184 4.202684 TGAGGTAGAGGAGAGGAAAGTTGA 60.203 45.833 0.00 0.00 0.00 3.18
177 187 5.247337 AGGTAGAGGAGAGGAAAGTTGAAAG 59.753 44.000 0.00 0.00 0.00 2.62
223 245 9.650539 ATCTGTTAGCATAATATGTCTCATCAC 57.349 33.333 1.92 0.00 0.00 3.06
224 246 7.809806 TCTGTTAGCATAATATGTCTCATCACG 59.190 37.037 1.92 0.00 0.00 4.35
241 263 9.967346 TCTCATCACGTTTTTAGGAATATCTAG 57.033 33.333 0.00 0.00 0.00 2.43
266 288 9.941325 AGTTATTGAAGATATGGCTAAGAGATG 57.059 33.333 0.00 0.00 0.00 2.90
272 294 4.530161 AGATATGGCTAAGAGATGACCCAC 59.470 45.833 0.00 0.00 0.00 4.61
349 372 8.383318 ACTATCTTATCAACCATTGTACATGC 57.617 34.615 0.00 0.00 0.00 4.06
350 373 6.639632 ATCTTATCAACCATTGTACATGCC 57.360 37.500 0.00 0.00 0.00 4.40
351 374 5.754782 TCTTATCAACCATTGTACATGCCT 58.245 37.500 0.00 0.00 0.00 4.75
352 375 6.186957 TCTTATCAACCATTGTACATGCCTT 58.813 36.000 0.00 0.00 0.00 4.35
353 376 7.342581 TCTTATCAACCATTGTACATGCCTTA 58.657 34.615 0.00 0.00 0.00 2.69
354 377 5.835113 ATCAACCATTGTACATGCCTTAC 57.165 39.130 0.00 0.00 0.00 2.34
355 378 4.657013 TCAACCATTGTACATGCCTTACA 58.343 39.130 0.00 0.00 0.00 2.41
356 379 5.260424 TCAACCATTGTACATGCCTTACAT 58.740 37.500 0.00 0.00 40.66 2.29
357 380 5.356751 TCAACCATTGTACATGCCTTACATC 59.643 40.000 0.00 0.00 36.64 3.06
363 386 0.107214 ACATGCCTTACATCACCCCG 60.107 55.000 0.00 0.00 36.64 5.73
365 388 1.920734 ATGCCTTACATCACCCCGCA 61.921 55.000 0.00 0.00 31.52 5.69
372 395 1.450312 CATCACCCCGCACTCCTTC 60.450 63.158 0.00 0.00 0.00 3.46
382 405 1.536943 GCACTCCTTCTCCCGTGTCT 61.537 60.000 0.00 0.00 0.00 3.41
384 407 1.216710 CTCCTTCTCCCGTGTCTGC 59.783 63.158 0.00 0.00 0.00 4.26
387 410 0.250295 CCTTCTCCCGTGTCTGCAAA 60.250 55.000 0.00 0.00 0.00 3.68
395 418 2.095567 CCCGTGTCTGCAAAGAAAGATG 60.096 50.000 0.00 0.00 0.00 2.90
402 425 3.012518 CTGCAAAGAAAGATGGGTCGAT 58.987 45.455 0.00 0.00 0.00 3.59
403 426 3.009723 TGCAAAGAAAGATGGGTCGATC 58.990 45.455 0.00 0.00 0.00 3.69
416 439 5.565592 TGGGTCGATCTTGATTTTGATTG 57.434 39.130 0.00 0.00 0.00 2.67
417 440 5.252547 TGGGTCGATCTTGATTTTGATTGA 58.747 37.500 0.00 0.00 32.45 2.57
418 441 5.887598 TGGGTCGATCTTGATTTTGATTGAT 59.112 36.000 0.00 0.00 36.05 2.57
419 442 6.377996 TGGGTCGATCTTGATTTTGATTGATT 59.622 34.615 0.00 0.00 36.05 2.57
448 471 6.324512 TGGTAAATTTCTTGAGCATGGCATAT 59.675 34.615 0.00 0.00 0.00 1.78
464 487 2.362077 GCATATCCGCCCAGTTCATTTT 59.638 45.455 0.00 0.00 0.00 1.82
465 488 3.181476 GCATATCCGCCCAGTTCATTTTT 60.181 43.478 0.00 0.00 0.00 1.94
466 489 4.037446 GCATATCCGCCCAGTTCATTTTTA 59.963 41.667 0.00 0.00 0.00 1.52
471 494 5.233988 TCCGCCCAGTTCATTTTTATTTTG 58.766 37.500 0.00 0.00 0.00 2.44
482 505 7.920160 TCATTTTTATTTTGGCCAGGATTTC 57.080 32.000 5.11 0.00 0.00 2.17
490 513 1.678970 GCCAGGATTTCCCGTGCTT 60.679 57.895 0.00 0.00 40.87 3.91
505 528 3.004734 CCGTGCTTTGAGAAGGAATTTGT 59.995 43.478 0.00 0.00 34.84 2.83
508 531 5.591099 GTGCTTTGAGAAGGAATTTGTCAA 58.409 37.500 0.00 0.00 44.53 3.18
527 550 5.408299 TGTCAACCTCGAGACAATGTAAATG 59.592 40.000 15.71 0.00 41.42 2.32
529 552 5.869344 TCAACCTCGAGACAATGTAAATGAG 59.131 40.000 15.71 0.00 0.00 2.90
533 556 6.102663 CCTCGAGACAATGTAAATGAGAAGT 58.897 40.000 15.71 0.00 0.00 3.01
536 559 6.590292 TCGAGACAATGTAAATGAGAAGTTCC 59.410 38.462 0.00 0.00 0.00 3.62
537 560 6.368791 CGAGACAATGTAAATGAGAAGTTCCA 59.631 38.462 0.00 0.00 0.00 3.53
618 646 7.008992 GTCAGCACAATAGCATTCTCATTTTTC 59.991 37.037 0.00 0.00 36.85 2.29
619 647 6.255020 CAGCACAATAGCATTCTCATTTTTCC 59.745 38.462 0.00 0.00 36.85 3.13
625 657 3.012161 AGCATTCTCATTTTTCCCCTCCT 59.988 43.478 0.00 0.00 0.00 3.69
734 766 5.613360 CGCGTCATGAATGGATAAAAGCTAG 60.613 44.000 0.00 0.00 0.00 3.42
735 767 5.683859 CGTCATGAATGGATAAAAGCTAGC 58.316 41.667 6.62 6.62 0.00 3.42
736 768 5.237127 CGTCATGAATGGATAAAAGCTAGCA 59.763 40.000 18.83 0.00 0.00 3.49
737 769 6.565435 CGTCATGAATGGATAAAAGCTAGCAG 60.565 42.308 18.83 0.00 0.00 4.24
738 770 6.484643 GTCATGAATGGATAAAAGCTAGCAGA 59.515 38.462 18.83 0.00 0.00 4.26
739 771 6.484643 TCATGAATGGATAAAAGCTAGCAGAC 59.515 38.462 18.83 1.88 0.00 3.51
826 858 1.375326 GTTTCTCCACCTCCGCCTT 59.625 57.895 0.00 0.00 0.00 4.35
827 859 0.611714 GTTTCTCCACCTCCGCCTTA 59.388 55.000 0.00 0.00 0.00 2.69
828 860 1.209747 GTTTCTCCACCTCCGCCTTAT 59.790 52.381 0.00 0.00 0.00 1.73
937 969 7.235812 CCAGGAAATAGCTTTAGTATAGTCCCT 59.764 40.741 0.00 0.00 0.00 4.20
939 972 8.652290 AGGAAATAGCTTTAGTATAGTCCCTTG 58.348 37.037 0.00 0.00 0.00 3.61
956 989 0.322975 TTGCAAGCAGAGGAGAGGAC 59.677 55.000 0.00 0.00 0.00 3.85
972 1005 2.123812 ACCGGAGAGGGGATCGAC 60.124 66.667 9.46 0.00 46.96 4.20
1173 1212 3.449227 CGCACCGTCAGCCTCCTA 61.449 66.667 0.00 0.00 0.00 2.94
1183 1222 2.829458 GCCTCCTACTCGACCGCT 60.829 66.667 0.00 0.00 0.00 5.52
1208 1251 1.578618 GTACGTACGAGTGCGGTCG 60.579 63.158 24.41 6.01 45.76 4.79
1223 1266 1.048724 GGTCGTCCATCCATCCTCCA 61.049 60.000 0.00 0.00 0.00 3.86
1237 1280 4.088351 TCCATCCTCCCCGGCTGA 62.088 66.667 0.00 0.00 30.24 4.26
1323 1368 3.453424 GGGCGTTTGTCTGTTTTTCATT 58.547 40.909 0.00 0.00 0.00 2.57
1324 1369 3.868661 GGGCGTTTGTCTGTTTTTCATTT 59.131 39.130 0.00 0.00 0.00 2.32
1325 1370 4.026062 GGGCGTTTGTCTGTTTTTCATTTC 60.026 41.667 0.00 0.00 0.00 2.17
1327 1372 5.234116 GGCGTTTGTCTGTTTTTCATTTCAT 59.766 36.000 0.00 0.00 0.00 2.57
1337 1382 6.269315 TGTTTTTCATTTCATGCAACGTACT 58.731 32.000 0.00 0.00 0.00 2.73
1338 1383 7.418408 TGTTTTTCATTTCATGCAACGTACTA 58.582 30.769 0.00 0.00 0.00 1.82
1368 1418 8.392612 CGTCAGTTAATGGTAATTAAAATCGGT 58.607 33.333 0.00 0.00 39.40 4.69
1429 1479 0.320334 TCTTCAGCGCGTCCATCAAA 60.320 50.000 8.43 0.00 0.00 2.69
1828 1878 0.801067 GCTACCGCGTCAACTACCAG 60.801 60.000 4.92 0.00 0.00 4.00
2067 2117 4.517703 CGTCGAGTCGGAGCGGAC 62.518 72.222 13.54 0.95 37.19 4.79
2068 2118 4.517703 GTCGAGTCGGAGCGGACG 62.518 72.222 13.54 0.00 41.81 4.79
2249 2299 5.825679 CGGAGATTTGGGTTGGTTGATTATA 59.174 40.000 0.00 0.00 0.00 0.98
2321 2376 2.125310 TTACTCGGCGGGCACATG 60.125 61.111 6.72 0.00 0.00 3.21
2322 2377 2.949909 TTACTCGGCGGGCACATGT 61.950 57.895 6.72 0.00 0.00 3.21
2344 2403 8.826710 CATGTATGAAAACATAACGACCTACAT 58.173 33.333 0.00 0.00 38.01 2.29
2366 2425 0.118144 AGTGCTCCCTTCCTTCCTCT 59.882 55.000 0.00 0.00 0.00 3.69
2396 2460 1.000486 CTCTCTTCTCCCCCACCGA 60.000 63.158 0.00 0.00 0.00 4.69
2402 2466 2.758327 CTCCCCCACCGACGATGA 60.758 66.667 0.00 0.00 0.00 2.92
2458 2526 6.857437 AGGTTTATCCTGGATTTTCTTTGG 57.143 37.500 15.55 0.00 46.19 3.28
2470 2538 5.048991 GGATTTTCTTTGGAAAGCTACGTCA 60.049 40.000 0.00 0.00 41.66 4.35
2505 2573 0.533032 GGTGTGGCTAGGTCTCAGTC 59.467 60.000 0.00 0.00 0.00 3.51
2510 2578 0.736053 GGCTAGGTCTCAGTCGACTG 59.264 60.000 34.76 34.76 45.08 3.51
2531 2599 4.651778 TGGGATTTAACCAAGTCTCAGTG 58.348 43.478 0.00 0.00 34.44 3.66
2543 2611 5.406780 CCAAGTCTCAGTGAAGTGACATAAC 59.593 44.000 12.13 0.00 35.17 1.89
2596 2669 4.853924 AATTTTGCAAAGATCTCCACGT 57.146 36.364 12.41 0.00 0.00 4.49
2602 2675 4.433615 TGCAAAGATCTCCACGTAAGATC 58.566 43.478 23.15 23.15 46.28 2.75
2610 2683 3.376234 TCTCCACGTAAGATCGAACGAAT 59.624 43.478 23.74 5.35 41.55 3.34
2691 2766 9.787435 AACTACATTATTGAAAGGTCAACACTA 57.213 29.630 0.00 0.00 46.40 2.74
2718 2793 4.353777 TGGGTGACTAGCTTTCATCTAGT 58.646 43.478 7.91 2.67 46.67 2.57
2719 2794 5.516044 TGGGTGACTAGCTTTCATCTAGTA 58.484 41.667 7.91 0.00 44.74 1.82
2720 2795 5.594725 TGGGTGACTAGCTTTCATCTAGTAG 59.405 44.000 7.91 0.00 44.74 2.57
2770 2845 3.687212 TCGTACATCATTTCATTTGGCGT 59.313 39.130 0.00 0.00 0.00 5.68
2832 2908 8.736751 TGTTAAATTAATCCGCTTTGAAAGTC 57.263 30.769 6.81 0.00 0.00 3.01
2867 2944 8.865590 TTTGCAAGTTACTATTTGAAAGGTTC 57.134 30.769 0.00 0.00 0.00 3.62
2922 2999 5.208463 TGGAAGCCTGGTTTCATTTTAAC 57.792 39.130 22.31 6.15 0.00 2.01
2923 3000 4.898861 TGGAAGCCTGGTTTCATTTTAACT 59.101 37.500 22.31 0.00 0.00 2.24
2936 3765 5.038033 TCATTTTAACTTTGCCACGTCAAC 58.962 37.500 0.00 0.00 0.00 3.18
2937 3766 3.423996 TTTAACTTTGCCACGTCAACC 57.576 42.857 0.00 0.00 0.00 3.77
2941 3770 2.128853 CTTTGCCACGTCAACCGCAT 62.129 55.000 0.00 0.00 41.42 4.73
2956 3785 1.717937 GCATGATGTGTGTCCTCGC 59.282 57.895 0.00 0.00 0.00 5.03
2958 3787 1.471501 GCATGATGTGTGTCCTCGCTA 60.472 52.381 0.00 0.00 0.00 4.26
2987 3816 6.553476 GGGCATATTTATCCCTTAGTGGTTTT 59.447 38.462 0.00 0.00 37.08 2.43
2989 3818 7.286775 GGCATATTTATCCCTTAGTGGTTTTGA 59.713 37.037 0.00 0.00 0.00 2.69
3014 3843 7.598189 TGATTGATAACAATGCAATTTGTGG 57.402 32.000 6.46 0.00 45.30 4.17
3024 3853 3.741249 TGCAATTTGTGGACTAACCGTA 58.259 40.909 0.00 0.00 42.61 4.02
3025 3854 3.499157 TGCAATTTGTGGACTAACCGTAC 59.501 43.478 0.00 0.00 42.61 3.67
3029 3858 4.576216 TTTGTGGACTAACCGTACGTAA 57.424 40.909 15.21 0.00 42.61 3.18
3035 3864 3.381590 GGACTAACCGTACGTAAGGGAAT 59.618 47.826 27.69 17.06 46.39 3.01
3037 3866 4.016444 ACTAACCGTACGTAAGGGAATGA 58.984 43.478 27.69 9.82 46.39 2.57
3038 3867 3.959535 AACCGTACGTAAGGGAATGAA 57.040 42.857 27.69 0.00 46.39 2.57
3053 3882 6.771573 AGGGAATGAAGCATGAAAATCAAAA 58.228 32.000 0.00 0.00 0.00 2.44
3094 3923 4.157656 CCCAAGATCTATCTAGGAGAAGCG 59.842 50.000 0.00 0.00 35.76 4.68
3138 3967 3.362581 TACGTACCCTCGTAGACCG 57.637 57.895 0.00 0.00 43.80 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.770097 CATGTACAATGGTTGATAAGATAGTCT 57.230 33.333 0.00 0.00 0.00 3.24
2 3 8.499162 GCATGTACAATGGTTGATAAGATAGTC 58.501 37.037 0.00 0.00 0.00 2.59
3 4 7.445402 GGCATGTACAATGGTTGATAAGATAGT 59.555 37.037 0.00 0.00 0.00 2.12
4 5 7.094634 GGGCATGTACAATGGTTGATAAGATAG 60.095 40.741 0.00 0.00 0.00 2.08
5 6 6.714810 GGGCATGTACAATGGTTGATAAGATA 59.285 38.462 0.00 0.00 0.00 1.98
6 7 5.536161 GGGCATGTACAATGGTTGATAAGAT 59.464 40.000 0.00 0.00 0.00 2.40
7 8 4.887071 GGGCATGTACAATGGTTGATAAGA 59.113 41.667 0.00 0.00 0.00 2.10
8 9 4.889409 AGGGCATGTACAATGGTTGATAAG 59.111 41.667 0.00 0.00 0.00 1.73
9 10 4.865905 AGGGCATGTACAATGGTTGATAA 58.134 39.130 0.00 0.00 0.00 1.75
10 11 4.518278 AGGGCATGTACAATGGTTGATA 57.482 40.909 0.00 0.00 0.00 2.15
11 12 3.386932 AGGGCATGTACAATGGTTGAT 57.613 42.857 0.00 0.00 0.00 2.57
12 13 2.897271 AGGGCATGTACAATGGTTGA 57.103 45.000 0.00 0.00 0.00 3.18
13 14 4.016444 ACTAAGGGCATGTACAATGGTTG 58.984 43.478 0.00 0.00 0.00 3.77
14 15 4.316025 ACTAAGGGCATGTACAATGGTT 57.684 40.909 0.00 0.00 0.00 3.67
15 16 4.316025 AACTAAGGGCATGTACAATGGT 57.684 40.909 0.00 0.00 0.00 3.55
16 17 4.201910 CGAAACTAAGGGCATGTACAATGG 60.202 45.833 0.00 0.00 0.00 3.16
17 18 4.201910 CCGAAACTAAGGGCATGTACAATG 60.202 45.833 0.00 0.12 0.00 2.82
18 19 3.945285 CCGAAACTAAGGGCATGTACAAT 59.055 43.478 0.00 0.00 0.00 2.71
19 20 3.340034 CCGAAACTAAGGGCATGTACAA 58.660 45.455 0.00 0.00 0.00 2.41
20 21 2.937873 GCCGAAACTAAGGGCATGTACA 60.938 50.000 0.00 0.00 46.13 2.90
21 22 1.669265 GCCGAAACTAAGGGCATGTAC 59.331 52.381 0.00 0.00 46.13 2.90
22 23 2.032680 GCCGAAACTAAGGGCATGTA 57.967 50.000 0.00 0.00 46.13 2.29
23 24 2.868253 GCCGAAACTAAGGGCATGT 58.132 52.632 0.00 0.00 46.13 3.21
28 29 0.743345 CTTCGGGCCGAAACTAAGGG 60.743 60.000 37.48 22.49 45.23 3.95
29 30 0.248289 TCTTCGGGCCGAAACTAAGG 59.752 55.000 37.48 25.87 45.23 2.69
30 31 1.641577 CTCTTCGGGCCGAAACTAAG 58.358 55.000 37.48 27.00 45.23 2.18
59 60 0.968405 TGCTGGGAAATTGCTGAACC 59.032 50.000 0.00 0.00 0.00 3.62
74 75 4.929198 CAAGGTCGTTTGCTGCTG 57.071 55.556 0.00 0.00 0.00 4.41
78 79 2.203153 ACGGCAAGGTCGTTTGCT 60.203 55.556 16.93 1.77 42.79 3.91
103 104 7.880195 CCTAAGATAGCACCATTATATATGCCC 59.120 40.741 3.03 0.00 38.92 5.36
108 109 8.696374 GCACTCCTAAGATAGCACCATTATATA 58.304 37.037 0.00 0.00 0.00 0.86
109 110 7.365117 GGCACTCCTAAGATAGCACCATTATAT 60.365 40.741 0.00 0.00 0.00 0.86
110 111 6.070767 GGCACTCCTAAGATAGCACCATTATA 60.071 42.308 0.00 0.00 0.00 0.98
111 112 5.280215 GGCACTCCTAAGATAGCACCATTAT 60.280 44.000 0.00 0.00 0.00 1.28
112 113 4.040461 GGCACTCCTAAGATAGCACCATTA 59.960 45.833 0.00 0.00 0.00 1.90
113 114 3.181450 GGCACTCCTAAGATAGCACCATT 60.181 47.826 0.00 0.00 0.00 3.16
157 167 5.896073 TTCTTTCAACTTTCCTCTCCTCT 57.104 39.130 0.00 0.00 0.00 3.69
160 170 6.944234 TCTTTTCTTTCAACTTTCCTCTCC 57.056 37.500 0.00 0.00 0.00 3.71
193 215 9.866798 TGAGACATATTATGCTAACAGATCATC 57.133 33.333 3.52 0.00 0.00 2.92
199 221 7.596621 ACGTGATGAGACATATTATGCTAACAG 59.403 37.037 3.52 0.00 0.00 3.16
201 223 7.875316 ACGTGATGAGACATATTATGCTAAC 57.125 36.000 3.52 0.00 0.00 2.34
208 230 9.878667 TTCCTAAAAACGTGATGAGACATATTA 57.121 29.630 0.00 0.00 0.00 0.98
241 263 9.935241 TCATCTCTTAGCCATATCTTCAATAAC 57.065 33.333 0.00 0.00 0.00 1.89
247 269 5.247110 TGGGTCATCTCTTAGCCATATCTTC 59.753 44.000 0.00 0.00 38.31 2.87
254 276 1.833630 CAGTGGGTCATCTCTTAGCCA 59.166 52.381 0.00 0.00 40.82 4.75
256 278 3.954904 TCTACAGTGGGTCATCTCTTAGC 59.045 47.826 0.00 0.00 0.00 3.09
261 283 4.744795 AATGTCTACAGTGGGTCATCTC 57.255 45.455 0.00 0.00 0.00 2.75
289 312 7.957002 AGTCATCCACGTAATTTAGAGATGAT 58.043 34.615 15.56 0.00 40.32 2.45
323 346 8.499162 GCATGTACAATGGTTGATAAGATAGTC 58.501 37.037 0.00 0.00 0.00 2.59
345 368 1.447317 GCGGGGTGATGTAAGGCATG 61.447 60.000 0.00 0.00 38.06 4.06
347 370 2.270850 GCGGGGTGATGTAAGGCA 59.729 61.111 0.00 0.00 0.00 4.75
349 372 0.462047 GAGTGCGGGGTGATGTAAGG 60.462 60.000 0.00 0.00 0.00 2.69
350 373 0.462047 GGAGTGCGGGGTGATGTAAG 60.462 60.000 0.00 0.00 0.00 2.34
351 374 0.907704 AGGAGTGCGGGGTGATGTAA 60.908 55.000 0.00 0.00 0.00 2.41
352 375 0.907704 AAGGAGTGCGGGGTGATGTA 60.908 55.000 0.00 0.00 0.00 2.29
353 376 2.185310 GAAGGAGTGCGGGGTGATGT 62.185 60.000 0.00 0.00 0.00 3.06
354 377 1.450312 GAAGGAGTGCGGGGTGATG 60.450 63.158 0.00 0.00 0.00 3.07
355 378 1.613630 AGAAGGAGTGCGGGGTGAT 60.614 57.895 0.00 0.00 0.00 3.06
356 379 2.203788 AGAAGGAGTGCGGGGTGA 60.204 61.111 0.00 0.00 0.00 4.02
357 380 2.266055 GAGAAGGAGTGCGGGGTG 59.734 66.667 0.00 0.00 0.00 4.61
363 386 1.079750 GACACGGGAGAAGGAGTGC 60.080 63.158 0.00 0.00 38.08 4.40
365 388 1.536943 GCAGACACGGGAGAAGGAGT 61.537 60.000 0.00 0.00 0.00 3.85
372 395 1.532868 CTTTCTTTGCAGACACGGGAG 59.467 52.381 0.00 0.00 0.00 4.30
382 405 2.559698 TCGACCCATCTTTCTTTGCA 57.440 45.000 0.00 0.00 0.00 4.08
384 407 4.937620 TCAAGATCGACCCATCTTTCTTTG 59.062 41.667 0.00 0.00 40.52 2.77
387 410 5.365021 AATCAAGATCGACCCATCTTTCT 57.635 39.130 0.00 0.00 40.52 2.52
395 418 5.818136 TCAATCAAAATCAAGATCGACCC 57.182 39.130 0.00 0.00 0.00 4.46
417 440 9.603921 CCATGCTCAAGAAATTTACCAAATAAT 57.396 29.630 0.00 0.00 0.00 1.28
418 441 7.548780 GCCATGCTCAAGAAATTTACCAAATAA 59.451 33.333 0.00 0.00 0.00 1.40
419 442 7.041107 GCCATGCTCAAGAAATTTACCAAATA 58.959 34.615 0.00 0.00 0.00 1.40
426 449 6.294120 CGGATATGCCATGCTCAAGAAATTTA 60.294 38.462 0.00 0.00 35.94 1.40
429 452 3.504906 CGGATATGCCATGCTCAAGAAAT 59.495 43.478 0.00 0.00 35.94 2.17
431 454 2.497138 CGGATATGCCATGCTCAAGAA 58.503 47.619 0.00 0.00 35.94 2.52
448 471 5.233988 CAAAATAAAAATGAACTGGGCGGA 58.766 37.500 0.00 0.00 0.00 5.54
464 487 2.763448 CGGGAAATCCTGGCCAAAATAA 59.237 45.455 7.01 0.00 38.76 1.40
465 488 2.291930 ACGGGAAATCCTGGCCAAAATA 60.292 45.455 7.01 0.00 46.75 1.40
466 489 1.194218 CGGGAAATCCTGGCCAAAAT 58.806 50.000 7.01 0.00 38.76 1.82
471 494 3.140814 GCACGGGAAATCCTGGCC 61.141 66.667 12.76 0.00 46.75 5.36
482 505 1.826385 ATTCCTTCTCAAAGCACGGG 58.174 50.000 0.00 0.00 0.00 5.28
490 513 4.515191 CGAGGTTGACAAATTCCTTCTCAA 59.485 41.667 0.00 0.00 0.00 3.02
505 528 5.789521 TCATTTACATTGTCTCGAGGTTGA 58.210 37.500 13.56 0.46 0.00 3.18
508 531 5.661056 TCTCATTTACATTGTCTCGAGGT 57.339 39.130 13.56 4.48 0.00 3.85
618 646 1.403687 GGACGGATTCAGAGGAGGGG 61.404 65.000 0.00 0.00 0.00 4.79
619 647 1.403687 GGGACGGATTCAGAGGAGGG 61.404 65.000 0.00 0.00 0.00 4.30
625 657 2.367202 GGCCAGGGACGGATTCAGA 61.367 63.158 0.00 0.00 0.00 3.27
659 691 0.037975 AAACGGACGCGTACAAGGAT 60.038 50.000 23.49 0.00 0.00 3.24
681 713 3.952535 ACGCGCAGATGGAAATTATTTC 58.047 40.909 5.73 9.03 38.94 2.17
714 746 6.484643 GTCTGCTAGCTTTTATCCATTCATGA 59.515 38.462 17.23 0.00 0.00 3.07
734 766 3.388272 GCTTAGGCTTAGGGTCTGC 57.612 57.895 2.34 0.00 35.22 4.26
826 858 5.893500 TCTTGGGTGGGTGACAAATTAATA 58.106 37.500 0.00 0.00 0.00 0.98
827 859 4.746466 TCTTGGGTGGGTGACAAATTAAT 58.254 39.130 0.00 0.00 0.00 1.40
828 860 4.186077 TCTTGGGTGGGTGACAAATTAA 57.814 40.909 0.00 0.00 0.00 1.40
937 969 0.322975 GTCCTCTCCTCTGCTTGCAA 59.677 55.000 0.00 0.00 0.00 4.08
939 972 1.220477 GGTCCTCTCCTCTGCTTGC 59.780 63.158 0.00 0.00 0.00 4.01
956 989 2.913060 GGTCGATCCCCTCTCCGG 60.913 72.222 0.00 0.00 0.00 5.14
1183 1222 1.003839 ACTCGTACGTACCGGTGGA 60.004 57.895 19.93 9.72 0.00 4.02
1208 1251 1.627834 GAGGATGGAGGATGGATGGAC 59.372 57.143 0.00 0.00 0.00 4.02
1365 1415 2.024590 GATGAACCCCGACCCTACCG 62.025 65.000 0.00 0.00 0.00 4.02
1368 1418 0.754217 CGAGATGAACCCCGACCCTA 60.754 60.000 0.00 0.00 0.00 3.53
1429 1479 2.960170 GTGTAGTCGGACGGCAGT 59.040 61.111 1.89 0.00 0.00 4.40
1483 1533 1.068417 CGTCTTGGGGAACACGTCA 59.932 57.895 0.00 0.00 0.00 4.35
2067 2117 1.738099 CCGCTGTCCTTGAACCTCG 60.738 63.158 0.00 0.00 0.00 4.63
2068 2118 2.035442 GCCGCTGTCCTTGAACCTC 61.035 63.158 0.00 0.00 0.00 3.85
2249 2299 2.812011 GCCAAATTCCGCCGAGTAATAT 59.188 45.455 0.00 0.00 0.00 1.28
2321 2376 7.493320 TCCATGTAGGTCGTTATGTTTTCATAC 59.507 37.037 0.00 0.00 39.33 2.39
2322 2377 7.557724 TCCATGTAGGTCGTTATGTTTTCATA 58.442 34.615 0.00 0.00 38.98 2.15
2366 2425 2.754552 GAGAAGAGAGAGCAGAGCAGAA 59.245 50.000 0.00 0.00 0.00 3.02
2396 2460 0.108615 CCTGAAACGGAGCTCATCGT 60.109 55.000 17.19 14.08 41.71 3.73
2436 2504 6.850752 TCCAAAGAAAATCCAGGATAAACC 57.149 37.500 1.02 0.00 39.35 3.27
2443 2511 4.879197 AGCTTTCCAAAGAAAATCCAGG 57.121 40.909 3.11 0.00 41.40 4.45
2458 2526 6.420008 TCAAAAGTTAGTCTGACGTAGCTTTC 59.580 38.462 18.98 0.00 0.00 2.62
2470 2538 4.461198 CCACACCCTTCAAAAGTTAGTCT 58.539 43.478 0.00 0.00 0.00 3.24
2510 2578 4.906618 TCACTGAGACTTGGTTAAATCCC 58.093 43.478 0.00 0.00 0.00 3.85
2602 2675 9.181805 ACAGTGAATACTATATTCATTCGTTCG 57.818 33.333 12.99 2.24 39.80 3.95
2604 2677 9.261180 CCACAGTGAATACTATATTCATTCGTT 57.739 33.333 12.99 0.00 39.80 3.85
2605 2678 8.638873 TCCACAGTGAATACTATATTCATTCGT 58.361 33.333 12.99 8.70 39.80 3.85
2610 2683 9.987272 CTCAATCCACAGTGAATACTATATTCA 57.013 33.333 0.62 7.09 34.74 2.57
2691 2766 4.164843 TGAAAGCTAGTCACCCAAAAGT 57.835 40.909 0.00 0.00 0.00 2.66
2841 2917 9.476202 GAACCTTTCAAATAGTAACTTGCAAAT 57.524 29.630 0.00 0.00 0.00 2.32
2842 2918 8.470805 TGAACCTTTCAAATAGTAACTTGCAAA 58.529 29.630 0.00 0.00 36.59 3.68
2867 2944 4.335594 AGAAGGAAACTCTGACGGTTTTTG 59.664 41.667 0.00 0.00 42.68 2.44
2922 2999 2.051345 GCGGTTGACGTGGCAAAG 60.051 61.111 0.00 0.00 46.52 2.77
2923 3000 2.190170 ATGCGGTTGACGTGGCAAA 61.190 52.632 0.00 0.00 46.52 3.68
2936 3765 1.423721 CGAGGACACACATCATGCGG 61.424 60.000 0.00 0.00 0.00 5.69
2937 3766 2.001357 CGAGGACACACATCATGCG 58.999 57.895 0.00 0.00 0.00 4.73
2941 3770 3.068165 CCTAATAGCGAGGACACACATCA 59.932 47.826 0.00 0.00 35.99 3.07
2987 3816 8.874816 CACAAATTGCATTGTTATCAATCATCA 58.125 29.630 2.91 0.00 41.44 3.07
2989 3818 8.041919 TCCACAAATTGCATTGTTATCAATCAT 58.958 29.630 2.91 0.00 41.44 2.45
3014 3843 4.096382 TCATTCCCTTACGTACGGTTAGTC 59.904 45.833 21.06 0.00 0.00 2.59
3024 3853 3.627395 TCATGCTTCATTCCCTTACGT 57.373 42.857 0.00 0.00 0.00 3.57
3025 3854 4.963276 TTTCATGCTTCATTCCCTTACG 57.037 40.909 0.00 0.00 0.00 3.18
3029 3858 6.363167 TTTGATTTTCATGCTTCATTCCCT 57.637 33.333 0.00 0.00 0.00 4.20
3057 3886 4.225267 AGATCTTGGGTGTTCGTAGGATTT 59.775 41.667 0.00 0.00 0.00 2.17
3058 3887 3.775316 AGATCTTGGGTGTTCGTAGGATT 59.225 43.478 0.00 0.00 0.00 3.01
3094 3923 0.741915 CTCTCCCCTCTCGTTGCTAC 59.258 60.000 0.00 0.00 0.00 3.58
3109 3938 2.677337 GAGGGTACGTAGACACACTCTC 59.323 54.545 10.55 4.79 41.06 3.20
3136 3965 2.833631 ATATACGCTTCCCCTTTCGG 57.166 50.000 0.00 0.00 0.00 4.30
3137 3966 3.671928 CGTTATATACGCTTCCCCTTTCG 59.328 47.826 0.00 0.00 44.26 3.46


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

AutoCloner maintained by Alex Coulton.