Multiple sequence alignment - TraesCS4D01G121300

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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 TraesCS4D01G121300 chr4D 100.000 4391 0 0 1 4391 102391149 102386759 0.000000e+00 8109.0
1 TraesCS4D01G121300 chr4D 78.909 275 35 15 3795 4065 462548414 462548159 9.770000e-37 165.0
2 TraesCS4D01G121300 chr4D 84.024 169 23 2 263 427 435967478 435967310 4.550000e-35 159.0
3 TraesCS4D01G121300 chr4A 92.537 3484 155 34 33 3439 472647857 472651312 0.000000e+00 4896.0
4 TraesCS4D01G121300 chr4A 93.945 578 24 5 3497 4066 472651329 472651903 0.000000e+00 863.0
5 TraesCS4D01G121300 chr4A 90.837 251 15 2 4146 4391 472651900 472652147 3.270000e-86 329.0
6 TraesCS4D01G121300 chr4A 75.112 446 102 9 1747 2187 694667021 694667462 2.680000e-47 200.0
7 TraesCS4D01G121300 chr4A 78.313 249 27 15 3794 4036 6491610 6491383 7.660000e-28 135.0
8 TraesCS4D01G121300 chr4A 88.636 44 5 0 99 142 696560311 696560354 2.000000e-03 54.7
9 TraesCS4D01G121300 chr4B 94.986 2812 99 19 664 3448 146559661 146556865 0.000000e+00 4373.0
10 TraesCS4D01G121300 chr4B 92.162 370 13 4 3563 3929 146534262 146533906 3.920000e-140 508.0
11 TraesCS4D01G121300 chr4B 92.430 251 10 2 4146 4391 146533670 146533424 2.510000e-92 350.0
12 TraesCS4D01G121300 chr4B 83.803 142 23 0 286 427 449514505 449514364 7.660000e-28 135.0
13 TraesCS4D01G121300 chr7A 76.923 858 171 21 1636 2481 32300762 32299920 3.090000e-126 462.0
14 TraesCS4D01G121300 chr7A 78.550 331 54 11 1005 1322 32301849 32301523 7.450000e-48 202.0
15 TraesCS4D01G121300 chr7D 76.163 860 180 19 1636 2484 31996480 31995635 3.140000e-116 429.0
16 TraesCS4D01G121300 chr7D 78.209 335 51 15 1005 1322 31997774 31997445 1.250000e-45 195.0
17 TraesCS4D01G121300 chr7D 95.789 95 3 1 4056 4150 52840542 52840449 7.610000e-33 152.0
18 TraesCS4D01G121300 chr7D 92.233 103 7 1 4058 4160 45835321 45835422 1.270000e-30 145.0
19 TraesCS4D01G121300 chrUn 75.607 865 182 23 1633 2484 366954297 366953449 6.840000e-108 401.0
20 TraesCS4D01G121300 chrUn 75.607 865 182 23 1633 2484 366956268 366955420 6.840000e-108 401.0
21 TraesCS4D01G121300 chrUn 77.265 563 118 8 1633 2190 444589950 444590507 5.480000e-84 322.0
22 TraesCS4D01G121300 chrUn 95.745 94 2 2 4065 4158 226012807 226012898 2.740000e-32 150.0
23 TraesCS4D01G121300 chrUn 75.072 349 62 18 1184 1515 366954732 366954392 5.920000e-29 139.0
24 TraesCS4D01G121300 chrUn 75.072 349 62 18 1184 1515 366956703 366956363 5.920000e-29 139.0
25 TraesCS4D01G121300 chrUn 75.072 349 62 18 1184 1515 444589515 444589855 5.920000e-29 139.0
26 TraesCS4D01G121300 chr5D 84.986 353 35 15 3669 4015 437445310 437444970 4.210000e-90 342.0
27 TraesCS4D01G121300 chr5D 81.081 333 36 10 3675 4006 6385389 6385695 1.580000e-59 241.0
28 TraesCS4D01G121300 chr5D 80.905 199 33 4 232 427 55830470 55830666 7.610000e-33 152.0
29 TraesCS4D01G121300 chr5D 96.703 91 3 0 4064 4154 322375748 322375838 7.610000e-33 152.0
30 TraesCS4D01G121300 chr5D 82.738 168 25 2 263 426 562432602 562432435 3.540000e-31 147.0
31 TraesCS4D01G121300 chr5D 92.308 104 4 2 4051 4153 386983948 386984048 1.270000e-30 145.0
32 TraesCS4D01G121300 chr3A 81.910 398 54 17 3675 4066 698686844 698687229 1.970000e-83 320.0
33 TraesCS4D01G121300 chr3B 82.709 347 43 12 3675 4009 759107207 759107548 4.300000e-75 292.0
34 TraesCS4D01G121300 chr5A 80.781 333 33 12 3675 4006 3286679 3286377 9.500000e-57 231.0
35 TraesCS4D01G121300 chr5A 78.571 392 45 21 3675 4065 455483302 455483655 5.720000e-54 222.0
36 TraesCS4D01G121300 chr5B 77.970 404 51 16 3665 4065 545190728 545190360 7.390000e-53 219.0
37 TraesCS4D01G121300 chr5B 96.774 93 3 0 4057 4149 603648385 603648293 5.880000e-34 156.0
38 TraesCS4D01G121300 chr5B 84.397 141 17 4 4065 4205 180061447 180061582 2.760000e-27 134.0
39 TraesCS4D01G121300 chr6A 88.811 143 16 0 286 428 224277331 224277189 4.510000e-40 176.0
40 TraesCS4D01G121300 chr1D 85.897 156 18 3 276 427 202315215 202315370 3.510000e-36 163.0
41 TraesCS4D01G121300 chr3D 80.808 198 35 3 231 427 613585398 613585593 7.610000e-33 152.0
42 TraesCS4D01G121300 chr1B 95.745 94 4 0 4059 4152 39580053 39580146 7.610000e-33 152.0
43 TraesCS4D01G121300 chr2A 94.845 97 4 1 4057 4153 678161259 678161354 2.740000e-32 150.0
44 TraesCS4D01G121300 chr6B 80.000 200 34 6 232 428 626881554 626881358 4.580000e-30 143.0
45 TraesCS4D01G121300 chr2D 87.097 62 8 0 1823 1884 64184858 64184797 2.190000e-08 71.3


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 TraesCS4D01G121300 chr4D 102386759 102391149 4390 True 8109.000000 8109 100.000000 1 4391 1 chr4D.!!$R1 4390
1 TraesCS4D01G121300 chr4A 472647857 472652147 4290 False 2029.333333 4896 92.439667 33 4391 3 chr4A.!!$F3 4358
2 TraesCS4D01G121300 chr4B 146556865 146559661 2796 True 4373.000000 4373 94.986000 664 3448 1 chr4B.!!$R1 2784
3 TraesCS4D01G121300 chr4B 146533424 146534262 838 True 429.000000 508 92.296000 3563 4391 2 chr4B.!!$R3 828
4 TraesCS4D01G121300 chr7A 32299920 32301849 1929 True 332.000000 462 77.736500 1005 2481 2 chr7A.!!$R1 1476
5 TraesCS4D01G121300 chr7D 31995635 31997774 2139 True 312.000000 429 77.186000 1005 2484 2 chr7D.!!$R2 1479
6 TraesCS4D01G121300 chrUn 366953449 366956703 3254 True 270.000000 401 75.339500 1184 2484 4 chrUn.!!$R1 1300
7 TraesCS4D01G121300 chrUn 444589515 444590507 992 False 230.500000 322 76.168500 1184 2190 2 chrUn.!!$F2 1006

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
173 176 0.321671 CAGTGCTTCTCGGAAAGGGA 59.678 55.0 0.00 0.0 0.0 4.20 F
1539 4279 0.610785 TGGGCCCCTTGTTCGAATTC 60.611 55.0 22.27 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 4426 0.548926 TGAGGTACATCCCCTTGCCA 60.549 55.0 4.87 0.0 36.75 4.92 R
3414 6188 0.037697 TGCACACCTACTAACCAGCG 60.038 55.0 0.00 0.0 0.00 5.18 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
19 20 1.318576 CCGAATGGGGTTAGATTGGC 58.681 55.000 0.00 0.00 0.00 4.52
20 21 0.944386 CGAATGGGGTTAGATTGGCG 59.056 55.000 0.00 0.00 0.00 5.69
21 22 1.474320 CGAATGGGGTTAGATTGGCGA 60.474 52.381 0.00 0.00 0.00 5.54
22 23 2.810400 CGAATGGGGTTAGATTGGCGAT 60.810 50.000 0.00 0.00 0.00 4.58
23 24 3.222603 GAATGGGGTTAGATTGGCGATT 58.777 45.455 0.00 0.00 0.00 3.34
24 25 2.818751 TGGGGTTAGATTGGCGATTT 57.181 45.000 0.00 0.00 0.00 2.17
25 26 2.374184 TGGGGTTAGATTGGCGATTTG 58.626 47.619 0.00 0.00 0.00 2.32
26 27 2.291282 TGGGGTTAGATTGGCGATTTGT 60.291 45.455 0.00 0.00 0.00 2.83
27 28 2.357952 GGGGTTAGATTGGCGATTTGTC 59.642 50.000 0.00 0.00 0.00 3.18
28 29 2.357952 GGGTTAGATTGGCGATTTGTCC 59.642 50.000 0.00 0.00 0.00 4.02
29 30 3.013921 GGTTAGATTGGCGATTTGTCCA 58.986 45.455 0.00 0.00 0.00 4.02
30 31 3.442273 GGTTAGATTGGCGATTTGTCCAA 59.558 43.478 0.00 0.00 45.35 3.53
31 32 4.438744 GGTTAGATTGGCGATTTGTCCAAG 60.439 45.833 0.00 0.00 44.59 3.61
63 64 6.865205 GGCACATATTTAATTCCATGAGAAGC 59.135 38.462 0.00 0.00 38.07 3.86
81 82 2.334307 CACAGTTGTGCTTCCCTGG 58.666 57.895 0.00 0.00 39.39 4.45
86 87 2.035066 CAGTTGTGCTTCCCTGGAAAAG 59.965 50.000 0.00 0.00 33.34 2.27
130 133 3.507162 TTTCTTCTCATGGAGGCACAA 57.493 42.857 0.00 0.00 0.00 3.33
139 142 5.415701 TCTCATGGAGGCACAAATTTACTTC 59.584 40.000 0.00 0.00 0.00 3.01
142 145 4.469657 TGGAGGCACAAATTTACTTCTGT 58.530 39.130 0.00 0.00 0.00 3.41
143 146 4.278170 TGGAGGCACAAATTTACTTCTGTG 59.722 41.667 2.03 2.03 41.68 3.66
155 158 2.724977 CTTCTGTGAGAAGTACGGCA 57.275 50.000 5.34 0.00 45.03 5.69
166 169 1.805945 GTACGGCAGTGCTTCTCGG 60.806 63.158 16.11 0.53 0.00 4.63
170 173 1.630244 CGGCAGTGCTTCTCGGAAAG 61.630 60.000 16.11 0.00 0.00 2.62
173 176 0.321671 CAGTGCTTCTCGGAAAGGGA 59.678 55.000 0.00 0.00 0.00 4.20
176 179 1.807142 GTGCTTCTCGGAAAGGGAAAG 59.193 52.381 0.00 0.00 39.18 2.62
194 197 8.525290 AGGGAAAGAAAATATGTACTTCCATG 57.475 34.615 6.96 0.00 0.00 3.66
210 213 9.906660 GTACTTCCATGAAAAACACATATTTGA 57.093 29.630 0.00 0.00 0.00 2.69
218 221 4.695217 AAACACATATTTGATTCCGCGT 57.305 36.364 4.92 0.00 0.00 6.01
260 263 1.755179 AAATCATGGTTCCAGCTCCG 58.245 50.000 0.00 0.00 0.00 4.63
261 264 0.749454 AATCATGGTTCCAGCTCCGC 60.749 55.000 0.00 0.00 0.00 5.54
279 284 3.626670 TCCGCGTTTTTCCTTTCAGTTTA 59.373 39.130 4.92 0.00 0.00 2.01
313 318 7.408132 AATATCGTCGAAACCTATTGACATG 57.592 36.000 0.00 0.00 33.99 3.21
333 338 5.710099 ACATGGTATGTGGTTTCGAAAATCT 59.290 36.000 13.10 0.00 43.01 2.40
335 340 5.309638 TGGTATGTGGTTTCGAAAATCTCA 58.690 37.500 13.10 14.32 0.00 3.27
341 346 2.096614 GGTTTCGAAAATCTCAACGCGA 60.097 45.455 15.93 0.00 0.00 5.87
353 358 4.443850 CTCAACGCGAGAAATCCAATAG 57.556 45.455 15.93 0.00 45.45 1.73
360 365 5.022021 CGCGAGAAATCCAATAGTGAAAAC 58.978 41.667 0.00 0.00 0.00 2.43
367 372 8.852135 AGAAATCCAATAGTGAAAACGGTTTAA 58.148 29.630 6.53 0.00 0.00 1.52
368 373 9.124807 GAAATCCAATAGTGAAAACGGTTTAAG 57.875 33.333 6.53 0.00 0.00 1.85
385 390 4.695217 TTAAGATTTGGACGCATGGTTC 57.305 40.909 0.00 0.00 0.00 3.62
451 456 1.973515 ACATGTCAGCACCTGAGAAGA 59.026 47.619 0.00 0.00 41.46 2.87
454 459 1.338484 TGTCAGCACCTGAGAAGATGC 60.338 52.381 0.00 0.00 41.46 3.91
466 471 4.825422 TGAGAAGATGCGAGTGATCTTTT 58.175 39.130 0.00 0.00 39.72 2.27
467 472 4.628766 TGAGAAGATGCGAGTGATCTTTTG 59.371 41.667 0.00 0.00 39.72 2.44
468 473 3.373439 AGAAGATGCGAGTGATCTTTTGC 59.627 43.478 0.00 0.00 39.72 3.68
511 516 2.489938 TTTTGCCGATTAGGAGCACT 57.510 45.000 0.00 0.00 45.00 4.40
512 517 2.024176 TTTGCCGATTAGGAGCACTC 57.976 50.000 0.00 0.00 45.00 3.51
513 518 1.195115 TTGCCGATTAGGAGCACTCT 58.805 50.000 0.00 0.00 45.00 3.24
538 543 3.731652 TTTTTGAGTGCTCACATTGGG 57.268 42.857 0.79 0.00 39.66 4.12
572 593 1.896660 TGACGAGGTTGGCCAAAGC 60.897 57.895 22.47 14.04 37.19 3.51
578 599 4.362476 GTTGGCCAAAGCGCTGGG 62.362 66.667 22.47 20.92 41.24 4.45
616 637 1.829096 TTGGACTGACCCACGTCGA 60.829 57.895 0.00 0.00 42.37 4.20
642 663 2.925706 TTACGGAGCTGGGCCACA 60.926 61.111 0.00 0.00 0.00 4.17
673 716 2.123683 CTAGGGCAGCGGAGGAGA 60.124 66.667 0.00 0.00 0.00 3.71
674 717 2.123683 TAGGGCAGCGGAGGAGAG 60.124 66.667 0.00 0.00 0.00 3.20
758 802 3.351416 GTCGTGGTTGGCCGGAAC 61.351 66.667 5.05 0.29 37.67 3.62
796 840 4.129737 CGTCCGGATCTGGTGCGT 62.130 66.667 20.32 0.00 40.39 5.24
951 998 7.067421 TGTCATAGGTGCTAATTCTACTAGGT 58.933 38.462 0.00 0.00 0.00 3.08
971 1018 1.169577 TGGTGTTTCTGTGCGTGTTT 58.830 45.000 0.00 0.00 0.00 2.83
989 1036 4.974438 TGGTCCCGGTGCTTCCCT 62.974 66.667 0.00 0.00 0.00 4.20
998 1045 4.329545 TGCTTCCCTGCCGGTGAC 62.330 66.667 1.90 0.00 0.00 3.67
1144 1191 3.437795 ACACCGAGTACCTCCGCG 61.438 66.667 0.00 0.00 0.00 6.46
1160 1207 4.514577 CGGCTTCCTGGATCGCGT 62.515 66.667 5.77 0.00 0.00 6.01
1176 1226 3.702048 GTACCACCAGGCGCCTCA 61.702 66.667 30.29 4.48 39.06 3.86
1358 3626 1.066114 CTCGGTCGTGCGAGAAAGTC 61.066 60.000 0.00 0.00 34.48 3.01
1362 3630 1.214367 GTCGTGCGAGAAAGTCCAAA 58.786 50.000 0.00 0.00 0.00 3.28
1413 4153 1.432270 GCCACGTCTAATGCAGCTCC 61.432 60.000 0.00 0.00 0.00 4.70
1467 4207 3.141488 ACCGCGGAGAAGCTCGAT 61.141 61.111 35.90 0.68 34.40 3.59
1526 4266 1.683385 GAAGATGTAAGCATTGGGCCC 59.317 52.381 17.59 17.59 46.50 5.80
1539 4279 0.610785 TGGGCCCCTTGTTCGAATTC 60.611 55.000 22.27 0.00 0.00 2.17
1667 4426 0.972983 CTGATCAGGGGGACAGACGT 60.973 60.000 15.38 0.00 32.90 4.34
2007 4777 0.317436 GCGTCTCAGCGACTGGATAG 60.317 60.000 6.95 0.00 40.59 2.08
2033 4803 3.190849 CCTCTGCGTGATGCCGTG 61.191 66.667 0.00 0.00 45.60 4.94
2375 5148 1.266718 GACGATGAAAAGGTGCAAGCA 59.733 47.619 0.00 0.00 36.26 3.91
2403 5176 3.643320 TGGTTTGTATGACAATTTGGGCA 59.357 39.130 0.78 0.00 38.00 5.36
2417 5190 1.032014 TGGGCAAGTTGAAGCTTGTC 58.968 50.000 2.10 5.94 46.85 3.18
2628 5401 4.766373 TGCTCTGCCAATTATGAAGAAACA 59.234 37.500 0.00 0.00 0.00 2.83
2693 5467 5.222631 CCTGTGTAAGCCTGATTTGTTTTC 58.777 41.667 0.00 0.00 0.00 2.29
2696 5470 5.362430 TGTGTAAGCCTGATTTGTTTTCCTT 59.638 36.000 0.00 0.00 0.00 3.36
2697 5471 6.547880 TGTGTAAGCCTGATTTGTTTTCCTTA 59.452 34.615 0.00 0.00 0.00 2.69
2713 5487 8.380099 TGTTTTCCTTATACTTAGCTTGAAGGA 58.620 33.333 0.00 0.00 40.47 3.36
2731 5505 9.191995 CTTGAAGGATTTGTGGTGTTATAAAAC 57.808 33.333 0.00 0.00 36.07 2.43
2754 5528 0.588252 CAGTCCAACAACCGCTGAAG 59.412 55.000 0.00 0.00 0.00 3.02
2766 5540 2.288886 ACCGCTGAAGAAGTTGTAGTCC 60.289 50.000 0.00 0.00 0.00 3.85
3118 5892 0.588980 CGCGACTGACATCGATCGAA 60.589 55.000 23.50 4.27 45.13 3.71
3228 6002 2.745102 GAGATAAGGGTACTTGAGCGC 58.255 52.381 0.00 0.00 37.53 5.92
3353 6127 1.645710 GAGGAGAGGGTGTCAGGAAA 58.354 55.000 0.00 0.00 0.00 3.13
3414 6188 3.004524 ACGACTATACGAGAGGAAATGGC 59.995 47.826 0.00 0.00 37.03 4.40
3448 6222 3.510360 GGTGTGCAGGACGTATATAGGAT 59.490 47.826 9.36 0.00 0.00 3.24
3449 6223 4.021368 GGTGTGCAGGACGTATATAGGATT 60.021 45.833 9.36 0.00 0.00 3.01
3451 6225 6.294899 GGTGTGCAGGACGTATATAGGATTTA 60.295 42.308 9.36 0.00 0.00 1.40
3453 6227 6.265876 TGTGCAGGACGTATATAGGATTTACA 59.734 38.462 9.36 4.39 0.00 2.41
3455 6229 7.275779 GTGCAGGACGTATATAGGATTTACATG 59.724 40.741 9.36 0.00 0.00 3.21
3456 6230 6.757010 GCAGGACGTATATAGGATTTACATGG 59.243 42.308 9.36 0.00 0.00 3.66
3457 6231 7.578955 GCAGGACGTATATAGGATTTACATGGT 60.579 40.741 9.36 0.00 0.00 3.55
3458 6232 7.759886 CAGGACGTATATAGGATTTACATGGTG 59.240 40.741 9.36 0.00 0.00 4.17
3459 6233 6.534079 GGACGTATATAGGATTTACATGGTGC 59.466 42.308 9.36 0.00 0.00 5.01
3460 6234 6.403878 ACGTATATAGGATTTACATGGTGCC 58.596 40.000 9.36 0.00 0.00 5.01
3461 6235 5.815740 CGTATATAGGATTTACATGGTGCCC 59.184 44.000 0.00 0.00 0.00 5.36
3462 6236 3.525800 ATAGGATTTACATGGTGCCCC 57.474 47.619 0.00 0.00 0.00 5.80
3464 6238 1.111277 GGATTTACATGGTGCCCCAC 58.889 55.000 0.00 0.00 45.65 4.61
3465 6239 1.341976 GGATTTACATGGTGCCCCACT 60.342 52.381 0.00 0.00 45.65 4.00
3466 6240 2.092103 GGATTTACATGGTGCCCCACTA 60.092 50.000 0.00 0.00 45.65 2.74
3467 6241 2.500392 TTTACATGGTGCCCCACTAC 57.500 50.000 0.00 0.00 45.65 2.73
3468 6242 0.621609 TTACATGGTGCCCCACTACC 59.378 55.000 0.00 0.00 45.65 3.18
3469 6243 1.276140 TACATGGTGCCCCACTACCC 61.276 60.000 0.00 0.00 45.65 3.69
3470 6244 2.204228 ATGGTGCCCCACTACCCA 60.204 61.111 0.00 0.00 45.65 4.51
3471 6245 1.854979 ATGGTGCCCCACTACCCAA 60.855 57.895 0.00 0.00 45.65 4.12
3472 6246 1.863155 ATGGTGCCCCACTACCCAAG 61.863 60.000 0.00 0.00 45.65 3.61
3473 6247 2.355115 GTGCCCCACTACCCAAGG 59.645 66.667 0.00 0.00 0.00 3.61
3474 6248 2.208640 TGCCCCACTACCCAAGGA 59.791 61.111 0.00 0.00 0.00 3.36
3475 6249 1.230149 TGCCCCACTACCCAAGGAT 60.230 57.895 0.00 0.00 0.00 3.24
3476 6250 0.849094 TGCCCCACTACCCAAGGATT 60.849 55.000 0.00 0.00 0.00 3.01
3477 6251 0.106669 GCCCCACTACCCAAGGATTC 60.107 60.000 0.00 0.00 0.00 2.52
3478 6252 1.596496 CCCCACTACCCAAGGATTCT 58.404 55.000 0.00 0.00 0.00 2.40
3479 6253 1.212935 CCCCACTACCCAAGGATTCTG 59.787 57.143 0.00 0.00 0.00 3.02
3480 6254 1.408822 CCCACTACCCAAGGATTCTGC 60.409 57.143 0.00 0.00 0.00 4.26
3481 6255 1.281867 CCACTACCCAAGGATTCTGCA 59.718 52.381 0.00 0.00 0.00 4.41
3482 6256 2.290896 CCACTACCCAAGGATTCTGCAA 60.291 50.000 0.00 0.00 0.00 4.08
3483 6257 3.012518 CACTACCCAAGGATTCTGCAAG 58.987 50.000 0.00 0.00 0.00 4.01
3484 6258 2.025887 ACTACCCAAGGATTCTGCAAGG 60.026 50.000 0.00 0.00 0.00 3.61
3485 6259 0.613012 ACCCAAGGATTCTGCAAGGC 60.613 55.000 0.00 0.00 0.00 4.35
3486 6260 0.324091 CCCAAGGATTCTGCAAGGCT 60.324 55.000 0.00 0.00 0.00 4.58
3487 6261 1.064463 CCCAAGGATTCTGCAAGGCTA 60.064 52.381 0.00 0.00 0.00 3.93
3488 6262 2.621407 CCCAAGGATTCTGCAAGGCTAA 60.621 50.000 0.00 0.00 0.00 3.09
3489 6263 2.686915 CCAAGGATTCTGCAAGGCTAAG 59.313 50.000 0.00 0.00 0.00 2.18
3490 6264 2.049888 AGGATTCTGCAAGGCTAAGC 57.950 50.000 5.03 5.03 0.00 3.09
3508 6282 2.833244 CCTAGGAGGCAGGAAGGAG 58.167 63.158 1.05 0.00 34.91 3.69
3604 6378 4.566004 TGATTCAGGTTGGAGAACTTACG 58.434 43.478 0.00 0.00 32.15 3.18
3628 6402 1.539388 TGTTTCCACTTTAGCATGCGG 59.461 47.619 13.01 6.36 0.00 5.69
3744 6523 3.018856 CACATGCCACATTATCACAGGT 58.981 45.455 0.00 0.00 0.00 4.00
3874 6653 1.824230 GCCCACCAAACATGCATAGAA 59.176 47.619 0.00 0.00 0.00 2.10
4011 6893 5.627172 TGCGTACAAGCAAATCTTATTGAC 58.373 37.500 0.00 0.00 45.06 3.18
4019 6901 8.604035 ACAAGCAAATCTTATTGACATACTACG 58.396 33.333 0.00 0.00 32.74 3.51
4064 6949 2.149578 ACGCTCGCGGTATTATCTAGT 58.850 47.619 16.18 0.00 44.69 2.57
4065 6950 3.329386 ACGCTCGCGGTATTATCTAGTA 58.671 45.455 16.18 0.00 44.69 1.82
4066 6951 3.124297 ACGCTCGCGGTATTATCTAGTAC 59.876 47.826 16.18 0.00 44.69 2.73
4067 6952 3.370366 CGCTCGCGGTATTATCTAGTACT 59.630 47.826 6.13 0.00 35.56 2.73
4068 6953 4.492247 CGCTCGCGGTATTATCTAGTACTC 60.492 50.000 6.13 0.00 35.56 2.59
4069 6954 4.201802 GCTCGCGGTATTATCTAGTACTCC 60.202 50.000 6.13 0.00 0.00 3.85
4070 6955 4.256920 TCGCGGTATTATCTAGTACTCCC 58.743 47.826 6.13 0.00 0.00 4.30
4071 6956 4.019860 TCGCGGTATTATCTAGTACTCCCT 60.020 45.833 6.13 0.00 0.00 4.20
4072 6957 4.332268 CGCGGTATTATCTAGTACTCCCTC 59.668 50.000 0.00 0.00 0.00 4.30
4073 6958 5.499313 GCGGTATTATCTAGTACTCCCTCT 58.501 45.833 0.00 0.00 0.00 3.69
4074 6959 5.354792 GCGGTATTATCTAGTACTCCCTCTG 59.645 48.000 0.00 0.00 0.00 3.35
4075 6960 6.474630 CGGTATTATCTAGTACTCCCTCTGT 58.525 44.000 0.00 0.00 0.00 3.41
4076 6961 7.619050 CGGTATTATCTAGTACTCCCTCTGTA 58.381 42.308 0.00 0.00 0.00 2.74
4077 6962 8.099537 CGGTATTATCTAGTACTCCCTCTGTAA 58.900 40.741 0.00 0.00 0.00 2.41
4078 6963 9.804977 GGTATTATCTAGTACTCCCTCTGTAAA 57.195 37.037 0.00 0.00 0.00 2.01
4091 6976 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
4092 6977 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
4093 6978 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
4094 6979 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
4095 6980 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
4143 7028 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
4144 7029 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
4145 7030 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
4146 7031 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
4293 7183 2.299297 TGCAACATTCAACCATGCATGA 59.701 40.909 28.31 7.94 41.67 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.318576 GCCAATCTAACCCCATTCGG 58.681 55.000 0.00 0.00 0.00 4.30
1 2 0.944386 CGCCAATCTAACCCCATTCG 59.056 55.000 0.00 0.00 0.00 3.34
2 3 2.341846 TCGCCAATCTAACCCCATTC 57.658 50.000 0.00 0.00 0.00 2.67
3 4 3.312736 AATCGCCAATCTAACCCCATT 57.687 42.857 0.00 0.00 0.00 3.16
4 5 2.958355 CAAATCGCCAATCTAACCCCAT 59.042 45.455 0.00 0.00 0.00 4.00
5 6 2.291282 ACAAATCGCCAATCTAACCCCA 60.291 45.455 0.00 0.00 0.00 4.96
6 7 2.357952 GACAAATCGCCAATCTAACCCC 59.642 50.000 0.00 0.00 0.00 4.95
7 8 2.357952 GGACAAATCGCCAATCTAACCC 59.642 50.000 0.00 0.00 0.00 4.11
8 9 3.013921 TGGACAAATCGCCAATCTAACC 58.986 45.455 0.00 0.00 0.00 2.85
9 10 4.156008 ACTTGGACAAATCGCCAATCTAAC 59.844 41.667 0.00 0.00 42.79 2.34
10 11 4.155826 CACTTGGACAAATCGCCAATCTAA 59.844 41.667 0.00 0.00 42.79 2.10
11 12 3.689161 CACTTGGACAAATCGCCAATCTA 59.311 43.478 0.00 0.00 42.79 1.98
12 13 2.489329 CACTTGGACAAATCGCCAATCT 59.511 45.455 0.00 0.00 42.79 2.40
13 14 2.228822 ACACTTGGACAAATCGCCAATC 59.771 45.455 0.00 0.00 42.79 2.67
14 15 2.030007 CACACTTGGACAAATCGCCAAT 60.030 45.455 0.00 0.00 42.79 3.16
15 16 1.336440 CACACTTGGACAAATCGCCAA 59.664 47.619 0.00 0.00 41.61 4.52
16 17 0.950836 CACACTTGGACAAATCGCCA 59.049 50.000 0.00 0.00 0.00 5.69
17 18 3.773117 CACACTTGGACAAATCGCC 57.227 52.632 0.00 0.00 0.00 5.54
139 142 1.702886 CACTGCCGTACTTCTCACAG 58.297 55.000 0.00 0.00 0.00 3.66
142 145 0.679505 AAGCACTGCCGTACTTCTCA 59.320 50.000 0.00 0.00 0.00 3.27
143 146 1.067495 AGAAGCACTGCCGTACTTCTC 60.067 52.381 15.74 0.00 46.15 2.87
153 156 1.301677 CCCTTTCCGAGAAGCACTGC 61.302 60.000 0.00 0.00 0.00 4.40
155 158 1.056660 TTCCCTTTCCGAGAAGCACT 58.943 50.000 0.00 0.00 0.00 4.40
164 167 7.625828 AGTACATATTTTCTTTCCCTTTCCG 57.374 36.000 0.00 0.00 0.00 4.30
166 169 9.020731 TGGAAGTACATATTTTCTTTCCCTTTC 57.979 33.333 0.00 0.00 0.00 2.62
170 173 8.519799 TCATGGAAGTACATATTTTCTTTCCC 57.480 34.615 0.00 0.00 0.00 3.97
194 197 5.571357 ACGCGGAATCAAATATGTGTTTTTC 59.429 36.000 12.47 0.00 0.00 2.29
202 205 5.568482 TCTTTTCACGCGGAATCAAATATG 58.432 37.500 12.47 0.00 34.91 1.78
210 213 6.921307 ACTTTTATTTTCTTTTCACGCGGAAT 59.079 30.769 12.47 0.00 34.91 3.01
256 259 1.602377 ACTGAAAGGAAAAACGCGGAG 59.398 47.619 12.47 0.00 39.30 4.63
257 260 1.670791 ACTGAAAGGAAAAACGCGGA 58.329 45.000 12.47 0.00 39.30 5.54
258 261 2.485266 AACTGAAAGGAAAAACGCGG 57.515 45.000 12.47 0.00 39.30 6.46
260 263 7.901002 TCAAAATAAACTGAAAGGAAAAACGC 58.099 30.769 0.00 0.00 39.30 4.84
291 296 5.163488 ACCATGTCAATAGGTTTCGACGATA 60.163 40.000 0.00 0.00 29.58 2.92
292 297 4.119862 CCATGTCAATAGGTTTCGACGAT 58.880 43.478 0.00 0.00 0.00 3.73
294 299 3.259064 ACCATGTCAATAGGTTTCGACG 58.741 45.455 0.00 0.00 29.58 5.12
297 302 5.007626 CCACATACCATGTCAATAGGTTTCG 59.992 44.000 0.00 0.00 42.70 3.46
309 314 5.710099 AGATTTTCGAAACCACATACCATGT 59.290 36.000 10.79 0.00 46.22 3.21
313 318 5.873179 TGAGATTTTCGAAACCACATACC 57.127 39.130 10.79 0.00 0.00 2.73
333 338 3.616821 CACTATTGGATTTCTCGCGTTGA 59.383 43.478 5.77 2.87 0.00 3.18
335 340 3.857052 TCACTATTGGATTTCTCGCGTT 58.143 40.909 5.77 0.00 0.00 4.84
341 346 6.894339 AACCGTTTTCACTATTGGATTTCT 57.106 33.333 0.00 0.00 0.00 2.52
353 358 5.397240 CGTCCAAATCTTAAACCGTTTTCAC 59.603 40.000 0.96 0.00 0.00 3.18
360 365 3.425404 CATGCGTCCAAATCTTAAACCG 58.575 45.455 0.00 0.00 0.00 4.44
367 372 2.198827 TGAACCATGCGTCCAAATCT 57.801 45.000 0.00 0.00 0.00 2.40
368 373 2.487762 TCTTGAACCATGCGTCCAAATC 59.512 45.455 0.00 0.00 0.00 2.17
426 431 3.118992 TCTCAGGTGCTGACATGTGTATC 60.119 47.826 1.15 0.00 35.39 2.24
427 432 2.833943 TCTCAGGTGCTGACATGTGTAT 59.166 45.455 1.15 0.00 35.39 2.29
428 433 2.247358 TCTCAGGTGCTGACATGTGTA 58.753 47.619 1.15 0.00 35.39 2.90
442 447 2.361757 AGATCACTCGCATCTTCTCAGG 59.638 50.000 0.00 0.00 0.00 3.86
451 456 2.163010 CCTTGCAAAAGATCACTCGCAT 59.837 45.455 0.00 0.00 0.00 4.73
454 459 2.426522 TCCCTTGCAAAAGATCACTCG 58.573 47.619 0.00 0.00 0.00 4.18
466 471 4.202524 ACTGGTTAAGTGTTATCCCTTGCA 60.203 41.667 0.00 0.00 37.88 4.08
467 472 4.332828 ACTGGTTAAGTGTTATCCCTTGC 58.667 43.478 0.00 0.00 37.88 4.01
951 998 1.169577 AACACGCACAGAAACACCAA 58.830 45.000 0.00 0.00 0.00 3.67
971 1018 3.961414 GGGAAGCACCGGGACCAA 61.961 66.667 6.32 0.00 40.11 3.67
1144 1191 1.591863 GTACGCGATCCAGGAAGCC 60.592 63.158 15.93 0.00 0.00 4.35
1160 1207 3.390521 CTGAGGCGCCTGGTGGTA 61.391 66.667 38.41 11.68 35.27 3.25
1223 1273 2.111384 ACGGCTTGATGTCCTCATACT 58.889 47.619 0.00 0.00 34.06 2.12
1349 3617 1.192534 GCACGACTTTGGACTTTCTCG 59.807 52.381 0.00 0.00 0.00 4.04
1358 3626 4.357142 ACGTATATACAGCACGACTTTGG 58.643 43.478 13.22 0.00 38.96 3.28
1362 3630 5.065602 TGAGAAACGTATATACAGCACGACT 59.934 40.000 13.22 4.38 38.96 4.18
1467 4207 2.355108 GCCATTGTAGAACAGCCTCTGA 60.355 50.000 0.29 0.00 35.18 3.27
1526 4266 3.253230 GGCCAAATGAATTCGAACAAGG 58.747 45.455 0.00 0.84 0.00 3.61
1539 4279 5.288015 TGACAAATATTATGCGGCCAAATG 58.712 37.500 2.24 0.00 0.00 2.32
1667 4426 0.548926 TGAGGTACATCCCCTTGCCA 60.549 55.000 4.87 0.00 36.75 4.92
2007 4777 2.435586 ACGCAGAGGAGCATGTGC 60.436 61.111 0.00 0.00 42.49 4.57
2087 4857 2.431683 GGCTTCCTGGCACACTCA 59.568 61.111 0.00 0.00 41.37 3.41
2375 5148 7.255801 CCCAAATTGTCATACAAACCAGTACTT 60.256 37.037 0.00 0.00 41.96 2.24
2403 5176 4.024556 CACAAGATCGACAAGCTTCAACTT 60.025 41.667 0.00 0.00 28.98 2.66
2417 5190 5.097529 CCAATTTTGACATCCACAAGATCG 58.902 41.667 0.00 0.00 30.59 3.69
2628 5401 4.453819 GCAGTGAAGTGCTAGTTCAATTCT 59.546 41.667 10.49 1.04 39.07 2.40
2693 5467 8.616076 CACAAATCCTTCAAGCTAAGTATAAGG 58.384 37.037 0.00 0.00 35.80 2.69
2696 5470 7.552687 CACCACAAATCCTTCAAGCTAAGTATA 59.447 37.037 0.00 0.00 0.00 1.47
2697 5471 6.375455 CACCACAAATCCTTCAAGCTAAGTAT 59.625 38.462 0.00 0.00 0.00 2.12
2713 5487 7.787028 ACTGTTGGTTTTATAACACCACAAAT 58.213 30.769 20.63 11.20 43.02 2.32
2731 5505 1.101049 AGCGGTTGTTGGACTGTTGG 61.101 55.000 0.00 0.00 0.00 3.77
2737 5511 1.264288 CTTCTTCAGCGGTTGTTGGAC 59.736 52.381 0.00 0.00 0.00 4.02
2776 5550 7.116376 TGTCGAGTCAAAATCATAGTGTTTCTC 59.884 37.037 0.00 0.00 0.00 2.87
2813 5587 2.798499 CGGTATCTGTAAAGACCTGGCG 60.798 54.545 0.00 0.00 0.00 5.69
3118 5892 3.430042 ACAGCAATTCTCCATGACAGT 57.570 42.857 0.00 0.00 0.00 3.55
3353 6127 3.770388 GGGAGTCTCTTGGCTAAAGTACT 59.230 47.826 0.00 0.00 36.52 2.73
3414 6188 0.037697 TGCACACCTACTAACCAGCG 60.038 55.000 0.00 0.00 0.00 5.18
3456 6230 1.571773 ATCCTTGGGTAGTGGGGCAC 61.572 60.000 0.00 0.00 34.10 5.01
3457 6231 0.849094 AATCCTTGGGTAGTGGGGCA 60.849 55.000 0.00 0.00 0.00 5.36
3458 6232 0.106669 GAATCCTTGGGTAGTGGGGC 60.107 60.000 0.00 0.00 0.00 5.80
3459 6233 1.212935 CAGAATCCTTGGGTAGTGGGG 59.787 57.143 0.00 0.00 0.00 4.96
3460 6234 1.408822 GCAGAATCCTTGGGTAGTGGG 60.409 57.143 0.00 0.00 0.00 4.61
3461 6235 1.281867 TGCAGAATCCTTGGGTAGTGG 59.718 52.381 0.00 0.00 0.00 4.00
3462 6236 2.787473 TGCAGAATCCTTGGGTAGTG 57.213 50.000 0.00 0.00 0.00 2.74
3463 6237 2.025887 CCTTGCAGAATCCTTGGGTAGT 60.026 50.000 0.00 0.00 0.00 2.73
3464 6238 2.648059 CCTTGCAGAATCCTTGGGTAG 58.352 52.381 0.00 0.00 0.00 3.18
3465 6239 1.340991 GCCTTGCAGAATCCTTGGGTA 60.341 52.381 0.00 0.00 0.00 3.69
3466 6240 0.613012 GCCTTGCAGAATCCTTGGGT 60.613 55.000 0.00 0.00 0.00 4.51
3467 6241 0.324091 AGCCTTGCAGAATCCTTGGG 60.324 55.000 0.00 0.00 0.00 4.12
3468 6242 2.425143 TAGCCTTGCAGAATCCTTGG 57.575 50.000 0.00 0.00 0.00 3.61
3469 6243 2.098770 GCTTAGCCTTGCAGAATCCTTG 59.901 50.000 0.00 0.00 0.00 3.61
3470 6244 2.373224 GCTTAGCCTTGCAGAATCCTT 58.627 47.619 0.00 0.00 0.00 3.36
3471 6245 1.409381 GGCTTAGCCTTGCAGAATCCT 60.409 52.381 17.16 0.00 46.69 3.24
3472 6246 1.028130 GGCTTAGCCTTGCAGAATCC 58.972 55.000 17.16 0.00 46.69 3.01
3490 6264 0.762461 CCTCCTTCCTGCCTCCTAGG 60.762 65.000 0.82 0.82 38.80 3.02
3491 6265 1.406860 GCCTCCTTCCTGCCTCCTAG 61.407 65.000 0.00 0.00 0.00 3.02
3492 6266 1.383248 GCCTCCTTCCTGCCTCCTA 60.383 63.158 0.00 0.00 0.00 2.94
3493 6267 2.690510 GCCTCCTTCCTGCCTCCT 60.691 66.667 0.00 0.00 0.00 3.69
3494 6268 3.803162 GGCCTCCTTCCTGCCTCC 61.803 72.222 0.00 0.00 42.01 4.30
3495 6269 2.549169 CTTGGCCTCCTTCCTGCCTC 62.549 65.000 3.32 0.00 45.56 4.70
3507 6281 4.929807 CCAACAAGGACTTGGCCT 57.070 55.556 15.72 0.00 44.45 5.19
3604 6378 3.429881 GCATGCTAAAGTGGAAACAAAGC 59.570 43.478 11.37 0.00 46.06 3.51
3744 6523 1.629861 TCTCATGCATGTTGAGGTGGA 59.370 47.619 25.43 9.56 40.80 4.02
4019 6901 5.703592 TGTGGCGGGAATATGTTGTAATATC 59.296 40.000 0.00 0.00 0.00 1.63
4065 6950 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
4066 6951 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
4067 6952 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
4068 6953 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
4069 6954 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
4117 7002 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
4118 7003 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
4119 7004 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
4120 7005 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
4121 7006 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
4122 7007 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4127 7012 9.683870 CTAGATACTCCCTCCGTAAACTAATAT 57.316 37.037 0.00 0.00 0.00 1.28
4128 7013 8.664079 ACTAGATACTCCCTCCGTAAACTAATA 58.336 37.037 0.00 0.00 0.00 0.98
4129 7014 7.525165 ACTAGATACTCCCTCCGTAAACTAAT 58.475 38.462 0.00 0.00 0.00 1.73
4130 7015 6.904626 ACTAGATACTCCCTCCGTAAACTAA 58.095 40.000 0.00 0.00 0.00 2.24
4131 7016 6.506538 ACTAGATACTCCCTCCGTAAACTA 57.493 41.667 0.00 0.00 0.00 2.24
4132 7017 5.385628 ACTAGATACTCCCTCCGTAAACT 57.614 43.478 0.00 0.00 0.00 2.66
4133 7018 7.094420 GGAATACTAGATACTCCCTCCGTAAAC 60.094 44.444 0.00 0.00 0.00 2.01
4134 7019 6.944862 GGAATACTAGATACTCCCTCCGTAAA 59.055 42.308 0.00 0.00 0.00 2.01
4135 7020 6.274200 AGGAATACTAGATACTCCCTCCGTAA 59.726 42.308 0.00 0.00 0.00 3.18
4136 7021 5.789575 AGGAATACTAGATACTCCCTCCGTA 59.210 44.000 0.00 0.00 0.00 4.02
4137 7022 4.602732 AGGAATACTAGATACTCCCTCCGT 59.397 45.833 0.00 0.00 0.00 4.69
4138 7023 5.182169 AGGAATACTAGATACTCCCTCCG 57.818 47.826 0.00 0.00 0.00 4.63
4139 7024 7.931046 TCTTAGGAATACTAGATACTCCCTCC 58.069 42.308 0.00 0.00 32.16 4.30
4140 7025 9.810870 TTTCTTAGGAATACTAGATACTCCCTC 57.189 37.037 0.00 0.00 32.16 4.30
4189 7074 2.227149 TGACATGCTTGCATGTTGAGAC 59.773 45.455 32.76 22.84 44.88 3.36
4212 7097 5.116882 GGTCACCCTATTCATAGTTGTGAC 58.883 45.833 23.32 23.32 46.69 3.67
4327 7217 7.164230 AGAATAATTAAATGAACACCCGCAA 57.836 32.000 0.00 0.00 0.00 4.85
4328 7218 6.767524 AGAATAATTAAATGAACACCCGCA 57.232 33.333 0.00 0.00 0.00 5.69
4329 7219 9.744468 AAATAGAATAATTAAATGAACACCCGC 57.256 29.630 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.