Multiple sequence alignment - TraesCS6B01G377900

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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 TraesCS6B01G377900 chr6B 100.000 3749 0 0 1 3749 653003802 653007550 0.000000e+00 6924.0
1 TraesCS6B01G377900 chr6B 77.615 956 167 31 1436 2372 7901625 7900698 1.530000e-148 536.0
2 TraesCS6B01G377900 chr6B 77.223 922 156 31 1436 2339 7823729 7822844 1.210000e-134 490.0
3 TraesCS6B01G377900 chr6B 77.031 923 156 32 1436 2345 8418318 8419197 2.620000e-131 479.0
4 TraesCS6B01G377900 chr6B 76.763 241 47 5 1052 1292 8417874 8418105 3.930000e-25 126.0
5 TraesCS6B01G377900 chr6D 91.648 1748 94 20 2031 3749 432877714 432879438 0.000000e+00 2372.0
6 TraesCS6B01G377900 chr6D 93.645 598 30 1 1436 2033 432876819 432877408 0.000000e+00 887.0
7 TraesCS6B01G377900 chr6D 90.174 631 49 10 813 1439 432876129 432876750 0.000000e+00 809.0
8 TraesCS6B01G377900 chr6D 91.200 500 31 9 2992 3483 432882156 432882650 0.000000e+00 667.0
9 TraesCS6B01G377900 chr6D 77.991 936 153 32 1436 2357 4281966 4281070 4.260000e-149 538.0
10 TraesCS6B01G377900 chr6D 77.754 926 152 30 1436 2345 4638339 4639226 1.540000e-143 520.0
11 TraesCS6B01G377900 chr6D 76.049 977 181 34 1436 2388 4055285 4054338 3.410000e-125 459.0
12 TraesCS6B01G377900 chr6D 78.049 451 74 16 1436 1867 4642893 4643337 1.030000e-65 261.0
13 TraesCS6B01G377900 chr6D 94.815 135 3 3 3617 3749 432883048 432883180 1.360000e-49 207.0
14 TraesCS6B01G377900 chr6D 81.250 176 31 1 2403 2578 3978113 3977940 1.400000e-29 141.0
15 TraesCS6B01G377900 chr6D 80.741 135 19 6 2665 2795 3822822 3822691 8.570000e-17 99.0
16 TraesCS6B01G377900 chr6A 92.605 933 37 6 2686 3598 578978602 578979522 0.000000e+00 1312.0
17 TraesCS6B01G377900 chr6A 79.052 907 139 28 1436 2330 2972714 2973581 3.250000e-160 575.0
18 TraesCS6B01G377900 chr6A 77.991 936 153 33 1436 2357 2730390 2729494 4.260000e-149 538.0
19 TraesCS6B01G377900 chr6A 77.754 926 149 37 1436 2339 3015363 3016253 2.000000e-142 516.0
20 TraesCS6B01G377900 chr6A 93.548 341 22 0 2272 2612 578978265 578978605 3.340000e-140 508.0
21 TraesCS6B01G377900 chr6A 79.045 377 64 6 1717 2093 2995485 2995846 1.040000e-60 244.0
22 TraesCS6B01G377900 chr6A 95.833 144 3 3 3609 3749 578979744 578979887 2.910000e-56 230.0
23 TraesCS6B01G377900 chr6A 78.214 280 58 2 1012 1288 3302994 3303273 3.850000e-40 176.0
24 TraesCS6B01G377900 chr6A 79.630 216 38 5 2401 2613 3613764 3613976 2.330000e-32 150.0
25 TraesCS6B01G377900 chr6A 78.241 216 41 5 2401 2613 3606055 3606267 2.350000e-27 134.0
26 TraesCS6B01G377900 chr6A 91.489 47 2 2 3410 3455 3312502 3312547 3.130000e-06 63.9
27 TraesCS6B01G377900 chr1D 90.435 805 68 8 1 801 420892779 420891980 0.000000e+00 1051.0
28 TraesCS6B01G377900 chr1D 73.490 811 175 26 3 802 346370056 346370837 1.720000e-68 270.0
29 TraesCS6B01G377900 chrUn 89.055 804 79 8 1 799 27389382 27390181 0.000000e+00 989.0
30 TraesCS6B01G377900 chrUn 78.602 701 123 14 1436 2131 51923649 51922971 4.450000e-119 438.0
31 TraesCS6B01G377900 chrUn 77.045 758 146 14 1436 2187 51908095 51908830 9.690000e-111 411.0
32 TraesCS6B01G377900 chrUn 77.045 758 146 14 1436 2187 290969281 290970016 9.690000e-111 411.0
33 TraesCS6B01G377900 chr1A 86.160 802 103 8 1 800 25836298 25837093 0.000000e+00 859.0
34 TraesCS6B01G377900 chr1A 88.060 603 66 6 200 800 435763995 435764593 0.000000e+00 710.0
35 TraesCS6B01G377900 chr1B 85.928 803 106 7 3 801 636556584 636555785 0.000000e+00 850.0
36 TraesCS6B01G377900 chr4D 79.743 701 126 13 1 694 35557787 35558478 9.350000e-136 494.0
37 TraesCS6B01G377900 chr4D 78.026 760 138 16 1436 2188 3224765 3224028 5.710000e-123 451.0
38 TraesCS6B01G377900 chr4A 78.486 753 134 14 1436 2182 602371683 602372413 5.670000e-128 468.0
39 TraesCS6B01G377900 chr5B 77.132 809 175 8 1 803 633300983 633301787 9.490000e-126 460.0
40 TraesCS6B01G377900 chr4B 76.953 768 146 17 1436 2195 2691888 2692632 3.490000e-110 409.0
41 TraesCS6B01G377900 chr4B 76.823 768 147 18 1436 2195 2703403 2704147 1.620000e-108 403.0
42 TraesCS6B01G377900 chr5D 75.155 809 167 25 3 801 390074562 390075346 2.140000e-92 350.0
43 TraesCS6B01G377900 chr2B 74.545 715 168 13 3 710 680866433 680865726 2.190000e-77 300.0
44 TraesCS6B01G377900 chr5A 77.299 511 104 10 297 800 671264451 671264956 1.320000e-74 291.0
45 TraesCS6B01G377900 chr5A 84.211 247 37 2 1 246 403754367 403754612 4.840000e-59 239.0


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 TraesCS6B01G377900 chr6B 653003802 653007550 3748 False 6924.000000 6924 100.000000 1 3749 1 chr6B.!!$F1 3748
1 TraesCS6B01G377900 chr6B 7900698 7901625 927 True 536.000000 536 77.615000 1436 2372 1 chr6B.!!$R2 936
2 TraesCS6B01G377900 chr6B 7822844 7823729 885 True 490.000000 490 77.223000 1436 2339 1 chr6B.!!$R1 903
3 TraesCS6B01G377900 chr6B 8417874 8419197 1323 False 302.500000 479 76.897000 1052 2345 2 chr6B.!!$F2 1293
4 TraesCS6B01G377900 chr6D 432876129 432883180 7051 False 988.400000 2372 92.296400 813 3749 5 chr6D.!!$F2 2936
5 TraesCS6B01G377900 chr6D 4281070 4281966 896 True 538.000000 538 77.991000 1436 2357 1 chr6D.!!$R4 921
6 TraesCS6B01G377900 chr6D 4054338 4055285 947 True 459.000000 459 76.049000 1436 2388 1 chr6D.!!$R3 952
7 TraesCS6B01G377900 chr6D 4638339 4643337 4998 False 390.500000 520 77.901500 1436 2345 2 chr6D.!!$F1 909
8 TraesCS6B01G377900 chr6A 578978265 578979887 1622 False 683.333333 1312 93.995333 2272 3749 3 chr6A.!!$F8 1477
9 TraesCS6B01G377900 chr6A 2972714 2973581 867 False 575.000000 575 79.052000 1436 2330 1 chr6A.!!$F1 894
10 TraesCS6B01G377900 chr6A 2729494 2730390 896 True 538.000000 538 77.991000 1436 2357 1 chr6A.!!$R1 921
11 TraesCS6B01G377900 chr6A 3015363 3016253 890 False 516.000000 516 77.754000 1436 2339 1 chr6A.!!$F3 903
12 TraesCS6B01G377900 chr1D 420891980 420892779 799 True 1051.000000 1051 90.435000 1 801 1 chr1D.!!$R1 800
13 TraesCS6B01G377900 chr1D 346370056 346370837 781 False 270.000000 270 73.490000 3 802 1 chr1D.!!$F1 799
14 TraesCS6B01G377900 chrUn 27389382 27390181 799 False 989.000000 989 89.055000 1 799 1 chrUn.!!$F1 798
15 TraesCS6B01G377900 chrUn 51922971 51923649 678 True 438.000000 438 78.602000 1436 2131 1 chrUn.!!$R1 695
16 TraesCS6B01G377900 chrUn 51908095 51908830 735 False 411.000000 411 77.045000 1436 2187 1 chrUn.!!$F2 751
17 TraesCS6B01G377900 chrUn 290969281 290970016 735 False 411.000000 411 77.045000 1436 2187 1 chrUn.!!$F3 751
18 TraesCS6B01G377900 chr1A 25836298 25837093 795 False 859.000000 859 86.160000 1 800 1 chr1A.!!$F1 799
19 TraesCS6B01G377900 chr1A 435763995 435764593 598 False 710.000000 710 88.060000 200 800 1 chr1A.!!$F2 600
20 TraesCS6B01G377900 chr1B 636555785 636556584 799 True 850.000000 850 85.928000 3 801 1 chr1B.!!$R1 798
21 TraesCS6B01G377900 chr4D 35557787 35558478 691 False 494.000000 494 79.743000 1 694 1 chr4D.!!$F1 693
22 TraesCS6B01G377900 chr4D 3224028 3224765 737 True 451.000000 451 78.026000 1436 2188 1 chr4D.!!$R1 752
23 TraesCS6B01G377900 chr4A 602371683 602372413 730 False 468.000000 468 78.486000 1436 2182 1 chr4A.!!$F1 746
24 TraesCS6B01G377900 chr5B 633300983 633301787 804 False 460.000000 460 77.132000 1 803 1 chr5B.!!$F1 802
25 TraesCS6B01G377900 chr4B 2691888 2692632 744 False 409.000000 409 76.953000 1436 2195 1 chr4B.!!$F1 759
26 TraesCS6B01G377900 chr4B 2703403 2704147 744 False 403.000000 403 76.823000 1436 2195 1 chr4B.!!$F2 759
27 TraesCS6B01G377900 chr5D 390074562 390075346 784 False 350.000000 350 75.155000 3 801 1 chr5D.!!$F1 798
28 TraesCS6B01G377900 chr2B 680865726 680866433 707 True 300.000000 300 74.545000 3 710 1 chr2B.!!$R1 707
29 TraesCS6B01G377900 chr5A 671264451 671264956 505 False 291.000000 291 77.299000 297 800 1 chr5A.!!$F2 503

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
360 377 0.108281 GCTGTTTCTAGGACGGGGAC 60.108 60.0 7.73 0.0 0.00 4.46 F
1377 1410 0.109532 TGATCAACAAGTGCCGGGAA 59.890 50.0 2.18 0.0 0.00 3.97 F
1401 1434 1.037493 TTGTCGTATCGGATCCCCTG 58.963 55.0 6.06 0.0 0.00 4.45 F
1477 1582 1.821216 ATCGAGCCCGTTCAAATTGT 58.179 45.0 0.00 0.0 37.05 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1720 0.033228 CAAAGTGCATTCCCGGCAAA 59.967 50.000 0.00 0.00 43.91 3.68 R
2221 2683 0.865769 CACCGGACCGACAAAGAAAG 59.134 55.000 17.49 0.00 0.00 2.62 R
2231 2694 1.065273 CCGTAAGATCACCGGACCG 59.935 63.158 9.46 6.99 44.41 4.79 R
3328 4184 1.303074 CCACATCAGCAGCCACAGT 60.303 57.895 0.00 0.00 0.00 3.55 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
34 35 4.794003 GCTTTGTCAAATGAGGAACTGGTG 60.794 45.833 0.00 0.00 41.55 4.17
116 117 1.078426 CTCCCGCCGGATCAGTTTT 60.078 57.895 5.05 0.00 37.60 2.43
152 153 2.101783 CACTATGGGCAATTTGGAGCA 58.898 47.619 0.00 0.00 0.00 4.26
153 154 2.100252 CACTATGGGCAATTTGGAGCAG 59.900 50.000 0.00 0.00 0.00 4.24
154 155 1.068127 CTATGGGCAATTTGGAGCAGC 59.932 52.381 0.00 0.00 0.00 5.25
245 246 5.930135 ACTTGGCGGATATTGAGTTTCTAT 58.070 37.500 0.00 0.00 0.00 1.98
247 248 5.290493 TGGCGGATATTGAGTTTCTATGT 57.710 39.130 0.00 0.00 0.00 2.29
292 309 3.685435 CCGAATGCAAGGCCAAGT 58.315 55.556 5.01 0.00 0.00 3.16
360 377 0.108281 GCTGTTTCTAGGACGGGGAC 60.108 60.000 7.73 0.00 0.00 4.46
361 378 1.558233 CTGTTTCTAGGACGGGGACT 58.442 55.000 0.00 0.00 0.00 3.85
400 417 1.218316 GTGTAGGGACGAAGCAGGG 59.782 63.158 0.00 0.00 0.00 4.45
401 418 1.987855 TGTAGGGACGAAGCAGGGG 60.988 63.158 0.00 0.00 0.00 4.79
482 500 3.384789 AGACCATAGCAATACGAGAAGCA 59.615 43.478 0.00 0.00 0.00 3.91
520 538 9.993454 CCAAGATCTCTATATCAACAAGATGAA 57.007 33.333 0.00 0.00 37.57 2.57
706 726 5.273674 AGTACGCTTTATCCTTAGGGTTC 57.726 43.478 0.00 0.00 38.36 3.62
830 853 2.872245 TCCAAAAACTTCTGCTCGTCTG 59.128 45.455 0.00 0.00 0.00 3.51
832 855 1.230324 AAAACTTCTGCTCGTCTGCC 58.770 50.000 0.00 0.00 0.00 4.85
879 902 2.303676 GCGCCTCTCCTAAATCGCG 61.304 63.158 0.00 0.00 42.33 5.87
881 904 1.956678 GCCTCTCCTAAATCGCGGC 60.957 63.158 6.13 0.00 0.00 6.53
882 905 1.661821 CCTCTCCTAAATCGCGGCG 60.662 63.158 17.70 17.70 0.00 6.46
919 942 0.549169 TTCCCGTTCCCTCCCTTCAT 60.549 55.000 0.00 0.00 0.00 2.57
934 957 2.409975 CTTCATTGCAAGCCCAAGTTG 58.590 47.619 4.94 0.00 0.00 3.16
951 975 1.745653 GTTGCTGCTTCTATTCCCCAC 59.254 52.381 0.00 0.00 0.00 4.61
970 994 3.871594 CCACTTCGTTTCTTGACACTCTT 59.128 43.478 0.00 0.00 0.00 2.85
982 1006 9.996554 TTTCTTGACACTCTTTCTATATTCACA 57.003 29.630 0.00 0.00 0.00 3.58
1069 1102 2.123251 TCCTCCGGGAGATCCTGC 60.123 66.667 25.60 0.00 41.13 4.85
1071 1104 2.506061 CCTCCGGGAGATCCTGCTG 61.506 68.421 25.60 1.89 41.13 4.41
1094 1127 1.617536 TCCCTCTGCAGCCATCCTT 60.618 57.895 9.47 0.00 0.00 3.36
1157 1190 2.189521 CTCCGACCCCCAATTCCG 59.810 66.667 0.00 0.00 0.00 4.30
1172 1205 4.741781 CCGCAAACGCTTCCGCAG 62.742 66.667 0.00 0.00 38.22 5.18
1182 1215 1.746615 CTTCCGCAGACACCATGGG 60.747 63.158 18.09 7.72 0.00 4.00
1220 1253 3.431725 CTTCGCGGGGCCTGTTTC 61.432 66.667 15.16 0.00 0.00 2.78
1227 1260 1.301293 GGGGCCTGTTTCCAGAGAG 59.699 63.158 0.84 0.00 41.50 3.20
1231 1264 0.250467 GCCTGTTTCCAGAGAGCACA 60.250 55.000 0.00 0.00 41.50 4.57
1285 1318 4.749310 CTGCCGCACGCTTCTCCT 62.749 66.667 0.00 0.00 38.78 3.69
1332 1365 2.430367 GACCGCTGGGACTTGGTT 59.570 61.111 0.00 0.00 34.12 3.67
1341 1374 2.594592 GACTTGGTTGGCTGCCGT 60.595 61.111 14.98 4.09 0.00 5.68
1375 1408 1.308069 CCTGATCAACAAGTGCCGGG 61.308 60.000 2.18 0.00 0.00 5.73
1377 1410 0.109532 TGATCAACAAGTGCCGGGAA 59.890 50.000 2.18 0.00 0.00 3.97
1401 1434 1.037493 TTGTCGTATCGGATCCCCTG 58.963 55.000 6.06 0.00 0.00 4.45
1477 1582 1.821216 ATCGAGCCCGTTCAAATTGT 58.179 45.000 0.00 0.00 37.05 2.71
1575 1695 5.354054 TCTCGGCGACTACAAATAGTATC 57.646 43.478 4.99 0.00 41.98 2.24
1597 1720 5.706447 TCTGTAGTATAAGGTCCAGCATCT 58.294 41.667 0.00 0.00 0.00 2.90
1776 1905 2.031683 CCTCGCTGTTTTGTCGAAACTT 59.968 45.455 15.27 0.00 46.25 2.66
1857 1986 2.029918 GCAGAAAACCATTCCACTGGAC 60.030 50.000 0.00 0.00 39.73 4.02
1889 2019 2.244695 ACGGAGAATGTGTAGTGACCA 58.755 47.619 0.00 0.00 0.00 4.02
1890 2020 2.631062 ACGGAGAATGTGTAGTGACCAA 59.369 45.455 0.00 0.00 0.00 3.67
1891 2021 3.070446 ACGGAGAATGTGTAGTGACCAAA 59.930 43.478 0.00 0.00 0.00 3.28
1892 2022 4.062293 CGGAGAATGTGTAGTGACCAAAA 58.938 43.478 0.00 0.00 0.00 2.44
1893 2023 4.513692 CGGAGAATGTGTAGTGACCAAAAA 59.486 41.667 0.00 0.00 0.00 1.94
1894 2024 5.334105 CGGAGAATGTGTAGTGACCAAAAAG 60.334 44.000 0.00 0.00 0.00 2.27
1895 2025 5.048713 GGAGAATGTGTAGTGACCAAAAAGG 60.049 44.000 0.00 0.00 45.67 3.11
1896 2026 4.827284 AGAATGTGTAGTGACCAAAAAGGG 59.173 41.667 0.00 0.00 43.89 3.95
2097 2541 7.873739 ATCTAGTACATTGCAAAAGCAAAAC 57.126 32.000 1.71 6.34 33.20 2.43
2099 2543 5.971895 AGTACATTGCAAAAGCAAAACAG 57.028 34.783 1.71 1.28 33.20 3.16
2100 2544 4.810491 AGTACATTGCAAAAGCAAAACAGG 59.190 37.500 1.71 0.00 33.20 4.00
2101 2545 2.944349 ACATTGCAAAAGCAAAACAGGG 59.056 40.909 1.71 0.00 33.20 4.45
2111 2558 3.790126 AGCAAAACAGGGGTCCATTTAT 58.210 40.909 0.00 0.00 0.00 1.40
2231 2694 9.736023 ATACATTGAGTTGTTTCTTTCTTTGTC 57.264 29.630 0.00 0.00 0.00 3.18
2330 2799 0.961019 TTGTTGTCTGGCCATTGCTC 59.039 50.000 5.51 0.00 37.74 4.26
2347 2816 6.498304 CATTGCTCAATGGTAACTTATGGTC 58.502 40.000 13.31 0.00 43.25 4.02
2361 2830 6.388619 ACTTATGGTCCTGTCCTTGTATTT 57.611 37.500 0.00 0.00 0.00 1.40
2398 2869 5.584253 AACTGGCAGTAGTATCAGTAGTG 57.416 43.478 22.37 0.00 39.26 2.74
2399 2870 4.601084 ACTGGCAGTAGTATCAGTAGTGT 58.399 43.478 20.61 0.00 38.52 3.55
2419 2892 3.563808 TGTGTGTGTGCTTAAGGATTGAC 59.436 43.478 4.29 1.13 0.00 3.18
2421 2894 4.994852 GTGTGTGTGCTTAAGGATTGACTA 59.005 41.667 4.29 0.00 0.00 2.59
2423 2896 4.392138 GTGTGTGCTTAAGGATTGACTACC 59.608 45.833 4.29 0.00 0.00 3.18
2555 3261 5.354234 GGGGATATATGTGGCTTCATTTACG 59.646 44.000 0.00 0.00 0.00 3.18
2561 3267 5.574891 ATGTGGCTTCATTTACGCATTTA 57.425 34.783 0.00 0.00 30.59 1.40
2608 3314 6.071391 CCTTTTGCCCTCAAGTTACATTACAT 60.071 38.462 0.00 0.00 33.12 2.29
2610 3316 5.435686 TGCCCTCAAGTTACATTACATCT 57.564 39.130 0.00 0.00 0.00 2.90
2612 3318 6.953101 TGCCCTCAAGTTACATTACATCTTA 58.047 36.000 0.00 0.00 0.00 2.10
2613 3319 6.821665 TGCCCTCAAGTTACATTACATCTTAC 59.178 38.462 0.00 0.00 0.00 2.34
2615 3321 7.224949 GCCCTCAAGTTACATTACATCTTACTC 59.775 40.741 0.00 0.00 0.00 2.59
2616 3322 8.258007 CCCTCAAGTTACATTACATCTTACTCA 58.742 37.037 0.00 0.00 0.00 3.41
2908 3642 9.753674 AATGGGTTGATAATCTAGAAAGTTCAA 57.246 29.630 0.00 1.83 0.00 2.69
2936 3671 0.182061 TCTGATGGAGGGCATTGAGC 59.818 55.000 0.00 0.00 44.65 4.26
2993 3728 6.607600 ACAGTAGAAGTTGATAGTCCATAGCA 59.392 38.462 0.00 0.00 0.00 3.49
3045 3786 4.884164 GCTAGGATGATAGCCAGTTTTGTT 59.116 41.667 0.00 0.00 41.96 2.83
3227 3976 9.689976 TGAGTTGTATAAATTGGTTTTGACATG 57.310 29.630 0.00 0.00 29.69 3.21
3250 3999 5.163513 GTGGCATTTATTGTTCTTCAGGTG 58.836 41.667 0.00 0.00 0.00 4.00
3324 4180 2.670509 GCTGCATGTCCTTCAGCTTTTC 60.671 50.000 13.16 0.00 46.93 2.29
3328 4184 5.744171 TGCATGTCCTTCAGCTTTTCTATA 58.256 37.500 0.00 0.00 0.00 1.31
3454 4311 8.448615 GGATTTAGTGTGTAATTCGCTAACTTT 58.551 33.333 0.00 0.00 37.53 2.66
3566 4441 5.130975 TGCCTGGATCTGTCAGTGTATTAAT 59.869 40.000 0.00 0.00 0.00 1.40
3676 5431 4.160626 AGCTAAATCGCTCTCCACTAAAGT 59.839 41.667 0.00 0.00 34.57 2.66
3677 5432 4.504826 GCTAAATCGCTCTCCACTAAAGTC 59.495 45.833 0.00 0.00 0.00 3.01
3685 5441 2.300152 TCTCCACTAAAGTCAGGCACAG 59.700 50.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.555199 GTAGTCATGGTCATGTGCTCC 58.445 52.381 10.32 0.00 39.72 4.70
116 117 2.613026 AGTGTGACCGTCATCAACAA 57.387 45.000 4.13 0.00 0.00 2.83
152 153 0.538118 TGTATAACTTTCCGGCGGCT 59.462 50.000 23.83 5.29 0.00 5.52
153 154 1.263217 CATGTATAACTTTCCGGCGGC 59.737 52.381 23.83 3.99 0.00 6.53
154 155 2.800544 CTCATGTATAACTTTCCGGCGG 59.199 50.000 22.51 22.51 0.00 6.13
245 246 6.374417 AAGTGCCCTATCTTTCTTCTTACA 57.626 37.500 0.00 0.00 0.00 2.41
247 248 6.106673 CGAAAGTGCCCTATCTTTCTTCTTA 58.893 40.000 13.24 0.00 43.94 2.10
256 257 0.462759 GCTGCGAAAGTGCCCTATCT 60.463 55.000 0.00 0.00 0.00 1.98
263 264 1.512734 CATTCGGCTGCGAAAGTGC 60.513 57.895 10.06 0.00 0.00 4.40
272 273 2.552585 CTTGGCCTTGCATTCGGCTG 62.553 60.000 18.09 8.30 45.57 4.85
280 281 0.178967 TCCATGAACTTGGCCTTGCA 60.179 50.000 3.32 0.00 36.66 4.08
292 309 1.202758 GGTGGTGGCGATATCCATGAA 60.203 52.381 0.00 0.00 38.57 2.57
382 399 1.218316 CCCTGCTTCGTCCCTACAC 59.782 63.158 0.00 0.00 0.00 2.90
400 417 0.536006 CGATGCTCCAAGGAATCCCC 60.536 60.000 0.00 0.00 0.00 4.81
401 418 0.469917 TCGATGCTCCAAGGAATCCC 59.530 55.000 0.00 0.00 0.00 3.85
410 427 1.344438 AGAACAAGTGTCGATGCTCCA 59.656 47.619 0.00 0.00 0.00 3.86
520 538 1.473965 CCTTGCAGTCCGATGCTATGT 60.474 52.381 8.37 0.00 46.63 2.29
611 629 9.959749 AAAATGCACGAAGAAAAATTACTAGAA 57.040 25.926 0.00 0.00 0.00 2.10
629 648 8.552034 GTCCTATACTCATGACTAAAAATGCAC 58.448 37.037 0.00 0.00 0.00 4.57
724 744 1.306141 AAGATCTCCGGGCTGACCA 60.306 57.895 0.00 0.00 40.22 4.02
801 824 6.178607 AGCAGAAGTTTTTGGATGGATTTT 57.821 33.333 0.00 0.00 0.00 1.82
802 825 5.565439 CGAGCAGAAGTTTTTGGATGGATTT 60.565 40.000 0.00 0.00 0.00 2.17
803 826 4.082571 CGAGCAGAAGTTTTTGGATGGATT 60.083 41.667 0.00 0.00 0.00 3.01
804 827 3.441572 CGAGCAGAAGTTTTTGGATGGAT 59.558 43.478 0.00 0.00 0.00 3.41
805 828 2.813754 CGAGCAGAAGTTTTTGGATGGA 59.186 45.455 0.00 0.00 0.00 3.41
806 829 2.554032 ACGAGCAGAAGTTTTTGGATGG 59.446 45.455 0.00 0.00 0.00 3.51
807 830 3.499918 AGACGAGCAGAAGTTTTTGGATG 59.500 43.478 0.00 0.00 0.00 3.51
808 831 3.499918 CAGACGAGCAGAAGTTTTTGGAT 59.500 43.478 0.00 0.00 0.00 3.41
809 832 2.872245 CAGACGAGCAGAAGTTTTTGGA 59.128 45.455 0.00 0.00 0.00 3.53
810 833 2.603173 GCAGACGAGCAGAAGTTTTTGG 60.603 50.000 0.00 0.00 0.00 3.28
811 834 2.603173 GGCAGACGAGCAGAAGTTTTTG 60.603 50.000 0.00 0.00 35.83 2.44
812 835 1.604278 GGCAGACGAGCAGAAGTTTTT 59.396 47.619 0.00 0.00 35.83 1.94
813 836 1.230324 GGCAGACGAGCAGAAGTTTT 58.770 50.000 0.00 0.00 35.83 2.43
814 837 0.603975 GGGCAGACGAGCAGAAGTTT 60.604 55.000 0.00 0.00 35.83 2.66
815 838 1.004440 GGGCAGACGAGCAGAAGTT 60.004 57.895 0.00 0.00 35.83 2.66
816 839 2.659610 GGGCAGACGAGCAGAAGT 59.340 61.111 0.00 0.00 35.83 3.01
871 894 1.663388 ATCGATGCGCCGCGATTTA 60.663 52.632 23.28 4.94 44.00 1.40
872 895 2.967076 ATCGATGCGCCGCGATTT 60.967 55.556 23.28 8.56 44.00 2.17
879 902 4.005472 CGCCTGAATCGATGCGCC 62.005 66.667 13.82 0.00 40.58 6.53
882 905 1.156645 AAGCTCGCCTGAATCGATGC 61.157 55.000 0.00 0.00 35.25 3.91
919 942 1.442567 CAGCAACTTGGGCTTGCAA 59.557 52.632 11.15 0.00 45.48 4.08
934 957 2.293170 GAAGTGGGGAATAGAAGCAGC 58.707 52.381 0.00 0.00 0.00 5.25
935 958 2.093447 ACGAAGTGGGGAATAGAAGCAG 60.093 50.000 0.00 0.00 42.51 4.24
936 959 1.906574 ACGAAGTGGGGAATAGAAGCA 59.093 47.619 0.00 0.00 42.51 3.91
951 975 5.975410 AGAAAGAGTGTCAAGAAACGAAG 57.025 39.130 0.00 0.00 0.00 3.79
970 994 6.183360 GCTAGGGTTGGACTGTGAATATAGAA 60.183 42.308 0.00 0.00 0.00 2.10
982 1006 2.114616 CATCTGAGCTAGGGTTGGACT 58.885 52.381 0.00 0.00 0.00 3.85
1030 1063 3.760035 CTCGTCGTCCAGTGGGGG 61.760 72.222 9.92 1.33 37.22 5.40
1069 1102 4.834453 CTGCAGAGGGAGGCGCAG 62.834 72.222 8.42 0.00 45.17 5.18
1082 1115 2.586245 CGAGGAAGGATGGCTGCA 59.414 61.111 0.50 0.00 0.00 4.41
1172 1205 1.826385 CAGAGGTTTCCCATGGTGTC 58.174 55.000 11.73 0.00 0.00 3.67
1182 1215 1.448717 GCCGAGGAGCAGAGGTTTC 60.449 63.158 0.00 0.00 0.00 2.78
1220 1253 2.418471 GGAGTGAAGATGTGCTCTCTGG 60.418 54.545 0.38 0.00 31.03 3.86
1285 1318 1.303561 GGCTCTGTGGCATGGTCAA 60.304 57.895 0.00 0.00 41.37 3.18
1375 1408 3.550436 GGATCCGATACGACAACCTCTTC 60.550 52.174 0.00 0.00 0.00 2.87
1377 1410 1.955080 GGATCCGATACGACAACCTCT 59.045 52.381 0.00 0.00 0.00 3.69
1477 1582 4.200838 TGTCTCCATTGCGTATCAAGAA 57.799 40.909 0.00 0.00 38.22 2.52
1509 1623 0.179067 CCGAGTCGTAGAGAGAGCCT 60.179 60.000 12.31 0.00 36.95 4.58
1575 1695 6.412362 AAGATGCTGGACCTTATACTACAG 57.588 41.667 0.00 0.00 0.00 2.74
1597 1720 0.033228 CAAAGTGCATTCCCGGCAAA 59.967 50.000 0.00 0.00 43.91 3.68
1776 1905 6.617784 TGTTCCTCACCCATAATTGGATAGTA 59.382 38.462 0.00 0.00 46.92 1.82
1857 1986 3.687698 ACATTCTCCGTTTAAACATCCCG 59.312 43.478 18.07 3.85 0.00 5.14
1947 2077 3.118884 GGAGCATGAAGTTGCCAATCATT 60.119 43.478 0.00 0.00 43.83 2.57
2097 2541 7.280652 CAGCAAAATAAAATAAATGGACCCCTG 59.719 37.037 0.00 0.00 0.00 4.45
2099 2543 6.542005 CCAGCAAAATAAAATAAATGGACCCC 59.458 38.462 0.00 0.00 0.00 4.95
2100 2544 6.038161 GCCAGCAAAATAAAATAAATGGACCC 59.962 38.462 0.00 0.00 0.00 4.46
2101 2545 6.038161 GGCCAGCAAAATAAAATAAATGGACC 59.962 38.462 0.00 0.00 0.00 4.46
2111 2558 6.294473 TCAAATGAAGGCCAGCAAAATAAAA 58.706 32.000 5.01 0.00 0.00 1.52
2221 2683 0.865769 CACCGGACCGACAAAGAAAG 59.134 55.000 17.49 0.00 0.00 2.62
2231 2694 1.065273 CCGTAAGATCACCGGACCG 59.935 63.158 9.46 6.99 44.41 4.79
2270 2734 7.029563 CCTGTTCTAACATTAATGAACCAAGC 58.970 38.462 22.16 6.96 38.41 4.01
2330 2799 4.881850 GGACAGGACCATAAGTTACCATTG 59.118 45.833 0.00 0.00 0.00 2.82
2335 2804 5.161943 ACAAGGACAGGACCATAAGTTAC 57.838 43.478 0.00 0.00 0.00 2.50
2398 2869 3.815401 AGTCAATCCTTAAGCACACACAC 59.185 43.478 0.00 0.00 0.00 3.82
2399 2870 4.085357 AGTCAATCCTTAAGCACACACA 57.915 40.909 0.00 0.00 0.00 3.72
2419 2892 9.529325 TGAAGAACTGTTCATAAATATCGGTAG 57.471 33.333 21.50 0.00 31.31 3.18
2421 2894 8.041323 AGTGAAGAACTGTTCATAAATATCGGT 58.959 33.333 21.50 0.00 38.68 4.69
2485 3191 9.847224 AATAATCATTACCAAGTAACGAAGGAT 57.153 29.630 0.00 0.00 30.49 3.24
2561 3267 6.904626 AGGCTATCTTTTGTGACAAGGATAT 58.095 36.000 17.04 6.64 0.00 1.63
2608 3314 8.662141 GCAAACGGTTATATTTTCTGAGTAAGA 58.338 33.333 0.00 0.00 0.00 2.10
2610 3316 8.325421 TGCAAACGGTTATATTTTCTGAGTAA 57.675 30.769 0.00 0.00 0.00 2.24
2612 3318 6.653320 TCTGCAAACGGTTATATTTTCTGAGT 59.347 34.615 0.00 0.00 0.00 3.41
2613 3319 7.072177 TCTGCAAACGGTTATATTTTCTGAG 57.928 36.000 0.00 0.00 0.00 3.35
2615 3321 7.218773 CACATCTGCAAACGGTTATATTTTCTG 59.781 37.037 0.00 0.00 0.00 3.02
2616 3322 7.120579 TCACATCTGCAAACGGTTATATTTTCT 59.879 33.333 0.00 0.00 0.00 2.52
2622 3339 4.570930 TGTCACATCTGCAAACGGTTATA 58.429 39.130 0.00 0.00 0.00 0.98
2628 3345 7.643528 AGTATATATGTCACATCTGCAAACG 57.356 36.000 0.00 0.00 0.00 3.60
2936 3671 1.523758 GAGGCAACCACTAGTGTTGG 58.476 55.000 25.79 13.42 37.17 3.77
2983 3718 6.466885 AGTTCGTAGTTTATGCTATGGACT 57.533 37.500 1.53 1.53 40.30 3.85
2985 3720 9.256477 CATTTAGTTCGTAGTTTATGCTATGGA 57.744 33.333 0.00 0.00 0.00 3.41
3018 3753 4.550076 ACTGGCTATCATCCTAGCAATC 57.450 45.455 5.55 0.00 44.84 2.67
3045 3786 5.604231 AGATGAATCATCCCAGCACTAGTAA 59.396 40.000 18.69 0.00 41.36 2.24
3227 3976 5.163513 CACCTGAAGAACAATAAATGCCAC 58.836 41.667 0.00 0.00 0.00 5.01
3250 3999 4.740268 ACAAACCGAAGAAAACTCCAAAC 58.260 39.130 0.00 0.00 0.00 2.93
3324 4180 3.129109 CACATCAGCAGCCACAGTATAG 58.871 50.000 0.00 0.00 0.00 1.31
3328 4184 1.303074 CCACATCAGCAGCCACAGT 60.303 57.895 0.00 0.00 0.00 3.55
3356 4212 6.564709 TTCTGCTCCATATATTGTCAATGC 57.435 37.500 8.39 1.96 0.00 3.56
3676 5431 0.685097 GGTAACTGACCTGTGCCTGA 59.315 55.000 0.00 0.00 45.89 3.86
3677 5432 3.233355 GGTAACTGACCTGTGCCTG 57.767 57.895 0.00 0.00 45.89 4.85


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

AutoCloner maintained by Alex Coulton.