Multiple sequence alignment - TraesCS1B01G431900

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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 TraesCS1B01G431900 chr1B 100.000 3223 0 0 1 3223 656423815 656420593 0.000000e+00 5952.0
1 TraesCS1B01G431900 chr1B 91.480 939 66 4 1478 2405 598446729 598445794 0.000000e+00 1279.0
2 TraesCS1B01G431900 chr1B 92.000 150 11 1 2367 2515 598445770 598445621 3.260000e-50 209.0
3 TraesCS1B01G431900 chr4A 88.680 2447 150 43 3 2398 598235674 598238044 0.000000e+00 2867.0
4 TraesCS1B01G431900 chr4A 93.289 149 8 2 2368 2515 598238076 598238223 5.410000e-53 219.0
5 TraesCS1B01G431900 chr6D 96.761 710 19 3 2515 3223 348105728 348105022 0.000000e+00 1181.0
6 TraesCS1B01G431900 chr6D 96.353 713 23 2 2512 3223 460401158 460400448 0.000000e+00 1170.0
7 TraesCS1B01G431900 chr5D 96.503 715 23 2 2511 3223 438665525 438664811 0.000000e+00 1181.0
8 TraesCS1B01G431900 chr5D 100.000 49 0 0 218 266 416873074 416873122 1.230000e-14 91.6
9 TraesCS1B01G431900 chr4D 96.751 708 23 0 2511 3218 508484209 508484916 0.000000e+00 1181.0
10 TraesCS1B01G431900 chr2D 96.197 710 24 2 2517 3223 394803442 394802733 0.000000e+00 1158.0
11 TraesCS1B01G431900 chr2D 85.386 479 49 12 1233 1694 587257904 587257430 8.090000e-131 477.0
12 TraesCS1B01G431900 chr2D 75.385 650 131 18 1611 2249 641190114 641190745 1.460000e-73 287.0
13 TraesCS1B01G431900 chr3B 95.258 717 30 3 2508 3223 458400796 458401509 0.000000e+00 1133.0
14 TraesCS1B01G431900 chr3B 95.077 711 32 2 2514 3223 752327808 752327100 0.000000e+00 1116.0
15 TraesCS1B01G431900 chr7B 95.467 706 32 0 2513 3218 293065477 293064772 0.000000e+00 1127.0
16 TraesCS1B01G431900 chr5B 95.231 713 33 1 2512 3223 710688789 710689501 0.000000e+00 1127.0
17 TraesCS1B01G431900 chr2A 80.890 1371 213 35 949 2299 732599374 732600715 0.000000e+00 1035.0
18 TraesCS1B01G431900 chr2A 79.598 1392 218 44 946 2299 732853340 732851977 0.000000e+00 937.0
19 TraesCS1B01G431900 chr2A 78.855 1031 165 27 1281 2294 722072241 722071247 0.000000e+00 647.0
20 TraesCS1B01G431900 chr2B 80.245 1387 211 40 949 2299 727084904 727086263 0.000000e+00 985.0
21 TraesCS1B01G431900 chr2B 79.986 1389 219 39 946 2299 727206457 727205093 0.000000e+00 970.0
22 TraesCS1B01G431900 chr2B 79.391 1150 175 33 1165 2294 709784449 709783342 0.000000e+00 754.0
23 TraesCS1B01G431900 chr1D 95.025 402 17 2 1 401 472291450 472291051 2.110000e-176 628.0


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 TraesCS1B01G431900 chr1B 656420593 656423815 3222 True 5952 5952 100.0000 1 3223 1 chr1B.!!$R1 3222
1 TraesCS1B01G431900 chr1B 598445621 598446729 1108 True 744 1279 91.7400 1478 2515 2 chr1B.!!$R2 1037
2 TraesCS1B01G431900 chr4A 598235674 598238223 2549 False 1543 2867 90.9845 3 2515 2 chr4A.!!$F1 2512
3 TraesCS1B01G431900 chr6D 348105022 348105728 706 True 1181 1181 96.7610 2515 3223 1 chr6D.!!$R1 708
4 TraesCS1B01G431900 chr6D 460400448 460401158 710 True 1170 1170 96.3530 2512 3223 1 chr6D.!!$R2 711
5 TraesCS1B01G431900 chr5D 438664811 438665525 714 True 1181 1181 96.5030 2511 3223 1 chr5D.!!$R1 712
6 TraesCS1B01G431900 chr4D 508484209 508484916 707 False 1181 1181 96.7510 2511 3218 1 chr4D.!!$F1 707
7 TraesCS1B01G431900 chr2D 394802733 394803442 709 True 1158 1158 96.1970 2517 3223 1 chr2D.!!$R1 706
8 TraesCS1B01G431900 chr2D 641190114 641190745 631 False 287 287 75.3850 1611 2249 1 chr2D.!!$F1 638
9 TraesCS1B01G431900 chr3B 458400796 458401509 713 False 1133 1133 95.2580 2508 3223 1 chr3B.!!$F1 715
10 TraesCS1B01G431900 chr3B 752327100 752327808 708 True 1116 1116 95.0770 2514 3223 1 chr3B.!!$R1 709
11 TraesCS1B01G431900 chr7B 293064772 293065477 705 True 1127 1127 95.4670 2513 3218 1 chr7B.!!$R1 705
12 TraesCS1B01G431900 chr5B 710688789 710689501 712 False 1127 1127 95.2310 2512 3223 1 chr5B.!!$F1 711
13 TraesCS1B01G431900 chr2A 732599374 732600715 1341 False 1035 1035 80.8900 949 2299 1 chr2A.!!$F1 1350
14 TraesCS1B01G431900 chr2A 732851977 732853340 1363 True 937 937 79.5980 946 2299 1 chr2A.!!$R2 1353
15 TraesCS1B01G431900 chr2A 722071247 722072241 994 True 647 647 78.8550 1281 2294 1 chr2A.!!$R1 1013
16 TraesCS1B01G431900 chr2B 727084904 727086263 1359 False 985 985 80.2450 949 2299 1 chr2B.!!$F1 1350
17 TraesCS1B01G431900 chr2B 727205093 727206457 1364 True 970 970 79.9860 946 2299 1 chr2B.!!$R2 1353
18 TraesCS1B01G431900 chr2B 709783342 709784449 1107 True 754 754 79.3910 1165 2294 1 chr2B.!!$R1 1129

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
846 858 0.027979 CGGTAATGTGCCGCAGAATG 59.972 55.0 0.00 0.00 42.82 2.67 F
1088 1109 0.179153 GGATGCGGCTTCTTCAAAGC 60.179 55.0 14.51 1.16 42.30 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 1901 0.107508 ATTGTGGCCTGGATCGTCTG 60.108 55.0 3.32 0.0 0.00 3.51 R
2596 2736 0.918983 TCCCTTGTATCTGCCTTGGG 59.081 55.0 0.00 0.0 34.76 4.12 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
41 42 2.901042 GGTGACGGATGGACTCCC 59.099 66.667 0.00 0.00 41.49 4.30
42 43 2.732619 GGTGACGGATGGACTCCCC 61.733 68.421 0.00 0.00 41.49 4.81
46 47 2.758327 CGGATGGACTCCCCGTGA 60.758 66.667 4.93 0.00 41.49 4.35
47 48 2.901042 GGATGGACTCCCCGTGAC 59.099 66.667 0.00 0.00 38.19 3.67
48 49 2.494918 GATGGACTCCCCGTGACG 59.505 66.667 0.00 0.00 37.93 4.35
58 59 4.796231 CCGTGACGGCTAGCGCTT 62.796 66.667 18.68 0.00 41.17 4.68
62 63 3.865830 GACGGCTAGCGCTTTGGC 61.866 66.667 18.68 20.23 36.09 4.52
73 74 3.107017 GCTTTGGCGATCGCTTTTT 57.893 47.368 36.25 0.00 41.60 1.94
90 91 8.845942 TCGCTTTTTAAGAAAGAAAACTAACC 57.154 30.769 11.78 0.00 0.00 2.85
121 122 2.705658 TCAGGTGGAAACAGACTCACAT 59.294 45.455 0.00 0.00 44.46 3.21
129 130 6.818644 GTGGAAACAGACTCACATACATATGT 59.181 38.462 13.93 13.93 44.53 2.29
141 142 6.233905 ACATACATATGTGCAGAAGGTACA 57.766 37.500 18.81 0.00 44.66 2.90
142 143 6.649155 ACATACATATGTGCAGAAGGTACAA 58.351 36.000 18.81 0.00 45.44 2.41
143 144 7.109501 ACATACATATGTGCAGAAGGTACAAA 58.890 34.615 18.81 0.00 45.44 2.83
144 145 7.280876 ACATACATATGTGCAGAAGGTACAAAG 59.719 37.037 18.81 0.00 45.44 2.77
145 146 5.560724 ACATATGTGCAGAAGGTACAAAGT 58.439 37.500 7.78 0.00 45.44 2.66
146 147 6.707290 ACATATGTGCAGAAGGTACAAAGTA 58.293 36.000 7.78 0.00 45.44 2.24
147 148 7.338710 ACATATGTGCAGAAGGTACAAAGTAT 58.661 34.615 7.78 0.00 45.44 2.12
148 149 7.280876 ACATATGTGCAGAAGGTACAAAGTATG 59.719 37.037 7.78 0.00 45.44 2.39
149 150 5.222079 TGTGCAGAAGGTACAAAGTATGA 57.778 39.130 0.00 0.00 39.28 2.15
150 151 5.616270 TGTGCAGAAGGTACAAAGTATGAA 58.384 37.500 0.00 0.00 39.28 2.57
151 152 5.468746 TGTGCAGAAGGTACAAAGTATGAAC 59.531 40.000 0.00 0.00 39.28 3.18
152 153 5.701290 GTGCAGAAGGTACAAAGTATGAACT 59.299 40.000 0.00 0.00 32.53 3.01
153 154 6.872020 GTGCAGAAGGTACAAAGTATGAACTA 59.128 38.462 0.00 0.00 31.57 2.24
154 155 6.872020 TGCAGAAGGTACAAAGTATGAACTAC 59.128 38.462 0.00 0.00 33.75 2.73
155 156 6.034683 GCAGAAGGTACAAAGTATGAACTACG 59.965 42.308 0.00 0.00 33.75 3.51
182 183 2.708325 GCCCCAGAAGGAATCATCTACT 59.292 50.000 0.00 0.00 38.24 2.57
187 188 5.221422 CCCAGAAGGAATCATCTACTGAGAC 60.221 48.000 0.00 0.00 35.67 3.36
265 266 6.113411 TCCTAGAACTTGTAATAAGCTTGCC 58.887 40.000 9.86 0.00 0.00 4.52
346 347 1.072965 GTCAGGATATGGCTTGAGGGG 59.927 57.143 0.00 0.00 0.00 4.79
353 354 1.803453 ATGGCTTGAGGGGCTTCCAA 61.803 55.000 0.00 0.00 38.24 3.53
356 357 1.269958 GCTTGAGGGGCTTCCAAATT 58.730 50.000 0.00 0.00 38.24 1.82
366 367 5.488561 AGGGGCTTCCAAATTTGATGTAATT 59.511 36.000 19.86 0.00 38.24 1.40
376 377 7.393327 CAAATTTGATGTAATTGTTCGGATGC 58.607 34.615 13.08 0.00 0.00 3.91
419 425 4.503296 GGTGTATAGAATCGGCTGTTCCAT 60.503 45.833 0.00 0.00 34.01 3.41
453 459 2.249309 ATCTCCTAAACTGGGTCGGT 57.751 50.000 0.00 0.00 0.00 4.69
473 481 2.370189 GTCTGGGCTGAGTATATGGCTT 59.630 50.000 0.00 0.00 0.00 4.35
498 508 5.749109 GCAAGATATATAATCCCGTCTTCCG 59.251 44.000 0.00 0.00 0.00 4.30
507 517 0.893447 CCCGTCTTCCGTAGAAACCT 59.107 55.000 0.00 0.00 33.81 3.50
509 519 2.334838 CCGTCTTCCGTAGAAACCTTG 58.665 52.381 0.00 0.00 33.81 3.61
532 544 4.700213 GGATCCAATCTGGTCGAAAGAAAA 59.300 41.667 6.95 0.00 45.01 2.29
547 559 0.802494 GAAAATCGCCGGAAGCAGAA 59.198 50.000 5.05 0.00 44.04 3.02
548 560 0.804989 AAAATCGCCGGAAGCAGAAG 59.195 50.000 5.05 0.00 44.04 2.85
550 562 0.741221 AATCGCCGGAAGCAGAAGAC 60.741 55.000 5.05 0.00 44.04 3.01
557 569 0.390472 GGAAGCAGAAGACCACCGAG 60.390 60.000 0.00 0.00 0.00 4.63
558 570 0.603569 GAAGCAGAAGACCACCGAGA 59.396 55.000 0.00 0.00 0.00 4.04
559 571 0.605589 AAGCAGAAGACCACCGAGAG 59.394 55.000 0.00 0.00 0.00 3.20
575 587 2.552315 CGAGAGGAGGAGATAGACAAGC 59.448 54.545 0.00 0.00 0.00 4.01
576 588 2.552315 GAGAGGAGGAGATAGACAAGCG 59.448 54.545 0.00 0.00 0.00 4.68
606 618 1.067582 CTACCGAGGCGATTGGTCC 59.932 63.158 2.82 0.00 42.71 4.46
616 628 1.227853 GATTGGTCCGGCGGCTTAT 60.228 57.895 23.83 11.65 0.00 1.73
649 661 1.203928 CATTCAGATCAGGCGACGAC 58.796 55.000 0.00 0.00 0.00 4.34
655 667 0.952280 GATCAGGCGACGACTCCATA 59.048 55.000 0.00 0.00 0.00 2.74
656 668 1.542030 GATCAGGCGACGACTCCATAT 59.458 52.381 0.00 0.00 0.00 1.78
682 694 3.557595 CGAACCAATATCTTCCTGCAGAC 59.442 47.826 17.39 0.00 0.00 3.51
706 718 2.568696 AGTTGATGACGAGATGGACG 57.431 50.000 0.00 0.00 0.00 4.79
709 721 3.065510 AGTTGATGACGAGATGGACGTAG 59.934 47.826 0.00 0.00 43.97 3.51
713 725 0.454600 GACGAGATGGACGTAGGCAA 59.545 55.000 0.00 0.00 43.97 4.52
720 732 1.448893 GGACGTAGGCAAATCGGCA 60.449 57.895 0.00 0.00 44.47 5.69
730 742 2.356135 GCAAATCGGCAGAGGAACTTA 58.644 47.619 0.00 0.00 41.55 2.24
747 759 2.287668 ACTTATTCCGGAGCTCGAATCG 60.288 50.000 17.03 10.80 42.43 3.34
749 761 0.249073 ATTCCGGAGCTCGAATCGTG 60.249 55.000 3.34 0.62 42.43 4.35
750 762 1.592400 TTCCGGAGCTCGAATCGTGT 61.592 55.000 3.34 0.00 42.43 4.49
753 765 1.134530 CGGAGCTCGAATCGTGTGTC 61.135 60.000 7.83 1.95 42.43 3.67
769 781 1.604278 GTGTCCAGGTGCTCAAAGAAC 59.396 52.381 0.00 0.00 0.00 3.01
772 784 1.202806 TCCAGGTGCTCAAAGAACTGG 60.203 52.381 0.00 0.00 0.00 4.00
814 826 0.600255 CTTCCACTCCAAGACGCGTT 60.600 55.000 15.53 0.00 0.00 4.84
817 829 0.041312 CCACTCCAAGACGCGTTTTG 60.041 55.000 29.63 29.63 0.00 2.44
846 858 0.027979 CGGTAATGTGCCGCAGAATG 59.972 55.000 0.00 0.00 42.82 2.67
848 860 1.331756 GGTAATGTGCCGCAGAATGAG 59.668 52.381 0.00 0.00 39.69 2.90
863 875 4.562789 CAGAATGAGTGAAGCGATTCGTAA 59.437 41.667 9.12 0.00 39.69 3.18
880 892 2.223021 CGTAACATGCACATTCTTCCCG 60.223 50.000 0.00 0.00 0.00 5.14
904 916 2.031919 CTGGCACCCAGCAACGTA 59.968 61.111 0.00 0.00 45.13 3.57
921 939 1.800655 CGTAGTGATCAGCAGCTGGAC 60.801 57.143 22.62 15.65 31.51 4.02
941 959 1.802960 CGTGAACAAGCAGAAGCAGAT 59.197 47.619 0.00 0.00 45.49 2.90
945 963 4.633126 GTGAACAAGCAGAAGCAGATGATA 59.367 41.667 0.00 0.00 45.49 2.15
956 974 6.746822 CAGAAGCAGATGATAGATGACGATAC 59.253 42.308 0.00 0.00 0.00 2.24
970 988 3.001634 TGACGATACGGACATAGACGAAC 59.998 47.826 0.00 0.00 0.00 3.95
977 995 2.279252 CATAGACGAACCGGCCCG 60.279 66.667 13.61 13.61 34.11 6.13
996 1017 3.118038 CCCGAGAATTAACCATGGAGGAA 60.118 47.826 21.47 9.46 41.22 3.36
998 1019 3.561725 CGAGAATTAACCATGGAGGAAGC 59.438 47.826 21.47 3.46 41.22 3.86
1040 1061 2.812358 TTCGCTTGCTACAGAAGTGA 57.188 45.000 0.00 0.00 38.00 3.41
1088 1109 0.179153 GGATGCGGCTTCTTCAAAGC 60.179 55.000 14.51 1.16 42.30 3.51
1128 1149 6.895607 TGCATGCATTATCACTCAATTTTG 57.104 33.333 18.46 0.00 0.00 2.44
1129 1150 5.292345 TGCATGCATTATCACTCAATTTTGC 59.708 36.000 18.46 0.00 0.00 3.68
1156 1180 4.384208 GCTAGCTACTTCCCATTTCCTTCA 60.384 45.833 7.70 0.00 0.00 3.02
1176 1200 6.204882 CCTTCACGTTCTTTTACCTTTGATCT 59.795 38.462 0.00 0.00 0.00 2.75
1177 1201 6.539649 TCACGTTCTTTTACCTTTGATCTG 57.460 37.500 0.00 0.00 0.00 2.90
1181 1205 5.625311 CGTTCTTTTACCTTTGATCTGTTGC 59.375 40.000 0.00 0.00 0.00 4.17
1200 1224 3.115390 TGCCCTTCCTTCTATAAGCTGT 58.885 45.455 0.00 0.00 0.00 4.40
1216 1240 2.110011 AGCTGTAAGGGAATGGGTTTGT 59.890 45.455 0.00 0.00 0.00 2.83
1222 1247 4.955811 AAGGGAATGGGTTTGTCTTTTC 57.044 40.909 0.00 0.00 0.00 2.29
1223 1248 3.922375 AGGGAATGGGTTTGTCTTTTCA 58.078 40.909 0.00 0.00 0.00 2.69
1224 1249 4.294347 AGGGAATGGGTTTGTCTTTTCAA 58.706 39.130 0.00 0.00 0.00 2.69
1359 1408 3.873952 GCGAATACCTTGCAGATCTTCTT 59.126 43.478 0.00 0.00 0.00 2.52
1371 1420 7.615582 TGCAGATCTTCTTCATTAAAATCGT 57.384 32.000 0.00 0.00 0.00 3.73
1388 1437 2.282407 TCGTAGAAATTAAAGGCGGCC 58.718 47.619 12.11 12.11 0.00 6.13
1404 1453 3.039202 GCCTCGAATGGCCGTTGTG 62.039 63.158 16.85 7.60 46.82 3.33
1466 1515 2.910688 TCGCAACCTTCTCTTCTGTT 57.089 45.000 0.00 0.00 0.00 3.16
1494 1543 2.026262 GGACAAGGAGCCAAATAGTCCA 60.026 50.000 0.00 0.00 42.65 4.02
1540 1593 5.769662 GCTTTTTCATTTTCCTTTTGGGGAT 59.230 36.000 0.00 0.00 40.87 3.85
1541 1594 6.939730 GCTTTTTCATTTTCCTTTTGGGGATA 59.060 34.615 0.00 0.00 40.87 2.59
1542 1595 7.611467 GCTTTTTCATTTTCCTTTTGGGGATAT 59.389 33.333 0.00 0.00 40.87 1.63
1544 1597 8.860780 TTTTCATTTTCCTTTTGGGGATATTG 57.139 30.769 0.00 0.00 40.87 1.90
1617 1682 3.245229 TGGGGTGATTGACTAATGCTTGT 60.245 43.478 0.00 0.00 0.00 3.16
1694 1759 5.452356 CCCTGTTGACTTTGAAATTCAGCTT 60.452 40.000 11.91 0.00 0.00 3.74
1700 1765 9.730420 GTTGACTTTGAAATTCAGCTTAAAGTA 57.270 29.630 9.24 0.00 38.17 2.24
1836 1901 2.181021 GCATGGAGCTGCTTGTGC 59.819 61.111 19.86 16.29 41.15 4.57
1925 1996 0.179100 GATGCCGAGTAGCTTGCTCA 60.179 55.000 15.33 0.00 33.45 4.26
2003 2074 1.344438 TCATCTGGTGAAGTCGTGCTT 59.656 47.619 0.00 0.00 40.76 3.91
2075 2146 2.279851 TCAAGGCGTGTGGTGTCG 60.280 61.111 0.00 0.00 0.00 4.35
2096 2167 3.310774 CGGTAGAACATGAAGAAGGCATG 59.689 47.826 0.00 0.00 46.49 4.06
2114 2185 2.831685 TGCTGGAACTCGTTGTACAT 57.168 45.000 0.00 0.00 0.00 2.29
2220 2291 5.861727 TCTATGTTGATGATGCTGTGCTAT 58.138 37.500 0.00 0.00 0.00 2.97
2253 2324 2.427506 CTTGGTCCTTCCTTGTAGCAC 58.572 52.381 0.00 0.00 37.07 4.40
2299 2370 4.149598 GTGGGTATTTGAAACCTCCAAGT 58.850 43.478 0.00 0.00 37.18 3.16
2319 2390 6.401474 CCAAGTAGTGAACAACAATGATCTCG 60.401 42.308 0.00 0.00 30.06 4.04
2357 2428 5.744666 TTTGAAACCTCCGTTTACTTGAG 57.255 39.130 0.00 0.00 42.34 3.02
2358 2429 4.675976 TGAAACCTCCGTTTACTTGAGA 57.324 40.909 0.00 0.00 42.34 3.27
2359 2430 5.223449 TGAAACCTCCGTTTACTTGAGAT 57.777 39.130 0.00 0.00 42.34 2.75
2361 2432 6.059484 TGAAACCTCCGTTTACTTGAGATTT 58.941 36.000 0.00 0.00 42.34 2.17
2362 2433 6.204108 TGAAACCTCCGTTTACTTGAGATTTC 59.796 38.462 0.00 0.00 42.34 2.17
2363 2434 5.223449 ACCTCCGTTTACTTGAGATTTCA 57.777 39.130 0.00 0.00 0.00 2.69
2364 2435 5.238583 ACCTCCGTTTACTTGAGATTTCAG 58.761 41.667 0.00 0.00 34.15 3.02
2365 2436 4.093556 CCTCCGTTTACTTGAGATTTCAGC 59.906 45.833 0.00 0.00 34.15 4.26
2410 2544 4.004982 TGATGATGTGTGTCCATTCAGTG 58.995 43.478 0.00 0.00 0.00 3.66
2413 2547 3.814842 TGATGTGTGTCCATTCAGTGTTC 59.185 43.478 0.00 0.00 0.00 3.18
2419 2553 6.038161 TGTGTGTCCATTCAGTGTTCTTTAAG 59.962 38.462 0.00 0.00 0.00 1.85
2429 2563 6.759272 TCAGTGTTCTTTAAGTGTGCTATCT 58.241 36.000 0.00 0.00 0.00 1.98
2595 2735 2.964925 CCCGACACCACACACACG 60.965 66.667 0.00 0.00 0.00 4.49
2596 2736 3.636043 CCGACACCACACACACGC 61.636 66.667 0.00 0.00 0.00 5.34
2717 2857 1.442184 CTCCACCGTGAACGAGTCG 60.442 63.158 11.85 11.85 43.02 4.18
3161 3302 0.107017 CCGGAGACCATCAAAGGCAT 60.107 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.457625 CTCCAGCGGCTCCCATCTG 62.458 68.421 0.00 0.00 0.00 2.90
1 2 3.160047 CTCCAGCGGCTCCCATCT 61.160 66.667 0.00 0.00 0.00 2.90
32 33 3.075005 CCGTCACGGGGAGTCCAT 61.075 66.667 8.94 0.00 44.15 3.41
42 43 2.809601 AAAGCGCTAGCCGTCACG 60.810 61.111 12.05 0.00 46.67 4.35
43 44 2.740714 CCAAAGCGCTAGCCGTCAC 61.741 63.158 12.05 0.00 46.67 3.67
44 45 2.434185 CCAAAGCGCTAGCCGTCA 60.434 61.111 12.05 0.00 46.67 4.35
45 46 3.865830 GCCAAAGCGCTAGCCGTC 61.866 66.667 12.05 0.00 46.67 4.79
58 59 4.214545 TCTTTCTTAAAAAGCGATCGCCAA 59.785 37.500 34.89 19.47 43.17 4.52
62 63 7.837898 AGTTTTCTTTCTTAAAAAGCGATCG 57.162 32.000 11.69 11.69 0.00 3.69
90 91 5.874810 TCTGTTTCCACCTGAATATTTCTCG 59.125 40.000 0.00 0.00 31.67 4.04
121 122 6.707290 ACTTTGTACCTTCTGCACATATGTA 58.293 36.000 8.32 0.00 0.00 2.29
129 130 5.865085 AGTTCATACTTTGTACCTTCTGCA 58.135 37.500 0.00 0.00 0.00 4.41
130 131 6.034683 CGTAGTTCATACTTTGTACCTTCTGC 59.965 42.308 0.00 0.00 35.78 4.26
131 132 7.272948 GTCGTAGTTCATACTTTGTACCTTCTG 59.727 40.741 0.00 0.00 35.78 3.02
132 133 7.040201 TGTCGTAGTTCATACTTTGTACCTTCT 60.040 37.037 0.00 0.00 35.78 2.85
133 134 7.086376 TGTCGTAGTTCATACTTTGTACCTTC 58.914 38.462 0.00 0.00 35.78 3.46
134 135 6.985117 TGTCGTAGTTCATACTTTGTACCTT 58.015 36.000 0.00 0.00 35.78 3.50
135 136 6.579666 TGTCGTAGTTCATACTTTGTACCT 57.420 37.500 0.00 0.00 35.78 3.08
136 137 7.620806 GCTTTGTCGTAGTTCATACTTTGTACC 60.621 40.741 0.00 0.00 35.78 3.34
137 138 7.225397 GCTTTGTCGTAGTTCATACTTTGTAC 58.775 38.462 0.00 0.00 35.78 2.90
138 139 6.366877 GGCTTTGTCGTAGTTCATACTTTGTA 59.633 38.462 0.00 0.00 35.78 2.41
139 140 5.178809 GGCTTTGTCGTAGTTCATACTTTGT 59.821 40.000 0.00 0.00 35.78 2.83
140 141 5.390567 GGGCTTTGTCGTAGTTCATACTTTG 60.391 44.000 0.00 0.00 35.78 2.77
141 142 4.694037 GGGCTTTGTCGTAGTTCATACTTT 59.306 41.667 0.00 0.00 35.78 2.66
142 143 4.251268 GGGCTTTGTCGTAGTTCATACTT 58.749 43.478 0.00 0.00 35.78 2.24
143 144 3.369157 GGGGCTTTGTCGTAGTTCATACT 60.369 47.826 0.00 0.00 38.44 2.12
144 145 2.934553 GGGGCTTTGTCGTAGTTCATAC 59.065 50.000 0.00 0.00 0.00 2.39
145 146 2.568062 TGGGGCTTTGTCGTAGTTCATA 59.432 45.455 0.00 0.00 0.00 2.15
146 147 1.349688 TGGGGCTTTGTCGTAGTTCAT 59.650 47.619 0.00 0.00 0.00 2.57
147 148 0.759959 TGGGGCTTTGTCGTAGTTCA 59.240 50.000 0.00 0.00 0.00 3.18
148 149 1.001633 TCTGGGGCTTTGTCGTAGTTC 59.998 52.381 0.00 0.00 0.00 3.01
149 150 1.053424 TCTGGGGCTTTGTCGTAGTT 58.947 50.000 0.00 0.00 0.00 2.24
150 151 1.002087 CTTCTGGGGCTTTGTCGTAGT 59.998 52.381 0.00 0.00 0.00 2.73
151 152 1.676014 CCTTCTGGGGCTTTGTCGTAG 60.676 57.143 0.00 0.00 0.00 3.51
152 153 0.323629 CCTTCTGGGGCTTTGTCGTA 59.676 55.000 0.00 0.00 0.00 3.43
153 154 1.073199 CCTTCTGGGGCTTTGTCGT 59.927 57.895 0.00 0.00 0.00 4.34
154 155 0.250727 TTCCTTCTGGGGCTTTGTCG 60.251 55.000 0.00 0.00 35.33 4.35
155 156 2.095461 GATTCCTTCTGGGGCTTTGTC 58.905 52.381 0.00 0.00 35.33 3.18
187 188 1.347817 GACGAGCAAAGAGACGGCTG 61.348 60.000 0.00 0.00 38.15 4.85
301 302 0.249031 GGCCCAAACGATGCTAATGC 60.249 55.000 0.00 0.00 40.20 3.56
346 347 7.411804 CCGAACAATTACATCAAATTTGGAAGC 60.412 37.037 17.90 0.00 0.00 3.86
353 354 6.042143 GGCATCCGAACAATTACATCAAATT 58.958 36.000 0.00 0.00 0.00 1.82
356 357 3.380004 GGGCATCCGAACAATTACATCAA 59.620 43.478 0.00 0.00 0.00 2.57
366 367 2.359850 GTGCTGGGCATCCGAACA 60.360 61.111 0.00 0.00 41.91 3.18
427 433 7.092757 ACCGACCCAGTTTAGGAGATTTATTTA 60.093 37.037 0.00 0.00 0.00 1.40
428 434 6.120220 CCGACCCAGTTTAGGAGATTTATTT 58.880 40.000 0.00 0.00 0.00 1.40
429 435 5.191124 ACCGACCCAGTTTAGGAGATTTATT 59.809 40.000 0.00 0.00 0.00 1.40
445 451 4.631740 TCAGCCCAGACCGACCCA 62.632 66.667 0.00 0.00 0.00 4.51
453 459 2.369860 CAAGCCATATACTCAGCCCAGA 59.630 50.000 0.00 0.00 0.00 3.86
473 481 6.627287 CGGAAGACGGGATTATATATCTTGCA 60.627 42.308 11.30 0.00 35.10 4.08
498 508 4.884164 CCAGATTGGATCCAAGGTTTCTAC 59.116 45.833 29.98 13.93 40.96 2.59
507 517 3.263170 TCTTTCGACCAGATTGGATCCAA 59.737 43.478 28.92 28.92 40.96 3.53
509 519 3.543680 TCTTTCGACCAGATTGGATCC 57.456 47.619 4.20 4.20 40.96 3.36
532 544 1.153549 GTCTTCTGCTTCCGGCGAT 60.154 57.895 9.30 0.00 45.43 4.58
547 559 1.208844 TCTCCTCCTCTCGGTGGTCT 61.209 60.000 0.00 0.00 43.14 3.85
548 560 0.106419 ATCTCCTCCTCTCGGTGGTC 60.106 60.000 0.00 0.00 43.14 4.02
550 562 1.422024 TCTATCTCCTCCTCTCGGTGG 59.578 57.143 0.00 0.00 43.84 4.61
557 569 1.611491 CCGCTTGTCTATCTCCTCCTC 59.389 57.143 0.00 0.00 0.00 3.71
558 570 1.215673 TCCGCTTGTCTATCTCCTCCT 59.784 52.381 0.00 0.00 0.00 3.69
559 571 1.693627 TCCGCTTGTCTATCTCCTCC 58.306 55.000 0.00 0.00 0.00 4.30
561 573 1.410882 GCTTCCGCTTGTCTATCTCCT 59.589 52.381 0.00 0.00 0.00 3.69
563 575 2.099921 TCTGCTTCCGCTTGTCTATCTC 59.900 50.000 0.00 0.00 36.97 2.75
564 576 2.103373 TCTGCTTCCGCTTGTCTATCT 58.897 47.619 0.00 0.00 36.97 1.98
565 577 2.586258 TCTGCTTCCGCTTGTCTATC 57.414 50.000 0.00 0.00 36.97 2.08
566 578 4.100189 AGTTATCTGCTTCCGCTTGTCTAT 59.900 41.667 0.00 0.00 36.97 1.98
567 579 3.447586 AGTTATCTGCTTCCGCTTGTCTA 59.552 43.478 0.00 0.00 36.97 2.59
568 580 2.234908 AGTTATCTGCTTCCGCTTGTCT 59.765 45.455 0.00 0.00 36.97 3.41
569 581 2.622436 AGTTATCTGCTTCCGCTTGTC 58.378 47.619 0.00 0.00 36.97 3.18
570 582 2.770164 AGTTATCTGCTTCCGCTTGT 57.230 45.000 0.00 0.00 36.97 3.16
571 583 2.866762 GGTAGTTATCTGCTTCCGCTTG 59.133 50.000 0.00 0.00 36.97 4.01
572 584 2.481449 CGGTAGTTATCTGCTTCCGCTT 60.481 50.000 0.00 0.00 36.97 4.68
573 585 1.067212 CGGTAGTTATCTGCTTCCGCT 59.933 52.381 0.00 0.00 36.97 5.52
574 586 1.066605 TCGGTAGTTATCTGCTTCCGC 59.933 52.381 5.67 0.00 36.99 5.54
575 587 2.287668 CCTCGGTAGTTATCTGCTTCCG 60.288 54.545 4.40 4.40 38.16 4.30
576 588 2.546162 GCCTCGGTAGTTATCTGCTTCC 60.546 54.545 0.00 0.00 0.00 3.46
583 595 2.035576 ACCAATCGCCTCGGTAGTTATC 59.964 50.000 0.00 0.00 0.00 1.75
606 618 0.600255 AATCTTCCGATAAGCCGCCG 60.600 55.000 0.00 0.00 0.00 6.46
682 694 3.118992 TCCATCTCGTCATCAACTTCCAG 60.119 47.826 0.00 0.00 0.00 3.86
690 702 1.947456 CCTACGTCCATCTCGTCATCA 59.053 52.381 0.00 0.00 41.72 3.07
706 718 0.178068 TCCTCTGCCGATTTGCCTAC 59.822 55.000 0.00 0.00 0.00 3.18
709 721 0.678048 AGTTCCTCTGCCGATTTGCC 60.678 55.000 0.00 0.00 0.00 4.52
730 742 0.249073 CACGATTCGAGCTCCGGAAT 60.249 55.000 13.95 14.46 39.14 3.01
747 759 0.947244 CTTTGAGCACCTGGACACAC 59.053 55.000 0.00 0.00 0.00 3.82
749 761 1.604278 GTTCTTTGAGCACCTGGACAC 59.396 52.381 0.00 0.00 0.00 3.67
750 762 1.490490 AGTTCTTTGAGCACCTGGACA 59.510 47.619 0.00 0.00 0.00 4.02
753 765 1.202806 TCCAGTTCTTTGAGCACCTGG 60.203 52.381 0.00 0.00 40.63 4.45
769 781 2.046507 GTGTCTGCCTGCCTCCAG 60.047 66.667 0.00 0.00 38.85 3.86
772 784 2.513026 ATCGTGTGTCTGCCTGCCTC 62.513 60.000 0.00 0.00 0.00 4.70
814 826 4.024387 GCACATTACCGACAACTCTTCAAA 60.024 41.667 0.00 0.00 0.00 2.69
817 829 2.415512 GGCACATTACCGACAACTCTTC 59.584 50.000 0.00 0.00 0.00 2.87
842 854 4.326278 TGTTACGAATCGCTTCACTCATTC 59.674 41.667 1.15 0.00 0.00 2.67
846 858 3.542291 GCATGTTACGAATCGCTTCACTC 60.542 47.826 1.15 0.00 0.00 3.51
848 860 2.093625 TGCATGTTACGAATCGCTTCAC 59.906 45.455 1.15 0.00 0.00 3.18
863 875 1.315257 GCCGGGAAGAATGTGCATGT 61.315 55.000 2.18 0.00 0.00 3.21
890 902 0.673644 ATCACTACGTTGCTGGGTGC 60.674 55.000 0.00 0.00 43.25 5.01
891 903 1.337728 TGATCACTACGTTGCTGGGTG 60.338 52.381 0.00 0.00 0.00 4.61
892 904 0.973632 TGATCACTACGTTGCTGGGT 59.026 50.000 0.00 0.00 0.00 4.51
893 905 1.645034 CTGATCACTACGTTGCTGGG 58.355 55.000 0.00 0.00 0.00 4.45
895 907 1.657594 CTGCTGATCACTACGTTGCTG 59.342 52.381 0.00 0.00 0.00 4.41
896 908 2.001812 CTGCTGATCACTACGTTGCT 57.998 50.000 0.00 0.00 0.00 3.91
897 909 0.371645 GCTGCTGATCACTACGTTGC 59.628 55.000 0.00 0.00 0.00 4.17
900 912 0.174389 CCAGCTGCTGATCACTACGT 59.826 55.000 30.10 0.00 32.44 3.57
902 914 1.800655 CGTCCAGCTGCTGATCACTAC 60.801 57.143 30.10 15.53 32.44 2.73
904 916 1.217511 CGTCCAGCTGCTGATCACT 59.782 57.895 30.10 0.00 32.44 3.41
921 939 1.220529 TCTGCTTCTGCTTGTTCACG 58.779 50.000 0.00 0.00 40.48 4.35
941 959 6.313164 GTCTATGTCCGTATCGTCATCTATCA 59.687 42.308 0.00 0.00 0.00 2.15
945 963 3.432592 CGTCTATGTCCGTATCGTCATCT 59.567 47.826 0.00 0.00 0.00 2.90
956 974 1.588139 GCCGGTTCGTCTATGTCCG 60.588 63.158 1.90 0.00 40.72 4.79
970 988 0.179029 ATGGTTAATTCTCGGGCCGG 60.179 55.000 27.98 17.02 0.00 6.13
977 995 3.561725 CGCTTCCTCCATGGTTAATTCTC 59.438 47.826 12.58 0.00 37.07 2.87
1012 1033 3.002791 TGTAGCAAGCGAAATCCTCTTG 58.997 45.455 0.00 0.00 39.95 3.02
1040 1061 3.525862 GATCCCCATCTAGATTCCCAGT 58.474 50.000 1.33 0.00 0.00 4.00
1088 1109 0.792640 GCATGTCAACTCACTCGTGG 59.207 55.000 0.00 0.00 0.00 4.94
1129 1150 5.071115 AGGAAATGGGAAGTAGCTAGCTAAG 59.929 44.000 25.74 0.00 0.00 2.18
1145 1169 5.240844 AGGTAAAAGAACGTGAAGGAAATGG 59.759 40.000 0.00 0.00 0.00 3.16
1156 1180 6.725246 CAACAGATCAAAGGTAAAAGAACGT 58.275 36.000 0.00 0.00 0.00 3.99
1176 1200 3.523564 AGCTTATAGAAGGAAGGGCAACA 59.476 43.478 0.00 0.00 33.02 3.33
1177 1201 3.879892 CAGCTTATAGAAGGAAGGGCAAC 59.120 47.826 0.00 0.00 32.84 4.17
1181 1205 5.221742 CCCTTACAGCTTATAGAAGGAAGGG 60.222 48.000 12.38 12.38 43.38 3.95
1200 1224 5.459505 TGAAAAGACAAACCCATTCCCTTA 58.540 37.500 0.00 0.00 0.00 2.69
1359 1408 9.710979 CGCCTTTAATTTCTACGATTTTAATGA 57.289 29.630 0.00 0.00 0.00 2.57
1371 1420 2.168936 TCGAGGCCGCCTTTAATTTCTA 59.831 45.455 14.70 0.00 31.76 2.10
1388 1437 1.227999 ACACACAACGGCCATTCGAG 61.228 55.000 2.24 0.00 0.00 4.04
1399 1448 2.294074 ACCACACCATACACACACAAC 58.706 47.619 0.00 0.00 0.00 3.32
1404 1453 1.266718 CAGCAACCACACCATACACAC 59.733 52.381 0.00 0.00 0.00 3.82
1435 1484 2.783135 AGGTTGCGATTGTGATCAACT 58.217 42.857 0.00 0.00 38.90 3.16
1466 1515 0.835971 TGGCTCCTTGTCCTACTGCA 60.836 55.000 0.00 0.00 0.00 4.41
1529 1582 3.130340 CGGTCAACAATATCCCCAAAAGG 59.870 47.826 0.00 0.00 0.00 3.11
1540 1593 1.904287 AAAGCAGGCGGTCAACAATA 58.096 45.000 0.00 0.00 0.00 1.90
1541 1594 1.039856 AAAAGCAGGCGGTCAACAAT 58.960 45.000 0.00 0.00 0.00 2.71
1542 1595 0.102120 CAAAAGCAGGCGGTCAACAA 59.898 50.000 0.00 0.00 0.00 2.83
1544 1597 0.102300 AACAAAAGCAGGCGGTCAAC 59.898 50.000 0.00 0.00 0.00 3.18
1694 1759 6.150976 CAGACATGGCTCCACATTTTACTTTA 59.849 38.462 0.00 0.00 0.00 1.85
1700 1765 2.173519 CCAGACATGGCTCCACATTTT 58.826 47.619 0.00 0.00 40.52 1.82
1836 1901 0.107508 ATTGTGGCCTGGATCGTCTG 60.108 55.000 3.32 0.00 0.00 3.51
1925 1996 1.004918 GCGTGAGTAGGGTGCTGTT 60.005 57.895 0.00 0.00 0.00 3.16
1967 2038 4.454847 CCAGATGAGGCATTAGCAACATAG 59.545 45.833 0.00 0.00 44.61 2.23
2003 2074 3.106827 TGCATGTCTACCAGGATCAAGA 58.893 45.455 0.00 0.00 0.00 3.02
2075 2146 3.065925 GCATGCCTTCTTCATGTTCTACC 59.934 47.826 6.36 0.00 42.34 3.18
2096 2167 1.128692 GCATGTACAACGAGTTCCAGC 59.871 52.381 0.00 0.00 0.00 4.85
2114 2185 1.133482 TCTCCGGATGATGAGTAGGCA 60.133 52.381 3.57 0.00 0.00 4.75
2220 2291 2.835764 AGGACCAAGCAACGGTAATCTA 59.164 45.455 0.00 0.00 36.69 1.98
2299 2370 5.778862 TCACGAGATCATTGTTGTTCACTA 58.221 37.500 0.00 0.00 0.00 2.74
2319 2390 1.133915 TCAAAACCCCACCAGTCTCAC 60.134 52.381 0.00 0.00 0.00 3.51
2357 2428 1.648467 GGTCCTGCACCGCTGAAATC 61.648 60.000 0.00 0.00 34.56 2.17
2358 2429 1.675641 GGTCCTGCACCGCTGAAAT 60.676 57.895 0.00 0.00 34.56 2.17
2359 2430 2.281484 GGTCCTGCACCGCTGAAA 60.281 61.111 0.00 0.00 34.56 2.69
2429 2563 8.706322 TGGACACTTCAGACATATAGCTAATA 57.294 34.615 0.00 0.00 0.00 0.98
2500 2634 4.735662 TTTTCGGTAAAATCACGGTCAG 57.264 40.909 0.00 0.00 29.59 3.51
2596 2736 0.918983 TCCCTTGTATCTGCCTTGGG 59.081 55.000 0.00 0.00 34.76 4.12
2632 2772 3.393278 TGCTTTGGGGTGTTTAGAGTAGT 59.607 43.478 0.00 0.00 0.00 2.73
2919 3059 1.755393 AAAACCTCGTCTGGCTCGGT 61.755 55.000 0.00 0.00 0.00 4.69
3093 3234 2.579201 GCGGGAGTTGCTAGCTCA 59.421 61.111 17.23 0.00 34.83 4.26
3098 3239 2.463589 CTTGGTGGCGGGAGTTGCTA 62.464 60.000 0.00 0.00 0.00 3.49
3121 3262 2.045926 GTCTGGATGCAAGGCGGT 60.046 61.111 0.00 0.00 0.00 5.68
3161 3302 2.048222 CGGTCGGCTCAAAGCTCA 60.048 61.111 0.00 0.00 41.99 4.26


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

AutoCloner maintained by Alex Coulton.