Multiple sequence alignment - TraesCS2B01G575900

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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 TraesCS2B01G575900 chr2B 100.000 3067 0 0 549 3615 765063561 765060495 0.000000e+00 5664
1 TraesCS2B01G575900 chr2B 100.000 255 0 0 1 255 765064109 765063855 4.220000e-129 472
2 TraesCS2B01G575900 chr2D 92.528 1432 86 6 1403 2816 622916664 622915236 0.000000e+00 2032
3 TraesCS2B01G575900 chr2D 81.109 487 64 15 644 1114 622917410 622916936 7.380000e-97 364
4 TraesCS2B01G575900 chr2D 81.513 357 36 15 2918 3252 622915190 622914842 2.140000e-67 267
5 TraesCS2B01G575900 chr2D 91.765 170 10 3 89 255 622917944 622917776 2.170000e-57 233
6 TraesCS2B01G575900 chr2D 89.726 146 11 3 1272 1417 622916887 622916746 2.220000e-42 183
7 TraesCS2B01G575900 chr2A 91.667 960 51 13 2211 3152 754349774 754348826 0.000000e+00 1303
8 TraesCS2B01G575900 chr2A 84.547 783 77 24 559 1311 754352879 754352111 0.000000e+00 736
9 TraesCS2B01G575900 chr2A 89.564 527 41 4 2159 2675 754340527 754340005 0.000000e+00 656
10 TraesCS2B01G575900 chr2A 92.537 402 24 5 1785 2181 754350248 754349848 4.050000e-159 571
11 TraesCS2B01G575900 chr2A 90.367 436 23 13 3150 3582 754348659 754348240 4.080000e-154 555
12 TraesCS2B01G575900 chr2A 88.545 323 21 4 1477 1791 754351853 754351539 9.470000e-101 377
13 TraesCS2B01G575900 chr2A 90.303 165 14 2 89 252 754353102 754352939 7.860000e-52 215
14 TraesCS2B01G575900 chr5D 90.464 388 37 0 2230 2617 41363440 41363827 2.490000e-141 512
15 TraesCS2B01G575900 chr5B 88.345 429 42 5 2197 2617 35530553 35530981 3.220000e-140 508
16 TraesCS2B01G575900 chr5A 88.361 421 45 4 2199 2617 29681791 29682209 1.500000e-138 503
17 TraesCS2B01G575900 chr7B 85.307 456 49 8 860 1308 84023104 84023548 4.250000e-124 455


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 TraesCS2B01G575900 chr2B 765060495 765064109 3614 True 3068.000000 5664 100.0000 1 3615 2 chr2B.!!$R1 3614
1 TraesCS2B01G575900 chr2D 622914842 622917944 3102 True 615.800000 2032 87.3282 89 3252 5 chr2D.!!$R1 3163
2 TraesCS2B01G575900 chr2A 754340005 754340527 522 True 656.000000 656 89.5640 2159 2675 1 chr2A.!!$R1 516
3 TraesCS2B01G575900 chr2A 754348240 754353102 4862 True 626.166667 1303 89.6610 89 3582 6 chr2A.!!$R2 3493

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
44 45 0.107459 AAGAAGCGGCCTGAATCCTC 60.107 55.0 0.00 0.00 0.0 3.71 F
80 81 0.172803 ACACAGTAATCGGAGGCGAC 59.827 55.0 0.00 0.00 0.0 5.19 F
1175 1454 0.390998 TCGAACATGCATCTTCGCCA 60.391 50.0 26.28 12.06 39.3 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 1437 0.804364 TGTGGCGAAGATGCATGTTC 59.196 50.0 23.14 23.14 36.28 3.18 R
1237 1516 0.889994 TGCCACCAATCACAGATTGC 59.110 50.0 12.93 4.10 0.00 3.56 R
2816 4649 0.601558 GTCAGGTCCTGTAACGAGCA 59.398 55.0 18.65 0.00 32.61 4.26 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
37 38 2.800881 AAAAGAAAAGAAGCGGCCTG 57.199 45.000 0.00 0.00 0.00 4.85
38 39 1.981256 AAAGAAAAGAAGCGGCCTGA 58.019 45.000 0.00 0.00 0.00 3.86
39 40 1.981256 AAGAAAAGAAGCGGCCTGAA 58.019 45.000 0.00 0.00 0.00 3.02
40 41 2.206576 AGAAAAGAAGCGGCCTGAAT 57.793 45.000 0.00 0.00 0.00 2.57
41 42 2.087646 AGAAAAGAAGCGGCCTGAATC 58.912 47.619 0.00 0.00 0.00 2.52
42 43 1.133216 GAAAAGAAGCGGCCTGAATCC 59.867 52.381 0.00 0.00 0.00 3.01
43 44 0.329596 AAAGAAGCGGCCTGAATCCT 59.670 50.000 0.00 0.00 0.00 3.24
44 45 0.107459 AAGAAGCGGCCTGAATCCTC 60.107 55.000 0.00 0.00 0.00 3.71
45 46 1.524849 GAAGCGGCCTGAATCCTCC 60.525 63.158 0.00 0.00 0.00 4.30
46 47 3.391665 AAGCGGCCTGAATCCTCCG 62.392 63.158 0.00 0.00 44.29 4.63
47 48 4.918201 GCGGCCTGAATCCTCCGG 62.918 72.222 0.00 0.00 41.96 5.14
50 51 4.570874 GCCTGAATCCTCCGGCCC 62.571 72.222 0.00 0.00 44.10 5.80
51 52 3.878667 CCTGAATCCTCCGGCCCC 61.879 72.222 0.00 0.00 0.00 5.80
52 53 4.241555 CTGAATCCTCCGGCCCCG 62.242 72.222 0.00 0.00 39.44 5.73
63 64 4.104183 GGCCCCGGGAAATCGACA 62.104 66.667 26.32 0.00 0.00 4.35
64 65 2.822701 GCCCCGGGAAATCGACAC 60.823 66.667 26.32 0.00 0.00 3.67
65 66 2.666207 CCCCGGGAAATCGACACA 59.334 61.111 26.32 0.00 0.00 3.72
66 67 1.449601 CCCCGGGAAATCGACACAG 60.450 63.158 26.32 0.00 0.00 3.66
67 68 1.295423 CCCGGGAAATCGACACAGT 59.705 57.895 18.48 0.00 0.00 3.55
68 69 0.533491 CCCGGGAAATCGACACAGTA 59.467 55.000 18.48 0.00 0.00 2.74
69 70 1.066716 CCCGGGAAATCGACACAGTAA 60.067 52.381 18.48 0.00 0.00 2.24
70 71 2.419574 CCCGGGAAATCGACACAGTAAT 60.420 50.000 18.48 0.00 0.00 1.89
71 72 2.864343 CCGGGAAATCGACACAGTAATC 59.136 50.000 0.00 0.00 0.00 1.75
72 73 2.534349 CGGGAAATCGACACAGTAATCG 59.466 50.000 0.00 0.74 39.72 3.34
73 74 2.864343 GGGAAATCGACACAGTAATCGG 59.136 50.000 6.56 0.00 38.86 4.18
74 75 3.429822 GGGAAATCGACACAGTAATCGGA 60.430 47.826 6.56 0.00 38.86 4.55
75 76 3.797256 GGAAATCGACACAGTAATCGGAG 59.203 47.826 6.56 0.00 38.86 4.63
76 77 3.438297 AATCGACACAGTAATCGGAGG 57.562 47.619 6.56 0.00 38.86 4.30
77 78 0.454600 TCGACACAGTAATCGGAGGC 59.545 55.000 6.56 0.00 38.86 4.70
78 79 0.866061 CGACACAGTAATCGGAGGCG 60.866 60.000 0.00 0.00 34.67 5.52
79 80 0.454600 GACACAGTAATCGGAGGCGA 59.545 55.000 0.00 0.00 0.00 5.54
80 81 0.172803 ACACAGTAATCGGAGGCGAC 59.827 55.000 0.00 0.00 0.00 5.19
81 82 0.866061 CACAGTAATCGGAGGCGACG 60.866 60.000 0.00 0.00 0.00 5.12
82 83 1.944676 CAGTAATCGGAGGCGACGC 60.945 63.158 12.43 12.43 0.00 5.19
83 84 2.103538 GTAATCGGAGGCGACGCA 59.896 61.111 23.09 0.00 0.00 5.24
84 85 1.299926 GTAATCGGAGGCGACGCAT 60.300 57.895 23.09 16.07 0.00 4.73
85 86 1.007734 TAATCGGAGGCGACGCATC 60.008 57.895 25.16 25.16 38.72 3.91
177 178 2.124570 CCATGGGGGACTGCTTCG 60.125 66.667 2.85 0.00 40.01 3.79
179 180 4.115199 ATGGGGGACTGCTTCGGC 62.115 66.667 0.00 0.00 42.19 5.54
204 208 4.162690 GCCTGAGGAATCGGCGGT 62.163 66.667 7.21 0.00 33.64 5.68
571 575 4.282195 TGGGCTTAAATAAATATTGGCCGG 59.718 41.667 0.00 0.00 37.43 6.13
604 611 0.601558 TTACAGAGGCCTGACGTGTC 59.398 55.000 12.00 0.00 43.02 3.67
637 644 2.437895 GGGCCCTGCTACCGTTTC 60.438 66.667 17.04 0.00 0.00 2.78
638 645 2.349755 GGCCCTGCTACCGTTTCA 59.650 61.111 0.00 0.00 0.00 2.69
639 646 2.038837 GGCCCTGCTACCGTTTCAC 61.039 63.158 0.00 0.00 0.00 3.18
642 649 1.373435 CCTGCTACCGTTTCACCCA 59.627 57.895 0.00 0.00 0.00 4.51
643 650 0.673644 CCTGCTACCGTTTCACCCAG 60.674 60.000 0.00 0.00 0.00 4.45
645 652 2.038837 GCTACCGTTTCACCCAGGC 61.039 63.158 0.00 0.00 0.00 4.85
646 653 1.376812 CTACCGTTTCACCCAGGCC 60.377 63.158 0.00 0.00 0.00 5.19
647 654 3.242897 TACCGTTTCACCCAGGCCG 62.243 63.158 0.00 0.00 0.00 6.13
648 655 4.636435 CCGTTTCACCCAGGCCGT 62.636 66.667 0.00 0.00 0.00 5.68
651 658 2.203422 TTTCACCCAGGCCGTTGG 60.203 61.111 3.95 3.95 38.00 3.77
652 659 2.758207 TTTCACCCAGGCCGTTGGA 61.758 57.895 12.62 0.00 40.87 3.53
687 926 4.351054 CCGGCAGAAACCCAGCCT 62.351 66.667 0.00 0.00 46.14 4.58
690 929 1.075659 GGCAGAAACCCAGCCTTCT 59.924 57.895 0.00 0.00 44.92 2.85
691 930 0.962855 GGCAGAAACCCAGCCTTCTC 60.963 60.000 0.00 0.00 44.92 2.87
694 933 0.988063 AGAAACCCAGCCTTCTCTCC 59.012 55.000 0.00 0.00 0.00 3.71
703 942 1.456705 CCTTCTCTCCCCCTCCTCG 60.457 68.421 0.00 0.00 0.00 4.63
708 947 2.231540 CTCTCCCCCTCCTCGTCCTT 62.232 65.000 0.00 0.00 0.00 3.36
781 1020 4.452733 CGCTCCCTTCCACCGGAC 62.453 72.222 9.46 0.00 0.00 4.79
824 1067 1.667722 GTTGCCTGAGCCCTTTTGG 59.332 57.895 0.00 0.00 38.69 3.28
834 1077 3.181423 TGAGCCCTTTTGGTGTAAGGAAT 60.181 43.478 3.28 0.00 44.01 3.01
842 1085 2.124411 TGGTGTAAGGAATCCCTAGCC 58.876 52.381 0.00 0.00 43.48 3.93
851 1094 2.865183 AATCCCTAGCCCTGCCTGGT 62.865 60.000 0.00 0.00 0.00 4.00
914 1169 2.109799 CACCGGCCCTGATGCTAG 59.890 66.667 0.00 0.00 0.00 3.42
931 1186 4.256090 GGCGCATTGATCCGTGGC 62.256 66.667 10.83 0.00 0.00 5.01
949 1204 2.287909 TGGCGGTGTTGCTGTAAAATTC 60.288 45.455 0.00 0.00 34.52 2.17
980 1245 0.973632 TTCTGCAGGAAAGCGTAGGA 59.026 50.000 15.13 0.00 37.31 2.94
981 1246 0.532573 TCTGCAGGAAAGCGTAGGAG 59.467 55.000 15.13 0.00 37.31 3.69
982 1247 0.532573 CTGCAGGAAAGCGTAGGAGA 59.467 55.000 5.57 0.00 37.31 3.71
983 1248 0.532573 TGCAGGAAAGCGTAGGAGAG 59.467 55.000 0.00 0.00 37.31 3.20
984 1249 0.818296 GCAGGAAAGCGTAGGAGAGA 59.182 55.000 0.00 0.00 0.00 3.10
985 1250 1.202359 GCAGGAAAGCGTAGGAGAGAG 60.202 57.143 0.00 0.00 0.00 3.20
987 1252 1.285373 AGGAAAGCGTAGGAGAGAGGA 59.715 52.381 0.00 0.00 0.00 3.71
988 1253 1.679153 GGAAAGCGTAGGAGAGAGGAG 59.321 57.143 0.00 0.00 0.00 3.69
991 1256 2.197605 GCGTAGGAGAGAGGAGGGC 61.198 68.421 0.00 0.00 0.00 5.19
992 1257 1.227664 CGTAGGAGAGAGGAGGGCA 59.772 63.158 0.00 0.00 0.00 5.36
993 1258 0.395862 CGTAGGAGAGAGGAGGGCAA 60.396 60.000 0.00 0.00 0.00 4.52
994 1259 1.116308 GTAGGAGAGAGGAGGGCAAC 58.884 60.000 0.00 0.00 0.00 4.17
995 1260 0.395862 TAGGAGAGAGGAGGGCAACG 60.396 60.000 0.00 0.00 37.60 4.10
996 1261 2.185608 GAGAGAGGAGGGCAACGC 59.814 66.667 0.00 0.00 37.60 4.84
997 1262 2.604686 AGAGAGGAGGGCAACGCA 60.605 61.111 0.00 0.00 37.60 5.24
1009 1274 1.854664 CAACGCAAAATGGCAGCAC 59.145 52.632 0.00 0.00 0.00 4.40
1020 1285 2.587247 GGCAGCACTCCTCAGGTCA 61.587 63.158 0.00 0.00 0.00 4.02
1070 1340 3.326297 AGCCTTCTCAAAGTCTTGCTACT 59.674 43.478 0.00 0.00 32.14 2.57
1085 1356 1.739371 GCTACTTGACCACCTTAGGCG 60.739 57.143 0.00 0.00 0.00 5.52
1086 1357 0.899720 TACTTGACCACCTTAGGCGG 59.100 55.000 3.37 3.37 0.00 6.13
1098 1369 1.804748 CTTAGGCGGTCCAAACTTGAC 59.195 52.381 0.00 0.00 33.74 3.18
1103 1374 1.068541 GCGGTCCAAACTTGACATTCC 60.069 52.381 0.00 0.00 0.00 3.01
1130 1409 7.504403 AGCAGTTACTTGATATTGTAGCAGAT 58.496 34.615 0.00 0.00 0.00 2.90
1158 1437 7.875316 AGTCAGTTTATATGGAATTCGATCG 57.125 36.000 9.36 9.36 0.00 3.69
1172 1451 2.119457 TCGATCGAACATGCATCTTCG 58.881 47.619 25.48 25.48 40.52 3.79
1174 1453 0.940126 ATCGAACATGCATCTTCGCC 59.060 50.000 26.28 0.00 39.30 5.54
1175 1454 0.390998 TCGAACATGCATCTTCGCCA 60.391 50.000 26.28 12.06 39.30 5.69
1195 1474 5.046529 GCCACATGTCATGTTTTTGTGTTA 58.953 37.500 15.98 0.00 42.70 2.41
1202 1481 7.984002 TGTCATGTTTTTGTGTTATCAGTTG 57.016 32.000 0.00 0.00 0.00 3.16
1237 1516 3.329743 AAGATCGAAATTGCTCGCATG 57.670 42.857 0.00 0.00 38.73 4.06
1308 1587 5.972107 ACCTTGGAGAAAAATCATGACTG 57.028 39.130 0.00 0.00 0.00 3.51
1322 1666 4.744570 TCATGACTGCTAGTTAAACCTCG 58.255 43.478 0.00 0.00 0.00 4.63
1345 1689 4.180057 GTCTGAATGGTCTGCTACTTGAG 58.820 47.826 0.00 0.00 0.00 3.02
1383 1727 5.483685 ACTTCAGACTATGTGTTTGCCTA 57.516 39.130 0.00 0.00 31.59 3.93
1447 1883 6.039047 GGATGTCATCATATGGTGATTATGGC 59.961 42.308 21.25 9.36 45.25 4.40
1520 1993 1.501582 GGAGTATCAGGGAAGCCTGT 58.498 55.000 0.00 0.00 38.77 4.00
1538 2011 7.430760 AGCCTGTATCTCTAGTCAAATCTTT 57.569 36.000 0.00 0.00 0.00 2.52
1546 2019 6.940739 TCTCTAGTCAAATCTTTTCTCAGGG 58.059 40.000 0.00 0.00 0.00 4.45
1604 2085 7.028962 TGTGATGCTTAGCAAAATAACATGAC 58.971 34.615 12.08 0.00 43.62 3.06
1635 2116 6.149474 CACTTTTCTTGGTCTATGTAGTTGGG 59.851 42.308 0.00 0.00 0.00 4.12
1686 2167 4.445710 TACGGGGGCGCTACCTCA 62.446 66.667 18.55 4.85 43.06 3.86
1725 2206 0.815615 GACCATCCCGTTCTGATGCC 60.816 60.000 0.00 0.00 38.61 4.40
1726 2207 1.526917 CCATCCCGTTCTGATGCCC 60.527 63.158 0.00 0.00 38.61 5.36
1808 3588 6.144078 ACCAACATGACCTTTTTAAGTCAC 57.856 37.500 0.00 0.00 0.00 3.67
1846 3626 3.745975 CGTGAGCACTCAAAAGTTCCATA 59.254 43.478 1.05 0.00 41.85 2.74
1874 3654 7.468141 TGTGTATATCTTCTATTGCTCCGAT 57.532 36.000 0.00 0.00 0.00 4.18
1947 3727 4.380867 GCTTGTGTTACTATTGCTGCCAAT 60.381 41.667 0.00 0.00 43.74 3.16
2084 3867 5.332581 GCATTTTTCTTTGCTCCGTTTTCTC 60.333 40.000 0.00 0.00 35.95 2.87
2148 3935 5.069781 TGCAAAACTAACAGGGTAATTGCTT 59.930 36.000 8.39 0.00 38.86 3.91
2152 3939 5.959618 ACTAACAGGGTAATTGCTTGAAC 57.040 39.130 5.82 0.00 0.00 3.18
2192 4015 8.773404 TTTCTTGAGGTACTTGTTTATCTAGC 57.227 34.615 0.00 0.00 41.55 3.42
2455 4288 0.322816 GTGCTGCCATGAAGAAGGGA 60.323 55.000 0.00 0.00 0.00 4.20
2485 4318 1.513158 CAGCGAGGTCCAGTTCGAT 59.487 57.895 3.32 0.00 39.06 3.59
2494 4327 2.076100 GTCCAGTTCGATGACAATGCA 58.924 47.619 0.00 0.00 0.00 3.96
2618 4451 3.492656 GGCCGAGCACATAGTTTGAGATA 60.493 47.826 0.00 0.00 0.00 1.98
2655 4488 5.183331 CCTGTATCTAGCTATTAGTTCCGCA 59.817 44.000 0.00 0.00 0.00 5.69
2764 4597 6.716628 TCTGTTTGCCAATAATCTCTGTTCTT 59.283 34.615 0.00 0.00 0.00 2.52
2765 4598 6.913170 TGTTTGCCAATAATCTCTGTTCTTC 58.087 36.000 0.00 0.00 0.00 2.87
2816 4649 6.374417 ACCAGACAAGGATATGTGTACTTT 57.626 37.500 0.00 0.00 32.57 2.66
2821 4654 4.870426 ACAAGGATATGTGTACTTTGCTCG 59.130 41.667 0.00 0.00 30.82 5.03
2825 4658 6.040878 AGGATATGTGTACTTTGCTCGTTAC 58.959 40.000 0.00 0.00 0.00 2.50
2831 4664 2.165319 ACTTTGCTCGTTACAGGACC 57.835 50.000 0.00 0.00 0.00 4.46
2841 4674 2.484065 CGTTACAGGACCTGACCAAACA 60.484 50.000 28.56 0.61 35.18 2.83
2844 4677 2.057922 ACAGGACCTGACCAAACATCT 58.942 47.619 28.56 0.00 35.18 2.90
2848 4681 2.039084 GGACCTGACCAAACATCTCACT 59.961 50.000 0.00 0.00 0.00 3.41
2852 4685 4.287067 ACCTGACCAAACATCTCACTACAT 59.713 41.667 0.00 0.00 0.00 2.29
2865 4698 5.816682 TCTCACTACATGAAGAGTGGAGTA 58.183 41.667 19.73 6.68 38.70 2.59
2955 4806 4.524749 TCTATCAGCGTCGTTTTATCTCG 58.475 43.478 0.00 0.00 0.00 4.04
2965 4816 6.294363 CGTCGTTTTATCTCGCTTTTAGTTT 58.706 36.000 0.00 0.00 0.00 2.66
3033 4905 6.204882 GGTTGTCTCTTGCTGTTAGTGTATTT 59.795 38.462 0.00 0.00 0.00 1.40
3041 4913 9.066892 TCTTGCTGTTAGTGTATTTCATCTTTT 57.933 29.630 0.00 0.00 0.00 2.27
3044 4916 8.506437 TGCTGTTAGTGTATTTCATCTTTTCTG 58.494 33.333 0.00 0.00 0.00 3.02
3094 4967 5.859205 ATTCCAAAAGGAGAATATGCACC 57.141 39.130 0.00 0.00 30.98 5.01
3118 4996 2.365293 TGAAGCTGTAGTGAGTGCTCAA 59.635 45.455 3.19 0.00 41.85 3.02
3121 4999 1.923204 GCTGTAGTGAGTGCTCAATCG 59.077 52.381 5.39 0.00 41.85 3.34
3128 5006 2.413453 GTGAGTGCTCAATCGGTTCTTC 59.587 50.000 3.19 0.00 41.85 2.87
3139 5017 7.165460 TCAATCGGTTCTTCTATGTTCAGTA 57.835 36.000 0.00 0.00 0.00 2.74
3140 5018 7.608153 TCAATCGGTTCTTCTATGTTCAGTAA 58.392 34.615 0.00 0.00 0.00 2.24
3141 5019 8.258007 TCAATCGGTTCTTCTATGTTCAGTAAT 58.742 33.333 0.00 0.00 0.00 1.89
3142 5020 8.883731 CAATCGGTTCTTCTATGTTCAGTAATT 58.116 33.333 0.00 0.00 0.00 1.40
3144 5022 8.922058 TCGGTTCTTCTATGTTCAGTAATTAC 57.078 34.615 7.57 7.57 0.00 1.89
3145 5023 8.746530 TCGGTTCTTCTATGTTCAGTAATTACT 58.253 33.333 12.50 12.50 36.90 2.24
3310 5374 9.710900 ACATTTTTCTTCTTTTCACTTCAAACT 57.289 25.926 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.693074 TCAGGCCGCTTCTTTTCTTTTT 59.307 40.909 0.00 0.00 0.00 1.94
18 19 2.306847 TCAGGCCGCTTCTTTTCTTTT 58.693 42.857 0.00 0.00 0.00 2.27
19 20 1.981256 TCAGGCCGCTTCTTTTCTTT 58.019 45.000 0.00 0.00 0.00 2.52
20 21 1.981256 TTCAGGCCGCTTCTTTTCTT 58.019 45.000 0.00 0.00 0.00 2.52
21 22 2.087646 GATTCAGGCCGCTTCTTTTCT 58.912 47.619 0.00 0.00 0.00 2.52
22 23 1.133216 GGATTCAGGCCGCTTCTTTTC 59.867 52.381 0.00 0.00 0.00 2.29
23 24 1.177401 GGATTCAGGCCGCTTCTTTT 58.823 50.000 0.00 0.00 0.00 2.27
24 25 0.329596 AGGATTCAGGCCGCTTCTTT 59.670 50.000 0.00 0.00 0.00 2.52
25 26 0.107459 GAGGATTCAGGCCGCTTCTT 60.107 55.000 0.00 0.00 0.00 2.52
26 27 1.524482 GAGGATTCAGGCCGCTTCT 59.476 57.895 0.00 0.00 0.00 2.85
27 28 1.524849 GGAGGATTCAGGCCGCTTC 60.525 63.158 0.00 0.00 0.00 3.86
28 29 2.592308 GGAGGATTCAGGCCGCTT 59.408 61.111 0.00 0.00 0.00 4.68
29 30 3.854669 CGGAGGATTCAGGCCGCT 61.855 66.667 0.00 0.00 37.08 5.52
46 47 4.104183 TGTCGATTTCCCGGGGCC 62.104 66.667 23.50 6.46 0.00 5.80
47 48 2.822701 GTGTCGATTTCCCGGGGC 60.823 66.667 23.50 7.09 0.00 5.80
48 49 1.449601 CTGTGTCGATTTCCCGGGG 60.450 63.158 23.50 6.77 0.00 5.73
49 50 0.533491 TACTGTGTCGATTTCCCGGG 59.467 55.000 16.85 16.85 0.00 5.73
50 51 2.373540 TTACTGTGTCGATTTCCCGG 57.626 50.000 0.00 0.00 0.00 5.73
51 52 2.534349 CGATTACTGTGTCGATTTCCCG 59.466 50.000 10.61 0.00 40.11 5.14
52 53 2.864343 CCGATTACTGTGTCGATTTCCC 59.136 50.000 15.79 0.00 40.11 3.97
53 54 3.777478 TCCGATTACTGTGTCGATTTCC 58.223 45.455 15.79 0.00 40.11 3.13
54 55 3.797256 CCTCCGATTACTGTGTCGATTTC 59.203 47.826 15.79 0.00 40.11 2.17
55 56 3.782046 CCTCCGATTACTGTGTCGATTT 58.218 45.455 15.79 0.00 40.11 2.17
56 57 2.481449 GCCTCCGATTACTGTGTCGATT 60.481 50.000 15.79 0.00 40.11 3.34
57 58 1.067212 GCCTCCGATTACTGTGTCGAT 59.933 52.381 15.79 0.00 40.11 3.59
58 59 0.454600 GCCTCCGATTACTGTGTCGA 59.545 55.000 15.79 0.00 40.11 4.20
59 60 0.866061 CGCCTCCGATTACTGTGTCG 60.866 60.000 9.52 9.52 36.29 4.35
60 61 0.454600 TCGCCTCCGATTACTGTGTC 59.545 55.000 0.00 0.00 38.82 3.67
61 62 0.172803 GTCGCCTCCGATTACTGTGT 59.827 55.000 0.00 0.00 46.38 3.72
62 63 0.866061 CGTCGCCTCCGATTACTGTG 60.866 60.000 0.00 0.00 46.38 3.66
63 64 1.432251 CGTCGCCTCCGATTACTGT 59.568 57.895 0.00 0.00 46.38 3.55
64 65 1.944676 GCGTCGCCTCCGATTACTG 60.945 63.158 5.75 0.00 46.38 2.74
65 66 1.735376 ATGCGTCGCCTCCGATTACT 61.735 55.000 15.88 0.00 46.38 2.24
66 67 1.276145 GATGCGTCGCCTCCGATTAC 61.276 60.000 15.88 0.00 46.38 1.89
67 68 1.007734 GATGCGTCGCCTCCGATTA 60.008 57.895 15.88 0.00 46.38 1.75
68 69 2.279517 GATGCGTCGCCTCCGATT 60.280 61.111 15.88 0.00 46.38 3.34
69 70 4.630785 CGATGCGTCGCCTCCGAT 62.631 66.667 16.48 0.00 46.38 4.18
78 79 3.684323 GGTAACGACCGATGCGTC 58.316 61.111 0.00 0.00 41.75 5.19
179 180 2.657102 GATTCCTCAGGCAGGCTCCG 62.657 65.000 0.00 0.00 43.08 4.63
189 190 2.464459 GCAACCGCCGATTCCTCAG 61.464 63.158 0.00 0.00 0.00 3.35
190 191 2.435938 GCAACCGCCGATTCCTCA 60.436 61.111 0.00 0.00 0.00 3.86
221 225 0.910088 GACTTCAGTAGCCCCCACCT 60.910 60.000 0.00 0.00 0.00 4.00
548 552 4.282195 CCGGCCAATATTTATTTAAGCCCA 59.718 41.667 2.24 0.00 33.47 5.36
549 553 4.525100 TCCGGCCAATATTTATTTAAGCCC 59.475 41.667 2.24 0.00 33.47 5.19
550 554 5.475564 TCTCCGGCCAATATTTATTTAAGCC 59.524 40.000 2.24 0.00 33.60 4.35
551 555 6.379386 GTCTCCGGCCAATATTTATTTAAGC 58.621 40.000 2.24 0.00 0.00 3.09
552 556 6.072119 GGGTCTCCGGCCAATATTTATTTAAG 60.072 42.308 2.24 0.00 0.00 1.85
553 557 5.771165 GGGTCTCCGGCCAATATTTATTTAA 59.229 40.000 2.24 0.00 0.00 1.52
554 558 5.318630 GGGTCTCCGGCCAATATTTATTTA 58.681 41.667 2.24 0.00 0.00 1.40
555 559 4.149598 GGGTCTCCGGCCAATATTTATTT 58.850 43.478 2.24 0.00 0.00 1.40
556 560 3.763057 GGGTCTCCGGCCAATATTTATT 58.237 45.455 2.24 0.00 0.00 1.40
557 561 3.434940 GGGTCTCCGGCCAATATTTAT 57.565 47.619 2.24 0.00 0.00 1.40
571 575 3.576648 CTCTGTAAACACTTCGGGTCTC 58.423 50.000 0.00 0.00 0.00 3.36
621 628 2.038837 GTGAAACGGTAGCAGGGCC 61.039 63.158 0.00 0.00 0.00 5.80
624 631 0.673644 CTGGGTGAAACGGTAGCAGG 60.674 60.000 0.00 0.00 38.12 4.85
634 641 2.203422 CCAACGGCCTGGGTGAAA 60.203 61.111 0.00 0.00 32.32 2.69
637 644 2.484287 AATCTCCAACGGCCTGGGTG 62.484 60.000 11.00 0.00 37.06 4.61
638 645 0.912487 TAATCTCCAACGGCCTGGGT 60.912 55.000 11.00 0.00 37.06 4.51
639 646 0.179045 CTAATCTCCAACGGCCTGGG 60.179 60.000 11.00 4.59 37.06 4.45
642 649 0.831307 GACCTAATCTCCAACGGCCT 59.169 55.000 0.00 0.00 0.00 5.19
643 650 0.529992 CGACCTAATCTCCAACGGCC 60.530 60.000 0.00 0.00 0.00 6.13
645 652 0.870307 CGCGACCTAATCTCCAACGG 60.870 60.000 0.00 0.00 0.00 4.44
646 653 1.480219 GCGCGACCTAATCTCCAACG 61.480 60.000 12.10 0.00 0.00 4.10
647 654 1.480219 CGCGCGACCTAATCTCCAAC 61.480 60.000 28.94 0.00 0.00 3.77
648 655 1.226859 CGCGCGACCTAATCTCCAA 60.227 57.895 28.94 0.00 0.00 3.53
651 658 3.030882 GGCGCGCGACCTAATCTC 61.031 66.667 37.18 12.28 0.00 2.75
652 659 4.925576 CGGCGCGCGACCTAATCT 62.926 66.667 37.18 0.00 0.00 2.40
683 922 2.250635 GAGGAGGGGGAGAGAAGGCT 62.251 65.000 0.00 0.00 0.00 4.58
684 923 1.764454 GAGGAGGGGGAGAGAAGGC 60.764 68.421 0.00 0.00 0.00 4.35
687 926 1.306970 GACGAGGAGGGGGAGAGAA 59.693 63.158 0.00 0.00 0.00 2.87
690 929 2.226149 GAAGGACGAGGAGGGGGAGA 62.226 65.000 0.00 0.00 0.00 3.71
691 930 1.758906 GAAGGACGAGGAGGGGGAG 60.759 68.421 0.00 0.00 0.00 4.30
694 933 2.038975 TGGAAGGACGAGGAGGGG 59.961 66.667 0.00 0.00 0.00 4.79
703 942 4.452733 CCGCTCCGGTGGAAGGAC 62.453 72.222 0.00 0.00 45.39 3.85
824 1067 2.104963 CAGGGCTAGGGATTCCTTACAC 59.895 54.545 0.00 0.00 41.56 2.90
834 1077 3.579451 AACCAGGCAGGGCTAGGGA 62.579 63.158 0.00 0.00 43.89 4.20
842 1085 2.912025 AACGGCAAACCAGGCAGG 60.912 61.111 0.00 0.00 45.67 4.85
851 1094 1.069771 GGAATCGAAACGAACGGCAAA 60.070 47.619 0.00 0.00 39.99 3.68
914 1169 4.256090 GCCACGGATCAATGCGCC 62.256 66.667 4.18 0.00 45.92 6.53
931 1186 3.479006 CTCGAATTTTACAGCAACACCG 58.521 45.455 0.00 0.00 0.00 4.94
949 1204 1.131883 CCTGCAGAAGAAAATGGCTCG 59.868 52.381 17.39 0.00 0.00 5.03
980 1245 1.768684 TTTGCGTTGCCCTCCTCTCT 61.769 55.000 0.00 0.00 0.00 3.10
981 1246 0.889186 TTTTGCGTTGCCCTCCTCTC 60.889 55.000 0.00 0.00 0.00 3.20
982 1247 0.251341 ATTTTGCGTTGCCCTCCTCT 60.251 50.000 0.00 0.00 0.00 3.69
983 1248 0.109132 CATTTTGCGTTGCCCTCCTC 60.109 55.000 0.00 0.00 0.00 3.71
984 1249 1.535204 CCATTTTGCGTTGCCCTCCT 61.535 55.000 0.00 0.00 0.00 3.69
985 1250 1.079888 CCATTTTGCGTTGCCCTCC 60.080 57.895 0.00 0.00 0.00 4.30
987 1252 2.343387 GCCATTTTGCGTTGCCCT 59.657 55.556 0.00 0.00 0.00 5.19
988 1253 2.028733 CTGCCATTTTGCGTTGCCC 61.029 57.895 0.00 0.00 0.00 5.36
991 1256 0.598158 AGTGCTGCCATTTTGCGTTG 60.598 50.000 0.00 0.00 0.00 4.10
992 1257 0.318955 GAGTGCTGCCATTTTGCGTT 60.319 50.000 0.00 0.00 0.00 4.84
993 1258 1.286880 GAGTGCTGCCATTTTGCGT 59.713 52.632 0.00 0.00 0.00 5.24
994 1259 1.444895 GGAGTGCTGCCATTTTGCG 60.445 57.895 0.00 0.00 0.00 4.85
995 1260 0.108945 GAGGAGTGCTGCCATTTTGC 60.109 55.000 0.00 0.00 0.00 3.68
996 1261 1.201647 CTGAGGAGTGCTGCCATTTTG 59.798 52.381 0.00 0.00 0.00 2.44
997 1262 1.542492 CTGAGGAGTGCTGCCATTTT 58.458 50.000 0.00 0.00 0.00 1.82
1009 1274 2.224066 ACGAACACTTTGACCTGAGGAG 60.224 50.000 4.99 0.00 0.00 3.69
1085 1356 3.440522 GCTAGGAATGTCAAGTTTGGACC 59.559 47.826 0.00 0.00 34.36 4.46
1086 1357 4.072131 TGCTAGGAATGTCAAGTTTGGAC 58.928 43.478 0.00 0.00 35.83 4.02
1088 1359 4.074970 ACTGCTAGGAATGTCAAGTTTGG 58.925 43.478 0.00 0.00 0.00 3.28
1098 1369 8.668510 ACAATATCAAGTAACTGCTAGGAATG 57.331 34.615 0.00 0.00 0.00 2.67
1103 1374 8.138074 TCTGCTACAATATCAAGTAACTGCTAG 58.862 37.037 0.00 0.00 0.00 3.42
1133 1412 8.789762 TCGATCGAATTCCATATAAACTGACTA 58.210 33.333 16.99 0.00 0.00 2.59
1138 1417 8.712363 CATGTTCGATCGAATTCCATATAAACT 58.288 33.333 31.24 7.35 36.45 2.66
1142 1421 6.162777 TGCATGTTCGATCGAATTCCATATA 58.837 36.000 31.24 18.04 36.45 0.86
1158 1437 0.804364 TGTGGCGAAGATGCATGTTC 59.196 50.000 23.14 23.14 36.28 3.18
1172 1451 3.456280 ACACAAAAACATGACATGTGGC 58.544 40.909 21.49 0.00 44.07 5.01
1174 1453 7.648908 ACTGATAACACAAAAACATGACATGTG 59.351 33.333 21.49 11.91 44.07 3.21
1233 1512 2.536365 CACCAATCACAGATTGCATGC 58.464 47.619 11.82 11.82 0.00 4.06
1237 1516 0.889994 TGCCACCAATCACAGATTGC 59.110 50.000 12.93 4.10 0.00 3.56
1285 1564 5.415701 GCAGTCATGATTTTTCTCCAAGGTA 59.584 40.000 0.00 0.00 0.00 3.08
1308 1587 3.863142 TCAGACCGAGGTTTAACTAGC 57.137 47.619 0.00 0.00 0.00 3.42
1322 1666 3.055819 TCAAGTAGCAGACCATTCAGACC 60.056 47.826 0.00 0.00 0.00 3.85
1345 1689 1.813178 GAAGTTTGGAGTGGCTAAGGC 59.187 52.381 0.00 0.00 37.82 4.35
1412 1848 7.128418 ACCATATGATGACATCCCTATAAGCAT 59.872 37.037 12.90 0.00 37.87 3.79
1434 1870 9.105844 AGTTATAGAGTTAGCCATAATCACCAT 57.894 33.333 0.00 0.00 0.00 3.55
1473 1910 6.485984 CCTGATCATTTTCTTATGGAGAGGTG 59.514 42.308 0.00 0.00 35.37 4.00
1479 1916 5.193527 TCCCACCTGATCATTTTCTTATGGA 59.806 40.000 0.00 0.00 0.00 3.41
1520 1993 8.700051 CCCTGAGAAAAGATTTGACTAGAGATA 58.300 37.037 0.00 0.00 0.00 1.98
1538 2011 4.584325 CACATTTCAAAGGAACCCTGAGAA 59.416 41.667 0.00 0.00 32.13 2.87
1543 2016 3.230976 GGTCACATTTCAAAGGAACCCT 58.769 45.455 0.00 0.00 33.87 4.34
1546 2019 4.918810 ACTGGTCACATTTCAAAGGAAC 57.081 40.909 0.00 0.00 31.35 3.62
1577 2056 8.087136 TCATGTTATTTTGCTAAGCATCACAAA 58.913 29.630 0.00 0.00 38.76 2.83
1604 2085 3.420839 AGACCAAGAAAAGTGTTTGCG 57.579 42.857 0.00 0.00 0.00 4.85
1635 2116 1.510480 GGCTTCCCATCATAGCACGC 61.510 60.000 0.00 0.00 36.64 5.34
1686 2167 3.689649 GTCTTGCCACCGTTTCAATAGAT 59.310 43.478 0.00 0.00 0.00 1.98
1713 2194 1.817099 GCAGAGGGCATCAGAACGG 60.817 63.158 0.58 0.00 43.97 4.44
1726 2207 2.634815 AGCATCAATACCTGGCAGAG 57.365 50.000 17.94 8.80 0.00 3.35
1808 3588 3.843510 GCTCACGACAAAAAGTTACCACG 60.844 47.826 0.00 0.00 0.00 4.94
1846 3626 7.600375 CGGAGCAATAGAAGATATACACATTGT 59.400 37.037 0.00 0.00 0.00 2.71
1874 3654 6.127101 AGGTAATACCGGATCATCGATATCA 58.873 40.000 9.46 0.00 44.90 2.15
1896 3676 7.894376 TCAACGATTTAACAAACTACCTAGG 57.106 36.000 7.41 7.41 0.00 3.02
1915 3695 6.682863 GCAATAGTAACACAAGCTATTCAACG 59.317 38.462 0.00 0.00 34.36 4.10
1947 3727 5.046663 GGCAACCAAAGAAAAATCCCAGATA 60.047 40.000 0.00 0.00 0.00 1.98
2034 3817 5.568392 AGAGAATGCCTCATGAAAAGAACT 58.432 37.500 0.00 0.00 44.40 3.01
2040 3823 4.847198 TGCTTAGAGAATGCCTCATGAAA 58.153 39.130 0.00 0.00 44.40 2.69
2084 3867 4.503714 TTATGGCCCTCTTCCAGTTTAG 57.496 45.455 0.00 0.00 36.98 1.85
2148 3935 9.230122 TCAAGAAAATTATGCATACTCAGTTCA 57.770 29.630 5.74 0.00 0.00 3.18
2152 3939 8.218338 ACCTCAAGAAAATTATGCATACTCAG 57.782 34.615 5.74 0.57 0.00 3.35
2192 4015 2.958355 ACCACTTGGAAAACATCTGTGG 59.042 45.455 1.14 0.00 43.11 4.17
2221 4054 1.074405 TGCTGAAACCAGAGCAGGAAT 59.926 47.619 0.00 0.00 40.30 3.01
2284 4117 1.738099 CTTGGCTCCGGAGTTGTCG 60.738 63.158 31.43 13.41 0.00 4.35
2494 4327 4.261572 CCCTTGTTGTTCACAATGACGATT 60.262 41.667 0.00 0.00 44.72 3.34
2503 4336 1.444119 GCTCGCCCTTGTTGTTCACA 61.444 55.000 0.00 0.00 0.00 3.58
2518 4351 3.197790 CGGGTGCCAATCAGCTCG 61.198 66.667 0.00 0.00 42.57 5.03
2618 4451 5.652014 GCTAGATACAGGTCAGCAGATAGAT 59.348 44.000 0.00 0.00 32.46 1.98
2764 4597 0.677288 ACACACTTCGGTTCCATCGA 59.323 50.000 0.00 0.00 34.62 3.59
2765 4598 1.194547 CAACACACTTCGGTTCCATCG 59.805 52.381 0.00 0.00 0.00 3.84
2816 4649 0.601558 GTCAGGTCCTGTAACGAGCA 59.398 55.000 18.65 0.00 32.61 4.26
2821 4654 3.202829 TGTTTGGTCAGGTCCTGTAAC 57.797 47.619 18.65 16.74 32.61 2.50
2825 4658 2.038952 TGAGATGTTTGGTCAGGTCCTG 59.961 50.000 13.21 13.21 0.00 3.86
2831 4664 5.482006 TCATGTAGTGAGATGTTTGGTCAG 58.518 41.667 0.00 0.00 31.80 3.51
2841 4674 5.268387 ACTCCACTCTTCATGTAGTGAGAT 58.732 41.667 20.01 7.76 44.79 2.75
2844 4677 7.482169 AAATACTCCACTCTTCATGTAGTGA 57.518 36.000 20.01 10.13 44.79 3.41
2955 4806 7.254084 CCCATTTCATTATGCGAAACTAAAAGC 60.254 37.037 0.00 0.00 35.31 3.51
2958 4809 6.039616 GCCCATTTCATTATGCGAAACTAAA 58.960 36.000 0.00 0.00 35.31 1.85
2965 4816 3.489355 AGATGCCCATTTCATTATGCGA 58.511 40.909 0.00 0.00 0.00 5.10
3033 4905 5.593909 ACACAAATGACCACAGAAAAGATGA 59.406 36.000 0.00 0.00 0.00 2.92
3041 4913 5.651387 TTGAAAACACAAATGACCACAGA 57.349 34.783 0.00 0.00 0.00 3.41
3044 4916 9.862585 GATATTTTTGAAAACACAAATGACCAC 57.137 29.630 0.00 0.00 39.09 4.16
3092 4965 0.603569 CTCACTACAGCTTCACCGGT 59.396 55.000 0.00 0.00 0.00 5.28
3094 4967 1.702886 CACTCACTACAGCTTCACCG 58.297 55.000 0.00 0.00 0.00 4.94
3118 4996 9.530633 GTAATTACTGAACATAGAAGAACCGAT 57.469 33.333 8.41 0.00 0.00 4.18
3139 5017 7.503566 AGATGCCATGCAGTGTAATTAGTAATT 59.496 33.333 12.61 12.61 43.65 1.40
3140 5018 7.000472 AGATGCCATGCAGTGTAATTAGTAAT 59.000 34.615 0.00 0.00 43.65 1.89
3141 5019 6.356556 AGATGCCATGCAGTGTAATTAGTAA 58.643 36.000 0.00 0.00 43.65 2.24
3142 5020 5.928976 AGATGCCATGCAGTGTAATTAGTA 58.071 37.500 0.00 0.00 43.65 1.82
3143 5021 4.785301 AGATGCCATGCAGTGTAATTAGT 58.215 39.130 0.00 0.00 43.65 2.24
3144 5022 5.762825 AAGATGCCATGCAGTGTAATTAG 57.237 39.130 0.00 0.00 43.65 1.73
3145 5023 6.601217 TGTTAAGATGCCATGCAGTGTAATTA 59.399 34.615 0.00 0.00 43.65 1.40
3153 5207 7.493320 ACAAAATAATGTTAAGATGCCATGCAG 59.507 33.333 0.00 0.00 43.65 4.41
3330 5394 9.667107 CCCAAGTAGTGATTTTACAGAAGATTA 57.333 33.333 0.00 0.00 0.00 1.75
3331 5395 7.611855 CCCCAAGTAGTGATTTTACAGAAGATT 59.388 37.037 0.00 0.00 0.00 2.40
3337 5401 4.918588 ACCCCCAAGTAGTGATTTTACAG 58.081 43.478 0.00 0.00 0.00 2.74
3348 5412 4.295141 TCATGTGTTTACCCCCAAGTAG 57.705 45.455 0.00 0.00 0.00 2.57
3351 5415 6.790232 AATATTCATGTGTTTACCCCCAAG 57.210 37.500 0.00 0.00 0.00 3.61
3402 5466 4.314740 TTTAAATGTGCCAGTGTTCCAC 57.685 40.909 0.00 0.00 34.10 4.02
3428 5492 5.680619 TGTCTTAAGTGAGGTGTTCATGTT 58.319 37.500 1.63 0.00 38.29 2.71
3490 5554 8.722342 TTCTTACAAAAATGCTCGTGTATTTC 57.278 30.769 12.78 0.00 37.48 2.17


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

AutoCloner maintained by Alex Coulton.