Multiple sequence alignment - TraesCS6B01G149300

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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 TraesCS6B01G149300 chr6B 100.000 3641 0 0 1 3641 150220857 150224497 0.000000e+00 6724.0
1 TraesCS6B01G149300 chr6B 76.066 422 67 25 2991 3405 204111704 204112098 4.800000e-44 189.0
2 TraesCS6B01G149300 chr6D 92.756 2540 118 23 2 2531 77622659 77625142 0.000000e+00 3611.0
3 TraesCS6B01G149300 chr6D 87.193 1671 168 27 995 2643 56928833 56927187 0.000000e+00 1858.0
4 TraesCS6B01G149300 chr6D 85.980 699 66 17 2529 3200 77625830 77626523 0.000000e+00 719.0
5 TraesCS6B01G149300 chr6D 90.991 444 36 4 3199 3639 77647719 77648161 2.420000e-166 595.0
6 TraesCS6B01G149300 chr6A 93.962 1474 82 3 1175 2642 93271286 93272758 0.000000e+00 2222.0
7 TraesCS6B01G149300 chr6A 87.713 1937 139 37 1417 3316 93205287 93207161 0.000000e+00 2167.0
8 TraesCS6B01G149300 chr6A 85.268 1025 89 34 2646 3639 93283832 93284825 0.000000e+00 1000.0
9 TraesCS6B01G149300 chr6A 87.723 839 70 5 1 830 93168324 93169138 0.000000e+00 948.0
10 TraesCS6B01G149300 chr6A 89.062 512 53 3 209 718 93266337 93266847 1.840000e-177 632.0
11 TraesCS6B01G149300 chr6A 85.787 591 53 13 209 796 93265532 93266094 6.730000e-167 597.0
12 TraesCS6B01G149300 chr6A 88.518 479 45 8 1 474 93147687 93148160 4.080000e-159 571.0
13 TraesCS6B01G149300 chr6A 88.235 238 28 0 1269 1506 93179712 93179949 5.950000e-73 285.0
14 TraesCS6B01G149300 chr6A 92.268 194 15 0 985 1178 93268408 93268601 3.580000e-70 276.0
15 TraesCS6B01G149300 chr6A 85.020 247 14 4 870 1113 93169136 93169362 2.830000e-56 230.0
16 TraesCS6B01G149300 chr6A 91.176 170 14 1 752 921 93267159 93267327 2.830000e-56 230.0
17 TraesCS6B01G149300 chr6A 88.079 151 12 2 1121 1271 93169587 93169731 1.340000e-39 174.0
18 TraesCS6B01G149300 chr2D 77.335 1681 296 54 1015 2643 610404621 610402974 0.000000e+00 915.0
19 TraesCS6B01G149300 chr2D 76.689 1673 319 46 1012 2643 610378183 610376541 0.000000e+00 863.0
20 TraesCS6B01G149300 chr2D 85.965 228 30 2 3414 3639 340483630 340483403 3.630000e-60 243.0
21 TraesCS6B01G149300 chr5B 77.204 930 171 28 1031 1947 94048379 94049280 4.200000e-139 505.0
22 TraesCS6B01G149300 chr5B 77.223 821 157 17 1133 1947 94087354 94088150 1.540000e-123 453.0
23 TraesCS6B01G149300 chr5D 76.923 936 173 29 1031 1955 88465071 88465974 3.270000e-135 492.0
24 TraesCS6B01G149300 chr5D 76.707 820 163 15 1133 1947 88469888 88470684 7.220000e-117 431.0
25 TraesCS6B01G149300 chr5D 89.447 199 19 2 3413 3609 473429485 473429287 2.170000e-62 250.0
26 TraesCS6B01G149300 chr5D 76.440 382 77 9 3032 3406 446874374 446873999 1.030000e-45 195.0
27 TraesCS6B01G149300 chr2A 80.542 627 117 4 2021 2643 743265932 743265307 9.150000e-131 477.0
28 TraesCS6B01G149300 chr2A 76.078 974 176 37 1012 1956 743266972 743266027 4.290000e-124 455.0
29 TraesCS6B01G149300 chr2A 77.500 240 50 3 3172 3408 677807493 677807731 1.360000e-29 141.0
30 TraesCS6B01G149300 chr2A 100.000 31 0 0 421 451 386009085 386009115 1.410000e-04 58.4
31 TraesCS6B01G149300 chr5A 76.979 821 159 14 1133 1947 82300079 82300875 3.340000e-120 442.0
32 TraesCS6B01G149300 chr2B 78.965 599 118 8 2024 2617 41473328 41472733 5.660000e-108 401.0
33 TraesCS6B01G149300 chr2B 80.153 393 73 5 2255 2643 745765444 745765053 4.600000e-74 289.0
34 TraesCS6B01G149300 chr7A 78.105 475 94 8 2940 3408 37838950 37839420 3.560000e-75 292.0
35 TraesCS6B01G149300 chr7A 86.792 53 4 3 400 451 303946907 303946957 5.080000e-04 56.5
36 TraesCS6B01G149300 chr3B 78.795 415 75 8 3001 3408 17107353 17106945 2.160000e-67 267.0
37 TraesCS6B01G149300 chr7D 78.933 375 68 10 3042 3408 448508840 448508469 1.010000e-60 244.0
38 TraesCS6B01G149300 chr7D 81.154 260 36 7 3020 3271 79377600 79377854 2.870000e-46 196.0
39 TraesCS6B01G149300 chr3A 85.022 227 32 2 3414 3639 291782289 291782064 2.830000e-56 230.0
40 TraesCS6B01G149300 chr3A 83.913 230 35 2 3411 3638 589443969 589444198 6.120000e-53 219.0
41 TraesCS6B01G149300 chr4B 84.783 230 31 4 3414 3641 484109014 484109241 1.020000e-55 228.0
42 TraesCS6B01G149300 chr3D 84.862 218 31 2 3414 3630 217683285 217683501 6.120000e-53 219.0
43 TraesCS6B01G149300 chr3D 100.000 29 0 0 423 451 449537855 449537827 2.000000e-03 54.7
44 TraesCS6B01G149300 chr1D 83.550 231 35 3 3413 3641 31755178 31754949 2.850000e-51 213.0
45 TraesCS6B01G149300 chr4D 93.478 46 1 2 410 454 37518766 37518810 2.350000e-07 67.6


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 TraesCS6B01G149300 chr6B 150220857 150224497 3640 False 6724.000000 6724 100.000000 1 3641 1 chr6B.!!$F1 3640
1 TraesCS6B01G149300 chr6D 77622659 77626523 3864 False 2165.000000 3611 89.368000 2 3200 2 chr6D.!!$F2 3198
2 TraesCS6B01G149300 chr6D 56927187 56928833 1646 True 1858.000000 1858 87.193000 995 2643 1 chr6D.!!$R1 1648
3 TraesCS6B01G149300 chr6A 93205287 93207161 1874 False 2167.000000 2167 87.713000 1417 3316 1 chr6A.!!$F3 1899
4 TraesCS6B01G149300 chr6A 93283832 93284825 993 False 1000.000000 1000 85.268000 2646 3639 1 chr6A.!!$F4 993
5 TraesCS6B01G149300 chr6A 93265532 93272758 7226 False 791.400000 2222 90.451000 209 2642 5 chr6A.!!$F6 2433
6 TraesCS6B01G149300 chr6A 93168324 93169731 1407 False 450.666667 948 86.940667 1 1271 3 chr6A.!!$F5 1270
7 TraesCS6B01G149300 chr2D 610402974 610404621 1647 True 915.000000 915 77.335000 1015 2643 1 chr2D.!!$R3 1628
8 TraesCS6B01G149300 chr2D 610376541 610378183 1642 True 863.000000 863 76.689000 1012 2643 1 chr2D.!!$R2 1631
9 TraesCS6B01G149300 chr5B 94048379 94049280 901 False 505.000000 505 77.204000 1031 1947 1 chr5B.!!$F1 916
10 TraesCS6B01G149300 chr5B 94087354 94088150 796 False 453.000000 453 77.223000 1133 1947 1 chr5B.!!$F2 814
11 TraesCS6B01G149300 chr5D 88465071 88470684 5613 False 461.500000 492 76.815000 1031 1955 2 chr5D.!!$F1 924
12 TraesCS6B01G149300 chr2A 743265307 743266972 1665 True 466.000000 477 78.310000 1012 2643 2 chr2A.!!$R1 1631
13 TraesCS6B01G149300 chr5A 82300079 82300875 796 False 442.000000 442 76.979000 1133 1947 1 chr5A.!!$F1 814
14 TraesCS6B01G149300 chr2B 41472733 41473328 595 True 401.000000 401 78.965000 2024 2617 1 chr2B.!!$R1 593

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
257 263 0.030092 ACCCCTAGCCCTATGAGCAA 60.030 55.0 0.0 0.0 0.00 3.91 F
1537 6647 0.908198 GGTCAATCTGCTCCAGGACT 59.092 55.0 0.0 0.0 31.51 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 6772 1.142688 ACTCCTGGAACCTGCCCAAT 61.143 55.0 0.0 0.0 32.53 3.16 R
2945 8854 0.252103 TAAGGTGACCGAGGAGGCTT 60.252 55.0 0.0 0.0 46.52 4.35 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 7.121315 ACAACCAGCTATTTTCAATCTCTTACC 59.879 37.037 0.00 0.00 0.00 2.85
207 212 8.562052 CAAACACATATACTCACATACATGCAT 58.438 33.333 0.00 0.00 0.00 3.96
257 263 0.030092 ACCCCTAGCCCTATGAGCAA 60.030 55.000 0.00 0.00 0.00 3.91
278 284 3.382832 CGGGAGACTGAGCCGGTT 61.383 66.667 1.90 0.00 39.98 4.44
293 299 1.271379 CCGGTTGGTCTTGAGGTTGAT 60.271 52.381 0.00 0.00 0.00 2.57
398 1220 2.978978 TCAAACCTGAGGTCTGATTCCA 59.021 45.455 2.94 0.00 33.12 3.53
405 1227 2.183679 GAGGTCTGATTCCAGGTGAGT 58.816 52.381 0.00 0.00 40.76 3.41
475 1297 8.732531 TCTCCGGTAAACATATTTAAAAACCAG 58.267 33.333 0.00 0.00 32.04 4.00
575 1410 6.915843 CAGTATGACAAACAAAACCTGGTTAC 59.084 38.462 13.37 2.63 39.69 2.50
580 1415 4.951094 ACAAACAAAACCTGGTTACTAGCA 59.049 37.500 13.37 0.00 31.23 3.49
596 1431 2.403252 AGCAAGAATAAGACACCCCG 57.597 50.000 0.00 0.00 0.00 5.73
646 1481 3.937706 TCGCTAAGTCGCTAGGGATATAC 59.062 47.826 13.18 0.44 36.31 1.47
647 1482 3.940221 CGCTAAGTCGCTAGGGATATACT 59.060 47.826 13.18 2.94 34.58 2.12
648 1483 4.034279 CGCTAAGTCGCTAGGGATATACTC 59.966 50.000 13.18 0.00 34.58 2.59
649 1484 4.336153 GCTAAGTCGCTAGGGATATACTCC 59.664 50.000 13.18 0.00 44.11 3.85
651 1486 2.305343 AGTCGCTAGGGATATACTCCGT 59.695 50.000 13.18 0.00 46.01 4.69
830 1992 1.188863 GTGGATTGGCTGCCTGATTT 58.811 50.000 21.03 0.00 0.00 2.17
831 1993 2.025037 AGTGGATTGGCTGCCTGATTTA 60.025 45.455 21.03 0.00 0.00 1.40
832 1994 2.961062 GTGGATTGGCTGCCTGATTTAT 59.039 45.455 21.03 3.71 0.00 1.40
833 1995 3.005155 GTGGATTGGCTGCCTGATTTATC 59.995 47.826 21.03 11.79 0.00 1.75
834 1996 3.117398 TGGATTGGCTGCCTGATTTATCT 60.117 43.478 21.03 0.00 0.00 1.98
835 1997 4.104579 TGGATTGGCTGCCTGATTTATCTA 59.895 41.667 21.03 8.03 0.00 1.98
836 1998 4.699257 GGATTGGCTGCCTGATTTATCTAG 59.301 45.833 21.03 0.00 0.00 2.43
837 1999 4.778213 TTGGCTGCCTGATTTATCTAGT 57.222 40.909 21.03 0.00 0.00 2.57
838 2000 4.342862 TGGCTGCCTGATTTATCTAGTC 57.657 45.455 21.03 0.00 0.00 2.59
839 2001 3.711190 TGGCTGCCTGATTTATCTAGTCA 59.289 43.478 21.03 0.00 0.00 3.41
840 2002 4.349048 TGGCTGCCTGATTTATCTAGTCAT 59.651 41.667 21.03 0.00 0.00 3.06
841 2003 5.163163 TGGCTGCCTGATTTATCTAGTCATT 60.163 40.000 21.03 0.00 0.00 2.57
842 2004 5.767168 GGCTGCCTGATTTATCTAGTCATTT 59.233 40.000 12.43 0.00 0.00 2.32
843 2005 6.293845 GGCTGCCTGATTTATCTAGTCATTTG 60.294 42.308 12.43 0.00 0.00 2.32
844 2006 6.624352 TGCCTGATTTATCTAGTCATTTGC 57.376 37.500 0.00 0.00 0.00 3.68
845 2007 6.359804 TGCCTGATTTATCTAGTCATTTGCT 58.640 36.000 0.00 0.00 0.00 3.91
846 2008 7.508687 TGCCTGATTTATCTAGTCATTTGCTA 58.491 34.615 0.00 0.00 0.00 3.49
847 2009 7.658982 TGCCTGATTTATCTAGTCATTTGCTAG 59.341 37.037 0.00 0.00 37.77 3.42
848 2010 7.659390 GCCTGATTTATCTAGTCATTTGCTAGT 59.341 37.037 0.00 0.00 37.69 2.57
849 2011 9.553064 CCTGATTTATCTAGTCATTTGCTAGTT 57.447 33.333 0.00 0.00 37.69 2.24
866 2028 9.515226 TTTGCTAGTTTATCTTATTGTCTTGGT 57.485 29.630 0.00 0.00 0.00 3.67
867 2029 9.515226 TTGCTAGTTTATCTTATTGTCTTGGTT 57.485 29.630 0.00 0.00 0.00 3.67
868 2030 9.162764 TGCTAGTTTATCTTATTGTCTTGGTTC 57.837 33.333 0.00 0.00 0.00 3.62
869 2031 9.162764 GCTAGTTTATCTTATTGTCTTGGTTCA 57.837 33.333 0.00 0.00 0.00 3.18
905 2067 6.131544 AGTTCTAGTTTTGTTCGCATTTGT 57.868 33.333 0.00 0.00 0.00 2.83
1326 6436 3.121030 GAGTGCTTCACGGCGCAT 61.121 61.111 10.83 0.00 44.17 4.73
1482 6592 4.891727 CCCCGCCTCGATGAACGG 62.892 72.222 8.17 8.17 45.21 4.44
1488 6598 2.180769 CTCGATGAACGGACGGCA 59.819 61.111 0.00 0.00 42.82 5.69
1537 6647 0.908198 GGTCAATCTGCTCCAGGACT 59.092 55.000 0.00 0.00 31.51 3.85
1947 7093 0.674895 AAGGCATCGTCTTGGTGAGC 60.675 55.000 0.00 0.00 0.00 4.26
1949 7095 0.955428 GGCATCGTCTTGGTGAGCAA 60.955 55.000 0.00 0.00 0.00 3.91
1985 7131 2.849294 TCATCAAACATGACACCGGA 57.151 45.000 9.46 0.00 0.00 5.14
1987 7133 4.479786 TCATCAAACATGACACCGGATA 57.520 40.909 9.46 0.00 0.00 2.59
1988 7134 5.034852 TCATCAAACATGACACCGGATAT 57.965 39.130 9.46 0.00 0.00 1.63
2203 7391 1.819632 CCCTACCTGCAATGCGTCC 60.820 63.158 0.00 0.00 0.00 4.79
2376 7564 1.699083 TCTCCAACAGAGTTCATGCCA 59.301 47.619 0.00 0.00 43.71 4.92
2386 7574 1.280421 AGTTCATGCCAGAGAGGTTCC 59.720 52.381 0.00 0.00 40.61 3.62
2476 7673 4.005472 CGATGCGCATTCTCGGCC 62.005 66.667 26.12 8.69 0.00 6.13
2521 7718 4.731853 TCCAGTGGGATGCCGGGA 62.732 66.667 9.92 0.00 38.64 5.14
2618 8505 0.039035 CCCCGGGAATTTGTCAAGGA 59.961 55.000 26.32 0.00 0.00 3.36
2622 8509 3.260632 CCCGGGAATTTGTCAAGGATTTT 59.739 43.478 18.48 0.00 0.00 1.82
2649 8536 3.609853 TGCTTCCACTTGATGTATCACC 58.390 45.455 0.00 0.00 36.36 4.02
2674 8561 3.117284 TGGAGTAAGGGCAGGTTTCTTTT 60.117 43.478 0.00 0.00 0.00 2.27
2680 8567 9.623000 GAGTAAGGGCAGGTTTCTTTTATTATA 57.377 33.333 0.00 0.00 0.00 0.98
2684 8571 9.487442 AAGGGCAGGTTTCTTTTATTATATGAA 57.513 29.630 0.00 0.00 0.00 2.57
2744 8651 1.829456 CACCTCCATGCCGACCATA 59.171 57.895 0.00 0.00 31.47 2.74
2748 8655 1.299541 CTCCATGCCGACCATACAAC 58.700 55.000 0.00 0.00 31.47 3.32
2749 8656 0.107410 TCCATGCCGACCATACAACC 60.107 55.000 0.00 0.00 31.47 3.77
2750 8657 1.436195 CCATGCCGACCATACAACCG 61.436 60.000 0.00 0.00 31.47 4.44
2751 8658 1.817941 ATGCCGACCATACAACCGC 60.818 57.895 0.00 0.00 30.69 5.68
2755 8662 0.655733 CCGACCATACAACCGCATTC 59.344 55.000 0.00 0.00 0.00 2.67
2857 8765 3.605634 CACCCGGTCACAATCAATAAGA 58.394 45.455 0.00 0.00 0.00 2.10
2865 8773 5.235186 GGTCACAATCAATAAGAGACGGATG 59.765 44.000 0.00 0.00 0.00 3.51
2866 8774 4.811024 TCACAATCAATAAGAGACGGATGC 59.189 41.667 0.00 0.00 0.00 3.91
2886 8794 2.187707 CTCATAGTTTTTGCATGCGCC 58.812 47.619 14.09 0.00 37.32 6.53
2888 8796 2.159393 TCATAGTTTTTGCATGCGCCTC 60.159 45.455 14.09 2.50 37.32 4.70
2889 8797 1.242989 TAGTTTTTGCATGCGCCTCA 58.757 45.000 14.09 0.00 37.32 3.86
2892 8800 0.108709 TTTTTGCATGCGCCTCATCC 60.109 50.000 14.09 0.00 37.32 3.51
2910 8819 4.517453 TCATCCCAAAAGTCCGTGTAAAAG 59.483 41.667 0.00 0.00 0.00 2.27
2917 8826 2.547990 AGTCCGTGTAAAAGAGGGGAT 58.452 47.619 0.00 0.00 0.00 3.85
2920 8829 4.077108 GTCCGTGTAAAAGAGGGGATTTT 58.923 43.478 0.00 0.00 34.40 1.82
2921 8830 4.155462 GTCCGTGTAAAAGAGGGGATTTTC 59.845 45.833 0.00 0.00 32.38 2.29
2945 8854 0.471211 CCCTCCTAACCGGCTATCCA 60.471 60.000 0.00 0.00 0.00 3.41
2956 8865 1.369321 GCTATCCAAGCCTCCTCGG 59.631 63.158 0.00 0.00 46.25 4.63
2962 8871 2.120718 AAGCCTCCTCGGTCACCT 59.879 61.111 0.00 0.00 34.25 4.00
2967 9172 0.613853 CCTCCTCGGTCACCTTACCA 60.614 60.000 0.00 0.00 39.71 3.25
2975 9180 1.229082 TCACCTTACCACCGCCTCT 60.229 57.895 0.00 0.00 0.00 3.69
2979 9184 1.265454 CCTTACCACCGCCTCTTCCT 61.265 60.000 0.00 0.00 0.00 3.36
3001 9206 0.750911 CCATCTGGCTCCTTCTTGGC 60.751 60.000 0.00 0.00 35.26 4.52
3018 9239 3.068881 CCGCCTCCTTCTTGACCA 58.931 61.111 0.00 0.00 0.00 4.02
3026 9247 2.307098 CTCCTTCTTGACCACCTCCATT 59.693 50.000 0.00 0.00 0.00 3.16
3055 9276 2.163010 CCAAGCGCTTCAACATCTTGAT 59.837 45.455 22.21 0.00 36.26 2.57
3057 9278 4.337763 CAAGCGCTTCAACATCTTGATAC 58.662 43.478 22.21 0.00 36.26 2.24
3065 9286 3.118445 TCAACATCTTGATACGGATGGCA 60.118 43.478 7.65 0.00 42.34 4.92
3076 9297 2.250485 GATGGCATGCACGATCGC 59.750 61.111 21.36 0.00 0.00 4.58
3138 9362 1.143183 GTATCCTTCGAAGCGGCCA 59.857 57.895 19.99 0.85 0.00 5.36
3139 9363 0.249911 GTATCCTTCGAAGCGGCCAT 60.250 55.000 19.99 8.05 0.00 4.40
3147 9371 1.746615 GAAGCGGCCATGAGCTCAA 60.747 57.895 22.50 4.23 43.78 3.02
3155 9379 1.615384 GCCATGAGCTCAACCCTTCTT 60.615 52.381 22.50 0.00 38.99 2.52
3200 9424 0.391793 CGAGGTTGAGCTTCTTCCCC 60.392 60.000 0.00 0.00 0.00 4.81
3205 9429 2.509561 GAGCTTCTTCCCCGTCGC 60.510 66.667 0.00 0.00 0.00 5.19
3206 9430 4.083862 AGCTTCTTCCCCGTCGCC 62.084 66.667 0.00 0.00 0.00 5.54
3219 9443 3.527427 TCGCCGCCATCGAGATGT 61.527 61.111 11.59 0.00 37.11 3.06
3230 9454 4.680708 GCCATCGAGATGTTAAACCTCTCA 60.681 45.833 11.59 2.15 39.05 3.27
3241 9465 5.891551 TGTTAAACCTCTCAGCCTTCTTTTT 59.108 36.000 0.00 0.00 0.00 1.94
3248 9472 4.646572 TCTCAGCCTTCTTTTTCTCCTTC 58.353 43.478 0.00 0.00 0.00 3.46
3251 9475 3.885297 CAGCCTTCTTTTTCTCCTTCACA 59.115 43.478 0.00 0.00 0.00 3.58
3264 9489 2.086869 CCTTCACATGGAACGCTTGAT 58.913 47.619 0.00 0.00 0.00 2.57
3270 9495 2.355756 ACATGGAACGCTTGATACATGC 59.644 45.455 0.00 0.00 39.30 4.06
3319 9544 0.904865 ACCTCTCCGTCATCTTGGCA 60.905 55.000 0.00 0.00 0.00 4.92
3358 10402 6.811665 GCTTCTCTTTCTTCTCTTCCTACTTC 59.188 42.308 0.00 0.00 0.00 3.01
3398 12111 2.069165 AACCTTCTTGGGCGGCTCTT 62.069 55.000 9.56 0.00 41.11 2.85
3419 12133 1.143277 TGGTTGGGTTGTTATGTCGGT 59.857 47.619 0.00 0.00 0.00 4.69
3421 12135 2.223745 GTTGGGTTGTTATGTCGGTGT 58.776 47.619 0.00 0.00 0.00 4.16
3426 12140 4.885907 TGGGTTGTTATGTCGGTGTTAAAA 59.114 37.500 0.00 0.00 0.00 1.52
3466 12256 2.604686 TCCCGAGCTGCTGGTCTT 60.605 61.111 18.80 0.00 38.45 3.01
3528 12318 3.062639 GGTTCGGACCCCTCGAAA 58.937 61.111 0.00 0.00 46.14 3.46
3536 12326 2.550639 CGGACCCCTCGAAAAGGTAAAA 60.551 50.000 0.94 0.00 44.56 1.52
3548 12338 5.566627 CGAAAAGGTAAAACCCTACGTCCTA 60.567 44.000 0.00 0.00 39.75 2.94
3615 12454 2.286294 CCTCAAGCTCGTATGATTGTGC 59.714 50.000 0.00 0.00 35.19 4.57
3624 12463 5.017294 TCGTATGATTGTGCTATGAACCA 57.983 39.130 0.00 0.00 0.00 3.67
3633 12472 2.291741 GTGCTATGAACCATAAGGCTGC 59.708 50.000 0.00 0.00 39.06 5.25
3639 12478 4.502105 TGAACCATAAGGCTGCTAATCA 57.498 40.909 0.00 0.00 39.06 2.57
3640 12479 5.052693 TGAACCATAAGGCTGCTAATCAT 57.947 39.130 0.00 0.00 39.06 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 172 2.206750 GTGTTTGTACCGTGCTTCTCA 58.793 47.619 0.00 0.00 0.00 3.27
173 178 4.865925 TGAGTATATGTGTTTGTACCGTGC 59.134 41.667 0.00 0.00 0.00 5.34
177 182 8.936070 TGTATGTGAGTATATGTGTTTGTACC 57.064 34.615 0.00 0.00 0.00 3.34
207 212 7.489160 AGAGCGTTTATGAACATGAGTGTATA 58.511 34.615 0.00 0.00 37.67 1.47
257 263 2.344203 CGGCTCAGTCTCCCGAAGT 61.344 63.158 0.00 0.00 44.55 3.01
278 284 3.390967 TGTCTTCATCAACCTCAAGACCA 59.609 43.478 7.92 0.00 42.75 4.02
293 299 1.002430 GAGGCATCTGTGGTGTCTTCA 59.998 52.381 0.00 0.00 30.36 3.02
331 337 4.067896 GAGTGTTCTTTCAATGAGAGGCA 58.932 43.478 0.78 0.00 0.00 4.75
332 338 4.153835 CAGAGTGTTCTTTCAATGAGAGGC 59.846 45.833 0.78 0.00 0.00 4.70
333 339 4.153835 GCAGAGTGTTCTTTCAATGAGAGG 59.846 45.833 0.78 0.00 0.00 3.69
334 340 4.153835 GGCAGAGTGTTCTTTCAATGAGAG 59.846 45.833 0.00 0.00 0.00 3.20
335 341 4.067896 GGCAGAGTGTTCTTTCAATGAGA 58.932 43.478 0.00 0.00 0.00 3.27
336 342 4.070716 AGGCAGAGTGTTCTTTCAATGAG 58.929 43.478 0.00 0.00 0.00 2.90
337 343 4.090761 AGGCAGAGTGTTCTTTCAATGA 57.909 40.909 0.00 0.00 0.00 2.57
338 344 4.843220 AAGGCAGAGTGTTCTTTCAATG 57.157 40.909 0.00 0.00 0.00 2.82
339 345 6.716628 TCATAAAGGCAGAGTGTTCTTTCAAT 59.283 34.615 0.00 0.00 32.53 2.57
340 346 6.061441 TCATAAAGGCAGAGTGTTCTTTCAA 58.939 36.000 0.00 0.00 32.53 2.69
341 347 5.620206 TCATAAAGGCAGAGTGTTCTTTCA 58.380 37.500 0.00 0.00 32.53 2.69
398 1220 1.697982 GGTTGTACTCCCAACTCACCT 59.302 52.381 4.29 0.00 43.36 4.00
405 1227 1.913419 GGAGGATGGTTGTACTCCCAA 59.087 52.381 7.94 0.00 42.87 4.12
475 1297 1.266175 TCGTCGTTTCACTCTCACTCC 59.734 52.381 0.00 0.00 0.00 3.85
575 1410 3.118738 ACGGGGTGTCTTATTCTTGCTAG 60.119 47.826 0.00 0.00 0.00 3.42
580 1415 4.529377 TCAACTACGGGGTGTCTTATTCTT 59.471 41.667 0.00 0.00 33.62 2.52
596 1431 8.564574 TGGATGACTGTTTTGTTAATCAACTAC 58.435 33.333 0.00 0.00 35.61 2.73
651 1486 2.825075 TACCGTCTGCCTACGCCAGA 62.825 60.000 2.60 0.00 41.51 3.86
840 2002 9.515226 ACCAAGACAATAAGATAAACTAGCAAA 57.485 29.630 0.00 0.00 0.00 3.68
841 2003 9.515226 AACCAAGACAATAAGATAAACTAGCAA 57.485 29.630 0.00 0.00 0.00 3.91
842 2004 9.162764 GAACCAAGACAATAAGATAAACTAGCA 57.837 33.333 0.00 0.00 0.00 3.49
843 2005 9.162764 TGAACCAAGACAATAAGATAAACTAGC 57.837 33.333 0.00 0.00 0.00 3.42
847 2009 9.573133 CCAATGAACCAAGACAATAAGATAAAC 57.427 33.333 0.00 0.00 0.00 2.01
848 2010 9.527157 TCCAATGAACCAAGACAATAAGATAAA 57.473 29.630 0.00 0.00 0.00 1.40
849 2011 8.956426 GTCCAATGAACCAAGACAATAAGATAA 58.044 33.333 0.00 0.00 0.00 1.75
850 2012 8.328758 AGTCCAATGAACCAAGACAATAAGATA 58.671 33.333 0.00 0.00 0.00 1.98
851 2013 7.177878 AGTCCAATGAACCAAGACAATAAGAT 58.822 34.615 0.00 0.00 0.00 2.40
852 2014 6.542821 AGTCCAATGAACCAAGACAATAAGA 58.457 36.000 0.00 0.00 0.00 2.10
853 2015 6.824305 AGTCCAATGAACCAAGACAATAAG 57.176 37.500 0.00 0.00 0.00 1.73
854 2016 7.595819 AAAGTCCAATGAACCAAGACAATAA 57.404 32.000 0.00 0.00 0.00 1.40
855 2017 7.286546 TCAAAAGTCCAATGAACCAAGACAATA 59.713 33.333 0.00 0.00 0.00 1.90
856 2018 6.098124 TCAAAAGTCCAATGAACCAAGACAAT 59.902 34.615 0.00 0.00 0.00 2.71
857 2019 5.420421 TCAAAAGTCCAATGAACCAAGACAA 59.580 36.000 0.00 0.00 0.00 3.18
858 2020 4.952957 TCAAAAGTCCAATGAACCAAGACA 59.047 37.500 0.00 0.00 0.00 3.41
859 2021 5.514274 TCAAAAGTCCAATGAACCAAGAC 57.486 39.130 0.00 0.00 0.00 3.01
860 2022 5.656416 ACTTCAAAAGTCCAATGAACCAAGA 59.344 36.000 0.00 0.00 37.02 3.02
861 2023 5.906073 ACTTCAAAAGTCCAATGAACCAAG 58.094 37.500 0.00 0.00 37.02 3.61
862 2024 5.930837 ACTTCAAAAGTCCAATGAACCAA 57.069 34.783 0.00 0.00 37.02 3.67
863 2025 5.656416 AGAACTTCAAAAGTCCAATGAACCA 59.344 36.000 0.00 0.00 41.91 3.67
864 2026 6.149129 AGAACTTCAAAAGTCCAATGAACC 57.851 37.500 0.00 0.00 41.91 3.62
865 2027 7.931275 ACTAGAACTTCAAAAGTCCAATGAAC 58.069 34.615 0.00 0.00 41.91 3.18
866 2028 8.519799 AACTAGAACTTCAAAAGTCCAATGAA 57.480 30.769 0.00 0.00 41.91 2.57
867 2029 8.519799 AAACTAGAACTTCAAAAGTCCAATGA 57.480 30.769 0.00 0.00 41.91 2.57
868 2030 9.023967 CAAAACTAGAACTTCAAAAGTCCAATG 57.976 33.333 0.00 0.00 41.91 2.82
869 2031 8.749354 ACAAAACTAGAACTTCAAAAGTCCAAT 58.251 29.630 0.00 0.00 41.91 3.16
870 2032 8.117813 ACAAAACTAGAACTTCAAAAGTCCAA 57.882 30.769 0.00 0.00 41.91 3.53
871 2033 7.696992 ACAAAACTAGAACTTCAAAAGTCCA 57.303 32.000 0.00 0.00 41.91 4.02
905 2067 5.637810 ACGATTCTTAAAGAAATCGTCAGCA 59.362 36.000 19.29 0.00 40.68 4.41
949 3141 6.183360 GCGCTTGCTATATAGTGCTAGTAGTA 60.183 42.308 11.38 0.00 42.91 1.82
950 3142 5.392165 GCGCTTGCTATATAGTGCTAGTAGT 60.392 44.000 11.38 0.00 42.91 2.73
951 3143 5.031578 GCGCTTGCTATATAGTGCTAGTAG 58.968 45.833 11.38 0.00 42.91 2.57
979 3171 1.559219 TGCCCTGAAAATCCTCGATCA 59.441 47.619 0.00 0.00 0.00 2.92
1520 6630 1.829849 CTGAGTCCTGGAGCAGATTGA 59.170 52.381 17.33 0.00 32.44 2.57
1647 6772 1.142688 ACTCCTGGAACCTGCCCAAT 61.143 55.000 0.00 0.00 32.53 3.16
1947 7093 5.527214 TGATGAAGGAATTACGGTGCTATTG 59.473 40.000 0.00 0.00 0.00 1.90
1949 7095 5.290493 TGATGAAGGAATTACGGTGCTAT 57.710 39.130 0.00 0.00 0.00 2.97
1985 7131 6.157211 GGACATTACGTTGCAGCTAGTATAT 58.843 40.000 0.00 0.00 0.00 0.86
1987 7133 4.142026 TGGACATTACGTTGCAGCTAGTAT 60.142 41.667 0.00 0.00 0.00 2.12
1988 7134 3.193903 TGGACATTACGTTGCAGCTAGTA 59.806 43.478 0.00 0.00 0.00 1.82
2358 7546 1.699083 TCTGGCATGAACTCTGTTGGA 59.301 47.619 0.00 0.00 0.00 3.53
2376 7564 0.961358 CCGTGTCGAGGAACCTCTCT 60.961 60.000 17.18 0.00 40.69 3.10
2467 7664 2.496817 GAGCGTCAGGCCGAGAAT 59.503 61.111 0.00 0.00 45.17 2.40
2521 7718 2.813754 CCATGTCAATGACACGACCTTT 59.186 45.455 19.17 0.00 45.65 3.11
2618 8505 4.978099 TCAAGTGGAAGCAGAGAGAAAAT 58.022 39.130 0.00 0.00 0.00 1.82
2622 8509 2.902486 ACATCAAGTGGAAGCAGAGAGA 59.098 45.455 0.00 0.00 0.00 3.10
2649 8536 3.456277 AGAAACCTGCCCTTACTCCATAG 59.544 47.826 0.00 0.00 0.00 2.23
2717 8604 1.153168 CATGGAGGTGCCCTAACGG 60.153 63.158 0.00 0.00 31.76 4.44
2718 8605 1.819632 GCATGGAGGTGCCCTAACG 60.820 63.158 0.00 0.00 39.18 3.18
2732 8619 2.013807 CGGTTGTATGGTCGGCATG 58.986 57.895 0.00 0.00 0.00 4.06
2733 8620 1.817941 GCGGTTGTATGGTCGGCAT 60.818 57.895 0.00 0.00 0.00 4.40
2734 8621 2.435234 GCGGTTGTATGGTCGGCA 60.435 61.111 0.00 0.00 0.00 5.69
2744 8651 3.008049 GGAGATATAGGGAATGCGGTTGT 59.992 47.826 0.00 0.00 0.00 3.32
2748 8655 1.137086 CCGGAGATATAGGGAATGCGG 59.863 57.143 0.00 0.00 38.50 5.69
2749 8656 1.825474 ACCGGAGATATAGGGAATGCG 59.175 52.381 9.46 0.00 0.00 4.73
2750 8657 2.832129 TGACCGGAGATATAGGGAATGC 59.168 50.000 9.46 0.00 0.00 3.56
2751 8658 3.449018 CCTGACCGGAGATATAGGGAATG 59.551 52.174 9.46 0.00 33.16 2.67
2755 8662 2.448453 GACCTGACCGGAGATATAGGG 58.552 57.143 9.46 0.84 36.31 3.53
2824 8731 2.238646 TGACCGGGTGCTAGAAAATCAT 59.761 45.455 3.30 0.00 0.00 2.45
2827 8734 1.349688 TGTGACCGGGTGCTAGAAAAT 59.650 47.619 3.30 0.00 0.00 1.82
2857 8765 3.375299 GCAAAAACTATGAGCATCCGTCT 59.625 43.478 0.00 0.00 0.00 4.18
2865 8773 1.585214 GCGCATGCAAAAACTATGAGC 59.415 47.619 19.57 4.19 42.15 4.26
2866 8774 2.159338 AGGCGCATGCAAAAACTATGAG 60.159 45.455 19.57 0.00 45.35 2.90
2886 8794 2.185004 ACACGGACTTTTGGGATGAG 57.815 50.000 0.00 0.00 0.00 2.90
2888 8796 4.517453 TCTTTTACACGGACTTTTGGGATG 59.483 41.667 0.00 0.00 0.00 3.51
2889 8797 4.721132 TCTTTTACACGGACTTTTGGGAT 58.279 39.130 0.00 0.00 0.00 3.85
2892 8800 3.252458 CCCTCTTTTACACGGACTTTTGG 59.748 47.826 0.00 0.00 0.00 3.28
2910 8819 2.238084 AGGGCAAAGAAAATCCCCTC 57.762 50.000 0.00 0.00 42.31 4.30
2917 8826 2.510613 CGGTTAGGAGGGCAAAGAAAA 58.489 47.619 0.00 0.00 0.00 2.29
2920 8829 1.988015 CCGGTTAGGAGGGCAAAGA 59.012 57.895 0.00 0.00 45.00 2.52
2921 8830 1.749258 GCCGGTTAGGAGGGCAAAG 60.749 63.158 1.90 0.00 46.13 2.77
2930 8839 3.307379 GCTTGGATAGCCGGTTAGG 57.693 57.895 1.90 0.00 44.48 2.69
2945 8854 0.252103 TAAGGTGACCGAGGAGGCTT 60.252 55.000 0.00 0.00 46.52 4.35
2956 8865 1.079336 GAGGCGGTGGTAAGGTGAC 60.079 63.158 0.00 0.00 0.00 3.67
2962 8871 0.543410 TGAGGAAGAGGCGGTGGTAA 60.543 55.000 0.00 0.00 0.00 2.85
2967 9172 1.613630 ATGGTGAGGAAGAGGCGGT 60.614 57.895 0.00 0.00 0.00 5.68
2975 9180 0.252881 AGGAGCCAGATGGTGAGGAA 60.253 55.000 0.00 0.00 37.57 3.36
2979 9184 1.280133 CAAGAAGGAGCCAGATGGTGA 59.720 52.381 0.00 0.00 37.57 4.02
3001 9206 1.376037 GTGGTCAAGAAGGAGGCGG 60.376 63.158 0.00 0.00 0.00 6.13
3018 9239 2.119484 TTGGCGGACGAAATGGAGGT 62.119 55.000 0.00 0.00 0.00 3.85
3055 9276 0.599991 GATCGTGCATGCCATCCGTA 60.600 55.000 16.68 3.54 0.00 4.02
3057 9278 2.941333 GATCGTGCATGCCATCCG 59.059 61.111 16.68 12.15 0.00 4.18
3076 9297 0.460109 TGAGTTGGATGACGATGCGG 60.460 55.000 0.00 0.00 0.00 5.69
3138 9362 3.515602 ACAAAGAAGGGTTGAGCTCAT 57.484 42.857 19.04 0.85 0.00 2.90
3139 9363 3.214328 GAACAAAGAAGGGTTGAGCTCA 58.786 45.455 13.74 13.74 0.00 4.26
3147 9371 2.495084 GAAGCTCGAACAAAGAAGGGT 58.505 47.619 0.00 0.00 0.00 4.34
3155 9379 0.959553 AGGAGACGAAGCTCGAACAA 59.040 50.000 11.64 0.00 43.74 2.83
3205 9429 1.597663 GGTTTAACATCTCGATGGCGG 59.402 52.381 11.25 0.00 42.91 6.13
3206 9430 2.540101 GAGGTTTAACATCTCGATGGCG 59.460 50.000 11.25 0.00 42.91 5.69
3219 9443 6.365520 AGAAAAAGAAGGCTGAGAGGTTTAA 58.634 36.000 0.00 0.00 0.00 1.52
3230 9454 4.170468 TGTGAAGGAGAAAAAGAAGGCT 57.830 40.909 0.00 0.00 0.00 4.58
3241 9465 0.976641 AGCGTTCCATGTGAAGGAGA 59.023 50.000 16.06 0.00 40.49 3.71
3248 9472 3.789791 GCATGTATCAAGCGTTCCATGTG 60.790 47.826 0.00 0.00 33.85 3.21
3251 9475 2.923121 AGCATGTATCAAGCGTTCCAT 58.077 42.857 0.00 0.00 33.06 3.41
3264 9489 3.262420 GCGAAGAAGGAGAAAGCATGTA 58.738 45.455 0.00 0.00 0.00 2.29
3270 9495 3.045601 TCTTGGCGAAGAAGGAGAAAG 57.954 47.619 8.90 0.00 35.14 2.62
3319 9544 1.075659 GAAGCAAGAAGGGGTGGCT 59.924 57.895 0.00 0.00 36.13 4.75
3365 10409 4.149090 AGAAGGTTAGAAGAGGGTTCCT 57.851 45.455 0.00 0.00 36.03 3.36
3398 12111 2.231529 CCGACATAACAACCCAACCAA 58.768 47.619 0.00 0.00 0.00 3.67
3419 12133 2.706890 GGAGATCCGCCAGTTTTAACA 58.293 47.619 0.00 0.00 0.00 2.41
3441 12231 2.681778 CAGCTCGGGACCTCCTGT 60.682 66.667 0.00 0.00 43.01 4.00
3466 12256 2.041081 CCCTCCTGTTACCATTGTTCCA 59.959 50.000 0.00 0.00 0.00 3.53
3482 12272 1.134670 CATCGTCTCCTGTTTCCCTCC 60.135 57.143 0.00 0.00 0.00 4.30
3484 12274 1.645710 ACATCGTCTCCTGTTTCCCT 58.354 50.000 0.00 0.00 0.00 4.20
3488 12278 4.618920 AGGTAAACATCGTCTCCTGTTT 57.381 40.909 6.02 6.02 45.07 2.83
3528 12318 4.420206 AGTAGGACGTAGGGTTTTACCTT 58.580 43.478 0.00 0.00 42.09 3.50
3556 12346 9.935241 GTACTTGATACTCCATCACATCAATAT 57.065 33.333 0.00 0.00 43.49 1.28
3563 12355 6.850752 TCTTGTACTTGATACTCCATCACA 57.149 37.500 0.00 0.00 43.49 3.58
3615 12454 6.233434 TGATTAGCAGCCTTATGGTTCATAG 58.767 40.000 0.00 0.00 35.27 2.23


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

AutoCloner maintained by Alex Coulton.