Multiple sequence alignment - TraesCS2D01G374100

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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 TraesCS2D01G374100 chr2D 100.000 4940 0 0 1 4940 477428346 477423407 0.000000e+00 9123
1 TraesCS2D01G374100 chr2D 97.154 527 14 1 1 526 614352392 614352918 0.000000e+00 889
2 TraesCS2D01G374100 chr2D 97.137 524 14 1 1 523 600610870 600610347 0.000000e+00 883
3 TraesCS2D01G374100 chr2D 80.258 932 166 12 2720 3636 650078873 650079801 0.000000e+00 686
4 TraesCS2D01G374100 chr2D 91.837 147 10 2 1980 2125 596662417 596662272 2.330000e-48 204
5 TraesCS2D01G374100 chr2D 82.514 183 27 3 2187 2368 15522866 15523044 6.620000e-34 156
6 TraesCS2D01G374100 chr2D 85.811 148 15 6 1980 2125 369895203 369895346 8.560000e-33 152
7 TraesCS2D01G374100 chr2D 81.383 188 30 4 2186 2371 499156506 499156322 1.110000e-31 148
8 TraesCS2D01G374100 chr2B 97.062 1770 40 6 2301 4058 559422873 559421104 0.000000e+00 2970
9 TraesCS2D01G374100 chr2B 92.067 1727 72 20 612 2305 559426869 559425175 0.000000e+00 2370
10 TraesCS2D01G374100 chr2B 79.104 938 167 22 2720 3636 786104804 786105733 1.950000e-173 619
11 TraesCS2D01G374100 chr2B 87.500 144 16 2 1983 2125 763653342 763653200 1.100000e-36 165
12 TraesCS2D01G374100 chr2B 97.674 86 2 0 527 612 559426983 559426898 1.110000e-31 148
13 TraesCS2D01G374100 chr2B 88.525 122 10 3 4126 4244 559420812 559420692 1.430000e-30 145
14 TraesCS2D01G374100 chr5D 98.540 685 8 2 4258 4940 101752302 101752986 0.000000e+00 1208
15 TraesCS2D01G374100 chr5D 98.080 677 12 1 4265 4940 44694123 44693447 0.000000e+00 1177
16 TraesCS2D01G374100 chr5D 97.637 677 15 1 4265 4940 565211069 565210393 0.000000e+00 1160
17 TraesCS2D01G374100 chr5D 97.345 678 17 1 4264 4940 501386913 501387590 0.000000e+00 1151
18 TraesCS2D01G374100 chr5D 98.050 359 6 1 169 526 538114090 538114448 1.510000e-174 623
19 TraesCS2D01G374100 chr5D 84.667 150 18 5 1980 2126 424135572 424135425 1.430000e-30 145
20 TraesCS2D01G374100 chr5D 81.183 186 28 5 2187 2368 459328865 459328683 5.150000e-30 143
21 TraesCS2D01G374100 chr3D 98.671 677 8 1 4265 4940 29285881 29286557 0.000000e+00 1199
22 TraesCS2D01G374100 chr3D 80.851 188 28 5 2187 2371 467289871 467289689 1.850000e-29 141
23 TraesCS2D01G374100 chr4D 97.932 677 13 1 4265 4940 361847444 361846768 0.000000e+00 1171
24 TraesCS2D01G374100 chr4D 97.784 677 14 1 4265 4940 145632031 145631355 0.000000e+00 1166
25 TraesCS2D01G374100 chr4D 97.637 677 15 1 4265 4940 439827310 439827986 0.000000e+00 1160
26 TraesCS2D01G374100 chr4D 98.102 527 9 1 1 526 348430793 348431319 0.000000e+00 917
27 TraesCS2D01G374100 chr6D 97.341 677 16 2 4265 4940 56791250 56791925 0.000000e+00 1149
28 TraesCS2D01G374100 chr7D 97.736 530 11 1 1 529 232372943 232373472 0.000000e+00 911
29 TraesCS2D01G374100 chr1D 97.348 528 13 1 1 527 16732631 16732104 0.000000e+00 896
30 TraesCS2D01G374100 chr1D 86.705 173 19 2 2187 2358 246517674 246517843 6.530000e-44 189
31 TraesCS2D01G374100 chr1D 86.034 179 20 3 2194 2370 395555599 395555774 2.350000e-43 187
32 TraesCS2D01G374100 chr2A 95.085 529 24 2 1 527 748156304 748156832 0.000000e+00 832
33 TraesCS2D01G374100 chr2A 80.759 1081 170 30 2720 3779 619771359 619770296 0.000000e+00 809
34 TraesCS2D01G374100 chr2A 94.318 528 28 2 1 527 114850053 114849527 0.000000e+00 808
35 TraesCS2D01G374100 chr2A 85.202 223 27 6 307 526 108517824 108518043 1.790000e-54 224
36 TraesCS2D01G374100 chr2A 84.865 185 24 2 2187 2370 770401194 770401013 3.040000e-42 183
37 TraesCS2D01G374100 chr3A 81.517 936 157 13 2720 3645 683214769 683215698 0.000000e+00 756
38 TraesCS2D01G374100 chr3B 81.303 936 158 14 2720 3645 723459798 723460726 0.000000e+00 743
39 TraesCS2D01G374100 chr4A 95.335 343 14 2 1 341 462051853 462052195 1.210000e-150 544
40 TraesCS2D01G374100 chr6A 85.870 184 22 2 2187 2369 319076520 319076700 5.050000e-45 193
41 TraesCS2D01G374100 chr6A 82.632 190 28 3 2184 2371 454802899 454803085 3.960000e-36 163
42 TraesCS2D01G374100 chr6A 89.109 101 8 2 7 106 130015231 130015329 6.720000e-24 122
43 TraesCS2D01G374100 chr1B 89.655 145 11 4 1980 2121 139068816 139068673 1.090000e-41 182
44 TraesCS2D01G374100 chr5A 71.390 734 188 21 2834 3556 535529390 535528668 6.570000e-39 172
45 TraesCS2D01G374100 chr6B 88.811 143 11 5 1982 2121 341760304 341760164 2.360000e-38 171
46 TraesCS2D01G374100 chr6B 88.276 145 12 5 1980 2121 707023941 707023799 8.500000e-38 169
47 TraesCS2D01G374100 chr7A 87.500 144 14 4 1982 2122 433054484 433054626 3.960000e-36 163
48 TraesCS2D01G374100 chr5B 83.824 136 22 0 3059 3194 508676182 508676047 4.010000e-26 130


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 TraesCS2D01G374100 chr2D 477423407 477428346 4939 True 9123.00 9123 100.000 1 4940 1 chr2D.!!$R1 4939
1 TraesCS2D01G374100 chr2D 614352392 614352918 526 False 889.00 889 97.154 1 526 1 chr2D.!!$F3 525
2 TraesCS2D01G374100 chr2D 600610347 600610870 523 True 883.00 883 97.137 1 523 1 chr2D.!!$R4 522
3 TraesCS2D01G374100 chr2D 650078873 650079801 928 False 686.00 686 80.258 2720 3636 1 chr2D.!!$F4 916
4 TraesCS2D01G374100 chr2B 559420692 559426983 6291 True 1408.25 2970 93.832 527 4244 4 chr2B.!!$R2 3717
5 TraesCS2D01G374100 chr2B 786104804 786105733 929 False 619.00 619 79.104 2720 3636 1 chr2B.!!$F1 916
6 TraesCS2D01G374100 chr5D 101752302 101752986 684 False 1208.00 1208 98.540 4258 4940 1 chr5D.!!$F1 682
7 TraesCS2D01G374100 chr5D 44693447 44694123 676 True 1177.00 1177 98.080 4265 4940 1 chr5D.!!$R1 675
8 TraesCS2D01G374100 chr5D 565210393 565211069 676 True 1160.00 1160 97.637 4265 4940 1 chr5D.!!$R4 675
9 TraesCS2D01G374100 chr5D 501386913 501387590 677 False 1151.00 1151 97.345 4264 4940 1 chr5D.!!$F2 676
10 TraesCS2D01G374100 chr3D 29285881 29286557 676 False 1199.00 1199 98.671 4265 4940 1 chr3D.!!$F1 675
11 TraesCS2D01G374100 chr4D 361846768 361847444 676 True 1171.00 1171 97.932 4265 4940 1 chr4D.!!$R2 675
12 TraesCS2D01G374100 chr4D 145631355 145632031 676 True 1166.00 1166 97.784 4265 4940 1 chr4D.!!$R1 675
13 TraesCS2D01G374100 chr4D 439827310 439827986 676 False 1160.00 1160 97.637 4265 4940 1 chr4D.!!$F2 675
14 TraesCS2D01G374100 chr4D 348430793 348431319 526 False 917.00 917 98.102 1 526 1 chr4D.!!$F1 525
15 TraesCS2D01G374100 chr6D 56791250 56791925 675 False 1149.00 1149 97.341 4265 4940 1 chr6D.!!$F1 675
16 TraesCS2D01G374100 chr7D 232372943 232373472 529 False 911.00 911 97.736 1 529 1 chr7D.!!$F1 528
17 TraesCS2D01G374100 chr1D 16732104 16732631 527 True 896.00 896 97.348 1 527 1 chr1D.!!$R1 526
18 TraesCS2D01G374100 chr2A 748156304 748156832 528 False 832.00 832 95.085 1 527 1 chr2A.!!$F2 526
19 TraesCS2D01G374100 chr2A 619770296 619771359 1063 True 809.00 809 80.759 2720 3779 1 chr2A.!!$R2 1059
20 TraesCS2D01G374100 chr2A 114849527 114850053 526 True 808.00 808 94.318 1 527 1 chr2A.!!$R1 526
21 TraesCS2D01G374100 chr3A 683214769 683215698 929 False 756.00 756 81.517 2720 3645 1 chr3A.!!$F1 925
22 TraesCS2D01G374100 chr3B 723459798 723460726 928 False 743.00 743 81.303 2720 3645 1 chr3B.!!$F1 925

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
569 573 0.320247 CATGGCGGCTATCACTCTCC 60.320 60.0 11.43 0.0 0.00 3.71 F
1659 1698 0.038166 TCCAAATGACCCAGCACTCC 59.962 55.0 0.00 0.0 0.00 3.85 F
1661 1700 0.038744 CAAATGACCCAGCACTCCCT 59.961 55.0 0.00 0.0 0.00 4.20 F
1664 1703 0.043334 ATGACCCAGCACTCCCTAGT 59.957 55.0 0.00 0.0 35.91 2.57 F
1764 1803 0.099082 CCACGCTCTACTCGTTCTCC 59.901 60.0 0.00 0.0 38.19 3.71 F
3729 6122 0.250901 GCTTGAACCTGAGAGGGCAA 60.251 55.0 0.00 0.0 40.58 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 1712 0.037697 CACACCCTCGTCGATGGAAA 60.038 55.000 21.62 0.0 0.00 3.13 R
2752 5125 2.154462 CACGGCAAGAAACAGAATCCT 58.846 47.619 0.00 0.0 0.00 3.24 R
3664 6057 2.740981 GCTTGATCGCCTCCATATCTTG 59.259 50.000 0.00 0.0 0.00 3.02 R
3729 6122 3.118956 CGTCCTTCATGCTAGGTCTCTTT 60.119 47.826 11.91 0.0 34.29 2.52 R
3833 6226 1.072015 CTCCATGCCAATCTCCTCCTC 59.928 57.143 0.00 0.0 0.00 3.71 R
4682 7312 1.883084 GATTCGGCGGCTTCACGAT 60.883 57.895 7.21 0.0 36.43 3.73 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
170 171 1.843832 TTGGTGGTGGTCCGGATCA 60.844 57.895 15.09 15.09 36.30 2.92
322 324 3.962694 AGGAGGCAGCTGCAGCAA 61.963 61.111 38.24 0.00 45.16 3.91
512 516 0.787787 CCTCGCGACATGTTTTTCGA 59.212 50.000 3.71 9.78 37.43 3.71
569 573 0.320247 CATGGCGGCTATCACTCTCC 60.320 60.000 11.43 0.00 0.00 3.71
581 585 3.767806 CTCTCCTGCCGCTGCTGA 61.768 66.667 8.56 1.08 38.61 4.26
699 732 4.228567 TCACCTGCGACGCCAACA 62.229 61.111 18.69 0.00 0.00 3.33
700 733 4.012895 CACCTGCGACGCCAACAC 62.013 66.667 18.69 0.00 0.00 3.32
709 742 3.963676 ACGCCAACACGTACAGTAA 57.036 47.368 0.00 0.00 46.19 2.24
1057 1091 3.323136 GCTGCCGCATCGACGTAG 61.323 66.667 0.00 0.00 35.78 3.51
1092 1126 0.859232 CGTTCACCCTCAACTTGTCG 59.141 55.000 0.00 0.00 0.00 4.35
1148 1182 3.691342 CTTCGTCACCGGCCAGGA 61.691 66.667 18.74 2.27 45.00 3.86
1164 1198 0.538057 AGGACAGGTACACGTTCCGA 60.538 55.000 0.00 0.00 0.00 4.55
1191 1225 2.271800 GATCTGGACCGTGACATTCAC 58.728 52.381 0.00 0.00 43.65 3.18
1193 1227 0.321671 CTGGACCGTGACATTCACCT 59.678 55.000 0.76 0.00 44.20 4.00
1203 1237 2.038426 TGACATTCACCTCGACATGGTT 59.962 45.455 0.00 0.00 35.28 3.67
1401 1435 2.668550 GTGCCGGACCAAGGTGAC 60.669 66.667 5.05 0.00 0.00 3.67
1413 1447 3.075641 GGTGACCCCCTCCGTCTC 61.076 72.222 0.00 0.00 0.00 3.36
1415 1449 2.037367 TGACCCCCTCCGTCTCTG 59.963 66.667 0.00 0.00 0.00 3.35
1416 1450 2.037527 GACCCCCTCCGTCTCTGT 59.962 66.667 0.00 0.00 0.00 3.41
1417 1451 2.037527 ACCCCCTCCGTCTCTGTC 59.962 66.667 0.00 0.00 0.00 3.51
1424 1463 1.135257 CCTCCGTCTCTGTCATGACAC 60.135 57.143 24.56 13.64 36.21 3.67
1425 1464 0.888619 TCCGTCTCTGTCATGACACC 59.111 55.000 24.56 11.37 36.21 4.16
1432 1471 2.676839 CTCTGTCATGACACCTGAATGC 59.323 50.000 24.56 0.00 36.21 3.56
1442 1481 3.614092 ACACCTGAATGCCAGTTGATAG 58.386 45.455 0.00 0.00 37.47 2.08
1453 1492 5.439721 TGCCAGTTGATAGCTATTTCATGT 58.560 37.500 7.87 0.00 0.00 3.21
1457 1496 7.519008 GCCAGTTGATAGCTATTTCATGTACAC 60.519 40.741 7.87 0.00 0.00 2.90
1463 1502 4.969816 AGCTATTTCATGTACACGTTTGC 58.030 39.130 0.00 0.00 0.00 3.68
1469 1508 3.925379 TCATGTACACGTTTGCTCTGAT 58.075 40.909 0.00 0.00 0.00 2.90
1473 1512 3.926527 TGTACACGTTTGCTCTGATCATC 59.073 43.478 0.00 0.00 0.00 2.92
1481 1520 6.072286 ACGTTTGCTCTGATCATCTTTTTCAT 60.072 34.615 0.00 0.00 0.00 2.57
1482 1521 6.805271 CGTTTGCTCTGATCATCTTTTTCATT 59.195 34.615 0.00 0.00 0.00 2.57
1483 1522 7.327761 CGTTTGCTCTGATCATCTTTTTCATTT 59.672 33.333 0.00 0.00 0.00 2.32
1508 1547 2.488153 GTCCAACAGTTTATGGCTCCAC 59.512 50.000 0.00 0.00 36.62 4.02
1509 1548 1.818674 CCAACAGTTTATGGCTCCACC 59.181 52.381 0.00 0.00 39.84 4.61
1590 1629 4.112341 GAGCTGGGCTGCTTTGCG 62.112 66.667 0.00 0.00 44.17 4.85
1659 1698 0.038166 TCCAAATGACCCAGCACTCC 59.962 55.000 0.00 0.00 0.00 3.85
1660 1699 0.967380 CCAAATGACCCAGCACTCCC 60.967 60.000 0.00 0.00 0.00 4.30
1661 1700 0.038744 CAAATGACCCAGCACTCCCT 59.961 55.000 0.00 0.00 0.00 4.20
1662 1701 1.281867 CAAATGACCCAGCACTCCCTA 59.718 52.381 0.00 0.00 0.00 3.53
1663 1702 1.207791 AATGACCCAGCACTCCCTAG 58.792 55.000 0.00 0.00 0.00 3.02
1664 1703 0.043334 ATGACCCAGCACTCCCTAGT 59.957 55.000 0.00 0.00 35.91 2.57
1665 1704 0.614979 TGACCCAGCACTCCCTAGTC 60.615 60.000 0.00 0.00 31.97 2.59
1666 1705 0.614979 GACCCAGCACTCCCTAGTCA 60.615 60.000 0.00 0.00 31.97 3.41
1667 1706 0.905337 ACCCAGCACTCCCTAGTCAC 60.905 60.000 0.00 0.00 31.97 3.67
1668 1707 1.617947 CCCAGCACTCCCTAGTCACC 61.618 65.000 0.00 0.00 31.97 4.02
1669 1708 1.513158 CAGCACTCCCTAGTCACCG 59.487 63.158 0.00 0.00 31.97 4.94
1670 1709 0.965866 CAGCACTCCCTAGTCACCGA 60.966 60.000 0.00 0.00 31.97 4.69
1671 1710 0.966370 AGCACTCCCTAGTCACCGAC 60.966 60.000 0.00 0.00 31.97 4.79
1672 1711 1.248785 GCACTCCCTAGTCACCGACA 61.249 60.000 0.00 0.00 34.60 4.35
1673 1712 1.475403 CACTCCCTAGTCACCGACAT 58.525 55.000 0.00 0.00 34.60 3.06
1674 1713 1.825474 CACTCCCTAGTCACCGACATT 59.175 52.381 0.00 0.00 34.60 2.71
1689 1728 0.902531 ACATTTCCATCGACGAGGGT 59.097 50.000 26.18 6.38 34.82 4.34
1764 1803 0.099082 CCACGCTCTACTCGTTCTCC 59.901 60.000 0.00 0.00 38.19 3.71
1785 1824 1.202698 GGAGAATCGGGGATGGTGAAG 60.203 57.143 0.00 0.00 34.37 3.02
1805 1844 2.797278 GGGCTGTCGATGACCCGAT 61.797 63.158 2.17 0.00 40.91 4.18
2047 2087 8.600449 AGAAGAAAAGAGAATGAGTACAACAG 57.400 34.615 0.00 0.00 0.00 3.16
2063 2103 4.843728 ACAACAGAGGGTACAATACATGG 58.156 43.478 0.00 0.00 0.00 3.66
2114 2154 1.554836 CAGAGCAGAGAGACAAGGGA 58.445 55.000 0.00 0.00 0.00 4.20
2125 2165 2.202236 GACAAGGGATGCTCAGGCCA 62.202 60.000 5.01 0.00 37.74 5.36
2131 2171 1.442526 GGATGCTCAGGCCACATTCG 61.443 60.000 5.01 0.00 37.74 3.34
2184 2249 8.774586 GTTTCTATAGATGCATTCGGTTTGTAT 58.225 33.333 2.58 0.00 0.00 2.29
2287 2353 4.860802 TGAGGCAATTCAATCCCTTAGA 57.139 40.909 0.00 0.00 0.00 2.10
2373 4745 1.135689 CAAACCGAATGAGCCCTTTCG 60.136 52.381 8.96 8.96 44.52 3.46
2405 4777 4.262635 CCAGGGAATTAGTACTGATCGCAT 60.263 45.833 5.39 0.00 32.86 4.73
2536 4908 4.214758 GCCTCGGAAGTTTTACTTGCTTTA 59.785 41.667 8.98 0.00 43.27 1.85
2547 4919 3.262142 TTGCTTTAGTTGCCCGCGC 62.262 57.895 0.00 0.00 0.00 6.86
2565 4937 2.276201 CGCGGGACAGATTTTGACATA 58.724 47.619 0.00 0.00 0.00 2.29
2589 4961 3.096489 GCAAGGAAGTGCAAAACATCA 57.904 42.857 0.00 0.00 44.29 3.07
2639 5011 8.109705 TGATTTTCAGCAAATTCAGCTAGTTA 57.890 30.769 5.18 0.00 41.14 2.24
2752 5125 4.121669 GACTGAGCTCTGGCGCGA 62.122 66.667 22.75 0.00 44.37 5.87
3729 6122 0.250901 GCTTGAACCTGAGAGGGCAA 60.251 55.000 0.00 0.00 40.58 4.52
3810 6203 2.290514 TGCTCCAGGAAAGGATGAAGTG 60.291 50.000 0.00 0.00 36.99 3.16
3833 6226 1.947456 TCGATCTCACCGTGATGTAGG 59.053 52.381 0.62 0.00 0.00 3.18
3960 6353 2.526888 TTGTACTCTCTCCGTCCCAT 57.473 50.000 0.00 0.00 0.00 4.00
3961 6354 1.763968 TGTACTCTCTCCGTCCCATG 58.236 55.000 0.00 0.00 0.00 3.66
3965 6358 1.186200 CTCTCTCCGTCCCATGTCAA 58.814 55.000 0.00 0.00 0.00 3.18
3970 6363 2.009774 CTCCGTCCCATGTCAATTGAC 58.990 52.381 28.10 28.10 44.97 3.18
3983 6385 4.161333 GTCAATTGACGCTGAAAAGGATG 58.839 43.478 22.09 0.00 35.12 3.51
4001 6403 8.824756 AAAGGATGTATCTAGACAACTACTCA 57.175 34.615 0.00 0.00 31.83 3.41
4005 6407 8.347035 GGATGTATCTAGACAACTACTCACTTC 58.653 40.741 0.00 0.00 31.83 3.01
4013 6415 7.865706 AGACAACTACTCACTTCAAACAAAT 57.134 32.000 0.00 0.00 0.00 2.32
4014 6416 7.697691 AGACAACTACTCACTTCAAACAAATG 58.302 34.615 0.00 0.00 0.00 2.32
4060 6479 0.668401 CACCGTAGTTTCGTCCCCAC 60.668 60.000 0.00 0.00 0.00 4.61
4071 6490 3.050339 TCCCCACGGACGTGTTAC 58.950 61.111 21.52 0.00 44.02 2.50
4085 6504 2.134346 GTGTTACGGGCGTTTTACTGA 58.866 47.619 0.00 0.00 0.00 3.41
4097 6516 6.315393 GGGCGTTTTACTGAATCTTCATCTAA 59.685 38.462 0.00 0.00 36.46 2.10
4098 6517 7.180748 GGCGTTTTACTGAATCTTCATCTAAC 58.819 38.462 0.00 0.00 36.46 2.34
4099 6518 7.064728 GGCGTTTTACTGAATCTTCATCTAACT 59.935 37.037 0.00 0.00 36.46 2.24
4100 6519 9.084164 GCGTTTTACTGAATCTTCATCTAACTA 57.916 33.333 0.00 0.00 36.46 2.24
4107 6526 8.646900 ACTGAATCTTCATCTAACTAATCTCCC 58.353 37.037 0.00 0.00 36.46 4.30
4108 6527 7.967908 TGAATCTTCATCTAACTAATCTCCCC 58.032 38.462 0.00 0.00 31.01 4.81
4109 6528 7.568738 TGAATCTTCATCTAACTAATCTCCCCA 59.431 37.037 0.00 0.00 31.01 4.96
4110 6529 7.937700 ATCTTCATCTAACTAATCTCCCCAA 57.062 36.000 0.00 0.00 0.00 4.12
4111 6530 7.937700 TCTTCATCTAACTAATCTCCCCAAT 57.062 36.000 0.00 0.00 0.00 3.16
4112 6531 8.337118 TCTTCATCTAACTAATCTCCCCAATT 57.663 34.615 0.00 0.00 0.00 2.32
4113 6532 8.781951 TCTTCATCTAACTAATCTCCCCAATTT 58.218 33.333 0.00 0.00 0.00 1.82
4114 6533 8.980481 TTCATCTAACTAATCTCCCCAATTTC 57.020 34.615 0.00 0.00 0.00 2.17
4115 6534 8.101309 TCATCTAACTAATCTCCCCAATTTCA 57.899 34.615 0.00 0.00 0.00 2.69
4116 6535 8.556589 TCATCTAACTAATCTCCCCAATTTCAA 58.443 33.333 0.00 0.00 0.00 2.69
4117 6536 8.624776 CATCTAACTAATCTCCCCAATTTCAAC 58.375 37.037 0.00 0.00 0.00 3.18
4118 6537 7.116736 TCTAACTAATCTCCCCAATTTCAACC 58.883 38.462 0.00 0.00 0.00 3.77
4119 6538 4.270008 ACTAATCTCCCCAATTTCAACCG 58.730 43.478 0.00 0.00 0.00 4.44
4120 6539 2.143876 ATCTCCCCAATTTCAACCGG 57.856 50.000 0.00 0.00 0.00 5.28
4121 6540 0.039035 TCTCCCCAATTTCAACCGGG 59.961 55.000 6.32 0.00 38.52 5.73
4123 6542 4.531351 CCCAATTTCAACCGGGGT 57.469 55.556 6.32 0.00 34.81 4.95
4124 6543 1.971418 CCCAATTTCAACCGGGGTG 59.029 57.895 5.48 5.48 34.81 4.61
4150 6778 1.979809 TGCCTCCCCTAATCTCCAAA 58.020 50.000 0.00 0.00 0.00 3.28
4153 6781 2.713708 GCCTCCCCTAATCTCCAAATCT 59.286 50.000 0.00 0.00 0.00 2.40
4168 6796 8.561738 TCTCCAAATCTATTGGTTCACTTTAC 57.438 34.615 7.07 0.00 40.40 2.01
4169 6797 8.383175 TCTCCAAATCTATTGGTTCACTTTACT 58.617 33.333 7.07 0.00 40.40 2.24
4176 6804 8.752766 TCTATTGGTTCACTTTACTTAGTTCG 57.247 34.615 0.00 0.00 0.00 3.95
4208 6838 1.407979 AGTAAATCCCCGTGCGTCTAG 59.592 52.381 0.00 0.00 0.00 2.43
4226 6856 4.096682 GTCTAGCATTACTCAGTTCCGTCT 59.903 45.833 0.00 0.00 0.00 4.18
4241 6871 6.766944 CAGTTCCGTCTCTATCCTACTCTTAA 59.233 42.308 0.00 0.00 0.00 1.85
4243 6873 7.282901 AGTTCCGTCTCTATCCTACTCTTAAAC 59.717 40.741 0.00 0.00 0.00 2.01
4244 6874 6.656902 TCCGTCTCTATCCTACTCTTAAACA 58.343 40.000 0.00 0.00 0.00 2.83
4245 6875 7.114754 TCCGTCTCTATCCTACTCTTAAACAA 58.885 38.462 0.00 0.00 0.00 2.83
4246 6876 7.282675 TCCGTCTCTATCCTACTCTTAAACAAG 59.717 40.741 0.00 0.00 0.00 3.16
4247 6877 7.067251 CCGTCTCTATCCTACTCTTAAACAAGT 59.933 40.741 0.00 0.00 0.00 3.16
4248 6878 7.911205 CGTCTCTATCCTACTCTTAAACAAGTG 59.089 40.741 0.00 0.00 0.00 3.16
4249 6879 8.192110 GTCTCTATCCTACTCTTAAACAAGTGG 58.808 40.741 0.00 0.00 0.00 4.00
4250 6880 7.894364 TCTCTATCCTACTCTTAAACAAGTGGT 59.106 37.037 0.00 0.00 0.00 4.16
4251 6881 8.431910 TCTATCCTACTCTTAAACAAGTGGTT 57.568 34.615 0.00 0.00 42.98 3.67
4252 6882 9.537852 TCTATCCTACTCTTAAACAAGTGGTTA 57.462 33.333 0.00 0.00 39.29 2.85
4255 6885 7.318141 TCCTACTCTTAAACAAGTGGTTATCG 58.682 38.462 0.00 0.00 39.29 2.92
4256 6886 6.534079 CCTACTCTTAAACAAGTGGTTATCGG 59.466 42.308 0.00 0.00 39.29 4.18
4257 6887 6.105397 ACTCTTAAACAAGTGGTTATCGGA 57.895 37.500 0.00 0.00 39.29 4.55
4258 6888 6.708285 ACTCTTAAACAAGTGGTTATCGGAT 58.292 36.000 0.00 0.00 39.29 4.18
4259 6889 6.594159 ACTCTTAAACAAGTGGTTATCGGATG 59.406 38.462 0.00 0.00 39.29 3.51
4260 6890 6.469410 TCTTAAACAAGTGGTTATCGGATGT 58.531 36.000 0.00 0.00 39.29 3.06
4261 6891 6.938030 TCTTAAACAAGTGGTTATCGGATGTT 59.062 34.615 0.00 0.00 39.29 2.71
4338 6968 4.274978 TCCATGTATAGTTGAGGACGTGA 58.725 43.478 0.00 0.00 31.73 4.35
4682 7312 2.119655 GCCGCTTCTACTCCTCCGA 61.120 63.158 0.00 0.00 0.00 4.55
4746 7376 2.427245 CCGCCACTCTTCCCGATCT 61.427 63.158 0.00 0.00 0.00 2.75
4932 7563 1.576920 CGACTGGCTAGCGATCGAT 59.423 57.895 21.57 16.78 34.77 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 3.390521 AAGGGCGATGCAGACCGA 61.391 61.111 9.64 0.00 46.30 4.69
230 231 7.264947 GTCATAAAAATGTTCGATTTCCCCAT 58.735 34.615 0.00 0.00 0.00 4.00
407 411 3.483869 AGAATCCCCAGCTCCGCC 61.484 66.667 0.00 0.00 0.00 6.13
512 516 0.917533 TGCTAGTACTCCCTCCGTCT 59.082 55.000 0.00 0.00 0.00 4.18
569 573 3.561213 CGTCATCAGCAGCGGCAG 61.561 66.667 12.44 2.56 44.61 4.85
581 585 4.393155 TGCGGCCAGAAGCGTCAT 62.393 61.111 2.24 0.00 45.17 3.06
699 732 0.964358 AGGAGGCGCTTACTGTACGT 60.964 55.000 2.12 0.00 0.00 3.57
700 733 0.525668 CAGGAGGCGCTTACTGTACG 60.526 60.000 22.95 0.00 0.00 3.67
701 734 0.806492 GCAGGAGGCGCTTACTGTAC 60.806 60.000 29.94 13.07 33.62 2.90
702 735 1.515954 GCAGGAGGCGCTTACTGTA 59.484 57.895 29.94 0.00 33.62 2.74
703 736 2.266055 GCAGGAGGCGCTTACTGT 59.734 61.111 29.94 0.00 33.62 3.55
890 924 4.794241 GCGACGCATGTTGGACGC 62.794 66.667 16.42 12.26 39.33 5.19
895 929 1.507713 CGAACAGCGACGCATGTTG 60.508 57.895 29.30 19.52 44.57 3.33
901 935 3.173240 GAGGACGAACAGCGACGC 61.173 66.667 13.03 13.03 44.57 5.19
902 936 2.870161 CGAGGACGAACAGCGACG 60.870 66.667 0.00 0.00 44.57 5.12
1081 1115 2.551270 GGTGCGCGACAAGTTGAG 59.449 61.111 12.10 4.33 0.00 3.02
1083 1117 4.368808 CCGGTGCGCGACAAGTTG 62.369 66.667 12.10 0.00 0.00 3.16
1110 1144 1.966451 GGTCAGTTTGTCCCGGCTG 60.966 63.158 0.00 0.00 0.00 4.85
1191 1225 1.141881 CGGAGGAACCATGTCGAGG 59.858 63.158 0.00 0.00 38.90 4.63
1345 1379 4.035102 GTTGCCGGAGAAGCCCCT 62.035 66.667 5.05 0.00 0.00 4.79
1389 1423 2.531942 AGGGGGTCACCTTGGTCC 60.532 66.667 0.00 0.00 37.69 4.46
1401 1435 1.381872 ATGACAGAGACGGAGGGGG 60.382 63.158 0.00 0.00 0.00 5.40
1413 1447 1.741706 GGCATTCAGGTGTCATGACAG 59.258 52.381 28.54 17.04 42.74 3.51
1415 1449 1.741706 CTGGCATTCAGGTGTCATGAC 59.258 52.381 19.27 19.27 39.76 3.06
1416 1450 2.118313 CTGGCATTCAGGTGTCATGA 57.882 50.000 0.00 0.00 39.76 3.07
1432 1471 7.306807 CGTGTACATGAAATAGCTATCAACTGG 60.307 40.741 9.62 0.00 0.00 4.00
1442 1481 4.969816 AGCAAACGTGTACATGAAATAGC 58.030 39.130 21.82 15.69 0.00 2.97
1453 1492 4.456280 AGATGATCAGAGCAAACGTGTA 57.544 40.909 0.09 0.00 0.00 2.90
1457 1496 5.692814 TGAAAAAGATGATCAGAGCAAACG 58.307 37.500 0.09 0.00 0.00 3.60
1463 1502 9.557338 GACAGAAAATGAAAAAGATGATCAGAG 57.443 33.333 0.09 0.00 0.00 3.35
1469 1508 7.780064 TGTTGGACAGAAAATGAAAAAGATGA 58.220 30.769 0.00 0.00 0.00 2.92
1590 1629 5.163258 ACATGTCAGGTAAAGATGGATCCTC 60.163 44.000 14.23 8.14 0.00 3.71
1659 1698 3.458189 GATGGAAATGTCGGTGACTAGG 58.542 50.000 0.00 0.00 33.15 3.02
1660 1699 3.116300 CGATGGAAATGTCGGTGACTAG 58.884 50.000 0.00 0.00 33.15 2.57
1661 1700 2.756207 TCGATGGAAATGTCGGTGACTA 59.244 45.455 0.00 0.00 33.15 2.59
1662 1701 1.548719 TCGATGGAAATGTCGGTGACT 59.451 47.619 0.00 0.00 33.15 3.41
1663 1702 1.659098 GTCGATGGAAATGTCGGTGAC 59.341 52.381 0.00 0.00 0.00 3.67
1664 1703 1.734377 CGTCGATGGAAATGTCGGTGA 60.734 52.381 0.00 0.00 0.00 4.02
1665 1704 0.645355 CGTCGATGGAAATGTCGGTG 59.355 55.000 0.00 0.00 0.00 4.94
1666 1705 0.528924 TCGTCGATGGAAATGTCGGT 59.471 50.000 4.48 0.00 0.00 4.69
1667 1706 1.200483 CTCGTCGATGGAAATGTCGG 58.800 55.000 4.48 0.00 0.00 4.79
1668 1707 1.200483 CCTCGTCGATGGAAATGTCG 58.800 55.000 4.48 0.00 0.00 4.35
1669 1708 1.134788 ACCCTCGTCGATGGAAATGTC 60.135 52.381 21.62 0.00 0.00 3.06
1670 1709 0.902531 ACCCTCGTCGATGGAAATGT 59.097 50.000 21.62 4.57 0.00 2.71
1671 1710 1.290203 CACCCTCGTCGATGGAAATG 58.710 55.000 21.62 7.30 0.00 2.32
1672 1711 0.902531 ACACCCTCGTCGATGGAAAT 59.097 50.000 21.62 5.13 0.00 2.17
1673 1712 0.037697 CACACCCTCGTCGATGGAAA 60.038 55.000 21.62 0.00 0.00 3.13
1674 1713 1.183030 ACACACCCTCGTCGATGGAA 61.183 55.000 21.62 0.00 0.00 3.53
1689 1728 2.416747 CGCTTCTGAATCCTCAACACA 58.583 47.619 0.00 0.00 0.00 3.72
1722 1761 2.945668 GTCTCGATCCCCCAAGAAATTG 59.054 50.000 0.00 0.00 0.00 2.32
1723 1762 2.576191 TGTCTCGATCCCCCAAGAAATT 59.424 45.455 0.00 0.00 0.00 1.82
1764 1803 1.069765 CACCATCCCCGATTCTCCG 59.930 63.158 0.00 0.00 0.00 4.63
1776 1815 1.021390 CGACAGCCCACTTCACCATC 61.021 60.000 0.00 0.00 0.00 3.51
1785 1824 2.125106 GGGTCATCGACAGCCCAC 60.125 66.667 13.31 0.00 40.76 4.61
1805 1844 4.783621 GCATCGCCTCCCTGCACA 62.784 66.667 0.00 0.00 35.96 4.57
1818 1857 4.065088 TGTACTCCTTGTTGTTCAGCATC 58.935 43.478 0.00 0.00 0.00 3.91
1951 1990 1.303561 TGCCTGTGCATCCACCTTC 60.304 57.895 0.00 0.00 44.23 3.46
1999 2039 3.674997 TCAAGGAAAGATACGCAAGCTT 58.325 40.909 0.00 0.00 45.62 3.74
2044 2084 2.843730 TGCCATGTATTGTACCCTCTGT 59.156 45.455 0.00 0.00 0.00 3.41
2047 2087 4.085357 TCATGCCATGTATTGTACCCTC 57.915 45.455 4.31 0.00 0.00 4.30
2063 2103 1.660560 ATGCCCTCTTGCGTTCATGC 61.661 55.000 0.00 0.00 0.00 4.06
2114 2154 1.452651 CCGAATGTGGCCTGAGCAT 60.453 57.895 3.32 0.25 42.56 3.79
2131 2171 2.945668 CTCCGGAATCCTCATTCAAACC 59.054 50.000 5.23 0.00 40.41 3.27
2158 2223 7.016361 ACAAACCGAATGCATCTATAGAAAC 57.984 36.000 6.52 2.52 0.00 2.78
2220 2285 5.924356 TGAGTGGATGTGTAGTTTCTTTCA 58.076 37.500 0.00 0.00 0.00 2.69
2221 2286 6.861065 TTGAGTGGATGTGTAGTTTCTTTC 57.139 37.500 0.00 0.00 0.00 2.62
2230 2295 7.759489 AAAATAAGCTTTGAGTGGATGTGTA 57.241 32.000 3.20 0.00 0.00 2.90
2257 2322 3.297134 TGAATTGCCTCATTCCTACCC 57.703 47.619 0.00 0.00 0.00 3.69
2266 2332 4.860802 TCTAAGGGATTGAATTGCCTCA 57.139 40.909 0.00 0.00 36.25 3.86
2287 2353 3.377253 AGGATGACACTTGCCATCATT 57.623 42.857 7.68 0.00 40.55 2.57
2547 4919 5.036737 GCAATTATGTCAAAATCTGTCCCG 58.963 41.667 0.00 0.00 0.00 5.14
2608 4980 7.227910 AGCTGAATTTGCTGAAAATCAAAATGT 59.772 29.630 6.17 0.00 37.51 2.71
2639 5011 3.005554 CTCGGATGATCTTGCAAAGTGT 58.994 45.455 0.00 0.00 46.34 3.55
2752 5125 2.154462 CACGGCAAGAAACAGAATCCT 58.846 47.619 0.00 0.00 0.00 3.24
3664 6057 2.740981 GCTTGATCGCCTCCATATCTTG 59.259 50.000 0.00 0.00 0.00 3.02
3729 6122 3.118956 CGTCCTTCATGCTAGGTCTCTTT 60.119 47.826 11.91 0.00 34.29 2.52
3810 6203 1.135083 ACATCACGGTGAGATCGAACC 60.135 52.381 16.84 9.22 0.00 3.62
3833 6226 1.072015 CTCCATGCCAATCTCCTCCTC 59.928 57.143 0.00 0.00 0.00 3.71
3960 6353 3.210227 TCCTTTTCAGCGTCAATTGACA 58.790 40.909 32.06 14.58 44.99 3.58
3961 6354 3.896648 TCCTTTTCAGCGTCAATTGAC 57.103 42.857 25.68 25.68 41.47 3.18
3965 6358 5.431765 AGATACATCCTTTTCAGCGTCAAT 58.568 37.500 0.00 0.00 0.00 2.57
3970 6363 5.592054 TGTCTAGATACATCCTTTTCAGCG 58.408 41.667 0.00 0.00 0.00 5.18
3971 6364 7.044798 AGTTGTCTAGATACATCCTTTTCAGC 58.955 38.462 0.00 0.00 0.00 4.26
3978 6380 7.579105 AGTGAGTAGTTGTCTAGATACATCCT 58.421 38.462 0.00 0.00 0.00 3.24
3983 6385 9.344309 GTTTGAAGTGAGTAGTTGTCTAGATAC 57.656 37.037 0.00 0.00 0.00 2.24
4001 6403 4.221703 TCACCACCAACATTTGTTTGAAGT 59.778 37.500 1.93 0.00 35.83 3.01
4005 6407 2.857152 CGTCACCACCAACATTTGTTTG 59.143 45.455 0.00 0.00 35.83 2.93
4013 6415 2.190843 CACCCGTCACCACCAACA 59.809 61.111 0.00 0.00 0.00 3.33
4014 6416 3.284449 GCACCCGTCACCACCAAC 61.284 66.667 0.00 0.00 0.00 3.77
4045 6449 1.966762 TCCGTGGGGACGAAACTAC 59.033 57.895 0.00 0.00 37.43 2.73
4060 6479 4.705519 ACGCCCGTAACACGTCCG 62.706 66.667 0.00 2.89 40.58 4.79
4064 6483 1.136557 CAGTAAAACGCCCGTAACACG 60.137 52.381 0.00 0.00 42.11 4.49
4071 6490 2.739913 TGAAGATTCAGTAAAACGCCCG 59.260 45.455 0.00 0.00 32.50 6.13
4074 6493 7.965045 AGTTAGATGAAGATTCAGTAAAACGC 58.035 34.615 1.32 0.00 41.08 4.84
4085 6504 7.937700 TGGGGAGATTAGTTAGATGAAGATT 57.062 36.000 0.00 0.00 0.00 2.40
4097 6516 4.270008 CGGTTGAAATTGGGGAGATTAGT 58.730 43.478 0.00 0.00 0.00 2.24
4098 6517 3.632145 CCGGTTGAAATTGGGGAGATTAG 59.368 47.826 0.00 0.00 0.00 1.73
4099 6518 3.626222 CCCGGTTGAAATTGGGGAGATTA 60.626 47.826 0.00 0.00 40.51 1.75
4100 6519 2.456577 CCGGTTGAAATTGGGGAGATT 58.543 47.619 0.00 0.00 0.00 2.40
4101 6520 1.341976 CCCGGTTGAAATTGGGGAGAT 60.342 52.381 0.00 0.00 40.51 2.75
4102 6521 0.039035 CCCGGTTGAAATTGGGGAGA 59.961 55.000 0.00 0.00 40.51 3.71
4103 6522 2.578683 CCCGGTTGAAATTGGGGAG 58.421 57.895 0.00 0.00 40.51 4.30
4104 6523 4.854587 CCCGGTTGAAATTGGGGA 57.145 55.556 0.00 0.00 40.51 4.81
4106 6525 1.540435 CCACCCCGGTTGAAATTGGG 61.540 60.000 0.00 0.00 42.23 4.12
4107 6526 1.540435 CCCACCCCGGTTGAAATTGG 61.540 60.000 0.00 0.00 0.00 3.16
4108 6527 1.971418 CCCACCCCGGTTGAAATTG 59.029 57.895 0.00 0.00 0.00 2.32
4109 6528 1.911269 GCCCACCCCGGTTGAAATT 60.911 57.895 0.00 0.00 0.00 1.82
4110 6529 2.283604 GCCCACCCCGGTTGAAAT 60.284 61.111 0.00 0.00 0.00 2.17
4111 6530 4.607025 GGCCCACCCCGGTTGAAA 62.607 66.667 0.00 0.00 0.00 2.69
4130 6758 1.979809 TTGGAGATTAGGGGAGGCAA 58.020 50.000 0.00 0.00 0.00 4.52
4150 6778 9.367444 CGAACTAAGTAAAGTGAACCAATAGAT 57.633 33.333 0.00 0.00 0.00 1.98
4153 6781 9.979578 TTACGAACTAAGTAAAGTGAACCAATA 57.020 29.630 0.00 0.00 31.89 1.90
4174 6802 6.762661 CGGGGATTTACTTAAGGATTTTACGA 59.237 38.462 7.53 0.00 0.00 3.43
4176 6804 7.680350 GCACGGGGATTTACTTAAGGATTTTAC 60.680 40.741 7.53 0.00 0.00 2.01
4208 6838 3.512033 AGAGACGGAACTGAGTAATGC 57.488 47.619 0.00 0.00 0.00 3.56
4218 6848 7.066766 TGTTTAAGAGTAGGATAGAGACGGAAC 59.933 40.741 0.00 0.00 0.00 3.62
4221 6851 6.939132 TGTTTAAGAGTAGGATAGAGACGG 57.061 41.667 0.00 0.00 0.00 4.79
4226 6856 8.431910 AACCACTTGTTTAAGAGTAGGATAGA 57.568 34.615 0.00 0.00 37.36 1.98
4241 6871 4.394729 ACAACATCCGATAACCACTTGTT 58.605 39.130 0.00 0.00 41.11 2.83
4243 6873 4.215399 ACAACAACATCCGATAACCACTTG 59.785 41.667 0.00 0.00 0.00 3.16
4244 6874 4.394729 ACAACAACATCCGATAACCACTT 58.605 39.130 0.00 0.00 0.00 3.16
4245 6875 4.015872 ACAACAACATCCGATAACCACT 57.984 40.909 0.00 0.00 0.00 4.00
4246 6876 4.214545 TCAACAACAACATCCGATAACCAC 59.785 41.667 0.00 0.00 0.00 4.16
4247 6877 4.390264 TCAACAACAACATCCGATAACCA 58.610 39.130 0.00 0.00 0.00 3.67
4248 6878 4.693566 TCTCAACAACAACATCCGATAACC 59.306 41.667 0.00 0.00 0.00 2.85
4249 6879 5.856126 TCTCAACAACAACATCCGATAAC 57.144 39.130 0.00 0.00 0.00 1.89
4250 6880 5.937540 ACATCTCAACAACAACATCCGATAA 59.062 36.000 0.00 0.00 0.00 1.75
4251 6881 5.487433 ACATCTCAACAACAACATCCGATA 58.513 37.500 0.00 0.00 0.00 2.92
4252 6882 4.326826 ACATCTCAACAACAACATCCGAT 58.673 39.130 0.00 0.00 0.00 4.18
4253 6883 3.738982 ACATCTCAACAACAACATCCGA 58.261 40.909 0.00 0.00 0.00 4.55
4254 6884 4.929211 TCTACATCTCAACAACAACATCCG 59.071 41.667 0.00 0.00 0.00 4.18
4255 6885 6.992063 ATCTACATCTCAACAACAACATCC 57.008 37.500 0.00 0.00 0.00 3.51
4256 6886 8.479313 TGTATCTACATCTCAACAACAACATC 57.521 34.615 0.00 0.00 0.00 3.06
4261 6891 9.533253 CACATATGTATCTACATCTCAACAACA 57.467 33.333 8.32 0.00 45.11 3.33
4565 7195 3.680196 TAGGGGTGGGAGAGGCGT 61.680 66.667 0.00 0.00 0.00 5.68
4669 7299 2.704464 TCACGATCGGAGGAGTAGAA 57.296 50.000 20.98 0.00 0.00 2.10
4682 7312 1.883084 GATTCGGCGGCTTCACGAT 60.883 57.895 7.21 0.00 36.43 3.73


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

AutoCloner maintained by Alex Coulton.