Multiple sequence alignment - TraesCS7A01G279400

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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 TraesCS7A01G279400 chr7A 100.000 2834 0 0 1 2834 298481452 298478619 0.000000e+00 5234.0
1 TraesCS7A01G279400 chr7A 97.222 36 1 0 735 770 543460942 543460907 8.480000e-06 62.1
2 TraesCS7A01G279400 chr7D 96.183 1336 38 4 1499 2831 269704239 269705564 0.000000e+00 2172.0
3 TraesCS7A01G279400 chr7D 97.153 562 16 0 951 1512 269702391 269702952 0.000000e+00 950.0
4 TraesCS7A01G279400 chr7B 95.789 1235 40 3 1600 2831 271250887 271252112 0.000000e+00 1982.0
5 TraesCS7A01G279400 chr7B 95.827 623 25 1 980 1602 271250163 271250784 0.000000e+00 1005.0
6 TraesCS7A01G279400 chr7B 94.828 58 3 0 733 790 721309904 721309961 1.080000e-14 91.6
7 TraesCS7A01G279400 chr7B 92.857 42 2 1 948 988 271249971 271250012 3.050000e-05 60.2
8 TraesCS7A01G279400 chr6D 83.470 974 113 29 1 929 292865113 292864143 0.000000e+00 863.0
9 TraesCS7A01G279400 chr6B 89.628 376 36 2 1 373 170869123 170869498 2.550000e-130 475.0
10 TraesCS7A01G279400 chr6B 83.811 488 46 14 419 873 170870259 170870746 1.560000e-117 433.0
11 TraesCS7A01G279400 chr4D 94.444 72 4 0 732 803 401774086 401774157 8.300000e-21 111.0
12 TraesCS7A01G279400 chr5D 88.000 75 8 1 596 670 528873305 528873378 1.400000e-13 87.9
13 TraesCS7A01G279400 chr6A 86.765 68 9 0 604 671 399697004 399697071 3.030000e-10 76.8
14 TraesCS7A01G279400 chr4A 100.000 33 0 0 537 569 16847203 16847235 8.480000e-06 62.1
15 TraesCS7A01G279400 chr4A 96.970 33 1 0 537 569 742098496 742098528 3.940000e-04 56.5
16 TraesCS7A01G279400 chr3B 92.500 40 3 0 541 580 429178856 429178817 1.100000e-04 58.4
17 TraesCS7A01G279400 chr5B 100.000 30 0 0 540 569 92453897 92453868 3.940000e-04 56.5
18 TraesCS7A01G279400 chr5A 96.970 33 1 0 537 569 572510648 572510680 3.940000e-04 56.5
19 TraesCS7A01G279400 chr4B 96.970 33 1 0 537 569 466618931 466618963 3.940000e-04 56.5


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 TraesCS7A01G279400 chr7A 298478619 298481452 2833 True 5234.000000 5234 100.000000 1 2834 1 chr7A.!!$R1 2833
1 TraesCS7A01G279400 chr7D 269702391 269705564 3173 False 1561.000000 2172 96.668000 951 2831 2 chr7D.!!$F1 1880
2 TraesCS7A01G279400 chr7B 271249971 271252112 2141 False 1015.733333 1982 94.824333 948 2831 3 chr7B.!!$F2 1883
3 TraesCS7A01G279400 chr6D 292864143 292865113 970 True 863.000000 863 83.470000 1 929 1 chr6D.!!$R1 928
4 TraesCS7A01G279400 chr6B 170869123 170870746 1623 False 454.000000 475 86.719500 1 873 2 chr6B.!!$F1 872

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
415 1127 0.108615 ATGTAGTCCACTGCAGCGAC 60.109 55.0 21.36 21.36 41.68 5.19 F
828 1581 0.326618 AAGGGGATCGATGGGAGTGT 60.327 55.0 0.54 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 2205 1.493861 CTCTCCATCTTCTGCTCCCA 58.506 55.0 0.0 0.0 0.0 4.37 R
2771 5091 0.680921 ACAAATGTCCCCCAGATGCG 60.681 55.0 0.0 0.0 0.0 4.73 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
56 57 4.568956 ACAAAATAGATGCCTGCCAAAAC 58.431 39.130 0.00 0.00 0.00 2.43
86 87 1.821216 ACTACCATTTCAAGTGGGCG 58.179 50.000 3.63 0.00 41.14 6.13
87 88 1.349688 ACTACCATTTCAAGTGGGCGA 59.650 47.619 3.63 0.00 41.14 5.54
91 92 1.470098 CCATTTCAAGTGGGCGAAGAG 59.530 52.381 0.00 0.00 32.98 2.85
113 114 2.930040 GCCACATATATATCGCGTTGCT 59.070 45.455 5.77 0.00 0.00 3.91
117 118 5.120053 CCACATATATATCGCGTTGCTGAAA 59.880 40.000 5.77 0.00 0.00 2.69
124 125 1.495951 GCGTTGCTGAAACTACCGG 59.504 57.895 0.00 0.00 36.56 5.28
126 127 1.873863 GTTGCTGAAACTACCGGGC 59.126 57.895 6.32 0.00 35.75 6.13
128 129 0.605319 TTGCTGAAACTACCGGGCTG 60.605 55.000 6.32 0.00 0.00 4.85
150 151 6.239600 GCTGATATAGGAGGACCACATGTAAA 60.240 42.308 0.00 0.00 38.94 2.01
172 173 1.959226 GCAACGCCGGAAACAGAGA 60.959 57.895 5.05 0.00 0.00 3.10
176 177 1.892209 ACGCCGGAAACAGAGAAAAT 58.108 45.000 5.05 0.00 0.00 1.82
180 181 2.094545 GCCGGAAACAGAGAAAATGCAT 60.095 45.455 5.05 0.00 0.00 3.96
185 186 4.309099 GAAACAGAGAAAATGCATGGCAA 58.691 39.130 0.00 0.00 43.62 4.52
254 255 1.745489 GGGTTAGAAGCTGGTGCCG 60.745 63.158 0.00 0.00 40.80 5.69
263 264 1.959042 AGCTGGTGCCGAATCTAATG 58.041 50.000 0.00 0.00 40.80 1.90
271 272 4.049186 GTGCCGAATCTAATGTCACGTAT 58.951 43.478 0.00 0.00 0.00 3.06
272 273 4.048504 TGCCGAATCTAATGTCACGTATG 58.951 43.478 0.00 0.00 0.00 2.39
273 274 3.428870 GCCGAATCTAATGTCACGTATGG 59.571 47.826 0.00 0.00 0.00 2.74
307 308 0.692476 TAGCAATCAGTGGCAGTGGT 59.308 50.000 21.53 12.77 0.00 4.16
355 359 6.995686 TGTTTAAAAACAGAGTGGATAGCTGA 59.004 34.615 4.19 0.00 43.45 4.26
376 1088 6.721704 TGATGCTTGTAGATCAGTAGATGT 57.278 37.500 0.00 0.00 33.72 3.06
380 1092 7.823745 TGCTTGTAGATCAGTAGATGTATGA 57.176 36.000 0.00 0.00 33.22 2.15
388 1100 5.079998 TCAGTAGATGTATGAGGGATGGT 57.920 43.478 0.00 0.00 0.00 3.55
395 1107 2.368548 TGTATGAGGGATGGTTGGATCG 59.631 50.000 0.00 0.00 0.00 3.69
399 1111 1.417890 GAGGGATGGTTGGATCGATGT 59.582 52.381 0.54 0.00 0.00 3.06
404 1116 3.555168 GGATGGTTGGATCGATGTAGTCC 60.555 52.174 0.54 0.00 0.00 3.85
405 1117 2.462723 TGGTTGGATCGATGTAGTCCA 58.537 47.619 0.54 0.48 40.13 4.02
406 1118 2.167693 TGGTTGGATCGATGTAGTCCAC 59.832 50.000 0.54 0.00 41.48 4.02
407 1119 2.431057 GGTTGGATCGATGTAGTCCACT 59.569 50.000 0.54 0.00 41.48 4.00
408 1120 3.448686 GTTGGATCGATGTAGTCCACTG 58.551 50.000 0.54 0.00 41.48 3.66
409 1121 1.409064 TGGATCGATGTAGTCCACTGC 59.591 52.381 0.54 0.00 37.12 4.40
411 1123 2.544694 GGATCGATGTAGTCCACTGCAG 60.545 54.545 13.48 13.48 41.68 4.41
412 1124 0.173481 TCGATGTAGTCCACTGCAGC 59.827 55.000 15.27 3.24 41.68 5.25
413 1125 2.670635 GATGTAGTCCACTGCAGCG 58.329 57.895 15.27 3.57 41.68 5.18
414 1126 0.173481 GATGTAGTCCACTGCAGCGA 59.827 55.000 15.27 6.83 41.68 4.93
415 1127 0.108615 ATGTAGTCCACTGCAGCGAC 60.109 55.000 21.36 21.36 41.68 5.19
416 1128 1.801913 GTAGTCCACTGCAGCGACG 60.802 63.158 22.17 7.31 0.00 5.12
417 1129 1.969589 TAGTCCACTGCAGCGACGA 60.970 57.895 22.17 17.15 0.00 4.20
418 1130 1.520600 TAGTCCACTGCAGCGACGAA 61.521 55.000 22.17 14.90 0.00 3.85
419 1131 2.049156 TCCACTGCAGCGACGAAG 60.049 61.111 15.27 0.00 0.00 3.79
451 1170 3.295273 AGTCCACTGCAGCGACGA 61.295 61.111 22.17 8.30 0.00 4.20
525 1244 4.408821 GAGGGCGCATGTGGGTGA 62.409 66.667 10.83 0.00 0.00 4.02
535 1269 1.779061 ATGTGGGTGAAGGCGGACTT 61.779 55.000 0.00 0.00 43.65 3.01
576 1329 3.003763 GGAGGCGGAGTGAAGGGT 61.004 66.667 0.00 0.00 0.00 4.34
685 1438 1.338136 AAGATACCCGTGGCTCCTGG 61.338 60.000 0.00 0.00 0.00 4.45
687 1440 1.306654 ATACCCGTGGCTCCTGGAA 60.307 57.895 0.00 0.00 0.00 3.53
730 1483 2.308722 GGGGAAGGGATCTGTGGCA 61.309 63.158 0.00 0.00 0.00 4.92
773 1526 2.586357 GGATCGAGGGCGCTTGAC 60.586 66.667 22.04 15.19 37.46 3.18
806 1559 0.810031 CGGCGACAAAGGGATCGATT 60.810 55.000 0.00 0.00 40.86 3.34
816 1569 1.068121 GGGATCGATTGGAAGGGGAT 58.932 55.000 0.00 0.00 0.00 3.85
819 1572 3.217321 TCGATTGGAAGGGGATCGA 57.783 52.632 3.81 3.81 46.43 3.59
820 1573 1.717032 TCGATTGGAAGGGGATCGAT 58.283 50.000 0.00 0.00 44.53 3.59
821 1574 1.344438 TCGATTGGAAGGGGATCGATG 59.656 52.381 0.54 0.00 44.53 3.84
822 1575 1.609061 CGATTGGAAGGGGATCGATGG 60.609 57.143 0.54 0.00 43.86 3.51
823 1576 0.773644 ATTGGAAGGGGATCGATGGG 59.226 55.000 0.54 0.00 0.00 4.00
824 1577 0.327095 TTGGAAGGGGATCGATGGGA 60.327 55.000 0.54 0.00 0.00 4.37
825 1578 0.764369 TGGAAGGGGATCGATGGGAG 60.764 60.000 0.54 0.00 0.00 4.30
826 1579 0.764752 GGAAGGGGATCGATGGGAGT 60.765 60.000 0.54 0.00 0.00 3.85
827 1580 0.394565 GAAGGGGATCGATGGGAGTG 59.605 60.000 0.54 0.00 0.00 3.51
828 1581 0.326618 AAGGGGATCGATGGGAGTGT 60.327 55.000 0.54 0.00 0.00 3.55
829 1582 0.326618 AGGGGATCGATGGGAGTGTT 60.327 55.000 0.54 0.00 0.00 3.32
830 1583 0.546598 GGGGATCGATGGGAGTGTTT 59.453 55.000 0.54 0.00 0.00 2.83
831 1584 1.064685 GGGGATCGATGGGAGTGTTTT 60.065 52.381 0.54 0.00 0.00 2.43
832 1585 2.289565 GGGATCGATGGGAGTGTTTTC 58.710 52.381 0.54 0.00 0.00 2.29
833 1586 2.092914 GGGATCGATGGGAGTGTTTTCT 60.093 50.000 0.54 0.00 0.00 2.52
834 1587 3.610911 GGATCGATGGGAGTGTTTTCTT 58.389 45.455 0.54 0.00 0.00 2.52
835 1588 4.010349 GGATCGATGGGAGTGTTTTCTTT 58.990 43.478 0.54 0.00 0.00 2.52
836 1589 4.459337 GGATCGATGGGAGTGTTTTCTTTT 59.541 41.667 0.54 0.00 0.00 2.27
837 1590 5.392057 GGATCGATGGGAGTGTTTTCTTTTC 60.392 44.000 0.54 0.00 0.00 2.29
838 1591 3.496884 TCGATGGGAGTGTTTTCTTTTCG 59.503 43.478 0.00 0.00 0.00 3.46
839 1592 3.364964 CGATGGGAGTGTTTTCTTTTCGG 60.365 47.826 0.00 0.00 0.00 4.30
840 1593 2.303175 TGGGAGTGTTTTCTTTTCGGG 58.697 47.619 0.00 0.00 0.00 5.14
841 1594 2.304092 GGGAGTGTTTTCTTTTCGGGT 58.696 47.619 0.00 0.00 0.00 5.28
842 1595 2.034179 GGGAGTGTTTTCTTTTCGGGTG 59.966 50.000 0.00 0.00 0.00 4.61
843 1596 2.686405 GGAGTGTTTTCTTTTCGGGTGT 59.314 45.455 0.00 0.00 0.00 4.16
844 1597 3.129813 GGAGTGTTTTCTTTTCGGGTGTT 59.870 43.478 0.00 0.00 0.00 3.32
845 1598 4.381185 GGAGTGTTTTCTTTTCGGGTGTTT 60.381 41.667 0.00 0.00 0.00 2.83
846 1599 5.142061 AGTGTTTTCTTTTCGGGTGTTTT 57.858 34.783 0.00 0.00 0.00 2.43
847 1600 5.543714 AGTGTTTTCTTTTCGGGTGTTTTT 58.456 33.333 0.00 0.00 0.00 1.94
862 1615 3.548488 TTTTTGCTGCCTGTGGGG 58.452 55.556 0.00 0.00 38.36 4.96
863 1616 1.382420 TTTTTGCTGCCTGTGGGGT 60.382 52.632 0.00 0.00 37.43 4.95
864 1617 1.684386 TTTTTGCTGCCTGTGGGGTG 61.684 55.000 0.00 0.00 37.43 4.61
865 1618 4.601794 TTGCTGCCTGTGGGGTGG 62.602 66.667 0.00 0.00 37.43 4.61
876 1629 3.702623 GGGGTGGGGAGGGGACTA 61.703 72.222 0.00 0.00 44.43 2.59
877 1630 2.457794 GGGTGGGGAGGGGACTAA 59.542 66.667 0.00 0.00 44.43 2.24
878 1631 1.230050 GGGTGGGGAGGGGACTAAA 60.230 63.158 0.00 0.00 44.43 1.85
879 1632 0.847758 GGGTGGGGAGGGGACTAAAA 60.848 60.000 0.00 0.00 44.43 1.52
880 1633 1.078115 GGTGGGGAGGGGACTAAAAA 58.922 55.000 0.00 0.00 44.43 1.94
916 1669 8.934507 AAAAACAGTTAAAAATGATGGAACGA 57.065 26.923 0.00 0.00 0.00 3.85
917 1670 9.541143 AAAAACAGTTAAAAATGATGGAACGAT 57.459 25.926 0.00 0.00 0.00 3.73
928 1681 9.787532 AAAATGATGGAACGATAATAAACTGTG 57.212 29.630 0.00 0.00 0.00 3.66
929 1682 8.731275 AATGATGGAACGATAATAAACTGTGA 57.269 30.769 0.00 0.00 0.00 3.58
930 1683 8.731275 ATGATGGAACGATAATAAACTGTGAA 57.269 30.769 0.00 0.00 0.00 3.18
931 1684 8.196802 TGATGGAACGATAATAAACTGTGAAG 57.803 34.615 0.00 0.00 0.00 3.02
932 1685 8.038351 TGATGGAACGATAATAAACTGTGAAGA 58.962 33.333 0.00 0.00 0.00 2.87
933 1686 7.591006 TGGAACGATAATAAACTGTGAAGAC 57.409 36.000 0.00 0.00 0.00 3.01
934 1687 7.383687 TGGAACGATAATAAACTGTGAAGACT 58.616 34.615 0.00 0.00 0.00 3.24
935 1688 8.525316 TGGAACGATAATAAACTGTGAAGACTA 58.475 33.333 0.00 0.00 0.00 2.59
936 1689 9.530633 GGAACGATAATAAACTGTGAAGACTAT 57.469 33.333 0.00 0.00 0.00 2.12
943 1696 8.635877 AATAAACTGTGAAGACTATCATCGAC 57.364 34.615 0.00 0.00 0.00 4.20
944 1697 5.906113 AACTGTGAAGACTATCATCGACT 57.094 39.130 0.00 0.00 0.00 4.18
945 1698 5.493133 ACTGTGAAGACTATCATCGACTC 57.507 43.478 0.00 0.00 0.00 3.36
946 1699 4.944317 ACTGTGAAGACTATCATCGACTCA 59.056 41.667 0.00 0.00 0.00 3.41
947 1700 5.065859 ACTGTGAAGACTATCATCGACTCAG 59.934 44.000 0.00 0.00 0.00 3.35
948 1701 5.186198 TGTGAAGACTATCATCGACTCAGA 58.814 41.667 0.00 0.00 0.00 3.27
949 1702 5.295540 TGTGAAGACTATCATCGACTCAGAG 59.704 44.000 0.00 0.00 0.00 3.35
950 1703 5.525745 GTGAAGACTATCATCGACTCAGAGA 59.474 44.000 3.79 0.00 0.00 3.10
951 1704 6.204688 GTGAAGACTATCATCGACTCAGAGAT 59.795 42.308 3.79 0.00 0.00 2.75
952 1705 6.204495 TGAAGACTATCATCGACTCAGAGATG 59.796 42.308 3.79 8.09 43.99 2.90
956 1709 1.406898 TCATCGACTCAGAGATGCACC 59.593 52.381 3.79 0.00 42.76 5.01
1064 1976 4.862092 AGATGCGCGCTGACCTCG 62.862 66.667 33.29 0.00 0.00 4.63
1195 2107 1.940883 TACATCCAGGTCGGTCGCAC 61.941 60.000 0.00 0.00 35.57 5.34
1218 2130 3.436243 CCACCCAAAGCCCTATTTAACA 58.564 45.455 0.00 0.00 0.00 2.41
1239 2151 1.867233 CATGCCCTTAATCCTTCGTCG 59.133 52.381 0.00 0.00 0.00 5.12
1292 2204 3.304826 GTGTTTCGTTTTGATTTTGCGGT 59.695 39.130 0.00 0.00 0.00 5.68
1293 2205 3.927142 TGTTTCGTTTTGATTTTGCGGTT 59.073 34.783 0.00 0.00 0.00 4.44
1321 2233 0.341258 AAGATGGAGAGGGAGAGGCA 59.659 55.000 0.00 0.00 0.00 4.75
1427 2339 5.030820 ACTGCCCTCTAGGTTACAGTTTAT 58.969 41.667 9.56 0.00 38.17 1.40
1532 3744 4.996434 ACTGCAGCTGCGTGGGTC 62.996 66.667 32.11 6.25 45.83 4.46
1630 3947 0.175760 TCGATGTGGCTAGAAGGTGC 59.824 55.000 0.00 0.00 0.00 5.01
1660 3977 3.245052 CCTCCATCCCTGAGAAAAGTGTT 60.245 47.826 0.00 0.00 31.26 3.32
1665 3982 5.514834 CCATCCCTGAGAAAAGTGTTTAGGA 60.515 44.000 0.00 0.00 0.00 2.94
1715 4035 4.463050 TCCAAGTTTTGTTATGGAGGGT 57.537 40.909 0.00 0.00 37.05 4.34
1719 4039 5.714806 CCAAGTTTTGTTATGGAGGGTATGT 59.285 40.000 0.00 0.00 34.82 2.29
1744 4064 8.511321 GTGAATGTTTTGATCATGTGTTACCTA 58.489 33.333 0.00 0.00 0.00 3.08
1746 4066 7.994425 ATGTTTTGATCATGTGTTACCTACA 57.006 32.000 0.00 0.00 0.00 2.74
1813 4133 6.716934 TGTGATAGAGTAGATGGAAAGGTC 57.283 41.667 0.00 0.00 0.00 3.85
1859 4179 1.971481 TGTGTGCTCAAGTGAAGCAT 58.029 45.000 0.66 0.00 40.84 3.79
1872 4192 9.269453 CTCAAGTGAAGCATTGATGATTATCTA 57.731 33.333 0.00 0.00 36.41 1.98
1888 4208 9.624373 ATGATTATCTATTTTGAGTTCAGCTGT 57.376 29.630 14.67 0.00 0.00 4.40
1961 4281 6.070881 AGTCTGATGAAAGCAACACTCTCTAT 60.071 38.462 0.00 0.00 0.00 1.98
2312 4632 7.961351 TCTGAAAAGAAAAGGCAATCCAATTA 58.039 30.769 0.00 0.00 33.74 1.40
2344 4664 2.293399 GGAAAGGTTCACGTCATTTGCT 59.707 45.455 0.00 0.00 0.00 3.91
2345 4665 3.500680 GGAAAGGTTCACGTCATTTGCTA 59.499 43.478 0.00 0.00 0.00 3.49
2371 4691 8.658499 AAACAAGTTCTTAATCGTGTTCTAGT 57.342 30.769 0.00 0.00 35.86 2.57
2372 4692 7.639162 ACAAGTTCTTAATCGTGTTCTAGTG 57.361 36.000 0.00 0.00 0.00 2.74
2373 4693 7.208080 ACAAGTTCTTAATCGTGTTCTAGTGT 58.792 34.615 0.00 0.00 0.00 3.55
2374 4694 8.355169 ACAAGTTCTTAATCGTGTTCTAGTGTA 58.645 33.333 0.00 0.00 0.00 2.90
2375 4695 9.355215 CAAGTTCTTAATCGTGTTCTAGTGTAT 57.645 33.333 0.00 0.00 0.00 2.29
2376 4696 9.570488 AAGTTCTTAATCGTGTTCTAGTGTATC 57.430 33.333 0.00 0.00 0.00 2.24
2377 4697 8.737175 AGTTCTTAATCGTGTTCTAGTGTATCA 58.263 33.333 0.00 0.00 0.00 2.15
2532 4852 4.262420 GGCCCTTTTGATGTAAGAAAAGCA 60.262 41.667 0.00 0.00 37.69 3.91
2585 4905 4.445453 CATGCCATGCTTCTTGTAGAGTA 58.555 43.478 0.00 0.00 0.00 2.59
2589 4909 4.260948 GCCATGCTTCTTGTAGAGTAATGC 60.261 45.833 0.00 0.00 0.00 3.56
2704 5024 6.256757 GCTGTTACTAACACATCTCTTCATCC 59.743 42.308 0.00 0.00 36.25 3.51
2771 5091 0.698818 AAGGTGACCCCATCTTGGAC 59.301 55.000 0.00 0.00 41.89 4.02
2832 5152 9.943163 GAGATGGAAGAATAAATTCTGTAAAGC 57.057 33.333 5.99 0.00 45.83 3.51
2833 5153 8.616076 AGATGGAAGAATAAATTCTGTAAAGCG 58.384 33.333 5.99 0.00 45.83 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.038402 GGCAGGCATCTATTTTGTATGCTT 59.962 41.667 6.49 0.00 44.29 3.91
86 87 4.045104 CGCGATATATATGTGGCCTCTTC 58.955 47.826 0.00 0.00 0.00 2.87
87 88 3.447586 ACGCGATATATATGTGGCCTCTT 59.552 43.478 15.93 0.49 0.00 2.85
91 92 2.030457 GCAACGCGATATATATGTGGCC 59.970 50.000 15.93 0.00 0.00 5.36
103 104 1.076332 GGTAGTTTCAGCAACGCGAT 58.924 50.000 15.93 0.00 40.75 4.58
113 114 3.576982 CCTATATCAGCCCGGTAGTTTCA 59.423 47.826 0.00 0.00 0.00 2.69
117 118 2.291670 CCTCCTATATCAGCCCGGTAGT 60.292 54.545 0.00 0.00 0.00 2.73
124 125 2.609747 TGTGGTCCTCCTATATCAGCC 58.390 52.381 0.00 0.00 34.23 4.85
126 127 6.918067 TTACATGTGGTCCTCCTATATCAG 57.082 41.667 9.11 0.00 34.23 2.90
128 129 7.155328 CAGTTTACATGTGGTCCTCCTATATC 58.845 42.308 9.11 0.00 34.23 1.63
161 162 3.504863 CCATGCATTTTCTCTGTTTCCG 58.495 45.455 0.00 0.00 0.00 4.30
172 173 2.627945 CATGAGCTTGCCATGCATTTT 58.372 42.857 0.00 0.00 38.76 1.82
202 203 5.734855 AATAGAATTTGTTCACGGGATCG 57.265 39.130 0.00 0.00 43.02 3.69
237 238 0.321298 TTCGGCACCAGCTTCTAACC 60.321 55.000 0.00 0.00 41.70 2.85
254 255 7.203910 AGAACTCCATACGTGACATTAGATTC 58.796 38.462 0.00 0.00 0.00 2.52
273 274 6.096282 ACTGATTGCTAGAAGGAGTAGAACTC 59.904 42.308 0.00 0.00 44.32 3.01
355 359 8.414629 TCATACATCTACTGATCTACAAGCAT 57.585 34.615 0.00 0.00 0.00 3.79
359 363 7.526918 TCCCTCATACATCTACTGATCTACAA 58.473 38.462 0.00 0.00 0.00 2.41
376 1088 2.970987 TCGATCCAACCATCCCTCATA 58.029 47.619 0.00 0.00 0.00 2.15
380 1092 1.511613 ACATCGATCCAACCATCCCT 58.488 50.000 0.00 0.00 0.00 4.20
388 1100 2.159099 GCAGTGGACTACATCGATCCAA 60.159 50.000 6.27 0.00 44.05 3.53
395 1107 0.173481 TCGCTGCAGTGGACTACATC 59.827 55.000 26.23 0.00 0.00 3.06
399 1111 1.520600 TTCGTCGCTGCAGTGGACTA 61.521 55.000 26.23 16.66 0.00 2.59
404 1116 1.372251 AGACTTCGTCGCTGCAGTG 60.372 57.895 21.43 21.43 37.67 3.66
405 1117 1.372251 CAGACTTCGTCGCTGCAGT 60.372 57.895 16.64 0.00 37.67 4.40
406 1118 1.081175 TCAGACTTCGTCGCTGCAG 60.081 57.895 10.11 10.11 37.67 4.41
407 1119 1.371758 GTCAGACTTCGTCGCTGCA 60.372 57.895 0.00 0.00 37.67 4.41
408 1120 2.429351 CGTCAGACTTCGTCGCTGC 61.429 63.158 0.00 0.00 37.67 5.25
409 1121 1.797933 CCGTCAGACTTCGTCGCTG 60.798 63.158 0.00 0.00 37.67 5.18
411 1123 2.249557 TAGCCGTCAGACTTCGTCGC 62.250 60.000 0.00 0.00 37.67 5.19
412 1124 0.520827 GTAGCCGTCAGACTTCGTCG 60.521 60.000 0.00 0.00 37.67 5.12
413 1125 0.520827 CGTAGCCGTCAGACTTCGTC 60.521 60.000 0.00 0.00 0.00 4.20
414 1126 1.500844 CGTAGCCGTCAGACTTCGT 59.499 57.895 0.00 0.00 0.00 3.85
415 1127 4.361827 CGTAGCCGTCAGACTTCG 57.638 61.111 0.00 0.00 0.00 3.79
462 1181 2.435693 GCTCCACTCCCGGCAGTAT 61.436 63.158 0.00 0.00 0.00 2.12
463 1182 3.075005 GCTCCACTCCCGGCAGTA 61.075 66.667 0.00 0.00 0.00 2.74
472 1191 2.267324 GGCTCCAGTGCTCCACTC 59.733 66.667 0.00 0.00 43.43 3.51
516 1235 1.779061 AAGTCCGCCTTCACCCACAT 61.779 55.000 0.00 0.00 0.00 3.21
519 1238 2.429930 CAAGTCCGCCTTCACCCA 59.570 61.111 0.00 0.00 0.00 4.51
525 1244 4.394712 CCTCCGCAAGTCCGCCTT 62.395 66.667 0.00 0.00 0.00 4.35
633 1386 3.823330 GCTCCGACACGATCCGGT 61.823 66.667 0.00 0.00 45.48 5.28
685 1438 2.666526 GCCGCCGATGATCCCTTC 60.667 66.667 0.00 0.00 0.00 3.46
687 1440 3.620785 GAGCCGCCGATGATCCCT 61.621 66.667 0.00 0.00 0.00 4.20
694 1447 4.537433 GCTTCAGGAGCCGCCGAT 62.537 66.667 0.00 0.00 46.01 4.18
714 1467 1.452833 GCTGCCACAGATCCCTTCC 60.453 63.158 0.00 0.00 32.44 3.46
794 1547 1.215423 CCCCTTCCAATCGATCCCTTT 59.785 52.381 0.00 0.00 0.00 3.11
806 1559 0.764369 CTCCCATCGATCCCCTTCCA 60.764 60.000 0.00 0.00 0.00 3.53
816 1569 3.496884 CGAAAAGAAAACACTCCCATCGA 59.503 43.478 0.00 0.00 0.00 3.59
819 1572 2.890945 CCCGAAAAGAAAACACTCCCAT 59.109 45.455 0.00 0.00 0.00 4.00
820 1573 2.303175 CCCGAAAAGAAAACACTCCCA 58.697 47.619 0.00 0.00 0.00 4.37
821 1574 2.034179 CACCCGAAAAGAAAACACTCCC 59.966 50.000 0.00 0.00 0.00 4.30
822 1575 2.686405 ACACCCGAAAAGAAAACACTCC 59.314 45.455 0.00 0.00 0.00 3.85
823 1576 4.365899 AACACCCGAAAAGAAAACACTC 57.634 40.909 0.00 0.00 0.00 3.51
824 1577 4.794278 AAACACCCGAAAAGAAAACACT 57.206 36.364 0.00 0.00 0.00 3.55
825 1578 5.849357 AAAAACACCCGAAAAGAAAACAC 57.151 34.783 0.00 0.00 0.00 3.32
845 1598 1.382420 ACCCCACAGGCAGCAAAAA 60.382 52.632 0.00 0.00 40.58 1.94
846 1599 2.132996 CACCCCACAGGCAGCAAAA 61.133 57.895 0.00 0.00 40.58 2.44
847 1600 2.521465 CACCCCACAGGCAGCAAA 60.521 61.111 0.00 0.00 40.58 3.68
848 1601 4.601794 CCACCCCACAGGCAGCAA 62.602 66.667 0.00 0.00 40.58 3.91
859 1612 2.793484 TTTAGTCCCCTCCCCACCCC 62.793 65.000 0.00 0.00 0.00 4.95
860 1613 0.847758 TTTTAGTCCCCTCCCCACCC 60.848 60.000 0.00 0.00 0.00 4.61
861 1614 1.078115 TTTTTAGTCCCCTCCCCACC 58.922 55.000 0.00 0.00 0.00 4.61
891 1644 8.934507 TCGTTCCATCATTTTTAACTGTTTTT 57.065 26.923 0.00 0.00 0.00 1.94
902 1655 9.787532 CACAGTTTATTATCGTTCCATCATTTT 57.212 29.630 0.00 0.00 0.00 1.82
903 1656 9.173021 TCACAGTTTATTATCGTTCCATCATTT 57.827 29.630 0.00 0.00 0.00 2.32
904 1657 8.731275 TCACAGTTTATTATCGTTCCATCATT 57.269 30.769 0.00 0.00 0.00 2.57
905 1658 8.731275 TTCACAGTTTATTATCGTTCCATCAT 57.269 30.769 0.00 0.00 0.00 2.45
906 1659 8.038351 TCTTCACAGTTTATTATCGTTCCATCA 58.962 33.333 0.00 0.00 0.00 3.07
907 1660 8.328864 GTCTTCACAGTTTATTATCGTTCCATC 58.671 37.037 0.00 0.00 0.00 3.51
908 1661 8.041323 AGTCTTCACAGTTTATTATCGTTCCAT 58.959 33.333 0.00 0.00 0.00 3.41
909 1662 7.383687 AGTCTTCACAGTTTATTATCGTTCCA 58.616 34.615 0.00 0.00 0.00 3.53
910 1663 7.829378 AGTCTTCACAGTTTATTATCGTTCC 57.171 36.000 0.00 0.00 0.00 3.62
917 1670 9.731819 GTCGATGATAGTCTTCACAGTTTATTA 57.268 33.333 0.00 0.00 0.00 0.98
918 1671 8.470805 AGTCGATGATAGTCTTCACAGTTTATT 58.529 33.333 0.00 0.00 0.00 1.40
919 1672 8.001881 AGTCGATGATAGTCTTCACAGTTTAT 57.998 34.615 0.00 0.00 0.00 1.40
920 1673 7.120726 TGAGTCGATGATAGTCTTCACAGTTTA 59.879 37.037 0.00 0.00 0.00 2.01
921 1674 6.071896 TGAGTCGATGATAGTCTTCACAGTTT 60.072 38.462 0.00 0.00 0.00 2.66
922 1675 5.416013 TGAGTCGATGATAGTCTTCACAGTT 59.584 40.000 0.00 0.00 0.00 3.16
923 1676 4.944317 TGAGTCGATGATAGTCTTCACAGT 59.056 41.667 0.00 0.00 0.00 3.55
924 1677 5.295540 TCTGAGTCGATGATAGTCTTCACAG 59.704 44.000 0.00 0.00 0.00 3.66
925 1678 5.186198 TCTGAGTCGATGATAGTCTTCACA 58.814 41.667 0.00 0.00 0.00 3.58
926 1679 5.525745 TCTCTGAGTCGATGATAGTCTTCAC 59.474 44.000 4.32 0.00 0.00 3.18
927 1680 5.675538 TCTCTGAGTCGATGATAGTCTTCA 58.324 41.667 4.32 0.00 0.00 3.02
928 1681 6.602179 CATCTCTGAGTCGATGATAGTCTTC 58.398 44.000 4.32 0.00 39.43 2.87
929 1682 5.048782 GCATCTCTGAGTCGATGATAGTCTT 60.049 44.000 15.08 0.00 39.43 3.01
930 1683 4.455533 GCATCTCTGAGTCGATGATAGTCT 59.544 45.833 15.08 0.00 39.43 3.24
931 1684 4.215185 TGCATCTCTGAGTCGATGATAGTC 59.785 45.833 15.08 2.35 39.43 2.59
932 1685 4.023279 GTGCATCTCTGAGTCGATGATAGT 60.023 45.833 15.08 0.00 39.43 2.12
933 1686 4.475028 GTGCATCTCTGAGTCGATGATAG 58.525 47.826 15.08 0.00 39.43 2.08
934 1687 3.254411 GGTGCATCTCTGAGTCGATGATA 59.746 47.826 15.08 4.30 39.43 2.15
935 1688 2.035704 GGTGCATCTCTGAGTCGATGAT 59.964 50.000 15.08 0.00 39.43 2.45
936 1689 1.406898 GGTGCATCTCTGAGTCGATGA 59.593 52.381 15.08 0.00 39.43 2.92
937 1690 1.135721 TGGTGCATCTCTGAGTCGATG 59.864 52.381 4.32 3.01 39.91 3.84
938 1691 1.478631 TGGTGCATCTCTGAGTCGAT 58.521 50.000 4.32 0.00 0.00 3.59
939 1692 1.067565 GTTGGTGCATCTCTGAGTCGA 60.068 52.381 4.32 0.00 0.00 4.20
940 1693 1.337167 TGTTGGTGCATCTCTGAGTCG 60.337 52.381 4.32 0.00 0.00 4.18
941 1694 2.462456 TGTTGGTGCATCTCTGAGTC 57.538 50.000 4.32 0.00 0.00 3.36
942 1695 2.498167 GTTGTTGGTGCATCTCTGAGT 58.502 47.619 4.32 0.00 0.00 3.41
943 1696 1.808945 GGTTGTTGGTGCATCTCTGAG 59.191 52.381 0.00 0.00 0.00 3.35
944 1697 1.545428 GGGTTGTTGGTGCATCTCTGA 60.545 52.381 0.00 0.00 0.00 3.27
945 1698 0.883833 GGGTTGTTGGTGCATCTCTG 59.116 55.000 0.00 0.00 0.00 3.35
946 1699 0.251341 GGGGTTGTTGGTGCATCTCT 60.251 55.000 0.00 0.00 0.00 3.10
947 1700 0.539438 TGGGGTTGTTGGTGCATCTC 60.539 55.000 0.00 0.00 0.00 2.75
948 1701 0.827507 GTGGGGTTGTTGGTGCATCT 60.828 55.000 0.00 0.00 0.00 2.90
949 1702 1.665442 GTGGGGTTGTTGGTGCATC 59.335 57.895 0.00 0.00 0.00 3.91
950 1703 1.836604 GGTGGGGTTGTTGGTGCAT 60.837 57.895 0.00 0.00 0.00 3.96
951 1704 2.443016 GGTGGGGTTGTTGGTGCA 60.443 61.111 0.00 0.00 0.00 4.57
952 1705 3.230990 GGGTGGGGTTGTTGGTGC 61.231 66.667 0.00 0.00 0.00 5.01
956 1709 1.681486 GGTGTTGGGTGGGGTTGTTG 61.681 60.000 0.00 0.00 0.00 3.33
1109 2021 4.742201 TCACTCAGAAGGCGCCGC 62.742 66.667 23.20 17.80 0.00 6.53
1195 2107 0.042581 AAATAGGGCTTTGGGTGGGG 59.957 55.000 0.00 0.00 0.00 4.96
1218 2130 2.741878 CGACGAAGGATTAAGGGCATGT 60.742 50.000 0.00 0.00 0.00 3.21
1292 2204 1.836166 CTCTCCATCTTCTGCTCCCAA 59.164 52.381 0.00 0.00 0.00 4.12
1293 2205 1.493861 CTCTCCATCTTCTGCTCCCA 58.506 55.000 0.00 0.00 0.00 4.37
1321 2233 4.097551 AGCTTTTTCTTGAGCTTCTCCT 57.902 40.909 0.00 0.00 46.55 3.69
1427 2339 1.550524 AGCCATTGAGAGTCTACGCAA 59.449 47.619 0.00 0.00 34.55 4.85
1557 3769 6.294508 GGTTTGACACTTGGCACTTGTAATAT 60.295 38.462 0.27 0.00 29.05 1.28
1566 3778 3.641031 GTGGTTTGACACTTGGCAC 57.359 52.632 0.00 0.00 38.32 5.01
1590 3802 4.125703 GACTTGGCATCTACCATTCAGAG 58.874 47.826 0.00 0.00 40.13 3.35
1630 3947 3.231298 GGGATGGAGGAGTTCCCG 58.769 66.667 0.00 0.00 46.19 5.14
1715 4035 9.838975 GTAACACATGATCAAAACATTCACATA 57.161 29.630 0.00 0.00 0.00 2.29
1719 4039 7.523293 AGGTAACACATGATCAAAACATTCA 57.477 32.000 0.00 0.00 41.41 2.57
1744 4064 2.498481 CCCATGATGCAACCATCTTTGT 59.502 45.455 0.00 0.00 46.43 2.83
1746 4066 3.104519 TCCCATGATGCAACCATCTTT 57.895 42.857 0.00 0.00 46.43 2.52
1800 4120 6.126863 ACACTTCATTGACCTTTCCATCTA 57.873 37.500 0.00 0.00 0.00 1.98
1813 4133 5.684626 GTCTTTCAGCTCAAACACTTCATTG 59.315 40.000 0.00 0.00 0.00 2.82
1872 4192 7.876936 ATCATATCACAGCTGAACTCAAAAT 57.123 32.000 23.35 1.92 0.00 1.82
1888 4208 8.839343 CAACATGTACTTAGCCAAATCATATCA 58.161 33.333 0.00 0.00 0.00 2.15
2091 4411 7.042119 CCAAATAAACACAATTGGACTGTTTCC 60.042 37.037 21.94 0.00 44.01 3.13
2174 4494 9.428097 GCTGATGAATTGATTAGAAAAGGTTTT 57.572 29.630 0.77 0.00 0.00 2.43
2312 4632 4.679372 CGTGAACCTTTCCCAAACAAACAT 60.679 41.667 0.00 0.00 0.00 2.71
2345 4665 9.106070 ACTAGAACACGATTAAGAACTTGTTTT 57.894 29.630 0.00 0.00 30.81 2.43
2371 4691 7.784633 TGCGACATAAATCAGATTTGATACA 57.215 32.000 17.38 6.40 43.20 2.29
2372 4692 8.947940 GTTTGCGACATAAATCAGATTTGATAC 58.052 33.333 17.38 6.73 43.20 2.24
2373 4693 8.672815 TGTTTGCGACATAAATCAGATTTGATA 58.327 29.630 17.38 0.00 36.84 2.15
2374 4694 7.485913 GTGTTTGCGACATAAATCAGATTTGAT 59.514 33.333 17.38 3.77 42.21 2.57
2375 4695 6.801377 GTGTTTGCGACATAAATCAGATTTGA 59.199 34.615 17.38 3.66 41.10 2.69
2376 4696 6.033831 GGTGTTTGCGACATAAATCAGATTTG 59.966 38.462 17.38 6.02 41.10 2.32
2377 4697 6.092748 GGTGTTTGCGACATAAATCAGATTT 58.907 36.000 13.06 13.06 41.10 2.17
2532 4852 6.616237 ATCAAGGGAAAATCTGAGCATTTT 57.384 33.333 3.43 3.43 38.43 1.82
2585 4905 8.685838 TTACTTAGAAACTGGTAAACTGCATT 57.314 30.769 0.00 0.00 0.00 3.56
2589 4909 8.784043 AGCAATTACTTAGAAACTGGTAAACTG 58.216 33.333 0.00 0.00 0.00 3.16
2704 5024 1.544825 TTCCCTCGGCCTTCTGTCAG 61.545 60.000 0.00 0.00 0.00 3.51
2771 5091 0.680921 ACAAATGTCCCCCAGATGCG 60.681 55.000 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.