Multiple sequence alignment - TraesCS6D01G228800

Loading Multiple Alignment...

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 TraesCS6D01G228800 chr6D 100.000 3773 0 0 1 3773 319710564 319706792 0.000000e+00 6968.0
1 TraesCS6D01G228800 chr6D 82.669 502 64 12 1851 2346 37430967 37431451 1.250000e-114 424.0
2 TraesCS6D01G228800 chr6B 94.679 1184 49 5 1883 3052 503522317 503523500 0.000000e+00 1825.0
3 TraesCS6D01G228800 chr6B 91.837 735 31 10 3044 3773 503528719 503529429 0.000000e+00 998.0
4 TraesCS6D01G228800 chr6B 91.139 711 26 11 523 1215 503521007 503521698 0.000000e+00 929.0
5 TraesCS6D01G228800 chr6B 88.312 462 31 7 32 472 503520532 503520991 2.000000e-147 532.0
6 TraesCS6D01G228800 chr6B 91.615 322 12 3 1197 1507 503521716 503522033 7.490000e-117 431.0
7 TraesCS6D01G228800 chr6B 91.176 272 17 2 1510 1781 503522002 503522266 2.770000e-96 363.0
8 TraesCS6D01G228800 chr6B 81.900 221 22 3 1805 2018 621822158 621822367 1.800000e-38 171.0
9 TraesCS6D01G228800 chr6A 91.445 1204 70 12 1781 2952 457403630 457402428 0.000000e+00 1622.0
10 TraesCS6D01G228800 chr6A 89.263 1276 53 22 229 1462 457405195 457403962 0.000000e+00 1520.0
11 TraesCS6D01G228800 chr6A 91.032 814 43 13 2976 3773 457402344 457401545 0.000000e+00 1072.0
12 TraesCS6D01G228800 chr4A 81.137 827 124 20 1550 2360 16032012 16032822 5.320000e-178 634.0
13 TraesCS6D01G228800 chr3D 82.883 555 65 14 1805 2346 579611411 579611948 4.410000e-129 472.0
14 TraesCS6D01G228800 chr3D 83.663 404 56 9 1905 2305 120909713 120910109 4.600000e-99 372.0
15 TraesCS6D01G228800 chr5B 82.310 554 69 14 1805 2346 133644749 133645285 1.600000e-123 453.0
16 TraesCS6D01G228800 chrUn 82.047 557 68 14 1805 2346 327382432 327382971 2.670000e-121 446.0
17 TraesCS6D01G228800 chr5A 81.239 549 73 14 1805 2342 526049575 526049046 2.100000e-112 416.0
18 TraesCS6D01G228800 chr1D 81.641 512 61 12 1851 2346 417545644 417546138 9.820000e-106 394.0
19 TraesCS6D01G228800 chr3B 83.951 405 56 7 1904 2305 569295751 569295353 2.750000e-101 379.0
20 TraesCS6D01G228800 chr2D 95.745 47 2 0 1007 1053 522987766 522987720 4.040000e-10 76.8
21 TraesCS6D01G228800 chr2A 95.556 45 2 0 1009 1053 668051606 668051562 5.230000e-09 73.1
22 TraesCS6D01G228800 chr2B 93.617 47 3 0 1007 1053 616475625 616475579 1.880000e-08 71.3


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 TraesCS6D01G228800 chr6D 319706792 319710564 3772 True 6968.000000 6968 100.0000 1 3773 1 chr6D.!!$R1 3772
1 TraesCS6D01G228800 chr6B 503528719 503529429 710 False 998.000000 998 91.8370 3044 3773 1 chr6B.!!$F1 729
2 TraesCS6D01G228800 chr6B 503520532 503523500 2968 False 816.000000 1825 91.3842 32 3052 5 chr6B.!!$F3 3020
3 TraesCS6D01G228800 chr6A 457401545 457405195 3650 True 1404.666667 1622 90.5800 229 3773 3 chr6A.!!$R1 3544
4 TraesCS6D01G228800 chr4A 16032012 16032822 810 False 634.000000 634 81.1370 1550 2360 1 chr4A.!!$F1 810
5 TraesCS6D01G228800 chr3D 579611411 579611948 537 False 472.000000 472 82.8830 1805 2346 1 chr3D.!!$F2 541
6 TraesCS6D01G228800 chr5B 133644749 133645285 536 False 453.000000 453 82.3100 1805 2346 1 chr5B.!!$F1 541
7 TraesCS6D01G228800 chrUn 327382432 327382971 539 False 446.000000 446 82.0470 1805 2346 1 chrUn.!!$F1 541
8 TraesCS6D01G228800 chr5A 526049046 526049575 529 True 416.000000 416 81.2390 1805 2342 1 chr5A.!!$R1 537

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
57 58 0.391661 CTTAGCATGGACGCACAGGT 60.392 55.0 0.0 0.0 0.00 4.00 F
1066 1123 0.320073 CAAGGTTTGCCTGCCACATG 60.320 55.0 0.0 0.0 46.33 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 2192 0.168348 TCTCGTACAACTGAGCGAGC 59.832 55.0 16.61 0.0 46.98 5.03 R
2844 3189 0.316278 CTACGAGATCGGACTGCACG 60.316 60.0 7.22 0.0 44.95 5.34 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
25 26 8.803397 AAATATTCAGTCAACTTACCCCTAAC 57.197 34.615 0.00 0.00 0.00 2.34
26 27 4.628963 TTCAGTCAACTTACCCCTAACC 57.371 45.455 0.00 0.00 0.00 2.85
27 28 3.589641 TCAGTCAACTTACCCCTAACCA 58.410 45.455 0.00 0.00 0.00 3.67
28 29 3.975312 TCAGTCAACTTACCCCTAACCAA 59.025 43.478 0.00 0.00 0.00 3.67
29 30 4.600111 TCAGTCAACTTACCCCTAACCAAT 59.400 41.667 0.00 0.00 0.00 3.16
30 31 4.941873 CAGTCAACTTACCCCTAACCAATC 59.058 45.833 0.00 0.00 0.00 2.67
53 54 1.726853 ACTTCTTAGCATGGACGCAC 58.273 50.000 0.00 0.00 0.00 5.34
57 58 0.391661 CTTAGCATGGACGCACAGGT 60.392 55.000 0.00 0.00 0.00 4.00
62 63 1.867233 GCATGGACGCACAGGTATAAG 59.133 52.381 0.00 0.00 0.00 1.73
67 68 3.068165 TGGACGCACAGGTATAAGAGATG 59.932 47.826 0.00 0.00 0.00 2.90
68 69 3.053455 GACGCACAGGTATAAGAGATGC 58.947 50.000 0.00 0.00 0.00 3.91
74 75 5.221541 GCACAGGTATAAGAGATGCCTAACT 60.222 44.000 0.00 0.00 32.74 2.24
75 76 6.015350 GCACAGGTATAAGAGATGCCTAACTA 60.015 42.308 0.00 0.00 32.74 2.24
79 80 8.301002 CAGGTATAAGAGATGCCTAACTACTTC 58.699 40.741 0.00 0.00 32.74 3.01
88 89 2.167075 GCCTAACTACTTCCGCACCTTA 59.833 50.000 0.00 0.00 0.00 2.69
98 99 0.455972 CCGCACCTTAATGGCAAACG 60.456 55.000 0.00 0.00 40.22 3.60
102 103 1.201414 CACCTTAATGGCAAACGGGAC 59.799 52.381 0.00 0.00 40.22 4.46
103 104 1.202952 ACCTTAATGGCAAACGGGACA 60.203 47.619 0.00 0.00 40.22 4.02
105 106 1.883275 CTTAATGGCAAACGGGACACA 59.117 47.619 0.00 0.00 0.00 3.72
116 117 1.305219 CGGGACACACGCCATTTGAT 61.305 55.000 0.00 0.00 0.00 2.57
132 133 6.432936 CCATTTGATCCGATATGTCTGTTTG 58.567 40.000 0.00 0.00 0.00 2.93
133 134 6.038603 CCATTTGATCCGATATGTCTGTTTGT 59.961 38.462 0.00 0.00 0.00 2.83
134 135 7.415541 CCATTTGATCCGATATGTCTGTTTGTT 60.416 37.037 0.00 0.00 0.00 2.83
136 137 5.729510 TGATCCGATATGTCTGTTTGTTGA 58.270 37.500 0.00 0.00 0.00 3.18
160 175 2.579207 TCGTTCGATGATCCAAGTCC 57.421 50.000 0.00 0.00 0.00 3.85
168 183 4.279420 TCGATGATCCAAGTCCTAGTCATG 59.721 45.833 0.00 0.00 0.00 3.07
171 186 5.854010 TGATCCAAGTCCTAGTCATGTAC 57.146 43.478 0.00 0.00 0.00 2.90
172 187 5.519808 TGATCCAAGTCCTAGTCATGTACT 58.480 41.667 0.00 0.00 42.62 2.73
173 188 5.360999 TGATCCAAGTCCTAGTCATGTACTG 59.639 44.000 7.74 0.00 39.39 2.74
179 200 5.373222 AGTCCTAGTCATGTACTGCTCTAG 58.627 45.833 7.74 2.24 39.39 2.43
183 204 6.890268 TCCTAGTCATGTACTGCTCTAGAAAA 59.110 38.462 13.22 0.00 39.39 2.29
221 242 7.782897 AGATATGGGATCTAACTGAATCGAA 57.217 36.000 0.00 0.00 0.00 3.71
265 286 2.801699 CGGTCCATAGTATTCTGCGCAA 60.802 50.000 13.05 0.00 0.00 4.85
323 344 1.182667 GCCCGGGTTTATGCTCTTTT 58.817 50.000 24.63 0.00 0.00 2.27
410 434 4.223964 GCATCGAAGGTTCCGCGC 62.224 66.667 0.00 0.00 0.00 6.86
457 481 4.386413 CTGCCGGCAGAGTTTTCT 57.614 55.556 46.72 0.00 46.30 2.52
459 483 1.808411 CTGCCGGCAGAGTTTTCTTA 58.192 50.000 46.72 12.87 46.30 2.10
460 484 2.151202 CTGCCGGCAGAGTTTTCTTAA 58.849 47.619 46.72 12.64 46.30 1.85
469 493 7.138736 CGGCAGAGTTTTCTTAATTTTCTTGA 58.861 34.615 0.00 0.00 0.00 3.02
470 494 7.113544 CGGCAGAGTTTTCTTAATTTTCTTGAC 59.886 37.037 0.00 0.00 0.00 3.18
477 501 9.967245 GTTTTCTTAATTTTCTTGACACAAACC 57.033 29.630 0.00 0.00 0.00 3.27
546 580 2.599281 TTCCGAGGCCGTGAGACA 60.599 61.111 0.00 0.00 0.00 3.41
689 732 2.267681 ATCCAGGACGAACGTCGAGC 62.268 60.000 18.57 7.44 43.74 5.03
700 743 2.354656 GTCGAGCAGCACGTCACA 60.355 61.111 12.17 0.00 0.00 3.58
701 744 2.050077 TCGAGCAGCACGTCACAG 60.050 61.111 12.17 0.00 0.00 3.66
703 746 3.771491 GAGCAGCACGTCACAGCG 61.771 66.667 0.00 0.00 35.48 5.18
707 750 4.592192 AGCACGTCACAGCGCACT 62.592 61.111 11.47 0.00 35.48 4.40
864 921 3.069318 GCCGTCGTCTCCCCTTCT 61.069 66.667 0.00 0.00 0.00 2.85
867 924 1.136984 CGTCGTCTCCCCTTCTTCG 59.863 63.158 0.00 0.00 0.00 3.79
1060 1117 2.644992 CCGTCAAGGTTTGCCTGC 59.355 61.111 0.00 0.00 46.33 4.85
1061 1118 2.644992 CGTCAAGGTTTGCCTGCC 59.355 61.111 0.00 0.00 46.33 4.85
1062 1119 2.192861 CGTCAAGGTTTGCCTGCCA 61.193 57.895 0.00 0.00 46.33 4.92
1063 1120 1.363807 GTCAAGGTTTGCCTGCCAC 59.636 57.895 0.00 0.00 46.33 5.01
1064 1121 1.076412 TCAAGGTTTGCCTGCCACA 60.076 52.632 0.00 0.00 46.33 4.17
1065 1122 0.469705 TCAAGGTTTGCCTGCCACAT 60.470 50.000 0.00 0.00 46.33 3.21
1066 1123 0.320073 CAAGGTTTGCCTGCCACATG 60.320 55.000 0.00 0.00 46.33 3.21
1067 1124 0.760189 AAGGTTTGCCTGCCACATGT 60.760 50.000 0.00 0.00 46.33 3.21
1068 1125 1.181098 AGGTTTGCCTGCCACATGTC 61.181 55.000 0.00 0.00 45.05 3.06
1069 1126 1.081242 GTTTGCCTGCCACATGTCG 60.081 57.895 0.00 0.00 0.00 4.35
1113 1187 2.107950 TCCGAATTTCGCATCCAAGT 57.892 45.000 13.26 0.00 38.82 3.16
1165 1239 4.179361 CACATGTGCACACCCCTT 57.821 55.556 24.37 2.07 0.00 3.95
1454 1579 9.443283 GTCATGTAATTCTCTTATTCATGTTGC 57.557 33.333 0.00 0.00 34.67 4.17
1460 1585 5.079689 TCTCTTATTCATGTTGCGGTGTA 57.920 39.130 0.00 0.00 0.00 2.90
1461 1586 5.670485 TCTCTTATTCATGTTGCGGTGTAT 58.330 37.500 0.00 0.00 0.00 2.29
1462 1587 6.811954 TCTCTTATTCATGTTGCGGTGTATA 58.188 36.000 0.00 0.00 0.00 1.47
1463 1588 7.269316 TCTCTTATTCATGTTGCGGTGTATAA 58.731 34.615 0.00 0.00 0.00 0.98
1469 1594 8.850454 ATTCATGTTGCGGTGTATAAATAAAC 57.150 30.769 0.00 0.00 0.00 2.01
1509 1768 6.795098 TTATACTGTCAAGTTTGCATTCGT 57.205 33.333 0.00 0.00 37.88 3.85
1510 1769 3.338818 ACTGTCAAGTTTGCATTCGTG 57.661 42.857 0.00 0.00 30.14 4.35
1511 1770 2.033299 ACTGTCAAGTTTGCATTCGTGG 59.967 45.455 0.00 0.00 30.14 4.94
1512 1771 2.020720 TGTCAAGTTTGCATTCGTGGT 58.979 42.857 0.00 0.00 0.00 4.16
1513 1772 3.206964 TGTCAAGTTTGCATTCGTGGTA 58.793 40.909 0.00 0.00 0.00 3.25
1514 1773 3.818210 TGTCAAGTTTGCATTCGTGGTAT 59.182 39.130 0.00 0.00 0.00 2.73
1515 1774 4.158384 GTCAAGTTTGCATTCGTGGTATG 58.842 43.478 0.00 0.00 0.00 2.39
1516 1775 2.916716 CAAGTTTGCATTCGTGGTATGC 59.083 45.455 0.00 0.00 46.63 3.14
1524 1783 3.723764 GCATTCGTGGTATGCATTTTACG 59.276 43.478 3.54 13.22 45.93 3.18
1525 1784 3.392769 TTCGTGGTATGCATTTTACGC 57.607 42.857 18.52 8.16 0.00 4.42
1526 1785 2.623535 TCGTGGTATGCATTTTACGCT 58.376 42.857 18.52 0.00 0.00 5.07
1527 1786 2.350192 TCGTGGTATGCATTTTACGCTG 59.650 45.455 18.52 6.57 0.00 5.18
1528 1787 2.095213 CGTGGTATGCATTTTACGCTGT 59.905 45.455 3.54 0.00 0.00 4.40
1529 1788 3.680789 GTGGTATGCATTTTACGCTGTC 58.319 45.455 3.54 0.00 0.00 3.51
1530 1789 3.126171 GTGGTATGCATTTTACGCTGTCA 59.874 43.478 3.54 0.00 0.00 3.58
1531 1790 3.753797 TGGTATGCATTTTACGCTGTCAA 59.246 39.130 3.54 0.00 0.00 3.18
1532 1791 4.142708 TGGTATGCATTTTACGCTGTCAAG 60.143 41.667 3.54 0.00 0.00 3.02
1533 1792 4.142687 GGTATGCATTTTACGCTGTCAAGT 60.143 41.667 3.54 0.00 0.00 3.16
1534 1793 3.980646 TGCATTTTACGCTGTCAAGTT 57.019 38.095 0.00 0.00 0.00 2.66
1535 1794 4.300189 TGCATTTTACGCTGTCAAGTTT 57.700 36.364 0.00 0.00 0.00 2.66
1536 1795 4.041049 TGCATTTTACGCTGTCAAGTTTG 58.959 39.130 0.00 0.00 0.00 2.93
1537 1796 3.425193 GCATTTTACGCTGTCAAGTTTGG 59.575 43.478 0.00 0.00 0.00 3.28
1538 1797 4.791411 GCATTTTACGCTGTCAAGTTTGGA 60.791 41.667 0.00 0.00 0.00 3.53
1539 1798 5.460646 CATTTTACGCTGTCAAGTTTGGAT 58.539 37.500 0.00 0.00 0.00 3.41
1540 1799 5.508200 TTTTACGCTGTCAAGTTTGGATT 57.492 34.783 0.00 0.00 0.00 3.01
1541 1800 4.481930 TTACGCTGTCAAGTTTGGATTG 57.518 40.909 0.00 0.00 0.00 2.67
1542 1801 2.297701 ACGCTGTCAAGTTTGGATTGT 58.702 42.857 0.00 0.00 0.00 2.71
1620 1879 8.915057 ATTGTTCTGCTAAATATGCATAGTCT 57.085 30.769 12.79 3.71 39.86 3.24
1712 1972 8.697507 AGAAAATTACTCTGATCAAGTTGGTT 57.302 30.769 13.40 6.31 0.00 3.67
1713 1973 9.136323 AGAAAATTACTCTGATCAAGTTGGTTT 57.864 29.630 13.40 11.13 0.00 3.27
1714 1974 9.185192 GAAAATTACTCTGATCAAGTTGGTTTG 57.815 33.333 13.40 0.00 0.00 2.93
1715 1975 6.824305 ATTACTCTGATCAAGTTGGTTTGG 57.176 37.500 13.40 0.00 0.00 3.28
1716 1976 4.437682 ACTCTGATCAAGTTGGTTTGGA 57.562 40.909 2.34 0.00 0.00 3.53
1717 1977 4.137543 ACTCTGATCAAGTTGGTTTGGAC 58.862 43.478 2.34 0.00 0.00 4.02
1742 2002 4.601084 TGGAGTTGGACAACCTGTTTTTA 58.399 39.130 11.28 0.00 42.06 1.52
1791 2086 5.779241 TGACTTCTGACTAATTCCCCATT 57.221 39.130 0.00 0.00 0.00 3.16
1833 2128 5.238650 ACTGAAAGGACGACCATTTTGTTAG 59.761 40.000 6.71 1.00 39.30 2.34
1890 2192 3.000727 GACCAATTCCAACTACACGGAG 58.999 50.000 0.00 0.00 31.51 4.63
1971 2274 8.738645 ATTAGTCCCTGATTTTCAGTTATGAC 57.261 34.615 4.00 5.19 42.80 3.06
2052 2355 2.203422 TTTGGTGGGCAGGAACCG 60.203 61.111 0.00 0.00 39.47 4.44
2184 2506 4.759183 GTCTCTGTTTCAGGCTGAAAGAAT 59.241 41.667 35.98 0.00 45.83 2.40
2233 2556 2.036604 TGACTTGCGTCCATGAACAGTA 59.963 45.455 0.00 0.00 39.47 2.74
2525 2869 3.202906 TGTTGCACCTGTCTACAAGTTC 58.797 45.455 0.00 0.00 0.00 3.01
2579 2923 5.241506 GGACAACATCAAATGGAACTTCTCA 59.758 40.000 0.00 0.00 33.60 3.27
2621 2965 1.597742 GGCATGTTGTGGATCGCTAT 58.402 50.000 0.00 0.00 0.00 2.97
2716 3060 3.395941 ACTTCCTTTCCTGATCTTGTGGT 59.604 43.478 0.00 0.00 0.00 4.16
2745 3089 3.267812 TCCTTGGATCTTTGCAGAAGGAT 59.732 43.478 0.00 0.00 30.27 3.24
2768 3112 0.243907 AAGAAGCTGCTCGCGAGTTA 59.756 50.000 34.46 23.18 45.59 2.24
2854 3199 1.024579 AATAAAGGCCGTGCAGTCCG 61.025 55.000 0.00 0.00 0.00 4.79
2895 3240 4.214980 CATGTAATGGATTTCGTGGAGC 57.785 45.455 0.00 0.00 41.79 4.70
2898 3243 1.369625 AATGGATTTCGTGGAGCGTC 58.630 50.000 0.00 0.00 42.13 5.19
2949 3295 3.321497 TCTGTGTTTTTGTTGTGGTTGC 58.679 40.909 0.00 0.00 0.00 4.17
2954 3300 3.119316 TGTTTTTGTTGTGGTTGCGAGAT 60.119 39.130 0.00 0.00 0.00 2.75
2959 3305 2.037902 TGTTGTGGTTGCGAGATTCCTA 59.962 45.455 0.00 0.00 0.00 2.94
2964 3310 2.771943 TGGTTGCGAGATTCCTATTCCT 59.228 45.455 0.00 0.00 0.00 3.36
3026 3432 2.814097 GCCTCTGTGTTACCAATGGTGT 60.814 50.000 16.41 0.00 36.19 4.16
3039 3445 3.976169 CAATGGTGTGTTCGTTGGAAAT 58.024 40.909 0.00 0.00 33.05 2.17
3083 3492 3.840437 TTTGCTGCAGGCGAAGTT 58.160 50.000 17.12 0.00 45.43 2.66
3086 3495 1.795170 TTGCTGCAGGCGAAGTTTCC 61.795 55.000 17.12 0.00 45.43 3.13
3119 3530 0.713883 AAACACGTCTATCTTGCGCG 59.286 50.000 0.00 0.00 0.00 6.86
3120 3531 0.109458 AACACGTCTATCTTGCGCGA 60.109 50.000 12.10 0.00 0.00 5.87
3128 3539 4.026804 CGTCTATCTTGCGCGAAAACTATT 60.027 41.667 12.10 0.00 0.00 1.73
3156 3567 9.970553 ACATATAGCAATGACATATTTGAGGAT 57.029 29.630 0.00 0.00 0.00 3.24
3227 3638 8.620116 TGTTCAGTTTCACAGATAAATCATCA 57.380 30.769 0.00 0.00 35.96 3.07
3400 3811 1.220206 CAGTCTCCATTGCCGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
3401 3812 1.088340 CAGTCTCCATTGCCGCTCTG 61.088 60.000 0.00 0.00 0.00 3.35
3402 3813 2.124983 TCTCCATTGCCGCTCTGC 60.125 61.111 0.00 0.00 0.00 4.26
3403 3814 2.124819 CTCCATTGCCGCTCTGCT 60.125 61.111 0.00 0.00 0.00 4.24
3404 3815 2.124983 TCCATTGCCGCTCTGCTC 60.125 61.111 0.00 0.00 0.00 4.26
3405 3816 2.124819 CCATTGCCGCTCTGCTCT 60.125 61.111 0.00 0.00 0.00 4.09
3442 3853 1.994779 GCTGCCATTTTCAATTCCACG 59.005 47.619 0.00 0.00 0.00 4.94
3451 3862 1.358877 TCAATTCCACGCACTCATCG 58.641 50.000 0.00 0.00 0.00 3.84
3468 3882 0.037046 TCGCCCCATCATCATCATCG 60.037 55.000 0.00 0.00 0.00 3.84
3478 3892 1.804748 CATCATCATCGTCAGCCATGG 59.195 52.381 7.63 7.63 0.00 3.66
3523 3937 2.026822 AGCTGAACATTCGGAATCCACT 60.027 45.455 0.00 0.00 35.56 4.00
3524 3938 2.352960 GCTGAACATTCGGAATCCACTC 59.647 50.000 0.00 0.00 35.56 3.51
3525 3939 3.599343 CTGAACATTCGGAATCCACTCA 58.401 45.455 0.00 1.23 35.56 3.41
3682 4104 0.108898 CTCAGAGTCTCCGCCTGTTG 60.109 60.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.832685 GGTTAGGGGTAAGTTGACTGAATATTT 59.167 37.037 0.00 0.00 0.00 1.40
1 2 7.037153 TGGTTAGGGGTAAGTTGACTGAATATT 60.037 37.037 0.00 0.00 0.00 1.28
2 3 6.445786 TGGTTAGGGGTAAGTTGACTGAATAT 59.554 38.462 0.00 0.00 0.00 1.28
3 4 5.786457 TGGTTAGGGGTAAGTTGACTGAATA 59.214 40.000 0.00 0.00 0.00 1.75
4 5 4.600111 TGGTTAGGGGTAAGTTGACTGAAT 59.400 41.667 0.00 0.00 0.00 2.57
5 6 3.975312 TGGTTAGGGGTAAGTTGACTGAA 59.025 43.478 0.00 0.00 0.00 3.02
6 7 3.589641 TGGTTAGGGGTAAGTTGACTGA 58.410 45.455 0.00 0.00 0.00 3.41
7 8 4.360951 TTGGTTAGGGGTAAGTTGACTG 57.639 45.455 0.00 0.00 0.00 3.51
8 9 4.018688 GGATTGGTTAGGGGTAAGTTGACT 60.019 45.833 0.00 0.00 0.00 3.41
9 10 4.018688 AGGATTGGTTAGGGGTAAGTTGAC 60.019 45.833 0.00 0.00 0.00 3.18
10 11 4.180723 AGGATTGGTTAGGGGTAAGTTGA 58.819 43.478 0.00 0.00 0.00 3.18
11 12 4.586306 AGGATTGGTTAGGGGTAAGTTG 57.414 45.455 0.00 0.00 0.00 3.16
12 13 5.794289 AGTTAGGATTGGTTAGGGGTAAGTT 59.206 40.000 0.00 0.00 0.00 2.66
13 14 5.356575 AGTTAGGATTGGTTAGGGGTAAGT 58.643 41.667 0.00 0.00 0.00 2.24
14 15 5.970501 AGTTAGGATTGGTTAGGGGTAAG 57.029 43.478 0.00 0.00 0.00 2.34
15 16 6.034003 AGAAGTTAGGATTGGTTAGGGGTAA 58.966 40.000 0.00 0.00 0.00 2.85
16 17 5.606761 AGAAGTTAGGATTGGTTAGGGGTA 58.393 41.667 0.00 0.00 0.00 3.69
17 18 4.445564 AGAAGTTAGGATTGGTTAGGGGT 58.554 43.478 0.00 0.00 0.00 4.95
18 19 5.452341 AAGAAGTTAGGATTGGTTAGGGG 57.548 43.478 0.00 0.00 0.00 4.79
19 20 6.056236 GCTAAGAAGTTAGGATTGGTTAGGG 58.944 44.000 0.00 0.00 36.83 3.53
20 21 6.650120 TGCTAAGAAGTTAGGATTGGTTAGG 58.350 40.000 0.00 0.00 36.83 2.69
21 22 7.227512 CCATGCTAAGAAGTTAGGATTGGTTAG 59.772 40.741 0.00 0.00 42.89 2.34
22 23 7.054124 CCATGCTAAGAAGTTAGGATTGGTTA 58.946 38.462 0.00 0.00 42.89 2.85
23 24 5.888161 CCATGCTAAGAAGTTAGGATTGGTT 59.112 40.000 0.00 0.00 42.89 3.67
24 25 5.191722 TCCATGCTAAGAAGTTAGGATTGGT 59.808 40.000 0.00 0.00 42.89 3.67
25 26 5.529060 GTCCATGCTAAGAAGTTAGGATTGG 59.471 44.000 0.00 3.71 42.89 3.16
26 27 5.235186 CGTCCATGCTAAGAAGTTAGGATTG 59.765 44.000 0.00 0.00 42.89 2.67
27 28 5.360591 CGTCCATGCTAAGAAGTTAGGATT 58.639 41.667 0.00 0.00 42.89 3.01
28 29 4.740934 GCGTCCATGCTAAGAAGTTAGGAT 60.741 45.833 0.00 0.00 45.47 3.24
29 30 3.430374 GCGTCCATGCTAAGAAGTTAGGA 60.430 47.826 0.00 0.00 40.51 2.94
30 31 2.866762 GCGTCCATGCTAAGAAGTTAGG 59.133 50.000 0.00 0.00 36.83 2.69
53 54 7.768807 AGTAGTTAGGCATCTCTTATACCTG 57.231 40.000 0.00 0.00 31.79 4.00
57 58 6.072064 GCGGAAGTAGTTAGGCATCTCTTATA 60.072 42.308 0.00 0.00 0.00 0.98
62 63 2.100916 TGCGGAAGTAGTTAGGCATCTC 59.899 50.000 4.16 0.00 0.00 2.75
67 68 0.535797 AGGTGCGGAAGTAGTTAGGC 59.464 55.000 0.00 0.00 0.00 3.93
68 69 4.460948 TTAAGGTGCGGAAGTAGTTAGG 57.539 45.455 0.00 0.00 0.00 2.69
74 75 1.279558 TGCCATTAAGGTGCGGAAGTA 59.720 47.619 0.00 0.00 40.61 2.24
75 76 0.037590 TGCCATTAAGGTGCGGAAGT 59.962 50.000 0.00 0.00 40.61 3.01
79 80 0.455972 CGTTTGCCATTAAGGTGCGG 60.456 55.000 0.00 0.00 40.61 5.69
88 89 1.791103 CGTGTGTCCCGTTTGCCATT 61.791 55.000 0.00 0.00 0.00 3.16
98 99 0.451783 GATCAAATGGCGTGTGTCCC 59.548 55.000 0.00 0.00 0.00 4.46
102 103 1.016627 ATCGGATCAAATGGCGTGTG 58.983 50.000 0.00 0.00 0.00 3.82
103 104 2.613026 TATCGGATCAAATGGCGTGT 57.387 45.000 0.00 0.00 0.00 4.49
105 106 3.067106 GACATATCGGATCAAATGGCGT 58.933 45.455 0.00 0.00 0.00 5.68
116 117 4.221924 TCCTCAACAAACAGACATATCGGA 59.778 41.667 0.00 0.00 0.00 4.55
132 133 3.491267 GGATCATCGAACGATTCCTCAAC 59.509 47.826 16.04 3.32 31.90 3.18
133 134 3.132111 TGGATCATCGAACGATTCCTCAA 59.868 43.478 20.83 6.49 34.35 3.02
134 135 2.693074 TGGATCATCGAACGATTCCTCA 59.307 45.455 20.83 10.61 34.35 3.86
136 137 3.133003 ACTTGGATCATCGAACGATTCCT 59.867 43.478 20.83 6.21 34.35 3.36
160 175 7.539436 TGTTTTCTAGAGCAGTACATGACTAG 58.461 38.462 0.00 3.58 35.64 2.57
202 223 5.183228 GGTTTTCGATTCAGTTAGATCCCA 58.817 41.667 0.00 0.00 0.00 4.37
205 226 4.868734 ACGGGTTTTCGATTCAGTTAGATC 59.131 41.667 0.00 0.00 0.00 2.75
213 234 0.589223 GTGCACGGGTTTTCGATTCA 59.411 50.000 0.00 0.00 0.00 2.57
214 235 0.589223 TGTGCACGGGTTTTCGATTC 59.411 50.000 13.13 0.00 0.00 2.52
221 242 1.739049 CCATTGTGTGCACGGGTTT 59.261 52.632 13.13 0.00 0.00 3.27
289 310 1.097547 CGGGCATCTTCGGCATCTTT 61.098 55.000 0.00 0.00 0.00 2.52
323 344 0.671251 GGCAAACACGGTGAAATGGA 59.329 50.000 16.29 0.00 0.00 3.41
410 434 2.739287 TAGCCGCAAACCGTTCGG 60.739 61.111 9.81 9.81 45.46 4.30
456 480 9.185192 GAGATGGTTTGTGTCAAGAAAATTAAG 57.815 33.333 0.00 0.00 0.00 1.85
457 481 8.141268 GGAGATGGTTTGTGTCAAGAAAATTAA 58.859 33.333 0.00 0.00 0.00 1.40
459 483 6.462909 GGGAGATGGTTTGTGTCAAGAAAATT 60.463 38.462 0.00 0.00 0.00 1.82
460 484 5.011023 GGGAGATGGTTTGTGTCAAGAAAAT 59.989 40.000 0.00 0.00 0.00 1.82
469 493 1.303317 GCCGGGAGATGGTTTGTGT 60.303 57.895 2.18 0.00 0.00 3.72
470 494 1.303236 TGCCGGGAGATGGTTTGTG 60.303 57.895 2.18 0.00 0.00 3.33
477 501 0.033228 CTTAGCTCTGCCGGGAGATG 59.967 60.000 27.14 19.97 35.52 2.90
546 580 2.325082 GCTGGCGAATTCACGGTGT 61.325 57.895 8.17 0.00 0.00 4.16
609 648 1.683441 GTGTGAAGGGAATCCGGGT 59.317 57.895 0.00 0.00 38.33 5.28
689 732 4.360027 GTGCGCTGTGACGTGCTG 62.360 66.667 9.73 0.00 40.87 4.41
703 746 2.171489 GACTTTGCGTTCCGGAGTGC 62.171 60.000 19.80 19.80 0.00 4.40
704 747 1.860078 GACTTTGCGTTCCGGAGTG 59.140 57.895 3.34 1.87 0.00 3.51
705 748 1.663702 CGACTTTGCGTTCCGGAGT 60.664 57.895 3.34 0.00 0.00 3.85
707 750 0.942410 CTTCGACTTTGCGTTCCGGA 60.942 55.000 0.00 0.00 0.00 5.14
900 957 4.235762 GGCTGCGCGAAGGGGATA 62.236 66.667 17.69 0.00 41.43 2.59
1113 1187 0.178975 ACACGGAAAATTGGCAGGGA 60.179 50.000 0.00 0.00 0.00 4.20
1161 1235 0.541863 AAGTGACAGCGGGATAAGGG 59.458 55.000 0.00 0.00 0.00 3.95
1165 1239 1.476891 GAGTGAAGTGACAGCGGGATA 59.523 52.381 0.00 0.00 0.00 2.59
1425 1549 9.035607 ACATGAATAAGAGAATTACATGACGAC 57.964 33.333 0.00 0.00 37.59 4.34
1503 1762 3.723764 GCGTAAAATGCATACCACGAATG 59.276 43.478 23.22 4.68 0.00 2.67
1507 1766 2.095213 ACAGCGTAAAATGCATACCACG 59.905 45.455 17.66 17.66 31.07 4.94
1508 1767 3.126171 TGACAGCGTAAAATGCATACCAC 59.874 43.478 0.00 0.00 31.07 4.16
1509 1768 3.339141 TGACAGCGTAAAATGCATACCA 58.661 40.909 0.00 0.00 31.07 3.25
1510 1769 4.142687 ACTTGACAGCGTAAAATGCATACC 60.143 41.667 0.00 0.00 31.07 2.73
1511 1770 4.969816 ACTTGACAGCGTAAAATGCATAC 58.030 39.130 0.00 0.00 31.07 2.39
1512 1771 5.621197 AACTTGACAGCGTAAAATGCATA 57.379 34.783 0.00 0.00 31.07 3.14
1513 1772 4.503741 AACTTGACAGCGTAAAATGCAT 57.496 36.364 0.00 0.00 31.07 3.96
1514 1773 3.980646 AACTTGACAGCGTAAAATGCA 57.019 38.095 0.00 0.00 31.07 3.96
1515 1774 3.425193 CCAAACTTGACAGCGTAAAATGC 59.575 43.478 0.00 0.00 0.00 3.56
1516 1775 4.854399 TCCAAACTTGACAGCGTAAAATG 58.146 39.130 0.00 0.00 0.00 2.32
1517 1776 5.705609 ATCCAAACTTGACAGCGTAAAAT 57.294 34.783 0.00 0.00 0.00 1.82
1518 1777 5.163602 ACAATCCAAACTTGACAGCGTAAAA 60.164 36.000 0.00 0.00 0.00 1.52
1519 1778 4.336993 ACAATCCAAACTTGACAGCGTAAA 59.663 37.500 0.00 0.00 0.00 2.01
1520 1779 3.880490 ACAATCCAAACTTGACAGCGTAA 59.120 39.130 0.00 0.00 0.00 3.18
1521 1780 3.472652 ACAATCCAAACTTGACAGCGTA 58.527 40.909 0.00 0.00 0.00 4.42
1522 1781 2.290641 GACAATCCAAACTTGACAGCGT 59.709 45.455 0.00 0.00 0.00 5.07
1523 1782 2.290367 TGACAATCCAAACTTGACAGCG 59.710 45.455 0.00 0.00 0.00 5.18
1524 1783 3.988379 TGACAATCCAAACTTGACAGC 57.012 42.857 0.00 0.00 0.00 4.40
1525 1784 5.696822 CAGATGACAATCCAAACTTGACAG 58.303 41.667 0.00 0.00 33.19 3.51
1526 1785 4.022935 GCAGATGACAATCCAAACTTGACA 60.023 41.667 0.00 0.00 33.95 3.58
1527 1786 4.022935 TGCAGATGACAATCCAAACTTGAC 60.023 41.667 0.00 0.00 32.77 3.18
1528 1787 4.143543 TGCAGATGACAATCCAAACTTGA 58.856 39.130 0.00 0.00 32.77 3.02
1529 1788 4.508461 TGCAGATGACAATCCAAACTTG 57.492 40.909 0.00 0.00 32.77 3.16
1530 1789 5.069516 ACTTTGCAGATGACAATCCAAACTT 59.930 36.000 0.00 0.00 32.77 2.66
1531 1790 4.586001 ACTTTGCAGATGACAATCCAAACT 59.414 37.500 0.00 0.00 32.77 2.66
1532 1791 4.874970 ACTTTGCAGATGACAATCCAAAC 58.125 39.130 0.00 0.00 32.77 2.93
1533 1792 5.068855 TCAACTTTGCAGATGACAATCCAAA 59.931 36.000 0.00 0.00 32.77 3.28
1534 1793 4.583907 TCAACTTTGCAGATGACAATCCAA 59.416 37.500 0.00 0.00 32.77 3.53
1535 1794 4.143543 TCAACTTTGCAGATGACAATCCA 58.856 39.130 0.00 0.00 32.77 3.41
1536 1795 4.217118 ACTCAACTTTGCAGATGACAATCC 59.783 41.667 0.00 0.00 32.77 3.01
1537 1796 5.368256 ACTCAACTTTGCAGATGACAATC 57.632 39.130 0.00 0.00 29.24 2.67
1538 1797 7.826252 ACTATACTCAACTTTGCAGATGACAAT 59.174 33.333 0.00 0.00 29.24 2.71
1539 1798 7.118245 CACTATACTCAACTTTGCAGATGACAA 59.882 37.037 0.00 0.00 29.24 3.18
1540 1799 6.591448 CACTATACTCAACTTTGCAGATGACA 59.409 38.462 0.00 0.00 29.24 3.58
1541 1800 6.591834 ACACTATACTCAACTTTGCAGATGAC 59.408 38.462 0.00 0.00 29.24 3.06
1542 1801 6.591448 CACACTATACTCAACTTTGCAGATGA 59.409 38.462 0.00 0.00 31.36 2.92
1712 1972 3.020984 GTTGTCCAACTCCAAAGTCCAA 58.979 45.455 2.95 0.00 38.25 3.53
1713 1973 2.650322 GTTGTCCAACTCCAAAGTCCA 58.350 47.619 2.95 0.00 38.25 4.02
1714 1974 1.954382 GGTTGTCCAACTCCAAAGTCC 59.046 52.381 9.79 0.00 40.94 3.85
1715 1975 2.618709 CAGGTTGTCCAACTCCAAAGTC 59.381 50.000 9.79 0.00 40.94 3.01
1716 1976 2.025321 ACAGGTTGTCCAACTCCAAAGT 60.025 45.455 9.79 0.00 40.94 2.66
1717 1977 2.654863 ACAGGTTGTCCAACTCCAAAG 58.345 47.619 9.79 0.00 40.94 2.77
1742 2002 6.238184 CGTCATGACACTTAATATGCACACAT 60.238 38.462 24.93 0.00 40.49 3.21
1791 2086 6.590234 TTCAGTACTTGCATCTCTCTACAA 57.410 37.500 0.00 0.00 0.00 2.41
1890 2192 0.168348 TCTCGTACAACTGAGCGAGC 59.832 55.000 16.61 0.00 46.98 5.03
1993 2296 3.138283 AGGATCTCAAAACCTGTGGTCAA 59.862 43.478 0.00 0.00 33.12 3.18
2052 2355 4.462483 TGAACAATTTCCTCATTAGTGCCC 59.538 41.667 0.00 0.00 0.00 5.36
2184 2506 6.517605 TGTACACTGTACACTAAAGCAATCA 58.482 36.000 16.61 0.00 0.00 2.57
2233 2556 7.814264 AGCTTTCCTCGATCAAATGATAATT 57.186 32.000 0.00 0.00 34.37 1.40
2525 2869 0.538057 TGCCTTTGCTGGACTTCAGG 60.538 55.000 0.00 0.00 43.54 3.86
2716 3060 3.244875 TGCAAAGATCCAAGGAGTAAGCA 60.245 43.478 0.00 0.00 0.00 3.91
2745 3089 0.455815 TCGCGAGCAGCTTCTTGATA 59.544 50.000 3.71 0.00 45.59 2.15
2768 3112 2.827322 TGATGCAGCAACAAGGCTTAAT 59.173 40.909 0.00 0.00 42.71 1.40
2844 3189 0.316278 CTACGAGATCGGACTGCACG 60.316 60.000 7.22 0.00 44.95 5.34
2894 3239 0.718343 CTGCAGCAGAAGTAAGACGC 59.282 55.000 18.42 0.00 32.44 5.19
2895 3240 2.095008 TCTCTGCAGCAGAAGTAAGACG 60.095 50.000 25.35 11.59 40.18 4.18
2898 3243 5.229423 GGATATCTCTGCAGCAGAAGTAAG 58.771 45.833 25.35 13.71 40.18 2.34
2959 3305 4.453480 TCCAAACTTGTTCCTCAGGAAT 57.547 40.909 10.09 0.00 44.04 3.01
2964 3310 4.531854 TCACATTCCAAACTTGTTCCTCA 58.468 39.130 0.00 0.00 0.00 3.86
3026 3432 7.090953 ACTACAGAAAAATTTCCAACGAACA 57.909 32.000 2.37 0.00 37.92 3.18
3039 3445 6.094061 CCGGACAAAACAAACTACAGAAAAA 58.906 36.000 0.00 0.00 0.00 1.94
3156 3567 8.651389 TGTATTTCTTCCTCTTCTTCTTCTTCA 58.349 33.333 0.00 0.00 0.00 3.02
3227 3638 4.218312 GGAGATATTTGTGGCCTTGGAAT 58.782 43.478 3.32 1.89 0.00 3.01
3334 3745 2.366435 GGTAGGGGTAGGCTGGCA 60.366 66.667 3.38 0.00 0.00 4.92
3367 3778 3.968568 CTGTGCCAAGCGCTTGCA 61.969 61.111 38.53 33.88 42.66 4.08
3370 3781 1.963338 GAGACTGTGCCAAGCGCTT 60.963 57.895 18.98 18.98 40.03 4.68
3371 3782 2.358003 GAGACTGTGCCAAGCGCT 60.358 61.111 2.64 2.64 40.03 5.92
3400 3811 1.187567 TGCTGTACCAGAGCAGAGCA 61.188 55.000 2.41 0.00 41.56 4.26
3401 3812 1.593787 TGCTGTACCAGAGCAGAGC 59.406 57.895 2.41 0.00 41.56 4.09
3405 3816 1.004560 GCACTGCTGTACCAGAGCA 60.005 57.895 13.75 10.39 45.08 4.26
3422 3833 1.994779 CGTGGAATTGAAAATGGCAGC 59.005 47.619 0.00 0.00 0.00 5.25
3424 3835 1.342496 TGCGTGGAATTGAAAATGGCA 59.658 42.857 0.00 0.00 0.00 4.92
3442 3853 1.228063 ATGATGGGGCGATGAGTGC 60.228 57.895 0.00 0.00 0.00 4.40
3451 3862 1.271001 TGACGATGATGATGATGGGGC 60.271 52.381 0.00 0.00 0.00 5.80
3468 3882 1.875963 CGTGGAAACCATGGCTGAC 59.124 57.895 13.04 0.38 36.92 3.51
3478 3892 2.750888 GCCGGATCTGCGTGGAAAC 61.751 63.158 5.05 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.