Multiple sequence alignment - TraesCS2A01G141900

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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 TraesCS2A01G141900 chr2A 100.000 3297 0 0 1 3297 87459526 87462822 0.000000e+00 6089.0
1 TraesCS2A01G141900 chr2A 100.000 405 0 0 3600 4004 87463125 87463529 0.000000e+00 749.0
2 TraesCS2A01G141900 chr2D 87.961 1628 83 30 98 1663 87268311 87269887 0.000000e+00 1816.0
3 TraesCS2A01G141900 chr2D 91.251 1223 79 18 1799 3006 87269934 87271143 0.000000e+00 1640.0
4 TraesCS2A01G141900 chr2D 94.802 404 19 2 3601 4004 87277336 87277737 2.630000e-176 628.0
5 TraesCS2A01G141900 chr2D 93.443 305 13 3 2998 3297 87277007 87277309 2.840000e-121 446.0
6 TraesCS2A01G141900 chr2D 84.712 399 59 2 3606 4004 43477509 43477113 8.060000e-107 398.0
7 TraesCS2A01G141900 chr2D 97.170 106 3 0 1 106 87261330 87261435 3.180000e-41 180.0
8 TraesCS2A01G141900 chr2D 83.889 180 11 5 335 497 561337711 561337533 5.360000e-34 156.0
9 TraesCS2A01G141900 chr2B 93.966 1044 50 10 2065 3101 139915711 139916748 0.000000e+00 1567.0
10 TraesCS2A01G141900 chr2B 92.780 651 25 9 504 1144 139913818 139914456 0.000000e+00 922.0
11 TraesCS2A01G141900 chr2B 89.293 523 36 11 1 504 139913268 139913789 4.360000e-179 638.0
12 TraesCS2A01G141900 chr2B 81.297 401 22 18 1491 1872 139914902 139915268 3.940000e-70 276.0
13 TraesCS2A01G141900 chr2B 75.000 340 73 9 3671 4004 1690451 1690118 3.220000e-31 147.0
14 TraesCS2A01G141900 chr2B 83.226 155 10 6 1885 2039 139915481 139915619 1.170000e-25 128.0
15 TraesCS2A01G141900 chr2B 83.654 104 16 1 3105 3208 68261926 68261824 3.290000e-16 97.1
16 TraesCS2A01G141900 chr2B 92.982 57 4 0 1150 1206 139914490 139914546 2.560000e-12 84.2
17 TraesCS2A01G141900 chr3A 86.869 396 50 2 3601 3996 514052881 514052488 3.670000e-120 442.0
18 TraesCS2A01G141900 chr4D 84.051 395 60 3 3608 4002 30300028 30299637 1.050000e-100 377.0
19 TraesCS2A01G141900 chr4D 84.466 103 11 2 3105 3207 393848503 393848406 3.290000e-16 97.1
20 TraesCS2A01G141900 chr1B 92.857 210 14 1 1 210 282079711 282079503 1.810000e-78 303.0
21 TraesCS2A01G141900 chr1B 92.857 210 14 1 1 210 282104038 282103830 1.810000e-78 303.0
22 TraesCS2A01G141900 chr7A 83.072 319 50 4 3688 4004 74605675 74605991 1.820000e-73 287.0
23 TraesCS2A01G141900 chr5A 90.094 212 20 1 1 212 203029891 203030101 1.420000e-69 274.0
24 TraesCS2A01G141900 chr5A 80.110 181 23 7 3103 3283 458557168 458557335 5.430000e-24 122.0
25 TraesCS2A01G141900 chrUn 84.177 158 14 2 326 472 62703781 62703938 4.170000e-30 143.0
26 TraesCS2A01G141900 chr6A 84.177 158 14 2 326 472 4583126 4583283 4.170000e-30 143.0
27 TraesCS2A01G141900 chr6A 81.481 162 24 2 3136 3297 29883493 29883338 1.170000e-25 128.0
28 TraesCS2A01G141900 chr6A 84.259 108 3 9 3105 3204 27062703 27062804 4.260000e-15 93.5
29 TraesCS2A01G141900 chr6D 82.424 165 18 5 3119 3283 27975746 27975899 2.510000e-27 134.0
30 TraesCS2A01G141900 chr3B 82.031 128 21 1 1967 2092 761295668 761295541 1.520000e-19 108.0
31 TraesCS2A01G141900 chr3B 84.375 96 11 1 3105 3200 147518939 147518848 1.530000e-14 91.6
32 TraesCS2A01G141900 chr4B 78.022 182 27 6 3116 3297 513054651 513054483 7.080000e-18 102.0
33 TraesCS2A01G141900 chr7B 86.813 91 9 3 2009 2097 740002670 740002759 9.160000e-17 99.0
34 TraesCS2A01G141900 chr7B 88.158 76 5 4 2011 2084 657546969 657547042 1.980000e-13 87.9
35 TraesCS2A01G141900 chr7B 100.000 34 0 0 336 369 574478120 574478153 3.340000e-06 63.9
36 TraesCS2A01G141900 chr7B 100.000 31 0 0 339 369 574478179 574478209 1.550000e-04 58.4
37 TraesCS2A01G141900 chr7B 100.000 29 0 0 339 367 574478235 574478263 2.000000e-03 54.7
38 TraesCS2A01G141900 chr3D 90.625 64 6 0 1992 2055 303406588 303406525 7.130000e-13 86.1


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 TraesCS2A01G141900 chr2A 87459526 87463529 4003 False 3419.000000 6089 100.0000 1 4004 2 chr2A.!!$F1 4003
1 TraesCS2A01G141900 chr2D 87268311 87271143 2832 False 1728.000000 1816 89.6060 98 3006 2 chr2D.!!$F2 2908
2 TraesCS2A01G141900 chr2D 87277007 87277737 730 False 537.000000 628 94.1225 2998 4004 2 chr2D.!!$F3 1006
3 TraesCS2A01G141900 chr2B 139913268 139916748 3480 False 602.533333 1567 88.9240 1 3101 6 chr2B.!!$F1 3100

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
440 479 0.030638 TGGTTTCAAAGAAGCGCTGC 59.969 50.0 12.58 9.98 0.00 5.25 F
1579 1790 0.037882 TCTTCTGTTCGCTCCAGCTG 60.038 55.0 6.78 6.78 39.32 4.24 F
1959 2402 0.729116 CTATCACCTTGTTGCCTGCG 59.271 55.0 0.00 0.00 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 1813 0.109153 ACAGAACATGAGCACCAGCA 59.891 50.0 0.00 0.0 45.49 4.41 R
2805 3322 0.446616 GTTTTGATCCCGAACCTCGC 59.553 55.0 0.00 0.0 38.82 5.03 R
3644 4170 0.478072 TGTGGACCACATGGAGCTTT 59.522 50.0 23.72 0.0 39.62 3.51 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
27 28 1.265095 CAAAGACTGCACTGACGCATT 59.735 47.619 0.00 0.00 42.06 3.56
36 37 0.319900 ACTGACGCATTGAAGCTCGT 60.320 50.000 0.00 0.00 37.92 4.18
67 68 4.796038 ATTTGAGCCTTTCATGTTCCAG 57.204 40.909 0.00 0.00 35.27 3.86
88 89 3.347216 GCAAAGGCTGAATCACCTCTTA 58.653 45.455 5.16 0.00 34.31 2.10
189 209 4.217159 GGGGTGCTAGGTACGGCG 62.217 72.222 4.80 4.80 35.09 6.46
221 241 3.198068 CAACATGACTAATCCTGACCGG 58.802 50.000 0.00 0.00 0.00 5.28
260 280 2.224113 GCCGTTGGAATCGGGACTAATA 60.224 50.000 6.50 0.00 46.90 0.98
303 323 1.590147 CCGACCGGAACTAGTGCTT 59.410 57.895 9.46 0.00 37.50 3.91
316 336 5.091261 ACTAGTGCTTCGGATGAAAGATT 57.909 39.130 0.00 0.00 32.66 2.40
333 353 9.944376 ATGAAAGATTAGTTTTCTACTAGTGCA 57.056 29.630 5.39 0.00 40.35 4.57
438 477 1.334869 CAGTGGTTTCAAAGAAGCGCT 59.665 47.619 2.64 2.64 45.58 5.92
440 479 0.030638 TGGTTTCAAAGAAGCGCTGC 59.969 50.000 12.58 9.98 0.00 5.25
441 480 0.664466 GGTTTCAAAGAAGCGCTGCC 60.664 55.000 12.58 6.27 0.00 4.85
469 508 3.012518 CCGCTTCCATCTTTCATGAAGT 58.987 45.455 8.41 0.00 36.70 3.01
476 515 7.649533 TTCCATCTTTCATGAAGTATGCATT 57.350 32.000 19.35 0.00 24.93 3.56
516 584 4.822350 AGATAATCACGACTCGAATCCTCA 59.178 41.667 5.20 0.00 0.00 3.86
548 616 5.121142 TCAAATCGACGGTTTGAAATAGACC 59.879 40.000 28.96 0.00 41.23 3.85
574 643 2.036475 CCTCTCGAAACATCGGATGGAT 59.964 50.000 21.19 9.85 35.09 3.41
583 652 3.045634 ACATCGGATGGATTTGGTAGGA 58.954 45.455 21.19 0.00 31.28 2.94
594 663 5.312178 TGGATTTGGTAGGAAGAAAAGGAGA 59.688 40.000 0.00 0.00 0.00 3.71
681 751 1.241315 ACTCAATGGAAAACCCGCGG 61.241 55.000 21.04 21.04 37.93 6.46
790 860 4.202030 CCGACAGTGTTAGTTAGGGATCTC 60.202 50.000 0.00 0.00 0.00 2.75
796 866 6.819146 CAGTGTTAGTTAGGGATCTCTTTTCC 59.181 42.308 0.00 0.00 0.00 3.13
799 869 7.980662 GTGTTAGTTAGGGATCTCTTTTCCTAC 59.019 40.741 0.00 0.00 32.22 3.18
832 905 3.058085 ACGGCAGGTAAACCATTTTAACG 60.058 43.478 1.26 0.00 39.54 3.18
850 923 1.869690 GCCGGCAGAAGAACACTTC 59.130 57.895 24.80 0.00 39.94 3.01
1041 1118 1.675720 GGATTGTCGGGGCAAATGGG 61.676 60.000 0.00 0.00 31.63 4.00
1042 1119 0.970427 GATTGTCGGGGCAAATGGGT 60.970 55.000 0.00 0.00 31.63 4.51
1043 1120 0.544120 ATTGTCGGGGCAAATGGGTT 60.544 50.000 0.00 0.00 31.63 4.11
1044 1121 1.182385 TTGTCGGGGCAAATGGGTTC 61.182 55.000 0.00 0.00 0.00 3.62
1045 1122 2.036572 TCGGGGCAAATGGGTTCC 59.963 61.111 0.00 0.00 0.00 3.62
1046 1123 2.283532 CGGGGCAAATGGGTTCCA 60.284 61.111 0.00 0.00 38.19 3.53
1047 1124 2.350458 CGGGGCAAATGGGTTCCAG 61.350 63.158 0.00 0.00 36.75 3.86
1148 1259 2.221981 CGCTGCTCTTCTTTTCTTTCGT 59.778 45.455 0.00 0.00 0.00 3.85
1231 1360 6.145338 TCTTGTAATCTAACCGCTTAGGAG 57.855 41.667 0.00 0.00 45.00 3.69
1236 1365 2.317040 TCTAACCGCTTAGGAGGATGG 58.683 52.381 0.49 0.00 45.00 3.51
1402 1550 0.605589 AAGCGGTTCTAGTGGGTTGC 60.606 55.000 0.00 0.00 0.00 4.17
1403 1551 2.038837 GCGGTTCTAGTGGGTTGCC 61.039 63.158 0.00 0.00 0.00 4.52
1404 1552 1.677552 CGGTTCTAGTGGGTTGCCT 59.322 57.895 0.00 0.00 0.00 4.75
1406 1554 1.405121 CGGTTCTAGTGGGTTGCCTAC 60.405 57.143 0.00 0.00 35.11 3.18
1407 1555 1.065636 GGTTCTAGTGGGTTGCCTACC 60.066 57.143 0.00 0.00 46.99 3.18
1414 1562 2.033602 GGTTGCCTACCGTTGCCT 59.966 61.111 0.00 0.00 37.12 4.75
1415 1563 1.297364 GGTTGCCTACCGTTGCCTA 59.703 57.895 0.00 0.00 37.12 3.93
1416 1564 0.107361 GGTTGCCTACCGTTGCCTAT 60.107 55.000 0.00 0.00 37.12 2.57
1417 1565 1.296727 GTTGCCTACCGTTGCCTATC 58.703 55.000 0.00 0.00 0.00 2.08
1418 1566 0.179094 TTGCCTACCGTTGCCTATCG 60.179 55.000 0.00 0.00 0.00 2.92
1419 1567 1.324740 TGCCTACCGTTGCCTATCGT 61.325 55.000 0.00 0.00 0.00 3.73
1420 1568 0.596859 GCCTACCGTTGCCTATCGTC 60.597 60.000 0.00 0.00 0.00 4.20
1421 1569 1.030457 CCTACCGTTGCCTATCGTCT 58.970 55.000 0.00 0.00 0.00 4.18
1428 1576 2.656085 GTTGCCTATCGTCTGAGATCG 58.344 52.381 0.00 0.00 32.39 3.69
1458 1606 9.364989 CTTCCAAGATCTCTTACTCTGTTTTAG 57.635 37.037 0.00 0.00 34.28 1.85
1463 1611 7.552459 AGATCTCTTACTCTGTTTTAGCTTCC 58.448 38.462 0.00 0.00 0.00 3.46
1464 1612 6.665992 TCTCTTACTCTGTTTTAGCTTCCA 57.334 37.500 0.00 0.00 0.00 3.53
1467 1615 8.157476 TCTCTTACTCTGTTTTAGCTTCCATTT 58.843 33.333 0.00 0.00 0.00 2.32
1468 1616 9.436957 CTCTTACTCTGTTTTAGCTTCCATTTA 57.563 33.333 0.00 0.00 0.00 1.40
1473 1621 7.173390 ACTCTGTTTTAGCTTCCATTTAGACAC 59.827 37.037 0.00 0.00 0.00 3.67
1501 1649 3.088194 AGTCAAATTGTTGCAGCACAG 57.912 42.857 1.37 0.00 34.50 3.66
1503 1651 3.319972 AGTCAAATTGTTGCAGCACAGAT 59.680 39.130 1.37 0.00 34.50 2.90
1563 1774 2.035066 GGTGAGCAATTGCAGTGTTCTT 59.965 45.455 30.89 8.75 45.16 2.52
1564 1775 3.303406 GTGAGCAATTGCAGTGTTCTTC 58.697 45.455 30.89 17.37 45.16 2.87
1565 1776 3.004106 GTGAGCAATTGCAGTGTTCTTCT 59.996 43.478 30.89 7.20 45.16 2.85
1579 1790 0.037882 TCTTCTGTTCGCTCCAGCTG 60.038 55.000 6.78 6.78 39.32 4.24
1580 1791 1.004560 TTCTGTTCGCTCCAGCTGG 60.005 57.895 27.87 27.87 39.32 4.85
1581 1792 1.758440 TTCTGTTCGCTCCAGCTGGT 61.758 55.000 31.58 0.00 39.32 4.00
1582 1793 1.302033 CTGTTCGCTCCAGCTGGTT 60.302 57.895 31.58 0.00 39.32 3.67
1583 1794 1.572085 CTGTTCGCTCCAGCTGGTTG 61.572 60.000 31.58 24.58 39.32 3.77
1584 1795 2.669569 TTCGCTCCAGCTGGTTGC 60.670 61.111 31.58 30.61 43.29 4.17
1593 1804 3.730761 GCTGGTTGCTGGTGCTCG 61.731 66.667 0.00 0.00 40.48 5.03
1594 1805 2.281070 CTGGTTGCTGGTGCTCGT 60.281 61.111 0.00 0.00 40.48 4.18
1595 1806 2.591429 TGGTTGCTGGTGCTCGTG 60.591 61.111 0.00 0.00 40.48 4.35
1596 1807 2.591715 GGTTGCTGGTGCTCGTGT 60.592 61.111 0.00 0.00 40.48 4.49
1597 1808 2.186826 GGTTGCTGGTGCTCGTGTT 61.187 57.895 0.00 0.00 40.48 3.32
1598 1809 1.279840 GTTGCTGGTGCTCGTGTTC 59.720 57.895 0.00 0.00 40.48 3.18
1602 1813 1.594293 CTGGTGCTCGTGTTCGGTT 60.594 57.895 0.00 0.00 37.69 4.44
1654 1870 1.372872 GTGGCCACAAATGAACGGC 60.373 57.895 31.23 0.00 44.10 5.68
1673 1889 1.581934 CTCGCTGTTTGAGTTGGTGA 58.418 50.000 0.00 0.00 0.00 4.02
1679 1914 3.366883 GCTGTTTGAGTTGGTGAACACAA 60.367 43.478 7.25 0.00 39.84 3.33
1697 1932 3.126343 CACAACGCTTAATTGGTACTCCC 59.874 47.826 0.00 0.00 0.00 4.30
1789 2024 8.373981 TGGTACAGAGGTAGTACTATGATCTAC 58.626 40.741 5.75 6.22 41.16 2.59
1790 2025 8.596293 GGTACAGAGGTAGTACTATGATCTACT 58.404 40.741 5.75 0.00 41.16 2.57
1791 2026 9.643693 GTACAGAGGTAGTACTATGATCTACTC 57.356 40.741 5.75 5.98 38.95 2.59
1792 2027 7.682628 ACAGAGGTAGTACTATGATCTACTCC 58.317 42.308 5.75 0.00 35.69 3.85
1793 2028 6.814644 CAGAGGTAGTACTATGATCTACTCCG 59.185 46.154 5.75 0.00 35.69 4.63
1794 2029 6.497954 AGAGGTAGTACTATGATCTACTCCGT 59.502 42.308 5.75 0.00 35.69 4.69
1795 2030 7.673504 AGAGGTAGTACTATGATCTACTCCGTA 59.326 40.741 5.75 0.00 35.69 4.02
1796 2031 7.839907 AGGTAGTACTATGATCTACTCCGTAG 58.160 42.308 5.75 0.00 37.47 3.51
1797 2032 7.454380 AGGTAGTACTATGATCTACTCCGTAGT 59.546 40.741 5.75 0.00 37.41 2.73
1798 2033 8.744652 GGTAGTACTATGATCTACTCCGTAGTA 58.255 40.741 5.75 0.00 37.41 1.82
1814 2049 7.498570 ACTCCGTAGTAACTTATACTGGAAGAG 59.501 40.741 0.00 0.00 33.24 2.85
1831 2066 9.077885 ACTGGAAGAGTTATTCAGCAATAAAAA 57.922 29.630 0.00 0.00 35.29 1.94
1866 2101 4.672801 GCTTTTGCTTCGTAGAAATCTGGG 60.673 45.833 0.00 0.00 43.35 4.45
1898 2341 5.300539 TCACAAAATAGTTGCTTTAGCCACA 59.699 36.000 8.43 0.00 38.95 4.17
1956 2399 0.995024 AGCCTATCACCTTGTTGCCT 59.005 50.000 0.00 0.00 0.00 4.75
1959 2402 0.729116 CTATCACCTTGTTGCCTGCG 59.271 55.000 0.00 0.00 0.00 5.18
1995 2438 0.976963 CGCGTTCATGTTTGATGTGC 59.023 50.000 0.00 0.00 0.00 4.57
1996 2439 1.662592 CGCGTTCATGTTTGATGTGCA 60.663 47.619 0.00 0.00 0.00 4.57
2017 2460 1.395826 ATCCTAGTCGTGCAGAGGCC 61.396 60.000 0.00 0.00 40.13 5.19
2020 2463 1.729470 CTAGTCGTGCAGAGGCCGAT 61.729 60.000 0.00 0.00 42.01 4.18
2048 2496 3.378427 GCTCATTGTGTTTGTATCCCCTC 59.622 47.826 0.00 0.00 0.00 4.30
2061 2509 2.910688 TCCCCTCGATGCTTCATTAC 57.089 50.000 0.08 0.00 0.00 1.89
2065 2513 1.789464 CCTCGATGCTTCATTACGAGC 59.211 52.381 0.00 0.00 45.59 5.03
2066 2514 2.544694 CCTCGATGCTTCATTACGAGCT 60.545 50.000 0.00 0.00 45.59 4.09
2068 2516 4.290969 CTCGATGCTTCATTACGAGCTAA 58.709 43.478 0.00 0.00 42.39 3.09
2118 2634 5.178809 AGTCACCGTGTAATTAAACTGCTTC 59.821 40.000 4.29 0.00 0.00 3.86
2122 2638 6.148150 CACCGTGTAATTAAACTGCTTCCTTA 59.852 38.462 4.29 0.00 0.00 2.69
2447 2964 2.484770 GCTGACCAACTACACCAAGTCA 60.485 50.000 0.00 0.00 33.51 3.41
2525 3042 2.049433 GACTGGGTGGTCGTCGTG 60.049 66.667 0.00 0.00 0.00 4.35
2600 3117 3.706373 GCTCCTTCGGTCCAGCCA 61.706 66.667 0.00 0.00 36.97 4.75
2661 3178 7.164122 AGTTTTGCTGATGAAGTGAGAAGATA 58.836 34.615 0.00 0.00 0.00 1.98
2662 3179 7.663081 AGTTTTGCTGATGAAGTGAGAAGATAA 59.337 33.333 0.00 0.00 0.00 1.75
2730 3247 2.602257 TGATCTTATGCCCGTGTCAG 57.398 50.000 0.00 0.00 0.00 3.51
2744 3261 3.366070 CCGTGTCAGTCGTTTCTGTATCT 60.366 47.826 0.00 0.00 36.85 1.98
2753 3270 7.329471 TCAGTCGTTTCTGTATCTTTCAGATTG 59.671 37.037 0.00 0.00 40.83 2.67
2798 3315 5.889289 TGACACCACAGTACAGTAGCATATA 59.111 40.000 0.00 0.00 0.00 0.86
2871 3388 0.860533 CACAATTGGCAACGGCTTTG 59.139 50.000 10.83 5.46 40.87 2.77
2872 3389 0.249826 ACAATTGGCAACGGCTTTGG 60.250 50.000 10.83 0.00 40.87 3.28
3089 3610 5.479306 TGCTAGGAGATAACTTGTGTGTTC 58.521 41.667 0.00 0.00 0.00 3.18
3164 3685 2.826979 CATCTCTTGATGCACACAGC 57.173 50.000 0.00 0.00 42.83 4.40
3165 3686 1.400846 CATCTCTTGATGCACACAGCC 59.599 52.381 0.00 0.00 42.83 4.85
3228 3749 4.587684 AGTCTTACGGACCTCAAAGAAAGA 59.412 41.667 2.62 0.00 45.54 2.52
3230 3751 5.177142 GTCTTACGGACCTCAAAGAAAGAAC 59.823 44.000 2.62 0.00 38.93 3.01
3252 3773 2.435372 AATGATATGCCACAACCGGT 57.565 45.000 0.00 0.00 0.00 5.28
3263 3789 1.281656 CAACCGGTGAGGCGAAAAC 59.718 57.895 8.52 0.00 46.52 2.43
3266 3792 1.301401 CCGGTGAGGCGAAAACAGA 60.301 57.895 0.00 0.00 0.00 3.41
3624 4150 1.731709 TCGTGCAACCATCTTTCATCG 59.268 47.619 0.00 0.00 0.00 3.84
3625 4151 1.202065 CGTGCAACCATCTTTCATCGG 60.202 52.381 0.00 0.00 0.00 4.18
3640 4166 2.948979 TCATCGGTTGCAACCCAATATC 59.051 45.455 36.75 15.13 46.53 1.63
3644 4170 3.117851 TCGGTTGCAACCCAATATCCATA 60.118 43.478 36.75 11.23 46.53 2.74
3657 4183 5.184479 CCAATATCCATAAAGCTCCATGTGG 59.816 44.000 6.72 5.47 0.00 4.17
3703 4229 0.978146 AGGTATCCAAGCTGACGCCT 60.978 55.000 0.00 0.00 36.60 5.52
3725 4251 7.307337 CGCCTTGAAGATAACTTGCAAATTTTT 60.307 33.333 0.00 0.00 36.39 1.94
3748 4274 7.397892 TTTGTGATGGTTTGTCTGTTAAAGA 57.602 32.000 0.00 0.00 0.00 2.52
3786 4312 7.358352 CGACAATTTCAAATGGCTCAAAGTAAC 60.358 37.037 0.00 0.00 0.00 2.50
3797 4323 2.206750 TCAAAGTAACGCACACACTCC 58.793 47.619 0.00 0.00 0.00 3.85
3814 4340 3.804325 CACTCCTACTCAAATATGTGCCG 59.196 47.826 0.00 0.00 0.00 5.69
3815 4341 3.451178 ACTCCTACTCAAATATGTGCCGT 59.549 43.478 0.00 0.00 0.00 5.68
3894 4420 4.452890 CGGAGCAACATTAAAGGATACG 57.547 45.455 0.00 0.00 46.39 3.06
3901 4427 6.597672 AGCAACATTAAAGGATACGTGAATGA 59.402 34.615 7.87 0.00 46.39 2.57
3903 4429 7.587757 GCAACATTAAAGGATACGTGAATGATC 59.412 37.037 7.87 0.00 46.39 2.92
3941 4467 1.692411 AGTGGGCAAAGGAGAAACAC 58.308 50.000 0.00 0.00 0.00 3.32
3978 4504 3.606846 CGTCGTGATCACAAAAGCAACAT 60.607 43.478 24.93 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.179086 TTCACAGCACACGAGCTTCA 60.179 50.000 0.00 0.00 43.70 3.02
36 37 1.985473 AGGCTCAAATTCACAGCACA 58.015 45.000 5.80 0.00 34.62 4.57
67 68 1.831580 AGAGGTGATTCAGCCTTTGC 58.168 50.000 12.07 0.00 34.81 3.68
88 89 5.280654 AGCCATCATTGAACACAAACTTT 57.719 34.783 0.00 0.00 0.00 2.66
157 158 2.758737 CCCCCTACGTCGAAGGCT 60.759 66.667 0.00 0.00 32.34 4.58
175 176 0.870307 CATGTCGCCGTACCTAGCAC 60.870 60.000 0.00 0.00 0.00 4.40
176 177 1.033202 TCATGTCGCCGTACCTAGCA 61.033 55.000 0.00 0.00 0.00 3.49
177 178 0.594284 GTCATGTCGCCGTACCTAGC 60.594 60.000 0.00 0.00 0.00 3.42
178 179 0.316772 CGTCATGTCGCCGTACCTAG 60.317 60.000 0.00 0.00 0.00 3.02
189 209 2.341257 AGTCATGTTGCTCGTCATGTC 58.659 47.619 0.00 0.00 41.22 3.06
221 241 2.766651 TATGAGTGGACGGGGGCC 60.767 66.667 0.00 0.00 0.00 5.80
232 252 1.202533 CCGATTCCAACGGCTATGAGT 60.203 52.381 0.00 0.00 43.74 3.41
260 280 1.349067 GGCCCGGGACTAATATGAGT 58.651 55.000 29.31 0.00 0.00 3.41
293 313 4.537135 TCTTTCATCCGAAGCACTAGTT 57.463 40.909 0.00 0.00 31.28 2.24
316 336 6.095160 GGAGCTAGTGCACTAGTAGAAAACTA 59.905 42.308 40.27 14.96 45.85 2.24
333 353 5.957771 TTGAAGAATGGTATGGAGCTAGT 57.042 39.130 0.00 0.00 0.00 2.57
516 584 7.315247 TCAAACCGTCGATTTGAAATATGAT 57.685 32.000 12.42 0.00 41.82 2.45
559 627 4.275936 CCTACCAAATCCATCCGATGTTTC 59.724 45.833 7.60 0.00 0.00 2.78
563 632 3.769739 TCCTACCAAATCCATCCGATG 57.230 47.619 0.93 0.93 0.00 3.84
566 635 3.838244 TCTTCCTACCAAATCCATCCG 57.162 47.619 0.00 0.00 0.00 4.18
574 643 5.535030 GCTTTCTCCTTTTCTTCCTACCAAA 59.465 40.000 0.00 0.00 0.00 3.28
583 652 3.066760 CGGTGTTGCTTTCTCCTTTTCTT 59.933 43.478 0.00 0.00 0.00 2.52
594 663 3.284449 GGGCGTCGGTGTTGCTTT 61.284 61.111 0.00 0.00 0.00 3.51
650 720 1.448985 CATTGAGTTGGTACCACCGG 58.551 55.000 16.04 0.00 42.58 5.28
651 721 1.002659 TCCATTGAGTTGGTACCACCG 59.997 52.381 16.04 0.00 42.58 4.94
652 722 2.871096 TCCATTGAGTTGGTACCACC 57.129 50.000 16.04 7.99 38.01 4.61
653 723 4.261867 GGTTTTCCATTGAGTTGGTACCAC 60.262 45.833 16.04 10.20 40.31 4.16
654 724 3.892588 GGTTTTCCATTGAGTTGGTACCA 59.107 43.478 11.60 11.60 40.31 3.25
655 725 3.257375 GGGTTTTCCATTGAGTTGGTACC 59.743 47.826 4.43 4.43 42.91 3.34
656 726 3.057806 CGGGTTTTCCATTGAGTTGGTAC 60.058 47.826 0.00 0.00 42.91 3.34
657 727 3.150767 CGGGTTTTCCATTGAGTTGGTA 58.849 45.455 0.00 0.00 42.91 3.25
658 728 1.960689 CGGGTTTTCCATTGAGTTGGT 59.039 47.619 0.00 0.00 42.91 3.67
659 729 1.336795 GCGGGTTTTCCATTGAGTTGG 60.337 52.381 0.00 0.00 42.91 3.77
660 730 1.665735 CGCGGGTTTTCCATTGAGTTG 60.666 52.381 0.00 0.00 42.91 3.16
681 751 1.535088 GAATTAAGAAAGCGGCGCAC 58.465 50.000 35.02 23.18 0.00 5.34
790 860 3.120649 CGTCGCTTTCTTGGTAGGAAAAG 60.121 47.826 0.00 0.00 33.17 2.27
796 866 0.669318 TGCCGTCGCTTTCTTGGTAG 60.669 55.000 0.00 0.00 35.36 3.18
799 869 2.680913 CCTGCCGTCGCTTTCTTGG 61.681 63.158 0.00 0.00 35.36 3.61
832 905 1.578206 GGAAGTGTTCTTCTGCCGGC 61.578 60.000 22.73 22.73 46.47 6.13
850 923 2.172419 CGGCGCTGTTGTTAACGG 59.828 61.111 8.45 0.00 40.80 4.44
980 1053 3.145551 CCTCCGACGGGTAGGGTG 61.146 72.222 15.25 0.00 30.99 4.61
1148 1259 0.883153 ATCACAAATGCAGCAGCGAA 59.117 45.000 0.00 0.00 46.23 4.70
1231 1360 0.320771 CGCCTACACTATGCCCATCC 60.321 60.000 0.00 0.00 0.00 3.51
1236 1365 1.616865 TCCATACGCCTACACTATGCC 59.383 52.381 0.00 0.00 0.00 4.40
1412 1560 1.807742 GACCCGATCTCAGACGATAGG 59.192 57.143 0.00 0.00 43.77 2.57
1413 1561 2.773487 AGACCCGATCTCAGACGATAG 58.227 52.381 0.00 0.00 35.30 2.08
1414 1562 2.932855 AGACCCGATCTCAGACGATA 57.067 50.000 0.00 0.00 28.16 2.92
1415 1563 1.950909 GAAGACCCGATCTCAGACGAT 59.049 52.381 0.00 0.00 36.27 3.73
1416 1564 1.380524 GAAGACCCGATCTCAGACGA 58.619 55.000 0.00 0.00 36.27 4.20
1417 1565 0.382515 GGAAGACCCGATCTCAGACG 59.617 60.000 0.00 0.00 36.27 4.18
1418 1566 1.475403 TGGAAGACCCGATCTCAGAC 58.525 55.000 0.00 0.00 36.27 3.51
1419 1567 2.103373 CTTGGAAGACCCGATCTCAGA 58.897 52.381 0.00 0.00 36.27 3.27
1420 1568 2.103373 TCTTGGAAGACCCGATCTCAG 58.897 52.381 0.00 0.00 36.27 3.35
1421 1569 2.231716 TCTTGGAAGACCCGATCTCA 57.768 50.000 0.00 0.00 36.27 3.27
1428 1576 4.959839 AGAGTAAGAGATCTTGGAAGACCC 59.040 45.833 5.34 0.00 37.98 4.46
1458 1606 8.366671 ACTAATTATCGTGTCTAAATGGAAGC 57.633 34.615 0.00 0.00 0.00 3.86
1468 1616 7.962918 GCAACAATTTGACTAATTATCGTGTCT 59.037 33.333 2.79 0.00 34.69 3.41
1473 1621 6.746822 TGCTGCAACAATTTGACTAATTATCG 59.253 34.615 0.00 0.00 34.69 2.92
1493 1641 2.941064 TGCTGAATCTTATCTGTGCTGC 59.059 45.455 0.00 0.00 0.00 5.25
1501 1649 6.371825 TCAGATCATGCATGCTGAATCTTATC 59.628 38.462 25.63 18.02 34.71 1.75
1503 1651 5.617252 TCAGATCATGCATGCTGAATCTTA 58.383 37.500 25.63 16.15 34.71 2.10
1579 1790 2.117941 GAACACGAGCACCAGCAACC 62.118 60.000 0.00 0.00 45.49 3.77
1580 1791 1.279840 GAACACGAGCACCAGCAAC 59.720 57.895 0.00 0.00 45.49 4.17
1581 1792 2.243957 CGAACACGAGCACCAGCAA 61.244 57.895 0.00 0.00 45.49 3.91
1582 1793 2.661537 CGAACACGAGCACCAGCA 60.662 61.111 0.00 0.00 45.49 4.41
1583 1794 3.414700 CCGAACACGAGCACCAGC 61.415 66.667 0.00 0.00 42.56 4.85
1584 1795 1.594293 AACCGAACACGAGCACCAG 60.594 57.895 0.00 0.00 0.00 4.00
1585 1796 1.885388 CAACCGAACACGAGCACCA 60.885 57.895 0.00 0.00 0.00 4.17
1586 1797 2.935955 CAACCGAACACGAGCACC 59.064 61.111 0.00 0.00 0.00 5.01
1587 1798 2.244651 AGCAACCGAACACGAGCAC 61.245 57.895 0.00 0.00 0.00 4.40
1588 1799 2.108157 AGCAACCGAACACGAGCA 59.892 55.556 0.00 0.00 0.00 4.26
1589 1800 2.551270 CAGCAACCGAACACGAGC 59.449 61.111 0.00 0.00 0.00 5.03
1590 1801 1.594293 ACCAGCAACCGAACACGAG 60.594 57.895 0.00 0.00 0.00 4.18
1591 1802 1.885388 CACCAGCAACCGAACACGA 60.885 57.895 0.00 0.00 0.00 4.35
1592 1803 2.631428 CACCAGCAACCGAACACG 59.369 61.111 0.00 0.00 0.00 4.49
1593 1804 2.117941 GAGCACCAGCAACCGAACAC 62.118 60.000 0.00 0.00 45.49 3.32
1594 1805 1.891919 GAGCACCAGCAACCGAACA 60.892 57.895 0.00 0.00 45.49 3.18
1595 1806 1.237285 ATGAGCACCAGCAACCGAAC 61.237 55.000 0.00 0.00 45.49 3.95
1596 1807 1.073025 ATGAGCACCAGCAACCGAA 59.927 52.632 0.00 0.00 45.49 4.30
1597 1808 1.672030 CATGAGCACCAGCAACCGA 60.672 57.895 0.00 0.00 45.49 4.69
1598 1809 1.518056 AACATGAGCACCAGCAACCG 61.518 55.000 0.00 0.00 45.49 4.44
1602 1813 0.109153 ACAGAACATGAGCACCAGCA 59.891 50.000 0.00 0.00 45.49 4.41
1654 1870 1.581934 TCACCAACTCAAACAGCGAG 58.418 50.000 0.00 0.00 36.53 5.03
1673 1889 4.214758 GGAGTACCAATTAAGCGTTGTGTT 59.785 41.667 0.00 0.00 35.97 3.32
1679 1914 2.169978 GGAGGGAGTACCAATTAAGCGT 59.830 50.000 0.00 0.00 43.89 5.07
1697 1932 4.668177 CGGCTTACACATTTTGTTACGGAG 60.668 45.833 0.00 0.00 39.91 4.63
1752 1987 3.279434 CCTCTGTACCAAAATGTAGGGC 58.721 50.000 0.00 0.00 0.00 5.19
1753 1988 4.569719 ACCTCTGTACCAAAATGTAGGG 57.430 45.455 0.00 0.00 0.00 3.53
1755 1990 8.064336 AGTACTACCTCTGTACCAAAATGTAG 57.936 38.462 0.00 0.00 40.61 2.74
1789 2024 7.498570 ACTCTTCCAGTATAAGTTACTACGGAG 59.501 40.741 0.00 0.00 31.37 4.63
1790 2025 7.341805 ACTCTTCCAGTATAAGTTACTACGGA 58.658 38.462 0.00 0.21 31.37 4.69
1791 2026 7.565323 ACTCTTCCAGTATAAGTTACTACGG 57.435 40.000 0.00 0.00 31.37 4.02
1798 2033 8.540388 TGCTGAATAACTCTTCCAGTATAAGTT 58.460 33.333 0.00 0.00 32.30 2.66
1831 2066 2.110578 AGCAAAAGCACTCCCAAGTTT 58.889 42.857 0.00 0.00 31.71 2.66
1851 2086 5.014858 AGTGAGTACCCAGATTTCTACGAA 58.985 41.667 0.00 0.00 0.00 3.85
1866 2101 6.787085 AGCAACTATTTTGTGAGTGAGTAC 57.213 37.500 0.00 0.00 0.00 2.73
1898 2341 3.823304 GGGTGCAGAGTTCTCTTCATTTT 59.177 43.478 5.59 0.00 0.00 1.82
1956 2399 2.324330 CCACACAAAGGATCGCGCA 61.324 57.895 8.75 0.00 0.00 6.09
1959 2402 2.877691 GCCCACACAAAGGATCGC 59.122 61.111 0.00 0.00 0.00 4.58
1995 2438 1.202348 CCTCTGCACGACTAGGATGTG 60.202 57.143 6.84 6.84 36.70 3.21
1996 2439 1.107114 CCTCTGCACGACTAGGATGT 58.893 55.000 0.00 0.00 0.00 3.06
2017 2460 2.975410 ACACAATGAGCACACAATCG 57.025 45.000 0.00 0.00 0.00 3.34
2020 2463 3.865011 ACAAACACAATGAGCACACAA 57.135 38.095 0.00 0.00 0.00 3.33
2048 2496 6.690704 TTATTAGCTCGTAATGAAGCATCG 57.309 37.500 0.00 0.00 33.16 3.84
2061 2509 5.611844 CGATAAAGGGCGTTTTATTAGCTCG 60.612 44.000 10.73 4.99 36.30 5.03
2065 2513 5.352643 CCCGATAAAGGGCGTTTTATTAG 57.647 43.478 10.73 6.55 45.72 1.73
2095 2610 5.352643 AAGCAGTTTAATTACACGGTGAC 57.647 39.130 16.29 0.17 0.00 3.67
2096 2611 4.453136 GGAAGCAGTTTAATTACACGGTGA 59.547 41.667 16.29 0.00 0.00 4.02
2097 2612 4.454504 AGGAAGCAGTTTAATTACACGGTG 59.545 41.667 6.58 6.58 0.00 4.94
2098 2613 4.648651 AGGAAGCAGTTTAATTACACGGT 58.351 39.130 4.25 0.00 0.00 4.83
2118 2634 7.120726 CCCTGAAAACAGTAACCAGTATTAAGG 59.879 40.741 0.00 0.00 0.00 2.69
2122 2638 5.073965 TCCCCTGAAAACAGTAACCAGTATT 59.926 40.000 0.00 0.00 0.00 1.89
2421 2938 1.602377 GGTGTAGTTGGTCAGCACAAC 59.398 52.381 0.00 0.00 46.44 3.32
2447 2964 1.416243 TGAGGAACCGGTTGTACTGT 58.584 50.000 27.87 0.00 0.00 3.55
2525 3042 4.687215 TCGGTGCTGGTGCTGAGC 62.687 66.667 0.00 0.00 40.48 4.26
2600 3117 3.181493 GCGAAACAATCATCCAGCTGAAT 60.181 43.478 17.39 0.00 0.00 2.57
2661 3178 3.610114 GCGAGATGAGCAACACAACATTT 60.610 43.478 0.00 0.00 34.19 2.32
2662 3179 2.095567 GCGAGATGAGCAACACAACATT 60.096 45.455 0.00 0.00 34.19 2.71
2744 3261 6.464222 ACCGAGTAGAAATGACAATCTGAAA 58.536 36.000 4.78 0.00 0.00 2.69
2753 3270 3.870633 ACTGGACCGAGTAGAAATGAC 57.129 47.619 0.00 0.00 0.00 3.06
2765 3282 0.880278 CTGTGGTGTCAACTGGACCG 60.880 60.000 0.00 0.00 46.38 4.79
2805 3322 0.446616 GTTTTGATCCCGAACCTCGC 59.553 55.000 0.00 0.00 38.82 5.03
2864 3381 1.676006 GACCACAATATCCCAAAGCCG 59.324 52.381 0.00 0.00 0.00 5.52
2871 3388 3.117888 ACATCACCTGACCACAATATCCC 60.118 47.826 0.00 0.00 0.00 3.85
2872 3389 3.879295 CACATCACCTGACCACAATATCC 59.121 47.826 0.00 0.00 0.00 2.59
3107 3628 5.778241 GGGGTATTCCTCCTTTTTGAAAGAA 59.222 40.000 2.15 0.00 35.33 2.52
3108 3629 5.330233 GGGGTATTCCTCCTTTTTGAAAGA 58.670 41.667 2.15 0.00 35.33 2.52
3161 3682 5.296780 ACTTGGACGTTTAATCATATGGCTG 59.703 40.000 2.13 0.00 0.00 4.85
3164 3685 7.315247 TGAACTTGGACGTTTAATCATATGG 57.685 36.000 2.13 0.00 0.00 2.74
3165 3686 9.619316 TTTTGAACTTGGACGTTTAATCATATG 57.381 29.630 0.00 0.00 0.00 1.78
3228 3749 4.493547 CGGTTGTGGCATATCATTTTGTT 58.506 39.130 0.00 0.00 0.00 2.83
3230 3751 3.119173 ACCGGTTGTGGCATATCATTTTG 60.119 43.478 0.00 0.00 0.00 2.44
3252 3773 5.351465 GTCATCTTTATCTGTTTTCGCCTCA 59.649 40.000 0.00 0.00 0.00 3.86
3599 4125 6.091305 CGATGAAAGATGGTTGCACGATATAT 59.909 38.462 0.00 0.00 0.00 0.86
3603 4129 2.352651 CGATGAAAGATGGTTGCACGAT 59.647 45.455 0.00 0.00 0.00 3.73
3625 4151 5.049828 GCTTTATGGATATTGGGTTGCAAC 58.950 41.667 21.59 21.59 0.00 4.17
3640 4166 2.301346 GGACCACATGGAGCTTTATGG 58.699 52.381 4.53 8.43 38.94 2.74
3644 4170 0.478072 TGTGGACCACATGGAGCTTT 59.522 50.000 23.72 0.00 39.62 3.51
3657 4183 2.945668 GTCCTTATTCAGCCATGTGGAC 59.054 50.000 2.55 0.00 37.39 4.02
3738 4264 6.147164 GTCGGAATGATGTTGTCTTTAACAGA 59.853 38.462 0.00 0.00 43.14 3.41
3748 4274 5.703978 TGAAATTGTCGGAATGATGTTGT 57.296 34.783 0.00 0.00 0.00 3.32
3786 4312 2.148916 TTTGAGTAGGAGTGTGTGCG 57.851 50.000 0.00 0.00 0.00 5.34
3797 4323 6.903883 AAACTACGGCACATATTTGAGTAG 57.096 37.500 16.59 16.59 0.00 2.57
3814 4340 4.774124 ACCGGGATTAAGCCTAAAACTAC 58.226 43.478 10.09 0.00 0.00 2.73
3815 4341 5.440207 AACCGGGATTAAGCCTAAAACTA 57.560 39.130 10.09 0.00 0.00 2.24
3827 4353 2.239402 GGGACTTGGTTAACCGGGATTA 59.761 50.000 19.65 0.00 39.43 1.75
3882 4408 5.408604 GCGGATCATTCACGTATCCTTTAAT 59.591 40.000 11.53 0.00 37.60 1.40
3894 4420 4.632153 AGTTACTATGGCGGATCATTCAC 58.368 43.478 0.00 0.00 0.00 3.18
3901 4427 3.275617 TGCAAAGTTACTATGGCGGAT 57.724 42.857 0.00 0.00 0.00 4.18
3903 4429 3.405170 CTTGCAAAGTTACTATGGCGG 57.595 47.619 0.00 0.00 39.70 6.13
3941 4467 5.509605 TCACGACGAAACAATAGAACATG 57.490 39.130 0.00 0.00 0.00 3.21
3978 4504 3.446442 AGTTGGGAAGGTAGTAGACGA 57.554 47.619 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.