Multiple sequence alignment - TraesCS1D01G010600

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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 TraesCS1D01G010600 chr1D 100.000 3991 0 0 1 3991 5453886 5457876 0.000000e+00 7371.0
1 TraesCS1D01G010600 chr1D 90.201 398 31 3 1595 1987 176205359 176205753 2.750000e-141 512.0
2 TraesCS1D01G010600 chr7A 86.485 2930 234 79 180 3021 692311355 692308500 0.000000e+00 3068.0
3 TraesCS1D01G010600 chr7A 84.727 275 32 9 3308 3578 692308345 692308077 2.360000e-67 267.0
4 TraesCS1D01G010600 chr1B 86.071 2326 201 67 888 3155 17832553 17830293 0.000000e+00 2386.0
5 TraesCS1D01G010600 chr1B 86.439 1438 118 39 1455 2860 8193219 8194611 0.000000e+00 1504.0
6 TraesCS1D01G010600 chr1B 86.469 1382 106 38 888 2219 639480886 639482236 0.000000e+00 1441.0
7 TraesCS1D01G010600 chr1B 90.760 671 37 12 193 850 17833210 17832552 0.000000e+00 872.0
8 TraesCS1D01G010600 chr1B 88.227 739 52 22 862 1588 8183600 8184315 0.000000e+00 850.0
9 TraesCS1D01G010600 chr1B 87.339 774 57 16 2266 3021 639482342 639483092 0.000000e+00 848.0
10 TraesCS1D01G010600 chr1B 90.861 569 28 11 286 850 639480339 639480887 0.000000e+00 741.0
11 TraesCS1D01G010600 chr1B 83.805 778 75 19 2266 3021 8184587 8185335 0.000000e+00 691.0
12 TraesCS1D01G010600 chr1B 86.385 639 60 15 246 866 8182948 8183577 0.000000e+00 673.0
13 TraesCS1D01G010600 chr1B 90.959 365 24 5 3631 3991 8195294 8195653 2.160000e-132 483.0
14 TraesCS1D01G010600 chr1B 78.827 699 105 31 2885 3566 8194609 8195281 7.920000e-117 431.0
15 TraesCS1D01G010600 chr1B 89.256 242 14 5 1995 2224 8184330 8184571 3.900000e-75 292.0
16 TraesCS1D01G010600 chr1B 85.283 265 27 9 3305 3566 639483244 639483499 3.060000e-66 263.0
17 TraesCS1D01G010600 chr1B 88.770 187 9 4 8 186 8182759 8182941 6.720000e-53 219.0
18 TraesCS1D01G010600 chr1B 87.500 152 10 3 3090 3241 8185336 8185478 2.470000e-37 167.0
19 TraesCS1D01G010600 chr1B 86.755 151 12 2 3090 3240 639483093 639483235 1.150000e-35 161.0
20 TraesCS1D01G010600 chr1B 88.710 124 12 2 3296 3418 8185475 8185597 2.480000e-32 150.0
21 TraesCS1D01G010600 chr1B 94.792 96 5 0 16 111 639450198 639450293 2.480000e-32 150.0
22 TraesCS1D01G010600 chr1B 88.991 109 5 4 72 177 17833369 17833265 1.160000e-25 128.0
23 TraesCS1D01G010600 chr1B 87.879 99 8 3 13 111 17833454 17833360 3.260000e-21 113.0
24 TraesCS1D01G010600 chr1B 94.872 39 2 0 3939 3977 30187802 30187840 1.200000e-05 62.1
25 TraesCS1D01G010600 chr1B 80.247 81 11 5 3897 3977 7228666 7228741 5.570000e-04 56.5
26 TraesCS1D01G010600 chr1A 86.807 1804 174 31 1460 3222 6634475 6632695 0.000000e+00 1954.0
27 TraesCS1D01G010600 chr1A 89.910 1447 87 26 1826 3250 6762090 6760681 0.000000e+00 1808.0
28 TraesCS1D01G010600 chr1A 83.542 1197 122 39 1460 2609 6721098 6719930 0.000000e+00 1050.0
29 TraesCS1D01G010600 chr1A 89.963 817 51 14 866 1663 6763132 6762328 0.000000e+00 1026.0
30 TraesCS1D01G010600 chr1A 94.610 538 20 3 3455 3991 6735788 6735259 0.000000e+00 824.0
31 TraesCS1D01G010600 chr1A 87.914 695 50 14 180 863 6763835 6763164 0.000000e+00 787.0
32 TraesCS1D01G010600 chr1A 91.209 364 24 4 3631 3991 6718808 6718450 4.640000e-134 488.0
33 TraesCS1D01G010600 chr1A 89.121 239 23 3 2885 3121 6719748 6719511 1.080000e-75 294.0
34 TraesCS1D01G010600 chr1A 96.296 162 6 0 3299 3460 6760690 6760529 2.360000e-67 267.0
35 TraesCS1D01G010600 chr1A 87.978 183 13 2 9 186 6764082 6763904 1.450000e-49 207.0
36 TraesCS1D01G010600 chr1A 93.220 118 8 0 2746 2863 6719860 6719743 1.470000e-39 174.0
37 TraesCS1D01G010600 chr6D 90.099 404 32 3 1589 1987 389252782 389253182 5.910000e-143 518.0
38 TraesCS1D01G010600 chr6A 90.452 398 29 4 1595 1987 608870133 608869740 2.130000e-142 516.0
39 TraesCS1D01G010600 chrUn 90.201 398 31 3 1595 1987 397078686 397078292 2.750000e-141 512.0
40 TraesCS1D01G010600 chr5D 90.201 398 31 3 1595 1987 503226329 503226723 2.750000e-141 512.0


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 TraesCS1D01G010600 chr1D 5453886 5457876 3990 False 7371.000000 7371 100.000000 1 3991 1 chr1D.!!$F1 3990
1 TraesCS1D01G010600 chr7A 692308077 692311355 3278 True 1667.500000 3068 85.606000 180 3578 2 chr7A.!!$R1 3398
2 TraesCS1D01G010600 chr1B 17830293 17833454 3161 True 874.750000 2386 88.425250 13 3155 4 chr1B.!!$R1 3142
3 TraesCS1D01G010600 chr1B 8193219 8195653 2434 False 806.000000 1504 85.408333 1455 3991 3 chr1B.!!$F5 2536
4 TraesCS1D01G010600 chr1B 639480339 639483499 3160 False 690.800000 1441 87.341400 286 3566 5 chr1B.!!$F6 3280
5 TraesCS1D01G010600 chr1B 8182759 8185597 2838 False 434.571429 850 87.521857 8 3418 7 chr1B.!!$F4 3410
6 TraesCS1D01G010600 chr1A 6632695 6634475 1780 True 1954.000000 1954 86.807000 1460 3222 1 chr1A.!!$R1 1762
7 TraesCS1D01G010600 chr1A 6735259 6735788 529 True 824.000000 824 94.610000 3455 3991 1 chr1A.!!$R2 536
8 TraesCS1D01G010600 chr1A 6760529 6764082 3553 True 819.000000 1808 90.412200 9 3460 5 chr1A.!!$R4 3451
9 TraesCS1D01G010600 chr1A 6718450 6721098 2648 True 501.500000 1050 89.273000 1460 3991 4 chr1A.!!$R3 2531

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
564 718 0.314935 AACAATGGAAAGCACGGCAG 59.685 50.000 0.00 0.00 0.00 4.85 F
1002 1254 1.269936 GGGTCCGGTTCGTATACCATG 60.270 57.143 0.00 0.00 38.12 3.66 F
2425 2963 0.855598 ATGCAATACCTGAGGGGCAT 59.144 50.000 13.82 13.82 39.10 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 1916 0.391263 GAATTGACCGAGGAGCCGTT 60.391 55.000 0.0 0.0 0.00 4.44 R
2453 2992 0.471617 GGTAGCTGATGCAGACCCAT 59.528 55.000 0.0 0.0 39.87 4.00 R
3544 4439 1.343789 TGTGTAATTGGAACCGACCGA 59.656 47.619 0.0 0.0 0.00 4.69 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
40 41 2.665185 GCGACTGTGGCGTCCTTT 60.665 61.111 0.00 0.00 0.00 3.11
63 64 4.629092 TGAATCTATCTGATGTGCTGCTC 58.371 43.478 0.00 0.00 35.21 4.26
111 145 3.350219 TCCTGCTTAGGGTTTAGCTTG 57.650 47.619 0.00 0.00 38.22 4.01
129 165 2.435693 GCCTACTCGCTGGGTGGAT 61.436 63.158 0.00 0.00 0.00 3.41
130 166 1.113517 GCCTACTCGCTGGGTGGATA 61.114 60.000 0.00 0.00 0.00 2.59
131 167 0.674534 CCTACTCGCTGGGTGGATAC 59.325 60.000 0.00 0.00 0.00 2.24
170 211 4.091509 CGGATCACTTTCGTTCCTAGTTTG 59.908 45.833 0.00 0.00 0.00 2.93
211 332 0.758123 CTTTGCAGCCTTTTTCCCCA 59.242 50.000 0.00 0.00 0.00 4.96
296 424 2.400399 CAGGTTCTTGTGCAAAGCATG 58.600 47.619 0.00 0.00 41.91 4.06
363 495 7.026562 CAGGATATCTCAGCACTATTCTTACG 58.973 42.308 2.05 0.00 0.00 3.18
419 551 2.682856 ACACGCTTGCCCATGTAATTAG 59.317 45.455 0.00 0.00 0.00 1.73
420 552 1.676006 ACGCTTGCCCATGTAATTAGC 59.324 47.619 0.00 0.00 0.00 3.09
421 553 1.949525 CGCTTGCCCATGTAATTAGCT 59.050 47.619 0.00 0.00 0.00 3.32
422 554 3.138304 CGCTTGCCCATGTAATTAGCTA 58.862 45.455 0.00 0.00 0.00 3.32
435 570 8.642885 CATGTAATTAGCTAGCTACTTTCATCG 58.357 37.037 28.53 22.62 31.82 3.84
463 599 1.004277 TGCCTCCGTGCCTTTATTCTT 59.996 47.619 0.00 0.00 0.00 2.52
471 607 4.396166 CCGTGCCTTTATTCTTGATCAGTT 59.604 41.667 0.00 0.00 0.00 3.16
472 608 5.106157 CCGTGCCTTTATTCTTGATCAGTTT 60.106 40.000 0.00 0.00 0.00 2.66
474 610 6.348458 CGTGCCTTTATTCTTGATCAGTTTGA 60.348 38.462 0.00 0.00 0.00 2.69
477 613 8.246180 TGCCTTTATTCTTGATCAGTTTGATTC 58.754 33.333 0.00 0.00 37.20 2.52
564 718 0.314935 AACAATGGAAAGCACGGCAG 59.685 50.000 0.00 0.00 0.00 4.85
615 777 3.864583 CAGGTTTGTTGTGGATGTGTTTG 59.135 43.478 0.00 0.00 0.00 2.93
616 778 3.766591 AGGTTTGTTGTGGATGTGTTTGA 59.233 39.130 0.00 0.00 0.00 2.69
617 779 4.405358 AGGTTTGTTGTGGATGTGTTTGAT 59.595 37.500 0.00 0.00 0.00 2.57
618 780 5.596361 AGGTTTGTTGTGGATGTGTTTGATA 59.404 36.000 0.00 0.00 0.00 2.15
624 786 7.199766 TGTTGTGGATGTGTTTGATAGTTTTC 58.800 34.615 0.00 0.00 0.00 2.29
666 829 7.397892 TTGGTTTGACAGACTCTAGATCTAG 57.602 40.000 21.81 21.81 34.56 2.43
850 1095 9.754382 ATTATGCAAATGTCTTATGTTGGATTC 57.246 29.630 0.00 0.00 34.43 2.52
851 1096 5.639757 TGCAAATGTCTTATGTTGGATTCG 58.360 37.500 0.00 0.00 0.00 3.34
852 1097 5.414144 TGCAAATGTCTTATGTTGGATTCGA 59.586 36.000 0.00 0.00 0.00 3.71
853 1098 6.095300 TGCAAATGTCTTATGTTGGATTCGAT 59.905 34.615 0.00 0.00 0.00 3.59
854 1099 6.634436 GCAAATGTCTTATGTTGGATTCGATC 59.366 38.462 0.00 0.00 0.00 3.69
855 1100 7.679400 GCAAATGTCTTATGTTGGATTCGATCA 60.679 37.037 0.00 0.00 0.00 2.92
856 1101 7.864108 AATGTCTTATGTTGGATTCGATCAA 57.136 32.000 0.00 0.00 0.00 2.57
857 1102 8.455903 AATGTCTTATGTTGGATTCGATCAAT 57.544 30.769 0.00 0.00 0.00 2.57
858 1103 7.864108 TGTCTTATGTTGGATTCGATCAATT 57.136 32.000 0.00 0.00 0.00 2.32
859 1104 7.696755 TGTCTTATGTTGGATTCGATCAATTG 58.303 34.615 0.00 0.00 0.00 2.32
860 1105 7.336679 TGTCTTATGTTGGATTCGATCAATTGT 59.663 33.333 5.13 0.00 0.00 2.71
861 1106 8.184192 GTCTTATGTTGGATTCGATCAATTGTT 58.816 33.333 5.13 0.00 0.00 2.83
862 1107 8.739039 TCTTATGTTGGATTCGATCAATTGTTT 58.261 29.630 5.13 0.00 0.00 2.83
863 1108 8.909708 TTATGTTGGATTCGATCAATTGTTTC 57.090 30.769 5.13 3.45 0.00 2.78
864 1109 6.324561 TGTTGGATTCGATCAATTGTTTCA 57.675 33.333 5.13 0.00 0.00 2.69
865 1110 6.923012 TGTTGGATTCGATCAATTGTTTCAT 58.077 32.000 5.13 0.00 0.00 2.57
866 1111 7.377398 TGTTGGATTCGATCAATTGTTTCATT 58.623 30.769 5.13 0.00 0.00 2.57
867 1112 8.518702 TGTTGGATTCGATCAATTGTTTCATTA 58.481 29.630 5.13 0.00 0.00 1.90
868 1113 9.520204 GTTGGATTCGATCAATTGTTTCATTAT 57.480 29.630 5.13 0.00 0.00 1.28
881 1126 8.907222 ATTGTTTCATTATATGATTTTGGCCC 57.093 30.769 0.00 0.00 39.39 5.80
882 1127 7.673641 TGTTTCATTATATGATTTTGGCCCT 57.326 32.000 0.00 0.00 39.39 5.19
883 1128 7.725251 TGTTTCATTATATGATTTTGGCCCTC 58.275 34.615 0.00 0.00 39.39 4.30
884 1129 7.564660 TGTTTCATTATATGATTTTGGCCCTCT 59.435 33.333 0.00 0.00 39.39 3.69
885 1130 9.077885 GTTTCATTATATGATTTTGGCCCTCTA 57.922 33.333 0.00 0.00 39.39 2.43
886 1131 8.868522 TTCATTATATGATTTTGGCCCTCTAG 57.131 34.615 0.00 0.00 39.39 2.43
887 1132 7.988937 TCATTATATGATTTTGGCCCTCTAGT 58.011 34.615 0.00 0.00 33.59 2.57
888 1133 8.448008 TCATTATATGATTTTGGCCCTCTAGTT 58.552 33.333 0.00 0.00 33.59 2.24
889 1134 9.082313 CATTATATGATTTTGGCCCTCTAGTTT 57.918 33.333 0.00 0.00 0.00 2.66
902 1147 5.868258 GCCCTCTAGTTTGTACAGTTCTTAC 59.132 44.000 0.00 0.00 0.00 2.34
1002 1254 1.269936 GGGTCCGGTTCGTATACCATG 60.270 57.143 0.00 0.00 38.12 3.66
1003 1255 1.410153 GGTCCGGTTCGTATACCATGT 59.590 52.381 0.00 0.00 38.12 3.21
1086 1343 5.760253 TCATTCTTTTAGGCGATCCAAGATC 59.240 40.000 0.00 0.00 33.74 2.75
1113 1370 5.508489 GCAACACCGAGGCTGTAATACTATA 60.508 44.000 0.00 0.00 0.00 1.31
1114 1371 6.688578 CAACACCGAGGCTGTAATACTATAT 58.311 40.000 0.00 0.00 0.00 0.86
1115 1372 7.576287 GCAACACCGAGGCTGTAATACTATATA 60.576 40.741 0.00 0.00 0.00 0.86
1116 1373 8.467598 CAACACCGAGGCTGTAATACTATATAT 58.532 37.037 0.00 0.00 0.00 0.86
1172 1433 8.806429 TGCTTTTGAAGTCATATCCAGAATTA 57.194 30.769 0.00 0.00 0.00 1.40
1210 1474 3.871594 GCCAGTATCTAAAGTTCACGCAT 59.128 43.478 0.00 0.00 0.00 4.73
1211 1475 5.047847 GCCAGTATCTAAAGTTCACGCATA 58.952 41.667 0.00 0.00 0.00 3.14
1213 1477 6.292381 GCCAGTATCTAAAGTTCACGCATAAG 60.292 42.308 0.00 0.00 0.00 1.73
1259 1523 2.047274 ATGTGGGTGACGAAGCGG 60.047 61.111 0.00 0.00 0.00 5.52
1600 1886 6.564499 GCGAAACAAAACAACGATACCTCTAA 60.564 38.462 0.00 0.00 0.00 2.10
1628 1916 4.935205 CCGTACATGAGATTTTCACCTCAA 59.065 41.667 0.00 0.00 42.02 3.02
1665 1953 6.598064 GTCAATTCTTTCGAAGGGATCCTTTA 59.402 38.462 9.45 0.00 44.82 1.85
1666 1954 7.283354 GTCAATTCTTTCGAAGGGATCCTTTAT 59.717 37.037 9.45 0.00 44.82 1.40
1674 1962 6.242396 TCGAAGGGATCCTTTATTTTGTTCA 58.758 36.000 9.45 0.00 44.82 3.18
1693 1981 1.002544 CAAGAGTCTCCGCCCTTCTTT 59.997 52.381 0.00 0.00 0.00 2.52
1734 2023 3.910648 ACTAAGACCAACTAAGTCACGC 58.089 45.455 0.00 0.00 36.68 5.34
1815 2136 5.021033 ACCAAACAAATGCAGATCAAACA 57.979 34.783 0.00 0.00 0.00 2.83
1816 2137 4.810491 ACCAAACAAATGCAGATCAAACAC 59.190 37.500 0.00 0.00 0.00 3.32
1817 2138 4.084952 CCAAACAAATGCAGATCAAACACG 60.085 41.667 0.00 0.00 0.00 4.49
1818 2139 3.988379 ACAAATGCAGATCAAACACGT 57.012 38.095 0.00 0.00 0.00 4.49
1819 2140 3.888934 ACAAATGCAGATCAAACACGTC 58.111 40.909 0.00 0.00 0.00 4.34
1851 2277 9.667989 GTAATAAGAAGAAATCTCTCTCGGTAC 57.332 37.037 0.00 0.00 37.42 3.34
1874 2300 1.228510 CCCCTTGCCCCTCATTCTC 59.771 63.158 0.00 0.00 0.00 2.87
1951 2384 8.401709 GGGCTCTTCTATCTTTGACTTATTTTG 58.598 37.037 0.00 0.00 0.00 2.44
2072 2510 1.546476 CTCCAAGAAGTCAGCCGTACT 59.454 52.381 0.00 0.00 0.00 2.73
2122 2574 6.174760 ACCGAAACATGTATACCTTGCTTAA 58.825 36.000 0.00 0.00 0.00 1.85
2229 2702 7.924358 AAGTACATGTCCATTATACACCCTA 57.076 36.000 0.00 0.00 0.00 3.53
2230 2703 7.924358 AGTACATGTCCATTATACACCCTAA 57.076 36.000 0.00 0.00 0.00 2.69
2239 2712 6.101588 TCCATTATACACCCTAACCCTAAACC 59.898 42.308 0.00 0.00 0.00 3.27
2281 2807 6.460399 CCGGTTTTTCTTTACATGTTCCTGAA 60.460 38.462 2.30 1.49 0.00 3.02
2301 2830 9.449719 TCCTGAAATTATCTACTTTCAAACCTC 57.550 33.333 4.84 0.00 39.97 3.85
2334 2863 3.470567 GTCCGTGCGACAGAAGCG 61.471 66.667 0.00 0.00 41.54 4.68
2413 2951 2.632996 AGTCGGCCTAGCTTATGCAATA 59.367 45.455 0.00 0.00 42.74 1.90
2417 2955 3.077359 GGCCTAGCTTATGCAATACCTG 58.923 50.000 0.00 0.00 42.74 4.00
2420 2958 4.573900 CCTAGCTTATGCAATACCTGAGG 58.426 47.826 0.00 0.00 42.74 3.86
2422 2960 2.107204 AGCTTATGCAATACCTGAGGGG 59.893 50.000 2.38 0.00 42.74 4.79
2423 2961 2.508526 CTTATGCAATACCTGAGGGGC 58.491 52.381 2.38 1.34 39.10 5.80
2424 2962 1.517238 TATGCAATACCTGAGGGGCA 58.483 50.000 2.38 7.66 39.10 5.36
2425 2963 0.855598 ATGCAATACCTGAGGGGCAT 59.144 50.000 13.82 13.82 39.10 4.40
2457 2996 7.660112 TGCTTACATGATTTGCTAATAATGGG 58.340 34.615 18.77 11.21 37.05 4.00
2483 3028 3.707793 CATCAGCTACCGTTCCTTCTAC 58.292 50.000 0.00 0.00 0.00 2.59
2492 3037 5.082251 ACCGTTCCTTCTACATTCTTACC 57.918 43.478 0.00 0.00 0.00 2.85
2897 3461 2.284190 GCTCTAGTTGCATTCCAGGAC 58.716 52.381 0.00 0.00 0.00 3.85
2996 3560 6.977502 GGAGTTCATCCGATGTATAGATGATG 59.022 42.308 8.24 3.97 44.27 3.07
3262 4089 9.944663 CAACTAGTTAACTTTTTCAGTTATGCA 57.055 29.630 14.49 0.00 45.65 3.96
3270 4097 7.935338 ACTTTTTCAGTTATGCAATGAAGTG 57.065 32.000 0.00 0.00 34.64 3.16
3271 4098 6.421801 ACTTTTTCAGTTATGCAATGAAGTGC 59.578 34.615 0.00 0.00 37.48 4.40
3272 4099 4.439305 TTCAGTTATGCAATGAAGTGCC 57.561 40.909 0.00 0.00 44.26 5.01
3273 4100 3.419943 TCAGTTATGCAATGAAGTGCCA 58.580 40.909 0.00 0.00 44.26 4.92
3274 4101 3.825585 TCAGTTATGCAATGAAGTGCCAA 59.174 39.130 0.00 0.00 44.26 4.52
3275 4102 4.463539 TCAGTTATGCAATGAAGTGCCAAT 59.536 37.500 0.00 0.00 44.26 3.16
3276 4103 5.651576 TCAGTTATGCAATGAAGTGCCAATA 59.348 36.000 0.00 0.00 44.26 1.90
3277 4104 5.975344 CAGTTATGCAATGAAGTGCCAATAG 59.025 40.000 0.00 0.00 44.26 1.73
3278 4105 5.887598 AGTTATGCAATGAAGTGCCAATAGA 59.112 36.000 0.00 0.00 44.26 1.98
3279 4106 6.548622 AGTTATGCAATGAAGTGCCAATAGAT 59.451 34.615 0.00 0.00 44.26 1.98
3280 4107 5.864418 ATGCAATGAAGTGCCAATAGATT 57.136 34.783 0.00 0.00 44.26 2.40
3281 4108 5.664294 TGCAATGAAGTGCCAATAGATTT 57.336 34.783 0.00 0.00 44.26 2.17
3282 4109 5.653507 TGCAATGAAGTGCCAATAGATTTC 58.346 37.500 0.00 0.00 44.26 2.17
3283 4110 5.185442 TGCAATGAAGTGCCAATAGATTTCA 59.815 36.000 0.00 0.00 44.26 2.69
3284 4111 6.101332 GCAATGAAGTGCCAATAGATTTCAA 58.899 36.000 0.00 0.00 38.66 2.69
3285 4112 6.591062 GCAATGAAGTGCCAATAGATTTCAAA 59.409 34.615 0.00 0.00 38.66 2.69
3286 4113 7.118101 GCAATGAAGTGCCAATAGATTTCAAAA 59.882 33.333 0.00 0.00 38.66 2.44
3287 4114 8.991026 CAATGAAGTGCCAATAGATTTCAAAAA 58.009 29.630 0.00 0.00 0.00 1.94
3411 4297 3.759581 ACTTCACACCATGAAAGCATCT 58.240 40.909 0.00 0.00 46.80 2.90
3436 4322 2.162208 TCATTTCGATTGAGTTGCTGGC 59.838 45.455 0.00 0.00 0.00 4.85
3534 4429 5.456921 TGAAAGGGAGCTGGAATCTTAAT 57.543 39.130 0.00 0.00 0.00 1.40
3543 4438 7.922811 GGGAGCTGGAATCTTAATTAAAATGTG 59.077 37.037 0.00 0.00 0.00 3.21
3544 4439 8.470002 GGAGCTGGAATCTTAATTAAAATGTGT 58.530 33.333 0.00 0.00 0.00 3.72
3545 4440 9.508567 GAGCTGGAATCTTAATTAAAATGTGTC 57.491 33.333 0.00 0.00 0.00 3.67
3546 4441 8.184192 AGCTGGAATCTTAATTAAAATGTGTCG 58.816 33.333 0.00 0.00 0.00 4.35
3568 4463 3.187842 GGTCGGTTCCAATTACACACTTC 59.812 47.826 0.00 0.00 0.00 3.01
3625 4521 8.736244 CATATATCATGATGCAACAGATTTGGA 58.264 33.333 18.72 0.00 0.00 3.53
3637 4533 3.834813 ACAGATTTGGACTACTCTCTGCA 59.165 43.478 0.00 0.00 34.80 4.41
3715 4611 0.253044 TGTACTGCTTGAGGGATGGC 59.747 55.000 0.00 0.00 0.00 4.40
3729 4627 4.413760 AGGGATGGCTTATTTGGATCATG 58.586 43.478 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.442706 TCAGATAGATTCAAAAGGACGCC 58.557 43.478 0.00 0.00 0.00 5.68
40 41 5.032327 AGCAGCACATCAGATAGATTCAA 57.968 39.130 0.00 0.00 33.72 2.69
63 64 2.722094 TGTAAGCTAAACCCCAGCATG 58.278 47.619 0.00 0.00 41.66 4.06
111 145 1.113517 TATCCACCCAGCGAGTAGGC 61.114 60.000 0.00 0.00 0.00 3.93
129 165 7.175467 AGTGATCCGTTAATCCGTATGTATGTA 59.825 37.037 0.00 0.00 0.00 2.29
130 166 6.015688 AGTGATCCGTTAATCCGTATGTATGT 60.016 38.462 0.00 0.00 0.00 2.29
131 167 6.387465 AGTGATCCGTTAATCCGTATGTATG 58.613 40.000 0.00 0.00 0.00 2.39
132 168 6.585695 AGTGATCCGTTAATCCGTATGTAT 57.414 37.500 0.00 0.00 0.00 2.29
206 327 3.511146 GCAATTCTCAATCAAAGTGGGGA 59.489 43.478 0.00 0.00 0.00 4.81
211 332 3.830755 AGGCTGCAATTCTCAATCAAAGT 59.169 39.130 0.50 0.00 0.00 2.66
296 424 4.506288 ACAAAGTTTTTGCAATCCGTTAGC 59.494 37.500 0.00 0.00 0.00 3.09
419 551 3.736759 GGTAAGCGATGAAAGTAGCTAGC 59.263 47.826 6.62 6.62 39.25 3.42
420 552 5.189659 AGGTAAGCGATGAAAGTAGCTAG 57.810 43.478 0.00 0.00 39.25 3.42
421 553 5.348986 CAAGGTAAGCGATGAAAGTAGCTA 58.651 41.667 0.00 0.00 39.25 3.32
422 554 4.184629 CAAGGTAAGCGATGAAAGTAGCT 58.815 43.478 0.00 0.00 42.35 3.32
435 570 2.399356 GCACGGAGGCAAGGTAAGC 61.399 63.158 0.00 0.00 0.00 3.09
463 599 7.381766 ACAATCGAATGAATCAAACTGATCA 57.618 32.000 7.64 0.00 35.76 2.92
471 607 6.292649 GGCGTGTATACAATCGAATGAATCAA 60.293 38.462 17.29 0.00 0.00 2.57
472 608 5.176774 GGCGTGTATACAATCGAATGAATCA 59.823 40.000 17.29 0.00 0.00 2.57
474 610 4.149922 CGGCGTGTATACAATCGAATGAAT 59.850 41.667 17.29 0.00 0.00 2.57
477 613 2.409752 GCGGCGTGTATACAATCGAATG 60.410 50.000 17.29 0.00 0.00 2.67
564 718 2.959071 GATCGCTGCTGCCGTCTC 60.959 66.667 10.24 0.00 35.36 3.36
636 798 9.965902 ATCTAGAGTCTGTCAAACCAATTAATT 57.034 29.630 1.86 0.00 0.00 1.40
637 799 9.606631 GATCTAGAGTCTGTCAAACCAATTAAT 57.393 33.333 1.86 0.00 0.00 1.40
638 800 8.816894 AGATCTAGAGTCTGTCAAACCAATTAA 58.183 33.333 1.86 0.00 0.00 1.40
639 801 8.367660 AGATCTAGAGTCTGTCAAACCAATTA 57.632 34.615 1.86 0.00 0.00 1.40
640 802 7.251321 AGATCTAGAGTCTGTCAAACCAATT 57.749 36.000 1.86 0.00 0.00 2.32
666 829 0.674895 AGAGTCAAGCACCGCCATTC 60.675 55.000 0.00 0.00 0.00 2.67
855 1100 9.341078 GGGCCAAAATCATATAATGAAACAATT 57.659 29.630 4.39 0.00 43.50 2.32
856 1101 8.716779 AGGGCCAAAATCATATAATGAAACAAT 58.283 29.630 6.18 0.00 43.50 2.71
857 1102 8.088463 AGGGCCAAAATCATATAATGAAACAA 57.912 30.769 6.18 0.00 43.50 2.83
858 1103 7.564660 AGAGGGCCAAAATCATATAATGAAACA 59.435 33.333 6.18 0.00 43.50 2.83
859 1104 7.955918 AGAGGGCCAAAATCATATAATGAAAC 58.044 34.615 6.18 0.00 43.50 2.78
860 1105 9.300681 CTAGAGGGCCAAAATCATATAATGAAA 57.699 33.333 6.18 0.00 43.50 2.69
861 1106 8.448008 ACTAGAGGGCCAAAATCATATAATGAA 58.552 33.333 6.18 0.00 43.50 2.57
862 1107 7.988937 ACTAGAGGGCCAAAATCATATAATGA 58.011 34.615 6.18 0.00 44.55 2.57
863 1108 8.641498 AACTAGAGGGCCAAAATCATATAATG 57.359 34.615 6.18 0.00 0.00 1.90
864 1109 9.082313 CAAACTAGAGGGCCAAAATCATATAAT 57.918 33.333 6.18 0.00 0.00 1.28
865 1110 8.058847 ACAAACTAGAGGGCCAAAATCATATAA 58.941 33.333 6.18 0.00 0.00 0.98
866 1111 7.582719 ACAAACTAGAGGGCCAAAATCATATA 58.417 34.615 6.18 0.00 0.00 0.86
867 1112 6.435164 ACAAACTAGAGGGCCAAAATCATAT 58.565 36.000 6.18 0.00 0.00 1.78
868 1113 5.826643 ACAAACTAGAGGGCCAAAATCATA 58.173 37.500 6.18 0.00 0.00 2.15
869 1114 4.677182 ACAAACTAGAGGGCCAAAATCAT 58.323 39.130 6.18 0.00 0.00 2.45
870 1115 4.112634 ACAAACTAGAGGGCCAAAATCA 57.887 40.909 6.18 0.00 0.00 2.57
871 1116 5.007682 TGTACAAACTAGAGGGCCAAAATC 58.992 41.667 6.18 0.00 0.00 2.17
872 1117 4.993028 TGTACAAACTAGAGGGCCAAAAT 58.007 39.130 6.18 0.00 0.00 1.82
873 1118 4.141344 ACTGTACAAACTAGAGGGCCAAAA 60.141 41.667 6.18 0.00 0.00 2.44
874 1119 3.393278 ACTGTACAAACTAGAGGGCCAAA 59.607 43.478 6.18 0.00 0.00 3.28
875 1120 2.976882 ACTGTACAAACTAGAGGGCCAA 59.023 45.455 6.18 0.00 0.00 4.52
876 1121 2.616524 ACTGTACAAACTAGAGGGCCA 58.383 47.619 6.18 0.00 0.00 5.36
877 1122 3.261137 AGAACTGTACAAACTAGAGGGCC 59.739 47.826 0.00 0.00 0.00 5.80
878 1123 4.538746 AGAACTGTACAAACTAGAGGGC 57.461 45.455 0.00 0.00 0.00 5.19
879 1124 6.210984 AGGTAAGAACTGTACAAACTAGAGGG 59.789 42.308 0.00 0.00 0.00 4.30
880 1125 7.039923 TCAGGTAAGAACTGTACAAACTAGAGG 60.040 40.741 0.00 0.00 37.25 3.69
881 1126 7.883217 TCAGGTAAGAACTGTACAAACTAGAG 58.117 38.462 0.00 0.00 37.25 2.43
882 1127 7.828508 TCAGGTAAGAACTGTACAAACTAGA 57.171 36.000 0.00 0.00 37.25 2.43
885 1130 9.436957 CATATTCAGGTAAGAACTGTACAAACT 57.563 33.333 0.00 0.00 37.25 2.66
886 1131 9.216117 ACATATTCAGGTAAGAACTGTACAAAC 57.784 33.333 0.00 0.00 37.25 2.93
887 1132 9.214957 CACATATTCAGGTAAGAACTGTACAAA 57.785 33.333 0.00 0.00 37.25 2.83
888 1133 8.590204 TCACATATTCAGGTAAGAACTGTACAA 58.410 33.333 0.00 0.00 37.25 2.41
889 1134 8.129496 TCACATATTCAGGTAAGAACTGTACA 57.871 34.615 0.00 0.00 37.25 2.90
987 1239 2.124903 GCTGACATGGTATACGAACCG 58.875 52.381 0.00 0.00 42.91 4.44
1086 1343 3.716006 CAGCCTCGGTGTTGCGTG 61.716 66.667 0.00 0.00 0.00 5.34
1127 1384 4.935885 CAGAATGACCTGCAACTAGAAC 57.064 45.455 0.00 0.00 39.69 3.01
1172 1433 3.247006 CTGGCACGGTGACTAATAAGT 57.753 47.619 16.16 0.00 39.21 2.24
1210 1474 7.447238 CAGAAATCTTCCAACCCTGTAAACTTA 59.553 37.037 0.00 0.00 0.00 2.24
1211 1475 6.265422 CAGAAATCTTCCAACCCTGTAAACTT 59.735 38.462 0.00 0.00 0.00 2.66
1213 1477 5.768164 TCAGAAATCTTCCAACCCTGTAAAC 59.232 40.000 0.00 0.00 0.00 2.01
1259 1523 2.423446 CAGGCATCGGCTAGACCC 59.577 66.667 0.00 0.00 40.87 4.46
1420 1701 7.230849 TCTTAGTAACCTGAAATGGACGTAA 57.769 36.000 0.00 0.00 0.00 3.18
1570 1856 5.607119 ATCGTTGTTTTGTTTCGCTATCT 57.393 34.783 0.00 0.00 0.00 1.98
1600 1886 5.411669 GGTGAAAATCTCATGTACGGTTCTT 59.588 40.000 0.00 0.00 36.14 2.52
1628 1916 0.391263 GAATTGACCGAGGAGCCGTT 60.391 55.000 0.00 0.00 0.00 4.44
1665 1953 2.814336 GGCGGAGACTCTTGAACAAAAT 59.186 45.455 1.74 0.00 0.00 1.82
1666 1954 2.218603 GGCGGAGACTCTTGAACAAAA 58.781 47.619 1.74 0.00 0.00 2.44
1674 1962 1.276705 GAAAGAAGGGCGGAGACTCTT 59.723 52.381 1.74 0.00 32.70 2.85
1693 1981 0.406750 TAGTCTTCGGGGTGGAGTGA 59.593 55.000 0.00 0.00 0.00 3.41
1842 2268 1.139058 CAAGGGGATTGGTACCGAGAG 59.861 57.143 8.13 0.00 35.08 3.20
1851 2277 1.953100 ATGAGGGGCAAGGGGATTGG 61.953 60.000 0.00 0.00 39.47 3.16
1874 2300 6.760298 TCGAAAAGGATCATTCTGATTCTCAG 59.240 38.462 0.00 0.00 41.75 3.35
1989 2422 6.455246 GCGACCTACAAGACAGTAAATTTAGC 60.455 42.308 0.00 0.00 0.00 3.09
2072 2510 3.268334 AGGCACCTACCCATATTTCAACA 59.732 43.478 0.00 0.00 0.00 3.33
2122 2574 6.098838 TGTTTCAGAGTGATATGTAGCTCCAT 59.901 38.462 0.00 0.00 0.00 3.41
2229 2702 1.386066 GGGGGTTAGGGTTTAGGGTT 58.614 55.000 0.00 0.00 0.00 4.11
2230 2703 3.125862 GGGGGTTAGGGTTTAGGGT 57.874 57.895 0.00 0.00 0.00 4.34
2249 2722 2.951457 AAAGAAAAACCGGTGTGTGG 57.049 45.000 8.52 0.00 0.00 4.17
2301 2830 2.293677 ACGGACAGTGCGATCCTAATAG 59.706 50.000 22.51 0.00 34.49 1.73
2305 2834 1.807226 CACGGACAGTGCGATCCTA 59.193 57.895 22.51 0.00 44.72 2.94
2319 2848 3.036084 AACGCTTCTGTCGCACGG 61.036 61.111 0.00 0.00 0.00 4.94
2325 2854 0.818040 ACCCAACCAACGCTTCTGTC 60.818 55.000 0.00 0.00 0.00 3.51
2334 2863 2.510664 TTGGCTGAACCCAACCAAC 58.489 52.632 0.00 0.00 41.98 3.77
2413 2951 2.159101 AACATGCATGCCCCTCAGGT 62.159 55.000 26.53 0.02 38.26 4.00
2417 2955 2.497770 GCAACATGCATGCCCCTC 59.502 61.111 26.53 7.82 44.26 4.30
2450 2989 3.244700 GGTAGCTGATGCAGACCCATTAT 60.245 47.826 0.00 0.00 39.87 1.28
2451 2990 2.104792 GGTAGCTGATGCAGACCCATTA 59.895 50.000 0.00 0.00 39.87 1.90
2452 2991 1.133976 GGTAGCTGATGCAGACCCATT 60.134 52.381 0.00 0.00 39.87 3.16
2453 2992 0.471617 GGTAGCTGATGCAGACCCAT 59.528 55.000 0.00 0.00 39.87 4.00
2457 2996 1.281899 GAACGGTAGCTGATGCAGAC 58.718 55.000 0.00 0.00 42.74 3.51
2483 3028 7.391554 TGAAAATGTCTCTTCAGGGTAAGAATG 59.608 37.037 0.00 0.00 35.14 2.67
2492 3037 7.597743 CCTGAAAATTGAAAATGTCTCTTCAGG 59.402 37.037 11.43 11.43 33.30 3.86
2897 3461 2.027460 GGCAACGCCTTGTGGTTG 59.973 61.111 0.00 0.00 46.69 3.77
2981 3545 6.389906 TGCCAGTAACATCATCTATACATCG 58.610 40.000 0.00 0.00 0.00 3.84
2996 3560 3.526931 TCTACAGCTCATGCCAGTAAC 57.473 47.619 0.00 0.00 40.80 2.50
3246 4073 6.421801 GCACTTCATTGCATAACTGAAAAAGT 59.578 34.615 0.00 0.00 42.49 2.66
3247 4074 6.128742 GGCACTTCATTGCATAACTGAAAAAG 60.129 38.462 0.00 0.00 44.94 2.27
3248 4075 5.695816 GGCACTTCATTGCATAACTGAAAAA 59.304 36.000 0.00 0.00 44.94 1.94
3249 4076 5.221402 TGGCACTTCATTGCATAACTGAAAA 60.221 36.000 0.00 0.00 44.94 2.29
3250 4077 4.280425 TGGCACTTCATTGCATAACTGAAA 59.720 37.500 0.00 0.00 44.94 2.69
3251 4078 3.825585 TGGCACTTCATTGCATAACTGAA 59.174 39.130 0.00 0.00 44.94 3.02
3252 4079 3.419943 TGGCACTTCATTGCATAACTGA 58.580 40.909 0.00 0.00 44.94 3.41
3253 4080 3.853831 TGGCACTTCATTGCATAACTG 57.146 42.857 0.00 0.00 44.94 3.16
3254 4081 5.887598 TCTATTGGCACTTCATTGCATAACT 59.112 36.000 0.00 0.00 44.94 2.24
3255 4082 6.135290 TCTATTGGCACTTCATTGCATAAC 57.865 37.500 0.00 0.00 44.94 1.89
3256 4083 6.964807 ATCTATTGGCACTTCATTGCATAA 57.035 33.333 0.00 0.00 44.94 1.90
3257 4084 6.964807 AATCTATTGGCACTTCATTGCATA 57.035 33.333 0.00 0.00 44.94 3.14
3258 4085 5.864418 AATCTATTGGCACTTCATTGCAT 57.136 34.783 0.00 0.00 44.94 3.96
3259 4086 5.185442 TGAAATCTATTGGCACTTCATTGCA 59.815 36.000 0.00 0.00 44.94 4.08
3260 4087 5.653507 TGAAATCTATTGGCACTTCATTGC 58.346 37.500 0.00 0.00 42.18 3.56
3261 4088 8.537049 TTTTGAAATCTATTGGCACTTCATTG 57.463 30.769 0.00 0.00 0.00 2.82
3411 4297 5.691305 CCAGCAACTCAATCGAAATGAAAAA 59.309 36.000 5.86 0.00 0.00 1.94
3436 4322 3.194329 TCAGTACACTGCAGAATCTCTGG 59.806 47.826 23.35 2.78 44.43 3.86
3534 4429 2.807392 GGAACCGACCGACACATTTTAA 59.193 45.455 0.00 0.00 0.00 1.52
3543 4438 1.728425 GTGTAATTGGAACCGACCGAC 59.272 52.381 0.00 0.00 0.00 4.79
3544 4439 1.343789 TGTGTAATTGGAACCGACCGA 59.656 47.619 0.00 0.00 0.00 4.69
3545 4440 1.461897 GTGTGTAATTGGAACCGACCG 59.538 52.381 0.00 0.00 0.00 4.79
3546 4441 2.774687 AGTGTGTAATTGGAACCGACC 58.225 47.619 0.00 0.00 0.00 4.79
3568 4463 8.726870 TCATTTTACTCCGGTTATCCTAAAAG 57.273 34.615 0.00 0.00 29.54 2.27
3605 4501 4.338012 AGTCCAAATCTGTTGCATCATGA 58.662 39.130 0.00 0.00 0.00 3.07
3609 4505 5.181748 AGAGTAGTCCAAATCTGTTGCATC 58.818 41.667 0.00 0.00 0.00 3.91
3615 4511 3.834813 TGCAGAGAGTAGTCCAAATCTGT 59.165 43.478 13.28 0.00 37.18 3.41
3625 4521 5.124036 AGGAAGATAGTGCAGAGAGTAGT 57.876 43.478 0.00 0.00 0.00 2.73
3637 4533 9.073475 GTATCATCACTTGACTAGGAAGATAGT 57.927 37.037 10.00 0.00 37.11 2.12
3682 4578 5.968387 AGCAGTACACGAACTTAATATGC 57.032 39.130 0.00 0.00 0.00 3.14
3683 4579 7.254117 CCTCAAGCAGTACACGAACTTAATATG 60.254 40.741 0.00 0.00 0.00 1.78
3684 4580 6.757010 CCTCAAGCAGTACACGAACTTAATAT 59.243 38.462 0.00 0.00 0.00 1.28
3685 4581 6.097356 CCTCAAGCAGTACACGAACTTAATA 58.903 40.000 0.00 0.00 0.00 0.98
3715 4611 7.284034 AGGTTACTCTTGCATGATCCAAATAAG 59.716 37.037 2.33 0.00 0.00 1.73
3729 4627 6.035758 CGGATTTACAAGTAGGTTACTCTTGC 59.964 42.308 12.21 0.00 41.22 4.01


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

AutoCloner maintained by Alex Coulton.