Multiple sequence alignment - TraesCS2A01G114900

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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 TraesCS2A01G114900 chr2A 100.000 3441 0 0 1 3441 65651763 65655203 0.000000e+00 6355
1 TraesCS2A01G114900 chr2B 90.175 3430 176 62 81 3440 100324826 100328164 0.000000e+00 4318
2 TraesCS2A01G114900 chr2D 89.123 3420 192 84 87 3440 64156371 64159676 0.000000e+00 4089
3 TraesCS2A01G114900 chr5D 93.421 76 3 2 2081 2155 40183814 40183888 1.010000e-20 111
4 TraesCS2A01G114900 chr5B 93.421 76 3 2 2081 2155 33556623 33556549 1.010000e-20 111
5 TraesCS2A01G114900 chr5A 93.333 75 5 0 2073 2147 28228880 28228954 1.010000e-20 111
6 TraesCS2A01G114900 chr4D 93.056 72 5 0 2076 2147 291587224 291587295 4.700000e-19 106


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 TraesCS2A01G114900 chr2A 65651763 65655203 3440 False 6355 6355 100.000 1 3441 1 chr2A.!!$F1 3440
1 TraesCS2A01G114900 chr2B 100324826 100328164 3338 False 4318 4318 90.175 81 3440 1 chr2B.!!$F1 3359
2 TraesCS2A01G114900 chr2D 64156371 64159676 3305 False 4089 4089 89.123 87 3440 1 chr2D.!!$F1 3353

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
896 953 0.111446 TCCCTCCGTTGCCATTTTCA 59.889 50.0 0.0 0.0 0.0 2.69 F
1261 1331 0.111253 AGGGGTGCAAGAAGAAGGTG 59.889 55.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2062 0.386838 GCTTTGTCTTTGGCTGCTGT 59.613 50.0 0.0 0.0 0.0 4.40 R
3185 3328 0.827507 ATTTGACCACTGCCACCACC 60.828 55.0 0.0 0.0 0.0 4.61 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
30 31 4.700213 TGGTTTAGCCAGTAATCTCAAAGC 59.300 41.667 0.00 0.00 43.61 3.51
31 32 4.944317 GGTTTAGCCAGTAATCTCAAAGCT 59.056 41.667 0.00 0.00 37.17 3.74
32 33 6.113411 GGTTTAGCCAGTAATCTCAAAGCTA 58.887 40.000 0.00 0.00 37.17 3.32
33 34 6.037281 GGTTTAGCCAGTAATCTCAAAGCTAC 59.963 42.308 0.00 0.00 37.17 3.58
34 35 6.546428 TTAGCCAGTAATCTCAAAGCTACT 57.454 37.500 0.00 0.00 31.51 2.57
35 36 5.017294 AGCCAGTAATCTCAAAGCTACTC 57.983 43.478 0.00 0.00 0.00 2.59
36 37 4.714308 AGCCAGTAATCTCAAAGCTACTCT 59.286 41.667 0.00 0.00 0.00 3.24
37 38 5.188751 AGCCAGTAATCTCAAAGCTACTCTT 59.811 40.000 0.00 0.00 36.34 2.85
38 39 5.293079 GCCAGTAATCTCAAAGCTACTCTTG 59.707 44.000 0.00 0.00 34.67 3.02
39 40 5.814705 CCAGTAATCTCAAAGCTACTCTTGG 59.185 44.000 0.00 0.00 34.67 3.61
40 41 6.351371 CCAGTAATCTCAAAGCTACTCTTGGA 60.351 42.308 0.00 0.00 34.67 3.53
41 42 6.533367 CAGTAATCTCAAAGCTACTCTTGGAC 59.467 42.308 0.00 0.00 34.67 4.02
42 43 5.753721 AATCTCAAAGCTACTCTTGGACT 57.246 39.130 0.00 0.00 34.67 3.85
43 44 6.859112 AATCTCAAAGCTACTCTTGGACTA 57.141 37.500 0.00 0.00 34.67 2.59
44 45 5.906113 TCTCAAAGCTACTCTTGGACTAG 57.094 43.478 0.00 0.00 34.67 2.57
45 46 5.326069 TCTCAAAGCTACTCTTGGACTAGT 58.674 41.667 0.00 0.00 34.67 2.57
46 47 6.482524 TCTCAAAGCTACTCTTGGACTAGTA 58.517 40.000 0.00 0.00 34.67 1.82
47 48 6.600032 TCTCAAAGCTACTCTTGGACTAGTAG 59.400 42.308 0.00 5.36 45.26 2.57
48 49 6.482524 TCAAAGCTACTCTTGGACTAGTAGA 58.517 40.000 12.46 0.00 45.29 2.59
49 50 6.374894 TCAAAGCTACTCTTGGACTAGTAGAC 59.625 42.308 12.46 0.00 45.29 2.59
50 51 5.438698 AGCTACTCTTGGACTAGTAGACA 57.561 43.478 12.46 0.00 45.29 3.41
51 52 5.433526 AGCTACTCTTGGACTAGTAGACAG 58.566 45.833 12.46 0.00 45.29 3.51
52 53 4.035909 GCTACTCTTGGACTAGTAGACAGC 59.964 50.000 12.46 1.75 45.29 4.40
53 54 4.310022 ACTCTTGGACTAGTAGACAGCT 57.690 45.455 3.59 0.00 0.00 4.24
54 55 4.013728 ACTCTTGGACTAGTAGACAGCTG 58.986 47.826 13.48 13.48 0.00 4.24
55 56 4.263550 ACTCTTGGACTAGTAGACAGCTGA 60.264 45.833 23.35 0.00 0.00 4.26
56 57 4.861196 TCTTGGACTAGTAGACAGCTGAT 58.139 43.478 23.35 11.17 0.00 2.90
57 58 4.884744 TCTTGGACTAGTAGACAGCTGATC 59.115 45.833 23.35 14.11 0.00 2.92
58 59 4.511786 TGGACTAGTAGACAGCTGATCT 57.488 45.455 23.35 20.32 0.00 2.75
60 61 3.004315 GGACTAGTAGACAGCTGATCTGC 59.996 52.174 23.35 20.69 46.76 4.26
61 62 3.625853 ACTAGTAGACAGCTGATCTGCA 58.374 45.455 23.35 11.80 46.76 4.41
62 63 4.214310 ACTAGTAGACAGCTGATCTGCAT 58.786 43.478 23.35 13.23 46.76 3.96
63 64 3.455990 AGTAGACAGCTGATCTGCATG 57.544 47.619 23.35 19.91 46.76 4.06
64 65 1.865970 GTAGACAGCTGATCTGCATGC 59.134 52.381 23.35 11.82 46.76 4.06
65 66 0.810426 AGACAGCTGATCTGCATGCG 60.810 55.000 23.35 8.20 46.76 4.73
66 67 1.773054 GACAGCTGATCTGCATGCGG 61.773 60.000 23.35 21.02 46.76 5.69
67 68 1.523032 CAGCTGATCTGCATGCGGA 60.523 57.895 30.50 30.50 35.78 5.54
68 69 1.523258 AGCTGATCTGCATGCGGAC 60.523 57.895 30.95 22.85 33.73 4.79
69 70 1.816679 GCTGATCTGCATGCGGACA 60.817 57.895 30.95 25.64 33.73 4.02
70 71 2.012237 CTGATCTGCATGCGGACAC 58.988 57.895 30.95 25.30 33.73 3.67
71 72 0.741927 CTGATCTGCATGCGGACACA 60.742 55.000 30.95 27.95 33.73 3.72
72 73 1.020861 TGATCTGCATGCGGACACAC 61.021 55.000 30.95 20.80 33.73 3.82
73 74 1.709147 GATCTGCATGCGGACACACC 61.709 60.000 30.95 13.82 33.73 4.16
74 75 2.467993 ATCTGCATGCGGACACACCA 62.468 55.000 30.95 7.87 38.90 4.17
75 76 2.203266 TGCATGCGGACACACCAA 60.203 55.556 14.09 0.00 38.90 3.67
76 77 1.794151 CTGCATGCGGACACACCAAA 61.794 55.000 22.55 0.00 38.90 3.28
77 78 1.081242 GCATGCGGACACACCAAAG 60.081 57.895 0.00 0.00 38.90 2.77
78 79 1.795170 GCATGCGGACACACCAAAGT 61.795 55.000 0.00 0.00 38.90 2.66
79 80 0.667993 CATGCGGACACACCAAAGTT 59.332 50.000 0.00 0.00 38.90 2.66
89 90 5.449451 GGACACACCAAAGTTTTACGAACAT 60.449 40.000 0.00 0.00 38.79 2.71
90 91 6.238429 GGACACACCAAAGTTTTACGAACATA 60.238 38.462 0.00 0.00 38.79 2.29
91 92 6.488817 ACACACCAAAGTTTTACGAACATAC 58.511 36.000 0.00 0.00 0.00 2.39
101 102 7.031975 AGTTTTACGAACATACTACCTGTAGC 58.968 38.462 4.25 0.00 36.66 3.58
136 137 4.159120 GCGGATAAGAACAAGAACAAAGC 58.841 43.478 0.00 0.00 0.00 3.51
181 184 1.333524 CGTATCCGCGTAGACGATTGT 60.334 52.381 13.81 0.00 43.02 2.71
195 198 4.155462 AGACGATTGTACAACGAGAGCTAA 59.845 41.667 26.26 0.00 0.00 3.09
202 205 1.751924 ACAACGAGAGCTAAGCCCTAG 59.248 52.381 0.00 0.00 0.00 3.02
272 281 1.550524 CCTCGTCAGATCAGGTTTCCA 59.449 52.381 0.00 0.00 0.00 3.53
290 303 2.875804 AAAAGCCAGCCAGCAAGCC 61.876 57.895 0.00 0.00 34.23 4.35
291 304 3.822636 AAAGCCAGCCAGCAAGCCT 62.823 57.895 0.00 0.00 34.23 4.58
292 305 2.430704 AAAGCCAGCCAGCAAGCCTA 62.431 55.000 0.00 0.00 34.23 3.93
347 363 1.242076 CAGCACTGAAAGGAACCCTG 58.758 55.000 0.00 0.00 39.30 4.45
363 381 2.092914 ACCCTGGTTATTACTCAGCTGC 60.093 50.000 9.47 0.00 0.00 5.25
407 425 1.371337 TTGAATGCTGCCGCTGCTAG 61.371 55.000 21.13 0.00 38.71 3.42
439 457 2.159198 GCTAATCTAACGACCCGTCCAA 60.159 50.000 0.00 0.00 39.99 3.53
488 531 0.248907 TAGTTATGAGCGGCGTCTGC 60.249 55.000 9.37 2.87 41.71 4.26
498 541 1.699656 CGGCGTCTGCATTCTTCTGG 61.700 60.000 0.00 0.00 45.35 3.86
499 542 0.391661 GGCGTCTGCATTCTTCTGGA 60.392 55.000 0.00 0.00 45.35 3.86
500 543 1.661341 GCGTCTGCATTCTTCTGGAT 58.339 50.000 0.00 0.00 42.15 3.41
501 544 1.596727 GCGTCTGCATTCTTCTGGATC 59.403 52.381 0.00 0.00 42.15 3.36
502 545 2.741228 GCGTCTGCATTCTTCTGGATCT 60.741 50.000 0.00 0.00 42.15 2.75
503 546 2.864946 CGTCTGCATTCTTCTGGATCTG 59.135 50.000 0.00 0.00 0.00 2.90
504 547 3.204526 GTCTGCATTCTTCTGGATCTGG 58.795 50.000 0.00 0.00 0.00 3.86
530 573 2.860051 CGAGATCACATCACGTCGG 58.140 57.895 0.00 0.00 38.33 4.79
604 648 4.521146 CTCACAAGATATTTGGAGGCAGT 58.479 43.478 0.00 0.00 0.00 4.40
605 649 4.264253 TCACAAGATATTTGGAGGCAGTG 58.736 43.478 0.00 0.00 0.00 3.66
617 661 1.129437 GAGGCAGTGCGAGTGAAAATC 59.871 52.381 9.45 0.00 0.00 2.17
669 713 0.532115 GGGTTGTCCAATGATGTGGC 59.468 55.000 0.00 0.00 38.68 5.01
684 728 3.723348 GGCGGCGTTGTGGTTCTC 61.723 66.667 9.37 0.00 0.00 2.87
750 799 4.629523 TGGTGGTTCGGTTCGGCC 62.630 66.667 0.00 0.00 0.00 6.13
751 800 4.324991 GGTGGTTCGGTTCGGCCT 62.325 66.667 0.00 0.00 34.25 5.19
752 801 2.741211 GTGGTTCGGTTCGGCCTC 60.741 66.667 0.00 0.00 34.25 4.70
753 802 4.367023 TGGTTCGGTTCGGCCTCG 62.367 66.667 0.00 0.00 34.25 4.63
883 940 1.510431 AAGGCCCCTTCTTTCCCTCC 61.510 60.000 0.00 0.00 0.00 4.30
891 948 0.404040 TTCTTTCCCTCCGTTGCCAT 59.596 50.000 0.00 0.00 0.00 4.40
893 950 1.203001 TCTTTCCCTCCGTTGCCATTT 60.203 47.619 0.00 0.00 0.00 2.32
894 951 1.618343 CTTTCCCTCCGTTGCCATTTT 59.382 47.619 0.00 0.00 0.00 1.82
895 952 1.253100 TTCCCTCCGTTGCCATTTTC 58.747 50.000 0.00 0.00 0.00 2.29
896 953 0.111446 TCCCTCCGTTGCCATTTTCA 59.889 50.000 0.00 0.00 0.00 2.69
1011 1071 4.456535 CCTCAGTCTCTGTAGCTTAGCTA 58.543 47.826 10.21 10.21 40.44 3.32
1023 1083 3.989056 AGCTTAGCTACCTTTCTCCTCT 58.011 45.455 4.30 0.00 36.99 3.69
1043 1103 2.196997 TTTCCATGGCGTCAGGGGAG 62.197 60.000 22.09 0.00 44.37 4.30
1081 1141 0.958822 ACGGTGAGCCATTCCAAAAC 59.041 50.000 0.00 0.00 34.09 2.43
1100 1160 1.270358 ACAGCTTCACCGTCTTCTTCC 60.270 52.381 0.00 0.00 0.00 3.46
1101 1161 1.001406 CAGCTTCACCGTCTTCTTCCT 59.999 52.381 0.00 0.00 0.00 3.36
1102 1162 1.273886 AGCTTCACCGTCTTCTTCCTC 59.726 52.381 0.00 0.00 0.00 3.71
1103 1163 1.273886 GCTTCACCGTCTTCTTCCTCT 59.726 52.381 0.00 0.00 0.00 3.69
1104 1164 2.289133 GCTTCACCGTCTTCTTCCTCTT 60.289 50.000 0.00 0.00 0.00 2.85
1105 1165 3.580731 CTTCACCGTCTTCTTCCTCTTC 58.419 50.000 0.00 0.00 0.00 2.87
1106 1166 1.893801 TCACCGTCTTCTTCCTCTTCC 59.106 52.381 0.00 0.00 0.00 3.46
1107 1167 1.896465 CACCGTCTTCTTCCTCTTCCT 59.104 52.381 0.00 0.00 0.00 3.36
1108 1168 2.094442 CACCGTCTTCTTCCTCTTCCTC 60.094 54.545 0.00 0.00 0.00 3.71
1109 1169 1.478916 CCGTCTTCTTCCTCTTCCTCC 59.521 57.143 0.00 0.00 0.00 4.30
1110 1170 2.452505 CGTCTTCTTCCTCTTCCTCCT 58.547 52.381 0.00 0.00 0.00 3.69
1111 1171 2.425668 CGTCTTCTTCCTCTTCCTCCTC 59.574 54.545 0.00 0.00 0.00 3.71
1112 1172 2.764010 GTCTTCTTCCTCTTCCTCCTCC 59.236 54.545 0.00 0.00 0.00 4.30
1113 1173 2.657459 TCTTCTTCCTCTTCCTCCTCCT 59.343 50.000 0.00 0.00 0.00 3.69
1114 1174 2.838637 TCTTCCTCTTCCTCCTCCTC 57.161 55.000 0.00 0.00 0.00 3.71
1115 1175 1.289530 TCTTCCTCTTCCTCCTCCTCC 59.710 57.143 0.00 0.00 0.00 4.30
1116 1176 1.290732 CTTCCTCTTCCTCCTCCTCCT 59.709 57.143 0.00 0.00 0.00 3.69
1117 1177 0.930726 TCCTCTTCCTCCTCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
1158 1221 2.158957 TCTTCTTCTTGTTGTGGCGAGT 60.159 45.455 0.00 0.00 0.00 4.18
1187 1256 2.483538 GCTGACATTGTGTTTGGGCTTT 60.484 45.455 0.00 0.00 0.00 3.51
1188 1257 3.125316 CTGACATTGTGTTTGGGCTTTG 58.875 45.455 0.00 0.00 0.00 2.77
1189 1258 1.866601 GACATTGTGTTTGGGCTTTGC 59.133 47.619 0.00 0.00 0.00 3.68
1261 1331 0.111253 AGGGGTGCAAGAAGAAGGTG 59.889 55.000 0.00 0.00 0.00 4.00
1301 1371 3.868757 TCGAAGGTACCAACTCATGAG 57.131 47.619 21.37 21.37 0.00 2.90
1336 1406 9.065871 GGTTAATTGATTGAACTTTCATTCTCG 57.934 33.333 12.66 0.00 38.03 4.04
1363 1433 3.059597 AGTTCATTCTTCTTGCAACGACG 60.060 43.478 0.00 0.00 0.00 5.12
1369 1439 5.856126 TTCTTCTTGCAACGACGATTAAT 57.144 34.783 0.00 0.00 0.00 1.40
1377 1447 3.742786 CAACGACGATTAATTGGTGTGG 58.257 45.455 0.00 0.00 0.00 4.17
1379 1449 3.666274 ACGACGATTAATTGGTGTGGAA 58.334 40.909 0.00 0.00 0.00 3.53
1380 1450 4.258543 ACGACGATTAATTGGTGTGGAAT 58.741 39.130 0.00 0.00 0.00 3.01
1427 1501 8.951243 TGGTTTTGATTAATCGAATGTGTATCA 58.049 29.630 17.11 7.28 30.68 2.15
1429 1503 9.438291 GTTTTGATTAATCGAATGTGTATCAGG 57.562 33.333 17.11 0.00 30.68 3.86
1430 1504 6.785488 TGATTAATCGAATGTGTATCAGGC 57.215 37.500 10.80 0.00 0.00 4.85
1777 1863 1.706575 CCAAGGAGGAGGGAGAGGA 59.293 63.158 0.00 0.00 41.22 3.71
1915 2001 0.475906 AACAAGCAGCAGAAGGAGGT 59.524 50.000 0.00 0.00 0.00 3.85
1985 2077 0.752743 AGCAACAGCAGCCAAAGACA 60.753 50.000 0.00 0.00 0.00 3.41
2302 2403 1.666553 CGCAGGAGCCGTACAACAA 60.667 57.895 0.00 0.00 37.52 2.83
2400 2509 4.237018 AGTCTGTAGTTAAAAGTGGGGGA 58.763 43.478 0.00 0.00 0.00 4.81
2406 2515 1.078159 GTTAAAAGTGGGGGATGGGGT 59.922 52.381 0.00 0.00 0.00 4.95
2407 2516 0.707616 TAAAAGTGGGGGATGGGGTG 59.292 55.000 0.00 0.00 0.00 4.61
2408 2517 2.105640 AAAAGTGGGGGATGGGGTGG 62.106 60.000 0.00 0.00 0.00 4.61
2546 2655 4.363999 ACTTGATTAGCTCGTCATGTAGC 58.636 43.478 14.36 8.72 39.08 3.58
2626 2735 9.951866 AATAATTTCCAATTTGGTACTATCCCT 57.048 29.630 14.98 0.00 39.03 4.20
2635 2744 8.802267 CAATTTGGTACTATCCCTTTTGAGAAA 58.198 33.333 0.00 0.00 0.00 2.52
2653 2762 9.574458 TTTGAGAAAATAGTCTATTCTGTCTCG 57.426 33.333 21.62 0.00 35.45 4.04
2704 2814 8.122952 CGAATCATGTCTACAAAAATAACCTCC 58.877 37.037 0.00 0.00 0.00 4.30
2707 2817 7.162761 TCATGTCTACAAAAATAACCTCCGAA 58.837 34.615 0.00 0.00 0.00 4.30
2768 2891 7.710907 TGAACTCATGCCTACAAGATAACATAC 59.289 37.037 0.00 0.00 0.00 2.39
2769 2892 7.124573 ACTCATGCCTACAAGATAACATACA 57.875 36.000 0.00 0.00 0.00 2.29
2770 2893 7.739825 ACTCATGCCTACAAGATAACATACAT 58.260 34.615 0.00 0.00 0.00 2.29
2771 2894 8.870116 ACTCATGCCTACAAGATAACATACATA 58.130 33.333 0.00 0.00 0.00 2.29
2772 2895 9.881649 CTCATGCCTACAAGATAACATACATAT 57.118 33.333 0.00 0.00 0.00 1.78
2773 2896 9.657419 TCATGCCTACAAGATAACATACATATG 57.343 33.333 0.00 0.00 39.55 1.78
2776 2899 9.657419 TGCCTACAAGATAACATACATATGATG 57.343 33.333 10.38 11.01 37.15 3.07
2795 2924 6.709145 TGATGCACAAAATAGCAACAAATC 57.291 33.333 0.00 0.00 44.88 2.17
2800 2929 5.613142 GCACAAAATAGCAACAAATCTGTGC 60.613 40.000 7.50 7.50 46.94 4.57
2801 2930 5.462729 CACAAAATAGCAACAAATCTGTGCA 59.537 36.000 0.00 0.00 35.37 4.57
2802 2931 6.146510 CACAAAATAGCAACAAATCTGTGCAT 59.853 34.615 0.00 0.00 35.37 3.96
2806 2935 7.816945 AATAGCAACAAATCTGTGCATAAAC 57.183 32.000 0.00 0.00 35.37 2.01
2837 2966 3.452990 TCCTGCGGTATCTGAATTTGGTA 59.547 43.478 0.00 0.00 0.00 3.25
2843 2973 4.461198 GGTATCTGAATTTGGTAGGGTGG 58.539 47.826 0.00 0.00 0.00 4.61
2865 2997 4.379918 GGTGCTTACATCTTTTGAGAAGCC 60.380 45.833 0.00 0.00 42.28 4.35
2873 3005 4.008074 TCTTTTGAGAAGCCGATCTTGT 57.992 40.909 0.00 0.00 34.56 3.16
2874 3006 3.748048 TCTTTTGAGAAGCCGATCTTGTG 59.252 43.478 0.00 0.00 34.56 3.33
2875 3007 3.401033 TTTGAGAAGCCGATCTTGTGA 57.599 42.857 0.00 0.00 34.56 3.58
2886 3018 4.740634 GCCGATCTTGTGATGATTCTGGTA 60.741 45.833 0.00 0.00 32.19 3.25
2889 3021 6.238211 CCGATCTTGTGATGATTCTGGTAAAC 60.238 42.308 0.00 0.00 32.19 2.01
2917 3049 6.648310 AGTGATGTCTAGTTCAAATGTGACAG 59.352 38.462 0.00 0.00 37.76 3.51
2939 3071 0.250513 CTAGGTCAGTGAAGTGGGGC 59.749 60.000 0.00 0.00 0.00 5.80
2941 3073 2.829384 GGTCAGTGAAGTGGGGCCA 61.829 63.158 4.39 0.00 0.00 5.36
2950 3082 3.763671 GTGGGGCCACTTCACTTG 58.236 61.111 6.53 0.00 43.12 3.16
3037 3169 5.178067 CAGGCTTTTTGTAATTTTCCTGCTG 59.822 40.000 0.00 0.00 34.26 4.41
3042 3174 7.041848 GCTTTTTGTAATTTTCCTGCTGTGATT 60.042 33.333 0.00 0.00 0.00 2.57
3089 3221 2.865119 TGATGGAGTTGTCACATGCT 57.135 45.000 0.00 0.00 0.00 3.79
3185 3328 0.758734 TCCGTAATGATGGAGCCCTG 59.241 55.000 0.00 0.00 35.69 4.45
3222 3365 0.915364 ATCAGGAGGGACAAAGAGCC 59.085 55.000 0.00 0.00 0.00 4.70
3233 3376 5.949952 AGGGACAAAGAGCCGTTTAAATTAT 59.050 36.000 0.00 0.00 0.00 1.28
3282 3425 4.542525 TCCCAATCCCATTGTTAAGTAGGT 59.457 41.667 0.00 0.00 38.59 3.08
3295 3438 3.868619 AAGTAGGTTAAACCACTGGCA 57.131 42.857 0.00 0.00 41.95 4.92
3399 3542 9.698309 ATAACTACATATCTCTTTTGACATCCG 57.302 33.333 0.00 0.00 0.00 4.18
3423 3572 0.374758 CCAATCCTGCGTGACATTCG 59.625 55.000 0.00 0.00 0.00 3.34
3426 3575 2.244117 ATCCTGCGTGACATTCGGCT 62.244 55.000 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.944317 AGCTTTGAGATTACTGGCTAAACC 59.056 41.667 0.00 0.00 39.84 3.27
9 10 6.819146 AGTAGCTTTGAGATTACTGGCTAAAC 59.181 38.462 0.00 0.00 33.57 2.01
10 11 6.947464 AGTAGCTTTGAGATTACTGGCTAAA 58.053 36.000 0.00 0.00 33.57 1.85
11 12 6.381420 AGAGTAGCTTTGAGATTACTGGCTAA 59.619 38.462 0.00 0.00 33.57 3.09
12 13 5.894393 AGAGTAGCTTTGAGATTACTGGCTA 59.106 40.000 0.00 0.00 0.00 3.93
13 14 4.714308 AGAGTAGCTTTGAGATTACTGGCT 59.286 41.667 0.00 0.00 0.00 4.75
14 15 5.017294 AGAGTAGCTTTGAGATTACTGGC 57.983 43.478 0.00 0.00 0.00 4.85
15 16 5.814705 CCAAGAGTAGCTTTGAGATTACTGG 59.185 44.000 0.00 0.00 33.60 4.00
16 17 6.533367 GTCCAAGAGTAGCTTTGAGATTACTG 59.467 42.308 0.00 0.00 33.60 2.74
17 18 6.439058 AGTCCAAGAGTAGCTTTGAGATTACT 59.561 38.462 0.00 0.00 33.60 2.24
18 19 6.635755 AGTCCAAGAGTAGCTTTGAGATTAC 58.364 40.000 0.00 0.00 33.60 1.89
19 20 6.859112 AGTCCAAGAGTAGCTTTGAGATTA 57.141 37.500 0.00 0.00 33.60 1.75
20 21 5.753721 AGTCCAAGAGTAGCTTTGAGATT 57.246 39.130 0.00 0.00 33.60 2.40
21 22 5.955355 ACTAGTCCAAGAGTAGCTTTGAGAT 59.045 40.000 0.00 0.00 38.68 2.75
22 23 5.326069 ACTAGTCCAAGAGTAGCTTTGAGA 58.674 41.667 0.00 0.00 38.68 3.27
23 24 5.652994 ACTAGTCCAAGAGTAGCTTTGAG 57.347 43.478 0.00 0.00 38.68 3.02
24 25 6.374894 GTCTACTAGTCCAAGAGTAGCTTTGA 59.625 42.308 0.00 0.00 43.24 2.69
25 26 6.151312 TGTCTACTAGTCCAAGAGTAGCTTTG 59.849 42.308 0.00 0.00 43.24 2.77
26 27 6.246919 TGTCTACTAGTCCAAGAGTAGCTTT 58.753 40.000 0.00 0.00 43.24 3.51
27 28 5.817784 TGTCTACTAGTCCAAGAGTAGCTT 58.182 41.667 0.00 0.00 43.24 3.74
28 29 5.433526 CTGTCTACTAGTCCAAGAGTAGCT 58.566 45.833 0.00 0.00 43.24 3.32
29 30 4.035909 GCTGTCTACTAGTCCAAGAGTAGC 59.964 50.000 0.00 6.61 43.24 3.58
30 31 5.295787 CAGCTGTCTACTAGTCCAAGAGTAG 59.704 48.000 5.25 5.16 44.37 2.57
31 32 5.045797 TCAGCTGTCTACTAGTCCAAGAGTA 60.046 44.000 14.67 0.00 0.00 2.59
32 33 4.013728 CAGCTGTCTACTAGTCCAAGAGT 58.986 47.826 5.25 0.00 0.00 3.24
33 34 4.265893 TCAGCTGTCTACTAGTCCAAGAG 58.734 47.826 14.67 0.00 0.00 2.85
34 35 4.302559 TCAGCTGTCTACTAGTCCAAGA 57.697 45.455 14.67 0.00 0.00 3.02
35 36 4.887071 AGATCAGCTGTCTACTAGTCCAAG 59.113 45.833 14.67 0.00 0.00 3.61
36 37 4.642437 CAGATCAGCTGTCTACTAGTCCAA 59.358 45.833 14.67 0.00 39.85 3.53
37 38 4.203226 CAGATCAGCTGTCTACTAGTCCA 58.797 47.826 14.67 0.00 39.85 4.02
38 39 3.004315 GCAGATCAGCTGTCTACTAGTCC 59.996 52.174 14.67 0.00 46.62 3.85
39 40 3.629855 TGCAGATCAGCTGTCTACTAGTC 59.370 47.826 14.67 1.06 46.62 2.59
40 41 3.625853 TGCAGATCAGCTGTCTACTAGT 58.374 45.455 14.67 0.00 46.62 2.57
41 42 4.548494 CATGCAGATCAGCTGTCTACTAG 58.452 47.826 14.67 5.51 46.62 2.57
42 43 3.243670 GCATGCAGATCAGCTGTCTACTA 60.244 47.826 14.21 6.28 46.62 1.82
43 44 2.483363 GCATGCAGATCAGCTGTCTACT 60.483 50.000 14.21 6.28 46.62 2.57
44 45 1.865970 GCATGCAGATCAGCTGTCTAC 59.134 52.381 14.21 10.94 46.62 2.59
45 46 1.537562 CGCATGCAGATCAGCTGTCTA 60.538 52.381 19.57 2.79 46.62 2.59
46 47 0.810426 CGCATGCAGATCAGCTGTCT 60.810 55.000 19.57 12.81 46.62 3.41
47 48 1.642215 CGCATGCAGATCAGCTGTC 59.358 57.895 19.57 10.66 46.62 3.51
48 49 1.818363 CCGCATGCAGATCAGCTGT 60.818 57.895 19.57 0.42 46.62 4.40
50 51 1.523258 GTCCGCATGCAGATCAGCT 60.523 57.895 19.57 0.00 34.99 4.24
51 52 1.816679 TGTCCGCATGCAGATCAGC 60.817 57.895 19.57 2.62 0.00 4.26
52 53 0.741927 TGTGTCCGCATGCAGATCAG 60.742 55.000 19.57 0.00 0.00 2.90
53 54 1.020861 GTGTGTCCGCATGCAGATCA 61.021 55.000 19.57 12.32 0.00 2.92
54 55 1.709147 GGTGTGTCCGCATGCAGATC 61.709 60.000 19.57 9.91 0.00 2.75
55 56 1.746615 GGTGTGTCCGCATGCAGAT 60.747 57.895 19.57 0.00 0.00 2.90
56 57 2.358615 GGTGTGTCCGCATGCAGA 60.359 61.111 19.57 9.42 0.00 4.26
57 58 1.794151 TTTGGTGTGTCCGCATGCAG 61.794 55.000 19.57 6.53 39.52 4.41
58 59 1.794151 CTTTGGTGTGTCCGCATGCA 61.794 55.000 19.57 0.00 39.52 3.96
59 60 1.081242 CTTTGGTGTGTCCGCATGC 60.081 57.895 7.91 7.91 39.52 4.06
60 61 0.667993 AACTTTGGTGTGTCCGCATG 59.332 50.000 0.00 0.00 39.52 4.06
61 62 1.398692 AAACTTTGGTGTGTCCGCAT 58.601 45.000 0.00 0.00 39.52 4.73
62 63 1.178276 AAAACTTTGGTGTGTCCGCA 58.822 45.000 0.00 0.00 39.52 5.69
63 64 2.723209 GTAAAACTTTGGTGTGTCCGC 58.277 47.619 0.00 0.00 39.52 5.54
64 65 2.608546 TCGTAAAACTTTGGTGTGTCCG 59.391 45.455 0.00 0.00 39.52 4.79
65 66 4.142643 TGTTCGTAAAACTTTGGTGTGTCC 60.143 41.667 0.00 0.00 0.00 4.02
66 67 4.972201 TGTTCGTAAAACTTTGGTGTGTC 58.028 39.130 0.00 0.00 0.00 3.67
67 68 5.570234 ATGTTCGTAAAACTTTGGTGTGT 57.430 34.783 0.00 0.00 0.00 3.72
68 69 6.721321 AGTATGTTCGTAAAACTTTGGTGTG 58.279 36.000 0.00 0.00 0.00 3.82
69 70 6.930667 AGTATGTTCGTAAAACTTTGGTGT 57.069 33.333 0.00 0.00 0.00 4.16
70 71 7.172019 AGGTAGTATGTTCGTAAAACTTTGGTG 59.828 37.037 0.00 0.00 0.00 4.17
71 72 7.172019 CAGGTAGTATGTTCGTAAAACTTTGGT 59.828 37.037 0.00 0.00 0.00 3.67
72 73 7.172019 ACAGGTAGTATGTTCGTAAAACTTTGG 59.828 37.037 0.00 0.00 0.00 3.28
73 74 8.080083 ACAGGTAGTATGTTCGTAAAACTTTG 57.920 34.615 0.00 0.00 0.00 2.77
74 75 9.415544 CTACAGGTAGTATGTTCGTAAAACTTT 57.584 33.333 0.00 0.00 32.02 2.66
75 76 7.543520 GCTACAGGTAGTATGTTCGTAAAACTT 59.456 37.037 8.16 0.00 35.65 2.66
76 77 7.031975 GCTACAGGTAGTATGTTCGTAAAACT 58.968 38.462 8.16 0.00 35.65 2.66
77 78 6.021153 CGCTACAGGTAGTATGTTCGTAAAAC 60.021 42.308 8.16 0.00 35.65 2.43
78 79 6.029607 CGCTACAGGTAGTATGTTCGTAAAA 58.970 40.000 8.16 0.00 35.65 1.52
79 80 5.572211 CGCTACAGGTAGTATGTTCGTAAA 58.428 41.667 8.16 0.00 35.65 2.01
89 90 5.768662 AGATCAAATAGCGCTACAGGTAGTA 59.231 40.000 21.49 0.00 35.65 1.82
90 91 4.585162 AGATCAAATAGCGCTACAGGTAGT 59.415 41.667 21.49 0.00 35.65 2.73
91 92 4.920340 CAGATCAAATAGCGCTACAGGTAG 59.080 45.833 21.49 7.02 36.29 3.18
181 184 1.848652 AGGGCTTAGCTCTCGTTGTA 58.151 50.000 0.00 0.00 31.40 2.41
195 198 1.758906 GCCTTCTCGACCTAGGGCT 60.759 63.158 14.26 0.00 36.96 5.19
202 205 2.221906 TTAGGTGCGCCTTCTCGACC 62.222 60.000 26.67 3.33 44.18 4.79
272 281 2.739132 GCTTGCTGGCTGGCTTTT 59.261 55.556 2.00 0.00 0.00 2.27
290 303 7.327275 GCTTGATTCATGGAGTACGAGTAATAG 59.673 40.741 0.00 0.00 0.00 1.73
291 304 7.145985 GCTTGATTCATGGAGTACGAGTAATA 58.854 38.462 0.00 0.00 0.00 0.98
292 305 5.986135 GCTTGATTCATGGAGTACGAGTAAT 59.014 40.000 0.00 0.00 0.00 1.89
347 363 2.603560 GACGTGCAGCTGAGTAATAACC 59.396 50.000 20.43 0.00 0.00 2.85
363 381 0.736636 AATGCAGCATCATGGACGTG 59.263 50.000 8.77 0.00 0.00 4.49
407 425 2.032680 TAGATTAGCCGGCAACAACC 57.967 50.000 31.54 10.68 0.00 3.77
439 457 0.104409 AGGGTTTGGTGAGGAGGAGT 60.104 55.000 0.00 0.00 0.00 3.85
488 531 2.172082 TGCCTCCAGATCCAGAAGAATG 59.828 50.000 0.00 0.00 0.00 2.67
498 541 2.159043 TGATCTCGTTTGCCTCCAGATC 60.159 50.000 0.00 0.00 39.91 2.75
499 542 1.833630 TGATCTCGTTTGCCTCCAGAT 59.166 47.619 0.00 0.00 0.00 2.90
500 543 1.066858 GTGATCTCGTTTGCCTCCAGA 60.067 52.381 0.00 0.00 0.00 3.86
501 544 1.338105 TGTGATCTCGTTTGCCTCCAG 60.338 52.381 0.00 0.00 0.00 3.86
502 545 0.684535 TGTGATCTCGTTTGCCTCCA 59.315 50.000 0.00 0.00 0.00 3.86
503 546 1.936547 GATGTGATCTCGTTTGCCTCC 59.063 52.381 0.00 0.00 0.00 4.30
504 547 2.349886 GTGATGTGATCTCGTTTGCCTC 59.650 50.000 0.00 0.00 0.00 4.70
530 573 2.023223 CAATTGCGCAAGGCCACAC 61.023 57.895 28.62 0.00 42.61 3.82
604 648 2.684374 CCATGATGGATTTTCACTCGCA 59.316 45.455 5.27 0.00 40.96 5.10
605 649 2.945008 TCCATGATGGATTTTCACTCGC 59.055 45.455 10.75 0.00 42.67 5.03
669 713 1.227999 ACATGAGAACCACAACGCCG 61.228 55.000 0.00 0.00 0.00 6.46
812 867 0.315886 TGAACGAGCAAGCGTAGGAA 59.684 50.000 0.00 0.00 44.86 3.36
883 940 1.879380 TCTGGAGTGAAAATGGCAACG 59.121 47.619 0.00 0.00 42.51 4.10
891 948 2.645838 AGCAGCTTCTGGAGTGAAAA 57.354 45.000 0.00 0.00 31.21 2.29
893 950 2.028658 CAGTAGCAGCTTCTGGAGTGAA 60.029 50.000 18.95 0.00 31.21 3.18
894 951 1.547820 CAGTAGCAGCTTCTGGAGTGA 59.452 52.381 18.95 0.00 31.21 3.41
895 952 2.006056 GCAGTAGCAGCTTCTGGAGTG 61.006 57.143 25.56 11.06 41.58 3.51
896 953 0.248843 GCAGTAGCAGCTTCTGGAGT 59.751 55.000 25.56 0.00 41.58 3.85
957 1017 3.791586 GAGTGGAGGAGCTGGGGC 61.792 72.222 0.00 0.00 39.06 5.80
1011 1071 3.815757 GCCATGGAAAAGAGGAGAAAGGT 60.816 47.826 18.40 0.00 0.00 3.50
1022 1082 1.315257 CCCCTGACGCCATGGAAAAG 61.315 60.000 18.40 6.56 30.61 2.27
1023 1083 1.304052 CCCCTGACGCCATGGAAAA 60.304 57.895 18.40 0.00 30.61 2.29
1081 1141 1.001406 AGGAAGAAGACGGTGAAGCTG 59.999 52.381 0.00 0.00 0.00 4.24
1100 1160 0.933700 AGGAGGAGGAGGAGGAAGAG 59.066 60.000 0.00 0.00 0.00 2.85
1101 1161 0.930726 GAGGAGGAGGAGGAGGAAGA 59.069 60.000 0.00 0.00 0.00 2.87
1102 1162 0.933700 AGAGGAGGAGGAGGAGGAAG 59.066 60.000 0.00 0.00 0.00 3.46
1103 1163 1.289530 GAAGAGGAGGAGGAGGAGGAA 59.710 57.143 0.00 0.00 0.00 3.36
1104 1164 0.930726 GAAGAGGAGGAGGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
1105 1165 0.933700 AGAAGAGGAGGAGGAGGAGG 59.066 60.000 0.00 0.00 0.00 4.30
1106 1166 2.244769 AGAAGAAGAGGAGGAGGAGGAG 59.755 54.545 0.00 0.00 0.00 3.69
1107 1167 2.293246 AGAAGAAGAGGAGGAGGAGGA 58.707 52.381 0.00 0.00 0.00 3.71
1108 1168 2.846665 AGAAGAAGAGGAGGAGGAGG 57.153 55.000 0.00 0.00 0.00 4.30
1109 1169 3.981212 AGAAGAAGAAGAGGAGGAGGAG 58.019 50.000 0.00 0.00 0.00 3.69
1110 1170 4.045334 AGAAGAAGAAGAAGAGGAGGAGGA 59.955 45.833 0.00 0.00 0.00 3.71
1111 1171 4.352893 AGAAGAAGAAGAAGAGGAGGAGG 58.647 47.826 0.00 0.00 0.00 4.30
1112 1172 5.716703 AGAAGAAGAAGAAGAAGAGGAGGAG 59.283 44.000 0.00 0.00 0.00 3.69
1113 1173 5.650283 AGAAGAAGAAGAAGAAGAGGAGGA 58.350 41.667 0.00 0.00 0.00 3.71
1114 1174 6.211384 AGAAGAAGAAGAAGAAGAAGAGGAGG 59.789 42.308 0.00 0.00 0.00 4.30
1115 1175 7.232118 AGAAGAAGAAGAAGAAGAAGAGGAG 57.768 40.000 0.00 0.00 0.00 3.69
1116 1176 7.508977 AGAAGAAGAAGAAGAAGAAGAAGAGGA 59.491 37.037 0.00 0.00 0.00 3.71
1117 1177 7.670364 AGAAGAAGAAGAAGAAGAAGAAGAGG 58.330 38.462 0.00 0.00 0.00 3.69
1261 1331 2.549332 GCTGTGGAGCACCTTCTTC 58.451 57.895 0.71 0.00 45.46 2.87
1357 1427 3.666274 TCCACACCAATTAATCGTCGTT 58.334 40.909 0.00 0.00 0.00 3.85
1363 1433 8.739972 ACAGAAAGTATTCCACACCAATTAATC 58.260 33.333 0.00 0.00 36.12 1.75
1369 1439 6.126409 AGAAACAGAAAGTATTCCACACCAA 58.874 36.000 0.00 0.00 36.12 3.67
1377 1447 8.807581 CCACAAACAAAGAAACAGAAAGTATTC 58.192 33.333 0.00 0.00 35.70 1.75
1379 1449 7.836842 ACCACAAACAAAGAAACAGAAAGTAT 58.163 30.769 0.00 0.00 0.00 2.12
1380 1450 7.222000 ACCACAAACAAAGAAACAGAAAGTA 57.778 32.000 0.00 0.00 0.00 2.24
1427 1501 1.006571 CGTCACCTTGTACACGCCT 60.007 57.895 0.00 0.00 0.00 5.52
1429 1503 0.989890 GATCGTCACCTTGTACACGC 59.010 55.000 0.00 0.00 32.21 5.34
1430 1504 1.135888 TCGATCGTCACCTTGTACACG 60.136 52.381 15.94 0.00 0.00 4.49
1636 1722 2.747507 CTTTTTGGGCTTGGCGTCCG 62.748 60.000 0.00 0.00 0.00 4.79
1777 1863 3.383223 CCCTTCTCCTTCTTCTCAGGAT 58.617 50.000 0.00 0.00 39.84 3.24
1970 2062 0.386838 GCTTTGTCTTTGGCTGCTGT 59.613 50.000 0.00 0.00 0.00 4.40
2240 2341 4.724022 CCGTACATGTACTCCGGC 57.276 61.111 28.53 6.64 34.04 6.13
2241 2342 1.066918 GGCCGTACATGTACTCCGG 59.933 63.158 28.53 25.39 41.50 5.14
2242 2343 1.066918 GGGCCGTACATGTACTCCG 59.933 63.158 28.53 18.10 34.04 4.63
2291 2392 3.040099 GTTGAACATGTTGTTGTACGGC 58.960 45.455 17.58 0.00 41.28 5.68
2302 2403 2.550208 GGGTTCTCCTCGTTGAACATGT 60.550 50.000 0.00 0.00 42.91 3.21
2400 2509 4.720443 AAGCCTCCCCCACCCCAT 62.720 66.667 0.00 0.00 0.00 4.00
2406 2515 1.062734 TCTATTACGAAGCCTCCCCCA 60.063 52.381 0.00 0.00 0.00 4.96
2407 2516 1.713297 TCTATTACGAAGCCTCCCCC 58.287 55.000 0.00 0.00 0.00 5.40
2408 2517 3.388345 CTTCTATTACGAAGCCTCCCC 57.612 52.381 0.00 0.00 34.59 4.81
2430 2539 2.300152 CACTCAGCCTAGACAAACCTCA 59.700 50.000 0.00 0.00 0.00 3.86
2431 2540 2.354203 CCACTCAGCCTAGACAAACCTC 60.354 54.545 0.00 0.00 0.00 3.85
2432 2541 1.625818 CCACTCAGCCTAGACAAACCT 59.374 52.381 0.00 0.00 0.00 3.50
2433 2542 1.623811 TCCACTCAGCCTAGACAAACC 59.376 52.381 0.00 0.00 0.00 3.27
2434 2543 2.300437 ACTCCACTCAGCCTAGACAAAC 59.700 50.000 0.00 0.00 0.00 2.93
2511 2620 7.215194 CGAGCTAATCAAGTCGAAAATTTGAAG 59.785 37.037 0.00 3.66 34.80 3.02
2512 2621 7.015289 CGAGCTAATCAAGTCGAAAATTTGAA 58.985 34.615 0.00 0.00 34.80 2.69
2575 2684 9.677567 TTGAAACAAGCTAGTAGCAAAAATAAG 57.322 29.630 23.77 6.74 45.56 1.73
2635 2744 6.641169 TCATGCGAGACAGAATAGACTATT 57.359 37.500 7.46 7.46 0.00 1.73
2644 2753 3.411446 ACCAAATTCATGCGAGACAGAA 58.589 40.909 0.00 0.00 0.00 3.02
2647 2756 3.684305 CAGTACCAAATTCATGCGAGACA 59.316 43.478 0.00 0.00 0.00 3.41
2653 2762 7.043854 CGAATCAATTCAGTACCAAATTCATGC 60.044 37.037 3.81 0.00 36.61 4.06
2704 2814 4.691860 AATTTGTGGATTCTCTGCTTCG 57.308 40.909 0.00 0.00 0.00 3.79
2733 2855 6.855836 TGTAGGCATGAGTTCAAATGAATTC 58.144 36.000 10.66 10.66 40.05 2.17
2768 2891 7.758613 TTGTTGCTATTTTGTGCATCATATG 57.241 32.000 0.00 0.00 38.27 1.78
2769 2892 8.951787 ATTTGTTGCTATTTTGTGCATCATAT 57.048 26.923 0.00 0.00 38.27 1.78
2770 2893 8.252417 AGATTTGTTGCTATTTTGTGCATCATA 58.748 29.630 0.00 0.00 38.27 2.15
2771 2894 7.064134 CAGATTTGTTGCTATTTTGTGCATCAT 59.936 33.333 0.00 0.00 38.27 2.45
2772 2895 6.366604 CAGATTTGTTGCTATTTTGTGCATCA 59.633 34.615 0.00 0.00 39.07 3.07
2773 2896 6.366877 ACAGATTTGTTGCTATTTTGTGCATC 59.633 34.615 0.00 0.00 39.07 3.91
2775 2898 5.462729 CACAGATTTGTTGCTATTTTGTGCA 59.537 36.000 0.00 0.00 34.62 4.57
2776 2899 5.908106 CACAGATTTGTTGCTATTTTGTGC 58.092 37.500 0.00 0.00 34.62 4.57
2784 2913 6.380995 CAGTTTATGCACAGATTTGTTGCTA 58.619 36.000 10.53 1.46 34.62 3.49
2795 2924 1.538047 ACTGCCCAGTTTATGCACAG 58.462 50.000 0.00 0.00 38.83 3.66
2821 2950 4.079958 ACCACCCTACCAAATTCAGATACC 60.080 45.833 0.00 0.00 0.00 2.73
2837 2966 3.157087 CAAAAGATGTAAGCACCACCCT 58.843 45.455 0.00 0.00 0.00 4.34
2843 2973 4.670221 CGGCTTCTCAAAAGATGTAAGCAC 60.670 45.833 15.01 7.78 44.09 4.40
2865 2997 6.313658 TGTTTACCAGAATCATCACAAGATCG 59.686 38.462 0.00 0.00 30.20 3.69
2873 3005 5.863965 TCACTGTGTTTACCAGAATCATCA 58.136 37.500 7.79 0.00 34.04 3.07
2874 3006 6.372659 ACATCACTGTGTTTACCAGAATCATC 59.627 38.462 7.79 0.00 33.22 2.92
2875 3007 6.240894 ACATCACTGTGTTTACCAGAATCAT 58.759 36.000 7.79 0.00 33.22 2.45
2886 3018 7.283127 ACATTTGAACTAGACATCACTGTGTTT 59.717 33.333 7.79 0.00 35.14 2.83
2889 3021 6.424812 TCACATTTGAACTAGACATCACTGTG 59.575 38.462 19.56 19.56 39.00 3.66
2917 3049 1.550976 CCCACTTCACTGACCTAGGAC 59.449 57.143 17.98 10.59 0.00 3.85
2939 3071 3.304928 GCCAAAGTGATCAAGTGAAGTGG 60.305 47.826 0.00 0.00 0.00 4.00
2941 3073 3.554934 TGCCAAAGTGATCAAGTGAAGT 58.445 40.909 0.00 0.00 0.00 3.01
2950 3082 2.232208 CCCCTTCTTTGCCAAAGTGATC 59.768 50.000 16.33 0.00 39.52 2.92
3037 3169 7.593825 ACTTTAGTTTGCAGGACAATAATCAC 58.406 34.615 5.28 0.00 38.31 3.06
3042 3174 6.601613 CCCATACTTTAGTTTGCAGGACAATA 59.398 38.462 5.28 0.00 38.31 1.90
3089 3221 9.836864 AAGAATCATCATTGCATTAGTAGTACA 57.163 29.630 2.52 0.00 0.00 2.90
3182 3325 3.850098 GACCACTGCCACCACCAGG 62.850 68.421 0.00 0.00 42.21 4.45
3185 3328 0.827507 ATTTGACCACTGCCACCACC 60.828 55.000 0.00 0.00 0.00 4.61
3233 3376 2.841266 TGGCAGGCAGTACCACTAATAA 59.159 45.455 0.00 0.00 43.14 1.40
3282 3425 3.957497 ACAAGTTGATGCCAGTGGTTTAA 59.043 39.130 11.74 0.00 0.00 1.52
3343 3486 5.954434 TGTATTCTAACATTTCCGCGTAC 57.046 39.130 4.92 0.00 0.00 3.67
3348 3491 8.310406 TCTGCATATGTATTCTAACATTTCCG 57.690 34.615 4.29 0.00 40.52 4.30
3381 3524 6.183361 TGGGATTCGGATGTCAAAAGAGATAT 60.183 38.462 0.00 0.00 0.00 1.63
3392 3535 2.498167 CAGGATTGGGATTCGGATGTC 58.502 52.381 0.00 0.00 0.00 3.06
3399 3542 1.017387 GTCACGCAGGATTGGGATTC 58.983 55.000 0.00 0.00 40.26 2.52


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

AutoCloner maintained by Alex Coulton.