Multiple sequence alignment - TraesCS2A01G290000

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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 TraesCS2A01G290000 chr2A 100.000 3525 0 0 1 3525 498842901 498839377 0.000000e+00 6510.0
1 TraesCS2A01G290000 chr2A 89.610 231 24 0 1737 1967 188903341 188903111 9.570000e-76 294.0
2 TraesCS2A01G290000 chr2A 84.615 299 33 10 2810 3104 141900642 141900353 5.760000e-73 285.0
3 TraesCS2A01G290000 chr2A 86.885 61 8 0 1160 1220 499578770 499578830 6.310000e-08 69.4
4 TraesCS2A01G290000 chr2B 89.133 2733 175 53 1 2688 437383945 437381290 0.000000e+00 3290.0
5 TraesCS2A01G290000 chr2B 89.655 377 30 6 3149 3524 437381164 437380796 4.120000e-129 472.0
6 TraesCS2A01G290000 chr2B 86.007 293 31 7 2810 3101 120240011 120240294 4.420000e-79 305.0
7 TraesCS2A01G290000 chr2B 89.286 84 5 3 2673 2752 437381273 437381190 6.230000e-18 102.0
8 TraesCS2A01G290000 chr2B 86.885 61 8 0 1160 1220 438458659 438458719 6.310000e-08 69.4
9 TraesCS2A01G290000 chr2D 90.630 2316 139 34 448 2739 368526800 368524539 0.000000e+00 3003.0
10 TraesCS2A01G290000 chr2D 88.443 424 20 11 1 422 368527480 368527084 5.290000e-133 484.0
11 TraesCS2A01G290000 chr2D 86.874 419 20 19 3108 3515 368524514 368524120 1.500000e-118 436.0
12 TraesCS2A01G290000 chr1A 89.610 231 24 0 1737 1967 464086768 464086538 9.570000e-76 294.0
13 TraesCS2A01G290000 chrUn 85.274 292 33 7 2810 3099 127021689 127021972 3.440000e-75 292.0
14 TraesCS2A01G290000 chrUn 84.589 292 35 7 2810 3099 49027487 49027770 7.450000e-72 281.0
15 TraesCS2A01G290000 chr5D 84.589 292 35 7 2810 3099 19111140 19111423 7.450000e-72 281.0
16 TraesCS2A01G290000 chr5D 90.625 96 9 0 2108 2203 28994708 28994803 1.030000e-25 128.0
17 TraesCS2A01G290000 chr4B 84.828 290 33 8 2812 3099 12110071 12109791 7.450000e-72 281.0
18 TraesCS2A01G290000 chr4B 88.745 231 24 1 1737 1967 211498271 211498499 7.450000e-72 281.0
19 TraesCS2A01G290000 chr1D 84.775 289 34 7 2813 3099 416482475 416482195 7.450000e-72 281.0
20 TraesCS2A01G290000 chr6D 84.459 296 33 10 2813 3104 34523945 34523659 2.680000e-71 279.0
21 TraesCS2A01G290000 chr4D 84.589 292 34 8 2810 3099 33237256 33237538 2.680000e-71 279.0
22 TraesCS2A01G290000 chr6A 86.364 220 19 3 1758 1976 602928520 602928311 2.740000e-56 230.0
23 TraesCS2A01G290000 chr6A 93.571 140 9 0 2108 2247 459674899 459675038 3.570000e-50 209.0
24 TraesCS2A01G290000 chr6A 86.232 138 18 1 1737 1874 617204830 617204694 7.880000e-32 148.0
25 TraesCS2A01G290000 chr3B 85.022 227 22 4 1758 1984 749767736 749767950 1.650000e-53 220.0
26 TraesCS2A01G290000 chr3B 90.991 111 7 3 1773 1882 430931844 430931736 2.840000e-31 147.0
27 TraesCS2A01G290000 chr6B 83.636 220 26 2 1760 1979 420841313 420841522 7.720000e-47 198.0
28 TraesCS2A01G290000 chr7A 93.069 101 6 1 1773 1873 13394019 13394118 2.840000e-31 147.0


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 TraesCS2A01G290000 chr2A 498839377 498842901 3524 True 6510.000000 6510 100.000 1 3525 1 chr2A.!!$R3 3524
1 TraesCS2A01G290000 chr2B 437380796 437383945 3149 True 1288.000000 3290 89.358 1 3524 3 chr2B.!!$R1 3523
2 TraesCS2A01G290000 chr2D 368524120 368527480 3360 True 1307.666667 3003 88.649 1 3515 3 chr2D.!!$R1 3514

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
938 1217 0.17691 CACACCCAACCCAACCAAAC 59.823 55.0 0.0 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2892 3268 0.179067 CATGCATTCAATGGCCCACC 60.179 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
57 58 3.421231 CGAGACGAGGCGTGAATAATAAC 59.579 47.826 0.00 0.00 41.37 1.89
91 92 4.107029 TGGCACGCCACTAGTACT 57.893 55.556 6.67 0.00 41.89 2.73
165 166 1.282875 GCCTGTGCCGTTGAAACTC 59.717 57.895 0.00 0.00 0.00 3.01
171 172 1.134694 GCCGTTGAAACTCATCCGC 59.865 57.895 0.00 0.00 0.00 5.54
172 173 1.573829 GCCGTTGAAACTCATCCGCA 61.574 55.000 0.00 0.00 0.00 5.69
173 174 1.086696 CCGTTGAAACTCATCCGCAT 58.913 50.000 0.00 0.00 0.00 4.73
174 175 1.062587 CCGTTGAAACTCATCCGCATC 59.937 52.381 0.00 0.00 0.00 3.91
175 176 1.062587 CGTTGAAACTCATCCGCATCC 59.937 52.381 0.00 0.00 0.00 3.51
176 177 1.401905 GTTGAAACTCATCCGCATCCC 59.598 52.381 0.00 0.00 0.00 3.85
267 268 3.904136 AACATTTCTTTCAGGTGAGCG 57.096 42.857 0.00 0.00 0.00 5.03
340 342 4.077184 CGTCCCCGTGCCTGCTTA 62.077 66.667 0.00 0.00 0.00 3.09
356 358 2.610374 TGCTTAGACGAACCACACAAAC 59.390 45.455 0.00 0.00 0.00 2.93
362 364 1.370587 CGAACCACACAAACCCACGT 61.371 55.000 0.00 0.00 0.00 4.49
371 373 5.411977 CCACACAAACCCACGTTATATTGTA 59.588 40.000 6.31 0.00 0.00 2.41
372 374 6.308675 CACACAAACCCACGTTATATTGTAC 58.691 40.000 6.31 0.00 0.00 2.90
374 376 7.331440 CACACAAACCCACGTTATATTGTACTA 59.669 37.037 6.31 0.00 0.00 1.82
375 377 7.546667 ACACAAACCCACGTTATATTGTACTAG 59.453 37.037 6.31 0.00 0.00 2.57
376 378 7.546667 CACAAACCCACGTTATATTGTACTAGT 59.453 37.037 0.00 0.00 0.00 2.57
377 379 8.748412 ACAAACCCACGTTATATTGTACTAGTA 58.252 33.333 0.00 0.00 0.00 1.82
378 380 9.241317 CAAACCCACGTTATATTGTACTAGTAG 57.759 37.037 1.87 0.00 0.00 2.57
379 381 8.525290 AACCCACGTTATATTGTACTAGTAGT 57.475 34.615 8.14 8.14 0.00 2.73
401 403 3.858247 AGAGTGTAAATTACTGTCGGCC 58.142 45.455 4.67 0.00 0.00 6.13
554 816 2.250646 GGAAAACGAGGGGGAAACG 58.749 57.895 0.00 0.00 0.00 3.60
607 870 4.473444 AGTGGCCCACCTTTATTATCATG 58.527 43.478 11.06 0.00 34.49 3.07
608 871 4.167892 AGTGGCCCACCTTTATTATCATGA 59.832 41.667 11.06 0.00 34.49 3.07
609 872 5.079643 GTGGCCCACCTTTATTATCATGAT 58.920 41.667 13.81 13.81 36.63 2.45
610 873 5.047802 GTGGCCCACCTTTATTATCATGATG 60.048 44.000 18.72 1.95 36.63 3.07
623 886 1.218450 TCATGATGATGCAACCCCCAT 59.782 47.619 0.00 0.00 0.00 4.00
650 913 2.603776 GACCACCACCGTCCTCCT 60.604 66.667 0.00 0.00 0.00 3.69
786 1051 3.319031 AGGCATTATTAAAGGCAGGCT 57.681 42.857 7.78 0.00 44.11 4.58
803 1068 1.070914 GGCTCGGAAAAGATAGGGAGG 59.929 57.143 0.00 0.00 0.00 4.30
804 1069 1.070914 GCTCGGAAAAGATAGGGAGGG 59.929 57.143 0.00 0.00 0.00 4.30
806 1071 2.630580 CTCGGAAAAGATAGGGAGGGAG 59.369 54.545 0.00 0.00 0.00 4.30
807 1072 2.246588 TCGGAAAAGATAGGGAGGGAGA 59.753 50.000 0.00 0.00 0.00 3.71
808 1073 3.116707 TCGGAAAAGATAGGGAGGGAGAT 60.117 47.826 0.00 0.00 0.00 2.75
811 1082 5.105146 CGGAAAAGATAGGGAGGGAGATATG 60.105 48.000 0.00 0.00 0.00 1.78
842 1116 2.753043 CCATCCGCTTTGGCTGCT 60.753 61.111 0.00 0.00 37.80 4.24
843 1117 2.488355 CATCCGCTTTGGCTGCTG 59.512 61.111 0.00 0.00 37.80 4.41
844 1118 3.446570 ATCCGCTTTGGCTGCTGC 61.447 61.111 7.10 7.10 37.80 5.25
881 1155 3.504520 TCCCCGTCAAAATAAACAAGAGC 59.495 43.478 0.00 0.00 0.00 4.09
908 1182 2.146073 CTTTTGTCCCCTTGCAGGCG 62.146 60.000 0.00 0.00 32.73 5.52
909 1183 2.632602 TTTTGTCCCCTTGCAGGCGA 62.633 55.000 0.00 0.00 32.73 5.54
910 1184 3.551496 TTGTCCCCTTGCAGGCGAG 62.551 63.158 1.35 1.35 32.73 5.03
911 1185 4.785453 GTCCCCTTGCAGGCGAGG 62.785 72.222 18.89 18.89 45.17 4.63
934 1213 2.131067 CCACACACCCAACCCAACC 61.131 63.158 0.00 0.00 0.00 3.77
935 1214 1.380515 CACACACCCAACCCAACCA 60.381 57.895 0.00 0.00 0.00 3.67
936 1215 0.972983 CACACACCCAACCCAACCAA 60.973 55.000 0.00 0.00 0.00 3.67
937 1216 0.252284 ACACACCCAACCCAACCAAA 60.252 50.000 0.00 0.00 0.00 3.28
938 1217 0.176910 CACACCCAACCCAACCAAAC 59.823 55.000 0.00 0.00 0.00 2.93
939 1218 0.978667 ACACCCAACCCAACCAAACC 60.979 55.000 0.00 0.00 0.00 3.27
940 1219 1.383386 ACCCAACCCAACCAAACCC 60.383 57.895 0.00 0.00 0.00 4.11
941 1220 1.383248 CCCAACCCAACCAAACCCA 60.383 57.895 0.00 0.00 0.00 4.51
942 1221 0.983378 CCCAACCCAACCAAACCCAA 60.983 55.000 0.00 0.00 0.00 4.12
943 1222 0.179234 CCAACCCAACCAAACCCAAC 59.821 55.000 0.00 0.00 0.00 3.77
1004 1283 3.787001 CTCCACGCCTCTTCCCCC 61.787 72.222 0.00 0.00 0.00 5.40
1019 1298 1.135960 CCCCCTCCATCTCTCTTTCC 58.864 60.000 0.00 0.00 0.00 3.13
1027 1306 3.323115 TCCATCTCTCTTTCCATCCATCG 59.677 47.826 0.00 0.00 0.00 3.84
1035 1314 0.461870 TTCCATCCATCGCAACTCCG 60.462 55.000 0.00 0.00 0.00 4.63
1075 1354 2.456119 CCAACTCCTCACGCATCGC 61.456 63.158 0.00 0.00 0.00 4.58
1133 1430 1.901085 GCCGTCTCCCAGACAAGAT 59.099 57.895 4.60 0.00 45.30 2.40
1134 1431 1.112113 GCCGTCTCCCAGACAAGATA 58.888 55.000 4.60 0.00 45.30 1.98
1135 1432 1.067821 GCCGTCTCCCAGACAAGATAG 59.932 57.143 4.60 0.00 45.30 2.08
1271 1568 3.069980 ATCTCCTGGACGAGCACGC 62.070 63.158 2.62 0.00 43.96 5.34
1272 1569 4.803426 CTCCTGGACGAGCACGCC 62.803 72.222 2.62 6.75 43.96 5.68
1317 1626 2.792500 TGGGAACAACACTGTGCTG 58.208 52.632 7.90 8.78 37.44 4.41
1362 1671 0.179225 CATGCAACGACAACTACGGC 60.179 55.000 0.00 0.00 34.93 5.68
1534 1843 2.439701 CGTCCACTAGCGGGAGGA 60.440 66.667 15.20 2.02 41.64 3.71
1545 1854 2.605299 GGGAGGATGGCCAATGCT 59.395 61.111 10.96 9.41 40.15 3.79
1599 1908 1.106944 TGGAGATGGACGCGCTCATA 61.107 55.000 5.73 0.00 0.00 2.15
1617 1926 4.301027 CGGCTCGAGGTATGCCCC 62.301 72.222 15.58 3.66 43.42 5.80
1638 1947 2.654912 CGCCTCGTTTTCTTCGCGT 61.655 57.895 5.77 0.00 35.15 6.01
1640 1949 0.450645 GCCTCGTTTTCTTCGCGTTC 60.451 55.000 5.77 0.00 0.00 3.95
1641 1950 0.856641 CCTCGTTTTCTTCGCGTTCA 59.143 50.000 5.77 0.00 0.00 3.18
1642 1951 1.459592 CCTCGTTTTCTTCGCGTTCAT 59.540 47.619 5.77 0.00 0.00 2.57
1644 1953 3.122278 CCTCGTTTTCTTCGCGTTCATAA 59.878 43.478 5.77 0.00 0.00 1.90
1655 1964 2.004017 GCGTTCATAATCGGGTTGTCA 58.996 47.619 0.00 0.00 0.00 3.58
1657 1966 3.726782 GCGTTCATAATCGGGTTGTCAAC 60.727 47.826 7.20 7.20 0.00 3.18
1658 1967 3.682858 CGTTCATAATCGGGTTGTCAACT 59.317 43.478 15.17 0.00 0.00 3.16
1659 1968 4.201685 CGTTCATAATCGGGTTGTCAACTC 60.202 45.833 15.17 10.63 0.00 3.01
1684 1993 4.288670 TGATCGAACGGTATCTCACTTC 57.711 45.455 0.00 0.00 0.00 3.01
1693 2002 5.202004 ACGGTATCTCACTTCCTTGTCTAT 58.798 41.667 0.00 0.00 0.00 1.98
1696 2005 6.405953 CGGTATCTCACTTCCTTGTCTATGTT 60.406 42.308 0.00 0.00 0.00 2.71
1700 2009 5.991606 TCTCACTTCCTTGTCTATGTTTGTG 59.008 40.000 0.00 0.00 0.00 3.33
1709 2018 2.157668 GTCTATGTTTGTGGTGCAGACG 59.842 50.000 0.00 0.00 35.21 4.18
1721 2030 0.888619 TGCAGACGGAGAGAATTCGT 59.111 50.000 0.00 0.00 39.99 3.85
2219 2528 2.048127 AAGAACGCCTCGCTCCAC 60.048 61.111 0.00 0.00 0.00 4.02
2255 2564 0.033796 CATCCAACTCCAGGCCATGT 60.034 55.000 5.01 0.00 0.00 3.21
2338 2647 9.209297 GTGTTCTGCAATATTTGTTTTTGTTTC 57.791 29.630 0.00 0.00 0.00 2.78
2392 2701 1.450134 TCACGTGATCAGGCCATGC 60.450 57.895 15.76 0.00 0.00 4.06
2393 2702 2.512286 ACGTGATCAGGCCATGCG 60.512 61.111 15.15 6.70 0.00 4.73
2394 2703 3.945434 CGTGATCAGGCCATGCGC 61.945 66.667 5.01 0.00 0.00 6.09
2428 2737 5.624159 TGGAATTTGCATGTAGATCCTAGG 58.376 41.667 0.82 0.82 0.00 3.02
2477 2792 5.256474 AGCCTGTTAATGTGCTGAACTAAT 58.744 37.500 0.00 0.00 31.70 1.73
2580 2906 0.179158 AAACCGTGTTGTTTCCGTGC 60.179 50.000 0.00 0.00 33.24 5.34
2599 2925 1.638388 CGATTGCTCCATGCGTGTGT 61.638 55.000 4.96 0.00 46.63 3.72
2616 2951 4.348656 GTGTGTAAAGATGCTGCATGATG 58.651 43.478 21.53 0.00 0.00 3.07
2630 2965 6.264970 TGCTGCATGATGGCAATATTTTACTA 59.735 34.615 0.00 0.00 44.40 1.82
2642 2977 7.857885 GGCAATATTTTACTATCACACTTGCTC 59.142 37.037 0.00 0.00 36.44 4.26
2643 2978 7.857885 GCAATATTTTACTATCACACTTGCTCC 59.142 37.037 0.00 0.00 34.12 4.70
2712 3079 6.542735 TCGTAGTAGTTCTACTTGAGCATCAT 59.457 38.462 16.10 0.00 42.78 2.45
2732 3103 5.590145 TCATCATGAATATTTTTGTGCCGG 58.410 37.500 0.00 0.00 0.00 6.13
2752 3128 2.611518 GTCGATCTTGACCAGTCCAAG 58.388 52.381 0.00 0.00 41.63 3.61
2753 3129 1.550524 TCGATCTTGACCAGTCCAAGG 59.449 52.381 0.00 0.00 40.88 3.61
2755 3131 0.329596 ATCTTGACCAGTCCAAGGCC 59.670 55.000 0.00 0.00 40.88 5.19
2756 3132 1.303643 CTTGACCAGTCCAAGGCCC 60.304 63.158 0.00 0.00 37.83 5.80
2758 3134 2.067932 TTGACCAGTCCAAGGCCCTG 62.068 60.000 0.00 0.00 0.00 4.45
2759 3135 2.450502 ACCAGTCCAAGGCCCTGT 60.451 61.111 0.00 0.00 0.00 4.00
2760 3136 1.151899 ACCAGTCCAAGGCCCTGTA 60.152 57.895 0.00 0.00 0.00 2.74
2761 3137 0.550147 ACCAGTCCAAGGCCCTGTAT 60.550 55.000 0.00 0.00 0.00 2.29
2762 3138 0.107017 CCAGTCCAAGGCCCTGTATG 60.107 60.000 0.00 0.00 0.00 2.39
2763 3139 0.107017 CAGTCCAAGGCCCTGTATGG 60.107 60.000 0.00 0.34 0.00 2.74
2764 3140 0.550147 AGTCCAAGGCCCTGTATGGT 60.550 55.000 0.00 0.00 34.50 3.55
2765 3141 0.331616 GTCCAAGGCCCTGTATGGTT 59.668 55.000 0.00 0.00 34.50 3.67
2766 3142 0.623723 TCCAAGGCCCTGTATGGTTC 59.376 55.000 0.00 0.00 34.50 3.62
2767 3143 0.331278 CCAAGGCCCTGTATGGTTCA 59.669 55.000 0.00 0.00 0.00 3.18
2768 3144 1.063717 CCAAGGCCCTGTATGGTTCAT 60.064 52.381 0.00 0.00 0.00 2.57
2769 3145 2.174639 CCAAGGCCCTGTATGGTTCATA 59.825 50.000 0.00 0.00 0.00 2.15
2770 3146 3.480470 CAAGGCCCTGTATGGTTCATAG 58.520 50.000 0.00 0.00 0.00 2.23
2771 3147 2.776665 AGGCCCTGTATGGTTCATAGT 58.223 47.619 0.00 0.00 0.00 2.12
2772 3148 2.706190 AGGCCCTGTATGGTTCATAGTC 59.294 50.000 0.00 0.00 0.00 2.59
2773 3149 2.224548 GGCCCTGTATGGTTCATAGTCC 60.225 54.545 0.00 0.00 0.00 3.85
2774 3150 2.706190 GCCCTGTATGGTTCATAGTCCT 59.294 50.000 0.00 0.00 0.00 3.85
2775 3151 3.244249 GCCCTGTATGGTTCATAGTCCTC 60.244 52.174 0.00 0.00 0.00 3.71
2776 3152 3.005897 CCCTGTATGGTTCATAGTCCTCG 59.994 52.174 0.00 0.00 0.00 4.63
2777 3153 3.005897 CCTGTATGGTTCATAGTCCTCGG 59.994 52.174 0.00 0.00 0.00 4.63
2778 3154 3.889538 CTGTATGGTTCATAGTCCTCGGA 59.110 47.826 0.00 0.00 0.00 4.55
2779 3155 3.635373 TGTATGGTTCATAGTCCTCGGAC 59.365 47.826 8.03 8.03 44.86 4.79
2791 3167 4.787260 GTCCTCGGACTTTTTCTAGACT 57.213 45.455 8.82 0.00 41.57 3.24
2792 3168 5.893897 GTCCTCGGACTTTTTCTAGACTA 57.106 43.478 8.82 0.00 41.57 2.59
2793 3169 6.264841 GTCCTCGGACTTTTTCTAGACTAA 57.735 41.667 8.82 0.00 41.57 2.24
2794 3170 6.685657 GTCCTCGGACTTTTTCTAGACTAAA 58.314 40.000 8.82 0.00 41.57 1.85
2795 3171 7.150640 GTCCTCGGACTTTTTCTAGACTAAAA 58.849 38.462 8.82 0.00 41.57 1.52
2796 3172 7.654923 GTCCTCGGACTTTTTCTAGACTAAAAA 59.345 37.037 8.82 0.00 41.57 1.94
2829 3205 9.707957 AAATGATCTCTAGTTCCTTCTTAGAGA 57.292 33.333 11.54 11.54 44.76 3.10
2851 3227 8.800332 AGAGATTATTAAATGATCATGTTGCCC 58.200 33.333 9.46 0.00 0.00 5.36
2852 3228 8.716674 AGATTATTAAATGATCATGTTGCCCT 57.283 30.769 9.46 0.00 0.00 5.19
2853 3229 9.812347 AGATTATTAAATGATCATGTTGCCCTA 57.188 29.630 9.46 0.00 0.00 3.53
2855 3231 8.995027 TTATTAAATGATCATGTTGCCCTAGT 57.005 30.769 9.46 0.00 0.00 2.57
2894 3270 8.593945 ACAATCAAACAATATTATGAGGTGGT 57.406 30.769 0.00 0.00 0.00 4.16
2895 3271 8.469200 ACAATCAAACAATATTATGAGGTGGTG 58.531 33.333 0.00 0.00 0.00 4.17
2896 3272 7.587037 ATCAAACAATATTATGAGGTGGTGG 57.413 36.000 0.00 0.00 0.00 4.61
2897 3273 5.890985 TCAAACAATATTATGAGGTGGTGGG 59.109 40.000 0.00 0.00 0.00 4.61
2898 3274 3.832527 ACAATATTATGAGGTGGTGGGC 58.167 45.455 0.00 0.00 0.00 5.36
2899 3275 3.157087 CAATATTATGAGGTGGTGGGCC 58.843 50.000 0.00 0.00 0.00 5.80
2900 3276 1.900254 TATTATGAGGTGGTGGGCCA 58.100 50.000 0.00 0.00 43.73 5.36
2908 3284 3.710926 TGGTGGGCCATTGAATGC 58.289 55.556 10.70 0.00 40.46 3.56
2909 3285 1.229114 TGGTGGGCCATTGAATGCA 60.229 52.632 10.70 0.00 40.46 3.96
2910 3286 0.618107 TGGTGGGCCATTGAATGCAT 60.618 50.000 10.70 0.00 40.46 3.96
2911 3287 0.179067 GGTGGGCCATTGAATGCATG 60.179 55.000 10.70 0.00 34.09 4.06
2912 3288 0.179067 GTGGGCCATTGAATGCATGG 60.179 55.000 10.70 0.00 38.45 3.66
2913 3289 0.325390 TGGGCCATTGAATGCATGGA 60.325 50.000 0.00 0.00 37.66 3.41
2914 3290 0.391597 GGGCCATTGAATGCATGGAG 59.608 55.000 4.39 0.00 37.66 3.86
2915 3291 0.391597 GGCCATTGAATGCATGGAGG 59.608 55.000 7.48 3.83 37.66 4.30
2916 3292 1.405872 GCCATTGAATGCATGGAGGA 58.594 50.000 7.48 0.00 37.66 3.71
2917 3293 1.068127 GCCATTGAATGCATGGAGGAC 59.932 52.381 7.48 0.00 37.66 3.85
2918 3294 1.684983 CCATTGAATGCATGGAGGACC 59.315 52.381 0.00 0.00 37.66 4.46
2927 3303 4.248908 TGGAGGACCATTGCTGGA 57.751 55.556 0.00 0.00 46.37 3.86
2928 3304 2.473768 TGGAGGACCATTGCTGGAA 58.526 52.632 0.00 0.00 46.37 3.53
2929 3305 0.776810 TGGAGGACCATTGCTGGAAA 59.223 50.000 0.00 0.00 46.37 3.13
2930 3306 1.146774 TGGAGGACCATTGCTGGAAAA 59.853 47.619 0.00 0.00 46.37 2.29
2931 3307 1.821136 GGAGGACCATTGCTGGAAAAG 59.179 52.381 0.00 0.00 46.37 2.27
2932 3308 2.519013 GAGGACCATTGCTGGAAAAGT 58.481 47.619 0.00 0.00 46.37 2.66
2933 3309 2.489722 GAGGACCATTGCTGGAAAAGTC 59.510 50.000 0.00 6.25 46.37 3.01
2934 3310 2.108952 AGGACCATTGCTGGAAAAGTCT 59.891 45.455 12.16 0.50 46.37 3.24
2935 3311 2.893489 GGACCATTGCTGGAAAAGTCTT 59.107 45.455 12.16 0.00 46.37 3.01
2936 3312 4.079253 GGACCATTGCTGGAAAAGTCTTA 58.921 43.478 12.16 0.00 46.37 2.10
2937 3313 4.522789 GGACCATTGCTGGAAAAGTCTTAA 59.477 41.667 12.16 0.00 46.37 1.85
2938 3314 5.010617 GGACCATTGCTGGAAAAGTCTTAAA 59.989 40.000 12.16 0.00 46.37 1.52
2939 3315 6.462347 GGACCATTGCTGGAAAAGTCTTAAAA 60.462 38.462 12.16 0.00 46.37 1.52
2940 3316 6.883744 ACCATTGCTGGAAAAGTCTTAAAAA 58.116 32.000 0.00 0.00 46.37 1.94
2941 3317 6.986231 ACCATTGCTGGAAAAGTCTTAAAAAG 59.014 34.615 0.00 0.00 46.37 2.27
2942 3318 6.986231 CCATTGCTGGAAAAGTCTTAAAAAGT 59.014 34.615 0.00 0.00 46.37 2.66
2943 3319 7.169813 CCATTGCTGGAAAAGTCTTAAAAAGTC 59.830 37.037 0.00 0.00 46.37 3.01
2944 3320 6.144078 TGCTGGAAAAGTCTTAAAAAGTCC 57.856 37.500 0.00 0.00 0.00 3.85
2945 3321 5.891551 TGCTGGAAAAGTCTTAAAAAGTCCT 59.108 36.000 0.00 0.00 0.00 3.85
2946 3322 7.057894 TGCTGGAAAAGTCTTAAAAAGTCCTA 58.942 34.615 0.00 0.00 0.00 2.94
2947 3323 7.558444 TGCTGGAAAAGTCTTAAAAAGTCCTAA 59.442 33.333 0.00 0.00 0.00 2.69
2948 3324 8.410912 GCTGGAAAAGTCTTAAAAAGTCCTAAA 58.589 33.333 0.00 0.00 0.00 1.85
2975 3351 7.118496 AGACTTTTCTTGAGAGTCTTCTTCA 57.882 36.000 0.00 0.00 45.77 3.02
2976 3352 7.734942 AGACTTTTCTTGAGAGTCTTCTTCAT 58.265 34.615 0.00 0.00 45.77 2.57
2977 3353 8.210265 AGACTTTTCTTGAGAGTCTTCTTCATT 58.790 33.333 0.00 0.00 45.77 2.57
2978 3354 8.744568 ACTTTTCTTGAGAGTCTTCTTCATTT 57.255 30.769 0.00 0.00 32.53 2.32
2979 3355 9.838339 ACTTTTCTTGAGAGTCTTCTTCATTTA 57.162 29.630 0.00 0.00 32.53 1.40
2981 3357 9.838339 TTTTCTTGAGAGTCTTCTTCATTTAGT 57.162 29.630 0.00 0.00 32.53 2.24
2982 3358 9.482627 TTTCTTGAGAGTCTTCTTCATTTAGTC 57.517 33.333 0.00 0.00 32.53 2.59
2983 3359 8.415950 TCTTGAGAGTCTTCTTCATTTAGTCT 57.584 34.615 0.00 0.00 32.53 3.24
2984 3360 8.519526 TCTTGAGAGTCTTCTTCATTTAGTCTC 58.480 37.037 0.00 0.00 37.23 3.36
2985 3361 7.767250 TGAGAGTCTTCTTCATTTAGTCTCA 57.233 36.000 0.00 0.00 41.83 3.27
2986 3362 8.183104 TGAGAGTCTTCTTCATTTAGTCTCAA 57.817 34.615 0.00 0.00 41.38 3.02
2987 3363 8.642432 TGAGAGTCTTCTTCATTTAGTCTCAAA 58.358 33.333 0.00 0.00 41.38 2.69
2988 3364 9.482627 GAGAGTCTTCTTCATTTAGTCTCAAAA 57.517 33.333 0.00 0.00 36.87 2.44
2989 3365 9.838339 AGAGTCTTCTTCATTTAGTCTCAAAAA 57.162 29.630 0.00 0.00 0.00 1.94
2992 3368 9.122613 GTCTTCTTCATTTAGTCTCAAAAATGC 57.877 33.333 3.50 0.00 41.01 3.56
2993 3369 8.299570 TCTTCTTCATTTAGTCTCAAAAATGCC 58.700 33.333 3.50 0.00 41.01 4.40
2994 3370 7.765695 TCTTCATTTAGTCTCAAAAATGCCT 57.234 32.000 3.50 0.00 41.01 4.75
2995 3371 8.862325 TCTTCATTTAGTCTCAAAAATGCCTA 57.138 30.769 3.50 0.00 41.01 3.93
2996 3372 9.295825 TCTTCATTTAGTCTCAAAAATGCCTAA 57.704 29.630 3.50 0.00 41.01 2.69
3004 3380 8.056407 AGTCTCAAAAATGCCTAATTTAGTCC 57.944 34.615 2.88 0.00 37.51 3.85
3005 3381 7.890655 AGTCTCAAAAATGCCTAATTTAGTCCT 59.109 33.333 2.88 0.00 37.51 3.85
3006 3382 8.523658 GTCTCAAAAATGCCTAATTTAGTCCTT 58.476 33.333 2.88 0.00 37.51 3.36
3007 3383 9.747898 TCTCAAAAATGCCTAATTTAGTCCTTA 57.252 29.630 2.88 0.00 37.51 2.69
3015 3391 8.927675 TGCCTAATTTAGTCCTTAAAAAGTCA 57.072 30.769 2.88 0.00 35.03 3.41
3016 3392 9.010029 TGCCTAATTTAGTCCTTAAAAAGTCAG 57.990 33.333 2.88 0.00 35.03 3.51
3017 3393 9.011095 GCCTAATTTAGTCCTTAAAAAGTCAGT 57.989 33.333 2.88 0.00 35.03 3.41
3020 3396 7.997773 ATTTAGTCCTTAAAAAGTCAGTCCC 57.002 36.000 0.00 0.00 35.03 4.46
3021 3397 6.758806 TTAGTCCTTAAAAAGTCAGTCCCT 57.241 37.500 0.00 0.00 0.00 4.20
3022 3398 5.230323 AGTCCTTAAAAAGTCAGTCCCTC 57.770 43.478 0.00 0.00 0.00 4.30
3023 3399 4.041815 AGTCCTTAAAAAGTCAGTCCCTCC 59.958 45.833 0.00 0.00 0.00 4.30
3024 3400 3.977999 TCCTTAAAAAGTCAGTCCCTCCA 59.022 43.478 0.00 0.00 0.00 3.86
3025 3401 4.041691 TCCTTAAAAAGTCAGTCCCTCCAG 59.958 45.833 0.00 0.00 0.00 3.86
3026 3402 4.202472 CCTTAAAAAGTCAGTCCCTCCAGT 60.202 45.833 0.00 0.00 0.00 4.00
3027 3403 3.953542 AAAAAGTCAGTCCCTCCAGTT 57.046 42.857 0.00 0.00 0.00 3.16
3028 3404 3.953542 AAAAGTCAGTCCCTCCAGTTT 57.046 42.857 0.00 0.00 0.00 2.66
3029 3405 2.938956 AAGTCAGTCCCTCCAGTTTG 57.061 50.000 0.00 0.00 0.00 2.93
3030 3406 1.059913 AGTCAGTCCCTCCAGTTTGG 58.940 55.000 0.00 0.00 39.43 3.28
3031 3407 0.765510 GTCAGTCCCTCCAGTTTGGT 59.234 55.000 0.00 0.00 39.03 3.67
3032 3408 0.764890 TCAGTCCCTCCAGTTTGGTG 59.235 55.000 0.00 0.00 39.03 4.17
3033 3409 0.764890 CAGTCCCTCCAGTTTGGTGA 59.235 55.000 0.00 0.00 39.03 4.02
3034 3410 1.142870 CAGTCCCTCCAGTTTGGTGAA 59.857 52.381 0.00 0.00 39.03 3.18
3035 3411 1.850345 AGTCCCTCCAGTTTGGTGAAA 59.150 47.619 0.00 0.00 39.03 2.69
3036 3412 2.243736 AGTCCCTCCAGTTTGGTGAAAA 59.756 45.455 0.00 0.00 39.03 2.29
3037 3413 3.028130 GTCCCTCCAGTTTGGTGAAAAA 58.972 45.455 0.00 0.00 39.03 1.94
3096 3472 4.994907 AAAGTCCCTGTAAACAAACACC 57.005 40.909 0.00 0.00 0.00 4.16
3097 3473 2.940158 AGTCCCTGTAAACAAACACCC 58.060 47.619 0.00 0.00 0.00 4.61
3098 3474 1.958579 GTCCCTGTAAACAAACACCCC 59.041 52.381 0.00 0.00 0.00 4.95
3099 3475 1.854280 TCCCTGTAAACAAACACCCCT 59.146 47.619 0.00 0.00 0.00 4.79
3100 3476 3.054576 TCCCTGTAAACAAACACCCCTA 58.945 45.455 0.00 0.00 0.00 3.53
3101 3477 3.073356 TCCCTGTAAACAAACACCCCTAG 59.927 47.826 0.00 0.00 0.00 3.02
3102 3478 3.181437 CCCTGTAAACAAACACCCCTAGT 60.181 47.826 0.00 0.00 0.00 2.57
3103 3479 4.070009 CCTGTAAACAAACACCCCTAGTC 58.930 47.826 0.00 0.00 0.00 2.59
3104 3480 4.445162 CCTGTAAACAAACACCCCTAGTCA 60.445 45.833 0.00 0.00 0.00 3.41
3105 3481 5.113446 TGTAAACAAACACCCCTAGTCAA 57.887 39.130 0.00 0.00 0.00 3.18
3106 3482 5.697067 TGTAAACAAACACCCCTAGTCAAT 58.303 37.500 0.00 0.00 0.00 2.57
3217 3593 1.823169 GCCAGTCCCACTGTCGGTTA 61.823 60.000 3.07 0.00 44.50 2.85
3376 3752 3.726517 CCCAAGGAACGCACGCAG 61.727 66.667 0.00 0.00 0.00 5.18
3412 3788 2.042831 GCTTGCTCTCAACCGCCAT 61.043 57.895 0.00 0.00 0.00 4.40
3428 3804 1.217882 CCATCCAGCCGTATCGTTTC 58.782 55.000 0.00 0.00 0.00 2.78
3444 3828 2.289444 CGTTTCTACCTGTGGTGATGGT 60.289 50.000 0.00 0.00 36.19 3.55
3450 3834 5.335261 TCTACCTGTGGTGATGGTAAACTA 58.665 41.667 0.00 0.00 36.19 2.24
3451 3835 4.553330 ACCTGTGGTGATGGTAAACTAG 57.447 45.455 0.00 0.00 32.98 2.57
3452 3836 3.908103 ACCTGTGGTGATGGTAAACTAGT 59.092 43.478 0.00 0.00 32.98 2.57
3453 3837 5.088730 ACCTGTGGTGATGGTAAACTAGTA 58.911 41.667 0.00 0.00 32.98 1.82
3454 3838 5.724854 ACCTGTGGTGATGGTAAACTAGTAT 59.275 40.000 0.00 0.00 32.98 2.12
3464 3848 7.985184 TGATGGTAAACTAGTATGCGAAATTCT 59.015 33.333 0.00 0.00 0.00 2.40
3471 3855 6.407202 ACTAGTATGCGAAATTCTCAAGGTT 58.593 36.000 0.00 0.00 0.00 3.50
3486 3872 4.655963 TCAAGGTTGTAGGAGTACGTACT 58.344 43.478 27.71 27.71 37.97 2.73
3524 3910 2.053627 GGTGTACGTACGTTTGGTGAG 58.946 52.381 27.92 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.070446 TCGGTCACAGGTTTGAATACACT 59.930 43.478 0.00 0.00 0.00 3.55
14 15 3.395639 GTCGGTCACAGGTTTGAATACA 58.604 45.455 0.00 0.00 0.00 2.29
91 92 0.680618 CCCACACACAACCTACCGTA 59.319 55.000 0.00 0.00 0.00 4.02
165 166 5.707298 AGTATTTTTAGATGGGATGCGGATG 59.293 40.000 0.00 0.00 0.00 3.51
213 214 4.334481 GCTCTACTACTCAGAAGTGGACTC 59.666 50.000 0.00 0.00 37.43 3.36
340 342 0.253610 TGGGTTTGTGTGGTTCGTCT 59.746 50.000 0.00 0.00 0.00 4.18
356 358 9.494271 TCTACTACTAGTACAATATAACGTGGG 57.506 37.037 0.00 0.00 0.00 4.61
374 376 7.414984 GCCGACAGTAATTTACACTCTACTACT 60.415 40.741 9.15 0.00 0.00 2.57
375 377 6.690528 GCCGACAGTAATTTACACTCTACTAC 59.309 42.308 9.15 0.00 0.00 2.73
376 378 6.183360 GGCCGACAGTAATTTACACTCTACTA 60.183 42.308 9.15 0.00 0.00 1.82
377 379 5.393896 GGCCGACAGTAATTTACACTCTACT 60.394 44.000 9.15 0.00 0.00 2.57
378 380 4.802563 GGCCGACAGTAATTTACACTCTAC 59.197 45.833 9.15 0.00 0.00 2.59
379 381 4.708421 AGGCCGACAGTAATTTACACTCTA 59.292 41.667 9.15 0.00 0.00 2.43
485 746 8.906636 ACGATACGCCTACATGTATTTATTAG 57.093 34.615 5.91 0.00 31.67 1.73
494 755 4.210537 GCAATTTACGATACGCCTACATGT 59.789 41.667 2.69 2.69 0.00 3.21
496 757 4.373527 TGCAATTTACGATACGCCTACAT 58.626 39.130 0.00 0.00 0.00 2.29
541 803 1.123246 TTCCTTCGTTTCCCCCTCGT 61.123 55.000 0.00 0.00 0.00 4.18
542 804 0.035739 TTTCCTTCGTTTCCCCCTCG 59.964 55.000 0.00 0.00 0.00 4.63
543 805 1.884579 GTTTTCCTTCGTTTCCCCCTC 59.115 52.381 0.00 0.00 0.00 4.30
544 806 1.816572 CGTTTTCCTTCGTTTCCCCCT 60.817 52.381 0.00 0.00 0.00 4.79
547 809 1.941975 TGACGTTTTCCTTCGTTTCCC 59.058 47.619 0.00 0.00 40.39 3.97
549 811 3.481028 GCTTTGACGTTTTCCTTCGTTTC 59.519 43.478 0.00 0.00 40.39 2.78
552 814 2.011222 TGCTTTGACGTTTTCCTTCGT 58.989 42.857 0.00 0.00 43.00 3.85
553 815 2.372350 GTGCTTTGACGTTTTCCTTCG 58.628 47.619 0.00 0.00 0.00 3.79
554 816 2.727777 GGTGCTTTGACGTTTTCCTTC 58.272 47.619 0.00 0.00 0.00 3.46
607 870 1.613836 GAGATGGGGGTTGCATCATC 58.386 55.000 0.00 0.00 37.02 2.92
608 871 0.186873 GGAGATGGGGGTTGCATCAT 59.813 55.000 0.00 0.00 0.00 2.45
609 872 1.614711 GGAGATGGGGGTTGCATCA 59.385 57.895 0.00 0.00 0.00 3.07
610 873 1.526917 CGGAGATGGGGGTTGCATC 60.527 63.158 0.00 0.00 0.00 3.91
650 913 1.406898 GAGAGTGATGTGAGATGCGGA 59.593 52.381 0.00 0.00 0.00 5.54
786 1051 2.246588 TCTCCCTCCCTATCTTTTCCGA 59.753 50.000 0.00 0.00 0.00 4.55
803 1068 0.976641 TGGACGGATGCCATATCTCC 59.023 55.000 0.00 0.00 0.00 3.71
804 1069 2.417719 GTTGGACGGATGCCATATCTC 58.582 52.381 0.00 0.00 34.90 2.75
806 1071 1.523758 GGTTGGACGGATGCCATATC 58.476 55.000 0.00 0.00 34.90 1.63
807 1072 0.110486 GGGTTGGACGGATGCCATAT 59.890 55.000 0.00 0.00 34.90 1.78
808 1073 1.275421 TGGGTTGGACGGATGCCATA 61.275 55.000 0.00 0.00 34.90 2.74
811 1082 1.823899 GATGGGTTGGACGGATGCC 60.824 63.158 0.00 0.00 0.00 4.40
842 1116 3.626596 AAGGGAGGGAGGGAGGCA 61.627 66.667 0.00 0.00 0.00 4.75
843 1117 2.770475 GAAGGGAGGGAGGGAGGC 60.770 72.222 0.00 0.00 0.00 4.70
844 1118 2.040359 GGAAGGGAGGGAGGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
845 1119 2.040359 GGGAAGGGAGGGAGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
846 1120 3.707189 GGGGAAGGGAGGGAGGGA 61.707 72.222 0.00 0.00 0.00 4.20
848 1122 4.416601 ACGGGGAAGGGAGGGAGG 62.417 72.222 0.00 0.00 0.00 4.30
849 1123 2.764547 GACGGGGAAGGGAGGGAG 60.765 72.222 0.00 0.00 0.00 4.30
850 1124 2.699607 TTTGACGGGGAAGGGAGGGA 62.700 60.000 0.00 0.00 0.00 4.20
851 1125 1.785353 TTTTGACGGGGAAGGGAGGG 61.785 60.000 0.00 0.00 0.00 4.30
852 1126 0.331616 ATTTTGACGGGGAAGGGAGG 59.668 55.000 0.00 0.00 0.00 4.30
934 1213 0.666374 GGGAAGACACGTTGGGTTTG 59.334 55.000 0.00 0.00 0.00 2.93
935 1214 0.466739 GGGGAAGACACGTTGGGTTT 60.467 55.000 0.00 0.00 0.00 3.27
936 1215 1.149854 GGGGAAGACACGTTGGGTT 59.850 57.895 0.00 0.00 0.00 4.11
937 1216 2.833957 GGGGAAGACACGTTGGGT 59.166 61.111 0.00 0.00 0.00 4.51
938 1217 2.358247 CGGGGAAGACACGTTGGG 60.358 66.667 0.00 0.00 0.00 4.12
939 1218 3.047877 GCGGGGAAGACACGTTGG 61.048 66.667 0.00 0.00 0.00 3.77
940 1219 2.280524 TGCGGGGAAGACACGTTG 60.281 61.111 0.00 0.00 0.00 4.10
941 1220 2.280592 GTGCGGGGAAGACACGTT 60.281 61.111 0.00 0.00 0.00 3.99
942 1221 4.309950 GGTGCGGGGAAGACACGT 62.310 66.667 0.00 0.00 35.11 4.49
985 1264 2.579738 GGGAAGAGGCGTGGAGTC 59.420 66.667 0.00 0.00 0.00 3.36
986 1265 3.003763 GGGGAAGAGGCGTGGAGT 61.004 66.667 0.00 0.00 0.00 3.85
998 1277 2.482494 GAAAGAGAGATGGAGGGGGAA 58.518 52.381 0.00 0.00 0.00 3.97
1004 1283 4.561123 CGATGGATGGAAAGAGAGATGGAG 60.561 50.000 0.00 0.00 0.00 3.86
1019 1298 1.769098 CTGCGGAGTTGCGATGGATG 61.769 60.000 0.00 0.00 37.81 3.51
1027 1306 3.595108 GAAACGGCTGCGGAGTTGC 62.595 63.158 14.45 5.45 0.00 4.17
1075 1354 3.467119 CGACGCAAAGGACGACGG 61.467 66.667 0.00 0.00 43.07 4.79
1118 1415 6.294286 GCTATGTACTATCTTGTCTGGGAGAC 60.294 46.154 0.00 0.00 45.26 3.36
1133 1430 1.407618 CACCAGCACCGCTATGTACTA 59.592 52.381 0.00 0.00 36.40 1.82
1134 1431 0.175760 CACCAGCACCGCTATGTACT 59.824 55.000 0.00 0.00 36.40 2.73
1135 1432 0.108329 ACACCAGCACCGCTATGTAC 60.108 55.000 3.85 0.00 36.40 2.90
1254 1551 3.749064 GCGTGCTCGTCCAGGAGA 61.749 66.667 10.18 0.00 39.49 3.71
1255 1552 4.803426 GGCGTGCTCGTCCAGGAG 62.803 72.222 10.18 0.00 39.49 3.69
1362 1671 3.121030 CGCTTCCTGGGCACGAAG 61.121 66.667 0.00 0.00 38.81 3.79
1425 1734 4.626081 AGAACCAAGCGCTGCCGT 62.626 61.111 12.58 4.25 36.67 5.68
1518 1827 1.742768 CATCCTCCCGCTAGTGGAC 59.257 63.158 24.31 0.00 0.00 4.02
1524 1833 1.770110 ATTGGCCATCCTCCCGCTA 60.770 57.895 6.09 0.00 0.00 4.26
1617 1926 1.130613 CGAAGAAAACGAGGCGCAG 59.869 57.895 10.83 1.82 0.00 5.18
1626 1935 4.019867 CCGATTATGAACGCGAAGAAAAC 58.980 43.478 15.93 0.00 0.00 2.43
1638 1947 3.930229 CGAGTTGACAACCCGATTATGAA 59.070 43.478 16.30 0.00 34.25 2.57
1640 1949 3.517602 TCGAGTTGACAACCCGATTATG 58.482 45.455 19.40 0.28 36.70 1.90
1641 1950 3.880047 TCGAGTTGACAACCCGATTAT 57.120 42.857 19.40 0.00 36.70 1.28
1661 1970 4.920640 AGTGAGATACCGTTCGATCAAT 57.079 40.909 0.00 0.00 0.00 2.57
1665 1974 3.288964 AGGAAGTGAGATACCGTTCGAT 58.711 45.455 0.00 0.00 0.00 3.59
1684 1993 2.884012 TGCACCACAAACATAGACAAGG 59.116 45.455 0.00 0.00 0.00 3.61
1693 2002 0.813610 CTCCGTCTGCACCACAAACA 60.814 55.000 0.00 0.00 0.00 2.83
1696 2005 1.112916 TCTCTCCGTCTGCACCACAA 61.113 55.000 0.00 0.00 0.00 3.33
1700 2009 1.646189 GAATTCTCTCCGTCTGCACC 58.354 55.000 0.00 0.00 0.00 5.01
1709 2018 1.521681 CCCCGCACGAATTCTCTCC 60.522 63.158 3.52 0.00 0.00 3.71
1760 2069 1.901085 CTCCACAGTAGCCAGGACC 59.099 63.158 0.00 0.00 0.00 4.46
1763 2072 2.185350 CGCTCCACAGTAGCCAGG 59.815 66.667 0.00 0.00 36.60 4.45
1764 2073 2.510238 GCGCTCCACAGTAGCCAG 60.510 66.667 0.00 0.00 36.60 4.85
1865 2174 4.227134 CCCTCCGCGGTCATCTGG 62.227 72.222 27.15 17.13 0.00 3.86
1943 2252 4.340246 TGCAGCAGCTGGTCCAGG 62.340 66.667 24.13 5.99 42.74 4.45
2194 2503 4.660938 AGGCGTTCTTGGTGGCCC 62.661 66.667 0.00 0.00 46.75 5.80
2219 2528 0.905357 ATGGTCAGGAAAGGAGGACG 59.095 55.000 0.00 0.00 0.00 4.79
2305 2614 1.803334 TATTGCAGAACACGACACCC 58.197 50.000 0.00 0.00 0.00 4.61
2338 2647 1.934220 CTGAAGCCCACATGCAGCAG 61.934 60.000 0.00 0.00 0.00 4.24
2447 2759 3.775316 AGCACATTAACAGGCTACCTACT 59.225 43.478 0.00 0.00 34.25 2.57
2454 2766 3.146104 AGTTCAGCACATTAACAGGCT 57.854 42.857 0.00 0.00 36.99 4.58
2477 2792 5.968676 ATTTAGCCACCCACATACTAAGA 57.031 39.130 0.00 0.00 0.00 2.10
2556 2881 2.263945 GGAAACAACACGGTTTTGGTG 58.736 47.619 11.33 0.00 40.85 4.17
2580 2906 1.061411 CACACGCATGGAGCAATCG 59.939 57.895 0.00 0.00 46.13 3.34
2599 2925 2.657143 TGCCATCATGCAGCATCTTTA 58.343 42.857 4.38 0.00 36.04 1.85
2616 2951 7.707104 AGCAAGTGTGATAGTAAAATATTGCC 58.293 34.615 0.00 0.00 39.98 4.52
2630 2965 2.936919 TTGACAGGAGCAAGTGTGAT 57.063 45.000 0.00 0.00 0.00 3.06
2712 3079 4.438065 CGACCGGCACAAAAATATTCATGA 60.438 41.667 0.00 0.00 0.00 3.07
2716 3083 3.750639 TCGACCGGCACAAAAATATTC 57.249 42.857 0.00 0.00 0.00 1.75
2732 3103 2.611518 CTTGGACTGGTCAAGATCGAC 58.388 52.381 3.10 0.00 42.94 4.20
2749 3125 2.442236 ATGAACCATACAGGGCCTTG 57.558 50.000 14.35 14.35 43.89 3.61
2752 3128 2.224548 GGACTATGAACCATACAGGGCC 60.225 54.545 0.00 0.00 43.89 5.80
2753 3129 2.706190 AGGACTATGAACCATACAGGGC 59.294 50.000 0.00 0.00 43.89 5.19
2755 3131 3.005897 CCGAGGACTATGAACCATACAGG 59.994 52.174 0.00 0.00 45.67 4.00
2756 3132 3.889538 TCCGAGGACTATGAACCATACAG 59.110 47.826 0.00 0.00 0.00 2.74
2758 3134 4.240175 GTCCGAGGACTATGAACCATAC 57.760 50.000 14.61 0.00 41.57 2.39
2770 3146 4.787260 AGTCTAGAAAAAGTCCGAGGAC 57.213 45.455 14.10 14.10 44.86 3.85
2771 3147 6.906157 TTTAGTCTAGAAAAAGTCCGAGGA 57.094 37.500 0.00 0.00 0.00 3.71
2772 3148 7.958053 TTTTTAGTCTAGAAAAAGTCCGAGG 57.042 36.000 0.00 0.00 32.29 4.63
2803 3179 9.707957 TCTCTAAGAAGGAACTAGAGATCATTT 57.292 33.333 0.00 0.00 38.49 2.32
2804 3180 9.881773 ATCTCTAAGAAGGAACTAGAGATCATT 57.118 33.333 12.82 0.00 45.99 2.57
2825 3201 8.800332 GGGCAACATGATCATTTAATAATCTCT 58.200 33.333 5.16 0.00 39.74 3.10
2826 3202 8.800332 AGGGCAACATGATCATTTAATAATCTC 58.200 33.333 5.16 0.00 39.74 2.75
2827 3203 8.716674 AGGGCAACATGATCATTTAATAATCT 57.283 30.769 5.16 0.00 39.74 2.40
2829 3205 9.592196 ACTAGGGCAACATGATCATTTAATAAT 57.408 29.630 5.16 0.00 39.74 1.28
2830 3206 8.995027 ACTAGGGCAACATGATCATTTAATAA 57.005 30.769 5.16 0.00 39.74 1.40
2868 3244 9.034800 ACCACCTCATAATATTGTTTGATTGTT 57.965 29.630 0.00 0.00 0.00 2.83
2869 3245 8.469200 CACCACCTCATAATATTGTTTGATTGT 58.531 33.333 0.00 0.00 0.00 2.71
2870 3246 7.922278 CCACCACCTCATAATATTGTTTGATTG 59.078 37.037 0.00 0.60 0.00 2.67
2871 3247 7.069826 CCCACCACCTCATAATATTGTTTGATT 59.930 37.037 0.00 0.00 0.00 2.57
2872 3248 6.550854 CCCACCACCTCATAATATTGTTTGAT 59.449 38.462 0.00 0.00 0.00 2.57
2873 3249 5.890985 CCCACCACCTCATAATATTGTTTGA 59.109 40.000 0.00 0.00 0.00 2.69
2874 3250 5.451798 GCCCACCACCTCATAATATTGTTTG 60.452 44.000 0.00 0.00 0.00 2.93
2875 3251 4.649218 GCCCACCACCTCATAATATTGTTT 59.351 41.667 0.00 0.00 0.00 2.83
2876 3252 4.215109 GCCCACCACCTCATAATATTGTT 58.785 43.478 0.00 0.00 0.00 2.83
2877 3253 3.436470 GGCCCACCACCTCATAATATTGT 60.436 47.826 0.00 0.00 35.26 2.71
2878 3254 3.157087 GGCCCACCACCTCATAATATTG 58.843 50.000 0.00 0.00 35.26 1.90
2879 3255 2.788807 TGGCCCACCACCTCATAATATT 59.211 45.455 0.00 0.00 42.67 1.28
2880 3256 2.427872 TGGCCCACCACCTCATAATAT 58.572 47.619 0.00 0.00 42.67 1.28
2881 3257 1.900254 TGGCCCACCACCTCATAATA 58.100 50.000 0.00 0.00 42.67 0.98
2882 3258 2.721966 TGGCCCACCACCTCATAAT 58.278 52.632 0.00 0.00 42.67 1.28
2883 3259 4.259694 TGGCCCACCACCTCATAA 57.740 55.556 0.00 0.00 42.67 1.90
2892 3268 0.179067 CATGCATTCAATGGCCCACC 60.179 55.000 0.00 0.00 0.00 4.61
2893 3269 0.179067 CCATGCATTCAATGGCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
2894 3270 0.325390 TCCATGCATTCAATGGCCCA 60.325 50.000 0.00 0.00 35.51 5.36
2895 3271 0.391597 CTCCATGCATTCAATGGCCC 59.608 55.000 0.00 0.00 35.51 5.80
2896 3272 0.391597 CCTCCATGCATTCAATGGCC 59.608 55.000 0.00 0.00 35.51 5.36
2897 3273 1.068127 GTCCTCCATGCATTCAATGGC 59.932 52.381 0.00 0.00 35.51 4.40
2898 3274 1.684983 GGTCCTCCATGCATTCAATGG 59.315 52.381 0.00 0.00 36.82 3.16
2899 3275 2.380941 TGGTCCTCCATGCATTCAATG 58.619 47.619 0.00 0.00 39.03 2.82
2900 3276 2.832643 TGGTCCTCCATGCATTCAAT 57.167 45.000 0.00 0.00 39.03 2.57
2911 3287 1.821136 CTTTTCCAGCAATGGTCCTCC 59.179 52.381 0.00 0.00 0.00 4.30
2912 3288 2.489722 GACTTTTCCAGCAATGGTCCTC 59.510 50.000 0.00 0.00 0.00 3.71
2913 3289 2.108952 AGACTTTTCCAGCAATGGTCCT 59.891 45.455 0.00 0.00 0.00 3.85
2914 3290 2.519013 AGACTTTTCCAGCAATGGTCC 58.481 47.619 0.00 0.00 0.00 4.46
2915 3291 5.705609 TTAAGACTTTTCCAGCAATGGTC 57.294 39.130 0.00 0.00 0.00 4.02
2916 3292 6.478512 TTTTAAGACTTTTCCAGCAATGGT 57.521 33.333 0.00 0.00 0.00 3.55
2917 3293 6.986231 ACTTTTTAAGACTTTTCCAGCAATGG 59.014 34.615 0.00 0.00 0.00 3.16
2918 3294 7.169813 GGACTTTTTAAGACTTTTCCAGCAATG 59.830 37.037 0.00 0.00 0.00 2.82
2919 3295 7.069950 AGGACTTTTTAAGACTTTTCCAGCAAT 59.930 33.333 0.00 0.00 0.00 3.56
2920 3296 6.379988 AGGACTTTTTAAGACTTTTCCAGCAA 59.620 34.615 0.00 0.00 0.00 3.91
2921 3297 5.891551 AGGACTTTTTAAGACTTTTCCAGCA 59.108 36.000 0.00 0.00 0.00 4.41
2922 3298 6.392625 AGGACTTTTTAAGACTTTTCCAGC 57.607 37.500 0.00 0.00 0.00 4.85
2952 3328 7.961325 ATGAAGAAGACTCTCAAGAAAAGTC 57.039 36.000 0.00 0.00 39.76 3.01
2953 3329 8.744568 AAATGAAGAAGACTCTCAAGAAAAGT 57.255 30.769 0.00 0.00 0.00 2.66
2955 3331 9.838339 ACTAAATGAAGAAGACTCTCAAGAAAA 57.162 29.630 0.00 0.00 0.00 2.29
2956 3332 9.482627 GACTAAATGAAGAAGACTCTCAAGAAA 57.517 33.333 0.00 0.00 0.00 2.52
2957 3333 8.865090 AGACTAAATGAAGAAGACTCTCAAGAA 58.135 33.333 0.00 0.00 0.00 2.52
2958 3334 8.415950 AGACTAAATGAAGAAGACTCTCAAGA 57.584 34.615 0.00 0.00 0.00 3.02
2959 3335 8.303156 TGAGACTAAATGAAGAAGACTCTCAAG 58.697 37.037 0.00 0.00 34.51 3.02
2960 3336 8.183104 TGAGACTAAATGAAGAAGACTCTCAA 57.817 34.615 0.00 0.00 34.51 3.02
2961 3337 7.767250 TGAGACTAAATGAAGAAGACTCTCA 57.233 36.000 0.00 0.00 34.51 3.27
2962 3338 9.482627 TTTTGAGACTAAATGAAGAAGACTCTC 57.517 33.333 0.00 0.00 34.51 3.20
2963 3339 9.838339 TTTTTGAGACTAAATGAAGAAGACTCT 57.162 29.630 0.00 0.00 34.51 3.24
2966 3342 9.122613 GCATTTTTGAGACTAAATGAAGAAGAC 57.877 33.333 11.66 0.00 41.86 3.01
2967 3343 8.299570 GGCATTTTTGAGACTAAATGAAGAAGA 58.700 33.333 11.66 0.00 41.86 2.87
2968 3344 8.302438 AGGCATTTTTGAGACTAAATGAAGAAG 58.698 33.333 11.66 0.00 41.86 2.85
2969 3345 8.181904 AGGCATTTTTGAGACTAAATGAAGAA 57.818 30.769 11.66 0.00 41.86 2.52
2970 3346 7.765695 AGGCATTTTTGAGACTAAATGAAGA 57.234 32.000 11.66 0.00 41.86 2.87
2978 3354 9.174166 GGACTAAATTAGGCATTTTTGAGACTA 57.826 33.333 8.28 0.00 36.43 2.59
2979 3355 7.890655 AGGACTAAATTAGGCATTTTTGAGACT 59.109 33.333 8.28 0.00 36.43 3.24
2980 3356 8.056407 AGGACTAAATTAGGCATTTTTGAGAC 57.944 34.615 8.28 0.00 36.43 3.36
2981 3357 8.650143 AAGGACTAAATTAGGCATTTTTGAGA 57.350 30.769 8.28 0.00 33.29 3.27
2989 3365 9.528489 TGACTTTTTAAGGACTAAATTAGGCAT 57.472 29.630 8.28 0.00 34.70 4.40
2990 3366 8.927675 TGACTTTTTAAGGACTAAATTAGGCA 57.072 30.769 8.28 0.00 34.70 4.75
2991 3367 9.011095 ACTGACTTTTTAAGGACTAAATTAGGC 57.989 33.333 4.92 0.46 29.52 3.93
2994 3370 9.511272 GGGACTGACTTTTTAAGGACTAAATTA 57.489 33.333 0.00 0.00 29.52 1.40
2995 3371 8.225416 AGGGACTGACTTTTTAAGGACTAAATT 58.775 33.333 0.00 0.00 37.18 1.82
2996 3372 7.756614 AGGGACTGACTTTTTAAGGACTAAAT 58.243 34.615 0.00 0.00 37.18 1.40
2997 3373 7.145474 AGGGACTGACTTTTTAAGGACTAAA 57.855 36.000 0.00 0.00 37.18 1.85
2998 3374 6.239800 GGAGGGACTGACTTTTTAAGGACTAA 60.240 42.308 0.00 0.00 41.55 2.24
2999 3375 5.247792 GGAGGGACTGACTTTTTAAGGACTA 59.752 44.000 0.00 0.00 41.55 2.59
3000 3376 4.041815 GGAGGGACTGACTTTTTAAGGACT 59.958 45.833 0.00 0.00 41.55 3.85
3001 3377 4.202430 TGGAGGGACTGACTTTTTAAGGAC 60.202 45.833 0.00 0.00 41.55 3.85
3002 3378 3.977999 TGGAGGGACTGACTTTTTAAGGA 59.022 43.478 0.00 0.00 41.55 3.36
3003 3379 4.202472 ACTGGAGGGACTGACTTTTTAAGG 60.202 45.833 0.00 0.00 41.55 2.69
3004 3380 4.974399 ACTGGAGGGACTGACTTTTTAAG 58.026 43.478 0.00 0.00 41.55 1.85
3005 3381 5.382664 AACTGGAGGGACTGACTTTTTAA 57.617 39.130 0.00 0.00 41.55 1.52
3006 3382 5.130350 CAAACTGGAGGGACTGACTTTTTA 58.870 41.667 0.00 0.00 41.55 1.52
3007 3383 3.953542 AACTGGAGGGACTGACTTTTT 57.046 42.857 0.00 0.00 41.55 1.94
3008 3384 3.555966 CAAACTGGAGGGACTGACTTTT 58.444 45.455 0.00 0.00 41.55 2.27
3009 3385 2.158608 CCAAACTGGAGGGACTGACTTT 60.159 50.000 0.00 0.00 41.55 2.66
3010 3386 1.421646 CCAAACTGGAGGGACTGACTT 59.578 52.381 0.00 0.00 41.55 3.01
3011 3387 1.059913 CCAAACTGGAGGGACTGACT 58.940 55.000 0.00 0.00 41.55 3.41
3012 3388 0.765510 ACCAAACTGGAGGGACTGAC 59.234 55.000 0.00 0.00 41.55 3.51
3013 3389 0.764890 CACCAAACTGGAGGGACTGA 59.235 55.000 0.00 0.00 41.55 3.41
3014 3390 0.764890 TCACCAAACTGGAGGGACTG 59.235 55.000 0.00 0.00 41.55 3.51
3016 3392 2.358322 TTTCACCAAACTGGAGGGAC 57.642 50.000 0.00 0.00 40.96 4.46
3017 3393 3.390175 TTTTTCACCAAACTGGAGGGA 57.610 42.857 0.00 0.00 40.96 4.20
3073 3449 5.337733 GGGTGTTTGTTTACAGGGACTTTTT 60.338 40.000 0.00 0.00 34.60 1.94
3074 3450 4.160814 GGGTGTTTGTTTACAGGGACTTTT 59.839 41.667 0.00 0.00 34.60 2.27
3075 3451 3.702548 GGGTGTTTGTTTACAGGGACTTT 59.297 43.478 0.00 0.00 34.60 2.66
3076 3452 3.293337 GGGTGTTTGTTTACAGGGACTT 58.707 45.455 0.00 0.00 34.60 3.01
3077 3453 2.423803 GGGGTGTTTGTTTACAGGGACT 60.424 50.000 0.00 0.00 43.88 3.85
3078 3454 1.958579 GGGGTGTTTGTTTACAGGGAC 59.041 52.381 0.00 0.00 0.00 4.46
3079 3455 1.854280 AGGGGTGTTTGTTTACAGGGA 59.146 47.619 0.00 0.00 0.00 4.20
3080 3456 2.375014 AGGGGTGTTTGTTTACAGGG 57.625 50.000 0.00 0.00 0.00 4.45
3081 3457 4.070009 GACTAGGGGTGTTTGTTTACAGG 58.930 47.826 0.00 0.00 0.00 4.00
3082 3458 4.710324 TGACTAGGGGTGTTTGTTTACAG 58.290 43.478 0.00 0.00 0.00 2.74
3083 3459 4.774660 TGACTAGGGGTGTTTGTTTACA 57.225 40.909 0.00 0.00 0.00 2.41
3084 3460 6.002082 AGATTGACTAGGGGTGTTTGTTTAC 58.998 40.000 0.00 0.00 0.00 2.01
3085 3461 6.001460 CAGATTGACTAGGGGTGTTTGTTTA 58.999 40.000 0.00 0.00 0.00 2.01
3086 3462 4.827284 CAGATTGACTAGGGGTGTTTGTTT 59.173 41.667 0.00 0.00 0.00 2.83
3087 3463 4.141251 ACAGATTGACTAGGGGTGTTTGTT 60.141 41.667 0.00 0.00 0.00 2.83
3088 3464 3.394606 ACAGATTGACTAGGGGTGTTTGT 59.605 43.478 0.00 0.00 0.00 2.83
3089 3465 4.003648 GACAGATTGACTAGGGGTGTTTG 58.996 47.826 0.00 0.00 0.00 2.93
3090 3466 3.009143 GGACAGATTGACTAGGGGTGTTT 59.991 47.826 0.00 0.00 0.00 2.83
3091 3467 2.572104 GGACAGATTGACTAGGGGTGTT 59.428 50.000 0.00 0.00 0.00 3.32
3092 3468 2.188817 GGACAGATTGACTAGGGGTGT 58.811 52.381 0.00 0.00 0.00 4.16
3093 3469 2.472029 AGGACAGATTGACTAGGGGTG 58.528 52.381 0.00 0.00 0.00 4.61
3094 3470 2.950990 AGGACAGATTGACTAGGGGT 57.049 50.000 0.00 0.00 0.00 4.95
3095 3471 3.643237 TGTAGGACAGATTGACTAGGGG 58.357 50.000 0.00 0.00 0.00 4.79
3096 3472 4.712337 AGTTGTAGGACAGATTGACTAGGG 59.288 45.833 0.00 0.00 0.00 3.53
3097 3473 5.186021 ACAGTTGTAGGACAGATTGACTAGG 59.814 44.000 0.00 0.00 0.00 3.02
3098 3474 6.096036 CACAGTTGTAGGACAGATTGACTAG 58.904 44.000 0.00 0.00 0.00 2.57
3099 3475 5.566826 GCACAGTTGTAGGACAGATTGACTA 60.567 44.000 0.00 0.00 0.00 2.59
3100 3476 4.800914 GCACAGTTGTAGGACAGATTGACT 60.801 45.833 0.00 0.00 0.00 3.41
3101 3477 3.433615 GCACAGTTGTAGGACAGATTGAC 59.566 47.826 0.00 0.00 0.00 3.18
3102 3478 3.557054 GGCACAGTTGTAGGACAGATTGA 60.557 47.826 0.00 0.00 0.00 2.57
3103 3479 2.744202 GGCACAGTTGTAGGACAGATTG 59.256 50.000 0.00 0.00 0.00 2.67
3104 3480 2.290323 GGGCACAGTTGTAGGACAGATT 60.290 50.000 0.00 0.00 0.00 2.40
3105 3481 1.279271 GGGCACAGTTGTAGGACAGAT 59.721 52.381 0.00 0.00 0.00 2.90
3106 3482 0.685097 GGGCACAGTTGTAGGACAGA 59.315 55.000 0.00 0.00 0.00 3.41
3168 3544 3.698820 AACTCACCCGTACGGCCC 61.699 66.667 29.15 0.00 33.26 5.80
3217 3593 2.120909 AATTTATGCGCTGCGGGCT 61.121 52.632 24.61 1.02 42.10 5.19
3376 3752 1.012486 GCAAGCAATTGAGCACCAGC 61.012 55.000 10.34 0.00 42.56 4.85
3385 3761 2.717580 TGAGAGCAAGCAAGCAATTG 57.282 45.000 0.00 0.00 36.85 2.32
3387 3763 2.719426 GTTGAGAGCAAGCAAGCAAT 57.281 45.000 3.19 0.00 34.01 3.56
3412 3788 1.406539 GGTAGAAACGATACGGCTGGA 59.593 52.381 0.00 0.00 0.00 3.86
3428 3804 4.553330 AGTTTACCATCACCACAGGTAG 57.447 45.455 0.00 0.00 38.96 3.18
3444 3828 8.038944 ACCTTGAGAATTTCGCATACTAGTTTA 58.961 33.333 0.00 0.00 0.00 2.01
3450 3834 5.003804 ACAACCTTGAGAATTTCGCATACT 58.996 37.500 3.60 0.00 0.00 2.12
3451 3835 5.296813 ACAACCTTGAGAATTTCGCATAC 57.703 39.130 3.60 0.00 0.00 2.39
3452 3836 5.584649 CCTACAACCTTGAGAATTTCGCATA 59.415 40.000 3.60 0.00 0.00 3.14
3453 3837 4.396166 CCTACAACCTTGAGAATTTCGCAT 59.604 41.667 3.60 0.00 0.00 4.73
3454 3838 3.751175 CCTACAACCTTGAGAATTTCGCA 59.249 43.478 0.00 0.00 0.00 5.10
3464 3848 4.655963 AGTACGTACTCCTACAACCTTGA 58.344 43.478 22.45 0.00 0.00 3.02
3494 3880 2.015587 GTACGTACACCCCTCAGAGAG 58.984 57.143 20.67 0.00 0.00 3.20
3496 3882 0.731417 CGTACGTACACCCCTCAGAG 59.269 60.000 24.50 1.32 0.00 3.35
3498 3884 0.883833 AACGTACGTACACCCCTCAG 59.116 55.000 23.12 8.72 0.00 3.35


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

AutoCloner maintained by Alex Coulton.