Multiple sequence alignment - TraesCS2A01G277100

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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 TraesCS2A01G277100 chr2A 100.000 4834 0 0 1 4834 458050107 458054940 0.000000e+00 8927.0
1 TraesCS2A01G277100 chr2A 98.780 82 1 0 4544 4625 458054567 458054648 3.900000e-31 147.0
2 TraesCS2A01G277100 chr2B 88.382 4252 288 88 86 4246 411144302 411140166 0.000000e+00 4926.0
3 TraesCS2A01G277100 chr2B 93.269 104 6 1 4440 4542 450718378 450718275 8.380000e-33 152.0
4 TraesCS2A01G277100 chr2B 93.269 104 6 1 4440 4542 492605251 492605148 8.380000e-33 152.0
5 TraesCS2A01G277100 chr2B 94.737 76 4 0 3 78 411144410 411144335 8.500000e-23 119.0
6 TraesCS2A01G277100 chr2D 89.015 3951 261 80 582 4444 345627230 345623365 0.000000e+00 4732.0
7 TraesCS2A01G277100 chr2D 86.911 573 44 12 3 574 345629722 345629180 8.890000e-172 614.0
8 TraesCS2A01G277100 chr2D 85.859 297 31 7 4534 4829 345623329 345623043 6.080000e-79 305.0
9 TraesCS2A01G277100 chr1B 79.783 277 49 7 75 347 356982212 356982485 1.370000e-45 195.0
10 TraesCS2A01G277100 chr1B 77.914 163 19 12 73 230 65281544 65281394 8.620000e-13 86.1
11 TraesCS2A01G277100 chr6D 77.338 278 54 8 66 338 345068792 345068519 6.480000e-34 156.0
12 TraesCS2A01G277100 chr5A 93.269 104 6 1 4440 4542 596587448 596587345 8.380000e-33 152.0
13 TraesCS2A01G277100 chr1A 93.269 104 6 1 4440 4542 569341815 569341712 8.380000e-33 152.0
14 TraesCS2A01G277100 chrUn 92.308 104 7 1 4440 4542 83540971 83540868 3.900000e-31 147.0
15 TraesCS2A01G277100 chr6B 92.308 104 7 1 4440 4542 712458076 712458179 3.900000e-31 147.0
16 TraesCS2A01G277100 chr6B 93.478 46 2 1 4628 4673 31517418 31517374 3.120000e-07 67.6
17 TraesCS2A01G277100 chr4B 92.308 104 7 1 4440 4542 398126322 398126425 3.900000e-31 147.0
18 TraesCS2A01G277100 chr4B 92.308 104 7 1 4440 4542 398161231 398161334 3.900000e-31 147.0
19 TraesCS2A01G277100 chr4B 92.308 104 7 1 4440 4542 398195993 398196096 3.900000e-31 147.0
20 TraesCS2A01G277100 chr7D 89.286 112 10 2 1117 1227 232811621 232811731 6.520000e-29 139.0
21 TraesCS2A01G277100 chr7A 89.286 112 10 2 1117 1227 246270526 246270416 6.520000e-29 139.0
22 TraesCS2A01G277100 chr4A 82.114 123 22 0 4545 4667 661977231 661977109 6.620000e-19 106.0


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 TraesCS2A01G277100 chr2A 458050107 458054940 4833 False 4537.000000 8927 99.390000 1 4834 2 chr2A.!!$F1 4833
1 TraesCS2A01G277100 chr2B 411140166 411144410 4244 True 2522.500000 4926 91.559500 3 4246 2 chr2B.!!$R3 4243
2 TraesCS2A01G277100 chr2D 345623043 345629722 6679 True 1883.666667 4732 87.261667 3 4829 3 chr2D.!!$R1 4826

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
442 468 0.328258 TTCTTGCAACTCCTAGCCCC 59.672 55.0 0.00 0.00 0.0 5.80 F
1237 3233 0.104120 CGAAGGTATGGATCACGGCA 59.896 55.0 0.00 0.00 0.0 5.69 F
2002 4013 0.595588 CCAGACTCGAGGATGGATCG 59.404 60.0 25.97 7.52 41.5 3.69 F
2602 4645 1.027357 ACTTGTTGCTTGCAGTGAGG 58.973 50.0 0.00 0.00 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 4013 0.038159 CCTCTGACTTGGACACGACC 60.038 60.0 0.00 0.0 0.0 4.79 R
3188 5240 0.110486 GCCTGTTCCCAAGGACAAGA 59.890 55.0 0.00 0.0 0.0 3.02 R
3189 5241 0.111253 AGCCTGTTCCCAAGGACAAG 59.889 55.0 0.00 0.0 0.0 3.16 R
4374 6476 0.179189 GACAAAAGCTTCGCGGATGG 60.179 55.0 6.13 0.0 0.0 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.836999 TTGGAGCTGCGCTTCCCTTA 61.837 55.000 18.89 6.30 39.88 2.69
47 48 0.400594 GCTTCCCTTAGTGTGGGTGT 59.599 55.000 0.00 0.00 44.84 4.16
54 55 3.306780 CCCTTAGTGTGGGTGTCTTAGTG 60.307 52.174 0.00 0.00 39.82 2.74
78 79 2.035066 GCACATGCCTTCTTGTGTTTCT 59.965 45.455 11.26 0.00 45.10 2.52
84 85 4.265893 TGCCTTCTTGTGTTTCTGTACAA 58.734 39.130 0.00 0.00 35.66 2.41
121 147 1.411493 GGGTCGATGTTCGTCTTCGC 61.411 60.000 0.00 8.13 41.35 4.70
122 148 0.456312 GGTCGATGTTCGTCTTCGCT 60.456 55.000 0.00 0.00 41.35 4.93
212 238 1.970917 CTTCGGTGTGCGATCTTGGC 61.971 60.000 0.00 0.00 0.00 4.52
217 243 2.892425 GTGCGATCTTGGCGAGGG 60.892 66.667 0.97 0.00 0.00 4.30
290 316 6.662414 TTGTGATGATTTTCACTCGGTATC 57.338 37.500 6.20 0.00 45.07 2.24
292 318 5.104941 TGTGATGATTTTCACTCGGTATCCT 60.105 40.000 6.20 0.00 45.07 3.24
305 331 9.139734 TCACTCGGTATCCTATTAATTAACTGT 57.860 33.333 0.00 0.00 0.00 3.55
326 352 9.832445 AACTGTGAACTCTCTTCTGTTTAATTA 57.168 29.630 0.00 0.00 0.00 1.40
334 360 9.401058 ACTCTCTTCTGTTTAATTAATGGATGG 57.599 33.333 0.00 0.00 0.00 3.51
338 364 5.776358 TCTGTTTAATTAATGGATGGGGCT 58.224 37.500 0.00 0.00 0.00 5.19
341 367 7.505585 TCTGTTTAATTAATGGATGGGGCTAAG 59.494 37.037 0.00 0.00 0.00 2.18
396 422 5.768164 TCTGCCATCGAGTATGTAGTGATTA 59.232 40.000 0.00 0.00 33.34 1.75
439 465 4.320567 GGAAGTTTTCTTGCAACTCCTAGC 60.321 45.833 0.00 0.00 45.53 3.42
440 466 3.149981 AGTTTTCTTGCAACTCCTAGCC 58.850 45.455 0.00 0.00 27.49 3.93
441 467 2.200373 TTTCTTGCAACTCCTAGCCC 57.800 50.000 0.00 0.00 0.00 5.19
442 468 0.328258 TTCTTGCAACTCCTAGCCCC 59.672 55.000 0.00 0.00 0.00 5.80
443 469 0.840288 TCTTGCAACTCCTAGCCCCA 60.840 55.000 0.00 0.00 0.00 4.96
444 470 0.393537 CTTGCAACTCCTAGCCCCAG 60.394 60.000 0.00 0.00 0.00 4.45
445 471 1.852157 TTGCAACTCCTAGCCCCAGG 61.852 60.000 0.00 0.00 37.00 4.45
465 491 1.325355 CCCCCAGCTATGCATTTCTG 58.675 55.000 3.54 12.35 0.00 3.02
481 507 5.452636 GCATTTCTGTACCCAACCTTGAAAA 60.453 40.000 0.00 0.00 30.34 2.29
522 553 7.621832 TTTTCTTCAAATATGCAAAGACACG 57.378 32.000 0.00 0.00 0.00 4.49
544 575 1.554617 TCTTTGGATCGGCTGACATCA 59.445 47.619 0.00 0.00 0.00 3.07
588 2561 3.764885 ACTCTTCACACTGTTTGTTGC 57.235 42.857 0.00 0.00 35.67 4.17
589 2562 3.081061 ACTCTTCACACTGTTTGTTGCA 58.919 40.909 0.00 0.00 35.67 4.08
605 2578 0.459489 TGCAGCCCAGTTGTCAAAAC 59.541 50.000 0.00 0.00 0.00 2.43
613 2586 4.082733 GCCCAGTTGTCAAAACTATCTTCC 60.083 45.833 0.00 0.00 0.00 3.46
615 2588 5.182001 CCCAGTTGTCAAAACTATCTTCCAG 59.818 44.000 0.00 0.00 0.00 3.86
626 2605 6.765915 AACTATCTTCCAGGAAAGAAATGC 57.234 37.500 2.72 0.00 38.69 3.56
665 2644 1.567504 AGTGAAACCAACGACGACTG 58.432 50.000 0.00 0.00 37.80 3.51
745 2726 1.685765 CCCACCGACCCTGATCTGA 60.686 63.158 0.38 0.00 0.00 3.27
746 2727 1.050988 CCCACCGACCCTGATCTGAT 61.051 60.000 0.38 0.00 0.00 2.90
747 2728 0.390860 CCACCGACCCTGATCTGATC 59.609 60.000 10.72 10.72 0.00 2.92
748 2729 1.407936 CACCGACCCTGATCTGATCT 58.592 55.000 17.82 0.00 0.00 2.75
749 2730 1.068281 CACCGACCCTGATCTGATCTG 59.932 57.143 17.82 16.49 0.00 2.90
834 2815 1.016130 ACGCAACAATCTCTGCTCCG 61.016 55.000 0.00 0.00 36.38 4.63
835 2816 1.427020 GCAACAATCTCTGCTCCGC 59.573 57.895 0.00 0.00 35.62 5.54
836 2817 1.986575 GCAACAATCTCTGCTCCGCC 61.987 60.000 0.00 0.00 35.62 6.13
837 2818 1.078143 AACAATCTCTGCTCCGCCC 60.078 57.895 0.00 0.00 0.00 6.13
854 2835 1.817740 GCCCGCCATATAAGAAGCCAA 60.818 52.381 0.00 0.00 0.00 4.52
953 2934 4.007659 ACCCGTTAATCGCTTCATCTTTT 58.992 39.130 0.00 0.00 38.35 2.27
954 2935 4.457949 ACCCGTTAATCGCTTCATCTTTTT 59.542 37.500 0.00 0.00 38.35 1.94
955 2936 4.793216 CCCGTTAATCGCTTCATCTTTTTG 59.207 41.667 0.00 0.00 38.35 2.44
1237 3233 0.104120 CGAAGGTATGGATCACGGCA 59.896 55.000 0.00 0.00 0.00 5.69
1238 3234 1.583054 GAAGGTATGGATCACGGCAC 58.417 55.000 0.00 0.00 0.00 5.01
1271 3267 3.133542 TCTGCATCTGATCACCCTAGTTG 59.866 47.826 0.00 0.00 0.00 3.16
1298 3294 3.624861 GCAACATCAGACCCAACAGATAG 59.375 47.826 0.00 0.00 0.00 2.08
1299 3295 4.623886 GCAACATCAGACCCAACAGATAGA 60.624 45.833 0.00 0.00 0.00 1.98
1300 3296 5.678583 CAACATCAGACCCAACAGATAGAT 58.321 41.667 0.00 0.00 0.00 1.98
1301 3297 5.287674 ACATCAGACCCAACAGATAGATG 57.712 43.478 0.00 0.00 38.02 2.90
1362 3358 3.827898 GCACTCTCCTCGACGGGG 61.828 72.222 7.70 7.70 32.98 5.73
1631 3627 2.637947 GGCATCTTCAAGAAGGTCCTC 58.362 52.381 9.73 0.00 38.88 3.71
1695 3691 5.368256 AGTTACTGGTACGTTGTGTCTAG 57.632 43.478 0.00 0.00 0.00 2.43
1728 3736 9.634163 GGTTTCGACCAAATTACTGAATATTTT 57.366 29.630 0.00 0.00 0.00 1.82
1760 3768 3.821033 ACTTGTGTTCTGCTAAACATCCC 59.179 43.478 7.56 0.00 40.96 3.85
1771 3779 3.120304 GCTAAACATCCCAAACTGTCGTC 60.120 47.826 0.00 0.00 0.00 4.20
1780 3788 4.994852 TCCCAAACTGTCGTCTGAAATTAG 59.005 41.667 0.00 0.00 0.00 1.73
1787 3795 5.050644 TGTCGTCTGAAATTAGCTAACGA 57.949 39.130 8.70 9.36 35.55 3.85
1790 3798 6.588756 TGTCGTCTGAAATTAGCTAACGAAAT 59.411 34.615 14.26 0.00 39.10 2.17
1791 3799 7.756272 TGTCGTCTGAAATTAGCTAACGAAATA 59.244 33.333 14.26 4.23 39.10 1.40
1852 3862 1.612199 GGGTTGCCGAACTGGAATGTA 60.612 52.381 0.00 0.00 42.00 2.29
1863 3873 5.561532 CGAACTGGAATGTACGTCGGTATAT 60.562 44.000 0.00 0.00 32.52 0.86
1883 3894 3.980646 TTCCAACGAAATGGTGAACTG 57.019 42.857 0.00 0.00 41.46 3.16
1884 3895 3.201353 TCCAACGAAATGGTGAACTGA 57.799 42.857 0.00 0.00 41.46 3.41
1984 3995 1.805945 CGCAGTCAAGTACGAGGCC 60.806 63.158 0.00 0.00 0.00 5.19
1990 4001 1.135344 GTCAAGTACGAGGCCAGACTC 60.135 57.143 5.01 0.00 0.00 3.36
2002 4013 0.595588 CCAGACTCGAGGATGGATCG 59.404 60.000 25.97 7.52 41.50 3.69
2120 4134 2.612672 CTCTGAATCGCTGATGCACAAT 59.387 45.455 0.00 0.00 39.64 2.71
2171 4185 1.285950 GGCACTTTCCAAAGCCGTC 59.714 57.895 0.00 0.00 39.63 4.79
2248 4262 4.813697 GCCATCTCTCCTCAAATCTGTTAC 59.186 45.833 0.00 0.00 0.00 2.50
2249 4263 5.363939 CCATCTCTCCTCAAATCTGTTACC 58.636 45.833 0.00 0.00 0.00 2.85
2250 4264 5.363939 CATCTCTCCTCAAATCTGTTACCC 58.636 45.833 0.00 0.00 0.00 3.69
2270 4295 3.636764 CCCTTGCTGTACTCCAAAAGTTT 59.363 43.478 0.00 0.00 39.55 2.66
2271 4296 4.261614 CCCTTGCTGTACTCCAAAAGTTTC 60.262 45.833 0.00 0.00 39.55 2.78
2272 4297 4.580580 CCTTGCTGTACTCCAAAAGTTTCT 59.419 41.667 0.00 0.00 39.55 2.52
2273 4298 5.499139 TTGCTGTACTCCAAAAGTTTCTG 57.501 39.130 0.00 0.00 39.55 3.02
2274 4299 4.776349 TGCTGTACTCCAAAAGTTTCTGA 58.224 39.130 0.00 0.00 39.55 3.27
2275 4300 4.574828 TGCTGTACTCCAAAAGTTTCTGAC 59.425 41.667 0.00 0.00 39.55 3.51
2276 4301 4.816925 GCTGTACTCCAAAAGTTTCTGACT 59.183 41.667 0.00 0.00 41.47 3.41
2277 4302 5.277538 GCTGTACTCCAAAAGTTTCTGACTG 60.278 44.000 0.00 0.00 39.00 3.51
2278 4303 5.123227 TGTACTCCAAAAGTTTCTGACTGG 58.877 41.667 0.00 0.00 39.00 4.00
2279 4304 2.952310 ACTCCAAAAGTTTCTGACTGGC 59.048 45.455 0.00 0.00 39.00 4.85
2280 4305 3.217626 CTCCAAAAGTTTCTGACTGGCT 58.782 45.455 0.00 0.00 39.00 4.75
2297 4322 7.933396 TGACTGGCTTCATAAATTGATATGTG 58.067 34.615 0.00 0.00 35.29 3.21
2311 4336 6.549912 TTGATATGTGCTGCATCTTATGAC 57.450 37.500 5.27 0.00 38.94 3.06
2388 4413 1.113788 CCCCGAATTCCACATTGCAT 58.886 50.000 0.00 0.00 0.00 3.96
2508 4533 2.590575 AACGACGGGGCAGTTGTG 60.591 61.111 0.00 0.00 38.64 3.33
2511 4536 2.426023 GACGGGGCAGTTGTGAGT 59.574 61.111 0.00 0.00 0.00 3.41
2533 4558 3.864686 CGCGGCGCACTGCTAATT 61.865 61.111 32.61 0.00 46.69 1.40
2540 4565 1.268896 GCGCACTGCTAATTCATGCAT 60.269 47.619 0.30 0.00 41.73 3.96
2541 4566 2.381589 CGCACTGCTAATTCATGCATG 58.618 47.619 21.07 21.07 38.59 4.06
2542 4567 2.124903 GCACTGCTAATTCATGCATGC 58.875 47.619 22.25 11.82 38.59 4.06
2543 4568 2.480587 GCACTGCTAATTCATGCATGCA 60.481 45.455 25.04 25.04 40.20 3.96
2544 4569 3.798889 GCACTGCTAATTCATGCATGCAT 60.799 43.478 27.46 27.46 40.20 3.96
2563 4588 4.517075 TGCATAACCTCGTGAAAATTGTCA 59.483 37.500 0.00 0.00 0.00 3.58
2602 4645 1.027357 ACTTGTTGCTTGCAGTGAGG 58.973 50.000 0.00 0.00 0.00 3.86
2846 4889 3.444034 CACCGTCTTCTATGAAGTGGAGA 59.556 47.826 19.68 0.00 0.00 3.71
2860 4903 3.665190 AGTGGAGATTGTTTCCTTCGAC 58.335 45.455 0.00 0.00 35.67 4.20
2908 4951 6.715344 TTGTCTGTTGTTTACATATCCGTC 57.285 37.500 0.00 0.00 35.85 4.79
2909 4952 6.032956 TGTCTGTTGTTTACATATCCGTCT 57.967 37.500 0.00 0.00 35.85 4.18
2910 4953 5.867174 TGTCTGTTGTTTACATATCCGTCTG 59.133 40.000 0.00 0.00 35.85 3.51
2911 4954 6.097356 GTCTGTTGTTTACATATCCGTCTGA 58.903 40.000 0.00 0.00 35.85 3.27
2912 4955 6.034683 GTCTGTTGTTTACATATCCGTCTGAC 59.965 42.308 0.00 0.00 35.85 3.51
2913 4956 5.172934 TGTTGTTTACATATCCGTCTGACC 58.827 41.667 1.55 0.00 0.00 4.02
2914 4957 4.036567 TGTTTACATATCCGTCTGACCG 57.963 45.455 1.55 0.00 0.00 4.79
2915 4958 3.444742 TGTTTACATATCCGTCTGACCGT 59.555 43.478 1.55 0.00 0.00 4.83
2920 4963 3.181457 ACATATCCGTCTGACCGTCTCTA 60.181 47.826 1.55 0.00 0.00 2.43
2945 4988 2.545526 CTGTCAGAAAGTGAACGCATGT 59.454 45.455 0.00 0.00 36.74 3.21
3094 5145 7.936301 GCTTCCAAGAGATATGAGAAGGTAAAT 59.064 37.037 0.00 0.00 33.08 1.40
3104 5155 6.966534 ATGAGAAGGTAAATAAAGGGCATG 57.033 37.500 0.00 0.00 0.00 4.06
3105 5156 5.200483 TGAGAAGGTAAATAAAGGGCATGG 58.800 41.667 0.00 0.00 0.00 3.66
3110 5161 3.889538 GGTAAATAAAGGGCATGGGTCTC 59.110 47.826 0.00 0.00 0.00 3.36
3117 5168 1.204146 GGGCATGGGTCTCTCAACTA 58.796 55.000 0.00 0.00 0.00 2.24
3125 5176 5.470047 TGGGTCTCTCAACTAAAAGTCTC 57.530 43.478 0.00 0.00 0.00 3.36
3133 5184 4.617959 TCAACTAAAAGTCTCGTCCTGTG 58.382 43.478 0.00 0.00 0.00 3.66
3144 5196 4.446719 GTCTCGTCCTGTGAAAAACGTATT 59.553 41.667 0.00 0.00 36.55 1.89
3174 5226 6.900568 GAATTGAGTTCCTGACTGACATAG 57.099 41.667 0.00 0.00 39.19 2.23
3176 5228 6.805016 ATTGAGTTCCTGACTGACATAGAT 57.195 37.500 0.00 0.00 39.19 1.98
3177 5229 5.588958 TGAGTTCCTGACTGACATAGATG 57.411 43.478 0.00 0.00 39.19 2.90
3178 5230 5.019470 TGAGTTCCTGACTGACATAGATGT 58.981 41.667 0.00 0.00 40.63 3.06
3179 5231 5.105595 TGAGTTCCTGACTGACATAGATGTG 60.106 44.000 0.00 0.00 38.98 3.21
3180 5232 3.808466 TCCTGACTGACATAGATGTGC 57.192 47.619 0.00 0.00 41.95 4.57
3181 5233 3.099141 TCCTGACTGACATAGATGTGCA 58.901 45.455 0.00 0.00 41.95 4.57
3182 5234 3.708121 TCCTGACTGACATAGATGTGCAT 59.292 43.478 0.00 0.00 41.95 3.96
3183 5235 4.056740 CCTGACTGACATAGATGTGCATC 58.943 47.826 0.00 4.12 41.95 3.91
3185 5237 5.349061 TGACTGACATAGATGTGCATCTT 57.651 39.130 18.34 2.66 45.31 2.40
3186 5238 5.737860 TGACTGACATAGATGTGCATCTTT 58.262 37.500 18.34 9.25 45.31 2.52
3187 5239 5.583457 TGACTGACATAGATGTGCATCTTTG 59.417 40.000 22.18 22.18 45.31 2.77
3198 5250 3.316029 TGTGCATCTTTGTCTTGTCCTTG 59.684 43.478 0.00 0.00 0.00 3.61
3211 5263 3.058160 CCTTGGGAACAGGCTGCG 61.058 66.667 15.89 0.00 44.54 5.18
3307 5359 0.316607 TAAACAACGCAGCGTGCAAG 60.317 50.000 23.78 14.29 45.36 4.01
3340 5392 7.446001 AAAGGATTACAAAGAAGCAGAGAAG 57.554 36.000 0.00 0.00 0.00 2.85
3355 5407 0.475906 AGAAGCTCTGCACCAAGGTT 59.524 50.000 3.76 3.76 36.01 3.50
3361 5413 2.851195 CTCTGCACCAAGGTTAGTGTT 58.149 47.619 0.00 0.00 36.35 3.32
3362 5414 3.805807 GCTCTGCACCAAGGTTAGTGTTA 60.806 47.826 0.00 0.00 36.35 2.41
3363 5415 3.735591 TCTGCACCAAGGTTAGTGTTAC 58.264 45.455 0.00 0.00 36.35 2.50
3364 5416 2.812011 CTGCACCAAGGTTAGTGTTACC 59.188 50.000 0.00 0.00 36.35 2.85
3374 5426 6.018589 AGGTTAGTGTTACCTTTCGAGTAC 57.981 41.667 0.00 0.00 43.45 2.73
3375 5427 4.853743 GGTTAGTGTTACCTTTCGAGTACG 59.146 45.833 0.00 0.00 35.41 3.67
3378 5430 9.884653 GGTTAGTGTTACCTTTCGAGTACGAGG 62.885 48.148 0.00 0.00 39.86 4.63
3388 5440 2.422479 TCGAGTACGAGGGTTTCATCAG 59.578 50.000 0.00 0.00 43.81 2.90
3389 5441 2.163815 CGAGTACGAGGGTTTCATCAGT 59.836 50.000 0.00 0.00 42.66 3.41
3392 5444 0.396435 ACGAGGGTTTCATCAGTGCA 59.604 50.000 0.00 0.00 0.00 4.57
3394 5446 1.197721 CGAGGGTTTCATCAGTGCAAC 59.802 52.381 0.00 0.00 31.78 4.17
3399 5451 3.578688 GGTTTCATCAGTGCAACCAATC 58.421 45.455 5.33 0.00 46.73 2.67
3400 5452 3.005684 GGTTTCATCAGTGCAACCAATCA 59.994 43.478 5.33 0.00 46.73 2.57
3402 5454 3.921119 TCATCAGTGCAACCAATCAAC 57.079 42.857 0.00 0.00 37.80 3.18
3403 5455 3.220940 TCATCAGTGCAACCAATCAACA 58.779 40.909 0.00 0.00 37.80 3.33
3404 5456 3.635836 TCATCAGTGCAACCAATCAACAA 59.364 39.130 0.00 0.00 37.80 2.83
3405 5457 3.435105 TCAGTGCAACCAATCAACAAC 57.565 42.857 0.00 0.00 37.80 3.32
3406 5458 2.757314 TCAGTGCAACCAATCAACAACA 59.243 40.909 0.00 0.00 37.80 3.33
3409 5461 2.602660 GTGCAACCAATCAACAACACAC 59.397 45.455 0.00 0.00 0.00 3.82
3413 5465 2.451490 ACCAATCAACAACACACCACA 58.549 42.857 0.00 0.00 0.00 4.17
3415 5467 3.181477 ACCAATCAACAACACACCACATG 60.181 43.478 0.00 0.00 0.00 3.21
3416 5468 3.067883 CCAATCAACAACACACCACATGA 59.932 43.478 0.00 0.00 0.00 3.07
3417 5469 4.262121 CCAATCAACAACACACCACATGAT 60.262 41.667 0.00 0.00 0.00 2.45
3422 5474 3.942829 ACAACACACCACATGATCCTAG 58.057 45.455 0.00 0.00 0.00 3.02
3451 5507 5.483231 TGGCATTATTGATCAGGTTTTGGAA 59.517 36.000 0.00 0.00 0.00 3.53
3529 5585 1.335882 TGGATCTGGAGCTGGCAGAG 61.336 60.000 20.86 6.64 0.00 3.35
3576 5632 1.202582 CGACCCAGACAACAGGTAGAG 59.797 57.143 0.00 0.00 32.81 2.43
3613 5670 3.582647 TCTGGAGATCAACAAGGCTACAA 59.417 43.478 0.00 0.00 0.00 2.41
3624 5683 6.419710 TCAACAAGGCTACAAATATCGTATCG 59.580 38.462 0.00 0.00 0.00 2.92
3631 5690 7.328737 AGGCTACAAATATCGTATCGATTTCAC 59.671 37.037 1.71 0.00 44.59 3.18
3638 5697 5.977489 ATCGTATCGATTTCACCTATGGA 57.023 39.130 1.71 0.00 44.59 3.41
3640 5699 6.340962 TCGTATCGATTTCACCTATGGATT 57.659 37.500 1.71 0.00 0.00 3.01
3641 5700 7.457024 TCGTATCGATTTCACCTATGGATTA 57.543 36.000 1.71 0.00 0.00 1.75
3652 5711 6.613699 TCACCTATGGATTATGGCTGATTTT 58.386 36.000 0.00 0.00 0.00 1.82
3749 5810 1.291272 GGACGCCAAGTTCTACGGT 59.709 57.895 0.00 0.00 0.00 4.83
4001 6063 5.550232 TTGCTCACGTACGATTCTAGTAA 57.450 39.130 24.41 13.03 0.00 2.24
4108 6170 6.901265 ACTCAAATTAATTGCACATTTTGGC 58.099 32.000 0.39 0.00 38.98 4.52
4110 6172 7.877097 ACTCAAATTAATTGCACATTTTGGCTA 59.123 29.630 0.39 0.00 38.98 3.93
4134 6196 2.797156 GGACATTGGAAGTGATCGATCG 59.203 50.000 20.03 9.36 0.00 3.69
4135 6197 3.448686 GACATTGGAAGTGATCGATCGT 58.551 45.455 20.03 7.56 0.00 3.73
4136 6198 4.499188 GGACATTGGAAGTGATCGATCGTA 60.499 45.833 20.03 0.83 0.00 3.43
4137 6199 5.201713 ACATTGGAAGTGATCGATCGTAT 57.798 39.130 20.03 8.49 0.00 3.06
4148 6237 5.034797 TGATCGATCGTATATTGCGGAATC 58.965 41.667 20.03 6.54 0.00 2.52
4157 6246 0.249120 ATTGCGGAATCTGACGTGGA 59.751 50.000 0.00 0.00 0.00 4.02
4212 6306 7.849322 TTAAAAGGATCTGGCCTAAAGTTTT 57.151 32.000 3.32 5.97 37.26 2.43
4233 6328 8.571336 AGTTTTTAGTCTGACCAATGATTTCAG 58.429 33.333 3.76 1.36 38.52 3.02
4254 6349 7.572523 TCAGCCATCCAATAGTAAAATTCAG 57.427 36.000 0.00 0.00 0.00 3.02
4275 6370 9.852091 ATTCAGAAGATAAAGCAAAAATGACTC 57.148 29.630 0.00 0.00 0.00 3.36
4276 6371 7.820648 TCAGAAGATAAAGCAAAAATGACTCC 58.179 34.615 0.00 0.00 0.00 3.85
4277 6372 7.031975 CAGAAGATAAAGCAAAAATGACTCCC 58.968 38.462 0.00 0.00 0.00 4.30
4285 6380 7.910441 AAGCAAAAATGACTCCCATAAAATG 57.090 32.000 0.00 0.00 34.45 2.32
4286 6381 7.008021 AGCAAAAATGACTCCCATAAAATGT 57.992 32.000 0.00 0.00 34.45 2.71
4287 6382 8.133024 AGCAAAAATGACTCCCATAAAATGTA 57.867 30.769 0.00 0.00 34.45 2.29
4313 6408 6.727824 ATCTCTGTTTCAAATTACTCGTGG 57.272 37.500 0.00 0.00 0.00 4.94
4314 6409 5.607477 TCTCTGTTTCAAATTACTCGTGGT 58.393 37.500 0.00 0.00 0.00 4.16
4315 6410 6.053005 TCTCTGTTTCAAATTACTCGTGGTT 58.947 36.000 0.00 0.00 0.00 3.67
4316 6411 6.540914 TCTCTGTTTCAAATTACTCGTGGTTT 59.459 34.615 0.00 0.00 0.00 3.27
4317 6412 7.066525 TCTCTGTTTCAAATTACTCGTGGTTTT 59.933 33.333 0.00 0.00 0.00 2.43
4318 6413 8.211116 TCTGTTTCAAATTACTCGTGGTTTTA 57.789 30.769 0.00 0.00 0.00 1.52
4319 6414 8.339714 TCTGTTTCAAATTACTCGTGGTTTTAG 58.660 33.333 0.00 0.00 0.00 1.85
4320 6415 7.987649 TGTTTCAAATTACTCGTGGTTTTAGT 58.012 30.769 0.00 0.00 0.00 2.24
4322 6417 8.950961 GTTTCAAATTACTCGTGGTTTTAGTTC 58.049 33.333 0.00 0.00 0.00 3.01
4324 6419 8.211116 TCAAATTACTCGTGGTTTTAGTTCAA 57.789 30.769 0.00 0.00 0.00 2.69
4332 6427 9.857957 ACTCGTGGTTTTAGTTCAAATTTAAAA 57.142 25.926 0.00 0.00 0.00 1.52
4334 6429 8.796278 TCGTGGTTTTAGTTCAAATTTAAAACG 58.204 29.630 15.13 8.76 43.26 3.60
4335 6430 8.585436 CGTGGTTTTAGTTCAAATTTAAAACGT 58.415 29.630 15.13 0.00 43.26 3.99
4361 6463 6.702723 ACGAAGTACATAAAGTGCAACTGTAA 59.297 34.615 0.00 0.00 46.51 2.41
4374 6476 3.933332 GCAACTGTAACATGTACTCCCTC 59.067 47.826 0.00 0.00 0.00 4.30
4381 6483 0.034059 CATGTACTCCCTCCATCCGC 59.966 60.000 0.00 0.00 0.00 5.54
4385 6487 1.107538 TACTCCCTCCATCCGCGAAG 61.108 60.000 8.23 0.00 0.00 3.79
4401 6503 3.788434 CGAAGCTTTTGTCTTTAGCGA 57.212 42.857 0.00 0.00 39.82 4.93
4402 6504 4.128554 CGAAGCTTTTGTCTTTAGCGAA 57.871 40.909 0.00 0.00 39.82 4.70
4423 6527 9.152595 AGCGAAAGTTTTAAAATTTTAACCACA 57.847 25.926 20.35 5.90 32.77 4.17
4459 6592 9.886132 AATAGTACTAGATCCGTTTTGAAATGT 57.114 29.630 8.85 0.00 0.00 2.71
4662 6795 6.850752 TGTACACTTATTCATGGACAGAGA 57.149 37.500 0.00 0.00 34.65 3.10
4668 6801 7.068103 ACACTTATTCATGGACAGAGAGAGTAG 59.932 40.741 0.00 0.00 0.00 2.57
4669 6802 7.284261 CACTTATTCATGGACAGAGAGAGTAGA 59.716 40.741 0.00 0.00 0.00 2.59
4670 6803 7.502226 ACTTATTCATGGACAGAGAGAGTAGAG 59.498 40.741 0.00 0.00 0.00 2.43
4671 6804 3.550820 TCATGGACAGAGAGAGTAGAGC 58.449 50.000 0.00 0.00 0.00 4.09
4675 6808 5.117406 TGGACAGAGAGAGTAGAGCAATA 57.883 43.478 0.00 0.00 0.00 1.90
4706 6839 1.852157 TTCATTTCTGAGCCCGGCCT 61.852 55.000 5.55 0.00 31.68 5.19
4714 6847 3.816367 GAGCCCGGCCTATCTGCAC 62.816 68.421 5.55 0.00 0.00 4.57
4716 6849 3.164269 CCCGGCCTATCTGCACCT 61.164 66.667 0.00 0.00 0.00 4.00
4727 6860 5.278758 GCCTATCTGCACCTAGTTAAGAGAG 60.279 48.000 0.00 0.00 0.00 3.20
4729 6862 6.719370 CCTATCTGCACCTAGTTAAGAGAGAT 59.281 42.308 0.00 0.00 29.68 2.75
4801 6934 0.327924 TGGAGGATGATTTGGTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
4803 6936 1.453155 GAGGATGATTTGGTGCGTGT 58.547 50.000 0.00 0.00 0.00 4.49
4804 6937 1.131126 GAGGATGATTTGGTGCGTGTG 59.869 52.381 0.00 0.00 0.00 3.82
4817 6950 1.569493 CGTGTGGTCCGCTTCAAAG 59.431 57.895 3.62 0.00 0.00 2.77
4824 6957 1.230324 GTCCGCTTCAAAGTTCAGCT 58.770 50.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.045955 GCTCCAACTCTGAAGGATAGTTTAG 58.954 44.000 0.00 0.00 31.21 1.85
1 2 5.721960 AGCTCCAACTCTGAAGGATAGTTTA 59.278 40.000 0.00 0.00 31.21 2.01
37 38 1.416401 CCACACTAAGACACCCACACT 59.584 52.381 0.00 0.00 0.00 3.55
121 147 1.738099 CAAGCGACCCCGACTTCAG 60.738 63.158 0.00 0.00 38.22 3.02
122 148 2.342279 CAAGCGACCCCGACTTCA 59.658 61.111 0.00 0.00 38.22 3.02
326 352 2.767960 CAAAAGCTTAGCCCCATCCATT 59.232 45.455 0.00 0.00 0.00 3.16
372 398 3.551846 TCACTACATACTCGATGGCAGA 58.448 45.455 0.00 0.00 40.18 4.26
374 400 4.937201 AATCACTACATACTCGATGGCA 57.063 40.909 0.00 0.00 40.18 4.92
396 422 2.224606 CATCAAGTCACTGGTGCAAGT 58.775 47.619 0.00 0.00 0.00 3.16
440 466 3.894638 CATAGCTGGGGGCCTGGG 61.895 72.222 0.84 0.00 43.05 4.45
441 467 4.593125 GCATAGCTGGGGGCCTGG 62.593 72.222 0.84 0.00 43.05 4.45
442 468 2.651841 AATGCATAGCTGGGGGCCTG 62.652 60.000 0.84 0.00 43.05 4.85
443 469 1.953100 AAATGCATAGCTGGGGGCCT 61.953 55.000 0.84 0.00 43.05 5.19
444 470 1.458209 AAATGCATAGCTGGGGGCC 60.458 57.895 0.00 0.00 43.05 5.80
445 471 0.468771 AGAAATGCATAGCTGGGGGC 60.469 55.000 0.00 0.00 42.19 5.80
446 472 1.325355 CAGAAATGCATAGCTGGGGG 58.675 55.000 16.85 0.00 0.00 5.40
447 473 2.062971 ACAGAAATGCATAGCTGGGG 57.937 50.000 24.26 7.84 32.82 4.96
465 491 6.897259 GAAAAAGTTTTCAAGGTTGGGTAC 57.103 37.500 10.87 0.00 44.48 3.34
522 553 0.036388 TGTCAGCCGATCCAAAGACC 60.036 55.000 0.00 0.00 0.00 3.85
588 2561 4.074970 AGATAGTTTTGACAACTGGGCTG 58.925 43.478 0.00 0.00 0.00 4.85
589 2562 4.373156 AGATAGTTTTGACAACTGGGCT 57.627 40.909 0.00 0.00 0.00 5.19
605 2578 6.118170 TCTGCATTTCTTTCCTGGAAGATAG 58.882 40.000 9.42 4.81 35.70 2.08
613 2586 5.188434 TGGACTATCTGCATTTCTTTCCTG 58.812 41.667 0.00 0.00 0.00 3.86
615 2588 4.578105 CCTGGACTATCTGCATTTCTTTCC 59.422 45.833 0.00 0.00 0.00 3.13
626 2605 0.911769 TTGTGGGCCTGGACTATCTG 59.088 55.000 4.53 0.00 0.00 2.90
745 2726 2.107901 GGATTGGGAGATGCTTCCAGAT 59.892 50.000 0.00 0.00 40.69 2.90
746 2727 1.492176 GGATTGGGAGATGCTTCCAGA 59.508 52.381 0.00 0.00 40.69 3.86
747 2728 1.213678 TGGATTGGGAGATGCTTCCAG 59.786 52.381 0.00 0.00 40.69 3.86
748 2729 1.297968 TGGATTGGGAGATGCTTCCA 58.702 50.000 0.00 0.00 37.36 3.53
749 2730 2.027385 GTTGGATTGGGAGATGCTTCC 58.973 52.381 0.00 0.00 36.46 3.46
834 2815 0.250727 TGGCTTCTTATATGGCGGGC 60.251 55.000 0.00 0.00 0.00 6.13
835 2816 1.880027 GTTGGCTTCTTATATGGCGGG 59.120 52.381 0.00 0.00 0.00 6.13
836 2817 1.531149 CGTTGGCTTCTTATATGGCGG 59.469 52.381 0.00 0.00 0.00 6.13
837 2818 2.479837 TCGTTGGCTTCTTATATGGCG 58.520 47.619 0.00 0.00 0.00 5.69
953 2934 1.210478 GGCTCTCTAGGTGGAATGCAA 59.790 52.381 0.00 0.00 0.00 4.08
954 2935 0.833287 GGCTCTCTAGGTGGAATGCA 59.167 55.000 0.00 0.00 0.00 3.96
955 2936 1.127343 AGGCTCTCTAGGTGGAATGC 58.873 55.000 0.00 0.00 0.00 3.56
1238 3234 3.746949 GATGCAGAGGGGACAGCCG 62.747 68.421 0.00 0.00 33.83 5.52
1239 3235 2.191641 GATGCAGAGGGGACAGCC 59.808 66.667 0.00 0.00 0.00 4.85
1240 3236 1.153208 CAGATGCAGAGGGGACAGC 60.153 63.158 0.00 0.00 0.00 4.40
1241 3237 1.070445 GATCAGATGCAGAGGGGACAG 59.930 57.143 0.00 0.00 0.00 3.51
1242 3238 1.126488 GATCAGATGCAGAGGGGACA 58.874 55.000 0.00 0.00 0.00 4.02
1271 3267 0.602638 TGGGTCTGATGTTGCGTGAC 60.603 55.000 0.00 0.00 0.00 3.67
1285 3281 5.230942 CGGTTATCATCTATCTGTTGGGTC 58.769 45.833 0.00 0.00 0.00 4.46
1298 3294 5.236478 ACATTCGTTCATTCCGGTTATCATC 59.764 40.000 0.00 0.00 0.00 2.92
1299 3295 5.123227 ACATTCGTTCATTCCGGTTATCAT 58.877 37.500 0.00 0.00 0.00 2.45
1300 3296 4.509616 ACATTCGTTCATTCCGGTTATCA 58.490 39.130 0.00 0.00 0.00 2.15
1301 3297 5.163794 ACAACATTCGTTCATTCCGGTTATC 60.164 40.000 0.00 0.00 31.13 1.75
1362 3358 1.716172 GGCTCGAATCGAACTTGGC 59.284 57.895 6.84 6.04 34.74 4.52
1631 3627 0.460284 CCCATTTCTGACCCTCGACG 60.460 60.000 0.00 0.00 0.00 5.12
1667 3663 2.982470 CAACGTACCAGTAACTTCGTCC 59.018 50.000 0.00 0.00 0.00 4.79
1695 3691 4.841443 AATTTGGTCGAAACCCAGTTAC 57.159 40.909 0.00 0.00 45.83 2.50
1728 3736 4.883585 AGCAGAACACAAGTCAGAATCAAA 59.116 37.500 0.00 0.00 0.00 2.69
1729 3737 4.454678 AGCAGAACACAAGTCAGAATCAA 58.545 39.130 0.00 0.00 0.00 2.57
1738 3746 3.821033 GGGATGTTTAGCAGAACACAAGT 59.179 43.478 7.01 0.00 41.86 3.16
1739 3747 3.820467 TGGGATGTTTAGCAGAACACAAG 59.180 43.478 7.01 0.00 41.86 3.16
1760 3768 5.597813 AGCTAATTTCAGACGACAGTTTG 57.402 39.130 0.00 0.00 34.16 2.93
1814 3822 5.338300 GCAACCCAAAATCATTAGGTTCCAT 60.338 40.000 0.00 0.00 38.76 3.41
1817 3827 4.503910 GGCAACCCAAAATCATTAGGTTC 58.496 43.478 0.00 0.00 38.76 3.62
1863 3873 3.546724 TCAGTTCACCATTTCGTTGGAA 58.453 40.909 8.44 0.00 39.25 3.53
1865 3875 3.253188 ACATCAGTTCACCATTTCGTTGG 59.747 43.478 1.17 1.17 42.82 3.77
1866 3876 4.488126 ACATCAGTTCACCATTTCGTTG 57.512 40.909 0.00 0.00 0.00 4.10
1898 3909 5.282055 AGAGCAGATCGATAACCATTTCA 57.718 39.130 0.00 0.00 0.00 2.69
1984 3995 0.595588 CCGATCCATCCTCGAGTCTG 59.404 60.000 12.31 8.02 38.38 3.51
1990 4001 1.008424 CACGACCGATCCATCCTCG 60.008 63.158 0.00 0.00 35.92 4.63
2002 4013 0.038159 CCTCTGACTTGGACACGACC 60.038 60.000 0.00 0.00 0.00 4.79
2120 4134 9.871175 AAGTAACCTGTAATTTTAAAGGGAGAA 57.129 29.630 10.60 0.00 41.62 2.87
2171 4185 1.089920 CGCCCTTCTTCATGGTCTTG 58.910 55.000 0.00 0.00 0.00 3.02
2248 4262 2.863809 ACTTTTGGAGTACAGCAAGGG 58.136 47.619 0.00 0.00 36.65 3.95
2249 4263 4.580580 AGAAACTTTTGGAGTACAGCAAGG 59.419 41.667 0.00 0.00 37.72 3.61
2250 4264 5.296780 TCAGAAACTTTTGGAGTACAGCAAG 59.703 40.000 0.00 0.00 37.72 4.01
2270 4295 7.994911 ACATATCAATTTATGAAGCCAGTCAGA 59.005 33.333 4.50 0.00 42.54 3.27
2271 4296 8.074370 CACATATCAATTTATGAAGCCAGTCAG 58.926 37.037 4.50 0.00 42.54 3.51
2272 4297 7.469043 GCACATATCAATTTATGAAGCCAGTCA 60.469 37.037 4.50 0.00 42.54 3.41
2273 4298 6.860023 GCACATATCAATTTATGAAGCCAGTC 59.140 38.462 4.50 0.00 42.54 3.51
2274 4299 6.548622 AGCACATATCAATTTATGAAGCCAGT 59.451 34.615 4.50 0.00 42.54 4.00
2275 4300 6.861572 CAGCACATATCAATTTATGAAGCCAG 59.138 38.462 4.50 1.91 42.54 4.85
2276 4301 6.736519 GCAGCACATATCAATTTATGAAGCCA 60.737 38.462 4.50 0.00 42.54 4.75
2277 4302 5.632347 GCAGCACATATCAATTTATGAAGCC 59.368 40.000 4.50 0.00 42.54 4.35
2278 4303 6.210796 TGCAGCACATATCAATTTATGAAGC 58.789 36.000 4.50 7.37 42.54 3.86
2279 4304 8.297426 AGATGCAGCACATATCAATTTATGAAG 58.703 33.333 4.07 0.00 39.58 3.02
2280 4305 8.173542 AGATGCAGCACATATCAATTTATGAA 57.826 30.769 4.07 0.00 39.58 2.57
2297 4322 1.863454 CTGTCCGTCATAAGATGCAGC 59.137 52.381 0.00 0.00 0.00 5.25
2311 4336 0.953471 TCGCCAAAACCATCTGTCCG 60.953 55.000 0.00 0.00 0.00 4.79
2388 4413 5.000591 CAGGAGACTAGCTCAAGATCGATA 58.999 45.833 0.00 0.00 45.81 2.92
2524 4549 5.508489 GGTTATGCATGCATGAATTAGCAGT 60.508 40.000 37.43 14.58 44.94 4.40
2533 4558 1.941975 CACGAGGTTATGCATGCATGA 59.058 47.619 37.43 29.35 37.82 3.07
2540 4565 4.517075 TGACAATTTTCACGAGGTTATGCA 59.483 37.500 0.00 0.00 0.00 3.96
2541 4566 5.041951 TGACAATTTTCACGAGGTTATGC 57.958 39.130 0.00 0.00 0.00 3.14
2542 4567 6.073276 TGTCTGACAATTTTCACGAGGTTATG 60.073 38.462 8.27 0.00 0.00 1.90
2543 4568 5.995282 TGTCTGACAATTTTCACGAGGTTAT 59.005 36.000 8.27 0.00 0.00 1.89
2544 4569 5.361427 TGTCTGACAATTTTCACGAGGTTA 58.639 37.500 8.27 0.00 0.00 2.85
2580 4623 3.548818 CCTCACTGCAAGCAACAAGTAAC 60.549 47.826 0.00 0.00 37.60 2.50
2587 4630 1.168407 TCAGCCTCACTGCAAGCAAC 61.168 55.000 0.00 0.00 46.76 4.17
2602 4645 1.796796 GTCCAACTTGCCGATCAGC 59.203 57.895 0.00 0.00 0.00 4.26
2676 4719 2.022240 GACCTGCTCCTCATCCGTCC 62.022 65.000 0.00 0.00 0.00 4.79
2860 4903 3.764237 ACCACCACAGTTAGTACCTTG 57.236 47.619 0.00 0.00 0.00 3.61
2865 4908 6.098695 AGACAAAGTAACCACCACAGTTAGTA 59.901 38.462 0.00 0.00 33.28 1.82
2866 4909 5.104652 AGACAAAGTAACCACCACAGTTAGT 60.105 40.000 0.00 0.00 35.37 2.24
2867 4910 5.236478 CAGACAAAGTAACCACCACAGTTAG 59.764 44.000 0.00 0.00 30.59 2.34
2908 4951 1.131504 GACAGCAGTAGAGACGGTCAG 59.868 57.143 11.27 0.00 0.00 3.51
2909 4952 1.166129 GACAGCAGTAGAGACGGTCA 58.834 55.000 11.27 0.00 0.00 4.02
2910 4953 1.131504 CTGACAGCAGTAGAGACGGTC 59.868 57.143 0.00 0.00 37.37 4.79
2911 4954 1.169577 CTGACAGCAGTAGAGACGGT 58.830 55.000 0.00 0.00 37.37 4.83
2912 4955 1.454201 TCTGACAGCAGTAGAGACGG 58.546 55.000 0.00 0.00 42.84 4.79
2913 4956 3.057876 ACTTTCTGACAGCAGTAGAGACG 60.058 47.826 0.00 0.00 42.84 4.18
2914 4957 4.022762 TCACTTTCTGACAGCAGTAGAGAC 60.023 45.833 0.00 0.00 42.84 3.36
2915 4958 4.145052 TCACTTTCTGACAGCAGTAGAGA 58.855 43.478 0.00 0.00 42.84 3.10
2920 4963 2.205074 CGTTCACTTTCTGACAGCAGT 58.795 47.619 0.00 0.00 42.84 4.40
2945 4988 4.659111 TCTCCTGAAACAGTAACACGAA 57.341 40.909 0.00 0.00 0.00 3.85
2953 4996 5.767168 CCAAGATTCTTTCTCCTGAAACAGT 59.233 40.000 0.00 0.00 37.27 3.55
3094 5145 1.965414 TGAGAGACCCATGCCCTTTA 58.035 50.000 0.00 0.00 0.00 1.85
3095 5146 1.075601 TTGAGAGACCCATGCCCTTT 58.924 50.000 0.00 0.00 0.00 3.11
3096 5147 0.329596 GTTGAGAGACCCATGCCCTT 59.670 55.000 0.00 0.00 0.00 3.95
3098 5149 1.204146 TAGTTGAGAGACCCATGCCC 58.796 55.000 0.00 0.00 0.00 5.36
3100 5151 4.327680 ACTTTTAGTTGAGAGACCCATGC 58.672 43.478 0.00 0.00 0.00 4.06
3104 5155 4.022155 ACGAGACTTTTAGTTGAGAGACCC 60.022 45.833 0.00 0.00 0.00 4.46
3105 5156 5.123805 ACGAGACTTTTAGTTGAGAGACC 57.876 43.478 0.00 0.00 0.00 3.85
3110 5161 4.681942 CACAGGACGAGACTTTTAGTTGAG 59.318 45.833 0.00 0.00 0.00 3.02
3117 5168 4.201783 CGTTTTTCACAGGACGAGACTTTT 60.202 41.667 0.00 0.00 37.69 2.27
3125 5176 4.718858 TCAATACGTTTTTCACAGGACG 57.281 40.909 0.00 0.00 41.00 4.79
3162 5214 4.946445 AGATGCACATCTATGTCAGTCAG 58.054 43.478 11.40 0.00 45.69 3.51
3166 5218 5.816258 AGACAAAGATGCACATCTATGTCAG 59.184 40.000 13.32 3.74 46.75 3.51
3167 5219 5.737860 AGACAAAGATGCACATCTATGTCA 58.262 37.500 13.32 0.00 46.75 3.58
3168 5220 6.093219 ACAAGACAAAGATGCACATCTATGTC 59.907 38.462 13.32 12.19 46.75 3.06
3169 5221 5.942236 ACAAGACAAAGATGCACATCTATGT 59.058 36.000 13.32 9.06 46.75 2.29
3170 5222 6.432607 ACAAGACAAAGATGCACATCTATG 57.567 37.500 13.32 8.55 46.75 2.23
3174 5226 3.755378 AGGACAAGACAAAGATGCACATC 59.245 43.478 2.28 2.28 38.09 3.06
3176 5228 3.213206 AGGACAAGACAAAGATGCACA 57.787 42.857 0.00 0.00 0.00 4.57
3177 5229 3.304928 CCAAGGACAAGACAAAGATGCAC 60.305 47.826 0.00 0.00 0.00 4.57
3178 5230 2.886523 CCAAGGACAAGACAAAGATGCA 59.113 45.455 0.00 0.00 0.00 3.96
3179 5231 2.229784 CCCAAGGACAAGACAAAGATGC 59.770 50.000 0.00 0.00 0.00 3.91
3180 5232 3.754965 TCCCAAGGACAAGACAAAGATG 58.245 45.455 0.00 0.00 0.00 2.90
3181 5233 4.145052 GTTCCCAAGGACAAGACAAAGAT 58.855 43.478 0.00 0.00 0.00 2.40
3182 5234 3.053991 TGTTCCCAAGGACAAGACAAAGA 60.054 43.478 0.00 0.00 0.00 2.52
3183 5235 3.287222 TGTTCCCAAGGACAAGACAAAG 58.713 45.455 0.00 0.00 0.00 2.77
3184 5236 3.287222 CTGTTCCCAAGGACAAGACAAA 58.713 45.455 0.00 0.00 0.00 2.83
3185 5237 2.422803 CCTGTTCCCAAGGACAAGACAA 60.423 50.000 0.00 0.00 0.00 3.18
3186 5238 1.142870 CCTGTTCCCAAGGACAAGACA 59.857 52.381 0.00 0.00 0.00 3.41
3187 5239 1.897560 CCTGTTCCCAAGGACAAGAC 58.102 55.000 0.00 0.00 0.00 3.01
3188 5240 0.110486 GCCTGTTCCCAAGGACAAGA 59.890 55.000 0.00 0.00 0.00 3.02
3189 5241 0.111253 AGCCTGTTCCCAAGGACAAG 59.889 55.000 0.00 0.00 0.00 3.16
3190 5242 0.178992 CAGCCTGTTCCCAAGGACAA 60.179 55.000 0.00 0.00 0.00 3.18
3191 5243 1.455849 CAGCCTGTTCCCAAGGACA 59.544 57.895 0.00 0.00 0.00 4.02
3192 5244 1.973812 GCAGCCTGTTCCCAAGGAC 60.974 63.158 0.00 0.00 0.00 3.85
3198 5250 1.019805 GTACTTCGCAGCCTGTTCCC 61.020 60.000 0.00 0.00 0.00 3.97
3211 5263 4.734917 AGCTGTCGTACTCAATGTACTTC 58.265 43.478 0.00 0.00 46.89 3.01
3226 5278 1.515952 CTCGCTGAAGGAGCTGTCG 60.516 63.158 0.00 0.00 46.64 4.35
3307 5359 6.743575 TCTTTGTAATCCTTTAGCTTCAGC 57.256 37.500 0.00 0.00 42.49 4.26
3313 5365 6.595716 TCTCTGCTTCTTTGTAATCCTTTAGC 59.404 38.462 0.00 0.00 0.00 3.09
3316 5368 6.072230 GCTTCTCTGCTTCTTTGTAATCCTTT 60.072 38.462 0.00 0.00 0.00 3.11
3340 5392 1.160137 CACTAACCTTGGTGCAGAGC 58.840 55.000 8.19 0.00 32.93 4.09
3355 5407 4.393062 CCTCGTACTCGAAAGGTAACACTA 59.607 45.833 0.00 0.00 45.61 2.74
3361 5413 2.496899 ACCCTCGTACTCGAAAGGTA 57.503 50.000 9.26 0.00 45.03 3.08
3362 5414 3.353342 ACCCTCGTACTCGAAAGGT 57.647 52.632 6.29 6.29 45.61 3.50
3363 5415 2.029649 TGAAACCCTCGTACTCGAAAGG 60.030 50.000 0.00 0.00 45.61 3.11
3364 5416 3.293311 TGAAACCCTCGTACTCGAAAG 57.707 47.619 0.00 0.00 45.61 2.62
3367 5419 2.422479 CTGATGAAACCCTCGTACTCGA 59.578 50.000 0.00 0.00 44.12 4.04
3368 5420 2.163815 ACTGATGAAACCCTCGTACTCG 59.836 50.000 0.00 0.00 38.55 4.18
3369 5421 3.512680 CACTGATGAAACCCTCGTACTC 58.487 50.000 0.00 0.00 0.00 2.59
3371 5423 2.000447 GCACTGATGAAACCCTCGTAC 59.000 52.381 0.00 0.00 0.00 3.67
3372 5424 1.621317 TGCACTGATGAAACCCTCGTA 59.379 47.619 0.00 0.00 0.00 3.43
3373 5425 0.396435 TGCACTGATGAAACCCTCGT 59.604 50.000 0.00 0.00 0.00 4.18
3374 5426 1.197721 GTTGCACTGATGAAACCCTCG 59.802 52.381 0.00 0.00 38.32 4.63
3375 5427 2.997485 GTTGCACTGATGAAACCCTC 57.003 50.000 0.00 0.00 38.32 4.30
3379 5431 4.241590 TGATTGGTTGCACTGATGAAAC 57.758 40.909 0.00 0.00 43.02 2.78
3381 5433 3.635836 TGTTGATTGGTTGCACTGATGAA 59.364 39.130 0.00 0.00 0.00 2.57
3383 5435 3.646611 TGTTGATTGGTTGCACTGATG 57.353 42.857 0.00 0.00 0.00 3.07
3384 5436 3.384146 TGTTGTTGATTGGTTGCACTGAT 59.616 39.130 0.00 0.00 0.00 2.90
3385 5437 2.757314 TGTTGTTGATTGGTTGCACTGA 59.243 40.909 0.00 0.00 0.00 3.41
3386 5438 2.859538 GTGTTGTTGATTGGTTGCACTG 59.140 45.455 0.00 0.00 0.00 3.66
3388 5440 2.602660 GTGTGTTGTTGATTGGTTGCAC 59.397 45.455 0.00 0.00 0.00 4.57
3389 5441 2.417924 GGTGTGTTGTTGATTGGTTGCA 60.418 45.455 0.00 0.00 0.00 4.08
3392 5444 2.828520 TGTGGTGTGTTGTTGATTGGTT 59.171 40.909 0.00 0.00 0.00 3.67
3394 5446 3.067883 TCATGTGGTGTGTTGTTGATTGG 59.932 43.478 0.00 0.00 0.00 3.16
3397 5449 3.507233 GGATCATGTGGTGTGTTGTTGAT 59.493 43.478 0.00 0.00 0.00 2.57
3399 5451 2.886523 AGGATCATGTGGTGTGTTGTTG 59.113 45.455 0.00 0.00 0.00 3.33
3400 5452 3.228188 AGGATCATGTGGTGTGTTGTT 57.772 42.857 0.00 0.00 0.00 2.83
3402 5454 3.935203 GTCTAGGATCATGTGGTGTGTTG 59.065 47.826 0.00 0.00 0.00 3.33
3403 5455 3.368427 CGTCTAGGATCATGTGGTGTGTT 60.368 47.826 0.00 0.00 0.00 3.32
3404 5456 2.166459 CGTCTAGGATCATGTGGTGTGT 59.834 50.000 0.00 0.00 0.00 3.72
3405 5457 2.481969 CCGTCTAGGATCATGTGGTGTG 60.482 54.545 0.00 0.00 45.00 3.82
3406 5458 1.757118 CCGTCTAGGATCATGTGGTGT 59.243 52.381 0.00 0.00 45.00 4.16
3409 5461 1.069204 CCACCGTCTAGGATCATGTGG 59.931 57.143 0.14 0.14 45.00 4.17
3413 5465 1.722034 ATGCCACCGTCTAGGATCAT 58.278 50.000 0.00 0.00 45.00 2.45
3415 5467 3.963428 ATAATGCCACCGTCTAGGATC 57.037 47.619 0.00 0.00 45.00 3.36
3416 5468 3.646162 TCAATAATGCCACCGTCTAGGAT 59.354 43.478 0.00 0.00 45.00 3.24
3417 5469 3.035363 TCAATAATGCCACCGTCTAGGA 58.965 45.455 0.00 0.00 45.00 2.94
3422 5474 2.549754 CCTGATCAATAATGCCACCGTC 59.450 50.000 0.00 0.00 0.00 4.79
3451 5507 0.464036 TGACGTTTGTGCTCTCCAGT 59.536 50.000 0.00 0.00 0.00 4.00
3529 5585 4.526262 TCCAGAGCCTTCTTGATATCTAGC 59.474 45.833 9.07 0.00 0.00 3.42
3576 5632 0.179936 CCAGAGAGATGGAAGGTGCC 59.820 60.000 0.00 0.00 43.57 5.01
3601 5658 6.509656 TCGATACGATATTTGTAGCCTTGTT 58.490 36.000 0.00 0.00 0.00 2.83
3603 5660 7.582435 AATCGATACGATATTTGTAGCCTTG 57.418 36.000 0.00 0.00 46.30 3.61
3604 5661 7.870954 TGAAATCGATACGATATTTGTAGCCTT 59.129 33.333 0.00 0.00 46.30 4.35
3613 5670 8.063200 TCCATAGGTGAAATCGATACGATATT 57.937 34.615 0.00 4.68 46.30 1.28
3624 5683 6.240894 TCAGCCATAATCCATAGGTGAAATC 58.759 40.000 0.00 0.00 0.00 2.17
3631 5690 7.528996 TGAAAAATCAGCCATAATCCATAGG 57.471 36.000 0.00 0.00 0.00 2.57
3638 5697 8.851541 AACAAACATGAAAAATCAGCCATAAT 57.148 26.923 0.00 0.00 0.00 1.28
3640 5699 8.149647 AGAAACAAACATGAAAAATCAGCCATA 58.850 29.630 0.00 0.00 0.00 2.74
3641 5700 6.993902 AGAAACAAACATGAAAAATCAGCCAT 59.006 30.769 0.00 0.00 0.00 4.40
3652 5711 2.364970 CTGGGGCAGAAACAAACATGAA 59.635 45.455 0.00 0.00 32.44 2.57
3749 5810 2.752354 CCTCCATTTGGCGAACATGTTA 59.248 45.455 11.95 0.00 34.44 2.41
3858 5919 0.324368 ACTAGTGCATCCAGACCCGA 60.324 55.000 0.00 0.00 0.00 5.14
4108 6170 5.419542 TCGATCACTTCCAATGTCCTTTAG 58.580 41.667 0.00 0.00 0.00 1.85
4110 6172 4.286297 TCGATCACTTCCAATGTCCTTT 57.714 40.909 0.00 0.00 0.00 3.11
4134 6196 3.428870 CCACGTCAGATTCCGCAATATAC 59.571 47.826 0.00 0.00 0.00 1.47
4135 6197 3.319689 TCCACGTCAGATTCCGCAATATA 59.680 43.478 0.00 0.00 0.00 0.86
4136 6198 2.102420 TCCACGTCAGATTCCGCAATAT 59.898 45.455 0.00 0.00 0.00 1.28
4137 6199 1.478916 TCCACGTCAGATTCCGCAATA 59.521 47.619 0.00 0.00 0.00 1.90
4148 6237 0.815734 ATTCGGGTACTCCACGTCAG 59.184 55.000 0.00 0.00 34.36 3.51
4157 6246 0.916086 TTCCCATGCATTCGGGTACT 59.084 50.000 19.03 0.00 43.57 2.73
4212 6306 4.943705 GGCTGAAATCATTGGTCAGACTAA 59.056 41.667 1.23 1.23 43.02 2.24
4233 6328 8.225603 TCTTCTGAATTTTACTATTGGATGGC 57.774 34.615 0.00 0.00 0.00 4.40
4254 6349 6.924111 TGGGAGTCATTTTTGCTTTATCTTC 58.076 36.000 0.00 0.00 0.00 2.87
4263 6358 8.947055 ATACATTTTATGGGAGTCATTTTTGC 57.053 30.769 0.00 0.00 37.30 3.68
4287 6382 8.883731 CCACGAGTAATTTGAAACAGAGATAAT 58.116 33.333 0.00 0.00 0.00 1.28
4291 6386 5.607477 ACCACGAGTAATTTGAAACAGAGA 58.393 37.500 0.00 0.00 0.00 3.10
4292 6387 5.924475 ACCACGAGTAATTTGAAACAGAG 57.076 39.130 0.00 0.00 0.00 3.35
4295 6390 7.987649 ACTAAAACCACGAGTAATTTGAAACA 58.012 30.769 0.00 0.00 0.00 2.83
4296 6391 8.845942 AACTAAAACCACGAGTAATTTGAAAC 57.154 30.769 0.00 0.00 0.00 2.78
4298 6393 8.211116 TGAACTAAAACCACGAGTAATTTGAA 57.789 30.769 0.00 0.00 0.00 2.69
4300 6395 8.844441 TTTGAACTAAAACCACGAGTAATTTG 57.156 30.769 0.00 0.00 0.00 2.32
4306 6401 9.857957 TTTTAAATTTGAACTAAAACCACGAGT 57.142 25.926 0.00 0.00 0.00 4.18
4318 6413 9.636965 GTACTTCGTACGTTTTAAATTTGAACT 57.363 29.630 16.05 0.32 29.20 3.01
4319 6414 9.419737 TGTACTTCGTACGTTTTAAATTTGAAC 57.580 29.630 16.05 5.22 41.41 3.18
4328 6423 7.380870 TGCACTTTATGTACTTCGTACGTTTTA 59.619 33.333 16.05 1.90 41.41 1.52
4329 6424 6.200665 TGCACTTTATGTACTTCGTACGTTTT 59.799 34.615 16.05 2.90 41.41 2.43
4330 6425 5.691305 TGCACTTTATGTACTTCGTACGTTT 59.309 36.000 16.05 3.27 41.41 3.60
4331 6426 5.221880 TGCACTTTATGTACTTCGTACGTT 58.778 37.500 16.05 3.64 41.41 3.99
4332 6427 4.797471 TGCACTTTATGTACTTCGTACGT 58.203 39.130 16.05 0.00 41.41 3.57
4333 6428 5.344128 AGTTGCACTTTATGTACTTCGTACG 59.656 40.000 9.53 9.53 41.41 3.67
4334 6429 6.145048 ACAGTTGCACTTTATGTACTTCGTAC 59.855 38.462 0.00 0.00 39.24 3.67
4335 6430 6.218019 ACAGTTGCACTTTATGTACTTCGTA 58.782 36.000 0.00 0.00 0.00 3.43
4337 6432 5.591643 ACAGTTGCACTTTATGTACTTCG 57.408 39.130 0.00 0.00 0.00 3.79
4339 6434 7.795482 TGTTACAGTTGCACTTTATGTACTT 57.205 32.000 0.00 0.00 0.00 2.24
4340 6435 7.444183 ACATGTTACAGTTGCACTTTATGTACT 59.556 33.333 0.00 0.00 0.00 2.73
4341 6436 7.581476 ACATGTTACAGTTGCACTTTATGTAC 58.419 34.615 0.00 0.00 0.00 2.90
4342 6437 7.737972 ACATGTTACAGTTGCACTTTATGTA 57.262 32.000 0.00 0.00 0.00 2.29
4343 6438 6.633500 ACATGTTACAGTTGCACTTTATGT 57.367 33.333 0.00 0.00 0.00 2.29
4344 6439 7.806690 AGTACATGTTACAGTTGCACTTTATG 58.193 34.615 2.30 0.00 0.00 1.90
4345 6440 7.119262 GGAGTACATGTTACAGTTGCACTTTAT 59.881 37.037 2.30 0.00 0.00 1.40
4346 6441 6.425721 GGAGTACATGTTACAGTTGCACTTTA 59.574 38.462 2.30 0.00 0.00 1.85
4357 6459 3.709653 GGATGGAGGGAGTACATGTTACA 59.290 47.826 2.30 0.00 0.00 2.41
4361 6463 1.414158 CGGATGGAGGGAGTACATGT 58.586 55.000 2.69 2.69 0.00 3.21
4374 6476 0.179189 GACAAAAGCTTCGCGGATGG 60.179 55.000 6.13 0.00 0.00 3.51
4381 6483 3.788434 TCGCTAAAGACAAAAGCTTCG 57.212 42.857 0.00 0.00 34.03 3.79
4385 6487 6.569228 AAAACTTTCGCTAAAGACAAAAGC 57.431 33.333 16.86 0.00 44.14 3.51
4397 6499 9.152595 TGTGGTTAAAATTTTAAAACTTTCGCT 57.847 25.926 21.81 0.00 34.71 4.93
4398 6500 9.923786 ATGTGGTTAAAATTTTAAAACTTTCGC 57.076 25.926 21.81 14.25 34.71 4.70
4642 6775 5.719085 ACTCTCTCTGTCCATGAATAAGTGT 59.281 40.000 0.00 0.00 0.00 3.55
4653 6786 3.441500 TTGCTCTACTCTCTCTGTCCA 57.558 47.619 0.00 0.00 0.00 4.02
4675 6808 8.146412 GGGCTCAGAAATGAATATTTGCTAAAT 58.854 33.333 0.00 0.00 36.66 1.40
4706 6839 9.815306 AATATCTCTCTTAACTAGGTGCAGATA 57.185 33.333 0.00 0.00 0.00 1.98
4775 6908 2.100252 CCAAATCATCCTCCATGCACAC 59.900 50.000 0.00 0.00 31.70 3.82
4789 6922 1.169661 GGACCACACGCACCAAATCA 61.170 55.000 0.00 0.00 0.00 2.57
4801 6934 1.305201 GAACTTTGAAGCGGACCACA 58.695 50.000 0.00 0.00 0.00 4.17
4803 6936 1.593196 CTGAACTTTGAAGCGGACCA 58.407 50.000 0.00 0.00 0.00 4.02
4804 6937 0.238553 GCTGAACTTTGAAGCGGACC 59.761 55.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.