Multiple sequence alignment - TraesCS5D01G095800

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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 TraesCS5D01G095800 chr5D 100.000 8105 0 0 1 8105 105341741 105349845 0.000000e+00 14968.0
1 TraesCS5D01G095800 chr5D 78.303 719 102 30 5194 5882 106808062 106807368 1.630000e-111 414.0
2 TraesCS5D01G095800 chr5D 80.760 421 59 15 6024 6440 106807306 106806904 7.900000e-80 309.0
3 TraesCS5D01G095800 chr5D 84.015 269 40 2 4867 5133 106808449 106808182 1.040000e-63 255.0
4 TraesCS5D01G095800 chr5D 92.000 50 2 2 3829 3877 105342902 105342950 1.460000e-07 69.4
5 TraesCS5D01G095800 chr5D 92.000 50 2 2 1162 1210 105345569 105345617 1.460000e-07 69.4
6 TraesCS5D01G095800 chr5B 93.563 4381 174 36 3227 7547 115314383 115318715 0.000000e+00 6429.0
7 TraesCS5D01G095800 chr5B 88.100 1832 139 42 16 1804 115309157 115310952 0.000000e+00 2102.0
8 TraesCS5D01G095800 chr5B 86.647 689 38 26 2525 3203 115313642 115314286 0.000000e+00 713.0
9 TraesCS5D01G095800 chr5B 88.296 581 34 9 7532 8105 115318734 115319287 0.000000e+00 665.0
10 TraesCS5D01G095800 chr5B 80.307 716 93 31 5188 5879 115349834 115350525 1.570000e-136 497.0
11 TraesCS5D01G095800 chr5B 80.348 402 57 14 6024 6421 115350590 115350973 1.330000e-72 285.0
12 TraesCS5D01G095800 chr5B 82.622 328 49 6 4807 5133 115349366 115349686 4.790000e-72 283.0
13 TraesCS5D01G095800 chr5B 90.226 133 7 3 1802 1928 115312055 115312187 1.400000e-37 169.0
14 TraesCS5D01G095800 chr5B 89.062 64 3 4 3829 3890 115310279 115310340 8.720000e-10 76.8
15 TraesCS5D01G095800 chr5B 91.837 49 4 0 1162 1210 115314986 115315034 1.460000e-07 69.4
16 TraesCS5D01G095800 chr5A 92.811 3283 144 36 3463 6696 109339199 109342438 0.000000e+00 4671.0
17 TraesCS5D01G095800 chr5A 94.965 1152 42 9 771 1911 109335408 109336554 0.000000e+00 1792.0
18 TraesCS5D01G095800 chr5A 95.249 842 39 1 6707 7547 109342594 109343435 0.000000e+00 1332.0
19 TraesCS5D01G095800 chr5A 93.362 693 32 8 2496 3184 109337958 109338640 0.000000e+00 1013.0
20 TraesCS5D01G095800 chr5A 91.001 689 48 6 108 787 109333435 109334118 0.000000e+00 917.0
21 TraesCS5D01G095800 chr5A 85.010 507 53 14 1973 2471 109336556 109337047 2.030000e-135 494.0
22 TraesCS5D01G095800 chr5A 80.247 648 83 29 5247 5871 109930677 109931302 5.770000e-121 446.0
23 TraesCS5D01G095800 chr5A 89.691 291 21 5 7532 7821 109343452 109343734 5.980000e-96 363.0
24 TraesCS5D01G095800 chr5A 95.631 206 8 1 7901 8105 109343766 109343971 6.060000e-86 329.0
25 TraesCS5D01G095800 chr5A 84.375 192 25 5 3182 3371 109339015 109339203 5.000000e-42 183.0
26 TraesCS5D01G095800 chr5A 92.000 50 2 2 3829 3877 109335798 109335846 1.460000e-07 69.4
27 TraesCS5D01G095800 chr5A 91.837 49 2 2 1162 1209 109339581 109339628 5.250000e-07 67.6
28 TraesCS5D01G095800 chr5A 97.368 38 1 0 7858 7895 109343736 109343773 1.890000e-06 65.8


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 TraesCS5D01G095800 chr5D 105341741 105349845 8104 False 14968.0 14968 100.000000 1 8105 1 chr5D.!!$F1 8104
1 TraesCS5D01G095800 chr5D 106806904 106808449 1545 True 326.0 414 81.026000 4867 6440 3 chr5D.!!$R1 1573
2 TraesCS5D01G095800 chr5B 115309157 115319287 10130 False 1460.6 6429 89.675857 16 8105 7 chr5B.!!$F1 8089
3 TraesCS5D01G095800 chr5B 115349366 115350973 1607 False 355.0 497 81.092333 4807 6421 3 chr5B.!!$F2 1614
4 TraesCS5D01G095800 chr5A 109333435 109343971 10536 False 941.4 4671 91.941667 108 8105 12 chr5A.!!$F2 7997
5 TraesCS5D01G095800 chr5A 109930677 109931302 625 False 446.0 446 80.247000 5247 5871 1 chr5A.!!$F1 624

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
268 269 0.107410 TGGTTCCATCATACGGTGCC 60.107 55.000 0.00 0.00 0.00 5.01 F
1778 3132 0.247185 AAATGAAATGCGTGCCCCTG 59.753 50.000 0.00 0.00 0.00 4.45 F
2322 5935 0.035439 AAGGTGGACAATGGCCTACG 60.035 55.000 6.71 0.00 0.00 3.51 F
2788 7291 0.320697 AAGTGGAGCCGTTGGAGTAC 59.679 55.000 0.00 0.00 0.00 2.73 F
4178 9160 1.227147 GCGGCGCTGGTCTGTATAA 60.227 57.895 26.86 0.00 0.00 0.98 F
5052 10058 1.001764 TGCCCTCAGTCATGCAAGG 60.002 57.895 0.00 0.00 0.00 3.61 F
5060 10066 1.538512 CAGTCATGCAAGGGACAACAG 59.461 52.381 15.92 3.06 36.50 3.16 F
6540 11679 0.249155 CAAGTGCAGTGGTTTGGCTG 60.249 55.000 0.00 0.00 35.93 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 5257 0.103937 AGAAGCATACCTCGCTGCTC 59.896 55.000 0.00 0.00 41.93 4.26 R
3414 8376 0.108804 TTTCCGGCGATCACTGTCTC 60.109 55.000 9.30 0.00 0.00 3.36 R
3607 8581 0.947180 GCGGTCGCTCCTTTGTTACA 60.947 55.000 8.20 0.00 38.26 2.41 R
4505 9497 0.250684 TCTGGTCCAAAATCAGCGCA 60.251 50.000 11.47 0.00 0.00 6.09 R
5388 10488 1.669779 GCAGTCCACAAGATGCTCATC 59.330 52.381 1.75 1.75 35.78 2.92 R
6295 11433 0.036294 GCACCAAGTAGTCCCTCCAC 60.036 60.000 0.00 0.00 0.00 4.02 R
6780 12068 1.228245 AAAGCATCACACCGCTGGT 60.228 52.632 0.00 0.00 38.82 4.00 R
7904 13239 0.103208 GCCTCAGTGTATCTCCCGTG 59.897 60.000 0.00 0.00 0.00 4.94 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
21 22 2.159462 CGTCGACAACCTAGTAACTCCC 60.159 54.545 17.16 0.00 0.00 4.30
26 27 3.113043 ACAACCTAGTAACTCCCCCATC 58.887 50.000 0.00 0.00 0.00 3.51
27 28 3.112263 CAACCTAGTAACTCCCCCATCA 58.888 50.000 0.00 0.00 0.00 3.07
31 32 2.176247 AGTAACTCCCCCATCATCGT 57.824 50.000 0.00 0.00 0.00 3.73
32 33 1.762957 AGTAACTCCCCCATCATCGTG 59.237 52.381 0.00 0.00 0.00 4.35
41 42 2.564771 CCCATCATCGTGTTGTAGCAT 58.435 47.619 0.00 0.00 0.00 3.79
43 44 2.219445 CCATCATCGTGTTGTAGCATCG 59.781 50.000 0.00 0.00 0.00 3.84
47 48 0.315886 TCGTGTTGTAGCATCGTGGT 59.684 50.000 0.00 0.00 0.00 4.16
49 50 1.917955 CGTGTTGTAGCATCGTGGTAG 59.082 52.381 0.00 0.00 30.19 3.18
63 64 2.038837 GGTAGCCGGTTCCAGCAAC 61.039 63.158 1.90 0.00 0.00 4.17
73 74 0.313672 TTCCAGCAACCAACGCAATC 59.686 50.000 0.00 0.00 0.00 2.67
79 80 1.072505 AACCAACGCAATCGGTCCT 59.927 52.632 0.00 0.00 40.69 3.85
81 82 0.108329 ACCAACGCAATCGGTCCTAG 60.108 55.000 0.00 0.00 40.69 3.02
82 83 1.429148 CCAACGCAATCGGTCCTAGC 61.429 60.000 0.00 0.00 40.69 3.42
95 96 2.290323 GGTCCTAGCAAACCATGTCACT 60.290 50.000 0.00 0.00 35.53 3.41
97 98 2.637382 TCCTAGCAAACCATGTCACTGA 59.363 45.455 0.00 0.00 0.00 3.41
132 133 2.742372 CTGCTCCCCAACGAACGG 60.742 66.667 0.00 0.00 0.00 4.44
264 265 1.931172 GTCGTTGGTTCCATCATACGG 59.069 52.381 11.94 0.00 0.00 4.02
268 269 0.107410 TGGTTCCATCATACGGTGCC 60.107 55.000 0.00 0.00 0.00 5.01
271 272 1.966901 TTCCATCATACGGTGCCGCT 61.967 55.000 10.87 1.06 44.19 5.52
288 289 1.514678 GCTGGTTGCAACATCACCGA 61.515 55.000 29.55 4.50 42.31 4.69
328 329 1.197721 CGACAGATGGTTCCAGCAAAC 59.802 52.381 9.74 0.00 0.00 2.93
348 349 1.071894 CGTCGCTCATGATAACTTGCG 60.072 52.381 16.13 16.13 43.95 4.85
399 400 1.313772 TAAAAGAAGCGCCACTTGCA 58.686 45.000 15.49 5.88 39.29 4.08
416 417 1.000052 TGCAGTCATTTGTGCACATGG 60.000 47.619 22.39 13.15 44.70 3.66
417 418 1.270274 GCAGTCATTTGTGCACATGGA 59.730 47.619 22.39 15.32 39.62 3.41
458 459 7.889469 AGTTGATTGTATGTTTCTTTCAGCAT 58.111 30.769 0.00 0.00 0.00 3.79
478 479 5.435557 GCATGACTACAATATGCTTCGAAC 58.564 41.667 0.00 0.00 42.84 3.95
617 621 4.159879 ACTCTCTCCGTCCGAAAATGTAAT 59.840 41.667 0.00 0.00 0.00 1.89
618 622 5.080969 TCTCTCCGTCCGAAAATGTAATT 57.919 39.130 0.00 0.00 38.98 1.40
752 768 9.626045 ATGAAGAAAAAGAATAAAAACGCTAGG 57.374 29.630 0.00 0.00 0.00 3.02
826 2148 2.814336 CAGGCTACCAGTTTTTGTCCTC 59.186 50.000 0.00 0.00 0.00 3.71
1221 2543 2.442056 GGTACGCATCCTCCCATCT 58.558 57.895 0.00 0.00 0.00 2.90
1236 2558 1.312815 CATCTCAAGAATTCCCCGGC 58.687 55.000 0.65 0.00 0.00 6.13
1386 2708 2.355363 TTCACGGCGTTCTCGGTG 60.355 61.111 11.19 0.00 37.56 4.94
1570 2892 2.094130 GGTAGAGTATATTCCTGGCGGC 60.094 54.545 0.00 0.00 0.00 6.53
1615 2939 3.834489 ATCTGTGGCGAAGATTCATCT 57.166 42.857 0.00 0.00 39.22 2.90
1773 3127 2.829928 CAAGCAAAATGAAATGCGTGC 58.170 42.857 1.12 0.00 46.98 5.34
1778 3132 0.247185 AAATGAAATGCGTGCCCCTG 59.753 50.000 0.00 0.00 0.00 4.45
1919 4387 1.227853 AAATATGAGGCGGGGCGAC 60.228 57.895 0.00 0.00 33.59 5.19
1959 5277 3.071580 GCAGCGAGGTATGCTTCTT 57.928 52.632 0.00 0.00 41.72 2.52
1960 5278 0.933796 GCAGCGAGGTATGCTTCTTC 59.066 55.000 0.00 0.00 41.72 2.87
1963 5281 1.410882 AGCGAGGTATGCTTCTTCTCC 59.589 52.381 0.00 0.00 40.48 3.71
1964 5282 1.539280 GCGAGGTATGCTTCTTCTCCC 60.539 57.143 0.00 0.00 0.00 4.30
1967 5285 2.774809 GAGGTATGCTTCTTCTCCCCTT 59.225 50.000 0.00 0.00 0.00 3.95
1968 5286 3.967987 GAGGTATGCTTCTTCTCCCCTTA 59.032 47.826 0.00 0.00 0.00 2.69
1969 5287 4.371681 AGGTATGCTTCTTCTCCCCTTAA 58.628 43.478 0.00 0.00 0.00 1.85
1970 5288 4.978388 AGGTATGCTTCTTCTCCCCTTAAT 59.022 41.667 0.00 0.00 0.00 1.40
1971 5289 5.072464 AGGTATGCTTCTTCTCCCCTTAATC 59.928 44.000 0.00 0.00 0.00 1.75
2008 5326 1.823169 TAGCCACGTCAACCCACCTC 61.823 60.000 0.00 0.00 0.00 3.85
2009 5327 2.357034 CCACGTCAACCCACCTCG 60.357 66.667 0.00 0.00 0.00 4.63
2010 5328 3.041940 CACGTCAACCCACCTCGC 61.042 66.667 0.00 0.00 0.00 5.03
2011 5329 4.309950 ACGTCAACCCACCTCGCC 62.310 66.667 0.00 0.00 0.00 5.54
2056 5383 2.436417 CCACGAACAATGAGGGTTGAT 58.564 47.619 0.00 0.00 33.37 2.57
2067 5394 2.213499 GAGGGTTGATGGCTATTGTCG 58.787 52.381 0.00 0.00 0.00 4.35
2076 5403 2.193306 GGCTATTGTCGCCAACATTG 57.807 50.000 0.00 0.00 46.77 2.82
2081 5408 3.361977 GTCGCCAACATTGCCGGT 61.362 61.111 1.90 0.00 0.00 5.28
2113 5442 1.762957 CATGACCATCCCTAAGTCCGT 59.237 52.381 0.00 0.00 0.00 4.69
2124 5453 2.385803 CTAAGTCCGTGGGTCATAGGT 58.614 52.381 0.00 0.00 0.00 3.08
2128 5457 2.027469 AGTCCGTGGGTCATAGGTTTTC 60.027 50.000 0.00 0.00 0.00 2.29
2146 5475 7.241628 AGGTTTTCCCTATCTGAAGACATTTT 58.758 34.615 0.00 0.00 43.87 1.82
2192 5801 7.681939 AAATTTAACGAGATAGGCAGTGAAA 57.318 32.000 0.00 0.00 0.00 2.69
2193 5802 7.865706 AATTTAACGAGATAGGCAGTGAAAT 57.134 32.000 0.00 0.00 31.05 2.17
2220 5829 4.465886 TCCTATCTCTTTCCCTTCTCTCG 58.534 47.826 0.00 0.00 0.00 4.04
2221 5830 3.572255 CCTATCTCTTTCCCTTCTCTCGG 59.428 52.174 0.00 0.00 0.00 4.63
2261 5870 3.118847 TCTCCGTGTAGATAGTCGACACT 60.119 47.826 19.50 15.46 46.33 3.55
2264 5873 3.487042 CCGTGTAGATAGTCGACACTTGG 60.487 52.174 19.50 8.67 46.33 3.61
2274 5883 5.424121 AGTCGACACTTGGAAAATGAAAG 57.576 39.130 19.50 0.00 0.00 2.62
2275 5884 4.275936 AGTCGACACTTGGAAAATGAAAGG 59.724 41.667 19.50 0.00 0.00 3.11
2280 5889 7.393234 TCGACACTTGGAAAATGAAAGGAATAT 59.607 33.333 0.00 0.00 0.00 1.28
2284 5893 9.362539 CACTTGGAAAATGAAAGGAATATGAAG 57.637 33.333 0.00 0.00 0.00 3.02
2312 5925 1.754226 GGAAAAGCAACAAGGTGGACA 59.246 47.619 0.00 0.00 0.00 4.02
2322 5935 0.035439 AAGGTGGACAATGGCCTACG 60.035 55.000 6.71 0.00 0.00 3.51
2325 5938 0.535335 GTGGACAATGGCCTACGAGA 59.465 55.000 6.71 0.00 0.00 4.04
2342 5955 3.499157 ACGAGAGTCAAGAGTGTCACTAC 59.501 47.826 5.21 0.15 44.19 2.73
2366 5979 2.033151 CCGAGTGTTTGAACCGAAGAAC 60.033 50.000 0.00 0.00 0.00 3.01
2374 5987 5.468746 TGTTTGAACCGAAGAACATAAGAGG 59.531 40.000 0.00 0.00 0.00 3.69
2398 6011 1.603678 GCGTCTCGGGTCAAACTAACA 60.604 52.381 0.00 0.00 0.00 2.41
2404 6017 1.944024 CGGGTCAAACTAACAAGTGCA 59.056 47.619 0.00 0.00 0.00 4.57
2438 6051 7.765695 ATGGTCTTTGTGAGATTTGTATTGT 57.234 32.000 0.00 0.00 36.61 2.71
2513 7012 1.998315 CACAGAGGCAGAAGTTGATCG 59.002 52.381 0.00 0.00 0.00 3.69
2788 7291 0.320697 AAGTGGAGCCGTTGGAGTAC 59.679 55.000 0.00 0.00 0.00 2.73
2797 7300 1.268896 CCGTTGGAGTACGCATACGAT 60.269 52.381 19.04 0.00 43.93 3.73
2798 7301 2.031769 CCGTTGGAGTACGCATACGATA 60.032 50.000 19.04 0.00 43.93 2.92
2799 7302 2.969306 CGTTGGAGTACGCATACGATAC 59.031 50.000 14.42 0.00 43.93 2.24
2800 7303 2.955607 TGGAGTACGCATACGATACG 57.044 50.000 0.00 0.00 43.93 3.06
2801 7304 2.482864 TGGAGTACGCATACGATACGA 58.517 47.619 0.00 0.00 43.93 3.43
2819 7322 2.009774 CGAGGATTACCCAAACAGCAG 58.990 52.381 0.00 0.00 37.41 4.24
2842 7345 7.368059 CAGCTGGATATGTACGTAAATAGACA 58.632 38.462 11.07 10.57 0.00 3.41
2963 7466 2.541907 AAGGTGTGCAGGCCAGGAT 61.542 57.895 5.01 0.00 0.00 3.24
2994 7497 8.394971 TGCTTTATGTGCTTATATAAGTGCAT 57.605 30.769 23.95 23.95 37.76 3.96
3011 7514 4.039730 AGTGCATCGTGGATCTTAAGCTAT 59.960 41.667 0.00 0.00 0.00 2.97
3047 7554 7.935338 CGGAGCGATTAATAACCTAAGTAAA 57.065 36.000 0.00 0.00 0.00 2.01
3054 7561 9.038803 CGATTAATAACCTAAGTAAACAGGGTC 57.961 37.037 0.00 0.00 36.15 4.46
3083 7590 1.227263 CGATGGATCCGTGTCACCC 60.227 63.158 12.38 0.00 0.00 4.61
3100 7607 2.092914 CACCCTCCTAAGTTGGACCATC 60.093 54.545 0.00 0.00 31.94 3.51
3107 7616 5.701224 TCCTAAGTTGGACCATCAAGTTTT 58.299 37.500 5.36 0.00 39.89 2.43
3108 7617 5.768164 TCCTAAGTTGGACCATCAAGTTTTC 59.232 40.000 5.36 0.00 39.89 2.29
3113 7622 7.839680 AGTTGGACCATCAAGTTTTCTTTAT 57.160 32.000 5.36 0.00 38.17 1.40
3145 7656 4.374689 TGGACCATTAAGTTGGCTGTAA 57.625 40.909 0.00 0.00 40.68 2.41
3146 7657 4.730966 TGGACCATTAAGTTGGCTGTAAA 58.269 39.130 0.00 0.00 40.68 2.01
3187 8075 6.645415 CGTGGTCTCAAGTTGAGTATTACTTT 59.355 38.462 27.83 0.00 44.58 2.66
3191 8079 9.274206 GGTCTCAAGTTGAGTATTACTTTCTTT 57.726 33.333 27.83 0.00 44.58 2.52
3209 8097 9.543783 ACTTTCTTTGTTCGAAATTACTCTAGT 57.456 29.630 0.00 0.00 30.75 2.57
3213 8101 8.975439 TCTTTGTTCGAAATTACTCTAGTTGTC 58.025 33.333 0.00 0.00 0.00 3.18
3215 8103 7.633361 TGTTCGAAATTACTCTAGTTGTCAC 57.367 36.000 0.00 0.00 0.00 3.67
3217 8105 7.594015 TGTTCGAAATTACTCTAGTTGTCACTC 59.406 37.037 0.00 0.00 34.06 3.51
3220 8108 6.466413 CGAAATTACTCTAGTTGTCACTCGAG 59.534 42.308 11.84 11.84 44.78 4.04
3221 8109 4.681835 TTACTCTAGTTGTCACTCGAGC 57.318 45.455 13.61 0.00 43.62 5.03
3224 8112 2.148768 TCTAGTTGTCACTCGAGCGAA 58.851 47.619 13.61 0.00 34.06 4.70
3230 8191 3.066369 TGTCACTCGAGCGAATGTATC 57.934 47.619 13.61 0.00 0.00 2.24
3306 8267 7.490657 TGTGGTTATAGTGAAGTGGAGTTAT 57.509 36.000 0.00 0.00 0.00 1.89
3364 8325 1.671979 CCCTACACTCACATGGCATG 58.328 55.000 25.31 25.31 0.00 4.06
3399 8361 2.300152 TCTTTCTCAACAGACGGCAGAT 59.700 45.455 0.00 0.00 0.00 2.90
3414 8376 2.159338 GGCAGATACACCAACAATGCAG 60.159 50.000 0.00 0.00 33.94 4.41
3421 8383 2.224606 CACCAACAATGCAGAGACAGT 58.775 47.619 0.00 0.00 0.00 3.55
3448 8410 4.615912 CGCCGGAAAGATCAGAACAAAAAT 60.616 41.667 5.05 0.00 0.00 1.82
3607 8581 4.410400 CCGGCCGCCTTCTCCTTT 62.410 66.667 22.85 0.00 0.00 3.11
4116 9098 1.808390 GTCCCGACATGGTGCGTAC 60.808 63.158 0.00 0.00 35.15 3.67
4162 9144 4.869215 AGACTCTCTGACATGATAATGCG 58.131 43.478 0.00 0.00 0.00 4.73
4163 9145 3.986572 GACTCTCTGACATGATAATGCGG 59.013 47.826 0.00 0.00 0.00 5.69
4178 9160 1.227147 GCGGCGCTGGTCTGTATAA 60.227 57.895 26.86 0.00 0.00 0.98
4258 9240 5.060427 TCATTCCCCTGAAAGAAGTTCAA 57.940 39.130 5.50 0.00 45.67 2.69
4347 9329 7.312657 TCGTAGTTGAGACGTTGATTATAGT 57.687 36.000 0.00 0.00 41.11 2.12
4371 9353 5.763698 TCAATTGATTTTCATTGGCTGCAAA 59.236 32.000 3.38 0.00 0.00 3.68
4372 9354 6.262496 TCAATTGATTTTCATTGGCTGCAAAA 59.738 30.769 3.38 0.00 0.00 2.44
4412 9395 6.707440 TTTGAATTGTGAGAAGTTTAGGCA 57.293 33.333 0.00 0.00 0.00 4.75
4418 9401 4.776349 TGTGAGAAGTTTAGGCACTTTGA 58.224 39.130 0.00 0.00 41.75 2.69
4427 9410 5.889289 AGTTTAGGCACTTTGACCTTGTTAA 59.111 36.000 0.00 0.00 41.75 2.01
4443 9426 8.383318 ACCTTGTTAATAAGATCATGGATTCG 57.617 34.615 13.07 0.00 0.00 3.34
4489 9481 1.768275 TCAGGGCTGAACTTCAGTTGA 59.232 47.619 18.16 15.72 45.94 3.18
4504 9496 7.440523 CTTCAGTTGAAGCCTAATTAGTTGT 57.559 36.000 11.50 0.00 44.10 3.32
4505 9497 7.817418 TTCAGTTGAAGCCTAATTAGTTGTT 57.183 32.000 11.50 1.88 0.00 2.83
4507 9499 5.858581 CAGTTGAAGCCTAATTAGTTGTTGC 59.141 40.000 11.50 7.08 0.00 4.17
4514 9506 4.438744 GCCTAATTAGTTGTTGCGCTGATT 60.439 41.667 9.73 0.00 0.00 2.57
4532 9524 4.079253 TGATTTTGGACCAGAACCTTAGC 58.921 43.478 0.00 0.00 0.00 3.09
4543 9535 3.373439 CAGAACCTTAGCTCTTGCATCAC 59.627 47.826 0.00 0.00 42.74 3.06
4559 9551 2.472695 TCACGTAGAGGCTTTGCATT 57.527 45.000 0.00 0.00 0.00 3.56
4566 9558 1.113788 GAGGCTTTGCATTATGGCCA 58.886 50.000 8.56 8.56 44.60 5.36
4574 9566 4.464069 TTGCATTATGGCCAAGTTTACC 57.536 40.909 10.96 0.00 0.00 2.85
4652 9644 2.576191 TGCCCTGTTTAGCTGGAGTAAT 59.424 45.455 0.00 0.00 38.33 1.89
4653 9645 2.945668 GCCCTGTTTAGCTGGAGTAATG 59.054 50.000 0.00 0.00 38.33 1.90
4658 9651 6.378280 CCCTGTTTAGCTGGAGTAATGAAAAT 59.622 38.462 0.00 0.00 38.33 1.82
4685 9678 8.325787 TCTCAACTAACCCAAATAGCTAATTCA 58.674 33.333 0.00 0.00 0.00 2.57
4698 9691 5.113502 AGCTAATTCAGTGAAGTGTTTGC 57.886 39.130 15.79 14.18 0.00 3.68
4832 9836 5.796935 CAGTAAACTCAACATGCTGCAATAC 59.203 40.000 6.36 0.00 0.00 1.89
4974 9980 7.913821 GCTTTCCAATAAACTATTTAGAACCCG 59.086 37.037 0.00 0.00 0.00 5.28
5052 10058 1.001764 TGCCCTCAGTCATGCAAGG 60.002 57.895 0.00 0.00 0.00 3.61
5060 10066 1.538512 CAGTCATGCAAGGGACAACAG 59.461 52.381 15.92 3.06 36.50 3.16
5140 10146 1.740585 GCACACAGGTACAACACACAA 59.259 47.619 0.00 0.00 0.00 3.33
5199 10298 3.931578 AGCAGTTGTTCATACCTCAGAC 58.068 45.455 0.00 0.00 0.00 3.51
5234 10333 2.751259 ACTTTCTGCACATAGGCACATG 59.249 45.455 0.00 0.00 39.25 3.21
5382 10482 7.890127 TCAATTTGGATCCTTTCAGTGTCTTAT 59.110 33.333 14.23 0.00 0.00 1.73
5383 10483 7.636150 ATTTGGATCCTTTCAGTGTCTTATG 57.364 36.000 14.23 0.00 0.00 1.90
5384 10484 6.373005 TTGGATCCTTTCAGTGTCTTATGA 57.627 37.500 14.23 0.00 0.00 2.15
5385 10485 5.734720 TGGATCCTTTCAGTGTCTTATGAC 58.265 41.667 14.23 1.85 43.20 3.06
5386 10486 5.485353 TGGATCCTTTCAGTGTCTTATGACT 59.515 40.000 14.23 0.00 43.29 3.41
5387 10487 6.013379 TGGATCCTTTCAGTGTCTTATGACTT 60.013 38.462 14.23 0.00 43.29 3.01
5388 10488 6.314896 GGATCCTTTCAGTGTCTTATGACTTG 59.685 42.308 3.84 8.35 43.29 3.16
5389 10489 6.419484 TCCTTTCAGTGTCTTATGACTTGA 57.581 37.500 9.87 10.17 43.29 3.02
5690 10807 4.730613 GCATATTCAGGTTTACAACAGGCG 60.731 45.833 0.00 0.00 0.00 5.52
6295 11433 3.076621 TGTTATCTTGCTTGCAGTCCAG 58.923 45.455 0.00 0.00 0.00 3.86
6472 11611 9.871238 TTTCTTGTACAGATACATCCTAGTTTC 57.129 33.333 0.00 0.00 41.02 2.78
6475 11614 5.601313 TGTACAGATACATCCTAGTTTCCCC 59.399 44.000 0.00 0.00 36.34 4.81
6477 11616 5.289510 ACAGATACATCCTAGTTTCCCCTT 58.710 41.667 0.00 0.00 0.00 3.95
6479 11618 6.058183 CAGATACATCCTAGTTTCCCCTTTG 58.942 44.000 0.00 0.00 0.00 2.77
6540 11679 0.249155 CAAGTGCAGTGGTTTGGCTG 60.249 55.000 0.00 0.00 35.93 4.85
6550 11689 0.608308 GGTTTGGCTGGTGGGTCTAC 60.608 60.000 0.00 0.00 0.00 2.59
6602 11742 9.818796 GAAAGTTCATATCTCAAAGTTTCAGAC 57.181 33.333 0.00 0.00 40.00 3.51
6650 11792 5.304614 AGATGCGGTCTACATACCTGTAAAT 59.695 40.000 0.00 0.00 37.41 1.40
6754 12041 5.888161 ACCTCGCCTTCAATGAAAAGATATT 59.112 36.000 0.00 0.00 0.00 1.28
6780 12068 7.497579 TGACGGCTGCTTCATCTTAAATAAATA 59.502 33.333 0.00 0.00 0.00 1.40
6791 12079 6.671614 TCTTAAATAAATACCAGCGGTGTG 57.328 37.500 14.40 7.66 36.19 3.82
6810 12098 5.697633 GGTGTGATGCTTTGATTTCATTTGT 59.302 36.000 0.00 0.00 0.00 2.83
6831 12120 4.950475 TGTTGTGGACCTTGTGTTAATGAA 59.050 37.500 0.00 0.00 0.00 2.57
6862 12151 8.614346 TGTATAATTTGGCACGTTCTATTTACC 58.386 33.333 0.00 0.00 0.00 2.85
6863 12152 5.968528 AATTTGGCACGTTCTATTTACCA 57.031 34.783 0.00 0.00 0.00 3.25
7027 12316 2.606308 GCAATGCTTATCTTGATGGCCG 60.606 50.000 0.00 0.00 0.00 6.13
7131 12420 1.621317 TCCTATTTCGGTGTGCAGACA 59.379 47.619 16.68 0.00 0.00 3.41
7183 12472 2.221169 CAGCATGTACAACCACACTGT 58.779 47.619 0.00 0.00 0.00 3.55
7194 12483 3.569194 ACCACACTGTTGTATTGACCA 57.431 42.857 0.00 0.00 33.30 4.02
7353 12642 0.449388 GAGAGTCGGCCTTGCATTTG 59.551 55.000 0.00 0.00 0.00 2.32
7388 12677 6.012745 ACTTTTCAATCTCCTGTTATTGCCT 58.987 36.000 0.00 0.00 33.91 4.75
7404 12693 3.319137 TGCCTATGACTGTGTCTTGTC 57.681 47.619 0.00 0.00 33.15 3.18
7485 12775 9.462174 TCAAACAAGTGATGATATTTTGTGTTC 57.538 29.630 0.00 0.00 32.75 3.18
7513 12803 7.993758 GGTAACCTATATCTTTCTCTGCCTTTT 59.006 37.037 0.00 0.00 0.00 2.27
7525 12815 3.620488 TCTGCCTTTTCATATGGGTCAC 58.380 45.455 2.13 0.00 0.00 3.67
7547 12837 4.576463 ACGATCCACCTGCAAAATAATCTC 59.424 41.667 0.00 0.00 0.00 2.75
7599 12925 3.304726 GCCCAAGTTCTAACTGAAACTGC 60.305 47.826 0.00 0.00 39.66 4.40
7600 12926 3.882888 CCCAAGTTCTAACTGAAACTGCA 59.117 43.478 0.00 0.00 39.66 4.41
7685 13020 1.188863 CCTGCCTTTCCATTTCCCAG 58.811 55.000 0.00 0.00 0.00 4.45
7686 13021 1.550869 CCTGCCTTTCCATTTCCCAGT 60.551 52.381 0.00 0.00 0.00 4.00
7687 13022 2.291540 CCTGCCTTTCCATTTCCCAGTA 60.292 50.000 0.00 0.00 0.00 2.74
7688 13023 3.019564 CTGCCTTTCCATTTCCCAGTAG 58.980 50.000 0.00 0.00 0.00 2.57
7689 13024 2.291540 TGCCTTTCCATTTCCCAGTAGG 60.292 50.000 0.00 0.00 0.00 3.18
7690 13025 2.379005 CCTTTCCATTTCCCAGTAGGC 58.621 52.381 0.00 0.00 34.51 3.93
7691 13026 2.291540 CCTTTCCATTTCCCAGTAGGCA 60.292 50.000 0.00 0.00 34.51 4.75
7743 13078 5.880332 ACAATACGCATAGTTGAAGGAACAT 59.120 36.000 0.00 0.00 36.98 2.71
7759 13094 7.812191 TGAAGGAACATAATAACATTGCAACAC 59.188 33.333 0.00 0.00 0.00 3.32
7768 13103 7.642071 AATAACATTGCAACACAGATGAAAC 57.358 32.000 0.00 0.00 0.00 2.78
7781 13116 5.180117 CACAGATGAAACTAAAGGAGTGGTG 59.820 44.000 0.00 0.00 38.87 4.17
7782 13117 5.163195 ACAGATGAAACTAAAGGAGTGGTGT 60.163 40.000 0.00 0.00 38.87 4.16
7787 13122 7.074653 TGAAACTAAAGGAGTGGTGTTAGAT 57.925 36.000 0.00 0.00 38.87 1.98
7788 13123 7.514721 TGAAACTAAAGGAGTGGTGTTAGATT 58.485 34.615 0.00 0.00 38.87 2.40
7831 13166 7.227512 ACCAGAAAATCAAGTGAAGTACTGAAG 59.772 37.037 0.00 0.00 40.26 3.02
7844 13179 5.840940 AGTACTGAAGCAAATGTACGTTC 57.159 39.130 0.00 0.00 39.87 3.95
7856 13191 5.718649 AATGTACGTTCAGATACATGCAC 57.281 39.130 0.00 0.00 40.36 4.57
7860 13195 2.860136 ACGTTCAGATACATGCACGATG 59.140 45.455 5.94 0.00 41.42 3.84
7899 13234 3.209266 TGGTACATCACACGCACTG 57.791 52.632 0.00 0.00 0.00 3.66
7900 13235 0.676736 TGGTACATCACACGCACTGA 59.323 50.000 0.00 0.00 0.00 3.41
7901 13236 1.275010 TGGTACATCACACGCACTGAT 59.725 47.619 0.00 0.00 0.00 2.90
7902 13237 1.927174 GGTACATCACACGCACTGATC 59.073 52.381 0.00 0.00 0.00 2.92
7903 13238 2.606108 GTACATCACACGCACTGATCA 58.394 47.619 0.00 0.00 0.00 2.92
7904 13239 1.432514 ACATCACACGCACTGATCAC 58.567 50.000 0.00 0.00 0.00 3.06
7905 13240 1.270252 ACATCACACGCACTGATCACA 60.270 47.619 0.00 0.00 0.00 3.58
7906 13241 1.127397 CATCACACGCACTGATCACAC 59.873 52.381 0.00 0.00 0.00 3.82
7907 13242 0.939106 TCACACGCACTGATCACACG 60.939 55.000 0.00 0.00 0.00 4.49
7921 13256 2.092323 TCACACGGGAGATACACTGAG 58.908 52.381 0.00 0.00 0.00 3.35
7944 13280 2.479566 AGATGGCTCACACGAACAAT 57.520 45.000 0.00 0.00 0.00 2.71
8049 13387 1.436336 GCAAATGCAGGCAGGCTAG 59.564 57.895 0.00 0.00 41.59 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.159462 GGGAGTTACTAGGTTGTCGACG 60.159 54.545 11.62 0.00 0.00 5.12
1 2 2.165234 GGGGAGTTACTAGGTTGTCGAC 59.835 54.545 9.11 9.11 0.00 4.20
2 3 2.450476 GGGGAGTTACTAGGTTGTCGA 58.550 52.381 0.00 0.00 0.00 4.20
3 4 1.479730 GGGGGAGTTACTAGGTTGTCG 59.520 57.143 0.00 0.00 0.00 4.35
4 5 2.543635 TGGGGGAGTTACTAGGTTGTC 58.456 52.381 0.00 0.00 0.00 3.18
5 6 2.727429 TGGGGGAGTTACTAGGTTGT 57.273 50.000 0.00 0.00 0.00 3.32
6 7 3.112263 TGATGGGGGAGTTACTAGGTTG 58.888 50.000 0.00 0.00 0.00 3.77
7 8 3.502051 TGATGGGGGAGTTACTAGGTT 57.498 47.619 0.00 0.00 0.00 3.50
8 9 3.588569 GATGATGGGGGAGTTACTAGGT 58.411 50.000 0.00 0.00 0.00 3.08
9 10 2.563179 CGATGATGGGGGAGTTACTAGG 59.437 54.545 0.00 0.00 0.00 3.02
10 11 3.005897 CACGATGATGGGGGAGTTACTAG 59.994 52.174 0.00 0.00 0.00 2.57
11 12 2.963101 CACGATGATGGGGGAGTTACTA 59.037 50.000 0.00 0.00 0.00 1.82
12 13 1.762957 CACGATGATGGGGGAGTTACT 59.237 52.381 0.00 0.00 0.00 2.24
13 14 1.485066 ACACGATGATGGGGGAGTTAC 59.515 52.381 0.00 0.00 0.00 2.50
14 15 1.874129 ACACGATGATGGGGGAGTTA 58.126 50.000 0.00 0.00 0.00 2.24
19 20 1.953559 CTACAACACGATGATGGGGG 58.046 55.000 0.00 0.00 0.00 5.40
21 22 2.022764 TGCTACAACACGATGATGGG 57.977 50.000 0.00 0.00 0.00 4.00
26 27 1.324435 CCACGATGCTACAACACGATG 59.676 52.381 0.00 0.00 0.00 3.84
27 28 1.067142 ACCACGATGCTACAACACGAT 60.067 47.619 0.00 0.00 0.00 3.73
31 32 1.404986 GGCTACCACGATGCTACAACA 60.405 52.381 0.00 0.00 0.00 3.33
32 33 1.287425 GGCTACCACGATGCTACAAC 58.713 55.000 0.00 0.00 0.00 3.32
41 42 2.601067 TGGAACCGGCTACCACGA 60.601 61.111 0.00 0.00 0.00 4.35
43 44 2.436115 GCTGGAACCGGCTACCAC 60.436 66.667 16.37 0.58 44.39 4.16
47 48 2.349755 GGTTGCTGGAACCGGCTA 59.650 61.111 22.64 14.32 45.00 3.93
63 64 1.429148 GCTAGGACCGATTGCGTTGG 61.429 60.000 0.00 0.00 37.40 3.77
66 67 0.036765 TTTGCTAGGACCGATTGCGT 60.037 50.000 0.00 0.00 35.23 5.24
73 74 1.338674 TGACATGGTTTGCTAGGACCG 60.339 52.381 0.00 0.00 38.81 4.79
79 80 4.009675 GGAATCAGTGACATGGTTTGCTA 58.990 43.478 0.00 0.00 0.00 3.49
81 82 2.557924 TGGAATCAGTGACATGGTTTGC 59.442 45.455 0.00 0.00 0.00 3.68
82 83 4.437794 CGATGGAATCAGTGACATGGTTTG 60.438 45.833 0.00 0.00 45.97 2.93
132 133 0.179037 TATGCTGGAGCTGATGGCAC 60.179 55.000 0.00 0.00 44.79 5.01
226 227 1.002087 GACATCGTCTGTTGGGAACCT 59.998 52.381 0.00 0.00 45.04 3.50
249 250 0.107410 GGCACCGTATGATGGAACCA 60.107 55.000 0.00 0.00 0.00 3.67
271 272 0.950836 CTTCGGTGATGTTGCAACCA 59.049 50.000 26.14 15.16 0.00 3.67
288 289 0.839946 ATGATGCTAGAACCGGCCTT 59.160 50.000 0.00 0.00 0.00 4.35
328 329 2.635141 GCAAGTTATCATGAGCGACG 57.365 50.000 0.09 0.00 0.00 5.12
348 349 3.531262 AAAACTGGTGCGTCGTATTTC 57.469 42.857 0.00 0.00 0.00 2.17
399 400 5.981088 TTAATCCATGTGCACAAATGACT 57.019 34.783 25.72 12.70 0.00 3.41
414 415 6.303054 TCAACTCTGGTGTCATTTTAATCCA 58.697 36.000 0.00 0.00 0.00 3.41
416 417 8.299570 ACAATCAACTCTGGTGTCATTTTAATC 58.700 33.333 0.00 0.00 0.00 1.75
417 418 8.181904 ACAATCAACTCTGGTGTCATTTTAAT 57.818 30.769 0.00 0.00 0.00 1.40
458 459 6.816140 TCATTGTTCGAAGCATATTGTAGTCA 59.184 34.615 0.00 0.00 0.00 3.41
631 644 7.095774 CGTCCGTCCTAAAATATAAGACCATTG 60.096 40.741 0.00 0.00 0.00 2.82
826 2148 5.342806 TGTGTTGCATAAGAAAAGACTCG 57.657 39.130 0.00 0.00 0.00 4.18
1125 2447 4.106925 GCCAGGCTGAGGAGGTGG 62.107 72.222 17.94 0.00 0.00 4.61
1221 2543 2.437716 GCGCCGGGGAATTCTTGA 60.438 61.111 24.68 0.00 0.00 3.02
1570 2892 0.248417 CAGCTCGAGATGTGTCGGAG 60.248 60.000 22.28 0.00 40.49 4.63
1578 2900 3.181488 ACAGATTCAGTCAGCTCGAGATG 60.181 47.826 24.40 24.40 0.00 2.90
1615 2939 2.229792 GCCAAATTCCACTGTCACTCA 58.770 47.619 0.00 0.00 0.00 3.41
1778 3132 3.051392 GCTACATTGGGCGTGGTGC 62.051 63.158 0.00 0.00 45.38 5.01
1780 3134 1.377202 CAGCTACATTGGGCGTGGT 60.377 57.895 0.00 0.00 0.00 4.16
1919 4387 1.798735 CTCAACAAGCGGCAGATGG 59.201 57.895 1.45 0.00 0.00 3.51
1939 5257 0.103937 AGAAGCATACCTCGCTGCTC 59.896 55.000 0.00 0.00 41.93 4.26
1941 5259 0.933796 GAAGAAGCATACCTCGCTGC 59.066 55.000 0.00 0.00 40.35 5.25
1953 5271 4.203226 CCAAGATTAAGGGGAGAAGAAGC 58.797 47.826 0.00 0.00 0.00 3.86
1963 5281 1.846439 TGGAGCTCCCAAGATTAAGGG 59.154 52.381 29.95 0.00 43.29 3.95
1987 5305 1.024579 GGTGGGTTGACGTGGCTATG 61.025 60.000 0.00 0.00 0.00 2.23
2081 5408 2.361104 GTCATGGGAAGGCGCCAA 60.361 61.111 31.54 8.85 0.00 4.52
2095 5422 1.191535 CACGGACTTAGGGATGGTCA 58.808 55.000 0.00 0.00 0.00 4.02
2166 5497 7.681939 TCACTGCCTATCTCGTTAAATTTTT 57.318 32.000 0.00 0.00 0.00 1.94
2168 5499 7.681939 TTTCACTGCCTATCTCGTTAAATTT 57.318 32.000 0.00 0.00 0.00 1.82
2182 5791 6.069731 AGAGATAGGAAAAGATTTCACTGCCT 60.070 38.462 5.32 0.00 0.00 4.75
2192 5801 7.627293 AGAGAAGGGAAAGAGATAGGAAAAGAT 59.373 37.037 0.00 0.00 0.00 2.40
2193 5802 6.962902 AGAGAAGGGAAAGAGATAGGAAAAGA 59.037 38.462 0.00 0.00 0.00 2.52
2244 5853 4.959596 TCCAAGTGTCGACTATCTACAC 57.040 45.455 17.92 5.11 41.63 2.90
2274 5883 8.253113 TGCTTTTCCTCATTTTCTTCATATTCC 58.747 33.333 0.00 0.00 0.00 3.01
2275 5884 9.643693 TTGCTTTTCCTCATTTTCTTCATATTC 57.356 29.630 0.00 0.00 0.00 1.75
2280 5889 6.219417 TGTTGCTTTTCCTCATTTTCTTCA 57.781 33.333 0.00 0.00 0.00 3.02
2284 5893 5.234972 CACCTTGTTGCTTTTCCTCATTTTC 59.765 40.000 0.00 0.00 0.00 2.29
2290 5903 2.034685 GTCCACCTTGTTGCTTTTCCTC 59.965 50.000 0.00 0.00 0.00 3.71
2298 5911 0.319813 GCCATTGTCCACCTTGTTGC 60.320 55.000 0.00 0.00 0.00 4.17
2312 5925 2.428890 CTCTTGACTCTCGTAGGCCATT 59.571 50.000 5.01 0.00 28.59 3.16
2322 5935 5.392595 GGATGTAGTGACACTCTTGACTCTC 60.393 48.000 12.39 6.19 38.76 3.20
2325 5938 3.191581 CGGATGTAGTGACACTCTTGACT 59.808 47.826 12.39 0.00 38.76 3.41
2334 5947 3.319689 TCAAACACTCGGATGTAGTGACA 59.680 43.478 10.02 0.00 45.89 3.58
2342 5955 1.790755 TCGGTTCAAACACTCGGATG 58.209 50.000 0.00 0.00 0.00 3.51
2366 5979 0.312416 CGAGACGCTCCCCTCTTATG 59.688 60.000 2.00 0.00 0.00 1.90
2374 5987 2.939261 TTTGACCCGAGACGCTCCC 61.939 63.158 2.00 0.00 0.00 4.30
2398 6011 6.561519 AAGACCATATACTAAGGTGCACTT 57.438 37.500 17.98 6.12 43.28 3.16
2404 6017 7.973048 TCTCACAAAGACCATATACTAAGGT 57.027 36.000 0.00 0.00 38.63 3.50
2493 6977 1.998315 CGATCAACTTCTGCCTCTGTG 59.002 52.381 0.00 0.00 0.00 3.66
2494 6978 1.674221 GCGATCAACTTCTGCCTCTGT 60.674 52.381 0.00 0.00 0.00 3.41
2535 7035 8.196771 TCTTACAAAAATGAGTGAAGTGCAAAT 58.803 29.630 0.00 0.00 0.00 2.32
2776 7279 1.477030 CGTATGCGTACTCCAACGGC 61.477 60.000 14.01 0.00 43.06 5.68
2788 7291 3.423571 GGTAATCCTCGTATCGTATGCG 58.576 50.000 0.00 0.00 39.81 4.73
2797 7300 2.568062 TGCTGTTTGGGTAATCCTCGTA 59.432 45.455 0.00 0.00 36.20 3.43
2798 7301 1.349688 TGCTGTTTGGGTAATCCTCGT 59.650 47.619 0.00 0.00 36.20 4.18
2799 7302 2.009774 CTGCTGTTTGGGTAATCCTCG 58.990 52.381 0.00 0.00 36.20 4.63
2800 7303 1.745653 GCTGCTGTTTGGGTAATCCTC 59.254 52.381 0.00 0.00 36.20 3.71
2801 7304 1.355720 AGCTGCTGTTTGGGTAATCCT 59.644 47.619 0.00 0.00 36.20 3.24
2819 7322 8.583810 TTTGTCTATTTACGTACATATCCAGC 57.416 34.615 2.05 0.00 0.00 4.85
2842 7345 3.427503 CGCCGATGGACATAAAGCTTTTT 60.428 43.478 18.47 6.68 0.00 1.94
2994 7497 4.497507 CGTGTCATAGCTTAAGATCCACGA 60.498 45.833 20.77 4.10 44.07 4.35
3035 7538 3.367292 CGCGACCCTGTTTACTTAGGTTA 60.367 47.826 0.00 0.00 31.99 2.85
3036 7539 2.611224 CGCGACCCTGTTTACTTAGGTT 60.611 50.000 0.00 0.00 31.99 3.50
3037 7540 1.067354 CGCGACCCTGTTTACTTAGGT 60.067 52.381 0.00 0.00 31.99 3.08
3038 7541 1.203052 TCGCGACCCTGTTTACTTAGG 59.797 52.381 3.71 0.00 0.00 2.69
3039 7542 2.642139 TCGCGACCCTGTTTACTTAG 57.358 50.000 3.71 0.00 0.00 2.18
3043 7550 1.127951 CAACATCGCGACCCTGTTTAC 59.872 52.381 20.67 0.00 30.99 2.01
3047 7554 1.374252 GACAACATCGCGACCCTGT 60.374 57.895 12.93 14.97 0.00 4.00
3083 7590 4.559862 ACTTGATGGTCCAACTTAGGAG 57.440 45.455 0.00 0.00 38.64 3.69
3187 8075 8.882415 ACAACTAGAGTAATTTCGAACAAAGA 57.118 30.769 0.00 0.00 0.00 2.52
3191 8079 7.431249 AGTGACAACTAGAGTAATTTCGAACA 58.569 34.615 0.00 0.00 33.79 3.18
3205 8093 2.613730 TTCGCTCGAGTGACAACTAG 57.386 50.000 27.52 2.04 36.52 2.57
3206 8094 2.228103 ACATTCGCTCGAGTGACAACTA 59.772 45.455 27.52 13.65 36.52 2.24
3207 8095 1.000163 ACATTCGCTCGAGTGACAACT 60.000 47.619 27.52 10.46 40.21 3.16
3208 8096 1.419374 ACATTCGCTCGAGTGACAAC 58.581 50.000 27.52 1.56 35.74 3.32
3209 8097 3.128764 AGATACATTCGCTCGAGTGACAA 59.871 43.478 27.52 15.16 35.74 3.18
3211 8099 3.341857 AGATACATTCGCTCGAGTGAC 57.658 47.619 27.52 15.06 35.74 3.67
3213 8101 3.230355 GCTAGATACATTCGCTCGAGTG 58.770 50.000 19.99 19.99 37.77 3.51
3215 8103 3.058570 AGTGCTAGATACATTCGCTCGAG 60.059 47.826 8.45 8.45 0.00 4.04
3217 8105 3.275400 AGTGCTAGATACATTCGCTCG 57.725 47.619 0.00 0.00 0.00 5.03
3220 8108 6.400091 CGGAATTTAGTGCTAGATACATTCGC 60.400 42.308 0.00 0.00 0.00 4.70
3221 8109 6.089551 CCGGAATTTAGTGCTAGATACATTCG 59.910 42.308 0.00 0.00 0.00 3.34
3224 8112 6.456501 GTCCGGAATTTAGTGCTAGATACAT 58.543 40.000 5.23 0.00 0.00 2.29
3230 8191 2.100252 TCCGTCCGGAATTTAGTGCTAG 59.900 50.000 5.23 0.00 42.05 3.42
3306 8267 0.976641 AGGATCTGCGTGTCTGGAAA 59.023 50.000 0.00 0.00 0.00 3.13
3375 8336 3.476552 TGCCGTCTGTTGAGAAAGATTT 58.523 40.909 0.00 0.00 0.00 2.17
3378 8339 1.686587 TCTGCCGTCTGTTGAGAAAGA 59.313 47.619 0.00 0.00 0.00 2.52
3379 8340 2.154854 TCTGCCGTCTGTTGAGAAAG 57.845 50.000 0.00 0.00 0.00 2.62
3381 8342 2.560981 TGTATCTGCCGTCTGTTGAGAA 59.439 45.455 0.00 0.00 0.00 2.87
3383 8344 2.263077 GTGTATCTGCCGTCTGTTGAG 58.737 52.381 0.00 0.00 0.00 3.02
3386 8347 0.973632 TGGTGTATCTGCCGTCTGTT 59.026 50.000 0.00 0.00 0.00 3.16
3399 8361 3.181455 ACTGTCTCTGCATTGTTGGTGTA 60.181 43.478 0.00 0.00 0.00 2.90
3414 8376 0.108804 TTTCCGGCGATCACTGTCTC 60.109 55.000 9.30 0.00 0.00 3.36
3421 8383 1.111277 TCTGATCTTTCCGGCGATCA 58.889 50.000 21.60 21.60 42.57 2.92
3606 8580 1.504359 CGGTCGCTCCTTTGTTACAA 58.496 50.000 0.00 0.00 0.00 2.41
3607 8581 0.947180 GCGGTCGCTCCTTTGTTACA 60.947 55.000 8.20 0.00 38.26 2.41
3675 8649 4.329545 AAGCAGCGCGAGGGGAAA 62.330 61.111 12.10 0.00 0.00 3.13
3921 8903 2.842058 CCAGGATCCCCATCAGGC 59.158 66.667 8.55 0.00 33.88 4.85
3954 8936 2.350895 CATGGAGACGGTGCCCAA 59.649 61.111 2.71 0.00 33.15 4.12
4019 9001 4.704833 CCCAGCCACCTGACCACG 62.705 72.222 0.00 0.00 41.77 4.94
4082 9064 1.335132 GGACCAGGTTGGCGAGGATA 61.335 60.000 0.00 0.00 42.67 2.59
4116 9098 2.801162 CTGTGCGACTCGTGACGG 60.801 66.667 4.70 0.00 32.46 4.79
4158 9140 1.744320 TATACAGACCAGCGCCGCAT 61.744 55.000 13.36 0.00 0.00 4.73
4162 9144 3.752796 TGTTATACAGACCAGCGCC 57.247 52.632 2.29 0.00 0.00 6.53
4178 9160 2.387757 AGCATCCAAACCAAACACTGT 58.612 42.857 0.00 0.00 0.00 3.55
4347 9329 4.895961 TGCAGCCAATGAAAATCAATTGA 58.104 34.783 11.26 11.26 0.00 2.57
4352 9334 3.814283 GGTTTTGCAGCCAATGAAAATCA 59.186 39.130 0.00 0.00 36.27 2.57
4359 9341 1.003476 GGGGGTTTTGCAGCCAATG 60.003 57.895 6.41 0.00 46.10 2.82
4387 9370 7.653311 GTGCCTAAACTTCTCACAATTCAAATT 59.347 33.333 0.00 0.00 0.00 1.82
4389 9372 6.321181 AGTGCCTAAACTTCTCACAATTCAAA 59.679 34.615 0.00 0.00 0.00 2.69
4412 9395 8.960591 CCATGATCTTATTAACAAGGTCAAAGT 58.039 33.333 13.20 0.00 46.06 2.66
4418 9401 8.210946 TCGAATCCATGATCTTATTAACAAGGT 58.789 33.333 0.00 0.00 0.00 3.50
4427 9410 9.007901 GGAAAGAATTCGAATCCATGATCTTAT 57.992 33.333 16.76 9.89 36.36 1.73
4443 9426 4.685169 TCAATGAGCACGGAAAGAATTC 57.315 40.909 0.00 0.00 34.66 2.17
4448 9431 2.416547 ACGAATCAATGAGCACGGAAAG 59.583 45.455 10.08 0.00 0.00 2.62
4489 9481 3.081804 AGCGCAACAACTAATTAGGCTT 58.918 40.909 16.73 0.17 0.00 4.35
4504 9496 0.597568 CTGGTCCAAAATCAGCGCAA 59.402 50.000 11.47 0.00 0.00 4.85
4505 9497 0.250684 TCTGGTCCAAAATCAGCGCA 60.251 50.000 11.47 0.00 0.00 6.09
4507 9499 1.200020 GGTTCTGGTCCAAAATCAGCG 59.800 52.381 0.00 0.00 0.00 5.18
4514 9506 2.979678 AGAGCTAAGGTTCTGGTCCAAA 59.020 45.455 0.00 0.00 31.86 3.28
4532 9524 1.135915 AGCCTCTACGTGATGCAAGAG 59.864 52.381 0.00 0.36 38.53 2.85
4543 9535 2.031682 GCCATAATGCAAAGCCTCTACG 60.032 50.000 0.00 0.00 0.00 3.51
4559 9551 2.355310 CGACCTGGTAAACTTGGCCATA 60.355 50.000 6.09 0.00 0.00 2.74
4566 9558 4.753107 CACAATGTACGACCTGGTAAACTT 59.247 41.667 0.00 0.00 0.00 2.66
4574 9566 3.258228 TGTATGCACAATGTACGACCTG 58.742 45.455 0.00 0.00 0.00 4.00
4597 9589 8.716646 TTGTGTTGTTCGACATATAGAATGAT 57.283 30.769 0.00 0.00 0.00 2.45
4599 9591 8.603181 TCATTGTGTTGTTCGACATATAGAATG 58.397 33.333 0.00 0.00 0.00 2.67
4609 9601 1.398451 CGGCTCATTGTGTTGTTCGAC 60.398 52.381 0.00 0.00 0.00 4.20
4652 9644 8.303876 GCTATTTGGGTTAGTTGAGAATTTTCA 58.696 33.333 0.00 0.00 0.00 2.69
4653 9645 8.523658 AGCTATTTGGGTTAGTTGAGAATTTTC 58.476 33.333 0.00 0.00 0.00 2.29
4658 9651 9.174166 GAATTAGCTATTTGGGTTAGTTGAGAA 57.826 33.333 5.63 0.00 0.00 2.87
4685 9678 3.616219 TGTTACCAGCAAACACTTCACT 58.384 40.909 0.00 0.00 32.07 3.41
4783 9785 9.137459 TGAACTTGAAAATAAATCCACTGGTAA 57.863 29.630 0.00 0.00 0.00 2.85
4832 9836 6.931281 TCAAGTTAACATCAAAGGAGTCTCAG 59.069 38.462 8.61 0.00 0.00 3.35
4974 9980 7.010460 GGGTATGTACGTTAACCAGACATAAAC 59.990 40.741 17.13 14.16 35.40 2.01
5060 10066 2.592287 TTGGACCGTCGGGCAAAC 60.592 61.111 21.19 1.51 36.48 2.93
5199 10298 8.534333 TGTGCAGAAAGTAATAGAAACTACAG 57.466 34.615 0.00 0.00 0.00 2.74
5234 10333 3.460648 CCTTGTAGCTGTACAGGGC 57.539 57.895 23.95 11.87 46.25 5.19
5382 10482 3.008266 TCCACAAGATGCTCATCAAGTCA 59.992 43.478 11.90 0.00 40.22 3.41
5383 10483 3.373439 GTCCACAAGATGCTCATCAAGTC 59.627 47.826 11.90 0.00 40.22 3.01
5384 10484 3.008813 AGTCCACAAGATGCTCATCAAGT 59.991 43.478 11.90 6.94 40.22 3.16
5385 10485 3.374367 CAGTCCACAAGATGCTCATCAAG 59.626 47.826 11.90 6.38 40.22 3.02
5386 10486 3.340928 CAGTCCACAAGATGCTCATCAA 58.659 45.455 11.90 0.00 40.22 2.57
5387 10487 2.938314 GCAGTCCACAAGATGCTCATCA 60.938 50.000 11.90 0.00 40.22 3.07
5388 10488 1.669779 GCAGTCCACAAGATGCTCATC 59.330 52.381 1.75 1.75 35.78 2.92
5389 10489 1.681166 GGCAGTCCACAAGATGCTCAT 60.681 52.381 0.00 0.00 38.71 2.90
5690 10807 6.713792 TTTTCTGTTGCTTACCAAACAAAC 57.286 33.333 0.00 0.00 34.68 2.93
6295 11433 0.036294 GCACCAAGTAGTCCCTCCAC 60.036 60.000 0.00 0.00 0.00 4.02
6472 11611 3.721087 ACAAGATCTGTACCAAAGGGG 57.279 47.619 0.00 0.00 44.81 4.79
6475 11614 9.410556 CCAAATAAAACAAGATCTGTACCAAAG 57.589 33.333 0.00 0.00 37.23 2.77
6477 11616 7.507616 ACCCAAATAAAACAAGATCTGTACCAA 59.492 33.333 0.00 0.00 37.23 3.67
6479 11618 7.462571 ACCCAAATAAAACAAGATCTGTACC 57.537 36.000 0.00 0.00 37.23 3.34
6540 11679 3.386716 TACCACCAGTAGACCCACC 57.613 57.895 0.00 0.00 0.00 4.61
6550 11689 7.519032 TTTTTCTGAAAATACCTACCACCAG 57.481 36.000 15.63 0.00 30.07 4.00
6631 11773 7.837202 TGAAAATTTACAGGTATGTAGACCG 57.163 36.000 0.00 0.00 44.88 4.79
6692 11834 9.377312 ACACAAAATTAAGTGTTTTTGCTACAT 57.623 25.926 9.35 0.00 46.04 2.29
6722 12009 5.924356 TCATTGAAGGCGAGGTAATAATCA 58.076 37.500 0.00 0.00 0.00 2.57
6754 12041 2.760634 TTAAGATGAAGCAGCCGTCA 57.239 45.000 0.00 0.00 34.04 4.35
6780 12068 1.228245 AAAGCATCACACCGCTGGT 60.228 52.632 0.00 0.00 38.82 4.00
6791 12079 6.424509 TCCACAACAAATGAAATCAAAGCATC 59.575 34.615 0.00 0.00 0.00 3.91
6810 12098 5.441500 TCTTCATTAACACAAGGTCCACAA 58.558 37.500 0.00 0.00 0.00 3.33
6831 12120 7.391148 AGAACGTGCCAAATTATACATTTCT 57.609 32.000 0.00 0.00 0.00 2.52
6889 12178 7.195646 TGTCATTTTTCAAGACAAGCTTAGTG 58.804 34.615 0.00 0.00 39.15 2.74
6966 12255 3.332919 GCTCAAGAAGAAGATGACTGCA 58.667 45.455 0.00 0.00 0.00 4.41
7027 12316 2.185103 AAGGAGACGACGAGTGACGC 62.185 60.000 0.00 0.00 46.94 5.19
7039 12328 1.882623 CAGGAACAAGCCAAAGGAGAC 59.117 52.381 0.00 0.00 0.00 3.36
7131 12420 0.318699 CATGTGGTGACGACGACACT 60.319 55.000 25.15 7.17 42.78 3.55
7156 12445 1.196808 GGTTGTACATGCTGTTGGTCG 59.803 52.381 0.00 0.00 0.00 4.79
7183 12472 8.100164 TCAGTTTCATATCACTGGTCAATACAA 58.900 33.333 6.44 0.00 40.81 2.41
7194 12483 7.487822 TCTTCCTTCTCAGTTTCATATCACT 57.512 36.000 0.00 0.00 0.00 3.41
7276 12565 1.068055 CCTCCAGCAAACAATGTCTGC 60.068 52.381 3.04 3.04 34.10 4.26
7353 12642 3.321968 AGATTGAAAAGTGGCAGGAAACC 59.678 43.478 0.00 0.00 0.00 3.27
7404 12693 9.730705 ATTATAATGGAGTATGTGATTCCTGTG 57.269 33.333 0.00 0.00 34.96 3.66
7485 12775 5.471257 GCAGAGAAAGATATAGGTTACCCG 58.529 45.833 0.00 0.00 35.12 5.28
7513 12803 1.691976 GGTGGATCGTGACCCATATGA 59.308 52.381 3.65 0.00 34.58 2.15
7525 12815 4.576053 TGAGATTATTTTGCAGGTGGATCG 59.424 41.667 0.00 0.00 0.00 3.69
7570 12894 4.103469 TCAGTTAGAACTTGGGCCTGTTTA 59.897 41.667 14.62 8.12 37.08 2.01
7619 12945 5.007626 CAGAACTTCATTCCTCAAACGAACA 59.992 40.000 0.00 0.00 38.16 3.18
7620 12946 5.236478 TCAGAACTTCATTCCTCAAACGAAC 59.764 40.000 0.00 0.00 38.16 3.95
7654 12989 2.435372 AAGGCAGGACACTTGACAAA 57.565 45.000 0.00 0.00 0.00 2.83
7655 12990 2.297701 GAAAGGCAGGACACTTGACAA 58.702 47.619 0.00 0.00 0.00 3.18
7656 12991 1.476833 GGAAAGGCAGGACACTTGACA 60.477 52.381 0.00 0.00 0.00 3.58
7657 12992 1.239347 GGAAAGGCAGGACACTTGAC 58.761 55.000 0.00 0.00 0.00 3.18
7658 12993 0.843309 TGGAAAGGCAGGACACTTGA 59.157 50.000 0.00 0.00 0.00 3.02
7659 12994 1.915141 ATGGAAAGGCAGGACACTTG 58.085 50.000 0.00 0.00 0.00 3.16
7660 12995 2.683211 AATGGAAAGGCAGGACACTT 57.317 45.000 0.00 0.00 0.00 3.16
7665 13000 0.783206 TGGGAAATGGAAAGGCAGGA 59.217 50.000 0.00 0.00 0.00 3.86
7689 13024 6.039270 TGTTCCATAATATTTGTGGCTACTGC 59.961 38.462 12.44 0.00 41.26 4.40
7690 13025 7.283127 AGTGTTCCATAATATTTGTGGCTACTG 59.717 37.037 12.44 0.00 41.26 2.74
7691 13026 7.346471 AGTGTTCCATAATATTTGTGGCTACT 58.654 34.615 12.44 12.31 41.26 2.57
7743 13078 8.575589 AGTTTCATCTGTGTTGCAATGTTATTA 58.424 29.630 0.59 0.00 0.00 0.98
7759 13094 5.308825 ACACCACTCCTTTAGTTTCATCTG 58.691 41.667 0.00 0.00 35.76 2.90
7768 13103 7.419711 TCCTAATCTAACACCACTCCTTTAG 57.580 40.000 0.00 0.00 0.00 1.85
7781 13116 7.201652 GGTTGTTGCTCTCATTCCTAATCTAAC 60.202 40.741 0.00 0.00 0.00 2.34
7782 13117 6.823689 GGTTGTTGCTCTCATTCCTAATCTAA 59.176 38.462 0.00 0.00 0.00 2.10
7787 13122 4.041567 TCTGGTTGTTGCTCTCATTCCTAA 59.958 41.667 0.00 0.00 0.00 2.69
7788 13123 3.582647 TCTGGTTGTTGCTCTCATTCCTA 59.417 43.478 0.00 0.00 0.00 2.94
7831 13166 4.963953 GCATGTATCTGAACGTACATTTGC 59.036 41.667 0.00 0.00 38.98 3.68
7856 13191 5.065090 TGAATAAACAGAGGAACATGCATCG 59.935 40.000 0.00 0.00 0.00 3.84
7860 13195 5.126061 ACCATGAATAAACAGAGGAACATGC 59.874 40.000 0.00 0.00 34.51 4.06
7895 13230 2.427095 TGTATCTCCCGTGTGATCAGTG 59.573 50.000 0.00 0.00 0.00 3.66
7896 13231 2.427453 GTGTATCTCCCGTGTGATCAGT 59.573 50.000 0.00 0.00 0.00 3.41
7897 13232 2.690497 AGTGTATCTCCCGTGTGATCAG 59.310 50.000 0.00 0.00 0.00 2.90
7898 13233 2.427095 CAGTGTATCTCCCGTGTGATCA 59.573 50.000 0.00 0.00 0.00 2.92
7899 13234 2.688446 TCAGTGTATCTCCCGTGTGATC 59.312 50.000 0.00 0.00 0.00 2.92
7900 13235 2.690497 CTCAGTGTATCTCCCGTGTGAT 59.310 50.000 0.00 0.00 0.00 3.06
7901 13236 2.092323 CTCAGTGTATCTCCCGTGTGA 58.908 52.381 0.00 0.00 0.00 3.58
7902 13237 1.135139 CCTCAGTGTATCTCCCGTGTG 59.865 57.143 0.00 0.00 0.00 3.82
7903 13238 1.475403 CCTCAGTGTATCTCCCGTGT 58.525 55.000 0.00 0.00 0.00 4.49
7904 13239 0.103208 GCCTCAGTGTATCTCCCGTG 59.897 60.000 0.00 0.00 0.00 4.94
7905 13240 0.324368 TGCCTCAGTGTATCTCCCGT 60.324 55.000 0.00 0.00 0.00 5.28
7906 13241 0.824109 TTGCCTCAGTGTATCTCCCG 59.176 55.000 0.00 0.00 0.00 5.14
7907 13242 2.111384 TCTTGCCTCAGTGTATCTCCC 58.889 52.381 0.00 0.00 0.00 4.30
7921 13256 0.955428 TTCGTGTGAGCCATCTTGCC 60.955 55.000 0.00 0.00 0.00 4.52
7944 13280 2.552743 CTCTGTACGTGTTGTCTCCAGA 59.447 50.000 0.00 0.00 32.38 3.86
7973 13309 7.534282 TGGTTACTAATGTATTGCATGTGTTG 58.466 34.615 0.00 0.00 37.96 3.33
7992 13330 2.754946 TTGTCTCCGGTGATGGTTAC 57.245 50.000 9.83 0.00 0.00 2.50
8049 13387 0.733150 GCCGCTTGGTAATGGAGAAC 59.267 55.000 0.00 0.00 34.16 3.01


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

AutoCloner maintained by Alex Coulton.