Multiple sequence alignment - TraesCS5D01G413200

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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 TraesCS5D01G413200 chr5D 100.000 3527 0 0 1 3527 476159895 476156369 0.000000e+00 6514.0
1 TraesCS5D01G413200 chr5D 91.707 410 15 9 1812 2221 286180270 286180660 5.150000e-153 551.0
2 TraesCS5D01G413200 chr5D 89.512 410 12 16 1812 2221 563675488 563675110 1.140000e-134 490.0
3 TraesCS5D01G413200 chr5D 88.400 250 18 2 955 1203 286178181 286178420 1.240000e-74 291.0
4 TraesCS5D01G413200 chr5D 88.824 170 9 3 1590 1751 286180102 286180269 2.150000e-47 200.0
5 TraesCS5D01G413200 chr5D 86.364 110 5 3 1650 1751 563675596 563675489 1.030000e-20 111.0
6 TraesCS5D01G413200 chr5D 97.778 45 1 0 1233 1277 286178422 286178466 1.050000e-10 78.7
7 TraesCS5D01G413200 chr5A 93.249 2755 120 25 14 2730 595543556 595540830 0.000000e+00 3997.0
8 TraesCS5D01G413200 chr5A 92.562 242 11 3 2772 3012 595540826 595540591 1.210000e-89 340.0
9 TraesCS5D01G413200 chr5A 79.381 388 72 8 92 477 444037284 444037665 2.090000e-67 267.0
10 TraesCS5D01G413200 chr5A 97.059 34 1 0 3270 3303 595540515 595540482 1.370000e-04 58.4
11 TraesCS5D01G413200 chr5B 94.962 2084 60 18 964 3012 583579477 583577404 0.000000e+00 3225.0
12 TraesCS5D01G413200 chr5B 88.281 896 79 12 77 957 583580407 583579523 0.000000e+00 1050.0
13 TraesCS5D01G413200 chr5B 94.634 205 6 3 3015 3214 583577444 583577240 2.640000e-81 313.0
14 TraesCS5D01G413200 chr5B 97.143 35 1 0 8 42 583581876 583581842 3.800000e-05 60.2
15 TraesCS5D01G413200 chr6B 88.444 900 60 12 1322 2201 615309139 615310014 0.000000e+00 1046.0
16 TraesCS5D01G413200 chr6B 78.142 366 34 20 956 1318 615295645 615295967 1.290000e-44 191.0
17 TraesCS5D01G413200 chr7D 91.707 410 15 9 1812 2221 529583687 529583297 5.150000e-153 551.0
18 TraesCS5D01G413200 chr7D 88.000 250 19 2 955 1203 529585900 529585661 5.760000e-73 285.0
19 TraesCS5D01G413200 chr7D 81.115 323 51 10 86 403 167511582 167511899 2.100000e-62 250.0
20 TraesCS5D01G413200 chr7D 81.765 170 6 6 1590 1751 529583840 529583688 6.180000e-23 119.0
21 TraesCS5D01G413200 chr7D 97.778 45 1 0 1233 1277 529585659 529585615 1.050000e-10 78.7
22 TraesCS5D01G413200 chr2A 91.463 410 16 9 1812 2221 102426203 102425813 2.390000e-151 545.0
23 TraesCS5D01G413200 chr2A 88.000 250 19 2 955 1203 102428278 102428039 5.760000e-73 285.0
24 TraesCS5D01G413200 chr2A 81.176 170 7 6 1590 1751 102426356 102426204 2.880000e-21 113.0
25 TraesCS5D01G413200 chr2A 97.778 45 1 0 1233 1277 102428037 102427993 1.050000e-10 78.7
26 TraesCS5D01G413200 chr3A 90.732 410 19 10 1812 2221 572018860 572018470 2.410000e-146 529.0
27 TraesCS5D01G413200 chr3A 81.293 433 63 16 57 481 568448506 568448928 5.640000e-88 335.0
28 TraesCS5D01G413200 chr3A 87.861 173 8 5 1590 1751 572019031 572018861 1.290000e-44 191.0
29 TraesCS5D01G413200 chr3A 100.000 28 0 0 1250 1277 572020698 572020671 6.000000e-03 52.8
30 TraesCS5D01G413200 chr2D 90.732 410 19 9 1812 2221 37310702 37310312 2.410000e-146 529.0
31 TraesCS5D01G413200 chr2D 87.967 241 19 1 963 1203 37312512 37312282 3.470000e-70 276.0
32 TraesCS5D01G413200 chr2D 97.778 45 1 0 1233 1277 37312280 37312236 1.050000e-10 78.7
33 TraesCS5D01G413200 chr2D 100.000 30 0 0 3264 3293 638503272 638503301 4.920000e-04 56.5
34 TraesCS5D01G413200 chr1B 80.872 413 61 11 87 494 45351701 45351302 3.420000e-80 309.0
35 TraesCS5D01G413200 chr1B 100.000 30 0 0 3328 3357 47489939 47489910 4.920000e-04 56.5
36 TraesCS5D01G413200 chr4D 83.041 342 48 7 95 431 88081614 88081278 5.720000e-78 302.0
37 TraesCS5D01G413200 chr4D 87.302 63 2 5 3330 3391 58394135 58394078 2.270000e-07 67.6
38 TraesCS5D01G413200 chr3B 78.744 414 72 15 86 490 31056113 31055707 2.700000e-66 263.0
39 TraesCS5D01G413200 chr4A 79.357 373 70 7 88 456 661431490 661431859 4.520000e-64 255.0
40 TraesCS5D01G413200 chr7A 82.456 285 45 5 77 359 458977812 458978093 9.780000e-61 244.0


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 TraesCS5D01G413200 chr5D 476156369 476159895 3526 True 6514.000000 6514 100.000000 1 3527 1 chr5D.!!$R1 3526
1 TraesCS5D01G413200 chr5D 286178181 286180660 2479 False 280.175000 551 91.677250 955 2221 4 chr5D.!!$F1 1266
2 TraesCS5D01G413200 chr5A 595540482 595543556 3074 True 1465.133333 3997 94.290000 14 3303 3 chr5A.!!$R1 3289
3 TraesCS5D01G413200 chr5B 583577240 583581876 4636 True 1162.050000 3225 93.755000 8 3214 4 chr5B.!!$R1 3206
4 TraesCS5D01G413200 chr6B 615309139 615310014 875 False 1046.000000 1046 88.444000 1322 2201 1 chr6B.!!$F2 879
5 TraesCS5D01G413200 chr7D 529583297 529585900 2603 True 258.425000 551 89.812500 955 2221 4 chr7D.!!$R1 1266
6 TraesCS5D01G413200 chr2A 102425813 102428278 2465 True 255.425000 545 89.604250 955 2221 4 chr2A.!!$R1 1266
7 TraesCS5D01G413200 chr3A 572018470 572020698 2228 True 257.600000 529 92.864333 1250 2221 3 chr3A.!!$R1 971
8 TraesCS5D01G413200 chr2D 37310312 37312512 2200 True 294.566667 529 92.159000 963 2221 3 chr2D.!!$R1 1258

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
531 1938 0.788995 CTGCGAATCTCCGATGCATC 59.211 55.000 17.1 17.1 34.66 3.91 F
947 2372 1.065600 CACACGGCACACCAAAAGG 59.934 57.895 0.0 0.0 34.57 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 4659 1.454663 GATCAGCTTGGGCCCTTCC 60.455 63.158 25.7 10.78 39.73 3.46 R
2678 5691 0.837272 ACATCCCAATACACCGAGGG 59.163 55.000 0.0 0.00 42.86 4.30 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
66 1451 1.624312 ACATGCATGCATTTGTGGGAA 59.376 42.857 30.32 0.00 33.90 3.97
67 1452 2.004017 CATGCATGCATTTGTGGGAAC 58.996 47.619 30.32 0.00 33.90 3.62
68 1453 1.046204 TGCATGCATTTGTGGGAACA 58.954 45.000 18.46 0.00 38.70 3.18
91 1492 2.149803 TTGTGGCACGTAGGTCCTCG 62.150 60.000 13.77 1.64 0.00 4.63
92 1493 3.755628 TGGCACGTAGGTCCTCGC 61.756 66.667 0.00 0.00 0.00 5.03
122 1524 8.901793 TGCTTTTATTTTTGGCTTCTGATTTTT 58.098 25.926 0.00 0.00 0.00 1.94
123 1525 9.385902 GCTTTTATTTTTGGCTTCTGATTTTTC 57.614 29.630 0.00 0.00 0.00 2.29
127 1529 7.862512 ATTTTTGGCTTCTGATTTTTCAACA 57.137 28.000 0.00 0.00 0.00 3.33
177 1579 8.905702 CCAAATAAGTTATGCTTTCATATTCGC 58.094 33.333 0.00 0.00 38.57 4.70
315 1717 5.132897 TCATGATTTTTGTGCCTACAACC 57.867 39.130 0.00 0.00 45.91 3.77
316 1718 4.586421 TCATGATTTTTGTGCCTACAACCA 59.414 37.500 0.00 0.00 45.91 3.67
436 1843 9.303116 TGAAACTTAAAATTTACTATGCCCTCA 57.697 29.630 0.00 0.00 0.00 3.86
462 1869 4.215399 TGGGATTCAACAACTTCACGAATC 59.785 41.667 0.00 0.00 40.67 2.52
463 1870 4.215399 GGGATTCAACAACTTCACGAATCA 59.785 41.667 11.33 0.00 42.33 2.57
477 1884 1.797046 CGAATCATGAGGCAATCGAGG 59.203 52.381 0.09 0.00 32.38 4.63
481 1888 3.466791 ATGAGGCAATCGAGGGGCG 62.467 63.158 6.96 0.00 42.69 6.13
482 1889 4.918201 GAGGCAATCGAGGGGCGG 62.918 72.222 6.96 0.00 41.33 6.13
531 1938 0.788995 CTGCGAATCTCCGATGCATC 59.211 55.000 17.10 17.10 34.66 3.91
537 1944 4.240888 CGAATCTCCGATGCATCTGTATT 58.759 43.478 23.73 18.89 0.00 1.89
548 1955 7.191551 CGATGCATCTGTATTGTTTTGAGATT 58.808 34.615 23.73 0.00 0.00 2.40
589 1996 1.365633 GCCCAAACGGACAAATGCA 59.634 52.632 0.00 0.00 0.00 3.96
636 2043 4.621991 CCTTCCGATACATCTACCAACAG 58.378 47.826 0.00 0.00 0.00 3.16
644 2052 7.709182 CCGATACATCTACCAACAGTATCAAAA 59.291 37.037 0.00 0.00 40.46 2.44
683 2100 1.304134 TCTCAGCAGTCGCCACCTA 60.304 57.895 0.00 0.00 39.83 3.08
695 2112 1.537562 CGCCACCTATTACCGGTTCTC 60.538 57.143 15.04 0.00 30.82 2.87
753 2178 1.745232 CTGCTCCACTCTACTCGTCT 58.255 55.000 0.00 0.00 0.00 4.18
947 2372 1.065600 CACACGGCACACCAAAAGG 59.934 57.895 0.00 0.00 34.57 3.11
1011 2481 2.196925 AAACCAAATGGCGACGGCA 61.197 52.632 27.04 27.04 43.52 5.69
1012 2482 1.739338 AAACCAAATGGCGACGGCAA 61.739 50.000 28.50 11.91 42.43 4.52
2259 5266 4.922026 AAGGACCCGCGCGTGTTT 62.922 61.111 29.95 13.00 0.00 2.83
2280 5287 4.883300 CGCGCCGAGGACTACGTC 62.883 72.222 0.00 0.00 0.00 4.34
2547 5554 0.921347 GCATCGCCACGTGTACTTAG 59.079 55.000 15.65 0.00 0.00 2.18
2678 5691 0.892358 GACCGGTTTTTCCCAGGGAC 60.892 60.000 8.12 0.00 0.00 4.46
2692 5705 0.981277 AGGGACCCTCGGTGTATTGG 60.981 60.000 7.44 0.00 35.25 3.16
2729 5751 2.907892 AGTCAGTGAGATGAAAGGGGA 58.092 47.619 0.00 0.00 0.00 4.81
2731 5753 2.303022 GTCAGTGAGATGAAAGGGGACA 59.697 50.000 0.00 0.00 0.00 4.02
2732 5754 3.054802 GTCAGTGAGATGAAAGGGGACAT 60.055 47.826 0.00 0.00 0.00 3.06
2733 5755 3.054875 TCAGTGAGATGAAAGGGGACATG 60.055 47.826 0.00 0.00 0.00 3.21
2734 5756 2.915604 AGTGAGATGAAAGGGGACATGT 59.084 45.455 0.00 0.00 0.00 3.21
2736 5758 4.080863 AGTGAGATGAAAGGGGACATGTAC 60.081 45.833 0.00 0.00 0.00 2.90
2737 5759 4.080863 GTGAGATGAAAGGGGACATGTACT 60.081 45.833 8.27 0.00 0.00 2.73
2739 5761 3.456277 AGATGAAAGGGGACATGTACTCC 59.544 47.826 3.62 5.88 0.00 3.85
2740 5762 2.915869 TGAAAGGGGACATGTACTCCT 58.084 47.619 3.62 8.32 0.00 3.69
2741 5763 4.069312 TGAAAGGGGACATGTACTCCTA 57.931 45.455 16.00 1.63 0.00 2.94
2742 5764 3.773119 TGAAAGGGGACATGTACTCCTAC 59.227 47.826 16.00 13.62 0.00 3.18
2743 5765 3.778622 AAGGGGACATGTACTCCTACT 57.221 47.619 16.00 6.34 0.00 2.57
2898 5923 0.326048 TGGGGGTGCAATTATTGGGG 60.326 55.000 7.08 0.00 0.00 4.96
2937 5963 0.332972 ACCTCCTTGGCTCCATTTCC 59.667 55.000 0.00 0.00 40.22 3.13
2992 6020 4.286447 GGCCAGGTTTTTGGACCA 57.714 55.556 0.00 0.00 40.63 4.02
3001 6029 0.752054 TTTTTGGACCAGGCTTGCAG 59.248 50.000 0.00 0.00 0.00 4.41
3002 6030 0.106268 TTTTGGACCAGGCTTGCAGA 60.106 50.000 0.00 0.00 0.00 4.26
3003 6031 0.106268 TTTGGACCAGGCTTGCAGAA 60.106 50.000 0.00 0.00 0.00 3.02
3004 6032 0.538057 TTGGACCAGGCTTGCAGAAG 60.538 55.000 0.00 0.00 0.00 2.85
3005 6033 1.073897 GGACCAGGCTTGCAGAAGT 59.926 57.895 0.00 0.00 0.00 3.01
3006 6034 0.957888 GGACCAGGCTTGCAGAAGTC 60.958 60.000 0.00 0.00 33.62 3.01
3007 6035 0.036022 GACCAGGCTTGCAGAAGTCT 59.964 55.000 0.00 0.00 45.45 3.24
3011 6039 2.399916 AGGCTTGCAGAAGTCTGATC 57.600 50.000 12.54 0.00 42.80 2.92
3012 6040 1.005340 GGCTTGCAGAAGTCTGATCG 58.995 55.000 12.54 0.46 46.59 3.69
3013 6041 1.005340 GCTTGCAGAAGTCTGATCGG 58.995 55.000 12.54 0.00 46.59 4.18
3014 6042 1.649664 CTTGCAGAAGTCTGATCGGG 58.350 55.000 12.54 0.00 46.59 5.14
3015 6043 0.391661 TTGCAGAAGTCTGATCGGGC 60.392 55.000 12.54 0.00 46.59 6.13
3016 6044 1.522580 GCAGAAGTCTGATCGGGCC 60.523 63.158 12.54 0.00 46.59 5.80
3017 6045 1.227089 CAGAAGTCTGATCGGGCCG 60.227 63.158 22.51 22.51 46.59 6.13
3018 6046 2.107141 GAAGTCTGATCGGGCCGG 59.893 66.667 27.98 10.15 0.00 6.13
3019 6047 3.447025 GAAGTCTGATCGGGCCGGG 62.447 68.421 27.98 13.85 0.00 5.73
3031 6059 4.986708 GCCGGGCTGGGTTTTGGA 62.987 66.667 15.62 0.00 38.63 3.53
3032 6060 2.989253 CCGGGCTGGGTTTTGGAC 60.989 66.667 3.77 0.00 0.00 4.02
3041 6069 1.299850 GGTTTTGGACCGTGCTTGC 60.300 57.895 0.00 0.00 39.00 4.01
3042 6070 1.435515 GTTTTGGACCGTGCTTGCA 59.564 52.632 0.00 0.00 0.00 4.08
3065 6093 2.711542 AGCCCGATCCTTAAACAACAG 58.288 47.619 0.00 0.00 0.00 3.16
3135 6167 0.831711 AGCAACCAAAAGCCCGGAAT 60.832 50.000 0.73 0.00 0.00 3.01
3214 6246 3.826265 GAAGCCCAAGCCCAACCCA 62.826 63.158 0.00 0.00 41.25 4.51
3215 6247 3.403008 AAGCCCAAGCCCAACCCAA 62.403 57.895 0.00 0.00 41.25 4.12
3216 6248 2.846754 GCCCAAGCCCAACCCAAA 60.847 61.111 0.00 0.00 0.00 3.28
3217 6249 2.447714 GCCCAAGCCCAACCCAAAA 61.448 57.895 0.00 0.00 0.00 2.44
3229 6261 2.563297 CCCAAAAGGTAAGCCCGAC 58.437 57.895 0.00 0.00 38.74 4.79
3230 6262 0.963856 CCCAAAAGGTAAGCCCGACC 60.964 60.000 0.00 0.00 38.74 4.79
3234 6266 3.709567 AGGTAAGCCCGACCTGAC 58.290 61.111 1.12 0.00 45.90 3.51
3235 6267 1.988406 AGGTAAGCCCGACCTGACC 60.988 63.158 1.12 1.61 45.90 4.02
3236 6268 1.988406 GGTAAGCCCGACCTGACCT 60.988 63.158 2.49 0.00 34.05 3.85
3239 6271 2.449967 TAAGCCCGACCTGACCTGGA 62.450 60.000 0.00 0.00 0.00 3.86
3240 6272 4.083862 GCCCGACCTGACCTGGAC 62.084 72.222 0.00 0.00 0.00 4.02
3241 6273 2.283966 CCCGACCTGACCTGGACT 60.284 66.667 0.00 0.00 0.00 3.85
3242 6274 2.650116 CCCGACCTGACCTGGACTG 61.650 68.421 0.00 0.00 0.00 3.51
3243 6275 2.650116 CCGACCTGACCTGGACTGG 61.650 68.421 17.73 17.73 0.00 4.00
3244 6276 2.650116 CGACCTGACCTGGACTGGG 61.650 68.421 21.77 14.31 0.00 4.45
3245 6277 1.536662 GACCTGACCTGGACTGGGT 60.537 63.158 21.77 16.82 40.13 4.51
3246 6278 1.073706 ACCTGACCTGGACTGGGTT 60.074 57.895 21.77 3.80 37.17 4.11
3247 6279 0.697854 ACCTGACCTGGACTGGGTTT 60.698 55.000 21.77 3.18 37.17 3.27
3248 6280 0.478507 CCTGACCTGGACTGGGTTTT 59.521 55.000 12.91 0.00 37.17 2.43
3249 6281 1.133482 CCTGACCTGGACTGGGTTTTT 60.133 52.381 12.91 0.00 37.17 1.94
3250 6282 1.956477 CTGACCTGGACTGGGTTTTTG 59.044 52.381 0.00 0.00 37.17 2.44
3251 6283 1.328279 GACCTGGACTGGGTTTTTGG 58.672 55.000 0.00 0.00 37.17 3.28
3252 6284 0.930726 ACCTGGACTGGGTTTTTGGA 59.069 50.000 0.00 0.00 32.46 3.53
3253 6285 1.133482 ACCTGGACTGGGTTTTTGGAG 60.133 52.381 0.00 0.00 32.46 3.86
3254 6286 0.961753 CTGGACTGGGTTTTTGGAGC 59.038 55.000 0.00 0.00 0.00 4.70
3255 6287 0.555769 TGGACTGGGTTTTTGGAGCT 59.444 50.000 0.00 0.00 0.00 4.09
3256 6288 0.961753 GGACTGGGTTTTTGGAGCTG 59.038 55.000 0.00 0.00 0.00 4.24
3257 6289 0.961753 GACTGGGTTTTTGGAGCTGG 59.038 55.000 0.00 0.00 0.00 4.85
3258 6290 0.469892 ACTGGGTTTTTGGAGCTGGG 60.470 55.000 0.00 0.00 0.00 4.45
3259 6291 1.820010 CTGGGTTTTTGGAGCTGGGC 61.820 60.000 0.00 0.00 0.00 5.36
3260 6292 1.533994 GGGTTTTTGGAGCTGGGCT 60.534 57.895 0.00 0.00 43.88 5.19
3261 6293 1.121407 GGGTTTTTGGAGCTGGGCTT 61.121 55.000 0.00 0.00 39.88 4.35
3262 6294 0.033920 GGTTTTTGGAGCTGGGCTTG 59.966 55.000 0.00 0.00 39.88 4.01
3263 6295 0.033920 GTTTTTGGAGCTGGGCTTGG 59.966 55.000 0.00 0.00 39.88 3.61
3264 6296 1.120795 TTTTTGGAGCTGGGCTTGGG 61.121 55.000 0.00 0.00 39.88 4.12
3265 6297 2.310930 TTTTGGAGCTGGGCTTGGGT 62.311 55.000 0.00 0.00 39.88 4.51
3266 6298 2.310930 TTTGGAGCTGGGCTTGGGTT 62.311 55.000 0.00 0.00 39.88 4.11
3267 6299 2.677875 GGAGCTGGGCTTGGGTTG 60.678 66.667 0.00 0.00 39.88 3.77
3268 6300 2.677875 GAGCTGGGCTTGGGTTGG 60.678 66.667 0.00 0.00 39.88 3.77
3299 6331 2.599408 TCAGGTTTACTCTCGGGTCT 57.401 50.000 0.00 0.00 0.00 3.85
3303 6335 3.700038 CAGGTTTACTCTCGGGTCTATGT 59.300 47.826 0.00 0.00 0.00 2.29
3304 6336 4.159879 CAGGTTTACTCTCGGGTCTATGTT 59.840 45.833 0.00 0.00 0.00 2.71
3305 6337 4.159879 AGGTTTACTCTCGGGTCTATGTTG 59.840 45.833 0.00 0.00 0.00 3.33
3306 6338 4.081807 GGTTTACTCTCGGGTCTATGTTGT 60.082 45.833 0.00 0.00 0.00 3.32
3307 6339 5.476614 GTTTACTCTCGGGTCTATGTTGTT 58.523 41.667 0.00 0.00 0.00 2.83
3308 6340 6.350445 GGTTTACTCTCGGGTCTATGTTGTTA 60.350 42.308 0.00 0.00 0.00 2.41
3309 6341 6.839124 TTACTCTCGGGTCTATGTTGTTAA 57.161 37.500 0.00 0.00 0.00 2.01
3310 6342 5.934402 ACTCTCGGGTCTATGTTGTTAAT 57.066 39.130 0.00 0.00 0.00 1.40
3311 6343 6.295719 ACTCTCGGGTCTATGTTGTTAATT 57.704 37.500 0.00 0.00 0.00 1.40
3312 6344 7.414222 ACTCTCGGGTCTATGTTGTTAATTA 57.586 36.000 0.00 0.00 0.00 1.40
3313 6345 7.263496 ACTCTCGGGTCTATGTTGTTAATTAC 58.737 38.462 0.00 0.00 0.00 1.89
3314 6346 7.123847 ACTCTCGGGTCTATGTTGTTAATTACT 59.876 37.037 0.00 0.00 0.00 2.24
3315 6347 7.844009 TCTCGGGTCTATGTTGTTAATTACTT 58.156 34.615 0.00 0.00 0.00 2.24
3316 6348 7.977853 TCTCGGGTCTATGTTGTTAATTACTTC 59.022 37.037 0.00 0.00 0.00 3.01
3317 6349 7.043565 TCGGGTCTATGTTGTTAATTACTTCC 58.956 38.462 0.00 0.00 0.00 3.46
3318 6350 7.046033 CGGGTCTATGTTGTTAATTACTTCCT 58.954 38.462 0.00 0.00 0.00 3.36
3319 6351 7.551617 CGGGTCTATGTTGTTAATTACTTCCTT 59.448 37.037 0.00 0.00 0.00 3.36
3320 6352 8.890718 GGGTCTATGTTGTTAATTACTTCCTTC 58.109 37.037 0.00 0.00 0.00 3.46
3321 6353 9.444600 GGTCTATGTTGTTAATTACTTCCTTCA 57.555 33.333 0.00 0.00 0.00 3.02
3325 6357 7.696992 TGTTGTTAATTACTTCCTTCATCCC 57.303 36.000 0.00 0.00 0.00 3.85
3326 6358 6.373216 TGTTGTTAATTACTTCCTTCATCCCG 59.627 38.462 0.00 0.00 0.00 5.14
3327 6359 6.057321 TGTTAATTACTTCCTTCATCCCGT 57.943 37.500 0.00 0.00 0.00 5.28
3328 6360 7.185318 TGTTAATTACTTCCTTCATCCCGTA 57.815 36.000 0.00 0.00 0.00 4.02
3329 6361 7.622713 TGTTAATTACTTCCTTCATCCCGTAA 58.377 34.615 0.00 0.00 0.00 3.18
3330 6362 7.550196 TGTTAATTACTTCCTTCATCCCGTAAC 59.450 37.037 0.00 0.00 0.00 2.50
3331 6363 5.952347 ATTACTTCCTTCATCCCGTAACT 57.048 39.130 0.00 0.00 0.00 2.24
3332 6364 7.427989 AATTACTTCCTTCATCCCGTAACTA 57.572 36.000 0.00 0.00 0.00 2.24
3333 6365 4.732672 ACTTCCTTCATCCCGTAACTAC 57.267 45.455 0.00 0.00 0.00 2.73
3334 6366 4.351127 ACTTCCTTCATCCCGTAACTACT 58.649 43.478 0.00 0.00 0.00 2.57
3335 6367 4.776308 ACTTCCTTCATCCCGTAACTACTT 59.224 41.667 0.00 0.00 0.00 2.24
3336 6368 4.996788 TCCTTCATCCCGTAACTACTTC 57.003 45.455 0.00 0.00 0.00 3.01
3337 6369 3.703052 TCCTTCATCCCGTAACTACTTCC 59.297 47.826 0.00 0.00 0.00 3.46
3338 6370 3.705072 CCTTCATCCCGTAACTACTTCCT 59.295 47.826 0.00 0.00 0.00 3.36
3339 6371 4.202131 CCTTCATCCCGTAACTACTTCCTC 60.202 50.000 0.00 0.00 0.00 3.71
3340 6372 3.294214 TCATCCCGTAACTACTTCCTCC 58.706 50.000 0.00 0.00 0.00 4.30
3341 6373 1.755179 TCCCGTAACTACTTCCTCCG 58.245 55.000 0.00 0.00 0.00 4.63
3342 6374 1.004745 TCCCGTAACTACTTCCTCCGT 59.995 52.381 0.00 0.00 0.00 4.69
3343 6375 1.403323 CCCGTAACTACTTCCTCCGTC 59.597 57.143 0.00 0.00 0.00 4.79
3344 6376 1.403323 CCGTAACTACTTCCTCCGTCC 59.597 57.143 0.00 0.00 0.00 4.79
3345 6377 1.403323 CGTAACTACTTCCTCCGTCCC 59.597 57.143 0.00 0.00 0.00 4.46
3346 6378 2.450476 GTAACTACTTCCTCCGTCCCA 58.550 52.381 0.00 0.00 0.00 4.37
3347 6379 2.249309 AACTACTTCCTCCGTCCCAT 57.751 50.000 0.00 0.00 0.00 4.00
3348 6380 3.393426 AACTACTTCCTCCGTCCCATA 57.607 47.619 0.00 0.00 0.00 2.74
3349 6381 3.393426 ACTACTTCCTCCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
3350 6382 3.924922 ACTACTTCCTCCGTCCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
3351 6383 5.070823 ACTACTTCCTCCGTCCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
3352 6384 5.652324 ACTACTTCCTCCGTCCCATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
3353 6385 6.797707 ACTACTTCCTCCGTCCCATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
3354 6386 6.890814 ACTACTTCCTCCGTCCCATAATATAG 59.109 42.308 0.00 0.00 0.00 1.31
3355 6387 5.024118 ACTTCCTCCGTCCCATAATATAGG 58.976 45.833 0.00 0.00 0.00 2.57
3356 6388 4.959522 TCCTCCGTCCCATAATATAGGA 57.040 45.455 0.00 0.00 0.00 2.94
3357 6389 5.279562 TCCTCCGTCCCATAATATAGGAA 57.720 43.478 0.00 0.00 0.00 3.36
3358 6390 5.269991 TCCTCCGTCCCATAATATAGGAAG 58.730 45.833 0.00 0.00 0.00 3.46
3359 6391 4.406003 CCTCCGTCCCATAATATAGGAAGG 59.594 50.000 12.03 12.03 46.97 3.46
3362 6394 5.012328 CGTCCCATAATATAGGAAGGAGC 57.988 47.826 0.00 0.00 0.00 4.70
3363 6395 4.466370 CGTCCCATAATATAGGAAGGAGCA 59.534 45.833 0.00 0.00 0.00 4.26
3364 6396 5.129485 CGTCCCATAATATAGGAAGGAGCAT 59.871 44.000 0.00 0.00 0.00 3.79
3365 6397 6.352222 CGTCCCATAATATAGGAAGGAGCATT 60.352 42.308 0.00 0.00 0.00 3.56
3366 6398 7.406104 GTCCCATAATATAGGAAGGAGCATTT 58.594 38.462 0.00 0.00 0.00 2.32
3367 6399 7.890655 GTCCCATAATATAGGAAGGAGCATTTT 59.109 37.037 0.00 0.00 0.00 1.82
3368 6400 8.456124 TCCCATAATATAGGAAGGAGCATTTTT 58.544 33.333 0.00 0.00 0.00 1.94
3422 6454 5.446143 AAACGCATATGTTTTCTTGGACA 57.554 34.783 4.29 0.00 38.89 4.02
3423 6455 5.446143 AACGCATATGTTTTCTTGGACAA 57.554 34.783 4.29 0.00 0.00 3.18
3424 6456 5.446143 ACGCATATGTTTTCTTGGACAAA 57.554 34.783 4.29 0.00 0.00 2.83
3425 6457 5.837437 ACGCATATGTTTTCTTGGACAAAA 58.163 33.333 4.29 0.00 0.00 2.44
3426 6458 6.276847 ACGCATATGTTTTCTTGGACAAAAA 58.723 32.000 4.29 0.00 0.00 1.94
3448 6480 6.780706 AAAACCGCTCTTATAATATGGACG 57.219 37.500 0.00 0.00 0.00 4.79
3449 6481 4.451629 ACCGCTCTTATAATATGGACGG 57.548 45.455 0.00 0.00 43.52 4.79
3450 6482 4.084287 ACCGCTCTTATAATATGGACGGA 58.916 43.478 4.44 0.00 40.49 4.69
3451 6483 4.525487 ACCGCTCTTATAATATGGACGGAA 59.475 41.667 4.44 0.00 40.49 4.30
3452 6484 5.103000 CCGCTCTTATAATATGGACGGAAG 58.897 45.833 0.00 0.00 40.49 3.46
3453 6485 5.105877 CCGCTCTTATAATATGGACGGAAGA 60.106 44.000 0.00 0.00 40.49 2.87
3454 6486 6.387465 CGCTCTTATAATATGGACGGAAGAA 58.613 40.000 0.00 0.00 0.00 2.52
3455 6487 6.528423 CGCTCTTATAATATGGACGGAAGAAG 59.472 42.308 0.00 0.00 0.00 2.85
3456 6488 7.379750 GCTCTTATAATATGGACGGAAGAAGT 58.620 38.462 0.00 0.00 0.00 3.01
3457 6489 8.521176 GCTCTTATAATATGGACGGAAGAAGTA 58.479 37.037 0.00 0.00 0.00 2.24
3459 6491 8.521176 TCTTATAATATGGACGGAAGAAGTAGC 58.479 37.037 0.00 0.00 0.00 3.58
3460 6492 6.665992 ATAATATGGACGGAAGAAGTAGCA 57.334 37.500 0.00 0.00 0.00 3.49
3461 6493 2.674796 ATGGACGGAAGAAGTAGCAC 57.325 50.000 0.00 0.00 0.00 4.40
3462 6494 1.629043 TGGACGGAAGAAGTAGCACT 58.371 50.000 0.00 0.00 0.00 4.40
3463 6495 1.968493 TGGACGGAAGAAGTAGCACTT 59.032 47.619 1.82 1.82 41.95 3.16
3464 6496 2.367567 TGGACGGAAGAAGTAGCACTTT 59.632 45.455 3.56 0.00 38.80 2.66
3465 6497 3.181458 TGGACGGAAGAAGTAGCACTTTT 60.181 43.478 3.56 0.00 38.80 2.27
3466 6498 3.813724 GGACGGAAGAAGTAGCACTTTTT 59.186 43.478 3.56 4.36 38.80 1.94
3484 6516 4.668138 TTTTTAAGCCTGGTGGTCCTAT 57.332 40.909 0.00 0.00 35.27 2.57
3485 6517 4.668138 TTTTAAGCCTGGTGGTCCTATT 57.332 40.909 0.00 0.00 35.27 1.73
3486 6518 3.644966 TTAAGCCTGGTGGTCCTATTG 57.355 47.619 0.00 0.00 35.27 1.90
3487 6519 0.034089 AAGCCTGGTGGTCCTATTGC 60.034 55.000 0.00 0.00 35.27 3.56
3488 6520 1.207488 AGCCTGGTGGTCCTATTGCA 61.207 55.000 0.00 0.00 35.27 4.08
3489 6521 0.106519 GCCTGGTGGTCCTATTGCAT 60.107 55.000 0.00 0.00 35.27 3.96
3490 6522 1.142870 GCCTGGTGGTCCTATTGCATA 59.857 52.381 0.00 0.00 35.27 3.14
3491 6523 2.811873 GCCTGGTGGTCCTATTGCATAG 60.812 54.545 0.00 0.00 35.27 2.23
3492 6524 2.439507 CCTGGTGGTCCTATTGCATAGT 59.560 50.000 0.00 0.00 34.23 2.12
3493 6525 3.117888 CCTGGTGGTCCTATTGCATAGTT 60.118 47.826 0.00 0.00 34.23 2.24
3494 6526 4.102524 CCTGGTGGTCCTATTGCATAGTTA 59.897 45.833 0.00 0.00 34.23 2.24
3495 6527 5.221925 CCTGGTGGTCCTATTGCATAGTTAT 60.222 44.000 0.00 0.00 34.23 1.89
3496 6528 6.013725 CCTGGTGGTCCTATTGCATAGTTATA 60.014 42.308 0.00 0.00 34.23 0.98
3497 6529 7.311297 CCTGGTGGTCCTATTGCATAGTTATAT 60.311 40.741 0.00 0.00 34.23 0.86
3498 6530 7.620880 TGGTGGTCCTATTGCATAGTTATATC 58.379 38.462 0.00 0.00 34.23 1.63
3499 6531 7.236640 TGGTGGTCCTATTGCATAGTTATATCA 59.763 37.037 0.00 0.00 34.23 2.15
3500 6532 7.766278 GGTGGTCCTATTGCATAGTTATATCAG 59.234 40.741 0.00 0.00 0.00 2.90
3501 6533 8.531982 GTGGTCCTATTGCATAGTTATATCAGA 58.468 37.037 0.00 0.00 0.00 3.27
3502 6534 8.531982 TGGTCCTATTGCATAGTTATATCAGAC 58.468 37.037 0.00 0.00 0.00 3.51
3503 6535 8.754080 GGTCCTATTGCATAGTTATATCAGACT 58.246 37.037 0.00 0.00 0.00 3.24
3506 6538 9.376075 CCTATTGCATAGTTATATCAGACTTGG 57.624 37.037 0.00 0.00 0.00 3.61
3507 6539 9.935241 CTATTGCATAGTTATATCAGACTTGGT 57.065 33.333 0.00 0.00 0.00 3.67
3510 6542 9.764363 TTGCATAGTTATATCAGACTTGGTAAG 57.236 33.333 0.00 0.00 0.00 2.34
3511 6543 8.367911 TGCATAGTTATATCAGACTTGGTAAGG 58.632 37.037 0.00 0.00 0.00 2.69
3512 6544 8.585881 GCATAGTTATATCAGACTTGGTAAGGA 58.414 37.037 0.00 0.00 0.00 3.36
3513 6545 9.915629 CATAGTTATATCAGACTTGGTAAGGAC 57.084 37.037 0.00 0.00 0.00 3.85
3515 6547 6.326843 AGTTATATCAGACTTGGTAAGGACCC 59.673 42.308 0.00 0.00 46.32 4.46
3516 6548 1.652947 TCAGACTTGGTAAGGACCCC 58.347 55.000 0.00 0.00 46.32 4.95
3517 6549 1.151413 TCAGACTTGGTAAGGACCCCT 59.849 52.381 0.00 0.00 46.32 4.79
3518 6550 2.384375 TCAGACTTGGTAAGGACCCCTA 59.616 50.000 0.00 0.00 46.32 3.53
3519 6551 3.178865 CAGACTTGGTAAGGACCCCTAA 58.821 50.000 0.00 0.00 46.32 2.69
3520 6552 3.585732 CAGACTTGGTAAGGACCCCTAAA 59.414 47.826 0.00 0.00 46.32 1.85
3521 6553 4.042435 CAGACTTGGTAAGGACCCCTAAAA 59.958 45.833 0.00 0.00 46.32 1.52
3522 6554 4.042560 AGACTTGGTAAGGACCCCTAAAAC 59.957 45.833 0.00 0.00 46.32 2.43
3523 6555 3.723154 ACTTGGTAAGGACCCCTAAAACA 59.277 43.478 0.00 0.00 46.32 2.83
3524 6556 4.168479 ACTTGGTAAGGACCCCTAAAACAA 59.832 41.667 0.00 0.00 46.32 2.83
3525 6557 4.810584 TGGTAAGGACCCCTAAAACAAA 57.189 40.909 0.00 0.00 46.32 2.83
3526 6558 5.342361 TGGTAAGGACCCCTAAAACAAAT 57.658 39.130 0.00 0.00 46.32 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.127682 ACCTCAAATCCATACAAAAGCCATC 59.872 40.000 0.00 0.00 0.00 3.51
1 2 5.025453 ACCTCAAATCCATACAAAAGCCAT 58.975 37.500 0.00 0.00 0.00 4.40
2 3 4.220382 CACCTCAAATCCATACAAAAGCCA 59.780 41.667 0.00 0.00 0.00 4.75
3 4 4.220602 ACACCTCAAATCCATACAAAAGCC 59.779 41.667 0.00 0.00 0.00 4.35
12 13 9.645128 TCAATCAATATAACACCTCAAATCCAT 57.355 29.630 0.00 0.00 0.00 3.41
66 1451 1.071699 ACCTACGTGCCACAAATCTGT 59.928 47.619 0.00 0.00 35.63 3.41
67 1452 1.732259 GACCTACGTGCCACAAATCTG 59.268 52.381 0.00 0.00 0.00 2.90
68 1453 1.338769 GGACCTACGTGCCACAAATCT 60.339 52.381 0.00 0.00 0.00 2.40
91 1492 1.461725 GCCAAAAATAAAAGCACGCGC 60.462 47.619 5.73 0.00 38.99 6.86
92 1493 2.058057 AGCCAAAAATAAAAGCACGCG 58.942 42.857 3.53 3.53 0.00 6.01
140 1542 8.806146 AGCATAACTTATTTGGACTGTTCATTT 58.194 29.630 0.00 0.00 0.00 2.32
143 1545 7.759489 AAGCATAACTTATTTGGACTGTTCA 57.241 32.000 0.00 0.00 36.62 3.18
249 1651 8.890718 ACTAAGTTTCAAGAGTTGAACCTTAAC 58.109 33.333 15.80 6.85 46.74 2.01
281 1683 8.719648 GCACAAAAATCATGATTTTATTGGTCA 58.280 29.630 35.08 0.00 46.76 4.02
353 1758 4.141711 TGTGGTTTTCTCACTGCTCTTACT 60.142 41.667 0.00 0.00 36.21 2.24
364 1770 7.873719 TTATCTCAAACTTGTGGTTTTCTCA 57.126 32.000 0.00 0.00 44.77 3.27
422 1828 3.576078 CCCACATGAGGGCATAGTAAA 57.424 47.619 15.85 0.00 43.10 2.01
436 1843 3.253188 CGTGAAGTTGTTGAATCCCACAT 59.747 43.478 0.00 0.00 0.00 3.21
462 1869 1.895707 GCCCCTCGATTGCCTCATG 60.896 63.158 0.00 0.00 0.00 3.07
463 1870 2.512896 GCCCCTCGATTGCCTCAT 59.487 61.111 0.00 0.00 0.00 2.90
485 1892 4.853142 CCTGCCATGCCATGCCCT 62.853 66.667 0.00 0.00 0.00 5.19
520 1927 5.065090 TCAAAACAATACAGATGCATCGGAG 59.935 40.000 29.91 20.92 0.00 4.63
548 1955 4.358494 ACCGTCGTGTTCATTTTCAAAA 57.642 36.364 0.00 0.00 0.00 2.44
589 1996 1.531149 CGCGGACAAGTCAACTGATTT 59.469 47.619 0.00 0.00 0.00 2.17
644 2052 8.515695 TGAGAGCATCATTTGACTAATTGATT 57.484 30.769 0.00 0.00 35.70 2.57
683 2100 0.743345 GCGCTTGGAGAACCGGTAAT 60.743 55.000 8.00 0.00 39.42 1.89
753 2178 1.671166 CCGGTGGTGTGTCTGATCA 59.329 57.895 0.00 0.00 0.00 2.92
1011 2481 0.539051 CGAAGGAGAGCTGGTGGATT 59.461 55.000 0.00 0.00 0.00 3.01
1012 2482 1.965754 GCGAAGGAGAGCTGGTGGAT 61.966 60.000 0.00 0.00 0.00 3.41
1680 4659 1.454663 GATCAGCTTGGGCCCTTCC 60.455 63.158 25.70 10.78 39.73 3.46
2280 5287 3.717294 CCCAGGAACCTGTCGGGG 61.717 72.222 17.92 9.36 42.15 5.73
2547 5554 4.813296 TCGAGAAAAGCAGAGGAAAAAC 57.187 40.909 0.00 0.00 0.00 2.43
2678 5691 0.837272 ACATCCCAATACACCGAGGG 59.163 55.000 0.00 0.00 42.86 4.30
2692 5705 5.634859 CACTGACTAATTGGCAAAAACATCC 59.365 40.000 3.01 0.00 30.26 3.51
2729 5751 6.966751 TCAGTAAGGTAGTAGGAGTACATGT 58.033 40.000 2.69 2.69 0.00 3.21
2731 5753 7.813331 TGATCAGTAAGGTAGTAGGAGTACAT 58.187 38.462 0.00 0.00 0.00 2.29
2732 5754 7.204243 TGATCAGTAAGGTAGTAGGAGTACA 57.796 40.000 0.00 0.00 0.00 2.90
2733 5755 7.255208 GCTTGATCAGTAAGGTAGTAGGAGTAC 60.255 44.444 0.00 0.00 0.00 2.73
2734 5756 6.771749 GCTTGATCAGTAAGGTAGTAGGAGTA 59.228 42.308 0.00 0.00 0.00 2.59
2736 5758 5.830991 AGCTTGATCAGTAAGGTAGTAGGAG 59.169 44.000 0.00 0.00 34.41 3.69
2737 5759 5.594725 CAGCTTGATCAGTAAGGTAGTAGGA 59.405 44.000 0.00 0.00 34.41 2.94
2739 5761 5.361285 ACCAGCTTGATCAGTAAGGTAGTAG 59.639 44.000 9.41 0.00 34.41 2.57
2740 5762 5.269991 ACCAGCTTGATCAGTAAGGTAGTA 58.730 41.667 9.41 0.00 34.41 1.82
2741 5763 4.097418 ACCAGCTTGATCAGTAAGGTAGT 58.903 43.478 9.41 1.31 34.41 2.73
2742 5764 4.744795 ACCAGCTTGATCAGTAAGGTAG 57.255 45.455 9.41 0.75 34.41 3.18
2743 5765 6.183360 GGATAACCAGCTTGATCAGTAAGGTA 60.183 42.308 10.99 0.00 34.41 3.08
2898 5923 6.404403 GGAGGTAGGTTTGCTGTTAAATTAGC 60.404 42.308 0.00 0.00 40.29 3.09
2937 5963 6.680131 GCCCGATGTATGATCATAGAGAGAAG 60.680 46.154 15.83 8.60 0.00 2.85
2992 6020 1.405256 CGATCAGACTTCTGCAAGCCT 60.405 52.381 0.99 0.00 43.46 4.58
3001 6029 2.107141 CCGGCCCGATCAGACTTC 59.893 66.667 3.71 0.00 0.00 3.01
3002 6030 3.470888 CCCGGCCCGATCAGACTT 61.471 66.667 3.71 0.00 0.00 3.01
3014 6042 4.986708 TCCAAAACCCAGCCCGGC 62.987 66.667 0.00 0.00 0.00 6.13
3015 6043 2.989253 GTCCAAAACCCAGCCCGG 60.989 66.667 0.00 0.00 0.00 5.73
3016 6044 2.989253 GGTCCAAAACCCAGCCCG 60.989 66.667 0.00 0.00 42.85 6.13
3017 6045 2.989253 CGGTCCAAAACCCAGCCC 60.989 66.667 0.00 0.00 46.27 5.19
3018 6046 2.203437 ACGGTCCAAAACCCAGCC 60.203 61.111 0.00 0.00 46.27 4.85
3019 6047 3.039134 CACGGTCCAAAACCCAGC 58.961 61.111 0.00 0.00 46.27 4.85
3020 6048 1.106944 AAGCACGGTCCAAAACCCAG 61.107 55.000 0.00 0.00 46.27 4.45
3021 6049 1.076632 AAGCACGGTCCAAAACCCA 60.077 52.632 0.00 0.00 46.27 4.51
3022 6050 1.362355 CAAGCACGGTCCAAAACCC 59.638 57.895 0.00 0.00 46.27 4.11
3023 6051 1.299850 GCAAGCACGGTCCAAAACC 60.300 57.895 0.00 0.00 45.45 3.27
3024 6052 0.179124 TTGCAAGCACGGTCCAAAAC 60.179 50.000 0.00 0.00 0.00 2.43
3025 6053 0.532573 TTTGCAAGCACGGTCCAAAA 59.467 45.000 0.00 0.00 0.00 2.44
3026 6054 0.532573 TTTTGCAAGCACGGTCCAAA 59.467 45.000 0.00 0.00 0.00 3.28
3027 6055 0.102120 CTTTTGCAAGCACGGTCCAA 59.898 50.000 0.00 0.00 0.00 3.53
3028 6056 1.732917 CTTTTGCAAGCACGGTCCA 59.267 52.632 0.00 0.00 0.00 4.02
3029 6057 4.633980 CTTTTGCAAGCACGGTCC 57.366 55.556 0.00 0.00 0.00 4.46
3040 6068 2.230266 TGTTTAAGGATCGGGCTTTTGC 59.770 45.455 0.00 0.00 46.64 3.68
3041 6069 4.234574 GTTGTTTAAGGATCGGGCTTTTG 58.765 43.478 0.00 0.00 0.00 2.44
3042 6070 3.892588 TGTTGTTTAAGGATCGGGCTTTT 59.107 39.130 0.00 0.00 0.00 2.27
3104 6135 5.350504 TTTTGGTTGCTTTTCAAGATGGA 57.649 34.783 0.00 0.00 34.91 3.41
3135 6167 1.304879 CCTGATTTTTGGGCCGGGA 60.305 57.895 2.18 0.00 0.00 5.14
3214 6246 1.061546 TCAGGTCGGGCTTACCTTTT 58.938 50.000 8.35 0.00 45.26 2.27
3215 6247 0.323957 GTCAGGTCGGGCTTACCTTT 59.676 55.000 8.35 0.00 45.26 3.11
3216 6248 1.551019 GGTCAGGTCGGGCTTACCTT 61.551 60.000 8.35 0.00 45.26 3.50
3221 6253 3.322466 CCAGGTCAGGTCGGGCTT 61.322 66.667 0.00 0.00 0.00 4.35
3222 6254 4.316823 TCCAGGTCAGGTCGGGCT 62.317 66.667 0.00 0.00 0.00 5.19
3223 6255 4.083862 GTCCAGGTCAGGTCGGGC 62.084 72.222 0.00 0.00 0.00 6.13
3226 6258 2.650116 CCCAGTCCAGGTCAGGTCG 61.650 68.421 0.00 0.00 0.00 4.79
3227 6259 1.128188 AACCCAGTCCAGGTCAGGTC 61.128 60.000 0.00 0.00 36.27 3.85
3228 6260 0.697854 AAACCCAGTCCAGGTCAGGT 60.698 55.000 0.00 0.00 36.27 4.00
3229 6261 0.478507 AAAACCCAGTCCAGGTCAGG 59.521 55.000 0.00 0.00 36.27 3.86
3230 6262 1.956477 CAAAAACCCAGTCCAGGTCAG 59.044 52.381 0.00 0.00 36.27 3.51
3231 6263 1.410932 CCAAAAACCCAGTCCAGGTCA 60.411 52.381 0.00 0.00 36.27 4.02
3233 6265 0.930726 TCCAAAAACCCAGTCCAGGT 59.069 50.000 0.00 0.00 40.14 4.00
3234 6266 1.620822 CTCCAAAAACCCAGTCCAGG 58.379 55.000 0.00 0.00 0.00 4.45
3235 6267 0.961753 GCTCCAAAAACCCAGTCCAG 59.038 55.000 0.00 0.00 0.00 3.86
3236 6268 0.555769 AGCTCCAAAAACCCAGTCCA 59.444 50.000 0.00 0.00 0.00 4.02
3239 6271 0.469892 CCCAGCTCCAAAAACCCAGT 60.470 55.000 0.00 0.00 0.00 4.00
3240 6272 1.820010 GCCCAGCTCCAAAAACCCAG 61.820 60.000 0.00 0.00 0.00 4.45
3241 6273 1.836604 GCCCAGCTCCAAAAACCCA 60.837 57.895 0.00 0.00 0.00 4.51
3242 6274 1.121407 AAGCCCAGCTCCAAAAACCC 61.121 55.000 0.00 0.00 38.25 4.11
3243 6275 0.033920 CAAGCCCAGCTCCAAAAACC 59.966 55.000 0.00 0.00 38.25 3.27
3244 6276 0.033920 CCAAGCCCAGCTCCAAAAAC 59.966 55.000 0.00 0.00 38.25 2.43
3245 6277 1.120795 CCCAAGCCCAGCTCCAAAAA 61.121 55.000 0.00 0.00 38.25 1.94
3246 6278 1.533753 CCCAAGCCCAGCTCCAAAA 60.534 57.895 0.00 0.00 38.25 2.44
3247 6279 2.118076 CCCAAGCCCAGCTCCAAA 59.882 61.111 0.00 0.00 38.25 3.28
3248 6280 2.777960 AACCCAAGCCCAGCTCCAA 61.778 57.895 0.00 0.00 38.25 3.53
3249 6281 3.185203 AACCCAAGCCCAGCTCCA 61.185 61.111 0.00 0.00 38.25 3.86
3250 6282 2.677875 CAACCCAAGCCCAGCTCC 60.678 66.667 0.00 0.00 38.25 4.70
3251 6283 2.677875 CCAACCCAAGCCCAGCTC 60.678 66.667 0.00 0.00 38.25 4.09
3252 6284 4.305956 CCCAACCCAAGCCCAGCT 62.306 66.667 0.00 0.00 42.56 4.24
3254 6286 4.305956 AGCCCAACCCAAGCCCAG 62.306 66.667 0.00 0.00 0.00 4.45
3255 6287 4.619320 CAGCCCAACCCAAGCCCA 62.619 66.667 0.00 0.00 0.00 5.36
3256 6288 4.621087 ACAGCCCAACCCAAGCCC 62.621 66.667 0.00 0.00 0.00 5.19
3257 6289 2.991540 GACAGCCCAACCCAAGCC 60.992 66.667 0.00 0.00 0.00 4.35
3258 6290 2.991540 GGACAGCCCAACCCAAGC 60.992 66.667 0.00 0.00 34.14 4.01
3259 6291 2.520458 TGGACAGCCCAACCCAAG 59.480 61.111 0.00 0.00 43.29 3.61
3267 6299 0.257039 AACCTGATCATGGACAGCCC 59.743 55.000 15.51 0.00 33.40 5.19
3268 6300 2.134789 AAACCTGATCATGGACAGCC 57.865 50.000 15.51 0.00 33.40 4.85
3299 6331 9.403583 GGGATGAAGGAAGTAATTAACAACATA 57.596 33.333 0.00 0.00 0.00 2.29
3303 6335 6.478129 ACGGGATGAAGGAAGTAATTAACAA 58.522 36.000 0.00 0.00 0.00 2.83
3304 6336 6.057321 ACGGGATGAAGGAAGTAATTAACA 57.943 37.500 0.00 0.00 0.00 2.41
3305 6337 7.767659 AGTTACGGGATGAAGGAAGTAATTAAC 59.232 37.037 0.00 0.00 0.00 2.01
3306 6338 7.854337 AGTTACGGGATGAAGGAAGTAATTAA 58.146 34.615 0.00 0.00 0.00 1.40
3307 6339 7.427989 AGTTACGGGATGAAGGAAGTAATTA 57.572 36.000 0.00 0.00 0.00 1.40
3308 6340 6.309389 AGTTACGGGATGAAGGAAGTAATT 57.691 37.500 0.00 0.00 0.00 1.40
3309 6341 5.952347 AGTTACGGGATGAAGGAAGTAAT 57.048 39.130 0.00 0.00 0.00 1.89
3310 6342 5.954150 AGTAGTTACGGGATGAAGGAAGTAA 59.046 40.000 0.00 0.00 0.00 2.24
3311 6343 5.513233 AGTAGTTACGGGATGAAGGAAGTA 58.487 41.667 0.00 0.00 0.00 2.24
3312 6344 4.351127 AGTAGTTACGGGATGAAGGAAGT 58.649 43.478 0.00 0.00 0.00 3.01
3313 6345 5.340439 AAGTAGTTACGGGATGAAGGAAG 57.660 43.478 0.00 0.00 0.00 3.46
3314 6346 4.161001 GGAAGTAGTTACGGGATGAAGGAA 59.839 45.833 0.00 0.00 0.00 3.36
3315 6347 3.703052 GGAAGTAGTTACGGGATGAAGGA 59.297 47.826 0.00 0.00 0.00 3.36
3316 6348 3.705072 AGGAAGTAGTTACGGGATGAAGG 59.295 47.826 0.00 0.00 0.00 3.46
3317 6349 4.202131 GGAGGAAGTAGTTACGGGATGAAG 60.202 50.000 0.00 0.00 0.00 3.02
3318 6350 3.703052 GGAGGAAGTAGTTACGGGATGAA 59.297 47.826 0.00 0.00 0.00 2.57
3319 6351 3.294214 GGAGGAAGTAGTTACGGGATGA 58.706 50.000 0.00 0.00 0.00 2.92
3320 6352 2.034305 CGGAGGAAGTAGTTACGGGATG 59.966 54.545 0.00 0.00 0.00 3.51
3321 6353 2.305009 CGGAGGAAGTAGTTACGGGAT 58.695 52.381 0.00 0.00 0.00 3.85
3322 6354 1.004745 ACGGAGGAAGTAGTTACGGGA 59.995 52.381 0.00 0.00 0.00 5.14
3323 6355 1.403323 GACGGAGGAAGTAGTTACGGG 59.597 57.143 0.00 0.00 0.00 5.28
3324 6356 1.403323 GGACGGAGGAAGTAGTTACGG 59.597 57.143 0.00 0.00 0.00 4.02
3325 6357 1.403323 GGGACGGAGGAAGTAGTTACG 59.597 57.143 0.00 0.00 0.00 3.18
3326 6358 2.450476 TGGGACGGAGGAAGTAGTTAC 58.550 52.381 0.00 0.00 0.00 2.50
3327 6359 2.905415 TGGGACGGAGGAAGTAGTTA 57.095 50.000 0.00 0.00 0.00 2.24
3328 6360 2.249309 ATGGGACGGAGGAAGTAGTT 57.751 50.000 0.00 0.00 0.00 2.24
3329 6361 3.393426 TTATGGGACGGAGGAAGTAGT 57.607 47.619 0.00 0.00 0.00 2.73
3330 6362 6.321690 CCTATATTATGGGACGGAGGAAGTAG 59.678 46.154 0.00 0.00 31.57 2.57
3331 6363 6.011362 TCCTATATTATGGGACGGAGGAAGTA 60.011 42.308 4.74 0.00 34.71 2.24
3332 6364 5.024118 CCTATATTATGGGACGGAGGAAGT 58.976 45.833 0.00 0.00 31.57 3.01
3333 6365 5.269991 TCCTATATTATGGGACGGAGGAAG 58.730 45.833 4.74 0.00 34.71 3.46
3334 6366 5.279562 TCCTATATTATGGGACGGAGGAA 57.720 43.478 4.74 0.00 34.71 3.36
3335 6367 4.959522 TCCTATATTATGGGACGGAGGA 57.040 45.455 4.74 0.00 34.71 3.71
3336 6368 5.599999 CTTCCTATATTATGGGACGGAGG 57.400 47.826 8.19 0.00 39.88 4.30
3339 6371 4.141914 GCTCCTTCCTATATTATGGGACGG 60.142 50.000 19.80 19.80 46.60 4.79
3340 6372 4.466370 TGCTCCTTCCTATATTATGGGACG 59.534 45.833 8.19 6.89 39.88 4.79
3341 6373 6.567602 ATGCTCCTTCCTATATTATGGGAC 57.432 41.667 8.19 0.00 39.88 4.46
3342 6374 7.588866 AAATGCTCCTTCCTATATTATGGGA 57.411 36.000 4.74 4.74 38.24 4.37
3343 6375 8.655935 AAAAATGCTCCTTCCTATATTATGGG 57.344 34.615 0.00 0.00 0.00 4.00
3398 6430 6.276847 TGTCCAAGAAAACATATGCGTTTTT 58.723 32.000 1.58 2.44 46.39 1.94
3400 6432 5.446143 TGTCCAAGAAAACATATGCGTTT 57.554 34.783 1.58 3.62 40.79 3.60
3401 6433 5.446143 TTGTCCAAGAAAACATATGCGTT 57.554 34.783 1.58 0.00 0.00 4.84
3402 6434 5.446143 TTTGTCCAAGAAAACATATGCGT 57.554 34.783 1.58 0.00 0.00 5.24
3403 6435 6.761731 TTTTTGTCCAAGAAAACATATGCG 57.238 33.333 1.58 0.00 0.00 4.73
3424 6456 6.204108 CCGTCCATATTATAAGAGCGGTTTTT 59.796 38.462 0.00 0.00 32.99 1.94
3425 6457 5.699458 CCGTCCATATTATAAGAGCGGTTTT 59.301 40.000 0.00 0.00 32.99 2.43
3426 6458 5.011329 TCCGTCCATATTATAAGAGCGGTTT 59.989 40.000 11.89 0.00 38.07 3.27
3427 6459 4.525487 TCCGTCCATATTATAAGAGCGGTT 59.475 41.667 11.89 0.00 38.07 4.44
3428 6460 4.084287 TCCGTCCATATTATAAGAGCGGT 58.916 43.478 11.89 0.00 38.07 5.68
3429 6461 4.713824 TCCGTCCATATTATAAGAGCGG 57.286 45.455 0.00 0.00 38.20 5.52
3430 6462 5.950883 TCTTCCGTCCATATTATAAGAGCG 58.049 41.667 0.00 0.00 0.00 5.03
3431 6463 7.379750 ACTTCTTCCGTCCATATTATAAGAGC 58.620 38.462 0.00 0.00 0.00 4.09
3433 6465 8.521176 GCTACTTCTTCCGTCCATATTATAAGA 58.479 37.037 0.00 0.00 0.00 2.10
3434 6466 8.304596 TGCTACTTCTTCCGTCCATATTATAAG 58.695 37.037 0.00 0.00 0.00 1.73
3435 6467 8.086522 GTGCTACTTCTTCCGTCCATATTATAA 58.913 37.037 0.00 0.00 0.00 0.98
3436 6468 7.450634 AGTGCTACTTCTTCCGTCCATATTATA 59.549 37.037 0.00 0.00 0.00 0.98
3437 6469 6.267928 AGTGCTACTTCTTCCGTCCATATTAT 59.732 38.462 0.00 0.00 0.00 1.28
3438 6470 5.597182 AGTGCTACTTCTTCCGTCCATATTA 59.403 40.000 0.00 0.00 0.00 0.98
3439 6471 4.406003 AGTGCTACTTCTTCCGTCCATATT 59.594 41.667 0.00 0.00 0.00 1.28
3440 6472 3.961408 AGTGCTACTTCTTCCGTCCATAT 59.039 43.478 0.00 0.00 0.00 1.78
3441 6473 3.362706 AGTGCTACTTCTTCCGTCCATA 58.637 45.455 0.00 0.00 0.00 2.74
3442 6474 2.180276 AGTGCTACTTCTTCCGTCCAT 58.820 47.619 0.00 0.00 0.00 3.41
3443 6475 1.629043 AGTGCTACTTCTTCCGTCCA 58.371 50.000 0.00 0.00 0.00 4.02
3444 6476 2.745515 AAGTGCTACTTCTTCCGTCC 57.254 50.000 0.00 0.00 31.77 4.79
3463 6495 4.668138 ATAGGACCACCAGGCTTAAAAA 57.332 40.909 0.00 0.00 39.06 1.94
3464 6496 4.340617 CAATAGGACCACCAGGCTTAAAA 58.659 43.478 0.00 0.00 39.06 1.52
3465 6497 3.876156 GCAATAGGACCACCAGGCTTAAA 60.876 47.826 0.00 0.00 39.06 1.52
3466 6498 2.356741 GCAATAGGACCACCAGGCTTAA 60.357 50.000 0.00 0.00 39.06 1.85
3467 6499 1.211949 GCAATAGGACCACCAGGCTTA 59.788 52.381 0.00 0.00 39.06 3.09
3468 6500 0.034089 GCAATAGGACCACCAGGCTT 60.034 55.000 0.00 0.00 39.06 4.35
3469 6501 1.207488 TGCAATAGGACCACCAGGCT 61.207 55.000 0.00 0.00 39.06 4.58
3470 6502 0.106519 ATGCAATAGGACCACCAGGC 60.107 55.000 0.00 0.00 39.06 4.85
3471 6503 3.131709 CTATGCAATAGGACCACCAGG 57.868 52.381 0.00 0.00 43.25 4.45
3484 6516 9.764363 CTTACCAAGTCTGATATAACTATGCAA 57.236 33.333 0.00 0.00 0.00 4.08
3485 6517 8.367911 CCTTACCAAGTCTGATATAACTATGCA 58.632 37.037 0.00 0.00 0.00 3.96
3486 6518 8.585881 TCCTTACCAAGTCTGATATAACTATGC 58.414 37.037 0.00 0.00 0.00 3.14
3487 6519 9.915629 GTCCTTACCAAGTCTGATATAACTATG 57.084 37.037 0.00 0.00 0.00 2.23
3488 6520 9.091220 GGTCCTTACCAAGTCTGATATAACTAT 57.909 37.037 0.00 0.00 45.98 2.12
3489 6521 8.474710 GGTCCTTACCAAGTCTGATATAACTA 57.525 38.462 0.00 0.00 45.98 2.24
3490 6522 7.362802 GGTCCTTACCAAGTCTGATATAACT 57.637 40.000 0.00 0.00 45.98 2.24


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

AutoCloner maintained by Alex Coulton.