Multiple sequence alignment - TraesCS2D01G006400

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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 TraesCS2D01G006400 chr2D 100.000 5323 0 0 1 5323 3020539 3015217 0.000000e+00 9830.0
1 TraesCS2D01G006400 chr2A 92.037 1306 78 14 3464 4752 2696270 2697566 0.000000e+00 1812.0
2 TraesCS2D01G006400 chr2A 87.187 1436 76 25 1 1403 2692623 2693983 0.000000e+00 1533.0
3 TraesCS2D01G006400 chr2A 93.653 646 34 5 1958 2598 2694971 2695614 0.000000e+00 959.0
4 TraesCS2D01G006400 chr2A 81.651 545 72 19 4740 5277 2697586 2698109 1.370000e-115 427.0
5 TraesCS2D01G006400 chr2A 88.636 308 23 10 1604 1901 2694517 2694822 1.090000e-96 364.0
6 TraesCS2D01G006400 chr2A 100.000 36 0 0 1926 1961 2694922 2694957 3.440000e-07 67.6
7 TraesCS2D01G006400 chr2B 90.228 1361 108 17 3413 4757 7657312 7658663 0.000000e+00 1753.0
8 TraesCS2D01G006400 chr2B 86.673 983 61 30 1505 2448 7655284 7656235 0.000000e+00 1026.0
9 TraesCS2D01G006400 chr2B 84.466 1030 98 24 2436 3413 7656260 7657279 0.000000e+00 959.0
10 TraesCS2D01G006400 chr2B 85.685 964 56 35 499 1424 7654365 7655284 0.000000e+00 941.0
11 TraesCS2D01G006400 chr2B 93.782 193 10 1 2 192 7652437 7652629 6.750000e-74 289.0
12 TraesCS2D01G006400 chr2B 87.879 165 6 7 350 504 7652784 7652944 1.180000e-41 182.0
13 TraesCS2D01G006400 chr2B 89.764 127 9 3 4861 4983 7658707 7658833 5.520000e-35 159.0
14 TraesCS2D01G006400 chr4B 100.000 29 0 0 4179 4207 304880588 304880616 3.000000e-03 54.7
15 TraesCS2D01G006400 chr1B 100.000 29 0 0 4179 4207 77166817 77166789 3.000000e-03 54.7


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 TraesCS2D01G006400 chr2D 3015217 3020539 5322 True 9830.000000 9830 100.000000 1 5323 1 chr2D.!!$R1 5322
1 TraesCS2D01G006400 chr2A 2692623 2698109 5486 False 860.433333 1812 90.527333 1 5277 6 chr2A.!!$F1 5276
2 TraesCS2D01G006400 chr2B 7652437 7658833 6396 False 758.428571 1753 88.353857 2 4983 7 chr2B.!!$F1 4981

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
995 2511 0.035630 AGCAGAGGCAGTGATTCACC 60.036 55.000 13.14 0.0 44.61 4.02 F
1815 3710 0.383949 TCCACAAAAACTTGCTCGGC 59.616 50.000 0.00 0.0 0.00 5.54 F
1983 3988 2.053627 CTTCAATGTTTTGAGCACGGC 58.946 47.619 0.00 0.0 42.60 5.68 F
2003 4008 2.233676 GCTGGAAAAGGGGGTTAACATG 59.766 50.000 8.10 0.0 0.00 3.21 F
3889 6125 0.818445 CATCACCAGCATCAGAGCCC 60.818 60.000 0.00 0.0 34.23 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 3911 0.038744 ATGACCTGGGGAGCACTTTG 59.961 55.000 0.00 0.00 0.00 2.77 R
3533 5769 1.226295 CGTCACTCGATGCTGCGTA 60.226 57.895 0.00 0.00 42.86 4.42 R
3872 6108 1.919816 TGGGCTCTGATGCTGGTGA 60.920 57.895 0.00 0.00 0.00 4.02 R
3935 6177 4.388499 TTCTGGAACTCCGCGGCC 62.388 66.667 23.51 17.02 39.43 6.13 R
4759 7018 0.036010 CTTGACCTCACCAATCGCCT 60.036 55.000 0.00 0.00 0.00 5.52 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
114 117 6.566914 AGGGAAACATTAAATGGGGTTTAGA 58.433 36.000 0.00 0.00 33.92 2.10
118 121 8.536175 GGAAACATTAAATGGGGTTTAGATTCA 58.464 33.333 0.00 0.00 33.92 2.57
165 168 1.202770 AGCCACCGGTAAATAGCATCC 60.203 52.381 6.87 0.00 0.00 3.51
170 173 0.321298 CGGTAAATAGCATCCCCCGG 60.321 60.000 0.00 0.00 0.00 5.73
219 223 3.403558 GTCTGGAGGGGCCTCACC 61.404 72.222 13.05 13.05 44.40 4.02
245 249 7.268186 TCAACATATCGTGTACAACTTAACG 57.732 36.000 0.00 0.00 41.14 3.18
246 250 6.862608 TCAACATATCGTGTACAACTTAACGT 59.137 34.615 0.00 0.00 41.14 3.99
248 252 7.041187 ACATATCGTGTACAACTTAACGTTG 57.959 36.000 11.99 13.08 45.02 4.10
256 293 3.131240 CAACTTAACGTTGCCATAGCC 57.869 47.619 11.99 0.00 45.70 3.93
269 306 5.744666 TGCCATAGCCGACTATTTAAAAC 57.255 39.130 0.00 0.00 36.96 2.43
314 351 2.993449 GAGGAGAACGTCGACTCTTT 57.007 50.000 14.70 3.77 34.11 2.52
315 352 3.285816 GAGGAGAACGTCGACTCTTTT 57.714 47.619 14.70 3.22 34.11 2.27
342 379 6.745794 TTTTTGGGTGAGAAATCTTCCAAT 57.254 33.333 11.73 0.00 33.91 3.16
343 380 5.982890 TTTGGGTGAGAAATCTTCCAATC 57.017 39.130 11.73 0.00 33.91 2.67
344 381 4.934797 TGGGTGAGAAATCTTCCAATCT 57.065 40.909 7.52 0.00 0.00 2.40
345 382 4.592942 TGGGTGAGAAATCTTCCAATCTG 58.407 43.478 7.52 0.00 0.00 2.90
346 383 4.043310 TGGGTGAGAAATCTTCCAATCTGT 59.957 41.667 7.52 0.00 0.00 3.41
347 384 5.012893 GGGTGAGAAATCTTCCAATCTGTT 58.987 41.667 7.52 0.00 0.00 3.16
348 385 5.124617 GGGTGAGAAATCTTCCAATCTGTTC 59.875 44.000 7.52 0.00 0.00 3.18
456 500 0.586319 AACGTGCCATGCGTATATGC 59.414 50.000 10.13 10.13 42.10 3.14
544 2027 0.758734 TCCATGTATTGCGGAGAGGG 59.241 55.000 0.00 0.00 0.00 4.30
545 2028 0.469917 CCATGTATTGCGGAGAGGGT 59.530 55.000 0.00 0.00 0.00 4.34
546 2029 1.541233 CCATGTATTGCGGAGAGGGTC 60.541 57.143 0.00 0.00 0.00 4.46
547 2030 0.389391 ATGTATTGCGGAGAGGGTCG 59.611 55.000 0.00 0.00 0.00 4.79
548 2031 1.067582 GTATTGCGGAGAGGGTCGG 59.932 63.158 0.00 0.00 0.00 4.79
596 2079 2.218953 TAAGCGCAACGATTAGGGAG 57.781 50.000 11.47 0.00 36.67 4.30
597 2080 0.462047 AAGCGCAACGATTAGGGAGG 60.462 55.000 11.47 0.00 32.48 4.30
598 2081 1.887707 GCGCAACGATTAGGGAGGG 60.888 63.158 0.30 0.00 0.00 4.30
599 2082 1.820581 CGCAACGATTAGGGAGGGA 59.179 57.895 0.00 0.00 0.00 4.20
600 2083 0.393077 CGCAACGATTAGGGAGGGAT 59.607 55.000 0.00 0.00 0.00 3.85
601 2084 1.873903 CGCAACGATTAGGGAGGGATG 60.874 57.143 0.00 0.00 0.00 3.51
602 2085 1.543429 GCAACGATTAGGGAGGGATGG 60.543 57.143 0.00 0.00 0.00 3.51
603 2086 0.765510 AACGATTAGGGAGGGATGGC 59.234 55.000 0.00 0.00 0.00 4.40
604 2087 1.293498 CGATTAGGGAGGGATGGCG 59.707 63.158 0.00 0.00 0.00 5.69
605 2088 1.679898 GATTAGGGAGGGATGGCGG 59.320 63.158 0.00 0.00 0.00 6.13
606 2089 1.842381 GATTAGGGAGGGATGGCGGG 61.842 65.000 0.00 0.00 0.00 6.13
677 2160 3.706373 CCCCACTCCACTCCACCG 61.706 72.222 0.00 0.00 0.00 4.94
698 2181 2.757868 GCCACATGCAAACCCTACATTA 59.242 45.455 0.00 0.00 40.77 1.90
747 2246 4.576216 GCACAAGCTATCTAGTCTAGCA 57.424 45.455 21.19 0.00 43.26 3.49
878 2388 6.366061 CCATCCGTCAAGTACATATACACATG 59.634 42.308 0.00 0.00 33.30 3.21
930 2440 1.668337 GCTGATCGATCCATCCTGTCG 60.668 57.143 22.31 1.63 36.75 4.35
950 2460 2.175184 CTGGTTGCGTTTGCTCGGAG 62.175 60.000 0.00 0.00 43.34 4.63
954 2470 1.933853 GTTGCGTTTGCTCGGAGATAT 59.066 47.619 9.69 0.00 43.34 1.63
955 2471 3.120792 GTTGCGTTTGCTCGGAGATATA 58.879 45.455 9.69 0.00 43.34 0.86
956 2472 3.660501 TGCGTTTGCTCGGAGATATAT 57.339 42.857 9.69 0.00 43.34 0.86
957 2473 4.776795 TGCGTTTGCTCGGAGATATATA 57.223 40.909 9.69 0.00 43.34 0.86
958 2474 4.733850 TGCGTTTGCTCGGAGATATATAG 58.266 43.478 9.69 0.00 43.34 1.31
959 2475 4.457949 TGCGTTTGCTCGGAGATATATAGA 59.542 41.667 9.69 0.00 43.34 1.98
960 2476 4.794246 GCGTTTGCTCGGAGATATATAGAC 59.206 45.833 9.69 0.00 38.39 2.59
961 2477 5.333513 CGTTTGCTCGGAGATATATAGACC 58.666 45.833 9.69 0.00 33.89 3.85
962 2478 5.333513 GTTTGCTCGGAGATATATAGACCG 58.666 45.833 9.69 14.52 44.09 4.79
963 2479 3.542648 TGCTCGGAGATATATAGACCGG 58.457 50.000 9.69 0.00 43.14 5.28
964 2480 3.054582 TGCTCGGAGATATATAGACCGGT 60.055 47.826 6.92 6.92 43.14 5.28
965 2481 3.946558 GCTCGGAGATATATAGACCGGTT 59.053 47.826 9.42 0.87 43.14 4.44
966 2482 4.201930 GCTCGGAGATATATAGACCGGTTG 60.202 50.000 9.42 12.50 43.14 3.77
967 2483 5.169992 TCGGAGATATATAGACCGGTTGA 57.830 43.478 9.42 0.00 43.14 3.18
968 2484 5.183969 TCGGAGATATATAGACCGGTTGAG 58.816 45.833 9.42 0.00 43.14 3.02
969 2485 4.201930 CGGAGATATATAGACCGGTTGAGC 60.202 50.000 9.42 0.00 39.92 4.26
970 2486 4.951094 GGAGATATATAGACCGGTTGAGCT 59.049 45.833 9.42 3.10 0.00 4.09
971 2487 5.163602 GGAGATATATAGACCGGTTGAGCTG 60.164 48.000 9.42 0.00 0.00 4.24
972 2488 5.571285 AGATATATAGACCGGTTGAGCTGA 58.429 41.667 9.42 0.00 0.00 4.26
973 2489 6.191315 AGATATATAGACCGGTTGAGCTGAT 58.809 40.000 9.42 2.22 0.00 2.90
974 2490 4.792521 ATATAGACCGGTTGAGCTGATC 57.207 45.455 9.42 0.00 0.00 2.92
995 2511 0.035630 AGCAGAGGCAGTGATTCACC 60.036 55.000 13.14 0.00 44.61 4.02
1122 2652 2.808206 CGCCGGGGAGCTCCTATTT 61.808 63.158 31.36 0.00 35.95 1.40
1230 2788 9.918630 TCGAAATTAGTTTGCTAGTACTACTTT 57.081 29.630 0.00 12.46 34.46 2.66
1272 2830 1.178276 ATCGATCATCGGGGACTAGC 58.822 55.000 7.33 0.00 40.88 3.42
1298 2856 5.511377 CAGTTTATGCGTTATTCGTTGCATT 59.489 36.000 3.71 0.00 45.16 3.56
1301 2859 1.135546 TGCGTTATTCGTTGCATTGGG 60.136 47.619 0.00 0.00 42.13 4.12
1306 2864 4.412207 GTTATTCGTTGCATTGGGAAGAC 58.588 43.478 0.00 0.00 0.00 3.01
1307 2865 1.974265 TTCGTTGCATTGGGAAGACA 58.026 45.000 0.00 0.00 0.00 3.41
1399 2957 9.092876 AGAGTGAAACGCAAAATTTTAAAATGA 57.907 25.926 14.04 0.00 45.86 2.57
1471 3187 7.827701 TGTATAAAAGATAGCTACTCCATCCG 58.172 38.462 0.00 0.00 0.00 4.18
1478 3194 1.414181 AGCTACTCCATCCGTTCCATG 59.586 52.381 0.00 0.00 0.00 3.66
1482 3198 4.503296 GCTACTCCATCCGTTCCATGTTAT 60.503 45.833 0.00 0.00 0.00 1.89
1483 3199 5.279306 GCTACTCCATCCGTTCCATGTTATA 60.279 44.000 0.00 0.00 0.00 0.98
1484 3200 5.623956 ACTCCATCCGTTCCATGTTATAA 57.376 39.130 0.00 0.00 0.00 0.98
1486 3202 4.968259 TCCATCCGTTCCATGTTATAAGG 58.032 43.478 0.00 0.00 0.00 2.69
1487 3203 4.410883 TCCATCCGTTCCATGTTATAAGGT 59.589 41.667 0.00 0.00 0.00 3.50
1488 3204 4.515191 CCATCCGTTCCATGTTATAAGGTG 59.485 45.833 0.00 0.00 0.00 4.00
1490 3206 5.168647 TCCGTTCCATGTTATAAGGTGTT 57.831 39.130 0.00 0.00 0.00 3.32
1491 3207 5.180271 TCCGTTCCATGTTATAAGGTGTTC 58.820 41.667 0.00 0.00 0.00 3.18
1492 3208 4.334481 CCGTTCCATGTTATAAGGTGTTCC 59.666 45.833 0.00 0.00 0.00 3.62
1493 3209 4.938832 CGTTCCATGTTATAAGGTGTTCCA 59.061 41.667 0.00 0.00 35.89 3.53
1494 3210 5.413213 CGTTCCATGTTATAAGGTGTTCCAA 59.587 40.000 0.00 0.00 35.89 3.53
1495 3211 6.617879 GTTCCATGTTATAAGGTGTTCCAAC 58.382 40.000 0.00 0.00 35.89 3.77
1496 3212 6.134535 TCCATGTTATAAGGTGTTCCAACT 57.865 37.500 0.00 0.00 35.89 3.16
1498 3214 7.007723 TCCATGTTATAAGGTGTTCCAACTTT 58.992 34.615 0.00 0.00 38.32 2.66
1500 3216 8.147704 CCATGTTATAAGGTGTTCCAACTTTTT 58.852 33.333 0.00 0.00 38.32 1.94
1601 3342 8.712285 TCTTATAATTTGAAACGGAGGTAGTG 57.288 34.615 0.00 0.00 0.00 2.74
1632 3524 2.784347 GGAAAAGCTCTAAGGTGTGCT 58.216 47.619 0.00 0.00 38.25 4.40
1669 3561 7.038445 TGCTCCCATTTCAAGAAAATAATCCAA 60.038 33.333 0.00 0.00 35.77 3.53
1758 3653 9.573133 AAGTTTCATGAAAATCGTAATTCATCC 57.427 29.630 22.07 5.17 42.72 3.51
1762 3657 3.619483 TGAAAATCGTAATTCATCCGCGT 59.381 39.130 4.92 0.00 30.94 6.01
1776 3671 3.290308 TCCGCGTGCAAAATAACAAAT 57.710 38.095 4.92 0.00 0.00 2.32
1815 3710 0.383949 TCCACAAAAACTTGCTCGGC 59.616 50.000 0.00 0.00 0.00 5.54
1827 3722 2.348998 CTCGGCCAAGGCTCACTT 59.651 61.111 11.40 0.00 41.00 3.16
1838 3733 6.055588 GCCAAGGCTCACTTTAATATCTACA 58.944 40.000 3.29 0.00 37.29 2.74
1917 3905 9.066892 GGAATTTTATGACATATAACAGGAGCA 57.933 33.333 0.00 0.00 0.00 4.26
1921 3909 8.800370 TTTATGACATATAACAGGAGCAAACA 57.200 30.769 0.00 0.00 0.00 2.83
1922 3910 6.932356 ATGACATATAACAGGAGCAAACAG 57.068 37.500 0.00 0.00 0.00 3.16
1923 3911 4.635765 TGACATATAACAGGAGCAAACAGC 59.364 41.667 0.00 0.00 46.19 4.40
1961 3949 6.070995 AGGTCATAAAATCCACTGTCGTCTTA 60.071 38.462 0.00 0.00 0.00 2.10
1983 3988 2.053627 CTTCAATGTTTTGAGCACGGC 58.946 47.619 0.00 0.00 42.60 5.68
1993 3998 2.282462 AGCACGGCTGGAAAAGGG 60.282 61.111 0.00 0.00 37.57 3.95
2003 4008 2.233676 GCTGGAAAAGGGGGTTAACATG 59.766 50.000 8.10 0.00 0.00 3.21
2177 4189 3.815809 CTGTCTCTCTCCTACCTACCTG 58.184 54.545 0.00 0.00 0.00 4.00
2185 4197 2.358267 CTCCTACCTACCTGCTAACACG 59.642 54.545 0.00 0.00 0.00 4.49
2218 4230 7.837863 TGAAAGATACTAGAACCCTGTACTTG 58.162 38.462 0.00 0.00 0.00 3.16
2224 4236 3.508845 AGAACCCTGTACTTGCACAAT 57.491 42.857 0.00 0.00 0.00 2.71
2227 4239 5.186198 AGAACCCTGTACTTGCACAATATC 58.814 41.667 0.00 0.00 0.00 1.63
2230 4242 5.186198 ACCCTGTACTTGCACAATATCTTC 58.814 41.667 0.00 0.00 0.00 2.87
2232 4244 5.295292 CCCTGTACTTGCACAATATCTTCAG 59.705 44.000 0.00 0.00 0.00 3.02
2233 4245 5.220739 CCTGTACTTGCACAATATCTTCAGC 60.221 44.000 0.00 0.00 0.00 4.26
2465 4515 6.385759 TCCTGGCACTCTCCTATTGTATAAAA 59.614 38.462 0.00 0.00 0.00 1.52
2562 4617 8.558700 TCGTACCACTTTTCACCTAAATAAAAC 58.441 33.333 0.00 0.00 0.00 2.43
2580 4635 9.453325 AAATAAAACGCTGAAGTTTCGAAAATA 57.547 25.926 13.10 0.00 42.81 1.40
2590 4645 9.140286 CTGAAGTTTCGAAAATAGATGTAGACA 57.860 33.333 13.10 1.71 0.00 3.41
2650 4712 2.898729 AAGGAGCATCTACATGTCGG 57.101 50.000 0.00 0.00 33.73 4.79
2672 4734 4.611366 GGTTTGCTTTGTTCGTATCTTTCG 59.389 41.667 0.00 0.00 0.00 3.46
2678 4740 5.668132 GCTTTGTTCGTATCTTTCGTTCCTC 60.668 44.000 0.00 0.00 0.00 3.71
2681 4743 4.022589 TGTTCGTATCTTTCGTTCCTCTGT 60.023 41.667 0.00 0.00 0.00 3.41
2683 4745 4.730657 TCGTATCTTTCGTTCCTCTGTTC 58.269 43.478 0.00 0.00 0.00 3.18
2943 5020 9.679661 ACCATACAAAAAGTCCTTGAAATTTTT 57.320 25.926 0.00 0.00 35.75 1.94
3000 5077 6.095377 GCACATTTCTAGAAAATGTTCCTGG 58.905 40.000 21.26 13.27 45.52 4.45
3026 5104 7.118971 GCATTTGTGAAAAGCCCAATAAATGTA 59.881 33.333 0.00 0.00 35.32 2.29
3027 5105 8.658609 CATTTGTGAAAAGCCCAATAAATGTAG 58.341 33.333 0.00 0.00 32.14 2.74
3046 5125 9.868277 AAATGTAGAAAAATGTTCAACACTTCA 57.132 25.926 0.00 0.00 0.00 3.02
3076 5155 6.478344 TGCTTCGCACATTTAAAAAGAATGTT 59.522 30.769 0.00 0.00 43.23 2.71
3109 5188 8.719560 TTTATGTAACTGTTCAGTGTGTGTTA 57.280 30.769 6.22 0.00 0.00 2.41
3110 5189 6.598753 ATGTAACTGTTCAGTGTGTGTTAC 57.401 37.500 6.22 16.37 39.72 2.50
3133 5212 9.941664 TTACAAAAATGTTTGCCATGTATTTTG 57.058 25.926 8.34 0.00 46.84 2.44
3137 5216 7.814264 AAATGTTTGCCATGTATTTTGGAAA 57.186 28.000 0.00 0.00 36.26 3.13
3145 5224 5.288472 GCCATGTATTTTGGAAATGTTCGAC 59.712 40.000 0.00 0.00 36.26 4.20
3156 5235 2.880822 ATGTTCGACGTGCATTTGAG 57.119 45.000 0.00 0.00 0.00 3.02
3185 5264 8.958175 TGTTCAACATGTAATCGGAAAAATAC 57.042 30.769 0.00 0.00 0.00 1.89
3191 5292 7.461107 ACATGTAATCGGAAAAATACTCAACG 58.539 34.615 0.00 0.00 0.00 4.10
3192 5293 5.860641 TGTAATCGGAAAAATACTCAACGC 58.139 37.500 0.00 0.00 0.00 4.84
3211 5312 6.471198 TCAACGCGTATCTATAAACTGTTCAG 59.529 38.462 14.46 0.00 0.00 3.02
3225 5326 6.573664 AACTGTTCAGCATGTATAAGCAAA 57.426 33.333 0.00 0.00 37.40 3.68
3228 5329 5.941733 TGTTCAGCATGTATAAGCAAAGTG 58.058 37.500 0.00 0.00 37.40 3.16
3233 5334 6.823182 TCAGCATGTATAAGCAAAGTGTACAT 59.177 34.615 0.00 0.00 36.67 2.29
3297 5414 8.732746 TTTTAAGACCTATGGAATAGCACTTC 57.267 34.615 0.00 0.00 45.64 3.01
3336 5455 6.800072 TGAGGTTTAACACTTCCCAAAAAT 57.200 33.333 0.00 0.00 30.10 1.82
3338 5457 5.924356 AGGTTTAACACTTCCCAAAAATGG 58.076 37.500 0.00 0.00 0.00 3.16
3353 5472 4.871933 AAAATGGGGCTTAACACTTGAG 57.128 40.909 0.00 0.00 0.00 3.02
3361 5482 5.278808 GGGGCTTAACACTTGAGTAAAAAGG 60.279 44.000 0.00 0.00 0.00 3.11
3457 5641 5.929697 TTGCACTCTTGTTCACTATTCTG 57.070 39.130 0.00 0.00 0.00 3.02
3499 5734 5.876651 AATTCTTCTTTTTGGTCTTGGCT 57.123 34.783 0.00 0.00 0.00 4.75
3519 5755 5.774690 TGGCTTTGATTCTATCCTTGTTTGT 59.225 36.000 0.00 0.00 0.00 2.83
3533 5769 4.202451 CCTTGTTTGTTTCCCCCATCAATT 60.202 41.667 0.00 0.00 0.00 2.32
3881 6117 2.827190 CAGCGCCATCACCAGCAT 60.827 61.111 2.29 0.00 0.00 3.79
3885 6121 1.153309 CGCCATCACCAGCATCAGA 60.153 57.895 0.00 0.00 0.00 3.27
3886 6122 1.158484 CGCCATCACCAGCATCAGAG 61.158 60.000 0.00 0.00 0.00 3.35
3889 6125 0.818445 CATCACCAGCATCAGAGCCC 60.818 60.000 0.00 0.00 34.23 5.19
3890 6126 1.276859 ATCACCAGCATCAGAGCCCA 61.277 55.000 0.00 0.00 34.23 5.36
3891 6127 1.748122 CACCAGCATCAGAGCCCAC 60.748 63.158 0.00 0.00 34.23 4.61
3892 6128 1.922369 ACCAGCATCAGAGCCCACT 60.922 57.895 0.00 0.00 34.23 4.00
3957 6199 1.355066 CGCGGAGTTCCAGAAGAAGC 61.355 60.000 0.00 0.00 34.29 3.86
4049 6291 2.541120 GGAGCTGCATCGCCATCAC 61.541 63.158 5.37 0.00 0.00 3.06
4050 6292 2.515523 AGCTGCATCGCCATCACC 60.516 61.111 1.02 0.00 0.00 4.02
4051 6293 2.825387 GCTGCATCGCCATCACCA 60.825 61.111 0.00 0.00 0.00 4.17
4253 6495 3.130164 TCATGAGGAAGAAGAAGAGCTCG 59.870 47.826 8.37 0.00 0.00 5.03
4256 6498 0.804156 GGAAGAAGAAGAGCTCGGCG 60.804 60.000 8.37 0.00 0.00 6.46
4257 6499 0.109039 GAAGAAGAAGAGCTCGGCGT 60.109 55.000 8.37 2.37 0.00 5.68
4326 6568 2.181021 GCCCGTCGTTCTGATCGT 59.819 61.111 7.88 0.00 0.00 3.73
4331 6573 1.664874 CCGTCGTTCTGATCGTTGACA 60.665 52.381 7.88 0.00 0.00 3.58
4349 6591 3.356639 ATCCGTCGTGATGCGTGCT 62.357 57.895 0.00 0.00 42.13 4.40
4363 6605 2.281484 TGCTTGCGGGAGTTGGTC 60.281 61.111 0.00 0.00 0.00 4.02
4364 6606 2.032681 GCTTGCGGGAGTTGGTCT 59.967 61.111 0.00 0.00 0.00 3.85
4365 6607 2.035442 GCTTGCGGGAGTTGGTCTC 61.035 63.158 0.00 0.00 42.07 3.36
4367 6609 0.035458 CTTGCGGGAGTTGGTCTCTT 59.965 55.000 0.00 0.00 42.40 2.85
4369 6611 1.118965 TGCGGGAGTTGGTCTCTTGA 61.119 55.000 0.00 0.00 42.40 3.02
4370 6612 0.390472 GCGGGAGTTGGTCTCTTGAG 60.390 60.000 0.00 0.00 42.40 3.02
4371 6613 0.969894 CGGGAGTTGGTCTCTTGAGT 59.030 55.000 0.00 0.00 42.40 3.41
4372 6614 1.067495 CGGGAGTTGGTCTCTTGAGTC 60.067 57.143 0.00 0.00 42.40 3.36
4373 6615 1.067495 GGGAGTTGGTCTCTTGAGTCG 60.067 57.143 0.00 0.00 42.40 4.18
4374 6616 1.614413 GGAGTTGGTCTCTTGAGTCGT 59.386 52.381 0.00 0.00 42.40 4.34
4387 6636 0.385723 GAGTCGTGAGTCGTGACACC 60.386 60.000 14.71 4.91 40.80 4.16
4388 6637 1.099295 AGTCGTGAGTCGTGACACCA 61.099 55.000 14.71 0.00 40.80 4.17
4390 6639 1.099295 TCGTGAGTCGTGACACCACT 61.099 55.000 5.47 5.47 41.06 4.00
4395 6644 3.189910 GTGAGTCGTGACACCACTATACA 59.810 47.826 5.79 0.00 41.06 2.29
4441 6690 1.535462 ACGTTTAGAGCATGCAACACC 59.465 47.619 21.98 3.25 0.00 4.16
4464 6717 8.889717 CACCTGTATATTTTTGTTTCTCGGTAT 58.110 33.333 0.00 0.00 0.00 2.73
4720 6977 3.367646 TCACCGAATCTCAGTCTACCT 57.632 47.619 0.00 0.00 0.00 3.08
4729 6988 3.951663 TCTCAGTCTACCTGTTCATCGA 58.048 45.455 0.00 0.00 42.19 3.59
4731 6990 5.681639 TCTCAGTCTACCTGTTCATCGATA 58.318 41.667 0.00 0.00 42.19 2.92
4760 7019 9.793252 AAATCAAATAAACGATGAGATTTGGAG 57.207 29.630 0.00 0.00 38.97 3.86
4761 7020 7.320443 TCAAATAAACGATGAGATTTGGAGG 57.680 36.000 6.40 0.00 38.97 4.30
4762 7021 5.757850 AATAAACGATGAGATTTGGAGGC 57.242 39.130 0.00 0.00 0.00 4.70
4763 7022 1.656652 AACGATGAGATTTGGAGGCG 58.343 50.000 0.00 0.00 0.00 5.52
4764 7023 0.824109 ACGATGAGATTTGGAGGCGA 59.176 50.000 0.00 0.00 0.00 5.54
4765 7024 1.414181 ACGATGAGATTTGGAGGCGAT 59.586 47.619 0.00 0.00 0.00 4.58
4768 7062 2.042686 TGAGATTTGGAGGCGATTGG 57.957 50.000 0.00 0.00 0.00 3.16
4790 7084 2.315386 GGTCAAGTGGCGGTTCGAC 61.315 63.158 0.00 0.00 34.27 4.20
4805 7099 2.107950 TCGACCAGGCGATCAATTTT 57.892 45.000 0.00 0.00 35.01 1.82
4808 7102 2.030946 CGACCAGGCGATCAATTTTCTC 59.969 50.000 0.00 0.00 0.00 2.87
4809 7103 2.009774 ACCAGGCGATCAATTTTCTCG 58.990 47.619 0.00 0.00 35.57 4.04
4817 7111 4.650985 CGATCAATTTTCTCGAATGTGCA 58.349 39.130 0.00 0.00 34.41 4.57
4822 7116 5.048852 TCAATTTTCTCGAATGTGCACATGA 60.049 36.000 31.98 23.31 36.56 3.07
4831 7125 4.609947 GAATGTGCACATGAAGAACAACA 58.390 39.130 31.98 0.00 36.56 3.33
4854 7148 2.851195 AGTTGATAATCGCCCATGACC 58.149 47.619 0.00 0.00 0.00 4.02
4880 7174 0.737715 AGGTTGTCGATGAGCGCTTC 60.738 55.000 13.26 4.92 40.61 3.86
4946 7242 3.756963 GGTAACTTGCTCGGAGGAAAAAT 59.243 43.478 13.08 5.15 0.00 1.82
5057 7356 9.846248 AATGCTGATTTTGTGATAGACTAAAAC 57.154 29.630 0.00 0.00 33.77 2.43
5058 7357 8.621532 TGCTGATTTTGTGATAGACTAAAACT 57.378 30.769 0.00 0.00 33.77 2.66
5083 7382 9.255304 CTAATTTTTGGAAAACCTCGATTTTCA 57.745 29.630 20.24 6.70 46.16 2.69
5097 7396 9.846248 ACCTCGATTTTCAAAAATAATCAAGAG 57.154 29.630 0.86 4.47 38.64 2.85
5098 7397 8.801913 CCTCGATTTTCAAAAATAATCAAGAGC 58.198 33.333 0.86 0.00 38.64 4.09
5104 7403 9.814899 TTTTCAAAAATAATCAAGAGCTTCACA 57.185 25.926 0.00 0.00 0.00 3.58
5199 7498 9.889128 AAGAAATGTTTGGAAATCTTTCAAAGA 57.111 25.926 1.30 1.30 42.69 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 121 7.095607 CGGCTAAAAGATATGAAAAGCGATAGT 60.096 37.037 0.00 0.00 39.35 2.12
165 168 2.478033 GCAAAGATAACGCCCGGGG 61.478 63.158 25.28 15.33 0.00 5.73
198 201 1.001760 GAGGCCCCTCCAGACACTA 59.998 63.158 0.00 0.00 37.11 2.74
199 202 2.284995 GAGGCCCCTCCAGACACT 60.285 66.667 0.00 0.00 37.11 3.55
200 203 2.607750 TGAGGCCCCTCCAGACAC 60.608 66.667 11.62 0.00 42.09 3.67
201 204 2.607750 GTGAGGCCCCTCCAGACA 60.608 66.667 11.62 0.00 42.09 3.41
219 223 7.462331 CGTTAAGTTGTACACGATATGTTGAGG 60.462 40.741 0.00 0.00 43.19 3.86
245 249 5.744666 TTTAAATAGTCGGCTATGGCAAC 57.255 39.130 10.93 0.19 37.92 4.17
246 250 5.648526 TGTTTTAAATAGTCGGCTATGGCAA 59.351 36.000 10.93 2.38 37.92 4.52
248 252 5.744666 TGTTTTAAATAGTCGGCTATGGC 57.255 39.130 10.93 0.00 37.92 4.40
269 306 8.620416 CGATAGAGAGGAGGATACTAATCAATG 58.380 40.741 0.00 0.00 46.49 2.82
319 356 6.554605 AGATTGGAAGATTTCTCACCCAAAAA 59.445 34.615 10.85 0.00 38.08 1.94
320 357 6.015180 CAGATTGGAAGATTTCTCACCCAAAA 60.015 38.462 10.85 0.00 38.08 2.44
321 358 5.477984 CAGATTGGAAGATTTCTCACCCAAA 59.522 40.000 10.85 0.00 38.08 3.28
322 359 5.012239 CAGATTGGAAGATTTCTCACCCAA 58.988 41.667 0.00 0.00 38.56 4.12
323 360 4.043310 ACAGATTGGAAGATTTCTCACCCA 59.957 41.667 0.00 0.00 0.00 4.51
324 361 4.593956 ACAGATTGGAAGATTTCTCACCC 58.406 43.478 0.00 0.00 0.00 4.61
325 362 5.707298 TGAACAGATTGGAAGATTTCTCACC 59.293 40.000 0.00 0.00 0.00 4.02
326 363 6.808008 TGAACAGATTGGAAGATTTCTCAC 57.192 37.500 0.00 0.00 0.00 3.51
327 364 9.690913 ATTATGAACAGATTGGAAGATTTCTCA 57.309 29.630 0.00 0.00 0.00 3.27
339 376 6.575267 TCCAATGCCAATTATGAACAGATTG 58.425 36.000 0.00 0.00 0.00 2.67
340 377 6.795144 TCCAATGCCAATTATGAACAGATT 57.205 33.333 0.00 0.00 0.00 2.40
341 378 6.989155 ATCCAATGCCAATTATGAACAGAT 57.011 33.333 0.00 0.00 0.00 2.90
342 379 6.491062 CCTATCCAATGCCAATTATGAACAGA 59.509 38.462 0.00 0.00 0.00 3.41
343 380 6.491062 TCCTATCCAATGCCAATTATGAACAG 59.509 38.462 0.00 0.00 0.00 3.16
344 381 6.372104 TCCTATCCAATGCCAATTATGAACA 58.628 36.000 0.00 0.00 0.00 3.18
345 382 6.071728 CCTCCTATCCAATGCCAATTATGAAC 60.072 42.308 0.00 0.00 0.00 3.18
346 383 6.012113 CCTCCTATCCAATGCCAATTATGAA 58.988 40.000 0.00 0.00 0.00 2.57
347 384 5.312974 TCCTCCTATCCAATGCCAATTATGA 59.687 40.000 0.00 0.00 0.00 2.15
348 385 5.573219 TCCTCCTATCCAATGCCAATTATG 58.427 41.667 0.00 0.00 0.00 1.90
355 392 5.398012 GGGTATTATCCTCCTATCCAATGCC 60.398 48.000 0.00 0.00 0.00 4.40
456 500 3.737266 AGCAAACGAAAGAAACATGCATG 59.263 39.130 25.09 25.09 34.89 4.06
457 501 3.737266 CAGCAAACGAAAGAAACATGCAT 59.263 39.130 0.00 0.00 34.89 3.96
458 502 3.114809 CAGCAAACGAAAGAAACATGCA 58.885 40.909 0.00 0.00 34.89 3.96
459 503 3.115554 ACAGCAAACGAAAGAAACATGC 58.884 40.909 0.00 0.00 0.00 4.06
544 2027 1.817099 CCTGATCAAGCCTGCCGAC 60.817 63.158 0.00 0.00 0.00 4.79
545 2028 1.989508 TCCTGATCAAGCCTGCCGA 60.990 57.895 0.00 0.00 0.00 5.54
546 2029 1.817099 GTCCTGATCAAGCCTGCCG 60.817 63.158 0.00 0.00 0.00 5.69
547 2030 1.452833 GGTCCTGATCAAGCCTGCC 60.453 63.158 0.00 0.00 0.00 4.85
548 2031 1.817099 CGGTCCTGATCAAGCCTGC 60.817 63.158 0.00 0.00 0.00 4.85
549 2032 0.036010 AACGGTCCTGATCAAGCCTG 60.036 55.000 0.00 0.00 0.00 4.85
550 2033 0.250513 GAACGGTCCTGATCAAGCCT 59.749 55.000 0.00 0.00 0.00 4.58
551 2034 0.036388 TGAACGGTCCTGATCAAGCC 60.036 55.000 0.00 0.00 0.00 4.35
552 2035 1.079503 GTGAACGGTCCTGATCAAGC 58.920 55.000 0.00 0.00 0.00 4.01
603 2086 3.242897 TAATATTCCCGCCCGCCCG 62.243 63.158 0.00 0.00 0.00 6.13
604 2087 1.673337 GTAATATTCCCGCCCGCCC 60.673 63.158 0.00 0.00 0.00 6.13
605 2088 0.953960 CTGTAATATTCCCGCCCGCC 60.954 60.000 0.00 0.00 0.00 6.13
606 2089 0.250166 ACTGTAATATTCCCGCCCGC 60.250 55.000 0.00 0.00 0.00 6.13
607 2090 1.069513 TCACTGTAATATTCCCGCCCG 59.930 52.381 0.00 0.00 0.00 6.13
608 2091 2.922740 TCACTGTAATATTCCCGCCC 57.077 50.000 0.00 0.00 0.00 6.13
609 2092 3.560068 CACTTCACTGTAATATTCCCGCC 59.440 47.826 0.00 0.00 0.00 6.13
610 2093 3.560068 CCACTTCACTGTAATATTCCCGC 59.440 47.826 0.00 0.00 0.00 6.13
611 2094 4.809426 GTCCACTTCACTGTAATATTCCCG 59.191 45.833 0.00 0.00 0.00 5.14
612 2095 4.809426 CGTCCACTTCACTGTAATATTCCC 59.191 45.833 0.00 0.00 0.00 3.97
677 2160 1.185315 ATGTAGGGTTTGCATGTGGC 58.815 50.000 0.00 0.00 45.13 5.01
734 2233 7.913821 CGTTGTTGTTGTATGCTAGACTAGATA 59.086 37.037 13.91 5.78 0.00 1.98
735 2234 6.752351 CGTTGTTGTTGTATGCTAGACTAGAT 59.248 38.462 13.91 6.66 0.00 1.98
736 2235 6.090783 CGTTGTTGTTGTATGCTAGACTAGA 58.909 40.000 13.91 0.00 0.00 2.43
737 2236 5.862323 ACGTTGTTGTTGTATGCTAGACTAG 59.138 40.000 5.03 5.03 0.00 2.57
738 2237 5.775686 ACGTTGTTGTTGTATGCTAGACTA 58.224 37.500 0.00 0.00 0.00 2.59
739 2238 4.628074 ACGTTGTTGTTGTATGCTAGACT 58.372 39.130 0.00 0.00 0.00 3.24
740 2239 4.143179 GGACGTTGTTGTTGTATGCTAGAC 60.143 45.833 0.00 0.00 0.00 2.59
741 2240 3.991773 GGACGTTGTTGTTGTATGCTAGA 59.008 43.478 0.00 0.00 0.00 2.43
742 2241 3.994392 AGGACGTTGTTGTTGTATGCTAG 59.006 43.478 0.00 0.00 0.00 3.42
743 2242 3.997762 AGGACGTTGTTGTTGTATGCTA 58.002 40.909 0.00 0.00 0.00 3.49
745 2244 4.460505 GTTAGGACGTTGTTGTTGTATGC 58.539 43.478 0.00 0.00 0.00 3.14
746 2245 4.753107 AGGTTAGGACGTTGTTGTTGTATG 59.247 41.667 0.00 0.00 0.00 2.39
747 2246 4.964593 AGGTTAGGACGTTGTTGTTGTAT 58.035 39.130 0.00 0.00 0.00 2.29
878 2388 2.212652 TGCATGCACATCGGAGAATAC 58.787 47.619 18.46 0.00 43.58 1.89
930 2440 2.427410 CGAGCAAACGCAACCAGC 60.427 61.111 0.00 0.00 40.87 4.85
950 2460 5.899120 TCAGCTCAACCGGTCTATATATC 57.101 43.478 8.04 0.00 0.00 1.63
954 2470 2.552743 CGATCAGCTCAACCGGTCTATA 59.447 50.000 8.04 0.00 0.00 1.31
955 2471 1.338337 CGATCAGCTCAACCGGTCTAT 59.662 52.381 8.04 0.00 0.00 1.98
956 2472 0.738975 CGATCAGCTCAACCGGTCTA 59.261 55.000 8.04 0.00 0.00 2.59
957 2473 0.965866 TCGATCAGCTCAACCGGTCT 60.966 55.000 8.04 0.00 0.00 3.85
958 2474 0.526524 CTCGATCAGCTCAACCGGTC 60.527 60.000 8.04 0.00 0.00 4.79
959 2475 1.513158 CTCGATCAGCTCAACCGGT 59.487 57.895 0.00 0.00 0.00 5.28
960 2476 1.880340 GCTCGATCAGCTCAACCGG 60.880 63.158 0.00 0.00 45.83 5.28
961 2477 3.698382 GCTCGATCAGCTCAACCG 58.302 61.111 9.16 0.00 45.83 4.44
969 2485 0.528033 CACTGCCTCTGCTCGATCAG 60.528 60.000 10.02 10.02 38.71 2.90
970 2486 0.967380 TCACTGCCTCTGCTCGATCA 60.967 55.000 0.00 0.00 38.71 2.92
971 2487 0.388659 ATCACTGCCTCTGCTCGATC 59.611 55.000 0.00 0.00 38.71 3.69
972 2488 0.829333 AATCACTGCCTCTGCTCGAT 59.171 50.000 0.00 0.00 38.71 3.59
973 2489 0.174389 GAATCACTGCCTCTGCTCGA 59.826 55.000 0.00 0.00 38.71 4.04
974 2490 0.108472 TGAATCACTGCCTCTGCTCG 60.108 55.000 0.00 0.00 38.71 5.03
1230 2788 4.776349 ACACGAATGAACATGGGCTAATA 58.224 39.130 0.00 0.00 0.00 0.98
1272 2830 4.339429 CAACGAATAACGCATAAACTGGG 58.661 43.478 0.00 0.00 46.94 4.45
1298 2856 3.795688 AAGCAAGATTCTGTCTTCCCA 57.204 42.857 0.00 0.00 45.35 4.37
1301 2859 4.762956 AGCAAAGCAAGATTCTGTCTTC 57.237 40.909 0.00 0.00 45.35 2.87
1455 3171 2.891580 TGGAACGGATGGAGTAGCTATC 59.108 50.000 0.00 0.00 34.02 2.08
1467 3183 5.367945 ACACCTTATAACATGGAACGGAT 57.632 39.130 0.00 0.00 0.00 4.18
1470 3186 4.938832 TGGAACACCTTATAACATGGAACG 59.061 41.667 0.00 0.00 0.00 3.95
1471 3187 6.433093 AGTTGGAACACCTTATAACATGGAAC 59.567 38.462 0.00 0.00 39.29 3.62
1498 3214 6.695713 CGTCTACATACATCTGATTCCGAAAA 59.304 38.462 0.00 0.00 0.00 2.29
1500 3216 5.298527 ACGTCTACATACATCTGATTCCGAA 59.701 40.000 0.00 0.00 0.00 4.30
1501 3217 4.820173 ACGTCTACATACATCTGATTCCGA 59.180 41.667 0.00 0.00 0.00 4.55
1502 3218 4.912187 CACGTCTACATACATCTGATTCCG 59.088 45.833 0.00 0.00 0.00 4.30
1503 3219 5.833082 ACACGTCTACATACATCTGATTCC 58.167 41.667 0.00 0.00 0.00 3.01
1569 3287 9.341899 CTCCGTTTCAAATTATAAGAGGTTTTG 57.658 33.333 3.19 3.19 0.00 2.44
1575 3293 8.818057 CACTACCTCCGTTTCAAATTATAAGAG 58.182 37.037 0.00 0.00 0.00 2.85
1581 3299 4.643463 TGCACTACCTCCGTTTCAAATTA 58.357 39.130 0.00 0.00 0.00 1.40
1601 3342 3.003480 AGAGCTTTTCCGACTAACATGC 58.997 45.455 0.00 0.00 0.00 4.06
1632 3524 0.106569 ATGGGAGCAAATGCATCCGA 60.107 50.000 8.28 9.10 45.16 4.55
1693 3587 2.785269 TGGGGTCCTTTGCATATGAGAT 59.215 45.455 6.97 0.00 0.00 2.75
1699 3594 2.378547 AGAACTTGGGGTCCTTTGCATA 59.621 45.455 0.00 0.00 0.00 3.14
1758 3653 3.181545 GGTCATTTGTTATTTTGCACGCG 60.182 43.478 3.53 3.53 0.00 6.01
1762 3657 4.754114 GCTTGGGTCATTTGTTATTTTGCA 59.246 37.500 0.00 0.00 0.00 4.08
1776 3671 3.070878 GGAAAAAGGAAATGCTTGGGTCA 59.929 43.478 0.00 0.00 0.00 4.02
1815 3710 7.011482 GTGTGTAGATATTAAAGTGAGCCTTGG 59.989 40.741 0.00 0.00 32.32 3.61
1827 3722 7.613585 TCAAGAAACGGGTGTGTAGATATTAA 58.386 34.615 0.00 0.00 0.00 1.40
1838 3733 5.331876 TGAAAAATTCAAGAAACGGGTGT 57.668 34.783 0.00 0.00 36.59 4.16
1875 3778 9.410556 CATAAAATTCCAAAACTGAGTTGGTAG 57.589 33.333 0.00 0.00 44.96 3.18
1922 3910 1.973812 GACCTGGGGAGCACTTTGC 60.974 63.158 0.00 0.00 45.46 3.68
1923 3911 0.038744 ATGACCTGGGGAGCACTTTG 59.961 55.000 0.00 0.00 0.00 2.77
1924 3912 1.668826 TATGACCTGGGGAGCACTTT 58.331 50.000 0.00 0.00 0.00 2.66
1961 3949 2.034558 CCGTGCTCAAAACATTGAAGGT 59.965 45.455 0.00 0.00 0.00 3.50
1983 3988 3.509967 GTCATGTTAACCCCCTTTTCCAG 59.490 47.826 2.48 0.00 0.00 3.86
1993 3998 8.665685 CACTTTATCTTACAGTCATGTTAACCC 58.334 37.037 2.48 0.00 41.01 4.11
2177 4189 4.491676 TCTTTCATAGTGTCCGTGTTAGC 58.508 43.478 0.00 0.00 0.00 3.09
2185 4197 7.288158 AGGGTTCTAGTATCTTTCATAGTGTCC 59.712 40.741 0.00 0.00 0.00 4.02
2218 4230 5.124457 TGAAAAGAGGCTGAAGATATTGTGC 59.876 40.000 0.00 0.00 0.00 4.57
2224 4236 7.624549 AGTGTAATGAAAAGAGGCTGAAGATA 58.375 34.615 0.00 0.00 0.00 1.98
2227 4239 6.876257 ACTAGTGTAATGAAAAGAGGCTGAAG 59.124 38.462 0.00 0.00 0.00 3.02
2230 4242 7.324178 ACTACTAGTGTAATGAAAAGAGGCTG 58.676 38.462 5.39 0.00 0.00 4.85
2232 4244 9.649167 TTAACTACTAGTGTAATGAAAAGAGGC 57.351 33.333 5.39 0.00 0.00 4.70
2278 4291 5.280573 CCAATCTGATCCCATCAATCTAGCT 60.281 44.000 0.00 0.00 39.11 3.32
2473 4523 5.759763 TGTGCCACTCATTGTCACATATATC 59.240 40.000 0.00 0.00 31.26 1.63
2530 4585 2.542595 GTGAAAAGTGGTACGACTGTGG 59.457 50.000 11.59 0.00 0.00 4.17
2535 4590 7.656707 TTATTTAGGTGAAAAGTGGTACGAC 57.343 36.000 0.00 0.00 0.00 4.34
2562 4617 5.858475 ACATCTATTTTCGAAACTTCAGCG 58.142 37.500 10.79 0.00 0.00 5.18
2650 4712 5.202640 ACGAAAGATACGAACAAAGCAAAC 58.797 37.500 0.00 0.00 34.70 2.93
2672 4734 6.625873 AGAATGTGAAAAGAACAGAGGAAC 57.374 37.500 0.00 0.00 0.00 3.62
2963 5040 9.809096 TTCTAGAAATGTGCAAAACAATTGTTA 57.191 25.926 23.53 7.91 43.61 2.41
2964 5041 8.715191 TTCTAGAAATGTGCAAAACAATTGTT 57.285 26.923 18.13 18.13 43.61 2.83
2965 5042 8.715191 TTTCTAGAAATGTGCAAAACAATTGT 57.285 26.923 13.99 4.92 43.61 2.71
2980 5057 7.486407 AATGCCAGGAACATTTTCTAGAAAT 57.514 32.000 18.37 3.75 34.05 2.17
2987 5064 4.630111 TCACAAATGCCAGGAACATTTTC 58.370 39.130 2.99 0.00 43.42 2.29
3000 5077 5.938438 TTTATTGGGCTTTTCACAAATGC 57.062 34.783 0.00 0.00 39.89 3.56
3026 5104 8.831715 ACTTTTGAAGTGTTGAACATTTTTCT 57.168 26.923 7.50 0.00 41.01 2.52
3070 5149 7.975616 ACAGTTACATAAATGCCATGAACATTC 59.024 33.333 12.53 1.93 36.74 2.67
3076 5155 6.658816 ACTGAACAGTTACATAAATGCCATGA 59.341 34.615 1.32 0.00 38.83 3.07
3109 5188 7.284034 TCCAAAATACATGGCAAACATTTTTGT 59.716 29.630 17.11 7.82 43.62 2.83
3110 5189 7.646314 TCCAAAATACATGGCAAACATTTTTG 58.354 30.769 11.35 12.79 44.42 2.44
3133 5212 2.611974 AATGCACGTCGAACATTTCC 57.388 45.000 0.00 0.00 29.94 3.13
3137 5216 2.412870 TCTCAAATGCACGTCGAACAT 58.587 42.857 0.00 0.00 0.00 2.71
3156 5235 8.514136 TTTTCCGATTACATGTTGAACATTTC 57.486 30.769 8.30 3.15 36.53 2.17
3173 5252 2.997986 ACGCGTTGAGTATTTTTCCGAT 59.002 40.909 5.58 0.00 0.00 4.18
3175 5254 2.867456 ACGCGTTGAGTATTTTTCCG 57.133 45.000 5.58 0.00 0.00 4.30
3184 5263 5.888105 ACAGTTTATAGATACGCGTTGAGT 58.112 37.500 20.78 0.55 0.00 3.41
3185 5264 6.471198 TGAACAGTTTATAGATACGCGTTGAG 59.529 38.462 20.78 0.00 0.00 3.02
3191 5292 6.201044 ACATGCTGAACAGTTTATAGATACGC 59.799 38.462 3.77 0.00 0.00 4.42
3192 5293 7.700322 ACATGCTGAACAGTTTATAGATACG 57.300 36.000 3.77 0.00 0.00 3.06
3204 5305 6.025896 CACTTTGCTTATACATGCTGAACAG 58.974 40.000 0.00 0.00 0.00 3.16
3211 5312 7.015226 TGATGTACACTTTGCTTATACATGC 57.985 36.000 0.00 0.00 36.77 4.06
3225 5326 9.703892 GAGAGAAAATATAGCATGATGTACACT 57.296 33.333 0.00 0.00 0.00 3.55
3273 5374 6.984474 CGAAGTGCTATTCCATAGGTCTTAAA 59.016 38.462 0.00 0.00 33.43 1.52
3274 5375 6.462487 CCGAAGTGCTATTCCATAGGTCTTAA 60.462 42.308 0.00 0.00 33.43 1.85
3275 5376 5.010719 CCGAAGTGCTATTCCATAGGTCTTA 59.989 44.000 0.00 0.00 33.43 2.10
3281 5382 5.921408 GTCTAACCGAAGTGCTATTCCATAG 59.079 44.000 0.00 0.00 35.94 2.23
3286 5403 5.109903 ACATGTCTAACCGAAGTGCTATTC 58.890 41.667 0.00 0.00 0.00 1.75
3289 5406 3.119245 GGACATGTCTAACCGAAGTGCTA 60.119 47.826 24.50 0.00 0.00 3.49
3297 5414 2.233922 ACCTCAAGGACATGTCTAACCG 59.766 50.000 24.50 10.99 38.94 4.44
3336 5455 4.440826 TTTACTCAAGTGTTAAGCCCCA 57.559 40.909 0.00 0.00 0.00 4.96
3338 5457 5.301045 ACCTTTTTACTCAAGTGTTAAGCCC 59.699 40.000 0.00 0.00 0.00 5.19
3419 5574 5.002464 AGTGCAAATTATAGCAAAGCTGG 57.998 39.130 1.04 0.00 43.20 4.85
3420 5575 5.888105 AGAGTGCAAATTATAGCAAAGCTG 58.112 37.500 1.04 0.00 43.20 4.24
3455 5639 2.736144 ATTGCACTGTTTGATGGCAG 57.264 45.000 0.00 0.00 35.68 4.85
3457 5641 6.369615 AGAATTTAATTGCACTGTTTGATGGC 59.630 34.615 0.00 0.00 0.00 4.40
3497 5732 7.329471 GGAAACAAACAAGGATAGAATCAAAGC 59.671 37.037 0.00 0.00 0.00 3.51
3499 5734 7.256154 GGGGAAACAAACAAGGATAGAATCAAA 60.256 37.037 0.00 0.00 0.00 2.69
3519 5755 2.374184 CTGCGTAATTGATGGGGGAAA 58.626 47.619 0.00 0.00 0.00 3.13
3533 5769 1.226295 CGTCACTCGATGCTGCGTA 60.226 57.895 0.00 0.00 42.86 4.42
3872 6108 1.919816 TGGGCTCTGATGCTGGTGA 60.920 57.895 0.00 0.00 0.00 4.02
3935 6177 4.388499 TTCTGGAACTCCGCGGCC 62.388 66.667 23.51 17.02 39.43 6.13
4049 6291 4.241999 GCGTAATGCGGCTGCTGG 62.242 66.667 20.27 4.37 43.34 4.85
4169 6411 2.328589 CCTCCCCTCCTCCTCCTCA 61.329 68.421 0.00 0.00 0.00 3.86
4321 6563 0.914551 CACGACGGATGTCAACGATC 59.085 55.000 0.00 0.00 45.80 3.69
4326 6568 2.749541 GCATCACGACGGATGTCAA 58.250 52.632 20.24 0.00 45.80 3.18
4349 6591 0.250295 CAAGAGACCAACTCCCGCAA 60.250 55.000 0.00 0.00 45.96 4.85
4363 6605 1.531578 TCACGACTCACGACTCAAGAG 59.468 52.381 0.00 0.00 45.77 2.85
4364 6606 1.263484 GTCACGACTCACGACTCAAGA 59.737 52.381 0.00 0.00 45.77 3.02
4365 6607 1.002792 TGTCACGACTCACGACTCAAG 60.003 52.381 0.00 0.00 45.77 3.02
4367 6609 0.306840 GTGTCACGACTCACGACTCA 59.693 55.000 0.00 0.00 45.77 3.41
4369 6611 1.099295 TGGTGTCACGACTCACGACT 61.099 55.000 0.00 0.00 45.77 4.18
4370 6612 0.933509 GTGGTGTCACGACTCACGAC 60.934 60.000 10.58 0.00 45.77 4.34
4371 6613 1.357690 GTGGTGTCACGACTCACGA 59.642 57.895 10.58 0.00 45.77 4.35
4387 6636 7.593825 TCATCACTATCACCGAATGTATAGTG 58.406 38.462 19.25 19.25 42.87 2.74
4388 6637 7.761038 TCATCACTATCACCGAATGTATAGT 57.239 36.000 0.00 0.00 34.58 2.12
4390 6639 8.802267 TGATTCATCACTATCACCGAATGTATA 58.198 33.333 0.00 0.00 0.00 1.47
4395 6644 9.559732 TTTATTGATTCATCACTATCACCGAAT 57.440 29.630 0.00 0.00 36.36 3.34
4428 6677 5.505173 AAATATACAGGTGTTGCATGCTC 57.495 39.130 20.33 12.47 30.99 4.26
4473 6726 3.937814 TGTCCATAGCAAATTCTGTCGT 58.062 40.909 0.00 0.00 0.00 4.34
4475 6728 7.934457 ACATATTGTCCATAGCAAATTCTGTC 58.066 34.615 0.00 0.00 0.00 3.51
4622 6877 6.098266 GGGGTGCAAGGAATTATGAAAGTATT 59.902 38.462 0.00 0.00 0.00 1.89
4744 7003 1.207089 TCGCCTCCAAATCTCATCGTT 59.793 47.619 0.00 0.00 0.00 3.85
4754 7013 0.322456 CCTCACCAATCGCCTCCAAA 60.322 55.000 0.00 0.00 0.00 3.28
4757 7016 1.153349 GACCTCACCAATCGCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
4758 7017 0.036388 TTGACCTCACCAATCGCCTC 60.036 55.000 0.00 0.00 0.00 4.70
4759 7018 0.036010 CTTGACCTCACCAATCGCCT 60.036 55.000 0.00 0.00 0.00 5.52
4760 7019 0.321653 ACTTGACCTCACCAATCGCC 60.322 55.000 0.00 0.00 0.00 5.54
4761 7020 0.798776 CACTTGACCTCACCAATCGC 59.201 55.000 0.00 0.00 0.00 4.58
4762 7021 1.442769 CCACTTGACCTCACCAATCG 58.557 55.000 0.00 0.00 0.00 3.34
4763 7022 1.168714 GCCACTTGACCTCACCAATC 58.831 55.000 0.00 0.00 0.00 2.67
4764 7023 0.606401 CGCCACTTGACCTCACCAAT 60.606 55.000 0.00 0.00 0.00 3.16
4765 7024 1.227823 CGCCACTTGACCTCACCAA 60.228 57.895 0.00 0.00 0.00 3.67
4768 7062 1.227853 AACCGCCACTTGACCTCAC 60.228 57.895 0.00 0.00 0.00 3.51
4790 7084 2.279741 TCGAGAAAATTGATCGCCTGG 58.720 47.619 0.00 0.00 36.43 4.45
4805 7099 3.317603 TCTTCATGTGCACATTCGAGA 57.682 42.857 29.48 25.44 33.61 4.04
4808 7102 3.541071 TGTTCTTCATGTGCACATTCG 57.459 42.857 29.48 19.10 33.61 3.34
4809 7103 4.442073 GTGTTGTTCTTCATGTGCACATTC 59.558 41.667 29.48 15.01 33.61 2.67
4831 7125 3.627577 GTCATGGGCGATTATCAACTTGT 59.372 43.478 0.00 0.00 0.00 3.16
4845 7139 0.912486 ACCTCTAAGTGGTCATGGGC 59.088 55.000 0.00 0.00 31.03 5.36
4846 7140 2.305927 ACAACCTCTAAGTGGTCATGGG 59.694 50.000 0.00 0.00 36.69 4.00
4854 7148 3.182967 GCTCATCGACAACCTCTAAGTG 58.817 50.000 0.00 0.00 0.00 3.16
4880 7174 2.295909 TCCTTCGGTTTGAGCAAAATGG 59.704 45.455 0.00 0.00 31.33 3.16
4904 7200 7.285401 AGTTACCCATCCATGTGATTTAACATC 59.715 37.037 14.48 0.00 38.75 3.06
4946 7242 9.066892 ACAGAACAACTTTGAAGAATAGCATTA 57.933 29.630 0.00 0.00 0.00 1.90
5053 7352 9.607988 AATCGAGGTTTTCCAAAAATTAGTTTT 57.392 25.926 0.00 0.00 43.73 2.43
5054 7353 9.607988 AAATCGAGGTTTTCCAAAAATTAGTTT 57.392 25.926 0.00 0.00 43.73 2.66
5055 7354 9.607988 AAAATCGAGGTTTTCCAAAAATTAGTT 57.392 25.926 0.00 0.00 43.73 2.24
5056 7355 9.256477 GAAAATCGAGGTTTTCCAAAAATTAGT 57.744 29.630 11.52 0.00 40.50 2.24
5057 7356 9.255304 TGAAAATCGAGGTTTTCCAAAAATTAG 57.745 29.630 17.35 0.00 43.89 1.73
5058 7357 9.601217 TTGAAAATCGAGGTTTTCCAAAAATTA 57.399 25.926 17.35 0.00 43.89 1.40
5072 7371 8.801913 GCTCTTGATTATTTTTGAAAATCGAGG 58.198 33.333 5.06 4.66 39.81 4.63
5083 7382 9.768662 ACATTTGTGAAGCTCTTGATTATTTTT 57.231 25.926 0.00 0.00 0.00 1.94
5097 7396 9.638239 TCTTAAATAAATGGACATTTGTGAAGC 57.362 29.630 17.92 0.00 40.83 3.86


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

AutoCloner maintained by Alex Coulton.