Multiple sequence alignment - TraesCS5B01G366600

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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 TraesCS5B01G366600 chr5B 100.000 1885 0 0 2121 4005 545405252 545407136 0.000000e+00 3482.0
1 TraesCS5B01G366600 chr5B 100.000 1844 0 0 1 1844 545403132 545404975 0.000000e+00 3406.0
2 TraesCS5B01G366600 chr5B 82.710 428 56 12 3500 3923 545427785 545428198 8.180000e-97 364.0
3 TraesCS5B01G366600 chr5B 84.639 319 47 2 2174 2491 545405257 545405574 2.320000e-82 316.0
4 TraesCS5B01G366600 chr5B 84.639 319 47 2 2126 2443 545405305 545405622 2.320000e-82 316.0
5 TraesCS5B01G366600 chr5B 86.239 109 14 1 1736 1844 545404826 545404933 2.530000e-22 117.0
6 TraesCS5B01G366600 chr5B 86.364 110 12 3 1695 1802 545404867 545404975 2.530000e-22 117.0
7 TraesCS5B01G366600 chr5D 87.879 1848 136 44 2174 3958 447240654 447238832 0.000000e+00 2091.0
8 TraesCS5B01G366600 chr5D 86.957 1472 117 30 1 1439 447242601 447241172 0.000000e+00 1585.0
9 TraesCS5B01G366600 chr5D 94.415 376 20 1 1469 1844 447241173 447240799 9.650000e-161 577.0
10 TraesCS5B01G366600 chr5D 90.030 331 29 4 2121 2449 447240659 447240331 3.700000e-115 425.0
11 TraesCS5B01G366600 chr5D 85.455 385 51 3 3500 3884 447207304 447206925 2.900000e-106 396.0
12 TraesCS5B01G366600 chr5A 85.473 1893 147 48 2 1844 565392300 565394114 0.000000e+00 1855.0
13 TraesCS5B01G366600 chr5A 90.138 1156 70 14 2174 3322 565394705 565395823 0.000000e+00 1463.0
14 TraesCS5B01G366600 chr5A 84.631 488 48 14 3409 3884 565395854 565396326 1.010000e-125 460.0
15 TraesCS5B01G366600 chr5A 84.797 467 43 14 3500 3955 565402962 565403411 1.020000e-120 444.0
16 TraesCS5B01G366600 chr5A 92.953 298 17 4 2121 2416 565394700 565394995 7.950000e-117 431.0
17 TraesCS5B01G366600 chr2D 83.333 252 36 6 2622 2870 536153400 536153648 1.120000e-55 228.0
18 TraesCS5B01G366600 chr2B 82.171 258 40 6 2618 2872 637576567 637576821 2.420000e-52 217.0
19 TraesCS5B01G366600 chr2A 82.540 252 38 6 2622 2870 678965364 678965612 2.420000e-52 217.0
20 TraesCS5B01G366600 chr3A 85.897 78 6 3 2771 2844 535727725 535727801 1.190000e-10 78.7
21 TraesCS5B01G366600 chr4D 87.719 57 7 0 2813 2869 506216839 506216783 2.580000e-07 67.6
22 TraesCS5B01G366600 chr3D 79.412 102 16 3 2771 2868 414637651 414637551 2.580000e-07 67.6
23 TraesCS5B01G366600 chrUn 97.436 39 0 1 3850 3888 53041206 53041169 9.290000e-07 65.8
24 TraesCS5B01G366600 chr7B 97.436 39 0 1 3850 3888 182139760 182139797 9.290000e-07 65.8
25 TraesCS5B01G366600 chr4A 97.436 39 0 1 3850 3888 546447127 546447090 9.290000e-07 65.8
26 TraesCS5B01G366600 chr3B 83.117 77 8 3 2772 2844 540476549 540476474 9.290000e-07 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 TraesCS5B01G366600 chr5B 545403132 545407136 4004 False 1292.333333 3482 90.31350 1 4005 6 chr5B.!!$F2 4004
1 TraesCS5B01G366600 chr5D 447238832 447242601 3769 True 1169.500000 2091 89.82025 1 3958 4 chr5D.!!$R2 3957
2 TraesCS5B01G366600 chr5A 565392300 565396326 4026 False 1052.250000 1855 88.29875 2 3884 4 chr5A.!!$F2 3882

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
479 482 0.109412 CGGTACCACTCGTCTGTTCC 60.109 60.0 13.54 0.0 0.0 3.62 F
1169 1197 0.249868 TGCGGTATGTATGCTCCTGC 60.250 55.0 0.00 0.0 40.2 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1298 1336 0.028770 TTTCAGCAAACTTCGGCGTG 59.971 50.0 6.85 3.77 34.54 5.34 R
3008 3456 0.109342 CTGTTGGGAGGCTGTTCTGT 59.891 55.0 0.00 0.00 0.00 3.41 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
144 145 5.551233 AGCTACTGCAGTTGAAAGATTGTA 58.449 37.500 28.83 5.00 42.74 2.41
167 169 3.754965 TGGTCTGACTTGGAGATTTTGG 58.245 45.455 7.85 0.00 0.00 3.28
168 170 2.489722 GGTCTGACTTGGAGATTTTGGC 59.510 50.000 7.85 0.00 0.00 4.52
183 185 5.929992 AGATTTTGGCTCAACATCATTTGTG 59.070 36.000 13.19 0.00 38.99 3.33
184 186 4.669206 TTTGGCTCAACATCATTTGTGT 57.331 36.364 0.00 0.00 38.99 3.72
192 194 5.863965 TCAACATCATTTGTGTCCTGTCTA 58.136 37.500 0.00 0.00 38.99 2.59
198 200 4.929211 TCATTTGTGTCCTGTCTATTCGTG 59.071 41.667 0.00 0.00 0.00 4.35
202 204 2.095364 GTGTCCTGTCTATTCGTGTCGT 60.095 50.000 0.00 0.00 0.00 4.34
217 219 1.217882 GTCGTGAGTGGAAACCTGTG 58.782 55.000 0.00 0.00 0.00 3.66
256 258 2.993899 GTTCCGTTGTCGATTGACTGAT 59.006 45.455 14.27 0.00 45.70 2.90
265 267 6.639632 TGTCGATTGACTGATGATATGAGA 57.360 37.500 14.27 0.00 45.70 3.27
266 268 6.675987 TGTCGATTGACTGATGATATGAGAG 58.324 40.000 14.27 0.00 45.70 3.20
271 273 7.639461 CGATTGACTGATGATATGAGAGTATCG 59.361 40.741 0.00 0.00 42.67 2.92
287 289 2.674796 ATCGTCAGCTCTGTAAACCC 57.325 50.000 0.00 0.00 0.00 4.11
341 343 2.154462 GTGCTGCTGTTGAGTACCATT 58.846 47.619 0.00 0.00 0.00 3.16
342 344 2.160417 GTGCTGCTGTTGAGTACCATTC 59.840 50.000 0.00 0.00 0.00 2.67
358 360 1.065358 ATTCGTTGTTAGCACCGTCG 58.935 50.000 0.00 0.00 32.23 5.12
369 371 1.083015 CACCGTCGTTTTGCCTTCG 60.083 57.895 0.00 0.00 0.00 3.79
438 441 5.971895 GCTTGTTTCAGCAAATTTCTCAA 57.028 34.783 0.00 0.00 39.83 3.02
466 469 2.093658 TGCAATTCTTCTCTCCGGTACC 60.094 50.000 0.16 0.16 0.00 3.34
475 478 0.675837 TCTCCGGTACCACTCGTCTG 60.676 60.000 13.54 0.00 0.00 3.51
479 482 0.109412 CGGTACCACTCGTCTGTTCC 60.109 60.000 13.54 0.00 0.00 3.62
480 483 1.254954 GGTACCACTCGTCTGTTCCT 58.745 55.000 7.15 0.00 0.00 3.36
525 528 1.375908 CCGCCTGTCTGCTGCTTTA 60.376 57.895 0.00 0.00 0.00 1.85
531 534 1.736645 GTCTGCTGCTTTACGCCGA 60.737 57.895 0.00 0.00 38.05 5.54
535 538 1.083806 TGCTGCTTTACGCCGATCTG 61.084 55.000 0.00 0.00 38.05 2.90
536 539 0.806102 GCTGCTTTACGCCGATCTGA 60.806 55.000 0.00 0.00 38.05 3.27
537 540 1.203928 CTGCTTTACGCCGATCTGAG 58.796 55.000 0.00 0.00 38.05 3.35
538 541 0.815095 TGCTTTACGCCGATCTGAGA 59.185 50.000 0.00 0.00 38.05 3.27
539 542 1.409064 TGCTTTACGCCGATCTGAGAT 59.591 47.619 0.00 0.00 38.05 2.75
584 598 6.808008 TTTGAACTTTCTGAGAATGCTAGG 57.192 37.500 7.87 0.00 0.00 3.02
594 608 2.076863 AGAATGCTAGGACGTGCAAAC 58.923 47.619 10.52 3.84 42.74 2.93
652 666 6.883129 TGAACACATTCTACAACATTACACG 58.117 36.000 0.00 0.00 35.69 4.49
658 672 3.527533 TCTACAACATTACACGGATGCC 58.472 45.455 0.00 0.00 0.00 4.40
672 686 3.551496 ATGCCGACCTGTGTGTGGG 62.551 63.158 0.00 0.00 37.20 4.61
706 720 1.909700 TGAGTGGATCCCAAGCAAAC 58.090 50.000 9.90 0.00 34.18 2.93
765 789 3.878519 CCCGCGTCTCTCCGTCTC 61.879 72.222 4.92 0.00 0.00 3.36
766 790 3.878519 CCGCGTCTCTCCGTCTCC 61.879 72.222 4.92 0.00 0.00 3.71
767 791 4.225340 CGCGTCTCTCCGTCTCCG 62.225 72.222 0.00 0.00 0.00 4.63
852 876 3.181487 CCCACCAACGAATCCAATCATTC 60.181 47.826 0.00 0.00 0.00 2.67
859 883 2.889045 CGAATCCAATCATTCCCATGCT 59.111 45.455 0.00 0.00 30.03 3.79
874 898 1.273269 ATGCTCTGCCTCTGCCTCTT 61.273 55.000 0.00 0.00 36.33 2.85
884 908 0.972134 TCTGCCTCTTCCTCAGTGTG 59.028 55.000 0.00 0.00 0.00 3.82
887 911 1.895798 TGCCTCTTCCTCAGTGTGTAG 59.104 52.381 0.00 0.00 0.00 2.74
888 912 1.896465 GCCTCTTCCTCAGTGTGTAGT 59.104 52.381 0.00 0.00 0.00 2.73
890 914 3.119424 GCCTCTTCCTCAGTGTGTAGTAC 60.119 52.174 0.00 0.00 0.00 2.73
891 915 3.444388 CCTCTTCCTCAGTGTGTAGTACC 59.556 52.174 0.00 0.00 0.00 3.34
892 916 4.079970 CTCTTCCTCAGTGTGTAGTACCA 58.920 47.826 0.00 0.00 0.00 3.25
894 918 4.897076 TCTTCCTCAGTGTGTAGTACCAAA 59.103 41.667 0.00 0.00 0.00 3.28
895 919 4.595762 TCCTCAGTGTGTAGTACCAAAC 57.404 45.455 0.00 0.00 0.00 2.93
897 921 4.056050 CCTCAGTGTGTAGTACCAAACAC 58.944 47.826 6.64 6.64 44.97 3.32
902 926 3.480505 GTGTAGTACCAAACACACCCT 57.519 47.619 15.25 0.00 44.30 4.34
905 929 5.367302 GTGTAGTACCAAACACACCCTAAA 58.633 41.667 15.25 0.00 44.30 1.85
906 930 5.467735 GTGTAGTACCAAACACACCCTAAAG 59.532 44.000 15.25 0.00 44.30 1.85
913 941 2.841442 ACACACCCTAAAGCTCACTC 57.159 50.000 0.00 0.00 0.00 3.51
1047 1075 0.968405 GCCCCTCATTGCACAGAAAA 59.032 50.000 0.00 0.00 0.00 2.29
1048 1076 1.344114 GCCCCTCATTGCACAGAAAAA 59.656 47.619 0.00 0.00 0.00 1.94
1086 1114 1.821332 GGAATGCAAGAGCTCCCGG 60.821 63.158 10.93 0.00 42.74 5.73
1134 1162 1.569003 CATTGTTGTCGTGCTCGCA 59.431 52.632 2.69 2.33 36.96 5.10
1169 1197 0.249868 TGCGGTATGTATGCTCCTGC 60.250 55.000 0.00 0.00 40.20 4.85
1173 1201 2.036475 CGGTATGTATGCTCCTGCTTCT 59.964 50.000 0.00 0.00 40.48 2.85
1174 1202 3.658709 GGTATGTATGCTCCTGCTTCTC 58.341 50.000 0.00 0.00 40.48 2.87
1180 1209 0.459078 TGCTCCTGCTTCTCTCATCG 59.541 55.000 0.00 0.00 40.48 3.84
1187 1216 5.076182 TCCTGCTTCTCTCATCGATCTTAT 58.924 41.667 0.00 0.00 0.00 1.73
1233 1262 3.537580 AGGACGCACACTTGAGTTTAAA 58.462 40.909 0.00 0.00 35.65 1.52
1277 1307 4.273235 CACCCCTCAACAAAATTTTGCTTC 59.727 41.667 26.94 0.00 41.79 3.86
1298 1336 2.603173 CCACTTGCTGCGAAAGAGTTTC 60.603 50.000 6.72 0.00 36.32 2.78
1304 1342 1.154654 GCGAAAGAGTTTCACGCCG 60.155 57.895 0.00 0.00 42.79 6.46
1307 1345 1.136611 CGAAAGAGTTTCACGCCGAAG 60.137 52.381 0.00 0.00 39.63 3.79
1343 1381 4.439305 TGCCAATTCTTACTGACAATGC 57.561 40.909 0.00 0.00 0.00 3.56
1353 1391 7.744087 TCTTACTGACAATGCTTTGTATGTT 57.256 32.000 17.09 5.94 46.01 2.71
1365 1403 5.689514 TGCTTTGTATGTTCAAATTCGGTTG 59.310 36.000 0.00 0.00 36.83 3.77
1390 1436 5.118990 TCTTAGCATGCTAACAGGTTGATC 58.881 41.667 31.53 0.00 35.06 2.92
1418 1464 4.142204 TGAAATTTTGCTCACACTTGCTGA 60.142 37.500 0.00 0.00 0.00 4.26
1424 1470 4.006780 TGCTCACACTTGCTGAGAAATA 57.993 40.909 4.21 0.00 37.90 1.40
1435 1481 7.117236 CACTTGCTGAGAAATATGTGCAAATTT 59.883 33.333 0.00 0.00 39.42 1.82
1439 1485 8.955388 TGCTGAGAAATATGTGCAAATTTAGTA 58.045 29.630 0.00 0.00 0.00 1.82
1465 1511 9.843334 AAAATTAACTTGACAAAACACTAACGA 57.157 25.926 0.00 0.00 0.00 3.85
1466 1512 8.831000 AATTAACTTGACAAAACACTAACGAC 57.169 30.769 0.00 0.00 0.00 4.34
1467 1513 7.599630 TTAACTTGACAAAACACTAACGACT 57.400 32.000 0.00 0.00 0.00 4.18
1568 1614 2.971452 GAGTCCGACCACCACTCC 59.029 66.667 0.00 0.00 31.93 3.85
1655 1701 3.930012 GCGCCCTCCTTCGCCTAT 61.930 66.667 0.00 0.00 45.01 2.57
1658 1704 1.668867 GCCCTCCTTCGCCTATCTC 59.331 63.158 0.00 0.00 0.00 2.75
2242 2660 3.249189 GGGCCACCAGAGGTCACA 61.249 66.667 4.39 0.00 34.02 3.58
2398 2816 4.394712 GTGACTCCCAGCCCACCG 62.395 72.222 0.00 0.00 0.00 4.94
2698 3134 4.129737 ATGGACTACGCGTGCGCT 62.130 61.111 24.59 0.00 44.19 5.92
2761 3197 2.040544 CAAGCCGGACACCATGACC 61.041 63.158 5.05 0.00 0.00 4.02
2863 3299 1.077429 GCTCATCACCAAGGACCCC 60.077 63.158 0.00 0.00 0.00 4.95
2937 3373 5.936686 TCTTTGCTCTTCTTGTGATTGAG 57.063 39.130 0.00 0.00 0.00 3.02
3008 3456 4.455533 GCCATTACAGTGTGATGTGAAGAA 59.544 41.667 22.35 0.08 34.56 2.52
3013 3461 4.769688 ACAGTGTGATGTGAAGAACAGAA 58.230 39.130 0.00 0.00 43.64 3.02
3014 3462 4.572389 ACAGTGTGATGTGAAGAACAGAAC 59.428 41.667 0.00 0.00 43.64 3.01
3016 3464 4.813161 AGTGTGATGTGAAGAACAGAACAG 59.187 41.667 0.00 0.00 43.64 3.16
3018 3466 3.058639 GTGATGTGAAGAACAGAACAGCC 60.059 47.826 0.00 0.00 43.64 4.85
3019 3467 3.181451 TGATGTGAAGAACAGAACAGCCT 60.181 43.478 0.00 0.00 43.64 4.58
3035 3491 1.105759 GCCTCCCAACAGATGCCATC 61.106 60.000 0.00 0.00 0.00 3.51
3050 3506 1.299541 CCATCAGTGGCGTATGGTTC 58.700 55.000 1.24 0.00 39.01 3.62
3086 3542 5.048224 CACCATTTTCTGCTCAAGTTCAGAT 60.048 40.000 0.00 0.00 38.90 2.90
3198 3658 8.177119 ACTTTTGCTTCCTTTTGACACATATA 57.823 30.769 0.00 0.00 0.00 0.86
3199 3659 8.806146 ACTTTTGCTTCCTTTTGACACATATAT 58.194 29.630 0.00 0.00 0.00 0.86
3285 3745 1.873355 GCGACCACGTTCGTCAGTTC 61.873 60.000 10.99 0.00 41.26 3.01
3315 3775 2.808543 CTGACAAAGGCTTCGCTAACTT 59.191 45.455 0.00 0.00 0.00 2.66
3316 3776 2.548057 TGACAAAGGCTTCGCTAACTTG 59.452 45.455 0.00 0.00 0.00 3.16
3317 3777 2.806244 GACAAAGGCTTCGCTAACTTGA 59.194 45.455 0.00 0.00 0.00 3.02
3318 3778 3.211045 ACAAAGGCTTCGCTAACTTGAA 58.789 40.909 0.00 0.00 0.00 2.69
3319 3779 3.003378 ACAAAGGCTTCGCTAACTTGAAC 59.997 43.478 0.00 0.00 0.00 3.18
3320 3780 2.543777 AGGCTTCGCTAACTTGAACA 57.456 45.000 0.00 0.00 0.00 3.18
3321 3781 3.059352 AGGCTTCGCTAACTTGAACAT 57.941 42.857 0.00 0.00 0.00 2.71
3327 3787 4.990543 TCGCTAACTTGAACATGAACAG 57.009 40.909 0.00 0.00 0.00 3.16
3328 3788 4.627058 TCGCTAACTTGAACATGAACAGA 58.373 39.130 0.00 0.00 0.00 3.41
3334 3794 6.949352 AACTTGAACATGAACAGAAGTGAT 57.051 33.333 0.00 0.00 0.00 3.06
3338 3798 4.756642 TGAACATGAACAGAAGTGATCACC 59.243 41.667 22.21 8.10 38.21 4.02
3350 3810 6.035435 CAGAAGTGATCACCGAGAACTATTTG 59.965 42.308 22.21 4.88 0.00 2.32
3352 3812 5.411781 AGTGATCACCGAGAACTATTTGAC 58.588 41.667 22.21 0.00 0.00 3.18
3354 3814 3.226346 TCACCGAGAACTATTTGACCG 57.774 47.619 0.00 0.00 0.00 4.79
3355 3815 2.821378 TCACCGAGAACTATTTGACCGA 59.179 45.455 0.00 0.00 0.00 4.69
3379 3841 4.765339 TCGACAGACTAAAGAACCAGATGA 59.235 41.667 0.00 0.00 0.00 2.92
3382 3844 6.693545 CGACAGACTAAAGAACCAGATGATAC 59.306 42.308 0.00 0.00 0.00 2.24
3399 3861 8.981647 CAGATGATACGATATTGTTTGACATGA 58.018 33.333 0.00 0.00 0.00 3.07
3400 3862 9.716531 AGATGATACGATATTGTTTGACATGAT 57.283 29.630 0.00 0.00 0.00 2.45
3406 3877 7.633621 ACGATATTGTTTGACATGATGATCAC 58.366 34.615 0.00 0.00 0.00 3.06
3449 3920 5.169032 GCTAAGTTCAATTTACGTAATGCGC 59.831 40.000 9.18 0.00 46.11 6.09
3466 3937 0.658829 CGCGCACAAAATCAACCGAA 60.659 50.000 8.75 0.00 0.00 4.30
3468 3939 1.862008 GCGCACAAAATCAACCGAACA 60.862 47.619 0.30 0.00 0.00 3.18
3497 3970 5.989168 TCTCTTCGACACACACATAAAACAT 59.011 36.000 0.00 0.00 0.00 2.71
3506 3979 7.812648 ACACACACATAAAACATGTATGGTAC 58.187 34.615 10.95 0.00 31.24 3.34
3512 3985 4.678509 AAAACATGTATGGTACGTGCTG 57.321 40.909 0.00 0.00 46.93 4.41
3516 3989 0.390603 TGTATGGTACGTGCTGCCAC 60.391 55.000 3.01 0.00 37.49 5.01
3544 4017 2.048127 AGGCTGGAACTTCGTCGC 60.048 61.111 0.00 0.00 0.00 5.19
3585 4058 2.990967 TAAACCGGGTCGCCGACT 60.991 61.111 17.76 0.00 34.88 4.18
3588 4061 3.871248 AACCGGGTCGCCGACTTTC 62.871 63.158 17.76 6.47 34.88 2.62
3593 4066 3.144605 GTCGCCGACTTTCACGAC 58.855 61.111 10.56 0.00 46.64 4.34
3636 4109 1.536073 CCGACTCCTTGCAGACCAGA 61.536 60.000 0.00 0.00 0.00 3.86
3651 4124 4.082125 AGACCAGATTTTGCCCAAAGTAG 58.918 43.478 0.00 0.00 0.00 2.57
3662 4135 2.562738 GCCCAAAGTAGACCTGCAAAAT 59.437 45.455 0.00 0.00 0.00 1.82
3663 4136 3.761752 GCCCAAAGTAGACCTGCAAAATA 59.238 43.478 0.00 0.00 0.00 1.40
3667 4140 6.127897 CCCAAAGTAGACCTGCAAAATAAGAG 60.128 42.308 0.00 0.00 0.00 2.85
3669 4142 7.148340 CCAAAGTAGACCTGCAAAATAAGAGAG 60.148 40.741 0.00 0.00 0.00 3.20
3670 4143 5.983540 AGTAGACCTGCAAAATAAGAGAGG 58.016 41.667 0.00 0.00 0.00 3.69
3671 4144 4.917906 AGACCTGCAAAATAAGAGAGGT 57.082 40.909 0.00 0.00 36.51 3.85
3672 4145 5.248380 AGACCTGCAAAATAAGAGAGGTT 57.752 39.130 0.00 0.00 33.89 3.50
3673 4146 6.374417 AGACCTGCAAAATAAGAGAGGTTA 57.626 37.500 0.00 0.00 33.89 2.85
3674 4147 6.779860 AGACCTGCAAAATAAGAGAGGTTAA 58.220 36.000 0.00 0.00 33.89 2.01
3676 4149 6.543735 ACCTGCAAAATAAGAGAGGTTAACT 58.456 36.000 5.42 0.00 29.17 2.24
3680 4160 8.911918 TGCAAAATAAGAGAGGTTAACTAACA 57.088 30.769 5.42 0.00 37.92 2.41
3690 4170 6.592870 AGAGGTTAACTAACAGCTTGTTCTT 58.407 36.000 5.42 2.54 40.22 2.52
3696 4176 8.701540 GTTAACTAACAGCTTGTTCTTCTACTC 58.298 37.037 0.00 0.00 40.22 2.59
3697 4177 6.658188 ACTAACAGCTTGTTCTTCTACTCT 57.342 37.500 5.04 0.00 40.22 3.24
3698 4178 7.056844 ACTAACAGCTTGTTCTTCTACTCTT 57.943 36.000 5.04 0.00 40.22 2.85
3699 4179 6.926272 ACTAACAGCTTGTTCTTCTACTCTTG 59.074 38.462 5.04 0.00 40.22 3.02
3700 4180 5.537300 ACAGCTTGTTCTTCTACTCTTGA 57.463 39.130 0.00 0.00 0.00 3.02
3701 4181 5.918608 ACAGCTTGTTCTTCTACTCTTGAA 58.081 37.500 0.00 0.00 0.00 2.69
3702 4182 5.988561 ACAGCTTGTTCTTCTACTCTTGAAG 59.011 40.000 0.00 0.00 41.46 3.02
3703 4183 5.407995 CAGCTTGTTCTTCTACTCTTGAAGG 59.592 44.000 0.00 0.00 40.73 3.46
3704 4184 5.071115 AGCTTGTTCTTCTACTCTTGAAGGT 59.929 40.000 0.00 0.00 40.73 3.50
3705 4185 6.267928 AGCTTGTTCTTCTACTCTTGAAGGTA 59.732 38.462 0.00 0.00 40.73 3.08
3706 4186 6.588373 GCTTGTTCTTCTACTCTTGAAGGTAG 59.412 42.308 11.99 11.99 40.73 3.18
3707 4187 6.026947 TGTTCTTCTACTCTTGAAGGTAGC 57.973 41.667 12.89 0.00 40.73 3.58
3717 4197 5.906113 TCTTGAAGGTAGCAAGAGTAGAG 57.094 43.478 0.00 0.00 44.81 2.43
3727 4207 5.652994 AGCAAGAGTAGAGTAGGTTGAAG 57.347 43.478 0.00 0.00 0.00 3.02
3733 4213 0.178873 AGAGTAGGTTGAAGGGGGCA 60.179 55.000 0.00 0.00 0.00 5.36
3738 4218 3.335484 AGTAGGTTGAAGGGGGCAATTAA 59.665 43.478 0.00 0.00 0.00 1.40
3746 4226 4.714308 TGAAGGGGGCAATTAATTACCTTG 59.286 41.667 20.93 6.05 37.01 3.61
3772 4252 4.180946 CTCGTGGCTCGGACGGAG 62.181 72.222 9.26 5.68 46.06 4.63
3800 4280 0.104120 CGGACCGGAATGTCAGCATA 59.896 55.000 9.46 0.00 36.97 3.14
3822 4305 0.394488 TTCTGTTGGTTCGGTGCCAA 60.394 50.000 2.89 2.89 43.04 4.52
3824 4307 2.335011 GTTGGTTCGGTGCCAAGC 59.665 61.111 6.52 0.00 45.50 4.01
3839 4322 1.470098 CCAAGCATTCCGTTCTCTTGG 59.530 52.381 5.12 5.12 45.07 3.61
3844 4327 3.751698 AGCATTCCGTTCTCTTGGTTAAC 59.248 43.478 0.00 0.00 0.00 2.01
3845 4328 3.500680 GCATTCCGTTCTCTTGGTTAACA 59.499 43.478 8.10 0.00 0.00 2.41
3867 4350 2.226962 AGGCACCTGAATCAGCAAAT 57.773 45.000 4.40 0.00 0.00 2.32
3869 4352 3.019564 AGGCACCTGAATCAGCAAATAC 58.980 45.455 4.40 0.00 0.00 1.89
3871 4354 3.382546 GGCACCTGAATCAGCAAATACAT 59.617 43.478 4.40 0.00 0.00 2.29
3935 4426 4.539870 CCTTGTGAATAAAGTGTGCACAG 58.460 43.478 22.40 3.15 40.16 3.66
3939 4430 3.916172 GTGAATAAAGTGTGCACAGCATG 59.084 43.478 22.40 0.00 41.91 4.06
3955 4446 4.337555 ACAGCATGCTATTGAATTCTGGTC 59.662 41.667 22.19 0.00 42.53 4.02
3958 4449 4.511454 GCATGCTATTGAATTCTGGTCGTA 59.489 41.667 11.37 0.00 0.00 3.43
3959 4450 5.007626 GCATGCTATTGAATTCTGGTCGTAA 59.992 40.000 11.37 0.00 0.00 3.18
3960 4451 6.422223 CATGCTATTGAATTCTGGTCGTAAC 58.578 40.000 7.05 0.00 0.00 2.50
3961 4452 4.565166 TGCTATTGAATTCTGGTCGTAACG 59.435 41.667 7.05 0.00 0.00 3.18
3962 4453 4.802039 GCTATTGAATTCTGGTCGTAACGA 59.198 41.667 7.05 0.00 0.00 3.85
3963 4454 5.290158 GCTATTGAATTCTGGTCGTAACGAA 59.710 40.000 7.05 0.00 37.72 3.85
3964 4455 4.977741 TTGAATTCTGGTCGTAACGAAC 57.022 40.909 7.05 0.00 44.56 3.95
3974 4465 5.827568 GGTCGTAACGAACAAGTTCATAA 57.172 39.130 12.86 0.00 43.67 1.90
3975 4466 6.399204 GGTCGTAACGAACAAGTTCATAAT 57.601 37.500 12.86 0.00 43.67 1.28
3976 4467 6.824557 GGTCGTAACGAACAAGTTCATAATT 58.175 36.000 12.86 4.48 43.67 1.40
3977 4468 7.952339 GGTCGTAACGAACAAGTTCATAATTA 58.048 34.615 12.86 3.67 43.67 1.40
3978 4469 8.598075 GGTCGTAACGAACAAGTTCATAATTAT 58.402 33.333 12.86 0.00 43.67 1.28
3979 4470 9.615779 GTCGTAACGAACAAGTTCATAATTATC 57.384 33.333 12.86 0.00 37.72 1.75
3980 4471 9.356433 TCGTAACGAACAAGTTCATAATTATCA 57.644 29.630 12.86 0.00 39.46 2.15
3981 4472 9.619727 CGTAACGAACAAGTTCATAATTATCAG 57.380 33.333 12.86 0.00 39.46 2.90
3999 4490 5.991328 ATCAGTATTGTGAAACCTATGCG 57.009 39.130 0.00 0.00 34.36 4.73
4000 4491 3.621268 TCAGTATTGTGAAACCTATGCGC 59.379 43.478 0.00 0.00 34.36 6.09
4001 4492 3.373748 CAGTATTGTGAAACCTATGCGCA 59.626 43.478 14.96 14.96 34.36 6.09
4002 4493 4.035558 CAGTATTGTGAAACCTATGCGCAT 59.964 41.667 28.23 28.23 34.36 4.73
4003 4494 3.698029 ATTGTGAAACCTATGCGCATC 57.302 42.857 29.11 13.25 34.36 3.91
4004 4495 2.106477 TGTGAAACCTATGCGCATCA 57.894 45.000 29.11 16.10 34.36 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.509737 GCACGGCGTCCCTCCTAC 62.510 72.222 10.85 0.00 0.00 3.18
144 145 4.768968 CCAAAATCTCCAAGTCAGACCAAT 59.231 41.667 0.00 0.00 0.00 3.16
167 169 3.254166 ACAGGACACAAATGATGTTGAGC 59.746 43.478 0.00 0.00 41.46 4.26
168 170 4.758674 AGACAGGACACAAATGATGTTGAG 59.241 41.667 0.00 0.00 41.46 3.02
183 185 2.161012 TCACGACACGAATAGACAGGAC 59.839 50.000 0.00 0.00 0.00 3.85
184 186 2.418976 CTCACGACACGAATAGACAGGA 59.581 50.000 0.00 0.00 0.00 3.86
192 194 2.132762 GTTTCCACTCACGACACGAAT 58.867 47.619 0.00 0.00 0.00 3.34
198 200 1.202486 TCACAGGTTTCCACTCACGAC 60.202 52.381 0.00 0.00 0.00 4.34
202 204 1.416401 GGTCTCACAGGTTTCCACTCA 59.584 52.381 0.00 0.00 0.00 3.41
217 219 4.865365 CGGAACAAATGACTTCTAGGTCTC 59.135 45.833 0.00 0.00 37.16 3.36
256 258 5.411053 CAGAGCTGACGATACTCTCATATCA 59.589 44.000 0.00 0.00 38.72 2.15
265 267 3.130693 GGGTTTACAGAGCTGACGATACT 59.869 47.826 4.21 0.00 0.00 2.12
266 268 3.445857 GGGTTTACAGAGCTGACGATAC 58.554 50.000 4.21 0.00 0.00 2.24
271 273 1.404315 CCTCGGGTTTACAGAGCTGAC 60.404 57.143 4.21 0.00 0.00 3.51
287 289 4.437239 AGACACTGCTAATTTCATCCTCG 58.563 43.478 0.00 0.00 0.00 4.63
372 375 1.447838 ATGGACACACGATCACGGC 60.448 57.895 0.00 0.00 44.46 5.68
373 376 1.083806 CCATGGACACACGATCACGG 61.084 60.000 5.56 0.00 44.46 4.94
438 441 4.276642 GGAGAGAAGAATTGCATTCCCTT 58.723 43.478 0.00 0.00 40.13 3.95
466 469 3.991367 AGGTAAAAGGAACAGACGAGTG 58.009 45.455 0.00 0.00 0.00 3.51
475 478 3.002553 TCGTTGCGAAAGGTAAAAGGAAC 59.997 43.478 0.00 0.00 31.06 3.62
479 482 4.151689 TCAGATCGTTGCGAAAGGTAAAAG 59.848 41.667 0.00 0.00 39.99 2.27
480 483 4.059511 TCAGATCGTTGCGAAAGGTAAAA 58.940 39.130 0.00 0.00 39.99 1.52
525 528 2.419198 GGCATCTCAGATCGGCGT 59.581 61.111 6.85 0.00 0.00 5.68
531 534 5.163374 GGCAAATTAAAAGGGCATCTCAGAT 60.163 40.000 0.00 0.00 0.00 2.90
535 538 3.447742 CGGCAAATTAAAAGGGCATCTC 58.552 45.455 0.00 0.00 0.00 2.75
536 539 2.418609 GCGGCAAATTAAAAGGGCATCT 60.419 45.455 0.00 0.00 0.00 2.90
537 540 1.933181 GCGGCAAATTAAAAGGGCATC 59.067 47.619 0.00 0.00 0.00 3.91
538 541 1.277557 TGCGGCAAATTAAAAGGGCAT 59.722 42.857 0.00 0.00 0.00 4.40
539 542 0.681733 TGCGGCAAATTAAAAGGGCA 59.318 45.000 0.00 0.00 0.00 5.36
594 608 9.965902 AAGGATCTTACCTTATTTATGGCATAG 57.034 33.333 7.35 0.00 46.81 2.23
606 620 2.235155 TGCACGCAAGGATCTTACCTTA 59.765 45.455 0.00 0.00 46.94 2.69
608 622 0.613260 TGCACGCAAGGATCTTACCT 59.387 50.000 0.00 0.00 46.39 3.08
609 623 1.331756 CATGCACGCAAGGATCTTACC 59.668 52.381 0.00 0.00 46.39 2.85
610 624 2.279741 TCATGCACGCAAGGATCTTAC 58.720 47.619 0.00 0.00 46.39 2.34
652 666 2.034879 CACACACAGGTCGGCATCC 61.035 63.158 0.00 0.00 0.00 3.51
658 672 2.280797 CACCCCACACACAGGTCG 60.281 66.667 0.00 0.00 0.00 4.79
662 676 3.174987 TCCCCACCCCACACACAG 61.175 66.667 0.00 0.00 0.00 3.66
672 686 0.611714 ACTCAACATACGTCCCCACC 59.388 55.000 0.00 0.00 0.00 4.61
706 720 0.324943 TGGCTCCTTTTTCCTCCTCG 59.675 55.000 0.00 0.00 0.00 4.63
767 791 4.112341 CTTGCTCGCTGCTTGCCC 62.112 66.667 10.33 0.00 43.37 5.36
768 792 4.773117 GCTTGCTCGCTGCTTGCC 62.773 66.667 10.33 0.00 43.37 4.52
769 793 3.547249 TTGCTTGCTCGCTGCTTGC 62.547 57.895 0.00 2.32 43.37 4.01
770 794 1.002250 CTTTGCTTGCTCGCTGCTTG 61.002 55.000 0.00 0.00 43.37 4.01
771 795 1.285023 CTTTGCTTGCTCGCTGCTT 59.715 52.632 0.00 0.00 43.37 3.91
778 802 1.978542 CACAGATGCTTTGCTTGCTC 58.021 50.000 0.00 0.00 0.00 4.26
852 876 2.516460 GCAGAGGCAGAGCATGGG 60.516 66.667 0.00 0.00 40.72 4.00
859 883 0.975040 GAGGAAGAGGCAGAGGCAGA 60.975 60.000 0.00 0.00 43.71 4.26
874 898 3.962063 TGTTTGGTACTACACACTGAGGA 59.038 43.478 0.00 0.00 0.00 3.71
884 908 4.453478 GCTTTAGGGTGTGTTTGGTACTAC 59.547 45.833 0.00 0.00 0.00 2.73
887 911 3.483421 AGCTTTAGGGTGTGTTTGGTAC 58.517 45.455 0.00 0.00 0.00 3.34
888 912 3.136809 TGAGCTTTAGGGTGTGTTTGGTA 59.863 43.478 0.00 0.00 0.00 3.25
890 914 2.293399 GTGAGCTTTAGGGTGTGTTTGG 59.707 50.000 0.00 0.00 0.00 3.28
891 915 3.214328 AGTGAGCTTTAGGGTGTGTTTG 58.786 45.455 0.00 0.00 0.00 2.93
892 916 3.136626 AGAGTGAGCTTTAGGGTGTGTTT 59.863 43.478 0.00 0.00 0.00 2.83
894 918 2.330216 AGAGTGAGCTTTAGGGTGTGT 58.670 47.619 0.00 0.00 0.00 3.72
895 919 3.409026 AAGAGTGAGCTTTAGGGTGTG 57.591 47.619 0.00 0.00 0.00 3.82
897 921 3.748568 GTGAAAGAGTGAGCTTTAGGGTG 59.251 47.826 0.00 0.00 38.16 4.61
899 923 4.278975 AGTGAAAGAGTGAGCTTTAGGG 57.721 45.455 0.00 0.00 38.16 3.53
901 925 5.988561 AGTGAAGTGAAAGAGTGAGCTTTAG 59.011 40.000 0.00 0.00 38.16 1.85
902 926 5.755375 CAGTGAAGTGAAAGAGTGAGCTTTA 59.245 40.000 0.00 0.00 38.16 1.85
905 929 3.494048 CCAGTGAAGTGAAAGAGTGAGCT 60.494 47.826 0.00 0.00 0.00 4.09
906 930 2.805099 CCAGTGAAGTGAAAGAGTGAGC 59.195 50.000 0.00 0.00 0.00 4.26
913 941 4.070716 AGCAGAATCCAGTGAAGTGAAAG 58.929 43.478 0.00 0.00 0.00 2.62
960 988 7.039993 GCAAAGGTTAAAGGTTAAAGGAGATGA 60.040 37.037 0.00 0.00 0.00 2.92
962 990 6.780522 TGCAAAGGTTAAAGGTTAAAGGAGAT 59.219 34.615 0.00 0.00 0.00 2.75
963 991 6.040054 GTGCAAAGGTTAAAGGTTAAAGGAGA 59.960 38.462 0.00 0.00 0.00 3.71
1027 1055 0.112995 TTTCTGTGCAATGAGGGGCT 59.887 50.000 0.00 0.00 0.00 5.19
1028 1056 0.968405 TTTTCTGTGCAATGAGGGGC 59.032 50.000 0.00 0.00 0.00 5.80
1047 1075 4.684134 ATGGCGGGCAGGTGCTTT 62.684 61.111 10.83 0.00 41.70 3.51
1059 1087 2.759149 TTGCATTCCCCCATGGCG 60.759 61.111 6.09 0.00 0.00 5.69
1134 1162 1.060937 GCATTGCGCGACGAAGAAT 59.939 52.632 12.10 0.00 0.00 2.40
1164 1192 2.942804 AGATCGATGAGAGAAGCAGGA 58.057 47.619 0.54 0.00 0.00 3.86
1169 1197 8.783093 AGAAGTGTATAAGATCGATGAGAGAAG 58.217 37.037 0.54 0.00 0.00 2.85
1173 1201 7.040340 GGGAAGAAGTGTATAAGATCGATGAGA 60.040 40.741 0.54 0.00 0.00 3.27
1174 1202 7.040062 AGGGAAGAAGTGTATAAGATCGATGAG 60.040 40.741 0.54 0.00 0.00 2.90
1180 1209 7.291411 TGCTAGGGAAGAAGTGTATAAGATC 57.709 40.000 0.00 0.00 0.00 2.75
1187 1216 3.838317 ACACATGCTAGGGAAGAAGTGTA 59.162 43.478 0.00 0.00 35.54 2.90
1277 1307 0.947244 AACTCTTTCGCAGCAAGTGG 59.053 50.000 0.00 0.00 0.00 4.00
1298 1336 0.028770 TTTCAGCAAACTTCGGCGTG 59.971 50.000 6.85 3.77 34.54 5.34
1304 1342 6.783892 TTGGCATAAATTTCAGCAAACTTC 57.216 33.333 14.40 0.41 0.00 3.01
1307 1345 7.368480 AGAATTGGCATAAATTTCAGCAAAC 57.632 32.000 14.40 2.32 29.89 2.93
1343 1381 8.023128 AGATCAACCGAATTTGAACATACAAAG 58.977 33.333 0.00 0.00 41.87 2.77
1353 1391 5.449041 GCATGCTAAGATCAACCGAATTTGA 60.449 40.000 11.37 0.00 39.79 2.69
1365 1403 5.118990 TCAACCTGTTAGCATGCTAAGATC 58.881 41.667 34.78 24.68 38.95 2.75
1390 1436 6.074676 GCAAGTGTGAGCAAAATTTCAGTAAG 60.075 38.462 0.00 0.00 0.00 2.34
1439 1485 9.843334 TCGTTAGTGTTTTGTCAAGTTAATTTT 57.157 25.926 0.00 0.00 0.00 1.82
1446 1492 4.933400 ACAGTCGTTAGTGTTTTGTCAAGT 59.067 37.500 0.00 0.00 35.69 3.16
1448 1494 4.930405 TGACAGTCGTTAGTGTTTTGTCAA 59.070 37.500 2.27 0.00 40.07 3.18
1450 1496 4.327898 TGTGACAGTCGTTAGTGTTTTGTC 59.672 41.667 0.00 0.00 39.44 3.18
1452 1498 4.328983 AGTGTGACAGTCGTTAGTGTTTTG 59.671 41.667 0.00 0.00 39.44 2.44
1478 1524 1.270252 GCACCCAACAAAACCCATCAG 60.270 52.381 0.00 0.00 0.00 2.90
1483 1529 0.250513 TTGTGCACCCAACAAAACCC 59.749 50.000 15.69 0.00 0.00 4.11
1805 1998 4.819761 GGCAGTGGCGCGATCTCA 62.820 66.667 12.10 0.00 42.47 3.27
2398 2816 2.346365 GGGAACGGTGTGACCTCC 59.654 66.667 0.00 0.00 35.66 4.30
2761 3197 4.208686 GCGTAGGAGGCGTGGGAG 62.209 72.222 0.00 0.00 0.00 4.30
2863 3299 2.350522 GTGAGGTGATGTGGCTTACTG 58.649 52.381 0.00 0.00 0.00 2.74
2937 3373 5.627499 TCAAGAAATGGTTACAGCATCAC 57.373 39.130 0.00 0.00 34.88 3.06
3008 3456 0.109342 CTGTTGGGAGGCTGTTCTGT 59.891 55.000 0.00 0.00 0.00 3.41
3013 3461 1.001641 GCATCTGTTGGGAGGCTGT 60.002 57.895 0.00 0.00 39.52 4.40
3014 3462 1.751927 GGCATCTGTTGGGAGGCTG 60.752 63.158 0.00 0.00 41.87 4.85
3016 3464 1.076485 ATGGCATCTGTTGGGAGGC 60.076 57.895 0.00 0.00 41.52 4.70
3018 3466 1.064906 ACTGATGGCATCTGTTGGGAG 60.065 52.381 27.91 17.63 38.11 4.30
3019 3467 0.994247 ACTGATGGCATCTGTTGGGA 59.006 50.000 27.91 7.58 38.11 4.37
3035 3491 0.249120 TCCAGAACCATACGCCACTG 59.751 55.000 0.00 0.00 0.00 3.66
3041 3497 1.207089 TCCAGCTTCCAGAACCATACG 59.793 52.381 0.00 0.00 0.00 3.06
3050 3506 1.915141 AAATGGTGTCCAGCTTCCAG 58.085 50.000 0.00 0.00 36.75 3.86
3086 3542 8.691661 TCTGTATGTATATCTGCACTACTTCA 57.308 34.615 0.00 0.00 0.00 3.02
3265 3725 3.458579 CTGACGAACGTGGTCGCG 61.459 66.667 7.30 0.00 45.00 5.87
3285 3745 4.328440 CGAAGCCTTTGTCAGAGACTTATG 59.672 45.833 0.00 0.00 33.15 1.90
3315 3775 4.756642 GGTGATCACTTCTGTTCATGTTCA 59.243 41.667 24.50 0.00 30.49 3.18
3316 3776 4.143030 CGGTGATCACTTCTGTTCATGTTC 60.143 45.833 24.50 2.67 30.49 3.18
3317 3777 3.748048 CGGTGATCACTTCTGTTCATGTT 59.252 43.478 24.50 0.00 30.49 2.71
3318 3778 3.006859 TCGGTGATCACTTCTGTTCATGT 59.993 43.478 24.50 0.00 30.49 3.21
3319 3779 3.588955 TCGGTGATCACTTCTGTTCATG 58.411 45.455 24.50 3.55 30.49 3.07
3320 3780 3.511540 TCTCGGTGATCACTTCTGTTCAT 59.488 43.478 24.50 0.00 30.49 2.57
3321 3781 2.890945 TCTCGGTGATCACTTCTGTTCA 59.109 45.455 24.50 0.00 0.00 3.18
3327 3787 6.035112 GTCAAATAGTTCTCGGTGATCACTTC 59.965 42.308 24.50 8.80 0.00 3.01
3328 3788 5.869888 GTCAAATAGTTCTCGGTGATCACTT 59.130 40.000 24.50 5.65 0.00 3.16
3334 3794 2.821378 TCGGTCAAATAGTTCTCGGTGA 59.179 45.455 0.00 0.00 0.00 4.02
3338 3798 3.724751 GTCGATCGGTCAAATAGTTCTCG 59.275 47.826 16.41 0.00 0.00 4.04
3350 3810 4.097012 GTTCTTTAGTCTGTCGATCGGTC 58.903 47.826 16.41 9.60 0.00 4.79
3352 3812 3.119602 TGGTTCTTTAGTCTGTCGATCGG 60.120 47.826 16.41 0.00 0.00 4.18
3354 3814 5.312120 TCTGGTTCTTTAGTCTGTCGATC 57.688 43.478 0.00 0.00 0.00 3.69
3355 3815 5.419155 TCATCTGGTTCTTTAGTCTGTCGAT 59.581 40.000 0.00 0.00 0.00 3.59
3379 3841 9.492973 TGATCATCATGTCAAACAATATCGTAT 57.507 29.630 0.00 0.00 0.00 3.06
3382 3844 6.788930 CGTGATCATCATGTCAAACAATATCG 59.211 38.462 0.00 0.00 0.00 2.92
3399 3861 1.361993 GCTCGAGGAGCGTGATCAT 59.638 57.895 15.58 0.00 45.85 2.45
3400 3862 2.801421 GCTCGAGGAGCGTGATCA 59.199 61.111 15.58 0.00 45.85 2.92
3449 3920 2.043411 CTGTTCGGTTGATTTTGTGCG 58.957 47.619 0.00 0.00 0.00 5.34
3497 3970 0.390603 GTGGCAGCACGTACCATACA 60.391 55.000 0.00 0.00 35.53 2.29
3544 4017 3.616956 TCTGCAGACATACCCTTCTTG 57.383 47.619 13.74 0.00 0.00 3.02
3585 4058 0.536460 GCAAAGGGAGGGTCGTGAAA 60.536 55.000 0.00 0.00 0.00 2.69
3588 4061 2.359975 GGCAAAGGGAGGGTCGTG 60.360 66.667 0.00 0.00 0.00 4.35
3593 4066 2.285773 GCAAAGGGCAAAGGGAGGG 61.286 63.158 0.00 0.00 43.97 4.30
3636 4109 2.562738 GCAGGTCTACTTTGGGCAAAAT 59.437 45.455 0.00 0.00 0.00 1.82
3651 4124 6.655425 AGTTAACCTCTCTTATTTTGCAGGTC 59.345 38.462 0.88 0.00 32.90 3.85
3662 4135 7.299246 ACAAGCTGTTAGTTAACCTCTCTTA 57.701 36.000 0.88 0.00 35.37 2.10
3663 4136 6.176014 ACAAGCTGTTAGTTAACCTCTCTT 57.824 37.500 0.88 0.00 35.37 2.85
3667 4140 6.706716 AGAAGAACAAGCTGTTAGTTAACCTC 59.293 38.462 0.88 0.00 41.28 3.85
3669 4142 6.862711 AGAAGAACAAGCTGTTAGTTAACC 57.137 37.500 0.88 0.00 41.28 2.85
3670 4143 8.590719 AGTAGAAGAACAAGCTGTTAGTTAAC 57.409 34.615 0.00 0.00 41.28 2.01
3671 4144 8.639761 AGAGTAGAAGAACAAGCTGTTAGTTAA 58.360 33.333 0.00 0.00 41.28 2.01
3672 4145 8.179509 AGAGTAGAAGAACAAGCTGTTAGTTA 57.820 34.615 0.00 0.00 41.28 2.24
3673 4146 7.056844 AGAGTAGAAGAACAAGCTGTTAGTT 57.943 36.000 0.00 0.00 41.28 2.24
3674 4147 6.658188 AGAGTAGAAGAACAAGCTGTTAGT 57.342 37.500 0.00 0.00 41.28 2.24
3676 4149 7.050970 TCAAGAGTAGAAGAACAAGCTGTTA 57.949 36.000 0.00 0.00 41.28 2.41
3680 4160 5.071115 ACCTTCAAGAGTAGAAGAACAAGCT 59.929 40.000 4.61 0.00 44.00 3.74
3696 4176 5.652994 ACTCTACTCTTGCTACCTTCAAG 57.347 43.478 0.00 0.00 41.57 3.02
3697 4177 5.652891 CCTACTCTACTCTTGCTACCTTCAA 59.347 44.000 0.00 0.00 0.00 2.69
3698 4178 5.194432 CCTACTCTACTCTTGCTACCTTCA 58.806 45.833 0.00 0.00 0.00 3.02
3699 4179 5.195185 ACCTACTCTACTCTTGCTACCTTC 58.805 45.833 0.00 0.00 0.00 3.46
3700 4180 5.195848 ACCTACTCTACTCTTGCTACCTT 57.804 43.478 0.00 0.00 0.00 3.50
3701 4181 4.866327 ACCTACTCTACTCTTGCTACCT 57.134 45.455 0.00 0.00 0.00 3.08
3702 4182 4.948621 TCAACCTACTCTACTCTTGCTACC 59.051 45.833 0.00 0.00 0.00 3.18
3703 4183 6.404954 CCTTCAACCTACTCTACTCTTGCTAC 60.405 46.154 0.00 0.00 0.00 3.58
3704 4184 5.652891 CCTTCAACCTACTCTACTCTTGCTA 59.347 44.000 0.00 0.00 0.00 3.49
3705 4185 4.464597 CCTTCAACCTACTCTACTCTTGCT 59.535 45.833 0.00 0.00 0.00 3.91
3706 4186 4.382147 CCCTTCAACCTACTCTACTCTTGC 60.382 50.000 0.00 0.00 0.00 4.01
3707 4187 4.160626 CCCCTTCAACCTACTCTACTCTTG 59.839 50.000 0.00 0.00 0.00 3.02
3715 4195 0.696501 TTGCCCCCTTCAACCTACTC 59.303 55.000 0.00 0.00 0.00 2.59
3717 4197 2.231716 AATTGCCCCCTTCAACCTAC 57.768 50.000 0.00 0.00 0.00 3.18
3727 4207 3.772572 ACACAAGGTAATTAATTGCCCCC 59.227 43.478 26.17 13.49 42.66 5.40
3738 4218 5.123344 GCCACGAGAATAAACACAAGGTAAT 59.877 40.000 0.00 0.00 0.00 1.89
3746 4226 1.659098 CCGAGCCACGAGAATAAACAC 59.341 52.381 2.48 0.00 45.77 3.32
3800 4280 1.021968 GCACCGAACCAACAGAAACT 58.978 50.000 0.00 0.00 0.00 2.66
3822 4305 2.568623 AACCAAGAGAACGGAATGCT 57.431 45.000 0.00 0.00 0.00 3.79
3824 4307 4.755123 ACTGTTAACCAAGAGAACGGAATG 59.245 41.667 2.48 0.00 34.27 2.67
3839 4322 4.575885 TGATTCAGGTGCCTACTGTTAAC 58.424 43.478 0.00 0.00 37.25 2.01
3844 4327 1.065926 TGCTGATTCAGGTGCCTACTG 60.066 52.381 15.28 0.00 37.30 2.74
3845 4328 1.279496 TGCTGATTCAGGTGCCTACT 58.721 50.000 15.28 0.00 31.21 2.57
3905 4388 7.973388 GCACACTTTATTCACAAGGCAATATAA 59.027 33.333 0.00 0.00 0.00 0.98
3911 4394 2.954989 TGCACACTTTATTCACAAGGCA 59.045 40.909 0.00 0.00 0.00 4.75
3912 4395 3.243367 TGTGCACACTTTATTCACAAGGC 60.243 43.478 17.42 0.00 35.08 4.35
3935 4426 3.313526 ACGACCAGAATTCAATAGCATGC 59.686 43.478 10.51 10.51 0.00 4.06
3939 4430 4.802039 TCGTTACGACCAGAATTCAATAGC 59.198 41.667 2.33 0.00 0.00 2.97
3943 4434 4.370049 TGTTCGTTACGACCAGAATTCAA 58.630 39.130 7.06 0.00 34.89 2.69
3950 4441 3.117794 TGAACTTGTTCGTTACGACCAG 58.882 45.455 7.06 6.23 34.89 4.00
3955 4446 9.619727 CTGATAATTATGAACTTGTTCGTTACG 57.380 33.333 12.61 0.00 0.00 3.18
3973 4464 8.559536 CGCATAGGTTTCACAATACTGATAATT 58.440 33.333 0.00 0.00 0.00 1.40
3974 4465 7.307989 GCGCATAGGTTTCACAATACTGATAAT 60.308 37.037 0.30 0.00 0.00 1.28
3975 4466 6.018262 GCGCATAGGTTTCACAATACTGATAA 60.018 38.462 0.30 0.00 0.00 1.75
3976 4467 5.465390 GCGCATAGGTTTCACAATACTGATA 59.535 40.000 0.30 0.00 0.00 2.15
3977 4468 4.273480 GCGCATAGGTTTCACAATACTGAT 59.727 41.667 0.30 0.00 0.00 2.90
3978 4469 3.621268 GCGCATAGGTTTCACAATACTGA 59.379 43.478 0.30 0.00 0.00 3.41
3979 4470 3.373748 TGCGCATAGGTTTCACAATACTG 59.626 43.478 5.66 0.00 0.00 2.74
3980 4471 3.605634 TGCGCATAGGTTTCACAATACT 58.394 40.909 5.66 0.00 0.00 2.12
3981 4472 4.035091 TGATGCGCATAGGTTTCACAATAC 59.965 41.667 25.40 5.92 0.00 1.89
3982 4473 4.195416 TGATGCGCATAGGTTTCACAATA 58.805 39.130 25.40 0.00 0.00 1.90
3983 4474 3.016031 TGATGCGCATAGGTTTCACAAT 58.984 40.909 25.40 0.00 0.00 2.71
3984 4475 2.431454 TGATGCGCATAGGTTTCACAA 58.569 42.857 25.40 0.00 0.00 3.33
3985 4476 2.106477 TGATGCGCATAGGTTTCACA 57.894 45.000 25.40 11.60 0.00 3.58


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

AutoCloner maintained by Alex Coulton.