Multiple sequence alignment - TraesCS2A01G388300

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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 TraesCS2A01G388300 chr2A 100.000 3606 0 0 1 3606 635509740 635513345 0.000000e+00 6660
1 TraesCS2A01G388300 chr2A 98.551 276 3 1 3331 3606 532842042 532842316 1.510000e-133 486
2 TraesCS2A01G388300 chr2D 91.086 2625 77 34 785 3334 491192682 491195224 0.000000e+00 3406
3 TraesCS2A01G388300 chr2D 89.697 495 28 9 263 746 491192200 491192682 8.560000e-171 610
4 TraesCS2A01G388300 chr2D 87.793 213 17 5 1 204 491191998 491192210 1.290000e-59 241
5 TraesCS2A01G388300 chr2B 91.279 2557 100 41 837 3334 575835006 575837498 0.000000e+00 3373
6 TraesCS2A01G388300 chr2B 88.235 867 50 19 3 845 575833689 575834527 0.000000e+00 989
7 TraesCS2A01G388300 chr2B 99.265 272 2 0 3335 3606 764753515 764753244 3.230000e-135 492
8 TraesCS2A01G388300 chr1A 98.901 273 3 0 3334 3606 144566323 144566051 4.180000e-134 488
9 TraesCS2A01G388300 chr1A 81.221 213 28 8 2349 2555 390709561 390709767 1.040000e-35 161
10 TraesCS2A01G388300 chr4B 98.529 272 4 0 3335 3606 141558335 141558606 7.000000e-132 481
11 TraesCS2A01G388300 chr4B 96.386 249 7 2 3335 3582 141564908 141564661 3.350000e-110 409
12 TraesCS2A01G388300 chr5B 97.426 272 7 0 3335 3606 212407028 212407299 7.050000e-127 464
13 TraesCS2A01G388300 chr5B 96.813 251 6 2 3333 3582 212410963 212410714 5.570000e-113 418
14 TraesCS2A01G388300 chr3A 95.203 271 8 5 3315 3582 102495284 102495552 1.200000e-114 424
15 TraesCS2A01G388300 chr3A 82.564 195 22 11 2349 2537 504024846 504025034 1.040000e-35 161
16 TraesCS2A01G388300 chr4A 96.787 249 6 2 3335 3582 37011919 37012166 7.200000e-112 414
17 TraesCS2A01G388300 chr6D 78.593 654 83 34 1980 2611 312558754 312559372 2.630000e-101 379
18 TraesCS2A01G388300 chr6B 78.321 655 83 43 1980 2611 514478652 514478034 5.690000e-98 368
19 TraesCS2A01G388300 chr6A 77.530 672 95 33 1960 2611 449181666 449182301 1.590000e-93 353
20 TraesCS2A01G388300 chr1B 80.569 211 33 8 2349 2555 420685667 420685873 4.820000e-34 156


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 TraesCS2A01G388300 chr2A 635509740 635513345 3605 False 6660 6660 100.000000 1 3606 1 chr2A.!!$F2 3605
1 TraesCS2A01G388300 chr2D 491191998 491195224 3226 False 1419 3406 89.525333 1 3334 3 chr2D.!!$F1 3333
2 TraesCS2A01G388300 chr2B 575833689 575837498 3809 False 2181 3373 89.757000 3 3334 2 chr2B.!!$F1 3331
3 TraesCS2A01G388300 chr6D 312558754 312559372 618 False 379 379 78.593000 1980 2611 1 chr6D.!!$F1 631
4 TraesCS2A01G388300 chr6B 514478034 514478652 618 True 368 368 78.321000 1980 2611 1 chr6B.!!$R1 631
5 TraesCS2A01G388300 chr6A 449181666 449182301 635 False 353 353 77.530000 1960 2611 1 chr6A.!!$F1 651

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
752 771 0.036294 GAAGGCCAGGGTCTACACAC 60.036 60.0 5.01 0.0 0.0 3.82 F
756 775 0.320771 GCCAGGGTCTACACACACAG 60.321 60.0 0.00 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2804 1.576421 CGTGCTTGGACTTCTTGGC 59.424 57.895 0.0 0.0 0.0 4.52 R
2738 3347 2.086869 CTCCAAACGGTACTACTCGGA 58.913 52.381 0.0 0.0 0.0 4.55 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
27 28 7.094205 ACCACTATTTTGCAAATCTTGGAGTAG 60.094 37.037 25.05 12.33 30.85 2.57
64 65 2.887151 AGTGGAAGCTGCCTGTATTT 57.113 45.000 13.40 0.00 0.00 1.40
80 81 1.305201 ATTTTGCGCCGGTATACAGG 58.695 50.000 16.88 16.88 0.00 4.00
119 120 9.864034 GTTTAAAGTGAATGGACGATATACATG 57.136 33.333 0.00 0.00 0.00 3.21
126 127 2.029020 TGGACGATATACATGCTGCTCC 60.029 50.000 0.00 0.00 0.00 4.70
204 214 7.541091 CCAAGATTTGTATGAATGCAGCATATC 59.459 37.037 8.75 9.19 31.54 1.63
206 216 8.405418 AGATTTGTATGAATGCAGCATATCTT 57.595 30.769 8.75 9.19 32.97 2.40
216 226 5.488645 TGCAGCATATCTTTGTACACATG 57.511 39.130 0.00 0.00 0.00 3.21
218 228 4.261322 GCAGCATATCTTTGTACACATGGG 60.261 45.833 0.00 0.00 0.00 4.00
219 229 4.883585 CAGCATATCTTTGTACACATGGGT 59.116 41.667 5.60 5.60 0.00 4.51
220 230 6.054941 CAGCATATCTTTGTACACATGGGTA 58.945 40.000 2.93 2.93 0.00 3.69
221 231 6.017934 CAGCATATCTTTGTACACATGGGTAC 60.018 42.308 27.97 27.97 43.08 3.34
222 232 5.050363 GCATATCTTTGTACACATGGGTACG 60.050 44.000 28.43 17.09 45.16 3.67
223 233 4.811969 ATCTTTGTACACATGGGTACGA 57.188 40.909 28.43 25.41 45.16 3.43
239 249 7.218228 TGGGTACGATACGATACAACATATT 57.782 36.000 0.00 0.00 0.00 1.28
242 252 9.065871 GGGTACGATACGATACAACATATTTAC 57.934 37.037 0.00 0.00 0.00 2.01
244 254 9.065871 GTACGATACGATACAACATATTTACCC 57.934 37.037 0.00 0.00 0.00 3.69
249 259 5.006941 ACGATACAACATATTTACCCGCAAC 59.993 40.000 0.00 0.00 0.00 4.17
253 263 4.762765 ACAACATATTTACCCGCAACAGAA 59.237 37.500 0.00 0.00 0.00 3.02
342 352 7.862512 AAAGGAGAGAAGAAAAGATATGCAG 57.137 36.000 0.00 0.00 0.00 4.41
346 356 5.927819 AGAGAAGAAAAGATATGCAGGGAG 58.072 41.667 0.00 0.00 0.00 4.30
541 560 2.784682 ACTTTACCTTAACCCACCCACA 59.215 45.455 0.00 0.00 0.00 4.17
543 562 1.364269 TACCTTAACCCACCCACAGG 58.636 55.000 0.00 0.00 40.04 4.00
560 579 1.448013 GGCCCCGAAGAGAAGAACG 60.448 63.158 0.00 0.00 0.00 3.95
561 580 1.448013 GCCCCGAAGAGAAGAACGG 60.448 63.158 0.00 0.00 44.16 4.44
562 581 1.885163 GCCCCGAAGAGAAGAACGGA 61.885 60.000 0.00 0.00 46.94 4.69
563 582 0.606604 CCCCGAAGAGAAGAACGGAA 59.393 55.000 0.00 0.00 46.94 4.30
564 583 1.672145 CCCCGAAGAGAAGAACGGAAC 60.672 57.143 0.00 0.00 46.94 3.62
657 676 3.488090 GACCGCTGCGCTGTTACC 61.488 66.667 18.00 0.00 0.00 2.85
742 761 0.462759 GGATGAGTTCGAAGGCCAGG 60.463 60.000 5.01 0.00 0.00 4.45
746 765 1.536662 AGTTCGAAGGCCAGGGTCT 60.537 57.895 5.01 0.00 0.00 3.85
748 767 0.108281 GTTCGAAGGCCAGGGTCTAC 60.108 60.000 5.01 0.00 0.00 2.59
750 769 1.218316 CGAAGGCCAGGGTCTACAC 59.782 63.158 5.01 0.00 0.00 2.90
751 770 1.541310 CGAAGGCCAGGGTCTACACA 61.541 60.000 5.01 0.00 0.00 3.72
752 771 0.036294 GAAGGCCAGGGTCTACACAC 60.036 60.000 5.01 0.00 0.00 3.82
753 772 0.766674 AAGGCCAGGGTCTACACACA 60.767 55.000 5.01 0.00 0.00 3.72
754 773 1.003718 GGCCAGGGTCTACACACAC 60.004 63.158 0.00 0.00 0.00 3.82
755 774 1.752198 GCCAGGGTCTACACACACA 59.248 57.895 0.00 0.00 0.00 3.72
756 775 0.320771 GCCAGGGTCTACACACACAG 60.321 60.000 0.00 0.00 0.00 3.66
757 776 1.048601 CCAGGGTCTACACACACAGT 58.951 55.000 0.00 0.00 0.00 3.55
759 778 2.231478 CCAGGGTCTACACACACAGTAG 59.769 54.545 0.00 0.00 40.18 2.57
763 795 4.652421 AGGGTCTACACACACAGTAGAAAA 59.348 41.667 4.78 0.00 46.70 2.29
800 832 3.123284 GTCGACCGATACCGAGAAGATAG 59.877 52.174 3.51 0.00 38.22 2.08
801 833 3.065655 CGACCGATACCGAGAAGATAGT 58.934 50.000 0.00 0.00 38.22 2.12
802 834 4.021981 TCGACCGATACCGAGAAGATAGTA 60.022 45.833 0.00 0.00 38.22 1.82
868 1387 2.158914 AGCACCAAAGGCCAAAGAAAAG 60.159 45.455 5.01 0.00 0.00 2.27
887 1406 0.458025 GGAGCGGACGAGACGAAAAT 60.458 55.000 0.00 0.00 0.00 1.82
1019 1549 1.237285 ATGCTCCACCAAACGCTCAC 61.237 55.000 0.00 0.00 0.00 3.51
1084 1620 2.668212 CCTTCGCCTCAAACGCCA 60.668 61.111 0.00 0.00 0.00 5.69
1085 1621 2.680913 CCTTCGCCTCAAACGCCAG 61.681 63.158 0.00 0.00 0.00 4.85
1086 1622 3.314388 CTTCGCCTCAAACGCCAGC 62.314 63.158 0.00 0.00 0.00 4.85
1182 1718 0.399233 CTCTGGTAAGGAGGGAGGGG 60.399 65.000 0.00 0.00 0.00 4.79
1189 1725 0.400093 AAGGAGGGAGGGGGATTACG 60.400 60.000 0.00 0.00 0.00 3.18
1208 1744 0.402504 GGGGGCGAGAGAGATAGAGA 59.597 60.000 0.00 0.00 0.00 3.10
1209 1745 1.005450 GGGGGCGAGAGAGATAGAGAT 59.995 57.143 0.00 0.00 0.00 2.75
1210 1746 2.240160 GGGGGCGAGAGAGATAGAGATA 59.760 54.545 0.00 0.00 0.00 1.98
1211 1747 3.541632 GGGGCGAGAGAGATAGAGATAG 58.458 54.545 0.00 0.00 0.00 2.08
1212 1748 3.199071 GGGGCGAGAGAGATAGAGATAGA 59.801 52.174 0.00 0.00 0.00 1.98
1213 1749 4.442706 GGGCGAGAGAGATAGAGATAGAG 58.557 52.174 0.00 0.00 0.00 2.43
1214 1750 4.161565 GGGCGAGAGAGATAGAGATAGAGA 59.838 50.000 0.00 0.00 0.00 3.10
1215 1751 5.163301 GGGCGAGAGAGATAGAGATAGAGAT 60.163 48.000 0.00 0.00 0.00 2.75
1283 1819 2.561478 TTTTCGGAGTGGAAGGAAGG 57.439 50.000 0.00 0.00 0.00 3.46
1328 1864 4.340617 TCTCAACTTGTGGTTCTTGGTTT 58.659 39.130 0.00 0.00 35.74 3.27
1349 1892 6.978659 GGTTTCGGGAATTTATGATTTTCCTC 59.021 38.462 0.00 0.00 39.12 3.71
1353 1896 7.570132 TCGGGAATTTATGATTTTCCTCTGTA 58.430 34.615 0.00 0.00 39.12 2.74
1355 1898 8.292448 CGGGAATTTATGATTTTCCTCTGTATG 58.708 37.037 0.00 0.00 39.12 2.39
1361 1919 4.599041 TGATTTTCCTCTGTATGTTGGGG 58.401 43.478 0.00 0.00 0.00 4.96
1734 2292 1.210870 GCTTTTGTCGTACGTGGTGA 58.789 50.000 16.05 0.00 0.00 4.02
1923 2487 4.468689 GCTACCCCAGCGACACCC 62.469 72.222 0.00 0.00 41.37 4.61
1924 2488 4.143333 CTACCCCAGCGACACCCG 62.143 72.222 0.00 0.00 42.21 5.28
2458 3063 4.077184 TACAAGTCCGGCCGGCTG 62.077 66.667 39.89 33.13 34.68 4.85
2473 3078 2.754658 CTGCTCCCCGAGTACCGT 60.755 66.667 0.00 0.00 36.31 4.83
2563 3168 3.391382 AAGAAGGAGGACGGCCCG 61.391 66.667 1.76 0.00 40.87 6.13
2613 3221 1.648756 CGTCGTTCTAGCTCGCTCG 60.649 63.158 0.00 0.00 0.00 5.03
2614 3222 1.935436 GTCGTTCTAGCTCGCTCGC 60.935 63.158 0.00 0.00 0.00 5.03
2697 3305 2.356135 TGTACTACCGTACTCGAACCC 58.644 52.381 0.00 0.00 44.97 4.11
2737 3346 7.614583 TCTCTGCTAGTATCATCATCATCATCA 59.385 37.037 0.00 0.00 0.00 3.07
2738 3347 8.307582 TCTGCTAGTATCATCATCATCATCAT 57.692 34.615 0.00 0.00 0.00 2.45
2739 3348 8.414778 TCTGCTAGTATCATCATCATCATCATC 58.585 37.037 0.00 0.00 0.00 2.92
2748 3357 6.886459 TCATCATCATCATCATCCGAGTAGTA 59.114 38.462 0.00 0.00 0.00 1.82
2810 3419 4.011698 TGTTAGGTTTTAGGAATTCGGCC 58.988 43.478 0.00 0.00 0.00 6.13
2823 3432 3.411517 CGGCCCCTCCAACTCCAT 61.412 66.667 0.00 0.00 34.01 3.41
2885 3494 2.433838 AGCAGTGCAGCACTAGCG 60.434 61.111 27.80 16.60 43.43 4.26
2935 3544 4.688021 AGGAGTTTTTCTATGAGCTAGCG 58.312 43.478 9.55 0.00 0.00 4.26
2976 3585 0.740737 AATCAATGGCGGTGCTTAGC 59.259 50.000 0.00 0.00 0.00 3.09
3130 3747 4.036144 CACATGGTGTTGTCACATGTAACA 59.964 41.667 8.30 8.30 45.45 2.41
3131 3748 4.275689 ACATGGTGTTGTCACATGTAACAG 59.724 41.667 11.95 4.71 45.45 3.16
3132 3749 2.616376 TGGTGTTGTCACATGTAACAGC 59.384 45.455 24.98 24.98 46.95 4.40
3133 3750 2.616376 GGTGTTGTCACATGTAACAGCA 59.384 45.455 26.02 21.23 46.38 4.41
3134 3751 3.253188 GGTGTTGTCACATGTAACAGCAT 59.747 43.478 26.02 0.00 46.38 3.79
3135 3752 4.848370 GGTGTTGTCACATGTAACAGCATG 60.848 45.833 26.02 4.71 46.38 4.06
3136 3753 4.024133 GTGTTGTCACATGTAACAGCATGA 60.024 41.667 20.04 0.00 46.65 3.07
3137 3754 4.761227 TGTTGTCACATGTAACAGCATGAT 59.239 37.500 14.11 0.00 46.65 2.45
3138 3755 4.950434 TGTCACATGTAACAGCATGATG 57.050 40.909 9.94 9.94 46.65 3.07
3139 3756 3.127376 TGTCACATGTAACAGCATGATGC 59.873 43.478 11.67 9.89 46.65 3.91
3178 3818 0.036022 GAGCAGACAGTTGAGGGCTT 59.964 55.000 0.00 0.00 0.00 4.35
3245 3885 1.060713 CCGCTGTCTGTTTCGTGTAG 58.939 55.000 0.00 0.00 0.00 2.74
3246 3886 1.335597 CCGCTGTCTGTTTCGTGTAGA 60.336 52.381 0.00 0.00 0.00 2.59
3247 3887 2.596452 CGCTGTCTGTTTCGTGTAGAT 58.404 47.619 0.00 0.00 0.00 1.98
3249 3889 2.668457 GCTGTCTGTTTCGTGTAGATGG 59.332 50.000 0.00 0.00 0.00 3.51
3252 3892 3.572682 TGTCTGTTTCGTGTAGATGGAGT 59.427 43.478 0.00 0.00 0.00 3.85
3284 3946 3.560105 GATGGCCCTGCTAATTTTCTCT 58.440 45.455 0.00 0.00 0.00 3.10
3285 3947 3.004752 TGGCCCTGCTAATTTTCTCTC 57.995 47.619 0.00 0.00 0.00 3.20
3289 3951 3.876320 GCCCTGCTAATTTTCTCTCTCAG 59.124 47.826 0.00 0.00 0.00 3.35
3290 3952 4.625083 GCCCTGCTAATTTTCTCTCTCAGT 60.625 45.833 0.00 0.00 0.00 3.41
3328 3992 4.382320 GTGGCCCTTCGCGGTGTA 62.382 66.667 6.13 0.00 38.94 2.90
3329 3993 4.077184 TGGCCCTTCGCGGTGTAG 62.077 66.667 6.13 0.00 38.94 2.74
3330 3994 4.078516 GGCCCTTCGCGGTGTAGT 62.079 66.667 6.13 0.00 38.94 2.73
3331 3995 2.508663 GCCCTTCGCGGTGTAGTC 60.509 66.667 6.13 0.00 0.00 2.59
3332 3996 2.202570 CCCTTCGCGGTGTAGTCG 60.203 66.667 6.13 0.00 0.00 4.18
3333 3997 2.564975 CCTTCGCGGTGTAGTCGT 59.435 61.111 6.13 0.00 0.00 4.34
3335 3999 1.800315 CTTCGCGGTGTAGTCGTGG 60.800 63.158 6.13 0.00 38.48 4.94
3336 4000 3.902162 TTCGCGGTGTAGTCGTGGC 62.902 63.158 6.13 0.00 38.48 5.01
3337 4001 4.710695 CGCGGTGTAGTCGTGGCA 62.711 66.667 0.00 0.00 34.88 4.92
3338 4002 2.356553 GCGGTGTAGTCGTGGCAA 60.357 61.111 0.00 0.00 0.00 4.52
3339 4003 1.740296 GCGGTGTAGTCGTGGCAAT 60.740 57.895 0.00 0.00 0.00 3.56
3340 4004 1.296056 GCGGTGTAGTCGTGGCAATT 61.296 55.000 0.00 0.00 0.00 2.32
3341 4005 1.153353 CGGTGTAGTCGTGGCAATTT 58.847 50.000 0.00 0.00 0.00 1.82
3342 4006 1.533731 CGGTGTAGTCGTGGCAATTTT 59.466 47.619 0.00 0.00 0.00 1.82
3343 4007 2.664424 CGGTGTAGTCGTGGCAATTTTG 60.664 50.000 0.00 0.00 0.00 2.44
3344 4008 2.550606 GGTGTAGTCGTGGCAATTTTGA 59.449 45.455 0.00 0.00 0.00 2.69
3345 4009 3.551551 GTGTAGTCGTGGCAATTTTGAC 58.448 45.455 0.00 0.00 36.50 3.18
3346 4010 3.002862 GTGTAGTCGTGGCAATTTTGACA 59.997 43.478 0.00 0.00 45.70 3.58
3355 4019 5.747951 TGGCAATTTTGACAATTTTGACC 57.252 34.783 11.79 12.04 44.72 4.02
3356 4020 5.435291 TGGCAATTTTGACAATTTTGACCT 58.565 33.333 11.79 0.00 44.72 3.85
3357 4021 6.586344 TGGCAATTTTGACAATTTTGACCTA 58.414 32.000 11.79 0.00 44.72 3.08
3358 4022 7.222872 TGGCAATTTTGACAATTTTGACCTAT 58.777 30.769 11.79 0.00 44.72 2.57
3359 4023 7.172875 TGGCAATTTTGACAATTTTGACCTATG 59.827 33.333 11.79 0.00 44.72 2.23
3360 4024 7.361116 GGCAATTTTGACAATTTTGACCTATGG 60.361 37.037 12.41 0.00 35.83 2.74
3361 4025 7.387397 GCAATTTTGACAATTTTGACCTATGGA 59.613 33.333 12.41 0.00 0.00 3.41
3362 4026 8.711457 CAATTTTGACAATTTTGACCTATGGAC 58.289 33.333 0.00 0.00 0.00 4.02
3363 4027 5.621197 TTGACAATTTTGACCTATGGACG 57.379 39.130 0.00 0.00 0.00 4.79
3364 4028 4.900684 TGACAATTTTGACCTATGGACGA 58.099 39.130 0.00 0.00 0.00 4.20
3365 4029 5.309638 TGACAATTTTGACCTATGGACGAA 58.690 37.500 0.00 0.00 0.00 3.85
3366 4030 5.765677 TGACAATTTTGACCTATGGACGAAA 59.234 36.000 0.00 4.51 35.83 3.46
3367 4031 6.432783 TGACAATTTTGACCTATGGACGAAAT 59.567 34.615 7.94 7.94 40.96 2.17
3368 4032 6.852664 ACAATTTTGACCTATGGACGAAATC 58.147 36.000 12.23 0.00 39.32 2.17
3369 4033 6.432783 ACAATTTTGACCTATGGACGAAATCA 59.567 34.615 12.23 0.00 39.32 2.57
3370 4034 7.040062 ACAATTTTGACCTATGGACGAAATCAA 60.040 33.333 12.23 0.00 39.32 2.57
3371 4035 7.645058 ATTTTGACCTATGGACGAAATCAAT 57.355 32.000 7.94 0.00 37.02 2.57
3372 4036 7.461182 TTTTGACCTATGGACGAAATCAATT 57.539 32.000 0.00 0.00 28.85 2.32
3373 4037 6.677781 TTGACCTATGGACGAAATCAATTC 57.322 37.500 0.00 0.00 34.52 2.17
3374 4038 5.739959 TGACCTATGGACGAAATCAATTCA 58.260 37.500 0.00 0.00 37.96 2.57
3375 4039 5.584649 TGACCTATGGACGAAATCAATTCAC 59.415 40.000 0.00 0.00 37.96 3.18
3376 4040 4.570772 ACCTATGGACGAAATCAATTCACG 59.429 41.667 0.00 0.00 37.96 4.35
3377 4041 4.024893 CCTATGGACGAAATCAATTCACGG 60.025 45.833 0.00 0.00 37.96 4.94
3378 4042 3.046968 TGGACGAAATCAATTCACGGA 57.953 42.857 0.00 0.00 37.96 4.69
3379 4043 3.403968 TGGACGAAATCAATTCACGGAA 58.596 40.909 0.00 0.00 37.96 4.30
3380 4044 4.006989 TGGACGAAATCAATTCACGGAAT 58.993 39.130 0.00 0.00 37.96 3.01
3381 4045 4.142708 TGGACGAAATCAATTCACGGAATG 60.143 41.667 0.00 0.00 37.96 2.67
3382 4046 4.094294 GGACGAAATCAATTCACGGAATGA 59.906 41.667 0.00 2.27 37.96 2.57
3389 4053 2.941210 TTCACGGAATGAACTGGCC 58.059 52.632 0.00 0.00 42.62 5.36
3390 4054 0.953471 TTCACGGAATGAACTGGCCG 60.953 55.000 0.00 0.00 42.62 6.13
3392 4056 3.177600 CGGAATGAACTGGCCGTG 58.822 61.111 0.00 0.00 38.99 4.94
3393 4057 1.375396 CGGAATGAACTGGCCGTGA 60.375 57.895 0.00 0.00 38.99 4.35
3394 4058 0.953471 CGGAATGAACTGGCCGTGAA 60.953 55.000 0.00 0.00 38.99 3.18
3395 4059 1.243902 GGAATGAACTGGCCGTGAAA 58.756 50.000 0.00 0.00 0.00 2.69
3396 4060 1.068541 GGAATGAACTGGCCGTGAAAC 60.069 52.381 0.00 0.00 0.00 2.78
3397 4061 1.880027 GAATGAACTGGCCGTGAAACT 59.120 47.619 0.00 0.00 31.75 2.66
3398 4062 2.851263 ATGAACTGGCCGTGAAACTA 57.149 45.000 0.00 0.00 31.75 2.24
3399 4063 2.851263 TGAACTGGCCGTGAAACTAT 57.149 45.000 0.00 0.00 31.75 2.12
3400 4064 3.134574 TGAACTGGCCGTGAAACTATT 57.865 42.857 0.00 0.00 31.75 1.73
3401 4065 3.482436 TGAACTGGCCGTGAAACTATTT 58.518 40.909 0.00 0.00 31.75 1.40
3402 4066 3.500680 TGAACTGGCCGTGAAACTATTTC 59.499 43.478 0.00 0.00 40.08 2.17
3403 4067 3.134574 ACTGGCCGTGAAACTATTTCA 57.865 42.857 0.00 0.00 46.68 2.69
3415 4079 7.817418 TGAAACTATTTCACAGCTTTAACCT 57.183 32.000 0.00 0.00 44.21 3.50
3416 4080 8.232913 TGAAACTATTTCACAGCTTTAACCTT 57.767 30.769 0.00 0.00 44.21 3.50
3417 4081 8.691797 TGAAACTATTTCACAGCTTTAACCTTT 58.308 29.630 0.00 0.00 44.21 3.11
3418 4082 9.529325 GAAACTATTTCACAGCTTTAACCTTTT 57.471 29.630 0.00 0.00 39.45 2.27
3419 4083 9.884636 AAACTATTTCACAGCTTTAACCTTTTT 57.115 25.926 0.00 0.00 0.00 1.94
3420 4084 8.871686 ACTATTTCACAGCTTTAACCTTTTTG 57.128 30.769 0.00 0.00 0.00 2.44
3421 4085 8.474831 ACTATTTCACAGCTTTAACCTTTTTGT 58.525 29.630 0.00 0.00 0.00 2.83
3422 4086 6.959671 TTTCACAGCTTTAACCTTTTTGTG 57.040 33.333 0.00 0.00 36.64 3.33
3423 4087 5.652994 TCACAGCTTTAACCTTTTTGTGT 57.347 34.783 0.00 0.00 36.67 3.72
3424 4088 6.761099 TCACAGCTTTAACCTTTTTGTGTA 57.239 33.333 0.00 0.00 36.67 2.90
3425 4089 6.791303 TCACAGCTTTAACCTTTTTGTGTAG 58.209 36.000 0.00 0.00 36.67 2.74
3426 4090 5.458779 CACAGCTTTAACCTTTTTGTGTAGC 59.541 40.000 0.00 0.00 32.13 3.58
3427 4091 4.675114 CAGCTTTAACCTTTTTGTGTAGCG 59.325 41.667 0.00 0.00 0.00 4.26
3428 4092 3.424198 GCTTTAACCTTTTTGTGTAGCGC 59.576 43.478 0.00 0.00 0.00 5.92
3429 4093 3.629438 TTAACCTTTTTGTGTAGCGCC 57.371 42.857 2.29 0.00 0.00 6.53
3430 4094 0.671796 AACCTTTTTGTGTAGCGCCC 59.328 50.000 2.29 0.00 0.00 6.13
3431 4095 1.209127 CCTTTTTGTGTAGCGCCCG 59.791 57.895 2.29 0.00 0.00 6.13
3432 4096 1.442017 CTTTTTGTGTAGCGCCCGC 60.442 57.895 2.29 4.20 42.33 6.13
3433 4097 2.796245 CTTTTTGTGTAGCGCCCGCC 62.796 60.000 2.29 0.00 43.17 6.13
3434 4098 4.627801 TTTGTGTAGCGCCCGCCA 62.628 61.111 2.29 0.00 43.17 5.69
3452 4116 3.755628 GGACGGCGCCACACTCTA 61.756 66.667 28.98 0.00 0.00 2.43
3453 4117 2.506438 GACGGCGCCACACTCTAC 60.506 66.667 28.98 3.88 0.00 2.59
3454 4118 4.415332 ACGGCGCCACACTCTACG 62.415 66.667 28.98 11.48 0.00 3.51
3456 4120 4.065281 GGCGCCACACTCTACGGT 62.065 66.667 24.80 0.00 0.00 4.83
3457 4121 2.809601 GCGCCACACTCTACGGTG 60.810 66.667 0.00 0.00 42.34 4.94
3458 4122 2.809601 CGCCACACTCTACGGTGC 60.810 66.667 0.00 0.00 40.52 5.01
3459 4123 2.342279 GCCACACTCTACGGTGCA 59.658 61.111 0.00 0.00 40.52 4.57
3460 4124 1.738099 GCCACACTCTACGGTGCAG 60.738 63.158 0.00 0.00 40.52 4.41
3461 4125 1.738099 CCACACTCTACGGTGCAGC 60.738 63.158 5.64 5.64 40.52 5.25
3462 4126 2.088763 CACACTCTACGGTGCAGCG 61.089 63.158 34.46 34.46 40.52 5.18
3463 4127 3.181967 CACTCTACGGTGCAGCGC 61.182 66.667 35.78 0.00 0.00 5.92
3464 4128 4.436998 ACTCTACGGTGCAGCGCC 62.437 66.667 35.78 15.72 0.00 6.53
3465 4129 4.135153 CTCTACGGTGCAGCGCCT 62.135 66.667 35.78 21.27 0.00 5.52
3466 4130 2.752640 TCTACGGTGCAGCGCCTA 60.753 61.111 35.78 21.25 0.00 3.93
3467 4131 2.278857 CTACGGTGCAGCGCCTAG 60.279 66.667 35.78 25.87 0.00 3.02
3490 4154 3.660111 GGGCGTTGCACACCAGTC 61.660 66.667 0.00 0.00 0.00 3.51
3491 4155 3.660111 GGCGTTGCACACCAGTCC 61.660 66.667 0.00 0.00 0.00 3.85
3492 4156 2.899838 GCGTTGCACACCAGTCCA 60.900 61.111 0.00 0.00 0.00 4.02
3493 4157 3.022287 CGTTGCACACCAGTCCAC 58.978 61.111 0.00 0.00 0.00 4.02
3494 4158 2.542907 CGTTGCACACCAGTCCACC 61.543 63.158 0.00 0.00 0.00 4.61
3495 4159 2.203139 TTGCACACCAGTCCACCG 60.203 61.111 0.00 0.00 0.00 4.94
3496 4160 3.037686 TTGCACACCAGTCCACCGT 62.038 57.895 0.00 0.00 0.00 4.83
3497 4161 2.972505 GCACACCAGTCCACCGTG 60.973 66.667 0.00 0.00 0.00 4.94
3498 4162 2.280797 CACACCAGTCCACCGTGG 60.281 66.667 11.73 11.73 39.43 4.94
3499 4163 4.250305 ACACCAGTCCACCGTGGC 62.250 66.667 13.19 8.17 37.47 5.01
3500 4164 4.248842 CACCAGTCCACCGTGGCA 62.249 66.667 13.19 0.00 37.47 4.92
3501 4165 3.941188 ACCAGTCCACCGTGGCAG 61.941 66.667 13.19 5.21 37.47 4.85
3528 4192 3.594775 CCGCAACCAGCAGTGCAA 61.595 61.111 19.20 0.00 46.13 4.08
3529 4193 2.353839 CGCAACCAGCAGTGCAAC 60.354 61.111 19.20 0.00 46.13 4.17
3530 4194 2.353839 GCAACCAGCAGTGCAACG 60.354 61.111 19.20 6.21 45.86 4.10
3531 4195 2.353839 CAACCAGCAGTGCAACGC 60.354 61.111 19.20 0.31 45.86 4.84
3532 4196 3.595758 AACCAGCAGTGCAACGCC 61.596 61.111 19.20 0.00 45.86 5.68
3533 4197 4.569180 ACCAGCAGTGCAACGCCT 62.569 61.111 19.20 0.00 45.86 5.52
3534 4198 3.730761 CCAGCAGTGCAACGCCTC 61.731 66.667 19.20 0.00 45.86 4.70
3535 4199 3.730761 CAGCAGTGCAACGCCTCC 61.731 66.667 19.20 0.00 45.86 4.30
3538 4202 3.114616 CAGTGCAACGCCTCCGAG 61.115 66.667 0.00 0.00 45.86 4.63
3541 4205 3.378602 TGCAACGCCTCCGAGCTA 61.379 61.111 0.00 0.00 38.86 3.32
3542 4206 2.583593 GCAACGCCTCCGAGCTAG 60.584 66.667 0.00 0.00 36.58 3.42
3543 4207 2.105128 CAACGCCTCCGAGCTAGG 59.895 66.667 6.52 6.52 38.29 3.02
3549 4213 4.577246 CTCCGAGCTAGGCGCCAC 62.577 72.222 31.54 17.93 40.39 5.01
3552 4216 4.135153 CGAGCTAGGCGCCACACT 62.135 66.667 31.54 21.99 40.39 3.55
3553 4217 2.266055 GAGCTAGGCGCCACACTT 59.734 61.111 31.54 10.27 40.39 3.16
3554 4218 2.046892 AGCTAGGCGCCACACTTG 60.047 61.111 31.54 10.03 40.39 3.16
3555 4219 2.358737 GCTAGGCGCCACACTTGT 60.359 61.111 31.54 8.51 0.00 3.16
3556 4220 1.079405 GCTAGGCGCCACACTTGTA 60.079 57.895 31.54 9.35 0.00 2.41
3557 4221 0.672401 GCTAGGCGCCACACTTGTAA 60.672 55.000 31.54 0.72 0.00 2.41
3558 4222 1.803334 CTAGGCGCCACACTTGTAAA 58.197 50.000 31.54 0.00 0.00 2.01
3570 4234 2.316119 CTTGTAAAGTGCAACGCCTC 57.684 50.000 0.00 0.00 45.86 4.70
3571 4235 0.948678 TTGTAAAGTGCAACGCCTCC 59.051 50.000 0.00 0.00 45.86 4.30
3572 4236 1.225376 TGTAAAGTGCAACGCCTCCG 61.225 55.000 0.00 0.00 45.86 4.63
3573 4237 0.947180 GTAAAGTGCAACGCCTCCGA 60.947 55.000 0.00 0.00 45.86 4.55
3574 4238 0.669318 TAAAGTGCAACGCCTCCGAG 60.669 55.000 0.00 0.00 45.86 4.63
3575 4239 3.883744 AAGTGCAACGCCTCCGAGG 62.884 63.158 10.41 10.41 45.86 4.63
3576 4240 4.681978 GTGCAACGCCTCCGAGGT 62.682 66.667 16.09 0.00 37.80 3.85
3577 4241 2.992689 TGCAACGCCTCCGAGGTA 60.993 61.111 16.09 0.00 37.80 3.08
3578 4242 2.202756 GCAACGCCTCCGAGGTAG 60.203 66.667 16.09 12.45 37.80 3.18
3579 4243 2.494918 CAACGCCTCCGAGGTAGG 59.505 66.667 16.09 8.27 37.80 3.18
3584 4248 2.439701 CCTCCGAGGTAGGCGTCA 60.440 66.667 6.24 0.00 0.00 4.35
3585 4249 2.772691 CCTCCGAGGTAGGCGTCAC 61.773 68.421 6.24 0.00 0.00 3.67
3586 4250 2.034532 TCCGAGGTAGGCGTCACA 59.965 61.111 0.00 0.00 0.00 3.58
3587 4251 2.181021 CCGAGGTAGGCGTCACAC 59.819 66.667 0.00 0.00 0.00 3.82
3588 4252 2.341101 CCGAGGTAGGCGTCACACT 61.341 63.158 0.00 0.00 0.00 3.55
3589 4253 1.585006 CGAGGTAGGCGTCACACTT 59.415 57.895 0.00 0.00 0.00 3.16
3590 4254 0.456312 CGAGGTAGGCGTCACACTTC 60.456 60.000 0.00 0.00 0.00 3.01
3591 4255 0.889306 GAGGTAGGCGTCACACTTCT 59.111 55.000 0.00 0.00 0.00 2.85
3592 4256 1.272769 GAGGTAGGCGTCACACTTCTT 59.727 52.381 0.00 0.00 0.00 2.52
3593 4257 2.490903 GAGGTAGGCGTCACACTTCTTA 59.509 50.000 0.00 0.00 0.00 2.10
3594 4258 2.895404 AGGTAGGCGTCACACTTCTTAA 59.105 45.455 0.00 0.00 0.00 1.85
3595 4259 3.056749 AGGTAGGCGTCACACTTCTTAAG 60.057 47.826 0.00 0.00 0.00 1.85
3596 4260 3.305881 GGTAGGCGTCACACTTCTTAAGT 60.306 47.826 1.63 0.00 44.06 2.24
3604 4268 2.544726 ACTTCTTAAGTGCAGCGCC 58.455 52.632 2.29 0.00 41.01 6.53
3605 4269 0.035458 ACTTCTTAAGTGCAGCGCCT 59.965 50.000 2.29 0.00 41.01 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 8.382875 GCTTCCACTTTTGACAAATAATTATGC 58.617 33.333 0.50 0.00 0.00 3.14
64 65 0.249676 TTTCCTGTATACCGGCGCAA 59.750 50.000 10.83 0.00 0.00 4.85
80 81 9.055248 CATTCACTTTAAACTGATGACGATTTC 57.945 33.333 0.00 0.00 0.00 2.17
119 120 0.250234 TGTGACTATGGTGGAGCAGC 59.750 55.000 0.00 0.00 0.00 5.25
178 182 5.001237 TGCTGCATTCATACAAATCTTGG 57.999 39.130 0.00 0.00 34.12 3.61
204 214 4.501559 CGTATCGTACCCATGTGTACAAAG 59.498 45.833 17.08 3.06 40.91 2.77
206 216 3.693578 TCGTATCGTACCCATGTGTACAA 59.306 43.478 17.08 0.41 40.91 2.41
216 226 9.065871 GTAAATATGTTGTATCGTATCGTACCC 57.934 37.037 0.00 0.00 0.00 3.69
218 228 9.065871 GGGTAAATATGTTGTATCGTATCGTAC 57.934 37.037 0.00 0.00 0.00 3.67
219 229 7.962373 CGGGTAAATATGTTGTATCGTATCGTA 59.038 37.037 0.00 0.00 0.00 3.43
220 230 6.803320 CGGGTAAATATGTTGTATCGTATCGT 59.197 38.462 0.00 0.00 0.00 3.73
221 231 6.237384 GCGGGTAAATATGTTGTATCGTATCG 60.237 42.308 0.00 0.00 0.00 2.92
222 232 6.587226 TGCGGGTAAATATGTTGTATCGTATC 59.413 38.462 0.00 0.00 0.00 2.24
223 233 6.457355 TGCGGGTAAATATGTTGTATCGTAT 58.543 36.000 0.00 0.00 0.00 3.06
260 270 9.712305 GCCTACAACTGTAAATATGATGTATCT 57.288 33.333 0.00 0.00 0.00 1.98
264 274 6.062095 GGGCCTACAACTGTAAATATGATGT 58.938 40.000 0.84 0.00 0.00 3.06
267 277 4.699637 CGGGCCTACAACTGTAAATATGA 58.300 43.478 0.84 0.00 0.00 2.15
342 352 1.373497 CGGATATGCTGACGCTCCC 60.373 63.158 0.00 0.00 36.97 4.30
346 356 3.406361 CGCCGGATATGCTGACGC 61.406 66.667 5.05 0.00 0.00 5.19
450 469 3.839432 CTTCCCTCCGGTCCGAGC 61.839 72.222 14.39 0.00 0.00 5.03
501 520 1.523938 GGGTGAGCGATTAGTGGCC 60.524 63.158 0.00 0.00 0.00 5.36
502 521 1.090052 GTGGGTGAGCGATTAGTGGC 61.090 60.000 0.00 0.00 0.00 5.01
541 560 1.889530 CGTTCTTCTCTTCGGGGCCT 61.890 60.000 0.84 0.00 0.00 5.19
543 562 1.448013 CCGTTCTTCTCTTCGGGGC 60.448 63.158 0.00 0.00 39.41 5.80
560 579 3.292500 GAGACGACGGGGTGGTTCC 62.293 68.421 0.00 0.00 0.00 3.62
561 580 2.260743 GAGACGACGGGGTGGTTC 59.739 66.667 0.00 0.00 0.00 3.62
562 581 3.677648 CGAGACGACGGGGTGGTT 61.678 66.667 0.00 0.00 0.00 3.67
563 582 4.962836 ACGAGACGACGGGGTGGT 62.963 66.667 0.00 0.00 37.61 4.16
564 583 4.112341 GACGAGACGACGGGGTGG 62.112 72.222 0.00 0.00 37.61 4.61
657 676 0.037605 AAAGAAGGGTGACGCTACCG 60.038 55.000 1.54 0.00 41.79 4.02
711 730 9.162764 CCTTCGAACTCATCCTCTTTATAAAAA 57.837 33.333 0.00 0.00 0.00 1.94
712 731 7.280205 GCCTTCGAACTCATCCTCTTTATAAAA 59.720 37.037 0.00 0.00 0.00 1.52
713 732 6.761714 GCCTTCGAACTCATCCTCTTTATAAA 59.238 38.462 0.00 0.00 0.00 1.40
714 733 6.281405 GCCTTCGAACTCATCCTCTTTATAA 58.719 40.000 0.00 0.00 0.00 0.98
715 734 5.221461 GGCCTTCGAACTCATCCTCTTTATA 60.221 44.000 0.00 0.00 0.00 0.98
716 735 4.443598 GGCCTTCGAACTCATCCTCTTTAT 60.444 45.833 0.00 0.00 0.00 1.40
717 736 3.118738 GGCCTTCGAACTCATCCTCTTTA 60.119 47.826 0.00 0.00 0.00 1.85
723 742 0.462759 CCTGGCCTTCGAACTCATCC 60.463 60.000 3.32 0.00 0.00 3.51
763 795 2.416972 GGTCGACTCGCCTACTCATTTT 60.417 50.000 16.46 0.00 0.00 1.82
800 832 0.101759 TTATGTCGCCACCTCGCTAC 59.898 55.000 0.00 0.00 0.00 3.58
801 833 0.818938 TTTATGTCGCCACCTCGCTA 59.181 50.000 0.00 0.00 0.00 4.26
802 834 0.036765 TTTTATGTCGCCACCTCGCT 60.037 50.000 0.00 0.00 0.00 4.93
868 1387 0.458025 ATTTTCGTCTCGTCCGCTCC 60.458 55.000 0.00 0.00 0.00 4.70
887 1406 1.374947 CTCCTCCCGCACTCCAAAA 59.625 57.895 0.00 0.00 0.00 2.44
1019 1549 0.323816 GAAGGCAAGGGAAGAAGGGG 60.324 60.000 0.00 0.00 0.00 4.79
1182 1718 1.807495 CTCTCTCGCCCCCGTAATCC 61.807 65.000 0.00 0.00 35.54 3.01
1189 1725 0.402504 TCTCTATCTCTCTCGCCCCC 59.597 60.000 0.00 0.00 0.00 5.40
1273 1809 0.320421 CGCTCGTTTCCTTCCTTCCA 60.320 55.000 0.00 0.00 0.00 3.53
1283 1819 4.209495 AGAAAGAGAAAGAACGCTCGTTTC 59.791 41.667 9.13 3.50 38.60 2.78
1328 1864 6.423182 ACAGAGGAAAATCATAAATTCCCGA 58.577 36.000 0.00 0.00 42.93 5.14
1349 1892 1.086696 CTTCACGCCCCAACATACAG 58.913 55.000 0.00 0.00 0.00 2.74
1353 1896 1.303317 GTCCTTCACGCCCCAACAT 60.303 57.895 0.00 0.00 0.00 2.71
1355 1898 3.047877 CGTCCTTCACGCCCCAAC 61.048 66.667 0.00 0.00 42.87 3.77
1506 2064 1.667830 CGGCTCGCAAAACTCCTCA 60.668 57.895 0.00 0.00 0.00 3.86
1734 2292 8.542926 AGCAAGGCAGGAAGAAATAATTAATTT 58.457 29.630 5.91 0.00 40.59 1.82
2104 2674 2.479650 GTGGTCGACGAGGACGAG 59.520 66.667 9.92 0.00 42.66 4.18
2234 2804 1.576421 CGTGCTTGGACTTCTTGGC 59.424 57.895 0.00 0.00 0.00 4.52
2458 3063 3.525545 GGACGGTACTCGGGGAGC 61.526 72.222 8.31 0.00 44.45 4.70
2563 3168 3.044305 GTGGCGGTGACTGTGAGC 61.044 66.667 0.00 0.00 0.00 4.26
2697 3305 7.446001 ACTAGCAGAGAAATGGAAGAAAAAG 57.554 36.000 0.00 0.00 0.00 2.27
2737 3346 2.686915 CTCCAAACGGTACTACTCGGAT 59.313 50.000 0.00 0.00 0.00 4.18
2738 3347 2.086869 CTCCAAACGGTACTACTCGGA 58.913 52.381 0.00 0.00 0.00 4.55
2739 3348 2.086869 TCTCCAAACGGTACTACTCGG 58.913 52.381 0.00 0.00 0.00 4.63
2748 3357 6.070424 TGGACTCTAATTAATCTCCAAACGGT 60.070 38.462 0.00 0.00 0.00 4.83
2810 3419 0.995024 AAGGTGATGGAGTTGGAGGG 59.005 55.000 0.00 0.00 0.00 4.30
2823 3432 4.288626 ACCCTAACAAGCTAATGAAGGTGA 59.711 41.667 0.00 0.00 35.65 4.02
2885 3494 5.532557 ACAAAGCTGGAAATAAAGTTCTGC 58.467 37.500 0.00 0.00 0.00 4.26
2935 3544 3.121738 ACACTACCCTAGCAAACACAC 57.878 47.619 0.00 0.00 0.00 3.82
2948 3557 3.064820 CACCGCCATTGATTTACACTACC 59.935 47.826 0.00 0.00 0.00 3.18
2976 3585 5.945784 TCTTCAACCCTGATGATGGTAAAAG 59.054 40.000 0.00 0.00 32.36 2.27
3083 3700 3.803082 CCAAGGGTGCACGCATCG 61.803 66.667 32.29 20.16 0.00 3.84
3132 3749 6.381481 TCCTAAAACTAAGCATGCATCATG 57.619 37.500 21.98 7.50 43.91 3.07
3133 3750 5.009410 GCTCCTAAAACTAAGCATGCATCAT 59.991 40.000 21.98 5.50 34.86 2.45
3134 3751 4.336433 GCTCCTAAAACTAAGCATGCATCA 59.664 41.667 21.98 2.90 34.86 3.07
3135 3752 4.336433 TGCTCCTAAAACTAAGCATGCATC 59.664 41.667 21.98 0.00 39.69 3.91
3136 3753 4.272489 TGCTCCTAAAACTAAGCATGCAT 58.728 39.130 21.98 11.22 39.69 3.96
3137 3754 3.684908 TGCTCCTAAAACTAAGCATGCA 58.315 40.909 21.98 0.00 39.69 3.96
3138 3755 3.941483 TCTGCTCCTAAAACTAAGCATGC 59.059 43.478 10.51 10.51 43.30 4.06
3139 3756 4.034975 GCTCTGCTCCTAAAACTAAGCATG 59.965 45.833 0.00 0.00 43.30 4.06
3140 3757 4.195416 GCTCTGCTCCTAAAACTAAGCAT 58.805 43.478 0.00 0.00 43.30 3.79
3141 3758 3.007940 TGCTCTGCTCCTAAAACTAAGCA 59.992 43.478 0.00 0.00 42.16 3.91
3142 3759 3.600388 TGCTCTGCTCCTAAAACTAAGC 58.400 45.455 0.00 0.00 35.31 3.09
3143 3760 4.867608 GTCTGCTCTGCTCCTAAAACTAAG 59.132 45.833 0.00 0.00 0.00 2.18
3144 3761 4.283467 TGTCTGCTCTGCTCCTAAAACTAA 59.717 41.667 0.00 0.00 0.00 2.24
3145 3762 3.832490 TGTCTGCTCTGCTCCTAAAACTA 59.168 43.478 0.00 0.00 0.00 2.24
3146 3763 2.634940 TGTCTGCTCTGCTCCTAAAACT 59.365 45.455 0.00 0.00 0.00 2.66
3147 3764 2.999355 CTGTCTGCTCTGCTCCTAAAAC 59.001 50.000 0.00 0.00 0.00 2.43
3148 3765 2.634940 ACTGTCTGCTCTGCTCCTAAAA 59.365 45.455 0.00 0.00 0.00 1.52
3149 3766 2.251818 ACTGTCTGCTCTGCTCCTAAA 58.748 47.619 0.00 0.00 0.00 1.85
3150 3767 1.930251 ACTGTCTGCTCTGCTCCTAA 58.070 50.000 0.00 0.00 0.00 2.69
3151 3768 1.547820 CAACTGTCTGCTCTGCTCCTA 59.452 52.381 0.00 0.00 0.00 2.94
3152 3769 0.321021 CAACTGTCTGCTCTGCTCCT 59.679 55.000 0.00 0.00 0.00 3.69
3153 3770 0.319728 TCAACTGTCTGCTCTGCTCC 59.680 55.000 0.00 0.00 0.00 4.70
3154 3771 1.672441 CCTCAACTGTCTGCTCTGCTC 60.672 57.143 0.00 0.00 0.00 4.26
3178 3818 0.039180 TTCTACCTCTCGCTGTCCCA 59.961 55.000 0.00 0.00 0.00 4.37
3245 3885 4.217118 GCCATCCATGAACAATACTCCATC 59.783 45.833 0.00 0.00 0.00 3.51
3246 3886 4.147321 GCCATCCATGAACAATACTCCAT 58.853 43.478 0.00 0.00 0.00 3.41
3247 3887 3.554934 GCCATCCATGAACAATACTCCA 58.445 45.455 0.00 0.00 0.00 3.86
3249 3889 2.887152 GGGCCATCCATGAACAATACTC 59.113 50.000 4.39 0.00 35.00 2.59
3252 3892 2.948115 CAGGGCCATCCATGAACAATA 58.052 47.619 6.18 0.00 46.59 1.90
3284 3946 4.196971 CTGCATGATTCATTGGACTGAGA 58.803 43.478 0.00 0.00 0.00 3.27
3285 3947 3.243101 GCTGCATGATTCATTGGACTGAG 60.243 47.826 0.00 0.00 0.00 3.35
3289 3951 1.268896 CCGCTGCATGATTCATTGGAC 60.269 52.381 0.00 0.00 0.00 4.02
3290 3952 1.026584 CCGCTGCATGATTCATTGGA 58.973 50.000 0.00 0.00 0.00 3.53
3323 3987 2.550606 TCAAAATTGCCACGACTACACC 59.449 45.455 0.00 0.00 0.00 4.16
3328 3992 4.320608 AATTGTCAAAATTGCCACGACT 57.679 36.364 0.00 0.00 0.00 4.18
3329 3993 5.006165 TCAAAATTGTCAAAATTGCCACGAC 59.994 36.000 8.21 0.00 0.00 4.34
3330 3994 5.006165 GTCAAAATTGTCAAAATTGCCACGA 59.994 36.000 8.21 0.00 0.00 4.35
3331 3995 5.196825 GTCAAAATTGTCAAAATTGCCACG 58.803 37.500 8.21 0.00 0.00 4.94
3332 3996 5.296531 AGGTCAAAATTGTCAAAATTGCCAC 59.703 36.000 18.32 10.44 0.00 5.01
3333 3997 5.435291 AGGTCAAAATTGTCAAAATTGCCA 58.565 33.333 18.32 0.00 0.00 4.92
3335 3999 7.387397 TCCATAGGTCAAAATTGTCAAAATTGC 59.613 33.333 8.21 5.04 0.00 3.56
3336 4000 8.711457 GTCCATAGGTCAAAATTGTCAAAATTG 58.289 33.333 7.16 7.16 0.00 2.32
3337 4001 7.598493 CGTCCATAGGTCAAAATTGTCAAAATT 59.402 33.333 0.00 0.00 0.00 1.82
3338 4002 7.040062 TCGTCCATAGGTCAAAATTGTCAAAAT 60.040 33.333 0.00 0.00 0.00 1.82
3339 4003 6.263392 TCGTCCATAGGTCAAAATTGTCAAAA 59.737 34.615 0.00 0.00 0.00 2.44
3340 4004 5.765677 TCGTCCATAGGTCAAAATTGTCAAA 59.234 36.000 0.00 0.00 0.00 2.69
3341 4005 5.309638 TCGTCCATAGGTCAAAATTGTCAA 58.690 37.500 0.00 0.00 0.00 3.18
3342 4006 4.900684 TCGTCCATAGGTCAAAATTGTCA 58.099 39.130 0.00 0.00 0.00 3.58
3343 4007 5.873179 TTCGTCCATAGGTCAAAATTGTC 57.127 39.130 0.00 0.00 0.00 3.18
3344 4008 6.432783 TGATTTCGTCCATAGGTCAAAATTGT 59.567 34.615 0.00 0.00 0.00 2.71
3345 4009 6.851609 TGATTTCGTCCATAGGTCAAAATTG 58.148 36.000 0.00 0.00 0.00 2.32
3346 4010 7.461182 TTGATTTCGTCCATAGGTCAAAATT 57.539 32.000 0.00 0.00 0.00 1.82
3347 4011 7.645058 ATTGATTTCGTCCATAGGTCAAAAT 57.355 32.000 0.00 0.00 0.00 1.82
3348 4012 7.175816 TGAATTGATTTCGTCCATAGGTCAAAA 59.824 33.333 0.00 0.00 37.13 2.44
3349 4013 6.657117 TGAATTGATTTCGTCCATAGGTCAAA 59.343 34.615 0.00 0.00 37.13 2.69
3350 4014 6.093495 GTGAATTGATTTCGTCCATAGGTCAA 59.907 38.462 0.00 0.00 37.13 3.18
3351 4015 5.584649 GTGAATTGATTTCGTCCATAGGTCA 59.415 40.000 0.00 0.00 37.13 4.02
3352 4016 5.276868 CGTGAATTGATTTCGTCCATAGGTC 60.277 44.000 0.00 0.00 37.13 3.85
3353 4017 4.570772 CGTGAATTGATTTCGTCCATAGGT 59.429 41.667 0.00 0.00 37.13 3.08
3354 4018 4.024893 CCGTGAATTGATTTCGTCCATAGG 60.025 45.833 0.00 0.00 37.13 2.57
3355 4019 4.808895 TCCGTGAATTGATTTCGTCCATAG 59.191 41.667 0.00 0.00 37.13 2.23
3356 4020 4.760878 TCCGTGAATTGATTTCGTCCATA 58.239 39.130 0.00 0.00 37.13 2.74
3357 4021 3.605634 TCCGTGAATTGATTTCGTCCAT 58.394 40.909 0.00 0.00 37.13 3.41
3358 4022 3.046968 TCCGTGAATTGATTTCGTCCA 57.953 42.857 0.00 0.00 37.13 4.02
3359 4023 4.094294 TCATTCCGTGAATTGATTTCGTCC 59.906 41.667 0.00 0.00 37.13 4.79
3360 4024 5.216566 TCATTCCGTGAATTGATTTCGTC 57.783 39.130 0.00 0.00 37.13 4.20
3361 4025 5.621197 TTCATTCCGTGAATTGATTTCGT 57.379 34.783 0.00 0.00 41.79 3.85
3371 4035 0.953471 CGGCCAGTTCATTCCGTGAA 60.953 55.000 2.24 0.00 44.36 3.18
3372 4036 1.375396 CGGCCAGTTCATTCCGTGA 60.375 57.895 2.24 0.00 37.33 4.35
3373 4037 3.177600 CGGCCAGTTCATTCCGTG 58.822 61.111 2.24 0.00 37.33 4.94
3375 4039 0.953471 TTCACGGCCAGTTCATTCCG 60.953 55.000 2.24 0.00 46.61 4.30
3376 4040 1.068541 GTTTCACGGCCAGTTCATTCC 60.069 52.381 2.24 0.00 0.00 3.01
3377 4041 1.880027 AGTTTCACGGCCAGTTCATTC 59.120 47.619 2.24 0.00 0.00 2.67
3378 4042 1.981256 AGTTTCACGGCCAGTTCATT 58.019 45.000 2.24 0.00 0.00 2.57
3379 4043 2.851263 TAGTTTCACGGCCAGTTCAT 57.149 45.000 2.24 0.00 0.00 2.57
3380 4044 2.851263 ATAGTTTCACGGCCAGTTCA 57.149 45.000 2.24 0.00 0.00 3.18
3381 4045 3.500680 TGAAATAGTTTCACGGCCAGTTC 59.499 43.478 2.24 0.00 44.21 3.01
3382 4046 3.482436 TGAAATAGTTTCACGGCCAGTT 58.518 40.909 2.24 0.00 44.21 3.16
3383 4047 3.134574 TGAAATAGTTTCACGGCCAGT 57.865 42.857 2.24 0.00 44.21 4.00
3391 4055 7.817418 AGGTTAAAGCTGTGAAATAGTTTCA 57.183 32.000 1.24 1.24 46.68 2.69
3392 4056 9.529325 AAAAGGTTAAAGCTGTGAAATAGTTTC 57.471 29.630 0.00 0.00 40.08 2.78
3393 4057 9.884636 AAAAAGGTTAAAGCTGTGAAATAGTTT 57.115 25.926 0.00 0.00 27.93 2.66
3394 4058 9.313118 CAAAAAGGTTAAAGCTGTGAAATAGTT 57.687 29.630 0.00 0.00 0.00 2.24
3395 4059 8.474831 ACAAAAAGGTTAAAGCTGTGAAATAGT 58.525 29.630 0.00 0.00 0.00 2.12
3396 4060 8.755018 CACAAAAAGGTTAAAGCTGTGAAATAG 58.245 33.333 0.00 0.00 35.78 1.73
3397 4061 8.254508 ACACAAAAAGGTTAAAGCTGTGAAATA 58.745 29.630 6.32 0.00 36.91 1.40
3398 4062 7.102993 ACACAAAAAGGTTAAAGCTGTGAAAT 58.897 30.769 6.32 0.00 36.91 2.17
3399 4063 6.459923 ACACAAAAAGGTTAAAGCTGTGAAA 58.540 32.000 6.32 0.00 36.91 2.69
3400 4064 6.031751 ACACAAAAAGGTTAAAGCTGTGAA 57.968 33.333 6.32 0.00 36.91 3.18
3401 4065 5.652994 ACACAAAAAGGTTAAAGCTGTGA 57.347 34.783 6.32 0.00 36.91 3.58
3402 4066 5.458779 GCTACACAAAAAGGTTAAAGCTGTG 59.541 40.000 0.00 0.00 38.85 3.66
3403 4067 5.588240 GCTACACAAAAAGGTTAAAGCTGT 58.412 37.500 0.00 0.00 0.00 4.40
3404 4068 4.675114 CGCTACACAAAAAGGTTAAAGCTG 59.325 41.667 0.00 0.00 0.00 4.24
3405 4069 4.791734 GCGCTACACAAAAAGGTTAAAGCT 60.792 41.667 0.00 0.00 0.00 3.74
3406 4070 3.424198 GCGCTACACAAAAAGGTTAAAGC 59.576 43.478 0.00 0.00 0.00 3.51
3407 4071 3.978855 GGCGCTACACAAAAAGGTTAAAG 59.021 43.478 7.64 0.00 0.00 1.85
3408 4072 3.243468 GGGCGCTACACAAAAAGGTTAAA 60.243 43.478 7.64 0.00 0.00 1.52
3409 4073 2.293955 GGGCGCTACACAAAAAGGTTAA 59.706 45.455 7.64 0.00 0.00 2.01
3410 4074 1.881324 GGGCGCTACACAAAAAGGTTA 59.119 47.619 7.64 0.00 0.00 2.85
3411 4075 0.671796 GGGCGCTACACAAAAAGGTT 59.328 50.000 7.64 0.00 0.00 3.50
3412 4076 1.512156 CGGGCGCTACACAAAAAGGT 61.512 55.000 7.64 0.00 0.00 3.50
3413 4077 1.209127 CGGGCGCTACACAAAAAGG 59.791 57.895 7.64 0.00 0.00 3.11
3414 4078 1.442017 GCGGGCGCTACACAAAAAG 60.442 57.895 7.64 0.00 38.26 2.27
3415 4079 2.640421 GCGGGCGCTACACAAAAA 59.360 55.556 7.64 0.00 38.26 1.94
3416 4080 3.358707 GGCGGGCGCTACACAAAA 61.359 61.111 7.64 0.00 41.60 2.44
3417 4081 4.627801 TGGCGGGCGCTACACAAA 62.628 61.111 7.64 0.00 41.60 2.83
3435 4099 3.755628 TAGAGTGTGGCGCCGTCC 61.756 66.667 23.90 12.95 0.00 4.79
3436 4100 2.506438 GTAGAGTGTGGCGCCGTC 60.506 66.667 23.90 17.98 0.00 4.79
3437 4101 4.415332 CGTAGAGTGTGGCGCCGT 62.415 66.667 23.90 5.96 0.00 5.68
3439 4103 4.065281 ACCGTAGAGTGTGGCGCC 62.065 66.667 22.73 22.73 0.00 6.53
3440 4104 2.809601 CACCGTAGAGTGTGGCGC 60.810 66.667 0.00 0.00 32.89 6.53
3441 4105 2.809601 GCACCGTAGAGTGTGGCG 60.810 66.667 0.00 0.00 40.04 5.69
3442 4106 1.738099 CTGCACCGTAGAGTGTGGC 60.738 63.158 0.00 0.00 40.04 5.01
3443 4107 1.738099 GCTGCACCGTAGAGTGTGG 60.738 63.158 0.00 0.00 40.04 4.17
3444 4108 2.088763 CGCTGCACCGTAGAGTGTG 61.089 63.158 0.00 0.00 40.04 3.82
3445 4109 2.258591 CGCTGCACCGTAGAGTGT 59.741 61.111 0.00 0.00 40.04 3.55
3446 4110 3.181967 GCGCTGCACCGTAGAGTG 61.182 66.667 0.00 0.00 40.88 3.51
3447 4111 4.436998 GGCGCTGCACCGTAGAGT 62.437 66.667 7.64 0.00 0.00 3.24
3448 4112 2.669808 CTAGGCGCTGCACCGTAGAG 62.670 65.000 7.64 0.00 0.00 2.43
3449 4113 2.752640 TAGGCGCTGCACCGTAGA 60.753 61.111 7.64 0.00 0.00 2.59
3450 4114 2.278857 CTAGGCGCTGCACCGTAG 60.279 66.667 7.64 2.34 0.00 3.51
3451 4115 4.508128 GCTAGGCGCTGCACCGTA 62.508 66.667 7.64 0.00 35.14 4.02
3475 4139 3.181169 GTGGACTGGTGTGCAACGC 62.181 63.158 0.00 0.00 45.76 4.84
3476 4140 2.542907 GGTGGACTGGTGTGCAACG 61.543 63.158 0.00 0.00 45.76 4.10
3477 4141 2.542907 CGGTGGACTGGTGTGCAAC 61.543 63.158 0.00 0.00 45.76 4.17
3478 4142 2.203139 CGGTGGACTGGTGTGCAA 60.203 61.111 0.00 0.00 45.76 4.08
3479 4143 3.475494 ACGGTGGACTGGTGTGCA 61.475 61.111 0.00 0.00 42.20 4.57
3480 4144 2.972505 CACGGTGGACTGGTGTGC 60.973 66.667 0.00 0.00 34.96 4.57
3481 4145 2.280797 CCACGGTGGACTGGTGTG 60.281 66.667 22.77 0.00 40.96 3.82
3482 4146 4.250305 GCCACGGTGGACTGGTGT 62.250 66.667 30.65 0.00 40.96 4.16
3483 4147 4.248842 TGCCACGGTGGACTGGTG 62.249 66.667 30.65 2.56 40.96 4.17
3484 4148 3.941188 CTGCCACGGTGGACTGGT 61.941 66.667 30.65 0.00 40.96 4.00
3512 4176 2.353839 GTTGCACTGCTGGTTGCG 60.354 61.111 1.98 0.00 46.63 4.85
3513 4177 2.353839 CGTTGCACTGCTGGTTGC 60.354 61.111 1.98 0.00 43.25 4.17
3514 4178 2.353839 GCGTTGCACTGCTGGTTG 60.354 61.111 1.98 0.00 0.00 3.77
3515 4179 3.595758 GGCGTTGCACTGCTGGTT 61.596 61.111 9.04 0.00 0.00 3.67
3516 4180 4.569180 AGGCGTTGCACTGCTGGT 62.569 61.111 9.04 0.00 0.00 4.00
3517 4181 3.730761 GAGGCGTTGCACTGCTGG 61.731 66.667 9.04 0.00 0.00 4.85
3518 4182 3.730761 GGAGGCGTTGCACTGCTG 61.731 66.667 9.04 0.00 0.00 4.41
3521 4185 3.114616 CTCGGAGGCGTTGCACTG 61.115 66.667 0.00 0.00 0.00 3.66
3523 4187 3.642778 TAGCTCGGAGGCGTTGCAC 62.643 63.158 7.20 0.00 37.29 4.57
3524 4188 3.356639 CTAGCTCGGAGGCGTTGCA 62.357 63.158 7.20 0.00 37.29 4.08
3525 4189 2.583593 CTAGCTCGGAGGCGTTGC 60.584 66.667 7.20 0.00 37.29 4.17
3526 4190 2.105128 CCTAGCTCGGAGGCGTTG 59.895 66.667 7.20 0.00 37.29 4.10
3539 4203 1.732259 CTTTACAAGTGTGGCGCCTAG 59.268 52.381 29.70 12.91 0.00 3.02
3540 4204 1.071071 ACTTTACAAGTGTGGCGCCTA 59.929 47.619 29.70 14.39 41.01 3.93
3541 4205 0.179029 ACTTTACAAGTGTGGCGCCT 60.179 50.000 29.70 7.80 41.01 5.52
3542 4206 2.327228 ACTTTACAAGTGTGGCGCC 58.673 52.632 22.73 22.73 41.01 6.53
3550 4214 1.602377 GAGGCGTTGCACTTTACAAGT 59.398 47.619 0.00 0.00 44.06 3.16
3551 4215 1.069227 GGAGGCGTTGCACTTTACAAG 60.069 52.381 0.00 0.00 0.00 3.16
3552 4216 0.948678 GGAGGCGTTGCACTTTACAA 59.051 50.000 0.00 0.00 0.00 2.41
3553 4217 1.225376 CGGAGGCGTTGCACTTTACA 61.225 55.000 0.00 0.00 0.00 2.41
3554 4218 0.947180 TCGGAGGCGTTGCACTTTAC 60.947 55.000 0.00 0.00 0.00 2.01
3555 4219 0.669318 CTCGGAGGCGTTGCACTTTA 60.669 55.000 0.00 0.00 0.00 1.85
3556 4220 1.961277 CTCGGAGGCGTTGCACTTT 60.961 57.895 0.00 0.00 0.00 2.66
3557 4221 2.357517 CTCGGAGGCGTTGCACTT 60.358 61.111 0.00 0.00 0.00 3.16
3558 4222 4.379243 CCTCGGAGGCGTTGCACT 62.379 66.667 11.83 0.00 0.00 4.40
3559 4223 3.291101 TACCTCGGAGGCGTTGCAC 62.291 63.158 23.84 0.00 39.63 4.57
3560 4224 2.992689 TACCTCGGAGGCGTTGCA 60.993 61.111 23.84 0.00 39.63 4.08
3561 4225 2.202756 CTACCTCGGAGGCGTTGC 60.203 66.667 23.84 0.00 39.63 4.17
3562 4226 2.494918 CCTACCTCGGAGGCGTTG 59.505 66.667 23.84 10.89 39.63 4.10
3567 4231 2.439701 TGACGCCTACCTCGGAGG 60.440 66.667 22.40 22.40 42.49 4.30
3568 4232 2.044555 TGTGACGCCTACCTCGGAG 61.045 63.158 0.00 0.00 0.00 4.63
3569 4233 2.034532 TGTGACGCCTACCTCGGA 59.965 61.111 0.00 0.00 0.00 4.55
3570 4234 1.874345 AAGTGTGACGCCTACCTCGG 61.874 60.000 0.00 0.00 0.00 4.63
3571 4235 0.456312 GAAGTGTGACGCCTACCTCG 60.456 60.000 0.00 0.00 0.00 4.63
3572 4236 0.889306 AGAAGTGTGACGCCTACCTC 59.111 55.000 0.00 0.00 0.00 3.85
3573 4237 1.339097 AAGAAGTGTGACGCCTACCT 58.661 50.000 0.00 0.00 0.00 3.08
3574 4238 3.251571 CTTAAGAAGTGTGACGCCTACC 58.748 50.000 0.00 0.00 0.00 3.18
3575 4239 3.910648 ACTTAAGAAGTGTGACGCCTAC 58.089 45.455 10.09 0.00 41.01 3.18
3586 4250 0.035458 AGGCGCTGCACTTAAGAAGT 59.965 50.000 10.09 0.00 44.06 3.01
3587 4251 2.846371 AGGCGCTGCACTTAAGAAG 58.154 52.632 10.09 4.96 0.00 2.85


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

AutoCloner maintained by Alex Coulton.