Multiple sequence alignment - TraesCS6A01G176800

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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 TraesCS6A01G176800 chr6A 100.000 3299 0 0 1 3299 195296362 195293064 0.000000e+00 6093.0
1 TraesCS6A01G176800 chr6A 92.308 39 3 0 851 889 595071141 595071103 4.600000e-04 56.5
2 TraesCS6A01G176800 chr6B 95.852 1977 55 9 882 2854 274385759 274387712 0.000000e+00 3171.0
3 TraesCS6A01G176800 chr6B 93.542 480 29 2 72 549 274385074 274385553 0.000000e+00 713.0
4 TraesCS6A01G176800 chr6B 92.063 189 6 4 2894 3081 274387893 274388073 1.170000e-64 257.0
5 TraesCS6A01G176800 chr6D 95.691 1880 52 10 820 2691 149882513 149884371 0.000000e+00 2996.0
6 TraesCS6A01G176800 chr6D 90.937 651 25 6 1 639 149881245 149881873 0.000000e+00 845.0
7 TraesCS6A01G176800 chr6D 91.713 362 23 4 2720 3080 149884372 149884727 2.290000e-136 496.0
8 TraesCS6A01G176800 chrUn 85.377 212 28 3 3089 3299 43585823 43585614 1.990000e-52 217.0
9 TraesCS6A01G176800 chr1B 83.732 209 32 2 3091 3299 599580279 599580073 2.600000e-46 196.0
10 TraesCS6A01G176800 chr1B 89.600 125 12 1 668 791 47629813 47629937 1.230000e-34 158.0
11 TraesCS6A01G176800 chr7D 83.920 199 31 1 3099 3297 422575302 422575105 4.350000e-44 189.0
12 TraesCS6A01G176800 chr7D 81.538 195 32 4 3104 3298 274262585 274262395 1.230000e-34 158.0
13 TraesCS6A01G176800 chr3B 81.250 224 39 3 3075 3297 780835334 780835555 9.410000e-41 178.0
14 TraesCS6A01G176800 chr3B 91.453 117 10 0 668 784 345712332 345712448 9.470000e-36 161.0
15 TraesCS6A01G176800 chr7B 92.308 117 9 0 668 784 5920135 5920251 2.040000e-37 167.0
16 TraesCS6A01G176800 chr7B 81.043 211 33 4 3089 3296 99106981 99107187 9.470000e-36 161.0
17 TraesCS6A01G176800 chr7B 90.323 124 11 1 668 790 491165300 491165177 9.470000e-36 161.0
18 TraesCS6A01G176800 chr7B 89.516 124 12 1 660 783 21200143 21200021 4.410000e-34 156.0
19 TraesCS6A01G176800 chr7B 79.897 194 37 2 3105 3297 705807868 705807676 1.230000e-29 141.0
20 TraesCS6A01G176800 chr4A 91.667 120 10 0 668 787 468419386 468419267 2.040000e-37 167.0
21 TraesCS6A01G176800 chr2B 91.379 116 10 0 668 783 148404590 148404475 3.410000e-35 159.0
22 TraesCS6A01G176800 chr3A 90.083 121 12 0 664 784 521303639 521303519 1.230000e-34 158.0
23 TraesCS6A01G176800 chr1A 89.600 125 12 1 666 789 91302040 91302164 1.230000e-34 158.0
24 TraesCS6A01G176800 chr1A 85.965 57 5 3 2785 2840 493825103 493825157 1.280000e-04 58.4
25 TraesCS6A01G176800 chr1A 100.000 28 0 0 851 878 547968643 547968670 6.000000e-03 52.8
26 TraesCS6A01G176800 chr2A 87.402 127 16 0 3173 3299 100598314 100598440 2.650000e-31 147.0
27 TraesCS6A01G176800 chr2A 95.238 42 2 0 2808 2849 191639449 191639408 2.120000e-07 67.6
28 TraesCS6A01G176800 chr7A 97.143 35 0 1 2807 2840 10420240 10420274 1.280000e-04 58.4


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 TraesCS6A01G176800 chr6A 195293064 195296362 3298 True 6093.000000 6093 100.000000 1 3299 1 chr6A.!!$R1 3298
1 TraesCS6A01G176800 chr6B 274385074 274388073 2999 False 1380.333333 3171 93.819000 72 3081 3 chr6B.!!$F1 3009
2 TraesCS6A01G176800 chr6D 149881245 149884727 3482 False 1445.666667 2996 92.780333 1 3080 3 chr6D.!!$F1 3079

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
774 1325 0.107848 AGACAAGTATTTCCGGGCGG 60.108 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2455 3047 0.034767 CTGCCCCACATGTCAGTGAT 60.035 55.0 0.0 0.0 42.05 3.06 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
22 23 5.611796 CAACATCCATATCCGTGTATTGG 57.388 43.478 0.00 0.00 0.00 3.16
30 31 2.234896 TCCGTGTATTGGTCCCTGTA 57.765 50.000 0.00 0.00 0.00 2.74
77 87 5.667466 CATTGAAGATGCCCTTTAAGCAAT 58.333 37.500 0.00 0.00 44.83 3.56
97 108 4.737855 ATATATAGGCCGAATGCGAACT 57.262 40.909 0.00 0.00 42.61 3.01
233 244 5.703592 TGGTCAAAAAGCTAACGTACATCAT 59.296 36.000 0.00 0.00 0.00 2.45
238 249 4.737855 AAGCTAACGTACATCATGGTCT 57.262 40.909 0.00 0.00 0.00 3.85
239 250 4.737855 AGCTAACGTACATCATGGTCTT 57.262 40.909 0.00 0.00 0.00 3.01
317 328 3.786101 CGACCTCGCTCAACCATG 58.214 61.111 0.00 0.00 0.00 3.66
325 336 0.926155 CGCTCAACCATGATCTCACG 59.074 55.000 0.00 0.00 34.37 4.35
351 362 6.589830 AATCACTGCACATACGATACTTTC 57.410 37.500 0.00 0.00 0.00 2.62
355 366 5.351465 CACTGCACATACGATACTTTCCTTT 59.649 40.000 0.00 0.00 0.00 3.11
549 560 1.697432 ACGGGAAAATGTCTCAGTCCA 59.303 47.619 0.00 0.00 0.00 4.02
564 575 3.438781 TCAGTCCAACGCCAATTAATGAC 59.561 43.478 0.00 0.00 0.00 3.06
565 576 2.752903 AGTCCAACGCCAATTAATGACC 59.247 45.455 0.00 0.00 0.00 4.02
584 597 8.408043 AATGACCATGAGTGTAAAAGAAATCA 57.592 30.769 0.00 0.00 0.00 2.57
613 626 8.543774 GTGGATGTCGAAATTCTTATAGAACTG 58.456 37.037 0.00 0.00 37.00 3.16
618 631 6.201234 GTCGAAATTCTTATAGAACTGCTCCC 59.799 42.308 0.00 0.00 37.00 4.30
625 638 1.640917 TAGAACTGCTCCCTCCGTTT 58.359 50.000 0.00 0.00 0.00 3.60
626 639 0.765510 AGAACTGCTCCCTCCGTTTT 59.234 50.000 0.00 0.00 0.00 2.43
639 652 7.067859 GCTCCCTCCGTTTTAAATTATTTAGGT 59.932 37.037 0.00 0.00 0.00 3.08
640 653 8.510243 TCCCTCCGTTTTAAATTATTTAGGTC 57.490 34.615 0.00 0.00 0.00 3.85
641 654 7.280652 TCCCTCCGTTTTAAATTATTTAGGTCG 59.719 37.037 0.00 4.66 0.00 4.79
671 1222 5.705609 TTTTTCTCCACTGGCAATTACTC 57.294 39.130 0.00 0.00 0.00 2.59
672 1223 3.350219 TTCTCCACTGGCAATTACTCC 57.650 47.619 0.00 0.00 0.00 3.85
673 1224 1.559682 TCTCCACTGGCAATTACTCCC 59.440 52.381 0.00 0.00 0.00 4.30
674 1225 1.561542 CTCCACTGGCAATTACTCCCT 59.438 52.381 0.00 0.00 0.00 4.20
675 1226 1.559682 TCCACTGGCAATTACTCCCTC 59.440 52.381 0.00 0.00 0.00 4.30
676 1227 1.408822 CCACTGGCAATTACTCCCTCC 60.409 57.143 0.00 0.00 0.00 4.30
677 1228 0.541863 ACTGGCAATTACTCCCTCCG 59.458 55.000 0.00 0.00 0.00 4.63
678 1229 0.541863 CTGGCAATTACTCCCTCCGT 59.458 55.000 0.00 0.00 0.00 4.69
679 1230 0.988832 TGGCAATTACTCCCTCCGTT 59.011 50.000 0.00 0.00 0.00 4.44
680 1231 1.065709 TGGCAATTACTCCCTCCGTTC 60.066 52.381 0.00 0.00 0.00 3.95
681 1232 1.287425 GCAATTACTCCCTCCGTTCG 58.713 55.000 0.00 0.00 0.00 3.95
682 1233 1.935933 CAATTACTCCCTCCGTTCGG 58.064 55.000 4.74 4.74 0.00 4.30
683 1234 1.479323 CAATTACTCCCTCCGTTCGGA 59.521 52.381 13.34 13.34 0.00 4.55
684 1235 1.856629 ATTACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.04 33.41 4.30
685 1236 1.631405 TTACTCCCTCCGTTCGGAAA 58.369 50.000 14.79 2.93 33.41 3.13
686 1237 1.856629 TACTCCCTCCGTTCGGAAAT 58.143 50.000 14.79 2.39 33.41 2.17
687 1238 1.856629 ACTCCCTCCGTTCGGAAATA 58.143 50.000 14.79 2.82 33.41 1.40
688 1239 2.395619 ACTCCCTCCGTTCGGAAATAT 58.604 47.619 14.79 0.00 33.41 1.28
689 1240 2.770232 ACTCCCTCCGTTCGGAAATATT 59.230 45.455 14.79 0.00 33.41 1.28
690 1241 3.199289 ACTCCCTCCGTTCGGAAATATTT 59.801 43.478 14.79 0.00 33.41 1.40
691 1242 3.537580 TCCCTCCGTTCGGAAATATTTG 58.462 45.455 14.79 1.97 33.41 2.32
692 1243 3.054948 TCCCTCCGTTCGGAAATATTTGT 60.055 43.478 14.79 0.00 33.41 2.83
693 1244 3.311596 CCCTCCGTTCGGAAATATTTGTC 59.688 47.826 14.79 0.00 33.41 3.18
694 1245 3.311596 CCTCCGTTCGGAAATATTTGTCC 59.688 47.826 14.79 0.46 33.41 4.02
695 1246 4.189231 CTCCGTTCGGAAATATTTGTCCT 58.811 43.478 14.79 0.00 33.41 3.85
696 1247 4.581868 TCCGTTCGGAAATATTTGTCCTT 58.418 39.130 11.66 0.00 0.00 3.36
697 1248 5.732633 TCCGTTCGGAAATATTTGTCCTTA 58.267 37.500 11.66 0.00 0.00 2.69
698 1249 6.171921 TCCGTTCGGAAATATTTGTCCTTAA 58.828 36.000 11.66 0.00 0.00 1.85
699 1250 6.654161 TCCGTTCGGAAATATTTGTCCTTAAA 59.346 34.615 11.66 0.00 0.00 1.52
700 1251 7.174599 TCCGTTCGGAAATATTTGTCCTTAAAA 59.825 33.333 11.66 0.00 0.00 1.52
701 1252 7.971722 CCGTTCGGAAATATTTGTCCTTAAAAT 59.028 33.333 5.17 0.00 0.00 1.82
702 1253 9.991388 CGTTCGGAAATATTTGTCCTTAAAATA 57.009 29.630 5.17 0.00 34.79 1.40
769 1320 6.827641 TCGATTTTGAAGACAAGTATTTCCG 58.172 36.000 0.00 0.00 37.32 4.30
770 1321 6.021596 CGATTTTGAAGACAAGTATTTCCGG 58.978 40.000 0.00 0.00 37.32 5.14
771 1322 5.699097 TTTTGAAGACAAGTATTTCCGGG 57.301 39.130 0.00 0.00 37.32 5.73
772 1323 2.706890 TGAAGACAAGTATTTCCGGGC 58.293 47.619 0.00 0.00 0.00 6.13
773 1324 1.664151 GAAGACAAGTATTTCCGGGCG 59.336 52.381 0.00 0.00 0.00 6.13
774 1325 0.107848 AGACAAGTATTTCCGGGCGG 60.108 55.000 0.00 0.00 0.00 6.13
775 1326 0.108041 GACAAGTATTTCCGGGCGGA 60.108 55.000 0.00 0.00 43.52 5.54
776 1327 0.107848 ACAAGTATTTCCGGGCGGAG 60.108 55.000 0.00 0.00 46.06 4.63
777 1328 0.814010 CAAGTATTTCCGGGCGGAGG 60.814 60.000 0.00 0.00 46.06 4.30
778 1329 0.979187 AAGTATTTCCGGGCGGAGGA 60.979 55.000 0.00 0.00 46.06 3.71
779 1330 0.979187 AGTATTTCCGGGCGGAGGAA 60.979 55.000 0.00 4.01 46.06 3.36
802 1353 3.782656 ACAAACATACTCCCTCCGTTT 57.217 42.857 0.00 0.00 0.00 3.60
818 1369 9.333724 TCCCTCCGTTTTAAATTATAAGATGTC 57.666 33.333 0.00 0.00 0.00 3.06
953 1539 2.352323 CCCATTTTGTCGGTAAACTGCC 60.352 50.000 0.00 0.00 0.00 4.85
999 1585 0.607217 TGTTCGGAGGACGTGAGCTA 60.607 55.000 0.00 0.00 44.69 3.32
1215 1801 2.603473 CTCACCGACCTCACCCCA 60.603 66.667 0.00 0.00 0.00 4.96
1374 1960 1.447838 GGCCGATGTTCTCTGCGAA 60.448 57.895 0.00 0.00 35.13 4.70
1504 2090 2.690778 GCTGTGATGCCCACCGTTC 61.691 63.158 4.22 0.00 45.09 3.95
1613 2199 2.738521 GACGCACGTGCTGGTGAT 60.739 61.111 35.27 15.27 40.38 3.06
1626 2212 1.137675 CTGGTGATGCTCGAGAATGGA 59.862 52.381 18.75 0.00 0.00 3.41
2219 2811 2.257371 CGTGAAGGAGACGGCGAA 59.743 61.111 16.62 0.00 33.08 4.70
2437 3029 6.743575 AGATAAACTGAAGTTGAAATCCCG 57.256 37.500 0.00 0.00 38.44 5.14
2455 3047 3.325425 TCCCGAATTTGACACTTGAGGTA 59.675 43.478 0.00 0.00 0.00 3.08
2472 3064 1.668419 GTATCACTGACATGTGGGGC 58.332 55.000 1.15 0.00 38.40 5.80
2473 3065 1.065491 GTATCACTGACATGTGGGGCA 60.065 52.381 1.15 0.00 38.40 5.36
2474 3066 0.034767 ATCACTGACATGTGGGGCAG 60.035 55.000 1.15 6.93 38.40 4.85
2475 3067 1.073722 CACTGACATGTGGGGCAGT 59.926 57.895 1.15 7.66 41.90 4.40
2476 3068 1.073722 ACTGACATGTGGGGCAGTG 59.926 57.895 15.06 0.00 39.88 3.66
2536 3128 5.107065 CGGGAGTTGTGAGATCTTTACAAAC 60.107 44.000 21.08 17.92 36.23 2.93
2559 3151 1.917872 AACCGCACATTACCATGGTT 58.082 45.000 25.38 2.07 34.27 3.67
2560 3152 1.459450 ACCGCACATTACCATGGTTC 58.541 50.000 25.38 4.92 34.27 3.62
2561 3153 1.271652 ACCGCACATTACCATGGTTCA 60.272 47.619 25.38 11.07 34.27 3.18
2639 3233 5.443185 AATACAGTATGAACCATGCATGC 57.557 39.130 21.69 11.82 39.69 4.06
2640 3234 2.725637 ACAGTATGAACCATGCATGCA 58.274 42.857 25.04 25.04 39.69 3.96
2641 3235 3.293337 ACAGTATGAACCATGCATGCAT 58.707 40.909 27.46 27.46 39.69 3.96
2642 3236 3.067601 ACAGTATGAACCATGCATGCATG 59.932 43.478 41.28 41.28 45.87 4.06
2666 3268 1.068610 GCATGCACCACGTGTTGTAAT 60.069 47.619 14.21 6.30 37.62 1.89
2718 3320 4.368315 TGACTGAGACACAACACACATAC 58.632 43.478 0.00 0.00 0.00 2.39
2743 3345 3.951037 CCCCACATCCGTTTCATATCAAA 59.049 43.478 0.00 0.00 0.00 2.69
2754 3356 7.812191 TCCGTTTCATATCAAATCTTGTTTTGG 59.188 33.333 4.87 0.00 37.23 3.28
2755 3357 7.598493 CCGTTTCATATCAAATCTTGTTTTGGT 59.402 33.333 4.87 1.20 37.23 3.67
2756 3358 8.977505 CGTTTCATATCAAATCTTGTTTTGGTT 58.022 29.630 4.87 0.00 37.23 3.67
2759 3361 9.619316 TTCATATCAAATCTTGTTTTGGTTACG 57.381 29.630 4.87 0.00 37.23 3.18
2760 3362 7.753132 TCATATCAAATCTTGTTTTGGTTACGC 59.247 33.333 4.87 0.00 37.23 4.42
2779 3381 3.411415 GCTTACGCAGCTTTCAATCAT 57.589 42.857 0.00 0.00 46.27 2.45
2780 3382 3.357897 GCTTACGCAGCTTTCAATCATC 58.642 45.455 0.00 0.00 46.27 2.92
2802 3404 3.182372 CGTGTCGGCATATTGATGTAGTG 59.818 47.826 0.00 0.00 35.30 2.74
2873 3501 6.723131 AGCACTCATCATGATATCAAATCG 57.277 37.500 9.99 0.00 0.00 3.34
3007 3751 9.853555 CAAAACTAATGTGCCAAGTAATATGAA 57.146 29.630 0.00 0.00 0.00 2.57
3013 3757 8.588290 AATGTGCCAAGTAATATGAAAGGTAA 57.412 30.769 0.00 0.00 0.00 2.85
3018 3762 9.420118 TGCCAAGTAATATGAAAGGTAAATCAT 57.580 29.630 0.00 0.00 39.50 2.45
3082 3826 9.979578 ATGTTAGTTGCATGAAAGTAAAAATGA 57.020 25.926 14.25 0.00 29.11 2.57
3083 3827 9.462174 TGTTAGTTGCATGAAAGTAAAAATGAG 57.538 29.630 14.25 0.00 29.11 2.90
3084 3828 9.677567 GTTAGTTGCATGAAAGTAAAAATGAGA 57.322 29.630 14.25 0.00 29.11 3.27
3085 3829 9.677567 TTAGTTGCATGAAAGTAAAAATGAGAC 57.322 29.630 10.80 0.00 0.00 3.36
3086 3830 7.715657 AGTTGCATGAAAGTAAAAATGAGACA 58.284 30.769 0.00 0.00 0.00 3.41
3087 3831 8.362639 AGTTGCATGAAAGTAAAAATGAGACAT 58.637 29.630 0.00 0.00 0.00 3.06
3088 3832 8.642020 GTTGCATGAAAGTAAAAATGAGACATC 58.358 33.333 0.00 0.00 0.00 3.06
3089 3833 7.022979 TGCATGAAAGTAAAAATGAGACATCG 58.977 34.615 0.00 0.00 0.00 3.84
3090 3834 7.094848 TGCATGAAAGTAAAAATGAGACATCGA 60.095 33.333 0.00 0.00 0.00 3.59
3091 3835 7.912250 GCATGAAAGTAAAAATGAGACATCGAT 59.088 33.333 0.00 0.00 0.00 3.59
3096 3840 9.613428 AAAGTAAAAATGAGACATCGATATCCA 57.387 29.630 0.00 0.00 0.00 3.41
3097 3841 9.784531 AAGTAAAAATGAGACATCGATATCCAT 57.215 29.630 0.00 1.22 0.00 3.41
3098 3842 9.429359 AGTAAAAATGAGACATCGATATCCATC 57.571 33.333 0.00 0.00 0.00 3.51
3099 3843 9.208022 GTAAAAATGAGACATCGATATCCATCA 57.792 33.333 0.00 0.00 0.00 3.07
3100 3844 7.664082 AAAATGAGACATCGATATCCATCAC 57.336 36.000 0.00 0.00 0.00 3.06
3101 3845 5.990120 ATGAGACATCGATATCCATCACA 57.010 39.130 0.00 0.00 0.00 3.58
3102 3846 5.126396 TGAGACATCGATATCCATCACAC 57.874 43.478 0.00 0.00 0.00 3.82
3103 3847 4.584325 TGAGACATCGATATCCATCACACA 59.416 41.667 0.00 0.00 0.00 3.72
3104 3848 5.244626 TGAGACATCGATATCCATCACACAT 59.755 40.000 0.00 0.00 0.00 3.21
3105 3849 5.476614 AGACATCGATATCCATCACACATG 58.523 41.667 0.00 0.00 0.00 3.21
3106 3850 5.011431 AGACATCGATATCCATCACACATGT 59.989 40.000 0.00 0.00 0.00 3.21
3107 3851 4.992951 ACATCGATATCCATCACACATGTG 59.007 41.667 24.25 24.25 46.91 3.21
3108 3852 3.993920 TCGATATCCATCACACATGTGG 58.006 45.455 28.64 17.57 45.65 4.17
3109 3853 2.481568 CGATATCCATCACACATGTGGC 59.518 50.000 28.64 5.00 45.65 5.01
3110 3854 3.479489 GATATCCATCACACATGTGGCA 58.521 45.455 28.64 15.36 45.65 4.92
3111 3855 2.447408 ATCCATCACACATGTGGCAT 57.553 45.000 28.64 16.90 45.65 4.40
3112 3856 3.581265 ATCCATCACACATGTGGCATA 57.419 42.857 28.64 11.81 45.65 3.14
3113 3857 3.362870 TCCATCACACATGTGGCATAA 57.637 42.857 28.64 10.09 45.65 1.90
3114 3858 3.694926 TCCATCACACATGTGGCATAAA 58.305 40.909 28.64 8.28 45.65 1.40
3115 3859 4.085009 TCCATCACACATGTGGCATAAAA 58.915 39.130 28.64 6.81 45.65 1.52
3116 3860 4.158209 TCCATCACACATGTGGCATAAAAG 59.842 41.667 28.64 10.23 45.65 2.27
3117 3861 4.426416 CATCACACATGTGGCATAAAAGG 58.574 43.478 28.64 7.42 45.65 3.11
3118 3862 2.230992 TCACACATGTGGCATAAAAGGC 59.769 45.455 28.64 0.00 45.65 4.35
3119 3863 2.029200 CACACATGTGGCATAAAAGGCA 60.029 45.455 28.64 0.00 42.10 4.75
3120 3864 2.833338 ACACATGTGGCATAAAAGGCAT 59.167 40.909 28.64 0.77 46.23 4.40
3121 3865 3.119029 ACACATGTGGCATAAAAGGCATC 60.119 43.478 28.64 0.00 46.23 3.91
3122 3866 2.431782 ACATGTGGCATAAAAGGCATCC 59.568 45.455 0.00 0.00 46.23 3.51
3123 3867 1.102154 TGTGGCATAAAAGGCATCCG 58.898 50.000 0.00 0.00 46.23 4.18
3124 3868 0.249031 GTGGCATAAAAGGCATCCGC 60.249 55.000 0.00 0.00 46.23 5.54
3125 3869 0.395586 TGGCATAAAAGGCATCCGCT 60.396 50.000 0.00 0.00 39.34 5.52
3126 3870 0.746659 GGCATAAAAGGCATCCGCTT 59.253 50.000 0.00 0.00 38.60 4.68
3127 3871 1.953686 GGCATAAAAGGCATCCGCTTA 59.046 47.619 0.00 0.00 38.60 3.09
3128 3872 2.558359 GGCATAAAAGGCATCCGCTTAT 59.442 45.455 0.00 0.00 38.60 1.73
3129 3873 3.756434 GGCATAAAAGGCATCCGCTTATA 59.244 43.478 0.00 0.00 38.60 0.98
3130 3874 4.399303 GGCATAAAAGGCATCCGCTTATAT 59.601 41.667 0.00 0.00 38.60 0.86
3131 3875 5.588648 GGCATAAAAGGCATCCGCTTATATA 59.411 40.000 0.00 0.00 38.60 0.86
3132 3876 6.458342 GGCATAAAAGGCATCCGCTTATATAC 60.458 42.308 0.00 0.00 38.60 1.47
3133 3877 6.458342 GCATAAAAGGCATCCGCTTATATACC 60.458 42.308 0.00 0.00 38.60 2.73
3134 3878 4.634012 AAAGGCATCCGCTTATATACCA 57.366 40.909 0.00 0.00 38.60 3.25
3135 3879 4.844349 AAGGCATCCGCTTATATACCAT 57.156 40.909 0.00 0.00 38.60 3.55
3136 3880 4.142609 AGGCATCCGCTTATATACCATG 57.857 45.455 0.00 0.00 38.60 3.66
3137 3881 3.519510 AGGCATCCGCTTATATACCATGT 59.480 43.478 0.00 0.00 38.60 3.21
3138 3882 3.623060 GGCATCCGCTTATATACCATGTG 59.377 47.826 0.00 0.00 38.60 3.21
3139 3883 4.253685 GCATCCGCTTATATACCATGTGT 58.746 43.478 0.00 0.00 34.30 3.72
3140 3884 4.093408 GCATCCGCTTATATACCATGTGTG 59.907 45.833 0.00 0.00 34.30 3.82
3141 3885 6.873095 GCATCCGCTTATATACCATGTGTGG 61.873 48.000 0.00 0.00 42.78 4.17
3153 3897 0.548031 ATGTGTGGCATGAGTAGGGG 59.452 55.000 0.00 0.00 36.26 4.79
3154 3898 1.224592 GTGTGGCATGAGTAGGGGG 59.775 63.158 0.00 0.00 0.00 5.40
3170 3914 4.643387 GGGCAGCCCACACGAACT 62.643 66.667 27.33 0.00 44.65 3.01
3171 3915 3.357079 GGCAGCCCACACGAACTG 61.357 66.667 0.00 0.00 0.00 3.16
3172 3916 2.591715 GCAGCCCACACGAACTGT 60.592 61.111 0.00 0.00 32.65 3.55
3181 3925 3.779303 CACGAACTGTGTGTGAACG 57.221 52.632 6.80 0.00 43.88 3.95
3182 3926 1.273688 CACGAACTGTGTGTGAACGA 58.726 50.000 6.80 0.00 43.88 3.85
3183 3927 1.656594 CACGAACTGTGTGTGAACGAA 59.343 47.619 6.80 0.00 43.88 3.85
3184 3928 1.657094 ACGAACTGTGTGTGAACGAAC 59.343 47.619 0.00 0.00 0.00 3.95
3185 3929 1.656594 CGAACTGTGTGTGAACGAACA 59.343 47.619 0.00 0.00 0.00 3.18
3186 3930 2.092995 CGAACTGTGTGTGAACGAACAA 59.907 45.455 0.00 0.00 0.00 2.83
3187 3931 3.242284 CGAACTGTGTGTGAACGAACAAT 60.242 43.478 0.00 0.00 0.00 2.71
3188 3932 4.026393 CGAACTGTGTGTGAACGAACAATA 60.026 41.667 0.00 0.00 0.00 1.90
3189 3933 5.501092 CGAACTGTGTGTGAACGAACAATAA 60.501 40.000 0.00 0.00 0.00 1.40
3190 3934 5.804692 ACTGTGTGTGAACGAACAATAAA 57.195 34.783 0.00 0.00 0.00 1.40
3191 3935 6.184580 ACTGTGTGTGAACGAACAATAAAA 57.815 33.333 0.00 0.00 0.00 1.52
3192 3936 6.791303 ACTGTGTGTGAACGAACAATAAAAT 58.209 32.000 0.00 0.00 0.00 1.82
3193 3937 7.254852 ACTGTGTGTGAACGAACAATAAAATT 58.745 30.769 0.00 0.00 0.00 1.82
3194 3938 7.219917 ACTGTGTGTGAACGAACAATAAAATTG 59.780 33.333 0.00 0.00 0.00 2.32
3195 3939 6.020281 TGTGTGTGAACGAACAATAAAATTGC 60.020 34.615 0.00 0.00 0.00 3.56
3196 3940 5.460419 TGTGTGAACGAACAATAAAATTGCC 59.540 36.000 0.00 0.00 0.00 4.52
3197 3941 4.985409 TGTGAACGAACAATAAAATTGCCC 59.015 37.500 0.00 0.00 0.00 5.36
3198 3942 4.985409 GTGAACGAACAATAAAATTGCCCA 59.015 37.500 0.00 0.00 0.00 5.36
3199 3943 4.985409 TGAACGAACAATAAAATTGCCCAC 59.015 37.500 0.00 0.00 0.00 4.61
3200 3944 4.592485 ACGAACAATAAAATTGCCCACA 57.408 36.364 0.00 0.00 0.00 4.17
3201 3945 4.303282 ACGAACAATAAAATTGCCCACAC 58.697 39.130 0.00 0.00 0.00 3.82
3202 3946 4.202161 ACGAACAATAAAATTGCCCACACA 60.202 37.500 0.00 0.00 0.00 3.72
3203 3947 4.928615 CGAACAATAAAATTGCCCACACAT 59.071 37.500 0.00 0.00 0.00 3.21
3204 3948 5.163972 CGAACAATAAAATTGCCCACACATG 60.164 40.000 0.00 0.00 0.00 3.21
3205 3949 5.226194 ACAATAAAATTGCCCACACATGT 57.774 34.783 0.00 0.00 0.00 3.21
3206 3950 6.352016 ACAATAAAATTGCCCACACATGTA 57.648 33.333 0.00 0.00 0.00 2.29
3207 3951 6.397272 ACAATAAAATTGCCCACACATGTAG 58.603 36.000 0.00 0.00 0.00 2.74
3208 3952 6.210385 ACAATAAAATTGCCCACACATGTAGA 59.790 34.615 0.00 0.00 0.00 2.59
3209 3953 4.519540 AAAATTGCCCACACATGTAGAC 57.480 40.909 0.00 0.00 0.00 2.59
3210 3954 1.737838 ATTGCCCACACATGTAGACG 58.262 50.000 0.00 0.00 0.00 4.18
3211 3955 0.953471 TTGCCCACACATGTAGACGC 60.953 55.000 0.00 0.00 0.00 5.19
3212 3956 1.375396 GCCCACACATGTAGACGCA 60.375 57.895 0.00 0.00 0.00 5.24
3213 3957 1.361668 GCCCACACATGTAGACGCAG 61.362 60.000 0.00 0.00 0.00 5.18
3214 3958 1.361668 CCCACACATGTAGACGCAGC 61.362 60.000 0.00 0.00 0.00 5.25
3215 3959 0.390340 CCACACATGTAGACGCAGCT 60.390 55.000 0.00 0.00 0.00 4.24
3216 3960 1.135112 CCACACATGTAGACGCAGCTA 60.135 52.381 0.00 0.00 0.00 3.32
3217 3961 1.920574 CACACATGTAGACGCAGCTAC 59.079 52.381 0.00 6.13 40.85 3.58
3218 3962 1.819288 ACACATGTAGACGCAGCTACT 59.181 47.619 0.00 0.00 41.01 2.57
3219 3963 2.231478 ACACATGTAGACGCAGCTACTT 59.769 45.455 0.00 5.40 41.01 2.24
3220 3964 2.854777 CACATGTAGACGCAGCTACTTC 59.145 50.000 0.00 0.00 41.01 3.01
3221 3965 2.112522 CATGTAGACGCAGCTACTTCG 58.887 52.381 12.52 0.00 41.01 3.79
3222 3966 1.162698 TGTAGACGCAGCTACTTCGT 58.837 50.000 12.52 2.80 41.01 3.85
3223 3967 1.135774 TGTAGACGCAGCTACTTCGTG 60.136 52.381 12.52 0.00 41.01 4.35
3224 3968 0.179171 TAGACGCAGCTACTTCGTGC 60.179 55.000 7.13 0.00 36.50 5.34
3225 3969 2.432628 ACGCAGCTACTTCGTGCC 60.433 61.111 0.00 0.00 34.92 5.01
3226 3970 2.432456 CGCAGCTACTTCGTGCCA 60.432 61.111 0.00 0.00 33.42 4.92
3227 3971 2.730672 CGCAGCTACTTCGTGCCAC 61.731 63.158 0.00 0.00 33.42 5.01
3228 3972 1.667830 GCAGCTACTTCGTGCCACA 60.668 57.895 0.00 0.00 0.00 4.17
3229 3973 1.901650 GCAGCTACTTCGTGCCACAC 61.902 60.000 0.00 0.00 0.00 3.82
3230 3974 0.599991 CAGCTACTTCGTGCCACACA 60.600 55.000 0.00 0.00 33.40 3.72
3231 3975 0.321671 AGCTACTTCGTGCCACACAT 59.678 50.000 0.00 0.00 33.40 3.21
3232 3976 0.721718 GCTACTTCGTGCCACACATC 59.278 55.000 0.00 0.00 33.40 3.06
3233 3977 1.359848 CTACTTCGTGCCACACATCC 58.640 55.000 0.00 0.00 33.40 3.51
3234 3978 0.682292 TACTTCGTGCCACACATCCA 59.318 50.000 0.00 0.00 33.40 3.41
3235 3979 0.179032 ACTTCGTGCCACACATCCAA 60.179 50.000 0.00 0.00 33.40 3.53
3236 3980 0.238289 CTTCGTGCCACACATCCAAC 59.762 55.000 0.00 0.00 33.40 3.77
3237 3981 0.464554 TTCGTGCCACACATCCAACA 60.465 50.000 0.00 0.00 33.40 3.33
3238 3982 0.464554 TCGTGCCACACATCCAACAA 60.465 50.000 0.00 0.00 33.40 2.83
3239 3983 0.040157 CGTGCCACACATCCAACAAG 60.040 55.000 0.00 0.00 33.40 3.16
3240 3984 1.032014 GTGCCACACATCCAACAAGT 58.968 50.000 0.00 0.00 34.08 3.16
3241 3985 2.226330 GTGCCACACATCCAACAAGTA 58.774 47.619 0.00 0.00 34.08 2.24
3242 3986 2.031157 GTGCCACACATCCAACAAGTAC 60.031 50.000 0.00 0.00 34.08 2.73
3243 3987 2.158682 TGCCACACATCCAACAAGTACT 60.159 45.455 0.00 0.00 0.00 2.73
3244 3988 3.071747 TGCCACACATCCAACAAGTACTA 59.928 43.478 0.00 0.00 0.00 1.82
3245 3989 3.435671 GCCACACATCCAACAAGTACTAC 59.564 47.826 0.00 0.00 0.00 2.73
3246 3990 4.802918 GCCACACATCCAACAAGTACTACT 60.803 45.833 0.00 0.00 0.00 2.57
3247 3991 4.929808 CCACACATCCAACAAGTACTACTC 59.070 45.833 0.00 0.00 0.00 2.59
3248 3992 5.510690 CCACACATCCAACAAGTACTACTCA 60.511 44.000 0.00 0.00 0.00 3.41
3249 3993 6.166279 CACACATCCAACAAGTACTACTCAT 58.834 40.000 0.00 0.00 0.00 2.90
3250 3994 6.311445 CACACATCCAACAAGTACTACTCATC 59.689 42.308 0.00 0.00 0.00 2.92
3251 3995 5.812642 CACATCCAACAAGTACTACTCATCC 59.187 44.000 0.00 0.00 0.00 3.51
3252 3996 5.721960 ACATCCAACAAGTACTACTCATCCT 59.278 40.000 0.00 0.00 0.00 3.24
3253 3997 5.916661 TCCAACAAGTACTACTCATCCTC 57.083 43.478 0.00 0.00 0.00 3.71
3254 3998 5.330233 TCCAACAAGTACTACTCATCCTCA 58.670 41.667 0.00 0.00 0.00 3.86
3255 3999 5.185249 TCCAACAAGTACTACTCATCCTCAC 59.815 44.000 0.00 0.00 0.00 3.51
3256 4000 5.186021 CCAACAAGTACTACTCATCCTCACT 59.814 44.000 0.00 0.00 0.00 3.41
3257 4001 6.326375 CAACAAGTACTACTCATCCTCACTC 58.674 44.000 0.00 0.00 0.00 3.51
3258 4002 4.636648 ACAAGTACTACTCATCCTCACTCG 59.363 45.833 0.00 0.00 0.00 4.18
3259 4003 3.811083 AGTACTACTCATCCTCACTCGG 58.189 50.000 0.00 0.00 0.00 4.63
3260 4004 1.394618 ACTACTCATCCTCACTCGGC 58.605 55.000 0.00 0.00 0.00 5.54
3261 4005 0.309302 CTACTCATCCTCACTCGGCG 59.691 60.000 0.00 0.00 0.00 6.46
3262 4006 1.725557 TACTCATCCTCACTCGGCGC 61.726 60.000 0.00 0.00 0.00 6.53
3263 4007 4.193334 TCATCCTCACTCGGCGCG 62.193 66.667 0.00 0.00 0.00 6.86
3264 4008 4.498520 CATCCTCACTCGGCGCGT 62.499 66.667 8.43 0.00 0.00 6.01
3265 4009 4.498520 ATCCTCACTCGGCGCGTG 62.499 66.667 22.90 22.90 0.00 5.34
3296 4040 3.663464 CAAATATGCTCACACGTCCTG 57.337 47.619 0.00 0.00 0.00 3.86
3297 4041 2.315925 AATATGCTCACACGTCCTGG 57.684 50.000 0.00 0.00 0.00 4.45
3298 4042 0.179073 ATATGCTCACACGTCCTGGC 60.179 55.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.288273 GCATCCGTCAGTATACAGGGAC 60.288 54.545 5.50 8.65 0.00 4.46
30 31 3.331150 TGTTTTTCGCATCCGTCAGTAT 58.669 40.909 0.00 0.00 35.54 2.12
77 87 5.648178 TTAGTTCGCATTCGGCCTATATA 57.352 39.130 0.00 0.00 40.31 0.86
97 108 5.350633 CGAACGGATGTACCTATGGTTTTA 58.649 41.667 0.00 0.00 37.09 1.52
233 244 2.158385 ACACCTTAAATGGCCAAGACCA 60.158 45.455 10.96 0.00 45.82 4.02
238 249 4.443598 GGAACAAACACCTTAAATGGCCAA 60.444 41.667 10.96 0.00 0.00 4.52
239 250 3.070302 GGAACAAACACCTTAAATGGCCA 59.930 43.478 8.56 8.56 0.00 5.36
317 328 2.349886 GTGCAGTGATTTCCGTGAGATC 59.650 50.000 0.00 0.00 0.00 2.75
325 336 5.050490 AGTATCGTATGTGCAGTGATTTCC 58.950 41.667 0.00 0.00 0.00 3.13
440 451 5.162794 ACAACGTTGCTATACATACGACAA 58.837 37.500 27.61 0.00 36.73 3.18
507 518 2.522185 TCTCCATACCATACTACCGCC 58.478 52.381 0.00 0.00 0.00 6.13
549 560 4.016444 ACTCATGGTCATTAATTGGCGTT 58.984 39.130 0.00 0.00 0.00 4.84
564 575 5.711976 ACCCTGATTTCTTTTACACTCATGG 59.288 40.000 0.00 0.00 0.00 3.66
565 576 6.349611 CCACCCTGATTTCTTTTACACTCATG 60.350 42.308 0.00 0.00 0.00 3.07
584 597 3.721087 AAGAATTTCGACATCCACCCT 57.279 42.857 0.00 0.00 0.00 4.34
613 626 7.067859 ACCTAAATAATTTAAAACGGAGGGAGC 59.932 37.037 0.00 0.00 0.00 4.70
618 631 8.200364 TCCGACCTAAATAATTTAAAACGGAG 57.800 34.615 0.00 0.00 37.64 4.63
662 1213 1.287425 CGAACGGAGGGAGTAATTGC 58.713 55.000 0.00 0.00 0.00 3.56
667 1218 1.856629 ATTTCCGAACGGAGGGAGTA 58.143 50.000 15.34 0.00 46.06 2.59
668 1219 1.856629 TATTTCCGAACGGAGGGAGT 58.143 50.000 15.34 1.96 46.06 3.85
669 1220 3.470645 AATATTTCCGAACGGAGGGAG 57.529 47.619 15.34 0.00 46.06 4.30
670 1221 3.054948 ACAAATATTTCCGAACGGAGGGA 60.055 43.478 15.34 7.17 46.06 4.20
671 1222 3.275999 ACAAATATTTCCGAACGGAGGG 58.724 45.455 15.34 5.11 46.06 4.30
672 1223 3.311596 GGACAAATATTTCCGAACGGAGG 59.688 47.826 15.34 4.52 46.06 4.30
673 1224 4.189231 AGGACAAATATTTCCGAACGGAG 58.811 43.478 15.34 5.60 46.06 4.63
674 1225 4.210724 AGGACAAATATTTCCGAACGGA 57.789 40.909 12.04 12.04 43.52 4.69
675 1226 4.957759 AAGGACAAATATTTCCGAACGG 57.042 40.909 6.94 6.94 36.95 4.44
676 1227 8.905103 ATTTTAAGGACAAATATTTCCGAACG 57.095 30.769 0.00 0.00 36.95 3.95
743 1294 8.600625 CGGAAATACTTGTCTTCAAAATCGATA 58.399 33.333 0.00 0.00 32.87 2.92
744 1295 7.414098 CCGGAAATACTTGTCTTCAAAATCGAT 60.414 37.037 0.00 0.00 32.87 3.59
745 1296 6.128391 CCGGAAATACTTGTCTTCAAAATCGA 60.128 38.462 0.00 0.00 32.87 3.59
746 1297 6.021596 CCGGAAATACTTGTCTTCAAAATCG 58.978 40.000 0.00 0.00 32.87 3.34
747 1298 6.322491 CCCGGAAATACTTGTCTTCAAAATC 58.678 40.000 0.73 0.00 32.87 2.17
748 1299 5.336451 GCCCGGAAATACTTGTCTTCAAAAT 60.336 40.000 0.73 0.00 32.87 1.82
749 1300 4.022676 GCCCGGAAATACTTGTCTTCAAAA 60.023 41.667 0.73 0.00 32.87 2.44
750 1301 3.504520 GCCCGGAAATACTTGTCTTCAAA 59.495 43.478 0.73 0.00 32.87 2.69
751 1302 3.078837 GCCCGGAAATACTTGTCTTCAA 58.921 45.455 0.73 0.00 0.00 2.69
752 1303 2.706890 GCCCGGAAATACTTGTCTTCA 58.293 47.619 0.73 0.00 0.00 3.02
753 1304 1.664151 CGCCCGGAAATACTTGTCTTC 59.336 52.381 0.73 0.00 0.00 2.87
754 1305 1.677820 CCGCCCGGAAATACTTGTCTT 60.678 52.381 0.73 0.00 37.50 3.01
755 1306 0.107848 CCGCCCGGAAATACTTGTCT 60.108 55.000 0.73 0.00 37.50 3.41
756 1307 0.108041 TCCGCCCGGAAATACTTGTC 60.108 55.000 0.73 0.00 42.05 3.18
757 1308 0.107848 CTCCGCCCGGAAATACTTGT 60.108 55.000 0.73 0.00 44.66 3.16
758 1309 0.814010 CCTCCGCCCGGAAATACTTG 60.814 60.000 0.73 0.00 44.66 3.16
759 1310 0.979187 TCCTCCGCCCGGAAATACTT 60.979 55.000 0.73 0.00 44.66 2.24
760 1311 0.979187 TTCCTCCGCCCGGAAATACT 60.979 55.000 0.73 0.00 44.66 2.12
761 1312 0.532196 CTTCCTCCGCCCGGAAATAC 60.532 60.000 0.73 0.00 44.66 1.89
762 1313 0.979187 ACTTCCTCCGCCCGGAAATA 60.979 55.000 0.73 0.00 44.66 1.40
763 1314 0.979187 TACTTCCTCCGCCCGGAAAT 60.979 55.000 0.73 0.00 44.66 2.17
764 1315 1.610086 TACTTCCTCCGCCCGGAAA 60.610 57.895 0.73 2.52 44.66 3.13
765 1316 2.037687 TACTTCCTCCGCCCGGAA 59.962 61.111 0.73 0.00 44.66 4.30
766 1317 2.757099 GTACTTCCTCCGCCCGGA 60.757 66.667 0.73 9.31 42.90 5.14
767 1318 2.175035 TTTGTACTTCCTCCGCCCGG 62.175 60.000 0.00 0.00 0.00 5.73
768 1319 1.017701 GTTTGTACTTCCTCCGCCCG 61.018 60.000 0.00 0.00 0.00 6.13
769 1320 0.035739 TGTTTGTACTTCCTCCGCCC 59.964 55.000 0.00 0.00 0.00 6.13
770 1321 2.109425 ATGTTTGTACTTCCTCCGCC 57.891 50.000 0.00 0.00 0.00 6.13
771 1322 3.858247 AGTATGTTTGTACTTCCTCCGC 58.142 45.455 0.00 0.00 30.95 5.54
772 1323 4.430908 GGAGTATGTTTGTACTTCCTCCG 58.569 47.826 0.00 0.00 35.14 4.63
773 1324 4.767478 GGGAGTATGTTTGTACTTCCTCC 58.233 47.826 4.48 0.00 44.04 4.30
776 1327 4.679905 CGGAGGGAGTATGTTTGTACTTCC 60.680 50.000 3.63 3.63 46.63 3.46
777 1328 4.081807 ACGGAGGGAGTATGTTTGTACTTC 60.082 45.833 0.00 0.00 35.14 3.01
778 1329 3.836562 ACGGAGGGAGTATGTTTGTACTT 59.163 43.478 0.00 0.00 35.14 2.24
779 1330 3.438183 ACGGAGGGAGTATGTTTGTACT 58.562 45.455 0.00 0.00 37.61 2.73
780 1331 3.881937 ACGGAGGGAGTATGTTTGTAC 57.118 47.619 0.00 0.00 0.00 2.90
890 1476 5.649782 AAAGAAATACTACTCCGTTCCGA 57.350 39.130 0.00 0.00 0.00 4.55
899 1485 7.168905 AGTAGCTTGCCAAAAGAAATACTACT 58.831 34.615 0.00 0.00 32.04 2.57
953 1539 8.706936 CAAGCAAGCTATATATACTCAACACAG 58.293 37.037 0.00 0.00 0.00 3.66
1190 1776 2.363147 GGTCGGTGAGGGAGAGCT 60.363 66.667 0.00 0.00 0.00 4.09
1215 1801 4.636435 CGGCGGAGGGTGTGGTTT 62.636 66.667 0.00 0.00 0.00 3.27
1504 2090 3.123620 GAGAGCCAGGCACGCTTG 61.124 66.667 15.80 0.00 36.48 4.01
1613 2199 2.427453 GAGTAGGTTCCATTCTCGAGCA 59.573 50.000 7.81 0.00 0.00 4.26
1950 2542 2.033141 AGCAGCGCCATGACAAGT 59.967 55.556 2.29 0.00 0.00 3.16
2219 2811 4.479993 GCATCCTCAGCACGGCCT 62.480 66.667 0.00 0.00 0.00 5.19
2437 3029 6.650807 TCAGTGATACCTCAAGTGTCAAATTC 59.349 38.462 0.00 0.00 46.71 2.17
2455 3047 0.034767 CTGCCCCACATGTCAGTGAT 60.035 55.000 0.00 0.00 42.05 3.06
2559 3151 6.826231 TCCGCCTTATTTGAACTATTTGATGA 59.174 34.615 0.00 0.00 0.00 2.92
2560 3152 6.912591 GTCCGCCTTATTTGAACTATTTGATG 59.087 38.462 0.00 0.00 0.00 3.07
2561 3153 6.039382 GGTCCGCCTTATTTGAACTATTTGAT 59.961 38.462 0.00 0.00 0.00 2.57
2598 3190 8.142994 CTGTATTTATTCCACAGTGATGTACC 57.857 38.462 0.62 0.00 35.91 3.34
2666 3268 1.372683 GTCTGCTGACTCTTGCCCA 59.627 57.895 15.81 0.00 39.94 5.36
2718 3320 2.710096 ATGAAACGGATGTGGGGTAG 57.290 50.000 0.00 0.00 0.00 3.18
2743 3345 5.025986 CGTAAGCGTAACCAAAACAAGAT 57.974 39.130 0.00 0.00 0.00 2.40
2760 3362 3.062639 ACGATGATTGAAAGCTGCGTAAG 59.937 43.478 0.00 0.00 43.44 2.34
2774 3376 3.727726 TCAATATGCCGACACGATGATT 58.272 40.909 0.00 0.00 0.00 2.57
2779 3381 2.595124 ACATCAATATGCCGACACGA 57.405 45.000 0.00 0.00 36.50 4.35
2780 3382 3.182372 CACTACATCAATATGCCGACACG 59.818 47.826 0.00 0.00 36.50 4.49
2873 3501 5.152623 TCCATGACCGATTTGAGGATATC 57.847 43.478 0.00 0.00 0.00 1.63
3013 3757 7.063426 CGGTAGCATATGTTGAATACGATGATT 59.937 37.037 4.29 0.00 0.00 2.57
3018 3762 5.190992 ACGGTAGCATATGTTGAATACGA 57.809 39.130 4.29 0.00 0.00 3.43
3081 3825 5.126396 TGTGTGATGGATATCGATGTCTC 57.874 43.478 19.85 12.04 36.04 3.36
3082 3826 5.011431 ACATGTGTGATGGATATCGATGTCT 59.989 40.000 19.85 3.05 36.04 3.41
3083 3827 5.233225 ACATGTGTGATGGATATCGATGTC 58.767 41.667 13.31 13.31 36.04 3.06
3084 3828 5.219343 ACATGTGTGATGGATATCGATGT 57.781 39.130 8.54 0.00 36.04 3.06
3098 3842 2.029200 TGCCTTTTATGCCACATGTGTG 60.029 45.455 23.79 15.96 45.23 3.82
3099 3843 2.246469 TGCCTTTTATGCCACATGTGT 58.754 42.857 23.79 8.80 0.00 3.72
3100 3844 3.450578 GATGCCTTTTATGCCACATGTG 58.549 45.455 19.31 19.31 0.00 3.21
3101 3845 2.431782 GGATGCCTTTTATGCCACATGT 59.568 45.455 0.00 0.00 0.00 3.21
3102 3846 2.544277 CGGATGCCTTTTATGCCACATG 60.544 50.000 0.00 0.00 0.00 3.21
3103 3847 1.682854 CGGATGCCTTTTATGCCACAT 59.317 47.619 0.00 0.00 0.00 3.21
3104 3848 1.102154 CGGATGCCTTTTATGCCACA 58.898 50.000 0.00 0.00 0.00 4.17
3105 3849 0.249031 GCGGATGCCTTTTATGCCAC 60.249 55.000 0.00 0.00 33.98 5.01
3106 3850 0.395586 AGCGGATGCCTTTTATGCCA 60.396 50.000 0.00 0.00 44.31 4.92
3107 3851 0.746659 AAGCGGATGCCTTTTATGCC 59.253 50.000 0.00 0.00 44.31 4.40
3108 3852 3.923017 ATAAGCGGATGCCTTTTATGC 57.077 42.857 0.00 0.00 44.31 3.14
3109 3853 6.597672 TGGTATATAAGCGGATGCCTTTTATG 59.402 38.462 7.86 0.00 44.31 1.90
3110 3854 6.717289 TGGTATATAAGCGGATGCCTTTTAT 58.283 36.000 0.00 0.53 44.31 1.40
3111 3855 6.116711 TGGTATATAAGCGGATGCCTTTTA 57.883 37.500 0.00 0.00 44.31 1.52
3112 3856 4.980573 TGGTATATAAGCGGATGCCTTTT 58.019 39.130 0.00 0.00 44.31 2.27
3113 3857 4.634012 TGGTATATAAGCGGATGCCTTT 57.366 40.909 0.00 0.00 44.31 3.11
3114 3858 4.019321 ACATGGTATATAAGCGGATGCCTT 60.019 41.667 0.00 0.00 44.31 4.35
3115 3859 3.519510 ACATGGTATATAAGCGGATGCCT 59.480 43.478 0.00 0.00 44.31 4.75
3116 3860 3.623060 CACATGGTATATAAGCGGATGCC 59.377 47.826 0.00 0.00 44.31 4.40
3117 3861 4.093408 CACACATGGTATATAAGCGGATGC 59.907 45.833 0.00 0.00 43.24 3.91
3118 3862 4.631377 CCACACATGGTATATAAGCGGATG 59.369 45.833 0.00 0.00 41.64 3.51
3119 3863 4.832248 CCACACATGGTATATAAGCGGAT 58.168 43.478 0.00 0.00 41.64 4.18
3120 3864 4.265904 CCACACATGGTATATAAGCGGA 57.734 45.455 0.00 0.00 41.64 5.54
3134 3878 0.548031 CCCCTACTCATGCCACACAT 59.452 55.000 0.00 0.00 40.66 3.21
3135 3879 1.561769 CCCCCTACTCATGCCACACA 61.562 60.000 0.00 0.00 0.00 3.72
3136 3880 1.224592 CCCCCTACTCATGCCACAC 59.775 63.158 0.00 0.00 0.00 3.82
3137 3881 3.739922 CCCCCTACTCATGCCACA 58.260 61.111 0.00 0.00 0.00 4.17
3153 3897 4.643387 AGTTCGTGTGGGCTGCCC 62.643 66.667 30.97 30.97 45.71 5.36
3154 3898 3.357079 CAGTTCGTGTGGGCTGCC 61.357 66.667 11.05 11.05 0.00 4.85
3155 3899 2.591715 ACAGTTCGTGTGGGCTGC 60.592 61.111 0.00 0.00 38.28 5.25
3164 3908 1.657094 GTTCGTTCACACACAGTTCGT 59.343 47.619 0.00 0.00 0.00 3.85
3165 3909 1.656594 TGTTCGTTCACACACAGTTCG 59.343 47.619 0.00 0.00 0.00 3.95
3166 3910 3.733024 TTGTTCGTTCACACACAGTTC 57.267 42.857 0.00 0.00 0.00 3.01
3167 3911 5.804692 TTATTGTTCGTTCACACACAGTT 57.195 34.783 0.00 0.00 0.00 3.16
3168 3912 5.804692 TTTATTGTTCGTTCACACACAGT 57.195 34.783 0.00 0.00 0.00 3.55
3169 3913 7.546277 CAATTTTATTGTTCGTTCACACACAG 58.454 34.615 0.00 0.00 0.00 3.66
3170 3914 6.020281 GCAATTTTATTGTTCGTTCACACACA 60.020 34.615 0.00 0.00 0.00 3.72
3171 3915 6.344032 GCAATTTTATTGTTCGTTCACACAC 58.656 36.000 0.00 0.00 0.00 3.82
3172 3916 5.460419 GGCAATTTTATTGTTCGTTCACACA 59.540 36.000 0.00 0.00 0.00 3.72
3173 3917 5.107645 GGGCAATTTTATTGTTCGTTCACAC 60.108 40.000 0.00 0.00 0.00 3.82
3174 3918 4.985409 GGGCAATTTTATTGTTCGTTCACA 59.015 37.500 0.00 0.00 0.00 3.58
3175 3919 4.985409 TGGGCAATTTTATTGTTCGTTCAC 59.015 37.500 0.00 0.00 0.00 3.18
3176 3920 4.985409 GTGGGCAATTTTATTGTTCGTTCA 59.015 37.500 0.00 0.00 0.00 3.18
3177 3921 4.985409 TGTGGGCAATTTTATTGTTCGTTC 59.015 37.500 0.00 0.00 0.00 3.95
3178 3922 4.747605 GTGTGGGCAATTTTATTGTTCGTT 59.252 37.500 0.00 0.00 0.00 3.85
3179 3923 4.202161 TGTGTGGGCAATTTTATTGTTCGT 60.202 37.500 0.00 0.00 0.00 3.85
3180 3924 4.302455 TGTGTGGGCAATTTTATTGTTCG 58.698 39.130 0.00 0.00 0.00 3.95
3181 3925 5.700373 ACATGTGTGGGCAATTTTATTGTTC 59.300 36.000 0.00 0.00 0.00 3.18
3182 3926 5.619220 ACATGTGTGGGCAATTTTATTGTT 58.381 33.333 0.00 0.00 0.00 2.83
3183 3927 5.226194 ACATGTGTGGGCAATTTTATTGT 57.774 34.783 0.00 0.00 0.00 2.71
3184 3928 6.531240 GTCTACATGTGTGGGCAATTTTATTG 59.469 38.462 9.11 0.00 31.07 1.90
3185 3929 6.624861 CGTCTACATGTGTGGGCAATTTTATT 60.625 38.462 9.11 0.00 29.98 1.40
3186 3930 5.163663 CGTCTACATGTGTGGGCAATTTTAT 60.164 40.000 9.11 0.00 29.98 1.40
3187 3931 4.155099 CGTCTACATGTGTGGGCAATTTTA 59.845 41.667 9.11 0.00 29.98 1.52
3188 3932 3.057596 CGTCTACATGTGTGGGCAATTTT 60.058 43.478 9.11 0.00 29.98 1.82
3189 3933 2.487762 CGTCTACATGTGTGGGCAATTT 59.512 45.455 9.11 0.00 29.98 1.82
3190 3934 2.083774 CGTCTACATGTGTGGGCAATT 58.916 47.619 9.11 0.00 29.98 2.32
3191 3935 1.737838 CGTCTACATGTGTGGGCAAT 58.262 50.000 9.11 0.00 29.98 3.56
3192 3936 0.953471 GCGTCTACATGTGTGGGCAA 60.953 55.000 9.11 0.00 29.98 4.52
3193 3937 1.375396 GCGTCTACATGTGTGGGCA 60.375 57.895 9.11 0.00 29.98 5.36
3194 3938 1.361668 CTGCGTCTACATGTGTGGGC 61.362 60.000 9.11 7.67 0.00 5.36
3195 3939 1.361668 GCTGCGTCTACATGTGTGGG 61.362 60.000 9.11 0.00 0.00 4.61
3196 3940 0.390340 AGCTGCGTCTACATGTGTGG 60.390 55.000 9.11 0.00 0.00 4.17
3197 3941 1.920574 GTAGCTGCGTCTACATGTGTG 59.079 52.381 9.11 1.17 38.93 3.82
3198 3942 1.819288 AGTAGCTGCGTCTACATGTGT 59.181 47.619 9.11 0.00 40.95 3.72
3199 3943 2.568696 AGTAGCTGCGTCTACATGTG 57.431 50.000 9.11 0.00 40.95 3.21
3200 3944 2.478031 CGAAGTAGCTGCGTCTACATGT 60.478 50.000 14.93 2.69 40.95 3.21
3201 3945 2.112522 CGAAGTAGCTGCGTCTACATG 58.887 52.381 14.93 0.00 40.95 3.21
3202 3946 1.743958 ACGAAGTAGCTGCGTCTACAT 59.256 47.619 14.93 5.55 42.77 2.29
3203 3947 1.135774 CACGAAGTAGCTGCGTCTACA 60.136 52.381 14.93 0.00 42.77 2.74
3204 3948 1.536149 CACGAAGTAGCTGCGTCTAC 58.464 55.000 14.93 6.99 42.77 2.59
3205 3949 0.179171 GCACGAAGTAGCTGCGTCTA 60.179 55.000 14.93 0.00 42.77 2.59
3206 3950 1.444553 GCACGAAGTAGCTGCGTCT 60.445 57.895 14.93 0.90 42.77 4.18
3207 3951 2.445438 GGCACGAAGTAGCTGCGTC 61.445 63.158 7.65 7.65 42.77 5.19
3209 3953 2.432456 TGGCACGAAGTAGCTGCG 60.432 61.111 0.00 0.00 41.61 5.18
3210 3954 1.667830 TGTGGCACGAAGTAGCTGC 60.668 57.895 13.77 0.00 41.61 5.25
3211 3955 0.599991 TGTGTGGCACGAAGTAGCTG 60.600 55.000 13.77 0.00 41.61 4.24
3212 3956 0.321671 ATGTGTGGCACGAAGTAGCT 59.678 50.000 13.77 0.00 41.61 3.32
3213 3957 0.721718 GATGTGTGGCACGAAGTAGC 59.278 55.000 13.77 0.00 41.61 3.58
3214 3958 1.337728 TGGATGTGTGGCACGAAGTAG 60.338 52.381 13.77 0.00 41.61 2.57
3215 3959 0.682292 TGGATGTGTGGCACGAAGTA 59.318 50.000 13.77 0.00 41.61 2.24
3217 3961 0.238289 GTTGGATGTGTGGCACGAAG 59.762 55.000 13.77 0.00 37.14 3.79
3218 3962 0.464554 TGTTGGATGTGTGGCACGAA 60.465 50.000 13.77 3.62 37.14 3.85
3219 3963 0.464554 TTGTTGGATGTGTGGCACGA 60.465 50.000 13.77 1.98 37.14 4.35
3220 3964 0.040157 CTTGTTGGATGTGTGGCACG 60.040 55.000 13.77 0.00 37.14 5.34
3221 3965 1.032014 ACTTGTTGGATGTGTGGCAC 58.968 50.000 11.55 11.55 34.56 5.01
3222 3966 2.158682 AGTACTTGTTGGATGTGTGGCA 60.159 45.455 0.00 0.00 0.00 4.92
3223 3967 2.504367 AGTACTTGTTGGATGTGTGGC 58.496 47.619 0.00 0.00 0.00 5.01
3224 3968 4.894784 AGTAGTACTTGTTGGATGTGTGG 58.105 43.478 0.00 0.00 0.00 4.17
3225 3969 5.538118 TGAGTAGTACTTGTTGGATGTGTG 58.462 41.667 0.00 0.00 0.00 3.82
3226 3970 5.801531 TGAGTAGTACTTGTTGGATGTGT 57.198 39.130 0.00 0.00 0.00 3.72
3227 3971 5.812642 GGATGAGTAGTACTTGTTGGATGTG 59.187 44.000 0.00 0.00 0.00 3.21
3228 3972 5.721960 AGGATGAGTAGTACTTGTTGGATGT 59.278 40.000 0.00 0.00 0.00 3.06
3229 3973 6.127338 TGAGGATGAGTAGTACTTGTTGGATG 60.127 42.308 0.00 0.00 0.00 3.51
3230 3974 5.958380 TGAGGATGAGTAGTACTTGTTGGAT 59.042 40.000 0.00 0.00 0.00 3.41
3231 3975 5.185249 GTGAGGATGAGTAGTACTTGTTGGA 59.815 44.000 0.00 0.00 0.00 3.53
3232 3976 5.186021 AGTGAGGATGAGTAGTACTTGTTGG 59.814 44.000 0.00 0.00 0.00 3.77
3233 3977 6.274157 AGTGAGGATGAGTAGTACTTGTTG 57.726 41.667 0.00 0.00 0.00 3.33
3234 3978 5.124138 CGAGTGAGGATGAGTAGTACTTGTT 59.876 44.000 0.00 0.00 0.00 2.83
3235 3979 4.636648 CGAGTGAGGATGAGTAGTACTTGT 59.363 45.833 0.00 0.00 0.00 3.16
3236 3980 4.035792 CCGAGTGAGGATGAGTAGTACTTG 59.964 50.000 0.00 0.00 0.00 3.16
3237 3981 4.200874 CCGAGTGAGGATGAGTAGTACTT 58.799 47.826 0.00 0.00 0.00 2.24
3238 3982 3.811083 CCGAGTGAGGATGAGTAGTACT 58.189 50.000 1.37 1.37 0.00 2.73
3239 3983 2.291190 GCCGAGTGAGGATGAGTAGTAC 59.709 54.545 0.00 0.00 0.00 2.73
3240 3984 2.573369 GCCGAGTGAGGATGAGTAGTA 58.427 52.381 0.00 0.00 0.00 1.82
3241 3985 1.394618 GCCGAGTGAGGATGAGTAGT 58.605 55.000 0.00 0.00 0.00 2.73
3242 3986 0.309302 CGCCGAGTGAGGATGAGTAG 59.691 60.000 0.00 0.00 0.00 2.57
3243 3987 1.725557 GCGCCGAGTGAGGATGAGTA 61.726 60.000 0.00 0.00 0.00 2.59
3244 3988 3.069980 GCGCCGAGTGAGGATGAGT 62.070 63.158 0.00 0.00 0.00 3.41
3245 3989 2.279120 GCGCCGAGTGAGGATGAG 60.279 66.667 0.00 0.00 0.00 2.90
3246 3990 4.193334 CGCGCCGAGTGAGGATGA 62.193 66.667 0.00 0.00 0.00 2.92
3247 3991 4.498520 ACGCGCCGAGTGAGGATG 62.499 66.667 5.73 0.00 0.00 3.51
3248 3992 4.498520 CACGCGCCGAGTGAGGAT 62.499 66.667 16.15 0.00 41.83 3.24
3263 4007 2.518949 CATATTTGCTTCGTGCCACAC 58.481 47.619 0.00 0.00 42.00 3.82
3264 4008 1.135431 GCATATTTGCTTCGTGCCACA 60.135 47.619 0.35 0.00 45.77 4.17
3265 4009 1.548986 GCATATTTGCTTCGTGCCAC 58.451 50.000 0.35 0.00 45.77 5.01
3276 4020 2.352651 CCAGGACGTGTGAGCATATTTG 59.647 50.000 0.00 0.00 0.00 2.32
3277 4021 2.632377 CCAGGACGTGTGAGCATATTT 58.368 47.619 0.00 0.00 0.00 1.40
3278 4022 1.743772 GCCAGGACGTGTGAGCATATT 60.744 52.381 0.00 0.00 0.00 1.28
3279 4023 0.179073 GCCAGGACGTGTGAGCATAT 60.179 55.000 0.00 0.00 0.00 1.78
3280 4024 1.218047 GCCAGGACGTGTGAGCATA 59.782 57.895 0.00 0.00 0.00 3.14
3281 4025 2.046892 GCCAGGACGTGTGAGCAT 60.047 61.111 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.