Multiple sequence alignment - TraesCS2A01G370200

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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 TraesCS2A01G370200 chr2A 100.000 7779 0 0 1 7779 612852884 612845106 0.000000e+00 14366
1 TraesCS2A01G370200 chr2D 92.883 6042 281 65 4 5962 471223404 471217429 0.000000e+00 8637
2 TraesCS2A01G370200 chr2D 91.899 1864 95 25 5957 7777 471217392 471215542 0.000000e+00 2555
3 TraesCS2A01G370200 chr2D 88.298 188 17 5 4 188 13075050 13075235 3.650000e-53 220
4 TraesCS2A01G370200 chr2D 88.172 186 19 3 4 187 170337025 170336841 1.310000e-52 219
5 TraesCS2A01G370200 chr2D 91.667 156 12 1 6924 7079 79056169 79056323 1.700000e-51 215
6 TraesCS2A01G370200 chr2B 90.489 4311 209 78 631 4886 550406307 550402143 0.000000e+00 5504
7 TraesCS2A01G370200 chr2B 90.671 1983 113 25 3987 5962 550403024 550401107 0.000000e+00 2571
8 TraesCS2A01G370200 chr2B 93.541 1316 61 17 5957 7262 550401070 550399769 0.000000e+00 1938
9 TraesCS2A01G370200 chr2B 91.623 573 45 3 4 576 550407214 550406645 0.000000e+00 789
10 TraesCS2A01G370200 chr2B 90.297 505 29 13 7291 7777 550399650 550399148 1.830000e-180 643
11 TraesCS2A01G370200 chr6A 82.343 572 75 18 5096 5663 446297731 446298280 2.540000e-129 473
12 TraesCS2A01G370200 chr6B 88.889 243 27 0 3036 3278 477218776 477219018 4.560000e-77 300
13 TraesCS2A01G370200 chr6B 88.298 188 20 2 1 187 84828753 84828939 2.820000e-54 224
14 TraesCS2A01G370200 chr6D 88.382 241 28 0 3038 3278 309581236 309581476 2.750000e-74 291
15 TraesCS2A01G370200 chr1B 93.038 158 10 1 6921 7078 507851747 507851903 6.070000e-56 230
16 TraesCS2A01G370200 chr1B 82.967 182 24 6 1908 2085 32765916 32765738 2.910000e-34 158
17 TraesCS2A01G370200 chr1B 88.776 98 11 0 6153 6250 340805833 340805930 3.810000e-23 121
18 TraesCS2A01G370200 chr1A 93.038 158 10 1 6921 7078 479836086 479836242 6.070000e-56 230
19 TraesCS2A01G370200 chr1A 82.716 162 13 7 6526 6682 555805693 555805844 6.330000e-26 130
20 TraesCS2A01G370200 chr4B 92.715 151 11 0 6921 7071 146469215 146469365 1.310000e-52 219
21 TraesCS2A01G370200 chr4B 91.304 161 12 2 6921 7081 438375180 438375338 1.310000e-52 219
22 TraesCS2A01G370200 chr4B 85.185 189 23 5 1 188 61357405 61357221 1.030000e-43 189
23 TraesCS2A01G370200 chr7B 91.250 160 13 1 6924 7083 505937316 505937474 4.730000e-52 217
24 TraesCS2A01G370200 chr4D 91.720 157 11 2 6920 7075 74079349 74079504 4.730000e-52 217
25 TraesCS2A01G370200 chr3A 85.185 189 25 3 1 188 352423028 352422842 2.860000e-44 191
26 TraesCS2A01G370200 chr7A 85.326 184 23 4 4 186 260871271 260871091 3.710000e-43 187
27 TraesCS2A01G370200 chr5D 85.106 188 22 6 2 187 342839949 342839766 3.710000e-43 187


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 TraesCS2A01G370200 chr2A 612845106 612852884 7778 True 14366 14366 100.0000 1 7779 1 chr2A.!!$R1 7778
1 TraesCS2A01G370200 chr2D 471215542 471223404 7862 True 5596 8637 92.3910 4 7777 2 chr2D.!!$R2 7773
2 TraesCS2A01G370200 chr2B 550399148 550407214 8066 True 2289 5504 91.3242 4 7777 5 chr2B.!!$R1 7773
3 TraesCS2A01G370200 chr6A 446297731 446298280 549 False 473 473 82.3430 5096 5663 1 chr6A.!!$F1 567

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
54 55 0.029834 CGAATTGCATAGCCCTGTGC 59.970 55.000 9.70 9.70 46.09 4.57 F
940 1242 0.745128 ATCCGACGAGCGAAGAGTCT 60.745 55.000 0.00 0.00 44.57 3.24 F
1422 1746 0.395686 GGACCCGGGGTTTAGATAGC 59.604 60.000 27.92 4.31 35.25 2.97 F
1805 2142 0.447801 GTTCATGATGACGGCCACAC 59.552 55.000 2.24 0.00 0.00 3.82 F
2374 2717 0.592148 CGCTACCAGACCGAGGTATC 59.408 60.000 0.00 0.00 40.62 2.24 F
3952 4318 0.027194 CGCGGAGAGAATCGACGTAA 59.973 55.000 0.00 0.00 42.67 3.18 F
4363 4731 0.385974 GCACAAAGGTAAGCAGCACG 60.386 55.000 0.00 0.00 0.00 5.34 F
4657 5045 0.466124 AGATAGAAGGCGAGGGTTGC 59.534 55.000 0.00 0.00 0.00 4.17 F
4689 5077 1.004918 AGTGGTGGTAGTTGCTCGC 60.005 57.895 0.00 0.00 0.00 5.03 F
4769 5157 1.486726 CTAAGCGATTTCCAGAGGGGT 59.513 52.381 0.00 0.00 38.11 4.95 F
5170 5559 1.966451 CCAACCTTCCGTGGAGCAC 60.966 63.158 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1175 1499 0.677098 CTGATGCTGAAGCTGCTGGT 60.677 55.000 1.35 0.00 42.66 4.00 R
1788 2125 1.447663 CGTGTGGCCGTCATCATGA 60.448 57.895 0.00 0.00 0.00 3.07 R
3033 3393 1.141657 AGTTGCAGTGACATCCTGTGT 59.858 47.619 0.00 0.00 45.83 3.72 R
3665 4025 2.061028 GCAATGCCAACTACAACAAGC 58.939 47.619 0.00 0.00 0.00 4.01 R
4363 4731 0.318784 CGGCTCCATACTACGGCTTC 60.319 60.000 0.00 0.00 0.00 3.86 R
5828 6219 0.395586 TGGACCACAAGCAAGCAAGT 60.396 50.000 0.00 0.00 0.00 3.16 R
6108 6562 3.833559 AAAGGAGACCAAATGACCCAT 57.166 42.857 0.00 0.00 0.00 4.00 R
6458 6913 1.750206 TGCCATCGAAAATCACCATGG 59.250 47.619 11.19 11.19 37.63 3.66 R
6634 7089 3.313803 GGAAAAAGCTATAGCACTCCTGC 59.686 47.826 26.07 8.30 45.16 4.85 R
6691 7148 1.552792 TCAATCCGATACCTGTGCACA 59.447 47.619 20.37 20.37 0.00 4.57 R
6904 7370 0.743701 GCAGTCCACATGAGGCAGAG 60.744 60.000 3.98 0.00 0.00 3.35 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
54 55 0.029834 CGAATTGCATAGCCCTGTGC 59.970 55.000 9.70 9.70 46.09 4.57
123 124 1.484356 CGCTCGGTTATTACCTTCCG 58.516 55.000 0.00 0.00 42.66 4.30
148 149 9.485591 CGGCTAACACATAGTTTATTTTGTTAG 57.514 33.333 12.76 12.76 41.64 2.34
201 202 9.571816 TTAATTCAAAAAGGCCTCATTTGATTT 57.428 25.926 31.25 31.25 41.26 2.17
206 207 8.811017 TCAAAAAGGCCTCATTTGATTTATACA 58.189 29.630 29.25 14.18 37.95 2.29
262 263 4.185467 AGCGAGGTAATATGCATCTCAG 57.815 45.455 0.19 1.61 0.00 3.35
294 295 5.120830 AGGAAAAGAGATGTCGTTTGATTCG 59.879 40.000 8.45 0.00 34.90 3.34
305 306 5.644206 TGTCGTTTGATTCGGGATTTGATTA 59.356 36.000 0.00 0.00 0.00 1.75
307 308 6.851330 GTCGTTTGATTCGGGATTTGATTATC 59.149 38.462 0.00 0.00 0.00 1.75
315 316 9.273016 GATTCGGGATTTGATTATCTTTCACTA 57.727 33.333 0.00 0.00 0.00 2.74
426 427 5.586877 TGGAGGCCTTAGTTAGTAGAGAAA 58.413 41.667 6.77 0.00 0.00 2.52
559 560 2.440253 TCTTTCCCCTTGTTCCGAGAAA 59.560 45.455 0.00 0.00 0.00 2.52
593 847 6.035758 GCAATGTAGTAGTACCAGCACTAAAC 59.964 42.308 5.26 0.00 32.92 2.01
609 864 7.757624 CAGCACTAAACACAGAAAAGGTAAAAA 59.242 33.333 0.00 0.00 0.00 1.94
610 865 8.474831 AGCACTAAACACAGAAAAGGTAAAAAT 58.525 29.630 0.00 0.00 0.00 1.82
656 940 5.180680 AGAAGCAAGGGAAACGTGTAAATAC 59.819 40.000 0.00 0.00 0.00 1.89
660 944 5.049267 GCAAGGGAAACGTGTAAATACAAGA 60.049 40.000 12.41 0.00 38.71 3.02
835 1136 2.290641 CAGAACGGAGGGACAAAGTTTG 59.709 50.000 14.13 14.13 0.00 2.93
907 1209 2.138320 CGTCGCTCCAAATCATAGCAT 58.862 47.619 0.00 0.00 35.98 3.79
933 1235 2.541288 GGATCTATCCGACGAGCGA 58.459 57.895 0.00 0.00 44.57 4.93
936 1238 1.799403 GATCTATCCGACGAGCGAAGA 59.201 52.381 0.00 4.86 44.57 2.87
937 1239 1.218763 TCTATCCGACGAGCGAAGAG 58.781 55.000 0.00 0.00 44.57 2.85
938 1240 0.938713 CTATCCGACGAGCGAAGAGT 59.061 55.000 0.00 0.00 44.57 3.24
939 1241 0.935898 TATCCGACGAGCGAAGAGTC 59.064 55.000 0.00 0.00 44.57 3.36
940 1242 0.745128 ATCCGACGAGCGAAGAGTCT 60.745 55.000 0.00 0.00 44.57 3.24
964 1267 2.137523 CTCTGCACAACCATTTTTGGC 58.862 47.619 0.00 0.00 0.00 4.52
1144 1459 2.675423 ACCAGCAGCAGCACATGG 60.675 61.111 3.17 5.02 45.49 3.66
1378 1702 6.573664 ATTGATTTGATTCGTTGACTTGGA 57.426 33.333 0.00 0.00 0.00 3.53
1391 1715 5.694910 CGTTGACTTGGAATAGTTGTGTACT 59.305 40.000 0.00 0.00 41.04 2.73
1392 1716 6.864685 CGTTGACTTGGAATAGTTGTGTACTA 59.135 38.462 0.00 0.00 43.29 1.82
1393 1717 7.061905 CGTTGACTTGGAATAGTTGTGTACTAG 59.938 40.741 0.00 0.00 42.44 2.57
1422 1746 0.395686 GGACCCGGGGTTTAGATAGC 59.604 60.000 27.92 4.31 35.25 2.97
1462 1786 4.095334 GGTGAAACTCGTGTACTTTTGGTT 59.905 41.667 0.00 0.00 36.74 3.67
1467 1791 5.978934 ACTCGTGTACTTTTGGTTGTAAG 57.021 39.130 0.00 0.00 0.00 2.34
1551 1875 6.179756 TCCAAGCATGAATTATGTGTACAGT 58.820 36.000 0.00 0.00 39.08 3.55
1593 1917 3.753272 CCTGGGCATTCTGTATTAATCCG 59.247 47.826 0.00 0.00 0.00 4.18
1682 2019 2.175878 AGTGCTGAGCAACTAACAGG 57.824 50.000 9.51 0.00 41.47 4.00
1788 2125 5.810074 GCGAATTAATGGCTATTTTGTGGTT 59.190 36.000 0.00 0.00 0.00 3.67
1805 2142 0.447801 GTTCATGATGACGGCCACAC 59.552 55.000 2.24 0.00 0.00 3.82
2063 2402 3.319137 TGTGTCTACAGTCCTGCATTC 57.681 47.619 0.00 0.00 31.91 2.67
2088 2427 3.433343 TCCTGCATCACATCCAAACAAT 58.567 40.909 0.00 0.00 0.00 2.71
2092 2431 5.105635 CCTGCATCACATCCAAACAATAGTT 60.106 40.000 0.00 0.00 40.40 2.24
2133 2476 8.311109 GTGATTTGGTGGTTGGAAATATAAAGT 58.689 33.333 0.00 0.00 0.00 2.66
2136 2479 4.464597 TGGTGGTTGGAAATATAAAGTGGC 59.535 41.667 0.00 0.00 0.00 5.01
2139 2482 4.709397 TGGTTGGAAATATAAAGTGGCCTG 59.291 41.667 3.32 0.00 0.00 4.85
2181 2524 6.095580 GGATGTAAATTTTCAGGAGGTTCCTC 59.904 42.308 10.13 10.13 45.66 3.71
2260 2603 8.861086 ACTGTTCTTCCAACGTAGATGATATAT 58.139 33.333 0.00 0.00 29.10 0.86
2287 2630 9.398538 CCTAGATATTGGTAGTAGCTAGTAAGG 57.601 40.741 9.92 6.37 36.77 2.69
2288 2631 9.398538 CTAGATATTGGTAGTAGCTAGTAAGGG 57.601 40.741 9.92 0.00 34.86 3.95
2289 2632 7.997915 AGATATTGGTAGTAGCTAGTAAGGGA 58.002 38.462 9.92 0.00 0.00 4.20
2290 2633 8.625571 AGATATTGGTAGTAGCTAGTAAGGGAT 58.374 37.037 9.92 5.39 0.00 3.85
2297 2640 8.575589 GGTAGTAGCTAGTAAGGGATTAAGTTC 58.424 40.741 9.92 0.00 0.00 3.01
2310 2653 6.655425 AGGGATTAAGTTCTACTTTTGCAGTC 59.345 38.462 0.00 0.00 39.51 3.51
2374 2717 0.592148 CGCTACCAGACCGAGGTATC 59.408 60.000 0.00 0.00 40.62 2.24
2416 2759 1.597742 TTCTTGTCAAGTGCTGCTCC 58.402 50.000 12.30 0.00 0.00 4.70
2424 2767 2.305635 TCAAGTGCTGCTCCCATTCTTA 59.694 45.455 0.00 0.00 0.00 2.10
2463 2806 6.258287 TGCAATGTTATATTTTTGCATGAGCC 59.742 34.615 0.00 0.00 46.76 4.70
2535 2878 9.544579 AGTTAGAAATAGAACTAGGTTGTAGGT 57.455 33.333 0.00 0.00 0.00 3.08
2628 2971 1.826385 CTCGTGGAAGGAAAAGGCAT 58.174 50.000 0.00 0.00 0.00 4.40
2629 2972 2.939640 GCTCGTGGAAGGAAAAGGCATA 60.940 50.000 0.00 0.00 0.00 3.14
2630 2973 3.545703 CTCGTGGAAGGAAAAGGCATAT 58.454 45.455 0.00 0.00 0.00 1.78
2631 2974 3.278574 TCGTGGAAGGAAAAGGCATATG 58.721 45.455 0.00 0.00 0.00 1.78
2632 2975 3.054728 TCGTGGAAGGAAAAGGCATATGA 60.055 43.478 6.97 0.00 0.00 2.15
2633 2976 3.885297 CGTGGAAGGAAAAGGCATATGAT 59.115 43.478 6.97 0.00 0.00 2.45
2685 3028 3.079578 CCAGTCGTACACTCCTACTTGA 58.920 50.000 0.00 0.00 30.26 3.02
2729 3072 6.147821 CCTGTTCCACTTTATGTTCTACAGTG 59.852 42.308 0.00 0.00 31.24 3.66
2730 3073 6.822442 TGTTCCACTTTATGTTCTACAGTGA 58.178 36.000 0.00 0.00 0.00 3.41
2731 3074 7.450074 TGTTCCACTTTATGTTCTACAGTGAT 58.550 34.615 0.00 0.00 0.00 3.06
2732 3075 7.936847 TGTTCCACTTTATGTTCTACAGTGATT 59.063 33.333 0.00 0.00 0.00 2.57
2733 3076 8.443937 GTTCCACTTTATGTTCTACAGTGATTC 58.556 37.037 0.00 0.00 0.00 2.52
2734 3077 7.676004 TCCACTTTATGTTCTACAGTGATTCA 58.324 34.615 0.00 0.00 0.00 2.57
2738 3086 8.774586 ACTTTATGTTCTACAGTGATTCAACAC 58.225 33.333 0.00 0.00 40.60 3.32
2827 3175 4.224433 GCGGCATTTGAGTTCATCATATG 58.776 43.478 0.00 0.00 45.20 1.78
2934 3282 5.974108 TCTACCTTCTTTCCGAAATACCTG 58.026 41.667 0.00 0.00 0.00 4.00
2935 3283 3.951663 ACCTTCTTTCCGAAATACCTGG 58.048 45.455 0.00 0.00 0.00 4.45
3029 3389 8.426489 TCCTGCTAAGTTAGTGTCTTCTTTTTA 58.574 33.333 11.51 0.00 0.00 1.52
3032 3392 9.216117 TGCTAAGTTAGTGTCTTCTTTTTATCC 57.784 33.333 11.51 0.00 0.00 2.59
3033 3393 9.216117 GCTAAGTTAGTGTCTTCTTTTTATCCA 57.784 33.333 11.51 0.00 0.00 3.41
3062 3422 5.183904 GGATGTCACTGCAACTAAAGGAAAT 59.816 40.000 0.00 0.00 0.00 2.17
3332 3692 6.767080 TGGAATTCGTGAAATTACGTACATG 58.233 36.000 0.00 0.00 40.59 3.21
3338 3698 5.574055 TCGTGAAATTACGTACATGGAGTTC 59.426 40.000 0.00 0.00 44.06 3.01
3341 3701 6.035758 GTGAAATTACGTACATGGAGTTCCTC 59.964 42.308 0.00 0.00 36.82 3.71
3374 3734 6.912051 GCAACGATCAAACATAAGCATATTCA 59.088 34.615 0.00 0.00 0.00 2.57
3377 3737 9.853555 AACGATCAAACATAAGCATATTCAAAA 57.146 25.926 0.00 0.00 0.00 2.44
3397 3757 7.581814 TCAAAATGATCATATCACCCTTACCA 58.418 34.615 9.04 0.00 43.01 3.25
3665 4025 8.734386 GCTTATTATGGATGAGGTATTTGAAGG 58.266 37.037 0.00 0.00 0.00 3.46
3690 4050 3.052036 GTTGTAGTTGGCATTGCTTGTG 58.948 45.455 8.82 0.00 0.00 3.33
3701 4061 7.792374 TGGCATTGCTTGTGTTTTAAATTAA 57.208 28.000 8.82 0.00 0.00 1.40
3702 4062 8.388484 TGGCATTGCTTGTGTTTTAAATTAAT 57.612 26.923 8.82 0.00 0.00 1.40
3703 4063 9.494271 TGGCATTGCTTGTGTTTTAAATTAATA 57.506 25.926 8.82 0.00 0.00 0.98
3768 4128 2.113860 TGGCATTCTACCACTGCTTC 57.886 50.000 0.00 0.00 36.18 3.86
3769 4129 1.630369 TGGCATTCTACCACTGCTTCT 59.370 47.619 0.00 0.00 36.18 2.85
3775 4135 6.127619 GGCATTCTACCACTGCTTCTTTTATT 60.128 38.462 0.00 0.00 36.18 1.40
3807 4172 3.446873 ACCAAACACTGCATTTCACAGAA 59.553 39.130 0.00 0.00 38.55 3.02
3841 4206 8.503458 AAATAGGAATGTATATCAGCAGATGC 57.497 34.615 1.18 0.00 42.49 3.91
3854 4219 1.813513 CAGATGCGTTCTCCACCTTT 58.186 50.000 0.00 0.00 29.93 3.11
3935 4301 6.643360 TGGCTTAAGAAATTTCCTTTTTACGC 59.357 34.615 14.61 13.94 0.00 4.42
3948 4314 2.184385 TTTACGCGGAGAGAATCGAC 57.816 50.000 12.47 0.00 42.67 4.20
3951 4317 1.086067 ACGCGGAGAGAATCGACGTA 61.086 55.000 12.47 0.00 42.67 3.57
3952 4318 0.027194 CGCGGAGAGAATCGACGTAA 59.973 55.000 0.00 0.00 42.67 3.18
3973 4339 6.370442 CGTAAACAATATGTCCTGAAGTTGGA 59.630 38.462 0.00 0.00 0.00 3.53
3990 4356 7.564660 TGAAGTTGGATTGGCCTTTGATAATAT 59.435 33.333 3.32 0.00 37.63 1.28
3998 4364 8.879427 ATTGGCCTTTGATAATATACCCTAAC 57.121 34.615 3.32 0.00 0.00 2.34
4016 4382 3.837213 AACTTGGTCTGCATTTGATCG 57.163 42.857 0.00 0.00 0.00 3.69
4064 4430 4.130118 GTGATTTGTCCTACATGCCCTAG 58.870 47.826 0.00 0.00 0.00 3.02
4067 4433 3.398318 TTGTCCTACATGCCCTAGAGA 57.602 47.619 0.00 0.00 0.00 3.10
4068 4434 3.619900 TGTCCTACATGCCCTAGAGAT 57.380 47.619 0.00 0.00 0.00 2.75
4069 4435 3.928754 TGTCCTACATGCCCTAGAGATT 58.071 45.455 0.00 0.00 0.00 2.40
4070 4436 4.298626 TGTCCTACATGCCCTAGAGATTT 58.701 43.478 0.00 0.00 0.00 2.17
4115 4481 8.627208 AGTTATCCATTTAAGGTGCATATGAG 57.373 34.615 6.97 0.00 0.00 2.90
4118 4484 7.756395 ATCCATTTAAGGTGCATATGAGAAG 57.244 36.000 6.97 0.00 0.00 2.85
4171 4539 4.368391 AGGCACTGCTGAAAGACG 57.632 55.556 0.00 0.00 37.18 4.18
4207 4575 1.280421 GAGGGTTTGCTCTGTCCAGAT 59.720 52.381 0.00 0.00 36.76 2.90
4208 4576 2.501723 GAGGGTTTGCTCTGTCCAGATA 59.498 50.000 0.00 0.00 36.76 1.98
4322 4690 1.539869 AAGGAAGGAGGAGGCAGCA 60.540 57.895 0.00 0.00 0.00 4.41
4361 4729 1.238439 GAGCACAAAGGTAAGCAGCA 58.762 50.000 0.00 0.00 0.00 4.41
4363 4731 0.385974 GCACAAAGGTAAGCAGCACG 60.386 55.000 0.00 0.00 0.00 5.34
4479 4847 8.202137 TGGATTTGTAGTATTTAGTGAGTAGGC 58.798 37.037 0.00 0.00 0.00 3.93
4480 4848 8.202137 GGATTTGTAGTATTTAGTGAGTAGGCA 58.798 37.037 0.00 0.00 0.00 4.75
4497 4865 1.156736 GCAATGGTGCGTAGTCTTGT 58.843 50.000 0.00 0.00 41.93 3.16
4501 4869 1.037493 TGGTGCGTAGTCTTGTCACT 58.963 50.000 0.00 0.00 0.00 3.41
4524 4892 2.029380 CCTCGTGACACTTGACATGGTA 60.029 50.000 3.68 0.00 0.00 3.25
4600 4988 1.365633 GGATCGCTGCCTCTAGGTG 59.634 63.158 0.00 0.00 37.57 4.00
4626 5014 1.954146 GTGCGCGGTTCTGTCTTGA 60.954 57.895 8.83 0.00 0.00 3.02
4628 5016 2.383527 GCGCGGTTCTGTCTTGAGG 61.384 63.158 8.83 0.00 0.00 3.86
4637 5025 0.972134 CTGTCTTGAGGGAGTGAGCA 59.028 55.000 0.00 0.00 0.00 4.26
4648 5036 2.484594 GGGAGTGAGCAAGATAGAAGGC 60.485 54.545 0.00 0.00 0.00 4.35
4657 5045 0.466124 AGATAGAAGGCGAGGGTTGC 59.534 55.000 0.00 0.00 0.00 4.17
4689 5077 1.004918 AGTGGTGGTAGTTGCTCGC 60.005 57.895 0.00 0.00 0.00 5.03
4704 5092 3.289834 CGCTGTGTGGGCTTGCTT 61.290 61.111 0.00 0.00 0.00 3.91
4727 5115 2.935481 TGGGGAGGACTTGCTGGG 60.935 66.667 0.00 0.00 0.00 4.45
4769 5157 1.486726 CTAAGCGATTTCCAGAGGGGT 59.513 52.381 0.00 0.00 38.11 4.95
4784 5172 3.262660 AGAGGGGTTTAAGGGTAACTTCG 59.737 47.826 0.00 0.00 40.64 3.79
4785 5173 2.981784 AGGGGTTTAAGGGTAACTTCGT 59.018 45.455 0.00 0.00 40.64 3.85
4786 5174 3.008375 AGGGGTTTAAGGGTAACTTCGTC 59.992 47.826 0.00 0.00 40.64 4.20
4791 5179 5.510349 GGTTTAAGGGTAACTTCGTCTCTGT 60.510 44.000 0.00 0.00 40.64 3.41
4800 5188 7.172019 GGGTAACTTCGTCTCTGTTTTTAATGA 59.828 37.037 0.00 0.00 0.00 2.57
4899 5287 8.903820 ACTTATGTTGTATAATCAAAGGCTTCC 58.096 33.333 0.00 0.00 0.00 3.46
4902 5290 4.764050 TGTATAATCAAAGGCTTCCCGA 57.236 40.909 0.00 0.00 35.76 5.14
4928 5316 3.053826 AGTTCCCTGGGTAAACACTCTT 58.946 45.455 13.56 0.00 0.00 2.85
4930 5318 4.286291 AGTTCCCTGGGTAAACACTCTTAG 59.714 45.833 13.56 0.00 0.00 2.18
5076 5465 2.304470 TGGTGGTGCAGCTGTAGATTTA 59.696 45.455 18.08 0.00 32.61 1.40
5170 5559 1.966451 CCAACCTTCCGTGGAGCAC 60.966 63.158 0.00 0.00 0.00 4.40
5634 6025 6.601332 AGTATTCCATGATTTCCGTAATGGT 58.399 36.000 0.00 0.00 40.44 3.55
5637 6028 2.034558 CCATGATTTCCGTAATGGTGCC 59.965 50.000 0.00 0.00 39.52 5.01
5731 6122 3.535561 CGAAGGACATTATTCTGTGGCT 58.464 45.455 0.00 0.00 0.00 4.75
5732 6123 4.693283 CGAAGGACATTATTCTGTGGCTA 58.307 43.478 0.00 0.00 0.00 3.93
5733 6124 5.300752 CGAAGGACATTATTCTGTGGCTAT 58.699 41.667 0.00 0.00 0.00 2.97
5734 6125 5.760253 CGAAGGACATTATTCTGTGGCTATT 59.240 40.000 0.00 0.00 0.00 1.73
5735 6126 6.260936 CGAAGGACATTATTCTGTGGCTATTT 59.739 38.462 0.00 0.00 0.00 1.40
5736 6127 7.441157 CGAAGGACATTATTCTGTGGCTATTTA 59.559 37.037 0.00 0.00 0.00 1.40
5737 6128 9.289782 GAAGGACATTATTCTGTGGCTATTTAT 57.710 33.333 0.00 0.00 0.00 1.40
5738 6129 9.646522 AAGGACATTATTCTGTGGCTATTTATT 57.353 29.630 0.00 0.00 0.00 1.40
5739 6130 9.646522 AGGACATTATTCTGTGGCTATTTATTT 57.353 29.630 0.00 0.00 0.00 1.40
5823 6214 4.884164 ACTGGCATTGAAGTTTAGGCTATC 59.116 41.667 0.00 0.00 0.00 2.08
5828 6219 5.125417 GCATTGAAGTTTAGGCTATCCACAA 59.875 40.000 0.00 0.10 33.74 3.33
5873 6264 5.679734 ACAATGCAGTTTCTACAGTGAAG 57.320 39.130 0.00 0.00 33.83 3.02
5874 6265 5.368145 ACAATGCAGTTTCTACAGTGAAGA 58.632 37.500 0.00 0.00 33.83 2.87
5875 6266 5.822519 ACAATGCAGTTTCTACAGTGAAGAA 59.177 36.000 0.00 0.00 33.83 2.52
5876 6267 6.318648 ACAATGCAGTTTCTACAGTGAAGAAA 59.681 34.615 0.00 0.00 39.91 2.52
5877 6268 7.013655 ACAATGCAGTTTCTACAGTGAAGAAAT 59.986 33.333 0.00 0.00 43.01 2.17
5878 6269 8.506437 CAATGCAGTTTCTACAGTGAAGAAATA 58.494 33.333 0.00 0.00 43.01 1.40
5879 6270 8.621532 ATGCAGTTTCTACAGTGAAGAAATAA 57.378 30.769 0.00 0.00 43.01 1.40
5880 6271 8.621532 TGCAGTTTCTACAGTGAAGAAATAAT 57.378 30.769 0.00 0.00 43.01 1.28
5881 6272 9.719355 TGCAGTTTCTACAGTGAAGAAATAATA 57.281 29.630 0.00 0.00 43.01 0.98
5917 6322 2.662006 TTTCTCATGGAGAGTCAGCG 57.338 50.000 0.00 0.00 44.98 5.18
5940 6345 5.687730 CGCATGTAGTTAGTATCTGACTTGG 59.312 44.000 0.00 0.00 39.81 3.61
5946 6352 8.812972 TGTAGTTAGTATCTGACTTGGTCAATT 58.187 33.333 2.04 0.00 42.26 2.32
5960 6407 7.596494 ACTTGGTCAATTCACATTACATTCAG 58.404 34.615 0.00 0.00 0.00 3.02
5974 6421 9.959721 ACATTACATTCAGTAGACCTTACAATT 57.040 29.630 0.00 0.00 33.43 2.32
5988 6435 5.167845 CCTTACAATTGGCATGTGGTTTAC 58.832 41.667 10.83 0.00 32.27 2.01
6044 6491 5.491635 ACTTGAAGTTTCACTGCTCTTTC 57.508 39.130 0.00 0.00 36.83 2.62
6045 6492 4.943705 ACTTGAAGTTTCACTGCTCTTTCA 59.056 37.500 0.00 0.00 36.83 2.69
6046 6493 5.591877 ACTTGAAGTTTCACTGCTCTTTCAT 59.408 36.000 0.00 0.00 36.83 2.57
6048 6495 7.283127 ACTTGAAGTTTCACTGCTCTTTCATTA 59.717 33.333 0.00 0.00 36.83 1.90
6140 6594 7.727578 TTTGGTCTCCTTTTTCTAACCTTTT 57.272 32.000 0.00 0.00 0.00 2.27
6201 6655 7.559590 AGATATCCAAGCTGTTAATGTTGTC 57.440 36.000 0.00 0.00 0.00 3.18
6254 6708 2.705658 CCTATCTCCACAGGGTATGCAA 59.294 50.000 0.00 0.00 34.93 4.08
6310 6764 8.484214 TCAGGCTATGACTAGTTCTAATGATT 57.516 34.615 0.00 0.00 31.12 2.57
6350 6804 9.585099 GCTGAATAATCCTCTACTAAGATGATG 57.415 37.037 0.00 0.00 37.23 3.07
6423 6877 3.713003 TCTTGCCTATCAGGAGTTCAGA 58.287 45.455 0.00 0.00 37.67 3.27
6485 6940 4.244862 GTGATTTTCGATGGCAAATTGGT 58.755 39.130 0.00 0.00 0.00 3.67
6492 6947 3.631686 TCGATGGCAAATTGGTAAGATGG 59.368 43.478 0.00 0.00 0.00 3.51
6611 7066 3.425659 TCTGATCACCTATGAGGATCGG 58.574 50.000 0.00 0.00 42.91 4.18
6630 7085 7.554835 AGGATCGGTTTAACTTGTATGCAATTA 59.445 33.333 0.00 0.00 33.65 1.40
6634 7089 9.347934 TCGGTTTAACTTGTATGCAATTATTTG 57.652 29.630 0.00 0.00 33.65 2.32
6856 7313 5.463724 GTGTAAATAGCAGCTCATCAGGTAC 59.536 44.000 0.00 0.00 0.00 3.34
6913 7379 1.753649 GTAGTGCATCTCTCTGCCTCA 59.246 52.381 0.00 0.00 41.58 3.86
6977 7443 9.177608 CCAACTCTTTTCTGAATTGGATGTATA 57.822 33.333 12.28 0.00 43.59 1.47
7016 7482 5.647658 TGTGTTTGTTCACTCATTTCAGTCT 59.352 36.000 0.00 0.00 38.90 3.24
7078 7544 3.104512 TGTGAACGGAGGGAAGTATCAT 58.895 45.455 0.00 0.00 0.00 2.45
7119 7586 6.400568 AGGATTGTGGCTGTTGATATTTTTG 58.599 36.000 0.00 0.00 0.00 2.44
7121 7588 3.573598 TGTGGCTGTTGATATTTTTGCG 58.426 40.909 0.00 0.00 0.00 4.85
7137 7604 0.525455 TGCGATCACGATCCACTTCG 60.525 55.000 1.50 0.00 44.56 3.79
7228 7695 2.772515 GGGGGAGCATTAAGAGTACTGT 59.227 50.000 0.00 0.00 0.00 3.55
7244 7711 3.441496 ACTGTTTCAACATGCACTTGG 57.559 42.857 6.19 0.00 38.41 3.61
7247 7714 2.757314 TGTTTCAACATGCACTTGGACA 59.243 40.909 6.19 8.31 33.17 4.02
7262 7815 9.116067 TGCACTTGGACACTATAAAATATTACC 57.884 33.333 0.00 0.00 0.00 2.85
7301 7858 9.968870 TTTTACCATTGTACTTTGATTTACCAC 57.031 29.630 0.00 0.00 0.00 4.16
7430 8008 1.134220 GGATTCCGGGCACTGATTGTA 60.134 52.381 0.00 0.00 36.31 2.41
7433 8011 1.813753 CCGGGCACTGATTGTACCG 60.814 63.158 0.00 0.00 43.51 4.02
7648 8226 2.706890 TGGCTAAGCTAAAACTTCCCG 58.293 47.619 0.00 0.00 0.00 5.14
7652 8230 3.124806 GCTAAGCTAAAACTTCCCGTCAC 59.875 47.826 0.00 0.00 0.00 3.67
7653 8231 3.487120 AAGCTAAAACTTCCCGTCACT 57.513 42.857 0.00 0.00 0.00 3.41
7691 8269 0.036875 GCTAACCAGGTGCCTGTTCT 59.963 55.000 16.15 3.88 42.15 3.01
7701 8279 2.139118 GTGCCTGTTCTGAGACTGTTC 58.861 52.381 0.00 0.00 0.00 3.18
7719 8297 7.923878 AGACTGTTCTCTCTAAAACTGAAAGAC 59.076 37.037 0.00 0.00 37.43 3.01
7767 8346 3.619979 GCTGGCTAGCTTTTTCTACAGGA 60.620 47.826 15.78 0.00 46.57 3.86
7774 8353 6.803807 GCTAGCTTTTTCTACAGGACATTTTG 59.196 38.462 7.70 0.00 0.00 2.44
7777 8356 5.920840 GCTTTTTCTACAGGACATTTTGACC 59.079 40.000 0.00 0.00 32.33 4.02
7778 8357 6.399639 TTTTTCTACAGGACATTTTGACCC 57.600 37.500 0.00 0.00 32.57 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.608130 TGTCGATTCCACAGGGAGTG 59.392 55.000 0.00 0.00 46.01 3.51
2 3 1.573108 ATGTCGATTCCACAGGGAGT 58.427 50.000 0.00 0.00 46.01 3.85
4 5 2.693591 GAGTATGTCGATTCCACAGGGA 59.306 50.000 0.00 0.00 43.03 4.20
5 6 2.695666 AGAGTATGTCGATTCCACAGGG 59.304 50.000 0.00 0.00 0.00 4.45
6 7 4.580995 AGTAGAGTATGTCGATTCCACAGG 59.419 45.833 0.00 0.00 0.00 4.00
54 55 1.301677 GCTTCAAGACTTGCGAGGGG 61.302 60.000 10.50 0.00 0.00 4.79
95 96 6.437865 GGTAATAACCGAGCGCTTTTGCTT 62.438 45.833 13.26 4.33 39.95 3.91
230 231 4.772886 ATTACCTCGCTTCCTATGGTTT 57.227 40.909 0.00 0.00 32.74 3.27
233 234 4.184629 GCATATTACCTCGCTTCCTATGG 58.815 47.826 0.00 0.00 0.00 2.74
262 263 7.222000 ACGACATCTCTTTTCCTATAGGATC 57.778 40.000 22.30 11.94 44.98 3.36
273 274 4.154195 CCCGAATCAAACGACATCTCTTTT 59.846 41.667 0.00 0.00 0.00 2.27
279 280 4.094294 TCAAATCCCGAATCAAACGACATC 59.906 41.667 0.00 0.00 0.00 3.06
294 295 8.214364 AGACCTAGTGAAAGATAATCAAATCCC 58.786 37.037 0.00 0.00 0.00 3.85
305 306 7.906199 ACTTAGCATAGACCTAGTGAAAGAT 57.094 36.000 0.00 0.00 0.00 2.40
307 308 8.779354 AAAACTTAGCATAGACCTAGTGAAAG 57.221 34.615 0.00 0.00 0.00 2.62
315 316 8.926092 AGAAAAGAAAAACTTAGCATAGACCT 57.074 30.769 0.00 0.00 37.93 3.85
483 484 2.095466 GGGTCGCATCGATGTTCAAAAA 60.095 45.455 25.47 2.40 38.42 1.94
491 492 3.032017 AGAAATAGGGTCGCATCGATG 57.968 47.619 21.27 21.27 38.42 3.84
494 495 5.119279 CAGAAATAGAAATAGGGTCGCATCG 59.881 44.000 0.00 0.00 0.00 3.84
559 560 6.126883 TGGTACTACTACATTGCAGGCTAAAT 60.127 38.462 0.00 0.00 0.00 1.40
593 847 8.711457 CATGCCTTTATTTTTACCTTTTCTGTG 58.289 33.333 0.00 0.00 0.00 3.66
609 864 6.374333 TCTTTAGTTCTTTCGCATGCCTTTAT 59.626 34.615 13.15 0.00 0.00 1.40
610 865 5.703592 TCTTTAGTTCTTTCGCATGCCTTTA 59.296 36.000 13.15 0.00 0.00 1.85
891 1193 2.227388 CCGGAATGCTATGATTTGGAGC 59.773 50.000 0.00 0.00 36.72 4.70
933 1235 0.676184 TGTGCAGAGCGAAGACTCTT 59.324 50.000 0.00 0.00 44.76 2.85
936 1238 0.601311 GGTTGTGCAGAGCGAAGACT 60.601 55.000 0.00 0.00 0.00 3.24
937 1239 0.880278 TGGTTGTGCAGAGCGAAGAC 60.880 55.000 0.00 0.00 0.00 3.01
938 1240 0.035317 ATGGTTGTGCAGAGCGAAGA 59.965 50.000 0.00 0.00 0.00 2.87
939 1241 0.877071 AATGGTTGTGCAGAGCGAAG 59.123 50.000 0.00 0.00 0.00 3.79
940 1242 1.317613 AAATGGTTGTGCAGAGCGAA 58.682 45.000 0.00 0.00 0.00 4.70
964 1267 0.386113 GGACCTTCTCCGGAATCGAG 59.614 60.000 5.23 0.65 39.00 4.04
1130 1445 2.750637 GCTCCATGTGCTGCTGCT 60.751 61.111 17.00 0.00 40.48 4.24
1138 1453 3.190849 CGACTGCCGCTCCATGTG 61.191 66.667 0.00 0.00 0.00 3.21
1160 1484 4.030452 GGTTGTGGTGCTGCGAGC 62.030 66.667 0.00 1.70 42.82 5.03
1175 1499 0.677098 CTGATGCTGAAGCTGCTGGT 60.677 55.000 1.35 0.00 42.66 4.00
1328 1652 5.782047 TGAGCATTTTGAACCAATACCAAG 58.218 37.500 0.00 0.00 0.00 3.61
1378 1702 8.964772 CCTAACCAGTACTAGTACACAACTATT 58.035 37.037 29.87 17.18 39.96 1.73
1422 1746 0.896940 ACCCATGCTGCACTTTCAGG 60.897 55.000 3.57 2.17 34.74 3.86
1462 1786 3.118408 ACAGAAACACTCACAGCCTTACA 60.118 43.478 0.00 0.00 0.00 2.41
1467 1791 1.668419 ACACAGAAACACTCACAGCC 58.332 50.000 0.00 0.00 0.00 4.85
1664 2001 1.801178 GTCCTGTTAGTTGCTCAGCAC 59.199 52.381 0.00 0.00 38.71 4.40
1788 2125 1.447663 CGTGTGGCCGTCATCATGA 60.448 57.895 0.00 0.00 0.00 3.07
1805 2142 7.953158 ACTAATTAGACACATCAATCATCCG 57.047 36.000 19.38 0.00 0.00 4.18
2063 2402 4.240096 GTTTGGATGTGATGCAGGAAAAG 58.760 43.478 0.00 0.00 0.00 2.27
2088 2427 4.148079 TCACAAAATGCCACATCCAACTA 58.852 39.130 0.00 0.00 0.00 2.24
2092 2431 4.316645 CAAATCACAAAATGCCACATCCA 58.683 39.130 0.00 0.00 0.00 3.41
2133 2476 3.266772 AGGATATTCACTTCAACAGGCCA 59.733 43.478 5.01 0.00 0.00 5.36
2136 2479 5.102953 TCCAGGATATTCACTTCAACAGG 57.897 43.478 0.00 0.00 0.00 4.00
2139 2482 8.506168 TTTACATCCAGGATATTCACTTCAAC 57.494 34.615 0.00 0.00 0.00 3.18
2181 2524 6.757897 ACCATATTTGTGGACAACTATGTG 57.242 37.500 20.04 15.79 42.76 3.21
2281 2624 8.161425 TGCAAAAGTAGAACTTAATCCCTTACT 58.839 33.333 0.00 0.00 37.47 2.24
2282 2625 8.331730 TGCAAAAGTAGAACTTAATCCCTTAC 57.668 34.615 0.00 0.00 37.47 2.34
2283 2626 8.161425 ACTGCAAAAGTAGAACTTAATCCCTTA 58.839 33.333 0.00 0.00 37.47 2.69
2284 2627 7.004691 ACTGCAAAAGTAGAACTTAATCCCTT 58.995 34.615 0.00 0.00 37.47 3.95
2285 2628 6.543735 ACTGCAAAAGTAGAACTTAATCCCT 58.456 36.000 0.00 0.00 37.47 4.20
2286 2629 6.127980 GGACTGCAAAAGTAGAACTTAATCCC 60.128 42.308 0.00 0.00 40.07 3.85
2287 2630 6.402226 CGGACTGCAAAAGTAGAACTTAATCC 60.402 42.308 0.00 0.00 40.07 3.01
2288 2631 6.534934 CGGACTGCAAAAGTAGAACTTAATC 58.465 40.000 0.00 0.00 40.07 1.75
2289 2632 5.106673 GCGGACTGCAAAAGTAGAACTTAAT 60.107 40.000 0.00 0.00 45.45 1.40
2290 2633 4.212636 GCGGACTGCAAAAGTAGAACTTAA 59.787 41.667 0.00 0.00 45.45 1.85
2310 2653 2.747855 GGCCTTCCAGTCTTGCGG 60.748 66.667 0.00 0.00 0.00 5.69
2416 2759 7.211573 TGCATGCCAAATCTTTATAAGAATGG 58.788 34.615 16.68 15.08 44.81 3.16
2463 2806 7.935338 AGAAAACATGTAAAGCAAGACAATG 57.065 32.000 0.00 0.00 0.00 2.82
2493 2836 8.918202 ATTTCTAACTTATGACAACCAGAACA 57.082 30.769 0.00 0.00 0.00 3.18
2547 2890 4.020396 TGCAATGTGCCTGGACATTAAAAT 60.020 37.500 15.29 0.00 43.29 1.82
2560 2903 3.208594 TGATATCTGACTGCAATGTGCC 58.791 45.455 3.98 0.00 44.23 5.01
2567 2910 8.697507 TCTTCTAATACTGATATCTGACTGCA 57.302 34.615 15.75 0.00 0.00 4.41
2628 2971 6.239217 ACCAAGAACACTATCAGCATCATA 57.761 37.500 0.00 0.00 0.00 2.15
2629 2972 5.108187 ACCAAGAACACTATCAGCATCAT 57.892 39.130 0.00 0.00 0.00 2.45
2630 2973 4.558226 ACCAAGAACACTATCAGCATCA 57.442 40.909 0.00 0.00 0.00 3.07
2631 2974 5.392380 CCAAACCAAGAACACTATCAGCATC 60.392 44.000 0.00 0.00 0.00 3.91
2632 2975 4.460382 CCAAACCAAGAACACTATCAGCAT 59.540 41.667 0.00 0.00 0.00 3.79
2633 2976 3.820467 CCAAACCAAGAACACTATCAGCA 59.180 43.478 0.00 0.00 0.00 4.41
2685 3028 1.777272 GGGTAGCCTCCCAAGAATGAT 59.223 52.381 2.95 0.00 46.30 2.45
2729 3072 8.767478 ATGATGATTTTCCTTTGTGTTGAATC 57.233 30.769 0.00 0.00 0.00 2.52
2800 3148 2.093890 TGAACTCAAATGCCGCATGAT 58.906 42.857 6.63 0.00 0.00 2.45
2801 3149 1.532523 TGAACTCAAATGCCGCATGA 58.467 45.000 6.63 1.25 0.00 3.07
2827 3175 2.488153 GTGTGACTATTGAGGGCAAACC 59.512 50.000 0.00 0.00 37.59 3.27
2889 3237 4.192317 AGGAGTCTTGACAAGTTGAACAC 58.808 43.478 14.75 4.89 0.00 3.32
2934 3282 4.514066 ACTTGACATTTAACTCGTCCAACC 59.486 41.667 0.00 0.00 0.00 3.77
2935 3283 5.668558 ACTTGACATTTAACTCGTCCAAC 57.331 39.130 0.00 0.00 0.00 3.77
3032 3392 1.265095 GTTGCAGTGACATCCTGTGTG 59.735 52.381 0.00 0.00 42.36 3.82
3033 3393 1.141657 AGTTGCAGTGACATCCTGTGT 59.858 47.619 0.00 0.00 45.83 3.72
3062 3422 8.017373 CGCTTCAGAAAATAGTCTTCAAATTCA 58.983 33.333 0.00 0.00 0.00 2.57
3338 3698 6.092092 TGTTTGATCGTTGCATAATTTGAGG 58.908 36.000 0.00 0.00 0.00 3.86
3341 3701 8.051909 GCTTATGTTTGATCGTTGCATAATTTG 58.948 33.333 10.23 4.04 33.38 2.32
3374 3734 9.438163 AAATGGTAAGGGTGATATGATCATTTT 57.562 29.630 14.65 1.75 42.04 1.82
3377 3737 7.529555 ACAAATGGTAAGGGTGATATGATCAT 58.470 34.615 13.81 13.81 42.04 2.45
3603 3963 5.217978 TCAGAATGCAAATGCCTTTCTTT 57.782 34.783 14.42 0.00 39.15 2.52
3665 4025 2.061028 GCAATGCCAACTACAACAAGC 58.939 47.619 0.00 0.00 0.00 4.01
3729 4089 4.262420 GCCATGCCAAAAAGGTTCTTTAGA 60.262 41.667 0.00 0.00 40.61 2.10
3730 4090 3.996363 GCCATGCCAAAAAGGTTCTTTAG 59.004 43.478 0.00 0.00 40.61 1.85
3787 4152 4.046462 CCTTCTGTGAAATGCAGTGTTTG 58.954 43.478 0.00 0.00 35.60 2.93
3795 4160 7.662604 ATTTCATTTTCCTTCTGTGAAATGC 57.337 32.000 9.93 0.00 43.77 3.56
3841 4206 6.270064 ACAAACAATTTAAAGGTGGAGAACG 58.730 36.000 6.62 0.00 0.00 3.95
3854 4219 8.445275 TCTCTGAACTAGCAACAAACAATTTA 57.555 30.769 0.00 0.00 0.00 1.40
3913 4279 7.079475 TCCGCGTAAAAAGGAAATTTCTTAAG 58.921 34.615 17.42 11.02 0.00 1.85
3924 4290 3.518590 GATTCTCTCCGCGTAAAAAGGA 58.481 45.455 4.92 0.00 0.00 3.36
3935 4301 3.127081 TGTTTACGTCGATTCTCTCCG 57.873 47.619 0.00 0.00 0.00 4.63
3948 4314 6.370442 TCCAACTTCAGGACATATTGTTTACG 59.630 38.462 0.00 0.00 0.00 3.18
3951 4317 7.309990 CCAATCCAACTTCAGGACATATTGTTT 60.310 37.037 0.00 0.00 38.13 2.83
3952 4318 6.153340 CCAATCCAACTTCAGGACATATTGTT 59.847 38.462 0.00 0.00 38.13 2.83
3973 4339 8.678798 AGTTAGGGTATATTATCAAAGGCCAAT 58.321 33.333 5.01 0.00 0.00 3.16
3990 4356 4.042311 TCAAATGCAGACCAAGTTAGGGTA 59.958 41.667 0.00 0.00 39.19 3.69
3998 4364 2.730090 GCACGATCAAATGCAGACCAAG 60.730 50.000 8.35 0.00 41.65 3.61
4016 4382 1.611977 GGACAACCAACTTAAGGGCAC 59.388 52.381 7.53 0.00 35.97 5.01
4042 4408 3.004752 AGGGCATGTAGGACAAATCAC 57.995 47.619 0.00 0.00 0.00 3.06
4115 4481 5.468540 AAAAAGGGGCAAACTGTATCTTC 57.531 39.130 0.00 0.00 0.00 2.87
4118 4484 4.462834 AGCTAAAAAGGGGCAAACTGTATC 59.537 41.667 0.00 0.00 0.00 2.24
4171 4539 0.735632 CCTCAAGAGAGCGCACTCAC 60.736 60.000 31.74 11.39 46.09 3.51
4178 4546 0.321122 AGCAAACCCTCAAGAGAGCG 60.321 55.000 0.00 0.00 40.68 5.03
4207 4575 1.564818 ACAGAGACGACCTGGGAGATA 59.435 52.381 0.00 0.00 36.03 1.98
4208 4576 0.333312 ACAGAGACGACCTGGGAGAT 59.667 55.000 0.00 0.00 36.03 2.75
4304 4672 0.918310 ATGCTGCCTCCTCCTTCCTT 60.918 55.000 0.00 0.00 0.00 3.36
4322 4690 3.674997 TCGGCTGCTTCTAAAAGTTCAT 58.325 40.909 0.00 0.00 34.79 2.57
4363 4731 0.318784 CGGCTCCATACTACGGCTTC 60.319 60.000 0.00 0.00 0.00 3.86
4375 4743 2.602267 TTTCCCTCGTCGGCTCCA 60.602 61.111 0.00 0.00 0.00 3.86
4428 4796 1.439679 GCAAACCAGAACTAGACCCG 58.560 55.000 0.00 0.00 0.00 5.28
4431 4799 3.686916 AGAGGCAAACCAGAACTAGAC 57.313 47.619 0.00 0.00 39.06 2.59
4437 4805 2.746279 TCCAAAGAGGCAAACCAGAA 57.254 45.000 0.00 0.00 39.06 3.02
4479 4847 2.157668 GTGACAAGACTACGCACCATTG 59.842 50.000 0.00 0.00 0.00 2.82
4480 4848 2.037251 AGTGACAAGACTACGCACCATT 59.963 45.455 0.00 0.00 0.00 3.16
4488 4856 2.095161 CACGAGGGAGTGACAAGACTAC 60.095 54.545 0.00 0.00 44.43 2.73
4489 4857 2.160205 CACGAGGGAGTGACAAGACTA 58.840 52.381 0.00 0.00 44.43 2.59
4501 4869 1.000843 CATGTCAAGTGTCACGAGGGA 59.999 52.381 0.00 0.00 0.00 4.20
4512 4880 1.668919 CGTCAGCGTACCATGTCAAGT 60.669 52.381 0.00 0.00 0.00 3.16
4549 4917 3.689347 TGTAGAGCATGCCACAAAGATT 58.311 40.909 15.66 0.00 0.00 2.40
4575 4963 2.125106 GGCAGCGATCCGGACTTT 60.125 61.111 6.12 0.00 0.00 2.66
4600 4988 4.264638 AACCGCGCACCAGCAAAC 62.265 61.111 8.75 0.00 42.27 2.93
4626 5014 3.037549 CCTTCTATCTTGCTCACTCCCT 58.962 50.000 0.00 0.00 0.00 4.20
4628 5016 2.801342 CGCCTTCTATCTTGCTCACTCC 60.801 54.545 0.00 0.00 0.00 3.85
4637 5025 1.134371 GCAACCCTCGCCTTCTATCTT 60.134 52.381 0.00 0.00 0.00 2.40
4657 5045 4.081030 CACTGGCTCTTGTGCGCG 62.081 66.667 0.00 0.00 0.00 6.86
4660 5048 2.263741 CCACCACTGGCTCTTGTGC 61.264 63.158 0.00 0.00 33.26 4.57
4664 5052 1.072331 CAACTACCACCACTGGCTCTT 59.928 52.381 0.00 0.00 42.08 2.85
4689 5077 1.228367 AGGAAGCAAGCCCACACAG 60.228 57.895 0.00 0.00 0.00 3.66
4704 5092 1.538876 CAAGTCCTCCCCACCAGGA 60.539 63.158 0.00 0.00 37.75 3.86
4727 5115 1.069227 CCCTTCACAAACGCTGCTTAC 60.069 52.381 0.00 0.00 0.00 2.34
4738 5126 0.618458 ATCGCTTAGGCCCTTCACAA 59.382 50.000 0.00 0.00 34.44 3.33
4784 5172 4.396478 GCCCCTCTCATTAAAAACAGAGAC 59.604 45.833 0.00 0.00 35.34 3.36
4785 5173 4.567747 GGCCCCTCTCATTAAAAACAGAGA 60.568 45.833 0.00 0.00 35.34 3.10
4786 5174 3.696548 GGCCCCTCTCATTAAAAACAGAG 59.303 47.826 0.00 0.00 33.44 3.35
4791 5179 3.372675 GGCTAGGCCCCTCTCATTAAAAA 60.373 47.826 4.61 0.00 44.06 1.94
4877 5265 5.299279 CGGGAAGCCTTTGATTATACAACAT 59.701 40.000 0.00 0.00 0.00 2.71
4899 5287 2.083628 ACCCAGGGAACTATAGTCGG 57.916 55.000 14.54 2.50 40.21 4.79
4902 5290 5.347978 AGTGTTTACCCAGGGAACTATAGT 58.652 41.667 14.54 0.00 40.21 2.12
4928 5316 9.770097 CCATTTTCTATCTATGTGAGCTTTCTA 57.230 33.333 0.00 0.00 0.00 2.10
4930 5318 8.668510 TCCATTTTCTATCTATGTGAGCTTTC 57.331 34.615 0.00 0.00 0.00 2.62
5004 5393 9.567776 TTTATTTCACGAATCCATACACCATAT 57.432 29.630 0.00 0.00 0.00 1.78
5634 6025 1.529010 CACAAGGTTCCTGCAGGCA 60.529 57.895 28.91 15.88 34.44 4.75
5637 6028 1.873591 GTACACACAAGGTTCCTGCAG 59.126 52.381 6.78 6.78 0.00 4.41
5710 6101 3.535561 AGCCACAGAATAATGTCCTTCG 58.464 45.455 0.00 0.00 0.00 3.79
5773 6164 6.273071 GGCAATAAATAAGGCCTACAGTTTG 58.727 40.000 5.16 7.76 43.09 2.93
5774 6165 6.465439 GGCAATAAATAAGGCCTACAGTTT 57.535 37.500 5.16 7.72 43.09 2.66
5823 6214 1.563111 CACAAGCAAGCAAGTTGTGG 58.437 50.000 14.33 0.00 44.79 4.17
5828 6219 0.395586 TGGACCACAAGCAAGCAAGT 60.396 50.000 0.00 0.00 0.00 3.16
5917 6322 6.574350 ACCAAGTCAGATACTAACTACATGC 58.426 40.000 0.00 0.00 37.50 4.06
5940 6345 8.391106 GGTCTACTGAATGTAATGTGAATTGAC 58.609 37.037 0.00 0.00 0.00 3.18
5946 6352 8.129496 TGTAAGGTCTACTGAATGTAATGTGA 57.871 34.615 0.00 0.00 0.00 3.58
5960 6407 4.096382 CCACATGCCAATTGTAAGGTCTAC 59.904 45.833 4.43 0.00 0.00 2.59
5974 6421 4.944619 TTGATTTGTAAACCACATGCCA 57.055 36.364 0.00 0.00 36.90 4.92
5975 6422 6.630071 ACTATTGATTTGTAAACCACATGCC 58.370 36.000 0.00 0.00 36.90 4.40
6108 6562 3.833559 AAAGGAGACCAAATGACCCAT 57.166 42.857 0.00 0.00 0.00 4.00
6201 6655 5.876460 GGTCTTGGGGAAATCAAAATTGATG 59.124 40.000 9.28 0.00 46.60 3.07
6267 6721 6.877236 AGCCTGAACACCAAAATATAAATGG 58.123 36.000 0.00 0.00 40.16 3.16
6387 6841 5.505173 AGGCAAGATGTATTCATTTTCCG 57.495 39.130 0.00 0.00 34.06 4.30
6398 6852 4.962362 TGAACTCCTGATAGGCAAGATGTA 59.038 41.667 0.00 0.00 34.61 2.29
6458 6913 1.750206 TGCCATCGAAAATCACCATGG 59.250 47.619 11.19 11.19 37.63 3.66
6467 6922 5.713792 TCTTACCAATTTGCCATCGAAAA 57.286 34.783 0.00 0.00 0.00 2.29
6485 6940 3.745975 CACAGAAACAAGTCGCCATCTTA 59.254 43.478 0.00 0.00 0.00 2.10
6492 6947 6.806120 ATTTTAAACACAGAAACAAGTCGC 57.194 33.333 0.00 0.00 0.00 5.19
6602 7057 4.873827 GCATACAAGTTAAACCGATCCTCA 59.126 41.667 0.00 0.00 0.00 3.86
6630 7085 3.853355 AGCTATAGCACTCCTGCAAAT 57.147 42.857 26.07 0.00 46.97 2.32
6634 7089 3.313803 GGAAAAAGCTATAGCACTCCTGC 59.686 47.826 26.07 8.30 45.16 4.85
6640 7095 5.470437 GGGTGATAGGAAAAAGCTATAGCAC 59.530 44.000 26.07 10.63 45.16 4.40
6691 7148 1.552792 TCAATCCGATACCTGTGCACA 59.447 47.619 20.37 20.37 0.00 4.57
6787 7244 4.520492 GGTGGGGCATACAAGATTAATCTG 59.480 45.833 18.61 14.21 37.19 2.90
6904 7370 0.743701 GCAGTCCACATGAGGCAGAG 60.744 60.000 3.98 0.00 0.00 3.35
6905 7371 1.196766 AGCAGTCCACATGAGGCAGA 61.197 55.000 3.98 0.00 0.00 4.26
6906 7372 0.743701 GAGCAGTCCACATGAGGCAG 60.744 60.000 3.98 0.00 0.00 4.85
6907 7373 1.297689 GAGCAGTCCACATGAGGCA 59.702 57.895 3.98 0.00 0.00 4.75
6913 7379 2.362369 CGGAGGGAGCAGTCCACAT 61.362 63.158 0.00 0.00 46.07 3.21
6977 7443 7.439955 TGAACAAACACAATAAGACGTGTCTAT 59.560 33.333 2.42 0.00 45.37 1.98
6991 7457 6.150976 AGACTGAAATGAGTGAACAAACACAA 59.849 34.615 0.00 0.00 42.45 3.33
7049 7515 6.659824 ACTTCCCTCCGTTCACAAATATAAT 58.340 36.000 0.00 0.00 0.00 1.28
7055 7521 3.325425 TGATACTTCCCTCCGTTCACAAA 59.675 43.478 0.00 0.00 0.00 2.83
7078 7544 9.762933 CCACAATCCTTATTTTGAAGAGAAAAA 57.237 29.630 0.00 0.00 0.00 1.94
7119 7586 2.208074 CGAAGTGGATCGTGATCGC 58.792 57.895 3.91 0.00 38.69 4.58
7137 7604 8.030106 GTGTTTCAGTCCCTATATCTGCTATAC 58.970 40.741 0.00 0.00 0.00 1.47
7228 7695 3.023119 AGTGTCCAAGTGCATGTTGAAA 58.977 40.909 12.16 0.00 0.00 2.69
7273 7826 9.968870 GGTAAATCAAAGTACAATGGTAAAACA 57.031 29.630 0.00 0.00 0.00 2.83
7279 7832 6.775629 ACTGTGGTAAATCAAAGTACAATGGT 59.224 34.615 0.00 0.00 33.73 3.55
7280 7833 7.214467 ACTGTGGTAAATCAAAGTACAATGG 57.786 36.000 0.00 0.00 33.73 3.16
7283 7836 8.788806 CCAATACTGTGGTAAATCAAAGTACAA 58.211 33.333 0.00 0.00 39.47 2.41
7284 7837 8.330466 CCAATACTGTGGTAAATCAAAGTACA 57.670 34.615 0.00 0.00 39.47 2.90
7301 7858 3.804325 CAGGAGTATTCGCACCAATACTG 59.196 47.826 14.41 2.29 45.63 2.74
7363 7920 9.515020 TCAGTTGACAAAACAGAATGATAAAAC 57.485 29.630 0.00 0.00 39.69 2.43
7366 7923 9.288576 AGATCAGTTGACAAAACAGAATGATAA 57.711 29.630 0.00 0.00 39.69 1.75
7367 7924 8.853077 AGATCAGTTGACAAAACAGAATGATA 57.147 30.769 0.00 0.00 39.69 2.15
7369 7926 6.073602 CGAGATCAGTTGACAAAACAGAATGA 60.074 38.462 0.00 0.00 39.69 2.57
7370 7927 6.073602 TCGAGATCAGTTGACAAAACAGAATG 60.074 38.462 0.00 0.00 46.00 2.67
7374 7931 5.852738 ATCGAGATCAGTTGACAAAACAG 57.147 39.130 0.00 0.00 0.00 3.16
7381 7959 5.726138 GCAACATCAATCGAGATCAGTTGAC 60.726 44.000 20.14 11.41 35.54 3.18
7422 8000 3.617263 GGCTGAAGTTACGGTACAATCAG 59.383 47.826 14.33 14.33 37.33 2.90
7430 8008 1.140252 ACACAAGGCTGAAGTTACGGT 59.860 47.619 0.00 0.00 0.00 4.83
7433 8011 3.181491 TGCAAACACAAGGCTGAAGTTAC 60.181 43.478 0.00 0.00 0.00 2.50
7652 8230 8.391106 GGTTAGCAACATTAACTATTGTCAGAG 58.609 37.037 0.00 0.00 32.81 3.35
7653 8231 7.880713 TGGTTAGCAACATTAACTATTGTCAGA 59.119 33.333 0.00 0.00 32.81 3.27
7701 8279 6.353404 AGGAGGTCTTTCAGTTTTAGAGAG 57.647 41.667 0.00 0.00 0.00 3.20
7704 8282 7.574607 AGAAAAGGAGGTCTTTCAGTTTTAGA 58.425 34.615 0.00 0.00 44.30 2.10
7719 8297 7.599998 CCAATACATTGTCAAAAGAAAAGGAGG 59.400 37.037 0.00 0.00 36.06 4.30


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

AutoCloner maintained by Alex Coulton.