Multiple sequence alignment - TraesCS4D01G272900

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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 TraesCS4D01G272900 chr4D 100.000 5860 0 0 1 5860 442894002 442899861 0.000000e+00 10822
1 TraesCS4D01G272900 chr4D 96.721 61 2 0 3078 3138 442897019 442897079 1.040000e-17 102
2 TraesCS4D01G272900 chr4D 96.721 61 2 0 3018 3078 442897079 442897139 1.040000e-17 102
3 TraesCS4D01G272900 chr4A 89.303 2337 127 60 3593 5860 24765543 24763261 0.000000e+00 2817
4 TraesCS4D01G272900 chr4A 92.717 1373 64 16 818 2163 24768395 24767032 0.000000e+00 1949
5 TraesCS4D01G272900 chr4A 87.019 832 58 18 1 790 24769593 24768770 0.000000e+00 893
6 TraesCS4D01G272900 chr4A 89.747 673 63 6 3546 4215 621565400 621564731 0.000000e+00 856
7 TraesCS4D01G272900 chr4A 89.504 524 51 4 3077 3599 24766086 24765566 0.000000e+00 660
8 TraesCS4D01G272900 chr4A 82.504 663 72 18 2076 2699 24767033 24766376 5.170000e-150 542
9 TraesCS4D01G272900 chr4A 84.250 527 66 10 1146 1658 621567451 621566928 1.130000e-136 497
10 TraesCS4D01G272900 chr4A 92.045 352 21 4 2730 3076 24766376 24766027 6.830000e-134 488
11 TraesCS4D01G272900 chr4A 89.922 258 26 0 1779 2036 621566865 621566608 3.380000e-87 333
12 TraesCS4D01G272900 chr4A 90.000 160 16 0 4702 4861 621564190 621564031 2.140000e-49 207
13 TraesCS4D01G272900 chr4B 89.134 1905 130 42 199 2053 552013246 552015123 0.000000e+00 2300
14 TraesCS4D01G272900 chr4B 89.651 1575 77 43 4328 5860 552017344 552018874 0.000000e+00 1927
15 TraesCS4D01G272900 chr4B 93.640 1195 65 7 3077 4268 552016142 552017328 0.000000e+00 1775
16 TraesCS4D01G272900 chr4B 84.242 660 60 23 2079 2699 552015199 552015853 2.340000e-168 603
17 TraesCS4D01G272900 chr4B 93.162 351 18 4 2730 3076 552015853 552016201 1.460000e-140 510
18 TraesCS4D01G272900 chr4B 87.692 65 7 1 2100 2163 552015135 552015199 2.260000e-09 75
19 TraesCS4D01G272900 chr5D 89.343 685 56 8 3546 4215 547608656 547607974 0.000000e+00 845
20 TraesCS4D01G272900 chr5D 85.496 524 60 11 1146 1658 547610661 547610143 3.110000e-147 532
21 TraesCS4D01G272900 chr5D 89.837 246 25 0 1791 2036 547610072 547609827 3.410000e-82 316
22 TraesCS4D01G272900 chr5D 90.000 160 16 0 4702 4861 547607428 547607269 2.140000e-49 207
23 TraesCS4D01G272900 chrUn 89.197 685 57 8 3546 4215 68496565 68495883 0.000000e+00 839
24 TraesCS4D01G272900 chrUn 84.733 524 64 11 1146 1658 68509191 68508673 1.460000e-140 510
25 TraesCS4D01G272900 chrUn 89.431 246 26 0 1791 2036 68508602 68508357 1.590000e-80 311
26 TraesCS4D01G272900 chrUn 89.375 160 17 0 4702 4861 68495337 68495178 9.960000e-48 202
27 TraesCS4D01G272900 chr5B 88.262 673 70 9 3546 4215 690908135 690908801 0.000000e+00 797
28 TraesCS4D01G272900 chr5B 84.470 528 57 18 1146 1658 690906368 690906885 1.130000e-136 497
29 TraesCS4D01G272900 chr5B 86.063 287 40 0 1774 2060 690906926 690907212 5.700000e-80 309
30 TraesCS4D01G272900 chr5B 86.034 179 25 0 4683 4861 690909322 690909500 5.990000e-45 193
31 TraesCS4D01G272900 chr5B 84.416 77 11 1 543 619 455507528 455507453 2.260000e-09 75
32 TraesCS4D01G272900 chr7D 93.897 213 13 0 1443 1655 180440130 180440342 7.330000e-84 322
33 TraesCS4D01G272900 chr6D 91.667 216 18 0 1443 1658 150886171 150885956 3.430000e-77 300
34 TraesCS4D01G272900 chr3A 91.667 216 18 0 1443 1658 703853064 703852849 3.430000e-77 300
35 TraesCS4D01G272900 chr7B 91.018 167 12 2 2532 2697 643031433 643031597 7.640000e-54 222
36 TraesCS4D01G272900 chr5A 79.365 189 32 5 479 665 673555420 673555237 6.160000e-25 126


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 TraesCS4D01G272900 chr4D 442894002 442899861 5859 False 3675.333333 10822 97.814000 1 5860 3 chr4D.!!$F1 5859
1 TraesCS4D01G272900 chr4A 24763261 24769593 6332 True 1224.833333 2817 88.848667 1 5860 6 chr4A.!!$R1 5859
2 TraesCS4D01G272900 chr4A 621564031 621567451 3420 True 473.250000 856 88.479750 1146 4861 4 chr4A.!!$R2 3715
3 TraesCS4D01G272900 chr4B 552013246 552018874 5628 False 1198.333333 2300 89.586833 199 5860 6 chr4B.!!$F1 5661
4 TraesCS4D01G272900 chr5D 547607269 547610661 3392 True 475.000000 845 88.669000 1146 4861 4 chr5D.!!$R1 3715
5 TraesCS4D01G272900 chrUn 68495178 68496565 1387 True 520.500000 839 89.286000 3546 4861 2 chrUn.!!$R1 1315
6 TraesCS4D01G272900 chrUn 68508357 68509191 834 True 410.500000 510 87.082000 1146 2036 2 chrUn.!!$R2 890
7 TraesCS4D01G272900 chr5B 690906368 690909500 3132 False 449.000000 797 86.207250 1146 4861 4 chr5B.!!$F1 3715

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
19 20 0.378257 CCGGAGAATGGAATGCAACG 59.622 55.000 0.00 0.0 0.00 4.10 F
558 614 1.361993 TTGCACGGCAATGTTCACC 59.638 52.632 7.15 0.0 43.99 4.02 F
2096 2566 0.179029 CACCCAGTGTTTTCCGGACT 60.179 55.000 1.83 0.0 0.00 3.85 F
2369 2975 0.108329 TGCTAGGCTTGCGACTAACC 60.108 55.000 15.83 0.0 28.11 2.85 F
3111 3774 0.250597 TGTGCTCATGTGCTGCTTCT 60.251 50.000 19.60 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1451 0.614979 CCCAGGACTTCTTCTCCGGA 60.615 60.0 2.93 2.93 32.45 5.14 R
2323 2922 0.670162 GCCACTGCTTTGCTTCTTGA 59.330 50.0 0.00 0.00 33.53 3.02 R
3092 3755 0.250597 AGAAGCAGCACATGAGCACA 60.251 50.0 17.61 0.00 36.85 4.57 R
4270 5225 0.319211 TTAACACCGCGACTGTCTGG 60.319 55.0 8.23 12.65 0.00 3.86 R
4867 5882 0.392998 CGCCACCTATTTCTGCCAGT 60.393 55.0 0.00 0.00 0.00 4.00 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
19 20 0.378257 CCGGAGAATGGAATGCAACG 59.622 55.000 0.00 0.00 0.00 4.10
23 24 3.181497 CGGAGAATGGAATGCAACGAAAT 60.181 43.478 0.00 0.00 0.00 2.17
38 39 5.790495 GCAACGAAATTTAGATCACACACTC 59.210 40.000 5.22 0.00 0.00 3.51
100 105 9.166173 CACACATGATAGAGTAGGAATCAAAAA 57.834 33.333 0.00 0.00 33.60 1.94
179 185 7.573283 GCCACAAAACCTATTCTTTAGAGACAC 60.573 40.741 0.00 0.00 0.00 3.67
190 196 6.764877 TCTTTAGAGACACGCAAAAACTAG 57.235 37.500 0.00 0.00 0.00 2.57
191 197 6.278363 TCTTTAGAGACACGCAAAAACTAGT 58.722 36.000 0.00 0.00 0.00 2.57
196 202 2.294479 CACGCAAAAACTAGTCCGTG 57.706 50.000 14.16 14.16 39.75 4.94
268 274 5.065218 CCGACTCAGGATTTGGTTATTTCTG 59.935 44.000 0.00 0.00 0.00 3.02
294 306 6.017770 TGTTACAACATCTAAAAGACCAACCG 60.018 38.462 0.00 0.00 33.17 4.44
430 452 5.473162 TGCATATTGACGATTTTATCTGGGG 59.527 40.000 0.00 0.00 0.00 4.96
453 475 9.533253 GGGGTTTCAATATAAATTTGACATCAG 57.467 33.333 0.00 0.00 33.03 2.90
454 476 9.533253 GGGTTTCAATATAAATTTGACATCAGG 57.467 33.333 0.00 0.00 33.03 3.86
474 496 9.771534 CATCAGGTTTTTAGGGTTAAAATTTGA 57.228 29.630 0.00 0.00 38.26 2.69
533 589 6.073657 CGGCATGACAATTTTTCTGTTGATTT 60.074 34.615 0.00 0.00 0.00 2.17
558 614 1.361993 TTGCACGGCAATGTTCACC 59.638 52.632 7.15 0.00 43.99 4.02
619 676 2.352503 ATCTGTTTTCGCATGGCAAC 57.647 45.000 0.00 0.00 0.00 4.17
630 687 1.660104 GCATGGCAACCATTTTTAGCG 59.340 47.619 0.00 0.00 42.23 4.26
663 720 6.934645 TCTGATGTCGGACTTTTAACATTTCT 59.065 34.615 9.88 0.00 32.70 2.52
666 723 6.295039 TGTCGGACTTTTAACATTTCTGTC 57.705 37.500 9.88 0.00 33.36 3.51
673 730 9.129209 GGACTTTTAACATTTCTGTCTATTTGC 57.871 33.333 0.00 0.00 33.36 3.68
688 745 5.118510 GTCTATTTGCGGTTTTGTTCCATTG 59.881 40.000 0.00 0.00 0.00 2.82
689 746 2.969628 TTGCGGTTTTGTTCCATTGT 57.030 40.000 0.00 0.00 0.00 2.71
692 749 3.600388 TGCGGTTTTGTTCCATTGTTTT 58.400 36.364 0.00 0.00 0.00 2.43
696 753 5.063564 GCGGTTTTGTTCCATTGTTTTAACA 59.936 36.000 0.00 0.00 37.08 2.41
811 1198 2.862674 TATTTGACGCTCGGGGGTGC 62.863 60.000 10.87 2.12 38.76 5.01
883 1300 4.570772 TCCGCTTACATGCTAAGCTAAAAG 59.429 41.667 24.58 15.18 45.55 2.27
899 1316 1.498865 AAAGAACACCTCACGCAGCG 61.499 55.000 14.82 14.82 0.00 5.18
1006 1428 2.031768 GATCTGCTCCGATGGCCC 59.968 66.667 0.00 0.00 0.00 5.80
1283 1722 4.796231 CCAAGCCGTACGCGCTCT 62.796 66.667 24.77 15.28 44.76 4.09
1284 1723 3.248171 CAAGCCGTACGCGCTCTC 61.248 66.667 24.77 5.14 44.76 3.20
1606 2058 2.398554 CGACCCCAACCGCAAGATG 61.399 63.158 0.00 0.00 43.02 2.90
1693 2152 0.390860 ACTCCCACGCTCTGATATGC 59.609 55.000 0.00 0.00 0.00 3.14
1694 2153 0.678395 CTCCCACGCTCTGATATGCT 59.322 55.000 0.00 0.00 0.00 3.79
1695 2154 0.676184 TCCCACGCTCTGATATGCTC 59.324 55.000 0.00 0.00 0.00 4.26
1767 2230 8.934697 TGATTCTGCTAGTTTTATACCCTGTAT 58.065 33.333 0.00 0.00 0.00 2.29
2037 2500 2.560504 CATATGCTTGCCGAGGTACAA 58.439 47.619 0.00 0.00 0.00 2.41
2045 2508 4.632688 GCTTGCCGAGGTACAATTTAGTTA 59.367 41.667 0.00 0.00 0.00 2.24
2068 2531 3.928992 TCTTGTCATCGATCTCTTTGTGC 59.071 43.478 0.00 0.00 0.00 4.57
2070 2533 1.590238 GTCATCGATCTCTTTGTGCCG 59.410 52.381 0.00 0.00 0.00 5.69
2090 2560 3.058501 CCGTTGATACACCCAGTGTTTTC 60.059 47.826 5.59 4.90 45.08 2.29
2095 2565 0.464916 ACACCCAGTGTTTTCCGGAC 60.465 55.000 1.83 0.00 45.08 4.79
2096 2566 0.179029 CACCCAGTGTTTTCCGGACT 60.179 55.000 1.83 0.00 0.00 3.85
2113 2583 7.145932 TCCGGACTACTTACTGTTAGTTTAC 57.854 40.000 0.00 0.00 0.00 2.01
2116 2598 6.521133 CGGACTACTTACTGTTAGTTTACACG 59.479 42.308 4.66 1.61 0.00 4.49
2145 2627 3.851098 ACAGTGAAGCGAGAAGGATAAC 58.149 45.455 0.00 0.00 0.00 1.89
2151 2633 3.983044 AGCGAGAAGGATAACAAGGTT 57.017 42.857 0.00 0.00 0.00 3.50
2187 2762 5.259632 AGGAGTTATTTCTCAGCTGCAAAT 58.740 37.500 20.69 20.69 36.30 2.32
2188 2763 5.125097 AGGAGTTATTTCTCAGCTGCAAATG 59.875 40.000 23.56 8.29 36.30 2.32
2205 2780 5.105269 TGCAAATGATAATGGCATTGACAGT 60.105 36.000 22.57 16.85 36.20 3.55
2249 2848 2.744202 AGATGGTTCTTAGCAGCAAACG 59.256 45.455 0.00 0.00 40.47 3.60
2258 2857 0.613260 AGCAGCAAACGATGAGGGTA 59.387 50.000 0.00 0.00 0.00 3.69
2266 2865 4.394920 GCAAACGATGAGGGTATTTTGAGA 59.605 41.667 0.00 0.00 0.00 3.27
2268 2867 6.719365 CAAACGATGAGGGTATTTTGAGATC 58.281 40.000 0.00 0.00 0.00 2.75
2270 2869 6.179906 ACGATGAGGGTATTTTGAGATCAT 57.820 37.500 0.00 0.00 0.00 2.45
2274 2873 6.566079 TGAGGGTATTTTGAGATCATGTCT 57.434 37.500 0.00 0.00 40.81 3.41
2291 2890 5.488919 TCATGTCTCATAGACCTTTCCCTTT 59.511 40.000 4.69 0.00 44.44 3.11
2298 2897 3.840124 AGACCTTTCCCTTTATAGCCG 57.160 47.619 0.00 0.00 0.00 5.52
2313 2912 1.585521 GCCGTCAGATGTACGTCGG 60.586 63.158 9.41 9.07 38.67 4.79
2323 2922 4.514441 CAGATGTACGTCGGTAACTATCCT 59.486 45.833 9.41 0.00 0.00 3.24
2362 2968 1.595489 CGCTTATTTGCTAGGCTTGCG 60.595 52.381 15.83 2.01 30.48 4.85
2369 2975 0.108329 TGCTAGGCTTGCGACTAACC 60.108 55.000 15.83 0.00 28.11 2.85
2414 3020 6.739112 ACTTTCTTGTGGCTTAACTGAAATC 58.261 36.000 0.00 0.00 0.00 2.17
2419 3032 7.147312 TCTTGTGGCTTAACTGAAATCAAATG 58.853 34.615 0.00 0.00 0.00 2.32
2423 3036 5.538053 TGGCTTAACTGAAATCAAATGACCA 59.462 36.000 0.00 0.00 0.00 4.02
2425 3038 6.753744 GGCTTAACTGAAATCAAATGACCATC 59.246 38.462 0.00 0.00 0.00 3.51
2428 3041 5.320549 ACTGAAATCAAATGACCATCAGC 57.679 39.130 15.96 0.00 36.04 4.26
2435 3048 5.894298 TCAAATGACCATCAGCCTAGTAT 57.106 39.130 0.00 0.00 0.00 2.12
2443 3056 4.716784 ACCATCAGCCTAGTATTGAGTCAA 59.283 41.667 8.27 8.27 0.00 3.18
2450 3063 7.070447 TCAGCCTAGTATTGAGTCAATGAATCT 59.930 37.037 25.48 18.82 35.54 2.40
2467 3080 8.403236 CAATGAATCTGAGTATGAAAGAATGCA 58.597 33.333 0.00 0.00 0.00 3.96
2471 3084 3.943381 CTGAGTATGAAAGAATGCAGCCA 59.057 43.478 0.00 0.00 0.00 4.75
2481 3094 2.961062 AGAATGCAGCCAGTGAAGTTTT 59.039 40.909 0.00 0.00 0.00 2.43
2537 3151 4.766373 TCATCATGGTGCAGTTGTGTTATT 59.234 37.500 0.00 0.00 0.00 1.40
2550 3164 7.083858 CAGTTGTGTTATTTTAGGTGTGATGG 58.916 38.462 0.00 0.00 0.00 3.51
2642 3261 8.429641 TCCAAGGACATAAATTAGTATGGAGTC 58.570 37.037 2.94 0.00 36.04 3.36
2661 3281 6.443849 TGGAGTCCCAACAGTAGAAATATTCT 59.556 38.462 6.74 0.00 40.09 2.40
2699 3323 1.327303 TTGGTGCGCTCAAAATTCCT 58.673 45.000 9.73 0.00 0.00 3.36
2702 3326 2.227865 TGGTGCGCTCAAAATTCCTTAC 59.772 45.455 9.73 0.00 0.00 2.34
2712 3336 5.385198 TCAAAATTCCTTACCTTGTCTGCT 58.615 37.500 0.00 0.00 0.00 4.24
2723 3347 3.072184 ACCTTGTCTGCTGATGAACTTCT 59.928 43.478 0.00 0.00 0.00 2.85
2725 3349 3.758755 TGTCTGCTGATGAACTTCTGT 57.241 42.857 0.00 0.00 0.00 3.41
2727 3351 2.999355 GTCTGCTGATGAACTTCTGTCC 59.001 50.000 0.00 0.00 0.00 4.02
2728 3352 2.634453 TCTGCTGATGAACTTCTGTCCA 59.366 45.455 0.00 0.00 0.00 4.02
2866 3493 6.486657 TGAAGGATATACAAAATAGTGCTGGC 59.513 38.462 0.00 0.00 0.00 4.85
2869 3496 2.483014 TACAAAATAGTGCTGGCGGT 57.517 45.000 0.00 0.00 0.00 5.68
2951 3582 1.888512 AGCTTGCACCTTGGTTACATG 59.111 47.619 0.00 0.00 0.00 3.21
2965 3596 5.953183 TGGTTACATGTCAAAATCAGATGC 58.047 37.500 0.00 0.00 0.00 3.91
2972 3632 6.986231 ACATGTCAAAATCAGATGCGAGTATA 59.014 34.615 0.00 0.00 0.00 1.47
2973 3633 7.658982 ACATGTCAAAATCAGATGCGAGTATAT 59.341 33.333 0.00 0.00 0.00 0.86
3001 3661 4.563140 TGTTGGGACTTGGTAGGTTATC 57.437 45.455 0.00 0.00 0.00 1.75
3010 3670 5.896073 CTTGGTAGGTTATCAAGGGAGAT 57.104 43.478 1.94 0.00 41.96 2.75
3050 3713 0.809385 ATGTGCTCATGTGCTGCTTC 59.191 50.000 19.60 6.84 32.51 3.86
3061 3724 3.282021 TGTGCTGCTTCTTGAACTTCTT 58.718 40.909 0.00 0.00 0.00 2.52
3062 3725 4.450976 TGTGCTGCTTCTTGAACTTCTTA 58.549 39.130 0.00 0.00 0.00 2.10
3063 3726 5.065914 TGTGCTGCTTCTTGAACTTCTTAT 58.934 37.500 0.00 0.00 0.00 1.73
3064 3727 5.180117 TGTGCTGCTTCTTGAACTTCTTATC 59.820 40.000 0.00 0.00 0.00 1.75
3065 3728 5.180117 GTGCTGCTTCTTGAACTTCTTATCA 59.820 40.000 0.00 0.00 0.00 2.15
3066 3729 5.764686 TGCTGCTTCTTGAACTTCTTATCAA 59.235 36.000 0.00 0.00 34.57 2.57
3067 3730 6.432162 TGCTGCTTCTTGAACTTCTTATCAAT 59.568 34.615 0.00 0.00 35.20 2.57
3068 3731 7.040201 TGCTGCTTCTTGAACTTCTTATCAATT 60.040 33.333 0.00 0.00 35.20 2.32
3069 3732 7.272948 GCTGCTTCTTGAACTTCTTATCAATTG 59.727 37.037 0.00 0.00 35.20 2.32
3070 3733 7.086376 TGCTTCTTGAACTTCTTATCAATTGC 58.914 34.615 0.00 0.00 35.20 3.56
3071 3734 7.040201 TGCTTCTTGAACTTCTTATCAATTGCT 60.040 33.333 0.00 0.00 35.20 3.91
3072 3735 8.454106 GCTTCTTGAACTTCTTATCAATTGCTA 58.546 33.333 0.00 0.00 35.20 3.49
3076 3739 9.512435 CTTGAACTTCTTATCAATTGCTAATGG 57.488 33.333 0.00 0.00 35.20 3.16
3077 3740 8.579850 TGAACTTCTTATCAATTGCTAATGGT 57.420 30.769 0.00 0.00 0.00 3.55
3078 3741 9.023962 TGAACTTCTTATCAATTGCTAATGGTT 57.976 29.630 0.00 7.20 0.00 3.67
3079 3742 9.508567 GAACTTCTTATCAATTGCTAATGGTTC 57.491 33.333 16.55 16.55 0.00 3.62
3080 3743 8.000780 ACTTCTTATCAATTGCTAATGGTTCC 57.999 34.615 0.00 0.00 0.00 3.62
3081 3744 7.836183 ACTTCTTATCAATTGCTAATGGTTCCT 59.164 33.333 0.00 0.00 0.00 3.36
3082 3745 9.342308 CTTCTTATCAATTGCTAATGGTTCCTA 57.658 33.333 0.00 0.00 0.00 2.94
3083 3746 9.866655 TTCTTATCAATTGCTAATGGTTCCTAT 57.133 29.630 0.00 0.00 0.00 2.57
3084 3747 9.288576 TCTTATCAATTGCTAATGGTTCCTATG 57.711 33.333 0.00 0.00 0.00 2.23
3085 3748 5.772825 TCAATTGCTAATGGTTCCTATGC 57.227 39.130 0.00 0.00 0.00 3.14
3086 3749 5.448654 TCAATTGCTAATGGTTCCTATGCT 58.551 37.500 0.00 0.00 0.00 3.79
3087 3750 5.532406 TCAATTGCTAATGGTTCCTATGCTC 59.468 40.000 0.00 0.00 0.00 4.26
3088 3751 4.778213 TTGCTAATGGTTCCTATGCTCT 57.222 40.909 0.00 0.00 0.00 4.09
3089 3752 4.077300 TGCTAATGGTTCCTATGCTCTG 57.923 45.455 0.00 0.00 0.00 3.35
3090 3753 3.455910 TGCTAATGGTTCCTATGCTCTGT 59.544 43.478 0.00 0.00 0.00 3.41
3091 3754 4.653801 TGCTAATGGTTCCTATGCTCTGTA 59.346 41.667 0.00 0.00 0.00 2.74
3092 3755 5.307976 TGCTAATGGTTCCTATGCTCTGTAT 59.692 40.000 0.00 0.00 0.00 2.29
3093 3756 5.641209 GCTAATGGTTCCTATGCTCTGTATG 59.359 44.000 0.00 0.00 0.00 2.39
3094 3757 5.636903 AATGGTTCCTATGCTCTGTATGT 57.363 39.130 0.00 0.00 0.00 2.29
3095 3758 4.406648 TGGTTCCTATGCTCTGTATGTG 57.593 45.455 0.00 0.00 0.00 3.21
3096 3759 3.134458 GGTTCCTATGCTCTGTATGTGC 58.866 50.000 0.00 0.00 35.88 4.57
3097 3760 3.181461 GGTTCCTATGCTCTGTATGTGCT 60.181 47.826 0.00 0.00 36.27 4.40
3098 3761 4.054671 GTTCCTATGCTCTGTATGTGCTC 58.945 47.826 0.00 0.00 36.27 4.26
3099 3762 3.299503 TCCTATGCTCTGTATGTGCTCA 58.700 45.455 0.00 0.00 36.27 4.26
3100 3763 3.899980 TCCTATGCTCTGTATGTGCTCAT 59.100 43.478 6.50 6.50 36.27 2.90
3101 3764 3.995048 CCTATGCTCTGTATGTGCTCATG 59.005 47.826 11.46 0.00 36.27 3.07
3102 3765 3.555527 ATGCTCTGTATGTGCTCATGT 57.444 42.857 11.46 0.00 36.27 3.21
3103 3766 2.624636 TGCTCTGTATGTGCTCATGTG 58.375 47.619 11.46 2.08 36.27 3.21
3104 3767 1.329906 GCTCTGTATGTGCTCATGTGC 59.670 52.381 12.78 12.78 35.70 4.57
3105 3768 2.902523 CTCTGTATGTGCTCATGTGCT 58.097 47.619 19.60 3.52 35.70 4.40
3106 3769 2.608090 CTCTGTATGTGCTCATGTGCTG 59.392 50.000 19.60 6.09 35.70 4.41
3107 3770 1.063616 CTGTATGTGCTCATGTGCTGC 59.936 52.381 19.60 12.98 35.70 5.25
3108 3771 1.339342 TGTATGTGCTCATGTGCTGCT 60.339 47.619 19.60 7.37 35.70 4.24
3109 3772 1.741706 GTATGTGCTCATGTGCTGCTT 59.258 47.619 19.60 12.67 35.70 3.91
3110 3773 0.809385 ATGTGCTCATGTGCTGCTTC 59.191 50.000 19.60 6.84 32.51 3.86
3111 3774 0.250597 TGTGCTCATGTGCTGCTTCT 60.251 50.000 19.60 0.00 0.00 2.85
3112 3775 0.879765 GTGCTCATGTGCTGCTTCTT 59.120 50.000 19.60 0.00 0.00 2.52
3113 3776 0.879090 TGCTCATGTGCTGCTTCTTG 59.121 50.000 19.60 3.46 0.00 3.02
3114 3777 1.162698 GCTCATGTGCTGCTTCTTGA 58.837 50.000 12.42 7.36 0.00 3.02
3115 3778 1.538512 GCTCATGTGCTGCTTCTTGAA 59.461 47.619 12.42 0.00 0.00 2.69
3116 3779 2.163815 GCTCATGTGCTGCTTCTTGAAT 59.836 45.455 12.42 0.00 0.00 2.57
3117 3780 3.367087 GCTCATGTGCTGCTTCTTGAATT 60.367 43.478 12.42 0.00 0.00 2.17
3118 3781 4.806330 CTCATGTGCTGCTTCTTGAATTT 58.194 39.130 0.00 0.00 0.00 1.82
3119 3782 4.801891 TCATGTGCTGCTTCTTGAATTTC 58.198 39.130 0.00 0.00 0.00 2.17
3161 3828 3.009805 GGTAGAGGCTTTGGAAAAGGGTA 59.990 47.826 2.19 0.00 0.00 3.69
3187 3854 6.509418 TTTCTTTATGCAGTGGGTTGTATC 57.491 37.500 0.00 0.00 0.00 2.24
3194 3861 3.509575 TGCAGTGGGTTGTATCCAATTTC 59.490 43.478 0.00 0.00 35.86 2.17
3195 3862 3.119137 GCAGTGGGTTGTATCCAATTTCC 60.119 47.826 0.00 0.00 35.86 3.13
3205 3874 7.384932 GGTTGTATCCAATTTCCAAGTTTTCTG 59.615 37.037 0.00 0.00 32.11 3.02
3213 3882 4.935352 TTCCAAGTTTTCTGGATTGTGG 57.065 40.909 0.00 0.00 31.12 4.17
3243 3912 9.260002 TCATTTTCTTTATTTTTGGAAGACTGC 57.740 29.630 0.00 0.00 0.00 4.40
3245 3914 9.783081 ATTTTCTTTATTTTTGGAAGACTGCAT 57.217 25.926 0.00 0.00 0.00 3.96
3254 3954 6.839124 TTTGGAAGACTGCATATTTCATGT 57.161 33.333 0.00 0.00 0.00 3.21
3272 3972 4.079844 TCATGTATGGGGCATCTTTGAAGA 60.080 41.667 0.00 0.00 39.78 2.87
3299 4006 8.537858 TGATAGTTTTAGGACTAGAAAGAACCC 58.462 37.037 0.00 0.00 35.72 4.11
3306 4013 8.763984 TTAGGACTAGAAAGAACCCTATACTG 57.236 38.462 0.00 0.00 0.00 2.74
3311 4018 5.422214 AGAAAGAACCCTATACTGTGGTG 57.578 43.478 0.00 0.00 31.32 4.17
3342 4049 9.800433 CTATGTAATTGGTTAATTGCACATTCA 57.200 29.630 5.83 0.00 46.67 2.57
3401 4178 5.633601 GCTGGTGTTATTGCCTTAGTTTTTC 59.366 40.000 0.00 0.00 0.00 2.29
3408 4185 8.261522 TGTTATTGCCTTAGTTTTTCCAAGTTT 58.738 29.630 0.00 0.00 0.00 2.66
3409 4186 9.104965 GTTATTGCCTTAGTTTTTCCAAGTTTT 57.895 29.630 0.00 0.00 0.00 2.43
3445 4222 6.312918 GCGTTGATATACTTTCAGTCCTCAAA 59.687 38.462 0.00 0.00 28.60 2.69
3488 4265 9.503427 GTGGATAATCTTTTGTAATGCTTGTAC 57.497 33.333 0.00 0.00 0.00 2.90
3502 4279 2.928116 GCTTGTACCTGTCGGTGTAATC 59.072 50.000 0.00 0.00 45.18 1.75
3542 4322 8.621532 TTCAACTAGCCTTGGCTATATAATTG 57.378 34.615 20.15 17.36 0.00 2.32
3586 4405 7.015098 TGTGATTGTTTCTGTTTCCATATGGTT 59.985 33.333 21.28 0.00 36.34 3.67
3648 4495 2.828520 TCTCTTCTCTGCGACCTTCAAT 59.171 45.455 0.00 0.00 0.00 2.57
3677 4524 4.338400 AGTGAAGGAGTTTGTTACAAAGGC 59.662 41.667 11.07 6.10 0.00 4.35
4060 4929 4.212425 CGTGCTATTTTGACACACCAGTTA 59.788 41.667 0.00 0.00 33.89 2.24
4250 5193 9.894783 GTCTATTATGTACATACACCACTGTAG 57.105 37.037 15.20 7.78 39.30 2.74
4251 5194 8.573885 TCTATTATGTACATACACCACTGTAGC 58.426 37.037 15.20 0.00 39.30 3.58
4277 5232 1.227527 TCAACACCGTGCCAGACAG 60.228 57.895 0.00 0.00 0.00 3.51
4279 5234 1.227556 AACACCGTGCCAGACAGTC 60.228 57.895 0.00 0.00 0.00 3.51
4280 5235 2.734723 CACCGTGCCAGACAGTCG 60.735 66.667 0.00 0.00 0.00 4.18
4281 5236 4.664677 ACCGTGCCAGACAGTCGC 62.665 66.667 0.00 0.00 0.00 5.19
4288 5243 1.287815 CCAGACAGTCGCGGTGTTA 59.712 57.895 14.89 0.00 0.00 2.41
4316 5272 7.075148 AGGAATTAAATGGCTTGGGATAATGA 58.925 34.615 0.00 0.00 0.00 2.57
4333 5289 7.556275 GGGATAATGACAGATTGAACCTGTTAA 59.444 37.037 0.00 0.00 44.14 2.01
4334 5290 8.398665 GGATAATGACAGATTGAACCTGTTAAC 58.601 37.037 0.00 0.00 44.14 2.01
4338 5294 5.705441 TGACAGATTGAACCTGTTAACCATC 59.295 40.000 2.48 0.00 44.14 3.51
4369 5325 5.450376 AACACGCTACATTTAGTCAATCG 57.550 39.130 0.00 0.00 0.00 3.34
4395 5351 3.010420 GCCTGTTTGTTCTAGCCTAAGG 58.990 50.000 0.00 0.00 0.00 2.69
4396 5352 3.307480 GCCTGTTTGTTCTAGCCTAAGGA 60.307 47.826 0.00 0.00 0.00 3.36
4498 5468 9.018582 TGATGTGACCATTGTTTGTTGATTATA 57.981 29.630 0.00 0.00 0.00 0.98
4506 5476 9.507280 CCATTGTTTGTTGATTATAGATGTCAC 57.493 33.333 0.00 0.00 0.00 3.67
4507 5477 9.213819 CATTGTTTGTTGATTATAGATGTCACG 57.786 33.333 0.00 0.00 0.00 4.35
4508 5478 7.899178 TGTTTGTTGATTATAGATGTCACGT 57.101 32.000 0.00 0.00 0.00 4.49
4509 5479 8.317891 TGTTTGTTGATTATAGATGTCACGTT 57.682 30.769 0.00 0.00 0.00 3.99
4516 5486 7.240674 TGATTATAGATGTCACGTTTGTTTGC 58.759 34.615 0.00 0.00 0.00 3.68
4519 5489 2.942376 AGATGTCACGTTTGTTTGCTCA 59.058 40.909 0.00 0.00 0.00 4.26
4525 5495 4.560819 GTCACGTTTGTTTGCTCATTTTCA 59.439 37.500 0.00 0.00 0.00 2.69
4527 5497 5.809562 TCACGTTTGTTTGCTCATTTTCATT 59.190 32.000 0.00 0.00 0.00 2.57
4568 5539 8.743714 GTTGTGATTTCCTATTTCTGGAGATTT 58.256 33.333 0.00 0.00 34.76 2.17
4617 5588 9.460019 TTTCATGATTTATCAGTTGGACACATA 57.540 29.630 0.00 0.00 40.64 2.29
4618 5589 9.460019 TTCATGATTTATCAGTTGGACACATAA 57.540 29.630 0.00 0.00 40.64 1.90
4626 5597 9.733556 TTATCAGTTGGACACATAATAAGTTGT 57.266 29.630 0.00 0.00 0.00 3.32
4627 5598 7.433708 TCAGTTGGACACATAATAAGTTGTG 57.566 36.000 1.74 1.74 46.76 3.33
4667 5674 5.183331 TGAGTTAATCGCTGTTGAGTAGAGT 59.817 40.000 0.00 0.00 0.00 3.24
4692 5699 4.700213 GCTTATCTTGTGGCCTAACTGAAA 59.300 41.667 3.32 0.00 0.00 2.69
4893 5908 2.166254 CAGAAATAGGTGGCGGCAAATT 59.834 45.455 15.50 11.35 0.00 1.82
4967 5982 2.483106 CAGATGCTTGTGTCTGGAGTTG 59.517 50.000 0.00 0.00 38.50 3.16
5010 6025 3.897505 TGCGATGAATTCTATGAGGGAGA 59.102 43.478 7.05 0.00 0.00 3.71
5022 6039 7.937700 TCTATGAGGGAGAGTCCATTTTTAT 57.062 36.000 0.00 0.00 38.64 1.40
5050 6086 4.348656 GTTCGTTTGAGGTTTTCAAGTCC 58.651 43.478 0.00 0.00 46.01 3.85
5076 6112 1.466950 ACACACGCCCATGTAATTTCG 59.533 47.619 0.00 0.00 0.00 3.46
5082 6118 3.119990 ACGCCCATGTAATTTCGTTTGAG 60.120 43.478 0.00 0.00 0.00 3.02
5137 6184 3.302935 GCATGTGTACAGATTGATCGCAG 60.303 47.826 2.09 0.00 0.00 5.18
5168 6215 4.860802 ACAAGATTCATCCCCATGTGTA 57.139 40.909 0.00 0.00 0.00 2.90
5190 6237 9.722056 GTGTAAGAATGTACATGATTGATTTCC 57.278 33.333 9.63 0.00 36.42 3.13
5194 6241 8.674263 AGAATGTACATGATTGATTTCCTCTC 57.326 34.615 9.63 0.00 0.00 3.20
5220 6267 1.854126 CTGTTGGCACGCAAGAAAAAG 59.146 47.619 0.00 0.00 43.62 2.27
5222 6269 1.107114 TTGGCACGCAAGAAAAAGGA 58.893 45.000 0.00 0.00 43.62 3.36
5224 6271 1.066908 TGGCACGCAAGAAAAAGGAAG 59.933 47.619 0.00 0.00 43.62 3.46
5225 6272 1.067060 GGCACGCAAGAAAAAGGAAGT 59.933 47.619 0.00 0.00 43.62 3.01
5254 6301 3.996614 TCGTGCTCGATGACCTGA 58.003 55.556 6.80 0.00 41.35 3.86
5376 6423 2.735772 CCGGGCTGCTCAGGTACAT 61.736 63.158 0.00 0.00 0.00 2.29
5441 6488 3.567164 AGACTGTCCAAGCAAATCACAAG 59.433 43.478 3.76 0.00 0.00 3.16
5445 6492 2.028748 GTCCAAGCAAATCACAAGCCAT 60.029 45.455 0.00 0.00 0.00 4.40
5468 6515 2.097680 TCATCAGTGAGCAATGCGAA 57.902 45.000 0.00 0.00 0.00 4.70
5471 6518 1.089112 TCAGTGAGCAATGCGAATGG 58.911 50.000 0.00 0.00 0.00 3.16
5472 6519 1.089112 CAGTGAGCAATGCGAATGGA 58.911 50.000 0.00 0.00 0.00 3.41
5473 6520 1.674441 CAGTGAGCAATGCGAATGGAT 59.326 47.619 0.00 0.00 0.00 3.41
5528 6599 1.156736 CGATGGTGGTGAACTTGGAC 58.843 55.000 0.00 0.00 0.00 4.02
5564 6635 1.226831 GCGCTTCTTCCTCTCCTCG 60.227 63.158 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.072230 TGTGATCTAAATTTCGTTGCATTCCA 60.072 34.615 0.00 0.00 0.00 3.53
18 19 7.036220 ACTAGGAGTGTGTGATCTAAATTTCG 58.964 38.462 0.00 0.00 0.00 3.46
19 20 8.779354 AACTAGGAGTGTGTGATCTAAATTTC 57.221 34.615 0.00 0.00 0.00 2.17
23 24 8.618677 CGTATAACTAGGAGTGTGTGATCTAAA 58.381 37.037 0.00 0.00 0.00 1.85
38 39 1.137513 GGCTTGCGCGTATAACTAGG 58.862 55.000 8.43 0.00 36.88 3.02
100 105 5.687166 TTCCCATGGTTTCTCTAATACGT 57.313 39.130 11.73 0.00 0.00 3.57
155 160 7.510630 CGTGTCTCTAAAGAATAGGTTTTGTG 58.489 38.462 0.00 0.00 31.93 3.33
179 185 3.924686 ACTATCACGGACTAGTTTTTGCG 59.075 43.478 0.00 0.00 0.00 4.85
190 196 4.038883 AGTGGCCTATAAACTATCACGGAC 59.961 45.833 3.32 0.00 0.00 4.79
191 197 4.220724 AGTGGCCTATAAACTATCACGGA 58.779 43.478 3.32 0.00 0.00 4.69
268 274 7.136772 GGTTGGTCTTTTAGATGTTGTAACAC 58.863 38.462 0.00 0.00 42.51 3.32
318 331 3.576648 ACTCTCGAGTTGGATTTTCGAC 58.423 45.455 13.13 0.00 38.83 4.20
379 392 4.158579 TGCCGGCAATTTGATACAACAATA 59.841 37.500 30.74 0.00 0.00 1.90
413 426 4.912586 TGAAACCCCAGATAAAATCGTCA 58.087 39.130 0.00 0.00 0.00 4.35
415 428 9.635404 TTATATTGAAACCCCAGATAAAATCGT 57.365 29.630 0.00 0.00 0.00 3.73
444 466 7.899648 TTTAACCCTAAAAACCTGATGTCAA 57.100 32.000 0.00 0.00 0.00 3.18
453 475 7.227116 GGGTGTCAAATTTTAACCCTAAAAACC 59.773 37.037 19.12 9.11 45.93 3.27
454 476 8.145316 GGGTGTCAAATTTTAACCCTAAAAAC 57.855 34.615 19.12 2.61 45.93 2.43
474 496 0.250793 TATGCGTTCAATCGGGGTGT 59.749 50.000 0.00 0.00 0.00 4.16
509 565 6.790285 AATCAACAGAAAAATTGTCATGCC 57.210 33.333 0.00 0.00 0.00 4.40
558 614 9.594038 GTGTATAATAATTTGCCATGTTCTACG 57.406 33.333 0.00 0.00 0.00 3.51
630 687 5.803020 AAGTCCGACATCAGATTTTTAGC 57.197 39.130 0.40 0.00 0.00 3.09
663 720 3.632604 TGGAACAAAACCGCAAATAGACA 59.367 39.130 0.00 0.00 31.92 3.41
673 730 6.648725 TGTTAAAACAATGGAACAAAACCG 57.351 33.333 0.00 0.00 36.23 4.44
727 796 9.147732 ACCTTAGTTTTTCCATTCTTTCAGAAT 57.852 29.630 0.00 0.00 45.23 2.40
739 808 5.245075 CAGCCCAATAACCTTAGTTTTTCCA 59.755 40.000 0.00 0.00 37.42 3.53
741 810 6.156519 CACAGCCCAATAACCTTAGTTTTTC 58.843 40.000 0.00 0.00 37.42 2.29
873 1290 3.744426 GCGTGAGGTGTTCTTTTAGCTTA 59.256 43.478 0.00 0.00 0.00 3.09
883 1300 4.077188 GCGCTGCGTGAGGTGTTC 62.077 66.667 24.04 0.00 0.00 3.18
899 1316 4.399303 CGATTTGGGAGGGGATTATATTGC 59.601 45.833 0.00 0.00 0.00 3.56
929 1350 2.427905 GTTCGCGTTTTTCCGGGC 60.428 61.111 5.77 0.00 40.21 6.13
1029 1451 0.614979 CCCAGGACTTCTTCTCCGGA 60.615 60.000 2.93 2.93 32.45 5.14
1117 1539 3.160748 GGAGGAGCAGGAGGAGGC 61.161 72.222 0.00 0.00 0.00 4.70
1123 1545 2.693017 GGAGGAGGAGGAGCAGGA 59.307 66.667 0.00 0.00 0.00 3.86
1125 1547 3.535962 GCGGAGGAGGAGGAGCAG 61.536 72.222 0.00 0.00 0.00 4.24
1693 2152 4.100653 TCCAATAACCAGATGAGAGCAGAG 59.899 45.833 0.00 0.00 0.00 3.35
1694 2153 4.033009 TCCAATAACCAGATGAGAGCAGA 58.967 43.478 0.00 0.00 0.00 4.26
1695 2154 4.412796 TCCAATAACCAGATGAGAGCAG 57.587 45.455 0.00 0.00 0.00 4.24
1768 2231 8.906867 CCAACCAATCAGAATCAGTACATTATT 58.093 33.333 0.00 0.00 0.00 1.40
1769 2232 8.055181 ACCAACCAATCAGAATCAGTACATTAT 58.945 33.333 0.00 0.00 0.00 1.28
2045 2508 4.569966 GCACAAAGAGATCGATGACAAGAT 59.430 41.667 0.54 0.00 0.00 2.40
2061 2524 1.199097 GGGTGTATCAACGGCACAAAG 59.801 52.381 0.00 0.00 35.05 2.77
2068 2531 2.178912 AACACTGGGTGTATCAACGG 57.821 50.000 3.69 0.00 46.79 4.44
2070 2533 3.058501 CGGAAAACACTGGGTGTATCAAC 60.059 47.826 3.69 0.00 46.79 3.18
2090 2560 6.803807 GTGTAAACTAACAGTAAGTAGTCCGG 59.196 42.308 0.00 0.00 0.00 5.14
2095 2565 7.663664 CATGCGTGTAAACTAACAGTAAGTAG 58.336 38.462 0.00 0.00 0.00 2.57
2096 2566 6.089820 GCATGCGTGTAAACTAACAGTAAGTA 59.910 38.462 0.00 0.00 0.00 2.24
2113 2583 1.464687 GCTTCACTGTTAGCATGCGTG 60.465 52.381 13.01 13.80 37.35 5.34
2116 2598 1.061711 CTCGCTTCACTGTTAGCATGC 59.938 52.381 10.51 10.51 37.23 4.06
2163 2738 5.420725 TTGCAGCTGAGAAATAACTCCTA 57.579 39.130 20.43 0.00 36.22 2.94
2187 2762 9.571816 TGAATATTACTGTCAATGCCATTATCA 57.428 29.630 0.00 0.00 0.00 2.15
2233 2832 3.181516 CCTCATCGTTTGCTGCTAAGAAC 60.182 47.826 0.00 0.42 0.00 3.01
2249 2848 7.222872 AGACATGATCTCAAAATACCCTCATC 58.777 38.462 0.00 0.00 28.16 2.92
2266 2865 5.222870 AGGGAAAGGTCTATGAGACATGAT 58.777 41.667 0.00 0.00 46.79 2.45
2268 2867 5.365021 AAGGGAAAGGTCTATGAGACATG 57.635 43.478 8.77 0.00 46.79 3.21
2270 2869 7.202011 GCTATAAAGGGAAAGGTCTATGAGACA 60.202 40.741 8.77 0.00 46.79 3.41
2274 2873 5.011738 CGGCTATAAAGGGAAAGGTCTATGA 59.988 44.000 0.00 0.00 0.00 2.15
2276 2875 4.906060 ACGGCTATAAAGGGAAAGGTCTAT 59.094 41.667 0.00 0.00 0.00 1.98
2285 2884 3.305720 ACATCTGACGGCTATAAAGGGA 58.694 45.455 0.00 0.00 0.00 4.20
2291 2890 2.477754 CGACGTACATCTGACGGCTATA 59.522 50.000 0.00 0.00 46.39 1.31
2298 2897 3.754188 AGTTACCGACGTACATCTGAC 57.246 47.619 0.00 0.00 0.00 3.51
2313 2912 5.643777 TGCTTTGCTTCTTGAGGATAGTTAC 59.356 40.000 0.00 0.00 29.59 2.50
2323 2922 0.670162 GCCACTGCTTTGCTTCTTGA 59.330 50.000 0.00 0.00 33.53 3.02
2343 2949 1.670811 TCGCAAGCCTAGCAAATAAGC 59.329 47.619 0.00 0.00 37.18 3.09
2348 2954 2.073816 GTTAGTCGCAAGCCTAGCAAA 58.926 47.619 0.00 0.00 37.18 3.68
2362 2968 2.355209 CCCAAGAGGAAGCAGGTTAGTC 60.355 54.545 0.00 0.00 38.24 2.59
2369 2975 1.280457 ACCTACCCAAGAGGAAGCAG 58.720 55.000 0.00 0.00 39.89 4.24
2407 3013 4.401519 AGGCTGATGGTCATTTGATTTCAG 59.598 41.667 10.53 10.53 33.83 3.02
2414 3020 6.057533 TCAATACTAGGCTGATGGTCATTTG 58.942 40.000 0.00 0.00 0.00 2.32
2419 3032 4.342378 TGACTCAATACTAGGCTGATGGTC 59.658 45.833 0.00 0.11 0.00 4.02
2423 3036 6.737720 TCATTGACTCAATACTAGGCTGAT 57.262 37.500 3.88 0.00 32.35 2.90
2425 3038 7.171167 CAGATTCATTGACTCAATACTAGGCTG 59.829 40.741 3.88 4.66 32.35 4.85
2428 3041 8.420222 ACTCAGATTCATTGACTCAATACTAGG 58.580 37.037 3.88 0.00 32.35 3.02
2435 3048 9.159364 CTTTCATACTCAGATTCATTGACTCAA 57.841 33.333 6.76 0.00 0.00 3.02
2443 3056 7.255173 GCTGCATTCTTTCATACTCAGATTCAT 60.255 37.037 0.00 0.00 0.00 2.57
2450 3063 3.943381 CTGGCTGCATTCTTTCATACTCA 59.057 43.478 0.50 0.00 0.00 3.41
2467 3080 4.137543 CAGGAGTAAAAACTTCACTGGCT 58.862 43.478 0.00 0.00 0.00 4.75
2471 3084 8.152023 AGGATATCAGGAGTAAAAACTTCACT 57.848 34.615 4.83 0.00 0.00 3.41
2481 3094 5.074746 TGCCACTAGGATATCAGGAGTAA 57.925 43.478 4.83 0.00 36.89 2.24
2537 3151 2.432444 CTTTCGGCCATCACACCTAAA 58.568 47.619 2.24 0.00 0.00 1.85
2550 3164 1.936547 CAGATACCAAGAGCTTTCGGC 59.063 52.381 0.00 0.00 42.19 5.54
2603 3222 3.454082 TGTCCTTGGAAAACAAATGCCTT 59.546 39.130 0.00 0.00 38.91 4.35
2604 3223 3.037549 TGTCCTTGGAAAACAAATGCCT 58.962 40.909 0.00 0.00 38.91 4.75
2633 3252 5.416271 TTTCTACTGTTGGGACTCCATAC 57.584 43.478 0.00 0.00 43.63 2.39
2683 3307 2.488153 AGGTAAGGAATTTTGAGCGCAC 59.512 45.455 11.47 3.13 0.00 5.34
2684 3308 2.790433 AGGTAAGGAATTTTGAGCGCA 58.210 42.857 11.47 0.00 0.00 6.09
2699 3323 4.623932 AGTTCATCAGCAGACAAGGTAA 57.376 40.909 0.00 0.00 0.00 2.85
2702 3326 3.436015 CAGAAGTTCATCAGCAGACAAGG 59.564 47.826 5.50 0.00 0.00 3.61
2712 3336 2.607038 CGTCGTGGACAGAAGTTCATCA 60.607 50.000 5.50 0.00 35.23 3.07
2723 3347 3.740397 CCCGCTACGTCGTGGACA 61.740 66.667 20.34 0.00 36.68 4.02
2727 3351 3.411418 ATGAGCCCGCTACGTCGTG 62.411 63.158 8.47 0.00 0.00 4.35
2728 3352 3.138798 ATGAGCCCGCTACGTCGT 61.139 61.111 2.21 2.21 0.00 4.34
2887 3514 7.985184 TGTCACAGTCAAAAGTAGTCAATTACT 59.015 33.333 0.00 0.00 42.62 2.24
2888 3515 8.138365 TGTCACAGTCAAAAGTAGTCAATTAC 57.862 34.615 0.00 0.00 0.00 1.89
2951 3582 9.162793 CAAAATATACTCGCATCTGATTTTGAC 57.837 33.333 10.25 0.00 41.77 3.18
2965 3596 7.553881 AGTCCCAACATTCAAAATATACTCG 57.446 36.000 0.00 0.00 0.00 4.18
2972 3632 5.245977 CCTACCAAGTCCCAACATTCAAAAT 59.754 40.000 0.00 0.00 0.00 1.82
2973 3633 4.586841 CCTACCAAGTCCCAACATTCAAAA 59.413 41.667 0.00 0.00 0.00 2.44
3001 3661 6.214412 AGCATAGGAATAGGTTATCTCCCTTG 59.786 42.308 0.00 0.00 33.35 3.61
3010 3670 7.444183 GCACATACAAAGCATAGGAATAGGTTA 59.556 37.037 0.00 0.00 0.00 2.85
3016 3676 5.439721 TGAGCACATACAAAGCATAGGAAT 58.560 37.500 0.00 0.00 0.00 3.01
3050 3713 9.512435 CCATTAGCAATTGATAAGAAGTTCAAG 57.488 33.333 19.81 3.57 35.47 3.02
3061 3724 7.233632 AGCATAGGAACCATTAGCAATTGATA 58.766 34.615 10.34 3.99 0.00 2.15
3062 3725 6.073314 AGCATAGGAACCATTAGCAATTGAT 58.927 36.000 10.34 5.28 0.00 2.57
3063 3726 5.448654 AGCATAGGAACCATTAGCAATTGA 58.551 37.500 10.34 0.00 0.00 2.57
3064 3727 5.533903 AGAGCATAGGAACCATTAGCAATTG 59.466 40.000 0.00 0.00 0.00 2.32
3065 3728 5.533903 CAGAGCATAGGAACCATTAGCAATT 59.466 40.000 0.00 0.00 0.00 2.32
3066 3729 5.068636 CAGAGCATAGGAACCATTAGCAAT 58.931 41.667 0.00 0.00 0.00 3.56
3067 3730 4.080356 ACAGAGCATAGGAACCATTAGCAA 60.080 41.667 0.00 0.00 0.00 3.91
3068 3731 3.455910 ACAGAGCATAGGAACCATTAGCA 59.544 43.478 0.00 0.00 0.00 3.49
3069 3732 4.078639 ACAGAGCATAGGAACCATTAGC 57.921 45.455 0.00 0.00 0.00 3.09
3070 3733 6.648310 CACATACAGAGCATAGGAACCATTAG 59.352 42.308 0.00 0.00 0.00 1.73
3071 3734 6.524734 CACATACAGAGCATAGGAACCATTA 58.475 40.000 0.00 0.00 0.00 1.90
3072 3735 5.371526 CACATACAGAGCATAGGAACCATT 58.628 41.667 0.00 0.00 0.00 3.16
3073 3736 4.744867 GCACATACAGAGCATAGGAACCAT 60.745 45.833 0.00 0.00 33.66 3.55
3074 3737 3.432186 GCACATACAGAGCATAGGAACCA 60.432 47.826 0.00 0.00 33.66 3.67
3075 3738 3.134458 GCACATACAGAGCATAGGAACC 58.866 50.000 0.00 0.00 33.66 3.62
3076 3739 4.054671 GAGCACATACAGAGCATAGGAAC 58.945 47.826 0.00 0.00 36.17 3.62
3077 3740 3.706086 TGAGCACATACAGAGCATAGGAA 59.294 43.478 0.00 0.00 36.17 3.36
3078 3741 3.299503 TGAGCACATACAGAGCATAGGA 58.700 45.455 0.00 0.00 36.17 2.94
3079 3742 3.740631 TGAGCACATACAGAGCATAGG 57.259 47.619 0.00 0.00 36.17 2.57
3080 3743 4.448060 CACATGAGCACATACAGAGCATAG 59.552 45.833 0.00 0.00 36.17 2.23
3081 3744 4.374399 CACATGAGCACATACAGAGCATA 58.626 43.478 0.00 0.00 36.17 3.14
3082 3745 3.203716 CACATGAGCACATACAGAGCAT 58.796 45.455 0.00 0.00 36.17 3.79
3083 3746 2.624636 CACATGAGCACATACAGAGCA 58.375 47.619 0.00 0.00 36.17 4.26
3084 3747 1.329906 GCACATGAGCACATACAGAGC 59.670 52.381 10.48 0.00 35.09 4.09
3085 3748 2.608090 CAGCACATGAGCACATACAGAG 59.392 50.000 17.61 0.00 35.09 3.35
3086 3749 2.624636 CAGCACATGAGCACATACAGA 58.375 47.619 17.61 0.00 35.09 3.41
3087 3750 1.063616 GCAGCACATGAGCACATACAG 59.936 52.381 17.61 0.00 35.09 2.74
3088 3751 1.089112 GCAGCACATGAGCACATACA 58.911 50.000 17.61 0.00 35.09 2.29
3089 3752 1.376543 AGCAGCACATGAGCACATAC 58.623 50.000 17.61 1.85 35.09 2.39
3090 3753 2.011947 GAAGCAGCACATGAGCACATA 58.988 47.619 17.61 0.00 35.09 2.29
3091 3754 0.809385 GAAGCAGCACATGAGCACAT 59.191 50.000 17.61 1.90 36.85 3.21
3092 3755 0.250597 AGAAGCAGCACATGAGCACA 60.251 50.000 17.61 0.00 36.85 4.57
3093 3756 0.879765 AAGAAGCAGCACATGAGCAC 59.120 50.000 17.61 8.80 36.85 4.40
3094 3757 0.879090 CAAGAAGCAGCACATGAGCA 59.121 50.000 17.61 0.00 36.85 4.26
3095 3758 1.162698 TCAAGAAGCAGCACATGAGC 58.837 50.000 7.07 7.07 0.00 4.26
3096 3759 4.436242 AATTCAAGAAGCAGCACATGAG 57.564 40.909 0.00 0.00 0.00 2.90
3097 3760 4.521639 AGAAATTCAAGAAGCAGCACATGA 59.478 37.500 0.00 0.00 0.00 3.07
3098 3761 4.806330 AGAAATTCAAGAAGCAGCACATG 58.194 39.130 0.00 0.00 0.00 3.21
3099 3762 5.464030 AAGAAATTCAAGAAGCAGCACAT 57.536 34.783 0.00 0.00 0.00 3.21
3100 3763 4.924305 AAGAAATTCAAGAAGCAGCACA 57.076 36.364 0.00 0.00 0.00 4.57
3101 3764 6.615088 TGATAAGAAATTCAAGAAGCAGCAC 58.385 36.000 0.00 0.00 0.00 4.40
3102 3765 6.822667 TGATAAGAAATTCAAGAAGCAGCA 57.177 33.333 0.00 0.00 0.00 4.41
3103 3766 8.592998 CAATTGATAAGAAATTCAAGAAGCAGC 58.407 33.333 0.00 0.00 35.47 5.25
3104 3767 8.592998 GCAATTGATAAGAAATTCAAGAAGCAG 58.407 33.333 10.34 0.00 35.47 4.24
3105 3768 8.308931 AGCAATTGATAAGAAATTCAAGAAGCA 58.691 29.630 10.34 0.00 35.47 3.91
3106 3769 8.699283 AGCAATTGATAAGAAATTCAAGAAGC 57.301 30.769 10.34 0.00 35.47 3.86
3115 3778 9.646522 ACCTACCATTAGCAATTGATAAGAAAT 57.353 29.630 19.81 9.16 28.80 2.17
3117 3780 9.778741 CTACCTACCATTAGCAATTGATAAGAA 57.221 33.333 19.81 1.22 28.80 2.52
3118 3781 9.154632 TCTACCTACCATTAGCAATTGATAAGA 57.845 33.333 19.81 7.01 28.80 2.10
3119 3782 9.429359 CTCTACCTACCATTAGCAATTGATAAG 57.571 37.037 19.81 10.82 28.80 1.73
3136 3799 4.262617 CCTTTTCCAAAGCCTCTACCTAC 58.737 47.826 0.00 0.00 0.00 3.18
3161 3828 6.173427 ACAACCCACTGCATAAAGAAAATT 57.827 33.333 0.00 0.00 0.00 1.82
3194 3861 5.982890 ATACCACAATCCAGAAAACTTGG 57.017 39.130 0.00 0.00 37.04 3.61
3195 3862 6.980593 TGAATACCACAATCCAGAAAACTTG 58.019 36.000 0.00 0.00 0.00 3.16
3235 3904 6.072286 CCCCATACATGAAATATGCAGTCTTC 60.072 42.308 0.00 0.00 0.00 2.87
3236 3905 5.771666 CCCCATACATGAAATATGCAGTCTT 59.228 40.000 0.00 0.00 0.00 3.01
3237 3906 5.319453 CCCCATACATGAAATATGCAGTCT 58.681 41.667 0.00 0.00 0.00 3.24
3240 3909 3.827876 TGCCCCATACATGAAATATGCAG 59.172 43.478 0.00 0.00 0.00 4.41
3241 3910 3.842206 TGCCCCATACATGAAATATGCA 58.158 40.909 0.00 0.00 0.00 3.96
3242 3911 4.708421 AGATGCCCCATACATGAAATATGC 59.292 41.667 0.00 0.00 0.00 3.14
3243 3912 6.845758 AAGATGCCCCATACATGAAATATG 57.154 37.500 0.00 0.00 0.00 1.78
3245 3914 6.372104 TCAAAGATGCCCCATACATGAAATA 58.628 36.000 0.00 0.00 0.00 1.40
3247 3916 4.608269 TCAAAGATGCCCCATACATGAAA 58.392 39.130 0.00 0.00 0.00 2.69
3287 3987 6.154706 ACACCACAGTATAGGGTTCTTTCTAG 59.845 42.308 0.00 0.00 31.03 2.43
3297 4004 5.128827 ACATAGAACACACCACAGTATAGGG 59.871 44.000 0.00 0.00 0.00 3.53
3299 4006 9.817809 AATTACATAGAACACACCACAGTATAG 57.182 33.333 0.00 0.00 0.00 1.31
3306 4013 6.569179 AACCAATTACATAGAACACACCAC 57.431 37.500 0.00 0.00 0.00 4.16
3311 4018 9.072294 GTGCAATTAACCAATTACATAGAACAC 57.928 33.333 0.00 0.00 31.62 3.32
3341 4048 9.653287 TTAAGATTACGATAATAGGAATGCCTG 57.347 33.333 0.88 0.00 46.45 4.85
3376 4153 3.433306 ACTAAGGCAATAACACCAGCA 57.567 42.857 0.00 0.00 0.00 4.41
3408 4185 7.566760 AGTATATCAACGCCATCAATGAAAA 57.433 32.000 0.00 0.00 0.00 2.29
3409 4186 7.566760 AAGTATATCAACGCCATCAATGAAA 57.433 32.000 0.00 0.00 0.00 2.69
3411 4188 6.765512 TGAAAGTATATCAACGCCATCAATGA 59.234 34.615 0.00 0.00 0.00 2.57
3445 4222 2.425143 CACCACATGGACAAGGCTAT 57.575 50.000 4.53 0.00 38.94 2.97
3488 4265 1.475034 CCATGGGATTACACCGACAGG 60.475 57.143 2.85 0.00 45.13 4.00
3542 4322 8.462016 ACAATCACATCTAACCAAGAATTTAGC 58.538 33.333 0.00 0.00 37.89 3.09
3648 4495 6.411376 TGTAACAAACTCCTTCACTTTCTCA 58.589 36.000 0.00 0.00 0.00 3.27
3663 4510 5.924254 GTCCTTAATGGCCTTTGTAACAAAC 59.076 40.000 13.96 0.49 35.26 2.93
3677 4524 6.709018 ATATTTGGTTTCCGTCCTTAATGG 57.291 37.500 0.00 0.00 35.07 3.16
4229 5098 6.532988 TGCTACAGTGGTGTATGTACATAA 57.467 37.500 17.07 5.55 38.51 1.90
4250 5193 1.467374 GCACGGTGTTGACCAATATGC 60.467 52.381 10.24 0.00 43.33 3.14
4251 5194 1.132262 GGCACGGTGTTGACCAATATG 59.868 52.381 10.24 0.00 43.33 1.78
4270 5225 0.319211 TTAACACCGCGACTGTCTGG 60.319 55.000 8.23 12.65 0.00 3.86
4277 5232 5.971895 TTAATTCCTATTAACACCGCGAC 57.028 39.130 8.23 0.00 32.60 5.19
4279 5234 6.140110 CCATTTAATTCCTATTAACACCGCG 58.860 40.000 0.00 0.00 36.27 6.46
4280 5235 5.918576 GCCATTTAATTCCTATTAACACCGC 59.081 40.000 0.00 0.00 36.27 5.68
4281 5236 7.272037 AGCCATTTAATTCCTATTAACACCG 57.728 36.000 0.00 0.00 36.27 4.94
4288 5243 9.619842 ATTATCCCAAGCCATTTAATTCCTATT 57.380 29.630 0.00 0.00 0.00 1.73
4316 5272 4.695455 CGATGGTTAACAGGTTCAATCTGT 59.305 41.667 8.10 0.00 46.22 3.41
4333 5289 1.396996 GCGTGTTTGCTTATCGATGGT 59.603 47.619 8.54 0.00 0.00 3.55
4334 5290 1.665679 AGCGTGTTTGCTTATCGATGG 59.334 47.619 8.54 1.88 44.46 3.51
4338 5294 3.925688 ATGTAGCGTGTTTGCTTATCG 57.074 42.857 0.00 0.00 44.46 2.92
4369 5325 4.010349 AGGCTAGAACAAACAGGCATTAC 58.990 43.478 0.00 0.00 37.32 1.89
4395 5351 3.141398 TGGTTCTGCTGACAAGTTCATC 58.859 45.455 0.00 0.00 32.17 2.92
4396 5352 3.144506 CTGGTTCTGCTGACAAGTTCAT 58.855 45.455 0.00 0.00 32.17 2.57
4498 5468 2.942376 TGAGCAAACAAACGTGACATCT 59.058 40.909 0.00 0.00 0.00 2.90
4506 5476 7.951706 AAAAATGAAAATGAGCAAACAAACG 57.048 28.000 0.00 0.00 0.00 3.60
4537 5508 6.094603 CCAGAAATAGGAAATCACAACCTCTG 59.905 42.308 0.00 0.00 35.52 3.35
4541 5512 6.180472 TCTCCAGAAATAGGAAATCACAACC 58.820 40.000 0.00 0.00 34.08 3.77
4550 5521 9.532494 TCAATTGAAAATCTCCAGAAATAGGAA 57.468 29.630 5.45 0.00 34.08 3.36
4588 5559 8.299570 GTGTCCAACTGATAAATCATGAAAACT 58.700 33.333 0.00 0.00 36.02 2.66
4634 5639 5.488341 ACAGCGATTAACTCATAAACTGGT 58.512 37.500 0.00 0.00 31.95 4.00
4644 5649 5.642686 ACTCTACTCAACAGCGATTAACTC 58.357 41.667 0.00 0.00 0.00 3.01
4647 5652 4.625742 GCAACTCTACTCAACAGCGATTAA 59.374 41.667 0.00 0.00 0.00 1.40
4667 5674 4.009675 CAGTTAGGCCACAAGATAAGCAA 58.990 43.478 5.01 0.00 0.00 3.91
4692 5699 1.145738 AGCTCCTGTCACCACCAAAAT 59.854 47.619 0.00 0.00 0.00 1.82
4862 5877 4.331968 CCACCTATTTCTGCCAGTAAACA 58.668 43.478 0.00 0.00 0.00 2.83
4867 5882 0.392998 CGCCACCTATTTCTGCCAGT 60.393 55.000 0.00 0.00 0.00 4.00
4893 5908 3.961477 ACATAATCAAATAAGCGCGCA 57.039 38.095 35.10 14.88 0.00 6.09
4967 5982 4.497006 GCATCAGCTCAACATAATCCACAC 60.497 45.833 0.00 0.00 37.91 3.82
5010 6025 4.454504 ACGAACGAGCAATAAAAATGGACT 59.545 37.500 0.14 0.00 0.00 3.85
5022 6039 1.658994 AACCTCAAACGAACGAGCAA 58.341 45.000 0.14 0.00 0.00 3.91
5050 6086 0.603707 ACATGGGCGTGTGTGAAGAG 60.604 55.000 0.00 0.00 0.00 2.85
5100 6136 5.885230 ACACATGCGTAGTAGTACAAGTA 57.115 39.130 8.43 0.00 0.00 2.24
5101 6137 4.778534 ACACATGCGTAGTAGTACAAGT 57.221 40.909 8.43 0.00 0.00 3.16
5102 6138 5.633927 TGTACACATGCGTAGTAGTACAAG 58.366 41.667 8.43 0.00 38.90 3.16
5103 6139 5.412286 TCTGTACACATGCGTAGTAGTACAA 59.588 40.000 8.43 0.00 40.59 2.41
5106 6142 6.316890 TCAATCTGTACACATGCGTAGTAGTA 59.683 38.462 0.00 0.00 0.00 1.82
5107 6143 5.124936 TCAATCTGTACACATGCGTAGTAGT 59.875 40.000 0.00 0.00 0.00 2.73
5108 6144 5.578776 TCAATCTGTACACATGCGTAGTAG 58.421 41.667 0.00 0.00 0.00 2.57
5110 6146 4.450082 TCAATCTGTACACATGCGTAGT 57.550 40.909 0.00 0.00 0.00 2.73
5111 6147 4.147133 CGATCAATCTGTACACATGCGTAG 59.853 45.833 0.00 0.00 0.00 3.51
5112 6148 4.041723 CGATCAATCTGTACACATGCGTA 58.958 43.478 0.00 0.00 0.00 4.42
5137 6184 3.378427 GGATGAATCTTGTAACTGCCCAC 59.622 47.826 0.00 0.00 0.00 4.61
5168 6215 9.118300 GAGAGGAAATCAATCATGTACATTCTT 57.882 33.333 5.37 0.00 0.00 2.52
5190 6237 2.600731 CGTGCCAACAGAGTTAGAGAG 58.399 52.381 0.00 0.00 0.00 3.20
5192 6239 1.071605 GCGTGCCAACAGAGTTAGAG 58.928 55.000 0.00 0.00 0.00 2.43
5194 6241 1.195448 CTTGCGTGCCAACAGAGTTAG 59.805 52.381 0.00 0.00 0.00 2.34
5220 6267 3.545426 GCACGACAACTTGTAACACTTCC 60.545 47.826 0.00 0.00 0.00 3.46
5222 6269 3.267483 AGCACGACAACTTGTAACACTT 58.733 40.909 0.00 0.00 0.00 3.16
5224 6271 2.347292 CGAGCACGACAACTTGTAACAC 60.347 50.000 0.00 0.00 42.66 3.32
5225 6272 1.855978 CGAGCACGACAACTTGTAACA 59.144 47.619 0.00 0.00 42.66 2.41
5257 6304 4.432741 GGCAAGGAGTGGAGGGGC 62.433 72.222 0.00 0.00 0.00 5.80
5376 6423 0.976073 GAGGATGGGGTTCGAGGACA 60.976 60.000 0.00 0.00 0.00 4.02
5441 6488 5.448768 GCATTGCTCACTGATGATATATGGC 60.449 44.000 0.16 0.00 33.22 4.40
5445 6492 5.138125 TCGCATTGCTCACTGATGATATA 57.862 39.130 7.12 0.00 33.22 0.86
5471 6518 1.340248 CTTGGCTTGGGATGCATCATC 59.660 52.381 27.25 18.46 39.87 2.92
5472 6519 1.063492 TCTTGGCTTGGGATGCATCAT 60.063 47.619 27.25 0.00 0.00 2.45
5473 6520 0.332293 TCTTGGCTTGGGATGCATCA 59.668 50.000 27.25 6.50 0.00 3.07
5528 6599 4.873129 ATCTACAGCACCGCGCCG 62.873 66.667 0.00 0.00 44.04 6.46


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

AutoCloner maintained by Alex Coulton.