Multiple sequence alignment - TraesCS6D01G257900

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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 TraesCS6D01G257900 chr6D 100.000 3165 0 0 1 3165 363465079 363461915 0.000000e+00 5845.0
1 TraesCS6D01G257900 chr6D 90.947 243 22 0 2653 2895 227008004 227007762 8.460000e-86 327.0
2 TraesCS6D01G257900 chr6B 88.110 2666 146 67 2 2597 548117166 548114602 0.000000e+00 3009.0
3 TraesCS6D01G257900 chr6A 90.975 1241 45 23 1400 2589 504472989 504471765 0.000000e+00 1609.0
4 TraesCS6D01G257900 chr6A 86.099 1374 92 47 2 1343 504474489 504473183 0.000000e+00 1387.0
5 TraesCS6D01G257900 chr6A 92.797 236 16 1 2930 3165 504471463 504471229 1.090000e-89 340.0
6 TraesCS6D01G257900 chr6A 90.400 250 20 4 2649 2896 190652677 190652430 3.040000e-85 326.0
7 TraesCS6D01G257900 chr4D 91.429 245 21 0 2651 2895 30506670 30506426 1.410000e-88 337.0
8 TraesCS6D01G257900 chr4D 87.500 288 32 4 2646 2931 325892195 325892480 2.350000e-86 329.0
9 TraesCS6D01G257900 chr4D 90.323 248 23 1 2652 2898 11504358 11504111 1.090000e-84 324.0
10 TraesCS6D01G257900 chr4D 95.122 41 2 0 2892 2932 484462757 484462717 7.330000e-07 65.8
11 TraesCS6D01G257900 chr4D 95.000 40 2 0 2892 2931 112074029 112073990 2.640000e-06 63.9
12 TraesCS6D01G257900 chr3D 91.020 245 21 1 2651 2895 511728398 511728155 2.350000e-86 329.0
13 TraesCS6D01G257900 chr3D 90.688 247 23 0 2652 2898 523192596 523192350 2.350000e-86 329.0
14 TraesCS6D01G257900 chr3D 88.806 268 24 6 2637 2902 129016840 129016577 1.090000e-84 324.0
15 TraesCS6D01G257900 chr2D 91.322 242 18 3 2655 2895 642827313 642827074 8.460000e-86 327.0
16 TraesCS6D01G257900 chr7D 89.241 158 15 2 2008 2165 190005354 190005509 2.490000e-46 196.0
17 TraesCS6D01G257900 chr7B 90.000 150 15 0 2016 2165 334487119 334487268 8.960000e-46 195.0
18 TraesCS6D01G257900 chr7A 88.608 158 16 2 2008 2165 194177270 194177115 1.160000e-44 191.0
19 TraesCS6D01G257900 chr3A 91.071 56 3 2 2603 2657 66275397 66275451 1.220000e-09 75.0
20 TraesCS6D01G257900 chr3A 91.667 48 1 3 2610 2656 540972263 540972218 2.640000e-06 63.9
21 TraesCS6D01G257900 chr3B 88.136 59 7 0 2598 2656 741635444 741635502 1.570000e-08 71.3
22 TraesCS6D01G257900 chr3B 88.136 59 7 0 2598 2656 741647662 741647720 1.570000e-08 71.3
23 TraesCS6D01G257900 chr2B 89.286 56 6 0 2602 2657 213885548 213885493 1.570000e-08 71.3
24 TraesCS6D01G257900 chr1A 90.385 52 4 1 2892 2943 583322164 583322214 2.040000e-07 67.6
25 TraesCS6D01G257900 chrUn 95.000 40 2 0 2892 2931 248124587 248124548 2.640000e-06 63.9
26 TraesCS6D01G257900 chrUn 95.000 40 2 0 2892 2931 346478602 346478641 2.640000e-06 63.9
27 TraesCS6D01G257900 chr4B 95.000 40 2 0 2892 2931 172735533 172735494 2.640000e-06 63.9
28 TraesCS6D01G257900 chr2A 89.796 49 3 2 2888 2934 76520611 76520563 9.480000e-06 62.1
29 TraesCS6D01G257900 chr5A 89.362 47 5 0 2892 2938 469275404 469275450 3.410000e-05 60.2


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 TraesCS6D01G257900 chr6D 363461915 363465079 3164 True 5845 5845 100.000 1 3165 1 chr6D.!!$R2 3164
1 TraesCS6D01G257900 chr6B 548114602 548117166 2564 True 3009 3009 88.110 2 2597 1 chr6B.!!$R1 2595
2 TraesCS6D01G257900 chr6A 504471229 504474489 3260 True 1112 1609 89.957 2 3165 3 chr6A.!!$R2 3163

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
834 852 0.031994 AGCACCAACCGAACAATTGC 59.968 50.0 5.05 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2811 3135 0.110056 TAACGAACGAGACCGACTGC 60.11 55.0 0.14 0.0 39.5 4.4 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
44 50 2.419990 CCTGTGGATAATTGGACTGCGA 60.420 50.000 0.00 0.00 0.00 5.10
134 141 3.119459 AGCGATTTAGCTCTCGTCTCAAA 60.119 43.478 12.90 0.00 45.67 2.69
135 142 3.000575 GCGATTTAGCTCTCGTCTCAAAC 60.001 47.826 12.90 0.00 37.23 2.93
136 143 4.416620 CGATTTAGCTCTCGTCTCAAACT 58.583 43.478 0.00 0.00 0.00 2.66
137 144 5.570344 CGATTTAGCTCTCGTCTCAAACTA 58.430 41.667 0.00 0.00 0.00 2.24
138 145 6.202937 CGATTTAGCTCTCGTCTCAAACTAT 58.797 40.000 0.00 0.00 0.00 2.12
142 152 9.871238 ATTTAGCTCTCGTCTCAAACTATTTTA 57.129 29.630 0.00 0.00 0.00 1.52
147 157 6.860080 TCTCGTCTCAAACTATTTTATCCGT 58.140 36.000 0.00 0.00 0.00 4.69
148 158 6.750501 TCTCGTCTCAAACTATTTTATCCGTG 59.249 38.462 0.00 0.00 0.00 4.94
175 185 6.040391 AGCACTTAGTTTGCAGTTTTTGGATA 59.960 34.615 0.00 0.00 42.83 2.59
204 214 3.119291 GCTGATACTCGGTCATTCAGTG 58.881 50.000 0.00 0.00 36.91 3.66
228 238 3.808728 TGGACCAAGCTATTCTGTATGC 58.191 45.455 0.00 0.00 0.00 3.14
279 289 0.662077 CACCGATGTCGTGTTCGTCA 60.662 55.000 1.44 0.00 39.07 4.35
327 337 4.500205 CGTAGCACGATATTCCTAAACCCA 60.500 45.833 3.04 0.00 46.05 4.51
340 350 3.831911 CCTAAACCCAATCCTCAAAAGCA 59.168 43.478 0.00 0.00 0.00 3.91
342 352 4.541973 AAACCCAATCCTCAAAAGCATC 57.458 40.909 0.00 0.00 0.00 3.91
364 374 0.607620 GCATAGCCAAACCAAAGCCA 59.392 50.000 0.00 0.00 0.00 4.75
393 403 4.081642 CGTCTTGAGAAAGTAGGAATCCCA 60.082 45.833 0.00 0.00 33.88 4.37
523 537 2.916716 GACAAATGTAAACCATGCGCAG 59.083 45.455 18.32 5.51 32.82 5.18
536 550 3.390521 CGCAGGCACCCACCTCTA 61.391 66.667 0.00 0.00 38.26 2.43
537 551 2.586792 GCAGGCACCCACCTCTAG 59.413 66.667 0.00 0.00 38.26 2.43
538 552 2.586792 CAGGCACCCACCTCTAGC 59.413 66.667 0.00 0.00 38.26 3.42
552 570 7.508636 ACCCACCTCTAGCATCATATATCTATG 59.491 40.741 0.00 1.66 36.79 2.23
560 578 6.753180 AGCATCATATATCTATGTAAGCCCG 58.247 40.000 6.49 0.00 36.80 6.13
562 580 6.459066 CATCATATATCTATGTAAGCCCGGG 58.541 44.000 19.09 19.09 36.80 5.73
692 710 1.526225 GGCCGTCCCTTTAGATGCC 60.526 63.158 0.00 0.00 31.85 4.40
760 778 2.353607 CGCTTAGGTAGGCGCTCG 60.354 66.667 7.64 0.00 44.43 5.03
761 779 2.806237 GCTTAGGTAGGCGCTCGT 59.194 61.111 7.64 2.83 0.00 4.18
762 780 1.141234 GCTTAGGTAGGCGCTCGTT 59.859 57.895 7.64 0.00 0.00 3.85
763 781 1.146358 GCTTAGGTAGGCGCTCGTTG 61.146 60.000 7.64 0.00 0.00 4.10
770 788 0.531090 TAGGCGCTCGTTGTTGTTGT 60.531 50.000 7.64 0.00 0.00 3.32
771 789 1.063488 GGCGCTCGTTGTTGTTGTT 59.937 52.632 7.64 0.00 0.00 2.83
833 851 2.552315 ACTAGCACCAACCGAACAATTG 59.448 45.455 3.24 3.24 0.00 2.32
834 852 0.031994 AGCACCAACCGAACAATTGC 59.968 50.000 5.05 0.00 0.00 3.56
839 857 1.608590 CCAACCGAACAATTGCTCAGT 59.391 47.619 5.05 0.00 0.00 3.41
840 858 2.350772 CCAACCGAACAATTGCTCAGTC 60.351 50.000 5.05 0.00 0.00 3.51
841 859 2.549754 CAACCGAACAATTGCTCAGTCT 59.450 45.455 5.05 0.00 0.00 3.24
843 861 2.037772 ACCGAACAATTGCTCAGTCTCT 59.962 45.455 5.05 0.00 0.00 3.10
859 888 6.702329 TCAGTCTCTCCTTCTTTAAATGGTC 58.298 40.000 0.00 0.00 0.00 4.02
861 890 5.548056 AGTCTCTCCTTCTTTAAATGGTCCA 59.452 40.000 0.00 0.00 0.00 4.02
862 891 6.216456 AGTCTCTCCTTCTTTAAATGGTCCAT 59.784 38.462 0.00 0.00 0.00 3.41
864 893 6.215431 TCTCTCCTTCTTTAAATGGTCCATCA 59.785 38.462 4.39 0.00 0.00 3.07
915 944 1.738099 CTAGCATGTATCCCGCGCC 60.738 63.158 0.00 0.00 0.00 6.53
1074 1112 0.390735 GTACGATGCGTCCCCTTGTT 60.391 55.000 0.00 0.00 41.54 2.83
1084 1122 3.550233 GCGTCCCCTTGTTTTCTTTTCTC 60.550 47.826 0.00 0.00 0.00 2.87
1088 1126 3.243873 CCCCTTGTTTTCTTTTCTCCTGC 60.244 47.826 0.00 0.00 0.00 4.85
1121 1159 8.968969 TCTGATGATTGATGATAGATAGTCCTG 58.031 37.037 0.00 0.00 0.00 3.86
1127 1166 6.720217 TGATGATAGATAGTCCTGGGTCTA 57.280 41.667 0.00 0.00 0.00 2.59
1140 1179 2.330041 GTCTAGAGAGCTCGCGCC 59.670 66.667 12.03 1.33 36.60 6.53
1154 1193 3.499737 CGCCTGGTTCACGGATGC 61.500 66.667 0.00 0.00 0.00 3.91
1185 1224 1.623311 TCGAACCATTCTCAAGCAGGA 59.377 47.619 0.00 0.00 0.00 3.86
1229 1268 1.534595 GCTGTTCTTTCTGGCAGAGTG 59.465 52.381 17.91 13.98 0.00 3.51
1302 1344 3.546670 CGTCGCTACAATTCAGTTCTACC 59.453 47.826 0.00 0.00 0.00 3.18
1350 1393 6.199154 CGTAAGTTTCTGTACCATAGCTCATG 59.801 42.308 0.00 0.00 0.00 3.07
1355 1398 0.679505 GTACCATAGCTCATGCCGGA 59.320 55.000 5.05 0.00 40.80 5.14
1356 1399 1.070134 GTACCATAGCTCATGCCGGAA 59.930 52.381 5.05 0.00 40.80 4.30
1357 1400 0.767375 ACCATAGCTCATGCCGGAAT 59.233 50.000 5.05 0.00 40.80 3.01
1358 1401 1.977854 ACCATAGCTCATGCCGGAATA 59.022 47.619 5.05 0.00 40.80 1.75
1359 1402 2.573462 ACCATAGCTCATGCCGGAATAT 59.427 45.455 5.05 0.00 40.80 1.28
1360 1403 2.941064 CCATAGCTCATGCCGGAATATG 59.059 50.000 5.05 6.53 40.80 1.78
1361 1404 3.603532 CATAGCTCATGCCGGAATATGT 58.396 45.455 5.05 0.00 40.80 2.29
1362 1405 2.645838 AGCTCATGCCGGAATATGTT 57.354 45.000 5.05 0.00 40.80 2.71
1363 1406 2.498167 AGCTCATGCCGGAATATGTTC 58.502 47.619 5.05 3.21 40.80 3.18
1364 1407 2.158769 AGCTCATGCCGGAATATGTTCA 60.159 45.455 5.05 0.00 40.80 3.18
1365 1408 2.225019 GCTCATGCCGGAATATGTTCAG 59.775 50.000 5.05 0.00 36.01 3.02
1366 1409 3.470709 CTCATGCCGGAATATGTTCAGT 58.529 45.455 5.05 0.00 36.01 3.41
1367 1410 3.879295 CTCATGCCGGAATATGTTCAGTT 59.121 43.478 5.05 0.00 36.01 3.16
1374 1417 4.452455 CCGGAATATGTTCAGTTGATAGCC 59.548 45.833 0.00 0.00 36.01 3.93
1446 1651 8.503196 GTGATCATATACTGTGTAGTCTCAGAG 58.497 40.741 0.00 0.00 38.36 3.35
1558 1763 3.319274 ATGGACTACGCCATGGCA 58.681 55.556 34.93 16.95 46.62 4.92
1660 1865 2.124320 ATGATCCCGCCAAACCCG 60.124 61.111 0.00 0.00 0.00 5.28
1865 2112 4.400109 CACCGCAGCAGCAGCAAG 62.400 66.667 10.77 2.97 45.49 4.01
2169 2428 1.875813 GCGCCATCGTCTGACTCTG 60.876 63.158 6.21 3.18 38.14 3.35
2232 2499 1.299926 GTTCTCCATCGCGCCGTAT 60.300 57.895 0.00 0.00 0.00 3.06
2294 2561 1.141234 CGGTTCCCTTCTCGTAGGC 59.859 63.158 0.00 0.00 33.73 3.93
2304 2571 2.554806 TCTCGTAGGCGTATGTTGTG 57.445 50.000 5.60 0.00 39.49 3.33
2310 2577 2.098298 GCGTATGTTGTGCAGGCG 59.902 61.111 0.00 0.00 0.00 5.52
2367 2634 2.411748 TGAGATGAACATTCGCGTTGTC 59.588 45.455 15.66 10.77 0.00 3.18
2383 2650 2.921754 GTTGTCTGGATTCGGTTCGTAG 59.078 50.000 0.00 0.00 0.00 3.51
2394 2661 6.805760 GGATTCGGTTCGTAGGATATTACTTC 59.194 42.308 0.00 0.00 0.00 3.01
2415 2683 2.637715 ATGATGCTCTTTTCGCGCGC 62.638 55.000 27.95 23.91 0.00 6.86
2424 2692 2.170260 TTTTCGCGCGCTTCTCTTGG 62.170 55.000 30.48 11.00 0.00 3.61
2442 2710 7.684529 TCTCTTGGAAAGCTAAGAAGAGATTT 58.315 34.615 17.23 0.00 45.70 2.17
2451 2719 7.608308 AGCTAAGAAGAGATTTGTCAATGAC 57.392 36.000 6.41 6.41 0.00 3.06
2476 2744 4.046286 TGGCCACCAAAGACAGATTAAT 57.954 40.909 0.00 0.00 0.00 1.40
2477 2745 4.415596 TGGCCACCAAAGACAGATTAATT 58.584 39.130 0.00 0.00 0.00 1.40
2479 2747 6.013379 TGGCCACCAAAGACAGATTAATTAA 58.987 36.000 0.00 0.00 0.00 1.40
2480 2748 6.152661 TGGCCACCAAAGACAGATTAATTAAG 59.847 38.462 0.00 0.00 0.00 1.85
2481 2749 6.036470 GCCACCAAAGACAGATTAATTAAGC 58.964 40.000 5.30 5.30 0.00 3.09
2482 2750 6.350110 GCCACCAAAGACAGATTAATTAAGCA 60.350 38.462 15.37 0.00 0.00 3.91
2483 2751 7.631377 GCCACCAAAGACAGATTAATTAAGCAT 60.631 37.037 15.37 3.34 0.00 3.79
2484 2752 8.902806 CCACCAAAGACAGATTAATTAAGCATA 58.097 33.333 15.37 0.00 0.00 3.14
2553 2821 2.391389 CCTTTCGCTGTCCTTCGGC 61.391 63.158 0.00 0.00 44.34 5.54
2592 2861 9.320352 TGATCAAATCATTGCAAAAATAGATGG 57.680 29.630 1.71 0.21 36.45 3.51
2597 2866 6.140303 TCATTGCAAAAATAGATGGAGAGC 57.860 37.500 1.71 0.00 0.00 4.09
2598 2867 5.889853 TCATTGCAAAAATAGATGGAGAGCT 59.110 36.000 1.71 0.00 0.00 4.09
2599 2868 5.824904 TTGCAAAAATAGATGGAGAGCTC 57.175 39.130 5.27 5.27 0.00 4.09
2600 2869 5.108187 TGCAAAAATAGATGGAGAGCTCT 57.892 39.130 18.28 18.28 0.00 4.09
2601 2870 5.121811 TGCAAAAATAGATGGAGAGCTCTC 58.878 41.667 31.89 31.89 42.14 3.20
2602 2871 5.104610 TGCAAAAATAGATGGAGAGCTCTCT 60.105 40.000 36.09 22.27 42.48 3.10
2616 2885 6.777213 AGAGCTCTCTCCGTTCTAAAATAA 57.223 37.500 11.45 0.00 40.22 1.40
2617 2886 6.801575 AGAGCTCTCTCCGTTCTAAAATAAG 58.198 40.000 11.45 0.00 40.22 1.73
2618 2887 6.378848 AGAGCTCTCTCCGTTCTAAAATAAGT 59.621 38.462 11.45 0.00 40.22 2.24
2619 2888 6.334202 AGCTCTCTCCGTTCTAAAATAAGTG 58.666 40.000 0.00 0.00 0.00 3.16
2621 2890 6.253942 GCTCTCTCCGTTCTAAAATAAGTGTC 59.746 42.308 0.00 0.00 0.00 3.67
2622 2891 7.463961 TCTCTCCGTTCTAAAATAAGTGTCT 57.536 36.000 0.00 0.00 0.00 3.41
2624 2893 9.017509 TCTCTCCGTTCTAAAATAAGTGTCTTA 57.982 33.333 0.00 0.00 0.00 2.10
2672 2996 6.652205 ATTAGTACTCCCTCCATTCCAAAA 57.348 37.500 0.00 0.00 0.00 2.44
2675 2999 6.848562 AGTACTCCCTCCATTCCAAAATAT 57.151 37.500 0.00 0.00 0.00 1.28
2676 3000 7.947782 AGTACTCCCTCCATTCCAAAATATA 57.052 36.000 0.00 0.00 0.00 0.86
2677 3001 7.978925 AGTACTCCCTCCATTCCAAAATATAG 58.021 38.462 0.00 0.00 0.00 1.31
2678 3002 6.848562 ACTCCCTCCATTCCAAAATATAGT 57.151 37.500 0.00 0.00 0.00 2.12
2679 3003 6.605119 ACTCCCTCCATTCCAAAATATAGTG 58.395 40.000 0.00 0.00 0.00 2.74
2681 3005 4.216257 CCCTCCATTCCAAAATATAGTGCG 59.784 45.833 0.00 0.00 0.00 5.34
2682 3006 4.821805 CCTCCATTCCAAAATATAGTGCGT 59.178 41.667 0.00 0.00 0.00 5.24
2683 3007 5.049405 CCTCCATTCCAAAATATAGTGCGTC 60.049 44.000 0.00 0.00 0.00 5.19
2684 3008 4.819630 TCCATTCCAAAATATAGTGCGTCC 59.180 41.667 0.00 0.00 0.00 4.79
2685 3009 4.319477 CCATTCCAAAATATAGTGCGTCCG 60.319 45.833 0.00 0.00 0.00 4.79
2686 3010 2.206750 TCCAAAATATAGTGCGTCCGC 58.793 47.619 4.42 4.42 42.35 5.54
2687 3011 1.070843 CCAAAATATAGTGCGTCCGCG 60.071 52.381 7.22 0.00 45.51 6.46
2705 3029 1.292541 GCTTCCCGAGGTCGAACTT 59.707 57.895 3.47 0.00 43.02 2.66
2706 3030 0.320508 GCTTCCCGAGGTCGAACTTT 60.321 55.000 3.47 0.00 43.02 2.66
2707 3031 1.429463 CTTCCCGAGGTCGAACTTTG 58.571 55.000 3.47 0.00 43.02 2.77
2709 3033 0.316204 TCCCGAGGTCGAACTTTGAC 59.684 55.000 3.47 0.86 43.02 3.18
2722 3046 8.142348 GTCGAACTTTGACCATAAATTTAACG 57.858 34.615 1.21 0.00 0.00 3.18
2723 3047 8.011106 GTCGAACTTTGACCATAAATTTAACGA 58.989 33.333 1.21 0.00 0.00 3.85
2724 3048 8.557864 TCGAACTTTGACCATAAATTTAACGAA 58.442 29.630 1.21 1.12 0.00 3.85
2725 3049 8.624028 CGAACTTTGACCATAAATTTAACGAAC 58.376 33.333 1.21 0.00 0.00 3.95
2726 3050 8.496872 AACTTTGACCATAAATTTAACGAACG 57.503 30.769 1.21 0.00 0.00 3.95
2727 3051 7.863666 ACTTTGACCATAAATTTAACGAACGA 58.136 30.769 1.21 0.00 0.00 3.85
2728 3052 8.013378 ACTTTGACCATAAATTTAACGAACGAG 58.987 33.333 1.21 0.01 0.00 4.18
2729 3053 7.655236 TTGACCATAAATTTAACGAACGAGA 57.345 32.000 1.21 0.00 0.00 4.04
2730 3054 7.052565 TGACCATAAATTTAACGAACGAGAC 57.947 36.000 1.21 0.00 0.00 3.36
2731 3055 6.091169 TGACCATAAATTTAACGAACGAGACC 59.909 38.462 1.21 0.00 0.00 3.85
2732 3056 5.062558 ACCATAAATTTAACGAACGAGACCG 59.937 40.000 1.21 0.00 42.50 4.79
2733 3057 5.289193 CCATAAATTTAACGAACGAGACCGA 59.711 40.000 1.21 0.00 39.50 4.69
2734 3058 6.019318 CCATAAATTTAACGAACGAGACCGAT 60.019 38.462 1.21 0.00 39.50 4.18
2735 3059 5.851047 AAATTTAACGAACGAGACCGATT 57.149 34.783 0.14 0.00 39.50 3.34
2736 3060 4.835199 ATTTAACGAACGAGACCGATTG 57.165 40.909 0.14 0.00 39.50 2.67
2737 3061 1.621107 TAACGAACGAGACCGATTGC 58.379 50.000 0.14 0.00 39.50 3.56
2738 3062 1.342082 AACGAACGAGACCGATTGCG 61.342 55.000 0.14 0.00 39.50 4.85
2763 3087 6.618287 CGGGAGCAAAAGTTATATCAATGA 57.382 37.500 0.00 0.00 0.00 2.57
2764 3088 7.026631 CGGGAGCAAAAGTTATATCAATGAA 57.973 36.000 0.00 0.00 0.00 2.57
2765 3089 7.651808 CGGGAGCAAAAGTTATATCAATGAAT 58.348 34.615 0.00 0.00 0.00 2.57
2766 3090 8.137437 CGGGAGCAAAAGTTATATCAATGAATT 58.863 33.333 0.00 0.00 0.00 2.17
2767 3091 9.468532 GGGAGCAAAAGTTATATCAATGAATTC 57.531 33.333 0.00 0.00 0.00 2.17
2768 3092 9.173939 GGAGCAAAAGTTATATCAATGAATTCG 57.826 33.333 0.04 0.00 0.00 3.34
2769 3093 9.722056 GAGCAAAAGTTATATCAATGAATTCGT 57.278 29.630 0.04 0.00 0.00 3.85
2809 3133 9.628746 TTTTAATTATGTAACTTTTTCTCCCGC 57.371 29.630 0.00 0.00 0.00 6.13
2810 3134 5.830000 ATTATGTAACTTTTTCTCCCGCC 57.170 39.130 0.00 0.00 0.00 6.13
2811 3135 1.515081 TGTAACTTTTTCTCCCGCCG 58.485 50.000 0.00 0.00 0.00 6.46
2812 3136 0.167470 GTAACTTTTTCTCCCGCCGC 59.833 55.000 0.00 0.00 0.00 6.53
2813 3137 0.250381 TAACTTTTTCTCCCGCCGCA 60.250 50.000 0.00 0.00 0.00 5.69
2814 3138 1.515521 AACTTTTTCTCCCGCCGCAG 61.516 55.000 0.00 0.00 0.00 5.18
2815 3139 1.966451 CTTTTTCTCCCGCCGCAGT 60.966 57.895 0.00 0.00 0.00 4.40
2816 3140 1.912371 CTTTTTCTCCCGCCGCAGTC 61.912 60.000 0.00 0.00 0.00 3.51
2817 3141 4.735132 TTTCTCCCGCCGCAGTCG 62.735 66.667 0.00 0.00 0.00 4.18
2827 3151 2.870161 CGCAGTCGGTCTCGTTCG 60.870 66.667 0.00 0.00 37.69 3.95
2828 3152 2.254651 GCAGTCGGTCTCGTTCGT 59.745 61.111 0.00 0.00 37.69 3.85
2829 3153 1.371389 GCAGTCGGTCTCGTTCGTT 60.371 57.895 0.00 0.00 37.69 3.85
2830 3154 0.110056 GCAGTCGGTCTCGTTCGTTA 60.110 55.000 0.00 0.00 37.69 3.18
2831 3155 1.664016 GCAGTCGGTCTCGTTCGTTAA 60.664 52.381 0.00 0.00 37.69 2.01
2832 3156 2.653890 CAGTCGGTCTCGTTCGTTAAA 58.346 47.619 0.00 0.00 37.69 1.52
2833 3157 3.240069 CAGTCGGTCTCGTTCGTTAAAT 58.760 45.455 0.00 0.00 37.69 1.40
2834 3158 3.671928 CAGTCGGTCTCGTTCGTTAAATT 59.328 43.478 0.00 0.00 37.69 1.82
2835 3159 4.149396 CAGTCGGTCTCGTTCGTTAAATTT 59.851 41.667 0.00 0.00 37.69 1.82
2836 3160 5.343058 CAGTCGGTCTCGTTCGTTAAATTTA 59.657 40.000 0.00 0.00 37.69 1.40
2837 3161 6.034256 CAGTCGGTCTCGTTCGTTAAATTTAT 59.966 38.462 0.00 0.00 37.69 1.40
2838 3162 6.034256 AGTCGGTCTCGTTCGTTAAATTTATG 59.966 38.462 0.00 0.00 37.69 1.90
2839 3163 5.289193 TCGGTCTCGTTCGTTAAATTTATGG 59.711 40.000 0.00 0.00 37.69 2.74
2840 3164 5.062558 CGGTCTCGTTCGTTAAATTTATGGT 59.937 40.000 0.00 0.00 0.00 3.55
2841 3165 6.472680 GGTCTCGTTCGTTAAATTTATGGTC 58.527 40.000 0.00 0.00 0.00 4.02
2842 3166 6.091169 GGTCTCGTTCGTTAAATTTATGGTCA 59.909 38.462 0.00 0.00 0.00 4.02
2843 3167 7.360269 GGTCTCGTTCGTTAAATTTATGGTCAA 60.360 37.037 0.00 0.00 0.00 3.18
2844 3168 8.011106 GTCTCGTTCGTTAAATTTATGGTCAAA 58.989 33.333 0.00 0.00 0.00 2.69
2845 3169 8.225107 TCTCGTTCGTTAAATTTATGGTCAAAG 58.775 33.333 0.00 0.00 0.00 2.77
2846 3170 7.863666 TCGTTCGTTAAATTTATGGTCAAAGT 58.136 30.769 0.00 0.00 0.00 2.66
2847 3171 8.344098 TCGTTCGTTAAATTTATGGTCAAAGTT 58.656 29.630 0.00 0.00 31.36 2.66
2848 3172 8.624028 CGTTCGTTAAATTTATGGTCAAAGTTC 58.376 33.333 0.00 0.00 29.44 3.01
2849 3173 8.624028 GTTCGTTAAATTTATGGTCAAAGTTCG 58.376 33.333 0.00 0.00 29.44 3.95
2850 3174 8.085720 TCGTTAAATTTATGGTCAAAGTTCGA 57.914 30.769 0.00 0.00 29.44 3.71
2851 3175 8.011106 TCGTTAAATTTATGGTCAAAGTTCGAC 58.989 33.333 0.00 0.00 29.44 4.20
2857 3181 3.879912 GTCAAAGTTCGACCTCGGA 57.120 52.632 0.00 0.00 40.29 4.55
2858 3182 2.144482 GTCAAAGTTCGACCTCGGAA 57.856 50.000 0.00 0.00 40.29 4.30
2859 3183 2.476821 GTCAAAGTTCGACCTCGGAAA 58.523 47.619 0.00 0.00 40.29 3.13
2860 3184 2.475487 GTCAAAGTTCGACCTCGGAAAG 59.525 50.000 0.00 0.00 40.29 2.62
2861 3185 1.194772 CAAAGTTCGACCTCGGAAAGC 59.805 52.381 0.00 0.00 40.29 3.51
2862 3186 0.666577 AAGTTCGACCTCGGAAAGCG 60.667 55.000 0.00 0.00 40.29 4.68
2863 3187 2.431942 TTCGACCTCGGAAAGCGC 60.432 61.111 0.00 0.00 40.29 5.92
2864 3188 4.771356 TCGACCTCGGAAAGCGCG 62.771 66.667 0.00 0.00 40.29 6.86
2878 3202 4.222589 CGCGGGCGCACTACATTG 62.223 66.667 8.62 0.00 42.06 2.82
2879 3203 3.124921 GCGGGCGCACTACATTGT 61.125 61.111 8.62 0.00 41.49 2.71
2880 3204 2.784596 CGGGCGCACTACATTGTG 59.215 61.111 8.62 0.00 40.62 3.33
2881 3205 2.749865 CGGGCGCACTACATTGTGG 61.750 63.158 8.62 0.00 38.31 4.17
2882 3206 1.376683 GGGCGCACTACATTGTGGA 60.377 57.895 10.83 0.00 38.31 4.02
2883 3207 0.958382 GGGCGCACTACATTGTGGAA 60.958 55.000 10.83 0.00 38.31 3.53
2884 3208 1.094785 GGCGCACTACATTGTGGAAT 58.905 50.000 10.83 0.00 38.31 3.01
2885 3209 1.202177 GGCGCACTACATTGTGGAATG 60.202 52.381 10.83 0.00 44.11 2.67
2886 3210 1.202177 GCGCACTACATTGTGGAATGG 60.202 52.381 0.30 0.00 43.00 3.16
2887 3211 2.355197 CGCACTACATTGTGGAATGGA 58.645 47.619 7.20 0.00 43.00 3.41
2888 3212 2.746904 CGCACTACATTGTGGAATGGAA 59.253 45.455 7.20 0.00 43.00 3.53
2889 3213 3.181507 CGCACTACATTGTGGAATGGAAG 60.182 47.826 7.20 0.00 43.00 3.46
2890 3214 3.129287 GCACTACATTGTGGAATGGAAGG 59.871 47.826 7.20 0.00 43.00 3.46
2891 3215 4.588899 CACTACATTGTGGAATGGAAGGA 58.411 43.478 7.20 0.00 43.00 3.36
2892 3216 4.637534 CACTACATTGTGGAATGGAAGGAG 59.362 45.833 7.20 0.00 43.00 3.69
2893 3217 3.814504 ACATTGTGGAATGGAAGGAGT 57.185 42.857 0.00 0.00 43.00 3.85
2894 3218 4.927267 ACATTGTGGAATGGAAGGAGTA 57.073 40.909 0.00 0.00 43.00 2.59
2897 3221 4.715534 TTGTGGAATGGAAGGAGTACAA 57.284 40.909 0.00 0.00 0.00 2.41
2899 3223 4.651778 TGTGGAATGGAAGGAGTACAAAG 58.348 43.478 0.00 0.00 0.00 2.77
2900 3224 4.104102 TGTGGAATGGAAGGAGTACAAAGT 59.896 41.667 0.00 0.00 0.00 2.66
2903 3227 5.163141 TGGAATGGAAGGAGTACAAAGTTGA 60.163 40.000 0.00 0.00 0.00 3.18
2908 3232 5.071788 TGGAAGGAGTACAAAGTTGAGACAT 59.928 40.000 0.00 0.00 0.00 3.06
2909 3233 5.998363 GGAAGGAGTACAAAGTTGAGACATT 59.002 40.000 0.00 0.00 0.00 2.71
2912 3236 9.220767 GAAGGAGTACAAAGTTGAGACATTTAT 57.779 33.333 0.00 0.00 0.00 1.40
2913 3237 9.574516 AAGGAGTACAAAGTTGAGACATTTATT 57.425 29.630 0.00 0.00 0.00 1.40
2922 3246 7.962964 AGTTGAGACATTTATTTTGAGACGA 57.037 32.000 0.00 0.00 0.00 4.20
2926 3250 7.158697 TGAGACATTTATTTTGAGACGAAGGA 58.841 34.615 0.00 0.00 0.00 3.36
2931 3255 8.718734 ACATTTATTTTGAGACGAAGGAAGTAC 58.281 33.333 0.00 0.00 0.00 2.73
2932 3256 8.936864 CATTTATTTTGAGACGAAGGAAGTACT 58.063 33.333 0.00 0.00 0.00 2.73
2942 3341 9.715123 GAGACGAAGGAAGTACTTACTTATTAC 57.285 37.037 29.14 20.17 43.40 1.89
2965 3364 9.743057 TTACTAAGGTTCATTGAACATTGTTTG 57.257 29.630 29.70 20.80 44.36 2.93
2970 3369 4.235939 TCATTGAACATTGTTTGTCCCG 57.764 40.909 3.08 0.00 37.68 5.14
3010 3409 7.960793 ACGCTACTTTCATGTACTAAATTGTC 58.039 34.615 0.00 0.00 0.00 3.18
3066 3465 1.683917 GTGCATCTCGACCATCCTACT 59.316 52.381 0.00 0.00 0.00 2.57
3095 3494 8.789762 GGTTCCTTCTAGATCTTGTATCTAGTC 58.210 40.741 17.33 6.69 44.79 2.59
3124 3523 2.901249 TCGTCTAGCCATTTTGCCTAC 58.099 47.619 0.00 0.00 0.00 3.18
3128 3527 1.003646 TAGCCATTTTGCCTACCCCA 58.996 50.000 0.00 0.00 0.00 4.96
3129 3528 0.614697 AGCCATTTTGCCTACCCCAC 60.615 55.000 0.00 0.00 0.00 4.61
3133 3532 1.067915 CATTTTGCCTACCCCACAACG 60.068 52.381 0.00 0.00 0.00 4.10
3158 3557 7.256286 GTCTTATGGACTACACGTATTTGACT 58.744 38.462 0.00 0.00 41.46 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.883217 AGGCAATCCATATGTCATCTATGAAC 59.117 38.462 1.24 0.00 34.86 3.18
134 141 4.755266 AGTGCTCCACGGATAAAATAGT 57.245 40.909 0.00 0.00 39.64 2.12
135 142 6.281405 ACTAAGTGCTCCACGGATAAAATAG 58.719 40.000 0.00 0.00 39.64 1.73
136 143 6.229936 ACTAAGTGCTCCACGGATAAAATA 57.770 37.500 0.00 0.00 39.64 1.40
137 144 5.099042 ACTAAGTGCTCCACGGATAAAAT 57.901 39.130 0.00 0.00 39.64 1.82
138 145 4.546829 ACTAAGTGCTCCACGGATAAAA 57.453 40.909 0.00 0.00 39.64 1.52
142 152 2.699954 CAAACTAAGTGCTCCACGGAT 58.300 47.619 0.00 0.00 39.64 4.18
147 157 2.638480 ACTGCAAACTAAGTGCTCCA 57.362 45.000 0.00 0.00 42.69 3.86
148 158 3.990318 AAACTGCAAACTAAGTGCTCC 57.010 42.857 0.00 0.00 42.69 4.70
175 185 1.043816 CCGAGTATCAGCTCCACCAT 58.956 55.000 0.00 0.00 33.17 3.55
204 214 5.449177 GCATACAGAATAGCTTGGTCCAAAC 60.449 44.000 5.64 0.68 0.00 2.93
228 238 3.119708 CCAAATCTCAAAGGGAAGCTTCG 60.120 47.826 19.91 6.18 0.00 3.79
236 246 3.256631 CACAAGGTCCAAATCTCAAAGGG 59.743 47.826 0.00 0.00 0.00 3.95
299 309 1.993370 GGAATATCGTGCTACGCATCC 59.007 52.381 4.15 5.46 41.91 3.51
327 337 2.715046 TGCTCGATGCTTTTGAGGATT 58.285 42.857 8.07 0.00 43.37 3.01
340 350 2.418368 TTGGTTTGGCTATGCTCGAT 57.582 45.000 0.00 0.00 0.00 3.59
342 352 1.468054 GCTTTGGTTTGGCTATGCTCG 60.468 52.381 0.00 0.00 0.00 5.03
364 374 5.507637 TCCTACTTTCTCAAGACGGATAGT 58.492 41.667 0.00 0.00 33.72 2.12
393 403 3.440173 CCTGAATTTACGCAGGTGTGAAT 59.560 43.478 0.00 0.00 45.21 2.57
523 537 1.147153 GATGCTAGAGGTGGGTGCC 59.853 63.158 0.00 0.00 0.00 5.01
535 549 7.039714 CCGGGCTTACATAGATATATGATGCTA 60.040 40.741 14.15 0.00 0.00 3.49
536 550 6.239430 CCGGGCTTACATAGATATATGATGCT 60.239 42.308 14.15 0.00 0.00 3.79
537 551 5.928839 CCGGGCTTACATAGATATATGATGC 59.071 44.000 14.15 12.89 0.00 3.91
538 552 6.459066 CCCGGGCTTACATAGATATATGATG 58.541 44.000 8.08 4.88 0.00 3.07
552 570 3.647649 AACGTACGCCCGGGCTTAC 62.648 63.158 39.20 39.20 40.84 2.34
560 578 3.798878 GGAAATTAGTAGAACGTACGCCC 59.201 47.826 16.72 7.31 0.00 6.13
562 580 5.576895 AGAGGAAATTAGTAGAACGTACGC 58.423 41.667 16.72 0.00 0.00 4.42
626 644 1.473965 CGGAGCCGACTGGTAGTAGTA 60.474 57.143 2.00 0.00 42.83 1.82
692 710 0.321122 GGAGTGGCACAGAACAGGAG 60.321 60.000 21.41 0.00 41.80 3.69
760 778 5.262588 AGAAGGAATCCAACAACAACAAC 57.737 39.130 0.61 0.00 0.00 3.32
761 779 5.930837 AAGAAGGAATCCAACAACAACAA 57.069 34.783 0.61 0.00 0.00 2.83
762 780 5.656416 AGAAAGAAGGAATCCAACAACAACA 59.344 36.000 0.61 0.00 0.00 3.33
763 781 6.149129 AGAAAGAAGGAATCCAACAACAAC 57.851 37.500 0.61 0.00 0.00 3.32
770 788 4.455877 GCTCGAAAGAAAGAAGGAATCCAA 59.544 41.667 0.61 0.00 41.32 3.53
771 789 4.003648 GCTCGAAAGAAAGAAGGAATCCA 58.996 43.478 0.61 0.00 41.32 3.41
801 819 1.080093 GTGCTAGTGCTACCGTGCA 60.080 57.895 0.00 0.00 41.05 4.57
833 851 5.584251 CCATTTAAAGAAGGAGAGACTGAGC 59.416 44.000 0.00 0.00 0.00 4.26
834 852 6.706295 ACCATTTAAAGAAGGAGAGACTGAG 58.294 40.000 10.16 0.00 0.00 3.35
839 857 6.215431 TGATGGACCATTTAAAGAAGGAGAGA 59.785 38.462 8.78 0.00 0.00 3.10
840 858 6.418101 TGATGGACCATTTAAAGAAGGAGAG 58.582 40.000 8.78 0.00 0.00 3.20
841 859 6.012508 ACTGATGGACCATTTAAAGAAGGAGA 60.013 38.462 8.78 0.00 0.00 3.71
843 861 6.139679 ACTGATGGACCATTTAAAGAAGGA 57.860 37.500 8.78 0.00 0.00 3.36
859 888 2.415893 GGCAACGAAATGGAACTGATGG 60.416 50.000 0.00 0.00 0.00 3.51
1074 1112 6.603201 TCAGAGAAAAAGCAGGAGAAAAGAAA 59.397 34.615 0.00 0.00 0.00 2.52
1084 1122 5.892160 TCAATCATCAGAGAAAAAGCAGG 57.108 39.130 0.00 0.00 0.00 4.85
1121 1159 3.027292 CGCGAGCTCTCTAGACCC 58.973 66.667 12.85 0.00 0.00 4.46
1140 1179 0.804989 GAAAGGCATCCGTGAACCAG 59.195 55.000 0.00 0.00 0.00 4.00
1185 1224 2.158780 AGGAAGGTCAAAGCTGCCT 58.841 52.632 0.00 0.00 46.83 4.75
1350 1393 4.083802 GCTATCAACTGAACATATTCCGGC 60.084 45.833 0.00 0.00 33.49 6.13
1355 1398 4.752101 GCTCGGCTATCAACTGAACATATT 59.248 41.667 0.00 0.00 0.00 1.28
1356 1399 4.039730 AGCTCGGCTATCAACTGAACATAT 59.960 41.667 0.00 0.00 36.99 1.78
1357 1400 3.384789 AGCTCGGCTATCAACTGAACATA 59.615 43.478 0.00 0.00 36.99 2.29
1358 1401 2.169352 AGCTCGGCTATCAACTGAACAT 59.831 45.455 0.00 0.00 36.99 2.71
1359 1402 1.550524 AGCTCGGCTATCAACTGAACA 59.449 47.619 0.00 0.00 36.99 3.18
1360 1403 2.301577 AGCTCGGCTATCAACTGAAC 57.698 50.000 0.00 0.00 36.99 3.18
1361 1404 3.002791 CAAAGCTCGGCTATCAACTGAA 58.997 45.455 0.00 0.00 38.25 3.02
1362 1405 2.621338 CAAAGCTCGGCTATCAACTGA 58.379 47.619 0.00 0.00 38.25 3.41
1363 1406 1.063174 GCAAAGCTCGGCTATCAACTG 59.937 52.381 2.52 0.00 38.25 3.16
1364 1407 1.065854 AGCAAAGCTCGGCTATCAACT 60.066 47.619 10.10 0.00 38.25 3.16
1365 1408 1.373570 AGCAAAGCTCGGCTATCAAC 58.626 50.000 10.10 0.00 38.25 3.18
1366 1409 2.483714 CCTAGCAAAGCTCGGCTATCAA 60.484 50.000 16.81 0.89 41.41 2.57
1367 1410 1.069204 CCTAGCAAAGCTCGGCTATCA 59.931 52.381 16.81 1.19 41.41 2.15
1374 1417 4.839668 ATACTACTCCTAGCAAAGCTCG 57.160 45.455 0.00 0.00 40.44 5.03
1446 1651 0.730265 TGTGTGACAAACGTTGGAGC 59.270 50.000 10.33 1.45 34.12 4.70
1663 1868 2.124193 TGTTGCTGCTGCTGTGGT 60.124 55.556 17.00 0.00 40.48 4.16
1864 2111 1.490490 TGTTGCTCCTGGTGTTCTTCT 59.510 47.619 0.00 0.00 0.00 2.85
1865 2112 1.876156 CTGTTGCTCCTGGTGTTCTTC 59.124 52.381 0.00 0.00 0.00 2.87
2169 2428 1.004440 ACTTCAAGCGCTCAGGGTC 60.004 57.895 12.06 0.00 0.00 4.46
2232 2499 2.487762 CGGTGCAAAGAGCTAATGGAAA 59.512 45.455 0.00 0.00 45.94 3.13
2294 2561 0.515127 TTTCGCCTGCACAACATACG 59.485 50.000 0.00 0.00 0.00 3.06
2304 2571 2.343426 CCCCCTTTCTTTCGCCTGC 61.343 63.158 0.00 0.00 0.00 4.85
2310 2577 4.023980 CCCAACTATTCCCCCTTTCTTTC 58.976 47.826 0.00 0.00 0.00 2.62
2367 2634 4.785511 ATATCCTACGAACCGAATCCAG 57.214 45.455 0.00 0.00 0.00 3.86
2383 2650 7.992754 AAAGAGCATCATGGAAGTAATATCC 57.007 36.000 0.00 0.00 37.82 2.59
2394 2661 0.590732 GCGCGAAAAGAGCATCATGG 60.591 55.000 12.10 0.00 45.36 3.66
2415 2683 6.696411 TCTCTTCTTAGCTTTCCAAGAGAAG 58.304 40.000 17.93 13.05 43.84 2.85
2424 2692 8.725148 TCATTGACAAATCTCTTCTTAGCTTTC 58.275 33.333 0.00 0.00 0.00 2.62
2442 2710 1.317613 GTGGCCAACAGTCATTGACA 58.682 50.000 18.57 0.00 34.60 3.58
2451 2719 0.670162 CTGTCTTTGGTGGCCAACAG 59.330 55.000 25.28 20.24 43.82 3.16
2476 2744 7.620880 ACACCTCTTAGACACATTATGCTTAA 58.379 34.615 0.00 0.00 0.00 1.85
2477 2745 7.182817 ACACCTCTTAGACACATTATGCTTA 57.817 36.000 0.00 0.00 0.00 3.09
2479 2747 5.683876 ACACCTCTTAGACACATTATGCT 57.316 39.130 0.00 0.00 0.00 3.79
2480 2748 6.073548 GCATACACCTCTTAGACACATTATGC 60.074 42.308 0.00 0.00 33.48 3.14
2481 2749 6.144563 CGCATACACCTCTTAGACACATTATG 59.855 42.308 0.00 0.00 0.00 1.90
2482 2750 6.040504 TCGCATACACCTCTTAGACACATTAT 59.959 38.462 0.00 0.00 0.00 1.28
2483 2751 5.358725 TCGCATACACCTCTTAGACACATTA 59.641 40.000 0.00 0.00 0.00 1.90
2484 2752 4.159693 TCGCATACACCTCTTAGACACATT 59.840 41.667 0.00 0.00 0.00 2.71
2553 2821 9.655769 CAATGATTTGATCACGTAAATTCTAGG 57.344 33.333 0.00 0.00 43.01 3.02
2597 2866 7.540299 AGACACTTATTTTAGAACGGAGAGAG 58.460 38.462 0.00 0.00 0.00 3.20
2598 2867 7.463961 AGACACTTATTTTAGAACGGAGAGA 57.536 36.000 0.00 0.00 0.00 3.10
2599 2868 9.635520 TTAAGACACTTATTTTAGAACGGAGAG 57.364 33.333 0.00 0.00 0.00 3.20
2645 2928 7.758820 TGGAATGGAGGGAGTACTAATTTTA 57.241 36.000 0.00 0.00 0.00 1.52
2648 2931 6.652205 TTTGGAATGGAGGGAGTACTAATT 57.348 37.500 0.00 0.00 0.00 1.40
2653 2977 7.661847 CACTATATTTTGGAATGGAGGGAGTAC 59.338 40.741 0.00 0.00 0.00 2.73
2659 2983 4.821805 ACGCACTATATTTTGGAATGGAGG 59.178 41.667 0.00 0.00 0.00 4.30
2662 2986 4.319477 CGGACGCACTATATTTTGGAATGG 60.319 45.833 0.00 0.00 0.00 3.16
2664 2988 3.250040 GCGGACGCACTATATTTTGGAAT 59.750 43.478 12.31 0.00 41.49 3.01
2667 2991 1.070843 CGCGGACGCACTATATTTTGG 60.071 52.381 17.35 0.00 42.06 3.28
2685 3009 4.430765 TTCGACCTCGGGAAGCGC 62.431 66.667 0.00 0.00 40.29 5.92
2686 3010 2.488087 AAGTTCGACCTCGGGAAGCG 62.488 60.000 0.00 0.00 40.29 4.68
2687 3011 0.320508 AAAGTTCGACCTCGGGAAGC 60.321 55.000 0.00 0.00 40.29 3.86
2688 3012 1.000506 TCAAAGTTCGACCTCGGGAAG 59.999 52.381 0.00 0.00 40.29 3.46
2689 3013 1.042229 TCAAAGTTCGACCTCGGGAA 58.958 50.000 0.00 0.00 40.29 3.97
2690 3014 0.316204 GTCAAAGTTCGACCTCGGGA 59.684 55.000 0.00 0.00 40.29 5.14
2691 3015 2.823628 GTCAAAGTTCGACCTCGGG 58.176 57.895 0.00 0.00 40.29 5.14
2697 3021 8.011106 TCGTTAAATTTATGGTCAAAGTTCGAC 58.989 33.333 0.00 0.00 29.44 4.20
2699 3023 8.624028 GTTCGTTAAATTTATGGTCAAAGTTCG 58.376 33.333 0.00 0.00 29.44 3.95
2705 3029 7.360269 GGTCTCGTTCGTTAAATTTATGGTCAA 60.360 37.037 0.00 0.00 0.00 3.18
2706 3030 6.091169 GGTCTCGTTCGTTAAATTTATGGTCA 59.909 38.462 0.00 0.00 0.00 4.02
2707 3031 6.472680 GGTCTCGTTCGTTAAATTTATGGTC 58.527 40.000 0.00 0.00 0.00 4.02
2709 3033 5.289193 TCGGTCTCGTTCGTTAAATTTATGG 59.711 40.000 0.00 0.00 37.69 2.74
2710 3034 6.321873 TCGGTCTCGTTCGTTAAATTTATG 57.678 37.500 0.00 0.00 37.69 1.90
2711 3035 7.396419 CAATCGGTCTCGTTCGTTAAATTTAT 58.604 34.615 0.00 0.00 37.69 1.40
2712 3036 6.670452 GCAATCGGTCTCGTTCGTTAAATTTA 60.670 38.462 0.00 0.00 37.69 1.40
2713 3037 5.614760 CAATCGGTCTCGTTCGTTAAATTT 58.385 37.500 0.00 0.00 37.69 1.82
2714 3038 4.435121 GCAATCGGTCTCGTTCGTTAAATT 60.435 41.667 0.00 0.00 37.69 1.82
2715 3039 3.061697 GCAATCGGTCTCGTTCGTTAAAT 59.938 43.478 0.00 0.00 37.69 1.40
2716 3040 2.409378 GCAATCGGTCTCGTTCGTTAAA 59.591 45.455 0.00 0.00 37.69 1.52
2717 3041 1.987770 GCAATCGGTCTCGTTCGTTAA 59.012 47.619 0.00 0.00 37.69 2.01
2718 3042 1.621107 GCAATCGGTCTCGTTCGTTA 58.379 50.000 0.00 0.00 37.69 3.18
2719 3043 1.342082 CGCAATCGGTCTCGTTCGTT 61.342 55.000 0.00 0.00 37.69 3.85
2732 3056 2.872337 CTTTTGCTCCCGCCGCAATC 62.872 60.000 5.33 0.00 45.67 2.67
2733 3057 2.988684 TTTTGCTCCCGCCGCAAT 60.989 55.556 5.33 0.00 45.67 3.56
2734 3058 3.669344 CTTTTGCTCCCGCCGCAA 61.669 61.111 0.00 0.00 44.83 4.85
2735 3059 4.887932 TATAACTTTTGCTCCCGCCGCA 62.888 50.000 0.00 0.00 35.22 5.69
2736 3060 1.654023 ATAACTTTTGCTCCCGCCGC 61.654 55.000 0.00 0.00 34.43 6.53
2737 3061 1.658994 TATAACTTTTGCTCCCGCCG 58.341 50.000 0.00 0.00 34.43 6.46
2738 3062 3.211045 TGATATAACTTTTGCTCCCGCC 58.789 45.455 0.00 0.00 34.43 6.13
2739 3063 4.893424 TTGATATAACTTTTGCTCCCGC 57.107 40.909 0.00 0.00 0.00 6.13
2740 3064 6.618287 TCATTGATATAACTTTTGCTCCCG 57.382 37.500 0.00 0.00 0.00 5.14
2741 3065 9.468532 GAATTCATTGATATAACTTTTGCTCCC 57.531 33.333 0.00 0.00 0.00 4.30
2742 3066 9.173939 CGAATTCATTGATATAACTTTTGCTCC 57.826 33.333 6.22 0.00 0.00 4.70
2743 3067 9.722056 ACGAATTCATTGATATAACTTTTGCTC 57.278 29.630 6.22 0.00 0.00 4.26
2783 3107 9.628746 GCGGGAGAAAAAGTTACATAATTAAAA 57.371 29.630 0.00 0.00 0.00 1.52
2784 3108 8.245491 GGCGGGAGAAAAAGTTACATAATTAAA 58.755 33.333 0.00 0.00 0.00 1.52
2785 3109 7.414319 CGGCGGGAGAAAAAGTTACATAATTAA 60.414 37.037 0.00 0.00 0.00 1.40
2786 3110 6.037391 CGGCGGGAGAAAAAGTTACATAATTA 59.963 38.462 0.00 0.00 0.00 1.40
2787 3111 5.163693 CGGCGGGAGAAAAAGTTACATAATT 60.164 40.000 0.00 0.00 0.00 1.40
2788 3112 4.334481 CGGCGGGAGAAAAAGTTACATAAT 59.666 41.667 0.00 0.00 0.00 1.28
2789 3113 3.685756 CGGCGGGAGAAAAAGTTACATAA 59.314 43.478 0.00 0.00 0.00 1.90
2790 3114 3.264104 CGGCGGGAGAAAAAGTTACATA 58.736 45.455 0.00 0.00 0.00 2.29
2791 3115 2.081462 CGGCGGGAGAAAAAGTTACAT 58.919 47.619 0.00 0.00 0.00 2.29
2792 3116 1.515081 CGGCGGGAGAAAAAGTTACA 58.485 50.000 0.00 0.00 0.00 2.41
2793 3117 0.167470 GCGGCGGGAGAAAAAGTTAC 59.833 55.000 9.78 0.00 0.00 2.50
2794 3118 0.250381 TGCGGCGGGAGAAAAAGTTA 60.250 50.000 9.78 0.00 0.00 2.24
2795 3119 1.515521 CTGCGGCGGGAGAAAAAGTT 61.516 55.000 9.78 0.00 32.53 2.66
2796 3120 1.966451 CTGCGGCGGGAGAAAAAGT 60.966 57.895 9.78 0.00 32.53 2.66
2797 3121 1.912371 GACTGCGGCGGGAGAAAAAG 61.912 60.000 19.55 0.00 35.29 2.27
2798 3122 1.964373 GACTGCGGCGGGAGAAAAA 60.964 57.895 19.55 0.00 35.29 1.94
2799 3123 2.358247 GACTGCGGCGGGAGAAAA 60.358 61.111 19.55 0.00 35.29 2.29
2800 3124 4.735132 CGACTGCGGCGGGAGAAA 62.735 66.667 19.55 0.00 35.29 2.52
2810 3134 2.870161 CGAACGAGACCGACTGCG 60.870 66.667 0.00 0.00 39.50 5.18
2811 3135 0.110056 TAACGAACGAGACCGACTGC 60.110 55.000 0.14 0.00 39.50 4.40
2812 3136 2.320805 TTAACGAACGAGACCGACTG 57.679 50.000 0.14 0.00 39.50 3.51
2813 3137 3.565905 ATTTAACGAACGAGACCGACT 57.434 42.857 0.14 0.00 39.50 4.18
2814 3138 4.635961 AAATTTAACGAACGAGACCGAC 57.364 40.909 0.14 0.00 39.50 4.79
2815 3139 5.289193 CCATAAATTTAACGAACGAGACCGA 59.711 40.000 1.21 0.00 39.50 4.69
2816 3140 5.062558 ACCATAAATTTAACGAACGAGACCG 59.937 40.000 1.21 0.00 42.50 4.79
2817 3141 6.091169 TGACCATAAATTTAACGAACGAGACC 59.909 38.462 1.21 0.00 0.00 3.85
2818 3142 7.052565 TGACCATAAATTTAACGAACGAGAC 57.947 36.000 1.21 0.00 0.00 3.36
2819 3143 7.655236 TTGACCATAAATTTAACGAACGAGA 57.345 32.000 1.21 0.00 0.00 4.04
2820 3144 8.013378 ACTTTGACCATAAATTTAACGAACGAG 58.987 33.333 1.21 0.01 0.00 4.18
2821 3145 7.863666 ACTTTGACCATAAATTTAACGAACGA 58.136 30.769 1.21 0.00 0.00 3.85
2822 3146 8.496872 AACTTTGACCATAAATTTAACGAACG 57.503 30.769 1.21 0.00 0.00 3.95
2823 3147 8.624028 CGAACTTTGACCATAAATTTAACGAAC 58.376 33.333 1.21 0.00 0.00 3.95
2824 3148 8.557864 TCGAACTTTGACCATAAATTTAACGAA 58.442 29.630 1.21 1.12 0.00 3.85
2825 3149 8.011106 GTCGAACTTTGACCATAAATTTAACGA 58.989 33.333 1.21 0.00 0.00 3.85
2826 3150 8.142348 GTCGAACTTTGACCATAAATTTAACG 57.858 34.615 1.21 0.00 0.00 3.18
2839 3163 2.144482 TTCCGAGGTCGAACTTTGAC 57.856 50.000 3.47 0.86 43.02 3.18
2840 3164 2.750948 CTTTCCGAGGTCGAACTTTGA 58.249 47.619 3.47 0.91 43.02 2.69
2841 3165 1.194772 GCTTTCCGAGGTCGAACTTTG 59.805 52.381 3.47 0.00 43.02 2.77
2842 3166 1.509703 GCTTTCCGAGGTCGAACTTT 58.490 50.000 3.47 0.00 43.02 2.66
2843 3167 0.666577 CGCTTTCCGAGGTCGAACTT 60.667 55.000 3.47 0.00 43.02 2.66
2844 3168 1.080705 CGCTTTCCGAGGTCGAACT 60.081 57.895 0.34 0.34 43.02 3.01
2845 3169 2.727684 GCGCTTTCCGAGGTCGAAC 61.728 63.158 0.00 0.00 43.02 3.95
2846 3170 2.431942 GCGCTTTCCGAGGTCGAA 60.432 61.111 0.00 0.00 43.02 3.71
2847 3171 4.771356 CGCGCTTTCCGAGGTCGA 62.771 66.667 5.56 0.00 43.02 4.20
2861 3185 4.222589 CAATGTAGTGCGCCCGCG 62.223 66.667 4.18 4.36 45.51 6.46
2862 3186 3.124921 ACAATGTAGTGCGCCCGC 61.125 61.111 4.18 5.60 42.35 6.13
2863 3187 2.749865 CCACAATGTAGTGCGCCCG 61.750 63.158 4.18 0.00 38.18 6.13
2864 3188 0.958382 TTCCACAATGTAGTGCGCCC 60.958 55.000 4.18 0.00 38.18 6.13
2865 3189 1.094785 ATTCCACAATGTAGTGCGCC 58.905 50.000 4.18 0.00 38.18 6.53
2866 3190 1.202177 CCATTCCACAATGTAGTGCGC 60.202 52.381 0.00 0.00 38.22 6.09
2867 3191 2.355197 TCCATTCCACAATGTAGTGCG 58.645 47.619 0.00 0.00 38.22 5.34
2868 3192 3.129287 CCTTCCATTCCACAATGTAGTGC 59.871 47.826 0.00 0.00 38.22 4.40
2869 3193 4.588899 TCCTTCCATTCCACAATGTAGTG 58.411 43.478 0.00 0.00 38.22 2.74
2870 3194 4.289672 ACTCCTTCCATTCCACAATGTAGT 59.710 41.667 0.00 0.00 38.22 2.73
2871 3195 4.848357 ACTCCTTCCATTCCACAATGTAG 58.152 43.478 0.00 0.00 38.22 2.74
2872 3196 4.927267 ACTCCTTCCATTCCACAATGTA 57.073 40.909 0.00 0.00 38.22 2.29
2873 3197 3.814504 ACTCCTTCCATTCCACAATGT 57.185 42.857 0.00 0.00 38.22 2.71
2874 3198 4.588899 TGTACTCCTTCCATTCCACAATG 58.411 43.478 0.00 0.00 39.45 2.82
2875 3199 4.927267 TGTACTCCTTCCATTCCACAAT 57.073 40.909 0.00 0.00 0.00 2.71
2876 3200 4.715534 TTGTACTCCTTCCATTCCACAA 57.284 40.909 0.00 0.00 0.00 3.33
2877 3201 4.104102 ACTTTGTACTCCTTCCATTCCACA 59.896 41.667 0.00 0.00 0.00 4.17
2878 3202 4.652822 ACTTTGTACTCCTTCCATTCCAC 58.347 43.478 0.00 0.00 0.00 4.02
2879 3203 4.993705 ACTTTGTACTCCTTCCATTCCA 57.006 40.909 0.00 0.00 0.00 3.53
2880 3204 5.313712 TCAACTTTGTACTCCTTCCATTCC 58.686 41.667 0.00 0.00 0.00 3.01
2881 3205 6.147985 GTCTCAACTTTGTACTCCTTCCATTC 59.852 42.308 0.00 0.00 0.00 2.67
2882 3206 5.998363 GTCTCAACTTTGTACTCCTTCCATT 59.002 40.000 0.00 0.00 0.00 3.16
2883 3207 5.071788 TGTCTCAACTTTGTACTCCTTCCAT 59.928 40.000 0.00 0.00 0.00 3.41
2884 3208 4.407621 TGTCTCAACTTTGTACTCCTTCCA 59.592 41.667 0.00 0.00 0.00 3.53
2885 3209 4.957296 TGTCTCAACTTTGTACTCCTTCC 58.043 43.478 0.00 0.00 0.00 3.46
2886 3210 7.497925 AAATGTCTCAACTTTGTACTCCTTC 57.502 36.000 0.00 0.00 0.00 3.46
2887 3211 9.574516 AATAAATGTCTCAACTTTGTACTCCTT 57.425 29.630 0.00 0.00 0.00 3.36
2888 3212 9.574516 AAATAAATGTCTCAACTTTGTACTCCT 57.425 29.630 0.00 0.00 0.00 3.69
2894 3218 9.736023 GTCTCAAAATAAATGTCTCAACTTTGT 57.264 29.630 0.00 0.00 0.00 2.83
2897 3221 8.378172 TCGTCTCAAAATAAATGTCTCAACTT 57.622 30.769 0.00 0.00 0.00 2.66
2899 3223 7.746475 CCTTCGTCTCAAAATAAATGTCTCAAC 59.254 37.037 0.00 0.00 0.00 3.18
2900 3224 7.659799 TCCTTCGTCTCAAAATAAATGTCTCAA 59.340 33.333 0.00 0.00 0.00 3.02
2903 3227 7.661847 ACTTCCTTCGTCTCAAAATAAATGTCT 59.338 33.333 0.00 0.00 0.00 3.41
2908 3232 8.897872 AAGTACTTCCTTCGTCTCAAAATAAA 57.102 30.769 1.12 0.00 0.00 1.40
2909 3233 9.415544 GTAAGTACTTCCTTCGTCTCAAAATAA 57.584 33.333 12.39 0.00 0.00 1.40
2912 3236 7.047460 AGTAAGTACTTCCTTCGTCTCAAAA 57.953 36.000 12.39 0.00 31.13 2.44
2913 3237 6.645790 AGTAAGTACTTCCTTCGTCTCAAA 57.354 37.500 12.39 0.00 31.13 2.69
2942 3341 7.382218 GGACAAACAATGTTCAATGAACCTTAG 59.618 37.037 21.75 14.59 44.12 2.18
2944 3343 6.048509 GGACAAACAATGTTCAATGAACCTT 58.951 36.000 21.75 15.84 44.12 3.50
2965 3364 4.288531 CGTTAATAGTCATGTCTCGGGAC 58.711 47.826 8.99 8.99 42.42 4.46
2970 3369 7.701078 TGAAAGTAGCGTTAATAGTCATGTCTC 59.299 37.037 0.00 0.00 0.00 3.36
2985 3384 7.601130 TGACAATTTAGTACATGAAAGTAGCGT 59.399 33.333 0.00 0.00 0.00 5.07
3007 3406 5.629133 GCTTTGGTTGATCCCTACTATGACA 60.629 44.000 0.00 0.00 34.77 3.58
3010 3409 4.137543 GGCTTTGGTTGATCCCTACTATG 58.862 47.826 0.00 0.00 34.77 2.23
3017 3416 2.052104 CGGGGCTTTGGTTGATCCC 61.052 63.158 0.00 0.00 36.25 3.85
3095 3494 4.592485 AATGGCTAGACGAAGATGGTAG 57.408 45.455 0.00 0.00 0.00 3.18
3124 3523 1.734163 GTCCATAAGACGTTGTGGGG 58.266 55.000 3.52 0.00 43.50 4.96
3133 3532 7.256286 AGTCAAATACGTGTAGTCCATAAGAC 58.744 38.462 0.00 0.00 46.71 3.01


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

AutoCloner maintained by Alex Coulton.