Multiple sequence alignment - TraesCS6A01G298300

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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 TraesCS6A01G298300 chr6A 100.000 3245 0 0 1286 4530 531525786 531522542 0.000000e+00 5993.0
1 TraesCS6A01G298300 chr6A 100.000 493 0 0 520 1012 531526552 531526060 0.000000e+00 911.0
2 TraesCS6A01G298300 chr6A 100.000 368 0 0 1 368 531527071 531526704 0.000000e+00 680.0
3 TraesCS6A01G298300 chr6A 88.539 349 22 11 2 341 448375265 448374926 1.520000e-109 407.0
4 TraesCS6A01G298300 chr6A 92.537 67 5 0 3631 3697 531523410 531523344 3.730000e-16 97.1
5 TraesCS6A01G298300 chr6A 92.537 67 5 0 3662 3728 531523441 531523375 3.730000e-16 97.1
6 TraesCS6A01G298300 chr6D 92.057 1473 90 12 2343 3803 386442931 386441474 0.000000e+00 2047.0
7 TraesCS6A01G298300 chr6D 94.965 854 29 3 1287 2127 386443900 386443048 0.000000e+00 1327.0
8 TraesCS6A01G298300 chr6D 90.489 736 45 11 3815 4530 386441432 386440702 0.000000e+00 948.0
9 TraesCS6A01G298300 chr6D 89.296 355 22 7 3 341 118306027 118305673 9.000000e-117 431.0
10 TraesCS6A01G298300 chr6D 92.883 281 14 6 736 1012 386444229 386443951 1.960000e-108 403.0
11 TraesCS6A01G298300 chr6D 92.398 171 9 3 2127 2296 48458135 48457968 1.630000e-59 241.0
12 TraesCS6A01G298300 chr6D 86.335 161 21 1 520 679 118305588 118305428 1.680000e-39 174.0
13 TraesCS6A01G298300 chr6D 94.030 67 4 0 3662 3728 386441647 386441581 8.020000e-18 102.0
14 TraesCS6A01G298300 chr6B 88.301 1171 64 29 3163 4276 577365825 577364671 0.000000e+00 1336.0
15 TraesCS6A01G298300 chr6B 94.014 852 30 3 1287 2126 577367630 577366788 0.000000e+00 1271.0
16 TraesCS6A01G298300 chr6B 90.107 839 66 8 2343 3178 577366672 577365848 0.000000e+00 1074.0
17 TraesCS6A01G298300 chr6B 92.063 252 7 2 4281 4530 577364607 577364367 4.340000e-90 342.0
18 TraesCS6A01G298300 chr6B 91.195 159 7 7 857 1012 577367835 577367681 4.590000e-50 209.0
19 TraesCS6A01G298300 chr6B 92.537 67 5 0 3662 3728 577365352 577365286 3.730000e-16 97.1
20 TraesCS6A01G298300 chr2D 92.090 354 13 7 3 341 454812081 454811728 6.810000e-133 484.0
21 TraesCS6A01G298300 chr2D 89.937 159 16 0 520 678 454811646 454811488 5.940000e-49 206.0
22 TraesCS6A01G298300 chr2D 84.706 170 23 3 521 687 512422521 512422690 2.800000e-37 167.0
23 TraesCS6A01G298300 chr7D 91.317 357 14 7 1 341 548071633 548071278 5.300000e-129 472.0
24 TraesCS6A01G298300 chr7D 89.888 356 20 9 1 341 54305073 54305427 1.160000e-120 444.0
25 TraesCS6A01G298300 chr7D 90.385 156 15 0 523 678 548071191 548071036 5.940000e-49 206.0
26 TraesCS6A01G298300 chr7D 87.821 156 17 2 527 681 54305926 54306080 1.000000e-41 182.0
27 TraesCS6A01G298300 chr1D 89.636 357 18 12 2 341 374737934 374738288 1.940000e-118 436.0
28 TraesCS6A01G298300 chr1D 85.621 153 21 1 520 671 374738367 374738519 4.690000e-35 159.0
29 TraesCS6A01G298300 chr5D 89.914 347 20 9 2 341 550181214 550181552 2.500000e-117 433.0
30 TraesCS6A01G298300 chr7B 89.296 355 20 7 2 341 89598747 89598396 3.240000e-116 429.0
31 TraesCS6A01G298300 chr7B 88.483 356 23 10 2 341 624370310 624370663 9.070000e-112 414.0
32 TraesCS6A01G298300 chr7B 88.304 171 18 2 520 690 89598313 89598145 2.140000e-48 204.0
33 TraesCS6A01G298300 chr7B 88.125 160 19 0 520 679 624370757 624370916 1.660000e-44 191.0
34 TraesCS6A01G298300 chr3A 88.825 349 22 10 2 341 675159055 675158715 3.260000e-111 412.0
35 TraesCS6A01G298300 chr3A 88.252 349 24 11 2 341 567653470 567653130 7.060000e-108 401.0
36 TraesCS6A01G298300 chr3A 92.899 169 9 2 2124 2292 600921020 600920855 4.530000e-60 243.0
37 TraesCS6A01G298300 chr1B 88.136 354 28 6 2 341 375985638 375985285 4.220000e-110 409.0
38 TraesCS6A01G298300 chr5A 94.545 165 6 2 2128 2292 320214244 320214405 7.520000e-63 252.0
39 TraesCS6A01G298300 chr5B 93.567 171 6 4 2123 2292 607838386 607838552 2.710000e-62 250.0
40 TraesCS6A01G298300 chr3D 93.413 167 8 2 2128 2294 87926000 87926163 1.260000e-60 244.0
41 TraesCS6A01G298300 chr3D 91.379 174 12 2 2128 2301 375693990 375693820 7.580000e-58 235.0
42 TraesCS6A01G298300 chr7A 92.857 168 9 2 2128 2295 494786990 494786826 1.630000e-59 241.0
43 TraesCS6A01G298300 chr1A 91.429 175 11 3 2127 2301 39439000 39438830 2.110000e-58 237.0
44 TraesCS6A01G298300 chr1A 89.785 186 12 6 2128 2309 181769427 181769609 9.800000e-57 231.0
45 TraesCS6A01G298300 chr3B 86.420 162 18 4 523 681 633218757 633218597 1.680000e-39 174.0


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 TraesCS6A01G298300 chr6A 531522542 531527071 4529 True 1555.640000 5993 97.0148 1 4530 5 chr6A.!!$R2 4529
1 TraesCS6A01G298300 chr6D 386440702 386444229 3527 True 965.400000 2047 92.8848 736 4530 5 chr6D.!!$R3 3794
2 TraesCS6A01G298300 chr6D 118305428 118306027 599 True 302.500000 431 87.8155 3 679 2 chr6D.!!$R2 676
3 TraesCS6A01G298300 chr6B 577364367 577367835 3468 True 721.516667 1336 91.3695 857 4530 6 chr6B.!!$R1 3673
4 TraesCS6A01G298300 chr2D 454811488 454812081 593 True 345.000000 484 91.0135 3 678 2 chr2D.!!$R1 675
5 TraesCS6A01G298300 chr7D 548071036 548071633 597 True 339.000000 472 90.8510 1 678 2 chr7D.!!$R1 677
6 TraesCS6A01G298300 chr7D 54305073 54306080 1007 False 313.000000 444 88.8545 1 681 2 chr7D.!!$F1 680
7 TraesCS6A01G298300 chr1D 374737934 374738519 585 False 297.500000 436 87.6285 2 671 2 chr1D.!!$F1 669
8 TraesCS6A01G298300 chr7B 89598145 89598747 602 True 316.500000 429 88.8000 2 690 2 chr7B.!!$R1 688
9 TraesCS6A01G298300 chr7B 624370310 624370916 606 False 302.500000 414 88.3040 2 679 2 chr7B.!!$F1 677

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
956 1298 0.031585 CAACAGTCGTTCGTCAGGGA 59.968 55.0 0.0 0.0 31.13 4.20 F
957 1299 0.031721 AACAGTCGTTCGTCAGGGAC 59.968 55.0 0.0 0.0 0.00 4.46 F
1784 2140 0.107165 CCCCAAATTCTCCTCCGGTC 60.107 60.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 2140 0.240145 TACCACTCAACGACAGCGAG 59.760 55.0 0.00 0.00 41.64 5.03 R
2015 2371 0.884704 GGAGCACCTTGTTCGAGCAA 60.885 55.0 14.26 14.26 0.00 3.91 R
3756 4225 0.387622 TACACTTGTACACGCTCGCC 60.388 55.0 0.00 0.00 0.00 5.54 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
123 125 8.258708 GTGTATAGAGGTTGAATCACTTACCTT 58.741 37.037 6.56 1.19 40.97 3.50
238 256 2.452600 ATCCTTGTGTTTGGTGGTGT 57.547 45.000 0.00 0.00 0.00 4.16
327 351 1.566703 AGAGGAGAGAACTGATCGGGA 59.433 52.381 6.47 0.00 0.00 5.14
365 412 1.049855 TGGGGTGGTAAGTCACGTGT 61.050 55.000 16.51 0.00 38.46 4.49
367 414 0.105408 GGGTGGTAAGTCACGTGTGT 59.895 55.000 16.51 4.57 38.46 3.72
575 912 1.966451 CGCGAAAGAAGGCTGGGTT 60.966 57.895 0.00 0.00 0.00 4.11
586 923 1.607467 GCTGGGTTGTGGATGGCTT 60.607 57.895 0.00 0.00 0.00 4.35
626 963 1.005867 GAAGGGACGCGGTTGTACA 60.006 57.895 12.47 0.00 0.00 2.90
671 1009 4.158025 CCATCAGTCGACTGGTAGTTAGTT 59.842 45.833 37.82 13.98 43.91 2.24
681 1019 6.429521 ACTGGTAGTTAGTTGCTTCCTTTA 57.570 37.500 0.00 0.00 0.00 1.85
686 1024 8.161425 TGGTAGTTAGTTGCTTCCTTTAGAAAT 58.839 33.333 0.00 0.00 32.88 2.17
701 1039 8.517056 TCCTTTAGAAATAAAGTTTTAAGGGCG 58.483 33.333 0.00 0.00 35.78 6.13
702 1040 8.301720 CCTTTAGAAATAAAGTTTTAAGGGCGT 58.698 33.333 0.00 0.00 35.78 5.68
707 1045 9.467258 AGAAATAAAGTTTTAAGGGCGTAAAAC 57.533 29.630 19.56 19.56 46.99 2.43
713 1051 6.890663 GTTTTAAGGGCGTAAAACAAAGTT 57.109 33.333 21.10 0.00 46.35 2.66
714 1052 7.293402 GTTTTAAGGGCGTAAAACAAAGTTT 57.707 32.000 21.10 0.00 46.35 2.66
715 1053 6.889019 TTTAAGGGCGTAAAACAAAGTTTG 57.111 33.333 14.13 14.13 0.00 2.93
716 1054 3.446310 AGGGCGTAAAACAAAGTTTGG 57.554 42.857 19.45 2.08 34.12 3.28
717 1055 3.025262 AGGGCGTAAAACAAAGTTTGGA 58.975 40.909 19.45 0.00 34.12 3.53
718 1056 3.067601 AGGGCGTAAAACAAAGTTTGGAG 59.932 43.478 19.45 5.47 34.12 3.86
719 1057 3.181484 GGGCGTAAAACAAAGTTTGGAGT 60.181 43.478 19.45 6.50 34.12 3.85
720 1058 3.794564 GGCGTAAAACAAAGTTTGGAGTG 59.205 43.478 19.45 5.68 34.12 3.51
721 1059 3.794564 GCGTAAAACAAAGTTTGGAGTGG 59.205 43.478 19.45 5.68 34.12 4.00
722 1060 4.439016 GCGTAAAACAAAGTTTGGAGTGGA 60.439 41.667 19.45 0.00 34.12 4.02
723 1061 5.735070 GCGTAAAACAAAGTTTGGAGTGGAT 60.735 40.000 19.45 1.93 34.12 3.41
724 1062 6.270064 CGTAAAACAAAGTTTGGAGTGGATT 58.730 36.000 19.45 0.41 34.12 3.01
725 1063 6.754675 CGTAAAACAAAGTTTGGAGTGGATTT 59.245 34.615 19.45 6.44 34.12 2.17
726 1064 7.276878 CGTAAAACAAAGTTTGGAGTGGATTTT 59.723 33.333 19.45 15.37 34.12 1.82
727 1065 7.994425 AAAACAAAGTTTGGAGTGGATTTTT 57.006 28.000 19.45 10.92 34.12 1.94
763 1101 3.590443 CTCAGTTCGCGACGGACGT 62.590 63.158 9.15 0.00 40.73 4.34
767 1105 3.353029 TTCGCGACGGACGTACCA 61.353 61.111 9.15 0.00 44.60 3.25
781 1119 0.452987 GTACCACGCACAGATACCGA 59.547 55.000 0.00 0.00 0.00 4.69
810 1148 0.942252 AAGAGGAAAACGCGTGGAAC 59.058 50.000 14.98 4.07 0.00 3.62
827 1165 3.072915 TGGAACAGGTGATGTGTGATTCT 59.927 43.478 0.00 0.00 43.00 2.40
833 1171 5.107824 CAGGTGATGTGTGATTCTAGACAG 58.892 45.833 0.00 0.00 0.00 3.51
877 1216 6.591448 GTGATGATGTGTGATTCTAGACAACA 59.409 38.462 0.00 0.00 32.69 3.33
881 1220 3.244422 TGTGTGATTCTAGACAACACCCC 60.244 47.826 20.77 12.34 0.00 4.95
883 1222 3.244422 TGTGATTCTAGACAACACCCCAC 60.244 47.826 15.69 0.00 0.00 4.61
887 1228 3.935818 TCTAGACAACACCCCACAAAA 57.064 42.857 0.00 0.00 0.00 2.44
956 1298 0.031585 CAACAGTCGTTCGTCAGGGA 59.968 55.000 0.00 0.00 31.13 4.20
957 1299 0.031721 AACAGTCGTTCGTCAGGGAC 59.968 55.000 0.00 0.00 0.00 4.46
998 1341 1.688811 CCAACTCCCGATTCCCCAA 59.311 57.895 0.00 0.00 0.00 4.12
1774 2130 1.919240 AACGGAGAACCCCCAAATTC 58.081 50.000 0.00 0.00 0.00 2.17
1784 2140 0.107165 CCCCAAATTCTCCTCCGGTC 60.107 60.000 0.00 0.00 0.00 4.79
1833 2189 2.224695 ACTAGGGTTAGTGGGTTTGTGC 60.225 50.000 0.00 0.00 38.69 4.57
1870 2226 3.045601 AGCTAGAAATCACGCTTGTGT 57.954 42.857 0.00 0.00 44.22 3.72
1891 2247 3.559655 GTCTGTGTGTGTGCTTTGATGTA 59.440 43.478 0.00 0.00 0.00 2.29
1894 2250 4.698575 TGTGTGTGTGCTTTGATGTACTA 58.301 39.130 0.00 0.00 0.00 1.82
1898 2254 5.820423 TGTGTGTGCTTTGATGTACTAACTT 59.180 36.000 0.00 0.00 0.00 2.66
2002 2358 1.061546 TTGGGTTCTACTGGGTGGTC 58.938 55.000 0.00 0.00 0.00 4.02
2071 2427 1.337074 CGTCGCCTTAAACCTACACCA 60.337 52.381 0.00 0.00 0.00 4.17
2088 2444 3.568007 ACACCAATCACGCACTACATTTT 59.432 39.130 0.00 0.00 0.00 1.82
2127 2483 8.177119 TGAATGCTTAATTTCTTGTGGTAACT 57.823 30.769 0.00 0.00 37.61 2.24
2129 2485 9.556030 GAATGCTTAATTTCTTGTGGTAACTAC 57.444 33.333 0.00 0.00 37.61 2.73
2130 2486 8.863872 ATGCTTAATTTCTTGTGGTAACTACT 57.136 30.769 0.00 0.00 37.61 2.57
2131 2487 8.319143 TGCTTAATTTCTTGTGGTAACTACTC 57.681 34.615 0.00 0.00 37.61 2.59
2132 2488 7.389607 TGCTTAATTTCTTGTGGTAACTACTCC 59.610 37.037 0.00 0.00 37.61 3.85
2133 2489 7.148289 GCTTAATTTCTTGTGGTAACTACTCCC 60.148 40.741 0.00 0.00 37.61 4.30
2134 2490 6.449830 AATTTCTTGTGGTAACTACTCCCT 57.550 37.500 0.00 0.00 37.61 4.20
2135 2491 5.479124 TTTCTTGTGGTAACTACTCCCTC 57.521 43.478 0.00 0.00 37.61 4.30
2136 2492 3.438183 TCTTGTGGTAACTACTCCCTCC 58.562 50.000 0.00 0.00 37.61 4.30
2137 2493 1.843368 TGTGGTAACTACTCCCTCCG 58.157 55.000 0.00 0.00 37.61 4.63
2138 2494 1.076024 TGTGGTAACTACTCCCTCCGT 59.924 52.381 0.00 0.00 37.61 4.69
2139 2495 2.174360 GTGGTAACTACTCCCTCCGTT 58.826 52.381 0.00 0.00 37.61 4.44
2140 2496 2.165234 GTGGTAACTACTCCCTCCGTTC 59.835 54.545 0.00 0.00 37.61 3.95
2141 2497 1.753649 GGTAACTACTCCCTCCGTTCC 59.246 57.143 0.00 0.00 0.00 3.62
2142 2498 2.622714 GGTAACTACTCCCTCCGTTCCT 60.623 54.545 0.00 0.00 0.00 3.36
2143 2499 3.372025 GGTAACTACTCCCTCCGTTCCTA 60.372 52.174 0.00 0.00 0.00 2.94
2144 2500 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
2145 2501 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2146 2502 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2147 2503 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2148 2504 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2149 2505 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2150 2506 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2151 2507 7.786464 ACTACTCCCTCCGTTCCTAAATATAAA 59.214 37.037 0.00 0.00 0.00 1.40
2152 2508 7.441903 ACTCCCTCCGTTCCTAAATATAAAA 57.558 36.000 0.00 0.00 0.00 1.52
2153 2509 7.506971 ACTCCCTCCGTTCCTAAATATAAAAG 58.493 38.462 0.00 0.00 0.00 2.27
2154 2510 7.126879 ACTCCCTCCGTTCCTAAATATAAAAGT 59.873 37.037 0.00 0.00 0.00 2.66
2155 2511 7.503549 TCCCTCCGTTCCTAAATATAAAAGTC 58.496 38.462 0.00 0.00 0.00 3.01
2156 2512 7.346436 TCCCTCCGTTCCTAAATATAAAAGTCT 59.654 37.037 0.00 0.00 0.00 3.24
2157 2513 7.991460 CCCTCCGTTCCTAAATATAAAAGTCTT 59.009 37.037 0.00 0.00 0.00 3.01
2158 2514 9.392259 CCTCCGTTCCTAAATATAAAAGTCTTT 57.608 33.333 0.00 0.00 0.00 2.52
2190 2546 4.280174 TCCAATAAGGACTACATACGGAGC 59.720 45.833 0.00 0.00 43.07 4.70
2191 2547 4.038763 CCAATAAGGACTACATACGGAGCA 59.961 45.833 0.00 0.00 41.22 4.26
2192 2548 5.452776 CCAATAAGGACTACATACGGAGCAA 60.453 44.000 0.00 0.00 41.22 3.91
2193 2549 5.864418 ATAAGGACTACATACGGAGCAAA 57.136 39.130 0.00 0.00 0.00 3.68
2194 2550 4.546829 AAGGACTACATACGGAGCAAAA 57.453 40.909 0.00 0.00 0.00 2.44
2195 2551 4.546829 AGGACTACATACGGAGCAAAAA 57.453 40.909 0.00 0.00 0.00 1.94
2196 2552 5.099042 AGGACTACATACGGAGCAAAAAT 57.901 39.130 0.00 0.00 0.00 1.82
2197 2553 4.876107 AGGACTACATACGGAGCAAAAATG 59.124 41.667 0.00 0.00 0.00 2.32
2198 2554 4.873827 GGACTACATACGGAGCAAAAATGA 59.126 41.667 0.00 0.00 0.00 2.57
2199 2555 5.006746 GGACTACATACGGAGCAAAAATGAG 59.993 44.000 0.00 0.00 0.00 2.90
2200 2556 5.488341 ACTACATACGGAGCAAAAATGAGT 58.512 37.500 0.00 0.00 0.00 3.41
2201 2557 4.685169 ACATACGGAGCAAAAATGAGTG 57.315 40.909 0.00 0.00 0.00 3.51
2202 2558 4.323417 ACATACGGAGCAAAAATGAGTGA 58.677 39.130 0.00 0.00 0.00 3.41
2203 2559 4.759693 ACATACGGAGCAAAAATGAGTGAA 59.240 37.500 0.00 0.00 0.00 3.18
2204 2560 5.415701 ACATACGGAGCAAAAATGAGTGAAT 59.584 36.000 0.00 0.00 0.00 2.57
2205 2561 4.425577 ACGGAGCAAAAATGAGTGAATC 57.574 40.909 0.00 0.00 0.00 2.52
2206 2562 3.191371 ACGGAGCAAAAATGAGTGAATCC 59.809 43.478 0.00 0.00 0.00 3.01
2207 2563 3.191162 CGGAGCAAAAATGAGTGAATCCA 59.809 43.478 0.00 0.00 0.00 3.41
2208 2564 4.488879 GGAGCAAAAATGAGTGAATCCAC 58.511 43.478 0.00 0.00 43.50 4.02
2209 2565 4.022068 GGAGCAAAAATGAGTGAATCCACA 60.022 41.667 0.00 0.00 45.54 4.17
2210 2566 4.874970 AGCAAAAATGAGTGAATCCACAC 58.125 39.130 0.00 0.00 45.54 3.82
2223 2579 8.723942 AGTGAATCCACACTCTAAAATATGTC 57.276 34.615 0.00 0.00 46.36 3.06
2224 2580 8.543774 AGTGAATCCACACTCTAAAATATGTCT 58.456 33.333 0.00 0.00 46.36 3.41
2225 2581 9.817809 GTGAATCCACACTCTAAAATATGTCTA 57.182 33.333 0.00 0.00 42.72 2.59
2251 2607 7.946655 ATACATTCGTATGTAGTCCACATTG 57.053 36.000 18.06 0.00 46.01 2.82
2252 2608 5.972935 ACATTCGTATGTAGTCCACATTGA 58.027 37.500 5.81 0.00 46.01 2.57
2253 2609 6.403049 ACATTCGTATGTAGTCCACATTGAA 58.597 36.000 5.81 2.12 46.01 2.69
2254 2610 6.876789 ACATTCGTATGTAGTCCACATTGAAA 59.123 34.615 5.81 0.00 46.01 2.69
2255 2611 7.552687 ACATTCGTATGTAGTCCACATTGAAAT 59.447 33.333 5.81 0.00 46.01 2.17
2256 2612 7.534085 TTCGTATGTAGTCCACATTGAAATC 57.466 36.000 0.00 0.00 46.01 2.17
2257 2613 6.873997 TCGTATGTAGTCCACATTGAAATCT 58.126 36.000 0.00 0.00 46.01 2.40
2258 2614 6.978659 TCGTATGTAGTCCACATTGAAATCTC 59.021 38.462 0.00 0.00 46.01 2.75
2259 2615 6.980978 CGTATGTAGTCCACATTGAAATCTCT 59.019 38.462 0.00 0.00 46.01 3.10
2260 2616 8.135529 CGTATGTAGTCCACATTGAAATCTCTA 58.864 37.037 0.00 0.00 46.01 2.43
2261 2617 9.817809 GTATGTAGTCCACATTGAAATCTCTAA 57.182 33.333 0.00 0.00 46.01 2.10
2263 2619 9.739276 ATGTAGTCCACATTGAAATCTCTAAAA 57.261 29.630 0.00 0.00 46.01 1.52
2264 2620 9.567776 TGTAGTCCACATTGAAATCTCTAAAAA 57.432 29.630 0.00 0.00 30.04 1.94
2266 2622 8.924511 AGTCCACATTGAAATCTCTAAAAAGA 57.075 30.769 0.00 0.00 0.00 2.52
2267 2623 8.787852 AGTCCACATTGAAATCTCTAAAAAGAC 58.212 33.333 0.00 0.00 0.00 3.01
2268 2624 8.787852 GTCCACATTGAAATCTCTAAAAAGACT 58.212 33.333 0.00 0.00 0.00 3.24
2269 2625 9.354673 TCCACATTGAAATCTCTAAAAAGACTT 57.645 29.630 0.00 0.00 0.00 3.01
2286 2642 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2290 2646 7.564292 AGACTTATATTTAGGAACGGAGGAAGT 59.436 37.037 0.00 0.00 0.00 3.01
2292 2648 9.205513 ACTTATATTTAGGAACGGAGGAAGTAA 57.794 33.333 0.00 0.00 0.00 2.24
2328 2684 3.389983 ACCTGTAACTGAAACCACTAGCA 59.610 43.478 0.00 0.00 0.00 3.49
2334 2690 6.993308 TGTAACTGAAACCACTAGCAACATAA 59.007 34.615 0.00 0.00 0.00 1.90
2365 2785 8.291191 TCATGTGTTATATCTGGAATTTTGCA 57.709 30.769 0.00 0.00 0.00 4.08
2368 2788 8.121305 TGTGTTATATCTGGAATTTTGCAACT 57.879 30.769 0.00 0.00 0.00 3.16
2428 2848 9.705471 CTCTTTTGTTGTTAATAAACGTGTACA 57.295 29.630 0.00 0.00 38.53 2.90
2459 2879 1.571460 CAAGTGCGCCAAGACACTC 59.429 57.895 4.18 0.00 46.17 3.51
2460 2880 1.146041 AAGTGCGCCAAGACACTCA 59.854 52.632 4.18 0.00 46.17 3.41
2475 2895 6.665992 AGACACTCATTGACTAAAGTGGTA 57.334 37.500 6.34 0.00 42.66 3.25
2476 2896 6.456501 AGACACTCATTGACTAAAGTGGTAC 58.543 40.000 6.34 0.00 42.66 3.34
2477 2897 6.041637 AGACACTCATTGACTAAAGTGGTACA 59.958 38.462 6.34 0.00 42.66 2.90
2493 2913 5.945784 AGTGGTACAATGCTGTCATATGTTT 59.054 36.000 1.90 0.00 44.16 2.83
2586 3008 7.045416 TGGTAAATACTTAATGCGACTGACAT 58.955 34.615 0.00 0.00 0.00 3.06
2639 3061 2.839486 TGGTGAGTGCTAACTTCCTG 57.161 50.000 0.00 0.00 36.52 3.86
2665 3087 2.832733 ACCTAACAGAGTTACCTGGCTC 59.167 50.000 0.00 0.00 38.44 4.70
2822 3244 3.976704 TGGTTGGCCAGGTAATCAG 57.023 52.632 5.11 0.00 40.46 2.90
2825 3247 2.092323 GGTTGGCCAGGTAATCAGTTC 58.908 52.381 5.11 0.00 34.09 3.01
2831 3253 4.473196 TGGCCAGGTAATCAGTTCATTCTA 59.527 41.667 0.00 0.00 0.00 2.10
2833 3255 5.428253 GCCAGGTAATCAGTTCATTCTACA 58.572 41.667 0.00 0.00 0.00 2.74
2836 3258 7.254932 GCCAGGTAATCAGTTCATTCTACATTC 60.255 40.741 0.00 0.00 0.00 2.67
2837 3259 7.989741 CCAGGTAATCAGTTCATTCTACATTCT 59.010 37.037 0.00 0.00 0.00 2.40
2869 3291 5.634020 GTCAGCTACCTTACTACACAAACTG 59.366 44.000 0.00 0.00 0.00 3.16
2958 3381 7.829706 GGTGTTCTCCCCAGATATAAATATTCC 59.170 40.741 0.00 0.00 0.00 3.01
3021 3444 9.682465 GGGGTTATGATTCCTATCCTTAATAAC 57.318 37.037 0.00 0.00 31.54 1.89
3031 3454 7.792032 TCCTATCCTTAATAACAGTGGAACAG 58.208 38.462 0.00 0.00 41.80 3.16
3082 3505 5.312079 AGGATGCTGTAAGGATTATGCTTC 58.688 41.667 1.42 0.00 45.52 3.86
3104 3527 8.267367 GCTTCGTGCTTTCTAATTGTATAGTAC 58.733 37.037 0.00 0.00 38.95 2.73
3105 3528 9.517609 CTTCGTGCTTTCTAATTGTATAGTACT 57.482 33.333 0.00 0.00 0.00 2.73
3145 3568 8.682128 TGATTTGTTTGTTTGTGTAGTTCTTC 57.318 30.769 0.00 0.00 0.00 2.87
3211 3679 5.658634 ACTAGAAGTGAGCATAACTGATCCA 59.341 40.000 0.00 0.00 36.97 3.41
3286 3754 7.009179 TCTATTCTCAGAGACCAAACAATGT 57.991 36.000 0.00 0.00 0.00 2.71
3288 3756 6.566197 ATTCTCAGAGACCAAACAATGTTC 57.434 37.500 0.00 0.00 0.00 3.18
3306 3774 9.787435 ACAATGTTCTGAACTACCTATACAAAA 57.213 29.630 20.18 0.00 0.00 2.44
3357 3825 1.470458 CGATGCTCTGCTGACAGCTTA 60.470 52.381 26.94 14.36 44.10 3.09
3715 4183 7.680730 AGTCTGTTTGTAAACTGGTGATATCT 58.319 34.615 3.98 0.00 39.59 1.98
3736 4205 4.101585 TCTGTGAGAGTTTGTGAGGATTGT 59.898 41.667 0.00 0.00 0.00 2.71
3756 4225 4.380531 TGTCTGTGCTTTCTGTTTAGGAG 58.619 43.478 0.00 0.00 0.00 3.69
3758 4227 2.485814 CTGTGCTTTCTGTTTAGGAGGC 59.514 50.000 0.00 0.00 0.00 4.70
3808 4277 4.795278 GCATTAACATAAAGTGTGCTCTGC 59.205 41.667 0.00 0.00 41.14 4.26
3834 4333 9.553064 CATAAGAAGGTCACAGAATAGCTTAAT 57.447 33.333 0.00 0.00 33.80 1.40
3836 4335 6.352516 AGAAGGTCACAGAATAGCTTAATGG 58.647 40.000 0.00 0.00 33.80 3.16
3867 4366 6.403866 TGGACTCACTTTATGCAAAATTGT 57.596 33.333 0.00 0.00 0.00 2.71
3871 4370 8.082242 GGACTCACTTTATGCAAAATTGTTACT 58.918 33.333 0.00 0.00 0.00 2.24
3872 4371 9.118236 GACTCACTTTATGCAAAATTGTTACTC 57.882 33.333 0.00 0.00 0.00 2.59
3918 4420 6.640518 TGGATGTAACAAGAATAGGAGTGAC 58.359 40.000 0.00 0.00 0.00 3.67
3961 4463 0.528684 GGTGAGTATCTGACGCTGCC 60.529 60.000 0.00 0.00 34.92 4.85
3965 4467 2.028112 TGAGTATCTGACGCTGCCTTTT 60.028 45.455 0.00 0.00 34.92 2.27
3990 4495 8.964476 TTTTATGACTGGAGATGACTATTTCC 57.036 34.615 0.00 0.00 37.92 3.13
3991 4496 7.921041 TTATGACTGGAGATGACTATTTCCT 57.079 36.000 0.00 0.00 38.19 3.36
4005 4518 6.750501 TGACTATTTCCTCGTCATTTTCTACG 59.249 38.462 0.00 0.00 40.40 3.51
4027 4540 2.906354 CTGGTAGAAACCTTCATCGGG 58.094 52.381 0.00 0.00 46.91 5.14
4095 4619 7.595130 GTGAACCAAGATCAAATTACTTGTTCC 59.405 37.037 0.00 0.00 39.19 3.62
4250 4801 1.571955 TTGTGAGCTGAGCATCCCTA 58.428 50.000 7.39 0.00 0.00 3.53
4252 4803 1.908619 TGTGAGCTGAGCATCCCTAAA 59.091 47.619 7.39 0.00 0.00 1.85
4264 4815 1.313889 TCCCTAAATCCCCATTGCCA 58.686 50.000 0.00 0.00 0.00 4.92
4315 4925 1.907807 GGCTGCACCCAATGACCAA 60.908 57.895 0.50 0.00 0.00 3.67
4341 4951 1.550524 GACCCTGTGTGAGCTGACATA 59.449 52.381 9.85 5.85 0.00 2.29
4518 5138 3.721087 TCCTTCTCCTCCATTGGTTTC 57.279 47.619 1.86 0.00 0.00 2.78
4524 5144 1.715931 TCCTCCATTGGTTTCCATGGT 59.284 47.619 12.58 0.00 35.34 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.577296 AGAACTAAATAAGAAAGCCAAAAGGAC 58.423 33.333 0.00 0.00 0.00 3.85
149 151 6.565435 CGCATGCTACTAGGAGAAATCAATTG 60.565 42.308 17.13 0.00 0.00 2.32
255 276 2.174360 CCGCTCCAGATCTGATCCATA 58.826 52.381 24.62 1.54 0.00 2.74
256 277 0.975135 CCGCTCCAGATCTGATCCAT 59.025 55.000 24.62 0.00 0.00 3.41
299 320 0.033894 GTTCTCTCCTCTCTCCCCGT 60.034 60.000 0.00 0.00 0.00 5.28
327 351 2.027653 CCAAAACCAAACAACCACCTGT 60.028 45.455 0.00 0.00 0.00 4.00
575 912 1.202758 ACTTCGACAAAGCCATCCACA 60.203 47.619 0.00 0.00 38.67 4.17
586 923 1.593209 GCGTGACCCACTTCGACAA 60.593 57.895 0.00 0.00 31.34 3.18
609 946 0.035739 ATTGTACAACCGCGTCCCTT 59.964 50.000 11.22 0.00 0.00 3.95
651 989 3.057736 GCAACTAACTACCAGTCGACTGA 60.058 47.826 40.21 23.93 46.59 3.41
681 1019 9.467258 GTTTTACGCCCTTAAAACTTTATTTCT 57.533 29.630 10.32 0.00 43.85 2.52
686 1024 8.249638 ACTTTGTTTTACGCCCTTAAAACTTTA 58.750 29.630 15.77 4.21 45.90 1.85
688 1026 6.632909 ACTTTGTTTTACGCCCTTAAAACTT 58.367 32.000 15.77 1.64 45.90 2.66
689 1027 6.211587 ACTTTGTTTTACGCCCTTAAAACT 57.788 33.333 15.77 0.00 45.90 2.66
690 1028 6.890663 AACTTTGTTTTACGCCCTTAAAAC 57.109 33.333 10.56 10.56 45.91 2.43
691 1029 6.313164 CCAAACTTTGTTTTACGCCCTTAAAA 59.687 34.615 0.88 0.00 0.00 1.52
692 1030 5.811100 CCAAACTTTGTTTTACGCCCTTAAA 59.189 36.000 0.88 0.00 0.00 1.52
693 1031 5.126707 TCCAAACTTTGTTTTACGCCCTTAA 59.873 36.000 0.88 0.00 0.00 1.85
694 1032 4.643784 TCCAAACTTTGTTTTACGCCCTTA 59.356 37.500 0.88 0.00 0.00 2.69
695 1033 3.447944 TCCAAACTTTGTTTTACGCCCTT 59.552 39.130 0.88 0.00 0.00 3.95
696 1034 3.025262 TCCAAACTTTGTTTTACGCCCT 58.975 40.909 0.88 0.00 0.00 5.19
697 1035 3.181484 ACTCCAAACTTTGTTTTACGCCC 60.181 43.478 0.88 0.00 0.00 6.13
698 1036 3.794564 CACTCCAAACTTTGTTTTACGCC 59.205 43.478 0.88 0.00 0.00 5.68
699 1037 3.794564 CCACTCCAAACTTTGTTTTACGC 59.205 43.478 0.88 0.00 0.00 4.42
700 1038 5.238006 TCCACTCCAAACTTTGTTTTACG 57.762 39.130 0.88 0.00 0.00 3.18
701 1039 8.487313 AAAATCCACTCCAAACTTTGTTTTAC 57.513 30.769 0.88 0.00 0.00 2.01
703 1041 7.994425 AAAAATCCACTCCAAACTTTGTTTT 57.006 28.000 0.88 0.00 0.00 2.43
727 1065 6.067263 ACTGAGCGCACAAATAAGTAAAAA 57.933 33.333 11.47 0.00 0.00 1.94
728 1066 5.682943 ACTGAGCGCACAAATAAGTAAAA 57.317 34.783 11.47 0.00 0.00 1.52
729 1067 5.613795 CGAACTGAGCGCACAAATAAGTAAA 60.614 40.000 11.47 0.00 0.00 2.01
730 1068 4.143200 CGAACTGAGCGCACAAATAAGTAA 60.143 41.667 11.47 0.00 0.00 2.24
731 1069 3.366724 CGAACTGAGCGCACAAATAAGTA 59.633 43.478 11.47 0.00 0.00 2.24
732 1070 2.157668 CGAACTGAGCGCACAAATAAGT 59.842 45.455 11.47 0.00 0.00 2.24
733 1071 2.762472 CGAACTGAGCGCACAAATAAG 58.238 47.619 11.47 0.00 0.00 1.73
734 1072 2.873170 CGAACTGAGCGCACAAATAA 57.127 45.000 11.47 0.00 0.00 1.40
760 1098 0.171903 GGTATCTGTGCGTGGTACGT 59.828 55.000 0.00 0.00 44.73 3.57
763 1101 1.395635 ATCGGTATCTGTGCGTGGTA 58.604 50.000 0.00 0.00 0.00 3.25
781 1119 4.201783 CGCGTTTTCCTCTTCCGAATTAAT 60.202 41.667 0.00 0.00 0.00 1.40
795 1133 1.281656 CCTGTTCCACGCGTTTTCC 59.718 57.895 10.22 0.00 0.00 3.13
810 1148 5.077134 TGTCTAGAATCACACATCACCTG 57.923 43.478 0.00 0.00 0.00 4.00
813 1151 5.105752 GGACTGTCTAGAATCACACATCAC 58.894 45.833 7.85 0.00 0.00 3.06
893 1234 2.673833 GAGTAACACTGAACACCTCGG 58.326 52.381 0.00 0.00 36.38 4.63
956 1298 1.901948 TCTTCTCGCACCTCCGTGT 60.902 57.895 0.00 0.00 42.39 4.49
957 1299 1.444553 GTCTTCTCGCACCTCCGTG 60.445 63.158 0.00 0.00 43.35 4.94
1583 1926 2.903357 CACTGCAGGGCGTATCCT 59.097 61.111 19.93 0.00 37.71 3.24
1784 2140 0.240145 TACCACTCAACGACAGCGAG 59.760 55.000 0.00 0.00 41.64 5.03
1833 2189 5.763088 TCTAGCTAAGCAGATATCACAACG 58.237 41.667 5.32 0.00 0.00 4.10
1870 2226 2.642427 ACATCAAAGCACACACACAGA 58.358 42.857 0.00 0.00 0.00 3.41
1891 2247 6.238648 ACGGAATCATCAAAAGGAAGTTAGT 58.761 36.000 0.00 0.00 0.00 2.24
1894 2250 6.715264 AGTAACGGAATCATCAAAAGGAAGTT 59.285 34.615 0.00 0.00 0.00 2.66
1898 2254 6.001460 ACAAGTAACGGAATCATCAAAAGGA 58.999 36.000 0.00 0.00 0.00 3.36
1912 2268 1.993370 GTAGAGCTGCACAAGTAACGG 59.007 52.381 1.02 0.00 0.00 4.44
2002 2358 4.988598 AGCAAGTCGCCACCGGTG 62.989 66.667 28.26 28.26 44.04 4.94
2015 2371 0.884704 GGAGCACCTTGTTCGAGCAA 60.885 55.000 14.26 14.26 0.00 3.91
2088 2444 4.686191 AGCATTCAAATTCCCACACAAA 57.314 36.364 0.00 0.00 0.00 2.83
2091 2447 7.603784 AGAAATTAAGCATTCAAATTCCCACAC 59.396 33.333 0.00 0.00 0.00 3.82
2127 2483 8.551682 TTTTATATTTAGGAACGGAGGGAGTA 57.448 34.615 0.00 0.00 0.00 2.59
2129 2485 7.506971 ACTTTTATATTTAGGAACGGAGGGAG 58.493 38.462 0.00 0.00 0.00 4.30
2130 2486 7.346436 AGACTTTTATATTTAGGAACGGAGGGA 59.654 37.037 0.00 0.00 0.00 4.20
2131 2487 7.506971 AGACTTTTATATTTAGGAACGGAGGG 58.493 38.462 0.00 0.00 0.00 4.30
2132 2488 8.959705 AAGACTTTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2167 2523 4.280174 GCTCCGTATGTAGTCCTTATTGGA 59.720 45.833 0.00 0.00 43.86 3.53
2168 2524 4.038763 TGCTCCGTATGTAGTCCTTATTGG 59.961 45.833 0.00 0.00 37.10 3.16
2169 2525 5.196341 TGCTCCGTATGTAGTCCTTATTG 57.804 43.478 0.00 0.00 0.00 1.90
2170 2526 5.864418 TTGCTCCGTATGTAGTCCTTATT 57.136 39.130 0.00 0.00 0.00 1.40
2171 2527 5.864418 TTTGCTCCGTATGTAGTCCTTAT 57.136 39.130 0.00 0.00 0.00 1.73
2172 2528 5.664294 TTTTGCTCCGTATGTAGTCCTTA 57.336 39.130 0.00 0.00 0.00 2.69
2173 2529 4.546829 TTTTGCTCCGTATGTAGTCCTT 57.453 40.909 0.00 0.00 0.00 3.36
2174 2530 4.546829 TTTTTGCTCCGTATGTAGTCCT 57.453 40.909 0.00 0.00 0.00 3.85
2175 2531 4.873827 TCATTTTTGCTCCGTATGTAGTCC 59.126 41.667 0.00 0.00 0.00 3.85
2176 2532 5.581085 ACTCATTTTTGCTCCGTATGTAGTC 59.419 40.000 0.00 0.00 0.00 2.59
2177 2533 5.351465 CACTCATTTTTGCTCCGTATGTAGT 59.649 40.000 0.00 0.00 0.00 2.73
2178 2534 5.580691 TCACTCATTTTTGCTCCGTATGTAG 59.419 40.000 0.00 0.00 0.00 2.74
2179 2535 5.483811 TCACTCATTTTTGCTCCGTATGTA 58.516 37.500 0.00 0.00 0.00 2.29
2180 2536 4.323417 TCACTCATTTTTGCTCCGTATGT 58.677 39.130 0.00 0.00 0.00 2.29
2181 2537 4.944962 TCACTCATTTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2182 2538 5.066505 GGATTCACTCATTTTTGCTCCGTAT 59.933 40.000 0.00 0.00 0.00 3.06
2183 2539 4.394920 GGATTCACTCATTTTTGCTCCGTA 59.605 41.667 0.00 0.00 0.00 4.02
2184 2540 3.191371 GGATTCACTCATTTTTGCTCCGT 59.809 43.478 0.00 0.00 0.00 4.69
2185 2541 3.191162 TGGATTCACTCATTTTTGCTCCG 59.809 43.478 0.00 0.00 0.00 4.63
2186 2542 4.022068 TGTGGATTCACTCATTTTTGCTCC 60.022 41.667 5.55 0.00 43.94 4.70
2187 2543 4.919754 GTGTGGATTCACTCATTTTTGCTC 59.080 41.667 5.55 0.00 43.94 4.26
2188 2544 4.586001 AGTGTGGATTCACTCATTTTTGCT 59.414 37.500 5.55 0.00 44.07 3.91
2189 2545 4.874970 AGTGTGGATTCACTCATTTTTGC 58.125 39.130 5.55 0.00 44.07 3.68
2199 2555 8.723942 AGACATATTTTAGAGTGTGGATTCAC 57.276 34.615 0.00 0.00 43.87 3.18
2220 2576 9.729281 TGGACTACATACGAATGTATATAGACA 57.271 33.333 2.07 2.07 45.33 3.41
2221 2577 9.985318 GTGGACTACATACGAATGTATATAGAC 57.015 37.037 7.52 2.40 45.33 2.59
2222 2578 9.729281 TGTGGACTACATACGAATGTATATAGA 57.271 33.333 7.52 0.00 45.33 1.98
2238 2594 9.567776 TTTTTAGAGATTTCAATGTGGACTACA 57.432 29.630 0.00 0.00 44.87 2.74
2241 2597 8.787852 GTCTTTTTAGAGATTTCAATGTGGACT 58.212 33.333 0.00 0.00 0.00 3.85
2242 2598 8.787852 AGTCTTTTTAGAGATTTCAATGTGGAC 58.212 33.333 0.00 0.00 0.00 4.02
2243 2599 8.924511 AGTCTTTTTAGAGATTTCAATGTGGA 57.075 30.769 0.00 0.00 0.00 4.02
2260 2616 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2261 2617 8.765517 TCCTCCGTTCCTAAATATAAGTCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
2262 2618 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
2263 2619 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
2264 2620 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2265 2621 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2266 2622 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2270 2626 9.338622 CAAATTACTTCCTCCGTTCCTAAATAT 57.661 33.333 0.00 0.00 0.00 1.28
2271 2627 7.281549 GCAAATTACTTCCTCCGTTCCTAAATA 59.718 37.037 0.00 0.00 0.00 1.40
2272 2628 6.095021 GCAAATTACTTCCTCCGTTCCTAAAT 59.905 38.462 0.00 0.00 0.00 1.40
2273 2629 5.413523 GCAAATTACTTCCTCCGTTCCTAAA 59.586 40.000 0.00 0.00 0.00 1.85
2274 2630 4.939439 GCAAATTACTTCCTCCGTTCCTAA 59.061 41.667 0.00 0.00 0.00 2.69
2275 2631 4.020039 TGCAAATTACTTCCTCCGTTCCTA 60.020 41.667 0.00 0.00 0.00 2.94
2276 2632 3.244770 TGCAAATTACTTCCTCCGTTCCT 60.245 43.478 0.00 0.00 0.00 3.36
2277 2633 3.078837 TGCAAATTACTTCCTCCGTTCC 58.921 45.455 0.00 0.00 0.00 3.62
2278 2634 4.759516 TTGCAAATTACTTCCTCCGTTC 57.240 40.909 0.00 0.00 0.00 3.95
2279 2635 5.469479 CAATTGCAAATTACTTCCTCCGTT 58.531 37.500 1.71 0.00 0.00 4.44
2280 2636 4.618227 GCAATTGCAAATTACTTCCTCCGT 60.618 41.667 25.36 0.00 41.59 4.69
2281 2637 3.859386 GCAATTGCAAATTACTTCCTCCG 59.141 43.478 25.36 0.00 41.59 4.63
2305 2661 4.589798 TGCTAGTGGTTTCAGTTACAGGTA 59.410 41.667 0.00 0.00 0.00 3.08
2307 2663 4.002906 TGCTAGTGGTTTCAGTTACAGG 57.997 45.455 0.00 0.00 0.00 4.00
2428 2848 1.812571 CGCACTTGCTCTGGGTTTATT 59.187 47.619 0.00 0.00 39.32 1.40
2429 2849 1.453155 CGCACTTGCTCTGGGTTTAT 58.547 50.000 0.00 0.00 39.32 1.40
2453 2873 6.220930 TGTACCACTTTAGTCAATGAGTGTC 58.779 40.000 0.00 0.00 38.21 3.67
2459 2879 6.072508 ACAGCATTGTACCACTTTAGTCAATG 60.073 38.462 13.49 13.49 42.45 2.82
2460 2880 6.003950 ACAGCATTGTACCACTTTAGTCAAT 58.996 36.000 0.00 0.00 35.25 2.57
2475 2895 9.524106 CATATTCAAAACATATGACAGCATTGT 57.476 29.630 10.38 0.00 36.93 2.71
2476 2896 9.738832 TCATATTCAAAACATATGACAGCATTG 57.261 29.630 10.38 5.37 38.27 2.82
2691 3113 6.763610 AGAAGACATCAAACGAGAGAAAAACT 59.236 34.615 0.00 0.00 0.00 2.66
2701 3123 2.731451 CAGCGAAGAAGACATCAAACGA 59.269 45.455 0.00 0.00 0.00 3.85
2822 3244 9.424319 TGACACTTTCTAGAATGTAGAATGAAC 57.576 33.333 20.17 10.21 34.02 3.18
2825 3247 7.763528 AGCTGACACTTTCTAGAATGTAGAATG 59.236 37.037 20.17 12.08 34.02 2.67
2831 3253 5.482175 AGGTAGCTGACACTTTCTAGAATGT 59.518 40.000 16.18 16.18 0.00 2.71
2833 3255 6.613153 AAGGTAGCTGACACTTTCTAGAAT 57.387 37.500 5.89 0.00 0.00 2.40
2836 3258 6.518208 AGTAAGGTAGCTGACACTTTCTAG 57.482 41.667 12.03 0.00 0.00 2.43
2837 3259 6.944290 TGTAGTAAGGTAGCTGACACTTTCTA 59.056 38.462 12.03 0.67 0.00 2.10
2840 3262 5.303589 TGTGTAGTAAGGTAGCTGACACTTT 59.696 40.000 20.80 0.00 37.27 2.66
2876 3298 8.921353 ATGCAAGAGAGAAAATAATGAGCTAT 57.079 30.769 0.00 0.00 0.00 2.97
2878 3300 8.784994 CATATGCAAGAGAGAAAATAATGAGCT 58.215 33.333 0.00 0.00 0.00 4.09
2886 3309 7.222872 CCTCCTACATATGCAAGAGAGAAAAT 58.777 38.462 14.77 0.00 0.00 1.82
2887 3310 6.408548 CCCTCCTACATATGCAAGAGAGAAAA 60.409 42.308 14.77 0.00 0.00 2.29
2888 3311 5.070981 CCCTCCTACATATGCAAGAGAGAAA 59.929 44.000 14.77 0.00 0.00 2.52
2898 3321 2.038952 TGATGCACCCTCCTACATATGC 59.961 50.000 1.58 0.00 0.00 3.14
2958 3381 2.034878 TCTCCATTCTCACTGGGATCG 58.965 52.381 0.00 0.00 34.36 3.69
3021 3444 1.571460 GCTCGTTGCTGTTCCACTG 59.429 57.895 0.00 0.00 38.95 3.66
3031 3454 1.058903 GAATCCGTTCGCTCGTTGC 59.941 57.895 0.00 0.00 38.57 4.17
3118 3541 9.651913 AAGAACTACACAAACAAACAAATCAAT 57.348 25.926 0.00 0.00 0.00 2.57
3189 3651 6.737720 ATGGATCAGTTATGCTCACTTCTA 57.262 37.500 0.00 0.00 0.00 2.10
3203 3665 7.122715 AGTTCTCTCTAGTGTAATGGATCAGT 58.877 38.462 0.00 0.00 0.00 3.41
3204 3666 7.581213 AGTTCTCTCTAGTGTAATGGATCAG 57.419 40.000 0.00 0.00 0.00 2.90
3205 3667 7.962995 AAGTTCTCTCTAGTGTAATGGATCA 57.037 36.000 0.00 0.00 0.00 2.92
3206 3668 7.223777 GCAAAGTTCTCTCTAGTGTAATGGATC 59.776 40.741 0.00 0.00 0.00 3.36
3207 3669 7.044798 GCAAAGTTCTCTCTAGTGTAATGGAT 58.955 38.462 0.00 0.00 0.00 3.41
3211 3679 7.390027 ACATGCAAAGTTCTCTCTAGTGTAAT 58.610 34.615 0.00 0.00 0.00 1.89
3255 3723 6.462552 TGGTCTCTGAGAATAGATTGTCTG 57.537 41.667 9.31 1.46 31.92 3.51
3274 3742 5.531287 AGGTAGTTCAGAACATTGTTTGGTC 59.469 40.000 15.85 0.00 42.84 4.02
3288 3756 9.319143 CCATTCTCTTTTGTATAGGTAGTTCAG 57.681 37.037 0.00 0.00 0.00 3.02
3306 3774 4.961730 AGATAGAACTGAGCACCATTCTCT 59.038 41.667 1.18 0.00 33.53 3.10
3307 3775 5.275067 AGATAGAACTGAGCACCATTCTC 57.725 43.478 1.18 0.00 33.53 2.87
3312 3780 4.861196 AGACTAGATAGAACTGAGCACCA 58.139 43.478 0.00 0.00 0.00 4.17
3357 3825 4.523943 TGCAGCATTCCTGTTAGAACAAAT 59.476 37.500 0.00 0.00 43.71 2.32
3715 4183 4.101585 AGACAATCCTCACAAACTCTCACA 59.898 41.667 0.00 0.00 0.00 3.58
3736 4205 3.807209 GCCTCCTAAACAGAAAGCACAGA 60.807 47.826 0.00 0.00 0.00 3.41
3756 4225 0.387622 TACACTTGTACACGCTCGCC 60.388 55.000 0.00 0.00 0.00 5.54
3785 4254 4.795278 GCAGAGCACACTTTATGTTAATGC 59.205 41.667 0.00 0.00 40.64 3.56
3808 4277 8.948631 TTAAGCTATTCTGTGACCTTCTTATG 57.051 34.615 0.00 0.00 0.00 1.90
3834 4333 4.447138 AAAGTGAGTCCATAACCAACCA 57.553 40.909 0.00 0.00 0.00 3.67
3836 4335 5.414454 TGCATAAAGTGAGTCCATAACCAAC 59.586 40.000 0.00 0.00 0.00 3.77
3871 4370 9.492730 TCCATAGCAATATACAGATATTCAGGA 57.507 33.333 0.00 0.00 36.31 3.86
3918 4420 2.349886 GCTGCTTCTACGATTTCTGTGG 59.650 50.000 0.00 0.00 0.00 4.17
3965 4467 8.772250 AGGAAATAGTCATCTCCAGTCATAAAA 58.228 33.333 0.00 0.00 0.00 1.52
3967 4469 7.255625 CGAGGAAATAGTCATCTCCAGTCATAA 60.256 40.741 0.00 0.00 34.80 1.90
3968 4470 6.207614 CGAGGAAATAGTCATCTCCAGTCATA 59.792 42.308 0.00 0.00 34.80 2.15
3969 4471 5.010516 CGAGGAAATAGTCATCTCCAGTCAT 59.989 44.000 0.00 0.00 34.80 3.06
3970 4472 4.339530 CGAGGAAATAGTCATCTCCAGTCA 59.660 45.833 0.00 0.00 34.80 3.41
3972 4474 4.282496 ACGAGGAAATAGTCATCTCCAGT 58.718 43.478 0.00 0.00 34.80 4.00
3985 4490 3.621715 GCCGTAGAAAATGACGAGGAAAT 59.378 43.478 0.00 0.00 41.60 2.17
3987 4492 2.232941 AGCCGTAGAAAATGACGAGGAA 59.767 45.455 0.00 0.00 41.60 3.36
3989 4494 1.927174 CAGCCGTAGAAAATGACGAGG 59.073 52.381 0.00 0.00 41.60 4.63
3990 4495 1.927174 CCAGCCGTAGAAAATGACGAG 59.073 52.381 0.00 0.00 41.60 4.18
3991 4496 1.274167 ACCAGCCGTAGAAAATGACGA 59.726 47.619 0.00 0.00 41.60 4.20
4027 4540 2.436173 ACCTAGGAGTATCAGCAAAGGC 59.564 50.000 17.98 0.00 36.25 4.35
4095 4619 3.123050 TGTTGATCTGTCGTGTGTCTTG 58.877 45.455 0.00 0.00 0.00 3.02
4150 4674 4.084171 CCGATAGCAATCTTGTGTGCATAG 60.084 45.833 0.00 0.00 43.42 2.23
4250 4801 1.077663 AGTCAGTGGCAATGGGGATTT 59.922 47.619 15.62 0.00 0.00 2.17
4252 4803 1.595311 TAGTCAGTGGCAATGGGGAT 58.405 50.000 15.62 1.56 0.00 3.85
4264 4815 5.934625 CCTTGCACTTCTTGTAATAGTCAGT 59.065 40.000 0.00 0.00 0.00 3.41
4315 4925 0.901124 GCTCACACAGGGTCTCTCAT 59.099 55.000 0.00 0.00 0.00 2.90
4341 4951 6.377146 AGTGTTGTTTACCACTGACTTTCATT 59.623 34.615 0.00 0.00 0.00 2.57
4367 4977 2.068519 GCAAATGGCTGGTAGTTTTGC 58.931 47.619 3.31 3.31 43.45 3.68


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

AutoCloner maintained by Alex Coulton.