Multiple sequence alignment - TraesCS3B01G539000

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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 TraesCS3B01G539000 chr3B 100.000 3164 0 0 1 3164 778452799 778455962 0.000000e+00 5843
1 TraesCS3B01G539000 chr3B 79.392 296 59 2 1012 1306 778875851 778876145 1.150000e-49 207
2 TraesCS3B01G539000 chr3B 79.054 296 60 2 1012 1306 778932577 778932871 5.350000e-48 202
3 TraesCS3B01G539000 chr3B 78.451 297 61 3 1012 1306 778704957 778705252 1.160000e-44 191
4 TraesCS3B01G539000 chr3D 93.446 1480 90 5 1 1474 582829709 582828231 0.000000e+00 2189
5 TraesCS3B01G539000 chr3D 91.708 1013 69 9 1464 2470 582828211 582827208 0.000000e+00 1391
6 TraesCS3B01G539000 chr3D 90.941 287 16 8 2463 2747 582827024 582826746 8.280000e-101 377
7 TraesCS3B01G539000 chr3D 94.898 196 6 3 2973 3164 582826708 582826513 1.430000e-78 303
8 TraesCS3B01G539000 chr3D 85.897 234 30 3 2744 2974 104811447 104811214 2.440000e-61 246
9 TraesCS3B01G539000 chr3D 85.837 233 28 5 2744 2974 58208597 58208826 3.150000e-60 243
10 TraesCS3B01G539000 chr3D 80.165 242 42 5 1061 1299 582056793 582056555 3.240000e-40 176
11 TraesCS3B01G539000 chr3D 76.074 326 71 5 998 1321 582849828 582849508 2.530000e-36 163
12 TraesCS3B01G539000 chr3D 77.778 180 26 10 1144 1315 482501497 482501670 7.220000e-17 99
13 TraesCS3B01G539000 chr2D 87.013 231 30 0 2744 2974 159382452 159382682 8.700000e-66 261
14 TraesCS3B01G539000 chr2D 85.657 251 30 5 2302 2552 645896530 645896774 3.130000e-65 259
15 TraesCS3B01G539000 chr2D 86.344 227 31 0 2744 2970 197307009 197306783 6.780000e-62 248
16 TraesCS3B01G539000 chr2D 85.776 232 31 2 2744 2974 404473089 404472859 8.770000e-61 244
17 TraesCS3B01G539000 chr2D 81.124 249 41 5 2304 2551 56196740 56196983 8.950000e-46 195
18 TraesCS3B01G539000 chr2A 87.225 227 28 1 2744 2970 522232269 522232044 1.130000e-64 257
19 TraesCS3B01G539000 chr2A 84.337 249 33 5 2302 2549 771620167 771620410 4.080000e-59 239
20 TraesCS3B01G539000 chr6A 86.607 224 30 0 2744 2967 294861705 294861482 6.780000e-62 248
21 TraesCS3B01G539000 chr7D 85.837 233 31 2 2744 2974 2093456 2093224 2.440000e-61 246
22 TraesCS3B01G539000 chr7D 85.408 233 33 1 2743 2974 407258821 407258589 1.130000e-59 241
23 TraesCS3B01G539000 chr7D 82.969 229 33 5 2324 2551 484439868 484439645 5.350000e-48 202
24 TraesCS3B01G539000 chr6D 85.153 229 29 5 2324 2551 440639720 440639496 2.450000e-56 230
25 TraesCS3B01G539000 chr4A 81.569 255 40 6 2313 2566 625241549 625241797 1.490000e-48 204
26 TraesCS3B01G539000 chr4D 81.452 248 40 6 2307 2551 74366658 74366414 6.920000e-47 198
27 TraesCS3B01G539000 chr5B 81.377 247 40 5 2305 2551 672621558 672621798 2.490000e-46 196
28 TraesCS3B01G539000 chr3A 78.212 179 27 6 1144 1315 625405631 625405804 1.550000e-18 104


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 TraesCS3B01G539000 chr3B 778452799 778455962 3163 False 5843 5843 100.00000 1 3164 1 chr3B.!!$F1 3163
1 TraesCS3B01G539000 chr3D 582826513 582829709 3196 True 1065 2189 92.74825 1 3164 4 chr3D.!!$R4 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
962 966 0.035534 ACAAGCACACACACCACAGA 60.036 50.0 0.00 0.00 0.0 3.41 F
1101 1105 0.592754 GAGTGCCGTACGAGCTCATC 60.593 60.0 18.76 12.99 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1860 0.390860 CCTCGCTAGGTTCCATCCAG 59.609 60.0 0.00 0.00 38.19 3.86 R
2963 3198 0.100682 CATCCGAAGTCCGTCGTGAT 59.899 55.0 2.23 2.45 39.43 3.06 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 4.448537 ACTCTTGATTGAGAGGTCTTCG 57.551 45.455 6.82 0.00 45.93 3.79
82 83 6.257193 GGTCTTCGTCGAATTAAACCATGTAT 59.743 38.462 8.36 0.00 0.00 2.29
101 102 2.601240 TGGGATGAGCCAAATGTTCA 57.399 45.000 0.00 0.00 38.95 3.18
110 111 4.402155 TGAGCCAAATGTTCACTTCTGTTT 59.598 37.500 0.00 0.00 0.00 2.83
181 182 1.473258 TGGAAATTCTGCAATCCCGG 58.527 50.000 0.00 0.00 0.00 5.73
216 217 5.923204 ACATTCTGCTAATCCCAGACTAAG 58.077 41.667 0.00 0.00 38.93 2.18
339 340 0.667993 AACGTGGCATGTTCAACTGG 59.332 50.000 19.04 0.00 0.00 4.00
345 346 4.688021 GTGGCATGTTCAACTGGTTTAAA 58.312 39.130 0.00 0.00 0.00 1.52
386 387 4.261801 CGGATTTAATCACCACAGACCTT 58.738 43.478 7.29 0.00 0.00 3.50
410 411 8.908172 TTGTTTTAAACAGGGTTTTACTTACG 57.092 30.769 10.51 0.00 43.27 3.18
414 415 5.996669 AAACAGGGTTTTACTTACGACTG 57.003 39.130 0.00 0.00 0.00 3.51
421 422 4.928020 GGTTTTACTTACGACTGGAGGAAG 59.072 45.833 0.00 0.00 0.00 3.46
431 432 1.916181 ACTGGAGGAAGTATTGGTGGG 59.084 52.381 0.00 0.00 0.00 4.61
432 433 1.212935 CTGGAGGAAGTATTGGTGGGG 59.787 57.143 0.00 0.00 0.00 4.96
442 443 1.926426 ATTGGTGGGGCAGAGGTAGC 61.926 60.000 0.00 0.00 0.00 3.58
445 446 1.222113 GTGGGGCAGAGGTAGCTTC 59.778 63.158 0.00 0.00 0.00 3.86
476 477 3.804036 TGATACTCATTACCGCCCAAAG 58.196 45.455 0.00 0.00 0.00 2.77
481 482 3.262405 ACTCATTACCGCCCAAAGTTCTA 59.738 43.478 0.00 0.00 0.00 2.10
587 590 2.035155 GTGGGGGTGTGGTTAGGC 59.965 66.667 0.00 0.00 0.00 3.93
606 609 2.030096 GGCTGTAGCTATAACCCTCGTC 60.030 54.545 0.00 0.00 41.70 4.20
607 610 2.885894 GCTGTAGCTATAACCCTCGTCT 59.114 50.000 0.00 0.00 38.21 4.18
620 623 2.744202 CCCTCGTCTGAACCAGATTTTG 59.256 50.000 0.00 0.00 42.73 2.44
649 652 5.105756 CCAACATTTGGTTCCTATCTTGACC 60.106 44.000 0.00 0.00 45.93 4.02
683 686 4.202202 ACAAAAATGATTTCACCGCTTCCA 60.202 37.500 0.00 0.00 0.00 3.53
686 689 1.533625 TGATTTCACCGCTTCCAAGG 58.466 50.000 0.00 0.00 0.00 3.61
780 783 4.023193 CGAGGGCAAGATAAGTTTGTTTGT 60.023 41.667 0.00 0.00 0.00 2.83
802 805 4.170292 ACTTCAAACATCAAGATGCAGC 57.830 40.909 9.85 0.00 42.39 5.25
805 808 3.151554 TCAAACATCAAGATGCAGCACT 58.848 40.909 4.07 0.00 42.39 4.40
813 816 7.275183 ACATCAAGATGCAGCACTAATAAGTA 58.725 34.615 4.07 0.00 42.39 2.24
863 866 5.715070 AGACAAAACAGACTCTATCGAAGG 58.285 41.667 0.00 0.00 0.00 3.46
955 959 1.198867 GACAACACACAAGCACACACA 59.801 47.619 0.00 0.00 0.00 3.72
962 966 0.035534 ACAAGCACACACACCACAGA 60.036 50.000 0.00 0.00 0.00 3.41
968 972 0.742990 ACACACACCACAGAACCACG 60.743 55.000 0.00 0.00 0.00 4.94
977 981 1.541147 CACAGAACCACGCCATTGAAT 59.459 47.619 0.00 0.00 0.00 2.57
982 986 1.668419 ACCACGCCATTGAATAGCTC 58.332 50.000 0.00 0.00 0.00 4.09
988 992 2.724349 GCCATTGAATAGCTCGCTTTG 58.276 47.619 0.00 0.00 0.00 2.77
992 996 4.095483 CCATTGAATAGCTCGCTTTGAAGT 59.905 41.667 0.00 0.00 0.00 3.01
1009 1013 4.579869 TGAAGTAAGAAGAATGGGTGAGC 58.420 43.478 0.00 0.00 0.00 4.26
1011 1015 2.912956 AGTAAGAAGAATGGGTGAGCCA 59.087 45.455 5.57 5.57 36.17 4.75
1057 1061 2.356553 GTACGTTCAGCCACCGCA 60.357 61.111 0.00 0.00 37.52 5.69
1101 1105 0.592754 GAGTGCCGTACGAGCTCATC 60.593 60.000 18.76 12.99 0.00 2.92
1130 1134 2.301346 CCTTCACAACAAGAGCCAACT 58.699 47.619 0.00 0.00 0.00 3.16
1132 1136 2.418368 TCACAACAAGAGCCAACTGT 57.582 45.000 0.00 0.00 0.00 3.55
1140 1144 4.164258 AGCCAACTGTTGCTCACC 57.836 55.556 14.94 1.06 30.33 4.02
1192 1196 3.633094 CTCCACGGCGACAGACCAG 62.633 68.421 16.62 0.00 0.00 4.00
1198 1202 2.181777 GCGACAGACCAGCGATCA 59.818 61.111 0.00 0.00 0.00 2.92
1269 1273 2.689034 CTCCTCCCCACTGACCCC 60.689 72.222 0.00 0.00 0.00 4.95
1311 1315 1.489481 TCTGGGCTCACTTCATCGAT 58.511 50.000 0.00 0.00 0.00 3.59
1312 1316 1.410517 TCTGGGCTCACTTCATCGATC 59.589 52.381 0.00 0.00 0.00 3.69
1322 1326 6.701841 GCTCACTTCATCGATCAAAAGGTATA 59.298 38.462 13.42 0.33 0.00 1.47
1371 1375 3.653344 TGTGTTGAGAACTTGAGATCCG 58.347 45.455 0.00 0.00 0.00 4.18
1375 1379 1.272781 GAGAACTTGAGATCCGTGCG 58.727 55.000 0.00 0.00 0.00 5.34
1376 1380 0.737715 AGAACTTGAGATCCGTGCGC 60.738 55.000 0.00 0.00 0.00 6.09
1378 1382 1.016130 AACTTGAGATCCGTGCGCAG 61.016 55.000 12.22 4.91 0.00 5.18
1380 1384 0.737367 CTTGAGATCCGTGCGCAGAA 60.737 55.000 12.22 0.00 0.00 3.02
1381 1385 1.014044 TTGAGATCCGTGCGCAGAAC 61.014 55.000 12.22 4.28 0.00 3.01
1435 1440 1.222936 GCAGGCCTAGAGCACATGT 59.777 57.895 3.98 0.00 46.50 3.21
1544 1580 9.585099 GATATTTATGTTGCAAAAAGACCATGA 57.415 29.630 0.00 0.00 0.00 3.07
1545 1581 9.941325 ATATTTATGTTGCAAAAAGACCATGAA 57.059 25.926 0.00 2.95 0.00 2.57
1561 1597 3.006110 CCATGAAACCATTTCTGCACACT 59.994 43.478 0.00 0.00 40.32 3.55
1562 1598 3.988379 TGAAACCATTTCTGCACACTC 57.012 42.857 3.19 0.00 40.32 3.51
1565 1601 5.316167 TGAAACCATTTCTGCACACTCTAT 58.684 37.500 3.19 0.00 40.32 1.98
1578 1614 7.278646 TCTGCACACTCTATTATTCATGTGTTC 59.721 37.037 0.00 0.00 39.65 3.18
1579 1615 7.105588 TGCACACTCTATTATTCATGTGTTCT 58.894 34.615 0.00 0.00 39.65 3.01
1580 1616 7.607607 TGCACACTCTATTATTCATGTGTTCTT 59.392 33.333 0.00 0.00 39.65 2.52
1617 1653 9.255304 GTTTCAAGTTCAAATATTGTTTGGCTA 57.745 29.630 6.11 0.00 0.00 3.93
1626 1662 9.034800 TCAAATATTGTTTGGCTAGGAAGAAAT 57.965 29.630 6.11 0.00 0.00 2.17
1669 1709 1.069227 GTTGACCACGAACCTTGATGC 60.069 52.381 0.00 0.00 0.00 3.91
1759 1801 2.376228 ATTTTGCACAACCCACGGGC 62.376 55.000 0.69 0.00 39.32 6.13
1769 1811 1.376683 CCCACGGGCGATCTGAAAA 60.377 57.895 0.00 0.00 0.00 2.29
1770 1812 0.748005 CCCACGGGCGATCTGAAAAT 60.748 55.000 0.00 0.00 0.00 1.82
1848 1890 2.329678 CTAGCGAGGCACAGAGACGG 62.330 65.000 0.00 0.00 0.00 4.79
1852 1894 2.203640 AGGCACAGAGACGGTCCA 60.204 61.111 4.14 0.00 0.00 4.02
2022 2064 2.495084 GTGGTCACCAAAGAGGAGTTC 58.505 52.381 0.00 0.00 41.22 3.01
2028 2070 1.377333 CAAAGAGGAGTTCCCGGCC 60.377 63.158 0.00 0.00 40.87 6.13
2055 2097 3.319972 GCCATTGGTCTAGACGGTATGTA 59.680 47.826 16.56 0.00 0.00 2.29
2056 2098 4.558898 GCCATTGGTCTAGACGGTATGTAG 60.559 50.000 16.56 8.80 0.00 2.74
2097 2139 3.316573 CTTGCCGGAGAGGGGTGAC 62.317 68.421 5.05 0.00 41.48 3.67
2152 2194 0.463474 TCGATCAATGGCAATGGCGA 60.463 50.000 14.33 14.33 42.47 5.54
2153 2195 0.594602 CGATCAATGGCAATGGCGAT 59.405 50.000 11.49 0.00 40.47 4.58
2194 2236 5.912955 GGTCCACTTTAATTCGTCTTTTGTG 59.087 40.000 0.00 0.00 0.00 3.33
2197 2239 7.165318 GTCCACTTTAATTCGTCTTTTGTGTTC 59.835 37.037 0.00 0.00 0.00 3.18
2200 2242 9.072294 CACTTTAATTCGTCTTTTGTGTTCTTT 57.928 29.630 0.00 0.00 0.00 2.52
2213 2255 3.628487 TGTGTTCTTTTACCACTTTCCCG 59.372 43.478 0.00 0.00 0.00 5.14
2228 2270 3.553828 TTCCCGCGATCTTATCCTTTT 57.446 42.857 8.23 0.00 0.00 2.27
2229 2271 3.553828 TCCCGCGATCTTATCCTTTTT 57.446 42.857 8.23 0.00 0.00 1.94
2253 2295 2.225491 TCCTTGCATTGTAACACGCTTC 59.775 45.455 0.00 0.00 0.00 3.86
2270 2312 4.392138 ACGCTTCTATGGTTTCTGCTAAAC 59.608 41.667 6.68 6.68 0.00 2.01
2311 2353 8.976353 TGAGAGCTTTCTTCAGAATAATACTCT 58.024 33.333 5.77 10.82 33.54 3.24
2319 2361 9.653516 TTCTTCAGAATAATACTCTCTCCATCT 57.346 33.333 0.00 0.00 0.00 2.90
2342 2384 8.478775 TCTCAATATACAAGGCTACTACACAT 57.521 34.615 0.00 0.00 0.00 3.21
2400 2442 4.798387 CCAACAAAAAGCGAGTTATATGCC 59.202 41.667 0.00 0.00 0.00 4.40
2413 2455 6.632834 CGAGTTATATGCCACAAAAAGTATGC 59.367 38.462 0.00 0.00 0.00 3.14
2547 2780 5.130477 GGTCTTGTATACAGAAATGGAGGGA 59.870 44.000 5.56 0.00 0.00 4.20
2640 2873 8.575649 AACCGAGAAATAACCATTTGTAGATT 57.424 30.769 0.00 0.00 34.44 2.40
2659 2893 3.309961 TTGATGATCATAGCCGCTCTC 57.690 47.619 8.54 0.00 0.00 3.20
2665 2899 2.010145 TCATAGCCGCTCTCACAAAC 57.990 50.000 0.00 0.00 0.00 2.93
2669 2904 2.301577 AGCCGCTCTCACAAACTATC 57.698 50.000 0.00 0.00 0.00 2.08
2690 2925 7.928706 ACTATCCATACTTCTATGTCAGCAAAC 59.071 37.037 0.00 0.00 0.00 2.93
2691 2926 6.048732 TCCATACTTCTATGTCAGCAAACA 57.951 37.500 0.00 0.00 0.00 2.83
2692 2927 6.472016 TCCATACTTCTATGTCAGCAAACAA 58.528 36.000 0.00 0.00 31.81 2.83
2751 2986 7.690952 AAAGATATCCACGATCTACTACCTC 57.309 40.000 0.00 0.00 33.20 3.85
2752 2987 5.747342 AGATATCCACGATCTACTACCTCC 58.253 45.833 0.00 0.00 31.72 4.30
2756 2991 1.872313 CACGATCTACTACCTCCGTCC 59.128 57.143 0.00 0.00 0.00 4.79
2757 2992 1.767681 ACGATCTACTACCTCCGTCCT 59.232 52.381 0.00 0.00 0.00 3.85
2758 2993 2.144730 CGATCTACTACCTCCGTCCTG 58.855 57.143 0.00 0.00 0.00 3.86
2759 2994 2.506444 GATCTACTACCTCCGTCCTGG 58.494 57.143 0.00 0.00 40.09 4.45
2760 2995 1.293062 TCTACTACCTCCGTCCTGGT 58.707 55.000 0.00 0.00 39.52 4.00
2761 2996 1.637553 TCTACTACCTCCGTCCTGGTT 59.362 52.381 0.00 0.00 39.52 3.67
2762 2997 2.042162 TCTACTACCTCCGTCCTGGTTT 59.958 50.000 0.00 0.00 39.52 3.27
2763 2998 2.610438 ACTACCTCCGTCCTGGTTTA 57.390 50.000 0.00 0.00 39.52 2.01
2764 2999 3.111741 ACTACCTCCGTCCTGGTTTAT 57.888 47.619 0.00 0.00 39.52 1.40
2765 3000 3.447950 ACTACCTCCGTCCTGGTTTATT 58.552 45.455 0.00 0.00 39.52 1.40
2766 3001 2.781681 ACCTCCGTCCTGGTTTATTG 57.218 50.000 0.00 0.00 39.52 1.90
2767 3002 1.982958 ACCTCCGTCCTGGTTTATTGT 59.017 47.619 0.00 0.00 39.52 2.71
2770 3005 1.279846 TCCGTCCTGGTTTATTGTCCC 59.720 52.381 0.00 0.00 39.52 4.46
2771 3006 1.680860 CCGTCCTGGTTTATTGTCCCC 60.681 57.143 0.00 0.00 0.00 4.81
2772 3007 1.680860 CGTCCTGGTTTATTGTCCCCC 60.681 57.143 0.00 0.00 0.00 5.40
2773 3008 1.639108 GTCCTGGTTTATTGTCCCCCT 59.361 52.381 0.00 0.00 0.00 4.79
2774 3009 2.042569 GTCCTGGTTTATTGTCCCCCTT 59.957 50.000 0.00 0.00 0.00 3.95
2777 3012 3.268595 CCTGGTTTATTGTCCCCCTTAGT 59.731 47.826 0.00 0.00 0.00 2.24
2779 3014 5.133830 CCTGGTTTATTGTCCCCCTTAGTAT 59.866 44.000 0.00 0.00 0.00 2.12
2780 3015 6.354477 CCTGGTTTATTGTCCCCCTTAGTATT 60.354 42.308 0.00 0.00 0.00 1.89
2783 3018 7.397761 TGGTTTATTGTCCCCCTTAGTATTTTG 59.602 37.037 0.00 0.00 0.00 2.44
2784 3019 7.398047 GGTTTATTGTCCCCCTTAGTATTTTGT 59.602 37.037 0.00 0.00 0.00 2.83
2785 3020 7.948034 TTATTGTCCCCCTTAGTATTTTGTG 57.052 36.000 0.00 0.00 0.00 3.33
2786 3021 3.692690 TGTCCCCCTTAGTATTTTGTGC 58.307 45.455 0.00 0.00 0.00 4.57
2787 3022 3.021695 GTCCCCCTTAGTATTTTGTGCC 58.978 50.000 0.00 0.00 0.00 5.01
2788 3023 2.650322 TCCCCCTTAGTATTTTGTGCCA 59.350 45.455 0.00 0.00 0.00 4.92
2789 3024 3.076182 TCCCCCTTAGTATTTTGTGCCAA 59.924 43.478 0.00 0.00 0.00 4.52
2790 3025 3.835395 CCCCCTTAGTATTTTGTGCCAAA 59.165 43.478 0.00 0.00 0.00 3.28
2791 3026 4.469586 CCCCCTTAGTATTTTGTGCCAAAT 59.530 41.667 1.89 0.00 0.00 2.32
2792 3027 5.045942 CCCCCTTAGTATTTTGTGCCAAATT 60.046 40.000 1.89 2.10 0.00 1.82
2793 3028 6.472016 CCCCTTAGTATTTTGTGCCAAATTT 58.528 36.000 1.89 0.00 0.00 1.82
2794 3029 6.939730 CCCCTTAGTATTTTGTGCCAAATTTT 59.060 34.615 1.89 0.00 0.00 1.82
2795 3030 7.094848 CCCCTTAGTATTTTGTGCCAAATTTTG 60.095 37.037 1.99 1.99 0.00 2.44
2796 3031 7.659390 CCCTTAGTATTTTGTGCCAAATTTTGA 59.341 33.333 10.72 0.00 0.00 2.69
2797 3032 8.495148 CCTTAGTATTTTGTGCCAAATTTTGAC 58.505 33.333 10.72 0.00 0.00 3.18
2798 3033 9.260002 CTTAGTATTTTGTGCCAAATTTTGACT 57.740 29.630 10.72 5.38 0.00 3.41
2801 3036 9.206870 AGTATTTTGTGCCAAATTTTGACTATG 57.793 29.630 10.72 0.00 0.00 2.23
2802 3037 9.202273 GTATTTTGTGCCAAATTTTGACTATGA 57.798 29.630 10.72 0.00 0.00 2.15
2803 3038 8.674263 ATTTTGTGCCAAATTTTGACTATGAA 57.326 26.923 10.72 0.30 0.00 2.57
2804 3039 8.674263 TTTTGTGCCAAATTTTGACTATGAAT 57.326 26.923 10.72 0.00 0.00 2.57
2805 3040 8.674263 TTTGTGCCAAATTTTGACTATGAATT 57.326 26.923 10.72 0.00 0.00 2.17
2806 3041 8.674263 TTGTGCCAAATTTTGACTATGAATTT 57.326 26.923 10.72 0.00 34.33 1.82
2807 3042 8.309163 TGTGCCAAATTTTGACTATGAATTTC 57.691 30.769 10.72 0.00 32.35 2.17
2808 3043 7.930325 TGTGCCAAATTTTGACTATGAATTTCA 59.070 29.630 10.72 0.75 32.35 2.69
2809 3044 8.938906 GTGCCAAATTTTGACTATGAATTTCAT 58.061 29.630 15.78 15.78 40.72 2.57
2810 3045 9.504708 TGCCAAATTTTGACTATGAATTTCATT 57.495 25.926 16.62 0.30 38.26 2.57
2834 3069 8.877808 TTAACAAAATGTTAATGCATGTCACA 57.122 26.923 0.00 4.00 44.93 3.58
2835 3070 7.783090 AACAAAATGTTAATGCATGTCACAA 57.217 28.000 0.00 0.00 39.09 3.33
2836 3071 7.783090 ACAAAATGTTAATGCATGTCACAAA 57.217 28.000 0.00 0.00 0.00 2.83
2837 3072 8.206325 ACAAAATGTTAATGCATGTCACAAAA 57.794 26.923 0.00 0.00 0.00 2.44
2838 3073 8.671921 ACAAAATGTTAATGCATGTCACAAAAA 58.328 25.926 0.00 0.00 0.00 1.94
2939 3174 8.798153 CAATTAAATCTATCGTCAAGTTTTGGC 58.202 33.333 0.00 0.00 0.00 4.52
2940 3175 5.957842 AAATCTATCGTCAAGTTTTGGCA 57.042 34.783 0.00 0.00 34.15 4.92
2941 3176 4.946784 ATCTATCGTCAAGTTTTGGCAC 57.053 40.909 0.00 0.00 34.15 5.01
2942 3177 3.734463 TCTATCGTCAAGTTTTGGCACA 58.266 40.909 0.00 0.00 34.15 4.57
2956 3191 3.334583 TGGCACAAACTATGAGAGGAC 57.665 47.619 0.00 0.00 31.92 3.85
2957 3192 2.027192 TGGCACAAACTATGAGAGGACC 60.027 50.000 0.00 0.00 31.92 4.46
2958 3193 2.027192 GGCACAAACTATGAGAGGACCA 60.027 50.000 0.00 0.00 0.00 4.02
2959 3194 3.559171 GGCACAAACTATGAGAGGACCAA 60.559 47.826 0.00 0.00 0.00 3.67
2960 3195 4.265073 GCACAAACTATGAGAGGACCAAT 58.735 43.478 0.00 0.00 0.00 3.16
2961 3196 5.428253 GCACAAACTATGAGAGGACCAATA 58.572 41.667 0.00 0.00 0.00 1.90
2962 3197 5.880332 GCACAAACTATGAGAGGACCAATAA 59.120 40.000 0.00 0.00 0.00 1.40
2963 3198 6.374333 GCACAAACTATGAGAGGACCAATAAA 59.626 38.462 0.00 0.00 0.00 1.40
2964 3199 7.067494 GCACAAACTATGAGAGGACCAATAAAT 59.933 37.037 0.00 0.00 0.00 1.40
2965 3200 8.616076 CACAAACTATGAGAGGACCAATAAATC 58.384 37.037 0.00 0.00 0.00 2.17
2966 3201 8.328758 ACAAACTATGAGAGGACCAATAAATCA 58.671 33.333 0.00 0.00 0.00 2.57
2967 3202 8.616076 CAAACTATGAGAGGACCAATAAATCAC 58.384 37.037 0.00 0.00 0.00 3.06
2968 3203 6.516718 ACTATGAGAGGACCAATAAATCACG 58.483 40.000 0.00 0.00 0.00 4.35
2969 3204 5.614324 ATGAGAGGACCAATAAATCACGA 57.386 39.130 0.00 0.00 0.00 4.35
2970 3205 4.755411 TGAGAGGACCAATAAATCACGAC 58.245 43.478 0.00 0.00 0.00 4.34
2971 3206 3.782046 AGAGGACCAATAAATCACGACG 58.218 45.455 0.00 0.00 0.00 5.12
3015 3250 5.290158 CGCTTGGAAACGTACACAATAGTAT 59.710 40.000 0.00 0.00 0.00 2.12
3019 3254 9.362539 CTTGGAAACGTACACAATAGTATTACT 57.637 33.333 1.30 1.30 0.00 2.24
3066 3301 4.024048 ACAAAGTCACCATCGTTTTGCTAG 60.024 41.667 0.00 0.00 33.28 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 5.911752 TCAATCAAGAGTAAGATGCTCCTC 58.088 41.667 0.00 0.00 33.69 3.71
64 65 6.485313 TCATCCCATACATGGTTTAATTCGAC 59.515 38.462 7.46 0.00 46.65 4.20
82 83 2.170166 GTGAACATTTGGCTCATCCCA 58.830 47.619 0.00 0.00 0.00 4.37
84 85 3.760684 AGAAGTGAACATTTGGCTCATCC 59.239 43.478 0.00 0.00 0.00 3.51
157 158 3.368739 GGGATTGCAGAATTTCCAACTGG 60.369 47.826 0.00 0.00 33.00 4.00
181 182 2.094545 AGCAGAATGTTGCCGGAAATTC 60.095 45.455 5.05 2.33 45.18 2.17
231 232 9.893305 ACGGAAATTCAGTTCACTTAAATTTAG 57.107 29.630 0.00 8.69 31.58 1.85
240 241 6.165659 CGATTAACGGAAATTCAGTTCACT 57.834 37.500 14.29 1.95 36.29 3.41
258 259 6.161381 GGTAGAGAACAACAAAGGACGATTA 58.839 40.000 0.00 0.00 0.00 1.75
259 260 4.995487 GGTAGAGAACAACAAAGGACGATT 59.005 41.667 0.00 0.00 0.00 3.34
339 340 9.983804 CGGTCCTGTCTCTAATAAAATTTAAAC 57.016 33.333 0.00 0.00 0.00 2.01
345 346 6.749036 ATCCGGTCCTGTCTCTAATAAAAT 57.251 37.500 0.00 0.00 0.00 1.82
352 353 5.068723 GTGATTAAATCCGGTCCTGTCTCTA 59.931 44.000 0.00 0.00 0.00 2.43
359 360 2.574369 TGTGGTGATTAAATCCGGTCCT 59.426 45.455 0.00 0.00 0.00 3.85
386 387 8.180920 GTCGTAAGTAAAACCCTGTTTAAAACA 58.819 33.333 0.00 0.00 38.12 2.83
410 411 2.092914 CCCACCAATACTTCCTCCAGTC 60.093 54.545 0.00 0.00 0.00 3.51
414 415 0.106669 GCCCCACCAATACTTCCTCC 60.107 60.000 0.00 0.00 0.00 4.30
421 422 1.141053 CTACCTCTGCCCCACCAATAC 59.859 57.143 0.00 0.00 0.00 1.89
431 432 0.822164 TAACCGAAGCTACCTCTGCC 59.178 55.000 0.00 0.00 0.00 4.85
432 433 1.471153 GGTAACCGAAGCTACCTCTGC 60.471 57.143 0.00 0.00 35.61 4.26
442 443 2.098607 TGAGTATCAGCGGTAACCGAAG 59.901 50.000 0.00 0.00 46.33 3.79
463 464 5.362105 TGTATAGAACTTTGGGCGGTAAT 57.638 39.130 0.00 0.00 0.00 1.89
516 517 9.546909 CCATTTCGATATAGTTTGTATGAATGC 57.453 33.333 0.00 0.00 0.00 3.56
522 523 9.730420 GCAAAACCATTTCGATATAGTTTGTAT 57.270 29.630 11.68 0.00 0.00 2.29
587 590 4.135306 TCAGACGAGGGTTATAGCTACAG 58.865 47.826 0.00 0.00 0.00 2.74
606 609 5.474532 TGTTGGATCTCAAAATCTGGTTCAG 59.525 40.000 0.00 0.00 37.08 3.02
607 610 5.384336 TGTTGGATCTCAAAATCTGGTTCA 58.616 37.500 0.00 0.00 37.08 3.18
677 680 0.721718 CATCGACGAACCTTGGAAGC 59.278 55.000 0.00 0.00 0.00 3.86
683 686 0.038526 AGCGTTCATCGACGAACCTT 60.039 50.000 17.82 4.31 45.47 3.50
686 689 0.362512 GTGAGCGTTCATCGACGAAC 59.637 55.000 14.12 14.12 45.47 3.95
780 783 4.761227 TGCTGCATCTTGATGTTTGAAGTA 59.239 37.500 11.61 1.20 0.00 2.24
790 793 8.915057 ATTACTTATTAGTGCTGCATCTTGAT 57.085 30.769 5.27 5.98 35.78 2.57
813 816 4.777896 TGGGACAAAGAGTACTCAGCTATT 59.222 41.667 24.44 7.05 31.92 1.73
830 833 7.428197 AGAGTCTGTTTTGTCTCTATGGGACA 61.428 42.308 0.00 0.00 41.23 4.02
880 884 2.816087 GGAAGATTGAGCTCTGCACAAA 59.184 45.455 16.19 0.00 41.70 2.83
933 937 2.675844 GTGTGTGCTTGTGTGTTGTCTA 59.324 45.455 0.00 0.00 0.00 2.59
955 959 1.150536 AATGGCGTGGTTCTGTGGT 59.849 52.632 0.00 0.00 0.00 4.16
962 966 2.017049 GAGCTATTCAATGGCGTGGTT 58.983 47.619 0.00 0.00 42.13 3.67
968 972 2.355756 TCAAAGCGAGCTATTCAATGGC 59.644 45.455 0.00 0.00 36.97 4.40
977 981 5.386958 TCTTCTTACTTCAAAGCGAGCTA 57.613 39.130 0.00 0.00 0.00 3.32
982 986 4.455877 ACCCATTCTTCTTACTTCAAAGCG 59.544 41.667 0.00 0.00 0.00 4.68
988 992 3.942115 GGCTCACCCATTCTTCTTACTTC 59.058 47.826 0.00 0.00 0.00 3.01
1009 1013 0.742281 CTGATGAGCTTCACCGGTGG 60.742 60.000 33.40 19.84 0.00 4.61
1011 1015 1.078848 GCTGATGAGCTTCACCGGT 60.079 57.895 0.00 0.00 42.52 5.28
1032 1036 0.739813 GGCTGAACGTACTGCCGAAT 60.740 55.000 9.32 0.00 42.86 3.34
1072 1076 4.749310 CGGCACTCGCTTCAGCCT 62.749 66.667 0.00 0.00 44.85 4.58
1083 1087 1.433879 GATGAGCTCGTACGGCACT 59.566 57.895 24.11 15.75 0.00 4.40
1101 1105 1.847818 TGTTGTGAAGGTCTTCGACG 58.152 50.000 6.28 0.00 42.28 5.12
1115 1119 1.134946 GCAACAGTTGGCTCTTGTTGT 59.865 47.619 15.28 2.55 41.10 3.32
1130 1134 1.454847 GGGTTGTGGGTGAGCAACA 60.455 57.895 9.20 0.00 44.70 3.33
1132 1136 2.017668 ATGGGGTTGTGGGTGAGCAA 62.018 55.000 0.00 0.00 0.00 3.91
1140 1144 0.112218 TCTTGTGGATGGGGTTGTGG 59.888 55.000 0.00 0.00 0.00 4.17
1212 1216 4.476862 CCTCATCCACGTACTCGATAATG 58.523 47.826 0.00 0.00 40.62 1.90
1251 1255 2.689034 GGGTCAGTGGGGAGGAGG 60.689 72.222 0.00 0.00 0.00 4.30
1311 1315 7.695480 TTACAGCTTTGCATATACCTTTTGA 57.305 32.000 0.00 0.00 0.00 2.69
1312 1316 7.008266 CGTTTACAGCTTTGCATATACCTTTTG 59.992 37.037 0.00 0.00 0.00 2.44
1322 1326 2.154462 AGCTCGTTTACAGCTTTGCAT 58.846 42.857 0.00 0.00 45.34 3.96
1394 1399 9.853921 CTGCAAAGTTCAAATGTATTTCTTTTC 57.146 29.630 0.00 0.00 0.00 2.29
1400 1405 4.996758 GGCCTGCAAAGTTCAAATGTATTT 59.003 37.500 0.00 0.00 0.00 1.40
1530 1566 5.759763 AGAAATGGTTTCATGGTCTTTTTGC 59.240 36.000 5.36 0.00 42.10 3.68
1537 1573 3.005684 TGTGCAGAAATGGTTTCATGGTC 59.994 43.478 5.36 0.00 42.10 4.02
1539 1575 3.006110 AGTGTGCAGAAATGGTTTCATGG 59.994 43.478 5.36 0.00 42.10 3.66
1544 1580 7.944729 ATAATAGAGTGTGCAGAAATGGTTT 57.055 32.000 0.00 0.00 0.00 3.27
1545 1581 7.611467 TGAATAATAGAGTGTGCAGAAATGGTT 59.389 33.333 0.00 0.00 0.00 3.67
1561 1597 7.067372 CCAGGCAAAGAACACATGAATAATAGA 59.933 37.037 0.00 0.00 0.00 1.98
1562 1598 7.067372 TCCAGGCAAAGAACACATGAATAATAG 59.933 37.037 0.00 0.00 0.00 1.73
1565 1601 5.076182 TCCAGGCAAAGAACACATGAATAA 58.924 37.500 0.00 0.00 0.00 1.40
1578 1614 4.391405 ACTTGAAACTTTCCAGGCAAAG 57.609 40.909 7.36 8.90 39.03 2.77
1579 1615 4.221703 TGAACTTGAAACTTTCCAGGCAAA 59.778 37.500 7.36 0.00 0.00 3.68
1580 1616 3.766591 TGAACTTGAAACTTTCCAGGCAA 59.233 39.130 7.36 0.00 0.00 4.52
1631 1667 7.227873 TGGTCAACCACTGTAGAATTGATTTA 58.772 34.615 0.00 0.00 42.01 1.40
1634 1670 5.241403 TGGTCAACCACTGTAGAATTGAT 57.759 39.130 0.00 0.00 42.01 2.57
1635 1671 4.698201 TGGTCAACCACTGTAGAATTGA 57.302 40.909 0.00 0.00 42.01 2.57
1649 1689 1.069227 GCATCAAGGTTCGTGGTCAAC 60.069 52.381 0.00 0.00 0.00 3.18
1651 1691 0.107643 TGCATCAAGGTTCGTGGTCA 59.892 50.000 0.00 0.00 0.00 4.02
1654 1694 3.302365 AATTTGCATCAAGGTTCGTGG 57.698 42.857 0.00 0.00 0.00 4.94
1657 1697 5.801947 CCTTCTAAATTTGCATCAAGGTTCG 59.198 40.000 0.00 0.00 0.00 3.95
1669 1709 4.714632 TCTATCCGGGCCTTCTAAATTTG 58.285 43.478 0.84 0.00 0.00 2.32
1742 1784 3.532155 GCCCGTGGGTTGTGCAAA 61.532 61.111 6.82 0.00 37.65 3.68
1747 1789 3.319198 AGATCGCCCGTGGGTTGT 61.319 61.111 6.82 0.00 37.65 3.32
1748 1790 2.796483 TTCAGATCGCCCGTGGGTTG 62.796 60.000 6.82 0.00 37.65 3.77
1755 1797 5.408299 TCAACATATATTTTCAGATCGCCCG 59.592 40.000 0.00 0.00 0.00 6.13
1818 1860 0.390860 CCTCGCTAGGTTCCATCCAG 59.609 60.000 0.00 0.00 38.19 3.86
1848 1890 1.408822 CCCTTTGCCTCTACCATGGAC 60.409 57.143 21.47 0.71 0.00 4.02
1852 1894 1.216990 CTCCCCTTTGCCTCTACCAT 58.783 55.000 0.00 0.00 0.00 3.55
2010 2052 1.377333 GGCCGGGAACTCCTCTTTG 60.377 63.158 2.18 0.00 35.95 2.77
2011 2053 2.603652 GGGCCGGGAACTCCTCTTT 61.604 63.158 2.18 0.00 35.95 2.52
2013 2055 3.564347 AAGGGCCGGGAACTCCTCT 62.564 63.158 2.18 0.00 35.95 3.69
2028 2070 2.009774 CGTCTAGACCAATGGCAAAGG 58.990 52.381 17.23 7.00 0.00 3.11
2041 2083 5.300411 TCATCACCTACATACCGTCTAGA 57.700 43.478 0.00 0.00 0.00 2.43
2055 2097 3.176411 TGTCTTCACATCCTCATCACCT 58.824 45.455 0.00 0.00 0.00 4.00
2056 2098 3.616956 TGTCTTCACATCCTCATCACC 57.383 47.619 0.00 0.00 0.00 4.02
2097 2139 1.081892 CAGAGAACATGGCAACGAGG 58.918 55.000 0.00 0.00 42.51 4.63
2152 2194 2.479566 CCACTTCACTACTGTGGCAT 57.520 50.000 0.00 0.00 43.61 4.40
2170 2212 5.912955 CACAAAAGACGAATTAAAGTGGACC 59.087 40.000 0.00 0.00 0.00 4.46
2184 2226 5.875930 AGTGGTAAAAGAACACAAAAGACG 58.124 37.500 0.00 0.00 37.58 4.18
2194 2236 2.350102 CGCGGGAAAGTGGTAAAAGAAC 60.350 50.000 0.00 0.00 0.00 3.01
2197 2239 1.515081 TCGCGGGAAAGTGGTAAAAG 58.485 50.000 6.13 0.00 0.00 2.27
2200 2242 0.899720 AGATCGCGGGAAAGTGGTAA 59.100 50.000 6.13 0.00 0.00 2.85
2228 2270 3.799420 GCGTGTTACAATGCAAGGAAAAA 59.201 39.130 6.05 0.00 0.00 1.94
2229 2271 3.067461 AGCGTGTTACAATGCAAGGAAAA 59.933 39.130 12.26 0.00 0.00 2.29
2253 2295 4.843728 TCCCAGTTTAGCAGAAACCATAG 58.156 43.478 9.84 0.76 0.00 2.23
2270 2312 7.772757 AGAAAGCTCTCACTTTATTAATCCCAG 59.227 37.037 0.00 0.00 39.93 4.45
2311 2353 7.013220 AGTAGCCTTGTATATTGAGATGGAGA 58.987 38.462 0.00 0.00 0.00 3.71
2377 2419 4.798387 GGCATATAACTCGCTTTTTGTTGG 59.202 41.667 0.00 0.00 0.00 3.77
2400 2442 4.330620 GCATCCAATGGCATACTTTTTGTG 59.669 41.667 0.00 0.00 0.00 3.33
2413 2455 4.823157 TCTTTCAAATGTGCATCCAATGG 58.177 39.130 0.00 0.00 0.00 3.16
2509 2742 8.740906 TGTATACAAGACCACTTTGTTTTTCAA 58.259 29.630 2.20 0.00 33.70 2.69
2510 2743 8.282455 TGTATACAAGACCACTTTGTTTTTCA 57.718 30.769 2.20 0.00 33.70 2.69
2525 2758 5.964477 ACTCCCTCCATTTCTGTATACAAGA 59.036 40.000 7.06 4.19 0.00 3.02
2608 2841 8.528090 AAATGGTTATTTCTCGGTTAACCGCG 62.528 42.308 36.63 31.90 44.55 6.46
2609 2842 5.392272 AAATGGTTATTTCTCGGTTAACCGC 60.392 40.000 36.63 21.83 44.55 5.68
2633 2866 4.221482 AGCGGCTATGATCATCAATCTACA 59.779 41.667 12.53 0.00 35.24 2.74
2634 2867 4.753233 AGCGGCTATGATCATCAATCTAC 58.247 43.478 12.53 0.00 35.24 2.59
2640 2873 2.029560 GTGAGAGCGGCTATGATCATCA 60.030 50.000 12.53 0.00 0.00 3.07
2659 2893 9.254133 CTGACATAGAAGTATGGATAGTTTGTG 57.746 37.037 0.00 0.00 40.53 3.33
2665 2899 7.928167 TGTTTGCTGACATAGAAGTATGGATAG 59.072 37.037 0.00 0.00 40.53 2.08
2669 2904 6.741992 TTGTTTGCTGACATAGAAGTATGG 57.258 37.500 0.00 0.00 40.53 2.74
2726 2961 7.828223 GGAGGTAGTAGATCGTGGATATCTTTA 59.172 40.741 2.05 0.00 35.36 1.85
2727 2962 6.660094 GGAGGTAGTAGATCGTGGATATCTTT 59.340 42.308 2.05 0.00 35.36 2.52
2730 2965 4.571580 CGGAGGTAGTAGATCGTGGATATC 59.428 50.000 0.00 0.00 0.00 1.63
2732 2967 3.326006 ACGGAGGTAGTAGATCGTGGATA 59.674 47.826 0.00 0.00 0.00 2.59
2747 2982 1.982958 ACAATAAACCAGGACGGAGGT 59.017 47.619 0.00 0.00 40.61 3.85
2748 2983 2.629051 GACAATAAACCAGGACGGAGG 58.371 52.381 0.00 0.00 38.63 4.30
2751 2986 1.680860 GGGGACAATAAACCAGGACGG 60.681 57.143 0.00 0.00 42.50 4.79
2752 2987 1.680860 GGGGGACAATAAACCAGGACG 60.681 57.143 0.00 0.00 0.00 4.79
2756 2991 4.586306 ACTAAGGGGGACAATAAACCAG 57.414 45.455 0.00 0.00 0.00 4.00
2757 2992 6.661740 AATACTAAGGGGGACAATAAACCA 57.338 37.500 0.00 0.00 0.00 3.67
2758 2993 7.398047 ACAAAATACTAAGGGGGACAATAAACC 59.602 37.037 0.00 0.00 0.00 3.27
2759 2994 8.248253 CACAAAATACTAAGGGGGACAATAAAC 58.752 37.037 0.00 0.00 0.00 2.01
2760 2995 7.093684 GCACAAAATACTAAGGGGGACAATAAA 60.094 37.037 0.00 0.00 0.00 1.40
2761 2996 6.378848 GCACAAAATACTAAGGGGGACAATAA 59.621 38.462 0.00 0.00 0.00 1.40
2762 2997 5.889289 GCACAAAATACTAAGGGGGACAATA 59.111 40.000 0.00 0.00 0.00 1.90
2763 2998 4.709886 GCACAAAATACTAAGGGGGACAAT 59.290 41.667 0.00 0.00 0.00 2.71
2764 2999 4.083565 GCACAAAATACTAAGGGGGACAA 58.916 43.478 0.00 0.00 0.00 3.18
2765 3000 3.562609 GGCACAAAATACTAAGGGGGACA 60.563 47.826 0.00 0.00 0.00 4.02
2766 3001 3.021695 GGCACAAAATACTAAGGGGGAC 58.978 50.000 0.00 0.00 0.00 4.46
2767 3002 2.650322 TGGCACAAAATACTAAGGGGGA 59.350 45.455 0.00 0.00 31.92 4.81
2783 3018 8.309163 TGAAATTCATAGTCAAAATTTGGCAC 57.691 30.769 13.11 1.41 37.85 5.01
2784 3019 9.504708 AATGAAATTCATAGTCAAAATTTGGCA 57.495 25.926 13.11 0.00 35.76 4.92
2810 3045 8.877808 TTGTGACATGCATTAACATTTTGTTA 57.122 26.923 0.00 0.00 41.45 2.41
2811 3046 7.783090 TTGTGACATGCATTAACATTTTGTT 57.217 28.000 0.00 0.00 43.88 2.83
2812 3047 7.783090 TTTGTGACATGCATTAACATTTTGT 57.217 28.000 0.00 0.00 0.00 2.83
2913 3148 8.798153 GCCAAAACTTGACGATAGATTTAATTG 58.202 33.333 0.00 0.00 41.38 2.32
2914 3149 8.519526 TGCCAAAACTTGACGATAGATTTAATT 58.480 29.630 0.00 0.00 41.38 1.40
2915 3150 7.968405 GTGCCAAAACTTGACGATAGATTTAAT 59.032 33.333 0.00 0.00 41.38 1.40
2916 3151 7.041030 TGTGCCAAAACTTGACGATAGATTTAA 60.041 33.333 0.00 0.00 41.38 1.52
2917 3152 6.428465 TGTGCCAAAACTTGACGATAGATTTA 59.572 34.615 0.00 0.00 41.38 1.40
2918 3153 5.240623 TGTGCCAAAACTTGACGATAGATTT 59.759 36.000 0.00 0.00 41.38 2.17
2919 3154 4.759693 TGTGCCAAAACTTGACGATAGATT 59.240 37.500 0.00 0.00 41.38 2.40
2920 3155 4.323417 TGTGCCAAAACTTGACGATAGAT 58.677 39.130 0.00 0.00 41.38 1.98
2921 3156 3.734463 TGTGCCAAAACTTGACGATAGA 58.266 40.909 0.00 0.00 41.38 1.98
2922 3157 4.481930 TTGTGCCAAAACTTGACGATAG 57.518 40.909 0.00 0.00 46.19 2.08
2923 3158 4.336993 AGTTTGTGCCAAAACTTGACGATA 59.663 37.500 7.79 0.00 45.84 2.92
2924 3159 3.130340 AGTTTGTGCCAAAACTTGACGAT 59.870 39.130 7.79 0.00 45.84 3.73
2925 3160 2.490115 AGTTTGTGCCAAAACTTGACGA 59.510 40.909 7.79 0.00 45.84 4.20
2926 3161 2.874849 AGTTTGTGCCAAAACTTGACG 58.125 42.857 7.79 0.00 45.84 4.35
2927 3162 5.587289 TCATAGTTTGTGCCAAAACTTGAC 58.413 37.500 16.32 0.00 45.84 3.18
2928 3163 5.592282 TCTCATAGTTTGTGCCAAAACTTGA 59.408 36.000 16.32 16.28 45.84 3.02
2929 3164 5.830912 TCTCATAGTTTGTGCCAAAACTTG 58.169 37.500 16.32 13.94 45.84 3.16
2930 3165 5.010012 CCTCTCATAGTTTGTGCCAAAACTT 59.990 40.000 16.32 5.25 45.84 2.66
2932 3167 4.518970 TCCTCTCATAGTTTGTGCCAAAAC 59.481 41.667 3.73 3.73 39.80 2.43
2933 3168 4.518970 GTCCTCTCATAGTTTGTGCCAAAA 59.481 41.667 2.47 0.00 0.00 2.44
2934 3169 4.072131 GTCCTCTCATAGTTTGTGCCAAA 58.928 43.478 0.00 0.00 0.00 3.28
2935 3170 3.559171 GGTCCTCTCATAGTTTGTGCCAA 60.559 47.826 0.00 0.00 0.00 4.52
2936 3171 2.027192 GGTCCTCTCATAGTTTGTGCCA 60.027 50.000 0.00 0.00 0.00 4.92
2937 3172 2.027192 TGGTCCTCTCATAGTTTGTGCC 60.027 50.000 0.00 0.00 0.00 5.01
2938 3173 3.334583 TGGTCCTCTCATAGTTTGTGC 57.665 47.619 0.00 0.00 0.00 4.57
2939 3174 7.921786 TTTATTGGTCCTCTCATAGTTTGTG 57.078 36.000 0.00 0.00 0.00 3.33
2940 3175 8.328758 TGATTTATTGGTCCTCTCATAGTTTGT 58.671 33.333 0.00 0.00 0.00 2.83
2941 3176 8.616076 GTGATTTATTGGTCCTCTCATAGTTTG 58.384 37.037 0.00 0.00 0.00 2.93
2942 3177 7.495934 CGTGATTTATTGGTCCTCTCATAGTTT 59.504 37.037 0.00 0.00 0.00 2.66
2943 3178 6.986817 CGTGATTTATTGGTCCTCTCATAGTT 59.013 38.462 0.00 0.00 0.00 2.24
2944 3179 6.323996 TCGTGATTTATTGGTCCTCTCATAGT 59.676 38.462 0.00 0.00 0.00 2.12
2945 3180 6.642950 GTCGTGATTTATTGGTCCTCTCATAG 59.357 42.308 0.00 0.00 0.00 2.23
2946 3181 6.513180 GTCGTGATTTATTGGTCCTCTCATA 58.487 40.000 0.00 0.00 0.00 2.15
2947 3182 5.360591 GTCGTGATTTATTGGTCCTCTCAT 58.639 41.667 0.00 0.00 0.00 2.90
2948 3183 4.676986 CGTCGTGATTTATTGGTCCTCTCA 60.677 45.833 0.00 0.00 0.00 3.27
2949 3184 3.797256 CGTCGTGATTTATTGGTCCTCTC 59.203 47.826 0.00 0.00 0.00 3.20
2950 3185 3.430374 CCGTCGTGATTTATTGGTCCTCT 60.430 47.826 0.00 0.00 0.00 3.69
2951 3186 2.864343 CCGTCGTGATTTATTGGTCCTC 59.136 50.000 0.00 0.00 0.00 3.71
2952 3187 2.498481 TCCGTCGTGATTTATTGGTCCT 59.502 45.455 0.00 0.00 0.00 3.85
2953 3188 2.606272 GTCCGTCGTGATTTATTGGTCC 59.394 50.000 0.00 0.00 0.00 4.46
2954 3189 3.518590 AGTCCGTCGTGATTTATTGGTC 58.481 45.455 0.00 0.00 0.00 4.02
2955 3190 3.604875 AGTCCGTCGTGATTTATTGGT 57.395 42.857 0.00 0.00 0.00 3.67
2956 3191 3.000078 CGAAGTCCGTCGTGATTTATTGG 60.000 47.826 0.00 0.00 36.26 3.16
2957 3192 3.000078 CCGAAGTCCGTCGTGATTTATTG 60.000 47.826 2.23 0.00 39.43 1.90
2958 3193 3.119388 TCCGAAGTCCGTCGTGATTTATT 60.119 43.478 2.23 0.00 39.43 1.40
2959 3194 2.424601 TCCGAAGTCCGTCGTGATTTAT 59.575 45.455 2.23 0.00 39.43 1.40
2960 3195 1.811965 TCCGAAGTCCGTCGTGATTTA 59.188 47.619 2.23 0.00 39.43 1.40
2961 3196 0.599558 TCCGAAGTCCGTCGTGATTT 59.400 50.000 2.23 0.00 39.43 2.17
2962 3197 0.815734 ATCCGAAGTCCGTCGTGATT 59.184 50.000 2.23 0.00 39.43 2.57
2963 3198 0.100682 CATCCGAAGTCCGTCGTGAT 59.899 55.000 2.23 2.45 39.43 3.06
2964 3199 1.504900 CATCCGAAGTCCGTCGTGA 59.495 57.895 2.23 0.39 39.43 4.35
2965 3200 2.158959 GCATCCGAAGTCCGTCGTG 61.159 63.158 2.23 0.00 39.43 4.35
2966 3201 2.181021 GCATCCGAAGTCCGTCGT 59.819 61.111 2.23 0.00 39.43 4.34
2967 3202 2.582498 GGCATCCGAAGTCCGTCG 60.582 66.667 0.00 0.00 40.77 5.12
2968 3203 0.462047 AATGGCATCCGAAGTCCGTC 60.462 55.000 0.00 0.00 36.31 4.79
2969 3204 0.744414 CAATGGCATCCGAAGTCCGT 60.744 55.000 0.00 0.00 36.31 4.69
2970 3205 2.016961 CAATGGCATCCGAAGTCCG 58.983 57.895 0.00 0.00 38.18 4.79
2971 3206 0.749454 AGCAATGGCATCCGAAGTCC 60.749 55.000 0.00 0.00 44.61 3.85
3019 3254 9.237187 TGTTTGACATGCCTATCAATTAAAGTA 57.763 29.630 0.00 0.00 34.87 2.24
3022 3257 9.421806 CTTTGTTTGACATGCCTATCAATTAAA 57.578 29.630 0.00 0.39 34.87 1.52
3033 3268 2.100584 TGGTGACTTTGTTTGACATGCC 59.899 45.455 0.00 0.00 0.00 4.40
3080 3315 3.254629 GCAGTGGGCAGATCAAAGA 57.745 52.632 0.00 0.00 43.97 2.52
3130 3369 0.250209 CAGCTGCAGGTCAGACAACT 60.250 55.000 17.16 0.00 45.72 3.16


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

AutoCloner maintained by Alex Coulton.