Multiple sequence alignment - TraesCS2B01G392200

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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 TraesCS2B01G392200 chr2B 100.000 2946 0 0 1 2946 556594687 556597632 0.000000e+00 5441.0
1 TraesCS2B01G392200 chr2B 90.361 1442 99 22 1115 2524 556517284 556518717 0.000000e+00 1857.0
2 TraesCS2B01G392200 chr2B 83.779 1159 86 42 765 1854 556675919 556677044 0.000000e+00 1005.0
3 TraesCS2B01G392200 chr2B 79.811 634 68 27 71 674 556661153 556661756 9.830000e-110 407.0
4 TraesCS2B01G392200 chr2B 77.370 654 65 30 132 770 556516460 556517045 7.930000e-81 311.0
5 TraesCS2B01G392200 chr2B 92.593 216 10 3 2528 2741 569130787 569130998 3.690000e-79 305.0
6 TraesCS2B01G392200 chr2B 94.149 188 7 1 2524 2711 438929181 438929364 1.730000e-72 283.0
7 TraesCS2B01G392200 chr2B 95.906 171 7 0 2776 2946 556558046 556558216 8.040000e-71 278.0
8 TraesCS2B01G392200 chr2B 98.000 50 1 0 2728 2777 556518714 556518763 1.450000e-13 87.9
9 TraesCS2B01G392200 chr2B 91.935 62 5 0 709 770 556675833 556675894 1.450000e-13 87.9
10 TraesCS2B01G392200 chr2D 87.299 1370 111 30 941 2273 475499076 475500419 0.000000e+00 1507.0
11 TraesCS2B01G392200 chr2D 83.912 1411 111 46 765 2102 475876578 475877945 0.000000e+00 1242.0
12 TraesCS2B01G392200 chr2D 83.219 1162 88 40 765 1854 475984532 475985658 0.000000e+00 966.0
13 TraesCS2B01G392200 chr2D 79.022 634 75 22 71 671 475981990 475982598 5.960000e-102 381.0
14 TraesCS2B01G392200 chr2D 77.982 654 71 37 142 770 475498282 475498887 2.810000e-90 342.0
15 TraesCS2B01G392200 chr2D 90.995 211 15 1 2520 2730 82889807 82890013 6.220000e-72 281.0
16 TraesCS2B01G392200 chr2D 88.649 185 18 1 2128 2312 475877941 475878122 3.820000e-54 222.0
17 TraesCS2B01G392200 chr2D 94.118 136 7 1 2812 2946 475878281 475878416 3.850000e-49 206.0
18 TraesCS2B01G392200 chr2D 83.333 216 19 7 82 297 475873808 475874006 1.800000e-42 183.0
19 TraesCS2B01G392200 chr2D 92.063 63 4 1 709 770 475984445 475984507 1.450000e-13 87.9
20 TraesCS2B01G392200 chr2D 86.364 66 5 1 709 770 475876488 475876553 5.270000e-08 69.4
21 TraesCS2B01G392200 chr2A 86.101 1367 96 38 949 2273 617730640 617731954 0.000000e+00 1386.0
22 TraesCS2B01G392200 chr2A 88.313 907 80 11 1412 2312 617762363 617763249 0.000000e+00 1064.0
23 TraesCS2B01G392200 chr2A 82.353 1156 98 51 765 1854 617812557 617813672 0.000000e+00 907.0
24 TraesCS2B01G392200 chr2A 88.552 594 37 13 142 712 617759141 617759726 0.000000e+00 691.0
25 TraesCS2B01G392200 chr2A 80.218 642 63 33 71 692 617729858 617730455 9.760000e-115 424.0
26 TraesCS2B01G392200 chr2A 78.022 637 65 32 82 669 617797551 617798161 6.090000e-87 331.0
27 TraesCS2B01G392200 chr2A 92.694 219 16 0 2728 2946 617789372 617789590 1.700000e-82 316.0
28 TraesCS2B01G392200 chr2A 96.774 93 3 0 890 982 617761470 617761562 3.930000e-34 156.0
29 TraesCS2B01G392200 chr2A 98.214 56 1 0 70 125 617759089 617759144 6.720000e-17 99.0
30 TraesCS2B01G392200 chr6B 81.416 452 80 4 1412 1861 473541094 473540645 1.670000e-97 366.0
31 TraesCS2B01G392200 chr4B 92.381 210 9 3 2521 2728 371788567 371788771 2.870000e-75 292.0
32 TraesCS2B01G392200 chr4D 91.905 210 13 1 2529 2738 470124616 470124411 1.030000e-74 291.0
33 TraesCS2B01G392200 chr7B 91.667 204 13 1 2525 2728 554524355 554524156 2.240000e-71 279.0
34 TraesCS2B01G392200 chr6D 92.079 202 11 2 2523 2723 43060630 43060433 2.240000e-71 279.0
35 TraesCS2B01G392200 chr6A 90.610 213 15 2 2520 2731 1763309 1763101 8.040000e-71 278.0
36 TraesCS2B01G392200 chr5D 90.952 210 12 2 2524 2733 530794836 530795038 2.890000e-70 276.0


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 TraesCS2B01G392200 chr2B 556594687 556597632 2945 False 5441.000000 5441 100.00000 1 2946 1 chr2B.!!$F3 2945
1 TraesCS2B01G392200 chr2B 556516460 556518763 2303 False 751.966667 1857 88.57700 132 2777 3 chr2B.!!$F6 2645
2 TraesCS2B01G392200 chr2B 556675833 556677044 1211 False 546.450000 1005 87.85700 709 1854 2 chr2B.!!$F7 1145
3 TraesCS2B01G392200 chr2B 556661153 556661756 603 False 407.000000 407 79.81100 71 674 1 chr2B.!!$F4 603
4 TraesCS2B01G392200 chr2D 475498282 475500419 2137 False 924.500000 1507 82.64050 142 2273 2 chr2D.!!$F2 2131
5 TraesCS2B01G392200 chr2D 475981990 475985658 3668 False 478.300000 966 84.76800 71 1854 3 chr2D.!!$F4 1783
6 TraesCS2B01G392200 chr2D 475873808 475878416 4608 False 384.480000 1242 87.27520 82 2946 5 chr2D.!!$F3 2864
7 TraesCS2B01G392200 chr2A 617812557 617813672 1115 False 907.000000 907 82.35300 765 1854 1 chr2A.!!$F3 1089
8 TraesCS2B01G392200 chr2A 617729858 617731954 2096 False 905.000000 1386 83.15950 71 2273 2 chr2A.!!$F4 2202
9 TraesCS2B01G392200 chr2A 617759089 617763249 4160 False 502.500000 1064 92.96325 70 2312 4 chr2A.!!$F5 2242
10 TraesCS2B01G392200 chr2A 617797551 617798161 610 False 331.000000 331 78.02200 82 669 1 chr2A.!!$F2 587

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
763 4970 0.032678 AGGCATCGTCGATCATGGTC 59.967 55.0 4.34 0.0 0.0 4.02 F
765 4972 0.249447 GCATCGTCGATCATGGTCCA 60.249 55.0 4.34 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 7980 0.033208 GCACCTTCATCCCATTCCCA 60.033 55.0 0.00 0.0 0.00 4.37 R
2651 8958 0.033228 TTTGGCGCTCAATTGGTTGG 59.967 50.0 7.64 0.0 35.99 3.77 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
23 24 6.817765 ATGTTCATAATATTTAGGCCCACG 57.182 37.500 0.00 0.00 0.00 4.94
24 25 5.686753 TGTTCATAATATTTAGGCCCACGT 58.313 37.500 0.00 0.00 0.00 4.49
25 26 5.529430 TGTTCATAATATTTAGGCCCACGTG 59.471 40.000 9.08 9.08 0.00 4.49
26 27 5.298989 TCATAATATTTAGGCCCACGTGT 57.701 39.130 15.65 0.00 0.00 4.49
27 28 5.302360 TCATAATATTTAGGCCCACGTGTC 58.698 41.667 15.65 5.64 0.00 3.67
28 29 3.637911 AATATTTAGGCCCACGTGTCA 57.362 42.857 15.65 0.00 0.00 3.58
29 30 3.637911 ATATTTAGGCCCACGTGTCAA 57.362 42.857 15.65 0.00 0.00 3.18
30 31 2.507407 ATTTAGGCCCACGTGTCAAT 57.493 45.000 15.65 0.18 0.00 2.57
31 32 1.529226 TTTAGGCCCACGTGTCAATG 58.471 50.000 15.65 0.00 0.00 2.82
32 33 0.687920 TTAGGCCCACGTGTCAATGA 59.312 50.000 15.65 0.00 0.00 2.57
33 34 0.036765 TAGGCCCACGTGTCAATGAC 60.037 55.000 15.65 6.41 0.00 3.06
34 35 2.332654 GGCCCACGTGTCAATGACC 61.333 63.158 15.65 1.54 0.00 4.02
35 36 2.332654 GCCCACGTGTCAATGACCC 61.333 63.158 15.65 0.00 0.00 4.46
36 37 1.072332 CCCACGTGTCAATGACCCA 59.928 57.895 15.65 0.00 0.00 4.51
37 38 0.536233 CCCACGTGTCAATGACCCAA 60.536 55.000 15.65 0.00 0.00 4.12
38 39 1.313772 CCACGTGTCAATGACCCAAA 58.686 50.000 15.65 0.00 0.00 3.28
39 40 1.266718 CCACGTGTCAATGACCCAAAG 59.733 52.381 15.65 0.00 0.00 2.77
40 41 1.946768 CACGTGTCAATGACCCAAAGT 59.053 47.619 11.24 0.00 0.00 2.66
41 42 2.032030 CACGTGTCAATGACCCAAAGTC 60.032 50.000 11.24 0.00 46.51 3.01
50 51 2.586648 GACCCAAAGTCAGGTTCCAT 57.413 50.000 0.00 0.00 45.55 3.41
51 52 2.876581 GACCCAAAGTCAGGTTCCATT 58.123 47.619 0.00 0.00 45.55 3.16
52 53 4.028993 GACCCAAAGTCAGGTTCCATTA 57.971 45.455 0.00 0.00 45.55 1.90
53 54 4.403734 GACCCAAAGTCAGGTTCCATTAA 58.596 43.478 0.00 0.00 45.55 1.40
54 55 4.407365 ACCCAAAGTCAGGTTCCATTAAG 58.593 43.478 0.00 0.00 29.94 1.85
55 56 3.763897 CCCAAAGTCAGGTTCCATTAAGG 59.236 47.826 0.00 0.00 39.47 2.69
56 57 3.193479 CCAAAGTCAGGTTCCATTAAGGC 59.807 47.826 0.00 0.00 37.29 4.35
57 58 3.806949 AAGTCAGGTTCCATTAAGGCA 57.193 42.857 0.00 0.00 37.29 4.75
58 59 3.073274 AGTCAGGTTCCATTAAGGCAC 57.927 47.619 0.00 0.00 37.29 5.01
61 62 3.562397 GGTTCCATTAAGGCACCGA 57.438 52.632 0.00 0.00 43.94 4.69
62 63 1.828979 GGTTCCATTAAGGCACCGAA 58.171 50.000 0.00 0.00 43.94 4.30
63 64 1.743394 GGTTCCATTAAGGCACCGAAG 59.257 52.381 0.00 0.00 43.94 3.79
64 65 3.521162 GGTTCCATTAAGGCACCGAAGG 61.521 54.545 0.00 0.00 43.94 3.46
65 66 0.393808 TCCATTAAGGCACCGAAGGC 60.394 55.000 0.00 0.00 46.79 4.35
122 132 1.227764 CATGGGTCGAGCCATCTGG 60.228 63.158 39.24 26.98 39.65 3.86
242 253 1.583495 CGCTGACTCAGACCACCGTA 61.583 60.000 10.45 0.00 32.44 4.02
264 277 1.588597 GCCCTGGAAGAAAAGCAGC 59.411 57.895 0.00 0.00 34.07 5.25
265 278 0.897401 GCCCTGGAAGAAAAGCAGCT 60.897 55.000 0.00 0.00 34.07 4.24
266 279 1.172175 CCCTGGAAGAAAAGCAGCTC 58.828 55.000 0.00 0.00 34.07 4.09
267 280 1.546323 CCCTGGAAGAAAAGCAGCTCA 60.546 52.381 0.00 0.00 34.07 4.26
269 282 2.551721 CCTGGAAGAAAAGCAGCTCAGA 60.552 50.000 0.00 0.00 34.07 3.27
270 283 2.483491 CTGGAAGAAAAGCAGCTCAGAC 59.517 50.000 0.00 0.00 34.07 3.51
311 359 2.021355 AGCTAACATGCACTGAGAGC 57.979 50.000 0.00 0.00 36.78 4.09
338 386 3.403057 CGAACGTGCAGTGACGGG 61.403 66.667 16.00 5.08 43.84 5.28
371 425 2.170985 CACGCGCGAACCTTCTTG 59.829 61.111 39.36 18.07 0.00 3.02
387 477 5.221461 ACCTTCTTGCTTCTTCTTCTTCGTA 60.221 40.000 0.00 0.00 0.00 3.43
388 478 5.119434 CCTTCTTGCTTCTTCTTCTTCGTAC 59.881 44.000 0.00 0.00 0.00 3.67
391 481 4.175787 TGCTTCTTCTTCTTCGTACTCC 57.824 45.455 0.00 0.00 0.00 3.85
418 526 4.778143 GGTGTAGGCCCCACTGCG 62.778 72.222 19.41 0.00 33.31 5.18
542 650 2.411904 CATCCGCTCAAAGCTATCTCC 58.588 52.381 0.00 0.00 39.60 3.71
556 672 3.123621 GCTATCTCCACTTTGAACACACG 59.876 47.826 0.00 0.00 0.00 4.49
571 687 1.164041 ACACGGCACTGCAAACCTAC 61.164 55.000 2.82 0.00 0.00 3.18
595 749 8.329203 ACAAATAATCTGAAGAGGAAAGTGAC 57.671 34.615 0.00 0.00 0.00 3.67
603 760 2.427506 AGAGGAAAGTGACAATTCGGC 58.572 47.619 0.00 0.00 0.00 5.54
612 769 2.254951 CAATTCGGCTGCGTTGCA 59.745 55.556 0.00 0.00 36.92 4.08
613 770 1.153978 CAATTCGGCTGCGTTGCAT 60.154 52.632 0.00 0.00 38.13 3.96
614 771 0.098552 CAATTCGGCTGCGTTGCATA 59.901 50.000 0.00 0.00 38.13 3.14
615 772 1.024271 AATTCGGCTGCGTTGCATAT 58.976 45.000 0.00 0.00 38.13 1.78
741 4944 1.685765 ATGTGACAGCCGGCTAGGA 60.686 57.895 32.30 12.93 45.00 2.94
761 4968 1.143305 GAAGGCATCGTCGATCATGG 58.857 55.000 4.34 0.00 0.00 3.66
762 4969 0.465705 AAGGCATCGTCGATCATGGT 59.534 50.000 4.34 0.00 0.00 3.55
763 4970 0.032678 AGGCATCGTCGATCATGGTC 59.967 55.000 4.34 0.00 0.00 4.02
764 4971 0.946221 GGCATCGTCGATCATGGTCC 60.946 60.000 4.34 0.00 0.00 4.46
765 4972 0.249447 GCATCGTCGATCATGGTCCA 60.249 55.000 4.34 0.00 0.00 4.02
774 5020 2.359848 CGATCATGGTCCATGCACAAAT 59.640 45.455 24.89 13.81 41.18 2.32
777 5023 2.492881 TCATGGTCCATGCACAAATGTC 59.507 45.455 24.89 0.00 41.18 3.06
784 5876 3.573569 TGCACAAATGTCTTGCAGC 57.426 47.368 0.00 0.00 41.29 5.25
828 6162 1.147153 CTAGGCAAGCACTAGGGGC 59.853 63.158 0.00 0.00 35.42 5.80
832 6166 3.010144 CAAGCACTAGGGGCCCAT 58.990 61.111 27.72 21.79 0.00 4.00
982 6599 4.689612 ATCCAGAGCTTATAAAAGGCGA 57.310 40.909 0.00 0.00 32.98 5.54
992 6609 1.269703 TAAAAGGCGACCCCCTCCTC 61.270 60.000 0.00 0.00 32.93 3.71
998 6615 2.448736 GACCCCCTCCTCCCCATC 60.449 72.222 0.00 0.00 0.00 3.51
1020 6637 3.731136 GCACGGAGCAACAAGTCA 58.269 55.556 0.00 0.00 44.79 3.41
1035 6674 0.389391 AGTCACAACTCACCTCACCG 59.611 55.000 0.00 0.00 0.00 4.94
1062 6702 2.038295 CTCAGACAGAGGCAGGAAACTT 59.962 50.000 0.00 0.00 38.78 2.66
1089 6729 2.197283 AAGGAAGGAAGCAGAGCAAG 57.803 50.000 0.00 0.00 0.00 4.01
1090 6730 1.063183 AGGAAGGAAGCAGAGCAAGT 58.937 50.000 0.00 0.00 0.00 3.16
1091 6731 1.003003 AGGAAGGAAGCAGAGCAAGTC 59.997 52.381 0.00 0.00 0.00 3.01
1092 6732 1.003003 GGAAGGAAGCAGAGCAAGTCT 59.997 52.381 0.00 0.00 35.00 3.24
1095 6738 1.696336 AGGAAGCAGAGCAAGTCTTCA 59.304 47.619 9.77 0.00 37.31 3.02
1128 6771 5.120519 TCGTCTTACGAGAGAAAGAAGTCTC 59.879 44.000 0.00 0.00 46.73 3.36
1163 6806 1.251251 ACAGCAAATGGAGAAGGCAC 58.749 50.000 0.00 0.00 0.00 5.01
1166 6809 0.881118 GCAAATGGAGAAGGCACGAA 59.119 50.000 0.00 0.00 0.00 3.85
1180 6823 1.898938 CACGAAATGCGCATGTGATT 58.101 45.000 26.63 17.25 46.04 2.57
1259 6923 1.355971 TGCAAAGTATTCGACGAGCC 58.644 50.000 0.00 0.00 0.00 4.70
1325 7028 1.672881 CTCGGGGCATCAAAGAACATC 59.327 52.381 0.00 0.00 0.00 3.06
1326 7029 1.281867 TCGGGGCATCAAAGAACATCT 59.718 47.619 0.00 0.00 0.00 2.90
1350 7053 2.381961 AGTCCTCCTTCAGTCCTTCTCT 59.618 50.000 0.00 0.00 0.00 3.10
1356 7059 3.333980 TCCTTCAGTCCTTCTCTAGTCCA 59.666 47.826 0.00 0.00 0.00 4.02
1511 7618 1.000955 GCGTGGAGAAAGTCTTCCAGA 59.999 52.381 0.00 0.00 32.30 3.86
1785 7898 4.034258 GCTGGTGACCGACGACGA 62.034 66.667 9.28 0.00 42.66 4.20
1824 7937 1.592223 GCTTCGTCAGCTACCAGGT 59.408 57.895 0.00 0.00 46.27 4.00
1856 7969 3.068064 TCGAGCAGGTCATCGGCA 61.068 61.111 0.00 0.00 39.07 5.69
1857 7970 2.107750 CGAGCAGGTCATCGGCAT 59.892 61.111 0.00 0.00 39.07 4.40
2019 8151 3.136763 CAGCATGCGTGATTTAGGAGAT 58.863 45.455 13.01 0.00 0.00 2.75
2028 8160 3.564644 GTGATTTAGGAGATCTCGTCGGA 59.435 47.826 20.66 9.05 0.00 4.55
2127 8320 3.590127 GCACGAGGCCTAGGTTATC 57.410 57.895 17.90 5.35 36.11 1.75
2128 8321 0.318784 GCACGAGGCCTAGGTTATCG 60.319 60.000 22.65 22.65 39.22 2.92
2129 8322 1.315690 CACGAGGCCTAGGTTATCGA 58.684 55.000 27.84 0.00 37.16 3.59
2130 8323 1.001597 CACGAGGCCTAGGTTATCGAC 60.002 57.143 27.84 5.75 37.16 4.20
2144 8337 1.956629 ATCGACCTGGTGGCTTACGG 61.957 60.000 2.82 0.00 36.63 4.02
2171 8369 1.693627 CTATACGTGAGGCTGGAGGT 58.306 55.000 0.00 0.00 0.00 3.85
2173 8371 1.330655 ATACGTGAGGCTGGAGGTGG 61.331 60.000 0.00 0.00 0.00 4.61
2181 8379 2.878429 CTGGAGGTGGACGACGAG 59.122 66.667 0.00 0.00 0.00 4.18
2274 8487 0.814010 GGCTTATCAATGGGCGTCGT 60.814 55.000 0.00 0.00 0.00 4.34
2296 8509 0.911769 TGGATTGGTAGGTGCTGGAG 59.088 55.000 0.00 0.00 0.00 3.86
2426 8733 6.970484 ACACTTAAGTAGCATTTGGTTTGAG 58.030 36.000 8.04 0.00 0.00 3.02
2429 8736 8.134895 CACTTAAGTAGCATTTGGTTTGAGAAA 58.865 33.333 8.04 0.00 0.00 2.52
2499 8806 4.252073 GAGGTTGCCTCTCATATGCATAG 58.748 47.826 12.79 0.18 46.41 2.23
2528 8835 7.593825 ACAATATGAACAAAGTACAAAGAGGC 58.406 34.615 0.00 0.00 0.00 4.70
2529 8836 7.448469 ACAATATGAACAAAGTACAAAGAGGCT 59.552 33.333 0.00 0.00 0.00 4.58
2530 8837 8.946085 CAATATGAACAAAGTACAAAGAGGCTA 58.054 33.333 0.00 0.00 0.00 3.93
2531 8838 9.515226 AATATGAACAAAGTACAAAGAGGCTAA 57.485 29.630 0.00 0.00 0.00 3.09
2532 8839 9.686683 ATATGAACAAAGTACAAAGAGGCTAAT 57.313 29.630 0.00 0.00 0.00 1.73
2533 8840 7.817418 TGAACAAAGTACAAAGAGGCTAATT 57.183 32.000 0.00 0.00 0.00 1.40
2534 8841 7.648142 TGAACAAAGTACAAAGAGGCTAATTG 58.352 34.615 9.50 9.50 0.00 2.32
2535 8842 6.575162 ACAAAGTACAAAGAGGCTAATTGG 57.425 37.500 14.14 1.56 0.00 3.16
2536 8843 6.068670 ACAAAGTACAAAGAGGCTAATTGGT 58.931 36.000 14.14 6.88 0.00 3.67
2537 8844 6.549736 ACAAAGTACAAAGAGGCTAATTGGTT 59.450 34.615 14.14 4.44 0.00 3.67
2538 8845 6.819397 AAGTACAAAGAGGCTAATTGGTTC 57.181 37.500 14.14 3.26 0.00 3.62
2539 8846 4.935808 AGTACAAAGAGGCTAATTGGTTCG 59.064 41.667 14.14 0.00 0.00 3.95
2540 8847 2.488153 ACAAAGAGGCTAATTGGTTCGC 59.512 45.455 14.14 0.00 0.00 4.70
2541 8848 2.749621 CAAAGAGGCTAATTGGTTCGCT 59.250 45.455 4.30 0.00 0.00 4.93
2542 8849 2.029838 AGAGGCTAATTGGTTCGCTG 57.970 50.000 0.00 0.00 0.00 5.18
2543 8850 0.378610 GAGGCTAATTGGTTCGCTGC 59.621 55.000 0.00 0.00 0.00 5.25
2544 8851 1.032114 AGGCTAATTGGTTCGCTGCC 61.032 55.000 0.00 0.00 39.19 4.85
2545 8852 1.312371 GGCTAATTGGTTCGCTGCCA 61.312 55.000 0.00 0.00 38.79 4.92
2549 8856 4.251246 TTGGTTCGCTGCCAAAGT 57.749 50.000 0.00 0.00 42.39 2.66
2550 8857 2.499214 TTGGTTCGCTGCCAAAGTT 58.501 47.368 0.00 0.00 42.39 2.66
2551 8858 0.820871 TTGGTTCGCTGCCAAAGTTT 59.179 45.000 0.00 0.00 42.39 2.66
2552 8859 0.102120 TGGTTCGCTGCCAAAGTTTG 59.898 50.000 8.73 8.73 32.29 2.93
2605 8912 5.881777 GGTAAAACCAAAACTTGCCAAAA 57.118 34.783 0.00 0.00 38.42 2.44
2606 8913 6.255596 GGTAAAACCAAAACTTGCCAAAAA 57.744 33.333 0.00 0.00 38.42 1.94
2631 8938 8.716646 AAAAATTGGTAACTTTTTGAGAGGTG 57.283 30.769 0.00 0.00 34.26 4.00
2632 8939 6.405278 AATTGGTAACTTTTTGAGAGGTGG 57.595 37.500 0.00 0.00 37.61 4.61
2633 8940 3.827722 TGGTAACTTTTTGAGAGGTGGG 58.172 45.455 0.00 0.00 37.61 4.61
2634 8941 2.557056 GGTAACTTTTTGAGAGGTGGGC 59.443 50.000 0.00 0.00 0.00 5.36
2635 8942 2.452600 AACTTTTTGAGAGGTGGGCA 57.547 45.000 0.00 0.00 0.00 5.36
2636 8943 2.452600 ACTTTTTGAGAGGTGGGCAA 57.547 45.000 0.00 0.00 0.00 4.52
2637 8944 2.310538 ACTTTTTGAGAGGTGGGCAAG 58.689 47.619 0.00 0.00 0.00 4.01
2638 8945 2.091885 ACTTTTTGAGAGGTGGGCAAGA 60.092 45.455 0.00 0.00 0.00 3.02
2639 8946 2.746279 TTTTGAGAGGTGGGCAAGAA 57.254 45.000 0.00 0.00 0.00 2.52
2640 8947 1.981256 TTTGAGAGGTGGGCAAGAAC 58.019 50.000 0.00 0.00 0.00 3.01
2641 8948 0.110486 TTGAGAGGTGGGCAAGAACC 59.890 55.000 0.00 0.00 36.66 3.62
2642 8949 1.059584 TGAGAGGTGGGCAAGAACCA 61.060 55.000 0.00 0.00 39.05 3.67
2643 8950 0.110486 GAGAGGTGGGCAAGAACCAA 59.890 55.000 0.00 0.00 40.24 3.67
2644 8951 0.779997 AGAGGTGGGCAAGAACCAAT 59.220 50.000 0.00 0.00 40.24 3.16
2645 8952 1.147817 AGAGGTGGGCAAGAACCAATT 59.852 47.619 0.00 0.00 40.24 2.32
2646 8953 1.273327 GAGGTGGGCAAGAACCAATTG 59.727 52.381 0.00 0.00 40.24 2.32
2647 8954 0.321346 GGTGGGCAAGAACCAATTGG 59.679 55.000 23.31 23.31 40.24 3.16
2665 8972 3.996825 GTAGCCAACCAATTGAGCG 57.003 52.632 7.12 0.00 38.15 5.03
2666 8973 0.179163 GTAGCCAACCAATTGAGCGC 60.179 55.000 7.12 0.00 38.15 5.92
2667 8974 1.312371 TAGCCAACCAATTGAGCGCC 61.312 55.000 7.12 0.00 38.15 6.53
2668 8975 2.929903 GCCAACCAATTGAGCGCCA 61.930 57.895 7.12 0.00 38.15 5.69
2669 8976 1.664873 CCAACCAATTGAGCGCCAA 59.335 52.632 7.12 8.96 38.15 4.52
2670 8977 0.033228 CCAACCAATTGAGCGCCAAA 59.967 50.000 7.12 5.19 38.15 3.28
2671 8978 1.338011 CCAACCAATTGAGCGCCAAAT 60.338 47.619 7.12 7.29 38.15 2.32
2672 8979 2.415776 CAACCAATTGAGCGCCAAATT 58.584 42.857 7.12 12.51 38.15 1.82
2673 8980 2.807392 CAACCAATTGAGCGCCAAATTT 59.193 40.909 13.56 4.06 38.15 1.82
2674 8981 3.124578 ACCAATTGAGCGCCAAATTTT 57.875 38.095 13.56 3.46 38.43 1.82
2675 8982 3.475575 ACCAATTGAGCGCCAAATTTTT 58.524 36.364 13.56 3.16 38.43 1.94
2676 8983 4.636249 ACCAATTGAGCGCCAAATTTTTA 58.364 34.783 13.56 0.00 38.43 1.52
2677 8984 4.690280 ACCAATTGAGCGCCAAATTTTTAG 59.310 37.500 13.56 7.27 38.43 1.85
2678 8985 4.928615 CCAATTGAGCGCCAAATTTTTAGA 59.071 37.500 13.56 0.00 38.43 2.10
2679 8986 5.163963 CCAATTGAGCGCCAAATTTTTAGAC 60.164 40.000 13.56 0.00 38.43 2.59
2680 8987 4.846779 TTGAGCGCCAAATTTTTAGACT 57.153 36.364 2.29 0.00 0.00 3.24
2681 8988 4.846779 TGAGCGCCAAATTTTTAGACTT 57.153 36.364 2.29 0.00 0.00 3.01
2682 8989 4.545610 TGAGCGCCAAATTTTTAGACTTG 58.454 39.130 2.29 0.00 0.00 3.16
2683 8990 3.317150 AGCGCCAAATTTTTAGACTTGC 58.683 40.909 2.29 0.00 0.00 4.01
2684 8991 2.411748 GCGCCAAATTTTTAGACTTGCC 59.588 45.455 0.00 0.00 0.00 4.52
2685 8992 3.648009 CGCCAAATTTTTAGACTTGCCA 58.352 40.909 0.00 0.00 0.00 4.92
2686 8993 4.054671 CGCCAAATTTTTAGACTTGCCAA 58.945 39.130 0.00 0.00 0.00 4.52
2687 8994 4.084589 CGCCAAATTTTTAGACTTGCCAAC 60.085 41.667 0.00 0.00 0.00 3.77
2688 8995 4.813697 GCCAAATTTTTAGACTTGCCAACA 59.186 37.500 0.00 0.00 0.00 3.33
2689 8996 5.295540 GCCAAATTTTTAGACTTGCCAACAA 59.704 36.000 0.00 0.00 0.00 2.83
2690 8997 6.017192 GCCAAATTTTTAGACTTGCCAACAAT 60.017 34.615 0.00 0.00 34.61 2.71
2691 8998 7.468494 GCCAAATTTTTAGACTTGCCAACAATT 60.468 33.333 0.00 0.00 34.61 2.32
2692 8999 7.856894 CCAAATTTTTAGACTTGCCAACAATTG 59.143 33.333 3.24 3.24 34.61 2.32
2720 9027 5.883503 CCAATTATTGGCAGCAAAACAAT 57.116 34.783 11.33 0.00 45.17 2.71
2721 9028 6.256912 CCAATTATTGGCAGCAAAACAATT 57.743 33.333 11.33 0.00 45.17 2.32
2722 9029 7.375106 CCAATTATTGGCAGCAAAACAATTA 57.625 32.000 11.33 0.00 45.17 1.40
2723 9030 7.814642 CCAATTATTGGCAGCAAAACAATTAA 58.185 30.769 11.33 0.00 45.17 1.40
2724 9031 7.964011 CCAATTATTGGCAGCAAAACAATTAAG 59.036 33.333 11.33 0.00 45.17 1.85
2725 9032 6.479095 TTATTGGCAGCAAAACAATTAAGC 57.521 33.333 0.00 0.00 36.36 3.09
2726 9033 3.749665 TGGCAGCAAAACAATTAAGCT 57.250 38.095 0.00 0.00 35.63 3.74
2727 9034 3.652274 TGGCAGCAAAACAATTAAGCTC 58.348 40.909 0.00 0.00 32.35 4.09
2728 9035 3.069300 TGGCAGCAAAACAATTAAGCTCA 59.931 39.130 0.00 0.00 32.35 4.26
2729 9036 4.057432 GGCAGCAAAACAATTAAGCTCAA 58.943 39.130 0.00 0.00 32.35 3.02
2730 9037 4.511082 GGCAGCAAAACAATTAAGCTCAAA 59.489 37.500 0.00 0.00 32.35 2.69
2777 9084 7.581011 ATTATCAAAATTTTCAGTGGCGTTC 57.419 32.000 0.00 0.00 0.00 3.95
2778 9085 4.377839 TCAAAATTTTCAGTGGCGTTCA 57.622 36.364 0.00 0.00 0.00 3.18
2779 9086 4.109050 TCAAAATTTTCAGTGGCGTTCAC 58.891 39.130 0.00 3.40 46.39 3.18
2790 9097 4.531659 GTGGCGTTCACCTTGATTATAC 57.468 45.455 0.53 0.00 40.39 1.47
2791 9098 4.189231 GTGGCGTTCACCTTGATTATACT 58.811 43.478 0.53 0.00 40.39 2.12
2792 9099 4.634443 GTGGCGTTCACCTTGATTATACTT 59.366 41.667 0.53 0.00 40.39 2.24
2793 9100 4.873827 TGGCGTTCACCTTGATTATACTTC 59.126 41.667 0.00 0.00 0.00 3.01
2794 9101 4.025979 GGCGTTCACCTTGATTATACTTCG 60.026 45.833 0.00 0.00 0.00 3.79
2795 9102 4.802039 GCGTTCACCTTGATTATACTTCGA 59.198 41.667 0.00 0.00 0.00 3.71
2796 9103 5.276254 GCGTTCACCTTGATTATACTTCGAC 60.276 44.000 0.00 0.00 0.00 4.20
2797 9104 5.231568 CGTTCACCTTGATTATACTTCGACC 59.768 44.000 0.00 0.00 0.00 4.79
2798 9105 4.928601 TCACCTTGATTATACTTCGACCG 58.071 43.478 0.00 0.00 0.00 4.79
2799 9106 3.489785 CACCTTGATTATACTTCGACCGC 59.510 47.826 0.00 0.00 0.00 5.68
2800 9107 3.131577 ACCTTGATTATACTTCGACCGCA 59.868 43.478 0.00 0.00 0.00 5.69
2801 9108 4.116961 CCTTGATTATACTTCGACCGCAA 58.883 43.478 0.00 0.00 0.00 4.85
2802 9109 4.569162 CCTTGATTATACTTCGACCGCAAA 59.431 41.667 0.00 0.00 0.00 3.68
2803 9110 5.459110 TTGATTATACTTCGACCGCAAAC 57.541 39.130 0.00 0.00 0.00 2.93
2804 9111 4.496360 TGATTATACTTCGACCGCAAACA 58.504 39.130 0.00 0.00 0.00 2.83
2805 9112 5.113383 TGATTATACTTCGACCGCAAACAT 58.887 37.500 0.00 0.00 0.00 2.71
2806 9113 4.850859 TTATACTTCGACCGCAAACATG 57.149 40.909 0.00 0.00 0.00 3.21
2807 9114 1.434555 TACTTCGACCGCAAACATGG 58.565 50.000 0.00 0.00 0.00 3.66
2808 9115 1.154225 CTTCGACCGCAAACATGGC 60.154 57.895 0.00 0.00 0.00 4.40
2809 9116 1.577328 CTTCGACCGCAAACATGGCT 61.577 55.000 0.00 0.00 0.00 4.75
2810 9117 1.169661 TTCGACCGCAAACATGGCTT 61.170 50.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.206634 CACGTGGGCCTAAATATTATGAACAT 59.793 38.462 7.95 0.00 0.00 2.71
1 2 5.529430 CACGTGGGCCTAAATATTATGAACA 59.471 40.000 7.95 0.00 0.00 3.18
2 3 5.529800 ACACGTGGGCCTAAATATTATGAAC 59.470 40.000 21.57 0.00 0.00 3.18
3 4 5.686753 ACACGTGGGCCTAAATATTATGAA 58.313 37.500 21.57 0.00 0.00 2.57
4 5 5.163290 TGACACGTGGGCCTAAATATTATGA 60.163 40.000 21.57 0.00 0.00 2.15
5 6 5.060506 TGACACGTGGGCCTAAATATTATG 58.939 41.667 21.57 0.00 0.00 1.90
6 7 5.298989 TGACACGTGGGCCTAAATATTAT 57.701 39.130 21.57 0.00 0.00 1.28
7 8 4.757019 TGACACGTGGGCCTAAATATTA 57.243 40.909 21.57 0.00 0.00 0.98
8 9 3.637911 TGACACGTGGGCCTAAATATT 57.362 42.857 21.57 0.00 0.00 1.28
9 10 3.637911 TTGACACGTGGGCCTAAATAT 57.362 42.857 21.57 0.00 0.00 1.28
10 11 3.055021 TCATTGACACGTGGGCCTAAATA 60.055 43.478 21.57 0.00 0.00 1.40
11 12 2.091541 CATTGACACGTGGGCCTAAAT 58.908 47.619 21.57 7.09 0.00 1.40
12 13 1.072489 TCATTGACACGTGGGCCTAAA 59.928 47.619 21.57 5.00 0.00 1.85
13 14 0.687920 TCATTGACACGTGGGCCTAA 59.312 50.000 21.57 7.51 0.00 2.69
14 15 0.036765 GTCATTGACACGTGGGCCTA 60.037 55.000 21.57 6.02 32.09 3.93
15 16 1.302511 GTCATTGACACGTGGGCCT 60.303 57.895 21.57 0.00 32.09 5.19
16 17 2.332654 GGTCATTGACACGTGGGCC 61.333 63.158 21.57 8.66 33.68 5.80
17 18 2.332654 GGGTCATTGACACGTGGGC 61.333 63.158 21.57 12.05 33.68 5.36
18 19 0.536233 TTGGGTCATTGACACGTGGG 60.536 55.000 21.57 3.86 39.08 4.61
19 20 1.266718 CTTTGGGTCATTGACACGTGG 59.733 52.381 21.57 0.90 39.08 4.94
20 21 1.946768 ACTTTGGGTCATTGACACGTG 59.053 47.619 15.48 15.48 39.08 4.49
21 22 2.218603 GACTTTGGGTCATTGACACGT 58.781 47.619 18.09 8.30 39.08 4.49
22 23 2.969443 GACTTTGGGTCATTGACACG 57.031 50.000 18.09 5.14 39.08 4.49
30 31 8.889263 CCTTAATGGAACCTGACTTTGGGTCA 62.889 46.154 0.00 0.00 44.78 4.02
31 32 2.586648 ATGGAACCTGACTTTGGGTC 57.413 50.000 0.00 0.00 44.70 4.46
32 33 4.407365 CTTAATGGAACCTGACTTTGGGT 58.593 43.478 0.00 0.00 37.44 4.51
33 34 3.763897 CCTTAATGGAACCTGACTTTGGG 59.236 47.826 0.00 0.00 38.35 4.12
34 35 3.193479 GCCTTAATGGAACCTGACTTTGG 59.807 47.826 0.00 0.00 38.35 3.28
35 36 3.826157 TGCCTTAATGGAACCTGACTTTG 59.174 43.478 0.00 0.00 38.35 2.77
36 37 3.826729 GTGCCTTAATGGAACCTGACTTT 59.173 43.478 0.00 0.00 38.50 2.66
37 38 3.421844 GTGCCTTAATGGAACCTGACTT 58.578 45.455 0.00 0.00 38.50 3.01
38 39 3.073274 GTGCCTTAATGGAACCTGACT 57.927 47.619 0.00 0.00 38.50 3.41
44 45 1.743394 CCTTCGGTGCCTTAATGGAAC 59.257 52.381 0.00 0.00 44.01 3.62
45 46 1.953311 GCCTTCGGTGCCTTAATGGAA 60.953 52.381 0.00 0.00 38.35 3.53
46 47 0.393808 GCCTTCGGTGCCTTAATGGA 60.394 55.000 0.00 0.00 38.35 3.41
47 48 1.714899 CGCCTTCGGTGCCTTAATGG 61.715 60.000 0.00 0.00 39.35 3.16
48 49 1.024579 ACGCCTTCGGTGCCTTAATG 61.025 55.000 0.00 0.00 40.69 1.90
49 50 0.743345 GACGCCTTCGGTGCCTTAAT 60.743 55.000 0.00 0.00 40.69 1.40
50 51 1.375013 GACGCCTTCGGTGCCTTAA 60.375 57.895 0.00 0.00 40.69 1.85
51 52 2.263540 GACGCCTTCGGTGCCTTA 59.736 61.111 0.00 0.00 40.69 2.69
52 53 4.699522 GGACGCCTTCGGTGCCTT 62.700 66.667 0.00 0.00 40.69 4.35
64 65 2.781595 ATTGTGAGACGGTGGGACGC 62.782 60.000 0.00 0.00 37.37 5.19
65 66 0.528924 TATTGTGAGACGGTGGGACG 59.471 55.000 0.00 0.00 40.31 4.79
66 67 1.134788 CCTATTGTGAGACGGTGGGAC 60.135 57.143 0.00 0.00 0.00 4.46
67 68 1.191535 CCTATTGTGAGACGGTGGGA 58.808 55.000 0.00 0.00 0.00 4.37
68 69 1.191535 TCCTATTGTGAGACGGTGGG 58.808 55.000 0.00 0.00 0.00 4.61
138 148 3.723348 GTTTGGTGGCGAGCCGTC 61.723 66.667 9.78 5.20 39.42 4.79
242 253 1.303643 CTTTTCTTCCAGGGCGCCT 60.304 57.895 28.56 9.77 0.00 5.52
249 262 2.483491 GTCTGAGCTGCTTTTCTTCCAG 59.517 50.000 2.53 4.74 0.00 3.86
264 277 2.495669 GGTTTCTCCTCTGAGGTCTGAG 59.504 54.545 22.50 12.93 39.23 3.35
265 278 2.158310 TGGTTTCTCCTCTGAGGTCTGA 60.158 50.000 22.50 15.80 39.23 3.27
266 279 2.251818 TGGTTTCTCCTCTGAGGTCTG 58.748 52.381 22.50 13.96 39.23 3.51
267 280 2.704190 TGGTTTCTCCTCTGAGGTCT 57.296 50.000 22.50 0.00 39.23 3.85
269 282 3.318313 TCTTTGGTTTCTCCTCTGAGGT 58.682 45.455 22.50 0.00 39.23 3.85
270 283 4.357918 TTCTTTGGTTTCTCCTCTGAGG 57.642 45.455 17.84 17.84 39.23 3.86
311 359 2.081212 GCACGTTCGGTCAGTCTCG 61.081 63.158 0.00 0.00 0.00 4.04
338 386 4.360643 TGCATGGAATGGAAGGCC 57.639 55.556 0.00 0.00 43.62 5.19
371 425 4.170256 CAGGAGTACGAAGAAGAAGAAGC 58.830 47.826 0.00 0.00 0.00 3.86
387 477 2.356535 CCTACACCCTACGTACAGGAGT 60.357 54.545 12.76 12.67 38.00 3.85
388 478 2.295885 CCTACACCCTACGTACAGGAG 58.704 57.143 12.76 8.02 38.00 3.69
391 481 0.743097 GGCCTACACCCTACGTACAG 59.257 60.000 0.00 0.00 0.00 2.74
413 521 3.119495 GGACTGGATAAAATTTGCGCAGT 60.119 43.478 11.31 0.00 0.00 4.40
418 526 4.427312 CAGCAGGACTGGATAAAATTTGC 58.573 43.478 1.01 0.00 43.19 3.68
542 650 0.732571 AGTGCCGTGTGTTCAAAGTG 59.267 50.000 0.00 0.00 0.00 3.16
556 672 4.513198 TTATTTGTAGGTTTGCAGTGCC 57.487 40.909 13.72 0.00 0.00 5.01
571 687 8.327941 TGTCACTTTCCTCTTCAGATTATTTG 57.672 34.615 0.00 0.00 0.00 2.32
595 749 0.098552 TATGCAACGCAGCCGAATTG 59.901 50.000 0.00 0.00 43.65 2.32
603 760 5.094429 TGCAAAGTATATATGCAACGCAG 57.906 39.130 6.97 0.00 46.23 5.18
614 771 9.646522 ATTAATCCCTGTTTCTGCAAAGTATAT 57.353 29.630 0.00 0.00 0.00 0.86
615 772 9.120538 GATTAATCCCTGTTTCTGCAAAGTATA 57.879 33.333 3.92 0.00 0.00 1.47
741 4944 1.269988 CCATGATCGACGATGCCTTCT 60.270 52.381 16.49 0.00 0.00 2.85
761 4968 2.288334 TGCAAGACATTTGTGCATGGAC 60.288 45.455 10.90 10.90 43.09 4.02
762 4969 1.962100 TGCAAGACATTTGTGCATGGA 59.038 42.857 0.00 0.00 43.09 3.41
763 4970 2.333926 CTGCAAGACATTTGTGCATGG 58.666 47.619 0.00 0.00 46.51 3.66
764 4971 1.724623 GCTGCAAGACATTTGTGCATG 59.275 47.619 0.00 0.00 46.51 4.06
765 4972 1.667756 CGCTGCAAGACATTTGTGCAT 60.668 47.619 0.00 0.00 46.51 3.96
774 5020 2.818169 AAGGGTCCGCTGCAAGACA 61.818 57.895 18.12 0.00 34.07 3.41
777 5023 3.741476 GCAAGGGTCCGCTGCAAG 61.741 66.667 8.56 0.00 36.09 4.01
828 6162 7.559170 GGATTCTGGATAAAATATGGAGATGGG 59.441 40.741 0.00 0.00 0.00 4.00
832 6166 8.727149 ACAAGGATTCTGGATAAAATATGGAGA 58.273 33.333 0.00 0.00 0.00 3.71
982 6599 4.124126 GGATGGGGAGGAGGGGGT 62.124 72.222 0.00 0.00 0.00 4.95
992 6609 3.083349 TCCGTGCTCTGGATGGGG 61.083 66.667 0.00 0.00 0.00 4.96
998 6615 1.572085 CTTGTTGCTCCGTGCTCTGG 61.572 60.000 0.00 0.00 43.37 3.86
1012 6629 3.270877 GTGAGGTGAGTTGTGACTTGTT 58.729 45.455 0.00 0.00 35.88 2.83
1013 6630 2.420129 GGTGAGGTGAGTTGTGACTTGT 60.420 50.000 0.00 0.00 35.88 3.16
1016 6633 0.389391 CGGTGAGGTGAGTTGTGACT 59.611 55.000 0.00 0.00 39.32 3.41
1017 6634 0.600255 CCGGTGAGGTGAGTTGTGAC 60.600 60.000 0.00 0.00 34.51 3.67
1018 6635 1.745890 CCGGTGAGGTGAGTTGTGA 59.254 57.895 0.00 0.00 34.51 3.58
1020 6637 1.978455 TTGCCGGTGAGGTGAGTTGT 61.978 55.000 1.90 0.00 43.70 3.32
1062 6702 0.676782 GCTTCCTTCCTTTGCGCCTA 60.677 55.000 4.18 0.00 0.00 3.93
1089 6729 0.168568 GACGACGAGGAGGTGAAGAC 59.831 60.000 0.00 0.00 0.00 3.01
1090 6730 0.036448 AGACGACGAGGAGGTGAAGA 59.964 55.000 0.00 0.00 0.00 2.87
1091 6731 0.882474 AAGACGACGAGGAGGTGAAG 59.118 55.000 0.00 0.00 0.00 3.02
1092 6732 1.808945 GTAAGACGACGAGGAGGTGAA 59.191 52.381 0.00 0.00 0.00 3.18
1095 6738 0.036952 TCGTAAGACGACGAGGAGGT 60.037 55.000 0.00 0.00 46.73 3.85
1121 6764 2.326664 GAACGAAGAACCGGAGACTTC 58.673 52.381 9.46 17.60 37.32 3.01
1128 6771 0.865769 CTGTTGGAACGAAGAACCGG 59.134 55.000 0.00 0.00 0.00 5.28
1163 6806 1.193644 CCAATCACATGCGCATTTCG 58.806 50.000 22.81 12.72 42.12 3.46
1166 6809 0.462375 ATGCCAATCACATGCGCATT 59.538 45.000 22.81 9.76 35.23 3.56
1170 6813 1.361271 GGGATGCCAATCACATGCG 59.639 57.895 0.00 0.00 36.13 4.73
1180 6823 2.672908 CTGCTCACTGGGATGCCA 59.327 61.111 5.57 5.57 0.00 4.92
1325 7028 4.775253 AGAAGGACTGAAGGAGGACTTAAG 59.225 45.833 0.00 0.00 42.57 1.85
1326 7029 4.753186 AGAAGGACTGAAGGAGGACTTAA 58.247 43.478 0.00 0.00 40.21 1.85
1356 7059 7.147408 ACCAGAGCTACAAAGATTTATCCAGAT 60.147 37.037 0.00 0.00 0.00 2.90
1511 7618 1.074423 TCTCGACCGAGAACCACCT 59.926 57.895 18.43 0.00 46.89 4.00
1785 7898 2.289694 CCCATGAACCAGAACTCGAAGT 60.290 50.000 0.00 0.00 0.00 3.01
1824 7937 4.007644 CGAGGTGCTGCAGGGACA 62.008 66.667 17.12 1.56 38.05 4.02
1867 7980 0.033208 GCACCTTCATCCCATTCCCA 60.033 55.000 0.00 0.00 0.00 4.37
1868 7981 0.756815 GGCACCTTCATCCCATTCCC 60.757 60.000 0.00 0.00 0.00 3.97
1869 7982 1.103398 CGGCACCTTCATCCCATTCC 61.103 60.000 0.00 0.00 0.00 3.01
1870 7983 0.394352 ACGGCACCTTCATCCCATTC 60.394 55.000 0.00 0.00 0.00 2.67
1871 7984 0.394352 GACGGCACCTTCATCCCATT 60.394 55.000 0.00 0.00 0.00 3.16
1872 7985 1.224592 GACGGCACCTTCATCCCAT 59.775 57.895 0.00 0.00 0.00 4.00
1979 8111 2.983136 CTGCTCGTGTTGTAAGTCAGAG 59.017 50.000 0.00 0.00 0.00 3.35
2013 8145 0.531090 CGAGTCCGACGAGATCTCCT 60.531 60.000 17.13 5.48 38.22 3.69
2019 8151 4.747529 TCGCCGAGTCCGACGAGA 62.748 66.667 0.00 0.00 45.08 4.04
2109 8302 0.318784 CGATAACCTAGGCCTCGTGC 60.319 60.000 9.68 0.00 40.16 5.34
2110 8303 1.001597 GTCGATAACCTAGGCCTCGTG 60.002 57.143 9.68 0.49 0.00 4.35
2111 8304 1.316651 GTCGATAACCTAGGCCTCGT 58.683 55.000 9.68 3.42 0.00 4.18
2112 8305 0.597072 GGTCGATAACCTAGGCCTCG 59.403 60.000 9.68 14.64 45.45 4.63
2122 8315 2.547826 GTAAGCCACCAGGTCGATAAC 58.452 52.381 0.00 0.00 37.19 1.89
2123 8316 1.135527 CGTAAGCCACCAGGTCGATAA 59.864 52.381 0.00 0.00 37.19 1.75
2124 8317 0.742505 CGTAAGCCACCAGGTCGATA 59.257 55.000 0.00 0.00 37.19 2.92
2125 8318 1.515954 CGTAAGCCACCAGGTCGAT 59.484 57.895 0.00 0.00 37.19 3.59
2126 8319 2.642254 CCGTAAGCCACCAGGTCGA 61.642 63.158 0.00 0.00 37.19 4.20
2127 8320 2.125673 CCGTAAGCCACCAGGTCG 60.126 66.667 0.00 0.00 37.19 4.79
2128 8321 2.267961 CCCGTAAGCCACCAGGTC 59.732 66.667 0.00 0.00 37.19 3.85
2129 8322 2.203877 TCCCGTAAGCCACCAGGT 60.204 61.111 0.00 0.00 37.19 4.00
2130 8323 2.267961 GTCCCGTAAGCCACCAGG 59.732 66.667 0.00 0.00 38.23 4.45
2131 8324 2.125673 CGTCCCGTAAGCCACCAG 60.126 66.667 0.00 0.00 0.00 4.00
2148 8341 0.674534 CCAGCCTCACGTATAGGGAC 59.325 60.000 15.81 2.87 34.46 4.46
2274 8487 1.212688 CCAGCACCTACCAATCCATGA 59.787 52.381 0.00 0.00 0.00 3.07
2296 8509 1.805428 AAACACATCGGTTGCAGGCC 61.805 55.000 0.00 0.00 0.00 5.19
2398 8705 6.476243 ACCAAATGCTACTTAAGTGTAACG 57.524 37.500 18.56 2.88 45.86 3.18
2524 8831 0.378610 GCAGCGAACCAATTAGCCTC 59.621 55.000 0.00 0.00 37.16 4.70
2525 8832 1.032114 GGCAGCGAACCAATTAGCCT 61.032 55.000 0.00 0.00 37.16 4.58
2526 8833 1.312371 TGGCAGCGAACCAATTAGCC 61.312 55.000 0.00 0.00 37.16 3.93
2527 8834 0.525761 TTGGCAGCGAACCAATTAGC 59.474 50.000 4.28 0.00 42.23 3.09
2528 8835 2.228822 ACTTTGGCAGCGAACCAATTAG 59.771 45.455 8.64 7.12 46.25 1.73
2529 8836 2.235016 ACTTTGGCAGCGAACCAATTA 58.765 42.857 8.64 0.00 46.25 1.40
2530 8837 1.039856 ACTTTGGCAGCGAACCAATT 58.960 45.000 8.64 0.00 46.25 2.32
2531 8838 1.039856 AACTTTGGCAGCGAACCAAT 58.960 45.000 8.64 0.00 46.25 3.16
2532 8839 0.820871 AAACTTTGGCAGCGAACCAA 59.179 45.000 4.28 4.28 45.37 3.67
2533 8840 0.102120 CAAACTTTGGCAGCGAACCA 59.898 50.000 0.00 0.00 34.65 3.67
2534 8841 0.597377 CCAAACTTTGGCAGCGAACC 60.597 55.000 7.63 0.00 45.17 3.62
2535 8842 2.885502 CCAAACTTTGGCAGCGAAC 58.114 52.632 7.63 0.00 45.17 3.95
2560 8867 6.817515 CCAAATGTTGGCTTGCCAAGTATTG 61.818 44.000 25.26 24.48 45.00 1.90
2561 8868 4.317488 CAAATGTTGGCTTGCCAAGTATT 58.683 39.130 25.26 22.81 0.00 1.89
2562 8869 3.306919 CCAAATGTTGGCTTGCCAAGTAT 60.307 43.478 25.26 19.10 45.17 2.12
2563 8870 2.036992 CCAAATGTTGGCTTGCCAAGTA 59.963 45.455 25.26 17.85 45.17 2.24
2564 8871 1.202675 CCAAATGTTGGCTTGCCAAGT 60.203 47.619 25.26 15.14 45.17 3.16
2565 8872 1.515081 CCAAATGTTGGCTTGCCAAG 58.485 50.000 25.26 13.96 45.17 3.61
2566 8873 3.702147 CCAAATGTTGGCTTGCCAA 57.298 47.368 21.59 21.59 45.17 4.52
2583 8890 5.881777 TTTTGGCAAGTTTTGGTTTTACC 57.118 34.783 0.00 0.00 39.22 2.85
2606 8913 7.768582 CCACCTCTCAAAAAGTTACCAATTTTT 59.231 33.333 0.00 0.00 38.74 1.94
2607 8914 7.272244 CCACCTCTCAAAAAGTTACCAATTTT 58.728 34.615 0.00 0.00 0.00 1.82
2608 8915 6.183360 CCCACCTCTCAAAAAGTTACCAATTT 60.183 38.462 0.00 0.00 0.00 1.82
2609 8916 5.304357 CCCACCTCTCAAAAAGTTACCAATT 59.696 40.000 0.00 0.00 0.00 2.32
2610 8917 4.832823 CCCACCTCTCAAAAAGTTACCAAT 59.167 41.667 0.00 0.00 0.00 3.16
2611 8918 4.211920 CCCACCTCTCAAAAAGTTACCAA 58.788 43.478 0.00 0.00 0.00 3.67
2612 8919 3.827722 CCCACCTCTCAAAAAGTTACCA 58.172 45.455 0.00 0.00 0.00 3.25
2613 8920 2.557056 GCCCACCTCTCAAAAAGTTACC 59.443 50.000 0.00 0.00 0.00 2.85
2614 8921 3.219281 TGCCCACCTCTCAAAAAGTTAC 58.781 45.455 0.00 0.00 0.00 2.50
2615 8922 3.586470 TGCCCACCTCTCAAAAAGTTA 57.414 42.857 0.00 0.00 0.00 2.24
2616 8923 2.452600 TGCCCACCTCTCAAAAAGTT 57.547 45.000 0.00 0.00 0.00 2.66
2617 8924 2.091885 TCTTGCCCACCTCTCAAAAAGT 60.092 45.455 0.00 0.00 0.00 2.66
2618 8925 2.586425 TCTTGCCCACCTCTCAAAAAG 58.414 47.619 0.00 0.00 0.00 2.27
2619 8926 2.693074 GTTCTTGCCCACCTCTCAAAAA 59.307 45.455 0.00 0.00 0.00 1.94
2620 8927 2.306847 GTTCTTGCCCACCTCTCAAAA 58.693 47.619 0.00 0.00 0.00 2.44
2621 8928 1.478654 GGTTCTTGCCCACCTCTCAAA 60.479 52.381 0.00 0.00 0.00 2.69
2622 8929 0.110486 GGTTCTTGCCCACCTCTCAA 59.890 55.000 0.00 0.00 0.00 3.02
2623 8930 1.059584 TGGTTCTTGCCCACCTCTCA 61.060 55.000 0.00 0.00 33.76 3.27
2624 8931 0.110486 TTGGTTCTTGCCCACCTCTC 59.890 55.000 0.00 0.00 33.76 3.20
2625 8932 0.779997 ATTGGTTCTTGCCCACCTCT 59.220 50.000 0.00 0.00 33.76 3.69
2626 8933 1.273327 CAATTGGTTCTTGCCCACCTC 59.727 52.381 0.00 0.00 33.76 3.85
2627 8934 1.341080 CAATTGGTTCTTGCCCACCT 58.659 50.000 0.00 0.00 33.76 4.00
2628 8935 0.321346 CCAATTGGTTCTTGCCCACC 59.679 55.000 16.90 0.00 0.00 4.61
2629 8936 3.912899 CCAATTGGTTCTTGCCCAC 57.087 52.632 16.90 0.00 0.00 4.61
2647 8954 0.179163 GCGCTCAATTGGTTGGCTAC 60.179 55.000 5.42 0.00 35.99 3.58
2648 8955 1.312371 GGCGCTCAATTGGTTGGCTA 61.312 55.000 7.64 0.00 35.99 3.93
2649 8956 2.639327 GGCGCTCAATTGGTTGGCT 61.639 57.895 7.64 0.00 35.99 4.75
2650 8957 2.125952 GGCGCTCAATTGGTTGGC 60.126 61.111 7.64 4.20 35.99 4.52
2651 8958 0.033228 TTTGGCGCTCAATTGGTTGG 59.967 50.000 7.64 0.00 35.99 3.77
2652 8959 2.083167 ATTTGGCGCTCAATTGGTTG 57.917 45.000 7.64 0.00 34.98 3.77
2653 8960 2.837532 AATTTGGCGCTCAATTGGTT 57.162 40.000 7.64 1.17 34.98 3.67
2654 8961 2.837532 AAATTTGGCGCTCAATTGGT 57.162 40.000 7.64 0.00 34.98 3.67
2655 8962 4.928615 TCTAAAAATTTGGCGCTCAATTGG 59.071 37.500 7.64 3.89 34.98 3.16
2656 8963 5.634859 AGTCTAAAAATTTGGCGCTCAATTG 59.365 36.000 7.64 0.00 34.98 2.32
2657 8964 5.783111 AGTCTAAAAATTTGGCGCTCAATT 58.217 33.333 7.64 9.41 34.98 2.32
2658 8965 5.391312 AGTCTAAAAATTTGGCGCTCAAT 57.609 34.783 7.64 2.72 34.98 2.57
2659 8966 4.846779 AGTCTAAAAATTTGGCGCTCAA 57.153 36.364 7.64 7.34 0.00 3.02
2660 8967 4.545610 CAAGTCTAAAAATTTGGCGCTCA 58.454 39.130 7.64 0.00 0.00 4.26
2661 8968 3.364920 GCAAGTCTAAAAATTTGGCGCTC 59.635 43.478 7.64 0.00 0.00 5.03
2662 8969 3.317150 GCAAGTCTAAAAATTTGGCGCT 58.683 40.909 7.64 0.00 0.00 5.92
2663 8970 2.411748 GGCAAGTCTAAAAATTTGGCGC 59.588 45.455 0.00 0.00 36.57 6.53
2664 8971 3.648009 TGGCAAGTCTAAAAATTTGGCG 58.352 40.909 0.00 0.00 45.69 5.69
2665 8972 4.813697 TGTTGGCAAGTCTAAAAATTTGGC 59.186 37.500 0.00 3.09 43.80 4.52
2666 8973 6.917217 TTGTTGGCAAGTCTAAAAATTTGG 57.083 33.333 0.00 0.00 0.00 3.28
2667 8974 7.856894 CCAATTGTTGGCAAGTCTAAAAATTTG 59.143 33.333 0.00 0.00 45.17 2.32
2668 8975 7.929159 CCAATTGTTGGCAAGTCTAAAAATTT 58.071 30.769 0.00 0.00 45.17 1.82
2669 8976 7.495135 CCAATTGTTGGCAAGTCTAAAAATT 57.505 32.000 0.00 0.00 45.17 1.82
2699 9006 7.482428 GCTTAATTGTTTTGCTGCCAATAATTG 59.518 33.333 18.41 9.63 0.00 2.32
2700 9007 7.391275 AGCTTAATTGTTTTGCTGCCAATAATT 59.609 29.630 15.61 15.61 32.32 1.40
2701 9008 6.880529 AGCTTAATTGTTTTGCTGCCAATAAT 59.119 30.769 0.00 0.00 32.32 1.28
2702 9009 6.229733 AGCTTAATTGTTTTGCTGCCAATAA 58.770 32.000 0.00 0.00 32.32 1.40
2703 9010 5.792741 AGCTTAATTGTTTTGCTGCCAATA 58.207 33.333 0.00 0.00 32.32 1.90
2704 9011 4.644498 AGCTTAATTGTTTTGCTGCCAAT 58.356 34.783 0.00 0.00 32.32 3.16
2705 9012 4.057432 GAGCTTAATTGTTTTGCTGCCAA 58.943 39.130 0.00 0.00 33.83 4.52
2706 9013 3.069300 TGAGCTTAATTGTTTTGCTGCCA 59.931 39.130 0.00 0.00 33.83 4.92
2707 9014 3.652274 TGAGCTTAATTGTTTTGCTGCC 58.348 40.909 0.00 0.00 33.83 4.85
2708 9015 5.655893 TTTGAGCTTAATTGTTTTGCTGC 57.344 34.783 0.00 0.00 33.83 5.25
2709 9016 8.080083 AGATTTTGAGCTTAATTGTTTTGCTG 57.920 30.769 0.00 0.00 33.83 4.41
2710 9017 8.667076 AAGATTTTGAGCTTAATTGTTTTGCT 57.333 26.923 0.00 0.00 36.63 3.91
2711 9018 9.161684 CAAAGATTTTGAGCTTAATTGTTTTGC 57.838 29.630 0.00 0.00 0.00 3.68
2773 9080 5.231568 GGTCGAAGTATAATCAAGGTGAACG 59.768 44.000 0.00 0.00 0.00 3.95
2777 9084 3.489785 GCGGTCGAAGTATAATCAAGGTG 59.510 47.826 0.00 0.00 0.00 4.00
2778 9085 3.131577 TGCGGTCGAAGTATAATCAAGGT 59.868 43.478 0.00 0.00 0.00 3.50
2779 9086 3.713288 TGCGGTCGAAGTATAATCAAGG 58.287 45.455 0.00 0.00 0.00 3.61
2780 9087 5.062934 TGTTTGCGGTCGAAGTATAATCAAG 59.937 40.000 0.00 0.00 0.00 3.02
2781 9088 4.930405 TGTTTGCGGTCGAAGTATAATCAA 59.070 37.500 0.00 0.00 0.00 2.57
2782 9089 4.496360 TGTTTGCGGTCGAAGTATAATCA 58.504 39.130 0.00 0.00 0.00 2.57
2783 9090 5.432157 CATGTTTGCGGTCGAAGTATAATC 58.568 41.667 0.00 0.00 0.00 1.75
2784 9091 4.272504 CCATGTTTGCGGTCGAAGTATAAT 59.727 41.667 0.00 0.00 0.00 1.28
2785 9092 3.619483 CCATGTTTGCGGTCGAAGTATAA 59.381 43.478 0.00 0.00 0.00 0.98
2786 9093 3.191669 CCATGTTTGCGGTCGAAGTATA 58.808 45.455 0.00 0.00 0.00 1.47
2787 9094 2.006888 CCATGTTTGCGGTCGAAGTAT 58.993 47.619 0.00 0.00 0.00 2.12
2788 9095 1.434555 CCATGTTTGCGGTCGAAGTA 58.565 50.000 0.00 0.00 0.00 2.24
2789 9096 1.852067 GCCATGTTTGCGGTCGAAGT 61.852 55.000 0.00 0.00 0.00 3.01
2790 9097 1.154225 GCCATGTTTGCGGTCGAAG 60.154 57.895 0.00 0.00 0.00 3.79
2791 9098 1.169661 AAGCCATGTTTGCGGTCGAA 61.170 50.000 0.00 0.00 0.00 3.71
2792 9099 0.320858 TAAGCCATGTTTGCGGTCGA 60.321 50.000 0.00 0.00 0.00 4.20
2793 9100 0.179200 GTAAGCCATGTTTGCGGTCG 60.179 55.000 0.00 0.00 0.00 4.79
2794 9101 1.165270 AGTAAGCCATGTTTGCGGTC 58.835 50.000 0.00 0.00 0.00 4.79
2795 9102 1.616159 AAGTAAGCCATGTTTGCGGT 58.384 45.000 0.00 0.00 0.00 5.68
2796 9103 2.723124 AAAGTAAGCCATGTTTGCGG 57.277 45.000 0.00 0.00 0.00 5.69
2797 9104 3.637432 TGAAAAGTAAGCCATGTTTGCG 58.363 40.909 0.00 0.00 0.00 4.85
2798 9105 6.202570 TCAATTGAAAAGTAAGCCATGTTTGC 59.797 34.615 5.45 0.00 0.00 3.68
2799 9106 7.712264 TCAATTGAAAAGTAAGCCATGTTTG 57.288 32.000 5.45 0.00 0.00 2.93
2800 9107 8.907222 ATTCAATTGAAAAGTAAGCCATGTTT 57.093 26.923 23.91 0.00 37.61 2.83
2910 9218 3.138839 TGTATGGTTCCATCCATGAGCAT 59.861 43.478 7.67 0.00 46.27 3.79
2918 9226 8.418597 TCTACTAGTATTGTATGGTTCCATCC 57.581 38.462 7.67 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.