Multiple sequence alignment - TraesCS4B01G399300

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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 TraesCS4B01G399300 chr4B 100.000 4508 0 0 1 4508 673256194 673251687 0.000000e+00 8325.0
1 TraesCS4B01G399300 chr4B 95.192 1227 57 2 2186 3412 673381042 673379818 0.000000e+00 1938.0
2 TraesCS4B01G399300 chr4B 87.839 847 79 14 939 1765 673298612 673297770 0.000000e+00 972.0
3 TraesCS4B01G399300 chr4B 85.338 948 75 22 1156 2068 673384096 673383178 0.000000e+00 922.0
4 TraesCS4B01G399300 chr4B 95.571 429 17 1 1 429 672431117 672431543 0.000000e+00 686.0
5 TraesCS4B01G399300 chr4B 95.105 429 19 1 1 429 512574040 512574466 0.000000e+00 675.0
6 TraesCS4B01G399300 chr4B 81.621 506 73 12 2787 3280 673334455 673333958 7.020000e-108 401.0
7 TraesCS4B01G399300 chr4B 95.582 249 10 1 4256 4504 673336040 673335793 9.090000e-107 398.0
8 TraesCS4B01G399300 chr4B 85.638 376 23 11 898 1273 673471081 673470737 2.560000e-97 366.0
9 TraesCS4B01G399300 chr4B 97.419 155 4 0 1856 2010 673470522 673470368 9.620000e-67 265.0
10 TraesCS4B01G399300 chr4B 98.347 121 2 0 4027 4147 673336276 673336156 3.530000e-51 213.0
11 TraesCS4B01G399300 chrUn 87.977 2279 165 44 1085 3304 99821698 99823926 0.000000e+00 2590.0
12 TraesCS4B01G399300 chrUn 90.052 955 39 23 3567 4508 99824195 99825106 0.000000e+00 1186.0
13 TraesCS4B01G399300 chrUn 87.195 984 86 22 1102 2068 99740741 99739781 0.000000e+00 1083.0
14 TraesCS4B01G399300 chrUn 86.108 871 78 17 2175 3021 99739656 99738805 0.000000e+00 898.0
15 TraesCS4B01G399300 chrUn 88.095 378 22 3 899 1273 99648460 99648817 1.160000e-115 427.0
16 TraesCS4B01G399300 chrUn 97.222 36 1 0 1043 1078 99821583 99821618 1.350000e-05 62.1
17 TraesCS4B01G399300 chr4D 89.673 1559 58 37 2024 3564 491373907 491375380 0.000000e+00 1892.0
18 TraesCS4B01G399300 chr4D 93.799 1145 55 9 898 2032 491372369 491373507 0.000000e+00 1707.0
19 TraesCS4B01G399300 chr4D 91.003 967 24 23 3563 4507 491378205 491379130 0.000000e+00 1245.0
20 TraesCS4B01G399300 chr4D 73.695 498 55 32 2760 3241 491369717 491370154 1.700000e-24 124.0
21 TraesCS4B01G399300 chr3A 88.471 850 60 11 2468 3304 703420515 703421339 0.000000e+00 992.0
22 TraesCS4B01G399300 chr3A 91.696 578 29 9 3566 4141 703421786 703422346 0.000000e+00 784.0
23 TraesCS4B01G399300 chr3A 95.968 248 10 0 4258 4505 703422392 703422639 1.950000e-108 403.0
24 TraesCS4B01G399300 chr3A 75.329 304 61 9 1202 1503 622814700 622814409 2.830000e-27 134.0
25 TraesCS4B01G399300 chr5A 91.852 540 11 14 1858 2367 707536756 707537292 0.000000e+00 723.0
26 TraesCS4B01G399300 chr5A 84.309 376 16 6 898 1273 707536215 707536547 1.210000e-85 327.0
27 TraesCS4B01G399300 chr7B 95.592 431 17 1 1 431 676554933 676554505 0.000000e+00 689.0
28 TraesCS4B01G399300 chr7B 95.360 431 18 1 1 431 175093642 175093214 0.000000e+00 684.0
29 TraesCS4B01G399300 chr7B 95.035 423 21 0 431 853 177216450 177216872 0.000000e+00 665.0
30 TraesCS4B01G399300 chr7B 94.563 423 23 0 431 853 175033934 175034356 0.000000e+00 654.0
31 TraesCS4B01G399300 chr7B 94.326 423 24 0 431 853 312990983 312990561 0.000000e+00 649.0
32 TraesCS4B01G399300 chr3B 95.592 431 17 1 1 431 635913108 635912680 0.000000e+00 689.0
33 TraesCS4B01G399300 chr3B 94.563 423 23 0 431 853 780198513 780198935 0.000000e+00 654.0
34 TraesCS4B01G399300 chr6B 95.571 429 17 1 1 429 431923467 431923041 0.000000e+00 686.0
35 TraesCS4B01G399300 chr6B 95.105 429 19 1 1 429 331830351 331830777 0.000000e+00 675.0
36 TraesCS4B01G399300 chr5B 95.105 429 19 1 1 429 228262815 228263241 0.000000e+00 675.0
37 TraesCS4B01G399300 chr5B 95.105 429 19 1 1 429 553371121 553370695 0.000000e+00 675.0
38 TraesCS4B01G399300 chr5B 95.272 423 20 0 431 853 480926988 480926566 0.000000e+00 671.0
39 TraesCS4B01G399300 chr5B 95.024 422 21 0 432 853 467904655 467905076 0.000000e+00 664.0
40 TraesCS4B01G399300 chr5B 94.326 423 24 0 431 853 228263692 228264114 0.000000e+00 649.0
41 TraesCS4B01G399300 chr5B 94.326 423 24 0 431 853 528756956 528757378 0.000000e+00 649.0
42 TraesCS4B01G399300 chr5B 72.634 391 82 22 1618 1998 241897629 241897254 6.170000e-19 106.0
43 TraesCS4B01G399300 chr2B 94.326 423 24 0 431 853 371944677 371944255 0.000000e+00 649.0
44 TraesCS4B01G399300 chr2B 75.951 1052 205 36 2191 3200 797208936 797209981 8.710000e-137 497.0
45 TraesCS4B01G399300 chr2B 75.452 1051 209 34 2191 3197 797255331 797256376 2.460000e-127 466.0
46 TraesCS4B01G399300 chr2B 74.388 1144 214 54 2184 3293 797183089 797184187 2.510000e-112 416.0
47 TraesCS4B01G399300 chr2A 75.376 1129 210 36 2200 3291 763917465 763916368 2.440000e-132 483.0
48 TraesCS4B01G399300 chr2A 75.374 601 115 20 2211 2802 762660035 762660611 4.470000e-65 259.0
49 TraesCS4B01G399300 chr2A 72.251 782 166 41 1246 1998 267879153 267878394 1.280000e-45 195.0
50 TraesCS4B01G399300 chr2A 80.000 150 24 3 3051 3194 763973972 763973823 6.170000e-19 106.0
51 TraesCS4B01G399300 chr2D 81.459 329 50 8 2211 2535 637354189 637353868 4.470000e-65 259.0
52 TraesCS4B01G399300 chr2D 77.692 260 46 7 2211 2461 638329597 638329853 1.010000e-31 148.0
53 TraesCS4B01G399300 chr2D 77.692 260 40 12 2953 3206 636946113 636945866 4.700000e-30 143.0
54 TraesCS4B01G399300 chr7A 71.943 777 153 49 1254 2003 21602010 21601272 2.790000e-37 167.0
55 TraesCS4B01G399300 chr7A 84.677 124 19 0 3083 3206 439730762 439730885 1.700000e-24 124.0
56 TraesCS4B01G399300 chr5D 74.877 406 72 25 1600 1992 110645413 110645025 1.680000e-34 158.0


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 TraesCS4B01G399300 chr4B 673251687 673256194 4507 True 8325.000000 8325 100.000000 1 4508 1 chr4B.!!$R1 4507
1 TraesCS4B01G399300 chr4B 673379818 673384096 4278 True 1430.000000 1938 90.265000 1156 3412 2 chr4B.!!$R4 2256
2 TraesCS4B01G399300 chr4B 673297770 673298612 842 True 972.000000 972 87.839000 939 1765 1 chr4B.!!$R2 826
3 TraesCS4B01G399300 chr4B 673333958 673336276 2318 True 337.333333 401 91.850000 2787 4504 3 chr4B.!!$R3 1717
4 TraesCS4B01G399300 chr4B 673470368 673471081 713 True 315.500000 366 91.528500 898 2010 2 chr4B.!!$R5 1112
5 TraesCS4B01G399300 chrUn 99821583 99825106 3523 False 1279.366667 2590 91.750333 1043 4508 3 chrUn.!!$F2 3465
6 TraesCS4B01G399300 chrUn 99738805 99740741 1936 True 990.500000 1083 86.651500 1102 3021 2 chrUn.!!$R1 1919
7 TraesCS4B01G399300 chr4D 491369717 491379130 9413 False 1242.000000 1892 87.042500 898 4507 4 chr4D.!!$F1 3609
8 TraesCS4B01G399300 chr3A 703420515 703422639 2124 False 726.333333 992 92.045000 2468 4505 3 chr3A.!!$F1 2037
9 TraesCS4B01G399300 chr5A 707536215 707537292 1077 False 525.000000 723 88.080500 898 2367 2 chr5A.!!$F1 1469
10 TraesCS4B01G399300 chr5B 228262815 228264114 1299 False 662.000000 675 94.715500 1 853 2 chr5B.!!$F3 852
11 TraesCS4B01G399300 chr2B 797208936 797209981 1045 False 497.000000 497 75.951000 2191 3200 1 chr2B.!!$F2 1009
12 TraesCS4B01G399300 chr2B 797255331 797256376 1045 False 466.000000 466 75.452000 2191 3197 1 chr2B.!!$F3 1006
13 TraesCS4B01G399300 chr2B 797183089 797184187 1098 False 416.000000 416 74.388000 2184 3293 1 chr2B.!!$F1 1109
14 TraesCS4B01G399300 chr2A 763916368 763917465 1097 True 483.000000 483 75.376000 2200 3291 1 chr2A.!!$R2 1091
15 TraesCS4B01G399300 chr2A 762660035 762660611 576 False 259.000000 259 75.374000 2211 2802 1 chr2A.!!$F1 591

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
879 1329 0.107214 TCATGATGGAAACCGAGGCC 60.107 55.000 0.00 0.00 0.00 5.19 F
882 1332 0.111446 TGATGGAAACCGAGGCCAAA 59.889 50.000 5.01 0.00 34.95 3.28 F
896 1346 0.932399 GCCAAAACGGATATACGCGT 59.068 50.000 19.17 19.17 36.56 6.01 F
924 2680 1.303091 CCGTTGTTTCCATCGTCCCC 61.303 60.000 0.00 0.00 33.04 4.81 F
961 2727 1.450848 CATCAGCACCACCGCATCT 60.451 57.895 0.00 0.00 0.00 2.90 F
1070 2858 1.665442 GTGCCTGCATTTTTCCGGT 59.335 52.632 0.00 0.00 0.00 5.28 F
2079 4493 2.100252 TCGGATTTCACCACGGAGATAC 59.900 50.000 0.00 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 6781 0.692419 CTGGTAGGAGGAGGCATGGT 60.692 60.000 0.00 0.0 0.00 3.55 R
3043 7640 0.393077 CACCTTGAAGGACCACGTCT 59.607 55.000 19.83 0.0 37.67 4.18 R
3306 7945 1.774217 TCAGCCCCCACACCTTCTT 60.774 57.895 0.00 0.0 0.00 2.52 R
3307 7946 2.121963 TCAGCCCCCACACCTTCT 60.122 61.111 0.00 0.0 0.00 2.85 R
3308 7947 2.352805 CTCAGCCCCCACACCTTC 59.647 66.667 0.00 0.0 0.00 3.46 R
3309 7948 3.260100 CCTCAGCCCCCACACCTT 61.260 66.667 0.00 0.0 0.00 3.50 R
3827 11438 2.031120 CCTTGAAAGGCCAACAGAACA 58.969 47.619 5.01 0.0 39.76 3.18 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
40 41 0.955919 CCTTGACCCGAGCAAGTTCC 60.956 60.000 0.00 0.00 40.79 3.62
51 52 0.238553 GCAAGTTCCGCTCAAAGGTC 59.761 55.000 0.00 0.00 0.00 3.85
120 121 1.153549 GGCGTCAGCTCCCTTACTG 60.154 63.158 0.00 0.00 44.37 2.74
121 122 1.592223 GCGTCAGCTCCCTTACTGT 59.408 57.895 0.00 0.00 41.01 3.55
175 176 5.995282 ACTCATCAAGTCGTTTATTGACCAA 59.005 36.000 0.00 0.00 38.19 3.67
217 218 0.244994 TCGAGTTGCCTCTTCAGCTC 59.755 55.000 0.00 0.00 39.81 4.09
239 240 1.475034 GCAAATCCATCAGTCCGGCTA 60.475 52.381 0.00 0.00 0.00 3.93
397 398 6.183360 TGCAAAACTGTCAAAAGGTATGTCAT 60.183 34.615 0.00 0.00 0.00 3.06
398 399 6.701400 GCAAAACTGTCAAAAGGTATGTCATT 59.299 34.615 0.00 0.00 0.00 2.57
431 432 1.007387 CAAAACCCGTCAGCAAGCC 60.007 57.895 0.00 0.00 0.00 4.35
432 433 2.551912 AAAACCCGTCAGCAAGCCG 61.552 57.895 0.00 0.00 0.00 5.52
484 934 1.377333 CCTCCGGGTCTTTGGAAGC 60.377 63.158 0.00 0.00 32.89 3.86
486 936 2.167398 CTCCGGGTCTTTGGAAGCGA 62.167 60.000 0.00 0.00 32.89 4.93
561 1011 1.346722 CCTTGACGGAGGTGGTAGTTT 59.653 52.381 0.00 0.00 33.16 2.66
566 1016 1.077663 ACGGAGGTGGTAGTTTCCCTA 59.922 52.381 0.00 0.00 0.00 3.53
622 1072 5.048364 CCTCCAACATTTTGATTAACACGGA 60.048 40.000 0.00 0.00 34.24 4.69
661 1111 2.761213 GGGGGTCGGACACCGTAT 60.761 66.667 22.52 0.00 44.60 3.06
671 1121 2.423577 GGACACCGTATCAGTTTTGCT 58.576 47.619 0.00 0.00 0.00 3.91
672 1122 2.812011 GGACACCGTATCAGTTTTGCTT 59.188 45.455 0.00 0.00 0.00 3.91
675 1125 1.196808 ACCGTATCAGTTTTGCTTGCG 59.803 47.619 0.00 0.00 0.00 4.85
677 1127 1.135972 CGTATCAGTTTTGCTTGCGCT 60.136 47.619 9.73 0.00 36.97 5.92
679 1129 3.242413 CGTATCAGTTTTGCTTGCGCTAT 60.242 43.478 9.73 0.00 36.97 2.97
681 1131 1.468520 TCAGTTTTGCTTGCGCTATCC 59.531 47.619 9.73 0.00 36.97 2.59
683 1133 1.200020 AGTTTTGCTTGCGCTATCCAC 59.800 47.619 9.73 0.00 36.97 4.02
684 1134 1.200020 GTTTTGCTTGCGCTATCCACT 59.800 47.619 9.73 0.00 36.97 4.00
686 1136 0.744414 TTGCTTGCGCTATCCACTCC 60.744 55.000 9.73 0.00 36.97 3.85
687 1137 1.144936 GCTTGCGCTATCCACTCCT 59.855 57.895 9.73 0.00 0.00 3.69
688 1138 1.156645 GCTTGCGCTATCCACTCCTG 61.157 60.000 9.73 0.00 0.00 3.86
689 1139 0.176680 CTTGCGCTATCCACTCCTGT 59.823 55.000 9.73 0.00 0.00 4.00
690 1140 0.175760 TTGCGCTATCCACTCCTGTC 59.824 55.000 9.73 0.00 0.00 3.51
691 1141 1.068250 GCGCTATCCACTCCTGTCC 59.932 63.158 0.00 0.00 0.00 4.02
704 1154 0.471617 CCTGTCCAAGGGATAGCTGG 59.528 60.000 0.00 0.00 43.15 4.85
706 1156 1.561542 CTGTCCAAGGGATAGCTGGTT 59.438 52.381 0.00 0.00 34.39 3.67
708 1158 3.186283 TGTCCAAGGGATAGCTGGTTAA 58.814 45.455 0.00 0.00 32.73 2.01
709 1159 3.589735 TGTCCAAGGGATAGCTGGTTAAA 59.410 43.478 0.00 0.00 32.73 1.52
710 1160 4.043561 TGTCCAAGGGATAGCTGGTTAAAA 59.956 41.667 0.00 0.00 32.73 1.52
712 1162 3.954258 CCAAGGGATAGCTGGTTAAAAGG 59.046 47.826 0.00 0.00 0.00 3.11
713 1163 3.298686 AGGGATAGCTGGTTAAAAGGC 57.701 47.619 0.00 0.00 0.00 4.35
717 1167 4.381612 GGGATAGCTGGTTAAAAGGCAAAC 60.382 45.833 0.00 0.00 0.00 2.93
720 1170 1.414550 GCTGGTTAAAAGGCAAACCCA 59.585 47.619 2.02 0.00 43.78 4.51
721 1171 2.038426 GCTGGTTAAAAGGCAAACCCAT 59.962 45.455 2.02 0.00 43.78 4.00
724 1174 3.906846 TGGTTAAAAGGCAAACCCATGAT 59.093 39.130 0.00 0.00 43.78 2.45
732 1182 5.151297 AGGCAAACCCATGATAAACAAAG 57.849 39.130 0.00 0.00 36.11 2.77
733 1183 4.020307 AGGCAAACCCATGATAAACAAAGG 60.020 41.667 0.00 0.00 36.11 3.11
734 1184 4.252878 GCAAACCCATGATAAACAAAGGG 58.747 43.478 0.00 0.00 46.54 3.95
737 1187 5.937975 AACCCATGATAAACAAAGGGATG 57.062 39.130 14.44 0.00 45.08 3.51
739 1189 5.780731 ACCCATGATAAACAAAGGGATGAT 58.219 37.500 14.44 0.00 45.08 2.45
740 1190 5.599656 ACCCATGATAAACAAAGGGATGATG 59.400 40.000 14.44 0.00 45.08 3.07
741 1191 5.599656 CCCATGATAAACAAAGGGATGATGT 59.400 40.000 0.00 0.00 45.08 3.06
742 1192 6.461927 CCCATGATAAACAAAGGGATGATGTG 60.462 42.308 0.00 0.00 45.08 3.21
743 1193 6.097270 CCATGATAAACAAAGGGATGATGTGT 59.903 38.462 0.00 0.00 0.00 3.72
744 1194 6.757897 TGATAAACAAAGGGATGATGTGTC 57.242 37.500 0.00 0.00 0.00 3.67
745 1195 5.652014 TGATAAACAAAGGGATGATGTGTCC 59.348 40.000 0.00 0.00 34.92 4.02
748 1198 1.065491 CAAAGGGATGATGTGTCCGGA 60.065 52.381 0.00 0.00 36.58 5.14
749 1199 0.541863 AAGGGATGATGTGTCCGGAC 59.458 55.000 28.17 28.17 36.58 4.79
759 1209 2.280552 TGTCCGGACACAGGGCTAC 61.281 63.158 33.23 4.24 36.21 3.58
760 1210 1.982938 GTCCGGACACAGGGCTACT 60.983 63.158 29.75 0.00 0.00 2.57
761 1211 1.229082 TCCGGACACAGGGCTACTT 60.229 57.895 0.00 0.00 0.00 2.24
763 1213 0.175073 CCGGACACAGGGCTACTTAC 59.825 60.000 0.00 0.00 0.00 2.34
764 1214 1.183549 CGGACACAGGGCTACTTACT 58.816 55.000 0.00 0.00 0.00 2.24
765 1215 1.549170 CGGACACAGGGCTACTTACTT 59.451 52.381 0.00 0.00 0.00 2.24
768 1218 3.368531 GGACACAGGGCTACTTACTTCAG 60.369 52.174 0.00 0.00 0.00 3.02
769 1219 3.240302 ACACAGGGCTACTTACTTCAGT 58.760 45.455 0.00 0.00 0.00 3.41
771 1221 5.024118 ACACAGGGCTACTTACTTCAGTAT 58.976 41.667 0.00 0.00 0.00 2.12
773 1223 4.650131 ACAGGGCTACTTACTTCAGTATCC 59.350 45.833 0.00 0.00 35.56 2.59
775 1225 3.005578 GGGCTACTTACTTCAGTATCCGG 59.994 52.174 0.00 0.00 36.68 5.14
777 1227 3.552478 GCTACTTACTTCAGTATCCGGGC 60.552 52.174 0.00 0.00 0.00 6.13
779 1229 1.679680 CTTACTTCAGTATCCGGGCGA 59.320 52.381 0.00 0.00 0.00 5.54
780 1230 1.991121 TACTTCAGTATCCGGGCGAT 58.009 50.000 0.00 0.00 34.73 4.58
781 1231 1.120530 ACTTCAGTATCCGGGCGATT 58.879 50.000 0.00 0.00 31.92 3.34
783 1233 0.531974 TTCAGTATCCGGGCGATTGC 60.532 55.000 0.00 0.00 41.71 3.56
785 1235 1.069765 AGTATCCGGGCGATTGCAG 59.930 57.895 7.38 0.00 45.35 4.41
788 1238 2.324014 TATCCGGGCGATTGCAGCTT 62.324 55.000 7.38 0.00 45.35 3.74
789 1239 2.324014 ATCCGGGCGATTGCAGCTTA 62.324 55.000 7.38 0.00 45.35 3.09
790 1240 2.537560 CCGGGCGATTGCAGCTTAG 61.538 63.158 7.38 0.00 45.35 2.18
791 1241 2.537560 CGGGCGATTGCAGCTTAGG 61.538 63.158 7.38 0.00 45.35 2.69
793 1243 2.718107 GCGATTGCAGCTTAGGCC 59.282 61.111 0.00 0.00 42.15 5.19
794 1244 2.114670 GCGATTGCAGCTTAGGCCA 61.115 57.895 5.01 0.00 42.15 5.36
795 1245 2.020131 CGATTGCAGCTTAGGCCAG 58.980 57.895 5.01 0.00 39.73 4.85
796 1246 1.732308 GATTGCAGCTTAGGCCAGC 59.268 57.895 5.01 6.16 40.44 4.85
801 1251 1.530771 CAGCTTAGGCCAGCATCCT 59.469 57.895 16.78 0.00 42.84 3.24
802 1252 0.534652 CAGCTTAGGCCAGCATCCTC 60.535 60.000 16.78 0.00 42.84 3.71
804 1254 1.070445 CTTAGGCCAGCATCCTCGG 59.930 63.158 5.01 0.00 35.21 4.63
805 1255 1.689233 TTAGGCCAGCATCCTCGGT 60.689 57.895 5.01 0.00 35.21 4.69
806 1256 1.686325 TTAGGCCAGCATCCTCGGTC 61.686 60.000 5.01 0.00 35.21 4.79
809 1259 1.817099 GCCAGCATCCTCGGTCAAG 60.817 63.158 0.00 0.00 0.00 3.02
810 1260 1.817099 CCAGCATCCTCGGTCAAGC 60.817 63.158 0.00 0.00 0.00 4.01
811 1261 1.817099 CAGCATCCTCGGTCAAGCC 60.817 63.158 0.00 0.00 0.00 4.35
836 1286 1.475441 GCGTCTCTTGCGATCCGAAG 61.475 60.000 0.00 0.00 0.00 3.79
838 1288 1.467543 CGTCTCTTGCGATCCGAAGAA 60.468 52.381 0.00 0.00 0.00 2.52
839 1289 2.796383 CGTCTCTTGCGATCCGAAGAAT 60.796 50.000 0.00 0.00 0.00 2.40
840 1290 3.548214 CGTCTCTTGCGATCCGAAGAATA 60.548 47.826 0.00 0.00 0.00 1.75
843 1293 4.098044 TCTCTTGCGATCCGAAGAATAGTT 59.902 41.667 0.00 0.00 0.00 2.24
844 1294 4.755411 TCTTGCGATCCGAAGAATAGTTT 58.245 39.130 0.00 0.00 0.00 2.66
845 1295 4.566759 TCTTGCGATCCGAAGAATAGTTTG 59.433 41.667 0.00 0.00 0.00 2.93
847 1297 5.001237 TGCGATCCGAAGAATAGTTTGTA 57.999 39.130 0.00 0.00 0.00 2.41
848 1298 4.802039 TGCGATCCGAAGAATAGTTTGTAC 59.198 41.667 0.00 0.00 0.00 2.90
849 1299 4.802039 GCGATCCGAAGAATAGTTTGTACA 59.198 41.667 0.00 0.00 0.00 2.90
850 1300 5.462398 GCGATCCGAAGAATAGTTTGTACAT 59.538 40.000 0.00 0.00 0.00 2.29
851 1301 6.345882 GCGATCCGAAGAATAGTTTGTACATC 60.346 42.308 0.00 0.00 0.00 3.06
852 1302 6.918569 CGATCCGAAGAATAGTTTGTACATCT 59.081 38.462 0.00 1.23 0.00 2.90
853 1303 7.096436 CGATCCGAAGAATAGTTTGTACATCTG 60.096 40.741 0.00 0.00 0.00 2.90
854 1304 6.338146 TCCGAAGAATAGTTTGTACATCTGG 58.662 40.000 0.00 0.00 0.00 3.86
856 1306 5.580691 CGAAGAATAGTTTGTACATCTGGCA 59.419 40.000 0.00 0.00 0.00 4.92
858 1308 7.201644 CGAAGAATAGTTTGTACATCTGGCATT 60.202 37.037 0.00 0.00 0.00 3.56
859 1309 7.325660 AGAATAGTTTGTACATCTGGCATTG 57.674 36.000 0.00 0.00 0.00 2.82
860 1310 6.886459 AGAATAGTTTGTACATCTGGCATTGT 59.114 34.615 0.00 8.11 0.00 2.71
863 1313 5.012239 AGTTTGTACATCTGGCATTGTCAT 58.988 37.500 6.50 0.00 0.00 3.06
865 1315 4.219264 TGTACATCTGGCATTGTCATGA 57.781 40.909 6.50 0.00 31.07 3.07
868 1318 2.956333 ACATCTGGCATTGTCATGATGG 59.044 45.455 22.81 12.45 36.56 3.51
869 1319 3.219281 CATCTGGCATTGTCATGATGGA 58.781 45.455 16.44 2.41 31.07 3.41
872 1322 3.444742 TCTGGCATTGTCATGATGGAAAC 59.555 43.478 0.00 0.00 31.07 2.78
875 1325 2.423185 GCATTGTCATGATGGAAACCGA 59.577 45.455 0.00 0.00 31.07 4.69
876 1326 3.488047 GCATTGTCATGATGGAAACCGAG 60.488 47.826 0.00 0.00 31.07 4.63
877 1327 2.401583 TGTCATGATGGAAACCGAGG 57.598 50.000 0.00 0.00 0.00 4.63
879 1329 0.107214 TCATGATGGAAACCGAGGCC 60.107 55.000 0.00 0.00 0.00 5.19
881 1331 0.331278 ATGATGGAAACCGAGGCCAA 59.669 50.000 5.01 0.00 34.95 4.52
882 1332 0.111446 TGATGGAAACCGAGGCCAAA 59.889 50.000 5.01 0.00 34.95 3.28
883 1333 1.253100 GATGGAAACCGAGGCCAAAA 58.747 50.000 5.01 0.00 34.95 2.44
884 1334 0.966179 ATGGAAACCGAGGCCAAAAC 59.034 50.000 5.01 0.00 34.95 2.43
885 1335 1.284715 GGAAACCGAGGCCAAAACG 59.715 57.895 5.01 5.02 0.00 3.60
894 1344 1.529865 GAGGCCAAAACGGATATACGC 59.470 52.381 7.41 0.00 36.56 4.42
896 1346 0.932399 GCCAAAACGGATATACGCGT 59.068 50.000 19.17 19.17 36.56 6.01
924 2680 1.303091 CCGTTGTTTCCATCGTCCCC 61.303 60.000 0.00 0.00 33.04 4.81
961 2727 1.450848 CATCAGCACCACCGCATCT 60.451 57.895 0.00 0.00 0.00 2.90
984 2750 3.387947 CGTACACCCGAGCCCCTT 61.388 66.667 0.00 0.00 0.00 3.95
1031 2798 3.260380 CCAAATATGTTGAACCAAGGGCA 59.740 43.478 0.00 0.00 0.00 5.36
1070 2858 1.665442 GTGCCTGCATTTTTCCGGT 59.335 52.632 0.00 0.00 0.00 5.28
1093 2954 2.292061 ACATCTACGGTGACCTAACCCT 60.292 50.000 0.00 0.00 36.84 4.34
1147 3008 2.929641 TCAATCCAACAGCTCACACAA 58.070 42.857 0.00 0.00 0.00 3.33
1204 3077 2.668550 GGCACGTGTCCCACCTTC 60.669 66.667 18.38 0.00 0.00 3.46
1219 3092 6.014584 GTCCCACCTTCTCCAAAACATTATTT 60.015 38.462 0.00 0.00 0.00 1.40
1291 3164 4.517453 CCTGGAACTTCAAACCATCGTAAA 59.483 41.667 0.00 0.00 33.08 2.01
2079 4493 2.100252 TCGGATTTCACCACGGAGATAC 59.900 50.000 0.00 0.00 0.00 2.24
2090 4504 2.695666 CACGGAGATACATGACCCTCTT 59.304 50.000 0.00 0.00 0.00 2.85
2092 4506 3.775316 ACGGAGATACATGACCCTCTTTT 59.225 43.478 0.00 0.00 0.00 2.27
2277 6749 4.735132 CCTTCGCCGCGGTCTTCA 62.735 66.667 28.70 5.73 0.00 3.02
3306 7945 4.918360 AGGTGTGGGGGCTGGTGA 62.918 66.667 0.00 0.00 0.00 4.02
3307 7946 3.897122 GGTGTGGGGGCTGGTGAA 61.897 66.667 0.00 0.00 0.00 3.18
3308 7947 2.282462 GTGTGGGGGCTGGTGAAG 60.282 66.667 0.00 0.00 0.00 3.02
3309 7948 2.449518 TGTGGGGGCTGGTGAAGA 60.450 61.111 0.00 0.00 0.00 2.87
3310 7949 2.081787 TGTGGGGGCTGGTGAAGAA 61.082 57.895 0.00 0.00 0.00 2.52
3311 7950 1.303643 GTGGGGGCTGGTGAAGAAG 60.304 63.158 0.00 0.00 0.00 2.85
3312 7951 2.356667 GGGGGCTGGTGAAGAAGG 59.643 66.667 0.00 0.00 0.00 3.46
3313 7952 2.539081 GGGGGCTGGTGAAGAAGGT 61.539 63.158 0.00 0.00 0.00 3.50
3314 7953 1.303643 GGGGCTGGTGAAGAAGGTG 60.304 63.158 0.00 0.00 0.00 4.00
3315 7954 1.456287 GGGCTGGTGAAGAAGGTGT 59.544 57.895 0.00 0.00 0.00 4.16
3316 7955 0.890996 GGGCTGGTGAAGAAGGTGTG 60.891 60.000 0.00 0.00 0.00 3.82
3317 7956 0.890996 GGCTGGTGAAGAAGGTGTGG 60.891 60.000 0.00 0.00 0.00 4.17
3318 7957 0.890996 GCTGGTGAAGAAGGTGTGGG 60.891 60.000 0.00 0.00 0.00 4.61
3319 7958 0.250901 CTGGTGAAGAAGGTGTGGGG 60.251 60.000 0.00 0.00 0.00 4.96
3320 7959 1.074951 GGTGAAGAAGGTGTGGGGG 59.925 63.158 0.00 0.00 0.00 5.40
3321 7960 1.603739 GTGAAGAAGGTGTGGGGGC 60.604 63.158 0.00 0.00 0.00 5.80
3322 7961 1.774217 TGAAGAAGGTGTGGGGGCT 60.774 57.895 0.00 0.00 0.00 5.19
3323 7962 1.303643 GAAGAAGGTGTGGGGGCTG 60.304 63.158 0.00 0.00 0.00 4.85
3324 7963 1.774217 AAGAAGGTGTGGGGGCTGA 60.774 57.895 0.00 0.00 0.00 4.26
3390 8029 3.947834 CGCTTCCATCTAAAGGTTCCATT 59.052 43.478 0.00 0.00 0.00 3.16
3619 11210 1.459592 CGTCCCGATGAACAACAAGAC 59.540 52.381 0.00 0.00 0.00 3.01
3707 11299 1.051008 CCATCCATCCATGTCCTCGA 58.949 55.000 0.00 0.00 0.00 4.04
3708 11300 1.627329 CCATCCATCCATGTCCTCGAT 59.373 52.381 0.00 0.00 0.00 3.59
3709 11301 2.354503 CCATCCATCCATGTCCTCGATC 60.355 54.545 0.00 0.00 0.00 3.69
3710 11302 0.961753 TCCATCCATGTCCTCGATCG 59.038 55.000 9.36 9.36 0.00 3.69
3807 11418 5.363580 GCTTTCCCCAATTCCATCTTATTCA 59.636 40.000 0.00 0.00 0.00 2.57
3830 11441 4.179361 CACCCAGGTGCATGTGTT 57.821 55.556 3.41 0.00 39.39 3.32
3875 11508 1.725665 CTCGTCTTCCGCGGTCATA 59.274 57.895 27.15 1.49 36.19 2.15
3950 11584 3.244700 GGGACCCTCTGAATCCATACATG 60.245 52.174 2.09 0.00 33.87 3.21
3951 11585 3.648067 GGACCCTCTGAATCCATACATGA 59.352 47.826 0.00 0.00 32.35 3.07
3952 11586 4.288105 GGACCCTCTGAATCCATACATGAT 59.712 45.833 0.00 0.00 32.35 2.45
3993 11627 6.650807 CACTAGACTAGAATGCTGGAACAAAA 59.349 38.462 16.55 0.00 38.70 2.44
4008 11642 7.042725 GCTGGAACAAAATTAAAGGAAAGACAC 60.043 37.037 0.00 0.00 38.70 3.67
4197 11831 5.634859 CAGTTGTATGGTTGCCAAAAGATTC 59.365 40.000 0.00 0.00 36.95 2.52
4198 11832 5.539955 AGTTGTATGGTTGCCAAAAGATTCT 59.460 36.000 0.00 0.00 36.95 2.40
4199 11833 5.389859 TGTATGGTTGCCAAAAGATTCTG 57.610 39.130 0.00 0.00 36.95 3.02
4200 11834 5.076182 TGTATGGTTGCCAAAAGATTCTGA 58.924 37.500 0.00 0.00 36.95 3.27
4219 11853 2.234661 TGACTGACAGATCACCATCACC 59.765 50.000 10.08 0.00 0.00 4.02
4251 11900 8.727149 TGGATATTTTGGATAGGAGAAGAACAT 58.273 33.333 0.00 0.00 0.00 2.71
4252 11901 9.579932 GGATATTTTGGATAGGAGAAGAACATT 57.420 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.228552 GGGTCAAGGAGCAAGCCAA 60.229 57.895 0.00 0.00 0.00 4.52
26 27 3.626924 AGCGGAACTTGCTCGGGT 61.627 61.111 0.00 0.00 38.62 5.28
40 41 1.151668 CTGTGGAAGACCTTTGAGCG 58.848 55.000 0.00 0.00 37.04 5.03
45 46 0.183492 TGCTGCTGTGGAAGACCTTT 59.817 50.000 0.00 0.00 37.04 3.11
51 52 2.623915 GGTGCTGCTGCTGTGGAAG 61.624 63.158 17.00 0.00 40.48 3.46
120 121 4.210304 GTTGCTCCGCGATCGCAC 62.210 66.667 36.45 23.12 42.06 5.34
217 218 1.439353 CCGGACTGATGGATTTGCCG 61.439 60.000 0.00 0.00 40.66 5.69
239 240 4.814294 GCGGATCGTTCGGTGGCT 62.814 66.667 3.40 0.00 0.00 4.75
279 280 8.961634 CCGAGGATCATAATCTCAGTTATAGAA 58.038 37.037 0.00 0.00 33.17 2.10
431 432 1.737793 CGGGGAAAGAAATCTGTTCCG 59.262 52.381 13.41 8.89 41.54 4.30
432 433 1.472878 GCGGGGAAAGAAATCTGTTCC 59.527 52.381 12.27 12.27 40.16 3.62
433 434 2.437413 AGCGGGGAAAGAAATCTGTTC 58.563 47.619 0.00 0.00 0.00 3.18
434 435 2.586648 AGCGGGGAAAGAAATCTGTT 57.413 45.000 0.00 0.00 0.00 3.16
484 934 1.118356 CCAGGGGGAGAAGAGGATCG 61.118 65.000 0.00 0.00 36.68 3.69
486 936 0.725133 TTCCAGGGGGAGAAGAGGAT 59.275 55.000 0.00 0.00 46.01 3.24
511 961 3.702045 CAGTAAGGGAGGAATCGAGAGTT 59.298 47.826 0.00 0.00 0.00 3.01
596 1046 5.856455 CGTGTTAATCAAAATGTTGGAGGTC 59.144 40.000 0.00 0.00 35.29 3.85
651 1101 2.423577 AGCAAAACTGATACGGTGTCC 58.576 47.619 2.29 0.00 0.00 4.02
652 1102 3.810373 CAAGCAAAACTGATACGGTGTC 58.190 45.455 0.00 0.00 0.00 3.67
653 1103 2.031157 GCAAGCAAAACTGATACGGTGT 60.031 45.455 0.00 0.00 0.00 4.16
654 1104 2.584791 GCAAGCAAAACTGATACGGTG 58.415 47.619 0.00 0.00 0.00 4.94
656 1106 1.882198 CGCAAGCAAAACTGATACGG 58.118 50.000 0.00 0.00 0.00 4.02
671 1121 0.175760 GACAGGAGTGGATAGCGCAA 59.824 55.000 11.47 0.00 0.00 4.85
672 1122 1.676678 GGACAGGAGTGGATAGCGCA 61.677 60.000 11.47 0.00 0.00 6.09
675 1125 2.611225 CTTGGACAGGAGTGGATAGC 57.389 55.000 0.00 0.00 0.00 2.97
686 1136 1.207791 ACCAGCTATCCCTTGGACAG 58.792 55.000 0.00 0.00 32.98 3.51
687 1137 1.668826 AACCAGCTATCCCTTGGACA 58.331 50.000 0.00 0.00 32.98 4.02
688 1138 3.926058 TTAACCAGCTATCCCTTGGAC 57.074 47.619 0.00 0.00 32.98 4.02
689 1139 4.325030 CCTTTTAACCAGCTATCCCTTGGA 60.325 45.833 0.00 0.00 35.89 3.53
690 1140 3.954258 CCTTTTAACCAGCTATCCCTTGG 59.046 47.826 0.00 0.00 37.98 3.61
691 1141 3.381590 GCCTTTTAACCAGCTATCCCTTG 59.618 47.826 0.00 0.00 0.00 3.61
696 1146 4.381612 GGGTTTGCCTTTTAACCAGCTATC 60.382 45.833 0.00 0.00 44.48 2.08
697 1147 3.513912 GGGTTTGCCTTTTAACCAGCTAT 59.486 43.478 0.00 0.00 44.48 2.97
699 1149 1.691976 GGGTTTGCCTTTTAACCAGCT 59.308 47.619 0.00 0.00 44.48 4.24
700 1150 1.414550 TGGGTTTGCCTTTTAACCAGC 59.585 47.619 0.00 0.00 44.48 4.85
703 1153 4.551702 ATCATGGGTTTGCCTTTTAACC 57.448 40.909 0.00 0.00 42.46 2.85
704 1154 6.931840 TGTTTATCATGGGTTTGCCTTTTAAC 59.068 34.615 0.00 0.00 34.45 2.01
706 1156 6.672266 TGTTTATCATGGGTTTGCCTTTTA 57.328 33.333 0.00 0.00 34.45 1.52
708 1158 5.559148 TTGTTTATCATGGGTTTGCCTTT 57.441 34.783 0.00 0.00 34.45 3.11
709 1159 5.512921 CCTTTGTTTATCATGGGTTTGCCTT 60.513 40.000 0.00 0.00 34.45 4.35
710 1160 4.020307 CCTTTGTTTATCATGGGTTTGCCT 60.020 41.667 0.00 0.00 34.45 4.75
712 1162 4.020662 TCCCTTTGTTTATCATGGGTTTGC 60.021 41.667 0.00 0.00 39.51 3.68
713 1163 5.736951 TCCCTTTGTTTATCATGGGTTTG 57.263 39.130 0.00 0.00 39.51 2.93
717 1167 5.599656 ACATCATCCCTTTGTTTATCATGGG 59.400 40.000 0.00 0.00 39.71 4.00
720 1170 6.322201 GGACACATCATCCCTTTGTTTATCAT 59.678 38.462 0.00 0.00 0.00 2.45
721 1171 5.652014 GGACACATCATCCCTTTGTTTATCA 59.348 40.000 0.00 0.00 0.00 2.15
724 1174 4.006989 CGGACACATCATCCCTTTGTTTA 58.993 43.478 0.00 0.00 31.99 2.01
732 1182 1.904771 TGTCCGGACACATCATCCC 59.095 57.895 33.23 3.57 36.21 3.85
741 1191 2.118732 TAGCCCTGTGTCCGGACA 59.881 61.111 33.23 33.23 39.32 4.02
742 1192 1.542187 AAGTAGCCCTGTGTCCGGAC 61.542 60.000 28.17 28.17 0.00 4.79
743 1193 0.040058 TAAGTAGCCCTGTGTCCGGA 59.960 55.000 0.00 0.00 0.00 5.14
744 1194 0.175073 GTAAGTAGCCCTGTGTCCGG 59.825 60.000 0.00 0.00 0.00 5.14
745 1195 1.183549 AGTAAGTAGCCCTGTGTCCG 58.816 55.000 0.00 0.00 0.00 4.79
748 1198 3.240302 ACTGAAGTAAGTAGCCCTGTGT 58.760 45.455 0.00 0.00 0.00 3.72
749 1199 3.963428 ACTGAAGTAAGTAGCCCTGTG 57.037 47.619 0.00 0.00 0.00 3.66
755 1205 3.552478 GCCCGGATACTGAAGTAAGTAGC 60.552 52.174 0.73 0.00 38.14 3.58
756 1206 3.304525 CGCCCGGATACTGAAGTAAGTAG 60.305 52.174 0.73 0.00 36.14 2.57
757 1207 2.620115 CGCCCGGATACTGAAGTAAGTA 59.380 50.000 0.73 0.00 37.08 2.24
759 1209 1.679680 TCGCCCGGATACTGAAGTAAG 59.320 52.381 0.73 0.00 33.76 2.34
760 1210 1.766494 TCGCCCGGATACTGAAGTAA 58.234 50.000 0.73 0.00 33.76 2.24
761 1211 1.991121 ATCGCCCGGATACTGAAGTA 58.009 50.000 0.73 0.00 32.17 2.24
763 1213 1.502231 CAATCGCCCGGATACTGAAG 58.498 55.000 0.73 0.00 34.08 3.02
764 1214 0.531974 GCAATCGCCCGGATACTGAA 60.532 55.000 0.73 0.00 34.08 3.02
765 1215 1.069090 GCAATCGCCCGGATACTGA 59.931 57.895 0.73 0.00 34.08 3.41
768 1218 2.607892 GCTGCAATCGCCCGGATAC 61.608 63.158 0.73 0.00 37.32 2.24
769 1219 2.280797 GCTGCAATCGCCCGGATA 60.281 61.111 0.73 0.00 37.32 2.59
771 1221 2.923426 CTAAGCTGCAATCGCCCGGA 62.923 60.000 0.73 0.00 37.32 5.14
773 1223 2.537560 CCTAAGCTGCAATCGCCCG 61.538 63.158 1.02 0.00 37.32 6.13
775 1225 2.718107 GCCTAAGCTGCAATCGCC 59.282 61.111 1.02 0.00 37.32 5.54
777 1227 2.020131 CTGGCCTAAGCTGCAATCG 58.980 57.895 3.32 0.00 39.73 3.34
779 1229 0.396695 ATGCTGGCCTAAGCTGCAAT 60.397 50.000 15.52 0.00 45.77 3.56
780 1230 1.000521 ATGCTGGCCTAAGCTGCAA 60.001 52.632 15.52 0.00 45.77 4.08
781 1231 1.452651 GATGCTGGCCTAAGCTGCA 60.453 57.895 15.52 10.67 46.32 4.41
783 1233 0.534652 GAGGATGCTGGCCTAAGCTG 60.535 60.000 15.52 0.00 43.90 4.24
785 1235 1.596477 CGAGGATGCTGGCCTAAGC 60.596 63.158 8.13 8.13 43.82 3.09
788 1238 2.041922 ACCGAGGATGCTGGCCTA 60.042 61.111 3.32 0.00 35.44 3.93
789 1239 3.474570 GACCGAGGATGCTGGCCT 61.475 66.667 3.32 0.00 38.81 5.19
790 1240 3.329542 TTGACCGAGGATGCTGGCC 62.330 63.158 0.00 0.00 0.00 5.36
791 1241 1.817099 CTTGACCGAGGATGCTGGC 60.817 63.158 0.00 0.00 0.00 4.85
793 1243 1.817099 GGCTTGACCGAGGATGCTG 60.817 63.158 0.00 0.00 0.00 4.41
794 1244 2.586792 GGCTTGACCGAGGATGCT 59.413 61.111 0.00 0.00 0.00 3.79
795 1245 2.514824 GGGCTTGACCGAGGATGC 60.515 66.667 0.00 0.00 40.62 3.91
825 1275 3.857052 ACAAACTATTCTTCGGATCGCA 58.143 40.909 0.00 0.00 0.00 5.10
826 1276 4.802039 TGTACAAACTATTCTTCGGATCGC 59.198 41.667 0.00 0.00 0.00 4.58
827 1277 6.918569 AGATGTACAAACTATTCTTCGGATCG 59.081 38.462 0.00 0.00 0.00 3.69
828 1278 7.169982 CCAGATGTACAAACTATTCTTCGGATC 59.830 40.741 0.00 0.00 0.00 3.36
830 1280 6.338146 CCAGATGTACAAACTATTCTTCGGA 58.662 40.000 0.00 0.00 0.00 4.55
832 1282 5.580691 TGCCAGATGTACAAACTATTCTTCG 59.419 40.000 0.00 0.00 0.00 3.79
833 1283 6.985188 TGCCAGATGTACAAACTATTCTTC 57.015 37.500 0.00 0.00 0.00 2.87
836 1286 7.088589 ACAATGCCAGATGTACAAACTATTC 57.911 36.000 0.00 0.00 0.00 1.75
838 1288 6.179756 TGACAATGCCAGATGTACAAACTAT 58.820 36.000 0.00 0.00 0.00 2.12
839 1289 5.555966 TGACAATGCCAGATGTACAAACTA 58.444 37.500 0.00 0.00 0.00 2.24
840 1290 4.397420 TGACAATGCCAGATGTACAAACT 58.603 39.130 0.00 0.00 0.00 2.66
843 1293 4.587891 TCATGACAATGCCAGATGTACAA 58.412 39.130 0.00 0.00 33.47 2.41
844 1294 4.219264 TCATGACAATGCCAGATGTACA 57.781 40.909 0.00 0.00 33.47 2.90
845 1295 4.023450 CCATCATGACAATGCCAGATGTAC 60.023 45.833 0.00 0.00 32.98 2.90
847 1297 2.956333 CCATCATGACAATGCCAGATGT 59.044 45.455 0.00 0.00 32.98 3.06
848 1298 3.219281 TCCATCATGACAATGCCAGATG 58.781 45.455 0.00 0.00 33.47 2.90
849 1299 3.588210 TCCATCATGACAATGCCAGAT 57.412 42.857 0.00 0.00 33.47 2.90
850 1300 3.369242 TTCCATCATGACAATGCCAGA 57.631 42.857 0.00 0.00 33.47 3.86
851 1301 3.429822 GGTTTCCATCATGACAATGCCAG 60.430 47.826 0.00 0.00 33.47 4.85
852 1302 2.496871 GGTTTCCATCATGACAATGCCA 59.503 45.455 0.00 0.00 33.47 4.92
853 1303 2.480073 CGGTTTCCATCATGACAATGCC 60.480 50.000 0.00 0.00 33.47 4.40
854 1304 2.423185 TCGGTTTCCATCATGACAATGC 59.577 45.455 0.00 0.00 33.47 3.56
856 1306 3.282021 CCTCGGTTTCCATCATGACAAT 58.718 45.455 0.00 0.00 0.00 2.71
858 1308 1.678728 GCCTCGGTTTCCATCATGACA 60.679 52.381 0.00 0.00 0.00 3.58
859 1309 1.017387 GCCTCGGTTTCCATCATGAC 58.983 55.000 0.00 0.00 0.00 3.06
860 1310 0.107214 GGCCTCGGTTTCCATCATGA 60.107 55.000 0.00 0.00 0.00 3.07
863 1313 0.111446 TTTGGCCTCGGTTTCCATCA 59.889 50.000 3.32 0.00 0.00 3.07
865 1315 0.966179 GTTTTGGCCTCGGTTTCCAT 59.034 50.000 3.32 0.00 0.00 3.41
868 1318 1.167781 TCCGTTTTGGCCTCGGTTTC 61.168 55.000 21.30 1.06 43.94 2.78
869 1319 0.538746 ATCCGTTTTGGCCTCGGTTT 60.539 50.000 21.30 12.19 43.94 3.27
872 1322 2.140717 GTATATCCGTTTTGGCCTCGG 58.859 52.381 18.06 18.06 44.76 4.63
875 1325 1.589803 GCGTATATCCGTTTTGGCCT 58.410 50.000 3.32 0.00 37.80 5.19
876 1326 0.233848 CGCGTATATCCGTTTTGGCC 59.766 55.000 0.00 0.00 37.80 5.36
877 1327 0.932399 ACGCGTATATCCGTTTTGGC 59.068 50.000 11.67 0.00 37.80 4.52
879 1329 1.523934 GGGACGCGTATATCCGTTTTG 59.476 52.381 13.97 0.00 37.87 2.44
881 1331 0.032540 GGGGACGCGTATATCCGTTT 59.967 55.000 13.97 0.00 37.87 3.60
882 1332 1.662044 GGGGACGCGTATATCCGTT 59.338 57.895 13.97 0.00 37.87 4.44
883 1333 3.359002 GGGGACGCGTATATCCGT 58.641 61.111 13.97 0.98 40.85 4.69
896 1346 4.572571 AAACAACGGCAGCGGGGA 62.573 61.111 4.79 0.00 0.00 4.81
1031 2798 4.496670 GCTGAACGACGGTGCTAT 57.503 55.556 0.00 0.00 0.00 2.97
1070 2858 2.756760 GGTTAGGTCACCGTAGATGTCA 59.243 50.000 0.00 0.00 0.00 3.58
1093 2954 2.050144 GATTAGATCTGGGCCTCACCA 58.950 52.381 5.18 0.00 42.05 4.17
1334 3270 8.328758 AGGTGAAAGTGTATTTCATAAGGATCA 58.671 33.333 6.34 0.00 40.12 2.92
1576 3536 9.744468 ATTTAAAGTCAACACAAATAGTTCCAC 57.256 29.630 0.00 0.00 0.00 4.02
2013 4000 1.251251 GCAGTTCAAGCCCAACTCAT 58.749 50.000 0.00 0.00 31.40 2.90
2309 6781 0.692419 CTGGTAGGAGGAGGCATGGT 60.692 60.000 0.00 0.00 0.00 3.55
3043 7640 0.393077 CACCTTGAAGGACCACGTCT 59.607 55.000 19.83 0.00 37.67 4.18
3306 7945 1.774217 TCAGCCCCCACACCTTCTT 60.774 57.895 0.00 0.00 0.00 2.52
3307 7946 2.121963 TCAGCCCCCACACCTTCT 60.122 61.111 0.00 0.00 0.00 2.85
3308 7947 2.352805 CTCAGCCCCCACACCTTC 59.647 66.667 0.00 0.00 0.00 3.46
3309 7948 3.260100 CCTCAGCCCCCACACCTT 61.260 66.667 0.00 0.00 0.00 3.50
3390 8029 9.325248 TGAACCAATGTATCTATCTATCATGGA 57.675 33.333 0.00 0.00 0.00 3.41
3707 11299 6.701841 CGATATTATTATTGGCTAGGCACGAT 59.298 38.462 20.09 13.38 0.00 3.73
3708 11300 6.040247 CGATATTATTATTGGCTAGGCACGA 58.960 40.000 20.09 5.72 0.00 4.35
3709 11301 6.040247 TCGATATTATTATTGGCTAGGCACG 58.960 40.000 20.09 14.59 0.00 5.34
3710 11302 7.928706 AGATCGATATTATTATTGGCTAGGCAC 59.071 37.037 20.09 2.26 0.00 5.01
3778 11370 4.537288 AGATGGAATTGGGGAAAGCAAAAT 59.463 37.500 0.00 0.00 0.00 1.82
3781 11373 3.188880 AGATGGAATTGGGGAAAGCAA 57.811 42.857 0.00 0.00 0.00 3.91
3782 11374 2.925966 AGATGGAATTGGGGAAAGCA 57.074 45.000 0.00 0.00 0.00 3.91
3783 11375 5.363580 TGAATAAGATGGAATTGGGGAAAGC 59.636 40.000 0.00 0.00 0.00 3.51
3784 11376 6.462067 GCTGAATAAGATGGAATTGGGGAAAG 60.462 42.308 0.00 0.00 0.00 2.62
3786 11378 4.895297 GCTGAATAAGATGGAATTGGGGAA 59.105 41.667 0.00 0.00 0.00 3.97
3787 11379 4.473444 GCTGAATAAGATGGAATTGGGGA 58.527 43.478 0.00 0.00 0.00 4.81
3823 11434 2.361757 TGAAAGGCCAACAGAACACATG 59.638 45.455 5.01 0.00 0.00 3.21
3825 11436 2.136298 TGAAAGGCCAACAGAACACA 57.864 45.000 5.01 0.00 0.00 3.72
3826 11437 2.223805 CCTTGAAAGGCCAACAGAACAC 60.224 50.000 5.01 0.00 39.76 3.32
3827 11438 2.031120 CCTTGAAAGGCCAACAGAACA 58.969 47.619 5.01 0.00 39.76 3.18
3829 11440 2.746279 TCCTTGAAAGGCCAACAGAA 57.254 45.000 5.01 0.00 46.06 3.02
3830 11441 2.978156 ATCCTTGAAAGGCCAACAGA 57.022 45.000 5.01 0.00 46.06 3.41
3875 11508 6.769822 CCTACTTATTGGCAGAATCACAAGAT 59.230 38.462 0.00 0.00 35.53 2.40
3950 11584 7.925483 AGTCTAGTGCTTTCTGATCAATGTATC 59.075 37.037 0.00 0.00 0.00 2.24
3951 11585 7.790027 AGTCTAGTGCTTTCTGATCAATGTAT 58.210 34.615 0.00 0.00 0.00 2.29
3952 11586 7.175347 AGTCTAGTGCTTTCTGATCAATGTA 57.825 36.000 0.00 0.00 0.00 2.29
3993 11627 7.255001 CCACAAGTAACGTGTCTTTCCTTTAAT 60.255 37.037 0.00 0.00 32.26 1.40
4008 11642 3.994392 ACACAAGCTATCCACAAGTAACG 59.006 43.478 0.00 0.00 0.00 3.18
4075 11709 3.128242 GCATGTGTTCCATCTTCCTCTTG 59.872 47.826 0.00 0.00 0.00 3.02
4155 11789 7.563888 ACAACTGAAACTCCTTTTTACCTAC 57.436 36.000 0.00 0.00 0.00 3.18
4197 11831 3.519579 GTGATGGTGATCTGTCAGTCAG 58.480 50.000 0.00 0.00 44.85 3.51
4198 11832 2.234661 GGTGATGGTGATCTGTCAGTCA 59.765 50.000 0.00 0.70 34.36 3.41
4199 11833 2.234661 TGGTGATGGTGATCTGTCAGTC 59.765 50.000 0.00 0.00 34.36 3.51
4200 11834 2.259917 TGGTGATGGTGATCTGTCAGT 58.740 47.619 0.00 0.00 34.36 3.41
4219 11853 7.683578 TCTCCTATCCAAAATATCCACTGATG 58.316 38.462 0.00 0.00 32.18 3.07
4232 11866 8.884124 AATCAAATGTTCTTCTCCTATCCAAA 57.116 30.769 0.00 0.00 0.00 3.28
4233 11867 8.884124 AAATCAAATGTTCTTCTCCTATCCAA 57.116 30.769 0.00 0.00 0.00 3.53
4251 11900 7.594758 GTGCTCTACAATGTAAGCAAAATCAAA 59.405 33.333 22.18 4.81 45.55 2.69
4252 11901 7.083858 GTGCTCTACAATGTAAGCAAAATCAA 58.916 34.615 22.18 5.32 45.55 2.57
4253 11902 6.349280 GGTGCTCTACAATGTAAGCAAAATCA 60.349 38.462 22.18 5.81 45.55 2.57
4254 11903 6.030228 GGTGCTCTACAATGTAAGCAAAATC 58.970 40.000 22.18 14.28 45.55 2.17
4395 12044 3.724374 TGGTTTCTGTACCTTTGAGTCG 58.276 45.455 0.00 0.00 39.04 4.18


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

AutoCloner maintained by Alex Coulton.