Multiple sequence alignment - TraesCS5D01G070400

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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 TraesCS5D01G070400 chr5D 100.000 7600 0 0 1 7600 68227938 68235537 0.000000e+00 14035.0
1 TraesCS5D01G070400 chr5D 87.730 2820 211 54 1218 3984 68088267 68091004 0.000000e+00 3166.0
2 TraesCS5D01G070400 chr5D 90.512 1876 108 25 4852 6669 68091263 68093126 0.000000e+00 2414.0
3 TraesCS5D01G070400 chr5D 88.146 793 43 16 6689 7456 489352545 489353311 0.000000e+00 896.0
4 TraesCS5D01G070400 chr5D 90.499 421 28 4 6696 7106 5805225 5804807 5.190000e-151 545.0
5 TraesCS5D01G070400 chr5D 86.770 257 31 3 4371 4624 68232175 68231919 4.490000e-72 283.0
6 TraesCS5D01G070400 chr5D 86.770 257 31 3 3982 4238 68232561 68232308 4.490000e-72 283.0
7 TraesCS5D01G070400 chr5D 91.018 167 10 3 4624 4789 68090991 68091153 3.570000e-53 220.0
8 TraesCS5D01G070400 chr5D 94.400 125 3 1 977 1101 68087737 68087857 1.010000e-43 189.0
9 TraesCS5D01G070400 chr5D 85.556 90 13 0 3486 3575 124913923 124913834 2.260000e-15 95.3
10 TraesCS5D01G070400 chr5D 85.393 89 10 3 5060 5146 68091554 68091467 1.050000e-13 89.8
11 TraesCS5D01G070400 chr5B 95.074 3106 84 20 1140 4211 74146233 74149303 0.000000e+00 4824.0
12 TraesCS5D01G070400 chr5B 97.302 1742 34 4 4599 6338 74150828 74152558 0.000000e+00 2944.0
13 TraesCS5D01G070400 chr5B 91.667 300 14 6 4282 4580 74150551 74150840 9.180000e-109 405.0
14 TraesCS5D01G070400 chr5B 87.124 233 30 0 4392 4624 74149306 74149074 1.630000e-66 265.0
15 TraesCS5D01G070400 chr5B 89.071 183 4 6 977 1143 74145991 74146173 5.970000e-51 213.0
16 TraesCS5D01G070400 chr5B 92.958 142 10 0 7459 7600 74178027 74178168 2.780000e-49 207.0
17 TraesCS5D01G070400 chr5B 80.919 283 11 15 6397 6650 74152577 74152845 4.680000e-42 183.0
18 TraesCS5D01G070400 chr5B 77.220 259 53 6 3982 4238 345866900 345867154 6.150000e-31 147.0
19 TraesCS5D01G070400 chr5B 94.030 67 4 0 4286 4352 74149729 74149663 1.350000e-17 102.0
20 TraesCS5D01G070400 chr5B 86.667 90 12 0 3486 3575 137689503 137689414 4.850000e-17 100.0
21 TraesCS5D01G070400 chr5B 95.556 45 1 1 5103 5146 301544513 301544469 3.800000e-08 71.3
22 TraesCS5D01G070400 chr5A 96.653 2181 41 8 1998 4154 55335178 55333006 0.000000e+00 3594.0
23 TraesCS5D01G070400 chr5A 91.995 1574 67 26 5144 6678 55332332 55330779 0.000000e+00 2154.0
24 TraesCS5D01G070400 chr5A 90.443 858 46 8 1157 2005 55336155 55335325 0.000000e+00 1098.0
25 TraesCS5D01G070400 chr5A 96.166 652 19 1 4436 5081 55332984 55332333 0.000000e+00 1061.0
26 TraesCS5D01G070400 chr5A 87.793 213 16 3 3982 4194 55332796 55332998 2.740000e-59 241.0
27 TraesCS5D01G070400 chr5A 91.061 179 15 1 4446 4624 55333001 55333178 2.740000e-59 241.0
28 TraesCS5D01G070400 chr5A 90.345 145 9 2 7459 7600 59142635 59142493 1.300000e-42 185.0
29 TraesCS5D01G070400 chr5A 91.200 125 7 1 977 1101 55336683 55336563 4.720000e-37 167.0
30 TraesCS5D01G070400 chr5A 95.455 44 2 0 1100 1143 55336539 55336496 3.800000e-08 71.3
31 TraesCS5D01G070400 chr6A 89.825 914 75 12 1 899 170757195 170758105 0.000000e+00 1157.0
32 TraesCS5D01G070400 chr6A 87.352 593 53 6 6696 7276 556656943 556656361 0.000000e+00 660.0
33 TraesCS5D01G070400 chr6A 100.000 39 0 0 5106 5144 83250790 83250752 1.060000e-08 73.1
34 TraesCS5D01G070400 chr6D 88.853 933 68 9 1 917 175507430 175508342 0.000000e+00 1114.0
35 TraesCS5D01G070400 chr6D 87.264 793 40 23 6688 7456 453583317 453582562 0.000000e+00 848.0
36 TraesCS5D01G070400 chr6D 97.500 40 1 0 5106 5145 65506057 65506096 1.370000e-07 69.4
37 TraesCS5D01G070400 chr3D 91.656 791 27 15 6696 7453 255446270 255447054 0.000000e+00 1059.0
38 TraesCS5D01G070400 chr3D 89.003 782 30 16 6696 7449 393666232 393665479 0.000000e+00 917.0
39 TraesCS5D01G070400 chr4D 90.476 777 45 14 6694 7449 208554952 208554184 0.000000e+00 998.0
40 TraesCS5D01G070400 chr4D 86.433 457 18 10 7008 7449 506131317 506130890 1.930000e-125 460.0
41 TraesCS5D01G070400 chr4D 87.941 340 18 12 7130 7450 341402440 341402105 5.570000e-101 379.0
42 TraesCS5D01G070400 chr4D 84.564 149 18 4 3982 4130 318239587 318239730 7.950000e-30 143.0
43 TraesCS5D01G070400 chr1D 89.394 792 43 16 6684 7460 383252309 383253074 0.000000e+00 959.0
44 TraesCS5D01G070400 chr1D 83.172 309 34 8 1 301 289422750 289422452 4.520000e-67 267.0
45 TraesCS5D01G070400 chr1D 95.238 42 1 1 5105 5145 452260420 452260461 1.770000e-06 65.8
46 TraesCS5D01G070400 chr1D 97.222 36 1 0 625 660 442711875 442711910 2.290000e-05 62.1
47 TraesCS5D01G070400 chr1A 89.386 782 49 14 6695 7449 549305162 549305936 0.000000e+00 953.0
48 TraesCS5D01G070400 chr1A 90.863 591 34 5 6696 7276 85835095 85835675 0.000000e+00 774.0
49 TraesCS5D01G070400 chr2D 88.745 773 34 18 6696 7449 526823795 526824533 0.000000e+00 896.0
50 TraesCS5D01G070400 chr2D 85.859 198 23 4 4430 4624 12983452 12983257 1.000000e-48 206.0
51 TraesCS5D01G070400 chr2D 84.184 196 30 1 4433 4627 94561160 94560965 1.010000e-43 189.0
52 TraesCS5D01G070400 chr2D 86.486 148 19 1 3981 4128 318503466 318503320 2.190000e-35 161.0
53 TraesCS5D01G070400 chr3B 88.107 782 36 26 6696 7449 650612492 650613244 0.000000e+00 876.0
54 TraesCS5D01G070400 chr4A 94.620 539 17 5 1 527 443441709 443441171 0.000000e+00 824.0
55 TraesCS5D01G070400 chr4A 85.938 320 32 8 527 843 443440780 443440471 5.690000e-86 329.0
56 TraesCS5D01G070400 chr4A 82.143 140 21 3 3982 4119 7901902 7902039 4.820000e-22 117.0
57 TraesCS5D01G070400 chr6B 93.254 504 24 4 1 494 679622081 679622584 0.000000e+00 734.0
58 TraesCS5D01G070400 chr6B 83.075 644 60 21 8 636 266420972 266421581 2.410000e-149 540.0
59 TraesCS5D01G070400 chr6B 93.617 47 1 2 5105 5149 686365194 686365240 1.370000e-07 69.4
60 TraesCS5D01G070400 chr2A 87.705 610 41 9 6696 7276 99785864 99786468 0.000000e+00 680.0
61 TraesCS5D01G070400 chr2A 85.577 104 12 3 5057 5159 35528035 35527934 1.040000e-18 106.0
62 TraesCS5D01G070400 chr1B 91.554 296 9 7 7168 7449 24495528 24495235 1.990000e-105 394.0
63 TraesCS5D01G070400 chr1B 77.898 371 51 22 4284 4624 646131793 646131424 1.290000e-47 202.0
64 TraesCS5D01G070400 chr1B 77.628 371 52 22 4284 4624 646101532 646101163 6.020000e-46 196.0
65 TraesCS5D01G070400 chrUn 88.235 340 17 12 7130 7450 298894470 298894805 1.200000e-102 385.0
66 TraesCS5D01G070400 chrUn 77.931 290 49 12 4298 4572 101390815 101390526 4.720000e-37 167.0
67 TraesCS5D01G070400 chr7D 88.372 129 14 1 3975 4103 565056953 565057080 3.670000e-33 154.0
68 TraesCS5D01G070400 chr7D 79.104 201 38 4 2031 2229 45781626 45781428 1.330000e-27 135.0
69 TraesCS5D01G070400 chr7A 72.832 519 99 30 2031 2531 48046998 48046504 1.030000e-28 139.0
70 TraesCS5D01G070400 chr7B 90.196 51 5 0 586 636 741337726 741337676 4.920000e-07 67.6


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 TraesCS5D01G070400 chr5D 68227938 68235537 7599 False 14035.00 14035 100.0000 1 7600 1 chr5D.!!$F1 7599
1 TraesCS5D01G070400 chr5D 68087737 68093126 5389 False 1497.25 3166 90.9150 977 6669 4 chr5D.!!$F3 5692
2 TraesCS5D01G070400 chr5D 489352545 489353311 766 False 896.00 896 88.1460 6689 7456 1 chr5D.!!$F2 767
3 TraesCS5D01G070400 chr5D 68231919 68232561 642 True 283.00 283 86.7700 3982 4624 2 chr5D.!!$R4 642
4 TraesCS5D01G070400 chr5B 74145991 74152845 6854 False 1713.80 4824 90.8066 977 6650 5 chr5B.!!$F3 5673
5 TraesCS5D01G070400 chr5A 55330779 55336683 5904 True 1357.55 3594 93.6520 977 6678 6 chr5A.!!$R2 5701
6 TraesCS5D01G070400 chr6A 170757195 170758105 910 False 1157.00 1157 89.8250 1 899 1 chr6A.!!$F1 898
7 TraesCS5D01G070400 chr6A 556656361 556656943 582 True 660.00 660 87.3520 6696 7276 1 chr6A.!!$R2 580
8 TraesCS5D01G070400 chr6D 175507430 175508342 912 False 1114.00 1114 88.8530 1 917 1 chr6D.!!$F2 916
9 TraesCS5D01G070400 chr6D 453582562 453583317 755 True 848.00 848 87.2640 6688 7456 1 chr6D.!!$R1 768
10 TraesCS5D01G070400 chr3D 255446270 255447054 784 False 1059.00 1059 91.6560 6696 7453 1 chr3D.!!$F1 757
11 TraesCS5D01G070400 chr3D 393665479 393666232 753 True 917.00 917 89.0030 6696 7449 1 chr3D.!!$R1 753
12 TraesCS5D01G070400 chr4D 208554184 208554952 768 True 998.00 998 90.4760 6694 7449 1 chr4D.!!$R1 755
13 TraesCS5D01G070400 chr1D 383252309 383253074 765 False 959.00 959 89.3940 6684 7460 1 chr1D.!!$F1 776
14 TraesCS5D01G070400 chr1A 549305162 549305936 774 False 953.00 953 89.3860 6695 7449 1 chr1A.!!$F2 754
15 TraesCS5D01G070400 chr1A 85835095 85835675 580 False 774.00 774 90.8630 6696 7276 1 chr1A.!!$F1 580
16 TraesCS5D01G070400 chr2D 526823795 526824533 738 False 896.00 896 88.7450 6696 7449 1 chr2D.!!$F1 753
17 TraesCS5D01G070400 chr3B 650612492 650613244 752 False 876.00 876 88.1070 6696 7449 1 chr3B.!!$F1 753
18 TraesCS5D01G070400 chr4A 443440471 443441709 1238 True 576.50 824 90.2790 1 843 2 chr4A.!!$R1 842
19 TraesCS5D01G070400 chr6B 679622081 679622584 503 False 734.00 734 93.2540 1 494 1 chr6B.!!$F2 493
20 TraesCS5D01G070400 chr6B 266420972 266421581 609 False 540.00 540 83.0750 8 636 1 chr6B.!!$F1 628
21 TraesCS5D01G070400 chr2A 99785864 99786468 604 False 680.00 680 87.7050 6696 7276 1 chr2A.!!$F1 580

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
830 1240 0.249398 AGGGCGATGCGAAACTAACT 59.751 50.000 0.00 0.00 0.00 2.24 F
1154 1954 0.702924 CGACGCCGTATGATCGATTG 59.297 55.000 0.00 0.00 36.70 2.67 F
1486 2301 0.731417 CCTGCGATTTCTCCTTGCTG 59.269 55.000 0.00 0.00 0.00 4.41 F
1560 2375 2.032550 CCATGCTTCATTTCGCTTCGAT 59.967 45.455 0.00 0.00 35.23 3.59 F
1637 2452 2.526304 TGTCAACTCGGAGTCAAAGG 57.474 50.000 11.71 0.00 0.00 3.11 F
2143 3115 2.710096 ATCCATTACCAAGGGACACG 57.290 50.000 0.00 0.00 45.19 4.49 F
4063 5086 0.108585 ATGTGACACTTTCCACCGCT 59.891 50.000 7.20 0.00 32.61 5.52 F
4587 6788 0.037605 AGTGGTAGTTTTCCGAGCGG 60.038 55.000 1.74 1.74 0.00 5.52 F
5606 7908 0.527565 ATGCATTCAACCGGACAAGC 59.472 50.000 9.46 4.83 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 3115 1.470098 CCACAGCAGCCAAGTGTAATC 59.530 52.381 8.82 0.00 0.00 1.75 R
3016 4022 3.791320 TCTTGGGATGTCTGACTAGGTT 58.209 45.455 9.51 0.00 0.00 3.50 R
3067 4073 7.710475 TGATTCTGCGATGAGATATGTAAAACA 59.290 33.333 0.00 0.00 0.00 2.83 R
3248 4261 9.785982 AGAAAAGAAGTTGAAGTAAAGCTAGAT 57.214 29.630 0.00 0.00 0.00 1.98 R
3737 4751 5.931146 AGCTATCTATGCATGTAAACAGAGC 59.069 40.000 10.16 7.22 0.00 4.09 R
4197 5220 0.545548 GAGAGTGAGGGAGGGTTGGT 60.546 60.000 0.00 0.00 0.00 3.67 R
5969 8289 0.980231 AGGCCTCTCCATGACAGTCC 60.980 60.000 0.00 0.00 37.29 3.85 R
6258 8581 2.057137 AACAGGAAGACAGCAGCAAA 57.943 45.000 0.00 0.00 0.00 3.68 R
6840 9227 0.249398 ACTTAAGCGCCCTCAACGAT 59.751 50.000 2.29 0.00 0.00 3.73 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
48 49 2.125552 CGCCGTTCAGCCTGATGA 60.126 61.111 0.00 0.00 0.00 2.92
427 438 1.420430 GTCGGGATGGGATAACTGGA 58.580 55.000 0.00 0.00 0.00 3.86
521 534 1.331214 CTGGGCAATGGACAAAGTGT 58.669 50.000 0.00 0.00 0.00 3.55
550 958 1.486310 CGATGGAGAAACTGGATGGGA 59.514 52.381 0.00 0.00 0.00 4.37
559 967 5.091552 AGAAACTGGATGGGAAGTGTACTA 58.908 41.667 0.00 0.00 0.00 1.82
673 1081 8.868103 AGAGATAGAGATTAATGTGATTGAGCA 58.132 33.333 0.00 0.00 0.00 4.26
781 1191 5.290158 GTGACGCGAAATATGGAAAGTTCTA 59.710 40.000 15.93 0.00 0.00 2.10
829 1239 0.651031 GAGGGCGATGCGAAACTAAC 59.349 55.000 0.00 0.00 0.00 2.34
830 1240 0.249398 AGGGCGATGCGAAACTAACT 59.751 50.000 0.00 0.00 0.00 2.24
884 1296 7.012704 CAGACGAAAATGATGGGACTATTCAAT 59.987 37.037 0.00 0.00 0.00 2.57
893 1305 5.160607 TGGGACTATTCAATCAACTCGTT 57.839 39.130 0.00 0.00 0.00 3.85
899 1311 9.046296 GGACTATTCAATCAACTCGTTCATTAT 57.954 33.333 0.00 0.00 0.00 1.28
932 1344 9.674068 AGATTAGATCTTGATGATTGATGATGG 57.326 33.333 0.00 0.00 35.76 3.51
933 1345 9.668497 GATTAGATCTTGATGATTGATGATGGA 57.332 33.333 0.00 0.00 35.14 3.41
1150 1686 1.665544 GCATCGACGCCGTATGATCG 61.666 60.000 4.26 0.00 37.05 3.69
1154 1954 0.702924 CGACGCCGTATGATCGATTG 59.297 55.000 0.00 0.00 36.70 2.67
1172 1972 5.468746 TCGATTGTTCTTCCTTGTTTCGAAT 59.531 36.000 0.00 0.00 31.02 3.34
1246 2046 0.994995 CGAACTTCAGATCCGCACTG 59.005 55.000 0.00 0.00 36.80 3.66
1287 2088 6.343693 CGATGAAATTTCGATTCGCTCATTTG 60.344 38.462 18.67 0.09 38.88 2.32
1486 2301 0.731417 CCTGCGATTTCTCCTTGCTG 59.269 55.000 0.00 0.00 0.00 4.41
1560 2375 2.032550 CCATGCTTCATTTCGCTTCGAT 59.967 45.455 0.00 0.00 35.23 3.59
1637 2452 2.526304 TGTCAACTCGGAGTCAAAGG 57.474 50.000 11.71 0.00 0.00 3.11
1673 2488 4.034394 CGCATGCAGCTAGTTGAAATCTTA 59.966 41.667 19.57 0.00 42.61 2.10
1713 2528 7.842887 AGTTCTTCTCCTTCTGTTACTACTT 57.157 36.000 0.00 0.00 0.00 2.24
1714 2529 8.937207 AGTTCTTCTCCTTCTGTTACTACTTA 57.063 34.615 0.00 0.00 0.00 2.24
1715 2530 8.795513 AGTTCTTCTCCTTCTGTTACTACTTAC 58.204 37.037 0.00 0.00 0.00 2.34
1716 2531 8.795513 GTTCTTCTCCTTCTGTTACTACTTACT 58.204 37.037 0.00 0.00 0.00 2.24
1718 2533 9.447157 TCTTCTCCTTCTGTTACTACTTACTAC 57.553 37.037 0.00 0.00 0.00 2.73
1719 2534 9.452287 CTTCTCCTTCTGTTACTACTTACTACT 57.548 37.037 0.00 0.00 0.00 2.57
1735 2550 2.899900 ACTACTGAGATGCTGTGTTCCA 59.100 45.455 0.00 0.00 0.00 3.53
1985 2803 5.995565 TGCCTACAATTACTGTCTACTGT 57.004 39.130 0.00 0.00 39.64 3.55
2064 3035 6.208402 TGGATATGTACTGCATTTTGTTGTGT 59.792 34.615 0.00 0.00 38.94 3.72
2143 3115 2.710096 ATCCATTACCAAGGGACACG 57.290 50.000 0.00 0.00 45.19 4.49
2416 3389 6.739331 TTTCCTTTTTCAGCCCAATAAAGA 57.261 33.333 0.00 0.00 0.00 2.52
2568 3541 7.394016 TGAATGTGTTCTGATTCCTTAAGCTA 58.606 34.615 0.00 0.00 35.33 3.32
3016 4022 5.304778 TGCTTCAGAGTTTGTACTGCATTA 58.695 37.500 0.00 0.00 33.84 1.90
3067 4073 3.141398 CCAGTGCTAAGTGTCACAACAT 58.859 45.455 5.62 0.00 37.81 2.71
3248 4261 5.208294 AGAATTGGAGAGGGAGTACTGTA 57.792 43.478 0.00 0.00 0.00 2.74
3737 4751 6.614160 TCAACAAAGCACACATATTCATGAG 58.386 36.000 0.00 0.00 35.96 2.90
3997 5020 9.330063 TCCTTTATATGAGTAAAATGCACAGAG 57.670 33.333 0.00 0.00 0.00 3.35
4063 5086 0.108585 ATGTGACACTTTCCACCGCT 59.891 50.000 7.20 0.00 32.61 5.52
4109 5132 6.826893 AAACACTGAACCAAAATTTGATCG 57.173 33.333 7.37 5.02 0.00 3.69
4183 5206 2.100631 CGGCCGTTAACTGCTCTGG 61.101 63.158 19.50 6.32 0.00 3.86
4197 5220 1.881903 CTCTGGCTGAAGCGACTGGA 61.882 60.000 0.00 0.00 43.26 3.86
4211 5234 1.538876 CTGGACCAACCCTCCCTCA 60.539 63.158 0.00 0.00 38.00 3.86
4228 5578 0.923358 TCACTCTCTCTCCCTCTCCC 59.077 60.000 0.00 0.00 0.00 4.30
4230 5580 1.133792 CACTCTCTCTCCCTCTCCCTC 60.134 61.905 0.00 0.00 0.00 4.30
4231 5581 0.478507 CTCTCTCTCCCTCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
4232 5582 0.996762 TCTCTCTCCCTCTCCCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
4233 5583 0.998945 CTCTCTCCCTCTCCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
4234 5584 0.996762 TCTCTCCCTCTCCCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
4236 5586 3.036959 TCCCTCTCCCTCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
4237 5587 3.039526 CCCTCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
4239 5589 2.328589 CCTCTCCCTCCCTCCCTGA 61.329 68.421 0.00 0.00 0.00 3.86
4240 5590 1.075600 CTCTCCCTCCCTCCCTGAC 60.076 68.421 0.00 0.00 0.00 3.51
4241 5591 1.547755 TCTCCCTCCCTCCCTGACT 60.548 63.158 0.00 0.00 0.00 3.41
4242 5592 1.156322 TCTCCCTCCCTCCCTGACTT 61.156 60.000 0.00 0.00 0.00 3.01
4245 5595 1.657162 TCCCTCCCTCCCTGACTTATT 59.343 52.381 0.00 0.00 0.00 1.40
4247 5597 2.482494 CCTCCCTCCCTGACTTATTGT 58.518 52.381 0.00 0.00 0.00 2.71
4248 5598 3.632645 CCCTCCCTCCCTGACTTATTGTA 60.633 52.174 0.00 0.00 0.00 2.41
4249 5599 4.037927 CCTCCCTCCCTGACTTATTGTAA 58.962 47.826 0.00 0.00 0.00 2.41
4250 5600 4.473559 CCTCCCTCCCTGACTTATTGTAAA 59.526 45.833 0.00 0.00 0.00 2.01
4252 5602 5.098663 TCCCTCCCTGACTTATTGTAAACT 58.901 41.667 0.00 0.00 0.00 2.66
4281 6444 1.668826 TGTAGCACAATCTTCCCCCT 58.331 50.000 0.00 0.00 0.00 4.79
4282 6445 2.840511 TGTAGCACAATCTTCCCCCTA 58.159 47.619 0.00 0.00 0.00 3.53
4283 6446 3.186283 TGTAGCACAATCTTCCCCCTAA 58.814 45.455 0.00 0.00 0.00 2.69
4284 6447 2.808906 AGCACAATCTTCCCCCTAAC 57.191 50.000 0.00 0.00 0.00 2.34
4285 6448 2.279173 AGCACAATCTTCCCCCTAACT 58.721 47.619 0.00 0.00 0.00 2.24
4382 6583 4.045334 AGAAAAAGGAGAGGGAGAGAGAGA 59.955 45.833 0.00 0.00 0.00 3.10
4388 6589 0.478507 GAGGGAGAGAGAGAGAGGGG 59.521 65.000 0.00 0.00 0.00 4.79
4389 6590 0.998945 AGGGAGAGAGAGAGAGGGGG 60.999 65.000 0.00 0.00 0.00 5.40
4390 6591 0.996762 GGGAGAGAGAGAGAGGGGGA 60.997 65.000 0.00 0.00 0.00 4.81
4391 6592 0.478507 GGAGAGAGAGAGAGGGGGAG 59.521 65.000 0.00 0.00 0.00 4.30
4435 6636 3.002246 CGCTTCAAACAGAGCAGTTAACA 59.998 43.478 8.61 0.00 0.00 2.41
4585 6786 4.060205 TGTAAAGTGGTAGTTTTCCGAGC 58.940 43.478 0.00 0.00 0.00 5.03
4587 6788 0.037605 AGTGGTAGTTTTCCGAGCGG 60.038 55.000 1.74 1.74 0.00 5.52
4744 6954 3.202151 ACCACCTAACATACAGATTGGGG 59.798 47.826 0.00 0.00 30.99 4.96
4853 7140 4.343231 TGGGATATGCTTCTTCTTTTGCA 58.657 39.130 0.00 0.00 39.83 4.08
5311 7612 4.818546 GCTGTAATCATTGTGCCAGATAGT 59.181 41.667 0.00 0.00 0.00 2.12
5411 7712 9.519191 TTATTACTACTATGATTACCTACCGCA 57.481 33.333 0.00 0.00 0.00 5.69
5606 7908 0.527565 ATGCATTCAACCGGACAAGC 59.472 50.000 9.46 4.83 0.00 4.01
5714 8016 2.752354 TGTTTATGCCGTTTCATGAGGG 59.248 45.455 0.00 0.15 0.00 4.30
5717 8019 3.680156 GCCGTTTCATGAGGGCAA 58.320 55.556 22.39 2.07 46.92 4.52
5718 8020 1.963679 GCCGTTTCATGAGGGCAAA 59.036 52.632 22.39 1.72 46.92 3.68
6197 8520 2.357034 GCGGTTGAAGGAGCGTCA 60.357 61.111 0.00 0.00 42.11 4.35
6258 8581 6.644347 ACCTTAATCGTGAACAGATTCAGAT 58.356 36.000 2.74 0.00 45.58 2.90
6265 8588 4.164294 GTGAACAGATTCAGATTTGCTGC 58.836 43.478 0.00 0.00 45.58 5.25
6442 8774 4.818642 TGTATTGGATTGTTGTTGGCATG 58.181 39.130 0.00 0.00 0.00 4.06
6592 8940 6.385649 TTCTCGTTTGCAAAGTAAAAGGAT 57.614 33.333 13.26 0.00 31.83 3.24
6596 8944 7.389330 TCTCGTTTGCAAAGTAAAAGGATATCA 59.611 33.333 13.26 0.00 31.83 2.15
6597 8945 7.526608 TCGTTTGCAAAGTAAAAGGATATCAG 58.473 34.615 13.26 0.00 0.00 2.90
6651 9018 8.749841 TTTTCGTTTGAAACAATATATGTGGG 57.250 30.769 8.93 0.00 43.54 4.61
6654 9021 5.514914 CGTTTGAAACAATATATGTGGGTGC 59.485 40.000 8.93 0.00 42.99 5.01
6678 9045 4.554134 GCATATGTTCGCTGTCGAGTAGTA 60.554 45.833 4.29 0.00 46.34 1.82
6679 9046 5.690816 CATATGTTCGCTGTCGAGTAGTAT 58.309 41.667 0.00 0.00 46.34 2.12
6680 9047 6.620089 GCATATGTTCGCTGTCGAGTAGTATA 60.620 42.308 4.29 0.00 46.34 1.47
6681 9048 5.746307 ATGTTCGCTGTCGAGTAGTATAA 57.254 39.130 0.00 0.00 46.34 0.98
6682 9049 5.550232 TGTTCGCTGTCGAGTAGTATAAA 57.450 39.130 0.00 0.00 46.34 1.40
6683 9050 5.566623 TGTTCGCTGTCGAGTAGTATAAAG 58.433 41.667 0.00 0.00 46.34 1.85
6684 9051 5.352293 TGTTCGCTGTCGAGTAGTATAAAGA 59.648 40.000 0.00 0.00 46.34 2.52
6685 9052 6.128200 TGTTCGCTGTCGAGTAGTATAAAGAA 60.128 38.462 0.00 0.00 46.34 2.52
6686 9053 6.045698 TCGCTGTCGAGTAGTATAAAGAAG 57.954 41.667 0.00 0.00 40.21 2.85
6687 9054 5.814188 TCGCTGTCGAGTAGTATAAAGAAGA 59.186 40.000 0.00 0.00 40.21 2.87
6688 9055 6.314648 TCGCTGTCGAGTAGTATAAAGAAGAA 59.685 38.462 0.00 0.00 40.21 2.52
6689 9056 7.012138 TCGCTGTCGAGTAGTATAAAGAAGAAT 59.988 37.037 0.00 0.00 40.21 2.40
6690 9057 7.112287 CGCTGTCGAGTAGTATAAAGAAGAATG 59.888 40.741 0.00 0.00 38.10 2.67
6762 9149 3.113260 AGCTAAACACTTCGCTTCTGT 57.887 42.857 0.00 0.00 29.66 3.41
6849 9236 0.179111 TGGCTAAGCGATCGTTGAGG 60.179 55.000 17.07 6.59 0.00 3.86
6902 9289 0.698818 ACAGGCTGGAGGTAAAAGGG 59.301 55.000 20.34 0.00 0.00 3.95
6903 9290 0.034089 CAGGCTGGAGGTAAAAGGGG 60.034 60.000 6.61 0.00 0.00 4.79
7012 9404 2.381109 CTGCTCCTGTTCAGCATCG 58.619 57.895 0.00 0.00 45.81 3.84
7120 9619 1.843992 CTGCTGCTGTTGTTTGGTTC 58.156 50.000 0.00 0.00 0.00 3.62
7123 9622 1.269257 GCTGCTGTTGTTTGGTTCCTC 60.269 52.381 0.00 0.00 0.00 3.71
7138 9654 2.360100 CTCCTGCTGCTGCTTGCT 60.360 61.111 17.00 0.00 43.37 3.91
7165 9681 6.349944 GCAGCTGCCATTTATCTTATATGCTT 60.350 38.462 28.76 0.00 34.31 3.91
7214 9735 2.355756 CTGTGTGAACCACTGAACCTTG 59.644 50.000 0.00 0.00 44.81 3.61
7275 9796 6.012858 TGAACCACTGAACCTCAACCTTATAT 60.013 38.462 0.00 0.00 0.00 0.86
7316 9837 7.676947 TCAGTTACCTATGTGCTATATTTCCC 58.323 38.462 0.00 0.00 0.00 3.97
7344 9878 8.954950 TTTATTCAAAAACAGCCAAATTCTGA 57.045 26.923 0.00 0.00 35.61 3.27
7355 9891 6.930722 ACAGCCAAATTCTGACCAATTTAAAG 59.069 34.615 0.00 0.00 34.77 1.85
7382 9919 2.639065 CTTAATCCCGGTTAAGCTGCA 58.361 47.619 10.62 0.00 35.57 4.41
7432 9971 1.226603 CGCTCCGCTTACGCTTACT 60.227 57.895 0.00 0.00 38.22 2.24
7451 9990 6.571150 GCTTACTGCTTTCTTGAACATTGGAT 60.571 38.462 0.00 0.00 38.95 3.41
7456 9995 8.462016 ACTGCTTTCTTGAACATTGGATAATAC 58.538 33.333 0.00 0.00 0.00 1.89
7524 10063 9.768662 ACTTTGATTAGTAAGTTTTTAGACGGA 57.231 29.630 0.00 0.00 30.72 4.69
7526 10065 8.767478 TTGATTAGTAAGTTTTTAGACGGAGG 57.233 34.615 0.00 0.00 0.00 4.30
7527 10066 6.815142 TGATTAGTAAGTTTTTAGACGGAGGC 59.185 38.462 0.00 0.00 0.00 4.70
7528 10067 4.612264 AGTAAGTTTTTAGACGGAGGCA 57.388 40.909 0.00 0.00 0.00 4.75
7529 10068 5.161943 AGTAAGTTTTTAGACGGAGGCAT 57.838 39.130 0.00 0.00 0.00 4.40
7530 10069 5.176592 AGTAAGTTTTTAGACGGAGGCATC 58.823 41.667 0.00 0.00 0.00 3.91
7531 10070 3.983044 AGTTTTTAGACGGAGGCATCT 57.017 42.857 0.00 0.00 0.00 2.90
7532 10071 3.600388 AGTTTTTAGACGGAGGCATCTG 58.400 45.455 5.47 5.47 37.86 2.90
7533 10072 2.024176 TTTTAGACGGAGGCATCTGC 57.976 50.000 7.20 0.12 41.14 4.26
7546 10085 3.942130 GCATCTGCCCAAACTTAAACT 57.058 42.857 0.00 0.00 34.31 2.66
7547 10086 3.578688 GCATCTGCCCAAACTTAAACTG 58.421 45.455 0.00 0.00 34.31 3.16
7548 10087 3.255642 GCATCTGCCCAAACTTAAACTGA 59.744 43.478 0.00 0.00 34.31 3.41
7549 10088 4.616835 GCATCTGCCCAAACTTAAACTGAG 60.617 45.833 0.00 0.00 34.31 3.35
7550 10089 3.486383 TCTGCCCAAACTTAAACTGAGG 58.514 45.455 0.00 0.00 0.00 3.86
7551 10090 1.960689 TGCCCAAACTTAAACTGAGGC 59.039 47.619 0.00 0.00 39.64 4.70
7552 10091 1.272490 GCCCAAACTTAAACTGAGGCC 59.728 52.381 0.00 0.00 32.93 5.19
7553 10092 2.593026 CCCAAACTTAAACTGAGGCCA 58.407 47.619 5.01 0.00 0.00 5.36
7554 10093 3.165071 CCCAAACTTAAACTGAGGCCAT 58.835 45.455 5.01 0.00 0.00 4.40
7555 10094 3.578282 CCCAAACTTAAACTGAGGCCATT 59.422 43.478 5.01 0.00 0.00 3.16
7556 10095 4.040339 CCCAAACTTAAACTGAGGCCATTT 59.960 41.667 5.01 2.32 0.00 2.32
7557 10096 5.245075 CCCAAACTTAAACTGAGGCCATTTA 59.755 40.000 5.01 1.25 0.00 1.40
7558 10097 6.156519 CCAAACTTAAACTGAGGCCATTTAC 58.843 40.000 5.01 0.00 0.00 2.01
7559 10098 6.239176 CCAAACTTAAACTGAGGCCATTTACA 60.239 38.462 5.01 0.00 0.00 2.41
7560 10099 5.959618 ACTTAAACTGAGGCCATTTACAC 57.040 39.130 5.01 0.00 0.00 2.90
7561 10100 5.381757 ACTTAAACTGAGGCCATTTACACA 58.618 37.500 5.01 0.00 0.00 3.72
7562 10101 6.010219 ACTTAAACTGAGGCCATTTACACAT 58.990 36.000 5.01 0.00 0.00 3.21
7563 10102 4.789012 AAACTGAGGCCATTTACACATG 57.211 40.909 5.01 0.00 0.00 3.21
7564 10103 2.094675 ACTGAGGCCATTTACACATGC 58.905 47.619 5.01 0.00 0.00 4.06
7565 10104 1.406539 CTGAGGCCATTTACACATGCC 59.593 52.381 5.01 0.00 0.00 4.40
7566 10105 1.272369 TGAGGCCATTTACACATGCCA 60.272 47.619 5.01 0.00 0.00 4.92
7567 10106 1.134946 GAGGCCATTTACACATGCCAC 59.865 52.381 5.01 0.00 0.00 5.01
7568 10107 0.894141 GGCCATTTACACATGCCACA 59.106 50.000 0.00 0.00 0.00 4.17
7569 10108 1.404047 GGCCATTTACACATGCCACAC 60.404 52.381 0.00 0.00 0.00 3.82
7570 10109 1.271934 GCCATTTACACATGCCACACA 59.728 47.619 0.00 0.00 0.00 3.72
7571 10110 2.288702 GCCATTTACACATGCCACACAA 60.289 45.455 0.00 0.00 0.00 3.33
7572 10111 3.577667 CCATTTACACATGCCACACAAG 58.422 45.455 0.00 0.00 0.00 3.16
7573 10112 3.005684 CCATTTACACATGCCACACAAGT 59.994 43.478 0.00 0.00 0.00 3.16
7574 10113 3.980646 TTTACACATGCCACACAAGTC 57.019 42.857 0.00 0.00 0.00 3.01
7575 10114 2.928801 TACACATGCCACACAAGTCT 57.071 45.000 0.00 0.00 0.00 3.24
7576 10115 2.057137 ACACATGCCACACAAGTCTT 57.943 45.000 0.00 0.00 0.00 3.01
7577 10116 3.207265 ACACATGCCACACAAGTCTTA 57.793 42.857 0.00 0.00 0.00 2.10
7578 10117 3.550820 ACACATGCCACACAAGTCTTAA 58.449 40.909 0.00 0.00 0.00 1.85
7579 10118 3.565482 ACACATGCCACACAAGTCTTAAG 59.435 43.478 0.00 0.00 0.00 1.85
7580 10119 3.058016 CACATGCCACACAAGTCTTAAGG 60.058 47.826 1.85 0.00 0.00 2.69
7581 10120 3.181445 ACATGCCACACAAGTCTTAAGGA 60.181 43.478 1.85 0.00 0.00 3.36
7582 10121 3.569194 TGCCACACAAGTCTTAAGGAA 57.431 42.857 1.85 0.00 0.00 3.36
7583 10122 3.892284 TGCCACACAAGTCTTAAGGAAA 58.108 40.909 1.85 0.00 0.00 3.13
7584 10123 3.630312 TGCCACACAAGTCTTAAGGAAAC 59.370 43.478 1.85 0.00 0.00 2.78
7585 10124 3.630312 GCCACACAAGTCTTAAGGAAACA 59.370 43.478 1.85 0.00 0.00 2.83
7586 10125 4.097286 GCCACACAAGTCTTAAGGAAACAA 59.903 41.667 1.85 0.00 0.00 2.83
7587 10126 5.393678 GCCACACAAGTCTTAAGGAAACAAA 60.394 40.000 1.85 0.00 0.00 2.83
7588 10127 6.265577 CCACACAAGTCTTAAGGAAACAAAG 58.734 40.000 1.85 0.00 0.00 2.77
7589 10128 6.127730 CCACACAAGTCTTAAGGAAACAAAGT 60.128 38.462 1.85 0.00 0.00 2.66
7590 10129 7.066525 CCACACAAGTCTTAAGGAAACAAAGTA 59.933 37.037 1.85 0.00 0.00 2.24
7591 10130 8.122952 CACACAAGTCTTAAGGAAACAAAGTAG 58.877 37.037 1.85 0.00 0.00 2.57
7592 10131 7.282450 ACACAAGTCTTAAGGAAACAAAGTAGG 59.718 37.037 1.85 0.00 0.00 3.18
7593 10132 7.497909 CACAAGTCTTAAGGAAACAAAGTAGGA 59.502 37.037 1.85 0.00 0.00 2.94
7594 10133 7.498239 ACAAGTCTTAAGGAAACAAAGTAGGAC 59.502 37.037 1.85 0.00 0.00 3.85
7595 10134 7.133133 AGTCTTAAGGAAACAAAGTAGGACA 57.867 36.000 1.85 0.00 0.00 4.02
7596 10135 7.217906 AGTCTTAAGGAAACAAAGTAGGACAG 58.782 38.462 1.85 0.00 0.00 3.51
7597 10136 7.070821 AGTCTTAAGGAAACAAAGTAGGACAGA 59.929 37.037 1.85 0.00 0.00 3.41
7598 10137 7.171167 GTCTTAAGGAAACAAAGTAGGACAGAC 59.829 40.741 1.85 0.00 0.00 3.51
7599 10138 3.991367 AGGAAACAAAGTAGGACAGACG 58.009 45.455 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.480419 CGAACAGCAAGAGGAACGATTT 59.520 45.455 0.00 0.00 0.00 2.17
239 240 4.873129 CGTCCGCCCTCGATGTGG 62.873 72.222 8.07 8.07 38.10 4.17
559 967 3.741476 GCTCCACCCGACGTACGT 61.741 66.667 23.04 23.04 40.78 3.57
647 1055 8.868103 TGCTCAATCACATTAATCTCTATCTCT 58.132 33.333 0.00 0.00 0.00 3.10
648 1056 9.486497 TTGCTCAATCACATTAATCTCTATCTC 57.514 33.333 0.00 0.00 0.00 2.75
732 1140 7.884354 ACCGGTTTAGTAATACCTTCATGAAAA 59.116 33.333 9.88 0.00 32.08 2.29
739 1149 4.800471 CGTCACCGGTTTAGTAATACCTTC 59.200 45.833 2.97 0.00 32.08 3.46
744 1154 2.421775 TCGCGTCACCGGTTTAGTAATA 59.578 45.455 2.97 0.00 33.68 0.98
800 1210 0.320683 CATCGCCCTCTCACACAACA 60.321 55.000 0.00 0.00 0.00 3.33
815 1225 1.320555 CACCGAGTTAGTTTCGCATCG 59.679 52.381 0.00 0.00 36.76 3.84
857 1269 3.981071 AGTCCCATCATTTTCGTCTGA 57.019 42.857 0.00 0.00 0.00 3.27
867 1279 5.994054 CGAGTTGATTGAATAGTCCCATCAT 59.006 40.000 3.72 0.00 0.00 2.45
870 1282 5.359194 ACGAGTTGATTGAATAGTCCCAT 57.641 39.130 0.00 0.00 0.00 4.00
957 1369 8.512813 GGGAATGACTATCTACTACCCCTATAT 58.487 40.741 0.00 0.00 0.00 0.86
958 1370 7.692044 AGGGAATGACTATCTACTACCCCTATA 59.308 40.741 0.00 0.00 38.58 1.31
959 1371 6.513260 AGGGAATGACTATCTACTACCCCTAT 59.487 42.308 0.00 0.00 38.58 2.57
960 1372 5.861798 AGGGAATGACTATCTACTACCCCTA 59.138 44.000 0.00 0.00 38.58 3.53
961 1373 4.675550 AGGGAATGACTATCTACTACCCCT 59.324 45.833 0.00 0.00 35.87 4.79
962 1374 5.013258 AGGGAATGACTATCTACTACCCC 57.987 47.826 0.00 0.00 35.87 4.95
963 1375 5.018149 GGAGGGAATGACTATCTACTACCC 58.982 50.000 0.00 0.00 35.53 3.69
964 1376 5.018149 GGGAGGGAATGACTATCTACTACC 58.982 50.000 0.00 0.00 0.00 3.18
965 1377 5.018149 GGGGAGGGAATGACTATCTACTAC 58.982 50.000 0.00 0.00 0.00 2.73
966 1378 4.263816 CGGGGAGGGAATGACTATCTACTA 60.264 50.000 0.00 0.00 0.00 1.82
967 1379 3.500654 CGGGGAGGGAATGACTATCTACT 60.501 52.174 0.00 0.00 0.00 2.57
968 1380 2.826725 CGGGGAGGGAATGACTATCTAC 59.173 54.545 0.00 0.00 0.00 2.59
969 1381 2.822006 GCGGGGAGGGAATGACTATCTA 60.822 54.545 0.00 0.00 0.00 1.98
970 1382 2.016905 CGGGGAGGGAATGACTATCT 57.983 55.000 0.00 0.00 0.00 1.98
971 1383 0.321996 GCGGGGAGGGAATGACTATC 59.678 60.000 0.00 0.00 0.00 2.08
972 1384 1.128188 GGCGGGGAGGGAATGACTAT 61.128 60.000 0.00 0.00 0.00 2.12
973 1385 1.764854 GGCGGGGAGGGAATGACTA 60.765 63.158 0.00 0.00 0.00 2.59
974 1386 3.090532 GGCGGGGAGGGAATGACT 61.091 66.667 0.00 0.00 0.00 3.41
975 1387 4.191015 GGGCGGGGAGGGAATGAC 62.191 72.222 0.00 0.00 0.00 3.06
1108 1581 1.692749 GTGGGAGGAGGCCATGGTA 60.693 63.158 14.67 0.00 0.00 3.25
1150 1686 6.438763 ACATTCGAAACAAGGAAGAACAATC 58.561 36.000 0.00 0.00 0.00 2.67
1172 1972 0.376852 GCACAAGCACAACTCGAACA 59.623 50.000 0.00 0.00 41.58 3.18
1246 2046 0.391263 ATCGGAAAACTCGCAGGGAC 60.391 55.000 0.00 0.00 0.00 4.46
1486 2301 2.637947 CCCTTCTTCTTTGCTAGCTCC 58.362 52.381 17.23 0.00 0.00 4.70
1713 2528 4.086457 TGGAACACAGCATCTCAGTAGTA 58.914 43.478 0.00 0.00 0.00 1.82
1714 2529 2.899900 TGGAACACAGCATCTCAGTAGT 59.100 45.455 0.00 0.00 0.00 2.73
1715 2530 3.599730 TGGAACACAGCATCTCAGTAG 57.400 47.619 0.00 0.00 0.00 2.57
2064 3035 3.385384 CTCGCAGTGCCCTGGAGA 61.385 66.667 10.11 0.00 37.81 3.71
2143 3115 1.470098 CCACAGCAGCCAAGTGTAATC 59.530 52.381 8.82 0.00 0.00 1.75
2376 3349 9.492973 AAAAAGGAAATGAATCACGATTTTGAT 57.507 25.926 0.00 0.00 37.87 2.57
2416 3389 7.768582 TGAGGTATGAAAATACGTGATGAACAT 59.231 33.333 0.00 0.00 0.00 2.71
2568 3541 8.644374 TTTCTACCCAACAAGTTATGCTTAAT 57.356 30.769 0.00 0.00 35.27 1.40
2643 3616 9.262358 CTTTAGAGGTAGGATTTATGCAGTAAC 57.738 37.037 0.00 0.00 0.00 2.50
3016 4022 3.791320 TCTTGGGATGTCTGACTAGGTT 58.209 45.455 9.51 0.00 0.00 3.50
3067 4073 7.710475 TGATTCTGCGATGAGATATGTAAAACA 59.290 33.333 0.00 0.00 0.00 2.83
3248 4261 9.785982 AGAAAAGAAGTTGAAGTAAAGCTAGAT 57.214 29.630 0.00 0.00 0.00 1.98
3737 4751 5.931146 AGCTATCTATGCATGTAAACAGAGC 59.069 40.000 10.16 7.22 0.00 4.09
4022 5045 6.295916 ACATTTTGTAAAGTGGTGGTTTTCCA 60.296 34.615 5.12 0.00 41.71 3.53
4063 5086 2.302260 TGCCACTGTCAAATTTTCGGA 58.698 42.857 6.11 0.00 0.00 4.55
4154 5177 2.139888 TAACGGCCGTTAGCGACACA 62.140 55.000 39.67 22.38 45.17 3.72
4156 5179 1.008361 GTTAACGGCCGTTAGCGACA 61.008 55.000 39.96 27.63 45.17 4.35
4183 5206 1.301716 TTGGTCCAGTCGCTTCAGC 60.302 57.895 0.00 0.00 37.78 4.26
4197 5220 0.545548 GAGAGTGAGGGAGGGTTGGT 60.546 60.000 0.00 0.00 0.00 3.67
4211 5234 1.222567 GAGGGAGAGGGAGAGAGAGT 58.777 60.000 0.00 0.00 0.00 3.24
4228 5578 5.189934 AGTTTACAATAAGTCAGGGAGGGAG 59.810 44.000 0.00 0.00 0.00 4.30
4230 5580 5.437191 AGTTTACAATAAGTCAGGGAGGG 57.563 43.478 0.00 0.00 0.00 4.30
4231 5581 9.462606 AATTAAGTTTACAATAAGTCAGGGAGG 57.537 33.333 0.00 0.00 0.00 4.30
4281 6444 0.320421 GGCGGTGAACAGAGCAGTTA 60.320 55.000 0.00 0.00 0.00 2.24
4282 6445 1.598130 GGCGGTGAACAGAGCAGTT 60.598 57.895 0.00 0.00 0.00 3.16
4283 6446 2.031163 GGCGGTGAACAGAGCAGT 59.969 61.111 0.00 0.00 0.00 4.40
4284 6447 1.302033 AAGGCGGTGAACAGAGCAG 60.302 57.895 0.00 0.00 0.00 4.24
4285 6448 1.597854 CAAGGCGGTGAACAGAGCA 60.598 57.895 0.00 0.00 0.00 4.26
4349 6550 1.024579 TCCTTTTTCTCGCGGGCATC 61.025 55.000 6.13 0.00 0.00 3.91
4382 6583 2.540910 TCACTCCCCTCCCCCTCT 60.541 66.667 0.00 0.00 0.00 3.69
4412 6613 0.947244 AACTGCTCTGTTTGAAGCGG 59.053 50.000 1.78 1.78 39.36 5.52
4526 6727 1.405821 ACCGCACCGAAAATTTGACAA 59.594 42.857 0.00 0.00 0.00 3.18
4585 6786 0.108804 ACCACTTCAGCGTCATACCG 60.109 55.000 0.00 0.00 0.00 4.02
4587 6788 1.337823 ACCACCACTTCAGCGTCATAC 60.338 52.381 0.00 0.00 0.00 2.39
4597 6798 7.151976 AGTAAAATGCATAAAACCACCACTTC 58.848 34.615 0.00 0.00 0.00 3.01
4648 6857 9.736414 ATTAGGGATGAGATCTATGAATTGTTG 57.264 33.333 0.00 0.00 0.00 3.33
4744 6954 4.699522 GACCCCACCACCGCAGTC 62.700 72.222 0.00 0.00 0.00 3.51
5097 7385 4.807304 TCGTGGTTTTAGTTCAAGTCTGAC 59.193 41.667 0.00 0.00 0.00 3.51
5311 7612 8.206189 TCATTGTCTTATGCAATCTATGACTCA 58.794 33.333 11.12 0.00 34.68 3.41
5593 7895 1.303236 CCATGGCTTGTCCGGTTGA 60.303 57.895 0.00 0.00 37.80 3.18
5606 7908 0.987294 ACTGAGGGTGACTTCCATGG 59.013 55.000 4.97 4.97 35.11 3.66
5714 8016 5.751990 CCAATTCAGGATAATGAAGCTTTGC 59.248 40.000 0.00 0.00 42.20 3.68
5715 8017 5.751990 GCCAATTCAGGATAATGAAGCTTTG 59.248 40.000 0.00 0.00 42.20 2.77
5716 8018 5.422970 TGCCAATTCAGGATAATGAAGCTTT 59.577 36.000 0.00 0.00 42.20 3.51
5717 8019 4.957954 TGCCAATTCAGGATAATGAAGCTT 59.042 37.500 0.00 0.00 42.20 3.74
5718 8020 4.539726 TGCCAATTCAGGATAATGAAGCT 58.460 39.130 0.00 0.00 42.20 3.74
5969 8289 0.980231 AGGCCTCTCCATGACAGTCC 60.980 60.000 0.00 0.00 37.29 3.85
5991 8311 3.057104 TCTTGCTGCCATGTGAATTTGAG 60.057 43.478 0.00 0.00 0.00 3.02
6197 8520 2.121948 TGCTTCACTATCCAGATGGCT 58.878 47.619 0.00 0.00 34.44 4.75
6245 8568 4.082895 ACAGCAGCAAATCTGAATCTGTTC 60.083 41.667 0.00 0.00 45.72 3.18
6258 8581 2.057137 AACAGGAAGACAGCAGCAAA 57.943 45.000 0.00 0.00 0.00 3.68
6265 8588 2.072298 GCTGCACTAACAGGAAGACAG 58.928 52.381 0.00 0.00 38.16 3.51
6402 8731 9.003121 TCCAATACAATGGACCTAACAGTAGGG 62.003 44.444 4.86 0.00 44.52 3.53
6483 8816 3.926616 AGAGACGACGACATTTCCAAAT 58.073 40.909 0.00 0.00 0.00 2.32
6592 8940 8.850156 CAGAAAAAGGAAGGTTTCTTTCTGATA 58.150 33.333 17.93 0.00 41.12 2.15
6596 8944 6.194967 TCCAGAAAAAGGAAGGTTTCTTTCT 58.805 36.000 0.00 0.00 41.12 2.52
6597 8945 6.465439 TCCAGAAAAAGGAAGGTTTCTTTC 57.535 37.500 0.00 0.00 41.12 2.62
6604 8952 6.560003 AAATGTTTCCAGAAAAAGGAAGGT 57.440 33.333 0.00 0.00 45.25 3.50
6605 8953 7.254421 CGAAAAATGTTTCCAGAAAAAGGAAGG 60.254 37.037 2.68 0.00 45.25 3.46
6606 8954 7.277760 ACGAAAAATGTTTCCAGAAAAAGGAAG 59.722 33.333 2.68 0.00 45.25 3.46
6607 8955 7.100409 ACGAAAAATGTTTCCAGAAAAAGGAA 58.900 30.769 2.68 0.00 43.13 3.36
6608 8956 6.635755 ACGAAAAATGTTTCCAGAAAAAGGA 58.364 32.000 2.68 0.00 40.13 3.36
6609 8957 6.902224 ACGAAAAATGTTTCCAGAAAAAGG 57.098 33.333 2.68 0.00 40.13 3.11
6654 9021 2.577225 TCGACAGCGAACATATGCG 58.423 52.632 1.58 0.10 44.78 4.73
6684 9051 9.415544 GCTTTCTTGAACATTGTTATCATTCTT 57.584 29.630 1.15 0.00 0.00 2.52
6685 9052 7.752239 CGCTTTCTTGAACATTGTTATCATTCT 59.248 33.333 1.15 0.00 0.00 2.40
6686 9053 7.538678 ACGCTTTCTTGAACATTGTTATCATTC 59.461 33.333 1.15 0.00 0.00 2.67
6687 9054 7.370383 ACGCTTTCTTGAACATTGTTATCATT 58.630 30.769 1.15 0.00 0.00 2.57
6688 9055 6.913170 ACGCTTTCTTGAACATTGTTATCAT 58.087 32.000 1.15 0.00 0.00 2.45
6689 9056 6.312399 ACGCTTTCTTGAACATTGTTATCA 57.688 33.333 1.15 0.00 0.00 2.15
6690 9057 7.623268 AAACGCTTTCTTGAACATTGTTATC 57.377 32.000 1.15 0.00 0.00 1.75
6762 9149 2.028748 ACGCTAAAACTTTCGCCTAGGA 60.029 45.455 14.75 0.00 0.00 2.94
6840 9227 0.249398 ACTTAAGCGCCCTCAACGAT 59.751 50.000 2.29 0.00 0.00 3.73
6844 9231 1.202710 TGAACACTTAAGCGCCCTCAA 60.203 47.619 2.29 0.00 0.00 3.02
6849 9236 2.471370 GCTTTTTGAACACTTAAGCGCC 59.529 45.455 2.29 0.00 32.86 6.53
6903 9290 1.153061 GCCAGGCCTTTATACCCCC 59.847 63.158 0.00 0.00 0.00 5.40
7012 9404 2.641305 AGAATGCATGGAGCTGAGTTC 58.359 47.619 0.00 0.00 45.94 3.01
7110 9609 1.691196 CAGCAGGAGGAACCAAACAA 58.309 50.000 0.00 0.00 42.04 2.83
7120 9619 3.441290 GCAAGCAGCAGCAGGAGG 61.441 66.667 3.17 0.00 45.49 4.30
7138 9654 6.570957 GCATATAAGATAAATGGCAGCTGCAA 60.571 38.462 37.63 30.16 44.36 4.08
7214 9735 6.699575 AATAGCCAAATAACACATGAGGAC 57.300 37.500 0.00 0.00 0.00 3.85
7316 9837 8.334632 AGAATTTGGCTGTTTTTGAATAAAACG 58.665 29.630 8.16 5.22 41.62 3.60
7344 9878 7.601130 GGGATTAAGCGTTTTCTTTAAATTGGT 59.399 33.333 0.00 0.00 0.00 3.67
7355 9891 4.655027 CTTAACCGGGATTAAGCGTTTTC 58.345 43.478 6.32 0.00 35.84 2.29
7382 9919 2.498167 CTTAGAGCAATGGCCGCTTAT 58.502 47.619 5.02 0.80 40.63 1.73
7432 9971 8.347004 TGTATTATCCAATGTTCAAGAAAGCA 57.653 30.769 0.00 0.00 0.00 3.91
7498 10037 9.768662 TCCGTCTAAAAACTTACTAATCAAAGT 57.231 29.630 0.00 0.00 37.54 2.66
7500 10039 9.211485 CCTCCGTCTAAAAACTTACTAATCAAA 57.789 33.333 0.00 0.00 0.00 2.69
7501 10040 7.332678 GCCTCCGTCTAAAAACTTACTAATCAA 59.667 37.037 0.00 0.00 0.00 2.57
7502 10041 6.815142 GCCTCCGTCTAAAAACTTACTAATCA 59.185 38.462 0.00 0.00 0.00 2.57
7503 10042 6.815142 TGCCTCCGTCTAAAAACTTACTAATC 59.185 38.462 0.00 0.00 0.00 1.75
7504 10043 6.704310 TGCCTCCGTCTAAAAACTTACTAAT 58.296 36.000 0.00 0.00 0.00 1.73
7505 10044 6.100404 TGCCTCCGTCTAAAAACTTACTAA 57.900 37.500 0.00 0.00 0.00 2.24
7506 10045 5.726980 TGCCTCCGTCTAAAAACTTACTA 57.273 39.130 0.00 0.00 0.00 1.82
7507 10046 4.612264 TGCCTCCGTCTAAAAACTTACT 57.388 40.909 0.00 0.00 0.00 2.24
7508 10047 5.063564 CAGATGCCTCCGTCTAAAAACTTAC 59.936 44.000 0.00 0.00 35.58 2.34
7509 10048 5.175859 CAGATGCCTCCGTCTAAAAACTTA 58.824 41.667 0.00 0.00 35.58 2.24
7510 10049 4.003648 CAGATGCCTCCGTCTAAAAACTT 58.996 43.478 0.00 0.00 35.58 2.66
7511 10050 3.600388 CAGATGCCTCCGTCTAAAAACT 58.400 45.455 0.00 0.00 35.58 2.66
7512 10051 2.096013 GCAGATGCCTCCGTCTAAAAAC 59.904 50.000 0.00 0.00 35.58 2.43
7513 10052 2.356135 GCAGATGCCTCCGTCTAAAAA 58.644 47.619 0.00 0.00 35.58 1.94
7514 10053 2.024176 GCAGATGCCTCCGTCTAAAA 57.976 50.000 0.00 0.00 35.58 1.52
7515 10054 3.760693 GCAGATGCCTCCGTCTAAA 57.239 52.632 0.00 0.00 35.58 1.85
7526 10065 3.255642 TCAGTTTAAGTTTGGGCAGATGC 59.744 43.478 0.00 0.00 41.14 3.91
7527 10066 4.082571 CCTCAGTTTAAGTTTGGGCAGATG 60.083 45.833 0.00 0.00 0.00 2.90
7528 10067 4.082125 CCTCAGTTTAAGTTTGGGCAGAT 58.918 43.478 0.00 0.00 0.00 2.90
7529 10068 3.486383 CCTCAGTTTAAGTTTGGGCAGA 58.514 45.455 0.00 0.00 0.00 4.26
7530 10069 2.029918 GCCTCAGTTTAAGTTTGGGCAG 60.030 50.000 0.00 0.00 38.35 4.85
7531 10070 1.960689 GCCTCAGTTTAAGTTTGGGCA 59.039 47.619 0.00 0.00 38.35 5.36
7532 10071 1.272490 GGCCTCAGTTTAAGTTTGGGC 59.728 52.381 0.00 0.00 37.82 5.36
7533 10072 2.593026 TGGCCTCAGTTTAAGTTTGGG 58.407 47.619 3.32 0.00 0.00 4.12
7534 10073 4.871933 AATGGCCTCAGTTTAAGTTTGG 57.128 40.909 3.32 0.00 0.00 3.28
7535 10074 6.640907 GTGTAAATGGCCTCAGTTTAAGTTTG 59.359 38.462 3.32 0.00 33.03 2.93
7536 10075 6.322712 TGTGTAAATGGCCTCAGTTTAAGTTT 59.677 34.615 3.32 0.00 33.03 2.66
7537 10076 5.830991 TGTGTAAATGGCCTCAGTTTAAGTT 59.169 36.000 3.32 0.00 33.03 2.66
7538 10077 5.381757 TGTGTAAATGGCCTCAGTTTAAGT 58.618 37.500 3.32 0.00 33.03 2.24
7539 10078 5.957842 TGTGTAAATGGCCTCAGTTTAAG 57.042 39.130 3.32 0.00 33.03 1.85
7540 10079 5.336372 GCATGTGTAAATGGCCTCAGTTTAA 60.336 40.000 3.32 0.00 33.03 1.52
7541 10080 4.157656 GCATGTGTAAATGGCCTCAGTTTA 59.842 41.667 3.32 1.79 33.03 2.01
7542 10081 3.056607 GCATGTGTAAATGGCCTCAGTTT 60.057 43.478 3.32 2.80 33.03 2.66
7543 10082 2.493278 GCATGTGTAAATGGCCTCAGTT 59.507 45.455 3.32 0.00 35.26 3.16
7544 10083 2.094675 GCATGTGTAAATGGCCTCAGT 58.905 47.619 3.32 0.00 0.00 3.41
7545 10084 1.406539 GGCATGTGTAAATGGCCTCAG 59.593 52.381 3.32 0.00 44.98 3.35
7546 10085 1.473258 GGCATGTGTAAATGGCCTCA 58.527 50.000 3.32 0.00 44.98 3.86
7551 10090 3.005684 ACTTGTGTGGCATGTGTAAATGG 59.994 43.478 0.00 0.00 34.66 3.16
7552 10091 4.022935 AGACTTGTGTGGCATGTGTAAATG 60.023 41.667 0.00 0.00 35.88 2.32
7553 10092 4.144297 AGACTTGTGTGGCATGTGTAAAT 58.856 39.130 0.00 0.00 35.88 1.40
7554 10093 3.550820 AGACTTGTGTGGCATGTGTAAA 58.449 40.909 0.00 0.00 35.88 2.01
7555 10094 3.207265 AGACTTGTGTGGCATGTGTAA 57.793 42.857 0.00 0.00 35.88 2.41
7556 10095 2.928801 AGACTTGTGTGGCATGTGTA 57.071 45.000 0.00 0.00 35.88 2.90
7557 10096 2.057137 AAGACTTGTGTGGCATGTGT 57.943 45.000 0.00 0.00 35.88 3.72
7558 10097 3.058016 CCTTAAGACTTGTGTGGCATGTG 60.058 47.826 3.36 0.00 35.88 3.21
7559 10098 3.149196 CCTTAAGACTTGTGTGGCATGT 58.851 45.455 3.36 0.00 38.06 3.21
7560 10099 3.411446 TCCTTAAGACTTGTGTGGCATG 58.589 45.455 3.36 0.00 0.00 4.06
7561 10100 3.788227 TCCTTAAGACTTGTGTGGCAT 57.212 42.857 3.36 0.00 0.00 4.40
7562 10101 3.569194 TTCCTTAAGACTTGTGTGGCA 57.431 42.857 3.36 0.00 0.00 4.92
7563 10102 3.630312 TGTTTCCTTAAGACTTGTGTGGC 59.370 43.478 3.36 0.00 0.00 5.01
7564 10103 5.828299 TTGTTTCCTTAAGACTTGTGTGG 57.172 39.130 3.36 0.00 0.00 4.17
7565 10104 6.852664 ACTTTGTTTCCTTAAGACTTGTGTG 58.147 36.000 3.36 0.00 0.00 3.82
7566 10105 7.282450 CCTACTTTGTTTCCTTAAGACTTGTGT 59.718 37.037 3.36 0.00 0.00 3.72
7567 10106 7.497909 TCCTACTTTGTTTCCTTAAGACTTGTG 59.502 37.037 3.36 0.00 0.00 3.33
7568 10107 7.498239 GTCCTACTTTGTTTCCTTAAGACTTGT 59.502 37.037 3.36 0.00 0.00 3.16
7569 10108 7.497909 TGTCCTACTTTGTTTCCTTAAGACTTG 59.502 37.037 3.36 0.00 0.00 3.16
7570 10109 7.571025 TGTCCTACTTTGTTTCCTTAAGACTT 58.429 34.615 3.36 0.00 0.00 3.01
7571 10110 7.070821 TCTGTCCTACTTTGTTTCCTTAAGACT 59.929 37.037 3.36 0.00 0.00 3.24
7572 10111 7.171167 GTCTGTCCTACTTTGTTTCCTTAAGAC 59.829 40.741 3.36 0.00 0.00 3.01
7573 10112 7.215085 GTCTGTCCTACTTTGTTTCCTTAAGA 58.785 38.462 3.36 0.00 0.00 2.10
7574 10113 6.145696 CGTCTGTCCTACTTTGTTTCCTTAAG 59.854 42.308 0.00 0.00 0.00 1.85
7575 10114 5.987347 CGTCTGTCCTACTTTGTTTCCTTAA 59.013 40.000 0.00 0.00 0.00 1.85
7576 10115 5.535333 CGTCTGTCCTACTTTGTTTCCTTA 58.465 41.667 0.00 0.00 0.00 2.69
7577 10116 4.377897 CGTCTGTCCTACTTTGTTTCCTT 58.622 43.478 0.00 0.00 0.00 3.36
7578 10117 3.991367 CGTCTGTCCTACTTTGTTTCCT 58.009 45.455 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.