Multiple sequence alignment - TraesCS2D01G418200

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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 TraesCS2D01G418200 chr2D 100.000 9167 0 0 1 9167 532185450 532176284 0.000000e+00 16929.0
1 TraesCS2D01G418200 chr2D 93.902 164 4 3 8738 8896 526525121 526524959 9.200000e-60 243.0
2 TraesCS2D01G418200 chr2D 91.716 169 8 4 8734 8897 73403052 73402885 7.160000e-56 230.0
3 TraesCS2D01G418200 chr2D 91.667 168 8 4 8735 8897 367501998 367502164 2.580000e-55 228.0
4 TraesCS2D01G418200 chr2D 90.000 140 12 1 8927 9066 532154706 532154569 7.310000e-41 180.0
5 TraesCS2D01G418200 chr2B 95.317 8819 303 44 1 8739 632173849 632165061 0.000000e+00 13897.0
6 TraesCS2D01G418200 chr2B 94.138 2030 84 18 6637 8640 632012099 632010079 0.000000e+00 3057.0
7 TraesCS2D01G418200 chr2B 96.018 226 6 2 8896 9118 632165062 632164837 1.880000e-96 364.0
8 TraesCS2D01G418200 chr2B 97.391 115 3 0 6518 6632 632018586 632018472 7.260000e-46 196.0
9 TraesCS2D01G418200 chr2B 90.411 146 7 3 8928 9066 632021650 632021505 1.570000e-42 185.0
10 TraesCS2D01G418200 chr2B 83.333 78 11 2 9091 9166 77798797 77798874 4.590000e-08 71.3
11 TraesCS2D01G418200 chr2A 94.126 8239 375 49 562 8738 676722934 676714743 0.000000e+00 12432.0
12 TraesCS2D01G418200 chr2A 88.869 548 33 12 1 521 676723477 676722931 0.000000e+00 649.0
13 TraesCS2D01G418200 chr2A 90.141 142 7 3 9033 9167 676714633 676714492 2.630000e-40 178.0
14 TraesCS2D01G418200 chr2A 92.784 97 2 1 8901 8997 676714721 676714630 1.610000e-27 135.0
15 TraesCS2D01G418200 chr2A 86.747 83 4 7 9087 9166 75292933 75293011 1.640000e-12 86.1
16 TraesCS2D01G418200 chr5B 88.568 796 65 13 5344 6128 530694598 530693818 0.000000e+00 942.0
17 TraesCS2D01G418200 chr5B 91.398 186 13 2 6233 6416 530693825 530693641 1.530000e-62 252.0
18 TraesCS2D01G418200 chr5B 88.571 70 4 4 9100 9166 26866925 26866857 2.120000e-11 82.4
19 TraesCS2D01G418200 chr5D 94.545 165 5 1 8738 8898 436422562 436422398 1.530000e-62 252.0
20 TraesCS2D01G418200 chr5D 89.888 178 11 4 8737 8908 575448 575272 1.200000e-53 222.0
21 TraesCS2D01G418200 chr6A 93.373 166 5 4 8737 8897 5939241 5939077 3.310000e-59 241.0
22 TraesCS2D01G418200 chr6A 91.667 168 8 3 8735 8897 48520206 48520040 2.580000e-55 228.0
23 TraesCS2D01G418200 chr3D 92.727 165 5 4 8738 8897 498263802 498263640 1.990000e-56 231.0
24 TraesCS2D01G418200 chr3B 90.698 172 10 3 8731 8897 428703830 428703660 3.330000e-54 224.0
25 TraesCS2D01G418200 chr6D 89.041 73 6 2 9096 9166 23163223 23163151 1.270000e-13 89.8
26 TraesCS2D01G418200 chr1B 87.838 74 4 5 9096 9166 604034269 604034198 2.120000e-11 82.4


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 TraesCS2D01G418200 chr2D 532176284 532185450 9166 True 16929.0 16929 100.0000 1 9167 1 chr2D.!!$R4 9166
1 TraesCS2D01G418200 chr2B 632164837 632173849 9012 True 7130.5 13897 95.6675 1 9118 2 chr2B.!!$R3 9117
2 TraesCS2D01G418200 chr2B 632010079 632012099 2020 True 3057.0 3057 94.1380 6637 8640 1 chr2B.!!$R1 2003
3 TraesCS2D01G418200 chr2A 676714492 676723477 8985 True 3348.5 12432 91.4800 1 9167 4 chr2A.!!$R1 9166
4 TraesCS2D01G418200 chr5B 530693641 530694598 957 True 597.0 942 89.9830 5344 6416 2 chr5B.!!$R2 1072

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
608 639 0.620556 TCTGGTCCTGATTGGCCTTC 59.379 55.000 3.32 1.19 34.48 3.46 F
611 642 1.034292 GGTCCTGATTGGCCTTCTGC 61.034 60.000 3.32 0.00 40.16 4.26 F
2359 2436 0.480252 AGATAAAGGGGCATGAGGGC 59.520 55.000 0.00 0.00 42.44 5.19 F
3266 3343 0.394488 ATCTTCGCTGGACTCCTCGA 60.394 55.000 8.36 8.36 0.00 4.04 F
3430 3507 0.679505 CACACTCCCGAAGACAGGAA 59.320 55.000 0.00 0.00 0.00 3.36 F
5218 5295 0.038251 TCAGTGCTAAGCTGGTCGTG 60.038 55.000 0.00 0.00 34.89 4.35 F
5413 5490 1.257415 GAAGCTCATGAGACGATTGCG 59.743 52.381 27.04 0.00 44.79 4.85 F
5879 5963 1.525197 TCGTGCACAAACTAAAGAGCG 59.475 47.619 18.64 0.00 0.00 5.03 F
7372 7465 1.683943 GGCATCTGGCTTATTGCTCA 58.316 50.000 0.00 0.00 44.01 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2358 2435 0.524862 CTGATGGTCAACAGCCTTGC 59.475 55.000 0.00 0.0 33.62 4.01 R
2632 2709 4.471025 TGCTCTTCCAGTTTCATCTCCATA 59.529 41.667 0.00 0.0 0.00 2.74 R
4011 4088 0.588252 TTGAGTTTCAAGCTCTGCGC 59.412 50.000 0.00 0.0 31.83 6.09 R
5218 5295 0.251354 TCTCCTGCAGCTCATCAACC 59.749 55.000 8.66 0.0 0.00 3.77 R
5361 5438 3.197766 ACTCTCAATTTCCGCATACCTCA 59.802 43.478 0.00 0.0 0.00 3.86 R
6272 6361 2.092646 TCCAGTGTGCTTTGGTACTTGT 60.093 45.455 0.00 0.0 35.89 3.16 R
7339 7432 2.555325 CAGATGCCTCAGAACAAAGCAA 59.445 45.455 0.00 0.0 36.95 3.91 R
7613 7706 0.676151 AAAGCAGCAGCAGGACTAGC 60.676 55.000 3.17 0.0 45.49 3.42 R
8881 9010 1.001282 ACTCTACTCCCTCCGTTCCT 58.999 55.000 0.00 0.0 0.00 3.36 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
146 147 3.124921 CGCCATTTCGGTCGGCTT 61.125 61.111 0.00 0.00 43.95 4.35
217 233 2.197605 TTGCTGTCGACGAGGACCA 61.198 57.895 11.62 1.19 36.07 4.02
220 236 1.934220 GCTGTCGACGAGGACCATGA 61.934 60.000 11.62 0.00 36.07 3.07
230 246 3.198068 CGAGGACCATGATGTTTCGATT 58.802 45.455 0.00 0.00 31.43 3.34
239 255 2.677836 TGATGTTTCGATTAGGCTGTGC 59.322 45.455 0.00 0.00 0.00 4.57
241 257 1.076332 GTTTCGATTAGGCTGTGCGT 58.924 50.000 0.00 0.00 0.00 5.24
318 337 4.103928 GGGTAGGAGGAGGGGGCA 62.104 72.222 0.00 0.00 0.00 5.36
411 434 2.488153 GTTGCTGGACTATTTGGTGGAC 59.512 50.000 0.00 0.00 0.00 4.02
413 436 2.084546 GCTGGACTATTTGGTGGACAC 58.915 52.381 0.00 0.00 0.00 3.67
465 488 3.149196 TCCAAAATTCAGTGTGAGCTCC 58.851 45.455 12.15 3.09 0.00 4.70
471 494 1.256812 TCAGTGTGAGCTCCGATCAA 58.743 50.000 12.15 0.00 0.00 2.57
472 495 1.067565 TCAGTGTGAGCTCCGATCAAC 60.068 52.381 12.15 1.61 0.00 3.18
473 496 1.067283 CAGTGTGAGCTCCGATCAACT 60.067 52.381 12.15 2.95 0.00 3.16
533 564 4.547367 CGATCCAACCCCGGCCTC 62.547 72.222 0.00 0.00 0.00 4.70
543 574 2.586245 CCGGCCTCTGCATCAAGA 59.414 61.111 0.00 0.00 40.13 3.02
608 639 0.620556 TCTGGTCCTGATTGGCCTTC 59.379 55.000 3.32 1.19 34.48 3.46
611 642 1.034292 GGTCCTGATTGGCCTTCTGC 61.034 60.000 3.32 0.00 40.16 4.26
624 655 1.822990 CCTTCTGCGGAGTTGGTACTA 59.177 52.381 3.10 0.00 33.84 1.82
625 656 2.416972 CCTTCTGCGGAGTTGGTACTAC 60.417 54.545 3.10 0.00 33.84 2.73
626 657 2.211250 TCTGCGGAGTTGGTACTACT 57.789 50.000 3.10 0.00 32.62 2.57
641 672 4.161754 GGTACTACTGCCTTTGACTGGTAT 59.838 45.833 0.00 0.00 0.00 2.73
644 675 4.775780 ACTACTGCCTTTGACTGGTATGTA 59.224 41.667 0.00 0.00 0.00 2.29
646 677 3.055094 ACTGCCTTTGACTGGTATGTAGG 60.055 47.826 0.00 0.00 0.00 3.18
647 678 2.910319 TGCCTTTGACTGGTATGTAGGT 59.090 45.455 0.00 0.00 0.00 3.08
648 679 3.329520 TGCCTTTGACTGGTATGTAGGTT 59.670 43.478 0.00 0.00 0.00 3.50
654 689 4.938028 TGACTGGTATGTAGGTTGTAGGA 58.062 43.478 0.00 0.00 0.00 2.94
881 916 3.960102 GCCTTGATTGGATCCCATTTGTA 59.040 43.478 9.90 0.00 31.53 2.41
891 926 3.260475 TCCCATTTGTAGGTGACATCG 57.740 47.619 0.00 0.00 38.07 3.84
911 946 8.131455 ACATCGTCATTACACATTATCTTGAC 57.869 34.615 0.00 0.00 0.00 3.18
920 955 4.811024 ACACATTATCTTGACGCCTGTATG 59.189 41.667 0.00 0.00 0.00 2.39
955 992 7.557358 TGATGTGAGTATTGATGCCAGTATTTT 59.443 33.333 0.00 0.00 0.00 1.82
968 1005 7.517614 TGCCAGTATTTTCTTGTTGTGAATA 57.482 32.000 0.00 0.00 0.00 1.75
969 1006 8.121305 TGCCAGTATTTTCTTGTTGTGAATAT 57.879 30.769 0.00 0.00 0.00 1.28
996 1033 3.297736 ACGAATACTAAGCTAGTGGCCT 58.702 45.455 3.32 0.00 43.05 5.19
1046 1083 2.283529 GCTCTGGGGAGACGACCAA 61.284 63.158 0.00 0.00 41.86 3.67
1062 1099 2.930682 GACCAATCTTAAGTCGCCTGAC 59.069 50.000 1.63 0.00 45.86 3.51
1091 1128 4.122776 CTGGTAAGGAGAACATTCATCCG 58.877 47.826 0.00 0.00 38.20 4.18
1093 1130 4.712829 TGGTAAGGAGAACATTCATCCGTA 59.287 41.667 0.00 0.00 38.20 4.02
1127 1165 2.230508 TGTCGAGATTCCAGCGTACTTT 59.769 45.455 0.00 0.00 0.00 2.66
1146 1184 7.328493 CGTACTTTCAGAAATGAGTGATGTGTA 59.672 37.037 0.00 0.00 0.00 2.90
1195 1233 7.961855 TGTTTCATTCATGTTCTGTTTTGTTG 58.038 30.769 0.00 0.00 0.00 3.33
1220 1258 3.270877 GGCGTCCAATACTTCTTGATGT 58.729 45.455 0.00 0.00 0.00 3.06
1273 1318 3.364460 TGGGTGGGTGACTGAAATATG 57.636 47.619 0.00 0.00 0.00 1.78
1281 1326 5.009510 TGGGTGACTGAAATATGTTGTTGTG 59.990 40.000 0.00 0.00 0.00 3.33
1305 1350 8.276325 GTGTTCAGTACTTTAGTCATTTGTCAG 58.724 37.037 0.00 0.00 0.00 3.51
1357 1402 9.309516 ACTTGAATATCATTCATTTGAACATGC 57.690 29.630 2.62 0.00 36.80 4.06
1358 1403 8.651391 TTGAATATCATTCATTTGAACATGCC 57.349 30.769 2.62 0.00 36.80 4.40
1359 1404 7.783042 TGAATATCATTCATTTGAACATGCCA 58.217 30.769 0.00 0.00 36.80 4.92
1395 1445 2.035783 GGGCCAAGTGACCCCTTC 59.964 66.667 4.39 0.00 40.56 3.46
1516 1567 1.210155 GAGAATTGTGGTGCGGTGC 59.790 57.895 0.00 0.00 0.00 5.01
1700 1758 9.912634 TGAGGACTTGTTTATTTTTCAATGATC 57.087 29.630 0.00 0.00 0.00 2.92
1899 1976 1.467920 GCAAGTCCCAAAGAGGATGG 58.532 55.000 0.00 0.00 41.22 3.51
1996 2073 9.696917 GAGCTTGAATCTGAAAAGGAAAAATTA 57.303 29.630 0.00 0.00 0.00 1.40
2062 2139 7.516198 AAACAATTCTCTACAAGAAGCACAT 57.484 32.000 0.00 0.00 46.95 3.21
2064 2141 8.621532 AACAATTCTCTACAAGAAGCACATAA 57.378 30.769 0.00 0.00 46.95 1.90
2146 2223 3.616379 GGTCTGAGCTTGAAATCTCGAAG 59.384 47.826 0.00 0.00 32.20 3.79
2286 2363 6.549952 CAGAACTTGATAAGATGCTGGAAAC 58.450 40.000 0.00 0.00 0.00 2.78
2354 2431 3.137176 TCAGGAAGAGATAAAGGGGCATG 59.863 47.826 0.00 0.00 0.00 4.06
2358 2435 2.061061 AGAGATAAAGGGGCATGAGGG 58.939 52.381 0.00 0.00 0.00 4.30
2359 2436 0.480252 AGATAAAGGGGCATGAGGGC 59.520 55.000 0.00 0.00 42.44 5.19
2632 2709 3.188048 CGAAGCTTCTGAGTTTGCAAGAT 59.812 43.478 23.50 0.00 0.00 2.40
2674 2751 4.723309 AGCATGTGAAGGAAAAAGAGACT 58.277 39.130 0.00 0.00 0.00 3.24
3118 3195 7.721286 ATCTGAGAATAAATTAGCCACTTCG 57.279 36.000 0.00 0.00 0.00 3.79
3253 3330 7.194278 AGAAGATGAATGAATTGCAATCTTCG 58.806 34.615 20.85 0.00 44.22 3.79
3259 3336 2.162208 TGAATTGCAATCTTCGCTGGAC 59.838 45.455 13.38 0.00 0.00 4.02
3266 3343 0.394488 ATCTTCGCTGGACTCCTCGA 60.394 55.000 8.36 8.36 0.00 4.04
3278 3355 4.082190 TGGACTCCTCGACATCTAAAACTG 60.082 45.833 0.00 0.00 0.00 3.16
3290 3367 7.410942 CGACATCTAAAACTGAGCTACTTGAAC 60.411 40.741 0.00 0.00 0.00 3.18
3322 3399 5.096443 AGGATCTGACTGACAAATTCTCC 57.904 43.478 0.00 0.00 0.00 3.71
3346 3423 4.156190 CAGCATCAAGAACAAGCTCATTCT 59.844 41.667 6.61 6.61 36.73 2.40
3352 3429 5.766670 TCAAGAACAAGCTCATTCTGTTCAT 59.233 36.000 23.41 13.38 40.68 2.57
3430 3507 0.679505 CACACTCCCGAAGACAGGAA 59.320 55.000 0.00 0.00 0.00 3.36
3788 3865 8.854312 CAAAACTGACAGAAGAAAAAGAAAGTC 58.146 33.333 10.08 0.00 0.00 3.01
3789 3866 7.687941 AACTGACAGAAGAAAAAGAAAGTCA 57.312 32.000 10.08 0.00 34.10 3.41
3954 4031 8.543774 AGAGGAGCTAGAACTGAATTTGAAATA 58.456 33.333 0.00 0.00 0.00 1.40
4225 4302 2.289002 GGCATACAAGGAGAAATCAGCG 59.711 50.000 0.00 0.00 0.00 5.18
4507 4584 1.598962 GCAGCTTGAGCACAGTGGA 60.599 57.895 1.84 0.00 45.16 4.02
4603 4680 1.944177 AGAAGCTCCAGCAAGTAGGA 58.056 50.000 0.48 0.00 45.16 2.94
4759 4836 5.620879 GCTCGAAGCCTTTGAAAATGAGATT 60.621 40.000 0.00 0.00 34.48 2.40
4897 4974 3.871485 AGAGGAACTTGATGCTAAGCTG 58.129 45.455 0.00 0.00 41.55 4.24
5060 5137 4.082408 CAGCTGAATCAAGGAATGCAGAAA 60.082 41.667 8.42 0.00 0.00 2.52
5216 5293 2.015736 AATCAGTGCTAAGCTGGTCG 57.984 50.000 0.00 0.00 34.89 4.79
5218 5295 0.038251 TCAGTGCTAAGCTGGTCGTG 60.038 55.000 0.00 0.00 34.89 4.35
5361 5438 1.949547 GCTCCAGTCTGCTGCTGAATT 60.950 52.381 10.92 0.27 41.26 2.17
5413 5490 1.257415 GAAGCTCATGAGACGATTGCG 59.743 52.381 27.04 0.00 44.79 4.85
5622 5699 3.552875 CTGCTCATGAGGGAACAATCAT 58.447 45.455 23.89 0.00 36.87 2.45
5629 5706 7.206789 TCATGAGGGAACAATCATAAACCTA 57.793 36.000 0.00 0.00 35.10 3.08
5879 5963 1.525197 TCGTGCACAAACTAAAGAGCG 59.475 47.619 18.64 0.00 0.00 5.03
5907 5991 4.828291 CACAACTTGCAGAAACACAAAG 57.172 40.909 0.00 0.00 0.00 2.77
6174 6262 2.426522 CTTAGTGCTGCTTGCCTGTTA 58.573 47.619 0.00 0.00 42.00 2.41
6270 6359 4.341366 TGAAGAGCATGAAGAACTGACA 57.659 40.909 0.00 0.00 0.00 3.58
6272 6361 5.125356 TGAAGAGCATGAAGAACTGACAAA 58.875 37.500 0.00 0.00 0.00 2.83
6313 6402 7.550551 CACTGGAAGAGAAGCAGATGTTAAATA 59.449 37.037 0.00 0.00 37.43 1.40
6441 6532 4.973168 AGAGGCAAATTACAGTGTCTGAA 58.027 39.130 0.00 0.00 35.18 3.02
6508 6599 6.947376 AACTAATTTGGGTCCTACAGTACT 57.053 37.500 0.00 0.00 0.00 2.73
6761 6852 1.883926 ACCAGGTAAATTGGCGTTGTC 59.116 47.619 0.00 0.00 39.39 3.18
6874 6965 3.450904 ACCCTATCTGCTGAACTGGTAA 58.549 45.455 8.79 0.00 0.00 2.85
7265 7357 3.587061 TCACCTGTTACATCTGATGGGTT 59.413 43.478 20.83 3.76 33.60 4.11
7339 7432 7.389232 CCTTCAAATCCTTAAATTTGGAAGCT 58.611 34.615 11.06 0.00 43.64 3.74
7372 7465 1.683943 GGCATCTGGCTTATTGCTCA 58.316 50.000 0.00 0.00 44.01 4.26
7386 7479 6.259608 GCTTATTGCTCAGCTTTCTCTCATTA 59.740 38.462 0.00 0.00 38.95 1.90
7393 7486 6.315891 GCTCAGCTTTCTCTCATTAAGAACAT 59.684 38.462 0.00 0.00 32.64 2.71
7520 7613 9.515226 AATAGCCTTTTCAATCTGTTGTAGTAA 57.485 29.630 0.00 0.00 36.69 2.24
7570 7663 9.399797 TGAAAAGCTGATAGATTCACACAATAT 57.600 29.630 0.00 0.00 0.00 1.28
7590 7683 8.378565 ACAATATCCCCATACTTCACATTAGAG 58.621 37.037 0.00 0.00 0.00 2.43
7601 7694 6.291377 ACTTCACATTAGAGAACTTGCTTCA 58.709 36.000 0.00 0.00 0.00 3.02
7604 7697 3.997021 ACATTAGAGAACTTGCTTCACCG 59.003 43.478 0.00 0.00 0.00 4.94
7613 7706 2.034558 ACTTGCTTCACCGTTGGAATTG 59.965 45.455 0.00 0.00 0.00 2.32
7622 7715 2.009774 CCGTTGGAATTGCTAGTCCTG 58.990 52.381 15.39 5.82 39.29 3.86
7749 7846 4.926238 AGAAACTCGCTCTTGTCAATACAG 59.074 41.667 0.00 0.00 36.83 2.74
7786 7883 3.701040 ACCAAAAATGTGAGCAAGAGTGT 59.299 39.130 0.00 0.00 0.00 3.55
7996 8095 0.539051 AGAATTCAGCCTGGACTCGG 59.461 55.000 8.44 0.00 0.00 4.63
8115 8214 1.272147 GCCTTCAAGTTCATCCTGGGT 60.272 52.381 0.00 0.00 0.00 4.51
8151 8250 1.375523 GGTCATCGGCGTGTTCCTT 60.376 57.895 6.85 0.00 0.00 3.36
8350 8450 1.661112 GAAGTCAGAAATCCGGAAGCG 59.339 52.381 9.01 0.00 0.00 4.68
8352 8452 1.822990 AGTCAGAAATCCGGAAGCGTA 59.177 47.619 9.01 0.00 0.00 4.42
8389 8490 6.718294 TCTCCCTATAGTTTCTTTTTGGGTC 58.282 40.000 0.00 0.00 35.20 4.46
8446 8547 0.034186 TTCCTACCCTTGGCATGCAG 60.034 55.000 21.36 9.17 0.00 4.41
8494 8595 1.001974 TGCTGTCGGTGAGCTTGTATT 59.998 47.619 0.00 0.00 37.35 1.89
8495 8596 2.232696 TGCTGTCGGTGAGCTTGTATTA 59.767 45.455 0.00 0.00 37.35 0.98
8497 8598 3.871594 GCTGTCGGTGAGCTTGTATTAAT 59.128 43.478 0.00 0.00 33.37 1.40
8520 8639 3.735591 TGTAAAAAGGAAGTCCGTCAGG 58.264 45.455 0.00 0.00 42.08 3.86
8579 8698 6.045318 GTGTCATATGCTGTACAATCACTCT 58.955 40.000 0.00 0.00 0.00 3.24
8622 8751 1.333636 TGGGTTGTTGGTTGGCAAGG 61.334 55.000 0.00 0.00 0.00 3.61
8676 8805 8.269317 AGATGGGTTTATCCACTCGTTTATTTA 58.731 33.333 0.00 0.00 39.97 1.40
8687 8816 8.028354 TCCACTCGTTTATTTACTCGTTTGATA 58.972 33.333 0.00 0.00 0.00 2.15
8710 8839 1.971695 GGGGTTCAGGCTTTCACCG 60.972 63.158 0.00 0.00 33.69 4.94
8712 8841 1.896660 GGTTCAGGCTTTCACCGCA 60.897 57.895 0.00 0.00 33.69 5.69
8739 8868 8.850156 ACCATTCATTACTTTCTTGCCATATAC 58.150 33.333 0.00 0.00 0.00 1.47
8743 8872 7.224297 TCATTACTTTCTTGCCATATACTCCC 58.776 38.462 0.00 0.00 0.00 4.30
8744 8873 6.824958 TTACTTTCTTGCCATATACTCCCT 57.175 37.500 0.00 0.00 0.00 4.20
8745 8874 5.297569 ACTTTCTTGCCATATACTCCCTC 57.702 43.478 0.00 0.00 0.00 4.30
8747 8876 2.248248 TCTTGCCATATACTCCCTCCG 58.752 52.381 0.00 0.00 0.00 4.63
8748 8877 1.971357 CTTGCCATATACTCCCTCCGT 59.029 52.381 0.00 0.00 0.00 4.69
8749 8878 2.097110 TGCCATATACTCCCTCCGTT 57.903 50.000 0.00 0.00 0.00 4.44
8750 8879 1.968493 TGCCATATACTCCCTCCGTTC 59.032 52.381 0.00 0.00 0.00 3.95
8752 8881 2.890814 CCATATACTCCCTCCGTTCCT 58.109 52.381 0.00 0.00 0.00 3.36
8753 8882 3.816842 GCCATATACTCCCTCCGTTCCTA 60.817 52.174 0.00 0.00 0.00 2.94
8754 8883 4.413760 CCATATACTCCCTCCGTTCCTAA 58.586 47.826 0.00 0.00 0.00 2.69
8755 8884 4.836736 CCATATACTCCCTCCGTTCCTAAA 59.163 45.833 0.00 0.00 0.00 1.85
8756 8885 5.484290 CCATATACTCCCTCCGTTCCTAAAT 59.516 44.000 0.00 0.00 0.00 1.40
8757 8886 6.666546 CCATATACTCCCTCCGTTCCTAAATA 59.333 42.308 0.00 0.00 0.00 1.40
8759 8888 9.417561 CATATACTCCCTCCGTTCCTAAATATA 57.582 37.037 0.00 0.00 0.00 0.86
8761 8890 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
8762 8891 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
8763 8892 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
8764 8893 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
8765 8894 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
8766 8895 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
8767 8896 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
8809 8938 7.684937 GACTACAGTCGGATGTATATACCTT 57.315 40.000 10.38 0.00 35.21 3.50
8810 8939 8.108551 GACTACAGTCGGATGTATATACCTTT 57.891 38.462 10.38 0.00 35.21 3.11
8811 8940 8.474710 ACTACAGTCGGATGTATATACCTTTT 57.525 34.615 10.38 0.00 35.21 2.27
8812 8941 9.578576 ACTACAGTCGGATGTATATACCTTTTA 57.421 33.333 10.38 0.00 35.21 1.52
8814 8943 8.701908 ACAGTCGGATGTATATACCTTTTAGA 57.298 34.615 10.38 0.59 0.00 2.10
8815 8944 8.794553 ACAGTCGGATGTATATACCTTTTAGAG 58.205 37.037 10.38 0.00 0.00 2.43
8816 8945 8.794553 CAGTCGGATGTATATACCTTTTAGAGT 58.205 37.037 10.38 3.36 0.00 3.24
8829 8958 9.710818 ATACCTTTTAGAGTATAGGTTCACTCA 57.289 33.333 0.00 0.00 42.99 3.41
8830 8959 8.611051 ACCTTTTAGAGTATAGGTTCACTCAT 57.389 34.615 4.70 0.00 42.99 2.90
8831 8960 9.047947 ACCTTTTAGAGTATAGGTTCACTCATT 57.952 33.333 4.70 0.00 42.99 2.57
8832 8961 9.892130 CCTTTTAGAGTATAGGTTCACTCATTT 57.108 33.333 4.70 0.00 42.99 2.32
8835 8964 8.718102 TTAGAGTATAGGTTCACTCATTTTGC 57.282 34.615 4.70 0.00 42.99 3.68
8836 8965 6.951971 AGAGTATAGGTTCACTCATTTTGCT 58.048 36.000 4.70 0.00 42.99 3.91
8837 8966 7.398024 AGAGTATAGGTTCACTCATTTTGCTT 58.602 34.615 4.70 0.00 42.99 3.91
8838 8967 7.550906 AGAGTATAGGTTCACTCATTTTGCTTC 59.449 37.037 4.70 0.00 42.99 3.86
8839 8968 3.904136 AGGTTCACTCATTTTGCTTCG 57.096 42.857 0.00 0.00 0.00 3.79
8840 8969 3.214328 AGGTTCACTCATTTTGCTTCGT 58.786 40.909 0.00 0.00 0.00 3.85
8841 8970 4.385825 AGGTTCACTCATTTTGCTTCGTA 58.614 39.130 0.00 0.00 0.00 3.43
8842 8971 5.003804 AGGTTCACTCATTTTGCTTCGTAT 58.996 37.500 0.00 0.00 0.00 3.06
8843 8972 5.088739 GGTTCACTCATTTTGCTTCGTATG 58.911 41.667 0.00 0.00 0.00 2.39
8844 8973 5.334879 GGTTCACTCATTTTGCTTCGTATGT 60.335 40.000 0.00 0.00 0.00 2.29
8845 8974 6.128391 GGTTCACTCATTTTGCTTCGTATGTA 60.128 38.462 0.00 0.00 0.00 2.29
8846 8975 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
8847 8976 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
8848 8977 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
8849 8978 6.311445 CACTCATTTTGCTTCGTATGTAGTCT 59.689 38.462 0.00 0.00 0.00 3.24
8850 8979 7.488150 CACTCATTTTGCTTCGTATGTAGTCTA 59.512 37.037 0.00 0.00 0.00 2.59
8851 8980 8.198109 ACTCATTTTGCTTCGTATGTAGTCTAT 58.802 33.333 0.00 0.00 0.00 1.98
8852 8981 9.678941 CTCATTTTGCTTCGTATGTAGTCTATA 57.321 33.333 0.00 0.00 0.00 1.31
8853 8982 9.678941 TCATTTTGCTTCGTATGTAGTCTATAG 57.321 33.333 0.00 0.00 0.00 1.31
8854 8983 9.464714 CATTTTGCTTCGTATGTAGTCTATAGT 57.535 33.333 0.00 0.00 0.00 2.12
8855 8984 8.851960 TTTTGCTTCGTATGTAGTCTATAGTG 57.148 34.615 0.00 0.00 0.00 2.74
8856 8985 7.797038 TTGCTTCGTATGTAGTCTATAGTGA 57.203 36.000 0.00 0.00 0.00 3.41
8857 8986 7.422878 TGCTTCGTATGTAGTCTATAGTGAG 57.577 40.000 0.00 0.00 0.00 3.51
8858 8987 7.215085 TGCTTCGTATGTAGTCTATAGTGAGA 58.785 38.462 0.00 0.00 0.00 3.27
8859 8988 7.713942 TGCTTCGTATGTAGTCTATAGTGAGAA 59.286 37.037 0.00 0.00 0.00 2.87
8860 8989 8.723311 GCTTCGTATGTAGTCTATAGTGAGAAT 58.277 37.037 0.00 0.00 0.00 2.40
8862 8991 9.999660 TTCGTATGTAGTCTATAGTGAGAATCT 57.000 33.333 0.00 0.00 34.92 2.40
8863 8992 9.642327 TCGTATGTAGTCTATAGTGAGAATCTC 57.358 37.037 2.75 2.75 34.92 2.75
8864 8993 9.647797 CGTATGTAGTCTATAGTGAGAATCTCT 57.352 37.037 11.92 0.00 42.35 3.10
8891 9020 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
8892 9021 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
8893 9022 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
8894 9023 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
8895 9024 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
8896 9025 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
8907 9036 3.118445 ACGGAGGGAGTAGAGTACTGTAC 60.118 52.174 19.81 19.81 39.59 2.90
9000 9130 4.083110 GGCGAATGGATCTGGTCATATTTG 60.083 45.833 0.00 0.00 0.00 2.32
9122 9261 8.479313 AGAAAGTCCAAAACAAAATTGAACTC 57.521 30.769 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.564027 GGGCGGCGATTCAGTTCG 61.564 66.667 12.98 0.00 41.99 3.95
74 75 4.556233 CGGCAGAATCGGAGTGATAATTA 58.444 43.478 0.00 0.00 35.84 1.40
82 83 3.077556 AGGCGGCAGAATCGGAGT 61.078 61.111 13.08 0.00 0.00 3.85
146 147 2.508439 GGAGCGAAATCGTGCGGA 60.508 61.111 4.59 0.00 42.22 5.54
217 233 3.313526 GCACAGCCTAATCGAAACATCAT 59.686 43.478 0.00 0.00 0.00 2.45
220 236 1.665679 CGCACAGCCTAATCGAAACAT 59.334 47.619 0.00 0.00 0.00 2.71
230 246 2.279502 GATCGGACACGCACAGCCTA 62.280 60.000 0.00 0.00 40.69 3.93
318 337 2.835431 CTCCCTCCCACGATCGCT 60.835 66.667 16.60 0.00 0.00 4.93
411 434 1.577328 CCAGCCTACCAAACGCAGTG 61.577 60.000 0.00 0.00 45.00 3.66
413 436 2.040544 CCCAGCCTACCAAACGCAG 61.041 63.158 0.00 0.00 0.00 5.18
478 501 7.837863 AGTAGTCGATTGAGTATTTTTCTCCA 58.162 34.615 0.69 0.00 32.77 3.86
484 507 8.827177 TCAACAAGTAGTCGATTGAGTATTTT 57.173 30.769 3.59 0.00 30.14 1.82
543 574 1.884464 CGTATGGCTGTGCGCATCT 60.884 57.895 15.91 0.00 41.67 2.90
552 583 0.891373 AGGATCCGATCGTATGGCTG 59.109 55.000 15.09 0.00 0.00 4.85
608 639 1.736032 GCAGTAGTACCAACTCCGCAG 60.736 57.143 0.00 0.00 37.15 5.18
611 642 1.183549 AGGCAGTAGTACCAACTCCG 58.816 55.000 0.00 0.00 37.15 4.63
624 655 3.055094 CCTACATACCAGTCAAAGGCAGT 60.055 47.826 0.00 0.00 0.00 4.40
625 656 3.055094 ACCTACATACCAGTCAAAGGCAG 60.055 47.826 0.00 0.00 0.00 4.85
626 657 2.910319 ACCTACATACCAGTCAAAGGCA 59.090 45.455 0.00 0.00 0.00 4.75
641 672 8.450434 TCCTGTATACATATCCTACAACCTACA 58.550 37.037 5.91 0.00 0.00 2.74
644 675 8.232412 TCTTCCTGTATACATATCCTACAACCT 58.768 37.037 5.91 0.00 0.00 3.50
646 677 9.915629 CTTCTTCCTGTATACATATCCTACAAC 57.084 37.037 5.91 0.00 0.00 3.32
647 678 9.877222 TCTTCTTCCTGTATACATATCCTACAA 57.123 33.333 5.91 0.00 0.00 2.41
881 916 3.953712 TGTGTAATGACGATGTCACCT 57.046 42.857 1.11 0.00 45.65 4.00
891 926 5.523916 AGGCGTCAAGATAATGTGTAATGAC 59.476 40.000 0.00 0.00 34.01 3.06
911 946 2.486918 TCATGAATGAGCATACAGGCG 58.513 47.619 0.00 0.00 39.27 5.52
920 955 6.856135 TCAATACTCACATCATGAATGAGC 57.144 37.500 27.92 0.00 43.04 4.26
955 992 7.722795 TTCGTTTCTGATATTCACAACAAGA 57.277 32.000 0.00 0.00 0.00 3.02
968 1005 7.203910 CCACTAGCTTAGTATTCGTTTCTGAT 58.796 38.462 0.00 0.00 37.23 2.90
969 1006 6.561614 CCACTAGCTTAGTATTCGTTTCTGA 58.438 40.000 0.00 0.00 37.23 3.27
996 1033 1.339438 GCCTGTTCTGCTTCCATCTCA 60.339 52.381 0.00 0.00 0.00 3.27
1046 1083 1.816835 TCGTGTCAGGCGACTTAAGAT 59.183 47.619 10.09 0.00 43.06 2.40
1062 1099 4.188247 TGTTCTCCTTACCAGAATCGTG 57.812 45.455 0.00 0.00 32.50 4.35
1091 1128 2.592194 TCGACATGCACTCGACTTTAC 58.408 47.619 13.04 0.00 35.26 2.01
1093 1130 1.269723 TCTCGACATGCACTCGACTTT 59.730 47.619 13.04 0.00 35.26 2.66
1127 1165 8.699130 AGATATGTACACATCACTCATTTCTGA 58.301 33.333 16.19 0.00 37.76 3.27
1175 1213 7.181418 CCAAACAACAAAACAGAACATGAATG 58.819 34.615 0.00 0.00 0.00 2.67
1186 1224 1.272490 TGGACGCCAAACAACAAAACA 59.728 42.857 0.00 0.00 0.00 2.83
1228 1266 4.023291 ACATGTTCAGAAACCACACCTTT 58.977 39.130 0.00 0.00 34.28 3.11
1231 1269 4.385358 AAACATGTTCAGAAACCACACC 57.615 40.909 12.39 0.00 34.28 4.16
1273 1318 7.298507 TGACTAAAGTACTGAACACAACAAC 57.701 36.000 0.00 0.00 0.00 3.32
1281 1326 8.366671 ACTGACAAATGACTAAAGTACTGAAC 57.633 34.615 0.00 0.00 0.00 3.18
1305 1350 7.437748 ACTAGCAGAGACCAATGTATATGAAC 58.562 38.462 0.00 0.00 26.27 3.18
1311 1356 6.607600 TCAAGTACTAGCAGAGACCAATGTAT 59.392 38.462 0.00 0.00 0.00 2.29
1312 1357 5.949952 TCAAGTACTAGCAGAGACCAATGTA 59.050 40.000 0.00 0.00 0.00 2.29
1353 1398 6.259167 CCCATTTTCATTACAGAAATGGCATG 59.741 38.462 17.37 0.00 44.42 4.06
1354 1399 6.350906 CCCATTTTCATTACAGAAATGGCAT 58.649 36.000 17.37 0.00 44.42 4.40
1355 1400 5.338219 CCCCATTTTCATTACAGAAATGGCA 60.338 40.000 17.37 0.00 44.42 4.92
1356 1401 5.118286 CCCCATTTTCATTACAGAAATGGC 58.882 41.667 17.37 0.00 44.42 4.40
1357 1402 5.673514 CCCCCATTTTCATTACAGAAATGG 58.326 41.667 16.33 16.33 44.42 3.16
1358 1403 5.118286 GCCCCCATTTTCATTACAGAAATG 58.882 41.667 0.00 0.00 45.47 2.32
1359 1404 4.164030 GGCCCCCATTTTCATTACAGAAAT 59.836 41.667 0.00 0.00 37.35 2.17
1487 1538 7.011950 CCGCACCACAATTCTCAATACTAATAA 59.988 37.037 0.00 0.00 0.00 1.40
1488 1539 6.481976 CCGCACCACAATTCTCAATACTAATA 59.518 38.462 0.00 0.00 0.00 0.98
1489 1540 5.296780 CCGCACCACAATTCTCAATACTAAT 59.703 40.000 0.00 0.00 0.00 1.73
1516 1567 5.008415 GTCTGAAAGTTATGCTGATCATGGG 59.992 44.000 0.00 0.00 33.99 4.00
1720 1778 7.427989 AGACATTGGCATATTTGGAATTTCT 57.572 32.000 0.00 0.00 0.00 2.52
1786 1863 4.262164 GGTGTTTCCTTCACATGCTGATTT 60.262 41.667 0.00 0.00 37.52 2.17
1791 1868 1.133513 TGGGTGTTTCCTTCACATGCT 60.134 47.619 0.00 0.00 37.52 3.79
1837 1914 4.019411 TCATCTACCAGCTCAAAACCATCA 60.019 41.667 0.00 0.00 0.00 3.07
1899 1976 4.279420 AGGTGGCAGATTCTGAAGTTTTTC 59.721 41.667 17.87 0.00 32.44 2.29
1963 2040 7.884877 TCCTTTTCAGATTCAAGCTCTTCAATA 59.115 33.333 0.00 0.00 0.00 1.90
1996 2073 4.008330 CTGCTTCTGTCATGTCCTTCATT 58.992 43.478 0.00 0.00 34.09 2.57
2039 2116 8.621532 TTATGTGCTTCTTGTAGAGAATTGTT 57.378 30.769 0.00 0.00 43.23 2.83
2146 2223 4.439837 GCCTCAATTTCTTGAATCCTCTGC 60.440 45.833 0.00 0.00 40.78 4.26
2286 2363 2.807967 TCTTTCATGTTCAACTGAGCCG 59.192 45.455 0.00 0.00 0.00 5.52
2350 2427 1.980772 AACAGCCTTGCCCTCATGC 60.981 57.895 0.00 0.00 0.00 4.06
2354 2431 1.973812 GGTCAACAGCCTTGCCCTC 60.974 63.158 0.00 0.00 0.00 4.30
2358 2435 0.524862 CTGATGGTCAACAGCCTTGC 59.475 55.000 0.00 0.00 33.62 4.01
2632 2709 4.471025 TGCTCTTCCAGTTTCATCTCCATA 59.529 41.667 0.00 0.00 0.00 2.74
2674 2751 4.222810 TGCTTCTCCAATGTAGCTTCACTA 59.777 41.667 0.00 0.00 34.77 2.74
2809 2886 2.359214 CTCTTCAGCCTGACGTAGCATA 59.641 50.000 0.00 0.00 0.00 3.14
2854 2931 0.179205 GCGACAATGCTTCTGACAGC 60.179 55.000 0.00 5.31 40.55 4.40
3102 3179 6.170506 TGTTCACTCGAAGTGGCTAATTTAT 58.829 36.000 12.89 0.00 45.94 1.40
3118 3195 4.574828 TCCAGCAACTTTACTTGTTCACTC 59.425 41.667 0.00 0.00 0.00 3.51
3226 3303 7.883391 AGATTGCAATTCATTCATCTTCTCT 57.117 32.000 14.33 0.00 0.00 3.10
3253 3330 1.681538 TAGATGTCGAGGAGTCCAGC 58.318 55.000 12.86 1.64 0.00 4.85
3259 3336 4.109050 GCTCAGTTTTAGATGTCGAGGAG 58.891 47.826 0.00 0.00 0.00 3.69
3266 3343 7.217200 TGTTCAAGTAGCTCAGTTTTAGATGT 58.783 34.615 0.00 0.00 0.00 3.06
3278 3355 5.178438 CCTTGACTTCTTGTTCAAGTAGCTC 59.822 44.000 15.51 12.93 38.22 4.09
3315 3392 4.038271 TGTTCTTGATGCTGGGAGAATT 57.962 40.909 0.00 0.00 31.52 2.17
3322 3399 2.156917 TGAGCTTGTTCTTGATGCTGG 58.843 47.619 0.00 0.00 33.83 4.85
3346 3423 9.076781 TCCAATTCAATACTTCTTTCATGAACA 57.923 29.630 7.89 0.00 30.46 3.18
3352 3429 8.924511 AACTCTCCAATTCAATACTTCTTTCA 57.075 30.769 0.00 0.00 0.00 2.69
3368 3445 5.559770 TGATGTATGAAGCAAACTCTCCAA 58.440 37.500 0.00 0.00 0.00 3.53
3430 3507 1.544314 GCTTCAAGTTCCTGCTCCAGT 60.544 52.381 0.00 0.00 0.00 4.00
3788 3865 1.511850 TCAGCAATGGTGTTCTCGTG 58.488 50.000 12.41 0.00 32.43 4.35
3789 3866 2.027745 AGATCAGCAATGGTGTTCTCGT 60.028 45.455 17.32 0.28 35.93 4.18
3954 4031 8.270030 TGGATTCAGTGTGAAGATCATTAAGAT 58.730 33.333 0.00 0.00 40.05 2.40
4011 4088 0.588252 TTGAGTTTCAAGCTCTGCGC 59.412 50.000 0.00 0.00 31.83 6.09
4603 4680 4.038642 GTCTCCTTCTGAGTCAAGTTGTCT 59.961 45.833 2.05 2.05 42.12 3.41
4759 4836 1.937191 TGGTGGTCTCATGAGTAGCA 58.063 50.000 21.92 19.30 0.00 3.49
4799 4876 2.411904 CTTTGACTCAGCACTGGAGAC 58.588 52.381 0.00 0.00 36.26 3.36
4831 4908 3.426568 GCCGTGCTCTCAGCCAAC 61.427 66.667 0.00 0.00 41.51 3.77
4897 4974 1.503542 CAGTTCATGAAGCACGGCC 59.496 57.895 8.80 0.00 0.00 6.13
5060 5137 3.829948 CTTCACGCATTTGAGCTTCAAT 58.170 40.909 0.00 0.00 36.11 2.57
5216 5293 0.321919 TCCTGCAGCTCATCAACCAC 60.322 55.000 8.66 0.00 0.00 4.16
5218 5295 0.251354 TCTCCTGCAGCTCATCAACC 59.749 55.000 8.66 0.00 0.00 3.77
5361 5438 3.197766 ACTCTCAATTTCCGCATACCTCA 59.802 43.478 0.00 0.00 0.00 3.86
5413 5490 7.604545 AGGTCTGTAACTTCAGCTTCTTTATTC 59.395 37.037 0.00 0.00 35.63 1.75
5569 5646 1.876156 ACAGCTTCTTCCTTTTCAGCG 59.124 47.619 0.00 0.00 35.53 5.18
5629 5706 2.418368 TTCTTGTGTGCACCTCTGTT 57.582 45.000 15.69 0.00 0.00 3.16
5907 5991 3.130340 TGTCTGGAAAAGTTCAACCTTGC 59.870 43.478 0.00 0.00 0.00 4.01
6174 6262 6.998074 TGGTATGAGAAATATTTCGAAGCCAT 59.002 34.615 19.86 18.64 41.92 4.40
6249 6338 4.341366 TGTCAGTTCTTCATGCTCTTCA 57.659 40.909 0.00 0.00 0.00 3.02
6270 6359 3.130340 CCAGTGTGCTTTGGTACTTGTTT 59.870 43.478 0.00 0.00 0.00 2.83
6272 6361 2.092646 TCCAGTGTGCTTTGGTACTTGT 60.093 45.455 0.00 0.00 35.89 3.16
6441 6532 6.146760 AGATACCTCCTCCATGTATTTCAGT 58.853 40.000 0.00 0.00 0.00 3.41
6444 6535 6.831976 ACAAGATACCTCCTCCATGTATTTC 58.168 40.000 0.00 0.00 0.00 2.17
6592 6683 3.552699 CAGTTGTTTCAACTTGCATGGTG 59.447 43.478 11.29 11.29 0.00 4.17
6839 6930 6.069963 AGCAGATAGGGTTGACAGTAAGAAAT 60.070 38.462 0.00 0.00 0.00 2.17
7265 7357 5.536161 GCTGCCTTAATCTTGGATCCATAAA 59.464 40.000 17.06 4.37 0.00 1.40
7339 7432 2.555325 CAGATGCCTCAGAACAAAGCAA 59.445 45.455 0.00 0.00 36.95 3.91
7372 7465 7.826252 TGCTTATGTTCTTAATGAGAGAAAGCT 59.174 33.333 0.00 0.00 37.36 3.74
7386 7479 6.204301 CCTTCGATCATGATGCTTATGTTCTT 59.796 38.462 14.30 0.00 0.00 2.52
7393 7486 3.758755 AGCCTTCGATCATGATGCTTA 57.241 42.857 14.30 0.00 0.00 3.09
7520 7613 9.599866 TCATCGTCAAGAATTTGTAAGTATGAT 57.400 29.630 0.00 0.00 35.73 2.45
7529 7622 5.916883 CAGCTTTTCATCGTCAAGAATTTGT 59.083 36.000 0.00 0.00 35.73 2.83
7532 7625 5.947228 TCAGCTTTTCATCGTCAAGAATT 57.053 34.783 0.00 0.00 0.00 2.17
7545 7638 9.875675 GATATTGTGTGAATCTATCAGCTTTTC 57.124 33.333 0.00 0.00 39.19 2.29
7570 7663 5.964477 AGTTCTCTAATGTGAAGTATGGGGA 59.036 40.000 0.00 0.00 30.39 4.81
7590 7683 1.305201 TCCAACGGTGAAGCAAGTTC 58.695 50.000 0.00 0.00 35.48 3.01
7601 7694 1.628846 AGGACTAGCAATTCCAACGGT 59.371 47.619 0.39 0.00 33.92 4.83
7604 7697 2.421424 CAGCAGGACTAGCAATTCCAAC 59.579 50.000 0.39 0.00 33.92 3.77
7613 7706 0.676151 AAAGCAGCAGCAGGACTAGC 60.676 55.000 3.17 0.00 45.49 3.42
7622 7715 3.565905 ATAAAGTGTCAAAGCAGCAGC 57.434 42.857 0.00 0.00 42.56 5.25
7767 7864 5.581126 TCAACACTCTTGCTCACATTTTT 57.419 34.783 0.00 0.00 0.00 1.94
7786 7883 5.309543 TCCTGTACCTTCTTCTCCATTTCAA 59.690 40.000 0.00 0.00 0.00 2.69
7996 8095 2.116366 CTGTTTGTTTTGCGGTGCTAC 58.884 47.619 0.00 0.00 0.00 3.58
8115 8214 3.233980 ACTGACAGCAGGGCGACA 61.234 61.111 1.25 0.00 46.60 4.35
8151 8250 2.092049 TCGGCACTAGTATCTCCTTCCA 60.092 50.000 0.00 0.00 0.00 3.53
8350 8450 4.828072 AGGGAGAACTCACCAAGAATAC 57.172 45.455 0.08 0.00 32.15 1.89
8352 8452 6.206042 ACTATAGGGAGAACTCACCAAGAAT 58.794 40.000 4.43 0.00 32.15 2.40
8446 8547 3.396260 AATTGCATGCATATGGCCTTC 57.604 42.857 23.37 0.00 43.89 3.46
8494 8595 7.040961 CCTGACGGACTTCCTTTTTACAAATTA 60.041 37.037 0.00 0.00 0.00 1.40
8495 8596 6.238925 CCTGACGGACTTCCTTTTTACAAATT 60.239 38.462 0.00 0.00 0.00 1.82
8497 8598 4.577283 CCTGACGGACTTCCTTTTTACAAA 59.423 41.667 0.00 0.00 0.00 2.83
8676 8805 4.019681 TGAACCCCATCTTATCAAACGAGT 60.020 41.667 0.00 0.00 0.00 4.18
8687 8816 1.428912 TGAAAGCCTGAACCCCATCTT 59.571 47.619 0.00 0.00 0.00 2.40
8710 8839 4.627035 GGCAAGAAAGTAATGAATGGTTGC 59.373 41.667 0.00 0.00 37.60 4.17
8712 8841 6.610075 ATGGCAAGAAAGTAATGAATGGTT 57.390 33.333 0.00 0.00 0.00 3.67
8739 8868 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
8741 8870 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
8769 8898 9.440784 CGACTGTAGTCTTTATAGTGAAATCTC 57.559 37.037 10.05 0.00 42.66 2.75
8770 8899 8.407064 CCGACTGTAGTCTTTATAGTGAAATCT 58.593 37.037 10.05 0.00 42.66 2.40
8771 8900 8.404000 TCCGACTGTAGTCTTTATAGTGAAATC 58.596 37.037 10.05 0.00 42.66 2.17
8772 8901 8.289939 TCCGACTGTAGTCTTTATAGTGAAAT 57.710 34.615 10.05 0.00 42.66 2.17
8773 8902 7.692460 TCCGACTGTAGTCTTTATAGTGAAA 57.308 36.000 10.05 0.00 42.66 2.69
8774 8903 7.338703 ACATCCGACTGTAGTCTTTATAGTGAA 59.661 37.037 10.05 0.00 42.66 3.18
8775 8904 6.827251 ACATCCGACTGTAGTCTTTATAGTGA 59.173 38.462 10.05 0.00 42.66 3.41
8776 8905 7.028926 ACATCCGACTGTAGTCTTTATAGTG 57.971 40.000 10.05 2.94 42.66 2.74
8777 8906 8.921353 ATACATCCGACTGTAGTCTTTATAGT 57.079 34.615 10.05 4.42 42.66 2.12
8781 8910 9.224267 GGTATATACATCCGACTGTAGTCTTTA 57.776 37.037 14.70 0.00 42.66 1.85
8782 8911 7.943447 AGGTATATACATCCGACTGTAGTCTTT 59.057 37.037 14.70 0.00 42.66 2.52
8783 8912 7.460071 AGGTATATACATCCGACTGTAGTCTT 58.540 38.462 14.70 0.00 42.66 3.01
8784 8913 7.018487 AGGTATATACATCCGACTGTAGTCT 57.982 40.000 14.70 0.00 42.66 3.24
8785 8914 7.684937 AAGGTATATACATCCGACTGTAGTC 57.315 40.000 14.70 1.92 41.47 2.59
8786 8915 8.474710 AAAAGGTATATACATCCGACTGTAGT 57.525 34.615 14.70 0.00 35.21 2.73
8788 8917 9.797642 TCTAAAAGGTATATACATCCGACTGTA 57.202 33.333 14.70 0.46 36.14 2.74
8789 8918 8.701908 TCTAAAAGGTATATACATCCGACTGT 57.298 34.615 14.70 0.00 0.00 3.55
8790 8919 8.794553 ACTCTAAAAGGTATATACATCCGACTG 58.205 37.037 14.70 2.28 0.00 3.51
8791 8920 8.937207 ACTCTAAAAGGTATATACATCCGACT 57.063 34.615 14.70 0.00 0.00 4.18
8803 8932 9.710818 TGAGTGAACCTATACTCTAAAAGGTAT 57.289 33.333 0.00 0.00 41.51 2.73
8804 8933 9.710818 ATGAGTGAACCTATACTCTAAAAGGTA 57.289 33.333 0.00 0.00 41.51 3.08
8805 8934 8.611051 ATGAGTGAACCTATACTCTAAAAGGT 57.389 34.615 0.00 0.00 44.24 3.50
8806 8935 9.892130 AAATGAGTGAACCTATACTCTAAAAGG 57.108 33.333 0.00 0.00 42.86 3.11
8809 8938 9.162764 GCAAAATGAGTGAACCTATACTCTAAA 57.837 33.333 0.00 0.00 42.86 1.85
8810 8939 8.540388 AGCAAAATGAGTGAACCTATACTCTAA 58.460 33.333 0.00 0.00 42.86 2.10
8811 8940 8.079211 AGCAAAATGAGTGAACCTATACTCTA 57.921 34.615 0.00 0.00 42.86 2.43
8812 8941 6.951971 AGCAAAATGAGTGAACCTATACTCT 58.048 36.000 0.00 0.00 42.86 3.24
8813 8942 7.464710 CGAAGCAAAATGAGTGAACCTATACTC 60.465 40.741 0.00 0.00 42.77 2.59
8814 8943 6.313905 CGAAGCAAAATGAGTGAACCTATACT 59.686 38.462 0.00 0.00 0.00 2.12
8815 8944 6.092259 ACGAAGCAAAATGAGTGAACCTATAC 59.908 38.462 0.00 0.00 0.00 1.47
8816 8945 6.170506 ACGAAGCAAAATGAGTGAACCTATA 58.829 36.000 0.00 0.00 0.00 1.31
8817 8946 5.003804 ACGAAGCAAAATGAGTGAACCTAT 58.996 37.500 0.00 0.00 0.00 2.57
8818 8947 4.385825 ACGAAGCAAAATGAGTGAACCTA 58.614 39.130 0.00 0.00 0.00 3.08
8819 8948 3.214328 ACGAAGCAAAATGAGTGAACCT 58.786 40.909 0.00 0.00 0.00 3.50
8820 8949 3.626028 ACGAAGCAAAATGAGTGAACC 57.374 42.857 0.00 0.00 0.00 3.62
8821 8950 5.689819 ACATACGAAGCAAAATGAGTGAAC 58.310 37.500 0.00 0.00 0.00 3.18
8822 8951 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
8823 8952 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
8824 8953 6.311445 AGACTACATACGAAGCAAAATGAGTG 59.689 38.462 0.00 0.00 0.00 3.51
8825 8954 6.398918 AGACTACATACGAAGCAAAATGAGT 58.601 36.000 0.00 0.00 0.00 3.41
8826 8955 6.893958 AGACTACATACGAAGCAAAATGAG 57.106 37.500 0.00 0.00 0.00 2.90
8827 8956 9.678941 CTATAGACTACATACGAAGCAAAATGA 57.321 33.333 0.00 0.00 0.00 2.57
8828 8957 9.464714 ACTATAGACTACATACGAAGCAAAATG 57.535 33.333 6.78 0.00 0.00 2.32
8829 8958 9.464714 CACTATAGACTACATACGAAGCAAAAT 57.535 33.333 6.78 0.00 0.00 1.82
8830 8959 8.680001 TCACTATAGACTACATACGAAGCAAAA 58.320 33.333 6.78 0.00 0.00 2.44
8831 8960 8.217131 TCACTATAGACTACATACGAAGCAAA 57.783 34.615 6.78 0.00 0.00 3.68
8832 8961 7.713942 TCTCACTATAGACTACATACGAAGCAA 59.286 37.037 6.78 0.00 0.00 3.91
8833 8962 7.215085 TCTCACTATAGACTACATACGAAGCA 58.785 38.462 6.78 0.00 0.00 3.91
8834 8963 7.655236 TCTCACTATAGACTACATACGAAGC 57.345 40.000 6.78 0.00 0.00 3.86
8836 8965 9.999660 AGATTCTCACTATAGACTACATACGAA 57.000 33.333 6.78 0.00 0.00 3.85
8837 8966 9.642327 GAGATTCTCACTATAGACTACATACGA 57.358 37.037 6.78 0.00 0.00 3.43
8838 8967 9.647797 AGAGATTCTCACTATAGACTACATACG 57.352 37.037 15.83 0.00 32.06 3.06
8866 8995 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
8867 8996 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
8868 8997 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
8869 8998 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
8870 8999 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
8871 9000 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
8872 9001 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
8873 9002 7.529555 TCTACTCCCTCCGTTCCTAAATATAA 58.470 38.462 0.00 0.00 0.00 0.98
8874 9003 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
8875 9004 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
8876 9005 5.103771 ACTCTACTCCCTCCGTTCCTAAATA 60.104 44.000 0.00 0.00 0.00 1.40
8877 9006 4.216708 CTCTACTCCCTCCGTTCCTAAAT 58.783 47.826 0.00 0.00 0.00 1.40
8878 9007 3.011032 ACTCTACTCCCTCCGTTCCTAAA 59.989 47.826 0.00 0.00 0.00 1.85
8879 9008 2.579860 ACTCTACTCCCTCCGTTCCTAA 59.420 50.000 0.00 0.00 0.00 2.69
8880 9009 2.203584 ACTCTACTCCCTCCGTTCCTA 58.796 52.381 0.00 0.00 0.00 2.94
8881 9010 1.001282 ACTCTACTCCCTCCGTTCCT 58.999 55.000 0.00 0.00 0.00 3.36
8882 9011 2.092484 AGTACTCTACTCCCTCCGTTCC 60.092 54.545 0.00 0.00 32.47 3.62
8883 9012 2.944349 CAGTACTCTACTCCCTCCGTTC 59.056 54.545 0.00 0.00 36.76 3.95
8884 9013 2.308275 ACAGTACTCTACTCCCTCCGTT 59.692 50.000 0.00 0.00 36.76 4.44
8885 9014 1.914798 ACAGTACTCTACTCCCTCCGT 59.085 52.381 0.00 0.00 36.76 4.69
8886 9015 2.713863 ACAGTACTCTACTCCCTCCG 57.286 55.000 0.00 0.00 36.76 4.63
8887 9016 3.459227 AGGTACAGTACTCTACTCCCTCC 59.541 52.174 10.62 0.00 36.76 4.30
8888 9017 4.080413 ACAGGTACAGTACTCTACTCCCTC 60.080 50.000 10.62 0.00 36.76 4.30
8889 9018 3.851374 ACAGGTACAGTACTCTACTCCCT 59.149 47.826 10.62 0.00 36.76 4.20
8890 9019 4.233632 ACAGGTACAGTACTCTACTCCC 57.766 50.000 10.62 0.00 36.76 4.30
8891 9020 5.588246 GGTTACAGGTACAGTACTCTACTCC 59.412 48.000 10.62 4.25 36.76 3.85
8892 9021 5.293079 CGGTTACAGGTACAGTACTCTACTC 59.707 48.000 10.62 0.00 36.76 2.59
8893 9022 5.181748 CGGTTACAGGTACAGTACTCTACT 58.818 45.833 10.62 0.00 40.28 2.57
8894 9023 4.201861 GCGGTTACAGGTACAGTACTCTAC 60.202 50.000 10.62 0.00 27.63 2.59
8895 9024 3.941483 GCGGTTACAGGTACAGTACTCTA 59.059 47.826 10.62 0.00 27.63 2.43
8896 9025 2.751806 GCGGTTACAGGTACAGTACTCT 59.248 50.000 10.62 3.60 27.63 3.24
9122 9261 6.312180 AGGGTTTAATTTAGCTTTCGTCTACG 59.688 38.462 0.00 0.00 41.45 3.51
9140 9279 8.713708 TTTCAGGATTACAAATTCAGGGTTTA 57.286 30.769 0.00 0.00 0.00 2.01
9141 9280 7.610580 TTTCAGGATTACAAATTCAGGGTTT 57.389 32.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.