Multiple sequence alignment - TraesCS3D01G391300

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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 TraesCS3D01G391300 chr3D 100.000 8361 0 0 1 8361 506179602 506171242 0.000000e+00 15440.0
1 TraesCS3D01G391300 chr3D 90.909 88 8 0 5322 5409 506174196 506174109 1.470000e-22 119.0
2 TraesCS3D01G391300 chr3D 90.909 88 8 0 5407 5494 506174281 506174194 1.470000e-22 119.0
3 TraesCS3D01G391300 chr3B 95.953 3435 77 11 2473 5848 668074888 668071457 0.000000e+00 5517.0
4 TraesCS3D01G391300 chr3B 93.938 2293 82 31 15 2290 668077132 668074880 0.000000e+00 3411.0
5 TraesCS3D01G391300 chr3B 94.079 1959 92 13 5843 7791 668071492 668069548 0.000000e+00 2953.0
6 TraesCS3D01G391300 chr3B 93.401 197 12 1 2279 2475 170337653 170337848 2.950000e-74 291.0
7 TraesCS3D01G391300 chr3B 93.401 197 12 1 2279 2475 429456125 429456320 2.950000e-74 291.0
8 TraesCS3D01G391300 chr3A 95.114 2804 70 15 2473 5211 644809045 644806244 0.000000e+00 4357.0
9 TraesCS3D01G391300 chr3A 92.172 2210 106 31 19 2198 644811426 644809254 0.000000e+00 3061.0
10 TraesCS3D01G391300 chr3A 95.043 1957 68 16 5843 7791 644805518 644803583 0.000000e+00 3049.0
11 TraesCS3D01G391300 chr3A 96.406 640 21 2 5210 5848 644806121 644805483 0.000000e+00 1053.0
12 TraesCS3D01G391300 chr3A 98.936 94 1 0 2197 2290 644809130 644809037 1.440000e-37 169.0
13 TraesCS3D01G391300 chr3A 90.909 88 8 0 5407 5494 644806009 644805922 1.470000e-22 119.0
14 TraesCS3D01G391300 chr3A 89.773 88 9 0 5322 5409 644805924 644805837 6.860000e-21 113.0
15 TraesCS3D01G391300 chr4D 95.833 576 23 1 7787 8361 450646077 450646652 0.000000e+00 929.0
16 TraesCS3D01G391300 chr5B 93.056 576 39 1 7787 8361 642347092 642346517 0.000000e+00 841.0
17 TraesCS3D01G391300 chr5B 88.889 576 44 5 7787 8361 642007527 642008083 0.000000e+00 691.0
18 TraesCS3D01G391300 chr5B 86.995 569 73 1 7794 8361 425720048 425719480 2.540000e-179 640.0
19 TraesCS3D01G391300 chr5B 86.643 569 75 1 7794 8361 437604916 437604348 5.510000e-176 628.0
20 TraesCS3D01G391300 chr5B 87.027 555 71 1 7808 8361 437575624 437575070 7.130000e-175 625.0
21 TraesCS3D01G391300 chr4B 89.410 576 59 2 7787 8361 28743695 28743121 0.000000e+00 725.0
22 TraesCS3D01G391300 chr1D 87.500 576 70 2 7787 8361 31909007 31908433 0.000000e+00 664.0
23 TraesCS3D01G391300 chr6B 86.596 567 75 1 7796 8361 179722046 179721480 7.130000e-175 625.0
24 TraesCS3D01G391300 chr2B 95.722 187 8 0 2289 2475 370571370 370571184 1.360000e-77 302.0
25 TraesCS3D01G391300 chr2B 96.875 32 0 1 5212 5243 247388936 247388966 1.500000e-02 52.8
26 TraesCS3D01G391300 chr1B 95.722 187 8 0 2289 2475 228468345 228468531 1.360000e-77 302.0
27 TraesCS3D01G391300 chr1B 93.401 197 12 1 2279 2475 63310799 63310994 2.950000e-74 291.0
28 TraesCS3D01G391300 chr6A 93.103 203 11 3 2282 2482 494463089 494463290 2.280000e-75 294.0
29 TraesCS3D01G391300 chr6A 90.566 212 17 3 2272 2481 537876464 537876254 2.300000e-70 278.0
30 TraesCS3D01G391300 chr5A 93.467 199 12 1 2285 2482 29678144 29678342 2.280000e-75 294.0
31 TraesCS3D01G391300 chr7A 79.007 443 81 10 2779 3216 33888200 33887765 8.210000e-75 292.0
32 TraesCS3D01G391300 chr7B 92.647 204 12 3 2282 2484 94186869 94187070 2.950000e-74 291.0
33 TraesCS3D01G391300 chr7D 78.808 453 74 12 2779 3216 33435938 33435493 1.370000e-72 285.0


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 TraesCS3D01G391300 chr3D 506171242 506179602 8360 True 15440.000000 15440 100.000000 1 8361 1 chr3D.!!$R1 8360
1 TraesCS3D01G391300 chr3B 668069548 668077132 7584 True 3960.333333 5517 94.656667 15 7791 3 chr3B.!!$R1 7776
2 TraesCS3D01G391300 chr3A 644803583 644811426 7843 True 1703.000000 4357 94.050429 19 7791 7 chr3A.!!$R1 7772
3 TraesCS3D01G391300 chr4D 450646077 450646652 575 False 929.000000 929 95.833000 7787 8361 1 chr4D.!!$F1 574
4 TraesCS3D01G391300 chr5B 642346517 642347092 575 True 841.000000 841 93.056000 7787 8361 1 chr5B.!!$R4 574
5 TraesCS3D01G391300 chr5B 642007527 642008083 556 False 691.000000 691 88.889000 7787 8361 1 chr5B.!!$F1 574
6 TraesCS3D01G391300 chr5B 425719480 425720048 568 True 640.000000 640 86.995000 7794 8361 1 chr5B.!!$R1 567
7 TraesCS3D01G391300 chr5B 437604348 437604916 568 True 628.000000 628 86.643000 7794 8361 1 chr5B.!!$R3 567
8 TraesCS3D01G391300 chr5B 437575070 437575624 554 True 625.000000 625 87.027000 7808 8361 1 chr5B.!!$R2 553
9 TraesCS3D01G391300 chr4B 28743121 28743695 574 True 725.000000 725 89.410000 7787 8361 1 chr4B.!!$R1 574
10 TraesCS3D01G391300 chr1D 31908433 31909007 574 True 664.000000 664 87.500000 7787 8361 1 chr1D.!!$R1 574
11 TraesCS3D01G391300 chr6B 179721480 179722046 566 True 625.000000 625 86.596000 7796 8361 1 chr6B.!!$R1 565

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
408 424 0.108585 CTCTCCCTCTCCCTCTCTCG 59.891 65.000 0.00 0.00 0.00 4.04 F
868 899 0.109132 GCTTCAGCCCAATTTGGTCG 60.109 55.000 14.26 1.26 35.17 4.79 F
1131 1162 1.365633 GGAGATCTACCAGCTGCCG 59.634 63.158 8.66 0.00 0.00 5.69 F
2627 2803 1.001633 ACGTTCTCTGCATTACCGGTT 59.998 47.619 15.04 0.00 0.00 4.44 F
3601 3816 2.224843 TGATGGACAAATCAGGTGCAGT 60.225 45.455 0.00 0.00 39.98 4.40 F
4169 4385 2.299013 TCTCTCGTACACTGCCAACATT 59.701 45.455 0.00 0.00 0.00 2.71 F
5436 5833 0.251354 AGCACTGGAATGATCGCAGT 59.749 50.000 0.00 0.00 37.48 4.40 F
7052 7481 0.037790 GCTTCAAGCACTCGAGGACT 60.038 55.000 18.41 10.57 41.89 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1335 1.067142 CGGGTTGGATTTCTCGAGACA 60.067 52.381 16.36 9.65 0.00 3.41 R
2608 2784 1.659098 GAACCGGTAATGCAGAGAACG 59.341 52.381 8.00 0.00 0.00 3.95 R
2631 2807 2.168521 TCCTATGACAGTACTTGCTGGC 59.831 50.000 0.00 0.00 44.53 4.85 R
4488 4704 0.036952 CACTCTGCGACCCATTGACT 60.037 55.000 0.00 0.00 0.00 3.41 R
5417 5814 0.251354 ACTGCGATCATTCCAGTGCT 59.749 50.000 4.99 0.00 38.32 4.40 R
5913 6342 0.250513 AACACCTTCTCCGAGATGGC 59.749 55.000 23.94 0.00 41.75 4.40 R
7070 7499 0.551879 TTTCTGGTCCGTTTTCCCCA 59.448 50.000 0.00 0.00 0.00 4.96 R
8281 8723 0.179134 CCATCTCCCACTCGTCGAAC 60.179 60.000 0.00 0.00 0.00 3.95 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
53 54 2.040278 CCCACCTGTCAGATTCCAGAAA 59.960 50.000 0.00 0.00 0.00 2.52
161 163 3.793144 CAACGCGCTTGCCTCTCC 61.793 66.667 5.73 0.00 34.11 3.71
163 165 4.749310 ACGCGCTTGCCTCTCCTG 62.749 66.667 5.73 0.00 34.11 3.86
164 166 4.441695 CGCGCTTGCCTCTCCTGA 62.442 66.667 5.56 0.00 34.11 3.86
165 167 2.511145 GCGCTTGCCTCTCCTGAG 60.511 66.667 0.00 0.00 39.92 3.35
166 168 2.511145 CGCTTGCCTCTCCTGAGC 60.511 66.667 0.00 0.00 38.93 4.26
167 169 2.988800 GCTTGCCTCTCCTGAGCT 59.011 61.111 0.00 0.00 38.93 4.09
168 170 1.449956 GCTTGCCTCTCCTGAGCTG 60.450 63.158 0.00 0.00 38.93 4.24
169 171 1.981636 CTTGCCTCTCCTGAGCTGT 59.018 57.895 0.00 0.00 38.93 4.40
170 172 0.391395 CTTGCCTCTCCTGAGCTGTG 60.391 60.000 0.00 0.00 38.93 3.66
171 173 2.125188 GCCTCTCCTGAGCTGTGC 60.125 66.667 0.00 0.00 38.93 4.57
172 174 2.583520 CCTCTCCTGAGCTGTGCC 59.416 66.667 0.00 0.00 38.93 5.01
173 175 2.583520 CTCTCCTGAGCTGTGCCC 59.416 66.667 0.00 0.00 33.12 5.36
248 250 0.691413 CTAGTCCTCCTCCAACCCCC 60.691 65.000 0.00 0.00 0.00 5.40
249 251 1.160289 TAGTCCTCCTCCAACCCCCT 61.160 60.000 0.00 0.00 0.00 4.79
384 400 3.470888 CCACCGGATTCGCCCTCT 61.471 66.667 9.46 0.00 34.56 3.69
385 401 2.107141 CACCGGATTCGCCCTCTC 59.893 66.667 9.46 0.00 34.56 3.20
386 402 2.042843 ACCGGATTCGCCCTCTCT 60.043 61.111 9.46 0.00 34.56 3.10
387 403 2.128507 ACCGGATTCGCCCTCTCTC 61.129 63.158 9.46 0.00 34.56 3.20
388 404 2.731374 CGGATTCGCCCTCTCTCC 59.269 66.667 0.00 0.00 0.00 3.71
389 405 2.862223 CGGATTCGCCCTCTCTCCC 61.862 68.421 0.00 0.00 0.00 4.30
390 406 1.458588 GGATTCGCCCTCTCTCCCT 60.459 63.158 0.00 0.00 0.00 4.20
391 407 1.468506 GGATTCGCCCTCTCTCCCTC 61.469 65.000 0.00 0.00 0.00 4.30
392 408 0.469144 GATTCGCCCTCTCTCCCTCT 60.469 60.000 0.00 0.00 0.00 3.69
400 416 0.478507 CTCTCTCCCTCTCCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
402 418 0.998945 CTCTCCCTCTCCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
405 421 0.996762 TCCCTCTCCCTCTCCCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
408 424 0.108585 CTCTCCCTCTCCCTCTCTCG 59.891 65.000 0.00 0.00 0.00 4.04
414 430 2.218115 CTCTCCCTCTCTCGGGTGGT 62.218 65.000 0.00 0.00 44.95 4.16
428 444 1.447314 GTGGTTGGATCCGTCGTCC 60.447 63.158 7.39 5.50 36.26 4.79
429 445 2.202703 GGTTGGATCCGTCGTCCG 60.203 66.667 7.39 0.00 38.64 4.79
430 446 2.884207 GTTGGATCCGTCGTCCGC 60.884 66.667 7.39 0.00 38.64 5.54
431 447 4.485834 TTGGATCCGTCGTCCGCG 62.486 66.667 7.39 0.00 38.64 6.46
440 456 4.268939 TCGTCCGCGGTTCGTTGT 62.269 61.111 30.94 0.00 38.89 3.32
445 461 2.664436 CCGCGGTTCGTTGTTCTCC 61.664 63.158 19.50 0.00 36.19 3.71
446 462 2.664436 CGCGGTTCGTTGTTCTCCC 61.664 63.158 0.00 0.00 0.00 4.30
448 464 0.883370 GCGGTTCGTTGTTCTCCCTT 60.883 55.000 0.00 0.00 0.00 3.95
460 476 0.840722 TCTCCCTTGTGTTCCCCTCC 60.841 60.000 0.00 0.00 0.00 4.30
516 534 4.377471 CGCGATCTGAGTTGCGTA 57.623 55.556 0.00 0.00 44.81 4.42
517 535 2.199152 CGCGATCTGAGTTGCGTAG 58.801 57.895 0.00 0.00 44.81 3.51
518 536 1.202973 CGCGATCTGAGTTGCGTAGG 61.203 60.000 0.00 0.00 44.81 3.18
519 537 0.872021 GCGATCTGAGTTGCGTAGGG 60.872 60.000 0.00 0.00 0.00 3.53
526 544 0.173708 GAGTTGCGTAGGGAGGACAG 59.826 60.000 0.00 0.00 0.00 3.51
547 565 4.513318 CAGTGGTTCTGAGGAAAAAGAGTC 59.487 45.833 0.00 0.00 46.27 3.36
676 694 4.489771 CCCGGGGAATTCGCTGCT 62.490 66.667 22.57 0.00 34.25 4.24
776 801 2.095461 TGATCTCAACCGAGTCTCCAG 58.905 52.381 0.00 0.00 40.44 3.86
868 899 0.109132 GCTTCAGCCCAATTTGGTCG 60.109 55.000 14.26 1.26 35.17 4.79
897 928 4.599047 AGAGAGTTCAGTTCTTGGAGTG 57.401 45.455 0.00 0.00 0.00 3.51
906 937 2.709125 TTCTTGGAGTGGCCGTCGTG 62.709 60.000 0.00 0.00 40.66 4.35
907 938 4.980805 TTGGAGTGGCCGTCGTGC 62.981 66.667 0.00 0.00 40.66 5.34
924 955 3.066814 CCAAAGAGGGCAGGCAGC 61.067 66.667 0.00 0.00 44.65 5.25
929 960 4.039092 GAGGGCAGGCAGCTGGAA 62.039 66.667 17.12 0.00 44.79 3.53
951 982 2.229039 CAGTTGTGCTGTCTCACCG 58.771 57.895 0.00 0.00 40.27 4.94
1131 1162 1.365633 GGAGATCTACCAGCTGCCG 59.634 63.158 8.66 0.00 0.00 5.69
1170 1202 3.192466 GCCTGCTAGCATTCCAATTTTG 58.808 45.455 19.72 1.84 0.00 2.44
1171 1203 6.424923 TGCCTGCTAGCATTCCAATTTTGG 62.425 45.833 19.72 12.67 43.20 3.28
1196 1228 7.124298 GGAATCATGGTAGTATAGTCCTGCATA 59.876 40.741 0.00 0.00 0.00 3.14
1223 1255 3.864583 GTGTGTTGCATTCAAATGTGTGT 59.135 39.130 4.76 0.00 38.65 3.72
1302 1335 3.555168 GGATCGGGAAACTCTGCGATTAT 60.555 47.826 0.00 0.00 0.00 1.28
1359 1396 1.672881 CATTCGCATCCTCCCTGTTTC 59.327 52.381 0.00 0.00 0.00 2.78
1383 1420 5.138276 TCTTACTATATCGTGTGGCCTCTT 58.862 41.667 3.32 0.00 0.00 2.85
1386 1423 5.197682 ACTATATCGTGTGGCCTCTTAAC 57.802 43.478 3.32 0.00 0.00 2.01
1391 1428 3.071479 TCGTGTGGCCTCTTAACAATTC 58.929 45.455 3.32 0.00 0.00 2.17
1699 1736 4.156556 TGCATTTGTGACTAATCTTGGCTC 59.843 41.667 0.00 0.00 0.00 4.70
2031 2068 3.624300 CGCCTTCGATCTGCTGCG 61.624 66.667 0.00 2.91 38.10 5.18
2118 2155 3.002791 CTGTCGTATGTTTGCCAGTCAT 58.997 45.455 0.00 0.00 0.00 3.06
2119 2156 3.407698 TGTCGTATGTTTGCCAGTCATT 58.592 40.909 0.00 0.00 0.00 2.57
2120 2157 3.818210 TGTCGTATGTTTGCCAGTCATTT 59.182 39.130 0.00 0.00 0.00 2.32
2121 2158 4.998033 TGTCGTATGTTTGCCAGTCATTTA 59.002 37.500 0.00 0.00 0.00 1.40
2122 2159 5.470437 TGTCGTATGTTTGCCAGTCATTTAA 59.530 36.000 0.00 0.00 0.00 1.52
2123 2160 6.021596 GTCGTATGTTTGCCAGTCATTTAAG 58.978 40.000 0.00 0.00 0.00 1.85
2130 2167 4.040936 TGCCAGTCATTTAAGGGCTTAA 57.959 40.909 0.00 0.00 44.85 1.85
2283 2445 7.876068 AGGTTTTCAACAGATAACGAGACATTA 59.124 33.333 0.00 0.00 0.00 1.90
2284 2446 8.665685 GGTTTTCAACAGATAACGAGACATTAT 58.334 33.333 0.00 0.00 0.00 1.28
2315 2477 9.591792 TCAGTTTGTCTAATTCACATCTAGATG 57.408 33.333 27.63 27.63 44.15 2.90
2342 2504 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
2343 2505 6.544928 TTAAGGATGTCACATCTAAGCTCA 57.455 37.500 17.46 0.00 0.00 4.26
2344 2506 4.399004 AGGATGTCACATCTAAGCTCAC 57.601 45.455 17.46 0.00 0.00 3.51
2345 2507 3.771479 AGGATGTCACATCTAAGCTCACA 59.229 43.478 17.46 0.00 0.00 3.58
2346 2508 3.868077 GGATGTCACATCTAAGCTCACAC 59.132 47.826 17.46 0.00 0.00 3.82
2347 2509 4.498241 GATGTCACATCTAAGCTCACACA 58.502 43.478 10.81 0.00 0.00 3.72
2348 2510 4.335400 TGTCACATCTAAGCTCACACAA 57.665 40.909 0.00 0.00 0.00 3.33
2349 2511 4.702831 TGTCACATCTAAGCTCACACAAA 58.297 39.130 0.00 0.00 0.00 2.83
2350 2512 5.308014 TGTCACATCTAAGCTCACACAAAT 58.692 37.500 0.00 0.00 0.00 2.32
2351 2513 6.463360 TGTCACATCTAAGCTCACACAAATA 58.537 36.000 0.00 0.00 0.00 1.40
2352 2514 7.105588 TGTCACATCTAAGCTCACACAAATAT 58.894 34.615 0.00 0.00 0.00 1.28
2353 2515 8.257306 TGTCACATCTAAGCTCACACAAATATA 58.743 33.333 0.00 0.00 0.00 0.86
2354 2516 9.265901 GTCACATCTAAGCTCACACAAATATAT 57.734 33.333 0.00 0.00 0.00 0.86
2360 2522 9.777297 TCTAAGCTCACACAAATATATAATGCA 57.223 29.630 0.00 0.00 0.00 3.96
2363 2525 8.224389 AGCTCACACAAATATATAATGCAACA 57.776 30.769 0.00 0.00 0.00 3.33
2364 2526 8.685427 AGCTCACACAAATATATAATGCAACAA 58.315 29.630 0.00 0.00 0.00 2.83
2365 2527 8.745837 GCTCACACAAATATATAATGCAACAAC 58.254 33.333 0.00 0.00 0.00 3.32
2366 2528 9.786105 CTCACACAAATATATAATGCAACAACA 57.214 29.630 0.00 0.00 0.00 3.33
2422 2584 4.410492 CACAAACAGAGTGGACATTAGC 57.590 45.455 0.00 0.00 33.43 3.09
2423 2585 4.067896 CACAAACAGAGTGGACATTAGCT 58.932 43.478 0.00 0.00 33.43 3.32
2424 2586 4.516698 CACAAACAGAGTGGACATTAGCTT 59.483 41.667 0.00 0.00 33.43 3.74
2425 2587 5.700832 CACAAACAGAGTGGACATTAGCTTA 59.299 40.000 0.00 0.00 33.43 3.09
2426 2588 5.934625 ACAAACAGAGTGGACATTAGCTTAG 59.065 40.000 0.00 0.00 0.00 2.18
2427 2589 6.166279 CAAACAGAGTGGACATTAGCTTAGA 58.834 40.000 0.00 0.00 0.00 2.10
2428 2590 6.552445 AACAGAGTGGACATTAGCTTAGAT 57.448 37.500 0.00 0.00 0.00 1.98
2429 2591 5.911752 ACAGAGTGGACATTAGCTTAGATG 58.088 41.667 0.00 0.00 0.00 2.90
2430 2592 5.423610 ACAGAGTGGACATTAGCTTAGATGT 59.576 40.000 9.09 9.09 39.09 3.06
2431 2593 5.752472 CAGAGTGGACATTAGCTTAGATGTG 59.248 44.000 12.89 0.00 36.67 3.21
2432 2594 5.658634 AGAGTGGACATTAGCTTAGATGTGA 59.341 40.000 12.89 0.46 36.67 3.58
2433 2595 5.665459 AGTGGACATTAGCTTAGATGTGAC 58.335 41.667 12.89 9.81 36.67 3.67
2434 2596 5.187772 AGTGGACATTAGCTTAGATGTGACA 59.812 40.000 12.89 9.63 36.67 3.58
2435 2597 6.051717 GTGGACATTAGCTTAGATGTGACAT 58.948 40.000 12.89 0.00 36.67 3.06
2436 2598 7.069950 AGTGGACATTAGCTTAGATGTGACATA 59.930 37.037 12.89 0.00 36.67 2.29
2437 2599 7.710907 GTGGACATTAGCTTAGATGTGACATAA 59.289 37.037 12.89 0.00 36.67 1.90
2438 2600 7.710907 TGGACATTAGCTTAGATGTGACATAAC 59.289 37.037 12.89 0.00 36.67 1.89
2439 2601 7.928706 GGACATTAGCTTAGATGTGACATAACT 59.071 37.037 12.89 0.00 36.67 2.24
2440 2602 9.967346 GACATTAGCTTAGATGTGACATAACTA 57.033 33.333 12.89 0.00 36.67 2.24
2470 2632 5.916661 TCTAGATGTGTCCTAGACAAACC 57.083 43.478 0.00 0.00 44.49 3.27
2471 2633 3.983044 AGATGTGTCCTAGACAAACCC 57.017 47.619 0.00 0.00 44.49 4.11
2472 2634 3.521727 AGATGTGTCCTAGACAAACCCT 58.478 45.455 0.00 0.00 44.49 4.34
2473 2635 3.910627 AGATGTGTCCTAGACAAACCCTT 59.089 43.478 0.00 0.00 44.49 3.95
2539 2701 2.134346 ACAATTTTTGTGCATCGTGCC 58.866 42.857 7.38 1.16 44.23 5.01
2627 2803 1.001633 ACGTTCTCTGCATTACCGGTT 59.998 47.619 15.04 0.00 0.00 4.44
2631 2807 2.972625 TCTCTGCATTACCGGTTCTTG 58.027 47.619 15.04 9.70 0.00 3.02
2669 2845 7.069578 TGTCATAGGAGTAGGAGTGATTAAACC 59.930 40.741 0.00 0.00 0.00 3.27
2981 3195 4.469945 AGGATCATCGGTTAGTGGAAAGAA 59.530 41.667 0.00 0.00 0.00 2.52
2985 3199 7.041984 GGATCATCGGTTAGTGGAAAGAAATAC 60.042 40.741 0.00 0.00 0.00 1.89
2988 3202 7.333423 TCATCGGTTAGTGGAAAGAAATACAAG 59.667 37.037 0.00 0.00 0.00 3.16
3153 3367 6.043012 AGCATCTCAGACTGGCTATCTAATTT 59.957 38.462 1.81 0.00 32.09 1.82
3331 3546 6.047870 GCTGATACAATGTGAGATCTTCTGT 58.952 40.000 0.00 0.00 0.00 3.41
3361 3576 4.339247 ACATTTTTAGATAGCAATGCGCCT 59.661 37.500 4.18 0.00 44.04 5.52
3541 3756 5.070001 CCACAATTACTGGTCTCCTGAAAA 58.930 41.667 0.00 0.00 0.00 2.29
3545 3760 4.993705 TTACTGGTCTCCTGAAAATGGT 57.006 40.909 0.00 0.00 0.00 3.55
3601 3816 2.224843 TGATGGACAAATCAGGTGCAGT 60.225 45.455 0.00 0.00 39.98 4.40
3871 4086 4.935205 TCAGTAACAATAGCGAGTGCAATT 59.065 37.500 0.00 0.00 46.23 2.32
4169 4385 2.299013 TCTCTCGTACACTGCCAACATT 59.701 45.455 0.00 0.00 0.00 2.71
4320 4536 9.151177 AGGACATCAATATTAATTGGCATTTCT 57.849 29.630 0.00 0.00 42.40 2.52
4431 4647 3.078837 ACACCGTGTTTTATCCACCATC 58.921 45.455 0.00 0.00 0.00 3.51
4443 4659 4.063967 ACCATCGTCGCGCCTTCA 62.064 61.111 0.00 0.00 0.00 3.02
4524 4740 3.636300 AGAGTGTGCTTTTGTTGGCATTA 59.364 39.130 0.00 0.00 40.66 1.90
4573 4789 4.756642 TGGATGAACTGCAGTCTAAAAGTG 59.243 41.667 21.95 0.00 0.00 3.16
4775 4992 6.607004 TTTTACCTTGGAGTTTTTGACCAA 57.393 33.333 0.00 0.00 40.68 3.67
4776 4993 5.585820 TTACCTTGGAGTTTTTGACCAAC 57.414 39.130 0.00 0.00 38.52 3.77
5034 5251 6.488683 AGAAGACCGTATCTCAAATAGAGGAG 59.511 42.308 0.00 0.00 44.81 3.69
5084 5327 2.692041 GGGCTTTGAGATCCTCATTTGG 59.308 50.000 0.00 0.00 40.39 3.28
5116 5359 7.011763 CAGTAATATCAATTGTACAGTGCTGCT 59.988 37.037 5.13 0.00 0.00 4.24
5287 5684 4.593206 CCATCCTAGGCTACTTATGGTGAA 59.407 45.833 14.22 0.00 31.11 3.18
5376 5773 4.155462 CACAGTTGGAATCCATTGAGTCAG 59.845 45.833 17.60 0.92 37.33 3.51
5417 5814 6.036953 GCACACCATTTGAATTTGTTCTGAAA 59.963 34.615 0.00 0.00 0.00 2.69
5436 5833 0.251354 AGCACTGGAATGATCGCAGT 59.749 50.000 0.00 0.00 37.48 4.40
5701 6098 3.394719 GAGGTTGTCTCTGAACCAAGAC 58.605 50.000 0.00 0.00 44.71 3.01
5713 6110 4.523083 TGAACCAAGACAGTAAGTTGCTT 58.477 39.130 0.00 0.00 0.00 3.91
5756 6153 7.768582 ACCAAAGAGTTGTTCCCTTTTTATTTG 59.231 33.333 0.00 0.00 32.40 2.32
5757 6154 7.226523 CCAAAGAGTTGTTCCCTTTTTATTTGG 59.773 37.037 0.00 0.00 36.80 3.28
5803 6201 5.470098 GTCCTCCATATTCGTATGCAACATT 59.530 40.000 0.00 0.00 0.00 2.71
5844 6273 3.264947 TGAATTCACGGCTTGATCTCAG 58.735 45.455 3.38 0.00 32.84 3.35
5845 6274 3.265791 GAATTCACGGCTTGATCTCAGT 58.734 45.455 0.00 0.00 32.84 3.41
5846 6275 4.081697 TGAATTCACGGCTTGATCTCAGTA 60.082 41.667 3.38 0.00 32.84 2.74
5847 6276 4.679373 ATTCACGGCTTGATCTCAGTAT 57.321 40.909 0.00 0.00 32.84 2.12
5848 6277 5.791336 ATTCACGGCTTGATCTCAGTATA 57.209 39.130 0.00 0.00 32.84 1.47
5849 6278 4.837896 TCACGGCTTGATCTCAGTATAG 57.162 45.455 0.00 0.00 0.00 1.31
5850 6279 4.207955 TCACGGCTTGATCTCAGTATAGT 58.792 43.478 0.00 0.00 0.00 2.12
5851 6280 5.374071 TCACGGCTTGATCTCAGTATAGTA 58.626 41.667 0.00 0.00 0.00 1.82
5852 6281 5.470437 TCACGGCTTGATCTCAGTATAGTAG 59.530 44.000 0.00 0.00 0.00 2.57
5853 6282 5.239744 CACGGCTTGATCTCAGTATAGTAGT 59.760 44.000 0.00 0.00 0.00 2.73
5854 6283 5.828859 ACGGCTTGATCTCAGTATAGTAGTT 59.171 40.000 0.00 0.00 0.00 2.24
5855 6284 6.146216 CGGCTTGATCTCAGTATAGTAGTTG 58.854 44.000 0.00 0.00 0.00 3.16
5856 6285 6.017026 CGGCTTGATCTCAGTATAGTAGTTGA 60.017 42.308 0.00 0.00 0.00 3.18
5857 6286 7.468768 CGGCTTGATCTCAGTATAGTAGTTGAA 60.469 40.741 0.00 0.00 0.00 2.69
5858 6287 8.364142 GGCTTGATCTCAGTATAGTAGTTGAAT 58.636 37.037 0.00 0.00 0.00 2.57
5859 6288 9.757227 GCTTGATCTCAGTATAGTAGTTGAATT 57.243 33.333 0.00 0.00 0.00 2.17
5865 6294 8.144478 TCTCAGTATAGTAGTTGAATTCATGGC 58.856 37.037 9.40 3.19 0.00 4.40
5866 6295 8.023021 TCAGTATAGTAGTTGAATTCATGGCT 57.977 34.615 9.40 10.37 0.00 4.75
5867 6296 8.486210 TCAGTATAGTAGTTGAATTCATGGCTT 58.514 33.333 9.40 0.00 0.00 4.35
5868 6297 8.554528 CAGTATAGTAGTTGAATTCATGGCTTG 58.445 37.037 9.40 0.00 0.00 4.01
5869 6298 8.486210 AGTATAGTAGTTGAATTCATGGCTTGA 58.514 33.333 9.40 0.00 0.00 3.02
5870 6299 9.277783 GTATAGTAGTTGAATTCATGGCTTGAT 57.722 33.333 9.40 1.32 33.34 2.57
5871 6300 6.690194 AGTAGTTGAATTCATGGCTTGATC 57.310 37.500 9.40 0.90 33.34 2.92
5872 6301 6.421485 AGTAGTTGAATTCATGGCTTGATCT 58.579 36.000 9.40 3.60 33.34 2.75
5873 6302 5.831702 AGTTGAATTCATGGCTTGATCTC 57.168 39.130 9.40 4.91 33.34 2.75
5874 6303 5.258841 AGTTGAATTCATGGCTTGATCTCA 58.741 37.500 9.40 7.24 33.34 3.27
5910 6339 5.069318 TCCACTGTAAATGAAGATGTTGCA 58.931 37.500 0.00 0.00 0.00 4.08
5913 6342 5.854866 CACTGTAAATGAAGATGTTGCACAG 59.145 40.000 0.00 0.00 37.48 3.66
5946 6375 4.394920 AGAAGGTGTTTGTATACAATGGCG 59.605 41.667 18.69 0.00 35.55 5.69
6090 6519 2.356135 GTCTACCCGCAATCACACATT 58.644 47.619 0.00 0.00 0.00 2.71
6205 6634 5.700832 TGTTACTTCTGCACAATCTTCGAAT 59.299 36.000 0.00 0.00 0.00 3.34
6206 6635 4.675190 ACTTCTGCACAATCTTCGAATG 57.325 40.909 0.00 0.00 0.00 2.67
6455 6884 5.526846 GCAGAAGTTTGATGGGATAGAAGAG 59.473 44.000 0.00 0.00 0.00 2.85
6479 6908 3.007831 AGCTTCTTCAAGAGTTCTCCCTG 59.992 47.826 0.00 0.00 0.00 4.45
6859 7288 8.221944 TGAAAACCCCTCTGTTCTCTTATAAAA 58.778 33.333 0.00 0.00 0.00 1.52
6860 7289 9.244292 GAAAACCCCTCTGTTCTCTTATAAAAT 57.756 33.333 0.00 0.00 0.00 1.82
6861 7290 8.581253 AAACCCCTCTGTTCTCTTATAAAATG 57.419 34.615 0.00 0.00 0.00 2.32
6863 7292 6.064717 CCCCTCTGTTCTCTTATAAAATGGG 58.935 44.000 0.00 0.00 0.00 4.00
6864 7293 5.532779 CCCTCTGTTCTCTTATAAAATGGGC 59.467 44.000 0.00 0.00 0.00 5.36
6865 7294 6.122277 CCTCTGTTCTCTTATAAAATGGGCA 58.878 40.000 0.00 0.00 0.00 5.36
6866 7295 6.261826 CCTCTGTTCTCTTATAAAATGGGCAG 59.738 42.308 0.00 0.00 0.00 4.85
6867 7296 6.721318 TCTGTTCTCTTATAAAATGGGCAGT 58.279 36.000 0.00 0.00 0.00 4.40
6868 7297 6.823689 TCTGTTCTCTTATAAAATGGGCAGTC 59.176 38.462 0.00 0.00 0.00 3.51
6869 7298 6.721318 TGTTCTCTTATAAAATGGGCAGTCT 58.279 36.000 0.00 0.00 0.00 3.24
6870 7299 7.175104 TGTTCTCTTATAAAATGGGCAGTCTT 58.825 34.615 0.00 0.00 0.00 3.01
6871 7300 7.669722 TGTTCTCTTATAAAATGGGCAGTCTTT 59.330 33.333 0.00 0.00 0.00 2.52
6877 7306 9.342308 CTTATAAAATGGGCAGTCTTTCTCATA 57.658 33.333 0.00 0.00 0.00 2.15
6878 7307 7.814264 ATAAAATGGGCAGTCTTTCTCATAG 57.186 36.000 0.00 0.00 0.00 2.23
6902 7331 5.758784 GGTTTGTACTTGAACTACTTGCTCT 59.241 40.000 0.00 0.00 0.00 4.09
6908 7337 4.101741 ACTTGAACTACTTGCTCTCAGGTT 59.898 41.667 0.00 0.00 34.20 3.50
6962 7391 1.347707 GTCTCCACCAATCCTGTGTCA 59.652 52.381 0.00 0.00 31.71 3.58
6980 7409 6.475504 TGTGTCATATGACCAAATGAAGAGT 58.524 36.000 28.64 0.00 44.15 3.24
6995 7424 4.582869 TGAAGAGTCAATGTGAATCCCTG 58.417 43.478 2.32 0.00 41.92 4.45
7052 7481 0.037790 GCTTCAAGCACTCGAGGACT 60.038 55.000 18.41 10.57 41.89 3.85
7085 7514 1.133450 TCAATTGGGGAAAACGGACCA 60.133 47.619 5.42 0.00 0.00 4.02
7106 7535 3.985279 CAGAAACAAATGAGGCATGTGTG 59.015 43.478 4.13 0.00 40.94 3.82
7134 7563 8.204836 TCCTATCAGATGTTCTTAACCTTAAGC 58.795 37.037 0.00 0.00 39.90 3.09
7135 7564 8.207545 CCTATCAGATGTTCTTAACCTTAAGCT 58.792 37.037 0.00 0.00 39.90 3.74
7136 7565 9.255304 CTATCAGATGTTCTTAACCTTAAGCTC 57.745 37.037 0.00 0.00 39.90 4.09
7137 7566 7.246171 TCAGATGTTCTTAACCTTAAGCTCT 57.754 36.000 0.00 0.00 39.90 4.09
7138 7567 7.324178 TCAGATGTTCTTAACCTTAAGCTCTC 58.676 38.462 0.00 0.00 39.90 3.20
7147 7576 5.375283 AACCTTAAGCTCTCCTAAATCCC 57.625 43.478 0.00 0.00 0.00 3.85
7168 7597 3.125316 CCGGCATCTTGTCAGTTTCTTAC 59.875 47.826 0.00 0.00 0.00 2.34
7169 7598 3.181530 CGGCATCTTGTCAGTTTCTTACG 60.182 47.826 0.00 0.00 0.00 3.18
7170 7599 3.994392 GGCATCTTGTCAGTTTCTTACGA 59.006 43.478 0.00 0.00 0.00 3.43
7171 7600 4.631813 GGCATCTTGTCAGTTTCTTACGAT 59.368 41.667 0.00 0.00 0.00 3.73
7172 7601 5.446473 GGCATCTTGTCAGTTTCTTACGATG 60.446 44.000 0.00 0.00 0.00 3.84
7183 7612 8.073768 TCAGTTTCTTACGATGTTGAAATTTCC 58.926 33.333 15.48 1.80 32.22 3.13
7190 7619 5.399013 ACGATGTTGAAATTTCCGAAATCC 58.601 37.500 15.48 3.63 0.00 3.01
7199 7628 3.762407 TTTCCGAAATCCTGACTGACA 57.238 42.857 0.00 0.00 0.00 3.58
7200 7629 3.762407 TTCCGAAATCCTGACTGACAA 57.238 42.857 0.00 0.00 0.00 3.18
7201 7630 3.981071 TCCGAAATCCTGACTGACAAT 57.019 42.857 0.00 0.00 0.00 2.71
7237 7667 3.262660 AGTCATCTGCTCAATCTGAACCA 59.737 43.478 0.00 0.00 0.00 3.67
7282 7712 3.124270 ATGCGGCGCAACGATTCA 61.124 55.556 39.46 13.38 43.62 2.57
7315 7745 3.121030 CGCTCCTTCAGGTTGCCG 61.121 66.667 7.62 0.00 36.34 5.69
7588 8020 8.080417 TGTAGTGTCTGAGTGTATGTACTTTTC 58.920 37.037 0.00 0.00 0.00 2.29
7669 8109 5.931441 ATCTGTGCTTGTCTGAGTTTTAC 57.069 39.130 0.00 0.00 0.00 2.01
7792 8234 9.571810 GAAAAGAAAACTTGCAAAATGGAAAAT 57.428 25.926 0.00 0.00 0.00 1.82
7805 8247 7.587392 GCAAAATGGAAAATTTACAGAGCAAAC 59.413 33.333 0.00 0.00 0.00 2.93
7831 8273 1.502231 ACATATCAATGAGCGGTCGC 58.498 50.000 10.46 7.32 37.72 5.19
7832 8274 1.202521 ACATATCAATGAGCGGTCGCA 60.203 47.619 17.71 0.00 38.92 5.10
7868 8310 3.054802 GGATGGTGTGAGAGGAAGATGTT 60.055 47.826 0.00 0.00 0.00 2.71
7899 8341 7.467947 GCTGCAAAAGAAGTTCTCTTAAAGTCT 60.468 37.037 5.70 0.00 44.00 3.24
8069 8511 3.708631 TGCATTGAAAAGTCAAAAGGGGA 59.291 39.130 0.00 0.00 46.66 4.81
8162 8604 2.186160 CGAACAGCTTGTGTGCCCA 61.186 57.895 0.00 0.00 40.26 5.36
8281 8723 1.897802 AGATGCTCAAAAAGGGCCTTG 59.102 47.619 21.72 8.68 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.821589 GTTGCGCGAGGGAGGGAG 62.822 72.222 12.10 0.00 0.00 4.30
53 54 1.963338 GTGGCTGCTCGTTGCTCTT 60.963 57.895 0.00 0.00 43.37 2.85
157 159 3.385384 CGGGCACAGCTCAGGAGA 61.385 66.667 0.00 0.00 0.00 3.71
158 160 3.699894 ACGGGCACAGCTCAGGAG 61.700 66.667 0.00 0.00 0.00 3.69
159 161 4.007644 CACGGGCACAGCTCAGGA 62.008 66.667 0.00 0.00 0.00 3.86
271 287 2.657237 CCTCGTCGGCTCCTTGTT 59.343 61.111 0.00 0.00 0.00 2.83
381 397 0.478507 GGAGAGGGAGAGGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
382 398 0.996762 GGGAGAGGGAGAGGGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
384 400 0.996762 GAGGGAGAGGGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
385 401 0.998945 AGAGGGAGAGGGAGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
386 402 0.996762 GAGAGGGAGAGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
387 403 0.998945 AGAGAGGGAGAGGGAGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
388 404 0.478507 GAGAGAGGGAGAGGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
389 405 0.108585 CGAGAGAGGGAGAGGGAGAG 59.891 65.000 0.00 0.00 0.00 3.20
390 406 1.349542 CCGAGAGAGGGAGAGGGAGA 61.350 65.000 0.00 0.00 0.00 3.71
391 407 1.150536 CCGAGAGAGGGAGAGGGAG 59.849 68.421 0.00 0.00 0.00 4.30
392 408 3.336820 CCGAGAGAGGGAGAGGGA 58.663 66.667 0.00 0.00 0.00 4.20
400 416 0.978146 ATCCAACCACCCGAGAGAGG 60.978 60.000 0.00 0.00 0.00 3.69
402 418 0.976073 GGATCCAACCACCCGAGAGA 60.976 60.000 6.95 0.00 0.00 3.10
405 421 2.186903 CGGATCCAACCACCCGAG 59.813 66.667 13.41 0.00 44.29 4.63
408 424 2.125269 CGACGGATCCAACCACCC 60.125 66.667 13.41 0.00 0.00 4.61
414 430 4.485834 CGCGGACGACGGATCCAA 62.486 66.667 13.41 0.00 43.93 3.53
429 445 0.883370 AAGGGAGAACAACGAACCGC 60.883 55.000 0.00 0.00 0.00 5.68
430 446 0.865769 CAAGGGAGAACAACGAACCG 59.134 55.000 0.00 0.00 0.00 4.44
431 447 1.602377 CACAAGGGAGAACAACGAACC 59.398 52.381 0.00 0.00 0.00 3.62
432 448 2.285977 ACACAAGGGAGAACAACGAAC 58.714 47.619 0.00 0.00 0.00 3.95
433 449 2.702592 ACACAAGGGAGAACAACGAA 57.297 45.000 0.00 0.00 0.00 3.85
434 450 2.557317 GAACACAAGGGAGAACAACGA 58.443 47.619 0.00 0.00 0.00 3.85
435 451 1.602377 GGAACACAAGGGAGAACAACG 59.398 52.381 0.00 0.00 0.00 4.10
440 456 1.064825 GAGGGGAACACAAGGGAGAA 58.935 55.000 0.00 0.00 0.00 2.87
445 461 0.615850 GAGAGGAGGGGAACACAAGG 59.384 60.000 0.00 0.00 0.00 3.61
446 462 0.615850 GGAGAGGAGGGGAACACAAG 59.384 60.000 0.00 0.00 0.00 3.16
448 464 0.252284 GAGGAGAGGAGGGGAACACA 60.252 60.000 0.00 0.00 0.00 3.72
515 533 1.431633 TCAGAACCACTGTCCTCCCTA 59.568 52.381 0.00 0.00 45.86 3.53
516 534 0.191064 TCAGAACCACTGTCCTCCCT 59.809 55.000 0.00 0.00 45.86 4.20
517 535 0.610687 CTCAGAACCACTGTCCTCCC 59.389 60.000 0.00 0.00 45.86 4.30
518 536 0.610687 CCTCAGAACCACTGTCCTCC 59.389 60.000 0.00 0.00 45.86 4.30
519 537 1.633774 TCCTCAGAACCACTGTCCTC 58.366 55.000 0.00 0.00 45.86 3.71
526 544 3.495001 CGACTCTTTTTCCTCAGAACCAC 59.505 47.826 0.00 0.00 0.00 4.16
547 565 2.117156 CAGCCCCTGCCAAAGATCG 61.117 63.158 0.00 0.00 38.69 3.69
681 699 1.692173 GGCCGGTGCTGGGACTATTA 61.692 60.000 1.90 0.00 37.74 0.98
684 702 4.715130 AGGCCGGTGCTGGGACTA 62.715 66.667 1.90 0.00 42.62 2.59
868 899 5.208463 AGAACTGAACTCTCTTGGACTTC 57.792 43.478 0.00 0.00 0.00 3.01
878 909 2.224402 GCCACTCCAAGAACTGAACTCT 60.224 50.000 0.00 0.00 0.00 3.24
907 938 3.066814 GCTGCCTGCCCTCTTTGG 61.067 66.667 0.00 0.00 35.15 3.28
918 949 0.541296 AACTGCAATTCCAGCTGCCT 60.541 50.000 8.66 0.00 37.79 4.75
920 951 0.316204 ACAACTGCAATTCCAGCTGC 59.684 50.000 8.66 0.00 33.37 5.25
924 955 2.060326 CAGCACAACTGCAATTCCAG 57.940 50.000 0.00 0.00 46.97 3.86
942 973 1.003003 TGATCCAAATGCGGTGAGACA 59.997 47.619 0.00 0.00 0.00 3.41
996 1027 2.510906 GACATCACCCCCATCCCG 59.489 66.667 0.00 0.00 0.00 5.14
1131 1162 1.166531 GCAGGATTGGACATACCGCC 61.167 60.000 0.00 0.00 42.61 6.13
1140 1171 1.273986 TGCTAGCAGGCAGGATTGGA 61.274 55.000 14.93 0.00 37.29 3.53
1170 1202 5.246203 TGCAGGACTATACTACCATGATTCC 59.754 44.000 0.00 0.00 0.00 3.01
1171 1203 6.346477 TGCAGGACTATACTACCATGATTC 57.654 41.667 0.00 0.00 0.00 2.52
1173 1205 8.481314 CATTATGCAGGACTATACTACCATGAT 58.519 37.037 0.00 0.00 0.00 2.45
1184 1216 3.459598 ACACACCCATTATGCAGGACTAT 59.540 43.478 0.00 0.00 0.00 2.12
1189 1221 1.135024 GCAACACACCCATTATGCAGG 60.135 52.381 0.00 0.00 34.10 4.85
1196 1228 3.834489 TTTGAATGCAACACACCCATT 57.166 38.095 0.00 0.00 32.79 3.16
1223 1255 5.947663 TCCCAAGTTCAATAAGGAAACTCA 58.052 37.500 0.00 0.00 42.68 3.41
1302 1335 1.067142 CGGGTTGGATTTCTCGAGACA 60.067 52.381 16.36 9.65 0.00 3.41
1359 1396 4.762765 AGAGGCCACACGATATAGTAAGAG 59.237 45.833 5.01 0.00 0.00 2.85
1383 1420 7.097192 GTGTAGTGATCCAGTGAGAATTGTTA 58.903 38.462 0.00 0.00 0.00 2.41
1386 1423 5.482006 TGTGTAGTGATCCAGTGAGAATTG 58.518 41.667 0.00 0.00 0.00 2.32
1391 1428 5.077134 TCAATGTGTAGTGATCCAGTGAG 57.923 43.478 0.00 0.00 29.67 3.51
1699 1736 4.389077 GTCTGAATAAGAAACCGGTCTGTG 59.611 45.833 8.04 0.00 36.40 3.66
2144 2181 8.621286 GTTCGACATGATTATTCCTGGTTTAAT 58.379 33.333 0.00 0.00 0.00 1.40
2289 2451 9.591792 CATCTAGATGTGAATTAGACAAACTGA 57.408 33.333 22.42 0.00 34.23 3.41
2317 2479 7.882791 TGAGCTTAGATGTGACATCCTTAAAAA 59.117 33.333 21.05 6.46 0.00 1.94
2318 2480 7.334421 GTGAGCTTAGATGTGACATCCTTAAAA 59.666 37.037 21.05 8.00 0.00 1.52
2319 2481 6.818644 GTGAGCTTAGATGTGACATCCTTAAA 59.181 38.462 21.05 10.18 0.00 1.52
2320 2482 6.070824 TGTGAGCTTAGATGTGACATCCTTAA 60.071 38.462 21.05 13.11 0.00 1.85
2321 2483 5.422012 TGTGAGCTTAGATGTGACATCCTTA 59.578 40.000 21.05 6.22 0.00 2.69
2322 2484 4.223700 TGTGAGCTTAGATGTGACATCCTT 59.776 41.667 21.05 7.22 0.00 3.36
2323 2485 3.771479 TGTGAGCTTAGATGTGACATCCT 59.229 43.478 21.05 11.37 0.00 3.24
2324 2486 3.868077 GTGTGAGCTTAGATGTGACATCC 59.132 47.826 21.05 6.69 0.00 3.51
2325 2487 4.498241 TGTGTGAGCTTAGATGTGACATC 58.502 43.478 17.46 17.46 0.00 3.06
2326 2488 4.541973 TGTGTGAGCTTAGATGTGACAT 57.458 40.909 0.00 0.00 0.00 3.06
2327 2489 4.335400 TTGTGTGAGCTTAGATGTGACA 57.665 40.909 0.00 0.00 0.00 3.58
2328 2490 5.869753 ATTTGTGTGAGCTTAGATGTGAC 57.130 39.130 0.00 0.00 0.00 3.67
2334 2496 9.777297 TGCATTATATATTTGTGTGAGCTTAGA 57.223 29.630 0.00 0.00 0.00 2.10
2337 2499 8.685427 TGTTGCATTATATATTTGTGTGAGCTT 58.315 29.630 0.00 0.00 0.00 3.74
2338 2500 8.224389 TGTTGCATTATATATTTGTGTGAGCT 57.776 30.769 0.00 0.00 0.00 4.09
2339 2501 8.745837 GTTGTTGCATTATATATTTGTGTGAGC 58.254 33.333 0.00 0.00 0.00 4.26
2340 2502 9.786105 TGTTGTTGCATTATATATTTGTGTGAG 57.214 29.630 0.00 0.00 0.00 3.51
2401 2563 4.067896 AGCTAATGTCCACTCTGTTTGTG 58.932 43.478 0.00 0.00 35.39 3.33
2402 2564 4.357918 AGCTAATGTCCACTCTGTTTGT 57.642 40.909 0.00 0.00 0.00 2.83
2403 2565 6.166279 TCTAAGCTAATGTCCACTCTGTTTG 58.834 40.000 0.00 0.00 0.00 2.93
2404 2566 6.360370 TCTAAGCTAATGTCCACTCTGTTT 57.640 37.500 0.00 0.00 0.00 2.83
2405 2567 6.070538 ACATCTAAGCTAATGTCCACTCTGTT 60.071 38.462 4.03 0.00 30.35 3.16
2406 2568 5.423610 ACATCTAAGCTAATGTCCACTCTGT 59.576 40.000 4.03 0.00 30.35 3.41
2407 2569 5.752472 CACATCTAAGCTAATGTCCACTCTG 59.248 44.000 6.38 0.00 33.92 3.35
2408 2570 5.658634 TCACATCTAAGCTAATGTCCACTCT 59.341 40.000 6.38 0.00 33.92 3.24
2409 2571 5.751028 GTCACATCTAAGCTAATGTCCACTC 59.249 44.000 6.38 0.00 33.92 3.51
2410 2572 5.187772 TGTCACATCTAAGCTAATGTCCACT 59.812 40.000 6.38 0.00 33.92 4.00
2411 2573 5.419542 TGTCACATCTAAGCTAATGTCCAC 58.580 41.667 6.38 7.15 33.92 4.02
2412 2574 5.675684 TGTCACATCTAAGCTAATGTCCA 57.324 39.130 6.38 4.73 33.92 4.02
2413 2575 7.928706 AGTTATGTCACATCTAAGCTAATGTCC 59.071 37.037 0.00 2.73 33.92 4.02
2414 2576 8.879342 AGTTATGTCACATCTAAGCTAATGTC 57.121 34.615 0.00 0.00 33.92 3.06
2446 2608 6.276847 GGTTTGTCTAGGACACATCTAGATG 58.723 44.000 27.63 27.63 42.60 2.90
2447 2609 5.364157 GGGTTTGTCTAGGACACATCTAGAT 59.636 44.000 0.00 0.00 42.60 1.98
2448 2610 4.710375 GGGTTTGTCTAGGACACATCTAGA 59.290 45.833 0.00 0.00 42.60 2.43
2449 2611 4.712337 AGGGTTTGTCTAGGACACATCTAG 59.288 45.833 0.00 0.00 42.60 2.43
2450 2612 4.684724 AGGGTTTGTCTAGGACACATCTA 58.315 43.478 0.00 0.00 42.60 1.98
2451 2613 3.521727 AGGGTTTGTCTAGGACACATCT 58.478 45.455 0.00 0.00 42.60 2.90
2452 2614 3.983044 AGGGTTTGTCTAGGACACATC 57.017 47.619 0.00 0.00 42.60 3.06
2453 2615 6.388619 AATAAGGGTTTGTCTAGGACACAT 57.611 37.500 0.00 0.00 42.60 3.21
2454 2616 5.836024 AATAAGGGTTTGTCTAGGACACA 57.164 39.130 0.00 0.00 42.60 3.72
2458 2620 9.043548 GCCTATATAATAAGGGTTTGTCTAGGA 57.956 37.037 0.00 0.00 33.17 2.94
2459 2621 9.047947 AGCCTATATAATAAGGGTTTGTCTAGG 57.952 37.037 0.00 0.00 40.68 3.02
2461 2623 9.839185 AGAGCCTATATAATAAGGGTTTGTCTA 57.161 33.333 5.60 0.00 43.50 2.59
2462 2624 8.743636 AGAGCCTATATAATAAGGGTTTGTCT 57.256 34.615 5.60 0.00 43.50 3.41
2544 2717 8.864024 CAAAGTACAGTACTATGACAGAACATG 58.136 37.037 13.87 0.00 38.26 3.21
2604 2780 2.601763 CCGGTAATGCAGAGAACGTAAC 59.398 50.000 0.00 0.00 0.00 2.50
2608 2784 1.659098 GAACCGGTAATGCAGAGAACG 59.341 52.381 8.00 0.00 0.00 3.95
2631 2807 2.168521 TCCTATGACAGTACTTGCTGGC 59.831 50.000 0.00 0.00 44.53 4.85
2981 3195 9.378551 TCGCTGAACTTTGATTATACTTGTATT 57.621 29.630 0.00 0.00 0.00 1.89
2985 3199 9.214953 GAATTCGCTGAACTTTGATTATACTTG 57.785 33.333 0.00 0.00 0.00 3.16
2988 3202 8.604035 TCAGAATTCGCTGAACTTTGATTATAC 58.396 33.333 0.00 0.00 41.65 1.47
3066 3280 5.186797 TGAATGGTTGTTTCTGGTTCACTTT 59.813 36.000 0.00 0.00 0.00 2.66
3153 3367 6.380846 CCTGGGTTCAAGAATGAATGGAAATA 59.619 38.462 0.00 0.00 46.67 1.40
3399 3614 1.835531 TGCTGGATTCTCAGATGCAGA 59.164 47.619 10.04 0.00 45.17 4.26
3541 3756 1.963515 GAACAGAAAGGGCAACACCAT 59.036 47.619 0.00 0.00 42.05 3.55
3545 3760 3.569194 TGTAGAACAGAAAGGGCAACA 57.431 42.857 0.00 0.00 39.74 3.33
3601 3816 8.188139 GCGAAGAAATTACATGGGAGAAAATTA 58.812 33.333 0.00 0.00 0.00 1.40
3871 4086 5.634439 TCGCAAGTGTTTTACTAAATCGCTA 59.366 36.000 6.23 0.00 39.18 4.26
4169 4385 4.876701 GACACTGTTGTCCTGGCA 57.123 55.556 0.00 0.00 45.77 4.92
4320 4536 4.458989 GGAAATGCCTGAGACATGTACAAA 59.541 41.667 0.00 0.00 0.00 2.83
4431 4647 0.650512 ATAACAATGAAGGCGCGACG 59.349 50.000 12.10 0.00 0.00 5.12
4443 4659 2.034124 GCTGACCATGGGCATAACAAT 58.966 47.619 23.87 0.00 0.00 2.71
4488 4704 0.036952 CACTCTGCGACCCATTGACT 60.037 55.000 0.00 0.00 0.00 3.41
5034 5251 2.626266 CAACAAGGGGGTAGGAACAAAC 59.374 50.000 0.00 0.00 0.00 2.93
5084 5327 9.601217 ACTGTACAATTGATATTACTGAGGTTC 57.399 33.333 13.59 0.00 0.00 3.62
5116 5359 5.943416 CCACATTGACCCTGTTTTAGACATA 59.057 40.000 0.00 0.00 37.69 2.29
5266 5663 5.468658 AGTTCACCATAAGTAGCCTAGGAT 58.531 41.667 14.75 9.51 0.00 3.24
5270 5667 6.614694 TTCAAGTTCACCATAAGTAGCCTA 57.385 37.500 0.00 0.00 0.00 3.93
5306 5703 8.752005 TTCAGAACAAAGCAATAGCCTTATAT 57.248 30.769 0.00 0.00 43.56 0.86
5376 5773 5.593010 TGGTGTGCAAAATACTGGTTAAAC 58.407 37.500 0.00 0.00 0.00 2.01
5417 5814 0.251354 ACTGCGATCATTCCAGTGCT 59.749 50.000 4.99 0.00 38.32 4.40
5436 5833 3.513912 ACTCGATGGATTCCAACTGTGTA 59.486 43.478 9.98 0.00 36.95 2.90
5615 6012 5.762179 TGACTGGAGGTCTGTCATAAAAT 57.238 39.130 0.00 0.00 45.32 1.82
5701 6098 3.983344 GGCAATGTTGAAGCAACTTACTG 59.017 43.478 11.11 3.59 43.85 2.74
5713 6110 2.942804 TGGTTTGAGAGGCAATGTTGA 58.057 42.857 0.00 0.00 36.15 3.18
5756 6153 9.087424 GGACATCATCTTTTGTTTTTAATAGCC 57.913 33.333 0.00 0.00 0.00 3.93
5757 6154 9.860898 AGGACATCATCTTTTGTTTTTAATAGC 57.139 29.630 0.00 0.00 0.00 2.97
5776 6174 4.820897 TGCATACGAATATGGAGGACATC 58.179 43.478 0.00 0.00 41.03 3.06
5844 6273 8.662781 TCAAGCCATGAATTCAACTACTATAC 57.337 34.615 13.09 0.00 34.30 1.47
5845 6274 9.494271 GATCAAGCCATGAATTCAACTACTATA 57.506 33.333 13.09 1.08 42.54 1.31
5846 6275 8.216423 AGATCAAGCCATGAATTCAACTACTAT 58.784 33.333 13.09 1.52 42.54 2.12
5847 6276 7.568349 AGATCAAGCCATGAATTCAACTACTA 58.432 34.615 13.09 0.00 42.54 1.82
5848 6277 6.421485 AGATCAAGCCATGAATTCAACTACT 58.579 36.000 13.09 5.11 42.54 2.57
5849 6278 6.317140 TGAGATCAAGCCATGAATTCAACTAC 59.683 38.462 13.09 2.76 42.54 2.73
5850 6279 6.417258 TGAGATCAAGCCATGAATTCAACTA 58.583 36.000 13.09 0.00 42.54 2.24
5851 6280 5.258841 TGAGATCAAGCCATGAATTCAACT 58.741 37.500 13.09 7.66 42.54 3.16
5852 6281 5.571784 TGAGATCAAGCCATGAATTCAAC 57.428 39.130 13.09 5.34 42.54 3.18
5853 6282 8.473358 AATATGAGATCAAGCCATGAATTCAA 57.527 30.769 13.09 0.00 42.54 2.69
5854 6283 8.473358 AAATATGAGATCAAGCCATGAATTCA 57.527 30.769 11.26 11.26 42.54 2.57
5855 6284 9.760077 AAAAATATGAGATCAAGCCATGAATTC 57.240 29.630 0.00 0.00 42.54 2.17
5856 6285 9.760077 GAAAAATATGAGATCAAGCCATGAATT 57.240 29.630 0.00 0.00 42.54 2.17
5857 6286 9.144298 AGAAAAATATGAGATCAAGCCATGAAT 57.856 29.630 0.00 0.00 42.54 2.57
5858 6287 8.529424 AGAAAAATATGAGATCAAGCCATGAA 57.471 30.769 0.00 0.00 42.54 2.57
5859 6288 8.529424 AAGAAAAATATGAGATCAAGCCATGA 57.471 30.769 0.00 0.00 43.67 3.07
5860 6289 9.595823 AAAAGAAAAATATGAGATCAAGCCATG 57.404 29.630 0.00 0.00 0.00 3.66
5862 6291 9.643693 GAAAAAGAAAAATATGAGATCAAGCCA 57.356 29.630 0.00 0.00 0.00 4.75
5863 6292 9.091784 GGAAAAAGAAAAATATGAGATCAAGCC 57.908 33.333 0.00 0.00 0.00 4.35
5864 6293 9.643693 TGGAAAAAGAAAAATATGAGATCAAGC 57.356 29.630 0.00 0.00 0.00 4.01
5910 6339 0.616111 ACCTTCTCCGAGATGGCTGT 60.616 55.000 23.94 7.83 41.75 4.40
5913 6342 0.250513 AACACCTTCTCCGAGATGGC 59.749 55.000 23.94 0.00 41.75 4.40
6090 6519 9.898576 ATAGCTCATACTAATTATATAGGGCCA 57.101 33.333 6.18 0.00 0.00 5.36
6205 6634 3.252215 CAGAACCGTAAAGCATTTCACCA 59.748 43.478 0.00 0.00 40.09 4.17
6206 6635 3.500680 TCAGAACCGTAAAGCATTTCACC 59.499 43.478 0.00 0.00 40.09 4.02
6419 6848 5.060506 TCAAACTTCTGCAATCCGTAAGAA 58.939 37.500 0.00 0.00 43.02 2.52
6455 6884 2.741517 GGAGAACTCTTGAAGAAGCTGC 59.258 50.000 0.00 0.00 0.00 5.25
6479 6908 4.202090 GCACCAAGAGGAAATGAATCATCC 60.202 45.833 0.00 0.00 38.69 3.51
6530 6959 4.213270 TCCTTTTCAGCGTACATTGAACAG 59.787 41.667 12.30 12.30 33.36 3.16
6806 7235 6.907212 GTGCCATTGTTTTAGAGATTGATACG 59.093 38.462 0.00 0.00 0.00 3.06
6859 7288 3.118531 ACCTATGAGAAAGACTGCCCAT 58.881 45.455 0.00 0.00 0.00 4.00
6860 7289 2.551270 ACCTATGAGAAAGACTGCCCA 58.449 47.619 0.00 0.00 0.00 5.36
6861 7290 3.636153 AACCTATGAGAAAGACTGCCC 57.364 47.619 0.00 0.00 0.00 5.36
6863 7292 6.166982 AGTACAAACCTATGAGAAAGACTGC 58.833 40.000 0.00 0.00 0.00 4.40
6864 7293 7.872993 TCAAGTACAAACCTATGAGAAAGACTG 59.127 37.037 0.00 0.00 0.00 3.51
6865 7294 7.963532 TCAAGTACAAACCTATGAGAAAGACT 58.036 34.615 0.00 0.00 0.00 3.24
6866 7295 8.496751 GTTCAAGTACAAACCTATGAGAAAGAC 58.503 37.037 0.00 0.00 0.00 3.01
6867 7296 8.429641 AGTTCAAGTACAAACCTATGAGAAAGA 58.570 33.333 0.00 0.00 0.00 2.52
6868 7297 8.608844 AGTTCAAGTACAAACCTATGAGAAAG 57.391 34.615 0.00 0.00 0.00 2.62
6869 7298 9.485206 GTAGTTCAAGTACAAACCTATGAGAAA 57.515 33.333 0.00 0.00 0.00 2.52
6870 7299 8.867097 AGTAGTTCAAGTACAAACCTATGAGAA 58.133 33.333 5.17 0.00 0.00 2.87
6871 7300 8.418597 AGTAGTTCAAGTACAAACCTATGAGA 57.581 34.615 5.17 0.00 0.00 3.27
6877 7306 5.681639 AGCAAGTAGTTCAAGTACAAACCT 58.318 37.500 5.17 0.00 0.00 3.50
6878 7307 5.758784 AGAGCAAGTAGTTCAAGTACAAACC 59.241 40.000 5.17 0.00 0.00 3.27
6902 7331 2.289882 CCTTGCTGTCTCATGAACCTGA 60.290 50.000 0.00 0.00 0.00 3.86
6908 7337 1.072806 ACTTGCCTTGCTGTCTCATGA 59.927 47.619 0.00 0.00 0.00 3.07
6962 7391 7.830697 TCACATTGACTCTTCATTTGGTCATAT 59.169 33.333 0.00 0.00 38.29 1.78
6980 7409 4.229353 TCCATTACCAGGGATTCACATTGA 59.771 41.667 0.00 0.00 0.00 2.57
6995 7424 3.758554 TCTTCTGCTGCTTTTCCATTACC 59.241 43.478 0.00 0.00 0.00 2.85
7052 7481 1.933181 CCAATTGAGCTACGCGAATCA 59.067 47.619 15.93 8.22 0.00 2.57
7070 7499 0.551879 TTTCTGGTCCGTTTTCCCCA 59.448 50.000 0.00 0.00 0.00 4.96
7085 7514 3.553508 GCACACATGCCTCATTTGTTTCT 60.554 43.478 0.00 0.00 46.97 2.52
7106 7535 6.168270 AGGTTAAGAACATCTGATAGGAGC 57.832 41.667 0.00 0.00 0.00 4.70
7112 7541 7.856415 AGAGCTTAAGGTTAAGAACATCTGAT 58.144 34.615 8.87 0.00 42.05 2.90
7118 7547 7.549147 TTAGGAGAGCTTAAGGTTAAGAACA 57.451 36.000 8.87 0.00 42.05 3.18
7134 7563 1.974236 AGATGCCGGGATTTAGGAGAG 59.026 52.381 10.83 0.00 0.00 3.20
7135 7564 2.103153 AGATGCCGGGATTTAGGAGA 57.897 50.000 10.83 0.00 0.00 3.71
7136 7565 2.158755 ACAAGATGCCGGGATTTAGGAG 60.159 50.000 10.83 0.13 0.00 3.69
7137 7566 1.843851 ACAAGATGCCGGGATTTAGGA 59.156 47.619 10.83 0.00 0.00 2.94
7138 7567 2.222027 GACAAGATGCCGGGATTTAGG 58.778 52.381 10.83 3.15 0.00 2.69
7147 7576 3.181530 CGTAAGAAACTGACAAGATGCCG 60.182 47.826 0.00 0.00 43.02 5.69
7168 7597 5.512788 CAGGATTTCGGAAATTTCAACATCG 59.487 40.000 19.49 12.88 0.00 3.84
7169 7598 6.528072 GTCAGGATTTCGGAAATTTCAACATC 59.472 38.462 19.49 13.34 0.00 3.06
7170 7599 6.209391 AGTCAGGATTTCGGAAATTTCAACAT 59.791 34.615 19.49 5.94 0.00 2.71
7171 7600 5.534654 AGTCAGGATTTCGGAAATTTCAACA 59.465 36.000 19.49 1.28 0.00 3.33
7172 7601 5.858581 CAGTCAGGATTTCGGAAATTTCAAC 59.141 40.000 19.49 12.52 0.00 3.18
7183 7612 5.149273 CAACAATTGTCAGTCAGGATTTCG 58.851 41.667 12.39 0.00 0.00 3.46
7190 7619 5.557514 GCAAAATGCAACAATTGTCAGTCAG 60.558 40.000 12.39 3.77 44.26 3.51
7315 7745 4.752879 TCGTACGGGCTTGCAGGC 62.753 66.667 16.52 13.24 40.51 4.85
7588 8020 1.616159 TTTTCTTTTCTGGCCCTCGG 58.384 50.000 0.00 0.00 0.00 4.63
7645 8081 5.841957 AAAACTCAGACAAGCACAGATTT 57.158 34.783 0.00 0.00 0.00 2.17
7646 8082 5.822519 TGTAAAACTCAGACAAGCACAGATT 59.177 36.000 0.00 0.00 0.00 2.40
7648 8084 4.765273 TGTAAAACTCAGACAAGCACAGA 58.235 39.130 0.00 0.00 0.00 3.41
7649 8085 5.679734 ATGTAAAACTCAGACAAGCACAG 57.320 39.130 0.00 0.00 0.00 3.66
7650 8086 6.318648 AGAAATGTAAAACTCAGACAAGCACA 59.681 34.615 0.00 0.00 0.00 4.57
7651 8087 6.729187 AGAAATGTAAAACTCAGACAAGCAC 58.271 36.000 0.00 0.00 0.00 4.40
7652 8088 6.542005 TGAGAAATGTAAAACTCAGACAAGCA 59.458 34.615 0.00 0.00 35.01 3.91
7653 8089 6.959361 TGAGAAATGTAAAACTCAGACAAGC 58.041 36.000 0.00 0.00 35.01 4.01
7663 8103 8.106247 TCAGGTACCAATGAGAAATGTAAAAC 57.894 34.615 15.94 0.00 0.00 2.43
7669 8109 9.347240 AGATTAATCAGGTACCAATGAGAAATG 57.653 33.333 15.94 0.00 0.00 2.32
7726 8166 5.706369 TCCTCTCGTGGATAGTATTTCTAGC 59.294 44.000 0.00 0.00 34.64 3.42
7792 8234 9.677567 GATATGTTCAAAAGTTTGCTCTGTAAA 57.322 29.630 0.00 0.00 38.05 2.01
7831 8273 1.479323 CCATCCTTGCACCCTTGATTG 59.521 52.381 0.00 0.00 0.00 2.67
7832 8274 1.077663 ACCATCCTTGCACCCTTGATT 59.922 47.619 0.00 0.00 0.00 2.57
7868 8310 5.065914 AGAGAACTTCTTTTGCAGCACATA 58.934 37.500 0.00 0.00 29.61 2.29
7899 8341 0.250553 CCGGTAAAGCTTGGACCACA 60.251 55.000 23.71 0.00 32.39 4.17
8281 8723 0.179134 CCATCTCCCACTCGTCGAAC 60.179 60.000 0.00 0.00 0.00 3.95
8334 8777 2.668212 CATGGACGTGGTGCCGTT 60.668 61.111 0.00 0.00 41.98 4.44


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

AutoCloner maintained by Alex Coulton.