Multiple sequence alignment - TraesCS5A01G232700

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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 TraesCS5A01G232700 chr5A 100.000 2762 0 0 1 2762 448089083 448091844 0.000000e+00 5101.0
1 TraesCS5A01G232700 chr5A 100.000 400 0 0 3016 3415 448092098 448092497 0.000000e+00 739.0
2 TraesCS5A01G232700 chr5D 87.985 2139 94 49 639 2704 344398614 344400662 0.000000e+00 2375.0
3 TraesCS5A01G232700 chr5D 83.407 452 27 19 1 445 344397637 344398047 3.220000e-100 375.0
4 TraesCS5A01G232700 chr5D 84.956 226 18 8 3016 3227 344400733 344400956 7.420000e-52 215.0
5 TraesCS5A01G232700 chr5B 87.846 2057 115 37 680 2668 407818575 407816586 0.000000e+00 2289.0
6 TraesCS5A01G232700 chr5B 79.596 446 37 23 1 445 407819594 407819202 1.560000e-68 270.0
7 TraesCS5A01G232700 chr5B 84.722 216 20 8 3016 3227 407816468 407816262 1.610000e-48 204.0
8 TraesCS5A01G232700 chr5B 89.655 58 6 0 3269 3326 407816178 407816121 1.310000e-09 75.0
9 TraesCS5A01G232700 chr2D 88.144 194 17 5 2024 2211 527547519 527547712 3.430000e-55 226.0
10 TraesCS5A01G232700 chr2A 88.021 192 17 5 2026 2211 672415937 672416128 4.440000e-54 222.0
11 TraesCS5A01G232700 chr2B 87.629 194 18 5 2024 2211 624892074 624892267 1.600000e-53 220.0
12 TraesCS5A01G232700 chr1B 82.759 203 20 10 2026 2213 418106021 418105819 2.110000e-37 167.0
13 TraesCS5A01G232700 chr1B 90.588 85 8 0 1649 1733 418106305 418106221 2.790000e-21 113.0
14 TraesCS5A01G232700 chr1A 82.759 203 20 10 2026 2213 387840975 387840773 2.110000e-37 167.0
15 TraesCS5A01G232700 chr1A 89.412 85 9 0 1649 1733 387841264 387841180 1.300000e-19 108.0
16 TraesCS5A01G232700 chr4B 90.244 123 12 0 2020 2142 491465480 491465602 9.810000e-36 161.0
17 TraesCS5A01G232700 chr4B 83.871 124 15 5 1608 1731 491464652 491464770 2.790000e-21 113.0
18 TraesCS5A01G232700 chr4A 90.244 123 12 0 2020 2142 56145029 56145151 9.810000e-36 161.0
19 TraesCS5A01G232700 chr4A 85.714 105 12 3 1627 1731 56144271 56144372 1.300000e-19 108.0
20 TraesCS5A01G232700 chr1D 89.412 85 9 0 1649 1733 308459917 308459833 1.300000e-19 108.0
21 TraesCS5A01G232700 chr4D 81.600 125 16 7 1608 1731 398669570 398669688 2.810000e-16 97.1
22 TraesCS5A01G232700 chr7D 85.366 82 12 0 1812 1893 46670548 46670467 6.070000e-13 86.1
23 TraesCS5A01G232700 chr7D 82.143 84 15 0 1813 1896 46711921 46711838 4.730000e-09 73.1


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 TraesCS5A01G232700 chr5A 448089083 448092497 3414 False 2920.000000 5101 100.000000 1 3415 2 chr5A.!!$F1 3414
1 TraesCS5A01G232700 chr5D 344397637 344400956 3319 False 988.333333 2375 85.449333 1 3227 3 chr5D.!!$F1 3226
2 TraesCS5A01G232700 chr5B 407816121 407819594 3473 True 709.500000 2289 85.454750 1 3326 4 chr5B.!!$R1 3325

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
883 1362 0.034960 CACACGGAGGAGAGAGAGGA 60.035 60.0 0.0 0.0 0.0 3.71 F
1387 1889 0.102481 ATCCGATCTGTTCCGTTCCG 59.898 55.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 2274 0.183014 TAAGCAAACGGGGTTGGTCA 59.817 50.0 1.18 0.0 38.23 4.02 R
3381 4005 0.108186 TTGACAGCTCCTGCGTATGG 60.108 55.0 0.00 0.0 45.42 2.74 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
26 27 1.959282 GTGGATGAGGAATTGATGGCC 59.041 52.381 0.00 0.00 0.00 5.36
53 54 4.582760 CGTGCCTGCATGCAAATT 57.417 50.000 22.88 0.00 44.11 1.82
75 78 1.270826 GCAGGGGAAGAAAAGAGTTGC 59.729 52.381 0.00 0.00 0.00 4.17
76 79 2.868899 CAGGGGAAGAAAAGAGTTGCT 58.131 47.619 0.00 0.00 0.00 3.91
77 80 2.555757 CAGGGGAAGAAAAGAGTTGCTG 59.444 50.000 0.00 0.00 0.00 4.41
78 81 1.270826 GGGGAAGAAAAGAGTTGCTGC 59.729 52.381 0.00 0.00 0.00 5.25
79 82 2.234143 GGGAAGAAAAGAGTTGCTGCT 58.766 47.619 0.00 0.00 0.00 4.24
80 83 3.412386 GGGAAGAAAAGAGTTGCTGCTA 58.588 45.455 0.00 0.00 0.00 3.49
81 84 3.189495 GGGAAGAAAAGAGTTGCTGCTAC 59.811 47.826 6.10 6.10 0.00 3.58
82 85 3.189495 GGAAGAAAAGAGTTGCTGCTACC 59.811 47.826 10.52 3.07 0.00 3.18
83 86 3.492102 AGAAAAGAGTTGCTGCTACCA 57.508 42.857 10.52 0.00 0.00 3.25
84 87 3.142174 AGAAAAGAGTTGCTGCTACCAC 58.858 45.455 10.52 5.88 0.00 4.16
85 88 2.938956 AAAGAGTTGCTGCTACCACT 57.061 45.000 10.52 7.92 0.00 4.00
86 89 4.040461 AGAAAAGAGTTGCTGCTACCACTA 59.960 41.667 10.52 0.00 0.00 2.74
108 111 0.905357 ACTTCTCTCCACATTCCCCG 59.095 55.000 0.00 0.00 0.00 5.73
190 193 1.164662 GCTCCTCACGCATGCATCAT 61.165 55.000 19.57 0.00 0.00 2.45
191 194 0.586802 CTCCTCACGCATGCATCATG 59.413 55.000 19.57 10.02 43.91 3.07
192 195 0.178533 TCCTCACGCATGCATCATGA 59.821 50.000 19.57 13.71 43.81 3.07
193 196 1.018910 CCTCACGCATGCATCATGAA 58.981 50.000 19.57 0.49 43.81 2.57
194 197 1.607148 CCTCACGCATGCATCATGAAT 59.393 47.619 19.57 0.00 43.81 2.57
195 198 2.034179 CCTCACGCATGCATCATGAATT 59.966 45.455 19.57 0.00 43.81 2.17
196 199 3.251487 CCTCACGCATGCATCATGAATTA 59.749 43.478 19.57 0.00 43.81 1.40
225 228 4.664891 GCATGCACGCATTTTCTTTCTTTC 60.665 41.667 14.21 0.00 33.90 2.62
229 232 5.231991 TGCACGCATTTTCTTTCTTTCTTTC 59.768 36.000 0.00 0.00 0.00 2.62
235 238 7.010460 CGCATTTTCTTTCTTTCTTTCTTTGGT 59.990 33.333 0.00 0.00 0.00 3.67
274 277 2.701423 TCATTCCATCCCATTGCCATTG 59.299 45.455 0.00 0.00 0.00 2.82
275 278 0.831966 TTCCATCCCATTGCCATTGC 59.168 50.000 0.00 0.00 38.26 3.56
276 279 1.049855 TCCATCCCATTGCCATTGCC 61.050 55.000 0.00 0.00 36.33 4.52
277 280 1.338890 CCATCCCATTGCCATTGCCA 61.339 55.000 0.00 0.00 36.33 4.92
278 281 0.762418 CATCCCATTGCCATTGCCAT 59.238 50.000 0.00 0.00 36.33 4.40
279 282 1.053424 ATCCCATTGCCATTGCCATC 58.947 50.000 0.00 0.00 36.33 3.51
280 283 1.068417 CCCATTGCCATTGCCATCG 59.932 57.895 0.00 0.00 36.33 3.84
312 315 9.911788 AATTATAGGCTCTAATTACCATCATGG 57.088 33.333 14.19 0.54 45.02 3.66
336 339 1.751927 CATGCAGGCCAGGGAGAAC 60.752 63.158 5.01 0.00 0.00 3.01
361 364 2.464157 TCATATGAACACACACGGCA 57.536 45.000 1.98 0.00 0.00 5.69
374 382 0.526954 CACGGCACCATCTACGTACC 60.527 60.000 0.00 0.00 37.85 3.34
391 399 2.425143 ACCGCACATTCATCATTCCT 57.575 45.000 0.00 0.00 0.00 3.36
395 403 2.547211 CGCACATTCATCATTCCTCCTC 59.453 50.000 0.00 0.00 0.00 3.71
405 413 6.496743 TCATCATTCCTCCTCTTTGGAAAAT 58.503 36.000 0.00 0.00 45.63 1.82
406 414 7.642186 TCATCATTCCTCCTCTTTGGAAAATA 58.358 34.615 0.00 0.00 45.63 1.40
407 415 7.557719 TCATCATTCCTCCTCTTTGGAAAATAC 59.442 37.037 0.00 0.00 45.63 1.89
408 416 6.789268 TCATTCCTCCTCTTTGGAAAATACA 58.211 36.000 0.00 0.00 45.63 2.29
409 417 6.886459 TCATTCCTCCTCTTTGGAAAATACAG 59.114 38.462 0.00 0.00 45.63 2.74
430 438 7.468141 ACAGTATCTTTTCCCATTCCTTTTC 57.532 36.000 0.00 0.00 0.00 2.29
445 453 2.167075 CCTTTTCTGCACCCATCATTCC 59.833 50.000 0.00 0.00 0.00 3.01
447 455 2.425143 TTCTGCACCCATCATTCCTC 57.575 50.000 0.00 0.00 0.00 3.71
448 456 1.588239 TCTGCACCCATCATTCCTCT 58.412 50.000 0.00 0.00 0.00 3.69
450 458 0.548031 TGCACCCATCATTCCTCTCC 59.452 55.000 0.00 0.00 0.00 3.71
452 460 1.516110 CACCCATCATTCCTCTCCCT 58.484 55.000 0.00 0.00 0.00 4.20
453 461 1.419387 CACCCATCATTCCTCTCCCTC 59.581 57.143 0.00 0.00 0.00 4.30
454 462 1.063183 CCCATCATTCCTCTCCCTCC 58.937 60.000 0.00 0.00 0.00 4.30
455 463 1.415716 CCCATCATTCCTCTCCCTCCT 60.416 57.143 0.00 0.00 0.00 3.69
458 466 1.324014 TCATTCCTCTCCCTCCTCCT 58.676 55.000 0.00 0.00 0.00 3.69
460 468 0.565674 ATTCCTCTCCCTCCTCCTCC 59.434 60.000 0.00 0.00 0.00 4.30
462 470 0.556380 TCCTCTCCCTCCTCCTCCTT 60.556 60.000 0.00 0.00 0.00 3.36
463 471 0.398381 CCTCTCCCTCCTCCTCCTTG 60.398 65.000 0.00 0.00 0.00 3.61
466 474 0.980231 CTCCCTCCTCCTCCTTGGTG 60.980 65.000 0.00 0.00 37.07 4.17
467 475 2.674220 CCCTCCTCCTCCTTGGTGC 61.674 68.421 0.00 0.00 37.07 5.01
468 476 1.614824 CCTCCTCCTCCTTGGTGCT 60.615 63.158 0.00 0.00 37.07 4.40
469 477 0.325671 CCTCCTCCTCCTTGGTGCTA 60.326 60.000 0.00 0.00 37.07 3.49
470 478 1.694048 CCTCCTCCTCCTTGGTGCTAT 60.694 57.143 0.00 0.00 37.07 2.97
471 479 1.415659 CTCCTCCTCCTTGGTGCTATG 59.584 57.143 0.00 0.00 37.07 2.23
472 480 0.179034 CCTCCTCCTTGGTGCTATGC 60.179 60.000 0.00 0.00 37.07 3.14
473 481 0.179034 CTCCTCCTTGGTGCTATGCC 60.179 60.000 0.00 0.00 37.07 4.40
474 482 1.152881 CCTCCTTGGTGCTATGCCC 60.153 63.158 0.00 0.00 0.00 5.36
475 483 1.152881 CTCCTTGGTGCTATGCCCC 60.153 63.158 0.00 0.00 0.00 5.80
476 484 1.619363 TCCTTGGTGCTATGCCCCT 60.619 57.895 0.00 0.00 0.00 4.79
477 485 0.327095 TCCTTGGTGCTATGCCCCTA 60.327 55.000 0.00 0.00 0.00 3.53
478 486 0.109342 CCTTGGTGCTATGCCCCTAG 59.891 60.000 0.00 0.00 0.00 3.02
497 625 4.213270 CCTAGCTAGAATCTCACTCGTCTG 59.787 50.000 22.70 0.00 0.00 3.51
512 640 3.997021 CTCGTCTGCACTCCAAAATTACT 59.003 43.478 0.00 0.00 0.00 2.24
518 659 6.426937 GTCTGCACTCCAAAATTACTTACTGA 59.573 38.462 0.00 0.00 0.00 3.41
519 660 6.426937 TCTGCACTCCAAAATTACTTACTGAC 59.573 38.462 0.00 0.00 0.00 3.51
535 676 3.941657 GACGCACAGCTCCAGGTCC 62.942 68.421 0.00 0.00 0.00 4.46
540 681 1.922369 ACAGCTCCAGGTCCAGCAT 60.922 57.895 1.61 0.00 38.18 3.79
541 682 1.451567 CAGCTCCAGGTCCAGCATG 60.452 63.158 1.61 0.00 38.18 4.06
547 688 2.046892 AGGTCCAGCATGCACGAC 60.047 61.111 21.98 22.22 31.97 4.34
548 689 3.490759 GGTCCAGCATGCACGACG 61.491 66.667 21.98 2.25 31.97 5.12
549 690 3.490759 GTCCAGCATGCACGACGG 61.491 66.667 21.98 11.75 31.97 4.79
550 691 4.758251 TCCAGCATGCACGACGGG 62.758 66.667 21.98 10.92 31.97 5.28
552 693 3.490759 CAGCATGCACGACGGGTC 61.491 66.667 21.98 0.00 0.00 4.46
589 730 6.294731 GGCATAAATTCGGCCATAAAGAATCT 60.295 38.462 2.24 0.00 46.92 2.40
591 732 4.574599 AATTCGGCCATAAAGAATCTGC 57.425 40.909 2.24 0.00 33.94 4.26
595 736 1.680338 GCCATAAAGAATCTGCGGGT 58.320 50.000 0.00 0.00 0.00 5.28
596 737 1.334869 GCCATAAAGAATCTGCGGGTG 59.665 52.381 0.00 0.00 0.00 4.61
597 738 1.334869 CCATAAAGAATCTGCGGGTGC 59.665 52.381 0.00 0.00 43.20 5.01
614 755 4.129737 CGCGGCCGGAGAAGAAGA 62.130 66.667 29.38 0.00 0.00 2.87
615 756 2.202810 GCGGCCGGAGAAGAAGAG 60.203 66.667 29.38 0.00 0.00 2.85
616 757 2.202810 CGGCCGGAGAAGAAGAGC 60.203 66.667 20.10 0.00 0.00 4.09
617 758 2.188207 GGCCGGAGAAGAAGAGCC 59.812 66.667 5.05 0.00 0.00 4.70
618 759 2.202810 GCCGGAGAAGAAGAGCCG 60.203 66.667 5.05 0.00 43.20 5.52
620 761 3.604629 CGGAGAAGAAGAGCCGGA 58.395 61.111 5.05 0.00 40.08 5.14
621 762 1.435515 CGGAGAAGAAGAGCCGGAG 59.564 63.158 5.05 0.00 40.08 4.63
622 763 1.032657 CGGAGAAGAAGAGCCGGAGA 61.033 60.000 5.05 0.00 40.08 3.71
623 764 0.744281 GGAGAAGAAGAGCCGGAGAG 59.256 60.000 5.05 0.00 0.00 3.20
624 765 0.744281 GAGAAGAAGAGCCGGAGAGG 59.256 60.000 5.05 0.00 44.97 3.69
625 766 0.333312 AGAAGAAGAGCCGGAGAGGA 59.667 55.000 5.05 0.00 45.00 3.71
626 767 0.744281 GAAGAAGAGCCGGAGAGGAG 59.256 60.000 5.05 0.00 45.00 3.69
627 768 0.686112 AAGAAGAGCCGGAGAGGAGG 60.686 60.000 5.05 0.00 45.00 4.30
628 769 1.076632 GAAGAGCCGGAGAGGAGGA 60.077 63.158 5.05 0.00 45.00 3.71
629 770 1.076339 AAGAGCCGGAGAGGAGGAG 60.076 63.158 5.05 0.00 45.00 3.69
630 771 3.223589 GAGCCGGAGAGGAGGAGC 61.224 72.222 5.05 0.00 45.00 4.70
635 776 2.841988 GGAGAGGAGGAGCGGCAT 60.842 66.667 1.45 0.00 0.00 4.40
636 777 2.420890 GAGAGGAGGAGCGGCATG 59.579 66.667 1.45 0.00 0.00 4.06
637 778 3.805891 GAGAGGAGGAGCGGCATGC 62.806 68.421 9.90 9.90 46.98 4.06
682 1127 1.024579 TTCTGGAAAAGATCGCGGGC 61.025 55.000 6.13 0.00 33.93 6.13
734 1179 3.436704 AGCCCGCGATAATGATTAACATG 59.563 43.478 8.23 0.00 39.39 3.21
747 1192 5.922546 TGATTAACATGATTATTACCGCGC 58.077 37.500 0.00 0.00 0.00 6.86
748 1193 4.735662 TTAACATGATTATTACCGCGCC 57.264 40.909 0.00 0.00 0.00 6.53
749 1194 1.144969 ACATGATTATTACCGCGCCG 58.855 50.000 0.00 0.00 0.00 6.46
790 1250 4.204891 GAACGCCGGAATCGCACG 62.205 66.667 5.05 0.00 39.28 5.34
866 1336 1.202651 ACCCGCCATTATAGCTCACAC 60.203 52.381 0.00 0.00 0.00 3.82
879 1358 0.808125 CTCACACACGGAGGAGAGAG 59.192 60.000 0.00 0.00 0.00 3.20
880 1359 0.400594 TCACACACGGAGGAGAGAGA 59.599 55.000 0.00 0.00 0.00 3.10
881 1360 0.808125 CACACACGGAGGAGAGAGAG 59.192 60.000 0.00 0.00 0.00 3.20
882 1361 0.322997 ACACACGGAGGAGAGAGAGG 60.323 60.000 0.00 0.00 0.00 3.69
883 1362 0.034960 CACACGGAGGAGAGAGAGGA 60.035 60.000 0.00 0.00 0.00 3.71
884 1363 0.254747 ACACGGAGGAGAGAGAGGAG 59.745 60.000 0.00 0.00 0.00 3.69
885 1364 0.465460 CACGGAGGAGAGAGAGGAGG 60.465 65.000 0.00 0.00 0.00 4.30
886 1365 1.150536 CGGAGGAGAGAGAGGAGGG 59.849 68.421 0.00 0.00 0.00 4.30
887 1366 1.349542 CGGAGGAGAGAGAGGAGGGA 61.350 65.000 0.00 0.00 0.00 4.20
888 1367 0.478507 GGAGGAGAGAGAGGAGGGAG 59.521 65.000 0.00 0.00 0.00 4.30
889 1368 0.478507 GAGGAGAGAGAGGAGGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
890 1369 0.998945 AGGAGAGAGAGGAGGGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
891 1370 0.996762 GGAGAGAGAGGAGGGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
892 1371 0.478507 GAGAGAGAGGAGGGAGGGAG 59.521 65.000 0.00 0.00 0.00 4.30
893 1372 0.998945 AGAGAGAGGAGGGAGGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
894 1373 2.018086 AGAGAGGAGGGAGGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
895 1374 2.015726 GAGAGGAGGGAGGGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
896 1375 2.018086 AGAGGAGGGAGGGAGGGAG 61.018 68.421 0.00 0.00 0.00 4.30
975 1454 2.741092 CGGTCCCATATCCCACCG 59.259 66.667 0.00 0.00 45.38 4.94
978 1457 1.366366 GTCCCATATCCCACCGTCG 59.634 63.158 0.00 0.00 0.00 5.12
1009 1506 1.976132 GCTGGTAGGCATGGAGCTGA 61.976 60.000 0.00 0.00 44.79 4.26
1059 1556 4.785453 GGCCGGGAGCTGGTTCTG 62.785 72.222 2.18 0.00 43.05 3.02
1128 1625 4.565850 GGCGAGGGGAGGAGGGAT 62.566 72.222 0.00 0.00 0.00 3.85
1131 1628 1.834822 CGAGGGGAGGAGGGATCAC 60.835 68.421 0.00 0.00 0.00 3.06
1262 1762 1.154131 CGTCCGAGAGCAGTGAGTG 60.154 63.158 0.00 0.00 0.00 3.51
1263 1763 1.578206 CGTCCGAGAGCAGTGAGTGA 61.578 60.000 0.00 0.00 0.00 3.41
1264 1764 0.814457 GTCCGAGAGCAGTGAGTGAT 59.186 55.000 0.00 0.00 0.00 3.06
1265 1765 0.813821 TCCGAGAGCAGTGAGTGATG 59.186 55.000 0.00 0.00 0.00 3.07
1266 1766 0.805322 CCGAGAGCAGTGAGTGATGC 60.805 60.000 0.00 0.00 42.87 3.91
1307 1809 4.037446 TCCTTTCCGTTTCTTGGATTTGTG 59.963 41.667 0.00 0.00 34.91 3.33
1308 1810 4.202111 CCTTTCCGTTTCTTGGATTTGTGT 60.202 41.667 0.00 0.00 34.91 3.72
1309 1811 4.993029 TTCCGTTTCTTGGATTTGTGTT 57.007 36.364 0.00 0.00 34.91 3.32
1310 1812 4.993029 TCCGTTTCTTGGATTTGTGTTT 57.007 36.364 0.00 0.00 0.00 2.83
1311 1813 4.677584 TCCGTTTCTTGGATTTGTGTTTG 58.322 39.130 0.00 0.00 0.00 2.93
1312 1814 4.158764 TCCGTTTCTTGGATTTGTGTTTGT 59.841 37.500 0.00 0.00 0.00 2.83
1325 1827 0.743688 TGTTTGTTTCTGCATGCCGT 59.256 45.000 16.68 0.00 0.00 5.68
1346 1848 3.905705 GATGAGATCGCCGCCGGAG 62.906 68.421 7.68 2.79 34.56 4.63
1351 1853 3.825833 GATCGCCGCCGGAGTAGTG 62.826 68.421 7.68 0.00 34.56 2.74
1383 1885 1.065928 GCGATCCGATCTGTTCCGT 59.934 57.895 6.81 0.00 0.00 4.69
1384 1886 0.527817 GCGATCCGATCTGTTCCGTT 60.528 55.000 6.81 0.00 0.00 4.44
1385 1887 1.478137 CGATCCGATCTGTTCCGTTC 58.522 55.000 6.81 0.00 0.00 3.95
1386 1888 1.854227 GATCCGATCTGTTCCGTTCC 58.146 55.000 0.75 0.00 0.00 3.62
1387 1889 0.102481 ATCCGATCTGTTCCGTTCCG 59.898 55.000 0.00 0.00 0.00 4.30
1388 1890 1.214589 CCGATCTGTTCCGTTCCGT 59.785 57.895 0.00 0.00 0.00 4.69
1389 1891 0.389426 CCGATCTGTTCCGTTCCGTT 60.389 55.000 0.00 0.00 0.00 4.44
1390 1892 0.989890 CGATCTGTTCCGTTCCGTTC 59.010 55.000 0.00 0.00 0.00 3.95
1391 1893 1.356938 GATCTGTTCCGTTCCGTTCC 58.643 55.000 0.00 0.00 0.00 3.62
1392 1894 0.974383 ATCTGTTCCGTTCCGTTCCT 59.026 50.000 0.00 0.00 0.00 3.36
1745 2268 1.202177 CCCGTAAGCATGCACATCAAC 60.202 52.381 21.98 7.19 0.00 3.18
1749 2272 0.241749 AAGCATGCACATCAACCACG 59.758 50.000 21.98 0.00 0.00 4.94
1751 2274 1.865788 GCATGCACATCAACCACGGT 61.866 55.000 14.21 0.00 0.00 4.83
1755 2278 1.852067 GCACATCAACCACGGTGACC 61.852 60.000 10.28 0.00 33.16 4.02
1800 2323 3.499737 CGTTCTGACGCCCATGGC 61.500 66.667 6.09 0.58 46.75 4.40
1926 2449 5.640783 GCCATGAAATCCTTTTCTTTTCCTG 59.359 40.000 0.00 0.00 41.54 3.86
1950 2473 2.159626 CCTTTGTCTCTCTCGTCTCGAC 60.160 54.545 0.00 0.00 0.00 4.20
1964 2487 1.066143 TCTCGACCAAGAATCTTGGCC 60.066 52.381 34.77 26.33 43.23 5.36
1973 2496 0.960364 GAATCTTGGCCGGTCAAGCA 60.960 55.000 38.20 27.77 42.68 3.91
1977 2500 0.103937 CTTGGCCGGTCAAGCAAAAA 59.896 50.000 34.01 4.84 37.84 1.94
1979 2502 1.300620 GGCCGGTCAAGCAAAAACC 60.301 57.895 0.00 0.00 0.00 3.27
1998 2521 3.434637 ACCATTAAATAAAAGCGCGCTG 58.565 40.909 37.24 19.51 0.00 5.18
2013 2536 2.344872 CTGGCTTTGGCTTTGGGC 59.655 61.111 0.00 0.00 38.73 5.36
2418 2953 1.797933 CCGTCGAGCTCGTGACTTG 60.798 63.158 33.33 17.61 40.80 3.16
2462 2997 0.655733 CCTGCTTGTAAATACGCCCG 59.344 55.000 0.00 0.00 0.00 6.13
2559 3096 4.410400 CCCCAGCCCGAGTGGAAC 62.410 72.222 0.00 0.00 37.23 3.62
2568 3105 3.112709 GAGTGGAACCGCGTCTGC 61.113 66.667 4.92 0.00 37.80 4.26
2582 3119 2.845019 TCTGCCGTCAGATTTGCTG 58.155 52.632 0.00 0.00 43.95 4.41
2584 3121 2.262471 CTGCCGTCAGATTTGCTGCC 62.262 60.000 0.00 0.00 44.52 4.85
2586 3123 2.753966 CCGTCAGATTTGCTGCCCG 61.754 63.158 0.00 0.00 44.52 6.13
2630 3170 2.907910 ATTGTTGCATCAGAGTTCGC 57.092 45.000 0.00 0.00 0.00 4.70
2636 3176 2.610433 TGCATCAGAGTTCGCTGTTAG 58.390 47.619 3.79 0.00 37.20 2.34
2640 3180 1.202582 TCAGAGTTCGCTGTTAGCCTC 59.797 52.381 3.79 0.00 38.18 4.70
2746 3298 0.966920 GTGAGGGAGGACGTGAAAGA 59.033 55.000 0.00 0.00 0.00 2.52
2747 3299 1.343465 GTGAGGGAGGACGTGAAAGAA 59.657 52.381 0.00 0.00 0.00 2.52
2748 3300 2.043992 TGAGGGAGGACGTGAAAGAAA 58.956 47.619 0.00 0.00 0.00 2.52
2749 3301 2.037251 TGAGGGAGGACGTGAAAGAAAG 59.963 50.000 0.00 0.00 0.00 2.62
3040 3592 2.856032 CTGTGGCGTTTCTGCTCG 59.144 61.111 0.00 0.00 34.52 5.03
3137 3689 1.878522 CATCGACGCCCACTACTGC 60.879 63.158 0.00 0.00 0.00 4.40
3185 3758 9.084164 GTGAGTGAAAGCGTAGATAAGATTTTA 57.916 33.333 0.00 0.00 0.00 1.52
3217 3790 1.134694 GGTGAAAAGATGCGGCGTC 59.865 57.895 14.27 14.27 0.00 5.19
3228 3801 3.983562 CGGCGTCGTGTGTGTGTG 61.984 66.667 0.00 0.00 0.00 3.82
3229 3802 2.888534 GGCGTCGTGTGTGTGTGT 60.889 61.111 0.00 0.00 0.00 3.72
3230 3803 2.319707 GCGTCGTGTGTGTGTGTG 59.680 61.111 0.00 0.00 0.00 3.82
3231 3804 3.002673 CGTCGTGTGTGTGTGTGG 58.997 61.111 0.00 0.00 0.00 4.17
3232 3805 1.807981 CGTCGTGTGTGTGTGTGGT 60.808 57.895 0.00 0.00 0.00 4.16
3233 3806 1.713246 GTCGTGTGTGTGTGTGGTG 59.287 57.895 0.00 0.00 0.00 4.17
3234 3807 2.103647 TCGTGTGTGTGTGTGGTGC 61.104 57.895 0.00 0.00 0.00 5.01
3235 3808 2.403186 GTGTGTGTGTGTGGTGCG 59.597 61.111 0.00 0.00 0.00 5.34
3245 3818 2.260154 TGTGGTGCGCTCAACCATG 61.260 57.895 19.68 0.00 35.82 3.66
3250 3823 2.100031 TGCGCTCAACCATGCTACG 61.100 57.895 9.73 0.00 0.00 3.51
3253 3826 0.458543 CGCTCAACCATGCTACGACT 60.459 55.000 0.00 0.00 0.00 4.18
3254 3827 1.281899 GCTCAACCATGCTACGACTC 58.718 55.000 0.00 0.00 0.00 3.36
3256 3829 2.930887 GCTCAACCATGCTACGACTCAA 60.931 50.000 0.00 0.00 0.00 3.02
3257 3830 3.325870 CTCAACCATGCTACGACTCAAA 58.674 45.455 0.00 0.00 0.00 2.69
3258 3831 3.064207 TCAACCATGCTACGACTCAAAC 58.936 45.455 0.00 0.00 0.00 2.93
3259 3832 3.067106 CAACCATGCTACGACTCAAACT 58.933 45.455 0.00 0.00 0.00 2.66
3260 3833 2.688507 ACCATGCTACGACTCAAACTG 58.311 47.619 0.00 0.00 0.00 3.16
3261 3834 2.037251 ACCATGCTACGACTCAAACTGT 59.963 45.455 0.00 0.00 0.00 3.55
3262 3835 3.067106 CCATGCTACGACTCAAACTGTT 58.933 45.455 0.00 0.00 0.00 3.16
3266 3890 3.242608 TGCTACGACTCAAACTGTTTTGC 60.243 43.478 2.41 0.00 41.78 3.68
3267 3891 3.242608 GCTACGACTCAAACTGTTTTGCA 60.243 43.478 2.41 0.00 41.78 4.08
3333 3957 3.683115 CAACAGTGCTTACTTACGACG 57.317 47.619 0.00 0.00 0.00 5.12
3334 3958 2.342910 ACAGTGCTTACTTACGACGG 57.657 50.000 0.00 0.00 0.00 4.79
3335 3959 1.881973 ACAGTGCTTACTTACGACGGA 59.118 47.619 0.00 0.00 0.00 4.69
3336 3960 2.490903 ACAGTGCTTACTTACGACGGAT 59.509 45.455 0.00 0.00 0.00 4.18
3337 3961 2.852413 CAGTGCTTACTTACGACGGATG 59.148 50.000 0.00 0.00 0.00 3.51
3338 3962 2.751259 AGTGCTTACTTACGACGGATGA 59.249 45.455 0.00 0.00 0.00 2.92
3339 3963 3.106672 GTGCTTACTTACGACGGATGAG 58.893 50.000 0.00 0.00 0.00 2.90
3340 3964 2.751259 TGCTTACTTACGACGGATGAGT 59.249 45.455 0.00 0.00 0.00 3.41
3341 3965 3.106672 GCTTACTTACGACGGATGAGTG 58.893 50.000 0.00 0.00 0.00 3.51
3342 3966 3.692576 CTTACTTACGACGGATGAGTGG 58.307 50.000 0.00 0.00 0.00 4.00
3343 3967 1.542492 ACTTACGACGGATGAGTGGT 58.458 50.000 0.00 0.00 36.95 4.16
3344 3968 1.471684 ACTTACGACGGATGAGTGGTC 59.528 52.381 0.00 0.00 34.89 4.02
3346 3970 2.875485 CGACGGATGAGTGGTCGT 59.125 61.111 4.78 0.00 46.07 4.34
3347 3971 2.092374 CGACGGATGAGTGGTCGTA 58.908 57.895 4.78 0.00 46.07 3.43
3348 3972 0.661552 CGACGGATGAGTGGTCGTAT 59.338 55.000 4.78 0.00 46.07 3.06
3349 3973 1.333881 CGACGGATGAGTGGTCGTATC 60.334 57.143 4.78 0.00 46.07 2.24
3350 3974 1.674441 GACGGATGAGTGGTCGTATCA 59.326 52.381 0.00 0.00 35.91 2.15
3351 3975 2.293677 GACGGATGAGTGGTCGTATCAT 59.706 50.000 0.00 0.00 36.40 2.45
3352 3976 2.293677 ACGGATGAGTGGTCGTATCATC 59.706 50.000 5.97 5.97 45.57 2.92
3356 3980 3.165058 TGAGTGGTCGTATCATCAAGC 57.835 47.619 0.00 0.00 0.00 4.01
3357 3981 2.120232 GAGTGGTCGTATCATCAAGCG 58.880 52.381 0.00 0.00 0.00 4.68
3358 3982 1.749063 AGTGGTCGTATCATCAAGCGA 59.251 47.619 0.00 0.00 0.00 4.93
3359 3983 2.120232 GTGGTCGTATCATCAAGCGAG 58.880 52.381 0.00 0.00 33.90 5.03
3360 3984 1.132588 GGTCGTATCATCAAGCGAGC 58.867 55.000 0.00 0.00 42.85 5.03
3361 3985 1.536072 GGTCGTATCATCAAGCGAGCA 60.536 52.381 9.56 0.00 46.68 4.26
3362 3986 1.518929 GTCGTATCATCAAGCGAGCAC 59.481 52.381 0.00 0.00 33.90 4.40
3363 3987 1.405463 TCGTATCATCAAGCGAGCACT 59.595 47.619 0.00 0.00 0.00 4.40
3364 3988 1.520174 CGTATCATCAAGCGAGCACTG 59.480 52.381 0.00 0.00 0.00 3.66
3365 3989 1.260033 GTATCATCAAGCGAGCACTGC 59.740 52.381 0.00 0.00 0.00 4.40
3366 3990 1.426816 ATCATCAAGCGAGCACTGCG 61.427 55.000 0.00 0.00 37.44 5.18
3396 4020 2.963854 CGCCATACGCAGGAGCTG 60.964 66.667 0.00 0.00 39.10 4.24
3397 4021 2.187946 GCCATACGCAGGAGCTGT 59.812 61.111 0.00 0.00 39.10 4.40
3398 4022 1.884926 GCCATACGCAGGAGCTGTC 60.885 63.158 0.00 0.00 39.10 3.51
3399 4023 1.517361 CCATACGCAGGAGCTGTCA 59.483 57.895 0.00 0.00 39.10 3.58
3400 4024 0.108186 CCATACGCAGGAGCTGTCAA 60.108 55.000 0.00 0.00 39.10 3.18
3401 4025 1.284657 CATACGCAGGAGCTGTCAAG 58.715 55.000 0.00 0.00 39.10 3.02
3402 4026 0.176680 ATACGCAGGAGCTGTCAAGG 59.823 55.000 0.00 0.00 39.10 3.61
3403 4027 0.898326 TACGCAGGAGCTGTCAAGGA 60.898 55.000 0.00 0.00 39.10 3.36
3404 4028 1.447489 CGCAGGAGCTGTCAAGGAG 60.447 63.158 0.00 0.00 39.10 3.69
3405 4029 1.676384 GCAGGAGCTGTCAAGGAGT 59.324 57.895 0.00 0.00 37.91 3.85
3406 4030 0.898320 GCAGGAGCTGTCAAGGAGTA 59.102 55.000 0.00 0.00 37.91 2.59
3407 4031 1.404851 GCAGGAGCTGTCAAGGAGTAC 60.405 57.143 0.00 0.00 37.91 2.73
3408 4032 2.175202 CAGGAGCTGTCAAGGAGTACT 58.825 52.381 0.00 0.00 0.00 2.73
3409 4033 3.357203 CAGGAGCTGTCAAGGAGTACTA 58.643 50.000 0.00 0.00 0.00 1.82
3410 4034 3.129638 CAGGAGCTGTCAAGGAGTACTAC 59.870 52.174 0.00 0.00 0.00 2.73
3411 4035 3.090037 GGAGCTGTCAAGGAGTACTACA 58.910 50.000 8.10 1.35 0.00 2.74
3412 4036 3.510360 GGAGCTGTCAAGGAGTACTACAA 59.490 47.826 8.10 0.00 0.00 2.41
3413 4037 4.487019 GAGCTGTCAAGGAGTACTACAAC 58.513 47.826 8.10 3.20 0.00 3.32
3414 4038 3.057456 AGCTGTCAAGGAGTACTACAACG 60.057 47.826 8.10 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.010797 GCAGGCACGCATGATTACG 60.011 57.895 8.03 0.00 0.00 3.18
51 52 3.849527 ACTCTTTTCTTCCCCTGCAAAT 58.150 40.909 0.00 0.00 0.00 2.32
52 53 3.312736 ACTCTTTTCTTCCCCTGCAAA 57.687 42.857 0.00 0.00 0.00 3.68
53 54 2.958355 CAACTCTTTTCTTCCCCTGCAA 59.042 45.455 0.00 0.00 0.00 4.08
59 62 2.234143 AGCAGCAACTCTTTTCTTCCC 58.766 47.619 0.00 0.00 0.00 3.97
61 64 3.815401 TGGTAGCAGCAACTCTTTTCTTC 59.185 43.478 0.00 0.00 0.00 2.87
75 78 4.577283 GGAGAGAAGTAGTAGTGGTAGCAG 59.423 50.000 0.00 0.00 0.00 4.24
76 79 4.018688 TGGAGAGAAGTAGTAGTGGTAGCA 60.019 45.833 0.00 0.00 0.00 3.49
77 80 4.336153 GTGGAGAGAAGTAGTAGTGGTAGC 59.664 50.000 0.00 0.00 0.00 3.58
78 81 5.498393 TGTGGAGAGAAGTAGTAGTGGTAG 58.502 45.833 0.00 0.00 0.00 3.18
79 82 5.509832 TGTGGAGAGAAGTAGTAGTGGTA 57.490 43.478 0.00 0.00 0.00 3.25
80 83 4.383931 TGTGGAGAGAAGTAGTAGTGGT 57.616 45.455 0.00 0.00 0.00 4.16
81 84 5.163499 GGAATGTGGAGAGAAGTAGTAGTGG 60.163 48.000 0.00 0.00 0.00 4.00
82 85 5.163499 GGGAATGTGGAGAGAAGTAGTAGTG 60.163 48.000 0.00 0.00 0.00 2.74
83 86 4.957327 GGGAATGTGGAGAGAAGTAGTAGT 59.043 45.833 0.00 0.00 0.00 2.73
84 87 4.342665 GGGGAATGTGGAGAGAAGTAGTAG 59.657 50.000 0.00 0.00 0.00 2.57
85 88 4.287552 GGGGAATGTGGAGAGAAGTAGTA 58.712 47.826 0.00 0.00 0.00 1.82
86 89 3.108376 GGGGAATGTGGAGAGAAGTAGT 58.892 50.000 0.00 0.00 0.00 2.73
108 111 2.583593 GAGCCGATCCGTGTCTGC 60.584 66.667 0.00 0.00 0.00 4.26
122 125 2.899044 CGGAGGAGATCGGTCGAGC 61.899 68.421 4.06 4.06 0.00 5.03
190 193 1.404748 CGTGCATGCCCATGTAATTCA 59.595 47.619 16.68 0.00 40.80 2.57
191 194 1.865248 GCGTGCATGCCCATGTAATTC 60.865 52.381 20.59 0.00 40.80 2.17
192 195 0.102844 GCGTGCATGCCCATGTAATT 59.897 50.000 20.59 0.00 40.80 1.40
193 196 1.036481 TGCGTGCATGCCCATGTAAT 61.036 50.000 27.43 0.00 40.80 1.89
194 197 1.036481 ATGCGTGCATGCCCATGTAA 61.036 50.000 27.43 7.89 40.80 2.41
195 198 1.036481 AATGCGTGCATGCCCATGTA 61.036 50.000 27.43 8.66 40.80 2.29
196 199 1.890625 AAATGCGTGCATGCCCATGT 61.891 50.000 27.43 8.24 40.80 3.21
262 265 1.068417 CGATGGCAATGGCAATGGG 59.932 57.895 14.81 0.00 42.43 4.00
274 277 2.733227 GCCTATAATTGCATGCGATGGC 60.733 50.000 23.88 23.88 40.52 4.40
275 278 2.751259 AGCCTATAATTGCATGCGATGG 59.249 45.455 21.25 17.61 0.00 3.51
276 279 3.688185 AGAGCCTATAATTGCATGCGATG 59.312 43.478 21.25 9.30 0.00 3.84
277 280 3.947868 AGAGCCTATAATTGCATGCGAT 58.052 40.909 15.05 15.05 0.00 4.58
278 281 3.407424 AGAGCCTATAATTGCATGCGA 57.593 42.857 10.79 10.79 0.00 5.10
279 282 5.808042 ATTAGAGCCTATAATTGCATGCG 57.192 39.130 14.09 0.00 0.00 4.73
280 283 7.121168 TGGTAATTAGAGCCTATAATTGCATGC 59.879 37.037 17.65 11.82 37.11 4.06
312 315 1.751927 CCTGGCCTGCATGGAAGTC 60.752 63.158 3.32 0.00 38.35 3.01
336 339 3.000222 CGTGTGTGTTCATATGATCGGTG 60.000 47.826 6.17 0.00 0.00 4.94
374 382 2.547211 GAGGAGGAATGATGAATGTGCG 59.453 50.000 0.00 0.00 0.00 5.34
405 413 8.390921 AGAAAAGGAATGGGAAAAGATACTGTA 58.609 33.333 0.00 0.00 0.00 2.74
406 414 7.177392 CAGAAAAGGAATGGGAAAAGATACTGT 59.823 37.037 0.00 0.00 0.00 3.55
407 415 7.542025 CAGAAAAGGAATGGGAAAAGATACTG 58.458 38.462 0.00 0.00 0.00 2.74
408 416 6.153510 GCAGAAAAGGAATGGGAAAAGATACT 59.846 38.462 0.00 0.00 0.00 2.12
409 417 6.071391 TGCAGAAAAGGAATGGGAAAAGATAC 60.071 38.462 0.00 0.00 0.00 2.24
418 426 0.897621 GGGTGCAGAAAAGGAATGGG 59.102 55.000 0.00 0.00 0.00 4.00
430 438 1.476471 GGAGAGGAATGATGGGTGCAG 60.476 57.143 0.00 0.00 0.00 4.41
445 453 0.398381 CCAAGGAGGAGGAGGGAGAG 60.398 65.000 0.00 0.00 41.22 3.20
447 455 0.980231 CACCAAGGAGGAGGAGGGAG 60.980 65.000 0.00 0.00 41.22 4.30
448 456 1.081092 CACCAAGGAGGAGGAGGGA 59.919 63.158 0.00 0.00 41.22 4.20
450 458 0.325671 TAGCACCAAGGAGGAGGAGG 60.326 60.000 0.00 0.00 41.22 4.30
452 460 1.500474 CATAGCACCAAGGAGGAGGA 58.500 55.000 0.00 0.00 41.22 3.71
453 461 0.179034 GCATAGCACCAAGGAGGAGG 60.179 60.000 0.00 0.00 41.22 4.30
454 462 0.179034 GGCATAGCACCAAGGAGGAG 60.179 60.000 0.00 0.00 41.22 3.69
455 463 1.635817 GGGCATAGCACCAAGGAGGA 61.636 60.000 0.00 0.00 41.22 3.71
467 475 4.159506 GTGAGATTCTAGCTAGGGGCATAG 59.840 50.000 20.58 0.00 44.79 2.23
468 476 4.090090 GTGAGATTCTAGCTAGGGGCATA 58.910 47.826 20.58 0.00 44.79 3.14
469 477 2.903135 GTGAGATTCTAGCTAGGGGCAT 59.097 50.000 20.58 7.95 44.79 4.40
470 478 2.091055 AGTGAGATTCTAGCTAGGGGCA 60.091 50.000 20.58 9.25 44.79 5.36
471 479 2.560981 GAGTGAGATTCTAGCTAGGGGC 59.439 54.545 20.58 9.76 42.19 5.80
472 480 2.817258 CGAGTGAGATTCTAGCTAGGGG 59.183 54.545 20.58 0.00 0.00 4.79
473 481 3.482436 ACGAGTGAGATTCTAGCTAGGG 58.518 50.000 20.58 0.00 0.00 3.53
474 482 4.213270 CAGACGAGTGAGATTCTAGCTAGG 59.787 50.000 20.58 3.07 0.00 3.02
475 483 4.319477 GCAGACGAGTGAGATTCTAGCTAG 60.319 50.000 15.01 15.01 0.00 3.42
476 484 3.562141 GCAGACGAGTGAGATTCTAGCTA 59.438 47.826 0.00 0.00 0.00 3.32
477 485 2.357637 GCAGACGAGTGAGATTCTAGCT 59.642 50.000 0.00 0.00 0.00 3.32
478 486 2.098280 TGCAGACGAGTGAGATTCTAGC 59.902 50.000 0.00 0.00 0.00 3.42
497 625 5.618561 CGTCAGTAAGTAATTTTGGAGTGC 58.381 41.667 0.00 0.00 0.00 4.40
512 640 0.038251 CTGGAGCTGTGCGTCAGTAA 60.038 55.000 0.00 0.00 45.23 2.24
518 659 4.008933 GGACCTGGAGCTGTGCGT 62.009 66.667 0.00 0.00 0.00 5.24
519 660 3.947132 CTGGACCTGGAGCTGTGCG 62.947 68.421 0.00 0.00 0.00 5.34
526 667 1.748122 GTGCATGCTGGACCTGGAG 60.748 63.158 20.33 0.00 32.15 3.86
535 676 3.490759 GACCCGTCGTGCATGCTG 61.491 66.667 20.33 11.68 0.00 4.41
561 702 3.115556 GGCCGAATTTATGCCGCA 58.884 55.556 0.00 0.00 35.08 5.69
565 706 6.583806 CAGATTCTTTATGGCCGAATTTATGC 59.416 38.462 0.00 0.00 0.00 3.14
575 716 0.954452 CCCGCAGATTCTTTATGGCC 59.046 55.000 0.00 0.00 0.00 5.36
597 738 4.129737 TCTTCTTCTCCGGCCGCG 62.130 66.667 22.85 13.93 0.00 6.46
598 739 2.202810 CTCTTCTTCTCCGGCCGC 60.203 66.667 22.85 0.00 0.00 6.53
599 740 2.202810 GCTCTTCTTCTCCGGCCG 60.203 66.667 21.04 21.04 0.00 6.13
600 741 2.188207 GGCTCTTCTTCTCCGGCC 59.812 66.667 0.00 0.00 0.00 6.13
601 742 2.202810 CGGCTCTTCTTCTCCGGC 60.203 66.667 0.00 0.00 38.35 6.13
603 744 1.032657 TCTCCGGCTCTTCTTCTCCG 61.033 60.000 0.00 0.00 41.41 4.63
604 745 0.744281 CTCTCCGGCTCTTCTTCTCC 59.256 60.000 0.00 0.00 0.00 3.71
605 746 0.744281 CCTCTCCGGCTCTTCTTCTC 59.256 60.000 0.00 0.00 0.00 2.87
606 747 0.333312 TCCTCTCCGGCTCTTCTTCT 59.667 55.000 0.00 0.00 0.00 2.85
607 748 0.744281 CTCCTCTCCGGCTCTTCTTC 59.256 60.000 0.00 0.00 0.00 2.87
608 749 0.686112 CCTCCTCTCCGGCTCTTCTT 60.686 60.000 0.00 0.00 0.00 2.52
609 750 1.076339 CCTCCTCTCCGGCTCTTCT 60.076 63.158 0.00 0.00 0.00 2.85
610 751 1.076632 TCCTCCTCTCCGGCTCTTC 60.077 63.158 0.00 0.00 0.00 2.87
611 752 1.076339 CTCCTCCTCTCCGGCTCTT 60.076 63.158 0.00 0.00 0.00 2.85
612 753 2.600731 CTCCTCCTCTCCGGCTCT 59.399 66.667 0.00 0.00 0.00 4.09
613 754 3.223589 GCTCCTCCTCTCCGGCTC 61.224 72.222 0.00 0.00 0.00 4.70
618 759 2.841988 ATGCCGCTCCTCCTCTCC 60.842 66.667 0.00 0.00 0.00 3.71
619 760 2.420890 CATGCCGCTCCTCCTCTC 59.579 66.667 0.00 0.00 0.00 3.20
620 761 3.859414 GCATGCCGCTCCTCCTCT 61.859 66.667 6.36 0.00 37.77 3.69
621 762 4.166888 TGCATGCCGCTCCTCCTC 62.167 66.667 16.68 0.00 43.06 3.71
622 763 4.172512 CTGCATGCCGCTCCTCCT 62.173 66.667 16.68 0.00 43.06 3.69
682 1127 5.890424 TCTTTCCCCTTTTATAAACAGCG 57.110 39.130 0.00 0.00 0.00 5.18
734 1179 0.584876 AAAGCGGCGCGGTAATAATC 59.415 50.000 27.59 0.00 36.27 1.75
749 1194 2.729491 GTGGTTCGCGGCAAAAGC 60.729 61.111 6.13 3.02 0.00 3.51
829 1289 1.170290 GGTTTGACCAGTTGACGGGG 61.170 60.000 5.34 0.00 38.42 5.73
830 1290 1.170290 GGGTTTGACCAGTTGACGGG 61.170 60.000 0.00 0.00 41.02 5.28
831 1291 1.503818 CGGGTTTGACCAGTTGACGG 61.504 60.000 0.00 0.00 41.02 4.79
866 1336 0.465460 CCTCCTCTCTCTCCTCCGTG 60.465 65.000 0.00 0.00 0.00 4.94
879 1358 2.612251 CTCCCTCCCTCCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
880 1359 3.039526 CCTCCCTCCCTCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
881 1360 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
882 1361 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
883 1362 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
884 1363 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
885 1364 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
886 1365 4.179599 CCCCTCCCTCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
887 1366 4.761304 TCCCCTCCCTCCCTCCCT 62.761 72.222 0.00 0.00 0.00 4.20
888 1367 4.179599 CTCCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
889 1368 3.369388 ACTCCCCTCCCTCCCTCC 61.369 72.222 0.00 0.00 0.00 4.30
890 1369 2.284151 GACTCCCCTCCCTCCCTC 59.716 72.222 0.00 0.00 0.00 4.30
891 1370 3.369388 GGACTCCCCTCCCTCCCT 61.369 72.222 0.00 0.00 0.00 4.20
978 1457 2.267681 CTACCAGCAGGACGGACGAC 62.268 65.000 0.35 0.00 38.69 4.34
1009 1506 3.013932 CTCCCCCAAGCTCAGCCT 61.014 66.667 0.00 0.00 0.00 4.58
1112 1609 2.920384 GATCCCTCCTCCCCTCGC 60.920 72.222 0.00 0.00 0.00 5.03
1113 1610 1.834822 GTGATCCCTCCTCCCCTCG 60.835 68.421 0.00 0.00 0.00 4.63
1286 1786 4.932146 ACACAAATCCAAGAAACGGAAAG 58.068 39.130 0.00 0.00 35.77 2.62
1307 1809 1.130955 CACGGCATGCAGAAACAAAC 58.869 50.000 24.99 0.00 0.00 2.93
1308 1810 3.566273 CACGGCATGCAGAAACAAA 57.434 47.368 24.99 0.00 0.00 2.83
1346 1848 1.215647 CCCGTCTCAGCACCACTAC 59.784 63.158 0.00 0.00 0.00 2.73
1383 1885 0.404040 AAATGCCCTGAGGAACGGAA 59.596 50.000 0.00 0.00 33.47 4.30
1384 1886 0.322456 CAAATGCCCTGAGGAACGGA 60.322 55.000 0.00 0.00 33.47 4.69
1385 1887 1.315257 CCAAATGCCCTGAGGAACGG 61.315 60.000 0.00 0.00 33.47 4.44
1386 1888 0.322456 TCCAAATGCCCTGAGGAACG 60.322 55.000 0.00 0.00 33.47 3.95
1387 1889 1.467920 CTCCAAATGCCCTGAGGAAC 58.532 55.000 0.00 0.00 33.47 3.62
1388 1890 0.332632 CCTCCAAATGCCCTGAGGAA 59.667 55.000 0.00 0.00 45.93 3.36
1389 1891 2.001803 CCTCCAAATGCCCTGAGGA 58.998 57.895 0.00 0.00 45.93 3.71
1390 1892 1.755783 GCCTCCAAATGCCCTGAGG 60.756 63.158 0.00 0.00 45.83 3.86
1391 1893 2.117156 CGCCTCCAAATGCCCTGAG 61.117 63.158 0.00 0.00 0.00 3.35
1392 1894 2.045045 CGCCTCCAAATGCCCTGA 60.045 61.111 0.00 0.00 0.00 3.86
1749 2272 2.852180 GCAAACGGGGTTGGTCACC 61.852 63.158 0.00 0.00 46.46 4.02
1751 2274 0.183014 TAAGCAAACGGGGTTGGTCA 59.817 50.000 1.18 0.00 38.23 4.02
1755 2278 1.033574 TGGTTAAGCAAACGGGGTTG 58.966 50.000 4.54 0.00 39.13 3.77
1808 2331 4.749310 ACCTTCTGCCTCTGCGCG 62.749 66.667 0.00 0.00 41.78 6.86
1926 2449 1.816224 AGACGAGAGAGACAAAGGAGC 59.184 52.381 0.00 0.00 0.00 4.70
1950 2473 0.322456 TGACCGGCCAAGATTCTTGG 60.322 55.000 32.46 32.46 42.37 3.61
1964 2487 7.644986 TTATTTAATGGTTTTTGCTTGACCG 57.355 32.000 0.00 0.00 36.22 4.79
1973 2496 5.407084 AGCGCGCTTTTATTTAATGGTTTTT 59.593 32.000 31.32 0.00 0.00 1.94
1977 2500 3.434637 CAGCGCGCTTTTATTTAATGGT 58.565 40.909 34.58 1.37 0.00 3.55
1979 2502 2.216263 GCCAGCGCGCTTTTATTTAATG 59.784 45.455 34.58 16.93 0.00 1.90
1998 2521 2.659016 GAGCCCAAAGCCAAAGCC 59.341 61.111 0.00 0.00 45.47 4.35
2375 2910 4.453892 AATGGAGGCTGGGGCTGC 62.454 66.667 0.00 5.74 45.89 5.25
2433 2968 4.120755 CAAGCAGGCCCTCCCTCC 62.121 72.222 0.00 0.00 44.09 4.30
2434 2969 1.562672 TTACAAGCAGGCCCTCCCTC 61.563 60.000 0.00 0.00 44.09 4.30
2462 2997 2.737252 CGAGGAGCGGAAATATTAAGGC 59.263 50.000 0.00 0.00 36.03 4.35
2551 3088 3.112709 GCAGACGCGGTTCCACTC 61.113 66.667 12.47 0.00 0.00 3.51
2586 3123 2.879813 TTTAAGCATCCGGGCCGTCC 62.880 60.000 26.32 9.65 0.00 4.79
2595 3132 5.700373 TGCAACAATTTTCCTTTAAGCATCC 59.300 36.000 0.00 0.00 0.00 3.51
2630 3170 3.648009 GGAGATTGATCGAGGCTAACAG 58.352 50.000 0.00 0.00 0.00 3.16
2636 3176 1.218230 GCACGGAGATTGATCGAGGC 61.218 60.000 0.00 0.00 0.00 4.70
2640 3180 3.680642 AAAATGCACGGAGATTGATCG 57.319 42.857 0.00 0.00 0.00 3.69
2721 3273 0.750911 ACGTCCTCCCTCACGGATAC 60.751 60.000 0.00 0.00 41.00 2.24
2722 3274 0.750546 CACGTCCTCCCTCACGGATA 60.751 60.000 0.00 0.00 41.00 2.59
2738 3290 5.030874 ACTAAATTCCGCTTTCTTTCACG 57.969 39.130 0.00 0.00 0.00 4.35
3022 3574 2.558313 GAGCAGAAACGCCACAGC 59.442 61.111 0.00 0.00 0.00 4.40
3040 3592 3.737172 AACACCATCGCGGCAAGC 61.737 61.111 6.13 0.00 43.95 4.01
3117 3669 2.954868 GTAGTGGGCGTCGATGCG 60.955 66.667 22.62 7.32 35.06 4.73
3122 3674 4.063967 TGGCAGTAGTGGGCGTCG 62.064 66.667 0.00 0.00 0.00 5.12
3137 3689 2.753452 TCTACCAGTAAAGAGCGAGTGG 59.247 50.000 0.00 0.00 41.28 4.00
3199 3772 1.134694 GACGCCGCATCTTTTCACC 59.865 57.895 0.00 0.00 0.00 4.02
3217 3790 2.403186 GCACCACACACACACACG 59.597 61.111 0.00 0.00 0.00 4.49
3227 3800 2.112928 ATGGTTGAGCGCACCACA 59.887 55.556 19.21 7.82 36.24 4.17
3228 3801 2.562912 CATGGTTGAGCGCACCAC 59.437 61.111 19.21 10.30 36.24 4.16
3229 3802 2.462125 TAGCATGGTTGAGCGCACCA 62.462 55.000 19.13 19.13 37.99 4.17
3230 3803 1.745115 TAGCATGGTTGAGCGCACC 60.745 57.895 11.47 9.68 35.48 5.01
3231 3804 1.425428 GTAGCATGGTTGAGCGCAC 59.575 57.895 11.47 3.13 35.48 5.34
3232 3805 2.100031 CGTAGCATGGTTGAGCGCA 61.100 57.895 11.47 0.00 35.48 6.09
3233 3806 1.809619 TCGTAGCATGGTTGAGCGC 60.810 57.895 1.12 0.00 35.48 5.92
3234 3807 0.458543 AGTCGTAGCATGGTTGAGCG 60.459 55.000 1.12 3.73 35.48 5.03
3235 3808 1.281899 GAGTCGTAGCATGGTTGAGC 58.718 55.000 1.12 0.00 0.00 4.26
3245 3818 3.242608 TGCAAAACAGTTTGAGTCGTAGC 60.243 43.478 0.00 0.00 45.99 3.58
3259 3832 4.831698 GCACTTGGCTGCAAAACA 57.168 50.000 0.50 0.00 40.25 2.83
3275 3899 7.359933 CGCTACTACACCATAGTTAGTACTAGC 60.360 44.444 8.59 8.59 40.09 3.42
3277 3901 7.500992 ACGCTACTACACCATAGTTAGTACTA 58.499 38.462 0.00 0.00 40.96 1.82
3278 3902 6.352516 ACGCTACTACACCATAGTTAGTACT 58.647 40.000 0.00 0.00 38.44 2.73
3283 3907 7.282901 TGTTCATACGCTACTACACCATAGTTA 59.717 37.037 0.00 0.00 0.00 2.24
3287 3911 6.453926 TTGTTCATACGCTACTACACCATA 57.546 37.500 0.00 0.00 0.00 2.74
3321 3945 3.128242 ACCACTCATCCGTCGTAAGTAAG 59.872 47.826 0.00 0.00 39.48 2.34
3326 3950 0.448990 CGACCACTCATCCGTCGTAA 59.551 55.000 0.00 0.00 43.29 3.18
3327 3951 2.092374 CGACCACTCATCCGTCGTA 58.908 57.895 0.00 0.00 43.29 3.43
3328 3952 2.875485 CGACCACTCATCCGTCGT 59.125 61.111 0.00 0.00 43.29 4.34
3330 3954 1.674441 TGATACGACCACTCATCCGTC 59.326 52.381 0.00 0.00 36.58 4.79
3331 3955 1.758936 TGATACGACCACTCATCCGT 58.241 50.000 0.00 0.00 38.82 4.69
3332 3956 2.293399 TGATGATACGACCACTCATCCG 59.707 50.000 8.76 0.00 42.92 4.18
3333 3957 4.302455 CTTGATGATACGACCACTCATCC 58.698 47.826 8.76 0.00 42.92 3.51
3334 3958 3.738282 GCTTGATGATACGACCACTCATC 59.262 47.826 5.11 5.11 43.54 2.92
3335 3959 3.722147 GCTTGATGATACGACCACTCAT 58.278 45.455 0.00 0.00 32.46 2.90
3336 3960 2.479560 CGCTTGATGATACGACCACTCA 60.480 50.000 0.00 0.00 0.00 3.41
3337 3961 2.120232 CGCTTGATGATACGACCACTC 58.880 52.381 0.00 0.00 0.00 3.51
3338 3962 1.749063 TCGCTTGATGATACGACCACT 59.251 47.619 0.00 0.00 0.00 4.00
3339 3963 2.120232 CTCGCTTGATGATACGACCAC 58.880 52.381 0.00 0.00 0.00 4.16
3340 3964 1.536072 GCTCGCTTGATGATACGACCA 60.536 52.381 0.00 0.00 0.00 4.02
3341 3965 1.132588 GCTCGCTTGATGATACGACC 58.867 55.000 0.00 0.00 0.00 4.79
3342 3966 1.518929 GTGCTCGCTTGATGATACGAC 59.481 52.381 0.00 0.00 0.00 4.34
3343 3967 1.405463 AGTGCTCGCTTGATGATACGA 59.595 47.619 0.00 0.00 0.00 3.43
3344 3968 1.520174 CAGTGCTCGCTTGATGATACG 59.480 52.381 0.00 0.00 0.00 3.06
3345 3969 1.260033 GCAGTGCTCGCTTGATGATAC 59.740 52.381 8.18 0.00 0.00 2.24
3346 3970 1.575244 GCAGTGCTCGCTTGATGATA 58.425 50.000 8.18 0.00 0.00 2.15
3347 3971 1.426816 CGCAGTGCTCGCTTGATGAT 61.427 55.000 14.33 0.00 0.00 2.45
3348 3972 2.096442 CGCAGTGCTCGCTTGATGA 61.096 57.895 14.33 0.00 0.00 2.92
3349 3973 2.398429 CGCAGTGCTCGCTTGATG 59.602 61.111 14.33 0.00 0.00 3.07
3380 4004 1.884926 GACAGCTCCTGCGTATGGC 60.885 63.158 0.00 0.00 45.42 4.40
3381 4005 0.108186 TTGACAGCTCCTGCGTATGG 60.108 55.000 0.00 0.00 45.42 2.74
3382 4006 1.284657 CTTGACAGCTCCTGCGTATG 58.715 55.000 0.00 0.00 45.42 2.39
3383 4007 0.176680 CCTTGACAGCTCCTGCGTAT 59.823 55.000 0.00 0.00 45.42 3.06
3384 4008 0.898326 TCCTTGACAGCTCCTGCGTA 60.898 55.000 0.00 0.00 45.42 4.42
3385 4009 2.164865 CTCCTTGACAGCTCCTGCGT 62.165 60.000 0.00 0.00 45.42 5.24
3386 4010 1.447489 CTCCTTGACAGCTCCTGCG 60.447 63.158 0.00 0.00 45.42 5.18
3387 4011 0.898320 TACTCCTTGACAGCTCCTGC 59.102 55.000 0.00 0.00 34.37 4.85
3388 4012 2.175202 AGTACTCCTTGACAGCTCCTG 58.825 52.381 0.00 0.00 37.52 3.86
3389 4013 2.614134 AGTACTCCTTGACAGCTCCT 57.386 50.000 0.00 0.00 0.00 3.69
3390 4014 3.090037 TGTAGTACTCCTTGACAGCTCC 58.910 50.000 0.00 0.00 0.00 4.70
3391 4015 4.487019 GTTGTAGTACTCCTTGACAGCTC 58.513 47.826 0.00 0.00 0.00 4.09
3392 4016 3.057456 CGTTGTAGTACTCCTTGACAGCT 60.057 47.826 0.00 0.00 0.00 4.24
3393 4017 3.243336 CGTTGTAGTACTCCTTGACAGC 58.757 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.