Multiple sequence alignment - TraesCS3B01G127400

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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 TraesCS3B01G127400 chr3B 100.000 3189 0 0 1 3189 106118962 106122150 0.000000e+00 5890
1 TraesCS3B01G127400 chr3D 86.083 2637 158 76 46 2536 64172758 64175331 0.000000e+00 2643
2 TraesCS3B01G127400 chr3D 79.383 616 101 17 2541 3135 567536768 567536158 8.230000e-111 411
3 TraesCS3B01G127400 chr3A 82.789 1685 136 68 905 2529 73929920 73931510 0.000000e+00 1363
4 TraesCS3B01G127400 chr3A 85.341 880 45 30 33 872 73929010 73929845 0.000000e+00 833
5 TraesCS3B01G127400 chr3A 79.698 596 96 13 2541 3115 702923062 702922471 1.070000e-109 407
6 TraesCS3B01G127400 chr5D 85.833 600 64 11 2541 3121 9634888 9634291 4.520000e-173 617
7 TraesCS3B01G127400 chr1D 84.039 614 74 13 2541 3134 24579837 24580446 1.280000e-158 569
8 TraesCS3B01G127400 chr1D 77.349 596 107 16 2542 3115 391111494 391110905 8.530000e-86 327
9 TraesCS3B01G127400 chr1D 86.260 131 18 0 1546 1676 125823234 125823364 3.320000e-30 143
10 TraesCS3B01G127400 chr2D 83.876 614 75 13 2541 3134 623441345 623441954 5.970000e-157 564
11 TraesCS3B01G127400 chr2D 83.333 612 79 12 2541 3132 466400676 466400068 7.780000e-151 544
12 TraesCS3B01G127400 chr1A 83.388 614 79 12 2541 3134 137913759 137913149 6.010000e-152 547
13 TraesCS3B01G127400 chr1A 87.786 131 16 0 1546 1676 139553681 139553811 1.530000e-33 154
14 TraesCS3B01G127400 chr5B 81.879 596 83 12 2541 3115 611724639 611724048 2.230000e-131 479
15 TraesCS3B01G127400 chr7D 80.806 620 92 16 2541 3137 53372289 53371674 8.060000e-126 460
16 TraesCS3B01G127400 chr7D 80.690 580 78 18 2541 3099 588796549 588797115 1.370000e-113 420
17 TraesCS3B01G127400 chr6B 80.556 612 88 18 2541 3129 697810871 697811474 2.920000e-120 442
18 TraesCS3B01G127400 chr1B 87.786 131 16 0 1546 1676 189584390 189584520 1.530000e-33 154


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 TraesCS3B01G127400 chr3B 106118962 106122150 3188 False 5890 5890 100.000 1 3189 1 chr3B.!!$F1 3188
1 TraesCS3B01G127400 chr3D 64172758 64175331 2573 False 2643 2643 86.083 46 2536 1 chr3D.!!$F1 2490
2 TraesCS3B01G127400 chr3D 567536158 567536768 610 True 411 411 79.383 2541 3135 1 chr3D.!!$R1 594
3 TraesCS3B01G127400 chr3A 73929010 73931510 2500 False 1098 1363 84.065 33 2529 2 chr3A.!!$F1 2496
4 TraesCS3B01G127400 chr3A 702922471 702923062 591 True 407 407 79.698 2541 3115 1 chr3A.!!$R1 574
5 TraesCS3B01G127400 chr5D 9634291 9634888 597 True 617 617 85.833 2541 3121 1 chr5D.!!$R1 580
6 TraesCS3B01G127400 chr1D 24579837 24580446 609 False 569 569 84.039 2541 3134 1 chr1D.!!$F1 593
7 TraesCS3B01G127400 chr1D 391110905 391111494 589 True 327 327 77.349 2542 3115 1 chr1D.!!$R1 573
8 TraesCS3B01G127400 chr2D 623441345 623441954 609 False 564 564 83.876 2541 3134 1 chr2D.!!$F1 593
9 TraesCS3B01G127400 chr2D 466400068 466400676 608 True 544 544 83.333 2541 3132 1 chr2D.!!$R1 591
10 TraesCS3B01G127400 chr1A 137913149 137913759 610 True 547 547 83.388 2541 3134 1 chr1A.!!$R1 593
11 TraesCS3B01G127400 chr5B 611724048 611724639 591 True 479 479 81.879 2541 3115 1 chr5B.!!$R1 574
12 TraesCS3B01G127400 chr7D 53371674 53372289 615 True 460 460 80.806 2541 3137 1 chr7D.!!$R1 596
13 TraesCS3B01G127400 chr7D 588796549 588797115 566 False 420 420 80.690 2541 3099 1 chr7D.!!$F1 558
14 TraesCS3B01G127400 chr6B 697810871 697811474 603 False 442 442 80.556 2541 3129 1 chr6B.!!$F1 588

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
51 52 0.033796 ATACACTCGGGAGTCGGGAA 60.034 55.0 0.0 0.0 43.26 3.97 F
901 1030 0.043053 CACGCTTGTGACTTGTCGTG 60.043 55.0 0.0 0.0 46.91 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1295 1463 0.17924 GTCAGATCAACGCTGCAACG 60.179 55.0 8.18 8.18 39.5 4.10 R
2465 2713 0.16747 CAACACCATTCGAGCAGCAG 59.833 55.0 0.00 0.00 0.0 4.24 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
21 22 4.672587 TCCAGCATATAGGACACTGTTC 57.327 45.455 0.00 0.00 0.00 3.18
22 23 3.388024 TCCAGCATATAGGACACTGTTCC 59.612 47.826 0.00 2.10 35.66 3.62
23 24 3.134623 CCAGCATATAGGACACTGTTCCA 59.865 47.826 10.30 0.46 38.25 3.53
24 25 4.384098 CCAGCATATAGGACACTGTTCCAA 60.384 45.833 10.30 0.00 38.25 3.53
25 26 4.813161 CAGCATATAGGACACTGTTCCAAG 59.187 45.833 10.30 0.00 38.25 3.61
26 27 4.471386 AGCATATAGGACACTGTTCCAAGT 59.529 41.667 10.30 0.00 38.25 3.16
27 28 5.661312 AGCATATAGGACACTGTTCCAAGTA 59.339 40.000 10.30 3.05 38.25 2.24
28 29 6.327626 AGCATATAGGACACTGTTCCAAGTAT 59.672 38.462 10.30 4.37 38.25 2.12
29 30 6.992715 GCATATAGGACACTGTTCCAAGTATT 59.007 38.462 10.30 0.00 38.25 1.89
30 31 7.499232 GCATATAGGACACTGTTCCAAGTATTT 59.501 37.037 10.30 0.00 38.25 1.40
31 32 9.396022 CATATAGGACACTGTTCCAAGTATTTT 57.604 33.333 10.30 0.00 38.25 1.82
37 38 8.448615 GGACACTGTTCCAAGTATTTTATACAC 58.551 37.037 0.00 0.00 35.49 2.90
39 40 9.216117 ACACTGTTCCAAGTATTTTATACACTC 57.784 33.333 0.00 0.00 0.00 3.51
51 52 0.033796 ATACACTCGGGAGTCGGGAA 60.034 55.000 0.00 0.00 43.26 3.97
183 185 7.093322 AGCCATCAGATCACAAAAGAATAAC 57.907 36.000 0.00 0.00 0.00 1.89
184 186 6.660521 AGCCATCAGATCACAAAAGAATAACA 59.339 34.615 0.00 0.00 0.00 2.41
199 201 6.126863 AGAATAACAGAAACAGTGGGATCA 57.873 37.500 0.00 0.00 0.00 2.92
213 215 5.975693 GTGGGATCACTTTTGTTTATGGA 57.024 39.130 0.00 0.00 40.58 3.41
214 216 6.530019 GTGGGATCACTTTTGTTTATGGAT 57.470 37.500 0.00 0.00 40.58 3.41
215 217 6.564328 GTGGGATCACTTTTGTTTATGGATC 58.436 40.000 0.00 0.00 40.58 3.36
218 220 5.893824 GGATCACTTTTGTTTATGGATCCCT 59.106 40.000 9.90 1.08 39.32 4.20
220 222 5.261216 TCACTTTTGTTTATGGATCCCTCC 58.739 41.667 9.90 0.00 42.45 4.30
221 223 4.402474 CACTTTTGTTTATGGATCCCTCCC 59.598 45.833 9.90 0.00 41.29 4.30
295 297 0.978667 ACAACCCAACCCAACCCAAC 60.979 55.000 0.00 0.00 0.00 3.77
299 301 0.978146 CCCAACCCAACCCAACACAA 60.978 55.000 0.00 0.00 0.00 3.33
300 302 0.176910 CCAACCCAACCCAACACAAC 59.823 55.000 0.00 0.00 0.00 3.32
301 303 0.898320 CAACCCAACCCAACACAACA 59.102 50.000 0.00 0.00 0.00 3.33
314 316 1.227556 ACAACACACACTCGCTCCC 60.228 57.895 0.00 0.00 0.00 4.30
323 325 0.682855 CACTCGCTCCCTCCTTCTCT 60.683 60.000 0.00 0.00 0.00 3.10
351 360 2.771763 AAACCCGCAGCAGAGAGACG 62.772 60.000 0.00 0.00 0.00 4.18
352 361 4.504916 CCCGCAGCAGAGAGACGG 62.505 72.222 0.00 0.00 43.44 4.79
353 362 3.443925 CCGCAGCAGAGAGACGGA 61.444 66.667 0.00 0.00 46.71 4.69
354 363 2.101965 CGCAGCAGAGAGACGGAG 59.898 66.667 0.00 0.00 0.00 4.63
355 364 2.402572 CGCAGCAGAGAGACGGAGA 61.403 63.158 0.00 0.00 0.00 3.71
356 365 1.138671 GCAGCAGAGAGACGGAGAC 59.861 63.158 0.00 0.00 0.00 3.36
376 385 2.875933 ACGAGATAGAAAGAGCGAGAGG 59.124 50.000 0.00 0.00 0.00 3.69
377 386 3.135225 CGAGATAGAAAGAGCGAGAGGA 58.865 50.000 0.00 0.00 0.00 3.71
378 387 3.186409 CGAGATAGAAAGAGCGAGAGGAG 59.814 52.174 0.00 0.00 0.00 3.69
379 388 4.385825 GAGATAGAAAGAGCGAGAGGAGA 58.614 47.826 0.00 0.00 0.00 3.71
380 389 4.389374 AGATAGAAAGAGCGAGAGGAGAG 58.611 47.826 0.00 0.00 0.00 3.20
438 460 2.281761 CCGTGCTTGGCTCTGGTT 60.282 61.111 0.00 0.00 0.00 3.67
439 461 1.898574 CCGTGCTTGGCTCTGGTTT 60.899 57.895 0.00 0.00 0.00 3.27
440 462 1.283793 CGTGCTTGGCTCTGGTTTG 59.716 57.895 0.00 0.00 0.00 2.93
441 463 1.662044 GTGCTTGGCTCTGGTTTGG 59.338 57.895 0.00 0.00 0.00 3.28
442 464 2.202395 TGCTTGGCTCTGGTTTGGC 61.202 57.895 0.00 0.00 0.00 4.52
443 465 2.935740 GCTTGGCTCTGGTTTGGCC 61.936 63.158 0.00 0.00 45.45 5.36
444 466 2.203625 TTGGCTCTGGTTTGGCCC 60.204 61.111 0.00 0.00 44.71 5.80
445 467 2.720144 CTTGGCTCTGGTTTGGCCCT 62.720 60.000 0.00 0.00 44.71 5.19
446 468 2.677875 GGCTCTGGTTTGGCCCTG 60.678 66.667 0.00 0.00 39.96 4.45
447 469 2.677875 GCTCTGGTTTGGCCCTGG 60.678 66.667 0.00 0.00 36.04 4.45
448 470 2.846532 CTCTGGTTTGGCCCTGGT 59.153 61.111 0.00 0.00 36.04 4.00
482 504 1.226018 CTCGTTTCATTTCGCGGCC 60.226 57.895 6.13 0.00 0.00 6.13
552 579 1.227674 GGCCTAGATTCGTGCCAGG 60.228 63.158 0.00 0.00 43.46 4.45
589 619 0.796927 GGGAGCCGTTTCTTTCTTCG 59.203 55.000 0.00 0.00 0.00 3.79
590 620 0.166161 GGAGCCGTTTCTTTCTTCGC 59.834 55.000 0.00 0.00 0.00 4.70
591 621 0.179248 GAGCCGTTTCTTTCTTCGCG 60.179 55.000 0.00 0.00 0.00 5.87
646 689 2.457778 GCTTTGAATACGCGCCCGA 61.458 57.895 5.73 0.00 38.29 5.14
647 690 1.347221 CTTTGAATACGCGCCCGAC 59.653 57.895 5.73 0.00 38.29 4.79
648 691 2.032185 CTTTGAATACGCGCCCGACC 62.032 60.000 5.73 0.00 38.29 4.79
649 692 2.510064 TTTGAATACGCGCCCGACCT 62.510 55.000 5.73 0.00 38.29 3.85
650 693 2.657620 GAATACGCGCCCGACCTC 60.658 66.667 5.73 0.00 38.29 3.85
651 694 4.217159 AATACGCGCCCGACCTCC 62.217 66.667 5.73 0.00 38.29 4.30
666 709 3.430497 TCCCTCCCTCCCTCCTCG 61.430 72.222 0.00 0.00 0.00 4.63
811 873 4.671590 TCGGTCTCAGGTGGGCGA 62.672 66.667 0.00 0.00 0.00 5.54
814 876 4.459089 GTCTCAGGTGGGCGAGCC 62.459 72.222 5.37 5.37 0.00 4.70
836 898 1.526917 GTCCAGCACCTGCACTGTT 60.527 57.895 0.00 0.00 45.16 3.16
865 945 3.162666 TCTCTTCCGCCATATATTCCGT 58.837 45.455 2.28 0.00 0.00 4.69
867 947 2.894765 TCTTCCGCCATATATTCCGTCA 59.105 45.455 2.28 0.00 0.00 4.35
872 952 1.346365 CCATATATTCCGTCACCGCG 58.654 55.000 0.00 0.00 0.00 6.46
873 953 0.713883 CATATATTCCGTCACCGCGC 59.286 55.000 0.00 0.00 0.00 6.86
900 1029 0.459585 ACACGCTTGTGACTTGTCGT 60.460 50.000 0.00 0.00 46.91 4.34
901 1030 0.043053 CACGCTTGTGACTTGTCGTG 60.043 55.000 0.00 0.00 46.91 4.35
902 1031 0.179121 ACGCTTGTGACTTGTCGTGA 60.179 50.000 0.00 0.00 0.00 4.35
903 1032 0.504384 CGCTTGTGACTTGTCGTGAG 59.496 55.000 0.00 0.00 0.00 3.51
984 1114 3.691342 CGAGGTTGCCAGGGACGA 61.691 66.667 0.00 0.00 0.00 4.20
1065 1200 2.835431 GAGCTCAGCCTCGGCCTA 60.835 66.667 9.40 0.00 43.17 3.93
1109 1271 0.447801 GCACCGACAGCAGGTAATTG 59.552 55.000 0.00 0.00 40.59 2.32
1170 1332 1.372582 TCATCCGAGCTTTCATGCAC 58.627 50.000 0.00 0.00 34.99 4.57
1206 1368 1.303317 GTCAGGTTTGGACGGGCAT 60.303 57.895 0.00 0.00 0.00 4.40
1250 1418 1.743252 CTCGCCAACCTCAAGGAGC 60.743 63.158 2.30 2.07 38.94 4.70
1257 1425 1.891150 CAACCTCAAGGAGCAAGCAAT 59.109 47.619 2.30 0.00 38.94 3.56
1287 1455 5.097742 AGGCCAAGTAAGCAAAAACTTTT 57.902 34.783 5.01 0.00 33.72 2.27
1289 1457 5.584649 AGGCCAAGTAAGCAAAAACTTTTTC 59.415 36.000 5.01 0.00 33.72 2.29
1294 1462 8.382875 CCAAGTAAGCAAAAACTTTTTCTTCAG 58.617 33.333 3.58 0.00 35.71 3.02
1295 1463 7.525688 AGTAAGCAAAAACTTTTTCTTCAGC 57.474 32.000 3.58 6.57 35.71 4.26
1328 1496 4.703897 TGATCTGACCGTCTTTGTTCTTT 58.296 39.130 0.00 0.00 0.00 2.52
1330 1498 5.926542 TGATCTGACCGTCTTTGTTCTTTAG 59.073 40.000 0.00 0.00 0.00 1.85
1334 1502 6.819649 TCTGACCGTCTTTGTTCTTTAGAAAA 59.180 34.615 0.00 0.00 35.58 2.29
1335 1503 7.334921 TCTGACCGTCTTTGTTCTTTAGAAAAA 59.665 33.333 0.00 0.00 35.58 1.94
1336 1504 7.992008 TGACCGTCTTTGTTCTTTAGAAAAAT 58.008 30.769 0.00 0.00 35.58 1.82
1339 1507 9.893305 ACCGTCTTTGTTCTTTAGAAAAATATG 57.107 29.630 0.00 0.00 35.58 1.78
1340 1508 9.893305 CCGTCTTTGTTCTTTAGAAAAATATGT 57.107 29.630 0.00 0.00 35.58 2.29
1368 1545 6.795098 TTTTTATGCTTCGTCTGTGTACAT 57.205 33.333 0.00 0.00 0.00 2.29
1509 1692 0.030235 GGCAACCAAAGACAACGACC 59.970 55.000 0.00 0.00 0.00 4.79
1687 1872 1.373435 CCGGTACACACCCACACAT 59.627 57.895 0.00 0.00 42.43 3.21
1711 1896 3.059120 CACACCATGCATCATCGATCTTC 60.059 47.826 0.00 0.00 0.00 2.87
1712 1897 2.483106 CACCATGCATCATCGATCTTCC 59.517 50.000 0.00 0.00 0.00 3.46
1713 1898 1.730612 CCATGCATCATCGATCTTCCG 59.269 52.381 0.00 0.00 0.00 4.30
1714 1899 2.410939 CATGCATCATCGATCTTCCGT 58.589 47.619 0.00 0.00 0.00 4.69
1715 1900 2.602257 TGCATCATCGATCTTCCGTT 57.398 45.000 0.00 0.00 0.00 4.44
1716 1901 2.473816 TGCATCATCGATCTTCCGTTC 58.526 47.619 0.00 0.00 0.00 3.95
1723 1908 0.736325 CGATCTTCCGTTCCGCTGTT 60.736 55.000 0.00 0.00 0.00 3.16
1755 1944 1.240256 ACTCTCGTGGTCTCACTCAC 58.760 55.000 0.00 0.00 41.53 3.51
1794 1983 1.350684 TGCATGTAGCTCAAAGGGACA 59.649 47.619 0.00 0.00 45.94 4.02
1799 1988 1.192146 TAGCTCAAAGGGACACCGCT 61.192 55.000 0.00 0.00 43.47 5.52
1900 2089 1.134401 CGTCCCATGGCAGTAAGTCAT 60.134 52.381 6.09 0.00 45.27 3.06
1901 2090 2.565841 GTCCCATGGCAGTAAGTCATC 58.434 52.381 6.09 0.00 41.62 2.92
1902 2091 1.138859 TCCCATGGCAGTAAGTCATCG 59.861 52.381 6.09 0.00 41.62 3.84
1903 2092 1.134401 CCCATGGCAGTAAGTCATCGT 60.134 52.381 6.09 0.00 41.62 3.73
1904 2093 2.632377 CCATGGCAGTAAGTCATCGTT 58.368 47.619 0.00 0.00 41.62 3.85
1906 2095 3.804325 CCATGGCAGTAAGTCATCGTTAG 59.196 47.826 0.00 0.00 41.62 2.34
1909 2098 4.491676 TGGCAGTAAGTCATCGTTAGAAC 58.508 43.478 0.00 0.00 0.00 3.01
1910 2099 4.021807 TGGCAGTAAGTCATCGTTAGAACA 60.022 41.667 0.00 0.00 0.00 3.18
1911 2100 4.563184 GGCAGTAAGTCATCGTTAGAACAG 59.437 45.833 0.00 0.00 0.00 3.16
1912 2101 5.162075 GCAGTAAGTCATCGTTAGAACAGT 58.838 41.667 0.00 0.00 0.00 3.55
1913 2102 5.634020 GCAGTAAGTCATCGTTAGAACAGTT 59.366 40.000 0.00 0.00 0.00 3.16
1920 2109 5.924825 GTCATCGTTAGAACAGTTACACCTT 59.075 40.000 0.00 0.00 0.00 3.50
1921 2110 5.924254 TCATCGTTAGAACAGTTACACCTTG 59.076 40.000 0.00 0.00 0.00 3.61
1931 2120 2.949644 AGTTACACCTTGGACAAGTTGC 59.050 45.455 9.17 0.00 34.65 4.17
1935 2124 1.750778 CACCTTGGACAAGTTGCAACT 59.249 47.619 26.36 26.36 42.04 3.16
1936 2125 2.948979 CACCTTGGACAAGTTGCAACTA 59.051 45.455 31.31 13.63 38.57 2.24
1937 2126 3.569701 CACCTTGGACAAGTTGCAACTAT 59.430 43.478 31.31 22.33 38.57 2.12
1938 2127 4.759693 CACCTTGGACAAGTTGCAACTATA 59.240 41.667 31.31 13.60 38.57 1.31
1960 2149 5.943706 ATATGCTGAATCTGATGAACTGC 57.056 39.130 0.00 3.33 0.00 4.40
1963 2162 2.613133 GCTGAATCTGATGAACTGCCTC 59.387 50.000 0.00 0.00 0.00 4.70
2056 2263 3.215151 TCATCGGTGAGTATCTCTGGAC 58.785 50.000 0.00 0.00 35.75 4.02
2057 2264 2.801077 TCGGTGAGTATCTCTGGACA 57.199 50.000 0.00 0.00 35.75 4.02
2070 2277 5.503634 TCTCTGGACAAAATCTGAATCCA 57.496 39.130 0.00 0.00 37.11 3.41
2071 2278 6.070951 TCTCTGGACAAAATCTGAATCCAT 57.929 37.500 0.00 0.00 38.74 3.41
2078 2292 6.057321 ACAAAATCTGAATCCATTGGCATT 57.943 33.333 0.00 0.00 0.00 3.56
2118 2332 6.458206 GCATTAACTGAACCAAATCGCTATCA 60.458 38.462 0.00 0.00 0.00 2.15
2272 2511 1.804151 TGAAATCACGGCTGCTGTAAC 59.196 47.619 14.72 5.00 0.00 2.50
2282 2521 1.404315 GCTGCTGTAACTAGAGCCGTT 60.404 52.381 0.00 0.00 41.45 4.44
2314 2554 1.573376 ACTGCTATTTTGGGGGCCATA 59.427 47.619 4.39 0.00 31.53 2.74
2416 2660 7.370383 AGTTTGTTCTTGGTATAATTGCACAG 58.630 34.615 0.00 0.00 0.00 3.66
2417 2661 5.895636 TGTTCTTGGTATAATTGCACAGG 57.104 39.130 0.00 0.00 0.00 4.00
2454 2702 2.882324 TCTTTGCCGGTTGTTTGTTTC 58.118 42.857 1.90 0.00 0.00 2.78
2455 2703 2.494073 TCTTTGCCGGTTGTTTGTTTCT 59.506 40.909 1.90 0.00 0.00 2.52
2456 2704 2.285827 TTGCCGGTTGTTTGTTTCTG 57.714 45.000 1.90 0.00 0.00 3.02
2457 2705 1.178276 TGCCGGTTGTTTGTTTCTGT 58.822 45.000 1.90 0.00 0.00 3.41
2458 2706 1.135257 TGCCGGTTGTTTGTTTCTGTG 60.135 47.619 1.90 0.00 0.00 3.66
2459 2707 1.801025 GCCGGTTGTTTGTTTCTGTGG 60.801 52.381 1.90 0.00 0.00 4.17
2460 2708 1.474879 CCGGTTGTTTGTTTCTGTGGT 59.525 47.619 0.00 0.00 0.00 4.16
2461 2709 2.525055 CGGTTGTTTGTTTCTGTGGTG 58.475 47.619 0.00 0.00 0.00 4.17
2462 2710 2.267426 GGTTGTTTGTTTCTGTGGTGC 58.733 47.619 0.00 0.00 0.00 5.01
2465 2713 1.135141 TGTTTGTTTCTGTGGTGCTGC 60.135 47.619 0.00 0.00 0.00 5.25
2494 2742 2.582052 GAATGGTGTTGGTTCAGGTCA 58.418 47.619 0.00 0.00 0.00 4.02
2556 2804 0.890542 TGCTGCACCTACCAAGCTTG 60.891 55.000 19.93 19.93 0.00 4.01
2615 2863 4.690280 CCTTCAGTGAGAGAGAGCTTTTTC 59.310 45.833 0.00 0.00 0.00 2.29
2617 2865 2.992543 CAGTGAGAGAGAGCTTTTTCGG 59.007 50.000 0.00 0.00 0.00 4.30
2629 2877 2.552315 GCTTTTTCGGACTGGACAATGA 59.448 45.455 0.00 0.00 0.00 2.57
2639 2887 4.885907 GGACTGGACAATGATGTTGATGAT 59.114 41.667 0.00 0.00 40.74 2.45
2646 2894 7.342541 TGGACAATGATGTTGATGATGGTTTAT 59.657 33.333 0.00 0.00 40.74 1.40
2651 2899 6.363882 TGATGTTGATGATGGTTTATAGCCA 58.636 36.000 1.32 1.32 40.68 4.75
2674 2924 4.717877 TGCAATCCAACTCTTCTCAAGAA 58.282 39.130 0.00 0.00 37.02 2.52
2679 2929 7.303998 CAATCCAACTCTTCTCAAGAAATCAC 58.696 38.462 0.00 0.00 37.02 3.06
2686 2936 6.072618 ACTCTTCTCAAGAAATCACTTGCATG 60.073 38.462 0.00 0.00 44.52 4.06
2690 2940 6.210796 TCTCAAGAAATCACTTGCATGTTTG 58.789 36.000 1.83 4.61 44.52 2.93
2691 2941 5.291178 TCAAGAAATCACTTGCATGTTTGG 58.709 37.500 1.83 0.00 44.52 3.28
2709 2975 0.891904 GGCGCCCACCTTCTGTTTTA 60.892 55.000 18.11 0.00 0.00 1.52
2710 2976 0.521735 GCGCCCACCTTCTGTTTTAG 59.478 55.000 0.00 0.00 0.00 1.85
2736 3002 8.504815 GTTAACCTCAATACCAAGAAAGAAGTC 58.495 37.037 0.00 0.00 0.00 3.01
2744 3010 8.526147 CAATACCAAGAAAGAAGTCCAAATCAT 58.474 33.333 0.00 0.00 0.00 2.45
2745 3011 6.336842 ACCAAGAAAGAAGTCCAAATCATG 57.663 37.500 0.00 0.00 0.00 3.07
2761 3030 3.581024 TCATGCAAATCCAGAGCAAAC 57.419 42.857 0.00 0.00 42.15 2.93
2793 3062 6.057533 TCAAATCTGACAAAAGAGCTCTCAA 58.942 36.000 18.55 2.48 0.00 3.02
2794 3063 6.713903 TCAAATCTGACAAAAGAGCTCTCAAT 59.286 34.615 18.55 3.57 0.00 2.57
2797 3066 5.371526 TCTGACAAAAGAGCTCTCAATTGT 58.628 37.500 28.42 28.42 40.69 2.71
2817 3086 5.261209 TGTTTCATTTGAGGAACTTGTGG 57.739 39.130 0.00 0.00 41.55 4.17
2829 3098 6.889177 TGAGGAACTTGTGGCAATTATATCAA 59.111 34.615 0.00 0.00 41.55 2.57
2941 3210 8.373992 GTTGTTGCAATTTTGTACTTAAACGAA 58.626 29.630 0.59 0.00 0.00 3.85
2963 3232 0.398664 TACCAGGCTCTAGGGGCTTC 60.399 60.000 17.63 0.00 40.17 3.86
2985 3254 8.688151 GCTTCTTTTAGTCCATAGAGAGACTTA 58.312 37.037 0.00 0.00 40.43 2.24
2993 3263 5.303078 GTCCATAGAGAGACTTATCAAGCCA 59.697 44.000 0.00 0.00 0.00 4.75
3009 3279 2.001361 GCCAGCACACATGAGATGGC 62.001 60.000 20.10 20.10 41.39 4.40
3023 3293 6.318144 ACATGAGATGGCTTGTTCTTATCTTG 59.682 38.462 0.00 0.00 33.60 3.02
3027 3297 7.448161 TGAGATGGCTTGTTCTTATCTTGAAAA 59.552 33.333 0.00 0.00 0.00 2.29
3031 3301 6.097554 TGGCTTGTTCTTATCTTGAAAACCAA 59.902 34.615 0.00 0.00 0.00 3.67
3062 3332 6.070251 TGCTTCATATACACTTCCTCTTCCAA 60.070 38.462 0.00 0.00 0.00 3.53
3071 3341 5.070001 CACTTCCTCTTCCAAAACACCATA 58.930 41.667 0.00 0.00 0.00 2.74
3100 3370 3.336468 GCATTCTGCATATCTAGCTGCT 58.664 45.455 7.57 7.57 44.26 4.24
3115 3385 1.759445 GCTGCTTGAGACTCCATCCTA 59.241 52.381 0.00 0.00 0.00 2.94
3118 3388 3.640498 CTGCTTGAGACTCCATCCTATGA 59.360 47.826 0.00 0.00 0.00 2.15
3121 3391 4.996122 GCTTGAGACTCCATCCTATGAATG 59.004 45.833 0.00 0.00 0.00 2.67
3137 3407 4.603989 TGAATGCAACAATGGACAACAT 57.396 36.364 0.00 0.00 43.07 2.71
3138 3408 4.308265 TGAATGCAACAATGGACAACATG 58.692 39.130 0.00 0.00 40.44 3.21
3139 3409 4.038883 TGAATGCAACAATGGACAACATGA 59.961 37.500 0.00 0.00 40.44 3.07
3140 3410 3.646611 TGCAACAATGGACAACATGAG 57.353 42.857 0.00 0.00 40.44 2.90
3141 3411 2.296752 TGCAACAATGGACAACATGAGG 59.703 45.455 0.00 0.00 40.44 3.86
3142 3412 2.297033 GCAACAATGGACAACATGAGGT 59.703 45.455 0.00 0.00 40.44 3.85
3143 3413 3.243839 GCAACAATGGACAACATGAGGTT 60.244 43.478 0.00 0.00 40.44 3.50
3144 3414 4.740334 GCAACAATGGACAACATGAGGTTT 60.740 41.667 0.00 0.00 40.44 3.27
3145 3415 5.358922 CAACAATGGACAACATGAGGTTTT 58.641 37.500 0.00 0.00 40.44 2.43
3146 3416 4.947645 ACAATGGACAACATGAGGTTTTG 58.052 39.130 0.00 0.00 40.44 2.44
3147 3417 3.665745 ATGGACAACATGAGGTTTTGC 57.334 42.857 0.00 0.00 38.70 3.68
3148 3418 2.382882 TGGACAACATGAGGTTTTGCA 58.617 42.857 0.00 0.00 37.72 4.08
3149 3419 2.361757 TGGACAACATGAGGTTTTGCAG 59.638 45.455 0.00 0.00 37.72 4.41
3150 3420 2.362077 GGACAACATGAGGTTTTGCAGT 59.638 45.455 0.00 0.00 37.72 4.40
3151 3421 3.181476 GGACAACATGAGGTTTTGCAGTT 60.181 43.478 0.00 0.00 37.72 3.16
3152 3422 4.432712 GACAACATGAGGTTTTGCAGTTT 58.567 39.130 0.00 0.00 37.72 2.66
3153 3423 4.831107 ACAACATGAGGTTTTGCAGTTTT 58.169 34.783 0.00 0.00 37.72 2.43
3154 3424 4.869861 ACAACATGAGGTTTTGCAGTTTTC 59.130 37.500 0.00 0.00 37.72 2.29
3155 3425 5.111293 CAACATGAGGTTTTGCAGTTTTCT 58.889 37.500 0.00 0.00 37.72 2.52
3156 3426 5.343307 ACATGAGGTTTTGCAGTTTTCTT 57.657 34.783 0.00 0.00 0.00 2.52
3157 3427 5.733676 ACATGAGGTTTTGCAGTTTTCTTT 58.266 33.333 0.00 0.00 0.00 2.52
3158 3428 6.172630 ACATGAGGTTTTGCAGTTTTCTTTT 58.827 32.000 0.00 0.00 0.00 2.27
3159 3429 6.313658 ACATGAGGTTTTGCAGTTTTCTTTTC 59.686 34.615 0.00 0.00 0.00 2.29
3160 3430 6.036577 TGAGGTTTTGCAGTTTTCTTTTCT 57.963 33.333 0.00 0.00 0.00 2.52
3161 3431 6.099341 TGAGGTTTTGCAGTTTTCTTTTCTC 58.901 36.000 0.00 0.00 0.00 2.87
3162 3432 5.419542 AGGTTTTGCAGTTTTCTTTTCTCC 58.580 37.500 0.00 0.00 0.00 3.71
3163 3433 5.187772 AGGTTTTGCAGTTTTCTTTTCTCCT 59.812 36.000 0.00 0.00 0.00 3.69
3164 3434 6.379988 AGGTTTTGCAGTTTTCTTTTCTCCTA 59.620 34.615 0.00 0.00 0.00 2.94
3165 3435 6.697455 GGTTTTGCAGTTTTCTTTTCTCCTAG 59.303 38.462 0.00 0.00 0.00 3.02
3166 3436 7.258441 GTTTTGCAGTTTTCTTTTCTCCTAGT 58.742 34.615 0.00 0.00 0.00 2.57
3167 3437 7.404671 TTTGCAGTTTTCTTTTCTCCTAGTT 57.595 32.000 0.00 0.00 0.00 2.24
3168 3438 7.404671 TTGCAGTTTTCTTTTCTCCTAGTTT 57.595 32.000 0.00 0.00 0.00 2.66
3169 3439 6.795399 TGCAGTTTTCTTTTCTCCTAGTTTG 58.205 36.000 0.00 0.00 0.00 2.93
3170 3440 6.183360 TGCAGTTTTCTTTTCTCCTAGTTTGG 60.183 38.462 0.00 0.00 0.00 3.28
3171 3441 6.183360 GCAGTTTTCTTTTCTCCTAGTTTGGT 60.183 38.462 0.00 0.00 0.00 3.67
3172 3442 7.418408 CAGTTTTCTTTTCTCCTAGTTTGGTC 58.582 38.462 0.00 0.00 0.00 4.02
3173 3443 7.283354 CAGTTTTCTTTTCTCCTAGTTTGGTCT 59.717 37.037 0.00 0.00 0.00 3.85
3174 3444 7.499563 AGTTTTCTTTTCTCCTAGTTTGGTCTC 59.500 37.037 0.00 0.00 0.00 3.36
3175 3445 6.494666 TTCTTTTCTCCTAGTTTGGTCTCA 57.505 37.500 0.00 0.00 0.00 3.27
3176 3446 6.688073 TCTTTTCTCCTAGTTTGGTCTCAT 57.312 37.500 0.00 0.00 0.00 2.90
3177 3447 6.467677 TCTTTTCTCCTAGTTTGGTCTCATG 58.532 40.000 0.00 0.00 0.00 3.07
3178 3448 4.826274 TTCTCCTAGTTTGGTCTCATGG 57.174 45.455 0.00 0.00 0.00 3.66
3179 3449 3.791320 TCTCCTAGTTTGGTCTCATGGT 58.209 45.455 0.00 0.00 0.00 3.55
3180 3450 3.515502 TCTCCTAGTTTGGTCTCATGGTG 59.484 47.826 0.00 0.00 0.00 4.17
3181 3451 3.248024 TCCTAGTTTGGTCTCATGGTGT 58.752 45.455 0.00 0.00 0.00 4.16
3182 3452 3.007940 TCCTAGTTTGGTCTCATGGTGTG 59.992 47.826 0.00 0.00 0.00 3.82
3183 3453 1.609208 AGTTTGGTCTCATGGTGTGC 58.391 50.000 0.00 0.00 0.00 4.57
3184 3454 1.133823 AGTTTGGTCTCATGGTGTGCA 60.134 47.619 0.00 0.00 0.00 4.57
3185 3455 1.680735 GTTTGGTCTCATGGTGTGCAA 59.319 47.619 0.00 0.00 0.00 4.08
3186 3456 2.064434 TTGGTCTCATGGTGTGCAAA 57.936 45.000 0.00 0.00 0.00 3.68
3187 3457 1.608055 TGGTCTCATGGTGTGCAAAG 58.392 50.000 0.00 0.00 0.00 2.77
3188 3458 1.142667 TGGTCTCATGGTGTGCAAAGA 59.857 47.619 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.388024 GGAACAGTGTCCTATATGCTGGA 59.612 47.826 0.00 0.00 34.56 3.86
1 2 3.134623 TGGAACAGTGTCCTATATGCTGG 59.865 47.826 0.00 0.00 38.62 4.85
2 3 4.406648 TGGAACAGTGTCCTATATGCTG 57.593 45.455 0.00 0.00 38.62 4.41
3 4 4.471386 ACTTGGAACAGTGTCCTATATGCT 59.529 41.667 0.00 0.00 42.39 3.79
4 5 4.770795 ACTTGGAACAGTGTCCTATATGC 58.229 43.478 0.00 0.00 42.39 3.14
5 6 8.964476 AAATACTTGGAACAGTGTCCTATATG 57.036 34.615 0.00 0.00 42.39 1.78
9 10 9.880157 GTATAAAATACTTGGAACAGTGTCCTA 57.120 33.333 0.00 0.00 42.39 2.94
10 11 8.380099 TGTATAAAATACTTGGAACAGTGTCCT 58.620 33.333 0.00 0.00 42.39 3.85
11 12 8.448615 GTGTATAAAATACTTGGAACAGTGTCC 58.551 37.037 0.00 0.21 42.39 4.02
12 13 9.216117 AGTGTATAAAATACTTGGAACAGTGTC 57.784 33.333 0.00 0.00 42.39 3.67
13 14 9.216117 GAGTGTATAAAATACTTGGAACAGTGT 57.784 33.333 0.00 0.00 42.39 3.55
14 15 8.380644 CGAGTGTATAAAATACTTGGAACAGTG 58.619 37.037 0.00 0.00 42.39 3.66
15 16 7.548075 CCGAGTGTATAAAATACTTGGAACAGT 59.452 37.037 0.00 0.00 45.10 3.55
16 17 7.011109 CCCGAGTGTATAAAATACTTGGAACAG 59.989 40.741 10.68 0.00 45.10 3.16
17 18 6.819649 CCCGAGTGTATAAAATACTTGGAACA 59.180 38.462 10.68 0.00 45.10 3.18
18 19 7.043565 TCCCGAGTGTATAAAATACTTGGAAC 58.956 38.462 10.68 0.00 45.10 3.62
19 20 7.093201 ACTCCCGAGTGTATAAAATACTTGGAA 60.093 37.037 10.68 0.00 45.10 3.53
20 21 6.381994 ACTCCCGAGTGTATAAAATACTTGGA 59.618 38.462 10.68 4.25 45.10 3.53
21 22 6.579865 ACTCCCGAGTGTATAAAATACTTGG 58.420 40.000 0.00 0.00 42.95 3.61
22 23 6.417044 CGACTCCCGAGTGTATAAAATACTTG 59.583 42.308 1.17 0.00 42.66 3.16
23 24 6.460676 CCGACTCCCGAGTGTATAAAATACTT 60.461 42.308 1.17 0.00 42.66 2.24
24 25 5.009410 CCGACTCCCGAGTGTATAAAATACT 59.991 44.000 1.17 0.00 42.66 2.12
25 26 5.218139 CCGACTCCCGAGTGTATAAAATAC 58.782 45.833 1.17 0.00 42.66 1.89
26 27 4.279169 CCCGACTCCCGAGTGTATAAAATA 59.721 45.833 1.17 0.00 42.66 1.40
27 28 3.069158 CCCGACTCCCGAGTGTATAAAAT 59.931 47.826 1.17 0.00 42.66 1.82
28 29 2.428171 CCCGACTCCCGAGTGTATAAAA 59.572 50.000 1.17 0.00 42.66 1.52
29 30 2.026641 CCCGACTCCCGAGTGTATAAA 58.973 52.381 1.17 0.00 42.66 1.40
30 31 1.212688 TCCCGACTCCCGAGTGTATAA 59.787 52.381 1.17 0.00 42.66 0.98
31 32 0.839277 TCCCGACTCCCGAGTGTATA 59.161 55.000 1.17 0.00 42.66 1.47
37 38 1.248785 TTGTCTTCCCGACTCCCGAG 61.249 60.000 0.00 0.00 43.25 4.63
39 40 0.034337 TTTTGTCTTCCCGACTCCCG 59.966 55.000 0.00 0.00 43.25 5.14
51 52 0.178990 GCACCCTCCCTGTTTTGTCT 60.179 55.000 0.00 0.00 0.00 3.41
173 175 7.505585 TGATCCCACTGTTTCTGTTATTCTTTT 59.494 33.333 0.00 0.00 0.00 2.27
199 201 4.294970 AGGGAGGGATCCATAAACAAAAGT 59.705 41.667 15.23 0.00 0.00 2.66
206 208 2.429383 GGAGGAGGGAGGGATCCATAAA 60.429 54.545 15.23 0.00 38.12 1.40
209 211 1.556561 GGAGGAGGGAGGGATCCAT 59.443 63.158 15.23 6.26 38.12 3.41
210 212 3.037715 GGAGGAGGGAGGGATCCA 58.962 66.667 15.23 0.00 38.12 3.41
211 213 2.203714 CGGAGGAGGGAGGGATCC 60.204 72.222 1.92 1.92 35.71 3.36
213 215 1.383248 CAACGGAGGAGGGAGGGAT 60.383 63.158 0.00 0.00 0.00 3.85
214 216 2.038975 CAACGGAGGAGGGAGGGA 59.961 66.667 0.00 0.00 0.00 4.20
215 217 3.787001 GCAACGGAGGAGGGAGGG 61.787 72.222 0.00 0.00 0.00 4.30
220 222 2.358737 AAAGCGCAACGGAGGAGG 60.359 61.111 11.47 0.00 0.00 4.30
221 223 2.391389 GGAAAGCGCAACGGAGGAG 61.391 63.158 11.47 0.00 0.00 3.69
295 297 1.498865 GGGAGCGAGTGTGTGTTGTG 61.499 60.000 0.00 0.00 0.00 3.33
299 301 2.574955 GGAGGGAGCGAGTGTGTGT 61.575 63.158 0.00 0.00 0.00 3.72
300 302 1.821061 AAGGAGGGAGCGAGTGTGTG 61.821 60.000 0.00 0.00 0.00 3.82
301 303 1.534235 AAGGAGGGAGCGAGTGTGT 60.534 57.895 0.00 0.00 0.00 3.72
314 316 3.333804 GTTTGAAGAGCCAGAGAAGGAG 58.666 50.000 0.00 0.00 0.00 3.69
323 325 1.600636 CTGCGGGTTTGAAGAGCCA 60.601 57.895 0.00 0.00 37.01 4.75
351 360 2.873472 TCGCTCTTTCTATCTCGTCTCC 59.127 50.000 0.00 0.00 0.00 3.71
352 361 3.805422 TCTCGCTCTTTCTATCTCGTCTC 59.195 47.826 0.00 0.00 0.00 3.36
353 362 3.799366 TCTCGCTCTTTCTATCTCGTCT 58.201 45.455 0.00 0.00 0.00 4.18
354 363 3.059188 CCTCTCGCTCTTTCTATCTCGTC 60.059 52.174 0.00 0.00 0.00 4.20
355 364 2.875933 CCTCTCGCTCTTTCTATCTCGT 59.124 50.000 0.00 0.00 0.00 4.18
356 365 3.135225 TCCTCTCGCTCTTTCTATCTCG 58.865 50.000 0.00 0.00 0.00 4.04
360 369 3.137544 TCCTCTCCTCTCGCTCTTTCTAT 59.862 47.826 0.00 0.00 0.00 1.98
365 374 0.916086 TCTCCTCTCCTCTCGCTCTT 59.084 55.000 0.00 0.00 0.00 2.85
376 385 1.452145 CGGCTGCCTACTCTCCTCTC 61.452 65.000 17.92 0.00 0.00 3.20
377 386 1.454847 CGGCTGCCTACTCTCCTCT 60.455 63.158 17.92 0.00 0.00 3.69
378 387 1.324005 AACGGCTGCCTACTCTCCTC 61.324 60.000 17.92 0.00 0.00 3.71
379 388 1.305381 AACGGCTGCCTACTCTCCT 60.305 57.895 17.92 0.00 0.00 3.69
380 389 1.153549 CAACGGCTGCCTACTCTCC 60.154 63.158 17.92 0.00 0.00 3.71
421 437 1.898574 AAACCAGAGCCAAGCACGG 60.899 57.895 0.00 0.00 0.00 4.94
472 494 2.512515 GAGCAGAGGCCGCGAAAT 60.513 61.111 8.23 0.00 42.56 2.17
482 504 1.739338 ATTCCGGCGTAGGAGCAGAG 61.739 60.000 6.01 0.00 41.98 3.35
552 579 0.590195 CCGATTGATTGCTAGCAGCC 59.410 55.000 18.45 13.79 41.51 4.85
646 689 3.369388 GGAGGGAGGGAGGGAGGT 61.369 72.222 0.00 0.00 0.00 3.85
647 690 3.039526 AGGAGGGAGGGAGGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
648 691 2.612251 GAGGAGGGAGGGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
649 692 3.430497 CGAGGAGGGAGGGAGGGA 61.430 72.222 0.00 0.00 0.00 4.20
650 693 2.531483 TTTCGAGGAGGGAGGGAGGG 62.531 65.000 0.00 0.00 0.00 4.30
651 694 1.001760 TTTCGAGGAGGGAGGGAGG 59.998 63.158 0.00 0.00 0.00 4.30
652 695 1.668101 CGTTTCGAGGAGGGAGGGAG 61.668 65.000 0.00 0.00 0.00 4.30
653 696 1.681327 CGTTTCGAGGAGGGAGGGA 60.681 63.158 0.00 0.00 0.00 4.20
654 697 2.893398 CGTTTCGAGGAGGGAGGG 59.107 66.667 0.00 0.00 0.00 4.30
655 698 2.184579 GCGTTTCGAGGAGGGAGG 59.815 66.667 0.00 0.00 0.00 4.30
656 699 1.139947 GAGCGTTTCGAGGAGGGAG 59.860 63.158 0.00 0.00 0.00 4.30
657 700 1.183030 TTGAGCGTTTCGAGGAGGGA 61.183 55.000 0.00 0.00 0.00 4.20
666 709 1.001706 GGGACAAGGTTTGAGCGTTTC 60.002 52.381 0.00 0.00 0.00 2.78
814 876 4.994471 TGCAGGTGCTGGACGCTG 62.994 66.667 3.18 11.47 42.66 5.18
815 877 4.996434 GTGCAGGTGCTGGACGCT 62.996 66.667 3.18 0.00 42.32 5.07
836 898 2.711922 GGCGGAAGAGAGAGGCGAA 61.712 63.158 0.00 0.00 0.00 4.70
865 945 3.749064 GTCTCTCCTGCGCGGTGA 61.749 66.667 16.49 17.16 34.31 4.02
867 947 4.057428 GTGTCTCTCCTGCGCGGT 62.057 66.667 16.49 0.00 0.00 5.68
872 952 1.005630 ACAAGCGTGTCTCTCCTGC 60.006 57.895 0.00 0.00 29.49 4.85
873 953 0.315251 TCACAAGCGTGTCTCTCCTG 59.685 55.000 1.00 0.00 44.02 3.86
900 1029 3.903714 TCAAGAAAGTGATGGAGACCTCA 59.096 43.478 0.00 0.00 0.00 3.86
901 1030 4.543590 TCAAGAAAGTGATGGAGACCTC 57.456 45.455 0.00 0.00 0.00 3.85
902 1031 5.511386 AATCAAGAAAGTGATGGAGACCT 57.489 39.130 0.00 0.00 38.28 3.85
903 1032 5.474876 ACAAATCAAGAAAGTGATGGAGACC 59.525 40.000 0.00 0.00 38.28 3.85
976 1106 2.178521 CTCGACCGTTCGTCCCTG 59.821 66.667 1.29 0.00 46.01 4.45
984 1114 0.243907 CCATGAGTGACTCGACCGTT 59.756 55.000 8.23 0.00 32.35 4.44
993 1125 2.103042 GCTCCACGCCATGAGTGAC 61.103 63.158 18.67 7.59 41.83 3.67
1065 1200 1.677552 CTTGGTGAAGTAGGCGGGT 59.322 57.895 0.00 0.00 0.00 5.28
1109 1271 0.321475 ACAGAGCAGCAAGAAGGAGC 60.321 55.000 0.00 0.00 0.00 4.70
1112 1274 1.552337 TCCTACAGAGCAGCAAGAAGG 59.448 52.381 0.00 0.00 0.00 3.46
1160 1322 3.441496 ACACAAACAGGTGCATGAAAG 57.559 42.857 0.00 0.00 42.55 2.62
1170 1332 2.230025 TGACACCACAAACACAAACAGG 59.770 45.455 0.00 0.00 0.00 4.00
1287 1455 1.436195 AACGCTGCAACGCTGAAGAA 61.436 50.000 9.87 0.00 36.19 2.52
1289 1457 1.723542 CAACGCTGCAACGCTGAAG 60.724 57.895 9.87 0.00 36.19 3.02
1294 1462 1.510623 CAGATCAACGCTGCAACGC 60.511 57.895 9.87 0.00 36.19 4.84
1295 1463 0.179240 GTCAGATCAACGCTGCAACG 60.179 55.000 8.18 8.18 39.50 4.10
1357 1534 2.327081 ACGTCGACATGTACACAGAC 57.673 50.000 17.16 4.83 0.00 3.51
1358 1535 2.159801 CGTACGTCGACATGTACACAGA 60.160 50.000 24.22 0.00 42.96 3.41
1359 1536 2.163638 CGTACGTCGACATGTACACAG 58.836 52.381 24.22 11.27 42.96 3.66
1360 1537 1.530720 ACGTACGTCGACATGTACACA 59.469 47.619 24.22 0.00 42.96 3.72
1361 1538 1.900603 CACGTACGTCGACATGTACAC 59.099 52.381 19.94 9.37 42.96 2.90
1362 1539 1.725611 GCACGTACGTCGACATGTACA 60.726 52.381 19.94 0.00 42.96 2.90
1363 1540 0.903187 GCACGTACGTCGACATGTAC 59.097 55.000 19.94 17.92 42.86 2.90
1364 1541 0.516439 TGCACGTACGTCGACATGTA 59.484 50.000 19.94 7.78 42.86 2.29
1365 1542 0.728129 CTGCACGTACGTCGACATGT 60.728 55.000 19.94 8.85 42.86 3.21
1366 1543 1.403225 CCTGCACGTACGTCGACATG 61.403 60.000 19.94 10.28 42.86 3.21
1367 1544 1.154093 CCTGCACGTACGTCGACAT 60.154 57.895 19.94 1.85 42.86 3.06
1368 1545 2.253154 CCTGCACGTACGTCGACA 59.747 61.111 19.94 15.68 42.86 4.35
1495 1678 1.566018 GGCGAGGTCGTTGTCTTTGG 61.566 60.000 0.69 0.00 42.22 3.28
1503 1686 2.049433 CTTGACGGCGAGGTCGTT 60.049 61.111 16.62 0.00 46.30 3.85
1589 1772 1.078848 CTTGAGCTCCACCTTCCGG 60.079 63.158 12.15 0.00 0.00 5.14
1687 1872 2.977772 TCGATGATGCATGGTGTGTA 57.022 45.000 2.46 0.00 0.00 2.90
1723 1908 3.069079 ACGAGAGTACAAGGCTGACTA 57.931 47.619 0.00 0.00 46.88 2.59
1755 1944 2.357517 AGGCAGGAAACACTCGCG 60.358 61.111 0.00 0.00 0.00 5.87
1758 1947 1.952263 GCACAGGCAGGAAACACTC 59.048 57.895 0.00 0.00 40.72 3.51
1900 2089 4.341806 TCCAAGGTGTAACTGTTCTAACGA 59.658 41.667 0.00 0.00 36.74 3.85
1901 2090 4.446719 GTCCAAGGTGTAACTGTTCTAACG 59.553 45.833 0.00 0.00 36.74 3.18
1902 2091 5.362263 TGTCCAAGGTGTAACTGTTCTAAC 58.638 41.667 0.00 0.00 36.74 2.34
1903 2092 5.617528 TGTCCAAGGTGTAACTGTTCTAA 57.382 39.130 0.00 0.00 36.74 2.10
1904 2093 5.129815 ACTTGTCCAAGGTGTAACTGTTCTA 59.870 40.000 11.45 0.00 42.53 2.10
1906 2095 4.196971 ACTTGTCCAAGGTGTAACTGTTC 58.803 43.478 11.45 0.00 42.53 3.18
1920 2109 6.260714 CAGCATATATAGTTGCAACTTGTCCA 59.739 38.462 35.20 18.73 41.35 4.02
1921 2110 6.483307 TCAGCATATATAGTTGCAACTTGTCC 59.517 38.462 35.20 15.46 41.35 4.02
1935 2124 7.767659 GGCAGTTCATCAGATTCAGCATATATA 59.232 37.037 0.00 0.00 0.00 0.86
1936 2125 6.598457 GGCAGTTCATCAGATTCAGCATATAT 59.402 38.462 0.00 0.00 0.00 0.86
1937 2126 5.936372 GGCAGTTCATCAGATTCAGCATATA 59.064 40.000 0.00 0.00 0.00 0.86
1938 2127 4.760715 GGCAGTTCATCAGATTCAGCATAT 59.239 41.667 0.00 0.00 0.00 1.78
1977 2184 1.075979 TCGCCGTGACGATGAACATG 61.076 55.000 6.54 0.00 37.09 3.21
2037 2244 3.298686 TGTCCAGAGATACTCACCGAT 57.701 47.619 0.00 0.00 32.06 4.18
2056 2263 5.233476 CGAATGCCAATGGATTCAGATTTTG 59.767 40.000 2.05 0.00 0.00 2.44
2057 2264 5.353938 CGAATGCCAATGGATTCAGATTTT 58.646 37.500 2.05 0.00 0.00 1.82
2085 2299 2.161609 GGTTCAGTTAATGCTGGTTCGG 59.838 50.000 0.00 0.00 37.12 4.30
2118 2332 1.299541 CTGCGAAGAACACACAAGGT 58.700 50.000 0.00 0.00 0.00 3.50
2249 2488 1.339438 ACAGCAGCCGTGATTTCATCT 60.339 47.619 0.00 0.00 0.00 2.90
2265 2504 2.924290 CAGAAACGGCTCTAGTTACAGC 59.076 50.000 0.00 0.00 34.65 4.40
2266 2505 3.921021 CACAGAAACGGCTCTAGTTACAG 59.079 47.826 0.00 0.00 0.00 2.74
2267 2506 3.570975 TCACAGAAACGGCTCTAGTTACA 59.429 43.478 0.00 0.00 0.00 2.41
2272 2511 1.929836 GCATCACAGAAACGGCTCTAG 59.070 52.381 0.00 0.00 0.00 2.43
2282 2521 5.355071 CCAAAATAGCAGTAGCATCACAGAA 59.645 40.000 0.00 0.00 45.49 3.02
2314 2554 2.128771 AGCATCAAAATACGGCCACT 57.871 45.000 2.24 0.00 0.00 4.00
2394 2635 5.772672 ACCTGTGCAATTATACCAAGAACAA 59.227 36.000 0.00 0.00 0.00 2.83
2416 2660 6.317857 GCAAAGATCAAGTTCATGAAGTACC 58.682 40.000 16.08 0.90 32.06 3.34
2417 2661 6.317857 GGCAAAGATCAAGTTCATGAAGTAC 58.682 40.000 16.08 1.89 32.06 2.73
2454 2702 4.039357 GCAGCAGCAGCACCACAG 62.039 66.667 4.63 0.00 45.49 3.66
2455 2703 4.574271 AGCAGCAGCAGCACCACA 62.574 61.111 12.92 0.00 45.49 4.17
2456 2704 3.735029 GAGCAGCAGCAGCACCAC 61.735 66.667 12.92 0.00 45.49 4.16
2459 2707 2.396955 ATTCGAGCAGCAGCAGCAC 61.397 57.895 12.92 4.74 45.49 4.40
2460 2708 2.046604 ATTCGAGCAGCAGCAGCA 60.047 55.556 12.92 0.00 45.49 4.41
2461 2709 2.403987 CATTCGAGCAGCAGCAGC 59.596 61.111 3.17 0.46 45.49 5.25
2462 2710 1.744368 ACCATTCGAGCAGCAGCAG 60.744 57.895 3.17 0.00 45.49 4.24
2465 2713 0.167470 CAACACCATTCGAGCAGCAG 59.833 55.000 0.00 0.00 0.00 4.24
2494 2742 4.932200 GGACACATCGATCAGAAGAAGTTT 59.068 41.667 0.00 0.00 0.00 2.66
2530 2778 2.122729 TAGGTGCAGCAGGTCCCT 59.877 61.111 19.63 6.85 0.00 4.20
2533 2781 0.674895 CTTGGTAGGTGCAGCAGGTC 60.675 60.000 19.63 5.22 0.00 3.85
2534 2782 1.376466 CTTGGTAGGTGCAGCAGGT 59.624 57.895 19.63 0.00 0.00 4.00
2535 2783 2.042831 GCTTGGTAGGTGCAGCAGG 61.043 63.158 19.63 0.00 32.17 4.85
2536 2784 0.607489 AAGCTTGGTAGGTGCAGCAG 60.607 55.000 19.63 7.26 34.49 4.24
2537 2785 0.890542 CAAGCTTGGTAGGTGCAGCA 60.891 55.000 19.14 0.00 34.49 4.41
2538 2786 0.890996 ACAAGCTTGGTAGGTGCAGC 60.891 55.000 29.18 8.11 31.15 5.25
2539 2787 0.877071 CACAAGCTTGGTAGGTGCAG 59.123 55.000 29.18 1.40 31.15 4.41
2556 2804 1.765314 AGAGGATGGCACCAGATACAC 59.235 52.381 8.48 0.00 0.00 2.90
2615 2863 2.698803 TCAACATCATTGTCCAGTCCG 58.301 47.619 0.00 0.00 34.06 4.79
2617 2865 5.220989 CCATCATCAACATCATTGTCCAGTC 60.221 44.000 0.00 0.00 34.06 3.51
2629 2877 6.294899 GCATGGCTATAAACCATCATCAACAT 60.295 38.462 4.32 0.00 44.85 2.71
2639 2887 3.908476 TGGATTGCATGGCTATAAACCA 58.092 40.909 0.00 0.00 42.61 3.67
2646 2894 3.054139 AGAAGAGTTGGATTGCATGGCTA 60.054 43.478 0.00 0.00 0.00 3.93
2651 2899 4.914983 TCTTGAGAAGAGTTGGATTGCAT 58.085 39.130 0.00 0.00 32.71 3.96
2674 2924 1.936203 GCGCCAAACATGCAAGTGATT 60.936 47.619 0.00 0.00 0.00 2.57
2679 2929 2.432972 GGGCGCCAAACATGCAAG 60.433 61.111 30.85 0.00 0.00 4.01
2686 2936 2.597510 AGAAGGTGGGCGCCAAAC 60.598 61.111 30.85 22.64 34.18 2.93
2690 2940 0.891904 TAAAACAGAAGGTGGGCGCC 60.892 55.000 21.18 21.18 0.00 6.53
2691 2941 0.521735 CTAAAACAGAAGGTGGGCGC 59.478 55.000 0.00 0.00 0.00 6.53
2709 2975 8.218488 ACTTCTTTCTTGGTATTGAGGTTAACT 58.782 33.333 5.42 0.00 0.00 2.24
2710 2976 8.392372 ACTTCTTTCTTGGTATTGAGGTTAAC 57.608 34.615 0.00 0.00 0.00 2.01
2736 3002 3.118920 TGCTCTGGATTTGCATGATTTGG 60.119 43.478 0.00 0.00 0.00 3.28
2761 3030 7.488187 TCTTTTGTCAGATTTGAACTCAGAG 57.512 36.000 0.00 0.00 34.49 3.35
2793 3062 6.282930 CCACAAGTTCCTCAAATGAAACAAT 58.717 36.000 1.99 0.00 0.00 2.71
2794 3063 5.659463 CCACAAGTTCCTCAAATGAAACAA 58.341 37.500 1.99 0.00 0.00 2.83
2797 3066 3.703556 TGCCACAAGTTCCTCAAATGAAA 59.296 39.130 0.00 0.00 0.00 2.69
2850 3119 8.877864 TCTACAATAAGTCCAAAACATCCATT 57.122 30.769 0.00 0.00 0.00 3.16
2880 3149 2.325484 TCAAAGTCTGGCACCTCACTA 58.675 47.619 0.00 0.00 0.00 2.74
2941 3210 0.691413 GCCCCTAGAGCCTGGTACTT 60.691 60.000 0.00 0.00 0.00 2.24
2949 3218 2.506231 ACTAAAAGAAGCCCCTAGAGCC 59.494 50.000 0.00 0.00 0.00 4.70
2985 3254 1.003928 TCTCATGTGTGCTGGCTTGAT 59.996 47.619 0.00 0.00 0.00 2.57
2993 3263 1.271762 ACAAGCCATCTCATGTGTGCT 60.272 47.619 0.00 0.00 0.00 4.40
3031 3301 5.426833 AGGAAGTGTATATGAAGCAACCTCT 59.573 40.000 0.00 0.00 0.00 3.69
3062 3332 5.920273 CAGAATGCGTTTCTTTATGGTGTTT 59.080 36.000 0.00 0.00 42.15 2.83
3089 3359 3.903467 TGGAGTCTCAAGCAGCTAGATA 58.097 45.455 0.00 0.00 0.00 1.98
3100 3370 4.409901 TGCATTCATAGGATGGAGTCTCAA 59.590 41.667 1.47 0.00 0.00 3.02
3115 3385 4.603989 TGTTGTCCATTGTTGCATTCAT 57.396 36.364 0.00 0.00 0.00 2.57
3118 3388 4.561938 CCTCATGTTGTCCATTGTTGCATT 60.562 41.667 0.00 0.00 0.00 3.56
3121 3391 2.297033 ACCTCATGTTGTCCATTGTTGC 59.703 45.455 0.00 0.00 0.00 4.17
3137 3407 6.036577 AGAAAAGAAAACTGCAAAACCTCA 57.963 33.333 0.00 0.00 0.00 3.86
3138 3408 5.520288 GGAGAAAAGAAAACTGCAAAACCTC 59.480 40.000 0.00 0.00 0.00 3.85
3139 3409 5.187772 AGGAGAAAAGAAAACTGCAAAACCT 59.812 36.000 0.00 0.00 0.00 3.50
3140 3410 5.419542 AGGAGAAAAGAAAACTGCAAAACC 58.580 37.500 0.00 0.00 0.00 3.27
3141 3411 7.258441 ACTAGGAGAAAAGAAAACTGCAAAAC 58.742 34.615 0.00 0.00 0.00 2.43
3142 3412 7.404671 ACTAGGAGAAAAGAAAACTGCAAAA 57.595 32.000 0.00 0.00 0.00 2.44
3143 3413 7.404671 AACTAGGAGAAAAGAAAACTGCAAA 57.595 32.000 0.00 0.00 0.00 3.68
3144 3414 7.257722 CAAACTAGGAGAAAAGAAAACTGCAA 58.742 34.615 0.00 0.00 0.00 4.08
3145 3415 6.183360 CCAAACTAGGAGAAAAGAAAACTGCA 60.183 38.462 0.00 0.00 0.00 4.41
3146 3416 6.183360 ACCAAACTAGGAGAAAAGAAAACTGC 60.183 38.462 0.00 0.00 0.00 4.40
3147 3417 7.283354 AGACCAAACTAGGAGAAAAGAAAACTG 59.717 37.037 0.00 0.00 0.00 3.16
3148 3418 7.347252 AGACCAAACTAGGAGAAAAGAAAACT 58.653 34.615 0.00 0.00 0.00 2.66
3149 3419 7.282450 TGAGACCAAACTAGGAGAAAAGAAAAC 59.718 37.037 0.00 0.00 0.00 2.43
3150 3420 7.343357 TGAGACCAAACTAGGAGAAAAGAAAA 58.657 34.615 0.00 0.00 0.00 2.29
3151 3421 6.895782 TGAGACCAAACTAGGAGAAAAGAAA 58.104 36.000 0.00 0.00 0.00 2.52
3152 3422 6.494666 TGAGACCAAACTAGGAGAAAAGAA 57.505 37.500 0.00 0.00 0.00 2.52
3153 3423 6.467677 CATGAGACCAAACTAGGAGAAAAGA 58.532 40.000 0.00 0.00 0.00 2.52
3154 3424 5.645497 CCATGAGACCAAACTAGGAGAAAAG 59.355 44.000 0.00 0.00 0.00 2.27
3155 3425 5.073144 ACCATGAGACCAAACTAGGAGAAAA 59.927 40.000 0.00 0.00 0.00 2.29
3156 3426 4.597507 ACCATGAGACCAAACTAGGAGAAA 59.402 41.667 0.00 0.00 0.00 2.52
3157 3427 4.020218 CACCATGAGACCAAACTAGGAGAA 60.020 45.833 0.00 0.00 0.00 2.87
3158 3428 3.515502 CACCATGAGACCAAACTAGGAGA 59.484 47.826 0.00 0.00 0.00 3.71
3159 3429 3.261897 ACACCATGAGACCAAACTAGGAG 59.738 47.826 0.00 0.00 0.00 3.69
3160 3430 3.007940 CACACCATGAGACCAAACTAGGA 59.992 47.826 0.00 0.00 0.00 2.94
3161 3431 3.338249 CACACCATGAGACCAAACTAGG 58.662 50.000 0.00 0.00 0.00 3.02
3162 3432 2.744202 GCACACCATGAGACCAAACTAG 59.256 50.000 0.00 0.00 0.00 2.57
3163 3433 2.105649 TGCACACCATGAGACCAAACTA 59.894 45.455 0.00 0.00 0.00 2.24
3164 3434 1.133823 TGCACACCATGAGACCAAACT 60.134 47.619 0.00 0.00 0.00 2.66
3165 3435 1.317613 TGCACACCATGAGACCAAAC 58.682 50.000 0.00 0.00 0.00 2.93
3166 3436 2.064434 TTGCACACCATGAGACCAAA 57.936 45.000 0.00 0.00 0.00 3.28
3167 3437 1.955778 CTTTGCACACCATGAGACCAA 59.044 47.619 0.00 0.00 0.00 3.67
3168 3438 1.142667 TCTTTGCACACCATGAGACCA 59.857 47.619 0.00 0.00 0.00 4.02
3169 3439 1.896220 TCTTTGCACACCATGAGACC 58.104 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.