Multiple sequence alignment - TraesCS3D01G003300

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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 TraesCS3D01G003300 chr3D 100.000 3268 0 0 272 3539 1348100 1344833 0.000000e+00 6035.0
1 TraesCS3D01G003300 chr3D 98.140 215 4 0 3267 3481 29994994 29995208 3.340000e-100 375.0
2 TraesCS3D01G003300 chr3D 97.674 215 5 0 3267 3481 549067851 549068065 1.550000e-98 370.0
3 TraesCS3D01G003300 chr3D 89.873 237 17 7 3274 3509 313301364 313301134 7.430000e-77 298.0
4 TraesCS3D01G003300 chr3D 100.000 45 0 0 1 45 1348371 1348327 2.260000e-12 84.2
5 TraesCS3D01G003300 chr3D 100.000 43 0 0 1 43 1348066 1348024 2.930000e-11 80.5
6 TraesCS3D01G003300 chr3B 95.506 2559 93 6 694 3233 3412492 3409937 0.000000e+00 4069.0
7 TraesCS3D01G003300 chr3B 95.109 2208 83 5 694 2887 5318425 5320621 0.000000e+00 3456.0
8 TraesCS3D01G003300 chr3B 94.888 313 14 2 2921 3233 5320624 5320934 4.110000e-134 488.0
9 TraesCS3D01G003300 chr3B 94.667 75 4 0 625 699 3477221 3477147 2.230000e-22 117.0
10 TraesCS3D01G003300 chr3B 93.333 75 5 0 625 699 5263756 5263830 1.040000e-20 111.0
11 TraesCS3D01G003300 chr3B 96.774 31 1 0 3235 3265 3409980 3409950 6.000000e-03 52.8
12 TraesCS3D01G003300 chr3B 96.774 31 1 0 3232 3262 5320888 5320918 6.000000e-03 52.8
13 TraesCS3D01G003300 chr2A 81.572 1769 294 22 905 2658 2876092 2877843 0.000000e+00 1432.0
14 TraesCS3D01G003300 chr2A 82.190 1589 253 18 976 2544 2405893 2407471 0.000000e+00 1339.0
15 TraesCS3D01G003300 chr2A 92.759 290 19 2 337 624 766716595 766716884 5.460000e-113 418.0
16 TraesCS3D01G003300 chr2A 87.042 355 29 13 280 626 20799556 20799211 5.540000e-103 385.0
17 TraesCS3D01G003300 chr2B 82.324 1601 274 9 958 2551 9199119 9197521 0.000000e+00 1380.0
18 TraesCS3D01G003300 chr2B 82.970 1515 255 3 1026 2539 454670150 454668638 0.000000e+00 1365.0
19 TraesCS3D01G003300 chr2B 82.663 1517 257 6 1026 2539 6914748 6913235 0.000000e+00 1339.0
20 TraesCS3D01G003300 chr2B 81.541 1609 285 10 1063 2665 30990143 30988541 0.000000e+00 1315.0
21 TraesCS3D01G003300 chrUn 83.059 1517 250 6 1026 2539 337610958 337612470 0.000000e+00 1371.0
22 TraesCS3D01G003300 chr4D 98.580 352 5 0 272 623 62735445 62735094 1.080000e-174 623.0
23 TraesCS3D01G003300 chr4D 89.873 237 17 7 3274 3509 362487834 362487604 7.430000e-77 298.0
24 TraesCS3D01G003300 chr4D 97.674 43 1 0 1 43 62735411 62735369 1.360000e-09 75.0
25 TraesCS3D01G003300 chr4D 95.122 41 2 0 1 41 62735498 62735458 8.200000e-07 65.8
26 TraesCS3D01G003300 chr6D 96.910 356 10 1 272 626 50734226 50733871 2.350000e-166 595.0
27 TraesCS3D01G003300 chr6D 95.517 290 12 1 337 625 300899279 300898990 2.490000e-126 462.0
28 TraesCS3D01G003300 chr6D 97.070 273 8 0 3267 3539 8482840 8483112 8.950000e-126 460.0
29 TraesCS3D01G003300 chr6D 100.000 45 0 0 1 45 50734736 50734692 2.260000e-12 84.2
30 TraesCS3D01G003300 chr6D 100.000 34 0 0 12 45 50734290 50734257 2.950000e-06 63.9
31 TraesCS3D01G003300 chr6D 100.000 33 0 0 13 45 50734248 50734216 1.060000e-05 62.1
32 TraesCS3D01G003300 chr6D 97.143 35 1 0 1 35 468777895 468777929 3.820000e-05 60.2
33 TraesCS3D01G003300 chr7D 95.211 355 16 1 289 643 127281525 127281172 8.580000e-156 560.0
34 TraesCS3D01G003300 chr7D 97.802 273 6 0 3267 3539 379833057 379833329 4.140000e-129 472.0
35 TraesCS3D01G003300 chr7D 97.674 43 1 0 1 43 127281508 127281466 1.360000e-09 75.0
36 TraesCS3D01G003300 chr2D 99.267 273 2 0 3267 3539 638450078 638449806 8.830000e-136 494.0
37 TraesCS3D01G003300 chr2D 91.471 340 19 8 291 624 592034929 592035264 3.220000e-125 459.0
38 TraesCS3D01G003300 chr7A 90.490 347 23 3 289 625 717412405 717412751 1.940000e-122 449.0
39 TraesCS3D01G003300 chr7A 92.542 295 18 4 333 624 707978992 707979285 1.520000e-113 420.0
40 TraesCS3D01G003300 chr1D 98.140 215 4 0 3267 3481 33317899 33317685 3.340000e-100 375.0
41 TraesCS3D01G003300 chr1D 96.744 215 6 1 3267 3481 33064310 33064097 1.210000e-94 357.0
42 TraesCS3D01G003300 chr1D 90.244 41 4 0 1 41 457070944 457070904 2.000000e-03 54.7
43 TraesCS3D01G003300 chr5D 78.671 286 40 9 2954 3230 548969406 548969133 1.690000e-38 171.0
44 TraesCS3D01G003300 chr5D 96.774 31 1 0 3235 3265 548969173 548969143 6.000000e-03 52.8


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 TraesCS3D01G003300 chr3D 1344833 1348371 3538 True 2066.566667 6035 100.000000 1 3539 3 chr3D.!!$R2 3538
1 TraesCS3D01G003300 chr3B 3409937 3412492 2555 True 2060.900000 4069 96.140000 694 3265 2 chr3B.!!$R2 2571
2 TraesCS3D01G003300 chr3B 5318425 5320934 2509 False 1332.266667 3456 95.590333 694 3262 3 chr3B.!!$F2 2568
3 TraesCS3D01G003300 chr2A 2876092 2877843 1751 False 1432.000000 1432 81.572000 905 2658 1 chr2A.!!$F2 1753
4 TraesCS3D01G003300 chr2A 2405893 2407471 1578 False 1339.000000 1339 82.190000 976 2544 1 chr2A.!!$F1 1568
5 TraesCS3D01G003300 chr2B 9197521 9199119 1598 True 1380.000000 1380 82.324000 958 2551 1 chr2B.!!$R2 1593
6 TraesCS3D01G003300 chr2B 454668638 454670150 1512 True 1365.000000 1365 82.970000 1026 2539 1 chr2B.!!$R4 1513
7 TraesCS3D01G003300 chr2B 6913235 6914748 1513 True 1339.000000 1339 82.663000 1026 2539 1 chr2B.!!$R1 1513
8 TraesCS3D01G003300 chr2B 30988541 30990143 1602 True 1315.000000 1315 81.541000 1063 2665 1 chr2B.!!$R3 1602
9 TraesCS3D01G003300 chrUn 337610958 337612470 1512 False 1371.000000 1371 83.059000 1026 2539 1 chrUn.!!$F1 1513
10 TraesCS3D01G003300 chr6D 50733871 50734736 865 True 201.300000 595 99.227500 1 626 4 chr6D.!!$R2 625

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
665 906 0.171455 GGCATCAAGAGACGACGTCT 59.829 55.0 29.59 29.59 46.42 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2624 2895 1.239296 ATTGCGATGGATGGATGCCG 61.239 55.0 0.0 0.0 0.0 5.69 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
420 660 8.909708 TGATTGCTTTTCATTTTTAGATACGG 57.090 30.769 0.00 0.00 0.00 4.02
423 663 5.126384 TGCTTTTCATTTTTAGATACGGGGG 59.874 40.000 0.00 0.00 0.00 5.40
580 821 4.612033 CGGATTAACGAGTTGGTGGTTTTC 60.612 45.833 0.00 0.00 35.47 2.29
626 867 5.300792 GGTGGTTTCTTACAATTGACTCCAA 59.699 40.000 13.59 0.00 36.61 3.53
627 868 6.183360 GGTGGTTTCTTACAATTGACTCCAAA 60.183 38.462 13.59 1.76 35.67 3.28
628 869 6.695713 GTGGTTTCTTACAATTGACTCCAAAC 59.304 38.462 13.59 12.75 35.67 2.93
629 870 6.605594 TGGTTTCTTACAATTGACTCCAAACT 59.394 34.615 13.59 0.00 35.67 2.66
630 871 7.776030 TGGTTTCTTACAATTGACTCCAAACTA 59.224 33.333 13.59 9.04 35.67 2.24
631 872 8.793592 GGTTTCTTACAATTGACTCCAAACTAT 58.206 33.333 13.59 0.00 35.67 2.12
639 880 9.911788 ACAATTGACTCCAAACTATATGAGATT 57.088 29.630 13.59 0.00 35.67 2.40
641 882 9.911788 AATTGACTCCAAACTATATGAGATTGT 57.088 29.630 0.00 0.00 36.46 2.71
642 883 8.722480 TTGACTCCAAACTATATGAGATTGTG 57.278 34.615 0.00 0.00 36.46 3.33
643 884 8.078060 TGACTCCAAACTATATGAGATTGTGA 57.922 34.615 0.00 0.00 36.46 3.58
644 885 8.708378 TGACTCCAAACTATATGAGATTGTGAT 58.292 33.333 0.00 0.00 36.46 3.06
645 886 8.899427 ACTCCAAACTATATGAGATTGTGATG 57.101 34.615 0.00 0.00 36.46 3.07
646 887 7.935755 ACTCCAAACTATATGAGATTGTGATGG 59.064 37.037 0.00 2.09 36.46 3.51
647 888 7.226441 TCCAAACTATATGAGATTGTGATGGG 58.774 38.462 6.80 0.00 36.46 4.00
648 889 6.072286 CCAAACTATATGAGATTGTGATGGGC 60.072 42.308 0.00 0.00 36.46 5.36
649 890 5.830799 ACTATATGAGATTGTGATGGGCA 57.169 39.130 0.00 0.00 0.00 5.36
650 891 6.384342 ACTATATGAGATTGTGATGGGCAT 57.616 37.500 0.00 0.00 0.00 4.40
651 892 6.413052 ACTATATGAGATTGTGATGGGCATC 58.587 40.000 0.00 0.00 38.29 3.91
652 893 3.588210 ATGAGATTGTGATGGGCATCA 57.412 42.857 0.00 0.00 44.83 3.07
659 900 3.766644 TGATGGGCATCAAGAGACG 57.233 52.632 0.00 0.00 44.14 4.18
660 901 1.194218 TGATGGGCATCAAGAGACGA 58.806 50.000 0.00 0.00 44.14 4.20
661 902 1.134699 TGATGGGCATCAAGAGACGAC 60.135 52.381 0.00 0.00 44.14 4.34
662 903 0.179100 ATGGGCATCAAGAGACGACG 60.179 55.000 0.00 0.00 0.00 5.12
663 904 1.215647 GGGCATCAAGAGACGACGT 59.784 57.895 0.00 0.00 0.00 4.34
664 905 0.802607 GGGCATCAAGAGACGACGTC 60.803 60.000 20.25 20.25 0.00 4.34
665 906 0.171455 GGCATCAAGAGACGACGTCT 59.829 55.000 29.59 29.59 46.42 4.18
666 907 1.400846 GGCATCAAGAGACGACGTCTA 59.599 52.381 29.28 15.12 43.53 2.59
667 908 2.539953 GGCATCAAGAGACGACGTCTAG 60.540 54.545 29.28 20.99 43.53 2.43
668 909 2.352034 GCATCAAGAGACGACGTCTAGA 59.648 50.000 29.28 24.86 43.53 2.43
669 910 3.545228 GCATCAAGAGACGACGTCTAGAG 60.545 52.174 29.28 20.34 43.53 2.43
670 911 3.316071 TCAAGAGACGACGTCTAGAGT 57.684 47.619 29.28 12.39 43.53 3.24
671 912 4.446994 TCAAGAGACGACGTCTAGAGTA 57.553 45.455 29.28 12.12 43.53 2.59
672 913 5.008619 TCAAGAGACGACGTCTAGAGTAT 57.991 43.478 29.28 6.94 43.53 2.12
673 914 5.042593 TCAAGAGACGACGTCTAGAGTATC 58.957 45.833 29.28 15.56 43.53 2.24
697 938 0.880441 CCGATGGTGCAACACATGAA 59.120 50.000 6.58 0.00 39.98 2.57
728 969 6.659824 ACCATTACAGGACGGAAATTAAGAT 58.340 36.000 0.00 0.00 0.00 2.40
778 1028 7.062839 CAGCATAGACAAGTGACTAGAAAGTTC 59.937 40.741 0.00 0.00 35.56 3.01
933 1188 6.538021 GGAGCTTGTCTATATATGAAGCCATG 59.462 42.308 13.16 0.00 39.93 3.66
960 1215 2.273557 GCCCATGCATGTTCATTGAAC 58.726 47.619 24.58 20.27 39.02 3.18
987 1245 9.088512 GATAAATCTATTAGTAGCATTCCCACG 57.911 37.037 0.00 0.00 0.00 4.94
1102 1370 6.116126 GCTAGTTGTAGATCAAAGAACCCAT 58.884 40.000 0.00 0.00 37.81 4.00
1374 1642 0.179062 GCAGCCTCTTCACCATCGAT 60.179 55.000 0.00 0.00 0.00 3.59
1388 1656 2.182791 CGATGGCGAGCTGTGTCT 59.817 61.111 0.00 0.00 40.82 3.41
1512 1780 2.118233 TTACCCACATGGCGAGCACA 62.118 55.000 0.00 0.00 37.83 4.57
1573 1841 0.602905 GTTTGACCTGGCTGCTACGT 60.603 55.000 0.00 0.00 0.00 3.57
1588 1856 0.671472 TACGTCTCTCTTCGGCGTGA 60.671 55.000 6.85 5.98 37.05 4.35
1710 1978 2.585330 TGCTGGAAGTTGATGAAGCAA 58.415 42.857 0.00 0.00 37.69 3.91
1895 2164 3.708403 TGCTGATGATGACTTGTTCCT 57.292 42.857 0.00 0.00 0.00 3.36
1956 2225 6.134535 ACAATTGGAACTACCCTAACATGA 57.865 37.500 10.83 0.00 38.00 3.07
2017 2286 3.333029 TCATCCGCAATGAACTCTCAA 57.667 42.857 0.00 0.00 41.49 3.02
2411 2680 3.186001 GCGATTATGCAGATGAAGACTGG 59.814 47.826 0.00 0.00 36.09 4.00
2490 2759 3.368248 ACCCAAGCCGTCTTGTATACTA 58.632 45.455 5.37 0.00 46.33 1.82
2494 2763 4.261656 CCAAGCCGTCTTGTATACTAGAGG 60.262 50.000 22.23 22.23 46.33 3.69
2559 2830 3.126831 ACTTTATGCTCTCTATGCGTGC 58.873 45.455 0.00 0.00 0.00 5.34
2590 2861 4.820894 AGGGCCACTAGTACAGTTTTAG 57.179 45.455 6.18 0.00 34.26 1.85
2624 2895 7.266335 GCAATCGCAGTATTGTCGAATTATAAC 59.734 37.037 8.33 0.00 38.78 1.89
2704 2980 3.766051 TGTTGTATGGCATGGCATTGTAA 59.234 39.130 36.03 24.66 0.00 2.41
2735 3011 1.382522 ACATAATCAAGCGGCACCAG 58.617 50.000 1.45 0.00 0.00 4.00
2839 3115 0.961753 GGCTGAACTTGTTTGAGGGG 59.038 55.000 0.00 0.00 0.00 4.79
2920 3196 9.780186 ATTTTAGTAACCAGCTCTATATGTTCC 57.220 33.333 0.00 0.00 0.00 3.62
2925 3201 3.259374 ACCAGCTCTATATGTTCCCATCG 59.741 47.826 0.00 0.00 32.29 3.84
2962 3238 2.124507 TTGTAGAAAGGGCGCTGGCT 62.125 55.000 7.64 7.47 39.81 4.75
3033 3309 2.191513 CAGGGCCATCCAATCTGCG 61.192 63.158 6.18 0.00 38.24 5.18
3053 3329 0.240945 CGCGAGCCCTTTGTTTCATT 59.759 50.000 0.00 0.00 0.00 2.57
3238 3514 4.119363 ATGGACGCTGCTGGCCAT 62.119 61.111 20.99 20.99 36.35 4.40
3252 3528 4.473520 CCATGGCCGCCTCGTCTT 62.474 66.667 11.61 0.00 0.00 3.01
3253 3529 3.197790 CATGGCCGCCTCGTCTTG 61.198 66.667 11.61 0.00 0.00 3.02
3257 3533 3.567797 GCCGCCTCGTCTTGCATC 61.568 66.667 0.00 0.00 0.00 3.91
3258 3534 2.185350 CCGCCTCGTCTTGCATCT 59.815 61.111 0.00 0.00 0.00 2.90
3259 3535 1.880340 CCGCCTCGTCTTGCATCTC 60.880 63.158 0.00 0.00 0.00 2.75
3260 3536 1.880340 CGCCTCGTCTTGCATCTCC 60.880 63.158 0.00 0.00 0.00 3.71
3261 3537 1.519719 GCCTCGTCTTGCATCTCCT 59.480 57.895 0.00 0.00 0.00 3.69
3262 3538 0.747255 GCCTCGTCTTGCATCTCCTA 59.253 55.000 0.00 0.00 0.00 2.94
3263 3539 1.269517 GCCTCGTCTTGCATCTCCTAG 60.270 57.143 0.00 0.00 0.00 3.02
3264 3540 1.269517 CCTCGTCTTGCATCTCCTAGC 60.270 57.143 0.00 0.00 0.00 3.42
3265 3541 1.406898 CTCGTCTTGCATCTCCTAGCA 59.593 52.381 0.00 0.00 39.32 3.49
3266 3542 1.135139 TCGTCTTGCATCTCCTAGCAC 59.865 52.381 0.00 0.00 41.05 4.40
3267 3543 1.804372 CGTCTTGCATCTCCTAGCACC 60.804 57.143 0.00 0.00 41.05 5.01
3268 3544 1.208052 GTCTTGCATCTCCTAGCACCA 59.792 52.381 0.00 0.00 41.05 4.17
3269 3545 1.208052 TCTTGCATCTCCTAGCACCAC 59.792 52.381 0.00 0.00 41.05 4.16
3270 3546 1.209019 CTTGCATCTCCTAGCACCACT 59.791 52.381 0.00 0.00 41.05 4.00
3271 3547 0.826715 TGCATCTCCTAGCACCACTC 59.173 55.000 0.00 0.00 35.51 3.51
3272 3548 0.105778 GCATCTCCTAGCACCACTCC 59.894 60.000 0.00 0.00 0.00 3.85
3273 3549 0.387202 CATCTCCTAGCACCACTCCG 59.613 60.000 0.00 0.00 0.00 4.63
3274 3550 0.757188 ATCTCCTAGCACCACTCCGG 60.757 60.000 0.00 0.00 42.50 5.14
3275 3551 3.075005 TCCTAGCACCACTCCGGC 61.075 66.667 0.00 0.00 39.03 6.13
3276 3552 4.162690 CCTAGCACCACTCCGGCC 62.163 72.222 0.00 0.00 39.03 6.13
3277 3553 4.514577 CTAGCACCACTCCGGCCG 62.515 72.222 21.04 21.04 39.03 6.13
3293 3569 4.116328 CGCGCCAGTTCCTCTCGA 62.116 66.667 0.00 0.00 0.00 4.04
3294 3570 2.496817 GCGCCAGTTCCTCTCGAT 59.503 61.111 0.00 0.00 0.00 3.59
3295 3571 1.590259 GCGCCAGTTCCTCTCGATC 60.590 63.158 0.00 0.00 0.00 3.69
3296 3572 1.066587 CGCCAGTTCCTCTCGATCC 59.933 63.158 0.00 0.00 0.00 3.36
3297 3573 1.066587 GCCAGTTCCTCTCGATCCG 59.933 63.158 0.00 0.00 0.00 4.18
3298 3574 1.384989 GCCAGTTCCTCTCGATCCGA 61.385 60.000 0.00 0.00 0.00 4.55
3299 3575 1.103803 CCAGTTCCTCTCGATCCGAA 58.896 55.000 0.00 0.00 34.74 4.30
3300 3576 1.202313 CCAGTTCCTCTCGATCCGAAC 60.202 57.143 9.45 9.45 34.74 3.95
3301 3577 0.733729 AGTTCCTCTCGATCCGAACG 59.266 55.000 10.96 0.00 39.63 3.95
3302 3578 0.248539 GTTCCTCTCGATCCGAACGG 60.249 60.000 6.94 6.94 34.74 4.44
3303 3579 1.381928 TTCCTCTCGATCCGAACGGG 61.382 60.000 13.29 0.00 34.74 5.28
3304 3580 2.026301 CTCTCGATCCGAACGGGC 59.974 66.667 13.29 5.36 34.74 6.13
3305 3581 2.752640 TCTCGATCCGAACGGGCA 60.753 61.111 13.29 0.00 34.74 5.36
3306 3582 2.076622 CTCTCGATCCGAACGGGCAT 62.077 60.000 13.29 0.30 34.74 4.40
3307 3583 1.661821 CTCGATCCGAACGGGCATC 60.662 63.158 13.29 8.76 34.74 3.91
3308 3584 3.030308 CGATCCGAACGGGCATCG 61.030 66.667 17.76 17.76 45.88 3.84
3313 3589 3.864686 CGAACGGGCATCGGCAAG 61.865 66.667 3.86 0.00 44.45 4.01
3314 3590 4.179579 GAACGGGCATCGGCAAGC 62.180 66.667 3.86 0.00 44.45 4.01
3338 3614 4.256813 GTCCGGACGAAGAACCAC 57.743 61.111 20.85 0.00 0.00 4.16
3339 3615 1.373873 GTCCGGACGAAGAACCACC 60.374 63.158 20.85 0.00 0.00 4.61
3340 3616 2.047560 CCGGACGAAGAACCACCC 60.048 66.667 0.00 0.00 0.00 4.61
3341 3617 2.047560 CGGACGAAGAACCACCCC 60.048 66.667 0.00 0.00 0.00 4.95
3342 3618 2.047560 GGACGAAGAACCACCCCG 60.048 66.667 0.00 0.00 0.00 5.73
3343 3619 2.576832 GGACGAAGAACCACCCCGA 61.577 63.158 0.00 0.00 0.00 5.14
3344 3620 1.080025 GACGAAGAACCACCCCGAG 60.080 63.158 0.00 0.00 0.00 4.63
3345 3621 1.530013 GACGAAGAACCACCCCGAGA 61.530 60.000 0.00 0.00 0.00 4.04
3346 3622 1.215647 CGAAGAACCACCCCGAGAG 59.784 63.158 0.00 0.00 0.00 3.20
3374 3650 3.601685 CACCGCGGCCAAACCTTT 61.602 61.111 28.58 0.00 35.61 3.11
3375 3651 3.292159 ACCGCGGCCAAACCTTTC 61.292 61.111 28.58 0.00 35.61 2.62
3376 3652 4.398598 CCGCGGCCAAACCTTTCG 62.399 66.667 14.67 0.00 35.61 3.46
3377 3653 3.350612 CGCGGCCAAACCTTTCGA 61.351 61.111 2.24 0.00 35.61 3.71
3378 3654 2.254350 GCGGCCAAACCTTTCGAC 59.746 61.111 2.24 0.00 35.61 4.20
3379 3655 2.554272 CGGCCAAACCTTTCGACG 59.446 61.111 2.24 0.00 35.61 5.12
3380 3656 2.951458 GGCCAAACCTTTCGACGG 59.049 61.111 0.00 0.00 34.51 4.79
3381 3657 2.254350 GCCAAACCTTTCGACGGC 59.746 61.111 0.00 0.00 0.00 5.68
3382 3658 2.554272 CCAAACCTTTCGACGGCG 59.446 61.111 2.87 2.87 39.35 6.46
3383 3659 2.554272 CAAACCTTTCGACGGCGG 59.446 61.111 12.58 0.00 38.28 6.13
3384 3660 3.351416 AAACCTTTCGACGGCGGC 61.351 61.111 12.58 7.52 38.28 6.53
3410 3686 3.539107 CGTAAGGGAACGCGCGAC 61.539 66.667 39.36 27.49 35.87 5.19
3411 3687 3.184003 GTAAGGGAACGCGCGACC 61.184 66.667 39.36 33.87 0.00 4.79
3412 3688 4.781959 TAAGGGAACGCGCGACCG 62.782 66.667 39.36 7.85 37.57 4.79
3423 3699 4.832608 GCGACCGGCGAAAGGGAT 62.833 66.667 20.06 0.00 44.57 3.85
3424 3700 2.890474 CGACCGGCGAAAGGGATG 60.890 66.667 9.30 0.00 44.57 3.51
3425 3701 2.513897 GACCGGCGAAAGGGATGG 60.514 66.667 9.30 0.00 0.00 3.51
3426 3702 3.325201 GACCGGCGAAAGGGATGGT 62.325 63.158 9.30 0.00 0.00 3.55
3427 3703 1.963464 GACCGGCGAAAGGGATGGTA 61.963 60.000 9.30 0.00 0.00 3.25
3428 3704 1.222387 CCGGCGAAAGGGATGGTAA 59.778 57.895 9.30 0.00 0.00 2.85
3429 3705 1.093496 CCGGCGAAAGGGATGGTAAC 61.093 60.000 9.30 0.00 0.00 2.50
3430 3706 1.426041 CGGCGAAAGGGATGGTAACG 61.426 60.000 0.00 0.00 42.51 3.18
3431 3707 1.093496 GGCGAAAGGGATGGTAACGG 61.093 60.000 0.00 0.00 42.51 4.44
3432 3708 1.712018 GCGAAAGGGATGGTAACGGC 61.712 60.000 0.00 0.00 42.51 5.68
3433 3709 1.426041 CGAAAGGGATGGTAACGGCG 61.426 60.000 4.80 4.80 42.51 6.46
3434 3710 1.712018 GAAAGGGATGGTAACGGCGC 61.712 60.000 6.90 0.00 42.51 6.53
3435 3711 3.692370 AAGGGATGGTAACGGCGCC 62.692 63.158 19.07 19.07 42.51 6.53
3436 3712 4.476752 GGGATGGTAACGGCGCCA 62.477 66.667 28.98 7.06 42.51 5.69
3437 3713 3.199891 GGATGGTAACGGCGCCAC 61.200 66.667 28.98 17.46 37.62 5.01
3438 3714 3.199891 GATGGTAACGGCGCCACC 61.200 66.667 28.98 26.16 37.62 4.61
3470 3746 2.261671 CGTCTCGGACACAAGGGG 59.738 66.667 5.15 0.00 32.09 4.79
3471 3747 2.273179 CGTCTCGGACACAAGGGGA 61.273 63.158 5.15 0.00 32.09 4.81
3472 3748 1.592223 GTCTCGGACACAAGGGGAG 59.408 63.158 0.00 0.00 32.09 4.30
3473 3749 2.266055 CTCGGACACAAGGGGAGC 59.734 66.667 0.00 0.00 0.00 4.70
3474 3750 2.525629 TCGGACACAAGGGGAGCA 60.526 61.111 0.00 0.00 0.00 4.26
3475 3751 2.046892 CGGACACAAGGGGAGCAG 60.047 66.667 0.00 0.00 0.00 4.24
3476 3752 2.583441 CGGACACAAGGGGAGCAGA 61.583 63.158 0.00 0.00 0.00 4.26
3477 3753 1.298014 GGACACAAGGGGAGCAGAG 59.702 63.158 0.00 0.00 0.00 3.35
3478 3754 1.298014 GACACAAGGGGAGCAGAGG 59.702 63.158 0.00 0.00 0.00 3.69
3479 3755 1.152030 ACACAAGGGGAGCAGAGGA 60.152 57.895 0.00 0.00 0.00 3.71
3480 3756 1.197430 ACACAAGGGGAGCAGAGGAG 61.197 60.000 0.00 0.00 0.00 3.69
3481 3757 0.906756 CACAAGGGGAGCAGAGGAGA 60.907 60.000 0.00 0.00 0.00 3.71
3482 3758 0.043940 ACAAGGGGAGCAGAGGAGAT 59.956 55.000 0.00 0.00 0.00 2.75
3483 3759 0.758123 CAAGGGGAGCAGAGGAGATC 59.242 60.000 0.00 0.00 0.00 2.75
3484 3760 0.399806 AAGGGGAGCAGAGGAGATCC 60.400 60.000 0.00 0.00 43.27 3.36
3493 3769 4.364318 AGGAGATCCTGGTCCGTG 57.636 61.111 0.00 0.00 46.55 4.94
3494 3770 2.060980 AGGAGATCCTGGTCCGTGC 61.061 63.158 0.00 0.00 46.55 5.34
3495 3771 2.501610 GAGATCCTGGTCCGTGCC 59.498 66.667 0.00 0.00 0.00 5.01
3496 3772 2.039624 AGATCCTGGTCCGTGCCT 59.960 61.111 0.00 0.00 0.00 4.75
3497 3773 2.022240 GAGATCCTGGTCCGTGCCTC 62.022 65.000 0.00 0.00 0.00 4.70
3498 3774 2.284625 ATCCTGGTCCGTGCCTCA 60.285 61.111 0.00 0.00 0.00 3.86
3499 3775 2.579684 GATCCTGGTCCGTGCCTCAC 62.580 65.000 0.00 0.00 0.00 3.51
3500 3776 3.625897 CCTGGTCCGTGCCTCACA 61.626 66.667 0.00 0.00 33.40 3.58
3501 3777 2.357517 CTGGTCCGTGCCTCACAC 60.358 66.667 0.00 0.00 46.45 3.82
3509 3785 3.810579 GTGCCTCACACTCTCTCTG 57.189 57.895 0.00 0.00 46.41 3.35
3510 3786 0.965439 GTGCCTCACACTCTCTCTGT 59.035 55.000 0.00 0.00 46.41 3.41
3511 3787 1.342819 GTGCCTCACACTCTCTCTGTT 59.657 52.381 0.00 0.00 46.41 3.16
3512 3788 1.342496 TGCCTCACACTCTCTCTGTTG 59.658 52.381 0.00 0.00 0.00 3.33
3513 3789 1.938926 GCCTCACACTCTCTCTGTTGC 60.939 57.143 0.00 0.00 0.00 4.17
3514 3790 1.668337 CCTCACACTCTCTCTGTTGCG 60.668 57.143 0.00 0.00 0.00 4.85
3515 3791 0.315251 TCACACTCTCTCTGTTGCGG 59.685 55.000 0.00 0.00 0.00 5.69
3516 3792 0.668706 CACACTCTCTCTGTTGCGGG 60.669 60.000 0.00 0.00 0.00 6.13
3517 3793 0.827925 ACACTCTCTCTGTTGCGGGA 60.828 55.000 0.00 0.00 0.00 5.14
3518 3794 0.108898 CACTCTCTCTGTTGCGGGAG 60.109 60.000 0.00 0.00 0.00 4.30
3519 3795 1.254284 ACTCTCTCTGTTGCGGGAGG 61.254 60.000 0.00 0.00 0.00 4.30
3520 3796 0.967887 CTCTCTCTGTTGCGGGAGGA 60.968 60.000 0.00 0.00 0.00 3.71
3521 3797 0.967887 TCTCTCTGTTGCGGGAGGAG 60.968 60.000 0.00 0.00 0.00 3.69
3522 3798 1.954362 CTCTCTGTTGCGGGAGGAGG 61.954 65.000 0.00 0.00 0.00 4.30
3523 3799 1.984570 CTCTGTTGCGGGAGGAGGA 60.985 63.158 0.00 0.00 0.00 3.71
3524 3800 1.954362 CTCTGTTGCGGGAGGAGGAG 61.954 65.000 0.00 0.00 0.00 3.69
3525 3801 1.984570 CTGTTGCGGGAGGAGGAGA 60.985 63.158 0.00 0.00 0.00 3.71
3526 3802 1.535444 TGTTGCGGGAGGAGGAGAA 60.535 57.895 0.00 0.00 0.00 2.87
3527 3803 1.125093 TGTTGCGGGAGGAGGAGAAA 61.125 55.000 0.00 0.00 0.00 2.52
3528 3804 0.391793 GTTGCGGGAGGAGGAGAAAG 60.392 60.000 0.00 0.00 0.00 2.62
3529 3805 0.544357 TTGCGGGAGGAGGAGAAAGA 60.544 55.000 0.00 0.00 0.00 2.52
3530 3806 0.544357 TGCGGGAGGAGGAGAAAGAA 60.544 55.000 0.00 0.00 0.00 2.52
3531 3807 0.176910 GCGGGAGGAGGAGAAAGAAG 59.823 60.000 0.00 0.00 0.00 2.85
3532 3808 0.176910 CGGGAGGAGGAGAAAGAAGC 59.823 60.000 0.00 0.00 0.00 3.86
3533 3809 1.280457 GGGAGGAGGAGAAAGAAGCA 58.720 55.000 0.00 0.00 0.00 3.91
3534 3810 1.209261 GGGAGGAGGAGAAAGAAGCAG 59.791 57.143 0.00 0.00 0.00 4.24
3535 3811 1.209261 GGAGGAGGAGAAAGAAGCAGG 59.791 57.143 0.00 0.00 0.00 4.85
3536 3812 2.183679 GAGGAGGAGAAAGAAGCAGGA 58.816 52.381 0.00 0.00 0.00 3.86
3537 3813 2.168313 GAGGAGGAGAAAGAAGCAGGAG 59.832 54.545 0.00 0.00 0.00 3.69
3538 3814 1.209261 GGAGGAGAAAGAAGCAGGAGG 59.791 57.143 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
419 659 4.178956 ACCAAATATCATACACACCCCC 57.821 45.455 0.00 0.00 0.00 5.40
420 660 4.202111 GCAACCAAATATCATACACACCCC 60.202 45.833 0.00 0.00 0.00 4.95
423 663 5.574891 TGGCAACCAAATATCATACACAC 57.425 39.130 0.00 0.00 0.00 3.82
558 799 4.517832 AGAAAACCACCAACTCGTTAATCC 59.482 41.667 0.00 0.00 0.00 3.01
565 806 1.021202 TGCAGAAAACCACCAACTCG 58.979 50.000 0.00 0.00 0.00 4.18
580 821 2.297033 ACATTTGTGGCTAGGTTTGCAG 59.703 45.455 0.00 0.00 0.00 4.41
613 854 9.911788 AATCTCATATAGTTTGGAGTCAATTGT 57.088 29.630 5.13 0.00 32.28 2.71
626 867 6.191657 TGCCCATCACAATCTCATATAGTT 57.808 37.500 0.00 0.00 0.00 2.24
627 868 5.830799 TGCCCATCACAATCTCATATAGT 57.169 39.130 0.00 0.00 0.00 2.12
628 869 6.412214 TGATGCCCATCACAATCTCATATAG 58.588 40.000 6.85 0.00 42.42 1.31
629 870 6.377245 TGATGCCCATCACAATCTCATATA 57.623 37.500 6.85 0.00 42.42 0.86
630 871 5.251182 TGATGCCCATCACAATCTCATAT 57.749 39.130 6.85 0.00 42.42 1.78
631 872 4.710313 TGATGCCCATCACAATCTCATA 57.290 40.909 6.85 0.00 42.42 2.15
632 873 3.588210 TGATGCCCATCACAATCTCAT 57.412 42.857 6.85 0.00 42.42 2.90
633 874 3.054213 TCTTGATGCCCATCACAATCTCA 60.054 43.478 10.30 0.00 46.49 3.27
634 875 3.548770 TCTTGATGCCCATCACAATCTC 58.451 45.455 10.30 0.00 46.49 2.75
635 876 3.201487 TCTCTTGATGCCCATCACAATCT 59.799 43.478 10.30 0.00 46.49 2.40
636 877 3.314635 GTCTCTTGATGCCCATCACAATC 59.685 47.826 10.30 0.00 46.49 2.67
637 878 3.285484 GTCTCTTGATGCCCATCACAAT 58.715 45.455 10.30 0.00 46.49 2.71
638 879 2.715046 GTCTCTTGATGCCCATCACAA 58.285 47.619 10.30 1.88 46.49 3.33
639 880 1.405933 CGTCTCTTGATGCCCATCACA 60.406 52.381 10.30 0.62 46.49 3.58
640 881 1.134699 TCGTCTCTTGATGCCCATCAC 60.135 52.381 10.30 0.00 46.49 3.06
641 882 1.134699 GTCGTCTCTTGATGCCCATCA 60.135 52.381 6.85 6.85 45.30 3.07
642 883 1.576356 GTCGTCTCTTGATGCCCATC 58.424 55.000 1.35 1.35 38.29 3.51
643 884 0.179100 CGTCGTCTCTTGATGCCCAT 60.179 55.000 0.00 0.00 0.00 4.00
644 885 1.215382 CGTCGTCTCTTGATGCCCA 59.785 57.895 0.00 0.00 0.00 5.36
645 886 0.802607 GACGTCGTCTCTTGATGCCC 60.803 60.000 18.09 0.00 0.00 5.36
646 887 0.171455 AGACGTCGTCTCTTGATGCC 59.829 55.000 22.05 0.00 38.71 4.40
647 888 2.352034 TCTAGACGTCGTCTCTTGATGC 59.648 50.000 30.11 0.00 42.40 3.91
648 889 3.619483 ACTCTAGACGTCGTCTCTTGATG 59.381 47.826 30.11 19.32 42.40 3.07
649 890 3.864243 ACTCTAGACGTCGTCTCTTGAT 58.136 45.455 30.11 11.53 42.40 2.57
650 891 3.316071 ACTCTAGACGTCGTCTCTTGA 57.684 47.619 30.11 22.89 42.40 3.02
651 892 5.045215 AGATACTCTAGACGTCGTCTCTTG 58.955 45.833 30.11 21.32 42.40 3.02
652 893 5.266733 AGATACTCTAGACGTCGTCTCTT 57.733 43.478 30.11 15.33 42.40 2.85
653 894 4.924305 AGATACTCTAGACGTCGTCTCT 57.076 45.455 30.11 16.74 42.40 3.10
654 895 5.042593 TGAAGATACTCTAGACGTCGTCTC 58.957 45.833 30.11 14.78 42.40 3.36
655 896 4.805192 GTGAAGATACTCTAGACGTCGTCT 59.195 45.833 29.25 29.25 45.54 4.18
656 897 4.025813 GGTGAAGATACTCTAGACGTCGTC 60.026 50.000 17.70 17.70 0.00 4.20
657 898 3.870419 GGTGAAGATACTCTAGACGTCGT 59.130 47.826 10.46 0.00 0.00 4.34
658 899 3.060406 CGGTGAAGATACTCTAGACGTCG 60.060 52.174 10.46 0.00 0.00 5.12
659 900 4.118410 TCGGTGAAGATACTCTAGACGTC 58.882 47.826 7.70 7.70 0.00 4.34
660 901 4.134379 TCGGTGAAGATACTCTAGACGT 57.866 45.455 0.00 0.00 0.00 4.34
661 902 4.083749 CCATCGGTGAAGATACTCTAGACG 60.084 50.000 0.00 0.00 0.00 4.18
662 903 4.822896 ACCATCGGTGAAGATACTCTAGAC 59.177 45.833 0.00 0.00 32.98 2.59
663 904 5.050126 ACCATCGGTGAAGATACTCTAGA 57.950 43.478 0.00 0.00 32.98 2.43
677 918 0.250684 TCATGTGTTGCACCATCGGT 60.251 50.000 0.00 0.00 35.62 4.69
678 919 0.880441 TTCATGTGTTGCACCATCGG 59.120 50.000 0.00 0.00 32.73 4.18
679 920 2.925578 ATTCATGTGTTGCACCATCG 57.074 45.000 0.00 0.00 32.73 3.84
680 921 4.150980 CACAAATTCATGTGTTGCACCATC 59.849 41.667 2.62 0.00 44.46 3.51
681 922 4.059511 CACAAATTCATGTGTTGCACCAT 58.940 39.130 2.62 0.00 44.46 3.55
682 923 3.455327 CACAAATTCATGTGTTGCACCA 58.545 40.909 2.62 0.00 44.46 4.17
691 932 6.009589 TCCTGTAATGGTCACAAATTCATGT 58.990 36.000 0.00 0.00 0.00 3.21
692 933 6.324819 GTCCTGTAATGGTCACAAATTCATG 58.675 40.000 0.00 0.00 0.00 3.07
697 938 3.008594 TCCGTCCTGTAATGGTCACAAAT 59.991 43.478 0.00 0.00 0.00 2.32
709 950 4.116961 CGCATCTTAATTTCCGTCCTGTA 58.883 43.478 0.00 0.00 0.00 2.74
728 969 2.894126 TGCCTTTTAATTCCCTTTCGCA 59.106 40.909 0.00 0.00 0.00 5.10
778 1028 3.676873 GCACTTCATTGGGTTGGCAATAG 60.677 47.826 1.92 0.00 0.00 1.73
960 1215 9.088512 GTGGGAATGCTACTAATAGATTTATCG 57.911 37.037 0.00 0.00 0.00 2.92
981 1239 3.792401 CATTGTTATCACTAGCGTGGGA 58.208 45.455 0.00 0.00 41.53 4.37
987 1245 6.382869 AGAATTGGCATTGTTATCACTAGC 57.617 37.500 0.00 0.00 0.00 3.42
1102 1370 1.679139 CAGTTTGTTGGGAGCACTGA 58.321 50.000 0.00 0.00 37.63 3.41
1374 1642 1.591703 CCTAAGACACAGCTCGCCA 59.408 57.895 0.00 0.00 0.00 5.69
1382 1650 2.432456 CGCGCTGCCTAAGACACA 60.432 61.111 5.56 0.00 0.00 3.72
1512 1780 3.319198 ATGTCGAACGGGGTGCCT 61.319 61.111 0.00 0.00 0.00 4.75
1573 1841 1.585006 GGTTCACGCCGAAGAGAGA 59.415 57.895 0.00 0.00 33.09 3.10
1588 1856 2.447959 GGATAGGAGGCCGGGGTT 60.448 66.667 2.18 0.00 0.00 4.11
1710 1978 1.482593 CTCTCAGGGCCGATGTTTAGT 59.517 52.381 0.00 0.00 0.00 2.24
1895 2164 6.128486 ACCATGTAACCAATCATCATAGCAA 58.872 36.000 0.00 0.00 0.00 3.91
1956 2225 4.168101 TCTGGGTGAGGTTGTAGAAGAAT 58.832 43.478 0.00 0.00 0.00 2.40
2017 2286 4.559153 GCTACTTTGTTTGATGCAATGGT 58.441 39.130 0.00 0.00 0.00 3.55
2411 2680 2.637025 ACAACATTGTGGCGACGC 59.363 55.556 12.43 12.43 40.49 5.19
2490 2759 1.661463 TGAGCCCATTCTTCACCTCT 58.339 50.000 0.00 0.00 0.00 3.69
2494 2763 2.134789 ACCATGAGCCCATTCTTCAC 57.865 50.000 0.00 0.00 0.00 3.18
2559 2830 4.755266 ACTAGTGGCCCTTAAGTATGTG 57.245 45.455 0.00 0.00 0.00 3.21
2607 2878 6.146510 TGGATGCCGTTATAATTCGACAATAC 59.853 38.462 0.00 0.00 0.00 1.89
2624 2895 1.239296 ATTGCGATGGATGGATGCCG 61.239 55.000 0.00 0.00 0.00 5.69
2704 2980 5.060816 CGCTTGATTATGTTTGATGCGTTTT 59.939 36.000 0.00 0.00 36.78 2.43
2735 3011 2.486592 CCACCTCGACAACCCAAATAAC 59.513 50.000 0.00 0.00 0.00 1.89
2839 3115 7.596749 TGTATAAAGTGCAAGAAGTAGCTTC 57.403 36.000 0.00 0.96 40.45 3.86
2920 3196 0.460722 TTTGCATTGGATGGCGATGG 59.539 50.000 0.00 0.00 0.00 3.51
2962 3238 2.044451 CAACTATTGGGCCGGCCA 60.044 61.111 44.46 28.13 37.98 5.36
3011 3287 1.530183 GATTGGATGGCCCTGGCTC 60.530 63.158 8.29 0.00 41.60 4.70
3033 3309 2.126850 GAAACAAAGGGCTCGCGC 60.127 61.111 0.00 0.00 0.00 6.86
3053 3329 1.460689 ACGACACAAGGGGAAGGGA 60.461 57.895 0.00 0.00 0.00 4.20
3115 3391 0.682209 AGGTGCAATCCATGGCTGTC 60.682 55.000 6.96 4.32 0.00 3.51
3200 3476 0.391661 GCCAGGAGATGCAAGACGAA 60.392 55.000 0.00 0.00 0.00 3.85
3235 3511 4.473520 AAGACGAGGCGGCCATGG 62.474 66.667 23.09 7.63 34.11 3.66
3236 3512 3.197790 CAAGACGAGGCGGCCATG 61.198 66.667 23.09 15.24 34.11 3.66
3240 3516 3.567797 GATGCAAGACGAGGCGGC 61.568 66.667 0.00 0.00 33.59 6.53
3241 3517 1.880340 GAGATGCAAGACGAGGCGG 60.880 63.158 0.00 0.00 0.00 6.13
3242 3518 1.880340 GGAGATGCAAGACGAGGCG 60.880 63.158 0.00 0.00 0.00 5.52
3243 3519 0.747255 TAGGAGATGCAAGACGAGGC 59.253 55.000 0.00 0.00 0.00 4.70
3244 3520 1.269517 GCTAGGAGATGCAAGACGAGG 60.270 57.143 0.00 0.00 0.00 4.63
3245 3521 1.406898 TGCTAGGAGATGCAAGACGAG 59.593 52.381 0.00 0.00 36.15 4.18
3246 3522 1.135139 GTGCTAGGAGATGCAAGACGA 59.865 52.381 0.00 0.00 41.10 4.20
3247 3523 1.565305 GTGCTAGGAGATGCAAGACG 58.435 55.000 0.00 0.00 41.10 4.18
3248 3524 1.208052 TGGTGCTAGGAGATGCAAGAC 59.792 52.381 0.00 0.00 41.10 3.01
3249 3525 1.208052 GTGGTGCTAGGAGATGCAAGA 59.792 52.381 0.00 0.00 41.10 3.02
3250 3526 1.209019 AGTGGTGCTAGGAGATGCAAG 59.791 52.381 0.00 0.00 41.10 4.01
3251 3527 1.208052 GAGTGGTGCTAGGAGATGCAA 59.792 52.381 0.00 0.00 41.10 4.08
3252 3528 0.826715 GAGTGGTGCTAGGAGATGCA 59.173 55.000 0.00 0.00 36.79 3.96
3253 3529 0.105778 GGAGTGGTGCTAGGAGATGC 59.894 60.000 0.00 0.00 0.00 3.91
3254 3530 0.387202 CGGAGTGGTGCTAGGAGATG 59.613 60.000 0.00 0.00 0.00 2.90
3255 3531 0.757188 CCGGAGTGGTGCTAGGAGAT 60.757 60.000 0.00 0.00 0.00 2.75
3256 3532 1.379977 CCGGAGTGGTGCTAGGAGA 60.380 63.158 0.00 0.00 0.00 3.71
3257 3533 3.082579 GCCGGAGTGGTGCTAGGAG 62.083 68.421 5.05 0.00 41.21 3.69
3258 3534 3.075005 GCCGGAGTGGTGCTAGGA 61.075 66.667 5.05 0.00 41.21 2.94
3259 3535 4.162690 GGCCGGAGTGGTGCTAGG 62.163 72.222 5.05 0.00 41.21 3.02
3260 3536 4.514577 CGGCCGGAGTGGTGCTAG 62.515 72.222 20.10 0.00 41.21 3.42
3276 3552 3.417275 ATCGAGAGGAACTGGCGCG 62.417 63.158 0.00 0.00 41.55 6.86
3277 3553 1.590259 GATCGAGAGGAACTGGCGC 60.590 63.158 0.00 0.00 41.55 6.53
3278 3554 1.066587 GGATCGAGAGGAACTGGCG 59.933 63.158 0.00 0.00 41.55 5.69
3279 3555 1.066587 CGGATCGAGAGGAACTGGC 59.933 63.158 0.00 0.00 41.55 4.85
3280 3556 1.103803 TTCGGATCGAGAGGAACTGG 58.896 55.000 0.00 0.00 41.55 4.00
3281 3557 1.532090 CGTTCGGATCGAGAGGAACTG 60.532 57.143 17.59 10.69 41.55 3.16
3283 3559 0.248539 CCGTTCGGATCGAGAGGAAC 60.249 60.000 9.88 12.61 37.14 3.62
3284 3560 1.381928 CCCGTTCGGATCGAGAGGAA 61.382 60.000 13.08 0.00 37.14 3.36
3285 3561 1.822613 CCCGTTCGGATCGAGAGGA 60.823 63.158 13.08 0.00 37.14 3.71
3286 3562 2.722487 CCCGTTCGGATCGAGAGG 59.278 66.667 13.08 0.00 37.14 3.69
3287 3563 2.026301 GCCCGTTCGGATCGAGAG 59.974 66.667 13.08 0.50 37.14 3.20
3288 3564 2.071844 GATGCCCGTTCGGATCGAGA 62.072 60.000 13.08 0.00 37.14 4.04
3289 3565 1.661821 GATGCCCGTTCGGATCGAG 60.662 63.158 13.08 0.00 37.14 4.04
3290 3566 2.415843 GATGCCCGTTCGGATCGA 59.584 61.111 13.08 0.00 0.00 3.59
3291 3567 3.030308 CGATGCCCGTTCGGATCG 61.030 66.667 16.46 16.46 36.22 3.69
3296 3572 3.864686 CTTGCCGATGCCCGTTCG 61.865 66.667 0.00 0.00 36.33 3.95
3297 3573 4.179579 GCTTGCCGATGCCCGTTC 62.180 66.667 0.00 0.00 36.33 3.95
3321 3597 1.373873 GGTGGTTCTTCGTCCGGAC 60.374 63.158 25.28 25.28 0.00 4.79
3322 3598 2.576832 GGGTGGTTCTTCGTCCGGA 61.577 63.158 0.00 0.00 0.00 5.14
3323 3599 2.047560 GGGTGGTTCTTCGTCCGG 60.048 66.667 0.00 0.00 0.00 5.14
3324 3600 2.047560 GGGGTGGTTCTTCGTCCG 60.048 66.667 0.00 0.00 0.00 4.79
3325 3601 2.047560 CGGGGTGGTTCTTCGTCC 60.048 66.667 0.00 0.00 0.00 4.79
3326 3602 1.080025 CTCGGGGTGGTTCTTCGTC 60.080 63.158 0.00 0.00 0.00 4.20
3327 3603 1.532316 TCTCGGGGTGGTTCTTCGT 60.532 57.895 0.00 0.00 0.00 3.85
3328 3604 1.215647 CTCTCGGGGTGGTTCTTCG 59.784 63.158 0.00 0.00 0.00 3.79
3329 3605 1.597461 CCTCTCGGGGTGGTTCTTC 59.403 63.158 0.00 0.00 0.00 2.87
3330 3606 3.807368 CCTCTCGGGGTGGTTCTT 58.193 61.111 0.00 0.00 0.00 2.52
3340 3616 4.803908 GCCCTTTGCCCCTCTCGG 62.804 72.222 0.00 0.00 0.00 4.63
3341 3617 4.033776 TGCCCTTTGCCCCTCTCG 62.034 66.667 0.00 0.00 40.16 4.04
3342 3618 2.361737 GTGCCCTTTGCCCCTCTC 60.362 66.667 0.00 0.00 40.16 3.20
3343 3619 3.984732 GGTGCCCTTTGCCCCTCT 61.985 66.667 0.00 0.00 40.16 3.69
3357 3633 3.551887 GAAAGGTTTGGCCGCGGTG 62.552 63.158 28.70 1.63 43.70 4.94
3358 3634 3.292159 GAAAGGTTTGGCCGCGGT 61.292 61.111 28.70 2.08 43.70 5.68
3359 3635 4.398598 CGAAAGGTTTGGCCGCGG 62.399 66.667 24.05 24.05 43.70 6.46
3360 3636 3.350612 TCGAAAGGTTTGGCCGCG 61.351 61.111 0.00 0.00 43.70 6.46
3361 3637 2.254350 GTCGAAAGGTTTGGCCGC 59.746 61.111 0.00 0.00 43.70 6.53
3362 3638 2.554272 CGTCGAAAGGTTTGGCCG 59.446 61.111 0.00 0.00 43.70 6.13
3363 3639 2.951458 CCGTCGAAAGGTTTGGCC 59.049 61.111 0.00 0.00 37.58 5.36
3364 3640 2.254350 GCCGTCGAAAGGTTTGGC 59.746 61.111 9.57 1.19 35.04 4.52
3365 3641 2.554272 CGCCGTCGAAAGGTTTGG 59.446 61.111 9.57 0.00 38.10 3.28
3366 3642 2.554272 CCGCCGTCGAAAGGTTTG 59.446 61.111 9.57 1.51 38.10 2.93
3367 3643 3.351416 GCCGCCGTCGAAAGGTTT 61.351 61.111 9.57 0.00 38.10 3.27
3384 3660 3.636313 TTCCCTTACGGTGAGCGCG 62.636 63.158 3.08 0.00 0.00 6.86
3385 3661 2.098831 GTTCCCTTACGGTGAGCGC 61.099 63.158 3.08 0.00 0.00 5.92
3386 3662 1.804326 CGTTCCCTTACGGTGAGCG 60.804 63.158 1.13 1.13 37.86 5.03
3387 3663 2.098831 GCGTTCCCTTACGGTGAGC 61.099 63.158 0.00 0.00 41.65 4.26
3388 3664 1.804326 CGCGTTCCCTTACGGTGAG 60.804 63.158 0.00 0.00 41.65 3.51
3389 3665 2.259204 CGCGTTCCCTTACGGTGA 59.741 61.111 0.00 0.00 41.65 4.02
3390 3666 3.484547 GCGCGTTCCCTTACGGTG 61.485 66.667 8.43 0.00 41.65 4.94
3392 3668 4.781959 TCGCGCGTTCCCTTACGG 62.782 66.667 30.98 0.00 41.65 4.02
3393 3669 3.539107 GTCGCGCGTTCCCTTACG 61.539 66.667 30.98 0.00 44.09 3.18
3394 3670 3.184003 GGTCGCGCGTTCCCTTAC 61.184 66.667 30.98 18.19 0.00 2.34
3395 3671 4.781959 CGGTCGCGCGTTCCCTTA 62.782 66.667 30.98 5.11 0.00 2.69
3406 3682 4.832608 ATCCCTTTCGCCGGTCGC 62.833 66.667 12.56 0.00 38.27 5.19
3407 3683 2.890474 CATCCCTTTCGCCGGTCG 60.890 66.667 1.90 7.73 40.15 4.79
3408 3684 1.963464 TACCATCCCTTTCGCCGGTC 61.963 60.000 1.90 0.00 0.00 4.79
3409 3685 1.555477 TTACCATCCCTTTCGCCGGT 61.555 55.000 1.90 0.00 0.00 5.28
3410 3686 1.093496 GTTACCATCCCTTTCGCCGG 61.093 60.000 0.00 0.00 0.00 6.13
3411 3687 1.426041 CGTTACCATCCCTTTCGCCG 61.426 60.000 0.00 0.00 0.00 6.46
3412 3688 1.093496 CCGTTACCATCCCTTTCGCC 61.093 60.000 0.00 0.00 0.00 5.54
3413 3689 1.712018 GCCGTTACCATCCCTTTCGC 61.712 60.000 0.00 0.00 0.00 4.70
3414 3690 1.426041 CGCCGTTACCATCCCTTTCG 61.426 60.000 0.00 0.00 0.00 3.46
3415 3691 1.712018 GCGCCGTTACCATCCCTTTC 61.712 60.000 0.00 0.00 0.00 2.62
3416 3692 1.747745 GCGCCGTTACCATCCCTTT 60.748 57.895 0.00 0.00 0.00 3.11
3417 3693 2.124860 GCGCCGTTACCATCCCTT 60.125 61.111 0.00 0.00 0.00 3.95
3418 3694 4.171103 GGCGCCGTTACCATCCCT 62.171 66.667 12.58 0.00 0.00 4.20
3419 3695 4.476752 TGGCGCCGTTACCATCCC 62.477 66.667 23.90 0.00 0.00 3.85
3420 3696 3.199891 GTGGCGCCGTTACCATCC 61.200 66.667 23.90 0.00 38.46 3.51
3421 3697 3.199891 GGTGGCGCCGTTACCATC 61.200 66.667 25.36 3.01 38.46 3.51
3453 3729 2.214181 CTCCCCTTGTGTCCGAGACG 62.214 65.000 0.00 0.00 34.95 4.18
3454 3730 1.592223 CTCCCCTTGTGTCCGAGAC 59.408 63.158 0.00 0.00 0.00 3.36
3455 3731 2.283529 GCTCCCCTTGTGTCCGAGA 61.284 63.158 0.00 0.00 0.00 4.04
3456 3732 2.266055 GCTCCCCTTGTGTCCGAG 59.734 66.667 0.00 0.00 0.00 4.63
3457 3733 2.525629 TGCTCCCCTTGTGTCCGA 60.526 61.111 0.00 0.00 0.00 4.55
3458 3734 2.046892 CTGCTCCCCTTGTGTCCG 60.047 66.667 0.00 0.00 0.00 4.79
3459 3735 1.298014 CTCTGCTCCCCTTGTGTCC 59.702 63.158 0.00 0.00 0.00 4.02
3460 3736 1.194781 TCCTCTGCTCCCCTTGTGTC 61.195 60.000 0.00 0.00 0.00 3.67
3461 3737 1.152030 TCCTCTGCTCCCCTTGTGT 60.152 57.895 0.00 0.00 0.00 3.72
3462 3738 0.906756 TCTCCTCTGCTCCCCTTGTG 60.907 60.000 0.00 0.00 0.00 3.33
3463 3739 0.043940 ATCTCCTCTGCTCCCCTTGT 59.956 55.000 0.00 0.00 0.00 3.16
3464 3740 0.758123 GATCTCCTCTGCTCCCCTTG 59.242 60.000 0.00 0.00 0.00 3.61
3465 3741 0.399806 GGATCTCCTCTGCTCCCCTT 60.400 60.000 0.00 0.00 0.00 3.95
3466 3742 1.235696 GGATCTCCTCTGCTCCCCT 59.764 63.158 0.00 0.00 0.00 4.79
3467 3743 1.120795 CAGGATCTCCTCTGCTCCCC 61.121 65.000 0.00 0.00 46.65 4.81
3468 3744 1.120795 CCAGGATCTCCTCTGCTCCC 61.121 65.000 0.00 0.00 46.65 4.30
3469 3745 0.398381 ACCAGGATCTCCTCTGCTCC 60.398 60.000 0.00 0.00 46.65 4.70
3470 3746 1.039856 GACCAGGATCTCCTCTGCTC 58.960 60.000 0.00 0.00 46.65 4.26
3471 3747 0.398381 GGACCAGGATCTCCTCTGCT 60.398 60.000 0.00 0.00 46.65 4.24
3472 3748 1.743321 CGGACCAGGATCTCCTCTGC 61.743 65.000 0.00 0.00 46.65 4.26
3473 3749 0.396417 ACGGACCAGGATCTCCTCTG 60.396 60.000 0.00 0.00 46.65 3.35
3474 3750 0.396417 CACGGACCAGGATCTCCTCT 60.396 60.000 0.00 0.00 46.65 3.69
3475 3751 2.022240 GCACGGACCAGGATCTCCTC 62.022 65.000 0.00 0.00 46.65 3.71
3477 3753 2.501610 GCACGGACCAGGATCTCC 59.498 66.667 0.00 0.00 0.00 3.71
3478 3754 2.022240 GAGGCACGGACCAGGATCTC 62.022 65.000 0.00 0.00 0.00 2.75
3479 3755 2.039624 AGGCACGGACCAGGATCT 59.960 61.111 0.00 0.00 0.00 2.75
3480 3756 2.359169 TGAGGCACGGACCAGGATC 61.359 63.158 0.00 0.00 0.00 3.36
3481 3757 2.284625 TGAGGCACGGACCAGGAT 60.285 61.111 0.00 0.00 0.00 3.24
3482 3758 3.311110 GTGAGGCACGGACCAGGA 61.311 66.667 0.00 0.00 0.00 3.86
3483 3759 3.625897 TGTGAGGCACGGACCAGG 61.626 66.667 0.00 0.00 37.14 4.45
3484 3760 2.357517 GTGTGAGGCACGGACCAG 60.358 66.667 0.00 0.00 38.45 4.00
3492 3768 1.342496 CAACAGAGAGAGTGTGAGGCA 59.658 52.381 0.00 0.00 0.00 4.75
3493 3769 1.938926 GCAACAGAGAGAGTGTGAGGC 60.939 57.143 0.00 0.00 0.00 4.70
3494 3770 1.668337 CGCAACAGAGAGAGTGTGAGG 60.668 57.143 0.00 0.00 0.00 3.86
3495 3771 1.668337 CCGCAACAGAGAGAGTGTGAG 60.668 57.143 0.00 0.00 0.00 3.51
3496 3772 0.315251 CCGCAACAGAGAGAGTGTGA 59.685 55.000 0.00 0.00 0.00 3.58
3497 3773 0.668706 CCCGCAACAGAGAGAGTGTG 60.669 60.000 0.00 0.00 0.00 3.82
3498 3774 0.827925 TCCCGCAACAGAGAGAGTGT 60.828 55.000 0.00 0.00 0.00 3.55
3499 3775 0.108898 CTCCCGCAACAGAGAGAGTG 60.109 60.000 0.00 0.00 31.43 3.51
3500 3776 1.254284 CCTCCCGCAACAGAGAGAGT 61.254 60.000 0.00 0.00 31.43 3.24
3501 3777 0.967887 TCCTCCCGCAACAGAGAGAG 60.968 60.000 0.00 0.00 31.43 3.20
3502 3778 0.967887 CTCCTCCCGCAACAGAGAGA 60.968 60.000 0.00 0.00 31.43 3.10
3503 3779 1.515020 CTCCTCCCGCAACAGAGAG 59.485 63.158 0.00 0.00 31.43 3.20
3504 3780 1.984570 CCTCCTCCCGCAACAGAGA 60.985 63.158 0.00 0.00 31.43 3.10
3505 3781 1.954362 CTCCTCCTCCCGCAACAGAG 61.954 65.000 0.00 0.00 0.00 3.35
3506 3782 1.984570 CTCCTCCTCCCGCAACAGA 60.985 63.158 0.00 0.00 0.00 3.41
3507 3783 1.544825 TTCTCCTCCTCCCGCAACAG 61.545 60.000 0.00 0.00 0.00 3.16
3508 3784 1.125093 TTTCTCCTCCTCCCGCAACA 61.125 55.000 0.00 0.00 0.00 3.33
3509 3785 0.391793 CTTTCTCCTCCTCCCGCAAC 60.392 60.000 0.00 0.00 0.00 4.17
3510 3786 0.544357 TCTTTCTCCTCCTCCCGCAA 60.544 55.000 0.00 0.00 0.00 4.85
3511 3787 0.544357 TTCTTTCTCCTCCTCCCGCA 60.544 55.000 0.00 0.00 0.00 5.69
3512 3788 0.176910 CTTCTTTCTCCTCCTCCCGC 59.823 60.000 0.00 0.00 0.00 6.13
3513 3789 0.176910 GCTTCTTTCTCCTCCTCCCG 59.823 60.000 0.00 0.00 0.00 5.14
3514 3790 1.209261 CTGCTTCTTTCTCCTCCTCCC 59.791 57.143 0.00 0.00 0.00 4.30
3515 3791 1.209261 CCTGCTTCTTTCTCCTCCTCC 59.791 57.143 0.00 0.00 0.00 4.30
3516 3792 2.168313 CTCCTGCTTCTTTCTCCTCCTC 59.832 54.545 0.00 0.00 0.00 3.71
3517 3793 2.187100 CTCCTGCTTCTTTCTCCTCCT 58.813 52.381 0.00 0.00 0.00 3.69
3518 3794 1.209261 CCTCCTGCTTCTTTCTCCTCC 59.791 57.143 0.00 0.00 0.00 4.30
3519 3795 2.689553 CCTCCTGCTTCTTTCTCCTC 57.310 55.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.