Multiple sequence alignment - TraesCS5B01G248600

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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 TraesCS5B01G248600 chr5B 100.000 4345 0 0 1 4345 430739454 430743798 0.000000e+00 8024
1 TraesCS5B01G248600 chr5B 96.552 116 4 0 4230 4345 562547495 562547380 4.430000e-45 193
2 TraesCS5B01G248600 chr5B 94.958 119 5 1 4227 4345 687198992 687199109 7.420000e-43 185
3 TraesCS5B01G248600 chr5A 92.828 2454 90 44 1 2392 466025184 466027613 0.000000e+00 3478
4 TraesCS5B01G248600 chr5A 89.290 1578 69 32 2282 3813 466027559 466029082 0.000000e+00 1886
5 TraesCS5B01G248600 chr5D 93.938 1732 58 21 579 2275 364744264 364745983 0.000000e+00 2573
6 TraesCS5B01G248600 chr5D 87.662 1775 63 48 2289 3990 364746039 364747730 0.000000e+00 1921
7 TraesCS5B01G248600 chr5D 93.058 605 19 9 17 599 364743652 364744255 0.000000e+00 863
8 TraesCS5B01G248600 chr5D 90.441 136 8 2 4092 4227 364747733 364747863 1.610000e-39 174
9 TraesCS5B01G248600 chr5D 92.593 81 6 0 1662 1742 394160599 394160679 2.750000e-22 117
10 TraesCS5B01G248600 chr5D 88.172 93 11 0 1662 1754 387715459 387715367 1.280000e-20 111
11 TraesCS5B01G248600 chr4A 96.552 116 4 0 4230 4345 666841738 666841623 4.430000e-45 193
12 TraesCS5B01G248600 chr4A 96.552 116 4 0 4230 4345 666845231 666845116 4.430000e-45 193
13 TraesCS5B01G248600 chr4A 96.522 115 4 0 4231 4345 542612489 542612375 1.590000e-44 191
14 TraesCS5B01G248600 chr4A 95.690 116 5 0 4230 4345 666827789 666827674 2.060000e-43 187
15 TraesCS5B01G248600 chr4A 95.690 116 5 0 4230 4345 666831259 666831144 2.060000e-43 187
16 TraesCS5B01G248600 chr4A 95.690 116 5 0 4230 4345 666838246 666838131 2.060000e-43 187
17 TraesCS5B01G248600 chr2B 93.548 124 7 1 4222 4345 616964484 616964362 2.670000e-42 183
18 TraesCS5B01G248600 chr2A 80.702 171 20 4 1584 1754 768206848 768206691 2.120000e-23 121


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 TraesCS5B01G248600 chr5B 430739454 430743798 4344 False 8024.00 8024 100.00000 1 4345 1 chr5B.!!$F1 4344
1 TraesCS5B01G248600 chr5A 466025184 466029082 3898 False 2682.00 3478 91.05900 1 3813 2 chr5A.!!$F1 3812
2 TraesCS5B01G248600 chr5D 364743652 364747863 4211 False 1382.75 2573 91.27475 17 4227 4 chr5D.!!$F2 4210

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
335 343 0.532573 TCTTTACGCCTGCTCCTCTG 59.467 55.000 0.00 0.0 0.0 3.35 F
925 1037 1.271102 GACCAGAGCACTTCGTCTTCT 59.729 52.381 2.07 0.0 0.0 2.85 F
2067 2216 0.798776 GGTGTTTCCGATCAGTGCTG 59.201 55.000 0.00 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2196 0.798776 CAGCACTGATCGGAAACACC 59.201 55.0 9.0 0.0 0.0 4.16 R
2408 2662 0.250338 AGGGAGCGAGTGTCAAAACC 60.250 55.0 0.0 0.0 0.0 3.27 R
3607 3926 0.104855 ACACGACCGATCCATCCATG 59.895 55.0 0.0 0.0 0.0 3.66 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 5.940617 TCACCTAAACCCTATCAATGATGG 58.059 41.667 5.91 2.41 0.00 3.51
27 28 5.072741 CACCTAAACCCTATCAATGATGGG 58.927 45.833 17.51 17.51 44.89 4.00
42 43 6.612049 TCAATGATGGGATGAAATGAAATGGA 59.388 34.615 0.00 0.00 0.00 3.41
43 49 6.665992 ATGATGGGATGAAATGAAATGGAG 57.334 37.500 0.00 0.00 0.00 3.86
184 191 3.676540 GTGTAAATAATTGCCCGTGTCG 58.323 45.455 0.00 0.00 0.00 4.35
335 343 0.532573 TCTTTACGCCTGCTCCTCTG 59.467 55.000 0.00 0.00 0.00 3.35
391 431 5.374071 CAAGTAAGTAACCAGGGAGTTGTT 58.626 41.667 0.00 0.00 0.00 2.83
514 557 8.561738 TTATTAAACAAAACAAAAACTGGCCA 57.438 26.923 4.71 4.71 0.00 5.36
549 592 1.339151 GCCCAGTTTGTGACTAGGAGG 60.339 57.143 0.00 0.00 39.26 4.30
560 613 1.493022 GACTAGGAGGAGAGCAGAGGA 59.507 57.143 0.00 0.00 0.00 3.71
568 621 2.107366 GGAGAGCAGAGGACTAAAGCT 58.893 52.381 0.00 0.00 38.43 3.74
573 626 3.406764 AGCAGAGGACTAAAGCTGTTTG 58.593 45.455 0.00 0.00 33.67 2.93
574 627 3.142174 GCAGAGGACTAAAGCTGTTTGT 58.858 45.455 0.00 0.00 0.00 2.83
575 628 3.565902 GCAGAGGACTAAAGCTGTTTGTT 59.434 43.478 0.00 0.00 0.00 2.83
576 629 4.555511 GCAGAGGACTAAAGCTGTTTGTTG 60.556 45.833 0.00 0.00 0.00 3.33
577 630 3.565902 AGAGGACTAAAGCTGTTTGTTGC 59.434 43.478 0.00 0.00 0.00 4.17
578 631 2.623416 AGGACTAAAGCTGTTTGTTGCC 59.377 45.455 0.00 0.00 0.00 4.52
579 632 2.623416 GGACTAAAGCTGTTTGTTGCCT 59.377 45.455 0.00 0.00 0.00 4.75
580 633 3.304726 GGACTAAAGCTGTTTGTTGCCTC 60.305 47.826 0.00 0.00 0.00 4.70
581 634 3.555966 ACTAAAGCTGTTTGTTGCCTCT 58.444 40.909 0.00 0.00 0.00 3.69
582 635 3.565902 ACTAAAGCTGTTTGTTGCCTCTC 59.434 43.478 0.00 0.00 0.00 3.20
583 636 2.355010 AAGCTGTTTGTTGCCTCTCT 57.645 45.000 0.00 0.00 0.00 3.10
584 637 1.889545 AGCTGTTTGTTGCCTCTCTC 58.110 50.000 0.00 0.00 0.00 3.20
585 638 1.419387 AGCTGTTTGTTGCCTCTCTCT 59.581 47.619 0.00 0.00 0.00 3.10
586 639 2.158696 AGCTGTTTGTTGCCTCTCTCTT 60.159 45.455 0.00 0.00 0.00 2.85
587 640 2.225255 GCTGTTTGTTGCCTCTCTCTTC 59.775 50.000 0.00 0.00 0.00 2.87
588 641 3.737850 CTGTTTGTTGCCTCTCTCTTCT 58.262 45.455 0.00 0.00 0.00 2.85
589 642 4.133078 CTGTTTGTTGCCTCTCTCTTCTT 58.867 43.478 0.00 0.00 0.00 2.52
590 643 4.526970 TGTTTGTTGCCTCTCTCTTCTTT 58.473 39.130 0.00 0.00 0.00 2.52
591 644 4.576463 TGTTTGTTGCCTCTCTCTTCTTTC 59.424 41.667 0.00 0.00 0.00 2.62
592 645 4.696479 TTGTTGCCTCTCTCTTCTTTCT 57.304 40.909 0.00 0.00 0.00 2.52
593 646 4.264460 TGTTGCCTCTCTCTTCTTTCTC 57.736 45.455 0.00 0.00 0.00 2.87
594 647 3.900601 TGTTGCCTCTCTCTTCTTTCTCT 59.099 43.478 0.00 0.00 0.00 3.10
595 648 4.021544 TGTTGCCTCTCTCTTCTTTCTCTC 60.022 45.833 0.00 0.00 0.00 3.20
596 649 4.046286 TGCCTCTCTCTTCTTTCTCTCT 57.954 45.455 0.00 0.00 0.00 3.10
597 650 4.016444 TGCCTCTCTCTTCTTTCTCTCTC 58.984 47.826 0.00 0.00 0.00 3.20
598 651 4.263905 TGCCTCTCTCTTCTTTCTCTCTCT 60.264 45.833 0.00 0.00 0.00 3.10
599 652 4.096984 GCCTCTCTCTTCTTTCTCTCTCTG 59.903 50.000 0.00 0.00 0.00 3.35
612 722 3.776969 TCTCTCTCTGGTTAACCATGCAT 59.223 43.478 27.24 0.00 46.46 3.96
632 742 4.816925 GCATAAAAACTAGTAGGGCCTCTG 59.183 45.833 10.74 0.85 0.00 3.35
633 743 5.368989 CATAAAAACTAGTAGGGCCTCTGG 58.631 45.833 10.74 11.94 0.00 3.86
634 744 2.644060 AAACTAGTAGGGCCTCTGGT 57.356 50.000 10.74 12.63 0.00 4.00
635 745 1.867363 AACTAGTAGGGCCTCTGGTG 58.133 55.000 10.74 0.03 0.00 4.17
853 965 2.301870 TCTTGCCGTTTCTGTCCATAGT 59.698 45.455 0.00 0.00 0.00 2.12
925 1037 1.271102 GACCAGAGCACTTCGTCTTCT 59.729 52.381 2.07 0.00 0.00 2.85
929 1041 1.816224 AGAGCACTTCGTCTTCTCTCC 59.184 52.381 0.00 0.00 28.82 3.71
942 1054 4.382541 TCTCCCGGCTGCCTCTCA 62.383 66.667 17.92 0.00 0.00 3.27
1154 1281 1.945387 CACATGATGGACTCCTTCGG 58.055 55.000 0.00 4.39 31.32 4.30
1500 1627 1.738099 CTGCTCGTCCAAAGGGTCG 60.738 63.158 0.00 0.00 45.37 4.79
1836 1984 2.914097 AACAGCCACAGCCTTGCC 60.914 61.111 0.00 0.00 41.25 4.52
1949 2097 5.733676 ACCATGGATGTTTTTATCCTTTGC 58.266 37.500 21.47 0.00 45.59 3.68
2048 2196 4.359706 CCTTTTTCCACCGAAAGAAGTTG 58.640 43.478 0.00 0.00 39.14 3.16
2056 2205 2.686405 ACCGAAAGAAGTTGGTGTTTCC 59.314 45.455 0.00 0.00 32.33 3.13
2064 2213 2.494059 AGTTGGTGTTTCCGATCAGTG 58.506 47.619 0.00 0.00 39.52 3.66
2067 2216 0.798776 GGTGTTTCCGATCAGTGCTG 59.201 55.000 0.00 0.00 0.00 4.41
2227 2377 5.457140 GTCTGAGAATCTATCTAGGCAACG 58.543 45.833 0.00 0.00 39.75 4.10
2231 2381 5.359860 TGAGAATCTATCTAGGCAACGTGAA 59.640 40.000 0.00 0.00 39.75 3.18
2260 2418 8.549338 ACTAGTAGGATTTTAGCTTTGAACAC 57.451 34.615 1.45 0.00 0.00 3.32
2324 2525 8.688151 ACTGAATACTTTGCTCTAGTAACTAGG 58.312 37.037 0.00 0.00 35.03 3.02
2539 2793 4.433186 AGCATCTCATCGCTCATACTAC 57.567 45.455 0.00 0.00 31.16 2.73
2541 2795 5.249420 AGCATCTCATCGCTCATACTACTA 58.751 41.667 0.00 0.00 31.16 1.82
2542 2796 5.707764 AGCATCTCATCGCTCATACTACTAA 59.292 40.000 0.00 0.00 31.16 2.24
2548 2802 7.448777 TCTCATCGCTCATACTACTAATTTCCT 59.551 37.037 0.00 0.00 0.00 3.36
2550 2804 8.082852 TCATCGCTCATACTACTAATTTCCTTC 58.917 37.037 0.00 0.00 0.00 3.46
2551 2805 6.746120 TCGCTCATACTACTAATTTCCTTCC 58.254 40.000 0.00 0.00 0.00 3.46
2552 2806 6.322969 TCGCTCATACTACTAATTTCCTTCCA 59.677 38.462 0.00 0.00 0.00 3.53
2554 2808 6.706716 GCTCATACTACTAATTTCCTTCCACC 59.293 42.308 0.00 0.00 0.00 4.61
2555 2809 7.635089 GCTCATACTACTAATTTCCTTCCACCA 60.635 40.741 0.00 0.00 0.00 4.17
2556 2810 7.792032 TCATACTACTAATTTCCTTCCACCAG 58.208 38.462 0.00 0.00 0.00 4.00
2558 2812 8.701895 CATACTACTAATTTCCTTCCACCAGTA 58.298 37.037 0.00 0.00 0.00 2.74
2559 2813 7.184067 ACTACTAATTTCCTTCCACCAGTAG 57.816 40.000 0.00 0.00 39.90 2.57
2597 2853 2.163810 ACTAACCATGCATGCCCAAT 57.836 45.000 21.69 7.10 0.00 3.16
2598 2854 3.311167 ACTAACCATGCATGCCCAATA 57.689 42.857 21.69 7.84 0.00 1.90
2599 2855 3.641046 ACTAACCATGCATGCCCAATAA 58.359 40.909 21.69 0.00 0.00 1.40
2600 2856 4.225573 ACTAACCATGCATGCCCAATAAT 58.774 39.130 21.69 0.00 0.00 1.28
2601 2857 5.392995 ACTAACCATGCATGCCCAATAATA 58.607 37.500 21.69 0.00 0.00 0.98
2602 2858 4.605640 AACCATGCATGCCCAATAATAC 57.394 40.909 21.69 0.00 0.00 1.89
2640 2896 0.545787 TTCTTCGCTTCCCTGGGGTA 60.546 55.000 14.00 0.19 36.47 3.69
2658 2914 0.949397 TATCTTCGTCGTCGATGGGG 59.051 55.000 14.28 7.71 45.65 4.96
2664 2920 1.654954 CGTCGTCGATGGGGTTCTCT 61.655 60.000 6.56 0.00 39.71 3.10
2825 3095 1.871080 AGCGTCTCTTCAACAACTGG 58.129 50.000 0.00 0.00 0.00 4.00
2838 3116 6.247229 TCAACAACTGGCATATACATACCT 57.753 37.500 0.00 0.00 0.00 3.08
2895 3176 8.094798 TGACACACCTCATTAAGATAAACAAC 57.905 34.615 0.00 0.00 0.00 3.32
2937 3220 2.320781 AGTACCTCAGCAGTCAACAGT 58.679 47.619 0.00 0.00 0.00 3.55
2987 3270 5.533154 GTGCTAGATAGACCATAGTGTGACT 59.467 44.000 0.00 0.00 0.00 3.41
2991 3274 5.136828 AGATAGACCATAGTGTGACTGAGG 58.863 45.833 0.00 0.00 32.09 3.86
2997 3280 1.460504 TAGTGTGACTGAGGCCTACG 58.539 55.000 4.42 1.28 0.00 3.51
2998 3281 1.446272 GTGTGACTGAGGCCTACGC 60.446 63.158 4.42 2.02 0.00 4.42
3085 3388 2.694213 ACAAGTACGTGCATGCATACA 58.306 42.857 25.64 8.85 0.00 2.29
3088 3391 4.507756 ACAAGTACGTGCATGCATACATAG 59.492 41.667 25.64 17.00 33.67 2.23
3089 3392 3.653344 AGTACGTGCATGCATACATAGG 58.347 45.455 25.64 7.64 33.67 2.57
3092 3395 3.390135 ACGTGCATGCATACATAGGTAC 58.610 45.455 25.64 5.57 33.67 3.34
3104 3407 2.827322 ACATAGGTACCTAACGTGTGCA 59.173 45.455 25.25 1.33 38.29 4.57
3156 3459 9.722056 GGATGATGAATTACTAACATGTTGAAC 57.278 33.333 21.42 6.16 0.00 3.18
3181 3485 4.708726 AGCTTGGTTGCTTGCTTATAAG 57.291 40.909 8.20 8.20 40.93 1.73
3293 3597 3.474570 ATGGGCTCCTCGCACTCC 61.475 66.667 0.00 0.00 44.45 3.85
3345 3649 1.084289 GGACGCCTACCAAATGTGAC 58.916 55.000 0.00 0.00 0.00 3.67
3346 3650 0.719465 GACGCCTACCAAATGTGACG 59.281 55.000 0.00 0.00 0.00 4.35
3422 3730 2.226674 GAGTTTGTTTGTCCAGCTAGCC 59.773 50.000 12.13 0.00 0.00 3.93
3557 3876 1.884067 GCACAGCTGGAGCCTTTAACT 60.884 52.381 19.93 0.00 43.38 2.24
3558 3877 2.079925 CACAGCTGGAGCCTTTAACTC 58.920 52.381 19.93 0.00 43.38 3.01
3564 3883 3.762674 GAGCCTTTAACTCCTCCCG 57.237 57.895 0.00 0.00 0.00 5.14
3605 3924 3.453424 CGTGTGTAAATCGATCCATGGA 58.547 45.455 18.88 18.88 0.00 3.41
3606 3925 4.058124 CGTGTGTAAATCGATCCATGGAT 58.942 43.478 27.66 27.66 37.59 3.41
3607 3926 4.150627 CGTGTGTAAATCGATCCATGGATC 59.849 45.833 35.76 35.76 45.42 3.36
3658 3978 0.825840 CGGGGCTGGAACTGGAAAAA 60.826 55.000 0.00 0.00 0.00 1.94
3710 4030 2.040544 CCTGTGGCGTGGAATGGAC 61.041 63.158 0.00 0.00 0.00 4.02
3823 4158 0.809241 CTCATCTCAGGGACGCAAGC 60.809 60.000 0.00 0.00 45.62 4.01
3824 4159 1.078918 CATCTCAGGGACGCAAGCA 60.079 57.895 0.00 0.00 45.62 3.91
3825 4160 1.078848 ATCTCAGGGACGCAAGCAC 60.079 57.895 0.00 0.00 45.62 4.40
3826 4161 1.830587 ATCTCAGGGACGCAAGCACA 61.831 55.000 0.00 0.00 45.62 4.57
3827 4162 1.597854 CTCAGGGACGCAAGCACAA 60.598 57.895 0.00 0.00 45.62 3.33
3838 4173 0.872881 CAAGCACAAGCACAACCAGC 60.873 55.000 0.00 0.00 45.49 4.85
3868 4203 4.202574 TATGGGGGTGCATGGCGG 62.203 66.667 0.00 0.00 0.00 6.13
3890 4225 3.058501 GTGTTCAAACATCGAACGGGAAT 60.059 43.478 0.00 0.00 44.63 3.01
3891 4226 3.187637 TGTTCAAACATCGAACGGGAATC 59.812 43.478 0.00 0.00 44.63 2.52
3892 4227 3.328382 TCAAACATCGAACGGGAATCT 57.672 42.857 0.00 0.00 0.00 2.40
3893 4228 3.259064 TCAAACATCGAACGGGAATCTC 58.741 45.455 0.00 0.00 0.00 2.75
3912 4253 0.319211 CCACCTGCACGAGTACGAAA 60.319 55.000 0.00 0.00 42.66 3.46
3951 4292 1.797713 GCGTCTCCGTCGATTGATTCA 60.798 52.381 0.00 0.00 36.15 2.57
3959 4300 2.621338 GTCGATTGATTCAGTGCTCCA 58.379 47.619 0.00 0.00 0.00 3.86
3963 4304 0.322816 TTGATTCAGTGCTCCAGGCC 60.323 55.000 0.00 0.00 40.92 5.19
3973 4314 4.680237 TCCAGGCCAGCACGAACG 62.680 66.667 5.01 0.00 0.00 3.95
3974 4315 4.988598 CCAGGCCAGCACGAACGT 62.989 66.667 5.01 0.00 0.00 3.99
3990 4331 2.337246 CGTTTTTACCAGCCCCGGG 61.337 63.158 15.80 15.80 0.00 5.73
4000 4341 3.942439 GCCCCGGGCTACCTCATC 61.942 72.222 22.31 0.00 46.69 2.92
4001 4342 2.445845 CCCCGGGCTACCTCATCA 60.446 66.667 17.73 0.00 33.28 3.07
4002 4343 1.843376 CCCCGGGCTACCTCATCAT 60.843 63.158 17.73 0.00 33.28 2.45
4003 4344 1.674057 CCCGGGCTACCTCATCATC 59.326 63.158 8.08 0.00 33.28 2.92
4004 4345 0.833834 CCCGGGCTACCTCATCATCT 60.834 60.000 8.08 0.00 33.28 2.90
4005 4346 1.051812 CCGGGCTACCTCATCATCTT 58.948 55.000 0.00 0.00 33.28 2.40
4006 4347 1.001406 CCGGGCTACCTCATCATCTTC 59.999 57.143 0.00 0.00 33.28 2.87
4007 4348 1.967066 CGGGCTACCTCATCATCTTCT 59.033 52.381 0.00 0.00 33.28 2.85
4008 4349 2.029470 CGGGCTACCTCATCATCTTCTC 60.029 54.545 0.00 0.00 33.28 2.87
4009 4350 2.029470 GGGCTACCTCATCATCTTCTCG 60.029 54.545 0.00 0.00 0.00 4.04
4010 4351 2.625790 GGCTACCTCATCATCTTCTCGT 59.374 50.000 0.00 0.00 0.00 4.18
4011 4352 3.821600 GGCTACCTCATCATCTTCTCGTA 59.178 47.826 0.00 0.00 0.00 3.43
4012 4353 4.083003 GGCTACCTCATCATCTTCTCGTAG 60.083 50.000 0.00 0.00 0.00 3.51
4013 4354 4.614993 GCTACCTCATCATCTTCTCGTAGC 60.615 50.000 0.00 0.00 40.25 3.58
4014 4355 2.292016 ACCTCATCATCTTCTCGTAGCG 59.708 50.000 0.00 0.00 0.00 4.26
4015 4356 2.292016 CCTCATCATCTTCTCGTAGCGT 59.708 50.000 0.00 0.00 0.00 5.07
4016 4357 3.295785 CTCATCATCTTCTCGTAGCGTG 58.704 50.000 0.00 0.00 0.00 5.34
4017 4358 2.683362 TCATCATCTTCTCGTAGCGTGT 59.317 45.455 0.00 0.00 0.00 4.49
4018 4359 3.128764 TCATCATCTTCTCGTAGCGTGTT 59.871 43.478 0.00 0.00 0.00 3.32
4019 4360 3.132629 TCATCTTCTCGTAGCGTGTTC 57.867 47.619 0.00 0.00 0.00 3.18
4020 4361 1.840741 CATCTTCTCGTAGCGTGTTCG 59.159 52.381 0.00 0.00 40.37 3.95
4021 4362 0.870393 TCTTCTCGTAGCGTGTTCGT 59.130 50.000 0.00 0.00 39.49 3.85
4022 4363 0.975544 CTTCTCGTAGCGTGTTCGTG 59.024 55.000 0.00 0.00 39.49 4.35
4023 4364 1.000233 TTCTCGTAGCGTGTTCGTGC 61.000 55.000 0.00 0.00 39.49 5.34
4024 4365 2.764925 CTCGTAGCGTGTTCGTGCG 61.765 63.158 0.00 0.00 39.49 5.34
4025 4366 3.095278 CGTAGCGTGTTCGTGCGT 61.095 61.111 0.00 0.00 39.49 5.24
4026 4367 2.464189 GTAGCGTGTTCGTGCGTG 59.536 61.111 0.00 0.00 39.49 5.34
4027 4368 2.731721 TAGCGTGTTCGTGCGTGG 60.732 61.111 0.00 0.00 39.49 4.94
4032 4373 4.281947 TGTTCGTGCGTGGCCGTA 62.282 61.111 0.00 0.00 36.15 4.02
4033 4374 2.812178 GTTCGTGCGTGGCCGTAT 60.812 61.111 0.00 0.00 36.15 3.06
4034 4375 2.811747 TTCGTGCGTGGCCGTATG 60.812 61.111 0.00 0.00 37.08 2.39
4035 4376 4.805231 TCGTGCGTGGCCGTATGG 62.805 66.667 0.00 0.00 36.49 2.74
4058 4399 4.595116 CAAATCGATTTGCTAGCTTCAGG 58.405 43.478 31.60 9.45 40.42 3.86
4059 4400 1.656652 TCGATTTGCTAGCTTCAGGC 58.343 50.000 17.23 0.00 42.19 4.85
4060 4401 7.161699 CAAATCGATTTGCTAGCTTCAGGCT 62.162 44.000 31.60 0.22 45.54 4.58
4061 4402 8.844812 CAAATCGATTTGCTAGCTTCAGGCTC 62.845 46.154 31.60 2.59 44.10 4.70
4068 4409 3.407657 GCTTCAGGCTCGCTGATG 58.592 61.111 0.00 0.00 38.06 3.07
4069 4410 2.821688 GCTTCAGGCTCGCTGATGC 61.822 63.158 11.61 11.61 42.05 3.91
4084 4425 3.055110 TGCGTTCGCATGCATGGT 61.055 55.556 27.34 0.00 40.20 3.55
4085 4426 2.277501 GCGTTCGCATGCATGGTC 60.278 61.111 27.34 11.26 34.70 4.02
4086 4427 3.037992 GCGTTCGCATGCATGGTCA 62.038 57.895 27.34 7.15 34.70 4.02
4087 4428 1.226101 CGTTCGCATGCATGGTCAC 60.226 57.895 27.34 15.82 0.00 3.67
4088 4429 1.875262 GTTCGCATGCATGGTCACA 59.125 52.632 27.34 0.00 0.00 3.58
4089 4430 0.454957 GTTCGCATGCATGGTCACAC 60.455 55.000 27.34 9.08 0.00 3.82
4090 4431 1.910216 TTCGCATGCATGGTCACACG 61.910 55.000 27.34 19.92 0.00 4.49
4105 4446 2.728383 ACGACACGACGAAAGCCG 60.728 61.111 0.00 0.00 44.72 5.52
4175 4516 2.492090 GTGCACGCAAACCCACAA 59.508 55.556 0.00 0.00 0.00 3.33
4185 4526 2.425668 GCAAACCCACAACACAGTACTT 59.574 45.455 0.00 0.00 0.00 2.24
4186 4527 3.119280 GCAAACCCACAACACAGTACTTT 60.119 43.478 0.00 0.00 0.00 2.66
4187 4528 4.619628 GCAAACCCACAACACAGTACTTTT 60.620 41.667 0.00 0.00 0.00 2.27
4188 4529 5.474825 CAAACCCACAACACAGTACTTTTT 58.525 37.500 0.00 0.00 0.00 1.94
4189 4530 6.622549 CAAACCCACAACACAGTACTTTTTA 58.377 36.000 0.00 0.00 0.00 1.52
4190 4531 5.823209 ACCCACAACACAGTACTTTTTAC 57.177 39.130 0.00 0.00 0.00 2.01
4191 4532 5.503002 ACCCACAACACAGTACTTTTTACT 58.497 37.500 0.00 0.00 0.00 2.24
4192 4533 6.652053 ACCCACAACACAGTACTTTTTACTA 58.348 36.000 0.00 0.00 0.00 1.82
4193 4534 6.539826 ACCCACAACACAGTACTTTTTACTAC 59.460 38.462 0.00 0.00 0.00 2.73
4202 4543 9.839589 CACAGTACTTTTTACTACTAAAACACG 57.160 33.333 0.00 0.00 32.59 4.49
4213 4554 6.313252 ACTACTAAAACACGAGTCGATCTTC 58.687 40.000 21.50 0.00 0.00 2.87
4227 4568 1.750778 GATCTTCGGGGTGGTACGTAA 59.249 52.381 0.00 0.00 0.00 3.18
4228 4569 0.887933 TCTTCGGGGTGGTACGTAAC 59.112 55.000 2.90 2.90 0.00 2.50
4229 4570 0.456653 CTTCGGGGTGGTACGTAACG 60.457 60.000 6.07 0.96 0.00 3.18
4230 4571 1.175983 TTCGGGGTGGTACGTAACGT 61.176 55.000 6.07 0.00 44.35 3.99
4231 4572 0.321741 TCGGGGTGGTACGTAACGTA 60.322 55.000 6.07 0.00 41.54 3.57
4240 4581 1.651987 TACGTAACGTACTCCCTCCG 58.348 55.000 0.00 0.00 41.54 4.63
4241 4582 0.321653 ACGTAACGTACTCCCTCCGT 60.322 55.000 0.00 0.00 38.73 4.69
4242 4583 0.804989 CGTAACGTACTCCCTCCGTT 59.195 55.000 0.00 0.00 45.65 4.44
4243 4584 1.202076 CGTAACGTACTCCCTCCGTTC 60.202 57.143 0.00 0.00 43.09 3.95
4244 4585 1.812571 GTAACGTACTCCCTCCGTTCA 59.187 52.381 0.00 0.00 43.09 3.18
4245 4586 0.600057 AACGTACTCCCTCCGTTCAC 59.400 55.000 0.00 0.00 40.46 3.18
4246 4587 1.136147 CGTACTCCCTCCGTTCACG 59.864 63.158 0.00 0.00 39.44 4.35
4247 4588 1.300971 CGTACTCCCTCCGTTCACGA 61.301 60.000 0.00 0.00 43.02 4.35
4248 4589 0.883833 GTACTCCCTCCGTTCACGAA 59.116 55.000 0.00 0.00 43.02 3.85
4249 4590 1.475682 GTACTCCCTCCGTTCACGAAT 59.524 52.381 0.00 0.00 43.02 3.34
4250 4591 1.843368 ACTCCCTCCGTTCACGAATA 58.157 50.000 0.00 0.00 43.02 1.75
4251 4592 2.173519 ACTCCCTCCGTTCACGAATAA 58.826 47.619 0.00 0.00 43.02 1.40
4252 4593 2.165845 ACTCCCTCCGTTCACGAATAAG 59.834 50.000 0.00 0.00 43.02 1.73
4253 4594 2.165845 CTCCCTCCGTTCACGAATAAGT 59.834 50.000 0.00 0.00 43.02 2.24
4254 4595 2.094390 TCCCTCCGTTCACGAATAAGTG 60.094 50.000 0.00 0.00 43.02 3.16
4255 4596 2.353406 CCCTCCGTTCACGAATAAGTGT 60.353 50.000 0.00 0.00 42.40 3.55
4256 4597 3.119388 CCCTCCGTTCACGAATAAGTGTA 60.119 47.826 0.00 0.00 42.40 2.90
4257 4598 3.855950 CCTCCGTTCACGAATAAGTGTAC 59.144 47.826 0.00 0.00 42.40 2.90
4258 4599 4.380233 CCTCCGTTCACGAATAAGTGTACT 60.380 45.833 0.00 0.00 42.40 2.73
4259 4600 5.125100 TCCGTTCACGAATAAGTGTACTT 57.875 39.130 0.00 2.51 42.40 2.24
4260 4601 5.156355 TCCGTTCACGAATAAGTGTACTTC 58.844 41.667 0.00 0.00 42.40 3.01
4261 4602 5.048504 TCCGTTCACGAATAAGTGTACTTCT 60.049 40.000 0.00 0.00 42.40 2.85
4262 4603 6.149308 TCCGTTCACGAATAAGTGTACTTCTA 59.851 38.462 0.00 0.00 42.40 2.10
4263 4604 6.468319 CCGTTCACGAATAAGTGTACTTCTAG 59.532 42.308 0.00 0.00 42.40 2.43
4264 4605 6.021626 CGTTCACGAATAAGTGTACTTCTAGC 60.022 42.308 0.00 0.00 42.40 3.42
4265 4606 6.754702 TCACGAATAAGTGTACTTCTAGCT 57.245 37.500 0.00 0.00 42.40 3.32
4266 4607 7.154435 TCACGAATAAGTGTACTTCTAGCTT 57.846 36.000 0.00 0.00 42.40 3.74
4267 4608 7.600065 TCACGAATAAGTGTACTTCTAGCTTT 58.400 34.615 0.00 0.00 42.40 3.51
4268 4609 8.086522 TCACGAATAAGTGTACTTCTAGCTTTT 58.913 33.333 0.00 0.00 42.40 2.27
4269 4610 8.162880 CACGAATAAGTGTACTTCTAGCTTTTG 58.837 37.037 0.00 0.00 37.40 2.44
4270 4611 7.871463 ACGAATAAGTGTACTTCTAGCTTTTGT 59.129 33.333 0.00 0.00 37.40 2.83
4271 4612 8.373992 CGAATAAGTGTACTTCTAGCTTTTGTC 58.626 37.037 0.00 0.00 37.40 3.18
4272 4613 8.549338 AATAAGTGTACTTCTAGCTTTTGTCC 57.451 34.615 0.00 0.00 37.40 4.02
4273 4614 5.810080 AGTGTACTTCTAGCTTTTGTCCT 57.190 39.130 0.00 0.00 0.00 3.85
4274 4615 6.912951 AGTGTACTTCTAGCTTTTGTCCTA 57.087 37.500 0.00 0.00 0.00 2.94
4275 4616 6.926313 AGTGTACTTCTAGCTTTTGTCCTAG 58.074 40.000 0.00 0.00 33.88 3.02
4276 4617 6.720288 AGTGTACTTCTAGCTTTTGTCCTAGA 59.280 38.462 0.00 0.00 38.53 2.43
4277 4618 7.397761 AGTGTACTTCTAGCTTTTGTCCTAGAT 59.602 37.037 0.00 0.00 39.62 1.98
4278 4619 8.035984 GTGTACTTCTAGCTTTTGTCCTAGATT 58.964 37.037 0.00 0.00 39.62 2.40
4279 4620 9.251440 TGTACTTCTAGCTTTTGTCCTAGATTA 57.749 33.333 0.00 0.00 39.62 1.75
4282 4623 9.660180 ACTTCTAGCTTTTGTCCTAGATTAAAG 57.340 33.333 0.00 0.00 39.62 1.85
4283 4624 9.660180 CTTCTAGCTTTTGTCCTAGATTAAAGT 57.340 33.333 0.00 0.00 39.62 2.66
4315 4656 9.996554 AACTTTGACCAATTTTATAGGGAAAAG 57.003 29.630 0.00 0.00 35.60 2.27
4316 4657 9.154632 ACTTTGACCAATTTTATAGGGAAAAGT 57.845 29.630 0.00 0.00 36.72 2.66
4319 4660 9.816787 TTGACCAATTTTATAGGGAAAAGTACT 57.183 29.630 0.00 0.00 32.06 2.73
4322 4663 9.404848 ACCAATTTTATAGGGAAAAGTACTAGC 57.595 33.333 0.00 0.00 32.06 3.42
4323 4664 9.403583 CCAATTTTATAGGGAAAAGTACTAGCA 57.596 33.333 0.00 0.00 32.06 3.49
4331 4672 9.780186 ATAGGGAAAAGTACTAGCATTTATGAC 57.220 33.333 0.00 0.00 0.00 3.06
4332 4673 7.630082 AGGGAAAAGTACTAGCATTTATGACA 58.370 34.615 0.00 0.00 0.00 3.58
4333 4674 7.553044 AGGGAAAAGTACTAGCATTTATGACAC 59.447 37.037 0.00 0.00 0.00 3.67
4334 4675 7.553044 GGGAAAAGTACTAGCATTTATGACACT 59.447 37.037 0.00 0.00 0.00 3.55
4335 4676 9.595823 GGAAAAGTACTAGCATTTATGACACTA 57.404 33.333 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.637483 TTCGCTCCATTTCATTTCATCC 57.363 40.909 0.00 0.00 0.00 3.51
27 28 4.501921 GCTTTCGCTCCATTTCATTTCATC 59.498 41.667 0.00 0.00 0.00 2.92
184 191 5.103290 TGTTTGCACTTCTTTAATCGGTC 57.897 39.130 0.00 0.00 0.00 4.79
391 431 7.013559 GGTGTTTACCTTTGCTTTCCTTTAGTA 59.986 37.037 0.00 0.00 43.97 1.82
549 592 2.495669 ACAGCTTTAGTCCTCTGCTCTC 59.504 50.000 0.00 0.00 0.00 3.20
560 613 3.555966 AGAGGCAACAAACAGCTTTAGT 58.444 40.909 0.00 0.00 41.41 2.24
568 621 3.845781 AGAAGAGAGAGGCAACAAACA 57.154 42.857 0.00 0.00 41.41 2.83
573 626 4.220602 AGAGAGAAAGAAGAGAGAGGCAAC 59.779 45.833 0.00 0.00 0.00 4.17
574 627 4.415596 AGAGAGAAAGAAGAGAGAGGCAA 58.584 43.478 0.00 0.00 0.00 4.52
575 628 4.016444 GAGAGAGAAAGAAGAGAGAGGCA 58.984 47.826 0.00 0.00 0.00 4.75
576 629 4.096984 CAGAGAGAGAAAGAAGAGAGAGGC 59.903 50.000 0.00 0.00 0.00 4.70
577 630 4.641989 CCAGAGAGAGAAAGAAGAGAGAGG 59.358 50.000 0.00 0.00 0.00 3.69
578 631 5.256474 ACCAGAGAGAGAAAGAAGAGAGAG 58.744 45.833 0.00 0.00 0.00 3.20
579 632 5.255397 ACCAGAGAGAGAAAGAAGAGAGA 57.745 43.478 0.00 0.00 0.00 3.10
580 633 5.982890 AACCAGAGAGAGAAAGAAGAGAG 57.017 43.478 0.00 0.00 0.00 3.20
581 634 6.209788 GGTTAACCAGAGAGAGAAAGAAGAGA 59.790 42.308 20.12 0.00 35.64 3.10
582 635 6.015010 TGGTTAACCAGAGAGAGAAAGAAGAG 60.015 42.308 23.69 0.00 42.01 2.85
583 636 5.839063 TGGTTAACCAGAGAGAGAAAGAAGA 59.161 40.000 23.69 0.00 42.01 2.87
584 637 6.102897 TGGTTAACCAGAGAGAGAAAGAAG 57.897 41.667 23.69 0.00 42.01 2.85
599 652 8.403236 CCTACTAGTTTTTATGCATGGTTAACC 58.597 37.037 18.27 18.27 0.00 2.85
612 722 4.224370 CACCAGAGGCCCTACTAGTTTTTA 59.776 45.833 0.00 0.00 0.00 1.52
632 742 3.785122 GACCACCACCACCACCACC 62.785 68.421 0.00 0.00 0.00 4.61
633 743 2.203294 GACCACCACCACCACCAC 60.203 66.667 0.00 0.00 0.00 4.16
634 744 2.277672 CTTGACCACCACCACCACCA 62.278 60.000 0.00 0.00 0.00 4.17
635 745 1.528309 CTTGACCACCACCACCACC 60.528 63.158 0.00 0.00 0.00 4.61
853 965 0.898320 AAGCTCTTAAGGCAGCGAGA 59.102 50.000 15.45 0.00 40.84 4.04
925 1037 4.382541 TGAGAGGCAGCCGGGAGA 62.383 66.667 5.55 0.00 0.00 3.71
929 1041 3.672295 GAACCTGAGAGGCAGCCGG 62.672 68.421 5.55 2.89 43.50 6.13
942 1054 2.358737 CGCTGGCCGAAAGAACCT 60.359 61.111 0.00 0.00 40.02 3.50
976 1088 0.313043 CCTGCTCCAACAACAAGCTG 59.687 55.000 0.00 0.00 36.96 4.24
977 1089 0.183492 TCCTGCTCCAACAACAAGCT 59.817 50.000 0.00 0.00 36.96 3.74
1062 1186 3.716195 CACTCCACGGGGATGCCA 61.716 66.667 6.99 0.00 43.91 4.92
1119 1246 4.746309 TGGGGATGCTGCTGGTGC 62.746 66.667 0.00 0.00 40.20 5.01
1362 1489 3.880846 CCGAAAGCGCTGCCCATC 61.881 66.667 12.58 3.94 35.83 3.51
1836 1984 3.066203 AGCAAAAACTGTGTACCCTTTCG 59.934 43.478 0.00 0.00 0.00 3.46
1949 2097 1.478510 TCTTCTCCCTTCTTAGCTGCG 59.521 52.381 0.00 0.00 0.00 5.18
1956 2104 4.682563 TCTCACTGATCTTCTCCCTTCTT 58.317 43.478 0.00 0.00 0.00 2.52
2048 2196 0.798776 CAGCACTGATCGGAAACACC 59.201 55.000 9.00 0.00 0.00 4.16
2056 2205 2.540515 ACGAAATACCAGCACTGATCG 58.459 47.619 0.00 4.20 35.36 3.69
2064 2213 4.616181 ACATTTGCTACGAAATACCAGC 57.384 40.909 0.00 0.00 34.56 4.85
2067 2216 7.311364 TCCTTTACATTTGCTACGAAATACC 57.689 36.000 0.00 0.00 0.00 2.73
2227 2377 9.819267 AAGCTAAAATCCTACTAGTATGTTCAC 57.181 33.333 2.33 0.00 0.00 3.18
2260 2418 1.607148 TGTACTCACCTGACACGAGTG 59.393 52.381 1.13 1.13 40.18 3.51
2286 2455 7.653713 AGCAAAGTATTCAGTTATCTGTATCCG 59.346 37.037 0.83 0.00 41.91 4.18
2358 2612 7.148340 ACGTACCAGTTACTAGAACACACTATC 60.148 40.741 0.00 0.00 0.00 2.08
2359 2613 6.656693 ACGTACCAGTTACTAGAACACACTAT 59.343 38.462 0.00 0.00 0.00 2.12
2408 2662 0.250338 AGGGAGCGAGTGTCAAAACC 60.250 55.000 0.00 0.00 0.00 3.27
2524 2778 7.526142 AGGAAATTAGTAGTATGAGCGATGA 57.474 36.000 0.00 0.00 0.00 2.92
2525 2779 7.329717 GGAAGGAAATTAGTAGTATGAGCGATG 59.670 40.741 0.00 0.00 0.00 3.84
2526 2780 7.015292 TGGAAGGAAATTAGTAGTATGAGCGAT 59.985 37.037 0.00 0.00 0.00 4.58
2527 2781 6.322969 TGGAAGGAAATTAGTAGTATGAGCGA 59.677 38.462 0.00 0.00 0.00 4.93
2529 2783 6.706716 GGTGGAAGGAAATTAGTAGTATGAGC 59.293 42.308 0.00 0.00 0.00 4.26
2530 2784 7.792032 TGGTGGAAGGAAATTAGTAGTATGAG 58.208 38.462 0.00 0.00 0.00 2.90
2531 2785 7.402071 ACTGGTGGAAGGAAATTAGTAGTATGA 59.598 37.037 0.00 0.00 0.00 2.15
2532 2786 7.565680 ACTGGTGGAAGGAAATTAGTAGTATG 58.434 38.462 0.00 0.00 0.00 2.39
2536 2790 6.049790 GCTACTGGTGGAAGGAAATTAGTAG 58.950 44.000 0.00 0.00 39.36 2.57
2537 2791 5.104652 GGCTACTGGTGGAAGGAAATTAGTA 60.105 44.000 0.00 0.00 0.00 1.82
2539 2793 4.080299 AGGCTACTGGTGGAAGGAAATTAG 60.080 45.833 0.00 0.00 0.00 1.73
2541 2795 2.649816 AGGCTACTGGTGGAAGGAAATT 59.350 45.455 0.00 0.00 0.00 1.82
2542 2796 2.279173 AGGCTACTGGTGGAAGGAAAT 58.721 47.619 0.00 0.00 0.00 2.17
2548 2802 2.224769 CCTTGAAAGGCTACTGGTGGAA 60.225 50.000 0.00 0.00 39.76 3.53
2550 2804 1.351017 TCCTTGAAAGGCTACTGGTGG 59.649 52.381 4.08 0.00 46.06 4.61
2551 2805 2.039084 ACTCCTTGAAAGGCTACTGGTG 59.961 50.000 4.08 0.00 46.06 4.17
2552 2806 2.039084 CACTCCTTGAAAGGCTACTGGT 59.961 50.000 4.08 0.00 46.06 4.00
2554 2808 3.330267 GACACTCCTTGAAAGGCTACTG 58.670 50.000 4.08 0.13 46.06 2.74
2555 2809 2.028930 CGACACTCCTTGAAAGGCTACT 60.029 50.000 4.08 0.00 46.06 2.57
2556 2810 2.029290 TCGACACTCCTTGAAAGGCTAC 60.029 50.000 4.08 0.00 46.06 3.58
2558 2812 1.048601 TCGACACTCCTTGAAAGGCT 58.951 50.000 4.08 0.00 46.06 4.58
2559 2813 1.531578 GTTCGACACTCCTTGAAAGGC 59.468 52.381 4.08 0.00 46.06 4.35
2597 2853 5.001232 GCTGTTGTTGACAAGGGAGTATTA 58.999 41.667 0.00 0.00 37.93 0.98
2598 2854 3.821033 GCTGTTGTTGACAAGGGAGTATT 59.179 43.478 0.00 0.00 37.93 1.89
2599 2855 3.073062 AGCTGTTGTTGACAAGGGAGTAT 59.927 43.478 0.00 0.00 37.93 2.12
2600 2856 2.438021 AGCTGTTGTTGACAAGGGAGTA 59.562 45.455 0.00 0.00 37.93 2.59
2601 2857 1.212935 AGCTGTTGTTGACAAGGGAGT 59.787 47.619 0.00 0.00 37.93 3.85
2602 2858 1.972872 AGCTGTTGTTGACAAGGGAG 58.027 50.000 0.00 0.00 37.93 4.30
2664 2920 2.796193 CGGGTGCATCATCTCCGGA 61.796 63.158 2.93 2.93 37.35 5.14
2838 3116 4.695396 TCGTTGCTGGAGTAACTAAACAA 58.305 39.130 6.13 0.00 38.28 2.83
2895 3176 6.935167 ACTATGGTTTTGGGAGCAAATTAAG 58.065 36.000 0.00 0.00 0.00 1.85
2937 3220 3.778629 GGTAGGTAGTGGATCTTTGGGAA 59.221 47.826 0.00 0.00 0.00 3.97
3085 3388 2.159142 GCTGCACACGTTAGGTACCTAT 60.159 50.000 22.36 5.03 0.00 2.57
3088 3391 0.320073 TGCTGCACACGTTAGGTACC 60.320 55.000 2.73 2.73 0.00 3.34
3089 3392 1.068474 CTGCTGCACACGTTAGGTAC 58.932 55.000 0.00 0.00 0.00 3.34
3092 3395 1.230635 AAGCTGCTGCACACGTTAGG 61.231 55.000 18.42 0.00 42.74 2.69
3104 3407 3.256383 TGTTGTTTATGCATGAAGCTGCT 59.744 39.130 10.16 0.00 45.94 4.24
3176 3480 6.712179 ACAAAACCAAACGGAAACCTTATA 57.288 33.333 0.00 0.00 0.00 0.98
3181 3485 3.327626 ACAACAAAACCAAACGGAAACC 58.672 40.909 0.00 0.00 0.00 3.27
3293 3597 2.575993 CTGAGGTCCTGCGAGTGG 59.424 66.667 0.00 0.00 0.00 4.00
3345 3649 2.124193 TGGCAATGGCATCTCCCG 60.124 61.111 5.05 0.00 43.71 5.14
3346 3650 2.496291 GCTGGCAATGGCATCTCCC 61.496 63.158 10.64 2.14 43.71 4.30
3372 3680 1.217779 GCTCTCAGCCTCAGGTCAC 59.782 63.158 0.00 0.00 34.48 3.67
3382 3690 4.459089 GGTCGGGTGGCTCTCAGC 62.459 72.222 0.00 0.00 42.74 4.26
3397 3705 1.675552 CTGGACAAACAAACTCGGGT 58.324 50.000 0.00 0.00 0.00 5.28
3422 3730 3.194329 TCAGATGATTGATAGCTAGGCCG 59.806 47.826 0.00 0.00 0.00 6.13
3462 3776 2.674033 GTGCATGTGGCCTCTGCA 60.674 61.111 20.66 20.66 43.20 4.41
3605 3924 1.001293 CACGACCGATCCATCCATGAT 59.999 52.381 0.00 0.00 0.00 2.45
3606 3925 0.389025 CACGACCGATCCATCCATGA 59.611 55.000 0.00 0.00 0.00 3.07
3607 3926 0.104855 ACACGACCGATCCATCCATG 59.895 55.000 0.00 0.00 0.00 3.66
3608 3927 0.830648 AACACGACCGATCCATCCAT 59.169 50.000 0.00 0.00 0.00 3.41
3609 3928 0.174845 GAACACGACCGATCCATCCA 59.825 55.000 0.00 0.00 0.00 3.41
3610 3929 0.460311 AGAACACGACCGATCCATCC 59.540 55.000 0.00 0.00 0.00 3.51
3611 3930 1.927174 CAAGAACACGACCGATCCATC 59.073 52.381 0.00 0.00 0.00 3.51
3710 4030 1.081892 CAGACAGAGCACAATTCCCG 58.918 55.000 0.00 0.00 0.00 5.14
3761 4081 1.378911 AATTCATCAGCCGCTGCCA 60.379 52.632 15.98 0.00 38.69 4.92
3822 4157 1.589727 GTGCTGGTTGTGCTTGTGC 60.590 57.895 0.00 0.00 40.20 4.57
3823 4158 1.298563 CGTGCTGGTTGTGCTTGTG 60.299 57.895 0.00 0.00 0.00 3.33
3824 4159 1.714899 GACGTGCTGGTTGTGCTTGT 61.715 55.000 0.00 0.00 0.00 3.16
3825 4160 1.009675 GACGTGCTGGTTGTGCTTG 60.010 57.895 0.00 0.00 0.00 4.01
3826 4161 2.186826 GGACGTGCTGGTTGTGCTT 61.187 57.895 0.00 0.00 0.00 3.91
3827 4162 2.591715 GGACGTGCTGGTTGTGCT 60.592 61.111 0.00 0.00 0.00 4.40
3868 4203 1.868498 TCCCGTTCGATGTTTGAACAC 59.132 47.619 0.00 0.00 44.63 3.32
3869 4204 2.242047 TCCCGTTCGATGTTTGAACA 57.758 45.000 8.05 0.00 44.63 3.18
3890 4225 1.583495 CGTACTCGTGCAGGTGGAGA 61.583 60.000 12.54 0.00 0.00 3.71
3891 4226 1.154016 CGTACTCGTGCAGGTGGAG 60.154 63.158 12.54 7.72 0.00 3.86
3892 4227 1.174078 TTCGTACTCGTGCAGGTGGA 61.174 55.000 12.54 1.27 38.33 4.02
3893 4228 0.319211 TTTCGTACTCGTGCAGGTGG 60.319 55.000 12.54 6.93 38.33 4.61
3912 4253 4.202441 ACGCTTAATCATCTTGCCATTCT 58.798 39.130 0.00 0.00 0.00 2.40
3959 4300 1.381165 AAAAACGTTCGTGCTGGCCT 61.381 50.000 3.32 0.00 0.00 5.19
3963 4304 2.635444 CTGGTAAAAACGTTCGTGCTG 58.365 47.619 0.00 0.00 0.00 4.41
3973 4314 2.642254 GCCCGGGGCTGGTAAAAAC 61.642 63.158 30.86 0.00 46.69 2.43
3974 4315 2.283316 GCCCGGGGCTGGTAAAAA 60.283 61.111 30.86 0.00 46.69 1.94
3990 4331 4.614993 GCTACGAGAAGATGATGAGGTAGC 60.615 50.000 4.38 4.38 42.99 3.58
3992 4333 3.498777 CGCTACGAGAAGATGATGAGGTA 59.501 47.826 0.00 0.00 0.00 3.08
3993 4334 2.292016 CGCTACGAGAAGATGATGAGGT 59.708 50.000 0.00 0.00 0.00 3.85
3994 4335 2.292016 ACGCTACGAGAAGATGATGAGG 59.708 50.000 0.00 0.00 0.00 3.86
3995 4336 3.242903 ACACGCTACGAGAAGATGATGAG 60.243 47.826 0.00 0.00 0.00 2.90
3996 4337 2.683362 ACACGCTACGAGAAGATGATGA 59.317 45.455 0.00 0.00 0.00 2.92
3997 4338 3.071786 ACACGCTACGAGAAGATGATG 57.928 47.619 0.00 0.00 0.00 3.07
3998 4339 3.696898 GAACACGCTACGAGAAGATGAT 58.303 45.455 0.00 0.00 0.00 2.45
3999 4340 2.475685 CGAACACGCTACGAGAAGATGA 60.476 50.000 0.00 0.00 0.00 2.92
4000 4341 1.840741 CGAACACGCTACGAGAAGATG 59.159 52.381 0.00 0.00 0.00 2.90
4001 4342 1.467734 ACGAACACGCTACGAGAAGAT 59.532 47.619 0.00 0.00 0.00 2.40
4002 4343 0.870393 ACGAACACGCTACGAGAAGA 59.130 50.000 0.00 0.00 0.00 2.87
4003 4344 0.975544 CACGAACACGCTACGAGAAG 59.024 55.000 0.00 0.00 0.00 2.85
4004 4345 1.000233 GCACGAACACGCTACGAGAA 61.000 55.000 0.00 0.00 0.00 2.87
4005 4346 1.441515 GCACGAACACGCTACGAGA 60.442 57.895 0.00 0.00 0.00 4.04
4006 4347 2.764925 CGCACGAACACGCTACGAG 61.765 63.158 0.00 0.00 0.00 4.18
4007 4348 2.797850 CGCACGAACACGCTACGA 60.798 61.111 0.00 0.00 0.00 3.43
4008 4349 3.095278 ACGCACGAACACGCTACG 61.095 61.111 0.00 0.00 0.00 3.51
4009 4350 2.464189 CACGCACGAACACGCTAC 59.536 61.111 0.00 0.00 0.00 3.58
4010 4351 2.731721 CCACGCACGAACACGCTA 60.732 61.111 0.00 0.00 0.00 4.26
4015 4356 3.576932 ATACGGCCACGCACGAACA 62.577 57.895 2.24 0.00 46.04 3.18
4016 4357 2.812178 ATACGGCCACGCACGAAC 60.812 61.111 2.24 0.00 46.04 3.95
4017 4358 2.811747 CATACGGCCACGCACGAA 60.812 61.111 2.24 0.00 46.04 3.85
4018 4359 4.805231 CCATACGGCCACGCACGA 62.805 66.667 2.24 0.00 46.04 4.35
4036 4377 5.021611 GCCTGAAGCTAGCAAATCGATTTG 61.022 45.833 35.70 35.70 43.22 2.32
4037 4378 3.065925 GCCTGAAGCTAGCAAATCGATTT 59.934 43.478 17.60 17.60 38.99 2.17
4038 4379 2.615912 GCCTGAAGCTAGCAAATCGATT 59.384 45.455 18.83 4.39 38.99 3.34
4039 4380 2.216898 GCCTGAAGCTAGCAAATCGAT 58.783 47.619 18.83 0.00 38.99 3.59
4040 4381 1.656652 GCCTGAAGCTAGCAAATCGA 58.343 50.000 18.83 0.00 38.99 3.59
4068 4409 2.277501 GACCATGCATGCGAACGC 60.278 61.111 21.69 12.33 42.35 4.84
4069 4410 1.226101 GTGACCATGCATGCGAACG 60.226 57.895 21.69 9.66 0.00 3.95
4070 4411 0.454957 GTGTGACCATGCATGCGAAC 60.455 55.000 21.69 16.97 0.00 3.95
4071 4412 1.875262 GTGTGACCATGCATGCGAA 59.125 52.632 21.69 5.27 0.00 4.70
4072 4413 2.389809 CGTGTGACCATGCATGCGA 61.390 57.895 21.69 3.80 0.00 5.10
4073 4414 2.098871 CGTGTGACCATGCATGCG 59.901 61.111 21.69 16.19 0.00 4.73
4074 4415 1.135315 GTCGTGTGACCATGCATGC 59.865 57.895 21.69 11.82 39.30 4.06
4075 4416 0.166597 GTGTCGTGTGACCATGCATG 59.833 55.000 20.19 20.19 44.86 4.06
4076 4417 1.291184 CGTGTCGTGTGACCATGCAT 61.291 55.000 0.00 0.00 44.86 3.96
4077 4418 1.953642 CGTGTCGTGTGACCATGCA 60.954 57.895 0.00 0.00 44.86 3.96
4078 4419 1.663388 TCGTGTCGTGTGACCATGC 60.663 57.895 0.00 0.00 44.86 4.06
4079 4420 1.605481 CGTCGTGTCGTGTGACCATG 61.605 60.000 0.00 0.00 44.86 3.66
4080 4421 1.371267 CGTCGTGTCGTGTGACCAT 60.371 57.895 0.00 0.00 44.86 3.55
4081 4422 1.991099 TTCGTCGTGTCGTGTGACCA 61.991 55.000 0.00 0.00 44.86 4.02
4082 4423 0.866906 TTTCGTCGTGTCGTGTGACC 60.867 55.000 0.00 0.00 44.86 4.02
4083 4424 0.497265 CTTTCGTCGTGTCGTGTGAC 59.503 55.000 0.00 0.00 45.71 3.67
4084 4425 1.204228 GCTTTCGTCGTGTCGTGTGA 61.204 55.000 0.00 0.00 0.00 3.58
4085 4426 1.198397 GCTTTCGTCGTGTCGTGTG 59.802 57.895 0.00 0.00 0.00 3.82
4086 4427 1.947642 GGCTTTCGTCGTGTCGTGT 60.948 57.895 0.00 0.00 0.00 4.49
4087 4428 2.844146 GGCTTTCGTCGTGTCGTG 59.156 61.111 0.00 0.00 0.00 4.35
4088 4429 2.728383 CGGCTTTCGTCGTGTCGT 60.728 61.111 0.00 0.00 32.61 4.34
4111 4452 2.034532 TCACCTGCATGCACTGGG 59.965 61.111 25.09 22.59 33.19 4.45
4167 4508 5.947566 AGTAAAAAGTACTGTGTTGTGGGTT 59.052 36.000 0.00 0.00 0.00 4.11
4185 4526 8.292448 AGATCGACTCGTGTTTTAGTAGTAAAA 58.708 33.333 10.79 10.79 36.05 1.52
4186 4527 7.810658 AGATCGACTCGTGTTTTAGTAGTAAA 58.189 34.615 0.00 0.00 0.00 2.01
4187 4528 7.369803 AGATCGACTCGTGTTTTAGTAGTAA 57.630 36.000 0.00 0.00 0.00 2.24
4188 4529 6.974932 AGATCGACTCGTGTTTTAGTAGTA 57.025 37.500 0.00 0.00 0.00 1.82
4189 4530 5.876612 AGATCGACTCGTGTTTTAGTAGT 57.123 39.130 0.00 0.00 0.00 2.73
4190 4531 5.448479 CGAAGATCGACTCGTGTTTTAGTAG 59.552 44.000 0.00 0.00 43.74 2.57
4191 4532 5.319139 CGAAGATCGACTCGTGTTTTAGTA 58.681 41.667 0.00 0.00 43.74 1.82
4192 4533 4.156915 CGAAGATCGACTCGTGTTTTAGT 58.843 43.478 0.00 0.00 43.74 2.24
4193 4534 3.542704 CCGAAGATCGACTCGTGTTTTAG 59.457 47.826 11.17 0.00 43.74 1.85
4202 4543 1.321074 ACCACCCCGAAGATCGACTC 61.321 60.000 0.58 0.00 43.74 3.36
4213 4554 2.176140 TACGTTACGTACCACCCCG 58.824 57.895 13.90 0.00 41.54 5.73
4227 4568 1.580845 CGTGAACGGAGGGAGTACGT 61.581 60.000 0.00 0.00 43.43 3.57
4228 4569 1.136147 CGTGAACGGAGGGAGTACG 59.864 63.158 0.00 0.00 35.37 3.67
4229 4570 0.883833 TTCGTGAACGGAGGGAGTAC 59.116 55.000 2.59 0.00 40.29 2.73
4230 4571 1.843368 ATTCGTGAACGGAGGGAGTA 58.157 50.000 2.59 0.00 40.29 2.59
4231 4572 1.843368 TATTCGTGAACGGAGGGAGT 58.157 50.000 2.59 0.00 40.29 3.85
4232 4573 2.165845 ACTTATTCGTGAACGGAGGGAG 59.834 50.000 2.59 0.00 40.29 4.30
4233 4574 2.094390 CACTTATTCGTGAACGGAGGGA 60.094 50.000 2.59 0.00 40.29 4.20
4234 4575 2.268298 CACTTATTCGTGAACGGAGGG 58.732 52.381 2.59 0.00 40.29 4.30
4235 4576 2.955614 ACACTTATTCGTGAACGGAGG 58.044 47.619 2.59 0.00 40.29 4.30
4236 4577 4.730657 AGTACACTTATTCGTGAACGGAG 58.269 43.478 2.59 0.00 40.29 4.63
4237 4578 4.771590 AGTACACTTATTCGTGAACGGA 57.228 40.909 2.59 0.00 40.29 4.69
4238 4579 5.159209 AGAAGTACACTTATTCGTGAACGG 58.841 41.667 2.59 0.00 38.27 4.44
4239 4580 6.021626 GCTAGAAGTACACTTATTCGTGAACG 60.022 42.308 0.00 0.00 38.27 3.95
4240 4581 7.028361 AGCTAGAAGTACACTTATTCGTGAAC 58.972 38.462 0.00 0.00 38.27 3.18
4241 4582 7.154435 AGCTAGAAGTACACTTATTCGTGAA 57.846 36.000 0.00 0.00 38.27 3.18
4242 4583 6.754702 AGCTAGAAGTACACTTATTCGTGA 57.245 37.500 0.00 0.00 38.27 4.35
4243 4584 7.813852 AAAGCTAGAAGTACACTTATTCGTG 57.186 36.000 0.00 0.00 40.67 4.35
4244 4585 7.871463 ACAAAAGCTAGAAGTACACTTATTCGT 59.129 33.333 0.00 0.00 36.11 3.85
4245 4586 8.240883 ACAAAAGCTAGAAGTACACTTATTCG 57.759 34.615 0.00 0.00 36.11 3.34
4246 4587 8.657729 GGACAAAAGCTAGAAGTACACTTATTC 58.342 37.037 0.00 0.00 36.11 1.75
4247 4588 8.376270 AGGACAAAAGCTAGAAGTACACTTATT 58.624 33.333 0.00 0.00 36.11 1.40
4248 4589 7.908453 AGGACAAAAGCTAGAAGTACACTTAT 58.092 34.615 0.00 0.00 36.11 1.73
4249 4590 7.299246 AGGACAAAAGCTAGAAGTACACTTA 57.701 36.000 0.00 0.00 36.11 2.24
4250 4591 6.176014 AGGACAAAAGCTAGAAGTACACTT 57.824 37.500 0.00 0.00 39.23 3.16
4251 4592 5.810080 AGGACAAAAGCTAGAAGTACACT 57.190 39.130 0.00 0.00 0.00 3.55
4252 4593 6.921914 TCTAGGACAAAAGCTAGAAGTACAC 58.078 40.000 0.00 0.00 0.00 2.90
4253 4594 7.719871 ATCTAGGACAAAAGCTAGAAGTACA 57.280 36.000 0.00 0.00 32.97 2.90
4256 4597 9.660180 CTTTAATCTAGGACAAAAGCTAGAAGT 57.340 33.333 0.00 0.00 32.97 3.01
4257 4598 9.660180 ACTTTAATCTAGGACAAAAGCTAGAAG 57.340 33.333 0.00 0.00 32.97 2.85
4289 4630 9.996554 CTTTTCCCTATAAAATTGGTCAAAGTT 57.003 29.630 0.00 0.00 0.00 2.66
4290 4631 9.154632 ACTTTTCCCTATAAAATTGGTCAAAGT 57.845 29.630 0.00 0.00 34.16 2.66
4293 4634 9.816787 AGTACTTTTCCCTATAAAATTGGTCAA 57.183 29.630 0.00 0.00 0.00 3.18
4296 4637 9.404848 GCTAGTACTTTTCCCTATAAAATTGGT 57.595 33.333 0.00 0.00 0.00 3.67
4297 4638 9.403583 TGCTAGTACTTTTCCCTATAAAATTGG 57.596 33.333 0.00 0.00 0.00 3.16
4305 4646 9.780186 GTCATAAATGCTAGTACTTTTCCCTAT 57.220 33.333 0.00 0.00 0.00 2.57
4306 4647 8.764558 TGTCATAAATGCTAGTACTTTTCCCTA 58.235 33.333 0.00 0.00 0.00 3.53
4307 4648 7.553044 GTGTCATAAATGCTAGTACTTTTCCCT 59.447 37.037 0.00 0.00 0.00 4.20
4308 4649 7.553044 AGTGTCATAAATGCTAGTACTTTTCCC 59.447 37.037 0.00 0.00 0.00 3.97
4309 4650 8.494016 AGTGTCATAAATGCTAGTACTTTTCC 57.506 34.615 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.