Multiple sequence alignment - TraesCS2A01G171100

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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 TraesCS2A01G171100 chr2A 100.000 4287 0 0 1 4287 126650548 126646262 0.000000e+00 7917.0
1 TraesCS2A01G171100 chr2B 94.527 3289 127 25 666 3916 175418328 175415055 0.000000e+00 5027.0
2 TraesCS2A01G171100 chr2B 83.206 131 22 0 788 918 5530277 5530407 2.090000e-23 121.0
3 TraesCS2A01G171100 chr2D 94.919 2086 80 15 668 2739 122400606 122398533 0.000000e+00 3241.0
4 TraesCS2A01G171100 chr2D 91.058 1163 58 24 2766 3916 122398544 122397416 0.000000e+00 1530.0
5 TraesCS2A01G171100 chr2D 87.179 78 7 3 4213 4287 122397416 122397339 7.640000e-13 86.1
6 TraesCS2A01G171100 chr6A 98.369 613 10 0 1 613 556886257 556886869 0.000000e+00 1077.0
7 TraesCS2A01G171100 chr3A 97.227 613 16 1 1 613 722239834 722240445 0.000000e+00 1037.0
8 TraesCS2A01G171100 chr3A 97.073 615 15 3 1 613 263166547 263165934 0.000000e+00 1033.0
9 TraesCS2A01G171100 chr3A 96.254 614 22 1 1 613 728544036 728543423 0.000000e+00 1005.0
10 TraesCS2A01G171100 chr3A 96.098 615 22 2 1 614 728594925 728594312 0.000000e+00 1002.0
11 TraesCS2A01G171100 chr3A 96.085 613 22 2 1 612 728574496 728573885 0.000000e+00 998.0
12 TraesCS2A01G171100 chr3A 96.072 611 19 5 4 613 54836023 54835417 0.000000e+00 990.0
13 TraesCS2A01G171100 chr3A 92.926 311 14 4 3911 4216 395477614 395477921 3.040000e-121 446.0
14 TraesCS2A01G171100 chr5A 97.674 602 10 4 13 613 481091115 481091713 0.000000e+00 1031.0
15 TraesCS2A01G171100 chr5A 94.814 617 23 9 1 614 440442521 440443131 0.000000e+00 953.0
16 TraesCS2A01G171100 chr5A 94.118 306 11 4 3915 4215 549204643 549204340 3.910000e-125 459.0
17 TraesCS2A01G171100 chr3D 93.891 311 13 4 3910 4215 22573662 22573971 8.400000e-127 464.0
18 TraesCS2A01G171100 chr1D 93.354 316 14 5 3905 4215 276505109 276504796 1.090000e-125 460.0
19 TraesCS2A01G171100 chr1D 100.000 42 0 0 3430 3471 51834544 51834503 1.280000e-10 78.7
20 TraesCS2A01G171100 chr1A 93.548 310 14 4 3911 4215 376346532 376346224 1.410000e-124 457.0
21 TraesCS2A01G171100 chr1A 93.831 308 11 4 3913 4215 540722865 540723169 1.410000e-124 457.0
22 TraesCS2A01G171100 chr7D 93.548 310 13 4 3911 4215 265508080 265507773 5.050000e-124 455.0
23 TraesCS2A01G171100 chr7D 93.506 308 12 4 3913 4215 539381771 539382075 6.540000e-123 451.0
24 TraesCS2A01G171100 chr5D 93.226 310 13 6 3911 4215 351152807 351153113 2.350000e-122 449.0
25 TraesCS2A01G171100 chrUn 100.000 42 0 0 3430 3471 261570348 261570307 1.280000e-10 78.7
26 TraesCS2A01G171100 chrUn 100.000 42 0 0 3430 3471 385510333 385510292 1.280000e-10 78.7
27 TraesCS2A01G171100 chrUn 100.000 42 0 0 3430 3471 388894520 388894561 1.280000e-10 78.7
28 TraesCS2A01G171100 chrUn 100.000 42 0 0 3430 3471 433905410 433905451 1.280000e-10 78.7
29 TraesCS2A01G171100 chrUn 100.000 42 0 0 3430 3471 453035632 453035591 1.280000e-10 78.7
30 TraesCS2A01G171100 chr6D 100.000 42 0 0 3430 3471 185541622 185541581 1.280000e-10 78.7
31 TraesCS2A01G171100 chr6D 100.000 42 0 0 3430 3471 388403099 388403140 1.280000e-10 78.7


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 TraesCS2A01G171100 chr2A 126646262 126650548 4286 True 7917.000000 7917 100.000 1 4287 1 chr2A.!!$R1 4286
1 TraesCS2A01G171100 chr2B 175415055 175418328 3273 True 5027.000000 5027 94.527 666 3916 1 chr2B.!!$R1 3250
2 TraesCS2A01G171100 chr2D 122397339 122400606 3267 True 1619.033333 3241 91.052 668 4287 3 chr2D.!!$R1 3619
3 TraesCS2A01G171100 chr6A 556886257 556886869 612 False 1077.000000 1077 98.369 1 613 1 chr6A.!!$F1 612
4 TraesCS2A01G171100 chr3A 722239834 722240445 611 False 1037.000000 1037 97.227 1 613 1 chr3A.!!$F2 612
5 TraesCS2A01G171100 chr3A 263165934 263166547 613 True 1033.000000 1033 97.073 1 613 1 chr3A.!!$R2 612
6 TraesCS2A01G171100 chr3A 728543423 728544036 613 True 1005.000000 1005 96.254 1 613 1 chr3A.!!$R3 612
7 TraesCS2A01G171100 chr3A 728594312 728594925 613 True 1002.000000 1002 96.098 1 614 1 chr3A.!!$R5 613
8 TraesCS2A01G171100 chr3A 728573885 728574496 611 True 998.000000 998 96.085 1 612 1 chr3A.!!$R4 611
9 TraesCS2A01G171100 chr3A 54835417 54836023 606 True 990.000000 990 96.072 4 613 1 chr3A.!!$R1 609
10 TraesCS2A01G171100 chr5A 481091115 481091713 598 False 1031.000000 1031 97.674 13 613 1 chr5A.!!$F2 600
11 TraesCS2A01G171100 chr5A 440442521 440443131 610 False 953.000000 953 94.814 1 614 1 chr5A.!!$F1 613

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
688 696 0.179171 ACGTTAGACATCTGCCGTCG 60.179 55.000 2.86 0.0 38.46 5.12 F
1833 1854 0.039527 GTTGGCACGGGACACATTTC 60.040 55.000 0.00 0.0 0.00 2.17 F
2262 2287 3.243367 TGTTTTCTGCTATGTGGTTGCAC 60.243 43.478 0.00 0.0 34.84 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 1983 4.067896 TCTCACAAGGAAAGATGCTGAAC 58.932 43.478 0.00 0.0 0.00 3.18 R
2750 2784 0.253160 TGGTGCCATAACCTCTCCCT 60.253 55.000 0.00 0.0 41.16 4.20 R
4209 4305 0.036671 CGGGCCGTTTACTTCTCCTT 60.037 55.000 19.97 0.0 0.00 3.36 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
614 622 1.235724 CGGCGAATAGGATTTTCCCC 58.764 55.000 0.00 0.00 37.19 4.81
615 623 1.617322 GGCGAATAGGATTTTCCCCC 58.383 55.000 0.00 0.00 37.19 5.40
616 624 1.133606 GGCGAATAGGATTTTCCCCCA 60.134 52.381 0.00 0.00 37.19 4.96
617 625 2.661718 GCGAATAGGATTTTCCCCCAA 58.338 47.619 0.00 0.00 37.19 4.12
618 626 2.361119 GCGAATAGGATTTTCCCCCAAC 59.639 50.000 0.00 0.00 37.19 3.77
619 627 3.626930 CGAATAGGATTTTCCCCCAACA 58.373 45.455 0.00 0.00 37.19 3.33
620 628 4.020543 CGAATAGGATTTTCCCCCAACAA 58.979 43.478 0.00 0.00 37.19 2.83
621 629 4.142249 CGAATAGGATTTTCCCCCAACAAC 60.142 45.833 0.00 0.00 37.19 3.32
622 630 2.785357 AGGATTTTCCCCCAACAACA 57.215 45.000 0.00 0.00 37.19 3.33
623 631 3.053359 AGGATTTTCCCCCAACAACAA 57.947 42.857 0.00 0.00 37.19 2.83
624 632 2.703536 AGGATTTTCCCCCAACAACAAC 59.296 45.455 0.00 0.00 37.19 3.32
625 633 2.436173 GGATTTTCCCCCAACAACAACA 59.564 45.455 0.00 0.00 0.00 3.33
626 634 3.462982 GATTTTCCCCCAACAACAACAC 58.537 45.455 0.00 0.00 0.00 3.32
627 635 1.938585 TTTCCCCCAACAACAACACA 58.061 45.000 0.00 0.00 0.00 3.72
628 636 2.166907 TTCCCCCAACAACAACACAT 57.833 45.000 0.00 0.00 0.00 3.21
629 637 1.407936 TCCCCCAACAACAACACATG 58.592 50.000 0.00 0.00 0.00 3.21
630 638 1.118838 CCCCCAACAACAACACATGT 58.881 50.000 0.00 0.00 46.82 3.21
659 667 7.861176 TTTTGAGTAACAACAAGAACAACAC 57.139 32.000 0.00 0.00 38.29 3.32
660 668 6.561737 TTGAGTAACAACAAGAACAACACA 57.438 33.333 0.00 0.00 33.18 3.72
661 669 6.751514 TGAGTAACAACAAGAACAACACAT 57.248 33.333 0.00 0.00 0.00 3.21
662 670 7.151999 TGAGTAACAACAAGAACAACACATT 57.848 32.000 0.00 0.00 0.00 2.71
663 671 8.270080 TGAGTAACAACAAGAACAACACATTA 57.730 30.769 0.00 0.00 0.00 1.90
664 672 8.178964 TGAGTAACAACAAGAACAACACATTAC 58.821 33.333 0.00 0.00 0.00 1.89
665 673 8.046294 AGTAACAACAAGAACAACACATTACA 57.954 30.769 0.00 0.00 0.00 2.41
666 674 7.966204 AGTAACAACAAGAACAACACATTACAC 59.034 33.333 0.00 0.00 0.00 2.90
667 675 6.260870 ACAACAAGAACAACACATTACACA 57.739 33.333 0.00 0.00 0.00 3.72
668 676 6.090129 ACAACAAGAACAACACATTACACAC 58.910 36.000 0.00 0.00 0.00 3.82
669 677 5.888691 ACAAGAACAACACATTACACACA 57.111 34.783 0.00 0.00 0.00 3.72
670 678 5.636837 ACAAGAACAACACATTACACACAC 58.363 37.500 0.00 0.00 0.00 3.82
671 679 4.530094 AGAACAACACATTACACACACG 57.470 40.909 0.00 0.00 0.00 4.49
672 680 3.936453 AGAACAACACATTACACACACGT 59.064 39.130 0.00 0.00 0.00 4.49
673 681 4.393680 AGAACAACACATTACACACACGTT 59.606 37.500 0.00 0.00 0.00 3.99
674 682 5.581479 AGAACAACACATTACACACACGTTA 59.419 36.000 0.00 0.00 0.00 3.18
675 683 5.398176 ACAACACATTACACACACGTTAG 57.602 39.130 0.00 0.00 0.00 2.34
676 684 5.110598 ACAACACATTACACACACGTTAGA 58.889 37.500 0.00 0.00 0.00 2.10
677 685 5.005971 ACAACACATTACACACACGTTAGAC 59.994 40.000 0.00 0.00 0.00 2.59
678 686 4.684877 ACACATTACACACACGTTAGACA 58.315 39.130 0.00 0.00 0.00 3.41
679 687 5.294356 ACACATTACACACACGTTAGACAT 58.706 37.500 0.00 0.00 0.00 3.06
680 688 5.404366 ACACATTACACACACGTTAGACATC 59.596 40.000 0.00 0.00 0.00 3.06
681 689 5.633601 CACATTACACACACGTTAGACATCT 59.366 40.000 0.00 0.00 0.00 2.90
682 690 5.633601 ACATTACACACACGTTAGACATCTG 59.366 40.000 0.00 0.00 0.00 2.90
685 693 0.992072 CACACGTTAGACATCTGCCG 59.008 55.000 0.00 0.00 0.00 5.69
688 696 0.179171 ACGTTAGACATCTGCCGTCG 60.179 55.000 2.86 0.00 38.46 5.12
692 700 2.776312 TAGACATCTGCCGTCGAATC 57.224 50.000 0.00 0.00 38.46 2.52
794 802 2.167861 GCTCGCTCCCACATCGAAC 61.168 63.158 0.00 0.00 0.00 3.95
1131 1140 0.252284 ATGAGGACTTCCCGGTCAGT 60.252 55.000 0.00 0.61 40.87 3.41
1135 1144 1.079750 GACTTCCCGGTCAGTCAGC 60.080 63.158 20.40 0.00 39.49 4.26
1173 1184 0.259356 CTCTCCCCCTTCTCCGTAGT 59.741 60.000 0.00 0.00 0.00 2.73
1176 1187 0.635009 TCCCCCTTCTCCGTAGTCAT 59.365 55.000 0.00 0.00 0.00 3.06
1235 1246 6.555463 TTAGTAGGATTCGGGATTCACTTT 57.445 37.500 0.00 0.00 0.00 2.66
1236 1247 5.024785 AGTAGGATTCGGGATTCACTTTC 57.975 43.478 0.00 0.00 0.00 2.62
1237 1248 4.717280 AGTAGGATTCGGGATTCACTTTCT 59.283 41.667 0.00 0.00 0.00 2.52
1239 1250 4.265073 AGGATTCGGGATTCACTTTCTTG 58.735 43.478 0.00 0.00 0.00 3.02
1240 1251 3.378427 GGATTCGGGATTCACTTTCTTGG 59.622 47.826 0.00 0.00 0.00 3.61
1241 1252 1.821216 TCGGGATTCACTTTCTTGGC 58.179 50.000 0.00 0.00 0.00 4.52
1242 1253 0.447801 CGGGATTCACTTTCTTGGCG 59.552 55.000 0.00 0.00 0.00 5.69
1243 1254 0.171231 GGGATTCACTTTCTTGGCGC 59.829 55.000 0.00 0.00 0.00 6.53
1395 1409 0.854218 TGCCCCCAAGAAAAGTACCA 59.146 50.000 0.00 0.00 0.00 3.25
1421 1435 7.489435 ACGACTCAACTTGTCATAACTGATATG 59.511 37.037 0.00 0.00 42.40 1.78
1422 1436 7.702348 CGACTCAACTTGTCATAACTGATATGA 59.298 37.037 3.78 3.78 46.41 2.15
1504 1524 5.703592 CACTAGTATGTAGCTAGAGGGAGTG 59.296 48.000 0.00 2.42 39.25 3.51
1833 1854 0.039527 GTTGGCACGGGACACATTTC 60.040 55.000 0.00 0.00 0.00 2.17
1962 1983 5.016051 TCCTTGCTAGCTCATAGAAACAG 57.984 43.478 17.23 0.00 32.76 3.16
2143 2164 5.168569 TCTGATAGGAAGCGTAAAACACAG 58.831 41.667 0.00 0.00 0.00 3.66
2262 2287 3.243367 TGTTTTCTGCTATGTGGTTGCAC 60.243 43.478 0.00 0.00 34.84 4.57
2297 2323 6.887002 CCCTTAATATTATCTCCCTTTCAGGC 59.113 42.308 0.00 0.00 32.73 4.85
2485 2511 6.887002 TGTTTGCACCATCCTATTTGTATGTA 59.113 34.615 0.00 0.00 0.00 2.29
2491 2517 9.448438 GCACCATCCTATTTGTATGTATATTCA 57.552 33.333 0.00 0.00 0.00 2.57
2733 2767 5.844004 CTGGTTTACAGTCTTACACTCTGT 58.156 41.667 0.00 0.00 42.42 3.41
2734 2768 6.229936 TGGTTTACAGTCTTACACTCTGTT 57.770 37.500 2.52 0.00 41.66 3.16
2735 2769 6.646267 TGGTTTACAGTCTTACACTCTGTTT 58.354 36.000 2.52 0.00 41.66 2.83
2736 2770 6.537301 TGGTTTACAGTCTTACACTCTGTTTG 59.463 38.462 2.52 0.00 41.66 2.93
2737 2771 6.759827 GGTTTACAGTCTTACACTCTGTTTGA 59.240 38.462 2.52 0.00 41.66 2.69
2738 2772 7.254353 GGTTTACAGTCTTACACTCTGTTTGAC 60.254 40.741 2.52 0.00 41.66 3.18
2739 2773 5.339008 ACAGTCTTACACTCTGTTTGACA 57.661 39.130 0.00 0.00 39.00 3.58
2740 2774 5.918608 ACAGTCTTACACTCTGTTTGACAT 58.081 37.500 0.00 0.00 39.00 3.06
2741 2775 6.349300 ACAGTCTTACACTCTGTTTGACATT 58.651 36.000 0.00 0.00 39.00 2.71
2742 2776 7.497595 ACAGTCTTACACTCTGTTTGACATTA 58.502 34.615 0.00 0.00 39.00 1.90
2743 2777 7.438459 ACAGTCTTACACTCTGTTTGACATTAC 59.562 37.037 0.00 0.00 39.00 1.89
2744 2778 6.641314 AGTCTTACACTCTGTTTGACATTACG 59.359 38.462 0.00 0.00 35.42 3.18
2745 2779 5.924254 TCTTACACTCTGTTTGACATTACGG 59.076 40.000 0.00 0.00 0.00 4.02
2746 2780 4.330944 ACACTCTGTTTGACATTACGGA 57.669 40.909 0.00 0.00 0.00 4.69
2747 2781 4.699637 ACACTCTGTTTGACATTACGGAA 58.300 39.130 0.00 0.00 0.00 4.30
2748 2782 5.120399 ACACTCTGTTTGACATTACGGAAA 58.880 37.500 0.00 0.00 0.00 3.13
2749 2783 5.763204 ACACTCTGTTTGACATTACGGAAAT 59.237 36.000 0.00 0.00 0.00 2.17
2750 2784 6.932400 ACACTCTGTTTGACATTACGGAAATA 59.068 34.615 0.00 0.00 0.00 1.40
2751 2785 7.117812 ACACTCTGTTTGACATTACGGAAATAG 59.882 37.037 0.00 0.00 0.00 1.73
2752 2786 6.594159 ACTCTGTTTGACATTACGGAAATAGG 59.406 38.462 0.00 0.00 0.00 2.57
2753 2787 5.878116 TCTGTTTGACATTACGGAAATAGGG 59.122 40.000 0.00 0.00 0.00 3.53
2754 2788 5.806818 TGTTTGACATTACGGAAATAGGGA 58.193 37.500 0.00 0.00 0.00 4.20
2755 2789 5.878116 TGTTTGACATTACGGAAATAGGGAG 59.122 40.000 0.00 0.00 0.00 4.30
2756 2790 5.943349 TTGACATTACGGAAATAGGGAGA 57.057 39.130 0.00 0.00 0.00 3.71
2757 2791 5.531122 TGACATTACGGAAATAGGGAGAG 57.469 43.478 0.00 0.00 0.00 3.20
2758 2792 4.344102 TGACATTACGGAAATAGGGAGAGG 59.656 45.833 0.00 0.00 0.00 3.69
2759 2793 4.296056 ACATTACGGAAATAGGGAGAGGT 58.704 43.478 0.00 0.00 0.00 3.85
2760 2794 4.720273 ACATTACGGAAATAGGGAGAGGTT 59.280 41.667 0.00 0.00 0.00 3.50
2761 2795 5.901276 ACATTACGGAAATAGGGAGAGGTTA 59.099 40.000 0.00 0.00 0.00 2.85
2762 2796 6.557633 ACATTACGGAAATAGGGAGAGGTTAT 59.442 38.462 0.00 0.00 0.00 1.89
2763 2797 4.957684 ACGGAAATAGGGAGAGGTTATG 57.042 45.455 0.00 0.00 0.00 1.90
2764 2798 3.646637 ACGGAAATAGGGAGAGGTTATGG 59.353 47.826 0.00 0.00 0.00 2.74
2924 3005 3.507233 CCATGGAACTTTATGCACTGTGT 59.493 43.478 5.56 0.00 0.00 3.72
2953 3034 7.162761 TCTTCGATGTAGAAAAATGGGTGTTA 58.837 34.615 0.00 0.00 0.00 2.41
3205 3287 3.879892 GCTATGCTACCTCCTTTTCCTTG 59.120 47.826 0.00 0.00 0.00 3.61
3214 3296 4.141158 ACCTCCTTTTCCTTGTGAATCAGT 60.141 41.667 0.00 0.00 31.67 3.41
3242 3324 4.844998 TGCATTGTAAAGCTTGCTAACA 57.155 36.364 0.00 0.00 36.10 2.41
3293 3375 4.244066 AGACTGCTATGATTGATGATCGC 58.756 43.478 0.00 0.00 37.60 4.58
3298 3380 4.081807 TGCTATGATTGATGATCGCTAGCT 60.082 41.667 13.93 0.00 42.86 3.32
3326 3408 7.569240 TGAAAAGGTTAACCCATTCAACATTT 58.431 30.769 27.74 15.11 37.83 2.32
3404 3486 7.287466 TGGAAGGTAGTGCGTAATTAGGTAATA 59.713 37.037 7.00 3.56 0.00 0.98
3405 3487 8.309656 GGAAGGTAGTGCGTAATTAGGTAATAT 58.690 37.037 6.68 0.00 0.00 1.28
3406 3488 9.351570 GAAGGTAGTGCGTAATTAGGTAATATC 57.648 37.037 6.68 6.36 0.00 1.63
3447 3529 3.563808 CGTTCAGGAGTTCATTTTGGTCA 59.436 43.478 0.00 0.00 0.00 4.02
3536 3620 0.179163 GTTTCTATTGCGGCTGTGCC 60.179 55.000 0.00 0.00 46.75 5.01
3693 3780 2.556189 TCGTTATGTTTGGCATGTGCTT 59.444 40.909 4.84 0.00 41.70 3.91
3743 3831 4.421058 AGCGTGTTTTGTTCTTTTTCTCC 58.579 39.130 0.00 0.00 0.00 3.71
3745 3833 4.676986 GCGTGTTTTGTTCTTTTTCTCCCT 60.677 41.667 0.00 0.00 0.00 4.20
3751 3839 9.952030 TGTTTTGTTCTTTTTCTCCCTAAAAAT 57.048 25.926 0.00 0.00 37.61 1.82
3776 3865 1.619654 TTCCTTGTGGTGCTTGGATG 58.380 50.000 0.00 0.00 34.23 3.51
3828 3917 4.577283 AGCTCCTCATACTCGTAGTTCTTC 59.423 45.833 0.00 0.00 0.00 2.87
3846 3935 1.586564 CCTCGATCGAACGGCTGTC 60.587 63.158 19.92 0.00 0.00 3.51
3854 3943 0.108804 CGAACGGCTGTCTGTGGTAT 60.109 55.000 0.00 0.00 0.00 2.73
3855 3944 1.359848 GAACGGCTGTCTGTGGTATG 58.640 55.000 0.00 0.00 0.00 2.39
3856 3945 0.685097 AACGGCTGTCTGTGGTATGT 59.315 50.000 0.00 0.00 0.00 2.29
3857 3946 1.552578 ACGGCTGTCTGTGGTATGTA 58.447 50.000 0.00 0.00 0.00 2.29
3858 3947 1.897133 ACGGCTGTCTGTGGTATGTAA 59.103 47.619 0.00 0.00 0.00 2.41
3860 3949 2.671396 CGGCTGTCTGTGGTATGTAAAC 59.329 50.000 0.00 0.00 0.00 2.01
3861 3950 3.670625 GGCTGTCTGTGGTATGTAAACA 58.329 45.455 0.00 0.00 0.00 2.83
3862 3951 4.261801 GGCTGTCTGTGGTATGTAAACAT 58.738 43.478 0.63 0.63 40.22 2.71
3863 3952 4.700213 GGCTGTCTGTGGTATGTAAACATT 59.300 41.667 0.12 0.00 37.76 2.71
3864 3953 5.391950 GGCTGTCTGTGGTATGTAAACATTG 60.392 44.000 0.12 0.00 37.76 2.82
3865 3954 5.411361 GCTGTCTGTGGTATGTAAACATTGA 59.589 40.000 0.12 0.00 37.76 2.57
3866 3955 6.094048 GCTGTCTGTGGTATGTAAACATTGAT 59.906 38.462 0.12 0.00 37.76 2.57
3915 4011 7.397761 ACCGATCCCCTCTAATCTCTAATTTAG 59.602 40.741 0.00 0.00 0.00 1.85
3916 4012 7.147811 CCGATCCCCTCTAATCTCTAATTTAGG 60.148 44.444 3.66 0.00 0.00 2.69
3917 4013 6.936968 TCCCCTCTAATCTCTAATTTAGGC 57.063 41.667 3.66 0.00 0.00 3.93
3918 4014 5.785940 TCCCCTCTAATCTCTAATTTAGGCC 59.214 44.000 0.00 0.00 0.00 5.19
3919 4015 5.788014 CCCCTCTAATCTCTAATTTAGGCCT 59.212 44.000 11.78 11.78 0.00 5.19
3920 4016 6.070481 CCCCTCTAATCTCTAATTTAGGCCTC 60.070 46.154 9.68 0.00 0.00 4.70
3921 4017 6.070481 CCCTCTAATCTCTAATTTAGGCCTCC 60.070 46.154 9.68 0.00 0.00 4.30
3922 4018 6.728632 CCTCTAATCTCTAATTTAGGCCTCCT 59.271 42.308 9.68 0.00 37.71 3.69
3923 4019 7.236640 CCTCTAATCTCTAATTTAGGCCTCCTT 59.763 40.741 9.68 3.79 34.61 3.36
3924 4020 8.568617 TCTAATCTCTAATTTAGGCCTCCTTT 57.431 34.615 9.68 3.58 34.61 3.11
3925 4021 8.432805 TCTAATCTCTAATTTAGGCCTCCTTTG 58.567 37.037 9.68 2.63 34.61 2.77
3926 4022 5.373812 TCTCTAATTTAGGCCTCCTTTGG 57.626 43.478 9.68 3.31 34.61 3.28
3927 4023 4.788617 TCTCTAATTTAGGCCTCCTTTGGT 59.211 41.667 9.68 0.00 34.61 3.67
3928 4024 5.253096 TCTCTAATTTAGGCCTCCTTTGGTT 59.747 40.000 9.68 0.00 34.61 3.67
3929 4025 5.506708 TCTAATTTAGGCCTCCTTTGGTTC 58.493 41.667 9.68 0.00 34.61 3.62
3930 4026 3.825908 ATTTAGGCCTCCTTTGGTTCA 57.174 42.857 9.68 0.00 34.61 3.18
3931 4027 3.825908 TTTAGGCCTCCTTTGGTTCAT 57.174 42.857 9.68 0.00 34.61 2.57
3932 4028 4.938575 TTTAGGCCTCCTTTGGTTCATA 57.061 40.909 9.68 0.00 34.61 2.15
3933 4029 4.503714 TTAGGCCTCCTTTGGTTCATAG 57.496 45.455 9.68 0.00 34.61 2.23
3934 4030 1.566231 AGGCCTCCTTTGGTTCATAGG 59.434 52.381 0.00 0.00 34.61 2.57
3935 4031 1.564348 GGCCTCCTTTGGTTCATAGGA 59.436 52.381 0.00 6.86 38.81 2.94
3936 4032 2.175715 GGCCTCCTTTGGTTCATAGGAT 59.824 50.000 0.00 0.00 39.94 3.24
3937 4033 3.394606 GGCCTCCTTTGGTTCATAGGATA 59.605 47.826 0.00 0.00 39.94 2.59
3938 4034 4.505742 GGCCTCCTTTGGTTCATAGGATAG 60.506 50.000 0.00 4.66 39.94 2.08
3939 4035 4.505742 GCCTCCTTTGGTTCATAGGATAGG 60.506 50.000 7.38 7.57 39.94 2.57
3940 4036 4.907875 CCTCCTTTGGTTCATAGGATAGGA 59.092 45.833 7.38 0.00 39.94 2.94
3941 4037 5.369699 CCTCCTTTGGTTCATAGGATAGGAA 59.630 44.000 7.38 0.00 39.94 3.36
3942 4038 6.126478 CCTCCTTTGGTTCATAGGATAGGAAA 60.126 42.308 7.38 0.00 43.51 3.13
3943 4039 7.278724 TCCTTTGGTTCATAGGATAGGAAAA 57.721 36.000 3.54 0.00 43.51 2.29
3944 4040 7.882755 TCCTTTGGTTCATAGGATAGGAAAAT 58.117 34.615 3.54 0.00 43.51 1.82
3945 4041 7.998964 TCCTTTGGTTCATAGGATAGGAAAATC 59.001 37.037 3.54 0.00 43.51 2.17
3946 4042 7.041098 CCTTTGGTTCATAGGATAGGAAAATCG 60.041 40.741 0.00 0.00 43.51 3.34
3947 4043 6.494666 TGGTTCATAGGATAGGAAAATCGT 57.505 37.500 0.00 0.00 43.51 3.73
3948 4044 7.606135 TGGTTCATAGGATAGGAAAATCGTA 57.394 36.000 0.00 0.00 43.51 3.43
3949 4045 7.667557 TGGTTCATAGGATAGGAAAATCGTAG 58.332 38.462 0.00 0.00 43.51 3.51
3950 4046 7.097834 GGTTCATAGGATAGGAAAATCGTAGG 58.902 42.308 0.00 0.00 43.51 3.18
3951 4047 7.039223 GGTTCATAGGATAGGAAAATCGTAGGA 60.039 40.741 0.00 0.00 43.51 2.94
3952 4048 8.365647 GTTCATAGGATAGGAAAATCGTAGGAA 58.634 37.037 8.64 8.64 43.51 3.36
3953 4049 8.666129 TCATAGGATAGGAAAATCGTAGGAAT 57.334 34.615 0.00 0.00 35.39 3.01
3954 4050 9.763837 TCATAGGATAGGAAAATCGTAGGAATA 57.236 33.333 0.00 0.00 35.39 1.75
3956 4052 9.992442 ATAGGATAGGAAAATCGTAGGAATAGA 57.008 33.333 0.00 0.00 31.73 1.98
3957 4053 8.356000 AGGATAGGAAAATCGTAGGAATAGAG 57.644 38.462 0.00 0.00 0.00 2.43
3958 4054 8.171400 AGGATAGGAAAATCGTAGGAATAGAGA 58.829 37.037 0.00 0.00 0.00 3.10
3959 4055 8.804204 GGATAGGAAAATCGTAGGAATAGAGAA 58.196 37.037 0.00 0.00 0.00 2.87
3960 4056 9.849166 GATAGGAAAATCGTAGGAATAGAGAAG 57.151 37.037 0.00 0.00 0.00 2.85
3961 4057 7.663043 AGGAAAATCGTAGGAATAGAGAAGT 57.337 36.000 0.00 0.00 0.00 3.01
3962 4058 7.718525 AGGAAAATCGTAGGAATAGAGAAGTC 58.281 38.462 0.00 0.00 0.00 3.01
3963 4059 7.342284 AGGAAAATCGTAGGAATAGAGAAGTCA 59.658 37.037 0.00 0.00 0.00 3.41
3964 4060 8.145122 GGAAAATCGTAGGAATAGAGAAGTCAT 58.855 37.037 0.00 0.00 0.00 3.06
3967 4063 7.931578 ATCGTAGGAATAGAGAAGTCATAGG 57.068 40.000 0.00 0.00 0.00 2.57
3968 4064 7.075851 TCGTAGGAATAGAGAAGTCATAGGA 57.924 40.000 0.00 0.00 0.00 2.94
3969 4065 7.515586 TCGTAGGAATAGAGAAGTCATAGGAA 58.484 38.462 0.00 0.00 0.00 3.36
3970 4066 7.997223 TCGTAGGAATAGAGAAGTCATAGGAAA 59.003 37.037 0.00 0.00 0.00 3.13
3971 4067 8.798402 CGTAGGAATAGAGAAGTCATAGGAAAT 58.202 37.037 0.00 0.00 0.00 2.17
3972 4068 9.921637 GTAGGAATAGAGAAGTCATAGGAAATG 57.078 37.037 0.00 0.00 0.00 2.32
3973 4069 8.789767 AGGAATAGAGAAGTCATAGGAAATGA 57.210 34.615 0.00 0.00 0.00 2.57
3974 4070 8.869109 AGGAATAGAGAAGTCATAGGAAATGAG 58.131 37.037 0.00 0.00 0.00 2.90
3975 4071 8.865090 GGAATAGAGAAGTCATAGGAAATGAGA 58.135 37.037 0.00 0.00 0.00 3.27
3978 4074 7.911130 AGAGAAGTCATAGGAAATGAGATGA 57.089 36.000 0.00 0.00 0.00 2.92
3979 4075 8.495160 AGAGAAGTCATAGGAAATGAGATGAT 57.505 34.615 0.00 0.00 31.35 2.45
3980 4076 9.599056 AGAGAAGTCATAGGAAATGAGATGATA 57.401 33.333 0.00 0.00 31.35 2.15
3983 4079 9.941325 GAAGTCATAGGAAATGAGATGATATGT 57.059 33.333 0.00 0.00 31.35 2.29
4019 4115 8.893563 CTATGAGTAGGAATAGGAAAGGAGAT 57.106 38.462 0.00 0.00 0.00 2.75
4020 4116 6.985653 TGAGTAGGAATAGGAAAGGAGATG 57.014 41.667 0.00 0.00 0.00 2.90
4021 4117 5.305644 TGAGTAGGAATAGGAAAGGAGATGC 59.694 44.000 0.00 0.00 0.00 3.91
4022 4118 4.595350 AGTAGGAATAGGAAAGGAGATGCC 59.405 45.833 0.00 0.00 0.00 4.40
4023 4119 2.713708 AGGAATAGGAAAGGAGATGCCC 59.286 50.000 0.00 0.00 37.37 5.36
4024 4120 2.713708 GGAATAGGAAAGGAGATGCCCT 59.286 50.000 0.00 0.00 38.42 5.19
4032 4128 3.744940 AAGGAGATGCCCTTTGATTCA 57.255 42.857 0.00 0.00 43.68 2.57
4033 4129 3.010200 AGGAGATGCCCTTTGATTCAC 57.990 47.619 0.00 0.00 37.37 3.18
4034 4130 2.309755 AGGAGATGCCCTTTGATTCACA 59.690 45.455 0.00 0.00 37.37 3.58
4035 4131 3.053095 AGGAGATGCCCTTTGATTCACAT 60.053 43.478 0.00 0.00 37.37 3.21
4036 4132 3.317430 GGAGATGCCCTTTGATTCACATC 59.683 47.826 6.23 6.23 35.31 3.06
4037 4133 3.949754 GAGATGCCCTTTGATTCACATCA 59.050 43.478 13.54 0.00 37.67 3.07
4038 4134 4.543689 AGATGCCCTTTGATTCACATCAT 58.456 39.130 13.54 2.83 39.28 2.45
4039 4135 5.698104 AGATGCCCTTTGATTCACATCATA 58.302 37.500 13.54 0.00 39.28 2.15
4040 4136 5.768662 AGATGCCCTTTGATTCACATCATAG 59.231 40.000 13.54 1.71 39.28 2.23
4105 4201 9.447279 TCCTATGAAATGTAAAGGATAGGAAGA 57.553 33.333 0.00 0.00 38.86 2.87
4130 4226 5.832539 TCCTCAGGAATAGGATTCCATTC 57.167 43.478 18.17 11.30 38.24 2.67
4140 4236 4.946160 AGGATTCCATTCCTACAAACCA 57.054 40.909 5.29 0.00 44.50 3.67
4141 4237 5.269554 AGGATTCCATTCCTACAAACCAA 57.730 39.130 5.29 0.00 44.50 3.67
4142 4238 5.650283 AGGATTCCATTCCTACAAACCAAA 58.350 37.500 5.29 0.00 44.50 3.28
4143 4239 5.716703 AGGATTCCATTCCTACAAACCAAAG 59.283 40.000 5.29 0.00 44.50 2.77
4144 4240 5.105351 GGATTCCATTCCTACAAACCAAAGG 60.105 44.000 0.00 0.00 32.68 3.11
4145 4241 3.773560 TCCATTCCTACAAACCAAAGGG 58.226 45.455 0.00 0.00 41.29 3.95
4202 4298 9.838339 TCCTATGAAATTCTTACAAGATTCCTC 57.162 33.333 0.00 0.00 34.49 3.71
4203 4299 9.844257 CCTATGAAATTCTTACAAGATTCCTCT 57.156 33.333 0.00 0.00 34.49 3.69
4215 4311 7.079451 ACAAGATTCCTCTAAACAAAGGAGA 57.921 36.000 0.00 0.00 42.49 3.71
4219 4315 8.437274 AGATTCCTCTAAACAAAGGAGAAGTA 57.563 34.615 0.00 0.00 42.49 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
569 577 2.853914 GGCAAACTGTCGAGCGAC 59.146 61.111 15.49 15.49 44.77 5.19
634 642 7.921214 TGTGTTGTTCTTGTTGTTACTCAAAAA 59.079 29.630 0.00 0.00 37.81 1.94
635 643 7.426410 TGTGTTGTTCTTGTTGTTACTCAAAA 58.574 30.769 0.00 0.00 37.81 2.44
636 644 6.971602 TGTGTTGTTCTTGTTGTTACTCAAA 58.028 32.000 0.00 0.00 37.81 2.69
637 645 6.561737 TGTGTTGTTCTTGTTGTTACTCAA 57.438 33.333 0.00 0.00 0.00 3.02
638 646 6.751514 ATGTGTTGTTCTTGTTGTTACTCA 57.248 33.333 0.00 0.00 0.00 3.41
639 647 8.178964 TGTAATGTGTTGTTCTTGTTGTTACTC 58.821 33.333 0.00 0.00 0.00 2.59
640 648 7.966204 GTGTAATGTGTTGTTCTTGTTGTTACT 59.034 33.333 0.00 0.00 0.00 2.24
641 649 7.751348 TGTGTAATGTGTTGTTCTTGTTGTTAC 59.249 33.333 0.00 0.00 0.00 2.50
642 650 7.751348 GTGTGTAATGTGTTGTTCTTGTTGTTA 59.249 33.333 0.00 0.00 0.00 2.41
643 651 6.584563 GTGTGTAATGTGTTGTTCTTGTTGTT 59.415 34.615 0.00 0.00 0.00 2.83
644 652 6.090129 GTGTGTAATGTGTTGTTCTTGTTGT 58.910 36.000 0.00 0.00 0.00 3.32
645 653 6.033407 GTGTGTGTAATGTGTTGTTCTTGTTG 59.967 38.462 0.00 0.00 0.00 3.33
646 654 6.090129 GTGTGTGTAATGTGTTGTTCTTGTT 58.910 36.000 0.00 0.00 0.00 2.83
647 655 5.636837 GTGTGTGTAATGTGTTGTTCTTGT 58.363 37.500 0.00 0.00 0.00 3.16
648 656 4.728131 CGTGTGTGTAATGTGTTGTTCTTG 59.272 41.667 0.00 0.00 0.00 3.02
649 657 4.393680 ACGTGTGTGTAATGTGTTGTTCTT 59.606 37.500 0.00 0.00 0.00 2.52
650 658 3.936453 ACGTGTGTGTAATGTGTTGTTCT 59.064 39.130 0.00 0.00 0.00 3.01
651 659 4.267357 ACGTGTGTGTAATGTGTTGTTC 57.733 40.909 0.00 0.00 0.00 3.18
652 660 4.688511 AACGTGTGTGTAATGTGTTGTT 57.311 36.364 0.00 0.00 0.00 2.83
653 661 5.005971 GTCTAACGTGTGTGTAATGTGTTGT 59.994 40.000 0.00 0.00 0.00 3.32
654 662 5.005875 TGTCTAACGTGTGTGTAATGTGTTG 59.994 40.000 0.00 0.00 0.00 3.33
655 663 5.110598 TGTCTAACGTGTGTGTAATGTGTT 58.889 37.500 0.00 0.00 0.00 3.32
656 664 4.684877 TGTCTAACGTGTGTGTAATGTGT 58.315 39.130 0.00 0.00 0.00 3.72
657 665 5.633601 AGATGTCTAACGTGTGTGTAATGTG 59.366 40.000 0.00 0.00 0.00 3.21
658 666 5.633601 CAGATGTCTAACGTGTGTGTAATGT 59.366 40.000 0.00 0.00 0.00 2.71
659 667 5.444613 GCAGATGTCTAACGTGTGTGTAATG 60.445 44.000 0.00 0.00 31.71 1.90
660 668 4.625742 GCAGATGTCTAACGTGTGTGTAAT 59.374 41.667 0.00 0.00 31.71 1.89
661 669 3.985279 GCAGATGTCTAACGTGTGTGTAA 59.015 43.478 0.00 0.00 31.71 2.41
662 670 3.571571 GCAGATGTCTAACGTGTGTGTA 58.428 45.455 0.00 0.00 31.71 2.90
663 671 2.404215 GCAGATGTCTAACGTGTGTGT 58.596 47.619 0.00 0.00 31.71 3.72
664 672 1.726791 GGCAGATGTCTAACGTGTGTG 59.273 52.381 0.00 0.00 31.71 3.82
665 673 1.668919 CGGCAGATGTCTAACGTGTGT 60.669 52.381 0.00 0.00 31.71 3.72
666 674 0.992072 CGGCAGATGTCTAACGTGTG 59.008 55.000 0.00 0.00 32.18 3.82
667 675 0.601558 ACGGCAGATGTCTAACGTGT 59.398 50.000 9.42 0.00 36.57 4.49
668 676 1.269166 GACGGCAGATGTCTAACGTG 58.731 55.000 13.47 0.00 37.53 4.49
669 677 0.179171 CGACGGCAGATGTCTAACGT 60.179 55.000 9.83 9.83 39.21 3.99
670 678 0.098200 TCGACGGCAGATGTCTAACG 59.902 55.000 0.00 4.62 34.17 3.18
671 679 2.273370 TTCGACGGCAGATGTCTAAC 57.727 50.000 0.00 0.00 34.17 2.34
672 680 2.223735 GGATTCGACGGCAGATGTCTAA 60.224 50.000 0.00 0.00 34.17 2.10
673 681 1.337071 GGATTCGACGGCAGATGTCTA 59.663 52.381 0.00 0.00 34.17 2.59
674 682 0.103208 GGATTCGACGGCAGATGTCT 59.897 55.000 0.00 0.00 34.17 3.41
675 683 0.179111 TGGATTCGACGGCAGATGTC 60.179 55.000 0.00 0.00 0.00 3.06
676 684 0.249120 TTGGATTCGACGGCAGATGT 59.751 50.000 0.00 0.00 0.00 3.06
677 685 0.933097 CTTGGATTCGACGGCAGATG 59.067 55.000 0.00 0.00 0.00 2.90
678 686 0.811616 GCTTGGATTCGACGGCAGAT 60.812 55.000 0.00 0.00 0.00 2.90
679 687 1.447838 GCTTGGATTCGACGGCAGA 60.448 57.895 0.00 0.00 0.00 4.26
680 688 2.464459 GGCTTGGATTCGACGGCAG 61.464 63.158 0.00 0.00 0.00 4.85
681 689 2.435938 GGCTTGGATTCGACGGCA 60.436 61.111 0.00 0.00 0.00 5.69
682 690 3.202706 GGGCTTGGATTCGACGGC 61.203 66.667 0.00 0.00 0.00 5.68
685 693 1.134401 TGAGATGGGCTTGGATTCGAC 60.134 52.381 0.00 0.00 0.00 4.20
688 696 3.219176 TGATGAGATGGGCTTGGATTC 57.781 47.619 0.00 0.00 0.00 2.52
692 700 2.295885 GTCTTGATGAGATGGGCTTGG 58.704 52.381 0.00 0.00 36.61 3.61
989 998 4.779733 ACGACATCCCGGGGAGCT 62.780 66.667 23.50 8.51 34.05 4.09
1113 1122 0.898789 GACTGACCGGGAAGTCCTCA 60.899 60.000 22.05 7.82 37.45 3.86
1155 1164 0.258194 GACTACGGAGAAGGGGGAGA 59.742 60.000 0.00 0.00 0.00 3.71
1173 1184 2.478989 GACCGAGTCGAGGTGATGA 58.521 57.895 15.64 0.00 43.01 2.92
1202 1213 4.511826 CCGAATCCTACTAATTCAGCCAAC 59.488 45.833 0.00 0.00 33.60 3.77
1395 1409 5.196341 TCAGTTATGACAAGTTGAGTCGT 57.804 39.130 10.54 1.63 38.83 4.34
1421 1435 5.759963 CAGCAAGAGGAAAATGAGCATATC 58.240 41.667 0.00 0.00 0.00 1.63
1422 1436 4.037684 GCAGCAAGAGGAAAATGAGCATAT 59.962 41.667 0.00 0.00 0.00 1.78
1423 1437 3.379372 GCAGCAAGAGGAAAATGAGCATA 59.621 43.478 0.00 0.00 0.00 3.14
1424 1438 2.165845 GCAGCAAGAGGAAAATGAGCAT 59.834 45.455 0.00 0.00 0.00 3.79
1425 1439 1.542915 GCAGCAAGAGGAAAATGAGCA 59.457 47.619 0.00 0.00 0.00 4.26
1459 1474 4.152402 GTGTAGAATCGAGAAGCAAAGCAA 59.848 41.667 0.00 0.00 0.00 3.91
1460 1475 3.679980 GTGTAGAATCGAGAAGCAAAGCA 59.320 43.478 0.00 0.00 0.00 3.91
1461 1476 3.929610 AGTGTAGAATCGAGAAGCAAAGC 59.070 43.478 0.00 0.00 0.00 3.51
1462 1477 6.326375 ACTAGTGTAGAATCGAGAAGCAAAG 58.674 40.000 0.00 0.00 0.00 2.77
1463 1478 6.268825 ACTAGTGTAGAATCGAGAAGCAAA 57.731 37.500 0.00 0.00 0.00 3.68
1504 1524 4.590850 ACTCCAAAGAAGCAAAATCCAC 57.409 40.909 0.00 0.00 0.00 4.02
1597 1618 4.737855 AACATAAGCAGTCCTGATACGT 57.262 40.909 0.00 0.00 0.00 3.57
1962 1983 4.067896 TCTCACAAGGAAAGATGCTGAAC 58.932 43.478 0.00 0.00 0.00 3.18
2536 2562 4.223953 TCCATGTAAGGGGTCAGAGTATC 58.776 47.826 0.00 0.00 39.14 2.24
2718 2752 6.851222 AATGTCAAACAGAGTGTAAGACTG 57.149 37.500 11.01 0.00 36.14 3.51
2726 2760 5.666969 TTTCCGTAATGTCAAACAGAGTG 57.333 39.130 0.00 0.00 0.00 3.51
2727 2761 6.594159 CCTATTTCCGTAATGTCAAACAGAGT 59.406 38.462 0.00 0.00 0.00 3.24
2728 2762 6.037172 CCCTATTTCCGTAATGTCAAACAGAG 59.963 42.308 0.00 0.00 0.00 3.35
2729 2763 5.878116 CCCTATTTCCGTAATGTCAAACAGA 59.122 40.000 0.00 0.00 0.00 3.41
2730 2764 5.878116 TCCCTATTTCCGTAATGTCAAACAG 59.122 40.000 0.00 0.00 0.00 3.16
2731 2765 5.806818 TCCCTATTTCCGTAATGTCAAACA 58.193 37.500 0.00 0.00 0.00 2.83
2732 2766 6.110707 TCTCCCTATTTCCGTAATGTCAAAC 58.889 40.000 0.00 0.00 0.00 2.93
2733 2767 6.302535 TCTCCCTATTTCCGTAATGTCAAA 57.697 37.500 0.00 0.00 0.00 2.69
2734 2768 5.163343 CCTCTCCCTATTTCCGTAATGTCAA 60.163 44.000 0.00 0.00 0.00 3.18
2735 2769 4.344102 CCTCTCCCTATTTCCGTAATGTCA 59.656 45.833 0.00 0.00 0.00 3.58
2736 2770 4.344390 ACCTCTCCCTATTTCCGTAATGTC 59.656 45.833 0.00 0.00 0.00 3.06
2737 2771 4.296056 ACCTCTCCCTATTTCCGTAATGT 58.704 43.478 0.00 0.00 0.00 2.71
2738 2772 4.957684 ACCTCTCCCTATTTCCGTAATG 57.042 45.455 0.00 0.00 0.00 1.90
2739 2773 6.013639 CCATAACCTCTCCCTATTTCCGTAAT 60.014 42.308 0.00 0.00 0.00 1.89
2740 2774 5.306160 CCATAACCTCTCCCTATTTCCGTAA 59.694 44.000 0.00 0.00 0.00 3.18
2741 2775 4.836736 CCATAACCTCTCCCTATTTCCGTA 59.163 45.833 0.00 0.00 0.00 4.02
2742 2776 3.646637 CCATAACCTCTCCCTATTTCCGT 59.353 47.826 0.00 0.00 0.00 4.69
2743 2777 3.557264 GCCATAACCTCTCCCTATTTCCG 60.557 52.174 0.00 0.00 0.00 4.30
2744 2778 3.394606 TGCCATAACCTCTCCCTATTTCC 59.605 47.826 0.00 0.00 0.00 3.13
2745 2779 4.390264 GTGCCATAACCTCTCCCTATTTC 58.610 47.826 0.00 0.00 0.00 2.17
2746 2780 3.138468 GGTGCCATAACCTCTCCCTATTT 59.862 47.826 0.00 0.00 37.24 1.40
2747 2781 2.711547 GGTGCCATAACCTCTCCCTATT 59.288 50.000 0.00 0.00 37.24 1.73
2748 2782 2.339769 GGTGCCATAACCTCTCCCTAT 58.660 52.381 0.00 0.00 37.24 2.57
2749 2783 1.009060 TGGTGCCATAACCTCTCCCTA 59.991 52.381 0.00 0.00 41.16 3.53
2750 2784 0.253160 TGGTGCCATAACCTCTCCCT 60.253 55.000 0.00 0.00 41.16 4.20
2751 2785 0.846693 ATGGTGCCATAACCTCTCCC 59.153 55.000 1.20 0.00 41.16 4.30
2752 2786 1.212935 ACATGGTGCCATAACCTCTCC 59.787 52.381 3.07 0.00 41.16 3.71
2753 2787 2.684881 CAACATGGTGCCATAACCTCTC 59.315 50.000 0.00 0.00 41.16 3.20
2754 2788 2.308570 TCAACATGGTGCCATAACCTCT 59.691 45.455 5.66 0.00 41.16 3.69
2755 2789 2.423538 GTCAACATGGTGCCATAACCTC 59.576 50.000 5.66 0.00 41.16 3.85
2756 2790 2.041620 AGTCAACATGGTGCCATAACCT 59.958 45.455 5.66 0.00 41.16 3.50
2757 2791 2.164219 CAGTCAACATGGTGCCATAACC 59.836 50.000 5.66 0.00 40.94 2.85
2758 2792 3.081061 TCAGTCAACATGGTGCCATAAC 58.919 45.455 5.66 0.00 34.91 1.89
2759 2793 3.431673 TCAGTCAACATGGTGCCATAA 57.568 42.857 5.66 0.00 34.91 1.90
2760 2794 3.650281 ATCAGTCAACATGGTGCCATA 57.350 42.857 5.66 0.00 34.91 2.74
2761 2795 2.519771 ATCAGTCAACATGGTGCCAT 57.480 45.000 5.66 0.00 37.08 4.40
2762 2796 3.650281 ATATCAGTCAACATGGTGCCA 57.350 42.857 5.66 0.00 0.00 4.92
2763 2797 4.440525 CCAAATATCAGTCAACATGGTGCC 60.441 45.833 5.66 0.00 0.00 5.01
2764 2798 4.158394 ACCAAATATCAGTCAACATGGTGC 59.842 41.667 5.66 1.03 38.44 5.01
2904 2985 5.789643 AAACACAGTGCATAAAGTTCCAT 57.210 34.783 0.00 0.00 0.00 3.41
2953 3034 6.521151 TTTTGCCAAAACCATGAACATTTT 57.479 29.167 0.00 0.00 0.00 1.82
3135 3217 0.896226 ACTTACGTGCTTCCTCCTCC 59.104 55.000 0.00 0.00 0.00 4.30
3188 3270 3.418684 TCACAAGGAAAAGGAGGTAGC 57.581 47.619 0.00 0.00 0.00 3.58
3252 3334 7.392673 AGCAGTCTTCATCTGTTACATGAAAAT 59.607 33.333 0.00 0.00 39.28 1.82
3293 3375 3.440522 GGGTTAACCTTTTCAGCAGCTAG 59.559 47.826 23.69 0.00 35.85 3.42
3298 3380 4.219115 TGAATGGGTTAACCTTTTCAGCA 58.781 39.130 25.73 15.62 37.24 4.41
3326 3408 7.386848 CGAAGAAGAATACCAAGAAACCTAACA 59.613 37.037 0.00 0.00 0.00 2.41
3404 3486 4.248859 CGCGGGAAGAATAATCATCTGAT 58.751 43.478 0.00 0.00 36.07 2.90
3405 3487 3.069586 ACGCGGGAAGAATAATCATCTGA 59.930 43.478 12.47 0.00 0.00 3.27
3406 3488 3.393800 ACGCGGGAAGAATAATCATCTG 58.606 45.455 12.47 0.00 0.00 2.90
3447 3529 8.656806 TCGTAGGATTCCATTTCTTAATACCAT 58.343 33.333 5.29 0.00 0.00 3.55
3536 3620 4.741676 GGGCAGATAAAATCGCATTTTCTG 59.258 41.667 9.24 11.63 41.26 3.02
3693 3780 0.465705 CTGAATCCTGGCCTAAGCGA 59.534 55.000 3.32 0.00 41.24 4.93
3743 3831 7.920682 GCACCACAAGGAATATGTATTTTTAGG 59.079 37.037 0.00 0.00 38.69 2.69
3745 3833 8.588290 AGCACCACAAGGAATATGTATTTTTA 57.412 30.769 0.00 0.00 38.69 1.52
3751 3839 4.018870 TCCAAGCACCACAAGGAATATGTA 60.019 41.667 0.00 0.00 38.69 2.29
3776 3865 5.585445 GGCATATGTGATGATCATCTTCCTC 59.415 44.000 30.65 17.80 38.60 3.71
3828 3917 1.586564 GACAGCCGTTCGATCGAGG 60.587 63.158 18.54 17.61 0.00 4.63
3846 3935 6.127925 ACTGCATCAATGTTTACATACCACAG 60.128 38.462 0.00 4.19 35.10 3.66
3854 3943 7.102993 TCTTAGCTACTGCATCAATGTTTACA 58.897 34.615 0.00 0.00 42.74 2.41
3855 3944 7.539712 TCTTAGCTACTGCATCAATGTTTAC 57.460 36.000 0.00 0.00 42.74 2.01
3856 3945 6.258727 GCTCTTAGCTACTGCATCAATGTTTA 59.741 38.462 0.00 0.00 42.74 2.01
3857 3946 5.065731 GCTCTTAGCTACTGCATCAATGTTT 59.934 40.000 0.00 0.00 42.74 2.83
3858 3947 4.574013 GCTCTTAGCTACTGCATCAATGTT 59.426 41.667 0.00 0.00 42.74 2.71
3860 3949 4.124970 TGCTCTTAGCTACTGCATCAATG 58.875 43.478 9.55 0.00 42.97 2.82
3861 3950 4.412796 TGCTCTTAGCTACTGCATCAAT 57.587 40.909 9.55 0.00 42.97 2.57
3862 3951 3.893326 TGCTCTTAGCTACTGCATCAA 57.107 42.857 9.55 0.00 42.97 2.57
3863 3952 3.525537 GTTGCTCTTAGCTACTGCATCA 58.474 45.455 13.11 0.51 42.32 3.07
3915 4011 1.564348 TCCTATGAACCAAAGGAGGCC 59.436 52.381 0.00 0.00 34.46 5.19
3916 4012 3.584733 ATCCTATGAACCAAAGGAGGC 57.415 47.619 0.00 0.00 42.53 4.70
3917 4013 4.907875 TCCTATCCTATGAACCAAAGGAGG 59.092 45.833 0.00 0.00 42.53 4.30
3918 4014 6.500589 TTCCTATCCTATGAACCAAAGGAG 57.499 41.667 0.00 0.00 42.53 3.69
3919 4015 6.901615 TTTCCTATCCTATGAACCAAAGGA 57.098 37.500 0.00 0.00 43.38 3.36
3920 4016 7.041098 CGATTTTCCTATCCTATGAACCAAAGG 60.041 40.741 0.00 0.00 0.00 3.11
3921 4017 7.499232 ACGATTTTCCTATCCTATGAACCAAAG 59.501 37.037 0.00 0.00 0.00 2.77
3922 4018 7.343357 ACGATTTTCCTATCCTATGAACCAAA 58.657 34.615 0.00 0.00 0.00 3.28
3923 4019 6.895782 ACGATTTTCCTATCCTATGAACCAA 58.104 36.000 0.00 0.00 0.00 3.67
3924 4020 6.494666 ACGATTTTCCTATCCTATGAACCA 57.505 37.500 0.00 0.00 0.00 3.67
3925 4021 7.039223 TCCTACGATTTTCCTATCCTATGAACC 60.039 40.741 0.00 0.00 0.00 3.62
3926 4022 7.893658 TCCTACGATTTTCCTATCCTATGAAC 58.106 38.462 0.00 0.00 0.00 3.18
3927 4023 8.486942 TTCCTACGATTTTCCTATCCTATGAA 57.513 34.615 0.00 0.00 0.00 2.57
3928 4024 8.666129 ATTCCTACGATTTTCCTATCCTATGA 57.334 34.615 0.00 0.00 0.00 2.15
3930 4026 9.992442 TCTATTCCTACGATTTTCCTATCCTAT 57.008 33.333 0.00 0.00 0.00 2.57
3931 4027 9.463902 CTCTATTCCTACGATTTTCCTATCCTA 57.536 37.037 0.00 0.00 0.00 2.94
3932 4028 8.171400 TCTCTATTCCTACGATTTTCCTATCCT 58.829 37.037 0.00 0.00 0.00 3.24
3933 4029 8.350852 TCTCTATTCCTACGATTTTCCTATCC 57.649 38.462 0.00 0.00 0.00 2.59
3934 4030 9.849166 CTTCTCTATTCCTACGATTTTCCTATC 57.151 37.037 0.00 0.00 0.00 2.08
3935 4031 9.369672 ACTTCTCTATTCCTACGATTTTCCTAT 57.630 33.333 0.00 0.00 0.00 2.57
3936 4032 8.763984 ACTTCTCTATTCCTACGATTTTCCTA 57.236 34.615 0.00 0.00 0.00 2.94
3937 4033 7.342284 TGACTTCTCTATTCCTACGATTTTCCT 59.658 37.037 0.00 0.00 0.00 3.36
3938 4034 7.490000 TGACTTCTCTATTCCTACGATTTTCC 58.510 38.462 0.00 0.00 0.00 3.13
3941 4037 8.798402 CCTATGACTTCTCTATTCCTACGATTT 58.202 37.037 0.00 0.00 0.00 2.17
3942 4038 8.164733 TCCTATGACTTCTCTATTCCTACGATT 58.835 37.037 0.00 0.00 0.00 3.34
3943 4039 7.691213 TCCTATGACTTCTCTATTCCTACGAT 58.309 38.462 0.00 0.00 0.00 3.73
3944 4040 7.075851 TCCTATGACTTCTCTATTCCTACGA 57.924 40.000 0.00 0.00 0.00 3.43
3945 4041 7.747155 TTCCTATGACTTCTCTATTCCTACG 57.253 40.000 0.00 0.00 0.00 3.51
3946 4042 9.921637 CATTTCCTATGACTTCTCTATTCCTAC 57.078 37.037 0.00 0.00 0.00 3.18
3947 4043 9.883293 TCATTTCCTATGACTTCTCTATTCCTA 57.117 33.333 0.00 0.00 0.00 2.94
3948 4044 8.789767 TCATTTCCTATGACTTCTCTATTCCT 57.210 34.615 0.00 0.00 0.00 3.36
3949 4045 8.865090 TCTCATTTCCTATGACTTCTCTATTCC 58.135 37.037 0.00 0.00 0.00 3.01
3952 4048 9.599056 TCATCTCATTTCCTATGACTTCTCTAT 57.401 33.333 0.00 0.00 0.00 1.98
3953 4049 9.599056 ATCATCTCATTTCCTATGACTTCTCTA 57.401 33.333 0.00 0.00 31.56 2.43
3954 4050 7.911130 TCATCTCATTTCCTATGACTTCTCT 57.089 36.000 0.00 0.00 0.00 3.10
3957 4053 9.941325 ACATATCATCTCATTTCCTATGACTTC 57.059 33.333 0.00 0.00 31.56 3.01
3994 4090 8.748412 CATCTCCTTTCCTATTCCTACTCATAG 58.252 40.741 0.00 0.00 0.00 2.23
3995 4091 7.179338 GCATCTCCTTTCCTATTCCTACTCATA 59.821 40.741 0.00 0.00 0.00 2.15
3996 4092 6.013812 GCATCTCCTTTCCTATTCCTACTCAT 60.014 42.308 0.00 0.00 0.00 2.90
3997 4093 5.305644 GCATCTCCTTTCCTATTCCTACTCA 59.694 44.000 0.00 0.00 0.00 3.41
3998 4094 5.279758 GGCATCTCCTTTCCTATTCCTACTC 60.280 48.000 0.00 0.00 0.00 2.59
3999 4095 4.595350 GGCATCTCCTTTCCTATTCCTACT 59.405 45.833 0.00 0.00 0.00 2.57
4000 4096 4.263112 GGGCATCTCCTTTCCTATTCCTAC 60.263 50.000 0.00 0.00 34.39 3.18
4001 4097 3.910627 GGGCATCTCCTTTCCTATTCCTA 59.089 47.826 0.00 0.00 34.39 2.94
4002 4098 2.713708 GGGCATCTCCTTTCCTATTCCT 59.286 50.000 0.00 0.00 34.39 3.36
4003 4099 2.713708 AGGGCATCTCCTTTCCTATTCC 59.286 50.000 0.00 0.00 32.13 3.01
4004 4100 4.445557 AAGGGCATCTCCTTTCCTATTC 57.554 45.455 0.00 0.00 44.14 1.75
4013 4109 2.309755 TGTGAATCAAAGGGCATCTCCT 59.690 45.455 0.00 0.00 39.17 3.69
4014 4110 2.726821 TGTGAATCAAAGGGCATCTCC 58.273 47.619 0.00 0.00 0.00 3.71
4015 4111 3.949754 TGATGTGAATCAAAGGGCATCTC 59.050 43.478 10.68 0.00 35.22 2.75
4016 4112 3.972133 TGATGTGAATCAAAGGGCATCT 58.028 40.909 10.68 0.00 35.22 2.90
4017 4113 4.931661 ATGATGTGAATCAAAGGGCATC 57.068 40.909 4.45 4.45 33.83 3.91
4018 4114 4.831155 CCTATGATGTGAATCAAAGGGCAT 59.169 41.667 0.00 0.00 33.83 4.40
4019 4115 4.079844 TCCTATGATGTGAATCAAAGGGCA 60.080 41.667 0.00 0.00 33.83 5.36
4020 4116 4.464008 TCCTATGATGTGAATCAAAGGGC 58.536 43.478 0.00 0.00 33.83 5.19
4021 4117 7.592885 AAATCCTATGATGTGAATCAAAGGG 57.407 36.000 0.00 0.00 33.83 3.95
4079 4175 9.447279 TCTTCCTATCCTTTACATTTCATAGGA 57.553 33.333 2.01 2.01 39.98 2.94
4084 4180 9.408648 GGAATTCTTCCTATCCTTTACATTTCA 57.591 33.333 5.23 0.00 46.57 2.69
4107 4203 5.073691 GGAATGGAATCCTATTCCTGAGGAA 59.926 44.000 23.95 17.46 46.19 3.36
4108 4204 4.599241 GGAATGGAATCCTATTCCTGAGGA 59.401 45.833 23.95 0.00 45.66 3.71
4109 4205 4.916183 GGAATGGAATCCTATTCCTGAGG 58.084 47.826 23.95 0.00 45.66 3.86
4120 4216 5.105351 CCTTTGGTTTGTAGGAATGGAATCC 60.105 44.000 0.00 0.00 39.96 3.01
4121 4217 5.105351 CCCTTTGGTTTGTAGGAATGGAATC 60.105 44.000 0.00 0.00 0.00 2.52
4122 4218 4.777366 CCCTTTGGTTTGTAGGAATGGAAT 59.223 41.667 0.00 0.00 0.00 3.01
4123 4219 4.156477 CCCTTTGGTTTGTAGGAATGGAA 58.844 43.478 0.00 0.00 0.00 3.53
4124 4220 3.141272 ACCCTTTGGTTTGTAGGAATGGA 59.859 43.478 0.00 0.00 44.75 3.41
4125 4221 3.506398 ACCCTTTGGTTTGTAGGAATGG 58.494 45.455 0.00 0.00 44.75 3.16
4176 4272 9.838339 GAGGAATCTTGTAAGAATTTCATAGGA 57.162 33.333 0.00 0.00 38.77 2.94
4177 4273 9.844257 AGAGGAATCTTGTAAGAATTTCATAGG 57.156 33.333 0.00 0.00 38.77 2.57
4186 4282 9.284968 CCTTTGTTTAGAGGAATCTTGTAAGAA 57.715 33.333 0.00 0.00 35.38 2.52
4187 4283 8.656806 TCCTTTGTTTAGAGGAATCTTGTAAGA 58.343 33.333 0.00 0.00 39.06 2.10
4188 4284 8.848474 TCCTTTGTTTAGAGGAATCTTGTAAG 57.152 34.615 0.00 0.00 39.06 2.34
4189 4285 8.656806 TCTCCTTTGTTTAGAGGAATCTTGTAA 58.343 33.333 0.00 0.00 41.33 2.41
4190 4286 8.202461 TCTCCTTTGTTTAGAGGAATCTTGTA 57.798 34.615 0.00 0.00 41.33 2.41
4191 4287 7.079451 TCTCCTTTGTTTAGAGGAATCTTGT 57.921 36.000 0.00 0.00 41.33 3.16
4192 4288 7.663493 ACTTCTCCTTTGTTTAGAGGAATCTTG 59.337 37.037 0.00 0.00 41.33 3.02
4193 4289 7.750655 ACTTCTCCTTTGTTTAGAGGAATCTT 58.249 34.615 0.00 0.00 41.33 2.40
4194 4290 7.323052 ACTTCTCCTTTGTTTAGAGGAATCT 57.677 36.000 0.00 0.00 41.33 2.40
4195 4291 9.503399 TTTACTTCTCCTTTGTTTAGAGGAATC 57.497 33.333 0.00 0.00 41.33 2.52
4196 4292 9.286170 GTTTACTTCTCCTTTGTTTAGAGGAAT 57.714 33.333 0.00 0.00 41.33 3.01
4197 4293 7.440255 CGTTTACTTCTCCTTTGTTTAGAGGAA 59.560 37.037 0.00 0.00 41.33 3.36
4198 4294 6.927381 CGTTTACTTCTCCTTTGTTTAGAGGA 59.073 38.462 0.00 0.00 39.69 3.71
4199 4295 6.147328 CCGTTTACTTCTCCTTTGTTTAGAGG 59.853 42.308 0.00 0.00 0.00 3.69
4200 4296 6.347483 GCCGTTTACTTCTCCTTTGTTTAGAG 60.347 42.308 0.00 0.00 0.00 2.43
4201 4297 5.467735 GCCGTTTACTTCTCCTTTGTTTAGA 59.532 40.000 0.00 0.00 0.00 2.10
4202 4298 5.334646 GGCCGTTTACTTCTCCTTTGTTTAG 60.335 44.000 0.00 0.00 0.00 1.85
4203 4299 4.516321 GGCCGTTTACTTCTCCTTTGTTTA 59.484 41.667 0.00 0.00 0.00 2.01
4204 4300 3.317149 GGCCGTTTACTTCTCCTTTGTTT 59.683 43.478 0.00 0.00 0.00 2.83
4205 4301 2.882761 GGCCGTTTACTTCTCCTTTGTT 59.117 45.455 0.00 0.00 0.00 2.83
4206 4302 2.501261 GGCCGTTTACTTCTCCTTTGT 58.499 47.619 0.00 0.00 0.00 2.83
4207 4303 1.810755 GGGCCGTTTACTTCTCCTTTG 59.189 52.381 0.00 0.00 0.00 2.77
4208 4304 1.609841 CGGGCCGTTTACTTCTCCTTT 60.610 52.381 19.97 0.00 0.00 3.11
4209 4305 0.036671 CGGGCCGTTTACTTCTCCTT 60.037 55.000 19.97 0.00 0.00 3.36
4210 4306 1.595357 CGGGCCGTTTACTTCTCCT 59.405 57.895 19.97 0.00 0.00 3.69
4211 4307 1.449070 CCGGGCCGTTTACTTCTCC 60.449 63.158 26.32 0.00 0.00 3.71
4215 4311 0.178767 GGATACCGGGCCGTTTACTT 59.821 55.000 26.32 2.79 0.00 2.24
4219 4315 1.897802 CTATAGGATACCGGGCCGTTT 59.102 52.381 26.32 14.01 37.17 3.60


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

AutoCloner maintained by Alex Coulton.