Multiple sequence alignment - TraesCS3D01G003400

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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 TraesCS3D01G003400 chr3D 100.000 4139 0 0 1 4139 1499503 1495365 0.000000e+00 7644.0
1 TraesCS3D01G003400 chr3D 96.305 406 11 1 624 1029 520636256 520635855 0.000000e+00 664.0
2 TraesCS3D01G003400 chr3D 92.233 103 8 0 928 1030 559488103 559488001 3.330000e-31 147.0
3 TraesCS3D01G003400 chr2D 88.332 3111 346 15 1030 4127 323098509 323101615 0.000000e+00 3718.0
4 TraesCS3D01G003400 chr2D 92.140 916 69 3 3216 4128 117250578 117249663 0.000000e+00 1290.0
5 TraesCS3D01G003400 chr2D 95.991 424 11 4 614 1036 650461252 650461670 0.000000e+00 684.0
6 TraesCS3D01G003400 chr2D 90.566 265 22 1 361 625 323098254 323098515 8.520000e-92 348.0
7 TraesCS3D01G003400 chr2D 86.260 262 32 4 107 365 323093950 323094210 8.760000e-72 281.0
8 TraesCS3D01G003400 chr6B 82.355 3117 514 31 1034 4131 602550988 602554087 0.000000e+00 2676.0
9 TraesCS3D01G003400 chr6B 86.441 59 2 4 900 957 554644510 554644457 4.470000e-05 60.2
10 TraesCS3D01G003400 chr2A 93.061 1643 113 1 1030 2672 55926199 55927840 0.000000e+00 2401.0
11 TraesCS3D01G003400 chr2A 94.398 1446 79 2 2696 4139 55927836 55929281 0.000000e+00 2220.0
12 TraesCS3D01G003400 chr2A 90.690 623 54 2 3 624 55925585 55926204 0.000000e+00 826.0
13 TraesCS3D01G003400 chr6D 96.749 646 18 2 3495 4139 267520911 267521554 0.000000e+00 1074.0
14 TraesCS3D01G003400 chr6D 94.776 134 5 1 3321 3454 267520783 267520914 1.510000e-49 207.0
15 TraesCS3D01G003400 chr6A 94.024 251 15 0 648 898 268992713 268992963 8.400000e-102 381.0
16 TraesCS3D01G003400 chr6A 90.040 251 10 8 648 898 268993507 268993742 1.120000e-80 311.0
17 TraesCS3D01G003400 chr5A 92.032 251 20 0 648 898 283095284 283095534 1.830000e-93 353.0
18 TraesCS3D01G003400 chr5A 91.667 252 21 0 647 898 283093864 283094115 2.370000e-92 350.0
19 TraesCS3D01G003400 chr5A 86.885 61 2 3 898 957 567048969 567048914 3.450000e-06 63.9
20 TraesCS3D01G003400 chr1A 82.464 211 30 7 3623 3829 22871888 22872095 1.180000e-40 178.0
21 TraesCS3D01G003400 chr5D 96.591 88 3 0 811 898 45599603 45599516 3.330000e-31 147.0
22 TraesCS3D01G003400 chr5D 84.404 109 13 4 923 1028 220779602 220779495 2.040000e-18 104.0
23 TraesCS3D01G003400 chr7B 88.776 98 11 0 717 814 658023454 658023357 2.020000e-23 121.0
24 TraesCS3D01G003400 chr7B 88.776 98 11 0 717 814 658024711 658024614 2.020000e-23 121.0
25 TraesCS3D01G003400 chr1B 88.421 95 6 4 937 1029 24205777 24205868 4.370000e-20 110.0
26 TraesCS3D01G003400 chr1B 88.421 95 6 4 937 1029 24254051 24254142 4.370000e-20 110.0
27 TraesCS3D01G003400 chr1B 88.298 94 6 4 936 1027 24251177 24251267 1.570000e-19 108.0
28 TraesCS3D01G003400 chr1B 87.368 95 7 4 937 1029 24207221 24207312 2.040000e-18 104.0
29 TraesCS3D01G003400 chr3B 88.172 93 7 3 939 1029 3772868 3772958 1.570000e-19 108.0
30 TraesCS3D01G003400 chr3B 97.143 35 1 0 917 951 74782932 74782966 4.470000e-05 60.2
31 TraesCS3D01G003400 chr1D 83.333 72 5 4 888 957 32887761 32887827 4.470000e-05 60.2
32 TraesCS3D01G003400 chr2B 97.059 34 1 0 917 950 152194958 152194991 1.610000e-04 58.4


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 TraesCS3D01G003400 chr3D 1495365 1499503 4138 True 7644.000000 7644 100.000000 1 4139 1 chr3D.!!$R1 4138
1 TraesCS3D01G003400 chr2D 323098254 323101615 3361 False 2033.000000 3718 89.449000 361 4127 2 chr2D.!!$F3 3766
2 TraesCS3D01G003400 chr2D 117249663 117250578 915 True 1290.000000 1290 92.140000 3216 4128 1 chr2D.!!$R1 912
3 TraesCS3D01G003400 chr6B 602550988 602554087 3099 False 2676.000000 2676 82.355000 1034 4131 1 chr6B.!!$F1 3097
4 TraesCS3D01G003400 chr2A 55925585 55929281 3696 False 1815.666667 2401 92.716333 3 4139 3 chr2A.!!$F1 4136
5 TraesCS3D01G003400 chr6D 267520783 267521554 771 False 640.500000 1074 95.762500 3321 4139 2 chr6D.!!$F1 818
6 TraesCS3D01G003400 chr6A 268992713 268993742 1029 False 346.000000 381 92.032000 648 898 2 chr6A.!!$F1 250
7 TraesCS3D01G003400 chr5A 283093864 283095534 1670 False 351.500000 353 91.849500 647 898 2 chr5A.!!$F1 251

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
959 2533 0.041312 CGTTGGTCGCCAGAAAACTG 60.041 55.0 0.00 0.0 33.81 3.16 F
1022 2596 0.033405 AGAGTTAGTCTAGGGCGGCA 60.033 55.0 12.47 0.0 31.71 5.69 F
1025 2599 0.248289 GTTAGTCTAGGGCGGCAACA 59.752 55.0 12.47 0.0 0.00 3.33 F
1223 2802 0.671781 GCTGAGGTCTGCATCGTGTT 60.672 55.0 4.14 0.0 40.06 3.32 F
2993 4573 0.182537 CAAGACCCCTTCACACCACA 59.817 55.0 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 3968 0.249120 CTGCACTCGGTTCCACCATA 59.751 55.000 0.00 0.0 38.47 2.74 R
2521 4101 0.460987 GTGGTCTCCTCCGAATGCAG 60.461 60.000 0.00 0.0 0.00 4.41 R
2549 4129 0.463654 TGCGATTATCTGTGGCACCC 60.464 55.000 16.26 0.0 0.00 4.61 R
3104 4686 0.179215 GAAGTTGCGACAATGCTCCG 60.179 55.000 6.90 0.0 35.36 4.63 R
3971 5556 4.962362 TGTAAGTGATCCTCCATAGCAAGA 59.038 41.667 0.00 0.0 0.00 3.02 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
88 90 2.741211 GACGTTCAACCCTCCCGC 60.741 66.667 0.00 0.00 0.00 6.13
125 127 4.754667 GGCGTCCACTTCCCCGTC 62.755 72.222 0.00 0.00 0.00 4.79
130 132 2.284699 CCACTTCCCCGTCCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
158 160 2.825836 GTCCATGGCTTCGCTGGG 60.826 66.667 6.96 0.00 0.00 4.45
165 167 2.964389 GCTTCGCTGGGATCTCGC 60.964 66.667 0.00 0.00 0.00 5.03
182 184 3.827898 CAGTCCGCCCTCCGTCTC 61.828 72.222 0.00 0.00 34.38 3.36
219 221 2.042843 AGGCCGGTGGTCTCTAGG 60.043 66.667 1.90 0.00 27.34 3.02
231 233 1.003646 TCTCTAGGCTGGGTCTGTCT 58.996 55.000 0.00 0.00 0.00 3.41
246 248 4.067512 TCTGGCTCTCCGGGCTCT 62.068 66.667 0.00 0.00 39.31 4.09
378 380 3.907260 TAGGTGGAGGCGTCGTCGT 62.907 63.158 3.66 0.85 39.49 4.34
380 382 4.338539 GTGGAGGCGTCGTCGTGT 62.339 66.667 3.66 0.00 39.49 4.49
381 383 3.598715 TGGAGGCGTCGTCGTGTT 61.599 61.111 3.66 0.00 39.49 3.32
444 446 0.753848 GTTCCTCCTCCTCCTCCTCG 60.754 65.000 0.00 0.00 0.00 4.63
546 548 2.835705 CGAGCCGCTCTGTATCCGT 61.836 63.158 18.14 0.00 0.00 4.69
623 625 4.681978 GGAAGCCCTGCGTCGTGT 62.682 66.667 0.00 0.00 37.89 4.49
624 626 3.414700 GAAGCCCTGCGTCGTGTG 61.415 66.667 0.00 0.00 0.00 3.82
625 627 4.235762 AAGCCCTGCGTCGTGTGT 62.236 61.111 0.00 0.00 0.00 3.72
626 628 3.750373 AAGCCCTGCGTCGTGTGTT 62.750 57.895 0.00 0.00 0.00 3.32
627 629 2.356553 GCCCTGCGTCGTGTGTTA 60.357 61.111 0.00 0.00 0.00 2.41
628 630 2.380410 GCCCTGCGTCGTGTGTTAG 61.380 63.158 0.00 0.00 0.00 2.34
629 631 1.287815 CCCTGCGTCGTGTGTTAGA 59.712 57.895 0.00 0.00 0.00 2.10
630 632 0.319211 CCCTGCGTCGTGTGTTAGAA 60.319 55.000 0.00 0.00 0.00 2.10
631 633 1.493772 CCTGCGTCGTGTGTTAGAAA 58.506 50.000 0.00 0.00 0.00 2.52
632 634 2.066262 CCTGCGTCGTGTGTTAGAAAT 58.934 47.619 0.00 0.00 0.00 2.17
633 635 3.247442 CCTGCGTCGTGTGTTAGAAATA 58.753 45.455 0.00 0.00 0.00 1.40
634 636 3.676172 CCTGCGTCGTGTGTTAGAAATAA 59.324 43.478 0.00 0.00 0.00 1.40
635 637 4.201589 CCTGCGTCGTGTGTTAGAAATAAG 60.202 45.833 0.00 0.00 0.00 1.73
636 638 3.122278 TGCGTCGTGTGTTAGAAATAAGC 59.878 43.478 0.00 0.00 0.00 3.09
637 639 3.483085 GCGTCGTGTGTTAGAAATAAGCC 60.483 47.826 0.00 0.00 0.00 4.35
638 640 3.676172 CGTCGTGTGTTAGAAATAAGCCA 59.324 43.478 0.00 0.00 0.00 4.75
639 641 4.328983 CGTCGTGTGTTAGAAATAAGCCAT 59.671 41.667 0.00 0.00 0.00 4.40
640 642 5.560148 GTCGTGTGTTAGAAATAAGCCATG 58.440 41.667 0.00 0.00 0.00 3.66
641 643 4.094294 TCGTGTGTTAGAAATAAGCCATGC 59.906 41.667 0.00 0.00 0.00 4.06
642 644 4.342772 GTGTGTTAGAAATAAGCCATGCG 58.657 43.478 0.00 0.00 0.00 4.73
643 645 4.006989 TGTGTTAGAAATAAGCCATGCGT 58.993 39.130 0.00 0.00 0.00 5.24
644 646 4.457603 TGTGTTAGAAATAAGCCATGCGTT 59.542 37.500 0.00 0.00 0.00 4.84
645 647 5.028375 GTGTTAGAAATAAGCCATGCGTTC 58.972 41.667 0.00 0.00 0.00 3.95
657 659 3.568743 GCGTTCACGTGTGTGGCA 61.569 61.111 16.51 0.00 46.42 4.92
660 662 1.370414 GTTCACGTGTGTGGCATGC 60.370 57.895 16.51 9.90 46.42 4.06
688 690 1.224722 GCTCGTGGCAATAGCTAGGC 61.225 60.000 13.50 10.83 41.70 3.93
697 699 0.179073 AATAGCTAGGCTGTGGCGTG 60.179 55.000 0.00 0.00 40.10 5.34
771 773 2.235016 GGTTGTTAGTGCATGGTGGAA 58.765 47.619 0.00 0.00 0.00 3.53
780 782 4.151883 AGTGCATGGTGGAATTAGTTTGT 58.848 39.130 0.00 0.00 0.00 2.83
785 787 5.127031 GCATGGTGGAATTAGTTTGTATGGT 59.873 40.000 0.00 0.00 0.00 3.55
799 801 0.968901 TATGGTCGAACGTGGAGGCT 60.969 55.000 5.15 0.00 0.00 4.58
898 2472 4.460263 TCATGTTTGTAGTGAGGCAGTTT 58.540 39.130 0.00 0.00 0.00 2.66
899 2473 4.887071 TCATGTTTGTAGTGAGGCAGTTTT 59.113 37.500 0.00 0.00 0.00 2.43
900 2474 4.630894 TGTTTGTAGTGAGGCAGTTTTG 57.369 40.909 0.00 0.00 0.00 2.44
901 2475 4.013728 TGTTTGTAGTGAGGCAGTTTTGT 58.986 39.130 0.00 0.00 0.00 2.83
902 2476 4.142491 TGTTTGTAGTGAGGCAGTTTTGTG 60.142 41.667 0.00 0.00 0.00 3.33
903 2477 1.946768 TGTAGTGAGGCAGTTTTGTGC 59.053 47.619 0.00 0.00 43.19 4.57
904 2478 2.222027 GTAGTGAGGCAGTTTTGTGCT 58.778 47.619 0.00 0.00 43.45 4.40
905 2479 1.027357 AGTGAGGCAGTTTTGTGCTG 58.973 50.000 0.00 0.00 43.45 4.41
906 2480 1.024271 GTGAGGCAGTTTTGTGCTGA 58.976 50.000 0.00 0.00 43.45 4.26
907 2481 1.405105 GTGAGGCAGTTTTGTGCTGAA 59.595 47.619 0.00 0.00 43.45 3.02
908 2482 2.035066 GTGAGGCAGTTTTGTGCTGAAT 59.965 45.455 0.00 0.00 43.45 2.57
909 2483 3.253188 GTGAGGCAGTTTTGTGCTGAATA 59.747 43.478 0.00 0.00 43.45 1.75
910 2484 3.253188 TGAGGCAGTTTTGTGCTGAATAC 59.747 43.478 0.00 0.00 43.45 1.89
911 2485 2.226437 AGGCAGTTTTGTGCTGAATACG 59.774 45.455 0.00 0.00 43.45 3.06
912 2486 2.031157 GGCAGTTTTGTGCTGAATACGT 60.031 45.455 0.00 0.00 43.45 3.57
913 2487 3.187637 GGCAGTTTTGTGCTGAATACGTA 59.812 43.478 0.00 0.00 43.45 3.57
914 2488 4.148891 GCAGTTTTGTGCTGAATACGTAC 58.851 43.478 0.00 0.00 40.54 3.67
915 2489 4.319190 GCAGTTTTGTGCTGAATACGTACA 60.319 41.667 0.00 0.00 40.54 2.90
916 2490 5.743467 CAGTTTTGTGCTGAATACGTACAA 58.257 37.500 0.00 0.00 36.12 2.41
917 2491 6.195868 CAGTTTTGTGCTGAATACGTACAAA 58.804 36.000 0.00 1.56 38.88 2.83
918 2492 6.689241 CAGTTTTGTGCTGAATACGTACAAAA 59.311 34.615 15.61 15.61 44.29 2.44
919 2493 6.910433 AGTTTTGTGCTGAATACGTACAAAAG 59.090 34.615 18.57 7.50 45.92 2.27
920 2494 6.606234 TTTGTGCTGAATACGTACAAAAGA 57.394 33.333 7.82 0.00 38.03 2.52
921 2495 6.606234 TTGTGCTGAATACGTACAAAAGAA 57.394 33.333 0.00 0.00 0.00 2.52
922 2496 6.223138 TGTGCTGAATACGTACAAAAGAAG 57.777 37.500 0.00 0.00 0.00 2.85
923 2497 5.178623 TGTGCTGAATACGTACAAAAGAAGG 59.821 40.000 0.00 0.00 0.00 3.46
924 2498 4.153475 TGCTGAATACGTACAAAAGAAGGC 59.847 41.667 0.00 0.00 0.00 4.35
925 2499 4.724036 GCTGAATACGTACAAAAGAAGGCG 60.724 45.833 0.00 0.00 0.00 5.52
926 2500 4.309099 TGAATACGTACAAAAGAAGGCGT 58.691 39.130 0.00 0.00 36.52 5.68
927 2501 4.751098 TGAATACGTACAAAAGAAGGCGTT 59.249 37.500 0.00 0.00 34.38 4.84
928 2502 5.236911 TGAATACGTACAAAAGAAGGCGTTT 59.763 36.000 0.00 0.00 34.38 3.60
929 2503 3.328237 ACGTACAAAAGAAGGCGTTTG 57.672 42.857 0.00 0.00 45.20 2.93
930 2504 2.032426 ACGTACAAAAGAAGGCGTTTGG 59.968 45.455 0.00 0.00 44.38 3.28
931 2505 2.603652 CGTACAAAAGAAGGCGTTTGGG 60.604 50.000 0.00 0.00 44.38 4.12
932 2506 0.104120 ACAAAAGAAGGCGTTTGGGC 59.896 50.000 0.00 0.00 44.38 5.36
933 2507 3.541824 ACAAAAGAAGGCGTTTGGGCG 62.542 52.381 0.00 0.00 44.38 6.13
957 2531 4.914291 CGTTGGTCGCCAGAAAAC 57.086 55.556 0.00 0.00 33.81 2.43
958 2532 2.317230 CGTTGGTCGCCAGAAAACT 58.683 52.632 0.00 0.00 33.81 2.66
959 2533 0.041312 CGTTGGTCGCCAGAAAACTG 60.041 55.000 0.00 0.00 33.81 3.16
960 2534 1.021968 GTTGGTCGCCAGAAAACTGT 58.978 50.000 0.00 0.00 33.81 3.55
961 2535 1.002792 GTTGGTCGCCAGAAAACTGTC 60.003 52.381 0.00 0.00 33.81 3.51
962 2536 0.534203 TGGTCGCCAGAAAACTGTCC 60.534 55.000 0.00 0.00 0.00 4.02
963 2537 0.534203 GGTCGCCAGAAAACTGTCCA 60.534 55.000 0.00 0.00 0.00 4.02
964 2538 1.523758 GTCGCCAGAAAACTGTCCAT 58.476 50.000 0.00 0.00 0.00 3.41
965 2539 1.464997 GTCGCCAGAAAACTGTCCATC 59.535 52.381 0.00 0.00 0.00 3.51
966 2540 1.347707 TCGCCAGAAAACTGTCCATCT 59.652 47.619 0.00 0.00 0.00 2.90
967 2541 2.154462 CGCCAGAAAACTGTCCATCTT 58.846 47.619 0.00 0.00 0.00 2.40
968 2542 2.095567 CGCCAGAAAACTGTCCATCTTG 60.096 50.000 0.00 0.00 0.00 3.02
969 2543 2.352127 GCCAGAAAACTGTCCATCTTGC 60.352 50.000 0.00 0.00 0.00 4.01
970 2544 2.229784 CCAGAAAACTGTCCATCTTGCC 59.770 50.000 0.00 0.00 0.00 4.52
971 2545 2.095567 CAGAAAACTGTCCATCTTGCCG 60.096 50.000 0.00 0.00 0.00 5.69
972 2546 1.880027 GAAAACTGTCCATCTTGCCGT 59.120 47.619 0.00 0.00 0.00 5.68
973 2547 2.851263 AAACTGTCCATCTTGCCGTA 57.149 45.000 0.00 0.00 0.00 4.02
974 2548 2.386661 AACTGTCCATCTTGCCGTAG 57.613 50.000 0.00 0.00 0.00 3.51
975 2549 1.267121 ACTGTCCATCTTGCCGTAGT 58.733 50.000 0.00 0.00 0.00 2.73
976 2550 1.204941 ACTGTCCATCTTGCCGTAGTC 59.795 52.381 0.00 0.00 0.00 2.59
977 2551 1.478510 CTGTCCATCTTGCCGTAGTCT 59.521 52.381 0.00 0.00 0.00 3.24
978 2552 2.688446 CTGTCCATCTTGCCGTAGTCTA 59.312 50.000 0.00 0.00 0.00 2.59
979 2553 2.426024 TGTCCATCTTGCCGTAGTCTAC 59.574 50.000 0.00 0.00 0.00 2.59
980 2554 2.029623 TCCATCTTGCCGTAGTCTACC 58.970 52.381 4.39 0.00 0.00 3.18
981 2555 2.032620 CCATCTTGCCGTAGTCTACCT 58.967 52.381 4.39 0.00 0.00 3.08
982 2556 2.034812 CCATCTTGCCGTAGTCTACCTC 59.965 54.545 4.39 0.00 0.00 3.85
983 2557 1.760192 TCTTGCCGTAGTCTACCTCC 58.240 55.000 4.39 0.00 0.00 4.30
984 2558 0.381089 CTTGCCGTAGTCTACCTCCG 59.619 60.000 4.39 0.00 0.00 4.63
985 2559 0.322816 TTGCCGTAGTCTACCTCCGT 60.323 55.000 4.39 0.00 0.00 4.69
986 2560 0.745845 TGCCGTAGTCTACCTCCGTC 60.746 60.000 4.39 0.00 0.00 4.79
987 2561 1.443322 GCCGTAGTCTACCTCCGTCC 61.443 65.000 4.39 0.00 0.00 4.79
988 2562 1.156645 CCGTAGTCTACCTCCGTCCG 61.157 65.000 4.39 0.00 0.00 4.79
989 2563 0.460987 CGTAGTCTACCTCCGTCCGT 60.461 60.000 4.39 0.00 0.00 4.69
990 2564 1.012841 GTAGTCTACCTCCGTCCGTG 58.987 60.000 0.00 0.00 0.00 4.94
991 2565 0.904649 TAGTCTACCTCCGTCCGTGA 59.095 55.000 0.00 0.00 0.00 4.35
992 2566 0.392729 AGTCTACCTCCGTCCGTGAG 60.393 60.000 0.00 0.00 0.00 3.51
993 2567 0.676151 GTCTACCTCCGTCCGTGAGT 60.676 60.000 5.07 0.00 0.00 3.41
994 2568 0.675837 TCTACCTCCGTCCGTGAGTG 60.676 60.000 5.07 1.11 0.00 3.51
995 2569 0.675837 CTACCTCCGTCCGTGAGTGA 60.676 60.000 5.07 0.00 0.00 3.41
996 2570 0.250858 TACCTCCGTCCGTGAGTGAA 60.251 55.000 5.07 0.00 0.00 3.18
997 2571 1.080705 CCTCCGTCCGTGAGTGAAC 60.081 63.158 5.07 0.00 0.00 3.18
998 2572 1.080705 CTCCGTCCGTGAGTGAACC 60.081 63.158 0.00 0.00 0.00 3.62
999 2573 1.802337 CTCCGTCCGTGAGTGAACCA 61.802 60.000 0.00 0.00 0.00 3.67
1000 2574 1.372997 CCGTCCGTGAGTGAACCAG 60.373 63.158 0.00 0.00 0.00 4.00
1001 2575 1.658114 CGTCCGTGAGTGAACCAGA 59.342 57.895 0.00 0.00 0.00 3.86
1002 2576 0.387367 CGTCCGTGAGTGAACCAGAG 60.387 60.000 0.00 0.00 0.00 3.35
1003 2577 0.959553 GTCCGTGAGTGAACCAGAGA 59.040 55.000 0.00 0.00 0.00 3.10
1004 2578 1.068194 GTCCGTGAGTGAACCAGAGAG 60.068 57.143 0.00 0.00 0.00 3.20
1005 2579 1.202891 TCCGTGAGTGAACCAGAGAGA 60.203 52.381 0.00 0.00 0.00 3.10
1006 2580 1.201181 CCGTGAGTGAACCAGAGAGAG 59.799 57.143 0.00 0.00 0.00 3.20
1007 2581 1.883275 CGTGAGTGAACCAGAGAGAGT 59.117 52.381 0.00 0.00 0.00 3.24
1008 2582 2.294791 CGTGAGTGAACCAGAGAGAGTT 59.705 50.000 0.00 0.00 0.00 3.01
1009 2583 3.502595 CGTGAGTGAACCAGAGAGAGTTA 59.497 47.826 0.00 0.00 0.00 2.24
1010 2584 4.378978 CGTGAGTGAACCAGAGAGAGTTAG 60.379 50.000 0.00 0.00 0.00 2.34
1011 2585 4.521256 GTGAGTGAACCAGAGAGAGTTAGT 59.479 45.833 0.00 0.00 0.00 2.24
1012 2586 4.762765 TGAGTGAACCAGAGAGAGTTAGTC 59.237 45.833 0.00 0.00 0.00 2.59
1013 2587 4.993028 AGTGAACCAGAGAGAGTTAGTCT 58.007 43.478 0.00 0.00 38.71 3.24
1014 2588 6.129414 AGTGAACCAGAGAGAGTTAGTCTA 57.871 41.667 0.00 0.00 34.71 2.59
1015 2589 6.177610 AGTGAACCAGAGAGAGTTAGTCTAG 58.822 44.000 0.00 0.00 34.71 2.43
1016 2590 5.355910 GTGAACCAGAGAGAGTTAGTCTAGG 59.644 48.000 0.00 0.00 34.71 3.02
1017 2591 4.513406 ACCAGAGAGAGTTAGTCTAGGG 57.487 50.000 0.00 0.00 34.71 3.53
1018 2592 3.219281 CCAGAGAGAGTTAGTCTAGGGC 58.781 54.545 0.00 0.00 34.71 5.19
1019 2593 2.875933 CAGAGAGAGTTAGTCTAGGGCG 59.124 54.545 0.00 0.00 34.71 6.13
1020 2594 2.158726 AGAGAGAGTTAGTCTAGGGCGG 60.159 54.545 0.00 0.00 34.71 6.13
1021 2595 0.669619 GAGAGTTAGTCTAGGGCGGC 59.330 60.000 0.00 0.00 34.71 6.53
1022 2596 0.033405 AGAGTTAGTCTAGGGCGGCA 60.033 55.000 12.47 0.00 31.71 5.69
1023 2597 0.822164 GAGTTAGTCTAGGGCGGCAA 59.178 55.000 12.47 0.00 0.00 4.52
1024 2598 0.535797 AGTTAGTCTAGGGCGGCAAC 59.464 55.000 12.47 4.53 0.00 4.17
1025 2599 0.248289 GTTAGTCTAGGGCGGCAACA 59.752 55.000 12.47 0.00 0.00 3.33
1026 2600 0.978151 TTAGTCTAGGGCGGCAACAA 59.022 50.000 12.47 0.00 0.00 2.83
1027 2601 0.248289 TAGTCTAGGGCGGCAACAAC 59.752 55.000 12.47 3.38 0.00 3.32
1028 2602 1.302192 GTCTAGGGCGGCAACAACA 60.302 57.895 12.47 0.00 0.00 3.33
1223 2802 0.671781 GCTGAGGTCTGCATCGTGTT 60.672 55.000 4.14 0.00 40.06 3.32
1314 2893 2.593436 CCGCCGGTTTCCTGTGTT 60.593 61.111 1.90 0.00 0.00 3.32
1369 2948 0.824595 TCCTCGACACCGTTTCTCCA 60.825 55.000 0.00 0.00 37.05 3.86
1572 3151 4.457496 CCATCGCACGCCTGGTCT 62.457 66.667 0.00 0.00 0.00 3.85
1869 3448 1.218230 GATCGCCGAGTTCAGATGGC 61.218 60.000 0.00 0.00 44.09 4.40
1878 3457 3.626996 TTCAGATGGCGGCAGTGGG 62.627 63.158 19.29 7.09 0.00 4.61
1961 3540 2.584608 GAGGGGTGTCCGTGATGG 59.415 66.667 0.00 0.00 41.52 3.51
2087 3666 1.296392 CGCCAATGGAGACTGGACA 59.704 57.895 2.05 0.00 34.35 4.02
2212 3792 1.595382 GTGTTGACAGCTGGCGAGT 60.595 57.895 19.93 0.00 0.00 4.18
2351 3931 4.558496 CGTCCTAGAGAAAGATCTGGATGC 60.558 50.000 0.00 0.00 35.54 3.91
2388 3968 4.404098 CCCTTGGTTACGGCGCCT 62.404 66.667 26.68 14.27 0.00 5.52
2468 4048 1.027357 GATCCGCATGCACAGGATTT 58.973 50.000 21.88 6.51 44.13 2.17
2549 4129 1.398692 GAGGAGACCACTCAGGCTAG 58.601 60.000 0.00 0.00 44.22 3.42
2566 4146 2.868044 GCTAGGGTGCCACAGATAATCG 60.868 54.545 0.00 0.00 0.00 3.34
2588 4168 2.742372 GAGGTGCGCGGTGATTGT 60.742 61.111 8.83 0.00 0.00 2.71
2592 4172 2.593148 TGCGCGGTGATTGTGGTT 60.593 55.556 8.83 0.00 0.00 3.67
2812 4392 2.032071 CGGCGTTTGGGACTCCTT 59.968 61.111 0.00 0.00 30.65 3.36
2910 4490 3.118956 TCAAAACATTTTGTGCGGGACTT 60.119 39.130 14.95 0.00 45.77 3.01
2950 4530 2.742053 CCGCTCCTCAAAGAAATCGAAA 59.258 45.455 0.00 0.00 0.00 3.46
2993 4573 0.182537 CAAGACCCCTTCACACCACA 59.817 55.000 0.00 0.00 0.00 4.17
3054 4634 4.742201 GCTTCGGCCGCTGAGACA 62.742 66.667 23.51 0.00 34.32 3.41
3071 4653 2.301583 AGACAGTCTTCTCAAAGCCCTC 59.698 50.000 0.00 0.00 32.18 4.30
3092 4674 1.070134 GGTATTGTGCCGGATGAGCTA 59.930 52.381 5.05 0.00 0.00 3.32
3102 4684 2.554142 CGGATGAGCTAGCAATCACAA 58.446 47.619 23.90 0.24 0.00 3.33
3104 4686 3.242543 CGGATGAGCTAGCAATCACAAAC 60.243 47.826 23.90 10.99 0.00 2.93
3119 4701 0.040514 CAAACGGAGCATTGTCGCAA 60.041 50.000 0.00 0.00 0.00 4.85
3161 4743 1.477558 CCACTCCAAGACAAGCACCTT 60.478 52.381 0.00 0.00 0.00 3.50
3235 4817 4.069869 CCAAGTGGTCACTGCCAG 57.930 61.111 4.22 0.00 41.58 4.85
3330 4913 1.124780 TTCGAGGGTTGAACAGTCCA 58.875 50.000 0.00 0.00 0.00 4.02
3726 5310 8.690203 TGGAGACTTTAATCTCATTTTGAACA 57.310 30.769 8.07 0.00 46.00 3.18
3755 5339 6.662755 TGATAAGAGTAATGCCAACCTTGAT 58.337 36.000 0.00 0.00 0.00 2.57
3971 5556 1.278985 TCAGACCATTGTCCGCTTCAT 59.721 47.619 0.00 0.00 42.81 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 74 4.324991 GGCGGGAGGGTTGAACGT 62.325 66.667 0.00 0.00 0.00 3.99
110 112 2.995574 AGGACGGGGAAGTGGACG 60.996 66.667 0.00 0.00 0.00 4.79
135 137 4.166011 GAAGCCATGGACGCGCAC 62.166 66.667 18.40 0.00 0.00 5.34
155 157 3.838271 GCGGACTGCGAGATCCCA 61.838 66.667 0.00 0.00 0.00 4.37
165 167 3.827898 GAGACGGAGGGCGGACTG 61.828 72.222 0.00 0.00 0.00 3.51
217 219 3.325753 GCCAGACAGACCCAGCCT 61.326 66.667 0.00 0.00 0.00 4.58
219 221 2.237534 GAGAGCCAGACAGACCCAGC 62.238 65.000 0.00 0.00 0.00 4.85
424 426 0.336737 GAGGAGGAGGAGGAGGAACA 59.663 60.000 0.00 0.00 0.00 3.18
425 427 0.753848 CGAGGAGGAGGAGGAGGAAC 60.754 65.000 0.00 0.00 0.00 3.62
426 428 1.615814 CGAGGAGGAGGAGGAGGAA 59.384 63.158 0.00 0.00 0.00 3.36
429 431 3.336820 TCCGAGGAGGAGGAGGAG 58.663 66.667 0.00 0.00 45.98 3.69
444 446 2.472909 CGGAATCAGCCGCCTTTCC 61.473 63.158 0.00 6.54 45.38 3.13
546 548 3.172106 TGCCCGGAGAACCCACAA 61.172 61.111 0.73 0.00 34.14 3.33
618 620 4.094294 GCATGGCTTATTTCTAACACACGA 59.906 41.667 0.00 0.00 0.00 4.35
619 621 4.342772 GCATGGCTTATTTCTAACACACG 58.657 43.478 0.00 0.00 0.00 4.49
620 622 4.142687 ACGCATGGCTTATTTCTAACACAC 60.143 41.667 0.00 0.00 0.00 3.82
621 623 4.006989 ACGCATGGCTTATTTCTAACACA 58.993 39.130 0.00 0.00 0.00 3.72
622 624 4.616181 ACGCATGGCTTATTTCTAACAC 57.384 40.909 0.00 0.00 0.00 3.32
623 625 4.697828 TGAACGCATGGCTTATTTCTAACA 59.302 37.500 0.00 0.00 0.00 2.41
624 626 5.028375 GTGAACGCATGGCTTATTTCTAAC 58.972 41.667 0.00 0.00 0.00 2.34
625 627 4.201773 CGTGAACGCATGGCTTATTTCTAA 60.202 41.667 0.00 0.00 0.00 2.10
626 628 3.308595 CGTGAACGCATGGCTTATTTCTA 59.691 43.478 0.00 0.00 0.00 2.10
627 629 2.095853 CGTGAACGCATGGCTTATTTCT 59.904 45.455 0.00 0.00 0.00 2.52
628 630 2.159572 ACGTGAACGCATGGCTTATTTC 60.160 45.455 2.11 0.00 44.43 2.17
629 631 1.810151 ACGTGAACGCATGGCTTATTT 59.190 42.857 2.11 0.00 44.43 1.40
630 632 1.130373 CACGTGAACGCATGGCTTATT 59.870 47.619 10.90 0.00 44.43 1.40
631 633 0.726827 CACGTGAACGCATGGCTTAT 59.273 50.000 10.90 0.00 44.43 1.73
632 634 0.601576 ACACGTGAACGCATGGCTTA 60.602 50.000 25.01 0.00 44.43 3.09
633 635 1.891919 ACACGTGAACGCATGGCTT 60.892 52.632 25.01 0.00 44.43 4.35
634 636 2.280797 ACACGTGAACGCATGGCT 60.281 55.556 25.01 0.00 44.43 4.75
635 637 2.127270 CACACGTGAACGCATGGC 60.127 61.111 25.01 0.00 44.43 4.40
636 638 1.082821 CACACACGTGAACGCATGG 60.083 57.895 25.01 3.39 46.80 3.66
637 639 1.082821 CCACACACGTGAACGCATG 60.083 57.895 25.01 11.44 46.80 4.06
638 640 2.892334 GCCACACACGTGAACGCAT 61.892 57.895 25.01 0.00 46.80 4.73
639 641 3.568743 GCCACACACGTGAACGCA 61.569 61.111 25.01 0.00 46.80 5.24
640 642 2.892334 ATGCCACACACGTGAACGC 61.892 57.895 25.01 17.26 46.80 4.84
641 643 1.082821 CATGCCACACACGTGAACG 60.083 57.895 25.01 12.52 46.80 3.95
642 644 1.370414 GCATGCCACACACGTGAAC 60.370 57.895 25.01 6.81 46.80 3.18
643 645 2.891221 CGCATGCCACACACGTGAA 61.891 57.895 25.01 0.33 46.80 3.18
644 646 3.345011 CGCATGCCACACACGTGA 61.345 61.111 25.01 0.00 46.80 4.35
645 647 3.648982 ACGCATGCCACACACGTG 61.649 61.111 15.48 15.48 43.21 4.49
657 659 4.314440 ACGAGCCCACACACGCAT 62.314 61.111 0.00 0.00 0.00 4.73
688 690 4.297891 CACACACGCACGCCACAG 62.298 66.667 0.00 0.00 0.00 3.66
771 773 4.628333 CCACGTTCGACCATACAAACTAAT 59.372 41.667 0.00 0.00 0.00 1.73
780 782 0.968901 AGCCTCCACGTTCGACCATA 60.969 55.000 0.00 0.00 0.00 2.74
785 787 0.242825 CTAACAGCCTCCACGTTCGA 59.757 55.000 0.00 0.00 0.00 3.71
799 801 2.048597 CACGCACCCTCGCTAACA 60.049 61.111 0.00 0.00 0.00 2.41
861 2435 1.745087 ACATGATTACAGCCGGCTTTG 59.255 47.619 30.60 21.13 0.00 2.77
862 2436 2.128771 ACATGATTACAGCCGGCTTT 57.871 45.000 30.60 25.21 0.00 3.51
898 2472 6.293190 CCTTCTTTTGTACGTATTCAGCACAA 60.293 38.462 0.00 0.00 0.00 3.33
899 2473 5.178623 CCTTCTTTTGTACGTATTCAGCACA 59.821 40.000 0.00 0.00 0.00 4.57
900 2474 5.618561 CCTTCTTTTGTACGTATTCAGCAC 58.381 41.667 0.00 0.00 0.00 4.40
901 2475 4.153475 GCCTTCTTTTGTACGTATTCAGCA 59.847 41.667 0.00 0.00 0.00 4.41
902 2476 4.648970 GCCTTCTTTTGTACGTATTCAGC 58.351 43.478 0.00 0.00 0.00 4.26
903 2477 4.387862 ACGCCTTCTTTTGTACGTATTCAG 59.612 41.667 0.00 0.00 31.03 3.02
904 2478 4.309099 ACGCCTTCTTTTGTACGTATTCA 58.691 39.130 0.00 0.00 31.03 2.57
905 2479 4.916099 ACGCCTTCTTTTGTACGTATTC 57.084 40.909 0.00 0.00 31.03 1.75
906 2480 5.445845 CAAACGCCTTCTTTTGTACGTATT 58.554 37.500 0.00 0.00 32.76 1.89
907 2481 4.083696 CCAAACGCCTTCTTTTGTACGTAT 60.084 41.667 0.00 0.00 31.72 3.06
908 2482 3.248125 CCAAACGCCTTCTTTTGTACGTA 59.752 43.478 0.00 0.00 31.72 3.57
909 2483 2.032426 CCAAACGCCTTCTTTTGTACGT 59.968 45.455 0.00 0.00 31.72 3.57
910 2484 2.603652 CCCAAACGCCTTCTTTTGTACG 60.604 50.000 0.00 0.00 31.72 3.67
911 2485 2.860971 GCCCAAACGCCTTCTTTTGTAC 60.861 50.000 0.00 0.00 31.72 2.90
912 2486 1.338655 GCCCAAACGCCTTCTTTTGTA 59.661 47.619 0.00 0.00 31.72 2.41
913 2487 0.104120 GCCCAAACGCCTTCTTTTGT 59.896 50.000 0.00 0.00 31.72 2.83
914 2488 0.939106 CGCCCAAACGCCTTCTTTTG 60.939 55.000 0.00 0.00 32.96 2.44
915 2489 1.362355 CGCCCAAACGCCTTCTTTT 59.638 52.632 0.00 0.00 0.00 2.27
916 2490 3.039134 CGCCCAAACGCCTTCTTT 58.961 55.556 0.00 0.00 0.00 2.52
940 2514 0.041312 CAGTTTTCTGGCGACCAACG 60.041 55.000 0.00 0.00 43.61 4.10
941 2515 3.845625 CAGTTTTCTGGCGACCAAC 57.154 52.632 0.00 0.00 43.61 3.77
951 2525 2.154462 CGGCAAGATGGACAGTTTTCT 58.846 47.619 0.00 0.00 0.00 2.52
952 2526 1.880027 ACGGCAAGATGGACAGTTTTC 59.120 47.619 0.00 0.00 0.00 2.29
953 2527 1.981256 ACGGCAAGATGGACAGTTTT 58.019 45.000 0.00 0.00 0.00 2.43
954 2528 2.038557 ACTACGGCAAGATGGACAGTTT 59.961 45.455 0.00 0.00 0.00 2.66
955 2529 1.623811 ACTACGGCAAGATGGACAGTT 59.376 47.619 0.00 0.00 0.00 3.16
956 2530 1.204941 GACTACGGCAAGATGGACAGT 59.795 52.381 0.00 0.00 0.00 3.55
957 2531 1.478510 AGACTACGGCAAGATGGACAG 59.521 52.381 0.00 0.00 0.00 3.51
958 2532 1.557099 AGACTACGGCAAGATGGACA 58.443 50.000 0.00 0.00 0.00 4.02
959 2533 2.223758 GGTAGACTACGGCAAGATGGAC 60.224 54.545 6.54 0.00 0.00 4.02
960 2534 2.029623 GGTAGACTACGGCAAGATGGA 58.970 52.381 6.54 0.00 0.00 3.41
961 2535 2.032620 AGGTAGACTACGGCAAGATGG 58.967 52.381 6.54 0.00 0.00 3.51
962 2536 2.034812 GGAGGTAGACTACGGCAAGATG 59.965 54.545 6.54 0.00 0.00 2.90
963 2537 2.308690 GGAGGTAGACTACGGCAAGAT 58.691 52.381 6.54 0.00 0.00 2.40
964 2538 1.760192 GGAGGTAGACTACGGCAAGA 58.240 55.000 6.54 0.00 0.00 3.02
971 2545 1.012841 CACGGACGGAGGTAGACTAC 58.987 60.000 3.86 3.86 0.00 2.73
972 2546 0.904649 TCACGGACGGAGGTAGACTA 59.095 55.000 0.00 0.00 0.00 2.59
973 2547 0.392729 CTCACGGACGGAGGTAGACT 60.393 60.000 0.00 0.00 0.00 3.24
974 2548 0.676151 ACTCACGGACGGAGGTAGAC 60.676 60.000 12.45 0.00 36.70 2.59
975 2549 0.675837 CACTCACGGACGGAGGTAGA 60.676 60.000 12.45 0.00 36.70 2.59
976 2550 0.675837 TCACTCACGGACGGAGGTAG 60.676 60.000 12.45 5.04 36.70 3.18
977 2551 0.250858 TTCACTCACGGACGGAGGTA 60.251 55.000 12.45 1.26 36.70 3.08
978 2552 1.529948 TTCACTCACGGACGGAGGT 60.530 57.895 12.45 0.00 36.70 3.85
979 2553 1.080705 GTTCACTCACGGACGGAGG 60.081 63.158 12.45 4.74 36.70 4.30
980 2554 1.080705 GGTTCACTCACGGACGGAG 60.081 63.158 8.11 8.11 38.36 4.63
981 2555 1.802337 CTGGTTCACTCACGGACGGA 61.802 60.000 0.00 0.00 0.00 4.69
982 2556 1.372997 CTGGTTCACTCACGGACGG 60.373 63.158 0.00 0.00 0.00 4.79
983 2557 0.387367 CTCTGGTTCACTCACGGACG 60.387 60.000 0.00 0.00 0.00 4.79
984 2558 0.959553 TCTCTGGTTCACTCACGGAC 59.040 55.000 0.00 0.00 0.00 4.79
985 2559 1.202891 TCTCTCTGGTTCACTCACGGA 60.203 52.381 0.00 0.00 0.00 4.69
986 2560 1.201181 CTCTCTCTGGTTCACTCACGG 59.799 57.143 0.00 0.00 0.00 4.94
987 2561 1.883275 ACTCTCTCTGGTTCACTCACG 59.117 52.381 0.00 0.00 0.00 4.35
988 2562 4.521256 ACTAACTCTCTCTGGTTCACTCAC 59.479 45.833 0.00 0.00 0.00 3.51
989 2563 4.730966 ACTAACTCTCTCTGGTTCACTCA 58.269 43.478 0.00 0.00 0.00 3.41
990 2564 5.007682 AGACTAACTCTCTCTGGTTCACTC 58.992 45.833 0.00 0.00 0.00 3.51
991 2565 4.993028 AGACTAACTCTCTCTGGTTCACT 58.007 43.478 0.00 0.00 0.00 3.41
992 2566 5.355910 CCTAGACTAACTCTCTCTGGTTCAC 59.644 48.000 0.00 0.00 0.00 3.18
993 2567 5.502079 CCTAGACTAACTCTCTCTGGTTCA 58.498 45.833 0.00 0.00 0.00 3.18
994 2568 4.885325 CCCTAGACTAACTCTCTCTGGTTC 59.115 50.000 0.00 0.00 0.00 3.62
995 2569 4.862371 CCCTAGACTAACTCTCTCTGGTT 58.138 47.826 0.00 0.00 0.00 3.67
996 2570 3.372241 GCCCTAGACTAACTCTCTCTGGT 60.372 52.174 0.00 0.00 0.00 4.00
997 2571 3.219281 GCCCTAGACTAACTCTCTCTGG 58.781 54.545 0.00 0.00 0.00 3.86
998 2572 2.875933 CGCCCTAGACTAACTCTCTCTG 59.124 54.545 0.00 0.00 0.00 3.35
999 2573 2.158726 CCGCCCTAGACTAACTCTCTCT 60.159 54.545 0.00 0.00 0.00 3.10
1000 2574 2.223745 CCGCCCTAGACTAACTCTCTC 58.776 57.143 0.00 0.00 0.00 3.20
1001 2575 1.751382 GCCGCCCTAGACTAACTCTCT 60.751 57.143 0.00 0.00 0.00 3.10
1002 2576 0.669619 GCCGCCCTAGACTAACTCTC 59.330 60.000 0.00 0.00 0.00 3.20
1003 2577 0.033405 TGCCGCCCTAGACTAACTCT 60.033 55.000 0.00 0.00 0.00 3.24
1004 2578 0.822164 TTGCCGCCCTAGACTAACTC 59.178 55.000 0.00 0.00 0.00 3.01
1005 2579 0.535797 GTTGCCGCCCTAGACTAACT 59.464 55.000 0.00 0.00 0.00 2.24
1006 2580 0.248289 TGTTGCCGCCCTAGACTAAC 59.752 55.000 0.00 0.00 0.00 2.34
1007 2581 0.978151 TTGTTGCCGCCCTAGACTAA 59.022 50.000 0.00 0.00 0.00 2.24
1008 2582 0.248289 GTTGTTGCCGCCCTAGACTA 59.752 55.000 0.00 0.00 0.00 2.59
1009 2583 1.003718 GTTGTTGCCGCCCTAGACT 60.004 57.895 0.00 0.00 0.00 3.24
1010 2584 0.676782 ATGTTGTTGCCGCCCTAGAC 60.677 55.000 0.00 0.00 0.00 2.59
1011 2585 0.392461 GATGTTGTTGCCGCCCTAGA 60.392 55.000 0.00 0.00 0.00 2.43
1012 2586 1.705337 CGATGTTGTTGCCGCCCTAG 61.705 60.000 0.00 0.00 0.00 3.02
1013 2587 1.743623 CGATGTTGTTGCCGCCCTA 60.744 57.895 0.00 0.00 0.00 3.53
1014 2588 3.055719 CGATGTTGTTGCCGCCCT 61.056 61.111 0.00 0.00 0.00 5.19
1015 2589 3.361977 ACGATGTTGTTGCCGCCC 61.362 61.111 0.00 0.00 0.00 6.13
1016 2590 2.126888 CACGATGTTGTTGCCGCC 60.127 61.111 0.00 0.00 0.00 6.13
1017 2591 1.440353 GACACGATGTTGTTGCCGC 60.440 57.895 0.00 0.00 0.00 6.53
1018 2592 1.154672 CGACACGATGTTGTTGCCG 60.155 57.895 0.00 0.00 0.00 5.69
1019 2593 0.110823 GACGACACGATGTTGTTGCC 60.111 55.000 10.91 0.00 44.56 4.52
1020 2594 0.579630 TGACGACACGATGTTGTTGC 59.420 50.000 10.91 2.92 44.56 4.17
1021 2595 2.470621 CGATGACGACACGATGTTGTTG 60.471 50.000 10.91 1.92 44.56 3.33
1022 2596 1.719246 CGATGACGACACGATGTTGTT 59.281 47.619 10.91 0.00 44.56 2.83
1024 2598 1.613270 TCGATGACGACACGATGTTG 58.387 50.000 7.99 0.00 43.81 3.33
1165 2741 1.766059 CGGACATCATGGGAGGGGA 60.766 63.158 0.00 0.00 0.00 4.81
1311 2890 4.083600 GCAATCGCCGCGTCAACA 62.084 61.111 13.39 0.00 0.00 3.33
1369 2948 2.885135 TCAGGATGGAACTTGTGCAT 57.115 45.000 0.00 0.00 41.75 3.96
1446 3025 3.507233 TGAACCTTGGATGCTCAATGAAC 59.493 43.478 0.00 0.00 0.00 3.18
1572 3151 0.249676 ACTCCGACGCTGTCTCTCTA 59.750 55.000 7.03 0.00 0.00 2.43
1581 3160 2.030562 CCCAACAACTCCGACGCT 59.969 61.111 0.00 0.00 0.00 5.07
1669 3248 1.647545 GGATCCACACACCATGCACG 61.648 60.000 6.95 0.00 0.00 5.34
1878 3457 4.329545 TCCGGCAACCCACTCTGC 62.330 66.667 0.00 0.00 37.86 4.26
2043 3622 2.515398 CAGGCCAAGGGACACACA 59.485 61.111 5.01 0.00 29.21 3.72
2087 3666 3.699894 CCTCCACTGCTGACGCCT 61.700 66.667 0.00 0.00 34.43 5.52
2212 3792 1.053424 GGTGGAGTAGGTGTGACCAA 58.947 55.000 0.00 0.00 41.95 3.67
2276 3856 0.970427 TGGCGTGACTAGCATCTGGA 60.970 55.000 0.00 0.00 36.08 3.86
2333 3913 5.510349 CCAATCGCATCCAGATCTTTCTCTA 60.510 44.000 0.00 0.00 0.00 2.43
2351 3931 0.933097 CGGATCAGCTTGTCCAATCG 59.067 55.000 13.18 0.00 34.05 3.34
2388 3968 0.249120 CTGCACTCGGTTCCACCATA 59.751 55.000 0.00 0.00 38.47 2.74
2487 4067 4.222847 GGCCTCACCGGATCCGTC 62.223 72.222 31.22 13.01 37.81 4.79
2521 4101 0.460987 GTGGTCTCCTCCGAATGCAG 60.461 60.000 0.00 0.00 0.00 4.41
2549 4129 0.463654 TGCGATTATCTGTGGCACCC 60.464 55.000 16.26 0.00 0.00 4.61
2812 4392 0.614697 TCCACAGCTGGAATCGGAGA 60.615 55.000 19.93 0.00 44.26 3.71
2910 4490 1.270041 GGTGGCGCCAATTTCTTCAAA 60.270 47.619 34.66 0.00 37.17 2.69
2950 4530 1.922447 TGGTCTAACTCCATTGGCCAT 59.078 47.619 6.09 0.00 0.00 4.40
3054 4634 0.610687 CCGAGGGCTTTGAGAAGACT 59.389 55.000 0.00 0.00 40.95 3.24
3086 4668 2.076100 CCGTTTGTGATTGCTAGCTCA 58.924 47.619 17.23 9.52 0.00 4.26
3092 4674 1.538047 ATGCTCCGTTTGTGATTGCT 58.462 45.000 0.00 0.00 0.00 3.91
3102 4684 0.884704 AGTTGCGACAATGCTCCGTT 60.885 50.000 6.90 0.00 35.36 4.44
3104 4686 0.179215 GAAGTTGCGACAATGCTCCG 60.179 55.000 6.90 0.00 35.36 4.63
3161 4743 1.067416 GATGGCAGCGATGGTACGA 59.933 57.895 1.46 0.00 35.09 3.43
3235 4817 1.377333 GGGTGGACAACTGCCTAGC 60.377 63.158 0.00 0.00 0.00 3.42
3266 4848 0.110238 CACGCGTGACATGGAAAAGG 60.110 55.000 34.93 0.93 0.00 3.11
3268 4850 1.300481 TTCACGCGTGACATGGAAAA 58.700 45.000 39.38 20.91 39.66 2.29
3330 4913 2.563179 TCTCAACGCTTTTCTCCTAGCT 59.437 45.455 0.00 0.00 35.25 3.32
3489 5072 3.075283 TCCACACCAAAATGATACCACCT 59.925 43.478 0.00 0.00 0.00 4.00
3726 5310 2.434336 TGGCATTACTCTTATCAGCCGT 59.566 45.455 0.00 0.00 43.35 5.68
3755 5339 7.715249 CGTCTAAATTTTCCCATCATTCTCCTA 59.285 37.037 0.00 0.00 0.00 2.94
3971 5556 4.962362 TGTAAGTGATCCTCCATAGCAAGA 59.038 41.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.