Multiple sequence alignment - TraesCS3B01G566500

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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 TraesCS3B01G566500 chr3B 100.000 5283 0 0 1 5283 798457184 798462466 0 9756
1 TraesCS3B01G566500 chr3D 89.496 4722 302 92 580 5230 595015892 595020490 0 5794
2 TraesCS3B01G566500 chr3A 89.832 3757 250 64 580 4281 726016621 726020300 0 4700
3 TraesCS3B01G566500 chr3A 88.583 981 70 19 4279 5230 726020423 726021390 0 1153
4 TraesCS3B01G566500 chr3A 96.522 575 18 2 1 573 547190736 547190162 0 950
5 TraesCS3B01G566500 chr2B 96.696 575 17 2 1 573 82063481 82062907 0 955
6 TraesCS3B01G566500 chr2B 96.373 579 18 3 1 576 659008756 659008178 0 950
7 TraesCS3B01G566500 chr6B 96.354 576 19 2 1 574 624524130 624524705 0 946
8 TraesCS3B01G566500 chr6B 96.348 575 19 2 1 573 135432191 135431617 0 944
9 TraesCS3B01G566500 chr6B 96.194 578 20 2 1 576 633348486 633347909 0 944
10 TraesCS3B01G566500 chr6B 96.187 577 20 2 1 575 645574248 645574824 0 942
11 TraesCS3B01G566500 chr4B 96.510 573 19 1 1 572 347642989 347643561 0 946
12 TraesCS3B01G566500 chr1B 96.354 576 20 1 1 575 678138218 678138793 0 946


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 TraesCS3B01G566500 chr3B 798457184 798462466 5282 False 9756.0 9756 100.0000 1 5283 1 chr3B.!!$F1 5282
1 TraesCS3B01G566500 chr3D 595015892 595020490 4598 False 5794.0 5794 89.4960 580 5230 1 chr3D.!!$F1 4650
2 TraesCS3B01G566500 chr3A 726016621 726021390 4769 False 2926.5 4700 89.2075 580 5230 2 chr3A.!!$F1 4650
3 TraesCS3B01G566500 chr3A 547190162 547190736 574 True 950.0 950 96.5220 1 573 1 chr3A.!!$R1 572
4 TraesCS3B01G566500 chr2B 82062907 82063481 574 True 955.0 955 96.6960 1 573 1 chr2B.!!$R1 572
5 TraesCS3B01G566500 chr2B 659008178 659008756 578 True 950.0 950 96.3730 1 576 1 chr2B.!!$R2 575
6 TraesCS3B01G566500 chr6B 624524130 624524705 575 False 946.0 946 96.3540 1 574 1 chr6B.!!$F1 573
7 TraesCS3B01G566500 chr6B 135431617 135432191 574 True 944.0 944 96.3480 1 573 1 chr6B.!!$R1 572
8 TraesCS3B01G566500 chr6B 633347909 633348486 577 True 944.0 944 96.1940 1 576 1 chr6B.!!$R2 575
9 TraesCS3B01G566500 chr6B 645574248 645574824 576 False 942.0 942 96.1870 1 575 1 chr6B.!!$F2 574
10 TraesCS3B01G566500 chr4B 347642989 347643561 572 False 946.0 946 96.5100 1 572 1 chr4B.!!$F1 571
11 TraesCS3B01G566500 chr1B 678138218 678138793 575 False 946.0 946 96.3540 1 575 1 chr1B.!!$F1 574

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
667 673 0.108424 CTTTCTCGTCTCCCTGCCTG 60.108 60.0 0.0 0.0 0.00 4.85 F
1463 1479 0.750182 CACTCCCTCTCCGTCTCCTC 60.750 65.0 0.0 0.0 0.00 3.71 F
1874 1905 0.107214 GATCGGAATCTGCCCACCAA 60.107 55.0 0.0 0.0 0.00 3.67 F
3393 3458 0.179034 CCATAAGGGACAGCAGGCTC 60.179 60.0 0.0 0.0 40.01 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 1886 0.107214 TTGGTGGGCAGATTCCGATC 60.107 55.0 0.00 0.00 0.00 3.69 R
2355 2389 0.659427 CGCCATCTGCATCGACAATT 59.341 50.0 0.00 0.00 41.33 2.32 R
3706 3771 0.241213 TGGACGAGCTTCGAGAAGTG 59.759 55.0 13.58 7.32 43.74 3.16 R
4683 4933 0.473501 GAGGAGGCCATGGAGGATCT 60.474 60.0 18.40 5.31 41.22 2.75 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
406 408 1.338107 TCGTTGTGTGAGAGGGTGAT 58.662 50.000 0.00 0.00 0.00 3.06
475 479 0.767446 TAAAACGGGTGGGAGGTGGA 60.767 55.000 0.00 0.00 0.00 4.02
484 488 1.982958 GTGGGAGGTGGAAGGAAGTAA 59.017 52.381 0.00 0.00 0.00 2.24
521 525 4.567597 ACCGGGTGAGGTGGGACA 62.568 66.667 6.32 0.00 44.07 4.02
532 536 5.069914 GGTGAGGTGGGACAAAAATAAAACT 59.930 40.000 0.00 0.00 44.16 2.66
539 543 6.752815 GTGGGACAAAAATAAAACTCGAAACA 59.247 34.615 0.00 0.00 44.16 2.83
575 579 8.918202 ACTGAGACATTAGGAGTAGAGATAAG 57.082 38.462 0.00 0.00 0.00 1.73
577 581 6.717540 TGAGACATTAGGAGTAGAGATAAGGC 59.282 42.308 0.00 0.00 0.00 4.35
578 582 6.615617 AGACATTAGGAGTAGAGATAAGGCA 58.384 40.000 0.00 0.00 0.00 4.75
579 583 7.069986 AGACATTAGGAGTAGAGATAAGGCAA 58.930 38.462 0.00 0.00 0.00 4.52
580 584 7.232534 AGACATTAGGAGTAGAGATAAGGCAAG 59.767 40.741 0.00 0.00 0.00 4.01
581 585 5.793030 TTAGGAGTAGAGATAAGGCAAGC 57.207 43.478 0.00 0.00 0.00 4.01
598 602 3.532155 CGGAGAGGGGGCGAGAAG 61.532 72.222 0.00 0.00 0.00 2.85
621 625 1.145119 AGAAAAGGAAAAGCCGAGGGT 59.855 47.619 0.00 0.00 43.43 4.34
622 626 1.269723 GAAAAGGAAAAGCCGAGGGTG 59.730 52.381 0.00 0.00 43.43 4.61
623 627 0.539669 AAAGGAAAAGCCGAGGGTGG 60.540 55.000 0.00 0.00 43.43 4.61
628 632 1.472878 GAAAAGCCGAGGGTGGAATTC 59.527 52.381 0.00 0.00 0.00 2.17
630 634 3.202706 GCCGAGGGTGGAATTCGC 61.203 66.667 0.00 0.00 33.25 4.70
663 669 1.205893 CCTTCCTTTCTCGTCTCCCTG 59.794 57.143 0.00 0.00 0.00 4.45
665 671 1.219393 CCTTTCTCGTCTCCCTGCC 59.781 63.158 0.00 0.00 0.00 4.85
667 673 0.108424 CTTTCTCGTCTCCCTGCCTG 60.108 60.000 0.00 0.00 0.00 4.85
669 675 4.154347 CTCGTCTCCCTGCCTGCC 62.154 72.222 0.00 0.00 0.00 4.85
671 677 4.463879 CGTCTCCCTGCCTGCCTG 62.464 72.222 0.00 0.00 0.00 4.85
679 685 3.709348 CTGCCTGCCTGCCTGCATA 62.709 63.158 3.59 0.00 41.16 3.14
681 687 2.273123 CCTGCCTGCCTGCATACA 59.727 61.111 0.00 0.00 41.16 2.29
682 688 2.117156 CCTGCCTGCCTGCATACAC 61.117 63.158 0.00 0.00 41.16 2.90
703 712 3.605749 CTCGCGCCTTCCTCCCAAA 62.606 63.158 0.00 0.00 0.00 3.28
704 713 2.438434 CGCGCCTTCCTCCCAAAT 60.438 61.111 0.00 0.00 0.00 2.32
709 718 1.686115 CGCCTTCCTCCCAAATCCAAT 60.686 52.381 0.00 0.00 0.00 3.16
713 722 3.310141 CCTTCCTCCCAAATCCAATTCCT 60.310 47.826 0.00 0.00 0.00 3.36
720 729 4.233989 TCCCAAATCCAATTCCTAATCCCA 59.766 41.667 0.00 0.00 0.00 4.37
721 730 4.968080 CCCAAATCCAATTCCTAATCCCAA 59.032 41.667 0.00 0.00 0.00 4.12
748 757 2.379459 GCCTCCCCCTTCCTTCCTC 61.379 68.421 0.00 0.00 0.00 3.71
831 840 3.712881 GCAAGCCACACGACCGAC 61.713 66.667 0.00 0.00 0.00 4.79
948 964 0.751452 CCTAGCTAGGGTTTCCGGTC 59.249 60.000 29.47 0.00 39.86 4.79
954 970 3.492068 GGGTTTCCGGTCCCTTCT 58.508 61.111 19.43 0.00 40.48 2.85
955 971 1.298993 GGGTTTCCGGTCCCTTCTC 59.701 63.158 19.43 0.00 40.48 2.87
956 972 1.298993 GGTTTCCGGTCCCTTCTCC 59.701 63.158 0.00 0.00 0.00 3.71
957 973 1.298993 GTTTCCGGTCCCTTCTCCC 59.701 63.158 0.00 0.00 0.00 4.30
1230 1246 2.583593 GCCTACTTCCGCTCGCTG 60.584 66.667 0.00 0.00 0.00 5.18
1457 1473 2.218115 CTCTCCCACTCCCTCTCCGT 62.218 65.000 0.00 0.00 0.00 4.69
1459 1475 2.218115 CTCCCACTCCCTCTCCGTCT 62.218 65.000 0.00 0.00 0.00 4.18
1460 1476 1.755008 CCCACTCCCTCTCCGTCTC 60.755 68.421 0.00 0.00 0.00 3.36
1462 1478 1.304952 CACTCCCTCTCCGTCTCCT 59.695 63.158 0.00 0.00 0.00 3.69
1463 1479 0.750182 CACTCCCTCTCCGTCTCCTC 60.750 65.000 0.00 0.00 0.00 3.71
1776 1807 1.738099 CTCGCCGTGGGACTTCTTG 60.738 63.158 0.00 0.00 0.00 3.02
1874 1905 0.107214 GATCGGAATCTGCCCACCAA 60.107 55.000 0.00 0.00 0.00 3.67
1993 2024 1.696832 GGCCGTCGTTGAAGATCAGC 61.697 60.000 0.00 0.00 0.00 4.26
2009 2040 3.119096 GCGCGTGAAGGGGAAGAC 61.119 66.667 8.43 0.00 0.00 3.01
2034 2065 0.613777 CTCCTGGTCCTACCACCAAC 59.386 60.000 0.00 0.00 44.79 3.77
2222 2253 2.031120 CTTGAAGGGTGCCAACTTTGA 58.969 47.619 0.00 0.00 0.00 2.69
2236 2267 2.241160 ACTTTGATGACATTGCTGGCA 58.759 42.857 0.00 0.00 46.86 4.92
2248 2279 3.076092 CTGGCAGCAACTCCTCCT 58.924 61.111 0.00 0.00 0.00 3.69
2249 2280 1.078567 CTGGCAGCAACTCCTCCTC 60.079 63.158 0.00 0.00 0.00 3.71
2250 2281 2.270527 GGCAGCAACTCCTCCTCC 59.729 66.667 0.00 0.00 0.00 4.30
2251 2282 2.125350 GCAGCAACTCCTCCTCCG 60.125 66.667 0.00 0.00 0.00 4.63
2253 2284 1.515020 CAGCAACTCCTCCTCCGAG 59.485 63.158 0.00 0.00 35.72 4.63
2355 2389 1.526887 GATTGATGAGGCCGGGTCA 59.473 57.895 2.18 0.00 0.00 4.02
2397 2431 2.813908 GGTAGCCACGGCAAGTCG 60.814 66.667 11.35 0.00 44.88 4.18
2472 2506 0.323816 AGAGAGATGTCGTGGAGGCA 60.324 55.000 0.00 0.00 39.68 4.75
2505 2539 2.786495 GGAGCGATTCGAGGAGGCA 61.786 63.158 10.88 0.00 0.00 4.75
2630 2664 5.069318 TGGAGCAACACATGTCTGAAATTA 58.931 37.500 8.37 0.00 0.00 1.40
2633 2667 5.957798 AGCAACACATGTCTGAAATTATGG 58.042 37.500 8.37 0.00 0.00 2.74
2646 2682 6.434028 TCTGAAATTATGGTATATGGGCAAGC 59.566 38.462 0.00 0.00 0.00 4.01
2648 2684 4.568072 ATTATGGTATATGGGCAAGCGA 57.432 40.909 0.00 0.00 0.00 4.93
2649 2685 2.185004 ATGGTATATGGGCAAGCGAC 57.815 50.000 0.00 0.00 0.00 5.19
2651 2687 1.202639 TGGTATATGGGCAAGCGACTG 60.203 52.381 0.00 0.00 0.00 3.51
2652 2688 1.070134 GGTATATGGGCAAGCGACTGA 59.930 52.381 0.00 0.00 0.00 3.41
2655 2691 1.737838 TATGGGCAAGCGACTGAAAG 58.262 50.000 0.00 0.00 42.29 2.62
2657 2693 1.600916 GGGCAAGCGACTGAAAGGT 60.601 57.895 0.00 0.00 39.30 3.50
2662 2698 1.939934 CAAGCGACTGAAAGGTTGACA 59.060 47.619 1.70 0.00 45.46 3.58
2663 2699 2.549754 CAAGCGACTGAAAGGTTGACAT 59.450 45.455 1.70 0.00 45.46 3.06
2665 2701 4.207891 AGCGACTGAAAGGTTGACATAT 57.792 40.909 0.00 0.00 39.30 1.78
2719 2756 0.390492 TGATGGAGCCTATGTCGCTG 59.610 55.000 0.00 0.00 36.48 5.18
2722 2759 1.300542 GGAGCCTATGTCGCTGAGC 60.301 63.158 0.00 0.00 36.48 4.26
2778 2815 2.098831 GGCGCTCAAGGTTACCGAC 61.099 63.158 7.64 0.00 0.00 4.79
2793 2830 0.824109 CCGACCACCTCAGCTTCATA 59.176 55.000 0.00 0.00 0.00 2.15
2794 2831 1.414181 CCGACCACCTCAGCTTCATAT 59.586 52.381 0.00 0.00 0.00 1.78
2800 2837 2.357009 CACCTCAGCTTCATATGCCAAC 59.643 50.000 0.00 0.00 0.00 3.77
2816 2853 2.094659 AACGGCAGAGAACATCGCG 61.095 57.895 0.00 0.00 0.00 5.87
2881 2918 6.227522 GGAAAAGAAGCTATATCAGGAGGTC 58.772 44.000 0.00 0.00 0.00 3.85
2932 2969 4.456911 ACAAGCTACAAGTGTCCATTCATG 59.543 41.667 0.00 0.00 0.00 3.07
2957 2994 8.736244 TGTTATCTCTTTATTTACTGCCCAAAC 58.264 33.333 0.00 0.00 0.00 2.93
3061 3098 1.810030 GCTAGACGAACAAGGGGCG 60.810 63.158 0.00 0.00 0.00 6.13
3108 3145 4.980805 GTCGGTGCGGGACTTGCA 62.981 66.667 0.00 0.00 40.70 4.08
3121 3158 1.651138 GACTTGCAGTCGAAGATCACG 59.349 52.381 0.00 0.28 40.67 4.35
3133 3170 4.800471 TCGAAGATCACGATCAACATCAAG 59.200 41.667 9.60 0.00 40.22 3.02
3202 3239 2.300437 ACTCTACCCTCAGCTTGTTGAC 59.700 50.000 0.00 0.00 0.00 3.18
3234 3298 5.675538 AGGGTATGATGAAGTTCTAGTTGC 58.324 41.667 4.17 0.00 0.00 4.17
3250 3314 2.798976 TTGCTCCACAACTTCATTGC 57.201 45.000 0.00 0.00 42.62 3.56
3305 3370 4.757594 TCATTGCTGCTCTTGTTTTTGTT 58.242 34.783 0.00 0.00 0.00 2.83
3306 3371 4.567558 TCATTGCTGCTCTTGTTTTTGTTG 59.432 37.500 0.00 0.00 0.00 3.33
3349 3414 1.003580 GGATGTGGAAGGCAGTTCTGA 59.996 52.381 3.84 0.00 35.25 3.27
3393 3458 0.179034 CCATAAGGGACAGCAGGCTC 60.179 60.000 0.00 0.00 40.01 4.70
3483 3548 0.606604 AGCTCACGAAATGGTACCGT 59.393 50.000 7.57 3.49 36.95 4.83
3500 3565 1.608590 CCGTTGCTTCAACAAGTGGAT 59.391 47.619 9.90 0.00 43.70 3.41
3528 3593 1.115467 AGAGGTCTTATGTGGAGGCG 58.885 55.000 0.00 0.00 0.00 5.52
3534 3599 1.009829 CTTATGTGGAGGCGCTGAAC 58.990 55.000 7.64 1.46 0.00 3.18
3669 3734 4.090588 TGGTTCCGGGCCATCGAC 62.091 66.667 13.50 0.00 0.00 4.20
3706 3771 1.710339 GCGCTGAAGTCAATCGACC 59.290 57.895 0.00 0.00 43.73 4.79
3713 3778 3.914312 TGAAGTCAATCGACCACTTCTC 58.086 45.455 23.37 8.72 44.32 2.87
3714 3779 2.638556 AGTCAATCGACCACTTCTCG 57.361 50.000 0.00 0.00 43.73 4.04
3741 3806 1.153667 CCACGAGCTGAGGAAGAGC 60.154 63.158 0.00 0.00 36.65 4.09
3747 3812 1.220477 GCTGAGGAAGAGCCAGGAC 59.780 63.158 0.00 0.00 40.02 3.85
3754 3819 2.875684 GAAGAGCCAGGACGACGAGC 62.876 65.000 0.00 0.00 0.00 5.03
3923 3988 1.829849 TCTGCACAAGATGAGGAGGAG 59.170 52.381 0.00 0.00 28.44 3.69
3924 3989 0.907486 TGCACAAGATGAGGAGGAGG 59.093 55.000 0.00 0.00 0.00 4.30
3932 3997 0.690411 ATGAGGAGGAGGCTGGACAG 60.690 60.000 0.00 0.00 0.00 3.51
4041 4106 0.107945 AGATCGCTGGCTTCTTCCAC 60.108 55.000 0.00 0.00 31.74 4.02
4044 4109 2.747855 GCTGGCTTCTTCCACGGG 60.748 66.667 0.00 0.00 31.74 5.28
4140 4226 3.136123 CTTGGCTGACGGCATGGG 61.136 66.667 8.86 0.00 45.87 4.00
4145 4231 2.438975 CTGACGGCATGGGCATGT 60.439 61.111 0.00 0.00 43.71 3.21
4147 4233 2.124570 GACGGCATGGGCATGTCT 60.125 61.111 0.00 0.00 41.05 3.41
4148 4234 1.750399 GACGGCATGGGCATGTCTT 60.750 57.895 0.00 0.00 41.05 3.01
4149 4235 1.304381 ACGGCATGGGCATGTCTTT 60.304 52.632 0.00 0.00 41.05 2.52
4151 4237 1.153509 GGCATGGGCATGTCTTTGC 60.154 57.895 14.15 14.15 43.71 3.68
4152 4238 1.592743 GCATGGGCATGTCTTTGCA 59.407 52.632 16.60 0.00 44.59 4.08
4153 4239 0.459585 GCATGGGCATGTCTTTGCAG 60.460 55.000 16.60 0.00 44.59 4.41
4154 4240 1.179152 CATGGGCATGTCTTTGCAGA 58.821 50.000 0.00 0.00 44.59 4.26
4155 4241 1.546923 CATGGGCATGTCTTTGCAGAA 59.453 47.619 0.00 0.00 44.59 3.02
4156 4242 1.250328 TGGGCATGTCTTTGCAGAAG 58.750 50.000 0.00 0.00 44.59 2.85
4157 4243 1.202915 TGGGCATGTCTTTGCAGAAGA 60.203 47.619 0.00 7.09 44.59 2.87
4158 4244 1.471684 GGGCATGTCTTTGCAGAAGAG 59.528 52.381 10.39 3.19 44.59 2.85
4159 4245 2.430465 GGCATGTCTTTGCAGAAGAGA 58.570 47.619 10.39 10.01 44.59 3.10
4160 4246 2.816087 GGCATGTCTTTGCAGAAGAGAA 59.184 45.455 10.39 4.77 44.59 2.87
4161 4247 3.119919 GGCATGTCTTTGCAGAAGAGAAG 60.120 47.826 10.39 8.35 44.59 2.85
4162 4248 3.750130 GCATGTCTTTGCAGAAGAGAAGA 59.250 43.478 10.39 2.48 42.31 2.87
4163 4249 4.378253 GCATGTCTTTGCAGAAGAGAAGAC 60.378 45.833 16.35 16.35 45.04 3.01
4165 4251 4.988708 GTCTTTGCAGAAGAGAAGACAG 57.011 45.455 17.70 0.00 44.50 3.51
4188 4275 4.974645 TTTTGTGACTGAGGTGGTAGAT 57.025 40.909 0.00 0.00 0.00 1.98
4191 4278 3.713003 TGTGACTGAGGTGGTAGATGAT 58.287 45.455 0.00 0.00 0.00 2.45
4213 4307 1.322538 GGGGTAGTGCTGGGCATTTG 61.323 60.000 0.00 0.00 41.91 2.32
4254 4349 0.254747 TCATTCTGGGGTTTAGGCCG 59.745 55.000 0.00 0.00 0.00 6.13
4260 4355 0.325602 TGGGGTTTAGGCCGTAGTTG 59.674 55.000 0.00 0.00 0.00 3.16
4293 4514 7.255242 CGGTTACGGTGGTAGATTAGATAGAAA 60.255 40.741 0.00 0.00 36.18 2.52
4294 4515 8.416329 GGTTACGGTGGTAGATTAGATAGAAAA 58.584 37.037 0.00 0.00 0.00 2.29
4295 4516 9.242477 GTTACGGTGGTAGATTAGATAGAAAAC 57.758 37.037 0.00 0.00 0.00 2.43
4333 4554 2.668279 CGTTTTTACTGATGGTGCCTGC 60.668 50.000 0.00 0.00 0.00 4.85
4336 4557 0.035152 TTACTGATGGTGCCTGCCTG 60.035 55.000 0.00 0.00 0.00 4.85
4339 4560 2.194388 CTGATGGTGCCTGCCTGACT 62.194 60.000 0.00 0.00 0.00 3.41
4357 4584 1.077993 ACTCACAGTAGAGGGGAGCTT 59.922 52.381 0.00 0.00 39.97 3.74
4360 4587 1.480137 CACAGTAGAGGGGAGCTTCAG 59.520 57.143 0.00 0.00 0.00 3.02
4362 4589 2.225394 ACAGTAGAGGGGAGCTTCAGAA 60.225 50.000 0.00 0.00 0.00 3.02
4379 4606 1.202818 AGAAGTTTCAGTGGTGCTCCC 60.203 52.381 1.59 0.00 0.00 4.30
4395 4629 5.594317 GGTGCTCCCATTTATTCTGTACATT 59.406 40.000 0.00 0.00 0.00 2.71
4400 4634 8.850156 GCTCCCATTTATTCTGTACATTGTTAT 58.150 33.333 0.00 0.00 0.00 1.89
4455 4690 7.275888 TCATTTTAGCAATGTGTTTGAGAGT 57.724 32.000 0.00 0.00 37.53 3.24
4503 4740 3.897819 CGCTACTTCGCATTTTCCC 57.102 52.632 0.00 0.00 0.00 3.97
4504 4741 0.377203 CGCTACTTCGCATTTTCCCC 59.623 55.000 0.00 0.00 0.00 4.81
4513 4754 4.289238 TCGCATTTTCCCCTTAACTGTA 57.711 40.909 0.00 0.00 0.00 2.74
4550 4791 3.223435 TCCCTTGAAACATAAACGGCAA 58.777 40.909 0.00 0.00 0.00 4.52
4577 4818 6.569994 GCTTCATTGCATTATTCCAGGATCTC 60.570 42.308 0.00 0.00 0.00 2.75
4584 4825 5.973565 GCATTATTCCAGGATCTCAAAAACG 59.026 40.000 0.00 0.00 0.00 3.60
4640 4881 2.261172 ATCGGTTCATCGTCGTCGCA 62.261 55.000 0.00 0.00 36.96 5.10
4646 4887 1.990799 TCATCGTCGTCGCATTTTCT 58.009 45.000 0.00 0.00 36.96 2.52
4649 4890 3.921630 TCATCGTCGTCGCATTTTCTTTA 59.078 39.130 0.00 0.00 36.96 1.85
4650 4891 3.693300 TCGTCGTCGCATTTTCTTTAC 57.307 42.857 0.00 0.00 36.96 2.01
4652 4893 2.410730 CGTCGTCGCATTTTCTTTACCT 59.589 45.455 0.00 0.00 0.00 3.08
4666 4908 5.156608 TCTTTACCTTTGTGCCTACTACC 57.843 43.478 0.00 0.00 0.00 3.18
4683 4933 2.047655 CGACCCCTAAGCGCAACA 60.048 61.111 11.47 0.00 0.00 3.33
4696 4946 1.442526 CGCAACAGATCCTCCATGGC 61.443 60.000 6.96 0.00 35.26 4.40
4717 4967 0.984230 TCCTCACTGGACCCAACATC 59.016 55.000 0.00 0.00 40.56 3.06
4718 4968 0.987294 CCTCACTGGACCCAACATCT 59.013 55.000 0.00 0.00 38.35 2.90
4725 4975 4.637534 CACTGGACCCAACATCTCAAATAG 59.362 45.833 0.00 0.00 0.00 1.73
4799 5050 0.672401 TCCGTCAGGCCATCGAAAAC 60.672 55.000 5.01 0.00 37.47 2.43
4822 5073 4.219507 CAGGTAGATGTCCAGGTATAGCAG 59.780 50.000 4.48 0.00 0.00 4.24
4849 5100 3.325293 TCTCAGCATCTCCTGAACAAC 57.675 47.619 0.00 0.00 41.02 3.32
4860 5111 1.891060 CTGAACAACTCCGCTGCGTC 61.891 60.000 21.59 10.27 0.00 5.19
4872 5124 4.111016 TGCGTCCCAGCTACGTCG 62.111 66.667 9.12 2.49 42.26 5.12
4892 5147 1.452399 GCCGCGAGATTCTATTTCGTC 59.548 52.381 8.23 0.00 36.74 4.20
4894 5149 2.820656 GCGAGATTCTATTTCGTCGC 57.179 50.000 0.00 0.00 45.00 5.19
4901 5162 3.726595 CTATTTCGTCGCGGCCCCA 62.727 63.158 4.51 0.00 0.00 4.96
4902 5163 2.989055 CTATTTCGTCGCGGCCCCAT 62.989 60.000 4.51 0.00 0.00 4.00
4927 5188 3.467803 ACGCAACTTCTATTGATAGGGC 58.532 45.455 0.00 0.00 0.00 5.19
5062 5329 2.202756 GGCGACGGACCTCATCAC 60.203 66.667 0.00 0.00 0.00 3.06
5084 5351 0.710567 CTTGCTGTCGCTTGTACTCG 59.289 55.000 0.00 0.00 36.97 4.18
5222 5489 7.430441 TCATCGAAATATGAGTTGTATCGGAA 58.570 34.615 0.00 0.00 32.18 4.30
5226 5493 6.346120 CGAAATATGAGTTGTATCGGAAGCAG 60.346 42.308 0.00 0.00 0.00 4.24
5227 5494 5.791336 ATATGAGTTGTATCGGAAGCAGA 57.209 39.130 0.00 0.00 0.00 4.26
5228 5495 4.679373 ATGAGTTGTATCGGAAGCAGAT 57.321 40.909 0.00 0.00 0.00 2.90
5229 5496 4.046938 TGAGTTGTATCGGAAGCAGATC 57.953 45.455 0.00 0.00 0.00 2.75
5230 5497 3.447229 TGAGTTGTATCGGAAGCAGATCA 59.553 43.478 0.00 0.00 0.00 2.92
5231 5498 4.081697 TGAGTTGTATCGGAAGCAGATCAA 60.082 41.667 0.00 0.00 0.00 2.57
5232 5499 4.832248 AGTTGTATCGGAAGCAGATCAAA 58.168 39.130 0.00 0.00 0.00 2.69
5233 5500 5.431765 AGTTGTATCGGAAGCAGATCAAAT 58.568 37.500 0.00 0.00 0.00 2.32
5234 5501 5.882557 AGTTGTATCGGAAGCAGATCAAATT 59.117 36.000 0.00 0.00 0.00 1.82
5235 5502 6.375455 AGTTGTATCGGAAGCAGATCAAATTT 59.625 34.615 0.00 0.00 0.00 1.82
5236 5503 6.122850 TGTATCGGAAGCAGATCAAATTTG 57.877 37.500 12.15 12.15 0.00 2.32
5237 5504 5.647658 TGTATCGGAAGCAGATCAAATTTGT 59.352 36.000 17.47 5.61 0.00 2.83
5238 5505 4.685169 TCGGAAGCAGATCAAATTTGTC 57.315 40.909 17.47 13.64 0.00 3.18
5239 5506 3.125146 TCGGAAGCAGATCAAATTTGTCG 59.875 43.478 17.47 11.17 0.00 4.35
5240 5507 3.125146 CGGAAGCAGATCAAATTTGTCGA 59.875 43.478 17.47 0.00 0.00 4.20
5241 5508 4.656041 GGAAGCAGATCAAATTTGTCGAG 58.344 43.478 17.47 12.49 0.00 4.04
5242 5509 3.754188 AGCAGATCAAATTTGTCGAGC 57.246 42.857 17.47 19.16 0.00 5.03
5243 5510 3.341823 AGCAGATCAAATTTGTCGAGCT 58.658 40.909 17.47 20.56 0.00 4.09
5244 5511 3.126514 AGCAGATCAAATTTGTCGAGCTG 59.873 43.478 24.41 20.77 44.09 4.24
5245 5512 3.125829 GCAGATCAAATTTGTCGAGCTGA 59.874 43.478 21.22 1.94 44.02 4.26
5246 5513 4.378770 GCAGATCAAATTTGTCGAGCTGAA 60.379 41.667 21.22 1.32 44.02 3.02
5247 5514 5.692814 CAGATCAAATTTGTCGAGCTGAAA 58.307 37.500 17.47 0.00 44.02 2.69
5248 5515 6.320171 CAGATCAAATTTGTCGAGCTGAAAT 58.680 36.000 17.47 0.08 44.02 2.17
5249 5516 6.468319 CAGATCAAATTTGTCGAGCTGAAATC 59.532 38.462 17.47 9.05 44.02 2.17
5250 5517 5.947228 TCAAATTTGTCGAGCTGAAATCT 57.053 34.783 17.47 0.00 0.00 2.40
5251 5518 6.317789 TCAAATTTGTCGAGCTGAAATCTT 57.682 33.333 17.47 0.00 0.00 2.40
5252 5519 6.144854 TCAAATTTGTCGAGCTGAAATCTTG 58.855 36.000 17.47 0.00 0.00 3.02
5253 5520 5.947228 AATTTGTCGAGCTGAAATCTTGA 57.053 34.783 0.00 0.00 0.00 3.02
5254 5521 4.997905 TTTGTCGAGCTGAAATCTTGAG 57.002 40.909 0.00 0.00 0.00 3.02
5255 5522 2.964740 TGTCGAGCTGAAATCTTGAGG 58.035 47.619 0.00 0.00 0.00 3.86
5256 5523 2.562738 TGTCGAGCTGAAATCTTGAGGA 59.437 45.455 0.00 0.00 0.00 3.71
5257 5524 3.006859 TGTCGAGCTGAAATCTTGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
5258 5525 3.997021 GTCGAGCTGAAATCTTGAGGAAA 59.003 43.478 0.00 0.00 0.00 3.13
5259 5526 4.633565 GTCGAGCTGAAATCTTGAGGAAAT 59.366 41.667 0.00 0.00 0.00 2.17
5260 5527 4.633126 TCGAGCTGAAATCTTGAGGAAATG 59.367 41.667 0.00 0.00 0.00 2.32
5261 5528 4.394300 CGAGCTGAAATCTTGAGGAAATGT 59.606 41.667 0.00 0.00 0.00 2.71
5262 5529 5.106396 CGAGCTGAAATCTTGAGGAAATGTT 60.106 40.000 0.00 0.00 0.00 2.71
5263 5530 6.022163 AGCTGAAATCTTGAGGAAATGTTG 57.978 37.500 0.00 0.00 0.00 3.33
5264 5531 5.047519 AGCTGAAATCTTGAGGAAATGTTGG 60.048 40.000 0.00 0.00 0.00 3.77
5265 5532 5.717119 CTGAAATCTTGAGGAAATGTTGGG 58.283 41.667 0.00 0.00 0.00 4.12
5266 5533 4.021192 TGAAATCTTGAGGAAATGTTGGGC 60.021 41.667 0.00 0.00 0.00 5.36
5267 5534 2.978156 TCTTGAGGAAATGTTGGGCT 57.022 45.000 0.00 0.00 0.00 5.19
5268 5535 4.591321 ATCTTGAGGAAATGTTGGGCTA 57.409 40.909 0.00 0.00 0.00 3.93
5269 5536 4.591321 TCTTGAGGAAATGTTGGGCTAT 57.409 40.909 0.00 0.00 0.00 2.97
5270 5537 5.708736 TCTTGAGGAAATGTTGGGCTATA 57.291 39.130 0.00 0.00 0.00 1.31
5271 5538 6.073447 TCTTGAGGAAATGTTGGGCTATAA 57.927 37.500 0.00 0.00 0.00 0.98
5272 5539 6.489603 TCTTGAGGAAATGTTGGGCTATAAA 58.510 36.000 0.00 0.00 0.00 1.40
5273 5540 6.603201 TCTTGAGGAAATGTTGGGCTATAAAG 59.397 38.462 0.00 0.00 0.00 1.85
5274 5541 5.200483 TGAGGAAATGTTGGGCTATAAAGG 58.800 41.667 0.00 0.00 0.00 3.11
5275 5542 5.044476 TGAGGAAATGTTGGGCTATAAAGGA 60.044 40.000 0.00 0.00 0.00 3.36
5276 5543 5.201243 AGGAAATGTTGGGCTATAAAGGAC 58.799 41.667 0.00 0.00 0.00 3.85
5277 5544 4.036380 GGAAATGTTGGGCTATAAAGGACG 59.964 45.833 0.00 0.00 0.00 4.79
5278 5545 2.702592 TGTTGGGCTATAAAGGACGG 57.297 50.000 0.00 0.00 0.00 4.79
5279 5546 1.306148 GTTGGGCTATAAAGGACGGC 58.694 55.000 0.00 0.00 0.00 5.68
5280 5547 0.913205 TTGGGCTATAAAGGACGGCA 59.087 50.000 0.00 0.00 0.00 5.69
5281 5548 1.136828 TGGGCTATAAAGGACGGCAT 58.863 50.000 0.00 0.00 0.00 4.40
5282 5549 1.071699 TGGGCTATAAAGGACGGCATC 59.928 52.381 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
294 296 8.815141 AAGAATCAATCACGATCAATCTCTAG 57.185 34.615 0.00 0.00 0.00 2.43
406 408 0.885596 CCCACCGGTTTAGTTTCGCA 60.886 55.000 2.97 0.00 0.00 5.10
475 479 8.584063 TTTTGGTACTTCTTTGTTACTTCCTT 57.416 30.769 0.00 0.00 0.00 3.36
539 543 5.067936 CCTAATGTCTCAGTTGGTAGATCGT 59.932 44.000 0.00 0.00 0.00 3.73
543 547 5.580998 ACTCCTAATGTCTCAGTTGGTAGA 58.419 41.667 0.00 0.00 0.00 2.59
581 585 3.532155 CTTCTCGCCCCCTCTCCG 61.532 72.222 0.00 0.00 0.00 4.63
594 598 3.570125 CGGCTTTTCCTTTTCTTCCTTCT 59.430 43.478 0.00 0.00 0.00 2.85
596 600 3.562182 TCGGCTTTTCCTTTTCTTCCTT 58.438 40.909 0.00 0.00 0.00 3.36
597 601 3.149981 CTCGGCTTTTCCTTTTCTTCCT 58.850 45.455 0.00 0.00 0.00 3.36
598 602 2.229062 CCTCGGCTTTTCCTTTTCTTCC 59.771 50.000 0.00 0.00 0.00 3.46
630 634 2.182030 GAAGGAGGAGGTCGCGTG 59.818 66.667 5.77 0.00 0.00 5.34
639 643 2.448453 GAGACGAGAAAGGAAGGAGGA 58.552 52.381 0.00 0.00 0.00 3.71
694 703 5.400189 GGATTAGGAATTGGATTTGGGAGGA 60.400 44.000 0.00 0.00 0.00 3.71
703 712 4.509122 CGGGATTGGGATTAGGAATTGGAT 60.509 45.833 0.00 0.00 0.00 3.41
704 713 3.181434 CGGGATTGGGATTAGGAATTGGA 60.181 47.826 0.00 0.00 0.00 3.53
709 718 0.476771 GCCGGGATTGGGATTAGGAA 59.523 55.000 2.18 0.00 0.00 3.36
713 722 2.833227 CGGCCGGGATTGGGATTA 59.167 61.111 20.10 0.00 0.00 1.75
734 743 3.090532 CGGGAGGAAGGAAGGGGG 61.091 72.222 0.00 0.00 0.00 5.40
735 744 3.798511 GCGGGAGGAAGGAAGGGG 61.799 72.222 0.00 0.00 0.00 4.79
736 745 3.798511 GGCGGGAGGAAGGAAGGG 61.799 72.222 0.00 0.00 0.00 3.95
889 905 2.127383 CCGGACGCGCTTTGTTTC 60.127 61.111 5.73 0.00 0.00 2.78
929 945 0.751452 GACCGGAAACCCTAGCTAGG 59.249 60.000 30.05 30.05 43.25 3.02
948 964 2.066999 CGAAGGGAGGGGAGAAGGG 61.067 68.421 0.00 0.00 0.00 3.95
953 969 3.157949 GAGGCGAAGGGAGGGGAG 61.158 72.222 0.00 0.00 0.00 4.30
954 970 4.798682 GGAGGCGAAGGGAGGGGA 62.799 72.222 0.00 0.00 0.00 4.81
955 971 4.806339 AGGAGGCGAAGGGAGGGG 62.806 72.222 0.00 0.00 0.00 4.79
956 972 3.157949 GAGGAGGCGAAGGGAGGG 61.158 72.222 0.00 0.00 0.00 4.30
957 973 3.532155 CGAGGAGGCGAAGGGAGG 61.532 72.222 0.00 0.00 0.00 4.30
1457 1473 2.125229 CGTCGTCGGAGGAGGAGA 60.125 66.667 13.45 0.00 37.71 3.71
1459 1475 2.435586 GTCGTCGTCGGAGGAGGA 60.436 66.667 16.41 16.41 37.71 3.71
1460 1476 3.862402 CGTCGTCGTCGGAGGAGG 61.862 72.222 12.71 12.71 37.71 4.30
1462 1478 2.812609 CTCGTCGTCGTCGGAGGA 60.813 66.667 11.74 0.00 38.33 3.71
1463 1479 3.862402 CCTCGTCGTCGTCGGAGG 61.862 72.222 11.74 11.45 38.44 4.30
1546 1577 2.097160 CTGATGCTGCGTCGTTGC 59.903 61.111 16.39 0.00 0.00 4.17
1548 1579 2.357396 TGCTGATGCTGCGTCGTT 60.357 55.556 16.39 0.00 40.48 3.85
1549 1580 3.114616 GTGCTGATGCTGCGTCGT 61.115 61.111 16.39 0.00 40.48 4.34
1550 1581 3.857854 GGTGCTGATGCTGCGTCG 61.858 66.667 16.39 12.09 40.48 5.12
1555 1586 2.857575 TAGTGGCGGTGCTGATGCTG 62.858 60.000 0.00 0.00 40.48 4.41
1556 1587 2.659063 TAGTGGCGGTGCTGATGCT 61.659 57.895 0.00 0.00 40.48 3.79
1557 1588 2.125147 TAGTGGCGGTGCTGATGC 60.125 61.111 0.00 0.00 40.20 3.91
1558 1589 0.462581 ATGTAGTGGCGGTGCTGATG 60.463 55.000 0.00 0.00 0.00 3.07
1559 1590 0.462581 CATGTAGTGGCGGTGCTGAT 60.463 55.000 0.00 0.00 0.00 2.90
1560 1591 1.079197 CATGTAGTGGCGGTGCTGA 60.079 57.895 0.00 0.00 0.00 4.26
1776 1807 2.047179 GTGGGCGTGAAGAGGTCC 60.047 66.667 0.00 0.00 31.96 4.46
1855 1886 0.107214 TTGGTGGGCAGATTCCGATC 60.107 55.000 0.00 0.00 0.00 3.69
1874 1905 0.324275 ATTGGCGTAATTGGGGCTGT 60.324 50.000 5.87 0.00 0.00 4.40
1993 2024 2.027625 GTGTCTTCCCCTTCACGCG 61.028 63.158 3.53 3.53 0.00 6.01
2042 2073 1.077429 GAGGAGGTGCCATTGGGAC 60.077 63.158 18.32 18.32 43.47 4.46
2049 2080 1.305633 CTCAGAGGAGGAGGTGCCA 60.306 63.158 0.00 0.00 40.02 4.92
2115 2146 2.672996 TTCCTTGGCAGCGGCTTC 60.673 61.111 9.17 0.00 40.87 3.86
2125 2156 0.804989 GGCACTGAATCGTTCCTTGG 59.195 55.000 0.00 0.00 0.00 3.61
2236 2267 0.251832 TTCTCGGAGGAGGAGTTGCT 60.252 55.000 4.96 0.00 40.85 3.91
2248 2279 3.511934 CCCTTCTTCTTCTTCTTCTCGGA 59.488 47.826 0.00 0.00 0.00 4.55
2249 2280 3.259625 ACCCTTCTTCTTCTTCTTCTCGG 59.740 47.826 0.00 0.00 0.00 4.63
2250 2281 4.241681 CACCCTTCTTCTTCTTCTTCTCG 58.758 47.826 0.00 0.00 0.00 4.04
2251 2282 4.994217 CACACCCTTCTTCTTCTTCTTCTC 59.006 45.833 0.00 0.00 0.00 2.87
2253 2284 3.500299 GCACACCCTTCTTCTTCTTCTTC 59.500 47.826 0.00 0.00 0.00 2.87
2355 2389 0.659427 CGCCATCTGCATCGACAATT 59.341 50.000 0.00 0.00 41.33 2.32
2382 2416 3.307906 ACCGACTTGCCGTGGCTA 61.308 61.111 12.84 3.37 42.51 3.93
2472 2506 0.915364 GCTCCTTGACCTCCTCCATT 59.085 55.000 0.00 0.00 0.00 3.16
2505 2539 2.436469 TCATCGCCGCAATGCAGT 60.436 55.556 5.91 0.00 0.00 4.40
2571 2605 6.884295 TCCATTACCCACATCTAAGAACTTTG 59.116 38.462 0.00 0.00 0.00 2.77
2630 2664 1.699634 AGTCGCTTGCCCATATACCAT 59.300 47.619 0.00 0.00 0.00 3.55
2633 2667 2.526304 TCAGTCGCTTGCCCATATAC 57.474 50.000 0.00 0.00 0.00 1.47
2679 2716 2.376518 ACCCTGGAAGAGAAATCTGCAA 59.623 45.455 0.00 0.00 34.07 4.08
2778 2815 1.134007 TGGCATATGAAGCTGAGGTGG 60.134 52.381 6.97 0.00 0.00 4.61
2782 2819 1.600957 CCGTTGGCATATGAAGCTGAG 59.399 52.381 6.97 0.00 0.00 3.35
2800 2837 2.202610 TCGCGATGTTCTCTGCCG 60.203 61.111 3.71 0.00 0.00 5.69
2810 2847 0.863538 CAGAGACTTCCGTCGCGATG 60.864 60.000 21.42 21.42 43.62 3.84
2816 2853 3.004944 AGAGTTGAACAGAGACTTCCGTC 59.995 47.826 0.00 0.00 40.54 4.79
2881 2918 2.094545 GGCCTCAAATGTGCTTACCTTG 60.095 50.000 0.00 0.00 0.00 3.61
2932 2969 8.736244 TGTTTGGGCAGTAAATAAAGAGATAAC 58.264 33.333 0.00 0.00 0.00 1.89
2957 2994 6.142818 TCACCTAACCTTTTTCAACACATG 57.857 37.500 0.00 0.00 0.00 3.21
3061 3098 1.214062 CTCTATCGCATCCGGCTCC 59.786 63.158 0.00 0.00 41.67 4.70
3108 3145 3.850122 TGTTGATCGTGATCTTCGACT 57.150 42.857 13.68 5.92 40.07 4.18
3121 3158 3.128242 CCTTGGCTGTCTTGATGTTGATC 59.872 47.826 0.00 0.00 0.00 2.92
3133 3170 1.743252 CGAGAAGGCCTTGGCTGTC 60.743 63.158 26.25 7.35 38.81 3.51
3184 3221 1.625818 AGGTCAACAAGCTGAGGGTAG 59.374 52.381 0.00 0.00 33.44 3.18
3234 3298 2.227388 GTCAGGCAATGAAGTTGTGGAG 59.773 50.000 0.00 0.00 40.43 3.86
3250 3314 6.751888 CAGTTTAAAGGTTTTGTTCTGTCAGG 59.248 38.462 0.00 0.00 0.00 3.86
3349 3414 1.476891 CAGCTGCTTCTCATGGCATTT 59.523 47.619 0.00 0.00 37.83 2.32
3435 3500 2.435938 TCCAGCGTCGCCAATTCC 60.436 61.111 14.86 0.00 0.00 3.01
3436 3501 3.093278 CTCCAGCGTCGCCAATTC 58.907 61.111 14.86 0.00 0.00 2.17
3437 3502 3.127533 GCTCCAGCGTCGCCAATT 61.128 61.111 14.86 0.00 0.00 2.32
3483 3548 2.294233 GCTGATCCACTTGTTGAAGCAA 59.706 45.455 0.00 0.00 31.68 3.91
3500 3565 1.406898 CATAAGACCTCTGCGAGCTGA 59.593 52.381 0.00 4.67 0.00 4.26
3528 3593 1.817099 CCTCAGCCATCCGTTCAGC 60.817 63.158 0.00 0.00 0.00 4.26
3534 3599 1.370437 CCATCTCCTCAGCCATCCG 59.630 63.158 0.00 0.00 0.00 4.18
3699 3764 1.546476 AGCTTCGAGAAGTGGTCGATT 59.454 47.619 13.58 0.00 45.41 3.34
3706 3771 0.241213 TGGACGAGCTTCGAGAAGTG 59.759 55.000 13.58 7.32 43.74 3.16
3732 3797 1.513622 GTCGTCCTGGCTCTTCCTC 59.486 63.158 0.00 0.00 35.26 3.71
3741 3806 4.778415 CGGTGCTCGTCGTCCTGG 62.778 72.222 0.00 0.00 0.00 4.45
3747 3812 4.717629 TTCTGCCGGTGCTCGTCG 62.718 66.667 1.90 0.00 38.71 5.12
3754 3819 1.078848 CCTTCCTCTTCTGCCGGTG 60.079 63.158 1.90 0.00 0.00 4.94
3888 3953 1.202973 GCAGATCGACGGTGTGATCG 61.203 60.000 9.78 9.29 44.47 3.69
3932 3997 3.869272 CGTGCTTGGCCATCTCGC 61.869 66.667 6.09 8.14 0.00 5.03
3961 4026 2.501650 CGCAAAATGGACGTGCCG 60.502 61.111 4.04 0.00 40.66 5.69
3966 4031 2.202298 GACGCCGCAAAATGGACG 60.202 61.111 0.00 0.00 33.96 4.79
4028 4093 0.955919 GTTCCCGTGGAAGAAGCCAG 60.956 60.000 5.71 0.00 42.88 4.85
4029 4094 1.072505 GTTCCCGTGGAAGAAGCCA 59.927 57.895 5.71 0.00 42.88 4.75
4132 4218 1.140161 CAAAGACATGCCCATGCCG 59.860 57.895 8.11 0.00 42.39 5.69
4140 4226 3.750130 TCTTCTCTTCTGCAAAGACATGC 59.250 43.478 7.09 0.00 46.58 4.06
4141 4227 5.280328 GTCTTCTCTTCTGCAAAGACATG 57.720 43.478 17.70 0.00 44.41 3.21
4145 4231 4.679373 ACTGTCTTCTCTTCTGCAAAGA 57.321 40.909 9.84 9.84 0.00 2.52
4147 4233 6.071952 ACAAAAACTGTCTTCTCTTCTGCAAA 60.072 34.615 0.00 0.00 29.87 3.68
4148 4234 5.415701 ACAAAAACTGTCTTCTCTTCTGCAA 59.584 36.000 0.00 0.00 29.87 4.08
4149 4235 4.943705 ACAAAAACTGTCTTCTCTTCTGCA 59.056 37.500 0.00 0.00 29.87 4.41
4151 4237 6.314896 AGTCACAAAAACTGTCTTCTCTTCTG 59.685 38.462 0.00 0.00 35.47 3.02
4152 4238 6.314896 CAGTCACAAAAACTGTCTTCTCTTCT 59.685 38.462 0.00 0.00 39.42 2.85
4153 4239 6.313905 TCAGTCACAAAAACTGTCTTCTCTTC 59.686 38.462 3.45 0.00 43.68 2.87
4154 4240 6.173339 TCAGTCACAAAAACTGTCTTCTCTT 58.827 36.000 3.45 0.00 43.68 2.85
4155 4241 5.734720 TCAGTCACAAAAACTGTCTTCTCT 58.265 37.500 3.45 0.00 43.68 3.10
4156 4242 5.007136 CCTCAGTCACAAAAACTGTCTTCTC 59.993 44.000 3.45 0.00 43.68 2.87
4157 4243 4.878397 CCTCAGTCACAAAAACTGTCTTCT 59.122 41.667 3.45 0.00 43.68 2.85
4158 4244 4.636206 ACCTCAGTCACAAAAACTGTCTTC 59.364 41.667 3.45 0.00 43.68 2.87
4159 4245 4.396166 CACCTCAGTCACAAAAACTGTCTT 59.604 41.667 3.45 0.00 43.68 3.01
4160 4246 3.941483 CACCTCAGTCACAAAAACTGTCT 59.059 43.478 3.45 0.00 43.68 3.41
4161 4247 3.065371 CCACCTCAGTCACAAAAACTGTC 59.935 47.826 3.45 0.00 43.68 3.51
4162 4248 3.016736 CCACCTCAGTCACAAAAACTGT 58.983 45.455 3.45 0.00 43.68 3.55
4163 4249 3.016736 ACCACCTCAGTCACAAAAACTG 58.983 45.455 0.00 0.00 44.43 3.16
4164 4250 3.366052 ACCACCTCAGTCACAAAAACT 57.634 42.857 0.00 0.00 0.00 2.66
4165 4251 4.448210 TCTACCACCTCAGTCACAAAAAC 58.552 43.478 0.00 0.00 0.00 2.43
4207 4297 7.358066 CAATGATCTATCTACACACCAAATGC 58.642 38.462 0.00 0.00 0.00 3.56
4208 4298 7.500227 ACCAATGATCTATCTACACACCAAATG 59.500 37.037 0.00 0.00 0.00 2.32
4213 4307 6.582636 TGAACCAATGATCTATCTACACACC 58.417 40.000 0.00 0.00 0.00 4.16
4254 4349 2.169179 CGTAACCGTCGTAGCAACTAC 58.831 52.381 0.00 0.00 33.99 2.73
4260 4355 1.514873 CCACCGTAACCGTCGTAGC 60.515 63.158 0.00 0.00 0.00 3.58
4269 4365 9.242477 GTTTTCTATCTAATCTACCACCGTAAC 57.758 37.037 0.00 0.00 0.00 2.50
4273 4369 6.501781 ACGTTTTCTATCTAATCTACCACCG 58.498 40.000 0.00 0.00 0.00 4.94
4293 4514 2.674357 ACGTCTGCAAAACACTAACGTT 59.326 40.909 5.88 5.88 34.79 3.99
4294 4515 2.273557 ACGTCTGCAAAACACTAACGT 58.726 42.857 0.00 0.00 34.04 3.99
4295 4516 3.313274 AACGTCTGCAAAACACTAACG 57.687 42.857 0.00 0.00 32.60 3.18
4312 4533 2.668279 GCAGGCACCATCAGTAAAAACG 60.668 50.000 0.00 0.00 0.00 3.60
4336 4557 1.107945 GCTCCCCTCTACTGTGAGTC 58.892 60.000 0.00 0.00 32.50 3.36
4339 4560 1.077169 TGAAGCTCCCCTCTACTGTGA 59.923 52.381 0.00 0.00 0.00 3.58
4357 4584 2.485479 GGAGCACCACTGAAACTTCTGA 60.485 50.000 0.00 0.00 35.97 3.27
4360 4587 1.239347 GGGAGCACCACTGAAACTTC 58.761 55.000 1.58 0.00 39.85 3.01
4362 4589 2.230664 TGGGAGCACCACTGAAACT 58.769 52.632 1.58 0.00 46.80 2.66
4401 4635 9.917129 TCGATTAGTAAGTTGAAGTTTCATGTA 57.083 29.630 0.00 0.00 37.00 2.29
4402 4636 8.827177 TCGATTAGTAAGTTGAAGTTTCATGT 57.173 30.769 0.00 0.00 37.00 3.21
4403 4637 9.907576 GATCGATTAGTAAGTTGAAGTTTCATG 57.092 33.333 0.00 0.00 37.00 3.07
4407 4641 9.706691 TGAAGATCGATTAGTAAGTTGAAGTTT 57.293 29.630 0.00 0.00 0.00 2.66
4408 4642 9.877178 ATGAAGATCGATTAGTAAGTTGAAGTT 57.123 29.630 0.00 0.00 0.00 2.66
4409 4643 9.877178 AATGAAGATCGATTAGTAAGTTGAAGT 57.123 29.630 0.00 0.00 0.00 3.01
4437 4671 9.502091 AACTATTAACTCTCAAACACATTGCTA 57.498 29.630 0.00 0.00 38.98 3.49
4499 4736 8.050930 GTCATTAGGATTTACAGTTAAGGGGAA 58.949 37.037 0.00 0.00 0.00 3.97
4501 4738 7.343357 TGTCATTAGGATTTACAGTTAAGGGG 58.657 38.462 0.00 0.00 0.00 4.79
4502 4739 7.012421 GCTGTCATTAGGATTTACAGTTAAGGG 59.988 40.741 0.00 0.00 39.74 3.95
4503 4740 7.770897 AGCTGTCATTAGGATTTACAGTTAAGG 59.229 37.037 0.00 0.00 39.74 2.69
4504 4741 8.723942 AGCTGTCATTAGGATTTACAGTTAAG 57.276 34.615 0.00 0.00 39.74 1.85
4513 4754 4.228210 TCAAGGGAGCTGTCATTAGGATTT 59.772 41.667 0.00 0.00 0.00 2.17
4550 4791 3.640029 CCTGGAATAATGCAATGAAGCCT 59.360 43.478 0.00 0.00 0.00 4.58
4610 4851 1.291184 TGAACCGATGCTCGCTGTTG 61.291 55.000 0.72 0.00 38.82 3.33
4640 4881 7.176165 GGTAGTAGGCACAAAGGTAAAGAAAAT 59.824 37.037 0.00 0.00 0.00 1.82
4646 4887 3.577848 TCGGTAGTAGGCACAAAGGTAAA 59.422 43.478 0.00 0.00 0.00 2.01
4649 4890 1.274447 GTCGGTAGTAGGCACAAAGGT 59.726 52.381 0.00 0.00 0.00 3.50
4650 4891 1.405121 GGTCGGTAGTAGGCACAAAGG 60.405 57.143 0.00 0.00 0.00 3.11
4652 4893 0.609662 GGGTCGGTAGTAGGCACAAA 59.390 55.000 0.00 0.00 0.00 2.83
4666 4908 2.047655 TGTTGCGCTTAGGGGTCG 60.048 61.111 9.73 0.00 0.00 4.79
4683 4933 0.473501 GAGGAGGCCATGGAGGATCT 60.474 60.000 18.40 5.31 41.22 2.75
4717 4967 4.574013 GTGGATGACTGAAGCCTATTTGAG 59.426 45.833 0.00 0.00 0.00 3.02
4718 4968 4.019411 TGTGGATGACTGAAGCCTATTTGA 60.019 41.667 0.00 0.00 0.00 2.69
4725 4975 0.737219 GCATGTGGATGACTGAAGCC 59.263 55.000 0.00 0.00 0.00 4.35
4799 5050 4.152647 TGCTATACCTGGACATCTACCTG 58.847 47.826 0.00 0.00 0.00 4.00
4869 5120 1.452399 GAAATAGAATCTCGCGGCGAC 59.548 52.381 22.69 11.89 0.00 5.19
4872 5124 1.452399 GACGAAATAGAATCTCGCGGC 59.548 52.381 6.13 0.00 36.03 6.53
4894 5149 3.369400 TTGCGTTTCATGGGGCCG 61.369 61.111 0.00 0.00 0.00 6.13
4901 5162 6.260936 CCCTATCAATAGAAGTTGCGTTTCAT 59.739 38.462 0.00 0.00 32.05 2.57
4902 5163 5.584649 CCCTATCAATAGAAGTTGCGTTTCA 59.415 40.000 0.00 0.00 32.05 2.69
5222 5489 3.126514 CAGCTCGACAAATTTGATCTGCT 59.873 43.478 24.64 21.35 0.00 4.24
5226 5493 6.549952 AGATTTCAGCTCGACAAATTTGATC 58.450 36.000 24.64 15.74 0.00 2.92
5227 5494 6.506500 AGATTTCAGCTCGACAAATTTGAT 57.493 33.333 24.64 8.92 0.00 2.57
5228 5495 5.947228 AGATTTCAGCTCGACAAATTTGA 57.053 34.783 24.64 1.45 0.00 2.69
5229 5496 6.144854 TCAAGATTTCAGCTCGACAAATTTG 58.855 36.000 16.67 16.67 0.00 2.32
5230 5497 6.317789 TCAAGATTTCAGCTCGACAAATTT 57.682 33.333 0.00 0.00 0.00 1.82
5231 5498 5.106396 CCTCAAGATTTCAGCTCGACAAATT 60.106 40.000 0.00 0.00 0.00 1.82
5232 5499 4.394300 CCTCAAGATTTCAGCTCGACAAAT 59.606 41.667 0.00 0.00 0.00 2.32
5233 5500 3.748048 CCTCAAGATTTCAGCTCGACAAA 59.252 43.478 0.00 0.00 0.00 2.83
5234 5501 3.006859 TCCTCAAGATTTCAGCTCGACAA 59.993 43.478 0.00 0.00 0.00 3.18
5235 5502 2.562738 TCCTCAAGATTTCAGCTCGACA 59.437 45.455 0.00 0.00 0.00 4.35
5236 5503 3.238108 TCCTCAAGATTTCAGCTCGAC 57.762 47.619 0.00 0.00 0.00 4.20
5237 5504 3.961480 TTCCTCAAGATTTCAGCTCGA 57.039 42.857 0.00 0.00 0.00 4.04
5238 5505 4.394300 ACATTTCCTCAAGATTTCAGCTCG 59.606 41.667 0.00 0.00 0.00 5.03
5239 5506 5.893897 ACATTTCCTCAAGATTTCAGCTC 57.106 39.130 0.00 0.00 0.00 4.09
5240 5507 5.047519 CCAACATTTCCTCAAGATTTCAGCT 60.048 40.000 0.00 0.00 0.00 4.24
5241 5508 5.166398 CCAACATTTCCTCAAGATTTCAGC 58.834 41.667 0.00 0.00 0.00 4.26
5242 5509 5.717119 CCCAACATTTCCTCAAGATTTCAG 58.283 41.667 0.00 0.00 0.00 3.02
5243 5510 4.021192 GCCCAACATTTCCTCAAGATTTCA 60.021 41.667 0.00 0.00 0.00 2.69
5244 5511 4.221482 AGCCCAACATTTCCTCAAGATTTC 59.779 41.667 0.00 0.00 0.00 2.17
5245 5512 4.162651 AGCCCAACATTTCCTCAAGATTT 58.837 39.130 0.00 0.00 0.00 2.17
5246 5513 3.782992 AGCCCAACATTTCCTCAAGATT 58.217 40.909 0.00 0.00 0.00 2.40
5247 5514 3.463048 AGCCCAACATTTCCTCAAGAT 57.537 42.857 0.00 0.00 0.00 2.40
5248 5515 2.978156 AGCCCAACATTTCCTCAAGA 57.022 45.000 0.00 0.00 0.00 3.02
5249 5516 6.183360 CCTTTATAGCCCAACATTTCCTCAAG 60.183 42.308 0.00 0.00 0.00 3.02
5250 5517 5.656416 CCTTTATAGCCCAACATTTCCTCAA 59.344 40.000 0.00 0.00 0.00 3.02
5251 5518 5.044476 TCCTTTATAGCCCAACATTTCCTCA 60.044 40.000 0.00 0.00 0.00 3.86
5252 5519 5.299531 GTCCTTTATAGCCCAACATTTCCTC 59.700 44.000 0.00 0.00 0.00 3.71
5253 5520 5.201243 GTCCTTTATAGCCCAACATTTCCT 58.799 41.667 0.00 0.00 0.00 3.36
5254 5521 4.036380 CGTCCTTTATAGCCCAACATTTCC 59.964 45.833 0.00 0.00 0.00 3.13
5255 5522 4.036380 CCGTCCTTTATAGCCCAACATTTC 59.964 45.833 0.00 0.00 0.00 2.17
5256 5523 3.951680 CCGTCCTTTATAGCCCAACATTT 59.048 43.478 0.00 0.00 0.00 2.32
5257 5524 3.551846 CCGTCCTTTATAGCCCAACATT 58.448 45.455 0.00 0.00 0.00 2.71
5258 5525 2.748465 GCCGTCCTTTATAGCCCAACAT 60.748 50.000 0.00 0.00 0.00 2.71
5259 5526 1.407712 GCCGTCCTTTATAGCCCAACA 60.408 52.381 0.00 0.00 0.00 3.33
5260 5527 1.306148 GCCGTCCTTTATAGCCCAAC 58.694 55.000 0.00 0.00 0.00 3.77
5261 5528 0.913205 TGCCGTCCTTTATAGCCCAA 59.087 50.000 0.00 0.00 0.00 4.12
5262 5529 1.071699 GATGCCGTCCTTTATAGCCCA 59.928 52.381 0.00 0.00 0.00 5.36
5263 5530 1.809684 GATGCCGTCCTTTATAGCCC 58.190 55.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.