Multiple sequence alignment - TraesCS1B01G415800

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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 TraesCS1B01G415800 chr1B 100.000 6079 0 0 1 6079 640850718 640844640 0.000000e+00 11226.0
1 TraesCS1B01G415800 chr1B 88.793 232 12 3 5811 6029 599175857 599175627 7.760000e-69 272.0
2 TraesCS1B01G415800 chr1A 92.940 6147 227 82 1 6029 556943765 556937708 0.000000e+00 8756.0
3 TraesCS1B01G415800 chr1A 89.811 265 14 5 371 633 556943332 556943079 1.630000e-85 327.0
4 TraesCS1B01G415800 chr1A 89.730 185 13 3 4502 4686 556830464 556830286 1.320000e-56 231.0
5 TraesCS1B01G415800 chr1A 87.719 57 3 2 440 496 556943371 556943319 5.090000e-06 63.9
6 TraesCS1B01G415800 chr1A 83.824 68 8 3 5948 6014 182151424 182151489 1.830000e-05 62.1
7 TraesCS1B01G415800 chr1D 92.144 3564 153 57 1 3503 464598721 464595224 0.000000e+00 4913.0
8 TraesCS1B01G415800 chr1D 94.410 2075 63 18 3485 5525 464595212 464593157 0.000000e+00 3140.0
9 TraesCS1B01G415800 chr1D 90.750 400 16 6 5644 6029 464593083 464592691 1.170000e-141 514.0
10 TraesCS1B01G415800 chr1D 90.661 257 12 4 371 626 464598277 464598032 1.260000e-86 331.0
11 TraesCS1B01G415800 chr1D 90.909 143 13 0 4544 4686 464404888 464404746 6.220000e-45 193.0
12 TraesCS1B01G415800 chr1D 87.719 57 3 2 440 496 464598316 464598264 5.090000e-06 63.9
13 TraesCS1B01G415800 chr1D 94.444 36 0 1 5981 6014 178833167 178833202 3.000000e-03 54.7
14 TraesCS1B01G415800 chr2D 83.725 639 69 20 3 625 627820490 627821109 6.840000e-159 571.0
15 TraesCS1B01G415800 chr5A 90.270 185 15 1 4502 4686 412229902 412230083 7.870000e-59 239.0
16 TraesCS1B01G415800 chr5A 98.182 55 1 0 6025 6079 10204591 10204537 5.020000e-16 97.1
17 TraesCS1B01G415800 chr4A 87.363 182 14 4 4502 4680 538724706 538724881 3.720000e-47 200.0
18 TraesCS1B01G415800 chr2B 83.482 224 22 8 406 626 770068961 770069172 1.730000e-45 195.0
19 TraesCS1B01G415800 chr2B 98.246 57 1 0 6023 6079 458500506 458500450 3.880000e-17 100.0
20 TraesCS1B01G415800 chr2B 98.246 57 1 0 6023 6079 733735846 733735902 3.880000e-17 100.0
21 TraesCS1B01G415800 chr5D 98.246 57 1 0 6023 6079 424907232 424907176 3.880000e-17 100.0
22 TraesCS1B01G415800 chr5B 100.000 54 0 0 6026 6079 274471267 274471320 3.880000e-17 100.0
23 TraesCS1B01G415800 chr5B 98.214 56 1 0 6024 6079 275309327 275309272 1.390000e-16 99.0
24 TraesCS1B01G415800 chr7B 98.214 56 1 0 6024 6079 431181952 431182007 1.390000e-16 99.0
25 TraesCS1B01G415800 chr3A 96.552 58 2 0 6022 6079 374342124 374342181 5.020000e-16 97.1
26 TraesCS1B01G415800 chr7A 100.000 51 0 0 6029 6079 24381145 24381095 1.800000e-15 95.3


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 TraesCS1B01G415800 chr1B 640844640 640850718 6078 True 11226.000000 11226 100.000000 1 6079 1 chr1B.!!$R2 6078
1 TraesCS1B01G415800 chr1A 556937708 556943765 6057 True 3048.966667 8756 90.156667 1 6029 3 chr1A.!!$R2 6028
2 TraesCS1B01G415800 chr1D 464592691 464598721 6030 True 1792.380000 4913 91.136800 1 6029 5 chr1D.!!$R2 6028
3 TraesCS1B01G415800 chr2D 627820490 627821109 619 False 571.000000 571 83.725000 3 625 1 chr2D.!!$F1 622

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
636 716 0.038166 TTTGCTTCCGATTGCTCCCT 59.962 50.000 0.00 0.0 0.00 4.20 F
865 953 0.040067 CGCTGTTCAAAGGCTGTTCC 60.040 55.000 0.00 0.0 0.00 3.62 F
867 955 1.000938 GCTGTTCAAAGGCTGTTCCTG 60.001 52.381 0.00 0.0 46.94 3.86 F
1459 1548 1.063717 TGAAGCCCATTCCTCCAATCC 60.064 52.381 0.00 0.0 37.08 3.01 F
2579 2669 1.135575 GGCTGAGCAGGAAACAATTCG 60.136 52.381 6.82 0.0 36.36 3.34 F
3074 3164 0.179004 TTGTGAAGGAACGTGGCCAT 60.179 50.000 9.72 0.0 0.00 4.40 F
4227 4383 0.747852 TTGCTCGTGTGTGTACCTCA 59.252 50.000 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1718 0.250252 CACCCCAAACATTTGCCACC 60.250 55.000 0.00 0.00 36.86 4.61 R
2546 2636 2.183858 CTCAGCCTCGTCGTCGACAA 62.184 60.000 24.13 5.97 41.35 3.18 R
2601 2691 2.564062 CAGTGGAAGATGCAAACCCAAT 59.436 45.455 0.00 0.00 0.00 3.16 R
2939 3029 4.222114 CAACGGAAAATTCTTCTGCAGAC 58.778 43.478 18.03 1.58 0.00 3.51 R
4092 4248 0.245539 CCCCAACAATGCAAGCTCTG 59.754 55.000 0.00 0.00 0.00 3.35 R
5067 5231 0.668706 CTCTGAAGTCACTGGCCACG 60.669 60.000 0.00 0.00 0.00 4.94 R
5305 5472 0.250513 CTCTACACTCCCAAGGCACC 59.749 60.000 0.00 0.00 0.00 5.01 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
89 90 9.638239 CTTTTCAGCATGGCTTTTAATTAAGTA 57.362 29.630 0.00 0.00 36.40 2.24
143 159 8.121708 GCATCAGTCTATTTCTCAACTTGAATC 58.878 37.037 0.00 0.00 0.00 2.52
263 279 4.080243 ACGAATATTGGTCATTGGGTGGTA 60.080 41.667 0.00 0.00 0.00 3.25
426 449 4.688413 GCTGTTCTGTAGTTCTTCTGGAAG 59.312 45.833 4.13 4.13 39.71 3.46
434 511 3.521727 AGTTCTTCTGGAAGCTCCCTTA 58.478 45.455 5.55 0.00 38.28 2.69
468 545 5.791336 TTCAGACAGTGACTGTTCTGTAT 57.209 39.130 27.86 11.79 45.44 2.29
469 546 5.126396 TCAGACAGTGACTGTTCTGTATG 57.874 43.478 27.86 22.95 45.44 2.39
471 548 5.069119 TCAGACAGTGACTGTTCTGTATGTT 59.931 40.000 27.86 5.27 45.44 2.71
472 549 5.403766 CAGACAGTGACTGTTCTGTATGTTC 59.596 44.000 20.42 2.69 45.44 3.18
473 550 5.303078 AGACAGTGACTGTTCTGTATGTTCT 59.697 40.000 20.42 5.10 45.44 3.01
475 552 6.349300 ACAGTGACTGTTCTGTATGTTCTTT 58.651 36.000 13.33 0.00 42.59 2.52
476 553 6.258727 ACAGTGACTGTTCTGTATGTTCTTTG 59.741 38.462 13.33 0.00 42.59 2.77
538 616 4.707105 CAAATCTCCTTTTGGCAAAACCT 58.293 39.130 20.81 2.23 40.22 3.50
539 617 5.741673 GCAAATCTCCTTTTGGCAAAACCTA 60.742 40.000 20.81 8.64 40.22 3.08
540 618 5.468540 AATCTCCTTTTGGCAAAACCTAC 57.531 39.130 20.81 0.00 40.22 3.18
541 619 3.227614 TCTCCTTTTGGCAAAACCTACC 58.772 45.455 20.81 0.00 40.22 3.18
542 620 3.117284 TCTCCTTTTGGCAAAACCTACCT 60.117 43.478 20.81 0.00 40.22 3.08
543 621 4.105057 TCTCCTTTTGGCAAAACCTACCTA 59.895 41.667 20.81 0.00 40.22 3.08
544 622 5.005628 TCCTTTTGGCAAAACCTACCTAT 57.994 39.130 20.81 0.00 40.22 2.57
545 623 6.012333 TCTCCTTTTGGCAAAACCTACCTATA 60.012 38.462 20.81 0.00 40.22 1.31
546 624 6.184789 TCCTTTTGGCAAAACCTACCTATAG 58.815 40.000 20.81 7.54 40.22 1.31
632 712 3.800628 GCTTTTGCTTCCGATTGCT 57.199 47.368 0.00 0.00 43.35 3.91
633 713 1.622232 GCTTTTGCTTCCGATTGCTC 58.378 50.000 0.00 0.00 43.35 4.26
634 714 1.733718 GCTTTTGCTTCCGATTGCTCC 60.734 52.381 0.00 0.00 43.35 4.70
635 715 0.887933 TTTTGCTTCCGATTGCTCCC 59.112 50.000 0.00 0.00 0.00 4.30
636 716 0.038166 TTTGCTTCCGATTGCTCCCT 59.962 50.000 0.00 0.00 0.00 4.20
637 717 0.677731 TTGCTTCCGATTGCTCCCTG 60.678 55.000 0.00 0.00 0.00 4.45
638 718 1.821332 GCTTCCGATTGCTCCCTGG 60.821 63.158 0.00 0.00 0.00 4.45
639 719 1.907739 CTTCCGATTGCTCCCTGGA 59.092 57.895 0.00 0.00 0.00 3.86
640 720 0.462759 CTTCCGATTGCTCCCTGGAC 60.463 60.000 0.00 0.00 0.00 4.02
641 721 1.198094 TTCCGATTGCTCCCTGGACA 61.198 55.000 0.00 0.00 0.00 4.02
642 722 1.198094 TCCGATTGCTCCCTGGACAA 61.198 55.000 0.00 0.00 0.00 3.18
643 723 0.322456 CCGATTGCTCCCTGGACAAA 60.322 55.000 0.00 0.00 0.00 2.83
644 724 1.683011 CCGATTGCTCCCTGGACAAAT 60.683 52.381 0.00 0.00 0.00 2.32
645 725 2.421388 CCGATTGCTCCCTGGACAAATA 60.421 50.000 0.00 0.00 0.00 1.40
646 726 3.480470 CGATTGCTCCCTGGACAAATAT 58.520 45.455 0.00 0.00 0.00 1.28
647 727 3.499918 CGATTGCTCCCTGGACAAATATC 59.500 47.826 0.00 0.00 0.00 1.63
648 728 3.297134 TTGCTCCCTGGACAAATATCC 57.703 47.619 0.00 0.00 39.45 2.59
649 729 2.492025 TGCTCCCTGGACAAATATCCT 58.508 47.619 0.00 0.00 39.75 3.24
650 730 2.852449 TGCTCCCTGGACAAATATCCTT 59.148 45.455 0.00 0.00 39.75 3.36
651 731 3.269381 TGCTCCCTGGACAAATATCCTTT 59.731 43.478 0.00 0.00 39.75 3.11
652 732 3.633986 GCTCCCTGGACAAATATCCTTTG 59.366 47.826 0.00 0.00 39.75 2.77
653 733 4.628715 GCTCCCTGGACAAATATCCTTTGA 60.629 45.833 0.00 0.00 39.75 2.69
654 734 4.855340 TCCCTGGACAAATATCCTTTGAC 58.145 43.478 0.00 0.00 39.75 3.18
688 768 3.641434 ATCAACTGCTATCTTGGCACT 57.359 42.857 0.00 0.00 35.71 4.40
694 774 2.170187 CTGCTATCTTGGCACTTCTCCT 59.830 50.000 0.00 0.00 35.71 3.69
695 775 2.573462 TGCTATCTTGGCACTTCTCCTT 59.427 45.455 0.00 0.00 34.56 3.36
696 776 3.009473 TGCTATCTTGGCACTTCTCCTTT 59.991 43.478 0.00 0.00 34.56 3.11
701 781 0.538057 TGGCACTTCTCCTTTGGCAG 60.538 55.000 0.00 0.00 40.56 4.85
702 782 0.538287 GGCACTTCTCCTTTGGCAGT 60.538 55.000 0.00 0.00 35.91 4.40
703 783 1.271379 GGCACTTCTCCTTTGGCAGTA 60.271 52.381 0.00 0.00 35.91 2.74
704 784 2.079925 GCACTTCTCCTTTGGCAGTAG 58.920 52.381 0.00 0.00 0.00 2.57
706 786 2.039084 CACTTCTCCTTTGGCAGTAGGT 59.961 50.000 14.94 0.00 33.15 3.08
707 787 2.711547 ACTTCTCCTTTGGCAGTAGGTT 59.288 45.455 14.94 0.00 33.15 3.50
709 789 4.349930 ACTTCTCCTTTGGCAGTAGGTTTA 59.650 41.667 14.94 2.87 33.15 2.01
710 790 4.553330 TCTCCTTTGGCAGTAGGTTTAG 57.447 45.455 14.94 7.70 33.15 1.85
711 791 3.010420 CTCCTTTGGCAGTAGGTTTAGC 58.990 50.000 14.94 0.00 33.15 3.09
712 792 2.642807 TCCTTTGGCAGTAGGTTTAGCT 59.357 45.455 14.94 0.00 33.15 3.32
713 793 3.073946 TCCTTTGGCAGTAGGTTTAGCTT 59.926 43.478 14.94 0.00 33.15 3.74
714 794 3.440522 CCTTTGGCAGTAGGTTTAGCTTC 59.559 47.826 9.02 0.00 0.00 3.86
715 795 3.780804 TTGGCAGTAGGTTTAGCTTCA 57.219 42.857 0.00 0.00 0.00 3.02
716 796 3.053831 TGGCAGTAGGTTTAGCTTCAC 57.946 47.619 0.00 0.00 0.00 3.18
717 797 2.637872 TGGCAGTAGGTTTAGCTTCACT 59.362 45.455 0.00 0.00 0.00 3.41
718 798 3.263261 GGCAGTAGGTTTAGCTTCACTC 58.737 50.000 0.00 0.00 0.00 3.51
719 799 3.263261 GCAGTAGGTTTAGCTTCACTCC 58.737 50.000 0.00 0.00 0.00 3.85
720 800 3.055747 GCAGTAGGTTTAGCTTCACTCCT 60.056 47.826 0.00 0.00 0.00 3.69
721 801 4.159879 GCAGTAGGTTTAGCTTCACTCCTA 59.840 45.833 0.00 0.00 0.00 2.94
722 802 5.163395 GCAGTAGGTTTAGCTTCACTCCTAT 60.163 44.000 0.00 0.00 28.15 2.57
723 803 6.508777 CAGTAGGTTTAGCTTCACTCCTATC 58.491 44.000 0.00 0.00 28.15 2.08
724 804 6.096987 CAGTAGGTTTAGCTTCACTCCTATCA 59.903 42.308 0.00 0.00 28.15 2.15
729 809 0.249657 GCTTCACTCCTATCAGGGCG 60.250 60.000 0.00 0.00 35.59 6.13
741 821 1.275666 TCAGGGCGAATCTCCTTTGA 58.724 50.000 0.00 0.00 0.00 2.69
745 825 1.339151 GGGCGAATCTCCTTTGACACT 60.339 52.381 0.00 0.00 0.00 3.55
805 885 2.482721 CCTTTGGCGGTTACTGTTACTG 59.517 50.000 1.54 1.54 0.00 2.74
829 909 2.852449 TCAGGGATCCTTTGGCATTAGT 59.148 45.455 12.58 0.00 0.00 2.24
833 913 5.071788 CAGGGATCCTTTGGCATTAGTACTA 59.928 44.000 12.58 0.00 0.00 1.82
855 943 1.153269 TGTGCTGACCGCTGTTCAA 60.153 52.632 0.00 0.00 40.11 2.69
858 946 1.165907 TGCTGACCGCTGTTCAAAGG 61.166 55.000 0.00 0.00 40.11 3.11
860 948 0.886490 CTGACCGCTGTTCAAAGGCT 60.886 55.000 0.00 0.00 0.00 4.58
865 953 0.040067 CGCTGTTCAAAGGCTGTTCC 60.040 55.000 0.00 0.00 0.00 3.62
867 955 1.000938 GCTGTTCAAAGGCTGTTCCTG 60.001 52.381 0.00 0.00 46.94 3.86
875 963 5.003804 TCAAAGGCTGTTCCTGAGTTTATC 58.996 41.667 0.00 0.00 46.94 1.75
877 965 4.851639 AGGCTGTTCCTGAGTTTATCAT 57.148 40.909 0.00 0.00 45.54 2.45
915 1004 3.634910 GCTTGTTACAAAGAGGTGGGAAA 59.365 43.478 0.00 0.00 0.00 3.13
916 1005 4.098807 GCTTGTTACAAAGAGGTGGGAAAA 59.901 41.667 0.00 0.00 0.00 2.29
961 1050 7.945033 AACACAATTGGTTGTTTCATATCAC 57.055 32.000 10.83 0.00 46.07 3.06
1069 1158 2.366916 AGTGACAGTGAGGACCAAGAAG 59.633 50.000 0.00 0.00 0.00 2.85
1070 1159 2.365617 GTGACAGTGAGGACCAAGAAGA 59.634 50.000 0.00 0.00 0.00 2.87
1071 1160 3.038280 TGACAGTGAGGACCAAGAAGAA 58.962 45.455 0.00 0.00 0.00 2.52
1083 1172 6.149474 AGGACCAAGAAGAATGTGAATTTACG 59.851 38.462 0.00 0.00 0.00 3.18
1092 1181 1.735018 TGTGAATTTACGGACCATGCG 59.265 47.619 0.00 0.00 37.19 4.73
1119 1208 3.623060 GCATCTTATCAAGCTTGGACGAA 59.377 43.478 25.73 13.28 0.00 3.85
1456 1545 1.075601 ACTGAAGCCCATTCCTCCAA 58.924 50.000 0.00 0.00 37.08 3.53
1459 1548 1.063717 TGAAGCCCATTCCTCCAATCC 60.064 52.381 0.00 0.00 37.08 3.01
1461 1550 1.312884 AGCCCATTCCTCCAATCCTT 58.687 50.000 0.00 0.00 0.00 3.36
1545 1634 3.222603 GTCCAAGTCAGGAACATGGTTT 58.777 45.455 0.00 0.00 45.19 3.27
1554 1643 3.127548 CAGGAACATGGTTTTCTGGATCG 59.872 47.826 0.00 0.00 0.00 3.69
1629 1718 2.609459 GCATGTGAACTGGATAACCTCG 59.391 50.000 0.00 0.00 37.04 4.63
1681 1770 2.932261 GTCCACCAAACTTTCAGGACT 58.068 47.619 0.00 0.00 41.67 3.85
1793 1882 2.701951 TCCCAAGTGAAGACCGTAAGTT 59.298 45.455 0.00 0.00 0.00 2.66
1868 1957 4.176271 GTTCTATGGCAAAATGGAAGCAC 58.824 43.478 0.00 0.00 28.87 4.40
1977 2066 4.530581 GCAGTAGAGGAAGCTGCC 57.469 61.111 0.73 0.73 46.93 4.85
2030 2119 1.975363 GATGCACTTGAGCGGACTGC 61.975 60.000 0.00 0.00 46.98 4.40
2086 2175 6.070596 TGACATTGTCAGATATGGAAGTGACT 60.071 38.462 15.41 0.00 37.67 3.41
2211 2300 2.295885 GAAGCAGATCTCACCAATGGG 58.704 52.381 3.55 0.00 41.29 4.00
2392 2481 7.835634 TTTGTTTTGTTGTGTTTTATCTCCC 57.164 32.000 0.00 0.00 0.00 4.30
2446 2536 7.952671 TCTGTCCAGACTATTGGTAACATATC 58.047 38.462 0.00 0.00 38.56 1.63
2546 2636 4.910195 TCTGTGAATGAGGTGCATACTTT 58.090 39.130 0.00 0.00 35.78 2.66
2579 2669 1.135575 GGCTGAGCAGGAAACAATTCG 60.136 52.381 6.82 0.00 36.36 3.34
2601 2691 4.579340 CGCCATGAGAGTACTAAGGTTAGA 59.421 45.833 0.00 0.00 34.84 2.10
2756 2846 8.514330 TTTCTACTTCTCCAAAACAGCTTTTA 57.486 30.769 0.00 0.00 0.00 1.52
2767 2857 7.221838 TCCAAAACAGCTTTTAATTTTCTGACG 59.778 33.333 0.00 0.00 0.00 4.35
2881 2971 8.974060 TTTCATAACTCTAAGGTCAAGTTGTT 57.026 30.769 2.11 0.00 35.08 2.83
2899 2989 5.590259 AGTTGTTGTTTCAGATTACTGCAGT 59.410 36.000 25.12 25.12 43.17 4.40
2905 2995 5.221722 TGTTTCAGATTACTGCAGTTCCTCT 60.222 40.000 27.06 20.07 43.17 3.69
2939 3029 4.502282 GTGAAGTCAGCAGATCTACATTCG 59.498 45.833 0.00 0.00 0.00 3.34
3074 3164 0.179004 TTGTGAAGGAACGTGGCCAT 60.179 50.000 9.72 0.00 0.00 4.40
3203 3293 9.816787 TGATATTTTAGGTTAAAAGAGGTTGGT 57.183 29.630 1.22 0.00 40.58 3.67
3299 3389 4.773674 TCCATTGCAAGTCCTTCATGAAAT 59.226 37.500 9.88 0.00 0.00 2.17
3449 3541 5.819825 ATAGCGATGTAGATGCGAATCTA 57.180 39.130 9.20 9.20 32.36 1.98
3546 3668 4.003648 AGCATGTTAAGGTTCCTTTCTCG 58.996 43.478 9.46 0.00 0.00 4.04
3597 3719 6.246420 AGATGATTGAAGTGAAAAAGGTCG 57.754 37.500 0.00 0.00 0.00 4.79
3603 3725 3.312421 TGAAGTGAAAAAGGTCGAGCTTG 59.688 43.478 28.91 0.00 0.00 4.01
3940 4074 1.059098 ATCACTTGTCTGCAGGGACA 58.941 50.000 15.13 9.44 43.41 4.02
4018 4174 9.859427 AACATGAAACATATTTTCTGGTACATG 57.141 29.630 0.00 0.00 38.20 3.21
4019 4175 9.023962 ACATGAAACATATTTTCTGGTACATGT 57.976 29.630 2.69 2.69 38.20 3.21
4227 4383 0.747852 TTGCTCGTGTGTGTACCTCA 59.252 50.000 0.00 0.00 0.00 3.86
4246 4402 1.028905 ACAGCTGAGATCGTCTAGCC 58.971 55.000 23.35 0.00 36.86 3.93
4275 4431 7.610305 TGAACAGTAACTTTCTTTTTCCAGTCT 59.390 33.333 0.00 0.00 0.00 3.24
4592 4748 2.946990 ACAAACCACCAAAGGTAAGTCG 59.053 45.455 0.00 0.00 42.25 4.18
4601 4757 3.139077 CAAAGGTAAGTCGCCAACTCTT 58.861 45.455 0.00 0.00 37.17 2.85
4786 4950 1.602311 ACTTCTGCTGCACCTTTCAG 58.398 50.000 0.00 0.00 34.79 3.02
4884 5048 1.000163 TCGTCAAGGAGCACTTCACTC 60.000 52.381 0.00 0.00 37.29 3.51
4888 5052 1.476007 AAGGAGCACTTCACTCGCCT 61.476 55.000 0.00 0.00 32.85 5.52
4950 5114 0.932123 CGATCTCGTCGGTCATGCTG 60.932 60.000 0.00 0.00 46.47 4.41
5096 5260 2.743928 CTTCAGAGCGGGCACACC 60.744 66.667 0.00 0.00 0.00 4.16
5097 5261 3.241530 TTCAGAGCGGGCACACCT 61.242 61.111 0.00 0.00 36.97 4.00
5098 5262 3.240134 TTCAGAGCGGGCACACCTC 62.240 63.158 0.00 0.00 36.97 3.85
5189 5356 0.040058 TGCCTGGCACATGATCCTTT 59.960 50.000 19.30 0.00 38.20 3.11
5195 5362 2.288948 TGGCACATGATCCTTTTGTTGC 60.289 45.455 0.00 0.00 0.00 4.17
5198 5365 2.981805 CACATGATCCTTTTGTTGCGTG 59.018 45.455 0.00 0.00 0.00 5.34
5200 5367 3.236816 CATGATCCTTTTGTTGCGTGAC 58.763 45.455 0.00 0.00 0.00 3.67
5230 5397 4.469657 TGTAAGATGGGAAAACTTGTGCT 58.530 39.130 0.00 0.00 0.00 4.40
5305 5472 5.518487 GGTGTGTAGTTTGGTTTGTGAAATG 59.482 40.000 0.00 0.00 0.00 2.32
5312 5479 2.114616 TGGTTTGTGAAATGGTGCCTT 58.885 42.857 0.00 0.00 0.00 4.35
5313 5480 2.158986 TGGTTTGTGAAATGGTGCCTTG 60.159 45.455 0.00 0.00 0.00 3.61
5314 5481 2.482864 GTTTGTGAAATGGTGCCTTGG 58.517 47.619 0.00 0.00 0.00 3.61
5315 5482 1.047002 TTGTGAAATGGTGCCTTGGG 58.953 50.000 0.00 0.00 0.00 4.12
5316 5483 0.187117 TGTGAAATGGTGCCTTGGGA 59.813 50.000 0.00 0.00 0.00 4.37
5317 5484 0.890683 GTGAAATGGTGCCTTGGGAG 59.109 55.000 0.00 0.00 0.00 4.30
5426 5593 3.884693 TGATGTGCCTGCAATAATACCAG 59.115 43.478 0.00 0.00 0.00 4.00
5427 5594 3.364460 TGTGCCTGCAATAATACCAGT 57.636 42.857 0.00 0.00 0.00 4.00
5431 5598 3.278574 GCCTGCAATAATACCAGTGTGA 58.721 45.455 0.00 0.00 0.00 3.58
5432 5599 3.694072 GCCTGCAATAATACCAGTGTGAA 59.306 43.478 0.00 0.00 0.00 3.18
5434 5601 5.640732 CCTGCAATAATACCAGTGTGAAAC 58.359 41.667 0.00 0.00 37.35 2.78
5460 5629 7.010183 CACGCACATTGCTAAATTACTACTACT 59.990 37.037 0.00 0.00 42.25 2.57
5461 5630 8.192774 ACGCACATTGCTAAATTACTACTACTA 58.807 33.333 0.00 0.00 42.25 1.82
5462 5631 8.477709 CGCACATTGCTAAATTACTACTACTAC 58.522 37.037 0.00 0.00 42.25 2.73
5503 5672 2.162681 CCCTGAGGTTTTCATGTCACC 58.837 52.381 0.00 0.00 34.68 4.02
5587 5756 6.351033 GGTCACACTAGTCATGTTCTAATGGA 60.351 42.308 0.00 5.74 0.00 3.41
5596 5765 6.947733 AGTCATGTTCTAATGGATTGTTGGAA 59.052 34.615 0.00 0.00 0.00 3.53
5597 5766 7.029563 GTCATGTTCTAATGGATTGTTGGAAC 58.970 38.462 7.78 7.78 43.28 3.62
5600 5769 6.068010 TGTTCTAATGGATTGTTGGAACACT 58.932 36.000 11.91 0.00 45.73 3.55
5601 5770 7.227873 TGTTCTAATGGATTGTTGGAACACTA 58.772 34.615 11.91 0.00 45.73 2.74
5602 5771 7.390440 TGTTCTAATGGATTGTTGGAACACTAG 59.610 37.037 11.91 0.00 45.73 2.57
5624 5793 5.717119 AGCCAAGCATTCTCTTAAAACATG 58.283 37.500 0.00 0.00 0.00 3.21
5746 5956 1.460504 GTGGTAGTAAAGCCAAGCCC 58.539 55.000 0.00 0.00 36.41 5.19
5752 5962 0.744771 GTAAAGCCAAGCCCTCTCCG 60.745 60.000 0.00 0.00 0.00 4.63
5804 6014 6.532657 TCTTTCGTCGTTTTCAAAGTAGAAGT 59.467 34.615 0.00 0.00 0.00 3.01
5805 6015 7.701924 TCTTTCGTCGTTTTCAAAGTAGAAGTA 59.298 33.333 0.00 0.00 0.00 2.24
5806 6016 6.738352 TCGTCGTTTTCAAAGTAGAAGTAC 57.262 37.500 0.00 0.00 0.00 2.73
5847 6057 5.568023 GCATATGCATGATAAACAATGCCCT 60.568 40.000 22.84 0.00 41.59 5.19
5852 6062 4.807304 GCATGATAAACAATGCCCTGAAAG 59.193 41.667 0.00 0.00 34.23 2.62
5914 6124 5.593968 TGCTTGTCGTGTTTCTAAGACTTA 58.406 37.500 0.00 0.00 34.92 2.24
6016 6241 6.641169 TGCACACAACCATTTATTAGAACA 57.359 33.333 0.00 0.00 0.00 3.18
6031 6256 6.759497 ATTAGAACAAACCAAGTATCAGGC 57.241 37.500 0.00 0.00 0.00 4.85
6032 6257 4.373156 AGAACAAACCAAGTATCAGGCT 57.627 40.909 0.00 0.00 0.00 4.58
6033 6258 4.074970 AGAACAAACCAAGTATCAGGCTG 58.925 43.478 8.58 8.58 0.00 4.85
6034 6259 2.795329 ACAAACCAAGTATCAGGCTGG 58.205 47.619 15.73 0.00 0.00 4.85
6035 6260 2.108250 ACAAACCAAGTATCAGGCTGGT 59.892 45.455 15.73 10.75 0.00 4.00
6036 6261 2.749621 CAAACCAAGTATCAGGCTGGTC 59.250 50.000 15.73 5.58 0.00 4.02
6037 6262 1.656587 ACCAAGTATCAGGCTGGTCA 58.343 50.000 15.73 0.00 0.00 4.02
6038 6263 2.200081 ACCAAGTATCAGGCTGGTCAT 58.800 47.619 15.73 3.37 0.00 3.06
6039 6264 3.384168 ACCAAGTATCAGGCTGGTCATA 58.616 45.455 15.73 2.30 0.00 2.15
6040 6265 3.389329 ACCAAGTATCAGGCTGGTCATAG 59.611 47.826 15.73 0.00 0.00 2.23
6041 6266 3.389329 CCAAGTATCAGGCTGGTCATAGT 59.611 47.826 15.73 5.48 0.00 2.12
6042 6267 4.375272 CAAGTATCAGGCTGGTCATAGTG 58.625 47.826 15.73 3.33 0.00 2.74
6043 6268 2.968574 AGTATCAGGCTGGTCATAGTGG 59.031 50.000 15.73 0.00 0.00 4.00
6044 6269 1.135094 ATCAGGCTGGTCATAGTGGG 58.865 55.000 15.73 0.00 0.00 4.61
6045 6270 0.982852 TCAGGCTGGTCATAGTGGGG 60.983 60.000 15.73 0.00 0.00 4.96
6046 6271 0.982852 CAGGCTGGTCATAGTGGGGA 60.983 60.000 6.61 0.00 0.00 4.81
6047 6272 0.692419 AGGCTGGTCATAGTGGGGAG 60.692 60.000 0.00 0.00 0.00 4.30
6048 6273 0.983378 GGCTGGTCATAGTGGGGAGT 60.983 60.000 0.00 0.00 0.00 3.85
6049 6274 1.691482 GGCTGGTCATAGTGGGGAGTA 60.691 57.143 0.00 0.00 0.00 2.59
6050 6275 2.116238 GCTGGTCATAGTGGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
6051 6276 2.158943 GCTGGTCATAGTGGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
6052 6277 3.375699 CTGGTCATAGTGGGGAGTAACT 58.624 50.000 0.00 0.00 0.00 2.24
6053 6278 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
6054 6279 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
6055 6280 4.960469 TGGTCATAGTGGGGAGTAACTTAG 59.040 45.833 0.00 0.00 0.00 2.18
6056 6281 5.206587 GGTCATAGTGGGGAGTAACTTAGA 58.793 45.833 0.00 0.00 0.00 2.10
6057 6282 5.068855 GGTCATAGTGGGGAGTAACTTAGAC 59.931 48.000 0.00 0.00 32.58 2.59
6058 6283 5.892686 GTCATAGTGGGGAGTAACTTAGACT 59.107 44.000 0.00 0.00 31.58 3.24
6059 6284 7.059156 GTCATAGTGGGGAGTAACTTAGACTA 58.941 42.308 0.00 0.00 31.58 2.59
6060 6285 7.229106 GTCATAGTGGGGAGTAACTTAGACTAG 59.771 44.444 0.00 0.00 31.58 2.57
6061 6286 5.533333 AGTGGGGAGTAACTTAGACTAGT 57.467 43.478 0.00 0.00 0.00 2.57
6062 6287 5.262804 AGTGGGGAGTAACTTAGACTAGTG 58.737 45.833 0.00 0.00 0.00 2.74
6063 6288 5.015515 GTGGGGAGTAACTTAGACTAGTGT 58.984 45.833 0.00 0.00 0.00 3.55
6064 6289 5.125257 GTGGGGAGTAACTTAGACTAGTGTC 59.875 48.000 0.00 0.00 43.22 3.67
6065 6290 5.222192 TGGGGAGTAACTTAGACTAGTGTCA 60.222 44.000 0.00 0.00 45.20 3.58
6066 6291 5.892686 GGGGAGTAACTTAGACTAGTGTCAT 59.107 44.000 0.00 0.00 45.20 3.06
6067 6292 6.183360 GGGGAGTAACTTAGACTAGTGTCATG 60.183 46.154 0.00 0.00 45.20 3.07
6068 6293 6.267070 GGAGTAACTTAGACTAGTGTCATGC 58.733 44.000 0.00 0.00 45.20 4.06
6069 6294 6.127703 GGAGTAACTTAGACTAGTGTCATGCA 60.128 42.308 0.00 0.00 45.20 3.96
6070 6295 7.411486 AGTAACTTAGACTAGTGTCATGCAT 57.589 36.000 0.00 0.00 45.20 3.96
6071 6296 8.521170 AGTAACTTAGACTAGTGTCATGCATA 57.479 34.615 0.00 0.00 45.20 3.14
6072 6297 9.137459 AGTAACTTAGACTAGTGTCATGCATAT 57.863 33.333 0.00 0.00 45.20 1.78
6073 6298 9.186323 GTAACTTAGACTAGTGTCATGCATATG 57.814 37.037 0.00 0.00 45.20 1.78
6074 6299 7.588497 ACTTAGACTAGTGTCATGCATATGA 57.412 36.000 6.97 0.00 45.20 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 130 7.329471 CACGATTCAAGTTGAGAAATAGACTGA 59.671 37.037 5.56 0.00 0.00 3.41
121 131 7.116948 ACACGATTCAAGTTGAGAAATAGACTG 59.883 37.037 5.56 0.00 0.00 3.51
165 181 8.463930 TCAGAAGAATGTTAATCCAACTGTTT 57.536 30.769 0.00 0.00 38.05 2.83
263 279 6.728089 TGAGAAGTCATCAGAGAATATGCT 57.272 37.500 0.00 0.00 0.00 3.79
352 369 6.069615 AGGAGATTTGCCCTAAAACTAGCTTA 60.070 38.462 0.00 0.00 32.28 3.09
403 426 4.258702 TCCAGAAGAACTACAGAACAGC 57.741 45.455 0.00 0.00 0.00 4.40
426 449 5.342333 TGAAATGTTCAGTGCTAAGGGAGC 61.342 45.833 0.00 0.00 42.62 4.70
455 532 5.063204 CCCAAAGAACATACAGAACAGTCA 58.937 41.667 0.00 0.00 0.00 3.41
468 545 2.158325 AGGAGATTTGCCCCAAAGAACA 60.158 45.455 0.00 0.00 36.76 3.18
469 546 2.529632 AGGAGATTTGCCCCAAAGAAC 58.470 47.619 0.00 0.00 36.76 3.01
471 548 2.899256 CAAAGGAGATTTGCCCCAAAGA 59.101 45.455 0.00 0.00 41.77 2.52
472 549 2.027837 CCAAAGGAGATTTGCCCCAAAG 60.028 50.000 0.00 0.00 45.85 2.77
473 550 1.977129 CCAAAGGAGATTTGCCCCAAA 59.023 47.619 0.00 0.00 45.85 3.28
475 552 0.904394 GCCAAAGGAGATTTGCCCCA 60.904 55.000 0.00 0.00 45.85 4.96
476 553 0.904394 TGCCAAAGGAGATTTGCCCC 60.904 55.000 0.00 0.00 45.85 5.80
545 623 5.010820 GGAGATTTGCCGAACTATAGGTACT 59.989 44.000 4.43 0.00 46.37 2.73
546 624 5.010820 AGGAGATTTGCCGAACTATAGGTAC 59.989 44.000 4.43 0.00 0.00 3.34
626 706 3.823304 GGATATTTGTCCAGGGAGCAATC 59.177 47.826 0.00 0.00 38.20 2.67
627 707 3.464833 AGGATATTTGTCCAGGGAGCAAT 59.535 43.478 0.00 0.00 40.90 3.56
628 708 2.852449 AGGATATTTGTCCAGGGAGCAA 59.148 45.455 0.00 0.00 40.90 3.91
629 709 2.492025 AGGATATTTGTCCAGGGAGCA 58.508 47.619 0.00 0.00 40.90 4.26
630 710 3.584733 AAGGATATTTGTCCAGGGAGC 57.415 47.619 0.00 0.00 40.90 4.70
631 711 4.884164 GTCAAAGGATATTTGTCCAGGGAG 59.116 45.833 0.74 0.00 40.90 4.30
632 712 4.290985 TGTCAAAGGATATTTGTCCAGGGA 59.709 41.667 0.74 0.00 40.90 4.20
633 713 4.599041 TGTCAAAGGATATTTGTCCAGGG 58.401 43.478 0.74 0.00 40.90 4.45
634 714 6.780457 AATGTCAAAGGATATTTGTCCAGG 57.220 37.500 0.74 0.00 40.90 4.45
635 715 7.284034 AGCTAATGTCAAAGGATATTTGTCCAG 59.716 37.037 0.00 0.00 40.90 3.86
636 716 7.118723 AGCTAATGTCAAAGGATATTTGTCCA 58.881 34.615 0.00 0.63 40.90 4.02
637 717 7.573968 AGCTAATGTCAAAGGATATTTGTCC 57.426 36.000 0.00 0.00 36.43 4.02
640 720 9.455847 GCTAAAGCTAATGTCAAAGGATATTTG 57.544 33.333 0.00 0.00 36.43 2.32
673 753 2.170187 AGGAGAAGTGCCAAGATAGCAG 59.830 50.000 0.00 0.00 41.87 4.24
688 768 3.876309 AAACCTACTGCCAAAGGAGAA 57.124 42.857 0.00 0.00 39.57 2.87
694 774 3.818773 GTGAAGCTAAACCTACTGCCAAA 59.181 43.478 0.00 0.00 0.00 3.28
695 775 3.072476 AGTGAAGCTAAACCTACTGCCAA 59.928 43.478 0.00 0.00 0.00 4.52
696 776 2.637872 AGTGAAGCTAAACCTACTGCCA 59.362 45.455 0.00 0.00 0.00 4.92
701 781 6.461788 CCTGATAGGAGTGAAGCTAAACCTAC 60.462 46.154 0.00 0.00 37.67 3.18
702 782 5.598830 CCTGATAGGAGTGAAGCTAAACCTA 59.401 44.000 0.00 0.00 37.67 3.08
703 783 4.407296 CCTGATAGGAGTGAAGCTAAACCT 59.593 45.833 0.00 0.00 37.67 3.50
704 784 4.443598 CCCTGATAGGAGTGAAGCTAAACC 60.444 50.000 0.00 0.00 37.67 3.27
706 786 3.134804 GCCCTGATAGGAGTGAAGCTAAA 59.865 47.826 0.00 0.00 37.67 1.85
707 787 2.700897 GCCCTGATAGGAGTGAAGCTAA 59.299 50.000 0.00 0.00 37.67 3.09
709 789 1.127343 GCCCTGATAGGAGTGAAGCT 58.873 55.000 0.00 0.00 37.67 3.74
710 790 0.249657 CGCCCTGATAGGAGTGAAGC 60.250 60.000 0.00 0.00 37.67 3.86
711 791 1.403814 TCGCCCTGATAGGAGTGAAG 58.596 55.000 0.00 0.00 37.67 3.02
712 792 1.860641 TTCGCCCTGATAGGAGTGAA 58.139 50.000 0.00 2.95 37.67 3.18
713 793 1.964223 GATTCGCCCTGATAGGAGTGA 59.036 52.381 0.00 0.00 37.67 3.41
714 794 1.967066 AGATTCGCCCTGATAGGAGTG 59.033 52.381 0.00 0.00 37.67 3.51
715 795 2.243810 GAGATTCGCCCTGATAGGAGT 58.756 52.381 0.00 0.00 37.67 3.85
716 796 1.548269 GGAGATTCGCCCTGATAGGAG 59.452 57.143 0.00 0.00 37.67 3.69
717 797 1.148027 AGGAGATTCGCCCTGATAGGA 59.852 52.381 2.46 0.00 37.67 2.94
718 798 1.638529 AGGAGATTCGCCCTGATAGG 58.361 55.000 2.46 0.00 34.30 2.57
719 799 3.070159 TCAAAGGAGATTCGCCCTGATAG 59.930 47.826 2.46 0.00 32.12 2.08
720 800 3.038280 TCAAAGGAGATTCGCCCTGATA 58.962 45.455 2.46 0.00 32.12 2.15
721 801 1.839994 TCAAAGGAGATTCGCCCTGAT 59.160 47.619 2.46 0.00 32.12 2.90
722 802 1.066143 GTCAAAGGAGATTCGCCCTGA 60.066 52.381 2.46 4.03 32.12 3.86
723 803 1.339055 TGTCAAAGGAGATTCGCCCTG 60.339 52.381 2.46 1.69 32.12 4.45
724 804 0.984230 TGTCAAAGGAGATTCGCCCT 59.016 50.000 2.46 0.00 0.00 5.19
729 809 9.660180 AGTAAGATTTAGTGTCAAAGGAGATTC 57.340 33.333 0.00 0.00 0.00 2.52
805 885 3.515602 ATGCCAAAGGATCCCTGATAC 57.484 47.619 8.55 0.76 32.13 2.24
858 946 7.658982 TGATGATATGATAAACTCAGGAACAGC 59.341 37.037 0.00 0.00 37.28 4.40
860 948 8.485392 TGTGATGATATGATAAACTCAGGAACA 58.515 33.333 0.00 0.00 37.28 3.18
865 953 9.538508 TGTTCTGTGATGATATGATAAACTCAG 57.461 33.333 0.00 0.00 37.28 3.35
875 963 6.432607 ACAAGCTTGTTCTGTGATGATATG 57.567 37.500 26.36 0.00 38.47 1.78
961 1050 6.249359 CAACACCACATTTTGTCATTTTGTG 58.751 36.000 0.00 0.00 37.90 3.33
1069 1158 4.351192 GCATGGTCCGTAAATTCACATTC 58.649 43.478 0.00 0.00 0.00 2.67
1070 1159 3.181501 CGCATGGTCCGTAAATTCACATT 60.182 43.478 0.00 0.00 0.00 2.71
1071 1160 2.354510 CGCATGGTCCGTAAATTCACAT 59.645 45.455 0.00 0.00 0.00 3.21
1092 1181 3.003482 CCAAGCTTGATAAGATGCTCTGC 59.997 47.826 28.05 0.00 34.38 4.26
1119 1208 2.646930 TCATCAATCTTGCCGATGCTT 58.353 42.857 0.00 0.00 37.14 3.91
1456 1545 7.486407 AATAAGGTGCATCTTCAAAAAGGAT 57.514 32.000 17.29 0.00 33.03 3.24
1545 1634 2.367202 GGCCCTCCACGATCCAGAA 61.367 63.158 0.00 0.00 0.00 3.02
1629 1718 0.250252 CACCCCAAACATTTGCCACC 60.250 55.000 0.00 0.00 36.86 4.61
1868 1957 3.922171 AAGGTTCTAGCCCAAGAGATG 57.078 47.619 1.71 0.00 0.00 2.90
1977 2066 2.452813 CCCAATCCGCTGACGTTCG 61.453 63.158 0.00 0.00 37.70 3.95
2130 2219 3.306294 CCCCAGTGCAAAAAGAGAAATCC 60.306 47.826 0.00 0.00 0.00 3.01
2211 2300 3.334583 TTCCTGCTAACTGTCATGGTC 57.665 47.619 0.00 0.00 0.00 4.02
2392 2481 8.792830 TGTATCTAGAAAAGATGGGTGAAAAG 57.207 34.615 0.00 0.00 44.95 2.27
2446 2536 6.591448 GCCTGAAATTGATACAAGGGAAAAAG 59.409 38.462 0.00 0.00 0.00 2.27
2450 2540 3.694072 CGCCTGAAATTGATACAAGGGAA 59.306 43.478 0.00 0.00 0.00 3.97
2522 2612 4.701765 AGTATGCACCTCATTCACAGATC 58.298 43.478 0.00 0.00 36.63 2.75
2546 2636 2.183858 CTCAGCCTCGTCGTCGACAA 62.184 60.000 24.13 5.97 41.35 3.18
2579 2669 6.658188 ATCTAACCTTAGTACTCTCATGGC 57.342 41.667 0.00 0.00 32.61 4.40
2601 2691 2.564062 CAGTGGAAGATGCAAACCCAAT 59.436 45.455 0.00 0.00 0.00 3.16
2643 2733 9.588774 CATCAAGTTGTTGCTTAAATTTCAATG 57.411 29.630 2.11 0.00 33.23 2.82
2756 2846 4.520492 AGAAGCCACATTCGTCAGAAAATT 59.480 37.500 0.00 0.00 40.15 1.82
2767 2857 5.241728 ACCAAAGAAACTAGAAGCCACATTC 59.758 40.000 0.00 0.00 0.00 2.67
2871 2961 6.414987 GCAGTAATCTGAAACAACAACTTGAC 59.585 38.462 0.00 0.00 43.76 3.18
2881 2971 4.973168 AGGAACTGCAGTAATCTGAAACA 58.027 39.130 22.01 0.00 40.13 2.83
2899 2989 7.223584 TGACTTCACAATTTGATACAGAGGAA 58.776 34.615 2.79 0.00 32.84 3.36
2905 2995 5.997129 TCTGCTGACTTCACAATTTGATACA 59.003 36.000 2.79 0.00 32.84 2.29
2939 3029 4.222114 CAACGGAAAATTCTTCTGCAGAC 58.778 43.478 18.03 1.58 0.00 3.51
3183 3273 7.835181 TCTTCAACCAACCTCTTTTAACCTAAA 59.165 33.333 0.00 0.00 0.00 1.85
3203 3293 6.655003 GTCCATTCCTGTTGTATCTTCTTCAA 59.345 38.462 0.00 0.00 0.00 2.69
3299 3389 5.775686 CAATGAGCCAGTGAAAAGATTCAA 58.224 37.500 0.00 0.00 46.66 2.69
3431 3523 6.261118 TCATGATAGATTCGCATCTACATCG 58.739 40.000 6.94 8.08 43.53 3.84
3432 3524 7.306690 GCATCATGATAGATTCGCATCTACATC 60.307 40.741 8.15 4.18 43.53 3.06
3433 3525 6.479331 GCATCATGATAGATTCGCATCTACAT 59.521 38.462 8.15 9.73 43.53 2.29
3434 3526 5.809051 GCATCATGATAGATTCGCATCTACA 59.191 40.000 8.15 8.04 43.53 2.74
3435 3527 5.809051 TGCATCATGATAGATTCGCATCTAC 59.191 40.000 8.15 3.00 43.53 2.59
3436 3528 5.969423 TGCATCATGATAGATTCGCATCTA 58.031 37.500 8.15 7.24 44.61 1.98
3437 3529 4.828829 TGCATCATGATAGATTCGCATCT 58.171 39.130 8.15 2.45 42.83 2.90
3438 3530 5.541098 TTGCATCATGATAGATTCGCATC 57.459 39.130 14.66 0.00 30.22 3.91
3587 3709 3.251004 ACATGACAAGCTCGACCTTTTTC 59.749 43.478 0.00 0.00 0.00 2.29
3597 3719 7.065085 ACAAGATAACATACACATGACAAGCTC 59.935 37.037 0.00 0.00 35.96 4.09
3603 3725 7.700322 ATCGACAAGATAACATACACATGAC 57.300 36.000 0.00 0.00 37.93 3.06
4018 4174 5.438761 AAGCAAAGAACACCATGTAAGAC 57.561 39.130 0.00 0.00 0.00 3.01
4019 4175 4.518970 GGAAGCAAAGAACACCATGTAAGA 59.481 41.667 0.00 0.00 0.00 2.10
4092 4248 0.245539 CCCCAACAATGCAAGCTCTG 59.754 55.000 0.00 0.00 0.00 3.35
4095 4251 1.823169 CTGCCCCAACAATGCAAGCT 61.823 55.000 0.00 0.00 34.06 3.74
4227 4383 1.028905 GGCTAGACGATCTCAGCTGT 58.971 55.000 14.67 0.00 34.41 4.40
4246 4402 5.681543 GGAAAAAGAAAGTTACTGTTCAGCG 59.318 40.000 0.00 0.00 0.00 5.18
4275 4431 2.100197 CCTCCGGAGTGATAGTGAACA 58.900 52.381 29.25 0.00 0.00 3.18
4395 4551 3.679980 GCAGCAGTTGAAGAATAGTCGAA 59.320 43.478 0.00 0.00 0.00 3.71
4402 4558 3.201708 AGGGATAGCAGCAGTTGAAGAAT 59.798 43.478 0.00 0.00 0.00 2.40
4592 4748 5.126396 AGTGCAGAATTTAAAGAGTTGGC 57.874 39.130 0.00 0.00 0.00 4.52
4601 4757 7.174253 AGGTCATTCGTTAAGTGCAGAATTTAA 59.826 33.333 0.00 0.00 31.70 1.52
4906 5070 1.432270 GAGGTATGCGTTGCAGGCTC 61.432 60.000 12.28 4.31 43.65 4.70
4950 5114 1.129326 GATATGTACGTGCTGTCGCC 58.871 55.000 4.97 0.00 34.43 5.54
5067 5231 0.668706 CTCTGAAGTCACTGGCCACG 60.669 60.000 0.00 0.00 0.00 4.94
5096 5260 3.285215 GCCATCGCCATGCAGGAG 61.285 66.667 0.00 0.00 41.22 3.69
5189 5356 1.163420 AAGATGCCGTCACGCAACAA 61.163 50.000 0.00 0.00 43.24 2.83
5195 5362 1.990799 TCTTACAAGATGCCGTCACG 58.009 50.000 0.00 0.00 0.00 4.35
5230 5397 2.682836 TCAGTTCATCGCGTCAATCAA 58.317 42.857 5.77 0.00 0.00 2.57
5305 5472 0.250513 CTCTACACTCCCAAGGCACC 59.749 60.000 0.00 0.00 0.00 5.01
5312 5479 2.179427 CCATCACACTCTACACTCCCA 58.821 52.381 0.00 0.00 0.00 4.37
5313 5480 2.457598 TCCATCACACTCTACACTCCC 58.542 52.381 0.00 0.00 0.00 4.30
5314 5481 3.511934 ACTTCCATCACACTCTACACTCC 59.488 47.826 0.00 0.00 0.00 3.85
5315 5482 4.792521 ACTTCCATCACACTCTACACTC 57.207 45.455 0.00 0.00 0.00 3.51
5316 5483 5.717178 ACATACTTCCATCACACTCTACACT 59.283 40.000 0.00 0.00 0.00 3.55
5317 5484 5.967088 ACATACTTCCATCACACTCTACAC 58.033 41.667 0.00 0.00 0.00 2.90
5426 5593 0.845768 GCAATGTGCGTGTTTCACAC 59.154 50.000 0.00 0.00 45.83 3.82
5427 5594 3.248626 GCAATGTGCGTGTTTCACA 57.751 47.368 0.00 0.00 46.86 3.58
5437 5604 9.530633 AGTAGTAGTAGTAATTTAGCAATGTGC 57.469 33.333 0.00 0.00 45.46 4.57
5460 5629 7.455638 AGGGTGATACCAAGTAAAGTACAAGTA 59.544 37.037 0.00 0.00 41.02 2.24
5461 5630 6.271624 AGGGTGATACCAAGTAAAGTACAAGT 59.728 38.462 0.00 0.00 41.02 3.16
5462 5631 6.594159 CAGGGTGATACCAAGTAAAGTACAAG 59.406 42.308 0.00 0.00 41.02 3.16
5503 5672 7.201257 CGTACATACAAACAAGCAAATCATGTG 60.201 37.037 0.00 0.00 0.00 3.21
5587 5756 2.558359 GCTTGGCTAGTGTTCCAACAAT 59.442 45.455 0.00 0.00 41.21 2.71
5596 5765 3.710209 AAGAGAATGCTTGGCTAGTGT 57.290 42.857 0.00 0.00 0.00 3.55
5597 5766 6.072508 TGTTTTAAGAGAATGCTTGGCTAGTG 60.073 38.462 0.00 0.00 0.00 2.74
5598 5767 6.003950 TGTTTTAAGAGAATGCTTGGCTAGT 58.996 36.000 0.00 0.00 0.00 2.57
5600 5769 6.434028 ACATGTTTTAAGAGAATGCTTGGCTA 59.566 34.615 0.00 0.00 0.00 3.93
5601 5770 5.244626 ACATGTTTTAAGAGAATGCTTGGCT 59.755 36.000 0.00 0.00 0.00 4.75
5602 5771 5.473039 ACATGTTTTAAGAGAATGCTTGGC 58.527 37.500 0.00 0.00 0.00 4.52
5804 6014 7.926555 GCATATGCAAGGAAGAAAGTAGTAGTA 59.073 37.037 22.84 0.00 41.59 1.82
5805 6015 6.763610 GCATATGCAAGGAAGAAAGTAGTAGT 59.236 38.462 22.84 0.00 41.59 2.73
5806 6016 7.183580 GCATATGCAAGGAAGAAAGTAGTAG 57.816 40.000 22.84 0.00 41.59 2.57
5886 6096 5.986741 TCTTAGAAACACGACAAGCAATACA 59.013 36.000 0.00 0.00 0.00 2.29
5914 6124 1.270907 AGCCATCTTGTTCTCGACCT 58.729 50.000 0.00 0.00 0.00 3.85
6016 6241 2.375174 TGACCAGCCTGATACTTGGTTT 59.625 45.455 0.00 0.00 43.65 3.27
6029 6254 0.983378 ACTCCCCACTATGACCAGCC 60.983 60.000 0.00 0.00 0.00 4.85
6030 6255 1.789523 TACTCCCCACTATGACCAGC 58.210 55.000 0.00 0.00 0.00 4.85
6031 6256 3.375699 AGTTACTCCCCACTATGACCAG 58.624 50.000 0.00 0.00 0.00 4.00
6032 6257 3.484953 AGTTACTCCCCACTATGACCA 57.515 47.619 0.00 0.00 0.00 4.02
6033 6258 5.068855 GTCTAAGTTACTCCCCACTATGACC 59.931 48.000 0.00 0.00 0.00 4.02
6034 6259 5.892686 AGTCTAAGTTACTCCCCACTATGAC 59.107 44.000 0.00 0.00 0.00 3.06
6035 6260 6.088541 AGTCTAAGTTACTCCCCACTATGA 57.911 41.667 0.00 0.00 0.00 2.15
6036 6261 7.013464 CACTAGTCTAAGTTACTCCCCACTATG 59.987 44.444 0.00 0.00 0.00 2.23
6037 6262 7.061688 CACTAGTCTAAGTTACTCCCCACTAT 58.938 42.308 0.00 0.00 0.00 2.12
6038 6263 6.012157 ACACTAGTCTAAGTTACTCCCCACTA 60.012 42.308 0.00 0.00 0.00 2.74
6039 6264 5.222296 ACACTAGTCTAAGTTACTCCCCACT 60.222 44.000 0.00 0.00 0.00 4.00
6040 6265 5.015515 ACACTAGTCTAAGTTACTCCCCAC 58.984 45.833 0.00 0.00 0.00 4.61
6041 6266 5.222192 TGACACTAGTCTAAGTTACTCCCCA 60.222 44.000 0.00 0.00 45.20 4.96
6042 6267 5.259632 TGACACTAGTCTAAGTTACTCCCC 58.740 45.833 0.00 0.00 45.20 4.81
6043 6268 6.680872 GCATGACACTAGTCTAAGTTACTCCC 60.681 46.154 0.00 0.00 45.20 4.30
6044 6269 6.127703 TGCATGACACTAGTCTAAGTTACTCC 60.128 42.308 0.00 0.00 45.20 3.85
6045 6270 6.853720 TGCATGACACTAGTCTAAGTTACTC 58.146 40.000 0.00 0.00 45.20 2.59
6046 6271 6.835819 TGCATGACACTAGTCTAAGTTACT 57.164 37.500 0.00 0.00 45.20 2.24
6047 6272 9.186323 CATATGCATGACACTAGTCTAAGTTAC 57.814 37.037 10.16 0.00 45.20 2.50
6048 6273 9.131791 TCATATGCATGACACTAGTCTAAGTTA 57.868 33.333 10.16 0.00 45.20 2.24
6049 6274 8.011844 TCATATGCATGACACTAGTCTAAGTT 57.988 34.615 10.16 0.00 45.20 2.66
6050 6275 7.588497 TCATATGCATGACACTAGTCTAAGT 57.412 36.000 10.16 0.00 45.20 2.24


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

AutoCloner maintained by Alex Coulton.