Multiple sequence alignment - TraesCS4D01G202400

Loading Multiple Alignment...

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 TraesCS4D01G202400 chr4D 100.000 3210 0 0 474 3683 349412176 349408967 0.000000e+00 5928.0
1 TraesCS4D01G202400 chr4D 98.636 220 3 0 474 693 418518877 418518658 1.240000e-104 390.0
2 TraesCS4D01G202400 chr4D 100.000 184 0 0 1 184 349412649 349412466 1.270000e-89 340.0
3 TraesCS4D01G202400 chr4D 96.739 184 6 0 1 184 418519101 418518918 1.280000e-79 307.0
4 TraesCS4D01G202400 chr4D 85.185 81 12 0 1751 1831 369861847 369861767 2.360000e-12 84.2
5 TraesCS4D01G202400 chr4D 85.185 81 12 0 1751 1831 369874733 369874813 2.360000e-12 84.2
6 TraesCS4D01G202400 chr4D 100.000 35 0 0 655 689 297379551 297379585 8.540000e-07 65.8
7 TraesCS4D01G202400 chr4B 91.685 2730 150 27 914 3606 432258445 432255756 0.000000e+00 3712.0
8 TraesCS4D01G202400 chr4B 91.946 149 9 3 684 829 432258740 432258592 4.820000e-49 206.0
9 TraesCS4D01G202400 chr4B 85.047 107 7 3 816 913 432258579 432258473 2.340000e-17 100.0
10 TraesCS4D01G202400 chr4B 83.562 73 12 0 1763 1835 455011815 455011743 6.600000e-08 69.4
11 TraesCS4D01G202400 chr4A 93.826 1717 78 9 1976 3669 115575133 115576844 0.000000e+00 2558.0
12 TraesCS4D01G202400 chr4A 90.623 1269 70 18 684 1922 115573615 115574864 0.000000e+00 1639.0
13 TraesCS4D01G202400 chr4A 82.278 79 13 1 1753 1831 94824199 94824276 2.370000e-07 67.6
14 TraesCS4D01G202400 chr5A 94.318 88 4 1 606 692 30418069 30418156 2.310000e-27 134.0
15 TraesCS4D01G202400 chr7B 83.824 136 17 5 560 692 702174402 702174269 1.390000e-24 124.0
16 TraesCS4D01G202400 chr7D 81.343 134 16 8 552 680 364626329 364626458 2.340000e-17 100.0
17 TraesCS4D01G202400 chr2D 100.000 40 0 0 655 694 628827424 628827463 1.420000e-09 75.0
18 TraesCS4D01G202400 chr1D 100.000 35 0 0 655 689 357456207 357456173 8.540000e-07 65.8


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 TraesCS4D01G202400 chr4D 349408967 349412649 3682 True 3134.000000 5928 100.000000 1 3683 2 chr4D.!!$R2 3682
1 TraesCS4D01G202400 chr4B 432255756 432258740 2984 True 1339.333333 3712 89.559333 684 3606 3 chr4B.!!$R2 2922
2 TraesCS4D01G202400 chr4A 115573615 115576844 3229 False 2098.500000 2558 92.224500 684 3669 2 chr4A.!!$F2 2985

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
71 72 0.031314 AGCAGCATCATCTACGACGG 59.969 55.0 0.00 0.00 0.0 4.79 F
508 509 0.033503 TCTGTAGGAGGGATGCGTGA 60.034 55.0 0.00 0.00 0.0 4.35 F
511 512 0.103208 GTAGGAGGGATGCGTGAGTG 59.897 60.0 0.00 0.00 0.0 3.51 F
582 583 0.175760 GTGGCTTCTCTGCGTGGATA 59.824 55.0 0.00 0.00 0.0 2.59 F
1535 1614 0.250234 CTGGATGACATGTCGGGTGT 59.750 55.0 20.54 4.48 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 1761 0.107654 CCGGACAAATGACCTCTCCC 60.108 60.000 0.00 0.0 0.00 4.30 R
1743 1834 0.189327 ATCTTGGGCCCCATTCCATC 59.811 55.000 22.27 0.0 31.53 3.51 R
2165 2496 1.463444 GATTCACCGAGGTTCCAAACG 59.537 52.381 0.00 0.0 0.00 3.60 R
2178 2509 1.463674 ATTGGACCGCTTGATTCACC 58.536 50.000 0.00 0.0 0.00 4.02 R
3481 3836 0.737715 GAGTCGAGGTGTCCATGTGC 60.738 60.000 0.00 0.0 0.00 4.57 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
17 18 3.788766 ACGCCGTGCTCAAATCGC 61.789 61.111 0.00 0.00 0.00 4.58
18 19 3.787676 CGCCGTGCTCAAATCGCA 61.788 61.111 0.00 0.00 34.52 5.10
19 20 2.099062 GCCGTGCTCAAATCGCAG 59.901 61.111 0.00 0.00 38.19 5.18
20 21 2.099062 CCGTGCTCAAATCGCAGC 59.901 61.111 0.00 0.00 38.19 5.25
21 22 2.393768 CCGTGCTCAAATCGCAGCT 61.394 57.895 0.00 0.00 38.19 4.24
22 23 1.059994 CGTGCTCAAATCGCAGCTC 59.940 57.895 0.00 0.00 38.19 4.09
23 24 1.059994 GTGCTCAAATCGCAGCTCG 59.940 57.895 0.00 0.00 38.19 5.03
40 41 3.945434 GACGGCCATGCGCAGATG 61.945 66.667 18.32 10.52 40.31 2.90
43 44 3.962421 GGCCATGCGCAGATGCTC 61.962 66.667 18.32 8.52 40.31 4.26
44 45 3.962421 GCCATGCGCAGATGCTCC 61.962 66.667 18.32 0.00 39.32 4.70
45 46 3.285215 CCATGCGCAGATGCTCCC 61.285 66.667 18.32 0.00 39.32 4.30
46 47 3.285215 CATGCGCAGATGCTCCCC 61.285 66.667 18.32 0.00 39.32 4.81
47 48 3.800833 ATGCGCAGATGCTCCCCA 61.801 61.111 18.32 0.00 39.32 4.96
48 49 3.129362 ATGCGCAGATGCTCCCCAT 62.129 57.895 18.32 0.00 39.32 4.00
54 55 2.976903 GATGCTCCCCATCGCAGC 60.977 66.667 0.00 0.00 40.84 5.25
55 56 3.762429 GATGCTCCCCATCGCAGCA 62.762 63.158 0.00 0.00 46.87 4.41
56 57 3.769369 ATGCTCCCCATCGCAGCAG 62.769 63.158 0.00 0.00 46.06 4.24
58 59 4.478371 CTCCCCATCGCAGCAGCA 62.478 66.667 0.82 0.00 42.27 4.41
59 60 3.769369 CTCCCCATCGCAGCAGCAT 62.769 63.158 0.82 0.00 42.27 3.79
60 61 3.285215 CCCCATCGCAGCAGCATC 61.285 66.667 0.82 0.00 42.27 3.91
61 62 2.515290 CCCATCGCAGCAGCATCA 60.515 61.111 0.82 0.00 42.27 3.07
62 63 1.897137 CCCATCGCAGCAGCATCAT 60.897 57.895 0.82 0.00 42.27 2.45
63 64 1.574925 CCATCGCAGCAGCATCATC 59.425 57.895 0.82 0.00 42.27 2.92
64 65 0.885150 CCATCGCAGCAGCATCATCT 60.885 55.000 0.82 0.00 42.27 2.90
65 66 1.607251 CCATCGCAGCAGCATCATCTA 60.607 52.381 0.82 0.00 42.27 1.98
66 67 1.459975 CATCGCAGCAGCATCATCTAC 59.540 52.381 0.82 0.00 42.27 2.59
67 68 0.595825 TCGCAGCAGCATCATCTACG 60.596 55.000 0.82 0.00 42.27 3.51
68 69 0.595825 CGCAGCAGCATCATCTACGA 60.596 55.000 0.82 0.00 42.27 3.43
69 70 0.857935 GCAGCAGCATCATCTACGAC 59.142 55.000 0.00 0.00 41.58 4.34
70 71 1.126890 CAGCAGCATCATCTACGACG 58.873 55.000 0.00 0.00 0.00 5.12
71 72 0.031314 AGCAGCATCATCTACGACGG 59.969 55.000 0.00 0.00 0.00 4.79
72 73 1.552348 GCAGCATCATCTACGACGGC 61.552 60.000 0.00 0.00 0.00 5.68
73 74 0.941463 CAGCATCATCTACGACGGCC 60.941 60.000 0.00 0.00 0.00 6.13
74 75 1.067416 GCATCATCTACGACGGCCA 59.933 57.895 2.24 0.00 0.00 5.36
75 76 0.319900 GCATCATCTACGACGGCCAT 60.320 55.000 2.24 0.00 0.00 4.40
76 77 1.422388 CATCATCTACGACGGCCATG 58.578 55.000 2.24 0.00 0.00 3.66
77 78 0.318441 ATCATCTACGACGGCCATGG 59.682 55.000 7.63 7.63 0.00 3.66
78 79 1.956170 CATCTACGACGGCCATGGC 60.956 63.158 29.47 29.47 41.06 4.40
105 106 3.534160 TCGCGTGTCGAAGCTTTC 58.466 55.556 5.77 0.00 45.36 2.62
106 107 2.019951 TCGCGTGTCGAAGCTTTCC 61.020 57.895 5.77 0.00 45.36 3.13
107 108 2.022129 CGCGTGTCGAAGCTTTCCT 61.022 57.895 0.00 0.00 41.67 3.36
108 109 1.782181 GCGTGTCGAAGCTTTCCTC 59.218 57.895 0.00 0.00 0.00 3.71
109 110 1.945776 GCGTGTCGAAGCTTTCCTCG 61.946 60.000 0.00 0.00 0.00 4.63
110 111 0.386858 CGTGTCGAAGCTTTCCTCGA 60.387 55.000 0.00 1.49 0.00 4.04
114 115 1.244816 TCGAAGCTTTCCTCGACTCA 58.755 50.000 0.00 0.00 0.00 3.41
115 116 1.819288 TCGAAGCTTTCCTCGACTCAT 59.181 47.619 0.00 0.00 0.00 2.90
116 117 1.923204 CGAAGCTTTCCTCGACTCATG 59.077 52.381 0.00 0.00 0.00 3.07
117 118 2.416027 CGAAGCTTTCCTCGACTCATGA 60.416 50.000 0.00 0.00 0.00 3.07
118 119 2.663826 AGCTTTCCTCGACTCATGAC 57.336 50.000 0.00 0.00 0.00 3.06
119 120 1.895798 AGCTTTCCTCGACTCATGACA 59.104 47.619 0.00 0.00 0.00 3.58
120 121 1.996191 GCTTTCCTCGACTCATGACAC 59.004 52.381 0.00 0.00 0.00 3.67
121 122 2.353208 GCTTTCCTCGACTCATGACACT 60.353 50.000 0.00 0.00 0.00 3.55
122 123 3.249091 CTTTCCTCGACTCATGACACTG 58.751 50.000 0.00 0.00 0.00 3.66
123 124 0.528017 TCCTCGACTCATGACACTGC 59.472 55.000 0.00 0.00 0.00 4.40
124 125 0.799917 CCTCGACTCATGACACTGCG 60.800 60.000 0.00 0.00 0.00 5.18
125 126 0.799917 CTCGACTCATGACACTGCGG 60.800 60.000 0.00 0.00 0.00 5.69
126 127 1.080501 CGACTCATGACACTGCGGT 60.081 57.895 0.00 0.00 0.00 5.68
127 128 1.073216 CGACTCATGACACTGCGGTC 61.073 60.000 0.00 0.00 38.29 4.79
128 129 1.073216 GACTCATGACACTGCGGTCG 61.073 60.000 0.00 0.00 40.72 4.79
129 130 2.432456 TCATGACACTGCGGTCGC 60.432 61.111 8.54 8.54 40.72 5.19
130 131 2.433145 CATGACACTGCGGTCGCT 60.433 61.111 16.36 0.00 40.72 4.93
131 132 2.433145 ATGACACTGCGGTCGCTG 60.433 61.111 18.05 18.05 40.72 5.18
165 166 4.086178 CACGCAGCTGCAGCAGTC 62.086 66.667 38.24 24.24 45.16 3.51
169 170 3.117171 CAGCTGCAGCAGTCCGTC 61.117 66.667 38.24 8.57 45.16 4.79
170 171 4.731612 AGCTGCAGCAGTCCGTCG 62.732 66.667 38.24 0.00 45.16 5.12
493 494 2.502745 AGGAGAGAGAGAGGGATCTGT 58.497 52.381 0.00 0.00 0.00 3.41
494 495 3.675613 AGGAGAGAGAGAGGGATCTGTA 58.324 50.000 0.00 0.00 0.00 2.74
495 496 3.652869 AGGAGAGAGAGAGGGATCTGTAG 59.347 52.174 0.00 0.00 0.00 2.74
496 497 3.244911 GGAGAGAGAGAGGGATCTGTAGG 60.245 56.522 0.00 0.00 0.00 3.18
497 498 3.650942 GAGAGAGAGAGGGATCTGTAGGA 59.349 52.174 0.00 0.00 0.00 2.94
498 499 3.652869 AGAGAGAGAGGGATCTGTAGGAG 59.347 52.174 0.00 0.00 0.00 3.69
499 500 2.716424 AGAGAGAGGGATCTGTAGGAGG 59.284 54.545 0.00 0.00 0.00 4.30
500 501 1.786441 AGAGAGGGATCTGTAGGAGGG 59.214 57.143 0.00 0.00 0.00 4.30
501 502 1.783979 GAGAGGGATCTGTAGGAGGGA 59.216 57.143 0.00 0.00 0.00 4.20
502 503 2.381961 GAGAGGGATCTGTAGGAGGGAT 59.618 54.545 0.00 0.00 0.00 3.85
503 504 2.111613 AGAGGGATCTGTAGGAGGGATG 59.888 54.545 0.00 0.00 0.00 3.51
504 505 0.980423 GGGATCTGTAGGAGGGATGC 59.020 60.000 0.00 0.00 0.00 3.91
505 506 0.605589 GGATCTGTAGGAGGGATGCG 59.394 60.000 0.00 0.00 0.00 4.73
506 507 1.333177 GATCTGTAGGAGGGATGCGT 58.667 55.000 0.00 0.00 0.00 5.24
507 508 1.000283 GATCTGTAGGAGGGATGCGTG 60.000 57.143 0.00 0.00 0.00 5.34
508 509 0.033503 TCTGTAGGAGGGATGCGTGA 60.034 55.000 0.00 0.00 0.00 4.35
509 510 0.387202 CTGTAGGAGGGATGCGTGAG 59.613 60.000 0.00 0.00 0.00 3.51
510 511 0.324368 TGTAGGAGGGATGCGTGAGT 60.324 55.000 0.00 0.00 0.00 3.41
511 512 0.103208 GTAGGAGGGATGCGTGAGTG 59.897 60.000 0.00 0.00 0.00 3.51
512 513 1.676678 TAGGAGGGATGCGTGAGTGC 61.677 60.000 0.00 0.00 0.00 4.40
513 514 2.887568 GAGGGATGCGTGAGTGCG 60.888 66.667 0.00 0.00 37.81 5.34
514 515 3.356639 GAGGGATGCGTGAGTGCGA 62.357 63.158 0.00 0.00 37.81 5.10
515 516 2.887568 GGGATGCGTGAGTGCGAG 60.888 66.667 0.00 0.00 37.81 5.03
516 517 2.887568 GGATGCGTGAGTGCGAGG 60.888 66.667 0.00 0.00 37.81 4.63
517 518 2.181777 GATGCGTGAGTGCGAGGA 59.818 61.111 0.00 0.00 37.81 3.71
518 519 1.446099 GATGCGTGAGTGCGAGGAA 60.446 57.895 0.00 0.00 37.81 3.36
519 520 1.416813 GATGCGTGAGTGCGAGGAAG 61.417 60.000 0.00 0.00 37.81 3.46
520 521 1.877576 ATGCGTGAGTGCGAGGAAGA 61.878 55.000 0.00 0.00 37.81 2.87
521 522 2.089349 GCGTGAGTGCGAGGAAGAC 61.089 63.158 0.00 0.00 0.00 3.01
522 523 1.797933 CGTGAGTGCGAGGAAGACG 60.798 63.158 0.00 0.00 0.00 4.18
523 524 1.579932 GTGAGTGCGAGGAAGACGA 59.420 57.895 0.00 0.00 0.00 4.20
524 525 0.729816 GTGAGTGCGAGGAAGACGAC 60.730 60.000 0.00 0.00 0.00 4.34
525 526 1.512310 GAGTGCGAGGAAGACGACG 60.512 63.158 0.00 0.00 0.00 5.12
526 527 3.173240 GTGCGAGGAAGACGACGC 61.173 66.667 0.00 0.00 44.85 5.19
528 529 3.173240 GCGAGGAAGACGACGCAC 61.173 66.667 0.00 0.00 44.36 5.34
529 530 2.504244 CGAGGAAGACGACGCACC 60.504 66.667 0.00 0.00 0.00 5.01
530 531 2.504244 GAGGAAGACGACGCACCG 60.504 66.667 0.00 0.00 0.00 4.94
531 532 2.974489 GAGGAAGACGACGCACCGA 61.974 63.158 0.00 0.00 0.00 4.69
532 533 2.804090 GGAAGACGACGCACCGAC 60.804 66.667 0.00 0.00 0.00 4.79
542 543 3.323136 GCACCGACGCAGCGATAG 61.323 66.667 24.65 11.44 0.00 2.08
543 544 2.655364 CACCGACGCAGCGATAGG 60.655 66.667 24.65 22.02 0.00 2.57
544 545 2.827190 ACCGACGCAGCGATAGGA 60.827 61.111 24.65 0.00 0.00 2.94
545 546 2.411701 CCGACGCAGCGATAGGAA 59.588 61.111 24.65 0.00 0.00 3.36
546 547 1.226859 CCGACGCAGCGATAGGAAA 60.227 57.895 24.65 0.00 0.00 3.13
547 548 1.209275 CCGACGCAGCGATAGGAAAG 61.209 60.000 24.65 2.93 0.00 2.62
548 549 0.248498 CGACGCAGCGATAGGAAAGA 60.248 55.000 24.65 0.00 0.00 2.52
549 550 1.797713 CGACGCAGCGATAGGAAAGAA 60.798 52.381 24.65 0.00 0.00 2.52
550 551 2.268298 GACGCAGCGATAGGAAAGAAA 58.732 47.619 24.65 0.00 0.00 2.52
551 552 2.671396 GACGCAGCGATAGGAAAGAAAA 59.329 45.455 24.65 0.00 0.00 2.29
552 553 3.071479 ACGCAGCGATAGGAAAGAAAAA 58.929 40.909 24.65 0.00 0.00 1.94
566 567 2.961768 AAAAATGAGCGGCCGTGG 59.038 55.556 28.70 0.00 0.00 4.94
567 568 3.281359 AAAAATGAGCGGCCGTGGC 62.281 57.895 28.70 16.61 41.06 5.01
568 569 4.722700 AAATGAGCGGCCGTGGCT 62.723 61.111 28.70 16.00 45.00 4.75
569 570 4.722700 AATGAGCGGCCGTGGCTT 62.723 61.111 28.70 12.92 41.72 4.35
578 579 3.114616 CCGTGGCTTCTCTGCGTG 61.115 66.667 0.00 0.00 0.00 5.34
579 580 3.114616 CGTGGCTTCTCTGCGTGG 61.115 66.667 0.00 0.00 0.00 4.94
580 581 2.343758 GTGGCTTCTCTGCGTGGA 59.656 61.111 0.00 0.00 0.00 4.02
581 582 1.078848 GTGGCTTCTCTGCGTGGAT 60.079 57.895 0.00 0.00 0.00 3.41
582 583 0.175760 GTGGCTTCTCTGCGTGGATA 59.824 55.000 0.00 0.00 0.00 2.59
583 584 0.901827 TGGCTTCTCTGCGTGGATAA 59.098 50.000 0.00 0.00 0.00 1.75
584 585 1.134699 TGGCTTCTCTGCGTGGATAAG 60.135 52.381 0.00 0.00 0.00 1.73
585 586 1.137086 GGCTTCTCTGCGTGGATAAGA 59.863 52.381 8.29 0.00 0.00 2.10
586 587 2.197577 GCTTCTCTGCGTGGATAAGAC 58.802 52.381 8.29 0.00 0.00 3.01
587 588 2.455032 CTTCTCTGCGTGGATAAGACG 58.545 52.381 0.00 0.00 39.87 4.18
588 589 0.738975 TCTCTGCGTGGATAAGACGG 59.261 55.000 0.00 0.00 37.30 4.79
589 590 0.738975 CTCTGCGTGGATAAGACGGA 59.261 55.000 0.00 0.00 37.30 4.69
590 591 3.258225 CTGCGTGGATAAGACGGAG 57.742 57.895 0.00 0.00 46.53 4.63
591 592 2.876581 TGCGTGGATAAGACGGAGA 58.123 52.632 0.00 0.00 37.30 3.71
592 593 1.399714 TGCGTGGATAAGACGGAGAT 58.600 50.000 0.00 0.00 37.30 2.75
593 594 1.067060 TGCGTGGATAAGACGGAGATG 59.933 52.381 0.00 0.00 37.30 2.90
594 595 1.603172 GCGTGGATAAGACGGAGATGG 60.603 57.143 0.00 0.00 37.30 3.51
595 596 1.000163 CGTGGATAAGACGGAGATGGG 60.000 57.143 0.00 0.00 33.08 4.00
596 597 2.040178 GTGGATAAGACGGAGATGGGT 58.960 52.381 0.00 0.00 0.00 4.51
597 598 2.039418 TGGATAAGACGGAGATGGGTG 58.961 52.381 0.00 0.00 0.00 4.61
598 599 2.317040 GGATAAGACGGAGATGGGTGA 58.683 52.381 0.00 0.00 0.00 4.02
599 600 2.297597 GGATAAGACGGAGATGGGTGAG 59.702 54.545 0.00 0.00 0.00 3.51
600 601 1.112113 TAAGACGGAGATGGGTGAGC 58.888 55.000 0.00 0.00 0.00 4.26
601 602 1.949847 AAGACGGAGATGGGTGAGCG 61.950 60.000 0.00 0.00 0.00 5.03
602 603 3.432051 GACGGAGATGGGTGAGCGG 62.432 68.421 0.00 0.00 0.00 5.52
603 604 4.899239 CGGAGATGGGTGAGCGGC 62.899 72.222 0.00 0.00 0.00 6.53
604 605 4.899239 GGAGATGGGTGAGCGGCG 62.899 72.222 0.51 0.51 0.00 6.46
632 633 4.129737 CCAGGGACGCGTGTCGAT 62.130 66.667 20.70 10.66 46.49 3.59
633 634 2.579787 CAGGGACGCGTGTCGATC 60.580 66.667 20.70 13.91 46.49 3.69
634 635 4.175489 AGGGACGCGTGTCGATCG 62.175 66.667 20.70 9.36 46.49 3.69
641 642 2.278206 CGTGTCGATCGCTGGAGG 60.278 66.667 11.09 0.00 0.00 4.30
642 643 2.761195 CGTGTCGATCGCTGGAGGA 61.761 63.158 11.09 0.00 0.00 3.71
643 644 1.064946 GTGTCGATCGCTGGAGGAG 59.935 63.158 11.09 0.00 0.00 3.69
644 645 2.121538 TGTCGATCGCTGGAGGAGG 61.122 63.158 11.09 0.00 0.00 4.30
645 646 3.219928 TCGATCGCTGGAGGAGGC 61.220 66.667 11.09 0.00 0.00 4.70
646 647 3.222855 CGATCGCTGGAGGAGGCT 61.223 66.667 0.26 0.00 0.00 4.58
647 648 2.790791 CGATCGCTGGAGGAGGCTT 61.791 63.158 0.26 0.00 0.00 4.35
648 649 1.227497 GATCGCTGGAGGAGGCTTG 60.227 63.158 0.00 0.00 0.00 4.01
649 650 3.397613 ATCGCTGGAGGAGGCTTGC 62.398 63.158 0.00 0.00 0.00 4.01
651 652 4.400961 GCTGGAGGAGGCTTGCGT 62.401 66.667 0.00 0.00 0.00 5.24
652 653 2.125350 CTGGAGGAGGCTTGCGTC 60.125 66.667 6.75 6.75 0.00 5.19
653 654 2.604686 TGGAGGAGGCTTGCGTCT 60.605 61.111 13.74 2.14 0.00 4.18
654 655 2.185608 GGAGGAGGCTTGCGTCTC 59.814 66.667 13.74 9.57 41.20 3.36
655 656 2.202676 GAGGAGGCTTGCGTCTCG 60.203 66.667 13.74 0.00 42.87 4.04
676 677 3.813529 CTGTTTTCAGCCGGTCTAAAG 57.186 47.619 1.90 0.00 41.24 1.85
677 678 1.877443 TGTTTTCAGCCGGTCTAAAGC 59.123 47.619 1.90 4.00 0.00 3.51
678 679 1.877443 GTTTTCAGCCGGTCTAAAGCA 59.123 47.619 1.90 0.00 0.00 3.91
679 680 2.264005 TTTCAGCCGGTCTAAAGCAA 57.736 45.000 1.90 0.00 0.00 3.91
680 681 1.808411 TTCAGCCGGTCTAAAGCAAG 58.192 50.000 1.90 0.00 0.00 4.01
681 682 0.673644 TCAGCCGGTCTAAAGCAAGC 60.674 55.000 1.90 0.00 0.00 4.01
682 683 1.741770 AGCCGGTCTAAAGCAAGCG 60.742 57.895 1.90 0.00 36.23 4.68
683 684 2.033194 GCCGGTCTAAAGCAAGCGT 61.033 57.895 1.90 0.00 34.76 5.07
684 685 1.574702 GCCGGTCTAAAGCAAGCGTT 61.575 55.000 1.90 0.00 34.76 4.84
685 686 0.872388 CCGGTCTAAAGCAAGCGTTT 59.128 50.000 0.00 0.00 34.76 3.60
686 687 1.265905 CCGGTCTAAAGCAAGCGTTTT 59.734 47.619 0.00 0.00 34.76 2.43
687 688 2.571206 CGGTCTAAAGCAAGCGTTTTC 58.429 47.619 0.00 0.00 0.00 2.29
736 738 8.855279 GCATACGCATTAAACAAAACTTGATAA 58.145 29.630 0.00 0.00 38.36 1.75
772 774 8.641499 ACTCATGTAAAGAATCGAGATCTTTC 57.359 34.615 24.23 17.97 43.96 2.62
813 815 1.600957 CGCGATCTGATCAAGCCAATT 59.399 47.619 17.19 0.00 0.00 2.32
864 893 2.093973 ACGCCAACTAATCAGTCTCCAG 60.094 50.000 0.00 0.00 32.29 3.86
878 916 9.911788 AATCAGTCTCCAGTAATTATCATGTTT 57.088 29.630 0.00 0.00 0.00 2.83
890 928 1.076777 CATGTTTCCCGGATGGCCT 60.077 57.895 0.73 0.00 0.00 5.19
910 948 2.755103 CTGATGATACGATCCGATCCCA 59.245 50.000 2.69 0.00 0.00 4.37
982 1047 7.464311 GCTTTCTAGTTTCGTTATAACCTGAGC 60.464 40.741 10.01 6.66 0.00 4.26
986 1051 5.169295 AGTTTCGTTATAACCTGAGCTGAC 58.831 41.667 10.01 1.84 0.00 3.51
1018 1083 3.475774 CGCCGCGTACAGTTGACC 61.476 66.667 4.92 0.00 0.00 4.02
1019 1084 2.048503 GCCGCGTACAGTTGACCT 60.049 61.111 4.92 0.00 0.00 3.85
1022 1087 1.372997 CGCGTACAGTTGACCTGCT 60.373 57.895 0.00 0.00 45.68 4.24
1051 1116 2.158856 TGATCCGCTCTGCATCAAGAAT 60.159 45.455 0.00 0.00 0.00 2.40
1063 1128 4.643334 TGCATCAAGAATCCAAGATCCAAG 59.357 41.667 0.00 0.00 0.00 3.61
1064 1129 4.499357 GCATCAAGAATCCAAGATCCAAGC 60.499 45.833 0.00 0.00 0.00 4.01
1065 1130 4.581309 TCAAGAATCCAAGATCCAAGCT 57.419 40.909 0.00 0.00 0.00 3.74
1066 1131 5.698741 TCAAGAATCCAAGATCCAAGCTA 57.301 39.130 0.00 0.00 0.00 3.32
1110 1175 0.814410 ATGATCCGCAGCAAGCAGAG 60.814 55.000 0.00 0.00 46.13 3.35
1112 1177 1.427592 GATCCGCAGCAAGCAGAGAC 61.428 60.000 0.00 0.00 46.13 3.36
1113 1178 2.176314 ATCCGCAGCAAGCAGAGACA 62.176 55.000 0.00 0.00 46.13 3.41
1185 1262 2.479730 CGTCTTCCTCAACTACATCGGG 60.480 54.545 0.00 0.00 0.00 5.14
1186 1263 1.480954 TCTTCCTCAACTACATCGGGC 59.519 52.381 0.00 0.00 0.00 6.13
1311 1390 2.401766 CCTGGATCACTGCAACGGC 61.402 63.158 0.00 0.00 41.68 5.68
1315 1394 2.045926 ATCACTGCAACGGCCTCC 60.046 61.111 0.00 0.00 40.13 4.30
1354 1433 0.878523 GCTGTACTGCGTGGTGAACA 60.879 55.000 9.10 0.00 0.00 3.18
1453 1532 3.264897 CGCATGGCTACGAGGTGC 61.265 66.667 0.00 0.00 0.00 5.01
1455 1534 1.884926 GCATGGCTACGAGGTGCTC 60.885 63.158 0.00 0.00 33.25 4.26
1498 1577 1.014564 GCCCAAGAAGTTCGACCTCG 61.015 60.000 0.00 0.00 41.45 4.63
1532 1611 0.392863 TTGCTGGATGACATGTCGGG 60.393 55.000 20.54 9.55 0.00 5.14
1533 1612 1.221840 GCTGGATGACATGTCGGGT 59.778 57.895 20.54 9.43 0.00 5.28
1535 1614 0.250234 CTGGATGACATGTCGGGTGT 59.750 55.000 20.54 4.48 0.00 4.16
1559 1638 1.107114 GAGGACGCAGAGAATGAGGA 58.893 55.000 0.00 0.00 32.12 3.71
1569 1648 4.695396 CAGAGAATGAGGACCAAGATGAG 58.305 47.826 0.00 0.00 0.00 2.90
1743 1834 1.240641 TGGCCAGTATGCAACAACCG 61.241 55.000 0.00 0.00 31.97 4.44
1877 1968 8.507524 AACTACAAAACTCCTTCCATTATAGC 57.492 34.615 0.00 0.00 0.00 2.97
1948 2041 8.893727 AGACTATCAACATTTTAGTTATGGTGC 58.106 33.333 0.00 0.00 39.89 5.01
1949 2042 8.574251 ACTATCAACATTTTAGTTATGGTGCA 57.426 30.769 0.00 0.00 39.89 4.57
1950 2043 9.189156 ACTATCAACATTTTAGTTATGGTGCAT 57.811 29.630 0.00 0.00 39.89 3.96
1952 2045 8.931385 ATCAACATTTTAGTTATGGTGCATTC 57.069 30.769 0.00 0.00 39.89 2.67
1953 2046 7.319646 TCAACATTTTAGTTATGGTGCATTCC 58.680 34.615 0.00 0.00 39.89 3.01
1954 2047 7.178274 TCAACATTTTAGTTATGGTGCATTCCT 59.822 33.333 0.00 0.00 39.89 3.36
1955 2048 6.866480 ACATTTTAGTTATGGTGCATTCCTG 58.134 36.000 0.00 0.00 0.00 3.86
1956 2049 5.913137 TTTTAGTTATGGTGCATTCCTGG 57.087 39.130 0.00 0.00 0.00 4.45
1957 2050 4.853468 TTAGTTATGGTGCATTCCTGGA 57.147 40.909 0.00 0.00 0.00 3.86
2025 2356 7.430441 AGCGAATAAATTTGTGTTTTGTAGGT 58.570 30.769 0.00 0.00 0.00 3.08
2165 2496 3.311596 ACAAGTACAACAACCTTCTTCGC 59.688 43.478 0.00 0.00 0.00 4.70
2178 2509 0.942410 TCTTCGCGTTTGGAACCTCG 60.942 55.000 5.77 0.00 0.00 4.63
2219 2550 8.324163 CAATAGATTGGGTACTAAAGCATACC 57.676 38.462 0.00 0.00 40.25 2.73
2309 2640 7.995488 CCTTGGATCTTAGAGGACAATAACAAT 59.005 37.037 0.00 0.00 0.00 2.71
2322 2653 7.067859 AGGACAATAACAATGATGATGTGGAAG 59.932 37.037 0.00 0.00 0.00 3.46
2324 2655 8.352137 ACAATAACAATGATGATGTGGAAGAA 57.648 30.769 0.00 0.00 0.00 2.52
2357 2688 6.255453 TGCCGCTAAAAGAAAATATTGAATGC 59.745 34.615 0.00 0.00 0.00 3.56
2411 2742 4.706842 AGGTGGTTGTGAAGAACAGTAT 57.293 40.909 0.00 0.00 40.74 2.12
2412 2743 5.818678 AGGTGGTTGTGAAGAACAGTATA 57.181 39.130 0.00 0.00 40.74 1.47
2476 2807 9.850628 GGTAATTTTCTTAGGGTTGTCATTTAC 57.149 33.333 0.00 0.00 0.00 2.01
2530 2861 4.529377 AGTCCAATACCTCGGAAAACTACA 59.471 41.667 0.00 0.00 31.67 2.74
2810 3141 7.598278 TGTACTTTTTATGCATTCGAACCAAT 58.402 30.769 3.54 0.00 0.00 3.16
2888 3219 3.054878 AGTACCGCAAAGTGTAGAAACG 58.945 45.455 0.00 0.00 0.00 3.60
3056 3389 6.748333 AGGCATTCATCAATGGTAATATCG 57.252 37.500 0.00 0.00 40.03 2.92
3165 3518 6.070538 AGCTTGGTATGATACACTCAAGAAGT 60.071 38.462 18.17 5.07 37.44 3.01
3285 3638 7.819900 GTGGATGATATTATCCTTCACAGTACC 59.180 40.741 23.07 0.00 45.59 3.34
3293 3646 2.557056 TCCTTCACAGTACCAACTCTCG 59.443 50.000 0.00 0.00 31.97 4.04
3345 3700 7.486647 AGCTGAAAATATCAAATGTCCATGAC 58.513 34.615 0.00 0.00 37.67 3.06
3357 3712 1.134491 GTCCATGACGGGGGAACTAAG 60.134 57.143 0.00 0.00 34.34 2.18
3364 3719 5.703730 TGACGGGGGAACTAAGAATATTT 57.296 39.130 0.00 0.00 0.00 1.40
3430 3785 2.515912 GAAAAATACCTCAAAGCCGCG 58.484 47.619 0.00 0.00 0.00 6.46
3481 3836 2.681848 GACATCAAGACTCCAATGCCAG 59.318 50.000 0.00 0.00 0.00 4.85
3546 3901 6.260050 TCGAACAAAAGGTATATTGCTCCATC 59.740 38.462 0.00 0.00 0.00 3.51
3592 3947 4.249638 TCTAGGCCCAACATTATGCTTT 57.750 40.909 0.00 0.00 0.00 3.51
3600 3955 4.451774 CCCAACATTATGCTTTGTGTTTGG 59.548 41.667 0.00 0.00 32.87 3.28
3606 3961 2.222007 TGCTTTGTGTTTGGATGTGC 57.778 45.000 0.00 0.00 0.00 4.57
3607 3962 1.479730 TGCTTTGTGTTTGGATGTGCA 59.520 42.857 0.00 0.00 0.00 4.57
3610 3965 3.719924 CTTTGTGTTTGGATGTGCACAT 58.280 40.909 31.82 31.82 40.82 3.21
3634 3989 4.257731 GAGGGTGAAGAAAACCAGAGATC 58.742 47.826 0.00 0.00 39.65 2.75
3640 3995 6.385033 GTGAAGAAAACCAGAGATCCAAATG 58.615 40.000 0.00 0.00 0.00 2.32
3660 4015 3.724478 TGTTCACCCTCCTATGATCACT 58.276 45.455 0.00 0.00 0.00 3.41
3669 4024 5.486526 CCTCCTATGATCACTTATCCTTGC 58.513 45.833 0.00 0.00 33.22 4.01
3670 4025 5.012458 CCTCCTATGATCACTTATCCTTGCA 59.988 44.000 0.00 0.00 33.22 4.08
3671 4026 5.858381 TCCTATGATCACTTATCCTTGCAC 58.142 41.667 0.00 0.00 33.22 4.57
3672 4027 5.604231 TCCTATGATCACTTATCCTTGCACT 59.396 40.000 0.00 0.00 33.22 4.40
3673 4028 6.782494 TCCTATGATCACTTATCCTTGCACTA 59.218 38.462 0.00 0.00 33.22 2.74
3674 4029 7.039434 TCCTATGATCACTTATCCTTGCACTAG 60.039 40.741 0.00 0.00 33.22 2.57
3675 4030 5.939764 TGATCACTTATCCTTGCACTAGT 57.060 39.130 0.00 0.00 33.22 2.57
3676 4031 7.603180 ATGATCACTTATCCTTGCACTAGTA 57.397 36.000 0.00 0.00 33.22 1.82
3677 4032 6.806751 TGATCACTTATCCTTGCACTAGTAC 58.193 40.000 0.00 0.00 33.22 2.73
3678 4033 5.244785 TCACTTATCCTTGCACTAGTACG 57.755 43.478 0.00 0.00 0.00 3.67
3679 4034 4.703575 TCACTTATCCTTGCACTAGTACGT 59.296 41.667 0.00 0.00 0.00 3.57
3680 4035 4.798907 CACTTATCCTTGCACTAGTACGTG 59.201 45.833 0.00 0.00 37.94 4.49
3681 4036 4.461781 ACTTATCCTTGCACTAGTACGTGT 59.538 41.667 0.00 0.00 37.24 4.49
3682 4037 3.505464 ATCCTTGCACTAGTACGTGTC 57.495 47.619 0.00 0.00 37.24 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.788766 GCGATTTGAGCACGGCGT 61.789 61.111 6.77 6.77 34.19 5.68
1 2 3.707156 CTGCGATTTGAGCACGGCG 62.707 63.158 4.80 4.80 40.01 6.46
2 3 2.099062 CTGCGATTTGAGCACGGC 59.901 61.111 0.00 0.00 40.01 5.68
3 4 2.099062 GCTGCGATTTGAGCACGG 59.901 61.111 0.00 0.00 40.01 4.94
4 5 1.059994 GAGCTGCGATTTGAGCACG 59.940 57.895 0.00 0.00 40.01 5.34
5 6 1.059994 CGAGCTGCGATTTGAGCAC 59.940 57.895 0.00 0.00 44.57 4.40
6 7 1.079888 TCGAGCTGCGATTTGAGCA 60.080 52.632 0.00 0.00 45.59 4.26
7 8 3.786101 TCGAGCTGCGATTTGAGC 58.214 55.556 0.00 0.00 45.59 4.26
23 24 3.945434 CATCTGCGCATGGCCGTC 61.945 66.667 12.24 0.00 42.61 4.79
30 31 3.129362 ATGGGGAGCATCTGCGCAT 62.129 57.895 12.24 11.03 46.43 4.73
31 32 3.762429 GATGGGGAGCATCTGCGCA 62.762 63.158 10.98 10.98 46.72 6.09
34 35 2.976903 GCGATGGGGAGCATCTGC 60.977 66.667 0.00 0.00 42.49 4.26
35 36 1.597302 CTGCGATGGGGAGCATCTG 60.597 63.158 0.00 0.00 33.73 2.90
36 37 2.827423 CTGCGATGGGGAGCATCT 59.173 61.111 0.00 0.00 33.73 2.90
41 42 3.769369 ATGCTGCTGCGATGGGGAG 62.769 63.158 11.21 0.00 43.34 4.30
42 43 3.762429 GATGCTGCTGCGATGGGGA 62.762 63.158 11.21 0.00 43.34 4.81
43 44 3.285215 GATGCTGCTGCGATGGGG 61.285 66.667 11.21 0.00 43.34 4.96
44 45 1.853114 GATGATGCTGCTGCGATGGG 61.853 60.000 11.21 0.00 43.34 4.00
45 46 0.885150 AGATGATGCTGCTGCGATGG 60.885 55.000 11.21 0.00 43.34 3.51
46 47 1.459975 GTAGATGATGCTGCTGCGATG 59.540 52.381 11.21 0.00 43.34 3.84
47 48 1.793258 GTAGATGATGCTGCTGCGAT 58.207 50.000 11.21 5.74 43.34 4.58
48 49 0.595825 CGTAGATGATGCTGCTGCGA 60.596 55.000 11.21 0.80 43.34 5.10
49 50 0.595825 TCGTAGATGATGCTGCTGCG 60.596 55.000 11.21 0.00 43.34 5.18
50 51 0.857935 GTCGTAGATGATGCTGCTGC 59.142 55.000 8.89 8.89 40.67 5.25
60 61 1.956170 GCCATGGCCGTCGTAGATG 60.956 63.158 27.24 0.00 44.47 2.90
61 62 2.421739 GCCATGGCCGTCGTAGAT 59.578 61.111 27.24 0.00 34.75 1.98
62 63 4.201679 CGCCATGGCCGTCGTAGA 62.202 66.667 30.79 0.00 37.98 2.59
89 90 1.945776 GAGGAAAGCTTCGACACGCG 61.946 60.000 3.53 3.53 42.69 6.01
90 91 1.782181 GAGGAAAGCTTCGACACGC 59.218 57.895 0.00 0.00 0.00 5.34
91 92 0.386858 TCGAGGAAAGCTTCGACACG 60.387 55.000 0.00 4.03 45.92 4.49
92 93 3.491581 TCGAGGAAAGCTTCGACAC 57.508 52.632 0.00 0.00 45.92 3.67
96 97 1.923204 CATGAGTCGAGGAAAGCTTCG 59.077 52.381 0.00 0.00 44.04 3.79
97 98 2.926838 GTCATGAGTCGAGGAAAGCTTC 59.073 50.000 0.00 0.00 0.00 3.86
98 99 2.300152 TGTCATGAGTCGAGGAAAGCTT 59.700 45.455 0.00 0.00 0.00 3.74
99 100 1.895798 TGTCATGAGTCGAGGAAAGCT 59.104 47.619 0.00 0.00 0.00 3.74
100 101 1.996191 GTGTCATGAGTCGAGGAAAGC 59.004 52.381 0.00 0.00 0.00 3.51
101 102 3.249091 CAGTGTCATGAGTCGAGGAAAG 58.751 50.000 0.00 0.00 0.00 2.62
102 103 2.610479 GCAGTGTCATGAGTCGAGGAAA 60.610 50.000 0.00 0.00 0.00 3.13
103 104 1.067565 GCAGTGTCATGAGTCGAGGAA 60.068 52.381 0.00 0.00 0.00 3.36
104 105 0.528017 GCAGTGTCATGAGTCGAGGA 59.472 55.000 0.00 0.00 0.00 3.71
105 106 0.799917 CGCAGTGTCATGAGTCGAGG 60.800 60.000 0.00 0.00 0.00 4.63
106 107 0.799917 CCGCAGTGTCATGAGTCGAG 60.800 60.000 0.00 0.00 0.00 4.04
107 108 1.212751 CCGCAGTGTCATGAGTCGA 59.787 57.895 0.00 0.00 0.00 4.20
108 109 1.073216 GACCGCAGTGTCATGAGTCG 61.073 60.000 0.00 0.00 35.29 4.18
109 110 1.073216 CGACCGCAGTGTCATGAGTC 61.073 60.000 0.00 0.00 34.88 3.36
110 111 1.080501 CGACCGCAGTGTCATGAGT 60.081 57.895 0.00 0.00 34.88 3.41
111 112 2.447887 GCGACCGCAGTGTCATGAG 61.448 63.158 9.73 0.00 41.49 2.90
112 113 2.432456 GCGACCGCAGTGTCATGA 60.432 61.111 9.73 0.00 41.49 3.07
113 114 2.433145 AGCGACCGCAGTGTCATG 60.433 61.111 16.97 0.00 44.88 3.07
114 115 2.433145 CAGCGACCGCAGTGTCAT 60.433 61.111 16.97 0.00 44.88 3.06
148 149 4.086178 GACTGCTGCAGCTGCGTG 62.086 66.667 36.60 26.68 45.83 5.34
152 153 3.117171 GACGGACTGCTGCAGCTG 61.117 66.667 35.49 35.49 44.21 4.24
153 154 4.731612 CGACGGACTGCTGCAGCT 62.732 66.667 36.61 20.34 42.66 4.24
473 474 2.502745 ACAGATCCCTCTCTCTCTCCT 58.497 52.381 0.00 0.00 0.00 3.69
474 475 3.244911 CCTACAGATCCCTCTCTCTCTCC 60.245 56.522 0.00 0.00 0.00 3.71
475 476 3.650942 TCCTACAGATCCCTCTCTCTCTC 59.349 52.174 0.00 0.00 0.00 3.20
476 477 3.652869 CTCCTACAGATCCCTCTCTCTCT 59.347 52.174 0.00 0.00 0.00 3.10
477 478 3.244911 CCTCCTACAGATCCCTCTCTCTC 60.245 56.522 0.00 0.00 0.00 3.20
478 479 2.716424 CCTCCTACAGATCCCTCTCTCT 59.284 54.545 0.00 0.00 0.00 3.10
479 480 2.225017 CCCTCCTACAGATCCCTCTCTC 60.225 59.091 0.00 0.00 0.00 3.20
480 481 1.786441 CCCTCCTACAGATCCCTCTCT 59.214 57.143 0.00 0.00 0.00 3.10
481 482 1.783979 TCCCTCCTACAGATCCCTCTC 59.216 57.143 0.00 0.00 0.00 3.20
482 483 1.928480 TCCCTCCTACAGATCCCTCT 58.072 55.000 0.00 0.00 0.00 3.69
483 484 2.534990 CATCCCTCCTACAGATCCCTC 58.465 57.143 0.00 0.00 0.00 4.30
484 485 1.484065 GCATCCCTCCTACAGATCCCT 60.484 57.143 0.00 0.00 0.00 4.20
485 486 0.980423 GCATCCCTCCTACAGATCCC 59.020 60.000 0.00 0.00 0.00 3.85
486 487 0.605589 CGCATCCCTCCTACAGATCC 59.394 60.000 0.00 0.00 0.00 3.36
487 488 1.000283 CACGCATCCCTCCTACAGATC 60.000 57.143 0.00 0.00 0.00 2.75
488 489 1.043816 CACGCATCCCTCCTACAGAT 58.956 55.000 0.00 0.00 0.00 2.90
489 490 0.033503 TCACGCATCCCTCCTACAGA 60.034 55.000 0.00 0.00 0.00 3.41
490 491 0.387202 CTCACGCATCCCTCCTACAG 59.613 60.000 0.00 0.00 0.00 2.74
491 492 0.324368 ACTCACGCATCCCTCCTACA 60.324 55.000 0.00 0.00 0.00 2.74
492 493 0.103208 CACTCACGCATCCCTCCTAC 59.897 60.000 0.00 0.00 0.00 3.18
493 494 1.676678 GCACTCACGCATCCCTCCTA 61.677 60.000 0.00 0.00 0.00 2.94
494 495 3.023949 GCACTCACGCATCCCTCCT 62.024 63.158 0.00 0.00 0.00 3.69
495 496 2.512515 GCACTCACGCATCCCTCC 60.513 66.667 0.00 0.00 0.00 4.30
496 497 2.887568 CGCACTCACGCATCCCTC 60.888 66.667 0.00 0.00 0.00 4.30
497 498 3.362399 CTCGCACTCACGCATCCCT 62.362 63.158 0.00 0.00 0.00 4.20
498 499 2.887568 CTCGCACTCACGCATCCC 60.888 66.667 0.00 0.00 0.00 3.85
499 500 2.835701 TTCCTCGCACTCACGCATCC 62.836 60.000 0.00 0.00 0.00 3.51
500 501 1.416813 CTTCCTCGCACTCACGCATC 61.417 60.000 0.00 0.00 0.00 3.91
501 502 1.446792 CTTCCTCGCACTCACGCAT 60.447 57.895 0.00 0.00 0.00 4.73
502 503 2.049156 CTTCCTCGCACTCACGCA 60.049 61.111 0.00 0.00 0.00 5.24
503 504 2.089349 GTCTTCCTCGCACTCACGC 61.089 63.158 0.00 0.00 0.00 5.34
504 505 1.797933 CGTCTTCCTCGCACTCACG 60.798 63.158 0.00 0.00 0.00 4.35
505 506 0.729816 GTCGTCTTCCTCGCACTCAC 60.730 60.000 0.00 0.00 0.00 3.51
506 507 1.579932 GTCGTCTTCCTCGCACTCA 59.420 57.895 0.00 0.00 0.00 3.41
507 508 1.512310 CGTCGTCTTCCTCGCACTC 60.512 63.158 0.00 0.00 0.00 3.51
508 509 2.561885 CGTCGTCTTCCTCGCACT 59.438 61.111 0.00 0.00 0.00 4.40
509 510 3.173240 GCGTCGTCTTCCTCGCAC 61.173 66.667 0.00 0.00 46.40 5.34
512 513 2.504244 GGTGCGTCGTCTTCCTCG 60.504 66.667 0.00 0.00 0.00 4.63
513 514 2.504244 CGGTGCGTCGTCTTCCTC 60.504 66.667 0.00 0.00 0.00 3.71
514 515 2.981909 TCGGTGCGTCGTCTTCCT 60.982 61.111 0.00 0.00 0.00 3.36
515 516 2.804090 GTCGGTGCGTCGTCTTCC 60.804 66.667 0.00 0.00 0.00 3.46
516 517 3.164011 CGTCGGTGCGTCGTCTTC 61.164 66.667 0.00 0.00 34.30 2.87
525 526 3.323136 CTATCGCTGCGTCGGTGC 61.323 66.667 22.48 0.00 0.00 5.01
526 527 2.607668 TTCCTATCGCTGCGTCGGTG 62.608 60.000 22.48 8.29 0.00 4.94
527 528 1.940883 TTTCCTATCGCTGCGTCGGT 61.941 55.000 22.48 9.27 0.00 4.69
528 529 1.209275 CTTTCCTATCGCTGCGTCGG 61.209 60.000 22.48 18.92 0.00 4.79
529 530 0.248498 TCTTTCCTATCGCTGCGTCG 60.248 55.000 22.48 10.97 0.00 5.12
530 531 1.922570 TTCTTTCCTATCGCTGCGTC 58.077 50.000 22.48 0.00 0.00 5.19
531 532 2.380084 TTTCTTTCCTATCGCTGCGT 57.620 45.000 22.48 11.78 0.00 5.24
532 533 3.740044 TTTTTCTTTCCTATCGCTGCG 57.260 42.857 17.25 17.25 0.00 5.18
549 550 2.961768 CCACGGCCGCTCATTTTT 59.038 55.556 28.58 0.00 0.00 1.94
550 551 3.747976 GCCACGGCCGCTCATTTT 61.748 61.111 28.58 0.00 34.56 1.82
551 552 4.722700 AGCCACGGCCGCTCATTT 62.723 61.111 28.58 0.00 43.17 2.32
552 553 4.722700 AAGCCACGGCCGCTCATT 62.723 61.111 28.58 13.02 43.17 2.57
561 562 3.114616 CACGCAGAGAAGCCACGG 61.115 66.667 0.00 0.00 0.00 4.94
562 563 2.842394 ATCCACGCAGAGAAGCCACG 62.842 60.000 0.00 0.00 0.00 4.94
563 564 0.175760 TATCCACGCAGAGAAGCCAC 59.824 55.000 0.00 0.00 0.00 5.01
564 565 0.901827 TTATCCACGCAGAGAAGCCA 59.098 50.000 0.00 0.00 0.00 4.75
565 566 1.137086 TCTTATCCACGCAGAGAAGCC 59.863 52.381 5.11 0.00 0.00 4.35
566 567 2.197577 GTCTTATCCACGCAGAGAAGC 58.802 52.381 5.11 0.00 0.00 3.86
567 568 2.455032 CGTCTTATCCACGCAGAGAAG 58.545 52.381 3.85 3.85 0.00 2.85
568 569 1.134367 CCGTCTTATCCACGCAGAGAA 59.866 52.381 0.00 0.00 35.87 2.87
569 570 0.738975 CCGTCTTATCCACGCAGAGA 59.261 55.000 0.00 0.00 35.87 3.10
570 571 0.738975 TCCGTCTTATCCACGCAGAG 59.261 55.000 0.00 0.00 35.87 3.35
571 572 0.738975 CTCCGTCTTATCCACGCAGA 59.261 55.000 0.00 0.00 35.87 4.26
572 573 0.738975 TCTCCGTCTTATCCACGCAG 59.261 55.000 0.00 0.00 35.87 5.18
573 574 1.067060 CATCTCCGTCTTATCCACGCA 59.933 52.381 0.00 0.00 35.87 5.24
574 575 1.603172 CCATCTCCGTCTTATCCACGC 60.603 57.143 0.00 0.00 35.87 5.34
575 576 1.000163 CCCATCTCCGTCTTATCCACG 60.000 57.143 0.00 0.00 36.99 4.94
576 577 2.040178 ACCCATCTCCGTCTTATCCAC 58.960 52.381 0.00 0.00 0.00 4.02
577 578 2.039418 CACCCATCTCCGTCTTATCCA 58.961 52.381 0.00 0.00 0.00 3.41
578 579 2.297597 CTCACCCATCTCCGTCTTATCC 59.702 54.545 0.00 0.00 0.00 2.59
579 580 2.288518 GCTCACCCATCTCCGTCTTATC 60.289 54.545 0.00 0.00 0.00 1.75
580 581 1.689273 GCTCACCCATCTCCGTCTTAT 59.311 52.381 0.00 0.00 0.00 1.73
581 582 1.112113 GCTCACCCATCTCCGTCTTA 58.888 55.000 0.00 0.00 0.00 2.10
582 583 1.901085 GCTCACCCATCTCCGTCTT 59.099 57.895 0.00 0.00 0.00 3.01
583 584 2.418910 CGCTCACCCATCTCCGTCT 61.419 63.158 0.00 0.00 0.00 4.18
584 585 2.105128 CGCTCACCCATCTCCGTC 59.895 66.667 0.00 0.00 0.00 4.79
585 586 3.461773 CCGCTCACCCATCTCCGT 61.462 66.667 0.00 0.00 0.00 4.69
586 587 4.899239 GCCGCTCACCCATCTCCG 62.899 72.222 0.00 0.00 0.00 4.63
587 588 4.899239 CGCCGCTCACCCATCTCC 62.899 72.222 0.00 0.00 0.00 3.71
615 616 4.129737 ATCGACACGCGTCCCTGG 62.130 66.667 9.86 0.00 39.11 4.45
616 617 2.579787 GATCGACACGCGTCCCTG 60.580 66.667 9.86 0.00 39.11 4.45
617 618 4.175489 CGATCGACACGCGTCCCT 62.175 66.667 9.86 0.00 39.11 4.20
624 625 2.278206 CCTCCAGCGATCGACACG 60.278 66.667 21.57 9.07 0.00 4.49
625 626 1.064946 CTCCTCCAGCGATCGACAC 59.935 63.158 21.57 0.32 0.00 3.67
626 627 2.121538 CCTCCTCCAGCGATCGACA 61.122 63.158 21.57 0.00 0.00 4.35
627 628 2.725008 CCTCCTCCAGCGATCGAC 59.275 66.667 21.57 10.46 0.00 4.20
628 629 3.219928 GCCTCCTCCAGCGATCGA 61.220 66.667 21.57 0.00 0.00 3.59
629 630 2.790791 AAGCCTCCTCCAGCGATCG 61.791 63.158 11.69 11.69 0.00 3.69
630 631 1.227497 CAAGCCTCCTCCAGCGATC 60.227 63.158 0.00 0.00 0.00 3.69
631 632 2.906458 CAAGCCTCCTCCAGCGAT 59.094 61.111 0.00 0.00 0.00 4.58
632 633 4.087892 GCAAGCCTCCTCCAGCGA 62.088 66.667 0.00 0.00 0.00 4.93
634 635 4.400961 ACGCAAGCCTCCTCCAGC 62.401 66.667 0.00 0.00 45.62 4.85
635 636 2.125350 GACGCAAGCCTCCTCCAG 60.125 66.667 0.00 0.00 45.62 3.86
636 637 2.604686 AGACGCAAGCCTCCTCCA 60.605 61.111 0.00 0.00 45.62 3.86
637 638 2.185608 GAGACGCAAGCCTCCTCC 59.814 66.667 0.00 0.00 41.45 4.30
638 639 2.202676 CGAGACGCAAGCCTCCTC 60.203 66.667 0.00 0.00 44.80 3.71
655 656 1.519408 TTAGACCGGCTGAAAACAGC 58.481 50.000 12.90 12.90 46.78 4.40
656 657 2.095718 GCTTTAGACCGGCTGAAAACAG 60.096 50.000 0.00 0.00 0.00 3.16
657 658 1.877443 GCTTTAGACCGGCTGAAAACA 59.123 47.619 0.00 0.00 0.00 2.83
658 659 1.877443 TGCTTTAGACCGGCTGAAAAC 59.123 47.619 0.00 0.00 0.00 2.43
659 660 2.264005 TGCTTTAGACCGGCTGAAAA 57.736 45.000 0.00 0.00 0.00 2.29
660 661 2.151202 CTTGCTTTAGACCGGCTGAAA 58.849 47.619 0.00 0.00 0.00 2.69
661 662 1.808411 CTTGCTTTAGACCGGCTGAA 58.192 50.000 0.00 1.91 0.00 3.02
662 663 0.673644 GCTTGCTTTAGACCGGCTGA 60.674 55.000 0.00 0.00 0.00 4.26
663 664 1.796796 GCTTGCTTTAGACCGGCTG 59.203 57.895 0.00 0.00 0.00 4.85
664 665 1.741770 CGCTTGCTTTAGACCGGCT 60.742 57.895 0.00 1.78 0.00 5.52
665 666 1.574702 AACGCTTGCTTTAGACCGGC 61.575 55.000 0.00 0.00 0.00 6.13
666 667 0.872388 AAACGCTTGCTTTAGACCGG 59.128 50.000 0.00 0.00 0.00 5.28
667 668 2.571206 GAAAACGCTTGCTTTAGACCG 58.429 47.619 0.00 0.00 0.00 4.79
668 669 2.552743 AGGAAAACGCTTGCTTTAGACC 59.447 45.455 0.00 0.00 0.00 3.85
669 670 3.898517 AGGAAAACGCTTGCTTTAGAC 57.101 42.857 0.00 0.00 0.00 2.59
670 671 4.578928 AGAAAGGAAAACGCTTGCTTTAGA 59.421 37.500 14.57 0.00 39.59 2.10
671 672 4.860072 AGAAAGGAAAACGCTTGCTTTAG 58.140 39.130 14.57 0.00 39.59 1.85
672 673 4.578928 AGAGAAAGGAAAACGCTTGCTTTA 59.421 37.500 14.57 0.00 39.59 1.85
673 674 3.381590 AGAGAAAGGAAAACGCTTGCTTT 59.618 39.130 14.52 14.52 41.64 3.51
674 675 2.952310 AGAGAAAGGAAAACGCTTGCTT 59.048 40.909 0.00 0.00 0.00 3.91
675 676 2.576615 AGAGAAAGGAAAACGCTTGCT 58.423 42.857 0.00 0.00 0.00 3.91
676 677 3.355626 AAGAGAAAGGAAAACGCTTGC 57.644 42.857 0.00 0.00 0.00 4.01
677 678 5.395486 CGTAAAAGAGAAAGGAAAACGCTTG 59.605 40.000 0.00 0.00 0.00 4.01
678 679 5.065602 ACGTAAAAGAGAAAGGAAAACGCTT 59.934 36.000 0.00 0.00 0.00 4.68
679 680 4.573607 ACGTAAAAGAGAAAGGAAAACGCT 59.426 37.500 0.00 0.00 0.00 5.07
680 681 4.840911 ACGTAAAAGAGAAAGGAAAACGC 58.159 39.130 0.00 0.00 0.00 4.84
681 682 6.019318 TGAGACGTAAAAGAGAAAGGAAAACG 60.019 38.462 0.00 0.00 0.00 3.60
682 683 7.242914 TGAGACGTAAAAGAGAAAGGAAAAC 57.757 36.000 0.00 0.00 0.00 2.43
683 684 7.852971 TTGAGACGTAAAAGAGAAAGGAAAA 57.147 32.000 0.00 0.00 0.00 2.29
684 685 8.342634 CAATTGAGACGTAAAAGAGAAAGGAAA 58.657 33.333 0.00 0.00 0.00 3.13
685 686 7.519970 GCAATTGAGACGTAAAAGAGAAAGGAA 60.520 37.037 10.34 0.00 0.00 3.36
686 687 6.073222 GCAATTGAGACGTAAAAGAGAAAGGA 60.073 38.462 10.34 0.00 0.00 3.36
687 688 6.080406 GCAATTGAGACGTAAAAGAGAAAGG 58.920 40.000 10.34 0.00 0.00 3.11
772 774 4.051237 CGCCCAAAAAGGAAGAAAGAAAG 58.949 43.478 0.00 0.00 41.22 2.62
813 815 4.679639 CGGTTCTCGTTCCTGGAATATTCA 60.680 45.833 17.07 3.07 0.00 2.57
817 819 2.449464 TCGGTTCTCGTTCCTGGAATA 58.551 47.619 13.07 3.43 40.32 1.75
818 820 1.263356 TCGGTTCTCGTTCCTGGAAT 58.737 50.000 13.07 0.00 40.32 3.01
819 821 1.203994 GATCGGTTCTCGTTCCTGGAA 59.796 52.381 4.68 4.68 40.32 3.53
858 887 6.288294 CGGGAAACATGATAATTACTGGAGA 58.712 40.000 0.00 0.00 0.00 3.71
864 893 5.335661 GCCATCCGGGAAACATGATAATTAC 60.336 44.000 0.00 0.00 40.01 1.89
878 916 0.178906 TATCATCAGGCCATCCGGGA 60.179 55.000 5.01 0.00 40.01 5.14
890 928 2.802719 TGGGATCGGATCGTATCATCA 58.197 47.619 11.62 3.83 0.00 3.07
910 948 1.076485 GCCCAGAGACCCAATGCAT 60.076 57.895 0.00 0.00 0.00 3.96
923 988 2.046988 TGTGCTGACGATGCCCAG 60.047 61.111 0.00 0.00 0.00 4.45
982 1047 2.825836 GCTTGGGCGGGATGTCAG 60.826 66.667 0.00 0.00 0.00 3.51
1018 1083 2.420890 GGATCAGCGGAGGAGCAG 59.579 66.667 0.00 0.00 40.15 4.24
1019 1084 3.531207 CGGATCAGCGGAGGAGCA 61.531 66.667 0.00 0.00 40.15 4.26
1022 1087 3.219928 GAGCGGATCAGCGGAGGA 61.220 66.667 12.29 0.00 43.00 3.71
1051 1116 2.968574 CCTAGCTAGCTTGGATCTTGGA 59.031 50.000 33.70 7.79 40.55 3.53
1299 1378 3.241530 AGGAGGCCGTTGCAGTGA 61.242 61.111 0.00 0.00 40.13 3.41
1311 1390 1.153549 GTTGCCGTAGAGCAGGAGG 60.154 63.158 0.00 0.00 45.13 4.30
1315 1394 1.811266 ATGCGTTGCCGTAGAGCAG 60.811 57.895 0.00 0.00 45.13 4.24
1332 1411 1.375908 CACCACGCAGTACAGCCAT 60.376 57.895 4.50 0.00 41.61 4.40
1476 1555 0.875059 GGTCGAACTTCTTGGGCTTG 59.125 55.000 0.00 0.00 0.00 4.01
1498 1577 3.627577 TCCAGCAAAGACAGAAACTCAAC 59.372 43.478 0.00 0.00 0.00 3.18
1532 1611 2.179517 CTGCGTCCTCCTCGACAC 59.820 66.667 0.00 0.00 32.74 3.67
1533 1612 2.033602 TCTGCGTCCTCCTCGACA 59.966 61.111 0.00 0.00 32.74 4.35
1535 1614 0.394488 ATTCTCTGCGTCCTCCTCGA 60.394 55.000 0.00 0.00 0.00 4.04
1559 1638 1.264749 TACAGCCGGCTCATCTTGGT 61.265 55.000 30.29 21.98 0.00 3.67
1569 1648 1.923227 GCAAAGGTTCTACAGCCGGC 61.923 60.000 21.89 21.89 0.00 6.13
1682 1761 0.107654 CCGGACAAATGACCTCTCCC 60.108 60.000 0.00 0.00 0.00 4.30
1743 1834 0.189327 ATCTTGGGCCCCATTCCATC 59.811 55.000 22.27 0.00 31.53 3.51
1832 1923 9.063615 TGTAGTTATGCACTTCGATCTAGAATA 57.936 33.333 0.00 0.00 36.88 1.75
1922 2015 8.893727 GCACCATAACTAAAATGTTGATAGTCT 58.106 33.333 0.00 0.00 0.00 3.24
1923 2016 8.673711 TGCACCATAACTAAAATGTTGATAGTC 58.326 33.333 0.00 0.00 0.00 2.59
1927 2020 7.981225 GGAATGCACCATAACTAAAATGTTGAT 59.019 33.333 0.00 0.00 0.00 2.57
1928 2021 7.178274 AGGAATGCACCATAACTAAAATGTTGA 59.822 33.333 0.00 0.00 0.00 3.18
1929 2022 7.276218 CAGGAATGCACCATAACTAAAATGTTG 59.724 37.037 0.00 0.00 0.00 3.33
1930 2023 7.322664 CAGGAATGCACCATAACTAAAATGTT 58.677 34.615 0.00 0.00 0.00 2.71
1931 2024 6.127366 CCAGGAATGCACCATAACTAAAATGT 60.127 38.462 0.00 0.00 0.00 2.71
1932 2025 6.096705 TCCAGGAATGCACCATAACTAAAATG 59.903 38.462 0.00 0.00 0.00 2.32
1933 2026 6.194235 TCCAGGAATGCACCATAACTAAAAT 58.806 36.000 0.00 0.00 0.00 1.82
1936 2029 4.853468 TCCAGGAATGCACCATAACTAA 57.147 40.909 0.00 0.00 0.00 2.24
1937 2030 5.387113 AATCCAGGAATGCACCATAACTA 57.613 39.130 0.00 0.00 0.00 2.24
1938 2031 3.959495 ATCCAGGAATGCACCATAACT 57.041 42.857 0.00 0.00 0.00 2.24
1939 2032 5.343307 AAAATCCAGGAATGCACCATAAC 57.657 39.130 0.00 0.00 0.00 1.89
2165 2496 1.463444 GATTCACCGAGGTTCCAAACG 59.537 52.381 0.00 0.00 0.00 3.60
2178 2509 1.463674 ATTGGACCGCTTGATTCACC 58.536 50.000 0.00 0.00 0.00 4.02
2219 2550 6.257411 ACAAAGTAGATTCATCAAGCTCGATG 59.743 38.462 8.43 8.43 43.50 3.84
2309 2640 5.416639 CACCATCTTTTCTTCCACATCATCA 59.583 40.000 0.00 0.00 0.00 3.07
2322 2653 3.190535 TCTTTTAGCGGCACCATCTTTTC 59.809 43.478 1.45 0.00 0.00 2.29
2324 2655 2.790433 TCTTTTAGCGGCACCATCTTT 58.210 42.857 1.45 0.00 0.00 2.52
2357 2688 8.538409 TCATTACATTATCATCATCGGAGTTG 57.462 34.615 0.00 0.00 0.00 3.16
2411 2742 9.137459 TGAAAACCCAAGAAATAAATGTGACTA 57.863 29.630 0.00 0.00 0.00 2.59
2412 2743 7.926018 GTGAAAACCCAAGAAATAAATGTGACT 59.074 33.333 0.00 0.00 0.00 3.41
2476 2807 6.293845 GCTATTCAAATGATAAGCCACTCCTG 60.294 42.308 6.34 0.00 0.00 3.86
2530 2861 2.558359 GCTGTGCAGTAATCTTTTGGGT 59.442 45.455 0.00 0.00 0.00 4.51
2756 3087 6.779860 ACATAACCAGATGACAAACTACCTT 58.220 36.000 0.00 0.00 0.00 3.50
2802 3133 4.776743 CAAGAAGACAACTGATTGGTTCG 58.223 43.478 0.00 0.00 40.42 3.95
2810 3141 5.858381 AGAACTATGCAAGAAGACAACTGA 58.142 37.500 0.00 0.00 0.00 3.41
3010 3343 7.380602 GCCTTTTCACATGCAATTGATATAGAC 59.619 37.037 10.34 0.00 0.00 2.59
3056 3389 6.566753 GCTTGTTTGACACATAGTTCTTCCTC 60.567 42.308 0.00 0.00 34.43 3.71
3171 3524 4.827284 CCTAGTTTGAAGCCCTTCTTTTCA 59.173 41.667 9.23 0.00 40.14 2.69
3274 3627 3.644884 ACGAGAGTTGGTACTGTGAAG 57.355 47.619 0.00 0.00 46.40 3.02
3323 3677 6.183360 CCCGTCATGGACATTTGATATTTTCA 60.183 38.462 0.00 0.00 42.00 2.69
3345 3700 7.255486 GGAATCAAAATATTCTTAGTTCCCCCG 60.255 40.741 0.00 0.00 36.34 5.73
3380 3735 8.696374 AGAGATAAAGATGTCATTCCGTTCTTA 58.304 33.333 0.00 0.00 0.00 2.10
3383 3738 6.980978 TGAGAGATAAAGATGTCATTCCGTTC 59.019 38.462 0.00 0.00 0.00 3.95
3430 3785 8.284693 CCAATTTTCCATGAAACATTTCTTCAC 58.715 33.333 5.97 0.00 35.70 3.18
3481 3836 0.737715 GAGTCGAGGTGTCCATGTGC 60.738 60.000 0.00 0.00 0.00 4.57
3495 3850 4.814771 GGTTTACCATTATCTTGGGAGTCG 59.185 45.833 0.00 0.00 41.35 4.18
3523 3878 6.430451 CGATGGAGCAATATACCTTTTGTTC 58.570 40.000 0.00 0.00 33.77 3.18
3525 3880 4.821805 CCGATGGAGCAATATACCTTTTGT 59.178 41.667 0.00 0.00 0.00 2.83
3526 3881 4.320494 GCCGATGGAGCAATATACCTTTTG 60.320 45.833 0.00 0.00 0.00 2.44
3558 3913 2.289320 GGGCCTAGATGCACACAGATAG 60.289 54.545 0.84 0.00 33.82 2.08
3592 3947 1.340568 CCATGTGCACATCCAAACACA 59.659 47.619 29.23 0.00 46.16 3.72
3600 3955 0.035152 TCACCCTCCATGTGCACATC 60.035 55.000 29.23 0.00 33.61 3.06
3606 3961 2.558359 GGTTTTCTTCACCCTCCATGTG 59.442 50.000 0.00 0.00 35.01 3.21
3607 3962 2.176798 TGGTTTTCTTCACCCTCCATGT 59.823 45.455 0.00 0.00 32.71 3.21
3610 3965 2.106511 CTCTGGTTTTCTTCACCCTCCA 59.893 50.000 0.00 0.00 32.71 3.86
3634 3989 4.235079 TCATAGGAGGGTGAACATTTGG 57.765 45.455 0.00 0.00 0.00 3.28
3640 3995 4.762289 AAGTGATCATAGGAGGGTGAAC 57.238 45.455 0.00 0.00 0.00 3.18
3660 4015 4.990257 GACACGTACTAGTGCAAGGATAA 58.010 43.478 11.70 0.00 45.45 1.75


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

AutoCloner maintained by Alex Coulton.