Multiple sequence alignment - TraesCS3B01G261800

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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 TraesCS3B01G261800 chr3B 100.000 3419 0 0 1 3419 419967990 419964572 0.000000e+00 6314.0
1 TraesCS3B01G261800 chr3D 90.190 3364 216 63 96 3419 301412256 301415545 0.000000e+00 4279.0
2 TraesCS3B01G261800 chr3A 89.777 2377 134 47 781 3092 434070541 434068209 0.000000e+00 2942.0
3 TraesCS3B01G261800 chr3A 91.818 330 25 1 3090 3419 434067184 434066857 3.110000e-125 459.0
4 TraesCS3B01G261800 chr1B 88.066 243 27 1 2037 2277 665061681 665061923 1.550000e-73 287.0
5 TraesCS3B01G261800 chr1D 87.243 243 29 1 2037 2277 477480536 477480778 3.360000e-70 276.0
6 TraesCS3B01G261800 chr1A 90.094 212 21 0 2051 2262 573921813 573922024 3.360000e-70 276.0
7 TraesCS3B01G261800 chr4A 78.603 229 36 11 2041 2264 143252299 143252519 4.600000e-29 139.0
8 TraesCS3B01G261800 chr4B 78.151 238 37 13 2045 2276 407056972 407056744 1.650000e-28 137.0
9 TraesCS3B01G261800 chr4D 77.679 224 37 11 2044 2262 327719429 327719214 1.290000e-24 124.0
10 TraesCS3B01G261800 chr7D 82.222 135 17 4 90 219 236640354 236640486 3.610000e-20 110.0
11 TraesCS3B01G261800 chr7D 79.012 162 28 4 74 229 368913864 368914025 4.670000e-19 106.0
12 TraesCS3B01G261800 chrUn 81.752 137 18 4 90 219 16310543 16310679 1.300000e-19 108.0
13 TraesCS3B01G261800 chrUn 81.119 143 20 4 90 225 381114649 381114507 1.300000e-19 108.0
14 TraesCS3B01G261800 chr6D 80.690 145 22 4 90 228 2855947 2855803 1.300000e-19 108.0
15 TraesCS3B01G261800 chr7B 78.528 163 28 4 74 229 313691564 313691402 2.170000e-17 100.0
16 TraesCS3B01G261800 chr5B 78.788 165 24 7 74 229 375641833 375641671 2.170000e-17 100.0
17 TraesCS3B01G261800 chr5A 78.049 164 27 5 74 229 421831517 421831355 1.010000e-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 TraesCS3B01G261800 chr3B 419964572 419967990 3418 True 6314.0 6314 100.0000 1 3419 1 chr3B.!!$R1 3418
1 TraesCS3B01G261800 chr3D 301412256 301415545 3289 False 4279.0 4279 90.1900 96 3419 1 chr3D.!!$F1 3323
2 TraesCS3B01G261800 chr3A 434066857 434070541 3684 True 1700.5 2942 90.7975 781 3419 2 chr3A.!!$R1 2638

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
512 514 0.031449 AAAACGCACCAACCGAATGG 59.969 50.0 5.05 5.05 46.38 3.16 F
755 758 0.041312 GCATAGGCCAATGTTACGCG 60.041 55.0 5.01 3.53 0.00 6.01 F
1027 1045 0.170561 CGTCCTTGATCGTCGTCCTT 59.829 55.0 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 1824 0.608640 AACGGACGGAGATGCTCTTT 59.391 50.000 0.0 0.0 0.0 2.52 R
2310 2354 1.079543 CAGACTGTGGCGGAAGAGG 60.080 63.158 0.0 0.0 0.0 3.69 R
2962 3043 0.249398 AAACGTAGCGGCCTTCTGAT 59.751 50.000 0.0 0.0 0.0 2.90 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
24 25 7.915293 TTTTCTATGGCCGGTATGTATAATG 57.085 36.000 1.90 0.00 0.00 1.90
25 26 6.860790 TTCTATGGCCGGTATGTATAATGA 57.139 37.500 1.90 0.00 0.00 2.57
26 27 6.860790 TCTATGGCCGGTATGTATAATGAA 57.139 37.500 1.90 0.00 0.00 2.57
27 28 7.247456 TCTATGGCCGGTATGTATAATGAAA 57.753 36.000 1.90 0.00 0.00 2.69
28 29 7.101054 TCTATGGCCGGTATGTATAATGAAAC 58.899 38.462 1.90 0.00 0.00 2.78
29 30 5.298989 TGGCCGGTATGTATAATGAAACT 57.701 39.130 1.90 0.00 0.00 2.66
30 31 6.422344 TGGCCGGTATGTATAATGAAACTA 57.578 37.500 1.90 0.00 0.00 2.24
31 32 7.011499 TGGCCGGTATGTATAATGAAACTAT 57.989 36.000 1.90 0.00 0.00 2.12
32 33 8.136563 TGGCCGGTATGTATAATGAAACTATA 57.863 34.615 1.90 0.00 0.00 1.31
33 34 8.036575 TGGCCGGTATGTATAATGAAACTATAC 58.963 37.037 1.90 0.00 0.00 1.47
34 35 8.036575 GGCCGGTATGTATAATGAAACTATACA 58.963 37.037 1.90 5.43 39.89 2.29
35 36 9.426837 GCCGGTATGTATAATGAAACTATACAA 57.573 33.333 1.90 0.00 39.29 2.41
47 48 9.632638 AATGAAACTATACAATAACAGATGGCT 57.367 29.630 0.00 0.00 0.00 4.75
52 53 9.856488 AACTATACAATAACAGATGGCTATACG 57.144 33.333 0.00 0.00 0.00 3.06
53 54 7.974501 ACTATACAATAACAGATGGCTATACGC 59.025 37.037 0.00 0.00 38.13 4.42
54 55 4.956085 ACAATAACAGATGGCTATACGCA 58.044 39.130 0.00 0.00 41.67 5.24
55 56 5.551233 ACAATAACAGATGGCTATACGCAT 58.449 37.500 0.00 0.00 41.67 4.73
56 57 5.639506 ACAATAACAGATGGCTATACGCATC 59.360 40.000 0.00 0.00 41.67 3.91
57 58 3.751479 AACAGATGGCTATACGCATCA 57.249 42.857 0.00 0.00 41.67 3.07
58 59 3.751479 ACAGATGGCTATACGCATCAA 57.249 42.857 0.00 0.00 41.67 2.57
59 60 3.657634 ACAGATGGCTATACGCATCAAG 58.342 45.455 0.00 0.00 41.67 3.02
60 61 2.414481 CAGATGGCTATACGCATCAAGC 59.586 50.000 0.00 0.00 41.67 4.01
69 70 4.275282 GCATCAAGCGCGAACATC 57.725 55.556 12.10 0.00 0.00 3.06
70 71 1.717937 GCATCAAGCGCGAACATCT 59.282 52.632 12.10 0.00 0.00 2.90
71 72 0.930310 GCATCAAGCGCGAACATCTA 59.070 50.000 12.10 0.00 0.00 1.98
72 73 1.070975 GCATCAAGCGCGAACATCTAG 60.071 52.381 12.10 0.00 0.00 2.43
73 74 2.196749 CATCAAGCGCGAACATCTAGT 58.803 47.619 12.10 0.00 0.00 2.57
74 75 3.372060 CATCAAGCGCGAACATCTAGTA 58.628 45.455 12.10 0.00 0.00 1.82
75 76 2.793933 TCAAGCGCGAACATCTAGTAC 58.206 47.619 12.10 0.00 0.00 2.73
76 77 2.422479 TCAAGCGCGAACATCTAGTACT 59.578 45.455 12.10 0.00 0.00 2.73
77 78 2.759538 AGCGCGAACATCTAGTACTC 57.240 50.000 12.10 0.00 0.00 2.59
78 79 2.290464 AGCGCGAACATCTAGTACTCT 58.710 47.619 12.10 0.00 0.00 3.24
79 80 2.288458 AGCGCGAACATCTAGTACTCTC 59.712 50.000 12.10 0.00 0.00 3.20
80 81 2.288458 GCGCGAACATCTAGTACTCTCT 59.712 50.000 12.10 0.00 0.00 3.10
81 82 3.605231 GCGCGAACATCTAGTACTCTCTC 60.605 52.174 12.10 0.00 0.00 3.20
82 83 3.059461 CGCGAACATCTAGTACTCTCTCC 60.059 52.174 0.00 0.00 0.00 3.71
83 84 3.059461 GCGAACATCTAGTACTCTCTCCG 60.059 52.174 0.00 0.00 0.00 4.63
84 85 3.059461 CGAACATCTAGTACTCTCTCCGC 60.059 52.174 0.00 0.00 0.00 5.54
85 86 2.853705 ACATCTAGTACTCTCTCCGCC 58.146 52.381 0.00 0.00 0.00 6.13
86 87 2.440253 ACATCTAGTACTCTCTCCGCCT 59.560 50.000 0.00 0.00 0.00 5.52
87 88 2.914695 TCTAGTACTCTCTCCGCCTC 57.085 55.000 0.00 0.00 0.00 4.70
88 89 1.417145 TCTAGTACTCTCTCCGCCTCC 59.583 57.143 0.00 0.00 0.00 4.30
89 90 1.141254 CTAGTACTCTCTCCGCCTCCA 59.859 57.143 0.00 0.00 0.00 3.86
90 91 0.331954 AGTACTCTCTCCGCCTCCAA 59.668 55.000 0.00 0.00 0.00 3.53
91 92 1.183549 GTACTCTCTCCGCCTCCAAA 58.816 55.000 0.00 0.00 0.00 3.28
92 93 1.757699 GTACTCTCTCCGCCTCCAAAT 59.242 52.381 0.00 0.00 0.00 2.32
93 94 2.160721 ACTCTCTCCGCCTCCAAATA 57.839 50.000 0.00 0.00 0.00 1.40
94 95 2.035632 ACTCTCTCCGCCTCCAAATAG 58.964 52.381 0.00 0.00 0.00 1.73
95 96 2.311463 CTCTCTCCGCCTCCAAATAGA 58.689 52.381 0.00 0.00 0.00 1.98
96 97 2.896685 CTCTCTCCGCCTCCAAATAGAT 59.103 50.000 0.00 0.00 0.00 1.98
97 98 2.630098 TCTCTCCGCCTCCAAATAGATG 59.370 50.000 0.00 0.00 0.00 2.90
98 99 1.694150 TCTCCGCCTCCAAATAGATGG 59.306 52.381 0.00 0.00 42.12 3.51
99 100 1.417890 CTCCGCCTCCAAATAGATGGT 59.582 52.381 0.00 0.00 41.46 3.55
100 101 1.140852 TCCGCCTCCAAATAGATGGTG 59.859 52.381 0.00 0.00 41.46 4.17
101 102 1.134098 CCGCCTCCAAATAGATGGTGT 60.134 52.381 0.00 0.00 41.46 4.16
102 103 2.104111 CCGCCTCCAAATAGATGGTGTA 59.896 50.000 0.00 0.00 41.46 2.90
103 104 3.244561 CCGCCTCCAAATAGATGGTGTAT 60.245 47.826 0.00 0.00 41.46 2.29
104 105 4.020573 CCGCCTCCAAATAGATGGTGTATA 60.021 45.833 0.00 0.00 41.46 1.47
105 106 5.512404 CCGCCTCCAAATAGATGGTGTATAA 60.512 44.000 0.00 0.00 41.46 0.98
106 107 5.995282 CGCCTCCAAATAGATGGTGTATAAA 59.005 40.000 0.00 0.00 41.46 1.40
107 108 6.485313 CGCCTCCAAATAGATGGTGTATAAAA 59.515 38.462 0.00 0.00 41.46 1.52
108 109 7.519970 CGCCTCCAAATAGATGGTGTATAAAAC 60.520 40.741 0.00 0.00 41.46 2.43
135 136 8.947055 AGTCAAAATTGCTTTGTAAGTTTGAT 57.053 26.923 19.98 11.00 46.63 2.57
247 249 0.896940 ACAGGGTTGGCAGAGCAATG 60.897 55.000 0.00 0.00 0.00 2.82
252 254 2.485302 GGGTTGGCAGAGCAATGTTTTT 60.485 45.455 0.00 0.00 0.00 1.94
293 295 5.500645 AGAGGCAACAGTTAAAAAGTCAC 57.499 39.130 0.00 0.00 41.41 3.67
294 296 4.338400 AGAGGCAACAGTTAAAAAGTCACC 59.662 41.667 0.00 0.00 41.41 4.02
306 308 0.036952 AAGTCACCGATGCAGACCAG 60.037 55.000 0.00 0.00 32.82 4.00
308 310 1.609210 TCACCGATGCAGACCAGGA 60.609 57.895 0.00 0.00 0.00 3.86
311 313 1.142748 CCGATGCAGACCAGGAGAC 59.857 63.158 0.00 0.00 0.00 3.36
312 314 1.226802 CGATGCAGACCAGGAGACG 60.227 63.158 0.00 0.00 0.00 4.18
329 331 3.807538 GCCGACGACCGCAGTCTA 61.808 66.667 0.00 0.00 41.16 2.59
330 332 2.099831 CCGACGACCGCAGTCTAC 59.900 66.667 0.00 0.00 41.16 2.59
331 333 2.276493 CGACGACCGCAGTCTACG 60.276 66.667 0.00 0.41 41.16 3.51
353 355 1.017387 GCAAATCGCCTTACCAGAGG 58.983 55.000 0.00 0.00 39.93 3.69
355 357 2.555199 CAAATCGCCTTACCAGAGGAG 58.445 52.381 0.00 0.00 39.25 3.69
359 361 2.253610 TCGCCTTACCAGAGGAGAAAA 58.746 47.619 0.00 0.00 41.76 2.29
360 362 2.028385 TCGCCTTACCAGAGGAGAAAAC 60.028 50.000 0.00 0.00 41.76 2.43
361 363 2.712709 GCCTTACCAGAGGAGAAAACC 58.287 52.381 0.00 0.00 39.25 3.27
362 364 2.039879 GCCTTACCAGAGGAGAAAACCA 59.960 50.000 0.00 0.00 39.25 3.67
363 365 3.676093 CCTTACCAGAGGAGAAAACCAC 58.324 50.000 0.00 0.00 39.25 4.16
364 366 3.328050 CCTTACCAGAGGAGAAAACCACT 59.672 47.826 0.00 0.00 39.25 4.00
382 384 4.466726 ACCACTGATAAGGACCTGTAGAAC 59.533 45.833 0.00 0.00 0.00 3.01
384 386 4.712337 CACTGATAAGGACCTGTAGAACCT 59.288 45.833 0.00 0.00 0.00 3.50
385 387 4.957327 ACTGATAAGGACCTGTAGAACCTC 59.043 45.833 0.00 0.00 31.89 3.85
392 394 3.083293 GACCTGTAGAACCTCGAAGACT 58.917 50.000 0.00 0.00 0.00 3.24
401 403 1.469308 ACCTCGAAGACTACAGAAGCG 59.531 52.381 0.00 0.00 0.00 4.68
405 407 0.533032 GAAGACTACAGAAGCGGGCT 59.467 55.000 0.00 0.00 0.00 5.19
435 437 0.544697 GGATCCACCGGAAGCCTAAA 59.455 55.000 9.46 0.00 34.34 1.85
438 440 1.128809 TCCACCGGAAGCCTAAACCA 61.129 55.000 9.46 0.00 0.00 3.67
447 449 2.640316 AGCCTAAACCAATCGGATCC 57.360 50.000 0.00 0.00 35.59 3.36
449 451 1.133915 GCCTAAACCAATCGGATCCCA 60.134 52.381 6.06 0.00 35.59 4.37
458 460 0.183731 ATCGGATCCCAAAAGGCCTC 59.816 55.000 5.23 0.00 34.51 4.70
460 462 1.697297 GGATCCCAAAAGGCCTCCA 59.303 57.895 5.23 0.00 37.22 3.86
461 463 0.396278 GGATCCCAAAAGGCCTCCAG 60.396 60.000 5.23 0.00 37.22 3.86
463 465 1.005924 GATCCCAAAAGGCCTCCAGAA 59.994 52.381 5.23 0.00 34.51 3.02
474 476 0.397941 CCTCCAGAAACACAGCTCCA 59.602 55.000 0.00 0.00 0.00 3.86
475 477 1.004044 CCTCCAGAAACACAGCTCCAT 59.996 52.381 0.00 0.00 0.00 3.41
479 481 2.612972 CCAGAAACACAGCTCCATACGT 60.613 50.000 0.00 0.00 0.00 3.57
480 482 2.668457 CAGAAACACAGCTCCATACGTC 59.332 50.000 0.00 0.00 0.00 4.34
484 486 1.107114 CACAGCTCCATACGTCCTCT 58.893 55.000 0.00 0.00 0.00 3.69
485 487 1.107114 ACAGCTCCATACGTCCTCTG 58.893 55.000 0.00 0.00 0.00 3.35
487 489 0.396417 AGCTCCATACGTCCTCTGCT 60.396 55.000 0.00 0.00 0.00 4.24
489 491 1.393603 CTCCATACGTCCTCTGCTGA 58.606 55.000 0.00 0.00 0.00 4.26
491 493 3.149981 CTCCATACGTCCTCTGCTGATA 58.850 50.000 0.00 0.00 0.00 2.15
512 514 0.031449 AAAACGCACCAACCGAATGG 59.969 50.000 5.05 5.05 46.38 3.16
521 523 1.768870 CCAACCGAATGGGGATAGAGT 59.231 52.381 0.00 0.00 41.60 3.24
522 524 2.485479 CCAACCGAATGGGGATAGAGTG 60.485 54.545 0.00 0.00 41.60 3.51
523 525 1.424638 ACCGAATGGGGATAGAGTGG 58.575 55.000 0.00 0.00 41.60 4.00
526 528 1.821088 GAATGGGGATAGAGTGGGGT 58.179 55.000 0.00 0.00 0.00 4.95
531 533 2.527057 TGGGGATAGAGTGGGGTAGAAT 59.473 50.000 0.00 0.00 0.00 2.40
568 570 1.404035 GGTAATGCCGCCTTAAACCAG 59.596 52.381 0.00 0.00 0.00 4.00
582 584 5.581085 CCTTAAACCAGACATAAAGACTCCG 59.419 44.000 0.00 0.00 0.00 4.63
583 585 2.674796 ACCAGACATAAAGACTCCGC 57.325 50.000 0.00 0.00 0.00 5.54
584 586 2.180276 ACCAGACATAAAGACTCCGCT 58.820 47.619 0.00 0.00 0.00 5.52
586 588 3.767673 ACCAGACATAAAGACTCCGCTAA 59.232 43.478 0.00 0.00 0.00 3.09
587 589 4.142138 ACCAGACATAAAGACTCCGCTAAG 60.142 45.833 0.00 0.00 0.00 2.18
588 590 4.363999 CAGACATAAAGACTCCGCTAAGG 58.636 47.826 0.00 0.00 42.97 2.69
602 604 3.197116 CCGCTAAGGAAAACCTAGGAAGA 59.803 47.826 17.98 0.00 45.00 2.87
633 635 2.943978 GCCACTGTACGACTGGCCT 61.944 63.158 14.50 0.00 44.15 5.19
636 638 2.283529 ACTGTACGACTGGCCTGGG 61.284 63.158 14.82 7.91 0.00 4.45
654 656 1.873698 GGTTTCAGAACCGTGCACTA 58.126 50.000 16.19 0.00 45.43 2.74
657 659 1.493772 TTCAGAACCGTGCACTAACG 58.506 50.000 16.19 0.67 43.20 3.18
660 662 2.667199 AACCGTGCACTAACGCCC 60.667 61.111 16.19 0.00 42.23 6.13
667 669 0.685097 TGCACTAACGCCCTCTTCTT 59.315 50.000 0.00 0.00 0.00 2.52
671 673 0.179108 CTAACGCCCTCTTCTTCCCG 60.179 60.000 0.00 0.00 0.00 5.14
674 676 1.227380 CGCCCTCTTCTTCCCGATG 60.227 63.158 0.00 0.00 0.00 3.84
720 723 9.334693 CAAACTCAGAAAGCTATGTGAATTTAC 57.665 33.333 0.00 0.00 0.00 2.01
724 727 6.092122 TCAGAAAGCTATGTGAATTTACACGG 59.908 38.462 5.03 3.02 42.86 4.94
747 750 3.317455 TCAATCCTTGCATAGGCCAAT 57.683 42.857 5.01 0.00 44.37 3.16
755 758 0.041312 GCATAGGCCAATGTTACGCG 60.041 55.000 5.01 3.53 0.00 6.01
759 762 0.391927 AGGCCAATGTTACGCGCTTA 60.392 50.000 5.73 0.00 0.00 3.09
812 816 4.436113 ACTACTACTACTGGCCTAGGTC 57.564 50.000 6.37 6.37 0.00 3.85
879 887 1.351017 ACAACCATGGACTGTACTGGG 59.649 52.381 21.47 6.30 32.89 4.45
952 960 1.076923 GGCTCCACGGTCTCCTCTA 60.077 63.158 0.00 0.00 0.00 2.43
980 988 2.939103 GCATGCTCCCCGCTATATAAAG 59.061 50.000 11.37 0.00 40.11 1.85
994 1002 2.969443 ATAAAGCACAACACACGCTC 57.031 45.000 0.00 0.00 34.11 5.03
1001 1009 1.968017 CAACACACGCTCCCTGCAT 60.968 57.895 0.00 0.00 43.06 3.96
1003 1021 1.518056 AACACACGCTCCCTGCATTG 61.518 55.000 0.00 0.00 43.06 2.82
1009 1027 3.136123 CTCCCTGCATTGCCCACG 61.136 66.667 6.12 0.00 0.00 4.94
1015 1033 2.203972 CTGCATTGCCCACGTCCTTG 62.204 60.000 6.12 0.00 0.00 3.61
1016 1034 1.971167 GCATTGCCCACGTCCTTGA 60.971 57.895 0.00 0.00 0.00 3.02
1020 1038 2.107041 TTGCCCACGTCCTTGATCGT 62.107 55.000 0.00 0.00 40.99 3.73
1025 1043 0.797249 CACGTCCTTGATCGTCGTCC 60.797 60.000 0.00 0.00 38.23 4.79
1026 1044 0.959372 ACGTCCTTGATCGTCGTCCT 60.959 55.000 0.00 0.00 35.30 3.85
1027 1045 0.170561 CGTCCTTGATCGTCGTCCTT 59.829 55.000 0.00 0.00 0.00 3.36
1028 1046 1.402456 CGTCCTTGATCGTCGTCCTTT 60.402 52.381 0.00 0.00 0.00 3.11
1029 1047 2.260481 GTCCTTGATCGTCGTCCTTTC 58.740 52.381 0.00 0.00 0.00 2.62
1030 1048 2.094649 GTCCTTGATCGTCGTCCTTTCT 60.095 50.000 0.00 0.00 0.00 2.52
1031 1049 2.163815 TCCTTGATCGTCGTCCTTTCTC 59.836 50.000 0.00 0.00 0.00 2.87
1032 1050 2.164624 CCTTGATCGTCGTCCTTTCTCT 59.835 50.000 0.00 0.00 0.00 3.10
1033 1051 3.430931 CTTGATCGTCGTCCTTTCTCTC 58.569 50.000 0.00 0.00 0.00 3.20
1034 1052 2.712709 TGATCGTCGTCCTTTCTCTCT 58.287 47.619 0.00 0.00 0.00 3.10
1035 1053 2.678836 TGATCGTCGTCCTTTCTCTCTC 59.321 50.000 0.00 0.00 0.00 3.20
1036 1054 2.476126 TCGTCGTCCTTTCTCTCTCT 57.524 50.000 0.00 0.00 0.00 3.10
1037 1055 2.348660 TCGTCGTCCTTTCTCTCTCTC 58.651 52.381 0.00 0.00 0.00 3.20
1038 1056 2.027929 TCGTCGTCCTTTCTCTCTCTCT 60.028 50.000 0.00 0.00 0.00 3.10
1039 1057 2.350498 CGTCGTCCTTTCTCTCTCTCTC 59.650 54.545 0.00 0.00 0.00 3.20
1040 1058 3.606687 GTCGTCCTTTCTCTCTCTCTCT 58.393 50.000 0.00 0.00 0.00 3.10
1041 1059 3.621715 GTCGTCCTTTCTCTCTCTCTCTC 59.378 52.174 0.00 0.00 0.00 3.20
1042 1060 3.517901 TCGTCCTTTCTCTCTCTCTCTCT 59.482 47.826 0.00 0.00 0.00 3.10
1043 1061 3.871594 CGTCCTTTCTCTCTCTCTCTCTC 59.128 52.174 0.00 0.00 0.00 3.20
1044 1062 4.383118 CGTCCTTTCTCTCTCTCTCTCTCT 60.383 50.000 0.00 0.00 0.00 3.10
1045 1063 5.119694 GTCCTTTCTCTCTCTCTCTCTCTC 58.880 50.000 0.00 0.00 0.00 3.20
1046 1064 5.032846 TCCTTTCTCTCTCTCTCTCTCTCT 58.967 45.833 0.00 0.00 0.00 3.10
1047 1065 5.129485 TCCTTTCTCTCTCTCTCTCTCTCTC 59.871 48.000 0.00 0.00 0.00 3.20
1048 1066 5.130145 CCTTTCTCTCTCTCTCTCTCTCTCT 59.870 48.000 0.00 0.00 0.00 3.10
1069 1087 2.840038 TCTCTCTCTCTCTCTCTGCACT 59.160 50.000 0.00 0.00 0.00 4.40
1084 1102 0.525761 GCACTTAATCCAGCGCCAAA 59.474 50.000 2.29 0.00 0.00 3.28
1092 1110 0.618458 TCCAGCGCCAAAGAGGTATT 59.382 50.000 2.29 0.00 40.61 1.89
1104 1122 6.826741 GCCAAAGAGGTATTACCAACATTCTA 59.173 38.462 15.19 0.00 41.95 2.10
1118 1162 5.345741 CCAACATTCTAAATTTTCCACTGCG 59.654 40.000 0.00 0.00 0.00 5.18
1169 1213 4.766891 ACATTTCGATCTGTTTGTTCCCAT 59.233 37.500 0.00 0.00 0.00 4.00
1178 1222 7.042456 CGATCTGTTTGTTCCCATAGAATACTG 60.042 40.741 0.00 0.00 36.69 2.74
1179 1223 7.016153 TCTGTTTGTTCCCATAGAATACTGT 57.984 36.000 0.00 0.00 36.69 3.55
1180 1224 8.141298 TCTGTTTGTTCCCATAGAATACTGTA 57.859 34.615 0.00 0.00 36.69 2.74
1181 1225 8.038944 TCTGTTTGTTCCCATAGAATACTGTAC 58.961 37.037 0.00 0.00 36.69 2.90
1474 1518 4.549516 GGAGACTACGACGGCGCC 62.550 72.222 19.07 19.07 42.48 6.53
1561 1605 1.644372 CGATCGCTACGAGCTCTGT 59.356 57.895 12.85 13.60 40.26 3.41
1564 1608 0.660488 ATCGCTACGAGCTCTGTCTG 59.340 55.000 12.85 9.08 39.91 3.51
1615 1659 3.214250 GATCCTCCGCCGCGAGAAT 62.214 63.158 15.93 0.00 30.97 2.40
1928 1972 3.192422 CGCATAATCTCCTCCTCTCGAAT 59.808 47.826 0.00 0.00 0.00 3.34
1944 1988 4.218200 TCTCGAATTGGCATTTGACATTGT 59.782 37.500 0.00 0.00 30.61 2.71
1945 1989 4.484236 TCGAATTGGCATTTGACATTGTC 58.516 39.130 9.93 9.93 30.06 3.18
1946 1990 3.301379 CGAATTGGCATTTGACATTGTCG 59.699 43.478 11.97 0.00 34.95 4.35
1947 1991 2.063156 TTGGCATTTGACATTGTCGC 57.937 45.000 11.97 8.74 34.95 5.19
1948 1992 0.957362 TGGCATTTGACATTGTCGCA 59.043 45.000 11.97 1.55 34.95 5.10
1949 1993 1.335780 TGGCATTTGACATTGTCGCAC 60.336 47.619 11.97 4.72 34.95 5.34
1950 1994 0.976963 GCATTTGACATTGTCGCACG 59.023 50.000 11.97 2.63 34.95 5.34
1951 1995 0.976963 CATTTGACATTGTCGCACGC 59.023 50.000 11.97 0.00 34.95 5.34
1952 1996 0.590682 ATTTGACATTGTCGCACGCA 59.409 45.000 11.97 0.00 34.95 5.24
1953 1997 0.316607 TTTGACATTGTCGCACGCAC 60.317 50.000 11.97 0.00 34.95 5.34
1954 1998 2.111932 TTGACATTGTCGCACGCACC 62.112 55.000 11.97 0.00 34.95 5.01
1989 2033 4.261781 GCGTACGCGGGACTAGGG 62.262 72.222 26.17 0.00 38.78 3.53
2031 2075 0.767375 AGGAGCAGAAGACCAAGCAA 59.233 50.000 0.00 0.00 0.00 3.91
2076 2120 1.786937 ACAACCAGGGCATGTTCAAA 58.213 45.000 0.00 0.00 0.00 2.69
2226 2270 3.414700 GTGCTCAACGGCGAGGTG 61.415 66.667 16.62 8.87 39.43 4.00
2310 2354 4.374702 CGTTGAGGCAGTGCACGC 62.375 66.667 18.61 20.56 0.00 5.34
2687 2757 1.853319 CGAAGTTGAGGTGACACGC 59.147 57.895 0.00 0.00 0.00 5.34
2692 2762 0.944386 GTTGAGGTGACACGCATGTT 59.056 50.000 0.00 0.00 39.95 2.71
2702 2772 5.031578 GTGACACGCATGTTTTCTTGTTTA 58.968 37.500 0.00 0.00 39.95 2.01
2707 2777 9.549509 GACACGCATGTTTTCTTGTTTATATTA 57.450 29.630 0.00 0.00 39.95 0.98
2835 2916 3.437049 GGCATCTTTCTCAGTACCAACAC 59.563 47.826 0.00 0.00 0.00 3.32
2859 2940 2.365941 GTTCCCGATTTGTCCCCAAAAA 59.634 45.455 0.00 0.00 43.43 1.94
2880 2961 9.573133 CAAAAACTCTGTTGTCTGTAAATCTTT 57.427 29.630 0.00 0.00 0.00 2.52
2925 3006 1.617322 TACTCCGCTGTGTCTGACTT 58.383 50.000 9.51 0.00 0.00 3.01
2938 3019 6.333416 TGTGTCTGACTTTCTCTATGTATGC 58.667 40.000 9.51 0.00 0.00 3.14
2959 3040 2.678336 CCTTTTCGGATGTACTCTTGGC 59.322 50.000 0.00 0.00 33.16 4.52
2962 3043 3.410631 TTCGGATGTACTCTTGGCAAA 57.589 42.857 0.00 0.00 0.00 3.68
2969 3050 5.065731 GGATGTACTCTTGGCAAATCAGAAG 59.934 44.000 0.00 0.00 0.00 2.85
2972 3053 1.475682 CTCTTGGCAAATCAGAAGGCC 59.524 52.381 0.00 0.00 46.58 5.19
3034 3122 0.450583 TGATCGGTACTGACGACTGC 59.549 55.000 6.52 0.00 43.78 4.40
3084 3172 6.171213 ACTTAACTCGCTTGTAAAAGGCTAT 58.829 36.000 0.00 0.00 0.00 2.97
3085 3173 4.946784 AACTCGCTTGTAAAAGGCTATG 57.053 40.909 0.00 0.00 0.00 2.23
3106 4221 1.544724 ATGTAAAATGCACGCCCTGT 58.455 45.000 0.00 0.00 0.00 4.00
3109 4224 0.250945 TAAAATGCACGCCCTGTCCA 60.251 50.000 0.00 0.00 0.00 4.02
3151 4266 8.386264 AGCCATAATATTATATCAGCATACCCC 58.614 37.037 7.65 0.00 0.00 4.95
3254 4369 8.725405 TTTTTCTGTCTGTGTTAGTTGTATCA 57.275 30.769 0.00 0.00 0.00 2.15
3255 4370 8.725405 TTTTCTGTCTGTGTTAGTTGTATCAA 57.275 30.769 0.00 0.00 0.00 2.57
3319 4434 6.276091 GGTGGATGATAATTTTGAGCTTTCC 58.724 40.000 0.00 0.00 0.00 3.13
3348 4463 9.734620 TTCAGAAAATGTCATGTTGTTCTAAAG 57.265 29.630 0.00 0.00 0.00 1.85
3376 4491 3.305744 GCCACCACACGACCAATTAAAAT 60.306 43.478 0.00 0.00 0.00 1.82
3415 4530 0.328450 AATATCACCCCCTCCCAGCA 60.328 55.000 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.681679 TCATTATACATACCGGCCATAGAAAA 58.318 34.615 0.00 0.00 0.00 2.29
2 3 6.860790 TCATTATACATACCGGCCATAGAA 57.139 37.500 0.00 0.00 0.00 2.10
3 4 6.860790 TTCATTATACATACCGGCCATAGA 57.139 37.500 0.00 0.00 0.00 1.98
4 5 7.103641 AGTTTCATTATACATACCGGCCATAG 58.896 38.462 0.00 0.00 0.00 2.23
6 7 5.876357 AGTTTCATTATACATACCGGCCAT 58.124 37.500 0.00 0.00 0.00 4.40
8 9 8.036575 TGTATAGTTTCATTATACATACCGGCC 58.963 37.037 0.00 0.00 38.44 6.13
9 10 8.991243 TGTATAGTTTCATTATACATACCGGC 57.009 34.615 0.00 0.00 38.44 6.13
21 22 9.632638 AGCCATCTGTTATTGTATAGTTTCATT 57.367 29.630 0.00 0.00 0.00 2.57
26 27 9.856488 CGTATAGCCATCTGTTATTGTATAGTT 57.144 33.333 0.00 0.00 0.00 2.24
27 28 7.974501 GCGTATAGCCATCTGTTATTGTATAGT 59.025 37.037 0.00 0.00 40.81 2.12
28 29 8.341477 GCGTATAGCCATCTGTTATTGTATAG 57.659 38.462 0.00 0.00 40.81 1.31
52 53 0.930310 TAGATGTTCGCGCTTGATGC 59.070 50.000 5.56 0.00 38.57 3.91
53 54 2.196749 ACTAGATGTTCGCGCTTGATG 58.803 47.619 5.56 0.00 0.00 3.07
54 55 2.586258 ACTAGATGTTCGCGCTTGAT 57.414 45.000 5.56 0.00 0.00 2.57
55 56 2.422479 AGTACTAGATGTTCGCGCTTGA 59.578 45.455 5.56 0.00 0.00 3.02
56 57 2.784380 GAGTACTAGATGTTCGCGCTTG 59.216 50.000 5.56 0.00 0.00 4.01
57 58 2.683867 AGAGTACTAGATGTTCGCGCTT 59.316 45.455 5.56 0.00 0.00 4.68
58 59 2.288458 GAGAGTACTAGATGTTCGCGCT 59.712 50.000 5.56 0.00 0.00 5.92
59 60 2.288458 AGAGAGTACTAGATGTTCGCGC 59.712 50.000 0.00 0.00 0.00 6.86
60 61 3.059461 GGAGAGAGTACTAGATGTTCGCG 60.059 52.174 0.00 0.00 0.00 5.87
61 62 3.059461 CGGAGAGAGTACTAGATGTTCGC 60.059 52.174 0.00 0.00 0.00 4.70
62 63 3.059461 GCGGAGAGAGTACTAGATGTTCG 60.059 52.174 0.00 0.00 0.00 3.95
63 64 3.251487 GGCGGAGAGAGTACTAGATGTTC 59.749 52.174 0.00 0.00 0.00 3.18
64 65 3.117813 AGGCGGAGAGAGTACTAGATGTT 60.118 47.826 0.00 0.00 0.00 2.71
65 66 2.440253 AGGCGGAGAGAGTACTAGATGT 59.560 50.000 0.00 0.00 0.00 3.06
66 67 3.071479 GAGGCGGAGAGAGTACTAGATG 58.929 54.545 0.00 0.00 0.00 2.90
67 68 2.039348 GGAGGCGGAGAGAGTACTAGAT 59.961 54.545 0.00 0.00 0.00 1.98
68 69 1.417145 GGAGGCGGAGAGAGTACTAGA 59.583 57.143 0.00 0.00 0.00 2.43
69 70 1.141254 TGGAGGCGGAGAGAGTACTAG 59.859 57.143 0.00 0.00 0.00 2.57
70 71 1.210538 TGGAGGCGGAGAGAGTACTA 58.789 55.000 0.00 0.00 0.00 1.82
71 72 0.331954 TTGGAGGCGGAGAGAGTACT 59.668 55.000 0.00 0.00 0.00 2.73
72 73 1.183549 TTTGGAGGCGGAGAGAGTAC 58.816 55.000 0.00 0.00 0.00 2.73
73 74 2.160721 ATTTGGAGGCGGAGAGAGTA 57.839 50.000 0.00 0.00 0.00 2.59
74 75 2.035632 CTATTTGGAGGCGGAGAGAGT 58.964 52.381 0.00 0.00 0.00 3.24
75 76 2.311463 TCTATTTGGAGGCGGAGAGAG 58.689 52.381 0.00 0.00 0.00 3.20
76 77 2.454336 TCTATTTGGAGGCGGAGAGA 57.546 50.000 0.00 0.00 0.00 3.10
77 78 2.289320 CCATCTATTTGGAGGCGGAGAG 60.289 54.545 0.00 0.00 39.25 3.20
78 79 1.694150 CCATCTATTTGGAGGCGGAGA 59.306 52.381 0.00 0.00 39.25 3.71
79 80 1.417890 ACCATCTATTTGGAGGCGGAG 59.582 52.381 0.00 0.00 39.25 4.63
80 81 1.140852 CACCATCTATTTGGAGGCGGA 59.859 52.381 0.00 0.00 39.25 5.54
81 82 1.134098 ACACCATCTATTTGGAGGCGG 60.134 52.381 0.00 0.00 39.25 6.13
82 83 2.332063 ACACCATCTATTTGGAGGCG 57.668 50.000 0.00 0.00 39.25 5.52
83 84 7.519970 CGTTTTATACACCATCTATTTGGAGGC 60.520 40.741 0.00 0.00 39.25 4.70
84 85 7.713507 TCGTTTTATACACCATCTATTTGGAGG 59.286 37.037 0.00 0.00 39.25 4.30
85 86 8.657074 TCGTTTTATACACCATCTATTTGGAG 57.343 34.615 0.00 0.00 39.25 3.86
86 87 8.262227 ACTCGTTTTATACACCATCTATTTGGA 58.738 33.333 0.00 0.00 39.25 3.53
87 88 8.433421 ACTCGTTTTATACACCATCTATTTGG 57.567 34.615 0.00 0.00 42.82 3.28
88 89 9.093970 TGACTCGTTTTATACACCATCTATTTG 57.906 33.333 0.00 0.00 0.00 2.32
89 90 9.661563 TTGACTCGTTTTATACACCATCTATTT 57.338 29.630 0.00 0.00 0.00 1.40
90 91 9.661563 TTTGACTCGTTTTATACACCATCTATT 57.338 29.630 0.00 0.00 0.00 1.73
91 92 9.661563 TTTTGACTCGTTTTATACACCATCTAT 57.338 29.630 0.00 0.00 0.00 1.98
92 93 9.661563 ATTTTGACTCGTTTTATACACCATCTA 57.338 29.630 0.00 0.00 0.00 1.98
93 94 7.972832 TTTTGACTCGTTTTATACACCATCT 57.027 32.000 0.00 0.00 0.00 2.90
94 95 9.061610 CAATTTTGACTCGTTTTATACACCATC 57.938 33.333 0.00 0.00 0.00 3.51
95 96 7.540745 GCAATTTTGACTCGTTTTATACACCAT 59.459 33.333 0.00 0.00 0.00 3.55
96 97 6.858993 GCAATTTTGACTCGTTTTATACACCA 59.141 34.615 0.00 0.00 0.00 4.17
97 98 7.081976 AGCAATTTTGACTCGTTTTATACACC 58.918 34.615 0.00 0.00 0.00 4.16
98 99 8.502161 AAGCAATTTTGACTCGTTTTATACAC 57.498 30.769 0.00 0.00 0.00 2.90
221 222 4.165180 TGCTCTGCCAACCCTGTATTAATA 59.835 41.667 0.00 0.00 0.00 0.98
223 224 2.307392 TGCTCTGCCAACCCTGTATTAA 59.693 45.455 0.00 0.00 0.00 1.40
252 254 4.098044 CCTCTACGAGCTCCTATGTTTCAA 59.902 45.833 8.47 0.00 0.00 2.69
253 255 3.632604 CCTCTACGAGCTCCTATGTTTCA 59.367 47.826 8.47 0.00 0.00 2.69
254 256 3.551250 GCCTCTACGAGCTCCTATGTTTC 60.551 52.174 8.47 0.00 0.00 2.78
256 258 1.957877 GCCTCTACGAGCTCCTATGTT 59.042 52.381 8.47 0.00 0.00 2.71
263 265 0.528470 ACTGTTGCCTCTACGAGCTC 59.472 55.000 2.73 2.73 0.00 4.09
278 280 3.880490 TGCATCGGTGACTTTTTAACTGT 59.120 39.130 0.00 0.00 0.00 3.55
280 282 4.213482 GTCTGCATCGGTGACTTTTTAACT 59.787 41.667 0.00 0.00 0.00 2.24
282 284 3.500680 GGTCTGCATCGGTGACTTTTTAA 59.499 43.478 0.00 0.00 0.00 1.52
283 285 3.071479 GGTCTGCATCGGTGACTTTTTA 58.929 45.455 0.00 0.00 0.00 1.52
284 286 1.880027 GGTCTGCATCGGTGACTTTTT 59.120 47.619 0.00 0.00 0.00 1.94
285 287 1.202758 TGGTCTGCATCGGTGACTTTT 60.203 47.619 0.00 0.00 0.00 2.27
287 289 0.036952 CTGGTCTGCATCGGTGACTT 60.037 55.000 0.00 0.00 0.00 3.01
293 295 1.142748 GTCTCCTGGTCTGCATCGG 59.857 63.158 0.00 0.00 0.00 4.18
294 296 1.226802 CGTCTCCTGGTCTGCATCG 60.227 63.158 0.00 0.00 0.00 3.84
312 314 3.807538 TAGACTGCGGTCGTCGGC 61.808 66.667 19.79 5.31 46.29 5.54
326 328 2.380084 AAGGCGATTTGCTTCGTAGA 57.620 45.000 0.00 0.00 45.43 2.59
328 330 2.273557 GGTAAGGCGATTTGCTTCGTA 58.726 47.619 0.00 0.00 45.43 3.43
329 331 1.084289 GGTAAGGCGATTTGCTTCGT 58.916 50.000 0.00 0.00 45.43 3.85
330 332 1.062587 CTGGTAAGGCGATTTGCTTCG 59.937 52.381 0.00 0.79 45.43 3.79
331 333 2.352960 CTCTGGTAAGGCGATTTGCTTC 59.647 50.000 0.00 0.00 45.43 3.86
353 355 4.938226 CAGGTCCTTATCAGTGGTTTTCTC 59.062 45.833 0.00 0.00 0.00 2.87
355 357 4.652822 ACAGGTCCTTATCAGTGGTTTTC 58.347 43.478 0.00 0.00 0.00 2.29
359 361 4.332683 TCTACAGGTCCTTATCAGTGGT 57.667 45.455 0.00 0.00 0.00 4.16
360 362 4.141914 GGTTCTACAGGTCCTTATCAGTGG 60.142 50.000 0.00 0.00 0.00 4.00
361 363 4.712337 AGGTTCTACAGGTCCTTATCAGTG 59.288 45.833 0.00 0.00 0.00 3.66
362 364 4.949121 AGGTTCTACAGGTCCTTATCAGT 58.051 43.478 0.00 0.00 0.00 3.41
363 365 4.036971 CGAGGTTCTACAGGTCCTTATCAG 59.963 50.000 0.00 0.00 0.00 2.90
364 366 3.952323 CGAGGTTCTACAGGTCCTTATCA 59.048 47.826 0.00 0.00 0.00 2.15
382 384 1.202200 CCGCTTCTGTAGTCTTCGAGG 60.202 57.143 0.00 0.00 0.00 4.63
384 386 0.809385 CCCGCTTCTGTAGTCTTCGA 59.191 55.000 0.00 0.00 0.00 3.71
385 387 0.802607 GCCCGCTTCTGTAGTCTTCG 60.803 60.000 0.00 0.00 0.00 3.79
392 394 0.178068 GGATTCAGCCCGCTTCTGTA 59.822 55.000 0.00 0.00 33.48 2.74
396 398 1.092345 GTCTGGATTCAGCCCGCTTC 61.092 60.000 0.00 0.00 40.69 3.86
401 403 3.309582 TCCGTCTGGATTCAGCCC 58.690 61.111 0.00 0.00 40.17 5.19
426 428 2.879026 GGATCCGATTGGTTTAGGCTTC 59.121 50.000 0.00 0.00 36.30 3.86
429 431 1.133915 TGGGATCCGATTGGTTTAGGC 60.134 52.381 5.45 0.00 36.30 3.93
435 437 1.959989 GCCTTTTGGGATCCGATTGGT 60.960 52.381 5.45 0.00 40.82 3.67
438 440 0.631212 AGGCCTTTTGGGATCCGATT 59.369 50.000 0.00 0.00 40.82 3.34
447 449 1.341209 GTGTTTCTGGAGGCCTTTTGG 59.659 52.381 6.77 0.00 44.18 3.28
449 451 2.310538 CTGTGTTTCTGGAGGCCTTTT 58.689 47.619 6.77 0.00 0.00 2.27
458 460 2.002586 CGTATGGAGCTGTGTTTCTGG 58.997 52.381 0.00 0.00 0.00 3.86
460 462 2.353803 GGACGTATGGAGCTGTGTTTCT 60.354 50.000 0.00 0.00 0.00 2.52
461 463 2.000447 GGACGTATGGAGCTGTGTTTC 59.000 52.381 0.00 0.00 0.00 2.78
463 465 1.204941 GAGGACGTATGGAGCTGTGTT 59.795 52.381 0.00 0.00 0.00 3.32
498 500 0.106918 TATCCCCATTCGGTTGGTGC 60.107 55.000 4.23 0.00 34.77 5.01
506 508 0.687354 CCCCACTCTATCCCCATTCG 59.313 60.000 0.00 0.00 0.00 3.34
507 509 1.821088 ACCCCACTCTATCCCCATTC 58.179 55.000 0.00 0.00 0.00 2.67
508 510 2.527057 TCTACCCCACTCTATCCCCATT 59.473 50.000 0.00 0.00 0.00 3.16
512 514 8.625467 AATAATATTCTACCCCACTCTATCCC 57.375 38.462 0.00 0.00 0.00 3.85
514 516 9.495382 AGGAATAATATTCTACCCCACTCTATC 57.505 37.037 12.19 0.00 0.00 2.08
544 546 0.106918 TTAAGGCGGCATTACCCAGG 60.107 55.000 13.08 0.00 33.26 4.45
546 548 1.465794 GTTTAAGGCGGCATTACCCA 58.534 50.000 13.08 0.00 33.26 4.51
547 549 0.742505 GGTTTAAGGCGGCATTACCC 59.257 55.000 13.08 6.57 33.26 3.69
550 552 2.290387 TGTCTGGTTTAAGGCGGCATTA 60.290 45.455 13.08 2.54 0.00 1.90
568 570 4.650754 TCCTTAGCGGAGTCTTTATGTC 57.349 45.455 0.00 0.00 36.69 3.06
611 613 0.246360 CCAGTCGTACAGTGGCATGA 59.754 55.000 0.00 0.00 38.87 3.07
622 624 1.122632 TGAAACCCAGGCCAGTCGTA 61.123 55.000 5.01 0.00 0.00 3.43
636 638 2.348218 CGTTAGTGCACGGTTCTGAAAC 60.348 50.000 12.01 0.00 36.47 2.78
652 654 0.179108 CGGGAAGAAGAGGGCGTTAG 60.179 60.000 0.00 0.00 0.00 2.34
654 656 1.265454 ATCGGGAAGAAGAGGGCGTT 61.265 55.000 0.00 0.00 0.00 4.84
657 659 0.761802 ATCATCGGGAAGAAGAGGGC 59.238 55.000 0.00 0.00 29.40 5.19
660 662 8.983724 GTATAGAAAAATCATCGGGAAGAAGAG 58.016 37.037 0.00 0.00 29.40 2.85
700 703 6.250819 CCGTGTAAATTCACATAGCTTTCTG 58.749 40.000 0.00 0.00 38.12 3.02
706 709 4.035091 TGATGCCGTGTAAATTCACATAGC 59.965 41.667 0.18 0.18 38.12 2.97
747 750 1.153329 CCCCCATAAGCGCGTAACA 60.153 57.895 8.43 0.00 0.00 2.41
777 781 9.640963 CAGTAGTAGTAGTTCTGCAACTAATTT 57.359 33.333 4.05 0.00 44.99 1.82
778 782 8.251721 CCAGTAGTAGTAGTTCTGCAACTAATT 58.748 37.037 4.05 0.00 44.99 1.40
779 783 7.630944 GCCAGTAGTAGTAGTTCTGCAACTAAT 60.631 40.741 4.17 4.17 44.99 1.73
812 816 3.057174 TGCCCTTGCTTATTTACCGTTTG 60.057 43.478 0.00 0.00 38.71 2.93
879 887 1.404851 CCGGAGCTCCTTCTTCTTGTC 60.405 57.143 29.73 0.00 0.00 3.18
980 988 2.591715 AGGGAGCGTGTGTTGTGC 60.592 61.111 0.00 0.00 0.00 4.57
994 1002 3.443045 GACGTGGGCAATGCAGGG 61.443 66.667 7.79 0.00 0.00 4.45
1001 1009 1.375396 CGATCAAGGACGTGGGCAA 60.375 57.895 0.00 0.00 0.00 4.52
1003 1021 1.810030 GACGATCAAGGACGTGGGC 60.810 63.158 0.00 0.00 42.74 5.36
1009 1027 2.094649 AGAAAGGACGACGATCAAGGAC 60.095 50.000 0.00 0.00 0.00 3.85
1015 1033 2.940410 AGAGAGAGAAAGGACGACGATC 59.060 50.000 0.00 0.00 0.00 3.69
1016 1034 2.940410 GAGAGAGAGAAAGGACGACGAT 59.060 50.000 0.00 0.00 0.00 3.73
1020 1038 3.517901 AGAGAGAGAGAGAGAAAGGACGA 59.482 47.826 0.00 0.00 0.00 4.20
1025 1043 6.098124 AGAGAGAGAGAGAGAGAGAGAGAAAG 59.902 46.154 0.00 0.00 0.00 2.62
1026 1044 5.960811 AGAGAGAGAGAGAGAGAGAGAGAAA 59.039 44.000 0.00 0.00 0.00 2.52
1027 1045 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
1028 1046 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1029 1047 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1030 1048 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1031 1049 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1032 1050 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1033 1051 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1034 1052 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1035 1053 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1036 1054 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1037 1055 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1038 1056 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1039 1057 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1040 1058 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1041 1059 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
1042 1060 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
1043 1061 4.501229 GCAGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
1044 1062 3.386078 GCAGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10
1045 1063 3.133542 TGCAGAGAGAGAGAGAGAGAGAG 59.866 52.174 0.00 0.00 0.00 3.20
1046 1064 3.106827 TGCAGAGAGAGAGAGAGAGAGA 58.893 50.000 0.00 0.00 0.00 3.10
1047 1065 3.118482 AGTGCAGAGAGAGAGAGAGAGAG 60.118 52.174 0.00 0.00 0.00 3.20
1048 1066 2.840038 AGTGCAGAGAGAGAGAGAGAGA 59.160 50.000 0.00 0.00 0.00 3.10
1069 1087 1.004277 ACCTCTTTGGCGCTGGATTAA 59.996 47.619 7.64 0.00 40.22 1.40
1092 1110 7.375053 GCAGTGGAAAATTTAGAATGTTGGTA 58.625 34.615 0.00 0.00 0.00 3.25
1104 1122 7.309920 ACGATATAAAACGCAGTGGAAAATTT 58.690 30.769 0.00 0.00 45.00 1.82
1169 1213 6.028146 TCCGCAAACAAGTACAGTATTCTA 57.972 37.500 0.00 0.00 0.00 2.10
1178 1222 3.500680 TGATTTCCTCCGCAAACAAGTAC 59.499 43.478 0.00 0.00 0.00 2.73
1179 1223 3.745799 TGATTTCCTCCGCAAACAAGTA 58.254 40.909 0.00 0.00 0.00 2.24
1180 1224 2.582052 TGATTTCCTCCGCAAACAAGT 58.418 42.857 0.00 0.00 0.00 3.16
1181 1225 3.191162 TGATGATTTCCTCCGCAAACAAG 59.809 43.478 0.00 0.00 0.00 3.16
1406 1450 1.658686 GAGAGCGAGACGGATGTGGT 61.659 60.000 0.00 0.00 0.00 4.16
1561 1605 4.671590 TCGGCGAGGTGGGACAGA 62.672 66.667 4.99 0.00 41.80 3.41
1661 1705 2.743928 CTCCTTGCCACCGAGCAC 60.744 66.667 0.00 0.00 43.97 4.40
1759 1803 3.684990 AGCACGGCGAGCTTCTCA 61.685 61.111 25.78 0.00 39.87 3.27
1780 1824 0.608640 AACGGACGGAGATGCTCTTT 59.391 50.000 0.00 0.00 0.00 2.52
1928 1972 1.339291 TGCGACAATGTCAAATGCCAA 59.661 42.857 14.24 0.00 32.09 4.52
1944 1988 4.794439 CGATCCAGGTGCGTGCGA 62.794 66.667 0.00 0.00 0.00 5.10
1947 1991 4.758251 TGCCGATCCAGGTGCGTG 62.758 66.667 3.62 0.00 0.00 5.34
1948 1992 4.457496 CTGCCGATCCAGGTGCGT 62.457 66.667 3.62 0.00 0.00 5.24
1950 1994 4.783621 TGCTGCCGATCCAGGTGC 62.784 66.667 0.00 1.83 33.44 5.01
1951 1995 2.513204 CTGCTGCCGATCCAGGTG 60.513 66.667 0.00 0.00 33.44 4.00
1952 1996 4.479993 GCTGCTGCCGATCCAGGT 62.480 66.667 3.85 0.00 33.44 4.00
2076 2120 1.402968 CACTTGTTGCACAGCTCTGTT 59.597 47.619 0.00 0.00 42.83 3.16
2122 2166 2.280797 GAACTGGCACTGGTCGCA 60.281 61.111 0.00 0.00 33.60 5.10
2307 2351 4.379243 CTGTGGCGGAAGAGGCGT 62.379 66.667 0.00 0.00 39.82 5.68
2310 2354 1.079543 CAGACTGTGGCGGAAGAGG 60.080 63.158 0.00 0.00 0.00 3.69
2591 2654 2.125269 CCCGCGTTCCCTCGAAAT 60.125 61.111 4.92 0.00 0.00 2.17
2707 2777 6.572119 GCTGCTATACAAGATCTACTGCTCAT 60.572 42.308 0.00 0.00 0.00 2.90
2805 2886 7.093068 TGGTACTGAGAAAGATGCCAACTTATA 60.093 37.037 0.00 0.00 0.00 0.98
2806 2887 6.116126 GGTACTGAGAAAGATGCCAACTTAT 58.884 40.000 0.00 0.00 0.00 1.73
2835 2916 1.173913 GGGGACAAATCGGGAACTTG 58.826 55.000 0.00 0.00 0.00 3.16
2925 3006 5.607939 TCCGAAAAGGCATACATAGAGAA 57.392 39.130 0.00 0.00 40.77 2.87
2938 3019 2.678336 GCCAAGAGTACATCCGAAAAGG 59.322 50.000 0.00 0.00 42.97 3.11
2959 3040 0.652592 CGTAGCGGCCTTCTGATTTG 59.347 55.000 0.00 0.00 0.00 2.32
2962 3043 0.249398 AAACGTAGCGGCCTTCTGAT 59.751 50.000 0.00 0.00 0.00 2.90
2972 3053 2.091122 GGTTCTTTACCGAAACGTAGCG 59.909 50.000 0.00 0.00 37.12 4.26
3034 3122 1.202290 ACACTTCAAGCTGCAAAACCG 60.202 47.619 1.02 0.00 0.00 4.44
3084 3172 2.094803 CAGGGCGTGCATTTTACATTCA 60.095 45.455 0.00 0.00 0.00 2.57
3085 3173 2.094752 ACAGGGCGTGCATTTTACATTC 60.095 45.455 7.17 0.00 0.00 2.67
3106 4221 1.136695 CTTTGTTGTTGCCTTGCTGGA 59.863 47.619 0.49 0.00 38.35 3.86
3109 4224 0.179076 GGCTTTGTTGTTGCCTTGCT 60.179 50.000 0.00 0.00 43.05 3.91
3239 4354 5.163290 TGTCACCCTTGATACAACTAACACA 60.163 40.000 0.00 0.00 33.11 3.72
3254 4369 4.503714 TTCTGAAGAAACTGTCACCCTT 57.496 40.909 0.00 0.00 0.00 3.95
3255 4370 4.713792 ATTCTGAAGAAACTGTCACCCT 57.286 40.909 0.00 0.00 37.61 4.34
3292 4407 5.271598 AGCTCAAAATTATCATCCACCCAA 58.728 37.500 0.00 0.00 0.00 4.12
3293 4408 4.870636 AGCTCAAAATTATCATCCACCCA 58.129 39.130 0.00 0.00 0.00 4.51
3295 4410 6.097412 AGGAAAGCTCAAAATTATCATCCACC 59.903 38.462 0.00 0.00 0.00 4.61
3296 4411 7.105241 AGGAAAGCTCAAAATTATCATCCAC 57.895 36.000 0.00 0.00 0.00 4.02
3297 4412 7.722949 AAGGAAAGCTCAAAATTATCATCCA 57.277 32.000 0.00 0.00 0.00 3.41
3319 4434 8.638685 AGAACAACATGACATTTTCTGAAAAG 57.361 30.769 19.14 13.66 33.22 2.27
3348 4463 1.647084 GTCGTGTGGTGGCAGTTTC 59.353 57.895 0.00 0.00 0.00 2.78
3376 4491 7.811713 TGATATTTGCGAACATTTTGATGACAA 59.188 29.630 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.