Multiple sequence alignment - TraesCS1D01G054900

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 TraesCS1D01G054900 chr1D 100.000 2882 0 0 1 2882 36324694 36321813 0.000000e+00 5323.0
1 TraesCS1D01G054900 chr1D 87.838 444 47 6 1 442 478127506 478127944 5.510000e-142 514.0
2 TraesCS1D01G054900 chr1D 95.556 90 3 1 443 532 36324341 36324253 2.990000e-30 143.0
3 TraesCS1D01G054900 chr1D 88.696 115 10 3 686 798 101104275 101104162 1.390000e-28 137.0
4 TraesCS1D01G054900 chr1D 87.069 116 11 4 686 798 90634569 90634455 8.380000e-26 128.0
5 TraesCS1D01G054900 chr1D 100.000 34 0 0 2171 2204 451635361 451635328 2.400000e-06 63.9
6 TraesCS1D01G054900 chr1D 97.059 34 1 0 2172 2205 316684059 316684092 1.120000e-04 58.4
7 TraesCS1D01G054900 chr1B 89.888 2047 123 28 887 2882 56063061 56061048 0.000000e+00 2556.0
8 TraesCS1D01G054900 chr1B 93.952 496 27 2 1630 2125 56134907 56135399 0.000000e+00 747.0
9 TraesCS1D01G054900 chr1B 86.636 434 40 6 2251 2671 56135481 56135909 5.620000e-127 464.0
10 TraesCS1D01G054900 chr1B 93.066 274 14 2 2610 2882 56135908 56136177 2.080000e-106 396.0
11 TraesCS1D01G054900 chr1B 87.554 233 20 5 1379 1611 56134694 56134917 7.920000e-66 261.0
12 TraesCS1D01G054900 chr1B 90.291 103 6 2 445 546 143061829 143061928 6.480000e-27 132.0
13 TraesCS1D01G054900 chr1B 86.957 115 12 3 686 798 486099683 486099570 3.010000e-25 126.0
14 TraesCS1D01G054900 chr1A 93.033 1378 64 20 788 2138 35544018 35542646 0.000000e+00 1984.0
15 TraesCS1D01G054900 chr1A 87.816 435 49 4 1 434 583882300 583882731 9.210000e-140 507.0
16 TraesCS1D01G054900 chr1A 89.286 336 23 5 2210 2536 35542647 35542316 2.670000e-110 409.0
17 TraesCS1D01G054900 chr1A 86.687 323 17 8 2582 2882 35542122 35541804 4.600000e-88 335.0
18 TraesCS1D01G054900 chr1A 87.826 115 11 3 686 798 530234442 530234329 6.480000e-27 132.0
19 TraesCS1D01G054900 chr1A 97.436 39 1 0 2167 2205 5494093 5494055 1.850000e-07 67.6
20 TraesCS1D01G054900 chr1A 97.368 38 1 0 2553 2590 35542322 35542285 6.670000e-07 65.8
21 TraesCS1D01G054900 chr1A 94.872 39 2 0 2167 2205 22295312 22295350 8.620000e-06 62.1
22 TraesCS1D01G054900 chr1A 90.476 42 4 0 2167 2208 537965748 537965789 4.010000e-04 56.5
23 TraesCS1D01G054900 chr5D 88.964 444 42 4 1 442 19508339 19508777 2.530000e-150 542.0
24 TraesCS1D01G054900 chr5D 87.613 444 50 3 1 442 204511363 204511803 7.120000e-141 510.0
25 TraesCS1D01G054900 chr5D 87.162 444 51 4 1 442 39698652 39698213 1.540000e-137 499.0
26 TraesCS1D01G054900 chr5D 93.750 96 3 1 445 540 19508693 19508785 1.080000e-29 141.0
27 TraesCS1D01G054900 chr5D 97.436 39 1 0 2167 2205 443649332 443649370 1.850000e-07 67.6
28 TraesCS1D01G054900 chr5D 94.872 39 2 0 2167 2205 412263368 412263330 8.620000e-06 62.1
29 TraesCS1D01G054900 chr5D 97.143 35 1 0 2171 2205 114807123 114807157 3.100000e-05 60.2
30 TraesCS1D01G054900 chr7B 88.539 445 42 5 1 442 449033400 449033838 5.470000e-147 531.0
31 TraesCS1D01G054900 chr7B 97.436 39 1 0 2167 2205 533773441 533773479 1.850000e-07 67.6
32 TraesCS1D01G054900 chr7B 100.000 35 0 0 2171 2205 686132208 686132242 6.670000e-07 65.8
33 TraesCS1D01G054900 chr7B 92.857 42 3 0 2167 2208 568677051 568677010 8.620000e-06 62.1
34 TraesCS1D01G054900 chr7B 92.857 42 3 0 2167 2208 750410817 750410776 8.620000e-06 62.1
35 TraesCS1D01G054900 chr3A 85.294 544 45 13 1 536 517446444 517446960 1.970000e-146 529.0
36 TraesCS1D01G054900 chr3A 88.136 59 4 2 2152 2208 584355047 584355104 1.850000e-07 67.6
37 TraesCS1D01G054900 chr2A 87.585 443 49 4 1 442 47226440 47226003 2.560000e-140 508.0
38 TraesCS1D01G054900 chr2A 93.478 92 3 1 443 534 47226089 47226001 1.800000e-27 134.0
39 TraesCS1D01G054900 chr2A 89.720 107 6 3 443 549 756522232 756522131 6.480000e-27 132.0
40 TraesCS1D01G054900 chr2B 86.937 444 52 4 1 442 785825896 785825457 7.170000e-136 494.0
41 TraesCS1D01G054900 chr2B 90.678 118 7 1 2742 2859 12056664 12056777 1.380000e-33 154.0
42 TraesCS1D01G054900 chr2B 100.000 28 0 0 610 637 735399699 735399726 5.000000e-03 52.8
43 TraesCS1D01G054900 chr7A 85.169 472 43 7 2210 2675 466521234 466520784 2.620000e-125 459.0
44 TraesCS1D01G054900 chr7A 97.436 39 1 0 2167 2205 573430916 573430954 1.850000e-07 67.6
45 TraesCS1D01G054900 chr4A 91.509 106 5 3 444 549 1134633 1134734 2.990000e-30 143.0
46 TraesCS1D01G054900 chr4A 86.842 114 14 1 686 798 109786709 109786822 3.010000e-25 126.0
47 TraesCS1D01G054900 chr4A 97.436 39 1 0 2167 2205 564893729 564893767 1.850000e-07 67.6
48 TraesCS1D01G054900 chr5B 90.654 107 5 3 445 549 703476799 703476696 1.390000e-28 137.0
49 TraesCS1D01G054900 chr5B 91.489 47 4 0 2167 2213 323708802 323708756 6.670000e-07 65.8
50 TraesCS1D01G054900 chr5A 92.784 97 4 1 443 539 624732330 624732237 1.390000e-28 137.0
51 TraesCS1D01G054900 chr7D 87.719 114 13 1 686 798 53975456 53975569 6.480000e-27 132.0
52 TraesCS1D01G054900 chr3B 87.826 115 11 3 686 798 227430846 227430733 6.480000e-27 132.0
53 TraesCS1D01G054900 chr4D 87.069 116 14 1 686 800 498041154 498041269 2.330000e-26 130.0
54 TraesCS1D01G054900 chr2D 87.069 116 14 1 686 800 420566134 420566019 2.330000e-26 130.0
55 TraesCS1D01G054900 chr6B 95.238 42 2 0 2167 2208 435830278 435830237 1.850000e-07 67.6
56 TraesCS1D01G054900 chr3D 95.000 40 2 0 2166 2205 524713631 524713592 2.400000e-06 63.9
57 TraesCS1D01G054900 chr3D 92.857 42 3 0 2167 2208 170239769 170239810 8.620000e-06 62.1
58 TraesCS1D01G054900 chr3D 94.872 39 2 0 2167 2205 558261187 558261149 8.620000e-06 62.1
59 TraesCS1D01G054900 chr3D 94.737 38 2 0 2167 2204 47480234 47480271 3.100000e-05 60.2
60 TraesCS1D01G054900 chr4B 96.875 32 1 0 2168 2199 42727243 42727274 1.000000e-03 54.7


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 TraesCS1D01G054900 chr1D 36321813 36324694 2881 True 2733.00 5323 97.7780 1 2882 2 chr1D.!!$R4 2881
1 TraesCS1D01G054900 chr1B 56061048 56063061 2013 True 2556.00 2556 89.8880 887 2882 1 chr1B.!!$R1 1995
2 TraesCS1D01G054900 chr1B 56134694 56136177 1483 False 467.00 747 90.3020 1379 2882 4 chr1B.!!$F2 1503
3 TraesCS1D01G054900 chr1A 35541804 35544018 2214 True 698.45 1984 91.5935 788 2882 4 chr1A.!!$R3 2094
4 TraesCS1D01G054900 chr3A 517446444 517446960 516 False 529.00 529 85.2940 1 536 1 chr3A.!!$F1 535

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
609 618 0.037975 GGACTCAAACGCGGGTTCTA 60.038 55.0 18.88 8.69 34.62 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2323 0.259938 GTGCTCCCTCCATCCCAAAT 59.74 55.0 0.0 0.0 0.0 2.32 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
84 86 7.412853 TTTTATTTAAGCCCACAATCCTACC 57.587 36.000 0.00 0.00 0.00 3.18
85 87 4.881157 ATTTAAGCCCACAATCCTACCT 57.119 40.909 0.00 0.00 0.00 3.08
86 88 4.668138 TTTAAGCCCACAATCCTACCTT 57.332 40.909 0.00 0.00 0.00 3.50
87 89 4.668138 TTAAGCCCACAATCCTACCTTT 57.332 40.909 0.00 0.00 0.00 3.11
88 90 5.782677 TTAAGCCCACAATCCTACCTTTA 57.217 39.130 0.00 0.00 0.00 1.85
89 91 4.668138 AAGCCCACAATCCTACCTTTAA 57.332 40.909 0.00 0.00 0.00 1.52
90 92 4.881157 AGCCCACAATCCTACCTTTAAT 57.119 40.909 0.00 0.00 0.00 1.40
91 93 5.206905 AGCCCACAATCCTACCTTTAATT 57.793 39.130 0.00 0.00 0.00 1.40
92 94 6.335781 AGCCCACAATCCTACCTTTAATTA 57.664 37.500 0.00 0.00 0.00 1.40
93 95 6.365520 AGCCCACAATCCTACCTTTAATTAG 58.634 40.000 0.00 0.00 0.00 1.73
94 96 5.009710 GCCCACAATCCTACCTTTAATTAGC 59.990 44.000 0.00 0.00 0.00 3.09
95 97 6.365520 CCCACAATCCTACCTTTAATTAGCT 58.634 40.000 0.00 0.00 0.00 3.32
96 98 6.486993 CCCACAATCCTACCTTTAATTAGCTC 59.513 42.308 0.00 0.00 0.00 4.09
97 99 7.054124 CCACAATCCTACCTTTAATTAGCTCA 58.946 38.462 0.00 0.00 0.00 4.26
98 100 7.721399 CCACAATCCTACCTTTAATTAGCTCAT 59.279 37.037 0.00 0.00 0.00 2.90
99 101 9.125026 CACAATCCTACCTTTAATTAGCTCATT 57.875 33.333 0.00 0.00 0.00 2.57
100 102 9.343539 ACAATCCTACCTTTAATTAGCTCATTC 57.656 33.333 0.00 0.00 0.00 2.67
101 103 8.499162 CAATCCTACCTTTAATTAGCTCATTCG 58.501 37.037 0.00 0.00 0.00 3.34
102 104 7.120923 TCCTACCTTTAATTAGCTCATTCGT 57.879 36.000 0.00 0.00 0.00 3.85
115 117 4.204581 GCTCATTCGTTTAATTAGCTCGC 58.795 43.478 0.00 0.00 40.30 5.03
124 126 5.007332 CGTTTAATTAGCTCGCCCTAAACAT 59.993 40.000 0.00 0.00 31.69 2.71
127 129 3.838244 TTAGCTCGCCCTAAACATGAT 57.162 42.857 0.00 0.00 0.00 2.45
138 140 4.012374 CCTAAACATGATGACTGCCACTT 58.988 43.478 0.00 0.00 0.00 3.16
147 149 7.992608 ACATGATGACTGCCACTTGTATATTTA 59.007 33.333 0.00 0.00 0.00 1.40
151 153 7.182817 TGACTGCCACTTGTATATTTAGAGT 57.817 36.000 0.00 0.00 0.00 3.24
158 160 7.764443 GCCACTTGTATATTTAGAGTGAGTTGA 59.236 37.037 3.56 0.00 39.97 3.18
175 177 9.778741 AGTGAGTTGAGATTAGTAAATGTGAAA 57.221 29.630 0.00 0.00 0.00 2.69
186 188 2.128771 AATGTGAAAGGCGCATAGGT 57.871 45.000 10.83 0.00 46.56 3.08
188 190 0.323302 TGTGAAAGGCGCATAGGTCA 59.677 50.000 10.83 4.12 30.65 4.02
195 197 0.381801 GGCGCATAGGTCATTGGTTG 59.618 55.000 10.83 0.00 0.00 3.77
206 208 5.067273 AGGTCATTGGTTGTTACATCGAAA 58.933 37.500 0.00 0.00 0.00 3.46
208 210 5.856455 GGTCATTGGTTGTTACATCGAAAAG 59.144 40.000 0.00 0.00 0.00 2.27
217 219 2.839486 ACATCGAAAAGCCAGACAGA 57.161 45.000 0.00 0.00 0.00 3.41
244 246 1.617850 TGTGTCCAATTCCCACAATGC 59.382 47.619 0.00 0.00 36.25 3.56
246 248 3.088532 GTGTCCAATTCCCACAATGCTA 58.911 45.455 0.00 0.00 0.00 3.49
274 276 5.830900 TTTTGACCCAATTATTTTTCGCG 57.169 34.783 0.00 0.00 0.00 5.87
277 279 3.119779 TGACCCAATTATTTTTCGCGGTC 60.120 43.478 6.13 0.91 39.19 4.79
280 282 3.488553 CCCAATTATTTTTCGCGGTCTCC 60.489 47.826 6.13 0.00 0.00 3.71
297 299 4.466015 GGTCTCCATGAAAGCCCATAAAAA 59.534 41.667 0.00 0.00 0.00 1.94
341 343 1.270305 GCCCAGATCGCTTAGCATGTA 60.270 52.381 4.70 0.00 0.00 2.29
354 356 2.826428 AGCATGTATACGAGCCAACAG 58.174 47.619 13.74 0.00 0.00 3.16
358 360 3.409851 TGTATACGAGCCAACAGTACG 57.590 47.619 0.00 0.00 0.00 3.67
361 364 2.336554 TACGAGCCAACAGTACGAAC 57.663 50.000 0.00 0.00 0.00 3.95
367 370 3.064931 AGCCAACAGTACGAACTTTAGC 58.935 45.455 0.00 0.00 31.97 3.09
380 383 2.561569 ACTTTAGCGTGCACTCAAACT 58.438 42.857 16.19 6.84 0.00 2.66
385 388 1.260561 AGCGTGCACTCAAACTAAACG 59.739 47.619 16.19 0.00 0.00 3.60
386 389 1.259507 GCGTGCACTCAAACTAAACGA 59.740 47.619 16.19 0.00 0.00 3.85
387 390 2.285950 GCGTGCACTCAAACTAAACGAA 60.286 45.455 16.19 0.00 0.00 3.85
426 429 6.667848 CCAAACCAAGAATACCTATTCCCTTT 59.332 38.462 2.04 0.00 42.29 3.11
476 485 1.268999 GCGTGCACTCAAACCAAATGA 60.269 47.619 16.19 0.00 0.00 2.57
477 486 2.797792 GCGTGCACTCAAACCAAATGAA 60.798 45.455 16.19 0.00 0.00 2.57
478 487 3.044986 CGTGCACTCAAACCAAATGAAG 58.955 45.455 16.19 0.00 0.00 3.02
492 501 7.050970 ACCAAATGAAGAAAAGGACTAAACC 57.949 36.000 0.00 0.00 0.00 3.27
579 588 7.853377 AAAAGAAAATCTTTAAGCACTACGC 57.147 32.000 5.83 0.00 45.19 4.42
580 589 5.618561 AAGAAAATCTTTAAGCACTACGCG 58.381 37.500 3.53 3.53 38.66 6.01
581 590 5.178809 AAGAAAATCTTTAAGCACTACGCGT 59.821 36.000 19.17 19.17 38.66 6.01
582 591 6.617953 AAGAAAATCTTTAAGCACTACGCGTC 60.618 38.462 18.63 0.00 38.66 5.19
583 592 8.894473 AAGAAAATCTTTAAGCACTACGCGTCA 61.894 37.037 18.63 0.96 38.66 4.35
588 597 2.506438 GCACTACGCGTCACCTCC 60.506 66.667 18.63 0.00 0.00 4.30
589 598 2.202440 CACTACGCGTCACCTCCG 60.202 66.667 18.63 0.00 0.00 4.63
590 599 3.437795 ACTACGCGTCACCTCCGG 61.438 66.667 18.63 0.00 0.00 5.14
591 600 4.189188 CTACGCGTCACCTCCGGG 62.189 72.222 18.63 0.00 43.05 5.73
592 601 4.720902 TACGCGTCACCTCCGGGA 62.721 66.667 18.63 0.00 40.27 5.14
595 604 4.131088 GCGTCACCTCCGGGACTC 62.131 72.222 0.00 0.00 36.25 3.36
596 605 2.675423 CGTCACCTCCGGGACTCA 60.675 66.667 0.00 0.00 36.25 3.41
597 606 2.273179 CGTCACCTCCGGGACTCAA 61.273 63.158 0.00 0.00 36.25 3.02
598 607 1.812686 CGTCACCTCCGGGACTCAAA 61.813 60.000 0.00 0.00 36.25 2.69
599 608 0.320508 GTCACCTCCGGGACTCAAAC 60.321 60.000 0.00 0.00 36.25 2.93
600 609 1.374252 CACCTCCGGGACTCAAACG 60.374 63.158 0.00 0.00 36.25 3.60
601 610 2.434359 CCTCCGGGACTCAAACGC 60.434 66.667 0.00 0.00 33.58 4.84
602 611 2.809601 CTCCGGGACTCAAACGCG 60.810 66.667 3.53 3.53 41.89 6.01
605 614 4.675029 CGGGACTCAAACGCGGGT 62.675 66.667 12.47 0.00 39.38 5.28
606 615 2.281276 GGGACTCAAACGCGGGTT 60.281 61.111 12.67 12.67 38.22 4.11
607 616 2.322830 GGGACTCAAACGCGGGTTC 61.323 63.158 18.88 5.50 34.62 3.62
608 617 1.301479 GGACTCAAACGCGGGTTCT 60.301 57.895 18.88 6.29 34.62 3.01
609 618 0.037975 GGACTCAAACGCGGGTTCTA 60.038 55.000 18.88 8.69 34.62 2.10
610 619 1.606224 GGACTCAAACGCGGGTTCTAA 60.606 52.381 18.88 6.25 34.62 2.10
611 620 1.725164 GACTCAAACGCGGGTTCTAAG 59.275 52.381 18.88 16.75 34.62 2.18
612 621 1.342174 ACTCAAACGCGGGTTCTAAGA 59.658 47.619 18.88 12.62 34.62 2.10
613 622 2.028385 ACTCAAACGCGGGTTCTAAGAT 60.028 45.455 18.88 0.00 34.62 2.40
614 623 3.000727 CTCAAACGCGGGTTCTAAGATT 58.999 45.455 18.88 0.00 34.62 2.40
615 624 3.404899 TCAAACGCGGGTTCTAAGATTT 58.595 40.909 18.88 0.00 34.62 2.17
616 625 3.187637 TCAAACGCGGGTTCTAAGATTTG 59.812 43.478 18.88 10.33 34.62 2.32
617 626 2.754946 ACGCGGGTTCTAAGATTTGA 57.245 45.000 12.47 0.00 0.00 2.69
618 627 3.048337 ACGCGGGTTCTAAGATTTGAA 57.952 42.857 12.47 0.00 0.00 2.69
619 628 2.740447 ACGCGGGTTCTAAGATTTGAAC 59.260 45.455 12.47 10.25 40.54 3.18
627 636 6.442513 GTTCTAAGATTTGAACCCTGATGG 57.557 41.667 8.20 0.00 37.08 3.51
637 646 2.599597 CCTGATGGGCTGGGGAAG 59.400 66.667 0.00 0.00 32.31 3.46
647 656 3.677963 CTGGGGAAGCTTGATTGGT 57.322 52.632 2.10 0.00 0.00 3.67
648 657 1.928868 CTGGGGAAGCTTGATTGGTT 58.071 50.000 2.10 0.00 0.00 3.67
649 658 2.250924 CTGGGGAAGCTTGATTGGTTT 58.749 47.619 2.10 0.00 0.00 3.27
650 659 1.969923 TGGGGAAGCTTGATTGGTTTG 59.030 47.619 2.10 0.00 0.00 2.93
651 660 2.247358 GGGGAAGCTTGATTGGTTTGA 58.753 47.619 2.10 0.00 0.00 2.69
652 661 2.833943 GGGGAAGCTTGATTGGTTTGAT 59.166 45.455 2.10 0.00 0.00 2.57
653 662 3.368739 GGGGAAGCTTGATTGGTTTGATG 60.369 47.826 2.10 0.00 0.00 3.07
654 663 3.256558 GGAAGCTTGATTGGTTTGATGC 58.743 45.455 2.10 0.00 0.00 3.91
655 664 3.256558 GAAGCTTGATTGGTTTGATGCC 58.743 45.455 2.10 0.00 0.00 4.40
656 665 2.250031 AGCTTGATTGGTTTGATGCCA 58.750 42.857 0.00 0.00 0.00 4.92
657 666 2.232941 AGCTTGATTGGTTTGATGCCAG 59.767 45.455 0.00 0.00 37.31 4.85
658 667 2.231964 GCTTGATTGGTTTGATGCCAGA 59.768 45.455 0.00 0.00 37.31 3.86
659 668 3.306225 GCTTGATTGGTTTGATGCCAGAA 60.306 43.478 0.00 0.00 37.31 3.02
660 669 4.800249 GCTTGATTGGTTTGATGCCAGAAA 60.800 41.667 0.00 0.00 37.31 2.52
661 670 5.484715 CTTGATTGGTTTGATGCCAGAAAT 58.515 37.500 0.00 0.00 37.31 2.17
662 671 5.486735 TGATTGGTTTGATGCCAGAAATT 57.513 34.783 0.00 0.00 37.31 1.82
663 672 5.239351 TGATTGGTTTGATGCCAGAAATTG 58.761 37.500 0.00 0.00 37.31 2.32
697 706 8.878769 CCAAATATTGGTTATTTACTTGCCAAC 58.121 33.333 0.87 0.00 45.93 3.77
698 707 8.878769 CAAATATTGGTTATTTACTTGCCAACC 58.121 33.333 0.00 0.00 41.30 3.77
699 708 7.726033 ATATTGGTTATTTACTTGCCAACCA 57.274 32.000 0.49 0.49 45.16 3.67
700 709 6.619329 ATTGGTTATTTACTTGCCAACCAT 57.381 33.333 5.40 0.00 45.87 3.55
701 710 5.652994 TGGTTATTTACTTGCCAACCATC 57.347 39.130 0.49 0.00 42.73 3.51
702 711 5.329399 TGGTTATTTACTTGCCAACCATCT 58.671 37.500 0.49 0.00 42.73 2.90
703 712 6.486056 TGGTTATTTACTTGCCAACCATCTA 58.514 36.000 0.49 0.00 42.73 1.98
704 713 6.948886 TGGTTATTTACTTGCCAACCATCTAA 59.051 34.615 0.49 0.00 42.73 2.10
705 714 7.122055 TGGTTATTTACTTGCCAACCATCTAAG 59.878 37.037 0.49 0.00 42.73 2.18
706 715 7.338449 GGTTATTTACTTGCCAACCATCTAAGA 59.662 37.037 0.00 0.00 38.79 2.10
707 716 8.398665 GTTATTTACTTGCCAACCATCTAAGAG 58.601 37.037 0.00 0.00 0.00 2.85
708 717 5.755409 TTACTTGCCAACCATCTAAGAGA 57.245 39.130 0.00 0.00 0.00 3.10
709 718 4.851639 ACTTGCCAACCATCTAAGAGAT 57.148 40.909 0.00 0.00 34.74 2.75
721 730 5.888105 CATCTAAGAGATGCCAGTTTTTGG 58.112 41.667 3.63 0.00 44.69 3.28
735 744 7.495135 CCAGTTTTTGGCAACTTTTGATATT 57.505 32.000 0.00 0.00 40.87 1.28
736 745 7.354257 CCAGTTTTTGGCAACTTTTGATATTG 58.646 34.615 0.00 0.00 40.87 1.90
737 746 6.852345 CAGTTTTTGGCAACTTTTGATATTGC 59.148 34.615 0.00 0.00 46.39 3.56
744 753 6.484818 GCAACTTTTGATATTGCCAATTGT 57.515 33.333 4.43 0.00 42.32 2.71
745 754 6.901265 GCAACTTTTGATATTGCCAATTGTT 58.099 32.000 4.43 0.00 42.32 2.83
746 755 6.797995 GCAACTTTTGATATTGCCAATTGTTG 59.202 34.615 4.43 0.16 42.32 3.33
767 776 5.327616 TGGCTCACCAAATATTGACAATG 57.672 39.130 11.05 0.00 45.37 2.82
768 777 4.160065 TGGCTCACCAAATATTGACAATGG 59.840 41.667 11.05 7.42 45.37 3.16
769 778 4.114794 GCTCACCAAATATTGACAATGGC 58.885 43.478 11.05 0.00 34.45 4.40
770 779 4.381825 GCTCACCAAATATTGACAATGGCA 60.382 41.667 11.05 0.00 34.45 4.92
771 780 5.722263 CTCACCAAATATTGACAATGGCAA 58.278 37.500 3.10 3.10 34.45 4.52
772 781 6.106648 TCACCAAATATTGACAATGGCAAA 57.893 33.333 5.29 0.00 34.45 3.68
773 782 6.709281 TCACCAAATATTGACAATGGCAAAT 58.291 32.000 5.29 0.00 34.45 2.32
774 783 7.845037 TCACCAAATATTGACAATGGCAAATA 58.155 30.769 5.29 0.00 34.45 1.40
775 784 8.484575 TCACCAAATATTGACAATGGCAAATAT 58.515 29.630 5.29 2.00 34.45 1.28
776 785 9.111613 CACCAAATATTGACAATGGCAAATATT 57.888 29.630 5.29 7.96 34.45 1.28
777 786 9.111613 ACCAAATATTGACAATGGCAAATATTG 57.888 29.630 5.29 10.71 40.48 1.90
778 787 8.561212 CCAAATATTGACAATGGCAAATATTGG 58.439 33.333 20.57 20.57 39.30 3.16
802 811 6.016777 GGCATCAAACCAATTATCCTCTACTG 60.017 42.308 0.00 0.00 0.00 2.74
803 812 6.543831 GCATCAAACCAATTATCCTCTACTGT 59.456 38.462 0.00 0.00 0.00 3.55
804 813 7.254932 GCATCAAACCAATTATCCTCTACTGTC 60.255 40.741 0.00 0.00 0.00 3.51
805 814 6.650120 TCAAACCAATTATCCTCTACTGTCC 58.350 40.000 0.00 0.00 0.00 4.02
807 816 5.878406 ACCAATTATCCTCTACTGTCCTG 57.122 43.478 0.00 0.00 0.00 3.86
808 817 4.656112 ACCAATTATCCTCTACTGTCCTGG 59.344 45.833 0.00 0.00 0.00 4.45
810 819 5.839063 CCAATTATCCTCTACTGTCCTGGTA 59.161 44.000 0.00 0.00 0.00 3.25
811 820 6.326583 CCAATTATCCTCTACTGTCCTGGTAA 59.673 42.308 0.00 0.00 0.00 2.85
812 821 6.980416 ATTATCCTCTACTGTCCTGGTAAC 57.020 41.667 0.00 0.00 0.00 2.50
813 822 3.097342 TCCTCTACTGTCCTGGTAACC 57.903 52.381 0.00 0.00 0.00 2.85
815 824 3.012502 TCCTCTACTGTCCTGGTAACCAT 59.987 47.826 0.00 0.00 30.82 3.55
819 836 1.628846 ACTGTCCTGGTAACCATCACC 59.371 52.381 0.00 0.00 36.54 4.02
864 881 6.163476 CACAGGAATGTTGTAGTAGCACTAA 58.837 40.000 0.00 0.00 31.62 2.24
979 997 1.279271 ACCATCTTCTTCTCAACCCCG 59.721 52.381 0.00 0.00 0.00 5.73
989 1007 2.282887 CAACCCCGAACCCCCAAG 60.283 66.667 0.00 0.00 0.00 3.61
1143 1175 4.171103 CCGTTGACCCCGATCCCC 62.171 72.222 0.00 0.00 0.00 4.81
1170 1202 1.455959 CTCCGACCCTTCCCTCGAT 60.456 63.158 0.00 0.00 31.24 3.59
1230 1262 2.362503 ATCTCCCGTGTCGAGGCA 60.363 61.111 0.00 0.00 0.00 4.75
1443 1485 2.684735 GACCCCGTCCTCTCCTCT 59.315 66.667 0.00 0.00 0.00 3.69
1533 1575 2.993853 GAGGAGCCCACCCTCTTG 59.006 66.667 0.00 0.00 45.18 3.02
1818 1860 2.263077 CATTTCTTCGAGGTGGACGAG 58.737 52.381 0.00 0.00 40.72 4.18
1863 1905 3.032265 AGTTCCCAAGCTTTGTCCTTT 57.968 42.857 0.00 0.00 0.00 3.11
1890 1932 8.650143 AGAAATTATCACTGTAACCCAATGTT 57.350 30.769 0.00 0.00 41.11 2.71
1898 1943 5.689961 CACTGTAACCCAATGTTTTACTTGC 59.310 40.000 3.82 0.00 38.42 4.01
1913 1958 6.735678 TTTACTTGCTTCGAGATGCATTTA 57.264 33.333 13.22 6.32 40.45 1.40
1939 1984 0.883833 CAGGGTTGGCATCTTCACAC 59.116 55.000 0.00 0.00 0.00 3.82
1945 1990 3.742369 GGTTGGCATCTTCACACAATTTG 59.258 43.478 0.00 0.00 0.00 2.32
1947 1992 4.669206 TGGCATCTTCACACAATTTGTT 57.331 36.364 0.00 0.00 35.67 2.83
2111 2157 7.407393 TGGCATCTTAATGAAATTCATCACA 57.593 32.000 9.11 0.00 35.76 3.58
2146 2278 8.757982 TGATTATATACTATTACCTCCGTCCC 57.242 38.462 0.00 0.00 0.00 4.46
2147 2279 8.338493 TGATTATATACTATTACCTCCGTCCCA 58.662 37.037 0.00 0.00 0.00 4.37
2148 2280 7.944729 TTATATACTATTACCTCCGTCCCAC 57.055 40.000 0.00 0.00 0.00 4.61
2149 2281 2.537633 ACTATTACCTCCGTCCCACA 57.462 50.000 0.00 0.00 0.00 4.17
2150 2282 2.385803 ACTATTACCTCCGTCCCACAG 58.614 52.381 0.00 0.00 0.00 3.66
2151 2283 1.687123 CTATTACCTCCGTCCCACAGG 59.313 57.143 0.00 0.00 0.00 4.00
2152 2284 0.042131 ATTACCTCCGTCCCACAGGA 59.958 55.000 0.00 0.00 41.08 3.86
2155 2287 3.793060 CTCCGTCCCACAGGAGTT 58.207 61.111 3.49 0.00 45.21 3.01
2156 2288 1.293498 CTCCGTCCCACAGGAGTTG 59.707 63.158 3.49 0.00 45.21 3.16
2157 2289 1.458777 TCCGTCCCACAGGAGTTGT 60.459 57.895 0.00 0.00 45.21 3.32
2158 2290 1.004918 CCGTCCCACAGGAGTTGTC 60.005 63.158 0.00 0.00 45.21 3.18
2159 2291 1.004918 CGTCCCACAGGAGTTGTCC 60.005 63.158 0.00 0.00 45.21 4.02
2176 2308 9.886132 GGAGTTGTCCTAGATTTATTTAGACAA 57.114 33.333 0.00 0.00 40.17 3.18
2197 2329 9.014297 AGACAAATCTAAGACAACTAATTTGGG 57.986 33.333 9.60 0.00 36.32 4.12
2198 2330 8.934023 ACAAATCTAAGACAACTAATTTGGGA 57.066 30.769 9.60 0.00 39.84 4.37
2199 2331 9.533831 ACAAATCTAAGACAACTAATTTGGGAT 57.466 29.630 9.60 0.00 39.84 3.85
2200 2332 9.793252 CAAATCTAAGACAACTAATTTGGGATG 57.207 33.333 0.00 0.00 39.84 3.51
2201 2333 8.525290 AATCTAAGACAACTAATTTGGGATGG 57.475 34.615 0.00 0.00 39.84 3.51
2202 2334 7.265599 TCTAAGACAACTAATTTGGGATGGA 57.734 36.000 0.00 0.00 39.84 3.41
2203 2335 7.338710 TCTAAGACAACTAATTTGGGATGGAG 58.661 38.462 0.00 0.00 39.84 3.86
2204 2336 4.860022 AGACAACTAATTTGGGATGGAGG 58.140 43.478 0.00 0.00 39.84 4.30
2205 2337 3.954258 GACAACTAATTTGGGATGGAGGG 59.046 47.826 0.00 0.00 39.84 4.30
2206 2338 3.596046 ACAACTAATTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 39.84 4.20
2207 2339 4.210331 CAACTAATTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
2208 2340 2.175715 ACTAATTTGGGATGGAGGGAGC 59.824 50.000 0.00 0.00 0.00 4.70
2256 2388 7.168219 AGATTCAGAGTTGGCATTTAACACTA 58.832 34.615 0.00 0.00 29.79 2.74
2363 2518 7.647907 ATCTTCATTTGCATTGAACAAGAAC 57.352 32.000 8.16 0.00 0.00 3.01
2372 2527 2.755836 TGAACAAGAACGAAAGCTGC 57.244 45.000 0.00 0.00 0.00 5.25
2375 2530 1.789739 CAAGAACGAAAGCTGCGCG 60.790 57.895 0.00 0.00 0.00 6.86
2376 2531 2.954753 AAGAACGAAAGCTGCGCGG 61.955 57.895 13.18 13.18 0.00 6.46
2455 2617 2.615493 CCAGTGTCCTGCGAGGTTTATT 60.615 50.000 0.00 0.00 37.38 1.40
2486 2653 4.975147 TGATATGGGAAATGGGTACTCTGT 59.025 41.667 0.00 0.00 0.00 3.41
2618 2964 5.530171 TGCTCAGAATGCAAGGAGAAATATC 59.470 40.000 10.35 0.00 37.51 1.63
2628 2974 6.261603 TGCAAGGAGAAATATCACACATGATC 59.738 38.462 0.00 0.00 42.15 2.92
2718 3124 6.086222 CACTCACATAACCAAAAGAAATCCG 58.914 40.000 0.00 0.00 0.00 4.18
2721 3127 7.119262 ACTCACATAACCAAAAGAAATCCGTAG 59.881 37.037 0.00 0.00 0.00 3.51
2763 3170 9.597681 ATTTATCTTTCTATTTCCATGAGCCAT 57.402 29.630 0.00 0.00 0.00 4.40
2869 3298 5.057149 GCTGTGATCTTTACATAACGGGAT 58.943 41.667 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 71 4.881157 ATTAAAGGTAGGATTGTGGGCT 57.119 40.909 0.00 0.00 0.00 5.19
94 96 4.318831 GGGCGAGCTAATTAAACGAATGAG 60.319 45.833 0.00 0.00 0.00 2.90
95 97 3.558418 GGGCGAGCTAATTAAACGAATGA 59.442 43.478 0.00 0.00 0.00 2.57
96 98 3.560068 AGGGCGAGCTAATTAAACGAATG 59.440 43.478 0.00 0.00 0.00 2.67
97 99 3.805207 AGGGCGAGCTAATTAAACGAAT 58.195 40.909 0.00 0.00 0.00 3.34
98 100 3.255969 AGGGCGAGCTAATTAAACGAA 57.744 42.857 0.00 0.00 0.00 3.85
99 101 2.973694 AGGGCGAGCTAATTAAACGA 57.026 45.000 0.00 0.00 0.00 3.85
100 102 4.330620 TGTTTAGGGCGAGCTAATTAAACG 59.669 41.667 0.00 0.00 35.08 3.60
101 103 5.806366 TGTTTAGGGCGAGCTAATTAAAC 57.194 39.130 0.00 0.00 33.72 2.01
102 104 6.116806 TCATGTTTAGGGCGAGCTAATTAAA 58.883 36.000 0.00 0.00 0.00 1.52
115 117 2.684881 GTGGCAGTCATCATGTTTAGGG 59.315 50.000 0.00 0.00 0.00 3.53
124 126 7.791029 TCTAAATATACAAGTGGCAGTCATCA 58.209 34.615 0.00 0.00 0.00 3.07
127 129 7.041721 CACTCTAAATATACAAGTGGCAGTCA 58.958 38.462 0.00 0.00 34.96 3.41
147 149 8.807118 TCACATTTACTAATCTCAACTCACTCT 58.193 33.333 0.00 0.00 0.00 3.24
151 153 9.219603 CCTTTCACATTTACTAATCTCAACTCA 57.780 33.333 0.00 0.00 0.00 3.41
158 160 4.941263 TGCGCCTTTCACATTTACTAATCT 59.059 37.500 4.18 0.00 0.00 2.40
175 177 0.255890 AACCAATGACCTATGCGCCT 59.744 50.000 4.18 0.00 0.00 5.52
186 188 5.457140 GCTTTTCGATGTAACAACCAATGA 58.543 37.500 0.00 0.00 0.00 2.57
188 190 4.279671 TGGCTTTTCGATGTAACAACCAAT 59.720 37.500 0.00 0.00 0.00 3.16
195 197 3.994392 TCTGTCTGGCTTTTCGATGTAAC 59.006 43.478 0.00 0.00 0.00 2.50
206 208 0.689623 CAGGACCTTCTGTCTGGCTT 59.310 55.000 0.00 0.00 43.89 4.35
208 210 0.321122 CACAGGACCTTCTGTCTGGC 60.321 60.000 0.00 0.00 45.24 4.85
217 219 1.075536 GGGAATTGGACACAGGACCTT 59.924 52.381 0.00 0.00 0.00 3.50
225 227 1.895131 AGCATTGTGGGAATTGGACAC 59.105 47.619 0.00 0.00 35.75 3.67
228 230 7.673641 ATAAATTAGCATTGTGGGAATTGGA 57.326 32.000 0.00 0.00 0.00 3.53
229 231 8.735692 AAATAAATTAGCATTGTGGGAATTGG 57.264 30.769 0.00 0.00 0.00 3.16
272 274 2.115291 GGGCTTTCATGGAGACCGC 61.115 63.158 6.19 0.00 31.36 5.68
274 276 3.297134 TTATGGGCTTTCATGGAGACC 57.703 47.619 13.30 13.30 43.03 3.85
297 299 5.253330 CAGGTACTTGTATGTTGATGGGTT 58.747 41.667 0.00 0.00 34.60 4.11
298 300 4.324254 CCAGGTACTTGTATGTTGATGGGT 60.324 45.833 4.10 0.00 34.60 4.51
299 301 4.199310 CCAGGTACTTGTATGTTGATGGG 58.801 47.826 4.10 0.00 34.60 4.00
308 310 2.263895 TCTGGGCCAGGTACTTGTAT 57.736 50.000 32.23 0.00 34.60 2.29
310 312 0.912486 GATCTGGGCCAGGTACTTGT 59.088 55.000 32.23 10.48 34.60 3.16
341 343 2.490903 AGTTCGTACTGTTGGCTCGTAT 59.509 45.455 0.00 0.00 31.99 3.06
354 356 2.056577 AGTGCACGCTAAAGTTCGTAC 58.943 47.619 12.01 0.00 37.14 3.67
358 360 3.002348 AGTTTGAGTGCACGCTAAAGTTC 59.998 43.478 21.44 8.30 0.00 3.01
361 364 4.725556 TTAGTTTGAGTGCACGCTAAAG 57.274 40.909 21.44 0.00 0.00 1.85
367 370 3.244345 TCTTCGTTTAGTTTGAGTGCACG 59.756 43.478 12.01 0.00 0.00 5.34
380 383 7.862512 TTGGTTTAGTCCTTTTCTTCGTTTA 57.137 32.000 0.00 0.00 0.00 2.01
385 388 6.459670 TGGTTTGGTTTAGTCCTTTTCTTC 57.540 37.500 0.00 0.00 0.00 2.87
386 389 6.666113 TCTTGGTTTGGTTTAGTCCTTTTCTT 59.334 34.615 0.00 0.00 0.00 2.52
387 390 6.192044 TCTTGGTTTGGTTTAGTCCTTTTCT 58.808 36.000 0.00 0.00 0.00 2.52
443 446 1.771291 GTGCACGCAAAAGTTTCGTAC 59.229 47.619 0.00 0.00 34.81 3.67
444 447 1.666700 AGTGCACGCAAAAGTTTCGTA 59.333 42.857 12.01 0.00 34.81 3.43
445 448 0.450184 AGTGCACGCAAAAGTTTCGT 59.550 45.000 12.01 0.00 36.84 3.85
446 449 1.112459 GAGTGCACGCAAAAGTTTCG 58.888 50.000 16.26 0.00 0.00 3.46
451 460 1.199624 GGTTTGAGTGCACGCAAAAG 58.800 50.000 38.58 0.00 44.74 2.27
455 464 0.743688 ATTTGGTTTGAGTGCACGCA 59.256 45.000 19.95 19.95 0.00 5.24
457 466 2.772568 TCATTTGGTTTGAGTGCACG 57.227 45.000 12.01 0.00 0.00 5.34
476 485 6.666113 TCTTGGTTTGGTTTAGTCCTTTTCTT 59.334 34.615 0.00 0.00 0.00 2.52
477 486 6.192044 TCTTGGTTTGGTTTAGTCCTTTTCT 58.808 36.000 0.00 0.00 0.00 2.52
478 487 6.459670 TCTTGGTTTGGTTTAGTCCTTTTC 57.540 37.500 0.00 0.00 0.00 2.29
492 501 7.718334 AAAGGGAATAGGTATTCTTGGTTTG 57.282 36.000 9.13 0.00 41.33 2.93
553 562 9.556030 GCGTAGTGCTTAAAGATTTTCTTTTAT 57.444 29.630 7.72 0.00 41.27 1.40
554 563 7.742963 CGCGTAGTGCTTAAAGATTTTCTTTTA 59.257 33.333 7.72 0.00 41.90 1.52
555 564 6.577427 CGCGTAGTGCTTAAAGATTTTCTTTT 59.423 34.615 7.72 0.00 41.90 2.27
556 565 6.077838 CGCGTAGTGCTTAAAGATTTTCTTT 58.922 36.000 0.00 7.57 44.55 2.52
557 566 5.178809 ACGCGTAGTGCTTAAAGATTTTCTT 59.821 36.000 11.67 0.00 45.12 2.52
558 567 4.689345 ACGCGTAGTGCTTAAAGATTTTCT 59.311 37.500 11.67 0.00 45.12 2.52
559 568 4.954442 ACGCGTAGTGCTTAAAGATTTTC 58.046 39.130 11.67 0.00 45.12 2.29
560 569 4.449743 TGACGCGTAGTGCTTAAAGATTTT 59.550 37.500 13.97 0.00 45.12 1.82
561 570 3.991773 TGACGCGTAGTGCTTAAAGATTT 59.008 39.130 13.97 0.00 45.12 2.17
562 571 3.367025 GTGACGCGTAGTGCTTAAAGATT 59.633 43.478 13.97 0.00 45.12 2.40
563 572 2.921754 GTGACGCGTAGTGCTTAAAGAT 59.078 45.455 13.97 0.00 45.12 2.40
564 573 2.322161 GTGACGCGTAGTGCTTAAAGA 58.678 47.619 13.97 0.00 45.12 2.52
565 574 1.389106 GGTGACGCGTAGTGCTTAAAG 59.611 52.381 13.97 0.00 45.12 1.85
566 575 1.000060 AGGTGACGCGTAGTGCTTAAA 60.000 47.619 13.97 0.00 45.12 1.52
567 576 0.599558 AGGTGACGCGTAGTGCTTAA 59.400 50.000 13.97 0.00 45.12 1.85
568 577 0.169672 GAGGTGACGCGTAGTGCTTA 59.830 55.000 13.97 0.00 45.12 3.09
569 578 1.080705 GAGGTGACGCGTAGTGCTT 60.081 57.895 13.97 0.00 45.12 3.91
570 579 2.567049 GAGGTGACGCGTAGTGCT 59.433 61.111 13.97 0.00 45.12 4.40
571 580 2.506438 GGAGGTGACGCGTAGTGC 60.506 66.667 13.97 0.00 45.12 4.40
585 594 2.809601 CGCGTTTGAGTCCCGGAG 60.810 66.667 0.73 0.00 0.00 4.63
586 595 4.367023 CCGCGTTTGAGTCCCGGA 62.367 66.667 0.73 0.00 41.34 5.14
588 597 4.675029 ACCCGCGTTTGAGTCCCG 62.675 66.667 4.92 0.00 0.00 5.14
589 598 2.281276 AACCCGCGTTTGAGTCCC 60.281 61.111 4.92 0.00 0.00 4.46
590 599 0.037975 TAGAACCCGCGTTTGAGTCC 60.038 55.000 4.92 0.00 30.30 3.85
591 600 1.725164 CTTAGAACCCGCGTTTGAGTC 59.275 52.381 4.92 0.00 30.30 3.36
592 601 1.342174 TCTTAGAACCCGCGTTTGAGT 59.658 47.619 4.92 0.00 30.30 3.41
593 602 2.074547 TCTTAGAACCCGCGTTTGAG 57.925 50.000 4.92 0.00 30.30 3.02
594 603 2.754946 ATCTTAGAACCCGCGTTTGA 57.245 45.000 4.92 0.00 30.30 2.69
595 604 3.187637 TCAAATCTTAGAACCCGCGTTTG 59.812 43.478 4.92 5.26 30.30 2.93
596 605 3.404899 TCAAATCTTAGAACCCGCGTTT 58.595 40.909 4.92 0.00 30.30 3.60
597 606 3.048337 TCAAATCTTAGAACCCGCGTT 57.952 42.857 4.92 0.00 33.88 4.84
598 607 2.740447 GTTCAAATCTTAGAACCCGCGT 59.260 45.455 4.92 0.00 38.49 6.01
599 608 3.385079 GTTCAAATCTTAGAACCCGCG 57.615 47.619 0.00 0.00 38.49 6.46
604 613 6.442513 CCATCAGGGTTCAAATCTTAGAAC 57.557 41.667 0.00 0.00 42.51 3.01
620 629 2.599597 CTTCCCCAGCCCATCAGG 59.400 66.667 0.00 0.00 39.47 3.86
621 630 2.123982 GCTTCCCCAGCCCATCAG 60.124 66.667 0.00 0.00 43.65 2.90
629 638 1.928868 AACCAATCAAGCTTCCCCAG 58.071 50.000 0.00 0.00 0.00 4.45
630 639 1.969923 CAAACCAATCAAGCTTCCCCA 59.030 47.619 0.00 0.00 0.00 4.96
631 640 2.247358 TCAAACCAATCAAGCTTCCCC 58.753 47.619 0.00 0.00 0.00 4.81
632 641 3.853475 CATCAAACCAATCAAGCTTCCC 58.147 45.455 0.00 0.00 0.00 3.97
633 642 3.256558 GCATCAAACCAATCAAGCTTCC 58.743 45.455 0.00 0.00 0.00 3.46
634 643 3.256558 GGCATCAAACCAATCAAGCTTC 58.743 45.455 0.00 0.00 0.00 3.86
635 644 2.633967 TGGCATCAAACCAATCAAGCTT 59.366 40.909 0.00 0.00 33.12 3.74
636 645 2.232941 CTGGCATCAAACCAATCAAGCT 59.767 45.455 0.00 0.00 36.56 3.74
637 646 2.231964 TCTGGCATCAAACCAATCAAGC 59.768 45.455 0.00 0.00 36.56 4.01
638 647 4.524316 TTCTGGCATCAAACCAATCAAG 57.476 40.909 0.00 0.00 36.56 3.02
639 648 4.952071 TTTCTGGCATCAAACCAATCAA 57.048 36.364 0.00 0.00 36.56 2.57
640 649 5.239351 CAATTTCTGGCATCAAACCAATCA 58.761 37.500 0.00 0.00 36.56 2.57
641 650 4.632688 CCAATTTCTGGCATCAAACCAATC 59.367 41.667 0.00 0.00 38.76 2.67
642 651 4.581868 CCAATTTCTGGCATCAAACCAAT 58.418 39.130 0.00 0.00 38.76 3.16
643 652 4.005487 CCAATTTCTGGCATCAAACCAA 57.995 40.909 0.00 0.00 38.76 3.67
644 653 3.681593 CCAATTTCTGGCATCAAACCA 57.318 42.857 0.00 0.00 38.76 3.67
672 681 8.878769 GGTTGGCAAGTAAATAACCAATATTTG 58.121 33.333 0.00 0.00 42.73 2.32
673 682 8.598041 TGGTTGGCAAGTAAATAACCAATATTT 58.402 29.630 0.00 0.00 45.46 1.40
674 683 8.140112 TGGTTGGCAAGTAAATAACCAATATT 57.860 30.769 0.00 0.00 45.46 1.28
675 684 7.726033 TGGTTGGCAAGTAAATAACCAATAT 57.274 32.000 0.00 0.00 45.46 1.28
680 689 5.914898 AGATGGTTGGCAAGTAAATAACC 57.085 39.130 0.00 0.00 40.83 2.85
681 690 8.276252 TCTTAGATGGTTGGCAAGTAAATAAC 57.724 34.615 0.00 0.00 0.00 1.89
682 691 8.325787 TCTCTTAGATGGTTGGCAAGTAAATAA 58.674 33.333 0.00 0.00 0.00 1.40
683 692 7.857456 TCTCTTAGATGGTTGGCAAGTAAATA 58.143 34.615 0.00 0.00 0.00 1.40
684 693 6.721318 TCTCTTAGATGGTTGGCAAGTAAAT 58.279 36.000 0.00 0.00 0.00 1.40
685 694 6.121776 TCTCTTAGATGGTTGGCAAGTAAA 57.878 37.500 0.00 0.00 0.00 2.01
686 695 5.755409 TCTCTTAGATGGTTGGCAAGTAA 57.245 39.130 0.00 0.00 0.00 2.24
687 696 5.674525 CATCTCTTAGATGGTTGGCAAGTA 58.325 41.667 0.00 0.00 46.34 2.24
688 697 4.521146 CATCTCTTAGATGGTTGGCAAGT 58.479 43.478 0.00 0.00 46.34 3.16
712 721 6.852345 GCAATATCAAAAGTTGCCAAAAACTG 59.148 34.615 0.00 0.00 41.67 3.16
713 722 6.958255 GCAATATCAAAAGTTGCCAAAAACT 58.042 32.000 0.00 0.00 41.67 2.66
721 730 6.484818 ACAATTGGCAATATCAAAAGTTGC 57.515 33.333 14.05 0.97 45.54 4.17
722 731 7.299586 CCAACAATTGGCAATATCAAAAGTTG 58.700 34.615 14.05 16.55 45.17 3.16
723 732 7.437793 CCAACAATTGGCAATATCAAAAGTT 57.562 32.000 14.05 7.18 45.17 2.66
745 754 4.160065 CCATTGTCAATATTTGGTGAGCCA 59.840 41.667 0.00 0.00 44.38 4.75
746 755 4.685924 CCATTGTCAATATTTGGTGAGCC 58.314 43.478 0.00 0.00 0.00 4.70
747 756 4.114794 GCCATTGTCAATATTTGGTGAGC 58.885 43.478 0.00 0.00 0.00 4.26
748 757 5.327616 TGCCATTGTCAATATTTGGTGAG 57.672 39.130 0.00 0.00 0.00 3.51
749 758 5.735285 TTGCCATTGTCAATATTTGGTGA 57.265 34.783 0.00 0.00 0.00 4.02
750 759 6.988622 ATTTGCCATTGTCAATATTTGGTG 57.011 33.333 0.00 0.00 0.00 4.17
751 760 9.111613 CAATATTTGCCATTGTCAATATTTGGT 57.888 29.630 0.00 0.00 0.00 3.67
752 761 8.561212 CCAATATTTGCCATTGTCAATATTTGG 58.439 33.333 0.00 0.00 32.55 3.28
753 762 8.071368 GCCAATATTTGCCATTGTCAATATTTG 58.929 33.333 0.00 0.00 32.55 2.32
754 763 7.774157 TGCCAATATTTGCCATTGTCAATATTT 59.226 29.630 8.89 0.00 32.55 1.40
755 764 7.281098 TGCCAATATTTGCCATTGTCAATATT 58.719 30.769 8.89 0.00 32.55 1.28
756 765 6.828788 TGCCAATATTTGCCATTGTCAATAT 58.171 32.000 8.89 0.00 32.55 1.28
757 766 6.231258 TGCCAATATTTGCCATTGTCAATA 57.769 33.333 8.89 0.00 32.55 1.90
758 767 5.100344 TGCCAATATTTGCCATTGTCAAT 57.900 34.783 8.89 0.00 32.55 2.57
759 768 4.548451 TGCCAATATTTGCCATTGTCAA 57.452 36.364 8.89 0.00 32.55 3.18
760 769 4.161754 TGATGCCAATATTTGCCATTGTCA 59.838 37.500 8.89 3.69 32.55 3.58
761 770 4.695396 TGATGCCAATATTTGCCATTGTC 58.305 39.130 8.89 1.52 32.55 3.18
762 771 4.757019 TGATGCCAATATTTGCCATTGT 57.243 36.364 8.89 0.00 32.55 2.71
763 772 5.220892 GGTTTGATGCCAATATTTGCCATTG 60.221 40.000 8.89 0.00 33.93 2.82
764 773 4.883006 GGTTTGATGCCAATATTTGCCATT 59.117 37.500 8.89 0.00 31.46 3.16
765 774 4.080469 TGGTTTGATGCCAATATTTGCCAT 60.080 37.500 8.89 3.28 32.29 4.40
766 775 3.262660 TGGTTTGATGCCAATATTTGCCA 59.737 39.130 8.89 0.00 32.29 4.92
767 776 3.871485 TGGTTTGATGCCAATATTTGCC 58.129 40.909 8.89 0.00 32.29 4.52
776 785 4.870636 AGAGGATAATTGGTTTGATGCCA 58.129 39.130 0.00 0.00 0.00 4.92
777 786 6.016777 CAGTAGAGGATAATTGGTTTGATGCC 60.017 42.308 0.00 0.00 0.00 4.40
778 787 6.543831 ACAGTAGAGGATAATTGGTTTGATGC 59.456 38.462 0.00 0.00 0.00 3.91
779 788 7.227512 GGACAGTAGAGGATAATTGGTTTGATG 59.772 40.741 0.00 0.00 0.00 3.07
780 789 7.127955 AGGACAGTAGAGGATAATTGGTTTGAT 59.872 37.037 0.00 0.00 0.00 2.57
781 790 6.443849 AGGACAGTAGAGGATAATTGGTTTGA 59.556 38.462 0.00 0.00 0.00 2.69
782 791 6.540189 CAGGACAGTAGAGGATAATTGGTTTG 59.460 42.308 0.00 0.00 0.00 2.93
783 792 6.353082 CCAGGACAGTAGAGGATAATTGGTTT 60.353 42.308 0.00 0.00 0.00 3.27
784 793 5.131142 CCAGGACAGTAGAGGATAATTGGTT 59.869 44.000 0.00 0.00 0.00 3.67
785 794 4.656112 CCAGGACAGTAGAGGATAATTGGT 59.344 45.833 0.00 0.00 0.00 3.67
786 795 4.656112 ACCAGGACAGTAGAGGATAATTGG 59.344 45.833 0.00 0.00 0.00 3.16
795 804 4.023980 TGATGGTTACCAGGACAGTAGAG 58.976 47.826 10.74 0.00 36.75 2.43
802 811 0.899720 TCGGTGATGGTTACCAGGAC 59.100 55.000 10.74 8.53 36.75 3.85
803 812 1.646912 TTCGGTGATGGTTACCAGGA 58.353 50.000 10.74 0.00 36.75 3.86
804 813 2.288666 CATTCGGTGATGGTTACCAGG 58.711 52.381 10.74 0.00 36.75 4.45
805 814 2.985896 ACATTCGGTGATGGTTACCAG 58.014 47.619 10.74 0.00 36.75 4.00
807 816 4.457949 AGAAAACATTCGGTGATGGTTACC 59.542 41.667 0.00 0.00 35.96 2.85
808 817 5.622770 AGAAAACATTCGGTGATGGTTAC 57.377 39.130 0.00 0.00 35.96 2.50
810 819 6.642707 TTTAGAAAACATTCGGTGATGGTT 57.357 33.333 0.00 0.00 38.54 3.67
811 820 6.642707 TTTTAGAAAACATTCGGTGATGGT 57.357 33.333 0.00 0.00 0.00 3.55
841 858 4.891992 AGTGCTACTACAACATTCCTGT 57.108 40.909 0.00 0.00 37.12 4.00
842 859 8.942338 TTATTAGTGCTACTACAACATTCCTG 57.058 34.615 0.00 0.00 28.93 3.86
843 860 9.765795 GATTATTAGTGCTACTACAACATTCCT 57.234 33.333 0.00 0.00 28.93 3.36
844 861 8.700644 CGATTATTAGTGCTACTACAACATTCC 58.299 37.037 0.00 0.00 28.93 3.01
846 863 7.170998 GCCGATTATTAGTGCTACTACAACATT 59.829 37.037 0.00 0.00 28.93 2.71
848 865 5.981315 GCCGATTATTAGTGCTACTACAACA 59.019 40.000 0.00 0.00 28.93 3.33
849 866 5.404667 GGCCGATTATTAGTGCTACTACAAC 59.595 44.000 0.00 0.00 28.93 3.32
850 867 5.510179 GGGCCGATTATTAGTGCTACTACAA 60.510 44.000 0.00 0.00 28.93 2.41
854 871 2.029290 CGGGCCGATTATTAGTGCTACT 60.029 50.000 24.41 0.00 0.00 2.57
864 881 4.411256 TTTTAAGAGACGGGCCGATTAT 57.589 40.909 35.78 14.52 0.00 1.28
979 997 3.922364 TTGGGGGCTTGGGGGTTC 61.922 66.667 0.00 0.00 0.00 3.62
1077 1109 4.736896 GTGACCGTGGCGTCTCCC 62.737 72.222 0.00 0.00 33.70 4.30
1080 1112 4.295119 GTGGTGACCGTGGCGTCT 62.295 66.667 0.00 0.00 33.70 4.18
1533 1575 1.815421 CTCGCAGTGGGGCATGTAC 60.815 63.158 7.42 0.00 0.00 2.90
1818 1860 2.876219 GTCCTCTGGTCGACGTCC 59.124 66.667 10.58 4.02 0.00 4.79
1863 1905 7.888021 ACATTGGGTTACAGTGATAATTTCTCA 59.112 33.333 0.00 0.00 38.97 3.27
1890 1932 5.627499 AAATGCATCTCGAAGCAAGTAAA 57.373 34.783 0.00 0.00 44.88 2.01
1898 1943 6.145858 CCTGAATCTCTAAATGCATCTCGAAG 59.854 42.308 0.00 0.00 0.00 3.79
1913 1958 2.203584 AGATGCCAACCCTGAATCTCT 58.796 47.619 0.00 0.00 0.00 3.10
1939 1984 7.878477 ATCACAGAATTGCAGTAACAAATTG 57.122 32.000 0.00 0.00 32.27 2.32
1945 1990 8.883731 AGTATACAATCACAGAATTGCAGTAAC 58.116 33.333 5.50 0.00 39.72 2.50
2005 2051 6.874288 AAATTATGCTCAGATGCTAACTCC 57.126 37.500 0.00 0.00 0.00 3.85
2134 2266 0.613853 CTCCTGTGGGACGGAGGTAA 60.614 60.000 0.00 0.00 42.46 2.85
2136 2268 2.283966 CTCCTGTGGGACGGAGGT 60.284 66.667 0.00 0.00 42.46 3.85
2139 2271 1.458777 ACAACTCCTGTGGGACGGA 60.459 57.895 0.00 0.00 36.69 4.69
2140 2272 1.004918 GACAACTCCTGTGGGACGG 60.005 63.158 0.00 0.00 38.84 4.79
2141 2273 1.004918 GGACAACTCCTGTGGGACG 60.005 63.158 0.00 0.00 38.84 4.79
2142 2274 2.453242 AGGACAACTCCTGTGGGAC 58.547 57.895 0.00 0.00 46.24 4.46
2150 2282 9.886132 TTGTCTAAATAAATCTAGGACAACTCC 57.114 33.333 0.00 0.00 36.71 3.85
2171 2303 9.014297 CCCAAATTAGTTGTCTTAGATTTGTCT 57.986 33.333 0.00 0.00 35.23 3.41
2172 2304 9.010029 TCCCAAATTAGTTGTCTTAGATTTGTC 57.990 33.333 0.00 0.00 35.23 3.18
2173 2305 8.934023 TCCCAAATTAGTTGTCTTAGATTTGT 57.066 30.769 0.00 0.00 35.23 2.83
2174 2306 9.793252 CATCCCAAATTAGTTGTCTTAGATTTG 57.207 33.333 0.00 0.00 35.23 2.32
2175 2307 8.971073 CCATCCCAAATTAGTTGTCTTAGATTT 58.029 33.333 0.00 0.00 35.23 2.17
2176 2308 8.336235 TCCATCCCAAATTAGTTGTCTTAGATT 58.664 33.333 0.00 0.00 35.23 2.40
2177 2309 7.872138 TCCATCCCAAATTAGTTGTCTTAGAT 58.128 34.615 0.00 0.00 35.23 1.98
2178 2310 7.265599 TCCATCCCAAATTAGTTGTCTTAGA 57.734 36.000 0.00 0.00 35.23 2.10
2179 2311 6.543831 CCTCCATCCCAAATTAGTTGTCTTAG 59.456 42.308 0.00 0.00 35.23 2.18
2180 2312 6.423182 CCTCCATCCCAAATTAGTTGTCTTA 58.577 40.000 0.00 0.00 35.23 2.10
2181 2313 5.264395 CCTCCATCCCAAATTAGTTGTCTT 58.736 41.667 0.00 0.00 35.23 3.01
2182 2314 4.325344 CCCTCCATCCCAAATTAGTTGTCT 60.325 45.833 0.00 0.00 35.23 3.41
2183 2315 3.954258 CCCTCCATCCCAAATTAGTTGTC 59.046 47.826 0.00 0.00 35.23 3.18
2184 2316 3.596046 TCCCTCCATCCCAAATTAGTTGT 59.404 43.478 0.00 0.00 35.23 3.32
2185 2317 4.210331 CTCCCTCCATCCCAAATTAGTTG 58.790 47.826 0.00 0.00 36.94 3.16
2186 2318 3.373110 GCTCCCTCCATCCCAAATTAGTT 60.373 47.826 0.00 0.00 0.00 2.24
2187 2319 2.175715 GCTCCCTCCATCCCAAATTAGT 59.824 50.000 0.00 0.00 0.00 2.24
2188 2320 2.175499 TGCTCCCTCCATCCCAAATTAG 59.825 50.000 0.00 0.00 0.00 1.73
2189 2321 2.091885 GTGCTCCCTCCATCCCAAATTA 60.092 50.000 0.00 0.00 0.00 1.40
2190 2322 1.009997 TGCTCCCTCCATCCCAAATT 58.990 50.000 0.00 0.00 0.00 1.82
2191 2323 0.259938 GTGCTCCCTCCATCCCAAAT 59.740 55.000 0.00 0.00 0.00 2.32
2192 2324 0.846427 AGTGCTCCCTCCATCCCAAA 60.846 55.000 0.00 0.00 0.00 3.28
2193 2325 0.846427 AAGTGCTCCCTCCATCCCAA 60.846 55.000 0.00 0.00 0.00 4.12
2194 2326 1.229951 AAGTGCTCCCTCCATCCCA 60.230 57.895 0.00 0.00 0.00 4.37
2195 2327 1.225704 CAAGTGCTCCCTCCATCCC 59.774 63.158 0.00 0.00 0.00 3.85
2196 2328 0.842635 ATCAAGTGCTCCCTCCATCC 59.157 55.000 0.00 0.00 0.00 3.51
2197 2329 2.295885 CAATCAAGTGCTCCCTCCATC 58.704 52.381 0.00 0.00 0.00 3.51
2198 2330 1.064166 CCAATCAAGTGCTCCCTCCAT 60.064 52.381 0.00 0.00 0.00 3.41
2199 2331 0.329261 CCAATCAAGTGCTCCCTCCA 59.671 55.000 0.00 0.00 0.00 3.86
2200 2332 0.620556 TCCAATCAAGTGCTCCCTCC 59.379 55.000 0.00 0.00 0.00 4.30
2201 2333 1.556911 TCTCCAATCAAGTGCTCCCTC 59.443 52.381 0.00 0.00 0.00 4.30
2202 2334 1.280421 GTCTCCAATCAAGTGCTCCCT 59.720 52.381 0.00 0.00 0.00 4.20
2203 2335 1.003580 TGTCTCCAATCAAGTGCTCCC 59.996 52.381 0.00 0.00 0.00 4.30
2204 2336 2.479566 TGTCTCCAATCAAGTGCTCC 57.520 50.000 0.00 0.00 0.00 4.70
2205 2337 5.048504 TGAATTTGTCTCCAATCAAGTGCTC 60.049 40.000 0.00 0.00 0.00 4.26
2206 2338 4.828939 TGAATTTGTCTCCAATCAAGTGCT 59.171 37.500 0.00 0.00 0.00 4.40
2207 2339 5.125100 TGAATTTGTCTCCAATCAAGTGC 57.875 39.130 0.00 0.00 0.00 4.40
2208 2340 8.272545 TCTATGAATTTGTCTCCAATCAAGTG 57.727 34.615 0.00 0.00 0.00 3.16
2269 2424 8.651588 GGAATGCATCTCTAATCAAGTAATACG 58.348 37.037 0.00 0.00 0.00 3.06
2344 2499 5.886715 TTCGTTCTTGTTCAATGCAAATG 57.113 34.783 0.00 0.00 0.00 2.32
2372 2527 7.373441 GTCTAAATTCAGAAATACAAATCCGCG 59.627 37.037 0.00 0.00 0.00 6.46
2455 2617 4.900652 CCCATTTCCCATATCAATCAACCA 59.099 41.667 0.00 0.00 0.00 3.67
2486 2653 5.128827 CAGCCTTACAGGTTATGTTCTAGGA 59.871 44.000 0.00 0.00 39.96 2.94
2547 2722 5.541868 TGGTTCCCTTTTAATGAAATCTGCA 59.458 36.000 0.00 0.00 0.00 4.41
2548 2723 6.036577 TGGTTCCCTTTTAATGAAATCTGC 57.963 37.500 0.00 0.00 0.00 4.26
2618 2964 5.121298 CAGTGTTCACCTTAGATCATGTGTG 59.879 44.000 0.00 0.00 0.00 3.82
2628 2974 2.072298 GCTGCTCAGTGTTCACCTTAG 58.928 52.381 0.00 0.00 0.00 2.18
2695 3101 5.768164 ACGGATTTCTTTTGGTTATGTGAGT 59.232 36.000 0.00 0.00 0.00 3.41
2718 3124 2.789323 TAGATCCTGGGGGTTCCTAC 57.211 55.000 0.00 0.00 36.20 3.18
2721 3127 4.852697 AGATAAATAGATCCTGGGGGTTCC 59.147 45.833 0.00 0.00 33.06 3.62
2802 3210 5.457686 AGAATGAGCTCAGGAGAGATTAGT 58.542 41.667 22.96 0.00 41.38 2.24


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

AutoCloner maintained by Alex Coulton.