Multiple sequence alignment - TraesCS4B01G338700

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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 TraesCS4B01G338700 chr4B 100.000 2814 0 0 1 2814 631610047 631607234 0.000000e+00 5197.0
1 TraesCS4B01G338700 chr4B 72.024 504 111 20 145 644 15741826 15741349 3.810000e-24 122.0
2 TraesCS4B01G338700 chr5A 87.197 2023 166 50 1 1963 673091133 673089144 0.000000e+00 2215.0
3 TraesCS4B01G338700 chr5A 93.103 406 14 9 1964 2363 673089098 673088701 1.450000e-162 582.0
4 TraesCS4B01G338700 chr5A 74.199 624 129 25 128 732 288258309 288257699 6.060000e-57 231.0
5 TraesCS4B01G338700 chr5A 86.935 199 14 3 2621 2814 673088329 673088138 2.200000e-51 213.0
6 TraesCS4B01G338700 chr4D 87.111 1994 168 49 1 1958 493015640 493017580 0.000000e+00 2176.0
7 TraesCS4B01G338700 chr4A 98.810 168 2 0 2435 2602 735482000 735481833 1.640000e-77 300.0
8 TraesCS4B01G338700 chr4A 71.930 399 93 15 129 519 631883311 631883698 6.420000e-17 99.0
9 TraesCS4B01G338700 chr3B 97.175 177 3 2 2431 2606 156649799 156649974 5.890000e-77 298.0
10 TraesCS4B01G338700 chr3B 97.143 175 4 1 2435 2609 461200410 461200583 7.620000e-76 294.0
11 TraesCS4B01G338700 chr3B 98.204 167 3 0 2435 2601 783212873 783212707 2.740000e-75 292.0
12 TraesCS4B01G338700 chr3B 73.469 441 93 20 145 572 673299530 673299959 8.120000e-31 145.0
13 TraesCS4B01G338700 chr6B 98.225 169 3 0 2430 2598 703686130 703685962 2.120000e-76 296.0
14 TraesCS4B01G338700 chr6B 72.745 521 111 21 145 661 51009478 51009971 2.260000e-31 147.0
15 TraesCS4B01G338700 chr5B 97.126 174 4 1 2435 2608 597857381 597857209 2.740000e-75 292.0
16 TraesCS4B01G338700 chr5B 94.149 188 6 5 2432 2617 64265976 64265792 5.930000e-72 281.0
17 TraesCS4B01G338700 chr5B 92.746 193 10 3 2424 2615 601327895 601327706 2.760000e-70 276.0
18 TraesCS4B01G338700 chr5B 73.710 407 89 13 344 736 589664762 589664360 2.920000e-30 143.0
19 TraesCS4B01G338700 chr5B 94.915 59 2 1 675 732 644867339 644867281 1.070000e-14 91.6
20 TraesCS4B01G338700 chr2B 95.055 182 8 1 2425 2605 425356478 425356297 4.590000e-73 285.0
21 TraesCS4B01G338700 chr2B 90.303 165 15 1 1355 1519 718396629 718396792 6.110000e-52 215.0
22 TraesCS4B01G338700 chr2B 89.697 165 16 1 1355 1519 756553094 756552931 2.840000e-50 209.0
23 TraesCS4B01G338700 chr2B 100.000 29 0 0 1715 1743 756552612 756552584 1.000000e-03 54.7
24 TraesCS4B01G338700 chr2D 92.121 165 12 1 1355 1519 592411285 592411448 6.060000e-57 231.0
25 TraesCS4B01G338700 chr2D 89.634 164 16 1 1355 1518 619046382 619046220 1.020000e-49 207.0
26 TraesCS4B01G338700 chr2D 97.297 37 1 0 1707 1743 619046047 619046011 2.340000e-06 63.9
27 TraesCS4B01G338700 chr2A 90.909 165 14 1 1355 1519 726986404 726986567 1.310000e-53 220.0
28 TraesCS4B01G338700 chr2A 90.244 164 15 1 1355 1518 749904132 749903970 2.200000e-51 213.0
29 TraesCS4B01G338700 chr3D 73.597 606 128 25 145 733 529837956 529838546 1.320000e-48 204.0
30 TraesCS4B01G338700 chr3D 71.707 615 134 30 145 732 561491644 561491043 4.890000e-28 135.0
31 TraesCS4B01G338700 chr3D 77.273 242 41 9 131 365 470876265 470876499 2.270000e-26 130.0
32 TraesCS4B01G338700 chr3D 83.200 125 21 0 1371 1495 500712380 500712504 6.370000e-22 115.0
33 TraesCS4B01G338700 chr5D 75.286 437 84 20 145 571 332073384 332072962 1.330000e-43 187.0
34 TraesCS4B01G338700 chr5D 80.606 165 27 3 130 293 45635818 45635978 3.810000e-24 122.0
35 TraesCS4B01G338700 chr5D 73.713 369 66 22 395 740 49668390 49668030 6.370000e-22 115.0
36 TraesCS4B01G338700 chr1D 74.877 406 86 11 344 737 227645174 227645575 1.340000e-38 171.0
37 TraesCS4B01G338700 chr7D 73.973 438 86 23 319 735 32209422 32209852 4.860000e-33 152.0
38 TraesCS4B01G338700 chr6A 71.761 602 128 30 145 733 73822610 73822038 6.320000e-27 132.0
39 TraesCS4B01G338700 chr7B 72.024 504 112 20 145 644 443336076 443335598 3.810000e-24 122.0
40 TraesCS4B01G338700 chr1A 73.278 363 78 15 383 732 531320156 531319800 6.370000e-22 115.0


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 TraesCS4B01G338700 chr4B 631607234 631610047 2813 True 5197.000000 5197 100.000000 1 2814 1 chr4B.!!$R2 2813
1 TraesCS4B01G338700 chr5A 673088138 673091133 2995 True 1003.333333 2215 89.078333 1 2814 3 chr5A.!!$R2 2813
2 TraesCS4B01G338700 chr5A 288257699 288258309 610 True 231.000000 231 74.199000 128 732 1 chr5A.!!$R1 604
3 TraesCS4B01G338700 chr4D 493015640 493017580 1940 False 2176.000000 2176 87.111000 1 1958 1 chr4D.!!$F1 1957
4 TraesCS4B01G338700 chr3D 529837956 529838546 590 False 204.000000 204 73.597000 145 733 1 chr3D.!!$F3 588

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
390 398 0.811219 CAGATCCGCAAGATTCGGCA 60.811 55.000 0.0 0.0 46.05 5.69 F
996 1024 1.079543 CCAGCGTCTCTCACCTTGG 60.080 63.158 0.0 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1265 1293 0.625849 AAGGGGTAGTCATTGCAGGG 59.374 55.0 0.00 0.0 0.0 4.45 R
2533 2657 0.528924 AGTGACTACATACGGCGCAA 59.471 50.0 10.83 0.0 0.0 4.85 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
47 48 4.853007 AGAGAAGGAAATCAATCACCCTG 58.147 43.478 0.00 0.00 0.00 4.45
71 72 7.445121 TGATACAATCAATATCTCTCGGCTTT 58.555 34.615 0.00 0.00 36.11 3.51
81 82 9.081997 CAATATCTCTCGGCTTTAACATATCTC 57.918 37.037 0.00 0.00 0.00 2.75
86 87 3.067601 TCGGCTTTAACATATCTCGAGCA 59.932 43.478 7.81 0.00 0.00 4.26
96 97 6.111768 ACATATCTCGAGCAAACAAACATC 57.888 37.500 7.81 0.00 0.00 3.06
97 99 5.065218 ACATATCTCGAGCAAACAAACATCC 59.935 40.000 7.81 0.00 0.00 3.51
117 119 2.620627 CCGTTAGGATTTCCCTTGCCTT 60.621 50.000 0.00 0.00 44.85 4.35
118 120 2.423538 CGTTAGGATTTCCCTTGCCTTG 59.576 50.000 0.00 0.00 44.85 3.61
123 125 2.643551 GATTTCCCTTGCCTTGATCGA 58.356 47.619 0.00 0.00 0.00 3.59
218 220 1.668919 GCGAGGGCTTTGTTTTTAGGC 60.669 52.381 0.00 0.00 35.83 3.93
273 276 3.132289 ACTCAGGAAGTCAAGTCAACGAA 59.868 43.478 0.00 0.00 30.02 3.85
275 278 7.131302 ACTCAGGAAGTCAAGTCAACGAAGT 62.131 44.000 0.00 0.00 35.75 3.01
299 302 4.259356 TCTCTGAAGATGGAATGCAGTTG 58.741 43.478 0.00 0.00 0.00 3.16
312 315 2.551270 TGCAGTTGTCCCCTTCTATCT 58.449 47.619 0.00 0.00 0.00 1.98
315 319 3.379452 CAGTTGTCCCCTTCTATCTCCT 58.621 50.000 0.00 0.00 0.00 3.69
316 320 4.547671 CAGTTGTCCCCTTCTATCTCCTA 58.452 47.826 0.00 0.00 0.00 2.94
319 323 4.405756 TGTCCCCTTCTATCTCCTATCC 57.594 50.000 0.00 0.00 0.00 2.59
323 327 3.502488 CCCCTTCTATCTCCTATCCCGTT 60.502 52.174 0.00 0.00 0.00 4.44
337 341 3.853330 CGTTCGGCGGTGCATCTG 61.853 66.667 7.21 0.00 36.85 2.90
380 387 1.984026 TGTCTCTGGCAGATCCGCA 60.984 57.895 19.11 11.41 37.80 5.69
390 398 0.811219 CAGATCCGCAAGATTCGGCA 60.811 55.000 0.00 0.00 46.05 5.69
404 412 1.082756 CGGCAGTGTTTGTCTTCGC 60.083 57.895 0.00 0.00 0.00 4.70
406 414 1.508632 GGCAGTGTTTGTCTTCGCTA 58.491 50.000 0.00 0.00 0.00 4.26
412 420 2.599082 GTGTTTGTCTTCGCTAGATCCG 59.401 50.000 0.00 0.00 34.79 4.18
414 422 1.103803 TTGTCTTCGCTAGATCCGCT 58.896 50.000 0.00 0.00 34.79 5.52
442 450 7.201530 GGATCTCATTTTCGTTCGTCTATGTTT 60.202 37.037 0.00 0.00 0.00 2.83
464 472 9.500785 TGTTTATGTGTCTACAGATTTTGATCA 57.499 29.630 0.00 0.00 40.79 2.92
494 502 9.194972 TGATCTACACTTCTCTTTATCAGTGAT 57.805 33.333 11.12 11.12 39.25 3.06
519 527 2.031163 GTTCTGGTGCGCTGGTCT 59.969 61.111 9.73 0.00 0.00 3.85
527 535 4.021925 GCGCTGGTCTTGAGGGGT 62.022 66.667 0.00 0.00 0.00 4.95
535 543 3.392616 CTGGTCTTGAGGGGTATTAGCAT 59.607 47.826 0.00 0.00 0.00 3.79
558 566 5.541845 TGATGAGTTTCCAACTGTCTACTG 58.458 41.667 0.00 0.00 43.03 2.74
597 606 3.477346 GGCGAGGGAGGGGGTAAC 61.477 72.222 0.00 0.00 0.00 2.50
623 634 3.758172 GCCGTTGGCTTTCTCCAA 58.242 55.556 0.00 0.00 46.69 3.53
625 636 1.459450 GCCGTTGGCTTTCTCCAATA 58.541 50.000 0.00 0.00 46.64 1.90
644 655 6.070995 TCCAATACTTGTAGTTGTCACTAGGG 60.071 42.308 0.00 0.00 36.09 3.53
645 656 6.070995 CCAATACTTGTAGTTGTCACTAGGGA 60.071 42.308 0.00 0.00 36.09 4.20
646 657 4.868314 ACTTGTAGTTGTCACTAGGGAC 57.132 45.455 18.69 18.69 36.09 4.46
647 658 4.220724 ACTTGTAGTTGTCACTAGGGACA 58.779 43.478 24.06 24.06 45.54 4.02
673 692 9.624373 AGTCTACGTAATCTCTATTACCTTTGA 57.376 33.333 0.00 0.00 43.04 2.69
722 741 9.784824 GTTGATGAATAGATCGAAAGTTATTCG 57.215 33.333 4.32 4.32 42.74 3.34
779 799 4.751767 AGAGAAATGCCGAGAAGAATCT 57.248 40.909 0.00 0.00 39.10 2.40
782 802 6.825610 AGAGAAATGCCGAGAAGAATCTAAT 58.174 36.000 0.00 0.00 35.54 1.73
783 803 7.957002 AGAGAAATGCCGAGAAGAATCTAATA 58.043 34.615 0.00 0.00 35.54 0.98
786 806 7.655328 AGAAATGCCGAGAAGAATCTAATACAG 59.345 37.037 0.00 0.00 35.54 2.74
788 808 6.465439 TGCCGAGAAGAATCTAATACAGAA 57.535 37.500 0.00 0.00 36.67 3.02
790 810 6.757010 TGCCGAGAAGAATCTAATACAGAAAC 59.243 38.462 0.00 0.00 36.67 2.78
794 814 8.587950 CGAGAAGAATCTAATACAGAAACACAC 58.412 37.037 0.00 0.00 36.67 3.82
795 815 9.424319 GAGAAGAATCTAATACAGAAACACACA 57.576 33.333 0.00 0.00 36.67 3.72
796 816 9.778741 AGAAGAATCTAATACAGAAACACACAA 57.221 29.630 0.00 0.00 36.67 3.33
810 830 2.487372 ACACACAAATACATGCATGCGA 59.513 40.909 26.53 15.18 0.00 5.10
840 860 1.199852 GACAAACAAGCAACACGCCG 61.200 55.000 0.00 0.00 44.04 6.46
860 880 2.202566 GTTGAAGCATAGTACTCCGGC 58.797 52.381 0.00 1.53 0.00 6.13
940 968 7.256154 GGCTATAAACTAAGAGAAGAGAGCCAT 60.256 40.741 0.00 0.00 43.25 4.40
968 996 3.242543 GCATGCCATATATGCTTAGCGTC 60.243 47.826 6.36 0.00 45.64 5.19
996 1024 1.079543 CCAGCGTCTCTCACCTTGG 60.080 63.158 0.00 0.00 0.00 3.61
1211 1239 3.522731 CCCTCAGCTCCTCCGTCG 61.523 72.222 0.00 0.00 0.00 5.12
1297 1325 2.241659 CCCCTTTGGCTTCCCCTCT 61.242 63.158 0.00 0.00 0.00 3.69
1299 1327 1.770324 CCTTTGGCTTCCCCTCTGT 59.230 57.895 0.00 0.00 0.00 3.41
1535 1563 2.352686 GCCTACGCGCGTATTCGA 60.353 61.111 39.19 21.95 39.71 3.71
1539 1567 1.118033 CTACGCGCGTATTCGACATT 58.882 50.000 39.19 15.12 39.71 2.71
1548 1576 3.486708 GCGTATTCGACATTGCCATTTGA 60.487 43.478 0.00 0.00 39.71 2.69
1549 1577 4.789481 GCGTATTCGACATTGCCATTTGAT 60.789 41.667 0.00 0.00 39.71 2.57
1550 1578 5.273170 CGTATTCGACATTGCCATTTGATT 58.727 37.500 0.00 0.00 39.71 2.57
1551 1579 6.426327 CGTATTCGACATTGCCATTTGATTA 58.574 36.000 0.00 0.00 39.71 1.75
1552 1580 6.574832 CGTATTCGACATTGCCATTTGATTAG 59.425 38.462 0.00 0.00 39.71 1.73
1556 1606 6.321717 TCGACATTGCCATTTGATTAGTTTC 58.678 36.000 0.00 0.00 0.00 2.78
1561 1611 5.465532 TGCCATTTGATTAGTTTCAAGCA 57.534 34.783 0.00 0.00 36.97 3.91
1588 1638 2.861935 GCAGCATTGTGATATTGGTTGC 59.138 45.455 0.00 0.00 0.00 4.17
1589 1639 3.450578 CAGCATTGTGATATTGGTTGCC 58.549 45.455 0.00 0.00 0.00 4.52
1594 1653 1.472082 TGTGATATTGGTTGCCTTGCG 59.528 47.619 0.00 0.00 0.00 4.85
1746 1820 4.552365 CCCCTGCGCCATGATCGT 62.552 66.667 4.18 0.00 0.00 3.73
1851 1925 4.100529 CAATGCATGTGCTTGCTACTTAC 58.899 43.478 0.00 0.00 43.18 2.34
1903 1977 9.948964 CTCTTGGTGATGGACATATCAATATTA 57.051 33.333 0.00 0.00 38.69 0.98
2037 2156 4.012374 CACAAGTAGGTGATGGCTGATTT 58.988 43.478 0.00 0.00 41.32 2.17
2038 2157 4.012374 ACAAGTAGGTGATGGCTGATTTG 58.988 43.478 0.00 0.00 0.00 2.32
2039 2158 4.012374 CAAGTAGGTGATGGCTGATTTGT 58.988 43.478 0.00 0.00 0.00 2.83
2040 2159 5.185454 CAAGTAGGTGATGGCTGATTTGTA 58.815 41.667 0.00 0.00 0.00 2.41
2041 2160 5.636903 AGTAGGTGATGGCTGATTTGTAT 57.363 39.130 0.00 0.00 0.00 2.29
2042 2161 5.371526 AGTAGGTGATGGCTGATTTGTATG 58.628 41.667 0.00 0.00 0.00 2.39
2043 2162 4.508551 AGGTGATGGCTGATTTGTATGA 57.491 40.909 0.00 0.00 0.00 2.15
2044 2163 5.057843 AGGTGATGGCTGATTTGTATGAT 57.942 39.130 0.00 0.00 0.00 2.45
2045 2164 6.191657 AGGTGATGGCTGATTTGTATGATA 57.808 37.500 0.00 0.00 0.00 2.15
2046 2165 6.787170 AGGTGATGGCTGATTTGTATGATAT 58.213 36.000 0.00 0.00 0.00 1.63
2055 2174 8.119226 GGCTGATTTGTATGATATAAAGATCGC 58.881 37.037 1.12 3.47 0.00 4.58
2065 2184 5.985530 TGATATAAAGATCGCTTGTGTGAGG 59.014 40.000 0.00 0.00 36.04 3.86
2066 2185 1.160137 AAAGATCGCTTGTGTGAGGC 58.840 50.000 0.00 0.00 36.04 4.70
2067 2186 0.674895 AAGATCGCTTGTGTGAGGCC 60.675 55.000 0.00 0.00 36.04 5.19
2119 2238 7.542130 CCTTTTGTTCCTGCTTTATATGTTGTC 59.458 37.037 0.00 0.00 0.00 3.18
2202 2321 0.318869 ACGCATGCACCACAAACATG 60.319 50.000 19.57 0.00 43.21 3.21
2249 2368 5.403766 GCTACTGTATCTATGTGTGCATGTC 59.596 44.000 0.00 0.00 36.58 3.06
2279 2403 4.631377 CGACAATGCTAATCTGGTGAGAAA 59.369 41.667 0.00 0.00 0.00 2.52
2280 2404 5.446473 CGACAATGCTAATCTGGTGAGAAAC 60.446 44.000 0.00 0.00 0.00 2.78
2284 2408 2.599082 GCTAATCTGGTGAGAAACGACG 59.401 50.000 0.00 0.00 0.00 5.12
2285 2409 2.814280 AATCTGGTGAGAAACGACGT 57.186 45.000 0.00 0.00 0.00 4.34
2287 2411 0.742505 TCTGGTGAGAAACGACGTGT 59.257 50.000 0.00 0.00 0.00 4.49
2293 2417 3.374745 GTGAGAAACGACGTGTTCCTAA 58.625 45.455 0.00 0.00 40.84 2.69
2319 2443 9.881773 ATTTCCTAATATGGTGTGTATTCCATT 57.118 29.630 2.05 0.00 43.22 3.16
2350 2474 9.846248 AAAGTTATGAGCTTTATCAACATTGAC 57.154 29.630 0.00 0.00 40.49 3.18
2351 2475 7.989826 AGTTATGAGCTTTATCAACATTGACC 58.010 34.615 0.00 0.00 40.49 4.02
2352 2476 7.611467 AGTTATGAGCTTTATCAACATTGACCA 59.389 33.333 0.00 0.00 40.49 4.02
2353 2477 6.839124 ATGAGCTTTATCAACATTGACCAA 57.161 33.333 0.00 0.00 40.49 3.67
2354 2478 6.258230 TGAGCTTTATCAACATTGACCAAG 57.742 37.500 0.00 3.79 40.49 3.61
2355 2479 5.769662 TGAGCTTTATCAACATTGACCAAGT 59.230 36.000 12.78 4.34 40.49 3.16
2356 2480 6.265196 TGAGCTTTATCAACATTGACCAAGTT 59.735 34.615 12.78 8.90 40.49 2.66
2357 2481 7.054491 AGCTTTATCAACATTGACCAAGTTT 57.946 32.000 12.78 3.88 40.49 2.66
2358 2482 7.500141 AGCTTTATCAACATTGACCAAGTTTT 58.500 30.769 12.78 2.25 40.49 2.43
2359 2483 8.637986 AGCTTTATCAACATTGACCAAGTTTTA 58.362 29.630 12.78 0.00 40.49 1.52
2360 2484 9.423061 GCTTTATCAACATTGACCAAGTTTTAT 57.577 29.630 12.78 0.00 40.49 1.40
2424 2548 9.916397 CGAATTAATCAACACCACTAGATTAAC 57.084 33.333 0.00 0.00 42.38 2.01
2436 2560 9.046296 CACCACTAGATTAACCATGAAATCTAC 57.954 37.037 15.44 0.00 41.50 2.59
2437 2561 8.993424 ACCACTAGATTAACCATGAAATCTACT 58.007 33.333 15.44 8.58 41.50 2.57
2438 2562 9.482627 CCACTAGATTAACCATGAAATCTACTC 57.517 37.037 15.44 0.00 41.50 2.59
2439 2563 9.482627 CACTAGATTAACCATGAAATCTACTCC 57.517 37.037 15.44 0.00 41.50 3.85
2441 2565 7.698163 AGATTAACCATGAAATCTACTCCCT 57.302 36.000 13.16 0.00 39.95 4.20
2442 2566 7.740805 AGATTAACCATGAAATCTACTCCCTC 58.259 38.462 13.16 0.00 39.95 4.30
2443 2567 4.779993 AACCATGAAATCTACTCCCTCC 57.220 45.455 0.00 0.00 0.00 4.30
2444 2568 2.700897 ACCATGAAATCTACTCCCTCCG 59.299 50.000 0.00 0.00 0.00 4.63
2446 2570 3.134804 CCATGAAATCTACTCCCTCCGTT 59.865 47.826 0.00 0.00 0.00 4.44
2447 2571 4.372656 CATGAAATCTACTCCCTCCGTTC 58.627 47.826 0.00 0.00 0.00 3.95
2448 2572 2.764572 TGAAATCTACTCCCTCCGTTCC 59.235 50.000 0.00 0.00 0.00 3.62
2449 2573 1.790818 AATCTACTCCCTCCGTTCCC 58.209 55.000 0.00 0.00 0.00 3.97
2450 2574 0.635009 ATCTACTCCCTCCGTTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
2454 2578 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2455 2579 1.558294 ACTCCCTCCGTTCCCAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
2457 2581 2.238898 CTCCCTCCGTTCCCAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
2458 2582 2.026636 TCCCTCCGTTCCCAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
2459 2583 2.290705 CCCTCCGTTCCCAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
2460 2584 3.007635 CCTCCGTTCCCAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
2462 2586 4.324267 CTCCGTTCCCAAATACTTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
2463 2587 4.721132 TCCGTTCCCAAATACTTGTCTTT 58.279 39.130 0.00 0.00 0.00 2.52
2464 2588 4.758165 TCCGTTCCCAAATACTTGTCTTTC 59.242 41.667 0.00 0.00 0.00 2.62
2465 2589 4.760204 CCGTTCCCAAATACTTGTCTTTCT 59.240 41.667 0.00 0.00 0.00 2.52
2466 2590 5.935789 CCGTTCCCAAATACTTGTCTTTCTA 59.064 40.000 0.00 0.00 0.00 2.10
2467 2591 6.092259 CCGTTCCCAAATACTTGTCTTTCTAG 59.908 42.308 0.00 0.00 0.00 2.43
2468 2592 6.092259 CGTTCCCAAATACTTGTCTTTCTAGG 59.908 42.308 0.00 0.00 0.00 3.02
2469 2593 5.497474 TCCCAAATACTTGTCTTTCTAGGC 58.503 41.667 0.00 0.00 0.00 3.93
2470 2594 5.013704 TCCCAAATACTTGTCTTTCTAGGCA 59.986 40.000 0.00 0.00 33.22 4.75
2471 2595 5.888161 CCCAAATACTTGTCTTTCTAGGCAT 59.112 40.000 0.00 0.00 35.56 4.40
2472 2596 6.378280 CCCAAATACTTGTCTTTCTAGGCATT 59.622 38.462 0.00 0.00 35.56 3.56
2473 2597 7.093771 CCCAAATACTTGTCTTTCTAGGCATTT 60.094 37.037 0.00 0.00 35.56 2.32
2474 2598 7.970614 CCAAATACTTGTCTTTCTAGGCATTTC 59.029 37.037 0.00 0.00 35.56 2.17
2475 2599 8.514594 CAAATACTTGTCTTTCTAGGCATTTCA 58.485 33.333 0.00 0.00 35.56 2.69
2476 2600 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
2477 2601 6.959639 ACTTGTCTTTCTAGGCATTTCAAA 57.040 33.333 0.00 0.00 35.56 2.69
2478 2602 7.530426 ACTTGTCTTTCTAGGCATTTCAAAT 57.470 32.000 0.00 0.00 35.56 2.32
2479 2603 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
2480 2604 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
2481 2605 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
2482 2606 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
2483 2607 6.151817 GTCTTTCTAGGCATTTCAAATGGACT 59.848 38.462 12.14 3.08 0.00 3.85
2484 2608 6.375455 TCTTTCTAGGCATTTCAAATGGACTC 59.625 38.462 12.14 0.00 0.00 3.36
2485 2609 5.178096 TCTAGGCATTTCAAATGGACTCA 57.822 39.130 12.14 0.00 0.00 3.41
2486 2610 5.569355 TCTAGGCATTTCAAATGGACTCAA 58.431 37.500 12.14 0.00 0.00 3.02
2487 2611 4.525912 AGGCATTTCAAATGGACTCAAC 57.474 40.909 12.14 0.00 0.00 3.18
2488 2612 3.896888 AGGCATTTCAAATGGACTCAACA 59.103 39.130 12.14 0.00 0.00 3.33
2489 2613 4.529377 AGGCATTTCAAATGGACTCAACAT 59.471 37.500 12.14 0.00 0.00 2.71
2490 2614 5.716228 AGGCATTTCAAATGGACTCAACATA 59.284 36.000 12.14 0.00 0.00 2.29
2491 2615 5.807011 GGCATTTCAAATGGACTCAACATAC 59.193 40.000 12.14 0.00 0.00 2.39
2492 2616 5.512788 GCATTTCAAATGGACTCAACATACG 59.487 40.000 12.14 0.00 0.00 3.06
2493 2617 6.622679 GCATTTCAAATGGACTCAACATACGA 60.623 38.462 12.14 0.00 0.00 3.43
2494 2618 6.869315 TTTCAAATGGACTCAACATACGAA 57.131 33.333 0.00 0.00 0.00 3.85
2495 2619 7.447374 TTTCAAATGGACTCAACATACGAAT 57.553 32.000 0.00 0.00 0.00 3.34
2496 2620 6.421377 TCAAATGGACTCAACATACGAATG 57.579 37.500 0.00 0.00 39.17 2.67
2498 2622 7.100409 TCAAATGGACTCAACATACGAATGTA 58.900 34.615 0.00 0.00 45.79 2.29
2499 2623 7.768582 TCAAATGGACTCAACATACGAATGTAT 59.231 33.333 0.00 0.00 45.79 2.29
2536 2660 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
2537 2661 5.536554 AGTGTAGATTCACTCATTTTGCG 57.463 39.130 0.00 0.00 44.07 4.85
2538 2662 4.091424 GTGTAGATTCACTCATTTTGCGC 58.909 43.478 0.00 0.00 35.68 6.09
2539 2663 2.927553 AGATTCACTCATTTTGCGCC 57.072 45.000 4.18 0.00 0.00 6.53
2540 2664 1.131126 AGATTCACTCATTTTGCGCCG 59.869 47.619 4.18 0.00 0.00 6.46
2541 2665 0.881118 ATTCACTCATTTTGCGCCGT 59.119 45.000 4.18 0.00 0.00 5.68
2542 2666 1.514003 TTCACTCATTTTGCGCCGTA 58.486 45.000 4.18 0.00 0.00 4.02
2543 2667 1.732941 TCACTCATTTTGCGCCGTAT 58.267 45.000 4.18 0.00 0.00 3.06
2544 2668 1.396648 TCACTCATTTTGCGCCGTATG 59.603 47.619 4.18 5.63 0.00 2.39
2545 2669 1.130373 CACTCATTTTGCGCCGTATGT 59.870 47.619 4.18 0.00 0.00 2.29
2546 2670 2.350192 CACTCATTTTGCGCCGTATGTA 59.650 45.455 4.18 0.00 0.00 2.29
2547 2671 2.607635 ACTCATTTTGCGCCGTATGTAG 59.392 45.455 4.18 7.56 0.00 2.74
2548 2672 2.607635 CTCATTTTGCGCCGTATGTAGT 59.392 45.455 4.18 0.00 0.00 2.73
2549 2673 2.605818 TCATTTTGCGCCGTATGTAGTC 59.394 45.455 4.18 0.00 0.00 2.59
2550 2674 2.081725 TTTTGCGCCGTATGTAGTCA 57.918 45.000 4.18 0.00 0.00 3.41
2551 2675 1.352114 TTTGCGCCGTATGTAGTCAC 58.648 50.000 4.18 0.00 0.00 3.67
2552 2676 0.528924 TTGCGCCGTATGTAGTCACT 59.471 50.000 4.18 0.00 0.00 3.41
2553 2677 0.528924 TGCGCCGTATGTAGTCACTT 59.471 50.000 4.18 0.00 0.00 3.16
2554 2678 0.921347 GCGCCGTATGTAGTCACTTG 59.079 55.000 0.00 0.00 0.00 3.16
2555 2679 1.734707 GCGCCGTATGTAGTCACTTGT 60.735 52.381 0.00 0.00 0.00 3.16
2556 2680 2.602878 CGCCGTATGTAGTCACTTGTT 58.397 47.619 0.00 0.00 0.00 2.83
2557 2681 3.761657 CGCCGTATGTAGTCACTTGTTA 58.238 45.455 0.00 0.00 0.00 2.41
2558 2682 4.168014 CGCCGTATGTAGTCACTTGTTAA 58.832 43.478 0.00 0.00 0.00 2.01
2559 2683 4.622313 CGCCGTATGTAGTCACTTGTTAAA 59.378 41.667 0.00 0.00 0.00 1.52
2560 2684 5.118971 CGCCGTATGTAGTCACTTGTTAAAA 59.881 40.000 0.00 0.00 0.00 1.52
2561 2685 6.183360 CGCCGTATGTAGTCACTTGTTAAAAT 60.183 38.462 0.00 0.00 0.00 1.82
2562 2686 7.178074 GCCGTATGTAGTCACTTGTTAAAATC 58.822 38.462 0.00 0.00 0.00 2.17
2563 2687 7.064253 GCCGTATGTAGTCACTTGTTAAAATCT 59.936 37.037 0.00 0.00 0.00 2.40
2564 2688 8.592998 CCGTATGTAGTCACTTGTTAAAATCTC 58.407 37.037 0.00 0.00 0.00 2.75
2565 2689 9.355215 CGTATGTAGTCACTTGTTAAAATCTCT 57.645 33.333 0.00 0.00 0.00 3.10
2588 2712 9.291664 CTCTAGAAAGACAAGTATTTAGGAACG 57.708 37.037 0.00 0.00 0.00 3.95
2589 2713 8.248945 TCTAGAAAGACAAGTATTTAGGAACGG 58.751 37.037 0.00 0.00 0.00 4.44
2590 2714 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
2591 2715 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
2592 2716 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2593 2717 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2594 2718 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2595 2719 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2610 2734 5.422331 ACGGAGGGAGTATATTCATATGGTG 59.578 44.000 2.13 0.00 0.00 4.17
2631 2755 8.830201 TGGTGTATGTTTAGTATTGTAAACGT 57.170 30.769 6.49 6.49 43.18 3.99
2632 2756 9.920133 TGGTGTATGTTTAGTATTGTAAACGTA 57.080 29.630 0.00 4.91 43.18 3.57
2639 2763 9.748708 TGTTTAGTATTGTAAACGTAGACAAGT 57.251 29.630 17.19 9.35 43.18 3.16
2677 3075 4.823442 TGATCAAAGTGTGTGAAGCTCAAT 59.177 37.500 0.00 0.00 0.00 2.57
2681 3079 5.806502 TCAAAGTGTGTGAAGCTCAATTTTG 59.193 36.000 0.00 0.00 36.95 2.44
2683 3081 4.925068 AGTGTGTGAAGCTCAATTTTGAC 58.075 39.130 0.00 0.00 32.90 3.18
2690 3088 3.643159 AGCTCAATTTTGACGGAAACC 57.357 42.857 0.00 0.00 32.90 3.27
2697 3095 1.698506 TTTGACGGAAACCAATGCCT 58.301 45.000 0.00 0.00 0.00 4.75
2716 3119 3.432890 GCCTGCTATATTATGGAGGGAGC 60.433 52.174 12.27 0.00 41.30 4.70
2778 3181 3.628769 GGCCCCAAATGGAGTATAAACCA 60.629 47.826 0.00 0.00 40.57 3.67
2780 3183 4.867086 CCCCAAATGGAGTATAAACCACT 58.133 43.478 0.00 0.00 39.06 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.608640 TTCCTTCTCTCCCGTTCAGC 59.391 55.000 0.00 0.00 0.00 4.26
47 48 7.897575 AAAGCCGAGAGATATTGATTGTATC 57.102 36.000 0.00 0.00 0.00 2.24
71 72 7.201609 GGATGTTTGTTTGCTCGAGATATGTTA 60.202 37.037 18.75 0.00 0.00 2.41
81 82 2.399396 AACGGATGTTTGTTTGCTCG 57.601 45.000 0.00 0.00 33.53 5.03
104 106 2.290896 TGTCGATCAAGGCAAGGGAAAT 60.291 45.455 0.00 0.00 0.00 2.17
117 119 4.923710 CGGCGGCGATGTCGATCA 62.924 66.667 29.19 0.00 39.90 2.92
118 120 4.624117 TCGGCGGCGATGTCGATC 62.624 66.667 31.46 0.00 41.70 3.69
123 125 2.852495 AAACAGATCGGCGGCGATGT 62.852 55.000 45.30 39.37 0.00 3.06
140 142 2.838202 CCTAAGGCCACAGGAGACTAAA 59.162 50.000 15.94 0.00 40.21 1.85
141 143 2.467880 CCTAAGGCCACAGGAGACTAA 58.532 52.381 15.94 0.00 40.21 2.24
199 201 1.611491 TGCCTAAAAACAAAGCCCTCG 59.389 47.619 0.00 0.00 0.00 4.63
228 231 5.327737 AGGACACAAACCCTAACCAAATA 57.672 39.130 0.00 0.00 0.00 1.40
261 264 3.883489 TCAGAGAGACTTCGTTGACTTGA 59.117 43.478 0.00 0.00 0.00 3.02
273 276 3.773667 TGCATTCCATCTTCAGAGAGACT 59.226 43.478 0.00 0.00 34.85 3.24
275 278 3.773667 ACTGCATTCCATCTTCAGAGAGA 59.226 43.478 0.00 0.00 34.85 3.10
299 302 3.715287 GGGATAGGAGATAGAAGGGGAC 58.285 54.545 0.00 0.00 0.00 4.46
337 341 4.778143 ATGCCCTCCGACAACGCC 62.778 66.667 0.00 0.00 38.29 5.68
340 344 2.040544 CCACATGCCCTCCGACAAC 61.041 63.158 0.00 0.00 0.00 3.32
342 346 2.184020 CTTCCACATGCCCTCCGACA 62.184 60.000 0.00 0.00 0.00 4.35
353 357 1.002888 CTGCCAGAGACACTTCCACAT 59.997 52.381 0.00 0.00 0.00 3.21
380 387 2.851195 AGACAAACACTGCCGAATCTT 58.149 42.857 0.00 0.00 0.00 2.40
390 398 3.673594 CGGATCTAGCGAAGACAAACACT 60.674 47.826 0.00 0.00 36.93 3.55
412 420 3.125316 ACGAACGAAAATGAGATCCAAGC 59.875 43.478 0.14 0.00 0.00 4.01
414 422 4.566004 AGACGAACGAAAATGAGATCCAA 58.434 39.130 0.14 0.00 0.00 3.53
422 430 7.955324 ACACATAAACATAGACGAACGAAAATG 59.045 33.333 0.14 4.04 0.00 2.32
467 475 9.025041 TCACTGATAAAGAGAAGTGTAGATCAA 57.975 33.333 0.00 0.00 40.69 2.57
476 484 8.944029 CAACAATCATCACTGATAAAGAGAAGT 58.056 33.333 0.00 0.00 41.34 3.01
485 493 6.372381 CACCAGAACAACAATCATCACTGATA 59.628 38.462 0.00 0.00 41.34 2.15
491 499 2.226200 CGCACCAGAACAACAATCATCA 59.774 45.455 0.00 0.00 0.00 3.07
494 502 0.310543 GCGCACCAGAACAACAATCA 59.689 50.000 0.30 0.00 0.00 2.57
519 527 4.660303 ACTCATCATGCTAATACCCCTCAA 59.340 41.667 0.00 0.00 0.00 3.02
623 634 6.014647 TGTCCCTAGTGACAACTACAAGTAT 58.985 40.000 5.49 0.00 42.06 2.12
625 636 4.220724 TGTCCCTAGTGACAACTACAAGT 58.779 43.478 5.49 0.00 42.06 3.16
644 655 8.606040 AGGTAATAGAGATTACGTAGACTGTC 57.394 38.462 0.00 0.00 45.79 3.51
645 656 8.977267 AAGGTAATAGAGATTACGTAGACTGT 57.023 34.615 8.03 7.03 45.79 3.55
646 657 9.666626 CAAAGGTAATAGAGATTACGTAGACTG 57.333 37.037 8.03 0.00 45.79 3.51
647 658 9.624373 TCAAAGGTAATAGAGATTACGTAGACT 57.376 33.333 0.00 0.00 45.79 3.24
652 663 9.530633 GAACATCAAAGGTAATAGAGATTACGT 57.469 33.333 0.00 0.00 45.79 3.57
653 664 9.751542 AGAACATCAAAGGTAATAGAGATTACG 57.248 33.333 2.62 0.00 45.79 3.18
673 692 4.460263 TGTCAAGGCAGTACAAAGAACAT 58.540 39.130 0.00 0.00 0.00 2.71
754 774 7.375053 AGATTCTTCTCGGCATTTCTCTATAC 58.625 38.462 0.00 0.00 0.00 1.47
779 799 8.787852 TGCATGTATTTGTGTGTTTCTGTATTA 58.212 29.630 0.00 0.00 0.00 0.98
782 802 6.625873 TGCATGTATTTGTGTGTTTCTGTA 57.374 33.333 0.00 0.00 0.00 2.74
783 803 5.512753 TGCATGTATTTGTGTGTTTCTGT 57.487 34.783 0.00 0.00 0.00 3.41
786 806 4.201513 CGCATGCATGTATTTGTGTGTTTC 60.202 41.667 26.79 4.98 0.00 2.78
788 808 3.057666 TCGCATGCATGTATTTGTGTGTT 60.058 39.130 26.79 0.00 0.00 3.32
790 810 3.134021 TCGCATGCATGTATTTGTGTG 57.866 42.857 26.79 7.69 0.00 3.82
794 814 2.121786 GGCTTCGCATGCATGTATTTG 58.878 47.619 26.79 14.56 0.00 2.32
795 815 1.750206 TGGCTTCGCATGCATGTATTT 59.250 42.857 26.79 0.00 0.00 1.40
796 816 1.066002 GTGGCTTCGCATGCATGTATT 59.934 47.619 26.79 0.00 0.00 1.89
797 817 0.664761 GTGGCTTCGCATGCATGTAT 59.335 50.000 26.79 0.00 0.00 2.29
798 818 0.676151 TGTGGCTTCGCATGCATGTA 60.676 50.000 26.79 13.55 0.00 2.29
799 819 1.972752 TGTGGCTTCGCATGCATGT 60.973 52.632 26.79 0.00 0.00 3.21
810 830 2.481795 GCTTGTTTGTCATGTGTGGCTT 60.482 45.455 0.00 0.00 0.00 4.35
816 836 2.531103 CGTGTTGCTTGTTTGTCATGTG 59.469 45.455 0.00 0.00 0.00 3.21
818 838 1.518102 GCGTGTTGCTTGTTTGTCATG 59.482 47.619 0.00 0.00 41.73 3.07
840 860 2.202566 GCCGGAGTACTATGCTTCAAC 58.797 52.381 5.05 0.00 0.00 3.18
860 880 2.086869 CTGGTGGGTGCAAGTAATCTG 58.913 52.381 0.00 0.00 0.00 2.90
892 920 3.842925 AACGCAACGCCCTGTCCAT 62.843 57.895 0.00 0.00 0.00 3.41
996 1024 2.500098 TGGCCTTCACCTAGTATGTGTC 59.500 50.000 3.32 0.00 35.25 3.67
1092 1120 3.434319 GGATGTGGCACCACTGCG 61.434 66.667 20.02 0.00 45.31 5.18
1098 1126 2.512515 GAGAGCGGATGTGGCACC 60.513 66.667 16.26 0.00 0.00 5.01
1101 1129 2.202987 CTGGAGAGCGGATGTGGC 60.203 66.667 0.00 0.00 0.00 5.01
1211 1239 2.027625 CGCCGTGGAAGGTGAACTC 61.028 63.158 0.00 0.00 44.18 3.01
1237 1265 3.384532 GAGGGCGTACCGGAACCA 61.385 66.667 9.46 0.00 46.96 3.67
1265 1293 0.625849 AAGGGGTAGTCATTGCAGGG 59.374 55.000 0.00 0.00 0.00 4.45
1297 1325 3.059982 CTGTTGGCTCCGGAGACA 58.940 61.111 36.71 36.71 46.54 3.41
1299 1327 2.922503 TGCTGTTGGCTCCGGAGA 60.923 61.111 35.69 12.78 42.39 3.71
1518 1546 2.352686 TCGAATACGCGCGTAGGC 60.353 61.111 40.57 32.51 39.58 3.93
1519 1547 0.659417 ATGTCGAATACGCGCGTAGG 60.659 55.000 40.57 31.58 39.58 3.18
1520 1548 1.118033 AATGTCGAATACGCGCGTAG 58.882 50.000 40.57 29.46 39.58 3.51
1521 1549 0.841356 CAATGTCGAATACGCGCGTA 59.159 50.000 40.65 40.65 39.58 4.42
1522 1550 1.628983 CAATGTCGAATACGCGCGT 59.371 52.632 39.05 39.05 39.58 6.01
1528 1556 7.417612 ACTAATCAAATGGCAATGTCGAATAC 58.582 34.615 0.00 0.00 0.00 1.89
1534 1562 7.412237 GCTTGAAACTAATCAAATGGCAATGTC 60.412 37.037 0.00 0.00 38.75 3.06
1535 1563 6.369615 GCTTGAAACTAATCAAATGGCAATGT 59.630 34.615 0.00 0.00 38.75 2.71
1539 1567 5.465532 TGCTTGAAACTAATCAAATGGCA 57.534 34.783 0.00 0.00 38.75 4.92
1561 1611 4.368315 CAATATCACAATGCTGCATGCTT 58.632 39.130 20.33 1.02 43.37 3.91
1575 1625 1.798813 GCGCAAGGCAACCAATATCAC 60.799 52.381 0.30 0.00 42.87 3.06
1811 1885 4.031426 GCATTGCGTAGTCTTGTACTGTAC 59.969 45.833 10.98 10.98 39.39 2.90
1812 1886 4.171005 GCATTGCGTAGTCTTGTACTGTA 58.829 43.478 0.00 0.00 39.39 2.74
1813 1887 2.993899 GCATTGCGTAGTCTTGTACTGT 59.006 45.455 0.00 0.00 39.39 3.55
1814 1888 2.993220 TGCATTGCGTAGTCTTGTACTG 59.007 45.455 3.84 0.00 39.39 2.74
1815 1889 3.313012 TGCATTGCGTAGTCTTGTACT 57.687 42.857 3.84 0.00 42.62 2.73
1816 1890 3.370978 ACATGCATTGCGTAGTCTTGTAC 59.629 43.478 2.41 0.00 0.00 2.90
1817 1891 3.370672 CACATGCATTGCGTAGTCTTGTA 59.629 43.478 2.41 0.00 0.00 2.41
1818 1892 2.160219 CACATGCATTGCGTAGTCTTGT 59.840 45.455 2.41 0.00 0.00 3.16
1851 1925 8.072567 GCTAGCTTTGGACAATTAATCATGTAG 58.927 37.037 7.70 0.00 0.00 2.74
1903 1977 3.270877 GCATAGTTCACGACTCCCATTT 58.729 45.455 0.00 0.00 39.86 2.32
2037 2156 8.141268 TCACACAAGCGATCTTTATATCATACA 58.859 33.333 0.00 0.00 0.00 2.29
2038 2157 8.520835 TCACACAAGCGATCTTTATATCATAC 57.479 34.615 0.00 0.00 0.00 2.39
2039 2158 7.814587 CCTCACACAAGCGATCTTTATATCATA 59.185 37.037 0.00 0.00 0.00 2.15
2040 2159 6.648310 CCTCACACAAGCGATCTTTATATCAT 59.352 38.462 0.00 0.00 0.00 2.45
2041 2160 5.985530 CCTCACACAAGCGATCTTTATATCA 59.014 40.000 0.00 0.00 0.00 2.15
2042 2161 5.107298 GCCTCACACAAGCGATCTTTATATC 60.107 44.000 0.00 0.00 0.00 1.63
2043 2162 4.752101 GCCTCACACAAGCGATCTTTATAT 59.248 41.667 0.00 0.00 0.00 0.86
2044 2163 4.119862 GCCTCACACAAGCGATCTTTATA 58.880 43.478 0.00 0.00 0.00 0.98
2045 2164 2.939103 GCCTCACACAAGCGATCTTTAT 59.061 45.455 0.00 0.00 0.00 1.40
2046 2165 2.346803 GCCTCACACAAGCGATCTTTA 58.653 47.619 0.00 0.00 0.00 1.85
2055 2174 3.052082 CTGGCGGCCTCACACAAG 61.052 66.667 21.46 2.99 0.00 3.16
2066 2185 4.789075 CCACGTACGGTCTGGCGG 62.789 72.222 21.06 4.24 0.00 6.13
2067 2186 2.552585 AATCCACGTACGGTCTGGCG 62.553 60.000 21.06 0.00 0.00 5.69
2119 2238 1.442148 GTCTTGCCCGCTAGGTAGG 59.558 63.158 0.00 0.00 38.26 3.18
2202 2321 6.036408 AGCTAACGAAATTAACGGTGAATACC 59.964 38.462 5.90 0.00 43.89 2.73
2249 2368 4.687948 CCAGATTAGCATTGTCGTCCATAG 59.312 45.833 0.00 0.00 0.00 2.23
2279 2403 3.672767 AGGAAATTAGGAACACGTCGT 57.327 42.857 0.00 0.00 0.00 4.34
2280 2404 7.095774 CCATATTAGGAAATTAGGAACACGTCG 60.096 40.741 0.00 0.00 0.00 5.12
2284 2408 8.621286 CACACCATATTAGGAAATTAGGAACAC 58.379 37.037 0.00 0.00 0.00 3.32
2285 2409 8.333235 ACACACCATATTAGGAAATTAGGAACA 58.667 33.333 0.00 0.00 0.00 3.18
2293 2417 9.881773 AATGGAATACACACCATATTAGGAAAT 57.118 29.630 0.00 0.00 44.79 2.17
2324 2448 9.846248 GTCAATGTTGATAAAGCTCATAACTTT 57.154 29.630 0.00 0.00 39.73 2.66
2327 2451 7.761409 TGGTCAATGTTGATAAAGCTCATAAC 58.239 34.615 0.00 0.00 39.73 1.89
2328 2452 7.936496 TGGTCAATGTTGATAAAGCTCATAA 57.064 32.000 0.00 0.00 39.73 1.90
2330 2454 6.435277 ACTTGGTCAATGTTGATAAAGCTCAT 59.565 34.615 14.90 0.00 39.73 2.90
2331 2455 5.769662 ACTTGGTCAATGTTGATAAAGCTCA 59.230 36.000 14.90 0.00 39.73 4.26
2332 2456 6.259550 ACTTGGTCAATGTTGATAAAGCTC 57.740 37.500 14.90 0.00 39.73 4.09
2334 2458 7.713764 AAAACTTGGTCAATGTTGATAAAGC 57.286 32.000 14.90 0.00 39.73 3.51
2390 2514 9.396022 AGTGGTGTTGATTAATTCGATATTCTT 57.604 29.630 0.00 0.00 0.00 2.52
2400 2524 9.747898 TGGTTAATCTAGTGGTGTTGATTAATT 57.252 29.630 0.00 0.00 40.85 1.40
2401 2525 9.920946 ATGGTTAATCTAGTGGTGTTGATTAAT 57.079 29.630 0.00 0.00 40.85 1.40
2402 2526 9.173021 CATGGTTAATCTAGTGGTGTTGATTAA 57.827 33.333 0.00 0.00 38.35 1.40
2403 2527 8.544622 TCATGGTTAATCTAGTGGTGTTGATTA 58.455 33.333 0.00 0.00 32.33 1.75
2415 2539 8.875168 AGGGAGTAGATTTCATGGTTAATCTAG 58.125 37.037 18.14 0.00 41.52 2.43
2424 2548 2.700897 ACGGAGGGAGTAGATTTCATGG 59.299 50.000 0.00 0.00 0.00 3.66
2436 2560 1.838077 AGTATTTGGGAACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
2437 2561 1.961133 AGTATTTGGGAACGGAGGGA 58.039 50.000 0.00 0.00 0.00 4.20
2438 2562 2.290705 ACAAGTATTTGGGAACGGAGGG 60.291 50.000 2.81 0.00 38.66 4.30
2439 2563 3.007635 GACAAGTATTTGGGAACGGAGG 58.992 50.000 2.81 0.00 38.66 4.30
2441 2565 4.360951 AAGACAAGTATTTGGGAACGGA 57.639 40.909 2.81 0.00 38.66 4.69
2442 2566 4.760204 AGAAAGACAAGTATTTGGGAACGG 59.240 41.667 2.81 0.00 38.66 4.44
2443 2567 5.941948 AGAAAGACAAGTATTTGGGAACG 57.058 39.130 2.81 0.00 38.66 3.95
2444 2568 6.127980 GCCTAGAAAGACAAGTATTTGGGAAC 60.128 42.308 2.81 0.00 38.66 3.62
2446 2570 5.013704 TGCCTAGAAAGACAAGTATTTGGGA 59.986 40.000 2.81 0.00 38.66 4.37
2447 2571 5.253330 TGCCTAGAAAGACAAGTATTTGGG 58.747 41.667 2.81 0.00 38.66 4.12
2448 2572 7.396540 AATGCCTAGAAAGACAAGTATTTGG 57.603 36.000 2.81 0.00 38.66 3.28
2449 2573 8.514594 TGAAATGCCTAGAAAGACAAGTATTTG 58.485 33.333 0.00 0.00 40.24 2.32
2450 2574 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
2454 2578 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
2455 2579 6.810182 CCATTTGAAATGCCTAGAAAGACAAG 59.190 38.462 12.26 0.00 0.00 3.16
2457 2581 6.009589 TCCATTTGAAATGCCTAGAAAGACA 58.990 36.000 12.26 0.00 0.00 3.41
2458 2582 6.151817 AGTCCATTTGAAATGCCTAGAAAGAC 59.848 38.462 12.26 10.86 0.00 3.01
2459 2583 6.248433 AGTCCATTTGAAATGCCTAGAAAGA 58.752 36.000 12.26 0.00 0.00 2.52
2460 2584 6.151648 TGAGTCCATTTGAAATGCCTAGAAAG 59.848 38.462 12.26 0.00 0.00 2.62
2462 2586 5.569355 TGAGTCCATTTGAAATGCCTAGAA 58.431 37.500 12.26 0.00 0.00 2.10
2463 2587 5.178096 TGAGTCCATTTGAAATGCCTAGA 57.822 39.130 12.26 1.83 0.00 2.43
2464 2588 5.183713 TGTTGAGTCCATTTGAAATGCCTAG 59.816 40.000 12.26 0.00 0.00 3.02
2465 2589 5.076182 TGTTGAGTCCATTTGAAATGCCTA 58.924 37.500 12.26 0.00 0.00 3.93
2466 2590 3.896888 TGTTGAGTCCATTTGAAATGCCT 59.103 39.130 12.26 9.70 0.00 4.75
2467 2591 4.255833 TGTTGAGTCCATTTGAAATGCC 57.744 40.909 12.26 5.23 0.00 4.40
2468 2592 5.512788 CGTATGTTGAGTCCATTTGAAATGC 59.487 40.000 12.26 0.23 0.00 3.56
2469 2593 6.841119 TCGTATGTTGAGTCCATTTGAAATG 58.159 36.000 10.84 10.84 0.00 2.32
2470 2594 7.447374 TTCGTATGTTGAGTCCATTTGAAAT 57.553 32.000 0.00 0.00 0.00 2.17
2471 2595 6.869315 TTCGTATGTTGAGTCCATTTGAAA 57.131 33.333 0.00 0.00 0.00 2.69
2472 2596 6.429692 ACATTCGTATGTTGAGTCCATTTGAA 59.570 34.615 1.31 0.00 42.29 2.69
2473 2597 5.937540 ACATTCGTATGTTGAGTCCATTTGA 59.062 36.000 1.31 0.00 42.29 2.69
2474 2598 6.182039 ACATTCGTATGTTGAGTCCATTTG 57.818 37.500 1.31 0.00 42.29 2.32
2475 2599 7.919690 CATACATTCGTATGTTGAGTCCATTT 58.080 34.615 13.12 0.00 46.70 2.32
2476 2600 7.482654 CATACATTCGTATGTTGAGTCCATT 57.517 36.000 13.12 0.00 46.70 3.16
2516 2640 4.091424 GCGCAAAATGAGTGAATCTACAC 58.909 43.478 0.30 0.00 40.60 2.90
2517 2641 3.126858 GGCGCAAAATGAGTGAATCTACA 59.873 43.478 10.83 0.00 0.00 2.74
2518 2642 3.685058 GGCGCAAAATGAGTGAATCTAC 58.315 45.455 10.83 0.00 0.00 2.59
2519 2643 2.351418 CGGCGCAAAATGAGTGAATCTA 59.649 45.455 10.83 0.00 0.00 1.98
2520 2644 1.131126 CGGCGCAAAATGAGTGAATCT 59.869 47.619 10.83 0.00 0.00 2.40
2521 2645 1.135689 ACGGCGCAAAATGAGTGAATC 60.136 47.619 10.83 0.00 0.00 2.52
2522 2646 0.881118 ACGGCGCAAAATGAGTGAAT 59.119 45.000 10.83 0.00 0.00 2.57
2523 2647 1.514003 TACGGCGCAAAATGAGTGAA 58.486 45.000 10.83 0.00 0.00 3.18
2524 2648 1.396648 CATACGGCGCAAAATGAGTGA 59.603 47.619 10.83 0.00 0.00 3.41
2525 2649 1.130373 ACATACGGCGCAAAATGAGTG 59.870 47.619 10.83 0.00 0.00 3.51
2526 2650 1.448985 ACATACGGCGCAAAATGAGT 58.551 45.000 10.83 0.00 0.00 3.41
2527 2651 2.607635 ACTACATACGGCGCAAAATGAG 59.392 45.455 10.83 10.39 0.00 2.90
2528 2652 2.605818 GACTACATACGGCGCAAAATGA 59.394 45.455 10.83 0.00 0.00 2.57
2529 2653 2.350192 TGACTACATACGGCGCAAAATG 59.650 45.455 10.83 11.57 0.00 2.32
2530 2654 2.350498 GTGACTACATACGGCGCAAAAT 59.650 45.455 10.83 0.00 0.00 1.82
2531 2655 1.727880 GTGACTACATACGGCGCAAAA 59.272 47.619 10.83 0.00 0.00 2.44
2532 2656 1.067425 AGTGACTACATACGGCGCAAA 60.067 47.619 10.83 0.00 0.00 3.68
2533 2657 0.528924 AGTGACTACATACGGCGCAA 59.471 50.000 10.83 0.00 0.00 4.85
2534 2658 0.528924 AAGTGACTACATACGGCGCA 59.471 50.000 10.83 0.00 0.00 6.09
2535 2659 0.921347 CAAGTGACTACATACGGCGC 59.079 55.000 6.90 0.00 0.00 6.53
2536 2660 2.273370 ACAAGTGACTACATACGGCG 57.727 50.000 4.80 4.80 0.00 6.46
2537 2661 6.470557 TTTTAACAAGTGACTACATACGGC 57.529 37.500 0.00 0.00 0.00 5.68
2538 2662 8.475331 AGATTTTAACAAGTGACTACATACGG 57.525 34.615 0.00 0.00 0.00 4.02
2539 2663 9.355215 AGAGATTTTAACAAGTGACTACATACG 57.645 33.333 0.00 0.00 0.00 3.06
2562 2686 9.291664 CGTTCCTAAATACTTGTCTTTCTAGAG 57.708 37.037 0.00 0.00 0.00 2.43
2563 2687 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
2564 2688 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
2565 2689 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
2566 2690 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
2567 2691 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
2568 2692 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2569 2693 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2570 2694 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
2571 2695 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
2572 2696 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
2573 2697 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
2574 2698 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
2575 2699 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
2576 2700 7.715266 ATATACTCCCTCCGTTCCTAAATAC 57.285 40.000 0.00 0.00 0.00 1.89
2577 2701 7.951806 TGAATATACTCCCTCCGTTCCTAAATA 59.048 37.037 0.00 0.00 0.00 1.40
2578 2702 6.785963 TGAATATACTCCCTCCGTTCCTAAAT 59.214 38.462 0.00 0.00 0.00 1.40
2579 2703 6.138263 TGAATATACTCCCTCCGTTCCTAAA 58.862 40.000 0.00 0.00 0.00 1.85
2580 2704 5.708544 TGAATATACTCCCTCCGTTCCTAA 58.291 41.667 0.00 0.00 0.00 2.69
2581 2705 5.329191 TGAATATACTCCCTCCGTTCCTA 57.671 43.478 0.00 0.00 0.00 2.94
2582 2706 4.194678 TGAATATACTCCCTCCGTTCCT 57.805 45.455 0.00 0.00 0.00 3.36
2583 2707 6.407074 CCATATGAATATACTCCCTCCGTTCC 60.407 46.154 3.65 0.00 0.00 3.62
2584 2708 6.154706 ACCATATGAATATACTCCCTCCGTTC 59.845 42.308 3.65 0.00 0.00 3.95
2585 2709 6.023603 ACCATATGAATATACTCCCTCCGTT 58.976 40.000 3.65 0.00 0.00 4.44
2586 2710 5.422331 CACCATATGAATATACTCCCTCCGT 59.578 44.000 3.65 0.00 0.00 4.69
2587 2711 5.422331 ACACCATATGAATATACTCCCTCCG 59.578 44.000 3.65 0.00 0.00 4.63
2588 2712 6.875972 ACACCATATGAATATACTCCCTCC 57.124 41.667 3.65 0.00 0.00 4.30
2589 2713 8.982723 ACATACACCATATGAATATACTCCCTC 58.017 37.037 3.65 0.00 0.00 4.30
2590 2714 8.917414 ACATACACCATATGAATATACTCCCT 57.083 34.615 3.65 0.00 0.00 4.20
2591 2715 9.959721 AAACATACACCATATGAATATACTCCC 57.040 33.333 3.65 0.00 0.00 4.30
2645 3043 7.977789 TCACACACTTTGATCAAGCTTATAA 57.022 32.000 8.41 0.00 35.65 0.98
2651 3049 3.004106 AGCTTCACACACTTTGATCAAGC 59.996 43.478 8.41 4.48 35.65 4.01
2658 3056 5.806502 TCAAAATTGAGCTTCACACACTTTG 59.193 36.000 0.00 0.00 32.50 2.77
2659 3057 5.807011 GTCAAAATTGAGCTTCACACACTTT 59.193 36.000 0.00 0.00 37.98 2.66
2660 3058 5.343249 GTCAAAATTGAGCTTCACACACTT 58.657 37.500 0.00 0.00 37.98 3.16
2661 3059 4.496341 CGTCAAAATTGAGCTTCACACACT 60.496 41.667 0.00 0.00 37.98 3.55
2662 3060 3.725740 CGTCAAAATTGAGCTTCACACAC 59.274 43.478 0.00 0.00 37.98 3.82
2663 3061 3.243035 CCGTCAAAATTGAGCTTCACACA 60.243 43.478 0.00 0.00 37.98 3.72
2677 3075 2.035632 AGGCATTGGTTTCCGTCAAAA 58.964 42.857 0.00 0.00 0.00 2.44
2681 3079 1.212751 GCAGGCATTGGTTTCCGTC 59.787 57.895 0.00 0.00 0.00 4.79
2683 3081 1.392589 ATAGCAGGCATTGGTTTCCG 58.607 50.000 0.00 0.00 38.70 4.30
2690 3088 4.885907 CCCTCCATAATATAGCAGGCATTG 59.114 45.833 0.00 0.00 0.00 2.82
2697 3095 4.429505 AGTGCTCCCTCCATAATATAGCA 58.570 43.478 0.00 0.00 36.23 3.49
2716 3119 4.932200 GTCAGGTTGTTTCCATCTCTAGTG 59.068 45.833 0.00 0.00 0.00 2.74
2742 3145 1.257750 GGGGCCATTTCCACTTGTCC 61.258 60.000 4.39 0.00 0.00 4.02
2778 3181 8.230486 CGTGCAAAGAAAAGAAATGATAGTAGT 58.770 33.333 0.00 0.00 0.00 2.73
2780 3183 7.389330 TCCGTGCAAAGAAAAGAAATGATAGTA 59.611 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.