Multiple sequence alignment - TraesCS5A01G070900

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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 TraesCS5A01G070900 chr5A 100.000 3681 0 0 1 3681 79276411 79280091 0.000000e+00 6798.0
1 TraesCS5A01G070900 chr5A 92.912 522 25 7 1 514 608274172 608273655 0.000000e+00 749.0
2 TraesCS5A01G070900 chr5D 92.232 2021 123 20 533 2541 84875238 84877236 0.000000e+00 2832.0
3 TraesCS5A01G070900 chr5D 83.226 936 99 23 2730 3632 84877420 84878330 0.000000e+00 806.0
4 TraesCS5A01G070900 chr5D 87.568 185 16 6 2592 2770 84877247 84877430 1.340000e-49 207.0
5 TraesCS5A01G070900 chr5B 91.477 1842 131 19 532 2359 92232262 92230433 0.000000e+00 2508.0
6 TraesCS5A01G070900 chr5B 80.282 568 78 12 3090 3625 50045108 50044543 7.410000e-107 398.0
7 TraesCS5A01G070900 chr5B 83.003 353 43 11 2659 3005 92230451 92230110 1.660000e-78 303.0
8 TraesCS5A01G070900 chr2A 93.678 522 21 7 1 514 25473335 25473852 0.000000e+00 771.0
9 TraesCS5A01G070900 chr2A 93.462 520 25 7 1 514 25461692 25462208 0.000000e+00 763.0
10 TraesCS5A01G070900 chr2A 82.848 309 43 9 2353 2656 434579961 434580264 6.060000e-68 268.0
11 TraesCS5A01G070900 chr2A 91.525 59 4 1 3624 3681 31083698 31083640 3.050000e-11 80.5
12 TraesCS5A01G070900 chr2A 90.000 60 4 2 3622 3680 735788961 735788903 3.940000e-10 76.8
13 TraesCS5A01G070900 chr2D 90.403 521 41 7 1 514 68570425 68570943 0.000000e+00 676.0
14 TraesCS5A01G070900 chr2D 90.019 521 41 10 1 514 68695714 68696230 0.000000e+00 664.0
15 TraesCS5A01G070900 chr2D 89.729 516 41 10 7 514 68661328 68661839 0.000000e+00 649.0
16 TraesCS5A01G070900 chr3D 89.272 522 46 9 1 514 510910915 510911434 0.000000e+00 645.0
17 TraesCS5A01G070900 chr3D 81.326 573 69 15 3090 3627 67624683 67624114 7.300000e-117 431.0
18 TraesCS5A01G070900 chr3D 84.106 453 56 3 3090 3526 114875651 114875199 1.220000e-114 424.0
19 TraesCS5A01G070900 chr3D 100.000 28 0 0 2732 2759 297675200 297675173 7.000000e-03 52.8
20 TraesCS5A01G070900 chr3B 89.038 520 45 10 1 514 309390248 309390761 5.190000e-178 634.0
21 TraesCS5A01G070900 chr2B 89.017 519 46 7 1 514 673716857 673717369 1.870000e-177 632.0
22 TraesCS5A01G070900 chr2B 98.000 50 1 0 3632 3681 314126036 314126085 1.820000e-13 87.9
23 TraesCS5A01G070900 chr1D 81.599 538 67 11 3090 3597 252560519 252561054 2.040000e-112 416.0
24 TraesCS5A01G070900 chr4B 79.562 548 73 14 3090 3607 139539869 139539331 4.520000e-94 355.0
25 TraesCS5A01G070900 chr7B 78.459 571 85 18 3090 3625 566300344 566299777 4.550000e-89 339.0
26 TraesCS5A01G070900 chr7B 82.468 308 45 8 2353 2656 413595117 413594815 1.010000e-65 261.0
27 TraesCS5A01G070900 chr6A 80.220 455 70 12 3188 3625 603625291 603624840 1.280000e-84 324.0
28 TraesCS5A01G070900 chr4D 82.353 340 59 1 3188 3526 150960280 150960619 1.000000e-75 294.0
29 TraesCS5A01G070900 chr4D 92.857 56 2 2 3627 3681 287561348 287561402 3.050000e-11 80.5
30 TraesCS5A01G070900 chrUn 78.556 457 74 15 3188 3625 58954017 58954468 2.800000e-71 279.0
31 TraesCS5A01G070900 chrUn 82.484 314 42 12 2353 2660 38615357 38615051 2.820000e-66 263.0
32 TraesCS5A01G070900 chrUn 88.889 63 3 3 3620 3681 88757147 88757206 1.420000e-09 75.0
33 TraesCS5A01G070900 chr7D 82.792 308 44 8 2353 2657 49806594 49806895 2.180000e-67 267.0
34 TraesCS5A01G070900 chr7D 82.085 307 45 9 2353 2656 101390986 101390687 1.700000e-63 254.0
35 TraesCS5A01G070900 chr7D 87.879 66 6 2 3618 3681 577365790 577365725 3.940000e-10 76.8
36 TraesCS5A01G070900 chr6B 82.792 308 43 8 2353 2656 40071727 40071426 2.180000e-67 267.0
37 TraesCS5A01G070900 chr6B 81.962 316 47 9 2346 2656 680182295 680182605 3.650000e-65 259.0
38 TraesCS5A01G070900 chr6B 75.551 454 91 12 3188 3625 77742141 77741692 4.820000e-49 206.0
39 TraesCS5A01G070900 chr4A 82.201 309 45 9 2353 2656 664934017 664934320 1.310000e-64 257.0
40 TraesCS5A01G070900 chr1A 92.188 64 4 1 3619 3681 223458357 223458420 5.060000e-14 89.8
41 TraesCS5A01G070900 chr7A 91.379 58 3 2 3625 3681 9434557 9434613 1.100000e-10 78.7
42 TraesCS5A01G070900 chr3A 92.727 55 3 1 3628 3681 78182569 78182515 1.100000e-10 78.7


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 TraesCS5A01G070900 chr5A 79276411 79280091 3680 False 6798.000000 6798 100.000000 1 3681 1 chr5A.!!$F1 3680
1 TraesCS5A01G070900 chr5A 608273655 608274172 517 True 749.000000 749 92.912000 1 514 1 chr5A.!!$R1 513
2 TraesCS5A01G070900 chr5D 84875238 84878330 3092 False 1281.666667 2832 87.675333 533 3632 3 chr5D.!!$F1 3099
3 TraesCS5A01G070900 chr5B 92230110 92232262 2152 True 1405.500000 2508 87.240000 532 3005 2 chr5B.!!$R2 2473
4 TraesCS5A01G070900 chr5B 50044543 50045108 565 True 398.000000 398 80.282000 3090 3625 1 chr5B.!!$R1 535
5 TraesCS5A01G070900 chr2A 25473335 25473852 517 False 771.000000 771 93.678000 1 514 1 chr2A.!!$F2 513
6 TraesCS5A01G070900 chr2A 25461692 25462208 516 False 763.000000 763 93.462000 1 514 1 chr2A.!!$F1 513
7 TraesCS5A01G070900 chr2D 68570425 68570943 518 False 676.000000 676 90.403000 1 514 1 chr2D.!!$F1 513
8 TraesCS5A01G070900 chr2D 68695714 68696230 516 False 664.000000 664 90.019000 1 514 1 chr2D.!!$F3 513
9 TraesCS5A01G070900 chr2D 68661328 68661839 511 False 649.000000 649 89.729000 7 514 1 chr2D.!!$F2 507
10 TraesCS5A01G070900 chr3D 510910915 510911434 519 False 645.000000 645 89.272000 1 514 1 chr3D.!!$F1 513
11 TraesCS5A01G070900 chr3D 67624114 67624683 569 True 431.000000 431 81.326000 3090 3627 1 chr3D.!!$R1 537
12 TraesCS5A01G070900 chr3B 309390248 309390761 513 False 634.000000 634 89.038000 1 514 1 chr3B.!!$F1 513
13 TraesCS5A01G070900 chr2B 673716857 673717369 512 False 632.000000 632 89.017000 1 514 1 chr2B.!!$F2 513
14 TraesCS5A01G070900 chr1D 252560519 252561054 535 False 416.000000 416 81.599000 3090 3597 1 chr1D.!!$F1 507
15 TraesCS5A01G070900 chr4B 139539331 139539869 538 True 355.000000 355 79.562000 3090 3607 1 chr4B.!!$R1 517
16 TraesCS5A01G070900 chr7B 566299777 566300344 567 True 339.000000 339 78.459000 3090 3625 1 chr7B.!!$R2 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
530 555 0.679960 ATTGAGCTACCAAACGGGGC 60.680 55.0 0.00 0.00 42.91 5.80 F
1451 1491 0.744874 CCGGTATCGTGTCCATCACT 59.255 55.0 0.00 0.00 44.16 3.41 F
2426 2472 0.244178 TACCTATGAACACGTGCGCA 59.756 50.0 17.22 5.66 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 2233 0.100325 CAGAACAGCAACGCAAACCA 59.900 50.0 0.0 0.0 0.00 3.67 R
2578 2625 0.108662 TCAAGTCACGATGCTCGCAT 60.109 50.0 3.7 3.7 45.12 4.73 R
3545 3667 0.035458 AACTTTAGCCACGCAGAGCT 59.965 50.0 0.0 0.0 42.48 4.09 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
417 436 7.708051 TCGTTCACAAATTCCAAAACTATTCA 58.292 30.769 0.00 0.00 0.00 2.57
515 540 9.811995 ACGCTAGTGTGTTTTCTTATATATTGA 57.188 29.630 8.45 0.00 32.25 2.57
527 552 8.827177 TTCTTATATATTGAGCTACCAAACGG 57.173 34.615 0.00 0.00 0.00 4.44
528 553 7.383687 TCTTATATATTGAGCTACCAAACGGG 58.616 38.462 0.00 0.00 44.81 5.28
529 554 2.702592 TATTGAGCTACCAAACGGGG 57.297 50.000 0.00 0.00 42.91 5.73
530 555 0.679960 ATTGAGCTACCAAACGGGGC 60.680 55.000 0.00 0.00 42.91 5.80
551 578 6.013639 GGGGCCTAAATGTATACTGTCATACT 60.014 42.308 0.84 0.00 33.37 2.12
646 675 6.872020 AGTTGGCTGATGAAAATTTGATGAAG 59.128 34.615 0.00 0.00 0.00 3.02
661 690 8.697507 ATTTGATGAAGTGGAATATACCTTCC 57.302 34.615 0.00 0.00 44.23 3.46
778 807 4.977739 TCCCTTCTATCTGACATTTCCCAT 59.022 41.667 0.00 0.00 0.00 4.00
779 808 5.068636 CCCTTCTATCTGACATTTCCCATG 58.931 45.833 0.00 0.00 0.00 3.66
867 896 8.793592 GTCAGAACCAGGATGTTATTTTACTTT 58.206 33.333 0.00 0.00 0.00 2.66
921 951 4.634012 TGACAGGGCACAACTAAACTAT 57.366 40.909 0.00 0.00 0.00 2.12
925 955 5.978814 ACAGGGCACAACTAAACTATAGAG 58.021 41.667 6.78 0.00 0.00 2.43
972 1004 4.202151 GCCCCCAGCAAGAACATTATTTAG 60.202 45.833 0.00 0.00 42.97 1.85
973 1005 4.202151 CCCCCAGCAAGAACATTATTTAGC 60.202 45.833 0.00 0.00 0.00 3.09
976 1008 6.321181 CCCCAGCAAGAACATTATTTAGCTAA 59.679 38.462 0.86 0.86 0.00 3.09
977 1009 7.196331 CCCAGCAAGAACATTATTTAGCTAAC 58.804 38.462 5.45 0.00 0.00 2.34
978 1010 7.067494 CCCAGCAAGAACATTATTTAGCTAACT 59.933 37.037 5.45 3.32 0.00 2.24
979 1011 9.109393 CCAGCAAGAACATTATTTAGCTAACTA 57.891 33.333 5.45 2.20 0.00 2.24
997 1037 6.127814 GCTAACTAATAACCCACCCTTGAAAC 60.128 42.308 0.00 0.00 0.00 2.78
1019 1059 8.474710 AAACCTCTATATAAGGCTTCGTAAGA 57.525 34.615 1.30 2.65 40.68 2.10
1108 1148 3.056250 CACTAGAGAATGGCAGACACTGT 60.056 47.826 0.00 0.00 33.43 3.55
1170 1210 2.669229 TCTACGACGACGGCACCA 60.669 61.111 12.58 0.00 44.46 4.17
1403 1443 3.458189 GTCGCTGTACCATTGCTTCTAT 58.542 45.455 0.00 0.00 0.00 1.98
1430 1470 2.123726 GCCGCTTCCATCCCCATT 60.124 61.111 0.00 0.00 0.00 3.16
1451 1491 0.744874 CCGGTATCGTGTCCATCACT 59.255 55.000 0.00 0.00 44.16 3.41
1538 1578 3.633094 GAAGTCGCTCGCTCAGCCA 62.633 63.158 0.00 0.00 46.74 4.75
1562 1602 1.192146 TGCTAGCTGAACCGGTCCTT 61.192 55.000 17.23 0.00 0.00 3.36
1619 1659 1.155424 TGGCCGACTTTTCACGTGTC 61.155 55.000 16.51 4.13 0.00 3.67
1634 1674 2.492484 ACGTGTCTTCCTGATAGGTGAC 59.508 50.000 12.92 12.92 38.95 3.67
1766 1806 3.691342 CGGTCCACTCCAAGCCGA 61.691 66.667 0.00 0.00 44.57 5.54
2020 2060 1.264749 AAGGATGTAGAGGTGGCGCA 61.265 55.000 10.83 0.00 0.00 6.09
2167 2207 1.335182 CTGTGTCGCTCGGATGTAGAT 59.665 52.381 0.00 0.00 0.00 1.98
2173 2213 1.202302 CGCTCGGATGTAGATGTGTGT 60.202 52.381 0.00 0.00 0.00 3.72
2188 2233 2.288666 GTGTGTCAGTGTGTGTCCATT 58.711 47.619 0.00 0.00 0.00 3.16
2267 2312 4.359706 GGTTTTGTGAATTGTGAGTGGTC 58.640 43.478 0.00 0.00 0.00 4.02
2271 2316 5.499139 TTGTGAATTGTGAGTGGTCTTTC 57.501 39.130 0.00 0.00 0.00 2.62
2304 2349 6.604396 AGCTGGAATGTAATGTGATGATTTCA 59.396 34.615 0.00 0.00 0.00 2.69
2305 2350 7.287005 AGCTGGAATGTAATGTGATGATTTCAT 59.713 33.333 0.00 0.00 36.54 2.57
2306 2351 8.570488 GCTGGAATGTAATGTGATGATTTCATA 58.430 33.333 0.00 0.00 36.54 2.15
2385 2431 3.267483 ACAAGTACACACTCAAACGCTT 58.733 40.909 0.00 0.00 32.29 4.68
2400 2446 4.966850 AACGCTTATATACACGTGCATC 57.033 40.909 17.22 0.00 39.00 3.91
2405 2451 4.386049 GCTTATATACACGTGCATCCACTC 59.614 45.833 17.22 0.00 39.86 3.51
2407 2453 2.988010 ATACACGTGCATCCACTCAT 57.012 45.000 17.22 0.00 39.86 2.90
2408 2454 5.722021 ATATACACGTGCATCCACTCATA 57.278 39.130 17.22 0.00 39.86 2.15
2420 2466 4.649088 TCCACTCATACCTATGAACACG 57.351 45.455 0.00 0.00 41.72 4.49
2421 2467 4.021229 TCCACTCATACCTATGAACACGT 58.979 43.478 0.00 0.00 41.72 4.49
2422 2468 4.112634 CCACTCATACCTATGAACACGTG 58.887 47.826 15.48 15.48 41.72 4.49
2424 2470 2.789339 CTCATACCTATGAACACGTGCG 59.211 50.000 17.22 0.00 41.72 5.34
2425 2471 1.257936 CATACCTATGAACACGTGCGC 59.742 52.381 17.22 8.48 35.75 6.09
2426 2472 0.244178 TACCTATGAACACGTGCGCA 59.756 50.000 17.22 5.66 0.00 6.09
2428 2474 1.288419 CCTATGAACACGTGCGCACA 61.288 55.000 37.03 19.36 0.00 4.57
2433 2479 0.442310 GAACACGTGCGCACATACAT 59.558 50.000 37.03 20.17 0.00 2.29
2434 2480 0.442310 AACACGTGCGCACATACATC 59.558 50.000 37.03 11.60 0.00 3.06
2435 2481 0.389817 ACACGTGCGCACATACATCT 60.390 50.000 37.03 11.20 0.00 2.90
2436 2482 0.721154 CACGTGCGCACATACATCTT 59.279 50.000 37.03 9.82 0.00 2.40
2437 2483 0.721154 ACGTGCGCACATACATCTTG 59.279 50.000 37.03 20.86 0.00 3.02
2440 2486 1.356624 GCGCACATACATCTTGCCC 59.643 57.895 0.30 0.00 32.31 5.36
2463 2509 2.491675 TGAGCACCTTCGAGAGACTA 57.508 50.000 0.00 0.00 41.84 2.59
2467 2513 1.795889 GCACCTTCGAGAGACTAAGCG 60.796 57.143 0.00 0.00 41.84 4.68
2477 2524 4.420168 GAGAGACTAAGCGGCATATCATC 58.580 47.826 1.45 0.00 0.00 2.92
2480 2527 5.712446 AGAGACTAAGCGGCATATCATCTTA 59.288 40.000 1.45 0.00 0.00 2.10
2489 2536 8.034058 AGCGGCATATCATCTTAAGATTTTAC 57.966 34.615 15.49 3.77 31.21 2.01
2490 2537 7.661437 AGCGGCATATCATCTTAAGATTTTACA 59.339 33.333 15.49 0.49 31.21 2.41
2499 2546 8.717821 TCATCTTAAGATTTTACAAAGACACCG 58.282 33.333 15.49 0.00 31.21 4.94
2502 2549 9.199982 TCTTAAGATTTTACAAAGACACCGTAG 57.800 33.333 0.00 0.00 0.00 3.51
2541 2588 1.410004 ACGTCTCCTTCCACTGAACA 58.590 50.000 0.00 0.00 0.00 3.18
2542 2589 1.068741 ACGTCTCCTTCCACTGAACAC 59.931 52.381 0.00 0.00 0.00 3.32
2545 2592 0.249868 CTCCTTCCACTGAACACGCA 60.250 55.000 0.00 0.00 0.00 5.24
2548 2595 1.511850 CTTCCACTGAACACGCATCA 58.488 50.000 0.00 0.00 0.00 3.07
2551 2598 1.492873 CACTGAACACGCATCACCG 59.507 57.895 0.00 0.00 0.00 4.94
2552 2599 0.943835 CACTGAACACGCATCACCGA 60.944 55.000 0.00 0.00 0.00 4.69
2553 2600 0.249699 ACTGAACACGCATCACCGAA 60.250 50.000 0.00 0.00 0.00 4.30
2554 2601 0.865111 CTGAACACGCATCACCGAAA 59.135 50.000 0.00 0.00 0.00 3.46
2555 2602 1.262950 CTGAACACGCATCACCGAAAA 59.737 47.619 0.00 0.00 0.00 2.29
2556 2603 1.876799 TGAACACGCATCACCGAAAAT 59.123 42.857 0.00 0.00 0.00 1.82
2557 2604 2.095969 TGAACACGCATCACCGAAAATC 60.096 45.455 0.00 0.00 0.00 2.17
2558 2605 0.802494 ACACGCATCACCGAAAATCC 59.198 50.000 0.00 0.00 0.00 3.01
2559 2606 1.086696 CACGCATCACCGAAAATCCT 58.913 50.000 0.00 0.00 0.00 3.24
2560 2607 1.086696 ACGCATCACCGAAAATCCTG 58.913 50.000 0.00 0.00 0.00 3.86
2561 2608 1.338674 ACGCATCACCGAAAATCCTGA 60.339 47.619 0.00 0.00 0.00 3.86
2562 2609 1.737236 CGCATCACCGAAAATCCTGAA 59.263 47.619 0.00 0.00 0.00 3.02
2563 2610 2.161410 CGCATCACCGAAAATCCTGAAA 59.839 45.455 0.00 0.00 0.00 2.69
2564 2611 3.181497 CGCATCACCGAAAATCCTGAAAT 60.181 43.478 0.00 0.00 0.00 2.17
2565 2612 4.035091 CGCATCACCGAAAATCCTGAAATA 59.965 41.667 0.00 0.00 0.00 1.40
2566 2613 5.448496 CGCATCACCGAAAATCCTGAAATAA 60.448 40.000 0.00 0.00 0.00 1.40
2567 2614 6.329496 GCATCACCGAAAATCCTGAAATAAA 58.671 36.000 0.00 0.00 0.00 1.40
2568 2615 6.980397 GCATCACCGAAAATCCTGAAATAAAT 59.020 34.615 0.00 0.00 0.00 1.40
2569 2616 7.168135 GCATCACCGAAAATCCTGAAATAAATC 59.832 37.037 0.00 0.00 0.00 2.17
2570 2617 7.095695 TCACCGAAAATCCTGAAATAAATCC 57.904 36.000 0.00 0.00 0.00 3.01
2571 2618 6.661377 TCACCGAAAATCCTGAAATAAATCCA 59.339 34.615 0.00 0.00 0.00 3.41
2572 2619 7.177568 TCACCGAAAATCCTGAAATAAATCCAA 59.822 33.333 0.00 0.00 0.00 3.53
2573 2620 7.489113 CACCGAAAATCCTGAAATAAATCCAAG 59.511 37.037 0.00 0.00 0.00 3.61
2574 2621 7.396055 ACCGAAAATCCTGAAATAAATCCAAGA 59.604 33.333 0.00 0.00 0.00 3.02
2575 2622 8.250332 CCGAAAATCCTGAAATAAATCCAAGAA 58.750 33.333 0.00 0.00 0.00 2.52
2576 2623 9.638239 CGAAAATCCTGAAATAAATCCAAGAAA 57.362 29.630 0.00 0.00 0.00 2.52
2581 2628 8.776376 TCCTGAAATAAATCCAAGAAAAATGC 57.224 30.769 0.00 0.00 0.00 3.56
2582 2629 7.545265 TCCTGAAATAAATCCAAGAAAAATGCG 59.455 33.333 0.00 0.00 0.00 4.73
2583 2630 7.545265 CCTGAAATAAATCCAAGAAAAATGCGA 59.455 33.333 0.00 0.00 0.00 5.10
2584 2631 8.464770 TGAAATAAATCCAAGAAAAATGCGAG 57.535 30.769 0.00 0.00 0.00 5.03
2585 2632 6.892310 AATAAATCCAAGAAAAATGCGAGC 57.108 33.333 0.00 0.00 0.00 5.03
2586 2633 3.940209 AATCCAAGAAAAATGCGAGCA 57.060 38.095 0.00 0.00 0.00 4.26
2587 2634 4.460948 AATCCAAGAAAAATGCGAGCAT 57.539 36.364 4.52 4.52 38.46 3.79
2588 2635 3.492421 TCCAAGAAAAATGCGAGCATC 57.508 42.857 11.26 0.00 35.31 3.91
2604 2651 3.928992 GAGCATCGTGACTTGAATTCTGA 59.071 43.478 7.05 0.00 0.00 3.27
2609 2656 3.928992 TCGTGACTTGAATTCTGATGAGC 59.071 43.478 7.05 0.00 0.00 4.26
2610 2657 3.241900 CGTGACTTGAATTCTGATGAGCG 60.242 47.826 7.05 0.40 0.00 5.03
2611 2658 3.928992 GTGACTTGAATTCTGATGAGCGA 59.071 43.478 7.05 0.00 0.00 4.93
2613 2660 4.082026 TGACTTGAATTCTGATGAGCGAGA 60.082 41.667 7.05 0.00 0.00 4.04
2620 2668 4.944619 TTCTGATGAGCGAGAATACCAT 57.055 40.909 0.00 0.00 0.00 3.55
2626 2674 2.766263 TGAGCGAGAATACCATTGTCCT 59.234 45.455 0.00 0.00 0.00 3.85
2663 2711 0.472471 AGGTTGGTTCGCCTCTTCAA 59.528 50.000 0.00 0.00 38.36 2.69
2669 2717 5.508320 GGTTGGTTCGCCTCTTCAATTAAAA 60.508 40.000 0.00 0.00 38.36 1.52
2750 2805 9.190858 TCTCATTATTATTGTTGTTGTTGTTGC 57.809 29.630 0.00 0.00 0.00 4.17
2753 2834 5.655893 ATTATTGTTGTTGTTGTTGCTGC 57.344 34.783 0.00 0.00 0.00 5.25
2770 2851 2.473984 GCTGCTGCTTGTGTGATTTTTC 59.526 45.455 8.53 0.00 36.03 2.29
2773 2854 2.730069 CTGCTTGTGTGATTTTTCGCA 58.270 42.857 0.00 0.00 0.00 5.10
2774 2855 3.311106 CTGCTTGTGTGATTTTTCGCAT 58.689 40.909 0.00 0.00 32.43 4.73
2775 2856 3.051327 TGCTTGTGTGATTTTTCGCATG 58.949 40.909 0.00 0.00 32.43 4.06
2776 2857 3.052036 GCTTGTGTGATTTTTCGCATGT 58.948 40.909 0.00 0.00 32.43 3.21
2777 2858 3.490526 GCTTGTGTGATTTTTCGCATGTT 59.509 39.130 0.00 0.00 32.43 2.71
2781 2862 4.269603 TGTGTGATTTTTCGCATGTTTTGG 59.730 37.500 0.00 0.00 32.43 3.28
2785 2871 6.925718 TGTGATTTTTCGCATGTTTTGGATTA 59.074 30.769 0.00 0.00 0.00 1.75
2843 2929 3.462954 TGAAATATTCAGATGGGGAGCCA 59.537 43.478 0.00 0.00 34.08 4.75
2854 2940 2.919043 GGAGCCATTCCATCCCGT 59.081 61.111 0.00 0.00 46.01 5.28
2857 2943 0.394352 GAGCCATTCCATCCCGTTGT 60.394 55.000 0.00 0.00 0.00 3.32
2928 3017 2.267324 GGAGTGAGTGAGGCAGGC 59.733 66.667 0.00 0.00 0.00 4.85
2939 3028 2.049627 GAGGCAGGCCATAGTGGGAG 62.050 65.000 13.63 0.00 38.19 4.30
2942 3031 1.926426 GCAGGCCATAGTGGGAGGTT 61.926 60.000 5.01 0.00 38.19 3.50
2943 3032 0.181350 CAGGCCATAGTGGGAGGTTC 59.819 60.000 5.01 0.00 38.19 3.62
2956 3045 6.210522 AGTGGGAGGTTCCATAAACTAGTAT 58.789 40.000 0.00 0.00 38.64 2.12
2963 3052 8.625467 AGGTTCCATAAACTAGTATTTCCTCT 57.375 34.615 0.00 0.00 38.02 3.69
3015 3105 6.105333 TCATGTCAAACTTTCAAAACAAGGG 58.895 36.000 0.00 0.00 0.00 3.95
3020 3110 7.547370 TGTCAAACTTTCAAAACAAGGGTTATG 59.453 33.333 0.00 0.00 35.82 1.90
3028 3118 4.911514 AAACAAGGGTTATGTGTCACAC 57.088 40.909 8.08 0.00 35.82 3.82
3030 3120 4.097286 AAACAAGGGTTATGTGTCACACAC 59.903 41.667 14.30 8.13 40.97 3.82
3052 3143 9.078753 CACACAAAAACTATTACCGAAAAGTTT 57.921 29.630 0.00 0.00 42.40 2.66
3074 3165 6.939132 TTTTTGAAATGTGCATCAAATGGT 57.061 29.167 12.63 0.00 43.04 3.55
3076 3167 8.442632 TTTTTGAAATGTGCATCAAATGGTAA 57.557 26.923 12.63 3.54 43.04 2.85
3077 3168 8.442632 TTTTGAAATGTGCATCAAATGGTAAA 57.557 26.923 12.63 0.00 43.04 2.01
3078 3169 8.442632 TTTGAAATGTGCATCAAATGGTAAAA 57.557 26.923 8.73 0.00 39.81 1.52
3079 3170 8.618702 TTGAAATGTGCATCAAATGGTAAAAT 57.381 26.923 0.00 0.00 32.89 1.82
3080 3171 8.254178 TGAAATGTGCATCAAATGGTAAAATC 57.746 30.769 0.00 0.00 0.00 2.17
3081 3172 8.095792 TGAAATGTGCATCAAATGGTAAAATCT 58.904 29.630 0.00 0.00 0.00 2.40
3082 3173 9.585099 GAAATGTGCATCAAATGGTAAAATCTA 57.415 29.630 0.00 0.00 0.00 1.98
3083 3174 9.941325 AAATGTGCATCAAATGGTAAAATCTAA 57.059 25.926 0.00 0.00 0.00 2.10
3084 3175 9.941325 AATGTGCATCAAATGGTAAAATCTAAA 57.059 25.926 0.00 0.00 0.00 1.85
3085 3176 8.755696 TGTGCATCAAATGGTAAAATCTAAAC 57.244 30.769 0.00 0.00 0.00 2.01
3086 3177 7.816995 TGTGCATCAAATGGTAAAATCTAAACC 59.183 33.333 0.00 0.00 0.00 3.27
3087 3178 7.816995 GTGCATCAAATGGTAAAATCTAAACCA 59.183 33.333 0.00 0.00 46.78 3.67
3145 3236 1.484038 TTTTGTGACTTGGCAGCCTT 58.516 45.000 14.15 0.00 0.00 4.35
3166 3257 4.386867 TCTGCTACGGAGTTCATTAAGG 57.613 45.455 0.00 0.00 37.78 2.69
3172 3263 7.784037 TGCTACGGAGTTCATTAAGGTTAATA 58.216 34.615 0.00 0.00 37.78 0.98
3198 3305 2.875317 TGCAAAAATACTGCGAGTGTGA 59.125 40.909 0.00 0.00 42.97 3.58
3211 3318 1.453015 GTGTGAGTGTGGTGGCCAA 60.453 57.895 7.24 0.00 34.18 4.52
3217 3324 2.203280 TGTGGTGGCCAAGAACCG 60.203 61.111 7.24 0.00 39.47 4.44
3220 3327 0.535553 GTGGTGGCCAAGAACCGTAA 60.536 55.000 7.24 0.00 39.47 3.18
3231 3338 4.154195 CCAAGAACCGTAATGGAGAAGTTG 59.846 45.833 0.00 0.00 42.00 3.16
3240 3347 6.086222 CGTAATGGAGAAGTTGTCATTTTGG 58.914 40.000 2.06 0.00 32.81 3.28
3247 3354 1.624813 AGTTGTCATTTTGGCATGGGG 59.375 47.619 0.00 0.00 29.04 4.96
3260 3367 2.427150 GGCATGGGGTTATATTGGGGTT 60.427 50.000 0.00 0.00 0.00 4.11
3285 3393 4.458989 GCAATAGTGTGGATGAAGTGGAAA 59.541 41.667 0.00 0.00 0.00 3.13
3292 3400 4.082125 GTGGATGAAGTGGAAATTGGAGT 58.918 43.478 0.00 0.00 0.00 3.85
3302 3410 2.238521 GAAATTGGAGTGACCCTTGCA 58.761 47.619 0.00 0.00 38.00 4.08
3318 3426 1.614996 TGCAGGGTTGTACATTGGTG 58.385 50.000 0.00 0.00 0.00 4.17
3326 3434 5.544948 AGGGTTGTACATTGGTGTTACTCTA 59.455 40.000 0.00 0.00 39.77 2.43
3327 3435 5.873164 GGGTTGTACATTGGTGTTACTCTAG 59.127 44.000 0.00 0.00 39.77 2.43
3351 3459 8.934023 AGACAAACCCATCATTTTAGAAACTA 57.066 30.769 0.00 0.00 0.00 2.24
3352 3460 9.014297 AGACAAACCCATCATTTTAGAAACTAG 57.986 33.333 0.00 0.00 0.00 2.57
3419 3527 8.602472 ACAGGTCTTCTCTAGTTGATCTAAAT 57.398 34.615 0.00 0.00 0.00 1.40
3463 3571 9.524106 TTTCAAGATGATGATAAATTGCATGAC 57.476 29.630 0.00 0.00 0.00 3.06
3483 3591 6.373005 TGACATCCAAGATTAACAGAAGGA 57.627 37.500 0.00 0.00 0.00 3.36
3491 3599 7.037586 TCCAAGATTAACAGAAGGACCAATAGT 60.038 37.037 0.00 0.00 0.00 2.12
3526 3634 9.746711 CGAGATTGTGAAGTTTAGTTTTGATAG 57.253 33.333 0.00 0.00 0.00 2.08
3527 3635 9.548208 GAGATTGTGAAGTTTAGTTTTGATAGC 57.452 33.333 0.00 0.00 0.00 2.97
3528 3636 9.289782 AGATTGTGAAGTTTAGTTTTGATAGCT 57.710 29.630 0.00 0.00 0.00 3.32
3535 3657 9.818796 GAAGTTTAGTTTTGATAGCTCTTCTTG 57.181 33.333 0.00 0.00 0.00 3.02
3545 3667 7.410120 TGATAGCTCTTCTTGATAGTGTTCA 57.590 36.000 0.00 0.00 0.00 3.18
3548 3670 4.222588 AGCTCTTCTTGATAGTGTTCAGCT 59.777 41.667 0.00 0.00 0.00 4.24
3565 3687 1.275291 AGCTCTGCGTGGCTAAAGTTA 59.725 47.619 0.00 0.00 37.00 2.24
3647 3770 9.973450 AAAATATGCATTTTGTAACACAGTACA 57.027 25.926 3.54 0.00 41.70 2.90
3648 3771 9.624697 AAATATGCATTTTGTAACACAGTACAG 57.375 29.630 3.54 0.00 35.47 2.74
3649 3772 6.875948 ATGCATTTTGTAACACAGTACAGA 57.124 33.333 0.00 0.00 35.47 3.41
3650 3773 6.055231 TGCATTTTGTAACACAGTACAGAC 57.945 37.500 0.00 0.00 35.47 3.51
3651 3774 5.586643 TGCATTTTGTAACACAGTACAGACA 59.413 36.000 0.00 0.00 35.47 3.41
3652 3775 5.907391 GCATTTTGTAACACAGTACAGACAC 59.093 40.000 0.00 0.00 35.47 3.67
3653 3776 6.457663 GCATTTTGTAACACAGTACAGACACA 60.458 38.462 0.00 0.00 35.47 3.72
3654 3777 7.468441 CATTTTGTAACACAGTACAGACACAA 58.532 34.615 0.00 0.00 35.47 3.33
3655 3778 6.656314 TTTGTAACACAGTACAGACACAAG 57.344 37.500 0.00 0.00 35.47 3.16
3656 3779 4.116961 TGTAACACAGTACAGACACAAGC 58.883 43.478 0.00 0.00 30.48 4.01
3657 3780 1.852942 ACACAGTACAGACACAAGCG 58.147 50.000 0.00 0.00 0.00 4.68
3658 3781 0.508641 CACAGTACAGACACAAGCGC 59.491 55.000 0.00 0.00 0.00 5.92
3659 3782 0.389391 ACAGTACAGACACAAGCGCT 59.611 50.000 2.64 2.64 0.00 5.92
3660 3783 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
3661 3784 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
3662 3785 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
3663 3786 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
3664 3787 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
3665 3788 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
3666 3789 3.448686 ACAGACACAAGCGCTCATATAC 58.551 45.455 12.06 1.00 0.00 1.47
3667 3790 3.119137 ACAGACACAAGCGCTCATATACA 60.119 43.478 12.06 0.00 0.00 2.29
3668 3791 3.243877 CAGACACAAGCGCTCATATACAC 59.756 47.826 12.06 0.00 0.00 2.90
3669 3792 3.119137 AGACACAAGCGCTCATATACACA 60.119 43.478 12.06 0.00 0.00 3.72
3670 3793 2.930040 ACACAAGCGCTCATATACACAC 59.070 45.455 12.06 0.00 0.00 3.82
3671 3794 2.034591 CACAAGCGCTCATATACACACG 60.035 50.000 12.06 0.00 0.00 4.49
3672 3795 1.071239 CAAGCGCTCATATACACACGC 60.071 52.381 12.06 0.00 46.20 5.34
3673 3796 2.588731 GCGCTCATATACACACGCA 58.411 52.632 0.00 0.00 45.25 5.24
3674 3797 1.139989 GCGCTCATATACACACGCAT 58.860 50.000 0.00 0.00 45.25 4.73
3675 3798 2.324860 GCGCTCATATACACACGCATA 58.675 47.619 0.00 0.00 45.25 3.14
3676 3799 2.090658 GCGCTCATATACACACGCATAC 59.909 50.000 0.00 0.00 45.25 2.39
3677 3800 3.305110 CGCTCATATACACACGCATACA 58.695 45.455 0.00 0.00 0.00 2.29
3678 3801 3.119628 CGCTCATATACACACGCATACAC 59.880 47.826 0.00 0.00 0.00 2.90
3679 3802 4.299155 GCTCATATACACACGCATACACT 58.701 43.478 0.00 0.00 0.00 3.55
3680 3803 4.383052 GCTCATATACACACGCATACACTC 59.617 45.833 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
324 342 7.492344 ACACAAACAATTTCTGAACATCTTTCC 59.508 33.333 0.00 0.00 0.00 3.13
384 403 7.834068 TTGGAATTTGTGAACGAAATTTGAA 57.166 28.000 0.00 0.00 34.00 2.69
481 506 7.982371 AGAAAACACACTAGCGTACATATAC 57.018 36.000 0.00 0.00 0.00 1.47
514 539 1.619807 TAGGCCCCGTTTGGTAGCTC 61.620 60.000 0.00 0.00 34.04 4.09
515 540 1.202769 TTAGGCCCCGTTTGGTAGCT 61.203 55.000 0.00 0.00 34.04 3.32
516 541 0.322726 TTTAGGCCCCGTTTGGTAGC 60.323 55.000 0.00 0.00 33.07 3.58
517 542 2.021457 CATTTAGGCCCCGTTTGGTAG 58.979 52.381 0.00 0.00 0.00 3.18
518 543 1.355043 ACATTTAGGCCCCGTTTGGTA 59.645 47.619 0.00 0.00 0.00 3.25
519 544 0.113580 ACATTTAGGCCCCGTTTGGT 59.886 50.000 0.00 0.00 0.00 3.67
520 545 2.131776 TACATTTAGGCCCCGTTTGG 57.868 50.000 0.00 0.00 0.00 3.28
521 546 4.274950 CAGTATACATTTAGGCCCCGTTTG 59.725 45.833 5.50 0.00 0.00 2.93
522 547 4.080186 ACAGTATACATTTAGGCCCCGTTT 60.080 41.667 5.50 0.00 0.00 3.60
523 548 3.457012 ACAGTATACATTTAGGCCCCGTT 59.543 43.478 5.50 0.00 0.00 4.44
524 549 3.043418 ACAGTATACATTTAGGCCCCGT 58.957 45.455 5.50 0.00 0.00 5.28
525 550 3.070446 TGACAGTATACATTTAGGCCCCG 59.930 47.826 5.50 0.00 0.00 5.73
526 551 4.699925 TGACAGTATACATTTAGGCCCC 57.300 45.455 5.50 0.00 0.00 5.80
527 552 6.874134 CAGTATGACAGTATACATTTAGGCCC 59.126 42.308 5.50 0.00 39.69 5.80
528 553 6.874134 CCAGTATGACAGTATACATTTAGGCC 59.126 42.308 5.50 0.00 39.69 5.19
529 554 6.369065 GCCAGTATGACAGTATACATTTAGGC 59.631 42.308 5.50 3.23 39.69 3.93
530 555 7.600375 CAGCCAGTATGACAGTATACATTTAGG 59.400 40.741 5.50 0.00 39.69 2.69
551 578 8.138928 AGTGTAATGATAGCTATATTCAGCCA 57.861 34.615 6.13 0.00 42.84 4.75
622 651 6.647895 ACTTCATCAAATTTTCATCAGCCAAC 59.352 34.615 0.00 0.00 0.00 3.77
661 690 5.633601 ACACGCTACATTATACATTCATCCG 59.366 40.000 0.00 0.00 0.00 4.18
691 720 3.195825 CCTTCCACGTTCTCCATAGAGTT 59.804 47.826 0.00 0.00 41.26 3.01
829 858 8.792633 CATCCTGGTTCTGACAAAATACTTTTA 58.207 33.333 0.00 0.00 0.00 1.52
867 896 7.831690 ACATTACTCTCTCTTGTCTCTATGTGA 59.168 37.037 0.00 0.00 0.00 3.58
925 955 8.456471 GGCGAGGGGTATTCATATTTATTAAAC 58.544 37.037 0.00 0.00 0.00 2.01
927 957 7.114095 GGGCGAGGGGTATTCATATTTATTAA 58.886 38.462 0.00 0.00 0.00 1.40
930 960 4.079958 GGGGCGAGGGGTATTCATATTTAT 60.080 45.833 0.00 0.00 0.00 1.40
931 961 3.264964 GGGGCGAGGGGTATTCATATTTA 59.735 47.826 0.00 0.00 0.00 1.40
933 963 1.633945 GGGGCGAGGGGTATTCATATT 59.366 52.381 0.00 0.00 0.00 1.28
935 965 0.838987 GGGGGCGAGGGGTATTCATA 60.839 60.000 0.00 0.00 0.00 2.15
937 967 2.770904 GGGGGCGAGGGGTATTCA 60.771 66.667 0.00 0.00 0.00 2.57
972 1004 5.106876 TCAAGGGTGGGTTATTAGTTAGC 57.893 43.478 0.00 0.00 0.00 3.09
973 1005 6.376299 GGTTTCAAGGGTGGGTTATTAGTTAG 59.624 42.308 0.00 0.00 0.00 2.34
976 1008 4.355889 AGGTTTCAAGGGTGGGTTATTAGT 59.644 41.667 0.00 0.00 0.00 2.24
977 1009 4.930696 AGGTTTCAAGGGTGGGTTATTAG 58.069 43.478 0.00 0.00 0.00 1.73
978 1010 4.604490 AGAGGTTTCAAGGGTGGGTTATTA 59.396 41.667 0.00 0.00 0.00 0.98
979 1011 3.401342 AGAGGTTTCAAGGGTGGGTTATT 59.599 43.478 0.00 0.00 0.00 1.40
980 1012 2.993863 AGAGGTTTCAAGGGTGGGTTAT 59.006 45.455 0.00 0.00 0.00 1.89
985 1025 6.534634 CCTTATATAGAGGTTTCAAGGGTGG 58.465 44.000 0.00 0.00 0.00 4.61
986 1026 5.998363 GCCTTATATAGAGGTTTCAAGGGTG 59.002 44.000 10.69 0.00 36.63 4.61
1019 1059 4.210331 GCTTGATGGGATGATAACCACTT 58.790 43.478 0.00 0.00 40.05 3.16
1108 1148 2.368548 TCCACTAGTTTCTTGCAGCAGA 59.631 45.455 0.00 0.00 0.00 4.26
1364 1404 2.058595 CCAGGTAGGGTCGGTCAGG 61.059 68.421 0.00 0.00 0.00 3.86
1418 1458 1.282653 TACCGGCAATGGGGATGGAA 61.283 55.000 0.00 0.00 0.00 3.53
1430 1470 1.324005 TGATGGACACGATACCGGCA 61.324 55.000 0.00 0.00 40.78 5.69
1451 1491 3.984186 CTCCGGAGCAAGGGGGAGA 62.984 68.421 20.67 0.00 36.10 3.71
1538 1578 2.993853 GGTTCAGCTAGCAGCCCT 59.006 61.111 18.83 0.00 43.77 5.19
1586 1626 3.435186 GCCACGGCCTTGAGCTTC 61.435 66.667 11.54 0.00 43.05 3.86
1619 1659 3.616956 TTGCTGTCACCTATCAGGAAG 57.383 47.619 0.00 0.00 37.67 3.46
1634 1674 1.601419 CCAGGTTGGCTCCATTGCTG 61.601 60.000 0.00 0.00 0.00 4.41
1728 1768 0.322546 GAGAAACCCGGGTTGAGCAT 60.323 55.000 38.87 23.50 38.47 3.79
1782 1822 1.079405 CGTACGGGTCCAGTTGCAT 60.079 57.895 7.57 0.00 0.00 3.96
2039 2079 3.133362 CGCCCTGGTTAAGGTAGAACATA 59.867 47.826 0.00 0.00 45.78 2.29
2167 2207 0.610687 TGGACACACACTGACACACA 59.389 50.000 0.00 0.00 0.00 3.72
2173 2213 2.687425 CAAACCAATGGACACACACTGA 59.313 45.455 6.16 0.00 0.00 3.41
2188 2233 0.100325 CAGAACAGCAACGCAAACCA 59.900 50.000 0.00 0.00 0.00 3.67
2267 2312 5.695851 ACATTCCAGCTAAACTGTGAAAG 57.304 39.130 0.00 0.00 45.68 2.62
2271 2316 6.149308 TCACATTACATTCCAGCTAAACTGTG 59.851 38.462 0.00 0.00 45.68 3.66
2360 2406 4.210537 GCGTTTGAGTGTGTACTTGTATGT 59.789 41.667 0.00 0.00 37.25 2.29
2361 2407 4.447724 AGCGTTTGAGTGTGTACTTGTATG 59.552 41.667 0.00 0.00 37.25 2.39
2362 2408 4.628074 AGCGTTTGAGTGTGTACTTGTAT 58.372 39.130 0.00 0.00 37.25 2.29
2363 2409 4.049546 AGCGTTTGAGTGTGTACTTGTA 57.950 40.909 0.00 0.00 37.25 2.41
2364 2410 2.901249 AGCGTTTGAGTGTGTACTTGT 58.099 42.857 0.00 0.00 37.25 3.16
2365 2411 3.944422 AAGCGTTTGAGTGTGTACTTG 57.056 42.857 0.00 0.00 37.25 3.16
2367 2413 7.487189 GTGTATATAAGCGTTTGAGTGTGTACT 59.513 37.037 0.00 0.00 40.66 2.73
2368 2414 7.512579 CGTGTATATAAGCGTTTGAGTGTGTAC 60.513 40.741 0.00 0.00 0.00 2.90
2369 2415 6.469915 CGTGTATATAAGCGTTTGAGTGTGTA 59.530 38.462 0.00 0.00 0.00 2.90
2372 2418 5.287752 CACGTGTATATAAGCGTTTGAGTGT 59.712 40.000 7.58 0.00 35.25 3.55
2373 2419 5.714272 CACGTGTATATAAGCGTTTGAGTG 58.286 41.667 7.58 0.00 35.25 3.51
2375 2421 4.266739 TGCACGTGTATATAAGCGTTTGAG 59.733 41.667 18.38 2.29 35.25 3.02
2376 2422 4.174762 TGCACGTGTATATAAGCGTTTGA 58.825 39.130 18.38 0.00 35.25 2.69
2377 2423 4.508376 TGCACGTGTATATAAGCGTTTG 57.492 40.909 18.38 3.14 35.25 2.93
2378 2424 4.210537 GGATGCACGTGTATATAAGCGTTT 59.789 41.667 19.47 0.00 35.25 3.60
2379 2425 3.739300 GGATGCACGTGTATATAAGCGTT 59.261 43.478 19.47 0.00 35.25 4.84
2380 2426 3.243602 TGGATGCACGTGTATATAAGCGT 60.244 43.478 19.47 1.54 38.14 5.07
2385 2431 5.722021 ATGAGTGGATGCACGTGTATATA 57.278 39.130 19.47 8.52 0.00 0.86
2400 2446 4.112634 CACGTGTTCATAGGTATGAGTGG 58.887 47.826 7.58 1.17 42.99 4.00
2405 2451 1.257936 GCGCACGTGTTCATAGGTATG 59.742 52.381 18.38 0.00 35.04 2.39
2407 2453 0.244178 TGCGCACGTGTTCATAGGTA 59.756 50.000 18.38 0.00 0.00 3.08
2408 2454 1.005512 TGCGCACGTGTTCATAGGT 60.006 52.632 18.38 0.00 0.00 3.08
2420 2466 0.248215 GGCAAGATGTATGTGCGCAC 60.248 55.000 33.11 33.11 39.22 5.34
2421 2467 1.375853 GGGCAAGATGTATGTGCGCA 61.376 55.000 5.66 5.66 46.93 6.09
2422 2468 1.356624 GGGCAAGATGTATGTGCGC 59.643 57.895 0.00 0.00 42.81 6.09
2424 2470 2.638480 TAGGGGCAAGATGTATGTGC 57.362 50.000 0.00 0.00 37.55 4.57
2425 2471 4.321718 CTCATAGGGGCAAGATGTATGTG 58.678 47.826 0.00 0.00 0.00 3.21
2426 2472 3.244700 GCTCATAGGGGCAAGATGTATGT 60.245 47.826 0.00 0.00 0.00 2.29
2428 2474 2.981784 TGCTCATAGGGGCAAGATGTAT 59.018 45.455 0.00 0.00 35.40 2.29
2433 2479 0.621571 AGGTGCTCATAGGGGCAAGA 60.622 55.000 2.11 0.00 40.26 3.02
2434 2480 0.257039 AAGGTGCTCATAGGGGCAAG 59.743 55.000 2.11 0.00 40.26 4.01
2435 2481 0.255890 GAAGGTGCTCATAGGGGCAA 59.744 55.000 2.11 0.00 40.26 4.52
2436 2482 1.915228 GAAGGTGCTCATAGGGGCA 59.085 57.895 0.00 0.00 36.01 5.36
2437 2483 1.227674 CGAAGGTGCTCATAGGGGC 60.228 63.158 0.00 0.00 0.00 5.80
2440 2486 2.034053 GTCTCTCGAAGGTGCTCATAGG 59.966 54.545 0.00 0.00 0.00 2.57
2463 2509 7.516198 AAAATCTTAAGATGATATGCCGCTT 57.484 32.000 18.61 2.65 34.49 4.68
2477 2524 8.440833 CCTACGGTGTCTTTGTAAAATCTTAAG 58.559 37.037 0.00 0.00 0.00 1.85
2480 2527 5.180680 GCCTACGGTGTCTTTGTAAAATCTT 59.819 40.000 0.00 0.00 0.00 2.40
2489 2536 4.667420 ACGCCTACGGTGTCTTTG 57.333 55.556 0.00 0.00 43.59 2.77
2499 2546 2.670635 TCGACTACGAGACGCCTAC 58.329 57.895 0.00 0.00 43.81 3.18
2524 2571 1.784525 CGTGTTCAGTGGAAGGAGAC 58.215 55.000 0.00 0.00 32.62 3.36
2541 2588 1.086696 CAGGATTTTCGGTGATGCGT 58.913 50.000 0.00 0.00 0.00 5.24
2542 2589 1.368641 TCAGGATTTTCGGTGATGCG 58.631 50.000 0.00 0.00 0.00 4.73
2545 2592 7.341769 TGGATTTATTTCAGGATTTTCGGTGAT 59.658 33.333 0.00 0.00 0.00 3.06
2548 2595 7.396055 TCTTGGATTTATTTCAGGATTTTCGGT 59.604 33.333 0.00 0.00 0.00 4.69
2555 2602 9.387257 GCATTTTTCTTGGATTTATTTCAGGAT 57.613 29.630 0.00 0.00 0.00 3.24
2556 2603 7.545265 CGCATTTTTCTTGGATTTATTTCAGGA 59.455 33.333 0.00 0.00 0.00 3.86
2557 2604 7.545265 TCGCATTTTTCTTGGATTTATTTCAGG 59.455 33.333 0.00 0.00 0.00 3.86
2558 2605 8.464770 TCGCATTTTTCTTGGATTTATTTCAG 57.535 30.769 0.00 0.00 0.00 3.02
2559 2606 7.063308 GCTCGCATTTTTCTTGGATTTATTTCA 59.937 33.333 0.00 0.00 0.00 2.69
2560 2607 7.063308 TGCTCGCATTTTTCTTGGATTTATTTC 59.937 33.333 0.00 0.00 0.00 2.17
2561 2608 6.873076 TGCTCGCATTTTTCTTGGATTTATTT 59.127 30.769 0.00 0.00 0.00 1.40
2562 2609 6.397272 TGCTCGCATTTTTCTTGGATTTATT 58.603 32.000 0.00 0.00 0.00 1.40
2563 2610 5.964758 TGCTCGCATTTTTCTTGGATTTAT 58.035 33.333 0.00 0.00 0.00 1.40
2564 2611 5.384063 TGCTCGCATTTTTCTTGGATTTA 57.616 34.783 0.00 0.00 0.00 1.40
2565 2612 4.255833 TGCTCGCATTTTTCTTGGATTT 57.744 36.364 0.00 0.00 0.00 2.17
2566 2613 3.940209 TGCTCGCATTTTTCTTGGATT 57.060 38.095 0.00 0.00 0.00 3.01
2567 2614 3.488047 CGATGCTCGCATTTTTCTTGGAT 60.488 43.478 5.79 0.00 36.70 3.41
2568 2615 2.159531 CGATGCTCGCATTTTTCTTGGA 60.160 45.455 5.79 0.00 36.70 3.53
2569 2616 2.179589 CGATGCTCGCATTTTTCTTGG 58.820 47.619 5.79 0.00 36.70 3.61
2570 2617 2.591148 CACGATGCTCGCATTTTTCTTG 59.409 45.455 5.79 0.00 45.12 3.02
2571 2618 2.483877 TCACGATGCTCGCATTTTTCTT 59.516 40.909 5.79 0.00 45.12 2.52
2572 2619 2.076100 TCACGATGCTCGCATTTTTCT 58.924 42.857 5.79 0.00 45.12 2.52
2573 2620 2.159653 AGTCACGATGCTCGCATTTTTC 60.160 45.455 5.79 0.00 45.12 2.29
2574 2621 1.806542 AGTCACGATGCTCGCATTTTT 59.193 42.857 5.79 0.00 45.12 1.94
2575 2622 1.442769 AGTCACGATGCTCGCATTTT 58.557 45.000 5.79 0.00 45.12 1.82
2576 2623 1.129251 CAAGTCACGATGCTCGCATTT 59.871 47.619 5.79 0.00 45.12 2.32
2577 2624 0.723414 CAAGTCACGATGCTCGCATT 59.277 50.000 5.79 0.00 45.12 3.56
2578 2625 0.108662 TCAAGTCACGATGCTCGCAT 60.109 50.000 3.70 3.70 45.12 4.73
2579 2626 0.319469 TTCAAGTCACGATGCTCGCA 60.319 50.000 5.63 0.00 45.12 5.10
2580 2627 1.002366 ATTCAAGTCACGATGCTCGC 58.998 50.000 5.63 0.00 45.12 5.03
2581 2628 2.926200 AGAATTCAAGTCACGATGCTCG 59.074 45.455 8.44 4.36 46.93 5.03
2582 2629 3.928992 TCAGAATTCAAGTCACGATGCTC 59.071 43.478 8.44 0.00 0.00 4.26
2583 2630 3.930336 TCAGAATTCAAGTCACGATGCT 58.070 40.909 8.44 0.00 0.00 3.79
2584 2631 4.330894 TCATCAGAATTCAAGTCACGATGC 59.669 41.667 8.44 0.00 31.89 3.91
2585 2632 5.502058 GCTCATCAGAATTCAAGTCACGATG 60.502 44.000 8.44 9.75 32.54 3.84
2586 2633 4.569966 GCTCATCAGAATTCAAGTCACGAT 59.430 41.667 8.44 0.00 0.00 3.73
2587 2634 3.928992 GCTCATCAGAATTCAAGTCACGA 59.071 43.478 8.44 0.00 0.00 4.35
2588 2635 3.241900 CGCTCATCAGAATTCAAGTCACG 60.242 47.826 8.44 0.00 0.00 4.35
2589 2636 3.928992 TCGCTCATCAGAATTCAAGTCAC 59.071 43.478 8.44 0.00 0.00 3.67
2590 2637 4.082026 TCTCGCTCATCAGAATTCAAGTCA 60.082 41.667 8.44 0.00 0.00 3.41
2599 2646 4.944619 ATGGTATTCTCGCTCATCAGAA 57.055 40.909 0.00 0.00 33.18 3.02
2600 2647 4.100035 ACAATGGTATTCTCGCTCATCAGA 59.900 41.667 0.00 0.00 0.00 3.27
2604 2651 3.389329 AGGACAATGGTATTCTCGCTCAT 59.611 43.478 0.00 0.00 0.00 2.90
2609 2656 5.290386 GTTAGGAGGACAATGGTATTCTCG 58.710 45.833 0.00 0.00 0.00 4.04
2610 2657 5.130477 TGGTTAGGAGGACAATGGTATTCTC 59.870 44.000 0.00 0.00 0.00 2.87
2611 2658 5.036916 TGGTTAGGAGGACAATGGTATTCT 58.963 41.667 0.00 0.00 0.00 2.40
2613 2660 5.163088 GGATGGTTAGGAGGACAATGGTATT 60.163 44.000 0.00 0.00 0.00 1.89
2620 2668 2.307686 GGTTGGATGGTTAGGAGGACAA 59.692 50.000 0.00 0.00 0.00 3.18
2626 2674 1.633432 CCTGTGGTTGGATGGTTAGGA 59.367 52.381 0.00 0.00 0.00 2.94
2654 2702 9.705290 TCTGGTTAAAATTTTAATTGAAGAGGC 57.295 29.630 22.66 9.28 35.35 4.70
2728 2777 7.656948 AGCAGCAACAACAACAACAATAATAAT 59.343 29.630 0.00 0.00 0.00 1.28
2734 2789 2.931325 CAGCAGCAACAACAACAACAAT 59.069 40.909 0.00 0.00 0.00 2.71
2750 2805 2.722629 CGAAAAATCACACAAGCAGCAG 59.277 45.455 0.00 0.00 0.00 4.24
2753 2834 2.730069 TGCGAAAAATCACACAAGCAG 58.270 42.857 0.00 0.00 0.00 4.24
2770 2851 5.009010 AGGAATAGCTAATCCAAAACATGCG 59.991 40.000 26.24 0.00 38.23 4.73
2818 2904 5.047519 GGCTCCCCATCTGAATATTTCATTG 60.048 44.000 0.00 0.00 39.30 2.82
2843 2929 3.696045 TGAATTGACAACGGGATGGAAT 58.304 40.909 0.00 0.00 0.00 3.01
2899 2988 6.315714 CCTCACTCACTCCCCTTTATCTATA 58.684 44.000 0.00 0.00 0.00 1.31
2928 3017 4.166144 AGTTTATGGAACCTCCCACTATGG 59.834 45.833 0.00 0.00 39.34 2.74
2956 3045 9.747898 TTGCCTTGTATAGAAAATTAGAGGAAA 57.252 29.630 0.00 0.00 0.00 3.13
2963 3052 7.335924 AGCGAAGTTGCCTTGTATAGAAAATTA 59.664 33.333 0.00 0.00 34.65 1.40
2965 3054 5.648092 AGCGAAGTTGCCTTGTATAGAAAAT 59.352 36.000 0.00 0.00 34.65 1.82
2970 3060 4.391830 TGAAAGCGAAGTTGCCTTGTATAG 59.608 41.667 0.00 0.00 34.65 1.31
2988 3078 8.170553 CCTTGTTTTGAAAGTTTGACATGAAAG 58.829 33.333 0.00 0.00 0.00 2.62
2993 3083 6.048732 ACCCTTGTTTTGAAAGTTTGACAT 57.951 33.333 0.00 0.00 0.00 3.06
3052 3143 8.442632 TTTACCATTTGATGCACATTTCAAAA 57.557 26.923 15.14 0.00 43.04 2.44
3058 3149 9.941325 TTTAGATTTTACCATTTGATGCACATT 57.059 25.926 0.00 0.00 0.00 2.71
3118 3209 5.186996 TGCCAAGTCACAAAATTCTCTTC 57.813 39.130 0.00 0.00 0.00 2.87
3145 3236 3.767673 ACCTTAATGAACTCCGTAGCAGA 59.232 43.478 0.00 0.00 0.00 4.26
3166 3257 9.232082 TCGCAGTATTTTTGCATCAATATTAAC 57.768 29.630 0.00 0.00 41.59 2.01
3172 3263 5.097529 CACTCGCAGTATTTTTGCATCAAT 58.902 37.500 0.00 0.00 41.59 2.57
3182 3273 3.059884 CACACTCACACTCGCAGTATTT 58.940 45.455 0.00 0.00 0.00 1.40
3183 3274 2.610479 CCACACTCACACTCGCAGTATT 60.610 50.000 0.00 0.00 0.00 1.89
3184 3275 1.067565 CCACACTCACACTCGCAGTAT 60.068 52.381 0.00 0.00 0.00 2.12
3185 3276 0.313987 CCACACTCACACTCGCAGTA 59.686 55.000 0.00 0.00 0.00 2.74
3186 3277 1.068083 CCACACTCACACTCGCAGT 59.932 57.895 0.00 0.00 0.00 4.40
3198 3305 1.152756 GGTTCTTGGCCACCACACT 60.153 57.895 3.88 0.00 30.78 3.55
3211 3318 4.039973 TGACAACTTCTCCATTACGGTTCT 59.960 41.667 0.00 0.00 35.57 3.01
3217 3324 5.863935 GCCAAAATGACAACTTCTCCATTAC 59.136 40.000 0.00 0.00 0.00 1.89
3220 3327 3.896888 TGCCAAAATGACAACTTCTCCAT 59.103 39.130 0.00 0.00 0.00 3.41
3231 3338 5.806654 ATATAACCCCATGCCAAAATGAC 57.193 39.130 0.00 0.00 0.00 3.06
3240 3347 2.694616 ACCCCAATATAACCCCATGC 57.305 50.000 0.00 0.00 0.00 4.06
3247 3354 6.978080 CACACTATTGCAAACCCCAATATAAC 59.022 38.462 1.71 0.00 35.35 1.89
3260 3367 3.758023 CCACTTCATCCACACTATTGCAA 59.242 43.478 0.00 0.00 0.00 4.08
3285 3393 3.658398 CTGCAAGGGTCACTCCAAT 57.342 52.632 0.00 0.00 38.11 3.16
3302 3410 4.349930 AGAGTAACACCAATGTACAACCCT 59.650 41.667 0.00 0.00 38.45 4.34
3318 3426 7.923414 AAATGATGGGTTTGTCTAGAGTAAC 57.077 36.000 0.00 0.31 0.00 2.50
3326 3434 7.839680 AGTTTCTAAAATGATGGGTTTGTCT 57.160 32.000 0.00 0.00 0.00 3.41
3327 3435 8.793592 ACTAGTTTCTAAAATGATGGGTTTGTC 58.206 33.333 0.00 0.00 0.00 3.18
3351 3459 6.551227 AGAAAAGAGGCCACAAAAGAATAACT 59.449 34.615 5.01 0.00 0.00 2.24
3352 3460 6.749139 AGAAAAGAGGCCACAAAAGAATAAC 58.251 36.000 5.01 0.00 0.00 1.89
3355 3463 5.453762 CCAAGAAAAGAGGCCACAAAAGAAT 60.454 40.000 5.01 0.00 0.00 2.40
3460 3568 6.173339 GTCCTTCTGTTAATCTTGGATGTCA 58.827 40.000 0.00 0.00 0.00 3.58
3463 3571 5.500234 TGGTCCTTCTGTTAATCTTGGATG 58.500 41.667 0.00 0.00 0.00 3.51
3483 3591 3.981308 GTGCGCCACACTATTGGT 58.019 55.556 4.18 0.00 46.41 3.67
3491 3599 2.030412 ACAATCTCGTGCGCCACA 59.970 55.556 4.18 0.00 33.40 4.17
3526 3634 4.502962 AGCTGAACACTATCAAGAAGAGC 58.497 43.478 0.00 0.00 0.00 4.09
3527 3635 5.806502 CAGAGCTGAACACTATCAAGAAGAG 59.193 44.000 0.00 0.00 0.00 2.85
3528 3636 5.718146 CAGAGCTGAACACTATCAAGAAGA 58.282 41.667 0.00 0.00 0.00 2.87
3535 3657 1.923204 CACGCAGAGCTGAACACTATC 59.077 52.381 0.85 0.00 0.00 2.08
3545 3667 0.035458 AACTTTAGCCACGCAGAGCT 59.965 50.000 0.00 0.00 42.48 4.09
3548 3670 3.861113 CGTTATAACTTTAGCCACGCAGA 59.139 43.478 13.56 0.00 0.00 4.26
3565 3687 7.548196 AAACATTCGTACAATCATCCGTTAT 57.452 32.000 0.00 0.00 0.00 1.89
3628 3751 5.907391 GTGTCTGTACTGTGTTACAAAATGC 59.093 40.000 0.00 0.00 0.00 3.56
3629 3752 7.010697 TGTGTCTGTACTGTGTTACAAAATG 57.989 36.000 0.00 0.00 0.00 2.32
3630 3753 7.618502 TTGTGTCTGTACTGTGTTACAAAAT 57.381 32.000 0.00 0.00 0.00 1.82
3631 3754 6.402766 GCTTGTGTCTGTACTGTGTTACAAAA 60.403 38.462 0.00 0.00 0.00 2.44
3632 3755 5.064198 GCTTGTGTCTGTACTGTGTTACAAA 59.936 40.000 0.00 0.00 0.00 2.83
3633 3756 4.569162 GCTTGTGTCTGTACTGTGTTACAA 59.431 41.667 0.00 4.57 0.00 2.41
3634 3757 4.116961 GCTTGTGTCTGTACTGTGTTACA 58.883 43.478 0.00 0.00 0.00 2.41
3635 3758 3.181774 CGCTTGTGTCTGTACTGTGTTAC 59.818 47.826 0.00 0.00 0.00 2.50
3636 3759 3.377439 CGCTTGTGTCTGTACTGTGTTA 58.623 45.455 0.00 0.00 0.00 2.41
3637 3760 2.201732 CGCTTGTGTCTGTACTGTGTT 58.798 47.619 0.00 0.00 0.00 3.32
3638 3761 1.852942 CGCTTGTGTCTGTACTGTGT 58.147 50.000 0.00 0.00 0.00 3.72
3639 3762 0.508641 GCGCTTGTGTCTGTACTGTG 59.491 55.000 0.00 0.00 0.00 3.66
3640 3763 0.389391 AGCGCTTGTGTCTGTACTGT 59.611 50.000 2.64 0.00 0.00 3.55
3641 3764 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
3642 3765 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
3643 3766 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
3644 3767 3.801114 ATATGAGCGCTTGTGTCTGTA 57.199 42.857 13.26 0.00 0.00 2.74
3645 3768 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
3646 3769 3.243877 GTGTATATGAGCGCTTGTGTCTG 59.756 47.826 13.26 0.00 0.00 3.51
3647 3770 3.119137 TGTGTATATGAGCGCTTGTGTCT 60.119 43.478 13.26 0.00 0.00 3.41
3648 3771 3.000322 GTGTGTATATGAGCGCTTGTGTC 60.000 47.826 13.26 0.00 0.00 3.67
3649 3772 2.930040 GTGTGTATATGAGCGCTTGTGT 59.070 45.455 13.26 4.27 0.00 3.72
3650 3773 2.034591 CGTGTGTATATGAGCGCTTGTG 60.035 50.000 13.26 0.00 0.00 3.33
3651 3774 2.193447 CGTGTGTATATGAGCGCTTGT 58.807 47.619 13.26 5.98 0.00 3.16
3652 3775 1.071239 GCGTGTGTATATGAGCGCTTG 60.071 52.381 13.26 0.00 41.37 4.01
3653 3776 1.209128 GCGTGTGTATATGAGCGCTT 58.791 50.000 13.26 0.00 41.37 4.68
3654 3777 0.102300 TGCGTGTGTATATGAGCGCT 59.898 50.000 11.27 11.27 44.34 5.92
3655 3778 1.139989 ATGCGTGTGTATATGAGCGC 58.860 50.000 0.00 0.00 44.29 5.92
3656 3779 3.119628 GTGTATGCGTGTGTATATGAGCG 59.880 47.826 0.00 0.00 0.00 5.03
3657 3780 4.299155 AGTGTATGCGTGTGTATATGAGC 58.701 43.478 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.