Multiple sequence alignment - TraesCS5A01G351600

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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 TraesCS5A01G351600 chr5A 100.000 5484 0 0 1 5484 554192843 554187360 0.000000e+00 10128.0
1 TraesCS5A01G351600 chr5A 80.365 1864 310 32 739 2565 554057133 554055289 0.000000e+00 1363.0
2 TraesCS5A01G351600 chr5A 81.169 1540 221 36 2982 4486 554054871 554053366 0.000000e+00 1173.0
3 TraesCS5A01G351600 chr5A 76.606 1526 287 55 2992 4484 553480352 553478864 0.000000e+00 776.0
4 TraesCS5A01G351600 chr5A 74.321 1289 286 34 989 2251 554221259 554219990 6.340000e-139 505.0
5 TraesCS5A01G351600 chr5A 73.354 1276 308 25 1022 2277 554063048 554061785 1.400000e-120 444.0
6 TraesCS5A01G351600 chr5A 77.966 590 97 22 3530 4097 553491200 553490622 6.800000e-89 339.0
7 TraesCS5A01G351600 chr5D 89.645 2482 200 22 238 2695 438577418 438574970 0.000000e+00 3107.0
8 TraesCS5A01G351600 chr5D 94.636 1510 73 7 3041 4543 438574964 438573456 0.000000e+00 2333.0
9 TraesCS5A01G351600 chr5D 76.726 1521 276 53 3031 4503 438559076 438557586 0.000000e+00 776.0
10 TraesCS5A01G351600 chr5D 76.934 1448 265 46 3035 4437 438545170 438543747 0.000000e+00 760.0
11 TraesCS5A01G351600 chr5D 78.578 1097 200 28 3033 4110 438589646 438588566 0.000000e+00 691.0
12 TraesCS5A01G351600 chr5D 86.645 629 48 9 4685 5279 438573223 438572597 0.000000e+00 664.0
13 TraesCS5A01G351600 chr5D 74.286 1365 301 36 983 2314 438457310 438455963 1.050000e-146 531.0
14 TraesCS5A01G351600 chr5D 74.316 1316 286 41 988 2268 438724688 438723390 1.360000e-140 510.0
15 TraesCS5A01G351600 chr5D 74.299 1319 281 47 989 2268 438660775 438659476 6.340000e-139 505.0
16 TraesCS5A01G351600 chr5D 73.976 1318 295 38 983 2271 438547401 438546103 1.780000e-134 490.0
17 TraesCS5A01G351600 chr5D 89.840 187 16 3 1 186 438577599 438577415 2.550000e-58 237.0
18 TraesCS5A01G351600 chr5D 94.656 131 5 2 4550 4678 438573397 438573267 9.310000e-48 202.0
19 TraesCS5A01G351600 chr5D 82.456 228 31 8 625 849 438661594 438661373 2.020000e-44 191.0
20 TraesCS5A01G351600 chr5D 100.000 35 0 0 4602 4636 438573257 438573223 1.280000e-06 65.8
21 TraesCS5A01G351600 chr5B 88.373 2563 262 20 1 2541 533482294 533479746 0.000000e+00 3049.0
22 TraesCS5A01G351600 chr5B 90.305 1609 114 16 2974 4549 533479171 533477572 0.000000e+00 2069.0
23 TraesCS5A01G351600 chr5B 76.741 1522 297 45 2992 4484 533018861 533017368 0.000000e+00 797.0
24 TraesCS5A01G351600 chr5B 89.748 556 41 11 4736 5287 533477393 533476850 0.000000e+00 697.0
25 TraesCS5A01G351600 chr5B 75.482 1505 303 46 3033 4499 533451377 533449901 0.000000e+00 675.0
26 TraesCS5A01G351600 chr5B 73.907 1349 308 34 1001 2327 533511473 533510147 8.200000e-138 501.0
27 TraesCS5A01G351600 chr5B 74.102 1309 287 44 989 2268 533525312 533524027 4.940000e-135 492.0
28 TraesCS5A01G351600 chr5B 73.289 1359 324 29 983 2315 533093271 533091926 3.870000e-126 462.0
29 TraesCS5A01G351600 chr5B 84.956 226 30 4 626 849 533576182 533575959 5.530000e-55 226.0
30 TraesCS5A01G351600 chr5B 90.411 146 12 1 4535 4678 533477536 533477391 2.020000e-44 191.0
31 TraesCS5A01G351600 chr5B 81.771 192 21 7 656 845 533526083 533525904 1.230000e-31 148.0
32 TraesCS5A01G351600 chr5B 86.014 143 10 4 5292 5434 533476748 533476616 1.590000e-30 145.0
33 TraesCS5A01G351600 chr5B 89.524 105 7 3 5380 5484 533476625 533476525 4.460000e-26 130.0
34 TraesCS5A01G351600 chr3B 81.282 1544 223 44 2992 4497 9570001 9568486 0.000000e+00 1190.0
35 TraesCS5A01G351600 chr3D 81.621 1431 197 46 3099 4497 7498355 7496959 0.000000e+00 1125.0
36 TraesCS5A01G351600 chr3D 74.579 1605 327 57 1006 2573 7501573 7500013 3.610000e-176 628.0
37 TraesCS5A01G351600 chr2B 78.165 1090 196 35 3032 4097 65047450 65048521 0.000000e+00 656.0
38 TraesCS5A01G351600 chr2A 75.055 1355 310 22 989 2324 14742727 14741382 6.080000e-169 604.0
39 TraesCS5A01G351600 chr2A 73.875 1378 316 32 998 2349 14705763 14704404 1.360000e-140 510.0


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 TraesCS5A01G351600 chr5A 554187360 554192843 5483 True 10128.000000 10128 100.000000 1 5484 1 chr5A.!!$R4 5483
1 TraesCS5A01G351600 chr5A 554053366 554057133 3767 True 1268.000000 1363 80.767000 739 4486 2 chr5A.!!$R6 3747
2 TraesCS5A01G351600 chr5A 553478864 553480352 1488 True 776.000000 776 76.606000 2992 4484 1 chr5A.!!$R1 1492
3 TraesCS5A01G351600 chr5A 554219990 554221259 1269 True 505.000000 505 74.321000 989 2251 1 chr5A.!!$R5 1262
4 TraesCS5A01G351600 chr5A 554061785 554063048 1263 True 444.000000 444 73.354000 1022 2277 1 chr5A.!!$R3 1255
5 TraesCS5A01G351600 chr5A 553490622 553491200 578 True 339.000000 339 77.966000 3530 4097 1 chr5A.!!$R2 567
6 TraesCS5A01G351600 chr5D 438572597 438577599 5002 True 1101.466667 3107 92.570333 1 5279 6 chr5D.!!$R6 5278
7 TraesCS5A01G351600 chr5D 438557586 438559076 1490 True 776.000000 776 76.726000 3031 4503 1 chr5D.!!$R2 1472
8 TraesCS5A01G351600 chr5D 438588566 438589646 1080 True 691.000000 691 78.578000 3033 4110 1 chr5D.!!$R3 1077
9 TraesCS5A01G351600 chr5D 438543747 438547401 3654 True 625.000000 760 75.455000 983 4437 2 chr5D.!!$R5 3454
10 TraesCS5A01G351600 chr5D 438455963 438457310 1347 True 531.000000 531 74.286000 983 2314 1 chr5D.!!$R1 1331
11 TraesCS5A01G351600 chr5D 438723390 438724688 1298 True 510.000000 510 74.316000 988 2268 1 chr5D.!!$R4 1280
12 TraesCS5A01G351600 chr5D 438659476 438661594 2118 True 348.000000 505 78.377500 625 2268 2 chr5D.!!$R7 1643
13 TraesCS5A01G351600 chr5B 533476525 533482294 5769 True 1046.833333 3049 89.062500 1 5484 6 chr5B.!!$R6 5483
14 TraesCS5A01G351600 chr5B 533017368 533018861 1493 True 797.000000 797 76.741000 2992 4484 1 chr5B.!!$R1 1492
15 TraesCS5A01G351600 chr5B 533449901 533451377 1476 True 675.000000 675 75.482000 3033 4499 1 chr5B.!!$R3 1466
16 TraesCS5A01G351600 chr5B 533510147 533511473 1326 True 501.000000 501 73.907000 1001 2327 1 chr5B.!!$R4 1326
17 TraesCS5A01G351600 chr5B 533091926 533093271 1345 True 462.000000 462 73.289000 983 2315 1 chr5B.!!$R2 1332
18 TraesCS5A01G351600 chr5B 533524027 533526083 2056 True 320.000000 492 77.936500 656 2268 2 chr5B.!!$R7 1612
19 TraesCS5A01G351600 chr3B 9568486 9570001 1515 True 1190.000000 1190 81.282000 2992 4497 1 chr3B.!!$R1 1505
20 TraesCS5A01G351600 chr3D 7496959 7501573 4614 True 876.500000 1125 78.100000 1006 4497 2 chr3D.!!$R1 3491
21 TraesCS5A01G351600 chr2B 65047450 65048521 1071 False 656.000000 656 78.165000 3032 4097 1 chr2B.!!$F1 1065
22 TraesCS5A01G351600 chr2A 14741382 14742727 1345 True 604.000000 604 75.055000 989 2324 1 chr2A.!!$R2 1335
23 TraesCS5A01G351600 chr2A 14704404 14705763 1359 True 510.000000 510 73.875000 998 2349 1 chr2A.!!$R1 1351

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
388 393 0.397675 TGCCCAACCAATCACCAACA 60.398 50.0 0.00 0.00 0.00 3.33 F
1941 2569 0.318441 GCTACTGTGACCAGACAGCA 59.682 55.0 12.71 0.00 46.28 4.41 F
2329 2968 0.106868 TGCAGGCTTAGATGCAGCAT 60.107 50.0 7.91 7.91 46.97 3.79 F
2858 3586 0.107831 TTCTTGTAGCACGCCAACCT 59.892 50.0 0.00 0.00 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2722 0.250467 ACATGAACTTGTCTGGCGCT 60.250 50.00 7.64 0.00 0.00 5.92 R
3039 5447 0.318445 GTGTTCTTGCCTGCTTGCAG 60.318 55.00 15.02 15.02 43.21 4.41 R
3817 6265 4.559153 GTGCTTGCATCTTGTTGGTTATT 58.441 39.13 0.00 0.00 0.00 1.40 R
4832 7493 0.321671 TGAACTGTCCTAGCACAGCC 59.678 55.00 13.96 6.77 46.81 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
38 39 6.255887 GGACTAGAACAAGACATTCCAATACG 59.744 42.308 0.00 0.00 0.00 3.06
46 47 4.517285 AGACATTCCAATACGCATGACTT 58.483 39.130 0.00 0.00 0.00 3.01
58 59 5.389642 ACGCATGACTTACACGAATTATG 57.610 39.130 0.00 0.00 0.00 1.90
59 60 4.868171 ACGCATGACTTACACGAATTATGT 59.132 37.500 0.00 0.86 0.00 2.29
202 204 9.535170 TCCCTAACAATAATTTATCAACCACAA 57.465 29.630 0.00 0.00 0.00 3.33
352 354 5.131142 CACCCTGTTATTCATCCTCCTACTT 59.869 44.000 0.00 0.00 0.00 2.24
374 379 1.817520 CTGTCGTTGTGTGTGCCCA 60.818 57.895 0.00 0.00 0.00 5.36
380 385 0.463620 GTTGTGTGTGCCCAACCAAT 59.536 50.000 0.00 0.00 35.93 3.16
388 393 0.397675 TGCCCAACCAATCACCAACA 60.398 50.000 0.00 0.00 0.00 3.33
395 400 4.261114 CCAACCAATCACCAACAATTTTGC 60.261 41.667 0.00 0.00 0.00 3.68
516 521 2.037772 CTCAGTCAACTGTTGGTAGCCT 59.962 50.000 19.55 6.30 44.12 4.58
520 525 3.118038 AGTCAACTGTTGGTAGCCTTTGA 60.118 43.478 19.55 0.00 0.00 2.69
552 560 2.295909 TCCTTTTCTTCCAATTGCACGG 59.704 45.455 0.00 0.00 0.00 4.94
620 629 8.355169 AGGAATAGTAAAACCCTTTCGAAAAAC 58.645 33.333 12.41 2.41 0.00 2.43
673 682 2.320587 CCAGCTGAGTTCACACCGC 61.321 63.158 17.39 0.00 0.00 5.68
676 685 2.738521 CTGAGTTCACACCGCCGG 60.739 66.667 0.00 0.00 0.00 6.13
693 702 1.006832 CGGTCGTTGCCATTCTAAGG 58.993 55.000 0.00 0.00 0.00 2.69
696 705 1.659098 GTCGTTGCCATTCTAAGGTCG 59.341 52.381 0.00 0.00 0.00 4.79
701 710 2.901249 TGCCATTCTAAGGTCGTAAGC 58.099 47.619 0.00 0.00 37.18 3.09
702 711 2.210961 GCCATTCTAAGGTCGTAAGCC 58.789 52.381 0.00 0.00 37.18 4.35
703 712 2.419574 GCCATTCTAAGGTCGTAAGCCA 60.420 50.000 0.00 0.00 36.22 4.75
782 796 5.417811 TCAAAGCTTTGCATTTTTCAGTCA 58.582 33.333 30.35 9.02 38.05 3.41
809 824 7.286087 CCCCTTTCATTATCAATCTGACATGAA 59.714 37.037 0.00 8.18 37.50 2.57
819 834 4.708576 ATCTGACATGAATGCTGGATCT 57.291 40.909 0.00 0.00 0.00 2.75
854 869 9.840427 ATTTGTCAAGAAATTAACACTAATCCG 57.160 29.630 0.00 0.00 0.00 4.18
862 877 2.961522 AACACTAATCCGTTGTTGCG 57.038 45.000 0.00 0.00 0.00 4.85
899 1451 3.476552 TCGATCCAGACTTTGCACTTTT 58.523 40.909 0.00 0.00 0.00 2.27
981 1545 1.201647 AGCACGTACGTACTGCAGAAT 59.798 47.619 32.34 19.59 34.80 2.40
1011 1576 1.271543 TGATCGATCATGGATTGGCCC 60.272 52.381 23.99 0.00 34.97 5.80
1251 1844 2.047179 GCCAACAGGGAGACGTCC 60.047 66.667 13.01 3.55 43.05 4.79
1269 1862 1.564622 CGTCACCAACAGCACTTCG 59.435 57.895 0.00 0.00 0.00 3.79
1711 2336 1.515521 GCAGGTTAACGGCAGCTTGT 61.516 55.000 13.98 0.00 40.25 3.16
1941 2569 0.318441 GCTACTGTGACCAGACAGCA 59.682 55.000 12.71 0.00 46.28 4.41
1992 2626 1.670406 CTTCGAGCCAGCAAGCACT 60.670 57.895 0.55 0.00 34.23 4.40
2088 2722 3.010472 TCTTGGCCTTGATGGAGATGAAA 59.990 43.478 3.32 0.00 38.35 2.69
2179 2813 2.629656 AATTGCTCCTGTGTGGCGC 61.630 57.895 0.00 0.00 46.22 6.53
2198 2832 2.745884 CGCATTCGCCAACCTGGA 60.746 61.111 0.00 0.00 40.96 3.86
2280 2919 2.167398 CTGGGAAGTTCGGCGAAGGA 62.167 60.000 24.41 0.00 0.00 3.36
2329 2968 0.106868 TGCAGGCTTAGATGCAGCAT 60.107 50.000 7.91 7.91 46.97 3.79
2383 3055 8.779303 TGTTATTTTGTCTATACCAACACACTG 58.221 33.333 0.00 0.00 0.00 3.66
2393 3065 8.197439 TCTATACCAACACACTGTCATGATTAG 58.803 37.037 0.00 3.44 0.00 1.73
2489 3168 0.521735 CTGGCAGTTTTAGGAACGGC 59.478 55.000 6.28 5.64 39.93 5.68
2557 3261 7.599998 TCAAAGGTACGTATACAGTTTTTCCTC 59.400 37.037 0.00 0.00 32.40 3.71
2568 3272 6.530019 ACAGTTTTTCCTCATGTGAAAGTT 57.470 33.333 11.20 2.58 33.58 2.66
2573 3277 7.922811 AGTTTTTCCTCATGTGAAAGTTCATTC 59.077 33.333 11.20 0.00 39.73 2.67
2575 3279 4.002982 TCCTCATGTGAAAGTTCATTCGG 58.997 43.478 0.00 0.00 39.73 4.30
2578 3282 1.243902 TGTGAAAGTTCATTCGGCCC 58.756 50.000 0.00 0.00 39.73 5.80
2579 3283 1.202879 TGTGAAAGTTCATTCGGCCCT 60.203 47.619 0.00 0.00 39.73 5.19
2580 3284 1.200020 GTGAAAGTTCATTCGGCCCTG 59.800 52.381 0.00 0.00 39.73 4.45
2581 3285 1.073125 TGAAAGTTCATTCGGCCCTGA 59.927 47.619 0.00 0.00 31.01 3.86
2584 3288 3.249687 GTTCATTCGGCCCTGAACT 57.750 52.632 23.44 2.79 44.94 3.01
2658 3383 8.821686 ATCACTGAACAATACCAAATAATCCA 57.178 30.769 0.00 0.00 0.00 3.41
2660 3385 9.253832 TCACTGAACAATACCAAATAATCCATT 57.746 29.630 0.00 0.00 0.00 3.16
2689 3417 2.959516 TCGAGTGTGACTTAGCCAATG 58.040 47.619 0.00 0.00 0.00 2.82
2696 3424 4.216257 GTGTGACTTAGCCAATGTGTCAAT 59.784 41.667 0.00 0.00 39.01 2.57
2697 3425 4.455533 TGTGACTTAGCCAATGTGTCAATC 59.544 41.667 0.00 0.00 39.01 2.67
2698 3426 3.684305 TGACTTAGCCAATGTGTCAATCG 59.316 43.478 0.00 0.00 35.15 3.34
2705 3433 4.574828 AGCCAATGTGTCAATCGTATAACC 59.425 41.667 0.00 0.00 0.00 2.85
2706 3434 4.334203 GCCAATGTGTCAATCGTATAACCA 59.666 41.667 0.00 0.00 0.00 3.67
2711 3439 6.415798 TGTGTCAATCGTATAACCACAATG 57.584 37.500 0.00 0.00 0.00 2.82
2717 3445 3.892284 TCGTATAACCACAATGGGCAAT 58.108 40.909 0.00 0.00 43.37 3.56
2721 3449 1.269012 AACCACAATGGGCAATCTGG 58.731 50.000 0.00 0.00 43.37 3.86
2727 3455 4.345837 CCACAATGGGCAATCTGGAATAAT 59.654 41.667 0.00 0.00 32.67 1.28
2729 3457 6.294899 CCACAATGGGCAATCTGGAATAATAG 60.295 42.308 0.00 0.00 32.67 1.73
2730 3458 5.244626 ACAATGGGCAATCTGGAATAATAGC 59.755 40.000 0.00 0.00 0.00 2.97
2731 3459 4.729552 TGGGCAATCTGGAATAATAGCT 57.270 40.909 0.00 0.00 0.00 3.32
2732 3460 4.655963 TGGGCAATCTGGAATAATAGCTC 58.344 43.478 0.00 0.00 0.00 4.09
2734 3462 4.319177 GGCAATCTGGAATAATAGCTCGT 58.681 43.478 0.00 0.00 0.00 4.18
2735 3463 4.390297 GGCAATCTGGAATAATAGCTCGTC 59.610 45.833 0.00 0.00 0.00 4.20
2736 3464 4.991056 GCAATCTGGAATAATAGCTCGTCA 59.009 41.667 0.00 0.00 0.00 4.35
2738 3466 6.401903 GCAATCTGGAATAATAGCTCGTCATG 60.402 42.308 0.00 0.00 0.00 3.07
2739 3467 5.139435 TCTGGAATAATAGCTCGTCATGG 57.861 43.478 0.00 0.00 0.00 3.66
2740 3468 4.588951 TCTGGAATAATAGCTCGTCATGGT 59.411 41.667 0.00 0.00 0.00 3.55
2743 3471 7.004555 TGGAATAATAGCTCGTCATGGTAAT 57.995 36.000 0.00 0.00 0.00 1.89
2747 3475 9.803315 GAATAATAGCTCGTCATGGTAATATGA 57.197 33.333 0.00 0.00 34.83 2.15
2749 3477 7.891183 AATAGCTCGTCATGGTAATATGAAC 57.109 36.000 0.00 0.00 38.69 3.18
2750 3478 5.537300 AGCTCGTCATGGTAATATGAACT 57.463 39.130 0.00 0.00 38.69 3.01
2751 3479 5.533482 AGCTCGTCATGGTAATATGAACTC 58.467 41.667 0.00 0.00 38.69 3.01
2754 3482 6.074088 GCTCGTCATGGTAATATGAACTCAAG 60.074 42.308 0.00 0.00 38.69 3.02
2755 3483 6.280643 TCGTCATGGTAATATGAACTCAAGG 58.719 40.000 0.00 0.00 38.69 3.61
2758 3486 8.088365 CGTCATGGTAATATGAACTCAAGGATA 58.912 37.037 0.00 0.00 38.69 2.59
2759 3487 9.209175 GTCATGGTAATATGAACTCAAGGATAC 57.791 37.037 0.00 0.00 38.69 2.24
2779 3507 8.871686 GGATACTTGTGTTCAAAACTTCAAAT 57.128 30.769 0.00 0.00 32.87 2.32
2780 3508 8.755018 GGATACTTGTGTTCAAAACTTCAAATG 58.245 33.333 0.00 0.00 32.87 2.32
2781 3509 9.301153 GATACTTGTGTTCAAAACTTCAAATGT 57.699 29.630 0.00 0.00 32.87 2.71
2782 3510 7.961325 ACTTGTGTTCAAAACTTCAAATGTT 57.039 28.000 0.00 0.00 32.87 2.71
2783 3511 8.376889 ACTTGTGTTCAAAACTTCAAATGTTT 57.623 26.923 0.00 0.00 39.03 2.83
2784 3512 8.281893 ACTTGTGTTCAAAACTTCAAATGTTTG 58.718 29.630 0.00 0.00 37.64 2.93
2785 3513 6.597614 TGTGTTCAAAACTTCAAATGTTTGC 58.402 32.000 0.66 0.00 37.64 3.68
2786 3514 6.426328 TGTGTTCAAAACTTCAAATGTTTGCT 59.574 30.769 0.66 0.00 37.64 3.91
2787 3515 7.041508 TGTGTTCAAAACTTCAAATGTTTGCTT 60.042 29.630 0.66 0.00 37.64 3.91
2788 3516 7.268872 GTGTTCAAAACTTCAAATGTTTGCTTG 59.731 33.333 0.66 1.09 37.64 4.01
2789 3517 6.419980 TCAAAACTTCAAATGTTTGCTTGG 57.580 33.333 0.66 0.00 37.64 3.61
2790 3518 5.353678 TCAAAACTTCAAATGTTTGCTTGGG 59.646 36.000 0.66 0.00 37.64 4.12
2791 3519 3.473923 ACTTCAAATGTTTGCTTGGGG 57.526 42.857 0.66 0.00 38.05 4.96
2792 3520 3.037549 ACTTCAAATGTTTGCTTGGGGA 58.962 40.909 0.66 0.00 38.05 4.81
2793 3521 3.070015 ACTTCAAATGTTTGCTTGGGGAG 59.930 43.478 0.66 0.00 38.05 4.30
2794 3522 2.956132 TCAAATGTTTGCTTGGGGAGA 58.044 42.857 0.66 0.00 38.05 3.71
2795 3523 2.892852 TCAAATGTTTGCTTGGGGAGAG 59.107 45.455 0.66 0.00 38.05 3.20
2796 3524 1.928868 AATGTTTGCTTGGGGAGAGG 58.071 50.000 0.00 0.00 0.00 3.69
2797 3525 1.075601 ATGTTTGCTTGGGGAGAGGA 58.924 50.000 0.00 0.00 0.00 3.71
2798 3526 1.075601 TGTTTGCTTGGGGAGAGGAT 58.924 50.000 0.00 0.00 0.00 3.24
2799 3527 1.272092 TGTTTGCTTGGGGAGAGGATG 60.272 52.381 0.00 0.00 0.00 3.51
2800 3528 0.332632 TTTGCTTGGGGAGAGGATGG 59.667 55.000 0.00 0.00 0.00 3.51
2801 3529 2.194326 GCTTGGGGAGAGGATGGC 59.806 66.667 0.00 0.00 0.00 4.40
2802 3530 2.683465 GCTTGGGGAGAGGATGGCA 61.683 63.158 0.00 0.00 0.00 4.92
2803 3531 2.004408 GCTTGGGGAGAGGATGGCAT 62.004 60.000 0.00 0.00 0.00 4.40
2804 3532 1.438469 CTTGGGGAGAGGATGGCATA 58.562 55.000 0.00 0.00 0.00 3.14
2805 3533 1.776667 CTTGGGGAGAGGATGGCATAA 59.223 52.381 0.00 0.00 0.00 1.90
2809 3537 2.979678 GGGGAGAGGATGGCATAAACTA 59.020 50.000 0.00 0.00 0.00 2.24
2819 3547 3.995636 TGGCATAAACTAGAGAGGAGGT 58.004 45.455 0.00 0.00 0.00 3.85
2821 3549 3.707102 GGCATAAACTAGAGAGGAGGTGT 59.293 47.826 0.00 0.00 0.00 4.16
2837 3565 4.019231 GGAGGTGTCTAGGGAGAAAATGTT 60.019 45.833 0.00 0.00 31.96 2.71
2844 3572 6.486657 TGTCTAGGGAGAAAATGTTGTTCTTG 59.513 38.462 0.00 0.00 35.46 3.02
2845 3573 6.486993 GTCTAGGGAGAAAATGTTGTTCTTGT 59.513 38.462 0.00 0.00 35.46 3.16
2846 3574 7.660208 GTCTAGGGAGAAAATGTTGTTCTTGTA 59.340 37.037 0.00 0.00 35.46 2.41
2847 3575 6.884280 AGGGAGAAAATGTTGTTCTTGTAG 57.116 37.500 0.00 0.00 35.46 2.74
2848 3576 5.241728 AGGGAGAAAATGTTGTTCTTGTAGC 59.758 40.000 0.00 0.00 35.46 3.58
2849 3577 5.009610 GGGAGAAAATGTTGTTCTTGTAGCA 59.990 40.000 0.00 0.00 35.46 3.49
2850 3578 5.915196 GGAGAAAATGTTGTTCTTGTAGCAC 59.085 40.000 0.00 0.00 35.46 4.40
2851 3579 5.510671 AGAAAATGTTGTTCTTGTAGCACG 58.489 37.500 0.00 0.00 31.10 5.34
2852 3580 2.969443 ATGTTGTTCTTGTAGCACGC 57.031 45.000 0.00 0.00 0.00 5.34
2853 3581 0.941542 TGTTGTTCTTGTAGCACGCC 59.058 50.000 0.00 0.00 0.00 5.68
2854 3582 0.941542 GTTGTTCTTGTAGCACGCCA 59.058 50.000 0.00 0.00 0.00 5.69
2855 3583 1.332375 GTTGTTCTTGTAGCACGCCAA 59.668 47.619 0.00 0.00 0.00 4.52
2856 3584 0.941542 TGTTCTTGTAGCACGCCAAC 59.058 50.000 0.00 0.00 0.00 3.77
2857 3585 0.237498 GTTCTTGTAGCACGCCAACC 59.763 55.000 0.00 0.00 0.00 3.77
2858 3586 0.107831 TTCTTGTAGCACGCCAACCT 59.892 50.000 0.00 0.00 0.00 3.50
2859 3587 0.320421 TCTTGTAGCACGCCAACCTC 60.320 55.000 0.00 0.00 0.00 3.85
2860 3588 0.602638 CTTGTAGCACGCCAACCTCA 60.603 55.000 0.00 0.00 0.00 3.86
2861 3589 0.179043 TTGTAGCACGCCAACCTCAA 60.179 50.000 0.00 0.00 0.00 3.02
2863 3591 1.165270 GTAGCACGCCAACCTCAATT 58.835 50.000 0.00 0.00 0.00 2.32
2864 3592 1.539827 GTAGCACGCCAACCTCAATTT 59.460 47.619 0.00 0.00 0.00 1.82
2865 3593 1.904287 AGCACGCCAACCTCAATTTA 58.096 45.000 0.00 0.00 0.00 1.40
2866 3594 1.812571 AGCACGCCAACCTCAATTTAG 59.187 47.619 0.00 0.00 0.00 1.85
2867 3595 1.810151 GCACGCCAACCTCAATTTAGA 59.190 47.619 0.00 0.00 0.00 2.10
2868 3596 2.414161 GCACGCCAACCTCAATTTAGAC 60.414 50.000 0.00 0.00 0.00 2.59
2878 3614 3.815401 CCTCAATTTAGACATTAGGCGGG 59.185 47.826 0.00 0.00 0.00 6.13
2881 3617 3.508845 ATTTAGACATTAGGCGGGCAT 57.491 42.857 3.78 0.00 0.00 4.40
2892 3628 0.461135 GGCGGGCATCATTTTGTCAT 59.539 50.000 0.00 0.00 0.00 3.06
2895 3631 2.098934 GCGGGCATCATTTTGTCATGTA 59.901 45.455 0.00 0.00 0.00 2.29
2910 3646 3.741344 GTCATGTATACCATCTTCCACGC 59.259 47.826 0.00 0.00 0.00 5.34
2928 5258 2.154854 GCTGACATAAGCGCCTATCA 57.845 50.000 2.29 0.00 32.56 2.15
2951 5281 8.017418 TCAAGTTATTTGATTTGGTTTCTGGT 57.983 30.769 0.00 0.00 40.82 4.00
2952 5282 8.141268 TCAAGTTATTTGATTTGGTTTCTGGTC 58.859 33.333 0.00 0.00 40.82 4.02
2955 5285 4.664150 TTTGATTTGGTTTCTGGTCCAC 57.336 40.909 0.00 0.00 33.12 4.02
2956 5286 3.304911 TGATTTGGTTTCTGGTCCACA 57.695 42.857 0.00 0.00 33.12 4.17
2958 5288 3.636300 TGATTTGGTTTCTGGTCCACAAG 59.364 43.478 0.00 0.00 33.12 3.16
2960 5290 2.638480 TGGTTTCTGGTCCACAAGAG 57.362 50.000 0.00 0.00 0.00 2.85
2963 5293 3.138283 TGGTTTCTGGTCCACAAGAGAAT 59.862 43.478 0.00 0.00 0.00 2.40
3015 5423 7.904977 CCTTTTTATGTCAATCATACACTCACG 59.095 37.037 0.00 0.00 38.55 4.35
3058 5466 0.318445 CTGCAAGCAGGCAAGAACAC 60.318 55.000 14.10 0.00 44.40 3.32
3062 5470 2.466846 CAAGCAGGCAAGAACACAAAG 58.533 47.619 0.00 0.00 0.00 2.77
3079 5490 5.095490 CACAAAGTGGAGAAAACACAAGAC 58.905 41.667 0.00 0.00 41.21 3.01
3082 5493 0.934496 TGGAGAAAACACAAGACGCG 59.066 50.000 3.53 3.53 0.00 6.01
3333 5768 7.246027 ACAGGGTCTAATTTCCCATTAAACTT 58.754 34.615 13.15 0.00 45.64 2.66
3586 6021 6.279882 ACAATCCACAATTTCACGAAACAAT 58.720 32.000 0.00 0.00 32.51 2.71
3817 6265 2.158813 GGTATGGCGAGGATCTTTGGAA 60.159 50.000 0.00 0.00 0.00 3.53
4120 6626 4.393371 GCCCACAAGAGTTCTATGAAGTTC 59.607 45.833 0.00 0.00 0.00 3.01
4486 7056 5.814705 CACTGAGATTGAGGGTAGATGAAAC 59.185 44.000 0.00 0.00 0.00 2.78
4533 7103 0.251341 AGCGCCTTTCCCAGTGAAAT 60.251 50.000 2.29 0.00 41.96 2.17
4573 7196 4.314121 TGTATTTCATTTTGTTGCCCTGC 58.686 39.130 0.00 0.00 0.00 4.85
4575 7198 2.529780 TTCATTTTGTTGCCCTGCTG 57.470 45.000 0.00 0.00 0.00 4.41
4582 7205 0.106569 TGTTGCCCTGCTGATATGGG 60.107 55.000 0.00 0.00 43.62 4.00
4642 7267 7.264221 TCAAACTGACAACATAACAGCAAAAT 58.736 30.769 0.00 0.00 35.38 1.82
4678 7303 3.994931 TTAGGTAGGGAGTTGCTTTCC 57.005 47.619 0.00 0.00 0.00 3.13
4679 7304 2.046280 AGGTAGGGAGTTGCTTTCCT 57.954 50.000 0.00 0.00 35.01 3.36
4681 7306 2.306219 AGGTAGGGAGTTGCTTTCCTTC 59.694 50.000 0.00 0.00 35.01 3.46
4682 7307 2.306219 GGTAGGGAGTTGCTTTCCTTCT 59.694 50.000 0.00 0.00 35.01 2.85
4683 7308 3.244946 GGTAGGGAGTTGCTTTCCTTCTT 60.245 47.826 0.00 0.00 35.01 2.52
4685 7310 4.936685 AGGGAGTTGCTTTCCTTCTTAT 57.063 40.909 2.53 0.00 35.01 1.73
4686 7311 5.262455 AGGGAGTTGCTTTCCTTCTTATT 57.738 39.130 2.53 0.00 35.01 1.40
4688 7313 6.418946 AGGGAGTTGCTTTCCTTCTTATTAG 58.581 40.000 2.53 0.00 35.01 1.73
4694 7355 9.301897 AGTTGCTTTCCTTCTTATTAGAAATGT 57.698 29.630 0.00 0.00 39.80 2.71
4718 7379 7.554835 TGTACATTTGTGTTTACCTTGAAGAGT 59.445 33.333 0.00 0.00 0.00 3.24
4782 7443 2.003301 GCTCGTCAAATCCTGGAAGTC 58.997 52.381 0.00 0.00 0.00 3.01
4802 7463 6.540438 AGTCGGATGTGGTTTCTAATCTTA 57.460 37.500 0.00 0.00 0.00 2.10
4844 7505 1.603842 CACCATGGCTGTGCTAGGA 59.396 57.895 13.04 0.00 0.00 2.94
4852 7513 1.433534 GCTGTGCTAGGACAGTTCAC 58.566 55.000 35.56 20.83 44.53 3.18
5006 7687 7.864686 TGCATATCTTTTATGGTCGATTTCTG 58.135 34.615 0.00 0.00 0.00 3.02
5095 7789 6.564125 CGCGAGTGACAATTCTATTTTATCCC 60.564 42.308 0.00 0.00 0.00 3.85
5179 7873 2.403259 TGTGTGTGTACTGATGAAGCG 58.597 47.619 0.00 0.00 0.00 4.68
5183 7877 4.025229 GTGTGTGTACTGATGAAGCGAAAA 60.025 41.667 0.00 0.00 0.00 2.29
5187 7881 7.119116 TGTGTGTACTGATGAAGCGAAAAATAT 59.881 33.333 0.00 0.00 0.00 1.28
5211 7905 8.997621 ATTTTATACTTTCTGCGACAGAGTTA 57.002 30.769 9.04 4.16 41.75 2.24
5260 7954 4.058817 GGACGAAATAGCACCAATCCTAG 58.941 47.826 0.00 0.00 0.00 3.02
5279 7973 3.885484 AGTTCAACAAATGAGCACTCG 57.115 42.857 0.00 0.00 41.36 4.18
5280 7974 2.031682 AGTTCAACAAATGAGCACTCGC 60.032 45.455 0.00 0.00 41.36 5.03
5283 7977 1.001487 CAACAAATGAGCACTCGCCAA 60.001 47.619 0.00 0.00 39.83 4.52
5284 7978 1.317613 ACAAATGAGCACTCGCCAAA 58.682 45.000 0.00 0.00 39.83 3.28
5287 7981 3.243839 ACAAATGAGCACTCGCCAAAAAT 60.244 39.130 0.00 0.00 39.83 1.82
5288 7982 2.642139 ATGAGCACTCGCCAAAAATG 57.358 45.000 0.00 0.00 39.83 2.32
5291 7985 0.242017 AGCACTCGCCAAAAATGAGC 59.758 50.000 0.00 0.00 39.83 4.26
5293 7987 1.689959 CACTCGCCAAAAATGAGCAC 58.310 50.000 0.00 0.00 32.98 4.40
5295 7989 1.537202 ACTCGCCAAAAATGAGCACTC 59.463 47.619 0.00 0.00 32.98 3.51
5296 7990 0.881118 TCGCCAAAAATGAGCACTCC 59.119 50.000 0.00 0.00 0.00 3.85
5297 7991 0.109132 CGCCAAAAATGAGCACTCCC 60.109 55.000 0.00 0.00 0.00 4.30
5298 7992 1.260544 GCCAAAAATGAGCACTCCCT 58.739 50.000 0.00 0.00 0.00 4.20
5299 7993 1.620323 GCCAAAAATGAGCACTCCCTT 59.380 47.619 0.00 0.00 0.00 3.95
5300 7994 2.611224 GCCAAAAATGAGCACTCCCTTG 60.611 50.000 0.00 0.00 0.00 3.61
5301 7995 2.892852 CCAAAAATGAGCACTCCCTTGA 59.107 45.455 0.00 0.00 0.00 3.02
5303 7997 4.301628 CAAAAATGAGCACTCCCTTGAAC 58.698 43.478 0.00 0.00 0.00 3.18
5305 7999 1.366319 ATGAGCACTCCCTTGAACCT 58.634 50.000 0.00 0.00 0.00 3.50
5308 8097 1.376037 GCACTCCCTTGAACCTCCG 60.376 63.158 0.00 0.00 0.00 4.63
5315 8104 2.920912 TTGAACCTCCGCCGGTCT 60.921 61.111 1.63 0.00 35.89 3.85
5330 8119 1.740380 CGGTCTGATGGTCCATGTGTC 60.740 57.143 9.76 0.00 0.00 3.67
5337 8126 5.248248 TCTGATGGTCCATGTGTCTTCTTAA 59.752 40.000 9.76 0.00 0.00 1.85
5338 8127 5.875224 TGATGGTCCATGTGTCTTCTTAAA 58.125 37.500 9.76 0.00 0.00 1.52
5339 8128 5.939883 TGATGGTCCATGTGTCTTCTTAAAG 59.060 40.000 9.76 0.00 0.00 1.85
5340 8129 5.304686 TGGTCCATGTGTCTTCTTAAAGT 57.695 39.130 0.00 0.00 33.95 2.66
5341 8130 6.428083 TGGTCCATGTGTCTTCTTAAAGTA 57.572 37.500 0.00 0.00 33.95 2.24
5342 8131 6.228258 TGGTCCATGTGTCTTCTTAAAGTAC 58.772 40.000 0.00 0.00 33.95 2.73
5343 8132 6.183361 TGGTCCATGTGTCTTCTTAAAGTACA 60.183 38.462 0.00 0.00 36.16 2.90
5347 8136 8.086522 TCCATGTGTCTTCTTAAAGTACAGTAC 58.913 37.037 2.05 2.05 35.64 2.73
5370 8159 6.484288 ACATTATTGTTTCATCAGGAGGTGA 58.516 36.000 0.00 0.00 33.65 4.02
5377 8166 1.839994 TCATCAGGAGGTGACATTCCC 59.160 52.381 5.58 0.00 38.28 3.97
5393 8227 2.442236 TCCCTCGACCCTAATACGTT 57.558 50.000 0.00 0.00 0.00 3.99
5429 8263 8.854979 TTGTTAACATTCACTTTTCATGACTG 57.145 30.769 9.56 0.00 34.02 3.51
5477 8311 1.603739 GAGGGGGTTGTGGTTCAGC 60.604 63.158 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 6.542852 ACAACATAATTCGTGTAAGTCATGC 58.457 36.000 0.00 0.00 33.44 4.06
46 47 7.170828 GCATCCATCTACAACATAATTCGTGTA 59.829 37.037 0.00 0.00 0.00 2.90
100 101 4.852138 CACAACTTGTGGAAGAACATGAG 58.148 43.478 13.36 0.00 44.27 2.90
142 143 8.704668 TGGTGTTGAAGAGCATATAGAAAGATA 58.295 33.333 0.00 0.00 0.00 1.98
235 237 4.450082 GGGTTTCCCACATCATTTGTAC 57.550 45.455 0.00 0.00 44.65 2.90
274 276 2.689983 GGCCATTTTAGACATGGTCAGG 59.310 50.000 0.00 0.00 44.66 3.86
352 354 1.976478 GCACACACAACGACAGCACA 61.976 55.000 0.00 0.00 0.00 4.57
374 379 3.882288 GGCAAAATTGTTGGTGATTGGTT 59.118 39.130 0.00 0.00 0.00 3.67
380 385 3.640498 TCATCTGGCAAAATTGTTGGTGA 59.360 39.130 0.00 0.00 0.00 4.02
388 393 5.818857 GCACCAATTATCATCTGGCAAAATT 59.181 36.000 0.00 0.00 33.19 1.82
395 400 3.251729 CGAAGGCACCAATTATCATCTGG 59.748 47.826 0.00 0.00 36.24 3.86
527 532 5.276820 CGTGCAATTGGAAGAAAAGGAAAAC 60.277 40.000 7.07 0.00 0.00 2.43
620 629 2.028763 CACGGTATGAATCCAAACGTCG 59.971 50.000 0.00 0.00 31.16 5.12
673 682 1.006832 CTTAGAATGGCAACGACCGG 58.993 55.000 0.00 0.00 42.51 5.28
676 685 1.659098 CGACCTTAGAATGGCAACGAC 59.341 52.381 0.00 0.00 42.51 4.34
693 702 2.431539 CACGTCAGTGGCTTACGAC 58.568 57.895 8.86 5.65 44.34 4.34
703 712 0.464036 TTTCAGCTGTCCACGTCAGT 59.536 50.000 14.67 0.00 35.60 3.41
782 796 6.078456 TGTCAGATTGATAATGAAAGGGGT 57.922 37.500 0.00 0.00 0.00 4.95
809 824 0.994247 TTGGTGACCAGATCCAGCAT 59.006 50.000 3.77 0.00 39.98 3.79
819 834 5.867903 ATTTCTTGACAAATTGGTGACCA 57.132 34.783 0.00 0.00 0.00 4.02
854 869 3.359654 CTTGGTCTTTACACGCAACAAC 58.640 45.455 0.00 0.00 0.00 3.32
862 877 3.309954 GGATCGATGCTTGGTCTTTACAC 59.690 47.826 9.99 0.00 0.00 2.90
899 1451 4.009002 TGCTAATGCTGACATGCTGTTAA 58.991 39.130 0.00 0.00 40.48 2.01
917 1471 5.163343 ACCTTGTTCAGTACTTCTGTTGCTA 60.163 40.000 0.00 0.00 43.97 3.49
981 1545 3.588955 CATGATCGATCAGGCCGAAATA 58.411 45.455 30.11 5.77 40.64 1.40
1011 1576 0.457509 CAGTGTAGCAGGTGAGAGCG 60.458 60.000 0.00 0.00 35.48 5.03
1110 1683 2.057503 CGTCATCGGAGATGATGGTC 57.942 55.000 19.23 6.39 44.68 4.02
1251 1844 1.151777 ACGAAGTGCTGTTGGTGACG 61.152 55.000 0.00 0.00 42.51 4.35
1269 1862 2.505118 GAGAGTGTCGGCGCAGAC 60.505 66.667 30.18 30.18 41.30 3.51
1678 2294 0.405585 ACCTGCTGGTATTGGTGCTT 59.594 50.000 14.47 0.00 46.43 3.91
1711 2336 1.344438 GGCCATGTAGATGATGACGGA 59.656 52.381 0.00 0.00 0.00 4.69
1794 2419 3.381908 CAGAGTAGGTCACCACATACCTC 59.618 52.174 0.00 0.00 42.60 3.85
1848 2473 3.324846 CGAGGATAACCCATGATGAGGAA 59.675 47.826 6.90 0.00 37.41 3.36
1992 2626 4.100084 CCAGCCGCCCACTCATCA 62.100 66.667 0.00 0.00 0.00 3.07
2088 2722 0.250467 ACATGAACTTGTCTGGCGCT 60.250 50.000 7.64 0.00 0.00 5.92
2179 2813 2.176546 CAGGTTGGCGAATGCGTG 59.823 61.111 0.00 0.00 44.10 5.34
2198 2832 2.219875 CCTCCAGACCTGCCACTGT 61.220 63.158 0.00 0.00 32.93 3.55
2296 2935 1.270839 GCCTGCAAGCCGGAGATATAA 60.271 52.381 5.05 0.00 34.28 0.98
2329 2968 2.158325 AGGGAGAAAATTTGGCACCAGA 60.158 45.455 9.06 0.00 0.00 3.86
2393 3065 6.633856 ACCATAAAAAGGCAAGTGAATGATC 58.366 36.000 0.00 0.00 0.00 2.92
2402 3074 5.931146 TGCACAAATACCATAAAAAGGCAAG 59.069 36.000 0.00 0.00 0.00 4.01
2489 3168 1.089920 GCATAGGACTGCCACAACAG 58.910 55.000 0.00 0.00 43.59 3.16
2557 3261 2.415893 GGGCCGAATGAACTTTCACATG 60.416 50.000 0.00 0.00 40.49 3.21
2568 3272 3.709653 ACTTATAGTTCAGGGCCGAATGA 59.290 43.478 12.63 2.19 0.00 2.57
2573 3277 3.606687 ACAAACTTATAGTTCAGGGCCG 58.393 45.455 0.00 0.00 37.47 6.13
2658 3383 4.957296 AGTCACACTCGAAACCACTTAAT 58.043 39.130 0.00 0.00 0.00 1.40
2660 3385 4.395959 AAGTCACACTCGAAACCACTTA 57.604 40.909 0.00 0.00 0.00 2.24
2689 3417 5.220777 CCCATTGTGGTTATACGATTGACAC 60.221 44.000 0.00 0.00 35.17 3.67
2696 3424 3.351794 TTGCCCATTGTGGTTATACGA 57.648 42.857 0.00 0.00 35.17 3.43
2697 3425 3.882888 AGATTGCCCATTGTGGTTATACG 59.117 43.478 0.00 0.00 35.17 3.06
2698 3426 4.037923 CCAGATTGCCCATTGTGGTTATAC 59.962 45.833 0.00 0.00 35.17 1.47
2705 3433 5.540400 ATTATTCCAGATTGCCCATTGTG 57.460 39.130 0.00 0.00 0.00 3.33
2706 3434 5.244626 GCTATTATTCCAGATTGCCCATTGT 59.755 40.000 0.00 0.00 0.00 2.71
2711 3439 3.686726 CGAGCTATTATTCCAGATTGCCC 59.313 47.826 0.00 0.00 0.00 5.36
2717 3445 4.588951 ACCATGACGAGCTATTATTCCAGA 59.411 41.667 0.00 0.00 0.00 3.86
2721 3449 9.803315 TCATATTACCATGACGAGCTATTATTC 57.197 33.333 0.00 0.00 29.93 1.75
2727 3455 6.264518 TGAGTTCATATTACCATGACGAGCTA 59.735 38.462 0.00 0.00 34.69 3.32
2729 3457 5.289595 TGAGTTCATATTACCATGACGAGC 58.710 41.667 0.00 0.00 34.69 5.03
2730 3458 6.422100 CCTTGAGTTCATATTACCATGACGAG 59.578 42.308 0.00 0.00 34.69 4.18
2731 3459 6.097696 TCCTTGAGTTCATATTACCATGACGA 59.902 38.462 0.00 0.00 34.69 4.20
2732 3460 6.280643 TCCTTGAGTTCATATTACCATGACG 58.719 40.000 0.00 0.00 34.69 4.35
2734 3462 9.159254 AGTATCCTTGAGTTCATATTACCATGA 57.841 33.333 0.00 0.00 33.10 3.07
2735 3463 9.784531 AAGTATCCTTGAGTTCATATTACCATG 57.215 33.333 0.00 0.00 0.00 3.66
2754 3482 8.755018 CATTTGAAGTTTTGAACACAAGTATCC 58.245 33.333 0.00 0.00 33.87 2.59
2755 3483 9.301153 ACATTTGAAGTTTTGAACACAAGTATC 57.699 29.630 0.00 0.00 33.87 2.24
2758 3486 7.961325 AACATTTGAAGTTTTGAACACAAGT 57.039 28.000 0.00 0.00 33.87 3.16
2759 3487 7.268872 GCAAACATTTGAAGTTTTGAACACAAG 59.731 33.333 8.54 0.00 40.55 3.16
2762 3490 6.830736 AGCAAACATTTGAAGTTTTGAACAC 58.169 32.000 8.54 0.00 40.55 3.32
2763 3491 7.296660 CAAGCAAACATTTGAAGTTTTGAACA 58.703 30.769 8.54 0.00 40.55 3.18
2764 3492 6.742264 CCAAGCAAACATTTGAAGTTTTGAAC 59.258 34.615 8.54 0.00 40.55 3.18
2766 3494 5.353678 CCCAAGCAAACATTTGAAGTTTTGA 59.646 36.000 8.54 0.00 40.55 2.69
2767 3495 5.448904 CCCCAAGCAAACATTTGAAGTTTTG 60.449 40.000 8.54 4.48 40.55 2.44
2768 3496 4.639755 CCCCAAGCAAACATTTGAAGTTTT 59.360 37.500 8.54 0.00 40.55 2.43
2769 3497 4.080638 TCCCCAAGCAAACATTTGAAGTTT 60.081 37.500 8.54 0.00 40.55 2.66
2770 3498 3.454082 TCCCCAAGCAAACATTTGAAGTT 59.546 39.130 8.54 0.00 40.55 2.66
2771 3499 3.037549 TCCCCAAGCAAACATTTGAAGT 58.962 40.909 8.54 0.00 40.55 3.01
2772 3500 3.321682 TCTCCCCAAGCAAACATTTGAAG 59.678 43.478 8.54 0.00 40.55 3.02
2773 3501 3.303938 TCTCCCCAAGCAAACATTTGAA 58.696 40.909 8.54 0.00 40.55 2.69
2774 3502 2.892852 CTCTCCCCAAGCAAACATTTGA 59.107 45.455 8.54 0.00 40.55 2.69
2775 3503 2.028748 CCTCTCCCCAAGCAAACATTTG 60.029 50.000 0.00 0.00 41.03 2.32
2776 3504 2.158325 TCCTCTCCCCAAGCAAACATTT 60.158 45.455 0.00 0.00 0.00 2.32
2777 3505 1.428912 TCCTCTCCCCAAGCAAACATT 59.571 47.619 0.00 0.00 0.00 2.71
2778 3506 1.075601 TCCTCTCCCCAAGCAAACAT 58.924 50.000 0.00 0.00 0.00 2.71
2779 3507 1.075601 ATCCTCTCCCCAAGCAAACA 58.924 50.000 0.00 0.00 0.00 2.83
2780 3508 1.467920 CATCCTCTCCCCAAGCAAAC 58.532 55.000 0.00 0.00 0.00 2.93
2781 3509 0.332632 CCATCCTCTCCCCAAGCAAA 59.667 55.000 0.00 0.00 0.00 3.68
2782 3510 2.001803 CCATCCTCTCCCCAAGCAA 58.998 57.895 0.00 0.00 0.00 3.91
2783 3511 2.683465 GCCATCCTCTCCCCAAGCA 61.683 63.158 0.00 0.00 0.00 3.91
2784 3512 2.004408 ATGCCATCCTCTCCCCAAGC 62.004 60.000 0.00 0.00 0.00 4.01
2785 3513 1.438469 TATGCCATCCTCTCCCCAAG 58.562 55.000 0.00 0.00 0.00 3.61
2786 3514 1.905839 TTATGCCATCCTCTCCCCAA 58.094 50.000 0.00 0.00 0.00 4.12
2787 3515 1.494721 GTTTATGCCATCCTCTCCCCA 59.505 52.381 0.00 0.00 0.00 4.96
2788 3516 1.777272 AGTTTATGCCATCCTCTCCCC 59.223 52.381 0.00 0.00 0.00 4.81
2789 3517 3.904339 TCTAGTTTATGCCATCCTCTCCC 59.096 47.826 0.00 0.00 0.00 4.30
2790 3518 4.835615 TCTCTAGTTTATGCCATCCTCTCC 59.164 45.833 0.00 0.00 0.00 3.71
2791 3519 5.047377 CCTCTCTAGTTTATGCCATCCTCTC 60.047 48.000 0.00 0.00 0.00 3.20
2792 3520 4.837860 CCTCTCTAGTTTATGCCATCCTCT 59.162 45.833 0.00 0.00 0.00 3.69
2793 3521 4.835615 TCCTCTCTAGTTTATGCCATCCTC 59.164 45.833 0.00 0.00 0.00 3.71
2794 3522 4.820775 TCCTCTCTAGTTTATGCCATCCT 58.179 43.478 0.00 0.00 0.00 3.24
2795 3523 4.020662 CCTCCTCTCTAGTTTATGCCATCC 60.021 50.000 0.00 0.00 0.00 3.51
2796 3524 4.591072 ACCTCCTCTCTAGTTTATGCCATC 59.409 45.833 0.00 0.00 0.00 3.51
2797 3525 4.346418 CACCTCCTCTCTAGTTTATGCCAT 59.654 45.833 0.00 0.00 0.00 4.40
2798 3526 3.706594 CACCTCCTCTCTAGTTTATGCCA 59.293 47.826 0.00 0.00 0.00 4.92
2799 3527 3.707102 ACACCTCCTCTCTAGTTTATGCC 59.293 47.826 0.00 0.00 0.00 4.40
2800 3528 4.647399 AGACACCTCCTCTCTAGTTTATGC 59.353 45.833 0.00 0.00 0.00 3.14
2801 3529 6.488683 CCTAGACACCTCCTCTCTAGTTTATG 59.511 46.154 0.00 0.00 34.16 1.90
2802 3530 6.411086 CCCTAGACACCTCCTCTCTAGTTTAT 60.411 46.154 0.00 0.00 34.16 1.40
2803 3531 5.104024 CCCTAGACACCTCCTCTCTAGTTTA 60.104 48.000 0.00 0.00 34.16 2.01
2804 3532 4.325501 CCCTAGACACCTCCTCTCTAGTTT 60.326 50.000 0.00 0.00 34.16 2.66
2805 3533 3.203487 CCCTAGACACCTCCTCTCTAGTT 59.797 52.174 0.00 0.00 34.16 2.24
2809 3537 1.850345 CTCCCTAGACACCTCCTCTCT 59.150 57.143 0.00 0.00 0.00 3.10
2819 3547 6.187727 AGAACAACATTTTCTCCCTAGACA 57.812 37.500 0.00 0.00 0.00 3.41
2821 3549 6.601332 ACAAGAACAACATTTTCTCCCTAGA 58.399 36.000 0.00 0.00 31.87 2.43
2837 3565 0.941542 GTTGGCGTGCTACAAGAACA 59.058 50.000 0.00 0.00 0.00 3.18
2844 3572 1.165270 AATTGAGGTTGGCGTGCTAC 58.835 50.000 0.00 0.00 0.00 3.58
2845 3573 1.904287 AAATTGAGGTTGGCGTGCTA 58.096 45.000 0.00 0.00 0.00 3.49
2846 3574 1.812571 CTAAATTGAGGTTGGCGTGCT 59.187 47.619 0.00 0.00 0.00 4.40
2847 3575 1.810151 TCTAAATTGAGGTTGGCGTGC 59.190 47.619 0.00 0.00 0.00 5.34
2848 3576 2.811431 TGTCTAAATTGAGGTTGGCGTG 59.189 45.455 0.00 0.00 0.00 5.34
2849 3577 3.134574 TGTCTAAATTGAGGTTGGCGT 57.865 42.857 0.00 0.00 0.00 5.68
2850 3578 4.701956 AATGTCTAAATTGAGGTTGGCG 57.298 40.909 0.00 0.00 0.00 5.69
2851 3579 5.450550 GCCTAATGTCTAAATTGAGGTTGGC 60.451 44.000 0.00 0.00 0.00 4.52
2852 3580 5.220854 CGCCTAATGTCTAAATTGAGGTTGG 60.221 44.000 0.00 0.00 0.00 3.77
2853 3581 5.220854 CCGCCTAATGTCTAAATTGAGGTTG 60.221 44.000 0.00 0.00 0.00 3.77
2854 3582 4.881850 CCGCCTAATGTCTAAATTGAGGTT 59.118 41.667 0.00 0.00 0.00 3.50
2855 3583 4.451900 CCGCCTAATGTCTAAATTGAGGT 58.548 43.478 0.00 0.00 0.00 3.85
2856 3584 3.815401 CCCGCCTAATGTCTAAATTGAGG 59.185 47.826 0.00 0.00 0.00 3.86
2857 3585 3.251004 GCCCGCCTAATGTCTAAATTGAG 59.749 47.826 0.00 0.00 0.00 3.02
2858 3586 3.211045 GCCCGCCTAATGTCTAAATTGA 58.789 45.455 0.00 0.00 0.00 2.57
2859 3587 2.948979 TGCCCGCCTAATGTCTAAATTG 59.051 45.455 0.00 0.00 0.00 2.32
2860 3588 3.290948 TGCCCGCCTAATGTCTAAATT 57.709 42.857 0.00 0.00 0.00 1.82
2861 3589 3.181445 TGATGCCCGCCTAATGTCTAAAT 60.181 43.478 0.00 0.00 0.00 1.40
2863 3591 1.765904 TGATGCCCGCCTAATGTCTAA 59.234 47.619 0.00 0.00 0.00 2.10
2864 3592 1.419381 TGATGCCCGCCTAATGTCTA 58.581 50.000 0.00 0.00 0.00 2.59
2865 3593 0.767375 ATGATGCCCGCCTAATGTCT 59.233 50.000 0.00 0.00 0.00 3.41
2866 3594 1.609208 AATGATGCCCGCCTAATGTC 58.391 50.000 0.00 0.00 0.00 3.06
2867 3595 2.071778 AAATGATGCCCGCCTAATGT 57.928 45.000 0.00 0.00 0.00 2.71
2868 3596 2.101249 ACAAAATGATGCCCGCCTAATG 59.899 45.455 0.00 0.00 0.00 1.90
2878 3614 7.879070 AGATGGTATACATGACAAAATGATGC 58.121 34.615 5.01 0.00 40.72 3.91
2881 3617 8.052141 TGGAAGATGGTATACATGACAAAATGA 58.948 33.333 5.01 0.00 40.72 2.57
2892 3628 3.028130 TCAGCGTGGAAGATGGTATACA 58.972 45.455 5.01 0.00 0.00 2.29
2895 3631 1.831106 TGTCAGCGTGGAAGATGGTAT 59.169 47.619 0.00 0.00 0.00 2.73
2910 3646 3.722147 ACTTGATAGGCGCTTATGTCAG 58.278 45.455 17.60 11.39 0.00 3.51
2927 5257 7.384932 GGACCAGAAACCAAATCAAATAACTTG 59.615 37.037 0.00 0.00 36.25 3.16
2928 5258 7.070571 TGGACCAGAAACCAAATCAAATAACTT 59.929 33.333 0.00 0.00 32.93 2.66
2938 5268 3.891366 CTCTTGTGGACCAGAAACCAAAT 59.109 43.478 5.46 0.00 37.94 2.32
2947 5277 4.013267 AGAACATTCTCTTGTGGACCAG 57.987 45.455 0.00 0.00 29.94 4.00
2949 5279 4.932200 CAGTAGAACATTCTCTTGTGGACC 59.068 45.833 0.00 0.00 38.70 4.46
2950 5280 4.932200 CCAGTAGAACATTCTCTTGTGGAC 59.068 45.833 0.00 0.00 38.70 4.02
2951 5281 4.593206 ACCAGTAGAACATTCTCTTGTGGA 59.407 41.667 14.05 0.00 38.70 4.02
2952 5282 4.692625 CACCAGTAGAACATTCTCTTGTGG 59.307 45.833 0.00 4.14 38.70 4.17
2955 5285 7.678947 ATTTCACCAGTAGAACATTCTCTTG 57.321 36.000 0.00 0.00 38.70 3.02
3039 5447 0.318445 GTGTTCTTGCCTGCTTGCAG 60.318 55.000 15.02 15.02 43.21 4.41
3058 5466 4.342772 CGTCTTGTGTTTTCTCCACTTTG 58.657 43.478 0.00 0.00 33.92 2.77
3062 5470 1.332904 CGCGTCTTGTGTTTTCTCCAC 60.333 52.381 0.00 0.00 0.00 4.02
3079 5490 5.900339 ACTTATACCATCAAATGTACGCG 57.100 39.130 3.53 3.53 0.00 6.01
3116 5527 1.363246 GTGGAGAGTTTCCTTCCCCT 58.637 55.000 0.77 0.00 46.92 4.79
3129 5540 5.757988 TGGAAATTCATGATCATGTGGAGA 58.242 37.500 30.01 12.07 39.72 3.71
3164 5576 5.862924 TTGTTGCTAGAGAAATTTCCTCG 57.137 39.130 14.61 8.70 35.88 4.63
3308 5736 6.800890 AGTTTAATGGGAAATTAGACCCTGT 58.199 36.000 13.83 6.66 45.74 4.00
3333 5768 7.874252 TCTTGCCCACCTAATAATACCTAAAA 58.126 34.615 0.00 0.00 0.00 1.52
3340 5775 5.592688 GCAACTTCTTGCCCACCTAATAATA 59.407 40.000 0.00 0.00 46.27 0.98
3586 6021 9.482627 AATAAACGTGAATTAATTTGCTTTGGA 57.517 25.926 1.43 0.00 0.00 3.53
3817 6265 4.559153 GTGCTTGCATCTTGTTGGTTATT 58.441 39.130 0.00 0.00 0.00 1.40
4642 7267 7.570982 TCCCTACCTAATTAATCCATTGAGTCA 59.429 37.037 0.00 0.00 0.00 3.41
4688 7313 9.522804 TTCAAGGTAAACACAAATGTACATTTC 57.477 29.630 27.12 15.63 38.45 2.17
4694 7355 7.771361 TCACTCTTCAAGGTAAACACAAATGTA 59.229 33.333 0.00 0.00 38.45 2.29
4718 7379 3.263489 TGAACAAGTACGTGGGTTTCA 57.737 42.857 13.47 10.67 0.00 2.69
4782 7443 8.094548 TGGATATAAGATTAGAAACCACATCCG 58.905 37.037 0.00 0.00 31.67 4.18
4802 7463 3.131396 GTCGTGCGGAAAAGATGGATAT 58.869 45.455 0.00 0.00 0.00 1.63
4832 7493 0.321671 TGAACTGTCCTAGCACAGCC 59.678 55.000 13.96 6.77 46.81 4.85
4837 7498 2.703536 TCCTTTGTGAACTGTCCTAGCA 59.296 45.455 0.00 0.00 0.00 3.49
4844 7505 3.281727 TCTTGCTCCTTTGTGAACTGT 57.718 42.857 0.00 0.00 0.00 3.55
4873 7534 7.151308 TGAAAATGCCGACATTAATCAGTTTT 58.849 30.769 0.00 0.00 45.90 2.43
4912 7573 4.489795 GTGCTGATGCGCGTCGTG 62.490 66.667 23.73 19.11 43.34 4.35
4941 7621 5.505181 AACATCAGTGAAGGGACTAACAT 57.495 39.130 0.00 0.00 38.49 2.71
4942 7622 4.974645 AACATCAGTGAAGGGACTAACA 57.025 40.909 0.00 0.00 38.49 2.41
4988 7669 8.928270 AGTAGTACAGAAATCGACCATAAAAG 57.072 34.615 2.52 0.00 0.00 2.27
4993 7674 9.886132 AAATTTAGTAGTACAGAAATCGACCAT 57.114 29.630 11.50 0.00 0.00 3.55
4994 7675 9.362539 GAAATTTAGTAGTACAGAAATCGACCA 57.637 33.333 11.50 0.00 0.00 4.02
5084 7778 9.010029 ACATACAAATTAGCGGGGATAAAATAG 57.990 33.333 0.00 0.00 0.00 1.73
5090 7784 5.012251 TGCTACATACAAATTAGCGGGGATA 59.988 40.000 0.00 0.00 41.02 2.59
5095 7789 5.922739 TCATGCTACATACAAATTAGCGG 57.077 39.130 0.00 0.00 41.02 5.52
5183 7877 9.601217 ACTCTGTCGCAGAAAGTATAAAATATT 57.399 29.630 10.12 0.00 43.75 1.28
5187 7881 8.086522 ACTAACTCTGTCGCAGAAAGTATAAAA 58.913 33.333 10.12 0.00 43.75 1.52
5191 7885 5.646577 ACTAACTCTGTCGCAGAAAGTAT 57.353 39.130 10.12 0.40 43.75 2.12
5200 7894 6.530534 TGATTTAGCTTAACTAACTCTGTCGC 59.469 38.462 0.00 0.00 40.63 5.19
5211 7905 7.492352 AGTTGTTCGTTGATTTAGCTTAACT 57.508 32.000 0.00 0.00 0.00 2.24
5260 7954 2.310577 GCGAGTGCTCATTTGTTGAAC 58.689 47.619 0.00 0.00 38.39 3.18
5279 7973 1.260544 AGGGAGTGCTCATTTTTGGC 58.739 50.000 1.41 0.00 0.00 4.52
5280 7974 2.892852 TCAAGGGAGTGCTCATTTTTGG 59.107 45.455 1.41 0.00 0.00 3.28
5283 7977 2.893489 GGTTCAAGGGAGTGCTCATTTT 59.107 45.455 1.41 0.00 0.00 1.82
5284 7978 2.108952 AGGTTCAAGGGAGTGCTCATTT 59.891 45.455 1.41 0.00 0.00 2.32
5287 7981 0.687354 GAGGTTCAAGGGAGTGCTCA 59.313 55.000 1.41 0.00 0.00 4.26
5288 7982 0.035915 GGAGGTTCAAGGGAGTGCTC 60.036 60.000 0.00 0.00 0.00 4.26
5291 7985 1.376037 GCGGAGGTTCAAGGGAGTG 60.376 63.158 0.00 0.00 0.00 3.51
5293 7987 2.269241 GGCGGAGGTTCAAGGGAG 59.731 66.667 0.00 0.00 0.00 4.30
5295 7989 4.778143 CCGGCGGAGGTTCAAGGG 62.778 72.222 24.41 0.00 0.00 3.95
5296 7990 3.952628 GACCGGCGGAGGTTCAAGG 62.953 68.421 35.78 1.17 46.09 3.61
5297 7991 2.434359 GACCGGCGGAGGTTCAAG 60.434 66.667 35.78 2.05 46.09 3.02
5298 7992 2.920912 AGACCGGCGGAGGTTCAA 60.921 61.111 35.78 0.00 46.09 2.69
5299 7993 3.691342 CAGACCGGCGGAGGTTCA 61.691 66.667 35.78 0.00 46.09 3.18
5300 7994 2.722201 ATCAGACCGGCGGAGGTTC 61.722 63.158 35.78 19.95 46.09 3.62
5301 7995 2.683933 ATCAGACCGGCGGAGGTT 60.684 61.111 35.78 10.44 46.09 3.50
5303 7997 4.227134 CCATCAGACCGGCGGAGG 62.227 72.222 35.78 20.62 37.30 4.30
5305 7999 3.458163 GACCATCAGACCGGCGGA 61.458 66.667 35.78 10.94 0.00 5.54
5308 8097 1.524621 CATGGACCATCAGACCGGC 60.525 63.158 3.21 0.00 0.00 6.13
5315 8104 5.497464 TTAAGAAGACACATGGACCATCA 57.503 39.130 3.21 0.00 0.00 3.07
5338 8127 9.383519 CCTGATGAAACAATAATGTACTGTACT 57.616 33.333 17.98 2.56 39.40 2.73
5339 8128 9.378551 TCCTGATGAAACAATAATGTACTGTAC 57.621 33.333 10.98 10.98 39.40 2.90
5340 8129 9.599866 CTCCTGATGAAACAATAATGTACTGTA 57.400 33.333 0.00 0.00 39.40 2.74
5341 8130 7.554118 CCTCCTGATGAAACAATAATGTACTGT 59.446 37.037 0.00 0.00 39.40 3.55
5342 8131 7.554118 ACCTCCTGATGAAACAATAATGTACTG 59.446 37.037 0.00 0.00 39.40 2.74
5343 8132 7.554118 CACCTCCTGATGAAACAATAATGTACT 59.446 37.037 0.00 0.00 39.40 2.73
5347 8136 6.375174 TGTCACCTCCTGATGAAACAATAATG 59.625 38.462 0.00 0.00 0.00 1.90
5370 8159 2.626743 CGTATTAGGGTCGAGGGAATGT 59.373 50.000 0.00 0.00 0.00 2.71
5377 8166 4.092383 CACCAAAAACGTATTAGGGTCGAG 59.908 45.833 0.00 0.00 0.00 4.04
5393 8227 9.442047 AAGTGAATGTTAACAAAATCACCAAAA 57.558 25.926 29.55 8.68 38.06 2.44
5424 8258 3.766151 CGCTTACGGAAGATTACAGTCA 58.234 45.455 12.84 0.00 34.25 3.41
5429 8263 2.281762 CACAGCGCTTACGGAAGATTAC 59.718 50.000 12.84 0.00 40.57 1.89
5453 8287 4.344865 CACAACCCCCTCCCCACG 62.345 72.222 0.00 0.00 0.00 4.94
5457 8291 2.426305 CTGAACCACAACCCCCTCCC 62.426 65.000 0.00 0.00 0.00 4.30
5460 8294 2.520968 GCTGAACCACAACCCCCT 59.479 61.111 0.00 0.00 0.00 4.79
5463 8297 1.822186 ACACGCTGAACCACAACCC 60.822 57.895 0.00 0.00 0.00 4.11
5464 8298 1.355210 CACACGCTGAACCACAACC 59.645 57.895 0.00 0.00 0.00 3.77
5466 8300 3.106552 GCACACGCTGAACCACAA 58.893 55.556 0.00 0.00 34.30 3.33


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

AutoCloner maintained by Alex Coulton.