Multiple sequence alignment - TraesCS1A01G216100

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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 TraesCS1A01G216100 chr1A 100.000 3020 0 0 1 3020 382099507 382102526 0.000000e+00 5578
1 TraesCS1A01G216100 chr1A 91.812 916 47 18 1 912 462343003 462343894 0.000000e+00 1251
2 TraesCS1A01G216100 chr1A 90.671 686 50 8 737 1413 462343845 462344525 0.000000e+00 900
3 TraesCS1A01G216100 chr1A 95.382 498 15 4 2523 3017 382088580 382089072 0.000000e+00 785
4 TraesCS1A01G216100 chr7A 86.369 2597 261 44 1 2524 606192642 606195218 0.000000e+00 2748
5 TraesCS1A01G216100 chr6B 97.543 1465 27 4 756 2213 673016361 673017823 0.000000e+00 2497
6 TraesCS1A01G216100 chr6B 85.489 1523 168 29 1039 2524 690878403 690876897 0.000000e+00 1539
7 TraesCS1A01G216100 chr6B 88.947 380 30 5 2137 2509 662108357 662107983 2.740000e-125 459
8 TraesCS1A01G216100 chr2A 87.272 1862 172 29 1 1815 572843875 572845718 0.000000e+00 2065
9 TraesCS1A01G216100 chr2A 85.942 1821 212 32 351 2153 173515062 173513268 0.000000e+00 1905
10 TraesCS1A01G216100 chr2A 89.038 894 81 13 1 885 779783196 779784081 0.000000e+00 1092
11 TraesCS1A01G216100 chr2A 88.702 894 85 12 1 885 779739689 779740575 0.000000e+00 1077
12 TraesCS1A01G216100 chr2A 83.055 419 61 10 2604 3017 78791966 78792379 3.680000e-99 372
13 TraesCS1A01G216100 chr6A 85.242 1816 226 29 352 2153 511525553 511527340 0.000000e+00 1831
14 TraesCS1A01G216100 chr6A 92.997 357 25 0 2162 2518 585576889 585576533 3.450000e-144 521
15 TraesCS1A01G216100 chr6A 81.742 356 62 3 2659 3013 209509614 209509967 8.190000e-76 294
16 TraesCS1A01G216100 chr3D 85.747 1761 191 36 804 2526 384008872 384010610 0.000000e+00 1807
17 TraesCS1A01G216100 chr3D 94.437 719 40 0 1 719 384008121 384008839 0.000000e+00 1107
18 TraesCS1A01G216100 chr3D 93.204 412 19 4 2126 2529 91381611 91381201 5.570000e-167 597
19 TraesCS1A01G216100 chr1D 94.652 1122 52 3 1414 2528 327013902 327015022 0.000000e+00 1733
20 TraesCS1A01G216100 chr1D 93.803 468 25 2 2553 3020 459701413 459701876 0.000000e+00 701
21 TraesCS1A01G216100 chr4B 94.013 1119 57 4 1414 2526 11609814 11610928 0.000000e+00 1687
22 TraesCS1A01G216100 chr4B 89.352 911 83 12 1 904 97890593 97889690 0.000000e+00 1133
23 TraesCS1A01G216100 chr4B 88.364 911 92 12 1 904 97793217 97792314 0.000000e+00 1083
24 TraesCS1A01G216100 chr4B 89.937 795 72 2 597 1383 11609021 11609815 0.000000e+00 1018
25 TraesCS1A01G216100 chr5B 93.450 1084 48 8 1416 2491 524503126 524504194 0.000000e+00 1587
26 TraesCS1A01G216100 chr5B 91.003 678 53 4 742 1413 524502376 524503051 0.000000e+00 907
27 TraesCS1A01G216100 chr7B 91.371 1043 82 6 1418 2454 88977538 88976498 0.000000e+00 1421
28 TraesCS1A01G216100 chr7B 85.777 682 80 9 744 1413 88978291 88977615 0.000000e+00 706
29 TraesCS1A01G216100 chr4D 87.500 1136 114 15 1417 2526 79009917 79011050 0.000000e+00 1286
30 TraesCS1A01G216100 chr4D 91.420 676 50 4 744 1413 349959022 349959695 0.000000e+00 920
31 TraesCS1A01G216100 chr4D 89.069 677 65 5 744 1413 79009167 79009841 0.000000e+00 832
32 TraesCS1A01G216100 chr6D 93.318 853 53 3 1 849 208551196 208550344 0.000000e+00 1256
33 TraesCS1A01G216100 chr6D 93.232 724 34 4 1808 2524 143474196 143474911 0.000000e+00 1051
34 TraesCS1A01G216100 chr6D 91.360 625 48 2 794 1413 208550441 208549818 0.000000e+00 850
35 TraesCS1A01G216100 chr6D 92.204 372 27 1 2162 2533 437344738 437344369 2.670000e-145 525
36 TraesCS1A01G216100 chr5A 91.475 915 50 17 1 912 354273741 354274630 0.000000e+00 1232
37 TraesCS1A01G216100 chr5A 89.133 865 80 9 1417 2274 354275336 354276193 0.000000e+00 1064
38 TraesCS1A01G216100 chr5A 89.838 679 54 9 744 1413 354274588 354275260 0.000000e+00 857
39 TraesCS1A01G216100 chr4A 92.024 840 57 4 1691 2524 340510974 340511809 0.000000e+00 1171
40 TraesCS1A01G216100 chr5D 93.803 468 25 2 2553 3020 370201568 370201105 0.000000e+00 701
41 TraesCS1A01G216100 chr5D 93.803 468 25 2 2553 3020 370249917 370249454 0.000000e+00 701
42 TraesCS1A01G216100 chr5D 95.068 365 18 0 2160 2524 47010396 47010760 2.610000e-160 575
43 TraesCS1A01G216100 chr7D 78.414 454 84 14 2575 3020 113456891 113456444 1.770000e-72 283
44 TraesCS1A01G216100 chr2D 78.810 420 84 5 2600 3017 94564240 94563824 8.250000e-71 278
45 TraesCS1A01G216100 chr2D 77.729 458 81 19 2575 3020 259175188 259174740 8.300000e-66 261


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 TraesCS1A01G216100 chr1A 382099507 382102526 3019 False 5578.0 5578 100.000000 1 3020 1 chr1A.!!$F2 3019
1 TraesCS1A01G216100 chr1A 462343003 462344525 1522 False 1075.5 1251 91.241500 1 1413 2 chr1A.!!$F3 1412
2 TraesCS1A01G216100 chr7A 606192642 606195218 2576 False 2748.0 2748 86.369000 1 2524 1 chr7A.!!$F1 2523
3 TraesCS1A01G216100 chr6B 673016361 673017823 1462 False 2497.0 2497 97.543000 756 2213 1 chr6B.!!$F1 1457
4 TraesCS1A01G216100 chr6B 690876897 690878403 1506 True 1539.0 1539 85.489000 1039 2524 1 chr6B.!!$R2 1485
5 TraesCS1A01G216100 chr2A 572843875 572845718 1843 False 2065.0 2065 87.272000 1 1815 1 chr2A.!!$F2 1814
6 TraesCS1A01G216100 chr2A 173513268 173515062 1794 True 1905.0 1905 85.942000 351 2153 1 chr2A.!!$R1 1802
7 TraesCS1A01G216100 chr2A 779783196 779784081 885 False 1092.0 1092 89.038000 1 885 1 chr2A.!!$F4 884
8 TraesCS1A01G216100 chr2A 779739689 779740575 886 False 1077.0 1077 88.702000 1 885 1 chr2A.!!$F3 884
9 TraesCS1A01G216100 chr6A 511525553 511527340 1787 False 1831.0 1831 85.242000 352 2153 1 chr6A.!!$F2 1801
10 TraesCS1A01G216100 chr3D 384008121 384010610 2489 False 1457.0 1807 90.092000 1 2526 2 chr3D.!!$F1 2525
11 TraesCS1A01G216100 chr1D 327013902 327015022 1120 False 1733.0 1733 94.652000 1414 2528 1 chr1D.!!$F1 1114
12 TraesCS1A01G216100 chr4B 11609021 11610928 1907 False 1352.5 1687 91.975000 597 2526 2 chr4B.!!$F1 1929
13 TraesCS1A01G216100 chr4B 97889690 97890593 903 True 1133.0 1133 89.352000 1 904 1 chr4B.!!$R2 903
14 TraesCS1A01G216100 chr4B 97792314 97793217 903 True 1083.0 1083 88.364000 1 904 1 chr4B.!!$R1 903
15 TraesCS1A01G216100 chr5B 524502376 524504194 1818 False 1247.0 1587 92.226500 742 2491 2 chr5B.!!$F1 1749
16 TraesCS1A01G216100 chr7B 88976498 88978291 1793 True 1063.5 1421 88.574000 744 2454 2 chr7B.!!$R1 1710
17 TraesCS1A01G216100 chr4D 79009167 79011050 1883 False 1059.0 1286 88.284500 744 2526 2 chr4D.!!$F2 1782
18 TraesCS1A01G216100 chr4D 349959022 349959695 673 False 920.0 920 91.420000 744 1413 1 chr4D.!!$F1 669
19 TraesCS1A01G216100 chr6D 208549818 208551196 1378 True 1053.0 1256 92.339000 1 1413 2 chr6D.!!$R2 1412
20 TraesCS1A01G216100 chr6D 143474196 143474911 715 False 1051.0 1051 93.232000 1808 2524 1 chr6D.!!$F1 716
21 TraesCS1A01G216100 chr5A 354273741 354276193 2452 False 1051.0 1232 90.148667 1 2274 3 chr5A.!!$F1 2273
22 TraesCS1A01G216100 chr4A 340510974 340511809 835 False 1171.0 1171 92.024000 1691 2524 1 chr4A.!!$F1 833

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
278 279 0.821711 TGTGAGGCCGGGTTTTCTTG 60.822 55.0 2.18 0.0 0.0 3.02 F
1017 1440 0.107214 TCATGAATTGGACTCCGCCC 60.107 55.0 0.00 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2473 0.871722 TTTGAACGATGCTTGACGGG 59.128 50.0 0.00 0.0 0.00 5.28 R
2387 2928 0.108281 TGCATGCTGAGCTGAGACTC 60.108 55.0 20.33 0.0 37.19 3.36 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
242 243 8.090831 GCTTGTTCATAGGAAAATTCTTCCTTT 58.909 33.333 20.08 13.26 46.21 3.11
278 279 0.821711 TGTGAGGCCGGGTTTTCTTG 60.822 55.000 2.18 0.00 0.00 3.02
328 329 4.030913 TGAAAGAGTATGGTCGAGGGAAT 58.969 43.478 0.00 0.00 0.00 3.01
724 763 4.713553 TGATGTGTGACTTGGTGTTGTAT 58.286 39.130 0.00 0.00 0.00 2.29
725 764 5.129634 TGATGTGTGACTTGGTGTTGTATT 58.870 37.500 0.00 0.00 0.00 1.89
726 765 5.592282 TGATGTGTGACTTGGTGTTGTATTT 59.408 36.000 0.00 0.00 0.00 1.40
776 1032 7.391148 TGGAATTCATTTTTAGGTGCTAGAC 57.609 36.000 7.93 0.00 0.00 2.59
792 1109 4.647853 TGCTAGACCGTCATTTATAGGTGT 59.352 41.667 0.40 0.00 37.07 4.16
820 1177 5.643379 TGTCATTTTTAGGTGCTGGAATC 57.357 39.130 0.00 0.00 0.00 2.52
857 1214 6.072008 TGCTGAAATACATTTTTGAGCTGCTA 60.072 34.615 0.15 0.00 32.55 3.49
861 1218 9.709495 TGAAATACATTTTTGAGCTGCTAAAAT 57.291 25.926 12.82 13.70 40.77 1.82
920 1341 5.880332 GCTGGGATGTGTTATTAACTTCTGA 59.120 40.000 7.99 0.00 0.00 3.27
1017 1440 0.107214 TCATGAATTGGACTCCGCCC 60.107 55.000 0.00 0.00 0.00 6.13
1178 1604 4.637091 TCAAGTGCACAATCATATCCACAG 59.363 41.667 21.04 0.00 0.00 3.66
1313 1744 2.162681 GGTATGCATGCTATCAACCCC 58.837 52.381 20.33 3.83 0.00 4.95
1563 2069 2.041701 GGGAATTATGCAATGGCCACT 58.958 47.619 8.16 0.00 40.13 4.00
1967 2473 6.618811 ACTTTGTGAAGATGAATGATGAAGC 58.381 36.000 0.00 0.00 36.69 3.86
2181 2697 2.749076 TGCACTGCTACAATTCATGGTC 59.251 45.455 1.98 0.00 0.00 4.02
2317 2856 3.115554 GGCAAAATATCCGTTCATGCAC 58.884 45.455 0.00 0.00 34.14 4.57
2335 2876 1.134580 CACCCTACCTCATGCAGTCTG 60.135 57.143 0.00 0.00 0.00 3.51
2387 2928 1.741706 CTGATGCAGGCTACCAAACAG 59.258 52.381 0.00 0.00 0.00 3.16
2410 2951 1.065709 TCTCAGCTCAGCATGCATCAA 60.066 47.619 21.98 0.57 34.76 2.57
2528 3069 2.812011 GCTACCAAACACACCCTTACAG 59.188 50.000 0.00 0.00 0.00 2.74
2529 3070 3.746432 GCTACCAAACACACCCTTACAGT 60.746 47.826 0.00 0.00 0.00 3.55
2530 3071 2.650322 ACCAAACACACCCTTACAGTG 58.350 47.619 0.00 0.00 41.15 3.66
2534 3075 4.771127 ACACCCTTACAGTGTGCG 57.229 55.556 5.88 0.00 46.43 5.34
2535 3076 1.597027 ACACCCTTACAGTGTGCGC 60.597 57.895 5.88 0.00 46.43 6.09
2536 3077 2.357034 ACCCTTACAGTGTGCGCG 60.357 61.111 5.88 0.00 0.00 6.86
2537 3078 3.118454 CCCTTACAGTGTGCGCGG 61.118 66.667 8.83 0.66 0.00 6.46
2538 3079 3.118454 CCTTACAGTGTGCGCGGG 61.118 66.667 8.83 0.00 0.00 6.13
2539 3080 3.118454 CTTACAGTGTGCGCGGGG 61.118 66.667 8.83 0.00 0.00 5.73
2561 3102 4.586235 GGGGCAGTGTGGCACAGT 62.586 66.667 22.75 22.31 46.74 3.55
2562 3103 2.429930 GGGCAGTGTGGCACAGTA 59.570 61.111 26.39 0.00 45.76 2.74
2563 3104 1.672356 GGGCAGTGTGGCACAGTAG 60.672 63.158 26.39 20.26 45.76 2.57
2564 3105 1.672356 GGCAGTGTGGCACAGTAGG 60.672 63.158 26.39 16.63 41.80 3.18
2565 3106 1.071471 GCAGTGTGGCACAGTAGGT 59.929 57.895 26.39 4.22 41.80 3.08
2573 3114 4.397348 CACAGTAGGTGTTGGGCC 57.603 61.111 0.00 0.00 42.75 5.80
2574 3115 1.761174 CACAGTAGGTGTTGGGCCT 59.239 57.895 4.53 0.00 42.75 5.19
2575 3116 0.110486 CACAGTAGGTGTTGGGCCTT 59.890 55.000 4.53 0.00 42.75 4.35
2576 3117 0.850784 ACAGTAGGTGTTGGGCCTTT 59.149 50.000 4.53 0.00 34.94 3.11
2577 3118 1.216930 ACAGTAGGTGTTGGGCCTTTT 59.783 47.619 4.53 0.00 34.94 2.27
2578 3119 1.886542 CAGTAGGTGTTGGGCCTTTTC 59.113 52.381 4.53 0.00 37.54 2.29
2579 3120 1.780919 AGTAGGTGTTGGGCCTTTTCT 59.219 47.619 4.53 0.00 37.54 2.52
2580 3121 2.177016 AGTAGGTGTTGGGCCTTTTCTT 59.823 45.455 4.53 0.00 37.54 2.52
2581 3122 1.704641 AGGTGTTGGGCCTTTTCTTC 58.295 50.000 4.53 0.00 31.04 2.87
2582 3123 1.217942 AGGTGTTGGGCCTTTTCTTCT 59.782 47.619 4.53 0.00 31.04 2.85
2583 3124 2.039418 GGTGTTGGGCCTTTTCTTCTT 58.961 47.619 4.53 0.00 0.00 2.52
2584 3125 2.035961 GGTGTTGGGCCTTTTCTTCTTC 59.964 50.000 4.53 0.00 0.00 2.87
2585 3126 2.959030 GTGTTGGGCCTTTTCTTCTTCT 59.041 45.455 4.53 0.00 0.00 2.85
2586 3127 3.384789 GTGTTGGGCCTTTTCTTCTTCTT 59.615 43.478 4.53 0.00 0.00 2.52
2587 3128 3.636764 TGTTGGGCCTTTTCTTCTTCTTC 59.363 43.478 4.53 0.00 0.00 2.87
2588 3129 3.884037 TGGGCCTTTTCTTCTTCTTCT 57.116 42.857 4.53 0.00 0.00 2.85
2589 3130 4.184649 TGGGCCTTTTCTTCTTCTTCTT 57.815 40.909 4.53 0.00 0.00 2.52
2590 3131 4.145052 TGGGCCTTTTCTTCTTCTTCTTC 58.855 43.478 4.53 0.00 0.00 2.87
2591 3132 3.508012 GGGCCTTTTCTTCTTCTTCTTCC 59.492 47.826 0.84 0.00 0.00 3.46
2592 3133 4.402829 GGCCTTTTCTTCTTCTTCTTCCT 58.597 43.478 0.00 0.00 0.00 3.36
2593 3134 4.830046 GGCCTTTTCTTCTTCTTCTTCCTT 59.170 41.667 0.00 0.00 0.00 3.36
2594 3135 5.303078 GGCCTTTTCTTCTTCTTCTTCCTTT 59.697 40.000 0.00 0.00 0.00 3.11
2595 3136 6.183360 GGCCTTTTCTTCTTCTTCTTCCTTTT 60.183 38.462 0.00 0.00 0.00 2.27
2596 3137 6.920758 GCCTTTTCTTCTTCTTCTTCCTTTTC 59.079 38.462 0.00 0.00 0.00 2.29
2597 3138 7.201866 GCCTTTTCTTCTTCTTCTTCCTTTTCT 60.202 37.037 0.00 0.00 0.00 2.52
2598 3139 8.134261 CCTTTTCTTCTTCTTCTTCCTTTTCTG 58.866 37.037 0.00 0.00 0.00 3.02
2599 3140 8.581253 TTTTCTTCTTCTTCTTCCTTTTCTGT 57.419 30.769 0.00 0.00 0.00 3.41
2600 3141 8.581253 TTTCTTCTTCTTCTTCCTTTTCTGTT 57.419 30.769 0.00 0.00 0.00 3.16
2601 3142 7.793927 TCTTCTTCTTCTTCCTTTTCTGTTC 57.206 36.000 0.00 0.00 0.00 3.18
2602 3143 7.569240 TCTTCTTCTTCTTCCTTTTCTGTTCT 58.431 34.615 0.00 0.00 0.00 3.01
2603 3144 8.049721 TCTTCTTCTTCTTCCTTTTCTGTTCTT 58.950 33.333 0.00 0.00 0.00 2.52
2604 3145 8.581253 TTCTTCTTCTTCCTTTTCTGTTCTTT 57.419 30.769 0.00 0.00 0.00 2.52
2605 3146 8.581253 TCTTCTTCTTCCTTTTCTGTTCTTTT 57.419 30.769 0.00 0.00 0.00 2.27
2606 3147 8.678199 TCTTCTTCTTCCTTTTCTGTTCTTTTC 58.322 33.333 0.00 0.00 0.00 2.29
2607 3148 8.581253 TTCTTCTTCCTTTTCTGTTCTTTTCT 57.419 30.769 0.00 0.00 0.00 2.52
2608 3149 7.989826 TCTTCTTCCTTTTCTGTTCTTTTCTG 58.010 34.615 0.00 0.00 0.00 3.02
2609 3150 7.611855 TCTTCTTCCTTTTCTGTTCTTTTCTGT 59.388 33.333 0.00 0.00 0.00 3.41
2610 3151 7.703058 TCTTCCTTTTCTGTTCTTTTCTGTT 57.297 32.000 0.00 0.00 0.00 3.16
2611 3152 8.122472 TCTTCCTTTTCTGTTCTTTTCTGTTT 57.878 30.769 0.00 0.00 0.00 2.83
2612 3153 8.244113 TCTTCCTTTTCTGTTCTTTTCTGTTTC 58.756 33.333 0.00 0.00 0.00 2.78
2613 3154 7.703058 TCCTTTTCTGTTCTTTTCTGTTTCT 57.297 32.000 0.00 0.00 0.00 2.52
2614 3155 8.122472 TCCTTTTCTGTTCTTTTCTGTTTCTT 57.878 30.769 0.00 0.00 0.00 2.52
2615 3156 8.585018 TCCTTTTCTGTTCTTTTCTGTTTCTTT 58.415 29.630 0.00 0.00 0.00 2.52
2616 3157 9.208022 CCTTTTCTGTTCTTTTCTGTTTCTTTT 57.792 29.630 0.00 0.00 0.00 2.27
2696 3237 9.941325 ATTATCATTTAAATCACTGCCACAAAA 57.059 25.926 0.00 0.00 0.00 2.44
2697 3238 7.894376 ATCATTTAAATCACTGCCACAAAAG 57.106 32.000 0.00 0.00 0.00 2.27
2698 3239 6.222389 TCATTTAAATCACTGCCACAAAAGG 58.778 36.000 0.00 0.00 0.00 3.11
2699 3240 5.606348 TTTAAATCACTGCCACAAAAGGT 57.394 34.783 0.00 0.00 0.00 3.50
2700 3241 5.606348 TTAAATCACTGCCACAAAAGGTT 57.394 34.783 0.00 0.00 0.00 3.50
2701 3242 4.486125 AAATCACTGCCACAAAAGGTTT 57.514 36.364 0.00 0.00 0.00 3.27
2702 3243 4.486125 AATCACTGCCACAAAAGGTTTT 57.514 36.364 0.00 0.00 0.00 2.43
2703 3244 5.606348 AATCACTGCCACAAAAGGTTTTA 57.394 34.783 0.00 0.00 0.00 1.52
2704 3245 4.379339 TCACTGCCACAAAAGGTTTTAC 57.621 40.909 0.00 0.00 0.00 2.01
2705 3246 4.020543 TCACTGCCACAAAAGGTTTTACT 58.979 39.130 0.00 0.00 0.00 2.24
2706 3247 4.097286 TCACTGCCACAAAAGGTTTTACTC 59.903 41.667 0.00 0.00 0.00 2.59
2707 3248 3.383505 ACTGCCACAAAAGGTTTTACTCC 59.616 43.478 0.00 0.00 0.00 3.85
2708 3249 3.366396 TGCCACAAAAGGTTTTACTCCA 58.634 40.909 0.00 0.00 0.00 3.86
2709 3250 3.769844 TGCCACAAAAGGTTTTACTCCAA 59.230 39.130 0.00 0.00 0.00 3.53
2710 3251 4.223032 TGCCACAAAAGGTTTTACTCCAAA 59.777 37.500 0.00 0.00 0.00 3.28
2711 3252 5.179533 GCCACAAAAGGTTTTACTCCAAAA 58.820 37.500 0.00 0.00 33.66 2.44
2712 3253 5.820423 GCCACAAAAGGTTTTACTCCAAAAT 59.180 36.000 0.00 0.00 38.36 1.82
2713 3254 6.317642 GCCACAAAAGGTTTTACTCCAAAATT 59.682 34.615 0.00 0.00 38.36 1.82
2714 3255 7.496263 GCCACAAAAGGTTTTACTCCAAAATTA 59.504 33.333 0.00 0.00 38.36 1.40
2715 3256 9.384764 CCACAAAAGGTTTTACTCCAAAATTAA 57.615 29.630 0.00 0.00 38.36 1.40
2789 3330 8.757164 AGCCACTATTTTAATTAGTTTTGTGC 57.243 30.769 0.00 0.00 0.00 4.57
2790 3331 8.364142 AGCCACTATTTTAATTAGTTTTGTGCA 58.636 29.630 0.00 0.00 0.00 4.57
2791 3332 9.150348 GCCACTATTTTAATTAGTTTTGTGCAT 57.850 29.630 0.00 0.00 0.00 3.96
2833 3374 9.574516 AAATGTGGTTTCTTCACTATTCTTACT 57.425 29.630 0.00 0.00 36.21 2.24
2834 3375 9.574516 AATGTGGTTTCTTCACTATTCTTACTT 57.425 29.630 0.00 0.00 36.21 2.24
2855 3396 9.952030 TTACTTATCAGTAATTTGTCACATCCA 57.048 29.630 0.00 0.00 40.06 3.41
2856 3397 8.498054 ACTTATCAGTAATTTGTCACATCCAG 57.502 34.615 0.00 0.00 0.00 3.86
2857 3398 8.321353 ACTTATCAGTAATTTGTCACATCCAGA 58.679 33.333 0.00 0.00 0.00 3.86
2858 3399 9.166173 CTTATCAGTAATTTGTCACATCCAGAA 57.834 33.333 0.00 0.00 0.00 3.02
2859 3400 6.801539 TCAGTAATTTGTCACATCCAGAAC 57.198 37.500 0.00 0.00 0.00 3.01
2860 3401 6.295249 TCAGTAATTTGTCACATCCAGAACA 58.705 36.000 0.00 0.00 0.00 3.18
2861 3402 6.942005 TCAGTAATTTGTCACATCCAGAACAT 59.058 34.615 0.00 0.00 0.00 2.71
2862 3403 7.448161 TCAGTAATTTGTCACATCCAGAACATT 59.552 33.333 0.00 0.00 0.00 2.71
2863 3404 8.084073 CAGTAATTTGTCACATCCAGAACATTT 58.916 33.333 0.00 0.00 0.00 2.32
2864 3405 8.641541 AGTAATTTGTCACATCCAGAACATTTT 58.358 29.630 0.00 0.00 0.00 1.82
2865 3406 9.906660 GTAATTTGTCACATCCAGAACATTTTA 57.093 29.630 0.00 0.00 0.00 1.52
2867 3408 7.581213 TTTGTCACATCCAGAACATTTTAGT 57.419 32.000 0.00 0.00 0.00 2.24
2868 3409 7.581213 TTGTCACATCCAGAACATTTTAGTT 57.419 32.000 0.00 0.00 0.00 2.24
2869 3410 7.581213 TGTCACATCCAGAACATTTTAGTTT 57.419 32.000 0.00 0.00 0.00 2.66
2870 3411 8.006298 TGTCACATCCAGAACATTTTAGTTTT 57.994 30.769 0.00 0.00 0.00 2.43
2871 3412 9.126151 TGTCACATCCAGAACATTTTAGTTTTA 57.874 29.630 0.00 0.00 0.00 1.52
2872 3413 9.959749 GTCACATCCAGAACATTTTAGTTTTAA 57.040 29.630 0.00 0.00 0.00 1.52
2938 3479 8.490355 TGAATATGAACGAGATTTGAATCATCG 58.510 33.333 16.59 16.59 39.58 3.84
2939 3480 7.953158 ATATGAACGAGATTTGAATCATCGT 57.047 32.000 17.42 17.42 43.84 3.73
2940 3481 5.454736 TGAACGAGATTTGAATCATCGTG 57.545 39.130 20.81 0.00 42.58 4.35
2941 3482 5.167845 TGAACGAGATTTGAATCATCGTGA 58.832 37.500 20.81 13.47 42.58 4.35
2942 3483 5.637387 TGAACGAGATTTGAATCATCGTGAA 59.363 36.000 20.81 14.19 42.58 3.18
2943 3484 6.147000 TGAACGAGATTTGAATCATCGTGAAA 59.853 34.615 20.81 12.73 42.58 2.69
2944 3485 5.858475 ACGAGATTTGAATCATCGTGAAAC 58.142 37.500 20.07 0.00 42.22 2.78
2945 3486 5.639506 ACGAGATTTGAATCATCGTGAAACT 59.360 36.000 20.07 0.00 42.22 2.66
2946 3487 6.811665 ACGAGATTTGAATCATCGTGAAACTA 59.188 34.615 20.07 0.00 42.22 2.24
2947 3488 7.330946 ACGAGATTTGAATCATCGTGAAACTAA 59.669 33.333 20.07 0.00 42.22 2.24
2948 3489 7.632515 CGAGATTTGAATCATCGTGAAACTAAC 59.367 37.037 6.50 0.00 37.89 2.34
2949 3490 8.322906 AGATTTGAATCATCGTGAAACTAACA 57.677 30.769 6.50 0.00 37.89 2.41
2950 3491 8.950210 AGATTTGAATCATCGTGAAACTAACAT 58.050 29.630 6.50 0.00 37.89 2.71
2951 3492 9.559958 GATTTGAATCATCGTGAAACTAACATT 57.440 29.630 0.00 0.00 35.49 2.71
2952 3493 9.912634 ATTTGAATCATCGTGAAACTAACATTT 57.087 25.926 0.00 0.00 31.75 2.32
2953 3494 8.726650 TTGAATCATCGTGAAACTAACATTTG 57.273 30.769 0.00 0.00 31.75 2.32
2954 3495 7.870826 TGAATCATCGTGAAACTAACATTTGT 58.129 30.769 0.00 0.00 31.75 2.83
2955 3496 8.994170 TGAATCATCGTGAAACTAACATTTGTA 58.006 29.630 0.00 0.00 31.75 2.41
2956 3497 9.820229 GAATCATCGTGAAACTAACATTTGTAA 57.180 29.630 0.00 0.00 31.75 2.41
2958 3499 9.988350 ATCATCGTGAAACTAACATTTGTAATC 57.012 29.630 0.00 0.00 31.75 1.75
2959 3500 8.166066 TCATCGTGAAACTAACATTTGTAATCG 58.834 33.333 0.00 0.00 31.75 3.34
2960 3501 7.410800 TCGTGAAACTAACATTTGTAATCGT 57.589 32.000 0.00 0.00 31.75 3.73
2961 3502 7.285069 TCGTGAAACTAACATTTGTAATCGTG 58.715 34.615 0.00 0.00 31.75 4.35
2962 3503 6.518395 CGTGAAACTAACATTTGTAATCGTGG 59.482 38.462 0.00 0.00 31.75 4.94
2963 3504 7.357303 GTGAAACTAACATTTGTAATCGTGGT 58.643 34.615 0.00 0.00 0.00 4.16
2964 3505 7.322699 GTGAAACTAACATTTGTAATCGTGGTG 59.677 37.037 0.00 0.00 0.00 4.17
2965 3506 7.226918 TGAAACTAACATTTGTAATCGTGGTGA 59.773 33.333 0.00 0.00 0.00 4.02
2966 3507 7.681939 AACTAACATTTGTAATCGTGGTGAT 57.318 32.000 0.00 0.00 39.67 3.06
2967 3508 7.072177 ACTAACATTTGTAATCGTGGTGATG 57.928 36.000 0.00 0.00 37.39 3.07
2968 3509 5.957842 AACATTTGTAATCGTGGTGATGT 57.042 34.783 0.00 0.00 37.39 3.06
2969 3510 5.295431 ACATTTGTAATCGTGGTGATGTG 57.705 39.130 0.00 0.00 37.39 3.21
2970 3511 4.155826 ACATTTGTAATCGTGGTGATGTGG 59.844 41.667 0.00 0.00 37.39 4.17
2971 3512 1.732941 TGTAATCGTGGTGATGTGGC 58.267 50.000 0.00 0.00 37.39 5.01
2972 3513 1.002544 TGTAATCGTGGTGATGTGGCA 59.997 47.619 0.00 0.00 37.39 4.92
2973 3514 2.288666 GTAATCGTGGTGATGTGGCAT 58.711 47.619 0.00 0.00 37.39 4.40
2974 3515 1.382522 AATCGTGGTGATGTGGCATC 58.617 50.000 0.00 2.44 37.39 3.91
2975 3516 0.252761 ATCGTGGTGATGTGGCATCA 59.747 50.000 7.63 7.63 35.45 3.07
2976 3517 0.252761 TCGTGGTGATGTGGCATCAT 59.747 50.000 13.88 0.00 30.53 2.45
2977 3518 1.097232 CGTGGTGATGTGGCATCATT 58.903 50.000 13.88 0.00 30.53 2.57
2978 3519 2.093235 TCGTGGTGATGTGGCATCATTA 60.093 45.455 13.88 5.04 30.53 1.90
2979 3520 2.288729 CGTGGTGATGTGGCATCATTAG 59.711 50.000 13.88 4.47 30.53 1.73
2980 3521 3.282021 GTGGTGATGTGGCATCATTAGT 58.718 45.455 13.88 0.00 30.53 2.24
2981 3522 4.450976 GTGGTGATGTGGCATCATTAGTA 58.549 43.478 13.88 0.00 30.53 1.82
2982 3523 4.512944 GTGGTGATGTGGCATCATTAGTAG 59.487 45.833 13.88 0.00 30.53 2.57
2983 3524 4.408596 TGGTGATGTGGCATCATTAGTAGA 59.591 41.667 13.88 0.00 0.00 2.59
2984 3525 4.993584 GGTGATGTGGCATCATTAGTAGAG 59.006 45.833 13.88 0.00 0.00 2.43
2985 3526 4.993584 GTGATGTGGCATCATTAGTAGAGG 59.006 45.833 13.88 0.00 0.00 3.69
2986 3527 4.040829 TGATGTGGCATCATTAGTAGAGGG 59.959 45.833 7.63 0.00 0.00 4.30
2987 3528 3.384168 TGTGGCATCATTAGTAGAGGGT 58.616 45.455 0.00 0.00 0.00 4.34
2988 3529 3.780294 TGTGGCATCATTAGTAGAGGGTT 59.220 43.478 0.00 0.00 0.00 4.11
2989 3530 4.966168 TGTGGCATCATTAGTAGAGGGTTA 59.034 41.667 0.00 0.00 0.00 2.85
2990 3531 5.163343 TGTGGCATCATTAGTAGAGGGTTAC 60.163 44.000 0.00 0.00 0.00 2.50
2991 3532 5.070580 GTGGCATCATTAGTAGAGGGTTACT 59.929 44.000 0.00 0.00 37.61 2.24
2992 3533 5.070446 TGGCATCATTAGTAGAGGGTTACTG 59.930 44.000 0.00 0.00 35.57 2.74
2993 3534 5.070580 GGCATCATTAGTAGAGGGTTACTGT 59.929 44.000 0.00 0.00 35.57 3.55
2994 3535 6.267014 GGCATCATTAGTAGAGGGTTACTGTA 59.733 42.308 0.00 0.00 35.57 2.74
2995 3536 7.371936 GCATCATTAGTAGAGGGTTACTGTAG 58.628 42.308 0.00 0.00 35.57 2.74
2996 3537 6.956202 TCATTAGTAGAGGGTTACTGTAGC 57.044 41.667 0.00 0.00 35.57 3.58
2997 3538 6.670617 TCATTAGTAGAGGGTTACTGTAGCT 58.329 40.000 1.71 0.00 35.57 3.32
2998 3539 7.124052 TCATTAGTAGAGGGTTACTGTAGCTT 58.876 38.462 0.00 0.00 35.57 3.74
2999 3540 8.277197 TCATTAGTAGAGGGTTACTGTAGCTTA 58.723 37.037 0.00 0.00 35.57 3.09
3000 3541 8.910944 CATTAGTAGAGGGTTACTGTAGCTTAA 58.089 37.037 0.00 0.00 35.57 1.85
3001 3542 9.657728 ATTAGTAGAGGGTTACTGTAGCTTAAT 57.342 33.333 0.00 0.00 35.57 1.40
3002 3543 7.974730 AGTAGAGGGTTACTGTAGCTTAATT 57.025 36.000 0.00 0.00 32.78 1.40
3004 3545 9.657728 AGTAGAGGGTTACTGTAGCTTAATTAT 57.342 33.333 0.00 0.00 32.78 1.28
3005 3546 9.911138 GTAGAGGGTTACTGTAGCTTAATTATC 57.089 37.037 0.00 0.00 0.00 1.75
3006 3547 7.964624 AGAGGGTTACTGTAGCTTAATTATCC 58.035 38.462 0.00 0.00 0.00 2.59
3007 3548 6.756221 AGGGTTACTGTAGCTTAATTATCCG 58.244 40.000 0.00 0.00 0.00 4.18
3008 3549 5.930569 GGGTTACTGTAGCTTAATTATCCGG 59.069 44.000 0.00 0.00 0.00 5.14
3009 3550 5.930569 GGTTACTGTAGCTTAATTATCCGGG 59.069 44.000 0.00 0.00 0.00 5.73
3010 3551 4.004196 ACTGTAGCTTAATTATCCGGGC 57.996 45.455 0.00 0.00 0.00 6.13
3011 3552 2.993899 CTGTAGCTTAATTATCCGGGCG 59.006 50.000 0.00 0.00 0.00 6.13
3012 3553 2.366266 TGTAGCTTAATTATCCGGGCGT 59.634 45.455 0.00 0.00 0.00 5.68
3013 3554 2.632987 AGCTTAATTATCCGGGCGTT 57.367 45.000 0.00 0.00 0.00 4.84
3014 3555 3.756933 AGCTTAATTATCCGGGCGTTA 57.243 42.857 0.00 0.00 0.00 3.18
3015 3556 3.396560 AGCTTAATTATCCGGGCGTTAC 58.603 45.455 0.00 0.00 0.00 2.50
3016 3557 3.132925 GCTTAATTATCCGGGCGTTACA 58.867 45.455 0.00 0.00 0.00 2.41
3017 3558 3.185797 GCTTAATTATCCGGGCGTTACAG 59.814 47.826 0.00 0.00 0.00 2.74
3018 3559 2.994186 AATTATCCGGGCGTTACAGT 57.006 45.000 0.00 0.00 0.00 3.55
3019 3560 2.994186 ATTATCCGGGCGTTACAGTT 57.006 45.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 124 1.211457 CAACCCATCTTCCCTCTCCAG 59.789 57.143 0.00 0.00 0.00 3.86
242 243 0.034574 ACAGCATACCCCGCATCAAA 60.035 50.000 0.00 0.00 0.00 2.69
328 329 4.410099 ACTCTTTGGCATTTTGAGGATGA 58.590 39.130 0.00 0.00 0.00 2.92
677 681 5.049398 TGTTTTACAACACCAAGACACAC 57.951 39.130 0.00 0.00 38.03 3.82
776 1032 5.588648 ACATTCCAACACCTATAAATGACGG 59.411 40.000 0.00 0.00 0.00 4.79
785 1102 7.673926 ACCTAAAAATGACATTCCAACACCTAT 59.326 33.333 0.05 0.00 0.00 2.57
792 1109 5.279406 CCAGCACCTAAAAATGACATTCCAA 60.279 40.000 0.05 0.00 0.00 3.53
861 1218 8.504812 TGATATTACAGCAGCTCAAAAACATA 57.495 30.769 0.00 0.00 0.00 2.29
865 1222 9.709495 AAAAATGATATTACAGCAGCTCAAAAA 57.291 25.926 0.00 0.00 0.00 1.94
1017 1440 3.490800 TTCAACATCATTGCCGACATG 57.509 42.857 0.00 0.00 0.00 3.21
1178 1604 1.153229 GTCCACCTATTCCGCCACC 60.153 63.158 0.00 0.00 0.00 4.61
1313 1744 4.024048 ACAACTCATTTCAGCAGGTAAACG 60.024 41.667 0.00 0.00 0.00 3.60
1776 2282 4.340950 TCACGGATAGCATCAGTCATGTTA 59.659 41.667 0.00 0.00 35.50 2.41
1794 2300 1.725641 TAGCACTTGCAATCTCACGG 58.274 50.000 0.00 0.00 45.16 4.94
1967 2473 0.871722 TTTGAACGATGCTTGACGGG 59.128 50.000 0.00 0.00 0.00 5.28
2081 2589 9.130312 GATTCATAGTACATAACCTCATTCGAC 57.870 37.037 0.00 0.00 0.00 4.20
2285 2804 5.351465 ACGGATATTTTGCCATATGATCGAC 59.649 40.000 3.65 0.00 0.00 4.20
2317 2856 0.179062 GCAGACTGCATGAGGTAGGG 60.179 60.000 22.62 0.00 44.26 3.53
2335 2876 1.891919 TGCTGAGACGGTGTTTGGC 60.892 57.895 0.00 0.00 0.00 4.52
2387 2928 0.108281 TGCATGCTGAGCTGAGACTC 60.108 55.000 20.33 0.00 37.19 3.36
2410 2951 6.038603 CAGCTGTTTGGTAGCAATGTATGTAT 59.961 38.462 8.40 0.00 43.53 2.29
2544 3085 3.190738 TACTGTGCCACACTGCCCC 62.191 63.158 0.00 0.00 36.91 5.80
2545 3086 1.672356 CTACTGTGCCACACTGCCC 60.672 63.158 0.00 0.00 36.91 5.36
2546 3087 1.672356 CCTACTGTGCCACACTGCC 60.672 63.158 0.00 0.00 36.91 4.85
2547 3088 1.071471 ACCTACTGTGCCACACTGC 59.929 57.895 0.00 0.00 36.91 4.40
2548 3089 2.918571 CACCTACTGTGCCACACTG 58.081 57.895 0.00 0.00 38.34 3.66
2557 3098 0.850784 AAAGGCCCAACACCTACTGT 59.149 50.000 0.00 0.00 36.14 3.55
2558 3099 1.886542 GAAAAGGCCCAACACCTACTG 59.113 52.381 0.00 0.00 36.14 2.74
2559 3100 1.780919 AGAAAAGGCCCAACACCTACT 59.219 47.619 0.00 0.00 36.14 2.57
2560 3101 2.287977 AGAAAAGGCCCAACACCTAC 57.712 50.000 0.00 0.00 36.14 3.18
2561 3102 2.445525 AGAAGAAAAGGCCCAACACCTA 59.554 45.455 0.00 0.00 36.14 3.08
2562 3103 1.217942 AGAAGAAAAGGCCCAACACCT 59.782 47.619 0.00 0.00 40.02 4.00
2563 3104 1.704641 AGAAGAAAAGGCCCAACACC 58.295 50.000 0.00 0.00 0.00 4.16
2564 3105 2.959030 AGAAGAAGAAAAGGCCCAACAC 59.041 45.455 0.00 0.00 0.00 3.32
2565 3106 3.312736 AGAAGAAGAAAAGGCCCAACA 57.687 42.857 0.00 0.00 0.00 3.33
2566 3107 3.891977 AGAAGAAGAAGAAAAGGCCCAAC 59.108 43.478 0.00 0.00 0.00 3.77
2567 3108 4.184649 AGAAGAAGAAGAAAAGGCCCAA 57.815 40.909 0.00 0.00 0.00 4.12
2568 3109 3.884037 AGAAGAAGAAGAAAAGGCCCA 57.116 42.857 0.00 0.00 0.00 5.36
2569 3110 3.508012 GGAAGAAGAAGAAGAAAAGGCCC 59.492 47.826 0.00 0.00 0.00 5.80
2570 3111 4.402829 AGGAAGAAGAAGAAGAAAAGGCC 58.597 43.478 0.00 0.00 0.00 5.19
2571 3112 6.398234 AAAGGAAGAAGAAGAAGAAAAGGC 57.602 37.500 0.00 0.00 0.00 4.35
2572 3113 8.134261 CAGAAAAGGAAGAAGAAGAAGAAAAGG 58.866 37.037 0.00 0.00 0.00 3.11
2573 3114 8.681806 ACAGAAAAGGAAGAAGAAGAAGAAAAG 58.318 33.333 0.00 0.00 0.00 2.27
2574 3115 8.581253 ACAGAAAAGGAAGAAGAAGAAGAAAA 57.419 30.769 0.00 0.00 0.00 2.29
2575 3116 8.581253 AACAGAAAAGGAAGAAGAAGAAGAAA 57.419 30.769 0.00 0.00 0.00 2.52
2576 3117 8.049721 AGAACAGAAAAGGAAGAAGAAGAAGAA 58.950 33.333 0.00 0.00 0.00 2.52
2577 3118 7.569240 AGAACAGAAAAGGAAGAAGAAGAAGA 58.431 34.615 0.00 0.00 0.00 2.87
2578 3119 7.800155 AGAACAGAAAAGGAAGAAGAAGAAG 57.200 36.000 0.00 0.00 0.00 2.85
2579 3120 8.581253 AAAGAACAGAAAAGGAAGAAGAAGAA 57.419 30.769 0.00 0.00 0.00 2.52
2580 3121 8.581253 AAAAGAACAGAAAAGGAAGAAGAAGA 57.419 30.769 0.00 0.00 0.00 2.87
2581 3122 8.681806 AGAAAAGAACAGAAAAGGAAGAAGAAG 58.318 33.333 0.00 0.00 0.00 2.85
2582 3123 8.462016 CAGAAAAGAACAGAAAAGGAAGAAGAA 58.538 33.333 0.00 0.00 0.00 2.52
2583 3124 7.611855 ACAGAAAAGAACAGAAAAGGAAGAAGA 59.388 33.333 0.00 0.00 0.00 2.87
2584 3125 7.766283 ACAGAAAAGAACAGAAAAGGAAGAAG 58.234 34.615 0.00 0.00 0.00 2.85
2585 3126 7.703058 ACAGAAAAGAACAGAAAAGGAAGAA 57.297 32.000 0.00 0.00 0.00 2.52
2586 3127 7.703058 AACAGAAAAGAACAGAAAAGGAAGA 57.297 32.000 0.00 0.00 0.00 2.87
2587 3128 8.246871 AGAAACAGAAAAGAACAGAAAAGGAAG 58.753 33.333 0.00 0.00 0.00 3.46
2588 3129 8.122472 AGAAACAGAAAAGAACAGAAAAGGAA 57.878 30.769 0.00 0.00 0.00 3.36
2589 3130 7.703058 AGAAACAGAAAAGAACAGAAAAGGA 57.297 32.000 0.00 0.00 0.00 3.36
2590 3131 8.763049 AAAGAAACAGAAAAGAACAGAAAAGG 57.237 30.769 0.00 0.00 0.00 3.11
2670 3211 9.941325 TTTTGTGGCAGTGATTTAAATGATAAT 57.059 25.926 5.17 0.00 0.00 1.28
2671 3212 9.421806 CTTTTGTGGCAGTGATTTAAATGATAA 57.578 29.630 5.17 0.00 0.00 1.75
2672 3213 8.034215 CCTTTTGTGGCAGTGATTTAAATGATA 58.966 33.333 5.17 0.00 0.00 2.15
2673 3214 6.875195 CCTTTTGTGGCAGTGATTTAAATGAT 59.125 34.615 5.17 0.00 0.00 2.45
2674 3215 6.183360 ACCTTTTGTGGCAGTGATTTAAATGA 60.183 34.615 5.17 0.00 0.00 2.57
2675 3216 5.990996 ACCTTTTGTGGCAGTGATTTAAATG 59.009 36.000 5.17 0.00 0.00 2.32
2676 3217 6.173427 ACCTTTTGTGGCAGTGATTTAAAT 57.827 33.333 0.00 0.00 0.00 1.40
2677 3218 5.606348 ACCTTTTGTGGCAGTGATTTAAA 57.394 34.783 0.00 0.00 0.00 1.52
2678 3219 5.606348 AACCTTTTGTGGCAGTGATTTAA 57.394 34.783 0.00 0.00 0.00 1.52
2679 3220 5.606348 AAACCTTTTGTGGCAGTGATTTA 57.394 34.783 0.00 0.00 0.00 1.40
2680 3221 4.486125 AAACCTTTTGTGGCAGTGATTT 57.514 36.364 0.00 0.00 0.00 2.17
2681 3222 4.486125 AAAACCTTTTGTGGCAGTGATT 57.514 36.364 0.00 0.00 0.00 2.57
2682 3223 4.649218 AGTAAAACCTTTTGTGGCAGTGAT 59.351 37.500 0.00 0.00 0.00 3.06
2683 3224 4.020543 AGTAAAACCTTTTGTGGCAGTGA 58.979 39.130 0.00 0.00 0.00 3.41
2684 3225 4.359706 GAGTAAAACCTTTTGTGGCAGTG 58.640 43.478 0.00 0.00 0.00 3.66
2685 3226 3.383505 GGAGTAAAACCTTTTGTGGCAGT 59.616 43.478 0.00 0.00 0.00 4.40
2686 3227 3.383185 TGGAGTAAAACCTTTTGTGGCAG 59.617 43.478 0.00 0.00 0.00 4.85
2687 3228 3.366396 TGGAGTAAAACCTTTTGTGGCA 58.634 40.909 0.00 0.00 0.00 4.92
2688 3229 4.394439 TTGGAGTAAAACCTTTTGTGGC 57.606 40.909 0.00 0.00 0.00 5.01
2689 3230 7.857734 AATTTTGGAGTAAAACCTTTTGTGG 57.142 32.000 0.00 0.00 40.80 4.17
2763 3304 9.849166 GCACAAAACTAATTAAAATAGTGGCTA 57.151 29.630 5.38 0.00 0.00 3.93
2764 3305 8.364142 TGCACAAAACTAATTAAAATAGTGGCT 58.636 29.630 5.38 0.00 0.00 4.75
2765 3306 8.527567 TGCACAAAACTAATTAAAATAGTGGC 57.472 30.769 5.38 5.83 0.00 5.01
2807 3348 9.574516 AGTAAGAATAGTGAAGAAACCACATTT 57.425 29.630 0.00 0.00 37.01 2.32
2808 3349 9.574516 AAGTAAGAATAGTGAAGAAACCACATT 57.425 29.630 0.00 0.00 37.01 2.71
2829 3370 9.952030 TGGATGTGACAAATTACTGATAAGTAA 57.048 29.630 5.08 5.08 38.44 2.24
2830 3371 9.599866 CTGGATGTGACAAATTACTGATAAGTA 57.400 33.333 0.00 0.00 0.00 2.24
2831 3372 8.321353 TCTGGATGTGACAAATTACTGATAAGT 58.679 33.333 0.00 0.00 0.00 2.24
2832 3373 8.722480 TCTGGATGTGACAAATTACTGATAAG 57.278 34.615 0.00 0.00 0.00 1.73
2833 3374 8.946085 GTTCTGGATGTGACAAATTACTGATAA 58.054 33.333 0.00 0.00 0.00 1.75
2834 3375 8.100164 TGTTCTGGATGTGACAAATTACTGATA 58.900 33.333 0.00 0.00 0.00 2.15
2835 3376 6.942005 TGTTCTGGATGTGACAAATTACTGAT 59.058 34.615 0.00 0.00 0.00 2.90
2836 3377 6.295249 TGTTCTGGATGTGACAAATTACTGA 58.705 36.000 0.00 0.00 0.00 3.41
2837 3378 6.558771 TGTTCTGGATGTGACAAATTACTG 57.441 37.500 0.00 0.00 0.00 2.74
2838 3379 7.765695 AATGTTCTGGATGTGACAAATTACT 57.234 32.000 0.00 0.00 0.00 2.24
2839 3380 8.816640 AAAATGTTCTGGATGTGACAAATTAC 57.183 30.769 0.00 0.00 0.00 1.89
2841 3382 8.641541 ACTAAAATGTTCTGGATGTGACAAATT 58.358 29.630 0.00 0.00 0.00 1.82
2842 3383 8.181904 ACTAAAATGTTCTGGATGTGACAAAT 57.818 30.769 0.00 0.00 0.00 2.32
2843 3384 7.581213 ACTAAAATGTTCTGGATGTGACAAA 57.419 32.000 0.00 0.00 0.00 2.83
2844 3385 7.581213 AACTAAAATGTTCTGGATGTGACAA 57.419 32.000 0.00 0.00 0.00 3.18
2845 3386 7.581213 AAACTAAAATGTTCTGGATGTGACA 57.419 32.000 0.00 0.00 0.00 3.58
2846 3387 9.959749 TTAAAACTAAAATGTTCTGGATGTGAC 57.040 29.630 0.00 0.00 0.00 3.67
2912 3453 8.490355 CGATGATTCAAATCTCGTTCATATTCA 58.510 33.333 4.50 0.00 36.39 2.57
2913 3454 8.491152 ACGATGATTCAAATCTCGTTCATATTC 58.509 33.333 16.99 0.00 41.69 1.75
2914 3455 8.278408 CACGATGATTCAAATCTCGTTCATATT 58.722 33.333 18.72 3.59 42.08 1.28
2915 3456 7.653311 TCACGATGATTCAAATCTCGTTCATAT 59.347 33.333 18.72 0.07 42.08 1.78
2916 3457 6.978080 TCACGATGATTCAAATCTCGTTCATA 59.022 34.615 18.72 9.08 42.08 2.15
2917 3458 5.812127 TCACGATGATTCAAATCTCGTTCAT 59.188 36.000 18.72 2.28 42.08 2.57
2918 3459 5.167845 TCACGATGATTCAAATCTCGTTCA 58.832 37.500 18.72 11.19 42.08 3.18
2919 3460 5.702622 TCACGATGATTCAAATCTCGTTC 57.297 39.130 18.72 6.54 42.08 3.95
2920 3461 6.147821 AGTTTCACGATGATTCAAATCTCGTT 59.852 34.615 18.72 8.75 42.08 3.85
2921 3462 5.639506 AGTTTCACGATGATTCAAATCTCGT 59.360 36.000 16.99 16.99 43.34 4.18
2922 3463 6.099579 AGTTTCACGATGATTCAAATCTCG 57.900 37.500 16.15 16.15 39.58 4.04
2923 3464 8.443160 TGTTAGTTTCACGATGATTCAAATCTC 58.557 33.333 4.50 0.00 36.39 2.75
2924 3465 8.322906 TGTTAGTTTCACGATGATTCAAATCT 57.677 30.769 4.50 0.00 36.39 2.40
2925 3466 9.559958 AATGTTAGTTTCACGATGATTCAAATC 57.440 29.630 0.00 0.00 35.97 2.17
2926 3467 9.912634 AAATGTTAGTTTCACGATGATTCAAAT 57.087 25.926 0.00 0.00 0.00 2.32
2927 3468 9.179552 CAAATGTTAGTTTCACGATGATTCAAA 57.820 29.630 0.00 0.00 0.00 2.69
2928 3469 8.349245 ACAAATGTTAGTTTCACGATGATTCAA 58.651 29.630 0.00 0.00 0.00 2.69
2929 3470 7.870826 ACAAATGTTAGTTTCACGATGATTCA 58.129 30.769 0.00 0.00 0.00 2.57
2930 3471 9.820229 TTACAAATGTTAGTTTCACGATGATTC 57.180 29.630 0.00 0.00 0.00 2.52
2932 3473 9.988350 GATTACAAATGTTAGTTTCACGATGAT 57.012 29.630 0.00 0.00 0.00 2.45
2933 3474 8.166066 CGATTACAAATGTTAGTTTCACGATGA 58.834 33.333 0.00 0.00 0.00 2.92
2934 3475 7.955324 ACGATTACAAATGTTAGTTTCACGATG 59.045 33.333 0.00 0.00 0.00 3.84
2935 3476 7.955324 CACGATTACAAATGTTAGTTTCACGAT 59.045 33.333 0.00 0.00 0.00 3.73
2936 3477 7.285069 CACGATTACAAATGTTAGTTTCACGA 58.715 34.615 0.00 0.00 0.00 4.35
2937 3478 6.518395 CCACGATTACAAATGTTAGTTTCACG 59.482 38.462 0.00 0.00 0.00 4.35
2938 3479 7.322699 CACCACGATTACAAATGTTAGTTTCAC 59.677 37.037 0.00 0.00 0.00 3.18
2939 3480 7.226918 TCACCACGATTACAAATGTTAGTTTCA 59.773 33.333 0.00 0.00 0.00 2.69
2940 3481 7.577979 TCACCACGATTACAAATGTTAGTTTC 58.422 34.615 0.00 0.00 0.00 2.78
2941 3482 7.499321 TCACCACGATTACAAATGTTAGTTT 57.501 32.000 0.00 0.00 0.00 2.66
2942 3483 7.174253 ACATCACCACGATTACAAATGTTAGTT 59.826 33.333 0.00 0.00 29.21 2.24
2943 3484 6.653320 ACATCACCACGATTACAAATGTTAGT 59.347 34.615 0.00 0.00 29.21 2.24
2944 3485 6.960992 CACATCACCACGATTACAAATGTTAG 59.039 38.462 0.00 0.00 29.21 2.34
2945 3486 6.128145 CCACATCACCACGATTACAAATGTTA 60.128 38.462 0.00 0.00 29.21 2.41
2946 3487 5.335583 CCACATCACCACGATTACAAATGTT 60.336 40.000 0.00 0.00 29.21 2.71
2947 3488 4.155826 CCACATCACCACGATTACAAATGT 59.844 41.667 0.00 0.00 29.21 2.71
2948 3489 4.661125 CCACATCACCACGATTACAAATG 58.339 43.478 0.00 0.00 29.21 2.32
2949 3490 3.128589 GCCACATCACCACGATTACAAAT 59.871 43.478 0.00 0.00 29.21 2.32
2950 3491 2.486203 GCCACATCACCACGATTACAAA 59.514 45.455 0.00 0.00 29.21 2.83
2951 3492 2.080693 GCCACATCACCACGATTACAA 58.919 47.619 0.00 0.00 29.21 2.41
2952 3493 1.002544 TGCCACATCACCACGATTACA 59.997 47.619 0.00 0.00 29.21 2.41
2953 3494 1.732941 TGCCACATCACCACGATTAC 58.267 50.000 0.00 0.00 29.21 1.89
2954 3495 2.093235 TGATGCCACATCACCACGATTA 60.093 45.455 6.17 0.00 29.21 1.75
2955 3496 1.339920 TGATGCCACATCACCACGATT 60.340 47.619 6.17 0.00 29.21 3.34
2956 3497 0.252761 TGATGCCACATCACCACGAT 59.747 50.000 6.17 0.00 33.27 3.73
2957 3498 0.252761 ATGATGCCACATCACCACGA 59.747 50.000 12.18 0.00 0.00 4.35
2958 3499 1.097232 AATGATGCCACATCACCACG 58.903 50.000 12.18 0.00 0.00 4.94
2959 3500 3.282021 ACTAATGATGCCACATCACCAC 58.718 45.455 12.18 0.00 0.00 4.16
2960 3501 3.650281 ACTAATGATGCCACATCACCA 57.350 42.857 12.18 3.19 0.00 4.17
2961 3502 4.960938 TCTACTAATGATGCCACATCACC 58.039 43.478 12.18 0.00 0.00 4.02
2962 3503 4.993584 CCTCTACTAATGATGCCACATCAC 59.006 45.833 12.18 0.00 0.00 3.06
2963 3504 4.040829 CCCTCTACTAATGATGCCACATCA 59.959 45.833 12.30 12.30 0.00 3.07
2964 3505 4.040952 ACCCTCTACTAATGATGCCACATC 59.959 45.833 0.55 0.55 0.00 3.06
2965 3506 3.976654 ACCCTCTACTAATGATGCCACAT 59.023 43.478 0.00 0.00 0.00 3.21
2966 3507 3.384168 ACCCTCTACTAATGATGCCACA 58.616 45.455 0.00 0.00 0.00 4.17
2967 3508 4.423625 AACCCTCTACTAATGATGCCAC 57.576 45.455 0.00 0.00 0.00 5.01
2968 3509 5.070446 CAGTAACCCTCTACTAATGATGCCA 59.930 44.000 0.00 0.00 30.77 4.92
2969 3510 5.070580 ACAGTAACCCTCTACTAATGATGCC 59.929 44.000 0.00 0.00 30.77 4.40
2970 3511 6.163135 ACAGTAACCCTCTACTAATGATGC 57.837 41.667 0.00 0.00 30.77 3.91
2971 3512 7.231722 AGCTACAGTAACCCTCTACTAATGATG 59.768 40.741 0.00 0.00 30.77 3.07
2972 3513 7.299134 AGCTACAGTAACCCTCTACTAATGAT 58.701 38.462 0.00 0.00 30.77 2.45
2973 3514 6.670617 AGCTACAGTAACCCTCTACTAATGA 58.329 40.000 0.00 0.00 30.77 2.57
2974 3515 6.963083 AGCTACAGTAACCCTCTACTAATG 57.037 41.667 0.00 0.00 30.77 1.90
2975 3516 9.657728 ATTAAGCTACAGTAACCCTCTACTAAT 57.342 33.333 0.00 0.00 30.77 1.73
2976 3517 9.484806 AATTAAGCTACAGTAACCCTCTACTAA 57.515 33.333 0.00 0.00 30.77 2.24
2978 3519 7.974730 AATTAAGCTACAGTAACCCTCTACT 57.025 36.000 0.00 0.00 32.13 2.57
2979 3520 9.911138 GATAATTAAGCTACAGTAACCCTCTAC 57.089 37.037 0.00 0.00 0.00 2.59
2980 3521 9.086758 GGATAATTAAGCTACAGTAACCCTCTA 57.913 37.037 0.00 0.00 0.00 2.43
2981 3522 7.255871 CGGATAATTAAGCTACAGTAACCCTCT 60.256 40.741 0.00 0.00 0.00 3.69
2982 3523 6.867293 CGGATAATTAAGCTACAGTAACCCTC 59.133 42.308 0.00 0.00 0.00 4.30
2983 3524 6.239515 CCGGATAATTAAGCTACAGTAACCCT 60.240 42.308 0.00 0.00 0.00 4.34
2984 3525 5.930569 CCGGATAATTAAGCTACAGTAACCC 59.069 44.000 0.00 0.00 0.00 4.11
2985 3526 5.930569 CCCGGATAATTAAGCTACAGTAACC 59.069 44.000 0.73 0.00 0.00 2.85
2986 3527 5.407691 GCCCGGATAATTAAGCTACAGTAAC 59.592 44.000 0.73 0.00 0.00 2.50
2987 3528 5.544650 GCCCGGATAATTAAGCTACAGTAA 58.455 41.667 0.73 0.00 0.00 2.24
2988 3529 4.321452 CGCCCGGATAATTAAGCTACAGTA 60.321 45.833 0.73 0.00 0.00 2.74
2989 3530 3.554337 CGCCCGGATAATTAAGCTACAGT 60.554 47.826 0.73 0.00 0.00 3.55
2990 3531 2.993899 CGCCCGGATAATTAAGCTACAG 59.006 50.000 0.73 0.00 0.00 2.74
2991 3532 2.366266 ACGCCCGGATAATTAAGCTACA 59.634 45.455 0.73 0.00 0.00 2.74
2992 3533 3.036075 ACGCCCGGATAATTAAGCTAC 57.964 47.619 0.73 0.00 0.00 3.58
2993 3534 3.756933 AACGCCCGGATAATTAAGCTA 57.243 42.857 0.73 0.00 0.00 3.32
2994 3535 2.632987 AACGCCCGGATAATTAAGCT 57.367 45.000 0.73 0.00 0.00 3.74
2995 3536 3.132925 TGTAACGCCCGGATAATTAAGC 58.867 45.455 0.73 0.00 0.00 3.09
2996 3537 4.374399 ACTGTAACGCCCGGATAATTAAG 58.626 43.478 0.73 0.00 0.00 1.85
2997 3538 4.405116 ACTGTAACGCCCGGATAATTAA 57.595 40.909 0.73 0.00 0.00 1.40
2998 3539 4.405116 AACTGTAACGCCCGGATAATTA 57.595 40.909 0.73 0.00 0.00 1.40
2999 3540 2.994186 ACTGTAACGCCCGGATAATT 57.006 45.000 0.73 0.00 0.00 1.40
3000 3541 2.994186 AACTGTAACGCCCGGATAAT 57.006 45.000 0.73 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.