Multiple sequence alignment - TraesCS6A01G249900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G249900 chr6A 100.000 3250 0 0 1 3250 463528154 463531403 0.000000e+00 6002.0
1 TraesCS6A01G249900 chr6D 96.571 2304 69 4 1 2299 325389902 325392200 0.000000e+00 3808.0
2 TraesCS6A01G249900 chr6D 87.613 993 85 24 295 1276 417474074 417473109 0.000000e+00 1118.0
3 TraesCS6A01G249900 chr6D 87.210 993 89 24 295 1276 416965093 416964128 0.000000e+00 1096.0
4 TraesCS6A01G249900 chr6D 83.861 948 120 26 828 1771 415515407 415514489 0.000000e+00 872.0
5 TraesCS6A01G249900 chr6D 84.626 722 63 16 1503 2224 416016236 416015563 0.000000e+00 675.0
6 TraesCS6A01G249900 chr6D 84.626 722 63 16 1503 2224 416123778 416123105 0.000000e+00 675.0
7 TraesCS6A01G249900 chr6D 84.488 722 64 16 1503 2224 417472835 417472162 0.000000e+00 669.0
8 TraesCS6A01G249900 chr6D 84.349 722 64 17 1503 2224 416963854 416963182 0.000000e+00 662.0
9 TraesCS6A01G249900 chr6D 94.408 304 16 1 974 1276 416016813 416016510 1.770000e-127 466.0
10 TraesCS6A01G249900 chr6D 94.408 304 16 1 974 1276 416124355 416124052 1.770000e-127 466.0
11 TraesCS6A01G249900 chr6D 80.882 476 52 20 295 768 417480564 417480126 4.020000e-89 339.0
12 TraesCS6A01G249900 chr6D 94.712 208 10 1 2507 2714 325392425 325392631 4.050000e-84 322.0
13 TraesCS6A01G249900 chr6D 89.744 234 24 0 1043 1276 417480132 417479899 1.900000e-77 300.0
14 TraesCS6A01G249900 chr6D 93.407 182 12 0 1363 1544 417479899 417479718 1.490000e-68 270.0
15 TraesCS6A01G249900 chr6D 92.308 182 14 0 1363 1544 416016510 416016329 3.220000e-65 259.0
16 TraesCS6A01G249900 chr6D 92.308 182 14 0 1363 1544 416124052 416123871 3.220000e-65 259.0
17 TraesCS6A01G249900 chr6D 92.308 182 14 0 1363 1544 416964128 416963947 3.220000e-65 259.0
18 TraesCS6A01G249900 chr6D 91.758 182 15 0 1363 1544 417473109 417472928 1.500000e-63 254.0
19 TraesCS6A01G249900 chr6D 93.750 160 10 0 2299 2458 325392268 325392427 1.170000e-59 241.0
20 TraesCS6A01G249900 chr6D 78.873 355 38 16 297 649 417480935 417480616 4.250000e-49 206.0
21 TraesCS6A01G249900 chr6D 79.114 316 31 19 337 649 416018151 416017868 5.540000e-43 185.0
22 TraesCS6A01G249900 chr6D 79.114 316 31 19 337 649 416126058 416125775 5.540000e-43 185.0
23 TraesCS6A01G249900 chr6D 79.114 316 31 19 337 649 416965428 416965145 5.540000e-43 185.0
24 TraesCS6A01G249900 chr6D 92.632 95 7 0 2926 3020 387885987 387886081 1.570000e-28 137.0
25 TraesCS6A01G249900 chr6D 87.179 117 6 6 1917 2025 417474330 417474215 1.220000e-24 124.0
26 TraesCS6A01G249900 chr6D 98.039 51 1 0 1004 1054 415199027 415198977 4.470000e-14 89.8
27 TraesCS6A01G249900 chr6D 100.000 30 0 0 2637 2666 325392682 325392711 4.530000e-04 56.5
28 TraesCS6A01G249900 chr6B 94.746 2322 74 14 1 2302 497888390 497886097 0.000000e+00 3568.0
29 TraesCS6A01G249900 chr6B 86.351 1077 91 24 295 1357 629580480 629581514 0.000000e+00 1123.0
30 TraesCS6A01G249900 chr6B 86.258 1077 92 24 295 1357 628894531 628895565 0.000000e+00 1118.0
31 TraesCS6A01G249900 chr6B 88.798 491 55 0 1054 1544 628893705 628894195 1.290000e-168 603.0
32 TraesCS6A01G249900 chr6B 88.798 491 55 0 1054 1544 629579654 629580144 1.290000e-168 603.0
33 TraesCS6A01G249900 chr6B 94.753 324 13 3 2299 2621 497886032 497885712 4.840000e-138 501.0
34 TraesCS6A01G249900 chr6B 82.068 474 52 18 295 767 628893258 628893699 1.100000e-99 374.0
35 TraesCS6A01G249900 chr6B 82.068 474 52 18 295 767 629579207 629579648 1.100000e-99 374.0
36 TraesCS6A01G249900 chr6B 89.362 282 26 3 1943 2224 628895567 628895844 5.160000e-93 351.0
37 TraesCS6A01G249900 chr6B 89.007 282 27 3 1943 2224 629581516 629581793 2.400000e-91 346.0
38 TraesCS6A01G249900 chr6B 92.969 128 8 1 2806 2932 497885633 497885506 5.540000e-43 185.0
39 TraesCS6A01G249900 chr6B 93.684 95 4 2 3013 3106 497885508 497885415 1.220000e-29 141.0
40 TraesCS6A01G249900 chr6B 89.524 105 9 2 2701 2805 13827627 13827525 7.320000e-27 132.0
41 TraesCS6A01G249900 chr6B 98.276 58 1 0 2653 2710 497885715 497885658 5.740000e-18 102.0
42 TraesCS6A01G249900 chr5D 95.484 155 6 1 3097 3250 115404095 115404249 2.500000e-61 246.0
43 TraesCS6A01G249900 chr5D 95.946 148 6 0 3103 3250 487559659 487559806 1.170000e-59 241.0
44 TraesCS6A01G249900 chr5B 96.599 147 5 0 3104 3250 146825611 146825757 9.010000e-61 244.0
45 TraesCS6A01G249900 chr5B 93.478 92 6 0 2716 2807 51965408 51965499 1.570000e-28 137.0
46 TraesCS6A01G249900 chr5B 92.045 88 7 0 2720 2807 241165147 241165060 1.220000e-24 124.0
47 TraesCS6A01G249900 chr2A 96.000 150 6 0 3101 3250 177665584 177665733 9.010000e-61 244.0
48 TraesCS6A01G249900 chr2A 94.505 91 5 0 2716 2806 39327509 39327419 1.220000e-29 141.0
49 TraesCS6A01G249900 chr3B 96.575 146 5 0 3105 3250 49950064 49949919 3.240000e-60 243.0
50 TraesCS6A01G249900 chr3B 96.575 146 5 0 3105 3250 235884226 235884081 3.240000e-60 243.0
51 TraesCS6A01G249900 chr3B 95.395 152 7 0 3099 3250 523158155 523158306 3.240000e-60 243.0
52 TraesCS6A01G249900 chr3B 96.512 86 3 0 2929 3014 70294016 70293931 3.380000e-30 143.0
53 TraesCS6A01G249900 chr3B 94.444 90 5 0 2719 2808 651703661 651703750 4.370000e-29 139.0
54 TraesCS6A01G249900 chr2B 95.425 153 6 1 3099 3250 711446787 711446939 3.240000e-60 243.0
55 TraesCS6A01G249900 chr3A 90.751 173 11 5 3081 3250 78571710 78571880 3.260000e-55 226.0
56 TraesCS6A01G249900 chr3A 91.667 96 8 0 2709 2804 710277873 710277968 2.030000e-27 134.0
57 TraesCS6A01G249900 chr7A 94.624 93 4 1 2717 2808 460121888 460121980 3.380000e-30 143.0
58 TraesCS6A01G249900 chr2D 92.708 96 7 0 2921 3016 341665952 341665857 4.370000e-29 139.0
59 TraesCS6A01G249900 chr1D 92.784 97 6 1 2925 3021 333465364 333465269 4.370000e-29 139.0
60 TraesCS6A01G249900 chr1D 94.505 91 4 1 2924 3013 355081125 355081215 4.370000e-29 139.0
61 TraesCS6A01G249900 chr7D 93.478 92 6 0 2922 3013 5068177 5068086 1.570000e-28 137.0
62 TraesCS6A01G249900 chr7D 88.393 112 9 1 2929 3040 141292172 141292065 7.320000e-27 132.0
63 TraesCS6A01G249900 chrUn 91.837 98 7 1 2708 2805 86631076 86630980 5.660000e-28 135.0
64 TraesCS6A01G249900 chr4D 91.837 98 7 1 2924 3020 455628465 455628562 5.660000e-28 135.0
65 TraesCS6A01G249900 chr3D 94.318 88 5 0 2929 3016 135380752 135380839 5.660000e-28 135.0
66 TraesCS6A01G249900 chr4B 91.667 96 8 0 2712 2807 648544183 648544278 2.030000e-27 134.0


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 TraesCS6A01G249900 chr6A 463528154 463531403 3249 False 6002.000 6002 100.00000 1 3250 1 chr6A.!!$F1 3249
1 TraesCS6A01G249900 chr6D 325389902 325392711 2809 False 1106.875 3808 96.25825 1 2714 4 chr6D.!!$F2 2713
2 TraesCS6A01G249900 chr6D 415514489 415515407 918 True 872.000 872 83.86100 828 1771 1 chr6D.!!$R2 943
3 TraesCS6A01G249900 chr6D 416963182 416965428 2246 True 550.500 1096 85.74525 295 2224 4 chr6D.!!$R5 1929
4 TraesCS6A01G249900 chr6D 417472162 417474330 2168 True 541.250 1118 87.75950 295 2224 4 chr6D.!!$R6 1929
5 TraesCS6A01G249900 chr6D 416015563 416018151 2588 True 396.250 675 87.61400 337 2224 4 chr6D.!!$R3 1887
6 TraesCS6A01G249900 chr6D 416123105 416126058 2953 True 396.250 675 87.61400 337 2224 4 chr6D.!!$R4 1887
7 TraesCS6A01G249900 chr6D 417479718 417480935 1217 True 278.750 339 85.72650 295 1544 4 chr6D.!!$R7 1249
8 TraesCS6A01G249900 chr6B 497885415 497888390 2975 True 899.400 3568 94.88560 1 3106 5 chr6B.!!$R2 3105
9 TraesCS6A01G249900 chr6B 628893258 628895844 2586 False 611.500 1118 86.62150 295 2224 4 chr6B.!!$F1 1929
10 TraesCS6A01G249900 chr6B 629579207 629581793 2586 False 611.500 1123 86.55600 295 2224 4 chr6B.!!$F2 1929

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
377 882 0.175989 CCAGGAACTAAGGCCTCGAC 59.824 60.000 5.23 0.88 36.02 4.20 F
636 1151 3.056607 GGTTGTCTGGTTCCATCCAATTG 60.057 47.826 0.00 0.00 37.01 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 3585 0.029433 TCCTCGTCATCATTCGCTCG 59.971 55.0 0.0 0.0 0.0 5.03 R
2316 5127 0.706433 ATCCCAGGACAGCAAACCAT 59.294 50.0 0.0 0.0 0.0 3.55 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
157 158 0.816421 CGGTTCCCGTGTTCTTGGTT 60.816 55.000 0.00 0.00 42.73 3.67
171 172 0.306533 TTGGTTCTCTTTCGCGTTGC 59.693 50.000 5.77 0.00 0.00 4.17
238 247 0.250295 TTTTCCCTGCCGTCAGTCTG 60.250 55.000 0.00 0.00 38.66 3.51
353 362 4.753107 TGGAACTGTTCGGTTTCTTGTATC 59.247 41.667 13.89 0.00 0.00 2.24
355 364 4.247267 ACTGTTCGGTTTCTTGTATCGA 57.753 40.909 0.00 0.00 0.00 3.59
377 882 0.175989 CCAGGAACTAAGGCCTCGAC 59.824 60.000 5.23 0.88 36.02 4.20
425 930 9.445878 TTCATAGGATTCTTGATTGATAGATGC 57.554 33.333 0.00 0.00 0.00 3.91
588 1103 6.580788 TCATACCAATGGTGCATTTATTTGG 58.419 36.000 16.41 12.49 36.19 3.28
593 1108 5.881443 CCAATGGTGCATTTATTTGGTCAAT 59.119 36.000 0.00 0.00 31.05 2.57
616 1131 6.078456 TCAACCAGATTAGGATGATTTGGT 57.922 37.500 0.00 0.00 42.04 3.67
636 1151 3.056607 GGTTGTCTGGTTCCATCCAATTG 60.057 47.826 0.00 0.00 37.01 2.32
1225 2837 5.320549 ACATGAATTTGAGACAATCCTGC 57.679 39.130 0.00 0.00 0.00 4.85
1501 3201 7.104326 ACTTTTTAACATGCATTTGTTAGCG 57.896 32.000 11.60 6.05 41.65 4.26
1529 3229 4.472833 ACTAGGGAGTTGCTCAGAATCAAT 59.527 41.667 0.00 0.00 28.61 2.57
1602 3628 1.696063 AATGGCTTGGGGAATGATCG 58.304 50.000 0.00 0.00 0.00 3.69
1706 4095 6.093219 GCATGCTCCTGATTATTGGTACATAG 59.907 42.308 11.37 0.00 39.30 2.23
1713 4102 9.822727 TCCTGATTATTGGTACATAGATGACTA 57.177 33.333 0.00 0.00 39.30 2.59
2171 4914 3.677648 CAGGCAGCCACCAACAGC 61.678 66.667 15.80 0.00 0.00 4.40
2225 4968 1.561643 TGTCTAGGACAGGAAGGCTG 58.438 55.000 0.00 0.00 37.67 4.85
2232 4975 4.437587 CAGGAAGGCTGCCCTGGG 62.438 72.222 21.94 8.86 44.68 4.45
2377 5188 1.067364 TGCAACACTTGGTCAGCATTG 59.933 47.619 0.00 0.00 36.07 2.82
2434 5245 5.011943 CCCATTGGAGAAGTGAAAAATTCCA 59.988 40.000 3.62 0.00 33.17 3.53
2449 5260 2.136298 TTCCACACTGTTGGCTTGAA 57.864 45.000 4.71 0.00 36.48 2.69
2469 5280 5.614308 TGAAGATTATGGTAGCATGGTCTG 58.386 41.667 17.58 0.00 0.00 3.51
2481 5292 4.449131 AGCATGGTCTGATGATACAAGTG 58.551 43.478 0.00 0.00 0.00 3.16
2482 5293 4.080695 AGCATGGTCTGATGATACAAGTGT 60.081 41.667 0.00 0.00 0.00 3.55
2504 5315 5.535030 TGTTCCCTTCTCTTTTCCTTTTAGC 59.465 40.000 0.00 0.00 0.00 3.09
2508 5319 5.405797 CCTTCTCTTTTCCTTTTAGCATGC 58.594 41.667 10.51 10.51 0.00 4.06
2525 5336 3.799366 CATGCCATTGGTTACATGCAAT 58.201 40.909 4.26 0.00 34.11 3.56
2682 5494 4.409247 AGGAGTAGACAAGAAACTGGTTGT 59.591 41.667 0.00 0.00 39.62 3.32
2710 5522 4.071961 TGCCACTGCCAATGTATACTAG 57.928 45.455 4.17 0.00 36.33 2.57
2711 5523 3.454447 TGCCACTGCCAATGTATACTAGT 59.546 43.478 0.00 0.00 36.33 2.57
2712 5524 4.651962 TGCCACTGCCAATGTATACTAGTA 59.348 41.667 4.77 4.77 36.33 1.82
2713 5525 4.989168 GCCACTGCCAATGTATACTAGTAC 59.011 45.833 4.31 0.00 0.00 2.73
2714 5526 5.452776 GCCACTGCCAATGTATACTAGTACA 60.453 44.000 4.31 2.48 38.79 2.90
2715 5527 6.216569 CCACTGCCAATGTATACTAGTACAG 58.783 44.000 4.31 7.90 37.93 2.74
2716 5528 6.183360 CCACTGCCAATGTATACTAGTACAGT 60.183 42.308 4.31 8.52 37.93 3.55
2717 5529 7.013942 CCACTGCCAATGTATACTAGTACAGTA 59.986 40.741 14.57 1.72 43.89 2.74
2718 5530 8.076781 CACTGCCAATGTATACTAGTACAGTAG 58.923 40.741 14.57 8.32 43.01 2.57
2719 5531 7.778853 ACTGCCAATGTATACTAGTACAGTAGT 59.221 37.037 13.77 8.32 43.01 2.73
2720 5532 9.281371 CTGCCAATGTATACTAGTACAGTAGTA 57.719 37.037 4.31 6.44 43.01 1.82
2730 5542 3.274095 GTACAGTAGTACTCCCTCCGT 57.726 52.381 0.00 0.00 45.66 4.69
2731 5543 4.408182 GTACAGTAGTACTCCCTCCGTA 57.592 50.000 0.00 0.00 45.66 4.02
2732 5544 4.770795 GTACAGTAGTACTCCCTCCGTAA 58.229 47.826 0.00 0.00 45.66 3.18
2733 5545 4.307032 ACAGTAGTACTCCCTCCGTAAA 57.693 45.455 0.00 0.00 0.00 2.01
2734 5546 4.013050 ACAGTAGTACTCCCTCCGTAAAC 58.987 47.826 0.00 0.00 0.00 2.01
2735 5547 4.012374 CAGTAGTACTCCCTCCGTAAACA 58.988 47.826 0.00 0.00 0.00 2.83
2736 5548 4.460382 CAGTAGTACTCCCTCCGTAAACAA 59.540 45.833 0.00 0.00 0.00 2.83
2737 5549 5.047802 CAGTAGTACTCCCTCCGTAAACAAA 60.048 44.000 0.00 0.00 0.00 2.83
2738 5550 5.718607 AGTAGTACTCCCTCCGTAAACAAAT 59.281 40.000 0.00 0.00 0.00 2.32
2739 5551 6.891908 AGTAGTACTCCCTCCGTAAACAAATA 59.108 38.462 0.00 0.00 0.00 1.40
2740 5552 6.803366 AGTACTCCCTCCGTAAACAAATAT 57.197 37.500 0.00 0.00 0.00 1.28
2741 5553 7.902920 AGTACTCCCTCCGTAAACAAATATA 57.097 36.000 0.00 0.00 0.00 0.86
2742 5554 8.310122 AGTACTCCCTCCGTAAACAAATATAA 57.690 34.615 0.00 0.00 0.00 0.98
2743 5555 8.419442 AGTACTCCCTCCGTAAACAAATATAAG 58.581 37.037 0.00 0.00 0.00 1.73
2744 5556 7.427989 ACTCCCTCCGTAAACAAATATAAGA 57.572 36.000 0.00 0.00 0.00 2.10
2745 5557 7.854337 ACTCCCTCCGTAAACAAATATAAGAA 58.146 34.615 0.00 0.00 0.00 2.52
2746 5558 7.767659 ACTCCCTCCGTAAACAAATATAAGAAC 59.232 37.037 0.00 0.00 0.00 3.01
2747 5559 7.622713 TCCCTCCGTAAACAAATATAAGAACA 58.377 34.615 0.00 0.00 0.00 3.18
2748 5560 8.269317 TCCCTCCGTAAACAAATATAAGAACAT 58.731 33.333 0.00 0.00 0.00 2.71
2749 5561 8.899771 CCCTCCGTAAACAAATATAAGAACATT 58.100 33.333 0.00 0.00 0.00 2.71
2778 5590 9.250624 GATCATTAAAGTAGTGATCTAAACGCT 57.749 33.333 11.46 0.00 44.08 5.07
2779 5591 8.630278 TCATTAAAGTAGTGATCTAAACGCTC 57.370 34.615 0.00 0.00 0.00 5.03
2780 5592 8.467598 TCATTAAAGTAGTGATCTAAACGCTCT 58.532 33.333 0.00 0.00 0.00 4.09
2781 5593 9.088512 CATTAAAGTAGTGATCTAAACGCTCTT 57.911 33.333 0.00 0.00 0.00 2.85
2790 5602 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
2798 5610 7.218145 ACGCTCTTATATTTGTTTACAGACG 57.782 36.000 0.00 0.00 0.00 4.18
2799 5611 6.255020 ACGCTCTTATATTTGTTTACAGACGG 59.745 38.462 0.00 0.00 0.00 4.79
2800 5612 6.474427 CGCTCTTATATTTGTTTACAGACGGA 59.526 38.462 0.00 0.00 0.00 4.69
2801 5613 7.306051 CGCTCTTATATTTGTTTACAGACGGAG 60.306 40.741 0.00 0.00 0.00 4.63
2818 5630 7.036220 CAGACGGAGTACTACTCAAAATTCAT 58.964 38.462 16.49 0.00 46.79 2.57
2848 5687 1.519234 TACGCCTGCTGCTTCATCG 60.519 57.895 0.00 0.28 38.05 3.84
2871 5710 4.008330 GGTTTAGGAGTACTTCTTTGGGC 58.992 47.826 9.53 0.00 0.00 5.36
2879 5718 5.488341 GAGTACTTCTTTGGGCAAGACATA 58.512 41.667 0.00 0.00 41.56 2.29
2886 5725 5.385198 TCTTTGGGCAAGACATAGAAGTTT 58.615 37.500 0.00 0.00 36.51 2.66
2893 5732 5.390991 GGCAAGACATAGAAGTTTAGCACAC 60.391 44.000 0.00 0.00 0.00 3.82
2928 5767 9.777297 TTTTAGCTATGCCTTTTCAAAAGAATT 57.223 25.926 11.73 0.00 0.00 2.17
2930 5769 9.855021 TTAGCTATGCCTTTTCAAAAGAATTAC 57.145 29.630 11.73 1.69 0.00 1.89
2931 5770 8.127150 AGCTATGCCTTTTCAAAAGAATTACT 57.873 30.769 11.73 3.64 0.00 2.24
2932 5771 8.246871 AGCTATGCCTTTTCAAAAGAATTACTC 58.753 33.333 11.73 0.00 0.00 2.59
2933 5772 7.489435 GCTATGCCTTTTCAAAAGAATTACTCC 59.511 37.037 11.73 0.00 0.00 3.85
2934 5773 6.096673 TGCCTTTTCAAAAGAATTACTCCC 57.903 37.500 11.73 0.00 0.00 4.30
2935 5774 5.838521 TGCCTTTTCAAAAGAATTACTCCCT 59.161 36.000 11.73 0.00 0.00 4.20
2936 5775 6.015434 TGCCTTTTCAAAAGAATTACTCCCTC 60.015 38.462 11.73 0.00 0.00 4.30
2937 5776 6.209589 GCCTTTTCAAAAGAATTACTCCCTCT 59.790 38.462 11.73 0.00 0.00 3.69
2938 5777 7.393515 GCCTTTTCAAAAGAATTACTCCCTCTA 59.606 37.037 11.73 0.00 0.00 2.43
2939 5778 9.467796 CCTTTTCAAAAGAATTACTCCCTCTAT 57.532 33.333 11.73 0.00 0.00 1.98
2942 5781 9.462606 TTTCAAAAGAATTACTCCCTCTATTCC 57.537 33.333 0.00 0.00 0.00 3.01
2943 5782 8.158025 TCAAAAGAATTACTCCCTCTATTCCA 57.842 34.615 0.00 0.00 0.00 3.53
2944 5783 8.781951 TCAAAAGAATTACTCCCTCTATTCCAT 58.218 33.333 0.00 0.00 0.00 3.41
2955 5794 9.207868 ACTCCCTCTATTCCATAATATAAGAGC 57.792 37.037 0.00 0.00 29.45 4.09
2956 5795 8.239038 TCCCTCTATTCCATAATATAAGAGCG 57.761 38.462 0.00 0.00 29.45 5.03
2957 5796 7.839705 TCCCTCTATTCCATAATATAAGAGCGT 59.160 37.037 0.00 0.00 29.45 5.07
2958 5797 8.478877 CCCTCTATTCCATAATATAAGAGCGTT 58.521 37.037 0.00 0.00 29.45 4.84
2959 5798 9.877178 CCTCTATTCCATAATATAAGAGCGTTT 57.123 33.333 0.00 0.00 29.45 3.60
2965 5804 8.725405 TCCATAATATAAGAGCGTTTTTGACA 57.275 30.769 0.00 0.00 0.00 3.58
2966 5805 8.609176 TCCATAATATAAGAGCGTTTTTGACAC 58.391 33.333 0.00 0.00 0.00 3.67
2967 5806 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
2970 5809 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
2971 5810 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
2972 5811 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
2973 5812 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
2974 5813 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
2975 5814 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
3005 5844 9.866655 AAAAATGCTCTTATATTATGGGACTGA 57.133 29.630 0.00 0.00 0.00 3.41
3006 5845 9.512588 AAAATGCTCTTATATTATGGGACTGAG 57.487 33.333 0.00 0.00 0.00 3.35
3007 5846 6.611613 TGCTCTTATATTATGGGACTGAGG 57.388 41.667 0.00 0.00 0.00 3.86
3008 5847 5.485353 TGCTCTTATATTATGGGACTGAGGG 59.515 44.000 0.00 0.00 0.00 4.30
3009 5848 5.721960 GCTCTTATATTATGGGACTGAGGGA 59.278 44.000 0.00 0.00 0.00 4.20
3010 5849 6.127196 GCTCTTATATTATGGGACTGAGGGAG 60.127 46.154 0.00 0.00 0.00 4.30
3011 5850 6.875469 TCTTATATTATGGGACTGAGGGAGT 58.125 40.000 0.00 0.00 37.76 3.85
3054 5893 9.985318 TCAACAATTTTGACACAAATTTGATTC 57.015 25.926 24.64 18.13 0.00 2.52
3100 5939 6.128418 TGCGATAATCTTTGTGAACGATGAAA 60.128 34.615 0.00 0.00 0.00 2.69
3106 5945 8.782533 AATCTTTGTGAACGATGAAAAAGTAC 57.217 30.769 0.00 0.00 0.00 2.73
3107 5946 7.548196 TCTTTGTGAACGATGAAAAAGTACT 57.452 32.000 0.00 0.00 0.00 2.73
3108 5947 8.651391 TCTTTGTGAACGATGAAAAAGTACTA 57.349 30.769 0.00 0.00 0.00 1.82
3109 5948 8.545420 TCTTTGTGAACGATGAAAAAGTACTAC 58.455 33.333 0.00 0.00 0.00 2.73
3110 5949 6.774354 TGTGAACGATGAAAAAGTACTACC 57.226 37.500 0.00 0.00 0.00 3.18
3111 5950 6.518493 TGTGAACGATGAAAAAGTACTACCT 58.482 36.000 0.00 0.00 0.00 3.08
3112 5951 6.643770 TGTGAACGATGAAAAAGTACTACCTC 59.356 38.462 0.00 0.00 0.00 3.85
3113 5952 6.090493 GTGAACGATGAAAAAGTACTACCTCC 59.910 42.308 0.00 0.00 0.00 4.30
3114 5953 4.741342 ACGATGAAAAAGTACTACCTCCG 58.259 43.478 0.00 0.00 0.00 4.63
3115 5954 4.219288 ACGATGAAAAAGTACTACCTCCGT 59.781 41.667 0.00 0.00 0.00 4.69
3116 5955 4.797349 CGATGAAAAAGTACTACCTCCGTC 59.203 45.833 0.00 0.00 0.00 4.79
3117 5956 4.525912 TGAAAAAGTACTACCTCCGTCC 57.474 45.455 0.00 0.00 0.00 4.79
3118 5957 4.154942 TGAAAAAGTACTACCTCCGTCCT 58.845 43.478 0.00 0.00 0.00 3.85
3119 5958 4.021719 TGAAAAAGTACTACCTCCGTCCTG 60.022 45.833 0.00 0.00 0.00 3.86
3120 5959 2.140839 AAGTACTACCTCCGTCCTGG 57.859 55.000 0.00 0.00 40.09 4.45
3121 5960 0.998145 AGTACTACCTCCGTCCTGGT 59.002 55.000 0.00 0.00 39.52 4.00
3122 5961 1.101331 GTACTACCTCCGTCCTGGTG 58.899 60.000 0.00 0.00 39.52 4.17
3123 5962 0.700564 TACTACCTCCGTCCTGGTGT 59.299 55.000 0.00 0.00 39.52 4.16
3124 5963 0.700564 ACTACCTCCGTCCTGGTGTA 59.299 55.000 0.00 0.00 39.52 2.90
3125 5964 1.287146 ACTACCTCCGTCCTGGTGTAT 59.713 52.381 0.00 0.00 39.52 2.29
3126 5965 2.511218 ACTACCTCCGTCCTGGTGTATA 59.489 50.000 0.00 0.00 39.52 1.47
3127 5966 2.537633 ACCTCCGTCCTGGTGTATAA 57.462 50.000 0.00 0.00 39.52 0.98
3128 5967 2.385803 ACCTCCGTCCTGGTGTATAAG 58.614 52.381 0.00 0.00 39.52 1.73
3129 5968 2.292061 ACCTCCGTCCTGGTGTATAAGT 60.292 50.000 0.00 0.00 39.52 2.24
3130 5969 2.361438 CCTCCGTCCTGGTGTATAAGTC 59.639 54.545 0.00 0.00 39.52 3.01
3131 5970 3.021695 CTCCGTCCTGGTGTATAAGTCA 58.978 50.000 0.00 0.00 39.52 3.41
3132 5971 3.637229 CTCCGTCCTGGTGTATAAGTCAT 59.363 47.826 0.00 0.00 39.52 3.06
3133 5972 4.028131 TCCGTCCTGGTGTATAAGTCATT 58.972 43.478 0.00 0.00 39.52 2.57
3134 5973 4.098960 TCCGTCCTGGTGTATAAGTCATTC 59.901 45.833 0.00 0.00 39.52 2.67
3135 5974 4.042398 CGTCCTGGTGTATAAGTCATTCG 58.958 47.826 0.00 0.00 0.00 3.34
3136 5975 3.802685 GTCCTGGTGTATAAGTCATTCGC 59.197 47.826 0.00 0.00 0.00 4.70
3137 5976 2.794910 CCTGGTGTATAAGTCATTCGCG 59.205 50.000 0.00 0.00 0.00 5.87
3138 5977 3.444916 CTGGTGTATAAGTCATTCGCGT 58.555 45.455 5.77 0.00 0.00 6.01
3139 5978 4.498513 CCTGGTGTATAAGTCATTCGCGTA 60.499 45.833 5.77 0.00 0.00 4.42
3140 5979 4.603985 TGGTGTATAAGTCATTCGCGTAG 58.396 43.478 5.77 0.00 0.00 3.51
3141 5980 4.096833 TGGTGTATAAGTCATTCGCGTAGT 59.903 41.667 5.77 0.00 0.00 2.73
3142 5981 5.039333 GGTGTATAAGTCATTCGCGTAGTT 58.961 41.667 5.77 2.59 0.00 2.24
3143 5982 5.172771 GGTGTATAAGTCATTCGCGTAGTTC 59.827 44.000 5.77 0.00 0.00 3.01
3144 5983 5.970023 GTGTATAAGTCATTCGCGTAGTTCT 59.030 40.000 5.77 0.00 0.00 3.01
3145 5984 7.128331 GTGTATAAGTCATTCGCGTAGTTCTA 58.872 38.462 5.77 0.00 0.00 2.10
3146 5985 7.320797 GTGTATAAGTCATTCGCGTAGTTCTAG 59.679 40.741 5.77 0.00 0.00 2.43
3147 5986 3.694535 AGTCATTCGCGTAGTTCTAGG 57.305 47.619 5.77 0.00 0.00 3.02
3148 5987 3.015327 AGTCATTCGCGTAGTTCTAGGT 58.985 45.455 5.77 0.00 0.00 3.08
3149 5988 3.065095 AGTCATTCGCGTAGTTCTAGGTC 59.935 47.826 5.77 0.00 0.00 3.85
3150 5989 3.011818 TCATTCGCGTAGTTCTAGGTCA 58.988 45.455 5.77 0.00 0.00 4.02
3151 5990 3.441222 TCATTCGCGTAGTTCTAGGTCAA 59.559 43.478 5.77 0.00 0.00 3.18
3152 5991 2.907910 TCGCGTAGTTCTAGGTCAAC 57.092 50.000 5.77 0.00 0.00 3.18
3153 5992 2.153645 TCGCGTAGTTCTAGGTCAACA 58.846 47.619 5.77 0.00 0.00 3.33
3154 5993 2.553602 TCGCGTAGTTCTAGGTCAACAA 59.446 45.455 5.77 0.00 0.00 2.83
3155 5994 3.192001 TCGCGTAGTTCTAGGTCAACAAT 59.808 43.478 5.77 0.00 0.00 2.71
3156 5995 3.924686 CGCGTAGTTCTAGGTCAACAATT 59.075 43.478 0.00 0.00 0.00 2.32
3157 5996 4.387862 CGCGTAGTTCTAGGTCAACAATTT 59.612 41.667 0.00 0.00 0.00 1.82
3158 5997 5.574055 CGCGTAGTTCTAGGTCAACAATTTA 59.426 40.000 0.00 0.00 0.00 1.40
3159 5998 6.089820 CGCGTAGTTCTAGGTCAACAATTTAA 59.910 38.462 0.00 0.00 0.00 1.52
3160 5999 7.232300 GCGTAGTTCTAGGTCAACAATTTAAC 58.768 38.462 0.00 0.00 0.00 2.01
3161 6000 7.117379 GCGTAGTTCTAGGTCAACAATTTAACT 59.883 37.037 0.00 0.00 0.00 2.24
3162 6001 9.630098 CGTAGTTCTAGGTCAACAATTTAACTA 57.370 33.333 0.00 0.00 0.00 2.24
3219 6058 7.715265 ATATTTAGAAACTACATCCGTGCAG 57.285 36.000 0.00 0.00 0.00 4.41
3220 6059 4.794278 TTAGAAACTACATCCGTGCAGA 57.206 40.909 0.00 0.00 0.00 4.26
3221 6060 3.678056 AGAAACTACATCCGTGCAGAA 57.322 42.857 0.00 0.00 0.00 3.02
3222 6061 4.002906 AGAAACTACATCCGTGCAGAAA 57.997 40.909 0.00 0.00 0.00 2.52
3223 6062 4.579869 AGAAACTACATCCGTGCAGAAAT 58.420 39.130 0.00 0.00 0.00 2.17
3224 6063 4.631813 AGAAACTACATCCGTGCAGAAATC 59.368 41.667 0.00 0.00 0.00 2.17
3225 6064 3.895232 ACTACATCCGTGCAGAAATCT 57.105 42.857 0.00 0.00 0.00 2.40
3226 6065 5.339008 AACTACATCCGTGCAGAAATCTA 57.661 39.130 0.00 0.00 0.00 1.98
3227 6066 4.938080 ACTACATCCGTGCAGAAATCTAG 58.062 43.478 0.00 0.00 0.00 2.43
3228 6067 3.895232 ACATCCGTGCAGAAATCTAGT 57.105 42.857 0.00 0.00 0.00 2.57
3229 6068 5.593095 ACTACATCCGTGCAGAAATCTAGTA 59.407 40.000 0.00 0.00 0.00 1.82
3230 6069 5.339008 ACATCCGTGCAGAAATCTAGTAA 57.661 39.130 0.00 0.00 0.00 2.24
3231 6070 5.918608 ACATCCGTGCAGAAATCTAGTAAT 58.081 37.500 0.00 0.00 0.00 1.89
3232 6071 7.050970 ACATCCGTGCAGAAATCTAGTAATA 57.949 36.000 0.00 0.00 0.00 0.98
3233 6072 7.671302 ACATCCGTGCAGAAATCTAGTAATAT 58.329 34.615 0.00 0.00 0.00 1.28
3234 6073 8.803235 ACATCCGTGCAGAAATCTAGTAATATA 58.197 33.333 0.00 0.00 0.00 0.86
3235 6074 9.077674 CATCCGTGCAGAAATCTAGTAATATAC 57.922 37.037 0.00 0.00 0.00 1.47
3236 6075 8.405418 TCCGTGCAGAAATCTAGTAATATACT 57.595 34.615 0.00 0.00 42.68 2.12
3237 6076 8.857098 TCCGTGCAGAAATCTAGTAATATACTT 58.143 33.333 0.00 0.00 40.14 2.24
3238 6077 9.477484 CCGTGCAGAAATCTAGTAATATACTTT 57.523 33.333 0.00 0.00 40.14 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 158 0.667487 CAGGAGCAACGCGAAAGAGA 60.667 55.000 15.93 0.00 33.96 3.10
271 280 0.107508 ATCGATGGAGCCCAACACAG 60.108 55.000 0.00 0.00 36.95 3.66
353 362 0.106894 GGCCTTAGTTCCTGGGATCG 59.893 60.000 0.00 0.00 0.00 3.69
355 364 1.512735 GAGGCCTTAGTTCCTGGGAT 58.487 55.000 6.77 0.00 31.71 3.85
425 930 3.873952 GAGTTTCCAATCGATTCCTGGAG 59.126 47.826 15.15 1.38 40.29 3.86
588 1103 7.814264 AATCATCCTAATCTGGTTGATTGAC 57.186 36.000 15.05 0.00 46.42 3.18
593 1108 6.078456 ACCAAATCATCCTAATCTGGTTGA 57.922 37.500 0.00 0.00 39.33 3.18
616 1131 3.843422 ACAATTGGATGGAACCAGACAA 58.157 40.909 10.83 12.75 41.19 3.18
636 1151 5.407502 ACAAAACTGGAAGCAACAAGTAAC 58.592 37.500 0.00 0.00 37.60 2.50
933 1836 2.036475 ACTGGATCCGTTAGCTGCATAG 59.964 50.000 7.39 0.00 0.00 2.23
1225 2837 3.189080 TCCAATCACGAGCTGAAACAATG 59.811 43.478 0.00 0.00 30.60 2.82
1307 2919 0.247736 GCACAATCCTCGACCTCTGT 59.752 55.000 0.00 0.00 0.00 3.41
1479 3179 5.986135 ACCGCTAACAAATGCATGTTAAAAA 59.014 32.000 12.64 0.00 43.21 1.94
1481 3181 5.127693 ACCGCTAACAAATGCATGTTAAA 57.872 34.783 12.64 0.00 43.21 1.52
1501 3201 3.514309 TCTGAGCAACTCCCTAGTTAACC 59.486 47.826 0.88 0.00 44.28 2.85
1556 3582 1.712877 CTCGTCATCATTCGCTCGATG 59.287 52.381 0.00 0.00 40.34 3.84
1559 3585 0.029433 TCCTCGTCATCATTCGCTCG 59.971 55.000 0.00 0.00 0.00 5.03
1706 4095 6.425114 ACAGTCACAAGTCACAAATAGTCATC 59.575 38.462 0.00 0.00 0.00 2.92
1713 4102 5.918608 ACTAGACAGTCACAAGTCACAAAT 58.081 37.500 2.66 0.00 37.23 2.32
1846 4391 6.782082 ACATCATAAGTGCTCTGTCTAGAA 57.218 37.500 0.00 0.00 31.21 2.10
1887 4432 4.371624 TCTGGGCTTCTTTCTGATTCAA 57.628 40.909 0.00 0.00 0.00 2.69
2171 4914 2.959030 TCTCTTGACACCATCTATCCGG 59.041 50.000 0.00 0.00 0.00 5.14
2232 4975 2.294233 TGGATCACAGAAAAGCAAGTGC 59.706 45.455 0.00 0.00 42.49 4.40
2316 5127 0.706433 ATCCCAGGACAGCAAACCAT 59.294 50.000 0.00 0.00 0.00 3.55
2377 5188 7.202016 TGTCACATTTAAGAATCTGTGTTCC 57.798 36.000 0.00 0.00 0.00 3.62
2425 5236 4.081198 TCAAGCCAACAGTGTGGAATTTTT 60.081 37.500 13.85 0.00 41.65 1.94
2434 5245 4.460382 CCATAATCTTCAAGCCAACAGTGT 59.540 41.667 0.00 0.00 0.00 3.55
2449 5260 5.545335 TCATCAGACCATGCTACCATAATCT 59.455 40.000 0.00 0.00 0.00 2.40
2469 5280 5.983540 AGAGAAGGGAACACTTGTATCATC 58.016 41.667 0.00 0.00 0.00 2.92
2481 5292 5.535030 TGCTAAAAGGAAAAGAGAAGGGAAC 59.465 40.000 0.00 0.00 0.00 3.62
2482 5293 5.701224 TGCTAAAAGGAAAAGAGAAGGGAA 58.299 37.500 0.00 0.00 0.00 3.97
2504 5315 2.963548 TGCATGTAACCAATGGCATG 57.036 45.000 12.20 12.20 40.96 4.06
2508 5319 4.395542 CCCAAAATTGCATGTAACCAATGG 59.604 41.667 0.00 0.00 32.40 3.16
2543 5354 8.301252 TCAGAACAGTATAGTACCTGCAAATA 57.699 34.615 0.00 0.00 0.00 1.40
2682 5494 3.098377 ACATTGGCAGTGGCATATTGAA 58.902 40.909 21.29 4.41 43.71 2.69
2710 5522 3.274095 ACGGAGGGAGTACTACTGTAC 57.726 52.381 4.77 0.00 46.89 2.90
2711 5523 5.186198 GTTTACGGAGGGAGTACTACTGTA 58.814 45.833 4.77 5.88 0.00 2.74
2712 5524 4.013050 GTTTACGGAGGGAGTACTACTGT 58.987 47.826 4.77 6.78 0.00 3.55
2713 5525 4.012374 TGTTTACGGAGGGAGTACTACTG 58.988 47.826 4.77 1.08 0.00 2.74
2714 5526 4.307032 TGTTTACGGAGGGAGTACTACT 57.693 45.455 4.77 1.85 0.00 2.57
2715 5527 5.391312 TTTGTTTACGGAGGGAGTACTAC 57.609 43.478 0.00 0.00 0.00 2.73
2716 5528 7.902920 ATATTTGTTTACGGAGGGAGTACTA 57.097 36.000 0.00 0.00 0.00 1.82
2717 5529 6.803366 ATATTTGTTTACGGAGGGAGTACT 57.197 37.500 0.00 0.00 0.00 2.73
2718 5530 8.416329 TCTTATATTTGTTTACGGAGGGAGTAC 58.584 37.037 0.00 0.00 0.00 2.73
2719 5531 8.537728 TCTTATATTTGTTTACGGAGGGAGTA 57.462 34.615 0.00 0.00 0.00 2.59
2720 5532 7.427989 TCTTATATTTGTTTACGGAGGGAGT 57.572 36.000 0.00 0.00 0.00 3.85
2721 5533 7.767198 TGTTCTTATATTTGTTTACGGAGGGAG 59.233 37.037 0.00 0.00 0.00 4.30
2722 5534 7.622713 TGTTCTTATATTTGTTTACGGAGGGA 58.377 34.615 0.00 0.00 0.00 4.20
2723 5535 7.852971 TGTTCTTATATTTGTTTACGGAGGG 57.147 36.000 0.00 0.00 0.00 4.30
2752 5564 9.250624 AGCGTTTAGATCACTACTTTAATGATC 57.749 33.333 7.60 7.60 46.04 2.92
2753 5565 9.250624 GAGCGTTTAGATCACTACTTTAATGAT 57.749 33.333 0.00 0.00 35.77 2.45
2754 5566 8.467598 AGAGCGTTTAGATCACTACTTTAATGA 58.532 33.333 0.00 0.00 37.82 2.57
2755 5567 8.635877 AGAGCGTTTAGATCACTACTTTAATG 57.364 34.615 0.00 0.00 37.82 1.90
2764 5576 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
2772 5584 8.166706 CGTCTGTAAACAAATATAAGAGCGTTT 58.833 33.333 0.00 0.00 0.00 3.60
2773 5585 7.201496 CCGTCTGTAAACAAATATAAGAGCGTT 60.201 37.037 0.00 0.00 0.00 4.84
2774 5586 6.255020 CCGTCTGTAAACAAATATAAGAGCGT 59.745 38.462 0.00 0.00 0.00 5.07
2775 5587 6.474427 TCCGTCTGTAAACAAATATAAGAGCG 59.526 38.462 0.00 0.00 0.00 5.03
2776 5588 7.491696 ACTCCGTCTGTAAACAAATATAAGAGC 59.508 37.037 0.00 0.00 0.00 4.09
2777 5589 8.928270 ACTCCGTCTGTAAACAAATATAAGAG 57.072 34.615 0.00 0.00 0.00 2.85
2778 5590 9.793252 GTACTCCGTCTGTAAACAAATATAAGA 57.207 33.333 0.00 0.00 0.00 2.10
2779 5591 9.798994 AGTACTCCGTCTGTAAACAAATATAAG 57.201 33.333 0.00 0.00 0.00 1.73
2782 5594 8.964772 AGTAGTACTCCGTCTGTAAACAAATAT 58.035 33.333 0.00 0.00 0.00 1.28
2783 5595 8.340618 AGTAGTACTCCGTCTGTAAACAAATA 57.659 34.615 0.00 0.00 0.00 1.40
2784 5596 7.040201 TGAGTAGTACTCCGTCTGTAAACAAAT 60.040 37.037 24.32 0.00 44.44 2.32
2785 5597 6.262944 TGAGTAGTACTCCGTCTGTAAACAAA 59.737 38.462 24.32 1.12 44.44 2.83
2786 5598 5.764686 TGAGTAGTACTCCGTCTGTAAACAA 59.235 40.000 24.32 1.53 44.44 2.83
2787 5599 5.308014 TGAGTAGTACTCCGTCTGTAAACA 58.692 41.667 24.32 2.33 44.44 2.83
2788 5600 5.869753 TGAGTAGTACTCCGTCTGTAAAC 57.130 43.478 24.32 0.00 44.44 2.01
2789 5601 6.882610 TTTGAGTAGTACTCCGTCTGTAAA 57.117 37.500 24.32 14.41 44.44 2.01
2790 5602 6.882610 TTTTGAGTAGTACTCCGTCTGTAA 57.117 37.500 24.32 9.74 44.44 2.41
2791 5603 7.175467 TGAATTTTGAGTAGTACTCCGTCTGTA 59.825 37.037 24.32 4.25 44.44 2.74
2792 5604 5.979288 ATTTTGAGTAGTACTCCGTCTGT 57.021 39.130 24.32 6.13 44.44 3.41
2793 5605 6.387465 TGAATTTTGAGTAGTACTCCGTCTG 58.613 40.000 24.32 0.00 44.44 3.51
2794 5606 6.585695 TGAATTTTGAGTAGTACTCCGTCT 57.414 37.500 24.32 7.99 44.44 4.18
2795 5607 7.829378 AATGAATTTTGAGTAGTACTCCGTC 57.171 36.000 24.32 15.02 44.44 4.79
2796 5608 9.886132 ATAAATGAATTTTGAGTAGTACTCCGT 57.114 29.630 24.32 8.87 44.44 4.69
2848 5687 4.586884 CCCAAAGAAGTACTCCTAAACCC 58.413 47.826 0.00 0.00 0.00 4.11
2871 5710 5.163953 CCGTGTGCTAAACTTCTATGTCTTG 60.164 44.000 0.00 0.00 0.00 3.02
2879 5718 5.548406 AGTAATTCCGTGTGCTAAACTTCT 58.452 37.500 0.00 0.00 0.00 2.85
2886 5725 5.484715 AGCTAAAAGTAATTCCGTGTGCTA 58.515 37.500 0.00 0.00 0.00 3.49
2893 5732 6.619801 AAGGCATAGCTAAAAGTAATTCCG 57.380 37.500 0.00 0.00 0.00 4.30
2929 5768 9.207868 GCTCTTATATTATGGAATAGAGGGAGT 57.792 37.037 0.00 0.00 30.58 3.85
2930 5769 8.356657 CGCTCTTATATTATGGAATAGAGGGAG 58.643 40.741 0.00 0.00 38.90 4.30
2931 5770 7.839705 ACGCTCTTATATTATGGAATAGAGGGA 59.160 37.037 16.73 1.31 38.90 4.20
2932 5771 8.012957 ACGCTCTTATATTATGGAATAGAGGG 57.987 38.462 0.00 0.00 40.58 4.30
2933 5772 9.877178 AAACGCTCTTATATTATGGAATAGAGG 57.123 33.333 0.00 0.00 30.58 3.69
2939 5778 9.168451 TGTCAAAAACGCTCTTATATTATGGAA 57.832 29.630 0.00 0.00 0.00 3.53
2940 5779 8.609176 GTGTCAAAAACGCTCTTATATTATGGA 58.391 33.333 0.00 0.00 35.42 3.41
2941 5780 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
2944 5783 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
2945 5784 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
2946 5785 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
2947 5786 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
2948 5787 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
2949 5788 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
2950 5789 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
2951 5790 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
2952 5791 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
2979 5818 9.866655 TCAGTCCCATAATATAAGAGCATTTTT 57.133 29.630 0.00 0.00 0.00 1.94
2980 5819 9.512588 CTCAGTCCCATAATATAAGAGCATTTT 57.487 33.333 0.00 0.00 0.00 1.82
2981 5820 8.105829 CCTCAGTCCCATAATATAAGAGCATTT 58.894 37.037 0.00 0.00 0.00 2.32
2982 5821 7.311549 CCCTCAGTCCCATAATATAAGAGCATT 60.312 40.741 0.00 0.00 0.00 3.56
2983 5822 6.157645 CCCTCAGTCCCATAATATAAGAGCAT 59.842 42.308 0.00 0.00 0.00 3.79
2984 5823 5.485353 CCCTCAGTCCCATAATATAAGAGCA 59.515 44.000 0.00 0.00 0.00 4.26
2985 5824 5.721960 TCCCTCAGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
2986 5825 6.957020 ACTCCCTCAGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
2987 5826 6.875469 ACTCCCTCAGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
2988 5827 7.896496 AGTACTCCCTCAGTCCCATAATATAAG 59.104 40.741 0.00 0.00 36.43 1.73
2989 5828 7.776745 AGTACTCCCTCAGTCCCATAATATAA 58.223 38.462 0.00 0.00 36.43 0.98
2990 5829 7.358255 AGTACTCCCTCAGTCCCATAATATA 57.642 40.000 0.00 0.00 36.43 0.86
2991 5830 6.234404 AGTACTCCCTCAGTCCCATAATAT 57.766 41.667 0.00 0.00 36.43 1.28
2992 5831 5.681494 AGTACTCCCTCAGTCCCATAATA 57.319 43.478 0.00 0.00 36.43 0.98
2993 5832 4.561254 AGTACTCCCTCAGTCCCATAAT 57.439 45.455 0.00 0.00 36.43 1.28
2994 5833 4.030913 CAAGTACTCCCTCAGTCCCATAA 58.969 47.826 0.00 0.00 36.43 1.90
2995 5834 3.643237 CAAGTACTCCCTCAGTCCCATA 58.357 50.000 0.00 0.00 36.43 2.74
2996 5835 2.472029 CAAGTACTCCCTCAGTCCCAT 58.528 52.381 0.00 0.00 36.43 4.00
2997 5836 1.938585 CAAGTACTCCCTCAGTCCCA 58.061 55.000 0.00 0.00 36.43 4.37
2998 5837 0.537653 GCAAGTACTCCCTCAGTCCC 59.462 60.000 0.00 0.00 36.43 4.46
2999 5838 1.562783 AGCAAGTACTCCCTCAGTCC 58.437 55.000 0.00 0.00 36.43 3.85
3000 5839 2.100087 GCTAGCAAGTACTCCCTCAGTC 59.900 54.545 10.63 0.00 36.43 3.51
3001 5840 2.104170 GCTAGCAAGTACTCCCTCAGT 58.896 52.381 10.63 0.00 39.41 3.41
3002 5841 1.066303 CGCTAGCAAGTACTCCCTCAG 59.934 57.143 16.45 0.00 0.00 3.35
3003 5842 1.103803 CGCTAGCAAGTACTCCCTCA 58.896 55.000 16.45 0.00 0.00 3.86
3004 5843 1.390565 TCGCTAGCAAGTACTCCCTC 58.609 55.000 16.45 0.00 0.00 4.30
3005 5844 1.848652 TTCGCTAGCAAGTACTCCCT 58.151 50.000 16.45 0.00 0.00 4.20
3006 5845 2.667473 TTTCGCTAGCAAGTACTCCC 57.333 50.000 16.45 0.00 0.00 4.30
3007 5846 4.630069 TGATTTTTCGCTAGCAAGTACTCC 59.370 41.667 16.45 0.00 0.00 3.85
3008 5847 5.779806 TGATTTTTCGCTAGCAAGTACTC 57.220 39.130 16.45 5.04 0.00 2.59
3009 5848 5.468746 TGTTGATTTTTCGCTAGCAAGTACT 59.531 36.000 16.45 0.00 0.00 2.73
3010 5849 5.685841 TGTTGATTTTTCGCTAGCAAGTAC 58.314 37.500 16.45 2.30 0.00 2.73
3011 5850 5.933187 TGTTGATTTTTCGCTAGCAAGTA 57.067 34.783 16.45 0.00 0.00 2.24
3054 5893 8.226543 TCGCAAGCAAATCATAAAACTTTAAG 57.773 30.769 0.00 0.00 37.18 1.85
3056 5895 9.847706 TTATCGCAAGCAAATCATAAAACTTTA 57.152 25.926 0.00 0.00 37.18 1.85
3059 5898 8.408601 AGATTATCGCAAGCAAATCATAAAACT 58.591 29.630 11.74 0.00 39.30 2.66
3060 5899 8.566008 AGATTATCGCAAGCAAATCATAAAAC 57.434 30.769 11.74 0.00 39.30 2.43
3065 5904 6.474427 CACAAAGATTATCGCAAGCAAATCAT 59.526 34.615 11.74 1.33 39.30 2.45
3073 5912 5.203358 TCGTTCACAAAGATTATCGCAAG 57.797 39.130 0.00 0.00 0.00 4.01
3100 5939 2.225217 ACCAGGACGGAGGTAGTACTTT 60.225 50.000 0.00 0.00 36.07 2.66
3106 5945 2.068834 ATACACCAGGACGGAGGTAG 57.931 55.000 0.00 0.00 36.07 3.18
3107 5946 3.053395 ACTTATACACCAGGACGGAGGTA 60.053 47.826 0.00 0.00 36.07 3.08
3108 5947 2.292061 ACTTATACACCAGGACGGAGGT 60.292 50.000 0.00 0.00 39.10 3.85
3109 5948 2.361438 GACTTATACACCAGGACGGAGG 59.639 54.545 0.00 0.00 38.63 4.30
3110 5949 3.021695 TGACTTATACACCAGGACGGAG 58.978 50.000 0.00 0.00 38.63 4.63
3111 5950 3.090210 TGACTTATACACCAGGACGGA 57.910 47.619 0.00 0.00 38.63 4.69
3112 5951 4.369182 GAATGACTTATACACCAGGACGG 58.631 47.826 0.00 0.00 42.50 4.79
3113 5952 4.042398 CGAATGACTTATACACCAGGACG 58.958 47.826 0.00 0.00 0.00 4.79
3114 5953 3.802685 GCGAATGACTTATACACCAGGAC 59.197 47.826 0.00 0.00 0.00 3.85
3115 5954 3.490249 CGCGAATGACTTATACACCAGGA 60.490 47.826 0.00 0.00 0.00 3.86
3116 5955 2.794910 CGCGAATGACTTATACACCAGG 59.205 50.000 0.00 0.00 0.00 4.45
3117 5956 3.444916 ACGCGAATGACTTATACACCAG 58.555 45.455 15.93 0.00 0.00 4.00
3118 5957 3.513680 ACGCGAATGACTTATACACCA 57.486 42.857 15.93 0.00 0.00 4.17
3119 5958 4.604976 ACTACGCGAATGACTTATACACC 58.395 43.478 15.93 0.00 0.00 4.16
3120 5959 5.970023 AGAACTACGCGAATGACTTATACAC 59.030 40.000 15.93 0.00 0.00 2.90
3121 5960 6.127810 AGAACTACGCGAATGACTTATACA 57.872 37.500 15.93 0.00 0.00 2.29
3122 5961 6.796072 CCTAGAACTACGCGAATGACTTATAC 59.204 42.308 15.93 0.00 0.00 1.47
3123 5962 6.484643 ACCTAGAACTACGCGAATGACTTATA 59.515 38.462 15.93 0.00 0.00 0.98
3124 5963 5.298777 ACCTAGAACTACGCGAATGACTTAT 59.701 40.000 15.93 0.00 0.00 1.73
3125 5964 4.637534 ACCTAGAACTACGCGAATGACTTA 59.362 41.667 15.93 0.00 0.00 2.24
3126 5965 3.442977 ACCTAGAACTACGCGAATGACTT 59.557 43.478 15.93 0.00 0.00 3.01
3127 5966 3.015327 ACCTAGAACTACGCGAATGACT 58.985 45.455 15.93 9.07 0.00 3.41
3128 5967 3.181503 TGACCTAGAACTACGCGAATGAC 60.182 47.826 15.93 0.66 0.00 3.06
3129 5968 3.011818 TGACCTAGAACTACGCGAATGA 58.988 45.455 15.93 0.00 0.00 2.57
3130 5969 3.416119 TGACCTAGAACTACGCGAATG 57.584 47.619 15.93 4.47 0.00 2.67
3131 5970 3.192001 TGTTGACCTAGAACTACGCGAAT 59.808 43.478 15.93 0.00 0.00 3.34
3132 5971 2.553602 TGTTGACCTAGAACTACGCGAA 59.446 45.455 15.93 0.00 0.00 4.70
3133 5972 2.153645 TGTTGACCTAGAACTACGCGA 58.846 47.619 15.93 0.00 0.00 5.87
3134 5973 2.624316 TGTTGACCTAGAACTACGCG 57.376 50.000 3.53 3.53 0.00 6.01
3135 5974 5.857822 AAATTGTTGACCTAGAACTACGC 57.142 39.130 0.00 0.00 0.00 4.42
3136 5975 8.530269 AGTTAAATTGTTGACCTAGAACTACG 57.470 34.615 0.00 0.00 0.00 3.51
3193 6032 9.424319 CTGCACGGATGTAGTTTCTAAATATAT 57.576 33.333 0.00 0.00 34.10 0.86
3194 6033 8.635328 TCTGCACGGATGTAGTTTCTAAATATA 58.365 33.333 0.00 0.00 39.42 0.86
3195 6034 7.497595 TCTGCACGGATGTAGTTTCTAAATAT 58.502 34.615 0.00 0.00 39.42 1.28
3196 6035 6.869695 TCTGCACGGATGTAGTTTCTAAATA 58.130 36.000 0.00 0.00 39.42 1.40
3197 6036 5.730550 TCTGCACGGATGTAGTTTCTAAAT 58.269 37.500 0.00 0.00 39.42 1.40
3198 6037 5.142061 TCTGCACGGATGTAGTTTCTAAA 57.858 39.130 0.00 0.00 39.42 1.85
3199 6038 4.794278 TCTGCACGGATGTAGTTTCTAA 57.206 40.909 0.00 0.00 39.42 2.10
3200 6039 4.794278 TTCTGCACGGATGTAGTTTCTA 57.206 40.909 0.00 0.00 39.42 2.10
3201 6040 3.678056 TTCTGCACGGATGTAGTTTCT 57.322 42.857 0.00 0.00 39.42 2.52
3202 6041 4.631813 AGATTTCTGCACGGATGTAGTTTC 59.368 41.667 0.00 0.00 39.42 2.78
3203 6042 4.579869 AGATTTCTGCACGGATGTAGTTT 58.420 39.130 0.00 0.00 39.42 2.66
3204 6043 4.207891 AGATTTCTGCACGGATGTAGTT 57.792 40.909 0.00 0.00 39.42 2.24
3205 6044 3.895232 AGATTTCTGCACGGATGTAGT 57.105 42.857 0.00 0.00 39.42 2.73
3206 6045 4.938080 ACTAGATTTCTGCACGGATGTAG 58.062 43.478 0.00 0.00 39.75 2.74
3207 6046 6.459670 TTACTAGATTTCTGCACGGATGTA 57.540 37.500 0.00 0.00 0.00 2.29
3208 6047 3.895232 ACTAGATTTCTGCACGGATGT 57.105 42.857 0.00 0.00 0.00 3.06
3209 6048 9.077674 GTATATTACTAGATTTCTGCACGGATG 57.922 37.037 0.00 0.00 0.00 3.51
3210 6049 9.026121 AGTATATTACTAGATTTCTGCACGGAT 57.974 33.333 0.00 0.00 37.23 4.18
3211 6050 8.405418 AGTATATTACTAGATTTCTGCACGGA 57.595 34.615 0.00 0.00 37.23 4.69
3212 6051 9.477484 AAAGTATATTACTAGATTTCTGCACGG 57.523 33.333 0.00 0.00 38.26 4.94


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

AutoCloner maintained by Alex Coulton.