Multiple sequence alignment - TraesCS5A01G289600

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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 TraesCS5A01G289600 chr5A 100.000 2694 0 0 771 3464 496287454 496284761 0.000000e+00 4975.0
1 TraesCS5A01G289600 chr5A 88.787 981 54 19 1391 2357 496571470 496570532 0.000000e+00 1151.0
2 TraesCS5A01G289600 chr5A 100.000 496 0 0 1 496 496288224 496287729 0.000000e+00 917.0
3 TraesCS5A01G289600 chr5A 96.327 490 18 0 7 496 496572815 496572326 0.000000e+00 806.0
4 TraesCS5A01G289600 chr5A 95.765 425 16 1 871 1293 496571893 496571469 0.000000e+00 684.0
5 TraesCS5A01G289600 chr5A 82.066 697 62 30 2640 3296 496570273 496569600 1.410000e-148 536.0
6 TraesCS5A01G289600 chr5A 79.751 321 51 7 2863 3179 631745064 631744754 1.620000e-53 220.0
7 TraesCS5A01G289600 chr5A 95.868 121 5 0 2499 2619 550650565 550650445 2.730000e-46 196.0
8 TraesCS5A01G289600 chr5B 91.071 1400 66 22 834 2218 474457779 474456424 0.000000e+00 1838.0
9 TraesCS5A01G289600 chr5B 91.006 656 31 8 1391 2032 474319146 474318505 0.000000e+00 859.0
10 TraesCS5A01G289600 chr5B 96.086 511 18 1 834 1342 428849411 428849921 0.000000e+00 832.0
11 TraesCS5A01G289600 chr5B 94.343 495 22 5 3 496 474458615 474458126 0.000000e+00 754.0
12 TraesCS5A01G289600 chr5B 96.364 385 11 1 920 1304 474319524 474319143 6.310000e-177 630.0
13 TraesCS5A01G289600 chr5B 81.393 833 74 34 2644 3416 428850899 428851710 3.820000e-169 604.0
14 TraesCS5A01G289600 chr5B 92.271 414 17 3 1339 1743 428850001 428850408 1.080000e-159 573.0
15 TraesCS5A01G289600 chr5B 82.837 571 49 16 2640 3168 474317775 474317212 1.880000e-127 466.0
16 TraesCS5A01G289600 chr5B 89.645 338 22 6 2030 2367 474318348 474318024 5.350000e-113 418.0
17 TraesCS5A01G289600 chr5B 83.333 330 35 9 2937 3246 474455706 474455377 1.570000e-73 287.0
18 TraesCS5A01G289600 chr5B 81.230 309 30 19 3164 3464 474445549 474445261 1.250000e-54 224.0
19 TraesCS5A01G289600 chr5B 84.821 224 17 9 3242 3464 474317210 474317003 3.500000e-50 209.0
20 TraesCS5A01G289600 chr5B 96.694 121 4 0 2499 2619 40789790 40789670 5.860000e-48 202.0
21 TraesCS5A01G289600 chr5B 96.364 110 4 0 2372 2481 474456137 474456028 7.640000e-42 182.0
22 TraesCS5A01G289600 chr5B 88.550 131 13 2 2239 2367 474456434 474456304 1.290000e-34 158.0
23 TraesCS5A01G289600 chr5B 86.395 147 9 3 2499 2635 140887160 140887015 2.150000e-32 150.0
24 TraesCS5A01G289600 chr5D 92.675 983 46 6 1236 2218 394585603 394584647 0.000000e+00 1393.0
25 TraesCS5A01G289600 chr5D 96.169 496 19 0 1 496 394586632 394586137 0.000000e+00 811.0
26 TraesCS5A01G289600 chr5D 95.556 495 20 2 3 496 394553205 394552712 0.000000e+00 791.0
27 TraesCS5A01G289600 chr5D 91.983 474 22 6 834 1304 394561215 394560755 0.000000e+00 651.0
28 TraesCS5A01G289600 chr5D 91.772 474 24 5 834 1304 394565321 394564860 0.000000e+00 645.0
29 TraesCS5A01G289600 chr5D 97.027 370 11 0 1 370 394565972 394565603 1.060000e-174 623.0
30 TraesCS5A01G289600 chr5D 96.448 366 11 1 834 1197 394585972 394585607 1.380000e-168 603.0
31 TraesCS5A01G289600 chr5D 82.163 712 58 31 2769 3464 394552366 394551708 6.540000e-152 547.0
32 TraesCS5A01G289600 chr5D 84.910 444 44 13 2924 3350 394282247 394281810 8.880000e-116 427.0
33 TraesCS5A01G289600 chr5D 93.040 273 5 1 1392 1650 394560748 394560476 1.510000e-103 387.0
34 TraesCS5A01G289600 chr5D 93.040 273 5 1 1392 1650 394564853 394564581 1.510000e-103 387.0
35 TraesCS5A01G289600 chr5D 79.757 494 60 28 2977 3464 394564233 394563774 4.310000e-84 322.0
36 TraesCS5A01G289600 chr5D 94.375 160 6 2 834 991 394552574 394552416 3.450000e-60 243.0
37 TraesCS5A01G289600 chr5D 82.237 304 29 17 2661 2955 394560463 394560176 4.470000e-59 239.0
38 TraesCS5A01G289600 chr5D 82.237 304 29 17 2661 2955 394564568 394564281 4.470000e-59 239.0
39 TraesCS5A01G289600 chr5D 93.130 131 7 2 2239 2367 394584657 394584527 1.270000e-44 191.0
40 TraesCS5A01G289600 chr5D 93.388 121 8 0 2499 2619 314893190 314893070 2.750000e-41 180.0
41 TraesCS5A01G289600 chr5D 93.519 108 7 0 2372 2479 27983047 27982940 9.950000e-36 161.0
42 TraesCS5A01G289600 chr5D 92.708 96 5 2 3370 3464 394583936 394583842 1.680000e-28 137.0
43 TraesCS5A01G289600 chr5D 95.000 60 3 0 774 833 394586100 394586041 1.020000e-15 95.3
44 TraesCS5A01G289600 chr5D 94.444 54 3 0 773 826 469800496 469800549 2.220000e-12 84.2
45 TraesCS5A01G289600 chrUn 90.854 656 32 8 1391 2032 359420512 359421153 0.000000e+00 854.0
46 TraesCS5A01G289600 chrUn 95.556 495 20 2 3 496 329882770 329882277 0.000000e+00 791.0
47 TraesCS5A01G289600 chrUn 91.772 474 24 5 834 1304 211149501 211149040 0.000000e+00 645.0
48 TraesCS5A01G289600 chrUn 91.772 474 24 5 834 1304 243175531 243175992 0.000000e+00 645.0
49 TraesCS5A01G289600 chrUn 96.134 388 12 1 917 1304 359420131 359420515 6.310000e-177 630.0
50 TraesCS5A01G289600 chrUn 97.027 370 11 0 1 370 211150591 211150222 1.060000e-174 623.0
51 TraesCS5A01G289600 chrUn 97.027 370 11 0 1 370 243174291 243174660 1.060000e-174 623.0
52 TraesCS5A01G289600 chrUn 97.027 370 11 0 1 370 319165180 319165549 1.060000e-174 623.0
53 TraesCS5A01G289600 chrUn 83.025 595 51 25 2769 3347 329881931 329881371 8.640000e-136 494.0
54 TraesCS5A01G289600 chrUn 93.040 273 5 1 1392 1650 211149033 211148761 1.510000e-103 387.0
55 TraesCS5A01G289600 chrUn 93.040 273 5 1 1392 1650 243175999 243176271 1.510000e-103 387.0
56 TraesCS5A01G289600 chrUn 79.757 494 60 28 2977 3464 211148413 211147954 4.310000e-84 322.0
57 TraesCS5A01G289600 chrUn 94.375 160 6 2 834 991 329882139 329881981 3.450000e-60 243.0
58 TraesCS5A01G289600 chrUn 82.237 304 29 17 2661 2955 211148748 211148461 4.470000e-59 239.0
59 TraesCS5A01G289600 chrUn 82.392 301 28 17 2661 2952 243176284 243176568 4.470000e-59 239.0
60 TraesCS5A01G289600 chrUn 80.117 342 48 16 2977 3313 243176619 243176945 1.610000e-58 237.0
61 TraesCS5A01G289600 chrUn 81.439 264 20 8 3209 3464 37336019 37335777 4.560000e-44 189.0
62 TraesCS5A01G289600 chr1D 82.283 762 84 25 1590 2346 32530991 32530276 2.290000e-171 612.0
63 TraesCS5A01G289600 chr1D 85.811 148 9 2 2499 2634 392701891 392702038 2.790000e-31 147.0
64 TraesCS5A01G289600 chr1A 79.423 763 105 22 1586 2343 31795529 31796244 3.110000e-135 492.0
65 TraesCS5A01G289600 chr1A 73.991 669 119 38 1589 2242 89966570 89965942 1.620000e-53 220.0
66 TraesCS5A01G289600 chr1A 89.286 140 4 4 2494 2622 284063221 284063360 7.690000e-37 165.0
67 TraesCS5A01G289600 chr1B 82.453 530 68 12 1824 2346 50155064 50154553 1.140000e-119 440.0
68 TraesCS5A01G289600 chr1B 89.313 131 4 4 2499 2619 529589268 529589138 4.630000e-34 156.0
69 TraesCS5A01G289600 chr3D 74.597 744 126 32 1616 2319 610430711 610429991 5.700000e-68 268.0
70 TraesCS5A01G289600 chr3D 93.382 136 8 1 2493 2628 131347671 131347805 2.110000e-47 200.0
71 TraesCS5A01G289600 chr3D 90.625 96 7 1 3218 3313 18429806 18429713 3.630000e-25 126.0
72 TraesCS5A01G289600 chr7A 95.200 125 6 0 2497 2621 2605541 2605665 7.580000e-47 198.0
73 TraesCS5A01G289600 chr7A 94.444 54 3 0 773 826 38582706 38582759 2.220000e-12 84.2
74 TraesCS5A01G289600 chr7A 94.444 54 3 0 773 826 38610314 38610367 2.220000e-12 84.2
75 TraesCS5A01G289600 chr7A 94.444 54 3 0 773 826 38621768 38621821 2.220000e-12 84.2
76 TraesCS5A01G289600 chr7A 94.444 54 3 0 773 826 38650523 38650576 2.220000e-12 84.2
77 TraesCS5A01G289600 chr6D 87.293 181 14 6 1292 1463 437544705 437544885 7.580000e-47 198.0
78 TraesCS5A01G289600 chr6D 95.413 109 4 1 2372 2479 14487022 14487130 4.600000e-39 172.0
79 TraesCS5A01G289600 chr6D 90.840 131 2 2 2499 2619 421801525 421801395 2.140000e-37 167.0
80 TraesCS5A01G289600 chr6D 91.667 60 5 0 773 832 110320177 110320118 2.220000e-12 84.2
81 TraesCS5A01G289600 chr4D 90.370 135 3 2 2495 2619 413008419 413008285 5.950000e-38 169.0
82 TraesCS5A01G289600 chr4B 89.844 128 12 1 1290 1416 105649670 105649543 2.770000e-36 163.0
83 TraesCS5A01G289600 chr2B 84.932 146 12 1 2493 2628 374276002 374276147 4.660000e-29 139.0
84 TraesCS5A01G289600 chr7B 95.455 66 3 0 2554 2619 27053309 27053244 4.730000e-19 106.0
85 TraesCS5A01G289600 chr7D 94.444 54 3 0 773 826 3715269 3715322 2.220000e-12 84.2
86 TraesCS5A01G289600 chr7D 83.784 74 11 1 399 471 236646673 236646600 6.200000e-08 69.4
87 TraesCS5A01G289600 chr3A 94.444 54 3 0 773 826 120846265 120846318 2.220000e-12 84.2
88 TraesCS5A01G289600 chr3B 97.059 34 1 0 2863 2896 674428351 674428384 1.340000e-04 58.4


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 TraesCS5A01G289600 chr5A 496284761 496288224 3463 True 2946.000000 4975 100.000000 1 3464 2 chr5A.!!$R3 3463
1 TraesCS5A01G289600 chr5A 496569600 496572815 3215 True 794.250000 1151 90.736250 7 3296 4 chr5A.!!$R4 3289
2 TraesCS5A01G289600 chr5B 428849411 428851710 2299 False 669.666667 832 89.916667 834 3416 3 chr5B.!!$F1 2582
3 TraesCS5A01G289600 chr5B 474455377 474458615 3238 True 643.800000 1838 90.732200 3 3246 5 chr5B.!!$R5 3243
4 TraesCS5A01G289600 chr5B 474317003 474319524 2521 True 516.400000 859 88.934600 920 3464 5 chr5B.!!$R4 2544
5 TraesCS5A01G289600 chr5D 394583842 394586632 2790 True 538.383333 1393 94.355000 1 3464 6 chr5D.!!$R6 3463
6 TraesCS5A01G289600 chr5D 394551708 394553205 1497 True 527.000000 791 90.698000 3 3464 3 chr5D.!!$R4 3461
7 TraesCS5A01G289600 chr5D 394560176 394565972 5796 True 436.625000 651 88.886625 1 3464 8 chr5D.!!$R5 3463
8 TraesCS5A01G289600 chrUn 359420131 359421153 1022 False 742.000000 854 93.494000 917 2032 2 chrUn.!!$F3 1115
9 TraesCS5A01G289600 chrUn 329881371 329882770 1399 True 509.333333 791 90.985333 3 3347 3 chrUn.!!$R3 3344
10 TraesCS5A01G289600 chrUn 211147954 211150591 2637 True 443.200000 645 88.766600 1 3464 5 chrUn.!!$R2 3463
11 TraesCS5A01G289600 chrUn 243174291 243176945 2654 False 426.200000 645 88.869600 1 3313 5 chrUn.!!$F2 3312
12 TraesCS5A01G289600 chr1D 32530276 32530991 715 True 612.000000 612 82.283000 1590 2346 1 chr1D.!!$R1 756
13 TraesCS5A01G289600 chr1A 31795529 31796244 715 False 492.000000 492 79.423000 1586 2343 1 chr1A.!!$F1 757
14 TraesCS5A01G289600 chr1A 89965942 89966570 628 True 220.000000 220 73.991000 1589 2242 1 chr1A.!!$R1 653
15 TraesCS5A01G289600 chr1B 50154553 50155064 511 True 440.000000 440 82.453000 1824 2346 1 chr1B.!!$R1 522
16 TraesCS5A01G289600 chr3D 610429991 610430711 720 True 268.000000 268 74.597000 1616 2319 1 chr3D.!!$R2 703

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
992 1406 1.134521 GTGTCTGTTCAGTGTCCACCA 60.135 52.381 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2659 3865 0.035458 CAACCACCCAGTCTCAGGAC 59.965 60.0 0.0 0.0 42.41 3.85 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
77 78 7.602644 TGTCTCTTGTGAGTTATTACATGAACC 59.397 37.037 0.00 0.00 40.98 3.62
265 266 1.210155 GAGCGCGCCTTCATTTGTT 59.790 52.632 30.33 4.23 0.00 2.83
333 335 6.038997 AGTATAACCAGGTCTGTTGAACTC 57.961 41.667 0.00 0.00 38.36 3.01
385 387 5.163468 TGTTTGAAAGCAAGCTAATTGGACA 60.163 36.000 0.00 0.00 39.47 4.02
439 441 3.138884 TGCTGGAAGTTACTTGATGCA 57.861 42.857 0.93 6.85 35.30 3.96
836 1246 5.841957 ATCATGACTTTCCCTGCATTTAC 57.158 39.130 0.00 0.00 0.00 2.01
992 1406 1.134521 GTGTCTGTTCAGTGTCCACCA 60.135 52.381 0.00 0.00 0.00 4.17
1132 1546 2.036346 AGATGCAAGGACACAAAAAGCC 59.964 45.455 0.00 0.00 0.00 4.35
1235 1649 3.352611 ACTACATCCCTGGCCTATTCT 57.647 47.619 3.32 0.00 0.00 2.40
1357 1865 9.283768 TCTAATTTACTTGTCTTTTGCTCATGA 57.716 29.630 0.00 0.00 0.00 3.07
1486 1998 2.698855 AATACTGCAGTGGTAGCCTG 57.301 50.000 29.57 6.17 0.00 4.85
1653 2195 0.254462 TTTGCAGACCAGGACACACA 59.746 50.000 0.00 0.00 0.00 3.72
1693 2236 1.142262 TCATCAGCTGGTCCATCATGG 59.858 52.381 15.13 0.00 39.43 3.66
1743 2308 4.438913 TGCTCCTTATAAGCTGGGGATAT 58.561 43.478 6.99 0.00 40.50 1.63
1794 2361 3.317608 CGAGACGCCGCTTTTACTA 57.682 52.632 0.00 0.00 0.00 1.82
1915 2499 3.132925 CAGCAATTTCCCACAAAAGTGG 58.867 45.455 7.66 7.66 43.86 4.00
1968 2566 1.269621 GCGAGGTAGGCGTGTATCATT 60.270 52.381 0.00 0.00 0.00 2.57
1977 2575 1.134340 GCGTGTATCATTGGGGTGGTA 60.134 52.381 0.00 0.00 0.00 3.25
2115 3076 6.570672 CAATAATGCTCATGTGCTTATCCT 57.429 37.500 19.60 2.71 0.00 3.24
2116 3077 6.379386 CAATAATGCTCATGTGCTTATCCTG 58.621 40.000 19.60 12.32 0.00 3.86
2117 3078 3.851458 ATGCTCATGTGCTTATCCTGA 57.149 42.857 19.60 0.00 0.00 3.86
2118 3079 3.632643 TGCTCATGTGCTTATCCTGAA 57.367 42.857 19.60 0.00 0.00 3.02
2119 3080 4.160642 TGCTCATGTGCTTATCCTGAAT 57.839 40.909 19.60 0.00 0.00 2.57
2120 3081 3.881089 TGCTCATGTGCTTATCCTGAATG 59.119 43.478 19.60 0.00 0.00 2.67
2121 3082 3.252701 GCTCATGTGCTTATCCTGAATGG 59.747 47.826 12.42 0.00 37.10 3.16
2214 3189 8.518430 TGCATATTGTTGTTGTATGTCCTATT 57.482 30.769 0.00 0.00 0.00 1.73
2239 3214 1.259609 CCAAAGTGATGGCATGTGGT 58.740 50.000 3.81 0.00 32.78 4.16
2240 3215 1.203052 CCAAAGTGATGGCATGTGGTC 59.797 52.381 3.81 0.00 32.78 4.02
2241 3216 1.203052 CAAAGTGATGGCATGTGGTCC 59.797 52.381 3.81 0.00 0.00 4.46
2290 3295 9.770097 TCCTAATTATCTCATCACTTGATTGAC 57.230 33.333 0.00 0.00 32.72 3.18
2319 3324 8.816640 AACAAATGGTAAATTCTGTAGCTTTG 57.183 30.769 0.00 0.00 0.00 2.77
2339 3344 2.260088 TATAACGGTGGTGCAGGGCC 62.260 60.000 0.00 0.00 0.00 5.80
2367 3372 5.412286 GGCCAAAATTGAGCATGTTAATGTT 59.588 36.000 0.00 0.00 36.08 2.71
2368 3373 6.308675 GCCAAAATTGAGCATGTTAATGTTG 58.691 36.000 11.49 11.49 36.08 3.33
2369 3374 6.621164 GCCAAAATTGAGCATGTTAATGTTGG 60.621 38.462 22.81 22.81 45.60 3.77
2370 3375 6.128227 CCAAAATTGAGCATGTTAATGTTGGG 60.128 38.462 21.07 10.81 41.95 4.12
2399 3573 1.303561 TTGGTCCTCATGGTGCTGC 60.304 57.895 0.00 0.00 34.23 5.25
2401 3575 2.821366 GTCCTCATGGTGCTGCCG 60.821 66.667 0.00 0.00 41.21 5.69
2440 3614 5.001232 TGCATTTTACTGAAGTGGGAGTAC 58.999 41.667 0.00 0.00 0.00 2.73
2465 3639 3.130516 CCAGTTCTCCACTCAGCGTAATA 59.869 47.826 0.00 0.00 30.92 0.98
2481 3655 7.067129 TCAGCGTAATATCCCTGTGATATACTC 59.933 40.741 0.00 0.00 44.27 2.59
2482 3656 6.321690 AGCGTAATATCCCTGTGATATACTCC 59.678 42.308 0.00 0.00 44.27 3.85
2483 3657 6.461231 GCGTAATATCCCTGTGATATACTCCC 60.461 46.154 0.00 0.00 44.27 4.30
2484 3658 6.605995 CGTAATATCCCTGTGATATACTCCCA 59.394 42.308 0.00 0.00 44.27 4.37
2485 3659 6.875972 AATATCCCTGTGATATACTCCCAC 57.124 41.667 0.00 0.00 44.27 4.61
2486 3660 3.993658 TCCCTGTGATATACTCCCACT 57.006 47.619 0.00 0.00 0.00 4.00
2488 3662 4.223953 TCCCTGTGATATACTCCCACTTC 58.776 47.826 0.00 0.00 0.00 3.01
2489 3663 3.967326 CCCTGTGATATACTCCCACTTCA 59.033 47.826 0.00 0.00 0.00 3.02
2490 3664 4.594920 CCCTGTGATATACTCCCACTTCAT 59.405 45.833 0.00 0.00 0.00 2.57
2492 3666 6.270000 CCCTGTGATATACTCCCACTTCATTA 59.730 42.308 0.00 0.00 0.00 1.90
2494 3668 6.745116 TGTGATATACTCCCACTTCATTACG 58.255 40.000 0.00 0.00 0.00 3.18
2495 3669 5.634020 GTGATATACTCCCACTTCATTACGC 59.366 44.000 0.00 0.00 0.00 4.42
2496 3670 5.538813 TGATATACTCCCACTTCATTACGCT 59.461 40.000 0.00 0.00 0.00 5.07
2497 3671 2.386661 ACTCCCACTTCATTACGCTG 57.613 50.000 0.00 0.00 0.00 5.18
2498 3672 1.899814 ACTCCCACTTCATTACGCTGA 59.100 47.619 0.00 0.00 0.00 4.26
2499 3673 2.093973 ACTCCCACTTCATTACGCTGAG 60.094 50.000 0.00 0.00 0.00 3.35
2500 3674 1.207089 TCCCACTTCATTACGCTGAGG 59.793 52.381 0.00 0.00 0.00 3.86
2505 3679 2.500098 ACTTCATTACGCTGAGGCCTTA 59.500 45.455 6.77 0.00 34.44 2.69
2506 3680 3.134804 ACTTCATTACGCTGAGGCCTTAT 59.865 43.478 6.77 0.00 34.44 1.73
2508 3682 3.728845 TCATTACGCTGAGGCCTTATTC 58.271 45.455 6.77 0.00 34.44 1.75
2509 3683 2.218953 TTACGCTGAGGCCTTATTCG 57.781 50.000 6.77 12.19 34.44 3.34
2510 3684 0.387929 TACGCTGAGGCCTTATTCGG 59.612 55.000 6.77 0.00 34.44 4.30
2511 3685 1.144057 CGCTGAGGCCTTATTCGGT 59.856 57.895 6.77 0.00 34.44 4.69
2512 3686 0.462047 CGCTGAGGCCTTATTCGGTT 60.462 55.000 6.77 0.00 34.44 4.44
2513 3687 1.017387 GCTGAGGCCTTATTCGGTTG 58.983 55.000 6.77 0.00 0.00 3.77
2514 3688 1.406887 GCTGAGGCCTTATTCGGTTGA 60.407 52.381 6.77 0.00 0.00 3.18
2515 3689 2.555199 CTGAGGCCTTATTCGGTTGAG 58.445 52.381 6.77 0.00 0.00 3.02
2516 3690 1.209504 TGAGGCCTTATTCGGTTGAGG 59.790 52.381 6.77 0.00 0.00 3.86
2517 3691 1.209747 GAGGCCTTATTCGGTTGAGGT 59.790 52.381 6.77 0.00 0.00 3.85
2518 3692 1.065418 AGGCCTTATTCGGTTGAGGTG 60.065 52.381 0.00 0.00 0.00 4.00
2519 3693 1.379527 GCCTTATTCGGTTGAGGTGG 58.620 55.000 0.00 0.00 0.00 4.61
2520 3694 1.339727 GCCTTATTCGGTTGAGGTGGT 60.340 52.381 0.00 0.00 0.00 4.16
2521 3695 2.878526 GCCTTATTCGGTTGAGGTGGTT 60.879 50.000 0.00 0.00 0.00 3.67
2522 3696 3.418047 CCTTATTCGGTTGAGGTGGTTT 58.582 45.455 0.00 0.00 0.00 3.27
2523 3697 3.824443 CCTTATTCGGTTGAGGTGGTTTT 59.176 43.478 0.00 0.00 0.00 2.43
2524 3698 4.279922 CCTTATTCGGTTGAGGTGGTTTTT 59.720 41.667 0.00 0.00 0.00 1.94
2525 3699 3.726291 ATTCGGTTGAGGTGGTTTTTG 57.274 42.857 0.00 0.00 0.00 2.44
2526 3700 2.421751 TCGGTTGAGGTGGTTTTTGA 57.578 45.000 0.00 0.00 0.00 2.69
2527 3701 2.724454 TCGGTTGAGGTGGTTTTTGAA 58.276 42.857 0.00 0.00 0.00 2.69
2528 3702 2.685897 TCGGTTGAGGTGGTTTTTGAAG 59.314 45.455 0.00 0.00 0.00 3.02
2529 3703 2.223711 CGGTTGAGGTGGTTTTTGAAGG 60.224 50.000 0.00 0.00 0.00 3.46
2530 3704 2.102420 GGTTGAGGTGGTTTTTGAAGGG 59.898 50.000 0.00 0.00 0.00 3.95
2531 3705 2.080654 TGAGGTGGTTTTTGAAGGGG 57.919 50.000 0.00 0.00 0.00 4.79
2532 3706 1.571457 TGAGGTGGTTTTTGAAGGGGA 59.429 47.619 0.00 0.00 0.00 4.81
2533 3707 2.023888 TGAGGTGGTTTTTGAAGGGGAA 60.024 45.455 0.00 0.00 0.00 3.97
2534 3708 3.239449 GAGGTGGTTTTTGAAGGGGAAT 58.761 45.455 0.00 0.00 0.00 3.01
2535 3709 2.972021 AGGTGGTTTTTGAAGGGGAATG 59.028 45.455 0.00 0.00 0.00 2.67
2536 3710 2.038426 GGTGGTTTTTGAAGGGGAATGG 59.962 50.000 0.00 0.00 0.00 3.16
2537 3711 1.696884 TGGTTTTTGAAGGGGAATGGC 59.303 47.619 0.00 0.00 0.00 4.40
2538 3712 1.696884 GGTTTTTGAAGGGGAATGGCA 59.303 47.619 0.00 0.00 0.00 4.92
2539 3713 2.105649 GGTTTTTGAAGGGGAATGGCAA 59.894 45.455 0.00 0.00 0.00 4.52
2540 3714 3.402110 GTTTTTGAAGGGGAATGGCAAG 58.598 45.455 0.00 0.00 0.00 4.01
2541 3715 1.643310 TTTGAAGGGGAATGGCAAGG 58.357 50.000 0.00 0.00 0.00 3.61
2542 3716 0.486879 TTGAAGGGGAATGGCAAGGT 59.513 50.000 0.00 0.00 0.00 3.50
2543 3717 0.486879 TGAAGGGGAATGGCAAGGTT 59.513 50.000 0.00 0.00 0.00 3.50
2544 3718 1.132881 TGAAGGGGAATGGCAAGGTTT 60.133 47.619 0.00 0.00 0.00 3.27
2545 3719 1.276138 GAAGGGGAATGGCAAGGTTTG 59.724 52.381 0.00 0.00 0.00 2.93
2546 3720 0.486879 AGGGGAATGGCAAGGTTTGA 59.513 50.000 0.00 0.00 0.00 2.69
2547 3721 0.897621 GGGGAATGGCAAGGTTTGAG 59.102 55.000 0.00 0.00 0.00 3.02
2548 3722 0.897621 GGGAATGGCAAGGTTTGAGG 59.102 55.000 0.00 0.00 0.00 3.86
2549 3723 0.897621 GGAATGGCAAGGTTTGAGGG 59.102 55.000 0.00 0.00 0.00 4.30
2550 3724 0.897621 GAATGGCAAGGTTTGAGGGG 59.102 55.000 0.00 0.00 0.00 4.79
2551 3725 0.545071 AATGGCAAGGTTTGAGGGGG 60.545 55.000 0.00 0.00 0.00 5.40
2552 3726 1.442886 ATGGCAAGGTTTGAGGGGGA 61.443 55.000 0.00 0.00 0.00 4.81
2553 3727 1.388133 GGCAAGGTTTGAGGGGGAT 59.612 57.895 0.00 0.00 0.00 3.85
2554 3728 0.252239 GGCAAGGTTTGAGGGGGATT 60.252 55.000 0.00 0.00 0.00 3.01
2555 3729 1.006639 GGCAAGGTTTGAGGGGGATTA 59.993 52.381 0.00 0.00 0.00 1.75
2556 3730 2.379005 GCAAGGTTTGAGGGGGATTAG 58.621 52.381 0.00 0.00 0.00 1.73
2557 3731 2.025321 GCAAGGTTTGAGGGGGATTAGA 60.025 50.000 0.00 0.00 0.00 2.10
2558 3732 3.373110 GCAAGGTTTGAGGGGGATTAGAT 60.373 47.826 0.00 0.00 0.00 1.98
2559 3733 4.464947 CAAGGTTTGAGGGGGATTAGATC 58.535 47.826 0.00 0.00 0.00 2.75
2570 3744 3.704800 GGATTAGATCCCCTACAAGCC 57.295 52.381 0.00 0.00 43.88 4.35
2571 3745 2.979678 GGATTAGATCCCCTACAAGCCA 59.020 50.000 0.00 0.00 43.88 4.75
2572 3746 3.394606 GGATTAGATCCCCTACAAGCCAA 59.605 47.826 0.00 0.00 43.88 4.52
2573 3747 4.141251 GGATTAGATCCCCTACAAGCCAAA 60.141 45.833 0.00 0.00 43.88 3.28
2574 3748 4.938575 TTAGATCCCCTACAAGCCAAAA 57.061 40.909 0.00 0.00 0.00 2.44
2575 3749 5.466127 TTAGATCCCCTACAAGCCAAAAT 57.534 39.130 0.00 0.00 0.00 1.82
2576 3750 3.903467 AGATCCCCTACAAGCCAAAATC 58.097 45.455 0.00 0.00 0.00 2.17
2577 3751 2.525105 TCCCCTACAAGCCAAAATCC 57.475 50.000 0.00 0.00 0.00 3.01
2578 3752 2.000048 TCCCCTACAAGCCAAAATCCT 59.000 47.619 0.00 0.00 0.00 3.24
2579 3753 2.025321 TCCCCTACAAGCCAAAATCCTC 60.025 50.000 0.00 0.00 0.00 3.71
2580 3754 2.024941 CCCCTACAAGCCAAAATCCTCT 60.025 50.000 0.00 0.00 0.00 3.69
2581 3755 3.282885 CCCTACAAGCCAAAATCCTCTC 58.717 50.000 0.00 0.00 0.00 3.20
2582 3756 3.282885 CCTACAAGCCAAAATCCTCTCC 58.717 50.000 0.00 0.00 0.00 3.71
2583 3757 2.978156 ACAAGCCAAAATCCTCTCCA 57.022 45.000 0.00 0.00 0.00 3.86
2584 3758 3.243359 ACAAGCCAAAATCCTCTCCAA 57.757 42.857 0.00 0.00 0.00 3.53
2585 3759 3.782992 ACAAGCCAAAATCCTCTCCAAT 58.217 40.909 0.00 0.00 0.00 3.16
2586 3760 3.766051 ACAAGCCAAAATCCTCTCCAATC 59.234 43.478 0.00 0.00 0.00 2.67
2587 3761 3.023939 AGCCAAAATCCTCTCCAATCC 57.976 47.619 0.00 0.00 0.00 3.01
2588 3762 2.584498 AGCCAAAATCCTCTCCAATCCT 59.416 45.455 0.00 0.00 0.00 3.24
2589 3763 2.954989 GCCAAAATCCTCTCCAATCCTC 59.045 50.000 0.00 0.00 0.00 3.71
2590 3764 3.372458 GCCAAAATCCTCTCCAATCCTCT 60.372 47.826 0.00 0.00 0.00 3.69
2591 3765 4.864726 CCAAAATCCTCTCCAATCCTCTT 58.135 43.478 0.00 0.00 0.00 2.85
2592 3766 4.643784 CCAAAATCCTCTCCAATCCTCTTG 59.356 45.833 0.00 0.00 0.00 3.02
2593 3767 4.516652 AAATCCTCTCCAATCCTCTTGG 57.483 45.455 0.00 0.00 40.87 3.61
2594 3768 1.885049 TCCTCTCCAATCCTCTTGGG 58.115 55.000 4.28 0.00 39.96 4.12
2608 3782 3.798202 CTCTTGGGAGGAGGATTAAACG 58.202 50.000 0.00 0.00 36.03 3.60
2609 3783 3.446968 TCTTGGGAGGAGGATTAAACGA 58.553 45.455 0.00 0.00 0.00 3.85
2610 3784 3.841845 TCTTGGGAGGAGGATTAAACGAA 59.158 43.478 0.00 0.00 0.00 3.85
2611 3785 3.622166 TGGGAGGAGGATTAAACGAAC 57.378 47.619 0.00 0.00 0.00 3.95
2612 3786 2.907696 TGGGAGGAGGATTAAACGAACA 59.092 45.455 0.00 0.00 0.00 3.18
2613 3787 3.328343 TGGGAGGAGGATTAAACGAACAA 59.672 43.478 0.00 0.00 0.00 2.83
2614 3788 3.939592 GGGAGGAGGATTAAACGAACAAG 59.060 47.826 0.00 0.00 0.00 3.16
2615 3789 3.939592 GGAGGAGGATTAAACGAACAAGG 59.060 47.826 0.00 0.00 0.00 3.61
2616 3790 3.344515 AGGAGGATTAAACGAACAAGGC 58.655 45.455 0.00 0.00 0.00 4.35
2617 3791 2.422479 GGAGGATTAAACGAACAAGGCC 59.578 50.000 0.00 0.00 0.00 5.19
2618 3792 3.344515 GAGGATTAAACGAACAAGGCCT 58.655 45.455 0.00 0.00 0.00 5.19
2619 3793 3.081804 AGGATTAAACGAACAAGGCCTG 58.918 45.455 5.69 2.82 0.00 4.85
2620 3794 3.078837 GGATTAAACGAACAAGGCCTGA 58.921 45.455 5.69 0.00 0.00 3.86
2621 3795 3.127030 GGATTAAACGAACAAGGCCTGAG 59.873 47.826 5.69 4.64 0.00 3.35
2658 3864 7.205297 CACACAAGGAAAAACATGATTCTTCT 58.795 34.615 0.00 0.00 0.00 2.85
2659 3865 7.168637 CACACAAGGAAAAACATGATTCTTCTG 59.831 37.037 0.00 0.00 0.00 3.02
2695 3906 2.415512 GGTTGTATTCAGAGAACCGCAC 59.584 50.000 0.00 0.00 0.00 5.34
2704 3934 3.260884 TCAGAGAACCGCACCTATTTTCT 59.739 43.478 0.00 0.00 0.00 2.52
2705 3935 4.003648 CAGAGAACCGCACCTATTTTCTT 58.996 43.478 0.00 0.00 0.00 2.52
2706 3936 5.046878 TCAGAGAACCGCACCTATTTTCTTA 60.047 40.000 0.00 0.00 0.00 2.10
2726 3956 5.893255 TCTTATTATGCTTGCCTTGAATGGT 59.107 36.000 0.00 0.00 0.00 3.55
2727 3957 7.059788 TCTTATTATGCTTGCCTTGAATGGTA 58.940 34.615 0.00 0.00 0.00 3.25
2859 4116 7.400439 TCTTGCTTAGGTAAGTACTCTACTCA 58.600 38.462 0.00 0.00 38.26 3.41
2860 4117 7.886970 TCTTGCTTAGGTAAGTACTCTACTCAA 59.113 37.037 0.00 0.57 38.26 3.02
2861 4118 8.413309 TTGCTTAGGTAAGTACTCTACTCAAA 57.587 34.615 0.00 0.00 38.26 2.69
2899 4156 7.591006 TCAGAACTTTGTAACGTAATCCATC 57.409 36.000 0.00 0.00 0.00 3.51
2907 4164 1.006832 ACGTAATCCATCAACAGCGC 58.993 50.000 0.00 0.00 0.00 5.92
2913 4170 2.229675 TCCATCAACAGCGCTATCAG 57.770 50.000 10.99 0.00 0.00 2.90
2987 4271 7.378966 GGTATCAATTACCGATCTGATTCTGA 58.621 38.462 0.00 0.00 41.10 3.27
2989 4273 9.429359 GTATCAATTACCGATCTGATTCTGATT 57.571 33.333 7.39 0.00 31.20 2.57
3013 4297 5.821516 AAATCGTGTGTTAACAGAAACCA 57.178 34.783 8.98 0.00 36.84 3.67
3016 4300 3.866910 TCGTGTGTTAACAGAAACCAGAC 59.133 43.478 8.98 0.00 36.84 3.51
3063 4347 1.069513 TGTTACCACGTCTTCCCTGTG 59.930 52.381 0.00 0.00 0.00 3.66
3079 4363 2.048603 GTGCAGCCCCATGGAGTTC 61.049 63.158 15.22 0.00 0.00 3.01
3080 4364 2.233566 TGCAGCCCCATGGAGTTCT 61.234 57.895 15.22 1.02 0.00 3.01
3088 4372 3.706373 ATGGAGTTCTGCGGCGGT 61.706 61.111 9.78 0.00 0.00 5.68
3090 4374 2.668550 GGAGTTCTGCGGCGGTTT 60.669 61.111 9.78 0.00 0.00 3.27
3092 4376 2.966309 GAGTTCTGCGGCGGTTTGG 61.966 63.158 9.78 0.00 0.00 3.28
3170 4787 2.104331 GGTGCCGACGATCACGAT 59.896 61.111 10.23 0.00 42.66 3.73
3319 4948 1.134580 CATCATCCAGCTGAACGAGGT 60.135 52.381 17.39 0.00 0.00 3.85
3324 4953 1.513158 CAGCTGAACGAGGTCGGAT 59.487 57.895 8.42 0.00 44.95 4.18
3338 4967 1.737793 GTCGGATTTCTCGTTGCCATT 59.262 47.619 0.00 0.00 0.00 3.16
3342 4971 2.476185 GGATTTCTCGTTGCCATTGTCG 60.476 50.000 0.00 0.00 0.00 4.35
3343 4972 0.871722 TTTCTCGTTGCCATTGTCGG 59.128 50.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 5.180868 ACTGAAAGCTTGCTGTTTCATAGAG 59.819 40.000 11.04 0.00 40.86 2.43
157 158 9.956720 AATATCATGCAAGCATTTAAGTAAGAC 57.043 29.630 4.52 0.00 33.90 3.01
385 387 3.932545 TTCATGCAAATAAACACCGCT 57.067 38.095 0.00 0.00 0.00 5.52
439 441 9.632638 ACATACAAATTATAAAGAGCACCTCAT 57.367 29.630 0.00 0.00 32.06 2.90
782 1123 9.914131 CGAACTATGTCTTTCATCCAATATAGA 57.086 33.333 0.00 0.00 37.91 1.98
787 1128 6.092670 CACACGAACTATGTCTTTCATCCAAT 59.907 38.462 0.00 0.00 37.91 3.16
992 1406 8.206189 CCAATTTAAATAGAGCCATTTGTGGAT 58.794 33.333 0.01 0.00 30.84 3.41
1105 1519 1.202794 TGTGTCCTTGCATCTTGCTCA 60.203 47.619 0.75 0.00 45.31 4.26
1132 1546 3.539604 CTCTAACCTTTCTGCATCCCAG 58.460 50.000 0.00 0.00 43.17 4.45
1194 1608 3.357079 CCTGTGGCAAGCACCGAC 61.357 66.667 0.00 0.00 0.00 4.79
1206 1620 2.169352 CCAGGGATGTAGTTCTCCTGTG 59.831 54.545 0.00 0.00 42.38 3.66
1235 1649 0.463295 GCAGCAGCTGAGGCATAGAA 60.463 55.000 27.39 0.00 41.70 2.10
1348 1856 0.038599 ACACCATGCCTCATGAGCAA 59.961 50.000 17.76 7.60 43.81 3.91
1357 1865 4.862641 ATAACCTAAAGACACCATGCCT 57.137 40.909 0.00 0.00 0.00 4.75
1486 1998 5.705609 TTTGGACAAGAAAATAGCAGGAC 57.294 39.130 0.00 0.00 0.00 3.85
1574 2093 7.226720 GGTATGCATGCAGTAAAGTTGTATAGT 59.773 37.037 26.69 5.53 0.00 2.12
1653 2195 2.573915 GACCAAGGACCTCTCCAGATTT 59.426 50.000 0.00 0.00 39.39 2.17
1693 2236 6.222038 TGATCTCAGTGAAGTTACATACCC 57.778 41.667 0.00 0.00 0.00 3.69
1915 2499 5.114081 ACAGTATAGCGAATTAACCCACAC 58.886 41.667 0.00 0.00 0.00 3.82
1968 2566 1.053424 GTTGACTCAGTACCACCCCA 58.947 55.000 0.00 0.00 0.00 4.96
1977 2575 5.278758 GCTTCTGACTCTTAGTTGACTCAGT 60.279 44.000 0.00 0.00 32.50 3.41
2075 2832 6.395629 CATTATTGCCCTCATCCATTTCATC 58.604 40.000 0.00 0.00 0.00 2.92
2113 3074 4.841422 AGAGTTCTGTTCATCCATTCAGG 58.159 43.478 0.00 0.00 39.47 3.86
2114 3075 6.871844 TCTAGAGTTCTGTTCATCCATTCAG 58.128 40.000 0.00 0.00 0.00 3.02
2115 3076 6.857437 TCTAGAGTTCTGTTCATCCATTCA 57.143 37.500 0.00 0.00 0.00 2.57
2116 3077 7.821846 AGTTTCTAGAGTTCTGTTCATCCATTC 59.178 37.037 0.00 0.00 0.00 2.67
2117 3078 7.684529 AGTTTCTAGAGTTCTGTTCATCCATT 58.315 34.615 0.00 0.00 0.00 3.16
2118 3079 7.251321 AGTTTCTAGAGTTCTGTTCATCCAT 57.749 36.000 0.00 0.00 0.00 3.41
2119 3080 6.672266 AGTTTCTAGAGTTCTGTTCATCCA 57.328 37.500 0.00 0.00 0.00 3.41
2120 3081 7.155328 TCAAGTTTCTAGAGTTCTGTTCATCC 58.845 38.462 0.00 0.00 0.00 3.51
2121 3082 8.594881 TTCAAGTTTCTAGAGTTCTGTTCATC 57.405 34.615 0.00 0.00 0.00 2.92
2122 3083 8.997323 CATTCAAGTTTCTAGAGTTCTGTTCAT 58.003 33.333 0.00 0.00 0.00 2.57
2123 3084 7.442364 CCATTCAAGTTTCTAGAGTTCTGTTCA 59.558 37.037 0.00 0.00 0.00 3.18
2203 3174 4.705023 ACTTTGGCAACCAATAGGACATAC 59.295 41.667 0.00 0.00 43.55 2.39
2206 3177 2.890311 CACTTTGGCAACCAATAGGACA 59.110 45.455 0.00 0.00 43.55 4.02
2225 3200 3.196040 ATGGACCACATGCCATCAC 57.804 52.632 0.00 0.00 40.83 3.06
2233 3208 4.927267 TTTAAGAGACCATGGACCACAT 57.073 40.909 21.47 5.43 41.57 3.21
2234 3209 4.715534 TTTTAAGAGACCATGGACCACA 57.284 40.909 21.47 0.00 0.00 4.17
2235 3210 4.142381 GCATTTTAAGAGACCATGGACCAC 60.142 45.833 21.47 9.74 0.00 4.16
2236 3211 4.016444 GCATTTTAAGAGACCATGGACCA 58.984 43.478 21.47 0.00 0.00 4.02
2237 3212 3.065371 CGCATTTTAAGAGACCATGGACC 59.935 47.826 21.47 9.85 0.00 4.46
2238 3213 3.487544 GCGCATTTTAAGAGACCATGGAC 60.488 47.826 21.47 13.40 0.00 4.02
2239 3214 2.682856 GCGCATTTTAAGAGACCATGGA 59.317 45.455 21.47 0.00 0.00 3.41
2240 3215 2.684881 AGCGCATTTTAAGAGACCATGG 59.315 45.455 11.19 11.19 0.00 3.66
2241 3216 4.361451 AAGCGCATTTTAAGAGACCATG 57.639 40.909 11.47 0.00 0.00 3.66
2290 3295 8.246180 AGCTACAGAATTTACCATTTGTTCATG 58.754 33.333 0.00 0.00 0.00 3.07
2319 3324 1.093496 GCCCTGCACCACCGTTATAC 61.093 60.000 0.00 0.00 0.00 1.47
2339 3344 0.108520 ATGCTCAATTTTGGCCTGCG 60.109 50.000 3.32 0.00 0.00 5.18
2367 3372 3.197983 AGGACCAAGGATGTAAATCCCA 58.802 45.455 8.45 0.00 41.65 4.37
2368 3373 3.202151 TGAGGACCAAGGATGTAAATCCC 59.798 47.826 8.45 0.00 41.65 3.85
2369 3374 4.503714 TGAGGACCAAGGATGTAAATCC 57.496 45.455 3.38 3.38 41.02 3.01
2370 3375 4.823989 CCATGAGGACCAAGGATGTAAATC 59.176 45.833 0.00 0.00 35.72 2.17
2399 3573 3.917988 TGCATATGATCTACTTCAGCGG 58.082 45.455 6.97 0.00 0.00 5.52
2401 3575 8.997323 AGTAAAATGCATATGATCTACTTCAGC 58.003 33.333 6.97 0.00 0.00 4.26
2440 3614 0.673022 GCTGAGTGGAGAACTGGCAG 60.673 60.000 14.16 14.16 40.07 4.85
2465 3639 4.493819 AGTGGGAGTATATCACAGGGAT 57.506 45.455 0.00 0.00 43.80 3.85
2481 3655 1.656652 CCTCAGCGTAATGAAGTGGG 58.343 55.000 0.00 0.00 0.00 4.61
2482 3656 1.009829 GCCTCAGCGTAATGAAGTGG 58.990 55.000 0.00 0.00 0.00 4.00
2483 3657 1.009829 GGCCTCAGCGTAATGAAGTG 58.990 55.000 0.00 0.00 41.24 3.16
2484 3658 0.905357 AGGCCTCAGCGTAATGAAGT 59.095 50.000 0.00 0.00 41.24 3.01
2485 3659 2.029838 AAGGCCTCAGCGTAATGAAG 57.970 50.000 5.23 0.00 41.24 3.02
2486 3660 3.838244 ATAAGGCCTCAGCGTAATGAA 57.162 42.857 5.23 0.00 41.24 2.57
2488 3662 2.476619 CGAATAAGGCCTCAGCGTAATG 59.523 50.000 5.23 0.00 41.24 1.90
2489 3663 2.548067 CCGAATAAGGCCTCAGCGTAAT 60.548 50.000 5.23 0.00 41.24 1.89
2490 3664 1.202486 CCGAATAAGGCCTCAGCGTAA 60.202 52.381 5.23 0.00 41.24 3.18
2492 3666 1.144057 CCGAATAAGGCCTCAGCGT 59.856 57.895 5.23 0.00 41.24 5.07
2494 3668 1.017387 CAACCGAATAAGGCCTCAGC 58.983 55.000 5.23 0.00 38.76 4.26
2495 3669 2.555199 CTCAACCGAATAAGGCCTCAG 58.445 52.381 5.23 0.00 33.69 3.35
2496 3670 1.209504 CCTCAACCGAATAAGGCCTCA 59.790 52.381 5.23 0.00 33.69 3.86
2497 3671 1.209747 ACCTCAACCGAATAAGGCCTC 59.790 52.381 5.23 0.00 31.79 4.70
2498 3672 1.065418 CACCTCAACCGAATAAGGCCT 60.065 52.381 0.00 0.00 31.79 5.19
2499 3673 1.379527 CACCTCAACCGAATAAGGCC 58.620 55.000 0.00 0.00 31.79 5.19
2500 3674 1.339727 ACCACCTCAACCGAATAAGGC 60.340 52.381 0.00 0.00 31.79 4.35
2505 3679 3.292460 TCAAAAACCACCTCAACCGAAT 58.708 40.909 0.00 0.00 0.00 3.34
2506 3680 2.724454 TCAAAAACCACCTCAACCGAA 58.276 42.857 0.00 0.00 0.00 4.30
2508 3682 2.223711 CCTTCAAAAACCACCTCAACCG 60.224 50.000 0.00 0.00 0.00 4.44
2509 3683 2.102420 CCCTTCAAAAACCACCTCAACC 59.898 50.000 0.00 0.00 0.00 3.77
2510 3684 2.102420 CCCCTTCAAAAACCACCTCAAC 59.898 50.000 0.00 0.00 0.00 3.18
2511 3685 2.023888 TCCCCTTCAAAAACCACCTCAA 60.024 45.455 0.00 0.00 0.00 3.02
2512 3686 1.571457 TCCCCTTCAAAAACCACCTCA 59.429 47.619 0.00 0.00 0.00 3.86
2513 3687 2.375014 TCCCCTTCAAAAACCACCTC 57.625 50.000 0.00 0.00 0.00 3.85
2514 3688 2.858787 TTCCCCTTCAAAAACCACCT 57.141 45.000 0.00 0.00 0.00 4.00
2515 3689 2.038426 CCATTCCCCTTCAAAAACCACC 59.962 50.000 0.00 0.00 0.00 4.61
2516 3690 2.549992 GCCATTCCCCTTCAAAAACCAC 60.550 50.000 0.00 0.00 0.00 4.16
2517 3691 1.696884 GCCATTCCCCTTCAAAAACCA 59.303 47.619 0.00 0.00 0.00 3.67
2518 3692 1.696884 TGCCATTCCCCTTCAAAAACC 59.303 47.619 0.00 0.00 0.00 3.27
2519 3693 3.402110 CTTGCCATTCCCCTTCAAAAAC 58.598 45.455 0.00 0.00 0.00 2.43
2520 3694 2.371510 CCTTGCCATTCCCCTTCAAAAA 59.628 45.455 0.00 0.00 0.00 1.94
2521 3695 1.977129 CCTTGCCATTCCCCTTCAAAA 59.023 47.619 0.00 0.00 0.00 2.44
2522 3696 1.132881 ACCTTGCCATTCCCCTTCAAA 60.133 47.619 0.00 0.00 0.00 2.69
2523 3697 0.486879 ACCTTGCCATTCCCCTTCAA 59.513 50.000 0.00 0.00 0.00 2.69
2524 3698 0.486879 AACCTTGCCATTCCCCTTCA 59.513 50.000 0.00 0.00 0.00 3.02
2525 3699 1.276138 CAAACCTTGCCATTCCCCTTC 59.724 52.381 0.00 0.00 0.00 3.46
2526 3700 1.132881 TCAAACCTTGCCATTCCCCTT 60.133 47.619 0.00 0.00 0.00 3.95
2527 3701 0.486879 TCAAACCTTGCCATTCCCCT 59.513 50.000 0.00 0.00 0.00 4.79
2528 3702 0.897621 CTCAAACCTTGCCATTCCCC 59.102 55.000 0.00 0.00 0.00 4.81
2529 3703 0.897621 CCTCAAACCTTGCCATTCCC 59.102 55.000 0.00 0.00 0.00 3.97
2530 3704 0.897621 CCCTCAAACCTTGCCATTCC 59.102 55.000 0.00 0.00 0.00 3.01
2531 3705 0.897621 CCCCTCAAACCTTGCCATTC 59.102 55.000 0.00 0.00 0.00 2.67
2532 3706 0.545071 CCCCCTCAAACCTTGCCATT 60.545 55.000 0.00 0.00 0.00 3.16
2533 3707 1.079073 CCCCCTCAAACCTTGCCAT 59.921 57.895 0.00 0.00 0.00 4.40
2534 3708 1.442886 ATCCCCCTCAAACCTTGCCA 61.443 55.000 0.00 0.00 0.00 4.92
2535 3709 0.252239 AATCCCCCTCAAACCTTGCC 60.252 55.000 0.00 0.00 0.00 4.52
2536 3710 2.025321 TCTAATCCCCCTCAAACCTTGC 60.025 50.000 0.00 0.00 0.00 4.01
2537 3711 4.464947 GATCTAATCCCCCTCAAACCTTG 58.535 47.826 0.00 0.00 0.00 3.61
2538 3712 3.463704 GGATCTAATCCCCCTCAAACCTT 59.536 47.826 0.00 0.00 43.88 3.50
2539 3713 3.056832 GGATCTAATCCCCCTCAAACCT 58.943 50.000 0.00 0.00 43.88 3.50
2540 3714 3.510531 GGATCTAATCCCCCTCAAACC 57.489 52.381 0.00 0.00 43.88 3.27
2551 3725 4.706842 TTGGCTTGTAGGGGATCTAATC 57.293 45.455 0.00 0.00 0.00 1.75
2552 3726 5.466127 TTTTGGCTTGTAGGGGATCTAAT 57.534 39.130 0.00 0.00 0.00 1.73
2553 3727 4.938575 TTTTGGCTTGTAGGGGATCTAA 57.061 40.909 0.00 0.00 0.00 2.10
2554 3728 4.141251 GGATTTTGGCTTGTAGGGGATCTA 60.141 45.833 0.00 0.00 0.00 1.98
2555 3729 3.373110 GGATTTTGGCTTGTAGGGGATCT 60.373 47.826 0.00 0.00 0.00 2.75
2556 3730 2.959030 GGATTTTGGCTTGTAGGGGATC 59.041 50.000 0.00 0.00 0.00 3.36
2557 3731 2.587307 AGGATTTTGGCTTGTAGGGGAT 59.413 45.455 0.00 0.00 0.00 3.85
2558 3732 2.000048 AGGATTTTGGCTTGTAGGGGA 59.000 47.619 0.00 0.00 0.00 4.81
2559 3733 2.024941 AGAGGATTTTGGCTTGTAGGGG 60.025 50.000 0.00 0.00 0.00 4.79
2560 3734 3.282885 GAGAGGATTTTGGCTTGTAGGG 58.717 50.000 0.00 0.00 0.00 3.53
2561 3735 3.282885 GGAGAGGATTTTGGCTTGTAGG 58.717 50.000 0.00 0.00 0.00 3.18
2562 3736 3.955471 TGGAGAGGATTTTGGCTTGTAG 58.045 45.455 0.00 0.00 0.00 2.74
2563 3737 4.380843 TTGGAGAGGATTTTGGCTTGTA 57.619 40.909 0.00 0.00 0.00 2.41
2564 3738 2.978156 TGGAGAGGATTTTGGCTTGT 57.022 45.000 0.00 0.00 0.00 3.16
2565 3739 3.131755 GGATTGGAGAGGATTTTGGCTTG 59.868 47.826 0.00 0.00 0.00 4.01
2566 3740 3.012161 AGGATTGGAGAGGATTTTGGCTT 59.988 43.478 0.00 0.00 0.00 4.35
2567 3741 2.584498 AGGATTGGAGAGGATTTTGGCT 59.416 45.455 0.00 0.00 0.00 4.75
2568 3742 2.954989 GAGGATTGGAGAGGATTTTGGC 59.045 50.000 0.00 0.00 0.00 4.52
2569 3743 4.516652 AGAGGATTGGAGAGGATTTTGG 57.483 45.455 0.00 0.00 0.00 3.28
2570 3744 4.643784 CCAAGAGGATTGGAGAGGATTTTG 59.356 45.833 0.12 0.00 42.06 2.44
2571 3745 4.325658 CCCAAGAGGATTGGAGAGGATTTT 60.326 45.833 8.20 0.00 42.06 1.82
2572 3746 3.203934 CCCAAGAGGATTGGAGAGGATTT 59.796 47.826 8.20 0.00 42.06 2.17
2573 3747 2.782341 CCCAAGAGGATTGGAGAGGATT 59.218 50.000 8.20 0.00 42.06 3.01
2574 3748 2.021639 TCCCAAGAGGATTGGAGAGGAT 60.022 50.000 8.20 0.00 40.93 3.24
2575 3749 1.366082 TCCCAAGAGGATTGGAGAGGA 59.634 52.381 8.20 0.00 40.93 3.71
2576 3750 1.767681 CTCCCAAGAGGATTGGAGAGG 59.232 57.143 8.20 0.00 46.33 3.69
2587 3761 3.451178 TCGTTTAATCCTCCTCCCAAGAG 59.549 47.826 0.00 0.00 40.09 2.85
2588 3762 3.446968 TCGTTTAATCCTCCTCCCAAGA 58.553 45.455 0.00 0.00 0.00 3.02
2589 3763 3.906720 TCGTTTAATCCTCCTCCCAAG 57.093 47.619 0.00 0.00 0.00 3.61
2590 3764 3.328343 TGTTCGTTTAATCCTCCTCCCAA 59.672 43.478 0.00 0.00 0.00 4.12
2591 3765 2.907696 TGTTCGTTTAATCCTCCTCCCA 59.092 45.455 0.00 0.00 0.00 4.37
2592 3766 3.622166 TGTTCGTTTAATCCTCCTCCC 57.378 47.619 0.00 0.00 0.00 4.30
2593 3767 3.939592 CCTTGTTCGTTTAATCCTCCTCC 59.060 47.826 0.00 0.00 0.00 4.30
2594 3768 3.374367 GCCTTGTTCGTTTAATCCTCCTC 59.626 47.826 0.00 0.00 0.00 3.71
2595 3769 3.344515 GCCTTGTTCGTTTAATCCTCCT 58.655 45.455 0.00 0.00 0.00 3.69
2596 3770 2.422479 GGCCTTGTTCGTTTAATCCTCC 59.578 50.000 0.00 0.00 0.00 4.30
2597 3771 3.127030 CAGGCCTTGTTCGTTTAATCCTC 59.873 47.826 0.00 0.00 0.00 3.71
2598 3772 3.081804 CAGGCCTTGTTCGTTTAATCCT 58.918 45.455 0.00 0.00 0.00 3.24
2599 3773 3.078837 TCAGGCCTTGTTCGTTTAATCC 58.921 45.455 0.00 0.00 0.00 3.01
2600 3774 3.751698 ACTCAGGCCTTGTTCGTTTAATC 59.248 43.478 0.00 0.00 0.00 1.75
2601 3775 3.502211 CACTCAGGCCTTGTTCGTTTAAT 59.498 43.478 0.00 0.00 0.00 1.40
2602 3776 2.875933 CACTCAGGCCTTGTTCGTTTAA 59.124 45.455 0.00 0.00 0.00 1.52
2603 3777 2.103432 TCACTCAGGCCTTGTTCGTTTA 59.897 45.455 0.00 0.00 0.00 2.01
2604 3778 1.134220 TCACTCAGGCCTTGTTCGTTT 60.134 47.619 0.00 0.00 0.00 3.60
2605 3779 0.468226 TCACTCAGGCCTTGTTCGTT 59.532 50.000 0.00 0.00 0.00 3.85
2606 3780 0.687354 ATCACTCAGGCCTTGTTCGT 59.313 50.000 0.00 0.00 0.00 3.85
2607 3781 1.081892 CATCACTCAGGCCTTGTTCG 58.918 55.000 0.00 0.00 0.00 3.95
2608 3782 2.191128 ACATCACTCAGGCCTTGTTC 57.809 50.000 0.00 0.00 0.00 3.18
2609 3783 2.639839 AGTACATCACTCAGGCCTTGTT 59.360 45.455 0.00 0.00 28.33 2.83
2610 3784 2.027745 CAGTACATCACTCAGGCCTTGT 60.028 50.000 0.00 6.64 34.26 3.16
2611 3785 2.625737 CAGTACATCACTCAGGCCTTG 58.374 52.381 0.00 0.00 34.26 3.61
2612 3786 1.065854 GCAGTACATCACTCAGGCCTT 60.066 52.381 0.00 0.00 34.26 4.35
2613 3787 0.539051 GCAGTACATCACTCAGGCCT 59.461 55.000 0.00 0.00 34.26 5.19
2614 3788 0.462759 GGCAGTACATCACTCAGGCC 60.463 60.000 0.00 0.00 36.87 5.19
2615 3789 0.250234 TGGCAGTACATCACTCAGGC 59.750 55.000 0.00 0.00 34.26 4.85
2616 3790 1.276138 TGTGGCAGTACATCACTCAGG 59.724 52.381 12.26 0.00 34.26 3.86
2617 3791 2.289010 TGTGTGGCAGTACATCACTCAG 60.289 50.000 12.26 0.00 34.26 3.35
2618 3792 1.691434 TGTGTGGCAGTACATCACTCA 59.309 47.619 12.26 11.76 34.26 3.41
2619 3793 2.455674 TGTGTGGCAGTACATCACTC 57.544 50.000 12.26 9.94 34.26 3.51
2620 3794 2.550855 CCTTGTGTGGCAGTACATCACT 60.551 50.000 5.47 0.00 38.32 3.41
2621 3795 1.806542 CCTTGTGTGGCAGTACATCAC 59.193 52.381 5.47 1.48 32.43 3.06
2658 3864 0.399949 AACCACCCAGTCTCAGGACA 60.400 55.000 0.00 0.00 44.36 4.02
2659 3865 0.035458 CAACCACCCAGTCTCAGGAC 59.965 60.000 0.00 0.00 42.41 3.85
2695 3906 8.632679 TCAAGGCAAGCATAATAAGAAAATAGG 58.367 33.333 0.00 0.00 0.00 2.57
2704 3934 7.838079 ATACCATTCAAGGCAAGCATAATAA 57.162 32.000 0.00 0.00 0.00 1.40
2706 3936 8.960591 GTATATACCATTCAAGGCAAGCATAAT 58.039 33.333 1.02 0.00 0.00 1.28
2726 3956 6.169557 AGGCACGTGGAATTGAAGTATATA 57.830 37.500 18.88 0.00 0.00 0.86
2727 3957 5.036117 AGGCACGTGGAATTGAAGTATAT 57.964 39.130 18.88 0.00 0.00 0.86
2795 4049 8.669055 TTATAAGTCCCAGTTACTAACTTCCA 57.331 34.615 9.28 0.00 40.46 3.53
2859 4116 5.016831 AGTTCTGAAACAAACACCTCCTTT 58.983 37.500 0.00 0.00 37.88 3.11
2860 4117 4.600062 AGTTCTGAAACAAACACCTCCTT 58.400 39.130 0.00 0.00 37.88 3.36
2861 4118 4.236527 AGTTCTGAAACAAACACCTCCT 57.763 40.909 0.00 0.00 37.88 3.69
2899 4156 1.520174 CGTCATCTGATAGCGCTGTTG 59.480 52.381 22.90 8.84 0.00 3.33
2907 4164 5.288015 ACAAGATTCAGCGTCATCTGATAG 58.712 41.667 0.00 0.00 42.12 2.08
2913 4170 3.189287 ACCAAACAAGATTCAGCGTCATC 59.811 43.478 0.00 0.00 0.00 2.92
2985 4269 9.440784 GTTTCTGTTAACACACGATTTTAATCA 57.559 29.630 3.59 0.00 35.11 2.57
2987 4271 8.407064 TGGTTTCTGTTAACACACGATTTTAAT 58.593 29.630 3.59 0.00 0.00 1.40
2989 4273 7.280428 TCTGGTTTCTGTTAACACACGATTTTA 59.720 33.333 3.59 0.00 0.00 1.52
3063 4347 1.751927 CAGAACTCCATGGGGCTGC 60.752 63.158 13.00 0.44 0.00 5.25
3088 4372 1.315981 TTGTCAGCCACAACGCCAAA 61.316 50.000 0.00 0.00 40.29 3.28
3090 4374 2.124529 TTGTCAGCCACAACGCCA 60.125 55.556 0.00 0.00 40.29 5.69
3092 4376 2.639286 CCTTGTCAGCCACAACGC 59.361 61.111 0.00 0.00 40.29 4.84
3211 4828 0.613853 CCTTCCTCCTCACCGGTGTA 60.614 60.000 32.74 18.79 0.00 2.90
3319 4948 1.737236 CAATGGCAACGAGAAATCCGA 59.263 47.619 0.00 0.00 42.51 4.55
3324 4953 0.871722 CCGACAATGGCAACGAGAAA 59.128 50.000 0.00 0.00 42.51 2.52
3401 5052 1.124477 AAGATCCTCGCCATCCCCTC 61.124 60.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.