Multiple sequence alignment - TraesCS2B01G467900

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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 TraesCS2B01G467900 chr2B 100.000 3071 0 0 1 3071 663885033 663888103 0.000000e+00 5672.0
1 TraesCS2B01G467900 chr2B 84.191 1360 130 51 767 2073 663837774 663839101 0.000000e+00 1242.0
2 TraesCS2B01G467900 chr2B 83.380 1426 141 39 719 2073 663828695 663830095 0.000000e+00 1232.0
3 TraesCS2B01G467900 chr2B 88.780 205 23 0 158 362 663827807 663828011 5.080000e-63 252.0
4 TraesCS2B01G467900 chr2B 75.817 306 50 18 212 506 663835064 663835356 1.920000e-27 134.0
5 TraesCS2B01G467900 chr2B 88.095 84 5 4 566 649 663837568 663837646 9.070000e-16 95.3
6 TraesCS2B01G467900 chr2B 85.263 95 9 3 2365 2457 663839387 663839478 3.260000e-15 93.5
7 TraesCS2B01G467900 chr2D 93.167 1566 78 5 691 2239 556407740 556409293 0.000000e+00 2272.0
8 TraesCS2B01G467900 chr2D 88.197 1686 124 35 719 2355 556618855 556620514 0.000000e+00 1941.0
9 TraesCS2B01G467900 chr2D 87.861 1697 147 37 691 2360 556365195 556366859 0.000000e+00 1938.0
10 TraesCS2B01G467900 chr2D 82.228 1553 164 44 769 2227 556266998 556268532 0.000000e+00 1236.0
11 TraesCS2B01G467900 chr2D 81.706 1454 160 51 861 2227 556350414 556351848 0.000000e+00 1114.0
12 TraesCS2B01G467900 chr2D 92.287 726 22 10 2 697 556406979 556407700 0.000000e+00 1000.0
13 TraesCS2B01G467900 chr2D 87.097 775 51 23 719 1489 556318178 556318907 0.000000e+00 832.0
14 TraesCS2B01G467900 chr2D 84.720 805 76 34 999 1767 556642397 556643190 0.000000e+00 761.0
15 TraesCS2B01G467900 chr2D 88.559 472 32 10 1484 1933 556333284 556333755 1.240000e-153 553.0
16 TraesCS2B01G467900 chr2D 89.549 421 39 3 1940 2360 556333871 556334286 2.100000e-146 529.0
17 TraesCS2B01G467900 chr2D 89.977 429 13 10 252 650 556364668 556365096 7.540000e-146 527.0
18 TraesCS2B01G467900 chr2D 85.484 434 43 8 2577 2992 556366931 556367362 4.700000e-118 435.0
19 TraesCS2B01G467900 chr2D 84.848 429 48 10 2577 2992 556334358 556334782 1.700000e-112 416.0
20 TraesCS2B01G467900 chr2D 87.209 344 31 4 175 506 556265349 556265691 2.230000e-101 379.0
21 TraesCS2B01G467900 chr2D 82.018 228 25 11 239 452 556618319 556618544 2.430000e-41 180.0
22 TraesCS2B01G467900 chr2D 84.337 166 17 4 217 377 556349767 556349928 1.470000e-33 154.0
23 TraesCS2B01G467900 chr2D 91.743 109 9 0 158 266 556364331 556364439 5.300000e-33 152.0
24 TraesCS2B01G467900 chr2D 87.179 117 12 3 533 649 556265801 556265914 2.490000e-26 130.0
25 TraesCS2B01G467900 chr2D 83.221 149 16 4 236 375 556315894 556316042 8.940000e-26 128.0
26 TraesCS2B01G467900 chr2D 94.915 59 1 1 2407 2465 556366878 556366934 1.170000e-14 91.6
27 TraesCS2B01G467900 chr2D 93.220 59 2 1 2407 2465 556334305 556334361 5.460000e-13 86.1
28 TraesCS2B01G467900 chr2D 100.000 29 0 0 102 130 639102601 639102629 2.000000e-03 54.7
29 TraesCS2B01G467900 chr2A 90.590 1424 91 20 964 2360 696219181 696220588 0.000000e+00 1847.0
30 TraesCS2B01G467900 chr2A 82.053 1783 176 70 572 2259 696040014 696041747 0.000000e+00 1387.0
31 TraesCS2B01G467900 chr2A 80.462 1602 178 69 769 2257 695998881 696000460 0.000000e+00 1099.0
32 TraesCS2B01G467900 chr2A 89.600 875 68 7 1589 2462 696307720 696308572 0.000000e+00 1090.0
33 TraesCS2B01G467900 chr2A 89.859 779 50 7 825 1577 696306861 696307636 0.000000e+00 974.0
34 TraesCS2B01G467900 chr2A 88.225 569 27 10 168 697 696218352 696218919 0.000000e+00 643.0
35 TraesCS2B01G467900 chr2A 85.781 429 44 8 2577 2992 696220660 696221084 3.640000e-119 438.0
36 TraesCS2B01G467900 chr2A 82.833 466 54 17 209 649 695998283 695998747 7.980000e-106 394.0
37 TraesCS2B01G467900 chr2A 90.909 297 16 4 219 507 696286892 696287185 3.710000e-104 388.0
38 TraesCS2B01G467900 chr2A 82.828 396 47 10 2579 2960 696308574 696308962 4.910000e-88 335.0
39 TraesCS2B01G467900 chr2A 97.122 139 3 1 533 671 696287245 696287382 1.840000e-57 233.0
40 TraesCS2B01G467900 chr2A 84.034 238 26 5 691 928 696218959 696219184 5.160000e-53 219.0
41 TraesCS2B01G467900 chr2A 91.304 138 7 2 691 828 696287434 696287566 1.880000e-42 183.0
42 TraesCS2B01G467900 chr2A 93.220 59 2 1 2407 2465 696220607 696220663 5.460000e-13 86.1
43 TraesCS2B01G467900 chr4B 85.470 117 16 1 2463 2579 364488514 364488629 1.500000e-23 121.0
44 TraesCS2B01G467900 chr4B 86.667 75 9 1 2994 3068 391542477 391542550 7.060000e-12 82.4
45 TraesCS2B01G467900 chr4B 100.000 35 0 0 96 130 13320852 13320818 7.110000e-07 65.8
46 TraesCS2B01G467900 chr4B 94.286 35 2 0 2995 3029 4772754 4772720 2.000000e-03 54.7
47 TraesCS2B01G467900 chr1A 84.874 119 18 0 2461 2579 432987723 432987841 1.500000e-23 121.0
48 TraesCS2B01G467900 chr1A 85.526 76 11 0 2504 2579 523071757 523071682 2.540000e-11 80.5
49 TraesCS2B01G467900 chr1A 83.099 71 8 4 2462 2530 21861016 21861084 9.190000e-06 62.1
50 TraesCS2B01G467900 chr1A 92.308 39 3 0 2463 2501 60706979 60706941 4.280000e-04 56.5
51 TraesCS2B01G467900 chr1A 100.000 29 0 0 102 130 257983643 257983671 2.000000e-03 54.7
52 TraesCS2B01G467900 chr5B 84.762 105 16 0 2472 2576 520176925 520177029 4.190000e-19 106.0
53 TraesCS2B01G467900 chr5B 97.222 36 1 0 622 657 623152559 623152594 9.190000e-06 62.1
54 TraesCS2B01G467900 chr5B 97.222 36 1 0 622 657 626817483 626817518 9.190000e-06 62.1
55 TraesCS2B01G467900 chr5B 100.000 28 0 0 100 127 369606704 369606731 6.000000e-03 52.8
56 TraesCS2B01G467900 chr7B 87.209 86 9 2 2463 2547 714632194 714632110 2.520000e-16 97.1
57 TraesCS2B01G467900 chr7B 83.146 89 13 2 2504 2590 583385393 583385305 2.540000e-11 80.5
58 TraesCS2B01G467900 chr3A 95.349 43 0 1 90 130 615161343 615161385 1.980000e-07 67.6
59 TraesCS2B01G467900 chr3B 84.746 59 9 0 2485 2543 569745592 569745534 3.310000e-05 60.2
60 TraesCS2B01G467900 chr6B 97.059 34 1 0 2996 3029 68415680 68415713 1.190000e-04 58.4
61 TraesCS2B01G467900 chr5D 94.444 36 2 0 2994 3029 257935596 257935561 4.280000e-04 56.5
62 TraesCS2B01G467900 chr3D 94.444 36 2 0 101 136 49608497 49608462 4.280000e-04 56.5
63 TraesCS2B01G467900 chr7A 100.000 29 0 0 102 130 405954285 405954313 2.000000e-03 54.7
64 TraesCS2B01G467900 chr7A 100.000 29 0 0 2994 3022 563927639 563927667 2.000000e-03 54.7
65 TraesCS2B01G467900 chr6A 86.000 50 7 0 2501 2550 583278337 583278288 2.000000e-03 54.7
66 TraesCS2B01G467900 chr5A 100.000 29 0 0 2994 3022 27264482 27264454 2.000000e-03 54.7
67 TraesCS2B01G467900 chr5A 100.000 29 0 0 2994 3022 402479571 402479599 2.000000e-03 54.7
68 TraesCS2B01G467900 chr4D 100.000 29 0 0 2994 3022 50931417 50931389 2.000000e-03 54.7
69 TraesCS2B01G467900 chr4A 100.000 29 0 0 2994 3022 345259865 345259837 2.000000e-03 54.7
70 TraesCS2B01G467900 chr1D 100.000 29 0 0 102 130 203458169 203458197 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G467900 chr2B 663885033 663888103 3070 False 5672.000000 5672 100.000000 1 3071 1 chr2B.!!$F1 3070
1 TraesCS2B01G467900 chr2B 663827807 663830095 2288 False 742.000000 1232 86.080000 158 2073 2 chr2B.!!$F2 1915
2 TraesCS2B01G467900 chr2B 663835064 663839478 4414 False 391.200000 1242 83.341500 212 2457 4 chr2B.!!$F3 2245
3 TraesCS2B01G467900 chr2D 556406979 556409293 2314 False 1636.000000 2272 92.727000 2 2239 2 chr2D.!!$F8 2237
4 TraesCS2B01G467900 chr2D 556618319 556620514 2195 False 1060.500000 1941 85.107500 239 2355 2 chr2D.!!$F9 2116
5 TraesCS2B01G467900 chr2D 556642397 556643190 793 False 761.000000 761 84.720000 999 1767 1 chr2D.!!$F1 768
6 TraesCS2B01G467900 chr2D 556349767 556351848 2081 False 634.000000 1114 83.021500 217 2227 2 chr2D.!!$F6 2010
7 TraesCS2B01G467900 chr2D 556364331 556367362 3031 False 628.720000 1938 89.996000 158 2992 5 chr2D.!!$F7 2834
8 TraesCS2B01G467900 chr2D 556265349 556268532 3183 False 581.666667 1236 85.538667 175 2227 3 chr2D.!!$F3 2052
9 TraesCS2B01G467900 chr2D 556315894 556318907 3013 False 480.000000 832 85.159000 236 1489 2 chr2D.!!$F4 1253
10 TraesCS2B01G467900 chr2D 556333284 556334782 1498 False 396.025000 553 89.044000 1484 2992 4 chr2D.!!$F5 1508
11 TraesCS2B01G467900 chr2A 696040014 696041747 1733 False 1387.000000 1387 82.053000 572 2259 1 chr2A.!!$F1 1687
12 TraesCS2B01G467900 chr2A 696306861 696308962 2101 False 799.666667 1090 87.429000 825 2960 3 chr2A.!!$F5 2135
13 TraesCS2B01G467900 chr2A 695998283 696000460 2177 False 746.500000 1099 81.647500 209 2257 2 chr2A.!!$F2 2048
14 TraesCS2B01G467900 chr2A 696218352 696221084 2732 False 646.620000 1847 88.370000 168 2992 5 chr2A.!!$F3 2824
15 TraesCS2B01G467900 chr2A 696286892 696287566 674 False 268.000000 388 93.111667 219 828 3 chr2A.!!$F4 609

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
32 33 1.210478 ACCACATGCATAGTCTCCACC 59.790 52.381 0.0 0.0 0.0 4.61 F
1327 6983 0.745845 CACAGAGCTTAGCCGCCATT 60.746 55.000 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 7541 0.179205 GAACGATGCTGCTGCTTGAC 60.179 55.0 17.0 4.8 40.48 3.18 R
2565 8562 0.179108 GACACGTACTCCCTCCATGC 60.179 60.0 0.0 0.0 0.00 4.06 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
28 29 8.783833 ATATATTTCACCACATGCATAGTCTC 57.216 34.615 0.00 0.00 0.00 3.36
32 33 1.210478 ACCACATGCATAGTCTCCACC 59.790 52.381 0.00 0.00 0.00 4.61
35 36 3.326006 CCACATGCATAGTCTCCACCTAT 59.674 47.826 0.00 0.00 0.00 2.57
36 37 4.562347 CCACATGCATAGTCTCCACCTATC 60.562 50.000 0.00 0.00 0.00 2.08
48 49 5.012251 GTCTCCACCTATCTTTTATCCTCCC 59.988 48.000 0.00 0.00 0.00 4.30
51 52 4.907875 CCACCTATCTTTTATCCTCCCAGA 59.092 45.833 0.00 0.00 0.00 3.86
73 74 2.095969 CGGATACTTTGCAAAGCGTTGA 60.096 45.455 33.72 17.21 39.63 3.18
77 78 6.090129 GGATACTTTGCAAAGCGTTGAATTA 58.910 36.000 33.72 18.72 39.63 1.40
93 94 6.238566 CGTTGAATTACTCTCTCCCGTATACA 60.239 42.308 3.32 0.00 0.00 2.29
109 110 4.876107 CGTATACAAGAGGAATTTGCAGGT 59.124 41.667 3.32 0.00 0.00 4.00
138 139 5.128033 TGGAGATGCCCTTAATGAATCAA 57.872 39.130 0.00 0.00 34.97 2.57
144 145 4.460263 TGCCCTTAATGAATCAATACGCT 58.540 39.130 0.00 0.00 0.00 5.07
162 163 2.550978 GCTAAGCTCTTGCGTATCCAA 58.449 47.619 0.00 0.00 45.42 3.53
843 6387 1.781786 ATCTGTCATGGGCTACGACT 58.218 50.000 0.00 0.00 0.00 4.18
853 6399 1.755380 GGGCTACGACTACTGAATGGT 59.245 52.381 0.00 0.00 0.00 3.55
859 6413 4.067972 ACGACTACTGAATGGTTGTGTT 57.932 40.909 0.00 0.00 35.16 3.32
886 6444 5.818678 ATATATACCTGGCCAACGAAAGA 57.181 39.130 7.01 0.00 0.00 2.52
907 6465 5.583495 AGAGTACACGAACATAGATTCTGC 58.417 41.667 0.00 0.00 0.00 4.26
1327 6983 0.745845 CACAGAGCTTAGCCGCCATT 60.746 55.000 0.00 0.00 0.00 3.16
1414 7107 4.776837 ACATGGATAAATTTCTGTTGGGCA 59.223 37.500 0.00 0.00 0.00 5.36
1491 7184 3.880490 TCAAAAACTACTGGAACACGCAT 59.120 39.130 0.00 0.00 0.00 4.73
1566 7259 1.525077 GTGCGACCAGACCAACCAA 60.525 57.895 0.00 0.00 0.00 3.67
1635 7424 2.600729 CCTTGGAGGCCTGAGCACT 61.601 63.158 12.00 0.00 42.56 4.40
1792 7606 0.175760 GATGAACTACCTGCAGCCGA 59.824 55.000 8.66 0.00 0.00 5.54
1860 7674 2.635714 CAGCAGCTGACCAATGATACA 58.364 47.619 20.43 0.00 32.44 2.29
1933 7756 2.487934 ACACTGCCGCTTCATATGATC 58.512 47.619 6.17 0.97 0.00 2.92
2055 7987 2.104792 CTGGAAGGACACACTGGAAGAA 59.895 50.000 0.00 0.00 37.43 2.52
2166 8132 5.398603 TTGTGTGTTCATTGTGGTTCTTT 57.601 34.783 0.00 0.00 0.00 2.52
2175 8141 8.514594 TGTTCATTGTGGTTCTTTCAATAGATC 58.485 33.333 0.00 0.00 31.76 2.75
2181 8150 7.806690 TGTGGTTCTTTCAATAGATCTTTTCG 58.193 34.615 0.00 0.00 0.00 3.46
2197 8167 5.430007 TCTTTTCGGTGAAGTTGAAGGTTA 58.570 37.500 0.00 0.00 0.00 2.85
2218 8214 6.477688 GGTTATCAATTGCTGATTTGATGTGG 59.522 38.462 0.00 0.00 42.46 4.17
2261 8258 3.814842 TCAGTTAACATGTTGCCACTCAG 59.185 43.478 21.42 9.15 0.00 3.35
2280 8277 1.736645 CACGAACGCGAGGACCATT 60.737 57.895 15.93 0.00 41.64 3.16
2390 8387 1.549203 ACAGTTGGGCCTTAGCAATG 58.451 50.000 4.53 2.09 42.56 2.82
2435 8432 3.178046 TGGTTTACTCACAGCCCATCTA 58.822 45.455 0.00 0.00 0.00 1.98
2436 8433 3.197766 TGGTTTACTCACAGCCCATCTAG 59.802 47.826 0.00 0.00 0.00 2.43
2465 8462 6.690194 ATACGAACGAACCTAAGATGTACT 57.310 37.500 0.14 0.00 0.00 2.73
2466 8463 4.979388 ACGAACGAACCTAAGATGTACTC 58.021 43.478 0.14 0.00 0.00 2.59
2467 8464 4.142513 ACGAACGAACCTAAGATGTACTCC 60.143 45.833 0.14 0.00 0.00 3.85
2468 8465 4.680702 GAACGAACCTAAGATGTACTCCC 58.319 47.826 0.00 0.00 0.00 4.30
2469 8466 3.978610 ACGAACCTAAGATGTACTCCCT 58.021 45.455 0.00 0.00 0.00 4.20
2470 8467 4.351127 ACGAACCTAAGATGTACTCCCTT 58.649 43.478 0.00 0.00 0.00 3.95
2471 8468 4.401837 ACGAACCTAAGATGTACTCCCTTC 59.598 45.833 0.00 0.00 0.00 3.46
2472 8469 4.497674 CGAACCTAAGATGTACTCCCTTCG 60.498 50.000 0.00 0.00 0.00 3.79
2473 8470 3.978610 ACCTAAGATGTACTCCCTTCGT 58.021 45.455 0.00 0.00 0.00 3.85
2474 8471 4.351127 ACCTAAGATGTACTCCCTTCGTT 58.649 43.478 0.00 0.00 0.00 3.85
2475 8472 4.401837 ACCTAAGATGTACTCCCTTCGTTC 59.598 45.833 0.00 0.00 0.00 3.95
2476 8473 3.505464 AAGATGTACTCCCTTCGTTCG 57.495 47.619 0.00 0.00 0.00 3.95
2477 8474 2.719739 AGATGTACTCCCTTCGTTCGA 58.280 47.619 0.00 0.00 0.00 3.71
2478 8475 3.087031 AGATGTACTCCCTTCGTTCGAA 58.913 45.455 7.40 7.40 0.00 3.71
2479 8476 3.508793 AGATGTACTCCCTTCGTTCGAAA 59.491 43.478 0.00 0.00 0.00 3.46
2480 8477 3.947910 TGTACTCCCTTCGTTCGAAAT 57.052 42.857 0.00 0.00 0.00 2.17
2481 8478 4.261578 TGTACTCCCTTCGTTCGAAATT 57.738 40.909 0.00 0.00 0.00 1.82
2482 8479 5.389859 TGTACTCCCTTCGTTCGAAATTA 57.610 39.130 0.00 0.00 0.00 1.40
2483 8480 5.969423 TGTACTCCCTTCGTTCGAAATTAT 58.031 37.500 0.00 0.00 0.00 1.28
2484 8481 6.400568 TGTACTCCCTTCGTTCGAAATTATT 58.599 36.000 0.00 0.00 0.00 1.40
2485 8482 6.875195 TGTACTCCCTTCGTTCGAAATTATTT 59.125 34.615 0.00 0.00 0.00 1.40
2486 8483 6.178239 ACTCCCTTCGTTCGAAATTATTTG 57.822 37.500 0.00 0.00 0.00 2.32
2487 8484 5.704053 ACTCCCTTCGTTCGAAATTATTTGT 59.296 36.000 0.00 0.00 0.00 2.83
2488 8485 6.128363 ACTCCCTTCGTTCGAAATTATTTGTC 60.128 38.462 0.00 0.00 0.00 3.18
2489 8486 5.019498 CCCTTCGTTCGAAATTATTTGTCG 58.981 41.667 0.00 0.00 36.12 4.35
2490 8487 5.390145 CCCTTCGTTCGAAATTATTTGTCGT 60.390 40.000 0.00 0.00 36.21 4.34
2491 8488 5.503376 CCTTCGTTCGAAATTATTTGTCGTG 59.497 40.000 0.00 0.00 36.21 4.35
2492 8489 5.825905 TCGTTCGAAATTATTTGTCGTGA 57.174 34.783 0.00 0.00 36.21 4.35
2493 8490 6.212934 TCGTTCGAAATTATTTGTCGTGAA 57.787 33.333 0.00 0.00 36.21 3.18
2494 8491 6.647569 TCGTTCGAAATTATTTGTCGTGAAA 58.352 32.000 0.00 0.00 36.21 2.69
2495 8492 7.124471 TCGTTCGAAATTATTTGTCGTGAAAA 58.876 30.769 0.00 0.00 36.21 2.29
2496 8493 7.799447 TCGTTCGAAATTATTTGTCGTGAAAAT 59.201 29.630 0.00 0.00 36.21 1.82
2497 8494 7.880757 CGTTCGAAATTATTTGTCGTGAAAATG 59.119 33.333 0.00 0.00 36.21 2.32
2498 8495 7.789341 TCGAAATTATTTGTCGTGAAAATGG 57.211 32.000 0.00 0.00 36.21 3.16
2499 8496 7.585867 TCGAAATTATTTGTCGTGAAAATGGA 58.414 30.769 0.00 0.00 36.21 3.41
2500 8497 8.240682 TCGAAATTATTTGTCGTGAAAATGGAT 58.759 29.630 0.00 0.00 36.21 3.41
2501 8498 9.497030 CGAAATTATTTGTCGTGAAAATGGATA 57.503 29.630 0.00 0.00 0.00 2.59
2543 8540 9.095065 AGAACTAAAATACGTCAACATACATCC 57.905 33.333 0.00 0.00 0.00 3.51
2544 8541 8.780846 AACTAAAATACGTCAACATACATCCA 57.219 30.769 0.00 0.00 0.00 3.41
2545 8542 8.958119 ACTAAAATACGTCAACATACATCCAT 57.042 30.769 0.00 0.00 0.00 3.41
2546 8543 9.391006 ACTAAAATACGTCAACATACATCCATT 57.609 29.630 0.00 0.00 0.00 3.16
2549 8546 8.506168 AAATACGTCAACATACATCCATTTCT 57.494 30.769 0.00 0.00 0.00 2.52
2550 8547 8.506168 AATACGTCAACATACATCCATTTCTT 57.494 30.769 0.00 0.00 0.00 2.52
2551 8548 6.817765 ACGTCAACATACATCCATTTCTTT 57.182 33.333 0.00 0.00 0.00 2.52
2552 8549 6.611381 ACGTCAACATACATCCATTTCTTTG 58.389 36.000 0.00 0.00 0.00 2.77
2553 8550 6.029607 CGTCAACATACATCCATTTCTTTGG 58.970 40.000 0.00 0.00 38.18 3.28
2554 8551 5.807011 GTCAACATACATCCATTTCTTTGGC 59.193 40.000 0.00 0.00 36.66 4.52
2555 8552 5.479724 TCAACATACATCCATTTCTTTGGCA 59.520 36.000 0.00 0.00 36.66 4.92
2556 8553 5.999205 ACATACATCCATTTCTTTGGCAA 57.001 34.783 0.00 0.00 36.66 4.52
2557 8554 5.969423 ACATACATCCATTTCTTTGGCAAG 58.031 37.500 0.00 0.00 36.66 4.01
2558 8555 5.481473 ACATACATCCATTTCTTTGGCAAGT 59.519 36.000 0.00 0.00 36.66 3.16
2559 8556 6.663093 ACATACATCCATTTCTTTGGCAAGTA 59.337 34.615 0.00 0.00 36.66 2.24
2560 8557 7.342799 ACATACATCCATTTCTTTGGCAAGTAT 59.657 33.333 0.00 0.00 36.66 2.12
2561 8558 6.610075 ACATCCATTTCTTTGGCAAGTATT 57.390 33.333 0.00 0.00 36.66 1.89
2562 8559 7.008021 ACATCCATTTCTTTGGCAAGTATTT 57.992 32.000 0.00 0.00 36.66 1.40
2563 8560 7.099120 ACATCCATTTCTTTGGCAAGTATTTC 58.901 34.615 0.00 0.00 36.66 2.17
2564 8561 6.036577 TCCATTTCTTTGGCAAGTATTTCC 57.963 37.500 0.00 0.00 36.66 3.13
2565 8562 4.864247 CCATTTCTTTGGCAAGTATTTCCG 59.136 41.667 0.00 0.00 0.00 4.30
2566 8563 3.569250 TTCTTTGGCAAGTATTTCCGC 57.431 42.857 0.00 0.00 0.00 5.54
2567 8564 2.509569 TCTTTGGCAAGTATTTCCGCA 58.490 42.857 0.00 0.00 0.00 5.69
2568 8565 3.088532 TCTTTGGCAAGTATTTCCGCAT 58.911 40.909 0.00 0.00 0.00 4.73
2569 8566 2.937469 TTGGCAAGTATTTCCGCATG 57.063 45.000 0.00 0.00 0.00 4.06
2570 8567 1.102154 TGGCAAGTATTTCCGCATGG 58.898 50.000 0.00 0.00 0.00 3.66
2571 8568 1.340502 TGGCAAGTATTTCCGCATGGA 60.341 47.619 0.00 0.00 44.61 3.41
2579 8576 3.950232 TCCGCATGGAGGGAGTAC 58.050 61.111 0.00 0.00 40.17 2.73
2584 8581 0.179108 GCATGGAGGGAGTACGTGTC 60.179 60.000 0.00 0.00 0.00 3.67
2605 8602 6.414987 GTGTCAAAAAGCTGAGTACATTTCAC 59.585 38.462 0.00 0.00 0.00 3.18
2611 8608 6.551385 AAGCTGAGTACATTTCACTTTCAG 57.449 37.500 0.00 0.00 0.00 3.02
2643 8642 2.249844 TTTCGAGGAACCAACAGGAC 57.750 50.000 0.00 0.00 0.00 3.85
2648 8647 2.437413 GAGGAACCAACAGGACCATTC 58.563 52.381 0.00 0.00 0.00 2.67
2710 8720 2.842208 TGTCAAACTTGCTGAAACCG 57.158 45.000 0.00 0.00 0.00 4.44
2761 8774 5.684550 AGAAAACCATACGGAAAACTGTC 57.315 39.130 0.00 0.00 35.59 3.51
2762 8775 4.517832 AGAAAACCATACGGAAAACTGTCC 59.482 41.667 0.00 0.00 35.59 4.02
2765 8778 1.365699 CATACGGAAAACTGTCCCGG 58.634 55.000 16.62 0.00 46.83 5.73
2770 8783 1.450025 GGAAAACTGTCCCGGTGATC 58.550 55.000 0.00 0.00 0.00 2.92
2782 8795 7.289317 ACTGTCCCGGTGATCTAGAATAAATAA 59.711 37.037 0.00 0.00 0.00 1.40
2801 8814 1.410004 AATATTCCTCGGTCGCCTCA 58.590 50.000 0.00 0.00 0.00 3.86
2818 8831 4.376146 GCCTCAAAAATAGCAAAACCACA 58.624 39.130 0.00 0.00 0.00 4.17
2821 8834 6.347644 GCCTCAAAAATAGCAAAACCACATTC 60.348 38.462 0.00 0.00 0.00 2.67
2822 8835 6.147656 CCTCAAAAATAGCAAAACCACATTCC 59.852 38.462 0.00 0.00 0.00 3.01
2859 8879 1.807742 TGGTTAAGGATGGTTTTCGCG 59.192 47.619 0.00 0.00 0.00 5.87
2963 8983 5.163513 AGCGCAAACCATTTTGAATAGAAG 58.836 37.500 11.47 0.00 44.38 2.85
2975 8995 9.121517 CATTTTGAATAGAAGCACACTTAACAG 57.878 33.333 0.00 0.00 35.82 3.16
2983 9003 3.616219 AGCACACTTAACAGTTGGACAA 58.384 40.909 0.00 0.00 0.00 3.18
2988 9008 6.312672 GCACACTTAACAGTTGGACAATTTTT 59.687 34.615 0.00 0.00 0.00 1.94
2992 9012 8.803799 CACTTAACAGTTGGACAATTTTTACAC 58.196 33.333 0.00 0.00 0.00 2.90
2993 9013 7.698970 ACTTAACAGTTGGACAATTTTTACACG 59.301 33.333 0.00 0.00 0.00 4.49
2994 9014 4.927422 ACAGTTGGACAATTTTTACACGG 58.073 39.130 0.00 0.00 0.00 4.94
2995 9015 4.641094 ACAGTTGGACAATTTTTACACGGA 59.359 37.500 0.00 0.00 0.00 4.69
2996 9016 5.212194 CAGTTGGACAATTTTTACACGGAG 58.788 41.667 0.00 0.00 0.00 4.63
2997 9017 5.008217 CAGTTGGACAATTTTTACACGGAGA 59.992 40.000 0.00 0.00 0.00 3.71
2998 9018 5.591067 AGTTGGACAATTTTTACACGGAGAA 59.409 36.000 0.00 0.00 0.00 2.87
2999 9019 6.264518 AGTTGGACAATTTTTACACGGAGAAT 59.735 34.615 0.00 0.00 0.00 2.40
3000 9020 7.446013 AGTTGGACAATTTTTACACGGAGAATA 59.554 33.333 0.00 0.00 0.00 1.75
3001 9021 7.931578 TGGACAATTTTTACACGGAGAATAT 57.068 32.000 0.00 0.00 0.00 1.28
3002 9022 7.981142 TGGACAATTTTTACACGGAGAATATC 58.019 34.615 0.00 0.00 0.00 1.63
3003 9023 7.608376 TGGACAATTTTTACACGGAGAATATCA 59.392 33.333 0.00 0.00 0.00 2.15
3004 9024 8.621286 GGACAATTTTTACACGGAGAATATCAT 58.379 33.333 0.00 0.00 0.00 2.45
3007 9027 9.580916 CAATTTTTACACGGAGAATATCATACG 57.419 33.333 0.00 0.00 0.00 3.06
3008 9028 7.703298 TTTTTACACGGAGAATATCATACGG 57.297 36.000 0.00 0.00 0.00 4.02
3009 9029 6.638096 TTTACACGGAGAATATCATACGGA 57.362 37.500 0.00 0.00 0.00 4.69
3010 9030 6.638096 TTACACGGAGAATATCATACGGAA 57.362 37.500 0.00 0.00 0.00 4.30
3011 9031 5.524971 ACACGGAGAATATCATACGGAAA 57.475 39.130 0.00 0.00 0.00 3.13
3012 9032 5.287226 ACACGGAGAATATCATACGGAAAC 58.713 41.667 0.00 0.00 0.00 2.78
3013 9033 4.684703 CACGGAGAATATCATACGGAAACC 59.315 45.833 0.00 0.00 0.00 3.27
3014 9034 4.342951 ACGGAGAATATCATACGGAAACCA 59.657 41.667 0.00 0.00 0.00 3.67
3015 9035 5.163385 ACGGAGAATATCATACGGAAACCAA 60.163 40.000 0.00 0.00 0.00 3.67
3016 9036 5.176958 CGGAGAATATCATACGGAAACCAAC 59.823 44.000 0.00 0.00 0.00 3.77
3017 9037 6.053005 GGAGAATATCATACGGAAACCAACA 58.947 40.000 0.00 0.00 0.00 3.33
3018 9038 6.710744 GGAGAATATCATACGGAAACCAACAT 59.289 38.462 0.00 0.00 0.00 2.71
3019 9039 7.228706 GGAGAATATCATACGGAAACCAACATT 59.771 37.037 0.00 0.00 0.00 2.71
3020 9040 8.519799 AGAATATCATACGGAAACCAACATTT 57.480 30.769 0.00 0.00 0.00 2.32
3021 9041 8.405531 AGAATATCATACGGAAACCAACATTTG 58.594 33.333 0.00 0.00 0.00 2.32
3022 9042 7.873719 ATATCATACGGAAACCAACATTTGA 57.126 32.000 0.00 0.00 0.00 2.69
3023 9043 6.582677 ATCATACGGAAACCAACATTTGAA 57.417 33.333 0.00 0.00 0.00 2.69
3024 9044 6.007936 TCATACGGAAACCAACATTTGAAG 57.992 37.500 0.00 0.00 0.00 3.02
3025 9045 5.765677 TCATACGGAAACCAACATTTGAAGA 59.234 36.000 0.00 0.00 0.00 2.87
3026 9046 4.993029 ACGGAAACCAACATTTGAAGAA 57.007 36.364 0.00 0.00 0.00 2.52
3027 9047 5.331876 ACGGAAACCAACATTTGAAGAAA 57.668 34.783 0.00 0.00 0.00 2.52
3028 9048 5.725362 ACGGAAACCAACATTTGAAGAAAA 58.275 33.333 0.00 0.00 0.00 2.29
3029 9049 6.345298 ACGGAAACCAACATTTGAAGAAAAT 58.655 32.000 0.00 0.00 39.13 1.82
3030 9050 6.821160 ACGGAAACCAACATTTGAAGAAAATT 59.179 30.769 0.00 0.00 36.28 1.82
3031 9051 7.335673 ACGGAAACCAACATTTGAAGAAAATTT 59.664 29.630 0.00 0.00 36.28 1.82
3032 9052 7.850492 CGGAAACCAACATTTGAAGAAAATTTC 59.150 33.333 0.00 0.00 36.28 2.17
3033 9053 8.672815 GGAAACCAACATTTGAAGAAAATTTCA 58.327 29.630 8.55 0.00 36.28 2.69
3036 9056 8.156994 ACCAACATTTGAAGAAAATTTCATGG 57.843 30.769 8.55 4.78 36.28 3.66
3037 9057 7.992033 ACCAACATTTGAAGAAAATTTCATGGA 59.008 29.630 8.55 0.00 36.28 3.41
3038 9058 8.838365 CCAACATTTGAAGAAAATTTCATGGAA 58.162 29.630 8.55 0.00 36.28 3.53
3041 9061 8.839343 ACATTTGAAGAAAATTTCATGGAAACC 58.161 29.630 8.55 0.00 36.28 3.27
3042 9062 8.838365 CATTTGAAGAAAATTTCATGGAAACCA 58.162 29.630 8.55 0.00 36.28 3.67
3043 9063 7.784633 TTGAAGAAAATTTCATGGAAACCAC 57.215 32.000 8.55 0.00 36.97 4.16
3044 9064 6.882656 TGAAGAAAATTTCATGGAAACCACA 58.117 32.000 8.55 0.00 35.80 4.17
3045 9065 7.507829 TGAAGAAAATTTCATGGAAACCACAT 58.492 30.769 8.55 0.00 35.80 3.21
3046 9066 7.992033 TGAAGAAAATTTCATGGAAACCACATT 59.008 29.630 8.55 0.00 35.80 2.71
3047 9067 8.750515 AAGAAAATTTCATGGAAACCACATTT 57.249 26.923 8.55 0.00 35.80 2.32
3048 9068 8.156994 AGAAAATTTCATGGAAACCACATTTG 57.843 30.769 8.55 0.00 35.80 2.32
3049 9069 7.992033 AGAAAATTTCATGGAAACCACATTTGA 59.008 29.630 8.55 0.00 35.80 2.69
3050 9070 8.517062 AAAATTTCATGGAAACCACATTTGAA 57.483 26.923 0.00 0.00 35.80 2.69
3051 9071 8.517062 AAATTTCATGGAAACCACATTTGAAA 57.483 26.923 15.00 15.00 40.60 2.69
3052 9072 7.733402 ATTTCATGGAAACCACATTTGAAAG 57.267 32.000 16.65 0.00 40.07 2.62
3053 9073 5.867903 TCATGGAAACCACATTTGAAAGT 57.132 34.783 0.00 0.00 35.80 2.66
3054 9074 6.232581 TCATGGAAACCACATTTGAAAGTT 57.767 33.333 0.00 0.00 35.80 2.66
3055 9075 6.047870 TCATGGAAACCACATTTGAAAGTTG 58.952 36.000 0.00 0.00 35.80 3.16
3056 9076 4.187694 TGGAAACCACATTTGAAAGTTGC 58.812 39.130 0.00 0.00 0.00 4.17
3057 9077 4.187694 GGAAACCACATTTGAAAGTTGCA 58.812 39.130 0.00 0.00 0.00 4.08
3058 9078 4.633565 GGAAACCACATTTGAAAGTTGCAA 59.366 37.500 0.00 0.00 0.00 4.08
3059 9079 5.220643 GGAAACCACATTTGAAAGTTGCAAG 60.221 40.000 0.00 0.00 0.00 4.01
3060 9080 4.734398 ACCACATTTGAAAGTTGCAAGA 57.266 36.364 0.00 0.00 0.00 3.02
3061 9081 5.083533 ACCACATTTGAAAGTTGCAAGAA 57.916 34.783 0.00 0.00 0.00 2.52
3062 9082 5.486526 ACCACATTTGAAAGTTGCAAGAAA 58.513 33.333 0.00 0.00 0.00 2.52
3063 9083 5.936956 ACCACATTTGAAAGTTGCAAGAAAA 59.063 32.000 0.00 0.00 0.00 2.29
3064 9084 6.429385 ACCACATTTGAAAGTTGCAAGAAAAA 59.571 30.769 0.00 0.00 0.00 1.94
3065 9085 7.121020 ACCACATTTGAAAGTTGCAAGAAAAAT 59.879 29.630 0.00 0.00 0.00 1.82
3066 9086 7.641020 CCACATTTGAAAGTTGCAAGAAAAATC 59.359 33.333 0.00 0.00 0.00 2.17
3067 9087 8.392612 CACATTTGAAAGTTGCAAGAAAAATCT 58.607 29.630 0.00 0.00 0.00 2.40
3068 9088 8.949177 ACATTTGAAAGTTGCAAGAAAAATCTT 58.051 25.926 0.00 0.00 0.00 2.40
3069 9089 9.777575 CATTTGAAAGTTGCAAGAAAAATCTTT 57.222 25.926 0.00 3.86 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.161404 GGAGACTATGCATGTGGTGAAATATA 58.839 38.462 10.16 0.00 0.00 0.86
28 29 4.907875 TCTGGGAGGATAAAAGATAGGTGG 59.092 45.833 0.00 0.00 0.00 4.61
32 33 4.833380 TCCGTCTGGGAGGATAAAAGATAG 59.167 45.833 0.00 0.00 40.94 2.08
35 36 3.110293 TCCGTCTGGGAGGATAAAAGA 57.890 47.619 0.00 0.00 40.94 2.52
48 49 2.474526 CGCTTTGCAAAGTATCCGTCTG 60.475 50.000 33.47 11.41 38.28 3.51
51 52 1.519408 ACGCTTTGCAAAGTATCCGT 58.481 45.000 33.47 29.67 38.28 4.69
73 74 6.490721 CCTCTTGTATACGGGAGAGAGTAATT 59.509 42.308 22.39 0.00 38.27 1.40
77 78 3.458857 TCCTCTTGTATACGGGAGAGAGT 59.541 47.826 22.39 0.00 38.27 3.24
93 94 1.826385 CCGACCTGCAAATTCCTCTT 58.174 50.000 0.00 0.00 0.00 2.85
126 127 8.304202 AGAGCTTAGCGTATTGATTCATTAAG 57.696 34.615 0.00 0.00 0.00 1.85
144 145 3.374058 GCTTTTGGATACGCAAGAGCTTA 59.626 43.478 8.22 0.00 43.62 3.09
162 163 0.397941 TGTAGCTCCTGTGCTGCTTT 59.602 50.000 0.00 0.00 44.19 3.51
530 2933 5.407387 CGTGTAGTGTAGCACCTGTAATTTT 59.593 40.000 0.00 0.00 34.49 1.82
531 2934 4.927425 CGTGTAGTGTAGCACCTGTAATTT 59.073 41.667 0.00 0.00 34.49 1.82
853 6399 6.785466 TGGCCAGGTATATATAGAGAACACAA 59.215 38.462 0.00 0.00 0.00 3.33
859 6413 5.823312 TCGTTGGCCAGGTATATATAGAGA 58.177 41.667 5.11 0.00 0.00 3.10
886 6444 4.142447 ACGCAGAATCTATGTTCGTGTACT 60.142 41.667 0.00 0.00 33.36 2.73
907 6465 2.802787 AGTGGACAGAAGTCAGAACG 57.197 50.000 0.00 0.00 46.80 3.95
1414 7107 3.611057 GCGATCGTCGACCACCTAATAAT 60.611 47.826 17.81 0.00 43.74 1.28
1473 7166 4.189231 GGATATGCGTGTTCCAGTAGTTT 58.811 43.478 5.16 0.00 0.00 2.66
1549 7242 1.525077 GTTGGTTGGTCTGGTCGCA 60.525 57.895 0.00 0.00 0.00 5.10
1550 7243 1.525077 TGTTGGTTGGTCTGGTCGC 60.525 57.895 0.00 0.00 0.00 5.19
1620 7409 3.324930 CCAGTGCTCAGGCCTCCA 61.325 66.667 0.00 0.00 37.74 3.86
1630 7419 4.790962 CATGAGGGCGCCAGTGCT 62.791 66.667 30.85 16.56 34.43 4.40
1746 7541 0.179205 GAACGATGCTGCTGCTTGAC 60.179 55.000 17.00 4.80 40.48 3.18
1860 7674 2.128507 GGAGCTCGTTCCCGGAGAT 61.129 63.158 0.73 0.00 33.95 2.75
1964 7896 4.056125 GCAAGCCGGCAAACTCCC 62.056 66.667 31.54 5.31 0.00 4.30
2055 7987 6.757010 CACAAGACATCTATAAACGGTAGCTT 59.243 38.462 0.00 0.00 0.00 3.74
2096 8051 5.243060 CACCGGTATGATGGATCTAACACTA 59.757 44.000 6.87 0.00 0.00 2.74
2128 8092 3.060406 CACACAAACAAATCAACGCATGG 60.060 43.478 0.00 0.00 0.00 3.66
2166 8132 7.158697 TCAACTTCACCGAAAAGATCTATTGA 58.841 34.615 0.00 0.00 0.00 2.57
2175 8141 4.632538 AACCTTCAACTTCACCGAAAAG 57.367 40.909 0.00 0.00 0.00 2.27
2181 8150 5.863935 GCAATTGATAACCTTCAACTTCACC 59.136 40.000 10.34 0.00 38.37 4.02
2218 8214 1.739067 AAGGAAATGGTAGCACGAGC 58.261 50.000 0.00 0.00 42.56 5.03
2229 8226 7.489113 GGCAACATGTTAACTGATAAGGAAATG 59.511 37.037 11.53 0.85 0.00 2.32
2230 8227 7.178274 TGGCAACATGTTAACTGATAAGGAAAT 59.822 33.333 11.53 0.00 46.17 2.17
2298 8295 6.930164 TGCGACCAAAGTGTTTTAGTTATCTA 59.070 34.615 0.00 0.00 0.00 1.98
2307 8304 4.039032 CGTTATTGCGACCAAAGTGTTTT 58.961 39.130 0.00 0.00 34.05 2.43
2317 8314 2.789249 GCCACCGTTATTGCGACC 59.211 61.111 0.00 0.00 0.00 4.79
2363 8360 4.202172 GCTAAGGCCCAACTGTAACAAAAA 60.202 41.667 0.00 0.00 0.00 1.94
2364 8361 3.319689 GCTAAGGCCCAACTGTAACAAAA 59.680 43.478 0.00 0.00 0.00 2.44
2365 8362 2.888414 GCTAAGGCCCAACTGTAACAAA 59.112 45.455 0.00 0.00 0.00 2.83
2366 8363 2.158593 TGCTAAGGCCCAACTGTAACAA 60.159 45.455 0.00 0.00 37.74 2.83
2367 8364 1.422024 TGCTAAGGCCCAACTGTAACA 59.578 47.619 0.00 0.00 37.74 2.41
2368 8365 2.194201 TGCTAAGGCCCAACTGTAAC 57.806 50.000 0.00 0.00 37.74 2.50
2369 8366 2.961531 TTGCTAAGGCCCAACTGTAA 57.038 45.000 0.00 0.00 37.74 2.41
2370 8367 2.620367 CCATTGCTAAGGCCCAACTGTA 60.620 50.000 0.00 0.00 37.74 2.74
2371 8368 1.549203 CATTGCTAAGGCCCAACTGT 58.451 50.000 0.00 0.00 37.74 3.55
2372 8369 0.819582 CCATTGCTAAGGCCCAACTG 59.180 55.000 0.00 0.00 37.74 3.16
2373 8370 0.704076 TCCATTGCTAAGGCCCAACT 59.296 50.000 0.00 0.00 37.74 3.16
2390 8387 7.094634 CCAGTATAACATTCCATTGCAGTATCC 60.095 40.741 0.00 0.00 0.00 2.59
2435 8432 5.587844 TCTTAGGTTCGTTCGTATTAGCTCT 59.412 40.000 0.00 0.00 0.00 4.09
2436 8433 5.814783 TCTTAGGTTCGTTCGTATTAGCTC 58.185 41.667 0.00 0.00 0.00 4.09
2465 8462 5.163933 CGACAAATAATTTCGAACGAAGGGA 60.164 40.000 9.46 0.00 35.38 4.20
2466 8463 5.019498 CGACAAATAATTTCGAACGAAGGG 58.981 41.667 9.46 0.00 35.38 3.95
2467 8464 5.503376 CACGACAAATAATTTCGAACGAAGG 59.497 40.000 9.46 0.00 36.58 3.46
2468 8465 6.293618 TCACGACAAATAATTTCGAACGAAG 58.706 36.000 9.46 0.23 36.58 3.79
2469 8466 6.212934 TCACGACAAATAATTTCGAACGAA 57.787 33.333 0.00 5.53 36.58 3.85
2470 8467 5.825905 TCACGACAAATAATTTCGAACGA 57.174 34.783 0.00 0.00 36.58 3.85
2471 8468 6.882312 TTTCACGACAAATAATTTCGAACG 57.118 33.333 0.00 0.00 36.58 3.95
2472 8469 8.153411 CCATTTTCACGACAAATAATTTCGAAC 58.847 33.333 0.00 0.00 36.58 3.95
2473 8470 8.076781 TCCATTTTCACGACAAATAATTTCGAA 58.923 29.630 3.62 0.00 36.58 3.71
2474 8471 7.585867 TCCATTTTCACGACAAATAATTTCGA 58.414 30.769 3.62 0.00 36.58 3.71
2475 8472 7.789341 TCCATTTTCACGACAAATAATTTCG 57.211 32.000 0.00 0.00 38.73 3.46
2517 8514 9.095065 GGATGTATGTTGACGTATTTTAGTTCT 57.905 33.333 0.00 0.00 0.00 3.01
2518 8515 8.875803 TGGATGTATGTTGACGTATTTTAGTTC 58.124 33.333 0.00 0.00 0.00 3.01
2519 8516 8.780846 TGGATGTATGTTGACGTATTTTAGTT 57.219 30.769 0.00 0.00 0.00 2.24
2520 8517 8.958119 ATGGATGTATGTTGACGTATTTTAGT 57.042 30.769 0.00 0.00 0.00 2.24
2523 8520 8.956426 AGAAATGGATGTATGTTGACGTATTTT 58.044 29.630 0.00 0.00 0.00 1.82
2524 8521 8.506168 AGAAATGGATGTATGTTGACGTATTT 57.494 30.769 0.00 0.00 0.00 1.40
2525 8522 8.506168 AAGAAATGGATGTATGTTGACGTATT 57.494 30.769 0.00 0.00 0.00 1.89
2526 8523 8.397906 CAAAGAAATGGATGTATGTTGACGTAT 58.602 33.333 0.00 0.00 0.00 3.06
2527 8524 7.148323 CCAAAGAAATGGATGTATGTTGACGTA 60.148 37.037 0.00 0.00 43.54 3.57
2528 8525 6.349280 CCAAAGAAATGGATGTATGTTGACGT 60.349 38.462 0.00 0.00 43.54 4.34
2529 8526 6.029607 CCAAAGAAATGGATGTATGTTGACG 58.970 40.000 0.00 0.00 43.54 4.35
2530 8527 5.807011 GCCAAAGAAATGGATGTATGTTGAC 59.193 40.000 0.00 0.00 43.54 3.18
2531 8528 5.479724 TGCCAAAGAAATGGATGTATGTTGA 59.520 36.000 0.00 0.00 43.54 3.18
2532 8529 5.722263 TGCCAAAGAAATGGATGTATGTTG 58.278 37.500 0.00 0.00 43.54 3.33
2533 8530 5.999205 TGCCAAAGAAATGGATGTATGTT 57.001 34.783 0.00 0.00 43.54 2.71
2534 8531 5.481473 ACTTGCCAAAGAAATGGATGTATGT 59.519 36.000 0.00 0.00 43.54 2.29
2535 8532 5.969423 ACTTGCCAAAGAAATGGATGTATG 58.031 37.500 0.00 0.00 43.54 2.39
2536 8533 7.902920 ATACTTGCCAAAGAAATGGATGTAT 57.097 32.000 0.00 0.25 43.54 2.29
2537 8534 7.716799 AATACTTGCCAAAGAAATGGATGTA 57.283 32.000 0.00 0.00 43.54 2.29
2538 8535 6.610075 AATACTTGCCAAAGAAATGGATGT 57.390 33.333 0.00 0.00 43.54 3.06
2539 8536 6.536224 GGAAATACTTGCCAAAGAAATGGATG 59.464 38.462 0.00 0.00 43.54 3.51
2540 8537 6.627953 CGGAAATACTTGCCAAAGAAATGGAT 60.628 38.462 0.00 0.00 43.54 3.41
2541 8538 5.336372 CGGAAATACTTGCCAAAGAAATGGA 60.336 40.000 0.00 0.00 43.54 3.41
2542 8539 4.864247 CGGAAATACTTGCCAAAGAAATGG 59.136 41.667 0.00 0.00 43.70 3.16
2543 8540 4.327087 GCGGAAATACTTGCCAAAGAAATG 59.673 41.667 0.00 0.00 36.84 2.32
2544 8541 4.021544 TGCGGAAATACTTGCCAAAGAAAT 60.022 37.500 0.00 0.00 36.84 2.17
2545 8542 3.319405 TGCGGAAATACTTGCCAAAGAAA 59.681 39.130 0.00 0.00 36.84 2.52
2546 8543 2.887783 TGCGGAAATACTTGCCAAAGAA 59.112 40.909 0.00 0.00 36.84 2.52
2547 8544 2.509569 TGCGGAAATACTTGCCAAAGA 58.490 42.857 0.00 0.00 36.84 2.52
2548 8545 3.181397 CATGCGGAAATACTTGCCAAAG 58.819 45.455 0.00 0.00 39.49 2.77
2549 8546 2.094286 CCATGCGGAAATACTTGCCAAA 60.094 45.455 0.00 0.00 0.00 3.28
2550 8547 1.476085 CCATGCGGAAATACTTGCCAA 59.524 47.619 0.00 0.00 0.00 4.52
2551 8548 1.102154 CCATGCGGAAATACTTGCCA 58.898 50.000 0.00 0.00 0.00 4.92
2552 8549 1.334869 CTCCATGCGGAAATACTTGCC 59.665 52.381 0.00 0.00 42.21 4.52
2553 8550 1.334869 CCTCCATGCGGAAATACTTGC 59.665 52.381 0.00 0.00 42.21 4.01
2554 8551 1.949525 CCCTCCATGCGGAAATACTTG 59.050 52.381 1.17 0.00 42.21 3.16
2555 8552 1.843851 TCCCTCCATGCGGAAATACTT 59.156 47.619 1.17 0.00 42.21 2.24
2556 8553 1.417890 CTCCCTCCATGCGGAAATACT 59.582 52.381 1.17 0.00 42.21 2.12
2557 8554 1.141053 ACTCCCTCCATGCGGAAATAC 59.859 52.381 1.17 0.00 42.21 1.89
2558 8555 1.507140 ACTCCCTCCATGCGGAAATA 58.493 50.000 1.17 0.00 42.21 1.40
2559 8556 1.141053 GTACTCCCTCCATGCGGAAAT 59.859 52.381 1.17 0.00 42.21 2.17
2560 8557 0.539986 GTACTCCCTCCATGCGGAAA 59.460 55.000 1.17 0.00 42.21 3.13
2561 8558 1.672854 CGTACTCCCTCCATGCGGAA 61.673 60.000 1.17 0.00 42.21 4.30
2562 8559 2.125326 CGTACTCCCTCCATGCGGA 61.125 63.158 1.17 0.00 39.79 5.54
2563 8560 2.417516 CGTACTCCCTCCATGCGG 59.582 66.667 0.00 0.00 0.00 5.69
2564 8561 1.226974 CACGTACTCCCTCCATGCG 60.227 63.158 0.00 0.00 0.00 4.73
2565 8562 0.179108 GACACGTACTCCCTCCATGC 60.179 60.000 0.00 0.00 0.00 4.06
2566 8563 1.182667 TGACACGTACTCCCTCCATG 58.817 55.000 0.00 0.00 0.00 3.66
2567 8564 1.933021 TTGACACGTACTCCCTCCAT 58.067 50.000 0.00 0.00 0.00 3.41
2568 8565 1.707106 TTTGACACGTACTCCCTCCA 58.293 50.000 0.00 0.00 0.00 3.86
2569 8566 2.825861 TTTTGACACGTACTCCCTCC 57.174 50.000 0.00 0.00 0.00 4.30
2570 8567 2.479275 GCTTTTTGACACGTACTCCCTC 59.521 50.000 0.00 0.00 0.00 4.30
2571 8568 2.104281 AGCTTTTTGACACGTACTCCCT 59.896 45.455 0.00 0.00 0.00 4.20
2572 8569 2.223377 CAGCTTTTTGACACGTACTCCC 59.777 50.000 0.00 0.00 0.00 4.30
2573 8570 3.128349 TCAGCTTTTTGACACGTACTCC 58.872 45.455 0.00 0.00 0.00 3.85
2574 8571 3.802685 ACTCAGCTTTTTGACACGTACTC 59.197 43.478 0.00 0.00 0.00 2.59
2575 8572 3.793559 ACTCAGCTTTTTGACACGTACT 58.206 40.909 0.00 0.00 0.00 2.73
2576 8573 4.505191 TGTACTCAGCTTTTTGACACGTAC 59.495 41.667 0.00 0.00 31.81 3.67
2577 8574 4.684877 TGTACTCAGCTTTTTGACACGTA 58.315 39.130 0.00 0.00 0.00 3.57
2578 8575 3.527533 TGTACTCAGCTTTTTGACACGT 58.472 40.909 0.00 0.00 0.00 4.49
2579 8576 4.732285 ATGTACTCAGCTTTTTGACACG 57.268 40.909 0.00 0.00 0.00 4.49
2584 8581 7.701924 TGAAAGTGAAATGTACTCAGCTTTTTG 59.298 33.333 0.00 0.00 30.88 2.44
2619 8617 2.949644 CTGTTGGTTCCTCGAAAAAGGT 59.050 45.455 0.00 0.00 37.69 3.50
2620 8618 2.293399 CCTGTTGGTTCCTCGAAAAAGG 59.707 50.000 0.00 0.00 37.81 3.11
2621 8619 3.003378 GTCCTGTTGGTTCCTCGAAAAAG 59.997 47.826 0.00 0.00 34.23 2.27
2643 8642 8.836268 TTTCTTCTTTCATGAAAATGGAATGG 57.164 30.769 20.82 10.58 0.00 3.16
2670 8669 9.612066 TTGACATGCTCTATACATAAAATGTCA 57.388 29.630 10.24 10.24 46.47 3.58
2693 8692 3.271729 TGTACGGTTTCAGCAAGTTTGA 58.728 40.909 0.00 0.00 0.00 2.69
2782 8795 1.410004 TGAGGCGACCGAGGAATATT 58.590 50.000 0.00 0.00 0.00 1.28
2801 8814 5.606505 ACGGAATGTGGTTTTGCTATTTTT 58.393 33.333 0.00 0.00 0.00 1.94
2844 8858 0.872388 GTCACGCGAAAACCATCCTT 59.128 50.000 15.93 0.00 0.00 3.36
2859 8879 7.474398 AACTTCTTTTAGGAAACTACGTCAC 57.526 36.000 0.00 0.00 44.30 3.67
2884 8904 5.061721 AGAAAATACCAGGTTCCAAGTGT 57.938 39.130 0.00 0.00 0.00 3.55
2963 8983 4.568152 ATTGTCCAACTGTTAAGTGTGC 57.432 40.909 0.00 0.00 36.51 4.57
2975 8995 5.427036 TCTCCGTGTAAAAATTGTCCAAC 57.573 39.130 0.00 0.00 0.00 3.77
2983 9003 8.145767 TCCGTATGATATTCTCCGTGTAAAAAT 58.854 33.333 0.00 0.00 0.00 1.82
2988 9008 6.441274 GTTTCCGTATGATATTCTCCGTGTA 58.559 40.000 0.00 0.00 0.00 2.90
2992 9012 4.878439 TGGTTTCCGTATGATATTCTCCG 58.122 43.478 0.00 0.00 0.00 4.63
2993 9013 6.053005 TGTTGGTTTCCGTATGATATTCTCC 58.947 40.000 0.00 0.00 0.00 3.71
2994 9014 7.730364 ATGTTGGTTTCCGTATGATATTCTC 57.270 36.000 0.00 0.00 0.00 2.87
2995 9015 8.405531 CAAATGTTGGTTTCCGTATGATATTCT 58.594 33.333 0.00 0.00 0.00 2.40
2996 9016 8.402472 TCAAATGTTGGTTTCCGTATGATATTC 58.598 33.333 0.00 0.00 0.00 1.75
2997 9017 8.287439 TCAAATGTTGGTTTCCGTATGATATT 57.713 30.769 0.00 0.00 0.00 1.28
2998 9018 7.873719 TCAAATGTTGGTTTCCGTATGATAT 57.126 32.000 0.00 0.00 0.00 1.63
2999 9019 7.608376 TCTTCAAATGTTGGTTTCCGTATGATA 59.392 33.333 0.00 0.00 0.00 2.15
3000 9020 6.432783 TCTTCAAATGTTGGTTTCCGTATGAT 59.567 34.615 0.00 0.00 0.00 2.45
3001 9021 5.765677 TCTTCAAATGTTGGTTTCCGTATGA 59.234 36.000 0.00 0.00 0.00 2.15
3002 9022 6.007936 TCTTCAAATGTTGGTTTCCGTATG 57.992 37.500 0.00 0.00 0.00 2.39
3003 9023 6.642707 TTCTTCAAATGTTGGTTTCCGTAT 57.357 33.333 0.00 0.00 0.00 3.06
3004 9024 6.452494 TTTCTTCAAATGTTGGTTTCCGTA 57.548 33.333 0.00 0.00 0.00 4.02
3005 9025 4.993029 TTCTTCAAATGTTGGTTTCCGT 57.007 36.364 0.00 0.00 0.00 4.69
3006 9026 6.843069 ATTTTCTTCAAATGTTGGTTTCCG 57.157 33.333 0.00 0.00 33.47 4.30
3007 9027 8.672815 TGAAATTTTCTTCAAATGTTGGTTTCC 58.327 29.630 10.33 0.00 35.09 3.13
3010 9030 8.623030 CCATGAAATTTTCTTCAAATGTTGGTT 58.377 29.630 10.33 0.00 38.75 3.67
3011 9031 7.992033 TCCATGAAATTTTCTTCAAATGTTGGT 59.008 29.630 10.33 0.00 38.75 3.67
3012 9032 8.380743 TCCATGAAATTTTCTTCAAATGTTGG 57.619 30.769 10.33 0.57 38.75 3.77
3015 9035 8.839343 GGTTTCCATGAAATTTTCTTCAAATGT 58.161 29.630 10.33 0.00 38.75 2.71
3016 9036 8.838365 TGGTTTCCATGAAATTTTCTTCAAATG 58.162 29.630 10.33 5.35 38.75 2.32
3017 9037 8.839343 GTGGTTTCCATGAAATTTTCTTCAAAT 58.161 29.630 10.33 0.00 38.75 2.32
3018 9038 7.826252 TGTGGTTTCCATGAAATTTTCTTCAAA 59.174 29.630 10.33 3.59 38.75 2.69
3019 9039 7.334090 TGTGGTTTCCATGAAATTTTCTTCAA 58.666 30.769 10.33 0.00 38.75 2.69
3020 9040 6.882656 TGTGGTTTCCATGAAATTTTCTTCA 58.117 32.000 10.33 0.00 39.56 3.02
3021 9041 7.967890 ATGTGGTTTCCATGAAATTTTCTTC 57.032 32.000 10.33 0.00 35.28 2.87
3022 9042 8.623030 CAAATGTGGTTTCCATGAAATTTTCTT 58.377 29.630 10.33 1.51 35.28 2.52
3023 9043 7.992033 TCAAATGTGGTTTCCATGAAATTTTCT 59.008 29.630 10.33 0.00 35.28 2.52
3024 9044 8.152309 TCAAATGTGGTTTCCATGAAATTTTC 57.848 30.769 2.05 2.05 35.28 2.29
3025 9045 8.517062 TTCAAATGTGGTTTCCATGAAATTTT 57.483 26.923 0.00 0.00 35.28 1.82
3026 9046 8.517062 TTTCAAATGTGGTTTCCATGAAATTT 57.483 26.923 9.68 0.00 35.33 1.82
3027 9047 7.774625 ACTTTCAAATGTGGTTTCCATGAAATT 59.225 29.630 12.53 7.30 37.81 1.82
3028 9048 7.281841 ACTTTCAAATGTGGTTTCCATGAAAT 58.718 30.769 12.53 4.87 37.81 2.17
3029 9049 6.648192 ACTTTCAAATGTGGTTTCCATGAAA 58.352 32.000 11.92 11.92 36.83 2.69
3030 9050 6.232581 ACTTTCAAATGTGGTTTCCATGAA 57.767 33.333 0.00 0.00 35.28 2.57
3031 9051 5.867903 ACTTTCAAATGTGGTTTCCATGA 57.132 34.783 0.00 0.00 35.28 3.07
3032 9052 5.277442 GCAACTTTCAAATGTGGTTTCCATG 60.277 40.000 0.00 0.00 35.28 3.66
3033 9053 4.815846 GCAACTTTCAAATGTGGTTTCCAT 59.184 37.500 0.00 0.00 35.28 3.41
3034 9054 4.187694 GCAACTTTCAAATGTGGTTTCCA 58.812 39.130 0.00 0.00 0.00 3.53
3035 9055 4.187694 TGCAACTTTCAAATGTGGTTTCC 58.812 39.130 0.00 0.00 0.00 3.13
3036 9056 5.580297 TCTTGCAACTTTCAAATGTGGTTTC 59.420 36.000 0.00 0.00 0.00 2.78
3037 9057 5.486526 TCTTGCAACTTTCAAATGTGGTTT 58.513 33.333 0.00 0.00 0.00 3.27
3038 9058 5.083533 TCTTGCAACTTTCAAATGTGGTT 57.916 34.783 0.00 0.00 0.00 3.67
3039 9059 4.734398 TCTTGCAACTTTCAAATGTGGT 57.266 36.364 0.00 0.00 0.00 4.16
3040 9060 6.419980 TTTTCTTGCAACTTTCAAATGTGG 57.580 33.333 0.00 0.00 0.00 4.17
3041 9061 8.392612 AGATTTTTCTTGCAACTTTCAAATGTG 58.607 29.630 0.00 0.00 0.00 3.21
3042 9062 8.496707 AGATTTTTCTTGCAACTTTCAAATGT 57.503 26.923 0.00 0.00 0.00 2.71
3043 9063 9.777575 AAAGATTTTTCTTGCAACTTTCAAATG 57.222 25.926 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.