Multiple sequence alignment - TraesCS1A01G413200

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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 TraesCS1A01G413200 chr1A 100.000 9275 0 0 1 9275 573219909 573210635 0.000000e+00 17128.0
1 TraesCS1A01G413200 chr1A 72.151 2869 711 81 2761 5583 448011625 448014451 0.000000e+00 791.0
2 TraesCS1A01G413200 chr1A 97.230 361 10 0 2421 2781 573212362 573212002 6.160000e-171 612.0
3 TraesCS1A01G413200 chr1A 97.230 361 10 0 7548 7908 573217489 573217129 6.160000e-171 612.0
4 TraesCS1A01G413200 chr6D 91.352 5504 414 35 2421 7908 431303903 431298446 0.000000e+00 7470.0
5 TraesCS1A01G413200 chr6D 81.691 3217 570 14 4222 7431 116747439 116744235 0.000000e+00 2660.0
6 TraesCS1A01G413200 chr6D 83.035 1285 190 17 2875 4154 116748715 116747454 0.000000e+00 1140.0
7 TraesCS1A01G413200 chr6D 92.067 479 34 4 200 676 263321650 263321174 0.000000e+00 671.0
8 TraesCS1A01G413200 chr6D 90.726 496 38 6 184 676 133006480 133006970 0.000000e+00 654.0
9 TraesCS1A01G413200 chr6D 85.405 370 40 13 2421 2781 431298810 431298446 1.140000e-98 372.0
10 TraesCS1A01G413200 chr3D 92.633 5199 342 26 2421 7590 573912231 573917417 0.000000e+00 7441.0
11 TraesCS1A01G413200 chr3D 91.736 484 38 2 194 676 140196799 140197281 0.000000e+00 671.0
12 TraesCS1A01G413200 chr3D 83.505 388 37 12 7548 7908 573912231 573912618 4.150000e-88 337.0
13 TraesCS1A01G413200 chr3D 87.970 266 23 9 2526 2782 573917535 573917800 1.170000e-78 305.0
14 TraesCS1A01G413200 chr3D 87.547 265 24 9 7653 7908 573917535 573917799 1.960000e-76 298.0
15 TraesCS1A01G413200 chr3D 85.859 99 10 3 8834 8931 572627135 572627230 1.650000e-17 102.0
16 TraesCS1A01G413200 chr5B 80.497 5517 971 89 2448 7908 647341591 647347058 0.000000e+00 4130.0
17 TraesCS1A01G413200 chr5B 90.221 1943 187 3 3993 5934 84916408 84918348 0.000000e+00 2532.0
18 TraesCS1A01G413200 chr5B 90.323 1643 157 2 3993 5634 84894973 84896614 0.000000e+00 2152.0
19 TraesCS1A01G413200 chr5B 89.111 1451 143 15 2418 3857 84892236 84893682 0.000000e+00 1790.0
20 TraesCS1A01G413200 chr5B 88.538 1361 141 15 6557 7908 84921899 84923253 0.000000e+00 1635.0
21 TraesCS1A01G413200 chr5B 90.688 494 43 3 184 676 61407789 61408280 0.000000e+00 654.0
22 TraesCS1A01G413200 chr5B 84.987 373 42 14 7546 7908 84892238 84892606 5.290000e-97 366.0
23 TraesCS1A01G413200 chr5B 87.543 289 36 0 5932 6220 84921614 84921902 1.490000e-87 335.0
24 TraesCS1A01G413200 chr5B 83.155 374 47 16 2421 2784 84922889 84923256 2.500000e-85 327.0
25 TraesCS1A01G413200 chr5B 85.294 170 23 2 6 174 702415049 702414881 3.440000e-39 174.0
26 TraesCS1A01G413200 chr5B 92.632 95 7 0 3763 3857 84896609 84896703 4.520000e-28 137.0
27 TraesCS1A01G413200 chr7A 94.252 2453 108 3 1 2421 144694433 144696884 0.000000e+00 3718.0
28 TraesCS1A01G413200 chr7A 98.147 1241 16 4 8041 9275 144697803 144699042 0.000000e+00 2158.0
29 TraesCS1A01G413200 chr7A 97.609 920 17 3 7908 8824 144696878 144697795 0.000000e+00 1572.0
30 TraesCS1A01G413200 chr7A 90.485 1135 81 16 676 1797 94143791 94142671 0.000000e+00 1472.0
31 TraesCS1A01G413200 chr7A 93.122 378 22 3 1792 2166 521797229 521796853 1.360000e-152 551.0
32 TraesCS1A01G413200 chr7A 89.710 379 33 5 1792 2166 521893072 521892696 6.510000e-131 479.0
33 TraesCS1A01G413200 chr7A 88.148 405 44 4 8859 9262 536151249 536151650 6.510000e-131 479.0
34 TraesCS1A01G413200 chr7A 83.267 251 36 4 7928 8172 33198890 33198640 9.370000e-55 226.0
35 TraesCS1A01G413200 chr7A 99.000 100 1 0 1634 1733 735870777 735870678 7.400000e-41 180.0
36 TraesCS1A01G413200 chr7A 85.030 167 23 2 10 174 112263100 112262934 1.600000e-37 169.0
37 TraesCS1A01G413200 chr6A 93.368 2322 87 8 129 2421 454705823 454708106 0.000000e+00 3373.0
38 TraesCS1A01G413200 chr6A 98.324 1372 18 3 7908 9275 454708100 454709470 0.000000e+00 2401.0
39 TraesCS1A01G413200 chr6A 90.846 1147 69 17 679 1797 19869784 19870922 0.000000e+00 1504.0
40 TraesCS1A01G413200 chr6A 88.745 231 18 6 1 224 454705592 454705821 9.170000e-70 276.0
41 TraesCS1A01G413200 chr5D 82.913 3769 597 39 3910 7658 514856155 514859896 0.000000e+00 3349.0
42 TraesCS1A01G413200 chr5A 92.709 2318 94 18 136 2421 548799350 548797076 0.000000e+00 3275.0
43 TraesCS1A01G413200 chr5A 98.104 1371 22 2 7908 9275 548797082 548795713 0.000000e+00 2385.0
44 TraesCS1A01G413200 chr5A 89.224 232 17 6 1 224 548799589 548799358 5.480000e-72 283.0
45 TraesCS1A01G413200 chr5A 82.328 232 27 10 697 921 487744205 487743981 1.230000e-43 189.0
46 TraesCS1A01G413200 chr5A 99.000 100 1 0 1634 1733 150805837 150805738 7.400000e-41 180.0
47 TraesCS1A01G413200 chr1B 90.129 2482 224 20 2421 4889 598708371 598710844 0.000000e+00 3206.0
48 TraesCS1A01G413200 chr1B 88.605 2580 277 17 5358 7928 598747087 598749658 0.000000e+00 3120.0
49 TraesCS1A01G413200 chr1B 87.935 431 44 7 8834 9262 678221999 678222423 1.390000e-137 501.0
50 TraesCS1A01G413200 chr1B 83.554 377 46 16 7544 7908 598708367 598708739 1.150000e-88 339.0
51 TraesCS1A01G413200 chr1B 82.749 371 49 15 2421 2782 598749277 598749641 5.410000e-82 316.0
52 TraesCS1A01G413200 chr1B 71.252 1214 311 36 2774 3969 380879959 380878766 3.300000e-69 274.0
53 TraesCS1A01G413200 chr3A 82.576 3369 523 51 2421 5768 418590321 418593646 0.000000e+00 2911.0
54 TraesCS1A01G413200 chr3A 91.648 874 42 12 935 1797 9980218 9981071 0.000000e+00 1181.0
55 TraesCS1A01G413200 chr3A 81.536 1159 188 25 6764 7908 418749810 418750956 0.000000e+00 931.0
56 TraesCS1A01G413200 chr3A 85.342 307 41 4 5950 6254 418749072 418749376 1.940000e-81 315.0
57 TraesCS1A01G413200 chr3A 79.718 355 56 9 694 1042 559497407 559497751 9.300000e-60 243.0
58 TraesCS1A01G413200 chr3A 93.220 59 4 0 804 862 559497559 559497617 4.610000e-13 87.9
59 TraesCS1A01G413200 chr2A 74.884 4300 996 66 2746 6998 36661794 36666056 0.000000e+00 1881.0
60 TraesCS1A01G413200 chr2A 88.642 405 42 4 8859 9262 24024637 24024236 3.010000e-134 490.0
61 TraesCS1A01G413200 chr2A 88.235 153 17 1 8 159 679960823 679960975 2.060000e-41 182.0
62 TraesCS1A01G413200 chr2A 84.884 172 21 5 6 174 685971647 685971478 1.600000e-37 169.0
63 TraesCS1A01G413200 chr2A 82.955 176 25 4 1 174 163674423 163674595 4.490000e-33 154.0
64 TraesCS1A01G413200 chr2A 78.873 142 26 4 8484 8623 674455679 674455540 9.920000e-15 93.5
65 TraesCS1A01G413200 chr2B 74.418 4296 1025 56 2746 6998 36986888 36991152 0.000000e+00 1777.0
66 TraesCS1A01G413200 chr2B 90.653 1134 80 15 676 1797 143014656 143013537 0.000000e+00 1483.0
67 TraesCS1A01G413200 chr2B 79.478 536 88 18 7146 7665 36991300 36991829 2.460000e-95 361.0
68 TraesCS1A01G413200 chr2B 79.781 366 49 14 703 1045 87538954 87538591 9.300000e-60 243.0
69 TraesCS1A01G413200 chr2B 79.651 172 23 6 735 899 41384127 41384293 7.610000e-21 113.0
70 TraesCS1A01G413200 chr1D 84.293 1719 265 4 5615 7331 409310532 409312247 0.000000e+00 1674.0
71 TraesCS1A01G413200 chr4D 92.887 478 30 4 202 676 272419443 272419919 0.000000e+00 691.0
72 TraesCS1A01G413200 chr4D 74.661 1180 279 19 3393 4563 111550399 111549231 1.070000e-138 505.0
73 TraesCS1A01G413200 chr4D 92.517 294 22 0 1239 1532 126935795 126935502 1.110000e-113 422.0
74 TraesCS1A01G413200 chr4D 94.203 69 3 1 1730 1797 198602377 198602309 4.580000e-18 104.0
75 TraesCS1A01G413200 chr2D 92.842 475 25 8 196 661 350310420 350310894 0.000000e+00 680.0
76 TraesCS1A01G413200 chr7D 92.593 378 24 3 1792 2166 474343239 474343615 2.950000e-149 540.0
77 TraesCS1A01G413200 chr7D 88.360 378 40 3 1792 2166 474271123 474271499 1.420000e-122 451.0
78 TraesCS1A01G413200 chr7D 83.271 269 39 5 7910 8172 32957330 32957062 9.300000e-60 243.0
79 TraesCS1A01G413200 chr7D 82.967 182 27 4 4 182 193241983 193241803 2.680000e-35 161.0
80 TraesCS1A01G413200 chr7B 92.593 378 24 3 1792 2166 498522521 498522897 2.950000e-149 540.0
81 TraesCS1A01G413200 chr7B 87.624 404 47 3 8859 9262 634562082 634562482 5.070000e-127 466.0
82 TraesCS1A01G413200 chr7B 87.863 379 40 5 1792 2166 498298452 498298828 3.070000e-119 440.0
83 TraesCS1A01G413200 chr7B 85.535 159 20 3 3 159 78268216 78268373 7.450000e-36 163.0
84 TraesCS1A01G413200 chrUn 87.654 405 45 5 8859 9262 421899650 421900050 5.070000e-127 466.0
85 TraesCS1A01G413200 chr4B 87.919 149 17 1 11 158 73494290 73494142 3.440000e-39 174.0


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 TraesCS1A01G413200 chr1A 573210635 573219909 9274 True 17128.000000 17128 100.000000 1 9275 1 chr1A.!!$R1 9274
1 TraesCS1A01G413200 chr1A 448011625 448014451 2826 False 791.000000 791 72.151000 2761 5583 1 chr1A.!!$F1 2822
2 TraesCS1A01G413200 chr6D 431298446 431303903 5457 True 7470.000000 7470 91.352000 2421 7908 1 chr6D.!!$R2 5487
3 TraesCS1A01G413200 chr6D 116744235 116748715 4480 True 1900.000000 2660 82.363000 2875 7431 2 chr6D.!!$R4 4556
4 TraesCS1A01G413200 chr3D 573912231 573917417 5186 False 7441.000000 7441 92.633000 2421 7590 1 chr3D.!!$F3 5169
5 TraesCS1A01G413200 chr5B 647341591 647347058 5467 False 4130.000000 4130 80.497000 2448 7908 1 chr5B.!!$F2 5460
6 TraesCS1A01G413200 chr5B 84916408 84923256 6848 False 1207.250000 2532 87.364250 2421 7908 4 chr5B.!!$F4 5487
7 TraesCS1A01G413200 chr5B 84892236 84896703 4467 False 1111.250000 2152 89.263250 2418 7908 4 chr5B.!!$F3 5490
8 TraesCS1A01G413200 chr7A 144694433 144699042 4609 False 2482.666667 3718 96.669333 1 9275 3 chr7A.!!$F2 9274
9 TraesCS1A01G413200 chr7A 94142671 94143791 1120 True 1472.000000 1472 90.485000 676 1797 1 chr7A.!!$R2 1121
10 TraesCS1A01G413200 chr6A 454705592 454709470 3878 False 2016.666667 3373 93.479000 1 9275 3 chr6A.!!$F2 9274
11 TraesCS1A01G413200 chr6A 19869784 19870922 1138 False 1504.000000 1504 90.846000 679 1797 1 chr6A.!!$F1 1118
12 TraesCS1A01G413200 chr5D 514856155 514859896 3741 False 3349.000000 3349 82.913000 3910 7658 1 chr5D.!!$F1 3748
13 TraesCS1A01G413200 chr5A 548795713 548799589 3876 True 1981.000000 3275 93.345667 1 9275 3 chr5A.!!$R3 9274
14 TraesCS1A01G413200 chr1B 598708367 598710844 2477 False 1772.500000 3206 86.841500 2421 7908 2 chr1B.!!$F2 5487
15 TraesCS1A01G413200 chr1B 598747087 598749658 2571 False 1718.000000 3120 85.677000 2421 7928 2 chr1B.!!$F3 5507
16 TraesCS1A01G413200 chr1B 380878766 380879959 1193 True 274.000000 274 71.252000 2774 3969 1 chr1B.!!$R1 1195
17 TraesCS1A01G413200 chr3A 418590321 418593646 3325 False 2911.000000 2911 82.576000 2421 5768 1 chr3A.!!$F2 3347
18 TraesCS1A01G413200 chr3A 9980218 9981071 853 False 1181.000000 1181 91.648000 935 1797 1 chr3A.!!$F1 862
19 TraesCS1A01G413200 chr3A 418749072 418750956 1884 False 623.000000 931 83.439000 5950 7908 2 chr3A.!!$F3 1958
20 TraesCS1A01G413200 chr2A 36661794 36666056 4262 False 1881.000000 1881 74.884000 2746 6998 1 chr2A.!!$F1 4252
21 TraesCS1A01G413200 chr2B 143013537 143014656 1119 True 1483.000000 1483 90.653000 676 1797 1 chr2B.!!$R2 1121
22 TraesCS1A01G413200 chr2B 36986888 36991829 4941 False 1069.000000 1777 76.948000 2746 7665 2 chr2B.!!$F2 4919
23 TraesCS1A01G413200 chr1D 409310532 409312247 1715 False 1674.000000 1674 84.293000 5615 7331 1 chr1D.!!$F1 1716
24 TraesCS1A01G413200 chr4D 111549231 111550399 1168 True 505.000000 505 74.661000 3393 4563 1 chr4D.!!$R1 1170

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
479 610 1.003464 TGGTGATGATGGTGTGTCTGG 59.997 52.381 0.00 0.0 0.00 3.86 F
1073 1317 0.612174 CACTCCCGTCTCTTCTCCCA 60.612 60.000 0.00 0.0 0.00 4.37 F
2507 2781 1.048160 GGAAGGAGAGCTGGAGAGGG 61.048 65.000 0.00 0.0 0.00 4.30 F
3242 3577 0.393537 CCACCATGAACTCTCTGGGC 60.394 60.000 0.00 0.0 34.21 5.36 F
3245 3580 0.460987 CCATGAACTCTCTGGGCGAC 60.461 60.000 0.00 0.0 0.00 5.19 F
3341 3676 1.153289 CTGAGCCAGAATCCACCCG 60.153 63.158 0.00 0.0 32.44 5.28 F
4850 6347 1.000896 ATTGCTGGGTACAGGCCAC 60.001 57.895 5.01 0.0 45.04 5.01 F
6450 11249 0.609131 TTTACTGCCCTTGCTCTGCC 60.609 55.000 0.00 0.0 38.71 4.85 F
7290 12100 0.672401 TTCGGCCACCTTCGTCAATC 60.672 55.000 2.24 0.0 0.00 2.67 F
7831 12658 0.177141 TCCTATTCAAACCTCCCGCG 59.823 55.000 0.00 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2472 0.029834 GCACACTGACAAGGCACAAG 59.970 55.000 0.00 0.00 0.00 3.16 R
2597 2922 1.267121 ATAAGCTCGAGTGGTGTGGT 58.733 50.000 15.13 0.00 0.00 4.16 R
4159 5653 0.322277 ACAGAAGCTGGCACTGGATG 60.322 55.000 17.92 0.00 35.51 3.51 R
4410 5904 0.689055 ACAGATCACCAGAGCTTGCA 59.311 50.000 0.00 0.00 38.74 4.08 R
4796 6293 1.630878 GGATTTCTGGGACTCACTGGT 59.369 52.381 0.00 0.00 0.00 4.00 R
5276 6793 4.646040 CCCTTGCCAGTCATTGATGAATTA 59.354 41.667 0.00 0.00 38.75 1.40 R
6789 11590 0.179056 CTGAACCTGGTGGACAACGT 60.179 55.000 0.00 0.00 37.04 3.99 R
7709 12529 0.734942 GTGGTGTGTCGGGTATCGTG 60.735 60.000 0.00 0.00 40.32 4.35 R
8183 13016 3.052490 AGAGCCATCTAGAACCTGTACCT 60.052 47.826 0.00 0.00 32.54 3.08 R
8824 14457 4.814294 GCTAGCCCACACCGACGG 62.814 72.222 13.61 13.61 0.00 4.79 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 6.095860 AGTGCACTACAACTTACGGATGTATA 59.904 38.462 20.16 0.00 33.74 1.47
78 79 6.417044 GTGCACTACAACTTACGGATGTATAG 59.583 42.308 10.32 4.27 33.74 1.31
307 438 9.131791 GATAGGAAGGAAACTATGGCAATTTTA 57.868 33.333 0.00 0.00 42.68 1.52
326 457 7.849322 ATTTTACAAAAAGATACCCACACCT 57.151 32.000 0.00 0.00 0.00 4.00
353 484 4.041444 TCCACATTTGCAAATAAGGCCTTT 59.959 37.500 26.08 8.91 0.00 3.11
355 486 4.996122 CACATTTGCAAATAAGGCCTTTCA 59.004 37.500 26.08 6.92 0.00 2.69
365 496 7.494211 CAAATAAGGCCTTTCATCATTCATCA 58.506 34.615 26.08 0.00 0.00 3.07
412 543 7.833786 ACTCATACAAATGCATCTTGATGTTT 58.166 30.769 20.96 3.63 32.76 2.83
448 579 4.693095 GGGCATCTTGCTAGCTTCTTATAC 59.307 45.833 17.23 0.29 44.28 1.47
475 606 2.373169 AGAGTTGGTGATGATGGTGTGT 59.627 45.455 0.00 0.00 0.00 3.72
479 610 1.003464 TGGTGATGATGGTGTGTCTGG 59.997 52.381 0.00 0.00 0.00 3.86
515 646 5.934402 AGGCCGTCCGATTTATATCTAAT 57.066 39.130 0.00 0.00 37.47 1.73
835 991 2.045242 TCCCTAGCTCGTGTCGCT 60.045 61.111 0.00 0.00 41.35 4.93
851 1059 2.045536 CTGGTGCCTCTCCCTTGC 60.046 66.667 0.00 0.00 0.00 4.01
852 1060 3.635268 CTGGTGCCTCTCCCTTGCC 62.635 68.421 0.00 0.00 0.00 4.52
853 1061 4.432741 GGTGCCTCTCCCTTGCCC 62.433 72.222 0.00 0.00 0.00 5.36
854 1062 4.785453 GTGCCTCTCCCTTGCCCG 62.785 72.222 0.00 0.00 0.00 6.13
858 1066 4.821589 CTCTCCCTTGCCCGCGTC 62.822 72.222 4.92 0.00 0.00 5.19
872 1080 4.803426 CGTCGCCAGTGCCTCTCC 62.803 72.222 0.00 0.00 0.00 3.71
873 1081 4.459089 GTCGCCAGTGCCTCTCCC 62.459 72.222 0.00 0.00 0.00 4.30
874 1082 4.704103 TCGCCAGTGCCTCTCCCT 62.704 66.667 0.00 0.00 0.00 4.20
875 1083 4.154347 CGCCAGTGCCTCTCCCTC 62.154 72.222 0.00 0.00 0.00 4.30
876 1084 4.154347 GCCAGTGCCTCTCCCTCG 62.154 72.222 0.00 0.00 0.00 4.63
945 1179 6.889198 AGATCTCATTTTTATTCTCCGGTGA 58.111 36.000 0.00 0.06 0.00 4.02
979 1213 1.672030 TCGGCTCGACCTACAACGA 60.672 57.895 0.00 0.00 35.61 3.85
1000 1234 2.111999 CTTCCTCCACTCCAACGCCA 62.112 60.000 0.00 0.00 0.00 5.69
1042 1276 2.757508 TCCCTCGCTCCTGCTCAG 60.758 66.667 0.00 0.00 36.97 3.35
1073 1317 0.612174 CACTCCCGTCTCTTCTCCCA 60.612 60.000 0.00 0.00 0.00 4.37
1090 1334 2.361357 ACTCTGACCCCGTCTCCG 60.361 66.667 0.00 0.00 33.15 4.63
1160 1404 3.957288 CCTTGGAAGGTTCACCGAT 57.043 52.632 0.00 0.00 41.41 4.18
1195 1439 1.075050 ACGGTCTGGTCTTCTCCACTA 59.925 52.381 0.00 0.00 33.55 2.74
1316 1560 2.649034 GAAGACCACCGCTCGTCA 59.351 61.111 0.00 0.00 0.00 4.35
1410 1654 2.024941 CACCCTCCTCCCTATTTGCTTT 60.025 50.000 0.00 0.00 0.00 3.51
1575 1830 2.655090 TGACTGCTGAAAATGGACCA 57.345 45.000 0.00 0.00 0.00 4.02
1954 2211 5.132502 TGGAAGATTGGCACCATTATGTAG 58.867 41.667 0.00 0.00 0.00 2.74
2143 2400 8.410141 AACCAATTGTTTTAATCGAGAGAACAA 58.590 29.630 16.41 16.41 42.32 2.83
2215 2472 2.559440 CTTGGCAGCTCCTGAGATTAC 58.441 52.381 0.00 0.00 32.44 1.89
2278 2535 3.278367 GCATATGCACATCACATGGAC 57.722 47.619 22.84 0.00 41.59 4.02
2331 2588 3.106242 TCGCTAGTTGTCTTTTGAGCA 57.894 42.857 0.00 0.00 0.00 4.26
2352 2609 9.213799 TGAGCAAAAACTGAAATTTAAGTTGTT 57.786 25.926 19.68 17.58 36.75 2.83
2373 2630 4.374689 TTGCTGAATTTGGGGTGTACTA 57.625 40.909 0.00 0.00 0.00 1.82
2382 2639 3.918294 TGGGGTGTACTATTGGTTAGC 57.082 47.619 0.00 0.00 0.00 3.09
2505 2779 1.341877 TGAGGAAGGAGAGCTGGAGAG 60.342 57.143 0.00 0.00 0.00 3.20
2507 2781 1.048160 GGAAGGAGAGCTGGAGAGGG 61.048 65.000 0.00 0.00 0.00 4.30
2508 2782 1.685355 GAAGGAGAGCTGGAGAGGGC 61.685 65.000 0.00 0.00 0.00 5.19
2531 2806 2.430244 GCGGACGCAACGAGAGAA 60.430 61.111 12.31 0.00 41.49 2.87
2532 2807 2.717809 GCGGACGCAACGAGAGAAC 61.718 63.158 12.31 0.00 41.49 3.01
2536 2811 1.066114 GACGCAACGAGAGAACGAGG 61.066 60.000 0.00 0.00 37.03 4.63
2537 2812 1.209383 CGCAACGAGAGAACGAGGA 59.791 57.895 0.00 0.00 37.03 3.71
2540 2815 1.983972 CAACGAGAGAACGAGGAAGG 58.016 55.000 0.00 0.00 37.03 3.46
2541 2816 1.540267 CAACGAGAGAACGAGGAAGGA 59.460 52.381 0.00 0.00 37.03 3.36
2564 2887 6.719370 GGAAGAGAGGATAAGCTCAGAGAATA 59.281 42.308 0.00 0.00 33.62 1.75
2597 2922 1.187974 ATTCCACGATACCCGACACA 58.812 50.000 0.00 0.00 41.76 3.72
2602 2927 1.180456 ACGATACCCGACACACCACA 61.180 55.000 0.00 0.00 41.76 4.17
2634 2959 6.091437 AGCTTATATATCCGCTCGTTACAAC 58.909 40.000 3.52 0.00 0.00 3.32
2656 2983 3.365265 GCCTCGGCCCAACACTTG 61.365 66.667 0.00 0.00 34.56 3.16
2704 3034 2.224066 ACTCCTATTCAAATCTCCCGCG 60.224 50.000 0.00 0.00 0.00 6.46
2722 3054 2.033194 GCTACGCTTCCGCCTTGTT 61.033 57.895 0.00 0.00 38.22 2.83
2831 3164 3.675995 TGCTGGTGCATCTGGAAAT 57.324 47.368 5.95 0.00 45.31 2.17
3104 3437 1.993369 GCTCCAACTTGTATGCCGCC 61.993 60.000 0.00 0.00 0.00 6.13
3194 3529 1.893137 ACCACTGACGACTGAGCATAA 59.107 47.619 0.00 0.00 0.00 1.90
3242 3577 0.393537 CCACCATGAACTCTCTGGGC 60.394 60.000 0.00 0.00 34.21 5.36
3245 3580 0.460987 CCATGAACTCTCTGGGCGAC 60.461 60.000 0.00 0.00 0.00 5.19
3341 3676 1.153289 CTGAGCCAGAATCCACCCG 60.153 63.158 0.00 0.00 32.44 5.28
3531 3869 4.378459 GCACTGCACACCTTAAGTACATTC 60.378 45.833 0.97 0.00 0.00 2.67
3554 3892 2.167487 GAGACACTGATTCACCCTCTCC 59.833 54.545 0.00 0.00 0.00 3.71
3787 4125 6.984474 TGACTGACTTTAGTAAACCTGTCAAG 59.016 38.462 19.41 14.25 34.64 3.02
3907 4830 2.227388 GGAGCAATCCAGGATATTTGCG 59.773 50.000 17.10 0.00 46.84 4.85
3955 5404 1.831343 GCACACTGCTTCACAAAGTG 58.169 50.000 0.67 0.67 45.46 3.16
4151 5645 3.818295 TGTAAAGTAAACCCAGGGCAT 57.182 42.857 4.91 0.00 0.00 4.40
4159 5653 3.777910 CCCAGGGCATGCCTTTGC 61.778 66.667 34.70 19.02 42.01 3.68
4197 5691 6.096673 TCTGTAACATGTCTTGAGCTACAA 57.903 37.500 0.00 0.00 36.97 2.41
4207 5701 2.680312 TGAGCTACAAGATCCACAGC 57.320 50.000 0.00 0.00 27.46 4.40
4400 5894 4.926238 AGTTCAGAAGTTAGCACTTGATCG 59.074 41.667 0.00 0.00 43.79 3.69
4541 6035 6.105333 CAGTTTCTGATTCTTCTGACCTAGG 58.895 44.000 7.41 7.41 32.44 3.02
4679 6176 2.320781 GGAGTAGAGGCCATAGCTTGA 58.679 52.381 5.01 0.00 39.73 3.02
4850 6347 1.000896 ATTGCTGGGTACAGGCCAC 60.001 57.895 5.01 0.00 45.04 5.01
5099 6615 5.163519 ACCAGGAAACAGAAAGTTCATGTTG 60.164 40.000 0.00 0.00 40.26 3.33
5158 6674 9.856162 AAAGGGTACAACTCTGAACTAAAATTA 57.144 29.630 0.00 0.00 0.00 1.40
5265 6782 4.151883 AGAAAACCATTTTGCTCCAGCTA 58.848 39.130 0.00 0.00 42.66 3.32
5266 6783 4.588528 AGAAAACCATTTTGCTCCAGCTAA 59.411 37.500 0.00 0.00 42.66 3.09
5267 6784 5.246883 AGAAAACCATTTTGCTCCAGCTAAT 59.753 36.000 0.00 0.00 42.66 1.73
5268 6785 5.488262 AAACCATTTTGCTCCAGCTAATT 57.512 34.783 0.00 0.00 42.66 1.40
5269 6786 4.725790 ACCATTTTGCTCCAGCTAATTC 57.274 40.909 0.00 0.00 42.66 2.17
5270 6787 4.088634 ACCATTTTGCTCCAGCTAATTCA 58.911 39.130 0.00 0.00 42.66 2.57
5271 6788 4.713321 ACCATTTTGCTCCAGCTAATTCAT 59.287 37.500 0.00 0.00 42.66 2.57
5272 6789 5.163478 ACCATTTTGCTCCAGCTAATTCATC 60.163 40.000 0.00 0.00 42.66 2.92
5273 6790 5.068723 CCATTTTGCTCCAGCTAATTCATCT 59.931 40.000 0.00 0.00 42.66 2.90
5274 6791 6.263842 CCATTTTGCTCCAGCTAATTCATCTA 59.736 38.462 0.00 0.00 42.66 1.98
5275 6792 6.932356 TTTTGCTCCAGCTAATTCATCTAG 57.068 37.500 0.00 0.00 42.66 2.43
5276 6793 5.620738 TTGCTCCAGCTAATTCATCTAGT 57.379 39.130 0.00 0.00 42.66 2.57
5321 6850 5.335976 GGGAAATCTGCTTTTTACTGTCAGG 60.336 44.000 4.53 0.00 0.00 3.86
5354 6883 9.740710 AGCTTTCTATAATCTACACAAAACCTT 57.259 29.630 0.00 0.00 0.00 3.50
5525 7054 0.953960 GTACAGCCCCACGAACCAAG 60.954 60.000 0.00 0.00 0.00 3.61
5625 7154 7.997773 AGTTCCTTAATAGGTTCAGGAAAAC 57.002 36.000 5.63 0.00 44.92 2.43
5771 7301 6.072508 GCAAAACTCCTTGTAATCTCACATCA 60.073 38.462 0.00 0.00 0.00 3.07
5777 7307 4.818546 CCTTGTAATCTCACATCATGTCCC 59.181 45.833 0.00 0.00 0.00 4.46
5835 7365 2.816087 CACTTCATCACTCCCCACTTTG 59.184 50.000 0.00 0.00 0.00 2.77
5873 7403 4.341806 CCCAAAATTATGTCATAGCTGCCA 59.658 41.667 0.00 0.00 0.00 4.92
5909 7439 3.133003 TCATAGGGCTAGTGAAGTTCTGC 59.867 47.826 4.17 3.70 0.00 4.26
5936 10734 3.016736 CAGCCACCAAGTTACATTAGGG 58.983 50.000 0.00 0.00 0.00 3.53
6039 10838 2.550830 TCTTTCCAACAGAGCCTGAC 57.449 50.000 8.91 0.00 35.18 3.51
6092 10891 3.181487 ACAACAGCAACACCACTTGATTC 60.181 43.478 0.00 0.00 0.00 2.52
6152 10951 1.152030 TCCTGACAGGGCCTGAACT 60.152 57.895 38.99 18.25 35.59 3.01
6210 11009 3.943381 CAGTGCATCCAACACTACATCAT 59.057 43.478 0.00 0.00 46.44 2.45
6212 11011 5.761726 CAGTGCATCCAACACTACATCATAT 59.238 40.000 0.00 0.00 46.44 1.78
6404 11203 3.088532 ACTGCTTCTAGAGTCCTGTCTG 58.911 50.000 0.00 0.00 0.00 3.51
6412 11211 1.342819 AGAGTCCTGTCTGCTTGTGAC 59.657 52.381 0.00 0.00 35.21 3.67
6444 11243 3.401033 AATTGGTTTTACTGCCCTTGC 57.599 42.857 0.00 0.00 38.26 4.01
6450 11249 0.609131 TTTACTGCCCTTGCTCTGCC 60.609 55.000 0.00 0.00 38.71 4.85
6494 11293 2.624316 CATACAGTGCAGCTTGTTGG 57.376 50.000 8.18 0.00 0.00 3.77
6553 11353 5.564848 GCAACTCTTCCTTTAAACCCATGAC 60.565 44.000 0.00 0.00 0.00 3.06
6691 11492 1.871080 AAGGACTGCAACAGTTCTCG 58.129 50.000 8.94 0.00 46.33 4.04
6782 11583 3.068732 TCTGTCTCACTGACTGAAACCAG 59.931 47.826 3.52 0.00 46.06 4.00
6789 11590 2.016318 CTGACTGAAACCAGTGTGCAA 58.984 47.619 2.50 0.00 44.34 4.08
6803 11604 1.821759 TGCAACGTTGTCCACCAGG 60.822 57.895 27.78 1.06 0.00 4.45
6857 11658 6.069673 TGTCAGGGATATTGTACAGTTGGAAT 60.070 38.462 0.00 0.00 0.00 3.01
6881 11682 4.776435 TGCCTCACATTGATCTATCCAA 57.224 40.909 0.00 0.00 0.00 3.53
7080 11881 1.697432 CCGCTCCCAATAACCCATCTA 59.303 52.381 0.00 0.00 0.00 1.98
7117 11918 4.312152 AACGGTCCCTCCCCTCGT 62.312 66.667 0.00 0.00 35.48 4.18
7137 11947 2.437180 CGCCCTGATTGCTCTGCA 60.437 61.111 0.00 0.00 36.47 4.41
7261 12071 1.147824 CATCCAGCGCCTCCAATCT 59.852 57.895 2.29 0.00 0.00 2.40
7290 12100 0.672401 TTCGGCCACCTTCGTCAATC 60.672 55.000 2.24 0.00 0.00 2.67
7374 12184 1.139095 CGCTCGAGGTACTTGGTCC 59.861 63.158 15.58 0.00 41.55 4.46
7399 12209 4.379143 GGGTTTGAACGCCGTCGC 62.379 66.667 0.00 0.00 39.84 5.19
7427 12237 1.072965 CTCTCTGAAGCAACCCACCTT 59.927 52.381 0.00 0.00 0.00 3.50
7618 12431 1.065709 GCCGGTAGAATTGGTGAGGAA 60.066 52.381 1.90 0.00 0.00 3.36
7619 12432 2.906354 CCGGTAGAATTGGTGAGGAAG 58.094 52.381 0.00 0.00 0.00 3.46
7620 12433 2.420129 CCGGTAGAATTGGTGAGGAAGG 60.420 54.545 0.00 0.00 0.00 3.46
7621 12434 2.500098 CGGTAGAATTGGTGAGGAAGGA 59.500 50.000 0.00 0.00 0.00 3.36
7626 12444 1.963985 ATTGGTGAGGAAGGAGAGCT 58.036 50.000 0.00 0.00 0.00 4.09
7635 12453 1.685355 GAAGGAGAGCTGGAGAGGGC 61.685 65.000 0.00 0.00 0.00 5.19
7659 12477 2.717809 GCGGACGCAACGAGAGAAC 61.718 63.158 12.31 0.00 41.49 3.01
7663 12481 1.066114 GACGCAACGAGAGAACGAGG 61.066 60.000 0.00 0.00 37.03 4.63
7664 12482 1.209383 CGCAACGAGAGAACGAGGA 59.791 57.895 0.00 0.00 37.03 3.71
7684 12503 3.005367 GGAAGGAAGAGAGGATAAGCTCG 59.995 52.174 0.00 0.00 36.29 5.03
7709 12529 9.455847 CGGAGAATAAGATTCAAATTCAATTCC 57.544 33.333 11.37 9.12 33.06 3.01
7724 12546 1.187974 ATTCCACGATACCCGACACA 58.812 50.000 0.00 0.00 41.76 3.72
7729 12551 1.180456 ACGATACCCGACACACCACA 61.180 55.000 0.00 0.00 41.76 4.17
7760 12582 6.263516 AGCTTATATATCCGCTCGTTACAA 57.736 37.500 3.52 0.00 0.00 2.41
7761 12583 6.091437 AGCTTATATATCCGCTCGTTACAAC 58.909 40.000 3.52 0.00 0.00 3.32
7783 12606 3.365265 GCCTCGGCCCAACACTTG 61.365 66.667 0.00 0.00 34.56 3.16
7784 12607 2.113139 CCTCGGCCCAACACTTGT 59.887 61.111 0.00 0.00 0.00 3.16
7785 12608 2.260869 CCTCGGCCCAACACTTGTG 61.261 63.158 0.00 0.00 0.00 3.33
7806 12633 2.325082 GCCCACACGCTAACACAGG 61.325 63.158 0.00 0.00 0.00 4.00
7831 12658 0.177141 TCCTATTCAAACCTCCCGCG 59.823 55.000 0.00 0.00 0.00 6.46
7913 12744 6.662865 AGTAGCTGCATACTGACAGATTAT 57.337 37.500 10.08 0.00 34.68 1.28
8156 12987 5.587844 TGCTTTTGTTGCATAACCATGTTTT 59.412 32.000 0.00 0.00 35.92 2.43
8157 12988 6.094603 TGCTTTTGTTGCATAACCATGTTTTT 59.905 30.769 0.00 0.00 35.92 1.94
8183 13016 3.119137 TCTGAAGCTACTTATGCAGCGAA 60.119 43.478 0.00 0.00 42.74 4.70
8226 13062 5.325239 TCTGTAGACAGTGAGAATGAGGAA 58.675 41.667 9.43 0.00 44.12 3.36
8824 14457 2.946329 TCAGAGTCCGAATAGCAGAGTC 59.054 50.000 0.00 0.00 0.00 3.36
9121 14754 7.895975 TTCAAGATACAAATCAGTCACTCAG 57.104 36.000 0.00 0.00 34.28 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 9.793259 TTTTTAGAGATTCCAACAAGTGACTAT 57.207 29.630 0.00 0.00 0.00 2.12
225 356 0.754217 GGCAGGCACACCATCATCAT 60.754 55.000 0.00 0.00 39.06 2.45
307 438 4.351111 AGAGAGGTGTGGGTATCTTTTTGT 59.649 41.667 0.00 0.00 0.00 2.83
326 457 4.158394 GCCTTATTTGCAAATGTGGAGAGA 59.842 41.667 31.67 13.71 0.00 3.10
353 484 6.189133 TGTGGGAGAAAATGATGAATGATGA 58.811 36.000 0.00 0.00 0.00 2.92
355 486 6.893554 TCTTGTGGGAGAAAATGATGAATGAT 59.106 34.615 0.00 0.00 0.00 2.45
365 496 8.383175 TGAGTAGTTTATCTTGTGGGAGAAAAT 58.617 33.333 0.00 0.00 31.46 1.82
448 579 4.279169 ACCATCATCACCAACTCTGTTTTG 59.721 41.667 0.00 0.00 0.00 2.44
475 606 3.415212 GCCTATATTGCAAGATGCCAGA 58.585 45.455 16.68 0.00 44.23 3.86
479 610 2.154462 ACGGCCTATATTGCAAGATGC 58.846 47.619 16.68 11.76 45.29 3.91
515 646 5.661503 TGCCATAATTTCCTTCCTATCCA 57.338 39.130 0.00 0.00 0.00 3.41
835 991 3.650950 GGCAAGGGAGAGGCACCA 61.651 66.667 0.00 0.00 0.00 4.17
855 1063 4.803426 GGAGAGGCACTGGCGACG 62.803 72.222 0.00 0.00 41.55 5.12
856 1064 4.459089 GGGAGAGGCACTGGCGAC 62.459 72.222 0.00 0.00 41.55 5.19
857 1065 4.704103 AGGGAGAGGCACTGGCGA 62.704 66.667 0.00 0.00 41.55 5.54
858 1066 4.154347 GAGGGAGAGGCACTGGCG 62.154 72.222 0.00 0.00 41.55 5.69
859 1067 4.154347 CGAGGGAGAGGCACTGGC 62.154 72.222 0.00 0.00 41.55 4.85
860 1068 4.154347 GCGAGGGAGAGGCACTGG 62.154 72.222 0.00 0.00 41.55 4.00
861 1069 4.154347 GGCGAGGGAGAGGCACTG 62.154 72.222 0.00 0.00 41.55 3.66
867 1075 3.827898 GACGTGGGCGAGGGAGAG 61.828 72.222 0.00 0.00 42.00 3.20
945 1179 0.732880 CCGACGCACTCGAAATCAGT 60.733 55.000 2.39 0.00 46.14 3.41
970 1204 1.067071 GTGGAGGAAGGTCGTTGTAGG 60.067 57.143 0.00 0.00 0.00 3.18
973 1207 0.680061 GAGTGGAGGAAGGTCGTTGT 59.320 55.000 0.00 0.00 0.00 3.32
979 1213 2.058675 CGTTGGAGTGGAGGAAGGT 58.941 57.895 0.00 0.00 0.00 3.50
1000 1234 0.104304 GAAGGGATGACGTACCGCAT 59.896 55.000 0.00 0.00 0.00 4.73
1042 1276 0.460987 CGGGAGTGAGTGAATCCAGC 60.461 60.000 0.00 0.00 34.62 4.85
1090 1334 1.299541 CATGGCATCGTCCTGGTAAC 58.700 55.000 0.00 0.00 0.00 2.50
1160 1404 2.009774 GACCGTACGTAGTTGCTCCTA 58.990 52.381 15.21 0.00 37.78 2.94
1195 1439 2.634940 CCTCCATGTCGATATCCCTGTT 59.365 50.000 0.00 0.00 0.00 3.16
1316 1560 1.682257 GGTGGAAGAAGCAGAGCCT 59.318 57.895 0.00 0.00 0.00 4.58
1410 1654 4.898320 TCTGAAGATAAGTTGCAGCAAGA 58.102 39.130 8.49 0.00 0.00 3.02
1462 1707 6.772716 ACTCCAAAGATTTCTGCAGTTTTCTA 59.227 34.615 14.67 0.00 0.00 2.10
1699 1955 9.665719 TGAAAATTACTGTATGATAGTGCAAGA 57.334 29.630 0.00 0.00 0.00 3.02
2143 2400 2.551071 GCAGCCCTCTCTTTGTACAAGT 60.551 50.000 8.56 0.00 0.00 3.16
2144 2401 2.079925 GCAGCCCTCTCTTTGTACAAG 58.920 52.381 8.56 3.78 0.00 3.16
2152 2409 0.255318 CAATGGAGCAGCCCTCTCTT 59.745 55.000 2.45 0.00 40.57 2.85
2215 2472 0.029834 GCACACTGACAAGGCACAAG 59.970 55.000 0.00 0.00 0.00 3.16
2331 2588 9.824534 CAGCAAACAACTTAAATTTCAGTTTTT 57.175 25.926 13.79 11.61 30.48 1.94
2350 2607 2.908688 ACACCCCAAATTCAGCAAAC 57.091 45.000 0.00 0.00 0.00 2.93
2352 2609 3.237268 AGTACACCCCAAATTCAGCAA 57.763 42.857 0.00 0.00 0.00 3.91
2373 2630 7.605309 GGTACTTACAGTAACAAGCTAACCAAT 59.395 37.037 0.00 0.00 38.27 3.16
2446 2703 2.440247 CCCAAATCTGGCGGTCCC 60.440 66.667 0.00 0.00 41.99 4.46
2477 2735 2.238395 GCTCTCCTTCCTCACCAATTCT 59.762 50.000 0.00 0.00 0.00 2.40
2531 2806 2.838637 ATCCTCTCTTCCTTCCTCGT 57.161 50.000 0.00 0.00 0.00 4.18
2532 2807 3.005367 GCTTATCCTCTCTTCCTTCCTCG 59.995 52.174 0.00 0.00 0.00 4.63
2536 2811 4.892934 TCTGAGCTTATCCTCTCTTCCTTC 59.107 45.833 0.00 0.00 33.02 3.46
2537 2812 4.877773 TCTGAGCTTATCCTCTCTTCCTT 58.122 43.478 0.00 0.00 33.02 3.36
2540 2815 6.655078 ATTCTCTGAGCTTATCCTCTCTTC 57.345 41.667 0.00 0.00 33.02 2.87
2541 2816 8.004215 TCTTATTCTCTGAGCTTATCCTCTCTT 58.996 37.037 0.00 0.00 33.02 2.85
2564 2887 8.190784 GGTATCGTGGAATTGAATTTGAATCTT 58.809 33.333 0.00 0.00 0.00 2.40
2597 2922 1.267121 ATAAGCTCGAGTGGTGTGGT 58.733 50.000 15.13 0.00 0.00 4.16
2602 2927 3.128938 GCGGATATATAAGCTCGAGTGGT 59.871 47.826 15.13 2.05 0.00 4.16
2681 3011 4.500887 CGCGGGAGATTTGAATAGGAGTTA 60.501 45.833 0.00 0.00 0.00 2.24
3104 3437 6.840780 AAGATATTGGAAAAAGTGGGAGTG 57.159 37.500 0.00 0.00 0.00 3.51
3194 3529 2.304180 AGTGTATCTGAAGTTGCAGCCT 59.696 45.455 0.00 0.00 35.86 4.58
3341 3676 7.094032 ACAAAATCTCTCAATCCTGATGTTTCC 60.094 37.037 0.00 0.00 0.00 3.13
3531 3869 0.898320 AGGGTGAATCAGTGTCTCGG 59.102 55.000 0.00 0.00 0.00 4.63
3620 3958 4.141251 ACCAGTTCTTTTTGGAAGGAGCTA 60.141 41.667 0.00 0.00 37.89 3.32
3907 4830 3.001533 CCAACAAGCAAAACATGAACTGC 59.998 43.478 0.00 4.58 34.96 4.40
3955 5404 3.378427 GGGTATGAAAACTGATGTGGAGC 59.622 47.826 0.00 0.00 0.00 4.70
4159 5653 0.322277 ACAGAAGCTGGCACTGGATG 60.322 55.000 17.92 0.00 35.51 3.51
4197 5691 5.663106 TCCTAAACTCTTATGCTGTGGATCT 59.337 40.000 0.00 0.00 0.00 2.75
4207 5701 6.546428 TTCAGGAGGTCCTAAACTCTTATG 57.454 41.667 0.00 0.00 46.65 1.90
4400 5894 0.964358 AGAGCTTGCATCACTTGGGC 60.964 55.000 0.00 0.00 0.00 5.36
4410 5904 0.689055 ACAGATCACCAGAGCTTGCA 59.311 50.000 0.00 0.00 38.74 4.08
4411 5905 1.818642 AACAGATCACCAGAGCTTGC 58.181 50.000 0.00 0.00 38.74 4.01
4796 6293 1.630878 GGATTTCTGGGACTCACTGGT 59.369 52.381 0.00 0.00 0.00 4.00
4982 6479 5.931146 AGATTTGAGAGAAGTGCTAACTGTG 59.069 40.000 0.00 0.00 36.51 3.66
5267 6784 9.551734 CCAGTCATTGATGAATTACTAGATGAA 57.448 33.333 0.00 0.00 38.75 2.57
5268 6785 7.658982 GCCAGTCATTGATGAATTACTAGATGA 59.341 37.037 0.00 0.00 38.75 2.92
5269 6786 7.443272 TGCCAGTCATTGATGAATTACTAGATG 59.557 37.037 0.00 0.00 38.75 2.90
5270 6787 7.512130 TGCCAGTCATTGATGAATTACTAGAT 58.488 34.615 0.00 0.00 38.75 1.98
5271 6788 6.888105 TGCCAGTCATTGATGAATTACTAGA 58.112 36.000 0.00 0.00 38.75 2.43
5272 6789 7.255035 CCTTGCCAGTCATTGATGAATTACTAG 60.255 40.741 0.00 0.00 38.75 2.57
5273 6790 6.543465 CCTTGCCAGTCATTGATGAATTACTA 59.457 38.462 0.00 0.00 38.75 1.82
5274 6791 5.359009 CCTTGCCAGTCATTGATGAATTACT 59.641 40.000 0.00 0.00 38.75 2.24
5275 6792 5.450965 CCCTTGCCAGTCATTGATGAATTAC 60.451 44.000 0.00 0.00 38.75 1.89
5276 6793 4.646040 CCCTTGCCAGTCATTGATGAATTA 59.354 41.667 0.00 0.00 38.75 1.40
5321 6850 7.442364 TGTGTAGATTATAGAAAGCTCAATGCC 59.558 37.037 0.00 0.00 44.23 4.40
5517 7046 3.557577 TCATGCAATCAACTTGGTTCG 57.442 42.857 0.00 0.00 35.25 3.95
5525 7054 6.455113 GCAGACAAATTGATCATGCAATCAAC 60.455 38.462 14.49 3.95 40.33 3.18
5597 7126 7.419711 TCCTGAACCTATTAAGGAACTACTG 57.580 40.000 0.00 0.00 41.97 2.74
5625 7154 8.258007 TGTATATGAGAAGTAAGACAAACAGGG 58.742 37.037 0.00 0.00 0.00 4.45
5719 7248 2.810852 CAGAAACCAGAACTGAAGGAGC 59.189 50.000 3.19 0.00 34.07 4.70
5771 7301 8.281531 TGGATTCAGTTTGATTATAAGGGACAT 58.718 33.333 0.00 0.00 0.00 3.06
5835 7365 1.484038 TTGGGCATGGATTGGTTAGC 58.516 50.000 0.00 0.00 0.00 3.09
5873 7403 3.005791 GCCCTATGAAAGTGTTGCAACTT 59.994 43.478 28.61 15.92 42.21 2.66
5909 7439 2.424842 TAACTTGGTGGCTGCAGGGG 62.425 60.000 17.12 0.00 0.00 4.79
5936 10734 9.400638 GATAAGCTACAGTGTACTGAATATGTC 57.599 37.037 18.18 5.25 46.59 3.06
6008 10807 7.255277 GCTCTGTTGGAAAGAATCAAGTTAACT 60.255 37.037 1.12 1.12 0.00 2.24
6039 10838 4.097135 TGGAAGTACACACACATTTGTTGG 59.903 41.667 0.00 0.00 31.66 3.77
6152 10951 5.047021 GCAGGAGGAATGTGCTACTATATCA 60.047 44.000 0.00 0.00 34.23 2.15
6332 11131 2.354203 GCAACTCAAGGAGTACAGGAGG 60.354 54.545 0.00 0.00 42.59 4.30
6444 11243 1.135333 GGAGAGGTTACTTCGGCAGAG 59.865 57.143 0.00 0.00 0.00 3.35
6450 11249 4.022242 TCAAGTTCAGGAGAGGTTACTTCG 60.022 45.833 0.00 0.00 0.00 3.79
6494 11293 1.527034 TGCAGTTGCCTGAATCTGTC 58.473 50.000 1.06 0.00 41.50 3.51
6553 11353 4.336433 ACACTCTGTTGGTCACAAGATTTG 59.664 41.667 0.00 0.00 37.25 2.32
6691 11492 4.501559 CCGAATTTGATGTGAATGTGCATC 59.498 41.667 0.00 0.00 41.19 3.91
6782 11583 1.063488 GGTGGACAACGTTGCACAC 59.937 57.895 31.65 31.65 37.37 3.82
6789 11590 0.179056 CTGAACCTGGTGGACAACGT 60.179 55.000 0.00 0.00 37.04 3.99
6803 11604 2.094700 TGTGGCGTCTACATCTCTGAAC 60.095 50.000 0.00 0.00 0.00 3.18
6857 11658 6.438186 TGGATAGATCAATGTGAGGCATTA 57.562 37.500 0.00 0.00 45.33 1.90
6875 11676 1.700985 GGGGGCAAGGGTTTGGATA 59.299 57.895 0.00 0.00 34.79 2.59
6881 11682 3.654143 GGTACGGGGGCAAGGGTT 61.654 66.667 0.00 0.00 0.00 4.11
7080 11881 2.203938 TCAAGTTCCCCCGCCTCT 60.204 61.111 0.00 0.00 0.00 3.69
7117 11918 1.144716 CAGAGCAATCAGGGCGCTA 59.855 57.895 7.64 0.00 39.45 4.26
7137 11947 3.883830 AGAGCAAGTTCAGTCGATGAT 57.116 42.857 0.00 0.00 37.89 2.45
7261 12071 2.032634 GTGGCCGAAATCTGCGACA 61.033 57.895 0.00 0.00 35.56 4.35
7374 12184 2.903547 CGTTCAAACCCAGTGCCCG 61.904 63.158 0.00 0.00 0.00 6.13
7399 12209 1.807573 GCTTCAGAGAGGAACGGCG 60.808 63.158 4.80 4.80 0.00 6.46
7604 12415 2.238395 GCTCTCCTTCCTCACCAATTCT 59.762 50.000 0.00 0.00 0.00 2.40
7607 12418 1.558756 CAGCTCTCCTTCCTCACCAAT 59.441 52.381 0.00 0.00 0.00 3.16
7618 12431 2.042025 GCCCTCTCCAGCTCTCCT 60.042 66.667 0.00 0.00 0.00 3.69
7619 12432 3.535962 CGCCCTCTCCAGCTCTCC 61.536 72.222 0.00 0.00 0.00 3.71
7620 12433 2.441164 TCGCCCTCTCCAGCTCTC 60.441 66.667 0.00 0.00 0.00 3.20
7621 12434 2.296945 ATCTCGCCCTCTCCAGCTCT 62.297 60.000 0.00 0.00 0.00 4.09
7626 12444 3.531207 CGCATCTCGCCCTCTCCA 61.531 66.667 0.00 0.00 37.30 3.86
7659 12477 3.005367 GCTTATCCTCTCTTCCTTCCTCG 59.995 52.174 0.00 0.00 0.00 4.63
7663 12481 3.005367 CCGAGCTTATCCTCTCTTCCTTC 59.995 52.174 0.00 0.00 0.00 3.46
7664 12482 2.962421 CCGAGCTTATCCTCTCTTCCTT 59.038 50.000 0.00 0.00 0.00 3.36
7709 12529 0.734942 GTGGTGTGTCGGGTATCGTG 60.735 60.000 0.00 0.00 40.32 4.35
7724 12546 6.127591 GGATATATAAGCTCGAGTGATGTGGT 60.128 42.308 15.13 0.00 0.00 4.16
7729 12551 4.884744 AGCGGATATATAAGCTCGAGTGAT 59.115 41.667 15.13 7.61 34.48 3.06
7778 12601 2.723746 GTGTGGGCTGCACAAGTG 59.276 61.111 5.97 0.00 36.88 3.16
7779 12602 2.901840 CGTGTGGGCTGCACAAGT 60.902 61.111 5.97 0.00 36.71 3.16
7780 12603 4.332637 GCGTGTGGGCTGCACAAG 62.333 66.667 5.97 3.78 36.71 3.16
7781 12604 2.949705 TTAGCGTGTGGGCTGCACAA 62.950 55.000 5.97 0.00 44.50 3.33
7783 12606 2.668212 TTAGCGTGTGGGCTGCAC 60.668 61.111 0.50 0.00 44.50 4.57
7784 12607 2.668212 GTTAGCGTGTGGGCTGCA 60.668 61.111 0.50 0.00 44.50 4.41
7785 12608 2.668212 TGTTAGCGTGTGGGCTGC 60.668 61.111 0.00 0.00 44.50 5.25
7806 12633 3.017442 GGAGGTTTGAATAGGAGTTGGC 58.983 50.000 0.00 0.00 0.00 4.52
8183 13016 3.052490 AGAGCCATCTAGAACCTGTACCT 60.052 47.826 0.00 0.00 32.54 3.08
8226 13062 9.730705 TCATTAGAATCTTCATGAGTTTGAGTT 57.269 29.630 0.00 0.00 0.00 3.01
8824 14457 4.814294 GCTAGCCCACACCGACGG 62.814 72.222 13.61 13.61 0.00 4.79
9121 14754 6.848451 TGTTTGGTAAGACAGACAAAAACTC 58.152 36.000 0.00 0.00 33.22 3.01


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

AutoCloner maintained by Alex Coulton.