Multiple sequence alignment - TraesCS5A01G008600

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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 TraesCS5A01G008600 chr5A 100.000 5062 0 0 1 5062 6252439 6257500 0.000000e+00 9348
1 TraesCS5A01G008600 chr5A 83.821 513 47 23 2777 3271 6255709 6255215 5.970000e-124 455
2 TraesCS5A01G008600 chr5A 79.377 514 84 20 1304 1804 6609510 6610014 4.850000e-90 342
3 TraesCS5A01G008600 chr5B 93.099 3420 144 39 787 4183 37371811 37375161 0.000000e+00 4924
4 TraesCS5A01G008600 chr5B 89.977 888 69 8 4184 5062 37376041 37376917 0.000000e+00 1129
5 TraesCS5A01G008600 chr5B 85.554 893 95 22 814 1700 32564932 32565796 0.000000e+00 904
6 TraesCS5A01G008600 chr5B 88.270 682 54 12 4389 5061 37266126 37265462 0.000000e+00 793
7 TraesCS5A01G008600 chr5B 84.748 813 96 12 784 1595 32422987 32423772 0.000000e+00 789
8 TraesCS5A01G008600 chr5B 86.477 562 50 19 3448 4004 32646999 32647539 1.210000e-165 593
9 TraesCS5A01G008600 chr5B 92.067 416 20 4 35 450 37370947 37371349 1.580000e-159 573
10 TraesCS5A01G008600 chr5B 96.382 304 11 0 486 789 37371343 37371646 7.570000e-138 501
11 TraesCS5A01G008600 chr5B 75.947 1056 179 39 1250 2269 7862673 7861657 1.650000e-129 473
12 TraesCS5A01G008600 chr5B 81.421 366 52 6 1917 2271 7995752 7995392 8.290000e-73 285
13 TraesCS5A01G008600 chr5B 92.000 200 14 2 4184 4382 37274028 37273830 3.860000e-71 279
14 TraesCS5A01G008600 chr5B 90.099 202 14 2 3989 4184 32648162 32648363 1.810000e-64 257
15 TraesCS5A01G008600 chr5B 84.921 252 34 4 2777 3025 120574784 120575034 8.410000e-63 252
16 TraesCS5A01G008600 chr5D 75.872 1061 173 41 1281 2305 7493050 7494063 9.930000e-127 464
17 TraesCS5A01G008600 chr5D 83.247 388 49 12 3044 3424 556557895 556557517 4.850000e-90 342
18 TraesCS5A01G008600 chr5D 85.098 255 29 7 2777 3024 64239919 64240171 8.410000e-63 252
19 TraesCS5A01G008600 chr7B 83.548 389 41 14 3044 3425 683436848 683437220 4.850000e-90 342
20 TraesCS5A01G008600 chr7B 82.206 399 42 20 3036 3425 327459820 327460198 2.940000e-82 316
21 TraesCS5A01G008600 chr7B 81.137 387 55 11 3044 3425 268510003 268509630 1.380000e-75 294
22 TraesCS5A01G008600 chr7B 84.959 246 33 4 2781 3024 268509781 268510024 3.910000e-61 246
23 TraesCS5A01G008600 chr6D 83.290 389 48 10 3044 3425 461709986 461709608 4.850000e-90 342
24 TraesCS5A01G008600 chr4B 82.732 388 49 12 3044 3425 391542851 391542476 3.780000e-86 329
25 TraesCS5A01G008600 chr1B 81.795 390 51 13 3044 3425 186803747 186803370 4.920000e-80 309
26 TraesCS5A01G008600 chr1B 86.047 258 29 6 2774 3025 565853311 565853567 2.320000e-68 270
27 TraesCS5A01G008600 chr2D 80.720 389 55 12 3044 3424 648235945 648235569 8.290000e-73 285
28 TraesCS5A01G008600 chr2D 86.957 253 26 5 2777 3024 370332551 370332801 1.390000e-70 278
29 TraesCS5A01G008600 chr7D 83.895 267 31 11 2763 3024 164102965 164103224 1.410000e-60 244
30 TraesCS5A01G008600 chr4A 83.209 268 35 10 2763 3024 444087222 444086959 2.360000e-58 237


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 TraesCS5A01G008600 chr5A 6252439 6257500 5061 False 9348.00 9348 100.00000 1 5062 1 chr5A.!!$F1 5061
1 TraesCS5A01G008600 chr5A 6609510 6610014 504 False 342.00 342 79.37700 1304 1804 1 chr5A.!!$F2 500
2 TraesCS5A01G008600 chr5B 37370947 37376917 5970 False 1781.75 4924 92.88125 35 5062 4 chr5B.!!$F5 5027
3 TraesCS5A01G008600 chr5B 32564932 32565796 864 False 904.00 904 85.55400 814 1700 1 chr5B.!!$F2 886
4 TraesCS5A01G008600 chr5B 37265462 37266126 664 True 793.00 793 88.27000 4389 5061 1 chr5B.!!$R3 672
5 TraesCS5A01G008600 chr5B 32422987 32423772 785 False 789.00 789 84.74800 784 1595 1 chr5B.!!$F1 811
6 TraesCS5A01G008600 chr5B 7861657 7862673 1016 True 473.00 473 75.94700 1250 2269 1 chr5B.!!$R1 1019
7 TraesCS5A01G008600 chr5B 32646999 32648363 1364 False 425.00 593 88.28800 3448 4184 2 chr5B.!!$F4 736
8 TraesCS5A01G008600 chr5D 7493050 7494063 1013 False 464.00 464 75.87200 1281 2305 1 chr5D.!!$F1 1024

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
272 273 0.108138 CATGGACGAACCCAGAGACC 60.108 60.000 0.00 0.00 39.97 3.85 F
1089 1264 0.107703 TGATTCGCGCAAAGGATCCT 60.108 50.000 9.02 9.02 0.00 3.24 F
1345 1520 1.050204 AACACAACCGTACTAGGCCA 58.950 50.000 5.01 0.00 33.69 5.36 F
2323 2531 1.338389 ACGTCAGATTGGGTTAACGGG 60.338 52.381 0.00 0.00 34.63 5.28 F
3583 3805 0.106217 GAGGGAGAGGGAGAGGAGTG 60.106 65.000 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 1520 0.396974 CTCCTGCAGGTAGAGGAGCT 60.397 60.0 31.58 0.00 46.90 4.09 R
2973 3185 0.179040 TGGAGACCGGTGAAAACCAC 60.179 55.0 14.63 0.00 44.95 4.16 R
3058 3270 2.600470 TTCGTGTAGTTTTCACCGGT 57.400 45.0 0.00 0.00 32.86 5.28 R
3586 3808 0.452287 CGACCACGTGTACTCACTCG 60.452 60.0 15.65 5.02 44.92 4.18 R
4608 6355 0.456824 TCGACTTGCTCACATCGCTC 60.457 55.0 0.00 0.00 34.59 5.03 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
19 20 4.260355 CGCATGCCATTCAGCGGG 62.260 66.667 13.15 0.00 45.83 6.13
20 21 3.908081 GCATGCCATTCAGCGGGG 61.908 66.667 6.36 0.00 34.65 5.73
21 22 2.124193 CATGCCATTCAGCGGGGA 60.124 61.111 0.00 0.00 34.65 4.81
22 23 1.753848 CATGCCATTCAGCGGGGAA 60.754 57.895 0.00 0.00 34.65 3.97
23 24 1.454479 ATGCCATTCAGCGGGGAAG 60.454 57.895 0.00 0.00 34.65 3.46
24 25 2.830370 GCCATTCAGCGGGGAAGG 60.830 66.667 0.00 0.00 0.00 3.46
25 26 2.124151 CCATTCAGCGGGGAAGGG 60.124 66.667 5.38 5.38 41.67 3.95
26 27 2.124151 CATTCAGCGGGGAAGGGG 60.124 66.667 0.00 0.00 0.00 4.79
27 28 2.614013 ATTCAGCGGGGAAGGGGT 60.614 61.111 0.00 0.00 0.00 4.95
28 29 2.680370 ATTCAGCGGGGAAGGGGTC 61.680 63.158 0.00 0.00 0.00 4.46
49 50 1.578618 CAAGCGCACGATCGAAAGC 60.579 57.895 24.34 21.40 0.00 3.51
60 61 2.456000 TCGAAAGCGATGCCAAGAC 58.544 52.632 0.00 0.00 42.51 3.01
71 72 4.012895 CCAAGACGCGCACGCTTT 62.013 61.111 13.70 0.00 45.53 3.51
94 95 4.526770 GGTGCGCCGGTAGTAAAT 57.473 55.556 4.18 0.00 0.00 1.40
130 131 1.251527 ACGAGCCGAACCAGTCTCAT 61.252 55.000 1.50 0.00 0.00 2.90
131 132 0.803768 CGAGCCGAACCAGTCTCATG 60.804 60.000 0.00 0.00 0.00 3.07
134 135 1.204941 AGCCGAACCAGTCTCATGTAC 59.795 52.381 0.00 0.00 0.00 2.90
240 241 8.186163 GGAAGAAAAGAGGAAAACGTTCTAAAA 58.814 33.333 0.00 0.00 33.92 1.52
267 268 0.251165 AAACCCATGGACGAACCCAG 60.251 55.000 15.22 0.00 39.97 4.45
272 273 0.108138 CATGGACGAACCCAGAGACC 60.108 60.000 0.00 0.00 39.97 3.85
322 323 3.123621 CACGAGATGAGAAACCCTTTTCG 59.876 47.826 0.00 0.00 45.15 3.46
363 364 4.427394 GGCGCACGAGATGAGAAT 57.573 55.556 10.83 0.00 0.00 2.40
380 381 0.982852 AATGATGTCGAGGGCCTCCA 60.983 55.000 27.36 20.21 34.83 3.86
381 382 1.406065 ATGATGTCGAGGGCCTCCAG 61.406 60.000 27.36 14.74 34.83 3.86
382 383 2.765807 ATGTCGAGGGCCTCCAGG 60.766 66.667 27.36 13.99 38.53 4.45
383 384 3.317436 ATGTCGAGGGCCTCCAGGA 62.317 63.158 27.36 16.17 37.39 3.86
384 385 2.444895 GTCGAGGGCCTCCAGGAT 60.445 66.667 27.36 0.00 37.39 3.24
385 386 2.123251 TCGAGGGCCTCCAGGATC 60.123 66.667 27.36 1.97 37.39 3.36
450 451 1.306482 TGGCAGAGGAAGAGGAGGG 60.306 63.158 0.00 0.00 0.00 4.30
451 452 2.069430 GGCAGAGGAAGAGGAGGGG 61.069 68.421 0.00 0.00 0.00 4.79
452 453 2.069430 GCAGAGGAAGAGGAGGGGG 61.069 68.421 0.00 0.00 0.00 5.40
453 454 1.394151 CAGAGGAAGAGGAGGGGGT 59.606 63.158 0.00 0.00 0.00 4.95
454 455 0.637195 CAGAGGAAGAGGAGGGGGTA 59.363 60.000 0.00 0.00 0.00 3.69
455 456 0.938192 AGAGGAAGAGGAGGGGGTAG 59.062 60.000 0.00 0.00 0.00 3.18
456 457 0.935194 GAGGAAGAGGAGGGGGTAGA 59.065 60.000 0.00 0.00 0.00 2.59
457 458 1.505977 GAGGAAGAGGAGGGGGTAGAT 59.494 57.143 0.00 0.00 0.00 1.98
458 459 1.505977 AGGAAGAGGAGGGGGTAGATC 59.494 57.143 0.00 0.00 0.00 2.75
459 460 1.505977 GGAAGAGGAGGGGGTAGATCT 59.494 57.143 0.00 0.00 0.00 2.75
460 461 2.492010 GGAAGAGGAGGGGGTAGATCTC 60.492 59.091 0.00 0.00 0.00 2.75
461 462 1.163408 AGAGGAGGGGGTAGATCTCC 58.837 60.000 0.00 0.06 45.46 3.71
463 464 3.151048 GGAGGGGGTAGATCTCCAC 57.849 63.158 0.00 1.28 44.72 4.02
464 465 0.563672 GGAGGGGGTAGATCTCCACT 59.436 60.000 4.90 4.90 44.72 4.00
465 466 2.003937 GAGGGGGTAGATCTCCACTC 57.996 60.000 15.10 15.10 45.08 3.51
466 467 0.563672 AGGGGGTAGATCTCCACTCC 59.436 60.000 6.03 6.03 38.77 3.85
467 468 0.264955 GGGGGTAGATCTCCACTCCA 59.735 60.000 15.17 0.00 37.00 3.86
468 469 1.415200 GGGGTAGATCTCCACTCCAC 58.585 60.000 9.38 0.00 35.20 4.02
469 470 1.033574 GGGTAGATCTCCACTCCACG 58.966 60.000 0.00 0.00 0.00 4.94
470 471 1.409802 GGGTAGATCTCCACTCCACGA 60.410 57.143 0.00 0.00 0.00 4.35
471 472 1.950909 GGTAGATCTCCACTCCACGAG 59.049 57.143 0.00 0.00 35.52 4.18
472 473 1.335496 GTAGATCTCCACTCCACGAGC 59.665 57.143 0.00 0.00 32.04 5.03
473 474 1.040339 AGATCTCCACTCCACGAGCC 61.040 60.000 0.00 0.00 32.04 4.70
474 475 2.022240 GATCTCCACTCCACGAGCCC 62.022 65.000 0.00 0.00 32.04 5.19
475 476 2.522198 ATCTCCACTCCACGAGCCCT 62.522 60.000 0.00 0.00 32.04 5.19
476 477 1.379977 CTCCACTCCACGAGCCCTA 60.380 63.158 0.00 0.00 32.04 3.53
477 478 1.379977 TCCACTCCACGAGCCCTAG 60.380 63.158 0.00 0.00 32.04 3.02
478 479 1.379977 CCACTCCACGAGCCCTAGA 60.380 63.158 0.00 0.00 32.04 2.43
479 480 0.757188 CCACTCCACGAGCCCTAGAT 60.757 60.000 0.00 0.00 32.04 1.98
480 481 0.671251 CACTCCACGAGCCCTAGATC 59.329 60.000 0.00 0.00 32.04 2.75
481 482 0.553819 ACTCCACGAGCCCTAGATCT 59.446 55.000 0.00 0.00 32.04 2.75
482 483 1.243902 CTCCACGAGCCCTAGATCTC 58.756 60.000 0.00 0.00 0.00 2.75
483 484 0.178987 TCCACGAGCCCTAGATCTCC 60.179 60.000 0.00 0.00 0.00 3.71
484 485 0.178975 CCACGAGCCCTAGATCTCCT 60.179 60.000 0.00 0.00 0.00 3.69
485 486 0.958091 CACGAGCCCTAGATCTCCTG 59.042 60.000 0.00 0.00 0.00 3.86
486 487 0.847373 ACGAGCCCTAGATCTCCTGA 59.153 55.000 0.00 0.00 0.00 3.86
487 488 1.243902 CGAGCCCTAGATCTCCTGAC 58.756 60.000 0.00 0.00 0.00 3.51
488 489 1.243902 GAGCCCTAGATCTCCTGACG 58.756 60.000 0.00 0.00 0.00 4.35
489 490 0.847373 AGCCCTAGATCTCCTGACGA 59.153 55.000 0.00 0.00 0.00 4.20
490 491 1.202879 AGCCCTAGATCTCCTGACGAG 60.203 57.143 0.00 0.00 40.30 4.18
491 492 1.243902 CCCTAGATCTCCTGACGAGC 58.756 60.000 0.00 0.00 38.62 5.03
512 513 0.179000 AGCTGGTCGAACATCCCATC 59.821 55.000 2.20 0.00 0.00 3.51
545 546 3.777925 CGGCCTTTGAGCACGACG 61.778 66.667 0.00 0.00 0.00 5.12
734 735 1.544093 CCCTACATACCCGACGAGCTA 60.544 57.143 0.00 0.00 0.00 3.32
747 748 1.074084 ACGAGCTAGCTGATAGGGCTA 59.926 52.381 24.99 0.00 40.74 3.93
810 978 1.284982 CGTGCTTGTTCTCTGACCCG 61.285 60.000 0.00 0.00 0.00 5.28
1089 1264 0.107703 TGATTCGCGCAAAGGATCCT 60.108 50.000 9.02 9.02 0.00 3.24
1160 1335 3.182152 AGGCTAAGGTGAGCTTCCTAAA 58.818 45.455 0.00 3.69 42.43 1.85
1161 1336 3.198853 AGGCTAAGGTGAGCTTCCTAAAG 59.801 47.826 0.00 11.96 42.43 1.85
1162 1337 3.055021 GGCTAAGGTGAGCTTCCTAAAGT 60.055 47.826 0.00 0.38 42.43 2.66
1163 1338 4.565861 GGCTAAGGTGAGCTTCCTAAAGTT 60.566 45.833 0.00 0.07 42.43 2.66
1164 1339 5.004448 GCTAAGGTGAGCTTCCTAAAGTTT 58.996 41.667 0.00 0.00 39.50 2.66
1235 1410 8.420222 AGACTTTCCTGATAGTTGATATCACAG 58.580 37.037 4.48 8.92 44.33 3.66
1242 1417 7.866898 CCTGATAGTTGATATCACAGAACTCTG 59.133 40.741 17.50 5.15 44.33 3.35
1294 1469 1.454653 GTGACGTAACTTTCACCGCTC 59.545 52.381 0.00 0.00 36.85 5.03
1345 1520 1.050204 AACACAACCGTACTAGGCCA 58.950 50.000 5.01 0.00 33.69 5.36
1410 1585 4.082245 AGGTTGAAGTTGACAAACCAGTTG 60.082 41.667 8.36 0.00 43.43 3.16
1618 1797 8.610248 TTCACTTTATGTTTTCTATTCCGACA 57.390 30.769 0.00 0.00 0.00 4.35
1848 2030 8.836413 CCTATTGTTCTTTGTTAGTTCTGTTGA 58.164 33.333 0.00 0.00 0.00 3.18
1872 2054 7.979537 TGAGTAATACACATGTCTTGTATGGTC 59.020 37.037 7.90 6.44 39.58 4.02
1881 2063 8.676401 CACATGTCTTGTATGGTCAATAATTCA 58.324 33.333 0.00 0.00 36.57 2.57
2054 2246 7.921786 TTGGTCTTATTGTTGAGAAGGTATG 57.078 36.000 0.00 0.00 0.00 2.39
2191 2399 6.885918 TCATATGCTGAGAAACTTGGAATCAA 59.114 34.615 0.00 0.00 0.00 2.57
2259 2467 4.114058 ACAATTGAGGTATGTGCATTGC 57.886 40.909 13.59 0.46 0.00 3.56
2288 2496 8.815565 TTTATTAGTTACTTGCCAATCCATCA 57.184 30.769 0.00 0.00 0.00 3.07
2305 2513 6.286240 TCCATCATAGATTAATCTCCCACG 57.714 41.667 21.17 8.78 38.32 4.94
2312 2520 5.878406 AGATTAATCTCCCACGTCAGATT 57.122 39.130 12.37 15.01 41.35 2.40
2323 2531 1.338389 ACGTCAGATTGGGTTAACGGG 60.338 52.381 0.00 0.00 34.63 5.28
2328 2536 2.888414 CAGATTGGGTTAACGGGTTGTT 59.112 45.455 0.00 0.00 44.78 2.83
2334 2542 5.197682 TGGGTTAACGGGTTGTTTTATTG 57.802 39.130 0.00 0.00 42.09 1.90
2405 2613 8.205512 TCTAGTTAATGTGGTGTTAGTTCAACA 58.794 33.333 0.00 0.00 44.97 3.33
2415 2623 4.798882 TGTTAGTTCAACAACCTCCCAAT 58.201 39.130 0.00 0.00 44.20 3.16
2421 2629 4.870123 TCAACAACCTCCCAATTCATTG 57.130 40.909 0.00 0.00 37.52 2.82
2501 2711 7.444629 TCAATTTGATGGAAGAGCATATAGC 57.555 36.000 0.00 0.00 46.19 2.97
2522 2732 3.799366 CTTACATTATACGGTGGGCACA 58.201 45.455 0.00 0.00 0.00 4.57
2552 2762 6.971726 TCCCGTAGCTAAGATCAAATAAGA 57.028 37.500 8.37 0.00 0.00 2.10
2604 2814 7.679453 TGTTAAATTGTACTTCTAGGGGGAGTA 59.321 37.037 0.00 0.00 0.00 2.59
2605 2815 8.712103 GTTAAATTGTACTTCTAGGGGGAGTAT 58.288 37.037 0.00 0.00 0.00 2.12
2727 2938 9.678941 TGATGTTCATTTGATAGTATCGAGTAC 57.321 33.333 5.68 0.00 0.00 2.73
2728 2939 9.678941 GATGTTCATTTGATAGTATCGAGTACA 57.321 33.333 5.68 3.89 35.67 2.90
2799 3010 9.247861 AGTATGGAGCTATGAAAAAGACAAATT 57.752 29.630 0.00 0.00 0.00 1.82
2809 3020 7.703298 TGAAAAAGACAAATTCAGCAATGAG 57.297 32.000 0.00 0.00 0.00 2.90
2812 3023 8.807667 AAAAAGACAAATTCAGCAATGAGTAG 57.192 30.769 0.00 0.00 0.00 2.57
2814 3025 6.492007 AGACAAATTCAGCAATGAGTAGTG 57.508 37.500 0.00 0.00 0.00 2.74
2815 3026 6.233434 AGACAAATTCAGCAATGAGTAGTGA 58.767 36.000 0.00 0.00 0.00 3.41
2816 3027 6.148480 AGACAAATTCAGCAATGAGTAGTGAC 59.852 38.462 0.00 0.00 0.00 3.67
2817 3028 5.764686 ACAAATTCAGCAATGAGTAGTGACA 59.235 36.000 0.00 0.00 0.00 3.58
2818 3029 6.432162 ACAAATTCAGCAATGAGTAGTGACAT 59.568 34.615 0.00 0.00 0.00 3.06
2819 3030 7.040201 ACAAATTCAGCAATGAGTAGTGACATT 60.040 33.333 0.00 0.00 37.22 2.71
2820 3031 8.453320 CAAATTCAGCAATGAGTAGTGACATTA 58.547 33.333 0.00 0.00 35.39 1.90
2821 3032 6.968131 TTCAGCAATGAGTAGTGACATTAC 57.032 37.500 0.00 0.00 35.39 1.89
2822 3033 6.286240 TCAGCAATGAGTAGTGACATTACT 57.714 37.500 10.16 10.16 35.39 2.24
2823 3034 6.101997 TCAGCAATGAGTAGTGACATTACTG 58.898 40.000 14.71 0.00 43.48 2.74
2824 3035 5.871524 CAGCAATGAGTAGTGACATTACTGT 59.128 40.000 14.71 1.84 40.27 3.55
2825 3036 6.369890 CAGCAATGAGTAGTGACATTACTGTT 59.630 38.462 14.71 7.27 40.27 3.16
2826 3037 6.936900 AGCAATGAGTAGTGACATTACTGTTT 59.063 34.615 14.71 5.99 35.14 2.83
2827 3038 7.017645 GCAATGAGTAGTGACATTACTGTTTG 58.982 38.462 14.71 16.17 35.14 2.93
2828 3039 7.521529 CAATGAGTAGTGACATTACTGTTTGG 58.478 38.462 14.71 0.00 35.14 3.28
2860 3072 8.975410 TGAATGCTGATTTGTCTTTTTCATAG 57.025 30.769 0.00 0.00 0.00 2.23
2868 3080 8.239314 TGATTTGTCTTTTTCATAGCTCACATC 58.761 33.333 0.00 0.00 0.00 3.06
2871 3083 4.034510 GTCTTTTTCATAGCTCACATCCCG 59.965 45.833 0.00 0.00 0.00 5.14
2928 3140 5.104259 AGAACATCACCCTCTTAACATCC 57.896 43.478 0.00 0.00 0.00 3.51
2945 3157 9.987272 CTTAACATCCCTTCTTTTGAGATTTTT 57.013 29.630 0.00 0.00 0.00 1.94
2973 3185 3.537806 AGTTCAAAACATCGTTTACGCG 58.462 40.909 3.53 3.53 39.60 6.01
2984 3196 1.745566 GTTTACGCGTGGTTTTCACC 58.254 50.000 24.59 0.00 43.23 4.02
3024 3236 5.880164 TGTTTCCGTATGATATTCTCCCA 57.120 39.130 0.00 0.00 0.00 4.37
3042 3254 3.721087 CCAGGTTATGGGAGAACAAGT 57.279 47.619 0.00 0.00 46.36 3.16
3058 3270 3.283751 ACAAGTCAACATTCGGTGGAAA 58.716 40.909 0.00 0.00 35.40 3.13
3059 3271 3.066203 ACAAGTCAACATTCGGTGGAAAC 59.934 43.478 0.00 0.00 35.40 2.78
3060 3272 2.227194 AGTCAACATTCGGTGGAAACC 58.773 47.619 0.00 0.00 35.40 3.27
3073 3285 2.944349 GTGGAAACCGGTGAAAACTACA 59.056 45.455 8.52 0.00 0.00 2.74
3075 3287 2.032636 GGAAACCGGTGAAAACTACACG 60.033 50.000 8.52 0.00 38.90 4.49
3096 3311 8.918961 ACACGAAAATATGTTTCAAAGTTTCA 57.081 26.923 0.00 0.00 0.00 2.69
3143 3358 2.173569 AGAGGGTGATGTTCTATTGCCC 59.826 50.000 0.00 0.00 35.04 5.36
3174 3389 6.869315 TTTCAGATTCAAACACATTACGGA 57.131 33.333 0.00 0.00 0.00 4.69
3271 3487 1.739466 TGTCTTTCCATTGCTCGCATC 59.261 47.619 0.00 0.00 0.00 3.91
3273 3489 0.383231 CTTTCCATTGCTCGCATCCC 59.617 55.000 0.00 0.00 0.00 3.85
3281 3497 3.945981 TTGCTCGCATCCCGTAATATA 57.054 42.857 0.00 0.00 38.35 0.86
3284 3500 3.194755 TGCTCGCATCCCGTAATATATGT 59.805 43.478 0.00 0.00 38.35 2.29
3392 3608 9.883142 TTCAAACATAGTTTCCATGAAGTTTTT 57.117 25.926 0.00 0.00 0.00 1.94
3417 3633 7.689446 TTTGAATGTTGGTTTCCGTATGATA 57.311 32.000 0.00 0.00 0.00 2.15
3418 3634 7.873719 TTGAATGTTGGTTTCCGTATGATAT 57.126 32.000 0.00 0.00 0.00 1.63
3419 3635 7.873719 TGAATGTTGGTTTCCGTATGATATT 57.126 32.000 0.00 0.00 0.00 1.28
3472 3688 7.285401 CCATGGGTTATACAGTATGCTCTTTTT 59.715 37.037 2.85 0.00 42.53 1.94
3482 3698 0.555769 TGCTCTTTTTGGGGAGGTGT 59.444 50.000 0.00 0.00 0.00 4.16
3515 3736 7.477144 TGAAATATCTGTTGTAGCCATTACG 57.523 36.000 0.00 0.00 34.87 3.18
3521 3742 6.656314 TCTGTTGTAGCCATTACGTATTTG 57.344 37.500 0.00 0.00 34.87 2.32
3574 3796 1.541672 GAGAGGGAGAGGGAGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
3575 3797 0.996762 GAGAGGGAGAGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
3576 3798 0.998945 AGAGGGAGAGGGAGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
3577 3799 0.996762 GAGGGAGAGGGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
3578 3800 0.998945 AGGGAGAGGGAGAGGGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
3580 3802 0.996762 GGAGAGGGAGAGGGAGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
3582 3804 0.254107 AGAGGGAGAGGGAGAGGAGT 60.254 60.000 0.00 0.00 0.00 3.85
3583 3805 0.106217 GAGGGAGAGGGAGAGGAGTG 60.106 65.000 0.00 0.00 0.00 3.51
3584 3806 0.553862 AGGGAGAGGGAGAGGAGTGA 60.554 60.000 0.00 0.00 0.00 3.41
3585 3807 0.560688 GGGAGAGGGAGAGGAGTGAT 59.439 60.000 0.00 0.00 0.00 3.06
3586 3808 1.480498 GGGAGAGGGAGAGGAGTGATC 60.480 61.905 0.00 0.00 0.00 2.92
3587 3809 1.604604 GAGAGGGAGAGGAGTGATCG 58.395 60.000 0.00 0.00 0.00 3.69
3588 3810 1.142060 GAGAGGGAGAGGAGTGATCGA 59.858 57.143 0.00 0.00 0.00 3.59
3665 3888 8.515414 GTGACAGACTCTTGGCTTTTATAATTT 58.485 33.333 0.00 0.00 0.00 1.82
3926 4149 7.154656 CCGTAATTGTATCTGATCATGGAGAA 58.845 38.462 0.00 0.00 0.00 2.87
4004 4862 6.367374 TCACCTTGAAGTCATTGGTGTATA 57.633 37.500 22.39 9.84 44.15 1.47
4167 5031 8.211181 CGAGTCTTAATTTATCGCATTTCTCTC 58.789 37.037 0.00 0.00 0.00 3.20
4228 5971 3.716353 TCACTTATATCACCATGGCAGGT 59.284 43.478 13.04 3.36 44.48 4.00
4250 5993 5.050159 GGTCCAGCACAAATCAATTTTGAAC 60.050 40.000 5.17 0.00 46.36 3.18
4314 6058 4.696479 ATAGTAAAGACTGGGAGCATGG 57.304 45.455 0.00 0.00 36.28 3.66
4358 6102 4.280929 GCAGGGGAAAGTAACAATCAAGTT 59.719 41.667 0.00 0.00 35.55 2.66
4411 6155 4.814771 TGCATGAAGAATAGTGATGCTCAG 59.185 41.667 0.00 0.00 40.11 3.35
4418 6162 3.876274 ATAGTGATGCTCAGACGTTGT 57.124 42.857 0.00 0.00 0.00 3.32
4433 6177 1.242076 GTTGTTGGTGCAGATCAGCT 58.758 50.000 11.68 0.00 43.32 4.24
4437 6181 4.215349 GGTGCAGATCAGCTCCAC 57.785 61.111 22.08 8.15 45.15 4.02
4445 6189 1.411977 AGATCAGCTCCACGATCAAGG 59.588 52.381 12.75 0.00 40.45 3.61
4483 6230 3.716353 AGGTGGACATTAGTGATGGCATA 59.284 43.478 0.00 0.00 46.30 3.14
4593 6340 9.656323 TTAGCTAGGATCTAAAAGGACTGAATA 57.344 33.333 0.00 0.00 0.00 1.75
4607 6354 4.651045 GGACTGAATAAAATGGATTGCCCT 59.349 41.667 0.00 0.00 35.38 5.19
4608 6355 5.452356 GGACTGAATAAAATGGATTGCCCTG 60.452 44.000 0.00 0.00 35.38 4.45
4609 6356 5.271598 ACTGAATAAAATGGATTGCCCTGA 58.728 37.500 0.00 0.00 35.38 3.86
4610 6357 5.361857 ACTGAATAAAATGGATTGCCCTGAG 59.638 40.000 0.00 0.00 35.38 3.35
4611 6358 4.099881 TGAATAAAATGGATTGCCCTGAGC 59.900 41.667 0.00 0.00 44.14 4.26
4615 6362 0.536687 ATGGATTGCCCTGAGCGATG 60.537 55.000 0.00 0.00 46.27 3.84
4616 6363 1.153086 GGATTGCCCTGAGCGATGT 60.153 57.895 0.00 0.00 46.27 3.06
4617 6364 1.442526 GGATTGCCCTGAGCGATGTG 61.443 60.000 0.00 0.00 46.27 3.21
4618 6365 0.462581 GATTGCCCTGAGCGATGTGA 60.463 55.000 0.00 0.00 46.27 3.58
4649 6398 3.567164 ACGTCGATATTAACCTCGTCCAT 59.433 43.478 0.00 0.00 36.33 3.41
4652 6401 5.619309 CGTCGATATTAACCTCGTCCATGAT 60.619 44.000 0.00 0.00 36.33 2.45
4656 6405 9.350951 TCGATATTAACCTCGTCCATGATATAT 57.649 33.333 0.00 0.00 36.33 0.86
4665 6414 6.378564 CCTCGTCCATGATATATTGGTAGACT 59.621 42.308 0.00 0.00 34.48 3.24
4667 6416 6.946009 TCGTCCATGATATATTGGTAGACTGA 59.054 38.462 0.00 1.34 34.48 3.41
4691 6443 4.643387 GCCAAGACCACCTGCGGT 62.643 66.667 0.00 0.00 43.91 5.68
4904 6656 1.992557 TCCCTGTTAATGCCTCAACCT 59.007 47.619 0.00 0.00 0.00 3.50
4905 6657 3.186283 TCCCTGTTAATGCCTCAACCTA 58.814 45.455 0.00 0.00 0.00 3.08
4906 6658 3.785887 TCCCTGTTAATGCCTCAACCTAT 59.214 43.478 0.00 0.00 0.00 2.57
4907 6659 4.972568 TCCCTGTTAATGCCTCAACCTATA 59.027 41.667 0.00 0.00 0.00 1.31
5013 6770 4.078363 AGTTTGTTCGTGTTGTTGACTG 57.922 40.909 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.918129 CCGCTGAATGGCATGCGC 62.918 66.667 21.12 15.98 40.41 6.09
2 3 4.260355 CCCGCTGAATGGCATGCG 62.260 66.667 19.99 19.99 40.98 4.73
3 4 3.908081 CCCCGCTGAATGGCATGC 61.908 66.667 9.90 9.90 0.00 4.06
4 5 1.731433 CTTCCCCGCTGAATGGCATG 61.731 60.000 0.00 0.00 0.00 4.06
5 6 1.454479 CTTCCCCGCTGAATGGCAT 60.454 57.895 0.00 0.00 0.00 4.40
6 7 2.045045 CTTCCCCGCTGAATGGCA 60.045 61.111 0.00 0.00 0.00 4.92
7 8 2.830370 CCTTCCCCGCTGAATGGC 60.830 66.667 0.00 0.00 0.00 4.40
8 9 2.124151 CCCTTCCCCGCTGAATGG 60.124 66.667 0.00 0.00 0.00 3.16
9 10 2.124151 CCCCTTCCCCGCTGAATG 60.124 66.667 0.00 0.00 0.00 2.67
10 11 2.614013 ACCCCTTCCCCGCTGAAT 60.614 61.111 0.00 0.00 0.00 2.57
11 12 3.327404 GACCCCTTCCCCGCTGAA 61.327 66.667 0.00 0.00 0.00 3.02
17 18 4.426313 CTTGGCGACCCCTTCCCC 62.426 72.222 0.00 0.00 0.00 4.81
29 30 2.886512 CTTTCGATCGTGCGCTTGGC 62.887 60.000 15.94 0.00 43.96 4.52
30 31 1.059369 CTTTCGATCGTGCGCTTGG 59.941 57.895 15.94 0.00 0.00 3.61
31 32 1.578618 GCTTTCGATCGTGCGCTTG 60.579 57.895 15.94 0.00 0.00 4.01
32 33 2.778679 GCTTTCGATCGTGCGCTT 59.221 55.556 15.94 0.00 0.00 4.68
33 34 3.545481 CGCTTTCGATCGTGCGCT 61.545 61.111 27.61 0.00 41.85 5.92
49 50 4.505217 GTGCGCGTCTTGGCATCG 62.505 66.667 8.43 0.00 41.83 3.84
77 78 0.741927 ACATTTACTACCGGCGCACC 60.742 55.000 10.83 0.00 0.00 5.01
78 79 1.081094 AACATTTACTACCGGCGCAC 58.919 50.000 10.83 0.00 0.00 5.34
79 80 1.733360 GAAACATTTACTACCGGCGCA 59.267 47.619 10.83 0.00 0.00 6.09
94 95 4.022676 GGCTCGTTTTGATTTAGGGAAACA 60.023 41.667 0.00 0.00 32.91 2.83
112 113 0.803768 CATGAGACTGGTTCGGCTCG 60.804 60.000 0.00 0.00 0.00 5.03
130 131 2.663520 CCAGCGCAACACCGTACA 60.664 61.111 11.47 0.00 0.00 2.90
131 132 2.663852 ACCAGCGCAACACCGTAC 60.664 61.111 11.47 0.00 0.00 3.67
240 241 3.301274 TCGTCCATGGGTTTTCCTTTTT 58.699 40.909 13.02 0.00 40.46 1.94
252 253 0.108138 GTCTCTGGGTTCGTCCATGG 60.108 60.000 4.97 4.97 36.05 3.66
267 268 3.450115 CCACGTCGAGGGGGTCTC 61.450 72.222 18.38 0.00 40.70 3.36
363 364 2.038813 TGGAGGCCCTCGACATCA 59.961 61.111 4.29 0.00 0.00 3.07
380 381 2.203771 GGTCATCGCCGAGGATCCT 61.204 63.158 16.13 16.13 0.00 3.24
381 382 2.340443 GGTCATCGCCGAGGATCC 59.660 66.667 4.25 2.48 0.00 3.36
382 383 2.340443 GGGTCATCGCCGAGGATC 59.660 66.667 4.25 3.57 0.00 3.36
383 384 3.606662 CGGGTCATCGCCGAGGAT 61.607 66.667 4.25 0.00 32.09 3.24
408 409 4.760047 GCCTCTTCGCTTCCCGCA 62.760 66.667 0.00 0.00 39.08 5.69
450 451 1.033574 CGTGGAGTGGAGATCTACCC 58.966 60.000 1.43 0.00 0.00 3.69
451 452 1.950909 CTCGTGGAGTGGAGATCTACC 59.049 57.143 1.43 3.43 31.90 3.18
452 453 1.335496 GCTCGTGGAGTGGAGATCTAC 59.665 57.143 0.00 0.00 31.90 2.59
453 454 1.681538 GCTCGTGGAGTGGAGATCTA 58.318 55.000 0.00 0.00 31.90 1.98
454 455 1.040339 GGCTCGTGGAGTGGAGATCT 61.040 60.000 0.00 0.00 31.90 2.75
455 456 1.439644 GGCTCGTGGAGTGGAGATC 59.560 63.158 0.00 0.00 31.90 2.75
456 457 2.060980 GGGCTCGTGGAGTGGAGAT 61.061 63.158 0.00 0.00 31.90 2.75
457 458 1.859841 TAGGGCTCGTGGAGTGGAGA 61.860 60.000 0.00 0.00 31.90 3.71
458 459 1.379977 TAGGGCTCGTGGAGTGGAG 60.380 63.158 0.00 0.00 31.39 3.86
459 460 1.379977 CTAGGGCTCGTGGAGTGGA 60.380 63.158 0.00 0.00 31.39 4.02
460 461 0.757188 ATCTAGGGCTCGTGGAGTGG 60.757 60.000 0.00 0.00 31.39 4.00
461 462 0.671251 GATCTAGGGCTCGTGGAGTG 59.329 60.000 0.00 0.00 31.39 3.51
462 463 0.553819 AGATCTAGGGCTCGTGGAGT 59.446 55.000 0.00 0.00 31.39 3.85
463 464 1.243902 GAGATCTAGGGCTCGTGGAG 58.756 60.000 0.00 0.00 0.00 3.86
464 465 0.178987 GGAGATCTAGGGCTCGTGGA 60.179 60.000 0.00 0.00 31.95 4.02
465 466 0.178975 AGGAGATCTAGGGCTCGTGG 60.179 60.000 0.00 0.00 31.95 4.94
466 467 0.958091 CAGGAGATCTAGGGCTCGTG 59.042 60.000 15.77 15.77 39.62 4.35
467 468 0.847373 TCAGGAGATCTAGGGCTCGT 59.153 55.000 0.00 4.96 31.95 4.18
468 469 1.243902 GTCAGGAGATCTAGGGCTCG 58.756 60.000 0.00 0.00 31.95 5.03
469 470 1.202830 TCGTCAGGAGATCTAGGGCTC 60.203 57.143 0.00 4.71 0.00 4.70
470 471 0.847373 TCGTCAGGAGATCTAGGGCT 59.153 55.000 0.00 0.00 0.00 5.19
471 472 1.243902 CTCGTCAGGAGATCTAGGGC 58.756 60.000 0.00 0.00 46.23 5.19
472 473 1.202879 AGCTCGTCAGGAGATCTAGGG 60.203 57.143 0.00 0.00 46.23 3.53
473 474 2.270352 AGCTCGTCAGGAGATCTAGG 57.730 55.000 0.00 0.00 46.23 3.02
474 475 2.742053 GCTAGCTCGTCAGGAGATCTAG 59.258 54.545 7.70 2.02 46.23 2.43
475 476 2.370519 AGCTAGCTCGTCAGGAGATCTA 59.629 50.000 12.68 0.00 46.23 1.98
476 477 1.142870 AGCTAGCTCGTCAGGAGATCT 59.857 52.381 12.68 0.00 46.23 2.75
477 478 1.266718 CAGCTAGCTCGTCAGGAGATC 59.733 57.143 16.15 0.00 46.23 2.75
478 479 1.317613 CAGCTAGCTCGTCAGGAGAT 58.682 55.000 16.15 0.00 46.23 2.75
479 480 0.749818 CCAGCTAGCTCGTCAGGAGA 60.750 60.000 16.15 0.00 46.23 3.71
480 481 1.034838 ACCAGCTAGCTCGTCAGGAG 61.035 60.000 21.49 6.29 46.06 3.69
481 482 1.000771 ACCAGCTAGCTCGTCAGGA 60.001 57.895 21.49 0.00 0.00 3.86
482 483 1.435515 GACCAGCTAGCTCGTCAGG 59.564 63.158 30.34 22.88 34.93 3.86
483 484 1.063327 CGACCAGCTAGCTCGTCAG 59.937 63.158 32.68 23.74 34.57 3.51
484 485 0.958876 TTCGACCAGCTAGCTCGTCA 60.959 55.000 32.68 20.99 34.57 4.35
485 486 0.523757 GTTCGACCAGCTAGCTCGTC 60.524 60.000 26.97 26.97 32.17 4.20
486 487 1.241990 TGTTCGACCAGCTAGCTCGT 61.242 55.000 15.32 15.32 0.00 4.18
487 488 0.101399 ATGTTCGACCAGCTAGCTCG 59.899 55.000 16.15 16.28 0.00 5.03
488 489 1.537135 GGATGTTCGACCAGCTAGCTC 60.537 57.143 16.15 2.95 0.00 4.09
489 490 0.461961 GGATGTTCGACCAGCTAGCT 59.538 55.000 12.68 12.68 0.00 3.32
490 491 0.530870 GGGATGTTCGACCAGCTAGC 60.531 60.000 6.62 6.62 0.00 3.42
491 492 0.824109 TGGGATGTTCGACCAGCTAG 59.176 55.000 0.00 0.00 0.00 3.42
512 513 0.943359 GCCGCGAAGATCATCTCTGG 60.943 60.000 8.23 0.00 33.29 3.86
545 546 2.496070 GTTTTACTTGGGATTGGGCTCC 59.504 50.000 0.00 0.00 34.31 4.70
597 598 4.222588 AGTCTGTCTTGATGAGGAGGAAAG 59.777 45.833 0.00 0.00 0.00 2.62
701 702 1.843368 TGTAGGGTTCGTAGAGTGGG 58.157 55.000 0.00 0.00 38.43 4.61
734 735 1.981495 GGATTGGTAGCCCTATCAGCT 59.019 52.381 5.96 0.00 42.66 4.24
747 748 2.203153 GCGTATGCCCGGATTGGT 60.203 61.111 0.73 0.00 35.15 3.67
779 780 3.357079 AGCACGAAGGCTTTGGCG 61.357 61.111 18.48 11.87 42.71 5.69
810 978 2.190578 CGGATGGGAAGGAGGCAC 59.809 66.667 0.00 0.00 0.00 5.01
955 1130 5.343307 AAGCAAACCAAAAGTCAGAACAT 57.657 34.783 0.00 0.00 0.00 2.71
1263 1438 6.476380 TGAAAGTTACGTCACTACATTTTCGT 59.524 34.615 2.20 0.00 35.73 3.85
1277 1452 1.612463 AGAGAGCGGTGAAAGTTACGT 59.388 47.619 0.00 0.00 0.00 3.57
1345 1520 0.396974 CTCCTGCAGGTAGAGGAGCT 60.397 60.000 31.58 0.00 46.90 4.09
1410 1585 1.538047 TCAATGAAAGTGGGCAGCTC 58.462 50.000 0.00 0.00 29.44 4.09
1848 2030 7.847096 TGACCATACAAGACATGTGTATTACT 58.153 34.615 1.15 0.00 43.77 2.24
1881 2063 8.134895 CACACAAATCTTAGGTGTAACATTGTT 58.865 33.333 7.30 7.30 43.41 2.83
1891 2073 7.447374 TGAATTACCACACAAATCTTAGGTG 57.553 36.000 0.00 0.00 38.47 4.00
1892 2074 8.650143 ATTGAATTACCACACAAATCTTAGGT 57.350 30.769 0.00 0.00 0.00 3.08
2071 2277 7.246171 AGGTGAAACTAGTAACATGAGTGAT 57.754 36.000 0.00 0.00 36.74 3.06
2092 2298 5.815581 TGCATATGAGGAACAACTTTAGGT 58.184 37.500 6.97 0.00 0.00 3.08
2145 2353 7.992754 ATGATCCTTTTGAGACCTAATATGC 57.007 36.000 0.00 0.00 0.00 3.14
2148 2356 8.884323 AGCATATGATCCTTTTGAGACCTAATA 58.116 33.333 6.97 0.00 0.00 0.98
2191 2399 4.998051 ACCTTCAATAACATCACCCTTGT 58.002 39.130 0.00 0.00 0.00 3.16
2259 2467 8.832521 TGGATTGGCAAGTAACTAATAAATACG 58.167 33.333 5.96 0.00 0.00 3.06
2288 2496 7.382110 CAATCTGACGTGGGAGATTAATCTAT 58.618 38.462 17.94 1.47 36.90 1.98
2305 2513 2.484742 ACCCGTTAACCCAATCTGAC 57.515 50.000 0.00 0.00 0.00 3.51
2312 2520 4.648307 ACAATAAAACAACCCGTTAACCCA 59.352 37.500 0.00 0.00 36.59 4.51
2323 2531 9.974980 TTCCCTCTTTGATTACAATAAAACAAC 57.025 29.630 0.00 0.00 35.85 3.32
2328 2536 7.446013 ACGTGTTCCCTCTTTGATTACAATAAA 59.554 33.333 0.00 0.00 35.85 1.40
2334 2542 6.592607 TGATTACGTGTTCCCTCTTTGATTAC 59.407 38.462 0.00 0.00 0.00 1.89
2421 2629 6.536787 AGATACTTATCCATGCAGAAAGCGC 61.537 44.000 0.00 0.00 38.68 5.92
2501 2711 3.799366 TGTGCCCACCGTATAATGTAAG 58.201 45.455 0.00 0.00 0.00 2.34
2513 2723 1.610624 CGGGATACATATGTGCCCACC 60.611 57.143 31.56 20.80 41.31 4.61
2515 2725 1.429930 ACGGGATACATATGTGCCCA 58.570 50.000 31.56 12.40 41.31 5.36
2522 2732 7.956328 TTGATCTTAGCTACGGGATACATAT 57.044 36.000 0.00 0.00 39.74 1.78
2574 2784 7.614192 CCCCCTAGAAGTACAATTTAACACATT 59.386 37.037 0.00 0.00 0.00 2.71
2770 2981 7.624549 TGTCTTTTTCATAGCTCCATACTCTT 58.375 34.615 0.00 0.00 0.00 2.85
2799 3010 6.286240 AGTAATGTCACTACTCATTGCTGA 57.714 37.500 7.45 0.00 42.24 4.26
2809 3020 4.755123 AGTGCCAAACAGTAATGTCACTAC 59.245 41.667 12.12 2.67 32.49 2.73
2812 3023 5.880054 ATAGTGCCAAACAGTAATGTCAC 57.120 39.130 0.00 0.30 37.72 3.67
2814 3025 6.494893 TCAATAGTGCCAAACAGTAATGTC 57.505 37.500 0.00 0.00 37.72 3.06
2815 3026 6.892658 TTCAATAGTGCCAAACAGTAATGT 57.107 33.333 0.00 0.00 37.72 2.71
2816 3027 6.254157 GCATTCAATAGTGCCAAACAGTAATG 59.746 38.462 0.00 0.00 37.72 1.90
2817 3028 6.153340 AGCATTCAATAGTGCCAAACAGTAAT 59.847 34.615 0.00 0.00 42.20 1.89
2818 3029 5.476599 AGCATTCAATAGTGCCAAACAGTAA 59.523 36.000 0.00 0.00 42.20 2.24
2819 3030 5.009631 AGCATTCAATAGTGCCAAACAGTA 58.990 37.500 0.00 0.00 42.20 2.74
2820 3031 3.828451 AGCATTCAATAGTGCCAAACAGT 59.172 39.130 0.00 0.00 42.20 3.55
2821 3032 4.082625 TCAGCATTCAATAGTGCCAAACAG 60.083 41.667 0.00 0.00 42.20 3.16
2822 3033 3.825585 TCAGCATTCAATAGTGCCAAACA 59.174 39.130 0.00 0.00 42.20 2.83
2823 3034 4.439305 TCAGCATTCAATAGTGCCAAAC 57.561 40.909 0.00 0.00 42.20 2.93
2824 3035 5.664294 AATCAGCATTCAATAGTGCCAAA 57.336 34.783 0.00 0.00 42.20 3.28
2825 3036 5.047164 ACAAATCAGCATTCAATAGTGCCAA 60.047 36.000 0.00 0.00 42.20 4.52
2826 3037 4.463539 ACAAATCAGCATTCAATAGTGCCA 59.536 37.500 0.00 0.00 42.20 4.92
2827 3038 5.002464 ACAAATCAGCATTCAATAGTGCC 57.998 39.130 0.00 0.00 42.20 5.01
2828 3039 5.888105 AGACAAATCAGCATTCAATAGTGC 58.112 37.500 0.00 0.00 41.57 4.40
2868 3080 1.810151 CAGGGTCAAACACATTACGGG 59.190 52.381 0.00 0.00 0.00 5.28
2871 3083 7.518211 GCAAAATTTCAGGGTCAAACACATTAC 60.518 37.037 0.00 0.00 0.00 1.89
2947 3159 6.021311 GCGTAAACGATGTTTTGAACTTTCAA 60.021 34.615 6.71 0.07 42.63 2.69
2948 3160 5.452944 GCGTAAACGATGTTTTGAACTTTCA 59.547 36.000 6.71 0.00 43.02 2.69
2953 3165 3.115098 CACGCGTAAACGATGTTTTGAAC 59.885 43.478 13.44 0.00 43.02 3.18
2964 3176 1.378347 GTGAAAACCACGCGTAAACG 58.622 50.000 13.44 0.00 38.02 3.60
2970 3182 3.231324 GACCGGTGAAAACCACGCG 62.231 63.158 14.63 3.53 46.62 6.01
2973 3185 0.179040 TGGAGACCGGTGAAAACCAC 60.179 55.000 14.63 0.00 44.95 4.16
3002 3214 5.221641 CCTGGGAGAATATCATACGGAAACA 60.222 44.000 0.00 0.00 0.00 2.83
3024 3236 4.104102 TGTTGACTTGTTCTCCCATAACCT 59.896 41.667 0.00 0.00 0.00 3.50
3033 3245 3.058914 CCACCGAATGTTGACTTGTTCTC 60.059 47.826 0.00 0.00 0.00 2.87
3058 3270 2.600470 TTCGTGTAGTTTTCACCGGT 57.400 45.000 0.00 0.00 32.86 5.28
3059 3271 3.948196 TTTTCGTGTAGTTTTCACCGG 57.052 42.857 0.00 0.00 32.86 5.28
3060 3272 6.595794 ACATATTTTCGTGTAGTTTTCACCG 58.404 36.000 0.00 0.00 32.86 4.94
3109 3324 6.314917 ACATCACCCTCTTAACATCCTTTTT 58.685 36.000 0.00 0.00 0.00 1.94
3143 3358 7.236674 TGTGTTTGAATCTGAAATTTTGCAG 57.763 32.000 0.00 0.00 0.00 4.41
3151 3366 6.869315 TCCGTAATGTGTTTGAATCTGAAA 57.131 33.333 0.00 0.00 0.00 2.69
3157 3372 4.992319 TCTCGTTCCGTAATGTGTTTGAAT 59.008 37.500 0.00 0.00 0.00 2.57
3202 3417 3.825585 TGTTTGGCACTATTCAATGCTGA 59.174 39.130 0.00 0.00 41.74 4.26
3392 3608 6.392625 TCATACGGAAACCAACATTCAAAA 57.607 33.333 0.00 0.00 0.00 2.44
3404 3620 5.855045 ACTGGGAGAATATCATACGGAAAC 58.145 41.667 0.00 0.00 0.00 2.78
3417 3633 6.688073 ATATCATACGGAAACTGGGAGAAT 57.312 37.500 0.00 0.00 0.00 2.40
3418 3634 6.326583 AGAATATCATACGGAAACTGGGAGAA 59.673 38.462 0.00 0.00 0.00 2.87
3419 3635 5.839063 AGAATATCATACGGAAACTGGGAGA 59.161 40.000 0.00 0.00 0.00 3.71
3489 3705 8.559536 CGTAATGGCTACAACAGATATTTCATT 58.440 33.333 0.00 0.00 0.00 2.57
3521 3742 9.328721 CAGATTTTTCTTGTTTTGTGGTTTTTC 57.671 29.630 0.00 0.00 0.00 2.29
3574 3796 2.639065 ACTCACTCGATCACTCCTCTC 58.361 52.381 0.00 0.00 0.00 3.20
3575 3797 2.799126 ACTCACTCGATCACTCCTCT 57.201 50.000 0.00 0.00 0.00 3.69
3576 3798 3.064271 GTGTACTCACTCGATCACTCCTC 59.936 52.174 0.00 0.00 40.98 3.71
3577 3799 3.011119 GTGTACTCACTCGATCACTCCT 58.989 50.000 0.00 0.00 40.98 3.69
3578 3800 2.223066 CGTGTACTCACTCGATCACTCC 60.223 54.545 0.00 0.00 42.71 3.85
3580 3802 2.159824 CACGTGTACTCACTCGATCACT 59.840 50.000 7.58 0.00 42.71 3.41
3582 3804 1.467342 CCACGTGTACTCACTCGATCA 59.533 52.381 15.65 0.00 42.71 2.92
3583 3805 1.467734 ACCACGTGTACTCACTCGATC 59.532 52.381 15.65 0.00 42.71 3.69
3584 3806 1.467734 GACCACGTGTACTCACTCGAT 59.532 52.381 15.65 0.00 42.71 3.59
3585 3807 0.870393 GACCACGTGTACTCACTCGA 59.130 55.000 15.65 0.00 42.71 4.04
3586 3808 0.452287 CGACCACGTGTACTCACTCG 60.452 60.000 15.65 5.02 44.92 4.18
3587 3809 3.379682 CGACCACGTGTACTCACTC 57.620 57.895 15.65 0.00 41.89 3.51
3599 3821 3.339253 AAAATACACCCCTACGACCAC 57.661 47.619 0.00 0.00 0.00 4.16
3628 3850 6.596888 CCAAGAGTCTGTCACATGAAATATGT 59.403 38.462 0.00 0.00 0.00 2.29
3629 3851 6.457934 GCCAAGAGTCTGTCACATGAAATATG 60.458 42.308 0.00 0.00 0.00 1.78
3680 3903 8.879227 TGATCCCAACATATGTCTATCAACATA 58.121 33.333 9.23 0.00 44.07 2.29
3914 4137 7.337689 CCTTTTACAATGTCTTCTCCATGATCA 59.662 37.037 0.00 0.00 0.00 2.92
3926 4149 6.599638 GGAGATGCTTACCTTTTACAATGTCT 59.400 38.462 0.00 0.00 0.00 3.41
4184 5048 9.220767 AGTGAATTTACTTTACCAAGAGCTAAG 57.779 33.333 0.00 0.00 33.72 2.18
4187 5051 9.740710 ATAAGTGAATTTACTTTACCAAGAGCT 57.259 29.630 19.38 0.00 41.01 4.09
4228 5971 5.668471 TGTTCAAAATTGATTTGTGCTGGA 58.332 33.333 0.00 0.00 46.89 3.86
4290 6034 4.487714 TGCTCCCAGTCTTTACTATTGG 57.512 45.455 0.00 0.00 33.48 3.16
4314 6058 4.159506 TGCCATAGTAAAATGCCTTGGTTC 59.840 41.667 0.00 0.00 0.00 3.62
4381 6125 7.201410 GCATCACTATTCTTCATGCAACTTTTG 60.201 37.037 0.00 0.00 39.76 2.44
4383 6127 6.152323 AGCATCACTATTCTTCATGCAACTTT 59.848 34.615 5.10 0.00 41.98 2.66
4384 6128 5.651139 AGCATCACTATTCTTCATGCAACTT 59.349 36.000 5.10 0.00 41.98 2.66
4387 6131 5.187687 TGAGCATCACTATTCTTCATGCAA 58.812 37.500 5.10 0.00 42.56 4.08
4411 6155 1.195448 CTGATCTGCACCAACAACGTC 59.805 52.381 0.00 0.00 0.00 4.34
4433 6177 1.191489 TCAGGCACCTTGATCGTGGA 61.191 55.000 10.30 0.00 0.00 4.02
4437 6181 1.811266 CCGTCAGGCACCTTGATCG 60.811 63.158 0.00 0.00 0.00 3.69
4457 6204 3.054434 CCATCACTAATGTCCACCTTCCA 60.054 47.826 0.00 0.00 33.13 3.53
4483 6230 2.071778 AGAGTTTGCAACCATGGTGT 57.928 45.000 20.60 5.92 0.00 4.16
4492 6239 7.606073 TGTGTATCTTAATGCTAGAGTTTGCAA 59.394 33.333 0.00 0.00 42.74 4.08
4573 6320 9.413734 CCATTTTATTCAGTCCTTTTAGATCCT 57.586 33.333 0.00 0.00 0.00 3.24
4574 6321 9.408648 TCCATTTTATTCAGTCCTTTTAGATCC 57.591 33.333 0.00 0.00 0.00 3.36
4593 6340 0.819582 CGCTCAGGGCAATCCATTTT 59.180 50.000 0.00 0.00 41.91 1.82
4603 6350 2.894387 GCTCACATCGCTCAGGGC 60.894 66.667 0.00 0.00 37.64 5.19
4607 6354 0.733909 CGACTTGCTCACATCGCTCA 60.734 55.000 0.00 0.00 0.00 4.26
4608 6355 0.456824 TCGACTTGCTCACATCGCTC 60.457 55.000 0.00 0.00 34.59 5.03
4609 6356 0.734253 GTCGACTTGCTCACATCGCT 60.734 55.000 8.70 0.00 34.59 4.93
4610 6357 1.704582 GTCGACTTGCTCACATCGC 59.295 57.895 8.70 0.00 34.59 4.58
4611 6358 0.729478 ACGTCGACTTGCTCACATCG 60.729 55.000 14.70 0.00 35.91 3.84
4612 6359 0.985549 GACGTCGACTTGCTCACATC 59.014 55.000 14.70 0.00 0.00 3.06
4613 6360 0.729478 CGACGTCGACTTGCTCACAT 60.729 55.000 33.35 0.00 43.02 3.21
4614 6361 1.370051 CGACGTCGACTTGCTCACA 60.370 57.895 33.35 0.00 43.02 3.58
4615 6362 1.082300 TCGACGTCGACTTGCTCAC 60.082 57.895 34.97 0.00 44.22 3.51
4616 6363 3.336566 TCGACGTCGACTTGCTCA 58.663 55.556 34.97 12.17 44.22 4.26
4643 6392 7.030165 GTCAGTCTACCAATATATCATGGACG 58.970 42.308 9.95 1.85 39.12 4.79
4649 6398 7.436933 CAAGCTGTCAGTCTACCAATATATCA 58.563 38.462 0.93 0.00 0.00 2.15
4652 6401 5.453339 GGCAAGCTGTCAGTCTACCAATATA 60.453 44.000 0.93 0.00 0.00 0.86
4656 6405 1.270839 GGCAAGCTGTCAGTCTACCAA 60.271 52.381 0.93 0.00 0.00 3.67
4665 6414 0.819259 GTGGTCTTGGCAAGCTGTCA 60.819 55.000 22.31 13.50 0.00 3.58
4667 6416 1.529244 GGTGGTCTTGGCAAGCTGT 60.529 57.895 22.31 0.00 0.00 4.40
4804 6556 4.523943 TGAGGCAACAAAATCAGCATTACT 59.476 37.500 0.00 0.00 41.41 2.24
4904 6656 7.956315 ACCCAGGAAGCAAGACTCTTATATATA 59.044 37.037 0.00 0.00 0.00 0.86
4905 6657 6.789959 ACCCAGGAAGCAAGACTCTTATATAT 59.210 38.462 0.00 0.00 0.00 0.86
4906 6658 6.042093 CACCCAGGAAGCAAGACTCTTATATA 59.958 42.308 0.00 0.00 0.00 0.86
4907 6659 4.971924 ACCCAGGAAGCAAGACTCTTATAT 59.028 41.667 0.00 0.00 0.00 0.86
4923 6675 3.321648 ACGCTGATGCACCCAGGA 61.322 61.111 16.75 0.00 39.64 3.86
4986 6743 3.241701 ACAACACGAACAAACTTTGCTG 58.758 40.909 1.14 0.00 0.00 4.41
4988 6745 3.670991 TCAACAACACGAACAAACTTTGC 59.329 39.130 1.14 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.