Multiple sequence alignment - TraesCS1D01G410900

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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 TraesCS1D01G410900 chr1D 100.000 3473 0 0 1 3473 472525921 472522449 0.000000e+00 6414.0
1 TraesCS1D01G410900 chr1D 96.053 76 3 0 416 491 280618787 280618712 1.310000e-24 124.0
2 TraesCS1D01G410900 chr1D 96.000 75 3 0 417 491 447392415 447392341 4.710000e-24 122.0
3 TraesCS1D01G410900 chr1D 94.521 73 4 0 253 325 472525413 472525341 2.830000e-21 113.0
4 TraesCS1D01G410900 chr1D 94.521 73 4 0 509 581 472525669 472525597 2.830000e-21 113.0
5 TraesCS1D01G410900 chr1B 91.539 2293 130 34 488 2757 657175131 657172880 0.000000e+00 3101.0
6 TraesCS1D01G410900 chr1B 79.268 656 71 36 2841 3473 657172836 657172223 6.980000e-107 398.0
7 TraesCS1D01G410900 chr1B 85.106 329 39 5 14 341 657175580 657175261 9.290000e-86 327.0
8 TraesCS1D01G410900 chr1B 89.362 94 10 0 488 581 657175370 657175277 6.090000e-23 119.0
9 TraesCS1D01G410900 chr1B 79.104 134 25 2 160 290 657175206 657175073 4.770000e-14 89.8
10 TraesCS1D01G410900 chr1A 91.837 882 40 10 1879 2757 566481009 566480157 0.000000e+00 1201.0
11 TraesCS1D01G410900 chr1A 94.692 697 30 6 1188 1880 566481861 566481168 0.000000e+00 1075.0
12 TraesCS1D01G410900 chr1A 90.275 473 41 3 764 1233 566482328 566481858 6.370000e-172 614.0
13 TraesCS1D01G410900 chr1A 84.887 397 38 14 3082 3463 566479897 566479508 7.030000e-102 381.0
14 TraesCS1D01G410900 chr1A 89.494 257 23 2 595 847 566482581 566482325 4.320000e-84 322.0
15 TraesCS1D01G410900 chr1A 84.043 188 25 4 2841 3025 566480113 566479928 3.560000e-40 176.0
16 TraesCS1D01G410900 chr1A 90.909 99 2 4 496 587 566482715 566482617 3.640000e-25 126.0
17 TraesCS1D01G410900 chr2D 97.368 76 2 0 416 491 526791647 526791572 2.810000e-26 130.0
18 TraesCS1D01G410900 chr2D 94.872 78 3 1 415 491 300783258 300783335 1.690000e-23 121.0
19 TraesCS1D01G410900 chr5D 97.333 75 2 0 417 491 390010034 390010108 1.010000e-25 128.0
20 TraesCS1D01G410900 chr4D 96.000 75 3 0 417 491 133809738 133809664 4.710000e-24 122.0
21 TraesCS1D01G410900 chr4D 94.872 78 3 1 415 491 396153809 396153886 1.690000e-23 121.0
22 TraesCS1D01G410900 chr4D 94.872 78 3 1 415 491 501584102 501584179 1.690000e-23 121.0
23 TraesCS1D01G410900 chr6D 91.860 86 4 3 409 491 455578455 455578540 2.190000e-22 117.0
24 TraesCS1D01G410900 chr7A 94.521 73 4 0 1835 1907 10887904 10887976 2.830000e-21 113.0


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 TraesCS1D01G410900 chr1D 472522449 472525921 3472 True 2213.333333 6414 96.347333 1 3473 3 chr1D.!!$R3 3472
1 TraesCS1D01G410900 chr1B 657172223 657175580 3357 True 806.960000 3101 84.875800 14 3473 5 chr1B.!!$R1 3459
2 TraesCS1D01G410900 chr1A 566479508 566482715 3207 True 556.428571 1201 89.448143 496 3463 7 chr1A.!!$R1 2967

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
462 499 0.034477 CAGCCCCACGGTCCTTTTAT 60.034 55.0 0.0 0.0 0.0 1.40 F
625 697 0.539986 ATGCCGGTGTTAGGTTCGAT 59.460 50.0 1.9 0.0 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2445 2822 0.391130 TGGATTCCTTGTTCTCGGCG 60.391 55.0 0.00 0.0 0.0 6.46 R
2601 2980 0.878523 GCATAGCGCGGTGGATAACA 60.879 55.0 23.02 0.0 0.0 2.41 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
17 18 4.124351 CGTAGCTTGGCGACCGGA 62.124 66.667 9.46 0.00 30.67 5.14
18 19 2.263540 GTAGCTTGGCGACCGGAA 59.736 61.111 9.46 0.00 0.00 4.30
19 20 1.375013 GTAGCTTGGCGACCGGAAA 60.375 57.895 9.46 0.00 0.00 3.13
20 21 1.079405 TAGCTTGGCGACCGGAAAG 60.079 57.895 9.46 4.86 0.00 2.62
21 22 1.537814 TAGCTTGGCGACCGGAAAGA 61.538 55.000 9.46 0.00 0.00 2.52
25 26 1.760479 TTGGCGACCGGAAAGAAGGA 61.760 55.000 9.46 0.00 0.00 3.36
29 30 1.711206 CGACCGGAAAGAAGGAACTC 58.289 55.000 9.46 0.00 38.49 3.01
30 31 1.000506 CGACCGGAAAGAAGGAACTCA 59.999 52.381 9.46 0.00 38.49 3.41
31 32 2.353803 CGACCGGAAAGAAGGAACTCAT 60.354 50.000 9.46 0.00 38.49 2.90
34 35 4.470602 ACCGGAAAGAAGGAACTCATTTT 58.529 39.130 9.46 0.00 38.49 1.82
39 40 6.017440 CGGAAAGAAGGAACTCATTTTGTGTA 60.017 38.462 0.00 0.00 38.49 2.90
40 41 7.308589 CGGAAAGAAGGAACTCATTTTGTGTAT 60.309 37.037 0.00 0.00 38.49 2.29
43 44 4.685169 AGGAACTCATTTTGTGTATGCG 57.315 40.909 0.00 0.00 0.00 4.73
49 50 2.158645 TCATTTTGTGTATGCGGTGTCG 59.841 45.455 0.00 0.00 39.81 4.35
92 93 4.939399 CAGGTCATGCATCGGACA 57.061 55.556 16.47 0.00 35.74 4.02
96 97 1.164411 GGTCATGCATCGGACACAAA 58.836 50.000 16.47 0.00 35.74 2.83
114 115 4.093850 CACAAATGATCGCAGATCTTGTCA 59.906 41.667 16.03 0.00 45.12 3.58
116 117 5.356190 ACAAATGATCGCAGATCTTGTCATT 59.644 36.000 15.99 12.43 45.12 2.57
124 125 5.693555 TCGCAGATCTTGTCATTGTATCATC 59.306 40.000 0.00 0.00 0.00 2.92
129 130 7.062022 CAGATCTTGTCATTGTATCATCTAGCG 59.938 40.741 0.00 0.00 0.00 4.26
130 131 4.984785 TCTTGTCATTGTATCATCTAGCGC 59.015 41.667 0.00 0.00 0.00 5.92
131 132 3.653344 TGTCATTGTATCATCTAGCGCC 58.347 45.455 2.29 0.00 0.00 6.53
133 134 2.899900 TCATTGTATCATCTAGCGCCCT 59.100 45.455 2.29 0.00 0.00 5.19
134 135 3.056536 TCATTGTATCATCTAGCGCCCTC 60.057 47.826 2.29 0.00 0.00 4.30
136 137 0.171455 GTATCATCTAGCGCCCTCGG 59.829 60.000 2.29 0.00 35.95 4.63
141 142 2.017559 ATCTAGCGCCCTCGGTTGTC 62.018 60.000 2.29 0.00 44.90 3.18
163 164 0.394216 TTTGCCATGCATAGCGAGGT 60.394 50.000 12.50 0.00 38.76 3.85
194 195 3.606153 CGGTGCTGTACTTTGTTACTTGC 60.606 47.826 0.00 0.00 0.00 4.01
196 197 4.319549 GGTGCTGTACTTTGTTACTTGCTC 60.320 45.833 0.00 0.00 0.00 4.26
199 200 2.473609 TGTACTTTGTTACTTGCTCGCG 59.526 45.455 0.00 0.00 0.00 5.87
210 211 2.104770 TTGCTCGCGTCAAGTGCTTG 62.105 55.000 5.77 5.63 41.71 4.01
219 220 3.123804 CGTCAAGTGCTTGTACTGAAGT 58.876 45.455 11.17 0.00 41.16 3.01
220 221 3.182572 CGTCAAGTGCTTGTACTGAAGTC 59.817 47.826 11.17 0.00 41.16 3.01
221 222 3.495001 GTCAAGTGCTTGTACTGAAGTCC 59.505 47.826 11.17 0.00 41.16 3.85
223 224 3.393089 AGTGCTTGTACTGAAGTCCTG 57.607 47.619 0.00 0.00 0.00 3.86
224 225 2.037772 AGTGCTTGTACTGAAGTCCTGG 59.962 50.000 0.00 0.00 0.00 4.45
234 235 3.954258 ACTGAAGTCCTGGGAAAAACTTG 59.046 43.478 2.78 0.00 32.34 3.16
239 240 5.061721 AGTCCTGGGAAAAACTTGTGTAT 57.938 39.130 0.00 0.00 0.00 2.29
241 242 6.790319 AGTCCTGGGAAAAACTTGTGTATAT 58.210 36.000 0.00 0.00 0.00 0.86
242 243 7.238710 AGTCCTGGGAAAAACTTGTGTATATT 58.761 34.615 0.00 0.00 0.00 1.28
244 245 9.016438 GTCCTGGGAAAAACTTGTGTATATTTA 57.984 33.333 0.00 0.00 0.00 1.40
294 295 3.658398 CTGTCAAGGACAATGGCCT 57.342 52.632 0.00 0.00 42.26 5.19
321 322 0.814457 AACGTTGCCACTTTTGCAGA 59.186 45.000 0.00 0.00 40.35 4.26
375 409 4.945246 TGCCATAGAGAGGTTAAATCGTC 58.055 43.478 0.00 0.00 0.00 4.20
377 411 4.261489 GCCATAGAGAGGTTAAATCGTCGA 60.261 45.833 0.00 0.00 0.00 4.20
383 417 1.933853 AGGTTAAATCGTCGATGCTGC 59.066 47.619 8.83 0.00 0.00 5.25
384 418 1.332028 GGTTAAATCGTCGATGCTGCG 60.332 52.381 8.83 0.00 0.00 5.18
388 422 1.756375 AATCGTCGATGCTGCGCTTC 61.756 55.000 8.83 0.00 0.00 3.86
392 426 0.247458 GTCGATGCTGCGCTTCTTTC 60.247 55.000 9.73 0.00 31.76 2.62
393 427 1.061570 CGATGCTGCGCTTCTTTCC 59.938 57.895 9.73 0.00 31.76 3.13
396 430 2.009774 GATGCTGCGCTTCTTTCCTTA 58.990 47.619 9.73 0.00 31.35 2.69
405 442 3.485877 CGCTTCTTTCCTTATTGGCTTCG 60.486 47.826 0.00 0.00 35.26 3.79
406 443 3.732169 GCTTCTTTCCTTATTGGCTTCGC 60.732 47.826 0.00 0.00 35.26 4.70
411 448 0.935196 CCTTATTGGCTTCGCGTACC 59.065 55.000 5.77 6.95 0.00 3.34
415 452 1.108776 ATTGGCTTCGCGTACCTCTA 58.891 50.000 5.77 0.00 0.00 2.43
418 455 1.479323 TGGCTTCGCGTACCTCTATTT 59.521 47.619 5.77 0.00 0.00 1.40
419 456 2.093869 TGGCTTCGCGTACCTCTATTTT 60.094 45.455 5.77 0.00 0.00 1.82
420 457 2.934553 GGCTTCGCGTACCTCTATTTTT 59.065 45.455 5.77 0.00 0.00 1.94
444 481 8.896320 TTTTGACTATTTACTGTAGAGCAACA 57.104 30.769 0.00 0.00 0.00 3.33
449 486 4.625800 CTGTAGAGCAACAGCCCC 57.374 61.111 1.57 0.00 40.40 5.80
450 487 1.679311 CTGTAGAGCAACAGCCCCA 59.321 57.895 1.57 0.00 40.40 4.96
451 488 0.674895 CTGTAGAGCAACAGCCCCAC 60.675 60.000 1.57 0.00 40.40 4.61
452 489 1.741770 GTAGAGCAACAGCCCCACG 60.742 63.158 0.00 0.00 0.00 4.94
453 490 2.954684 TAGAGCAACAGCCCCACGG 61.955 63.158 0.00 0.00 0.00 4.94
454 491 4.643387 GAGCAACAGCCCCACGGT 62.643 66.667 0.00 0.00 0.00 4.83
455 492 4.643387 AGCAACAGCCCCACGGTC 62.643 66.667 0.00 0.00 0.00 4.79
457 494 3.953775 CAACAGCCCCACGGTCCT 61.954 66.667 0.00 0.00 0.00 3.85
458 495 3.175710 AACAGCCCCACGGTCCTT 61.176 61.111 0.00 0.00 0.00 3.36
459 496 2.763645 AACAGCCCCACGGTCCTTT 61.764 57.895 0.00 0.00 0.00 3.11
460 497 2.115266 CAGCCCCACGGTCCTTTT 59.885 61.111 0.00 0.00 0.00 2.27
461 498 1.377229 CAGCCCCACGGTCCTTTTA 59.623 57.895 0.00 0.00 0.00 1.52
462 499 0.034477 CAGCCCCACGGTCCTTTTAT 60.034 55.000 0.00 0.00 0.00 1.40
463 500 0.702316 AGCCCCACGGTCCTTTTATT 59.298 50.000 0.00 0.00 0.00 1.40
464 501 1.100510 GCCCCACGGTCCTTTTATTC 58.899 55.000 0.00 0.00 0.00 1.75
465 502 1.758936 CCCCACGGTCCTTTTATTCC 58.241 55.000 0.00 0.00 0.00 3.01
466 503 1.004979 CCCCACGGTCCTTTTATTCCA 59.995 52.381 0.00 0.00 0.00 3.53
467 504 2.365582 CCCACGGTCCTTTTATTCCAG 58.634 52.381 0.00 0.00 0.00 3.86
468 505 2.026636 CCCACGGTCCTTTTATTCCAGA 60.027 50.000 0.00 0.00 0.00 3.86
469 506 3.560453 CCCACGGTCCTTTTATTCCAGAA 60.560 47.826 0.00 0.00 0.00 3.02
470 507 4.076394 CCACGGTCCTTTTATTCCAGAAA 58.924 43.478 0.00 0.00 0.00 2.52
471 508 4.705023 CCACGGTCCTTTTATTCCAGAAAT 59.295 41.667 0.00 0.00 0.00 2.17
472 509 5.185056 CCACGGTCCTTTTATTCCAGAAATT 59.815 40.000 0.00 0.00 0.00 1.82
473 510 6.295067 CCACGGTCCTTTTATTCCAGAAATTT 60.295 38.462 0.00 0.00 0.00 1.82
474 511 7.151976 CACGGTCCTTTTATTCCAGAAATTTT 58.848 34.615 0.00 0.00 0.00 1.82
475 512 7.655732 CACGGTCCTTTTATTCCAGAAATTTTT 59.344 33.333 0.00 0.00 0.00 1.94
476 513 7.655732 ACGGTCCTTTTATTCCAGAAATTTTTG 59.344 33.333 1.75 1.75 0.00 2.44
477 514 7.360017 CGGTCCTTTTATTCCAGAAATTTTTGC 60.360 37.037 3.20 0.00 0.00 3.68
478 515 7.094805 GGTCCTTTTATTCCAGAAATTTTTGCC 60.095 37.037 3.20 0.00 0.00 4.52
479 516 6.939730 TCCTTTTATTCCAGAAATTTTTGCCC 59.060 34.615 3.20 0.00 0.00 5.36
480 517 6.714356 CCTTTTATTCCAGAAATTTTTGCCCA 59.286 34.615 3.20 0.00 0.00 5.36
481 518 7.230309 CCTTTTATTCCAGAAATTTTTGCCCAA 59.770 33.333 3.20 0.00 0.00 4.12
482 519 7.742556 TTTATTCCAGAAATTTTTGCCCAAG 57.257 32.000 3.20 0.00 0.00 3.61
483 520 3.124578 TCCAGAAATTTTTGCCCAAGC 57.875 42.857 3.20 0.00 40.48 4.01
484 521 2.153645 CCAGAAATTTTTGCCCAAGCC 58.846 47.619 3.20 0.00 38.69 4.35
485 522 2.224597 CCAGAAATTTTTGCCCAAGCCT 60.225 45.455 3.20 0.00 38.69 4.58
486 523 2.809696 CAGAAATTTTTGCCCAAGCCTG 59.190 45.455 0.00 0.00 38.69 4.85
494 531 0.966875 TGCCCAAGCCTGCTTATGTG 60.967 55.000 3.71 0.00 38.69 3.21
560 598 4.327680 AGGACAATAGCCTTGTTCAGAAC 58.672 43.478 6.32 6.32 30.35 3.01
597 669 4.037923 CAGTTATTGCTTGTCACCCTGTTT 59.962 41.667 0.00 0.00 0.00 2.83
625 697 0.539986 ATGCCGGTGTTAGGTTCGAT 59.460 50.000 1.90 0.00 0.00 3.59
630 702 3.788937 CCGGTGTTAGGTTCGATGTTAT 58.211 45.455 0.00 0.00 0.00 1.89
642 714 7.383687 AGGTTCGATGTTATGACTTAGAAACA 58.616 34.615 13.75 0.00 35.86 2.83
653 725 4.816385 TGACTTAGAAACACTTCTGCAAGG 59.184 41.667 0.00 0.00 42.11 3.61
744 822 8.966868 CAGGATGGGTTACACAGTTTTATTTAT 58.033 33.333 0.00 0.00 0.00 1.40
793 958 5.764686 TGTGTGTCTTATTGCATTGACTTCT 59.235 36.000 0.00 0.00 0.00 2.85
802 967 9.371136 CTTATTGCATTGACTTCTCAGTACTTA 57.629 33.333 0.00 0.00 31.22 2.24
831 996 6.724263 TGTAAACATGTTCTTTGTACTGCTG 58.276 36.000 12.39 0.00 0.00 4.41
834 999 3.003689 ACATGTTCTTTGTACTGCTGCAC 59.996 43.478 0.00 0.00 0.00 4.57
842 1007 3.417069 TGTACTGCTGCACTATGGTTT 57.583 42.857 0.00 0.00 0.00 3.27
904 1071 2.765699 TCCAATTTTTCTATGCCCTGGC 59.234 45.455 0.00 0.00 42.35 4.85
1026 1193 3.257873 CGGAGAAGCCATCTGATGATACT 59.742 47.826 18.92 10.03 38.96 2.12
1127 1294 3.276857 CATCAGCACAGCAAGAGGTATT 58.723 45.455 0.00 0.00 0.00 1.89
1414 1625 6.808321 ATGTATAAAGCAGTCAGGGAAGTA 57.192 37.500 0.00 0.00 0.00 2.24
1448 1659 9.693739 TTTTAGCTCCATATCCATTAGTTTCAA 57.306 29.630 0.00 0.00 0.00 2.69
1456 1667 8.184192 CCATATCCATTAGTTTCAACTGTGTTC 58.816 37.037 2.26 0.00 40.07 3.18
1463 1674 8.745837 CATTAGTTTCAACTGTGTTCAAATGTC 58.254 33.333 2.26 0.00 40.07 3.06
1523 1735 1.564348 TGGGCTCTGGGAAAGGTATTC 59.436 52.381 0.00 0.00 0.00 1.75
1660 1872 2.335712 GCCCCTTGAAGCACTTCGG 61.336 63.158 5.95 2.26 42.28 4.30
1723 1935 6.967199 GCAAGAATGTGCTTACCTTGTATTAC 59.033 38.462 0.00 0.00 41.51 1.89
1744 1956 5.086104 ACACCACTGTTGATACTGTATCC 57.914 43.478 21.63 10.29 35.03 2.59
1749 1961 5.291128 CCACTGTTGATACTGTATCCGTTTC 59.709 44.000 21.63 10.13 35.03 2.78
1776 1988 3.099267 TCCGCTAGCTCTTTCATTAGC 57.901 47.619 13.93 0.00 39.08 3.09
1777 1989 2.430694 TCCGCTAGCTCTTTCATTAGCA 59.569 45.455 13.93 0.00 41.32 3.49
1807 2021 7.582719 TGCTGGTCTTTCTATTAACCCAATAT 58.417 34.615 0.00 0.00 0.00 1.28
1809 2023 9.740710 GCTGGTCTTTCTATTAACCCAATATAT 57.259 33.333 0.00 0.00 0.00 0.86
1915 2290 4.334552 TGTGGAGCTGATTTTGCTATCAA 58.665 39.130 0.00 0.00 41.30 2.57
1927 2302 6.470557 TTTTGCTATCAAACGTACTACACC 57.529 37.500 0.00 0.00 41.48 4.16
1982 2357 1.026718 GCTAGCTGTCCCATTTGCGT 61.027 55.000 7.70 0.00 0.00 5.24
1991 2366 1.190643 CCCATTTGCGTATTTGGGGT 58.809 50.000 11.91 0.00 44.29 4.95
2029 2404 8.908786 TCCAATAGATCACATATCCAGTTTTC 57.091 34.615 0.00 0.00 0.00 2.29
2086 2461 1.880027 ACGTTTTGCCACCTCATTCTC 59.120 47.619 0.00 0.00 0.00 2.87
2092 2467 1.291132 GCCACCTCATTCTCGTTAGC 58.709 55.000 0.00 0.00 0.00 3.09
2096 2471 2.349886 CACCTCATTCTCGTTAGCAAGC 59.650 50.000 0.00 0.00 0.00 4.01
2135 2512 5.653507 TGATATCCTTTTGCTGTCAAATGC 58.346 37.500 0.00 0.00 41.37 3.56
2295 2672 9.706691 CGGTACTTCATATTTACAAGATACCAT 57.293 33.333 0.00 0.00 30.81 3.55
2299 2676 9.060347 ACTTCATATTTACAAGATACCATGCAG 57.940 33.333 0.00 0.00 0.00 4.41
2327 2704 5.056480 TCCAGTACATTTATCTTGCCATCG 58.944 41.667 0.00 0.00 0.00 3.84
2413 2790 2.663196 CGAACCAGGAGTCCACCC 59.337 66.667 12.86 0.00 0.00 4.61
2414 2791 1.913762 CGAACCAGGAGTCCACCCT 60.914 63.158 12.86 0.00 0.00 4.34
2419 2796 2.284995 AGGAGTCCACCCTGAGCC 60.285 66.667 12.86 0.00 31.66 4.70
2420 2797 2.607750 GGAGTCCACCCTGAGCCA 60.608 66.667 3.60 0.00 0.00 4.75
2421 2798 2.664081 GGAGTCCACCCTGAGCCAG 61.664 68.421 3.60 0.00 0.00 4.85
2430 2807 2.985456 CTGAGCCAGGAGTCCACC 59.015 66.667 12.86 0.00 0.00 4.61
2549 2927 8.566260 TCTCGTTGCTCTAGTAATAAGTATTCC 58.434 37.037 0.00 0.00 0.00 3.01
2701 3080 4.034258 GCACCGAGTGTCGTCCGA 62.034 66.667 6.02 0.00 38.40 4.55
2703 3082 2.281345 ACCGAGTGTCGTCCGAGT 60.281 61.111 0.00 0.00 38.40 4.18
2704 3083 2.323580 ACCGAGTGTCGTCCGAGTC 61.324 63.158 0.00 0.00 38.40 3.36
2705 3084 2.096030 CGAGTGTCGTCCGAGTCG 59.904 66.667 5.29 5.29 34.72 4.18
2726 3105 2.603560 GGACTCGGACAGAATAAAAGCG 59.396 50.000 0.00 0.00 0.00 4.68
2728 3107 2.993899 ACTCGGACAGAATAAAAGCGTG 59.006 45.455 0.00 0.00 0.00 5.34
2729 3108 3.250744 CTCGGACAGAATAAAAGCGTGA 58.749 45.455 0.00 0.00 0.00 4.35
2740 3119 2.191128 AAAGCGTGAGAGCCTGAAAT 57.809 45.000 0.00 0.00 38.01 2.17
2745 3124 3.624861 AGCGTGAGAGCCTGAAATTTATG 59.375 43.478 0.00 0.00 38.01 1.90
2757 3136 5.309323 TGAAATTTATGCTGGTACTGTGC 57.691 39.130 0.00 0.00 0.00 4.57
2759 3138 6.176896 TGAAATTTATGCTGGTACTGTGCTA 58.823 36.000 0.00 0.00 0.00 3.49
2760 3139 6.316140 TGAAATTTATGCTGGTACTGTGCTAG 59.684 38.462 4.93 4.93 0.00 3.42
2761 3140 4.819105 TTTATGCTGGTACTGTGCTAGT 57.181 40.909 10.59 0.12 43.56 2.57
2763 3142 3.703001 ATGCTGGTACTGTGCTAGTTT 57.297 42.857 10.59 0.00 40.89 2.66
2764 3143 3.040147 TGCTGGTACTGTGCTAGTTTC 57.960 47.619 10.59 0.00 40.89 2.78
2765 3144 2.632996 TGCTGGTACTGTGCTAGTTTCT 59.367 45.455 10.59 0.00 40.89 2.52
2766 3145 3.254892 GCTGGTACTGTGCTAGTTTCTC 58.745 50.000 10.59 0.00 40.89 2.87
2767 3146 3.851098 CTGGTACTGTGCTAGTTTCTCC 58.149 50.000 1.18 0.78 40.89 3.71
2768 3147 2.230508 TGGTACTGTGCTAGTTTCTCCG 59.769 50.000 0.00 0.00 40.89 4.63
2769 3148 2.230750 GGTACTGTGCTAGTTTCTCCGT 59.769 50.000 0.00 0.00 40.89 4.69
2771 3150 1.272769 ACTGTGCTAGTTTCTCCGTCC 59.727 52.381 0.00 0.00 35.67 4.79
2772 3151 1.546476 CTGTGCTAGTTTCTCCGTCCT 59.454 52.381 0.00 0.00 0.00 3.85
2773 3152 1.272490 TGTGCTAGTTTCTCCGTCCTG 59.728 52.381 0.00 0.00 0.00 3.86
2774 3153 0.246635 TGCTAGTTTCTCCGTCCTGC 59.753 55.000 0.00 0.00 0.00 4.85
2775 3154 0.246635 GCTAGTTTCTCCGTCCTGCA 59.753 55.000 0.00 0.00 0.00 4.41
2776 3155 1.737363 GCTAGTTTCTCCGTCCTGCAG 60.737 57.143 6.78 6.78 0.00 4.41
2777 3156 1.546476 CTAGTTTCTCCGTCCTGCAGT 59.454 52.381 13.81 0.00 0.00 4.40
2778 3157 0.034059 AGTTTCTCCGTCCTGCAGTG 59.966 55.000 13.81 4.33 0.00 3.66
2779 3158 1.301716 TTTCTCCGTCCTGCAGTGC 60.302 57.895 13.81 8.58 0.00 4.40
2780 3159 1.758440 TTTCTCCGTCCTGCAGTGCT 61.758 55.000 17.60 0.00 0.00 4.40
2781 3160 2.433838 CTCCGTCCTGCAGTGCTG 60.434 66.667 17.60 16.00 0.00 4.41
2782 3161 2.917227 TCCGTCCTGCAGTGCTGA 60.917 61.111 22.25 13.04 0.00 4.26
2783 3162 2.740055 CCGTCCTGCAGTGCTGAC 60.740 66.667 22.25 21.72 0.00 3.51
2784 3163 3.108289 CGTCCTGCAGTGCTGACG 61.108 66.667 31.32 31.32 43.28 4.35
2785 3164 2.740055 GTCCTGCAGTGCTGACGG 60.740 66.667 22.25 13.85 0.00 4.79
2786 3165 3.233980 TCCTGCAGTGCTGACGGT 61.234 61.111 22.25 0.00 0.00 4.83
2787 3166 1.906333 TCCTGCAGTGCTGACGGTA 60.906 57.895 22.25 0.00 0.00 4.02
2788 3167 1.738099 CCTGCAGTGCTGACGGTAC 60.738 63.158 22.25 0.00 0.00 3.34
2789 3168 1.738099 CTGCAGTGCTGACGGTACC 60.738 63.158 17.60 0.16 0.00 3.34
2790 3169 2.809601 GCAGTGCTGACGGTACCG 60.810 66.667 32.22 32.22 46.03 4.02
2818 3197 1.601759 GGCTGCCTGCTGTCTGAAA 60.602 57.895 12.43 0.00 42.39 2.69
2819 3198 1.578423 GCTGCCTGCTGTCTGAAAC 59.422 57.895 0.00 0.00 38.95 2.78
2820 3199 1.860484 GCTGCCTGCTGTCTGAAACC 61.860 60.000 0.00 0.00 38.95 3.27
2821 3200 0.250640 CTGCCTGCTGTCTGAAACCT 60.251 55.000 0.00 0.00 0.00 3.50
2822 3201 0.535780 TGCCTGCTGTCTGAAACCTG 60.536 55.000 0.00 0.00 0.00 4.00
2823 3202 1.239968 GCCTGCTGTCTGAAACCTGG 61.240 60.000 0.00 0.00 0.00 4.45
2824 3203 0.607489 CCTGCTGTCTGAAACCTGGG 60.607 60.000 0.00 0.00 0.00 4.45
2825 3204 0.397941 CTGCTGTCTGAAACCTGGGA 59.602 55.000 0.00 0.00 0.00 4.37
2826 3205 1.004044 CTGCTGTCTGAAACCTGGGAT 59.996 52.381 0.00 0.00 0.00 3.85
2827 3206 1.271543 TGCTGTCTGAAACCTGGGATG 60.272 52.381 0.00 0.00 0.00 3.51
2828 3207 1.271597 GCTGTCTGAAACCTGGGATGT 60.272 52.381 0.00 0.00 0.00 3.06
2829 3208 2.815589 GCTGTCTGAAACCTGGGATGTT 60.816 50.000 0.00 0.00 0.00 2.71
2830 3209 3.490348 CTGTCTGAAACCTGGGATGTTT 58.510 45.455 0.00 0.00 38.57 2.83
2835 3214 2.445145 TGAAACCTGGGATGTTTCCTCA 59.555 45.455 11.94 0.00 46.98 3.86
2837 3216 0.324943 ACCTGGGATGTTTCCTCACG 59.675 55.000 0.00 0.00 42.20 4.35
2839 3218 0.321564 CTGGGATGTTTCCTCACGCA 60.322 55.000 0.00 0.00 42.20 5.24
2851 3230 2.158871 TCCTCACGCACTGTAAGGTTTT 60.159 45.455 0.00 0.00 39.30 2.43
2853 3232 3.131396 CTCACGCACTGTAAGGTTTTCT 58.869 45.455 0.00 0.00 39.30 2.52
2861 3240 5.515270 GCACTGTAAGGTTTTCTGTTTGAAC 59.485 40.000 0.00 0.00 39.30 3.18
2862 3241 6.616947 CACTGTAAGGTTTTCTGTTTGAACA 58.383 36.000 0.00 0.00 39.30 3.18
2873 3254 2.600731 TGTTTGAACAGTGCGGTTTTG 58.399 42.857 0.00 0.00 34.30 2.44
2881 3262 1.002468 CAGTGCGGTTTTGTGAAGGAG 60.002 52.381 0.00 0.00 0.00 3.69
2884 3265 0.591659 GCGGTTTTGTGAAGGAGTCC 59.408 55.000 0.00 0.00 0.00 3.85
2909 3291 1.757682 TCCTGTTTGGTGTGTTGGTC 58.242 50.000 0.00 0.00 37.07 4.02
2923 3305 2.708861 TGTTGGTCTATGGTGTCTTGGT 59.291 45.455 0.00 0.00 0.00 3.67
2943 3325 1.435577 ACCACATAACGGTTTCGCTC 58.564 50.000 0.00 0.00 40.63 5.03
2949 3331 3.434299 ACATAACGGTTTCGCTCGAAATT 59.566 39.130 18.55 12.26 44.52 1.82
2950 3332 4.083696 ACATAACGGTTTCGCTCGAAATTT 60.084 37.500 18.55 14.28 44.52 1.82
3025 3410 6.541111 AACAAGATAACTGGAGAACGTTTC 57.459 37.500 0.46 2.05 0.00 2.78
3029 3414 5.480205 AGATAACTGGAGAACGTTTCTTCC 58.520 41.667 16.20 16.20 40.87 3.46
3036 3421 3.305608 GGAGAACGTTTCTTCCGGACTTA 60.306 47.826 1.83 0.00 40.87 2.24
3040 3425 5.184671 AGAACGTTTCTTCCGGACTTATAGT 59.815 40.000 1.83 0.00 36.36 2.12
3113 3508 8.635765 AAAACATAGCCAAAAGTTGAGAGATA 57.364 30.769 0.00 0.00 0.00 1.98
3282 3683 3.188786 GCCGACATGCGAGTCCAC 61.189 66.667 10.48 0.00 44.57 4.02
3297 3698 0.963856 TCCACGGAGTACACGCTGAT 60.964 55.000 9.50 0.00 41.61 2.90
3365 3777 2.556782 GCTTACCCAAACCCTAAAGCCT 60.557 50.000 0.00 0.00 34.64 4.58
3367 3779 0.037734 ACCCAAACCCTAAAGCCTCG 59.962 55.000 0.00 0.00 0.00 4.63
3393 3805 2.833582 TCCTCCTCCATCGCGTCC 60.834 66.667 5.77 0.00 0.00 4.79
3411 3823 1.076014 CCACCCAACCCTAACCCAC 59.924 63.158 0.00 0.00 0.00 4.61
3412 3824 1.721093 CCACCCAACCCTAACCCACA 61.721 60.000 0.00 0.00 0.00 4.17
3415 3827 1.302993 CCAACCCTAACCCACACCG 60.303 63.158 0.00 0.00 0.00 4.94
3418 3830 4.770874 CCCTAACCCACACCGCCG 62.771 72.222 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.359459 CTTTCCGGTCGCCAAGCTAC 61.359 60.000 0.00 0.00 0.00 3.58
2 3 1.079405 CTTTCCGGTCGCCAAGCTA 60.079 57.895 0.00 0.00 0.00 3.32
3 4 2.358737 CTTTCCGGTCGCCAAGCT 60.359 61.111 0.00 0.00 0.00 3.74
4 5 1.912371 CTTCTTTCCGGTCGCCAAGC 61.912 60.000 0.00 0.00 0.00 4.01
5 6 1.298859 CCTTCTTTCCGGTCGCCAAG 61.299 60.000 0.00 0.00 0.00 3.61
6 7 1.302192 CCTTCTTTCCGGTCGCCAA 60.302 57.895 0.00 0.00 0.00 4.52
7 8 1.760479 TTCCTTCTTTCCGGTCGCCA 61.760 55.000 0.00 0.00 0.00 5.69
8 9 1.004200 TTCCTTCTTTCCGGTCGCC 60.004 57.895 0.00 0.00 0.00 5.54
9 10 0.320508 AGTTCCTTCTTTCCGGTCGC 60.321 55.000 0.00 0.00 0.00 5.19
10 11 1.000506 TGAGTTCCTTCTTTCCGGTCG 59.999 52.381 0.00 0.00 0.00 4.79
11 12 2.833631 TGAGTTCCTTCTTTCCGGTC 57.166 50.000 0.00 0.00 0.00 4.79
12 13 3.790089 AATGAGTTCCTTCTTTCCGGT 57.210 42.857 0.00 0.00 0.00 5.28
13 14 4.278419 ACAAAATGAGTTCCTTCTTTCCGG 59.722 41.667 0.00 0.00 0.00 5.14
14 15 5.215160 CACAAAATGAGTTCCTTCTTTCCG 58.785 41.667 0.00 0.00 0.00 4.30
15 16 6.149129 ACACAAAATGAGTTCCTTCTTTCC 57.851 37.500 0.00 0.00 0.00 3.13
16 17 7.327032 GCATACACAAAATGAGTTCCTTCTTTC 59.673 37.037 0.00 0.00 0.00 2.62
17 18 7.147976 GCATACACAAAATGAGTTCCTTCTTT 58.852 34.615 0.00 0.00 0.00 2.52
18 19 6.568462 CGCATACACAAAATGAGTTCCTTCTT 60.568 38.462 0.00 0.00 0.00 2.52
19 20 5.106555 CGCATACACAAAATGAGTTCCTTCT 60.107 40.000 0.00 0.00 0.00 2.85
20 21 5.088739 CGCATACACAAAATGAGTTCCTTC 58.911 41.667 0.00 0.00 0.00 3.46
21 22 4.082787 CCGCATACACAAAATGAGTTCCTT 60.083 41.667 0.00 0.00 0.00 3.36
25 26 3.568007 ACACCGCATACACAAAATGAGTT 59.432 39.130 0.00 0.00 0.00 3.01
28 29 2.158645 CGACACCGCATACACAAAATGA 59.841 45.455 0.00 0.00 0.00 2.57
29 30 2.504868 CGACACCGCATACACAAAATG 58.495 47.619 0.00 0.00 0.00 2.32
30 31 2.892373 CGACACCGCATACACAAAAT 57.108 45.000 0.00 0.00 0.00 1.82
43 44 0.317020 GTGCAGAAAACAGCGACACC 60.317 55.000 0.00 0.00 0.00 4.16
49 50 0.746659 AACCCAGTGCAGAAAACAGC 59.253 50.000 0.00 0.00 0.00 4.40
55 56 0.751277 CCACACAACCCAGTGCAGAA 60.751 55.000 0.00 0.00 43.23 3.02
56 57 1.152984 CCACACAACCCAGTGCAGA 60.153 57.895 0.00 0.00 43.23 4.26
88 89 3.201290 AGATCTGCGATCATTTGTGTCC 58.799 45.455 16.97 0.00 0.00 4.02
92 93 4.256110 TGACAAGATCTGCGATCATTTGT 58.744 39.130 17.53 17.53 0.00 2.83
96 97 4.449131 ACAATGACAAGATCTGCGATCAT 58.551 39.130 16.97 0.76 0.00 2.45
114 115 2.094494 CGAGGGCGCTAGATGATACAAT 60.094 50.000 7.64 0.00 0.00 2.71
116 117 0.881796 CGAGGGCGCTAGATGATACA 59.118 55.000 7.64 0.00 0.00 2.29
124 125 2.202756 GACAACCGAGGGCGCTAG 60.203 66.667 7.64 3.00 35.83 3.42
134 135 0.798009 GCATGGCAAATCGACAACCG 60.798 55.000 0.00 0.00 34.96 4.44
136 137 2.282701 ATGCATGGCAAATCGACAAC 57.717 45.000 0.00 0.00 43.62 3.32
141 142 0.587768 TCGCTATGCATGGCAAATCG 59.412 50.000 30.96 16.47 43.62 3.34
171 172 2.762745 AGTAACAAAGTACAGCACCGG 58.237 47.619 0.00 0.00 0.00 5.28
172 173 3.606153 GCAAGTAACAAAGTACAGCACCG 60.606 47.826 0.00 0.00 31.45 4.94
173 174 3.564225 AGCAAGTAACAAAGTACAGCACC 59.436 43.478 0.00 0.00 32.72 5.01
174 175 4.608445 CGAGCAAGTAACAAAGTACAGCAC 60.608 45.833 0.00 0.00 32.72 4.40
194 195 0.435008 GTACAAGCACTTGACGCGAG 59.565 55.000 15.93 1.31 42.93 5.03
196 197 0.161658 CAGTACAAGCACTTGACGCG 59.838 55.000 16.95 3.53 42.93 6.01
199 200 3.495001 GGACTTCAGTACAAGCACTTGAC 59.505 47.826 16.95 10.24 42.93 3.18
205 206 1.347707 CCCAGGACTTCAGTACAAGCA 59.652 52.381 0.00 0.00 0.00 3.91
206 207 1.623811 TCCCAGGACTTCAGTACAAGC 59.376 52.381 0.00 0.00 0.00 4.01
210 211 4.715713 AGTTTTTCCCAGGACTTCAGTAC 58.284 43.478 0.00 0.00 0.00 2.73
219 220 9.762381 ATAAATATACACAAGTTTTTCCCAGGA 57.238 29.630 0.00 0.00 0.00 3.86
234 235 8.122952 GTCAACCTGCACTTGATAAATATACAC 58.877 37.037 5.55 0.00 30.46 2.90
239 240 6.741992 CAGTCAACCTGCACTTGATAAATA 57.258 37.500 5.55 0.00 33.59 1.40
294 295 0.107410 AGTGGCAACGTTCTGGACAA 60.107 50.000 0.00 0.00 42.51 3.18
296 297 1.021968 AAAGTGGCAACGTTCTGGAC 58.978 50.000 0.00 0.00 42.51 4.02
298 299 1.838913 CAAAAGTGGCAACGTTCTGG 58.161 50.000 0.00 0.00 42.51 3.86
344 374 6.759497 AACCTCTCTATGGCAAATTAACAC 57.241 37.500 0.00 0.00 0.00 3.32
349 379 6.828785 ACGATTTAACCTCTCTATGGCAAATT 59.171 34.615 0.00 0.00 0.00 1.82
357 387 5.241949 AGCATCGACGATTTAACCTCTCTAT 59.758 40.000 7.83 0.00 0.00 1.98
383 417 3.485877 CGAAGCCAATAAGGAAAGAAGCG 60.486 47.826 0.00 0.00 41.22 4.68
384 418 4.021191 CGAAGCCAATAAGGAAAGAAGC 57.979 45.455 0.00 0.00 41.22 3.86
418 455 9.332502 TGTTGCTCTACAGTAAATAGTCAAAAA 57.667 29.630 0.00 0.00 0.00 1.94
419 456 8.896320 TGTTGCTCTACAGTAAATAGTCAAAA 57.104 30.769 0.00 0.00 0.00 2.44
420 457 7.117812 GCTGTTGCTCTACAGTAAATAGTCAAA 59.882 37.037 11.77 0.00 45.76 2.69
421 458 6.590292 GCTGTTGCTCTACAGTAAATAGTCAA 59.410 38.462 11.77 0.00 45.76 3.18
423 460 5.520649 GGCTGTTGCTCTACAGTAAATAGTC 59.479 44.000 11.77 0.00 45.76 2.59
424 461 5.420409 GGCTGTTGCTCTACAGTAAATAGT 58.580 41.667 11.77 0.00 45.76 2.12
425 462 4.811557 GGGCTGTTGCTCTACAGTAAATAG 59.188 45.833 11.77 0.00 45.76 1.73
426 463 4.383770 GGGGCTGTTGCTCTACAGTAAATA 60.384 45.833 11.77 0.00 45.76 1.40
427 464 3.610911 GGGCTGTTGCTCTACAGTAAAT 58.389 45.455 11.77 0.00 45.76 1.40
428 465 2.290071 GGGGCTGTTGCTCTACAGTAAA 60.290 50.000 11.77 0.00 45.76 2.01
429 466 1.278127 GGGGCTGTTGCTCTACAGTAA 59.722 52.381 11.77 0.00 45.76 2.24
432 469 1.679311 TGGGGCTGTTGCTCTACAG 59.321 57.895 7.02 7.02 46.55 2.74
433 470 3.899371 TGGGGCTGTTGCTCTACA 58.101 55.556 0.00 0.00 40.19 2.74
434 471 1.741770 CGTGGGGCTGTTGCTCTAC 60.742 63.158 0.00 0.00 46.05 2.59
435 472 2.662596 CGTGGGGCTGTTGCTCTA 59.337 61.111 0.00 0.00 40.19 2.43
436 473 4.335647 CCGTGGGGCTGTTGCTCT 62.336 66.667 0.00 0.00 40.19 4.09
437 474 4.643387 ACCGTGGGGCTGTTGCTC 62.643 66.667 0.00 0.00 39.42 4.26
438 475 4.643387 GACCGTGGGGCTGTTGCT 62.643 66.667 0.00 0.00 39.59 3.91
440 477 2.976494 AAAGGACCGTGGGGCTGTTG 62.976 60.000 0.00 0.00 36.48 3.33
441 478 2.292785 AAAAGGACCGTGGGGCTGTT 62.293 55.000 0.00 0.00 36.48 3.16
442 479 1.420532 TAAAAGGACCGTGGGGCTGT 61.421 55.000 0.00 0.00 36.48 4.40
443 480 0.034477 ATAAAAGGACCGTGGGGCTG 60.034 55.000 0.00 0.00 36.48 4.85
444 481 0.702316 AATAAAAGGACCGTGGGGCT 59.298 50.000 0.00 0.00 36.48 5.19
445 482 1.100510 GAATAAAAGGACCGTGGGGC 58.899 55.000 0.00 0.00 36.48 5.80
446 483 1.004979 TGGAATAAAAGGACCGTGGGG 59.995 52.381 0.00 0.00 40.11 4.96
447 484 2.026636 TCTGGAATAAAAGGACCGTGGG 60.027 50.000 0.00 0.00 0.00 4.61
448 485 3.343941 TCTGGAATAAAAGGACCGTGG 57.656 47.619 0.00 0.00 0.00 4.94
449 486 5.897377 ATTTCTGGAATAAAAGGACCGTG 57.103 39.130 0.00 0.00 0.00 4.94
450 487 6.911250 AAATTTCTGGAATAAAAGGACCGT 57.089 33.333 0.00 0.00 0.00 4.83
451 488 7.360017 GCAAAAATTTCTGGAATAAAAGGACCG 60.360 37.037 0.00 0.00 0.00 4.79
452 489 7.094805 GGCAAAAATTTCTGGAATAAAAGGACC 60.095 37.037 0.00 0.00 0.00 4.46
453 490 7.094805 GGGCAAAAATTTCTGGAATAAAAGGAC 60.095 37.037 0.00 0.00 0.00 3.85
454 491 6.939730 GGGCAAAAATTTCTGGAATAAAAGGA 59.060 34.615 0.00 0.00 0.00 3.36
455 492 6.714356 TGGGCAAAAATTTCTGGAATAAAAGG 59.286 34.615 0.00 0.00 0.00 3.11
456 493 7.742556 TGGGCAAAAATTTCTGGAATAAAAG 57.257 32.000 0.00 0.00 0.00 2.27
457 494 7.255416 GCTTGGGCAAAAATTTCTGGAATAAAA 60.255 33.333 0.00 0.00 38.54 1.52
458 495 6.206438 GCTTGGGCAAAAATTTCTGGAATAAA 59.794 34.615 0.00 0.00 38.54 1.40
459 496 5.704978 GCTTGGGCAAAAATTTCTGGAATAA 59.295 36.000 0.00 0.00 38.54 1.40
460 497 5.244755 GCTTGGGCAAAAATTTCTGGAATA 58.755 37.500 0.00 0.00 38.54 1.75
461 498 4.074259 GCTTGGGCAAAAATTTCTGGAAT 58.926 39.130 0.00 0.00 38.54 3.01
462 499 3.475575 GCTTGGGCAAAAATTTCTGGAA 58.524 40.909 0.00 0.00 38.54 3.53
463 500 2.224499 GGCTTGGGCAAAAATTTCTGGA 60.224 45.455 0.00 0.00 40.87 3.86
464 501 2.153645 GGCTTGGGCAAAAATTTCTGG 58.846 47.619 0.00 0.00 40.87 3.86
465 502 2.809696 CAGGCTTGGGCAAAAATTTCTG 59.190 45.455 0.00 0.00 40.87 3.02
466 503 2.811504 GCAGGCTTGGGCAAAAATTTCT 60.812 45.455 0.00 0.00 40.87 2.52
467 504 1.536766 GCAGGCTTGGGCAAAAATTTC 59.463 47.619 0.00 0.00 40.87 2.17
468 505 1.143481 AGCAGGCTTGGGCAAAAATTT 59.857 42.857 0.00 0.00 40.87 1.82
469 506 0.766752 AGCAGGCTTGGGCAAAAATT 59.233 45.000 0.00 0.00 40.87 1.82
470 507 0.766752 AAGCAGGCTTGGGCAAAAAT 59.233 45.000 5.60 0.00 40.87 1.82
471 508 1.418334 TAAGCAGGCTTGGGCAAAAA 58.582 45.000 16.37 0.00 40.87 1.94
472 509 1.275856 CATAAGCAGGCTTGGGCAAAA 59.724 47.619 16.37 0.00 40.87 2.44
473 510 0.896923 CATAAGCAGGCTTGGGCAAA 59.103 50.000 16.37 0.00 40.87 3.68
474 511 0.251742 ACATAAGCAGGCTTGGGCAA 60.252 50.000 16.37 0.00 40.87 4.52
475 512 0.966875 CACATAAGCAGGCTTGGGCA 60.967 55.000 16.37 0.00 40.87 5.36
476 513 1.811860 CACATAAGCAGGCTTGGGC 59.188 57.895 16.37 0.00 37.47 5.36
477 514 0.966875 TGCACATAAGCAGGCTTGGG 60.967 55.000 16.37 10.32 40.11 4.12
478 515 2.570365 TGCACATAAGCAGGCTTGG 58.430 52.632 16.37 10.65 40.11 3.61
486 523 2.001872 GCCCAACAAATGCACATAAGC 58.998 47.619 0.00 0.00 0.00 3.09
494 531 1.079612 GCCTGAGCCCAACAAATGC 60.080 57.895 0.00 0.00 0.00 3.56
557 595 1.199624 CTGCAAAAGTGGCAACGTTC 58.800 50.000 0.00 0.00 41.39 3.95
560 598 2.483583 TAACTGCAAAAGTGGCAACG 57.516 45.000 0.00 0.00 41.39 4.10
589 633 2.102578 GCATGCCATCTTAAACAGGGT 58.897 47.619 6.36 0.00 0.00 4.34
591 635 1.066002 CGGCATGCCATCTTAAACAGG 59.934 52.381 34.93 11.33 35.37 4.00
597 669 0.034574 AACACCGGCATGCCATCTTA 60.035 50.000 34.93 0.00 35.37 2.10
625 697 6.989759 TGCAGAAGTGTTTCTAAGTCATAACA 59.010 34.615 0.00 0.00 41.71 2.41
630 702 4.816385 CCTTGCAGAAGTGTTTCTAAGTCA 59.184 41.667 0.00 0.00 41.71 3.41
642 714 2.656947 TTAACAGGCCTTGCAGAAGT 57.343 45.000 0.00 0.00 0.00 3.01
653 725 2.814336 CTGGTCCAGTTCTTTAACAGGC 59.186 50.000 11.09 0.00 40.98 4.85
772 937 6.148480 ACTGAGAAGTCAATGCAATAAGACAC 59.852 38.462 11.89 6.95 34.90 3.67
862 1029 8.924511 TTGGAAAGAAATCTGAAACATAGTCT 57.075 30.769 0.00 0.00 0.00 3.24
891 1058 0.037590 AAACACGCCAGGGCATAGAA 59.962 50.000 11.42 0.00 42.06 2.10
904 1071 9.009327 CATCAAAATTAGTAGGCATAAAACACG 57.991 33.333 0.00 0.00 0.00 4.49
954 1121 6.240894 ACAAGCTACAAGAAGATGGATTTCA 58.759 36.000 0.00 0.00 0.00 2.69
961 1128 5.049198 TGCTCAAACAAGCTACAAGAAGATG 60.049 40.000 0.00 0.00 42.94 2.90
1151 1318 3.321682 ACATGCAAGCACACAAGGTTAAT 59.678 39.130 0.00 0.00 0.00 1.40
1414 1625 9.597681 AATGGATATGGAGCTAAAATTGATCTT 57.402 29.630 0.00 0.00 0.00 2.40
1448 1659 5.934625 GTCCTGATAGACATTTGAACACAGT 59.065 40.000 0.00 0.00 36.73 3.55
1456 1667 4.514441 GCTCATGGTCCTGATAGACATTTG 59.486 45.833 0.00 0.00 38.59 2.32
1463 1674 1.336702 GCTCGCTCATGGTCCTGATAG 60.337 57.143 0.00 0.00 0.00 2.08
1523 1735 7.306632 CCATATAGCTTTCGAAAAGAACGGTAG 60.307 40.741 12.41 0.00 41.92 3.18
1527 1739 6.583912 TCCATATAGCTTTCGAAAAGAACG 57.416 37.500 12.41 0.80 38.83 3.95
1645 1857 2.680913 CGGCCGAAGTGCTTCAAGG 61.681 63.158 24.07 7.02 39.46 3.61
1660 1872 4.082949 AGTTTTAGCACCTGTAATTTCGGC 60.083 41.667 0.00 0.00 0.00 5.54
1723 1935 4.112634 CGGATACAGTATCAACAGTGGTG 58.887 47.826 20.17 0.21 36.91 4.17
1744 1956 3.123804 AGCTAGCGGATAATGTGAAACG 58.876 45.455 9.55 0.00 42.39 3.60
1749 1961 4.371786 TGAAAGAGCTAGCGGATAATGTG 58.628 43.478 9.55 0.00 0.00 3.21
1776 1988 8.352942 GGGTTAATAGAAAGACCAGCAAATATG 58.647 37.037 0.00 0.00 33.81 1.78
1777 1989 8.058847 TGGGTTAATAGAAAGACCAGCAAATAT 58.941 33.333 0.00 0.00 33.81 1.28
1828 2042 9.219603 TGAACTGAGTTCATTTTGAATAGTAGG 57.780 33.333 23.02 0.00 45.88 3.18
1915 2290 4.580167 TCAACAGTAGTGGTGTAGTACGTT 59.420 41.667 15.19 0.00 42.60 3.99
1927 2302 5.710984 ACGGAGAAAGTATCAACAGTAGTG 58.289 41.667 0.00 0.00 0.00 2.74
1982 2357 5.891551 GGATTGCTAGAAAGAACCCCAAATA 59.108 40.000 0.00 0.00 0.00 1.40
1991 2366 8.267183 TGTGATCTATTGGATTGCTAGAAAGAA 58.733 33.333 0.00 0.00 34.33 2.52
2074 2449 2.672961 TGCTAACGAGAATGAGGTGG 57.327 50.000 0.00 0.00 0.00 4.61
2106 2481 2.547211 CAGCAAAAGGATATCAGCTCCG 59.453 50.000 4.83 0.00 37.88 4.63
2242 2619 4.507710 TGTCAGTAGATGCATGAAGGAAC 58.492 43.478 2.46 0.00 0.00 3.62
2295 2672 2.512692 AATGTACTGGATTGCCTGCA 57.487 45.000 0.00 0.00 36.65 4.41
2299 2676 5.523369 GCAAGATAAATGTACTGGATTGCC 58.477 41.667 0.00 0.00 35.63 4.52
2413 2790 2.985456 GGTGGACTCCTGGCTCAG 59.015 66.667 0.00 0.00 0.00 3.35
2414 2791 2.997315 CGGTGGACTCCTGGCTCA 60.997 66.667 0.00 0.00 0.00 4.26
2415 2792 2.680352 TCGGTGGACTCCTGGCTC 60.680 66.667 0.00 0.00 0.00 4.70
2416 2793 2.681778 CTCGGTGGACTCCTGGCT 60.682 66.667 0.00 0.00 0.00 4.75
2417 2794 3.775654 CCTCGGTGGACTCCTGGC 61.776 72.222 0.00 0.00 38.35 4.85
2418 2795 2.037367 TCCTCGGTGGACTCCTGG 59.963 66.667 0.00 0.00 40.56 4.45
2419 2796 2.055042 CCTCCTCGGTGGACTCCTG 61.055 68.421 0.00 0.00 40.56 3.86
2420 2797 2.360980 CCTCCTCGGTGGACTCCT 59.639 66.667 0.00 0.00 40.56 3.69
2421 2798 3.462678 GCCTCCTCGGTGGACTCC 61.463 72.222 8.19 0.00 40.56 3.85
2422 2799 3.462678 GGCCTCCTCGGTGGACTC 61.463 72.222 8.19 0.00 40.56 3.36
2423 2800 3.846405 TTGGCCTCCTCGGTGGACT 62.846 63.158 10.98 0.00 40.56 3.85
2424 2801 3.316573 CTTGGCCTCCTCGGTGGAC 62.317 68.421 3.32 5.60 40.56 4.02
2425 2802 3.003173 CTTGGCCTCCTCGGTGGA 61.003 66.667 3.32 0.00 43.86 4.02
2426 2803 4.101448 CCTTGGCCTCCTCGGTGG 62.101 72.222 3.32 0.00 34.25 4.61
2427 2804 4.785453 GCCTTGGCCTCCTCGGTG 62.785 72.222 3.32 0.00 34.25 4.94
2445 2822 0.391130 TGGATTCCTTGTTCTCGGCG 60.391 55.000 0.00 0.00 0.00 6.46
2549 2927 3.167945 GGCGTTACACGACGTCCG 61.168 66.667 10.58 7.63 46.05 4.79
2601 2980 0.878523 GCATAGCGCGGTGGATAACA 60.879 55.000 23.02 0.00 0.00 2.41
2701 3080 2.414994 TATTCTGTCCGAGTCCGACT 57.585 50.000 12.01 0.00 38.22 4.18
2703 3082 3.675228 GCTTTTATTCTGTCCGAGTCCGA 60.675 47.826 0.00 0.00 38.22 4.55
2704 3083 2.603560 GCTTTTATTCTGTCCGAGTCCG 59.396 50.000 0.00 0.00 0.00 4.79
2705 3084 2.603560 CGCTTTTATTCTGTCCGAGTCC 59.396 50.000 0.00 0.00 0.00 3.85
2706 3085 3.060895 CACGCTTTTATTCTGTCCGAGTC 59.939 47.826 0.00 0.00 0.00 3.36
2707 3086 2.993899 CACGCTTTTATTCTGTCCGAGT 59.006 45.455 0.00 0.00 0.00 4.18
2708 3087 3.250744 TCACGCTTTTATTCTGTCCGAG 58.749 45.455 0.00 0.00 0.00 4.63
2726 3105 4.201990 CCAGCATAAATTTCAGGCTCTCAC 60.202 45.833 7.86 0.00 31.30 3.51
2728 3107 3.950395 ACCAGCATAAATTTCAGGCTCTC 59.050 43.478 7.86 0.00 31.30 3.20
2729 3108 3.973425 ACCAGCATAAATTTCAGGCTCT 58.027 40.909 7.86 0.00 31.30 4.09
2740 3119 4.819105 ACTAGCACAGTACCAGCATAAA 57.181 40.909 4.85 0.00 34.98 1.40
2745 3124 3.254892 GAGAAACTAGCACAGTACCAGC 58.745 50.000 0.00 0.00 36.04 4.85
2757 3136 1.546476 ACTGCAGGACGGAGAAACTAG 59.454 52.381 19.93 0.00 36.36 2.57
2759 3138 0.034059 CACTGCAGGACGGAGAAACT 59.966 55.000 19.93 0.00 36.36 2.66
2760 3139 1.569479 GCACTGCAGGACGGAGAAAC 61.569 60.000 19.93 0.00 36.36 2.78
2761 3140 1.301716 GCACTGCAGGACGGAGAAA 60.302 57.895 19.93 0.00 36.36 2.52
2763 3142 2.601666 AGCACTGCAGGACGGAGA 60.602 61.111 19.93 0.00 36.36 3.71
2764 3143 2.433838 CAGCACTGCAGGACGGAG 60.434 66.667 19.93 1.55 39.42 4.63
2765 3144 2.917227 TCAGCACTGCAGGACGGA 60.917 61.111 19.93 12.52 0.00 4.69
2766 3145 2.740055 GTCAGCACTGCAGGACGG 60.740 66.667 19.93 10.25 0.00 4.79
2767 3146 3.108289 CGTCAGCACTGCAGGACG 61.108 66.667 24.46 24.46 45.79 4.79
2768 3147 2.154798 TACCGTCAGCACTGCAGGAC 62.155 60.000 19.93 14.14 33.80 3.85
2769 3148 1.906333 TACCGTCAGCACTGCAGGA 60.906 57.895 19.93 2.02 33.34 3.86
2771 3150 1.738099 GGTACCGTCAGCACTGCAG 60.738 63.158 13.48 13.48 0.00 4.41
2772 3151 2.342279 GGTACCGTCAGCACTGCA 59.658 61.111 3.30 0.00 0.00 4.41
2773 3152 2.809601 CGGTACCGTCAGCACTGC 60.810 66.667 26.39 0.00 34.35 4.40
2783 3162 2.807895 CGGTTCAGCACGGTACCG 60.808 66.667 32.22 32.22 46.22 4.02
2784 3163 2.433664 CCGGTTCAGCACGGTACC 60.434 66.667 0.16 0.16 44.85 3.34
2818 3197 0.324943 CGTGAGGAAACATCCCAGGT 59.675 55.000 0.00 0.00 0.00 4.00
2819 3198 1.026718 GCGTGAGGAAACATCCCAGG 61.027 60.000 0.00 0.00 0.00 4.45
2820 3199 0.321564 TGCGTGAGGAAACATCCCAG 60.322 55.000 0.00 0.00 0.00 4.45
2821 3200 0.605319 GTGCGTGAGGAAACATCCCA 60.605 55.000 0.00 0.00 0.00 4.37
2822 3201 0.321653 AGTGCGTGAGGAAACATCCC 60.322 55.000 0.00 0.00 0.00 3.85
2823 3202 0.798776 CAGTGCGTGAGGAAACATCC 59.201 55.000 0.00 0.00 0.00 3.51
2824 3203 1.512926 ACAGTGCGTGAGGAAACATC 58.487 50.000 0.00 0.00 0.00 3.06
2825 3204 2.831685 TACAGTGCGTGAGGAAACAT 57.168 45.000 0.00 0.00 0.00 2.71
2826 3205 2.479837 CTTACAGTGCGTGAGGAAACA 58.520 47.619 0.00 0.00 0.00 2.83
2835 3214 2.914059 ACAGAAAACCTTACAGTGCGT 58.086 42.857 0.00 0.00 0.00 5.24
2837 3216 5.243426 TCAAACAGAAAACCTTACAGTGC 57.757 39.130 0.00 0.00 0.00 4.40
2839 3218 6.827586 TGTTCAAACAGAAAACCTTACAGT 57.172 33.333 0.00 0.00 38.13 3.55
2853 3232 2.029828 ACAAAACCGCACTGTTCAAACA 60.030 40.909 0.00 0.00 37.37 2.83
2861 3240 1.002468 CTCCTTCACAAAACCGCACTG 60.002 52.381 0.00 0.00 0.00 3.66
2862 3241 1.308998 CTCCTTCACAAAACCGCACT 58.691 50.000 0.00 0.00 0.00 4.40
2863 3242 1.002792 GACTCCTTCACAAAACCGCAC 60.003 52.381 0.00 0.00 0.00 5.34
2866 3245 1.873591 CAGGACTCCTTCACAAAACCG 59.126 52.381 0.00 0.00 0.00 4.44
2872 3253 3.515502 CAGGATTACAGGACTCCTTCACA 59.484 47.826 0.00 0.00 37.30 3.58
2873 3254 3.515901 ACAGGATTACAGGACTCCTTCAC 59.484 47.826 0.00 0.00 37.30 3.18
2881 3262 3.502211 CACACCAAACAGGATTACAGGAC 59.498 47.826 0.00 0.00 41.22 3.85
2884 3265 4.261572 CCAACACACCAAACAGGATTACAG 60.262 45.833 0.00 0.00 41.22 2.74
2909 3291 3.973206 TGTGGTACCAAGACACCATAG 57.027 47.619 18.31 0.00 46.15 2.23
2923 3305 2.609350 GAGCGAAACCGTTATGTGGTA 58.391 47.619 0.00 0.00 39.29 3.25
2927 3309 2.068837 TTCGAGCGAAACCGTTATGT 57.931 45.000 2.42 0.00 0.00 2.29
2928 3310 3.651562 ATTTCGAGCGAAACCGTTATG 57.348 42.857 18.81 0.00 45.34 1.90
2929 3311 4.436451 GGAAATTTCGAGCGAAACCGTTAT 60.436 41.667 18.81 1.13 45.34 1.89
2932 3314 1.196127 GGAAATTTCGAGCGAAACCGT 59.804 47.619 18.81 8.26 45.34 4.83
2943 3325 4.087930 CACGTTTGGAATTCGGAAATTTCG 59.912 41.667 11.95 7.72 35.21 3.46
2949 3331 2.943690 TGAACACGTTTGGAATTCGGAA 59.056 40.909 0.00 0.00 0.00 4.30
2950 3332 2.562635 TGAACACGTTTGGAATTCGGA 58.437 42.857 0.00 0.00 0.00 4.55
3025 3410 6.424207 GCTTGGATTTACTATAAGTCCGGAAG 59.576 42.308 5.23 1.06 0.00 3.46
3029 3414 6.201044 CAGTGCTTGGATTTACTATAAGTCCG 59.799 42.308 5.86 0.00 0.00 4.79
3036 3421 4.235079 TGGCAGTGCTTGGATTTACTAT 57.765 40.909 16.11 0.00 0.00 2.12
3040 3425 3.193267 GTGATTGGCAGTGCTTGGATTTA 59.807 43.478 16.11 0.00 0.00 1.40
3089 3484 8.680903 CATATCTCTCAACTTTTGGCTATGTTT 58.319 33.333 0.00 0.00 0.00 2.83
3272 3673 1.601477 TGTACTCCGTGGACTCGCA 60.601 57.895 0.00 0.00 0.00 5.10
3274 3675 1.134075 CGTGTACTCCGTGGACTCG 59.866 63.158 0.00 0.00 0.00 4.18
3282 3683 2.385315 CACATATCAGCGTGTACTCCG 58.615 52.381 0.00 0.00 0.00 4.63
3287 3688 0.105964 GGCCCACATATCAGCGTGTA 59.894 55.000 0.00 0.00 0.00 2.90
3325 3726 8.837389 GGGTAAGCGAATATTTATTTTCTGAGT 58.163 33.333 0.00 0.00 0.00 3.41
3393 3805 1.076014 GTGGGTTAGGGTTGGGTGG 59.924 63.158 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.