Multiple sequence alignment - TraesCS2A01G109900

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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 TraesCS2A01G109900 chr2A 100.000 3885 0 0 1 3885 61492122 61488238 0.000000e+00 7175.0
1 TraesCS2A01G109900 chr2A 81.148 122 20 3 2286 2404 411110994 411111115 1.150000e-15 95.3
2 TraesCS2A01G109900 chr2B 89.583 1440 119 14 684 2107 95799579 95798155 0.000000e+00 1799.0
3 TraesCS2A01G109900 chr2B 86.740 1267 104 25 2603 3820 95797673 95796422 0.000000e+00 1351.0
4 TraesCS2A01G109900 chr2B 91.129 248 16 4 403 649 95802720 95802478 8.050000e-87 331.0
5 TraesCS2A01G109900 chr2B 89.453 256 19 5 122 374 95803108 95802858 2.250000e-82 316.0
6 TraesCS2A01G109900 chr2B 87.568 185 21 2 2106 2288 95798041 95797857 3.040000e-51 213.0
7 TraesCS2A01G109900 chr2B 81.143 175 13 6 2402 2556 95797858 95797684 5.270000e-24 122.0
8 TraesCS2A01G109900 chr2B 100.000 39 0 0 82 120 95803232 95803194 5.380000e-09 73.1
9 TraesCS2A01G109900 chr2D 91.494 1258 78 16 771 2012 61025113 61023869 0.000000e+00 1703.0
10 TraesCS2A01G109900 chr2D 89.362 752 58 8 2401 3132 61023526 61022777 0.000000e+00 926.0
11 TraesCS2A01G109900 chr2D 84.375 672 57 22 3248 3885 61022336 61021679 1.980000e-172 616.0
12 TraesCS2A01G109900 chr2D 92.025 326 24 2 1 325 61025661 61025337 1.270000e-124 457.0
13 TraesCS2A01G109900 chr2D 87.324 213 18 4 499 711 61025334 61025131 6.490000e-58 235.0
14 TraesCS2A01G109900 chr2D 87.831 189 20 3 2106 2292 61023710 61023523 6.540000e-53 219.0
15 TraesCS2A01G109900 chr2D 87.179 78 8 1 2032 2107 61023870 61023793 1.920000e-13 87.9
16 TraesCS2A01G109900 chr4A 76.886 623 109 27 1084 1685 215248574 215247966 1.740000e-83 320.0
17 TraesCS2A01G109900 chr4A 86.705 173 23 0 3499 3671 3351736 3351564 3.960000e-45 193.0
18 TraesCS2A01G109900 chr4A 86.228 167 22 1 2718 2884 215224057 215223892 3.080000e-41 180.0
19 TraesCS2A01G109900 chr4D 76.688 622 113 26 1084 1685 294349461 294350070 2.250000e-82 316.0
20 TraesCS2A01G109900 chr4D 87.805 164 20 0 2718 2881 294351952 294352115 3.960000e-45 193.0
21 TraesCS2A01G109900 chr4D 86.127 173 24 0 3496 3668 467636119 467636291 1.840000e-43 187.0
22 TraesCS2A01G109900 chr4B 76.763 624 110 24 1084 1685 362146899 362147509 2.250000e-82 316.0
23 TraesCS2A01G109900 chr4B 87.283 173 22 0 3496 3668 585822368 585822540 8.510000e-47 198.0
24 TraesCS2A01G109900 chr4B 87.805 164 20 0 2718 2881 362149449 362149612 3.960000e-45 193.0
25 TraesCS2A01G109900 chr4B 85.795 176 24 1 3493 3668 585963794 585963968 6.630000e-43 185.0
26 TraesCS2A01G109900 chr5D 88.038 209 23 2 3497 3704 412960964 412960757 3.000000e-61 246.0
27 TraesCS2A01G109900 chr5A 88.038 209 23 2 3497 3704 525026298 525026091 3.000000e-61 246.0
28 TraesCS2A01G109900 chr5B 87.500 208 24 2 3498 3704 497504868 497504662 5.020000e-59 239.0
29 TraesCS2A01G109900 chr5B 80.833 120 19 3 2288 2403 590183643 590183762 1.490000e-14 91.6
30 TraesCS2A01G109900 chr5B 91.837 49 4 0 2356 2404 61587 61635 6.970000e-08 69.4
31 TraesCS2A01G109900 chr5B 85.965 57 8 0 2348 2404 72083942 72083886 1.170000e-05 62.1
32 TraesCS2A01G109900 chr3A 91.837 49 4 0 2356 2404 103430474 103430522 6.970000e-08 69.4
33 TraesCS2A01G109900 chrUn 89.796 49 5 0 2356 2404 261272592 261272640 3.240000e-06 63.9
34 TraesCS2A01G109900 chrUn 89.796 49 5 0 2356 2404 278230630 278230678 3.240000e-06 63.9
35 TraesCS2A01G109900 chr6D 88.462 52 6 0 2356 2407 343461015 343460964 3.240000e-06 63.9
36 TraesCS2A01G109900 chr6D 88.462 52 6 0 2356 2407 422737463 422737412 3.240000e-06 63.9


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 TraesCS2A01G109900 chr2A 61488238 61492122 3884 True 7175.000000 7175 100.000000 1 3885 1 chr2A.!!$R1 3884
1 TraesCS2A01G109900 chr2B 95796422 95803232 6810 True 600.728571 1799 89.373714 82 3820 7 chr2B.!!$R1 3738
2 TraesCS2A01G109900 chr2D 61021679 61025661 3982 True 606.271429 1703 88.512857 1 3885 7 chr2D.!!$R1 3884
3 TraesCS2A01G109900 chr4A 215247966 215248574 608 True 320.000000 320 76.886000 1084 1685 1 chr4A.!!$R3 601
4 TraesCS2A01G109900 chr4D 294349461 294352115 2654 False 254.500000 316 82.246500 1084 2881 2 chr4D.!!$F2 1797
5 TraesCS2A01G109900 chr4B 362146899 362149612 2713 False 254.500000 316 82.284000 1084 2881 2 chr4B.!!$F3 1797

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
495 693 0.035317 ACAGAAGCCTCATCGTTGCA 59.965 50.0 0.00 0.0 0.00 4.08 F
1492 4617 0.169230 TGTTTGTGGTTGTGACACGC 59.831 50.0 0.22 0.0 41.64 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 6849 0.040067 CAAGAAGGAACAGCGGCAAC 60.04 55.0 1.45 0.0 0.0 4.17 R
2893 7473 0.030235 GTGACAAGGGTGCCGAAAAC 59.97 55.0 0.00 0.0 0.0 2.43 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
37 38 8.917655 ACAATAAACCACACGTAAAATTAATGC 58.082 29.630 0.00 0.00 0.00 3.56
49 50 6.692681 CGTAAAATTAATGCATCACCAAGGAG 59.307 38.462 0.00 0.00 0.00 3.69
57 58 2.482839 GCATCACCAAGGAGCTCTAGTC 60.483 54.545 14.64 0.00 0.00 2.59
58 59 1.853963 TCACCAAGGAGCTCTAGTCC 58.146 55.000 14.64 0.00 0.00 3.85
62 63 1.480137 CCAAGGAGCTCTAGTCCAGTG 59.520 57.143 14.64 0.01 36.43 3.66
63 64 2.451490 CAAGGAGCTCTAGTCCAGTGA 58.549 52.381 14.64 0.00 36.43 3.41
120 121 7.087409 TGTATGCTGGTTATTTTGTCATCTG 57.913 36.000 0.00 0.00 0.00 2.90
124 209 4.860907 GCTGGTTATTTTGTCATCTGCAAG 59.139 41.667 0.00 0.00 0.00 4.01
133 218 0.750546 TCATCTGCAAGCCATGAGCC 60.751 55.000 0.00 0.00 45.47 4.70
142 227 2.128771 AGCCATGAGCCGTAACAAAT 57.871 45.000 0.00 0.00 45.47 2.32
179 264 2.460757 ATGGTGCACAATTTCCTTGC 57.539 45.000 20.43 0.00 38.50 4.01
192 277 8.649841 CACAATTTCCTTGCATGTGTTTATTAG 58.350 33.333 6.25 0.00 38.50 1.73
225 310 1.683011 CCCCTCAGCAAGTTATGGGTG 60.683 57.143 0.00 0.00 33.13 4.61
253 338 3.245371 TGGGCTGATCCATGTCTCTTTTT 60.245 43.478 0.00 0.00 36.21 1.94
275 360 4.273318 TCTGCTGTGCTATCTACTTCAGA 58.727 43.478 0.00 0.00 37.79 3.27
310 395 0.035439 CAAGCCTACATGTTCCCGGT 60.035 55.000 2.30 0.00 0.00 5.28
314 399 0.828022 CCTACATGTTCCCGGTGCTA 59.172 55.000 2.30 0.00 0.00 3.49
332 417 2.678336 GCTACAAAGCGTGCCTAATCTT 59.322 45.455 0.00 0.00 39.39 2.40
333 418 3.242446 GCTACAAAGCGTGCCTAATCTTC 60.242 47.826 0.00 0.00 39.39 2.87
336 421 3.437049 ACAAAGCGTGCCTAATCTTCTTC 59.563 43.478 0.00 0.00 0.00 2.87
338 423 3.172229 AGCGTGCCTAATCTTCTTCTC 57.828 47.619 0.00 0.00 0.00 2.87
341 426 3.553917 GCGTGCCTAATCTTCTTCTCTTC 59.446 47.826 0.00 0.00 0.00 2.87
365 453 1.102154 TTTGCGATGGGTGCCTAATG 58.898 50.000 0.00 0.00 0.00 1.90
374 462 6.173339 CGATGGGTGCCTAATGATTTATAGT 58.827 40.000 0.00 0.00 0.00 2.12
375 463 7.327975 CGATGGGTGCCTAATGATTTATAGTA 58.672 38.462 0.00 0.00 0.00 1.82
376 464 7.822334 CGATGGGTGCCTAATGATTTATAGTAA 59.178 37.037 0.00 0.00 0.00 2.24
379 467 8.275758 TGGGTGCCTAATGATTTATAGTAACAA 58.724 33.333 0.00 0.00 0.00 2.83
380 468 8.784043 GGGTGCCTAATGATTTATAGTAACAAG 58.216 37.037 0.00 0.00 0.00 3.16
381 469 9.555727 GGTGCCTAATGATTTATAGTAACAAGA 57.444 33.333 0.00 0.00 0.00 3.02
398 595 5.048846 ACAAGAAAGACATAACACCAGGT 57.951 39.130 0.00 0.00 0.00 4.00
399 596 5.445964 ACAAGAAAGACATAACACCAGGTT 58.554 37.500 0.00 0.00 43.62 3.50
401 598 6.379988 ACAAGAAAGACATAACACCAGGTTTT 59.620 34.615 0.00 0.00 40.96 2.43
411 608 1.682854 CACCAGGTTTTGCACTGTGAT 59.317 47.619 12.86 0.00 32.90 3.06
414 611 2.288395 CCAGGTTTTGCACTGTGATTCC 60.288 50.000 12.86 5.98 32.90 3.01
416 613 1.606668 GGTTTTGCACTGTGATTCCGA 59.393 47.619 12.86 0.00 0.00 4.55
418 615 2.254546 TTTGCACTGTGATTCCGACT 57.745 45.000 12.86 0.00 0.00 4.18
448 646 4.268884 CACAACAAAACAATAAACCACCGG 59.731 41.667 0.00 0.00 0.00 5.28
482 680 0.670162 CCACCAAGCACCAACAGAAG 59.330 55.000 0.00 0.00 0.00 2.85
484 682 1.109323 ACCAAGCACCAACAGAAGCC 61.109 55.000 0.00 0.00 0.00 4.35
490 688 1.081892 CACCAACAGAAGCCTCATCG 58.918 55.000 0.00 0.00 0.00 3.84
495 693 0.035317 ACAGAAGCCTCATCGTTGCA 59.965 50.000 0.00 0.00 0.00 4.08
525 723 2.167693 TGTACCACCTCCTTATCGCAAG 59.832 50.000 0.00 0.00 0.00 4.01
600 798 4.816385 GTCTGTCTGAACATCCAAACTTCA 59.184 41.667 0.00 0.00 34.13 3.02
613 811 6.072112 TCCAAACTTCAAATAGTTGAGCAC 57.928 37.500 5.67 0.00 44.49 4.40
621 819 5.847367 TCAAATAGTTGAGCACGAGTGCAC 61.847 45.833 27.08 21.81 45.84 4.57
644 842 3.679389 ACTCACCTTGATCACATGTTCC 58.321 45.455 0.00 0.00 0.00 3.62
649 847 3.822735 ACCTTGATCACATGTTCCAAGTG 59.177 43.478 20.86 16.62 34.86 3.16
651 849 3.786368 TGATCACATGTTCCAAGTGGA 57.214 42.857 0.00 0.00 43.73 4.02
652 850 3.678289 TGATCACATGTTCCAAGTGGAG 58.322 45.455 0.00 0.00 46.36 3.86
653 851 3.327464 TGATCACATGTTCCAAGTGGAGA 59.673 43.478 0.00 0.00 46.36 3.71
654 852 3.407424 TCACATGTTCCAAGTGGAGAG 57.593 47.619 0.00 0.00 46.36 3.20
655 853 2.972021 TCACATGTTCCAAGTGGAGAGA 59.028 45.455 0.00 0.00 46.36 3.10
656 854 3.007290 TCACATGTTCCAAGTGGAGAGAG 59.993 47.826 0.00 0.00 46.36 3.20
657 855 3.007290 CACATGTTCCAAGTGGAGAGAGA 59.993 47.826 0.00 0.00 46.36 3.10
679 3741 7.886970 AGAGAGAGAGAGAGAAATATCATCTGG 59.113 40.741 0.00 0.00 0.00 3.86
680 3742 6.435277 AGAGAGAGAGAGAAATATCATCTGGC 59.565 42.308 0.00 0.00 0.00 4.85
682 3744 7.469343 AGAGAGAGAGAAATATCATCTGGCTA 58.531 38.462 0.00 0.00 0.00 3.93
711 3773 6.072508 CCAGCACAATAAGCTCTTCACTTTTA 60.073 38.462 0.00 0.00 41.14 1.52
712 3774 6.798959 CAGCACAATAAGCTCTTCACTTTTAC 59.201 38.462 0.00 0.00 41.14 2.01
716 3778 9.736023 CACAATAAGCTCTTCACTTTTACTTTT 57.264 29.630 0.00 0.00 0.00 2.27
739 3801 6.723298 TTTTTGGAAATAAGCTCTTCACCA 57.277 33.333 0.00 0.00 0.00 4.17
741 3803 6.515272 TTTGGAAATAAGCTCTTCACCATC 57.485 37.500 0.00 0.00 0.00 3.51
759 3821 4.996788 CATCTTTTGGAGGCAATAAGCT 57.003 40.909 0.00 0.00 44.79 3.74
768 3830 3.376546 GGAGGCAATAAGCTCTTCACTTG 59.623 47.826 0.00 0.00 44.79 3.16
770 3832 4.853007 AGGCAATAAGCTCTTCACTTGAT 58.147 39.130 0.00 0.00 44.79 2.57
772 3834 5.713861 AGGCAATAAGCTCTTCACTTGATTT 59.286 36.000 0.00 0.00 44.79 2.17
773 3835 6.886459 AGGCAATAAGCTCTTCACTTGATTTA 59.114 34.615 0.00 0.00 44.79 1.40
774 3836 7.559170 AGGCAATAAGCTCTTCACTTGATTTAT 59.441 33.333 0.00 0.00 44.79 1.40
775 3837 8.193438 GGCAATAAGCTCTTCACTTGATTTATT 58.807 33.333 0.00 0.00 44.79 1.40
776 3838 9.578439 GCAATAAGCTCTTCACTTGATTTATTT 57.422 29.630 0.00 0.00 41.15 1.40
824 3886 3.602205 AAGGAACAAGGAAGGCTTCTT 57.398 42.857 25.25 16.64 0.00 2.52
938 4005 1.272425 CCATCCAAAACCCTAGCACCA 60.272 52.381 0.00 0.00 0.00 4.17
1018 4091 4.342862 ACCATGGTAATCTCTCATTCCG 57.657 45.455 18.10 0.00 0.00 4.30
1029 4102 1.753368 CTCATTCCGCTCCCTCCTCC 61.753 65.000 0.00 0.00 0.00 4.30
1047 4120 2.163412 CTCCTCGTCTTCCTCTGAACTG 59.837 54.545 0.00 0.00 0.00 3.16
1077 4150 4.289245 ACACCGTCCGTTCCCGTG 62.289 66.667 0.00 0.00 0.00 4.94
1249 4370 4.339247 AGGGATTCAGATTTACCGCAATTG 59.661 41.667 0.00 0.00 0.00 2.32
1251 4372 4.338118 GGATTCAGATTTACCGCAATTGGA 59.662 41.667 7.72 0.00 0.00 3.53
1283 4404 1.142097 GCTCTACCGCTTCCTGGTC 59.858 63.158 0.00 0.00 40.96 4.02
1352 4473 4.660938 AGCAAGACCAACCGCCCC 62.661 66.667 0.00 0.00 0.00 5.80
1411 4532 1.457009 AAGGTATCCCTCTCTCGCGC 61.457 60.000 0.00 0.00 41.56 6.86
1412 4533 2.252855 GTATCCCTCTCTCGCGCG 59.747 66.667 26.76 26.76 0.00 6.86
1413 4534 3.661131 TATCCCTCTCTCGCGCGC 61.661 66.667 27.95 23.91 0.00 6.86
1487 4612 1.658686 GGCGGTGTTTGTGGTTGTGA 61.659 55.000 0.00 0.00 0.00 3.58
1488 4613 0.524604 GCGGTGTTTGTGGTTGTGAC 60.525 55.000 0.00 0.00 0.00 3.67
1489 4614 0.805614 CGGTGTTTGTGGTTGTGACA 59.194 50.000 0.00 0.00 0.00 3.58
1490 4615 1.466697 CGGTGTTTGTGGTTGTGACAC 60.467 52.381 0.00 0.00 39.76 3.67
1491 4616 1.466697 GGTGTTTGTGGTTGTGACACG 60.467 52.381 0.22 0.00 41.01 4.49
1492 4617 0.169230 TGTTTGTGGTTGTGACACGC 59.831 50.000 0.22 0.00 41.64 5.34
1519 4661 2.362397 GGAGGACAAGATCGCTGTGATA 59.638 50.000 3.28 0.00 37.47 2.15
1654 4796 0.669318 TTACCTTTGACCAGCTCGCG 60.669 55.000 0.00 0.00 0.00 5.87
1744 5138 7.549842 TGCTAATATTGCTGTTTGATGCATTTT 59.450 29.630 0.00 0.00 39.07 1.82
1763 5157 9.519191 TGCATTTTATATTGCATGAGGTAGTAT 57.481 29.630 0.00 0.00 43.54 2.12
1770 5166 3.808728 TGCATGAGGTAGTATCCAAAGC 58.191 45.455 0.00 0.00 0.00 3.51
1778 5174 7.630082 TGAGGTAGTATCCAAAGCTTTACAAT 58.370 34.615 12.25 8.20 0.00 2.71
1793 5189 6.542852 GCTTTACAATCGAAGCAGACAATTA 58.457 36.000 0.00 0.00 45.74 1.40
1828 5225 7.222000 ACTATTAAGTATGCTAGACTCCTGC 57.778 40.000 0.00 0.00 32.84 4.85
1865 5262 7.765307 ACCAAGTTTATTGTTCATGCTCATAG 58.235 34.615 0.00 0.00 0.00 2.23
1887 5285 9.347934 CATAGTGTGTTACAGAGAGACTTTTAG 57.652 37.037 0.00 0.00 0.00 1.85
1914 5809 3.265995 AGGTTGTGGTAGGGTATTCAAGG 59.734 47.826 0.00 0.00 0.00 3.61
1951 5846 7.753309 TTTTTCTGATTCATCGGTTTTCCTA 57.247 32.000 0.00 0.00 37.95 2.94
1967 5862 6.072119 GGTTTTCCTATTGTCAGGTGTTAAGG 60.072 42.308 0.00 0.00 36.99 2.69
2017 6057 9.742144 ATCTGTCTAAATCTATATCGTGTACCT 57.258 33.333 0.00 0.00 0.00 3.08
2020 6060 9.783081 TGTCTAAATCTATATCGTGTACCTACA 57.217 33.333 0.00 0.00 0.00 2.74
2022 6062 8.944029 TCTAAATCTATATCGTGTACCTACAGC 58.056 37.037 0.00 0.00 36.78 4.40
2023 6063 6.512342 AATCTATATCGTGTACCTACAGCC 57.488 41.667 0.00 0.00 36.78 4.85
2024 6064 4.976864 TCTATATCGTGTACCTACAGCCA 58.023 43.478 0.00 0.00 36.78 4.75
2025 6065 5.379187 TCTATATCGTGTACCTACAGCCAA 58.621 41.667 0.00 0.00 36.78 4.52
2026 6066 6.008331 TCTATATCGTGTACCTACAGCCAAT 58.992 40.000 0.00 0.00 36.78 3.16
2027 6067 3.906720 ATCGTGTACCTACAGCCAATT 57.093 42.857 0.00 0.00 36.78 2.32
2028 6068 2.967362 TCGTGTACCTACAGCCAATTG 58.033 47.619 0.00 0.00 36.78 2.32
2029 6069 1.396996 CGTGTACCTACAGCCAATTGC 59.603 52.381 0.00 0.00 36.78 3.56
2030 6070 2.432444 GTGTACCTACAGCCAATTGCA 58.568 47.619 0.00 0.00 44.83 4.08
2073 6201 3.299503 ACAGCTGGTCAAATTTCCAACT 58.700 40.909 19.93 0.00 33.06 3.16
2074 6202 3.706086 ACAGCTGGTCAAATTTCCAACTT 59.294 39.130 19.93 0.00 33.06 2.66
2075 6203 4.162131 ACAGCTGGTCAAATTTCCAACTTT 59.838 37.500 19.93 0.00 33.06 2.66
2179 6423 6.259167 TGCTTATTTTATGGTAGTAGTTGCGG 59.741 38.462 0.00 0.00 0.00 5.69
2181 6425 7.517893 GCTTATTTTATGGTAGTAGTTGCGGTC 60.518 40.741 0.00 0.00 0.00 4.79
2190 6434 2.366266 AGTAGTTGCGGTCTTGGTTACA 59.634 45.455 0.00 0.00 0.00 2.41
2239 6483 9.952341 CTTTGTTAAGAGTTGTTTAAAACTTGC 57.048 29.630 0.00 0.00 40.48 4.01
2295 6618 8.738645 AATCTTTGTTGATTCATAGTACTCCC 57.261 34.615 0.00 0.00 31.72 4.30
2296 6619 7.496346 TCTTTGTTGATTCATAGTACTCCCT 57.504 36.000 0.00 0.00 0.00 4.20
2297 6620 7.556844 TCTTTGTTGATTCATAGTACTCCCTC 58.443 38.462 0.00 0.00 0.00 4.30
2299 6622 4.341235 TGTTGATTCATAGTACTCCCTCCG 59.659 45.833 0.00 0.00 0.00 4.63
2300 6623 4.180377 TGATTCATAGTACTCCCTCCGT 57.820 45.455 0.00 0.00 0.00 4.69
2301 6624 4.142790 TGATTCATAGTACTCCCTCCGTC 58.857 47.826 0.00 0.00 0.00 4.79
2302 6625 2.653234 TCATAGTACTCCCTCCGTCC 57.347 55.000 0.00 0.00 0.00 4.79
2304 6627 2.158652 TCATAGTACTCCCTCCGTCCTG 60.159 54.545 0.00 0.00 0.00 3.86
2305 6628 0.549950 TAGTACTCCCTCCGTCCTGG 59.450 60.000 0.00 0.00 40.09 4.45
2315 6638 2.953466 TCCGTCCTGGATACTTTTCG 57.047 50.000 0.00 0.00 43.74 3.46
2316 6639 1.134907 TCCGTCCTGGATACTTTTCGC 60.135 52.381 0.00 0.00 43.74 4.70
2317 6640 0.921347 CGTCCTGGATACTTTTCGCG 59.079 55.000 0.00 0.00 37.61 5.87
2318 6641 1.287425 GTCCTGGATACTTTTCGCGG 58.713 55.000 6.13 0.00 37.61 6.46
2319 6642 1.134907 GTCCTGGATACTTTTCGCGGA 60.135 52.381 6.13 0.00 37.61 5.54
2320 6643 1.551430 TCCTGGATACTTTTCGCGGAA 59.449 47.619 6.13 0.00 37.61 4.30
2321 6644 2.169769 TCCTGGATACTTTTCGCGGAAT 59.830 45.455 6.13 0.00 37.61 3.01
2322 6645 2.287915 CCTGGATACTTTTCGCGGAATG 59.712 50.000 6.13 9.18 37.61 2.67
2323 6646 3.194861 CTGGATACTTTTCGCGGAATGA 58.805 45.455 18.98 4.19 37.61 2.57
2324 6647 3.601435 TGGATACTTTTCGCGGAATGAA 58.399 40.909 18.98 0.00 37.61 2.57
2334 6755 6.912203 TTTCGCGGAATGAATAGAAATGTA 57.088 33.333 6.13 0.00 0.00 2.29
2336 6757 6.466308 TCGCGGAATGAATAGAAATGTATG 57.534 37.500 6.13 0.00 0.00 2.39
2340 6761 7.417612 GCGGAATGAATAGAAATGTATGTGTT 58.582 34.615 0.00 0.00 0.00 3.32
2341 6762 8.556194 GCGGAATGAATAGAAATGTATGTGTTA 58.444 33.333 0.00 0.00 0.00 2.41
2376 6797 9.698309 ATATGTCTAGATTCATCCACTTTTACG 57.302 33.333 0.00 0.00 0.00 3.18
2377 6798 7.165460 TGTCTAGATTCATCCACTTTTACGA 57.835 36.000 0.00 0.00 0.00 3.43
2378 6799 7.033791 TGTCTAGATTCATCCACTTTTACGAC 58.966 38.462 0.00 0.00 0.00 4.34
2379 6800 7.033791 GTCTAGATTCATCCACTTTTACGACA 58.966 38.462 0.00 0.00 0.00 4.35
2380 6801 7.544566 GTCTAGATTCATCCACTTTTACGACAA 59.455 37.037 0.00 0.00 0.00 3.18
2381 6802 6.727824 AGATTCATCCACTTTTACGACAAG 57.272 37.500 0.00 0.00 0.00 3.16
2382 6803 6.231211 AGATTCATCCACTTTTACGACAAGT 58.769 36.000 0.00 0.00 34.67 3.16
2383 6804 7.383687 AGATTCATCCACTTTTACGACAAGTA 58.616 34.615 0.00 0.00 32.48 2.24
2384 6805 7.876068 AGATTCATCCACTTTTACGACAAGTAA 59.124 33.333 0.00 0.00 43.05 2.24
2385 6806 7.972832 TTCATCCACTTTTACGACAAGTAAT 57.027 32.000 0.00 0.00 44.03 1.89
2386 6807 7.972832 TCATCCACTTTTACGACAAGTAATT 57.027 32.000 0.00 0.00 44.03 1.40
2387 6808 8.025243 TCATCCACTTTTACGACAAGTAATTC 57.975 34.615 0.00 0.00 44.03 2.17
2388 6809 6.790285 TCCACTTTTACGACAAGTAATTCC 57.210 37.500 0.00 0.00 44.03 3.01
2389 6810 5.406175 TCCACTTTTACGACAAGTAATTCCG 59.594 40.000 0.00 0.00 44.03 4.30
2390 6811 5.390145 CCACTTTTACGACAAGTAATTCCGG 60.390 44.000 0.00 0.00 44.03 5.14
2391 6812 5.406175 CACTTTTACGACAAGTAATTCCGGA 59.594 40.000 0.00 0.00 44.03 5.14
2392 6813 5.406477 ACTTTTACGACAAGTAATTCCGGAC 59.594 40.000 1.83 0.00 44.03 4.79
2393 6814 4.517952 TTACGACAAGTAATTCCGGACA 57.482 40.909 1.83 0.00 40.15 4.02
2394 6815 2.955614 ACGACAAGTAATTCCGGACAG 58.044 47.619 1.83 0.00 0.00 3.51
2395 6816 2.559668 ACGACAAGTAATTCCGGACAGA 59.440 45.455 1.83 0.00 0.00 3.41
2396 6817 3.179830 CGACAAGTAATTCCGGACAGAG 58.820 50.000 1.83 0.00 0.00 3.35
2397 6818 3.522553 GACAAGTAATTCCGGACAGAGG 58.477 50.000 1.83 0.00 0.00 3.69
2398 6819 2.236395 ACAAGTAATTCCGGACAGAGGG 59.764 50.000 1.83 0.00 0.00 4.30
2399 6820 2.500098 CAAGTAATTCCGGACAGAGGGA 59.500 50.000 1.83 0.00 0.00 4.20
2404 6825 0.679002 TTCCGGACAGAGGGAGTACG 60.679 60.000 1.83 0.00 42.81 3.67
2421 6844 5.288712 GGAGTACGTGATAATTCAGTGTGTG 59.711 44.000 0.00 0.00 30.85 3.82
2426 6849 5.139482 CGTGATAATTCAGTGTGTGTGTTG 58.861 41.667 0.00 0.00 30.85 3.33
2448 6871 0.884704 GCCGCTGTTCCTTCTTGACA 60.885 55.000 0.00 0.00 0.00 3.58
2451 6874 1.466167 CGCTGTTCCTTCTTGACATGG 59.534 52.381 0.00 0.00 0.00 3.66
2455 6878 4.392940 CTGTTCCTTCTTGACATGGTCTT 58.607 43.478 0.00 0.00 33.15 3.01
2469 6892 7.259882 TGACATGGTCTTTATGATTTCATTGC 58.740 34.615 0.00 0.00 34.32 3.56
2470 6893 6.267817 ACATGGTCTTTATGATTTCATTGCG 58.732 36.000 0.00 0.00 37.76 4.85
2515 6958 6.686630 AGTACATGCTACTGATGCTAGAATC 58.313 40.000 3.43 3.43 0.00 2.52
2520 6963 5.363101 TGCTACTGATGCTAGAATCTTTGG 58.637 41.667 12.15 2.28 0.00 3.28
2521 6964 5.104776 TGCTACTGATGCTAGAATCTTTGGT 60.105 40.000 12.15 7.98 0.00 3.67
2549 6992 6.607600 TGTAGTCATGTAGAGGTATTTGCTCT 59.392 38.462 0.00 0.00 0.00 4.09
2556 6999 8.768955 CATGTAGAGGTATTTGCTCTGATTTAC 58.231 37.037 0.00 0.00 0.00 2.01
2686 7131 6.437928 TGAAGCGTTATTCATGGATAAATGC 58.562 36.000 18.30 18.30 34.31 3.56
2687 7132 5.376854 AGCGTTATTCATGGATAAATGCC 57.623 39.130 20.71 5.64 31.00 4.40
2689 7134 5.477984 AGCGTTATTCATGGATAAATGCCAT 59.522 36.000 20.71 7.82 46.76 4.40
2707 7286 6.266168 TGCCATAGACAACCATTTTAACAG 57.734 37.500 0.00 0.00 0.00 3.16
2708 7287 5.772672 TGCCATAGACAACCATTTTAACAGT 59.227 36.000 0.00 0.00 0.00 3.55
2824 7404 0.886490 CCAAGCCATATGTCCGCTCC 60.886 60.000 5.56 0.00 30.92 4.70
2893 7473 2.178912 TCAAGGTTTAAGCCGTGGAG 57.821 50.000 20.73 3.95 38.32 3.86
2897 7477 2.940158 AGGTTTAAGCCGTGGAGTTTT 58.060 42.857 2.33 0.00 0.00 2.43
2898 7478 2.882761 AGGTTTAAGCCGTGGAGTTTTC 59.117 45.455 2.33 0.00 0.00 2.29
2904 7484 2.613506 CCGTGGAGTTTTCGGCACC 61.614 63.158 0.00 0.00 37.90 5.01
2910 7490 0.591659 GAGTTTTCGGCACCCTTGTC 59.408 55.000 0.00 0.00 0.00 3.18
2911 7491 0.106918 AGTTTTCGGCACCCTTGTCA 60.107 50.000 0.00 0.00 0.00 3.58
2915 7495 0.179004 TTCGGCACCCTTGTCACATT 60.179 50.000 0.00 0.00 0.00 2.71
2917 7497 0.039256 CGGCACCCTTGTCACATTTG 60.039 55.000 0.00 0.00 0.00 2.32
2918 7498 0.319813 GGCACCCTTGTCACATTTGC 60.320 55.000 0.00 0.00 0.00 3.68
2921 7501 1.682854 CACCCTTGTCACATTTGCTGT 59.317 47.619 0.00 0.00 39.20 4.40
2929 7515 3.435327 TGTCACATTTGCTGTTATCGGTC 59.565 43.478 0.00 0.00 35.29 4.79
2930 7516 3.435327 GTCACATTTGCTGTTATCGGTCA 59.565 43.478 0.00 0.00 35.29 4.02
2934 7520 4.943705 ACATTTGCTGTTATCGGTCAATCT 59.056 37.500 0.00 0.00 32.90 2.40
2939 7525 4.184629 GCTGTTATCGGTCAATCTTCACT 58.815 43.478 0.00 0.00 0.00 3.41
2977 7563 7.924947 CAGAATCATACTGCTTTAGATGTCAGA 59.075 37.037 0.00 0.00 0.00 3.27
2988 7574 3.567576 AGATGTCAGAGTCTTGTGTCG 57.432 47.619 0.00 0.00 0.00 4.35
3009 7595 5.517054 GTCGATGAGTATTCAGAACCAGTTC 59.483 44.000 2.19 2.19 36.61 3.01
3052 7640 2.522185 ACTTGAGACCATGCTTGCAAT 58.478 42.857 0.00 0.00 0.00 3.56
3104 7692 1.003866 GTTGTCTCCGTTTGCAGTGTC 60.004 52.381 0.00 0.00 0.00 3.67
3115 7703 1.577468 TGCAGTGTCGTTGGTGTTAG 58.423 50.000 0.00 0.00 0.00 2.34
3168 7802 8.603242 ATGTAACTTTTCAGTGTTCGTTAGAT 57.397 30.769 0.00 0.00 31.60 1.98
3243 8156 1.197721 GATGACAGTGGCCGTCAAAAG 59.802 52.381 14.81 0.00 45.91 2.27
3246 8159 1.283793 CAGTGGCCGTCAAAAGCAG 59.716 57.895 0.00 0.00 0.00 4.24
3266 8179 8.631480 AAGCAGATCATAATTCATCATAAGCA 57.369 30.769 0.00 0.00 0.00 3.91
3267 8180 8.041829 AGCAGATCATAATTCATCATAAGCAC 57.958 34.615 0.00 0.00 0.00 4.40
3311 8225 9.378551 AGCAATATTACATGTAGAAGAAACGAA 57.621 29.630 5.56 0.00 0.00 3.85
3340 8254 7.839680 TTCTATCTATCACATAGGCACTTGA 57.160 36.000 0.00 0.00 41.75 3.02
3342 8256 4.327982 TCTATCACATAGGCACTTGAGC 57.672 45.455 0.00 0.00 41.75 4.26
3353 8267 1.678360 CACTTGAGCGTTGATGTTGC 58.322 50.000 0.00 0.00 0.00 4.17
3444 8376 1.327690 ATGTACGACGGCTGGTGGAT 61.328 55.000 0.00 0.00 0.00 3.41
3454 8386 4.424711 TGGTGGATGAAGCCGGCC 62.425 66.667 26.15 9.73 0.00 6.13
3712 8656 3.535962 CTGCTCGGCTCCTCCTCC 61.536 72.222 0.00 0.00 0.00 4.30
3719 8663 4.828925 GCTCCTCCTCCGCTGCAC 62.829 72.222 0.00 0.00 0.00 4.57
3774 8725 0.457035 GGTACGTTCGGGCACAGATA 59.543 55.000 0.00 0.00 29.39 1.98
3775 8726 1.535437 GGTACGTTCGGGCACAGATAG 60.535 57.143 0.00 0.00 29.39 2.08
3776 8727 1.133790 GTACGTTCGGGCACAGATAGT 59.866 52.381 0.00 0.00 29.39 2.12
3778 8729 1.133790 ACGTTCGGGCACAGATAGTAC 59.866 52.381 0.00 0.00 29.39 2.73
3780 8731 1.133790 GTTCGGGCACAGATAGTACGT 59.866 52.381 0.00 0.00 29.39 3.57
3782 8733 2.216046 TCGGGCACAGATAGTACGTAG 58.784 52.381 0.00 0.00 0.00 3.51
3783 8734 1.266175 CGGGCACAGATAGTACGTAGG 59.734 57.143 0.00 0.00 0.00 3.18
3784 8735 2.579873 GGGCACAGATAGTACGTAGGA 58.420 52.381 0.00 0.00 0.00 2.94
3785 8736 2.553172 GGGCACAGATAGTACGTAGGAG 59.447 54.545 0.00 0.00 0.00 3.69
3786 8737 2.030981 GGCACAGATAGTACGTAGGAGC 60.031 54.545 0.00 0.00 0.00 4.70
3787 8738 2.617308 GCACAGATAGTACGTAGGAGCA 59.383 50.000 0.00 0.00 0.00 4.26
3788 8739 3.066342 GCACAGATAGTACGTAGGAGCAA 59.934 47.826 0.00 0.00 0.00 3.91
3789 8740 4.790123 GCACAGATAGTACGTAGGAGCAAG 60.790 50.000 0.00 0.00 0.00 4.01
3790 8741 4.335874 CACAGATAGTACGTAGGAGCAAGT 59.664 45.833 0.00 0.00 0.00 3.16
3804 8755 1.443194 CAAGTGCTTGGCGTGATGC 60.443 57.895 4.13 0.00 45.38 3.91
3811 8762 0.647410 CTTGGCGTGATGCTAGAACG 59.353 55.000 0.00 0.00 45.43 3.95
3830 8797 1.739067 GTGATGGTACCTTGGTGCTC 58.261 55.000 14.36 0.00 0.00 4.26
3831 8798 1.003118 GTGATGGTACCTTGGTGCTCA 59.997 52.381 14.36 5.03 0.00 4.26
3834 8801 1.377333 GGTACCTTGGTGCTCAGGC 60.377 63.158 4.06 0.00 39.26 4.85
3836 8803 2.214216 TACCTTGGTGCTCAGGCGT 61.214 57.895 2.03 0.00 42.25 5.68
3840 8807 1.572085 CTTGGTGCTCAGGCGTGAAG 61.572 60.000 10.76 6.09 42.25 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.916654 TGCATTAATTTTACGTGTGGTTTATTG 58.083 29.630 0.00 0.00 0.00 1.90
17 18 6.584563 GTGATGCATTAATTTTACGTGTGGTT 59.415 34.615 0.00 0.00 0.00 3.67
23 24 6.151985 TCCTTGGTGATGCATTAATTTTACGT 59.848 34.615 0.00 0.00 0.00 3.57
24 25 6.559810 TCCTTGGTGATGCATTAATTTTACG 58.440 36.000 0.00 0.00 0.00 3.18
37 38 2.102252 GGACTAGAGCTCCTTGGTGATG 59.898 54.545 10.93 0.00 0.00 3.07
49 50 6.040391 ACAGATTATTCTCACTGGACTAGAGC 59.960 42.308 0.00 0.00 35.08 4.09
57 58 6.430925 TGGTCAAAACAGATTATTCTCACTGG 59.569 38.462 0.00 0.00 35.08 4.00
58 59 7.361542 CCTGGTCAAAACAGATTATTCTCACTG 60.362 40.741 0.00 0.00 38.20 3.66
62 63 5.163612 GGCCTGGTCAAAACAGATTATTCTC 60.164 44.000 0.00 0.00 38.20 2.87
63 64 4.706962 GGCCTGGTCAAAACAGATTATTCT 59.293 41.667 0.00 0.00 38.20 2.40
120 121 1.305219 TGTTACGGCTCATGGCTTGC 61.305 55.000 6.20 0.39 41.46 4.01
124 209 1.742831 TGATTTGTTACGGCTCATGGC 59.257 47.619 0.00 0.00 40.90 4.40
133 218 6.678663 GCGCTATTGCTATATGATTTGTTACG 59.321 38.462 0.00 0.00 36.97 3.18
142 227 4.392754 CACCATTGCGCTATTGCTATATGA 59.607 41.667 9.73 0.00 36.97 2.15
179 264 8.119226 GCTTAGAACTGCTCTAATAAACACATG 58.881 37.037 1.33 0.00 44.06 3.21
192 277 0.905357 TGAGGGGCTTAGAACTGCTC 59.095 55.000 0.00 0.00 0.00 4.26
225 310 2.363359 GACATGGATCAGCCCAAATTCC 59.637 50.000 0.00 0.00 40.04 3.01
253 338 4.273318 TCTGAAGTAGATAGCACAGCAGA 58.727 43.478 0.00 0.00 0.00 4.26
275 360 2.076863 GCTTGACATGCGTTAGGAACT 58.923 47.619 0.00 0.00 46.37 3.01
314 399 3.059352 AGAAGATTAGGCACGCTTTGT 57.941 42.857 0.00 0.00 0.00 2.83
320 405 5.004922 AGAAGAGAAGAAGATTAGGCACG 57.995 43.478 0.00 0.00 0.00 5.34
353 441 7.807198 TGTTACTATAAATCATTAGGCACCCA 58.193 34.615 0.00 0.00 0.00 4.51
374 462 6.597562 ACCTGGTGTTATGTCTTTCTTGTTA 58.402 36.000 0.00 0.00 0.00 2.41
375 463 5.445964 ACCTGGTGTTATGTCTTTCTTGTT 58.554 37.500 0.00 0.00 0.00 2.83
376 464 5.048846 ACCTGGTGTTATGTCTTTCTTGT 57.951 39.130 0.00 0.00 0.00 3.16
379 467 5.221244 GCAAAACCTGGTGTTATGTCTTTCT 60.221 40.000 0.99 0.00 35.67 2.52
380 468 4.982295 GCAAAACCTGGTGTTATGTCTTTC 59.018 41.667 0.99 0.00 35.67 2.62
381 469 4.404073 TGCAAAACCTGGTGTTATGTCTTT 59.596 37.500 0.99 0.00 35.67 2.52
382 470 3.957497 TGCAAAACCTGGTGTTATGTCTT 59.043 39.130 0.99 0.00 35.67 3.01
383 471 3.317993 GTGCAAAACCTGGTGTTATGTCT 59.682 43.478 0.99 0.00 35.67 3.41
384 472 3.317993 AGTGCAAAACCTGGTGTTATGTC 59.682 43.478 0.99 0.00 35.67 3.06
385 473 3.068024 CAGTGCAAAACCTGGTGTTATGT 59.932 43.478 0.99 0.00 35.67 2.29
386 474 3.068024 ACAGTGCAAAACCTGGTGTTATG 59.932 43.478 0.99 2.44 35.67 1.90
387 475 3.068024 CACAGTGCAAAACCTGGTGTTAT 59.932 43.478 0.99 0.00 35.67 1.89
388 476 2.425312 CACAGTGCAAAACCTGGTGTTA 59.575 45.455 0.99 0.00 35.67 2.41
389 477 1.204467 CACAGTGCAAAACCTGGTGTT 59.796 47.619 0.00 0.00 39.43 3.32
390 478 0.817013 CACAGTGCAAAACCTGGTGT 59.183 50.000 0.00 0.00 0.00 4.16
391 479 1.102154 TCACAGTGCAAAACCTGGTG 58.898 50.000 0.00 3.59 0.00 4.17
392 480 2.071778 ATCACAGTGCAAAACCTGGT 57.928 45.000 6.95 0.00 0.00 4.00
393 481 2.288395 GGAATCACAGTGCAAAACCTGG 60.288 50.000 6.95 0.00 0.00 4.45
394 482 2.605338 CGGAATCACAGTGCAAAACCTG 60.605 50.000 0.00 0.75 0.00 4.00
398 595 2.548057 GAGTCGGAATCACAGTGCAAAA 59.452 45.455 0.00 0.00 0.00 2.44
399 596 2.143122 GAGTCGGAATCACAGTGCAAA 58.857 47.619 0.00 0.00 0.00 3.68
401 598 0.969149 AGAGTCGGAATCACAGTGCA 59.031 50.000 8.28 0.00 0.00 4.57
411 608 6.316640 TGTTTTGTTGTGATTTAGAGTCGGAA 59.683 34.615 0.00 0.00 0.00 4.30
414 611 9.658475 TTATTGTTTTGTTGTGATTTAGAGTCG 57.342 29.630 0.00 0.00 0.00 4.18
441 639 2.125269 GACTTATGCGCCGGTGGT 60.125 61.111 18.41 5.22 0.00 4.16
448 646 1.432270 GGTGGAGCTGACTTATGCGC 61.432 60.000 0.00 0.00 0.00 6.09
525 723 7.269084 CGATCATGTAATATTTCGTTTGCCATC 59.731 37.037 0.00 0.00 0.00 3.51
621 819 2.964740 ACATGTGATCAAGGTGAGTCG 58.035 47.619 0.00 0.00 0.00 4.18
644 842 4.080919 TCTCTCTCTCTCTCTCTCCACTTG 60.081 50.000 0.00 0.00 0.00 3.16
649 847 7.453393 TGATATTTCTCTCTCTCTCTCTCTCC 58.547 42.308 0.00 0.00 0.00 3.71
651 849 8.888419 AGATGATATTTCTCTCTCTCTCTCTCT 58.112 37.037 0.00 0.00 0.00 3.10
652 850 8.944029 CAGATGATATTTCTCTCTCTCTCTCTC 58.056 40.741 0.00 0.00 0.00 3.20
653 851 7.886970 CCAGATGATATTTCTCTCTCTCTCTCT 59.113 40.741 0.00 0.00 0.00 3.10
654 852 7.362401 GCCAGATGATATTTCTCTCTCTCTCTC 60.362 44.444 0.00 0.00 0.00 3.20
655 853 6.435277 GCCAGATGATATTTCTCTCTCTCTCT 59.565 42.308 0.00 0.00 0.00 3.10
656 854 6.435277 AGCCAGATGATATTTCTCTCTCTCTC 59.565 42.308 0.00 0.00 0.00 3.20
657 855 6.317312 AGCCAGATGATATTTCTCTCTCTCT 58.683 40.000 0.00 0.00 0.00 3.10
680 3742 2.478134 GAGCTTATTGTGCTGGCGATAG 59.522 50.000 0.00 0.00 41.30 2.08
682 3744 1.134280 AGAGCTTATTGTGCTGGCGAT 60.134 47.619 0.00 0.00 41.30 4.58
689 3751 6.903419 AGTAAAAGTGAAGAGCTTATTGTGC 58.097 36.000 0.00 0.00 0.00 4.57
716 3778 6.723298 TGGTGAAGAGCTTATTTCCAAAAA 57.277 33.333 0.00 0.00 0.00 1.94
717 3779 6.721208 AGATGGTGAAGAGCTTATTTCCAAAA 59.279 34.615 11.44 0.00 0.00 2.44
718 3780 6.248433 AGATGGTGAAGAGCTTATTTCCAAA 58.752 36.000 11.44 0.00 0.00 3.28
719 3781 5.819991 AGATGGTGAAGAGCTTATTTCCAA 58.180 37.500 11.44 0.00 0.00 3.53
720 3782 5.441718 AGATGGTGAAGAGCTTATTTCCA 57.558 39.130 0.00 0.69 0.00 3.53
721 3783 6.765915 AAAGATGGTGAAGAGCTTATTTCC 57.234 37.500 0.00 0.00 0.00 3.13
722 3784 7.031975 CCAAAAGATGGTGAAGAGCTTATTTC 58.968 38.462 0.00 0.00 44.85 2.17
724 3786 6.521151 CCAAAAGATGGTGAAGAGCTTATT 57.479 37.500 0.00 0.00 44.85 1.40
739 3801 4.864726 AGAGCTTATTGCCTCCAAAAGAT 58.135 39.130 0.00 0.00 44.23 2.40
741 3803 4.460382 TGAAGAGCTTATTGCCTCCAAAAG 59.540 41.667 0.00 0.00 44.23 2.27
747 3809 4.256920 TCAAGTGAAGAGCTTATTGCCTC 58.743 43.478 0.00 0.00 44.23 4.70
748 3810 4.292186 TCAAGTGAAGAGCTTATTGCCT 57.708 40.909 0.00 0.00 44.23 4.75
777 3839 4.277423 GGATGACGAGTTTTCCCTCAAAAA 59.723 41.667 0.00 0.00 35.68 1.94
779 3841 3.408634 GGATGACGAGTTTTCCCTCAAA 58.591 45.455 0.00 0.00 0.00 2.69
780 3842 3.053831 GGATGACGAGTTTTCCCTCAA 57.946 47.619 0.00 0.00 0.00 3.02
781 3843 2.762535 GGATGACGAGTTTTCCCTCA 57.237 50.000 0.00 0.00 0.00 3.86
794 3856 3.934068 TCCTTGTTCCTTAACGGATGAC 58.066 45.455 0.00 0.00 42.70 3.06
808 3870 2.319844 CCCAAAGAAGCCTTCCTTGTT 58.680 47.619 13.32 0.00 38.56 2.83
811 3873 0.542938 GGCCCAAAGAAGCCTTCCTT 60.543 55.000 0.00 0.00 46.14 3.36
824 3886 1.137282 GTTTCTTTCGTTTGGGCCCAA 59.863 47.619 34.07 34.07 0.00 4.12
1018 4091 1.380650 AAGACGAGGAGGAGGGAGC 60.381 63.158 0.00 0.00 0.00 4.70
1029 4102 3.425094 CGTACAGTTCAGAGGAAGACGAG 60.425 52.174 0.00 0.00 32.31 4.18
1047 4120 1.226603 CGGTGTCAGCTAGGCGTAC 60.227 63.158 0.00 0.00 0.00 3.67
1077 4150 2.504519 GTCGATACCCTGGGTGCC 59.495 66.667 28.64 17.49 36.19 5.01
1207 4328 3.372554 GAGCAGTAGACGGGGGTGC 62.373 68.421 0.00 0.00 0.00 5.01
1210 4331 2.427245 CCTGAGCAGTAGACGGGGG 61.427 68.421 0.00 0.00 0.00 5.40
1249 4370 3.528597 AGAGCTACGAACAGGAAATCC 57.471 47.619 0.00 0.00 0.00 3.01
1251 4372 3.181489 CGGTAGAGCTACGAACAGGAAAT 60.181 47.826 0.00 0.00 36.94 2.17
1283 4404 3.003173 TGGCTCTTGGTCCTCCGG 61.003 66.667 0.00 0.00 36.30 5.14
1427 4549 5.125578 GGATTCATCCTGACCAAAGGTAAAC 59.874 44.000 0.00 0.00 43.73 2.01
1487 4612 1.457823 TTGTCCTCCTACACGCGTGT 61.458 55.000 42.29 42.29 46.87 4.49
1488 4613 0.732880 CTTGTCCTCCTACACGCGTG 60.733 60.000 35.99 35.99 0.00 5.34
1489 4614 0.892358 TCTTGTCCTCCTACACGCGT 60.892 55.000 5.58 5.58 0.00 6.01
1490 4615 0.456221 ATCTTGTCCTCCTACACGCG 59.544 55.000 3.53 3.53 0.00 6.01
1491 4616 1.534175 CGATCTTGTCCTCCTACACGC 60.534 57.143 0.00 0.00 0.00 5.34
1492 4617 1.534175 GCGATCTTGTCCTCCTACACG 60.534 57.143 0.00 0.00 0.00 4.49
1496 4638 1.751351 CACAGCGATCTTGTCCTCCTA 59.249 52.381 0.00 0.00 0.00 2.94
1519 4661 2.300967 ATCGGTGATGGTGCCCACT 61.301 57.895 0.00 0.00 35.80 4.00
1744 5138 7.824289 GCTTTGGATACTACCTCATGCAATATA 59.176 37.037 0.00 0.00 33.31 0.86
1757 5151 7.766219 TCGATTGTAAAGCTTTGGATACTAC 57.234 36.000 22.02 10.23 37.61 2.73
1763 5157 3.818210 TGCTTCGATTGTAAAGCTTTGGA 59.182 39.130 22.02 7.62 46.34 3.53
1778 5174 8.262715 TCAAACAATATAATTGTCTGCTTCGA 57.737 30.769 5.79 0.00 0.00 3.71
1813 5210 2.034878 CACCTGCAGGAGTCTAGCATA 58.965 52.381 39.19 0.00 37.68 3.14
1828 5225 6.183360 ACAATAAACTTGGTTTTCTCCACCTG 60.183 38.462 0.99 0.00 37.01 4.00
1865 5262 6.421202 CACCTAAAAGTCTCTCTGTAACACAC 59.579 42.308 0.00 0.00 0.00 3.82
1887 5285 1.355112 ACCCTACCACAACCTACACC 58.645 55.000 0.00 0.00 0.00 4.16
1942 5837 6.072119 CCTTAACACCTGACAATAGGAAAACC 60.072 42.308 0.00 0.00 40.42 3.27
1951 5846 4.103469 TGTGTACCCTTAACACCTGACAAT 59.897 41.667 4.09 0.00 45.33 2.71
2009 6049 1.396996 GCAATTGGCTGTAGGTACACG 59.603 52.381 7.72 0.00 40.25 4.49
2010 6050 2.420022 CTGCAATTGGCTGTAGGTACAC 59.580 50.000 7.72 0.00 45.15 2.90
2011 6051 2.710377 CTGCAATTGGCTGTAGGTACA 58.290 47.619 7.72 0.00 45.15 2.90
2190 6434 9.642343 AAAGGAAAATAAAGTAGACAAGACCTT 57.358 29.630 0.00 0.00 33.78 3.50
2273 6595 6.763610 GGAGGGAGTACTATGAATCAACAAAG 59.236 42.308 0.00 0.00 0.00 2.77
2288 6611 1.305623 TCCAGGACGGAGGGAGTAC 59.694 63.158 0.00 0.00 39.64 2.73
2289 6612 3.845559 TCCAGGACGGAGGGAGTA 58.154 61.111 0.00 0.00 39.64 2.59
2297 6620 1.287425 GCGAAAAGTATCCAGGACGG 58.713 55.000 0.00 0.00 0.00 4.79
2299 6622 1.134907 TCCGCGAAAAGTATCCAGGAC 60.135 52.381 8.23 0.00 0.00 3.85
2300 6623 1.187974 TCCGCGAAAAGTATCCAGGA 58.812 50.000 8.23 0.00 0.00 3.86
2301 6624 2.018542 TTCCGCGAAAAGTATCCAGG 57.981 50.000 8.23 0.00 0.00 4.45
2302 6625 3.194861 TCATTCCGCGAAAAGTATCCAG 58.805 45.455 8.23 0.00 0.00 3.86
2304 6627 4.813296 ATTCATTCCGCGAAAAGTATCC 57.187 40.909 8.23 0.00 0.00 2.59
2305 6628 6.764877 TCTATTCATTCCGCGAAAAGTATC 57.235 37.500 8.23 0.00 0.00 2.24
2307 6630 6.971527 TTTCTATTCATTCCGCGAAAAGTA 57.028 33.333 8.23 0.00 0.00 2.24
2308 6631 5.873179 TTTCTATTCATTCCGCGAAAAGT 57.127 34.783 8.23 0.00 0.00 2.66
2309 6632 6.258160 ACATTTCTATTCATTCCGCGAAAAG 58.742 36.000 8.23 0.00 0.00 2.27
2310 6633 6.189677 ACATTTCTATTCATTCCGCGAAAA 57.810 33.333 8.23 1.06 0.00 2.29
2311 6634 5.811399 ACATTTCTATTCATTCCGCGAAA 57.189 34.783 8.23 0.00 0.00 3.46
2312 6635 6.481976 ACATACATTTCTATTCATTCCGCGAA 59.518 34.615 8.23 0.00 0.00 4.70
2314 6637 6.073369 CACATACATTTCTATTCATTCCGCG 58.927 40.000 0.00 0.00 0.00 6.46
2315 6638 6.959361 ACACATACATTTCTATTCATTCCGC 58.041 36.000 0.00 0.00 0.00 5.54
2350 6771 9.698309 CGTAAAAGTGGATGAATCTAGACATAT 57.302 33.333 0.00 0.00 0.00 1.78
2352 6773 7.707035 GTCGTAAAAGTGGATGAATCTAGACAT 59.293 37.037 0.00 0.00 0.00 3.06
2353 6774 7.033791 GTCGTAAAAGTGGATGAATCTAGACA 58.966 38.462 0.00 0.00 0.00 3.41
2354 6775 7.033791 TGTCGTAAAAGTGGATGAATCTAGAC 58.966 38.462 0.00 0.00 0.00 2.59
2356 6777 7.545965 ACTTGTCGTAAAAGTGGATGAATCTAG 59.454 37.037 0.51 0.00 36.52 2.43
2358 6779 6.231211 ACTTGTCGTAAAAGTGGATGAATCT 58.769 36.000 0.51 0.00 36.52 2.40
2359 6780 6.481954 ACTTGTCGTAAAAGTGGATGAATC 57.518 37.500 0.51 0.00 36.52 2.52
2361 6782 7.972832 ATTACTTGTCGTAAAAGTGGATGAA 57.027 32.000 9.39 0.00 41.17 2.57
2362 6783 7.118680 GGAATTACTTGTCGTAAAAGTGGATGA 59.881 37.037 9.39 0.00 41.17 2.92
2363 6784 7.241376 GGAATTACTTGTCGTAAAAGTGGATG 58.759 38.462 9.39 0.00 41.17 3.51
2364 6785 6.091713 CGGAATTACTTGTCGTAAAAGTGGAT 59.908 38.462 9.39 3.14 41.17 3.41
2365 6786 5.406175 CGGAATTACTTGTCGTAAAAGTGGA 59.594 40.000 9.39 1.43 41.17 4.02
2366 6787 5.390145 CCGGAATTACTTGTCGTAAAAGTGG 60.390 44.000 0.00 0.26 41.17 4.00
2367 6788 5.406175 TCCGGAATTACTTGTCGTAAAAGTG 59.594 40.000 0.00 0.00 41.17 3.16
2368 6789 5.406477 GTCCGGAATTACTTGTCGTAAAAGT 59.594 40.000 5.23 5.68 41.17 2.66
2369 6790 5.406175 TGTCCGGAATTACTTGTCGTAAAAG 59.594 40.000 5.23 0.00 41.17 2.27
2370 6791 5.295950 TGTCCGGAATTACTTGTCGTAAAA 58.704 37.500 5.23 0.00 41.17 1.52
2371 6792 4.880759 TGTCCGGAATTACTTGTCGTAAA 58.119 39.130 5.23 0.00 41.17 2.01
2372 6793 4.218200 TCTGTCCGGAATTACTTGTCGTAA 59.782 41.667 5.23 0.00 41.97 3.18
2373 6794 3.758023 TCTGTCCGGAATTACTTGTCGTA 59.242 43.478 5.23 0.00 0.00 3.43
2374 6795 2.559668 TCTGTCCGGAATTACTTGTCGT 59.440 45.455 5.23 0.00 0.00 4.34
2375 6796 3.179830 CTCTGTCCGGAATTACTTGTCG 58.820 50.000 5.23 0.00 0.00 4.35
2376 6797 3.522553 CCTCTGTCCGGAATTACTTGTC 58.477 50.000 5.23 0.00 0.00 3.18
2377 6798 2.236395 CCCTCTGTCCGGAATTACTTGT 59.764 50.000 5.23 0.00 0.00 3.16
2378 6799 2.500098 TCCCTCTGTCCGGAATTACTTG 59.500 50.000 5.23 0.00 0.00 3.16
2379 6800 2.766828 CTCCCTCTGTCCGGAATTACTT 59.233 50.000 5.23 0.00 0.00 2.24
2380 6801 2.292323 ACTCCCTCTGTCCGGAATTACT 60.292 50.000 5.23 0.00 0.00 2.24
2381 6802 2.108970 ACTCCCTCTGTCCGGAATTAC 58.891 52.381 5.23 0.00 0.00 1.89
2382 6803 2.544844 ACTCCCTCTGTCCGGAATTA 57.455 50.000 5.23 0.00 0.00 1.40
2383 6804 2.108970 GTACTCCCTCTGTCCGGAATT 58.891 52.381 5.23 0.00 0.00 2.17
2384 6805 1.777941 GTACTCCCTCTGTCCGGAAT 58.222 55.000 5.23 0.00 0.00 3.01
2385 6806 0.679002 CGTACTCCCTCTGTCCGGAA 60.679 60.000 5.23 0.00 0.00 4.30
2386 6807 1.077930 CGTACTCCCTCTGTCCGGA 60.078 63.158 0.00 0.00 0.00 5.14
2387 6808 1.378250 ACGTACTCCCTCTGTCCGG 60.378 63.158 0.00 0.00 0.00 5.14
2388 6809 0.675837 TCACGTACTCCCTCTGTCCG 60.676 60.000 0.00 0.00 0.00 4.79
2389 6810 1.765230 ATCACGTACTCCCTCTGTCC 58.235 55.000 0.00 0.00 0.00 4.02
2390 6811 5.067413 TGAATTATCACGTACTCCCTCTGTC 59.933 44.000 0.00 0.00 0.00 3.51
2391 6812 4.954202 TGAATTATCACGTACTCCCTCTGT 59.046 41.667 0.00 0.00 0.00 3.41
2392 6813 5.067936 ACTGAATTATCACGTACTCCCTCTG 59.932 44.000 0.00 0.00 0.00 3.35
2393 6814 5.067936 CACTGAATTATCACGTACTCCCTCT 59.932 44.000 0.00 0.00 0.00 3.69
2394 6815 5.163540 ACACTGAATTATCACGTACTCCCTC 60.164 44.000 0.00 0.00 0.00 4.30
2395 6816 4.710375 ACACTGAATTATCACGTACTCCCT 59.290 41.667 0.00 0.00 0.00 4.20
2396 6817 4.804139 CACACTGAATTATCACGTACTCCC 59.196 45.833 0.00 0.00 0.00 4.30
2397 6818 5.288712 CACACACTGAATTATCACGTACTCC 59.711 44.000 0.00 0.00 0.00 3.85
2398 6819 5.862323 ACACACACTGAATTATCACGTACTC 59.138 40.000 0.00 0.00 0.00 2.59
2399 6820 5.633601 CACACACACTGAATTATCACGTACT 59.366 40.000 0.00 0.00 0.00 2.73
2404 6825 6.060028 ACAACACACACACTGAATTATCAC 57.940 37.500 0.00 0.00 0.00 3.06
2421 6844 1.299089 GGAACAGCGGCAACAACAC 60.299 57.895 1.45 0.00 0.00 3.32
2426 6849 0.040067 CAAGAAGGAACAGCGGCAAC 60.040 55.000 1.45 0.00 0.00 4.17
2448 6871 6.455360 ACGCAATGAAATCATAAAGACCAT 57.545 33.333 0.00 0.00 35.10 3.55
2451 6874 5.004726 GGCAACGCAATGAAATCATAAAGAC 59.995 40.000 0.00 0.00 35.10 3.01
2515 6958 7.556844 ACCTCTACATGACTACAATACCAAAG 58.443 38.462 0.00 0.00 0.00 2.77
2520 6963 8.979574 GCAAATACCTCTACATGACTACAATAC 58.020 37.037 0.00 0.00 0.00 1.89
2521 6964 8.924303 AGCAAATACCTCTACATGACTACAATA 58.076 33.333 0.00 0.00 0.00 1.90
2549 6992 8.852135 ACAAAAGAAAAAGGATACCGTAAATCA 58.148 29.630 0.00 0.00 37.17 2.57
2556 6999 7.918562 TCTCAAAACAAAAGAAAAAGGATACCG 59.081 33.333 0.00 0.00 37.17 4.02
2659 7103 9.299963 CATTTATCCATGAATAACGCTTCAAAA 57.700 29.630 0.00 0.00 38.55 2.44
2686 7131 9.620660 GTAAACTGTTAAAATGGTTGTCTATGG 57.379 33.333 0.00 0.00 0.00 2.74
2824 7404 2.113860 TCTCGAATTTCCTGCCCTTG 57.886 50.000 0.00 0.00 0.00 3.61
2887 7467 2.613506 GGGTGCCGAAAACTCCACG 61.614 63.158 0.00 0.00 0.00 4.94
2893 7473 0.030235 GTGACAAGGGTGCCGAAAAC 59.970 55.000 0.00 0.00 0.00 2.43
2897 7477 0.179004 AAATGTGACAAGGGTGCCGA 60.179 50.000 0.00 0.00 0.00 5.54
2898 7478 0.039256 CAAATGTGACAAGGGTGCCG 60.039 55.000 0.00 0.00 0.00 5.69
2902 7482 2.071778 ACAGCAAATGTGACAAGGGT 57.928 45.000 0.00 0.00 41.91 4.34
2904 7484 4.406069 CGATAACAGCAAATGTGACAAGG 58.594 43.478 0.00 0.00 43.00 3.61
2910 7490 4.418013 TTGACCGATAACAGCAAATGTG 57.582 40.909 0.00 0.00 43.00 3.21
2911 7491 4.943705 AGATTGACCGATAACAGCAAATGT 59.056 37.500 0.00 0.00 46.97 2.71
2915 7495 4.391830 GTGAAGATTGACCGATAACAGCAA 59.608 41.667 0.00 0.00 0.00 3.91
2917 7497 4.184629 AGTGAAGATTGACCGATAACAGC 58.815 43.478 0.00 0.00 0.00 4.40
2918 7498 6.727824 AAAGTGAAGATTGACCGATAACAG 57.272 37.500 0.00 0.00 0.00 3.16
2962 7548 5.221521 ACACAAGACTCTGACATCTAAAGCA 60.222 40.000 0.00 0.00 0.00 3.91
2977 7563 5.416013 TCTGAATACTCATCGACACAAGACT 59.584 40.000 0.00 0.00 0.00 3.24
2988 7574 7.768120 AGAATGAACTGGTTCTGAATACTCATC 59.232 37.037 13.54 0.00 40.14 2.92
3009 7595 8.356533 AGTTGCAAAATACTGAAACAAGAATG 57.643 30.769 0.00 0.00 37.32 2.67
3104 7692 0.238289 CAAGCAGCCTAACACCAACG 59.762 55.000 0.00 0.00 0.00 4.10
3115 7703 1.399791 GTAGAATGAGCACAAGCAGCC 59.600 52.381 0.00 0.00 45.49 4.85
3158 7792 5.900339 TCGCCAAATATCATCTAACGAAC 57.100 39.130 0.00 0.00 0.00 3.95
3212 7846 3.243873 GCCACTGTCATCGGATCTTGATA 60.244 47.826 0.00 0.00 0.00 2.15
3243 8156 7.813645 TGTGCTTATGATGAATTATGATCTGC 58.186 34.615 0.00 0.00 0.00 4.26
3285 8198 8.942338 TCGTTTCTTCTACATGTAATATTGCT 57.058 30.769 7.06 0.00 0.00 3.91
3307 8221 8.353684 CCTATGTGATAGATAGAAACTGTTCGT 58.646 37.037 0.00 0.00 35.52 3.85
3308 8222 7.327275 GCCTATGTGATAGATAGAAACTGTTCG 59.673 40.741 0.00 0.00 35.52 3.95
3311 8225 7.288852 AGTGCCTATGTGATAGATAGAAACTGT 59.711 37.037 0.00 0.00 34.77 3.55
3353 8267 2.363683 GATGGAGCTCTGGAACTTTGG 58.636 52.381 14.64 0.00 0.00 3.28
3418 8332 4.805231 CCGTCGTACATGGCGCCA 62.805 66.667 34.80 34.80 0.00 5.69
3737 8686 1.318576 CCGTGAAAACCTTCTGCCTT 58.681 50.000 0.00 0.00 32.33 4.35
3738 8687 0.182775 ACCGTGAAAACCTTCTGCCT 59.817 50.000 0.00 0.00 32.33 4.75
3746 8695 0.508213 CCGAACGTACCGTGAAAACC 59.492 55.000 9.00 0.00 39.99 3.27
3747 8696 0.508213 CCCGAACGTACCGTGAAAAC 59.492 55.000 9.00 0.00 39.99 2.43
3749 8698 1.664333 GCCCGAACGTACCGTGAAA 60.664 57.895 9.00 0.00 39.99 2.69
3750 8699 2.049248 GCCCGAACGTACCGTGAA 60.049 61.111 9.00 0.00 39.99 3.18
3761 8710 1.466856 ACGTACTATCTGTGCCCGAA 58.533 50.000 0.00 0.00 0.00 4.30
3785 8736 1.443194 CATCACGCCAAGCACTTGC 60.443 57.895 4.82 0.00 39.16 4.01
3786 8737 1.443194 GCATCACGCCAAGCACTTG 60.443 57.895 3.32 3.32 40.13 3.16
3787 8738 0.321564 TAGCATCACGCCAAGCACTT 60.322 50.000 0.00 0.00 44.04 3.16
3788 8739 0.742281 CTAGCATCACGCCAAGCACT 60.742 55.000 0.00 0.00 44.04 4.40
3789 8740 0.740868 TCTAGCATCACGCCAAGCAC 60.741 55.000 0.00 0.00 44.04 4.40
3790 8741 0.036483 TTCTAGCATCACGCCAAGCA 60.036 50.000 0.00 0.00 44.04 3.91
3793 8744 0.037697 ACGTTCTAGCATCACGCCAA 60.038 50.000 0.00 0.00 44.04 4.52
3796 8747 1.256376 CATCACGTTCTAGCATCACGC 59.744 52.381 0.00 0.00 37.44 5.34
3797 8748 1.854743 CCATCACGTTCTAGCATCACG 59.145 52.381 0.00 0.00 39.86 4.35
3798 8749 2.893637 ACCATCACGTTCTAGCATCAC 58.106 47.619 0.00 0.00 0.00 3.06
3799 8750 3.181479 GGTACCATCACGTTCTAGCATCA 60.181 47.826 7.15 0.00 0.00 3.07
3800 8751 3.068307 AGGTACCATCACGTTCTAGCATC 59.932 47.826 15.94 0.00 0.00 3.91
3801 8752 3.031736 AGGTACCATCACGTTCTAGCAT 58.968 45.455 15.94 0.00 0.00 3.79
3804 8755 3.194968 ACCAAGGTACCATCACGTTCTAG 59.805 47.826 15.94 0.00 0.00 2.43
3811 8762 1.003118 TGAGCACCAAGGTACCATCAC 59.997 52.381 15.94 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.