Multiple sequence alignment - TraesCS3A01G029800

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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 TraesCS3A01G029800 chr3A 100.000 3763 0 0 1 3763 15689284 15693046 0.000000e+00 6950
1 TraesCS3A01G029800 chr3A 92.280 557 40 1 902 1458 15701508 15702061 0.000000e+00 787
2 TraesCS3A01G029800 chr3A 91.423 548 44 1 911 1458 15561383 15560839 0.000000e+00 749
3 TraesCS3A01G029800 chr3A 79.567 1155 138 54 2334 3434 15702845 15703955 0.000000e+00 736
4 TraesCS3A01G029800 chr3A 85.265 509 65 7 1914 2416 15690739 15691243 2.000000e-142 516
5 TraesCS3A01G029800 chr3A 85.265 509 65 7 1456 1960 15691197 15691699 2.000000e-142 516
6 TraesCS3A01G029800 chr3A 90.937 331 29 1 916 1245 15612416 15612086 9.590000e-121 444
7 TraesCS3A01G029800 chr3A 84.682 346 33 15 1 341 36743063 36743393 1.010000e-85 327
8 TraesCS3A01G029800 chr3A 85.981 321 26 12 22 338 36805904 36806209 3.620000e-85 326
9 TraesCS3A01G029800 chr3A 86.076 316 18 10 36 349 15700405 15700696 2.180000e-82 316
10 TraesCS3A01G029800 chr3A 85.944 249 31 4 411 657 36875131 36875377 2.880000e-66 263
11 TraesCS3A01G029800 chr3A 86.486 222 14 9 53 269 36791637 36791847 2.920000e-56 230
12 TraesCS3A01G029800 chr3A 88.144 194 13 7 141 333 36874535 36874719 4.890000e-54 222
13 TraesCS3A01G029800 chr3A 89.623 106 11 0 1353 1458 15701821 15701926 6.560000e-28 135
14 TraesCS3A01G029800 chr3A 76.786 280 41 8 447 725 36806212 36806468 6.560000e-28 135
15 TraesCS3A01G029800 chr3A 88.679 106 12 0 1353 1458 15690501 15690606 3.050000e-26 130
16 TraesCS3A01G029800 chrUn 92.051 2642 166 27 916 3538 35265031 35262415 0.000000e+00 3675
17 TraesCS3A01G029800 chrUn 91.920 2500 158 27 1057 3538 35262052 35259579 0.000000e+00 3458
18 TraesCS3A01G029800 chrUn 77.963 1257 159 57 2337 3542 35062775 35061586 0.000000e+00 678
19 TraesCS3A01G029800 chrUn 82.535 710 90 25 41 725 35422125 35422825 9.000000e-166 593
20 TraesCS3A01G029800 chrUn 85.855 509 62 7 1456 1960 35261195 35260693 1.990000e-147 532
21 TraesCS3A01G029800 chrUn 85.855 509 62 7 1456 1960 35264032 35263530 1.990000e-147 532
22 TraesCS3A01G029800 chrUn 89.896 386 26 7 524 908 35064937 35064564 5.650000e-133 484
23 TraesCS3A01G029800 chrUn 91.940 335 24 1 911 1245 35063678 35063347 2.050000e-127 466
24 TraesCS3A01G029800 chrUn 90.310 258 25 0 1165 1422 35063469 35063212 4.660000e-89 339
25 TraesCS3A01G029800 chrUn 83.333 312 36 11 30 341 35421722 35422017 1.330000e-69 274
26 TraesCS3A01G029800 chrUn 82.645 242 42 0 1215 1456 35423280 35423521 8.190000e-52 215
27 TraesCS3A01G029800 chrUn 83.893 149 24 0 1217 1365 35423417 35423565 3.920000e-30 143
28 TraesCS3A01G029800 chr3D 93.103 1769 92 20 1688 3436 5614969 5613211 0.000000e+00 2564
29 TraesCS3A01G029800 chr3D 90.377 478 42 2 903 1380 5615531 5615058 3.190000e-175 625
30 TraesCS3A01G029800 chr3D 82.895 684 78 25 66 725 41606530 41607198 2.520000e-161 579
31 TraesCS3A01G029800 chr3D 85.127 511 64 10 1456 1960 5614740 5614236 2.590000e-141 512
32 TraesCS3A01G029800 chr3D 83.590 585 54 19 7 570 5617344 5616781 9.320000e-141 510
33 TraesCS3A01G029800 chr3D 80.994 684 71 41 66 725 5632855 5632207 4.370000e-134 488
34 TraesCS3A01G029800 chr3D 91.239 331 28 1 916 1245 5657525 5657855 2.060000e-122 449
35 TraesCS3A01G029800 chr3D 90.370 270 16 1 643 912 5616779 5616520 2.780000e-91 346
36 TraesCS3A01G029800 chr3D 84.758 269 38 3 447 715 26653839 26654104 2.230000e-67 267
37 TraesCS3A01G029800 chr3D 85.830 247 21 6 411 657 26654248 26654480 2.240000e-62 250
38 TraesCS3A01G029800 chr3D 86.441 177 15 3 1460 1636 5631305 5631138 6.420000e-43 185
39 TraesCS3A01G029800 chr3D 85.714 175 16 3 1462 1636 41608133 41608298 3.860000e-40 176
40 TraesCS3A01G029800 chr3D 93.396 106 7 0 1353 1458 5615220 5615115 1.400000e-34 158
41 TraesCS3A01G029800 chr3D 85.350 157 15 4 2 154 26653537 26653689 5.030000e-34 156
42 TraesCS3A01G029800 chr3B 94.157 890 46 3 1688 2571 12319759 12320648 0.000000e+00 1351
43 TraesCS3A01G029800 chr3B 80.264 1059 123 48 2520 3542 12320651 12321659 0.000000e+00 719
44 TraesCS3A01G029800 chr3B 89.895 475 44 2 900 1374 12319194 12319664 3.210000e-170 608
45 TraesCS3A01G029800 chr3B 85.686 510 64 8 1456 1960 12319987 12320492 2.570000e-146 529
46 TraesCS3A01G029800 chr3B 82.911 632 60 22 30 639 12318576 12319181 3.330000e-145 525
47 TraesCS3A01G029800 chr3B 77.090 323 55 4 441 763 4330064 4329761 6.460000e-38 169
48 TraesCS3A01G029800 chr7B 75.254 295 54 4 455 749 7206263 7205988 5.100000e-24 122
49 TraesCS3A01G029800 chr7B 76.763 241 38 3 522 762 138608547 138608325 6.600000e-23 119
50 TraesCS3A01G029800 chr7A 73.521 355 68 14 423 772 49781805 49781472 1.100000e-20 111


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 TraesCS3A01G029800 chr3A 15689284 15693046 3762 False 2028.000000 6950 89.802250 1 3763 4 chr3A.!!$F3 3762
1 TraesCS3A01G029800 chr3A 15560839 15561383 544 True 749.000000 749 91.423000 911 1458 1 chr3A.!!$R1 547
2 TraesCS3A01G029800 chr3A 15700405 15703955 3550 False 493.500000 787 86.886500 36 3434 4 chr3A.!!$F4 3398
3 TraesCS3A01G029800 chr3A 36874535 36875377 842 False 242.500000 263 87.044000 141 657 2 chr3A.!!$F6 516
4 TraesCS3A01G029800 chr3A 36805904 36806468 564 False 230.500000 326 81.383500 22 725 2 chr3A.!!$F5 703
5 TraesCS3A01G029800 chrUn 35259579 35265031 5452 True 2049.250000 3675 88.920250 916 3538 4 chrUn.!!$R2 2622
6 TraesCS3A01G029800 chrUn 35061586 35064937 3351 True 491.750000 678 87.527250 524 3542 4 chrUn.!!$R1 3018
7 TraesCS3A01G029800 chrUn 35421722 35423565 1843 False 306.250000 593 83.101500 30 1456 4 chrUn.!!$F1 1426
8 TraesCS3A01G029800 chr3D 5613211 5617344 4133 True 785.833333 2564 89.327167 7 3436 6 chr3D.!!$R1 3429
9 TraesCS3A01G029800 chr3D 41606530 41608298 1768 False 377.500000 579 84.304500 66 1636 2 chr3D.!!$F3 1570
10 TraesCS3A01G029800 chr3D 5631138 5632855 1717 True 336.500000 488 83.717500 66 1636 2 chr3D.!!$R2 1570
11 TraesCS3A01G029800 chr3D 26653537 26654480 943 False 224.333333 267 85.312667 2 715 3 chr3D.!!$F2 713
12 TraesCS3A01G029800 chr3B 12318576 12321659 3083 False 746.400000 1351 86.582600 30 3542 5 chr3B.!!$F1 3512

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
813 1581 0.968901 ATCCTGCATTGCTGGTGGTG 60.969 55.0 27.50 8.07 45.76 4.17 F
1364 3339 0.519077 GCACCTCTTGTTGCAGCTAC 59.481 55.0 1.17 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 3639 0.255033 TGAGTCGGTAGAGGCAGCTA 59.745 55.0 0.0 0.0 0.00 3.32 R
2842 7970 0.851469 ATGCAGAGAGATGGGGCAAT 59.149 50.0 0.0 0.0 38.08 3.56 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
26 27 3.221771 TGGAATGTGTTGAACAGAAGGG 58.778 45.455 0.00 0.00 43.64 3.95
156 162 3.552604 ATAACACATCAACACAACGCC 57.447 42.857 0.00 0.00 0.00 5.68
166 172 3.995048 TCAACACAACGCCGATACATAAA 59.005 39.130 0.00 0.00 0.00 1.40
169 175 3.936453 ACACAACGCCGATACATAAACAT 59.064 39.130 0.00 0.00 0.00 2.71
170 176 4.033587 ACACAACGCCGATACATAAACATC 59.966 41.667 0.00 0.00 0.00 3.06
171 177 4.033472 CACAACGCCGATACATAAACATCA 59.967 41.667 0.00 0.00 0.00 3.07
172 178 4.270084 ACAACGCCGATACATAAACATCAG 59.730 41.667 0.00 0.00 0.00 2.90
173 179 2.800544 ACGCCGATACATAAACATCAGC 59.199 45.455 0.00 0.00 0.00 4.26
174 180 2.159973 CGCCGATACATAAACATCAGCG 60.160 50.000 0.00 0.00 40.44 5.18
175 181 3.057019 GCCGATACATAAACATCAGCGA 58.943 45.455 0.00 0.00 0.00 4.93
176 182 3.679980 GCCGATACATAAACATCAGCGAT 59.320 43.478 0.00 0.00 0.00 4.58
266 674 1.268079 GTGAAGCTGAGGAAACTTGGC 59.732 52.381 0.00 0.00 44.43 4.52
269 677 1.075659 GCTGAGGAAACTTGGCCCT 59.924 57.895 0.00 0.00 44.43 5.19
333 742 7.599245 CCTCTAGTATAAGGTTTGCTATTTCCG 59.401 40.741 0.00 0.00 0.00 4.30
341 750 3.760151 GGTTTGCTATTTCCGTACCCTTT 59.240 43.478 0.00 0.00 0.00 3.11
346 812 4.141869 TGCTATTTCCGTACCCTTTCTACC 60.142 45.833 0.00 0.00 0.00 3.18
416 1179 4.367450 TGCAACCACATTTTAGCTTGAAC 58.633 39.130 0.00 0.00 0.00 3.18
420 1183 6.509997 GCAACCACATTTTAGCTTGAACAAAG 60.510 38.462 0.00 0.00 39.07 2.77
459 1222 1.135139 GGAGCTATGCGACTGAAGTGA 59.865 52.381 0.00 0.00 0.00 3.41
461 1224 1.134965 AGCTATGCGACTGAAGTGACC 60.135 52.381 0.00 0.00 0.00 4.02
502 1265 6.331369 ACTCAACAATGTCATTCGGATTTT 57.669 33.333 0.00 0.00 0.00 1.82
530 1295 2.224499 TGCTTGGTCTGACATTGTAGCA 60.224 45.455 10.38 12.38 35.26 3.49
563 1328 5.542635 ACATGACCAGACTACCTTCTGTTTA 59.457 40.000 0.00 0.00 41.40 2.01
666 1433 7.117285 TGAAGCTAGATTATTTCAGAGCTCA 57.883 36.000 17.77 0.00 42.15 4.26
669 1436 8.798859 AAGCTAGATTATTTCAGAGCTCAAAA 57.201 30.769 17.77 15.75 42.15 2.44
710 1477 5.687285 CGGTTAAGATGAATTATGCAAAGCC 59.313 40.000 0.00 0.00 0.00 4.35
734 1502 7.592164 GCCATGTTTACGTTAAATTGTAACTGT 59.408 33.333 0.00 0.00 30.74 3.55
769 1537 2.158914 TGCTCCTATGTACAGTGCCATG 60.159 50.000 0.33 0.00 0.00 3.66
805 1573 3.863142 AAAACAGAGATCCTGCATTGC 57.137 42.857 0.46 0.46 46.81 3.56
813 1581 0.968901 ATCCTGCATTGCTGGTGGTG 60.969 55.000 27.50 8.07 45.76 4.17
836 1604 7.033185 GTGCTGGTGGTTAAAAGTAAATATGG 58.967 38.462 0.00 0.00 0.00 2.74
1054 2936 8.996271 GTGATCATGATATTATTGACTTGAGCA 58.004 33.333 8.54 0.00 33.15 4.26
1055 2937 9.216117 TGATCATGATATTATTGACTTGAGCAG 57.784 33.333 8.54 0.00 32.34 4.24
1056 2938 7.430992 TCATGATATTATTGACTTGAGCAGC 57.569 36.000 0.00 0.00 0.00 5.25
1069 2951 3.260483 GCAGCAGCGATGACGAGG 61.260 66.667 4.02 0.00 42.66 4.63
1160 3042 1.743252 CTGGTGAAGGAAGCCGAGC 60.743 63.158 0.00 0.00 0.00 5.03
1364 3339 0.519077 GCACCTCTTGTTGCAGCTAC 59.481 55.000 1.17 0.00 0.00 3.58
1366 3341 2.612972 GCACCTCTTGTTGCAGCTACTA 60.613 50.000 8.50 0.00 0.00 1.82
1387 3362 5.645497 ACTAAAGGAAGTCAAGATGTGCATC 59.355 40.000 4.12 4.12 38.09 3.91
1476 3493 0.583438 CCAAGTCAGTGCGTGTGAAG 59.417 55.000 0.00 0.00 0.00 3.02
1477 3494 0.583438 CAAGTCAGTGCGTGTGAAGG 59.417 55.000 0.00 0.00 0.00 3.46
1487 3504 1.663643 GCGTGTGAAGGCGAAATATCA 59.336 47.619 0.00 0.00 0.00 2.15
1508 3525 6.401047 TCATAAGAAGAACTACCATACCGG 57.599 41.667 0.00 0.00 42.50 5.28
1520 3537 1.410004 CATACCGGCACTCCTAGGAA 58.590 55.000 13.77 0.00 0.00 3.36
1556 3573 7.254795 GCTTATACAGATGGGTGAATGTTGTAC 60.255 40.741 0.00 0.00 0.00 2.90
1558 3575 3.073798 ACAGATGGGTGAATGTTGTACCA 59.926 43.478 0.00 0.00 36.19 3.25
1584 3601 2.188994 GAAGAGCCAGCAGCCGAT 59.811 61.111 0.00 0.00 45.47 4.18
1585 3602 1.451028 GAAGAGCCAGCAGCCGATT 60.451 57.895 0.00 0.00 45.47 3.34
1598 3615 1.405821 AGCCGATTACAAGAGGTCTCG 59.594 52.381 0.00 0.00 35.63 4.04
1601 3618 2.223829 CCGATTACAAGAGGTCTCGCAT 60.224 50.000 0.00 0.00 34.95 4.73
1622 3639 0.393537 CTCGGGCCAGCAGAAGAATT 60.394 55.000 4.39 0.00 0.00 2.17
1639 3656 2.074729 ATTAGCTGCCTCTACCGACT 57.925 50.000 0.00 0.00 0.00 4.18
1695 3712 1.402984 GGATCAGCGAGTTGTCTTCGT 60.403 52.381 0.00 0.00 0.00 3.85
1712 3733 1.204704 TCGTTCTCCAACATCAGCGAT 59.795 47.619 0.00 0.00 32.14 4.58
1795 3824 5.670485 ACGATCCATATCAAGCAAACACTA 58.330 37.500 0.00 0.00 31.93 2.74
1851 3885 5.543790 AGTGGCCTTCCTGAAAAATGTTAAT 59.456 36.000 3.32 0.00 0.00 1.40
1856 3890 6.147656 GCCTTCCTGAAAAATGTTAATGTTGG 59.852 38.462 0.00 0.00 0.00 3.77
1879 3913 0.107654 GCTGTAGGCCCGACTTTCAT 60.108 55.000 0.00 0.00 34.27 2.57
1937 6437 4.183865 CAAAGTCAGTGAGTGTGAAGACA 58.816 43.478 12.22 0.00 0.00 3.41
2002 6505 1.135094 AGGCTCATACAGATGGGTGG 58.865 55.000 0.00 0.00 35.77 4.61
2091 7058 4.744137 CAGAAGAATCAGTTGCCTCTATCG 59.256 45.833 0.00 0.00 0.00 2.92
2135 7102 0.180642 CTCTGCCACATGCTGGATCT 59.819 55.000 15.81 0.00 43.95 2.75
2490 7553 0.940126 ACATGCTGAATCGCCGAATC 59.060 50.000 0.00 0.00 0.00 2.52
2513 7576 2.046023 CGCCCTCCAACATCAGCA 60.046 61.111 0.00 0.00 0.00 4.41
2514 7577 1.452651 CGCCCTCCAACATCAGCAT 60.453 57.895 0.00 0.00 0.00 3.79
2654 7773 4.767255 CCTGCTGCAGGTCCGACC 62.767 72.222 35.03 9.81 45.82 4.79
2738 7857 3.067180 TGAAACGTCGTAGGAAGAACTGT 59.933 43.478 0.00 0.00 0.00 3.55
2763 7883 3.009143 ACCCTGCAAACTAACTCCTTAGG 59.991 47.826 0.00 0.00 34.62 2.69
2821 7949 4.085357 ACCACTCTTGTTGCATCTGTAA 57.915 40.909 0.00 0.00 0.00 2.41
2833 7961 3.265791 GCATCTGTAATGGGATCGATCC 58.734 50.000 32.57 32.57 46.41 3.36
2842 7970 2.639853 GATCGATCCGAGCTCGCA 59.360 61.111 30.49 18.14 39.28 5.10
2930 8060 6.048073 TCGTCAAGCACATCATTAATTAGC 57.952 37.500 0.00 0.00 0.00 3.09
2954 8084 4.837860 TGGTATTTTGGTGAGCTTGGAAAT 59.162 37.500 0.00 0.00 0.00 2.17
2977 8109 1.789078 CGCAGCTGCTGTTTTCTGGT 61.789 55.000 34.22 0.00 39.32 4.00
2988 8120 6.003950 TGCTGTTTTCTGGTAGCTTAAGAAT 58.996 36.000 6.67 0.00 37.10 2.40
3038 8181 4.469657 AGCTGAGATGTAACCAAACCAAA 58.530 39.130 0.00 0.00 0.00 3.28
3042 8185 6.705825 GCTGAGATGTAACCAAACCAAAAATT 59.294 34.615 0.00 0.00 0.00 1.82
3117 8260 4.980573 AGTGTGTTTGGCTTTGGTAGATA 58.019 39.130 0.00 0.00 0.00 1.98
3146 8295 5.093457 TGAAGCGATAGTTTAGTTCTGTCG 58.907 41.667 7.49 7.49 44.84 4.35
3151 8300 2.457366 AGTTTAGTTCTGTCGGCAGG 57.543 50.000 18.55 0.00 42.78 4.85
3256 8412 3.582208 ACCTTTTGGAGCATGGCATTTTA 59.418 39.130 0.00 0.00 44.07 1.52
3261 8417 7.336427 CCTTTTGGAGCATGGCATTTTATTTTA 59.664 33.333 0.00 0.00 44.07 1.52
3263 8419 6.543430 TGGAGCATGGCATTTTATTTTAGT 57.457 33.333 0.00 0.00 0.00 2.24
3264 8420 6.945218 TGGAGCATGGCATTTTATTTTAGTT 58.055 32.000 0.00 0.00 0.00 2.24
3267 8423 7.254084 GGAGCATGGCATTTTATTTTAGTTTCG 60.254 37.037 0.00 0.00 0.00 3.46
3382 8542 5.865013 CAGCTAGAAGATATGCATCTGACAG 59.135 44.000 0.19 0.00 40.81 3.51
3405 8565 1.417890 ACGGGAAGATAGGAGGCAATG 59.582 52.381 0.00 0.00 0.00 2.82
3476 8638 7.777095 TGTATTTAACAAACTATGAATGGGCC 58.223 34.615 0.00 0.00 34.29 5.80
3489 8651 4.237843 TGAATGGGCCATAGAGAGAGATT 58.762 43.478 21.54 0.00 0.00 2.40
3491 8653 4.637387 ATGGGCCATAGAGAGAGATTTG 57.363 45.455 19.68 0.00 0.00 2.32
3492 8654 2.707791 TGGGCCATAGAGAGAGATTTGG 59.292 50.000 0.00 0.00 0.00 3.28
3493 8655 2.975489 GGGCCATAGAGAGAGATTTGGA 59.025 50.000 4.39 0.00 0.00 3.53
3494 8656 3.392616 GGGCCATAGAGAGAGATTTGGAA 59.607 47.826 4.39 0.00 0.00 3.53
3495 8657 4.042684 GGGCCATAGAGAGAGATTTGGAAT 59.957 45.833 4.39 0.00 0.00 3.01
3496 8658 5.457342 GGGCCATAGAGAGAGATTTGGAATT 60.457 44.000 4.39 0.00 0.00 2.17
3497 8659 6.067350 GGCCATAGAGAGAGATTTGGAATTT 58.933 40.000 0.00 0.00 0.00 1.82
3542 8706 6.658816 TCCATTAGAAAAGCTAACAATGCAGA 59.341 34.615 0.00 0.00 41.64 4.26
3543 8707 7.340232 TCCATTAGAAAAGCTAACAATGCAGAT 59.660 33.333 0.00 0.00 41.64 2.90
3544 8708 7.977853 CCATTAGAAAAGCTAACAATGCAGATT 59.022 33.333 0.00 0.00 41.64 2.40
3545 8709 9.362539 CATTAGAAAAGCTAACAATGCAGATTT 57.637 29.630 0.00 0.00 41.64 2.17
3546 8710 8.970691 TTAGAAAAGCTAACAATGCAGATTTC 57.029 30.769 0.00 3.81 34.21 2.17
3547 8711 7.224522 AGAAAAGCTAACAATGCAGATTTCT 57.775 32.000 0.00 5.50 36.38 2.52
3548 8712 7.664758 AGAAAAGCTAACAATGCAGATTTCTT 58.335 30.769 0.00 0.00 37.08 2.52
3549 8713 8.796475 AGAAAAGCTAACAATGCAGATTTCTTA 58.204 29.630 0.00 0.00 37.08 2.10
3550 8714 9.578439 GAAAAGCTAACAATGCAGATTTCTTAT 57.422 29.630 0.00 0.00 29.57 1.73
3575 8739 6.861065 TTTGTACATGTCTTCTCTTTGACC 57.139 37.500 0.00 0.00 32.67 4.02
3576 8740 5.808366 TGTACATGTCTTCTCTTTGACCT 57.192 39.130 0.00 0.00 32.67 3.85
3577 8741 5.541845 TGTACATGTCTTCTCTTTGACCTG 58.458 41.667 0.00 0.00 35.79 4.00
3578 8742 4.013267 ACATGTCTTCTCTTTGACCTGG 57.987 45.455 0.00 0.00 34.61 4.45
3579 8743 3.648067 ACATGTCTTCTCTTTGACCTGGA 59.352 43.478 0.00 0.00 34.61 3.86
3580 8744 4.103153 ACATGTCTTCTCTTTGACCTGGAA 59.897 41.667 0.00 0.00 34.61 3.53
3581 8745 4.342862 TGTCTTCTCTTTGACCTGGAAG 57.657 45.455 0.00 0.00 35.93 3.46
3582 8746 3.070748 GTCTTCTCTTTGACCTGGAAGC 58.929 50.000 0.00 0.00 34.98 3.86
3583 8747 2.039084 TCTTCTCTTTGACCTGGAAGCC 59.961 50.000 0.00 0.00 34.98 4.35
3584 8748 1.434188 TCTCTTTGACCTGGAAGCCA 58.566 50.000 0.00 0.00 0.00 4.75
3585 8749 1.988107 TCTCTTTGACCTGGAAGCCAT 59.012 47.619 0.00 0.00 30.82 4.40
3586 8750 2.026822 TCTCTTTGACCTGGAAGCCATC 60.027 50.000 0.00 0.00 30.82 3.51
3587 8751 1.988107 TCTTTGACCTGGAAGCCATCT 59.012 47.619 0.00 0.00 30.82 2.90
3588 8752 2.376518 TCTTTGACCTGGAAGCCATCTT 59.623 45.455 0.00 0.00 30.82 2.40
3589 8753 2.978156 TTGACCTGGAAGCCATCTTT 57.022 45.000 0.00 0.00 30.82 2.52
3590 8754 4.042809 TCTTTGACCTGGAAGCCATCTTTA 59.957 41.667 0.00 0.00 30.82 1.85
3591 8755 3.634397 TGACCTGGAAGCCATCTTTAG 57.366 47.619 0.00 0.00 30.82 1.85
3592 8756 2.912956 TGACCTGGAAGCCATCTTTAGT 59.087 45.455 0.00 0.00 30.82 2.24
3593 8757 3.274288 GACCTGGAAGCCATCTTTAGTG 58.726 50.000 0.00 0.00 30.82 2.74
3594 8758 2.019984 CCTGGAAGCCATCTTTAGTGC 58.980 52.381 0.00 0.00 30.82 4.40
3595 8759 2.618816 CCTGGAAGCCATCTTTAGTGCA 60.619 50.000 0.00 0.00 30.82 4.57
3596 8760 2.681848 CTGGAAGCCATCTTTAGTGCAG 59.318 50.000 0.00 0.00 30.82 4.41
3597 8761 2.040278 TGGAAGCCATCTTTAGTGCAGT 59.960 45.455 0.00 0.00 31.48 4.40
3598 8762 3.084786 GGAAGCCATCTTTAGTGCAGTT 58.915 45.455 0.00 0.00 31.48 3.16
3599 8763 3.119708 GGAAGCCATCTTTAGTGCAGTTG 60.120 47.826 0.00 0.00 31.48 3.16
3600 8764 3.423539 AGCCATCTTTAGTGCAGTTGA 57.576 42.857 0.00 0.00 0.00 3.18
3601 8765 3.754965 AGCCATCTTTAGTGCAGTTGAA 58.245 40.909 0.00 0.00 0.00 2.69
3602 8766 4.144297 AGCCATCTTTAGTGCAGTTGAAA 58.856 39.130 0.00 0.00 0.00 2.69
3603 8767 4.768968 AGCCATCTTTAGTGCAGTTGAAAT 59.231 37.500 0.00 0.00 0.00 2.17
3604 8768 5.098211 GCCATCTTTAGTGCAGTTGAAATC 58.902 41.667 0.00 0.00 0.00 2.17
3605 8769 5.335897 GCCATCTTTAGTGCAGTTGAAATCA 60.336 40.000 0.00 0.00 0.00 2.57
3606 8770 6.088824 CCATCTTTAGTGCAGTTGAAATCAC 58.911 40.000 0.00 0.00 0.00 3.06
3607 8771 6.294120 CCATCTTTAGTGCAGTTGAAATCACA 60.294 38.462 0.00 0.00 32.25 3.58
3608 8772 6.060028 TCTTTAGTGCAGTTGAAATCACAC 57.940 37.500 0.00 0.00 32.25 3.82
3609 8773 5.588246 TCTTTAGTGCAGTTGAAATCACACA 59.412 36.000 0.00 0.00 32.25 3.72
3610 8774 6.262944 TCTTTAGTGCAGTTGAAATCACACAT 59.737 34.615 0.00 0.00 32.25 3.21
3611 8775 7.443879 TCTTTAGTGCAGTTGAAATCACACATA 59.556 33.333 0.00 0.00 32.25 2.29
3612 8776 5.362556 AGTGCAGTTGAAATCACACATAC 57.637 39.130 0.00 0.00 32.25 2.39
3613 8777 5.065914 AGTGCAGTTGAAATCACACATACT 58.934 37.500 0.00 0.00 32.25 2.12
3614 8778 6.230472 AGTGCAGTTGAAATCACACATACTA 58.770 36.000 0.00 0.00 32.25 1.82
3615 8779 6.369890 AGTGCAGTTGAAATCACACATACTAG 59.630 38.462 0.00 0.00 32.25 2.57
3616 8780 6.368791 GTGCAGTTGAAATCACACATACTAGA 59.631 38.462 0.00 0.00 0.00 2.43
3617 8781 6.934083 TGCAGTTGAAATCACACATACTAGAA 59.066 34.615 0.00 0.00 0.00 2.10
3618 8782 7.607607 TGCAGTTGAAATCACACATACTAGAAT 59.392 33.333 0.00 0.00 0.00 2.40
3619 8783 7.907045 GCAGTTGAAATCACACATACTAGAATG 59.093 37.037 0.00 0.00 0.00 2.67
3620 8784 9.154847 CAGTTGAAATCACACATACTAGAATGA 57.845 33.333 0.00 0.00 0.00 2.57
3621 8785 9.896645 AGTTGAAATCACACATACTAGAATGAT 57.103 29.630 0.00 0.00 0.00 2.45
3622 8786 9.926751 GTTGAAATCACACATACTAGAATGATG 57.073 33.333 0.00 0.00 0.00 3.07
3623 8787 9.889128 TTGAAATCACACATACTAGAATGATGA 57.111 29.630 0.00 0.00 33.34 2.92
3626 8790 9.842775 AAATCACACATACTAGAATGATGATGT 57.157 29.630 0.00 0.39 36.86 3.06
3629 8793 9.136323 TCACACATACTAGAATGATGATGTAGT 57.864 33.333 0.00 0.00 0.00 2.73
3644 8808 9.549078 TGATGATGTAGTAGTAGTAGAAGTGAG 57.451 37.037 0.00 0.00 0.00 3.51
3645 8809 7.789273 TGATGTAGTAGTAGTAGAAGTGAGC 57.211 40.000 0.00 0.00 0.00 4.26
3646 8810 7.336396 TGATGTAGTAGTAGTAGAAGTGAGCA 58.664 38.462 0.00 0.00 0.00 4.26
3647 8811 7.993758 TGATGTAGTAGTAGTAGAAGTGAGCAT 59.006 37.037 0.00 0.00 0.00 3.79
3648 8812 8.754991 ATGTAGTAGTAGTAGAAGTGAGCATT 57.245 34.615 0.00 0.00 0.00 3.56
3649 8813 8.211116 TGTAGTAGTAGTAGAAGTGAGCATTC 57.789 38.462 0.00 0.00 0.00 2.67
3650 8814 7.827729 TGTAGTAGTAGTAGAAGTGAGCATTCA 59.172 37.037 0.00 0.00 0.00 2.57
3651 8815 7.889873 AGTAGTAGTAGAAGTGAGCATTCAT 57.110 36.000 0.00 0.00 35.39 2.57
3652 8816 8.299990 AGTAGTAGTAGAAGTGAGCATTCATT 57.700 34.615 0.00 0.00 35.39 2.57
3653 8817 8.410141 AGTAGTAGTAGAAGTGAGCATTCATTC 58.590 37.037 0.00 0.00 35.39 2.67
3654 8818 7.175347 AGTAGTAGAAGTGAGCATTCATTCA 57.825 36.000 0.00 0.00 35.39 2.57
3655 8819 7.615403 AGTAGTAGAAGTGAGCATTCATTCAA 58.385 34.615 0.00 0.00 35.39 2.69
3656 8820 8.097038 AGTAGTAGAAGTGAGCATTCATTCAAA 58.903 33.333 0.00 0.00 35.39 2.69
3657 8821 7.750229 AGTAGAAGTGAGCATTCATTCAAAA 57.250 32.000 0.00 0.00 35.39 2.44
3658 8822 8.345724 AGTAGAAGTGAGCATTCATTCAAAAT 57.654 30.769 0.00 0.00 35.39 1.82
3659 8823 8.800332 AGTAGAAGTGAGCATTCATTCAAAATT 58.200 29.630 0.00 0.00 35.39 1.82
3660 8824 9.415544 GTAGAAGTGAGCATTCATTCAAAATTT 57.584 29.630 0.00 0.00 35.39 1.82
3662 8826 9.985730 AGAAGTGAGCATTCATTCAAAATTTAA 57.014 25.926 0.00 0.00 35.39 1.52
3670 8834 9.333497 GCATTCATTCAAAATTTAAAAGAAGGC 57.667 29.630 17.27 17.27 34.04 4.35
3671 8835 9.532697 CATTCATTCAAAATTTAAAAGAAGGCG 57.467 29.630 0.00 0.00 0.00 5.52
3672 8836 8.655651 TTCATTCAAAATTTAAAAGAAGGCGT 57.344 26.923 0.00 0.00 0.00 5.68
3673 8837 8.071122 TCATTCAAAATTTAAAAGAAGGCGTG 57.929 30.769 0.00 0.00 0.00 5.34
3674 8838 6.836577 TTCAAAATTTAAAAGAAGGCGTGG 57.163 33.333 0.00 0.00 0.00 4.94
3675 8839 5.293560 TCAAAATTTAAAAGAAGGCGTGGG 58.706 37.500 0.00 0.00 0.00 4.61
3676 8840 4.948341 AAATTTAAAAGAAGGCGTGGGT 57.052 36.364 0.00 0.00 0.00 4.51
3677 8841 3.934457 ATTTAAAAGAAGGCGTGGGTG 57.066 42.857 0.00 0.00 0.00 4.61
3678 8842 1.611519 TTAAAAGAAGGCGTGGGTGG 58.388 50.000 0.00 0.00 0.00 4.61
3679 8843 0.891904 TAAAAGAAGGCGTGGGTGGC 60.892 55.000 0.00 0.00 0.00 5.01
3680 8844 2.920076 AAAAGAAGGCGTGGGTGGCA 62.920 55.000 0.00 0.00 36.77 4.92
3681 8845 2.713531 AAAGAAGGCGTGGGTGGCAT 62.714 55.000 0.00 0.00 36.77 4.40
3682 8846 3.134127 GAAGGCGTGGGTGGCATC 61.134 66.667 0.00 0.00 36.77 3.91
3683 8847 4.740822 AAGGCGTGGGTGGCATCC 62.741 66.667 10.69 10.69 36.77 3.51
3686 8850 4.722700 GCGTGGGTGGCATCCAGT 62.723 66.667 22.39 0.00 34.56 4.00
3687 8851 2.436646 CGTGGGTGGCATCCAGTC 60.437 66.667 22.39 8.70 34.56 3.51
3688 8852 2.044946 GTGGGTGGCATCCAGTCC 60.045 66.667 22.39 4.67 34.56 3.85
3689 8853 2.531428 TGGGTGGCATCCAGTCCA 60.531 61.111 17.39 2.03 36.26 4.02
3690 8854 2.159490 TGGGTGGCATCCAGTCCAA 61.159 57.895 17.39 0.00 35.89 3.53
3691 8855 1.076549 GGGTGGCATCCAGTCCAAA 59.923 57.895 13.13 0.00 32.34 3.28
3692 8856 0.541764 GGGTGGCATCCAGTCCAAAA 60.542 55.000 13.13 0.00 32.34 2.44
3693 8857 1.560505 GGTGGCATCCAGTCCAAAAT 58.439 50.000 0.00 0.00 32.34 1.82
3694 8858 1.901833 GGTGGCATCCAGTCCAAAATT 59.098 47.619 0.00 0.00 32.34 1.82
3695 8859 2.302733 GGTGGCATCCAGTCCAAAATTT 59.697 45.455 0.00 0.00 32.34 1.82
3696 8860 3.513515 GGTGGCATCCAGTCCAAAATTTA 59.486 43.478 0.00 0.00 32.34 1.40
3697 8861 4.020662 GGTGGCATCCAGTCCAAAATTTAA 60.021 41.667 0.00 0.00 32.34 1.52
3698 8862 5.512232 GGTGGCATCCAGTCCAAAATTTAAA 60.512 40.000 0.00 0.00 32.34 1.52
3699 8863 5.994668 GTGGCATCCAGTCCAAAATTTAAAA 59.005 36.000 0.00 0.00 32.34 1.52
3700 8864 5.994668 TGGCATCCAGTCCAAAATTTAAAAC 59.005 36.000 0.00 0.00 0.00 2.43
3701 8865 5.994668 GGCATCCAGTCCAAAATTTAAAACA 59.005 36.000 0.00 0.00 0.00 2.83
3702 8866 6.484977 GGCATCCAGTCCAAAATTTAAAACAA 59.515 34.615 0.00 0.00 0.00 2.83
3703 8867 7.174772 GGCATCCAGTCCAAAATTTAAAACAAT 59.825 33.333 0.00 0.00 0.00 2.71
3704 8868 8.016801 GCATCCAGTCCAAAATTTAAAACAATG 58.983 33.333 0.00 0.00 0.00 2.82
3705 8869 9.270640 CATCCAGTCCAAAATTTAAAACAATGA 57.729 29.630 0.00 0.00 0.00 2.57
3707 8871 9.270640 TCCAGTCCAAAATTTAAAACAATGATG 57.729 29.630 0.00 0.00 0.00 3.07
3708 8872 9.270640 CCAGTCCAAAATTTAAAACAATGATGA 57.729 29.630 0.00 0.00 0.00 2.92
3750 8914 9.740239 TCATATGAAAAATTAAGAGAATGCTGC 57.260 29.630 1.98 0.00 0.00 5.25
3751 8915 9.745880 CATATGAAAAATTAAGAGAATGCTGCT 57.254 29.630 0.00 0.00 0.00 4.24
3754 8918 7.243487 TGAAAAATTAAGAGAATGCTGCTACG 58.757 34.615 0.00 0.00 0.00 3.51
3755 8919 5.741388 AAATTAAGAGAATGCTGCTACGG 57.259 39.130 0.00 0.00 0.00 4.02
3756 8920 3.887621 TTAAGAGAATGCTGCTACGGT 57.112 42.857 0.00 0.00 0.00 4.83
3757 8921 2.015736 AAGAGAATGCTGCTACGGTG 57.984 50.000 0.00 0.00 0.00 4.94
3758 8922 0.460987 AGAGAATGCTGCTACGGTGC 60.461 55.000 0.00 0.00 0.00 5.01
3759 8923 0.460987 GAGAATGCTGCTACGGTGCT 60.461 55.000 0.00 0.00 0.00 4.40
3760 8924 0.036010 AGAATGCTGCTACGGTGCTT 60.036 50.000 0.00 0.00 0.00 3.91
3761 8925 0.804989 GAATGCTGCTACGGTGCTTT 59.195 50.000 0.00 0.00 0.00 3.51
3762 8926 1.200020 GAATGCTGCTACGGTGCTTTT 59.800 47.619 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.762661 CCTTCTGTTCAACACATTCCAAAAAT 59.237 34.615 0.00 0.00 33.76 1.82
9 10 5.388654 AGAAATCCCTTCTGTTCAACACAT 58.611 37.500 0.00 0.00 43.09 3.21
15 16 6.070656 ACATTGAAGAAATCCCTTCTGTTCA 58.929 36.000 0.00 0.00 44.00 3.18
26 27 8.273557 GCATATGCAAATGACATTGAAGAAATC 58.726 33.333 22.84 0.00 41.59 2.17
135 141 3.608241 CGGCGTTGTGTTGATGTGTTATT 60.608 43.478 0.00 0.00 0.00 1.40
136 142 2.095969 CGGCGTTGTGTTGATGTGTTAT 60.096 45.455 0.00 0.00 0.00 1.89
156 162 6.452244 TGAATCGCTGATGTTTATGTATCG 57.548 37.500 0.00 0.00 0.00 2.92
166 172 2.103771 AGGTATGCTGAATCGCTGATGT 59.896 45.455 0.00 0.00 0.00 3.06
169 175 2.988010 AAGGTATGCTGAATCGCTGA 57.012 45.000 0.00 0.00 0.00 4.26
170 176 3.624861 AGAAAAGGTATGCTGAATCGCTG 59.375 43.478 0.00 0.00 0.00 5.18
171 177 3.873952 GAGAAAAGGTATGCTGAATCGCT 59.126 43.478 0.00 0.00 0.00 4.93
172 178 3.002759 GGAGAAAAGGTATGCTGAATCGC 59.997 47.826 0.00 0.00 0.00 4.58
173 179 4.446371 AGGAGAAAAGGTATGCTGAATCG 58.554 43.478 0.00 0.00 0.00 3.34
174 180 7.011857 CAGTAAGGAGAAAAGGTATGCTGAATC 59.988 40.741 0.00 0.00 0.00 2.52
175 181 6.825721 CAGTAAGGAGAAAAGGTATGCTGAAT 59.174 38.462 0.00 0.00 0.00 2.57
176 182 6.173339 CAGTAAGGAGAAAAGGTATGCTGAA 58.827 40.000 0.00 0.00 0.00 3.02
266 674 3.703052 AGCCAATCTTCTTAAATGCAGGG 59.297 43.478 0.00 0.00 0.00 4.45
269 677 3.378112 CGGAGCCAATCTTCTTAAATGCA 59.622 43.478 0.00 0.00 0.00 3.96
333 742 8.303780 AGATAGTAAACAGGTAGAAAGGGTAC 57.696 38.462 0.00 0.00 0.00 3.34
363 832 9.103861 CCTCAGTTTCACTCTAAGAAAATATCC 57.896 37.037 0.00 0.00 36.80 2.59
392 868 5.973899 TCAAGCTAAAATGTGGTTGCATA 57.026 34.783 0.00 0.00 40.27 3.14
395 871 4.367450 TGTTCAAGCTAAAATGTGGTTGC 58.633 39.130 0.00 0.00 40.27 4.17
420 1183 6.872920 AGCTCCATATCTACTAGCTAAATGC 58.127 40.000 0.00 0.00 41.56 3.56
439 1202 1.135139 TCACTTCAGTCGCATAGCTCC 59.865 52.381 0.00 0.00 0.00 4.70
459 1222 9.668497 GTTGAGTATAGAAATACTGAAAAGGGT 57.332 33.333 2.88 0.00 46.71 4.34
502 1265 6.237901 ACAATGTCAGACCAAGCAGTATAAA 58.762 36.000 0.00 0.00 0.00 1.40
504 1267 5.420725 ACAATGTCAGACCAAGCAGTATA 57.579 39.130 0.00 0.00 0.00 1.47
519 1282 9.013490 GTCATGTAAAAATGATGCTACAATGTC 57.987 33.333 0.00 0.00 38.76 3.06
530 1295 7.633789 AGGTAGTCTGGTCATGTAAAAATGAT 58.366 34.615 0.00 0.00 38.76 2.45
563 1328 5.951747 ACAACATAGTTTGGCTGGATATTGT 59.048 36.000 0.00 0.00 0.00 2.71
734 1502 2.039418 AGGAGCATACGAATGGCACTA 58.961 47.619 0.00 0.00 33.38 2.74
769 1537 7.861630 TCTCTGTTTTACTGTTCAACATAAGC 58.138 34.615 0.00 0.00 30.18 3.09
805 1573 0.179004 TTAACCACCAGCACCACCAG 60.179 55.000 0.00 0.00 0.00 4.00
813 1581 7.165460 ACCATATTTACTTTTAACCACCAGC 57.835 36.000 0.00 0.00 0.00 4.85
836 1604 7.422399 TGAAAGTTGTGCTTATCCTAAACAAC 58.578 34.615 8.53 8.53 46.92 3.32
1054 2936 3.456365 AGCCTCGTCATCGCTGCT 61.456 61.111 0.00 0.00 38.23 4.24
1055 2937 3.260483 CAGCCTCGTCATCGCTGC 61.260 66.667 0.00 0.00 43.12 5.25
1069 2951 3.204526 CAATCTGATCCTCCTGAACAGC 58.795 50.000 0.00 0.00 42.10 4.40
1364 3339 5.065731 GGATGCACATCTTGACTTCCTTTAG 59.934 44.000 10.30 0.00 37.92 1.85
1366 3341 3.760684 GGATGCACATCTTGACTTCCTTT 59.239 43.478 10.30 0.00 37.92 3.11
1387 3362 1.949525 ACTAGCTGCAACAAACACAGG 59.050 47.619 1.02 0.00 31.94 4.00
1476 3493 7.656137 TGGTAGTTCTTCTTATGATATTTCGCC 59.344 37.037 0.00 0.00 0.00 5.54
1477 3494 8.589335 TGGTAGTTCTTCTTATGATATTTCGC 57.411 34.615 0.00 0.00 0.00 4.70
1487 3504 4.652421 TGCCGGTATGGTAGTTCTTCTTAT 59.348 41.667 1.90 0.00 41.21 1.73
1520 3537 5.308237 CCCATCTGTATAAGCCTAGGACTTT 59.692 44.000 14.75 5.90 0.00 2.66
1556 3573 1.298014 GGCTCTTCCACAGGACTGG 59.702 63.158 4.14 0.00 34.19 4.00
1558 3575 1.835927 GCTGGCTCTTCCACAGGACT 61.836 60.000 0.00 0.00 40.72 3.85
1584 3601 1.550524 AGCATGCGAGACCTCTTGTAA 59.449 47.619 13.01 0.00 0.00 2.41
1585 3602 1.135139 GAGCATGCGAGACCTCTTGTA 59.865 52.381 13.01 0.00 0.00 2.41
1601 3618 4.399395 CTTCTGCTGGCCCGAGCA 62.399 66.667 16.33 16.33 46.87 4.26
1622 3639 0.255033 TGAGTCGGTAGAGGCAGCTA 59.745 55.000 0.00 0.00 0.00 3.32
1681 3698 1.061485 GGAGAACGAAGACAACTCGC 58.939 55.000 0.00 0.00 0.00 5.03
1695 3712 4.051237 CGAATATCGCTGATGTTGGAGAA 58.949 43.478 5.55 0.00 31.14 2.87
1712 3733 5.272283 AGAGAAGAATTTACCGGCGAATA 57.728 39.130 9.30 0.00 0.00 1.75
1720 3741 6.482524 ACAAAGGGGTAGAGAAGAATTTACC 58.517 40.000 0.00 0.00 35.82 2.85
1729 3750 5.546499 ACTGTAATGACAAAGGGGTAGAGAA 59.454 40.000 0.00 0.00 34.35 2.87
1879 3913 1.621992 AGTCTGAGCTTTCGGAGTGA 58.378 50.000 0.00 0.00 0.00 3.41
1962 6465 3.837399 AGGACTTCTCCTAGGAGTGTT 57.163 47.619 33.14 20.25 46.16 3.32
1988 6491 3.889815 ACAACATCCACCCATCTGTATG 58.110 45.455 0.00 0.00 0.00 2.39
2002 6505 2.301870 TCCACAGGACTGGTACAACATC 59.698 50.000 4.14 0.00 38.70 3.06
2091 7058 1.527311 GACAACCGTTTCAGCTGAGTC 59.473 52.381 17.43 14.55 0.00 3.36
2135 7102 2.490509 TGGAGAGCGAAGACAATTCGTA 59.509 45.455 11.18 0.00 43.24 3.43
2255 7229 7.883391 TGTTAACTTCAAACACCAGGAATTA 57.117 32.000 7.22 0.00 32.07 1.40
2490 7553 2.907897 GATGTTGGAGGGCGAGGACG 62.908 65.000 0.00 0.00 42.93 4.79
2513 7576 7.750229 ACACAACTGTAATGACAAGAATGAT 57.250 32.000 0.00 0.00 34.35 2.45
2514 7577 7.566760 AACACAACTGTAATGACAAGAATGA 57.433 32.000 0.00 0.00 34.35 2.57
2654 7773 2.232298 GAGCCTTCGGACTGGTGGAG 62.232 65.000 0.00 0.00 0.00 3.86
2675 7794 1.554392 CGTCGCCATCTTCTGAGAAG 58.446 55.000 15.90 15.90 35.07 2.85
2677 7796 1.139734 GCGTCGCCATCTTCTGAGA 59.860 57.895 5.75 0.00 36.09 3.27
2686 7805 3.434319 CCAGCTTTGCGTCGCCAT 61.434 61.111 15.88 0.00 0.00 4.40
2738 7857 1.001633 GGAGTTAGTTTGCAGGGTCGA 59.998 52.381 0.00 0.00 0.00 4.20
2763 7883 6.305693 ACTACAACAACAGAAAGATTCAGC 57.694 37.500 0.00 0.00 0.00 4.26
2821 7949 1.590610 CGAGCTCGGATCGATCCCAT 61.591 60.000 33.51 19.27 44.24 4.00
2842 7970 0.851469 ATGCAGAGAGATGGGGCAAT 59.149 50.000 0.00 0.00 38.08 3.56
2930 8060 3.420893 TCCAAGCTCACCAAAATACCAG 58.579 45.455 0.00 0.00 0.00 4.00
3014 8157 4.469657 TGGTTTGGTTACATCTCAGCTTT 58.530 39.130 0.00 0.00 0.00 3.51
3038 8181 4.219288 GCTCTCACAAATCTGGGTCAATTT 59.781 41.667 0.00 0.00 0.00 1.82
3042 8185 1.699083 TGCTCTCACAAATCTGGGTCA 59.301 47.619 0.00 0.00 0.00 4.02
3117 8260 4.833390 ACTAAACTATCGCTTCAGCCTTT 58.167 39.130 0.00 0.00 37.91 3.11
3146 8295 2.514803 ACACCAGTAAATTCACCTGCC 58.485 47.619 0.00 0.00 0.00 4.85
3151 8300 5.008613 TCAGCAAGAACACCAGTAAATTCAC 59.991 40.000 0.00 0.00 0.00 3.18
3382 8542 1.485066 TGCCTCCTATCTTCCCGTTTC 59.515 52.381 0.00 0.00 0.00 2.78
3436 8596 8.603983 TGTTAAATACAACACGTTCTTTCAAC 57.396 30.769 0.00 0.00 33.55 3.18
3438 8598 9.063739 GTTTGTTAAATACAACACGTTCTTTCA 57.936 29.630 0.00 0.00 46.09 2.69
3439 8599 9.281075 AGTTTGTTAAATACAACACGTTCTTTC 57.719 29.630 0.00 0.00 46.09 2.62
3468 8630 4.906747 AATCTCTCTCTATGGCCCATTC 57.093 45.455 0.00 0.00 0.00 2.67
3515 8679 6.658816 TGCATTGTTAGCTTTTCTAATGGAGA 59.341 34.615 0.00 0.00 39.29 3.71
3549 8713 9.167311 GGTCAAAGAGAAGACATGTACAAATAT 57.833 33.333 0.00 0.00 36.50 1.28
3550 8714 8.375506 AGGTCAAAGAGAAGACATGTACAAATA 58.624 33.333 0.00 0.00 36.50 1.40
3551 8715 7.173907 CAGGTCAAAGAGAAGACATGTACAAAT 59.826 37.037 0.00 0.00 40.51 2.32
3552 8716 6.483307 CAGGTCAAAGAGAAGACATGTACAAA 59.517 38.462 0.00 0.00 40.51 2.83
3553 8717 5.991606 CAGGTCAAAGAGAAGACATGTACAA 59.008 40.000 0.00 0.00 40.51 2.41
3554 8718 5.511373 CCAGGTCAAAGAGAAGACATGTACA 60.511 44.000 0.00 0.00 42.97 2.90
3555 8719 4.932200 CCAGGTCAAAGAGAAGACATGTAC 59.068 45.833 0.00 0.00 42.97 2.90
3556 8720 4.838423 TCCAGGTCAAAGAGAAGACATGTA 59.162 41.667 0.00 0.00 42.97 2.29
3557 8721 3.648067 TCCAGGTCAAAGAGAAGACATGT 59.352 43.478 0.00 0.00 42.97 3.21
3558 8722 4.277515 TCCAGGTCAAAGAGAAGACATG 57.722 45.455 0.00 0.00 43.80 3.21
3559 8723 4.805609 GCTTCCAGGTCAAAGAGAAGACAT 60.806 45.833 0.00 0.00 36.83 3.06
3560 8724 3.495100 GCTTCCAGGTCAAAGAGAAGACA 60.495 47.826 0.00 0.00 36.83 3.41
3561 8725 3.070748 GCTTCCAGGTCAAAGAGAAGAC 58.929 50.000 0.00 0.00 36.83 3.01
3562 8726 2.039084 GGCTTCCAGGTCAAAGAGAAGA 59.961 50.000 0.00 0.00 36.83 2.87
3563 8727 2.224621 TGGCTTCCAGGTCAAAGAGAAG 60.225 50.000 0.00 0.00 37.57 2.85
3564 8728 1.774254 TGGCTTCCAGGTCAAAGAGAA 59.226 47.619 0.00 0.00 0.00 2.87
3565 8729 1.434188 TGGCTTCCAGGTCAAAGAGA 58.566 50.000 0.00 0.00 0.00 3.10
3566 8730 2.026449 AGATGGCTTCCAGGTCAAAGAG 60.026 50.000 0.00 0.00 36.75 2.85
3567 8731 1.988107 AGATGGCTTCCAGGTCAAAGA 59.012 47.619 0.00 0.00 36.75 2.52
3568 8732 2.503895 AGATGGCTTCCAGGTCAAAG 57.496 50.000 0.00 0.00 36.75 2.77
3569 8733 2.978156 AAGATGGCTTCCAGGTCAAA 57.022 45.000 0.00 0.00 36.75 2.69
3570 8734 2.978156 AAAGATGGCTTCCAGGTCAA 57.022 45.000 0.00 0.00 36.75 3.18
3571 8735 2.912956 ACTAAAGATGGCTTCCAGGTCA 59.087 45.455 0.00 0.00 36.75 4.02
3572 8736 3.274288 CACTAAAGATGGCTTCCAGGTC 58.726 50.000 0.00 0.00 36.75 3.85
3573 8737 2.619074 GCACTAAAGATGGCTTCCAGGT 60.619 50.000 0.00 0.00 36.75 4.00
3574 8738 2.019984 GCACTAAAGATGGCTTCCAGG 58.980 52.381 0.00 0.00 36.75 4.45
3575 8739 2.681848 CTGCACTAAAGATGGCTTCCAG 59.318 50.000 0.00 0.00 36.75 3.86
3576 8740 2.040278 ACTGCACTAAAGATGGCTTCCA 59.960 45.455 0.00 0.00 38.19 3.53
3577 8741 2.716217 ACTGCACTAAAGATGGCTTCC 58.284 47.619 0.00 0.00 31.82 3.46
3578 8742 3.753272 TCAACTGCACTAAAGATGGCTTC 59.247 43.478 0.00 0.00 31.82 3.86
3579 8743 3.754965 TCAACTGCACTAAAGATGGCTT 58.245 40.909 0.00 0.00 35.37 4.35
3580 8744 3.423539 TCAACTGCACTAAAGATGGCT 57.576 42.857 0.00 0.00 0.00 4.75
3581 8745 4.503741 TTTCAACTGCACTAAAGATGGC 57.496 40.909 0.00 0.00 0.00 4.40
3582 8746 6.088824 GTGATTTCAACTGCACTAAAGATGG 58.911 40.000 0.00 0.00 0.00 3.51
3583 8747 6.580041 GTGTGATTTCAACTGCACTAAAGATG 59.420 38.462 0.00 0.00 32.69 2.90
3584 8748 6.262944 TGTGTGATTTCAACTGCACTAAAGAT 59.737 34.615 0.00 0.00 32.69 2.40
3585 8749 5.588246 TGTGTGATTTCAACTGCACTAAAGA 59.412 36.000 0.00 0.00 32.69 2.52
3586 8750 5.820131 TGTGTGATTTCAACTGCACTAAAG 58.180 37.500 0.00 0.00 32.69 1.85
3587 8751 5.826601 TGTGTGATTTCAACTGCACTAAA 57.173 34.783 0.00 0.00 32.69 1.85
3588 8752 6.710295 AGTATGTGTGATTTCAACTGCACTAA 59.290 34.615 0.00 0.00 32.69 2.24
3589 8753 6.230472 AGTATGTGTGATTTCAACTGCACTA 58.770 36.000 0.00 0.00 32.69 2.74
3590 8754 5.065914 AGTATGTGTGATTTCAACTGCACT 58.934 37.500 0.00 0.00 32.69 4.40
3591 8755 5.362556 AGTATGTGTGATTTCAACTGCAC 57.637 39.130 0.00 0.00 0.00 4.57
3592 8756 6.463360 TCTAGTATGTGTGATTTCAACTGCA 58.537 36.000 0.00 0.00 0.00 4.41
3593 8757 6.968131 TCTAGTATGTGTGATTTCAACTGC 57.032 37.500 0.00 0.00 0.00 4.40
3594 8758 9.154847 TCATTCTAGTATGTGTGATTTCAACTG 57.845 33.333 8.95 0.00 0.00 3.16
3595 8759 9.896645 ATCATTCTAGTATGTGTGATTTCAACT 57.103 29.630 8.95 0.00 0.00 3.16
3596 8760 9.926751 CATCATTCTAGTATGTGTGATTTCAAC 57.073 33.333 8.95 0.00 0.00 3.18
3597 8761 9.889128 TCATCATTCTAGTATGTGTGATTTCAA 57.111 29.630 8.95 0.00 0.00 2.69
3600 8764 9.842775 ACATCATCATTCTAGTATGTGTGATTT 57.157 29.630 19.73 15.06 33.73 2.17
3603 8767 9.136323 ACTACATCATCATTCTAGTATGTGTGA 57.864 33.333 16.17 16.17 0.00 3.58
3618 8782 9.549078 CTCACTTCTACTACTACTACATCATCA 57.451 37.037 0.00 0.00 0.00 3.07
3619 8783 8.500773 GCTCACTTCTACTACTACTACATCATC 58.499 40.741 0.00 0.00 0.00 2.92
3620 8784 7.993758 TGCTCACTTCTACTACTACTACATCAT 59.006 37.037 0.00 0.00 0.00 2.45
3621 8785 7.336396 TGCTCACTTCTACTACTACTACATCA 58.664 38.462 0.00 0.00 0.00 3.07
3622 8786 7.789273 TGCTCACTTCTACTACTACTACATC 57.211 40.000 0.00 0.00 0.00 3.06
3623 8787 8.754991 AATGCTCACTTCTACTACTACTACAT 57.245 34.615 0.00 0.00 0.00 2.29
3624 8788 7.827729 TGAATGCTCACTTCTACTACTACTACA 59.172 37.037 0.00 0.00 0.00 2.74
3625 8789 8.211116 TGAATGCTCACTTCTACTACTACTAC 57.789 38.462 0.00 0.00 0.00 2.73
3626 8790 8.982091 ATGAATGCTCACTTCTACTACTACTA 57.018 34.615 0.00 0.00 33.30 1.82
3627 8791 7.889873 ATGAATGCTCACTTCTACTACTACT 57.110 36.000 0.00 0.00 33.30 2.57
3628 8792 8.191446 TGAATGAATGCTCACTTCTACTACTAC 58.809 37.037 0.00 0.00 33.30 2.73
3629 8793 8.293699 TGAATGAATGCTCACTTCTACTACTA 57.706 34.615 0.00 0.00 33.30 1.82
3630 8794 7.175347 TGAATGAATGCTCACTTCTACTACT 57.825 36.000 0.00 0.00 33.30 2.57
3631 8795 7.834068 TTGAATGAATGCTCACTTCTACTAC 57.166 36.000 0.00 0.00 33.30 2.73
3632 8796 8.846943 TTTTGAATGAATGCTCACTTCTACTA 57.153 30.769 0.00 0.00 33.30 1.82
3633 8797 7.750229 TTTTGAATGAATGCTCACTTCTACT 57.250 32.000 0.00 0.00 33.30 2.57
3634 8798 8.976986 AATTTTGAATGAATGCTCACTTCTAC 57.023 30.769 0.00 0.00 33.30 2.59
3636 8800 9.985730 TTAAATTTTGAATGAATGCTCACTTCT 57.014 25.926 0.00 0.00 33.30 2.85
3644 8808 9.333497 GCCTTCTTTTAAATTTTGAATGAATGC 57.667 29.630 17.54 17.54 0.00 3.56
3645 8809 9.532697 CGCCTTCTTTTAAATTTTGAATGAATG 57.467 29.630 12.37 11.30 0.00 2.67
3646 8810 9.271828 ACGCCTTCTTTTAAATTTTGAATGAAT 57.728 25.926 12.37 0.75 0.00 2.57
3647 8811 8.547069 CACGCCTTCTTTTAAATTTTGAATGAA 58.453 29.630 0.00 11.77 0.00 2.57
3648 8812 7.170658 CCACGCCTTCTTTTAAATTTTGAATGA 59.829 33.333 0.00 0.00 0.00 2.57
3649 8813 7.290118 CCACGCCTTCTTTTAAATTTTGAATG 58.710 34.615 0.00 0.00 0.00 2.67
3650 8814 6.426633 CCCACGCCTTCTTTTAAATTTTGAAT 59.573 34.615 0.00 0.00 0.00 2.57
3651 8815 5.755861 CCCACGCCTTCTTTTAAATTTTGAA 59.244 36.000 0.00 0.00 0.00 2.69
3652 8816 5.163395 ACCCACGCCTTCTTTTAAATTTTGA 60.163 36.000 0.00 0.00 0.00 2.69
3653 8817 5.050431 CACCCACGCCTTCTTTTAAATTTTG 60.050 40.000 0.00 0.00 0.00 2.44
3654 8818 5.053811 CACCCACGCCTTCTTTTAAATTTT 58.946 37.500 0.00 0.00 0.00 1.82
3655 8819 4.502431 CCACCCACGCCTTCTTTTAAATTT 60.502 41.667 0.00 0.00 0.00 1.82
3656 8820 3.006430 CCACCCACGCCTTCTTTTAAATT 59.994 43.478 0.00 0.00 0.00 1.82
3657 8821 2.560981 CCACCCACGCCTTCTTTTAAAT 59.439 45.455 0.00 0.00 0.00 1.40
3658 8822 1.957877 CCACCCACGCCTTCTTTTAAA 59.042 47.619 0.00 0.00 0.00 1.52
3659 8823 1.611519 CCACCCACGCCTTCTTTTAA 58.388 50.000 0.00 0.00 0.00 1.52
3660 8824 0.891904 GCCACCCACGCCTTCTTTTA 60.892 55.000 0.00 0.00 0.00 1.52
3661 8825 2.200337 GCCACCCACGCCTTCTTTT 61.200 57.895 0.00 0.00 0.00 2.27
3662 8826 2.597510 GCCACCCACGCCTTCTTT 60.598 61.111 0.00 0.00 0.00 2.52
3663 8827 3.210012 ATGCCACCCACGCCTTCTT 62.210 57.895 0.00 0.00 0.00 2.52
3664 8828 3.628646 GATGCCACCCACGCCTTCT 62.629 63.158 0.00 0.00 0.00 2.85
3665 8829 3.134127 GATGCCACCCACGCCTTC 61.134 66.667 0.00 0.00 0.00 3.46
3666 8830 4.740822 GGATGCCACCCACGCCTT 62.741 66.667 0.00 0.00 0.00 4.35
3669 8833 4.722700 ACTGGATGCCACCCACGC 62.723 66.667 0.00 0.00 0.00 5.34
3670 8834 2.436646 GACTGGATGCCACCCACG 60.437 66.667 0.00 0.00 0.00 4.94
3671 8835 2.044946 GGACTGGATGCCACCCAC 60.045 66.667 0.00 0.00 0.00 4.61
3672 8836 1.724148 TTTGGACTGGATGCCACCCA 61.724 55.000 0.00 0.00 33.01 4.51
3673 8837 0.541764 TTTTGGACTGGATGCCACCC 60.542 55.000 0.00 0.00 33.01 4.61
3674 8838 1.560505 ATTTTGGACTGGATGCCACC 58.439 50.000 0.00 0.00 33.01 4.61
3675 8839 3.683365 AAATTTTGGACTGGATGCCAC 57.317 42.857 0.00 0.00 33.01 5.01
3676 8840 5.815233 TTTAAATTTTGGACTGGATGCCA 57.185 34.783 0.00 0.00 0.00 4.92
3677 8841 5.994668 TGTTTTAAATTTTGGACTGGATGCC 59.005 36.000 0.00 0.00 0.00 4.40
3678 8842 7.489574 TTGTTTTAAATTTTGGACTGGATGC 57.510 32.000 0.00 0.00 0.00 3.91
3679 8843 9.270640 TCATTGTTTTAAATTTTGGACTGGATG 57.729 29.630 0.00 1.10 0.00 3.51
3681 8845 9.270640 CATCATTGTTTTAAATTTTGGACTGGA 57.729 29.630 0.00 0.00 0.00 3.86
3682 8846 9.270640 TCATCATTGTTTTAAATTTTGGACTGG 57.729 29.630 0.00 0.00 0.00 4.00
3724 8888 9.740239 GCAGCATTCTCTTAATTTTTCATATGA 57.260 29.630 0.00 0.00 0.00 2.15
3725 8889 9.745880 AGCAGCATTCTCTTAATTTTTCATATG 57.254 29.630 0.00 0.00 0.00 1.78
3728 8892 7.912250 CGTAGCAGCATTCTCTTAATTTTTCAT 59.088 33.333 0.00 0.00 0.00 2.57
3729 8893 7.243487 CGTAGCAGCATTCTCTTAATTTTTCA 58.757 34.615 0.00 0.00 0.00 2.69
3730 8894 6.688813 CCGTAGCAGCATTCTCTTAATTTTTC 59.311 38.462 0.00 0.00 0.00 2.29
3731 8895 6.151144 ACCGTAGCAGCATTCTCTTAATTTTT 59.849 34.615 0.00 0.00 0.00 1.94
3732 8896 5.648092 ACCGTAGCAGCATTCTCTTAATTTT 59.352 36.000 0.00 0.00 0.00 1.82
3733 8897 5.065218 CACCGTAGCAGCATTCTCTTAATTT 59.935 40.000 0.00 0.00 0.00 1.82
3734 8898 4.572389 CACCGTAGCAGCATTCTCTTAATT 59.428 41.667 0.00 0.00 0.00 1.40
3735 8899 4.122776 CACCGTAGCAGCATTCTCTTAAT 58.877 43.478 0.00 0.00 0.00 1.40
3736 8900 3.521560 CACCGTAGCAGCATTCTCTTAA 58.478 45.455 0.00 0.00 0.00 1.85
3737 8901 2.738643 GCACCGTAGCAGCATTCTCTTA 60.739 50.000 0.00 0.00 0.00 2.10
3738 8902 2.009042 GCACCGTAGCAGCATTCTCTT 61.009 52.381 0.00 0.00 0.00 2.85
3739 8903 0.460987 GCACCGTAGCAGCATTCTCT 60.461 55.000 0.00 0.00 0.00 3.10
3740 8904 0.460987 AGCACCGTAGCAGCATTCTC 60.461 55.000 0.00 0.00 36.85 2.87
3741 8905 0.036010 AAGCACCGTAGCAGCATTCT 60.036 50.000 0.00 0.00 36.85 2.40
3742 8906 0.804989 AAAGCACCGTAGCAGCATTC 59.195 50.000 0.00 0.00 36.85 2.67
3743 8907 1.247567 AAAAGCACCGTAGCAGCATT 58.752 45.000 0.00 0.00 36.85 3.56
3744 8908 2.946947 AAAAGCACCGTAGCAGCAT 58.053 47.368 0.00 0.00 36.85 3.79
3745 8909 4.473643 AAAAGCACCGTAGCAGCA 57.526 50.000 0.00 0.00 36.85 4.41


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

AutoCloner maintained by Alex Coulton.