Multiple sequence alignment - TraesCS1B01G463100

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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 TraesCS1B01G463100 chr1B 100.000 4918 0 0 1 4918 675372947 675377864 0.000000e+00 9082.0
1 TraesCS1B01G463100 chr1B 82.705 451 43 10 3084 3523 675552473 675552899 7.780000e-98 368.0
2 TraesCS1B01G463100 chr1B 82.857 420 46 15 2678 3093 675542785 675543182 2.180000e-93 353.0
3 TraesCS1B01G463100 chr1B 87.333 300 35 2 3009 3308 675543219 675543515 1.700000e-89 340.0
4 TraesCS1B01G463100 chr1B 82.421 347 37 17 4014 4351 675552946 675553277 1.040000e-71 281.0
5 TraesCS1B01G463100 chr1B 87.425 167 14 1 3188 3354 675551891 675552050 8.410000e-43 185.0
6 TraesCS1B01G463100 chr1B 79.365 252 29 17 4375 4615 675544022 675544261 6.590000e-34 156.0
7 TraesCS1B01G463100 chr1A 92.910 3399 181 29 1554 4918 582277229 582280601 0.000000e+00 4887.0
8 TraesCS1B01G463100 chr1A 87.867 1533 99 32 2237 3762 582292258 582293710 0.000000e+00 1720.0
9 TraesCS1B01G463100 chr1A 81.100 1164 122 49 3448 4573 582412065 582413168 0.000000e+00 841.0
10 TraesCS1B01G463100 chr1A 81.023 1017 55 46 567 1527 582276299 582277233 0.000000e+00 682.0
11 TraesCS1B01G463100 chr1A 83.221 745 78 22 2678 3414 582358357 582359062 1.490000e-179 640.0
12 TraesCS1B01G463100 chr1A 88.608 474 44 6 1 471 582275215 582275681 7.140000e-158 568.0
13 TraesCS1B01G463100 chr1A 81.304 583 58 20 1914 2476 582357633 582358184 4.550000e-115 425.0
14 TraesCS1B01G463100 chr1A 91.844 282 15 5 3842 4118 582293713 582293991 2.150000e-103 387.0
15 TraesCS1B01G463100 chr1A 82.751 458 43 12 3084 3529 582411350 582411783 4.650000e-100 375.0
16 TraesCS1B01G463100 chr1A 88.024 167 13 1 3188 3354 582410771 582410930 1.810000e-44 191.0
17 TraesCS1B01G463100 chr1D 90.365 1671 115 22 1554 3210 485054271 485055909 0.000000e+00 2152.0
18 TraesCS1B01G463100 chr1D 85.000 1400 131 40 2965 4351 485099053 485100386 0.000000e+00 1349.0
19 TraesCS1B01G463100 chr1D 92.484 918 47 10 3294 4209 485055917 485056814 0.000000e+00 1293.0
20 TraesCS1B01G463100 chr1D 84.965 1011 51 46 564 1527 485053319 485054275 0.000000e+00 931.0
21 TraesCS1B01G463100 chr1D 89.348 629 30 18 4296 4918 485056814 485057411 0.000000e+00 756.0
22 TraesCS1B01G463100 chr1D 88.556 568 56 4 1 568 485052734 485053292 0.000000e+00 680.0
23 TraesCS1B01G463100 chr1D 85.024 414 45 8 3007 3414 485090195 485090597 5.930000e-109 405.0
24 TraesCS1B01G463100 chr1D 81.295 417 40 17 2678 3091 485089777 485090158 2.220000e-78 303.0
25 TraesCS1B01G463100 chr2B 90.000 230 20 2 3009 3238 94929785 94929559 1.340000e-75 294.0
26 TraesCS1B01G463100 chr2B 90.805 87 8 0 176 262 215925392 215925306 3.110000e-22 117.0
27 TraesCS1B01G463100 chr2B 88.542 96 10 1 176 270 777546613 777546708 1.120000e-21 115.0
28 TraesCS1B01G463100 chr2B 90.476 84 6 2 4375 4456 94929487 94929404 5.200000e-20 110.0
29 TraesCS1B01G463100 chr7D 89.130 138 13 2 1 137 60485150 60485286 2.350000e-38 171.0
30 TraesCS1B01G463100 chr3D 88.542 96 11 0 173 268 606566357 606566452 3.110000e-22 117.0
31 TraesCS1B01G463100 chr3D 87.500 96 12 0 173 268 606595372 606595467 1.450000e-20 111.0
32 TraesCS1B01G463100 chr3D 90.385 52 5 0 4866 4917 535511236 535511287 8.830000e-08 69.4
33 TraesCS1B01G463100 chr3D 100.000 35 0 0 570 604 272290715 272290749 1.140000e-06 65.8
34 TraesCS1B01G463100 chr2A 87.629 97 11 1 175 270 611336580 611336676 1.450000e-20 111.0
35 TraesCS1B01G463100 chr5B 86.275 102 13 1 169 269 443276391 443276492 5.200000e-20 110.0
36 TraesCS1B01G463100 chr5B 93.220 59 4 0 1624 1682 617277297 617277355 2.440000e-13 87.9
37 TraesCS1B01G463100 chr5B 79.646 113 23 0 1624 1736 617038599 617038487 1.130000e-11 82.4
38 TraesCS1B01G463100 chr5A 86.408 103 11 3 166 268 6529806 6529905 5.200000e-20 110.0
39 TraesCS1B01G463100 chr5A 80.952 126 23 1 1618 1742 622212771 622212646 1.130000e-16 99.0
40 TraesCS1B01G463100 chr5A 92.308 65 5 0 1618 1682 622224980 622225044 5.240000e-15 93.5
41 TraesCS1B01G463100 chr5A 77.632 152 32 2 1618 1768 622145002 622145152 1.890000e-14 91.6
42 TraesCS1B01G463100 chr5A 100.000 35 0 0 570 604 408199473 408199439 1.140000e-06 65.8
43 TraesCS1B01G463100 chr5D 88.406 69 8 0 1618 1686 498027400 498027468 3.150000e-12 84.2
44 TraesCS1B01G463100 chr5D 100.000 35 0 0 570 604 431182028 431181994 1.140000e-06 65.8
45 TraesCS1B01G463100 chr6B 97.561 41 0 1 566 605 452527643 452527683 8.830000e-08 69.4
46 TraesCS1B01G463100 chr3B 100.000 37 0 0 568 604 159560859 159560823 8.830000e-08 69.4
47 TraesCS1B01G463100 chr3B 100.000 35 0 0 570 604 506972671 506972637 1.140000e-06 65.8
48 TraesCS1B01G463100 chr4A 95.122 41 2 0 570 610 407215238 407215278 1.140000e-06 65.8
49 TraesCS1B01G463100 chr4A 100.000 35 0 0 570 604 514761368 514761334 1.140000e-06 65.8
50 TraesCS1B01G463100 chr6A 94.872 39 2 0 570 608 428728 428690 1.480000e-05 62.1


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 TraesCS1B01G463100 chr1B 675372947 675377864 4917 False 9082.000000 9082 100.000000 1 4918 1 chr1B.!!$F1 4917
1 TraesCS1B01G463100 chr1B 675542785 675544261 1476 False 283.000000 353 83.185000 2678 4615 3 chr1B.!!$F2 1937
2 TraesCS1B01G463100 chr1B 675551891 675553277 1386 False 278.000000 368 84.183667 3084 4351 3 chr1B.!!$F3 1267
3 TraesCS1B01G463100 chr1A 582275215 582280601 5386 False 2045.666667 4887 87.513667 1 4918 3 chr1A.!!$F1 4917
4 TraesCS1B01G463100 chr1A 582292258 582293991 1733 False 1053.500000 1720 89.855500 2237 4118 2 chr1A.!!$F2 1881
5 TraesCS1B01G463100 chr1A 582357633 582359062 1429 False 532.500000 640 82.262500 1914 3414 2 chr1A.!!$F3 1500
6 TraesCS1B01G463100 chr1A 582410771 582413168 2397 False 469.000000 841 83.958333 3084 4573 3 chr1A.!!$F4 1489
7 TraesCS1B01G463100 chr1D 485099053 485100386 1333 False 1349.000000 1349 85.000000 2965 4351 1 chr1D.!!$F1 1386
8 TraesCS1B01G463100 chr1D 485052734 485057411 4677 False 1162.400000 2152 89.143600 1 4918 5 chr1D.!!$F2 4917
9 TraesCS1B01G463100 chr1D 485089777 485090597 820 False 354.000000 405 83.159500 2678 3414 2 chr1D.!!$F3 736

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
661 1190 0.104855 ATCACATCACACGGATCCGG 59.895 55.000 35.87 26.1 44.69 5.14 F
1522 2115 0.176680 ACCTGCTCTGCGATTCGATT 59.823 50.000 10.88 0.0 0.00 3.34 F
1706 2299 0.669318 TTCTCGATGCGTGTGGTTCC 60.669 55.000 0.00 0.0 0.00 3.62 F
1742 2335 1.065928 CGTGCCGTACTCTGATCCC 59.934 63.158 0.00 0.0 0.00 3.85 F
3178 4095 1.672881 GGTGCTAGCTGTGCTAATTGG 59.327 52.381 17.23 0.0 40.82 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 2138 0.187117 TGGTGGAAACAGGGCATGAA 59.813 50.000 5.99 0.0 44.46 2.57 R
3414 4370 0.949105 GTGTGCCAGTAACTCCGGTG 60.949 60.000 0.00 0.0 0.00 4.94 R
3532 4851 1.062587 GCACTGCACAATAAGGTAGCG 59.937 52.381 0.00 0.0 0.00 4.26 R
3554 4873 9.031360 GTTCTATAAGCATCGTTGAACAAGATA 57.969 33.333 0.00 0.0 34.36 1.98 R
4885 6302 1.710809 AGGTGTGGTCAGCCCTTTATT 59.289 47.619 0.00 0.0 42.30 1.40 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
79 82 6.514947 ACACGTATTACTATATTTTGGCCGA 58.485 36.000 0.00 0.00 0.00 5.54
115 118 3.091545 TGAGTCATTTGCCCCTTTGATC 58.908 45.455 0.00 0.00 0.00 2.92
127 130 4.442052 GCCCCTTTGATCTTTAATTCCTGC 60.442 45.833 0.00 0.00 0.00 4.85
307 310 2.365293 AGGTTCACCCATTTTGCTTCAC 59.635 45.455 0.00 0.00 36.42 3.18
320 323 6.741992 TTTTGCTTCACATGTAGTCCATAG 57.258 37.500 0.00 0.00 30.71 2.23
368 371 3.189287 CCGGAGCCAGTATTAATTGCATC 59.811 47.826 0.00 0.00 0.00 3.91
371 374 5.048504 CGGAGCCAGTATTAATTGCATCAAT 60.049 40.000 0.00 0.00 35.39 2.57
390 393 6.140303 TCAATTGCAGATAATCTTGGAAGC 57.860 37.500 0.00 0.00 0.00 3.86
395 398 3.243002 GCAGATAATCTTGGAAGCAGCAC 60.243 47.826 0.00 0.00 0.00 4.40
398 401 5.819379 CAGATAATCTTGGAAGCAGCACTAA 59.181 40.000 0.00 0.00 0.00 2.24
404 407 5.500234 TCTTGGAAGCAGCACTAATTACAT 58.500 37.500 0.00 0.00 0.00 2.29
405 408 5.945784 TCTTGGAAGCAGCACTAATTACATT 59.054 36.000 0.00 0.00 0.00 2.71
406 409 7.109501 TCTTGGAAGCAGCACTAATTACATTA 58.890 34.615 0.00 0.00 0.00 1.90
407 410 6.677781 TGGAAGCAGCACTAATTACATTAC 57.322 37.500 0.00 0.00 0.00 1.89
411 414 6.530913 AGCAGCACTAATTACATTACATCG 57.469 37.500 0.00 0.00 0.00 3.84
414 417 7.442364 AGCAGCACTAATTACATTACATCGATT 59.558 33.333 0.00 0.00 0.00 3.34
425 428 6.649436 ACATTACATCGATTGCAACTATTCG 58.351 36.000 12.77 12.77 0.00 3.34
429 432 1.483004 TCGATTGCAACTATTCGGGGA 59.517 47.619 17.43 0.00 32.67 4.81
430 433 1.597663 CGATTGCAACTATTCGGGGAC 59.402 52.381 11.43 0.00 0.00 4.46
431 434 2.639065 GATTGCAACTATTCGGGGACA 58.361 47.619 0.00 0.00 0.00 4.02
433 436 1.816074 TGCAACTATTCGGGGACAAC 58.184 50.000 0.00 0.00 0.00 3.32
434 437 1.072489 TGCAACTATTCGGGGACAACA 59.928 47.619 0.00 0.00 0.00 3.33
435 438 2.290641 TGCAACTATTCGGGGACAACAT 60.291 45.455 0.00 0.00 0.00 2.71
437 440 3.942748 GCAACTATTCGGGGACAACATTA 59.057 43.478 0.00 0.00 0.00 1.90
503 996 1.131420 GCGCAAAGAAGCTGAGACG 59.869 57.895 0.30 0.00 0.00 4.18
504 997 1.284982 GCGCAAAGAAGCTGAGACGA 61.285 55.000 0.30 0.00 0.00 4.20
505 998 0.436531 CGCAAAGAAGCTGAGACGAC 59.563 55.000 0.00 0.00 0.00 4.34
520 1013 1.263217 GACGACCAAAAGACGCAACAT 59.737 47.619 0.00 0.00 37.13 2.71
521 1014 1.002900 ACGACCAAAAGACGCAACATG 60.003 47.619 0.00 0.00 37.13 3.21
556 1053 2.418628 TCACTTCCGCCAATCGAAAATC 59.581 45.455 0.00 0.00 41.67 2.17
568 1065 1.127766 TCGAAAATCGCCACGACAATG 59.872 47.619 0.00 0.00 40.21 2.82
600 1129 7.550196 ACGCTTTTATATTTCTTTACGAAGGGA 59.450 33.333 0.00 0.00 33.56 4.20
601 1130 8.062448 CGCTTTTATATTTCTTTACGAAGGGAG 58.938 37.037 0.00 0.00 33.56 4.30
602 1131 8.890718 GCTTTTATATTTCTTTACGAAGGGAGT 58.109 33.333 0.00 0.00 33.56 3.85
621 1150 4.082949 GGAGTAGTACAAAATGTGTTGCCC 60.083 45.833 2.52 0.00 41.98 5.36
631 1160 1.602323 GTGTTGCCCGGTCCATCAA 60.602 57.895 0.00 0.00 0.00 2.57
639 1168 1.949525 CCCGGTCCATCAAATCACATC 59.050 52.381 0.00 0.00 0.00 3.06
640 1169 2.421952 CCCGGTCCATCAAATCACATCT 60.422 50.000 0.00 0.00 0.00 2.90
641 1170 2.874701 CCGGTCCATCAAATCACATCTC 59.125 50.000 0.00 0.00 0.00 2.75
642 1171 3.534554 CGGTCCATCAAATCACATCTCA 58.465 45.455 0.00 0.00 0.00 3.27
643 1172 4.132336 CGGTCCATCAAATCACATCTCAT 58.868 43.478 0.00 0.00 0.00 2.90
644 1173 4.212847 CGGTCCATCAAATCACATCTCATC 59.787 45.833 0.00 0.00 0.00 2.92
645 1174 5.128205 GGTCCATCAAATCACATCTCATCA 58.872 41.667 0.00 0.00 0.00 3.07
646 1175 5.008415 GGTCCATCAAATCACATCTCATCAC 59.992 44.000 0.00 0.00 0.00 3.06
647 1176 5.587443 GTCCATCAAATCACATCTCATCACA 59.413 40.000 0.00 0.00 0.00 3.58
648 1177 6.262496 GTCCATCAAATCACATCTCATCACAT 59.738 38.462 0.00 0.00 0.00 3.21
661 1190 0.104855 ATCACATCACACGGATCCGG 59.895 55.000 35.87 26.10 44.69 5.14
744 1278 1.609555 CCCATCACCTACTCTACGAGC 59.390 57.143 0.00 0.00 32.04 5.03
745 1279 2.298610 CCATCACCTACTCTACGAGCA 58.701 52.381 0.00 0.00 32.04 4.26
746 1280 2.292016 CCATCACCTACTCTACGAGCAG 59.708 54.545 0.00 0.00 32.04 4.24
752 1286 0.735471 TACTCTACGAGCAGCAGCAG 59.265 55.000 3.17 0.00 45.49 4.24
802 1336 0.179156 CGGTCTAAAACGGCTCGCTA 60.179 55.000 0.00 0.00 0.00 4.26
861 1395 3.402681 CCTCGCCTCACCACCCAT 61.403 66.667 0.00 0.00 0.00 4.00
862 1396 2.187946 CTCGCCTCACCACCCATC 59.812 66.667 0.00 0.00 0.00 3.51
863 1397 2.606213 TCGCCTCACCACCCATCA 60.606 61.111 0.00 0.00 0.00 3.07
864 1398 2.436646 CGCCTCACCACCCATCAC 60.437 66.667 0.00 0.00 0.00 3.06
866 1400 2.905996 GCCTCACCACCCATCACCA 61.906 63.158 0.00 0.00 0.00 4.17
867 1401 1.767036 CCTCACCACCCATCACCAA 59.233 57.895 0.00 0.00 0.00 3.67
869 1403 0.609131 CTCACCACCCATCACCAACC 60.609 60.000 0.00 0.00 0.00 3.77
1083 1631 2.059190 GTCGTCCCCCTCCTTCTCC 61.059 68.421 0.00 0.00 0.00 3.71
1085 1633 3.471806 GTCCCCCTCCTTCTCCGC 61.472 72.222 0.00 0.00 0.00 5.54
1086 1634 4.798682 TCCCCCTCCTTCTCCGCC 62.799 72.222 0.00 0.00 0.00 6.13
1087 1635 4.806339 CCCCCTCCTTCTCCGCCT 62.806 72.222 0.00 0.00 0.00 5.52
1259 1807 0.178990 ACCTTCACCAACCTCAAGGC 60.179 55.000 0.00 0.00 39.33 4.35
1274 1822 3.134127 GGCGCAGGGCAAGGTAAG 61.134 66.667 10.83 0.00 46.16 2.34
1275 1823 2.046314 GCGCAGGGCAAGGTAAGA 60.046 61.111 0.30 0.00 42.87 2.10
1276 1824 1.452108 GCGCAGGGCAAGGTAAGAT 60.452 57.895 0.30 0.00 42.87 2.40
1277 1825 0.179056 GCGCAGGGCAAGGTAAGATA 60.179 55.000 0.30 0.00 42.87 1.98
1278 1826 1.745827 GCGCAGGGCAAGGTAAGATAA 60.746 52.381 0.30 0.00 42.87 1.75
1318 1866 1.344438 ACTGCTCGTGTCTTGATTCCA 59.656 47.619 0.00 0.00 0.00 3.53
1325 1873 4.112634 TCGTGTCTTGATTCCATCGATTC 58.887 43.478 0.00 0.00 0.00 2.52
1377 1956 7.476540 ACTACTGTATGTATTGTCTTGGTGA 57.523 36.000 0.00 0.00 0.00 4.02
1391 1970 5.067153 TGTCTTGGTGACCATGTTTACTTTG 59.933 40.000 15.98 0.00 44.75 2.77
1409 1999 2.169832 TGCTCTGCAACTTGTAGTCC 57.830 50.000 6.75 1.12 34.76 3.85
1423 2013 2.631062 TGTAGTCCTCCATGTGTTCGTT 59.369 45.455 0.00 0.00 0.00 3.85
1424 2014 2.457366 AGTCCTCCATGTGTTCGTTC 57.543 50.000 0.00 0.00 0.00 3.95
1425 2015 1.971357 AGTCCTCCATGTGTTCGTTCT 59.029 47.619 0.00 0.00 0.00 3.01
1431 2021 3.325870 TCCATGTGTTCGTTCTTGCTAG 58.674 45.455 0.00 0.00 0.00 3.42
1432 2022 3.067106 CCATGTGTTCGTTCTTGCTAGT 58.933 45.455 0.00 0.00 0.00 2.57
1434 2024 4.688879 CCATGTGTTCGTTCTTGCTAGTAA 59.311 41.667 0.00 0.00 0.00 2.24
1436 2026 5.900339 TGTGTTCGTTCTTGCTAGTAAAG 57.100 39.130 0.00 0.00 0.00 1.85
1437 2027 4.748102 TGTGTTCGTTCTTGCTAGTAAAGG 59.252 41.667 7.27 0.00 0.00 3.11
1439 2029 5.638234 GTGTTCGTTCTTGCTAGTAAAGGAT 59.362 40.000 7.27 0.00 0.00 3.24
1440 2030 6.147328 GTGTTCGTTCTTGCTAGTAAAGGATT 59.853 38.462 7.27 0.00 0.00 3.01
1441 2031 7.330208 GTGTTCGTTCTTGCTAGTAAAGGATTA 59.670 37.037 7.27 0.00 0.00 1.75
1442 2032 7.874016 TGTTCGTTCTTGCTAGTAAAGGATTAA 59.126 33.333 7.27 0.00 0.00 1.40
1443 2033 8.880750 GTTCGTTCTTGCTAGTAAAGGATTAAT 58.119 33.333 7.27 0.00 0.00 1.40
1484 2077 3.894759 ACAAATCCCCTCAGATGTGATG 58.105 45.455 0.00 0.00 35.39 3.07
1486 2079 4.264083 ACAAATCCCCTCAGATGTGATGTT 60.264 41.667 0.00 0.00 35.39 2.71
1487 2080 4.598036 AATCCCCTCAGATGTGATGTTT 57.402 40.909 0.00 0.00 30.18 2.83
1488 2081 5.715439 AATCCCCTCAGATGTGATGTTTA 57.285 39.130 0.00 0.00 30.18 2.01
1489 2082 5.919348 ATCCCCTCAGATGTGATGTTTAT 57.081 39.130 0.00 0.00 30.18 1.40
1490 2083 7.392766 AATCCCCTCAGATGTGATGTTTATA 57.607 36.000 0.00 0.00 30.18 0.98
1491 2084 7.579940 ATCCCCTCAGATGTGATGTTTATAT 57.420 36.000 0.00 0.00 30.18 0.86
1492 2085 7.009179 TCCCCTCAGATGTGATGTTTATATC 57.991 40.000 0.00 0.00 30.18 1.63
1493 2086 6.558394 TCCCCTCAGATGTGATGTTTATATCA 59.442 38.462 0.00 0.00 34.83 2.15
1522 2115 0.176680 ACCTGCTCTGCGATTCGATT 59.823 50.000 10.88 0.00 0.00 3.34
1523 2116 1.293924 CCTGCTCTGCGATTCGATTT 58.706 50.000 10.88 0.00 0.00 2.17
1524 2117 1.004185 CCTGCTCTGCGATTCGATTTG 60.004 52.381 10.88 0.00 0.00 2.32
1525 2118 1.662629 CTGCTCTGCGATTCGATTTGT 59.337 47.619 10.88 0.00 0.00 2.83
1526 2119 2.076100 TGCTCTGCGATTCGATTTGTT 58.924 42.857 10.88 0.00 0.00 2.83
1527 2120 2.094258 TGCTCTGCGATTCGATTTGTTC 59.906 45.455 10.88 0.00 0.00 3.18
1528 2121 2.094258 GCTCTGCGATTCGATTTGTTCA 59.906 45.455 10.88 0.00 0.00 3.18
1529 2122 3.663908 CTCTGCGATTCGATTTGTTCAC 58.336 45.455 10.88 0.00 0.00 3.18
1530 2123 3.063485 TCTGCGATTCGATTTGTTCACA 58.937 40.909 10.88 0.00 0.00 3.58
1531 2124 3.123453 TCTGCGATTCGATTTGTTCACAG 59.877 43.478 10.88 4.39 0.00 3.66
1532 2125 3.063485 TGCGATTCGATTTGTTCACAGA 58.937 40.909 10.88 0.00 0.00 3.41
1533 2126 3.684305 TGCGATTCGATTTGTTCACAGAT 59.316 39.130 10.88 0.00 0.00 2.90
1534 2127 4.201714 TGCGATTCGATTTGTTCACAGATC 60.202 41.667 10.88 1.20 35.02 2.75
1535 2128 4.201714 GCGATTCGATTTGTTCACAGATCA 60.202 41.667 10.88 0.00 37.33 2.92
1536 2129 5.487581 CGATTCGATTTGTTCACAGATCAG 58.512 41.667 0.00 0.00 37.33 2.90
1537 2130 4.668576 TTCGATTTGTTCACAGATCAGC 57.331 40.909 10.23 0.00 37.33 4.26
1538 2131 2.667969 TCGATTTGTTCACAGATCAGCG 59.332 45.455 10.23 0.00 37.33 5.18
1539 2132 2.413112 CGATTTGTTCACAGATCAGCGT 59.587 45.455 10.23 0.00 37.33 5.07
1540 2133 3.482598 CGATTTGTTCACAGATCAGCGTC 60.483 47.826 10.23 0.00 37.33 5.19
1541 2134 2.820059 TTGTTCACAGATCAGCGTCT 57.180 45.000 0.00 0.00 0.00 4.18
1542 2135 3.934457 TTGTTCACAGATCAGCGTCTA 57.066 42.857 0.00 0.00 0.00 2.59
1543 2136 3.217599 TGTTCACAGATCAGCGTCTAC 57.782 47.619 0.00 0.00 0.00 2.59
1544 2137 2.556622 TGTTCACAGATCAGCGTCTACA 59.443 45.455 0.00 0.00 0.00 2.74
1545 2138 3.193479 TGTTCACAGATCAGCGTCTACAT 59.807 43.478 0.00 0.00 0.00 2.29
1546 2139 4.177026 GTTCACAGATCAGCGTCTACATT 58.823 43.478 0.00 0.00 0.00 2.71
1547 2140 4.033990 TCACAGATCAGCGTCTACATTC 57.966 45.455 0.00 0.00 0.00 2.67
1548 2141 3.443681 TCACAGATCAGCGTCTACATTCA 59.556 43.478 0.00 0.00 0.00 2.57
1549 2142 4.098501 TCACAGATCAGCGTCTACATTCAT 59.901 41.667 0.00 0.00 0.00 2.57
1550 2143 4.208666 CACAGATCAGCGTCTACATTCATG 59.791 45.833 0.00 0.00 0.00 3.07
1551 2144 3.183976 CAGATCAGCGTCTACATTCATGC 59.816 47.826 0.00 0.00 0.00 4.06
1552 2145 1.939974 TCAGCGTCTACATTCATGCC 58.060 50.000 0.00 0.00 0.00 4.40
1571 2164 3.268334 TGCCCTGTTTCCACCATAACTAT 59.732 43.478 0.00 0.00 0.00 2.12
1576 2169 6.872020 CCCTGTTTCCACCATAACTATATACG 59.128 42.308 0.00 0.00 0.00 3.06
1582 2175 5.541101 TCCACCATAACTATATACGGTTGCT 59.459 40.000 0.00 0.00 0.00 3.91
1583 2176 5.637810 CCACCATAACTATATACGGTTGCTG 59.362 44.000 0.00 1.97 0.00 4.41
1611 2204 1.333308 TGTGTTCTGATGGTGTTTGCG 59.667 47.619 0.00 0.00 0.00 4.85
1613 2206 2.226437 GTGTTCTGATGGTGTTTGCGAT 59.774 45.455 0.00 0.00 0.00 4.58
1706 2299 0.669318 TTCTCGATGCGTGTGGTTCC 60.669 55.000 0.00 0.00 0.00 3.62
1742 2335 1.065928 CGTGCCGTACTCTGATCCC 59.934 63.158 0.00 0.00 0.00 3.85
1800 2393 7.122501 ACAATGTTAAATATGCACATGTCCTGA 59.877 33.333 0.00 0.00 31.37 3.86
1803 2396 6.658816 TGTTAAATATGCACATGTCCTGAAGT 59.341 34.615 0.00 0.00 0.00 3.01
1805 2398 6.683974 AAATATGCACATGTCCTGAAGTAC 57.316 37.500 0.00 0.00 0.00 2.73
1940 2534 6.118170 CACCACATTTGAGGATGTTATCTCT 58.882 40.000 0.80 0.00 38.15 3.10
1952 2546 7.731054 AGGATGTTATCTCTATGGTGAAAGAC 58.269 38.462 0.00 0.00 0.00 3.01
2060 2654 3.132925 TGTAAAAGAAGCCGGTGTACAC 58.867 45.455 18.01 18.01 0.00 2.90
2074 2668 3.192466 GTGTACACGGTAATGCCCTTAG 58.808 50.000 10.84 0.00 0.00 2.18
2107 2701 4.810790 AGGTTCAGTGATGTTCTTCTACG 58.189 43.478 0.00 0.00 0.00 3.51
2193 2790 7.520614 GCACTGTTTCTGCTGTATCTTAGTTTT 60.521 37.037 0.00 0.00 0.00 2.43
2243 2847 6.808212 ACGATTGAGGATTAAAAAGTTGCATG 59.192 34.615 0.00 0.00 0.00 4.06
2260 2864 5.479124 TGCATGACAGCATAGACAGATAT 57.521 39.130 0.00 0.00 40.11 1.63
2337 2960 4.270084 TGCTGTTGTAAAGTTCTGTTCTCG 59.730 41.667 0.00 0.00 0.00 4.04
2378 3001 2.346766 TGTATTACCATGCTGCAGGG 57.653 50.000 29.75 29.75 41.50 4.45
2468 3091 1.944177 AGCTGGTAGGCTCTCTTTGA 58.056 50.000 0.00 0.00 38.24 2.69
2714 3364 7.125811 TCAGGTGCTAAGTAGTCTGGAATATTT 59.874 37.037 0.00 0.00 0.00 1.40
2752 3402 5.574830 TGTTTGTGCAGTTGTTTACATCAAC 59.425 36.000 0.00 0.00 43.51 3.18
2906 3560 7.926018 GTGTCCAGAACTCCAAATTATTTTTGT 59.074 33.333 0.00 0.00 0.00 2.83
2951 3606 3.983741 AGCACATTCTCCTTATCGCTAC 58.016 45.455 0.00 0.00 0.00 3.58
3121 4028 7.995289 TGTCATGCTTTTTCTCTTTAACAGAA 58.005 30.769 0.00 0.00 0.00 3.02
3155 4070 5.415389 ACATGCTTTTGTGCTGACATGTATA 59.585 36.000 0.00 0.00 44.49 1.47
3178 4095 1.672881 GGTGCTAGCTGTGCTAATTGG 59.327 52.381 17.23 0.00 40.82 3.16
3257 4176 5.801380 TGGTTATGTTCTGTAACTTCTCCC 58.199 41.667 0.00 0.00 36.51 4.30
3377 4333 6.226787 AGGCAGTTACATGATATGCTACTTC 58.773 40.000 0.00 0.00 37.08 3.01
3414 4370 6.884280 ATATTTGCTATTCAGGTAAGCACC 57.116 37.500 0.00 0.00 45.41 5.01
3510 4829 9.387123 GTTTGCTAAGTCTTCTCTTTATTGTTG 57.613 33.333 0.00 0.00 0.00 3.33
3517 4836 7.671302 AGTCTTCTCTTTATTGTTGCTCAGTA 58.329 34.615 0.00 0.00 0.00 2.74
3532 4851 5.061179 TGCTCAGTAAACTAGTTTTGGTCC 58.939 41.667 25.07 10.80 34.23 4.46
3554 4873 2.346803 CTACCTTATTGTGCAGTGCGT 58.653 47.619 11.20 1.86 0.00 5.24
3934 5261 7.903995 TTCCATGAAACAAGCATTTTTATCC 57.096 32.000 0.00 0.00 0.00 2.59
3940 5268 8.140677 TGAAACAAGCATTTTTATCCTTTGTG 57.859 30.769 0.00 0.00 0.00 3.33
4105 5439 9.744468 AAATTAATTGAGGTTAGTGTGACAAAC 57.256 29.630 0.39 0.00 0.00 2.93
4110 5444 3.399330 AGGTTAGTGTGACAAACGATGG 58.601 45.455 0.00 0.00 0.00 3.51
4111 5445 3.070446 AGGTTAGTGTGACAAACGATGGA 59.930 43.478 0.00 0.00 0.00 3.41
4119 5453 5.977129 GTGTGACAAACGATGGAAAAAGATT 59.023 36.000 0.00 0.00 0.00 2.40
4210 5549 8.664798 TCATTCCTCACTGTTTATCATTTTACG 58.335 33.333 0.00 0.00 0.00 3.18
4278 5617 5.066505 GCGTGATTAAATGGAGGAATGACTT 59.933 40.000 0.00 0.00 0.00 3.01
4302 5641 0.029834 CGCCAAGCTTGCATCATACC 59.970 55.000 21.43 0.63 0.00 2.73
4361 5733 6.650120 TGTTTTGCTATAAAAACCCCAACAA 58.350 32.000 9.30 0.00 45.39 2.83
4364 5736 8.931775 GTTTTGCTATAAAAACCCCAACAATAG 58.068 33.333 2.56 0.00 41.92 1.73
4410 5784 1.871080 AGGTTGAGCAAGAACTGTCG 58.129 50.000 0.00 0.00 0.00 4.35
4525 5903 8.643752 CCAATTTACTTGTTTGGTTAAATAGCG 58.356 33.333 0.00 0.00 36.08 4.26
4538 5916 6.183360 TGGTTAAATAGCGAGGAAGATTCGTA 60.183 38.462 0.00 0.00 40.08 3.43
4594 6000 4.633565 TCCTGCAAAAATCAAACAACCAAC 59.366 37.500 0.00 0.00 0.00 3.77
4595 6001 4.394300 CCTGCAAAAATCAAACAACCAACA 59.606 37.500 0.00 0.00 0.00 3.33
4598 6004 6.738114 TGCAAAAATCAAACAACCAACAAAA 58.262 28.000 0.00 0.00 0.00 2.44
4599 6005 7.202526 TGCAAAAATCAAACAACCAACAAAAA 58.797 26.923 0.00 0.00 0.00 1.94
4600 6006 7.869429 TGCAAAAATCAAACAACCAACAAAAAT 59.131 25.926 0.00 0.00 0.00 1.82
4616 6022 9.500785 CCAACAAAAATAATCAATTTACTGGGT 57.499 29.630 0.00 0.00 36.76 4.51
4641 6047 3.255642 TGCCAGACTGTTATTTTCTTGGC 59.744 43.478 0.93 5.28 35.67 4.52
4680 6086 5.423015 TCAGATGAAGACCACATAGCTTTC 58.577 41.667 0.00 0.00 0.00 2.62
4686 6092 6.577103 TGAAGACCACATAGCTTTCTAGATG 58.423 40.000 0.00 0.00 0.00 2.90
4885 6302 9.948964 TCTCTCAAGATTCAAATACTCATCAAA 57.051 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 7.591006 ACATCGGCCAAAATATAGTAATACG 57.409 36.000 2.24 0.00 0.00 3.06
67 70 9.612066 AAATTTTGATAACATCGGCCAAAATAT 57.388 25.926 2.24 0.00 42.83 1.28
70 73 7.442364 TCAAAATTTTGATAACATCGGCCAAAA 59.558 29.630 26.01 0.00 41.88 2.44
232 235 4.202398 ACACATTAGGGAGGTAGCATCATG 60.202 45.833 0.00 0.00 0.00 3.07
280 283 1.821216 AAATGGGTGAACCTACGCTG 58.179 50.000 0.00 0.00 41.11 5.18
288 291 3.451141 TGTGAAGCAAAATGGGTGAAC 57.549 42.857 0.00 0.00 0.00 3.18
368 371 5.898174 TGCTTCCAAGATTATCTGCAATTG 58.102 37.500 0.00 0.00 0.00 2.32
371 374 3.379372 GCTGCTTCCAAGATTATCTGCAA 59.621 43.478 0.00 0.00 0.00 4.08
374 377 4.197750 AGTGCTGCTTCCAAGATTATCTG 58.802 43.478 0.00 0.00 0.00 2.90
389 392 6.525121 TCGATGTAATGTAATTAGTGCTGC 57.475 37.500 0.00 0.00 39.94 5.25
390 393 7.531871 GCAATCGATGTAATGTAATTAGTGCTG 59.468 37.037 0.00 0.00 39.94 4.41
404 407 4.509970 CCCGAATAGTTGCAATCGATGTAA 59.490 41.667 19.00 0.00 37.48 2.41
405 408 4.055360 CCCGAATAGTTGCAATCGATGTA 58.945 43.478 19.00 0.00 37.48 2.29
406 409 2.872245 CCCGAATAGTTGCAATCGATGT 59.128 45.455 19.00 0.00 37.48 3.06
407 410 2.224079 CCCCGAATAGTTGCAATCGATG 59.776 50.000 19.00 10.77 37.48 3.84
411 414 2.639065 TGTCCCCGAATAGTTGCAATC 58.361 47.619 0.59 0.00 0.00 2.67
414 417 1.072489 TGTTGTCCCCGAATAGTTGCA 59.928 47.619 0.00 0.00 0.00 4.08
424 427 8.194104 TCATGAAATTAATTAATGTTGTCCCCG 58.806 33.333 11.42 0.00 0.00 5.73
425 428 9.883142 TTCATGAAATTAATTAATGTTGTCCCC 57.117 29.630 11.42 0.00 0.00 4.81
503 996 2.290641 AGACATGTTGCGTCTTTTGGTC 59.709 45.455 0.00 0.00 40.89 4.02
504 997 2.297701 AGACATGTTGCGTCTTTTGGT 58.702 42.857 0.00 0.00 40.89 3.67
520 1013 1.887242 GTGACACCGCTGCAAGACA 60.887 57.895 0.00 0.00 34.07 3.41
521 1014 1.160329 AAGTGACACCGCTGCAAGAC 61.160 55.000 0.84 0.00 34.07 3.01
526 1019 3.414700 CGGAAGTGACACCGCTGC 61.415 66.667 0.84 0.00 42.55 5.25
556 1053 1.201769 CGTTTAGACATTGTCGTGGCG 60.202 52.381 11.01 10.72 37.67 5.69
588 1117 7.601508 ACATTTTGTACTACTCCCTTCGTAAAG 59.398 37.037 0.00 0.00 0.00 1.85
600 1129 3.500680 CGGGCAACACATTTTGTACTACT 59.499 43.478 0.00 0.00 37.51 2.57
601 1130 3.365565 CCGGGCAACACATTTTGTACTAC 60.366 47.826 0.00 0.00 37.51 2.73
602 1131 2.814919 CCGGGCAACACATTTTGTACTA 59.185 45.455 0.00 0.00 37.51 1.82
621 1150 3.534554 TGAGATGTGATTTGATGGACCG 58.465 45.455 0.00 0.00 0.00 4.79
631 1160 4.569564 CGTGTGATGTGATGAGATGTGATT 59.430 41.667 0.00 0.00 0.00 2.57
639 1168 2.477825 GGATCCGTGTGATGTGATGAG 58.522 52.381 0.00 0.00 32.41 2.90
640 1169 1.202405 CGGATCCGTGTGATGTGATGA 60.202 52.381 26.35 0.00 32.41 2.92
641 1170 1.211743 CGGATCCGTGTGATGTGATG 58.788 55.000 26.35 0.00 32.41 3.07
642 1171 0.104855 CCGGATCCGTGTGATGTGAT 59.895 55.000 31.22 0.00 37.81 3.06
643 1172 1.515487 CCGGATCCGTGTGATGTGA 59.485 57.895 31.22 0.00 37.81 3.58
644 1173 1.521457 CCCGGATCCGTGTGATGTG 60.521 63.158 31.22 13.95 37.81 3.21
645 1174 1.676678 CTCCCGGATCCGTGTGATGT 61.677 60.000 31.22 0.00 37.81 3.06
646 1175 1.068083 CTCCCGGATCCGTGTGATG 59.932 63.158 31.22 15.39 37.81 3.07
647 1176 2.134287 CCTCCCGGATCCGTGTGAT 61.134 63.158 31.22 0.00 37.81 3.06
648 1177 2.758327 CCTCCCGGATCCGTGTGA 60.758 66.667 31.22 22.18 37.81 3.58
664 1193 4.516195 GAAGCCGTCGCCTCTCCC 62.516 72.222 0.00 0.00 34.57 4.30
744 1278 0.722469 CGTTTTACGTGCTGCTGCTG 60.722 55.000 17.00 11.40 36.74 4.41
745 1279 1.569493 CGTTTTACGTGCTGCTGCT 59.431 52.632 17.00 0.00 36.74 4.24
746 1280 2.074920 GCGTTTTACGTGCTGCTGC 61.075 57.895 8.89 8.89 44.73 5.25
752 1286 2.253154 GGGTGGCGTTTTACGTGC 59.747 61.111 0.00 0.00 44.73 5.34
788 1322 1.353609 GGCGTTAGCGAGCCGTTTTA 61.354 55.000 2.07 0.00 44.22 1.52
861 1395 2.004120 AGTGTGGGTGGGTTGGTGA 61.004 57.895 0.00 0.00 0.00 4.02
862 1396 1.827789 CAGTGTGGGTGGGTTGGTG 60.828 63.158 0.00 0.00 0.00 4.17
863 1397 2.004120 TCAGTGTGGGTGGGTTGGT 61.004 57.895 0.00 0.00 0.00 3.67
864 1398 1.528309 GTCAGTGTGGGTGGGTTGG 60.528 63.158 0.00 0.00 0.00 3.77
866 1400 0.395173 GTTGTCAGTGTGGGTGGGTT 60.395 55.000 0.00 0.00 0.00 4.11
867 1401 1.226262 GTTGTCAGTGTGGGTGGGT 59.774 57.895 0.00 0.00 0.00 4.51
869 1403 2.631160 TAAGTTGTCAGTGTGGGTGG 57.369 50.000 0.00 0.00 0.00 4.61
985 1533 4.181010 CATGGGTGCGAGGGAGGG 62.181 72.222 0.00 0.00 0.00 4.30
1242 1790 1.856265 GCGCCTTGAGGTTGGTGAAG 61.856 60.000 0.00 0.00 36.02 3.02
1259 1807 2.325583 TTATCTTACCTTGCCCTGCG 57.674 50.000 0.00 0.00 0.00 5.18
1274 1822 3.249320 GTCGGGGCGGTAAGAATTTTATC 59.751 47.826 0.00 0.00 0.00 1.75
1275 1823 3.208594 GTCGGGGCGGTAAGAATTTTAT 58.791 45.455 0.00 0.00 0.00 1.40
1276 1824 2.631267 GTCGGGGCGGTAAGAATTTTA 58.369 47.619 0.00 0.00 0.00 1.52
1277 1825 1.456296 GTCGGGGCGGTAAGAATTTT 58.544 50.000 0.00 0.00 0.00 1.82
1278 1826 0.741927 CGTCGGGGCGGTAAGAATTT 60.742 55.000 0.00 0.00 0.00 1.82
1303 1851 3.801114 ATCGATGGAATCAAGACACGA 57.199 42.857 0.00 0.00 45.97 4.35
1309 1857 2.032549 GCACCGAATCGATGGAATCAAG 60.033 50.000 3.36 0.00 45.97 3.02
1318 1866 2.684001 TTTACTGGCACCGAATCGAT 57.316 45.000 3.36 0.00 0.00 3.59
1325 1873 7.730364 ATAGAATTATCTTTTACTGGCACCG 57.270 36.000 0.00 0.00 37.10 4.94
1373 1952 3.821033 AGAGCAAAGTAAACATGGTCACC 59.179 43.478 15.69 0.00 42.45 4.02
1377 1956 3.221771 TGCAGAGCAAAGTAAACATGGT 58.778 40.909 0.00 0.00 34.76 3.55
1391 1970 2.342179 GAGGACTACAAGTTGCAGAGC 58.658 52.381 10.16 1.79 0.00 4.09
1408 1998 1.197721 GCAAGAACGAACACATGGAGG 59.802 52.381 0.00 0.00 0.00 4.30
1409 1999 2.146342 AGCAAGAACGAACACATGGAG 58.854 47.619 0.00 0.00 0.00 3.86
1446 2036 8.529476 GGGGATTTGTTAGTACTCGATATACAT 58.471 37.037 0.00 0.00 0.00 2.29
1447 2037 7.727186 AGGGGATTTGTTAGTACTCGATATACA 59.273 37.037 0.00 0.00 0.00 2.29
1448 2038 8.120140 AGGGGATTTGTTAGTACTCGATATAC 57.880 38.462 0.00 0.00 0.00 1.47
1454 2044 4.401519 TCTGAGGGGATTTGTTAGTACTCG 59.598 45.833 0.00 0.00 0.00 4.18
1455 2045 5.934402 TCTGAGGGGATTTGTTAGTACTC 57.066 43.478 0.00 0.00 0.00 2.59
1464 2057 3.894759 ACATCACATCTGAGGGGATTTG 58.105 45.455 4.00 0.00 32.16 2.32
1465 2058 4.598036 AACATCACATCTGAGGGGATTT 57.402 40.909 4.00 0.00 32.16 2.17
1468 2061 6.558394 TGATATAAACATCACATCTGAGGGGA 59.442 38.462 0.00 0.00 32.16 4.81
1469 2062 6.772605 TGATATAAACATCACATCTGAGGGG 58.227 40.000 0.00 0.00 32.16 4.79
1488 2081 7.708322 CGCAGAGCAGGTAACATATAATGATAT 59.292 37.037 0.00 0.00 41.41 1.63
1489 2082 7.035612 CGCAGAGCAGGTAACATATAATGATA 58.964 38.462 0.00 0.00 41.41 2.15
1490 2083 5.871524 CGCAGAGCAGGTAACATATAATGAT 59.128 40.000 0.00 0.00 41.41 2.45
1491 2084 5.010617 TCGCAGAGCAGGTAACATATAATGA 59.989 40.000 0.00 0.00 41.41 2.57
1492 2085 5.230182 TCGCAGAGCAGGTAACATATAATG 58.770 41.667 0.00 0.00 41.41 1.90
1493 2086 5.468540 TCGCAGAGCAGGTAACATATAAT 57.531 39.130 0.00 0.00 41.41 1.28
1522 2115 2.820059 AGACGCTGATCTGTGAACAA 57.180 45.000 18.70 0.00 0.00 2.83
1523 2116 2.556622 TGTAGACGCTGATCTGTGAACA 59.443 45.455 18.70 15.15 0.00 3.18
1524 2117 3.217599 TGTAGACGCTGATCTGTGAAC 57.782 47.619 18.70 13.19 0.00 3.18
1525 2118 4.082245 TGAATGTAGACGCTGATCTGTGAA 60.082 41.667 18.70 2.58 0.00 3.18
1526 2119 3.443681 TGAATGTAGACGCTGATCTGTGA 59.556 43.478 18.70 0.00 0.00 3.58
1527 2120 3.774066 TGAATGTAGACGCTGATCTGTG 58.226 45.455 11.20 11.20 0.00 3.66
1528 2121 4.366586 CATGAATGTAGACGCTGATCTGT 58.633 43.478 1.27 0.00 0.00 3.41
1529 2122 3.183976 GCATGAATGTAGACGCTGATCTG 59.816 47.826 0.00 0.00 0.00 2.90
1530 2123 3.388308 GCATGAATGTAGACGCTGATCT 58.612 45.455 0.00 0.00 0.00 2.75
1531 2124 2.478134 GGCATGAATGTAGACGCTGATC 59.522 50.000 0.00 0.00 0.00 2.92
1532 2125 2.487934 GGCATGAATGTAGACGCTGAT 58.512 47.619 0.00 0.00 0.00 2.90
1533 2126 1.473257 GGGCATGAATGTAGACGCTGA 60.473 52.381 0.00 0.00 0.00 4.26
1534 2127 0.940126 GGGCATGAATGTAGACGCTG 59.060 55.000 0.00 0.00 0.00 5.18
1535 2128 0.833287 AGGGCATGAATGTAGACGCT 59.167 50.000 0.00 0.00 0.00 5.07
1536 2129 0.940126 CAGGGCATGAATGTAGACGC 59.060 55.000 0.00 0.00 0.00 5.19
1537 2130 2.315925 ACAGGGCATGAATGTAGACG 57.684 50.000 5.99 0.00 0.00 4.18
1538 2131 3.378427 GGAAACAGGGCATGAATGTAGAC 59.622 47.826 5.99 0.00 0.00 2.59
1539 2132 3.010027 TGGAAACAGGGCATGAATGTAGA 59.990 43.478 5.99 0.00 35.01 2.59
1540 2133 3.129287 GTGGAAACAGGGCATGAATGTAG 59.871 47.826 5.99 0.00 44.46 2.74
1541 2134 3.088532 GTGGAAACAGGGCATGAATGTA 58.911 45.455 5.99 0.00 44.46 2.29
1542 2135 1.895131 GTGGAAACAGGGCATGAATGT 59.105 47.619 5.99 0.00 44.46 2.71
1543 2136 1.205417 GGTGGAAACAGGGCATGAATG 59.795 52.381 5.99 0.00 44.46 2.67
1544 2137 1.203162 TGGTGGAAACAGGGCATGAAT 60.203 47.619 5.99 0.00 44.46 2.57
1545 2138 0.187117 TGGTGGAAACAGGGCATGAA 59.813 50.000 5.99 0.00 44.46 2.57
1546 2139 0.409092 ATGGTGGAAACAGGGCATGA 59.591 50.000 5.99 0.00 44.46 3.07
1547 2140 2.142356 TATGGTGGAAACAGGGCATG 57.858 50.000 0.00 0.00 44.46 4.06
1548 2141 2.042979 AGTTATGGTGGAAACAGGGCAT 59.957 45.455 0.00 0.00 44.46 4.40
1549 2142 1.427368 AGTTATGGTGGAAACAGGGCA 59.573 47.619 0.00 0.00 44.46 5.36
1550 2143 2.215942 AGTTATGGTGGAAACAGGGC 57.784 50.000 0.00 0.00 44.46 5.19
1551 2144 6.872020 CGTATATAGTTATGGTGGAAACAGGG 59.128 42.308 0.00 0.00 44.46 4.45
1552 2145 6.872020 CCGTATATAGTTATGGTGGAAACAGG 59.128 42.308 0.00 0.00 44.46 4.00
1571 2164 5.239744 ACACAAAAATGACAGCAACCGTATA 59.760 36.000 0.00 0.00 0.00 1.47
1576 2169 4.268405 CAGAACACAAAAATGACAGCAACC 59.732 41.667 0.00 0.00 0.00 3.77
1582 2175 5.126869 ACACCATCAGAACACAAAAATGACA 59.873 36.000 0.00 0.00 0.00 3.58
1583 2176 5.591099 ACACCATCAGAACACAAAAATGAC 58.409 37.500 0.00 0.00 0.00 3.06
1611 2204 3.303395 GGGATGAACGCGATCTGAAAATC 60.303 47.826 15.93 9.12 0.00 2.17
1613 2206 2.006888 GGGATGAACGCGATCTGAAAA 58.993 47.619 15.93 0.00 0.00 2.29
1788 2381 2.738846 CACAGTACTTCAGGACATGTGC 59.261 50.000 9.70 9.70 31.30 4.57
1800 2393 9.534565 CATACAGAATACAATAGCACAGTACTT 57.465 33.333 0.00 0.00 0.00 2.24
1805 2398 8.972349 CACTACATACAGAATACAATAGCACAG 58.028 37.037 0.00 0.00 0.00 3.66
1940 2534 1.609580 GGCACCACGTCTTTCACCATA 60.610 52.381 0.00 0.00 0.00 2.74
1952 2546 2.740055 GACAGCTCAGGCACCACG 60.740 66.667 0.00 0.00 41.70 4.94
2060 2654 3.626217 GGAAAACTCTAAGGGCATTACCG 59.374 47.826 0.00 0.00 40.62 4.02
2074 2668 5.940470 ACATCACTGAACCTATGGAAAACTC 59.060 40.000 0.00 0.00 0.00 3.01
2130 2724 8.877864 ATTCAGATAATTAACAAGGTGACCAA 57.122 30.769 3.63 0.00 0.00 3.67
2178 2772 8.649973 ATGCACTAGTAAAACTAAGATACAGC 57.350 34.615 0.00 0.00 29.00 4.40
2193 2790 6.893554 TCTACCTGAAACCTTATGCACTAGTA 59.106 38.462 0.00 0.00 0.00 1.82
2260 2864 5.444877 GCGTCGTGTAAAATATAACTGTGCA 60.445 40.000 0.00 0.00 0.00 4.57
2267 2879 5.862860 TCACTGTGCGTCGTGTAAAATATAA 59.137 36.000 2.12 0.00 33.07 0.98
2378 3001 2.084546 GGAACATCAGGTACCACAAGC 58.915 52.381 15.94 0.00 0.00 4.01
2524 3147 6.480651 CCCTAATGGGTTTAAACACAAAACAC 59.519 38.462 26.11 0.00 46.84 3.32
2525 3148 6.583562 CCCTAATGGGTTTAAACACAAAACA 58.416 36.000 26.11 11.05 46.84 2.83
2697 3347 8.718656 AGGCATCTTAAATATTCCAGACTACTT 58.281 33.333 0.00 0.00 0.00 2.24
2699 3349 8.371699 AGAGGCATCTTAAATATTCCAGACTAC 58.628 37.037 0.00 0.00 28.57 2.73
2714 3364 4.340666 TGCACAAACAAAAGAGGCATCTTA 59.659 37.500 14.93 0.00 45.25 2.10
2906 3560 8.204836 GCTATATGAGAACAGAGTTTAAGGGAA 58.795 37.037 0.00 0.00 0.00 3.97
2951 3606 5.188434 TGGCCATTATGAGAACTTTCTGAG 58.812 41.667 0.00 0.00 37.73 3.35
3121 4028 1.342174 CAAAAGCATGTCAACCCAGCT 59.658 47.619 0.00 0.00 37.08 4.24
3155 4070 0.976641 TTAGCACAGCTAGCACCAGT 59.023 50.000 18.83 6.90 42.34 4.00
3200 4117 7.919091 TCAGTCTTTGTAAACAGTAGTGTACAG 59.081 37.037 3.00 0.00 46.32 2.74
3257 4176 7.712264 TTGTTTATGAATCACAAAGCCAAAG 57.288 32.000 0.00 0.00 0.00 2.77
3336 4292 3.609853 TGCCTAACTGGTTATGCTCAAG 58.390 45.455 16.97 0.00 37.50 3.02
3348 4304 5.994054 AGCATATCATGTAACTGCCTAACTG 59.006 40.000 0.00 0.00 33.34 3.16
3349 4305 6.179906 AGCATATCATGTAACTGCCTAACT 57.820 37.500 0.00 0.00 33.34 2.24
3350 4306 7.155328 AGTAGCATATCATGTAACTGCCTAAC 58.845 38.462 0.00 0.00 33.34 2.34
3351 4307 7.303182 AGTAGCATATCATGTAACTGCCTAA 57.697 36.000 0.00 0.00 33.34 2.69
3352 4308 6.918067 AGTAGCATATCATGTAACTGCCTA 57.082 37.500 0.00 0.00 33.34 3.93
3353 4309 5.815233 AGTAGCATATCATGTAACTGCCT 57.185 39.130 0.00 0.00 33.34 4.75
3354 4310 5.409826 GGAAGTAGCATATCATGTAACTGCC 59.590 44.000 0.00 5.02 36.41 4.85
3355 4311 6.226787 AGGAAGTAGCATATCATGTAACTGC 58.773 40.000 0.00 0.00 31.05 4.40
3377 4333 9.884465 GAATAGCAAATATTACTGCAACTTAGG 57.116 33.333 13.26 0.00 41.17 2.69
3414 4370 0.949105 GTGTGCCAGTAACTCCGGTG 60.949 60.000 0.00 0.00 0.00 4.94
3498 4817 9.209175 ACTAGTTTACTGAGCAACAATAAAGAG 57.791 33.333 0.00 0.00 32.20 2.85
3510 4829 4.151867 CGGACCAAAACTAGTTTACTGAGC 59.848 45.833 20.83 11.01 31.63 4.26
3532 4851 1.062587 GCACTGCACAATAAGGTAGCG 59.937 52.381 0.00 0.00 0.00 4.26
3554 4873 9.031360 GTTCTATAAGCATCGTTGAACAAGATA 57.969 33.333 0.00 0.00 34.36 1.98
3757 5080 9.624697 TCTGCAATTTTTGTAGACAATATTGAC 57.375 29.630 22.16 15.61 45.48 3.18
3824 5147 2.048603 GCCCAACTGCCTCACCATC 61.049 63.158 0.00 0.00 0.00 3.51
4099 5433 4.981674 TGCAATCTTTTTCCATCGTTTGTC 59.018 37.500 0.00 0.00 0.00 3.18
4184 5523 8.664798 CGTAAAATGATAAACAGTGAGGAATGA 58.335 33.333 0.00 0.00 0.00 2.57
4210 5549 4.437930 GCACTGTCATATTGAAGCCACTTC 60.438 45.833 0.32 0.32 40.54 3.01
4260 5599 5.878116 CGTACCAAGTCATTCCTCCATTTAA 59.122 40.000 0.00 0.00 0.00 1.52
4288 5627 5.242393 GGAATGTAATGGTATGATGCAAGCT 59.758 40.000 0.00 0.00 0.00 3.74
4302 5641 8.846211 ACAGGAATATTAAACCGGAATGTAATG 58.154 33.333 9.46 0.00 0.00 1.90
4410 5784 3.194005 TCCAGGAAGTGACTTGAACAC 57.806 47.619 0.90 0.00 38.38 3.32
4525 5903 7.790823 ACTAACTAGACTACGAATCTTCCTC 57.209 40.000 0.00 0.00 0.00 3.71
4538 5916 7.104290 GCCCAAGTGATTTTACTAACTAGACT 58.896 38.462 0.00 0.00 0.00 3.24
4598 6004 8.546083 TGGCATTACCCAGTAAATTGATTATT 57.454 30.769 0.00 0.00 37.83 1.40
4599 6005 8.181904 CTGGCATTACCCAGTAAATTGATTAT 57.818 34.615 0.10 0.00 45.87 1.28
4600 6006 7.581213 CTGGCATTACCCAGTAAATTGATTA 57.419 36.000 0.10 0.00 45.87 1.75
4616 6022 6.350110 GCCAAGAAAATAACAGTCTGGCATTA 60.350 38.462 4.53 0.00 36.46 1.90
4641 6047 2.328473 TCTGAGTCGTTTGATGCGAAG 58.672 47.619 0.00 0.00 40.19 3.79
4830 6244 6.261158 AGAAGAAAAGGAGAAGAAAGAAACGG 59.739 38.462 0.00 0.00 0.00 4.44
4885 6302 1.710809 AGGTGTGGTCAGCCCTTTATT 59.289 47.619 0.00 0.00 42.30 1.40


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

AutoCloner maintained by Alex Coulton.