Multiple sequence alignment - TraesCS5B01G108300

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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 TraesCS5B01G108300 chr5B 100.000 4969 0 0 1 4969 147422379 147427347 0.000000e+00 9177
1 TraesCS5B01G108300 chr5B 87.129 101 12 1 1980 2079 219085328 219085228 4.070000e-21 113
2 TraesCS5B01G108300 chr5D 88.408 1941 120 38 2653 4548 135643832 135645712 0.000000e+00 2241
3 TraesCS5B01G108300 chr5D 94.737 741 27 6 723 1452 135641672 135642411 0.000000e+00 1142
4 TraesCS5B01G108300 chr5D 90.166 661 46 12 1602 2246 135642719 135643376 0.000000e+00 843
5 TraesCS5B01G108300 chr5D 87.770 417 29 11 2224 2619 135643411 135643826 7.530000e-128 468
6 TraesCS5B01G108300 chr5D 89.394 132 9 1 1479 1605 135642403 135642534 1.430000e-35 161
7 TraesCS5B01G108300 chr5D 88.785 107 10 2 1971 2076 310557475 310557370 4.040000e-26 130
8 TraesCS5B01G108300 chr5D 87.273 110 13 1 1971 2079 462417544 462417653 1.880000e-24 124
9 TraesCS5B01G108300 chr5A 90.516 1687 82 37 723 2368 169311529 169309880 0.000000e+00 2158
10 TraesCS5B01G108300 chr5A 89.558 1379 81 29 2365 3692 169309778 169308412 0.000000e+00 1690
11 TraesCS5B01G108300 chr5A 91.346 728 31 10 4244 4969 169307916 169307219 0.000000e+00 966
12 TraesCS5B01G108300 chr5A 94.824 483 18 6 3772 4252 169308415 169307938 0.000000e+00 747
13 TraesCS5B01G108300 chr2B 87.952 747 60 19 1 720 706122982 706122239 0.000000e+00 854
14 TraesCS5B01G108300 chr6D 90.373 644 56 3 81 719 385943923 385944565 0.000000e+00 841
15 TraesCS5B01G108300 chr6D 92.560 336 22 3 82 415 2415798 2415464 3.480000e-131 479
16 TraesCS5B01G108300 chr6D 87.037 108 12 2 1971 2077 82143453 82143559 2.430000e-23 121
17 TraesCS5B01G108300 chr3A 88.925 623 61 5 82 698 54274883 54274263 0.000000e+00 761
18 TraesCS5B01G108300 chr3A 86.275 102 10 4 1980 2079 43010518 43010419 1.890000e-19 108
19 TraesCS5B01G108300 chr4A 84.105 648 96 4 74 715 187560769 187560123 1.960000e-173 619
20 TraesCS5B01G108300 chr1A 87.963 108 11 2 1973 2079 132412262 132412156 5.220000e-25 126
21 TraesCS5B01G108300 chrUn 86.916 107 11 3 1971 2076 108693379 108693275 3.140000e-22 117


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 TraesCS5B01G108300 chr5B 147422379 147427347 4968 False 9177.00 9177 100.000 1 4969 1 chr5B.!!$F1 4968
1 TraesCS5B01G108300 chr5D 135641672 135645712 4040 False 971.00 2241 90.095 723 4548 5 chr5D.!!$F2 3825
2 TraesCS5B01G108300 chr5A 169307219 169311529 4310 True 1390.25 2158 91.561 723 4969 4 chr5A.!!$R1 4246
3 TraesCS5B01G108300 chr2B 706122239 706122982 743 True 854.00 854 87.952 1 720 1 chr2B.!!$R1 719
4 TraesCS5B01G108300 chr6D 385943923 385944565 642 False 841.00 841 90.373 81 719 1 chr6D.!!$F2 638
5 TraesCS5B01G108300 chr3A 54274263 54274883 620 True 761.00 761 88.925 82 698 1 chr3A.!!$R2 616
6 TraesCS5B01G108300 chr4A 187560123 187560769 646 True 619.00 619 84.105 74 715 1 chr4A.!!$R1 641

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
820 851 0.454196 AAGGTTTTCAAACGCACGCT 59.546 45.0 0.00 0.0 39.77 5.07 F
1447 1498 0.166814 GTGCCTGCAACTTCGATGTC 59.833 55.0 4.21 0.0 0.00 3.06 F
2047 2320 0.104855 GCATGATGAGTAGCACCGGA 59.895 55.0 9.46 0.0 0.00 5.14 F
2492 2948 0.742281 CAGAATGAGGACCCTGTGCG 60.742 60.0 0.00 0.0 39.69 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 2178 1.064060 GACCACAGTCCGCATTTATGC 59.936 52.381 4.63 4.63 40.91 3.14 R
3172 3671 0.109342 AGAACACTGGCAACTGAGGG 59.891 55.000 0.00 0.00 39.15 4.30 R
3699 4209 0.529378 GAGGGCCAATGAGCAACAAG 59.471 55.000 6.18 0.00 0.00 3.16 R
4463 5013 0.376152 ATCTGAATTTGCAGCTCGCG 59.624 50.000 0.00 0.00 46.97 5.87 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
31 32 5.016831 TCACAATGGCTACTCTTGTAGAGA 58.983 41.667 10.50 0.00 45.07 3.10
44 45 7.773864 CTCTTGTAGAGAGTCACGATACTAA 57.226 40.000 0.00 0.00 45.07 2.24
78 103 0.602638 TGTGGCTGAGTTAAGTGGCG 60.603 55.000 0.00 0.00 0.00 5.69
117 143 2.851071 GCGAGATAGTCCGGCAGCT 61.851 63.158 0.00 0.00 0.00 4.24
126 152 3.376078 CCGGCAGCTGCACCAAAT 61.376 61.111 37.63 0.00 44.36 2.32
242 269 6.342111 CAAGGAGAGGAGTGGTTAAGATTAC 58.658 44.000 0.00 0.00 0.00 1.89
276 303 6.060028 TCATTTAGCGCAGAAAATATGTCC 57.940 37.500 11.47 0.00 0.00 4.02
300 327 2.351244 TAGAGGAGCAGTGGCACGG 61.351 63.158 13.67 13.67 44.61 4.94
312 339 1.077787 GGCACGGGATGAACATGGA 60.078 57.895 0.00 0.00 0.00 3.41
326 353 6.299805 TGAACATGGAGAGTTTATAGCTGT 57.700 37.500 0.00 0.00 0.00 4.40
368 395 2.347490 GGTGTGAGTGGATGCGGT 59.653 61.111 0.00 0.00 0.00 5.68
369 396 2.034879 GGTGTGAGTGGATGCGGTG 61.035 63.158 0.00 0.00 0.00 4.94
476 503 4.409342 CGATGCTCTCGGTTCTGG 57.591 61.111 1.87 0.00 43.82 3.86
484 511 3.070446 TGCTCTCGGTTCTGGAACTTTTA 59.930 43.478 12.34 0.00 40.94 1.52
525 552 8.643324 GCTATCCTTCTGGAAAGTAAAGAGATA 58.357 37.037 0.00 0.00 46.80 1.98
532 559 5.978814 TGGAAAGTAAAGAGATAGGTCTGC 58.021 41.667 0.00 0.00 33.97 4.26
556 583 7.182761 GCACTATGCAAAGTATGAAGTAAGTG 58.817 38.462 0.00 0.00 44.26 3.16
557 584 7.182761 CACTATGCAAAGTATGAAGTAAGTGC 58.817 38.462 0.00 0.00 0.00 4.40
558 585 5.567138 ATGCAAAGTATGAAGTAAGTGCC 57.433 39.130 0.00 0.00 0.00 5.01
559 586 3.756434 TGCAAAGTATGAAGTAAGTGCCC 59.244 43.478 0.00 0.00 0.00 5.36
560 587 4.010349 GCAAAGTATGAAGTAAGTGCCCT 58.990 43.478 0.00 0.00 0.00 5.19
562 589 3.802948 AGTATGAAGTAAGTGCCCTCG 57.197 47.619 0.00 0.00 0.00 4.63
574 605 1.298667 GCCCTCGGGAAGCAAACTA 59.701 57.895 6.08 0.00 37.50 2.24
575 606 1.025113 GCCCTCGGGAAGCAAACTAC 61.025 60.000 6.08 0.00 37.50 2.73
609 640 5.693555 TGTATAGCAAAATCATCTCTCGCTG 59.306 40.000 0.00 0.00 0.00 5.18
636 667 7.502060 AGATCTTCTGAGGTTTGGAAAGATA 57.498 36.000 0.00 0.00 0.00 1.98
640 671 7.612677 TCTTCTGAGGTTTGGAAAGATACTAC 58.387 38.462 0.00 0.00 0.00 2.73
654 685 6.416631 AAGATACTACCCCGGACTTTATTC 57.583 41.667 0.73 0.00 0.00 1.75
664 695 5.511545 CCCCGGACTTTATTCCTCATCTTAG 60.512 48.000 0.73 0.00 32.88 2.18
679 710 7.036220 CCTCATCTTAGTGTAAACAATCTCGT 58.964 38.462 0.00 0.00 0.00 4.18
767 798 1.660355 CTCTCCGCTGGCGCTATTA 59.340 57.895 7.64 0.00 38.24 0.98
820 851 0.454196 AAGGTTTTCAAACGCACGCT 59.546 45.000 0.00 0.00 39.77 5.07
821 852 0.454196 AGGTTTTCAAACGCACGCTT 59.546 45.000 0.00 0.00 39.77 4.68
1044 1075 2.574399 GAGCTCCTCGCGTTTCCT 59.426 61.111 5.77 0.00 45.59 3.36
1413 1458 9.984590 ATTTTAGGGTGTGTAAATGGTACTATT 57.015 29.630 0.00 0.00 0.00 1.73
1447 1498 0.166814 GTGCCTGCAACTTCGATGTC 59.833 55.000 4.21 0.00 0.00 3.06
1450 1501 1.470098 GCCTGCAACTTCGATGTCATT 59.530 47.619 4.21 0.00 0.00 2.57
1451 1502 2.095059 GCCTGCAACTTCGATGTCATTT 60.095 45.455 4.21 0.00 0.00 2.32
1452 1503 3.495193 CCTGCAACTTCGATGTCATTTG 58.505 45.455 4.21 0.81 0.00 2.32
1453 1504 3.058016 CCTGCAACTTCGATGTCATTTGT 60.058 43.478 4.21 0.00 0.00 2.83
1454 1505 4.539870 CTGCAACTTCGATGTCATTTGTT 58.460 39.130 4.21 0.00 0.00 2.83
1455 1506 4.930963 TGCAACTTCGATGTCATTTGTTT 58.069 34.783 4.21 0.00 0.00 2.83
1456 1507 5.347342 TGCAACTTCGATGTCATTTGTTTT 58.653 33.333 4.21 0.00 0.00 2.43
1457 1508 5.809562 TGCAACTTCGATGTCATTTGTTTTT 59.190 32.000 4.21 0.00 0.00 1.94
1458 1509 6.019961 TGCAACTTCGATGTCATTTGTTTTTC 60.020 34.615 4.21 0.00 0.00 2.29
1459 1510 6.562086 GCAACTTCGATGTCATTTGTTTTTCC 60.562 38.462 4.21 0.00 0.00 3.13
1460 1511 6.391227 ACTTCGATGTCATTTGTTTTTCCT 57.609 33.333 0.00 0.00 0.00 3.36
1461 1512 7.504924 ACTTCGATGTCATTTGTTTTTCCTA 57.495 32.000 0.00 0.00 0.00 2.94
1462 1513 7.360361 ACTTCGATGTCATTTGTTTTTCCTAC 58.640 34.615 0.00 0.00 0.00 3.18
1463 1514 6.249035 TCGATGTCATTTGTTTTTCCTACC 57.751 37.500 0.00 0.00 0.00 3.18
1464 1515 5.182380 TCGATGTCATTTGTTTTTCCTACCC 59.818 40.000 0.00 0.00 0.00 3.69
1465 1516 4.839668 TGTCATTTGTTTTTCCTACCCG 57.160 40.909 0.00 0.00 0.00 5.28
1466 1517 4.208746 TGTCATTTGTTTTTCCTACCCGT 58.791 39.130 0.00 0.00 0.00 5.28
1467 1518 4.645588 TGTCATTTGTTTTTCCTACCCGTT 59.354 37.500 0.00 0.00 0.00 4.44
1468 1519 4.979815 GTCATTTGTTTTTCCTACCCGTTG 59.020 41.667 0.00 0.00 0.00 4.10
1469 1520 4.038162 TCATTTGTTTTTCCTACCCGTTGG 59.962 41.667 0.00 0.00 37.80 3.77
1470 1521 1.320507 TGTTTTTCCTACCCGTTGGC 58.679 50.000 0.00 0.00 33.59 4.52
1471 1522 0.239082 GTTTTTCCTACCCGTTGGCG 59.761 55.000 0.00 0.00 33.59 5.69
1472 1523 0.179023 TTTTTCCTACCCGTTGGCGT 60.179 50.000 0.00 0.00 36.15 5.68
1473 1524 0.885596 TTTTCCTACCCGTTGGCGTG 60.886 55.000 0.00 0.00 36.15 5.34
1474 1525 2.734948 TTTCCTACCCGTTGGCGTGG 62.735 60.000 0.00 0.00 36.15 4.94
1475 1526 3.697747 CCTACCCGTTGGCGTGGA 61.698 66.667 0.00 0.00 36.15 4.02
1476 1527 2.582436 CTACCCGTTGGCGTGGAT 59.418 61.111 0.00 0.00 36.15 3.41
1477 1528 1.078708 CTACCCGTTGGCGTGGATT 60.079 57.895 0.00 0.00 36.15 3.01
1478 1529 0.176219 CTACCCGTTGGCGTGGATTA 59.824 55.000 0.00 0.00 36.15 1.75
1479 1530 0.831966 TACCCGTTGGCGTGGATTAT 59.168 50.000 0.00 0.00 36.15 1.28
1480 1531 0.746563 ACCCGTTGGCGTGGATTATG 60.747 55.000 0.00 0.00 36.15 1.90
1481 1532 0.462937 CCCGTTGGCGTGGATTATGA 60.463 55.000 0.00 0.00 36.15 2.15
1482 1533 1.593196 CCGTTGGCGTGGATTATGAT 58.407 50.000 0.00 0.00 36.15 2.45
1483 1534 2.549134 CCCGTTGGCGTGGATTATGATA 60.549 50.000 0.00 0.00 36.15 2.15
1484 1535 3.135225 CCGTTGGCGTGGATTATGATAA 58.865 45.455 0.00 0.00 36.15 1.75
1518 1596 2.221169 TCATGGAGTGCTGTTTGTGTC 58.779 47.619 0.00 0.00 0.00 3.67
1521 1599 1.230324 GGAGTGCTGTTTGTGTCTCC 58.770 55.000 0.00 0.00 35.45 3.71
1537 1615 4.097892 GTGTCTCCAGTTTCATGGTTTGTT 59.902 41.667 0.00 0.00 41.43 2.83
1543 1621 5.539574 TCCAGTTTCATGGTTTGTTGATGAT 59.460 36.000 0.00 0.00 41.43 2.45
1547 1625 4.787260 TCATGGTTTGTTGATGATGGTG 57.213 40.909 0.00 0.00 0.00 4.17
1588 1671 3.955650 TTTGTAGCCTCAGTACTGGTC 57.044 47.619 22.48 11.59 0.00 4.02
1600 1871 4.597507 TCAGTACTGGTCCTTTTTCCTGAT 59.402 41.667 22.48 0.00 0.00 2.90
1615 1886 9.941664 CTTTTTCCTGATATGTTGTATAGCAAG 57.058 33.333 0.00 0.00 37.83 4.01
1618 1889 9.851686 TTTCCTGATATGTTGTATAGCAAGAAT 57.148 29.630 0.00 0.00 37.83 2.40
1627 1898 5.294734 TGTATAGCAAGAATCAGGATGCA 57.705 39.130 0.00 0.00 41.18 3.96
1637 1908 4.820716 AGAATCAGGATGCAGAACTAATGC 59.179 41.667 0.00 0.00 44.11 3.56
1711 1982 2.698797 ACTATTGAGTATGGACCACCCG 59.301 50.000 0.00 0.00 33.39 5.28
1725 1996 1.072332 ACCCGTGCTGTATGTTGCA 59.928 52.632 0.00 0.00 36.79 4.08
1732 2003 0.179103 GCTGTATGTTGCAATGGGCC 60.179 55.000 0.59 0.00 43.89 5.80
1743 2014 1.405933 GCAATGGGCCCAGATTTCAAC 60.406 52.381 31.97 9.49 36.11 3.18
1755 2026 0.469705 ATTTCAACCCTGTGCTGGCA 60.470 50.000 0.00 0.00 0.00 4.92
1768 2039 1.598517 CTGGCAGGAAATTTGGGGC 59.401 57.895 6.61 0.00 0.00 5.80
1785 2056 3.054802 TGGGGCATTTGTCTGTTTTGTTT 60.055 39.130 0.00 0.00 0.00 2.83
1833 2104 6.095860 CACTGAATTTGGGAATAAGCTCATCA 59.904 38.462 0.00 0.00 0.00 3.07
1868 2139 1.080772 GCCAGCGCCCTTGTTTAAC 60.081 57.895 2.29 0.00 0.00 2.01
1872 2143 1.336755 CAGCGCCCTTGTTTAACTGTT 59.663 47.619 2.29 0.00 0.00 3.16
1907 2178 6.183360 CCTTACAGTGATGCAAATCTTCTGAG 60.183 42.308 14.89 7.10 32.37 3.35
1961 2232 2.035449 TGACCGTGGAAGTTACTCAGTG 59.965 50.000 0.00 0.00 0.00 3.66
1975 2246 3.891049 ACTCAGTGCCCATCCTATTTTC 58.109 45.455 0.00 0.00 0.00 2.29
1990 2262 5.820947 TCCTATTTTCTTCGATAAAGGGCAC 59.179 40.000 0.00 0.00 35.54 5.01
1999 2271 8.795842 TCTTCGATAAAGGGCACTTTTATTAA 57.204 30.769 21.06 8.78 44.26 1.40
2038 2311 4.142609 ACGGATACAAAGCATGATGAGT 57.857 40.909 0.00 0.00 0.00 3.41
2045 2318 1.945387 AAGCATGATGAGTAGCACCG 58.055 50.000 0.00 0.00 0.00 4.94
2047 2320 0.104855 GCATGATGAGTAGCACCGGA 59.895 55.000 9.46 0.00 0.00 5.14
2048 2321 1.270518 GCATGATGAGTAGCACCGGAT 60.271 52.381 9.46 0.00 0.00 4.18
2051 2324 1.957177 TGATGAGTAGCACCGGATCTC 59.043 52.381 9.46 8.67 0.00 2.75
2053 2326 3.181443 TGATGAGTAGCACCGGATCTCTA 60.181 47.826 9.46 0.15 0.00 2.43
2082 2355 1.610522 AGATGCACACAGCCAAAACTC 59.389 47.619 0.00 0.00 44.83 3.01
2086 2359 1.135141 GCACACAGCCAAAACTCACAA 60.135 47.619 0.00 0.00 37.23 3.33
2087 2360 2.673610 GCACACAGCCAAAACTCACAAA 60.674 45.455 0.00 0.00 37.23 2.83
2089 2362 4.736168 GCACACAGCCAAAACTCACAAATA 60.736 41.667 0.00 0.00 37.23 1.40
2090 2363 5.531634 CACACAGCCAAAACTCACAAATAT 58.468 37.500 0.00 0.00 0.00 1.28
2095 2388 6.435277 ACAGCCAAAACTCACAAATATCAGAT 59.565 34.615 0.00 0.00 0.00 2.90
2234 2528 3.577805 ACCCTGGCTGTAATATGGAAC 57.422 47.619 0.00 0.00 0.00 3.62
2237 2531 3.393800 CCTGGCTGTAATATGGAACGAG 58.606 50.000 0.00 0.00 0.00 4.18
2256 2606 6.149129 ACGAGATGAAGTATGTGCTATTGA 57.851 37.500 0.00 0.00 0.00 2.57
2295 2645 5.570973 GCACTCTGATATGTATGCGAACTAG 59.429 44.000 0.00 0.00 0.00 2.57
2335 2685 8.193250 TCTTTCGTATTTACATAGAAACTGCC 57.807 34.615 0.00 0.00 0.00 4.85
2338 2688 7.908827 TCGTATTTACATAGAAACTGCCAAA 57.091 32.000 0.00 0.00 0.00 3.28
2382 2836 6.101734 ACATCTGGTACATGAGAAATACCCAT 59.898 38.462 0.00 0.00 38.07 4.00
2389 2843 4.168675 ACATGAGAAATACCCATGGTCCAT 59.831 41.667 11.73 0.00 41.28 3.41
2393 2847 5.222109 TGAGAAATACCCATGGTCCATATGG 60.222 44.000 16.25 16.25 43.77 2.74
2459 2915 2.095567 CACACACCTGCAGCAAGATTAC 60.096 50.000 8.66 0.00 0.00 1.89
2468 2924 6.150140 ACCTGCAGCAAGATTACTAAAGAAAG 59.850 38.462 8.66 0.00 0.00 2.62
2475 2931 6.094186 GCAAGATTACTAAAGAAAGGTCCCAG 59.906 42.308 0.00 0.00 0.00 4.45
2492 2948 0.742281 CAGAATGAGGACCCTGTGCG 60.742 60.000 0.00 0.00 39.69 5.34
2544 3018 2.028020 GCCTGACTACTAAGCACCTTGT 60.028 50.000 0.00 0.00 0.00 3.16
2568 3042 1.638529 AGGTAGCTCAGTTGCAGACT 58.361 50.000 0.00 0.00 39.89 3.24
2622 3097 7.177216 TGCCAAAATATCTGTGAACTTCTCATT 59.823 33.333 0.00 0.00 36.14 2.57
2625 3100 8.954350 CAAAATATCTGTGAACTTCTCATTCCT 58.046 33.333 0.00 0.00 36.14 3.36
2642 3117 8.949177 TCTCATTCCTTTATTTTTACCCGTAAC 58.051 33.333 0.00 0.00 0.00 2.50
2650 3125 7.814264 TTATTTTTACCCGTAACAAGGACAA 57.186 32.000 0.00 0.00 0.00 3.18
2786 3284 7.608761 TCCAGTACAACATTGTTTAACCTATCC 59.391 37.037 1.98 0.00 42.35 2.59
2816 3314 4.513318 AGAGAAGTAAAACAGAGTGCTTGC 59.487 41.667 0.00 0.00 0.00 4.01
2822 3320 3.705043 AAACAGAGTGCTTGCAGAAAG 57.295 42.857 0.00 0.00 39.07 2.62
2845 3344 2.159014 TCCACCACATTACTGTATCCGC 60.159 50.000 0.00 0.00 33.14 5.54
2867 3366 6.156932 GCATTTCTTGCCAATCTTGTAAAC 57.843 37.500 0.00 0.00 46.15 2.01
2873 3372 7.701539 TCTTGCCAATCTTGTAAACATATGT 57.298 32.000 1.41 1.41 0.00 2.29
2950 3449 5.512788 CACCTCATTAATGCAAGCTTTAACG 59.487 40.000 10.76 7.47 31.48 3.18
2981 3480 2.254152 ACCTCCCAATCTCAGTGCTA 57.746 50.000 0.00 0.00 0.00 3.49
3005 3504 9.671279 CTATATGAATCATTATAACTGCCCACA 57.329 33.333 0.00 0.00 0.00 4.17
3006 3505 6.639632 ATGAATCATTATAACTGCCCACAC 57.360 37.500 0.00 0.00 0.00 3.82
3007 3506 5.504853 TGAATCATTATAACTGCCCACACA 58.495 37.500 0.00 0.00 0.00 3.72
3039 3538 3.182887 TCAAACACAGGGCCCATATTT 57.817 42.857 27.56 15.67 0.00 1.40
3076 3575 2.167075 ACAAGCCAAAGATGCTATTGCC 59.833 45.455 0.00 0.00 38.34 4.52
3122 3621 9.740710 ATCCATTGCTAGTAACTTTAAGTTCTT 57.259 29.630 14.03 6.45 39.51 2.52
3159 3658 6.312399 TCTTGTATAATTTTATGGCCTGCG 57.688 37.500 3.32 0.00 0.00 5.18
3210 3709 9.257651 AGTGTTCTTGTAACTATTTGTGTACTC 57.742 33.333 0.00 0.00 0.00 2.59
3212 3711 9.772973 TGTTCTTGTAACTATTTGTGTACTCAT 57.227 29.630 0.00 0.00 0.00 2.90
3220 3719 7.891183 ACTATTTGTGTACTCATCTGTTGTC 57.109 36.000 0.00 0.00 0.00 3.18
3256 3756 5.163237 GGGGAAGACCTGCATGTAGTTATTA 60.163 44.000 10.09 0.00 40.03 0.98
3284 3784 3.971468 TTAGCTTGCCCCTGGATTATT 57.029 42.857 0.00 0.00 0.00 1.40
3486 3992 3.098377 TGTACTAATAGCACCGGAACCA 58.902 45.455 9.46 0.00 0.00 3.67
3711 4221 7.156673 AGTTAATGCATTTCTTGTTGCTCATT 58.843 30.769 18.75 0.00 39.60 2.57
3718 4228 0.529378 CTTGTTGCTCATTGGCCCTC 59.471 55.000 0.00 0.00 0.00 4.30
3760 4270 2.400399 CAGCATTTTTGGCACAGACAG 58.600 47.619 0.00 0.00 42.39 3.51
3774 4284 5.536554 CACAGACAGTGTTAATGGCTTAG 57.463 43.478 0.00 0.00 43.40 2.18
3802 4312 6.634805 TGCAAACAATACCTTCTGTTTTCAA 58.365 32.000 0.00 0.00 41.77 2.69
3803 4313 7.271511 TGCAAACAATACCTTCTGTTTTCAAT 58.728 30.769 0.00 0.00 41.77 2.57
3804 4314 8.417106 TGCAAACAATACCTTCTGTTTTCAATA 58.583 29.630 0.00 0.00 41.77 1.90
3805 4315 8.699749 GCAAACAATACCTTCTGTTTTCAATAC 58.300 33.333 0.00 0.00 41.77 1.89
3807 4317 9.965824 AAACAATACCTTCTGTTTTCAATACAG 57.034 29.630 1.72 1.72 41.77 2.74
3808 4318 8.691661 ACAATACCTTCTGTTTTCAATACAGT 57.308 30.769 7.74 0.00 42.77 3.55
3809 4319 9.787435 ACAATACCTTCTGTTTTCAATACAGTA 57.213 29.630 7.74 0.00 42.77 2.74
3811 4321 6.803154 ACCTTCTGTTTTCAATACAGTAGC 57.197 37.500 7.74 0.00 42.77 3.58
3813 4323 6.428159 ACCTTCTGTTTTCAATACAGTAGCAG 59.572 38.462 7.74 0.33 42.77 4.24
3817 4327 7.861630 TCTGTTTTCAATACAGTAGCAGTTTC 58.138 34.615 7.74 0.00 42.77 2.78
3818 4328 6.966021 TGTTTTCAATACAGTAGCAGTTTCC 58.034 36.000 0.00 0.00 0.00 3.13
3854 4364 2.365293 GTGTTTTTGCAACCAGGATCCT 59.635 45.455 9.02 9.02 0.00 3.24
4079 4589 6.370442 CGTAATTCTGGTTTGAGAATGGTACA 59.630 38.462 0.00 0.00 41.02 2.90
4232 4743 4.038402 GGTGGATCATCACATTTTCCCATC 59.962 45.833 4.76 0.00 39.27 3.51
4237 4748 4.529897 TCATCACATTTTCCCATCCTCTG 58.470 43.478 0.00 0.00 0.00 3.35
4381 4930 2.953466 AATGATTGCGCTGCTGAAAT 57.047 40.000 9.73 0.00 0.00 2.17
4398 4947 3.119531 TGAAATTGTCGGCTAGCATTTGG 60.120 43.478 18.24 0.00 0.00 3.28
4471 5023 1.016130 ACATTTCTCCACGCGAGCTG 61.016 55.000 15.93 0.00 38.62 4.24
4489 5046 2.165845 GCTGCAAATTCAGATCAAGCCT 59.834 45.455 0.00 0.00 36.19 4.58
4519 5076 3.055530 AGAATTCTGTGCTTCAGGTCGAT 60.056 43.478 7.30 0.00 43.76 3.59
4523 5080 2.125552 TGCTTCAGGTCGATGCGG 60.126 61.111 0.00 0.00 45.50 5.69
4563 5120 2.949447 AGTTGGTTGATGCCTTTGACT 58.051 42.857 0.00 0.00 0.00 3.41
4571 5128 0.877071 ATGCCTTTGACTGTTGCTCG 59.123 50.000 0.00 0.00 0.00 5.03
4582 5139 1.377202 GTTGCTCGCCCCATTCTGA 60.377 57.895 0.00 0.00 0.00 3.27
4584 5141 0.677731 TTGCTCGCCCCATTCTGAAG 60.678 55.000 0.00 0.00 0.00 3.02
4629 5186 2.202544 GAGTGCTCGCTCGACAGG 60.203 66.667 0.00 0.00 0.00 4.00
4676 5233 1.004560 TGCTCCTCAACAGCTTCCG 60.005 57.895 0.00 0.00 37.79 4.30
4684 5241 1.148310 CAACAGCTTCCGTGGTACTG 58.852 55.000 0.00 0.00 0.00 2.74
4688 5245 1.798813 CAGCTTCCGTGGTACTGAAAC 59.201 52.381 0.00 0.00 0.00 2.78
4763 5320 2.158943 GCCGCTCTACTTTTCCATAGGT 60.159 50.000 0.00 0.00 0.00 3.08
4765 5322 3.871594 CCGCTCTACTTTTCCATAGGTTG 59.128 47.826 0.00 0.00 0.00 3.77
4797 5354 9.226606 CTTGGACAACTCACCTATAATTAACAA 57.773 33.333 0.00 0.00 0.00 2.83
4820 5377 6.038997 ACTAACAAACCTCTCTACCATGTC 57.961 41.667 0.00 0.00 0.00 3.06
4821 5378 3.983044 ACAAACCTCTCTACCATGTCC 57.017 47.619 0.00 0.00 0.00 4.02
4822 5379 3.521727 ACAAACCTCTCTACCATGTCCT 58.478 45.455 0.00 0.00 0.00 3.85
4823 5380 3.261897 ACAAACCTCTCTACCATGTCCTG 59.738 47.826 0.00 0.00 0.00 3.86
4824 5381 2.930109 ACCTCTCTACCATGTCCTGT 57.070 50.000 0.00 0.00 0.00 4.00
4825 5382 3.191888 ACCTCTCTACCATGTCCTGTT 57.808 47.619 0.00 0.00 0.00 3.16
4826 5383 4.332683 ACCTCTCTACCATGTCCTGTTA 57.667 45.455 0.00 0.00 0.00 2.41
4827 5384 4.282496 ACCTCTCTACCATGTCCTGTTAG 58.718 47.826 0.00 0.00 0.00 2.34
4828 5385 3.068873 CCTCTCTACCATGTCCTGTTAGC 59.931 52.174 0.00 0.00 0.00 3.09
4829 5386 3.957497 CTCTCTACCATGTCCTGTTAGCT 59.043 47.826 0.00 0.00 0.00 3.32
4830 5387 3.701542 TCTCTACCATGTCCTGTTAGCTG 59.298 47.826 0.00 0.00 0.00 4.24
4831 5388 3.441101 TCTACCATGTCCTGTTAGCTGT 58.559 45.455 0.00 0.00 0.00 4.40
4832 5389 3.838317 TCTACCATGTCCTGTTAGCTGTT 59.162 43.478 0.00 0.00 0.00 3.16
4843 5400 4.814234 CCTGTTAGCTGTTACTCACAACAA 59.186 41.667 0.00 0.00 37.93 2.83
4847 5404 8.439993 TGTTAGCTGTTACTCACAACAAATTA 57.560 30.769 0.00 0.00 37.93 1.40
4850 5407 7.568199 AGCTGTTACTCACAACAAATTAACT 57.432 32.000 0.00 0.00 37.93 2.24
4851 5408 7.417612 AGCTGTTACTCACAACAAATTAACTG 58.582 34.615 0.00 0.00 37.93 3.16
4852 5409 7.067008 AGCTGTTACTCACAACAAATTAACTGT 59.933 33.333 0.00 0.00 37.93 3.55
4853 5410 7.165812 GCTGTTACTCACAACAAATTAACTGTG 59.834 37.037 7.17 7.17 37.93 3.66
4854 5411 8.270080 TGTTACTCACAACAAATTAACTGTGA 57.730 30.769 12.98 12.98 44.38 3.58
4855 5412 8.731605 TGTTACTCACAACAAATTAACTGTGAA 58.268 29.630 14.02 2.68 45.47 3.18
4856 5413 9.221775 GTTACTCACAACAAATTAACTGTGAAG 57.778 33.333 14.02 11.37 45.47 3.02
4857 5414 7.391148 ACTCACAACAAATTAACTGTGAAGT 57.609 32.000 14.02 11.78 45.47 3.01
4858 5415 7.826690 ACTCACAACAAATTAACTGTGAAGTT 58.173 30.769 14.02 0.00 45.47 2.66
4859 5416 7.754924 ACTCACAACAAATTAACTGTGAAGTTG 59.245 33.333 14.73 14.73 45.47 3.16
4860 5417 6.529829 TCACAACAAATTAACTGTGAAGTTGC 59.470 34.615 15.92 0.00 43.81 4.17
4861 5418 5.810074 ACAACAAATTAACTGTGAAGTTGCC 59.190 36.000 15.92 0.00 38.82 4.52
4862 5419 5.590530 ACAAATTAACTGTGAAGTTGCCA 57.409 34.783 15.92 0.00 35.77 4.92
4863 5420 5.348164 ACAAATTAACTGTGAAGTTGCCAC 58.652 37.500 15.92 0.00 35.77 5.01
4904 5461 4.336713 TCGTTGATCATCTCCAGACAGTAG 59.663 45.833 0.00 0.00 0.00 2.57
4930 5487 3.947834 GGGAAATCATCTGTCGTTGGAAT 59.052 43.478 0.00 0.00 0.00 3.01
4932 5489 4.396166 GGAAATCATCTGTCGTTGGAATGT 59.604 41.667 0.00 0.00 0.00 2.71
4933 5490 5.106157 GGAAATCATCTGTCGTTGGAATGTT 60.106 40.000 0.00 0.00 0.00 2.71
4934 5491 6.093495 GGAAATCATCTGTCGTTGGAATGTTA 59.907 38.462 0.00 0.00 0.00 2.41
4945 5502 9.878667 TGTCGTTGGAATGTTATTATTCTAGAA 57.121 29.630 7.82 7.82 37.26 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.826385 GCCACTTAACTCAGCCACAT 58.174 50.000 0.00 0.00 0.00 3.21
63 64 0.388134 TCGTCGCCACTTAACTCAGC 60.388 55.000 0.00 0.00 0.00 4.26
64 65 1.337821 GTCGTCGCCACTTAACTCAG 58.662 55.000 0.00 0.00 0.00 3.35
65 66 0.386352 CGTCGTCGCCACTTAACTCA 60.386 55.000 0.00 0.00 0.00 3.41
66 67 0.110056 TCGTCGTCGCCACTTAACTC 60.110 55.000 0.00 0.00 36.96 3.01
67 68 0.386478 GTCGTCGTCGCCACTTAACT 60.386 55.000 0.00 0.00 36.96 2.24
68 69 0.661187 TGTCGTCGTCGCCACTTAAC 60.661 55.000 0.00 0.00 36.96 2.01
70 71 0.030504 TTTGTCGTCGTCGCCACTTA 59.969 50.000 0.00 0.00 36.96 2.24
72 73 0.599204 AATTTGTCGTCGTCGCCACT 60.599 50.000 0.00 0.00 36.96 4.00
126 152 7.021790 CGCTAGAACTCGTATTGATATAGCAA 58.978 38.462 5.78 5.78 34.25 3.91
242 269 3.040795 GCGCTAAATGATGCATCAACAG 58.959 45.455 31.79 25.95 40.69 3.16
276 303 1.140589 CACTGCTCCTCTACCTGCG 59.859 63.158 0.00 0.00 0.00 5.18
284 311 4.767255 CCCGTGCCACTGCTCCTC 62.767 72.222 0.00 0.00 38.71 3.71
300 327 6.426328 CAGCTATAAACTCTCCATGTTCATCC 59.574 42.308 0.00 0.00 0.00 3.51
326 353 2.008045 GCGGTATGAAACGGGCTACAA 61.008 52.381 0.00 0.00 0.00 2.41
334 361 1.083489 ACCACATGCGGTATGAAACG 58.917 50.000 13.15 0.04 39.21 3.60
336 363 1.809547 CACACCACATGCGGTATGAAA 59.190 47.619 5.16 0.00 35.33 2.69
368 395 5.764686 CCATTCCGAATAACAATCATCTCCA 59.235 40.000 0.00 0.00 0.00 3.86
369 396 5.765182 ACCATTCCGAATAACAATCATCTCC 59.235 40.000 0.00 0.00 0.00 3.71
469 496 2.557056 GCCCAGTAAAAGTTCCAGAACC 59.443 50.000 6.91 0.00 42.06 3.62
470 497 3.219281 TGCCCAGTAAAAGTTCCAGAAC 58.781 45.455 2.19 2.19 41.45 3.01
476 503 4.438744 CCGATTCATGCCCAGTAAAAGTTC 60.439 45.833 0.00 0.00 0.00 3.01
484 511 0.767375 ATAGCCGATTCATGCCCAGT 59.233 50.000 0.00 0.00 0.00 4.00
532 559 7.182761 GCACTTACTTCATACTTTGCATAGTG 58.817 38.462 18.71 4.47 0.00 2.74
556 583 1.025113 GTAGTTTGCTTCCCGAGGGC 61.025 60.000 2.58 0.00 34.68 5.19
557 584 0.739813 CGTAGTTTGCTTCCCGAGGG 60.740 60.000 0.65 0.65 0.00 4.30
558 585 0.037605 ACGTAGTTTGCTTCCCGAGG 60.038 55.000 0.00 0.00 37.78 4.63
559 586 2.527100 CTACGTAGTTTGCTTCCCGAG 58.473 52.381 14.66 0.00 37.78 4.63
560 587 1.403249 GCTACGTAGTTTGCTTCCCGA 60.403 52.381 22.98 0.00 37.78 5.14
562 589 2.000447 CAGCTACGTAGTTTGCTTCCC 59.000 52.381 22.98 3.91 44.03 3.97
574 605 6.761242 TGATTTTGCTATACAATCAGCTACGT 59.239 34.615 0.00 0.00 38.31 3.57
575 606 7.177498 TGATTTTGCTATACAATCAGCTACG 57.823 36.000 0.00 0.00 38.31 3.51
609 640 5.422214 TTCCAAACCTCAGAAGATCTACC 57.578 43.478 0.00 0.00 0.00 3.18
636 667 3.036819 GAGGAATAAAGTCCGGGGTAGT 58.963 50.000 0.00 0.00 43.03 2.73
640 671 2.706190 AGATGAGGAATAAAGTCCGGGG 59.294 50.000 0.00 0.00 43.03 5.73
654 685 7.036220 ACGAGATTGTTTACACTAAGATGAGG 58.964 38.462 0.00 0.00 0.00 3.86
664 695 9.478019 CTCAAATAATGACGAGATTGTTTACAC 57.522 33.333 0.00 0.00 33.47 2.90
718 749 9.543783 TTACACAAAACCGCCTTTTTATATTTT 57.456 25.926 0.00 0.00 28.85 1.82
719 750 9.713713 ATTACACAAAACCGCCTTTTTATATTT 57.286 25.926 0.00 0.00 28.85 1.40
720 751 9.713713 AATTACACAAAACCGCCTTTTTATATT 57.286 25.926 0.00 0.00 28.85 1.28
721 752 9.713713 AAATTACACAAAACCGCCTTTTTATAT 57.286 25.926 0.00 0.00 28.85 0.86
729 760 2.364002 AGCAAATTACACAAAACCGCCT 59.636 40.909 0.00 0.00 0.00 5.52
767 798 3.434596 GGGAGGCAACGGTAGGATAAATT 60.435 47.826 0.00 0.00 46.39 1.82
820 851 1.589113 GGCTGGTATTGGCGCAAAA 59.411 52.632 10.83 2.88 0.00 2.44
821 852 2.695759 CGGCTGGTATTGGCGCAAA 61.696 57.895 10.83 3.91 45.58 3.68
859 890 3.822192 CGTCAGCCGTCGGATGGA 61.822 66.667 27.96 12.94 39.86 3.41
881 912 1.341383 GGACTAGTAGAACGGGTGGGA 60.341 57.143 3.59 0.00 0.00 4.37
1413 1458 3.792401 CAGGCACGAAACTATCATACCA 58.208 45.455 0.00 0.00 0.00 3.25
1427 1478 1.133253 CATCGAAGTTGCAGGCACG 59.867 57.895 0.00 0.00 0.00 5.34
1447 1498 4.303282 CCAACGGGTAGGAAAAACAAATG 58.697 43.478 0.00 0.00 0.00 2.32
1450 1501 1.682323 GCCAACGGGTAGGAAAAACAA 59.318 47.619 0.00 0.00 36.17 2.83
1451 1502 1.320507 GCCAACGGGTAGGAAAAACA 58.679 50.000 0.00 0.00 36.17 2.83
1452 1503 0.239082 CGCCAACGGGTAGGAAAAAC 59.761 55.000 0.00 0.00 36.17 2.43
1453 1504 0.179023 ACGCCAACGGGTAGGAAAAA 60.179 50.000 0.00 0.00 46.04 1.94
1454 1505 0.885596 CACGCCAACGGGTAGGAAAA 60.886 55.000 0.00 0.00 46.04 2.29
1455 1506 1.301874 CACGCCAACGGGTAGGAAA 60.302 57.895 0.00 0.00 46.04 3.13
1456 1507 2.344500 CACGCCAACGGGTAGGAA 59.656 61.111 0.00 0.00 46.04 3.36
1457 1508 3.697747 CCACGCCAACGGGTAGGA 61.698 66.667 0.00 0.00 42.77 2.94
1458 1509 2.530958 AATCCACGCCAACGGGTAGG 62.531 60.000 0.00 0.00 42.77 3.18
1459 1510 0.176219 TAATCCACGCCAACGGGTAG 59.824 55.000 0.00 0.00 42.77 3.18
1460 1511 0.831966 ATAATCCACGCCAACGGGTA 59.168 50.000 0.00 0.00 42.77 3.69
1461 1512 0.746563 CATAATCCACGCCAACGGGT 60.747 55.000 0.00 0.00 42.77 5.28
1462 1513 0.462937 TCATAATCCACGCCAACGGG 60.463 55.000 0.00 0.00 46.04 5.28
1463 1514 1.593196 ATCATAATCCACGCCAACGG 58.407 50.000 0.00 0.00 46.04 4.44
1465 1516 6.795114 CGTTAATTATCATAATCCACGCCAAC 59.205 38.462 7.89 0.00 0.00 3.77
1466 1517 6.072948 CCGTTAATTATCATAATCCACGCCAA 60.073 38.462 12.77 0.00 0.00 4.52
1467 1518 5.410132 CCGTTAATTATCATAATCCACGCCA 59.590 40.000 12.77 0.00 0.00 5.69
1468 1519 5.410439 ACCGTTAATTATCATAATCCACGCC 59.590 40.000 12.77 0.00 0.00 5.68
1469 1520 6.476243 ACCGTTAATTATCATAATCCACGC 57.524 37.500 12.77 0.00 0.00 5.34
1470 1521 9.146984 ACATACCGTTAATTATCATAATCCACG 57.853 33.333 11.79 11.79 0.00 4.94
1478 1529 9.567776 TCCATGAAACATACCGTTAATTATCAT 57.432 29.630 0.00 0.00 36.59 2.45
1479 1530 8.966069 TCCATGAAACATACCGTTAATTATCA 57.034 30.769 0.00 0.00 36.59 2.15
1480 1531 9.052759 ACTCCATGAAACATACCGTTAATTATC 57.947 33.333 0.00 0.00 36.59 1.75
1481 1532 8.836413 CACTCCATGAAACATACCGTTAATTAT 58.164 33.333 0.00 0.00 36.59 1.28
1482 1533 7.201661 GCACTCCATGAAACATACCGTTAATTA 60.202 37.037 0.00 0.00 36.59 1.40
1483 1534 6.404293 GCACTCCATGAAACATACCGTTAATT 60.404 38.462 0.00 0.00 36.59 1.40
1484 1535 5.065988 GCACTCCATGAAACATACCGTTAAT 59.934 40.000 0.00 0.00 36.59 1.40
1518 1596 4.916983 TCAACAAACCATGAAACTGGAG 57.083 40.909 0.00 0.00 39.73 3.86
1521 1599 5.636121 CCATCATCAACAAACCATGAAACTG 59.364 40.000 0.00 0.00 30.43 3.16
1537 1615 6.260714 CCGAGATATTGAAAACACCATCATCA 59.739 38.462 0.00 0.00 0.00 3.07
1543 1621 4.457603 CCAACCGAGATATTGAAAACACCA 59.542 41.667 0.00 0.00 0.00 4.17
1547 1625 7.312899 ACAAATCCAACCGAGATATTGAAAAC 58.687 34.615 0.00 0.00 0.00 2.43
1588 1671 8.450578 TGCTATACAACATATCAGGAAAAAGG 57.549 34.615 0.00 0.00 0.00 3.11
1600 1871 7.388776 GCATCCTGATTCTTGCTATACAACATA 59.611 37.037 0.00 0.00 33.68 2.29
1615 1886 4.820716 AGCATTAGTTCTGCATCCTGATTC 59.179 41.667 0.00 0.00 42.15 2.52
1618 1889 3.054875 ACAGCATTAGTTCTGCATCCTGA 60.055 43.478 0.00 0.00 42.15 3.86
1627 1898 5.939764 TGACCATAGACAGCATTAGTTCT 57.060 39.130 0.00 0.00 0.00 3.01
1637 1908 8.642432 TCCTATTATTCACTTGACCATAGACAG 58.358 37.037 0.00 0.00 0.00 3.51
1711 1982 1.736696 GCCCATTGCAACATACAGCAC 60.737 52.381 0.00 0.00 41.05 4.40
1725 1996 1.571955 GGTTGAAATCTGGGCCCATT 58.428 50.000 28.82 18.16 0.00 3.16
1732 2003 1.542915 CAGCACAGGGTTGAAATCTGG 59.457 52.381 0.00 0.00 33.19 3.86
1755 2026 3.008266 CAGACAAATGCCCCAAATTTCCT 59.992 43.478 0.00 0.00 0.00 3.36
1768 2039 8.550376 CCCTAAATCAAACAAAACAGACAAATG 58.450 33.333 0.00 0.00 0.00 2.32
1785 2056 3.949586 TGCATGGTCATCCCTAAATCA 57.050 42.857 0.00 0.00 0.00 2.57
1833 2104 1.280710 TGGCCAACGACATAACCAGAT 59.719 47.619 0.61 0.00 0.00 2.90
1887 2158 3.439129 TGCTCAGAAGATTTGCATCACTG 59.561 43.478 0.00 0.00 37.40 3.66
1889 2160 4.634184 ATGCTCAGAAGATTTGCATCAC 57.366 40.909 0.00 0.00 39.79 3.06
1907 2178 1.064060 GACCACAGTCCGCATTTATGC 59.936 52.381 4.63 4.63 40.91 3.14
1944 2215 1.429463 GGCACTGAGTAACTTCCACG 58.571 55.000 0.00 0.00 0.00 4.94
1961 2232 6.072452 CCTTTATCGAAGAAAATAGGATGGGC 60.072 42.308 0.00 0.00 43.58 5.36
1975 2246 8.674607 AGTTAATAAAAGTGCCCTTTATCGAAG 58.325 33.333 0.00 0.00 40.01 3.79
1999 2271 7.931407 TGTATCCGTTTGATGCTAATTATGAGT 59.069 33.333 0.00 0.00 37.04 3.41
2017 2290 4.142609 ACTCATCATGCTTTGTATCCGT 57.857 40.909 0.00 0.00 0.00 4.69
2038 2311 3.082548 GCTATGTAGAGATCCGGTGCTA 58.917 50.000 0.00 0.00 0.00 3.49
2045 2318 6.071672 TGTGCATCTTAGCTATGTAGAGATCC 60.072 42.308 6.53 0.00 34.99 3.36
2047 2320 6.266330 TGTGTGCATCTTAGCTATGTAGAGAT 59.734 38.462 6.53 3.16 34.99 2.75
2048 2321 5.594317 TGTGTGCATCTTAGCTATGTAGAGA 59.406 40.000 6.53 0.83 34.99 3.10
2051 2324 4.447054 GCTGTGTGCATCTTAGCTATGTAG 59.553 45.833 6.53 0.00 42.31 2.74
2053 2326 3.201290 GCTGTGTGCATCTTAGCTATGT 58.799 45.455 6.53 0.00 42.31 2.29
2234 2528 6.920210 TCTTCAATAGCACATACTTCATCTCG 59.080 38.462 0.00 0.00 0.00 4.04
2237 2531 6.989169 ACCTCTTCAATAGCACATACTTCATC 59.011 38.462 0.00 0.00 0.00 2.92
2256 2606 2.173569 AGAGTGCACCTTTGAACCTCTT 59.826 45.455 14.63 0.00 30.15 2.85
2295 2645 1.809547 GAAAGAGAAGTGCCAGCCTTC 59.190 52.381 10.90 10.90 38.87 3.46
2335 2685 5.611796 TGCTTGTGCACTAGTAATCTTTG 57.388 39.130 25.57 2.59 45.31 2.77
2382 2836 5.742562 AATTTTAGACCCCATATGGACCA 57.257 39.130 24.00 0.00 37.39 4.02
2389 2843 9.206690 TGCATATTTCAAATTTTAGACCCCATA 57.793 29.630 0.00 0.00 0.00 2.74
2393 2847 7.492344 CAGGTGCATATTTCAAATTTTAGACCC 59.508 37.037 0.00 0.00 0.00 4.46
2459 2915 5.045578 TCCTCATTCTGGGACCTTTCTTTAG 60.046 44.000 0.00 0.00 0.00 1.85
2475 2931 1.450312 CCGCACAGGGTCCTCATTC 60.450 63.158 0.00 0.00 35.97 2.67
2509 2983 2.963782 AGTCAGGCCTATAAGGTAACCG 59.036 50.000 3.98 0.00 37.80 4.44
2544 3018 2.422479 CTGCAACTGAGCTACCTACGTA 59.578 50.000 0.00 0.00 34.99 3.57
2568 3042 2.270257 GCCCAGTCACAAGCATGCA 61.270 57.895 21.98 0.00 0.00 3.96
2622 3097 7.174772 GTCCTTGTTACGGGTAAAAATAAAGGA 59.825 37.037 12.25 12.25 0.00 3.36
2625 3100 7.814264 TGTCCTTGTTACGGGTAAAAATAAA 57.186 32.000 0.00 0.00 0.00 1.40
2729 3206 7.285858 AGTCTGTATGATAAAGTAGTGTCCCTC 59.714 40.741 0.00 0.00 0.00 4.30
2761 3239 7.392113 TGGATAGGTTAAACAATGTTGTACTGG 59.608 37.037 0.00 0.00 41.31 4.00
2774 3252 9.668497 ACTTCTCTATTTGTGGATAGGTTAAAC 57.332 33.333 0.00 0.00 31.83 2.01
2786 3284 8.012241 GCACTCTGTTTTACTTCTCTATTTGTG 58.988 37.037 0.00 0.00 0.00 3.33
2816 3314 4.821805 ACAGTAATGTGGTGGAACTTTCTG 59.178 41.667 0.00 0.00 36.74 3.02
2822 3320 3.869246 CGGATACAGTAATGTGGTGGAAC 59.131 47.826 5.98 0.00 0.00 3.62
2845 3344 7.894376 ATGTTTACAAGATTGGCAAGAAATG 57.106 32.000 5.96 4.92 0.00 2.32
2867 3366 8.543862 AACTACATCTGTGCATATGACATATG 57.456 34.615 25.13 25.13 44.25 1.78
2873 3372 9.696917 CTATGTAAACTACATCTGTGCATATGA 57.303 33.333 6.97 1.93 45.83 2.15
2981 3480 7.944000 TGTGTGGGCAGTTATAATGATTCATAT 59.056 33.333 0.00 0.00 0.00 1.78
3005 3504 5.221028 CCTGTGTTTGAATATGTGTGTGTGT 60.221 40.000 0.00 0.00 0.00 3.72
3006 3505 5.214417 CCTGTGTTTGAATATGTGTGTGTG 58.786 41.667 0.00 0.00 0.00 3.82
3007 3506 4.278170 CCCTGTGTTTGAATATGTGTGTGT 59.722 41.667 0.00 0.00 0.00 3.72
3039 3538 2.355716 GCTTGTGGTCCAGGCAGTTATA 60.356 50.000 0.00 0.00 45.05 0.98
3076 3575 1.855978 TGTTCAGTAAGCACGTTCACG 59.144 47.619 0.00 0.00 46.33 4.35
3122 3621 8.995027 AATTATACAAGATTGAAGGCCACATA 57.005 30.769 5.01 0.00 0.00 2.29
3172 3671 0.109342 AGAACACTGGCAACTGAGGG 59.891 55.000 0.00 0.00 39.15 4.30
3256 3756 4.140947 TCCAGGGGCAAGCTAATGATAAAT 60.141 41.667 0.00 0.00 0.00 1.40
3272 3772 9.689501 TTAAGTAACTAACAAATAATCCAGGGG 57.310 33.333 0.00 0.00 0.00 4.79
3324 3827 0.584396 GATTGAACGCACAACGGTGA 59.416 50.000 7.88 0.00 46.28 4.02
3486 3992 9.995003 TTCCACAGCAGACAATATTTAATTTTT 57.005 25.926 0.00 0.00 0.00 1.94
3699 4209 0.529378 GAGGGCCAATGAGCAACAAG 59.471 55.000 6.18 0.00 0.00 3.16
3774 4284 3.005791 ACAGAAGGTATTGTTTGCAAGGC 59.994 43.478 0.00 0.00 38.10 4.35
3802 4312 6.769512 TCAGAAAAGGAAACTGCTACTGTAT 58.230 36.000 0.00 0.00 42.68 2.29
3803 4313 6.169557 TCAGAAAAGGAAACTGCTACTGTA 57.830 37.500 0.00 0.00 42.68 2.74
3804 4314 5.036117 TCAGAAAAGGAAACTGCTACTGT 57.964 39.130 0.00 0.00 42.68 3.55
3805 4315 6.429385 AGATTCAGAAAAGGAAACTGCTACTG 59.571 38.462 0.00 0.00 42.68 2.74
3807 4317 6.809630 AGATTCAGAAAAGGAAACTGCTAC 57.190 37.500 0.00 0.00 42.68 3.58
3808 4318 8.103305 ACATAGATTCAGAAAAGGAAACTGCTA 58.897 33.333 0.00 0.00 42.68 3.49
3809 4319 6.944862 ACATAGATTCAGAAAAGGAAACTGCT 59.055 34.615 0.00 0.00 42.68 4.24
3810 4320 7.025963 CACATAGATTCAGAAAAGGAAACTGC 58.974 38.462 0.00 0.00 42.68 4.40
3811 4321 8.103948 ACACATAGATTCAGAAAAGGAAACTG 57.896 34.615 0.00 0.00 42.68 3.16
3813 4323 9.750125 AAAACACATAGATTCAGAAAAGGAAAC 57.250 29.630 0.00 0.00 0.00 2.78
3817 4327 7.652909 TGCAAAAACACATAGATTCAGAAAAGG 59.347 33.333 0.00 0.00 0.00 3.11
3818 4328 8.578308 TGCAAAAACACATAGATTCAGAAAAG 57.422 30.769 0.00 0.00 0.00 2.27
3854 4364 6.975197 CGCAGACTATTATCTTCTTGTTCTCA 59.025 38.462 0.00 0.00 0.00 3.27
3997 4507 7.317390 TGATACAACTGTCTTCGCTAATACAA 58.683 34.615 0.00 0.00 0.00 2.41
4237 4748 8.478877 AGGCCAAACAGCATATATATAGACTAC 58.521 37.037 5.01 0.00 0.00 2.73
4381 4930 1.164411 CACCAAATGCTAGCCGACAA 58.836 50.000 13.29 0.00 0.00 3.18
4398 4947 7.493971 ACAGTTTCAGATACAATCATAGAGCAC 59.506 37.037 0.00 0.00 0.00 4.40
4441 4990 4.320870 GTGGAGAAATGTTCCTTCGGTAA 58.679 43.478 0.00 0.00 35.67 2.85
4442 4991 3.615592 CGTGGAGAAATGTTCCTTCGGTA 60.616 47.826 0.00 0.00 35.67 4.02
4456 5005 2.987282 TTTGCAGCTCGCGTGGAGAA 62.987 55.000 5.77 0.00 46.23 2.87
4458 5008 1.915614 AATTTGCAGCTCGCGTGGAG 61.916 55.000 5.77 0.00 46.97 3.86
4461 5011 0.791983 CTGAATTTGCAGCTCGCGTG 60.792 55.000 5.77 4.44 46.97 5.34
4462 5012 0.950555 TCTGAATTTGCAGCTCGCGT 60.951 50.000 5.77 0.00 46.97 6.01
4463 5013 0.376152 ATCTGAATTTGCAGCTCGCG 59.624 50.000 0.00 0.00 46.97 5.87
4471 5023 2.159142 CCCAGGCTTGATCTGAATTTGC 60.159 50.000 0.00 0.00 34.36 3.68
4489 5046 2.544721 AGCACAGAATTCTCTCTCCCA 58.455 47.619 4.57 0.00 0.00 4.37
4523 5080 2.789203 GAGAATGTGACGCGCGGTC 61.789 63.158 35.22 26.66 46.27 4.79
4529 5086 1.873591 ACCAACTTGAGAATGTGACGC 59.126 47.619 0.00 0.00 0.00 5.19
4563 5120 1.675310 CAGAATGGGGCGAGCAACA 60.675 57.895 0.00 0.00 0.00 3.33
4571 5128 1.064463 TCCACATCTTCAGAATGGGGC 60.064 52.381 0.51 0.00 38.70 5.80
4582 5139 0.040058 TTGCCAGCCATCCACATCTT 59.960 50.000 0.00 0.00 0.00 2.40
4584 5141 0.966875 TGTTGCCAGCCATCCACATC 60.967 55.000 0.00 0.00 0.00 3.06
4629 5186 2.099831 GCATGTGAAGCAGCTCGC 59.900 61.111 0.00 0.00 42.91 5.03
4684 5241 3.078837 TCCGTAAGCAGGATTTGGTTTC 58.921 45.455 0.00 0.00 44.75 2.78
4688 5245 1.949525 CCATCCGTAAGCAGGATTTGG 59.050 52.381 0.00 0.00 45.59 3.28
4763 5320 1.340502 TGAGTTGTCCAAGTGCACCAA 60.341 47.619 14.63 7.33 0.00 3.67
4765 5322 0.663153 GTGAGTTGTCCAAGTGCACC 59.337 55.000 14.63 0.00 0.00 5.01
4797 5354 5.046520 GGACATGGTAGAGAGGTTTGTTAGT 60.047 44.000 0.00 0.00 0.00 2.24
4820 5377 4.377021 TGTTGTGAGTAACAGCTAACAGG 58.623 43.478 0.00 0.00 40.45 4.00
4821 5378 5.984233 TTGTTGTGAGTAACAGCTAACAG 57.016 39.130 0.00 0.00 41.18 3.16
4822 5379 6.935741 ATTTGTTGTGAGTAACAGCTAACA 57.064 33.333 0.00 0.00 41.18 2.41
4823 5380 9.166126 GTTAATTTGTTGTGAGTAACAGCTAAC 57.834 33.333 0.00 0.00 41.18 2.34
4824 5381 9.116067 AGTTAATTTGTTGTGAGTAACAGCTAA 57.884 29.630 0.00 0.00 41.18 3.09
4825 5382 8.556194 CAGTTAATTTGTTGTGAGTAACAGCTA 58.444 33.333 0.00 0.00 41.18 3.32
4826 5383 7.067008 ACAGTTAATTTGTTGTGAGTAACAGCT 59.933 33.333 0.00 0.00 41.18 4.24
4827 5384 7.165812 CACAGTTAATTTGTTGTGAGTAACAGC 59.834 37.037 9.14 0.00 42.61 4.40
4828 5385 8.394877 TCACAGTTAATTTGTTGTGAGTAACAG 58.605 33.333 12.00 0.00 43.43 3.16
4829 5386 8.270080 TCACAGTTAATTTGTTGTGAGTAACA 57.730 30.769 12.00 0.00 43.43 2.41
4843 5400 4.644685 ACAGTGGCAACTTCACAGTTAATT 59.355 37.500 0.00 0.00 41.69 1.40
4847 5404 1.745087 CACAGTGGCAACTTCACAGTT 59.255 47.619 0.00 0.00 44.72 3.16
4850 5407 2.016318 CTTCACAGTGGCAACTTCACA 58.984 47.619 0.00 0.00 37.58 3.58
4851 5408 2.017049 ACTTCACAGTGGCAACTTCAC 58.983 47.619 0.00 0.00 32.98 3.18
4852 5409 2.418368 ACTTCACAGTGGCAACTTCA 57.582 45.000 0.00 0.00 32.98 3.02
4853 5410 3.070429 CAACTTCACAGTGGCAACTTC 57.930 47.619 0.00 0.00 32.98 3.01
4860 5417 0.947244 GAGTGGCAACTTCACAGTGG 59.053 55.000 0.00 0.00 36.52 4.00
4861 5418 1.667236 TGAGTGGCAACTTCACAGTG 58.333 50.000 0.00 0.00 36.52 3.66
4862 5419 2.498167 GATGAGTGGCAACTTCACAGT 58.502 47.619 0.00 0.00 36.52 3.55
4863 5420 1.462283 CGATGAGTGGCAACTTCACAG 59.538 52.381 0.00 0.00 36.52 3.66
4904 5461 3.160777 ACGACAGATGATTTCCCGTAC 57.839 47.619 0.00 0.00 0.00 3.67
4945 5502 4.953940 TTGAGCCCAAGCAAAGTAAATT 57.046 36.364 0.00 0.00 43.56 1.82


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

AutoCloner maintained by Alex Coulton.