Multiple sequence alignment - TraesCS3A01G113200

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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 TraesCS3A01G113200 chr3A 100.000 6556 0 0 1 6556 80420020 80413465 0.000000e+00 12107.0
1 TraesCS3A01G113200 chr3A 93.305 239 14 2 6319 6556 80288869 80289106 1.050000e-92 351.0
2 TraesCS3A01G113200 chr3A 95.000 60 3 0 6200 6259 80410129 80410188 1.950000e-15 95.3
3 TraesCS3A01G113200 chr3B 92.242 3042 148 26 717 3731 112458229 112461209 0.000000e+00 4229.0
4 TraesCS3A01G113200 chr3B 91.790 1486 69 15 3717 5172 112461232 112462694 0.000000e+00 2019.0
5 TraesCS3A01G113200 chr3B 87.518 713 50 12 5167 5855 112463835 112464532 0.000000e+00 787.0
6 TraesCS3A01G113200 chr3B 81.877 618 51 23 5947 6556 112464713 112465277 1.290000e-126 464.0
7 TraesCS3A01G113200 chr3B 92.469 239 16 2 6319 6556 113504317 113504080 2.260000e-89 340.0
8 TraesCS3A01G113200 chr3B 84.140 372 27 19 6200 6556 112835323 112835677 1.360000e-86 331.0
9 TraesCS3A01G113200 chr3B 91.129 248 11 3 6319 6556 112947782 112948028 6.340000e-85 326.0
10 TraesCS3A01G113200 chr3B 83.333 372 30 19 6200 6556 113298549 113298903 1.370000e-81 315.0
11 TraesCS3A01G113200 chr3B 80.631 222 20 11 6203 6422 113487499 113487299 4.100000e-32 150.0
12 TraesCS3A01G113200 chr3B 96.774 62 2 0 6200 6261 112947695 112947756 3.230000e-18 104.0
13 TraesCS3A01G113200 chr3B 92.537 67 5 0 6195 6261 112496507 112496573 5.410000e-16 97.1
14 TraesCS3A01G113200 chr3D 91.476 3062 159 33 715 3735 68849146 68846146 0.000000e+00 4115.0
15 TraesCS3A01G113200 chr3D 87.078 2933 204 83 3717 6556 68846126 68843276 0.000000e+00 3155.0
16 TraesCS3A01G113200 chr3D 88.268 358 30 10 6200 6556 68389864 68389518 1.020000e-112 418.0
17 TraesCS3A01G113200 chr3D 87.709 358 28 12 6200 6556 68431255 68430913 2.850000e-108 403.0
18 TraesCS3A01G113200 chr3D 93.427 213 9 1 6349 6556 68833828 68833616 1.780000e-80 311.0
19 TraesCS3A01G113200 chr3D 92.925 212 9 3 6350 6556 68335234 68335444 2.970000e-78 303.0
20 TraesCS3A01G113200 chr3D 98.361 61 1 0 6200 6260 68335172 68335232 2.500000e-19 108.0
21 TraesCS3A01G113200 chr7D 84.976 619 71 12 49 661 61736880 61736278 5.620000e-170 608.0
22 TraesCS3A01G113200 chr6B 83.857 669 66 26 15 661 138706573 138707221 3.380000e-167 599.0
23 TraesCS3A01G113200 chr6B 82.234 394 40 18 287 661 441273117 441273499 4.940000e-81 313.0
24 TraesCS3A01G113200 chr6B 81.750 400 41 18 287 664 442249653 442249264 8.260000e-79 305.0
25 TraesCS3A01G113200 chr6B 89.326 178 15 3 484 661 27386325 27386498 3.080000e-53 220.0
26 TraesCS3A01G113200 chr1A 85.347 505 55 15 1 499 557866915 557866424 7.590000e-139 505.0
27 TraesCS3A01G113200 chr2A 88.854 323 24 8 1123 1442 274628 274941 2.870000e-103 387.0
28 TraesCS3A01G113200 chr1B 82.489 474 49 21 208 661 409158 409617 1.030000e-102 385.0
29 TraesCS3A01G113200 chr1B 81.607 473 52 20 211 663 126388820 126388363 6.250000e-95 359.0
30 TraesCS3A01G113200 chr7B 82.241 473 51 18 211 664 424968524 424968066 1.730000e-100 377.0
31 TraesCS3A01G113200 chr7B 91.453 234 18 2 6324 6556 603657835 603657603 2.950000e-83 320.0
32 TraesCS3A01G113200 chr5B 86.149 296 28 10 208 499 444820090 444820376 2.300000e-79 307.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G113200 chr3A 80413465 80420020 6555 True 12107.00 12107 100.00000 1 6556 1 chr3A.!!$R1 6555
1 TraesCS3A01G113200 chr3B 112458229 112465277 7048 False 1874.75 4229 88.35675 717 6556 4 chr3B.!!$F4 5839
2 TraesCS3A01G113200 chr3D 68843276 68849146 5870 True 3635.00 4115 89.27700 715 6556 2 chr3D.!!$R4 5841
3 TraesCS3A01G113200 chr7D 61736278 61736880 602 True 608.00 608 84.97600 49 661 1 chr7D.!!$R1 612
4 TraesCS3A01G113200 chr6B 138706573 138707221 648 False 599.00 599 83.85700 15 661 1 chr6B.!!$F2 646

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
647 676 0.527565 GGTGACTCGGCATTTGCATT 59.472 50.0 4.74 0.0 44.36 3.56 F
1766 1805 0.106519 ATATTGCCCTCAGGTGTGGC 60.107 55.0 0.00 6.4 45.56 5.01 F
2141 2185 0.888736 TGATGGCCACAGTTTCACCG 60.889 55.0 8.16 0.0 0.00 4.94 F
3685 3755 0.178767 TCCCATTCCAGCGACAGATG 59.821 55.0 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 1975 0.183492 TGCAATCCCAGGGAGTATGC 59.817 55.000 26.42 26.42 38.97 3.14 R
3197 3243 0.606604 TACGCAGGGAGGTTGAAGAC 59.393 55.000 0.00 0.00 0.00 3.01 R
3863 3971 2.167075 AGCAAGCTCTTTGTTTGTTGCT 59.833 40.909 1.61 1.61 44.37 3.91 R
5612 6906 0.038251 TGTGTCTCCGACATGTCAGC 60.038 55.000 24.93 12.04 44.63 4.26 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
76 77 9.912634 AATACAGTCCAAATTACTGAAATTGTG 57.087 29.630 12.70 0.00 45.89 3.33
77 78 6.748132 ACAGTCCAAATTACTGAAATTGTGG 58.252 36.000 12.70 2.64 45.89 4.17
378 384 7.717436 TGACACATTACTGAAAATTACAGTCCA 59.283 33.333 17.49 9.43 45.58 4.02
389 395 8.192110 TGAAAATTACAGTCCAAAAACCACTAC 58.808 33.333 0.00 0.00 0.00 2.73
446 456 2.496111 ACAGGGCAAAAATGCACATTG 58.504 42.857 5.78 0.00 41.47 2.82
452 462 6.002704 AGGGCAAAAATGCACATTGAATTAA 58.997 32.000 5.78 0.00 41.47 1.40
475 486 6.787085 AACTGTAACTACAACAGATTCAGC 57.213 37.500 10.02 0.00 45.89 4.26
483 495 7.426929 ACTACAACAGATTCAGCTAAAACTG 57.573 36.000 5.37 5.37 39.12 3.16
499 511 9.014297 AGCTAAAACTGAAATTGCTATTACACT 57.986 29.630 0.00 0.00 0.00 3.55
500 512 9.065871 GCTAAAACTGAAATTGCTATTACACTG 57.934 33.333 0.00 0.00 0.00 3.66
504 516 6.476378 ACTGAAATTGCTATTACACTGGACT 58.524 36.000 0.00 0.00 0.00 3.85
507 536 7.390823 TGAAATTGCTATTACACTGGACTACA 58.609 34.615 0.00 0.00 0.00 2.74
510 539 5.183014 TGCTATTACACTGGACTACATCG 57.817 43.478 0.00 0.00 0.00 3.84
511 540 3.982058 GCTATTACACTGGACTACATCGC 59.018 47.826 0.00 0.00 0.00 4.58
520 549 2.202566 GGACTACATCGCACTTAAGCC 58.797 52.381 1.29 0.00 0.00 4.35
617 646 6.596888 CACCAAATAACACATCTCATGAGACT 59.403 38.462 27.37 12.85 40.75 3.24
621 650 7.840342 AATAACACATCTCATGAGACTCAAC 57.160 36.000 27.37 0.00 40.75 3.18
626 655 4.771577 ACATCTCATGAGACTCAACTGACT 59.228 41.667 27.37 4.94 40.75 3.41
636 665 2.814919 ACTCAACTGACTAGGTGACTCG 59.185 50.000 0.00 0.00 45.47 4.18
647 676 0.527565 GGTGACTCGGCATTTGCATT 59.472 50.000 4.74 0.00 44.36 3.56
661 690 5.242393 GCATTTGCATTCATACATCTAGGGT 59.758 40.000 0.00 0.00 41.59 4.34
662 691 6.239120 GCATTTGCATTCATACATCTAGGGTT 60.239 38.462 0.00 0.00 41.59 4.11
663 692 7.685155 GCATTTGCATTCATACATCTAGGGTTT 60.685 37.037 0.00 0.00 41.59 3.27
664 693 7.716799 TTTGCATTCATACATCTAGGGTTTT 57.283 32.000 0.00 0.00 0.00 2.43
665 694 7.716799 TTGCATTCATACATCTAGGGTTTTT 57.283 32.000 0.00 0.00 0.00 1.94
689 718 8.848474 TTTTAGACAAACTCCTCCTCAATTAG 57.152 34.615 0.00 0.00 0.00 1.73
690 719 7.554959 TTAGACAAACTCCTCCTCAATTAGT 57.445 36.000 0.00 0.00 0.00 2.24
691 720 6.441088 AGACAAACTCCTCCTCAATTAGTT 57.559 37.500 0.00 0.00 31.94 2.24
692 721 6.842676 AGACAAACTCCTCCTCAATTAGTTT 58.157 36.000 0.00 0.00 40.13 2.66
693 722 7.290813 AGACAAACTCCTCCTCAATTAGTTTT 58.709 34.615 0.00 0.00 38.08 2.43
694 723 7.780271 AGACAAACTCCTCCTCAATTAGTTTTT 59.220 33.333 0.00 0.00 38.08 1.94
717 746 6.978343 TTTATTATGAGTCCAGACAAACGG 57.022 37.500 0.00 0.00 0.00 4.44
718 747 3.328382 TTATGAGTCCAGACAAACGGG 57.672 47.619 0.00 0.00 35.19 5.28
851 880 2.040884 CTCCCTCCCCCGATTCCA 60.041 66.667 0.00 0.00 0.00 3.53
906 935 4.548513 CCCTCTCCCCTCCCCTCG 62.549 77.778 0.00 0.00 0.00 4.63
907 936 4.548513 CCTCTCCCCTCCCCTCGG 62.549 77.778 0.00 0.00 0.00 4.63
960 989 1.139947 GCCGAAGAACCTCTCCTCG 59.860 63.158 0.00 0.00 0.00 4.63
968 997 2.045242 CCTCTCCTCGTCGACCCA 60.045 66.667 10.58 0.00 0.00 4.51
971 1000 0.961358 CTCTCCTCGTCGACCCACTT 60.961 60.000 10.58 0.00 0.00 3.16
1044 1073 1.803519 GCAGAAGCTCGACTCCGTG 60.804 63.158 0.00 0.00 37.91 4.94
1209 1238 0.179043 TCATCTCCTCCGACCTCTCG 60.179 60.000 0.00 0.00 39.83 4.04
1218 1247 2.039405 CGACCTCTCGTCTCCGGTT 61.039 63.158 0.00 0.00 39.56 4.44
1301 1330 0.393537 CTGCTCCCCAGGTGAACATC 60.394 60.000 0.00 0.00 37.93 3.06
1320 1349 2.560504 TCGGAATCCAATTCATGACGG 58.439 47.619 0.00 0.00 41.03 4.79
1325 1354 4.520492 GGAATCCAATTCATGACGGCTAAT 59.480 41.667 0.00 0.00 41.03 1.73
1352 1381 3.084039 ACCAGTTCCATGCTGTGTTATG 58.916 45.455 0.00 0.00 32.41 1.90
1377 1406 1.566563 CTCGTGTGCTGTGCTGTTC 59.433 57.895 0.00 0.00 0.00 3.18
1393 1422 0.179034 GTTCTGCAGCTATGGGAGGG 60.179 60.000 9.47 0.00 0.00 4.30
1395 1424 1.050988 TCTGCAGCTATGGGAGGGTC 61.051 60.000 9.47 0.00 0.00 4.46
1410 1439 1.683418 GGGTCGGGTATCTGGACACC 61.683 65.000 0.00 0.00 32.39 4.16
1477 1506 3.632189 CACATCGTCGATGAAGCTATCA 58.368 45.455 35.44 0.00 42.09 2.15
1491 1520 4.046938 AGCTATCACAGGTTCATACACG 57.953 45.455 0.00 0.00 0.00 4.49
1492 1521 3.123804 GCTATCACAGGTTCATACACGG 58.876 50.000 0.00 0.00 0.00 4.94
1496 1525 0.394938 ACAGGTTCATACACGGTGCA 59.605 50.000 8.30 0.00 0.00 4.57
1497 1526 1.003118 ACAGGTTCATACACGGTGCAT 59.997 47.619 8.30 0.00 0.00 3.96
1518 1547 2.679082 AGCGATAGGGTGTTAGTGGAT 58.321 47.619 0.00 0.00 0.00 3.41
1535 1564 5.705400 AGTGGATAGGATTTTATGTTGGGG 58.295 41.667 0.00 0.00 0.00 4.96
1536 1565 4.280929 GTGGATAGGATTTTATGTTGGGGC 59.719 45.833 0.00 0.00 0.00 5.80
1633 1670 0.110486 GGGAGGCAGAAAGGTGTGAA 59.890 55.000 0.00 0.00 0.00 3.18
1637 1674 3.057245 GGAGGCAGAAAGGTGTGAAATTC 60.057 47.826 0.00 0.00 0.00 2.17
1671 1710 7.489160 TCTTCTAGCTTGCGAAGTGATTAATA 58.511 34.615 15.38 0.00 38.20 0.98
1679 1718 6.448053 TGCGAAGTGATTAATAGCGATTAC 57.552 37.500 0.00 0.00 0.00 1.89
1682 1721 7.537649 TGCGAAGTGATTAATAGCGATTACTAG 59.462 37.037 0.00 0.00 0.00 2.57
1683 1722 7.537991 GCGAAGTGATTAATAGCGATTACTAGT 59.462 37.037 0.00 0.00 0.00 2.57
1684 1723 9.395707 CGAAGTGATTAATAGCGATTACTAGTT 57.604 33.333 0.00 0.00 0.00 2.24
1686 1725 9.477484 AAGTGATTAATAGCGATTACTAGTTGG 57.523 33.333 0.00 0.00 0.00 3.77
1687 1726 8.088981 AGTGATTAATAGCGATTACTAGTTGGG 58.911 37.037 0.00 0.00 0.00 4.12
1688 1727 6.872020 TGATTAATAGCGATTACTAGTTGGGC 59.128 38.462 0.00 0.00 0.00 5.36
1689 1728 4.957684 AATAGCGATTACTAGTTGGGCT 57.042 40.909 0.00 8.08 0.00 5.19
1690 1729 4.957684 ATAGCGATTACTAGTTGGGCTT 57.042 40.909 0.00 0.00 0.00 4.35
1735 1774 7.054855 CTTACTGCTTAGTAAGTTCTTGCTG 57.945 40.000 15.57 3.84 43.59 4.41
1744 1783 6.699575 AGTAAGTTCTTGCTGTGATGTTTT 57.300 33.333 2.63 0.00 0.00 2.43
1766 1805 0.106519 ATATTGCCCTCAGGTGTGGC 60.107 55.000 0.00 6.40 45.56 5.01
1770 1809 2.048603 GCCCTCAGGTGTGGCATTC 61.049 63.158 0.00 0.00 44.70 2.67
1775 1819 3.420893 CCTCAGGTGTGGCATTCTTTTA 58.579 45.455 0.00 0.00 0.00 1.52
1788 1832 6.096846 TGGCATTCTTTTAATTCTAAGGGAGC 59.903 38.462 0.00 0.00 0.00 4.70
1793 1837 8.706322 TTCTTTTAATTCTAAGGGAGCAGTTT 57.294 30.769 0.00 0.00 0.00 2.66
1803 1847 1.682257 GAGCAGTTTCTGGCCTCCT 59.318 57.895 3.32 0.00 31.21 3.69
1813 1857 2.607750 GGCCTCCTGGTCCTGACA 60.608 66.667 0.00 0.00 35.27 3.58
1822 1866 4.425772 TCCTGGTCCTGACATTTCTAGAA 58.574 43.478 0.00 0.00 0.00 2.10
1830 1874 4.629200 CCTGACATTTCTAGAAGTGCACTC 59.371 45.833 21.95 15.78 32.11 3.51
1831 1875 5.213891 TGACATTTCTAGAAGTGCACTCA 57.786 39.130 21.95 17.74 32.11 3.41
1839 1883 8.445275 TTTCTAGAAGTGCACTCAAATGTTTA 57.555 30.769 21.95 1.90 0.00 2.01
1893 1937 4.154195 AGGTTTTGTGCTATAAGTGCTTCG 59.846 41.667 0.00 0.00 0.00 3.79
1898 1942 5.270893 TGTGCTATAAGTGCTTCGGAATA 57.729 39.130 0.00 0.00 0.00 1.75
1914 1958 6.490566 TCGGAATAAAAGAGCAACTTAACC 57.509 37.500 0.00 0.00 37.93 2.85
1923 1967 5.914898 AGAGCAACTTAACCAACAAAACT 57.085 34.783 0.00 0.00 0.00 2.66
1925 1969 6.330278 AGAGCAACTTAACCAACAAAACTTC 58.670 36.000 0.00 0.00 0.00 3.01
1931 1975 3.904800 AACCAACAAAACTTCCAAGGG 57.095 42.857 0.00 0.00 0.00 3.95
1974 2018 7.806014 GCAACTTTAGGTCGTTTCAATATTTCA 59.194 33.333 0.00 0.00 0.00 2.69
1975 2019 9.329913 CAACTTTAGGTCGTTTCAATATTTCAG 57.670 33.333 0.00 0.00 0.00 3.02
2020 2064 6.951062 TGACCATCACTGTGAAATGTTTTA 57.049 33.333 15.31 1.63 0.00 1.52
2141 2185 0.888736 TGATGGCCACAGTTTCACCG 60.889 55.000 8.16 0.00 0.00 4.94
2148 2192 2.755836 CACAGTTTCACCGTGGAAAG 57.244 50.000 0.00 0.00 37.44 2.62
2180 2224 3.432252 GTCCAGAACGACCTACATTTGTG 59.568 47.826 0.00 0.00 0.00 3.33
2276 2320 1.998315 CTTCGATCTGTTGCTCACCAG 59.002 52.381 0.00 0.00 0.00 4.00
2387 2432 5.156355 GGAACTGTCAATGTGCTATTTGTG 58.844 41.667 0.00 0.00 0.00 3.33
2413 2459 3.195471 AGGTAGCCTTTTAGATTCCGC 57.805 47.619 0.00 0.00 0.00 5.54
2480 2526 6.014327 TCCTTTCTAATGCCTGCATTTCTTTT 60.014 34.615 21.18 0.94 43.32 2.27
2602 2648 4.013728 TGAAAAATATCGTTGTCCTGGGG 58.986 43.478 0.00 0.00 0.00 4.96
2956 3002 9.244799 GATTCCTTGTCAAAATCGTAAGTTTTT 57.755 29.630 0.00 0.00 46.84 1.94
3008 3054 8.628882 AGTAAATGTCAAAAACTGTTACAAGC 57.371 30.769 0.00 0.00 33.65 4.01
3016 3062 6.821665 TCAAAAACTGTTACAAGCTGAGTAGT 59.178 34.615 0.00 0.00 0.00 2.73
3026 3072 8.823818 GTTACAAGCTGAGTAGTTAAAAGACAA 58.176 33.333 0.00 0.00 0.00 3.18
3060 3106 9.167311 GTCTTCCTAGTGTTTTGATGAATATGT 57.833 33.333 0.00 0.00 0.00 2.29
3202 3248 2.102084 GGTATACCGGTTGAGGGTCTTC 59.898 54.545 15.04 0.00 38.99 2.87
3221 3267 2.742348 TCAACCTCCCTGCGTATCTTA 58.258 47.619 0.00 0.00 0.00 2.10
3309 3379 7.596494 ACTTGGATGAATATTGTTGTTGACTG 58.404 34.615 0.00 0.00 0.00 3.51
3337 3407 5.476614 ACAATAACTTCCGGTCTCTTGTAC 58.523 41.667 0.00 0.00 0.00 2.90
3415 3485 6.672593 TGAATTTGCCATACTTTCTCCCTAT 58.327 36.000 0.00 0.00 0.00 2.57
3430 3500 7.510675 TTCTCCCTATGATTCTACCAGTTTT 57.489 36.000 0.00 0.00 0.00 2.43
3482 3552 6.044871 CCATCCCAGGAGATTAGGAATTACTT 59.955 42.308 0.00 0.00 30.71 2.24
3670 3740 4.641989 GCTTCTTTGATGAATAAGCTCCCA 59.358 41.667 5.59 0.00 41.61 4.37
3678 3748 1.876156 GAATAAGCTCCCATTCCAGCG 59.124 52.381 0.00 0.00 40.84 5.18
3685 3755 0.178767 TCCCATTCCAGCGACAGATG 59.821 55.000 0.00 0.00 0.00 2.90
3899 4007 0.830648 TTGCTTATGCCCTAGCGTCT 59.169 50.000 0.00 0.00 44.31 4.18
4061 4172 6.588719 TTGGCTTATTGCAAGAAATACAGT 57.411 33.333 8.03 0.00 45.15 3.55
4090 4205 5.937111 ACACCTCAGTAATTGTTTGGTAGT 58.063 37.500 0.00 0.00 0.00 2.73
4108 4223 7.016153 TGGTAGTCAATTGTTGATACCTTCT 57.984 36.000 20.87 7.58 42.47 2.85
4152 4267 1.226542 CATGACCATGGCCTCTGCT 59.773 57.895 13.04 0.00 37.74 4.24
4174 4289 7.337938 TGCTTTCAGGATTAGTTATGTCATGA 58.662 34.615 0.00 0.00 31.68 3.07
4194 4309 1.675483 ACTCAAATGCGCTGTTTGACA 59.325 42.857 26.47 14.57 39.81 3.58
4211 4326 6.183360 TGTTTGACATGAGTAGAACCTCTGAA 60.183 38.462 0.00 0.00 32.50 3.02
4224 4339 4.917906 ACCTCTGAATTAGCTGAAGGTT 57.082 40.909 0.00 0.00 0.00 3.50
4248 4374 0.874607 GGCGTAAATCGAGTCCGCAT 60.875 55.000 24.38 0.00 45.70 4.73
4297 4423 4.714770 GCAAGGGCAGTCAATGAAATTGC 61.715 47.826 6.98 6.98 46.50 3.56
4412 4542 7.659390 AGCTAGCTATTGAATTACTTCATGACC 59.341 37.037 17.69 0.00 40.95 4.02
4559 4693 3.691609 GTGGAAGATCCTGTGATTTCACC 59.308 47.826 8.16 0.00 39.16 4.02
4563 4697 5.495640 GAAGATCCTGTGATTTCACCTCTT 58.504 41.667 8.16 10.17 45.88 2.85
4761 4895 5.010213 GGTACTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
4763 4897 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
4765 4899 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4767 4901 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4769 4903 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4792 4926 9.045223 TCTCTCATGCACACATATTTGTAATAC 57.955 33.333 0.00 0.00 33.67 1.89
4793 4927 8.962884 TCTCATGCACACATATTTGTAATACT 57.037 30.769 0.00 0.00 33.67 2.12
4804 4938 4.912317 TTTGTAATACTGCACCTACCCA 57.088 40.909 0.00 0.00 0.00 4.51
4806 4940 4.415881 TGTAATACTGCACCTACCCATG 57.584 45.455 0.00 0.00 0.00 3.66
4814 4948 5.190677 ACTGCACCTACCCATGTATTAAAC 58.809 41.667 0.00 0.00 0.00 2.01
4821 4955 6.657541 ACCTACCCATGTATTAAACTTGTGTG 59.342 38.462 0.00 0.00 32.63 3.82
4936 5070 6.204688 TGTTGAACATCTTCAAAGCGTAGATT 59.795 34.615 0.00 0.00 45.89 2.40
4977 5111 6.547510 TCATTGAGATTCCGAGATCTGTTCTA 59.452 38.462 0.00 0.00 36.54 2.10
4999 5133 1.025113 GGTAACCTTCTTCGCCTGGC 61.025 60.000 9.11 9.11 0.00 4.85
5086 5220 8.880878 AGTGGAGCGTTTTAACAAATTATTTT 57.119 26.923 0.00 0.00 0.00 1.82
5087 5221 9.320352 AGTGGAGCGTTTTAACAAATTATTTTT 57.680 25.926 0.00 0.00 0.00 1.94
5278 6564 2.203209 CCCCTAATGCCACGAGCC 60.203 66.667 0.00 0.00 42.71 4.70
5303 6589 2.723658 GAGAGAATCAAGCTGTATCGCG 59.276 50.000 0.00 0.00 37.82 5.87
5358 6651 5.413309 AGATGCAACTACTAACTCTTGCT 57.587 39.130 0.00 0.00 39.81 3.91
5563 6857 4.808895 TGCAGATACTATGTAAACCTTGCG 59.191 41.667 0.00 0.00 0.00 4.85
5574 6868 0.586319 AACCTTGCGTCATGTTCGTG 59.414 50.000 12.58 5.82 0.00 4.35
5575 6869 0.531974 ACCTTGCGTCATGTTCGTGT 60.532 50.000 12.58 5.14 0.00 4.49
5586 6880 5.558083 CGTCATGTTCGTGTCTTCATTTTCA 60.558 40.000 0.00 0.00 0.00 2.69
5587 6881 6.373779 GTCATGTTCGTGTCTTCATTTTCAT 58.626 36.000 0.00 0.00 0.00 2.57
5603 6897 2.549064 TCATTGGAGATGTATGGCGG 57.451 50.000 0.00 0.00 0.00 6.13
5607 6901 1.006102 GGAGATGTATGGCGGTCGG 60.006 63.158 0.00 0.00 0.00 4.79
5609 6903 0.104304 GAGATGTATGGCGGTCGGTT 59.896 55.000 0.00 0.00 0.00 4.44
5610 6904 0.179084 AGATGTATGGCGGTCGGTTG 60.179 55.000 0.00 0.00 0.00 3.77
5612 6906 2.512974 GTATGGCGGTCGGTTGGG 60.513 66.667 0.00 0.00 0.00 4.12
5676 6970 5.710099 ACCATCTTATTTTGTGTACCCAGTG 59.290 40.000 0.00 0.00 0.00 3.66
5804 7124 3.743567 TCACGTTTAGTTGTGCGTTTT 57.256 38.095 0.00 0.00 36.06 2.43
5843 7163 2.101770 GCGCAAATCAGGCAGCTC 59.898 61.111 0.30 0.00 0.00 4.09
5855 7175 3.015327 CAGGCAGCTCTATTTTGCTCTT 58.985 45.455 0.00 0.00 37.44 2.85
5860 7180 4.083110 GCAGCTCTATTTTGCTCTTTGTCA 60.083 41.667 0.00 0.00 37.44 3.58
5897 7253 4.521639 TGAAAATCACTTCAAGATGCAGCT 59.478 37.500 0.00 0.00 32.39 4.24
5898 7254 5.010314 TGAAAATCACTTCAAGATGCAGCTT 59.990 36.000 12.34 12.34 32.39 3.74
5936 7317 8.621286 AGCTTATATCAAAAATTTCCTGGTACG 58.379 33.333 0.00 0.00 0.00 3.67
5942 7323 5.121142 TCAAAAATTTCCTGGTACGTCGATC 59.879 40.000 0.00 0.00 0.00 3.69
5965 7375 7.189693 TCTCATATGTGTAATCGAATTTGGC 57.810 36.000 1.90 0.00 0.00 4.52
5997 7407 4.207165 GAGTTTTCCTAGCATAATGGGCA 58.793 43.478 0.00 0.00 0.00 5.36
6028 7438 6.073003 GCAGGAGGAAACCTTAATATGATTCG 60.073 42.308 0.00 0.00 38.32 3.34
6035 7445 7.041303 GGAAACCTTAATATGATTCGTCCTTCC 60.041 40.741 0.00 0.00 0.00 3.46
6038 7448 5.934625 CCTTAATATGATTCGTCCTTCCCAG 59.065 44.000 0.00 0.00 0.00 4.45
6059 7469 1.620822 AGCCAGACATCAAAACACCC 58.379 50.000 0.00 0.00 0.00 4.61
6061 7471 1.270550 GCCAGACATCAAAACACCCAG 59.729 52.381 0.00 0.00 0.00 4.45
6069 7479 5.144100 ACATCAAAACACCCAGGATTTGTA 58.856 37.500 11.33 3.62 35.01 2.41
6072 7482 7.619302 ACATCAAAACACCCAGGATTTGTATAT 59.381 33.333 11.33 0.00 35.01 0.86
6076 7486 5.975988 ACACCCAGGATTTGTATATCTGT 57.024 39.130 0.00 0.00 0.00 3.41
6078 7488 6.357367 ACACCCAGGATTTGTATATCTGTTC 58.643 40.000 0.00 0.00 0.00 3.18
6081 7491 7.503566 CACCCAGGATTTGTATATCTGTTCAAT 59.496 37.037 0.00 0.00 0.00 2.57
6082 7492 8.061304 ACCCAGGATTTGTATATCTGTTCAATT 58.939 33.333 0.00 0.00 0.00 2.32
6098 7509 9.323985 TCTGTTCAATTTTTCACCTAAATTTGG 57.676 29.630 0.00 0.00 34.01 3.28
6120 7531 2.165357 ATTCTGGCTCCAATTTCCCC 57.835 50.000 0.00 0.00 0.00 4.81
6135 7549 0.323360 TCCCCAGGTACAAATGCAGC 60.323 55.000 0.00 0.00 0.00 5.25
6148 7563 6.930667 ACAAATGCAGCTTTCAAAATTTCT 57.069 29.167 0.00 0.00 0.00 2.52
6150 7565 8.080083 ACAAATGCAGCTTTCAAAATTTCTAG 57.920 30.769 0.00 0.00 0.00 2.43
6153 7568 8.530269 AATGCAGCTTTCAAAATTTCTAGAAG 57.470 30.769 5.12 0.00 0.00 2.85
6166 7582 3.596940 TCTAGAAGACGGGCCTCTAAT 57.403 47.619 0.84 0.00 0.00 1.73
6167 7583 3.488363 TCTAGAAGACGGGCCTCTAATC 58.512 50.000 0.84 0.00 0.00 1.75
6169 7585 3.596940 AGAAGACGGGCCTCTAATCTA 57.403 47.619 0.84 0.00 0.00 1.98
6170 7586 3.912248 AGAAGACGGGCCTCTAATCTAA 58.088 45.455 0.84 0.00 0.00 2.10
6171 7587 3.637694 AGAAGACGGGCCTCTAATCTAAC 59.362 47.826 0.84 0.00 0.00 2.34
6172 7588 3.315880 AGACGGGCCTCTAATCTAACT 57.684 47.619 0.84 0.00 0.00 2.24
6173 7589 3.644335 AGACGGGCCTCTAATCTAACTT 58.356 45.455 0.84 0.00 0.00 2.66
6174 7590 4.801164 AGACGGGCCTCTAATCTAACTTA 58.199 43.478 0.84 0.00 0.00 2.24
6197 7615 4.965042 AAAACGCGCTTCAAAATTAAGG 57.035 36.364 5.73 0.00 0.00 2.69
6234 7652 2.653702 CGAGGCCGGAGATCATCC 59.346 66.667 5.05 0.00 45.64 3.51
6235 7653 2.936912 CGAGGCCGGAGATCATCCC 61.937 68.421 5.05 0.00 46.50 3.85
6252 7670 5.265191 TCATCCCCATTTCCATTAACGAAA 58.735 37.500 0.00 2.87 33.94 3.46
6266 7684 6.074569 CCATTAACGAAACATCAAACAACCAC 60.075 38.462 0.00 0.00 0.00 4.16
6300 7718 1.546476 CAGACAGTACACACCCTCTCC 59.454 57.143 0.00 0.00 0.00 3.71
6322 7740 7.295196 TCTCCCTCAGATAACCATACTACTAGT 59.705 40.741 0.00 0.00 0.00 2.57
6359 7777 2.499289 ACAGACACTCCCATCACTCATC 59.501 50.000 0.00 0.00 0.00 2.92
6364 7782 1.836166 ACTCCCATCACTCATCACAGG 59.164 52.381 0.00 0.00 0.00 4.00
6365 7783 2.113807 CTCCCATCACTCATCACAGGA 58.886 52.381 0.00 0.00 0.00 3.86
6371 7789 3.303881 TCACTCATCACAGGAAACTCG 57.696 47.619 0.00 0.00 40.21 4.18
6484 7907 3.112709 GGCAGCTTGTCGACGGTC 61.113 66.667 11.62 0.00 0.00 4.79
6541 7964 1.519455 CTCCATGTCGGCGTTCTCC 60.519 63.158 6.85 0.00 33.14 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.537848 GTAATTTGGACTGTATTTGTAAGTTCG 57.462 33.333 0.00 0.00 0.00 3.95
166 168 9.832445 TTGTTAAATGTGCATTTTAACCCTTAA 57.168 25.926 27.53 19.19 40.99 1.85
167 169 9.832445 TTTGTTAAATGTGCATTTTAACCCTTA 57.168 25.926 27.53 16.26 40.99 2.69
168 170 8.738645 TTTGTTAAATGTGCATTTTAACCCTT 57.261 26.923 27.53 0.98 40.99 3.95
213 218 6.265196 TGCATCTTTTCAGTAATTTGGACTGT 59.735 34.615 6.72 0.00 43.95 3.55
216 221 6.583806 CAGTGCATCTTTTCAGTAATTTGGAC 59.416 38.462 0.00 0.00 0.00 4.02
260 266 8.870160 TCCAATTCAAATTGTCAGTTTTACAG 57.130 30.769 12.99 0.00 43.24 2.74
278 284 9.859427 TGTCATATGATTTGAAACTTCCAATTC 57.141 29.630 9.02 0.00 0.00 2.17
293 299 6.319658 CCCTGCAACTTTACTGTCATATGATT 59.680 38.462 9.02 0.00 0.00 2.57
335 341 7.652524 ATGTGTCACTTCTAGTGTATCTGAT 57.347 36.000 4.27 0.00 46.03 2.90
339 345 8.459635 TCAGTAATGTGTCACTTCTAGTGTATC 58.540 37.037 4.27 1.18 46.03 2.24
340 346 8.349568 TCAGTAATGTGTCACTTCTAGTGTAT 57.650 34.615 4.27 0.00 46.03 2.29
378 384 9.984190 TTTTTCAGTTAAGTTGTAGTGGTTTTT 57.016 25.926 0.00 0.00 0.00 1.94
411 417 0.331278 CCTGTAATCTGTTGGGGGCA 59.669 55.000 0.00 0.00 0.00 5.36
417 423 4.389687 GCATTTTTGCCCTGTAATCTGTTG 59.610 41.667 0.00 0.00 0.00 3.33
452 462 6.525629 AGCTGAATCTGTTGTAGTTACAGTT 58.474 36.000 0.00 0.00 42.77 3.16
460 470 7.658179 TCAGTTTTAGCTGAATCTGTTGTAG 57.342 36.000 21.88 3.53 41.93 2.74
475 486 9.559958 CCAGTGTAATAGCAATTTCAGTTTTAG 57.440 33.333 0.00 0.00 0.00 1.85
483 495 7.843490 TGTAGTCCAGTGTAATAGCAATTTC 57.157 36.000 0.00 0.00 0.00 2.17
499 511 2.418197 GGCTTAAGTGCGATGTAGTCCA 60.418 50.000 4.02 0.00 0.00 4.02
500 512 2.202566 GGCTTAAGTGCGATGTAGTCC 58.797 52.381 4.02 0.00 0.00 3.85
504 516 2.658373 TTCGGCTTAAGTGCGATGTA 57.342 45.000 4.02 0.00 0.00 2.29
507 536 2.354821 GGATTTTCGGCTTAAGTGCGAT 59.645 45.455 4.02 0.00 0.00 4.58
510 539 2.488153 AGTGGATTTTCGGCTTAAGTGC 59.512 45.455 4.02 0.00 0.00 4.40
511 540 3.751175 TGAGTGGATTTTCGGCTTAAGTG 59.249 43.478 4.02 0.00 0.00 3.16
520 549 7.168972 TGCAGTTTAATTTTGAGTGGATTTTCG 59.831 33.333 0.00 0.00 0.00 3.46
599 628 6.209391 TCAGTTGAGTCTCATGAGATGTGTTA 59.791 38.462 27.51 9.42 39.97 2.41
607 636 4.704540 ACCTAGTCAGTTGAGTCTCATGAG 59.295 45.833 17.07 17.07 0.00 2.90
617 646 2.160205 CCGAGTCACCTAGTCAGTTGA 58.840 52.381 0.00 0.00 0.00 3.18
621 650 1.107114 ATGCCGAGTCACCTAGTCAG 58.893 55.000 0.00 0.00 0.00 3.51
626 655 0.323302 TGCAAATGCCGAGTCACCTA 59.677 50.000 2.46 0.00 41.18 3.08
636 665 5.336213 CCCTAGATGTATGAATGCAAATGCC 60.336 44.000 2.46 0.00 41.18 4.40
663 692 9.284968 CTAATTGAGGAGGAGTTTGTCTAAAAA 57.715 33.333 0.00 0.00 0.00 1.94
664 693 8.437575 ACTAATTGAGGAGGAGTTTGTCTAAAA 58.562 33.333 0.00 0.00 0.00 1.52
665 694 7.974504 ACTAATTGAGGAGGAGTTTGTCTAAA 58.025 34.615 0.00 0.00 0.00 1.85
666 695 7.554959 ACTAATTGAGGAGGAGTTTGTCTAA 57.445 36.000 0.00 0.00 0.00 2.10
667 696 7.554959 AACTAATTGAGGAGGAGTTTGTCTA 57.445 36.000 0.00 0.00 0.00 2.59
668 697 6.441088 AACTAATTGAGGAGGAGTTTGTCT 57.559 37.500 0.00 0.00 0.00 3.41
669 698 7.511959 AAAACTAATTGAGGAGGAGTTTGTC 57.488 36.000 1.98 0.00 39.60 3.18
670 699 7.898014 AAAAACTAATTGAGGAGGAGTTTGT 57.102 32.000 1.98 0.00 39.60 2.83
692 721 7.094549 CCCGTTTGTCTGGACTCATAATAAAAA 60.095 37.037 2.38 0.00 0.00 1.94
693 722 6.373216 CCCGTTTGTCTGGACTCATAATAAAA 59.627 38.462 2.38 0.00 0.00 1.52
694 723 5.878116 CCCGTTTGTCTGGACTCATAATAAA 59.122 40.000 2.38 0.00 0.00 1.40
695 724 5.424757 CCCGTTTGTCTGGACTCATAATAA 58.575 41.667 2.38 0.00 0.00 1.40
696 725 4.141801 CCCCGTTTGTCTGGACTCATAATA 60.142 45.833 2.38 0.00 0.00 0.98
697 726 3.370527 CCCCGTTTGTCTGGACTCATAAT 60.371 47.826 2.38 0.00 0.00 1.28
698 727 2.027561 CCCCGTTTGTCTGGACTCATAA 60.028 50.000 2.38 0.00 0.00 1.90
699 728 1.553248 CCCCGTTTGTCTGGACTCATA 59.447 52.381 2.38 0.00 0.00 2.15
700 729 0.324943 CCCCGTTTGTCTGGACTCAT 59.675 55.000 2.38 0.00 0.00 2.90
701 730 0.761323 TCCCCGTTTGTCTGGACTCA 60.761 55.000 2.38 0.00 0.00 3.41
702 731 0.395312 TTCCCCGTTTGTCTGGACTC 59.605 55.000 2.38 0.00 0.00 3.36
703 732 0.108019 GTTCCCCGTTTGTCTGGACT 59.892 55.000 2.38 0.00 0.00 3.85
704 733 0.179040 TGTTCCCCGTTTGTCTGGAC 60.179 55.000 0.00 0.00 0.00 4.02
705 734 0.768622 ATGTTCCCCGTTTGTCTGGA 59.231 50.000 0.00 0.00 0.00 3.86
706 735 1.616159 AATGTTCCCCGTTTGTCTGG 58.384 50.000 0.00 0.00 0.00 3.86
707 736 2.288152 CCAAATGTTCCCCGTTTGTCTG 60.288 50.000 6.34 0.00 44.95 3.51
708 737 1.960689 CCAAATGTTCCCCGTTTGTCT 59.039 47.619 6.34 0.00 44.95 3.41
709 738 1.604438 GCCAAATGTTCCCCGTTTGTC 60.604 52.381 6.34 0.00 44.95 3.18
710 739 0.391228 GCCAAATGTTCCCCGTTTGT 59.609 50.000 6.34 0.00 44.95 2.83
711 740 0.320334 GGCCAAATGTTCCCCGTTTG 60.320 55.000 0.00 0.00 45.65 2.93
712 741 1.476845 GGGCCAAATGTTCCCCGTTT 61.477 55.000 4.39 0.00 33.91 3.60
713 742 1.911269 GGGCCAAATGTTCCCCGTT 60.911 57.895 4.39 0.00 33.91 4.44
714 743 2.283604 GGGCCAAATGTTCCCCGT 60.284 61.111 4.39 0.00 33.91 5.28
715 744 2.283532 TGGGCCAAATGTTCCCCG 60.284 61.111 2.13 0.00 40.50 5.73
716 745 2.645192 CGTGGGCCAAATGTTCCCC 61.645 63.158 8.40 0.00 39.30 4.81
717 746 1.182385 TTCGTGGGCCAAATGTTCCC 61.182 55.000 8.40 0.00 40.47 3.97
718 747 0.038618 GTTCGTGGGCCAAATGTTCC 60.039 55.000 8.40 0.00 0.00 3.62
798 827 4.463879 CGGCTGCTCCTCCCACAG 62.464 72.222 0.00 0.00 34.48 3.66
800 829 4.154347 CTCGGCTGCTCCTCCCAC 62.154 72.222 0.00 0.00 0.00 4.61
803 832 4.828925 GTGCTCGGCTGCTCCTCC 62.829 72.222 0.00 0.00 0.00 4.30
804 833 4.828925 GGTGCTCGGCTGCTCCTC 62.829 72.222 0.00 0.00 41.72 3.71
915 944 1.051812 AGAGAATGAGCCGGGTATGG 58.948 55.000 5.91 0.00 0.00 2.74
916 945 3.555168 GGTTAGAGAATGAGCCGGGTATG 60.555 52.174 5.91 0.00 0.00 2.39
917 946 2.633481 GGTTAGAGAATGAGCCGGGTAT 59.367 50.000 5.91 0.00 0.00 2.73
918 947 2.037144 GGTTAGAGAATGAGCCGGGTA 58.963 52.381 5.91 0.00 0.00 3.69
919 948 0.831307 GGTTAGAGAATGAGCCGGGT 59.169 55.000 5.45 5.45 0.00 5.28
929 958 0.245539 CTTCGGCGGTGGTTAGAGAA 59.754 55.000 7.21 0.00 0.00 2.87
930 959 0.609957 TCTTCGGCGGTGGTTAGAGA 60.610 55.000 7.21 0.00 0.00 3.10
960 989 2.606826 AGGGGGAAGTGGGTCGAC 60.607 66.667 7.13 7.13 0.00 4.20
1177 1206 2.186903 GATGACGTCGGTGGCCAT 59.813 61.111 9.72 0.00 0.00 4.40
1188 1217 0.464735 AGAGGTCGGAGGAGATGACG 60.465 60.000 0.00 0.00 33.45 4.35
1209 1238 1.080705 CACGAGGACAACCGGAGAC 60.081 63.158 9.46 0.00 41.83 3.36
1301 1330 1.002468 GCCGTCATGAATTGGATTCCG 60.002 52.381 12.74 2.42 38.50 4.30
1320 1349 8.814506 CAGCATGGAACTGGTGCTAAATTAGC 62.815 46.154 17.42 17.42 46.67 3.09
1325 1354 2.161855 CAGCATGGAACTGGTGCTAAA 58.838 47.619 0.00 0.00 46.67 1.85
1333 1362 5.631026 GTTACATAACACAGCATGGAACTG 58.369 41.667 0.00 0.00 41.07 3.16
1335 1364 5.631026 CAGTTACATAACACAGCATGGAAC 58.369 41.667 4.67 2.13 43.48 3.62
1337 1366 3.689161 GCAGTTACATAACACAGCATGGA 59.311 43.478 4.67 0.00 38.62 3.41
1352 1381 0.508641 CACAGCACACGAGCAGTTAC 59.491 55.000 0.00 0.00 36.85 2.50
1377 1406 1.449353 GACCCTCCCATAGCTGCAG 59.551 63.158 10.11 10.11 0.00 4.41
1386 1415 1.075525 CAGATACCCGACCCTCCCA 60.076 63.158 0.00 0.00 0.00 4.37
1393 1422 1.033746 TCGGTGTCCAGATACCCGAC 61.034 60.000 7.87 0.00 39.14 4.79
1395 1424 1.436336 GTCGGTGTCCAGATACCCG 59.564 63.158 7.87 4.12 39.14 5.28
1477 1506 0.394938 TGCACCGTGTATGAACCTGT 59.605 50.000 0.00 0.00 0.00 4.00
1491 1520 0.393077 ACACCCTATCGCTATGCACC 59.607 55.000 0.00 0.00 0.00 5.01
1492 1521 2.240493 AACACCCTATCGCTATGCAC 57.760 50.000 0.00 0.00 0.00 4.57
1496 1525 3.840991 TCCACTAACACCCTATCGCTAT 58.159 45.455 0.00 0.00 0.00 2.97
1497 1526 3.301794 TCCACTAACACCCTATCGCTA 57.698 47.619 0.00 0.00 0.00 4.26
1501 1530 6.936968 AATCCTATCCACTAACACCCTATC 57.063 41.667 0.00 0.00 0.00 2.08
1518 1547 3.655615 ACGCCCCAACATAAAATCCTA 57.344 42.857 0.00 0.00 0.00 2.94
1535 1564 3.121544 GGAACTAGCATACCACTAACGC 58.878 50.000 0.00 0.00 0.00 4.84
1536 1565 4.097437 TGAGGAACTAGCATACCACTAACG 59.903 45.833 0.00 0.00 41.55 3.18
1621 1658 6.432403 AGAGAGAGAATTTCACACCTTTCT 57.568 37.500 0.00 0.00 0.00 2.52
1633 1670 6.818142 GCAAGCTAGAAGAAAGAGAGAGAATT 59.182 38.462 0.00 0.00 0.00 2.17
1637 1674 4.104776 CGCAAGCTAGAAGAAAGAGAGAG 58.895 47.826 0.00 0.00 0.00 3.20
1671 1710 2.766828 AGAAGCCCAACTAGTAATCGCT 59.233 45.455 0.00 0.00 0.00 4.93
1679 1718 2.586648 AACCCAAGAAGCCCAACTAG 57.413 50.000 0.00 0.00 0.00 2.57
1682 1721 1.893137 CCTAAACCCAAGAAGCCCAAC 59.107 52.381 0.00 0.00 0.00 3.77
1683 1722 1.783979 TCCTAAACCCAAGAAGCCCAA 59.216 47.619 0.00 0.00 0.00 4.12
1684 1723 1.451449 TCCTAAACCCAAGAAGCCCA 58.549 50.000 0.00 0.00 0.00 5.36
1685 1724 2.597578 TTCCTAAACCCAAGAAGCCC 57.402 50.000 0.00 0.00 0.00 5.19
1686 1725 3.696548 CAGATTCCTAAACCCAAGAAGCC 59.303 47.826 0.00 0.00 0.00 4.35
1687 1726 4.156739 CACAGATTCCTAAACCCAAGAAGC 59.843 45.833 0.00 0.00 0.00 3.86
1688 1727 4.156739 GCACAGATTCCTAAACCCAAGAAG 59.843 45.833 0.00 0.00 0.00 2.85
1689 1728 4.079253 GCACAGATTCCTAAACCCAAGAA 58.921 43.478 0.00 0.00 0.00 2.52
1690 1729 3.330701 AGCACAGATTCCTAAACCCAAGA 59.669 43.478 0.00 0.00 0.00 3.02
1733 1772 7.546358 TGAGGGCAATATTTAAAACATCACAG 58.454 34.615 0.00 0.00 0.00 3.66
1735 1774 6.980397 CCTGAGGGCAATATTTAAAACATCAC 59.020 38.462 0.00 0.00 0.00 3.06
1744 1783 3.897239 CCACACCTGAGGGCAATATTTA 58.103 45.455 2.38 0.00 35.63 1.40
1766 1805 8.286191 ACTGCTCCCTTAGAATTAAAAGAATG 57.714 34.615 1.69 0.00 0.00 2.67
1770 1809 8.239998 CAGAAACTGCTCCCTTAGAATTAAAAG 58.760 37.037 0.00 0.00 0.00 2.27
1775 1819 4.593956 CCAGAAACTGCTCCCTTAGAATT 58.406 43.478 0.00 0.00 0.00 2.17
1788 1832 0.322008 GACCAGGAGGCCAGAAACTG 60.322 60.000 5.01 5.33 39.06 3.16
1793 1837 2.284921 CAGGACCAGGAGGCCAGA 60.285 66.667 5.01 0.00 39.06 3.86
1803 1847 4.563580 GCACTTCTAGAAATGTCAGGACCA 60.564 45.833 14.87 0.00 0.00 4.02
1813 1857 7.516198 AACATTTGAGTGCACTTCTAGAAAT 57.484 32.000 22.65 15.95 0.00 2.17
1822 1866 7.264221 TGTGAATTTAAACATTTGAGTGCACT 58.736 30.769 21.88 21.88 0.00 4.40
1882 1926 5.880332 TGCTCTTTTATTCCGAAGCACTTAT 59.120 36.000 0.00 0.00 0.00 1.73
1885 1929 3.674997 TGCTCTTTTATTCCGAAGCACT 58.325 40.909 0.00 0.00 0.00 4.40
1893 1937 7.430441 TGTTGGTTAAGTTGCTCTTTTATTCC 58.570 34.615 0.68 0.00 37.56 3.01
1898 1942 7.158697 AGTTTTGTTGGTTAAGTTGCTCTTTT 58.841 30.769 0.68 0.00 37.56 2.27
1914 1958 2.977772 TGCCCTTGGAAGTTTTGTTG 57.022 45.000 0.00 0.00 0.00 3.33
1931 1975 0.183492 TGCAATCCCAGGGAGTATGC 59.817 55.000 26.42 26.42 38.97 3.14
1974 2018 5.488262 AAATTAAGAATGTTTGGCTGGCT 57.512 34.783 2.00 0.00 0.00 4.75
1975 2019 5.700373 TCAAAATTAAGAATGTTTGGCTGGC 59.300 36.000 0.00 0.00 32.91 4.85
2113 2157 6.041409 TGAAACTGTGGCCATCAATTTCTAAA 59.959 34.615 26.97 14.67 31.03 1.85
2141 2185 2.948979 TGGACATTGACACACTTTCCAC 59.051 45.455 0.00 0.00 0.00 4.02
2148 2192 2.221055 GTCGTTCTGGACATTGACACAC 59.779 50.000 0.00 0.00 36.91 3.82
2252 2296 3.178267 GTGAGCAACAGATCGAAGAGAG 58.822 50.000 0.00 0.00 43.63 3.20
2276 2320 6.246420 ACACAGAACATGCATTAAGAGAAC 57.754 37.500 0.00 0.00 0.00 3.01
2387 2432 6.282167 GGAATCTAAAAGGCTACCTAGTGAC 58.718 44.000 0.00 0.00 31.13 3.67
2445 2491 7.120726 GCAGGCATTAGAAAGGAAACTAAGTTA 59.879 37.037 0.00 0.00 42.68 2.24
2602 2648 3.319122 ACAATCAAAGGAAGCACTTCACC 59.681 43.478 12.21 0.00 41.20 4.02
3026 3072 9.965902 ATCAAAACACTAGGAAGACTATTTGAT 57.034 29.630 0.00 0.00 0.00 2.57
3197 3243 0.606604 TACGCAGGGAGGTTGAAGAC 59.393 55.000 0.00 0.00 0.00 3.01
3202 3248 2.431057 ACTAAGATACGCAGGGAGGTTG 59.569 50.000 0.00 0.00 0.00 3.77
3221 3267 3.243724 AGTTGCTCCTAGGACTCAAACT 58.756 45.455 18.42 16.08 0.00 2.66
3288 3358 5.105797 TGCCAGTCAACAACAATATTCATCC 60.106 40.000 0.00 0.00 0.00 3.51
3309 3379 2.817844 AGACCGGAAGTTATTGTTTGCC 59.182 45.455 9.46 0.00 0.00 4.52
3370 3440 6.882610 TCAGTACTCATTGTTCATTTGCTT 57.117 33.333 0.00 0.00 0.00 3.91
3415 3485 4.155826 CCGCAATCAAAACTGGTAGAATCA 59.844 41.667 0.00 0.00 0.00 2.57
3565 3635 3.066291 TGACCAGGCATAAACGATTGT 57.934 42.857 0.00 0.00 0.00 2.71
3568 3638 3.845781 AGATGACCAGGCATAAACGAT 57.154 42.857 0.00 0.00 0.00 3.73
3670 3740 6.057533 TGAATAATTCATCTGTCGCTGGAAT 58.942 36.000 0.00 0.00 34.08 3.01
3763 3871 5.452302 CGCTTTAACGATCTTGGCAATTTAG 59.548 40.000 0.00 0.00 34.06 1.85
3771 3879 3.682858 TCTTTCCGCTTTAACGATCTTGG 59.317 43.478 0.00 0.00 34.06 3.61
3863 3971 2.167075 AGCAAGCTCTTTGTTTGTTGCT 59.833 40.909 1.61 1.61 44.37 3.91
3899 4007 3.653164 TGATACTTCATAGGGTGGCAGA 58.347 45.455 0.00 0.00 0.00 4.26
4039 4150 5.709631 TGACTGTATTTCTTGCAATAAGCCA 59.290 36.000 0.00 0.00 44.83 4.75
4061 4172 6.016360 CCAAACAATTACTGAGGTGTTGATGA 60.016 38.462 0.00 0.00 34.54 2.92
4090 4205 7.665559 AGTGCTTAAGAAGGTATCAACAATTGA 59.334 33.333 13.59 0.00 45.01 2.57
4152 4267 8.539544 TGAGTCATGACATAACTAATCCTGAAA 58.460 33.333 27.02 0.00 0.00 2.69
4174 4289 1.675483 TGTCAAACAGCGCATTTGAGT 59.325 42.857 29.38 9.32 44.55 3.41
4194 4309 6.609212 TCAGCTAATTCAGAGGTTCTACTCAT 59.391 38.462 0.00 0.00 39.97 2.90
4211 4326 3.270877 CGCCTAACAACCTTCAGCTAAT 58.729 45.455 0.00 0.00 0.00 1.73
4224 4339 2.478370 CGGACTCGATTTACGCCTAACA 60.478 50.000 0.00 0.00 42.26 2.41
4248 4374 3.101437 TGGTCGGCACCTTATCTTTCTA 58.899 45.455 7.47 0.00 44.17 2.10
4412 4542 9.942850 ATCTTGGGTTAAAAATCAAACTAATGG 57.057 29.630 0.00 0.00 0.00 3.16
4490 4624 3.246463 CACCAACGCAAAATAAAACCCAC 59.754 43.478 0.00 0.00 0.00 4.61
4559 4693 4.997565 TCAGTGCTTTCAAAAACCAAGAG 58.002 39.130 0.00 0.00 0.00 2.85
4563 4697 4.493547 CTGTTCAGTGCTTTCAAAAACCA 58.506 39.130 0.00 0.00 0.00 3.67
4684 4818 1.343142 TCGCAGGTGTGTCACAACTAT 59.657 47.619 22.95 0.00 45.99 2.12
4761 4895 3.804786 ATGTGTGCATGAGAGAGAGAG 57.195 47.619 0.00 0.00 33.37 3.20
4763 4897 5.816258 ACAAATATGTGTGCATGAGAGAGAG 59.184 40.000 0.00 0.00 38.69 3.20
4765 4899 7.543947 TTACAAATATGTGTGCATGAGAGAG 57.456 36.000 8.91 0.00 40.84 3.20
4767 4901 9.049523 AGTATTACAAATATGTGTGCATGAGAG 57.950 33.333 8.91 0.00 40.84 3.20
4769 4903 7.588854 GCAGTATTACAAATATGTGTGCATGAG 59.411 37.037 8.91 0.00 40.84 2.90
4792 4926 5.437060 AGTTTAATACATGGGTAGGTGCAG 58.563 41.667 0.00 0.00 31.88 4.41
4793 4927 5.444744 AGTTTAATACATGGGTAGGTGCA 57.555 39.130 0.00 0.00 31.88 4.57
4977 5111 1.002087 CAGGCGAAGAAGGTTACCTGT 59.998 52.381 3.99 0.00 39.85 4.00
4999 5133 8.230486 GTGCCCATTAATCTTGATAAAGTATCG 58.770 37.037 0.00 0.00 38.02 2.92
5086 5220 9.423061 GCTAATTCCTTTCTGATTTAGCAAAAA 57.577 29.630 16.62 0.00 45.09 1.94
5087 5221 8.986477 GCTAATTCCTTTCTGATTTAGCAAAA 57.014 30.769 16.62 0.00 45.09 2.44
5109 5248 9.509956 GAGAGGAGATAACTAACTCTAATGCTA 57.490 37.037 6.67 0.00 39.21 3.49
5122 5261 9.836179 ATTGATTATGGTAGAGAGGAGATAACT 57.164 33.333 0.00 0.00 0.00 2.24
5128 5267 9.618890 TTCAAAATTGATTATGGTAGAGAGGAG 57.381 33.333 0.00 0.00 37.00 3.69
5172 5311 8.456904 TCGACAAAGTATACATTACTTGTGAC 57.543 34.615 5.50 1.63 39.48 3.67
5173 5312 7.274904 GCTCGACAAAGTATACATTACTTGTGA 59.725 37.037 5.50 6.34 39.48 3.58
5174 5313 7.275779 AGCTCGACAAAGTATACATTACTTGTG 59.724 37.037 5.50 3.60 39.48 3.33
5175 5314 7.321153 AGCTCGACAAAGTATACATTACTTGT 58.679 34.615 5.50 6.37 42.62 3.16
5182 6467 7.599245 GCCTATTAAGCTCGACAAAGTATACAT 59.401 37.037 5.50 0.00 0.00 2.29
5263 6549 1.819632 GTGGGCTCGTGGCATTAGG 60.820 63.158 13.29 0.00 44.01 2.69
5278 6564 2.376808 ACAGCTTGATTCTCTCGTGG 57.623 50.000 0.00 0.00 0.00 4.94
5303 6589 6.942532 ATTGATGGTCCATATGTTACACAC 57.057 37.500 3.72 0.00 0.00 3.82
5358 6651 3.183373 GCAACAAAATTTCAATTCGCGGA 59.817 39.130 6.13 0.00 0.00 5.54
5563 6857 5.747565 TGAAAATGAAGACACGAACATGAC 58.252 37.500 0.00 0.00 0.00 3.06
5574 6868 8.133627 CCATACATCTCCAATGAAAATGAAGAC 58.866 37.037 0.00 0.00 0.00 3.01
5575 6869 7.201848 GCCATACATCTCCAATGAAAATGAAGA 60.202 37.037 0.00 0.00 0.00 2.87
5586 6880 1.270305 CGACCGCCATACATCTCCAAT 60.270 52.381 0.00 0.00 0.00 3.16
5587 6881 0.104120 CGACCGCCATACATCTCCAA 59.896 55.000 0.00 0.00 0.00 3.53
5603 6897 1.298859 GACATGTCAGCCCAACCGAC 61.299 60.000 21.07 0.00 0.00 4.79
5607 6901 1.003839 TCCGACATGTCAGCCCAAC 60.004 57.895 24.93 0.00 0.00 3.77
5609 6903 1.609210 TCTCCGACATGTCAGCCCA 60.609 57.895 24.93 2.24 0.00 5.36
5610 6904 1.153549 GTCTCCGACATGTCAGCCC 60.154 63.158 24.93 5.35 32.09 5.19
5612 6906 0.038251 TGTGTCTCCGACATGTCAGC 60.038 55.000 24.93 12.04 44.63 4.26
5620 6914 1.563111 TTTCGTGTTGTGTCTCCGAC 58.437 50.000 0.00 0.00 0.00 4.79
5635 6929 6.683974 AGATGGTCCACTATCAAAATTTCG 57.316 37.500 0.00 0.00 36.45 3.46
5676 6970 9.706846 CAGAAAAATCAGTTCAAAAATTTCACC 57.293 29.630 0.00 0.00 0.00 4.02
5778 7094 3.602946 CGCACAACTAAACGTGATTTCGT 60.603 43.478 0.00 0.00 46.19 3.85
5779 7095 2.894000 CGCACAACTAAACGTGATTTCG 59.106 45.455 0.00 0.00 35.02 3.46
5883 7239 4.449131 TGGAGATAAGCTGCATCTTGAAG 58.551 43.478 12.98 0.00 40.31 3.02
5892 7248 3.212685 AGCTGATTTGGAGATAAGCTGC 58.787 45.455 0.00 0.00 41.39 5.25
5931 7312 4.485024 ACACATATGAGATCGACGTACC 57.515 45.455 10.38 0.00 0.00 3.34
5936 7317 8.454293 AATTCGATTACACATATGAGATCGAC 57.546 34.615 23.28 7.30 44.58 4.20
5942 7323 6.073369 CGCCAAATTCGATTACACATATGAG 58.927 40.000 10.38 3.79 0.00 2.90
5965 7375 2.080286 AGGAAAACTCACCATCGACG 57.920 50.000 0.00 0.00 0.00 5.12
5997 7407 3.532641 AAGGTTTCCTCCTGCAATCTT 57.467 42.857 0.00 0.00 37.93 2.40
6028 7438 0.035915 GTCTGGCTTCTGGGAAGGAC 60.036 60.000 8.98 4.94 0.00 3.85
6035 7445 2.886523 TGTTTTGATGTCTGGCTTCTGG 59.113 45.455 0.00 0.00 0.00 3.86
6038 7448 2.029918 GGGTGTTTTGATGTCTGGCTTC 60.030 50.000 0.00 0.00 0.00 3.86
6072 7482 9.323985 CCAAATTTAGGTGAAAAATTGAACAGA 57.676 29.630 0.00 0.00 36.81 3.41
6076 7486 8.511604 TTGCCAAATTTAGGTGAAAAATTGAA 57.488 26.923 0.00 0.00 36.81 2.69
6078 7488 9.396938 GAATTGCCAAATTTAGGTGAAAAATTG 57.603 29.630 0.00 0.00 36.81 2.32
6081 7491 7.228308 CCAGAATTGCCAAATTTAGGTGAAAAA 59.772 33.333 0.00 0.00 36.10 1.94
6082 7492 6.709846 CCAGAATTGCCAAATTTAGGTGAAAA 59.290 34.615 0.00 0.00 36.10 2.29
6098 7509 2.419159 GGGAAATTGGAGCCAGAATTGC 60.419 50.000 0.00 0.00 0.00 3.56
6120 7531 3.921119 TGAAAGCTGCATTTGTACCTG 57.079 42.857 1.02 0.00 0.00 4.00
6135 7549 6.086871 GCCCGTCTTCTAGAAATTTTGAAAG 58.913 40.000 6.63 0.00 0.00 2.62
6148 7563 3.596940 AGATTAGAGGCCCGTCTTCTA 57.403 47.619 0.00 0.00 0.00 2.10
6150 7565 3.637694 AGTTAGATTAGAGGCCCGTCTTC 59.362 47.826 0.00 0.00 0.00 2.87
6153 7568 5.526506 TTAAGTTAGATTAGAGGCCCGTC 57.473 43.478 0.00 0.00 0.00 4.79
6218 7636 2.588201 GGGGATGATCTCCGGCCTC 61.588 68.421 0.00 0.00 46.01 4.70
6220 7638 1.783250 AATGGGGATGATCTCCGGCC 61.783 60.000 6.89 0.00 40.96 6.13
6223 7641 1.421268 TGGAAATGGGGATGATCTCCG 59.579 52.381 6.89 0.00 40.96 4.63
6229 7647 4.511786 TCGTTAATGGAAATGGGGATGA 57.488 40.909 0.00 0.00 0.00 2.92
6234 7652 5.960113 TGATGTTTCGTTAATGGAAATGGG 58.040 37.500 7.61 0.00 35.97 4.00
6235 7653 7.383572 TGTTTGATGTTTCGTTAATGGAAATGG 59.616 33.333 7.61 0.00 35.97 3.16
6252 7670 2.875933 CGTACTGGTGGTTGTTTGATGT 59.124 45.455 0.00 0.00 0.00 3.06
6266 7684 0.318360 TGTCTGTTCGTGCGTACTGG 60.318 55.000 1.24 0.00 0.00 4.00
6322 7740 7.009179 AGTGTCTGTCCTTTGATTTCATCTA 57.991 36.000 0.00 0.00 0.00 1.98
6334 7752 1.625818 GTGATGGGAGTGTCTGTCCTT 59.374 52.381 0.00 0.00 34.16 3.36
6345 7763 2.113807 TCCTGTGATGAGTGATGGGAG 58.886 52.381 0.00 0.00 0.00 4.30
6346 7764 2.252535 TCCTGTGATGAGTGATGGGA 57.747 50.000 0.00 0.00 0.00 4.37
6359 7777 0.320374 TGGGTAGCGAGTTTCCTGTG 59.680 55.000 0.00 0.00 0.00 3.66
6364 7782 1.000506 TGTGAGTGGGTAGCGAGTTTC 59.999 52.381 0.00 0.00 0.00 2.78
6365 7783 1.045407 TGTGAGTGGGTAGCGAGTTT 58.955 50.000 0.00 0.00 0.00 2.66
6371 7789 1.257743 TCAGAGTGTGAGTGGGTAGC 58.742 55.000 0.00 0.00 0.00 3.58
6475 7898 2.126965 CTCACCGTGACCGTCGAC 60.127 66.667 5.18 5.18 0.00 4.20


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

AutoCloner maintained by Alex Coulton.