Multiple sequence alignment - TraesCS4D01G290400

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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 TraesCS4D01G290400 chr4D 100.000 4851 0 0 1 4851 461493915 461489065 0.000000e+00 8959.0
1 TraesCS4D01G290400 chr4D 92.593 243 15 3 1628 1869 417622900 417623140 3.590000e-91 346.0
2 TraesCS4D01G290400 chr4D 90.909 242 20 2 1630 1870 76023283 76023523 1.680000e-84 324.0
3 TraesCS4D01G290400 chr4A 92.685 2652 166 20 2208 4851 7165909 7168540 0.000000e+00 3797.0
4 TraesCS4D01G290400 chr4A 93.391 1498 55 13 99 1581 7164014 7165482 0.000000e+00 2178.0
5 TraesCS4D01G290400 chr4A 93.822 259 13 2 1865 2122 7165560 7165816 2.120000e-103 387.0
6 TraesCS4D01G290400 chr4A 90.741 108 9 1 1 107 7163357 7163464 5.060000e-30 143.0
7 TraesCS4D01G290400 chr4A 87.500 80 9 1 1554 1632 7165485 7165564 1.860000e-14 91.6
8 TraesCS4D01G290400 chr4B 91.554 2510 168 31 2356 4851 577002131 576999652 0.000000e+00 3421.0
9 TraesCS4D01G290400 chr4B 95.270 909 37 6 730 1632 577003463 577002555 0.000000e+00 1435.0
10 TraesCS4D01G290400 chr4B 92.975 726 45 5 1 725 577005649 577004929 0.000000e+00 1053.0
11 TraesCS4D01G290400 chr4B 94.253 261 14 1 1865 2125 577002559 577002300 9.780000e-107 398.0
12 TraesCS4D01G290400 chr5D 92.562 242 14 3 1633 1870 525668102 525667861 1.290000e-90 344.0
13 TraesCS4D01G290400 chr7D 92.469 239 18 0 1630 1868 614375904 614376142 4.650000e-90 342.0
14 TraesCS4D01G290400 chr7D 82.123 179 30 2 556 732 566135311 566135133 8.410000e-33 152.0
15 TraesCS4D01G290400 chr7D 82.500 80 14 0 472 551 4583890 4583811 2.420000e-08 71.3
16 TraesCS4D01G290400 chr2D 92.373 236 18 0 1630 1865 589493914 589494149 2.160000e-88 337.0
17 TraesCS4D01G290400 chr6D 91.093 247 20 2 1625 1870 91083566 91083811 2.800000e-87 333.0
18 TraesCS4D01G290400 chr1A 91.632 239 20 0 1630 1868 352138382 352138144 1.010000e-86 331.0
19 TraesCS4D01G290400 chr1A 90.795 239 22 0 1630 1868 500078725 500078963 2.180000e-83 320.0
20 TraesCS4D01G290400 chr1A 76.015 271 56 9 469 734 519270387 519270121 1.100000e-26 132.0
21 TraesCS4D01G290400 chr3D 90.833 240 19 3 1630 1868 54369198 54368961 7.840000e-83 318.0
22 TraesCS4D01G290400 chr3D 82.576 132 20 3 591 722 563049668 563049540 3.970000e-21 113.0
23 TraesCS4D01G290400 chr3D 83.117 77 10 3 473 547 49488487 49488412 3.130000e-07 67.6
24 TraesCS4D01G290400 chr7A 83.688 141 21 2 556 694 652492502 652492362 1.100000e-26 132.0
25 TraesCS4D01G290400 chr7A 82.955 88 10 5 471 556 204635920 204636004 1.870000e-09 75.0
26 TraesCS4D01G290400 chr7A 82.432 74 7 5 471 540 393762367 393762296 5.240000e-05 60.2
27 TraesCS4D01G290400 chr1D 75.926 270 57 8 469 734 423268629 423268364 1.100000e-26 132.0
28 TraesCS4D01G290400 chr1D 84.259 108 16 1 355 461 106421763 106421870 2.390000e-18 104.0
29 TraesCS4D01G290400 chr7B 80.663 181 23 7 556 732 617818402 617818230 3.940000e-26 130.0
30 TraesCS4D01G290400 chr3A 81.818 132 21 3 591 722 697872378 697872250 1.850000e-19 108.0
31 TraesCS4D01G290400 chr6A 84.848 66 7 3 470 534 7191424 7191361 4.050000e-06 63.9
32 TraesCS4D01G290400 chr5B 82.432 74 10 2 468 540 263518968 263518897 1.460000e-05 62.1
33 TraesCS4D01G290400 chr5A 81.081 74 11 2 468 540 313877033 313876962 6.780000e-04 56.5


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 TraesCS4D01G290400 chr4D 461489065 461493915 4850 True 8959.00 8959 100.0000 1 4851 1 chr4D.!!$R1 4850
1 TraesCS4D01G290400 chr4A 7163357 7168540 5183 False 1319.32 3797 91.6278 1 4851 5 chr4A.!!$F1 4850
2 TraesCS4D01G290400 chr4B 576999652 577005649 5997 True 1576.75 3421 93.5130 1 4851 4 chr4B.!!$R1 4850

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
759 2788 1.041447 CGTTGTAGGGACCTCGGGAT 61.041 60.000 0.00 0.00 0.00 3.85 F
1921 3997 0.108329 TTCCCGAGCTGATTCGAACC 60.108 55.000 0.00 0.00 43.03 3.62 F
2183 4259 0.034186 TGCCAGGGAAGTAGCAATGG 60.034 55.000 0.00 0.00 30.97 3.16 F
2184 4260 1.387295 GCCAGGGAAGTAGCAATGGC 61.387 60.000 0.00 0.00 45.61 4.40 F
2189 4265 1.410153 GGGAAGTAGCAATGGCATTGG 59.590 52.381 34.19 19.82 44.61 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 4240 0.034186 CCATTGCTACTTCCCTGGCA 60.034 55.000 0.00 0.00 0.00 4.92 R
3601 5698 0.460311 GCATGTAGCAGTACGGAGGT 59.540 55.000 0.00 0.00 44.79 3.85 R
3814 5911 1.702401 TCCATAGTGTTGGCTTGGACA 59.298 47.619 0.00 0.00 36.66 4.02 R
3838 5935 3.566322 CGTCATGGGTTTAACCTGTTTCA 59.434 43.478 14.27 3.34 38.64 2.69 R
4180 6279 5.779241 TCCCACATGGAAGAGAGTAAAAT 57.221 39.130 0.00 0.00 41.40 1.82 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
77 78 8.730680 GGATTTTGCTAACAATAGAAGAACTGA 58.269 33.333 0.00 0.00 35.21 3.41
86 87 6.407202 ACAATAGAAGAACTGACCCATGTAC 58.593 40.000 0.00 0.00 0.00 2.90
132 692 3.310774 CGGGAGATAGCATCAGTTTTGTG 59.689 47.826 0.00 0.00 0.00 3.33
133 693 3.629398 GGGAGATAGCATCAGTTTTGTGG 59.371 47.826 0.00 0.00 0.00 4.17
134 694 4.265073 GGAGATAGCATCAGTTTTGTGGT 58.735 43.478 0.00 0.00 0.00 4.16
135 695 4.333926 GGAGATAGCATCAGTTTTGTGGTC 59.666 45.833 0.00 0.00 0.00 4.02
136 696 4.910195 AGATAGCATCAGTTTTGTGGTCA 58.090 39.130 0.00 0.00 0.00 4.02
188 748 2.423947 GGTTGGGAGATGCATGAAGGAT 60.424 50.000 2.46 0.00 0.00 3.24
206 766 8.818141 TGAAGGATACATAAGATCGAATCAAC 57.182 34.615 0.00 0.00 41.41 3.18
285 845 1.620819 GATCCCTGACATATCTGCGGT 59.379 52.381 0.00 0.00 0.00 5.68
340 901 2.117206 GTGCCCCCACAATCACCA 59.883 61.111 0.00 0.00 41.67 4.17
491 1052 1.076024 AGGTCCACCTCAACATGCAAT 59.924 47.619 0.00 0.00 44.77 3.56
516 1077 1.399440 CATGGAGCAAAGATCACCACG 59.601 52.381 0.00 0.00 33.38 4.94
527 1088 2.093288 AGATCACCACGACATGCAATCT 60.093 45.455 0.00 0.00 0.00 2.40
700 1261 6.780457 ATTACAAGCAATTCCTGTAGCAAT 57.220 33.333 0.00 0.00 0.00 3.56
725 1286 5.501156 CTTGGGCTATCACCTAGTTCTTTT 58.499 41.667 0.00 0.00 0.00 2.27
727 1288 6.824958 TGGGCTATCACCTAGTTCTTTTAT 57.175 37.500 0.00 0.00 0.00 1.40
728 1289 7.208064 TGGGCTATCACCTAGTTCTTTTATT 57.792 36.000 0.00 0.00 0.00 1.40
729 1290 7.639378 TGGGCTATCACCTAGTTCTTTTATTT 58.361 34.615 0.00 0.00 0.00 1.40
730 1291 8.113462 TGGGCTATCACCTAGTTCTTTTATTTT 58.887 33.333 0.00 0.00 0.00 1.82
731 1292 8.967918 GGGCTATCACCTAGTTCTTTTATTTTT 58.032 33.333 0.00 0.00 0.00 1.94
759 2788 1.041447 CGTTGTAGGGACCTCGGGAT 61.041 60.000 0.00 0.00 0.00 3.85
846 2875 8.734386 GGACATGATCAAGAAAATTAGTCTGTT 58.266 33.333 4.68 0.00 0.00 3.16
927 2966 2.167281 GCAGATAGAGCCTTGAGTGACA 59.833 50.000 0.00 0.00 0.00 3.58
950 2990 9.606631 GACATCTGTTCCCTTTCCATATATATC 57.393 37.037 0.00 0.00 0.00 1.63
981 3021 4.767928 AGTACACAACAACCAAACCTCAAA 59.232 37.500 0.00 0.00 0.00 2.69
1167 3207 4.742649 TCTCTCCTCCGCGCCTGT 62.743 66.667 0.00 0.00 0.00 4.00
1195 3235 0.601576 CACCGACGACCAATGGTTCA 60.602 55.000 6.30 0.00 35.25 3.18
1324 3364 1.989165 GACTCATCTTGACGCAGACAC 59.011 52.381 0.00 0.00 0.00 3.67
1503 3543 0.957395 GGGTCGGTCGTGACTCTGTA 60.957 60.000 0.00 0.00 36.39 2.74
1518 3558 5.217978 ACTCTGTAACGGTATGGACAAAA 57.782 39.130 0.00 0.00 0.00 2.44
1634 3709 9.535878 CAAGAAGAAACCTATATGAAGTACTCC 57.464 37.037 0.00 0.00 0.00 3.85
1635 3710 8.252624 AGAAGAAACCTATATGAAGTACTCCC 57.747 38.462 0.00 0.00 0.00 4.30
1636 3711 8.068733 AGAAGAAACCTATATGAAGTACTCCCT 58.931 37.037 0.00 0.00 0.00 4.20
1637 3712 7.842887 AGAAACCTATATGAAGTACTCCCTC 57.157 40.000 0.00 0.00 0.00 4.30
1638 3713 6.783482 AGAAACCTATATGAAGTACTCCCTCC 59.217 42.308 0.00 0.00 0.00 4.30
1639 3714 4.664392 ACCTATATGAAGTACTCCCTCCG 58.336 47.826 0.00 0.00 0.00 4.63
1640 3715 4.106019 ACCTATATGAAGTACTCCCTCCGT 59.894 45.833 0.00 0.00 0.00 4.69
1641 3716 4.701171 CCTATATGAAGTACTCCCTCCGTC 59.299 50.000 0.00 0.00 0.00 4.79
1642 3717 1.777941 ATGAAGTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
1643 3718 0.679002 TGAAGTACTCCCTCCGTCCG 60.679 60.000 0.00 0.00 0.00 4.79
1644 3719 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
1645 3720 2.832201 GTACTCCCTCCGTCCGGG 60.832 72.222 0.00 0.00 43.38 5.73
1646 3721 3.341629 TACTCCCTCCGTCCGGGT 61.342 66.667 0.00 0.00 42.56 5.28
1647 3722 2.922704 TACTCCCTCCGTCCGGGTT 61.923 63.158 0.00 0.00 42.56 4.11
1648 3723 2.445492 TACTCCCTCCGTCCGGGTTT 62.445 60.000 0.00 0.00 42.56 3.27
1649 3724 1.683365 CTCCCTCCGTCCGGGTTTA 60.683 63.158 0.00 0.00 42.56 2.01
1650 3725 1.002017 TCCCTCCGTCCGGGTTTAT 59.998 57.895 0.00 0.00 42.56 1.40
1651 3726 0.618393 TCCCTCCGTCCGGGTTTATT 60.618 55.000 0.00 0.00 42.56 1.40
1652 3727 1.122227 CCCTCCGTCCGGGTTTATTA 58.878 55.000 0.00 0.00 36.91 0.98
1653 3728 1.485895 CCCTCCGTCCGGGTTTATTAA 59.514 52.381 0.00 0.00 36.91 1.40
1654 3729 2.484241 CCCTCCGTCCGGGTTTATTAAG 60.484 54.545 0.00 0.00 36.91 1.85
1655 3730 2.484241 CCTCCGTCCGGGTTTATTAAGG 60.484 54.545 0.00 0.00 37.00 2.69
1656 3731 1.134431 TCCGTCCGGGTTTATTAAGGC 60.134 52.381 0.00 0.00 37.00 4.35
1657 3732 1.302366 CGTCCGGGTTTATTAAGGCC 58.698 55.000 0.00 0.00 0.00 5.19
1658 3733 1.683943 GTCCGGGTTTATTAAGGCCC 58.316 55.000 0.00 7.65 37.79 5.80
1659 3734 0.552363 TCCGGGTTTATTAAGGCCCC 59.448 55.000 0.00 0.00 37.89 5.80
1660 3735 0.554305 CCGGGTTTATTAAGGCCCCT 59.446 55.000 0.00 0.00 37.89 4.79
1661 3736 1.063492 CCGGGTTTATTAAGGCCCCTT 60.063 52.381 0.00 4.77 37.89 3.95
1662 3737 2.624822 CCGGGTTTATTAAGGCCCCTTT 60.625 50.000 4.68 0.00 37.89 3.11
1663 3738 2.691526 CGGGTTTATTAAGGCCCCTTTC 59.308 50.000 4.68 0.00 37.89 2.62
1664 3739 3.715287 GGGTTTATTAAGGCCCCTTTCA 58.285 45.455 4.68 0.00 37.47 2.69
1665 3740 4.295201 GGGTTTATTAAGGCCCCTTTCAT 58.705 43.478 4.68 1.40 37.47 2.57
1666 3741 4.719773 GGGTTTATTAAGGCCCCTTTCATT 59.280 41.667 4.68 0.00 37.47 2.57
1667 3742 5.190925 GGGTTTATTAAGGCCCCTTTCATTT 59.809 40.000 4.68 0.00 37.47 2.32
1668 3743 6.296778 GGGTTTATTAAGGCCCCTTTCATTTT 60.297 38.462 4.68 0.00 37.47 1.82
1669 3744 6.597672 GGTTTATTAAGGCCCCTTTCATTTTG 59.402 38.462 4.68 0.00 37.47 2.44
1670 3745 7.390823 GTTTATTAAGGCCCCTTTCATTTTGA 58.609 34.615 4.68 0.00 37.47 2.69
1671 3746 5.682234 ATTAAGGCCCCTTTCATTTTGAG 57.318 39.130 4.68 0.00 37.47 3.02
1672 3747 2.999185 AGGCCCCTTTCATTTTGAGA 57.001 45.000 0.00 0.00 0.00 3.27
1673 3748 2.529632 AGGCCCCTTTCATTTTGAGAC 58.470 47.619 0.00 0.00 0.00 3.36
1674 3749 2.158325 AGGCCCCTTTCATTTTGAGACA 60.158 45.455 0.00 0.00 0.00 3.41
1675 3750 2.632512 GGCCCCTTTCATTTTGAGACAA 59.367 45.455 0.00 0.00 0.00 3.18
1676 3751 3.070878 GGCCCCTTTCATTTTGAGACAAA 59.929 43.478 0.00 0.00 0.00 2.83
1677 3752 4.309933 GCCCCTTTCATTTTGAGACAAAG 58.690 43.478 0.00 0.00 0.00 2.77
1678 3753 4.202253 GCCCCTTTCATTTTGAGACAAAGT 60.202 41.667 0.00 0.00 0.00 2.66
1679 3754 5.684813 GCCCCTTTCATTTTGAGACAAAGTT 60.685 40.000 0.00 0.00 0.00 2.66
1680 3755 6.348498 CCCCTTTCATTTTGAGACAAAGTTT 58.652 36.000 0.00 0.00 0.00 2.66
1681 3756 6.258507 CCCCTTTCATTTTGAGACAAAGTTTG 59.741 38.462 14.13 14.13 0.00 2.93
1682 3757 7.041107 CCCTTTCATTTTGAGACAAAGTTTGA 58.959 34.615 22.23 0.00 0.00 2.69
1683 3758 7.010460 CCCTTTCATTTTGAGACAAAGTTTGAC 59.990 37.037 22.23 15.71 0.00 3.18
1684 3759 7.010460 CCTTTCATTTTGAGACAAAGTTTGACC 59.990 37.037 22.23 12.55 0.00 4.02
1685 3760 6.522625 TCATTTTGAGACAAAGTTTGACCA 57.477 33.333 22.23 12.51 0.00 4.02
1686 3761 7.111247 TCATTTTGAGACAAAGTTTGACCAT 57.889 32.000 22.23 1.13 0.00 3.55
1687 3762 6.979817 TCATTTTGAGACAAAGTTTGACCATG 59.020 34.615 22.23 12.05 0.00 3.66
1688 3763 6.522625 TTTTGAGACAAAGTTTGACCATGA 57.477 33.333 22.23 6.03 0.00 3.07
1689 3764 6.522625 TTTGAGACAAAGTTTGACCATGAA 57.477 33.333 22.23 6.76 0.00 2.57
1690 3765 6.713762 TTGAGACAAAGTTTGACCATGAAT 57.286 33.333 22.23 0.00 0.00 2.57
1691 3766 6.713762 TGAGACAAAGTTTGACCATGAATT 57.286 33.333 22.23 0.00 0.00 2.17
1692 3767 7.111247 TGAGACAAAGTTTGACCATGAATTT 57.889 32.000 22.23 0.00 0.00 1.82
1693 3768 8.231692 TGAGACAAAGTTTGACCATGAATTTA 57.768 30.769 22.23 0.00 0.00 1.40
1694 3769 8.690884 TGAGACAAAGTTTGACCATGAATTTAA 58.309 29.630 22.23 0.00 0.00 1.52
1695 3770 8.871686 AGACAAAGTTTGACCATGAATTTAAC 57.128 30.769 22.23 0.00 0.00 2.01
1696 3771 8.695456 AGACAAAGTTTGACCATGAATTTAACT 58.305 29.630 22.23 0.00 0.00 2.24
1697 3772 9.959749 GACAAAGTTTGACCATGAATTTAACTA 57.040 29.630 22.23 0.00 0.00 2.24
1740 3815 9.661563 ATGTCACGAAAACTATACCATAGAAAA 57.338 29.630 0.00 0.00 0.00 2.29
1741 3816 8.928733 TGTCACGAAAACTATACCATAGAAAAC 58.071 33.333 0.00 0.00 0.00 2.43
1742 3817 8.385858 GTCACGAAAACTATACCATAGAAAACC 58.614 37.037 0.00 0.00 0.00 3.27
1743 3818 8.316214 TCACGAAAACTATACCATAGAAAACCT 58.684 33.333 0.00 0.00 0.00 3.50
1744 3819 8.601476 CACGAAAACTATACCATAGAAAACCTC 58.399 37.037 0.00 0.00 0.00 3.85
1745 3820 8.537858 ACGAAAACTATACCATAGAAAACCTCT 58.462 33.333 0.00 0.00 38.28 3.69
1746 3821 9.379791 CGAAAACTATACCATAGAAAACCTCTT 57.620 33.333 0.30 0.00 35.41 2.85
1755 3830 8.934023 ACCATAGAAAACCTCTTTCAAATACA 57.066 30.769 0.52 0.00 35.41 2.29
1756 3831 9.362151 ACCATAGAAAACCTCTTTCAAATACAA 57.638 29.630 0.52 0.00 35.41 2.41
1761 3836 8.923270 AGAAAACCTCTTTCAAATACAAATCCA 58.077 29.630 0.52 0.00 0.00 3.41
1762 3837 9.541143 GAAAACCTCTTTCAAATACAAATCCAA 57.459 29.630 0.00 0.00 0.00 3.53
1763 3838 8.887036 AAACCTCTTTCAAATACAAATCCAAC 57.113 30.769 0.00 0.00 0.00 3.77
1764 3839 7.595819 ACCTCTTTCAAATACAAATCCAACA 57.404 32.000 0.00 0.00 0.00 3.33
1765 3840 8.017418 ACCTCTTTCAAATACAAATCCAACAA 57.983 30.769 0.00 0.00 0.00 2.83
1766 3841 8.650490 ACCTCTTTCAAATACAAATCCAACAAT 58.350 29.630 0.00 0.00 0.00 2.71
1777 3852 7.790782 ACAAATCCAACAATATACTTTGGGT 57.209 32.000 9.09 1.35 40.31 4.51
1778 3853 8.887264 ACAAATCCAACAATATACTTTGGGTA 57.113 30.769 9.09 0.00 40.31 3.69
1779 3854 8.966868 ACAAATCCAACAATATACTTTGGGTAG 58.033 33.333 9.09 3.53 40.31 3.18
1780 3855 7.582667 AATCCAACAATATACTTTGGGTAGC 57.417 36.000 9.09 0.00 40.31 3.58
1781 3856 6.068461 TCCAACAATATACTTTGGGTAGCA 57.932 37.500 9.09 0.00 40.31 3.49
1782 3857 6.668645 TCCAACAATATACTTTGGGTAGCAT 58.331 36.000 9.09 0.00 40.31 3.79
1783 3858 7.807198 TCCAACAATATACTTTGGGTAGCATA 58.193 34.615 9.09 0.00 40.31 3.14
1784 3859 8.444783 TCCAACAATATACTTTGGGTAGCATAT 58.555 33.333 9.09 0.00 40.31 1.78
1785 3860 8.514594 CCAACAATATACTTTGGGTAGCATATG 58.485 37.037 0.00 0.00 36.84 1.78
1786 3861 7.687941 ACAATATACTTTGGGTAGCATATGC 57.312 36.000 20.36 20.36 42.49 3.14
1839 3914 9.244799 GTCAAACTTAGACCCAAAATACAAAAG 57.755 33.333 0.00 0.00 0.00 2.27
1840 3915 8.417884 TCAAACTTAGACCCAAAATACAAAAGG 58.582 33.333 0.00 0.00 0.00 3.11
1841 3916 6.911250 ACTTAGACCCAAAATACAAAAGGG 57.089 37.500 0.00 0.00 45.20 3.95
1842 3917 5.245301 ACTTAGACCCAAAATACAAAAGGGC 59.755 40.000 0.00 0.00 43.47 5.19
1843 3918 2.903784 AGACCCAAAATACAAAAGGGCC 59.096 45.455 0.00 0.00 43.47 5.80
1844 3919 2.903784 GACCCAAAATACAAAAGGGCCT 59.096 45.455 0.00 0.00 43.47 5.19
1845 3920 4.090819 GACCCAAAATACAAAAGGGCCTA 58.909 43.478 6.41 0.00 43.47 3.93
1846 3921 4.494591 ACCCAAAATACAAAAGGGCCTAA 58.505 39.130 6.41 0.00 43.47 2.69
1847 3922 5.097948 ACCCAAAATACAAAAGGGCCTAAT 58.902 37.500 6.41 0.00 43.47 1.73
1848 3923 6.265304 ACCCAAAATACAAAAGGGCCTAATA 58.735 36.000 6.41 0.00 43.47 0.98
1849 3924 6.731448 ACCCAAAATACAAAAGGGCCTAATAA 59.269 34.615 6.41 0.00 43.47 1.40
1850 3925 7.237887 ACCCAAAATACAAAAGGGCCTAATAAA 59.762 33.333 6.41 0.00 43.47 1.40
1851 3926 7.551262 CCCAAAATACAAAAGGGCCTAATAAAC 59.449 37.037 6.41 0.00 31.81 2.01
1852 3927 7.551262 CCAAAATACAAAAGGGCCTAATAAACC 59.449 37.037 6.41 0.00 0.00 3.27
1853 3928 6.801718 AATACAAAAGGGCCTAATAAACCC 57.198 37.500 6.41 0.00 44.62 4.11
1857 3932 3.409201 GGGCCTAATAAACCCGGAC 57.591 57.895 0.73 0.00 32.92 4.79
1858 3933 0.533531 GGGCCTAATAAACCCGGACG 60.534 60.000 0.73 0.00 32.92 4.79
1859 3934 0.465287 GGCCTAATAAACCCGGACGA 59.535 55.000 0.73 0.00 0.00 4.20
1860 3935 1.134431 GGCCTAATAAACCCGGACGAA 60.134 52.381 0.73 0.00 0.00 3.85
1861 3936 2.207590 GCCTAATAAACCCGGACGAAG 58.792 52.381 0.73 0.00 0.00 3.79
1862 3937 2.830104 CCTAATAAACCCGGACGAAGG 58.170 52.381 0.73 0.00 0.00 3.46
1863 3938 2.169144 CCTAATAAACCCGGACGAAGGT 59.831 50.000 0.73 0.00 38.27 3.50
1917 3993 1.331756 CCATTTTCCCGAGCTGATTCG 59.668 52.381 0.00 0.00 40.18 3.34
1921 3997 0.108329 TTCCCGAGCTGATTCGAACC 60.108 55.000 0.00 0.00 43.03 3.62
2063 4139 5.268387 AGAGTATTCTTCTCTGAGCTTCCA 58.732 41.667 0.00 0.00 40.26 3.53
2102 4178 3.269381 TGGCATTACAAAGAGGAAGGGAT 59.731 43.478 0.00 0.00 0.00 3.85
2137 4213 9.771534 CTCCTTAGGTTATTTATTCTTCTCTGG 57.228 37.037 0.00 0.00 0.00 3.86
2138 4214 9.502035 TCCTTAGGTTATTTATTCTTCTCTGGA 57.498 33.333 0.00 0.00 0.00 3.86
2154 4230 8.700051 TCTTCTCTGGAGTAGATATTTTTCTGG 58.300 37.037 3.40 0.00 34.21 3.86
2155 4231 8.609617 TTCTCTGGAGTAGATATTTTTCTGGA 57.390 34.615 0.00 0.00 34.21 3.86
2157 4233 8.700051 TCTCTGGAGTAGATATTTTTCTGGAAG 58.300 37.037 0.00 0.00 34.21 3.46
2159 4235 9.488762 TCTGGAGTAGATATTTTTCTGGAAGTA 57.511 33.333 0.00 0.00 33.76 2.24
2161 4237 9.488762 TGGAGTAGATATTTTTCTGGAAGTAGA 57.511 33.333 0.00 0.00 33.76 2.59
2167 4243 8.907885 AGATATTTTTCTGGAAGTAGAAATGCC 58.092 33.333 0.00 0.00 43.84 4.40
2168 4244 6.916360 ATTTTTCTGGAAGTAGAAATGCCA 57.084 33.333 0.00 0.00 43.84 4.92
2169 4245 5.964958 TTTTCTGGAAGTAGAAATGCCAG 57.035 39.130 0.00 0.00 43.84 4.85
2170 4246 3.634397 TCTGGAAGTAGAAATGCCAGG 57.366 47.619 0.00 0.00 44.78 4.45
2172 4248 2.239654 CTGGAAGTAGAAATGCCAGGGA 59.760 50.000 0.00 0.00 41.81 4.20
2173 4249 2.647299 TGGAAGTAGAAATGCCAGGGAA 59.353 45.455 0.00 0.00 0.00 3.97
2174 4250 3.282885 GGAAGTAGAAATGCCAGGGAAG 58.717 50.000 0.00 0.00 0.00 3.46
2175 4251 3.308473 GGAAGTAGAAATGCCAGGGAAGT 60.308 47.826 0.00 0.00 0.00 3.01
2177 4253 4.762289 AGTAGAAATGCCAGGGAAGTAG 57.238 45.455 0.00 0.00 0.00 2.57
2178 4254 2.426842 AGAAATGCCAGGGAAGTAGC 57.573 50.000 0.00 0.00 0.00 3.58
2183 4259 0.034186 TGCCAGGGAAGTAGCAATGG 60.034 55.000 0.00 0.00 30.97 3.16
2184 4260 1.387295 GCCAGGGAAGTAGCAATGGC 61.387 60.000 0.00 0.00 45.61 4.40
2186 4262 1.410648 CCAGGGAAGTAGCAATGGCAT 60.411 52.381 0.00 0.00 44.61 4.40
2188 4264 2.100252 CAGGGAAGTAGCAATGGCATTG 59.900 50.000 30.96 30.96 44.61 2.82
2189 4265 1.410153 GGGAAGTAGCAATGGCATTGG 59.590 52.381 34.19 19.82 44.61 3.16
2193 4269 4.427312 GAAGTAGCAATGGCATTGGAAAG 58.573 43.478 34.19 14.85 44.61 2.62
2194 4270 3.434309 AGTAGCAATGGCATTGGAAAGT 58.566 40.909 34.19 11.99 44.61 2.66
2196 4272 4.641989 AGTAGCAATGGCATTGGAAAGTAG 59.358 41.667 34.19 12.85 44.61 2.57
2197 4273 3.700538 AGCAATGGCATTGGAAAGTAGA 58.299 40.909 34.19 0.00 44.61 2.59
2198 4274 3.445096 AGCAATGGCATTGGAAAGTAGAC 59.555 43.478 34.19 18.12 44.61 2.59
2203 4296 5.860941 TGGCATTGGAAAGTAGACAAAAA 57.139 34.783 0.00 0.00 0.00 1.94
2278 4371 5.073311 AGAGTAAAAGCAAGCACTCGATA 57.927 39.130 0.00 0.00 41.80 2.92
2290 4383 2.159476 GCACTCGATAACTGGTCGTGTA 60.159 50.000 3.43 0.00 41.92 2.90
2324 4417 7.610865 ACAACGAAAATGATGAAAATACCCAT 58.389 30.769 0.00 0.00 0.00 4.00
2432 4525 6.208599 AGCATACTAGCTCCTTAAGAGATGAC 59.791 42.308 3.36 0.00 46.50 3.06
2480 4573 6.613153 AAGGCTAGAGGGTCAATATGATAC 57.387 41.667 0.00 0.00 0.00 2.24
2541 4638 6.317140 CACAAGGTGATGCAATACACTTCTAT 59.683 38.462 17.07 2.45 35.23 1.98
2765 4862 4.326826 CCAAGAGTCAGCTACCATCAAAA 58.673 43.478 0.00 0.00 0.00 2.44
3002 5099 2.529744 GGTGCCCACTCCCTCACTT 61.530 63.158 0.00 0.00 0.00 3.16
3023 5120 2.217750 TGGAAGACATTGTGGACAACG 58.782 47.619 0.00 0.00 38.86 4.10
3094 5191 3.226777 CTTCATGATCCGGTACCTCTCT 58.773 50.000 10.90 0.00 0.00 3.10
3096 5193 4.022413 TCATGATCCGGTACCTCTCTAG 57.978 50.000 10.90 0.00 0.00 2.43
3174 5271 7.579589 TTTGCTTCCATATTTGATTCAAACG 57.420 32.000 13.80 6.11 36.13 3.60
3209 5306 9.967451 TTCTTCTACACCATGGAAATTAATGTA 57.033 29.630 21.47 13.39 0.00 2.29
3269 5366 6.029346 AGATTGCACAGAATAAAAACCCAG 57.971 37.500 0.00 0.00 0.00 4.45
3290 5387 5.055812 CAGAAGATGCTCTAACTTGGGATC 58.944 45.833 0.00 0.00 0.00 3.36
3385 5482 3.751698 GCTTCCGAACAACTACCAAAGAT 59.248 43.478 0.00 0.00 0.00 2.40
3435 5532 6.381801 CAAAAGGCTGGAAAGTAAGTACATG 58.618 40.000 0.00 0.00 0.00 3.21
3440 5537 5.404946 GCTGGAAAGTAAGTACATGTACGA 58.595 41.667 26.17 17.42 40.80 3.43
3488 5585 2.032302 CGTCCCGAGAACTCTATCACAG 59.968 54.545 0.41 0.00 0.00 3.66
3500 5597 9.244292 AGAACTCTATCACAGACAAGTAACATA 57.756 33.333 0.00 0.00 0.00 2.29
3501 5598 9.856488 GAACTCTATCACAGACAAGTAACATAA 57.144 33.333 0.00 0.00 0.00 1.90
3502 5599 9.862371 AACTCTATCACAGACAAGTAACATAAG 57.138 33.333 0.00 0.00 0.00 1.73
3601 5698 3.616284 TCGGTTTGAGAAATCCGCA 57.384 47.368 3.63 0.00 42.28 5.69
3661 5758 1.904287 TGTGCCCTGGTAATGTGTTC 58.096 50.000 0.00 0.00 0.00 3.18
3814 5911 2.368548 GTTGAGACCCCTTGCCAAAAAT 59.631 45.455 0.00 0.00 0.00 1.82
3838 5935 3.780294 TCCAAGCCAACACTATGGATACT 59.220 43.478 0.00 0.00 43.54 2.12
3860 5957 3.566322 TGAAACAGGTTAAACCCATGACG 59.434 43.478 0.00 0.00 39.75 4.35
3963 6060 1.382522 AAGGCACGCTATTCCATGTG 58.617 50.000 0.00 0.00 35.48 3.21
3964 6061 0.253044 AGGCACGCTATTCCATGTGT 59.747 50.000 0.00 0.00 34.86 3.72
4024 6121 7.246171 ACAATGTAAAGATGTGTCTCCTACT 57.754 36.000 0.00 0.00 32.15 2.57
4220 6319 5.365605 TGTGGGACCTAGTCGATGATAAAAT 59.634 40.000 0.00 0.00 32.65 1.82
4257 6356 2.037772 CTGGATGGAAGGGTCGGATTAG 59.962 54.545 0.00 0.00 0.00 1.73
4298 6397 3.190118 GGAGTGCTCTTTCCATTGAACTG 59.810 47.826 0.00 0.00 33.55 3.16
4318 6417 2.336554 CGCTAAGCACTGCACAAAAT 57.663 45.000 3.30 0.00 0.00 1.82
4319 6418 3.469899 CGCTAAGCACTGCACAAAATA 57.530 42.857 3.30 0.00 0.00 1.40
4349 6448 3.318275 CCTGGCAAAGAAGATCATCCATG 59.682 47.826 0.00 0.00 0.00 3.66
4376 6475 0.250467 AGAGGCGTGTGCTTGAATGT 60.250 50.000 0.00 0.00 42.25 2.71
4401 6500 0.884704 CCCCGAATGCCTTGATACCG 60.885 60.000 0.00 0.00 0.00 4.02
4404 6503 1.502231 CGAATGCCTTGATACCGAGG 58.498 55.000 0.00 0.00 45.23 4.63
4409 6508 0.466124 GCCTTGATACCGAGGAAGCT 59.534 55.000 0.00 0.00 45.27 3.74
4413 6512 3.574396 CCTTGATACCGAGGAAGCTATGA 59.426 47.826 0.00 0.00 45.27 2.15
4538 6641 9.073475 AGATAAGAAGATGTACATGGTACTCTC 57.927 37.037 14.43 3.05 0.00 3.20
4603 6706 0.752658 TCATCCTACGCACTCCATGG 59.247 55.000 4.97 4.97 0.00 3.66
4634 6737 7.036154 TGGATTAATCTTGGGATGCAGATAT 57.964 36.000 14.95 0.00 31.75 1.63
4738 6842 7.471890 TGGGGACTAACCAACTAATAAATGTT 58.528 34.615 0.00 0.00 41.20 2.71
4739 6843 7.394923 TGGGGACTAACCAACTAATAAATGTTG 59.605 37.037 0.00 0.00 42.05 3.33
4808 6914 3.649023 TGGTACCAACTGTCCAAGTACAT 59.351 43.478 13.60 0.00 38.56 2.29
4811 6917 4.640771 ACCAACTGTCCAAGTACATGAT 57.359 40.909 0.00 0.00 38.56 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.890489 CATCCATGTGGGCATATGGTG 59.110 52.381 4.56 0.00 46.39 4.17
71 72 1.906574 TCTGGGTACATGGGTCAGTTC 59.093 52.381 0.00 0.00 0.00 3.01
77 78 0.118346 TGGAGTCTGGGTACATGGGT 59.882 55.000 0.00 0.00 0.00 4.51
86 87 5.178797 CAAAACACTAGTATGGAGTCTGGG 58.821 45.833 0.00 0.00 0.00 4.45
132 692 4.284378 GCTTTTGCTGATATGACTGACC 57.716 45.455 0.00 0.00 43.35 4.02
257 817 6.939163 GCAGATATGTCAGGGATCAAAATAGT 59.061 38.462 0.00 0.00 0.00 2.12
285 845 0.253894 TCTCCTATCCACGGACACGA 59.746 55.000 0.00 0.00 44.60 4.35
340 901 7.356680 TGAATTTGAGGATTTGGATATGAGGT 58.643 34.615 0.00 0.00 0.00 3.85
508 1069 2.408271 AGATTGCATGTCGTGGTGAT 57.592 45.000 0.00 0.00 0.00 3.06
700 1261 1.879575 ACTAGGTGATAGCCCAAGCA 58.120 50.000 0.00 0.00 43.56 3.91
727 1288 7.449086 AGGTCCCTACAACGATATTTTGAAAAA 59.551 33.333 0.00 0.00 0.00 1.94
728 1289 6.943718 AGGTCCCTACAACGATATTTTGAAAA 59.056 34.615 0.00 0.00 0.00 2.29
729 1290 6.478129 AGGTCCCTACAACGATATTTTGAAA 58.522 36.000 0.00 0.00 0.00 2.69
730 1291 6.057321 AGGTCCCTACAACGATATTTTGAA 57.943 37.500 0.00 0.00 0.00 2.69
731 1292 5.667466 GAGGTCCCTACAACGATATTTTGA 58.333 41.667 0.00 0.00 0.00 2.69
732 1293 4.506654 CGAGGTCCCTACAACGATATTTTG 59.493 45.833 0.00 0.00 0.00 2.44
759 2788 1.852157 AAGGAATGCGGCAGGGAAGA 61.852 55.000 9.25 0.00 0.00 2.87
846 2875 6.757947 CGATGGTAAAAGGAATTCCGTTAGTA 59.242 38.462 23.49 12.15 42.08 1.82
847 2876 5.583457 CGATGGTAAAAGGAATTCCGTTAGT 59.417 40.000 23.49 13.07 42.08 2.24
849 2878 5.352016 CACGATGGTAAAAGGAATTCCGTTA 59.648 40.000 23.49 19.22 42.08 3.18
853 2882 3.442273 TGCACGATGGTAAAAGGAATTCC 59.558 43.478 17.31 17.31 0.00 3.01
855 2884 5.461032 TTTGCACGATGGTAAAAGGAATT 57.539 34.783 0.00 0.00 0.00 2.17
856 2885 5.650543 GATTTGCACGATGGTAAAAGGAAT 58.349 37.500 0.00 0.00 0.00 3.01
857 2886 4.378978 CGATTTGCACGATGGTAAAAGGAA 60.379 41.667 0.00 0.00 0.00 3.36
858 2887 3.126171 CGATTTGCACGATGGTAAAAGGA 59.874 43.478 0.00 0.00 0.00 3.36
859 2888 3.119990 ACGATTTGCACGATGGTAAAAGG 60.120 43.478 1.86 0.00 34.70 3.11
860 2889 3.845775 CACGATTTGCACGATGGTAAAAG 59.154 43.478 1.86 0.00 34.70 2.27
927 2966 9.965902 GTTGATATATATGGAAAGGGAACAGAT 57.034 33.333 0.00 0.00 0.00 2.90
950 2990 3.619483 TGGTTGTTGTGTACTCGAAGTTG 59.381 43.478 0.00 0.00 0.00 3.16
969 3009 2.031870 GGTGAAGCTTTGAGGTTTGGT 58.968 47.619 0.00 0.00 35.86 3.67
1133 3173 4.023536 GGAGAGAGAAAGTACTGCCGATAG 60.024 50.000 0.00 0.00 0.00 2.08
1167 3207 4.273257 TCGTCGGTGTTGCTGCGA 62.273 61.111 0.00 0.00 32.56 5.10
1195 3235 3.068307 CCGTATTTCTTGATCCGGTCTCT 59.932 47.826 0.00 0.00 0.00 3.10
1303 3343 1.889170 TGTCTGCGTCAAGATGAGTCT 59.111 47.619 0.00 0.00 35.82 3.24
1503 3543 4.454504 CAGTAAGCTTTTGTCCATACCGTT 59.545 41.667 3.20 0.00 0.00 4.44
1627 3702 2.274760 CCGGACGGAGGGAGTACT 59.725 66.667 4.40 0.00 37.50 2.73
1634 3709 2.484241 CCTTAATAAACCCGGACGGAGG 60.484 54.545 13.13 4.42 37.50 4.30
1635 3710 2.830104 CCTTAATAAACCCGGACGGAG 58.170 52.381 13.13 5.04 37.50 4.63
1636 3711 1.134431 GCCTTAATAAACCCGGACGGA 60.134 52.381 13.13 0.00 37.50 4.69
1637 3712 1.302366 GCCTTAATAAACCCGGACGG 58.698 55.000 0.73 3.25 37.81 4.79
1638 3713 1.302366 GGCCTTAATAAACCCGGACG 58.698 55.000 0.73 0.00 0.00 4.79
1639 3714 1.683943 GGGCCTTAATAAACCCGGAC 58.316 55.000 0.73 0.00 31.32 4.79
1640 3715 0.552363 GGGGCCTTAATAAACCCGGA 59.448 55.000 0.73 0.00 43.82 5.14
1641 3716 0.554305 AGGGGCCTTAATAAACCCGG 59.446 55.000 0.84 0.00 46.10 5.73
1642 3717 2.447408 AAGGGGCCTTAATAAACCCG 57.553 50.000 0.84 0.00 46.10 5.28
1643 3718 3.715287 TGAAAGGGGCCTTAATAAACCC 58.285 45.455 0.84 2.90 42.01 4.11
1644 3719 5.950544 AATGAAAGGGGCCTTAATAAACC 57.049 39.130 0.84 0.00 34.84 3.27
1645 3720 7.390823 TCAAAATGAAAGGGGCCTTAATAAAC 58.609 34.615 0.84 0.00 34.84 2.01
1646 3721 7.456269 TCTCAAAATGAAAGGGGCCTTAATAAA 59.544 33.333 0.84 0.00 34.84 1.40
1647 3722 6.957020 TCTCAAAATGAAAGGGGCCTTAATAA 59.043 34.615 0.84 0.00 34.84 1.40
1648 3723 6.379988 GTCTCAAAATGAAAGGGGCCTTAATA 59.620 38.462 0.84 0.00 34.84 0.98
1649 3724 5.187772 GTCTCAAAATGAAAGGGGCCTTAAT 59.812 40.000 0.84 0.00 34.84 1.40
1650 3725 4.526650 GTCTCAAAATGAAAGGGGCCTTAA 59.473 41.667 0.84 0.00 34.84 1.85
1651 3726 4.086457 GTCTCAAAATGAAAGGGGCCTTA 58.914 43.478 0.84 0.00 34.84 2.69
1652 3727 2.899900 GTCTCAAAATGAAAGGGGCCTT 59.100 45.455 0.84 0.00 37.98 4.35
1653 3728 2.158325 TGTCTCAAAATGAAAGGGGCCT 60.158 45.455 0.84 0.00 0.00 5.19
1654 3729 2.247358 TGTCTCAAAATGAAAGGGGCC 58.753 47.619 0.00 0.00 0.00 5.80
1655 3730 4.202253 ACTTTGTCTCAAAATGAAAGGGGC 60.202 41.667 0.00 0.00 0.00 5.80
1656 3731 5.535753 ACTTTGTCTCAAAATGAAAGGGG 57.464 39.130 0.00 0.00 0.00 4.79
1657 3732 7.010460 GTCAAACTTTGTCTCAAAATGAAAGGG 59.990 37.037 1.44 0.00 0.00 3.95
1658 3733 7.010460 GGTCAAACTTTGTCTCAAAATGAAAGG 59.990 37.037 1.44 0.00 0.00 3.11
1659 3734 7.545265 TGGTCAAACTTTGTCTCAAAATGAAAG 59.455 33.333 1.44 0.00 0.00 2.62
1660 3735 7.382110 TGGTCAAACTTTGTCTCAAAATGAAA 58.618 30.769 1.44 0.00 0.00 2.69
1661 3736 6.929625 TGGTCAAACTTTGTCTCAAAATGAA 58.070 32.000 1.44 0.00 0.00 2.57
1662 3737 6.522625 TGGTCAAACTTTGTCTCAAAATGA 57.477 33.333 1.44 0.00 0.00 2.57
1663 3738 6.979817 TCATGGTCAAACTTTGTCTCAAAATG 59.020 34.615 1.44 0.00 0.00 2.32
1664 3739 7.111247 TCATGGTCAAACTTTGTCTCAAAAT 57.889 32.000 1.44 0.00 0.00 1.82
1665 3740 6.522625 TCATGGTCAAACTTTGTCTCAAAA 57.477 33.333 1.44 0.00 0.00 2.44
1666 3741 6.522625 TTCATGGTCAAACTTTGTCTCAAA 57.477 33.333 1.44 0.00 0.00 2.69
1667 3742 6.713762 ATTCATGGTCAAACTTTGTCTCAA 57.286 33.333 1.44 0.00 0.00 3.02
1668 3743 6.713762 AATTCATGGTCAAACTTTGTCTCA 57.286 33.333 1.44 0.42 0.00 3.27
1669 3744 8.968242 GTTAAATTCATGGTCAAACTTTGTCTC 58.032 33.333 1.44 0.00 0.00 3.36
1670 3745 8.695456 AGTTAAATTCATGGTCAAACTTTGTCT 58.305 29.630 1.44 0.00 0.00 3.41
1671 3746 8.871686 AGTTAAATTCATGGTCAAACTTTGTC 57.128 30.769 1.44 0.00 0.00 3.18
1714 3789 9.661563 TTTTCTATGGTATAGTTTTCGTGACAT 57.338 29.630 0.00 0.00 0.00 3.06
1715 3790 8.928733 GTTTTCTATGGTATAGTTTTCGTGACA 58.071 33.333 0.00 0.00 0.00 3.58
1716 3791 8.385858 GGTTTTCTATGGTATAGTTTTCGTGAC 58.614 37.037 0.00 0.00 0.00 3.67
1717 3792 8.316214 AGGTTTTCTATGGTATAGTTTTCGTGA 58.684 33.333 0.00 0.00 0.00 4.35
1718 3793 8.488651 AGGTTTTCTATGGTATAGTTTTCGTG 57.511 34.615 0.00 0.00 0.00 4.35
1719 3794 8.537858 AGAGGTTTTCTATGGTATAGTTTTCGT 58.462 33.333 0.00 0.00 33.23 3.85
1720 3795 8.943909 AGAGGTTTTCTATGGTATAGTTTTCG 57.056 34.615 0.00 0.00 33.23 3.46
1730 3805 8.934023 TGTATTTGAAAGAGGTTTTCTATGGT 57.066 30.769 1.88 0.00 34.14 3.55
1735 3810 8.923270 TGGATTTGTATTTGAAAGAGGTTTTCT 58.077 29.630 1.88 0.00 37.93 2.52
1736 3811 9.541143 TTGGATTTGTATTTGAAAGAGGTTTTC 57.459 29.630 0.00 0.00 0.00 2.29
1737 3812 9.325198 GTTGGATTTGTATTTGAAAGAGGTTTT 57.675 29.630 0.00 0.00 0.00 2.43
1738 3813 8.482128 TGTTGGATTTGTATTTGAAAGAGGTTT 58.518 29.630 0.00 0.00 0.00 3.27
1739 3814 8.017418 TGTTGGATTTGTATTTGAAAGAGGTT 57.983 30.769 0.00 0.00 0.00 3.50
1740 3815 7.595819 TGTTGGATTTGTATTTGAAAGAGGT 57.404 32.000 0.00 0.00 0.00 3.85
1751 3826 9.487442 ACCCAAAGTATATTGTTGGATTTGTAT 57.513 29.630 11.61 0.00 43.82 2.29
1752 3827 8.887264 ACCCAAAGTATATTGTTGGATTTGTA 57.113 30.769 11.61 0.00 43.82 2.41
1753 3828 7.790782 ACCCAAAGTATATTGTTGGATTTGT 57.209 32.000 11.61 1.84 43.82 2.83
1754 3829 7.920682 GCTACCCAAAGTATATTGTTGGATTTG 59.079 37.037 11.61 0.00 43.82 2.32
1755 3830 7.617723 TGCTACCCAAAGTATATTGTTGGATTT 59.382 33.333 11.61 2.10 43.82 2.17
1756 3831 7.122715 TGCTACCCAAAGTATATTGTTGGATT 58.877 34.615 11.61 3.86 43.82 3.01
1757 3832 6.668645 TGCTACCCAAAGTATATTGTTGGAT 58.331 36.000 11.61 0.49 43.82 3.41
1758 3833 6.068461 TGCTACCCAAAGTATATTGTTGGA 57.932 37.500 11.61 0.00 43.82 3.53
1759 3834 6.959639 ATGCTACCCAAAGTATATTGTTGG 57.040 37.500 5.47 5.47 41.30 3.77
1760 3835 8.023128 GCATATGCTACCCAAAGTATATTGTTG 58.977 37.037 20.64 0.00 33.93 3.33
1761 3836 8.110860 GCATATGCTACCCAAAGTATATTGTT 57.889 34.615 20.64 0.00 33.93 2.83
1762 3837 7.687941 GCATATGCTACCCAAAGTATATTGT 57.312 36.000 20.64 0.00 33.93 2.71
1813 3888 9.244799 CTTTTGTATTTTGGGTCTAAGTTTGAC 57.755 33.333 8.72 8.72 0.00 3.18
1814 3889 8.417884 CCTTTTGTATTTTGGGTCTAAGTTTGA 58.582 33.333 0.00 0.00 0.00 2.69
1815 3890 7.655732 CCCTTTTGTATTTTGGGTCTAAGTTTG 59.344 37.037 0.00 0.00 33.49 2.93
1816 3891 7.688328 GCCCTTTTGTATTTTGGGTCTAAGTTT 60.688 37.037 0.00 0.00 39.97 2.66
1817 3892 6.239487 GCCCTTTTGTATTTTGGGTCTAAGTT 60.239 38.462 0.00 0.00 39.97 2.66
1818 3893 5.245301 GCCCTTTTGTATTTTGGGTCTAAGT 59.755 40.000 0.00 0.00 39.97 2.24
1819 3894 5.337250 GGCCCTTTTGTATTTTGGGTCTAAG 60.337 44.000 0.00 0.00 39.33 2.18
1820 3895 4.528987 GGCCCTTTTGTATTTTGGGTCTAA 59.471 41.667 0.00 0.00 39.33 2.10
1821 3896 4.090819 GGCCCTTTTGTATTTTGGGTCTA 58.909 43.478 0.00 0.00 39.33 2.59
1822 3897 2.903784 GGCCCTTTTGTATTTTGGGTCT 59.096 45.455 0.00 0.00 39.33 3.85
1823 3898 2.903784 AGGCCCTTTTGTATTTTGGGTC 59.096 45.455 0.00 0.00 42.50 4.46
1824 3899 2.984672 AGGCCCTTTTGTATTTTGGGT 58.015 42.857 0.00 0.00 39.97 4.51
1825 3900 5.692115 ATTAGGCCCTTTTGTATTTTGGG 57.308 39.130 0.00 0.00 40.74 4.12
1826 3901 7.551262 GGTTTATTAGGCCCTTTTGTATTTTGG 59.449 37.037 0.00 0.00 0.00 3.28
1827 3902 7.551262 GGGTTTATTAGGCCCTTTTGTATTTTG 59.449 37.037 0.00 0.00 39.31 2.44
1828 3903 7.579916 CGGGTTTATTAGGCCCTTTTGTATTTT 60.580 37.037 0.00 0.00 40.22 1.82
1829 3904 6.127281 CGGGTTTATTAGGCCCTTTTGTATTT 60.127 38.462 0.00 0.00 40.22 1.40
1830 3905 5.361571 CGGGTTTATTAGGCCCTTTTGTATT 59.638 40.000 0.00 0.00 40.22 1.89
1831 3906 4.891168 CGGGTTTATTAGGCCCTTTTGTAT 59.109 41.667 0.00 0.00 40.22 2.29
1832 3907 4.271661 CGGGTTTATTAGGCCCTTTTGTA 58.728 43.478 0.00 0.00 40.22 2.41
1833 3908 3.093814 CGGGTTTATTAGGCCCTTTTGT 58.906 45.455 0.00 0.00 40.22 2.83
1834 3909 2.429250 CCGGGTTTATTAGGCCCTTTTG 59.571 50.000 0.00 0.00 40.22 2.44
1835 3910 2.312440 TCCGGGTTTATTAGGCCCTTTT 59.688 45.455 0.00 0.00 40.22 2.27
1836 3911 1.924552 TCCGGGTTTATTAGGCCCTTT 59.075 47.619 0.00 0.00 40.22 3.11
1837 3912 1.213678 GTCCGGGTTTATTAGGCCCTT 59.786 52.381 0.00 0.00 40.22 3.95
1838 3913 0.841961 GTCCGGGTTTATTAGGCCCT 59.158 55.000 0.00 0.00 40.22 5.19
1839 3914 0.533531 CGTCCGGGTTTATTAGGCCC 60.534 60.000 0.00 0.00 39.03 5.80
1840 3915 0.465287 TCGTCCGGGTTTATTAGGCC 59.535 55.000 0.00 0.00 0.00 5.19
1841 3916 2.207590 CTTCGTCCGGGTTTATTAGGC 58.792 52.381 0.00 0.00 0.00 3.93
1842 3917 2.169144 ACCTTCGTCCGGGTTTATTAGG 59.831 50.000 0.00 2.47 30.80 2.69
1843 3918 3.531934 ACCTTCGTCCGGGTTTATTAG 57.468 47.619 0.00 0.00 30.80 1.73
1844 3919 4.023291 ACTACCTTCGTCCGGGTTTATTA 58.977 43.478 0.00 0.00 37.07 0.98
1845 3920 2.833943 ACTACCTTCGTCCGGGTTTATT 59.166 45.455 0.00 0.00 37.07 1.40
1846 3921 2.460669 ACTACCTTCGTCCGGGTTTAT 58.539 47.619 0.00 0.00 37.07 1.40
1847 3922 1.923356 ACTACCTTCGTCCGGGTTTA 58.077 50.000 0.00 0.00 37.07 2.01
1848 3923 1.546029 GTACTACCTTCGTCCGGGTTT 59.454 52.381 0.00 0.00 37.07 3.27
1849 3924 1.177401 GTACTACCTTCGTCCGGGTT 58.823 55.000 0.00 0.00 37.07 4.11
1850 3925 0.038166 TGTACTACCTTCGTCCGGGT 59.962 55.000 0.00 0.00 39.40 5.28
1851 3926 0.737219 CTGTACTACCTTCGTCCGGG 59.263 60.000 0.00 0.00 0.00 5.73
1852 3927 1.457346 ACTGTACTACCTTCGTCCGG 58.543 55.000 0.00 0.00 0.00 5.14
1853 3928 3.002791 TGTACTGTACTACCTTCGTCCG 58.997 50.000 17.98 0.00 0.00 4.79
1854 3929 6.874288 ATATGTACTGTACTACCTTCGTCC 57.126 41.667 17.98 0.00 0.00 4.79
1855 3930 9.017669 CAAAATATGTACTGTACTACCTTCGTC 57.982 37.037 17.98 0.00 0.00 4.20
1856 3931 7.490402 GCAAAATATGTACTGTACTACCTTCGT 59.510 37.037 17.98 0.00 0.00 3.85
1857 3932 7.705325 AGCAAAATATGTACTGTACTACCTTCG 59.295 37.037 17.98 4.74 0.00 3.79
1858 3933 8.943909 AGCAAAATATGTACTGTACTACCTTC 57.056 34.615 17.98 2.61 0.00 3.46
1859 3934 8.537016 TGAGCAAAATATGTACTGTACTACCTT 58.463 33.333 17.98 5.16 0.00 3.50
1860 3935 7.980099 GTGAGCAAAATATGTACTGTACTACCT 59.020 37.037 17.98 4.36 0.00 3.08
1861 3936 7.224167 GGTGAGCAAAATATGTACTGTACTACC 59.776 40.741 17.98 6.46 0.00 3.18
1862 3937 7.980099 AGGTGAGCAAAATATGTACTGTACTAC 59.020 37.037 17.98 0.00 0.00 2.73
1863 3938 8.074613 AGGTGAGCAAAATATGTACTGTACTA 57.925 34.615 17.98 8.96 0.00 1.82
1921 3997 7.654022 ATGTGTTACATTGTTATTTAGGGGG 57.346 36.000 0.00 0.00 34.67 5.40
1984 4060 5.943706 TCTACGATAATGTAGACTGAGCC 57.056 43.478 0.00 0.00 44.39 4.70
2072 4148 5.190528 TCCTCTTTGTAATGCCAGAGAAGAT 59.809 40.000 0.00 0.00 35.70 2.40
2128 4204 8.700051 CCAGAAAAATATCTACTCCAGAGAAGA 58.300 37.037 0.70 0.00 36.48 2.87
2129 4205 8.700051 TCCAGAAAAATATCTACTCCAGAGAAG 58.300 37.037 0.70 0.00 36.48 2.85
2130 4206 8.609617 TCCAGAAAAATATCTACTCCAGAGAA 57.390 34.615 0.70 0.00 36.48 2.87
2131 4207 8.609617 TTCCAGAAAAATATCTACTCCAGAGA 57.390 34.615 0.70 0.00 36.48 3.10
2132 4208 8.482128 ACTTCCAGAAAAATATCTACTCCAGAG 58.518 37.037 0.00 0.00 36.48 3.35
2133 4209 8.380742 ACTTCCAGAAAAATATCTACTCCAGA 57.619 34.615 0.00 0.00 37.79 3.86
2134 4210 9.757227 CTACTTCCAGAAAAATATCTACTCCAG 57.243 37.037 0.00 0.00 0.00 3.86
2141 4217 8.907885 GGCATTTCTACTTCCAGAAAAATATCT 58.092 33.333 2.70 0.00 45.17 1.98
2142 4218 8.686334 TGGCATTTCTACTTCCAGAAAAATATC 58.314 33.333 2.70 0.00 45.17 1.63
2147 4223 4.766891 CCTGGCATTTCTACTTCCAGAAAA 59.233 41.667 8.05 0.00 45.17 2.29
2149 4225 3.308402 CCCTGGCATTTCTACTTCCAGAA 60.308 47.826 8.05 0.00 45.31 3.02
2151 4227 2.239654 TCCCTGGCATTTCTACTTCCAG 59.760 50.000 0.00 0.00 42.87 3.86
2152 4228 2.274542 TCCCTGGCATTTCTACTTCCA 58.725 47.619 0.00 0.00 0.00 3.53
2153 4229 3.282885 CTTCCCTGGCATTTCTACTTCC 58.717 50.000 0.00 0.00 0.00 3.46
2154 4230 3.956744 ACTTCCCTGGCATTTCTACTTC 58.043 45.455 0.00 0.00 0.00 3.01
2155 4231 4.626529 GCTACTTCCCTGGCATTTCTACTT 60.627 45.833 0.00 0.00 0.00 2.24
2157 4233 3.206964 GCTACTTCCCTGGCATTTCTAC 58.793 50.000 0.00 0.00 0.00 2.59
2159 4235 1.635487 TGCTACTTCCCTGGCATTTCT 59.365 47.619 0.00 0.00 0.00 2.52
2161 4237 2.603075 TTGCTACTTCCCTGGCATTT 57.397 45.000 0.00 0.00 34.59 2.32
2164 4240 0.034186 CCATTGCTACTTCCCTGGCA 60.034 55.000 0.00 0.00 0.00 4.92
2166 4242 0.034186 TGCCATTGCTACTTCCCTGG 60.034 55.000 0.00 0.00 38.71 4.45
2167 4243 2.062971 ATGCCATTGCTACTTCCCTG 57.937 50.000 0.00 0.00 38.71 4.45
2168 4244 2.381911 CAATGCCATTGCTACTTCCCT 58.618 47.619 4.18 0.00 38.71 4.20
2169 4245 1.410153 CCAATGCCATTGCTACTTCCC 59.590 52.381 12.01 0.00 38.92 3.97
2170 4246 2.378038 TCCAATGCCATTGCTACTTCC 58.622 47.619 12.01 0.00 38.92 3.46
2172 4248 3.834231 ACTTTCCAATGCCATTGCTACTT 59.166 39.130 12.01 0.00 38.92 2.24
2173 4249 3.434309 ACTTTCCAATGCCATTGCTACT 58.566 40.909 12.01 0.00 38.92 2.57
2174 4250 3.874392 ACTTTCCAATGCCATTGCTAC 57.126 42.857 12.01 0.00 38.92 3.58
2175 4251 4.640201 GTCTACTTTCCAATGCCATTGCTA 59.360 41.667 12.01 0.00 38.92 3.49
2177 4253 3.193267 TGTCTACTTTCCAATGCCATTGC 59.807 43.478 12.01 0.00 38.92 3.56
2178 4254 5.389859 TTGTCTACTTTCCAATGCCATTG 57.610 39.130 10.52 10.52 39.94 2.82
2203 4296 4.014406 CGGCCAGGGTTTAGATTACTTTT 58.986 43.478 2.24 0.00 0.00 2.27
2204 4297 3.617284 CGGCCAGGGTTTAGATTACTTT 58.383 45.455 2.24 0.00 0.00 2.66
2206 4299 1.489230 CCGGCCAGGGTTTAGATTACT 59.511 52.381 2.24 0.00 35.97 2.24
2220 4313 4.141228 TCCATAATAAATGGTTACCGGCCA 60.141 41.667 0.00 0.10 40.06 5.36
2290 4383 4.582701 TCATTTTCGTTGTTGCTGGAAT 57.417 36.364 0.00 0.00 0.00 3.01
2400 4493 7.945109 TCTTAAGGAGCTAGTATGCTTCATCTA 59.055 37.037 1.85 0.00 44.17 1.98
2432 4525 5.941948 ACACAAGTAGAAAAATCCCTTCG 57.058 39.130 0.00 0.00 0.00 3.79
2480 4573 4.819105 TTTATGGTGCCCCTCGATATAG 57.181 45.455 0.00 0.00 0.00 1.31
2765 4862 3.701040 ACAAAATCAGTGCACAGTCCTTT 59.299 39.130 21.04 9.94 0.00 3.11
2866 4963 6.662414 TTTGTGATAGCCTTTCGTATCTTG 57.338 37.500 0.00 0.00 0.00 3.02
2941 5038 6.400834 GCATGTAGCTGATGAAGTCATTATCG 60.401 42.308 10.85 0.00 41.15 2.92
3002 5099 2.616376 CGTTGTCCACAATGTCTTCCAA 59.384 45.455 3.81 0.00 37.90 3.53
3094 5191 4.546674 TGTCAAGGATATCTGGCTCACTA 58.453 43.478 2.05 0.00 0.00 2.74
3096 5193 3.827008 TGTCAAGGATATCTGGCTCAC 57.173 47.619 2.05 0.00 0.00 3.51
3174 5271 7.054124 TCCATGGTGTAGAAGAAATTACCATC 58.946 38.462 12.58 0.00 44.61 3.51
3207 5304 9.727627 CAGAAGATCAAAAGGCATAAAGATTAC 57.272 33.333 0.00 0.00 0.00 1.89
3209 5306 7.093640 TGCAGAAGATCAAAAGGCATAAAGATT 60.094 33.333 0.00 0.00 0.00 2.40
3290 5387 8.974408 CCACATATATTTCATCTTTGCAACATG 58.026 33.333 0.00 4.84 0.00 3.21
3385 5482 7.037153 GGGATATGGTAACCCTGGTATTCAATA 60.037 40.741 0.00 0.00 40.39 1.90
3468 5565 3.065648 GTCTGTGATAGAGTTCTCGGGAC 59.934 52.174 0.00 0.00 35.70 4.46
3488 5585 6.149474 ACCTGCATGTTCTTATGTTACTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
3500 5597 3.144506 CTGTGAAGACCTGCATGTTCTT 58.855 45.455 0.00 0.18 0.00 2.52
3501 5598 2.775890 CTGTGAAGACCTGCATGTTCT 58.224 47.619 0.00 0.00 0.00 3.01
3502 5599 1.198637 GCTGTGAAGACCTGCATGTTC 59.801 52.381 0.00 0.00 0.00 3.18
3518 5615 1.024046 TGTGTGACACTTTGCGCTGT 61.024 50.000 17.47 3.85 35.11 4.40
3601 5698 0.460311 GCATGTAGCAGTACGGAGGT 59.540 55.000 0.00 0.00 44.79 3.85
3661 5758 2.936498 CACCATAGTTTCTACCCTTGCG 59.064 50.000 0.00 0.00 0.00 4.85
3769 5866 7.559897 AACTTGAGTTTAATTGGAAGTCCAAGA 59.440 33.333 17.38 6.21 46.49 3.02
3814 5911 1.702401 TCCATAGTGTTGGCTTGGACA 59.298 47.619 0.00 0.00 36.66 4.02
3838 5935 3.566322 CGTCATGGGTTTAACCTGTTTCA 59.434 43.478 14.27 3.34 38.64 2.69
3860 5957 8.981724 ATGCATGTATCATCATAATTTTGCTC 57.018 30.769 0.00 0.00 0.00 4.26
3998 6095 8.812972 AGTAGGAGACACATCTTTACATTGTAA 58.187 33.333 5.14 5.14 34.34 2.41
4001 6098 9.823647 ATAAGTAGGAGACACATCTTTACATTG 57.176 33.333 0.00 0.00 34.34 2.82
4024 6121 9.067963 TGGGGGAATGAAATATATAGCTCATAA 57.932 33.333 8.89 0.00 0.00 1.90
4090 6189 9.765795 GTAACTAGTAGAATTACCATTGCATCT 57.234 33.333 3.59 0.00 0.00 2.90
4175 6274 8.802267 CCCACATGGAAGAGAGTAAAATTTTAA 58.198 33.333 12.14 0.00 37.39 1.52
4177 6276 7.010160 TCCCACATGGAAGAGAGTAAAATTTT 58.990 34.615 8.75 8.75 41.40 1.82
4178 6277 6.552008 TCCCACATGGAAGAGAGTAAAATTT 58.448 36.000 0.00 0.00 41.40 1.82
4179 6278 6.139679 TCCCACATGGAAGAGAGTAAAATT 57.860 37.500 0.00 0.00 41.40 1.82
4180 6279 5.779241 TCCCACATGGAAGAGAGTAAAAT 57.221 39.130 0.00 0.00 41.40 1.82
4227 6326 3.529319 ACCCTTCCATCCAGCTAGATTTT 59.471 43.478 0.00 0.00 0.00 1.82
4238 6337 1.270893 GCTAATCCGACCCTTCCATCC 60.271 57.143 0.00 0.00 0.00 3.51
4277 6376 3.365767 GCAGTTCAATGGAAAGAGCACTC 60.366 47.826 0.00 0.00 34.13 3.51
4298 6397 0.317770 TTTTGTGCAGTGCTTAGCGC 60.318 50.000 17.60 10.07 41.40 5.92
4310 6409 2.612721 CCAGGCCCAACTTATTTTGTGC 60.613 50.000 0.00 0.00 0.00 4.57
4318 6417 0.480690 TCTTTGCCAGGCCCAACTTA 59.519 50.000 9.64 0.00 0.00 2.24
4319 6418 0.398381 TTCTTTGCCAGGCCCAACTT 60.398 50.000 9.64 0.00 0.00 2.66
4394 6493 4.278669 GTCTTCATAGCTTCCTCGGTATCA 59.721 45.833 0.00 0.00 0.00 2.15
4401 6500 8.857694 AGTATACTAGTCTTCATAGCTTCCTC 57.142 38.462 2.75 0.00 0.00 3.71
4450 6549 9.777297 AAATGCATAGTAATTTTCCACAAGTTT 57.223 25.926 0.00 0.00 0.00 2.66
4452 6551 8.584157 TGAAATGCATAGTAATTTTCCACAAGT 58.416 29.630 0.00 0.00 0.00 3.16
4453 6552 8.984891 TGAAATGCATAGTAATTTTCCACAAG 57.015 30.769 0.00 0.00 0.00 3.16
4525 6628 9.940974 TTTAACCCTTATAGAGAGTACCATGTA 57.059 33.333 0.00 0.00 0.00 2.29
4567 6670 9.372369 CGTAGGATGAGAAAAGATAAAGAGTTT 57.628 33.333 0.00 0.00 0.00 2.66
4575 6678 5.221263 GGAGTGCGTAGGATGAGAAAAGATA 60.221 44.000 0.00 0.00 0.00 1.98
4576 6679 4.442192 GGAGTGCGTAGGATGAGAAAAGAT 60.442 45.833 0.00 0.00 0.00 2.40
4603 6706 6.678900 GCATCCCAAGATTAATCCATATTCGC 60.679 42.308 11.92 4.77 0.00 4.70
4605 6708 7.613022 TCTGCATCCCAAGATTAATCCATATTC 59.387 37.037 11.92 0.00 0.00 1.75
4703 6807 6.663523 AGTTGGTTAGTCCCCAAAATGATAAG 59.336 38.462 0.00 0.00 43.30 1.73
4708 6812 6.850752 ATTAGTTGGTTAGTCCCCAAAATG 57.149 37.500 0.00 0.00 43.30 2.32
4738 6842 7.271511 ACACCACAAATAGAATTTTGCTTTCA 58.728 30.769 0.00 0.00 39.65 2.69
4739 6843 7.713764 ACACCACAAATAGAATTTTGCTTTC 57.286 32.000 0.00 0.00 39.65 2.62


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

AutoCloner maintained by Alex Coulton.