Multiple sequence alignment - TraesCS2A01G472800

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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 TraesCS2A01G472800 chr2A 100.000 5686 0 0 1 5686 714213575 714207890 0.000000e+00 10501.0
1 TraesCS2A01G472800 chr2A 93.478 46 1 2 1 45 79314022 79314066 3.680000e-07 67.6
2 TraesCS2A01G472800 chr2D 92.087 3387 187 35 2330 5686 576195300 576191965 0.000000e+00 4695.0
3 TraesCS2A01G472800 chr2D 93.133 830 41 9 808 1628 576196727 576195905 0.000000e+00 1203.0
4 TraesCS2A01G472800 chr2D 91.532 555 26 7 137 677 576197306 576196759 0.000000e+00 745.0
5 TraesCS2A01G472800 chr2D 85.302 728 68 19 1642 2364 576195922 576195229 0.000000e+00 715.0
6 TraesCS2A01G472800 chr2B 92.661 1676 71 8 2588 4244 692166110 692164468 0.000000e+00 2366.0
7 TraesCS2A01G472800 chr2B 95.376 1449 60 7 4242 5686 692164309 692162864 0.000000e+00 2298.0
8 TraesCS2A01G472800 chr2B 92.398 763 48 2 829 1588 692168111 692167356 0.000000e+00 1079.0
9 TraesCS2A01G472800 chr2B 95.652 460 18 2 1687 2146 692167353 692166896 0.000000e+00 737.0
10 TraesCS2A01G472800 chr2B 91.205 523 32 9 269 786 692168617 692168104 0.000000e+00 699.0
11 TraesCS2A01G472800 chr2B 95.511 401 11 1 2197 2597 692166747 692166354 8.040000e-178 634.0
12 TraesCS2A01G472800 chr2B 92.737 179 5 3 37 215 692168807 692168637 9.460000e-63 252.0
13 TraesCS2A01G472800 chr7B 80.998 521 64 24 1665 2154 673310883 673310367 1.160000e-101 381.0
14 TraesCS2A01G472800 chr7B 78.172 536 65 30 4534 5066 171090649 171091135 1.550000e-75 294.0
15 TraesCS2A01G472800 chr6B 80.370 540 71 19 4537 5066 173817496 173816982 1.500000e-100 377.0
16 TraesCS2A01G472800 chr7D 82.057 457 61 14 1718 2154 595729929 595729474 2.500000e-98 370.0
17 TraesCS2A01G472800 chr7A 82.135 459 57 19 1718 2154 688692269 688691814 2.500000e-98 370.0
18 TraesCS2A01G472800 chr7A 97.619 42 1 0 1 42 25115274 25115315 7.900000e-09 73.1
19 TraesCS2A01G472800 chr7A 97.561 41 1 0 1 41 632643098 632643058 2.840000e-08 71.3
20 TraesCS2A01G472800 chr7A 97.561 41 0 1 1 41 632597039 632597000 1.020000e-07 69.4
21 TraesCS2A01G472800 chr7A 93.333 45 2 1 1 45 700396414 700396371 1.320000e-06 65.8
22 TraesCS2A01G472800 chr1B 80.405 296 38 11 4771 5066 87189385 87189660 2.080000e-49 207.0
23 TraesCS2A01G472800 chr5D 82.101 257 31 7 4810 5066 181607176 181607417 7.470000e-49 206.0
24 TraesCS2A01G472800 chr4A 92.683 82 5 1 4971 5051 20573330 20573249 3.600000e-22 117.0
25 TraesCS2A01G472800 chr6A 97.561 41 1 0 1 41 609266274 609266234 2.840000e-08 71.3
26 TraesCS2A01G472800 chr1A 100.000 38 0 0 1 38 49354589 49354626 2.840000e-08 71.3
27 TraesCS2A01G472800 chr1A 100.000 38 0 0 1 38 406143837 406143800 2.840000e-08 71.3
28 TraesCS2A01G472800 chr1A 100.000 38 0 0 1 38 548573447 548573484 2.840000e-08 71.3


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 TraesCS2A01G472800 chr2A 714207890 714213575 5685 True 10501.000000 10501 100.000000 1 5686 1 chr2A.!!$R1 5685
1 TraesCS2A01G472800 chr2D 576191965 576197306 5341 True 1839.500000 4695 90.513500 137 5686 4 chr2D.!!$R1 5549
2 TraesCS2A01G472800 chr2B 692162864 692168807 5943 True 1152.142857 2366 93.648571 37 5686 7 chr2B.!!$R1 5649
3 TraesCS2A01G472800 chr7B 673310367 673310883 516 True 381.000000 381 80.998000 1665 2154 1 chr7B.!!$R1 489
4 TraesCS2A01G472800 chr6B 173816982 173817496 514 True 377.000000 377 80.370000 4537 5066 1 chr6B.!!$R1 529

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
258 259 0.181350 GCCATTAGACACCCCTCCAG 59.819 60.000 0.00 0.0 0.00 3.86 F
430 441 0.320073 TACTTTTCCCGTGCTCCGTG 60.320 55.000 0.00 0.0 33.66 4.94 F
1086 1101 0.321653 GTGTGGATCTCAACCGGCTT 60.322 55.000 0.00 0.0 0.00 4.35 F
1681 1708 0.171903 CAAAGCCAAATGAGGGAGCG 59.828 55.000 0.00 0.0 0.00 5.03 F
1801 1862 0.328926 TGGCAGATGAGGTGAATGCA 59.671 50.000 0.00 0.0 38.63 3.96 F
2824 3259 0.661483 GAGGAAACAACGCAAGCAGC 60.661 55.000 0.00 0.0 45.62 5.25 F
2830 3265 0.801836 ACAACGCAAGCAGCACAAAC 60.802 50.000 0.00 0.0 46.13 2.93 F
3824 4262 1.980765 ACTTGATCAGGTGAGCTTCCA 59.019 47.619 10.05 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 1688 0.108472 GCTCCCTCATTTGGCTTTGC 60.108 55.000 0.00 0.00 0.00 3.68 R
1662 1689 0.171903 CGCTCCCTCATTTGGCTTTG 59.828 55.000 0.00 0.00 0.00 2.77 R
3083 3518 0.181350 GCTAGGCCAGTTGCAGGTAT 59.819 55.000 5.01 0.00 43.89 2.73 R
3159 3597 1.555967 ACCAGTGTTGTTGTGCCTTT 58.444 45.000 0.00 0.00 0.00 3.11 R
3531 3969 1.985159 TCACCTATGCACCCTTCAAGT 59.015 47.619 0.00 0.00 0.00 3.16 R
4088 4547 1.927174 CAACTCGAGGCATCTTTACCG 59.073 52.381 18.41 0.00 0.00 4.02 R
4104 4563 2.325583 TCTTCACGGTTTGAGCAACT 57.674 45.000 0.00 0.00 34.94 3.16 R
5605 6237 2.821810 GAGCTCTTTGGCCCGCTC 60.822 66.667 6.43 6.31 41.60 5.03 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
21 22 2.969443 ATGAGCGCTTGTGTTTGTAC 57.031 45.000 13.26 0.00 0.00 2.90
22 23 1.948104 TGAGCGCTTGTGTTTGTACT 58.052 45.000 13.26 0.00 0.00 2.73
23 24 1.597195 TGAGCGCTTGTGTTTGTACTG 59.403 47.619 13.26 0.00 0.00 2.74
24 25 1.864711 GAGCGCTTGTGTTTGTACTGA 59.135 47.619 13.26 0.00 0.00 3.41
25 26 2.480419 GAGCGCTTGTGTTTGTACTGAT 59.520 45.455 13.26 0.00 0.00 2.90
26 27 2.224079 AGCGCTTGTGTTTGTACTGATG 59.776 45.455 2.64 0.00 0.00 3.07
27 28 2.574322 CGCTTGTGTTTGTACTGATGC 58.426 47.619 0.00 0.00 0.00 3.91
28 29 2.224079 CGCTTGTGTTTGTACTGATGCT 59.776 45.455 0.00 0.00 0.00 3.79
29 30 3.431912 CGCTTGTGTTTGTACTGATGCTA 59.568 43.478 0.00 0.00 0.00 3.49
30 31 4.084066 CGCTTGTGTTTGTACTGATGCTAA 60.084 41.667 0.00 0.00 0.00 3.09
31 32 5.559991 CGCTTGTGTTTGTACTGATGCTAAA 60.560 40.000 0.00 0.00 0.00 1.85
32 33 6.205784 GCTTGTGTTTGTACTGATGCTAAAA 58.794 36.000 0.00 0.00 0.00 1.52
33 34 6.695278 GCTTGTGTTTGTACTGATGCTAAAAA 59.305 34.615 0.00 0.00 0.00 1.94
76 77 2.599082 CGACCATTGACTCGCTTCTTAC 59.401 50.000 0.00 0.00 0.00 2.34
77 78 2.599082 GACCATTGACTCGCTTCTTACG 59.401 50.000 0.00 0.00 0.00 3.18
78 79 1.927174 CCATTGACTCGCTTCTTACGG 59.073 52.381 0.00 0.00 0.00 4.02
79 80 2.607187 CATTGACTCGCTTCTTACGGT 58.393 47.619 0.00 0.00 0.00 4.83
81 82 4.360563 CATTGACTCGCTTCTTACGGTAT 58.639 43.478 0.00 0.00 0.00 2.73
82 83 5.506815 CCATTGACTCGCTTCTTACGGTATA 60.507 44.000 0.00 0.00 0.00 1.47
84 85 5.565592 TGACTCGCTTCTTACGGTATAAA 57.434 39.130 0.00 0.00 0.00 1.40
85 86 5.953183 TGACTCGCTTCTTACGGTATAAAA 58.047 37.500 0.00 0.00 0.00 1.52
86 87 6.389091 TGACTCGCTTCTTACGGTATAAAAA 58.611 36.000 0.00 0.00 0.00 1.94
87 88 6.529125 TGACTCGCTTCTTACGGTATAAAAAG 59.471 38.462 0.00 0.00 0.00 2.27
88 89 6.624423 ACTCGCTTCTTACGGTATAAAAAGA 58.376 36.000 0.00 0.00 0.00 2.52
90 91 7.763071 ACTCGCTTCTTACGGTATAAAAAGATT 59.237 33.333 0.00 0.00 0.00 2.40
91 92 7.902032 TCGCTTCTTACGGTATAAAAAGATTG 58.098 34.615 0.00 0.00 0.00 2.67
92 93 7.546667 TCGCTTCTTACGGTATAAAAAGATTGT 59.453 33.333 0.00 0.00 0.00 2.71
93 94 8.173130 CGCTTCTTACGGTATAAAAAGATTGTT 58.827 33.333 0.00 0.00 0.00 2.83
94 95 9.836076 GCTTCTTACGGTATAAAAAGATTGTTT 57.164 29.630 0.00 0.00 0.00 2.83
258 259 0.181350 GCCATTAGACACCCCTCCAG 59.819 60.000 0.00 0.00 0.00 3.86
259 260 1.584724 CCATTAGACACCCCTCCAGT 58.415 55.000 0.00 0.00 0.00 4.00
283 288 2.781431 TACCACTCTCCCAGCGCTGA 62.781 60.000 38.06 18.82 0.00 4.26
312 317 1.167851 ATGCATTGACCGGTTGACTG 58.832 50.000 9.42 5.77 0.00 3.51
317 322 1.052124 TTGACCGGTTGACTGACCCT 61.052 55.000 9.42 0.00 36.28 4.34
354 365 1.901948 TCAGTCCCTCGCTCGTTGT 60.902 57.895 0.00 0.00 0.00 3.32
430 441 0.320073 TACTTTTCCCGTGCTCCGTG 60.320 55.000 0.00 0.00 33.66 4.94
449 460 0.807496 GGGCTTTCATGTGAGTGAGC 59.193 55.000 0.00 6.58 0.00 4.26
451 462 1.432514 GCTTTCATGTGAGTGAGCGA 58.567 50.000 0.00 0.00 0.00 4.93
668 683 7.487189 CACATCTCATTTCCTCATTACTTTTGC 59.513 37.037 0.00 0.00 0.00 3.68
698 713 8.093927 TGTTTGTTTGATTCTTTTGGTTTCTCT 58.906 29.630 0.00 0.00 0.00 3.10
699 714 8.382875 GTTTGTTTGATTCTTTTGGTTTCTCTG 58.617 33.333 0.00 0.00 0.00 3.35
701 716 6.379703 TGTTTGATTCTTTTGGTTTCTCTGGA 59.620 34.615 0.00 0.00 0.00 3.86
702 717 6.639632 TTGATTCTTTTGGTTTCTCTGGAG 57.360 37.500 0.00 0.00 0.00 3.86
703 718 5.694995 TGATTCTTTTGGTTTCTCTGGAGT 58.305 37.500 0.00 0.00 0.00 3.85
704 719 6.837312 TGATTCTTTTGGTTTCTCTGGAGTA 58.163 36.000 0.00 0.00 0.00 2.59
705 720 6.936900 TGATTCTTTTGGTTTCTCTGGAGTAG 59.063 38.462 0.00 0.00 0.00 2.57
723 738 4.084888 GCGCGCACAAGGTACCAC 62.085 66.667 29.10 0.00 0.00 4.16
735 750 4.712337 ACAAGGTACCACTAGAATCTCAGG 59.288 45.833 15.94 0.00 0.00 3.86
744 759 6.014840 ACCACTAGAATCTCAGGTTCGTTTTA 60.015 38.462 0.00 0.00 0.00 1.52
746 761 7.148623 CCACTAGAATCTCAGGTTCGTTTTAAC 60.149 40.741 0.00 0.00 0.00 2.01
794 809 5.952526 TTTTTCCGTGTCTTCCCTTTATC 57.047 39.130 0.00 0.00 0.00 1.75
795 810 4.903045 TTTCCGTGTCTTCCCTTTATCT 57.097 40.909 0.00 0.00 0.00 1.98
796 811 3.887621 TCCGTGTCTTCCCTTTATCTG 57.112 47.619 0.00 0.00 0.00 2.90
797 812 3.437213 TCCGTGTCTTCCCTTTATCTGA 58.563 45.455 0.00 0.00 0.00 3.27
798 813 3.835978 TCCGTGTCTTCCCTTTATCTGAA 59.164 43.478 0.00 0.00 0.00 3.02
799 814 4.285003 TCCGTGTCTTCCCTTTATCTGAAA 59.715 41.667 0.00 0.00 0.00 2.69
800 815 5.045869 TCCGTGTCTTCCCTTTATCTGAAAT 60.046 40.000 0.00 0.00 0.00 2.17
801 816 5.648092 CCGTGTCTTCCCTTTATCTGAAATT 59.352 40.000 0.00 0.00 0.00 1.82
802 817 6.183360 CCGTGTCTTCCCTTTATCTGAAATTC 60.183 42.308 0.00 0.00 0.00 2.17
803 818 6.595716 CGTGTCTTCCCTTTATCTGAAATTCT 59.404 38.462 0.00 0.00 0.00 2.40
804 819 7.413438 CGTGTCTTCCCTTTATCTGAAATTCTG 60.413 40.741 0.00 0.00 0.00 3.02
805 820 7.607991 GTGTCTTCCCTTTATCTGAAATTCTGA 59.392 37.037 5.07 5.07 0.00 3.27
806 821 8.163408 TGTCTTCCCTTTATCTGAAATTCTGAA 58.837 33.333 6.66 0.00 0.00 3.02
838 853 3.508012 GCTCTCTCCAGTAGTGTCTTGAA 59.492 47.826 0.00 0.00 0.00 2.69
877 892 1.902508 TCTTCAGTAGCCCAGGAACAG 59.097 52.381 0.00 0.00 0.00 3.16
995 1010 1.000506 TCTTGCCAGGTAACGACAGTC 59.999 52.381 0.00 0.00 46.39 3.51
1061 1076 2.942804 TGTTGAATTCAGGGAGCAACA 58.057 42.857 8.41 5.55 44.38 3.33
1062 1077 3.499338 TGTTGAATTCAGGGAGCAACAT 58.501 40.909 8.41 0.00 42.49 2.71
1086 1101 0.321653 GTGTGGATCTCAACCGGCTT 60.322 55.000 0.00 0.00 0.00 4.35
1109 1124 5.947228 TTGGAAATAGCAAACACTGAGAG 57.053 39.130 0.00 0.00 0.00 3.20
1215 1230 1.125748 CGTCTTTCTGAGCAGCGAAAG 59.874 52.381 12.66 12.66 44.56 2.62
1236 1251 4.147321 AGGAGATTGAGCAAAAGAAGCAA 58.853 39.130 0.00 0.00 0.00 3.91
1453 1471 8.772250 TGGAGGAGTATATGAAGAAATTTCAGT 58.228 33.333 19.99 7.49 0.00 3.41
1466 1484 2.702592 TTTCAGTCAGAAACACCGGT 57.297 45.000 0.00 0.00 41.17 5.28
1470 1488 0.834612 AGTCAGAAACACCGGTGGAA 59.165 50.000 36.47 13.35 34.19 3.53
1483 1501 1.373570 GGTGGAAGAATTCTCTGCGG 58.626 55.000 8.78 0.00 46.56 5.69
1485 1503 2.093658 GGTGGAAGAATTCTCTGCGGTA 60.094 50.000 8.78 0.00 46.56 4.02
1493 1511 7.148306 GGAAGAATTCTCTGCGGTATTAAAACA 60.148 37.037 8.78 0.00 46.56 2.83
1494 1512 7.073342 AGAATTCTCTGCGGTATTAAAACAC 57.927 36.000 0.88 0.00 0.00 3.32
1528 1546 3.228188 TGCACCTGATTCTCCAAAGTT 57.772 42.857 0.00 0.00 0.00 2.66
1534 1552 3.265791 CTGATTCTCCAAAGTTCTCCCG 58.734 50.000 0.00 0.00 0.00 5.14
1566 1593 2.239402 TCATCAGGTCTGCCTTTATGCA 59.761 45.455 0.00 0.00 44.18 3.96
1571 1598 2.684881 AGGTCTGCCTTTATGCATTTCG 59.315 45.455 3.54 0.00 44.18 3.46
1584 1611 4.481930 TGCATTTCGACACCTTTTACAG 57.518 40.909 0.00 0.00 0.00 2.74
1585 1612 3.234386 GCATTTCGACACCTTTTACAGC 58.766 45.455 0.00 0.00 0.00 4.40
1586 1613 3.058224 GCATTTCGACACCTTTTACAGCT 60.058 43.478 0.00 0.00 0.00 4.24
1588 1615 4.806342 TTTCGACACCTTTTACAGCTTC 57.194 40.909 0.00 0.00 0.00 3.86
1589 1616 2.762745 TCGACACCTTTTACAGCTTCC 58.237 47.619 0.00 0.00 0.00 3.46
1590 1617 2.367567 TCGACACCTTTTACAGCTTCCT 59.632 45.455 0.00 0.00 0.00 3.36
1591 1618 3.575256 TCGACACCTTTTACAGCTTCCTA 59.425 43.478 0.00 0.00 0.00 2.94
1592 1619 4.222145 TCGACACCTTTTACAGCTTCCTAT 59.778 41.667 0.00 0.00 0.00 2.57
1593 1620 5.419788 TCGACACCTTTTACAGCTTCCTATA 59.580 40.000 0.00 0.00 0.00 1.31
1594 1621 6.097839 TCGACACCTTTTACAGCTTCCTATAT 59.902 38.462 0.00 0.00 0.00 0.86
1595 1622 6.761714 CGACACCTTTTACAGCTTCCTATATT 59.238 38.462 0.00 0.00 0.00 1.28
1596 1623 7.280205 CGACACCTTTTACAGCTTCCTATATTT 59.720 37.037 0.00 0.00 0.00 1.40
1597 1624 8.507524 ACACCTTTTACAGCTTCCTATATTTC 57.492 34.615 0.00 0.00 0.00 2.17
1598 1625 8.329502 ACACCTTTTACAGCTTCCTATATTTCT 58.670 33.333 0.00 0.00 0.00 2.52
1599 1626 9.832445 CACCTTTTACAGCTTCCTATATTTCTA 57.168 33.333 0.00 0.00 0.00 2.10
1620 1647 7.136822 TCTATGTACATTTAGGTGGCATTCT 57.863 36.000 14.77 0.00 0.00 2.40
1625 1652 4.455606 ACATTTAGGTGGCATTCTAGAGC 58.544 43.478 0.00 0.00 0.00 4.09
1628 1655 4.778213 TTAGGTGGCATTCTAGAGCATT 57.222 40.909 6.34 0.00 0.00 3.56
1629 1656 3.205784 AGGTGGCATTCTAGAGCATTC 57.794 47.619 6.34 0.00 0.00 2.67
1632 1659 1.134431 TGGCATTCTAGAGCATTCGCA 60.134 47.619 6.34 0.00 42.27 5.10
1633 1660 1.942657 GGCATTCTAGAGCATTCGCAA 59.057 47.619 6.34 0.00 42.27 4.85
1634 1661 2.355756 GGCATTCTAGAGCATTCGCAAA 59.644 45.455 6.34 0.00 42.27 3.68
1635 1662 3.181497 GGCATTCTAGAGCATTCGCAAAA 60.181 43.478 6.34 0.00 42.27 2.44
1636 1663 4.414852 GCATTCTAGAGCATTCGCAAAAA 58.585 39.130 0.00 0.00 42.27 1.94
1655 1682 3.967332 AAAAATGGTGGCATTCCAGAG 57.033 42.857 3.08 0.00 44.48 3.35
1656 1683 2.905415 AAATGGTGGCATTCCAGAGA 57.095 45.000 3.08 0.00 44.48 3.10
1657 1684 2.905415 AATGGTGGCATTCCAGAGAA 57.095 45.000 3.08 0.00 44.48 2.87
1658 1685 2.905415 ATGGTGGCATTCCAGAGAAA 57.095 45.000 3.08 0.00 44.48 2.52
1659 1686 1.909700 TGGTGGCATTCCAGAGAAAC 58.090 50.000 0.00 0.00 44.48 2.78
1660 1687 1.144708 TGGTGGCATTCCAGAGAAACA 59.855 47.619 0.00 0.00 44.48 2.83
1661 1688 1.815003 GGTGGCATTCCAGAGAAACAG 59.185 52.381 0.00 0.00 44.48 3.16
1662 1689 1.200948 GTGGCATTCCAGAGAAACAGC 59.799 52.381 0.00 0.00 44.48 4.40
1663 1690 1.202915 TGGCATTCCAGAGAAACAGCA 60.203 47.619 0.00 0.00 37.47 4.41
1681 1708 0.171903 CAAAGCCAAATGAGGGAGCG 59.828 55.000 0.00 0.00 0.00 5.03
1801 1862 0.328926 TGGCAGATGAGGTGAATGCA 59.671 50.000 0.00 0.00 38.63 3.96
1813 1874 0.818938 TGAATGCATTTGCCGCTGAT 59.181 45.000 14.33 0.00 41.18 2.90
1842 1903 0.890542 TCCACATTGTGTGCTGCTCC 60.891 55.000 15.34 0.00 46.51 4.70
1877 1938 6.872920 ACTTCAAGTTGTAATTTTTGGCTGA 58.127 32.000 2.11 0.00 0.00 4.26
1878 1939 6.756542 ACTTCAAGTTGTAATTTTTGGCTGAC 59.243 34.615 2.11 0.00 0.00 3.51
1940 2002 3.581101 TGAGATATTGTCAGGAGAGGGG 58.419 50.000 0.00 0.00 0.00 4.79
1997 2059 2.435437 GGCCAAGGGTATACCGACTAAA 59.565 50.000 15.80 0.00 46.96 1.85
2188 2250 8.736751 TTAATTTCCGTTGCTTCAAAATCTAC 57.263 30.769 0.00 0.00 0.00 2.59
2774 3206 6.509418 TTGCATTTAGGTTCAGAATGGTAC 57.491 37.500 0.00 0.00 36.16 3.34
2798 3230 6.377712 ACACTGAGTACTCCCACTTATCTAAC 59.622 42.308 20.11 0.00 0.00 2.34
2807 3242 5.674525 TCCCACTTATCTAACAATGCAGAG 58.325 41.667 0.00 0.00 0.00 3.35
2816 3251 3.354089 AACAATGCAGAGGAAACAACG 57.646 42.857 0.00 0.00 0.00 4.10
2823 3258 0.947244 AGAGGAAACAACGCAAGCAG 59.053 50.000 0.00 0.00 45.62 4.24
2824 3259 0.661483 GAGGAAACAACGCAAGCAGC 60.661 55.000 0.00 0.00 45.62 5.25
2830 3265 0.801836 ACAACGCAAGCAGCACAAAC 60.802 50.000 0.00 0.00 46.13 2.93
2944 3379 3.059352 ACATCAGTTGCTGGAGGTTAC 57.941 47.619 0.00 0.00 31.51 2.50
3022 3457 9.892130 CTCCAAAGTAGAGTCAGGTATTTAAAT 57.108 33.333 5.89 5.89 0.00 1.40
3107 3545 2.828128 GCAACTGGCCTAGCGCATC 61.828 63.158 11.47 0.00 40.31 3.91
3128 3566 5.766150 TCACTAACTTGACAATTGGTTGG 57.234 39.130 10.83 8.50 39.70 3.77
3159 3597 8.621532 AGTACTGATTCAGTTCTTTTAATGCA 57.378 30.769 23.53 0.00 42.59 3.96
3221 3659 9.111613 TGTTGACTAATTTTAATATGGTACGGG 57.888 33.333 0.00 0.00 0.00 5.28
3222 3660 7.733402 TGACTAATTTTAATATGGTACGGGC 57.267 36.000 0.00 0.00 0.00 6.13
3223 3661 6.711645 TGACTAATTTTAATATGGTACGGGCC 59.288 38.462 0.00 0.00 0.00 5.80
3224 3662 6.005823 ACTAATTTTAATATGGTACGGGCCC 58.994 40.000 13.57 13.57 0.00 5.80
3225 3663 4.734843 ATTTTAATATGGTACGGGCCCT 57.265 40.909 22.43 9.76 0.00 5.19
3247 3685 7.689559 GCCCTGGCCCATATATCTAATAGTTAC 60.690 44.444 0.00 0.00 34.56 2.50
3308 3746 7.958025 GTGGAGATGAGTTTTAAGATTCGTTTC 59.042 37.037 0.00 0.00 0.00 2.78
3310 3748 8.171840 GGAGATGAGTTTTAAGATTCGTTTCAG 58.828 37.037 4.47 0.00 0.00 3.02
3530 3968 8.737168 TCGTCATTTATGAAGAAGGAATTGAT 57.263 30.769 5.99 0.00 41.20 2.57
3531 3969 9.830975 TCGTCATTTATGAAGAAGGAATTGATA 57.169 29.630 5.99 0.00 41.20 2.15
3600 4038 7.988599 ACAATTATCCATATTTTGTTGCATGCT 59.011 29.630 20.33 0.00 0.00 3.79
3801 4239 5.798934 CGCAAAAGATTCAGGAAATTCTGAG 59.201 40.000 0.00 0.00 43.64 3.35
3803 4241 7.545489 GCAAAAGATTCAGGAAATTCTGAGAT 58.455 34.615 0.00 0.00 43.64 2.75
3824 4262 1.980765 ACTTGATCAGGTGAGCTTCCA 59.019 47.619 10.05 0.00 0.00 3.53
3838 4276 6.276091 GTGAGCTTCCATTTCATTTATTCCC 58.724 40.000 0.00 0.00 0.00 3.97
3842 4280 6.669154 AGCTTCCATTTCATTTATTCCCAAGA 59.331 34.615 0.00 0.00 0.00 3.02
3911 4355 8.364894 ACATGCTTGGATATAGTACGAAACATA 58.635 33.333 4.44 0.00 0.00 2.29
4104 4563 1.395635 TAGCGGTAAAGATGCCTCGA 58.604 50.000 0.00 0.00 0.00 4.04
4293 4914 6.573664 TCACTTGACAGGGAAACATTTATG 57.426 37.500 0.00 0.00 25.02 1.90
4335 4956 7.274447 TCTGATTCATTTTTGCTGGTTCTTTT 58.726 30.769 0.00 0.00 0.00 2.27
4368 4989 4.713814 TCATCTGCAGAGAAGTCATTACCT 59.286 41.667 22.96 0.00 0.00 3.08
4400 5021 6.005823 TCAAGAGGTATATTCATGCCAATGG 58.994 40.000 0.00 0.00 39.29 3.16
4404 5025 5.895807 AGGTATATTCATGCCAATGGTGAT 58.104 37.500 0.00 0.00 39.29 3.06
4422 5043 7.953005 TGGTGATCATACAACAAAATATGGT 57.047 32.000 0.00 0.00 34.39 3.55
4552 5174 9.418045 GCCTTTGTATGTGTAAAAATTGTGTAT 57.582 29.630 0.00 0.00 0.00 2.29
4611 5234 1.248785 GGGCGGTACTCTCACTGTGA 61.249 60.000 10.50 10.50 0.00 3.58
4679 5303 1.808945 ACAATTCCTGCAAGAGAAGCG 59.191 47.619 0.00 0.00 34.07 4.68
4726 5350 5.632034 AAACTCCTGTACCAGAACTTTCT 57.368 39.130 0.00 0.00 38.25 2.52
4742 5366 7.746703 AGAACTTTCTGGGAGTACTACATTTT 58.253 34.615 7.57 0.00 35.89 1.82
4743 5367 8.218488 AGAACTTTCTGGGAGTACTACATTTTT 58.782 33.333 7.57 0.00 35.89 1.94
5145 5777 6.726490 TCTGAACCAGAGTAAAACAGTACT 57.274 37.500 0.00 0.00 35.39 2.73
5515 6147 3.523157 TCCCATCTTTGCAGTTATCAGGA 59.477 43.478 0.00 0.00 0.00 3.86
5572 6204 4.108336 CGAATATCATAGGCTCCATGTCG 58.892 47.826 0.00 0.00 0.00 4.35
5605 6237 2.095364 GCACTCTGTGGCATTTTCTCTG 60.095 50.000 0.00 0.00 33.64 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.093408 CAGTACAAACACAAGCGCTCATAT 59.907 41.667 12.06 0.00 0.00 1.78
1 2 3.431912 CAGTACAAACACAAGCGCTCATA 59.568 43.478 12.06 0.00 0.00 2.15
2 3 2.224079 CAGTACAAACACAAGCGCTCAT 59.776 45.455 12.06 0.00 0.00 2.90
3 4 1.597195 CAGTACAAACACAAGCGCTCA 59.403 47.619 12.06 0.00 0.00 4.26
4 5 1.864711 TCAGTACAAACACAAGCGCTC 59.135 47.619 12.06 0.00 0.00 5.03
5 6 1.948104 TCAGTACAAACACAAGCGCT 58.052 45.000 2.64 2.64 0.00 5.92
6 7 2.574322 CATCAGTACAAACACAAGCGC 58.426 47.619 0.00 0.00 0.00 5.92
7 8 2.224079 AGCATCAGTACAAACACAAGCG 59.776 45.455 0.00 0.00 0.00 4.68
8 9 3.904136 AGCATCAGTACAAACACAAGC 57.096 42.857 0.00 0.00 0.00 4.01
33 34 6.144402 GTCGTGATGCTTGATTTGATGTTTTT 59.856 34.615 0.00 0.00 0.00 1.94
34 35 5.630680 GTCGTGATGCTTGATTTGATGTTTT 59.369 36.000 0.00 0.00 0.00 2.43
35 36 5.156355 GTCGTGATGCTTGATTTGATGTTT 58.844 37.500 0.00 0.00 0.00 2.83
49 50 0.647410 CGAGTCAATGGTCGTGATGC 59.353 55.000 0.00 0.00 0.00 3.91
172 173 2.476686 GGGAAACAGTATAAAACGCGGC 60.477 50.000 12.47 0.00 0.00 6.53
258 259 1.404843 CTGGGAGAGTGGTAGGCTAC 58.595 60.000 16.40 16.40 0.00 3.58
259 260 0.397254 GCTGGGAGAGTGGTAGGCTA 60.397 60.000 0.00 0.00 0.00 3.93
289 294 1.675483 TCAACCGGTCAATGCATATGC 59.325 47.619 21.09 21.09 42.50 3.14
290 295 2.945008 AGTCAACCGGTCAATGCATATG 59.055 45.455 8.04 0.00 0.00 1.78
291 296 2.945008 CAGTCAACCGGTCAATGCATAT 59.055 45.455 8.04 0.00 0.00 1.78
292 297 2.027653 TCAGTCAACCGGTCAATGCATA 60.028 45.455 8.04 0.00 0.00 3.14
293 298 1.167851 CAGTCAACCGGTCAATGCAT 58.832 50.000 8.04 0.00 0.00 3.96
294 299 0.107643 TCAGTCAACCGGTCAATGCA 59.892 50.000 8.04 0.00 0.00 3.96
317 322 4.144727 GGAGAGCGGGGGAGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
402 413 1.593265 GGGAAAAGTACCTCGCGGA 59.407 57.895 6.13 0.00 0.00 5.54
405 416 1.632948 GCACGGGAAAAGTACCTCGC 61.633 60.000 0.00 0.00 0.00 5.03
430 441 0.807496 GCTCACTCACATGAAAGCCC 59.193 55.000 0.00 0.00 0.00 5.19
449 460 4.039601 GATCGCGCGCACTCATCG 62.040 66.667 32.61 13.04 0.00 3.84
451 462 0.527600 TTAAGATCGCGCGCACTCAT 60.528 50.000 32.61 20.67 0.00 2.90
549 560 2.227865 GCTACGATCCAGATCCTCTGTC 59.772 54.545 2.11 0.00 42.80 3.51
654 669 5.518487 ACAAACAAACGCAAAAGTAATGAGG 59.482 36.000 0.00 0.00 0.00 3.86
668 683 6.826612 ACCAAAAGAATCAAACAAACAAACG 58.173 32.000 0.00 0.00 0.00 3.60
698 713 3.932580 CTTGTGCGCGCCTACTCCA 62.933 63.158 30.77 12.35 0.00 3.86
699 714 3.188786 CTTGTGCGCGCCTACTCC 61.189 66.667 30.77 9.73 0.00 3.85
701 716 2.642254 TACCTTGTGCGCGCCTACT 61.642 57.895 30.77 7.45 0.00 2.57
702 717 2.125832 TACCTTGTGCGCGCCTAC 60.126 61.111 30.77 21.76 0.00 3.18
703 718 2.125832 GTACCTTGTGCGCGCCTA 60.126 61.111 30.77 15.11 0.00 3.93
723 738 7.292129 GGTTAAAACGAACCTGAGATTCTAG 57.708 40.000 0.00 0.00 44.75 2.43
776 791 3.437213 TCAGATAAAGGGAAGACACGGA 58.563 45.455 0.00 0.00 0.00 4.69
778 793 6.595716 AGAATTTCAGATAAAGGGAAGACACG 59.404 38.462 0.00 0.00 0.00 4.49
779 794 7.607991 TCAGAATTTCAGATAAAGGGAAGACAC 59.392 37.037 0.00 0.00 0.00 3.67
780 795 7.689299 TCAGAATTTCAGATAAAGGGAAGACA 58.311 34.615 0.00 0.00 0.00 3.41
781 796 8.567285 TTCAGAATTTCAGATAAAGGGAAGAC 57.433 34.615 0.00 0.00 0.00 3.01
810 825 6.789268 AGACACTACTGGAGAGAGCATATAT 58.211 40.000 0.00 0.00 0.00 0.86
821 836 6.763610 ACTTTCTTTTCAAGACACTACTGGAG 59.236 38.462 0.00 0.00 37.23 3.86
838 853 2.052782 AAGGTGCCGTCACTTTCTTT 57.947 45.000 0.00 0.00 37.93 2.52
877 892 5.853282 GCTGATGAACACAATTTACTGTCAC 59.147 40.000 0.00 0.00 0.00 3.67
995 1010 3.386932 TCCCAGGATTCTCCATTTTGG 57.613 47.619 0.00 0.00 39.61 3.28
1061 1076 1.066143 GGTTGAGATCCACACGACCAT 60.066 52.381 0.00 0.00 41.33 3.55
1062 1077 0.320374 GGTTGAGATCCACACGACCA 59.680 55.000 0.00 0.00 41.33 4.02
1086 1101 6.061441 TCTCTCAGTGTTTGCTATTTCCAAA 58.939 36.000 0.00 0.00 0.00 3.28
1109 1124 1.336240 ACTGCATTTGAAAAGCGCCTC 60.336 47.619 2.29 0.00 0.00 4.70
1215 1230 4.233005 GTTGCTTCTTTTGCTCAATCTCC 58.767 43.478 0.00 0.00 0.00 3.71
1236 1251 2.567615 ACGTTCCTCCTCTAGCATTTGT 59.432 45.455 0.00 0.00 0.00 2.83
1453 1471 1.124780 TCTTCCACCGGTGTTTCTGA 58.875 50.000 31.80 19.03 0.00 3.27
1466 1484 4.487714 AATACCGCAGAGAATTCTTCCA 57.512 40.909 9.87 0.00 0.00 3.53
1470 1488 6.183360 CGTGTTTTAATACCGCAGAGAATTCT 60.183 38.462 7.95 7.95 0.00 2.40
1483 1501 8.730427 CAAGAAATAATCGGCGTGTTTTAATAC 58.270 33.333 6.85 0.00 0.00 1.89
1485 1503 6.252655 GCAAGAAATAATCGGCGTGTTTTAAT 59.747 34.615 6.85 0.00 0.00 1.40
1493 1511 1.400494 GGTGCAAGAAATAATCGGCGT 59.600 47.619 6.85 0.00 36.42 5.68
1494 1512 1.670811 AGGTGCAAGAAATAATCGGCG 59.329 47.619 0.00 0.00 36.42 6.46
1528 1546 3.055458 TGATGAGCAATTACAACGGGAGA 60.055 43.478 0.00 0.00 0.00 3.71
1534 1552 4.437930 GCAGACCTGATGAGCAATTACAAC 60.438 45.833 0.47 0.00 0.00 3.32
1566 1593 4.215613 GGAAGCTGTAAAAGGTGTCGAAAT 59.784 41.667 0.00 0.00 36.51 2.17
1571 1598 8.507524 AAATATAGGAAGCTGTAAAAGGTGTC 57.492 34.615 0.00 0.00 36.51 3.67
1592 1619 9.860650 AATGCCACCTAAATGTACATAGAAATA 57.139 29.630 9.21 0.00 0.00 1.40
1593 1620 8.766994 AATGCCACCTAAATGTACATAGAAAT 57.233 30.769 9.21 0.00 0.00 2.17
1594 1621 8.052748 AGAATGCCACCTAAATGTACATAGAAA 58.947 33.333 9.21 0.00 0.00 2.52
1595 1622 7.573710 AGAATGCCACCTAAATGTACATAGAA 58.426 34.615 9.21 0.00 0.00 2.10
1596 1623 7.136822 AGAATGCCACCTAAATGTACATAGA 57.863 36.000 9.21 0.00 0.00 1.98
1597 1624 8.367911 TCTAGAATGCCACCTAAATGTACATAG 58.632 37.037 9.21 3.63 0.00 2.23
1598 1625 8.257602 TCTAGAATGCCACCTAAATGTACATA 57.742 34.615 9.21 0.00 0.00 2.29
1599 1626 7.136822 TCTAGAATGCCACCTAAATGTACAT 57.863 36.000 1.41 1.41 0.00 2.29
1613 1640 1.586422 TGCGAATGCTCTAGAATGCC 58.414 50.000 1.83 0.00 43.34 4.40
1635 1662 3.509442 TCTCTGGAATGCCACCATTTTT 58.491 40.909 0.00 0.00 41.60 1.94
1636 1663 3.173953 TCTCTGGAATGCCACCATTTT 57.826 42.857 0.00 0.00 41.60 1.82
1637 1664 2.905415 TCTCTGGAATGCCACCATTT 57.095 45.000 0.00 0.00 41.60 2.32
1638 1665 2.827921 GTTTCTCTGGAATGCCACCATT 59.172 45.455 0.00 0.00 44.11 3.16
1639 1666 2.225091 TGTTTCTCTGGAATGCCACCAT 60.225 45.455 0.00 0.00 39.92 3.55
1640 1667 1.144708 TGTTTCTCTGGAATGCCACCA 59.855 47.619 0.00 0.00 39.92 4.17
1641 1668 1.815003 CTGTTTCTCTGGAATGCCACC 59.185 52.381 0.00 0.00 39.92 4.61
1642 1669 1.200948 GCTGTTTCTCTGGAATGCCAC 59.799 52.381 0.00 0.00 39.92 5.01
1643 1670 1.202915 TGCTGTTTCTCTGGAATGCCA 60.203 47.619 0.00 0.00 43.47 4.92
1644 1671 1.538047 TGCTGTTTCTCTGGAATGCC 58.462 50.000 0.00 0.00 0.00 4.40
1645 1672 3.572584 CTTTGCTGTTTCTCTGGAATGC 58.427 45.455 0.00 0.00 0.00 3.56
1646 1673 3.572584 GCTTTGCTGTTTCTCTGGAATG 58.427 45.455 0.00 0.00 0.00 2.67
1647 1674 2.560105 GGCTTTGCTGTTTCTCTGGAAT 59.440 45.455 0.00 0.00 0.00 3.01
1648 1675 1.956477 GGCTTTGCTGTTTCTCTGGAA 59.044 47.619 0.00 0.00 0.00 3.53
1649 1676 1.133823 TGGCTTTGCTGTTTCTCTGGA 60.134 47.619 0.00 0.00 0.00 3.86
1650 1677 1.321474 TGGCTTTGCTGTTTCTCTGG 58.679 50.000 0.00 0.00 0.00 3.86
1651 1678 3.441496 TTTGGCTTTGCTGTTTCTCTG 57.559 42.857 0.00 0.00 0.00 3.35
1652 1679 3.638160 TCATTTGGCTTTGCTGTTTCTCT 59.362 39.130 0.00 0.00 0.00 3.10
1653 1680 3.981211 TCATTTGGCTTTGCTGTTTCTC 58.019 40.909 0.00 0.00 0.00 2.87
1654 1681 3.243975 CCTCATTTGGCTTTGCTGTTTCT 60.244 43.478 0.00 0.00 0.00 2.52
1655 1682 3.062042 CCTCATTTGGCTTTGCTGTTTC 58.938 45.455 0.00 0.00 0.00 2.78
1656 1683 2.224354 CCCTCATTTGGCTTTGCTGTTT 60.224 45.455 0.00 0.00 0.00 2.83
1657 1684 1.345415 CCCTCATTTGGCTTTGCTGTT 59.655 47.619 0.00 0.00 0.00 3.16
1658 1685 0.971386 CCCTCATTTGGCTTTGCTGT 59.029 50.000 0.00 0.00 0.00 4.40
1659 1686 1.203994 CTCCCTCATTTGGCTTTGCTG 59.796 52.381 0.00 0.00 0.00 4.41
1660 1687 1.553706 CTCCCTCATTTGGCTTTGCT 58.446 50.000 0.00 0.00 0.00 3.91
1661 1688 0.108472 GCTCCCTCATTTGGCTTTGC 60.108 55.000 0.00 0.00 0.00 3.68
1662 1689 0.171903 CGCTCCCTCATTTGGCTTTG 59.828 55.000 0.00 0.00 0.00 2.77
1663 1690 0.967380 CCGCTCCCTCATTTGGCTTT 60.967 55.000 0.00 0.00 0.00 3.51
1877 1938 6.469782 ACATCCTGAAAACAAATTGTGAGT 57.530 33.333 0.00 0.00 0.00 3.41
1878 1939 9.480053 AATAACATCCTGAAAACAAATTGTGAG 57.520 29.630 0.00 0.00 0.00 3.51
1940 2002 7.877003 TCTTGACCTTATTCATCTCGTCTATC 58.123 38.462 0.00 0.00 0.00 2.08
1997 2059 9.965902 AATGGAGTATCAAATACAAACTCTCTT 57.034 29.630 0.00 0.00 38.21 2.85
2054 2116 0.600255 ACTTGCTGAAGACCGGTTCG 60.600 55.000 9.42 1.10 32.98 3.95
2154 2216 6.385649 AGCAACGGAAATTAAAGAAACAGA 57.614 33.333 0.00 0.00 0.00 3.41
2155 2217 6.695278 TGAAGCAACGGAAATTAAAGAAACAG 59.305 34.615 0.00 0.00 0.00 3.16
2156 2218 6.565234 TGAAGCAACGGAAATTAAAGAAACA 58.435 32.000 0.00 0.00 0.00 2.83
2157 2219 7.458038 TTGAAGCAACGGAAATTAAAGAAAC 57.542 32.000 0.00 0.00 0.00 2.78
2158 2220 8.480643 TTTTGAAGCAACGGAAATTAAAGAAA 57.519 26.923 0.00 0.00 0.00 2.52
2159 2221 8.655651 ATTTTGAAGCAACGGAAATTAAAGAA 57.344 26.923 0.00 0.00 0.00 2.52
2160 2222 8.141268 AGATTTTGAAGCAACGGAAATTAAAGA 58.859 29.630 0.00 0.00 0.00 2.52
2161 2223 8.298030 AGATTTTGAAGCAACGGAAATTAAAG 57.702 30.769 0.00 0.00 0.00 1.85
2162 2224 9.187455 GTAGATTTTGAAGCAACGGAAATTAAA 57.813 29.630 0.00 0.00 0.00 1.52
2289 2468 3.000322 GGATGACGACGCTATTTTCACTG 60.000 47.826 0.00 0.00 0.00 3.66
2301 2480 1.068474 GACCAACAAGGATGACGACG 58.932 55.000 0.00 0.00 41.22 5.12
2456 2635 6.074648 TGTGGAAAATACCCTCAAACTCAAT 58.925 36.000 0.00 0.00 0.00 2.57
2468 2647 2.678336 CTCGGCTCTTGTGGAAAATACC 59.322 50.000 0.00 0.00 0.00 2.73
2586 3018 9.102757 GCATTGAAGTAGATACAATTCAGAAGA 57.897 33.333 0.00 0.00 33.53 2.87
2711 3143 8.172352 AGTAAAATGTACAACATGCAAACCTA 57.828 30.769 0.00 0.00 37.97 3.08
2759 3191 3.904339 ACTCAGTGTACCATTCTGAACCT 59.096 43.478 0.00 0.00 37.68 3.50
2774 3206 6.377429 TGTTAGATAAGTGGGAGTACTCAGTG 59.623 42.308 23.91 0.00 29.65 3.66
2785 3217 4.818546 CCTCTGCATTGTTAGATAAGTGGG 59.181 45.833 0.00 0.00 0.00 4.61
2798 3230 1.001487 TGCGTTGTTTCCTCTGCATTG 60.001 47.619 0.00 0.00 0.00 2.82
2807 3242 1.065600 TGCTGCTTGCGTTGTTTCC 59.934 52.632 0.00 0.00 46.63 3.13
2816 3251 0.727122 CTAGCGTTTGTGCTGCTTGC 60.727 55.000 0.00 0.00 46.70 4.01
2823 3258 0.240945 ATTGTGGCTAGCGTTTGTGC 59.759 50.000 9.00 0.00 0.00 4.57
2824 3259 1.266718 ACATTGTGGCTAGCGTTTGTG 59.733 47.619 9.00 7.50 0.00 3.33
2830 3265 1.063027 CATGTGACATTGTGGCTAGCG 59.937 52.381 9.00 0.00 0.00 4.26
2936 3371 1.537562 CCAGCGGATAACGTAACCTCC 60.538 57.143 0.00 0.00 46.52 4.30
2974 3409 0.839277 ACCAAGGATGCCATCGATCA 59.161 50.000 0.00 0.00 0.00 2.92
2979 3414 1.202746 GGAGAGACCAAGGATGCCATC 60.203 57.143 0.00 0.00 38.79 3.51
3065 3500 6.547510 GCAGGTATCTAGGAAATCCAACAATT 59.452 38.462 1.67 0.00 38.89 2.32
3082 3517 1.811941 GCTAGGCCAGTTGCAGGTATC 60.812 57.143 5.01 0.00 43.89 2.24
3083 3518 0.181350 GCTAGGCCAGTTGCAGGTAT 59.819 55.000 5.01 0.00 43.89 2.73
3084 3519 1.602237 GCTAGGCCAGTTGCAGGTA 59.398 57.895 5.01 0.00 43.89 3.08
3085 3520 2.352805 GCTAGGCCAGTTGCAGGT 59.647 61.111 5.01 0.00 43.89 4.00
3086 3521 2.821366 CGCTAGGCCAGTTGCAGG 60.821 66.667 5.01 0.00 43.89 4.85
3107 3545 5.514274 ACCAACCAATTGTCAAGTTAGTG 57.486 39.130 4.43 0.00 33.60 2.74
3159 3597 1.555967 ACCAGTGTTGTTGTGCCTTT 58.444 45.000 0.00 0.00 0.00 3.11
3221 3659 4.660771 ACTATTAGATATATGGGCCAGGGC 59.339 45.833 13.78 3.77 41.06 5.19
3222 3660 6.831664 AACTATTAGATATATGGGCCAGGG 57.168 41.667 13.78 0.00 0.00 4.45
3223 3661 7.069578 ACGTAACTATTAGATATATGGGCCAGG 59.930 40.741 13.78 0.00 0.00 4.45
3224 3662 7.921214 CACGTAACTATTAGATATATGGGCCAG 59.079 40.741 13.78 0.00 0.00 4.85
3225 3663 7.398047 ACACGTAACTATTAGATATATGGGCCA 59.602 37.037 9.61 9.61 0.00 5.36
3247 3685 7.060600 TCATTCTTGACTTATTTGCTACACG 57.939 36.000 0.00 0.00 0.00 4.49
3308 3746 5.577164 ACGACCGACTTTTGAGATATTTCTG 59.423 40.000 0.00 0.00 30.30 3.02
3310 3748 5.724223 GCACGACCGACTTTTGAGATATTTC 60.724 44.000 0.00 0.00 0.00 2.17
3530 3968 3.178046 TCACCTATGCACCCTTCAAGTA 58.822 45.455 0.00 0.00 0.00 2.24
3531 3969 1.985159 TCACCTATGCACCCTTCAAGT 59.015 47.619 0.00 0.00 0.00 3.16
3626 4064 8.557864 TGGATTCAAGTTGCAAAAACATTAATG 58.442 29.630 14.01 14.01 0.00 1.90
3635 4073 4.275443 GGCAATTGGATTCAAGTTGCAAAA 59.725 37.500 23.58 0.00 42.36 2.44
3758 4196 3.119352 TGCGCATCAGCTATGACCTATAG 60.119 47.826 5.66 0.00 41.46 1.31
3801 4239 4.141846 TGGAAGCTCACCTGATCAAGTATC 60.142 45.833 10.53 0.00 34.93 2.24
3803 4241 3.173151 TGGAAGCTCACCTGATCAAGTA 58.827 45.455 10.53 0.00 0.00 2.24
3824 4262 8.917088 CCAGTATGTCTTGGGAATAAATGAAAT 58.083 33.333 0.00 0.00 0.00 2.17
3838 4276 5.734720 TCTTAAGAAGGCCAGTATGTCTTG 58.265 41.667 5.01 0.00 29.91 3.02
3842 4280 4.104831 ACCTCTTAAGAAGGCCAGTATGT 58.895 43.478 5.01 0.00 0.00 2.29
3886 4326 7.658179 ATGTTTCGTACTATATCCAAGCATG 57.342 36.000 0.00 0.00 0.00 4.06
4088 4547 1.927174 CAACTCGAGGCATCTTTACCG 59.073 52.381 18.41 0.00 0.00 4.02
4090 4549 2.605366 GAGCAACTCGAGGCATCTTTAC 59.395 50.000 18.41 0.00 0.00 2.01
4104 4563 2.325583 TCTTCACGGTTTGAGCAACT 57.674 45.000 0.00 0.00 34.94 3.16
4293 4914 8.055279 TGAATCAGAAACATATTCCAGAAACC 57.945 34.615 0.00 0.00 0.00 3.27
4335 4956 3.644738 TCTCTGCAGATGATCATAAGCCA 59.355 43.478 18.63 11.51 0.00 4.75
4368 4989 8.677300 GCATGAATATACCTCTTGAACAGAAAA 58.323 33.333 0.00 0.00 0.00 2.29
4389 5010 4.167652 TGTATGATCACCATTGGCATGA 57.832 40.909 1.54 0.07 36.71 3.07
4400 5021 7.068103 TCCCACCATATTTTGTTGTATGATCAC 59.932 37.037 0.00 0.00 31.48 3.06
4404 5025 6.249192 TGTCCCACCATATTTTGTTGTATGA 58.751 36.000 0.00 0.00 31.48 2.15
4504 5126 8.910351 AGGCAGAAACACCTTAATAATATCTC 57.090 34.615 0.00 0.00 29.74 2.75
4513 5135 5.830991 ACATACAAAGGCAGAAACACCTTAA 59.169 36.000 0.00 0.00 45.62 1.85
4514 5136 5.240623 CACATACAAAGGCAGAAACACCTTA 59.759 40.000 0.00 0.00 45.62 2.69
4524 5146 7.437862 ACACAATTTTTACACATACAAAGGCAG 59.562 33.333 0.00 0.00 0.00 4.85
4560 5182 6.071784 TCCACCTGAATCATTGTGAAAATCAG 60.072 38.462 12.71 10.97 36.38 2.90
4611 5234 8.383175 TGTTGACCCTTCATTCTCTTTACTAAT 58.617 33.333 0.00 0.00 0.00 1.73
5145 5777 4.040829 CACCTTATCATGGACTGATAGGCA 59.959 45.833 0.00 0.00 45.36 4.75
5491 6123 4.706476 CCTGATAACTGCAAAGATGGGAAA 59.294 41.667 0.00 0.00 0.00 3.13
5494 6126 3.889815 TCCTGATAACTGCAAAGATGGG 58.110 45.455 0.00 0.00 0.00 4.00
5515 6147 3.904339 ACTTCATCTACACAGACACCCTT 59.096 43.478 0.00 0.00 32.25 3.95
5572 6204 4.118410 CCACAGAGTGCATCAAGATAGAC 58.882 47.826 0.00 0.00 31.34 2.59
5605 6237 2.821810 GAGCTCTTTGGCCCGCTC 60.822 66.667 6.43 6.31 41.60 5.03


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

AutoCloner maintained by Alex Coulton.