Multiple sequence alignment - TraesCS6A01G170100

Loading Multiple Alignment...

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 TraesCS6A01G170100 chr6A 100.000 2216 0 0 1 2216 180370123 180372338 0.000000e+00 4093.0
1 TraesCS6A01G170100 chr6A 80.750 800 74 43 702 1451 180313706 180314475 3.220000e-153 551.0
2 TraesCS6A01G170100 chr6D 88.962 915 34 13 698 1564 137528402 137529297 0.000000e+00 1068.0
3 TraesCS6A01G170100 chr6D 80.699 772 84 35 698 1451 137500998 137501722 6.960000e-150 540.0
4 TraesCS6A01G170100 chr6D 90.821 207 13 5 1895 2098 137529494 137529697 2.800000e-69 272.0
5 TraesCS6A01G170100 chr6D 89.904 208 16 2 1671 1877 137529308 137529511 1.690000e-66 263.0
6 TraesCS6A01G170100 chr6B 86.828 911 55 28 698 1560 237111548 237112441 0.000000e+00 957.0
7 TraesCS6A01G170100 chr6B 86.709 632 65 12 55 671 703465305 703465932 0.000000e+00 684.0
8 TraesCS6A01G170100 chr6B 80.491 815 71 38 698 1451 237108329 237109116 5.380000e-151 544.0
9 TraesCS6A01G170100 chr6B 93.237 207 9 4 1895 2098 237112631 237112835 1.290000e-77 300.0
10 TraesCS6A01G170100 chr6B 83.491 212 12 7 1671 1877 237112455 237112648 2.260000e-40 176.0
11 TraesCS6A01G170100 chr4B 86.099 669 74 12 43 695 16081845 16082510 0.000000e+00 702.0
12 TraesCS6A01G170100 chr7A 86.846 631 63 11 56 671 10222744 10222119 0.000000e+00 688.0
13 TraesCS6A01G170100 chr3D 86.427 641 71 9 45 671 505410155 505410793 0.000000e+00 688.0
14 TraesCS6A01G170100 chr7B 85.845 657 76 10 54 697 636462130 636461478 0.000000e+00 682.0
15 TraesCS6A01G170100 chr5B 86.000 650 73 10 54 687 530709911 530709264 0.000000e+00 680.0
16 TraesCS6A01G170100 chr5B 86.022 651 70 14 54 688 606279652 606280297 0.000000e+00 678.0
17 TraesCS6A01G170100 chr2B 85.823 656 74 10 54 692 436266734 436266081 0.000000e+00 678.0
18 TraesCS6A01G170100 chr1D 85.542 664 77 11 39 687 384471848 384471189 0.000000e+00 676.0
19 TraesCS6A01G170100 chr1D 95.575 113 5 0 2104 2216 19339314 19339202 4.860000e-42 182.0
20 TraesCS6A01G170100 chr1A 100.000 119 0 0 2098 2216 379860345 379860227 1.030000e-53 220.0
21 TraesCS6A01G170100 chr1A 100.000 119 0 0 2098 2216 519694354 519694236 1.030000e-53 220.0
22 TraesCS6A01G170100 chr1A 92.683 82 6 0 2099 2180 519681525 519681606 3.870000e-23 119.0
23 TraesCS6A01G170100 chr1A 100.000 61 0 0 2099 2159 379856146 379856206 1.800000e-21 113.0
24 TraesCS6A01G170100 chrUn 95.868 121 5 0 2096 2216 68355458 68355338 1.740000e-46 196.0
25 TraesCS6A01G170100 chr5A 85.981 107 15 0 2091 2197 132181059 132180953 5.000000e-22 115.0
26 TraesCS6A01G170100 chr7D 84.071 113 18 0 2098 2210 63990208 63990096 2.330000e-20 110.0
27 TraesCS6A01G170100 chr2A 85.000 100 15 0 2098 2197 374718311 374718410 3.890000e-18 102.0
28 TraesCS6A01G170100 chr3A 93.478 46 1 1 1609 1654 53747389 53747432 1.420000e-07 67.6


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 TraesCS6A01G170100 chr6A 180370123 180372338 2215 False 4093.000000 4093 100.000000 1 2216 1 chr6A.!!$F2 2215
1 TraesCS6A01G170100 chr6A 180313706 180314475 769 False 551.000000 551 80.750000 702 1451 1 chr6A.!!$F1 749
2 TraesCS6A01G170100 chr6D 137500998 137501722 724 False 540.000000 540 80.699000 698 1451 1 chr6D.!!$F1 753
3 TraesCS6A01G170100 chr6D 137528402 137529697 1295 False 534.333333 1068 89.895667 698 2098 3 chr6D.!!$F2 1400
4 TraesCS6A01G170100 chr6B 703465305 703465932 627 False 684.000000 684 86.709000 55 671 1 chr6B.!!$F1 616
5 TraesCS6A01G170100 chr6B 237108329 237112835 4506 False 494.250000 957 86.011750 698 2098 4 chr6B.!!$F2 1400
6 TraesCS6A01G170100 chr4B 16081845 16082510 665 False 702.000000 702 86.099000 43 695 1 chr4B.!!$F1 652
7 TraesCS6A01G170100 chr7A 10222119 10222744 625 True 688.000000 688 86.846000 56 671 1 chr7A.!!$R1 615
8 TraesCS6A01G170100 chr3D 505410155 505410793 638 False 688.000000 688 86.427000 45 671 1 chr3D.!!$F1 626
9 TraesCS6A01G170100 chr7B 636461478 636462130 652 True 682.000000 682 85.845000 54 697 1 chr7B.!!$R1 643
10 TraesCS6A01G170100 chr5B 530709264 530709911 647 True 680.000000 680 86.000000 54 687 1 chr5B.!!$R1 633
11 TraesCS6A01G170100 chr5B 606279652 606280297 645 False 678.000000 678 86.022000 54 688 1 chr5B.!!$F1 634
12 TraesCS6A01G170100 chr2B 436266081 436266734 653 True 678.000000 678 85.823000 54 692 1 chr2B.!!$R1 638
13 TraesCS6A01G170100 chr1D 384471189 384471848 659 True 676.000000 676 85.542000 39 687 1 chr1D.!!$R2 648

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
721 740 0.030504 TGGTCGCACGTTTAGTCGAA 59.969 50.0 0.0 0.0 35.43 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 4995 0.102844 TCGTTCGGTTTTCGTCCAGT 59.897 50.0 0.0 0.0 40.32 4.0 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
28 29 7.849804 ACTTTGCATATAGTGTGTTCTTAGG 57.150 36.000 0.00 0.00 0.00 2.69
29 30 6.823689 ACTTTGCATATAGTGTGTTCTTAGGG 59.176 38.462 0.00 0.00 0.00 3.53
30 31 6.553953 TTGCATATAGTGTGTTCTTAGGGA 57.446 37.500 0.00 0.00 0.00 4.20
31 32 5.914033 TGCATATAGTGTGTTCTTAGGGAC 58.086 41.667 0.00 0.00 0.00 4.46
32 33 5.163343 TGCATATAGTGTGTTCTTAGGGACC 60.163 44.000 0.00 0.00 0.00 4.46
33 34 5.070580 GCATATAGTGTGTTCTTAGGGACCT 59.929 44.000 0.00 0.00 0.00 3.85
34 35 6.267014 GCATATAGTGTGTTCTTAGGGACCTA 59.733 42.308 0.00 0.00 0.00 3.08
35 36 7.659186 CATATAGTGTGTTCTTAGGGACCTAC 58.341 42.308 0.00 0.00 0.00 3.18
36 37 2.824341 AGTGTGTTCTTAGGGACCTACG 59.176 50.000 0.00 0.00 0.00 3.51
37 38 2.560105 GTGTGTTCTTAGGGACCTACGT 59.440 50.000 0.00 0.00 0.00 3.57
38 39 2.559668 TGTGTTCTTAGGGACCTACGTG 59.440 50.000 0.00 0.00 0.00 4.49
39 40 2.821969 GTGTTCTTAGGGACCTACGTGA 59.178 50.000 0.00 0.00 0.00 4.35
40 41 3.256631 GTGTTCTTAGGGACCTACGTGAA 59.743 47.826 0.00 1.36 0.00 3.18
41 42 3.508793 TGTTCTTAGGGACCTACGTGAAG 59.491 47.826 0.00 0.00 0.00 3.02
42 43 2.097825 TCTTAGGGACCTACGTGAAGC 58.902 52.381 0.00 0.00 0.00 3.86
43 44 1.136500 CTTAGGGACCTACGTGAAGCC 59.864 57.143 0.00 0.00 0.00 4.35
44 45 0.685458 TAGGGACCTACGTGAAGCCC 60.685 60.000 0.00 4.14 35.79 5.19
45 46 1.988406 GGGACCTACGTGAAGCCCT 60.988 63.158 0.00 0.00 32.78 5.19
48 49 1.472188 GACCTACGTGAAGCCCTAGT 58.528 55.000 0.00 0.00 0.00 2.57
52 53 1.471684 CTACGTGAAGCCCTAGTCGTT 59.528 52.381 0.00 0.00 33.70 3.85
66 71 0.321996 GTCGTTGCCTCCTCCTTCTT 59.678 55.000 0.00 0.00 0.00 2.52
88 94 4.532834 TCACAAAAAGCTAGGGTTTCTGT 58.467 39.130 0.00 0.00 35.09 3.41
91 97 5.067805 CACAAAAAGCTAGGGTTTCTGTCTT 59.932 40.000 0.00 0.00 32.93 3.01
94 100 2.621070 AGCTAGGGTTTCTGTCTTCCA 58.379 47.619 0.00 0.00 0.00 3.53
95 101 3.185455 AGCTAGGGTTTCTGTCTTCCAT 58.815 45.455 0.00 0.00 0.00 3.41
147 153 2.375173 CCCTAGGGCTGGGGGTAA 59.625 66.667 16.90 0.00 46.58 2.85
157 165 1.596496 CTGGGGGTAAGGTGGATCTT 58.404 55.000 0.00 0.00 0.00 2.40
243 253 0.319555 TCAGAAAGACAAGACGGCGG 60.320 55.000 13.24 0.00 0.00 6.13
244 254 1.668151 AGAAAGACAAGACGGCGGC 60.668 57.895 13.24 8.92 0.00 6.53
271 281 4.140536 CTCCCTGAAGATGGAATAAAGGC 58.859 47.826 0.00 0.00 0.00 4.35
275 285 4.141298 CCTGAAGATGGAATAAAGGCCTCT 60.141 45.833 5.23 0.00 0.00 3.69
278 288 3.397527 AGATGGAATAAAGGCCTCTCCA 58.602 45.455 21.61 21.61 40.36 3.86
353 369 1.068588 CGGCGGATCTATCTTTGGTGA 59.931 52.381 0.00 0.00 0.00 4.02
382 398 2.194271 GGATCTCATCGTTGTTCGTCC 58.806 52.381 0.00 0.00 40.80 4.79
384 400 3.448686 GATCTCATCGTTGTTCGTCCAT 58.551 45.455 0.00 0.00 40.80 3.41
400 416 1.338655 TCCATGTTCGTGTGTCTTCGA 59.661 47.619 0.00 0.00 0.00 3.71
470 486 4.065281 GTGCGCTGGTCCTACGGT 62.065 66.667 9.73 0.00 0.00 4.83
523 539 0.738389 CAACAAGTTGTGCCCGACTT 59.262 50.000 9.79 0.00 44.58 3.01
526 542 0.878523 CAAGTTGTGCCCGACTTCGA 60.879 55.000 0.00 0.00 42.33 3.71
589 605 3.631145 AGTGTTTGTAGTCGTCGCTAA 57.369 42.857 0.00 0.00 0.00 3.09
599 615 1.466167 GTCGTCGCTAAGTGGTCTACA 59.534 52.381 0.00 0.00 0.00 2.74
603 619 3.181499 CGTCGCTAAGTGGTCTACAGATT 60.181 47.826 0.00 0.00 0.00 2.40
606 622 4.461431 TCGCTAAGTGGTCTACAGATTTGA 59.539 41.667 0.00 0.00 0.00 2.69
617 633 8.999431 TGGTCTACAGATTTGAGTGTAATTTTC 58.001 33.333 0.00 0.00 0.00 2.29
664 683 7.714813 TGCCATGATTAAAAATGAGTAGATCGA 59.285 33.333 0.00 0.00 0.00 3.59
721 740 0.030504 TGGTCGCACGTTTAGTCGAA 59.969 50.000 0.00 0.00 35.43 3.71
850 892 2.768492 GCTTCATGGCGCCTTCCTG 61.768 63.158 29.70 18.83 0.00 3.86
942 1024 3.058160 CCGTGCCAAGAGCCCAAG 61.058 66.667 0.00 0.00 42.71 3.61
992 1074 2.498078 AGGGAAGAAGCTAAGAACCGAG 59.502 50.000 0.00 0.00 0.00 4.63
1241 1356 1.375140 CGGAGCTGAGCAAGAGCAA 60.375 57.895 7.39 0.00 45.49 3.91
1246 1361 0.099082 GCTGAGCAAGAGCAAGATGC 59.901 55.000 0.00 0.00 45.49 3.91
1377 4697 8.904099 AAATAATTAGTGAAGAAGATACGGGG 57.096 34.615 0.00 0.00 0.00 5.73
1379 4699 5.952347 ATTAGTGAAGAAGATACGGGGTT 57.048 39.130 0.00 0.00 0.00 4.11
1380 4700 3.611766 AGTGAAGAAGATACGGGGTTG 57.388 47.619 0.00 0.00 0.00 3.77
1381 4701 2.904434 AGTGAAGAAGATACGGGGTTGT 59.096 45.455 0.00 0.00 0.00 3.32
1422 4750 7.148950 GCTTATATTACTCGTGTGTGCAGTATC 60.149 40.741 0.00 0.00 0.00 2.24
1432 4764 7.882179 TCGTGTGTGCAGTATCTATGTATATT 58.118 34.615 0.00 0.00 0.00 1.28
1493 4836 5.632034 AAGATTATCCTTGGTACTGGGAC 57.368 43.478 0.00 0.00 33.45 4.46
1503 4846 2.235402 TGGTACTGGGACTCGATTTTCC 59.765 50.000 0.00 0.00 0.00 3.13
1526 4869 2.663119 GCAATGCATCCTCGTGAAAAAC 59.337 45.455 0.00 0.00 0.00 2.43
1565 4908 9.515020 TTCATTCGAATTTCATAGGTAAATTGC 57.485 29.630 8.21 0.00 36.82 3.56
1567 4910 9.299963 CATTCGAATTTCATAGGTAAATTGCAA 57.700 29.630 8.21 0.00 36.82 4.08
1568 4911 8.682128 TTCGAATTTCATAGGTAAATTGCAAC 57.318 30.769 0.00 0.00 36.82 4.17
1570 4913 6.964370 CGAATTTCATAGGTAAATTGCAACGA 59.036 34.615 0.00 0.00 36.82 3.85
1571 4914 7.643764 CGAATTTCATAGGTAAATTGCAACGAT 59.356 33.333 0.00 0.00 36.82 3.73
1602 4945 4.974368 TTTTTCTTTCGAAACAGAGGCA 57.026 36.364 6.47 0.00 38.77 4.75
1603 4946 3.963383 TTTCTTTCGAAACAGAGGCAC 57.037 42.857 6.47 0.00 34.35 5.01
1604 4947 1.878953 TCTTTCGAAACAGAGGCACC 58.121 50.000 6.47 0.00 0.00 5.01
1605 4948 1.416401 TCTTTCGAAACAGAGGCACCT 59.584 47.619 6.47 0.00 0.00 4.00
1606 4949 1.801178 CTTTCGAAACAGAGGCACCTC 59.199 52.381 6.47 8.74 43.03 3.85
1607 4950 0.756294 TTCGAAACAGAGGCACCTCA 59.244 50.000 18.67 0.00 44.99 3.86
1608 4951 0.976641 TCGAAACAGAGGCACCTCAT 59.023 50.000 18.67 3.67 44.99 2.90
1609 4952 1.066858 TCGAAACAGAGGCACCTCATC 60.067 52.381 18.67 9.81 44.99 2.92
1610 4953 1.363744 GAAACAGAGGCACCTCATCG 58.636 55.000 18.67 8.98 44.99 3.84
1611 4954 0.976641 AAACAGAGGCACCTCATCGA 59.023 50.000 18.67 0.00 44.99 3.59
1612 4955 1.198713 AACAGAGGCACCTCATCGAT 58.801 50.000 18.67 0.00 44.99 3.59
1613 4956 1.198713 ACAGAGGCACCTCATCGATT 58.801 50.000 18.67 0.00 44.99 3.34
1614 4957 2.388735 ACAGAGGCACCTCATCGATTA 58.611 47.619 18.67 0.00 44.99 1.75
1615 4958 2.766263 ACAGAGGCACCTCATCGATTAA 59.234 45.455 18.67 0.00 44.99 1.40
1616 4959 3.389329 ACAGAGGCACCTCATCGATTAAT 59.611 43.478 18.67 0.00 44.99 1.40
1617 4960 4.141620 ACAGAGGCACCTCATCGATTAATT 60.142 41.667 18.67 0.00 44.99 1.40
1618 4961 5.070446 ACAGAGGCACCTCATCGATTAATTA 59.930 40.000 18.67 0.00 44.99 1.40
1619 4962 5.991606 CAGAGGCACCTCATCGATTAATTAA 59.008 40.000 18.67 0.00 44.99 1.40
1620 4963 6.146837 CAGAGGCACCTCATCGATTAATTAAG 59.853 42.308 18.67 0.00 44.99 1.85
1621 4964 6.042093 AGAGGCACCTCATCGATTAATTAAGA 59.958 38.462 18.67 0.00 44.99 2.10
1622 4965 6.591935 AGGCACCTCATCGATTAATTAAGAA 58.408 36.000 3.94 0.00 0.00 2.52
1623 4966 6.708054 AGGCACCTCATCGATTAATTAAGAAG 59.292 38.462 3.94 0.00 0.00 2.85
1624 4967 6.706270 GGCACCTCATCGATTAATTAAGAAGA 59.294 38.462 3.94 3.72 0.00 2.87
1625 4968 7.226720 GGCACCTCATCGATTAATTAAGAAGAA 59.773 37.037 3.94 0.00 0.00 2.52
1626 4969 8.612619 GCACCTCATCGATTAATTAAGAAGAAA 58.387 33.333 3.94 0.00 0.00 2.52
1656 4999 9.757227 TTGTCCAATTAATTAACAGAAAACTGG 57.243 29.630 12.67 2.98 0.00 4.00
1657 5000 9.137459 TGTCCAATTAATTAACAGAAAACTGGA 57.863 29.630 0.00 0.00 0.00 3.86
1658 5001 9.406828 GTCCAATTAATTAACAGAAAACTGGAC 57.593 33.333 10.26 10.26 40.66 4.02
1659 5002 8.293867 TCCAATTAATTAACAGAAAACTGGACG 58.706 33.333 0.00 0.00 0.00 4.79
1660 5003 8.293867 CCAATTAATTAACAGAAAACTGGACGA 58.706 33.333 0.00 0.00 0.00 4.20
1661 5004 9.672086 CAATTAATTAACAGAAAACTGGACGAA 57.328 29.630 0.00 0.00 0.00 3.85
1664 5007 7.980742 AATTAACAGAAAACTGGACGAAAAC 57.019 32.000 0.00 0.00 0.00 2.43
1665 5008 4.365899 AACAGAAAACTGGACGAAAACC 57.634 40.909 0.00 0.00 0.00 3.27
1666 5009 2.353579 ACAGAAAACTGGACGAAAACCG 59.646 45.455 0.00 0.00 45.44 4.44
1667 5010 2.610374 CAGAAAACTGGACGAAAACCGA 59.390 45.455 0.00 0.00 41.76 4.69
1668 5011 3.064271 CAGAAAACTGGACGAAAACCGAA 59.936 43.478 0.00 0.00 41.76 4.30
1669 5012 3.064408 AGAAAACTGGACGAAAACCGAAC 59.936 43.478 0.00 0.00 41.76 3.95
1695 5038 9.836076 CGATGCATGATTATCAGAATATGTTTT 57.164 29.630 2.46 0.00 0.00 2.43
1699 5042 9.754382 GCATGATTATCAGAATATGTTTTTGGT 57.246 29.630 0.00 0.00 0.00 3.67
1722 5065 0.737219 GGATGGCTCATTGTCACTGC 59.263 55.000 0.00 0.00 30.59 4.40
1725 5068 1.241165 TGGCTCATTGTCACTGCAAG 58.759 50.000 0.00 0.00 42.29 4.01
1730 5073 3.004106 GCTCATTGTCACTGCAAGAACTT 59.996 43.478 0.00 0.00 37.43 2.66
1731 5074 4.534168 CTCATTGTCACTGCAAGAACTTG 58.466 43.478 9.82 9.82 43.14 3.16
1760 5103 1.160137 CTAGGTGGTGCACTGCTTTC 58.840 55.000 17.98 0.00 34.40 2.62
1787 5130 2.561569 TCAGACATCAGAGCATGCATG 58.438 47.619 22.70 22.70 0.00 4.06
1831 5174 8.597227 CACTAATTTTCCATGCATGTTGTTATG 58.403 33.333 24.58 8.13 0.00 1.90
1833 5176 6.971527 ATTTTCCATGCATGTTGTTATGTG 57.028 33.333 24.58 6.69 0.00 3.21
1865 5213 4.121317 CACTGATCATCAAGAGAGAAGGC 58.879 47.826 0.00 0.00 0.00 4.35
1875 5223 5.243981 TCAAGAGAGAAGGCAAGATTTCTG 58.756 41.667 0.00 0.00 33.97 3.02
1876 5224 3.608796 AGAGAGAAGGCAAGATTTCTGC 58.391 45.455 0.00 0.00 33.97 4.26
1881 5229 2.498077 GGCAAGATTTCTGCCTCCC 58.502 57.895 6.59 0.00 44.72 4.30
1882 5230 1.379642 GGCAAGATTTCTGCCTCCCG 61.380 60.000 6.59 0.00 44.72 5.14
1883 5231 1.997928 GCAAGATTTCTGCCTCCCGC 61.998 60.000 0.00 0.00 38.31 6.13
1925 5273 4.401519 AGATTTCTGCACCCTGAATGATTG 59.598 41.667 0.00 0.00 0.00 2.67
1928 5276 0.971959 TGCACCCTGAATGATTGCCC 60.972 55.000 0.00 0.00 31.94 5.36
1946 5294 1.893137 CCCTGTTTTTCCTTAGGCCAC 59.107 52.381 5.01 0.00 0.00 5.01
1949 5297 3.222603 CTGTTTTTCCTTAGGCCACTGT 58.777 45.455 5.01 0.00 0.00 3.55
1950 5298 2.955660 TGTTTTTCCTTAGGCCACTGTG 59.044 45.455 5.01 0.00 0.00 3.66
1951 5299 2.956333 GTTTTTCCTTAGGCCACTGTGT 59.044 45.455 5.01 0.00 0.00 3.72
1979 5327 7.117285 AGATTCAGTTCATATGTCAGCTACA 57.883 36.000 1.90 0.00 43.86 2.74
1993 5341 2.105477 CAGCTACACATGGCCTTCCTAT 59.895 50.000 3.32 0.00 31.21 2.57
1994 5342 3.324846 CAGCTACACATGGCCTTCCTATA 59.675 47.826 3.32 0.00 31.21 1.31
2004 5355 7.616935 CACATGGCCTTCCTATATATGGAAATT 59.383 37.037 3.32 0.00 42.29 1.82
2098 5449 2.484264 GGAAGAAACCATGTCCAAGTCG 59.516 50.000 0.00 0.00 0.00 4.18
2099 5450 2.185004 AGAAACCATGTCCAAGTCGG 57.815 50.000 0.00 0.00 0.00 4.79
2100 5451 1.697432 AGAAACCATGTCCAAGTCGGA 59.303 47.619 0.00 0.00 43.61 4.55
2107 5458 4.887957 TCCAAGTCGGACTGGGAT 57.112 55.556 27.02 2.11 43.32 3.85
2108 5459 2.591915 TCCAAGTCGGACTGGGATC 58.408 57.895 27.02 0.00 43.32 3.36
2109 5460 0.252057 TCCAAGTCGGACTGGGATCA 60.252 55.000 27.02 8.61 43.32 2.92
2110 5461 0.176680 CCAAGTCGGACTGGGATCAG 59.823 60.000 24.78 0.00 42.14 2.90
2111 5462 0.176680 CAAGTCGGACTGGGATCAGG 59.823 60.000 12.12 0.00 44.99 3.86
2112 5463 0.252284 AAGTCGGACTGGGATCAGGT 60.252 55.000 12.12 0.00 44.99 4.00
2113 5464 0.972983 AGTCGGACTGGGATCAGGTG 60.973 60.000 10.41 0.00 44.99 4.00
2114 5465 0.970937 GTCGGACTGGGATCAGGTGA 60.971 60.000 0.00 0.00 44.99 4.02
2115 5466 0.970937 TCGGACTGGGATCAGGTGAC 60.971 60.000 0.00 0.00 44.99 3.67
2116 5467 1.257750 CGGACTGGGATCAGGTGACA 61.258 60.000 0.00 0.00 44.99 3.58
2117 5468 1.207791 GGACTGGGATCAGGTGACAT 58.792 55.000 0.00 0.00 44.99 3.06
2118 5469 1.134280 GGACTGGGATCAGGTGACATG 60.134 57.143 0.00 0.00 44.99 3.21
2119 5470 0.254178 ACTGGGATCAGGTGACATGC 59.746 55.000 0.00 0.00 44.99 4.06
2120 5471 0.465097 CTGGGATCAGGTGACATGCC 60.465 60.000 0.00 0.00 37.36 4.40
2121 5472 0.915872 TGGGATCAGGTGACATGCCT 60.916 55.000 0.00 0.00 36.66 4.75
2122 5473 0.179034 GGGATCAGGTGACATGCCTC 60.179 60.000 0.00 0.00 33.31 4.70
2123 5474 0.835941 GGATCAGGTGACATGCCTCT 59.164 55.000 0.00 0.00 33.31 3.69
2124 5475 1.211457 GGATCAGGTGACATGCCTCTT 59.789 52.381 0.00 0.00 33.31 2.85
2125 5476 2.286872 GATCAGGTGACATGCCTCTTG 58.713 52.381 0.00 0.00 33.31 3.02
2126 5477 0.325933 TCAGGTGACATGCCTCTTGG 59.674 55.000 0.00 0.00 33.31 3.61
2136 5487 2.743928 CCTCTTGGCAGTCACCGC 60.744 66.667 0.00 0.00 0.00 5.68
2137 5488 3.114616 CTCTTGGCAGTCACCGCG 61.115 66.667 0.00 0.00 0.00 6.46
2138 5489 3.865929 CTCTTGGCAGTCACCGCGT 62.866 63.158 4.92 0.00 0.00 6.01
2139 5490 2.048597 CTTGGCAGTCACCGCGTA 60.049 61.111 4.92 0.00 0.00 4.42
2140 5491 1.666553 CTTGGCAGTCACCGCGTAA 60.667 57.895 4.92 0.00 0.00 3.18
2141 5492 1.897398 CTTGGCAGTCACCGCGTAAC 61.897 60.000 4.92 0.00 0.00 2.50
2142 5493 2.356553 GGCAGTCACCGCGTAACA 60.357 61.111 4.92 0.00 0.00 2.41
2143 5494 1.740296 GGCAGTCACCGCGTAACAT 60.740 57.895 4.92 0.00 0.00 2.71
2144 5495 1.419922 GCAGTCACCGCGTAACATG 59.580 57.895 4.92 0.00 0.00 3.21
2145 5496 1.419922 CAGTCACCGCGTAACATGC 59.580 57.895 4.92 0.00 0.00 4.06
2153 5504 2.895372 CGTAACATGCGCCCTCCC 60.895 66.667 4.18 0.00 0.00 4.30
2154 5505 2.270850 GTAACATGCGCCCTCCCA 59.729 61.111 4.18 0.00 0.00 4.37
2155 5506 1.152963 GTAACATGCGCCCTCCCAT 60.153 57.895 4.18 0.00 0.00 4.00
2156 5507 1.148273 TAACATGCGCCCTCCCATC 59.852 57.895 4.18 0.00 0.00 3.51
2157 5508 2.337879 TAACATGCGCCCTCCCATCC 62.338 60.000 4.18 0.00 0.00 3.51
2158 5509 4.193893 CATGCGCCCTCCCATCCA 62.194 66.667 4.18 0.00 0.00 3.41
2159 5510 4.195334 ATGCGCCCTCCCATCCAC 62.195 66.667 4.18 0.00 0.00 4.02
2164 5515 2.445845 CCCTCCCATCCACCGCTA 60.446 66.667 0.00 0.00 0.00 4.26
2165 5516 1.843376 CCCTCCCATCCACCGCTAT 60.843 63.158 0.00 0.00 0.00 2.97
2166 5517 1.418908 CCCTCCCATCCACCGCTATT 61.419 60.000 0.00 0.00 0.00 1.73
2167 5518 0.474184 CCTCCCATCCACCGCTATTT 59.526 55.000 0.00 0.00 0.00 1.40
2168 5519 1.133792 CCTCCCATCCACCGCTATTTT 60.134 52.381 0.00 0.00 0.00 1.82
2169 5520 2.654863 CTCCCATCCACCGCTATTTTT 58.345 47.619 0.00 0.00 0.00 1.94
2188 5539 4.695217 TTTTCATCCAACGGTTATCAGC 57.305 40.909 0.00 0.00 0.00 4.26
2203 5554 6.894828 GGTTATCAGCGAACAAAGTAAAAGA 58.105 36.000 0.00 0.00 0.00 2.52
2204 5555 7.357303 GGTTATCAGCGAACAAAGTAAAAGAA 58.643 34.615 0.00 0.00 0.00 2.52
2205 5556 7.534239 GGTTATCAGCGAACAAAGTAAAAGAAG 59.466 37.037 0.00 0.00 0.00 2.85
2206 5557 5.418310 TCAGCGAACAAAGTAAAAGAAGG 57.582 39.130 0.00 0.00 0.00 3.46
2207 5558 3.975035 CAGCGAACAAAGTAAAAGAAGGC 59.025 43.478 0.00 0.00 0.00 4.35
2208 5559 3.630312 AGCGAACAAAGTAAAAGAAGGCA 59.370 39.130 0.00 0.00 0.00 4.75
2209 5560 4.097286 AGCGAACAAAGTAAAAGAAGGCAA 59.903 37.500 0.00 0.00 0.00 4.52
2210 5561 4.206404 GCGAACAAAGTAAAAGAAGGCAAC 59.794 41.667 0.00 0.00 0.00 4.17
2211 5562 5.336744 CGAACAAAGTAAAAGAAGGCAACA 58.663 37.500 0.00 0.00 41.41 3.33
2212 5563 5.455525 CGAACAAAGTAAAAGAAGGCAACAG 59.544 40.000 0.00 0.00 41.41 3.16
2213 5564 4.682787 ACAAAGTAAAAGAAGGCAACAGC 58.317 39.130 0.00 0.00 41.41 4.40
2214 5565 4.402474 ACAAAGTAAAAGAAGGCAACAGCT 59.598 37.500 0.00 0.00 41.41 4.24
2215 5566 5.592688 ACAAAGTAAAAGAAGGCAACAGCTA 59.407 36.000 0.00 0.00 41.41 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.378551 CCTAAGAACACACTATATGCAAAGTAA 57.621 33.333 0.00 0.00 0.00 2.24
6 7 6.821665 GTCCCTAAGAACACACTATATGCAAA 59.178 38.462 0.00 0.00 0.00 3.68
7 8 6.346096 GTCCCTAAGAACACACTATATGCAA 58.654 40.000 0.00 0.00 0.00 4.08
8 9 5.163343 GGTCCCTAAGAACACACTATATGCA 60.163 44.000 0.00 0.00 29.87 3.96
9 10 5.070580 AGGTCCCTAAGAACACACTATATGC 59.929 44.000 0.00 0.00 33.03 3.14
10 11 6.732896 AGGTCCCTAAGAACACACTATATG 57.267 41.667 0.00 0.00 33.03 1.78
11 12 6.489361 CGTAGGTCCCTAAGAACACACTATAT 59.511 42.308 0.51 0.00 33.03 0.86
12 13 5.824624 CGTAGGTCCCTAAGAACACACTATA 59.175 44.000 0.51 0.00 33.03 1.31
13 14 4.643784 CGTAGGTCCCTAAGAACACACTAT 59.356 45.833 0.51 0.00 33.03 2.12
14 15 4.012374 CGTAGGTCCCTAAGAACACACTA 58.988 47.826 0.51 0.00 33.03 2.74
15 16 2.824341 CGTAGGTCCCTAAGAACACACT 59.176 50.000 0.51 0.00 33.03 3.55
16 17 2.560105 ACGTAGGTCCCTAAGAACACAC 59.440 50.000 12.40 0.00 33.03 3.82
17 18 2.559668 CACGTAGGTCCCTAAGAACACA 59.440 50.000 12.40 0.00 33.03 3.72
18 19 2.821969 TCACGTAGGTCCCTAAGAACAC 59.178 50.000 12.40 0.00 33.03 3.32
19 20 3.159213 TCACGTAGGTCCCTAAGAACA 57.841 47.619 12.40 0.00 33.03 3.18
20 21 3.675502 GCTTCACGTAGGTCCCTAAGAAC 60.676 52.174 12.40 0.00 33.38 3.01
21 22 2.494870 GCTTCACGTAGGTCCCTAAGAA 59.505 50.000 12.40 8.12 33.38 2.52
22 23 2.097825 GCTTCACGTAGGTCCCTAAGA 58.902 52.381 12.40 1.31 33.38 2.10
23 24 1.136500 GGCTTCACGTAGGTCCCTAAG 59.864 57.143 4.95 4.95 34.87 2.18
24 25 1.188863 GGCTTCACGTAGGTCCCTAA 58.811 55.000 0.00 0.00 0.00 2.69
25 26 0.685458 GGGCTTCACGTAGGTCCCTA 60.685 60.000 7.61 0.00 0.00 3.53
26 27 1.988406 GGGCTTCACGTAGGTCCCT 60.988 63.158 7.61 0.00 0.00 4.20
27 28 0.685458 TAGGGCTTCACGTAGGTCCC 60.685 60.000 6.94 6.94 0.00 4.46
28 29 0.745468 CTAGGGCTTCACGTAGGTCC 59.255 60.000 0.00 0.00 0.00 4.46
29 30 1.404748 GACTAGGGCTTCACGTAGGTC 59.595 57.143 0.00 0.00 34.14 3.85
30 31 1.472188 GACTAGGGCTTCACGTAGGT 58.528 55.000 0.00 0.00 34.14 3.08
31 32 0.381089 CGACTAGGGCTTCACGTAGG 59.619 60.000 0.00 0.00 34.14 3.18
32 33 1.093159 ACGACTAGGGCTTCACGTAG 58.907 55.000 0.00 0.00 35.53 3.51
33 34 1.200716 CAACGACTAGGGCTTCACGTA 59.799 52.381 0.00 0.00 33.76 3.57
34 35 0.038526 CAACGACTAGGGCTTCACGT 60.039 55.000 0.00 0.00 35.56 4.49
35 36 1.352156 GCAACGACTAGGGCTTCACG 61.352 60.000 0.00 0.00 0.00 4.35
36 37 1.019805 GGCAACGACTAGGGCTTCAC 61.020 60.000 0.00 0.00 0.00 3.18
37 38 1.192146 AGGCAACGACTAGGGCTTCA 61.192 55.000 0.00 0.00 46.39 3.02
38 39 0.460459 GAGGCAACGACTAGGGCTTC 60.460 60.000 0.00 0.00 46.39 3.86
39 40 1.597461 GAGGCAACGACTAGGGCTT 59.403 57.895 0.00 0.00 46.39 4.35
40 41 2.359967 GGAGGCAACGACTAGGGCT 61.360 63.158 0.00 0.00 46.39 5.19
41 42 2.187163 GGAGGCAACGACTAGGGC 59.813 66.667 0.00 0.00 46.39 5.19
42 43 1.677637 GGAGGAGGCAACGACTAGGG 61.678 65.000 0.00 0.00 46.39 3.53
43 44 0.684805 AGGAGGAGGCAACGACTAGG 60.685 60.000 0.00 0.00 46.39 3.02
44 45 1.135333 GAAGGAGGAGGCAACGACTAG 59.865 57.143 0.00 0.00 46.39 2.57
45 46 1.183549 GAAGGAGGAGGCAACGACTA 58.816 55.000 0.00 0.00 46.39 2.59
48 49 0.608640 GAAGAAGGAGGAGGCAACGA 59.391 55.000 0.00 0.00 46.39 3.85
52 53 1.434188 TTGTGAAGAAGGAGGAGGCA 58.566 50.000 0.00 0.00 0.00 4.75
66 71 4.532834 ACAGAAACCCTAGCTTTTTGTGA 58.467 39.130 0.00 0.00 30.27 3.58
88 94 4.508128 GGCGACGCCGATGGAAGA 62.508 66.667 25.24 0.00 39.62 2.87
139 145 1.295020 CAAGATCCACCTTACCCCCA 58.705 55.000 0.00 0.00 0.00 4.96
140 146 0.551396 CCAAGATCCACCTTACCCCC 59.449 60.000 0.00 0.00 0.00 5.40
141 147 0.106669 GCCAAGATCCACCTTACCCC 60.107 60.000 0.00 0.00 0.00 4.95
145 151 1.284785 CCCTTGCCAAGATCCACCTTA 59.715 52.381 5.89 0.00 0.00 2.69
146 152 0.040204 CCCTTGCCAAGATCCACCTT 59.960 55.000 5.89 0.00 0.00 3.50
147 153 1.142688 ACCCTTGCCAAGATCCACCT 61.143 55.000 5.89 0.00 0.00 4.00
215 225 3.134623 TCTTGTCTTTCTGAGCAGGACAA 59.865 43.478 9.15 9.15 42.23 3.18
228 238 3.041940 CGCCGCCGTCTTGTCTTT 61.042 61.111 0.00 0.00 0.00 2.52
243 253 4.537433 ATCTTCAGGGAGCCGCGC 62.537 66.667 0.00 0.00 0.00 6.86
244 254 2.587194 CATCTTCAGGGAGCCGCG 60.587 66.667 0.00 0.00 0.00 6.46
271 281 1.910772 CGGGGGCTAGATGGAGAGG 60.911 68.421 0.00 0.00 0.00 3.69
275 285 1.306654 ACAACGGGGGCTAGATGGA 60.307 57.895 0.00 0.00 0.00 3.41
278 288 1.635817 ATGCACAACGGGGGCTAGAT 61.636 55.000 5.18 0.00 0.00 1.98
353 369 3.185246 ACGATGAGATCCGAGCAAATT 57.815 42.857 0.00 0.00 0.00 1.82
480 496 5.117355 AGTAGACAGTCGAAAAATCGTCA 57.883 39.130 0.00 0.00 0.00 4.35
486 502 7.037438 ACTTGTTGTAGTAGACAGTCGAAAAA 58.963 34.615 0.00 0.00 39.88 1.94
489 505 5.762825 ACTTGTTGTAGTAGACAGTCGAA 57.237 39.130 0.00 0.00 39.88 3.71
490 506 5.066893 ACAACTTGTTGTAGTAGACAGTCGA 59.933 40.000 16.35 0.00 39.88 4.20
523 539 2.125326 ATCGCCCCTTCATCGTCGA 61.125 57.895 0.00 0.00 0.00 4.20
526 542 1.144057 GTCATCGCCCCTTCATCGT 59.856 57.895 0.00 0.00 0.00 3.73
559 575 4.258899 CGACTACAAACACTAAATCGAGCG 60.259 45.833 0.00 0.00 0.00 5.03
565 581 4.553323 AGCGACGACTACAAACACTAAAT 58.447 39.130 0.00 0.00 0.00 1.40
568 584 4.214119 ACTTAGCGACGACTACAAACACTA 59.786 41.667 0.00 0.00 0.00 2.74
589 605 6.665992 TTACACTCAAATCTGTAGACCACT 57.334 37.500 0.00 0.00 0.00 4.00
695 714 4.746729 ACTAAACGTGCGACCACATTATA 58.253 39.130 0.00 0.00 42.17 0.98
696 715 3.592059 ACTAAACGTGCGACCACATTAT 58.408 40.909 0.00 0.00 42.17 1.28
721 740 1.189524 TCCGACGGTCAGGATTGGTT 61.190 55.000 14.79 0.00 0.00 3.67
815 853 3.843240 CGAGCGAGCGAGTTTGGC 61.843 66.667 0.00 0.00 0.00 4.52
816 854 3.843240 GCGAGCGAGCGAGTTTGG 61.843 66.667 1.41 0.00 0.00 3.28
818 856 2.049063 AAGCGAGCGAGCGAGTTT 60.049 55.556 1.41 0.00 43.00 2.66
819 857 2.505118 GAAGCGAGCGAGCGAGTT 60.505 61.111 1.41 0.00 43.00 3.01
911 953 1.595357 CACGGTGGGGGAGTTAGTC 59.405 63.158 0.00 0.00 0.00 2.59
992 1074 3.694538 AACCGCCCATTGCCTTGC 61.695 61.111 0.00 0.00 36.24 4.01
1368 4688 4.230745 AGCATTAAACAACCCCGTATCT 57.769 40.909 0.00 0.00 0.00 1.98
1371 4691 4.556592 ACTAGCATTAAACAACCCCGTA 57.443 40.909 0.00 0.00 0.00 4.02
1372 4692 3.428413 ACTAGCATTAAACAACCCCGT 57.572 42.857 0.00 0.00 0.00 5.28
1373 4693 4.331717 CACTACTAGCATTAAACAACCCCG 59.668 45.833 0.00 0.00 0.00 5.73
1408 4736 8.427774 CAAATATACATAGATACTGCACACACG 58.572 37.037 0.00 0.00 0.00 4.49
1432 4764 7.011950 CCGTATCCTGAGCAAATTTACATACAA 59.988 37.037 0.00 0.00 0.00 2.41
1493 4836 2.925578 TGCATTGCAGGAAAATCGAG 57.074 45.000 7.38 0.00 33.32 4.04
1503 4846 1.089112 TTCACGAGGATGCATTGCAG 58.911 50.000 17.52 5.42 43.65 4.41
1526 4869 4.577693 ATTCGAATGAATCACCAGATGTGG 59.422 41.667 10.50 7.49 44.70 4.17
1541 4884 8.854979 TGCAATTTACCTATGAAATTCGAATG 57.145 30.769 12.25 0.00 34.93 2.67
1583 4926 5.511601 GAGGTGCCTCTGTTTCGAAAGAAA 61.512 45.833 11.66 0.00 46.58 2.52
1584 4927 4.050344 GAGGTGCCTCTGTTTCGAAAGAA 61.050 47.826 11.66 1.77 43.07 2.52
1585 4928 1.416401 AGGTGCCTCTGTTTCGAAAGA 59.584 47.619 11.66 9.46 39.20 2.52
1586 4929 1.801178 GAGGTGCCTCTGTTTCGAAAG 59.199 52.381 11.66 0.00 39.80 2.62
1587 4930 1.140052 TGAGGTGCCTCTGTTTCGAAA 59.860 47.619 17.96 6.47 43.12 3.46
1588 4931 0.756294 TGAGGTGCCTCTGTTTCGAA 59.244 50.000 17.96 0.00 43.12 3.71
1589 4932 0.976641 ATGAGGTGCCTCTGTTTCGA 59.023 50.000 17.96 0.00 43.12 3.71
1590 4933 1.363744 GATGAGGTGCCTCTGTTTCG 58.636 55.000 17.96 0.00 43.12 3.46
1591 4934 1.066858 TCGATGAGGTGCCTCTGTTTC 60.067 52.381 17.96 9.40 43.12 2.78
1592 4935 0.976641 TCGATGAGGTGCCTCTGTTT 59.023 50.000 17.96 2.33 43.12 2.83
1593 4936 1.198713 ATCGATGAGGTGCCTCTGTT 58.801 50.000 17.96 4.57 43.12 3.16
1594 4937 1.198713 AATCGATGAGGTGCCTCTGT 58.801 50.000 17.96 7.88 43.12 3.41
1595 4938 3.459232 TTAATCGATGAGGTGCCTCTG 57.541 47.619 17.96 8.98 43.12 3.35
1596 4939 4.696479 AATTAATCGATGAGGTGCCTCT 57.304 40.909 17.96 5.10 43.12 3.69
1597 4940 6.223852 TCTTAATTAATCGATGAGGTGCCTC 58.776 40.000 11.13 11.13 43.01 4.70
1598 4941 6.174720 TCTTAATTAATCGATGAGGTGCCT 57.825 37.500 0.00 0.00 0.00 4.75
1599 4942 6.706270 TCTTCTTAATTAATCGATGAGGTGCC 59.294 38.462 0.00 0.00 0.00 5.01
1600 4943 7.715265 TCTTCTTAATTAATCGATGAGGTGC 57.285 36.000 0.00 0.00 0.00 5.01
1630 4973 9.757227 CCAGTTTTCTGTTAATTAATTGGACAA 57.243 29.630 11.05 0.00 45.68 3.18
1631 4974 9.137459 TCCAGTTTTCTGTTAATTAATTGGACA 57.863 29.630 11.05 13.24 45.68 4.02
1632 4975 9.406828 GTCCAGTTTTCTGTTAATTAATTGGAC 57.593 33.333 11.05 10.59 43.51 4.02
1633 4976 8.293867 CGTCCAGTTTTCTGTTAATTAATTGGA 58.706 33.333 11.05 2.27 45.68 3.53
1634 4977 8.293867 TCGTCCAGTTTTCTGTTAATTAATTGG 58.706 33.333 11.05 0.00 45.68 3.16
1635 4978 9.672086 TTCGTCCAGTTTTCTGTTAATTAATTG 57.328 29.630 11.05 0.00 45.68 2.32
1638 4981 9.505995 GTTTTCGTCCAGTTTTCTGTTAATTAA 57.494 29.630 0.00 0.00 45.68 1.40
1639 4982 8.130469 GGTTTTCGTCCAGTTTTCTGTTAATTA 58.870 33.333 0.00 0.00 45.68 1.40
1640 4983 6.976349 GGTTTTCGTCCAGTTTTCTGTTAATT 59.024 34.615 0.00 0.00 45.68 1.40
1641 4984 6.500910 GGTTTTCGTCCAGTTTTCTGTTAAT 58.499 36.000 0.00 0.00 45.68 1.40
1642 4985 5.447548 CGGTTTTCGTCCAGTTTTCTGTTAA 60.448 40.000 0.00 0.00 45.68 2.01
1643 4986 4.034279 CGGTTTTCGTCCAGTTTTCTGTTA 59.966 41.667 0.00 0.00 45.68 2.41
1644 4987 3.181504 CGGTTTTCGTCCAGTTTTCTGTT 60.182 43.478 0.00 0.00 45.68 3.16
1645 4988 2.353579 CGGTTTTCGTCCAGTTTTCTGT 59.646 45.455 0.00 0.00 45.68 3.41
1646 4989 2.610374 TCGGTTTTCGTCCAGTTTTCTG 59.390 45.455 0.00 0.00 42.45 3.02
1647 4990 2.908916 TCGGTTTTCGTCCAGTTTTCT 58.091 42.857 0.00 0.00 40.32 2.52
1648 4991 3.357021 GTTCGGTTTTCGTCCAGTTTTC 58.643 45.455 0.00 0.00 40.32 2.29
1649 4992 2.223089 CGTTCGGTTTTCGTCCAGTTTT 60.223 45.455 0.00 0.00 40.32 2.43
1650 4993 1.328374 CGTTCGGTTTTCGTCCAGTTT 59.672 47.619 0.00 0.00 40.32 2.66
1651 4994 0.932399 CGTTCGGTTTTCGTCCAGTT 59.068 50.000 0.00 0.00 40.32 3.16
1652 4995 0.102844 TCGTTCGGTTTTCGTCCAGT 59.897 50.000 0.00 0.00 40.32 4.00
1653 4996 1.126113 CATCGTTCGGTTTTCGTCCAG 59.874 52.381 0.00 0.00 40.32 3.86
1654 4997 1.141645 CATCGTTCGGTTTTCGTCCA 58.858 50.000 0.00 0.00 40.32 4.02
1655 4998 0.179233 GCATCGTTCGGTTTTCGTCC 60.179 55.000 0.00 0.00 40.32 4.79
1656 4999 0.509499 TGCATCGTTCGGTTTTCGTC 59.491 50.000 0.00 0.00 40.32 4.20
1657 5000 1.136085 CATGCATCGTTCGGTTTTCGT 60.136 47.619 0.00 0.00 40.32 3.85
1658 5001 1.127766 TCATGCATCGTTCGGTTTTCG 59.872 47.619 0.00 0.00 40.90 3.46
1659 5002 2.892373 TCATGCATCGTTCGGTTTTC 57.108 45.000 0.00 0.00 0.00 2.29
1660 5003 3.848272 AATCATGCATCGTTCGGTTTT 57.152 38.095 0.00 0.00 0.00 2.43
1661 5004 4.574421 TGATAATCATGCATCGTTCGGTTT 59.426 37.500 0.00 0.00 0.00 3.27
1662 5005 4.126437 TGATAATCATGCATCGTTCGGTT 58.874 39.130 0.00 0.00 0.00 4.44
1663 5006 3.727726 TGATAATCATGCATCGTTCGGT 58.272 40.909 0.00 0.00 0.00 4.69
1664 5007 3.989817 TCTGATAATCATGCATCGTTCGG 59.010 43.478 0.00 0.00 0.00 4.30
1665 5008 5.580911 TTCTGATAATCATGCATCGTTCG 57.419 39.130 0.00 0.00 0.00 3.95
1666 5009 8.663025 ACATATTCTGATAATCATGCATCGTTC 58.337 33.333 0.00 0.00 0.00 3.95
1667 5010 8.557592 ACATATTCTGATAATCATGCATCGTT 57.442 30.769 0.00 0.00 0.00 3.85
1668 5011 8.557592 AACATATTCTGATAATCATGCATCGT 57.442 30.769 0.00 0.00 0.00 3.73
1669 5012 9.836076 AAAACATATTCTGATAATCATGCATCG 57.164 29.630 0.00 0.00 0.00 3.84
1695 5038 2.291735 ACAATGAGCCATCCATCACCAA 60.292 45.455 0.00 0.00 0.00 3.67
1699 5042 2.240414 AGTGACAATGAGCCATCCATCA 59.760 45.455 0.00 0.00 0.00 3.07
1703 5046 0.737219 GCAGTGACAATGAGCCATCC 59.263 55.000 7.16 0.00 0.00 3.51
1722 5065 1.079503 GGCCGAGTAGCAAGTTCTTG 58.920 55.000 8.04 8.04 0.00 3.02
1725 5068 1.202428 CCTAGGCCGAGTAGCAAGTTC 60.202 57.143 12.29 0.00 0.00 3.01
1730 5073 1.756950 CCACCTAGGCCGAGTAGCA 60.757 63.158 9.30 0.00 0.00 3.49
1731 5074 1.757340 ACCACCTAGGCCGAGTAGC 60.757 63.158 9.30 0.00 43.14 3.58
1736 5079 3.702048 GTGCACCACCTAGGCCGA 61.702 66.667 9.30 0.00 43.14 5.54
1739 5082 2.747855 GCAGTGCACCACCTAGGC 60.748 66.667 14.63 2.50 43.14 3.93
1814 5157 5.718724 TTTCACATAACAACATGCATGGA 57.281 34.783 29.41 11.51 0.00 3.41
1851 5199 5.881443 CAGAAATCTTGCCTTCTCTCTTGAT 59.119 40.000 0.00 0.00 29.29 2.57
1865 5213 2.101700 GCGGGAGGCAGAAATCTTG 58.898 57.895 0.00 0.00 42.87 3.02
1887 5235 9.914131 GTGCAGAAATCTTACCTTCTTATTTTT 57.086 29.630 0.00 0.00 29.29 1.94
1888 5236 8.523658 GGTGCAGAAATCTTACCTTCTTATTTT 58.476 33.333 0.00 0.00 31.45 1.82
1889 5237 7.122799 GGGTGCAGAAATCTTACCTTCTTATTT 59.877 37.037 11.37 0.00 33.47 1.40
1890 5238 6.603599 GGGTGCAGAAATCTTACCTTCTTATT 59.396 38.462 11.37 0.00 33.47 1.40
1891 5239 6.069381 AGGGTGCAGAAATCTTACCTTCTTAT 60.069 38.462 11.37 0.00 33.47 1.73
1892 5240 5.250774 AGGGTGCAGAAATCTTACCTTCTTA 59.749 40.000 11.37 0.00 33.47 2.10
1893 5241 4.043435 AGGGTGCAGAAATCTTACCTTCTT 59.957 41.667 11.37 0.00 33.47 2.52
1894 5242 3.589288 AGGGTGCAGAAATCTTACCTTCT 59.411 43.478 11.37 2.12 33.47 2.85
1895 5243 3.691609 CAGGGTGCAGAAATCTTACCTTC 59.308 47.826 11.37 0.39 33.47 3.46
1896 5244 3.330701 TCAGGGTGCAGAAATCTTACCTT 59.669 43.478 11.37 3.95 33.47 3.50
1897 5245 2.912956 TCAGGGTGCAGAAATCTTACCT 59.087 45.455 11.37 0.00 33.47 3.08
1898 5246 3.350219 TCAGGGTGCAGAAATCTTACC 57.650 47.619 0.00 5.46 32.65 2.85
1899 5247 4.943705 TCATTCAGGGTGCAGAAATCTTAC 59.056 41.667 0.00 0.00 0.00 2.34
1900 5248 5.178096 TCATTCAGGGTGCAGAAATCTTA 57.822 39.130 0.00 0.00 0.00 2.10
1901 5249 4.038271 TCATTCAGGGTGCAGAAATCTT 57.962 40.909 0.00 0.00 0.00 2.40
1902 5250 3.726557 TCATTCAGGGTGCAGAAATCT 57.273 42.857 0.00 0.00 0.00 2.40
1903 5251 4.679662 CAATCATTCAGGGTGCAGAAATC 58.320 43.478 0.00 0.00 0.00 2.17
1904 5252 3.118884 GCAATCATTCAGGGTGCAGAAAT 60.119 43.478 0.00 0.00 35.28 2.17
1905 5253 2.231964 GCAATCATTCAGGGTGCAGAAA 59.768 45.455 0.00 0.00 35.28 2.52
1906 5254 1.820519 GCAATCATTCAGGGTGCAGAA 59.179 47.619 0.00 0.00 35.28 3.02
1907 5255 1.466856 GCAATCATTCAGGGTGCAGA 58.533 50.000 0.00 0.00 35.28 4.26
1908 5256 0.458669 GGCAATCATTCAGGGTGCAG 59.541 55.000 0.00 0.00 36.93 4.41
1909 5257 0.971959 GGGCAATCATTCAGGGTGCA 60.972 55.000 0.00 0.00 36.93 4.57
1925 5273 0.895530 GGCCTAAGGAAAAACAGGGC 59.104 55.000 0.00 0.00 45.16 5.19
1928 5276 3.004734 CACAGTGGCCTAAGGAAAAACAG 59.995 47.826 3.32 0.00 0.00 3.16
1946 5294 8.939201 ACATATGAACTGAATCTTCTACACAG 57.061 34.615 10.38 0.00 35.14 3.66
1949 5297 7.708322 GCTGACATATGAACTGAATCTTCTACA 59.292 37.037 10.38 0.00 0.00 2.74
1950 5298 7.925483 AGCTGACATATGAACTGAATCTTCTAC 59.075 37.037 10.38 0.00 0.00 2.59
1951 5299 8.016301 AGCTGACATATGAACTGAATCTTCTA 57.984 34.615 10.38 0.00 0.00 2.10
1979 5327 6.718593 TTTCCATATATAGGAAGGCCATGT 57.281 37.500 5.01 0.00 45.25 3.21
2015 5366 9.553064 TGGCACTTCAATTAATTATTGTTTGTT 57.447 25.926 0.00 0.00 43.41 2.83
2098 5449 1.134280 CATGTCACCTGATCCCAGTCC 60.134 57.143 0.00 0.00 38.74 3.85
2099 5450 1.745141 GCATGTCACCTGATCCCAGTC 60.745 57.143 0.00 0.00 38.74 3.51
2100 5451 0.254178 GCATGTCACCTGATCCCAGT 59.746 55.000 0.00 0.00 38.74 4.00
2101 5452 0.465097 GGCATGTCACCTGATCCCAG 60.465 60.000 0.00 0.00 40.09 4.45
2102 5453 0.915872 AGGCATGTCACCTGATCCCA 60.916 55.000 0.00 0.00 35.72 4.37
2103 5454 0.179034 GAGGCATGTCACCTGATCCC 60.179 60.000 0.00 0.00 37.77 3.85
2104 5455 0.835941 AGAGGCATGTCACCTGATCC 59.164 55.000 0.00 0.00 37.77 3.36
2105 5456 2.286872 CAAGAGGCATGTCACCTGATC 58.713 52.381 0.00 0.00 37.77 2.92
2106 5457 1.064906 CCAAGAGGCATGTCACCTGAT 60.065 52.381 0.00 0.00 37.77 2.90
2107 5458 0.325933 CCAAGAGGCATGTCACCTGA 59.674 55.000 0.00 0.00 37.77 3.86
2108 5459 2.864114 CCAAGAGGCATGTCACCTG 58.136 57.895 0.00 0.00 37.77 4.00
2119 5470 2.743928 GCGGTGACTGCCAAGAGG 60.744 66.667 4.74 0.00 38.23 3.69
2120 5471 2.486636 TACGCGGTGACTGCCAAGAG 62.487 60.000 12.47 0.00 0.00 2.85
2121 5472 2.089887 TTACGCGGTGACTGCCAAGA 62.090 55.000 12.47 0.00 0.00 3.02
2122 5473 1.666553 TTACGCGGTGACTGCCAAG 60.667 57.895 12.47 0.00 0.00 3.61
2123 5474 1.957186 GTTACGCGGTGACTGCCAA 60.957 57.895 12.47 2.30 0.00 4.52
2124 5475 2.356553 GTTACGCGGTGACTGCCA 60.357 61.111 12.47 0.00 0.00 4.92
2125 5476 1.740296 ATGTTACGCGGTGACTGCC 60.740 57.895 12.47 0.00 0.00 4.85
2126 5477 1.419922 CATGTTACGCGGTGACTGC 59.580 57.895 12.47 6.27 0.00 4.40
2127 5478 1.419922 GCATGTTACGCGGTGACTG 59.580 57.895 12.47 3.28 0.00 3.51
2128 5479 3.870606 GCATGTTACGCGGTGACT 58.129 55.556 12.47 0.00 0.00 3.41
2136 5487 2.895372 GGGAGGGCGCATGTTACG 60.895 66.667 10.83 0.00 0.00 3.18
2137 5488 1.152963 ATGGGAGGGCGCATGTTAC 60.153 57.895 10.83 0.00 44.87 2.50
2138 5489 1.148273 GATGGGAGGGCGCATGTTA 59.852 57.895 10.83 0.00 46.33 2.41
2139 5490 2.124151 GATGGGAGGGCGCATGTT 60.124 61.111 10.83 0.00 46.33 2.71
2140 5491 4.195334 GGATGGGAGGGCGCATGT 62.195 66.667 10.83 0.00 46.33 3.21
2141 5492 4.193893 TGGATGGGAGGGCGCATG 62.194 66.667 10.83 0.00 46.33 4.06
2147 5498 1.418908 AATAGCGGTGGATGGGAGGG 61.419 60.000 0.00 0.00 0.00 4.30
2148 5499 0.474184 AAATAGCGGTGGATGGGAGG 59.526 55.000 0.00 0.00 0.00 4.30
2149 5500 2.348411 AAAATAGCGGTGGATGGGAG 57.652 50.000 0.00 0.00 0.00 4.30
2150 5501 2.818751 AAAAATAGCGGTGGATGGGA 57.181 45.000 0.00 0.00 0.00 4.37
2166 5517 4.378978 CGCTGATAACCGTTGGATGAAAAA 60.379 41.667 0.00 0.00 0.00 1.94
2167 5518 3.126171 CGCTGATAACCGTTGGATGAAAA 59.874 43.478 0.00 0.00 0.00 2.29
2168 5519 2.675844 CGCTGATAACCGTTGGATGAAA 59.324 45.455 0.00 0.00 0.00 2.69
2169 5520 2.093921 TCGCTGATAACCGTTGGATGAA 60.094 45.455 0.00 0.00 0.00 2.57
2170 5521 1.478916 TCGCTGATAACCGTTGGATGA 59.521 47.619 0.00 0.00 0.00 2.92
2171 5522 1.934589 TCGCTGATAACCGTTGGATG 58.065 50.000 0.00 0.00 0.00 3.51
2172 5523 2.277084 GTTCGCTGATAACCGTTGGAT 58.723 47.619 0.00 0.00 0.00 3.41
2173 5524 1.001068 TGTTCGCTGATAACCGTTGGA 59.999 47.619 0.00 0.00 0.00 3.53
2174 5525 1.434555 TGTTCGCTGATAACCGTTGG 58.565 50.000 0.00 0.00 0.00 3.77
2175 5526 3.059188 ACTTTGTTCGCTGATAACCGTTG 60.059 43.478 0.00 0.00 0.00 4.10
2176 5527 3.135994 ACTTTGTTCGCTGATAACCGTT 58.864 40.909 0.00 0.00 0.00 4.44
2177 5528 2.762745 ACTTTGTTCGCTGATAACCGT 58.237 42.857 0.00 0.00 0.00 4.83
2178 5529 4.914312 TTACTTTGTTCGCTGATAACCG 57.086 40.909 0.00 0.00 0.00 4.44
2179 5530 6.894828 TCTTTTACTTTGTTCGCTGATAACC 58.105 36.000 0.00 0.00 0.00 2.85
2180 5531 7.534239 CCTTCTTTTACTTTGTTCGCTGATAAC 59.466 37.037 0.00 0.00 0.00 1.89
2181 5532 7.581476 CCTTCTTTTACTTTGTTCGCTGATAA 58.419 34.615 0.00 0.00 0.00 1.75
2182 5533 6.348213 GCCTTCTTTTACTTTGTTCGCTGATA 60.348 38.462 0.00 0.00 0.00 2.15
2183 5534 5.562890 GCCTTCTTTTACTTTGTTCGCTGAT 60.563 40.000 0.00 0.00 0.00 2.90
2184 5535 4.261031 GCCTTCTTTTACTTTGTTCGCTGA 60.261 41.667 0.00 0.00 0.00 4.26
2185 5536 3.975035 GCCTTCTTTTACTTTGTTCGCTG 59.025 43.478 0.00 0.00 0.00 5.18
2186 5537 3.630312 TGCCTTCTTTTACTTTGTTCGCT 59.370 39.130 0.00 0.00 0.00 4.93
2187 5538 3.959943 TGCCTTCTTTTACTTTGTTCGC 58.040 40.909 0.00 0.00 0.00 4.70
2188 5539 5.336744 TGTTGCCTTCTTTTACTTTGTTCG 58.663 37.500 0.00 0.00 0.00 3.95
2189 5540 5.232202 GCTGTTGCCTTCTTTTACTTTGTTC 59.768 40.000 0.00 0.00 0.00 3.18
2190 5541 5.105351 AGCTGTTGCCTTCTTTTACTTTGTT 60.105 36.000 0.00 0.00 40.80 2.83
2191 5542 4.402474 AGCTGTTGCCTTCTTTTACTTTGT 59.598 37.500 0.00 0.00 40.80 2.83
2192 5543 4.936891 AGCTGTTGCCTTCTTTTACTTTG 58.063 39.130 0.00 0.00 40.80 2.77


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

AutoCloner maintained by Alex Coulton.