Multiple sequence alignment - TraesCS3D01G092500

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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 TraesCS3D01G092500 chr3D 100.000 8735 0 0 1 8735 46551936 46560670 0.000000e+00 16131.0
1 TraesCS3D01G092500 chr3D 88.372 301 31 4 3805 4102 369413409 369413708 8.340000e-95 359.0
2 TraesCS3D01G092500 chr3D 87.582 306 35 2 3798 4102 332631111 332630808 1.400000e-92 351.0
3 TraesCS3D01G092500 chr3A 93.419 5774 214 58 2272 7953 57960379 57954680 0.000000e+00 8405.0
4 TraesCS3D01G092500 chr3A 93.592 5571 197 51 2145 7654 57960481 57955010 0.000000e+00 8163.0
5 TraesCS3D01G092500 chr3A 90.761 1104 47 17 850 1912 57961805 57960716 0.000000e+00 1423.0
6 TraesCS3D01G092500 chr3A 96.589 645 19 3 1 644 108900588 108901230 0.000000e+00 1066.0
7 TraesCS3D01G092500 chr3A 94.545 220 6 4 1942 2158 57960717 57960501 1.410000e-87 335.0
8 TraesCS3D01G092500 chr3A 93.827 81 4 1 779 858 57962074 57961994 4.280000e-23 121.0
9 TraesCS3D01G092500 chr3B 94.089 4974 173 41 779 5686 72934065 72938983 0.000000e+00 7444.0
10 TraesCS3D01G092500 chr3B 95.336 1951 70 10 5710 7654 72938980 72940915 0.000000e+00 3079.0
11 TraesCS3D01G092500 chr3B 86.427 501 64 2 282 779 548076568 548077067 5.960000e-151 545.0
12 TraesCS3D01G092500 chr5D 97.951 781 15 1 1 780 495488043 495488823 0.000000e+00 1352.0
13 TraesCS3D01G092500 chr5D 96.692 786 25 1 7950 8735 65482799 65482015 0.000000e+00 1306.0
14 TraesCS3D01G092500 chr5D 96.301 784 28 1 7952 8735 65473946 65473164 0.000000e+00 1286.0
15 TraesCS3D01G092500 chr5D 95.833 792 32 1 7944 8735 339345171 339344381 0.000000e+00 1279.0
16 TraesCS3D01G092500 chr5D 95.934 787 31 1 7949 8735 339336327 339335542 0.000000e+00 1275.0
17 TraesCS3D01G092500 chr5D 89.869 306 29 2 3799 4102 115401775 115401470 8.220000e-105 392.0
18 TraesCS3D01G092500 chr5D 84.691 307 23 11 1 288 106688327 106688026 1.440000e-72 285.0
19 TraesCS3D01G092500 chr6D 97.946 779 14 2 1 779 80087276 80088052 0.000000e+00 1349.0
20 TraesCS3D01G092500 chr6D 97.078 787 23 0 7949 8735 168815323 168816109 0.000000e+00 1327.0
21 TraesCS3D01G092500 chr6D 95.293 786 37 0 7950 8735 162408318 162407533 0.000000e+00 1247.0
22 TraesCS3D01G092500 chr6D 95.122 287 11 2 1 286 199696830 199696546 4.810000e-122 449.0
23 TraesCS3D01G092500 chr7D 97.922 770 16 0 1 770 3713613 3714382 0.000000e+00 1334.0
24 TraesCS3D01G092500 chr7D 86.056 502 60 6 286 780 449990084 449989586 1.670000e-146 531.0
25 TraesCS3D01G092500 chr2D 95.455 792 32 4 7945 8735 500123303 500122515 0.000000e+00 1260.0
26 TraesCS3D01G092500 chr2D 95.299 787 36 1 7949 8735 567848613 567847828 0.000000e+00 1247.0
27 TraesCS3D01G092500 chr2D 95.165 786 37 1 7950 8735 567857452 567856668 0.000000e+00 1240.0
28 TraesCS3D01G092500 chr2D 91.855 221 16 1 2290 2510 196365211 196365429 3.060000e-79 307.0
29 TraesCS3D01G092500 chr2D 85.764 288 27 9 1 285 78797250 78797526 8.580000e-75 292.0
30 TraesCS3D01G092500 chr2D 84.574 188 24 5 5824 6009 196365739 196365923 1.940000e-41 182.0
31 TraesCS3D01G092500 chr5A 96.899 645 19 1 1 644 412520488 412521132 0.000000e+00 1079.0
32 TraesCS3D01G092500 chr5A 89.251 307 30 2 3799 4102 121412055 121411749 1.780000e-101 381.0
33 TraesCS3D01G092500 chr4B 90.760 487 41 2 302 785 14885856 14885371 0.000000e+00 647.0
34 TraesCS3D01G092500 chr5B 88.034 468 46 5 315 779 7147120 7147580 5.960000e-151 545.0
35 TraesCS3D01G092500 chr5B 90.196 306 28 2 3799 4102 126598771 126598466 1.770000e-106 398.0
36 TraesCS3D01G092500 chr7A 95.122 287 12 2 1 286 692715317 692715032 1.340000e-122 451.0
37 TraesCS3D01G092500 chr7B 90.523 306 28 1 3798 4102 13823711 13823406 3.800000e-108 403.0
38 TraesCS3D01G092500 chr7B 91.018 167 15 0 2290 2456 147586614 147586448 8.820000e-55 226.0
39 TraesCS3D01G092500 chr7B 88.991 109 9 3 5647 5752 147586409 147586301 1.980000e-26 132.0
40 TraesCS3D01G092500 chr4D 87.220 313 34 6 3794 4103 421335522 421335213 1.400000e-92 351.0
41 TraesCS3D01G092500 chr6B 83.871 310 41 5 5254 5558 51999486 51999791 3.990000e-73 287.0
42 TraesCS3D01G092500 chr6B 85.965 228 24 7 1561 1782 157774322 157774547 4.080000e-58 237.0
43 TraesCS3D01G092500 chr6B 79.235 183 30 7 1563 1739 15811396 15811576 4.280000e-23 121.0
44 TraesCS3D01G092500 chr6A 90.419 167 16 0 2290 2456 576945102 576944936 4.110000e-53 220.0
45 TraesCS3D01G092500 chr6A 88.991 109 9 3 5647 5752 576944897 576944789 1.980000e-26 132.0
46 TraesCS3D01G092500 chrUn 89.820 167 17 0 2290 2456 50316819 50316653 1.910000e-51 215.0
47 TraesCS3D01G092500 chrUn 89.820 167 17 0 2290 2456 307457563 307457397 1.910000e-51 215.0
48 TraesCS3D01G092500 chrUn 89.908 109 8 3 5647 5752 50316614 50316506 4.250000e-28 137.0
49 TraesCS3D01G092500 chrUn 89.908 109 8 3 5647 5752 307457358 307457250 4.250000e-28 137.0
50 TraesCS3D01G092500 chr1B 100.000 29 0 0 1568 1596 508998921 508998893 4.000000e-03 54.7
51 TraesCS3D01G092500 chr1A 100.000 29 0 0 1568 1596 480738932 480738904 4.000000e-03 54.7


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 TraesCS3D01G092500 chr3D 46551936 46560670 8734 False 16131.0 16131 100.00000 1 8735 1 chr3D.!!$F1 8734
1 TraesCS3D01G092500 chr3A 57954680 57960379 5699 True 8405.0 8405 93.41900 2272 7953 1 chr3A.!!$R1 5681
2 TraesCS3D01G092500 chr3A 57955010 57962074 7064 True 2510.5 8163 93.18125 779 7654 4 chr3A.!!$R2 6875
3 TraesCS3D01G092500 chr3A 108900588 108901230 642 False 1066.0 1066 96.58900 1 644 1 chr3A.!!$F1 643
4 TraesCS3D01G092500 chr3B 72934065 72940915 6850 False 5261.5 7444 94.71250 779 7654 2 chr3B.!!$F2 6875
5 TraesCS3D01G092500 chr5D 495488043 495488823 780 False 1352.0 1352 97.95100 1 780 1 chr5D.!!$F1 779
6 TraesCS3D01G092500 chr5D 65482015 65482799 784 True 1306.0 1306 96.69200 7950 8735 1 chr5D.!!$R2 785
7 TraesCS3D01G092500 chr5D 65473164 65473946 782 True 1286.0 1286 96.30100 7952 8735 1 chr5D.!!$R1 783
8 TraesCS3D01G092500 chr5D 339344381 339345171 790 True 1279.0 1279 95.83300 7944 8735 1 chr5D.!!$R6 791
9 TraesCS3D01G092500 chr5D 339335542 339336327 785 True 1275.0 1275 95.93400 7949 8735 1 chr5D.!!$R5 786
10 TraesCS3D01G092500 chr6D 80087276 80088052 776 False 1349.0 1349 97.94600 1 779 1 chr6D.!!$F1 778
11 TraesCS3D01G092500 chr6D 168815323 168816109 786 False 1327.0 1327 97.07800 7949 8735 1 chr6D.!!$F2 786
12 TraesCS3D01G092500 chr6D 162407533 162408318 785 True 1247.0 1247 95.29300 7950 8735 1 chr6D.!!$R1 785
13 TraesCS3D01G092500 chr7D 3713613 3714382 769 False 1334.0 1334 97.92200 1 770 1 chr7D.!!$F1 769
14 TraesCS3D01G092500 chr2D 500122515 500123303 788 True 1260.0 1260 95.45500 7945 8735 1 chr2D.!!$R1 790
15 TraesCS3D01G092500 chr2D 567847828 567848613 785 True 1247.0 1247 95.29900 7949 8735 1 chr2D.!!$R2 786
16 TraesCS3D01G092500 chr2D 567856668 567857452 784 True 1240.0 1240 95.16500 7950 8735 1 chr2D.!!$R3 785
17 TraesCS3D01G092500 chr2D 196365211 196365923 712 False 244.5 307 88.21450 2290 6009 2 chr2D.!!$F2 3719
18 TraesCS3D01G092500 chr5A 412520488 412521132 644 False 1079.0 1079 96.89900 1 644 1 chr5A.!!$F1 643

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
863 1064 0.467659 GGAGCCCTAAGCCTCTCGTA 60.468 60.000 0.00 0.0 45.47 3.43 F
1482 1697 2.169561 GAGGGGTTGAATCTCTCCTGTC 59.830 54.545 0.00 0.0 0.00 3.51 F
1689 1912 2.042404 TTTTACTCCGTGGTGGCCGT 62.042 55.000 0.00 0.0 37.80 5.68 F
3324 3612 1.435563 TCTGTAAGGGAAGGTGAGGGA 59.564 52.381 0.00 0.0 0.00 4.20 F
3765 4055 0.314935 AATGTGCACCGCTCTTTTGG 59.685 50.000 15.69 0.0 0.00 3.28 F
3897 4187 1.209019 AGGTGCAAGCCACTATCTCTG 59.791 52.381 0.00 0.0 44.08 3.35 F
4302 4592 1.288037 TCAGGGAAGCTCTACAGGCTA 59.712 52.381 0.00 0.0 39.30 3.93 F
5989 6374 0.250513 GGAGTCAAACCCGCTGAGAT 59.749 55.000 0.00 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1903 0.183014 TTTAAAGGTCACGGCCACCA 59.817 50.000 12.97 0.0 36.23 4.17 R
3310 3598 0.621862 GATGGTCCCTCACCTTCCCT 60.622 60.000 0.00 0.0 46.98 4.20 R
3563 3853 1.565759 TCATGGGCTGACCTTTGCTAT 59.434 47.619 0.00 0.0 41.11 2.97 R
4291 4581 2.467880 TGGGTTCCTTAGCCTGTAGAG 58.532 52.381 0.00 0.0 45.03 2.43 R
5604 5926 3.565905 ACGAGGGAAGTAGTGTTTACG 57.434 47.619 0.00 0.0 0.00 3.18 R
5896 6281 2.441750 ACCCTGTCTGCTTTTACCAAGA 59.558 45.455 0.00 0.0 0.00 3.02 R
6113 6498 2.007360 AAGATGCGTGAGAGAAGCTG 57.993 50.000 0.00 0.0 0.00 4.24 R
7744 8194 0.316204 TCTTCGGTTTCACCTCGTCC 59.684 55.000 0.00 0.0 35.66 4.79 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 3.592898 TGCATGTTCGTCAGTACTCAT 57.407 42.857 0.00 0.00 0.00 2.90
394 397 7.220740 TGTTTGTATCAGATTTGTGTGAGGTA 58.779 34.615 0.00 0.00 0.00 3.08
577 580 3.295626 TGTGGTCGTATGAACGCACCA 62.296 52.381 12.22 14.08 46.93 4.17
787 790 4.333095 CGATCCCGATCTAGTACACTATGG 59.667 50.000 0.00 0.00 38.22 2.74
863 1064 0.467659 GGAGCCCTAAGCCTCTCGTA 60.468 60.000 0.00 0.00 45.47 3.43
974 1175 7.228706 CCATGTGTTTATTACTCCACTTATCCC 59.771 40.741 0.00 0.00 0.00 3.85
1029 1230 3.058160 CAAGGCAAGGACGCTGGG 61.058 66.667 0.00 0.00 0.00 4.45
1442 1657 9.917129 TGAATTTCACTTGAATACGTACTTCTA 57.083 29.630 0.00 0.23 33.54 2.10
1454 1669 9.517609 GAATACGTACTTCTATCTGTTTGTGAT 57.482 33.333 0.00 0.00 0.00 3.06
1455 1670 8.858003 ATACGTACTTCTATCTGTTTGTGATG 57.142 34.615 0.00 0.00 0.00 3.07
1456 1671 5.577164 ACGTACTTCTATCTGTTTGTGATGC 59.423 40.000 0.00 0.00 0.00 3.91
1457 1672 5.576774 CGTACTTCTATCTGTTTGTGATGCA 59.423 40.000 0.00 0.00 0.00 3.96
1458 1673 6.090763 CGTACTTCTATCTGTTTGTGATGCAA 59.909 38.462 0.00 0.00 34.87 4.08
1459 1674 7.201556 CGTACTTCTATCTGTTTGTGATGCAAT 60.202 37.037 0.00 0.00 36.89 3.56
1460 1675 9.098355 GTACTTCTATCTGTTTGTGATGCAATA 57.902 33.333 0.00 0.00 36.89 1.90
1482 1697 2.169561 GAGGGGTTGAATCTCTCCTGTC 59.830 54.545 0.00 0.00 0.00 3.51
1487 1702 3.604582 GTTGAATCTCTCCTGTCTTGGG 58.395 50.000 0.00 0.00 0.00 4.12
1489 1704 2.834549 TGAATCTCTCCTGTCTTGGGAC 59.165 50.000 0.00 0.00 42.42 4.46
1523 1738 3.822594 TTTATGGTGCATCGTCACAAC 57.177 42.857 0.00 0.00 38.66 3.32
1524 1739 2.760634 TATGGTGCATCGTCACAACT 57.239 45.000 0.00 0.00 38.66 3.16
1526 1741 2.535012 TGGTGCATCGTCACAACTAA 57.465 45.000 0.00 0.00 38.66 2.24
1528 1743 3.407698 TGGTGCATCGTCACAACTAATT 58.592 40.909 0.00 0.00 38.66 1.40
1529 1744 4.570930 TGGTGCATCGTCACAACTAATTA 58.429 39.130 0.00 0.00 38.66 1.40
1530 1745 4.629634 TGGTGCATCGTCACAACTAATTAG 59.370 41.667 11.05 11.05 38.66 1.73
1531 1746 4.494199 GGTGCATCGTCACAACTAATTAGC 60.494 45.833 12.54 0.00 38.66 3.09
1532 1747 4.092821 GTGCATCGTCACAACTAATTAGCA 59.907 41.667 12.54 0.00 36.97 3.49
1533 1748 4.329801 TGCATCGTCACAACTAATTAGCAG 59.670 41.667 12.54 7.69 0.00 4.24
1548 1770 8.138712 ACTAATTAGCAGTAAGAGAGCACATAC 58.861 37.037 12.54 0.00 0.00 2.39
1564 1786 6.870769 AGCACATACGGTTAGTTATGTTAGT 58.129 36.000 0.00 0.00 31.51 2.24
1608 1831 9.857957 CTTATAATCGGTTAGAGGAGGATAAAC 57.142 37.037 0.00 0.00 0.00 2.01
1653 1876 4.383444 GCACCTAACCGAACCCTTATAACT 60.383 45.833 0.00 0.00 0.00 2.24
1664 1887 6.350780 CGAACCCTTATAACTGTTAGTGGAGT 60.351 42.308 6.40 5.81 0.00 3.85
1689 1912 2.042404 TTTTACTCCGTGGTGGCCGT 62.042 55.000 0.00 0.00 37.80 5.68
1707 1930 3.061697 GCCGTGACCTTTAAACATACTCG 59.938 47.826 0.00 0.00 0.00 4.18
1713 1936 2.277084 CTTTAAACATACTCGGCCGCT 58.723 47.619 23.51 10.67 0.00 5.52
1766 1994 2.187946 CTCTTCCATTCCGCCGCT 59.812 61.111 0.00 0.00 0.00 5.52
1881 2132 5.237344 GTGAGTCTAGCTGTGTTGATTTTGT 59.763 40.000 0.00 0.00 0.00 2.83
1921 2172 8.870116 AGTGGTCTGCTAATTATATGATGTGTA 58.130 33.333 0.00 0.00 0.00 2.90
1924 2175 9.360093 GGTCTGCTAATTATATGATGTGTACTC 57.640 37.037 0.00 0.00 0.00 2.59
2057 2309 4.816385 TCACACTCACTTCATTCTTCAACC 59.184 41.667 0.00 0.00 0.00 3.77
2083 2335 4.679373 ATCAGTAGGTGCAGAATACTGG 57.321 45.455 22.91 11.47 44.19 4.00
2223 2510 6.070538 ACTGTACTCCTCTGTTCAGCATATTT 60.071 38.462 0.00 0.00 38.40 1.40
2225 2512 6.818644 TGTACTCCTCTGTTCAGCATATTTTC 59.181 38.462 0.00 0.00 0.00 2.29
2228 2515 5.569355 TCCTCTGTTCAGCATATTTTCCAA 58.431 37.500 0.00 0.00 0.00 3.53
2233 2520 6.267471 TCTGTTCAGCATATTTTCCAACCTTT 59.733 34.615 0.00 0.00 0.00 3.11
2442 2729 6.391227 TCTGGTTCCTCAAAATTTCTCAAC 57.609 37.500 0.00 0.00 0.00 3.18
2563 2850 4.141824 CCTGGAATCCTCTTGTAAGTCTCC 60.142 50.000 0.00 0.00 0.00 3.71
2696 2983 3.269381 ACCAGCCATATCTGAAAGGGAAA 59.731 43.478 0.00 0.00 36.19 3.13
3048 3336 6.651225 AGAGGTCAGCACTGAAAATTTACTAC 59.349 38.462 1.05 0.00 41.85 2.73
3307 3595 2.081462 TCACAGCTGTGCATGAATCTG 58.919 47.619 36.76 13.93 45.25 2.90
3310 3598 3.437741 CACAGCTGTGCATGAATCTGTAA 59.562 43.478 32.39 0.00 39.39 2.41
3324 3612 1.435563 TCTGTAAGGGAAGGTGAGGGA 59.564 52.381 0.00 0.00 0.00 4.20
3378 3666 3.339253 AATGCTGAGCACTGACACATA 57.661 42.857 10.33 0.00 43.04 2.29
3380 3668 2.624636 TGCTGAGCACTGACACATATG 58.375 47.619 1.40 0.00 31.71 1.78
3465 3755 4.788925 TGTTTCCCCAGAAGAAGAGAAA 57.211 40.909 0.00 0.00 32.35 2.52
3563 3853 2.092968 GGCATATGGTCACAGAACCTGA 60.093 50.000 4.56 0.00 40.20 3.86
3633 3923 5.361427 GGTTCTAGTAAGCTTCATCCTTCC 58.639 45.833 0.00 0.00 0.00 3.46
3672 3962 2.611518 CTTCTAAGAACCGCTCCTGTG 58.388 52.381 0.00 0.00 0.00 3.66
3765 4055 0.314935 AATGTGCACCGCTCTTTTGG 59.685 50.000 15.69 0.00 0.00 3.28
3803 4093 9.453830 AGATGGTTTTCCTTCCTAATATACTCT 57.546 33.333 0.00 0.00 42.85 3.24
3897 4187 1.209019 AGGTGCAAGCCACTATCTCTG 59.791 52.381 0.00 0.00 44.08 3.35
3921 4211 3.621558 CTCTTTAATTCCCCACCTCCAC 58.378 50.000 0.00 0.00 0.00 4.02
3954 4244 4.019411 TGCATGTAGAAAATGAGGAGACCA 60.019 41.667 0.00 0.00 0.00 4.02
3955 4245 5.128919 GCATGTAGAAAATGAGGAGACCAT 58.871 41.667 0.00 0.00 0.00 3.55
3956 4246 5.008415 GCATGTAGAAAATGAGGAGACCATG 59.992 44.000 0.00 0.00 0.00 3.66
3963 4253 3.623906 ATGAGGAGACCATGTGTTGAG 57.376 47.619 0.00 0.00 0.00 3.02
3994 4284 2.621998 GCTTGATTCCCATGTGATGAGG 59.378 50.000 0.00 0.00 0.00 3.86
4039 4329 4.851639 AGTGCATTGGGAAGATAGAAGT 57.148 40.909 0.00 0.00 0.00 3.01
4074 4364 5.918011 GTGGACAAATTTCGAATGCTAAACA 59.082 36.000 0.00 0.00 0.00 2.83
4076 4366 7.753132 GTGGACAAATTTCGAATGCTAAACATA 59.247 33.333 0.00 0.00 38.34 2.29
4194 4484 9.944376 AAAGCTTACAATAAGACAGAATACTGA 57.056 29.630 0.00 0.00 46.03 3.41
4195 4485 9.944376 AAGCTTACAATAAGACAGAATACTGAA 57.056 29.630 0.00 0.00 46.03 3.02
4230 4520 5.523438 AAATTTCCGCTGTTCTTTGGTTA 57.477 34.783 0.00 0.00 0.00 2.85
4240 4530 7.383843 CCGCTGTTCTTTGGTTAACAATTATTT 59.616 33.333 8.10 0.00 39.21 1.40
4291 4581 4.946478 AGTACTCATGTATCAGGGAAGC 57.054 45.455 0.00 0.00 0.00 3.86
4293 4583 4.586841 AGTACTCATGTATCAGGGAAGCTC 59.413 45.833 0.00 0.00 0.00 4.09
4302 4592 1.288037 TCAGGGAAGCTCTACAGGCTA 59.712 52.381 0.00 0.00 39.30 3.93
4356 4646 4.576216 ATCAGCGTATGACTCTTCGAAT 57.424 40.909 0.00 0.00 41.91 3.34
4586 4883 7.595819 TTTATTGAGACTCAAACCCATTTGT 57.404 32.000 21.29 4.85 44.76 2.83
4611 4908 9.929180 GTAGATCTATGTGCCAATTATTGTCTA 57.071 33.333 5.57 0.00 0.00 2.59
4652 4949 6.811170 ACATTAAGTTGGTTTTGACAGTGTTG 59.189 34.615 0.00 0.00 0.00 3.33
4723 5020 5.125900 CCTATTTGTTTGTCATCTCATGCCA 59.874 40.000 0.00 0.00 0.00 4.92
4734 5031 3.657398 TCTCATGCCACATTGGAGATT 57.343 42.857 0.00 0.00 40.96 2.40
4737 5034 6.438186 TCTCATGCCACATTGGAGATTATA 57.562 37.500 0.00 0.00 40.96 0.98
4841 5142 9.886132 AGTACTACTAGGTAACAATTTGAATGG 57.114 33.333 2.79 0.00 41.41 3.16
4856 5157 3.482436 TGAATGGCCAACGTTAAACTCT 58.518 40.909 10.96 0.00 0.00 3.24
4869 5170 8.645487 CAACGTTAAACTCTAGAGGTTTGATAC 58.355 37.037 27.40 17.84 39.43 2.24
4920 5221 3.706600 ATGCCAACAATGCTTTCCATT 57.293 38.095 0.00 0.00 44.86 3.16
4980 5281 9.982651 TTATGTACACTATTTAGCCTGATTCTC 57.017 33.333 0.00 0.00 0.00 2.87
4998 5299 6.915300 TGATTCTCGGTGTTTTAAACAATGTG 59.085 34.615 12.37 8.72 44.16 3.21
5017 5318 5.528043 TGTGTATGCATGGTTGAAAAGTT 57.472 34.783 10.16 0.00 0.00 2.66
5018 5319 6.641169 TGTGTATGCATGGTTGAAAAGTTA 57.359 33.333 10.16 0.00 0.00 2.24
5019 5320 7.043961 TGTGTATGCATGGTTGAAAAGTTAA 57.956 32.000 10.16 0.00 0.00 2.01
5020 5321 7.492524 TGTGTATGCATGGTTGAAAAGTTAAA 58.507 30.769 10.16 0.00 0.00 1.52
5021 5322 8.147058 TGTGTATGCATGGTTGAAAAGTTAAAT 58.853 29.630 10.16 0.00 0.00 1.40
5022 5323 9.632807 GTGTATGCATGGTTGAAAAGTTAAATA 57.367 29.630 10.16 0.00 0.00 1.40
5096 5406 8.862325 TGCTCCATGTTCTAATCTTTCTTAAA 57.138 30.769 0.00 0.00 0.00 1.52
5148 5458 6.438763 CACCTCTGTTGAATTGTTTCCTTAC 58.561 40.000 0.00 0.00 0.00 2.34
5157 5467 1.588674 TGTTTCCTTACACAGCCACG 58.411 50.000 0.00 0.00 0.00 4.94
5161 5471 2.335316 TCCTTACACAGCCACGTTTT 57.665 45.000 0.00 0.00 0.00 2.43
5162 5472 1.944024 TCCTTACACAGCCACGTTTTG 59.056 47.619 0.00 0.00 0.00 2.44
5163 5473 1.673920 CCTTACACAGCCACGTTTTGT 59.326 47.619 0.00 0.00 0.00 2.83
5165 5475 3.312973 CCTTACACAGCCACGTTTTGTAA 59.687 43.478 0.00 0.00 32.95 2.41
5166 5476 4.201930 CCTTACACAGCCACGTTTTGTAAA 60.202 41.667 0.00 0.00 33.44 2.01
5169 5479 5.502153 ACACAGCCACGTTTTGTAAATAA 57.498 34.783 0.00 0.00 0.00 1.40
5170 5480 5.275494 ACACAGCCACGTTTTGTAAATAAC 58.725 37.500 0.00 0.00 0.00 1.89
5171 5481 5.163642 ACACAGCCACGTTTTGTAAATAACA 60.164 36.000 0.00 0.00 35.88 2.41
5896 6281 3.394606 TCAAACTTGTTTAGGGAGAGGCT 59.605 43.478 0.00 0.00 0.00 4.58
5989 6374 0.250513 GGAGTCAAACCCGCTGAGAT 59.749 55.000 0.00 0.00 0.00 2.75
5995 6380 2.565391 TCAAACCCGCTGAGATGTTCTA 59.435 45.455 0.00 0.00 0.00 2.10
6047 6432 2.287909 GCGCACATTGTTTTTACCTCCA 60.288 45.455 0.30 0.00 0.00 3.86
6162 6547 8.980481 ATTGGAACTTATTAACTCATACTGGG 57.020 34.615 0.00 0.00 0.00 4.45
6321 6706 6.686378 GCAGGATAGGTGTAACAGATTCATGA 60.686 42.308 0.00 0.00 39.98 3.07
6560 6945 1.813513 ACGACCTGGAATTGCTCTTG 58.186 50.000 0.00 0.00 0.00 3.02
6817 7221 7.762615 TCTTCAAGAAATTGCATTCATTGGATC 59.237 33.333 3.04 0.00 0.00 3.36
6874 7278 1.300697 GCGGAACTCTTGGACGTGT 60.301 57.895 0.00 0.00 0.00 4.49
6881 7285 3.577649 ACTCTTGGACGTGTCACTATG 57.422 47.619 0.00 0.00 0.00 2.23
6890 7294 1.189403 GTGTCACTATGCTACGACGC 58.811 55.000 0.00 0.00 0.00 5.19
6908 7312 3.004024 CGCAAGTGAAAGAGCACAATT 57.996 42.857 0.00 0.00 41.19 2.32
6939 7343 9.040259 TCTAATAGGATTGATTAGTCATCCTGG 57.960 37.037 19.97 12.12 40.01 4.45
6976 7380 5.186198 GCTGTGTGAATTAGTACCTTGGAT 58.814 41.667 0.00 0.00 0.00 3.41
7193 7600 3.797671 AGAGGGGTGGTTAGGACTTAT 57.202 47.619 0.00 0.00 0.00 1.73
7200 7607 7.086920 AGGGGTGGTTAGGACTTATTATATGT 58.913 38.462 0.00 0.00 0.00 2.29
7320 7738 1.334869 GAACAGTTCTTGGTGTGGCAG 59.665 52.381 6.00 0.00 0.00 4.85
7386 7804 1.557443 GCAACTCTGACGTGGGTTCG 61.557 60.000 0.00 0.00 0.00 3.95
7402 7823 6.091713 CGTGGGTTCGAACTACTATTTGAATT 59.908 38.462 26.32 0.00 35.05 2.17
7404 7825 8.938906 GTGGGTTCGAACTACTATTTGAATTTA 58.061 33.333 26.32 0.00 35.05 1.40
7481 7902 8.963725 TCTTTTGTTGCTAAGATTCATCATCAT 58.036 29.630 0.00 0.00 33.75 2.45
7491 7912 7.606858 AAGATTCATCATCATACCTTATGCG 57.393 36.000 0.00 0.00 36.14 4.73
7497 7918 3.493129 TCATCATACCTTATGCGCGTTTC 59.507 43.478 7.78 0.00 36.14 2.78
7500 7921 3.554324 TCATACCTTATGCGCGTTTCTTC 59.446 43.478 7.78 0.00 36.14 2.87
7557 7979 2.772077 TTTCAGCAGCGGTTACCATA 57.228 45.000 1.13 0.00 0.00 2.74
7566 7988 2.132762 GCGGTTACCATAGATTCACGG 58.867 52.381 1.13 0.00 0.00 4.94
7654 8076 9.498176 TGATGTGATGGTCAAAATATCTATCTG 57.502 33.333 0.00 0.00 0.00 2.90
7655 8077 8.859236 ATGTGATGGTCAAAATATCTATCTGG 57.141 34.615 0.00 0.00 0.00 3.86
7656 8078 7.805163 TGTGATGGTCAAAATATCTATCTGGT 58.195 34.615 0.00 0.00 0.00 4.00
7657 8079 7.716560 TGTGATGGTCAAAATATCTATCTGGTG 59.283 37.037 0.00 0.00 0.00 4.17
7696 8146 2.280628 CCGACCCTTAGCTCATGAAAC 58.719 52.381 0.00 0.00 0.00 2.78
7697 8147 2.280628 CGACCCTTAGCTCATGAAACC 58.719 52.381 0.00 0.00 0.00 3.27
7717 8167 2.797156 CCGATTCACTCTTATGAAGCCG 59.203 50.000 0.00 3.10 41.02 5.52
7719 8169 1.640428 TTCACTCTTATGAAGCCGCG 58.360 50.000 0.00 0.00 33.62 6.46
7782 8232 5.058008 CGAAGAACATGCGATAAACAAACAC 59.942 40.000 0.00 0.00 0.00 3.32
7803 8254 4.388469 CACAAGGAAAACCAACACAACTTG 59.612 41.667 0.00 0.00 39.76 3.16
7804 8255 3.885724 AGGAAAACCAACACAACTTGG 57.114 42.857 0.00 0.00 45.62 3.61
7816 8267 6.282930 CAACACAACTTGGGAGATTTTTCAT 58.717 36.000 0.00 0.00 0.00 2.57
7827 8278 5.166398 GGAGATTTTTCATTGGAGTTGCAG 58.834 41.667 0.00 0.00 0.00 4.41
7829 8280 5.776744 AGATTTTTCATTGGAGTTGCAGAC 58.223 37.500 0.00 0.00 0.00 3.51
7839 8290 2.945668 GGAGTTGCAGACACTTGTTCTT 59.054 45.455 0.00 0.00 0.00 2.52
7843 8294 2.564771 TGCAGACACTTGTTCTTCTGG 58.435 47.619 0.00 0.00 36.72 3.86
7859 8310 4.287067 TCTTCTGGACAGTTGAAGCCTTAT 59.713 41.667 0.00 0.00 37.63 1.73
7860 8311 3.942829 TCTGGACAGTTGAAGCCTTATG 58.057 45.455 0.00 0.00 0.00 1.90
7861 8312 3.012518 CTGGACAGTTGAAGCCTTATGG 58.987 50.000 0.00 0.00 0.00 2.74
7862 8313 2.375174 TGGACAGTTGAAGCCTTATGGT 59.625 45.455 0.00 0.00 35.27 3.55
7886 8339 2.890311 AGCTCTCCTCCATCAATCTACG 59.110 50.000 0.00 0.00 0.00 3.51
7892 8345 2.103094 CCTCCATCAATCTACGAAGGCA 59.897 50.000 0.00 0.00 0.00 4.75
7894 8347 4.384056 CTCCATCAATCTACGAAGGCATT 58.616 43.478 0.00 0.00 0.00 3.56
7926 8379 5.410439 CCTATTAGGTAAAGCACACAAACGT 59.590 40.000 1.17 0.00 0.00 3.99
7937 8390 5.539048 AGCACACAAACGTAACTCTCTTAT 58.461 37.500 0.00 0.00 0.00 1.73
8020 8473 4.021104 ACAATCAAGATCAAGGACTCACGA 60.021 41.667 0.00 0.00 0.00 4.35
8155 8608 5.005779 CGGAAGCAACAATATCTGAGTACAC 59.994 44.000 0.00 0.00 0.00 2.90
8205 8658 3.690460 AGGCTAGCACAAAAGTAGCAAT 58.310 40.909 18.24 0.00 40.87 3.56
8215 8668 6.143758 GCACAAAAGTAGCAATGATCGAAAAA 59.856 34.615 0.00 0.00 0.00 1.94
8253 8706 3.880168 GGAGCCTCCTAACTACTCCTA 57.120 52.381 2.64 0.00 42.99 2.94
8256 8709 4.386648 GGAGCCTCCTAACTACTCCTAGTT 60.387 50.000 2.64 0.00 44.14 2.24
8443 8896 7.560991 ACATATGCAACATTATCAAAGGAAGGA 59.439 33.333 1.58 0.00 0.00 3.36
8473 8926 0.964358 GACTGGGCTGCAGAAATGCT 60.964 55.000 20.43 0.00 35.49 3.79
8659 9112 6.382570 AGAGCCATACTATCCAGTTATCATCC 59.617 42.308 0.00 0.00 36.14 3.51
8731 9184 3.764237 ACAACTCCAAGTGTCCGTTAT 57.236 42.857 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.768968 CACAATCAAAATTCCCTCTGGAGT 59.231 41.667 0.00 0.00 43.07 3.85
54 55 3.254060 GAGTACTGACGAACATGCATGT 58.746 45.455 26.61 26.61 44.20 3.21
77 78 8.327271 AGAAATGAGGAGAAATGAAAGAGATGA 58.673 33.333 0.00 0.00 0.00 2.92
138 140 3.540314 TTTTTGCTGTTTGGCACATCT 57.460 38.095 0.00 0.00 42.27 2.90
394 397 4.533815 TGTCGATGTACTTCATAGGGACT 58.466 43.478 9.22 0.00 46.37 3.85
577 580 5.591877 CAGTTTATAAGGCAGGATCAAGCTT 59.408 40.000 0.00 0.00 0.00 3.74
787 790 2.626840 GTGAGAGGAACCTTGCATCTC 58.373 52.381 4.60 4.60 37.50 2.75
863 1064 0.188587 TGAGTGCGGAGGATAGGGAT 59.811 55.000 0.00 0.00 0.00 3.85
974 1175 3.564225 GGGCCGAATAAAATGGTACTGAG 59.436 47.826 0.00 0.00 0.00 3.35
1133 1335 0.687757 AGTAGAGCTGGGAATCCGCA 60.688 55.000 0.00 0.00 35.86 5.69
1361 1576 5.424121 AATAATCGCAAGTAATCTGCACC 57.576 39.130 0.00 0.00 39.48 5.01
1433 1648 5.576774 TGCATCACAAACAGATAGAAGTACG 59.423 40.000 0.00 0.00 0.00 3.67
1442 1657 4.885907 CCCTCTATTGCATCACAAACAGAT 59.114 41.667 0.00 0.00 42.86 2.90
1454 1669 3.782523 AGAGATTCAACCCCTCTATTGCA 59.217 43.478 0.00 0.00 35.68 4.08
1455 1670 4.384940 GAGAGATTCAACCCCTCTATTGC 58.615 47.826 0.00 0.00 37.40 3.56
1456 1671 4.657969 AGGAGAGATTCAACCCCTCTATTG 59.342 45.833 0.00 0.00 37.40 1.90
1457 1672 4.657969 CAGGAGAGATTCAACCCCTCTATT 59.342 45.833 0.00 0.00 37.40 1.73
1458 1673 4.230455 CAGGAGAGATTCAACCCCTCTAT 58.770 47.826 0.00 0.00 37.40 1.98
1459 1674 3.012959 ACAGGAGAGATTCAACCCCTCTA 59.987 47.826 0.00 0.00 37.40 2.43
1460 1675 2.225753 ACAGGAGAGATTCAACCCCTCT 60.226 50.000 0.00 0.00 39.73 3.69
1482 1697 2.001076 AAAAGCCTTCCTGTCCCAAG 57.999 50.000 0.00 0.00 0.00 3.61
1509 1724 4.092821 TGCTAATTAGTTGTGACGATGCAC 59.907 41.667 13.91 0.00 39.22 4.57
1515 1730 7.027760 TCTCTTACTGCTAATTAGTTGTGACG 58.972 38.462 13.91 6.54 0.00 4.35
1523 1738 7.324856 CGTATGTGCTCTCTTACTGCTAATTAG 59.675 40.741 8.20 8.20 0.00 1.73
1524 1739 7.139392 CGTATGTGCTCTCTTACTGCTAATTA 58.861 38.462 0.00 0.00 0.00 1.40
1526 1741 5.508153 CCGTATGTGCTCTCTTACTGCTAAT 60.508 44.000 0.00 0.00 0.00 1.73
1528 1743 3.315470 CCGTATGTGCTCTCTTACTGCTA 59.685 47.826 0.00 0.00 0.00 3.49
1529 1744 2.099921 CCGTATGTGCTCTCTTACTGCT 59.900 50.000 0.00 0.00 0.00 4.24
1530 1745 2.159226 ACCGTATGTGCTCTCTTACTGC 60.159 50.000 0.00 0.00 0.00 4.40
1531 1746 3.784701 ACCGTATGTGCTCTCTTACTG 57.215 47.619 0.00 0.00 0.00 2.74
1532 1747 4.948621 ACTAACCGTATGTGCTCTCTTACT 59.051 41.667 0.00 0.00 0.00 2.24
1533 1748 5.246145 ACTAACCGTATGTGCTCTCTTAC 57.754 43.478 0.00 0.00 0.00 2.34
1548 1770 6.273825 AGAGATGCACTAACATAACTAACCG 58.726 40.000 0.00 0.00 0.00 4.44
1564 1786 2.088104 AGGGATCGGTTAGAGATGCA 57.912 50.000 0.00 0.00 38.05 3.96
1608 1831 4.150804 GCACTTTAGAGGAGAAAACGTGAG 59.849 45.833 0.00 0.00 0.00 3.51
1680 1903 0.183014 TTTAAAGGTCACGGCCACCA 59.817 50.000 12.97 0.00 36.23 4.17
1689 1912 3.602483 GGCCGAGTATGTTTAAAGGTCA 58.398 45.455 0.00 0.00 0.00 4.02
1713 1936 2.078392 GAATTTTTACTCCGCGGGTGA 58.922 47.619 27.83 15.94 0.00 4.02
1827 2067 2.680841 TCACTTAAAATGGCCGAATCCG 59.319 45.455 0.00 0.00 0.00 4.18
1832 2072 5.710099 AGATTTCTTCACTTAAAATGGCCGA 59.290 36.000 0.00 0.00 0.00 5.54
1932 2183 5.129320 CCCGGGTGATTATCATGATATCTCA 59.871 44.000 14.18 17.22 35.41 3.27
1933 2184 5.129485 ACCCGGGTGATTATCATGATATCTC 59.871 44.000 29.69 15.15 0.00 2.75
2057 2309 2.654749 TCTGCACCTACTGATTCACG 57.345 50.000 0.00 0.00 0.00 4.35
2181 2468 4.608948 ACAGTAGAGTTTTGGACAGAGG 57.391 45.455 0.00 0.00 0.00 3.69
2223 2510 4.538746 AACCAAAACGAAAAGGTTGGAA 57.461 36.364 8.22 0.00 42.42 3.53
2225 2512 6.421501 GGTAATAACCAAAACGAAAAGGTTGG 59.578 38.462 14.19 0.00 45.98 3.77
2442 2729 6.653273 AAGATCACACAAGACAATGATACG 57.347 37.500 0.00 0.00 31.96 3.06
2563 2850 7.809331 TCAAAAGTTGCAGCATTATCAACTAAG 59.191 33.333 2.55 2.19 46.63 2.18
2641 2928 4.973396 TGAAGCTAAAGATCGCATGTTTG 58.027 39.130 0.00 0.00 0.00 2.93
2844 3131 0.883370 GTGGAATATCCGGTTCCGGC 60.883 60.000 23.57 10.31 46.49 6.13
3031 3319 7.688578 GTGATTCTCGTAGTAAATTTTCAGTGC 59.311 37.037 0.00 0.00 0.00 4.40
3048 3336 6.565234 ACTAACCACTTATCTGTGATTCTCG 58.435 40.000 0.00 0.00 40.12 4.04
3274 3562 3.743396 ACAGCTGTGAAGTTCTCGATTTC 59.257 43.478 20.97 0.00 0.00 2.17
3307 3595 0.910338 GGTCCCTCACCTTCCCTTAC 59.090 60.000 0.00 0.00 42.84 2.34
3310 3598 0.621862 GATGGTCCCTCACCTTCCCT 60.622 60.000 0.00 0.00 46.98 4.20
3378 3666 4.228210 ACAACACACCAGATAATCCCTCAT 59.772 41.667 0.00 0.00 0.00 2.90
3380 3668 4.080863 AGACAACACACCAGATAATCCCTC 60.081 45.833 0.00 0.00 0.00 4.30
3465 3755 4.018960 ACTTGACCATACTGAGAAAGCCAT 60.019 41.667 0.00 0.00 0.00 4.40
3563 3853 1.565759 TCATGGGCTGACCTTTGCTAT 59.434 47.619 0.00 0.00 41.11 2.97
3672 3962 4.153117 ACAAGATCAAGATGAACTTCACGC 59.847 41.667 0.00 0.00 37.39 5.34
3765 4055 4.338400 GGAAAACCATCTATGCCTTGGTAC 59.662 45.833 0.00 0.00 42.85 3.34
3803 4093 3.194968 GTCCACTTATTTGAGGACGGAGA 59.805 47.826 0.00 0.00 40.89 3.71
3853 4143 4.019174 CCCAATGCATTTTCTACTCCACT 58.981 43.478 9.83 0.00 0.00 4.00
3897 4187 3.371702 GGAGGTGGGGAATTAAAGAGGAC 60.372 52.174 0.00 0.00 0.00 3.85
3921 4211 6.314648 TCATTTTCTACATGCACTTAGCTCAG 59.685 38.462 0.00 0.00 45.94 3.35
3954 4244 3.766545 AGCCCAATAACACTCAACACAT 58.233 40.909 0.00 0.00 0.00 3.21
3955 4245 3.222173 AGCCCAATAACACTCAACACA 57.778 42.857 0.00 0.00 0.00 3.72
3956 4246 3.568007 TCAAGCCCAATAACACTCAACAC 59.432 43.478 0.00 0.00 0.00 3.32
3963 4253 3.801114 GGGAATCAAGCCCAATAACAC 57.199 47.619 0.00 0.00 45.31 3.32
4074 4364 4.101119 CCCTCCGTCCTCAAATAAGTGTAT 59.899 45.833 0.00 0.00 0.00 2.29
4076 4366 2.236395 CCCTCCGTCCTCAAATAAGTGT 59.764 50.000 0.00 0.00 0.00 3.55
4136 4426 8.094548 TGGTACCTGATATAGAAAATTCCATCG 58.905 37.037 14.36 0.00 0.00 3.84
4190 4480 8.076178 CGGAAATTTTTCTTCACAGTATTCAGT 58.924 33.333 3.28 0.00 37.35 3.41
4191 4481 7.061094 GCGGAAATTTTTCTTCACAGTATTCAG 59.939 37.037 3.28 0.00 37.35 3.02
4192 4482 6.861055 GCGGAAATTTTTCTTCACAGTATTCA 59.139 34.615 3.28 0.00 37.35 2.57
4193 4483 7.061094 CAGCGGAAATTTTTCTTCACAGTATTC 59.939 37.037 3.28 0.00 37.35 1.75
4194 4484 6.863126 CAGCGGAAATTTTTCTTCACAGTATT 59.137 34.615 3.28 0.00 37.35 1.89
4195 4485 6.016276 ACAGCGGAAATTTTTCTTCACAGTAT 60.016 34.615 3.28 0.00 37.35 2.12
4230 4520 7.309770 TGGAGTTTTAGGCCAAATAATTGTT 57.690 32.000 5.01 0.00 34.60 2.83
4240 4530 6.321821 AGTATTACATGGAGTTTTAGGCCA 57.678 37.500 5.01 0.00 35.91 5.36
4291 4581 2.467880 TGGGTTCCTTAGCCTGTAGAG 58.532 52.381 0.00 0.00 45.03 2.43
4293 4583 2.681097 GCTTGGGTTCCTTAGCCTGTAG 60.681 54.545 0.00 0.00 45.03 2.74
4302 4592 3.832490 GGTATTTTCTGCTTGGGTTCCTT 59.168 43.478 0.00 0.00 0.00 3.36
4434 4724 3.967332 TCATGAGCAACATCAGACAGA 57.033 42.857 0.00 0.00 37.07 3.41
4572 4869 7.467811 GCACATAGATCTACAAATGGGTTTGAG 60.468 40.741 4.10 0.00 46.03 3.02
4652 4949 8.748380 AATAAGCTGAAAATAGCACAAAGTTC 57.252 30.769 0.00 0.00 46.07 3.01
4723 5020 7.946219 TGCTTCCAATCATATAATCTCCAATGT 59.054 33.333 0.00 0.00 0.00 2.71
4836 5137 4.933400 TCTAGAGTTTAACGTTGGCCATTC 59.067 41.667 6.09 1.70 0.00 2.67
4841 5142 3.922910 ACCTCTAGAGTTTAACGTTGGC 58.077 45.455 18.42 0.59 0.00 4.52
4967 5268 3.695830 AAACACCGAGAATCAGGCTAA 57.304 42.857 0.00 0.00 33.12 3.09
4980 5281 5.687730 TGCATACACATTGTTTAAAACACCG 59.312 36.000 0.00 0.00 41.97 4.94
5105 5415 6.380560 AGAGGTGGTACTCCAAACTTCTATAC 59.619 42.308 9.52 0.00 45.79 1.47
5148 5458 5.274718 TGTTATTTACAAAACGTGGCTGTG 58.725 37.500 7.49 0.00 32.64 3.66
5163 5473 9.973450 TGCTGATGCTTTAAGTTTTGTTATTTA 57.027 25.926 0.00 0.00 40.48 1.40
5165 5475 8.143835 AGTGCTGATGCTTTAAGTTTTGTTATT 58.856 29.630 0.00 0.00 40.48 1.40
5166 5476 7.596248 CAGTGCTGATGCTTTAAGTTTTGTTAT 59.404 33.333 0.00 0.00 40.48 1.89
5169 5479 5.067674 TCAGTGCTGATGCTTTAAGTTTTGT 59.932 36.000 0.00 0.00 40.48 2.83
5170 5480 5.522456 TCAGTGCTGATGCTTTAAGTTTTG 58.478 37.500 0.00 0.00 40.48 2.44
5171 5481 5.772825 TCAGTGCTGATGCTTTAAGTTTT 57.227 34.783 0.00 0.00 40.48 2.43
5604 5926 3.565905 ACGAGGGAAGTAGTGTTTACG 57.434 47.619 0.00 0.00 0.00 3.18
5677 5999 7.715249 AGCACACAAAAGAGAAATAACTGTAGA 59.285 33.333 0.00 0.00 0.00 2.59
5872 6257 3.746492 CCTCTCCCTAAACAAGTTTGACG 59.254 47.826 8.37 0.00 34.23 4.35
5896 6281 2.441750 ACCCTGTCTGCTTTTACCAAGA 59.558 45.455 0.00 0.00 0.00 3.02
5989 6374 4.168101 ACAGGGGTTCAGAGATTAGAACA 58.832 43.478 7.49 0.00 44.46 3.18
5995 6380 3.200825 CCATGTACAGGGGTTCAGAGATT 59.799 47.826 18.94 0.00 0.00 2.40
6113 6498 2.007360 AAGATGCGTGAGAGAAGCTG 57.993 50.000 0.00 0.00 0.00 4.24
6162 6547 7.205297 AGCAAATTATGTTCAACATATGCTCC 58.795 34.615 23.05 9.40 44.85 4.70
6321 6706 2.107750 CAGGACTGCCGCGATGAT 59.892 61.111 8.23 0.00 39.96 2.45
6403 6788 5.163343 GGTTTCCTACATGCAGTACAGGATA 60.163 44.000 9.25 3.61 35.44 2.59
6404 6789 4.384208 GGTTTCCTACATGCAGTACAGGAT 60.384 45.833 9.25 0.00 35.44 3.24
6728 7129 7.450124 AATGAAGCTGAAATCCATAGCATAG 57.550 36.000 0.00 0.00 39.84 2.23
6785 7186 7.143340 TGAATGCAATTTCTTGAAGAACTGAG 58.857 34.615 16.36 6.90 36.07 3.35
6817 7221 2.287069 CCTCGGCTACTGTTCTACATCG 60.287 54.545 0.00 0.00 0.00 3.84
6874 7278 2.731027 CACTTGCGTCGTAGCATAGTGA 60.731 50.000 25.17 8.85 46.51 3.41
6881 7285 1.387084 CTCTTTCACTTGCGTCGTAGC 59.613 52.381 0.00 0.00 37.71 3.58
6890 7294 3.553508 CCCCAATTGTGCTCTTTCACTTG 60.554 47.826 4.43 0.00 37.81 3.16
6906 7310 8.525729 ACTAATCAATCCTATTAGACCCCAAT 57.474 34.615 9.25 0.00 38.61 3.16
6908 7312 7.079700 TGACTAATCAATCCTATTAGACCCCA 58.920 38.462 9.25 1.20 38.61 4.96
6955 7359 6.821665 GCTTATCCAAGGTACTAATTCACACA 59.178 38.462 0.00 0.00 38.49 3.72
6976 7380 5.733676 TGTCATATGCAAGAGACTTGCTTA 58.266 37.500 28.10 25.73 45.13 3.09
7193 7600 8.410141 GCAATTAGGCCAAAAGTACACATATAA 58.590 33.333 5.01 0.00 0.00 0.98
7200 7607 5.538433 AGAAAGCAATTAGGCCAAAAGTACA 59.462 36.000 5.01 0.00 0.00 2.90
7280 7688 6.294176 CTGTTCTTTACATAGCCATATTGGGC 60.294 42.308 0.00 0.00 44.64 5.36
7320 7738 2.808543 GTTGAACCCACATCAGAGTGAC 59.191 50.000 0.00 0.00 42.05 3.67
7404 7825 9.909644 CACACTAAAGTACTAGTAAATCACTGT 57.090 33.333 3.61 0.00 38.24 3.55
7418 7839 7.846107 CACGATGAATTATGCACACTAAAGTAC 59.154 37.037 0.00 0.00 0.00 2.73
7481 7902 1.921887 CGAAGAAACGCGCATAAGGTA 59.078 47.619 5.73 0.00 0.00 3.08
7491 7912 1.493311 CTGCAGGACGAAGAAACGC 59.507 57.895 5.57 0.00 36.70 4.84
7497 7918 2.743928 GGTGCCTGCAGGACGAAG 60.744 66.667 37.21 9.14 37.39 3.79
7500 7921 3.947132 CTCTGGTGCCTGCAGGACG 62.947 68.421 37.21 17.47 37.39 4.79
7620 8042 4.707030 TGACCATCACATCAAATGCTTC 57.293 40.909 0.00 0.00 0.00 3.86
7654 8076 2.352715 GGCCAGCAAATCAACTAACACC 60.353 50.000 0.00 0.00 0.00 4.16
7655 8077 2.352715 GGGCCAGCAAATCAACTAACAC 60.353 50.000 4.39 0.00 0.00 3.32
7656 8078 1.892474 GGGCCAGCAAATCAACTAACA 59.108 47.619 4.39 0.00 0.00 2.41
7657 8079 1.204704 GGGGCCAGCAAATCAACTAAC 59.795 52.381 4.39 0.00 0.00 2.34
7685 8135 3.055530 AGAGTGAATCGGTTTCATGAGCT 60.056 43.478 4.92 0.00 45.77 4.09
7696 8146 2.797156 CGGCTTCATAAGAGTGAATCGG 59.203 50.000 0.00 0.00 37.47 4.18
7697 8147 2.219674 GCGGCTTCATAAGAGTGAATCG 59.780 50.000 0.00 0.00 37.47 3.34
7744 8194 0.316204 TCTTCGGTTTCACCTCGTCC 59.684 55.000 0.00 0.00 35.66 4.79
7747 8197 1.860676 TGTTCTTCGGTTTCACCTCG 58.139 50.000 0.00 0.00 35.66 4.63
7758 8208 5.058008 GTGTTTGTTTATCGCATGTTCTTCG 59.942 40.000 0.00 0.00 0.00 3.79
7782 8232 3.932089 CCAAGTTGTGTTGGTTTTCCTTG 59.068 43.478 1.45 0.00 41.96 3.61
7803 8254 4.021192 TGCAACTCCAATGAAAAATCTCCC 60.021 41.667 0.00 0.00 0.00 4.30
7804 8255 5.047802 TCTGCAACTCCAATGAAAAATCTCC 60.048 40.000 0.00 0.00 0.00 3.71
7816 8267 2.418368 ACAAGTGTCTGCAACTCCAA 57.582 45.000 0.00 0.00 0.00 3.53
7827 8278 3.798202 ACTGTCCAGAAGAACAAGTGTC 58.202 45.455 0.40 0.00 0.00 3.67
7829 8280 4.191544 TCAACTGTCCAGAAGAACAAGTG 58.808 43.478 0.40 0.00 0.00 3.16
7839 8290 3.307691 CCATAAGGCTTCAACTGTCCAGA 60.308 47.826 1.30 0.00 0.00 3.86
7843 8294 3.674997 TCACCATAAGGCTTCAACTGTC 58.325 45.455 1.30 0.00 39.06 3.51
7859 8310 1.198713 GATGGAGGAGAGCTTCACCA 58.801 55.000 0.00 0.00 37.88 4.17
7860 8311 1.198713 TGATGGAGGAGAGCTTCACC 58.801 55.000 0.00 0.00 0.00 4.02
7861 8312 3.134442 AGATTGATGGAGGAGAGCTTCAC 59.866 47.826 0.00 0.00 0.00 3.18
7862 8313 3.382278 AGATTGATGGAGGAGAGCTTCA 58.618 45.455 0.00 0.00 0.00 3.02
7886 8339 5.998363 CCTAATAGGAACTGGTAATGCCTTC 59.002 44.000 0.00 0.00 41.52 3.46
7892 8345 7.991460 GTGCTTTACCTAATAGGAACTGGTAAT 59.009 37.037 14.17 0.00 41.04 1.89
7894 8347 6.441284 TGTGCTTTACCTAATAGGAACTGGTA 59.559 38.462 14.17 0.00 41.52 3.25
7937 8390 3.709653 AGGGCGTCACAATTATCTAGGAA 59.290 43.478 0.00 0.00 0.00 3.36
7999 8452 4.464244 TCTCGTGAGTCCTTGATCTTGATT 59.536 41.667 0.00 0.00 0.00 2.57
8020 8473 8.247562 GTCTAGAGTTGTGTTGTGATATCTTCT 58.752 37.037 3.98 0.00 0.00 2.85
8155 8608 4.516698 AGGCAAACTTGTCTAACTCATGTG 59.483 41.667 0.00 0.00 42.19 3.21
8205 8658 1.812571 GAGGCCTTGCTTTTTCGATCA 59.187 47.619 6.77 0.00 0.00 2.92
8253 8706 1.658673 GTGGAGACCGTCGACAACT 59.341 57.895 17.16 10.87 34.15 3.16
8256 8709 1.293963 CTACGTGGAGACCGTCGACA 61.294 60.000 17.16 0.00 38.08 4.35
8443 8896 2.224621 GCAGCCCAGTCCACATATACAT 60.225 50.000 0.00 0.00 0.00 2.29
8473 8926 5.613544 AGGACTAGGCCTTCTCTCTATTCTA 59.386 44.000 12.97 0.00 33.46 2.10
8513 8966 2.627699 GCAAGATGGTGGTTTCCAGAAA 59.372 45.455 0.00 0.00 41.05 2.52
8633 9086 7.561722 GGATGATAACTGGATAGTATGGCTCTA 59.438 40.741 0.00 0.00 35.69 2.43
8659 9112 9.421806 GATACTTGAGATGAGACTTGGATATTG 57.578 37.037 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.