Multiple sequence alignment - TraesCS3B01G426700

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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 TraesCS3B01G426700 chr3B 100.000 2378 0 0 1317 3694 665257814 665260191 0.000000e+00 4392.0
1 TraesCS3B01G426700 chr3B 100.000 1087 0 0 1 1087 665256498 665257584 0.000000e+00 2008.0
2 TraesCS3B01G426700 chr3B 97.727 44 1 0 2988 3031 665258285 665258242 3.960000e-10 76.8
3 TraesCS3B01G426700 chr3B 97.727 44 1 0 1745 1788 665259528 665259485 3.960000e-10 76.8
4 TraesCS3B01G426700 chr3B 100.000 41 0 0 2025 2065 753954754 753954714 3.960000e-10 76.8
5 TraesCS3B01G426700 chr3D 86.807 1948 146 57 1317 3192 503856865 503858773 0.000000e+00 2071.0
6 TraesCS3B01G426700 chr3D 86.411 574 46 15 1 557 503855733 503856291 1.900000e-167 599.0
7 TraesCS3B01G426700 chr3D 87.028 424 24 9 3276 3692 503858794 503859193 2.020000e-122 449.0
8 TraesCS3B01G426700 chr3D 91.765 85 7 0 3192 3276 22679060 22679144 6.480000e-23 119.0
9 TraesCS3B01G426700 chr3D 89.362 94 10 0 3192 3285 22767898 22767805 6.480000e-23 119.0
10 TraesCS3B01G426700 chr3A 90.269 1634 73 30 2118 3693 642159568 642161173 0.000000e+00 2058.0
11 TraesCS3B01G426700 chr3A 80.137 1168 99 61 1 1087 642157647 642158762 0.000000e+00 749.0
12 TraesCS3B01G426700 chr3A 81.323 771 80 33 1340 2085 642158842 642159573 5.350000e-158 568.0
13 TraesCS3B01G426700 chr3A 92.941 85 6 0 3192 3276 374427550 374427634 1.390000e-24 124.0
14 TraesCS3B01G426700 chr5B 94.118 85 5 0 3192 3276 162772861 162772777 2.990000e-26 130.0
15 TraesCS3B01G426700 chr5B 100.000 28 0 0 2729 2756 202328063 202328090 7.000000e-03 52.8
16 TraesCS3B01G426700 chr4A 87.611 113 12 2 3175 3286 214314521 214314410 2.990000e-26 130.0
17 TraesCS3B01G426700 chr2A 92.941 85 6 0 3192 3276 4139303 4139219 1.390000e-24 124.0
18 TraesCS3B01G426700 chr6D 91.011 89 8 0 3188 3276 2784223 2784311 1.800000e-23 121.0
19 TraesCS3B01G426700 chr6D 73.663 243 54 8 3456 3694 63801940 63802176 6.570000e-13 86.1
20 TraesCS3B01G426700 chr1A 84.746 118 12 5 3159 3276 209362043 209362154 3.020000e-21 113.0
21 TraesCS3B01G426700 chr6A 97.059 34 0 1 1580 1612 396873956 396873923 5.150000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G426700 chr3B 665256498 665260191 3693 False 3200.000000 4392 100.000000 1 3694 2 chr3B.!!$F1 3693
1 TraesCS3B01G426700 chr3D 503855733 503859193 3460 False 1039.666667 2071 86.748667 1 3692 3 chr3D.!!$F2 3691
2 TraesCS3B01G426700 chr3A 642157647 642161173 3526 False 1125.000000 2058 83.909667 1 3693 3 chr3A.!!$F2 3692

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
598 664 0.036294 GGTTCTCAAGGAGGGGAACG 60.036 60.000 0.00 0.0 38.94 3.95 F
605 671 0.105913 AAGGAGGGGAACGCCAAAAA 60.106 50.000 10.35 0.0 44.92 1.94 F
953 1056 0.618981 CCCTGGAAGTGGAAGGGTAC 59.381 60.000 0.00 0.0 44.95 3.34 F
986 1089 1.060622 GATCGTCGTCTTCGTCGCT 59.939 57.895 0.00 0.0 44.86 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 1771 0.179018 AACGGAGGCAAAAGCTCTGT 60.179 50.000 0.0 0.0 38.23 3.41 R
1657 1858 0.676184 AGCGTGATGTGCGGATCTAT 59.324 50.000 0.0 0.0 37.44 1.98 R
2525 2764 0.896923 AGTGCCCATAACCGTCGTAA 59.103 50.000 0.0 0.0 0.00 3.18 R
2759 2999 1.063469 CGAACGAAACCAAGTTGCAGT 59.937 47.619 0.0 0.0 0.00 4.40 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
75 76 0.677731 TCTTTGCCGCCTTCTCATGG 60.678 55.000 0.00 0.00 0.00 3.66
116 117 1.009829 CCTGCCTTGTTACGAGATGC 58.990 55.000 0.31 0.00 0.00 3.91
118 119 1.929836 CTGCCTTGTTACGAGATGCTC 59.070 52.381 0.31 0.00 0.00 4.26
121 122 2.815478 CCTTGTTACGAGATGCTCCTC 58.185 52.381 0.31 0.00 0.00 3.71
122 123 2.428890 CCTTGTTACGAGATGCTCCTCT 59.571 50.000 0.31 0.00 0.00 3.69
123 124 3.490078 CCTTGTTACGAGATGCTCCTCTC 60.490 52.174 0.31 3.68 38.64 3.20
131 143 3.734597 CGAGATGCTCCTCTCTTTCAGTG 60.735 52.174 9.00 0.00 39.65 3.66
157 169 3.668596 ACCGTTTGTTCTCTTTTGTCG 57.331 42.857 0.00 0.00 0.00 4.35
161 173 5.524646 ACCGTTTGTTCTCTTTTGTCGATAA 59.475 36.000 0.00 0.00 0.00 1.75
162 174 6.204108 ACCGTTTGTTCTCTTTTGTCGATAAT 59.796 34.615 0.00 0.00 0.00 1.28
175 187 3.117491 TCGATAATACGACGACCCTCT 57.883 47.619 0.00 0.00 37.37 3.69
176 188 2.804527 TCGATAATACGACGACCCTCTG 59.195 50.000 0.00 0.00 37.37 3.35
177 189 2.664971 CGATAATACGACGACCCTCTGC 60.665 54.545 0.00 0.00 35.09 4.26
178 190 1.753930 TAATACGACGACCCTCTGCA 58.246 50.000 0.00 0.00 0.00 4.41
216 231 0.325933 CTCCATGGTCCTGTGAAGCA 59.674 55.000 12.58 0.00 0.00 3.91
288 303 2.905075 TGTTCACGATAATCCTGCTGG 58.095 47.619 2.58 2.58 0.00 4.85
306 321 0.326264 GGTTGCTCATCCAGGTGAGT 59.674 55.000 9.57 0.00 45.80 3.41
328 344 2.176798 TGGGTTCCTTTTGTCCTGTCAT 59.823 45.455 0.00 0.00 0.00 3.06
342 361 3.134623 TCCTGTCATTGATTATCGGCTGT 59.865 43.478 0.00 0.00 0.00 4.40
386 410 1.067060 CCTCGCCGAGATAATGACACA 59.933 52.381 17.19 0.00 0.00 3.72
387 411 2.120232 CTCGCCGAGATAATGACACAC 58.880 52.381 8.82 0.00 0.00 3.82
388 412 1.749063 TCGCCGAGATAATGACACACT 59.251 47.619 0.00 0.00 0.00 3.55
389 413 1.854743 CGCCGAGATAATGACACACTG 59.145 52.381 0.00 0.00 0.00 3.66
391 415 2.860735 GCCGAGATAATGACACACTGAC 59.139 50.000 0.00 0.00 0.00 3.51
392 416 3.676049 GCCGAGATAATGACACACTGACA 60.676 47.826 0.00 0.00 0.00 3.58
393 417 4.686972 CCGAGATAATGACACACTGACAT 58.313 43.478 0.00 0.00 34.44 3.06
394 418 4.505556 CCGAGATAATGACACACTGACATG 59.494 45.833 0.00 0.00 33.39 3.21
395 419 4.505556 CGAGATAATGACACACTGACATGG 59.494 45.833 0.00 0.00 33.39 3.66
396 420 4.194640 AGATAATGACACACTGACATGGC 58.805 43.478 0.00 0.00 33.39 4.40
397 421 1.538047 AATGACACACTGACATGGCC 58.462 50.000 0.00 0.00 33.39 5.36
398 422 0.401356 ATGACACACTGACATGGCCA 59.599 50.000 8.56 8.56 31.98 5.36
399 423 0.250424 TGACACACTGACATGGCCAG 60.250 55.000 13.05 13.67 37.64 4.85
400 424 0.957395 GACACACTGACATGGCCAGG 60.957 60.000 17.55 17.55 36.03 4.45
419 443 2.361104 GCCAGGGCCGACATGAAA 60.361 61.111 0.00 0.00 31.04 2.69
476 506 1.661509 CTTGCGTCTGACAGCACGA 60.662 57.895 22.95 10.91 43.69 4.35
478 508 0.599991 TTGCGTCTGACAGCACGAAT 60.600 50.000 22.95 0.00 43.69 3.34
480 510 1.959899 GCGTCTGACAGCACGAATGG 61.960 60.000 22.95 3.47 38.32 3.16
481 511 0.667487 CGTCTGACAGCACGAATGGT 60.667 55.000 17.22 0.00 38.32 3.55
482 512 1.071605 GTCTGACAGCACGAATGGTC 58.928 55.000 2.24 0.00 33.06 4.02
496 530 4.766891 ACGAATGGTCAGGTTCATTTTCAT 59.233 37.500 0.00 0.00 34.18 2.57
515 549 3.403057 CACGTGCTGTCCCGTTCG 61.403 66.667 0.82 0.00 34.59 3.95
587 653 0.319555 CTTGGTCGAGCGGTTCTCAA 60.320 55.000 10.46 0.00 41.98 3.02
596 662 1.838073 GCGGTTCTCAAGGAGGGGAA 61.838 60.000 0.00 0.00 0.00 3.97
598 664 0.036294 GGTTCTCAAGGAGGGGAACG 60.036 60.000 0.00 0.00 38.94 3.95
601 667 2.528127 TCAAGGAGGGGAACGCCA 60.528 61.111 10.35 0.00 44.92 5.69
605 671 0.105913 AAGGAGGGGAACGCCAAAAA 60.106 50.000 10.35 0.00 44.92 1.94
624 690 2.102357 CGCCGCTCGCTCTAAAGA 59.898 61.111 0.00 0.00 34.21 2.52
637 708 7.868415 GCTCGCTCTAAAGAGGATTTAATTAGA 59.132 37.037 8.99 0.00 42.29 2.10
638 709 9.921637 CTCGCTCTAAAGAGGATTTAATTAGAT 57.078 33.333 8.99 0.00 42.29 1.98
671 747 0.882474 CGGTTATTTGTGGCGGGAAA 59.118 50.000 0.00 0.00 0.00 3.13
672 748 1.135517 CGGTTATTTGTGGCGGGAAAG 60.136 52.381 0.00 0.00 0.00 2.62
792 882 1.518302 GGGACGAGGAGGAGAAAGC 59.482 63.158 0.00 0.00 0.00 3.51
793 883 1.518302 GGACGAGGAGGAGAAAGCC 59.482 63.158 0.00 0.00 0.00 4.35
794 884 1.139947 GACGAGGAGGAGAAAGCCG 59.860 63.158 0.00 0.00 0.00 5.52
795 885 2.286127 GACGAGGAGGAGAAAGCCGG 62.286 65.000 0.00 0.00 0.00 6.13
796 886 2.188207 GAGGAGGAGAAAGCCGGC 59.812 66.667 21.89 21.89 0.00 6.13
797 887 3.393149 GAGGAGGAGAAAGCCGGCC 62.393 68.421 26.15 8.19 0.00 6.13
798 888 3.403558 GGAGGAGAAAGCCGGCCT 61.404 66.667 26.15 14.08 0.00 5.19
799 889 2.124942 GAGGAGAAAGCCGGCCTG 60.125 66.667 26.15 0.00 0.00 4.85
827 917 1.153249 GAATCCGATTCCACGCCCA 60.153 57.895 9.66 0.00 33.17 5.36
857 947 0.763035 AACCCGCCACTTTCTGTAGT 59.237 50.000 0.00 0.00 0.00 2.73
876 966 1.134068 GTAACATTCCTGCCTCCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
877 967 1.575447 AACATTCCTGCCTCCCTCCC 61.575 60.000 0.00 0.00 0.00 4.30
878 968 1.695597 CATTCCTGCCTCCCTCCCT 60.696 63.158 0.00 0.00 0.00 4.20
879 969 1.385206 ATTCCTGCCTCCCTCCCTC 60.385 63.158 0.00 0.00 0.00 4.30
888 978 2.904866 CCCTCCCTCTCGCTCTCG 60.905 72.222 0.00 0.00 0.00 4.04
890 980 3.591835 CTCCCTCTCGCTCTCGGC 61.592 72.222 0.00 0.00 36.13 5.54
894 984 3.947841 CTCTCGCTCTCGGCCTCG 61.948 72.222 0.00 0.00 37.74 4.63
919 1009 5.360999 GCTTTGCTTATTATTCCTTCCACCT 59.639 40.000 0.00 0.00 0.00 4.00
922 1012 3.570125 GCTTATTATTCCTTCCACCTGCC 59.430 47.826 0.00 0.00 0.00 4.85
929 1029 2.121506 TTCCACCTGCCTCCCCTT 60.122 61.111 0.00 0.00 0.00 3.95
931 1031 4.101448 CCACCTGCCTCCCCTTCG 62.101 72.222 0.00 0.00 0.00 3.79
943 1043 2.750350 CCTTCGTGCCCTGGAAGT 59.250 61.111 0.00 0.00 38.34 3.01
951 1054 3.922366 CCCTGGAAGTGGAAGGGT 58.078 61.111 0.00 0.00 44.95 4.34
953 1056 0.618981 CCCTGGAAGTGGAAGGGTAC 59.381 60.000 0.00 0.00 44.95 3.34
968 1071 3.136123 TACGAAGAGGGCCGACCG 61.136 66.667 0.00 3.37 46.96 4.79
986 1089 1.060622 GATCGTCGTCTTCGTCGCT 59.939 57.895 0.00 0.00 44.86 4.93
1032 1141 4.147449 CTCCCACCGCTGCGATCA 62.147 66.667 25.45 1.28 0.00 2.92
1036 1145 1.815003 CCACCGCTGCGATCAATCA 60.815 57.895 25.45 0.00 0.00 2.57
1040 1149 1.069204 ACCGCTGCGATCAATCAGTAT 59.931 47.619 25.45 0.00 33.09 2.12
1045 1154 3.062763 CTGCGATCAATCAGTATGTCCC 58.937 50.000 0.00 0.00 37.40 4.46
1056 1165 2.102252 CAGTATGTCCCCTGCTTCTCTC 59.898 54.545 0.00 0.00 0.00 3.20
1337 1458 2.036346 GCTTCTTTGCCATGGTTTGTCT 59.964 45.455 14.67 0.00 0.00 3.41
1338 1459 3.645884 CTTCTTTGCCATGGTTTGTCTG 58.354 45.455 14.67 0.00 0.00 3.51
1339 1460 2.665165 TCTTTGCCATGGTTTGTCTGT 58.335 42.857 14.67 0.00 0.00 3.41
1340 1461 2.622942 TCTTTGCCATGGTTTGTCTGTC 59.377 45.455 14.67 0.00 0.00 3.51
1349 1474 3.466836 TGGTTTGTCTGTCTGTGATCAC 58.533 45.455 19.27 19.27 0.00 3.06
1367 1492 1.284408 CTACGATCTCGAGCCTGGC 59.716 63.158 11.65 11.65 43.02 4.85
1370 1495 2.420890 GATCTCGAGCCTGGCCTG 59.579 66.667 16.57 8.35 0.00 4.85
1439 1569 8.792831 TGAATCGGTATTAAACTAATCGACTC 57.207 34.615 0.00 0.00 30.57 3.36
1456 1586 2.957006 GACTCGTTAAGATGCCTCCCTA 59.043 50.000 0.00 0.00 0.00 3.53
1467 1597 3.028094 TGCCTCCCTAGTCTTATTCGT 57.972 47.619 0.00 0.00 0.00 3.85
1469 1599 2.296752 GCCTCCCTAGTCTTATTCGTCC 59.703 54.545 0.00 0.00 0.00 4.79
1473 1603 2.553172 CCCTAGTCTTATTCGTCCTCCG 59.447 54.545 0.00 0.00 38.13 4.63
1490 1620 3.743396 CCTCCGTATTTTGCTATCTCTGC 59.257 47.826 0.00 0.00 0.00 4.26
1519 1656 5.874810 TGTATGACTAGTTTAAAGCAGCAGG 59.125 40.000 0.00 0.00 0.00 4.85
1543 1741 5.803967 GCTTTGCATATTCAACAAGGAAGAG 59.196 40.000 0.00 0.00 0.00 2.85
1544 1742 6.571150 GCTTTGCATATTCAACAAGGAAGAGT 60.571 38.462 0.00 0.00 0.00 3.24
1545 1743 6.500684 TTGCATATTCAACAAGGAAGAGTC 57.499 37.500 0.00 0.00 0.00 3.36
1547 1745 6.003326 TGCATATTCAACAAGGAAGAGTCAA 58.997 36.000 0.00 0.00 0.00 3.18
1548 1746 6.660521 TGCATATTCAACAAGGAAGAGTCAAT 59.339 34.615 0.00 0.00 0.00 2.57
1549 1747 7.828717 TGCATATTCAACAAGGAAGAGTCAATA 59.171 33.333 0.00 0.00 0.00 1.90
1550 1748 8.844244 GCATATTCAACAAGGAAGAGTCAATAT 58.156 33.333 0.00 0.00 0.00 1.28
1577 1775 9.730705 AAAGAAATTGTAATGAGATGAGACAGA 57.269 29.630 0.00 0.00 0.00 3.41
1578 1776 8.945481 AGAAATTGTAATGAGATGAGACAGAG 57.055 34.615 0.00 0.00 0.00 3.35
1579 1777 7.495279 AGAAATTGTAATGAGATGAGACAGAGC 59.505 37.037 0.00 0.00 0.00 4.09
1580 1778 5.929058 TTGTAATGAGATGAGACAGAGCT 57.071 39.130 0.00 0.00 0.00 4.09
1581 1779 5.929058 TGTAATGAGATGAGACAGAGCTT 57.071 39.130 0.00 0.00 0.00 3.74
1582 1780 6.291648 TGTAATGAGATGAGACAGAGCTTT 57.708 37.500 0.00 0.00 0.00 3.51
1583 1781 6.705302 TGTAATGAGATGAGACAGAGCTTTT 58.295 36.000 0.00 0.00 0.00 2.27
1584 1782 6.592994 TGTAATGAGATGAGACAGAGCTTTTG 59.407 38.462 0.00 0.00 0.00 2.44
1596 1794 3.957383 GCTTTTGCCTCCGTTTCAA 57.043 47.368 0.00 0.00 40.15 2.69
1597 1795 2.217429 GCTTTTGCCTCCGTTTCAAA 57.783 45.000 0.00 0.00 40.15 2.69
1598 1796 2.545731 GCTTTTGCCTCCGTTTCAAAA 58.454 42.857 0.00 0.00 40.15 2.44
1599 1797 3.130633 GCTTTTGCCTCCGTTTCAAAAT 58.869 40.909 0.00 0.00 38.51 1.82
1600 1798 4.303282 GCTTTTGCCTCCGTTTCAAAATA 58.697 39.130 0.00 0.00 38.51 1.40
1601 1799 4.747605 GCTTTTGCCTCCGTTTCAAAATAA 59.252 37.500 0.00 0.00 38.51 1.40
1602 1800 5.235401 GCTTTTGCCTCCGTTTCAAAATAAA 59.765 36.000 0.00 0.00 38.51 1.40
1603 1801 6.073276 GCTTTTGCCTCCGTTTCAAAATAAAT 60.073 34.615 0.00 0.00 38.51 1.40
1604 1802 7.117092 GCTTTTGCCTCCGTTTCAAAATAAATA 59.883 33.333 0.00 0.00 38.51 1.40
1605 1803 8.888579 TTTTGCCTCCGTTTCAAAATAAATAA 57.111 26.923 0.00 0.00 35.53 1.40
1606 1804 8.888579 TTTGCCTCCGTTTCAAAATAAATAAA 57.111 26.923 0.00 0.00 0.00 1.40
1607 1805 9.495572 TTTGCCTCCGTTTCAAAATAAATAAAT 57.504 25.926 0.00 0.00 0.00 1.40
1661 1863 2.118679 CCACCTGGGATGTGTGATAGA 58.881 52.381 0.00 0.00 40.01 1.98
1662 1864 2.707791 CCACCTGGGATGTGTGATAGAT 59.292 50.000 0.00 0.00 40.01 1.98
1667 1869 2.820059 GGATGTGTGATAGATCCGCA 57.180 50.000 0.00 0.00 39.21 5.69
1722 1926 5.825593 AACTCTCCAAGTGGTTGATTCTA 57.174 39.130 0.00 0.00 38.58 2.10
1726 1930 6.013379 ACTCTCCAAGTGGTTGATTCTAATGA 60.013 38.462 0.00 0.00 36.65 2.57
1747 1951 6.030548 TGAGATTTTCAGACTGATCGAGTT 57.969 37.500 5.87 0.00 33.83 3.01
1748 1952 5.866092 TGAGATTTTCAGACTGATCGAGTTG 59.134 40.000 5.87 2.21 33.83 3.16
1749 1953 4.629200 AGATTTTCAGACTGATCGAGTTGC 59.371 41.667 5.87 0.00 33.83 4.17
1750 1954 3.667497 TTTCAGACTGATCGAGTTGCT 57.333 42.857 5.87 0.00 33.83 3.91
1751 1955 3.667497 TTCAGACTGATCGAGTTGCTT 57.333 42.857 5.87 0.00 33.83 3.91
1752 1956 3.223423 TCAGACTGATCGAGTTGCTTC 57.777 47.619 0.00 0.00 33.83 3.86
1753 1957 1.916651 CAGACTGATCGAGTTGCTTCG 59.083 52.381 0.00 0.40 41.79 3.79
1768 1972 1.874562 CTTCGAAGCAATTGTCAGCG 58.125 50.000 13.09 6.56 35.48 5.18
1769 1973 1.460743 CTTCGAAGCAATTGTCAGCGA 59.539 47.619 13.09 8.72 35.48 4.93
1770 1974 1.507562 TCGAAGCAATTGTCAGCGAA 58.492 45.000 7.40 0.00 35.48 4.70
1771 1975 2.076100 TCGAAGCAATTGTCAGCGAAT 58.924 42.857 7.40 0.00 35.48 3.34
1772 1976 2.094258 TCGAAGCAATTGTCAGCGAATC 59.906 45.455 7.40 0.00 35.48 2.52
1773 1977 2.159667 CGAAGCAATTGTCAGCGAATCA 60.160 45.455 7.40 0.00 35.48 2.57
1774 1978 3.667695 CGAAGCAATTGTCAGCGAATCAA 60.668 43.478 7.40 0.00 35.48 2.57
1775 1979 3.921119 AGCAATTGTCAGCGAATCAAA 57.079 38.095 7.40 0.00 35.48 2.69
1778 1982 3.922240 GCAATTGTCAGCGAATCAAATGT 59.078 39.130 7.40 0.00 0.00 2.71
1802 2006 1.818060 TCCGCATTTCTGAACATTGGG 59.182 47.619 0.00 0.00 0.00 4.12
1811 2015 2.076863 CTGAACATTGGGAACTCGACC 58.923 52.381 0.00 0.00 0.00 4.79
1812 2016 1.076332 GAACATTGGGAACTCGACCG 58.924 55.000 0.00 0.00 0.00 4.79
2000 2236 7.037438 TCCATGCAATTTTAGCAAAAGAGATC 58.963 34.615 0.00 0.00 46.27 2.75
2016 2253 2.781595 GATCGCTGACCCACCGTTGT 62.782 60.000 0.00 0.00 0.00 3.32
2115 2352 2.363788 TTGTGTACATCAGAGCCGTC 57.636 50.000 0.00 0.00 0.00 4.79
2121 2359 2.100605 ACATCAGAGCCGTCTTTTCC 57.899 50.000 0.00 0.00 0.00 3.13
2227 2466 4.678509 TTATGTGAATCTTTGGTGCGAC 57.321 40.909 0.00 0.00 0.00 5.19
2352 2591 2.820197 GGGTAGGCACCTTTCTTTCTTG 59.180 50.000 0.00 0.00 45.04 3.02
2353 2592 2.229062 GGTAGGCACCTTTCTTTCTTGC 59.771 50.000 0.00 0.00 42.11 4.01
2354 2593 3.894257 GGCACCTTTCTTTCTTGCC 57.106 52.632 0.00 0.00 45.64 4.52
2356 2595 2.428888 GCACCTTTCTTTCTTGCCTG 57.571 50.000 0.00 0.00 0.00 4.85
2357 2596 1.603931 GCACCTTTCTTTCTTGCCTGC 60.604 52.381 0.00 0.00 0.00 4.85
2370 2609 5.465532 TCTTGCCTGCAATCAATTTGTAA 57.534 34.783 4.84 0.00 37.65 2.41
2483 2722 2.196742 ACCCCAGGATCATAGCAGAA 57.803 50.000 0.00 0.00 0.00 3.02
2489 2728 4.226846 CCCAGGATCATAGCAGAATATGGT 59.773 45.833 0.00 0.00 43.56 3.55
2498 2737 6.956435 TCATAGCAGAATATGGTCAGGAGTAT 59.044 38.462 0.00 0.00 40.89 2.12
2525 2764 1.227734 CAACCCGGTCCGTGTTCTT 60.228 57.895 9.34 0.00 0.00 2.52
2709 2949 2.728922 CGTAGCTAACCGGAGAATGAC 58.271 52.381 9.46 0.00 0.00 3.06
2710 2950 2.728922 GTAGCTAACCGGAGAATGACG 58.271 52.381 9.46 0.00 0.00 4.35
2711 2951 0.179108 AGCTAACCGGAGAATGACGC 60.179 55.000 9.46 0.00 0.00 5.19
2712 2952 1.480219 GCTAACCGGAGAATGACGCG 61.480 60.000 9.46 3.53 0.00 6.01
2713 2953 0.870307 CTAACCGGAGAATGACGCGG 60.870 60.000 9.46 0.00 0.00 6.46
2714 2954 1.597797 TAACCGGAGAATGACGCGGT 61.598 55.000 9.46 0.00 36.47 5.68
2747 2987 8.638629 TGTAAGCTTCTTCTACTACTTCTTCT 57.361 34.615 0.00 0.00 0.00 2.85
2748 2988 9.736414 TGTAAGCTTCTTCTACTACTTCTTCTA 57.264 33.333 0.00 0.00 0.00 2.10
2749 2989 9.992910 GTAAGCTTCTTCTACTACTTCTTCTAC 57.007 37.037 0.00 0.00 0.00 2.59
2750 2990 8.873186 AAGCTTCTTCTACTACTTCTTCTACT 57.127 34.615 0.00 0.00 0.00 2.57
2751 2991 9.962809 AAGCTTCTTCTACTACTTCTTCTACTA 57.037 33.333 0.00 0.00 0.00 1.82
2753 2993 9.387257 GCTTCTTCTACTACTTCTTCTACTACT 57.613 37.037 0.00 0.00 0.00 2.57
2814 3069 3.927142 GCGGTATAGCACATATGGAAGTC 59.073 47.826 7.80 0.00 37.05 3.01
2932 3190 3.813166 ACTGCATAAACTTACACTGCGTT 59.187 39.130 0.00 0.00 35.63 4.84
3000 3259 3.159472 TGAAAGCTTGCTGATGGACATT 58.841 40.909 5.89 0.00 0.00 2.71
3009 3268 2.357009 GCTGATGGACATTTGATTCGCT 59.643 45.455 0.00 0.00 0.00 4.93
3044 3303 0.874390 GCAACTGAATTCTCACGGCA 59.126 50.000 7.05 0.00 0.00 5.69
3049 3308 2.095059 ACTGAATTCTCACGGCAAATGC 60.095 45.455 7.05 0.00 41.14 3.56
3064 3347 5.565259 CGGCAAATGCGAATACAATCTTATC 59.435 40.000 0.00 0.00 43.26 1.75
3081 3364 7.865706 ATCTTATCTTGTTATGTTGGTCACC 57.134 36.000 0.00 0.00 0.00 4.02
3112 3395 7.727181 TCCTCTAGGATTGCTACATAGAAAAC 58.273 38.462 0.00 0.00 39.78 2.43
3199 3482 3.906218 TGCCTATCGAGTACTACTCCCTA 59.094 47.826 10.14 2.55 42.12 3.53
3210 3493 7.699812 CGAGTACTACTCCCTATGTAAACAAAC 59.300 40.741 10.14 0.00 42.12 2.93
3216 3499 9.326413 CTACTCCCTATGTAAACAAACATAAGG 57.674 37.037 5.61 5.61 42.02 2.69
3217 3500 7.116736 ACTCCCTATGTAAACAAACATAAGGG 58.883 38.462 16.95 16.95 41.41 3.95
3232 3515 8.567948 CAAACATAAGGGCGTTTAGATCAATAT 58.432 33.333 0.00 0.00 33.68 1.28
3272 3555 8.319057 TGCTCTTATATTTCTTTACAGAGGGA 57.681 34.615 0.00 0.00 0.00 4.20
3286 3581 8.603898 TTTACAGAGGGAGTAGTGATGATTAA 57.396 34.615 0.00 0.00 0.00 1.40
3372 3674 6.812160 GTGGCTCTTTTCTACGAAGATAGAAA 59.188 38.462 4.28 4.28 45.27 2.52
3381 3683 7.596749 TCTACGAAGATAGAAAAAGCTTTGG 57.403 36.000 13.54 0.00 0.00 3.28
3382 3684 7.383687 TCTACGAAGATAGAAAAAGCTTTGGA 58.616 34.615 13.54 0.00 0.00 3.53
3383 3685 6.877611 ACGAAGATAGAAAAAGCTTTGGAA 57.122 33.333 13.54 0.00 0.00 3.53
3384 3686 6.903419 ACGAAGATAGAAAAAGCTTTGGAAG 58.097 36.000 13.54 0.00 0.00 3.46
3385 3687 6.486993 ACGAAGATAGAAAAAGCTTTGGAAGT 59.513 34.615 13.54 0.00 0.00 3.01
3386 3688 7.660208 ACGAAGATAGAAAAAGCTTTGGAAGTA 59.340 33.333 13.54 1.26 0.00 2.24
3387 3689 7.958025 CGAAGATAGAAAAAGCTTTGGAAGTAC 59.042 37.037 13.54 2.75 0.00 2.73
3388 3690 7.689446 AGATAGAAAAAGCTTTGGAAGTACC 57.311 36.000 13.54 0.00 39.54 3.34
3389 3691 7.462590 AGATAGAAAAAGCTTTGGAAGTACCT 58.537 34.615 13.54 1.36 39.86 3.08
3390 3692 8.603304 AGATAGAAAAAGCTTTGGAAGTACCTA 58.397 33.333 13.54 6.13 39.86 3.08
3391 3693 9.227777 GATAGAAAAAGCTTTGGAAGTACCTAA 57.772 33.333 13.54 0.00 39.86 2.69
3406 3708 7.705752 GGAAGTACCTAAGTTAAAAGATCGGAG 59.294 40.741 0.00 0.00 35.41 4.63
3422 3747 1.804748 CGGAGGTACCAGACAAAAAGC 59.195 52.381 15.94 0.00 38.90 3.51
3441 3766 2.003301 GCTGGCTCTTTTCTACGAAGG 58.997 52.381 0.00 0.00 0.00 3.46
3503 3828 2.612212 TCAAAGAGAAACGGTGCAGAAC 59.388 45.455 0.00 0.00 0.00 3.01
3529 3854 1.002274 ATCCCAGCTCGGAGGTTCT 59.998 57.895 6.16 0.00 36.56 3.01
3552 3877 0.539986 TGGATTTGCTCGGGAGTACC 59.460 55.000 0.00 0.00 0.00 3.34
3693 4019 4.077108 GGTGGTACCGGAGAAATTTCTTT 58.923 43.478 21.33 9.37 37.73 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 7.010552 GCAGGCTATATATACATTGTACAGTGC 59.989 40.741 17.45 1.11 0.00 4.40
116 117 3.674528 TGCTTCACTGAAAGAGAGGAG 57.325 47.619 0.00 0.00 34.30 3.69
118 119 2.810852 GGTTGCTTCACTGAAAGAGAGG 59.189 50.000 0.00 0.00 34.30 3.69
121 122 2.213499 ACGGTTGCTTCACTGAAAGAG 58.787 47.619 0.00 0.00 37.43 2.85
122 123 2.325583 ACGGTTGCTTCACTGAAAGA 57.674 45.000 0.00 0.00 37.43 2.52
123 124 3.108144 CAAACGGTTGCTTCACTGAAAG 58.892 45.455 0.00 0.00 42.29 2.62
131 143 3.692791 AAGAGAACAAACGGTTGCTTC 57.307 42.857 14.43 15.46 40.63 3.86
157 169 2.292569 TGCAGAGGGTCGTCGTATTATC 59.707 50.000 0.00 0.00 0.00 1.75
161 173 0.385751 CATGCAGAGGGTCGTCGTAT 59.614 55.000 0.00 0.00 0.00 3.06
162 174 1.807226 CATGCAGAGGGTCGTCGTA 59.193 57.895 0.00 0.00 0.00 3.43
167 179 1.812922 GTGAGCATGCAGAGGGTCG 60.813 63.158 21.98 0.00 33.04 4.79
168 180 0.743701 CAGTGAGCATGCAGAGGGTC 60.744 60.000 21.98 7.99 0.00 4.46
169 181 1.196766 TCAGTGAGCATGCAGAGGGT 61.197 55.000 21.98 0.00 0.00 4.34
170 182 0.743701 GTCAGTGAGCATGCAGAGGG 60.744 60.000 21.98 6.40 0.00 4.30
172 184 1.666189 CATGTCAGTGAGCATGCAGAG 59.334 52.381 21.98 4.89 36.49 3.35
173 185 1.002773 ACATGTCAGTGAGCATGCAGA 59.997 47.619 21.98 6.59 44.43 4.26
174 186 1.130561 CACATGTCAGTGAGCATGCAG 59.869 52.381 21.98 17.22 44.43 4.41
175 187 1.161843 CACATGTCAGTGAGCATGCA 58.838 50.000 21.98 8.64 44.43 3.96
176 188 0.450583 CCACATGTCAGTGAGCATGC 59.549 55.000 23.90 10.51 44.43 4.06
177 189 1.092348 CCCACATGTCAGTGAGCATG 58.908 55.000 23.04 23.04 45.61 4.06
178 190 0.679002 GCCCACATGTCAGTGAGCAT 60.679 55.000 0.00 0.00 42.10 3.79
216 231 2.820197 GCCTCCCTGAAGAACGAAATTT 59.180 45.455 0.00 0.00 0.00 1.82
270 285 3.270027 CAACCAGCAGGATTATCGTGAA 58.730 45.455 17.65 0.00 34.44 3.18
306 321 2.024846 TGACAGGACAAAAGGAACCCAA 60.025 45.455 0.00 0.00 0.00 4.12
328 344 2.287644 CGCATCAACAGCCGATAATCAA 59.712 45.455 0.00 0.00 0.00 2.57
342 361 2.027285 TCTGGATCCTTTCACGCATCAA 60.027 45.455 14.23 0.00 0.00 2.57
373 395 4.272018 GCCATGTCAGTGTGTCATTATCTC 59.728 45.833 0.00 0.00 0.00 2.75
380 402 0.250424 CTGGCCATGTCAGTGTGTCA 60.250 55.000 5.51 0.00 29.72 3.58
386 410 4.052518 GCCCCTGGCCATGTCAGT 62.053 66.667 5.51 0.00 44.06 3.41
404 428 0.107017 ATCCTTTCATGTCGGCCCTG 60.107 55.000 0.00 0.00 0.00 4.45
419 443 3.744940 TTTTTCCCTCTCATGCATCCT 57.255 42.857 0.00 0.00 0.00 3.24
476 506 6.458210 GTGAATGAAAATGAACCTGACCATT 58.542 36.000 0.00 0.00 34.75 3.16
478 508 4.023279 CGTGAATGAAAATGAACCTGACCA 60.023 41.667 0.00 0.00 0.00 4.02
480 510 4.911610 CACGTGAATGAAAATGAACCTGAC 59.088 41.667 10.90 0.00 0.00 3.51
481 511 4.556501 GCACGTGAATGAAAATGAACCTGA 60.557 41.667 22.23 0.00 0.00 3.86
482 512 3.670055 GCACGTGAATGAAAATGAACCTG 59.330 43.478 22.23 0.00 0.00 4.00
515 549 0.025513 GCACAATCATCTCGTGCGAC 59.974 55.000 0.00 0.00 45.69 5.19
523 557 3.745975 TCGAAACGAAAGCACAATCATCT 59.254 39.130 0.00 0.00 31.06 2.90
587 653 0.539669 CTTTTTGGCGTTCCCCTCCT 60.540 55.000 0.00 0.00 0.00 3.69
624 690 8.782927 GGGCCTCCTATAATCTAATTAAATCCT 58.217 37.037 0.84 0.00 0.00 3.24
637 708 0.104090 AACCGGGGGCCTCCTATAAT 60.104 55.000 22.56 0.00 35.33 1.28
638 709 0.567182 TAACCGGGGGCCTCCTATAA 59.433 55.000 22.56 0.00 35.33 0.98
639 710 0.794934 ATAACCGGGGGCCTCCTATA 59.205 55.000 22.56 10.36 35.33 1.31
640 711 0.104090 AATAACCGGGGGCCTCCTAT 60.104 55.000 22.56 8.25 35.33 2.57
641 712 0.327770 AAATAACCGGGGGCCTCCTA 60.328 55.000 22.56 5.68 35.33 2.94
642 713 1.621514 AAATAACCGGGGGCCTCCT 60.622 57.895 22.56 2.87 35.33 3.69
643 714 1.455032 CAAATAACCGGGGGCCTCC 60.455 63.158 13.54 13.54 0.00 4.30
644 715 1.035385 CACAAATAACCGGGGGCCTC 61.035 60.000 6.32 0.00 0.00 4.70
645 716 1.000145 CACAAATAACCGGGGGCCT 60.000 57.895 6.32 0.00 0.00 5.19
646 717 2.055633 CCACAAATAACCGGGGGCC 61.056 63.158 6.32 0.00 0.00 5.80
776 866 1.139947 CGGCTTTCTCCTCCTCGTC 59.860 63.158 0.00 0.00 0.00 4.20
777 867 2.352032 CCGGCTTTCTCCTCCTCGT 61.352 63.158 0.00 0.00 0.00 4.18
778 868 2.496817 CCGGCTTTCTCCTCCTCG 59.503 66.667 0.00 0.00 0.00 4.63
779 869 2.188207 GCCGGCTTTCTCCTCCTC 59.812 66.667 22.15 0.00 0.00 3.71
780 870 3.403558 GGCCGGCTTTCTCCTCCT 61.404 66.667 28.56 0.00 0.00 3.69
781 871 3.403558 AGGCCGGCTTTCTCCTCC 61.404 66.667 28.56 5.83 0.00 4.30
782 872 2.124942 CAGGCCGGCTTTCTCCTC 60.125 66.667 28.56 6.68 0.00 3.71
783 873 4.416738 GCAGGCCGGCTTTCTCCT 62.417 66.667 28.56 11.02 0.00 3.69
784 874 4.416738 AGCAGGCCGGCTTTCTCC 62.417 66.667 25.87 8.41 42.71 3.71
785 875 3.130160 CAGCAGGCCGGCTTTCTC 61.130 66.667 28.94 9.28 42.71 2.87
786 876 2.697147 TTTCAGCAGGCCGGCTTTCT 62.697 55.000 28.94 17.06 42.71 2.52
787 877 1.805428 TTTTCAGCAGGCCGGCTTTC 61.805 55.000 28.94 14.47 42.71 2.62
788 878 1.809567 CTTTTCAGCAGGCCGGCTTT 61.810 55.000 28.94 12.72 42.71 3.51
789 879 2.203480 TTTTCAGCAGGCCGGCTT 60.203 55.556 28.94 18.19 42.71 4.35
791 881 2.985847 ACTTTTCAGCAGGCCGGC 60.986 61.111 21.36 21.36 0.00 6.13
792 882 1.172180 TTCACTTTTCAGCAGGCCGG 61.172 55.000 0.00 0.00 0.00 6.13
793 883 0.883833 ATTCACTTTTCAGCAGGCCG 59.116 50.000 0.00 0.00 0.00 6.13
794 884 1.203287 GGATTCACTTTTCAGCAGGCC 59.797 52.381 0.00 0.00 0.00 5.19
795 885 1.135575 CGGATTCACTTTTCAGCAGGC 60.136 52.381 0.00 0.00 0.00 4.85
796 886 2.426522 TCGGATTCACTTTTCAGCAGG 58.573 47.619 0.00 0.00 0.00 4.85
797 887 4.437930 GGAATCGGATTCACTTTTCAGCAG 60.438 45.833 26.93 0.00 41.03 4.24
798 888 3.440173 GGAATCGGATTCACTTTTCAGCA 59.560 43.478 26.93 0.00 41.03 4.41
799 889 3.440173 TGGAATCGGATTCACTTTTCAGC 59.560 43.478 26.93 10.73 41.03 4.26
857 947 1.213296 GGAGGGAGGCAGGAATGTTA 58.787 55.000 0.00 0.00 0.00 2.41
876 966 3.591835 GAGGCCGAGAGCGAGAGG 61.592 72.222 0.00 0.00 45.17 3.69
877 967 3.947841 CGAGGCCGAGAGCGAGAG 61.948 72.222 0.00 0.00 45.17 3.20
888 978 1.675552 TAATAAGCAAAGCCGAGGCC 58.324 50.000 10.95 0.00 43.17 5.19
890 980 4.137543 AGGAATAATAAGCAAAGCCGAGG 58.862 43.478 0.00 0.00 0.00 4.63
891 981 5.278022 GGAAGGAATAATAAGCAAAGCCGAG 60.278 44.000 0.00 0.00 0.00 4.63
894 984 5.451937 GGTGGAAGGAATAATAAGCAAAGCC 60.452 44.000 0.00 0.00 0.00 4.35
922 1012 4.101448 CCAGGGCACGAAGGGGAG 62.101 72.222 0.00 0.00 0.00 4.30
929 1029 2.111999 CTTCCACTTCCAGGGCACGA 62.112 60.000 0.00 0.00 0.00 4.35
931 1031 1.303643 CCTTCCACTTCCAGGGCAC 60.304 63.158 0.00 0.00 0.00 5.01
943 1043 1.262640 GCCCTCTTCGTACCCTTCCA 61.263 60.000 0.00 0.00 0.00 3.53
951 1054 2.898920 ATCGGTCGGCCCTCTTCGTA 62.899 60.000 0.00 0.00 0.00 3.43
953 1056 3.486252 GATCGGTCGGCCCTCTTCG 62.486 68.421 0.00 0.00 0.00 3.79
1020 1126 0.459899 TACTGATTGATCGCAGCGGT 59.540 50.000 16.42 7.99 35.57 5.68
1032 1141 3.118531 AGAAGCAGGGGACATACTGATT 58.881 45.455 0.00 0.00 44.98 2.57
1036 1145 2.023501 AGAGAGAAGCAGGGGACATACT 60.024 50.000 0.00 0.00 0.00 2.12
1040 1149 0.411452 AGAGAGAGAAGCAGGGGACA 59.589 55.000 0.00 0.00 0.00 4.02
1045 1154 2.348660 CAAGCAAGAGAGAGAAGCAGG 58.651 52.381 0.00 0.00 0.00 4.85
1056 1165 0.165511 GAAGACGCAGCAAGCAAGAG 59.834 55.000 0.00 0.00 46.13 2.85
1316 1437 2.036346 AGACAAACCATGGCAAAGAAGC 59.964 45.455 13.04 0.00 40.75 3.86
1317 1438 3.068590 ACAGACAAACCATGGCAAAGAAG 59.931 43.478 13.04 0.00 40.75 2.85
1318 1439 3.030291 ACAGACAAACCATGGCAAAGAA 58.970 40.909 13.04 0.00 40.75 2.52
1320 1441 2.624838 AGACAGACAAACCATGGCAAAG 59.375 45.455 13.04 1.75 40.75 2.77
1330 1451 4.383052 CGTAGTGATCACAGACAGACAAAC 59.617 45.833 27.02 8.25 0.00 2.93
1349 1474 1.284408 GCCAGGCTCGAGATCGTAG 59.716 63.158 18.75 0.00 40.80 3.51
1367 1492 1.631071 GCTCTTTCCTCCCCTCCAGG 61.631 65.000 0.00 0.00 0.00 4.45
1370 1495 2.736826 CCGCTCTTTCCTCCCCTCC 61.737 68.421 0.00 0.00 0.00 4.30
1439 1569 2.959707 AGACTAGGGAGGCATCTTAACG 59.040 50.000 0.00 0.00 30.20 3.18
1467 1597 4.501571 GCAGAGATAGCAAAATACGGAGGA 60.502 45.833 0.00 0.00 0.00 3.71
1469 1599 3.743396 GGCAGAGATAGCAAAATACGGAG 59.257 47.826 0.00 0.00 0.00 4.63
1473 1603 4.274459 CAGTGGGCAGAGATAGCAAAATAC 59.726 45.833 0.00 0.00 0.00 1.89
1490 1620 6.170506 TGCTTTAAACTAGTCATACAGTGGG 58.829 40.000 0.00 0.00 0.00 4.61
1519 1656 5.713025 TCTTCCTTGTTGAATATGCAAAGC 58.287 37.500 0.00 0.00 0.00 3.51
1551 1749 9.730705 TCTGTCTCATCTCATTACAATTTCTTT 57.269 29.630 0.00 0.00 0.00 2.52
1552 1750 9.381033 CTCTGTCTCATCTCATTACAATTTCTT 57.619 33.333 0.00 0.00 0.00 2.52
1553 1751 7.495279 GCTCTGTCTCATCTCATTACAATTTCT 59.505 37.037 0.00 0.00 0.00 2.52
1554 1752 7.495279 AGCTCTGTCTCATCTCATTACAATTTC 59.505 37.037 0.00 0.00 0.00 2.17
1555 1753 7.337167 AGCTCTGTCTCATCTCATTACAATTT 58.663 34.615 0.00 0.00 0.00 1.82
1556 1754 6.887013 AGCTCTGTCTCATCTCATTACAATT 58.113 36.000 0.00 0.00 0.00 2.32
1557 1755 6.482898 AGCTCTGTCTCATCTCATTACAAT 57.517 37.500 0.00 0.00 0.00 2.71
1558 1756 5.929058 AGCTCTGTCTCATCTCATTACAA 57.071 39.130 0.00 0.00 0.00 2.41
1559 1757 5.929058 AAGCTCTGTCTCATCTCATTACA 57.071 39.130 0.00 0.00 0.00 2.41
1560 1758 6.456718 GCAAAAGCTCTGTCTCATCTCATTAC 60.457 42.308 0.00 0.00 0.00 1.89
1561 1759 5.583854 GCAAAAGCTCTGTCTCATCTCATTA 59.416 40.000 0.00 0.00 0.00 1.90
1562 1760 4.395542 GCAAAAGCTCTGTCTCATCTCATT 59.604 41.667 0.00 0.00 0.00 2.57
1563 1761 3.940221 GCAAAAGCTCTGTCTCATCTCAT 59.060 43.478 0.00 0.00 0.00 2.90
1564 1762 3.332919 GCAAAAGCTCTGTCTCATCTCA 58.667 45.455 0.00 0.00 0.00 3.27
1565 1763 2.677337 GGCAAAAGCTCTGTCTCATCTC 59.323 50.000 0.00 0.00 0.00 2.75
1566 1764 2.305343 AGGCAAAAGCTCTGTCTCATCT 59.695 45.455 0.00 0.00 0.00 2.90
1567 1765 2.677337 GAGGCAAAAGCTCTGTCTCATC 59.323 50.000 20.12 0.47 43.59 2.92
1568 1766 2.617532 GGAGGCAAAAGCTCTGTCTCAT 60.618 50.000 24.12 0.00 45.49 2.90
1569 1767 1.271054 GGAGGCAAAAGCTCTGTCTCA 60.271 52.381 24.12 0.00 45.49 3.27
1570 1768 1.447945 GGAGGCAAAAGCTCTGTCTC 58.552 55.000 17.88 17.88 43.43 3.36
1571 1769 0.321122 CGGAGGCAAAAGCTCTGTCT 60.321 55.000 2.67 2.67 0.00 3.41
1572 1770 0.603975 ACGGAGGCAAAAGCTCTGTC 60.604 55.000 0.00 0.00 31.79 3.51
1573 1771 0.179018 AACGGAGGCAAAAGCTCTGT 60.179 50.000 0.00 0.00 38.23 3.41
1574 1772 0.954452 AAACGGAGGCAAAAGCTCTG 59.046 50.000 0.00 0.00 0.00 3.35
1575 1773 1.239347 GAAACGGAGGCAAAAGCTCT 58.761 50.000 0.00 0.00 0.00 4.09
1576 1774 0.951558 TGAAACGGAGGCAAAAGCTC 59.048 50.000 0.00 0.00 0.00 4.09
1577 1775 1.398692 TTGAAACGGAGGCAAAAGCT 58.601 45.000 0.00 0.00 0.00 3.74
1578 1776 2.217429 TTTGAAACGGAGGCAAAAGC 57.783 45.000 0.00 0.00 0.00 3.51
1579 1777 6.836577 TTTATTTTGAAACGGAGGCAAAAG 57.163 33.333 0.00 0.00 42.56 2.27
1580 1778 8.888579 TTATTTATTTTGAAACGGAGGCAAAA 57.111 26.923 0.00 0.00 43.18 2.44
1581 1779 8.888579 TTTATTTATTTTGAAACGGAGGCAAA 57.111 26.923 0.00 0.00 0.00 3.68
1657 1858 0.676184 AGCGTGATGTGCGGATCTAT 59.324 50.000 0.00 0.00 37.44 1.98
1661 1863 1.145759 CGTAAGCGTGATGTGCGGAT 61.146 55.000 0.00 0.00 37.44 4.18
1662 1864 1.803922 CGTAAGCGTGATGTGCGGA 60.804 57.895 0.00 0.00 37.44 5.54
1667 1869 2.125269 GCCCCGTAAGCGTGATGT 60.125 61.111 0.00 0.00 36.15 3.06
1722 1926 6.638610 ACTCGATCAGTCTGAAAATCTCATT 58.361 36.000 6.64 0.00 32.14 2.57
1726 1930 4.629200 GCAACTCGATCAGTCTGAAAATCT 59.371 41.667 6.64 0.00 32.30 2.40
1749 1953 1.460743 TCGCTGACAATTGCTTCGAAG 59.539 47.619 21.02 21.02 0.00 3.79
1750 1954 1.507562 TCGCTGACAATTGCTTCGAA 58.492 45.000 5.05 0.00 0.00 3.71
1751 1955 1.507562 TTCGCTGACAATTGCTTCGA 58.492 45.000 5.05 6.95 0.00 3.71
1752 1956 2.159667 TGATTCGCTGACAATTGCTTCG 60.160 45.455 5.05 4.61 0.00 3.79
1753 1957 3.476295 TGATTCGCTGACAATTGCTTC 57.524 42.857 5.05 0.00 0.00 3.86
1754 1958 3.921119 TTGATTCGCTGACAATTGCTT 57.079 38.095 5.05 0.00 0.00 3.91
1755 1959 3.921119 TTTGATTCGCTGACAATTGCT 57.079 38.095 5.05 0.00 0.00 3.91
1756 1960 3.922240 ACATTTGATTCGCTGACAATTGC 59.078 39.130 5.05 0.00 32.08 3.56
1757 1961 4.560035 GGACATTTGATTCGCTGACAATTG 59.440 41.667 3.24 3.24 33.81 2.32
1758 1962 4.218200 TGGACATTTGATTCGCTGACAATT 59.782 37.500 0.00 0.00 0.00 2.32
1759 1963 3.758023 TGGACATTTGATTCGCTGACAAT 59.242 39.130 0.00 0.00 0.00 2.71
1760 1964 3.145286 TGGACATTTGATTCGCTGACAA 58.855 40.909 0.00 0.00 0.00 3.18
1761 1965 2.777094 TGGACATTTGATTCGCTGACA 58.223 42.857 0.00 0.00 0.00 3.58
1762 1966 3.242870 GGATGGACATTTGATTCGCTGAC 60.243 47.826 0.00 0.00 0.00 3.51
1763 1967 2.945008 GGATGGACATTTGATTCGCTGA 59.055 45.455 0.00 0.00 0.00 4.26
1764 1968 2.286595 CGGATGGACATTTGATTCGCTG 60.287 50.000 0.00 0.00 0.00 5.18
1765 1969 1.942657 CGGATGGACATTTGATTCGCT 59.057 47.619 0.00 0.00 0.00 4.93
1766 1970 1.597937 GCGGATGGACATTTGATTCGC 60.598 52.381 0.00 0.00 0.00 4.70
1767 1971 1.670295 TGCGGATGGACATTTGATTCG 59.330 47.619 0.00 0.00 0.00 3.34
1768 1972 3.996150 ATGCGGATGGACATTTGATTC 57.004 42.857 0.00 0.00 0.00 2.52
1769 1973 4.403432 AGAAATGCGGATGGACATTTGATT 59.597 37.500 5.75 0.00 44.36 2.57
1770 1974 3.956199 AGAAATGCGGATGGACATTTGAT 59.044 39.130 5.75 0.00 44.36 2.57
1771 1975 3.129113 CAGAAATGCGGATGGACATTTGA 59.871 43.478 5.75 0.00 44.36 2.69
1772 1976 3.129113 TCAGAAATGCGGATGGACATTTG 59.871 43.478 5.75 0.00 44.36 2.32
1773 1977 3.355378 TCAGAAATGCGGATGGACATTT 58.645 40.909 0.00 0.88 46.37 2.32
1774 1978 3.003394 TCAGAAATGCGGATGGACATT 57.997 42.857 0.00 0.00 38.11 2.71
1775 1979 2.684881 GTTCAGAAATGCGGATGGACAT 59.315 45.455 0.00 0.00 0.00 3.06
1778 1982 2.488204 TGTTCAGAAATGCGGATGGA 57.512 45.000 0.00 0.00 0.00 3.41
1802 2006 2.476821 TCCTGAAAAACGGTCGAGTTC 58.523 47.619 0.00 0.00 32.43 3.01
1811 2015 4.076394 TCCCCTGTAATTCCTGAAAAACG 58.924 43.478 0.00 0.00 0.00 3.60
1812 2016 4.082949 CGTCCCCTGTAATTCCTGAAAAAC 60.083 45.833 0.00 0.00 0.00 2.43
1867 2093 1.228094 GCCTCTCCTTATGCAGGCC 60.228 63.158 0.00 0.00 45.04 5.19
1973 2209 7.388437 TCTCTTTTGCTAAAATTGCATGGAAT 58.612 30.769 6.63 6.63 40.34 3.01
2207 2446 2.670905 CGTCGCACCAAAGATTCACATA 59.329 45.455 0.00 0.00 0.00 2.29
2352 2591 7.832503 ATAAACTTACAAATTGATTGCAGGC 57.167 32.000 0.00 0.00 43.13 4.85
2398 2637 3.304861 GCAAGCAGTGTTGACATTCATCA 60.305 43.478 8.92 0.00 0.00 3.07
2401 2640 2.022934 TGCAAGCAGTGTTGACATTCA 58.977 42.857 8.92 0.00 0.00 2.57
2483 2722 3.328931 CCTTGCCATACTCCTGACCATAT 59.671 47.826 0.00 0.00 0.00 1.78
2489 2728 1.951209 TGTCCTTGCCATACTCCTGA 58.049 50.000 0.00 0.00 0.00 3.86
2498 2737 3.485346 GACCGGGTTGTCCTTGCCA 62.485 63.158 6.32 0.00 0.00 4.92
2525 2764 0.896923 AGTGCCCATAACCGTCGTAA 59.103 50.000 0.00 0.00 0.00 3.18
2595 2834 1.144969 TTGCGCAGTGTTGTACTAGC 58.855 50.000 11.31 0.00 37.60 3.42
2711 2951 3.221956 GCTTACATAGCGCGACCG 58.778 61.111 12.10 0.00 40.71 4.79
2745 2985 6.213677 CAAGTTGCAGTGTTGTAGTAGTAGA 58.786 40.000 0.00 0.00 0.00 2.59
2746 2986 5.405571 CCAAGTTGCAGTGTTGTAGTAGTAG 59.594 44.000 0.00 0.00 0.00 2.57
2747 2987 5.163385 ACCAAGTTGCAGTGTTGTAGTAGTA 60.163 40.000 0.00 0.00 0.00 1.82
2748 2988 4.127171 CCAAGTTGCAGTGTTGTAGTAGT 58.873 43.478 0.00 0.00 0.00 2.73
2749 2989 4.127171 ACCAAGTTGCAGTGTTGTAGTAG 58.873 43.478 0.00 0.00 0.00 2.57
2750 2990 4.145365 ACCAAGTTGCAGTGTTGTAGTA 57.855 40.909 0.00 0.00 0.00 1.82
2751 2991 2.999331 ACCAAGTTGCAGTGTTGTAGT 58.001 42.857 0.00 0.00 0.00 2.73
2753 2993 3.181505 CGAAACCAAGTTGCAGTGTTGTA 60.182 43.478 0.00 0.00 0.00 2.41
2754 2994 2.415357 CGAAACCAAGTTGCAGTGTTGT 60.415 45.455 0.00 0.00 0.00 3.32
2756 2996 1.816224 ACGAAACCAAGTTGCAGTGTT 59.184 42.857 0.00 0.00 0.00 3.32
2757 2997 1.459450 ACGAAACCAAGTTGCAGTGT 58.541 45.000 0.00 0.00 0.00 3.55
2758 2998 2.450160 GAACGAAACCAAGTTGCAGTG 58.550 47.619 0.00 0.00 0.00 3.66
2759 2999 1.063469 CGAACGAAACCAAGTTGCAGT 59.937 47.619 0.00 0.00 0.00 4.40
2932 3190 6.127479 ACACAAAACACTCCATTTTAAGCTGA 60.127 34.615 0.00 0.00 0.00 4.26
3000 3259 3.667695 CGAAGCAATTGTCAGCGAATCAA 60.668 43.478 7.40 0.00 35.48 2.57
3064 3347 5.371115 AAATCGGTGACCAACATAACAAG 57.629 39.130 1.11 0.00 0.00 3.16
3112 3395 8.874816 TCAAATGATGATTATGCACACATTTTG 58.125 29.630 0.00 2.48 36.71 2.44
3199 3482 5.715434 AACGCCCTTATGTTTGTTTACAT 57.285 34.783 0.00 0.00 41.43 2.29
3216 3499 9.813080 GATCACTAAAATATTGATCTAAACGCC 57.187 33.333 6.97 0.00 40.02 5.68
3266 3549 8.875168 CCTTTATTAATCATCACTACTCCCTCT 58.125 37.037 0.00 0.00 0.00 3.69
3286 3581 1.767088 GGTTCCGGGCTAGTCCTTTAT 59.233 52.381 12.53 0.00 34.39 1.40
3328 3630 1.202952 ACCTTTGAACGTGCCCCATAA 60.203 47.619 0.00 0.00 0.00 1.90
3372 3674 8.756486 TTTAACTTAGGTACTTCCAAAGCTTT 57.244 30.769 5.69 5.69 41.75 3.51
3374 3676 8.215736 TCTTTTAACTTAGGTACTTCCAAAGCT 58.784 33.333 0.00 0.00 41.75 3.74
3379 3681 7.178983 TCCGATCTTTTAACTTAGGTACTTCCA 59.821 37.037 0.00 0.00 41.75 3.53
3380 3682 7.550712 TCCGATCTTTTAACTTAGGTACTTCC 58.449 38.462 0.00 0.00 41.75 3.46
3381 3683 7.705752 CCTCCGATCTTTTAACTTAGGTACTTC 59.294 40.741 0.00 0.00 41.75 3.01
3382 3684 7.179872 ACCTCCGATCTTTTAACTTAGGTACTT 59.820 37.037 0.00 0.00 41.75 2.24
3383 3685 6.666980 ACCTCCGATCTTTTAACTTAGGTACT 59.333 38.462 0.00 0.00 46.37 2.73
3384 3686 6.871844 ACCTCCGATCTTTTAACTTAGGTAC 58.128 40.000 0.00 0.00 33.17 3.34
3385 3687 7.068716 GGTACCTCCGATCTTTTAACTTAGGTA 59.931 40.741 4.06 0.00 36.31 3.08
3386 3688 6.127225 GGTACCTCCGATCTTTTAACTTAGGT 60.127 42.308 4.06 0.00 38.35 3.08
3387 3689 6.127253 TGGTACCTCCGATCTTTTAACTTAGG 60.127 42.308 14.36 0.00 39.52 2.69
3388 3690 6.870769 TGGTACCTCCGATCTTTTAACTTAG 58.129 40.000 14.36 0.00 39.52 2.18
3389 3691 6.664816 TCTGGTACCTCCGATCTTTTAACTTA 59.335 38.462 14.36 0.00 39.52 2.24
3390 3692 5.482878 TCTGGTACCTCCGATCTTTTAACTT 59.517 40.000 14.36 0.00 39.52 2.66
3391 3693 5.021458 TCTGGTACCTCCGATCTTTTAACT 58.979 41.667 14.36 0.00 39.52 2.24
3392 3694 5.107824 GTCTGGTACCTCCGATCTTTTAAC 58.892 45.833 14.36 0.00 39.52 2.01
3393 3695 4.773674 TGTCTGGTACCTCCGATCTTTTAA 59.226 41.667 14.36 0.00 39.52 1.52
3394 3696 4.346730 TGTCTGGTACCTCCGATCTTTTA 58.653 43.478 14.36 0.00 39.52 1.52
3395 3697 3.170717 TGTCTGGTACCTCCGATCTTTT 58.829 45.455 14.36 0.00 39.52 2.27
3396 3698 2.816411 TGTCTGGTACCTCCGATCTTT 58.184 47.619 14.36 0.00 39.52 2.52
3397 3699 2.526888 TGTCTGGTACCTCCGATCTT 57.473 50.000 14.36 0.00 39.52 2.40
3398 3700 2.526888 TTGTCTGGTACCTCCGATCT 57.473 50.000 14.36 0.00 39.52 2.75
3399 3701 3.604875 TTTTGTCTGGTACCTCCGATC 57.395 47.619 14.36 3.52 39.52 3.69
3400 3702 3.868754 GCTTTTTGTCTGGTACCTCCGAT 60.869 47.826 14.36 0.00 39.52 4.18
3401 3703 2.549349 GCTTTTTGTCTGGTACCTCCGA 60.549 50.000 14.36 4.26 39.52 4.55
3402 3704 1.804748 GCTTTTTGTCTGGTACCTCCG 59.195 52.381 14.36 1.70 39.52 4.63
3422 3747 3.320673 ACCTTCGTAGAAAAGAGCCAG 57.679 47.619 0.00 0.00 45.90 4.85
3441 3766 4.113354 CGGTACTTCCAAGCATCTTCTAC 58.887 47.826 0.00 0.00 35.57 2.59
3503 3828 1.664873 CGAGCTGGGATCTAGCCTG 59.335 63.158 15.69 7.64 42.07 4.85
3529 3854 1.281867 ACTCCCGAGCAAATCCATTCA 59.718 47.619 0.00 0.00 0.00 2.57
3552 3877 1.348064 TGAGTCCCATTATAGGCCCG 58.652 55.000 0.00 0.00 0.00 6.13
3555 3880 3.756117 CCCTTTGAGTCCCATTATAGGC 58.244 50.000 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.