Multiple sequence alignment - TraesCS7D01G510800

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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 TraesCS7D01G510800 chr7D 100.000 7122 0 0 1 7122 613607301 613614422 0.000000e+00 13152.0
1 TraesCS7D01G510800 chr7D 85.212 825 74 22 1 786 613598749 613599564 0.000000e+00 804.0
2 TraesCS7D01G510800 chr7D 96.875 32 1 0 3086 3117 613610295 613610326 4.000000e-03 54.7
3 TraesCS7D01G510800 chr7D 96.875 32 1 0 2995 3026 613610386 613610417 4.000000e-03 54.7
4 TraesCS7D01G510800 chr7A 94.978 3903 131 24 3110 7010 705270237 705274076 0.000000e+00 6061.0
5 TraesCS7D01G510800 chr7A 88.836 3171 193 61 1 3072 705267133 705270241 0.000000e+00 3746.0
6 TraesCS7D01G510800 chr7A 84.531 821 83 24 1 786 705251627 705252438 0.000000e+00 773.0
7 TraesCS7D01G510800 chr7A 96.875 32 1 0 3086 3117 705270164 705270195 4.000000e-03 54.7
8 TraesCS7D01G510800 chr7B 94.733 3873 126 31 3110 6964 704269372 704273184 0.000000e+00 5951.0
9 TraesCS7D01G510800 chr7B 90.916 1398 63 21 1734 3072 704267984 704269376 0.000000e+00 1820.0
10 TraesCS7D01G510800 chr7B 82.875 1092 81 49 554 1593 704266714 704267751 0.000000e+00 883.0
11 TraesCS7D01G510800 chr2D 76.695 472 70 22 1946 2406 632272096 632272538 7.190000e-55 226.0
12 TraesCS7D01G510800 chr4D 76.432 454 68 21 1955 2398 207780518 207780094 7.240000e-50 209.0


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 TraesCS7D01G510800 chr7D 613607301 613614422 7121 False 13152.000000 13152 100.000 1 7122 1 chr7D.!!$F2 7121
1 TraesCS7D01G510800 chr7D 613598749 613599564 815 False 804.000000 804 85.212 1 786 1 chr7D.!!$F1 785
2 TraesCS7D01G510800 chr7A 705267133 705274076 6943 False 3287.233333 6061 93.563 1 7010 3 chr7A.!!$F2 7009
3 TraesCS7D01G510800 chr7A 705251627 705252438 811 False 773.000000 773 84.531 1 786 1 chr7A.!!$F1 785
4 TraesCS7D01G510800 chr7B 704266714 704273184 6470 False 2884.666667 5951 89.508 554 6964 3 chr7B.!!$F1 6410

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
537 575 0.470341 GGTAGGGAGCATGAAGGACC 59.530 60.000 0.00 0.0 0.00 4.46 F
1623 1777 0.253327 GGGCTGTAGCTTGGCTTACT 59.747 55.000 3.63 0.0 40.44 2.24 F
1925 2242 0.032403 TAACGCACCAAGCAGTACGT 59.968 50.000 0.00 0.0 46.13 3.57 F
3701 4073 0.248843 CTGGTTCAGGTGCTCTCTCC 59.751 60.000 0.00 0.0 0.00 3.71 F
3808 4180 1.002868 GTCAGCCTGACCAGCATGT 60.003 57.895 14.04 0.0 41.37 3.21 F
4657 5029 2.260844 TTCTCTGTTCCTGTGCCTTG 57.739 50.000 0.00 0.0 0.00 3.61 F
4660 5032 2.594303 TGTTCCTGTGCCTTGGCG 60.594 61.111 7.18 0.0 0.00 5.69 F
5179 5574 5.182950 TGTGATCAGTGTTTCTCTCTCTCTC 59.817 44.000 0.00 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2210 0.175760 TGCGTTACTGCAGAGGATCC 59.824 55.000 23.35 2.48 40.62 3.36 R
3197 3568 2.826128 GGGGATGTCTTTTCTGGGAAAC 59.174 50.000 0.00 0.00 0.00 2.78 R
3800 4172 0.038166 ACCCACTACCAACATGCTGG 59.962 55.000 13.73 13.73 42.68 4.85 R
5672 6067 1.605753 AAACTTGGAACGAGGGAAGC 58.394 50.000 0.00 0.00 0.00 3.86 R
5727 6124 0.806868 ATTGCGCATGTTCCAGACTG 59.193 50.000 12.75 0.00 0.00 3.51 R
5728 6125 1.089920 GATTGCGCATGTTCCAGACT 58.910 50.000 12.75 0.00 0.00 3.24 R
5884 6285 1.334059 CCATCGGAATTTTCGCCATCG 60.334 52.381 0.00 0.00 0.00 3.84 R
7044 7461 0.458669 GCCCCGACTATCACGAGAAA 59.541 55.000 0.00 0.00 0.00 2.52 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
202 224 2.093106 CTAGTGAACCGTCAGCTACCT 58.907 52.381 0.00 0.00 33.27 3.08
231 253 5.406780 GTCCAGAAGACAGTGATTACAACTG 59.593 44.000 0.00 2.13 45.55 3.16
241 263 6.716628 ACAGTGATTACAACTGAATCCAACAT 59.283 34.615 10.35 0.00 33.18 2.71
379 401 5.010012 GCTTGGCCTTACATAAGTGCAATAT 59.990 40.000 3.32 0.00 33.80 1.28
380 402 6.206634 GCTTGGCCTTACATAAGTGCAATATA 59.793 38.462 3.32 0.00 33.80 0.86
423 445 3.216800 AGTTGGAGTTAAACCCCGTTTC 58.783 45.455 0.00 0.00 37.01 2.78
463 490 0.822164 CCGTGGATACCGGTTTCTCT 59.178 55.000 22.09 0.00 43.00 3.10
466 493 2.734492 CGTGGATACCGGTTTCTCTGTC 60.734 54.545 22.09 7.91 0.00 3.51
468 495 2.108970 GGATACCGGTTTCTCTGTCCT 58.891 52.381 22.09 0.00 0.00 3.85
471 498 0.471211 ACCGGTTTCTCTGTCCTGGA 60.471 55.000 0.00 0.00 0.00 3.86
490 517 0.618458 AAAGGGCGCATAACTCCAGA 59.382 50.000 10.83 0.00 0.00 3.86
537 575 0.470341 GGTAGGGAGCATGAAGGACC 59.530 60.000 0.00 0.00 0.00 4.46
590 638 5.925506 TCTAGGGTTGTGTATGATTTCGA 57.074 39.130 0.00 0.00 0.00 3.71
600 648 5.937540 TGTGTATGATTTCGACTCCATTGTT 59.062 36.000 0.00 0.00 0.00 2.83
899 988 3.003173 CCTCCGTCCCAGCTCCAA 61.003 66.667 0.00 0.00 0.00 3.53
908 997 0.693767 CCCAGCTCCAATCTCCCTCT 60.694 60.000 0.00 0.00 0.00 3.69
1238 1364 4.818314 GGGTCCAGTGATCCCTCT 57.182 61.111 13.15 0.00 35.54 3.69
1239 1365 3.013682 GGGTCCAGTGATCCCTCTT 57.986 57.895 13.15 0.00 35.54 2.85
1255 1381 0.523546 TCTTCGCGAGCGTCAGATTC 60.524 55.000 17.24 0.00 40.74 2.52
1256 1382 1.792506 CTTCGCGAGCGTCAGATTCG 61.793 60.000 17.24 0.00 40.74 3.34
1257 1383 3.315521 CGCGAGCGTCAGATTCGG 61.316 66.667 0.00 0.00 35.05 4.30
1258 1384 3.621394 GCGAGCGTCAGATTCGGC 61.621 66.667 0.00 0.00 35.05 5.54
1259 1385 3.315521 CGAGCGTCAGATTCGGCG 61.316 66.667 0.00 0.00 0.00 6.46
1262 1388 3.918220 GCGTCAGATTCGGCGCTG 61.918 66.667 10.86 10.86 45.48 5.18
1263 1389 2.202610 CGTCAGATTCGGCGCTGA 60.203 61.111 16.69 16.69 38.72 4.26
1265 1391 2.202610 TCAGATTCGGCGCTGACG 60.203 61.111 20.84 8.55 44.07 4.35
1274 1400 2.689766 GCGCTGACGTGTTCGATC 59.310 61.111 0.00 0.00 42.83 3.69
1279 1405 2.884207 GACGTGTTCGATCCCGCC 60.884 66.667 0.00 0.00 40.62 6.13
1292 1418 4.183686 CCGCCGCTGGATTGCTTG 62.184 66.667 0.00 0.00 0.00 4.01
1293 1419 4.842091 CGCCGCTGGATTGCTTGC 62.842 66.667 0.00 0.00 0.00 4.01
1294 1420 4.842091 GCCGCTGGATTGCTTGCG 62.842 66.667 8.53 8.53 46.74 4.85
1297 1423 2.101770 GCTGGATTGCTTGCGCTC 59.898 61.111 9.73 0.00 36.97 5.03
1300 1426 2.033328 CTGGATTGCTTGCGCTCTCG 62.033 60.000 9.73 0.00 36.97 4.04
1502 1656 3.193691 ACTGATTCAGTGACTAGGGTTCG 59.806 47.826 18.35 0.00 43.63 3.95
1514 1668 3.447944 ACTAGGGTTCGGACTTCTGAATC 59.552 47.826 3.83 3.30 42.55 2.52
1522 1676 4.307432 TCGGACTTCTGAATCTCAACAAC 58.693 43.478 0.00 0.00 0.00 3.32
1532 1686 7.004086 TCTGAATCTCAACAACTTGGGTTTAT 58.996 34.615 0.00 0.00 32.73 1.40
1533 1687 6.980593 TGAATCTCAACAACTTGGGTTTATG 58.019 36.000 0.00 0.00 32.73 1.90
1534 1688 6.775142 TGAATCTCAACAACTTGGGTTTATGA 59.225 34.615 0.00 0.00 32.73 2.15
1535 1689 7.286546 TGAATCTCAACAACTTGGGTTTATGAA 59.713 33.333 0.00 0.00 32.73 2.57
1536 1690 7.781324 ATCTCAACAACTTGGGTTTATGAAT 57.219 32.000 0.00 0.00 32.73 2.57
1537 1691 7.595819 TCTCAACAACTTGGGTTTATGAATT 57.404 32.000 0.00 0.00 32.73 2.17
1538 1692 8.017418 TCTCAACAACTTGGGTTTATGAATTT 57.983 30.769 0.00 0.00 32.73 1.82
1539 1693 8.482128 TCTCAACAACTTGGGTTTATGAATTTT 58.518 29.630 0.00 0.00 32.73 1.82
1540 1694 9.757227 CTCAACAACTTGGGTTTATGAATTTTA 57.243 29.630 0.00 0.00 32.73 1.52
1541 1695 9.535878 TCAACAACTTGGGTTTATGAATTTTAC 57.464 29.630 0.00 0.00 32.73 2.01
1542 1696 8.769891 CAACAACTTGGGTTTATGAATTTTACC 58.230 33.333 0.00 0.00 32.73 2.85
1543 1697 8.024145 ACAACTTGGGTTTATGAATTTTACCA 57.976 30.769 0.00 0.00 32.73 3.25
1544 1698 7.929245 ACAACTTGGGTTTATGAATTTTACCAC 59.071 33.333 0.00 0.00 32.73 4.16
1545 1699 6.999950 ACTTGGGTTTATGAATTTTACCACC 58.000 36.000 0.00 0.00 0.00 4.61
1546 1700 6.014070 ACTTGGGTTTATGAATTTTACCACCC 60.014 38.462 8.48 8.48 42.73 4.61
1548 1702 5.482175 TGGGTTTATGAATTTTACCACCCAG 59.518 40.000 12.48 0.00 46.27 4.45
1549 1703 5.482526 GGGTTTATGAATTTTACCACCCAGT 59.517 40.000 9.96 0.00 42.09 4.00
1550 1704 6.014070 GGGTTTATGAATTTTACCACCCAGTT 60.014 38.462 9.96 0.00 42.09 3.16
1551 1705 6.871492 GGTTTATGAATTTTACCACCCAGTTG 59.129 38.462 0.00 0.00 0.00 3.16
1552 1706 6.597832 TTATGAATTTTACCACCCAGTTGG 57.402 37.500 0.00 0.00 43.04 3.77
1602 1756 6.040842 GGGCTTATGAATTTTATCAGCCTGAA 59.959 38.462 19.83 0.00 42.11 3.02
1616 1770 1.386533 CCTGAATGGGCTGTAGCTTG 58.613 55.000 3.63 0.00 41.70 4.01
1619 1773 0.394899 GAATGGGCTGTAGCTTGGCT 60.395 55.000 3.63 0.00 43.41 4.75
1621 1775 0.918983 ATGGGCTGTAGCTTGGCTTA 59.081 50.000 3.63 0.00 40.44 3.09
1623 1777 0.253327 GGGCTGTAGCTTGGCTTACT 59.747 55.000 3.63 0.00 40.44 2.24
1626 1780 2.420687 GGCTGTAGCTTGGCTTACTGAT 60.421 50.000 3.63 0.00 40.44 2.90
1632 1786 6.075315 TGTAGCTTGGCTTACTGATCCTATA 58.925 40.000 0.00 0.00 40.44 1.31
1721 1882 3.244345 TCTTTTATTATTCCGAGCGTGCG 59.756 43.478 0.00 0.00 0.00 5.34
1732 1893 2.222931 CCGAGCGTGCGATTAAATTGAA 60.223 45.455 0.00 0.00 0.00 2.69
1772 2072 2.361789 TGTGTGATGATCATGCCTGTG 58.638 47.619 14.30 0.00 0.00 3.66
1775 2076 0.256464 TGATGATCATGCCTGTGCCA 59.744 50.000 14.30 0.00 36.33 4.92
1784 2085 1.340088 TGCCTGTGCCATGTTTGAAT 58.660 45.000 0.00 0.00 36.33 2.57
1787 2088 2.673043 GCCTGTGCCATGTTTGAATGAG 60.673 50.000 0.00 0.00 0.00 2.90
1798 2099 6.404403 CCATGTTTGAATGAGAGACATCCTTG 60.404 42.308 0.00 0.00 38.38 3.61
1808 2109 2.429610 GAGACATCCTTGCCATGCATTT 59.570 45.455 0.00 0.00 38.76 2.32
1850 2151 2.030274 ACCAACTGAATAACGCCTTTGC 60.030 45.455 0.00 0.00 0.00 3.68
1868 2169 1.134848 TGCACTGAAAAACACCTTGGC 60.135 47.619 0.00 0.00 0.00 4.52
1875 2176 5.048991 ACTGAAAAACACCTTGGCTAATACG 60.049 40.000 0.00 0.00 0.00 3.06
1893 2210 1.485066 ACGCTCATTACTAGGGGTTGG 59.515 52.381 0.00 0.00 0.00 3.77
1916 2233 0.602638 CCTCTGCAGTAACGCACCAA 60.603 55.000 14.67 0.00 36.86 3.67
1925 2242 0.032403 TAACGCACCAAGCAGTACGT 59.968 50.000 0.00 0.00 46.13 3.57
1926 2243 1.219522 AACGCACCAAGCAGTACGTC 61.220 55.000 0.00 0.00 46.13 4.34
1927 2244 2.380410 CGCACCAAGCAGTACGTCC 61.380 63.158 0.00 0.00 46.13 4.79
1958 2279 5.341872 TTTTTACTGATCCCATGCATTGG 57.658 39.130 10.62 10.62 46.00 3.16
1996 2317 7.498900 CCCAAAAAGGAAAGAAATTAACTGCTT 59.501 33.333 0.00 0.00 41.22 3.91
2180 2501 4.209538 AGCTCATATTTATTGCCTGCACA 58.790 39.130 0.00 0.00 0.00 4.57
2192 2513 2.061220 CTGCACACAGGAGGGAAGA 58.939 57.895 0.00 0.00 40.48 2.87
2270 2591 3.228188 TCTTGGATTGCTCAAACACCT 57.772 42.857 0.00 0.00 0.00 4.00
2357 2679 7.898014 ACCCTCTTGTTTTTCTCACTTATTT 57.102 32.000 0.00 0.00 0.00 1.40
2358 2680 7.941919 ACCCTCTTGTTTTTCTCACTTATTTC 58.058 34.615 0.00 0.00 0.00 2.17
2359 2681 7.559897 ACCCTCTTGTTTTTCTCACTTATTTCA 59.440 33.333 0.00 0.00 0.00 2.69
2360 2682 8.413229 CCCTCTTGTTTTTCTCACTTATTTCAA 58.587 33.333 0.00 0.00 0.00 2.69
2457 2779 6.925610 TGTGCTATAACAAAATGAGCTAGG 57.074 37.500 0.00 0.00 34.19 3.02
2478 2800 5.070685 AGGTGGGAATACAAGTGAGAAAAC 58.929 41.667 0.00 0.00 0.00 2.43
2488 2810 4.806247 ACAAGTGAGAAAACTTCGACAGAG 59.194 41.667 0.00 0.00 38.34 3.35
2507 2830 8.420189 CGACAGAGCATAAAAAGACAAAAATTC 58.580 33.333 0.00 0.00 0.00 2.17
2633 2979 5.922544 TGTAGATGATATCTTGCATGTCACG 59.077 40.000 3.98 0.00 40.76 4.35
2924 3281 3.758023 TGGGAGTGCATTTTATGAGTGTG 59.242 43.478 0.00 0.00 0.00 3.82
3071 3440 7.786943 TCCTGATAGAAGAAAGGATGACTATGT 59.213 37.037 0.00 0.00 33.85 2.29
3072 3441 8.428063 CCTGATAGAAGAAAGGATGACTATGTT 58.572 37.037 0.00 0.00 30.92 2.71
3073 3442 9.829507 CTGATAGAAGAAAGGATGACTATGTTT 57.170 33.333 0.00 0.00 0.00 2.83
3074 3443 9.605275 TGATAGAAGAAAGGATGACTATGTTTG 57.395 33.333 0.00 0.00 0.00 2.93
3075 3444 9.823647 GATAGAAGAAAGGATGACTATGTTTGA 57.176 33.333 0.00 0.00 0.00 2.69
3076 3445 7.913674 AGAAGAAAGGATGACTATGTTTGAC 57.086 36.000 0.00 0.00 0.00 3.18
3077 3446 7.684529 AGAAGAAAGGATGACTATGTTTGACT 58.315 34.615 0.00 0.00 0.00 3.41
3078 3447 8.816894 AGAAGAAAGGATGACTATGTTTGACTA 58.183 33.333 0.00 0.00 0.00 2.59
3079 3448 9.606631 GAAGAAAGGATGACTATGTTTGACTAT 57.393 33.333 0.00 0.00 0.00 2.12
3080 3449 8.954950 AGAAAGGATGACTATGTTTGACTATG 57.045 34.615 0.00 0.00 0.00 2.23
3081 3450 8.543774 AGAAAGGATGACTATGTTTGACTATGT 58.456 33.333 0.00 0.00 0.00 2.29
3082 3451 9.167311 GAAAGGATGACTATGTTTGACTATGTT 57.833 33.333 0.00 0.00 0.00 2.71
3083 3452 8.723942 AAGGATGACTATGTTTGACTATGTTC 57.276 34.615 0.00 0.00 0.00 3.18
3084 3453 7.851228 AGGATGACTATGTTTGACTATGTTCA 58.149 34.615 0.00 0.00 0.00 3.18
3085 3454 7.766278 AGGATGACTATGTTTGACTATGTTCAC 59.234 37.037 0.00 0.00 0.00 3.18
3086 3455 7.549134 GGATGACTATGTTTGACTATGTTCACA 59.451 37.037 0.00 0.00 0.00 3.58
3087 3456 9.102757 GATGACTATGTTTGACTATGTTCACAT 57.897 33.333 0.00 0.00 40.22 3.21
3098 3467 9.725019 TTGACTATGTTCACATATTTCTTGAGT 57.275 29.630 0.06 0.00 38.09 3.41
3127 3496 6.091577 ACAATTGTATGTCATTTGCAATGCTG 59.908 34.615 9.97 0.00 39.53 4.41
3164 3535 8.716646 TTTGTTTATATCATCACTCATCGTGT 57.283 30.769 0.00 0.00 44.16 4.49
3286 3657 5.483811 GTTGCTTCTAGAAGAGGTTAGCTT 58.516 41.667 32.16 0.00 40.79 3.74
3323 3694 3.631686 TGCTACATTCTGTTGTGCTTTGT 59.368 39.130 0.00 0.00 0.00 2.83
3358 3729 9.372369 CTTGTGGTTCTAAAAATGTTTTGGTTA 57.628 29.630 0.00 0.00 0.00 2.85
3497 3869 5.202765 TGTGCATGGTCCATAATGAAGATT 58.797 37.500 3.38 0.00 0.00 2.40
3498 3870 5.657745 TGTGCATGGTCCATAATGAAGATTT 59.342 36.000 3.38 0.00 0.00 2.17
3499 3871 6.154877 TGTGCATGGTCCATAATGAAGATTTT 59.845 34.615 3.38 0.00 0.00 1.82
3500 3872 7.043565 GTGCATGGTCCATAATGAAGATTTTT 58.956 34.615 3.38 0.00 0.00 1.94
3501 3873 8.196771 GTGCATGGTCCATAATGAAGATTTTTA 58.803 33.333 3.38 0.00 0.00 1.52
3502 3874 8.926374 TGCATGGTCCATAATGAAGATTTTTAT 58.074 29.630 3.38 0.00 0.00 1.40
3503 3875 9.768662 GCATGGTCCATAATGAAGATTTTTATT 57.231 29.630 3.38 0.00 0.00 1.40
3544 3916 5.461078 GTGCATTGATCCATGTCTTAATTGC 59.539 40.000 8.45 0.00 0.00 3.56
3547 3919 3.277715 TGATCCATGTCTTAATTGCGCA 58.722 40.909 5.66 5.66 0.00 6.09
3550 3922 3.277715 TCCATGTCTTAATTGCGCATGA 58.722 40.909 12.75 0.00 39.21 3.07
3668 4040 1.470890 AGCAGTACAGACTCTTCTCGC 59.529 52.381 0.00 0.00 31.73 5.03
3701 4073 0.248843 CTGGTTCAGGTGCTCTCTCC 59.751 60.000 0.00 0.00 0.00 3.71
3709 4081 1.251527 GGTGCTCTCTCCGAGTCCAA 61.252 60.000 0.00 0.00 41.98 3.53
3719 4091 6.889198 TCTCTCCGAGTCCAATCAAATAAAT 58.111 36.000 0.00 0.00 0.00 1.40
3722 4094 5.750524 TCCGAGTCCAATCAAATAAATCCA 58.249 37.500 0.00 0.00 0.00 3.41
3737 4109 4.618920 AAATCCAGGACTTGTTCGTAGT 57.381 40.909 0.00 0.00 0.00 2.73
3787 4159 4.262635 CGGTGTGCTGGGAGAATCTATATT 60.263 45.833 0.00 0.00 33.73 1.28
3795 4167 6.629291 GCTGGGAGAATCTATATTAGGTCAGC 60.629 46.154 0.00 0.00 33.39 4.26
3800 4172 7.363443 GGAGAATCTATATTAGGTCAGCCTGAC 60.363 44.444 16.63 16.63 39.81 3.51
3808 4180 1.002868 GTCAGCCTGACCAGCATGT 60.003 57.895 14.04 0.00 41.37 3.21
3829 4201 3.019799 TGGTAGTGGGTCAAAAAGCAA 57.980 42.857 0.00 0.00 0.00 3.91
3877 4249 2.726821 TGATGGAAGGAATGGTTCAGC 58.273 47.619 0.00 0.00 0.00 4.26
3897 4269 2.567615 GCAGAGTCTTCCAAGGGAGTAA 59.432 50.000 0.00 0.00 31.21 2.24
3923 4295 9.917887 ATTTCTGAAGAGGATTGTGATTCTAAT 57.082 29.630 0.00 0.00 0.00 1.73
3935 4307 2.489619 TGATTCTAATCCTGGCCATGCC 60.490 50.000 5.51 0.00 40.91 4.40
3962 4334 6.943146 GGAAGGATTCTTCTGAAAGTTTAGGT 59.057 38.462 13.57 0.00 46.56 3.08
3986 4358 6.809630 AGTGATTTGAGTTCTTTAAGAGGC 57.190 37.500 0.00 0.00 0.00 4.70
3995 4367 7.450074 TGAGTTCTTTAAGAGGCAGTGAATTA 58.550 34.615 0.00 0.00 0.00 1.40
4001 4373 7.336931 TCTTTAAGAGGCAGTGAATTATCAACC 59.663 37.037 0.00 0.00 37.30 3.77
4199 4571 2.685388 GCAAAGAAGAATAGGGACAGCC 59.315 50.000 0.00 0.00 0.00 4.85
4657 5029 2.260844 TTCTCTGTTCCTGTGCCTTG 57.739 50.000 0.00 0.00 0.00 3.61
4660 5032 2.594303 TGTTCCTGTGCCTTGGCG 60.594 61.111 7.18 0.00 0.00 5.69
5116 5511 7.781324 ACCAACTCATCAATGTTTCCTTAAT 57.219 32.000 0.00 0.00 0.00 1.40
5117 5512 8.193953 ACCAACTCATCAATGTTTCCTTAATT 57.806 30.769 0.00 0.00 0.00 1.40
5118 5513 8.306761 ACCAACTCATCAATGTTTCCTTAATTC 58.693 33.333 0.00 0.00 0.00 2.17
5119 5514 8.306038 CCAACTCATCAATGTTTCCTTAATTCA 58.694 33.333 0.00 0.00 0.00 2.57
5120 5515 9.695526 CAACTCATCAATGTTTCCTTAATTCAA 57.304 29.630 0.00 0.00 0.00 2.69
5121 5516 9.918630 AACTCATCAATGTTTCCTTAATTCAAG 57.081 29.630 0.00 0.00 0.00 3.02
5122 5517 8.031277 ACTCATCAATGTTTCCTTAATTCAAGC 58.969 33.333 0.00 0.00 32.41 4.01
5123 5518 8.125978 TCATCAATGTTTCCTTAATTCAAGCT 57.874 30.769 0.00 0.00 32.41 3.74
5124 5519 8.587608 TCATCAATGTTTCCTTAATTCAAGCTT 58.412 29.630 0.00 0.00 32.41 3.74
5125 5520 8.866956 CATCAATGTTTCCTTAATTCAAGCTTC 58.133 33.333 0.00 0.00 32.41 3.86
5126 5521 8.181904 TCAATGTTTCCTTAATTCAAGCTTCT 57.818 30.769 0.00 0.00 32.41 2.85
5127 5522 8.084073 TCAATGTTTCCTTAATTCAAGCTTCTG 58.916 33.333 0.00 0.00 32.41 3.02
5128 5523 6.959639 TGTTTCCTTAATTCAAGCTTCTGT 57.040 33.333 0.00 0.00 32.41 3.41
5129 5524 7.346751 TGTTTCCTTAATTCAAGCTTCTGTT 57.653 32.000 0.00 0.00 32.41 3.16
5130 5525 7.425606 TGTTTCCTTAATTCAAGCTTCTGTTC 58.574 34.615 0.00 0.00 32.41 3.18
5131 5526 7.068103 TGTTTCCTTAATTCAAGCTTCTGTTCA 59.932 33.333 0.00 0.00 32.41 3.18
5132 5527 6.560253 TCCTTAATTCAAGCTTCTGTTCAC 57.440 37.500 0.00 0.00 32.41 3.18
5133 5528 6.299141 TCCTTAATTCAAGCTTCTGTTCACT 58.701 36.000 0.00 0.00 32.41 3.41
5134 5529 6.772716 TCCTTAATTCAAGCTTCTGTTCACTT 59.227 34.615 0.00 0.00 32.41 3.16
5135 5530 7.936847 TCCTTAATTCAAGCTTCTGTTCACTTA 59.063 33.333 0.00 0.00 32.41 2.24
5136 5531 8.734386 CCTTAATTCAAGCTTCTGTTCACTTAT 58.266 33.333 0.00 0.00 32.41 1.73
5179 5574 5.182950 TGTGATCAGTGTTTCTCTCTCTCTC 59.817 44.000 0.00 0.00 0.00 3.20
5180 5575 5.415701 GTGATCAGTGTTTCTCTCTCTCTCT 59.584 44.000 0.00 0.00 0.00 3.10
5672 6067 9.485206 TTTTAACTTGAAAGTACTGTAGCTAGG 57.515 33.333 0.00 0.00 38.57 3.02
5710 6105 7.866898 CCAAGTTTTGATCATGAATGTGTTACA 59.133 33.333 0.00 0.00 0.00 2.41
5727 6124 8.697846 TGTGTTACATGTCAGCTAATTAGTAC 57.302 34.615 13.91 10.17 0.00 2.73
5728 6125 8.308207 TGTGTTACATGTCAGCTAATTAGTACA 58.692 33.333 13.91 14.70 0.00 2.90
5947 6348 0.037790 GCGAAGACTCAAGCCTCACT 60.038 55.000 0.00 0.00 0.00 3.41
5962 6363 3.249091 CCTCACTGATGAAGAGACAACG 58.751 50.000 0.00 0.00 33.30 4.10
6260 6666 3.827898 CCCTCTGGTCTCGGCGTC 61.828 72.222 6.85 0.00 0.00 5.19
6261 6667 4.180946 CCTCTGGTCTCGGCGTCG 62.181 72.222 1.15 1.15 37.82 5.12
6262 6668 3.432588 CTCTGGTCTCGGCGTCGT 61.433 66.667 10.18 0.00 37.69 4.34
6504 6918 0.038159 GTGGTGAGGTGAGAACTCCG 60.038 60.000 0.00 0.00 35.16 4.63
6516 6930 2.500183 GAACTCCGCTGCGCAGTTTC 62.500 60.000 35.80 24.41 30.32 2.78
6539 6953 4.324874 CCTCCAGACCAATCTTCTTCCATT 60.325 45.833 0.00 0.00 30.42 3.16
6543 6957 4.096081 CAGACCAATCTTCTTCCATTGAGC 59.904 45.833 0.00 0.00 32.56 4.26
6628 7042 0.744414 TGCCGAGCTGTTGATAAGCC 60.744 55.000 0.00 0.00 41.82 4.35
6672 7087 9.774742 GACCAGTTATGAATATGTTTTCTGTTC 57.225 33.333 0.00 0.00 0.00 3.18
6705 7120 7.768120 AGAAGCAAAATGGTTTTACATGAAACA 59.232 29.630 0.00 0.00 38.31 2.83
6721 7136 7.483119 CATGAAACATAACGAACTTCATGTG 57.517 36.000 12.68 0.00 44.15 3.21
6763 7178 4.343811 TTTTTGAAAGTCGTGCGAGAAA 57.656 36.364 0.00 0.00 0.00 2.52
6772 7187 1.719246 TCGTGCGAGAAATGAAACTCG 59.281 47.619 11.36 11.36 0.00 4.18
6827 7244 8.862325 AATTCTTGTGACCAGTTGTGAATATA 57.138 30.769 0.00 0.00 0.00 0.86
6858 7275 6.698329 TGCTTCATGTGAGAAATGAAAGTTTG 59.302 34.615 0.00 0.00 42.04 2.93
6888 7305 3.970610 CGAAGCCTAATGAAATTCGCATG 59.029 43.478 0.00 0.00 37.87 4.06
6926 7343 8.984891 TCATGCGATAAATGAAATGTTTCTTT 57.015 26.923 6.99 4.36 38.02 2.52
6927 7344 9.075519 TCATGCGATAAATGAAATGTTTCTTTC 57.924 29.630 6.99 0.00 38.02 2.62
6928 7345 9.079833 CATGCGATAAATGAAATGTTTCTTTCT 57.920 29.630 6.99 0.00 38.02 2.52
6929 7346 9.643693 ATGCGATAAATGAAATGTTTCTTTCTT 57.356 25.926 6.99 0.00 38.02 2.52
6970 7387 4.093408 TCATGTTTGCTATTCTTCAGTCGC 59.907 41.667 0.00 0.00 0.00 5.19
6975 7392 2.028112 TGCTATTCTTCAGTCGCTTGGT 60.028 45.455 0.00 0.00 0.00 3.67
6988 7405 2.556622 TCGCTTGGTGAAAAATCCCTTC 59.443 45.455 0.00 0.00 0.00 3.46
7026 7443 3.322466 CTGCCGGTGGAAGGGAGT 61.322 66.667 1.90 0.00 41.55 3.85
7027 7444 3.316573 CTGCCGGTGGAAGGGAGTC 62.317 68.421 1.90 0.00 41.55 3.36
7028 7445 4.097361 GCCGGTGGAAGGGAGTCC 62.097 72.222 1.90 0.00 38.27 3.85
7029 7446 3.400054 CCGGTGGAAGGGAGTCCC 61.400 72.222 21.81 21.81 45.90 4.46
7038 7455 3.078817 GGGAGTCCCAGGGTTGAC 58.921 66.667 24.35 0.00 44.65 3.18
7039 7456 1.846124 GGGAGTCCCAGGGTTGACA 60.846 63.158 24.35 0.00 44.65 3.58
7040 7457 1.208165 GGGAGTCCCAGGGTTGACAT 61.208 60.000 24.35 0.00 44.65 3.06
7041 7458 0.698818 GGAGTCCCAGGGTTGACATT 59.301 55.000 5.01 0.00 33.89 2.71
7042 7459 1.075536 GGAGTCCCAGGGTTGACATTT 59.924 52.381 5.01 0.00 33.89 2.32
7043 7460 2.162681 GAGTCCCAGGGTTGACATTTG 58.837 52.381 5.01 0.00 33.89 2.32
7044 7461 1.499007 AGTCCCAGGGTTGACATTTGT 59.501 47.619 5.01 0.00 33.89 2.83
7045 7462 2.091333 AGTCCCAGGGTTGACATTTGTT 60.091 45.455 5.01 0.00 33.89 2.83
7046 7463 2.698274 GTCCCAGGGTTGACATTTGTTT 59.302 45.455 5.01 0.00 0.00 2.83
7047 7464 2.962421 TCCCAGGGTTGACATTTGTTTC 59.038 45.455 5.01 0.00 0.00 2.78
7048 7465 2.965147 CCCAGGGTTGACATTTGTTTCT 59.035 45.455 0.00 0.00 0.00 2.52
7049 7466 3.005791 CCCAGGGTTGACATTTGTTTCTC 59.994 47.826 0.00 0.00 0.00 2.87
7050 7467 3.304659 CCAGGGTTGACATTTGTTTCTCG 60.305 47.826 0.00 0.00 0.00 4.04
7051 7468 3.315191 CAGGGTTGACATTTGTTTCTCGT 59.685 43.478 0.00 0.00 0.00 4.18
7052 7469 3.315191 AGGGTTGACATTTGTTTCTCGTG 59.685 43.478 0.00 0.00 0.00 4.35
7053 7470 3.314080 GGGTTGACATTTGTTTCTCGTGA 59.686 43.478 0.00 0.00 0.00 4.35
7054 7471 4.023193 GGGTTGACATTTGTTTCTCGTGAT 60.023 41.667 0.00 0.00 0.00 3.06
7055 7472 5.180492 GGGTTGACATTTGTTTCTCGTGATA 59.820 40.000 0.00 0.00 0.00 2.15
7056 7473 6.307155 GGTTGACATTTGTTTCTCGTGATAG 58.693 40.000 0.00 0.00 0.00 2.08
7057 7474 6.073222 GGTTGACATTTGTTTCTCGTGATAGT 60.073 38.462 0.00 0.00 0.00 2.12
7058 7475 6.706055 TGACATTTGTTTCTCGTGATAGTC 57.294 37.500 0.00 0.00 0.00 2.59
7059 7476 5.344933 TGACATTTGTTTCTCGTGATAGTCG 59.655 40.000 0.00 0.00 0.00 4.18
7060 7477 4.625742 ACATTTGTTTCTCGTGATAGTCGG 59.374 41.667 0.00 0.00 0.00 4.79
7061 7478 2.933495 TGTTTCTCGTGATAGTCGGG 57.067 50.000 0.00 0.00 0.00 5.14
7062 7479 1.475280 TGTTTCTCGTGATAGTCGGGG 59.525 52.381 0.00 0.00 0.00 5.73
7063 7480 0.458669 TTTCTCGTGATAGTCGGGGC 59.541 55.000 0.00 0.00 0.00 5.80
7064 7481 1.721664 TTCTCGTGATAGTCGGGGCG 61.722 60.000 0.00 0.00 0.00 6.13
7065 7482 2.438975 TCGTGATAGTCGGGGCGT 60.439 61.111 0.00 0.00 0.00 5.68
7066 7483 2.025727 CGTGATAGTCGGGGCGTC 59.974 66.667 0.00 0.00 0.00 5.19
7067 7484 2.025727 GTGATAGTCGGGGCGTCG 59.974 66.667 0.00 0.00 0.00 5.12
7068 7485 3.214123 TGATAGTCGGGGCGTCGG 61.214 66.667 0.00 0.00 0.00 4.79
7069 7486 4.642542 GATAGTCGGGGCGTCGGC 62.643 72.222 10.88 10.88 38.90 5.54
7085 7502 2.125188 GCAGTCAGCAGAGGAGGC 60.125 66.667 0.00 0.00 44.79 4.70
7086 7503 2.183811 CAGTCAGCAGAGGAGGCG 59.816 66.667 0.00 0.00 36.08 5.52
7087 7504 3.073735 AGTCAGCAGAGGAGGCGG 61.074 66.667 0.00 0.00 36.08 6.13
7088 7505 3.386237 GTCAGCAGAGGAGGCGGT 61.386 66.667 0.00 0.00 36.08 5.68
7089 7506 3.385384 TCAGCAGAGGAGGCGGTG 61.385 66.667 0.00 0.00 36.08 4.94
7095 7512 3.461773 GAGGAGGCGGTGCAGCTA 61.462 66.667 14.92 0.00 37.29 3.32
7096 7513 3.724914 GAGGAGGCGGTGCAGCTAC 62.725 68.421 14.92 6.46 37.29 3.58
7098 7515 4.129737 GAGGCGGTGCAGCTACGA 62.130 66.667 14.92 0.00 37.29 3.43
7099 7516 4.436998 AGGCGGTGCAGCTACGAC 62.437 66.667 14.92 9.88 37.29 4.34
7102 7519 4.778415 CGGTGCAGCTACGACGCT 62.778 66.667 14.92 0.00 41.90 5.07
7108 7525 4.436998 AGCTACGACGCTGGCCAC 62.437 66.667 0.00 0.00 39.16 5.01
7109 7526 4.735132 GCTACGACGCTGGCCACA 62.735 66.667 0.00 0.00 0.00 4.17
7111 7528 3.989698 CTACGACGCTGGCCACAGG 62.990 68.421 0.00 0.00 45.04 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 184 7.231317 TCACTAGACAGGCAATCTTTTCAATTT 59.769 33.333 0.00 0.00 0.00 1.82
202 224 2.876581 TCACTGTCTTCTGGACTAGCA 58.123 47.619 0.00 0.00 44.74 3.49
212 234 6.650807 TGGATTCAGTTGTAATCACTGTCTTC 59.349 38.462 0.24 0.00 35.46 2.87
256 278 7.434013 ACGTTTTGATTACCTTTTCATGTTGAC 59.566 33.333 0.00 0.00 0.00 3.18
270 292 5.009310 ACTTCCCTTTGGACGTTTTGATTAC 59.991 40.000 0.00 0.00 40.01 1.89
272 294 3.958147 ACTTCCCTTTGGACGTTTTGATT 59.042 39.130 0.00 0.00 40.01 2.57
379 401 3.057104 CCAACCGGTATATGCATCTCGTA 60.057 47.826 8.00 0.00 0.00 3.43
380 402 2.288825 CCAACCGGTATATGCATCTCGT 60.289 50.000 8.00 0.00 0.00 4.18
423 445 0.680280 TCGGAGAAGAAGAGGACCCG 60.680 60.000 0.00 0.00 37.08 5.28
456 483 2.784347 CCCTTTCCAGGACAGAGAAAC 58.216 52.381 3.93 0.00 44.19 2.78
463 490 1.558167 TATGCGCCCTTTCCAGGACA 61.558 55.000 4.18 0.00 44.19 4.02
466 493 0.394352 AGTTATGCGCCCTTTCCAGG 60.394 55.000 4.18 0.00 40.45 4.45
468 495 0.393808 GGAGTTATGCGCCCTTTCCA 60.394 55.000 4.18 0.00 0.00 3.53
471 498 0.618458 TCTGGAGTTATGCGCCCTTT 59.382 50.000 4.18 0.00 36.09 3.11
515 553 0.695803 CCTTCATGCTCCCTACCCCT 60.696 60.000 0.00 0.00 0.00 4.79
547 585 5.246307 AGAAGAAAAGGGAAATACAGTCCG 58.754 41.667 0.00 0.00 35.86 4.79
884 973 1.306141 AGATTGGAGCTGGGACGGA 60.306 57.895 0.00 0.00 36.31 4.69
886 975 1.144936 GGAGATTGGAGCTGGGACG 59.855 63.158 0.00 0.00 0.00 4.79
888 977 0.692419 GAGGGAGATTGGAGCTGGGA 60.692 60.000 0.00 0.00 0.00 4.37
889 978 0.693767 AGAGGGAGATTGGAGCTGGG 60.694 60.000 0.00 0.00 0.00 4.45
1157 1263 2.286121 AGGCGGGGAATTCAGGGA 60.286 61.111 7.93 0.00 0.00 4.20
1158 1264 2.193248 GAGGCGGGGAATTCAGGG 59.807 66.667 7.93 0.00 0.00 4.45
1159 1265 2.044806 ATCGAGGCGGGGAATTCAGG 62.045 60.000 7.93 0.00 0.00 3.86
1216 1323 4.176752 GATCACTGGACCCCGGCC 62.177 72.222 0.00 0.00 32.02 6.13
1224 1350 1.667154 CGCGAAGAGGGATCACTGGA 61.667 60.000 0.00 0.00 34.27 3.86
1226 1352 0.248825 CTCGCGAAGAGGGATCACTG 60.249 60.000 11.33 0.00 43.20 3.66
1227 1353 2.010582 GCTCGCGAAGAGGGATCACT 62.011 60.000 11.33 0.00 46.91 3.41
1236 1362 0.523546 GAATCTGACGCTCGCGAAGA 60.524 55.000 18.98 18.51 42.83 2.87
1238 1364 1.867812 CGAATCTGACGCTCGCGAA 60.868 57.895 18.98 4.88 42.83 4.70
1239 1365 2.277310 CGAATCTGACGCTCGCGA 60.277 61.111 18.98 9.26 42.83 5.87
1256 1382 2.789203 GATCGAACACGTCAGCGCC 61.789 63.158 2.29 0.00 42.83 6.53
1257 1383 2.689766 GATCGAACACGTCAGCGC 59.310 61.111 0.00 0.00 42.83 5.92
1258 1384 2.158959 GGGATCGAACACGTCAGCG 61.159 63.158 0.00 0.00 44.93 5.18
1259 1385 2.158959 CGGGATCGAACACGTCAGC 61.159 63.158 9.43 0.00 39.00 4.26
1260 1386 2.158959 GCGGGATCGAACACGTCAG 61.159 63.158 18.87 0.00 39.03 3.51
1261 1387 2.126228 GCGGGATCGAACACGTCA 60.126 61.111 18.87 0.00 39.03 4.35
1262 1388 2.884207 GGCGGGATCGAACACGTC 60.884 66.667 18.87 13.20 39.03 4.34
1263 1389 4.789075 CGGCGGGATCGAACACGT 62.789 66.667 18.87 0.00 39.03 4.49
1265 1391 4.814294 AGCGGCGGGATCGAACAC 62.814 66.667 9.78 0.00 39.00 3.32
1297 1423 2.811317 GTGGAGAGCAACCGCGAG 60.811 66.667 8.23 0.00 45.49 5.03
1301 1427 2.907897 GATCGGGTGGAGAGCAACCG 62.908 65.000 0.00 0.00 45.52 4.44
1302 1428 1.153349 GATCGGGTGGAGAGCAACC 60.153 63.158 0.00 0.00 35.59 3.77
1343 1472 2.486128 CAACGAAATCGAGCTGAAACG 58.514 47.619 10.16 0.00 43.02 3.60
1502 1656 5.049129 CCAAGTTGTTGAGATTCAGAAGTCC 60.049 44.000 1.45 0.00 35.46 3.85
1514 1668 8.661352 AAAATTCATAAACCCAAGTTGTTGAG 57.339 30.769 1.45 0.00 35.97 3.02
1522 1676 6.403049 GGGTGGTAAAATTCATAAACCCAAG 58.597 40.000 11.73 0.00 44.52 3.61
1545 1699 5.186797 TGGTAAAATTCATAAGCCCAACTGG 59.813 40.000 0.00 0.00 37.09 4.00
1546 1700 6.279513 TGGTAAAATTCATAAGCCCAACTG 57.720 37.500 0.00 0.00 0.00 3.16
1547 1701 5.105351 GCTGGTAAAATTCATAAGCCCAACT 60.105 40.000 0.00 0.00 0.00 3.16
1548 1702 5.109210 GCTGGTAAAATTCATAAGCCCAAC 58.891 41.667 0.00 0.00 0.00 3.77
1549 1703 4.161377 GGCTGGTAAAATTCATAAGCCCAA 59.839 41.667 0.00 0.00 42.32 4.12
1550 1704 3.704061 GGCTGGTAAAATTCATAAGCCCA 59.296 43.478 0.00 0.00 42.32 5.36
1551 1705 3.704061 TGGCTGGTAAAATTCATAAGCCC 59.296 43.478 8.22 0.00 46.53 5.19
1553 1707 5.582689 ACTGGCTGGTAAAATTCATAAGC 57.417 39.130 0.00 0.00 0.00 3.09
1554 1708 6.332630 CCAACTGGCTGGTAAAATTCATAAG 58.667 40.000 0.00 0.00 0.00 1.73
1555 1709 5.186797 CCCAACTGGCTGGTAAAATTCATAA 59.813 40.000 0.00 0.00 34.33 1.90
1556 1710 4.709397 CCCAACTGGCTGGTAAAATTCATA 59.291 41.667 0.00 0.00 34.33 2.15
1557 1711 3.515104 CCCAACTGGCTGGTAAAATTCAT 59.485 43.478 0.00 0.00 34.33 2.57
1602 1756 0.918983 TAAGCCAAGCTACAGCCCAT 59.081 50.000 0.00 0.00 43.38 4.00
1616 1770 8.760980 ACTATCAGATATAGGATCAGTAAGCC 57.239 38.462 0.00 0.00 0.00 4.35
1619 1773 9.533831 TGCAACTATCAGATATAGGATCAGTAA 57.466 33.333 0.00 0.00 0.00 2.24
1621 1775 8.606754 ATGCAACTATCAGATATAGGATCAGT 57.393 34.615 0.00 0.00 0.00 3.41
1623 1777 9.662947 CAAATGCAACTATCAGATATAGGATCA 57.337 33.333 0.00 0.00 0.00 2.92
1626 1780 8.874156 ACTCAAATGCAACTATCAGATATAGGA 58.126 33.333 0.00 0.00 0.00 2.94
1632 1786 5.496133 GCACTCAAATGCAACTATCAGAT 57.504 39.130 0.00 0.00 45.39 2.90
1721 1882 6.460261 GGCAGGCCTAAGAGTTCAATTTAATC 60.460 42.308 3.98 0.00 0.00 1.75
1772 2072 4.201990 GGATGTCTCTCATTCAAACATGGC 60.202 45.833 0.00 0.00 36.83 4.40
1775 2076 5.125097 GCAAGGATGTCTCTCATTCAAACAT 59.875 40.000 0.00 0.00 36.83 2.71
1784 2085 1.407851 GCATGGCAAGGATGTCTCTCA 60.408 52.381 0.00 0.00 30.51 3.27
1787 2088 1.688772 ATGCATGGCAAGGATGTCTC 58.311 50.000 0.00 0.00 43.62 3.36
1798 2099 1.668751 CATTTCTGGCAAATGCATGGC 59.331 47.619 13.67 13.67 45.44 4.40
1850 2151 4.647424 TTAGCCAAGGTGTTTTTCAGTG 57.353 40.909 0.00 0.00 0.00 3.66
1868 2169 5.979288 ACCCCTAGTAATGAGCGTATTAG 57.021 43.478 0.00 0.00 0.00 1.73
1875 2176 2.124411 TCCCAACCCCTAGTAATGAGC 58.876 52.381 0.00 0.00 0.00 4.26
1893 2210 0.175760 TGCGTTACTGCAGAGGATCC 59.824 55.000 23.35 2.48 40.62 3.36
1958 2279 3.389656 TCCTTTTTGGGTGGGAACAAATC 59.610 43.478 0.00 0.00 36.57 2.17
1996 2317 5.163364 ACAAAATATCCACTTGGTTGTGCAA 60.163 36.000 0.00 0.00 36.68 4.08
2180 2501 0.396811 CGGTGTTTCTTCCCTCCTGT 59.603 55.000 0.00 0.00 0.00 4.00
2192 2513 2.750712 GTTATGTGGCCATACGGTGTTT 59.249 45.455 9.72 0.00 33.29 2.83
2357 2679 6.373005 TGATTGACTAAACTCCTGGATTGA 57.627 37.500 0.00 0.00 0.00 2.57
2358 2680 7.636150 ATTGATTGACTAAACTCCTGGATTG 57.364 36.000 0.00 0.00 0.00 2.67
2359 2681 8.655935 AAATTGATTGACTAAACTCCTGGATT 57.344 30.769 0.00 0.00 0.00 3.01
2360 2682 8.526147 CAAAATTGATTGACTAAACTCCTGGAT 58.474 33.333 0.00 0.00 31.84 3.41
2414 2736 6.425721 AGCACAAAGTTTTAATACTAGCGACA 59.574 34.615 0.00 0.00 0.00 4.35
2457 2779 6.565999 CGAAGTTTTCTCACTTGTATTCCCAC 60.566 42.308 0.00 0.00 37.11 4.61
2478 2800 5.845985 TGTCTTTTTATGCTCTGTCGAAG 57.154 39.130 0.00 0.00 0.00 3.79
2488 2810 8.127954 TGCCAAAGAATTTTTGTCTTTTTATGC 58.872 29.630 10.27 0.47 41.47 3.14
3022 3385 9.425248 AGGAACACATCAAATATGGAAATATGT 57.575 29.630 0.00 0.00 0.00 2.29
3072 3441 9.725019 ACTCAAGAAATATGTGAACATAGTCAA 57.275 29.630 8.94 0.00 41.58 3.18
3099 3468 8.605746 GCATTGCAAATGACATACAATTGTTAT 58.394 29.630 17.78 5.63 40.37 1.89
3100 3469 7.818446 AGCATTGCAAATGACATACAATTGTTA 59.182 29.630 17.78 3.36 40.37 2.41
3101 3470 6.651643 AGCATTGCAAATGACATACAATTGTT 59.348 30.769 17.78 0.00 40.37 2.83
3102 3471 6.091577 CAGCATTGCAAATGACATACAATTGT 59.908 34.615 16.68 16.68 40.37 2.71
3103 3472 6.091577 ACAGCATTGCAAATGACATACAATTG 59.908 34.615 11.91 3.24 40.96 2.32
3104 3473 6.167685 ACAGCATTGCAAATGACATACAATT 58.832 32.000 11.91 0.00 0.00 2.32
3105 3474 5.726397 ACAGCATTGCAAATGACATACAAT 58.274 33.333 11.91 5.76 0.00 2.71
3106 3475 5.136816 ACAGCATTGCAAATGACATACAA 57.863 34.783 11.91 0.00 0.00 2.41
3107 3476 4.787260 ACAGCATTGCAAATGACATACA 57.213 36.364 11.91 0.00 0.00 2.29
3108 3477 6.291955 GCATTACAGCATTGCAAATGACATAC 60.292 38.462 23.97 10.43 34.96 2.39
3120 3489 6.715344 ACAAAATCTTGCATTACAGCATTG 57.285 33.333 0.00 0.00 45.19 2.82
3161 3532 7.499232 AGCTGAAATATGGGAGTATTGTAACAC 59.501 37.037 0.00 0.00 0.00 3.32
3171 3542 4.130118 CGCTTAAGCTGAAATATGGGAGT 58.870 43.478 24.33 0.00 39.32 3.85
3197 3568 2.826128 GGGGATGTCTTTTCTGGGAAAC 59.174 50.000 0.00 0.00 0.00 2.78
3286 3657 8.465999 CAGAATGTAGCAATTAACAATGGGTAA 58.534 33.333 0.00 0.00 0.00 2.85
3358 3729 5.094387 TCCTCCAAAGTATTCCTTCTCTGT 58.906 41.667 0.00 0.00 31.27 3.41
3668 4040 4.135306 CTGAACCAGGATCATCAGAATGG 58.865 47.826 0.00 0.00 41.38 3.16
3701 4073 5.822519 TCCTGGATTTATTTGATTGGACTCG 59.177 40.000 0.00 0.00 0.00 4.18
3709 4081 6.659242 ACGAACAAGTCCTGGATTTATTTGAT 59.341 34.615 14.88 4.50 0.00 2.57
3719 4091 4.338012 TGATACTACGAACAAGTCCTGGA 58.662 43.478 0.00 0.00 0.00 3.86
3722 4094 5.124138 CAGACTGATACTACGAACAAGTCCT 59.876 44.000 0.00 0.00 0.00 3.85
3737 4109 4.950475 CCAGTTACTCCTGTCAGACTGATA 59.050 45.833 16.41 4.95 35.56 2.15
3800 4172 0.038166 ACCCACTACCAACATGCTGG 59.962 55.000 13.73 13.73 42.68 4.85
3808 4180 3.019799 TGCTTTTTGACCCACTACCAA 57.980 42.857 0.00 0.00 0.00 3.67
3817 4189 3.118775 ACCCTGTTTCTTGCTTTTTGACC 60.119 43.478 0.00 0.00 0.00 4.02
3829 4201 3.877508 CGAAAAGACAAGACCCTGTTTCT 59.122 43.478 0.00 0.00 0.00 2.52
3877 4249 5.428184 AATTACTCCCTTGGAAGACTCTG 57.572 43.478 0.00 0.00 0.00 3.35
3897 4269 9.917887 ATTAGAATCACAATCCTCTTCAGAAAT 57.082 29.630 0.00 0.00 0.00 2.17
3929 4301 0.106519 AAGAATCCTTCCGGGCATGG 60.107 55.000 0.00 0.00 34.39 3.66
3962 4334 7.450074 TGCCTCTTAAAGAACTCAAATCACTA 58.550 34.615 0.00 0.00 0.00 2.74
3986 4358 3.290710 CCCTGGGGTTGATAATTCACTG 58.709 50.000 4.27 0.00 0.00 3.66
3995 4367 0.345502 TACTAGCCCCTGGGGTTGAT 59.654 55.000 31.95 20.32 46.51 2.57
4001 4373 1.054978 GGGAACTACTAGCCCCTGGG 61.055 65.000 5.50 5.50 35.76 4.45
4046 4418 2.501723 ACTATGTCCATCCACACCACTC 59.498 50.000 0.00 0.00 0.00 3.51
4199 4571 7.333921 GCTATGAGATCCTCCATATCAGTTTTG 59.666 40.741 0.00 0.00 36.16 2.44
5138 5533 9.409918 ACTGATCACATACAACTAGTATACTGT 57.590 33.333 15.90 8.07 41.47 3.55
5145 5540 7.671302 AGAAACACTGATCACATACAACTAGT 58.329 34.615 0.00 0.00 0.00 2.57
5672 6067 1.605753 AAACTTGGAACGAGGGAAGC 58.394 50.000 0.00 0.00 0.00 3.86
5710 6105 6.607600 TCCAGACTGTACTAATTAGCTGACAT 59.392 38.462 12.54 5.33 0.00 3.06
5727 6124 0.806868 ATTGCGCATGTTCCAGACTG 59.193 50.000 12.75 0.00 0.00 3.51
5728 6125 1.089920 GATTGCGCATGTTCCAGACT 58.910 50.000 12.75 0.00 0.00 3.24
5769 6170 8.630917 TCAGCAGGAAAGATAGTAAGTACATAC 58.369 37.037 0.00 0.00 0.00 2.39
5770 6171 8.762481 TCAGCAGGAAAGATAGTAAGTACATA 57.238 34.615 0.00 0.00 0.00 2.29
5771 6172 7.661536 TCAGCAGGAAAGATAGTAAGTACAT 57.338 36.000 0.00 0.00 0.00 2.29
5772 6173 7.661536 ATCAGCAGGAAAGATAGTAAGTACA 57.338 36.000 0.00 0.00 0.00 2.90
5884 6285 1.334059 CCATCGGAATTTTCGCCATCG 60.334 52.381 0.00 0.00 0.00 3.84
5947 6348 5.139435 ACATCTTCGTTGTCTCTTCATCA 57.861 39.130 0.00 0.00 0.00 3.07
5962 6363 2.999355 GAGCAGGTCAGACAACATCTTC 59.001 50.000 2.17 0.00 34.41 2.87
6260 6666 2.181021 GACAGTACCGCCTCCACG 59.819 66.667 0.00 0.00 0.00 4.94
6261 6667 2.181021 CGACAGTACCGCCTCCAC 59.819 66.667 0.00 0.00 0.00 4.02
6262 6668 2.282674 ACGACAGTACCGCCTCCA 60.283 61.111 0.00 0.00 0.00 3.86
6516 6930 2.573462 TGGAAGAAGATTGGTCTGGAGG 59.427 50.000 0.00 0.00 34.13 4.30
6557 6971 1.422402 TCTTTCCCGGGTTACAAAGCT 59.578 47.619 22.86 0.00 0.00 3.74
6558 6972 1.900245 TCTTTCCCGGGTTACAAAGC 58.100 50.000 22.86 0.00 0.00 3.51
6568 6982 3.412386 AGAGAACACAATTCTTTCCCGG 58.588 45.455 0.00 0.00 0.00 5.73
6569 6983 4.065088 TGAGAGAACACAATTCTTTCCCG 58.935 43.478 5.13 0.00 31.03 5.14
6628 7042 2.512885 GTCACAGCAATTCAAGATGCG 58.487 47.619 0.00 0.00 46.98 4.73
6705 7120 4.569943 AGAGCACACATGAAGTTCGTTAT 58.430 39.130 0.00 0.00 0.00 1.89
6718 7133 7.846644 ATTTCAAAATTTTCAAGAGCACACA 57.153 28.000 0.00 0.00 0.00 3.72
6744 7159 3.558006 TCATTTCTCGCACGACTTTCAAA 59.442 39.130 0.00 0.00 0.00 2.69
6763 7178 1.556911 AGGATGCTCCACGAGTTTCAT 59.443 47.619 0.00 0.00 39.61 2.57
6827 7244 7.223260 TCATTTCTCACATGAAGCAGAAAAT 57.777 32.000 0.00 0.00 38.15 1.82
6858 7275 7.007099 CGAATTTCATTAGGCTTCGTGTAAAAC 59.993 37.037 0.00 0.00 35.29 2.43
6863 7280 3.181510 GCGAATTTCATTAGGCTTCGTGT 60.182 43.478 0.00 0.00 40.45 4.49
6926 7343 8.859090 ACATGAATCATTAGGTTTCACAAAAGA 58.141 29.630 0.00 0.00 37.87 2.52
6927 7344 9.480053 AACATGAATCATTAGGTTTCACAAAAG 57.520 29.630 0.00 0.00 37.87 2.27
6928 7345 9.829507 AAACATGAATCATTAGGTTTCACAAAA 57.170 25.926 0.00 0.00 37.87 2.44
6929 7346 9.258826 CAAACATGAATCATTAGGTTTCACAAA 57.741 29.630 0.00 0.00 37.87 2.83
6970 7387 4.321527 GCTCTGAAGGGATTTTTCACCAAG 60.322 45.833 0.00 0.00 31.66 3.61
6975 7392 3.157087 GGTGCTCTGAAGGGATTTTTCA 58.843 45.455 0.00 0.00 33.76 2.69
7010 7427 3.319198 GACTCCCTTCCACCGGCA 61.319 66.667 0.00 0.00 0.00 5.69
7011 7428 4.097361 GGACTCCCTTCCACCGGC 62.097 72.222 0.00 0.00 35.49 6.13
7012 7429 3.400054 GGGACTCCCTTCCACCGG 61.400 72.222 6.90 0.00 41.34 5.28
7013 7430 2.606519 TGGGACTCCCTTCCACCG 60.607 66.667 15.64 0.00 45.70 4.94
7014 7431 2.301738 CCTGGGACTCCCTTCCACC 61.302 68.421 15.64 0.00 45.70 4.61
7015 7432 2.301738 CCCTGGGACTCCCTTCCAC 61.302 68.421 15.64 0.00 45.70 4.02
7016 7433 2.124996 CCCTGGGACTCCCTTCCA 59.875 66.667 15.64 0.00 45.70 3.53
7017 7434 1.541620 AACCCTGGGACTCCCTTCC 60.542 63.158 22.23 0.00 45.70 3.46
7018 7435 0.840722 TCAACCCTGGGACTCCCTTC 60.841 60.000 22.23 0.00 45.70 3.46
7019 7436 1.134438 GTCAACCCTGGGACTCCCTT 61.134 60.000 22.23 0.00 45.70 3.95
7020 7437 1.539124 GTCAACCCTGGGACTCCCT 60.539 63.158 22.23 0.00 45.70 4.20
7021 7438 1.208165 ATGTCAACCCTGGGACTCCC 61.208 60.000 22.23 7.25 45.71 4.30
7022 7439 0.698818 AATGTCAACCCTGGGACTCC 59.301 55.000 22.23 5.02 35.11 3.85
7023 7440 2.162681 CAAATGTCAACCCTGGGACTC 58.837 52.381 22.23 7.33 35.11 3.36
7024 7441 1.499007 ACAAATGTCAACCCTGGGACT 59.501 47.619 22.23 2.54 35.11 3.85
7025 7442 1.995376 ACAAATGTCAACCCTGGGAC 58.005 50.000 22.23 8.03 34.63 4.46
7026 7443 2.765689 AACAAATGTCAACCCTGGGA 57.234 45.000 22.23 0.00 0.00 4.37
7027 7444 2.965147 AGAAACAAATGTCAACCCTGGG 59.035 45.455 12.28 12.28 0.00 4.45
7028 7445 3.304659 CGAGAAACAAATGTCAACCCTGG 60.305 47.826 0.00 0.00 0.00 4.45
7029 7446 3.315191 ACGAGAAACAAATGTCAACCCTG 59.685 43.478 0.00 0.00 0.00 4.45
7030 7447 3.315191 CACGAGAAACAAATGTCAACCCT 59.685 43.478 0.00 0.00 0.00 4.34
7031 7448 3.314080 TCACGAGAAACAAATGTCAACCC 59.686 43.478 0.00 0.00 0.00 4.11
7032 7449 4.545823 TCACGAGAAACAAATGTCAACC 57.454 40.909 0.00 0.00 0.00 3.77
7033 7450 6.888430 ACTATCACGAGAAACAAATGTCAAC 58.112 36.000 0.00 0.00 0.00 3.18
7034 7451 6.128929 CGACTATCACGAGAAACAAATGTCAA 60.129 38.462 0.00 0.00 0.00 3.18
7035 7452 5.344933 CGACTATCACGAGAAACAAATGTCA 59.655 40.000 0.00 0.00 0.00 3.58
7036 7453 5.220228 CCGACTATCACGAGAAACAAATGTC 60.220 44.000 0.00 0.00 0.00 3.06
7037 7454 4.625742 CCGACTATCACGAGAAACAAATGT 59.374 41.667 0.00 0.00 0.00 2.71
7038 7455 4.032900 CCCGACTATCACGAGAAACAAATG 59.967 45.833 0.00 0.00 0.00 2.32
7039 7456 4.181578 CCCGACTATCACGAGAAACAAAT 58.818 43.478 0.00 0.00 0.00 2.32
7040 7457 3.581755 CCCGACTATCACGAGAAACAAA 58.418 45.455 0.00 0.00 0.00 2.83
7041 7458 2.094390 CCCCGACTATCACGAGAAACAA 60.094 50.000 0.00 0.00 0.00 2.83
7042 7459 1.475280 CCCCGACTATCACGAGAAACA 59.525 52.381 0.00 0.00 0.00 2.83
7043 7460 1.801765 GCCCCGACTATCACGAGAAAC 60.802 57.143 0.00 0.00 0.00 2.78
7044 7461 0.458669 GCCCCGACTATCACGAGAAA 59.541 55.000 0.00 0.00 0.00 2.52
7045 7462 1.721664 CGCCCCGACTATCACGAGAA 61.722 60.000 0.00 0.00 0.00 2.87
7046 7463 2.184830 CGCCCCGACTATCACGAGA 61.185 63.158 0.00 0.00 0.00 4.04
7047 7464 2.331805 CGCCCCGACTATCACGAG 59.668 66.667 0.00 0.00 0.00 4.18
7048 7465 2.438975 ACGCCCCGACTATCACGA 60.439 61.111 0.00 0.00 0.00 4.35
7049 7466 2.025727 GACGCCCCGACTATCACG 59.974 66.667 0.00 0.00 0.00 4.35
7050 7467 2.025727 CGACGCCCCGACTATCAC 59.974 66.667 0.00 0.00 0.00 3.06
7051 7468 3.214123 CCGACGCCCCGACTATCA 61.214 66.667 0.00 0.00 0.00 2.15
7052 7469 4.642542 GCCGACGCCCCGACTATC 62.643 72.222 0.00 0.00 0.00 2.08
7062 7479 4.724602 TCTGCTGACTGCCGACGC 62.725 66.667 1.50 0.00 42.00 5.19
7063 7480 2.505777 CTCTGCTGACTGCCGACG 60.506 66.667 1.50 0.00 42.00 5.12
7064 7481 2.125753 CCTCTGCTGACTGCCGAC 60.126 66.667 1.50 0.00 42.00 4.79
7065 7482 2.283173 TCCTCTGCTGACTGCCGA 60.283 61.111 1.50 0.12 42.00 5.54
7066 7483 2.183811 CTCCTCTGCTGACTGCCG 59.816 66.667 1.50 0.00 42.00 5.69
7067 7484 2.583520 CCTCCTCTGCTGACTGCC 59.416 66.667 1.50 0.00 42.00 4.85
7068 7485 2.125188 GCCTCCTCTGCTGACTGC 60.125 66.667 0.00 0.00 43.25 4.40
7069 7486 2.183811 CGCCTCCTCTGCTGACTG 59.816 66.667 0.00 0.00 0.00 3.51
7070 7487 3.073735 CCGCCTCCTCTGCTGACT 61.074 66.667 0.00 0.00 0.00 3.41
7071 7488 3.386237 ACCGCCTCCTCTGCTGAC 61.386 66.667 0.00 0.00 0.00 3.51
7072 7489 3.385384 CACCGCCTCCTCTGCTGA 61.385 66.667 0.00 0.00 0.00 4.26
7077 7494 3.965026 TAGCTGCACCGCCTCCTCT 62.965 63.158 1.02 0.00 0.00 3.69
7078 7495 3.461773 TAGCTGCACCGCCTCCTC 61.462 66.667 1.02 0.00 0.00 3.71
7079 7496 3.775654 GTAGCTGCACCGCCTCCT 61.776 66.667 1.02 0.00 0.00 3.69
7081 7498 4.129737 TCGTAGCTGCACCGCCTC 62.130 66.667 1.02 0.00 0.00 4.70
7082 7499 4.436998 GTCGTAGCTGCACCGCCT 62.437 66.667 1.02 0.00 0.00 5.52
7092 7509 4.735132 TGTGGCCAGCGTCGTAGC 62.735 66.667 5.11 0.00 37.41 3.58
7093 7510 2.507102 CTGTGGCCAGCGTCGTAG 60.507 66.667 5.11 0.00 0.00 3.51
7094 7511 4.063967 CCTGTGGCCAGCGTCGTA 62.064 66.667 5.11 0.00 37.38 3.43


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

AutoCloner maintained by Alex Coulton.