Multiple sequence alignment - TraesCS2D01G355400

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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 TraesCS2D01G355400 chr2D 100.000 4045 0 0 1 4045 457650443 457654487 0.000000e+00 7470.0
1 TraesCS2D01G355400 chr2D 94.643 56 1 2 3992 4045 469977579 469977634 7.200000e-13 86.1
2 TraesCS2D01G355400 chr2D 94.118 51 1 2 3992 4040 469975972 469976022 4.340000e-10 76.8
3 TraesCS2D01G355400 chr2B 90.990 3840 173 62 1 3770 538951451 538955187 0.000000e+00 5014.0
4 TraesCS2D01G355400 chr2A 90.408 1543 77 23 2251 3770 601336567 601338061 0.000000e+00 1964.0
5 TraesCS2D01G355400 chr2A 88.669 1668 97 30 586 2189 601334931 601336570 0.000000e+00 1949.0
6 TraesCS2D01G355400 chr2A 86.577 298 21 11 52 332 601334268 601334563 1.090000e-80 311.0
7 TraesCS2D01G355400 chr2A 94.203 69 4 0 1 69 601334184 601334252 5.530000e-19 106.0
8 TraesCS2D01G355400 chr2A 83.486 109 6 5 3948 4045 601338063 601338170 1.550000e-14 91.6
9 TraesCS2D01G355400 chr5A 86.875 160 20 1 319 477 451733167 451733008 1.160000e-40 178.0
10 TraesCS2D01G355400 chr5A 81.905 105 18 1 319 422 662726661 662726557 2.000000e-13 87.9
11 TraesCS2D01G355400 chr5A 94.118 51 1 2 3997 4045 471693808 471693758 4.340000e-10 76.8
12 TraesCS2D01G355400 chr6A 81.022 137 23 2 321 454 453569998 453569862 5.530000e-19 106.0
13 TraesCS2D01G355400 chr3B 95.918 49 2 0 3997 4045 821733022 821733070 3.350000e-11 80.5
14 TraesCS2D01G355400 chr3B 94.595 37 1 1 442 477 139417761 139417725 5.650000e-04 56.5
15 TraesCS2D01G355400 chr7D 95.833 48 2 0 3998 4045 199564314 199564267 1.210000e-10 78.7
16 TraesCS2D01G355400 chr7A 95.833 48 2 0 3998 4045 209593020 209592973 1.210000e-10 78.7
17 TraesCS2D01G355400 chr3A 95.833 48 2 0 3998 4045 728885049 728885096 1.210000e-10 78.7
18 TraesCS2D01G355400 chr5B 95.833 48 1 1 3998 4045 437910330 437910284 4.340000e-10 76.8
19 TraesCS2D01G355400 chr7B 97.500 40 1 0 2208 2247 618503294 618503255 7.250000e-08 69.4
20 TraesCS2D01G355400 chr1D 95.238 42 2 0 2214 2255 141706014 141705973 2.610000e-07 67.6
21 TraesCS2D01G355400 chr1B 95.238 42 2 0 2214 2255 195591238 195591197 2.610000e-07 67.6
22 TraesCS2D01G355400 chr4B 94.595 37 2 0 2227 2263 649472188 649472152 1.570000e-04 58.4


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 TraesCS2D01G355400 chr2D 457650443 457654487 4044 False 7470.00 7470 100.0000 1 4045 1 chr2D.!!$F1 4044
1 TraesCS2D01G355400 chr2B 538951451 538955187 3736 False 5014.00 5014 90.9900 1 3770 1 chr2B.!!$F1 3769
2 TraesCS2D01G355400 chr2A 601334184 601338170 3986 False 884.32 1964 88.6686 1 4045 5 chr2A.!!$F1 4044

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
94 126 0.395312 ATCCGTGGTTTGTTCCGTCT 59.605 50.000 0.00 0.0 0.00 4.18 F
334 383 1.374947 CCAGGGCTTCTTCGGTTCA 59.625 57.895 0.00 0.0 0.00 3.18 F
1358 1635 0.179111 TCGGCGGACTGAATTAGCAG 60.179 55.000 7.21 0.0 41.63 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1280 1543 0.608035 TCAACCGACAGGCCCATTTC 60.608 55.0 0.00 0.0 42.76 2.17 R
1422 1707 0.679321 GAGCCCTGCAAAGGAAGGAG 60.679 60.0 6.62 0.0 43.45 3.69 R
3092 3404 0.878416 TGCTCGGTGTGGTAAAATGC 59.122 50.0 0.00 0.0 0.00 3.56 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
94 126 0.395312 ATCCGTGGTTTGTTCCGTCT 59.605 50.000 0.00 0.00 0.00 4.18
104 147 3.462483 TTGTTCCGTCTATGTGTGTGT 57.538 42.857 0.00 0.00 0.00 3.72
105 148 2.749776 TGTTCCGTCTATGTGTGTGTG 58.250 47.619 0.00 0.00 0.00 3.82
106 149 1.459592 GTTCCGTCTATGTGTGTGTGC 59.540 52.381 0.00 0.00 0.00 4.57
128 171 4.443621 CGGCCAAACCTTTTTCCTTTTTA 58.556 39.130 2.24 0.00 35.61 1.52
131 174 6.706716 CGGCCAAACCTTTTTCCTTTTTATTA 59.293 34.615 2.24 0.00 35.61 0.98
133 176 9.727859 GGCCAAACCTTTTTCCTTTTTATTATA 57.272 29.630 0.00 0.00 34.51 0.98
138 181 9.917129 AACCTTTTTCCTTTTTATTATACCGTG 57.083 29.630 0.00 0.00 0.00 4.94
139 182 9.299465 ACCTTTTTCCTTTTTATTATACCGTGA 57.701 29.630 0.00 0.00 0.00 4.35
277 326 2.289382 TGTCGTGCATCACCACTAACAT 60.289 45.455 0.00 0.00 33.60 2.71
278 327 2.742053 GTCGTGCATCACCACTAACATT 59.258 45.455 0.00 0.00 33.60 2.71
285 334 1.621317 TCACCACTAACATTCGCCTCA 59.379 47.619 0.00 0.00 0.00 3.86
328 377 2.264120 GAGGAGGCCAGGGCTTCTTC 62.264 65.000 24.95 20.00 44.44 2.87
334 383 1.374947 CCAGGGCTTCTTCGGTTCA 59.625 57.895 0.00 0.00 0.00 3.18
340 472 1.807142 GGCTTCTTCGGTTCAAAGGAG 59.193 52.381 0.00 0.00 33.22 3.69
342 474 2.480802 GCTTCTTCGGTTCAAAGGAGTC 59.519 50.000 0.00 0.00 32.74 3.36
404 537 3.073678 CCTGTGATGGTCGTTTGATTCA 58.926 45.455 0.00 0.00 0.00 2.57
447 582 5.659440 TTTTCTTCATAGGGTCCATTTGC 57.341 39.130 0.00 0.00 0.00 3.68
484 620 8.575649 GAGGAAAATTTCATCCACCTACTTTA 57.424 34.615 9.00 0.00 38.23 1.85
492 628 4.473196 TCATCCACCTACTTTATTCCTGCA 59.527 41.667 0.00 0.00 0.00 4.41
524 739 6.353323 TCATTCCTGCGTTTTGATAATCCTA 58.647 36.000 0.00 0.00 0.00 2.94
547 762 2.172082 GGTTACGGATTAAAGAGGCCCT 59.828 50.000 0.00 0.00 0.00 5.19
599 814 2.556287 GTGTGCGGGCGAAAGAAG 59.444 61.111 0.00 0.00 0.00 2.85
1139 1394 3.157949 CTTCTCCTCCCCCGCCTC 61.158 72.222 0.00 0.00 0.00 4.70
1140 1395 4.798682 TTCTCCTCCCCCGCCTCC 62.799 72.222 0.00 0.00 0.00 4.30
1224 1479 4.147449 CTCCAGTCCATCGCGCCA 62.147 66.667 0.00 0.00 0.00 5.69
1228 1483 4.148825 AGTCCATCGCGCCAGGTC 62.149 66.667 0.00 0.50 0.00 3.85
1279 1542 2.223409 ACGCGCGATTCTCTACATAACA 60.223 45.455 39.36 0.00 0.00 2.41
1280 1543 2.402049 CGCGCGATTCTCTACATAACAG 59.598 50.000 28.94 0.00 0.00 3.16
1290 1553 4.721776 TCTCTACATAACAGAAATGGGCCT 59.278 41.667 4.53 0.00 0.00 5.19
1306 1576 1.174783 GCCTGTCGGTTGAGACTAGA 58.825 55.000 0.00 0.00 41.47 2.43
1316 1586 6.593382 GTCGGTTGAGACTAGAGTTAACTAGA 59.407 42.308 8.42 0.00 41.42 2.43
1323 1593 8.275758 TGAGACTAGAGTTAACTAGATGGATGT 58.724 37.037 8.42 0.00 41.42 3.06
1358 1635 0.179111 TCGGCGGACTGAATTAGCAG 60.179 55.000 7.21 0.00 41.63 4.24
1399 1684 7.882179 ACGCTTTTAACTGGATTGATAAACTT 58.118 30.769 0.00 0.00 0.00 2.66
1410 1695 9.258826 CTGGATTGATAAACTTATCTCTGACAG 57.741 37.037 10.11 0.00 40.11 3.51
1422 1707 3.149196 TCTCTGACAGGGTTTTGCATTC 58.851 45.455 1.35 0.00 0.00 2.67
1479 1764 3.136443 TCAGGTTTGAGCTCCTTCTTCAA 59.864 43.478 12.15 0.00 30.91 2.69
1482 1767 3.304996 GGTTTGAGCTCCTTCTTCAAAGC 60.305 47.826 12.15 9.75 40.08 3.51
1485 1770 0.038890 AGCTCCTTCTTCAAAGCCCC 59.961 55.000 0.00 0.00 35.32 5.80
1491 1776 4.149598 TCCTTCTTCAAAGCCCCTTTAAC 58.850 43.478 0.00 0.00 31.96 2.01
1567 1852 7.475137 AAAACAAGAGAGAGTATAGCTGACT 57.525 36.000 0.00 0.00 0.00 3.41
1572 1857 6.001449 AGAGAGAGTATAGCTGACTTCTGT 57.999 41.667 0.00 2.33 0.00 3.41
1691 1976 1.652124 CCGACACAATTTAGACGTCCG 59.348 52.381 13.01 4.22 0.00 4.79
1742 2027 3.826157 GGTGTCATTCTTCACAATTCCCA 59.174 43.478 0.00 0.00 36.43 4.37
1751 2036 4.102210 TCTTCACAATTCCCATTGCCAAAA 59.898 37.500 0.00 0.00 43.39 2.44
1756 2041 5.704515 CACAATTCCCATTGCCAAAATGTTA 59.295 36.000 0.00 0.00 43.39 2.41
1757 2042 6.206243 CACAATTCCCATTGCCAAAATGTTAA 59.794 34.615 0.00 0.00 43.39 2.01
1764 2049 7.286316 TCCCATTGCCAAAATGTTAAAACAAAT 59.714 29.630 0.00 0.00 43.03 2.32
1766 2051 8.753175 CCATTGCCAAAATGTTAAAACAAATTG 58.247 29.630 13.08 13.08 43.03 2.32
1775 2060 4.872691 TGTTAAAACAAATTGGTGCCTGTG 59.127 37.500 0.00 0.00 35.67 3.66
1793 2078 4.024556 CCTGTGAGCAGTACTGAAGTTTTG 60.025 45.833 27.08 9.57 41.02 2.44
2013 2311 9.599866 CTATTGAATGACCTAGTGTACATTTGA 57.400 33.333 0.00 0.00 33.92 2.69
2047 2357 6.255453 CCAAATATAATTGGGAAAAGCGTGTG 59.745 38.462 11.25 0.00 45.03 3.82
2048 2358 6.524101 AATATAATTGGGAAAAGCGTGTGT 57.476 33.333 0.00 0.00 0.00 3.72
2049 2359 4.864704 ATAATTGGGAAAAGCGTGTGTT 57.135 36.364 0.00 0.00 0.00 3.32
2050 2360 3.535280 AATTGGGAAAAGCGTGTGTTT 57.465 38.095 0.00 0.00 0.00 2.83
2051 2361 3.535280 ATTGGGAAAAGCGTGTGTTTT 57.465 38.095 0.00 0.00 0.00 2.43
2052 2362 3.320673 TTGGGAAAAGCGTGTGTTTTT 57.679 38.095 0.00 0.00 40.61 1.94
2064 2374 7.276953 AGCGTGTGTTTTTCATTATATTTGC 57.723 32.000 0.00 0.00 0.00 3.68
2065 2375 7.090173 AGCGTGTGTTTTTCATTATATTTGCT 58.910 30.769 0.00 0.00 0.00 3.91
2083 2393 4.494350 TGCTCAGAGTTTTGATGCTTTC 57.506 40.909 0.00 0.00 0.00 2.62
2179 2490 2.838286 GCTCACAAGCTCAGGTCTG 58.162 57.895 0.00 0.00 45.55 3.51
2200 2511 7.201750 GGTCTGACTATTACTACCTCTGTTCAG 60.202 44.444 7.85 0.00 0.00 3.02
2210 2521 9.918630 TTACTACCTCTGTTCAGTAATGTAAAC 57.081 33.333 0.00 0.00 30.55 2.01
2224 2535 7.867403 CAGTAATGTAAACTGAACTGCCAAAAT 59.133 33.333 0.00 0.00 45.89 1.82
2369 2681 7.401484 AGCACATTAACATTAAAACCAAACG 57.599 32.000 0.00 0.00 0.00 3.60
2389 2701 6.980051 AACGTGGATTACTTCCTGTTATTC 57.020 37.500 0.00 0.00 45.68 1.75
2420 2732 1.555075 GTGATTACTCCCCTGCACTGA 59.445 52.381 0.00 0.00 0.00 3.41
2546 2858 5.189736 TGGCTTTCACCTACATAACTCATCT 59.810 40.000 0.00 0.00 0.00 2.90
2634 2946 2.149578 CCAAGTTCTTGTGAGCTGGAG 58.850 52.381 10.93 0.00 33.98 3.86
2667 2979 4.961438 AATTCCTTTTCACATGGTTGCT 57.039 36.364 0.00 0.00 0.00 3.91
2674 2986 4.734398 TTTCACATGGTTGCTTCTGTTT 57.266 36.364 0.00 0.00 0.00 2.83
2697 3009 4.922206 TGAGGCTATGTTGACTGGAAAAT 58.078 39.130 0.00 0.00 0.00 1.82
2761 3073 0.530870 GAGCGTACCAAGGAGATGGC 60.531 60.000 0.00 0.00 44.75 4.40
3048 3360 0.739813 GACCACCGCACGATAGCTTT 60.740 55.000 0.00 0.00 42.67 3.51
3089 3401 4.737054 CAGGTAAAAGTATTTGCAGCAGG 58.263 43.478 0.00 0.00 39.02 4.85
3124 3443 3.198068 CACCGAGCAATGTTAGCTGTAT 58.802 45.455 0.00 0.00 43.58 2.29
3154 3473 4.083537 ACGTGTAATGTTTGCCAGTGTATG 60.084 41.667 0.00 0.00 25.44 2.39
3155 3474 4.153296 CGTGTAATGTTTGCCAGTGTATGA 59.847 41.667 0.00 0.00 0.00 2.15
3156 3475 5.390613 GTGTAATGTTTGCCAGTGTATGAC 58.609 41.667 0.00 0.00 0.00 3.06
3304 3637 1.541588 GATCAAAAGGCGGTTTCTGCT 59.458 47.619 0.66 0.00 0.00 4.24
3309 3642 0.818040 AAGGCGGTTTCTGCTTTCGT 60.818 50.000 0.66 0.00 0.00 3.85
3355 3688 4.565022 TGCAGTTTGATTCACAGTATCGA 58.435 39.130 0.00 0.00 0.00 3.59
3356 3689 4.627035 TGCAGTTTGATTCACAGTATCGAG 59.373 41.667 0.00 0.00 0.00 4.04
3357 3690 4.493220 GCAGTTTGATTCACAGTATCGAGC 60.493 45.833 0.00 0.00 0.00 5.03
3358 3691 4.867047 CAGTTTGATTCACAGTATCGAGCT 59.133 41.667 0.00 0.00 29.93 4.09
3359 3692 5.349817 CAGTTTGATTCACAGTATCGAGCTT 59.650 40.000 0.00 0.00 28.05 3.74
3360 3693 5.578727 AGTTTGATTCACAGTATCGAGCTTC 59.421 40.000 0.00 0.00 0.00 3.86
3361 3694 4.718940 TGATTCACAGTATCGAGCTTCA 57.281 40.909 0.00 0.00 0.00 3.02
3364 3697 3.510388 TCACAGTATCGAGCTTCAAGG 57.490 47.619 0.00 0.00 0.00 3.61
3391 3724 3.016736 GCTATTTTTACCAGCAGGCTCA 58.983 45.455 0.00 0.00 39.06 4.26
3431 3776 9.959749 TGCTTTACTTTTCGTCTTTATTTTCAT 57.040 25.926 0.00 0.00 0.00 2.57
3437 3782 9.965824 ACTTTTCGTCTTTATTTTCATGATGTT 57.034 25.926 0.00 0.00 0.00 2.71
3439 3784 9.958234 TTTTCGTCTTTATTTTCATGATGTTCA 57.042 25.926 0.00 0.00 0.00 3.18
3440 3785 8.948853 TTCGTCTTTATTTTCATGATGTTCAC 57.051 30.769 0.00 0.00 0.00 3.18
3441 3786 7.526608 TCGTCTTTATTTTCATGATGTTCACC 58.473 34.615 0.00 0.00 0.00 4.02
3442 3787 7.174080 TCGTCTTTATTTTCATGATGTTCACCA 59.826 33.333 0.00 0.00 0.00 4.17
3449 3794 5.885230 TTCATGATGTTCACCAAGATGAC 57.115 39.130 0.00 0.00 29.21 3.06
3490 3835 5.887214 AGTGCTTGGTACCATCATATGTA 57.113 39.130 17.17 0.00 0.00 2.29
3508 3853 8.145122 TCATATGTACGGAATGTGCACTATTTA 58.855 33.333 19.41 0.00 46.29 1.40
3595 3943 5.001232 TCAGTGCTTGTAGTTGGGAAATAC 58.999 41.667 0.00 0.00 32.89 1.89
3596 3944 4.156008 CAGTGCTTGTAGTTGGGAAATACC 59.844 45.833 0.00 0.00 31.33 2.73
3597 3945 4.042934 AGTGCTTGTAGTTGGGAAATACCT 59.957 41.667 0.00 0.00 38.98 3.08
3598 3946 4.765339 GTGCTTGTAGTTGGGAAATACCTT 59.235 41.667 0.00 0.00 38.98 3.50
3599 3947 5.243060 GTGCTTGTAGTTGGGAAATACCTTT 59.757 40.000 0.00 0.00 38.98 3.11
3600 3948 5.836358 TGCTTGTAGTTGGGAAATACCTTTT 59.164 36.000 0.00 0.00 38.98 2.27
3601 3949 6.325286 TGCTTGTAGTTGGGAAATACCTTTTT 59.675 34.615 0.00 0.00 38.98 1.94
3687 4036 5.664457 CACCAGTATATGAACTGCTCAGAA 58.336 41.667 3.60 0.00 44.56 3.02
3728 4077 5.063880 GCGAAATGTAATACTCCCTCCATT 58.936 41.667 0.00 0.00 0.00 3.16
3747 4096 7.761249 CCTCCATTCCAAATGTGTAATCTTTTC 59.239 37.037 0.00 0.00 0.00 2.29
3773 4122 2.431954 CCAGCAGGTTCATGGAGATT 57.568 50.000 0.00 0.00 36.09 2.40
3774 4123 3.565764 CCAGCAGGTTCATGGAGATTA 57.434 47.619 0.00 0.00 36.09 1.75
3775 4124 3.474600 CCAGCAGGTTCATGGAGATTAG 58.525 50.000 0.00 0.00 36.09 1.73
3776 4125 2.877168 CAGCAGGTTCATGGAGATTAGC 59.123 50.000 0.00 0.00 0.00 3.09
3777 4126 2.776536 AGCAGGTTCATGGAGATTAGCT 59.223 45.455 0.00 0.00 0.00 3.32
3778 4127 3.201708 AGCAGGTTCATGGAGATTAGCTT 59.798 43.478 0.00 0.00 0.00 3.74
3779 4128 3.314635 GCAGGTTCATGGAGATTAGCTTG 59.685 47.826 0.00 0.00 0.00 4.01
3780 4129 4.521146 CAGGTTCATGGAGATTAGCTTGT 58.479 43.478 0.00 0.00 0.00 3.16
3781 4130 4.334759 CAGGTTCATGGAGATTAGCTTGTG 59.665 45.833 0.00 0.00 0.00 3.33
3782 4131 4.018960 AGGTTCATGGAGATTAGCTTGTGT 60.019 41.667 0.00 0.00 0.00 3.72
3783 4132 5.189736 AGGTTCATGGAGATTAGCTTGTGTA 59.810 40.000 0.00 0.00 0.00 2.90
3784 4133 5.880332 GGTTCATGGAGATTAGCTTGTGTAA 59.120 40.000 0.00 0.00 0.00 2.41
3785 4134 6.543831 GGTTCATGGAGATTAGCTTGTGTAAT 59.456 38.462 0.00 0.00 0.00 1.89
3786 4135 7.254932 GGTTCATGGAGATTAGCTTGTGTAATC 60.255 40.741 0.00 0.00 37.22 1.75
3787 4136 7.129457 TCATGGAGATTAGCTTGTGTAATCT 57.871 36.000 8.15 8.15 45.74 2.40
3788 4137 7.568349 TCATGGAGATTAGCTTGTGTAATCTT 58.432 34.615 9.49 0.00 43.99 2.40
3789 4138 8.049117 TCATGGAGATTAGCTTGTGTAATCTTT 58.951 33.333 9.49 0.00 43.99 2.52
3790 4139 8.680903 CATGGAGATTAGCTTGTGTAATCTTTT 58.319 33.333 9.49 0.00 43.99 2.27
3791 4140 8.635765 TGGAGATTAGCTTGTGTAATCTTTTT 57.364 30.769 9.49 0.00 43.99 1.94
3814 4163 7.929941 TTTTTGGGCAAAGTCAAAAGTAATT 57.070 28.000 0.00 0.00 41.77 1.40
3815 4164 7.929941 TTTTGGGCAAAGTCAAAAGTAATTT 57.070 28.000 0.00 0.00 37.76 1.82
3816 4165 9.449719 TTTTTGGGCAAAGTCAAAAGTAATTTA 57.550 25.926 0.00 0.00 41.77 1.40
3817 4166 9.620259 TTTTGGGCAAAGTCAAAAGTAATTTAT 57.380 25.926 0.00 0.00 37.76 1.40
3818 4167 9.620259 TTTGGGCAAAGTCAAAAGTAATTTATT 57.380 25.926 0.00 0.00 30.96 1.40
3819 4168 9.620259 TTGGGCAAAGTCAAAAGTAATTTATTT 57.380 25.926 0.00 0.00 0.00 1.40
3837 4186 7.663043 TTTATTTATTTATTGCGGGGAAGGT 57.337 32.000 0.00 0.00 0.00 3.50
3838 4187 5.784578 ATTTATTTATTGCGGGGAAGGTC 57.215 39.130 0.00 0.00 0.00 3.85
3839 4188 2.818751 ATTTATTGCGGGGAAGGTCA 57.181 45.000 0.00 0.00 0.00 4.02
3840 4189 2.588464 TTTATTGCGGGGAAGGTCAA 57.412 45.000 0.00 0.00 0.00 3.18
3841 4190 2.588464 TTATTGCGGGGAAGGTCAAA 57.412 45.000 0.00 0.00 0.00 2.69
3842 4191 2.818751 TATTGCGGGGAAGGTCAAAT 57.181 45.000 0.00 0.00 0.00 2.32
3843 4192 1.185315 ATTGCGGGGAAGGTCAAATG 58.815 50.000 0.00 0.00 0.00 2.32
3844 4193 0.178975 TTGCGGGGAAGGTCAAATGT 60.179 50.000 0.00 0.00 0.00 2.71
3845 4194 0.693622 TGCGGGGAAGGTCAAATGTA 59.306 50.000 0.00 0.00 0.00 2.29
3846 4195 1.074084 TGCGGGGAAGGTCAAATGTAA 59.926 47.619 0.00 0.00 0.00 2.41
3847 4196 2.291282 TGCGGGGAAGGTCAAATGTAAT 60.291 45.455 0.00 0.00 0.00 1.89
3848 4197 2.758423 GCGGGGAAGGTCAAATGTAATT 59.242 45.455 0.00 0.00 38.98 1.40
3849 4198 3.181490 GCGGGGAAGGTCAAATGTAATTC 60.181 47.826 0.00 0.00 33.67 2.17
3850 4199 4.013728 CGGGGAAGGTCAAATGTAATTCA 58.986 43.478 0.00 0.00 33.67 2.57
3851 4200 4.096382 CGGGGAAGGTCAAATGTAATTCAG 59.904 45.833 0.00 0.00 33.67 3.02
3852 4201 4.402474 GGGGAAGGTCAAATGTAATTCAGG 59.598 45.833 0.00 0.00 33.67 3.86
3853 4202 5.016831 GGGAAGGTCAAATGTAATTCAGGT 58.983 41.667 0.00 0.00 33.67 4.00
3854 4203 5.125578 GGGAAGGTCAAATGTAATTCAGGTC 59.874 44.000 0.00 0.00 33.67 3.85
3855 4204 5.710099 GGAAGGTCAAATGTAATTCAGGTCA 59.290 40.000 0.00 0.00 33.67 4.02
3856 4205 6.127897 GGAAGGTCAAATGTAATTCAGGTCAG 60.128 42.308 0.00 0.00 33.67 3.51
3857 4206 4.702131 AGGTCAAATGTAATTCAGGTCAGC 59.298 41.667 0.00 0.00 33.67 4.26
3858 4207 4.458989 GGTCAAATGTAATTCAGGTCAGCA 59.541 41.667 0.00 0.00 33.67 4.41
3859 4208 5.393962 GTCAAATGTAATTCAGGTCAGCAC 58.606 41.667 0.00 0.00 33.67 4.40
3860 4209 5.048782 GTCAAATGTAATTCAGGTCAGCACA 60.049 40.000 0.00 0.00 33.67 4.57
3861 4210 5.711506 TCAAATGTAATTCAGGTCAGCACAT 59.288 36.000 0.00 0.00 33.67 3.21
3862 4211 6.883756 TCAAATGTAATTCAGGTCAGCACATA 59.116 34.615 0.00 0.00 33.67 2.29
3863 4212 7.392953 TCAAATGTAATTCAGGTCAGCACATAA 59.607 33.333 0.00 0.00 33.67 1.90
3864 4213 7.701539 AATGTAATTCAGGTCAGCACATAAA 57.298 32.000 0.00 0.00 0.00 1.40
3865 4214 6.494893 TGTAATTCAGGTCAGCACATAAAC 57.505 37.500 0.00 0.00 0.00 2.01
3866 4215 4.685169 AATTCAGGTCAGCACATAAACG 57.315 40.909 0.00 0.00 0.00 3.60
3867 4216 2.831685 TCAGGTCAGCACATAAACGT 57.168 45.000 0.00 0.00 0.00 3.99
3868 4217 3.945981 TCAGGTCAGCACATAAACGTA 57.054 42.857 0.00 0.00 0.00 3.57
3869 4218 3.581755 TCAGGTCAGCACATAAACGTAC 58.418 45.455 0.00 0.00 0.00 3.67
3870 4219 3.257375 TCAGGTCAGCACATAAACGTACT 59.743 43.478 0.00 0.00 0.00 2.73
3871 4220 3.612860 CAGGTCAGCACATAAACGTACTC 59.387 47.826 0.00 0.00 0.00 2.59
3872 4221 2.928116 GGTCAGCACATAAACGTACTCC 59.072 50.000 0.00 0.00 0.00 3.85
3873 4222 2.928116 GTCAGCACATAAACGTACTCCC 59.072 50.000 0.00 0.00 0.00 4.30
3874 4223 2.829720 TCAGCACATAAACGTACTCCCT 59.170 45.455 0.00 0.00 0.00 4.20
3875 4224 3.119245 TCAGCACATAAACGTACTCCCTC 60.119 47.826 0.00 0.00 0.00 4.30
3876 4225 2.167900 AGCACATAAACGTACTCCCTCC 59.832 50.000 0.00 0.00 0.00 4.30
3877 4226 2.805845 CACATAAACGTACTCCCTCCG 58.194 52.381 0.00 0.00 0.00 4.63
3878 4227 2.424601 CACATAAACGTACTCCCTCCGA 59.575 50.000 0.00 0.00 0.00 4.55
3879 4228 3.067742 CACATAAACGTACTCCCTCCGAT 59.932 47.826 0.00 0.00 0.00 4.18
3880 4229 3.317430 ACATAAACGTACTCCCTCCGATC 59.683 47.826 0.00 0.00 0.00 3.69
3881 4230 1.109609 AAACGTACTCCCTCCGATCC 58.890 55.000 0.00 0.00 0.00 3.36
3882 4231 0.033796 AACGTACTCCCTCCGATCCA 60.034 55.000 0.00 0.00 0.00 3.41
3883 4232 0.185416 ACGTACTCCCTCCGATCCAT 59.815 55.000 0.00 0.00 0.00 3.41
3884 4233 1.422781 ACGTACTCCCTCCGATCCATA 59.577 52.381 0.00 0.00 0.00 2.74
3885 4234 2.041350 ACGTACTCCCTCCGATCCATAT 59.959 50.000 0.00 0.00 0.00 1.78
3886 4235 3.090037 CGTACTCCCTCCGATCCATATT 58.910 50.000 0.00 0.00 0.00 1.28
3887 4236 3.119459 CGTACTCCCTCCGATCCATATTG 60.119 52.174 0.00 0.00 0.00 1.90
3888 4237 1.625818 ACTCCCTCCGATCCATATTGC 59.374 52.381 0.00 0.00 0.00 3.56
3889 4238 1.905215 CTCCCTCCGATCCATATTGCT 59.095 52.381 0.00 0.00 0.00 3.91
3890 4239 2.304180 CTCCCTCCGATCCATATTGCTT 59.696 50.000 0.00 0.00 0.00 3.91
3891 4240 2.303022 TCCCTCCGATCCATATTGCTTC 59.697 50.000 0.00 0.00 0.00 3.86
3892 4241 2.616510 CCCTCCGATCCATATTGCTTCC 60.617 54.545 0.00 0.00 0.00 3.46
3893 4242 2.304180 CCTCCGATCCATATTGCTTCCT 59.696 50.000 0.00 0.00 0.00 3.36
3894 4243 3.332919 CTCCGATCCATATTGCTTCCTG 58.667 50.000 0.00 0.00 0.00 3.86
3895 4244 2.972021 TCCGATCCATATTGCTTCCTGA 59.028 45.455 0.00 0.00 0.00 3.86
3896 4245 3.007290 TCCGATCCATATTGCTTCCTGAG 59.993 47.826 0.00 0.00 0.00 3.35
3897 4246 3.244353 CCGATCCATATTGCTTCCTGAGT 60.244 47.826 0.00 0.00 0.00 3.41
3898 4247 4.021104 CCGATCCATATTGCTTCCTGAGTA 60.021 45.833 0.00 0.00 0.00 2.59
3899 4248 4.926238 CGATCCATATTGCTTCCTGAGTAC 59.074 45.833 0.00 0.00 0.00 2.73
3900 4249 5.279206 CGATCCATATTGCTTCCTGAGTACT 60.279 44.000 0.00 0.00 0.00 2.73
3901 4250 5.537300 TCCATATTGCTTCCTGAGTACTC 57.463 43.478 16.32 16.32 0.00 2.59
3902 4251 4.962362 TCCATATTGCTTCCTGAGTACTCA 59.038 41.667 23.80 23.80 38.06 3.41
3916 4265 6.544928 TGAGTACTCAGGAAATAATCTGCA 57.455 37.500 21.74 0.00 34.14 4.41
3917 4266 6.341316 TGAGTACTCAGGAAATAATCTGCAC 58.659 40.000 21.74 0.00 34.14 4.57
3918 4267 5.675538 AGTACTCAGGAAATAATCTGCACC 58.324 41.667 0.00 0.00 0.00 5.01
3919 4268 4.851639 ACTCAGGAAATAATCTGCACCT 57.148 40.909 0.00 0.00 0.00 4.00
3920 4269 4.521146 ACTCAGGAAATAATCTGCACCTG 58.479 43.478 8.96 8.96 44.02 4.00
3921 4270 4.018960 ACTCAGGAAATAATCTGCACCTGT 60.019 41.667 13.57 0.00 43.39 4.00
3922 4271 5.189736 ACTCAGGAAATAATCTGCACCTGTA 59.810 40.000 13.57 3.00 43.39 2.74
3923 4272 5.674525 TCAGGAAATAATCTGCACCTGTAG 58.325 41.667 13.57 0.00 43.39 2.74
3924 4273 5.425217 TCAGGAAATAATCTGCACCTGTAGA 59.575 40.000 13.57 0.00 43.39 2.59
3925 4274 6.070251 TCAGGAAATAATCTGCACCTGTAGAA 60.070 38.462 13.57 0.00 43.39 2.10
3926 4275 6.599244 CAGGAAATAATCTGCACCTGTAGAAA 59.401 38.462 7.40 0.00 40.08 2.52
3927 4276 7.284034 CAGGAAATAATCTGCACCTGTAGAAAT 59.716 37.037 7.40 0.00 40.08 2.17
3928 4277 7.284034 AGGAAATAATCTGCACCTGTAGAAATG 59.716 37.037 0.00 0.00 40.08 2.32
3929 4278 7.067494 GGAAATAATCTGCACCTGTAGAAATGT 59.933 37.037 0.00 0.00 40.08 2.71
3930 4279 7.559590 AATAATCTGCACCTGTAGAAATGTC 57.440 36.000 0.00 0.00 40.08 3.06
3931 4280 4.558226 ATCTGCACCTGTAGAAATGTCA 57.442 40.909 0.00 0.00 40.08 3.58
3932 4281 3.930336 TCTGCACCTGTAGAAATGTCAG 58.070 45.455 0.00 0.00 33.87 3.51
3933 4282 3.324846 TCTGCACCTGTAGAAATGTCAGT 59.675 43.478 0.00 0.00 33.87 3.41
3934 4283 4.067896 CTGCACCTGTAGAAATGTCAGTT 58.932 43.478 0.00 0.00 0.00 3.16
3935 4284 4.460263 TGCACCTGTAGAAATGTCAGTTT 58.540 39.130 0.00 0.00 0.00 2.66
3936 4285 4.275689 TGCACCTGTAGAAATGTCAGTTTG 59.724 41.667 0.00 0.00 0.00 2.93
3937 4286 4.515191 GCACCTGTAGAAATGTCAGTTTGA 59.485 41.667 0.00 0.00 0.00 2.69
3938 4287 5.008613 GCACCTGTAGAAATGTCAGTTTGAA 59.991 40.000 0.00 0.00 0.00 2.69
3939 4288 6.459573 GCACCTGTAGAAATGTCAGTTTGAAA 60.460 38.462 0.00 0.00 0.00 2.69
3940 4289 7.479980 CACCTGTAGAAATGTCAGTTTGAAAA 58.520 34.615 0.00 0.00 0.00 2.29
3941 4290 7.973388 CACCTGTAGAAATGTCAGTTTGAAAAA 59.027 33.333 0.00 0.00 0.00 1.94
3961 4310 2.041153 AAAAAGGCCCGTGCAGAAG 58.959 52.632 0.00 0.00 40.13 2.85
3978 4327 6.426937 GTGCAGAAGGAGTAAATGTCAGTTTA 59.573 38.462 0.00 0.00 0.00 2.01
3979 4328 6.995686 TGCAGAAGGAGTAAATGTCAGTTTAA 59.004 34.615 0.00 0.00 0.00 1.52
4001 4350 0.253327 AAAAAGGCCCCGTGCAAAAA 59.747 45.000 0.00 0.00 43.89 1.94
4003 4352 2.038814 AAAGGCCCCGTGCAAAAAGG 62.039 55.000 0.00 0.00 43.89 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 126 0.819666 TTTGGCCGCACACACACATA 60.820 50.000 0.00 0.00 0.00 2.29
104 147 1.045911 AGGAAAAAGGTTTGGCCGCA 61.046 50.000 0.00 0.00 43.70 5.69
105 148 0.105964 AAGGAAAAAGGTTTGGCCGC 59.894 50.000 0.00 0.00 43.70 6.53
106 149 2.613026 AAAGGAAAAAGGTTTGGCCG 57.387 45.000 0.00 0.00 43.70 6.13
135 178 1.660575 GGCCGATCACCGTATCACG 60.661 63.158 0.00 0.00 42.11 4.35
136 179 0.179094 TTGGCCGATCACCGTATCAC 60.179 55.000 0.00 0.00 36.31 3.06
138 181 0.935196 GTTTGGCCGATCACCGTATC 59.065 55.000 0.00 0.00 36.31 2.24
139 182 0.539986 AGTTTGGCCGATCACCGTAT 59.460 50.000 0.00 0.00 36.31 3.06
140 183 0.390603 CAGTTTGGCCGATCACCGTA 60.391 55.000 0.00 0.00 36.31 4.02
141 184 1.671054 CAGTTTGGCCGATCACCGT 60.671 57.895 0.00 0.00 36.31 4.83
143 186 2.046285 CCCAGTTTGGCCGATCACC 61.046 63.158 0.00 0.00 35.79 4.02
171 218 6.749216 ATCATCACGACGTTGATAACATAC 57.251 37.500 10.51 0.00 34.29 2.39
277 326 1.148273 AGTGGTGCTTTGAGGCGAA 59.852 52.632 0.00 0.00 34.52 4.70
278 327 1.597854 CAGTGGTGCTTTGAGGCGA 60.598 57.895 0.00 0.00 34.52 5.54
328 377 3.447586 TCCTATGAGACTCCTTTGAACCG 59.552 47.826 0.00 0.00 0.00 4.44
334 383 6.642733 TCCAAAATCCTATGAGACTCCTTT 57.357 37.500 0.00 0.00 0.00 3.11
340 472 7.557719 TCAAATCCTTCCAAAATCCTATGAGAC 59.442 37.037 0.00 0.00 0.00 3.36
342 474 7.886629 TCAAATCCTTCCAAAATCCTATGAG 57.113 36.000 0.00 0.00 0.00 2.90
394 526 6.859715 GATTTCAATCCTGTGAATCAAACG 57.140 37.500 0.00 0.00 37.36 3.60
429 562 3.624777 AGTGCAAATGGACCCTATGAAG 58.375 45.455 1.14 0.00 37.04 3.02
447 582 9.143631 GATGAAATTTTCCTCCAAAATGTAGTG 57.856 33.333 6.68 0.00 42.86 2.74
524 739 2.419159 GGCCTCTTTAATCCGTAACCGT 60.419 50.000 0.00 0.00 0.00 4.83
547 762 0.604243 ACTTGCGCCCACATCGTTTA 60.604 50.000 4.18 0.00 0.00 2.01
584 799 4.445545 CGCTTCTTTCGCCCGCAC 62.446 66.667 0.00 0.00 0.00 5.34
599 814 4.451652 GTCGCAAGCCAGCTTCGC 62.452 66.667 0.90 8.96 33.42 4.70
731 985 0.890996 GTGGGCAGTGAAGGTTCAGG 60.891 60.000 0.00 0.00 37.98 3.86
732 986 0.890996 GGTGGGCAGTGAAGGTTCAG 60.891 60.000 0.00 0.00 37.98 3.02
733 987 1.150536 GGTGGGCAGTGAAGGTTCA 59.849 57.895 0.00 0.00 34.20 3.18
734 988 1.603739 GGGTGGGCAGTGAAGGTTC 60.604 63.158 0.00 0.00 0.00 3.62
1234 1497 1.178534 GCGAGATCTGAGGAGAGGGG 61.179 65.000 0.00 0.00 0.00 4.79
1242 1505 1.297967 CGTCGGTGCGAGATCTGAG 60.298 63.158 0.00 0.00 36.23 3.35
1279 1542 0.609131 CAACCGACAGGCCCATTTCT 60.609 55.000 0.00 0.00 42.76 2.52
1280 1543 0.608035 TCAACCGACAGGCCCATTTC 60.608 55.000 0.00 0.00 42.76 2.17
1290 1553 5.068636 AGTTAACTCTAGTCTCAACCGACA 58.931 41.667 1.12 0.00 36.38 4.35
1306 1576 5.045578 AGCAACCACATCCATCTAGTTAACT 60.046 40.000 13.68 13.68 0.00 2.24
1316 1586 3.949754 CACTCATAAGCAACCACATCCAT 59.050 43.478 0.00 0.00 0.00 3.41
1323 1593 1.943968 GCCGACACTCATAAGCAACCA 60.944 52.381 0.00 0.00 0.00 3.67
1372 1649 9.174166 AGTTTATCAATCCAGTTAAAAGCGTAT 57.826 29.630 0.00 0.00 0.00 3.06
1390 1675 7.496346 AACCCTGTCAGAGATAAGTTTATCA 57.504 36.000 12.89 0.00 41.52 2.15
1399 1684 4.574674 ATGCAAAACCCTGTCAGAGATA 57.425 40.909 0.00 0.00 0.00 1.98
1402 1687 3.152341 AGAATGCAAAACCCTGTCAGAG 58.848 45.455 0.00 0.00 0.00 3.35
1410 1695 2.529632 AGGAAGGAGAATGCAAAACCC 58.470 47.619 0.00 0.00 0.00 4.11
1422 1707 0.679321 GAGCCCTGCAAAGGAAGGAG 60.679 60.000 6.62 0.00 43.45 3.69
1485 1770 9.319143 CTGGATAATACTGAACCTCTGTTAAAG 57.681 37.037 0.00 0.00 33.97 1.85
1491 1776 6.723298 AGACTGGATAATACTGAACCTCTG 57.277 41.667 0.00 0.00 0.00 3.35
1567 1852 1.406180 TGACGTCGTTCTCCAACAGAA 59.594 47.619 11.62 0.00 38.95 3.02
1572 1857 1.135527 ACAAGTGACGTCGTTCTCCAA 59.864 47.619 11.62 0.00 0.00 3.53
1662 1947 2.879103 AATTGTGTCGGAGGGTGATT 57.121 45.000 0.00 0.00 0.00 2.57
1691 1976 2.143876 ACAGGCATGTCAATAACCCC 57.856 50.000 0.00 0.00 32.99 4.95
1742 2027 8.473219 ACCAATTTGTTTTAACATTTTGGCAAT 58.527 25.926 23.32 11.41 45.56 3.56
1751 2036 5.526846 CACAGGCACCAATTTGTTTTAACAT 59.473 36.000 0.00 0.00 38.95 2.71
1756 2041 3.795877 CTCACAGGCACCAATTTGTTTT 58.204 40.909 0.00 0.00 0.00 2.43
1757 2042 2.483538 GCTCACAGGCACCAATTTGTTT 60.484 45.455 0.00 0.00 0.00 2.83
1775 2060 7.095732 GGTTACTACAAAACTTCAGTACTGCTC 60.096 40.741 18.45 0.00 0.00 4.26
1881 2166 6.566376 GCCTGATACTTAACTCGCTAGTAGTC 60.566 46.154 0.00 0.00 33.75 2.59
1888 2173 2.101582 CCAGCCTGATACTTAACTCGCT 59.898 50.000 0.00 0.00 0.00 4.93
2053 2363 8.965172 GCATCAAAACTCTGAGCAAATATAATG 58.035 33.333 4.19 0.93 0.00 1.90
2054 2364 8.910944 AGCATCAAAACTCTGAGCAAATATAAT 58.089 29.630 4.19 0.00 0.00 1.28
2055 2365 8.284945 AGCATCAAAACTCTGAGCAAATATAA 57.715 30.769 4.19 0.00 0.00 0.98
2056 2366 7.870509 AGCATCAAAACTCTGAGCAAATATA 57.129 32.000 4.19 0.00 0.00 0.86
2057 2367 6.770746 AGCATCAAAACTCTGAGCAAATAT 57.229 33.333 4.19 0.00 0.00 1.28
2058 2368 6.579666 AAGCATCAAAACTCTGAGCAAATA 57.420 33.333 4.19 0.00 0.00 1.40
2059 2369 5.464030 AAGCATCAAAACTCTGAGCAAAT 57.536 34.783 4.19 0.00 0.00 2.32
2060 2370 4.924305 AAGCATCAAAACTCTGAGCAAA 57.076 36.364 4.19 0.00 0.00 3.68
2061 2371 4.555313 CGAAAGCATCAAAACTCTGAGCAA 60.555 41.667 4.19 0.00 0.00 3.91
2062 2372 3.058708 CGAAAGCATCAAAACTCTGAGCA 60.059 43.478 4.19 0.00 0.00 4.26
2063 2373 3.058639 ACGAAAGCATCAAAACTCTGAGC 60.059 43.478 4.19 0.00 0.00 4.26
2064 2374 4.461405 CACGAAAGCATCAAAACTCTGAG 58.539 43.478 2.45 2.45 0.00 3.35
2065 2375 3.250762 CCACGAAAGCATCAAAACTCTGA 59.749 43.478 0.00 0.00 0.00 3.27
2083 2393 4.937696 TTGTTCACATTAGCATACCACG 57.062 40.909 0.00 0.00 0.00 4.94
2112 2423 6.155475 AGAACTACAGCATCATAAGTCCTC 57.845 41.667 0.00 0.00 0.00 3.71
2179 2490 9.953697 CATTACTGAACAGAGGTAGTAATAGTC 57.046 37.037 8.87 0.00 41.74 2.59
2200 2511 8.587952 AATTTTGGCAGTTCAGTTTACATTAC 57.412 30.769 0.00 0.00 0.00 1.89
2224 2535 8.548877 ACAGCCTCTGTTCCTAAATATAAGAAA 58.451 33.333 0.00 0.00 42.59 2.52
2247 2558 7.041780 GGATGGTATTGCACATAAGAAGTACAG 60.042 40.741 0.00 0.00 0.00 2.74
2389 2701 3.902467 GGGAGTAATCACCCCTTACTAGG 59.098 52.174 0.00 0.00 39.04 3.02
2500 2812 2.032528 TGCAGGTGTGGTGCTAGC 59.967 61.111 8.10 8.10 41.78 3.42
2634 2946 7.969314 TGTGAAAAGGAATTTACAACAAAAGC 58.031 30.769 0.00 0.00 0.00 3.51
2667 2979 5.239306 CAGTCAACATAGCCTCAAAACAGAA 59.761 40.000 0.00 0.00 0.00 3.02
2674 2986 4.365514 TTTCCAGTCAACATAGCCTCAA 57.634 40.909 0.00 0.00 0.00 3.02
2761 3073 3.070018 AGGAGATCAACAAACTGCTTCG 58.930 45.455 0.00 0.00 0.00 3.79
3089 3401 1.154112 CGGTGTGGTAAAATGCCGC 60.154 57.895 0.00 0.00 37.06 6.53
3092 3404 0.878416 TGCTCGGTGTGGTAAAATGC 59.122 50.000 0.00 0.00 0.00 3.56
3124 3443 2.222886 CAAACATTACACGTGGACCCA 58.777 47.619 21.57 0.00 0.00 4.51
3154 3473 4.537135 TCAACTGGGACAACTCATAGTC 57.463 45.455 0.00 0.00 38.70 2.59
3155 3474 4.348168 ACTTCAACTGGGACAACTCATAGT 59.652 41.667 0.00 0.00 38.70 2.12
3156 3475 4.899502 ACTTCAACTGGGACAACTCATAG 58.100 43.478 0.00 0.00 38.70 2.23
3304 3637 5.050023 TGTGCATTACTGAATTTCGACGAAA 60.050 36.000 23.98 23.98 35.94 3.46
3309 3642 5.643348 AGATGTGTGCATTACTGAATTTCGA 59.357 36.000 0.00 0.00 35.07 3.71
3356 3689 6.586463 GGTAAAAATAGCTTGAACCTTGAAGC 59.414 38.462 0.00 1.36 45.86 3.86
3357 3690 7.657336 TGGTAAAAATAGCTTGAACCTTGAAG 58.343 34.615 0.00 0.00 0.00 3.02
3358 3691 7.589958 TGGTAAAAATAGCTTGAACCTTGAA 57.410 32.000 0.00 0.00 0.00 2.69
3359 3692 6.294508 GCTGGTAAAAATAGCTTGAACCTTGA 60.295 38.462 0.00 0.00 34.70 3.02
3360 3693 5.863935 GCTGGTAAAAATAGCTTGAACCTTG 59.136 40.000 0.00 0.00 34.70 3.61
3361 3694 5.538433 TGCTGGTAAAAATAGCTTGAACCTT 59.462 36.000 0.00 0.00 38.25 3.50
3364 3697 5.402398 CCTGCTGGTAAAAATAGCTTGAAC 58.598 41.667 0.51 0.00 38.25 3.18
3391 3724 5.690464 AGTAAAGCAAGATCTGTCTCCAT 57.310 39.130 0.00 0.00 32.15 3.41
3431 3776 2.076100 GCGTCATCTTGGTGAACATCA 58.924 47.619 0.00 0.00 0.00 3.07
3432 3777 2.076100 TGCGTCATCTTGGTGAACATC 58.924 47.619 0.00 0.00 0.00 3.06
3433 3778 1.806542 GTGCGTCATCTTGGTGAACAT 59.193 47.619 0.00 0.00 0.00 2.71
3434 3779 1.225855 GTGCGTCATCTTGGTGAACA 58.774 50.000 0.00 0.00 0.00 3.18
3435 3780 1.225855 TGTGCGTCATCTTGGTGAAC 58.774 50.000 0.00 0.00 0.00 3.18
3436 3781 2.076100 GATGTGCGTCATCTTGGTGAA 58.924 47.619 12.47 0.00 46.64 3.18
3437 3782 1.725641 GATGTGCGTCATCTTGGTGA 58.274 50.000 12.47 0.00 46.64 4.02
3449 3794 4.041049 CACTAGCTCTAAGAAGATGTGCG 58.959 47.826 0.00 0.00 0.00 5.34
3490 3835 6.238374 GCTAACATAAATAGTGCACATTCCGT 60.238 38.462 21.04 10.98 0.00 4.69
3508 3853 3.264193 TGAAGGTGTCTCCATGCTAACAT 59.736 43.478 0.00 0.00 39.02 2.71
3537 3882 1.901464 GTGCCTCCGCCCTTCAAAA 60.901 57.895 0.00 0.00 0.00 2.44
3552 3900 6.145696 CACTGAACAGTACTAACTTAAGGTGC 59.854 42.308 2.38 0.00 40.20 5.01
3602 3950 8.494016 AAACAAATGGTATTCCGTTTCAAAAA 57.506 26.923 5.64 0.00 46.38 1.94
3603 3951 8.391106 CAAAACAAATGGTATTCCGTTTCAAAA 58.609 29.630 5.64 0.00 46.38 2.44
3604 3952 7.011482 CCAAAACAAATGGTATTCCGTTTCAAA 59.989 33.333 5.64 0.00 46.38 2.69
3605 3953 6.480320 CCAAAACAAATGGTATTCCGTTTCAA 59.520 34.615 5.64 0.00 46.38 2.69
3606 3954 5.986135 CCAAAACAAATGGTATTCCGTTTCA 59.014 36.000 5.64 0.00 46.38 2.69
3607 3955 5.107259 GCCAAAACAAATGGTATTCCGTTTC 60.107 40.000 5.64 0.00 46.38 2.78
3609 3957 4.039852 AGCCAAAACAAATGGTATTCCGTT 59.960 37.500 0.00 0.00 43.99 4.44
3610 3958 3.576550 AGCCAAAACAAATGGTATTCCGT 59.423 39.130 0.00 0.00 40.23 4.69
3611 3959 4.186856 AGCCAAAACAAATGGTATTCCG 57.813 40.909 0.00 0.00 40.23 4.30
3612 3960 5.179182 CACAAGCCAAAACAAATGGTATTCC 59.821 40.000 0.00 0.00 40.23 3.01
3613 3961 5.757808 ACACAAGCCAAAACAAATGGTATTC 59.242 36.000 0.00 0.00 40.23 1.75
3614 3962 5.679601 ACACAAGCCAAAACAAATGGTATT 58.320 33.333 0.00 0.00 40.23 1.89
3615 3963 5.289083 ACACAAGCCAAAACAAATGGTAT 57.711 34.783 0.00 0.00 40.23 2.73
3616 3964 4.744795 ACACAAGCCAAAACAAATGGTA 57.255 36.364 0.00 0.00 40.23 3.25
3617 3965 3.625649 ACACAAGCCAAAACAAATGGT 57.374 38.095 0.00 0.00 40.23 3.55
3687 4036 1.067635 CGCCTGGTGCAGCTTTTATTT 60.068 47.619 18.08 0.00 41.33 1.40
3790 4139 7.929941 AATTACTTTTGACTTTGCCCAAAAA 57.070 28.000 0.00 0.00 40.41 1.94
3791 4140 7.929941 AAATTACTTTTGACTTTGCCCAAAA 57.070 28.000 0.00 0.00 39.19 2.44
3792 4141 9.620259 AATAAATTACTTTTGACTTTGCCCAAA 57.380 25.926 0.00 0.00 0.00 3.28
3793 4142 9.620259 AAATAAATTACTTTTGACTTTGCCCAA 57.380 25.926 0.00 0.00 0.00 4.12
3811 4160 8.710239 ACCTTCCCCGCAATAAATAAATAAATT 58.290 29.630 0.00 0.00 0.00 1.82
3812 4161 8.257602 ACCTTCCCCGCAATAAATAAATAAAT 57.742 30.769 0.00 0.00 0.00 1.40
3813 4162 7.342284 TGACCTTCCCCGCAATAAATAAATAAA 59.658 33.333 0.00 0.00 0.00 1.40
3814 4163 6.834451 TGACCTTCCCCGCAATAAATAAATAA 59.166 34.615 0.00 0.00 0.00 1.40
3815 4164 6.366340 TGACCTTCCCCGCAATAAATAAATA 58.634 36.000 0.00 0.00 0.00 1.40
3816 4165 5.205056 TGACCTTCCCCGCAATAAATAAAT 58.795 37.500 0.00 0.00 0.00 1.40
3817 4166 4.601084 TGACCTTCCCCGCAATAAATAAA 58.399 39.130 0.00 0.00 0.00 1.40
3818 4167 4.237976 TGACCTTCCCCGCAATAAATAA 57.762 40.909 0.00 0.00 0.00 1.40
3819 4168 3.935818 TGACCTTCCCCGCAATAAATA 57.064 42.857 0.00 0.00 0.00 1.40
3820 4169 2.818751 TGACCTTCCCCGCAATAAAT 57.181 45.000 0.00 0.00 0.00 1.40
3821 4170 2.588464 TTGACCTTCCCCGCAATAAA 57.412 45.000 0.00 0.00 0.00 1.40
3822 4171 2.588464 TTTGACCTTCCCCGCAATAA 57.412 45.000 0.00 0.00 0.00 1.40
3823 4172 2.291282 ACATTTGACCTTCCCCGCAATA 60.291 45.455 0.00 0.00 0.00 1.90
3824 4173 1.185315 CATTTGACCTTCCCCGCAAT 58.815 50.000 0.00 0.00 0.00 3.56
3825 4174 0.178975 ACATTTGACCTTCCCCGCAA 60.179 50.000 0.00 0.00 0.00 4.85
3826 4175 0.693622 TACATTTGACCTTCCCCGCA 59.306 50.000 0.00 0.00 0.00 5.69
3827 4176 1.828979 TTACATTTGACCTTCCCCGC 58.171 50.000 0.00 0.00 0.00 6.13
3828 4177 4.013728 TGAATTACATTTGACCTTCCCCG 58.986 43.478 0.00 0.00 0.00 5.73
3829 4178 4.402474 CCTGAATTACATTTGACCTTCCCC 59.598 45.833 0.00 0.00 0.00 4.81
3830 4179 5.016831 ACCTGAATTACATTTGACCTTCCC 58.983 41.667 0.00 0.00 0.00 3.97
3831 4180 5.710099 TGACCTGAATTACATTTGACCTTCC 59.290 40.000 0.00 0.00 0.00 3.46
3832 4181 6.623767 GCTGACCTGAATTACATTTGACCTTC 60.624 42.308 0.00 0.00 0.00 3.46
3833 4182 5.183904 GCTGACCTGAATTACATTTGACCTT 59.816 40.000 0.00 0.00 0.00 3.50
3834 4183 4.702131 GCTGACCTGAATTACATTTGACCT 59.298 41.667 0.00 0.00 0.00 3.85
3835 4184 4.458989 TGCTGACCTGAATTACATTTGACC 59.541 41.667 0.00 0.00 0.00 4.02
3836 4185 5.048782 TGTGCTGACCTGAATTACATTTGAC 60.049 40.000 0.00 0.00 0.00 3.18
3837 4186 5.069318 TGTGCTGACCTGAATTACATTTGA 58.931 37.500 0.00 0.00 0.00 2.69
3838 4187 5.375417 TGTGCTGACCTGAATTACATTTG 57.625 39.130 0.00 0.00 0.00 2.32
3839 4188 7.701539 TTATGTGCTGACCTGAATTACATTT 57.298 32.000 0.00 0.00 0.00 2.32
3840 4189 7.538575 GTTTATGTGCTGACCTGAATTACATT 58.461 34.615 0.00 0.00 0.00 2.71
3841 4190 6.183360 CGTTTATGTGCTGACCTGAATTACAT 60.183 38.462 0.00 0.00 0.00 2.29
3842 4191 5.121611 CGTTTATGTGCTGACCTGAATTACA 59.878 40.000 0.00 0.00 0.00 2.41
3843 4192 5.121768 ACGTTTATGTGCTGACCTGAATTAC 59.878 40.000 0.00 0.00 0.00 1.89
3844 4193 5.242434 ACGTTTATGTGCTGACCTGAATTA 58.758 37.500 0.00 0.00 0.00 1.40
3845 4194 4.072131 ACGTTTATGTGCTGACCTGAATT 58.928 39.130 0.00 0.00 0.00 2.17
3846 4195 3.674997 ACGTTTATGTGCTGACCTGAAT 58.325 40.909 0.00 0.00 0.00 2.57
3847 4196 3.120321 ACGTTTATGTGCTGACCTGAA 57.880 42.857 0.00 0.00 0.00 3.02
3848 4197 2.831685 ACGTTTATGTGCTGACCTGA 57.168 45.000 0.00 0.00 0.00 3.86
3849 4198 3.585862 AGTACGTTTATGTGCTGACCTG 58.414 45.455 0.00 0.00 33.31 4.00
3850 4199 3.368116 GGAGTACGTTTATGTGCTGACCT 60.368 47.826 0.00 0.00 34.80 3.85
3851 4200 2.928116 GGAGTACGTTTATGTGCTGACC 59.072 50.000 0.00 0.00 34.80 4.02
3852 4201 2.928116 GGGAGTACGTTTATGTGCTGAC 59.072 50.000 0.00 0.00 34.80 3.51
3853 4202 2.829720 AGGGAGTACGTTTATGTGCTGA 59.170 45.455 0.00 0.00 34.80 4.26
3854 4203 3.187700 GAGGGAGTACGTTTATGTGCTG 58.812 50.000 0.00 0.00 34.80 4.41
3855 4204 2.167900 GGAGGGAGTACGTTTATGTGCT 59.832 50.000 0.00 0.00 37.52 4.40
3856 4205 2.547826 GGAGGGAGTACGTTTATGTGC 58.452 52.381 0.00 0.00 0.00 4.57
3857 4206 2.424601 TCGGAGGGAGTACGTTTATGTG 59.575 50.000 0.00 0.00 0.00 3.21
3858 4207 2.726821 TCGGAGGGAGTACGTTTATGT 58.273 47.619 0.00 0.00 0.00 2.29
3859 4208 3.305199 GGATCGGAGGGAGTACGTTTATG 60.305 52.174 0.00 0.00 0.00 1.90
3860 4209 2.889678 GGATCGGAGGGAGTACGTTTAT 59.110 50.000 0.00 0.00 0.00 1.40
3861 4210 2.301346 GGATCGGAGGGAGTACGTTTA 58.699 52.381 0.00 0.00 0.00 2.01
3862 4211 1.109609 GGATCGGAGGGAGTACGTTT 58.890 55.000 0.00 0.00 0.00 3.60
3863 4212 0.033796 TGGATCGGAGGGAGTACGTT 60.034 55.000 0.00 0.00 0.00 3.99
3864 4213 0.185416 ATGGATCGGAGGGAGTACGT 59.815 55.000 0.00 0.00 0.00 3.57
3865 4214 2.195741 TATGGATCGGAGGGAGTACG 57.804 55.000 0.00 0.00 0.00 3.67
3866 4215 3.368531 GCAATATGGATCGGAGGGAGTAC 60.369 52.174 0.00 0.00 0.00 2.73
3867 4216 2.832129 GCAATATGGATCGGAGGGAGTA 59.168 50.000 0.00 0.00 0.00 2.59
3868 4217 1.625818 GCAATATGGATCGGAGGGAGT 59.374 52.381 0.00 0.00 0.00 3.85
3869 4218 1.905215 AGCAATATGGATCGGAGGGAG 59.095 52.381 0.00 0.00 0.00 4.30
3870 4219 2.030027 AGCAATATGGATCGGAGGGA 57.970 50.000 0.00 0.00 0.00 4.20
3871 4220 2.616510 GGAAGCAATATGGATCGGAGGG 60.617 54.545 0.00 0.00 0.00 4.30
3872 4221 2.304180 AGGAAGCAATATGGATCGGAGG 59.696 50.000 0.00 0.00 0.00 4.30
3873 4222 3.007290 TCAGGAAGCAATATGGATCGGAG 59.993 47.826 0.00 0.00 0.00 4.63
3874 4223 2.972021 TCAGGAAGCAATATGGATCGGA 59.028 45.455 0.00 0.00 0.00 4.55
3875 4224 3.244353 ACTCAGGAAGCAATATGGATCGG 60.244 47.826 0.00 0.00 0.00 4.18
3876 4225 4.000331 ACTCAGGAAGCAATATGGATCG 58.000 45.455 0.00 0.00 0.00 3.69
3877 4226 6.107901 AGTACTCAGGAAGCAATATGGATC 57.892 41.667 0.00 0.00 0.00 3.36
3878 4227 5.604231 TGAGTACTCAGGAAGCAATATGGAT 59.396 40.000 21.74 0.00 34.14 3.41
3879 4228 4.962362 TGAGTACTCAGGAAGCAATATGGA 59.038 41.667 21.74 0.00 34.14 3.41
3880 4229 5.282055 TGAGTACTCAGGAAGCAATATGG 57.718 43.478 21.74 0.00 34.14 2.74
3893 4242 6.341316 GTGCAGATTATTTCCTGAGTACTCA 58.659 40.000 23.80 23.80 38.06 3.41
3894 4243 5.755861 GGTGCAGATTATTTCCTGAGTACTC 59.244 44.000 16.32 16.32 32.37 2.59
3895 4244 5.426833 AGGTGCAGATTATTTCCTGAGTACT 59.573 40.000 0.00 0.00 32.37 2.73
3896 4245 5.525378 CAGGTGCAGATTATTTCCTGAGTAC 59.475 44.000 9.52 0.00 43.28 2.73
3897 4246 5.189736 ACAGGTGCAGATTATTTCCTGAGTA 59.810 40.000 19.31 0.00 43.28 2.59
3898 4247 4.018960 ACAGGTGCAGATTATTTCCTGAGT 60.019 41.667 19.31 0.00 43.28 3.41
3899 4248 4.521146 ACAGGTGCAGATTATTTCCTGAG 58.479 43.478 19.31 0.00 43.28 3.35
3900 4249 4.574674 ACAGGTGCAGATTATTTCCTGA 57.425 40.909 19.31 0.00 43.28 3.86
3901 4250 5.674525 TCTACAGGTGCAGATTATTTCCTG 58.325 41.667 12.74 12.74 45.24 3.86
3902 4251 5.957771 TCTACAGGTGCAGATTATTTCCT 57.042 39.130 0.00 0.00 0.00 3.36
3903 4252 7.067494 ACATTTCTACAGGTGCAGATTATTTCC 59.933 37.037 0.00 0.00 0.00 3.13
3904 4253 7.989826 ACATTTCTACAGGTGCAGATTATTTC 58.010 34.615 0.00 0.00 0.00 2.17
3905 4254 7.611467 TGACATTTCTACAGGTGCAGATTATTT 59.389 33.333 0.00 0.00 0.00 1.40
3906 4255 7.112122 TGACATTTCTACAGGTGCAGATTATT 58.888 34.615 0.00 0.00 0.00 1.40
3907 4256 6.653020 TGACATTTCTACAGGTGCAGATTAT 58.347 36.000 0.00 0.00 0.00 1.28
3908 4257 6.048732 TGACATTTCTACAGGTGCAGATTA 57.951 37.500 0.00 0.00 0.00 1.75
3909 4258 4.910195 TGACATTTCTACAGGTGCAGATT 58.090 39.130 0.00 0.00 0.00 2.40
3910 4259 4.019860 ACTGACATTTCTACAGGTGCAGAT 60.020 41.667 0.00 0.00 36.17 2.90
3911 4260 3.324846 ACTGACATTTCTACAGGTGCAGA 59.675 43.478 0.00 0.00 36.17 4.26
3912 4261 3.668447 ACTGACATTTCTACAGGTGCAG 58.332 45.455 0.00 0.00 36.17 4.41
3913 4262 3.769739 ACTGACATTTCTACAGGTGCA 57.230 42.857 0.00 0.00 36.17 4.57
3914 4263 4.515191 TCAAACTGACATTTCTACAGGTGC 59.485 41.667 0.00 0.00 36.17 5.01
3915 4264 6.618287 TTCAAACTGACATTTCTACAGGTG 57.382 37.500 0.00 0.00 36.17 4.00
3916 4265 7.639113 TTTTCAAACTGACATTTCTACAGGT 57.361 32.000 0.00 0.00 36.17 4.00
3943 4292 1.463553 CCTTCTGCACGGGCCTTTTT 61.464 55.000 7.46 0.00 40.13 1.94
3944 4293 1.903404 CCTTCTGCACGGGCCTTTT 60.903 57.895 7.46 0.00 40.13 2.27
3945 4294 2.282462 CCTTCTGCACGGGCCTTT 60.282 61.111 7.46 0.00 40.13 3.11
3946 4295 3.249189 TCCTTCTGCACGGGCCTT 61.249 61.111 7.46 0.00 40.13 4.35
3949 4298 0.321298 TTTACTCCTTCTGCACGGGC 60.321 55.000 0.34 0.34 41.68 6.13
3987 4336 2.915137 TCCTTTTTGCACGGGGCC 60.915 61.111 0.00 0.00 43.89 5.80
3988 4337 2.200337 ACTCCTTTTTGCACGGGGC 61.200 57.895 0.00 0.00 45.13 5.80
3989 4338 1.659794 CACTCCTTTTTGCACGGGG 59.340 57.895 0.00 0.00 0.00 5.73
3996 4345 2.493278 CTGTATGGGCCACTCCTTTTTG 59.507 50.000 9.28 0.00 34.39 2.44
4001 4350 0.983378 GACCTGTATGGGCCACTCCT 60.983 60.000 9.28 0.00 38.13 3.69


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

AutoCloner maintained by Alex Coulton.