Multiple sequence alignment - TraesCS4D01G350500

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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 TraesCS4D01G350500 chr4D 100.000 5516 0 0 1 5516 502707459 502712974 0.000000e+00 10187.0
1 TraesCS4D01G350500 chr4D 75.367 613 91 34 4454 5032 502725705 502726291 1.990000e-59 241.0
2 TraesCS4D01G350500 chr5A 88.053 5692 341 163 42 5516 687147917 687153486 0.000000e+00 6431.0
3 TraesCS4D01G350500 chr5A 77.295 414 64 21 5116 5515 687160934 687161331 3.350000e-52 217.0
4 TraesCS4D01G350500 chr5A 79.433 282 37 6 4554 4822 687160404 687160677 4.390000e-41 180.0
5 TraesCS4D01G350500 chr5A 100.000 34 0 0 484 517 687148402 687148435 4.610000e-06 63.9
6 TraesCS4D01G350500 chr4B 90.426 1901 131 36 1448 3312 647623176 647625061 0.000000e+00 2455.0
7 TraesCS4D01G350500 chr4B 82.414 1450 151 47 4120 5516 647625884 647627282 0.000000e+00 1170.0
8 TraesCS4D01G350500 chr4B 89.570 930 51 19 554 1451 647622221 647623136 0.000000e+00 1138.0
9 TraesCS4D01G350500 chr4B 84.123 718 62 36 3337 4016 647625115 647625818 0.000000e+00 647.0
10 TraesCS4D01G350500 chr4B 84.698 464 30 10 1 435 647621627 647622078 5.110000e-115 425.0
11 TraesCS4D01G350500 chr2B 79.885 870 157 13 2180 3043 446081469 446082326 6.070000e-174 621.0
12 TraesCS4D01G350500 chr2A 79.862 869 155 16 2182 3043 508031562 508032417 7.850000e-173 617.0
13 TraesCS4D01G350500 chr2D 79.632 869 161 11 2180 3043 375593926 375594783 1.310000e-170 610.0
14 TraesCS4D01G350500 chr7D 84.000 125 16 4 2908 3030 4794787 4794909 3.490000e-22 117.0
15 TraesCS4D01G350500 chr4A 82.576 132 19 4 2901 3030 738888596 738888467 4.520000e-21 113.0
16 TraesCS4D01G350500 chr4A 88.136 59 7 0 2169 2227 738961913 738961971 2.760000e-08 71.3


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 TraesCS4D01G350500 chr4D 502707459 502712974 5515 False 10187 10187 100.0000 1 5516 1 chr4D.!!$F1 5515
1 TraesCS4D01G350500 chr4D 502725705 502726291 586 False 241 241 75.3670 4454 5032 1 chr4D.!!$F2 578
2 TraesCS4D01G350500 chr5A 687147917 687153486 5569 False 6431 6431 88.0530 42 5516 1 chr5A.!!$F1 5474
3 TraesCS4D01G350500 chr4B 647621627 647627282 5655 False 1167 2455 86.2462 1 5516 5 chr4B.!!$F1 5515
4 TraesCS4D01G350500 chr2B 446081469 446082326 857 False 621 621 79.8850 2180 3043 1 chr2B.!!$F1 863
5 TraesCS4D01G350500 chr2A 508031562 508032417 855 False 617 617 79.8620 2182 3043 1 chr2A.!!$F1 861
6 TraesCS4D01G350500 chr2D 375593926 375594783 857 False 610 610 79.6320 2180 3043 1 chr2D.!!$F1 863

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
774 919 0.324943 ACTTGACCCTTGACCGGATG 59.675 55.0 9.46 0.00 0.00 3.51 F
1361 1526 0.249447 TCCGTAATGCCGATGCTGAG 60.249 55.0 0.00 0.00 38.71 3.35 F
2112 2377 0.033503 TAGGATGGCCACTCGAGACA 60.034 55.0 21.68 12.44 36.29 3.41 F
3062 3356 0.100146 CGTCCTTACTACGTGCTCCC 59.900 60.0 0.00 0.00 35.66 4.30 F
3289 3583 0.109342 ACTTTGAGGTCACTGGCCTG 59.891 55.0 7.01 8.29 36.29 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 2123 0.678048 AGGAATTGGGTCGCAGAAGC 60.678 55.0 0.00 0.00 39.69 3.86 R
3071 3365 0.904865 TGATGAACCGAGCAGAGGGT 60.905 55.0 0.00 0.00 38.44 4.34 R
3666 4028 0.318699 TGAAACGAGGAGTGCACGAG 60.319 55.0 12.01 4.93 0.00 4.18 R
4431 4817 0.035343 TCACCCCGTTGTTGAACACA 60.035 50.0 0.00 0.00 31.78 3.72 R
5136 5622 1.112113 ATCCCACTACCAGTACTGCG 58.888 55.0 17.86 12.86 0.00 5.18 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
31 32 1.142870 CACTTTTCCCTCCACTGTCCA 59.857 52.381 0.00 0.00 0.00 4.02
32 33 1.421646 ACTTTTCCCTCCACTGTCCAG 59.578 52.381 0.00 0.00 0.00 3.86
220 249 5.012354 TCCACAGTTAAATAGGACCGAAACT 59.988 40.000 0.00 0.00 0.00 2.66
226 255 9.460906 CAGTTAAATAGGACCGAAACTATCTAC 57.539 37.037 0.00 0.00 0.00 2.59
227 256 9.418839 AGTTAAATAGGACCGAAACTATCTACT 57.581 33.333 0.00 0.00 0.00 2.57
230 259 7.432350 AATAGGACCGAAACTATCTACTACG 57.568 40.000 0.00 0.00 0.00 3.51
231 260 5.028549 AGGACCGAAACTATCTACTACGA 57.971 43.478 0.00 0.00 0.00 3.43
232 261 4.813697 AGGACCGAAACTATCTACTACGAC 59.186 45.833 0.00 0.00 0.00 4.34
233 262 4.813697 GGACCGAAACTATCTACTACGACT 59.186 45.833 0.00 0.00 0.00 4.18
277 306 1.005450 TGGCCTTGTGGTAGAATTCCC 59.995 52.381 3.32 0.00 35.27 3.97
278 307 1.685180 GGCCTTGTGGTAGAATTCCCC 60.685 57.143 0.65 3.26 35.27 4.81
279 308 1.685180 GCCTTGTGGTAGAATTCCCCC 60.685 57.143 0.65 2.88 35.27 5.40
326 360 2.095567 GTGCTGACATGACAATGACACC 60.096 50.000 0.00 0.00 34.25 4.16
398 439 1.109609 TGCAAGACATGTTGGTGCAA 58.890 45.000 22.30 11.15 41.95 4.08
400 441 2.063266 GCAAGACATGTTGGTGCAATG 58.937 47.619 18.89 0.00 35.28 2.82
402 443 3.311106 CAAGACATGTTGGTGCAATGTC 58.689 45.455 17.09 17.09 41.21 3.06
517 634 6.616947 TGTTTTCATCGACAGTCAAGTTTTT 58.383 32.000 0.41 0.00 0.00 1.94
518 635 6.526325 TGTTTTCATCGACAGTCAAGTTTTTG 59.474 34.615 0.41 0.00 35.57 2.44
519 636 5.811399 TTCATCGACAGTCAAGTTTTTGT 57.189 34.783 0.41 0.00 35.73 2.83
520 637 5.811399 TCATCGACAGTCAAGTTTTTGTT 57.189 34.783 0.41 0.00 35.73 2.83
521 638 5.806286 TCATCGACAGTCAAGTTTTTGTTC 58.194 37.500 0.41 0.00 35.73 3.18
522 639 5.584649 TCATCGACAGTCAAGTTTTTGTTCT 59.415 36.000 0.41 0.00 35.73 3.01
523 640 5.464965 TCGACAGTCAAGTTTTTGTTCTC 57.535 39.130 0.41 0.00 35.73 2.87
524 641 4.331717 TCGACAGTCAAGTTTTTGTTCTCC 59.668 41.667 0.41 0.00 35.73 3.71
525 642 4.332819 CGACAGTCAAGTTTTTGTTCTCCT 59.667 41.667 0.41 0.00 35.73 3.69
526 643 5.163754 CGACAGTCAAGTTTTTGTTCTCCTT 60.164 40.000 0.41 0.00 35.73 3.36
527 644 6.590234 ACAGTCAAGTTTTTGTTCTCCTTT 57.410 33.333 0.00 0.00 35.73 3.11
528 645 6.993079 ACAGTCAAGTTTTTGTTCTCCTTTT 58.007 32.000 0.00 0.00 35.73 2.27
529 646 7.441836 ACAGTCAAGTTTTTGTTCTCCTTTTT 58.558 30.769 0.00 0.00 35.73 1.94
549 666 2.900716 TTTTCTTTCTTTTGCGGGGG 57.099 45.000 0.00 0.00 0.00 5.40
563 680 4.599036 GGGGGTGCAGTCAAGTTT 57.401 55.556 0.00 0.00 0.00 2.66
564 681 2.820845 GGGGGTGCAGTCAAGTTTT 58.179 52.632 0.00 0.00 0.00 2.43
565 682 0.389025 GGGGGTGCAGTCAAGTTTTG 59.611 55.000 0.00 0.00 0.00 2.44
566 683 1.111277 GGGGTGCAGTCAAGTTTTGT 58.889 50.000 0.00 0.00 0.00 2.83
567 684 2.303175 GGGGTGCAGTCAAGTTTTGTA 58.697 47.619 0.00 0.00 0.00 2.41
568 685 2.890945 GGGGTGCAGTCAAGTTTTGTAT 59.109 45.455 0.00 0.00 0.00 2.29
574 691 6.363473 GTGCAGTCAAGTTTTGTATACTCAC 58.637 40.000 4.17 0.00 0.00 3.51
610 727 5.641155 AGGGAATAAAACACAGCTTTACCT 58.359 37.500 0.00 0.00 0.00 3.08
682 815 9.865321 GACAAACTAGTGATACTATTTGGTACA 57.135 33.333 0.00 0.00 35.70 2.90
770 915 2.841215 TGTAAACTTGACCCTTGACCG 58.159 47.619 0.00 0.00 0.00 4.79
771 916 2.148768 GTAAACTTGACCCTTGACCGG 58.851 52.381 0.00 0.00 0.00 5.28
772 917 0.841289 AAACTTGACCCTTGACCGGA 59.159 50.000 9.46 0.00 0.00 5.14
773 918 1.064825 AACTTGACCCTTGACCGGAT 58.935 50.000 9.46 0.00 0.00 4.18
774 919 0.324943 ACTTGACCCTTGACCGGATG 59.675 55.000 9.46 0.00 0.00 3.51
856 1003 3.201726 TGCAAAATTCTAAGCAGCGTC 57.798 42.857 0.00 0.00 32.48 5.19
888 1035 5.626543 CACATGCGGCATATAGAAAATTCAC 59.373 40.000 16.21 0.00 0.00 3.18
1131 1292 2.044946 GTGCCGGCCTCCATTCTT 60.045 61.111 26.77 0.00 0.00 2.52
1209 1370 0.543749 AGATACCCACTGCTCTTGCC 59.456 55.000 0.00 0.00 38.71 4.52
1231 1392 3.516615 GGACTTGTCTGAATCTTCTCCG 58.483 50.000 0.61 0.00 0.00 4.63
1232 1393 3.516615 GACTTGTCTGAATCTTCTCCGG 58.483 50.000 0.00 0.00 0.00 5.14
1233 1394 2.275318 CTTGTCTGAATCTTCTCCGGC 58.725 52.381 0.00 0.00 0.00 6.13
1234 1395 0.537188 TGTCTGAATCTTCTCCGGCC 59.463 55.000 0.00 0.00 0.00 6.13
1251 1412 0.462759 GCCTGTTTATGCTCCGCTCT 60.463 55.000 0.00 0.00 0.00 4.09
1261 1422 1.074752 GCTCCGCTCTGTCTTCAAAG 58.925 55.000 0.00 0.00 0.00 2.77
1281 1442 5.699097 AAGTAGATATGGCTCTCGTTCTC 57.301 43.478 0.00 0.00 0.00 2.87
1295 1456 4.388773 TCTCGTTCTCAAATACACACATGC 59.611 41.667 0.00 0.00 0.00 4.06
1361 1526 0.249447 TCCGTAATGCCGATGCTGAG 60.249 55.000 0.00 0.00 38.71 3.35
1415 1581 4.091945 CGGATACAACATCACAGACAACAG 59.908 45.833 0.00 0.00 0.00 3.16
1515 1724 2.948979 CCAAGTGTTAGTTTGACCAGCA 59.051 45.455 0.00 0.00 0.00 4.41
1533 1742 0.602562 CAAAAAGATTGCAGCCCGGA 59.397 50.000 0.73 0.00 0.00 5.14
1596 1807 2.454538 CCGTGTTAGTTAGGGAGTCCT 58.545 52.381 9.58 0.00 46.96 3.85
1615 1826 2.030451 CCTGCAGCTGTTTTCTTCTTCC 60.030 50.000 16.64 0.00 0.00 3.46
1712 1924 1.300481 TGCCACGAATCGTTGTTCAA 58.700 45.000 5.20 0.00 38.32 2.69
1789 2016 8.567948 AGTTGTTTTATGTGTCCTCTAATTGTG 58.432 33.333 0.00 0.00 0.00 3.33
1842 2073 4.392940 CTTGTCTCTTTGGGTGTCTGATT 58.607 43.478 0.00 0.00 0.00 2.57
1844 2075 2.485814 GTCTCTTTGGGTGTCTGATTGC 59.514 50.000 0.00 0.00 0.00 3.56
1906 2137 2.575893 TACGGCTTCTGCGACCCAA 61.576 57.895 0.00 0.00 40.82 4.12
2028 2260 9.425577 AGACCAAATTTAAGTTTTGTTTTTCGA 57.574 25.926 2.37 0.00 33.23 3.71
2103 2368 4.096681 CAGTGTATAGGATAGGATGGCCA 58.903 47.826 8.56 8.56 36.29 5.36
2104 2369 4.081420 CAGTGTATAGGATAGGATGGCCAC 60.081 50.000 8.16 1.35 36.29 5.01
2105 2370 4.097418 GTGTATAGGATAGGATGGCCACT 58.903 47.826 8.16 3.79 36.29 4.00
2106 2371 4.160626 GTGTATAGGATAGGATGGCCACTC 59.839 50.000 8.16 7.14 36.29 3.51
2109 2374 0.605589 GGATAGGATGGCCACTCGAG 59.394 60.000 8.16 11.84 36.29 4.04
2112 2377 0.033503 TAGGATGGCCACTCGAGACA 60.034 55.000 21.68 12.44 36.29 3.41
2116 2386 1.734465 GATGGCCACTCGAGACAAAAG 59.266 52.381 21.68 1.72 0.00 2.27
2154 2437 2.676839 CAGCTAGCTGACATGTTTGAGG 59.323 50.000 36.47 7.18 46.30 3.86
2156 2439 2.938756 GCTAGCTGACATGTTTGAGGCT 60.939 50.000 7.70 8.29 33.19 4.58
2172 2463 1.119684 GGCTTGGTTTTGGAACAGGT 58.880 50.000 0.00 0.00 42.39 4.00
2202 2493 0.991920 ACAAGGGATGGTACCACCTG 59.008 55.000 21.63 17.93 39.58 4.00
2316 2607 2.420568 CGCCATCAAGCCCAGCATT 61.421 57.895 0.00 0.00 0.00 3.56
2641 2932 2.731571 GCCATCCTGTACCGGAGCA 61.732 63.158 9.46 5.37 36.31 4.26
3062 3356 0.100146 CGTCCTTACTACGTGCTCCC 59.900 60.000 0.00 0.00 35.66 4.30
3074 3368 2.832498 GCTCCCCAGCATCTACCC 59.168 66.667 0.00 0.00 46.06 3.69
3076 3370 1.763546 GCTCCCCAGCATCTACCCTC 61.764 65.000 0.00 0.00 46.06 4.30
3078 3372 0.399091 TCCCCAGCATCTACCCTCTG 60.399 60.000 0.00 0.00 0.00 3.35
3083 3377 1.112315 AGCATCTACCCTCTGCTCGG 61.112 60.000 0.00 0.00 42.35 4.63
3084 3378 1.395826 GCATCTACCCTCTGCTCGGT 61.396 60.000 0.00 0.00 36.08 4.69
3086 3380 1.067821 CATCTACCCTCTGCTCGGTTC 59.932 57.143 0.00 0.00 33.36 3.62
3088 3382 1.115467 CTACCCTCTGCTCGGTTCAT 58.885 55.000 0.00 0.00 33.36 2.57
3089 3383 1.067821 CTACCCTCTGCTCGGTTCATC 59.932 57.143 0.00 0.00 33.36 2.92
3091 3385 0.467384 CCCTCTGCTCGGTTCATCAT 59.533 55.000 0.00 0.00 0.00 2.45
3093 3387 0.935898 CTCTGCTCGGTTCATCATGC 59.064 55.000 0.00 0.00 0.00 4.06
3095 3389 1.134310 TCTGCTCGGTTCATCATGCAT 60.134 47.619 0.00 0.00 0.00 3.96
3098 3392 2.212652 GCTCGGTTCATCATGCATACA 58.787 47.619 0.00 0.00 0.00 2.29
3100 3394 3.721035 CTCGGTTCATCATGCATACAGA 58.279 45.455 0.00 0.00 0.00 3.41
3103 3397 4.122046 CGGTTCATCATGCATACAGAAGA 58.878 43.478 0.00 0.00 0.00 2.87
3104 3398 4.210746 CGGTTCATCATGCATACAGAAGAG 59.789 45.833 0.00 0.00 0.00 2.85
3108 3402 8.090831 GGTTCATCATGCATACAGAAGAGTATA 58.909 37.037 0.00 0.00 33.12 1.47
3109 3403 9.650539 GTTCATCATGCATACAGAAGAGTATAT 57.349 33.333 0.00 0.00 33.12 0.86
3289 3583 0.109342 ACTTTGAGGTCACTGGCCTG 59.891 55.000 7.01 8.29 36.29 4.85
3323 3617 1.903860 TCAGTACCACCACCATGTACC 59.096 52.381 0.00 0.00 36.38 3.34
3356 3679 1.006314 GAGTGCAGTCAGTGTCGCTC 61.006 60.000 16.85 0.00 34.72 5.03
3510 3855 3.038710 GCTTGCAACTCTCGTTTTCAAG 58.961 45.455 0.00 10.25 40.48 3.02
3517 3862 2.289133 ACTCTCGTTTTCAAGCTCCCTC 60.289 50.000 0.00 0.00 0.00 4.30
3518 3863 1.971357 TCTCGTTTTCAAGCTCCCTCT 59.029 47.619 0.00 0.00 0.00 3.69
3519 3864 2.368875 TCTCGTTTTCAAGCTCCCTCTT 59.631 45.455 0.00 0.00 0.00 2.85
3520 3865 3.576982 TCTCGTTTTCAAGCTCCCTCTTA 59.423 43.478 0.00 0.00 0.00 2.10
3521 3866 3.660865 TCGTTTTCAAGCTCCCTCTTAC 58.339 45.455 0.00 0.00 0.00 2.34
3522 3867 3.070446 TCGTTTTCAAGCTCCCTCTTACA 59.930 43.478 0.00 0.00 0.00 2.41
3523 3868 3.433615 CGTTTTCAAGCTCCCTCTTACAG 59.566 47.826 0.00 0.00 0.00 2.74
3553 3902 3.054948 TCACACATCTGCATCATCCTCAA 60.055 43.478 0.00 0.00 0.00 3.02
3554 3903 3.064958 CACACATCTGCATCATCCTCAAC 59.935 47.826 0.00 0.00 0.00 3.18
3555 3904 2.617308 CACATCTGCATCATCCTCAACC 59.383 50.000 0.00 0.00 0.00 3.77
3556 3905 2.508716 ACATCTGCATCATCCTCAACCT 59.491 45.455 0.00 0.00 0.00 3.50
3573 3922 3.417069 ACCTCACGATTTGAATGGTCA 57.583 42.857 0.00 0.00 28.58 4.02
3580 3929 5.240403 TCACGATTTGAATGGTCATTTGTCA 59.760 36.000 0.00 0.00 32.48 3.58
3584 3933 6.128035 CGATTTGAATGGTCATTTGTCACCTA 60.128 38.462 0.00 0.00 32.48 3.08
3585 3934 5.957842 TTGAATGGTCATTTGTCACCTAC 57.042 39.130 0.00 0.00 32.48 3.18
3586 3935 4.000325 TGAATGGTCATTTGTCACCTACG 59.000 43.478 0.00 0.00 33.36 3.51
3587 3936 3.973206 ATGGTCATTTGTCACCTACGA 57.027 42.857 0.00 0.00 33.36 3.43
3588 3937 3.034721 TGGTCATTTGTCACCTACGAC 57.965 47.619 0.00 0.00 36.40 4.34
3589 3938 2.631062 TGGTCATTTGTCACCTACGACT 59.369 45.455 0.00 0.00 36.82 4.18
3590 3939 3.827876 TGGTCATTTGTCACCTACGACTA 59.172 43.478 0.00 0.00 36.82 2.59
3591 3940 4.171754 GGTCATTTGTCACCTACGACTAC 58.828 47.826 0.00 0.00 36.82 2.73
3592 3941 4.082354 GGTCATTTGTCACCTACGACTACT 60.082 45.833 0.00 0.00 36.82 2.57
3593 3942 5.124457 GGTCATTTGTCACCTACGACTACTA 59.876 44.000 0.00 0.00 36.82 1.82
3594 3943 6.256686 GTCATTTGTCACCTACGACTACTAG 58.743 44.000 0.00 0.00 36.82 2.57
3604 3953 3.940657 ACGACTACTAGTACATCACGC 57.059 47.619 0.00 0.00 0.00 5.34
3606 3955 3.686241 ACGACTACTAGTACATCACGCAA 59.314 43.478 0.00 0.00 0.00 4.85
3665 4027 2.455674 TGTTGGTCCAGATTCGTCAG 57.544 50.000 0.00 0.00 0.00 3.51
3666 4028 1.079503 GTTGGTCCAGATTCGTCAGC 58.920 55.000 0.00 0.00 0.00 4.26
3702 4064 5.043248 CGTTTCATTTCCAAACAAGCTTCT 58.957 37.500 0.00 0.00 33.99 2.85
3703 4065 5.519927 CGTTTCATTTCCAAACAAGCTTCTT 59.480 36.000 0.00 0.00 33.99 2.52
3704 4066 6.291796 CGTTTCATTTCCAAACAAGCTTCTTC 60.292 38.462 0.00 0.00 33.99 2.87
3718 4080 4.557705 AGCTTCTTCCCTGGCTAATACTA 58.442 43.478 0.00 0.00 32.94 1.82
3724 4086 6.017192 TCTTCCCTGGCTAATACTAATCGAT 58.983 40.000 0.00 0.00 0.00 3.59
3725 4087 5.916661 TCCCTGGCTAATACTAATCGATC 57.083 43.478 0.00 0.00 0.00 3.69
3726 4088 4.398358 TCCCTGGCTAATACTAATCGATCG 59.602 45.833 9.36 9.36 0.00 3.69
3727 4089 4.398358 CCCTGGCTAATACTAATCGATCGA 59.602 45.833 21.86 21.86 0.00 3.59
3769 4140 1.536943 GGAGGTGAGCTTCGAGGTGT 61.537 60.000 0.00 0.00 0.00 4.16
4016 4387 4.314522 TCACCACATCTCTCTCTCTCTT 57.685 45.455 0.00 0.00 0.00 2.85
4019 4390 4.462132 CACCACATCTCTCTCTCTCTTTCA 59.538 45.833 0.00 0.00 0.00 2.69
4020 4391 4.462483 ACCACATCTCTCTCTCTCTTTCAC 59.538 45.833 0.00 0.00 0.00 3.18
4026 4397 1.748493 CTCTCTCTCTTTCACCTCCCG 59.252 57.143 0.00 0.00 0.00 5.14
4036 4407 2.297698 TCACCTCCCGTCAACTTCTA 57.702 50.000 0.00 0.00 0.00 2.10
4071 4451 8.279970 TGTCCATAGATTTCAAGTGTAAATGG 57.720 34.615 0.00 0.00 0.00 3.16
4074 4454 8.112822 TCCATAGATTTCAAGTGTAAATGGGAA 58.887 33.333 0.00 0.00 0.00 3.97
4102 4485 8.040716 AGTATTGCCAGTACATTTTAACTCAC 57.959 34.615 0.00 0.00 0.00 3.51
4105 4488 4.759693 TGCCAGTACATTTTAACTCACCTG 59.240 41.667 0.00 0.00 0.00 4.00
4113 4496 6.981722 ACATTTTAACTCACCTGACCATTTC 58.018 36.000 0.00 0.00 0.00 2.17
4221 4604 1.390565 TTCGTCCGGGAAGATCTCTC 58.609 55.000 13.46 0.00 0.00 3.20
4239 4622 2.229062 TCTCTGAGAAGCTTGGTACGTG 59.771 50.000 2.10 0.00 0.00 4.49
4243 4626 1.461127 GAGAAGCTTGGTACGTGCAAG 59.539 52.381 2.10 8.47 0.00 4.01
4244 4627 1.202651 AGAAGCTTGGTACGTGCAAGT 60.203 47.619 10.83 10.83 0.00 3.16
4247 4631 0.941542 GCTTGGTACGTGCAAGTTCA 59.058 50.000 11.38 7.46 0.00 3.18
4265 4649 8.550376 GCAAGTTCATTTGTAACATCATTTTGT 58.450 29.630 0.00 0.00 0.00 2.83
4272 4656 9.897744 CATTTGTAACATCATTTTGTCTAGTGT 57.102 29.630 0.00 0.00 0.00 3.55
4304 4690 5.938322 TCAAAGGAGTATTTGAATTGCGTC 58.062 37.500 0.00 0.00 44.14 5.19
4312 4698 1.300481 TTGAATTGCGTCGACCAACA 58.700 45.000 17.86 11.64 0.00 3.33
4315 4701 3.067833 TGAATTGCGTCGACCAACATTA 58.932 40.909 17.86 7.70 0.00 1.90
4320 4706 4.491234 TGCGTCGACCAACATTAATTTT 57.509 36.364 10.58 0.00 0.00 1.82
4338 4724 5.682943 ATTTTTGTTTTCAGATCGACCGA 57.317 34.783 0.00 0.00 0.00 4.69
4422 4808 2.508439 GCGATCGGGAAAGACGCA 60.508 61.111 18.30 0.00 46.75 5.24
4425 4811 1.683790 CGATCGGGAAAGACGCACAC 61.684 60.000 7.38 0.00 0.00 3.82
4431 4817 2.433436 GGGAAAGACGCACACCTTTAT 58.567 47.619 0.00 0.00 33.23 1.40
4518 4914 5.132502 CCAATGATGAATGGTGCCTAAGTA 58.867 41.667 0.00 0.00 31.84 2.24
4519 4915 5.240183 CCAATGATGAATGGTGCCTAAGTAG 59.760 44.000 0.00 0.00 31.84 2.57
4520 4916 5.636903 ATGATGAATGGTGCCTAAGTAGT 57.363 39.130 0.00 0.00 0.00 2.73
4521 4917 6.747414 ATGATGAATGGTGCCTAAGTAGTA 57.253 37.500 0.00 0.00 0.00 1.82
4522 4918 6.747414 TGATGAATGGTGCCTAAGTAGTAT 57.253 37.500 0.00 0.00 0.00 2.12
4523 4919 7.849322 TGATGAATGGTGCCTAAGTAGTATA 57.151 36.000 0.00 0.00 0.00 1.47
4524 4920 8.435931 TGATGAATGGTGCCTAAGTAGTATAT 57.564 34.615 0.00 0.00 0.00 0.86
4525 4921 9.541884 TGATGAATGGTGCCTAAGTAGTATATA 57.458 33.333 0.00 0.00 0.00 0.86
4526 4922 9.804758 GATGAATGGTGCCTAAGTAGTATATAC 57.195 37.037 4.60 4.60 0.00 1.47
4527 4923 8.130671 TGAATGGTGCCTAAGTAGTATATACC 57.869 38.462 9.32 0.00 0.00 2.73
4655 5056 8.514330 AAGTGGTTAGAGAAATTTGTTGTACA 57.486 30.769 0.00 0.00 0.00 2.90
4708 5109 0.832626 ACATGATGATCCCACGCTGA 59.167 50.000 0.00 0.00 0.00 4.26
4712 5122 1.134699 TGATGATCCCACGCTGAAGAC 60.135 52.381 0.00 0.00 0.00 3.01
4863 5306 2.229062 CTCGGTGAAGTCAGAAGCACTA 59.771 50.000 0.00 0.00 0.00 2.74
4864 5307 2.229062 TCGGTGAAGTCAGAAGCACTAG 59.771 50.000 0.00 0.00 0.00 2.57
4865 5308 2.029828 CGGTGAAGTCAGAAGCACTAGT 60.030 50.000 0.00 0.00 0.00 2.57
4866 5309 3.553096 CGGTGAAGTCAGAAGCACTAGTT 60.553 47.826 0.00 0.00 0.00 2.24
4867 5310 4.381411 GGTGAAGTCAGAAGCACTAGTTT 58.619 43.478 0.00 0.00 0.00 2.66
4876 5319 7.178628 AGTCAGAAGCACTAGTTTCCTTGTATA 59.821 37.037 0.00 0.00 35.79 1.47
4883 5326 6.313164 GCACTAGTTTCCTTGTATAAGTCACC 59.687 42.308 0.00 0.00 31.80 4.02
4884 5327 7.383687 CACTAGTTTCCTTGTATAAGTCACCA 58.616 38.462 0.00 0.00 31.80 4.17
5058 5544 8.658609 TGCAGATTATTCTTTTTGCAAATAAGC 58.341 29.630 13.65 10.73 33.58 3.09
5062 5548 7.954788 TTATTCTTTTTGCAAATAAGCGGTT 57.045 28.000 13.65 4.76 37.31 4.44
5136 5622 7.806409 TGAAAAAGGTTAGTGGTAGGTTTAC 57.194 36.000 0.00 0.00 0.00 2.01
5186 5672 7.330946 ACATGATCGTGATTAAGTTCGAAAAGA 59.669 33.333 21.75 0.00 35.99 2.52
5261 5748 7.964604 ATGTTGTCCTGAAAAGAAGTACTAC 57.035 36.000 0.00 0.00 0.00 2.73
5392 5895 2.037053 CCGAATTGCACCCACAACA 58.963 52.632 0.00 0.00 31.03 3.33
5417 5920 1.298602 CACTGCACTGCACAACACTA 58.701 50.000 0.00 0.00 33.79 2.74
5419 5922 1.875514 ACTGCACTGCACAACACTATG 59.124 47.619 0.00 0.00 33.79 2.23
5422 5925 2.687425 TGCACTGCACAACACTATGTTT 59.313 40.909 0.00 0.00 33.81 2.83
5423 5926 3.879892 TGCACTGCACAACACTATGTTTA 59.120 39.130 0.00 0.00 33.81 2.01
5424 5927 4.518590 TGCACTGCACAACACTATGTTTAT 59.481 37.500 0.00 0.00 33.81 1.40
5459 5962 3.944650 TGTTTTGGTAGCGCATACATCAT 59.055 39.130 11.47 0.00 35.96 2.45
5470 5973 7.258022 AGCGCATACATCATGTGTAATTTAA 57.742 32.000 11.47 0.00 45.87 1.52
5473 5976 9.051027 GCGCATACATCATGTGTAATTTAATAC 57.949 33.333 0.30 0.00 45.87 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.073199 AGTGGAGGGAAAAGTGGCG 59.927 57.895 0.00 0.00 0.00 5.69
12 13 1.421646 CTGGACAGTGGAGGGAAAAGT 59.578 52.381 0.00 0.00 0.00 2.66
20 21 4.281182 ACACTTACTTACTGGACAGTGGAG 59.719 45.833 14.86 13.72 42.52 3.86
31 32 7.870954 TGATGATTTCGTTGACACTTACTTACT 59.129 33.333 0.00 0.00 0.00 2.24
32 33 8.014322 TGATGATTTCGTTGACACTTACTTAC 57.986 34.615 0.00 0.00 0.00 2.34
175 203 4.427312 GAAAAATGCAGTAATGCTCAGGG 58.573 43.478 17.03 0.00 35.49 4.45
233 262 5.866335 GAGAAAAGTCTCTGACTCGTAGA 57.134 43.478 0.42 0.00 45.99 2.59
277 306 3.027533 TCCAAGAGGATGAAGGGGG 57.972 57.895 0.00 0.00 39.61 5.40
343 377 4.262164 GCCAGAACATTCAACTTGGTCATT 60.262 41.667 0.00 0.00 33.09 2.57
398 439 5.817296 TCATGCAGCTAAGTTATTTCGACAT 59.183 36.000 0.00 0.00 0.00 3.06
400 441 5.718649 TCATGCAGCTAAGTTATTTCGAC 57.281 39.130 0.00 0.00 0.00 4.20
402 443 6.718388 TCATTCATGCAGCTAAGTTATTTCG 58.282 36.000 0.00 0.00 0.00 3.46
529 646 3.186702 CCCCCGCAAAAGAAAGAAAAA 57.813 42.857 0.00 0.00 0.00 1.94
530 647 2.900716 CCCCCGCAAAAGAAAGAAAA 57.099 45.000 0.00 0.00 0.00 2.29
546 663 0.389025 CAAAACTTGACTGCACCCCC 59.611 55.000 0.00 0.00 0.00 5.40
547 664 1.111277 ACAAAACTTGACTGCACCCC 58.889 50.000 0.00 0.00 0.00 4.95
548 665 4.760204 AGTATACAAAACTTGACTGCACCC 59.240 41.667 5.50 0.00 0.00 4.61
549 666 5.468746 TGAGTATACAAAACTTGACTGCACC 59.531 40.000 5.50 0.00 0.00 5.01
550 667 6.363473 GTGAGTATACAAAACTTGACTGCAC 58.637 40.000 5.50 0.00 0.00 4.57
551 668 5.176774 CGTGAGTATACAAAACTTGACTGCA 59.823 40.000 5.50 0.00 0.00 4.41
552 669 5.404366 TCGTGAGTATACAAAACTTGACTGC 59.596 40.000 5.50 0.00 0.00 4.40
553 670 7.402811 TTCGTGAGTATACAAAACTTGACTG 57.597 36.000 5.50 0.00 0.00 3.51
554 671 8.333186 GTTTTCGTGAGTATACAAAACTTGACT 58.667 33.333 15.82 0.00 33.65 3.41
555 672 8.333186 AGTTTTCGTGAGTATACAAAACTTGAC 58.667 33.333 18.32 5.63 37.92 3.18
556 673 8.428186 AGTTTTCGTGAGTATACAAAACTTGA 57.572 30.769 18.32 1.81 37.92 3.02
557 674 9.155053 GAAGTTTTCGTGAGTATACAAAACTTG 57.845 33.333 29.55 8.46 42.85 3.16
655 786 9.865321 GTACCAAATAGTATCACTAGTTTGTCA 57.135 33.333 6.54 0.74 36.93 3.58
656 787 9.865321 TGTACCAAATAGTATCACTAGTTTGTC 57.135 33.333 6.54 2.21 36.93 3.18
657 788 9.871238 CTGTACCAAATAGTATCACTAGTTTGT 57.129 33.333 0.00 7.91 36.93 2.83
658 789 9.871238 ACTGTACCAAATAGTATCACTAGTTTG 57.129 33.333 0.00 0.00 36.93 2.93
661 792 7.772292 TCGACTGTACCAAATAGTATCACTAGT 59.228 37.037 0.00 0.00 33.66 2.57
723 868 3.508845 AGTTTGGTTGCTACTCCATGT 57.491 42.857 0.00 0.00 33.50 3.21
724 869 4.201950 GCATAGTTTGGTTGCTACTCCATG 60.202 45.833 0.00 0.00 33.50 3.66
725 870 3.947834 GCATAGTTTGGTTGCTACTCCAT 59.052 43.478 0.00 0.00 33.50 3.41
726 871 3.343617 GCATAGTTTGGTTGCTACTCCA 58.656 45.455 0.00 0.00 33.61 3.86
727 872 2.683362 GGCATAGTTTGGTTGCTACTCC 59.317 50.000 0.00 0.00 36.62 3.85
770 915 1.152881 GGCACCACTCCATCCATCC 60.153 63.158 0.00 0.00 0.00 3.51
771 916 0.749454 GTGGCACCACTCCATCCATC 60.749 60.000 12.66 0.00 43.12 3.51
772 917 1.304282 GTGGCACCACTCCATCCAT 59.696 57.895 12.66 0.00 43.12 3.41
773 918 2.756400 GTGGCACCACTCCATCCA 59.244 61.111 12.66 0.00 43.12 3.41
888 1035 2.594962 GCGCGTATGACCAATCGGG 61.595 63.158 8.43 0.00 44.81 5.14
1011 1172 2.048316 GGCGCAACCACCCATTTG 60.048 61.111 10.83 0.00 38.86 2.32
1209 1370 3.516615 GGAGAAGATTCAGACAAGTCCG 58.483 50.000 0.00 0.00 0.00 4.79
1251 1412 6.460261 CGAGAGCCATATCTACTTTGAAGACA 60.460 42.308 0.00 0.00 0.00 3.41
1261 1422 5.440234 TTGAGAACGAGAGCCATATCTAC 57.560 43.478 0.00 0.00 0.00 2.59
1281 1442 6.144854 GGCTACATATGCATGTGTGTATTTG 58.855 40.000 32.07 17.88 45.17 2.32
1295 1456 4.753610 CCTGACATGTTCTGGCTACATATG 59.246 45.833 0.00 0.00 36.60 1.78
1361 1526 3.549070 ACGAACAGAACACACGTCTAAAC 59.451 43.478 0.00 0.00 31.69 2.01
1472 1681 5.528320 TGGCTACAAACTAACCACAAACTAC 59.472 40.000 0.00 0.00 0.00 2.73
1515 1724 0.603065 GTCCGGGCTGCAATCTTTTT 59.397 50.000 0.00 0.00 0.00 1.94
1596 1807 2.620115 CTGGAAGAAGAAAACAGCTGCA 59.380 45.455 15.27 0.00 34.07 4.41
1615 1826 3.185391 GCTCGACTTTTCTCAAGGAACTG 59.815 47.826 0.00 0.00 40.86 3.16
1755 1967 9.227777 GAGGACACATAAAACAACTATTAAGGT 57.772 33.333 0.00 0.00 0.00 3.50
1756 1968 9.449719 AGAGGACACATAAAACAACTATTAAGG 57.550 33.333 0.00 0.00 0.00 2.69
1763 1975 8.567948 CACAATTAGAGGACACATAAAACAACT 58.432 33.333 0.00 0.00 0.00 3.16
1766 1978 8.729756 CATCACAATTAGAGGACACATAAAACA 58.270 33.333 0.00 0.00 0.00 2.83
1767 1979 7.698130 GCATCACAATTAGAGGACACATAAAAC 59.302 37.037 0.00 0.00 0.00 2.43
1768 1980 7.611467 AGCATCACAATTAGAGGACACATAAAA 59.389 33.333 0.00 0.00 0.00 1.52
1770 1982 6.653020 AGCATCACAATTAGAGGACACATAA 58.347 36.000 0.00 0.00 0.00 1.90
1772 1984 5.108187 AGCATCACAATTAGAGGACACAT 57.892 39.130 0.00 0.00 0.00 3.21
1773 1985 4.558226 AGCATCACAATTAGAGGACACA 57.442 40.909 0.00 0.00 0.00 3.72
1774 1986 4.095483 CCAAGCATCACAATTAGAGGACAC 59.905 45.833 0.00 0.00 0.00 3.67
1776 1988 4.265073 ACCAAGCATCACAATTAGAGGAC 58.735 43.478 0.00 0.00 0.00 3.85
1778 1990 4.946157 AGAACCAAGCATCACAATTAGAGG 59.054 41.667 0.00 0.00 0.00 3.69
1779 1991 7.615582 TTAGAACCAAGCATCACAATTAGAG 57.384 36.000 0.00 0.00 0.00 2.43
1780 1992 8.579850 AATTAGAACCAAGCATCACAATTAGA 57.420 30.769 0.00 0.00 0.00 2.10
1783 2010 8.806146 AGTTAATTAGAACCAAGCATCACAATT 58.194 29.630 0.00 0.00 0.00 2.32
1789 2016 9.476202 AAAACAAGTTAATTAGAACCAAGCATC 57.524 29.630 0.00 0.00 0.00 3.91
1820 2051 3.475566 TCAGACACCCAAAGAGACAAG 57.524 47.619 0.00 0.00 0.00 3.16
1844 2075 2.745884 TTGCCGTCCCAGCAATCG 60.746 61.111 0.00 0.00 44.95 3.34
1866 2097 2.820197 CCATTCGGATCTGGAGTCGATA 59.180 50.000 0.62 0.00 34.24 2.92
1892 2123 0.678048 AGGAATTGGGTCGCAGAAGC 60.678 55.000 0.00 0.00 39.69 3.86
1906 2137 6.252995 AGAAGACAGAGACAAGTAGAGGAAT 58.747 40.000 0.00 0.00 0.00 3.01
2068 2300 6.472016 TCCTATACACTGCACATCTTTTTCA 58.528 36.000 0.00 0.00 0.00 2.69
2075 2307 5.984695 TCCTATCCTATACACTGCACATC 57.015 43.478 0.00 0.00 0.00 3.06
2078 2310 4.621747 GCCATCCTATCCTATACACTGCAC 60.622 50.000 0.00 0.00 0.00 4.57
2103 2368 3.733337 AGTTGCATCTTTTGTCTCGAGT 58.267 40.909 13.13 0.00 0.00 4.18
2104 2369 4.024556 ACAAGTTGCATCTTTTGTCTCGAG 60.025 41.667 5.93 5.93 0.00 4.04
2105 2370 3.876914 ACAAGTTGCATCTTTTGTCTCGA 59.123 39.130 7.31 0.00 0.00 4.04
2106 2371 3.970610 CACAAGTTGCATCTTTTGTCTCG 59.029 43.478 13.28 2.50 31.84 4.04
2154 2437 1.068588 GGACCTGTTCCAAAACCAAGC 59.931 52.381 0.00 0.00 45.10 4.01
2156 2439 1.394618 CGGACCTGTTCCAAAACCAA 58.605 50.000 0.00 0.00 46.29 3.67
2172 2463 2.307768 CATCCCTTGTAGTAGAGCGGA 58.692 52.381 0.00 0.00 0.00 5.54
2175 2466 3.321396 GGTACCATCCCTTGTAGTAGAGC 59.679 52.174 7.15 0.00 0.00 4.09
2202 2493 3.558533 CCTTGGGGTTGTACTGGTAGAAC 60.559 52.174 10.91 10.91 38.24 3.01
2298 2589 2.345880 GAATGCTGGGCTTGATGGCG 62.346 60.000 0.00 0.00 42.84 5.69
2316 2607 2.747460 CCGTACTGGTCGGTCGGA 60.747 66.667 12.27 0.00 43.22 4.55
2641 2932 1.062488 ACCCAGTGCTTGAAGTCCCT 61.062 55.000 0.00 0.00 0.00 4.20
2777 3068 2.942710 TCTTGAGCACGTACTTGTAGC 58.057 47.619 0.93 0.00 0.00 3.58
3070 3364 1.112113 GATGAACCGAGCAGAGGGTA 58.888 55.000 0.00 0.00 34.85 3.69
3071 3365 0.904865 TGATGAACCGAGCAGAGGGT 60.905 55.000 0.00 0.00 38.44 4.34
3074 3368 0.935898 GCATGATGAACCGAGCAGAG 59.064 55.000 0.00 0.00 0.00 3.35
3076 3370 1.306148 ATGCATGATGAACCGAGCAG 58.694 50.000 0.00 0.00 35.26 4.24
3078 3372 2.212652 TGTATGCATGATGAACCGAGC 58.787 47.619 10.16 0.00 0.00 5.03
3083 3377 7.959689 ATACTCTTCTGTATGCATGATGAAC 57.040 36.000 10.16 0.00 32.51 3.18
3108 3402 5.889853 AGCACAACCAATCAGTTCATCATAT 59.110 36.000 0.00 0.00 0.00 1.78
3109 3403 5.124297 CAGCACAACCAATCAGTTCATCATA 59.876 40.000 0.00 0.00 0.00 2.15
3110 3404 4.082408 CAGCACAACCAATCAGTTCATCAT 60.082 41.667 0.00 0.00 0.00 2.45
3111 3405 3.253921 CAGCACAACCAATCAGTTCATCA 59.746 43.478 0.00 0.00 0.00 3.07
3112 3406 3.829948 CAGCACAACCAATCAGTTCATC 58.170 45.455 0.00 0.00 0.00 2.92
3289 3583 1.477295 GTACTGACCTGGTAGGACTGC 59.523 57.143 0.00 0.00 37.67 4.40
3313 3607 5.057149 GGATTTAGCAGTAGGTACATGGTG 58.943 45.833 0.00 0.00 0.00 4.17
3314 3608 4.202223 CGGATTTAGCAGTAGGTACATGGT 60.202 45.833 0.00 0.00 0.00 3.55
3323 3617 3.119291 CTGCACTCGGATTTAGCAGTAG 58.881 50.000 0.00 0.00 45.57 2.57
3356 3679 3.019799 TGGACCAGAAGCTACCTAGAG 57.980 52.381 0.00 0.00 0.00 2.43
3510 3855 5.351740 GTGAATGTAAACTGTAAGAGGGAGC 59.648 44.000 0.00 0.00 37.43 4.70
3517 3862 7.017645 GCAGATGTGTGAATGTAAACTGTAAG 58.982 38.462 0.00 0.00 42.29 2.34
3518 3863 6.484977 TGCAGATGTGTGAATGTAAACTGTAA 59.515 34.615 0.00 0.00 0.00 2.41
3519 3864 5.994668 TGCAGATGTGTGAATGTAAACTGTA 59.005 36.000 0.00 0.00 0.00 2.74
3520 3865 4.821260 TGCAGATGTGTGAATGTAAACTGT 59.179 37.500 0.00 0.00 0.00 3.55
3521 3866 5.361135 TGCAGATGTGTGAATGTAAACTG 57.639 39.130 0.00 0.00 0.00 3.16
3522 3867 5.706833 TGATGCAGATGTGTGAATGTAAACT 59.293 36.000 0.00 0.00 0.00 2.66
3523 3868 5.941733 TGATGCAGATGTGTGAATGTAAAC 58.058 37.500 0.00 0.00 0.00 2.01
3553 3902 3.417069 TGACCATTCAAATCGTGAGGT 57.583 42.857 0.00 0.00 37.47 3.85
3554 3903 4.970662 AATGACCATTCAAATCGTGAGG 57.029 40.909 0.00 0.00 37.61 3.86
3555 3904 5.702865 ACAAATGACCATTCAAATCGTGAG 58.297 37.500 0.00 0.00 37.61 3.51
3556 3905 5.240403 TGACAAATGACCATTCAAATCGTGA 59.760 36.000 0.00 0.00 34.61 4.35
3573 3922 6.881065 TGTACTAGTAGTCGTAGGTGACAAAT 59.119 38.462 5.96 0.00 41.41 2.32
3580 3929 5.046529 CGTGATGTACTAGTAGTCGTAGGT 58.953 45.833 5.96 0.00 0.00 3.08
3584 3933 3.264947 TGCGTGATGTACTAGTAGTCGT 58.735 45.455 5.96 0.35 0.00 4.34
3585 3934 3.938778 TGCGTGATGTACTAGTAGTCG 57.061 47.619 5.96 4.31 0.00 4.18
3586 3935 4.978186 TGTTGCGTGATGTACTAGTAGTC 58.022 43.478 5.96 5.63 0.00 2.59
3587 3936 5.381174 TTGTTGCGTGATGTACTAGTAGT 57.619 39.130 8.14 8.14 0.00 2.73
3588 3937 6.291112 CGATTTGTTGCGTGATGTACTAGTAG 60.291 42.308 1.87 0.00 0.00 2.57
3589 3938 5.513849 CGATTTGTTGCGTGATGTACTAGTA 59.486 40.000 0.00 0.00 0.00 1.82
3590 3939 4.326278 CGATTTGTTGCGTGATGTACTAGT 59.674 41.667 0.00 0.00 0.00 2.57
3591 3940 4.326278 ACGATTTGTTGCGTGATGTACTAG 59.674 41.667 0.00 0.00 39.56 2.57
3592 3941 4.239304 ACGATTTGTTGCGTGATGTACTA 58.761 39.130 0.00 0.00 39.56 1.82
3593 3942 3.064207 ACGATTTGTTGCGTGATGTACT 58.936 40.909 0.00 0.00 39.56 2.73
3594 3943 3.404564 GACGATTTGTTGCGTGATGTAC 58.595 45.455 0.00 0.00 41.34 2.90
3604 3953 3.126858 ACGGATTGATGGACGATTTGTTG 59.873 43.478 0.00 0.00 0.00 3.33
3606 3955 2.936498 GACGGATTGATGGACGATTTGT 59.064 45.455 0.00 0.00 0.00 2.83
3665 4027 1.618640 GAAACGAGGAGTGCACGAGC 61.619 60.000 12.01 5.00 42.57 5.03
3666 4028 0.318699 TGAAACGAGGAGTGCACGAG 60.319 55.000 12.01 4.93 0.00 4.18
3702 4064 5.105877 CGATCGATTAGTATTAGCCAGGGAA 60.106 44.000 10.26 0.00 0.00 3.97
3703 4065 4.398358 CGATCGATTAGTATTAGCCAGGGA 59.602 45.833 10.26 0.00 0.00 4.20
3704 4066 4.398358 TCGATCGATTAGTATTAGCCAGGG 59.602 45.833 15.15 0.00 0.00 4.45
3718 4080 5.639506 ACTGTCAAAATCAAGTCGATCGATT 59.360 36.000 22.50 14.99 31.11 3.34
3724 4086 4.745125 GTCAGACTGTCAAAATCAAGTCGA 59.255 41.667 10.88 0.00 0.00 4.20
3725 4087 4.375405 CGTCAGACTGTCAAAATCAAGTCG 60.375 45.833 10.88 0.00 0.00 4.18
3726 4088 4.508124 ACGTCAGACTGTCAAAATCAAGTC 59.492 41.667 10.88 0.00 0.00 3.01
3727 4089 4.271049 CACGTCAGACTGTCAAAATCAAGT 59.729 41.667 10.88 0.00 0.00 3.16
4016 4387 1.420430 AGAAGTTGACGGGAGGTGAA 58.580 50.000 0.00 0.00 0.00 3.18
4019 4390 3.236896 TCTTTAGAAGTTGACGGGAGGT 58.763 45.455 0.00 0.00 0.00 3.85
4020 4391 3.510360 TCTCTTTAGAAGTTGACGGGAGG 59.490 47.826 0.00 0.00 0.00 4.30
4026 4397 7.155328 TGGACAGATTCTCTTTAGAAGTTGAC 58.845 38.462 0.00 0.00 44.79 3.18
4036 4407 9.393512 CTTGAAATCTATGGACAGATTCTCTTT 57.606 33.333 0.00 0.00 43.01 2.52
4071 4451 3.906720 TGTACTGGCAATACTCCTTCC 57.093 47.619 7.68 0.00 0.00 3.46
4074 4454 7.402862 AGTTAAAATGTACTGGCAATACTCCT 58.597 34.615 7.68 0.00 0.00 3.69
4087 4470 7.448748 AATGGTCAGGTGAGTTAAAATGTAC 57.551 36.000 0.00 0.00 0.00 2.90
4120 4503 3.181491 CCTGTCGGCACAAAAGAAAAAGA 60.181 43.478 0.00 0.00 29.82 2.52
4121 4504 3.115554 CCTGTCGGCACAAAAGAAAAAG 58.884 45.455 0.00 0.00 29.82 2.27
4122 4505 2.494073 ACCTGTCGGCACAAAAGAAAAA 59.506 40.909 0.00 0.00 29.82 1.94
4123 4506 2.096248 ACCTGTCGGCACAAAAGAAAA 58.904 42.857 0.00 0.00 29.82 2.29
4221 4604 1.071605 GCACGTACCAAGCTTCTCAG 58.928 55.000 0.00 0.00 0.00 3.35
4239 4622 8.550376 ACAAAATGATGTTACAAATGAACTTGC 58.450 29.630 0.00 0.00 0.00 4.01
4284 4668 4.092968 GTCGACGCAATTCAAATACTCCTT 59.907 41.667 0.00 0.00 0.00 3.36
4286 4670 3.242316 GGTCGACGCAATTCAAATACTCC 60.242 47.826 9.92 0.00 0.00 3.85
4300 4684 4.677832 ACAAAAATTAATGTTGGTCGACGC 59.322 37.500 9.92 3.20 0.00 5.19
4301 4685 6.741448 AACAAAAATTAATGTTGGTCGACG 57.259 33.333 9.92 0.00 38.29 5.12
4304 4690 8.812329 TCTGAAAACAAAAATTAATGTTGGTCG 58.188 29.630 13.77 7.22 39.57 4.79
4312 4698 8.293867 TCGGTCGATCTGAAAACAAAAATTAAT 58.706 29.630 0.00 0.00 0.00 1.40
4315 4701 6.067263 TCGGTCGATCTGAAAACAAAAATT 57.933 33.333 0.00 0.00 0.00 1.82
4338 4724 0.108615 CGAAGCTCTCAACCACCGAT 60.109 55.000 0.00 0.00 0.00 4.18
4425 4811 3.305064 CCCCGTTGTTGAACACATAAAGG 60.305 47.826 0.00 0.00 34.43 3.11
4431 4817 0.035343 TCACCCCGTTGTTGAACACA 60.035 50.000 0.00 0.00 31.78 3.72
4497 4883 6.006275 ACTACTTAGGCACCATTCATCATT 57.994 37.500 0.00 0.00 0.00 2.57
4523 4919 9.832445 AAACTCATGAGAAAACATATACGGTAT 57.168 29.630 29.27 5.87 0.00 2.73
4525 4921 9.661563 TTAAACTCATGAGAAAACATATACGGT 57.338 29.630 29.27 0.00 0.00 4.83
4542 4938 7.768120 TGGCATTCAACAAAAACTTAAACTCAT 59.232 29.630 0.00 0.00 0.00 2.90
4543 4939 7.099764 TGGCATTCAACAAAAACTTAAACTCA 58.900 30.769 0.00 0.00 0.00 3.41
4582 4979 3.460114 CAATCAGTTGCGTGGTGTG 57.540 52.632 0.00 0.00 0.00 3.82
4655 5056 7.648142 ACAACACGTGACAGAAATTATCAATT 58.352 30.769 25.01 0.00 0.00 2.32
4863 5306 9.331634 AAGGCTGGTGACTTATACAAGGAAACT 62.332 40.741 0.00 0.00 40.32 2.66
4864 5307 4.395231 GGCTGGTGACTTATACAAGGAAAC 59.605 45.833 0.00 0.00 35.97 2.78
4865 5308 4.288626 AGGCTGGTGACTTATACAAGGAAA 59.711 41.667 0.00 0.00 35.97 3.13
4866 5309 3.844211 AGGCTGGTGACTTATACAAGGAA 59.156 43.478 0.00 0.00 35.97 3.36
4867 5310 3.450904 AGGCTGGTGACTTATACAAGGA 58.549 45.455 0.00 0.00 35.97 3.36
4876 5319 2.310538 CCAAAAGAAGGCTGGTGACTT 58.689 47.619 0.00 0.00 45.81 3.01
5062 5548 5.813672 GGCATGTTAGTAACGGTTAATCTGA 59.186 40.000 3.89 0.00 0.00 3.27
5136 5622 1.112113 ATCCCACTACCAGTACTGCG 58.888 55.000 17.86 12.86 0.00 5.18
5224 5710 5.637810 TCAGGACAACATAAGCTTTTCGTAG 59.362 40.000 3.20 0.00 0.00 3.51
5227 5713 5.356882 TTCAGGACAACATAAGCTTTTCG 57.643 39.130 3.20 0.00 0.00 3.46
5261 5748 6.204301 CACCTGGAGATCATAAGCTTTACATG 59.796 42.308 3.20 2.37 0.00 3.21
5363 5850 3.938334 GGTGCAATTCGGCCATTTATTTT 59.062 39.130 2.24 0.00 0.00 1.82
5371 5858 2.988684 GTGGGTGCAATTCGGCCA 60.989 61.111 2.24 0.00 0.00 5.36
5470 5973 8.512138 GTTGCAACCTGTAATTTCAACTAGTAT 58.488 33.333 19.15 0.00 32.19 2.12
5473 5976 6.734137 TGTTGCAACCTGTAATTTCAACTAG 58.266 36.000 26.14 0.00 34.95 2.57
5474 5977 6.701145 TGTTGCAACCTGTAATTTCAACTA 57.299 33.333 26.14 0.00 34.95 2.24
5475 5978 5.590530 TGTTGCAACCTGTAATTTCAACT 57.409 34.783 26.14 0.00 34.95 3.16


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

AutoCloner maintained by Alex Coulton.