Multiple sequence alignment - TraesCS2D01G495100

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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 TraesCS2D01G495100 chr2D 100.000 2953 0 0 1 2953 592030125 592033077 0.000000e+00 5454.0
1 TraesCS2D01G495100 chr2D 81.142 753 84 34 1076 1799 592092256 592092979 4.300000e-153 551.0
2 TraesCS2D01G495100 chr2D 86.024 508 45 16 1076 1580 592115491 592115975 3.370000e-144 521.0
3 TraesCS2D01G495100 chr2D 83.681 527 61 16 1076 1599 592080436 592080940 9.580000e-130 473.0
4 TraesCS2D01G495100 chr2D 79.441 608 53 43 834 1415 592273907 592274468 6.010000e-97 364.0
5 TraesCS2D01G495100 chr2A 84.080 1451 88 57 649 2049 726560448 726561805 0.000000e+00 1267.0
6 TraesCS2D01G495100 chr2A 80.055 727 96 28 1076 1799 726592775 726593455 7.350000e-136 494.0
7 TraesCS2D01G495100 chr2A 81.132 689 56 25 148 818 726568012 726568644 4.430000e-133 484.0
8 TraesCS2D01G495100 chr2A 79.568 602 54 39 834 1415 726755851 726756403 1.670000e-97 366.0
9 TraesCS2D01G495100 chr2A 78.797 349 40 14 160 499 726559869 726560192 1.390000e-48 204.0
10 TraesCS2D01G495100 chr2A 87.324 142 17 1 129 270 726555717 726555857 8.470000e-36 161.0
11 TraesCS2D01G495100 chr2A 76.617 201 30 12 2195 2380 603372401 603372203 8.710000e-16 95.3
12 TraesCS2D01G495100 chr2A 92.308 52 2 1 2500 2549 726568834 726568885 4.080000e-09 73.1
13 TraesCS2D01G495100 chr2B 89.562 958 52 16 949 1872 717678529 717679472 0.000000e+00 1171.0
14 TraesCS2D01G495100 chr2B 85.584 659 71 14 140 776 717676902 717677558 0.000000e+00 669.0
15 TraesCS2D01G495100 chr2B 81.889 646 77 16 1907 2550 717679466 717680073 2.630000e-140 508.0
16 TraesCS2D01G495100 chr2B 88.620 413 44 3 2536 2946 717680094 717680505 1.580000e-137 499.0
17 TraesCS2D01G495100 chr2B 84.061 527 61 16 1076 1599 717775791 717776297 1.230000e-133 486.0
18 TraesCS2D01G495100 chr2B 80.306 589 67 29 848 1415 717895833 717896393 1.650000e-107 399.0
19 TraesCS2D01G495100 chr2B 84.416 77 10 2 2703 2778 339109733 339109658 1.140000e-09 75.0
20 TraesCS2D01G495100 chr7A 77.872 235 37 6 2715 2935 3527266 3527499 6.640000e-27 132.0
21 TraesCS2D01G495100 chr7A 87.179 78 5 5 2305 2377 139150443 139150520 1.890000e-12 84.2
22 TraesCS2D01G495100 chrUn 90.541 74 7 0 2330 2403 277302878 277302805 6.740000e-17 99.0
23 TraesCS2D01G495100 chrUn 90.541 74 7 0 2330 2403 283234095 283234022 6.740000e-17 99.0
24 TraesCS2D01G495100 chr3A 90.541 74 7 0 2330 2403 727191820 727191893 6.740000e-17 99.0
25 TraesCS2D01G495100 chr7B 87.209 86 8 2 2320 2402 132139398 132139313 8.710000e-16 95.3
26 TraesCS2D01G495100 chr4B 87.500 80 9 1 2302 2380 588691966 588691887 1.130000e-14 91.6
27 TraesCS2D01G495100 chr7D 91.071 56 5 0 2037 2092 130925750 130925805 3.160000e-10 76.8
28 TraesCS2D01G495100 chr7D 91.071 56 5 0 2037 2092 130926441 130926496 3.160000e-10 76.8
29 TraesCS2D01G495100 chr3D 82.927 82 12 2 2300 2380 560117150 560117070 4.080000e-09 73.1
30 TraesCS2D01G495100 chr6A 93.182 44 2 1 2321 2363 162426300 162426257 2.460000e-06 63.9


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 TraesCS2D01G495100 chr2D 592030125 592033077 2952 False 5454.00 5454 100.00000 1 2953 1 chr2D.!!$F1 2952
1 TraesCS2D01G495100 chr2D 592092256 592092979 723 False 551.00 551 81.14200 1076 1799 1 chr2D.!!$F3 723
2 TraesCS2D01G495100 chr2D 592080436 592080940 504 False 473.00 473 83.68100 1076 1599 1 chr2D.!!$F2 523
3 TraesCS2D01G495100 chr2D 592273907 592274468 561 False 364.00 364 79.44100 834 1415 1 chr2D.!!$F5 581
4 TraesCS2D01G495100 chr2A 726559869 726561805 1936 False 735.50 1267 81.43850 160 2049 2 chr2A.!!$F4 1889
5 TraesCS2D01G495100 chr2A 726592775 726593455 680 False 494.00 494 80.05500 1076 1799 1 chr2A.!!$F2 723
6 TraesCS2D01G495100 chr2A 726755851 726756403 552 False 366.00 366 79.56800 834 1415 1 chr2A.!!$F3 581
7 TraesCS2D01G495100 chr2A 726568012 726568885 873 False 278.55 484 86.72000 148 2549 2 chr2A.!!$F5 2401
8 TraesCS2D01G495100 chr2B 717676902 717680505 3603 False 711.75 1171 86.41375 140 2946 4 chr2B.!!$F3 2806
9 TraesCS2D01G495100 chr2B 717775791 717776297 506 False 486.00 486 84.06100 1076 1599 1 chr2B.!!$F1 523
10 TraesCS2D01G495100 chr2B 717895833 717896393 560 False 399.00 399 80.30600 848 1415 1 chr2B.!!$F2 567

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
28 29 0.035439 GGCTTGAATCGGGGAACAGA 60.035 55.0 0.0 0.0 39.42 3.41 F
1730 2966 0.107017 ATCTGATTGAAGGGCGTGGG 60.107 55.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 3006 1.737793 GCCGTCTCCGATTCACAATTT 59.262 47.619 0.0 0.0 35.63 1.82 R
2909 4225 1.253044 GCGCAAACACAAAGTCGTCG 61.253 55.000 0.3 0.0 0.00 5.12 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
20 21 2.291365 TGATGTCATGGCTTGAATCGG 58.709 47.619 4.47 0.00 35.70 4.18
21 22 1.605710 GATGTCATGGCTTGAATCGGG 59.394 52.381 4.47 0.00 35.70 5.14
22 23 0.394216 TGTCATGGCTTGAATCGGGG 60.394 55.000 4.47 0.00 35.70 5.73
23 24 0.107214 GTCATGGCTTGAATCGGGGA 60.107 55.000 4.47 0.00 35.70 4.81
24 25 0.623194 TCATGGCTTGAATCGGGGAA 59.377 50.000 0.00 0.00 0.00 3.97
25 26 0.740737 CATGGCTTGAATCGGGGAAC 59.259 55.000 0.00 0.00 0.00 3.62
26 27 0.331278 ATGGCTTGAATCGGGGAACA 59.669 50.000 0.00 0.00 0.00 3.18
27 28 0.322456 TGGCTTGAATCGGGGAACAG 60.322 55.000 0.00 0.00 0.00 3.16
28 29 0.035439 GGCTTGAATCGGGGAACAGA 60.035 55.000 0.00 0.00 39.42 3.41
36 37 3.550437 ATCGGGGAACAGATTCTTCAG 57.450 47.619 0.00 0.00 42.99 3.02
37 38 2.257207 TCGGGGAACAGATTCTTCAGT 58.743 47.619 0.00 0.00 34.98 3.41
38 39 2.233922 TCGGGGAACAGATTCTTCAGTC 59.766 50.000 0.00 0.00 34.98 3.51
39 40 2.622436 GGGGAACAGATTCTTCAGTCG 58.378 52.381 0.00 0.00 34.98 4.18
40 41 2.003301 GGGAACAGATTCTTCAGTCGC 58.997 52.381 0.00 0.00 34.98 5.19
41 42 1.656095 GGAACAGATTCTTCAGTCGCG 59.344 52.381 0.00 0.00 34.98 5.87
42 43 2.329379 GAACAGATTCTTCAGTCGCGT 58.671 47.619 5.77 0.00 31.55 6.01
43 44 1.983972 ACAGATTCTTCAGTCGCGTC 58.016 50.000 5.77 0.00 0.00 5.19
44 45 1.542030 ACAGATTCTTCAGTCGCGTCT 59.458 47.619 5.77 1.88 0.00 4.18
45 46 2.181205 CAGATTCTTCAGTCGCGTCTC 58.819 52.381 5.77 0.00 0.00 3.36
46 47 1.813178 AGATTCTTCAGTCGCGTCTCA 59.187 47.619 5.77 0.00 0.00 3.27
47 48 2.229062 AGATTCTTCAGTCGCGTCTCAA 59.771 45.455 5.77 0.00 0.00 3.02
48 49 1.767289 TTCTTCAGTCGCGTCTCAAC 58.233 50.000 5.77 0.00 0.00 3.18
58 59 4.047059 GTCTCAACGCCGGGTCGA 62.047 66.667 15.84 0.00 0.00 4.20
59 60 4.047059 TCTCAACGCCGGGTCGAC 62.047 66.667 7.13 7.13 0.00 4.20
78 79 3.392431 CTCGCCGAGCAAGATGTG 58.608 61.111 0.00 0.00 0.00 3.21
114 115 5.682943 GTTGTGCTAATCAACTGTTACCA 57.317 39.130 0.00 0.00 41.04 3.25
115 116 5.449304 GTTGTGCTAATCAACTGTTACCAC 58.551 41.667 0.00 0.00 41.04 4.16
116 117 4.968259 TGTGCTAATCAACTGTTACCACT 58.032 39.130 0.00 0.00 0.00 4.00
117 118 6.104146 TGTGCTAATCAACTGTTACCACTA 57.896 37.500 0.00 0.00 0.00 2.74
118 119 6.163476 TGTGCTAATCAACTGTTACCACTAG 58.837 40.000 0.00 0.00 0.00 2.57
119 120 6.164176 GTGCTAATCAACTGTTACCACTAGT 58.836 40.000 0.00 0.00 0.00 2.57
120 121 7.039574 TGTGCTAATCAACTGTTACCACTAGTA 60.040 37.037 0.00 0.00 0.00 1.82
121 122 7.816031 GTGCTAATCAACTGTTACCACTAGTAA 59.184 37.037 0.00 0.00 38.65 2.24
185 190 3.134127 GTGGCCTGGAATCCGCAC 61.134 66.667 3.32 0.00 33.28 5.34
187 192 4.467084 GGCCTGGAATCCGCACGA 62.467 66.667 0.00 0.00 0.00 4.35
195 200 2.280628 GGAATCCGCACGAAGATCTTT 58.719 47.619 9.87 0.00 0.00 2.52
207 212 4.520492 ACGAAGATCTTTTGAAAGCCACAT 59.480 37.500 9.87 0.00 35.99 3.21
209 214 5.397142 AAGATCTTTTGAAAGCCACATCC 57.603 39.130 0.88 0.00 35.99 3.51
372 398 2.100631 CGGCACCTGACCGTTCATC 61.101 63.158 0.00 0.00 45.70 2.92
478 505 3.544567 CGTAACGCCCGTAACGGC 61.545 66.667 0.20 0.20 46.86 5.68
534 590 4.634184 TGTCTAATAACTCTGGAGCGTC 57.366 45.455 0.00 0.00 0.00 5.19
539 770 2.561733 TAACTCTGGAGCGTCGATTG 57.438 50.000 0.00 0.00 0.00 2.67
541 772 1.880340 CTCTGGAGCGTCGATTGGC 60.880 63.158 0.00 0.00 0.00 4.52
542 773 2.125552 CTGGAGCGTCGATTGGCA 60.126 61.111 0.00 0.00 0.00 4.92
543 774 2.125552 TGGAGCGTCGATTGGCAG 60.126 61.111 0.00 0.00 0.00 4.85
544 775 3.567797 GGAGCGTCGATTGGCAGC 61.568 66.667 0.00 0.00 0.00 5.25
549 780 3.430862 GTCGATTGGCAGCCGCAA 61.431 61.111 7.03 0.00 41.24 4.85
550 781 2.671276 TCGATTGGCAGCCGCAAA 60.671 55.556 7.03 0.00 41.24 3.68
551 782 2.257980 CGATTGGCAGCCGCAAAA 59.742 55.556 7.03 0.00 41.24 2.44
552 783 1.802715 CGATTGGCAGCCGCAAAAG 60.803 57.895 7.03 0.00 41.24 2.27
553 784 2.047939 ATTGGCAGCCGCAAAAGC 60.048 55.556 7.03 0.00 41.24 3.51
580 811 0.705094 GAGCGCGATATCGATGTGTG 59.295 55.000 28.63 10.67 43.02 3.82
639 870 4.413928 CCAAAATGGGGCAGACGA 57.586 55.556 0.00 0.00 32.67 4.20
679 910 1.808411 TTTCAGCACCGGATTCAGTC 58.192 50.000 9.46 0.00 0.00 3.51
690 921 2.611518 GGATTCAGTCAAGTCACGAGG 58.388 52.381 0.00 0.00 0.00 4.63
721 953 1.467883 CGTGCATGTAACAAGGCCATG 60.468 52.381 5.01 5.77 39.13 3.66
771 1005 7.040409 AGGACAAGTTTTGACTAACATTGGATC 60.040 37.037 0.00 0.00 0.00 3.36
788 1870 2.028112 GGATCAATAGCCGCCTGACATA 60.028 50.000 0.00 0.00 0.00 2.29
789 1871 2.526304 TCAATAGCCGCCTGACATAC 57.474 50.000 0.00 0.00 0.00 2.39
790 1872 2.039418 TCAATAGCCGCCTGACATACT 58.961 47.619 0.00 0.00 0.00 2.12
791 1873 2.035961 TCAATAGCCGCCTGACATACTC 59.964 50.000 0.00 0.00 0.00 2.59
792 1874 0.969894 ATAGCCGCCTGACATACTCC 59.030 55.000 0.00 0.00 0.00 3.85
815 1897 6.014755 TCCATGTGGCTCAAAATGTGAATAAA 60.015 34.615 0.00 0.00 35.22 1.40
821 1903 9.255304 GTGGCTCAAAATGTGAATAAAAACTAA 57.745 29.630 0.00 0.00 35.22 2.24
822 1904 9.995003 TGGCTCAAAATGTGAATAAAAACTAAT 57.005 25.926 0.00 0.00 35.22 1.73
937 2083 2.424601 CAACATTTCCGTGCCTCATCAT 59.575 45.455 0.00 0.00 0.00 2.45
947 2093 2.553602 GTGCCTCATCATCACACACAAA 59.446 45.455 0.00 0.00 0.00 2.83
958 2106 6.401394 TCATCACACACAAAAACATTTCCAA 58.599 32.000 0.00 0.00 0.00 3.53
980 2128 4.116113 ACATCCTATAAAACCTCCCACCA 58.884 43.478 0.00 0.00 0.00 4.17
1039 2190 3.175714 AACTCGTCCTCCCCCAGGT 62.176 63.158 0.00 0.00 43.95 4.00
1420 2612 3.878519 CGCGTCTCCTCCGAGGAC 61.879 72.222 13.54 4.66 40.06 3.85
1544 2736 0.537188 ACGGATCGATGGAAGCAACT 59.463 50.000 0.54 0.00 0.00 3.16
1550 2742 0.729116 CGATGGAAGCAACTCGCATT 59.271 50.000 0.00 0.00 46.13 3.56
1564 2756 1.153784 GCATTGGCCATTCGGTGTG 60.154 57.895 6.09 0.00 33.28 3.82
1589 2781 2.615869 CTCTGTTCTCAGGCAAGCTAC 58.384 52.381 0.00 0.00 41.59 3.58
1600 2792 2.047560 AAGCTACCCGTGGCGAAC 60.048 61.111 0.00 0.00 42.26 3.95
1730 2966 0.107017 ATCTGATTGAAGGGCGTGGG 60.107 55.000 0.00 0.00 0.00 4.61
1731 2967 2.361104 TGATTGAAGGGCGTGGGC 60.361 61.111 0.00 0.00 38.90 5.36
1835 3100 1.430632 GCGTGCGTAGTACCAGCTA 59.569 57.895 6.41 0.00 41.02 3.32
1837 3102 1.265095 GCGTGCGTAGTACCAGCTATA 59.735 52.381 6.41 0.00 41.02 1.31
1849 3123 6.071984 AGTACCAGCTATATACTGCTTGACT 58.928 40.000 3.56 4.87 37.44 3.41
1939 3215 4.322057 ACACTCCTTGCTGGGAATAATT 57.678 40.909 0.42 0.00 34.66 1.40
1985 3262 0.630673 CATGATGTTGGGGAGGGGAA 59.369 55.000 0.00 0.00 0.00 3.97
1986 3263 1.006998 CATGATGTTGGGGAGGGGAAA 59.993 52.381 0.00 0.00 0.00 3.13
2011 3288 5.708736 TTTTGGGAATGGCTAGATGTAGA 57.291 39.130 0.05 0.00 0.00 2.59
2029 3306 6.613755 TGTAGATCGTCTGATTGTCGAATA 57.386 37.500 0.00 0.00 39.36 1.75
2031 3308 7.649057 TGTAGATCGTCTGATTGTCGAATATT 58.351 34.615 0.00 0.00 39.36 1.28
2039 3316 5.812127 TCTGATTGTCGAATATTGGTCAGTG 59.188 40.000 12.43 0.00 34.84 3.66
2051 3328 2.327228 GTCAGTGGACCGTTTTGGG 58.673 57.895 0.00 0.00 44.64 4.12
2078 3355 0.179045 ATGTAGATCCAACAGCGGGC 60.179 55.000 4.94 0.00 0.00 6.13
2093 3370 1.379176 GGGCAGCCCTTCTTCTTCC 60.379 63.158 24.99 0.00 41.34 3.46
2097 3374 0.107945 CAGCCCTTCTTCTTCCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
2099 3376 1.265454 GCCCTTCTTCTTCCTCCGGA 61.265 60.000 2.93 2.93 0.00 5.14
2102 3379 1.067821 CCTTCTTCTTCCTCCGGATCG 59.932 57.143 3.57 0.00 0.00 3.69
2111 3388 0.386113 CCTCCGGATCGTCTCTTTCC 59.614 60.000 3.57 0.00 0.00 3.13
2114 3391 2.950309 CTCCGGATCGTCTCTTTCCTTA 59.050 50.000 3.57 0.00 0.00 2.69
2118 3395 4.038162 CCGGATCGTCTCTTTCCTTAGAAT 59.962 45.833 0.00 0.00 0.00 2.40
2120 3397 5.216648 GGATCGTCTCTTTCCTTAGAATCG 58.783 45.833 0.00 0.00 0.00 3.34
2123 3400 3.459145 GTCTCTTTCCTTAGAATCGCCC 58.541 50.000 0.00 0.00 0.00 6.13
2125 3402 3.133003 TCTCTTTCCTTAGAATCGCCCAG 59.867 47.826 0.00 0.00 0.00 4.45
2145 3422 4.410400 GCCACCAGCCTAACCGCT 62.410 66.667 0.00 0.00 40.65 5.52
2153 3430 2.124570 CCTAACCGCTGCTGCCAT 60.125 61.111 10.24 0.00 35.36 4.40
2154 3431 2.475466 CCTAACCGCTGCTGCCATG 61.475 63.158 10.24 1.63 35.36 3.66
2155 3432 2.438254 TAACCGCTGCTGCCATGG 60.438 61.111 7.63 7.63 35.36 3.66
2156 3433 3.266686 TAACCGCTGCTGCCATGGT 62.267 57.895 14.67 8.79 35.36 3.55
2231 3509 4.012895 CCACTGTCGTGTTGCCGC 62.013 66.667 0.00 0.00 39.55 6.53
2247 3525 4.964241 GCCCTCCCCGCCTATCCT 62.964 72.222 0.00 0.00 0.00 3.24
2255 3533 1.545706 CCCGCCTATCCTTCTAGCCC 61.546 65.000 0.00 0.00 0.00 5.19
2259 3537 1.545706 CCTATCCTTCTAGCCCCGGC 61.546 65.000 0.00 0.00 42.33 6.13
2260 3538 0.832135 CTATCCTTCTAGCCCCGGCA 60.832 60.000 8.74 0.00 44.88 5.69
2263 3541 4.530857 CTTCTAGCCCCGGCACCG 62.531 72.222 8.74 1.02 44.88 4.94
2277 3555 1.804748 GGCACCGACGAAGATTTTCTT 59.195 47.619 0.00 0.00 39.87 2.52
2278 3556 5.527676 CGGCACCGACGAAGATTTTCTTC 62.528 52.174 2.01 7.11 44.22 2.87
2296 3574 3.189080 TCTTCGATGAAATTGCACCACTG 59.811 43.478 0.00 0.00 0.00 3.66
2306 3584 4.974721 CACCACTGCCCCACCACC 62.975 72.222 0.00 0.00 0.00 4.61
2313 3591 3.956314 GCCCCACCACCACCGTTA 61.956 66.667 0.00 0.00 0.00 3.18
2314 3592 3.083386 CCCCACCACCACCGTTAT 58.917 61.111 0.00 0.00 0.00 1.89
2315 3593 1.381076 CCCCACCACCACCGTTATT 59.619 57.895 0.00 0.00 0.00 1.40
2316 3594 0.251430 CCCCACCACCACCGTTATTT 60.251 55.000 0.00 0.00 0.00 1.40
2317 3595 1.170442 CCCACCACCACCGTTATTTC 58.830 55.000 0.00 0.00 0.00 2.17
2318 3596 0.800012 CCACCACCACCGTTATTTCG 59.200 55.000 0.00 0.00 0.00 3.46
2319 3597 1.515081 CACCACCACCGTTATTTCGT 58.485 50.000 0.00 0.00 0.00 3.85
2320 3598 1.461897 CACCACCACCGTTATTTCGTC 59.538 52.381 0.00 0.00 0.00 4.20
2321 3599 1.081094 CCACCACCGTTATTTCGTCC 58.919 55.000 0.00 0.00 0.00 4.79
2322 3600 1.081094 CACCACCGTTATTTCGTCCC 58.919 55.000 0.00 0.00 0.00 4.46
2323 3601 0.036105 ACCACCGTTATTTCGTCCCC 60.036 55.000 0.00 0.00 0.00 4.81
2324 3602 0.036199 CCACCGTTATTTCGTCCCCA 60.036 55.000 0.00 0.00 0.00 4.96
2325 3603 1.081094 CACCGTTATTTCGTCCCCAC 58.919 55.000 0.00 0.00 0.00 4.61
2326 3604 0.036105 ACCGTTATTTCGTCCCCACC 60.036 55.000 0.00 0.00 0.00 4.61
2327 3605 0.745486 CCGTTATTTCGTCCCCACCC 60.745 60.000 0.00 0.00 0.00 4.61
2328 3606 0.745486 CGTTATTTCGTCCCCACCCC 60.745 60.000 0.00 0.00 0.00 4.95
2329 3607 0.394762 GTTATTTCGTCCCCACCCCC 60.395 60.000 0.00 0.00 0.00 5.40
2330 3608 0.845543 TTATTTCGTCCCCACCCCCA 60.846 55.000 0.00 0.00 0.00 4.96
2331 3609 1.564483 TATTTCGTCCCCACCCCCAC 61.564 60.000 0.00 0.00 0.00 4.61
2332 3610 3.958337 TATTTCGTCCCCACCCCCACT 62.958 57.143 0.00 0.00 0.00 4.00
2347 3625 5.046735 CACCCCCACTCTAAGATAGATGATG 60.047 48.000 0.00 0.00 33.66 3.07
2360 3638 1.831652 GATGATGGGGTAGCCCTCCG 61.832 65.000 29.64 0.00 44.66 4.63
2375 3653 2.232298 CTCCGGCGAGCTCCTTTCTT 62.232 60.000 9.30 0.00 0.00 2.52
2376 3654 1.811679 CCGGCGAGCTCCTTTCTTC 60.812 63.158 9.30 0.00 0.00 2.87
2377 3655 1.811679 CGGCGAGCTCCTTTCTTCC 60.812 63.158 8.47 0.00 0.00 3.46
2378 3656 1.450491 GGCGAGCTCCTTTCTTCCC 60.450 63.158 8.47 0.00 0.00 3.97
2379 3657 1.599576 GCGAGCTCCTTTCTTCCCT 59.400 57.895 8.47 0.00 0.00 4.20
2380 3658 0.461163 GCGAGCTCCTTTCTTCCCTC 60.461 60.000 8.47 0.00 0.00 4.30
2381 3659 0.179124 CGAGCTCCTTTCTTCCCTCG 60.179 60.000 8.47 0.00 36.65 4.63
2382 3660 0.176910 GAGCTCCTTTCTTCCCTCGG 59.823 60.000 0.87 0.00 0.00 4.63
2383 3661 1.222113 GCTCCTTTCTTCCCTCGGG 59.778 63.158 0.00 0.00 0.00 5.14
2384 3662 1.222113 CTCCTTTCTTCCCTCGGGC 59.778 63.158 0.00 0.00 34.68 6.13
2385 3663 2.258748 CTCCTTTCTTCCCTCGGGCC 62.259 65.000 0.00 0.00 34.68 5.80
2409 3687 3.756434 CCCTCTGGCGAACTTTAAAATCA 59.244 43.478 0.00 0.00 0.00 2.57
2411 3689 5.105756 CCCTCTGGCGAACTTTAAAATCAAT 60.106 40.000 0.00 0.00 0.00 2.57
2434 3712 8.749499 CAATTGACTCAAAATCAAAAGTCAGTC 58.251 33.333 0.00 0.00 46.24 3.51
2441 3719 3.703001 ATCAAAAGTCAGTCCATCCGT 57.297 42.857 0.00 0.00 0.00 4.69
2452 3730 1.079127 CCATCCGTGTGGGTCTCAC 60.079 63.158 0.00 0.00 46.23 3.51
2467 3745 1.012086 CTCACCGGATGCACAATGAG 58.988 55.000 9.46 3.91 0.00 2.90
2470 3748 0.615331 ACCGGATGCACAATGAGACT 59.385 50.000 9.46 0.00 0.00 3.24
2471 3749 1.003580 ACCGGATGCACAATGAGACTT 59.996 47.619 9.46 0.00 0.00 3.01
2473 3751 1.399440 CGGATGCACAATGAGACTTGG 59.601 52.381 0.00 0.00 0.00 3.61
2475 3753 2.421424 GGATGCACAATGAGACTTGGTC 59.579 50.000 0.00 0.00 0.00 4.02
2598 3913 7.639113 ACTGTCACTTTTTACAAATTCTCCA 57.361 32.000 0.00 0.00 0.00 3.86
2608 3923 7.843490 TTTACAAATTCTCCATCGACTAAGG 57.157 36.000 0.00 0.00 0.00 2.69
2617 3932 6.516718 TCTCCATCGACTAAGGATTTTCATC 58.483 40.000 0.00 0.00 0.00 2.92
2618 3933 6.098266 TCTCCATCGACTAAGGATTTTCATCA 59.902 38.462 0.00 0.00 0.00 3.07
2619 3934 6.649155 TCCATCGACTAAGGATTTTCATCAA 58.351 36.000 0.00 0.00 0.00 2.57
2620 3935 7.282585 TCCATCGACTAAGGATTTTCATCAAT 58.717 34.615 0.00 0.00 0.00 2.57
2624 3939 5.506317 CGACTAAGGATTTTCATCAATGGGC 60.506 44.000 0.00 0.00 0.00 5.36
2626 3941 4.476628 AAGGATTTTCATCAATGGGCAC 57.523 40.909 0.00 0.00 0.00 5.01
2662 3977 9.816354 ATTTTGTTAACTATGGAAATACATGCC 57.184 29.630 7.22 0.00 32.39 4.40
2668 3983 1.593196 TGGAAATACATGCCGCTAGC 58.407 50.000 4.06 4.06 44.14 3.42
2675 3990 0.824109 ACATGCCGCTAGCTACAAGA 59.176 50.000 13.93 0.00 44.23 3.02
2677 3992 2.158900 ACATGCCGCTAGCTACAAGATT 60.159 45.455 13.93 0.00 44.23 2.40
2688 4003 7.570507 CGCTAGCTACAAGATTGTGTGTTTAAA 60.571 37.037 13.93 0.00 42.31 1.52
2696 4011 3.907894 TTGTGTGTTTAAATCGGCCTC 57.092 42.857 0.00 0.00 0.00 4.70
2701 4016 5.473846 TGTGTGTTTAAATCGGCCTCAATTA 59.526 36.000 0.00 0.00 0.00 1.40
2710 4025 9.959749 TTAAATCGGCCTCAATTACATTTATTC 57.040 29.630 0.00 0.00 0.00 1.75
2717 4032 8.138074 GGCCTCAATTACATTTATTCCTTCTTC 58.862 37.037 0.00 0.00 0.00 2.87
2863 4178 4.406003 ACGCTAGAAAGAACATATGACCCT 59.594 41.667 10.38 0.17 0.00 4.34
2864 4179 5.597182 ACGCTAGAAAGAACATATGACCCTA 59.403 40.000 10.38 1.68 0.00 3.53
2879 4194 9.347240 CATATGACCCTATGATATTTTGATCCC 57.653 37.037 0.00 0.00 31.92 3.85
2880 4195 6.778542 TGACCCTATGATATTTTGATCCCA 57.221 37.500 0.00 0.00 0.00 4.37
2883 4198 6.546484 ACCCTATGATATTTTGATCCCACTG 58.454 40.000 0.00 0.00 0.00 3.66
2884 4199 6.103205 ACCCTATGATATTTTGATCCCACTGT 59.897 38.462 0.00 0.00 0.00 3.55
2885 4200 7.006509 CCCTATGATATTTTGATCCCACTGTT 58.993 38.462 0.00 0.00 0.00 3.16
2926 4242 3.307339 TTACGACGACTTTGTGTTTGC 57.693 42.857 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.291365 CCGATTCAAGCCATGACATCA 58.709 47.619 0.00 0.00 37.92 3.07
1 2 1.605710 CCCGATTCAAGCCATGACATC 59.394 52.381 0.00 0.00 37.92 3.06
2 3 1.683943 CCCGATTCAAGCCATGACAT 58.316 50.000 0.00 0.00 37.92 3.06
3 4 0.394216 CCCCGATTCAAGCCATGACA 60.394 55.000 0.00 0.00 37.92 3.58
4 5 0.107214 TCCCCGATTCAAGCCATGAC 60.107 55.000 0.00 0.00 37.92 3.06
5 6 0.623194 TTCCCCGATTCAAGCCATGA 59.377 50.000 0.00 0.00 35.85 3.07
6 7 0.740737 GTTCCCCGATTCAAGCCATG 59.259 55.000 0.00 0.00 0.00 3.66
7 8 0.331278 TGTTCCCCGATTCAAGCCAT 59.669 50.000 0.00 0.00 0.00 4.40
8 9 0.322456 CTGTTCCCCGATTCAAGCCA 60.322 55.000 0.00 0.00 0.00 4.75
9 10 0.035439 TCTGTTCCCCGATTCAAGCC 60.035 55.000 0.00 0.00 0.00 4.35
10 11 2.044123 ATCTGTTCCCCGATTCAAGC 57.956 50.000 0.00 0.00 0.00 4.01
11 12 3.878778 AGAATCTGTTCCCCGATTCAAG 58.121 45.455 12.74 0.00 44.90 3.02
12 13 4.261801 GAAGAATCTGTTCCCCGATTCAA 58.738 43.478 12.74 0.00 44.90 2.69
13 14 3.263170 TGAAGAATCTGTTCCCCGATTCA 59.737 43.478 12.74 0.00 44.90 2.57
14 15 3.873910 TGAAGAATCTGTTCCCCGATTC 58.126 45.455 0.00 0.00 43.56 2.52
15 16 3.264450 ACTGAAGAATCTGTTCCCCGATT 59.736 43.478 0.00 0.00 34.44 3.34
16 17 2.840651 ACTGAAGAATCTGTTCCCCGAT 59.159 45.455 0.00 0.00 34.44 4.18
17 18 2.233922 GACTGAAGAATCTGTTCCCCGA 59.766 50.000 0.00 0.00 37.80 5.14
18 19 2.622436 GACTGAAGAATCTGTTCCCCG 58.378 52.381 0.00 0.00 37.80 5.73
19 20 2.622436 CGACTGAAGAATCTGTTCCCC 58.378 52.381 0.00 0.00 37.80 4.81
20 21 2.003301 GCGACTGAAGAATCTGTTCCC 58.997 52.381 0.00 0.00 37.80 3.97
21 22 1.656095 CGCGACTGAAGAATCTGTTCC 59.344 52.381 0.00 0.00 37.80 3.62
22 23 2.329379 ACGCGACTGAAGAATCTGTTC 58.671 47.619 15.93 0.00 37.80 3.18
23 24 2.029828 AGACGCGACTGAAGAATCTGTT 60.030 45.455 15.93 0.00 37.80 3.16
24 25 1.542030 AGACGCGACTGAAGAATCTGT 59.458 47.619 15.93 0.00 40.06 3.41
25 26 2.181205 GAGACGCGACTGAAGAATCTG 58.819 52.381 17.32 0.00 0.00 2.90
26 27 1.813178 TGAGACGCGACTGAAGAATCT 59.187 47.619 17.32 2.32 0.00 2.40
27 28 2.264109 TGAGACGCGACTGAAGAATC 57.736 50.000 17.32 0.01 0.00 2.52
28 29 2.329379 GTTGAGACGCGACTGAAGAAT 58.671 47.619 17.32 0.00 0.00 2.40
29 30 1.767289 GTTGAGACGCGACTGAAGAA 58.233 50.000 17.32 0.50 0.00 2.52
30 31 0.385598 CGTTGAGACGCGACTGAAGA 60.386 55.000 17.32 0.00 43.03 2.87
31 32 2.054801 CGTTGAGACGCGACTGAAG 58.945 57.895 17.32 4.51 43.03 3.02
32 33 4.221873 CGTTGAGACGCGACTGAA 57.778 55.556 17.32 11.56 43.03 3.02
41 42 4.047059 TCGACCCGGCGTTGAGAC 62.047 66.667 6.01 0.00 30.81 3.36
42 43 4.047059 GTCGACCCGGCGTTGAGA 62.047 66.667 3.51 0.00 35.42 3.27
61 62 3.392431 CACATCTTGCTCGGCGAG 58.608 61.111 31.40 31.40 41.13 5.03
79 80 2.826979 GCACAACTGCTGATGATCAG 57.173 50.000 17.83 17.83 46.90 2.90
92 93 5.682943 TGGTAACAGTTGATTAGCACAAC 57.317 39.130 0.00 0.00 46.17 3.32
121 122 0.949105 CGCCCGTCAACTTGCTAAGT 60.949 55.000 0.00 0.00 45.46 2.24
122 123 1.787847 CGCCCGTCAACTTGCTAAG 59.212 57.895 0.00 0.00 0.00 2.18
123 124 2.322081 GCGCCCGTCAACTTGCTAA 61.322 57.895 0.00 0.00 0.00 3.09
124 125 2.740826 GCGCCCGTCAACTTGCTA 60.741 61.111 0.00 0.00 0.00 3.49
125 126 4.927782 TGCGCCCGTCAACTTGCT 62.928 61.111 4.18 0.00 0.00 3.91
126 127 3.667429 GATGCGCCCGTCAACTTGC 62.667 63.158 4.18 0.00 0.00 4.01
127 128 2.480555 GATGCGCCCGTCAACTTG 59.519 61.111 4.18 0.00 0.00 3.16
128 129 2.746277 GGATGCGCCCGTCAACTT 60.746 61.111 4.18 0.00 0.00 2.66
185 190 4.488126 TGTGGCTTTCAAAAGATCTTCG 57.512 40.909 8.78 3.43 38.28 3.79
187 192 4.221482 GGGATGTGGCTTTCAAAAGATCTT 59.779 41.667 0.88 0.88 38.28 2.40
195 200 1.304052 CCGGGGATGTGGCTTTCAA 60.304 57.895 0.00 0.00 0.00 2.69
207 212 1.189524 CGGTATATCCTTGCCGGGGA 61.190 60.000 2.18 0.89 40.45 4.81
209 214 1.375523 GCGGTATATCCTTGCCGGG 60.376 63.158 2.18 0.00 43.90 5.73
241 246 2.810486 CGGTATCTCGCCGGATTTC 58.190 57.895 5.05 0.00 44.98 2.17
377 403 0.457851 AAGAGAATCGTCTGGCCTCG 59.542 55.000 3.32 6.77 42.67 4.63
381 407 2.167487 AGAAGGAAGAGAATCGTCTGGC 59.833 50.000 0.00 0.00 43.41 4.85
445 472 4.156622 CGCAGGCTCACATGCACG 62.157 66.667 3.51 0.00 42.68 5.34
478 505 3.481903 CACAGTGCTGCGCCGTAG 61.482 66.667 9.97 0.00 0.00 3.51
523 579 1.880340 GCCAATCGACGCTCCAGAG 60.880 63.158 0.00 0.00 0.00 3.35
534 590 1.802715 CTTTTGCGGCTGCCAATCG 60.803 57.895 20.29 5.53 41.78 3.34
547 778 0.936297 GCGCTCACTGTTGGCTTTTG 60.936 55.000 0.00 0.00 0.00 2.44
548 779 1.360192 GCGCTCACTGTTGGCTTTT 59.640 52.632 0.00 0.00 0.00 2.27
549 780 2.896801 CGCGCTCACTGTTGGCTTT 61.897 57.895 5.56 0.00 0.00 3.51
550 781 3.349006 CGCGCTCACTGTTGGCTT 61.349 61.111 5.56 0.00 0.00 4.35
551 782 2.225791 TATCGCGCTCACTGTTGGCT 62.226 55.000 5.56 0.00 0.00 4.75
552 783 1.154205 ATATCGCGCTCACTGTTGGC 61.154 55.000 5.56 0.00 0.00 4.52
553 784 0.855349 GATATCGCGCTCACTGTTGG 59.145 55.000 5.56 0.00 0.00 3.77
580 811 2.348872 CGCCAGTATGATCATCGCAAAC 60.349 50.000 12.53 4.37 39.69 2.93
666 897 2.069273 GTGACTTGACTGAATCCGGTG 58.931 52.381 0.00 0.00 30.59 4.94
721 953 3.242641 ACGAAACTTGAAAAACGAGGAGC 60.243 43.478 0.00 0.00 34.46 4.70
723 955 3.933955 TGACGAAACTTGAAAAACGAGGA 59.066 39.130 0.00 0.00 34.46 3.71
771 1005 2.408050 GAGTATGTCAGGCGGCTATTG 58.592 52.381 12.74 0.00 0.00 1.90
776 1010 0.882042 CATGGAGTATGTCAGGCGGC 60.882 60.000 0.00 0.00 31.92 6.53
788 1870 2.559668 CACATTTTGAGCCACATGGAGT 59.440 45.455 0.87 0.00 37.39 3.85
789 1871 2.821378 TCACATTTTGAGCCACATGGAG 59.179 45.455 0.87 0.00 37.39 3.86
790 1872 2.874014 TCACATTTTGAGCCACATGGA 58.126 42.857 0.87 0.00 37.39 3.41
791 1873 3.663995 TTCACATTTTGAGCCACATGG 57.336 42.857 0.00 0.00 34.94 3.66
792 1874 7.655236 TTTTATTCACATTTTGAGCCACATG 57.345 32.000 0.00 0.00 34.94 3.21
826 1908 8.046708 GGGGCTTTGTTCTTCCATTTAATATTT 58.953 33.333 0.00 0.00 0.00 1.40
827 1909 7.564793 GGGGCTTTGTTCTTCCATTTAATATT 58.435 34.615 0.00 0.00 0.00 1.28
828 1910 6.183360 CGGGGCTTTGTTCTTCCATTTAATAT 60.183 38.462 0.00 0.00 0.00 1.28
829 1911 5.126384 CGGGGCTTTGTTCTTCCATTTAATA 59.874 40.000 0.00 0.00 0.00 0.98
830 1912 4.081697 CGGGGCTTTGTTCTTCCATTTAAT 60.082 41.667 0.00 0.00 0.00 1.40
831 1913 3.257127 CGGGGCTTTGTTCTTCCATTTAA 59.743 43.478 0.00 0.00 0.00 1.52
832 1914 2.823154 CGGGGCTTTGTTCTTCCATTTA 59.177 45.455 0.00 0.00 0.00 1.40
937 2083 5.541845 TGTTGGAAATGTTTTTGTGTGTGA 58.458 33.333 0.00 0.00 0.00 3.58
947 2093 9.100197 AGGTTTTATAGGATGTTGGAAATGTTT 57.900 29.630 0.00 0.00 0.00 2.83
958 2106 4.079958 GTGGTGGGAGGTTTTATAGGATGT 60.080 45.833 0.00 0.00 0.00 3.06
980 2128 4.070552 GCTTCTCGTGGAGGGCGT 62.071 66.667 0.00 0.00 0.00 5.68
1039 2190 1.909986 TGGTCGATGGTGGGTTAATGA 59.090 47.619 0.00 0.00 0.00 2.57
1051 2202 3.561213 CTGCGCTGCTGGTCGATG 61.561 66.667 9.73 0.00 0.00 3.84
1544 2736 2.045438 ACCGAATGGCCAATGCGA 60.045 55.556 21.98 0.00 40.05 5.10
1550 2742 4.634703 ACGCACACCGAATGGCCA 62.635 61.111 8.56 8.56 41.02 5.36
1564 2756 2.386660 GCCTGAGAACAGAGCACGC 61.387 63.158 0.00 0.00 46.03 5.34
1625 2851 2.278336 CATGCTTGCGCCATTCCG 60.278 61.111 4.18 0.00 34.43 4.30
1733 2969 4.404098 CCACTACCACCGGCCACC 62.404 72.222 0.00 0.00 0.00 4.61
1764 3006 1.737793 GCCGTCTCCGATTCACAATTT 59.262 47.619 0.00 0.00 35.63 1.82
1822 3071 6.148976 TCAAGCAGTATATAGCTGGTACTACG 59.851 42.308 13.67 0.00 42.91 3.51
1835 3100 3.543680 AACCGCAGTCAAGCAGTATAT 57.456 42.857 0.00 0.00 0.00 0.86
1837 3102 2.496070 TCTAACCGCAGTCAAGCAGTAT 59.504 45.455 0.00 0.00 0.00 2.12
1849 3123 5.992829 TCATTACAAGTTTCTTCTAACCGCA 59.007 36.000 0.00 0.00 0.00 5.69
1939 3215 3.330701 AGGAAGACAAGCTTGTAATGGGA 59.669 43.478 31.20 0.00 42.43 4.37
1993 3270 3.511934 ACGATCTACATCTAGCCATTCCC 59.488 47.826 0.00 0.00 0.00 3.97
2011 3288 5.601662 ACCAATATTCGACAATCAGACGAT 58.398 37.500 0.00 0.00 43.37 3.73
2039 3316 2.312436 CGACGTCCCAAAACGGTCC 61.312 63.158 10.58 0.00 46.72 4.46
2078 3355 0.107945 CGGAGGAAGAAGAAGGGCTG 60.108 60.000 0.00 0.00 0.00 4.85
2093 3370 1.394618 AGGAAAGAGACGATCCGGAG 58.605 55.000 11.34 0.00 38.31 4.63
2097 3374 5.216648 CGATTCTAAGGAAAGAGACGATCC 58.783 45.833 0.00 0.00 34.90 3.36
2099 3376 4.500035 GGCGATTCTAAGGAAAGAGACGAT 60.500 45.833 0.00 0.00 34.90 3.73
2102 3379 3.118738 TGGGCGATTCTAAGGAAAGAGAC 60.119 47.826 0.00 0.00 34.90 3.36
2111 3388 2.247437 GCGGCTGGGCGATTCTAAG 61.247 63.158 20.08 0.00 0.00 2.18
2123 3400 4.408821 TTAGGCTGGTGGCGGCTG 62.409 66.667 11.43 0.00 44.18 4.85
2134 3411 4.785453 GGCAGCAGCGGTTAGGCT 62.785 66.667 0.00 0.00 46.13 4.58
2231 3509 2.122369 AAGGATAGGCGGGGAGGG 60.122 66.667 0.00 0.00 0.00 4.30
2240 3518 1.545706 GCCGGGGCTAGAAGGATAGG 61.546 65.000 2.18 0.00 38.26 2.57
2255 3533 1.296056 AAAATCTTCGTCGGTGCCGG 61.296 55.000 10.94 0.00 40.25 6.13
2270 3548 5.634859 GTGGTGCAATTTCATCGAAGAAAAT 59.365 36.000 18.57 8.75 43.58 1.82
2296 3574 2.774687 AATAACGGTGGTGGTGGGGC 62.775 60.000 0.00 0.00 0.00 5.80
2304 3582 0.036105 GGGGACGAAATAACGGTGGT 60.036 55.000 0.00 0.00 37.61 4.16
2306 3584 1.081094 GTGGGGACGAAATAACGGTG 58.919 55.000 0.00 0.00 37.61 4.94
2310 3588 0.394762 GGGGGTGGGGACGAAATAAC 60.395 60.000 0.00 0.00 0.00 1.89
2311 3589 0.845543 TGGGGGTGGGGACGAAATAA 60.846 55.000 0.00 0.00 0.00 1.40
2312 3590 1.229886 TGGGGGTGGGGACGAAATA 60.230 57.895 0.00 0.00 0.00 1.40
2313 3591 2.533232 TGGGGGTGGGGACGAAAT 60.533 61.111 0.00 0.00 0.00 2.17
2314 3592 3.572222 GTGGGGGTGGGGACGAAA 61.572 66.667 0.00 0.00 0.00 3.46
2315 3593 4.585216 AGTGGGGGTGGGGACGAA 62.585 66.667 0.00 0.00 0.00 3.85
2317 3595 3.612115 TAGAGTGGGGGTGGGGACG 62.612 68.421 0.00 0.00 0.00 4.79
2318 3596 1.229723 TTAGAGTGGGGGTGGGGAC 60.230 63.158 0.00 0.00 0.00 4.46
2319 3597 1.082206 CTTAGAGTGGGGGTGGGGA 59.918 63.158 0.00 0.00 0.00 4.81
2320 3598 0.327576 ATCTTAGAGTGGGGGTGGGG 60.328 60.000 0.00 0.00 0.00 4.96
2321 3599 2.090719 TCTATCTTAGAGTGGGGGTGGG 60.091 54.545 0.00 0.00 0.00 4.61
2322 3600 3.330126 TCTATCTTAGAGTGGGGGTGG 57.670 52.381 0.00 0.00 0.00 4.61
2323 3601 4.483950 TCATCTATCTTAGAGTGGGGGTG 58.516 47.826 0.00 0.00 38.38 4.61
2324 3602 4.834406 TCATCTATCTTAGAGTGGGGGT 57.166 45.455 0.00 0.00 38.38 4.95
2325 3603 4.469227 CCATCATCTATCTTAGAGTGGGGG 59.531 50.000 0.00 0.00 38.38 5.40
2326 3604 4.469227 CCCATCATCTATCTTAGAGTGGGG 59.531 50.000 16.86 9.79 44.20 4.96
2327 3605 4.469227 CCCCATCATCTATCTTAGAGTGGG 59.531 50.000 17.31 17.31 45.73 4.61
2328 3606 5.090139 ACCCCATCATCTATCTTAGAGTGG 58.910 45.833 0.00 6.49 38.38 4.00
2329 3607 6.127479 GCTACCCCATCATCTATCTTAGAGTG 60.127 46.154 0.00 0.00 38.38 3.51
2330 3608 5.955355 GCTACCCCATCATCTATCTTAGAGT 59.045 44.000 0.00 0.00 38.38 3.24
2331 3609 5.362430 GGCTACCCCATCATCTATCTTAGAG 59.638 48.000 0.00 0.00 38.38 2.43
2332 3610 5.273208 GGCTACCCCATCATCTATCTTAGA 58.727 45.833 0.00 0.00 39.50 2.10
2360 3638 1.450491 GGGAAGAAAGGAGCTCGCC 60.450 63.158 7.83 0.00 0.00 5.54
2368 3646 2.258748 GAGGCCCGAGGGAAGAAAGG 62.259 65.000 13.28 0.00 37.50 3.11
2384 3662 0.902531 TAAAGTTCGCCAGAGGGAGG 59.097 55.000 0.00 0.00 36.16 4.30
2385 3663 2.762535 TTAAAGTTCGCCAGAGGGAG 57.237 50.000 0.00 0.00 36.16 4.30
2392 3670 6.744112 AGTCAATTGATTTTAAAGTTCGCCA 58.256 32.000 12.12 0.00 0.00 5.69
2409 3687 7.922811 GGACTGACTTTTGATTTTGAGTCAATT 59.077 33.333 6.36 0.00 45.42 2.32
2411 3689 6.376864 TGGACTGACTTTTGATTTTGAGTCAA 59.623 34.615 0.08 0.08 45.42 3.18
2421 3699 3.244561 ACACGGATGGACTGACTTTTGAT 60.245 43.478 0.00 0.00 0.00 2.57
2422 3700 2.104111 ACACGGATGGACTGACTTTTGA 59.896 45.455 0.00 0.00 0.00 2.69
2424 3702 2.494059 CACACGGATGGACTGACTTTT 58.506 47.619 0.00 0.00 0.00 2.27
2434 3712 1.079127 GTGAGACCCACACGGATGG 60.079 63.158 0.28 0.28 45.03 3.51
2452 3730 1.399440 CAAGTCTCATTGTGCATCCGG 59.601 52.381 0.00 0.00 0.00 5.14
2490 3768 3.131577 CACTAGTTGGCTACGTATTCCCA 59.868 47.826 10.42 8.18 0.00 4.37
2491 3769 3.714391 CACTAGTTGGCTACGTATTCCC 58.286 50.000 10.42 6.00 0.00 3.97
2495 3773 5.509163 CCAATAGCACTAGTTGGCTACGTAT 60.509 44.000 15.10 0.87 44.62 3.06
2496 3774 4.202080 CCAATAGCACTAGTTGGCTACGTA 60.202 45.833 15.10 0.00 44.62 3.57
2497 3775 3.430374 CCAATAGCACTAGTTGGCTACGT 60.430 47.826 15.10 5.95 44.62 3.57
2498 3776 3.123804 CCAATAGCACTAGTTGGCTACG 58.876 50.000 15.10 10.34 44.62 3.51
2576 3891 7.227711 TCGATGGAGAATTTGTAAAAAGTGACA 59.772 33.333 0.00 0.00 0.00 3.58
2578 3893 7.444183 AGTCGATGGAGAATTTGTAAAAAGTGA 59.556 33.333 0.00 0.00 0.00 3.41
2580 3895 7.745620 AGTCGATGGAGAATTTGTAAAAAGT 57.254 32.000 0.00 0.00 0.00 2.66
2581 3896 9.760660 CTTAGTCGATGGAGAATTTGTAAAAAG 57.239 33.333 0.00 0.00 0.00 2.27
2589 3904 7.829211 TGAAAATCCTTAGTCGATGGAGAATTT 59.171 33.333 0.00 0.00 34.95 1.82
2598 3913 6.488006 CCCATTGATGAAAATCCTTAGTCGAT 59.512 38.462 0.00 0.00 0.00 3.59
2608 3923 3.781079 TCGTGCCCATTGATGAAAATC 57.219 42.857 0.00 0.00 0.00 2.17
2617 3932 6.313411 ACAAAATTATGAAATCGTGCCCATTG 59.687 34.615 0.00 0.00 0.00 2.82
2618 3933 6.405538 ACAAAATTATGAAATCGTGCCCATT 58.594 32.000 0.00 0.00 0.00 3.16
2619 3934 5.976458 ACAAAATTATGAAATCGTGCCCAT 58.024 33.333 0.00 0.00 0.00 4.00
2620 3935 5.398603 ACAAAATTATGAAATCGTGCCCA 57.601 34.783 0.00 0.00 0.00 5.36
2651 3966 3.390135 TGTAGCTAGCGGCATGTATTTC 58.610 45.455 9.55 0.00 44.79 2.17
2662 3977 3.254060 ACACACAATCTTGTAGCTAGCG 58.746 45.455 9.55 0.00 39.91 4.26
2668 3983 6.523201 GCCGATTTAAACACACAATCTTGTAG 59.477 38.462 0.00 0.00 39.91 2.74
2675 3990 3.823873 TGAGGCCGATTTAAACACACAAT 59.176 39.130 0.00 0.00 0.00 2.71
2677 3992 2.852449 TGAGGCCGATTTAAACACACA 58.148 42.857 0.00 0.00 0.00 3.72
2688 4003 6.306987 AGGAATAAATGTAATTGAGGCCGAT 58.693 36.000 0.00 0.00 36.10 4.18
2839 4154 5.104900 AGGGTCATATGTTCTTTCTAGCGTT 60.105 40.000 1.90 0.00 0.00 4.84
2863 4178 7.581814 TCCAACAGTGGGATCAAAATATCATA 58.418 34.615 0.00 0.00 46.01 2.15
2864 4179 6.434302 TCCAACAGTGGGATCAAAATATCAT 58.566 36.000 0.00 0.00 46.01 2.45
2875 4190 4.222336 TCACATTTTTCCAACAGTGGGAT 58.778 39.130 0.00 0.00 46.01 3.85
2879 4194 5.641209 TGGTTTTCACATTTTTCCAACAGTG 59.359 36.000 0.00 0.00 0.00 3.66
2880 4195 5.641636 GTGGTTTTCACATTTTTCCAACAGT 59.358 36.000 0.00 0.00 45.39 3.55
2905 4221 3.602946 CGCAAACACAAAGTCGTCGTAAT 60.603 43.478 0.00 0.00 0.00 1.89
2909 4225 1.253044 GCGCAAACACAAAGTCGTCG 61.253 55.000 0.30 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.