Multiple sequence alignment - TraesCS2A01G413100

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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 TraesCS2A01G413100 chr2A 100.000 3178 0 0 1 3178 670316235 670313058 0.000000e+00 5869.0
1 TraesCS2A01G413100 chr2A 83.333 90 13 2 1614 1703 140365144 140365057 7.310000e-12 82.4
2 TraesCS2A01G413100 chr2D 88.564 1644 65 37 628 2197 524933029 524931435 0.000000e+00 1881.0
3 TraesCS2A01G413100 chr2D 83.898 590 64 22 1 570 524933711 524933133 4.670000e-148 534.0
4 TraesCS2A01G413100 chr2D 86.100 259 22 6 2929 3178 524930511 524930258 1.880000e-67 267.0
5 TraesCS2A01G413100 chr2D 80.531 226 27 11 2240 2451 524931361 524931139 1.180000e-34 158.0
6 TraesCS2A01G413100 chr2B 84.643 1973 107 73 725 2566 620862124 620860217 0.000000e+00 1784.0
7 TraesCS2A01G413100 chr2B 88.750 400 32 3 185 571 620862991 620862592 7.980000e-131 477.0
8 TraesCS2A01G413100 chr2B 78.871 549 60 16 2664 3178 620859970 620859444 1.420000e-83 320.0
9 TraesCS2A01G413100 chr2B 91.667 84 6 1 628 711 620862496 620862414 7.200000e-22 115.0
10 TraesCS2A01G413100 chr6A 76.249 981 133 65 1144 2044 461644941 461645901 2.270000e-116 429.0
11 TraesCS2A01G413100 chr6D 76.165 944 132 63 1144 2009 324248449 324249377 8.200000e-111 411.0
12 TraesCS2A01G413100 chr1D 87.500 64 8 0 1637 1700 300025613 300025550 1.220000e-09 75.0
13 TraesCS2A01G413100 chr1B 87.500 64 8 0 1637 1700 404897886 404897823 1.220000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G413100 chr2A 670313058 670316235 3177 True 5869 5869 100.00000 1 3178 1 chr2A.!!$R2 3177
1 TraesCS2A01G413100 chr2D 524930258 524933711 3453 True 710 1881 84.77325 1 3178 4 chr2D.!!$R1 3177
2 TraesCS2A01G413100 chr2B 620859444 620862991 3547 True 674 1784 85.98275 185 3178 4 chr2B.!!$R1 2993
3 TraesCS2A01G413100 chr6A 461644941 461645901 960 False 429 429 76.24900 1144 2044 1 chr6A.!!$F1 900
4 TraesCS2A01G413100 chr6D 324248449 324249377 928 False 411 411 76.16500 1144 2009 1 chr6D.!!$F1 865

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
103 104 0.028637 GCCCTAGTACTACGACGTGC 59.971 60.0 11.56 0.0 0.0 5.34 F
383 414 0.040942 TTGTCCCCATCACCCCATTG 59.959 55.0 0.00 0.0 0.0 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1083 1494 0.253207 GGGAGGAAGGAAGGGAAGGA 60.253 60.0 0.0 0.0 0.0 3.36 R
2281 2904 0.030908 GCCCGATCTACTCTGTTCCG 59.969 60.0 0.0 0.0 0.0 4.30 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
48 49 1.338674 TGATGGACGTGTCATGGGTTC 60.339 52.381 0.00 0.00 0.00 3.62
49 50 0.984230 ATGGACGTGTCATGGGTTCT 59.016 50.000 0.00 0.00 0.00 3.01
50 51 0.320374 TGGACGTGTCATGGGTTCTC 59.680 55.000 0.00 0.00 0.00 2.87
51 52 0.736325 GGACGTGTCATGGGTTCTCG 60.736 60.000 0.00 0.00 0.00 4.04
52 53 0.242825 GACGTGTCATGGGTTCTCGA 59.757 55.000 0.00 0.00 0.00 4.04
53 54 0.895530 ACGTGTCATGGGTTCTCGAT 59.104 50.000 0.00 0.00 0.00 3.59
54 55 1.135083 ACGTGTCATGGGTTCTCGATC 60.135 52.381 0.00 0.00 0.00 3.69
55 56 1.560923 GTGTCATGGGTTCTCGATCG 58.439 55.000 9.36 9.36 0.00 3.69
56 57 1.134367 GTGTCATGGGTTCTCGATCGA 59.866 52.381 18.32 18.32 0.00 3.59
57 58 1.405463 TGTCATGGGTTCTCGATCGAG 59.595 52.381 34.20 34.20 43.21 4.04
59 60 1.676529 TCATGGGTTCTCGATCGAGTC 59.323 52.381 36.68 29.45 42.49 3.36
60 61 1.678627 CATGGGTTCTCGATCGAGTCT 59.321 52.381 36.68 17.68 42.49 3.24
61 62 1.095600 TGGGTTCTCGATCGAGTCTG 58.904 55.000 36.68 18.62 42.49 3.51
62 63 1.339727 TGGGTTCTCGATCGAGTCTGA 60.340 52.381 36.68 20.51 42.49 3.27
96 97 0.871057 CGTAGGCGCCCTAGTACTAC 59.129 60.000 26.15 16.05 36.71 2.73
103 104 0.028637 GCCCTAGTACTACGACGTGC 59.971 60.000 11.56 0.00 0.00 5.34
105 106 2.826428 CCCTAGTACTACGACGTGCTA 58.174 52.381 11.56 6.94 32.10 3.49
113 114 0.731514 TACGACGTGCTACTTGCTGC 60.732 55.000 11.56 0.00 43.37 5.25
116 117 1.355066 GACGTGCTACTTGCTGCTCC 61.355 60.000 0.00 0.00 43.37 4.70
117 118 2.103042 CGTGCTACTTGCTGCTCCC 61.103 63.158 0.00 0.00 43.37 4.30
118 119 1.003355 GTGCTACTTGCTGCTCCCA 60.003 57.895 0.00 0.00 43.37 4.37
119 120 1.003355 TGCTACTTGCTGCTCCCAC 60.003 57.895 0.00 0.00 43.37 4.61
130 161 3.706373 CTCCCACCACCACCTCCG 61.706 72.222 0.00 0.00 0.00 4.63
147 178 1.450211 CGGCTCCGGGGTCATAATT 59.550 57.895 6.79 0.00 35.56 1.40
148 179 0.179029 CGGCTCCGGGGTCATAATTT 60.179 55.000 6.79 0.00 35.56 1.82
149 180 1.605753 GGCTCCGGGGTCATAATTTC 58.394 55.000 0.00 0.00 0.00 2.17
150 181 1.143073 GGCTCCGGGGTCATAATTTCT 59.857 52.381 0.00 0.00 0.00 2.52
152 183 3.400255 GCTCCGGGGTCATAATTTCTAC 58.600 50.000 1.62 0.00 0.00 2.59
154 185 4.632153 CTCCGGGGTCATAATTTCTACAG 58.368 47.826 0.00 0.00 0.00 2.74
156 187 4.127171 CCGGGGTCATAATTTCTACAGTG 58.873 47.826 0.00 0.00 0.00 3.66
157 188 4.141801 CCGGGGTCATAATTTCTACAGTGA 60.142 45.833 0.00 0.00 0.00 3.41
158 189 5.454755 CCGGGGTCATAATTTCTACAGTGAT 60.455 44.000 0.00 0.00 0.00 3.06
159 190 6.055588 CGGGGTCATAATTTCTACAGTGATT 58.944 40.000 0.00 0.00 0.00 2.57
161 192 7.713507 CGGGGTCATAATTTCTACAGTGATTTA 59.286 37.037 0.00 0.00 0.00 1.40
162 193 9.403583 GGGGTCATAATTTCTACAGTGATTTAA 57.596 33.333 0.00 0.00 0.00 1.52
195 226 1.885887 TCCAAAGCGAATGGGAAAGTG 59.114 47.619 5.76 0.00 38.54 3.16
202 233 2.035321 GCGAATGGGAAAGTGGTGAAAA 59.965 45.455 0.00 0.00 0.00 2.29
204 235 3.067461 CGAATGGGAAAGTGGTGAAAACA 59.933 43.478 0.00 0.00 0.00 2.83
213 244 1.102154 TGGTGAAAACAGTGGTGCAG 58.898 50.000 0.00 0.00 0.00 4.41
218 249 2.680841 TGAAAACAGTGGTGCAGTGTAC 59.319 45.455 2.25 2.25 45.83 2.90
278 309 3.514645 CACAGCTGATTAATTTGCCACC 58.485 45.455 23.35 0.00 0.00 4.61
294 325 0.258484 CACCTATCACCAATGCCCCA 59.742 55.000 0.00 0.00 0.00 4.96
297 328 1.063717 CCTATCACCAATGCCCCAAGT 60.064 52.381 0.00 0.00 0.00 3.16
299 330 0.409092 ATCACCAATGCCCCAAGTCA 59.591 50.000 0.00 0.00 0.00 3.41
314 345 0.107456 AGTCACACTCCACCTTGCAG 59.893 55.000 0.00 0.00 0.00 4.41
358 389 0.390472 CGCTCTCCTTCTTGTCACCC 60.390 60.000 0.00 0.00 0.00 4.61
363 394 1.002544 CTCCTTCTTGTCACCCACTCC 59.997 57.143 0.00 0.00 0.00 3.85
383 414 0.040942 TTGTCCCCATCACCCCATTG 59.959 55.000 0.00 0.00 0.00 2.82
384 415 1.145900 TGTCCCCATCACCCCATTGT 61.146 55.000 0.00 0.00 0.00 2.71
385 416 0.684153 GTCCCCATCACCCCATTGTG 60.684 60.000 0.00 0.00 37.59 3.33
420 451 2.755655 CCCTACTCAACTCACTGATCGT 59.244 50.000 0.00 0.00 0.00 3.73
447 486 2.370445 CCGGAGCAAGGTGGAGGAT 61.370 63.158 0.00 0.00 0.00 3.24
458 498 0.620556 GTGGAGGATGGAAGCAAGGA 59.379 55.000 0.00 0.00 0.00 3.36
468 508 0.371645 GAAGCAAGGAAGCATCGTCG 59.628 55.000 0.00 0.00 36.85 5.12
548 593 4.275689 TCATATTGCGCAAGTCCCATAAAG 59.724 41.667 28.62 11.30 41.68 1.85
571 616 1.180029 AGAATTGACAGCCATGTGCC 58.820 50.000 2.95 0.00 40.68 5.01
572 617 0.889994 GAATTGACAGCCATGTGCCA 59.110 50.000 2.95 0.00 40.68 4.92
574 619 1.340088 ATTGACAGCCATGTGCCAAA 58.660 45.000 2.95 0.00 40.68 3.28
575 620 1.340088 TTGACAGCCATGTGCCAAAT 58.660 45.000 2.95 0.00 40.68 2.32
576 621 2.212812 TGACAGCCATGTGCCAAATA 57.787 45.000 2.95 0.00 40.68 1.40
597 724 3.198409 TCACATACCATCTCACATGGC 57.802 47.619 0.00 0.00 42.82 4.40
598 725 2.504996 TCACATACCATCTCACATGGCA 59.495 45.455 0.00 0.00 42.82 4.92
599 726 3.054508 TCACATACCATCTCACATGGCAA 60.055 43.478 0.00 0.00 42.82 4.52
600 727 3.314357 CACATACCATCTCACATGGCAAG 59.686 47.826 0.00 0.00 42.82 4.01
601 728 3.054139 ACATACCATCTCACATGGCAAGT 60.054 43.478 0.00 0.00 42.82 3.16
602 729 2.592102 ACCATCTCACATGGCAAGTT 57.408 45.000 0.00 0.00 42.82 2.66
603 730 3.719268 ACCATCTCACATGGCAAGTTA 57.281 42.857 0.00 0.00 42.82 2.24
604 731 4.240881 ACCATCTCACATGGCAAGTTAT 57.759 40.909 0.00 0.00 42.82 1.89
605 732 4.202441 ACCATCTCACATGGCAAGTTATC 58.798 43.478 0.00 0.00 42.82 1.75
606 733 4.201657 CCATCTCACATGGCAAGTTATCA 58.798 43.478 0.00 0.00 31.75 2.15
607 734 4.641541 CCATCTCACATGGCAAGTTATCAA 59.358 41.667 0.00 0.00 31.75 2.57
608 735 5.220989 CCATCTCACATGGCAAGTTATCAAG 60.221 44.000 0.00 0.00 31.75 3.02
609 736 3.691118 TCTCACATGGCAAGTTATCAAGC 59.309 43.478 0.00 0.00 0.00 4.01
610 737 3.419943 TCACATGGCAAGTTATCAAGCA 58.580 40.909 0.00 0.00 0.00 3.91
611 738 3.191162 TCACATGGCAAGTTATCAAGCAC 59.809 43.478 0.00 0.00 0.00 4.40
612 739 3.057386 CACATGGCAAGTTATCAAGCACA 60.057 43.478 0.00 0.00 0.00 4.57
613 740 3.573538 ACATGGCAAGTTATCAAGCACAA 59.426 39.130 0.00 0.00 0.00 3.33
614 741 4.039004 ACATGGCAAGTTATCAAGCACAAA 59.961 37.500 0.00 0.00 0.00 2.83
615 742 4.870123 TGGCAAGTTATCAAGCACAAAT 57.130 36.364 0.00 0.00 0.00 2.32
616 743 4.808558 TGGCAAGTTATCAAGCACAAATC 58.191 39.130 0.00 0.00 0.00 2.17
617 744 4.523943 TGGCAAGTTATCAAGCACAAATCT 59.476 37.500 0.00 0.00 0.00 2.40
618 745 5.098211 GGCAAGTTATCAAGCACAAATCTC 58.902 41.667 0.00 0.00 0.00 2.75
619 746 4.790140 GCAAGTTATCAAGCACAAATCTCG 59.210 41.667 0.00 0.00 0.00 4.04
620 747 4.606457 AGTTATCAAGCACAAATCTCGC 57.394 40.909 0.00 0.00 0.00 5.03
621 748 4.002982 AGTTATCAAGCACAAATCTCGCA 58.997 39.130 0.00 0.00 0.00 5.10
622 749 4.455533 AGTTATCAAGCACAAATCTCGCAA 59.544 37.500 0.00 0.00 0.00 4.85
623 750 3.921119 ATCAAGCACAAATCTCGCAAA 57.079 38.095 0.00 0.00 0.00 3.68
624 751 3.706802 TCAAGCACAAATCTCGCAAAA 57.293 38.095 0.00 0.00 0.00 2.44
625 752 4.039151 TCAAGCACAAATCTCGCAAAAA 57.961 36.364 0.00 0.00 0.00 1.94
662 789 5.164158 GCACAACTTATGCAAAATCGTTCAG 60.164 40.000 0.00 0.00 42.88 3.02
671 798 4.634004 TGCAAAATCGTTCAGGTATGGTAG 59.366 41.667 0.00 0.00 0.00 3.18
695 822 5.221303 GCAAATAATGGCTTGATTCCTGCTA 60.221 40.000 1.66 0.00 0.00 3.49
712 839 6.403878 TCCTGCTACTACCAAAAGTGTAATC 58.596 40.000 0.00 0.00 0.00 1.75
718 1123 1.883926 ACCAAAAGTGTAATCCCGTGC 59.116 47.619 0.00 0.00 0.00 5.34
719 1124 1.883275 CCAAAAGTGTAATCCCGTGCA 59.117 47.619 0.00 0.00 0.00 4.57
720 1125 2.294791 CCAAAAGTGTAATCCCGTGCAA 59.705 45.455 0.00 0.00 0.00 4.08
746 1151 0.239879 AACCGTGCTAAACAATGCGG 59.760 50.000 0.00 0.00 40.36 5.69
803 1208 6.480524 TGGATTCAGTACATTTCTTTCGTG 57.519 37.500 0.00 0.00 0.00 4.35
807 1212 3.186409 TCAGTACATTTCTTTCGTGCTGC 59.814 43.478 0.00 0.00 41.43 5.25
808 1213 3.187227 CAGTACATTTCTTTCGTGCTGCT 59.813 43.478 0.00 0.00 36.74 4.24
809 1214 2.693797 ACATTTCTTTCGTGCTGCTG 57.306 45.000 0.00 0.00 0.00 4.41
810 1215 1.334054 CATTTCTTTCGTGCTGCTGC 58.666 50.000 8.89 8.89 40.20 5.25
811 1216 1.068748 CATTTCTTTCGTGCTGCTGCT 60.069 47.619 17.00 0.00 40.48 4.24
812 1217 0.308684 TTTCTTTCGTGCTGCTGCTG 59.691 50.000 17.00 9.33 40.48 4.41
895 1306 3.368248 ACAGAGCAAATACCAATGGCAT 58.632 40.909 0.00 0.00 0.00 4.40
896 1307 3.131577 ACAGAGCAAATACCAATGGCATG 59.868 43.478 0.00 0.00 0.00 4.06
897 1308 2.696707 AGAGCAAATACCAATGGCATGG 59.303 45.455 0.00 7.58 46.38 3.66
898 1309 1.139455 AGCAAATACCAATGGCATGGC 59.861 47.619 13.29 13.29 44.75 4.40
899 1310 1.134461 GCAAATACCAATGGCATGGCA 60.134 47.619 25.52 25.52 44.75 4.92
900 1311 2.485835 GCAAATACCAATGGCATGGCAT 60.486 45.455 27.75 27.75 44.75 4.40
901 1312 3.244146 GCAAATACCAATGGCATGGCATA 60.244 43.478 32.36 18.79 44.75 3.14
902 1313 4.562082 CAAATACCAATGGCATGGCATAG 58.438 43.478 32.36 27.05 44.75 2.23
903 1314 3.530928 ATACCAATGGCATGGCATAGT 57.469 42.857 32.36 30.39 44.75 2.12
904 1315 4.656100 ATACCAATGGCATGGCATAGTA 57.344 40.909 32.36 31.28 44.75 1.82
905 1316 2.867624 ACCAATGGCATGGCATAGTAG 58.132 47.619 32.36 22.35 44.75 2.57
927 1338 4.591924 AGTAATAAGTGGAGAATACGGGGG 59.408 45.833 0.00 0.00 0.00 5.40
943 1354 4.468689 GGGCCGTCCGGGAAAGAG 62.469 72.222 7.97 0.00 38.47 2.85
944 1355 3.387947 GGCCGTCCGGGAAAGAGA 61.388 66.667 7.97 0.00 38.47 3.10
945 1356 2.184579 GCCGTCCGGGAAAGAGAG 59.815 66.667 7.97 0.00 38.47 3.20
946 1357 2.893398 CCGTCCGGGAAAGAGAGG 59.107 66.667 0.00 0.00 38.47 3.69
955 1366 2.689034 AAAGAGAGGGAGGGGGCG 60.689 66.667 0.00 0.00 0.00 6.13
984 1395 5.993748 AAAGAATGGAATAAAAGGCGGAA 57.006 34.783 0.00 0.00 0.00 4.30
985 1396 5.582689 AAGAATGGAATAAAAGGCGGAAG 57.417 39.130 0.00 0.00 0.00 3.46
986 1397 3.954258 AGAATGGAATAAAAGGCGGAAGG 59.046 43.478 0.00 0.00 0.00 3.46
987 1398 3.662759 ATGGAATAAAAGGCGGAAGGA 57.337 42.857 0.00 0.00 0.00 3.36
988 1399 3.443145 TGGAATAAAAGGCGGAAGGAA 57.557 42.857 0.00 0.00 0.00 3.36
989 1400 3.352648 TGGAATAAAAGGCGGAAGGAAG 58.647 45.455 0.00 0.00 0.00 3.46
990 1401 2.688446 GGAATAAAAGGCGGAAGGAAGG 59.312 50.000 0.00 0.00 0.00 3.46
991 1402 2.437085 ATAAAAGGCGGAAGGAAGGG 57.563 50.000 0.00 0.00 0.00 3.95
1031 1442 0.319555 TTCCAACTTCCGCAGACGAG 60.320 55.000 0.00 0.00 43.93 4.18
1082 1493 1.173444 ACTCTCTCGCACACTCCGTT 61.173 55.000 0.00 0.00 0.00 4.44
1083 1494 0.039074 CTCTCTCGCACACTCCGTTT 60.039 55.000 0.00 0.00 0.00 3.60
1084 1495 0.039437 TCTCTCGCACACTCCGTTTC 60.039 55.000 0.00 0.00 0.00 2.78
1085 1496 1.006571 TCTCGCACACTCCGTTTCC 60.007 57.895 0.00 0.00 0.00 3.13
1086 1497 1.006102 CTCGCACACTCCGTTTCCT 60.006 57.895 0.00 0.00 0.00 3.36
1087 1498 0.600255 CTCGCACACTCCGTTTCCTT 60.600 55.000 0.00 0.00 0.00 3.36
1088 1499 0.599204 TCGCACACTCCGTTTCCTTC 60.599 55.000 0.00 0.00 0.00 3.46
1089 1500 1.566018 CGCACACTCCGTTTCCTTCC 61.566 60.000 0.00 0.00 0.00 3.46
1090 1501 1.235281 GCACACTCCGTTTCCTTCCC 61.235 60.000 0.00 0.00 0.00 3.97
1130 1546 4.617959 TCGTATTTTTAGCCATCTCTCGG 58.382 43.478 0.00 0.00 0.00 4.63
2044 2590 1.602888 AGGCCACTGAAGCAAGCAG 60.603 57.895 5.01 0.00 39.26 4.24
2085 2649 2.424705 TTCCTTTCGGTCGGTCGGTG 62.425 60.000 0.00 0.00 0.00 4.94
2105 2669 1.614317 GGGTTGGTTCCAGTGGAGATG 60.614 57.143 12.67 0.00 31.21 2.90
2118 2682 1.298014 GAGATGGATGATCCGGGCC 59.702 63.158 7.03 0.00 40.17 5.80
2125 2689 0.321122 GATGATCCGGGCCTGTGATC 60.321 60.000 25.08 25.08 36.33 2.92
2173 2737 5.838529 GCAGTAAGCCAAAAAGGTAAAGAA 58.161 37.500 0.00 0.00 40.61 2.52
2174 2738 5.920840 GCAGTAAGCCAAAAAGGTAAAGAAG 59.079 40.000 0.00 0.00 40.61 2.85
2175 2739 6.238925 GCAGTAAGCCAAAAAGGTAAAGAAGA 60.239 38.462 0.00 0.00 40.61 2.87
2197 2761 7.825331 AGAAAAGGGTTAAGAAAAAGAGAGG 57.175 36.000 0.00 0.00 0.00 3.69
2202 2766 4.399618 GGGTTAAGAAAAAGAGAGGCATCC 59.600 45.833 0.00 0.00 0.00 3.51
2207 2771 3.769844 AGAAAAAGAGAGGCATCCGTCTA 59.230 43.478 0.00 0.00 36.40 2.59
2224 2806 6.275335 TCCGTCTATGGGTAGTTATTTTTCG 58.725 40.000 0.00 0.00 0.00 3.46
2238 2861 6.147328 AGTTATTTTTCGTGCTGTAGTTCTCC 59.853 38.462 0.00 0.00 0.00 3.71
2247 2870 2.294074 CTGTAGTTCTCCTCTCCCTCG 58.706 57.143 0.00 0.00 0.00 4.63
2281 2904 7.115663 TGTGTCTTTTTGTTTGTTTCAAGCTAC 59.884 33.333 0.00 0.00 0.00 3.58
2319 2946 1.579932 CAGCAAACAGAGCCAGCTG 59.420 57.895 6.78 6.78 45.44 4.24
2335 2962 2.586258 GCTGCTGCTGCTAGTTAGTA 57.414 50.000 22.10 0.00 40.48 1.82
2337 2964 3.462021 GCTGCTGCTGCTAGTTAGTATT 58.538 45.455 22.10 0.00 40.48 1.89
2338 2965 3.247173 GCTGCTGCTGCTAGTTAGTATTG 59.753 47.826 22.10 0.00 40.48 1.90
2341 2968 5.245531 TGCTGCTGCTAGTTAGTATTGTTT 58.754 37.500 17.00 0.00 40.48 2.83
2342 2969 5.351465 TGCTGCTGCTAGTTAGTATTGTTTC 59.649 40.000 17.00 0.00 40.48 2.78
2343 2970 5.582665 GCTGCTGCTAGTTAGTATTGTTTCT 59.417 40.000 8.53 0.00 36.03 2.52
2344 2971 6.237969 GCTGCTGCTAGTTAGTATTGTTTCTC 60.238 42.308 8.53 0.00 36.03 2.87
2346 2973 7.386851 TGCTGCTAGTTAGTATTGTTTCTCTT 58.613 34.615 0.00 0.00 0.00 2.85
2347 2974 7.878127 TGCTGCTAGTTAGTATTGTTTCTCTTT 59.122 33.333 0.00 0.00 0.00 2.52
2348 2975 8.722394 GCTGCTAGTTAGTATTGTTTCTCTTTT 58.278 33.333 0.00 0.00 0.00 2.27
2353 2980 8.100508 AGTTAGTATTGTTTCTCTTTTGGCTC 57.899 34.615 0.00 0.00 0.00 4.70
2411 3060 3.134458 AGCTAAACTGTTGCTGTCTGTC 58.866 45.455 4.75 0.00 35.54 3.51
2443 3092 2.945668 GCTGTTCTTGTTCCAACTGTCT 59.054 45.455 0.00 0.00 0.00 3.41
2452 3101 5.276461 TGTTCCAACTGTCTATCGCATAT 57.724 39.130 0.00 0.00 0.00 1.78
2453 3102 5.670485 TGTTCCAACTGTCTATCGCATATT 58.330 37.500 0.00 0.00 0.00 1.28
2454 3103 6.811954 TGTTCCAACTGTCTATCGCATATTA 58.188 36.000 0.00 0.00 0.00 0.98
2455 3104 6.923508 TGTTCCAACTGTCTATCGCATATTAG 59.076 38.462 0.00 0.00 0.00 1.73
2456 3105 5.470368 TCCAACTGTCTATCGCATATTAGC 58.530 41.667 0.00 0.00 0.00 3.09
2457 3106 5.010617 TCCAACTGTCTATCGCATATTAGCA 59.989 40.000 0.00 0.00 0.00 3.49
2458 3107 5.871524 CCAACTGTCTATCGCATATTAGCAT 59.128 40.000 0.00 0.00 0.00 3.79
2459 3108 7.035612 CCAACTGTCTATCGCATATTAGCATA 58.964 38.462 0.00 0.00 0.00 3.14
2471 3120 1.250328 TTAGCATAGCATGGCATGGC 58.750 50.000 27.48 21.19 0.00 4.40
2473 3122 0.541998 AGCATAGCATGGCATGGCAT 60.542 50.000 27.75 27.75 0.00 4.40
2474 3123 0.389817 GCATAGCATGGCATGGCATG 60.390 55.000 42.44 42.44 0.00 4.06
2475 3124 0.246360 CATAGCATGGCATGGCATGG 59.754 55.000 44.47 31.51 0.00 3.66
2482 3131 3.290567 GCATGGCATGGCACTTCA 58.709 55.556 25.84 0.45 0.00 3.02
2528 3193 2.437359 GGCAGGCAGGCAGTAGTG 60.437 66.667 0.00 0.00 43.51 2.74
2556 3234 6.401367 GCCATAAGCAACAAAATAGCAACAAG 60.401 38.462 0.00 0.00 42.97 3.16
2566 3244 4.978083 AATAGCAACAAGAATGCAGGAG 57.022 40.909 0.00 0.00 46.22 3.69
2591 3428 0.958822 AAAAGGGCCGCTGTACTTTG 59.041 50.000 0.00 0.00 33.79 2.77
2618 3455 3.390521 TAGCCCAGCCCACGTCTG 61.391 66.667 0.00 0.00 0.00 3.51
2622 3459 4.767255 CCAGCCCACGTCTGCCTC 62.767 72.222 2.35 0.00 0.00 4.70
2645 3482 1.384191 GCTTCCCACCACATTCCCT 59.616 57.895 0.00 0.00 0.00 4.20
2662 3540 0.749454 CCTTCCCCATACTGTGCTGC 60.749 60.000 0.00 0.00 0.00 5.25
2692 3570 3.322211 TGAATCCTGCAAGCAAAATGG 57.678 42.857 0.00 0.00 0.00 3.16
2701 3585 2.857748 GCAAGCAAAATGGCCGTATAAC 59.142 45.455 0.00 0.00 0.00 1.89
2714 3598 5.038683 GGCCGTATAACCAACAAATAAAGC 58.961 41.667 0.00 0.00 0.00 3.51
2761 3654 2.386661 ACAGCCGTGAAGATTACCTG 57.613 50.000 0.00 0.00 0.00 4.00
2770 3663 3.065925 GTGAAGATTACCTGCTCCATTGC 59.934 47.826 0.00 0.00 0.00 3.56
2773 3666 1.336125 GATTACCTGCTCCATTGCTGC 59.664 52.381 0.00 0.00 0.00 5.25
2777 3670 1.506718 CTGCTCCATTGCTGCTGTG 59.493 57.895 0.00 0.00 0.00 3.66
2784 3677 0.663269 CATTGCTGCTGTGCACTGTG 60.663 55.000 22.70 16.83 43.20 3.66
2861 3754 2.922503 GGGGCTGGGTTTGTTGGG 60.923 66.667 0.00 0.00 0.00 4.12
2866 3759 2.038814 GCTGGGTTTGTTGGGTTGGG 62.039 60.000 0.00 0.00 0.00 4.12
2879 3772 1.225704 GTTGGGGCCTGGATCTCTG 59.774 63.158 0.84 0.00 0.00 3.35
2881 3774 1.274703 TTGGGGCCTGGATCTCTGTC 61.275 60.000 0.84 0.00 0.00 3.51
2884 3777 0.107459 GGGCCTGGATCTCTGTCAAC 60.107 60.000 0.84 0.00 0.00 3.18
2887 3780 1.277557 GCCTGGATCTCTGTCAACAGT 59.722 52.381 9.82 0.00 44.12 3.55
2889 3782 3.332919 CCTGGATCTCTGTCAACAGTTG 58.667 50.000 6.99 6.99 44.12 3.16
2892 3812 2.303022 GGATCTCTGTCAACAGTTGGGA 59.697 50.000 13.52 8.48 44.12 4.37
2905 3825 3.950861 TTGGGAGGGAGGCCTCTGG 62.951 68.421 31.36 0.00 37.05 3.86
2909 3829 2.285743 AGGGAGGCCTCTGGAACC 60.286 66.667 31.36 22.82 0.00 3.62
2931 3874 0.687757 AGCCGATTCTGCAGGAGGTA 60.688 55.000 15.13 0.00 0.00 3.08
2935 3878 2.544685 CGATTCTGCAGGAGGTAGTTG 58.455 52.381 15.13 0.00 0.00 3.16
3004 3951 3.130633 CCTATGTTTGGATTCGCATCGA 58.869 45.455 0.00 0.00 0.00 3.59
3014 3966 1.532604 TTCGCATCGACTGGTCAGGT 61.533 55.000 2.87 0.00 34.89 4.00
3025 3977 2.357517 GTCAGGTCAGTGGCCACG 60.358 66.667 29.68 23.21 36.20 4.94
3026 3978 2.523168 TCAGGTCAGTGGCCACGA 60.523 61.111 29.68 25.01 36.20 4.35
3029 3981 2.668550 GGTCAGTGGCCACGAACC 60.669 66.667 33.24 33.24 35.02 3.62
3031 3983 1.668151 GTCAGTGGCCACGAACCTC 60.668 63.158 29.68 13.68 36.20 3.85
3066 4018 4.271049 CGATATTGACTAACTTGTGCTGGG 59.729 45.833 0.00 0.00 0.00 4.45
3091 4043 0.928229 CAGGATAGTTAACGCACGCC 59.072 55.000 0.00 0.00 0.00 5.68
3097 4049 1.648504 AGTTAACGCACGCCTAATCC 58.351 50.000 0.00 0.00 0.00 3.01
3101 4053 4.215742 CGCACGCCTAATCCGGGA 62.216 66.667 0.00 0.00 0.00 5.14
3112 4064 5.337330 CGCCTAATCCGGGATTATTCTTAGT 60.337 44.000 25.56 3.89 34.57 2.24
3127 4079 3.703420 TCTTAGTTTAATCGGCTCGCTC 58.297 45.455 0.00 0.00 0.00 5.03
3141 4093 2.589492 CGCTCTTGCTAATCGCCGG 61.589 63.158 0.00 0.00 38.05 6.13
3142 4094 2.886782 GCTCTTGCTAATCGCCGGC 61.887 63.158 19.07 19.07 38.05 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.570663 GATCAGCGTCGTCCCGGG 62.571 72.222 16.85 16.85 0.00 5.73
18 19 0.101399 ACGTCCATCAGATCAGCGTC 59.899 55.000 0.00 0.00 0.00 5.19
21 22 1.134995 TGACACGTCCATCAGATCAGC 60.135 52.381 0.00 0.00 0.00 4.26
27 28 0.250234 ACCCATGACACGTCCATCAG 59.750 55.000 0.00 0.00 0.00 2.90
48 49 3.181525 CCGTATCATCAGACTCGATCGAG 60.182 52.174 36.95 36.95 46.91 4.04
49 50 2.737252 CCGTATCATCAGACTCGATCGA 59.263 50.000 18.32 18.32 0.00 3.59
50 51 2.726373 GCCGTATCATCAGACTCGATCG 60.726 54.545 9.36 9.36 0.00 3.69
51 52 2.726373 CGCCGTATCATCAGACTCGATC 60.726 54.545 0.00 0.00 0.00 3.69
52 53 1.197949 CGCCGTATCATCAGACTCGAT 59.802 52.381 0.00 0.00 0.00 3.59
53 54 0.586802 CGCCGTATCATCAGACTCGA 59.413 55.000 0.00 0.00 0.00 4.04
54 55 0.586802 TCGCCGTATCATCAGACTCG 59.413 55.000 0.00 0.00 0.00 4.18
55 56 1.333931 TGTCGCCGTATCATCAGACTC 59.666 52.381 0.00 0.00 0.00 3.36
56 57 1.335182 CTGTCGCCGTATCATCAGACT 59.665 52.381 0.00 0.00 0.00 3.24
57 58 1.759994 CTGTCGCCGTATCATCAGAC 58.240 55.000 0.00 0.00 0.00 3.51
59 60 1.271446 CGCTGTCGCCGTATCATCAG 61.271 60.000 0.00 0.00 0.00 2.90
60 61 1.299089 CGCTGTCGCCGTATCATCA 60.299 57.895 0.00 0.00 0.00 3.07
61 62 0.040692 TACGCTGTCGCCGTATCATC 60.041 55.000 0.00 0.00 39.88 2.92
62 63 0.040336 CTACGCTGTCGCCGTATCAT 60.040 55.000 0.00 0.00 40.01 2.45
87 88 4.781570 GCAAGTAGCACGTCGTAGTACTAG 60.782 50.000 15.55 0.00 44.79 2.57
103 104 0.674895 GTGGTGGGAGCAGCAAGTAG 60.675 60.000 0.00 0.00 34.15 2.57
105 106 2.113986 GTGGTGGGAGCAGCAAGT 59.886 61.111 0.00 0.00 34.15 3.16
113 114 3.706373 CGGAGGTGGTGGTGGGAG 61.706 72.222 0.00 0.00 0.00 4.30
130 161 1.143073 AGAAATTATGACCCCGGAGCC 59.857 52.381 0.73 0.00 0.00 4.70
171 202 4.141824 ACTTTCCCATTCGCTTTGGAAAAA 60.142 37.500 0.00 5.24 44.01 1.94
172 203 3.386402 ACTTTCCCATTCGCTTTGGAAAA 59.614 39.130 0.00 0.00 44.01 2.29
173 204 2.962421 ACTTTCCCATTCGCTTTGGAAA 59.038 40.909 0.00 0.00 42.86 3.13
174 205 2.295909 CACTTTCCCATTCGCTTTGGAA 59.704 45.455 0.31 0.00 36.26 3.53
175 206 1.885887 CACTTTCCCATTCGCTTTGGA 59.114 47.619 0.31 0.00 36.26 3.53
176 207 1.067635 CCACTTTCCCATTCGCTTTGG 60.068 52.381 0.00 0.00 0.00 3.28
177 208 1.613437 ACCACTTTCCCATTCGCTTTG 59.387 47.619 0.00 0.00 0.00 2.77
178 209 1.613437 CACCACTTTCCCATTCGCTTT 59.387 47.619 0.00 0.00 0.00 3.51
179 210 1.202879 TCACCACTTTCCCATTCGCTT 60.203 47.619 0.00 0.00 0.00 4.68
180 211 0.400213 TCACCACTTTCCCATTCGCT 59.600 50.000 0.00 0.00 0.00 4.93
181 212 1.243902 TTCACCACTTTCCCATTCGC 58.756 50.000 0.00 0.00 0.00 4.70
182 213 3.067461 TGTTTTCACCACTTTCCCATTCG 59.933 43.478 0.00 0.00 0.00 3.34
183 214 4.099419 ACTGTTTTCACCACTTTCCCATTC 59.901 41.667 0.00 0.00 0.00 2.67
195 226 1.102978 ACTGCACCACTGTTTTCACC 58.897 50.000 0.00 0.00 0.00 4.02
202 233 0.529773 CACGTACACTGCACCACTGT 60.530 55.000 0.00 0.00 0.00 3.55
204 235 0.249322 GTCACGTACACTGCACCACT 60.249 55.000 0.00 0.00 0.00 4.00
213 244 1.300388 ACGCAAGGGTCACGTACAC 60.300 57.895 0.00 0.00 46.39 2.90
260 291 5.300286 GTGATAGGTGGCAAATTAATCAGCT 59.700 40.000 10.36 10.36 40.44 4.24
278 309 2.301346 GACTTGGGGCATTGGTGATAG 58.699 52.381 0.00 0.00 0.00 2.08
294 325 0.546122 TGCAAGGTGGAGTGTGACTT 59.454 50.000 0.00 0.00 0.00 3.01
383 414 5.828859 TGAGTAGGGTAGATAAAGAGCTCAC 59.171 44.000 17.77 2.80 0.00 3.51
384 415 6.014771 TGAGTAGGGTAGATAAAGAGCTCA 57.985 41.667 17.77 0.00 0.00 4.26
385 416 6.548251 AGTTGAGTAGGGTAGATAAAGAGCTC 59.452 42.308 5.27 5.27 0.00 4.09
447 486 0.036732 ACGATGCTTCCTTGCTTCCA 59.963 50.000 0.00 0.00 34.79 3.53
458 498 0.392998 AATCAAGGGCGACGATGCTT 60.393 50.000 0.00 0.00 34.52 3.91
468 508 1.690352 CCATCCATCCAAATCAAGGGC 59.310 52.381 0.00 0.00 0.00 5.19
548 593 2.165030 CACATGGCTGTCAATTCTTCCC 59.835 50.000 0.00 0.00 31.62 3.97
571 616 7.574404 GCCATGTGAGATGGTATGTGATATTTG 60.574 40.741 10.53 0.00 41.17 2.32
572 617 6.432162 GCCATGTGAGATGGTATGTGATATTT 59.568 38.462 10.53 0.00 41.17 1.40
574 619 5.013391 TGCCATGTGAGATGGTATGTGATAT 59.987 40.000 10.53 0.00 41.17 1.63
575 620 4.347583 TGCCATGTGAGATGGTATGTGATA 59.652 41.667 10.53 0.00 41.17 2.15
576 621 3.136992 TGCCATGTGAGATGGTATGTGAT 59.863 43.478 10.53 0.00 41.17 3.06
597 724 4.790140 GCGAGATTTGTGCTTGATAACTTG 59.210 41.667 0.00 0.00 0.00 3.16
598 725 4.455533 TGCGAGATTTGTGCTTGATAACTT 59.544 37.500 0.00 0.00 0.00 2.66
599 726 4.002982 TGCGAGATTTGTGCTTGATAACT 58.997 39.130 0.00 0.00 0.00 2.24
600 727 4.340894 TGCGAGATTTGTGCTTGATAAC 57.659 40.909 0.00 0.00 0.00 1.89
601 728 5.369685 TTTGCGAGATTTGTGCTTGATAA 57.630 34.783 0.00 0.00 0.00 1.75
602 729 5.369685 TTTTGCGAGATTTGTGCTTGATA 57.630 34.783 0.00 0.00 0.00 2.15
603 730 3.921119 TTTGCGAGATTTGTGCTTGAT 57.079 38.095 0.00 0.00 0.00 2.57
604 731 3.706802 TTTTGCGAGATTTGTGCTTGA 57.293 38.095 0.00 0.00 0.00 3.02
625 752 7.925483 TGCATAAGTTGTGCTTGATAACTTTTT 59.075 29.630 22.91 0.00 41.77 1.94
626 753 7.432869 TGCATAAGTTGTGCTTGATAACTTTT 58.567 30.769 22.91 0.00 41.77 2.27
662 789 5.534654 TCAAGCCATTATTTGCTACCATACC 59.465 40.000 0.00 0.00 36.66 2.73
671 798 3.805971 GCAGGAATCAAGCCATTATTTGC 59.194 43.478 0.00 0.00 0.00 3.68
695 822 4.320870 CACGGGATTACACTTTTGGTAGT 58.679 43.478 0.00 0.00 0.00 2.73
731 1136 1.270971 CATGCCGCATTGTTTAGCAC 58.729 50.000 2.16 0.00 36.06 4.40
746 1151 4.101790 CCGCGTTGTGGTCCATGC 62.102 66.667 4.92 0.00 0.00 4.06
781 1186 5.122396 AGCACGAAAGAAATGTACTGAATCC 59.878 40.000 0.00 0.00 0.00 3.01
803 1208 4.090642 CGTAAGTATATTAGCAGCAGCAGC 59.909 45.833 3.17 0.46 45.49 5.25
807 1212 7.911205 GGTAGATCGTAAGTATATTAGCAGCAG 59.089 40.741 0.00 0.00 39.48 4.24
808 1213 7.392393 TGGTAGATCGTAAGTATATTAGCAGCA 59.608 37.037 0.00 0.00 39.48 4.41
809 1214 7.759465 TGGTAGATCGTAAGTATATTAGCAGC 58.241 38.462 0.00 0.00 39.48 5.25
840 1246 4.497473 TTTTGCCGAGTTATTGTTCTGG 57.503 40.909 0.00 0.00 0.00 3.86
865 1271 7.994425 TTGGTATTTGCTCTGTAGAAATCAA 57.006 32.000 0.00 0.00 0.00 2.57
866 1272 7.067372 CCATTGGTATTTGCTCTGTAGAAATCA 59.933 37.037 0.00 0.00 0.00 2.57
867 1273 7.420800 CCATTGGTATTTGCTCTGTAGAAATC 58.579 38.462 0.00 0.00 0.00 2.17
868 1274 6.183360 GCCATTGGTATTTGCTCTGTAGAAAT 60.183 38.462 4.26 0.00 0.00 2.17
869 1275 5.125417 GCCATTGGTATTTGCTCTGTAGAAA 59.875 40.000 4.26 0.00 0.00 2.52
870 1276 4.640201 GCCATTGGTATTTGCTCTGTAGAA 59.360 41.667 4.26 0.00 0.00 2.10
882 1293 3.848303 ACTATGCCATGCCATTGGTATT 58.152 40.909 3.20 0.00 38.77 1.89
895 1306 7.907841 TTCTCCACTTATTACTACTATGCCA 57.092 36.000 0.00 0.00 0.00 4.92
896 1307 9.857957 GTATTCTCCACTTATTACTACTATGCC 57.142 37.037 0.00 0.00 0.00 4.40
897 1308 9.557338 CGTATTCTCCACTTATTACTACTATGC 57.443 37.037 0.00 0.00 0.00 3.14
899 1310 9.240734 CCCGTATTCTCCACTTATTACTACTAT 57.759 37.037 0.00 0.00 0.00 2.12
900 1311 7.667219 CCCCGTATTCTCCACTTATTACTACTA 59.333 40.741 0.00 0.00 0.00 1.82
901 1312 6.492772 CCCCGTATTCTCCACTTATTACTACT 59.507 42.308 0.00 0.00 0.00 2.57
902 1313 6.294955 CCCCCGTATTCTCCACTTATTACTAC 60.295 46.154 0.00 0.00 0.00 2.73
903 1314 5.776716 CCCCCGTATTCTCCACTTATTACTA 59.223 44.000 0.00 0.00 0.00 1.82
904 1315 4.591924 CCCCCGTATTCTCCACTTATTACT 59.408 45.833 0.00 0.00 0.00 2.24
905 1316 4.891260 CCCCCGTATTCTCCACTTATTAC 58.109 47.826 0.00 0.00 0.00 1.89
927 1338 3.372554 CTCTCTTTCCCGGACGGCC 62.373 68.421 0.73 0.00 0.00 6.13
935 1346 1.694525 CCCCCTCCCTCTCTTTCCC 60.695 68.421 0.00 0.00 0.00 3.97
937 1348 2.736826 CGCCCCCTCCCTCTCTTTC 61.737 68.421 0.00 0.00 0.00 2.62
943 1354 3.798511 CCTTTCGCCCCCTCCCTC 61.799 72.222 0.00 0.00 0.00 4.30
944 1355 3.883822 TTCCTTTCGCCCCCTCCCT 62.884 63.158 0.00 0.00 0.00 4.20
945 1356 2.435120 TTTTCCTTTCGCCCCCTCCC 62.435 60.000 0.00 0.00 0.00 4.30
946 1357 0.965866 CTTTTCCTTTCGCCCCCTCC 60.966 60.000 0.00 0.00 0.00 4.30
955 1366 7.063426 CGCCTTTTATTCCATTCTTTTCCTTTC 59.937 37.037 0.00 0.00 0.00 2.62
984 1395 1.430369 AACTGCCAAGCTCCCTTCCT 61.430 55.000 0.00 0.00 0.00 3.36
985 1396 0.962855 GAACTGCCAAGCTCCCTTCC 60.963 60.000 0.00 0.00 0.00 3.46
986 1397 0.962855 GGAACTGCCAAGCTCCCTTC 60.963 60.000 0.00 0.00 33.19 3.46
987 1398 1.075659 GGAACTGCCAAGCTCCCTT 59.924 57.895 0.00 0.00 33.19 3.95
988 1399 2.759795 GGAACTGCCAAGCTCCCT 59.240 61.111 0.00 0.00 33.19 4.20
989 1400 2.747855 CGGAACTGCCAAGCTCCC 60.748 66.667 0.00 0.00 35.54 4.30
990 1401 3.435186 GCGGAACTGCCAAGCTCC 61.435 66.667 0.00 0.00 35.61 4.70
991 1402 3.793144 CGCGGAACTGCCAAGCTC 61.793 66.667 0.00 0.00 35.94 4.09
1082 1493 1.670059 GGAGGAAGGAAGGGAAGGAA 58.330 55.000 0.00 0.00 0.00 3.36
1083 1494 0.253207 GGGAGGAAGGAAGGGAAGGA 60.253 60.000 0.00 0.00 0.00 3.36
1084 1495 0.550147 TGGGAGGAAGGAAGGGAAGG 60.550 60.000 0.00 0.00 0.00 3.46
1085 1496 1.372501 TTGGGAGGAAGGAAGGGAAG 58.627 55.000 0.00 0.00 0.00 3.46
1086 1497 1.710809 CTTTGGGAGGAAGGAAGGGAA 59.289 52.381 0.00 0.00 0.00 3.97
1087 1498 1.372501 CTTTGGGAGGAAGGAAGGGA 58.627 55.000 0.00 0.00 0.00 4.20
1088 1499 0.323816 GCTTTGGGAGGAAGGAAGGG 60.324 60.000 0.00 0.00 0.00 3.95
1089 1500 0.701147 AGCTTTGGGAGGAAGGAAGG 59.299 55.000 0.00 0.00 0.00 3.46
1090 1501 1.677217 CGAGCTTTGGGAGGAAGGAAG 60.677 57.143 0.00 0.00 0.00 3.46
1247 1685 2.653448 CGACGAGATCTGCTGCGG 60.653 66.667 0.00 0.95 0.00 5.69
1512 1986 0.396060 GGAGAGCATCATGAGGGACC 59.604 60.000 9.76 0.53 37.82 4.46
2044 2590 3.127533 ACGCCGGATTGCTTGCTC 61.128 61.111 5.05 0.00 0.00 4.26
2085 2649 0.698818 ATCTCCACTGGAACCAACCC 59.301 55.000 0.00 0.00 0.00 4.11
2105 2669 1.772819 ATCACAGGCCCGGATCATCC 61.773 60.000 0.73 0.00 0.00 3.51
2125 2689 1.448540 ACCATCTTTCTCGCCAGCG 60.449 57.895 5.50 5.50 41.35 5.18
2132 2696 1.339438 TGCCTGAGCACCATCTTTCTC 60.339 52.381 0.00 0.00 46.52 2.87
2173 2737 6.265649 GCCTCTCTTTTTCTTAACCCTTTTCT 59.734 38.462 0.00 0.00 0.00 2.52
2174 2738 6.040504 TGCCTCTCTTTTTCTTAACCCTTTTC 59.959 38.462 0.00 0.00 0.00 2.29
2175 2739 5.897250 TGCCTCTCTTTTTCTTAACCCTTTT 59.103 36.000 0.00 0.00 0.00 2.27
2197 2761 4.803098 ATAACTACCCATAGACGGATGC 57.197 45.455 0.00 0.00 32.23 3.91
2202 2766 6.509039 GCACGAAAAATAACTACCCATAGACG 60.509 42.308 0.00 0.00 32.23 4.18
2207 2771 5.007682 ACAGCACGAAAAATAACTACCCAT 58.992 37.500 0.00 0.00 0.00 4.00
2224 2806 1.478916 GGGAGAGGAGAACTACAGCAC 59.521 57.143 0.00 0.00 0.00 4.40
2238 2861 2.043450 ACCAGAGCCGAGGGAGAG 60.043 66.667 0.00 0.00 0.00 3.20
2247 2870 2.024414 ACAAAAAGACACACCAGAGCC 58.976 47.619 0.00 0.00 0.00 4.70
2281 2904 0.030908 GCCCGATCTACTCTGTTCCG 59.969 60.000 0.00 0.00 0.00 4.30
2319 2946 5.582665 AGAAACAATACTAACTAGCAGCAGC 59.417 40.000 0.00 0.00 42.56 5.25
2322 2949 7.835634 AAGAGAAACAATACTAACTAGCAGC 57.164 36.000 0.00 0.00 0.00 5.25
2325 2952 7.963465 GCCAAAAGAGAAACAATACTAACTAGC 59.037 37.037 0.00 0.00 0.00 3.42
2326 2953 9.220767 AGCCAAAAGAGAAACAATACTAACTAG 57.779 33.333 0.00 0.00 0.00 2.57
2328 2955 7.095187 CGAGCCAAAAGAGAAACAATACTAACT 60.095 37.037 0.00 0.00 0.00 2.24
2332 2959 5.305585 TCGAGCCAAAAGAGAAACAATACT 58.694 37.500 0.00 0.00 0.00 2.12
2333 2960 5.607119 TCGAGCCAAAAGAGAAACAATAC 57.393 39.130 0.00 0.00 0.00 1.89
2335 2962 5.006386 AGATCGAGCCAAAAGAGAAACAAT 58.994 37.500 0.00 0.00 0.00 2.71
2337 2964 4.008074 AGATCGAGCCAAAAGAGAAACA 57.992 40.909 0.00 0.00 0.00 2.83
2338 2965 4.378874 CCAAGATCGAGCCAAAAGAGAAAC 60.379 45.833 0.00 0.00 0.00 2.78
2341 2968 2.303022 ACCAAGATCGAGCCAAAAGAGA 59.697 45.455 0.00 0.00 0.00 3.10
2342 2969 2.704572 ACCAAGATCGAGCCAAAAGAG 58.295 47.619 0.00 0.00 0.00 2.85
2343 2970 2.859165 ACCAAGATCGAGCCAAAAGA 57.141 45.000 0.00 0.00 0.00 2.52
2344 2971 2.352960 GCTACCAAGATCGAGCCAAAAG 59.647 50.000 0.00 0.00 0.00 2.27
2346 2973 2.024176 GCTACCAAGATCGAGCCAAA 57.976 50.000 0.00 0.00 0.00 3.28
2347 2974 3.760693 GCTACCAAGATCGAGCCAA 57.239 52.632 0.00 0.00 0.00 4.52
2353 2980 4.386867 TTCTTGTAGGCTACCAAGATCG 57.613 45.455 25.86 7.60 34.22 3.69
2443 3092 4.751600 GCCATGCTATGCTAATATGCGATA 59.248 41.667 0.00 0.00 35.36 2.92
2452 3101 1.250328 GCCATGCCATGCTATGCTAA 58.750 50.000 0.00 0.00 0.00 3.09
2453 3102 0.110869 TGCCATGCCATGCTATGCTA 59.889 50.000 0.00 0.00 0.00 3.49
2454 3103 0.541998 ATGCCATGCCATGCTATGCT 60.542 50.000 0.00 0.00 0.00 3.79
2455 3104 0.389817 CATGCCATGCCATGCTATGC 60.390 55.000 3.39 0.00 36.52 3.14
2456 3105 0.246360 CCATGCCATGCCATGCTATG 59.754 55.000 11.13 5.87 40.92 2.23
2457 3106 1.541310 GCCATGCCATGCCATGCTAT 61.541 55.000 11.13 0.00 40.92 2.97
2458 3107 2.204461 GCCATGCCATGCCATGCTA 61.204 57.895 11.13 0.00 40.92 3.49
2459 3108 3.546543 GCCATGCCATGCCATGCT 61.547 61.111 11.13 0.00 40.92 3.79
2471 3120 0.675083 TTGCTTGGTGAAGTGCCATG 59.325 50.000 0.00 0.00 35.71 3.66
2473 3122 1.391157 GGTTGCTTGGTGAAGTGCCA 61.391 55.000 0.00 0.00 0.00 4.92
2474 3123 1.363807 GGTTGCTTGGTGAAGTGCC 59.636 57.895 0.00 0.00 0.00 5.01
2475 3124 1.008538 CGGTTGCTTGGTGAAGTGC 60.009 57.895 0.00 0.00 0.00 4.40
2476 3125 1.197721 GATCGGTTGCTTGGTGAAGTG 59.802 52.381 0.00 0.00 0.00 3.16
2477 3126 1.202758 TGATCGGTTGCTTGGTGAAGT 60.203 47.619 0.00 0.00 0.00 3.01
2482 3131 3.270877 GAGTAATGATCGGTTGCTTGGT 58.729 45.455 3.47 0.00 0.00 3.67
2520 3185 2.632377 TGCTTATGGCTTCACTACTGC 58.368 47.619 0.00 0.00 42.39 4.40
2521 3186 4.002982 TGTTGCTTATGGCTTCACTACTG 58.997 43.478 0.00 0.00 42.39 2.74
2522 3187 4.286297 TGTTGCTTATGGCTTCACTACT 57.714 40.909 0.00 0.00 42.39 2.57
2523 3188 5.371115 TTTGTTGCTTATGGCTTCACTAC 57.629 39.130 0.00 0.00 42.39 2.73
2528 3193 5.410067 TGCTATTTTGTTGCTTATGGCTTC 58.590 37.500 0.00 0.00 42.39 3.86
2571 3249 1.068541 CAAAGTACAGCGGCCCTTTTC 60.069 52.381 0.00 0.00 0.00 2.29
2591 3428 3.483869 CTGGGCTACAGGGGGAGC 61.484 72.222 0.00 0.00 43.70 4.70
2619 3456 4.821589 GGTGGGAAGCGAGCGAGG 62.822 72.222 0.00 0.00 0.00 4.63
2620 3457 4.069232 TGGTGGGAAGCGAGCGAG 62.069 66.667 0.00 0.00 0.00 5.03
2621 3458 4.373116 GTGGTGGGAAGCGAGCGA 62.373 66.667 0.00 0.00 0.00 4.93
2622 3459 3.958147 ATGTGGTGGGAAGCGAGCG 62.958 63.158 0.00 0.00 0.00 5.03
2645 3482 1.078497 CGCAGCACAGTATGGGGAA 60.078 57.895 0.00 0.00 42.43 3.97
2662 3540 1.205657 GCAGGATTCAATGCAATGCG 58.794 50.000 0.00 0.00 42.11 4.73
2683 3561 2.729194 TGGTTATACGGCCATTTTGCT 58.271 42.857 2.24 0.00 0.00 3.91
2684 3562 3.183754 GTTGGTTATACGGCCATTTTGC 58.816 45.455 2.24 0.00 34.37 3.68
2692 3570 4.731480 CGCTTTATTTGTTGGTTATACGGC 59.269 41.667 0.00 0.00 0.00 5.68
2701 3585 1.467374 CCGAGCCGCTTTATTTGTTGG 60.467 52.381 0.00 0.00 0.00 3.77
2714 3598 1.011968 TGAAACGACATTCCGAGCCG 61.012 55.000 0.00 0.00 0.00 5.52
2748 3641 3.065925 GCAATGGAGCAGGTAATCTTCAC 59.934 47.826 0.00 0.00 0.00 3.18
2761 3654 2.181021 GCACAGCAGCAATGGAGC 59.819 61.111 0.00 0.00 0.00 4.70
2777 3670 2.111878 ACAGACCCTGCACAGTGC 59.888 61.111 19.37 19.37 45.29 4.40
2784 3677 1.807142 GAAAAGCTACACAGACCCTGC 59.193 52.381 0.00 0.00 34.37 4.85
2789 3682 5.734855 TGAAAGTGAAAAGCTACACAGAC 57.265 39.130 16.80 9.79 39.18 3.51
2838 3731 0.621862 ACAAACCCAGCCCCCAAAAA 60.622 50.000 0.00 0.00 0.00 1.94
2846 3739 1.445518 CAACCCAACAAACCCAGCC 59.554 57.895 0.00 0.00 0.00 4.85
2861 3754 1.225704 CAGAGATCCAGGCCCCAAC 59.774 63.158 0.00 0.00 0.00 3.77
2866 3759 0.615331 TGTTGACAGAGATCCAGGCC 59.385 55.000 0.00 0.00 0.00 5.19
2879 3772 0.036875 CCTCCCTCCCAACTGTTGAC 59.963 60.000 21.49 0.00 0.00 3.18
2881 3774 1.303643 GCCTCCCTCCCAACTGTTG 60.304 63.158 13.50 13.50 0.00 3.33
2884 3777 2.612115 AGGCCTCCCTCCCAACTG 60.612 66.667 0.00 0.00 36.46 3.16
2892 3812 2.285743 GGTTCCAGAGGCCTCCCT 60.286 66.667 29.54 9.19 46.74 4.20
2905 3825 3.093278 CAGAATCGGCTGCGGTTC 58.907 61.111 7.10 8.01 0.00 3.62
3004 3951 2.520536 GGCCACTGACCTGACCAGT 61.521 63.158 0.00 0.00 44.92 4.00
3014 3966 2.741092 GAGGTTCGTGGCCACTGA 59.259 61.111 32.28 26.28 0.00 3.41
3031 3983 4.602259 ATATCGCCCACGCCACCG 62.602 66.667 0.00 0.00 39.84 4.94
3045 3997 5.435686 TCCCAGCACAAGTTAGTCAATAT 57.564 39.130 0.00 0.00 0.00 1.28
3066 4018 4.148348 CGTGCGTTAACTATCCTGCTAATC 59.852 45.833 3.71 0.00 0.00 1.75
3097 4049 6.649557 AGCCGATTAAACTAAGAATAATCCCG 59.350 38.462 0.00 0.00 34.18 5.14
3101 4053 6.929606 AGCGAGCCGATTAAACTAAGAATAAT 59.070 34.615 0.00 0.00 0.00 1.28
3112 4064 1.006832 GCAAGAGCGAGCCGATTAAA 58.993 50.000 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.