Multiple sequence alignment - TraesCS7A01G363100

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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 TraesCS7A01G363100 chr7A 100.000 2433 0 0 846 3278 537662373 537664805 0.000000e+00 4494.0
1 TraesCS7A01G363100 chr7A 100.000 660 0 0 1 660 537661528 537662187 0.000000e+00 1219.0
2 TraesCS7A01G363100 chr7D 91.410 2107 97 51 846 2902 462282339 462280267 0.000000e+00 2811.0
3 TraesCS7A01G363100 chr7D 92.090 670 28 10 2 660 462283044 462282389 0.000000e+00 920.0
4 TraesCS7A01G363100 chr7D 85.283 265 14 7 3016 3258 462280269 462280008 1.950000e-62 250.0
5 TraesCS7A01G363100 chr7B 90.643 2052 93 54 846 2833 485431319 485429303 0.000000e+00 2634.0
6 TraesCS7A01G363100 chr7B 90.244 369 10 11 301 660 485431714 485431363 2.980000e-125 459.0
7 TraesCS7A01G363100 chr7B 93.581 296 15 2 2 297 485432069 485431778 3.880000e-119 438.0
8 TraesCS7A01G363100 chr7B 84.151 265 17 10 3016 3258 485429248 485428987 1.970000e-57 233.0
9 TraesCS7A01G363100 chr6A 89.873 79 8 0 1619 1697 219561955 219561877 5.790000e-18 102.0
10 TraesCS7A01G363100 chr6D 88.608 79 9 0 1619 1697 160429236 160429158 2.690000e-16 97.1
11 TraesCS7A01G363100 chrUn 87.342 79 10 0 1619 1697 453960257 453960335 1.250000e-14 91.6
12 TraesCS7A01G363100 chrUn 87.342 79 10 0 1619 1697 466322493 466322571 1.250000e-14 91.6
13 TraesCS7A01G363100 chr6B 87.342 79 10 0 1619 1697 290596916 290596838 1.250000e-14 91.6
14 TraesCS7A01G363100 chr6B 87.342 79 10 0 1619 1697 290628474 290628396 1.250000e-14 91.6
15 TraesCS7A01G363100 chr6B 87.342 79 10 0 1619 1697 290656979 290656901 1.250000e-14 91.6


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 TraesCS7A01G363100 chr7A 537661528 537664805 3277 False 2856.5 4494 100.000000 1 3278 2 chr7A.!!$F1 3277
1 TraesCS7A01G363100 chr7D 462280008 462283044 3036 True 1327.0 2811 89.594333 2 3258 3 chr7D.!!$R1 3256
2 TraesCS7A01G363100 chr7B 485428987 485432069 3082 True 941.0 2634 89.654750 2 3258 4 chr7B.!!$R1 3256

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
605 677 0.038744 CATCCCTTTCCTGTGCCTGT 59.961 55.0 0.00 0.0 0.00 4.00 F
1700 1786 0.039618 CTTGTGGCCCCAAGGTATGT 59.960 55.0 19.34 0.0 38.51 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 2214 0.099082 GGTGTCGACGAGATCACTCC 59.901 60.000 11.62 3.67 39.76 3.85 R
2810 2948 1.405105 ACTGTGCGCACTGACAAAAAT 59.595 42.857 41.96 22.43 34.80 1.82 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
32 33 5.279456 CCCACATCTACACCAATATGATCGA 60.279 44.000 0.00 0.00 0.00 3.59
33 34 6.401394 CCACATCTACACCAATATGATCGAT 58.599 40.000 0.00 0.00 0.00 3.59
34 35 6.533012 CCACATCTACACCAATATGATCGATC 59.467 42.308 18.72 18.72 0.00 3.69
36 37 6.151144 ACATCTACACCAATATGATCGATCGA 59.849 38.462 21.86 21.86 0.00 3.59
37 38 6.183309 TCTACACCAATATGATCGATCGAG 57.817 41.667 23.84 9.44 0.00 4.04
38 39 3.579709 ACACCAATATGATCGATCGAGC 58.420 45.455 25.65 25.65 0.00 5.03
39 40 3.005791 ACACCAATATGATCGATCGAGCA 59.994 43.478 34.91 34.91 44.87 4.26
40 41 3.366121 CACCAATATGATCGATCGAGCAC 59.634 47.826 35.45 21.95 43.55 4.40
43 44 3.560902 ATATGATCGATCGAGCACGTT 57.439 42.857 35.45 23.20 43.55 3.99
59 60 0.394216 CGTTGCCTCCATGGGATGAA 60.394 55.000 13.02 0.00 35.58 2.57
172 173 1.774639 GTGTGGTGGTGTACGTGTAG 58.225 55.000 0.00 0.00 0.00 2.74
284 285 4.273148 ACGAAGGTTTGATGAGCTAAGT 57.727 40.909 0.00 0.00 0.00 2.24
326 387 4.080129 AGCCACAAACTATGGATGATGAGT 60.080 41.667 0.00 0.00 39.87 3.41
435 503 2.346847 ACGCTACAGTAGACGTACGAAG 59.653 50.000 24.41 7.01 37.00 3.79
462 530 2.547855 GCCACATAGGATCATACGCACA 60.548 50.000 0.00 0.00 41.22 4.57
464 532 3.492482 CCACATAGGATCATACGCACACA 60.492 47.826 0.00 0.00 41.22 3.72
465 533 3.490896 CACATAGGATCATACGCACACAC 59.509 47.826 0.00 0.00 0.00 3.82
466 534 3.132111 ACATAGGATCATACGCACACACA 59.868 43.478 0.00 0.00 0.00 3.72
579 649 1.364171 CTGTTCCCCGCCGATCTAG 59.636 63.158 0.00 0.00 0.00 2.43
602 674 1.034292 GCTCATCCCTTTCCTGTGCC 61.034 60.000 0.00 0.00 0.00 5.01
603 675 0.622665 CTCATCCCTTTCCTGTGCCT 59.377 55.000 0.00 0.00 0.00 4.75
604 676 0.329261 TCATCCCTTTCCTGTGCCTG 59.671 55.000 0.00 0.00 0.00 4.85
605 677 0.038744 CATCCCTTTCCTGTGCCTGT 59.961 55.000 0.00 0.00 0.00 4.00
606 678 0.038744 ATCCCTTTCCTGTGCCTGTG 59.961 55.000 0.00 0.00 0.00 3.66
607 679 2.270986 CCCTTTCCTGTGCCTGTGC 61.271 63.158 0.00 0.00 38.26 4.57
608 680 1.228367 CCTTTCCTGTGCCTGTGCT 60.228 57.895 0.00 0.00 38.71 4.40
610 682 0.250640 CTTTCCTGTGCCTGTGCTCT 60.251 55.000 0.00 0.00 38.71 4.09
611 683 0.250467 TTTCCTGTGCCTGTGCTCTC 60.250 55.000 0.00 0.00 38.71 3.20
612 684 2.046507 CCTGTGCCTGTGCTCTCC 60.047 66.667 0.00 0.00 38.71 3.71
613 685 2.591072 CCTGTGCCTGTGCTCTCCT 61.591 63.158 0.00 0.00 38.71 3.69
614 686 1.079266 CTGTGCCTGTGCTCTCCTC 60.079 63.158 0.00 0.00 38.71 3.71
615 687 2.267324 GTGCCTGTGCTCTCCTCC 59.733 66.667 0.00 0.00 38.71 4.30
616 688 3.005539 TGCCTGTGCTCTCCTCCC 61.006 66.667 0.00 0.00 38.71 4.30
617 689 2.686835 GCCTGTGCTCTCCTCCCT 60.687 66.667 0.00 0.00 33.53 4.20
879 951 1.964933 TCTCTCTCGATCGGCTCTCTA 59.035 52.381 16.41 0.00 0.00 2.43
943 1015 1.907936 CTCCCCATCTCATCCTGATCC 59.092 57.143 0.00 0.00 0.00 3.36
946 1018 0.612229 CCATCTCATCCTGATCCCCG 59.388 60.000 0.00 0.00 0.00 5.73
947 1019 1.346062 CATCTCATCCTGATCCCCGT 58.654 55.000 0.00 0.00 0.00 5.28
959 1031 0.532862 ATCCCCGTTTATCTGCGCTG 60.533 55.000 9.73 8.88 0.00 5.18
961 1033 2.709475 CCGTTTATCTGCGCTGCC 59.291 61.111 9.73 0.00 0.00 4.85
962 1034 1.815421 CCGTTTATCTGCGCTGCCT 60.815 57.895 9.73 1.47 0.00 4.75
963 1035 0.529773 CCGTTTATCTGCGCTGCCTA 60.530 55.000 9.73 0.42 0.00 3.93
964 1036 0.855349 CGTTTATCTGCGCTGCCTAG 59.145 55.000 9.73 0.00 0.00 3.02
965 1037 0.583917 GTTTATCTGCGCTGCCTAGC 59.416 55.000 9.73 0.00 46.62 3.42
1033 1105 2.465813 ACATGAGCCAGCTCTCTACTT 58.534 47.619 19.71 0.00 43.12 2.24
1168 1240 0.737715 CCCTAGCGACAACAGCAGTC 60.738 60.000 0.00 0.00 37.01 3.51
1169 1241 0.244994 CCTAGCGACAACAGCAGTCT 59.755 55.000 0.00 0.00 37.01 3.24
1170 1242 1.623359 CTAGCGACAACAGCAGTCTC 58.377 55.000 0.00 0.00 37.01 3.36
1171 1243 0.109735 TAGCGACAACAGCAGTCTCG 60.110 55.000 5.28 5.28 37.01 4.04
1236 1311 1.678101 GATCAGCCCCAACATGTAAGC 59.322 52.381 0.00 0.00 0.00 3.09
1241 1316 1.755179 CCCCAACATGTAAGCTGGAG 58.245 55.000 14.67 0.00 0.00 3.86
1242 1317 1.004745 CCCCAACATGTAAGCTGGAGT 59.995 52.381 14.67 0.00 0.00 3.85
1243 1318 2.086869 CCCAACATGTAAGCTGGAGTG 58.913 52.381 14.67 0.00 0.00 3.51
1251 1326 5.645497 ACATGTAAGCTGGAGTGATTTCTTC 59.355 40.000 0.00 0.00 0.00 2.87
1252 1327 5.489792 TGTAAGCTGGAGTGATTTCTTCT 57.510 39.130 0.00 0.00 0.00 2.85
1253 1328 5.240891 TGTAAGCTGGAGTGATTTCTTCTG 58.759 41.667 0.00 0.00 0.00 3.02
1254 1329 4.363991 AAGCTGGAGTGATTTCTTCTGT 57.636 40.909 0.00 0.00 0.00 3.41
1255 1330 3.936564 AGCTGGAGTGATTTCTTCTGTC 58.063 45.455 0.00 0.00 0.00 3.51
1256 1331 3.006247 GCTGGAGTGATTTCTTCTGTCC 58.994 50.000 0.00 0.00 0.00 4.02
1258 1333 4.081420 GCTGGAGTGATTTCTTCTGTCCTA 60.081 45.833 0.00 0.00 31.56 2.94
1259 1334 5.396213 GCTGGAGTGATTTCTTCTGTCCTAT 60.396 44.000 0.00 0.00 31.56 2.57
1261 1336 7.020827 TGGAGTGATTTCTTCTGTCCTATTT 57.979 36.000 0.00 0.00 31.56 1.40
1262 1337 6.881065 TGGAGTGATTTCTTCTGTCCTATTTG 59.119 38.462 0.00 0.00 31.56 2.32
1264 1339 7.607991 GGAGTGATTTCTTCTGTCCTATTTGAA 59.392 37.037 0.00 0.00 0.00 2.69
1265 1340 9.171877 GAGTGATTTCTTCTGTCCTATTTGAAT 57.828 33.333 0.00 0.00 0.00 2.57
1277 1362 8.477984 TGTCCTATTTGAATTAATTTGCTTGC 57.522 30.769 1.43 0.00 0.00 4.01
1287 1372 8.575589 TGAATTAATTTGCTTGCTCACTTTCTA 58.424 29.630 1.43 0.00 0.00 2.10
1293 1378 3.259374 TGCTTGCTCACTTTCTAGCTAGT 59.741 43.478 20.10 0.22 41.64 2.57
1295 1380 4.693095 GCTTGCTCACTTTCTAGCTAGTTT 59.307 41.667 20.10 0.93 41.64 2.66
1309 1394 8.425577 TCTAGCTAGTTTCTCAATTAACATGC 57.574 34.615 20.10 0.00 0.00 4.06
1310 1395 8.040727 TCTAGCTAGTTTCTCAATTAACATGCA 58.959 33.333 20.10 0.00 31.72 3.96
1311 1396 7.636150 AGCTAGTTTCTCAATTAACATGCAT 57.364 32.000 0.00 0.00 31.72 3.96
1330 1416 5.593968 TGCATGATCCTTTGATTGTTATGC 58.406 37.500 0.00 0.00 36.27 3.14
1343 1429 5.239963 TGATTGTTATGCGCATCAGATGATT 59.760 36.000 29.11 2.18 31.21 2.57
1358 1444 2.245159 TGATTGGTGGATCATCGAGC 57.755 50.000 0.00 0.00 31.35 5.03
1364 1450 1.359848 GTGGATCATCGAGCGTGTTT 58.640 50.000 0.00 0.00 0.00 2.83
1491 1577 1.372087 GCTCAAGATCGGCAAGTGGG 61.372 60.000 0.00 0.00 0.00 4.61
1544 1630 1.360911 GAGGAAGACGAGCGATCCC 59.639 63.158 0.00 0.00 32.15 3.85
1589 1675 0.941463 CGCAGGCATACGAGGATCAC 60.941 60.000 0.00 0.00 33.17 3.06
1655 1741 0.110056 GCTCTGATTGCAACACCACG 60.110 55.000 0.00 0.00 0.00 4.94
1699 1785 2.886382 CTTGTGGCCCCAAGGTATG 58.114 57.895 19.34 0.00 38.51 2.39
1700 1786 0.039618 CTTGTGGCCCCAAGGTATGT 59.960 55.000 19.34 0.00 38.51 2.29
1711 1807 5.889289 GCCCCAAGGTATGTCTTGTTAATTA 59.111 40.000 8.42 0.00 41.72 1.40
1712 1808 6.039382 GCCCCAAGGTATGTCTTGTTAATTAG 59.961 42.308 8.42 0.00 41.72 1.73
1713 1809 7.116736 CCCCAAGGTATGTCTTGTTAATTAGT 58.883 38.462 8.42 0.00 41.72 2.24
1714 1810 8.269317 CCCCAAGGTATGTCTTGTTAATTAGTA 58.731 37.037 8.42 0.00 41.72 1.82
1715 1811 9.847224 CCCAAGGTATGTCTTGTTAATTAGTAT 57.153 33.333 8.42 0.00 41.72 2.12
1731 1827 7.490657 AATTAGTATGTGGTCACTTGGTAGA 57.509 36.000 2.66 0.00 0.00 2.59
1735 1831 6.014647 AGTATGTGGTCACTTGGTAGAAGTA 58.985 40.000 2.66 0.00 0.00 2.24
1736 1832 4.595762 TGTGGTCACTTGGTAGAAGTAC 57.404 45.455 2.66 0.00 0.00 2.73
1737 1833 4.220724 TGTGGTCACTTGGTAGAAGTACT 58.779 43.478 2.66 0.00 0.00 2.73
1738 1834 4.280174 TGTGGTCACTTGGTAGAAGTACTC 59.720 45.833 0.00 0.00 0.00 2.59
1739 1835 3.830755 TGGTCACTTGGTAGAAGTACTCC 59.169 47.826 0.00 0.00 0.00 3.85
1757 1853 5.242795 ACTCCACAAGTTAGTTAATGGCT 57.757 39.130 0.00 0.00 33.03 4.75
1955 2055 3.258123 GTGAAGAAGGAGAAGAGAGCTGT 59.742 47.826 0.00 0.00 0.00 4.40
2020 2120 0.957395 CCAGGATCACACTGCCACAC 60.957 60.000 0.00 0.00 34.65 3.82
2024 2124 0.599991 GATCACACTGCCACACACGA 60.600 55.000 0.00 0.00 0.00 4.35
2086 2198 3.311110 TCGTCCCCACCACTGCTC 61.311 66.667 0.00 0.00 0.00 4.26
2151 2263 1.268283 ACTGGAGCAAGAGCCCTACC 61.268 60.000 0.00 0.00 43.56 3.18
2153 2265 2.202946 GAGCAAGAGCCCTACCGC 60.203 66.667 0.00 0.00 43.56 5.68
2429 2550 0.974383 AGTGTAACCCTGCGCTACTT 59.026 50.000 9.73 0.00 37.80 2.24
2459 2583 6.612247 TGTGATTCGTTTGTGTGTAAGATT 57.388 33.333 0.00 0.00 0.00 2.40
2461 2585 8.144155 TGTGATTCGTTTGTGTGTAAGATTAA 57.856 30.769 0.00 0.00 0.00 1.40
2462 2586 8.279800 TGTGATTCGTTTGTGTGTAAGATTAAG 58.720 33.333 0.00 0.00 0.00 1.85
2463 2587 7.744715 GTGATTCGTTTGTGTGTAAGATTAAGG 59.255 37.037 0.00 0.00 0.00 2.69
2464 2588 5.600908 TCGTTTGTGTGTAAGATTAAGGC 57.399 39.130 0.00 0.00 0.00 4.35
2465 2589 5.057819 TCGTTTGTGTGTAAGATTAAGGCA 58.942 37.500 0.00 0.00 0.00 4.75
2466 2590 5.178623 TCGTTTGTGTGTAAGATTAAGGCAG 59.821 40.000 0.00 0.00 0.00 4.85
2467 2591 5.049680 CGTTTGTGTGTAAGATTAAGGCAGT 60.050 40.000 0.00 0.00 0.00 4.40
2468 2592 5.940192 TTGTGTGTAAGATTAAGGCAGTG 57.060 39.130 0.00 0.00 0.00 3.66
2469 2593 5.222079 TGTGTGTAAGATTAAGGCAGTGA 57.778 39.130 0.00 0.00 0.00 3.41
2470 2594 5.237815 TGTGTGTAAGATTAAGGCAGTGAG 58.762 41.667 0.00 0.00 0.00 3.51
2471 2595 4.631813 GTGTGTAAGATTAAGGCAGTGAGG 59.368 45.833 0.00 0.00 0.00 3.86
2489 2613 5.072329 AGTGAGGAAGAGAGAGATCTAGAGG 59.928 48.000 0.00 0.00 0.00 3.69
2514 2638 5.261216 AGAGAGGTAGAAACAAGGAGAGAG 58.739 45.833 0.00 0.00 0.00 3.20
2515 2639 4.349365 AGAGGTAGAAACAAGGAGAGAGG 58.651 47.826 0.00 0.00 0.00 3.69
2534 2663 9.362151 GAGAGAGGAGAGAAGAGGATAAAAATA 57.638 37.037 0.00 0.00 0.00 1.40
2587 2716 3.473923 TCTGCAAACACTGTGAGATCA 57.526 42.857 15.86 6.16 0.00 2.92
2590 2719 2.291465 TGCAAACACTGTGAGATCAAGC 59.709 45.455 15.86 8.61 0.00 4.01
2591 2720 2.663879 GCAAACACTGTGAGATCAAGCG 60.664 50.000 15.86 0.00 0.00 4.68
2604 2733 3.496130 AGATCAAGCGTGAGTTCAGTTTG 59.504 43.478 8.63 0.00 37.14 2.93
2627 2756 2.820197 AGTAGCTAGCTTTTTGTTGCCC 59.180 45.455 24.88 0.00 0.00 5.36
2629 2758 0.037326 GCTAGCTTTTTGTTGCCCCC 60.037 55.000 7.70 0.00 0.00 5.40
2631 2760 1.182385 TAGCTTTTTGTTGCCCCCGG 61.182 55.000 0.00 0.00 0.00 5.73
2653 2783 3.377485 GCTAGTTAAGCCAAAAGGCTACC 59.623 47.826 9.76 1.04 46.25 3.18
2705 2836 2.742053 CTCGAACCATTTGTACTGTGGG 59.258 50.000 13.70 5.11 37.33 4.61
2706 2837 1.199097 CGAACCATTTGTACTGTGGGC 59.801 52.381 13.70 6.71 37.33 5.36
2707 2838 2.514803 GAACCATTTGTACTGTGGGCT 58.485 47.619 13.70 3.68 37.33 5.19
2708 2839 2.200373 ACCATTTGTACTGTGGGCTC 57.800 50.000 13.70 0.00 37.33 4.70
2709 2840 1.086696 CCATTTGTACTGTGGGCTCG 58.913 55.000 0.00 0.00 0.00 5.03
2710 2841 1.610624 CCATTTGTACTGTGGGCTCGT 60.611 52.381 0.00 0.00 0.00 4.18
2712 2843 3.331150 CATTTGTACTGTGGGCTCGTAA 58.669 45.455 0.00 0.00 0.00 3.18
2713 2844 3.688694 TTTGTACTGTGGGCTCGTAAT 57.311 42.857 0.00 0.00 0.00 1.89
2724 2858 4.992951 GTGGGCTCGTAATAATACCGAAAT 59.007 41.667 0.00 0.00 0.00 2.17
2786 2924 6.617879 TCATGACTTTTGCTTCTGATGATTG 58.382 36.000 0.00 0.00 0.00 2.67
2810 2948 7.330262 TGTATGTCAGTGATGATCTGCTTTAA 58.670 34.615 0.00 0.00 33.48 1.52
2821 2959 8.579006 TGATGATCTGCTTTAATTTTTGTCAGT 58.421 29.630 0.00 0.00 0.00 3.41
2855 2993 2.943036 TTCTAACCTTTTCCCGCTGT 57.057 45.000 0.00 0.00 0.00 4.40
2857 2995 3.217681 TCTAACCTTTTCCCGCTGTTT 57.782 42.857 0.00 0.00 0.00 2.83
2887 3025 7.504911 AGGCAAACATTCTCTTTATCATATGCT 59.495 33.333 0.00 0.00 0.00 3.79
2899 3037 4.881019 ATCATATGCTAACCGAGAAGCT 57.119 40.909 0.00 0.00 39.53 3.74
2900 3038 4.672587 TCATATGCTAACCGAGAAGCTT 57.327 40.909 0.00 0.00 39.53 3.74
2901 3039 5.784578 TCATATGCTAACCGAGAAGCTTA 57.215 39.130 0.00 3.62 39.53 3.09
2902 3040 6.346477 TCATATGCTAACCGAGAAGCTTAT 57.654 37.500 0.00 0.00 38.75 1.73
2903 3041 7.462571 TCATATGCTAACCGAGAAGCTTATA 57.537 36.000 0.00 0.00 37.11 0.98
2904 3042 7.313646 TCATATGCTAACCGAGAAGCTTATAC 58.686 38.462 0.00 0.00 37.11 1.47
2905 3043 5.793030 ATGCTAACCGAGAAGCTTATACT 57.207 39.130 0.00 0.00 39.53 2.12
2906 3044 5.184340 TGCTAACCGAGAAGCTTATACTC 57.816 43.478 0.00 0.71 39.53 2.59
2907 3045 4.888239 TGCTAACCGAGAAGCTTATACTCT 59.112 41.667 0.00 0.00 39.53 3.24
2908 3046 5.008811 TGCTAACCGAGAAGCTTATACTCTC 59.991 44.000 0.00 0.00 39.53 3.20
2909 3047 5.239963 GCTAACCGAGAAGCTTATACTCTCT 59.760 44.000 0.00 0.00 35.80 3.10
2910 3048 5.761165 AACCGAGAAGCTTATACTCTCTC 57.239 43.478 0.00 0.00 0.00 3.20
2911 3049 4.139038 ACCGAGAAGCTTATACTCTCTCC 58.861 47.826 0.00 0.00 0.00 3.71
2912 3050 4.141344 ACCGAGAAGCTTATACTCTCTCCT 60.141 45.833 0.00 0.00 0.00 3.69
2913 3051 5.072058 ACCGAGAAGCTTATACTCTCTCCTA 59.928 44.000 0.00 0.00 0.00 2.94
2914 3052 6.177610 CCGAGAAGCTTATACTCTCTCCTAT 58.822 44.000 0.00 0.00 0.00 2.57
2915 3053 6.315393 CCGAGAAGCTTATACTCTCTCCTATC 59.685 46.154 0.00 0.00 0.00 2.08
2916 3054 6.315393 CGAGAAGCTTATACTCTCTCCTATCC 59.685 46.154 0.00 0.00 0.00 2.59
2917 3055 6.490492 AGAAGCTTATACTCTCTCCTATCCC 58.510 44.000 0.00 0.00 0.00 3.85
2918 3056 6.277044 AGAAGCTTATACTCTCTCCTATCCCT 59.723 42.308 0.00 0.00 0.00 4.20
2919 3057 7.462972 AGAAGCTTATACTCTCTCCTATCCCTA 59.537 40.741 0.00 0.00 0.00 3.53
2920 3058 7.591854 AGCTTATACTCTCTCCTATCCCTAA 57.408 40.000 0.00 0.00 0.00 2.69
2921 3059 7.639378 AGCTTATACTCTCTCCTATCCCTAAG 58.361 42.308 0.00 0.00 0.00 2.18
2922 3060 7.241039 AGCTTATACTCTCTCCTATCCCTAAGT 59.759 40.741 0.00 0.00 0.00 2.24
2923 3061 7.338449 GCTTATACTCTCTCCTATCCCTAAGTG 59.662 44.444 0.00 0.00 0.00 3.16
2924 3062 6.790177 ATACTCTCTCCTATCCCTAAGTGT 57.210 41.667 0.00 0.00 0.00 3.55
2925 3063 5.056553 ACTCTCTCCTATCCCTAAGTGTC 57.943 47.826 0.00 0.00 0.00 3.67
2926 3064 4.729881 ACTCTCTCCTATCCCTAAGTGTCT 59.270 45.833 0.00 0.00 0.00 3.41
2927 3065 5.194942 ACTCTCTCCTATCCCTAAGTGTCTT 59.805 44.000 0.00 0.00 0.00 3.01
2928 3066 6.390461 ACTCTCTCCTATCCCTAAGTGTCTTA 59.610 42.308 0.00 0.00 0.00 2.10
2929 3067 7.091902 ACTCTCTCCTATCCCTAAGTGTCTTAA 60.092 40.741 0.00 0.00 0.00 1.85
2930 3068 7.649715 TCTCTCCTATCCCTAAGTGTCTTAAA 58.350 38.462 0.00 0.00 0.00 1.52
2931 3069 8.290277 TCTCTCCTATCCCTAAGTGTCTTAAAT 58.710 37.037 0.00 0.00 0.00 1.40
2932 3070 8.855804 TCTCCTATCCCTAAGTGTCTTAAATT 57.144 34.615 0.00 0.00 0.00 1.82
2933 3071 9.280456 TCTCCTATCCCTAAGTGTCTTAAATTT 57.720 33.333 0.00 0.00 0.00 1.82
2953 3091 8.934023 AAATTTAGTAGAACTTTGGTCATCCA 57.066 30.769 0.00 0.00 42.66 3.41
2954 3092 8.567285 AATTTAGTAGAACTTTGGTCATCCAG 57.433 34.615 0.00 0.00 45.22 3.86
2955 3093 6.928348 TTAGTAGAACTTTGGTCATCCAGA 57.072 37.500 0.00 0.00 45.22 3.86
2956 3094 5.825593 AGTAGAACTTTGGTCATCCAGAA 57.174 39.130 0.00 0.00 45.22 3.02
2957 3095 6.187727 AGTAGAACTTTGGTCATCCAGAAA 57.812 37.500 0.00 0.00 45.22 2.52
2958 3096 6.784031 AGTAGAACTTTGGTCATCCAGAAAT 58.216 36.000 0.00 0.00 45.22 2.17
2959 3097 7.918076 AGTAGAACTTTGGTCATCCAGAAATA 58.082 34.615 0.00 0.00 45.22 1.40
2960 3098 8.383175 AGTAGAACTTTGGTCATCCAGAAATAA 58.617 33.333 0.00 0.00 45.22 1.40
2961 3099 7.693969 AGAACTTTGGTCATCCAGAAATAAG 57.306 36.000 0.00 0.00 45.22 1.73
2962 3100 7.234355 AGAACTTTGGTCATCCAGAAATAAGT 58.766 34.615 0.00 0.00 45.22 2.24
2963 3101 6.824305 ACTTTGGTCATCCAGAAATAAGTG 57.176 37.500 0.00 0.00 45.22 3.16
2964 3102 6.306987 ACTTTGGTCATCCAGAAATAAGTGT 58.693 36.000 0.00 0.00 45.22 3.55
2965 3103 6.431234 ACTTTGGTCATCCAGAAATAAGTGTC 59.569 38.462 0.00 0.00 45.22 3.67
2966 3104 5.762179 TGGTCATCCAGAAATAAGTGTCT 57.238 39.130 0.00 0.00 39.03 3.41
2967 3105 5.734720 TGGTCATCCAGAAATAAGTGTCTC 58.265 41.667 0.00 0.00 39.03 3.36
2968 3106 5.248248 TGGTCATCCAGAAATAAGTGTCTCA 59.752 40.000 0.00 0.00 39.03 3.27
2969 3107 6.173339 GGTCATCCAGAAATAAGTGTCTCAA 58.827 40.000 0.00 0.00 0.00 3.02
2970 3108 6.092807 GGTCATCCAGAAATAAGTGTCTCAAC 59.907 42.308 0.00 0.00 0.00 3.18
2971 3109 6.876257 GTCATCCAGAAATAAGTGTCTCAACT 59.124 38.462 0.00 0.00 0.00 3.16
2972 3110 7.389053 GTCATCCAGAAATAAGTGTCTCAACTT 59.611 37.037 0.00 0.00 42.89 2.66
2973 3111 7.604164 TCATCCAGAAATAAGTGTCTCAACTTC 59.396 37.037 0.00 0.00 40.77 3.01
2974 3112 6.826668 TCCAGAAATAAGTGTCTCAACTTCA 58.173 36.000 0.00 0.00 40.77 3.02
2975 3113 6.931281 TCCAGAAATAAGTGTCTCAACTTCAG 59.069 38.462 0.00 0.00 40.77 3.02
2976 3114 6.708054 CCAGAAATAAGTGTCTCAACTTCAGT 59.292 38.462 0.00 0.00 40.77 3.41
2977 3115 7.872993 CCAGAAATAAGTGTCTCAACTTCAGTA 59.127 37.037 0.00 0.00 40.77 2.74
2978 3116 9.261180 CAGAAATAAGTGTCTCAACTTCAGTAA 57.739 33.333 0.00 0.00 40.77 2.24
2979 3117 9.832445 AGAAATAAGTGTCTCAACTTCAGTAAA 57.168 29.630 0.00 0.00 40.77 2.01
2982 3120 9.614792 AATAAGTGTCTCAACTTCAGTAAAACT 57.385 29.630 0.00 0.00 40.77 2.66
2983 3121 7.923414 AAGTGTCTCAACTTCAGTAAAACTT 57.077 32.000 0.00 0.00 35.44 2.66
2984 3122 7.923414 AGTGTCTCAACTTCAGTAAAACTTT 57.077 32.000 0.00 0.00 0.00 2.66
2985 3123 9.444600 AAGTGTCTCAACTTCAGTAAAACTTTA 57.555 29.630 0.00 0.00 35.44 1.85
2986 3124 9.099454 AGTGTCTCAACTTCAGTAAAACTTTAG 57.901 33.333 0.00 0.00 0.00 1.85
2987 3125 8.880750 GTGTCTCAACTTCAGTAAAACTTTAGT 58.119 33.333 0.00 0.00 0.00 2.24
2992 3130 9.880157 TCAACTTCAGTAAAACTTTAGTACACT 57.120 29.630 0.00 0.00 0.00 3.55
3006 3144 9.428097 ACTTTAGTACACTTATTTTTAGGACGG 57.572 33.333 0.00 0.00 0.00 4.79
3007 3145 9.643693 CTTTAGTACACTTATTTTTAGGACGGA 57.356 33.333 0.00 0.00 0.00 4.69
3008 3146 9.643693 TTTAGTACACTTATTTTTAGGACGGAG 57.356 33.333 0.00 0.00 0.00 4.63
3009 3147 6.637657 AGTACACTTATTTTTAGGACGGAGG 58.362 40.000 0.00 0.00 0.00 4.30
3010 3148 5.750352 ACACTTATTTTTAGGACGGAGGA 57.250 39.130 0.00 0.00 0.00 3.71
3011 3149 6.117975 ACACTTATTTTTAGGACGGAGGAA 57.882 37.500 0.00 0.00 0.00 3.36
3012 3150 6.171213 ACACTTATTTTTAGGACGGAGGAAG 58.829 40.000 0.00 0.00 0.00 3.46
3013 3151 6.171213 CACTTATTTTTAGGACGGAGGAAGT 58.829 40.000 0.00 0.00 0.00 3.01
3014 3152 7.038799 ACACTTATTTTTAGGACGGAGGAAGTA 60.039 37.037 0.00 0.00 0.00 2.24
3069 3232 3.877559 TCATGCTAGTAGCTTTGCACAT 58.122 40.909 22.34 3.54 42.97 3.21
3081 3245 3.777478 CTTTGCACATAAAGGAGGCATG 58.223 45.455 0.00 0.00 34.73 4.06
3164 3346 5.630415 TCAAACCTTAGATGGGGTATCAG 57.370 43.478 0.00 0.00 38.31 2.90
3165 3347 5.036916 TCAAACCTTAGATGGGGTATCAGT 58.963 41.667 0.00 0.00 38.31 3.41
3168 3350 7.349859 TCAAACCTTAGATGGGGTATCAGTAAT 59.650 37.037 0.00 0.00 38.31 1.89
3169 3351 8.656806 CAAACCTTAGATGGGGTATCAGTAATA 58.343 37.037 0.00 0.00 38.31 0.98
3170 3352 8.808240 AACCTTAGATGGGGTATCAGTAATAA 57.192 34.615 0.00 0.00 38.31 1.40
3171 3353 8.437274 ACCTTAGATGGGGTATCAGTAATAAG 57.563 38.462 0.00 0.00 38.31 1.73
3172 3354 8.017251 ACCTTAGATGGGGTATCAGTAATAAGT 58.983 37.037 0.00 0.00 38.31 2.24
3173 3355 8.532819 CCTTAGATGGGGTATCAGTAATAAGTC 58.467 40.741 0.00 0.00 38.31 3.01
3187 3373 8.467598 TCAGTAATAAGTCAGTAGTAAGCCAAG 58.532 37.037 0.00 0.00 0.00 3.61
3218 3404 4.339872 TGCCTCATCTGCAAAACAAAAT 57.660 36.364 0.00 0.00 35.40 1.82
3224 3410 7.254727 GCCTCATCTGCAAAACAAAATTTACAA 60.255 33.333 0.00 0.00 0.00 2.41
3231 3417 7.486647 TGCAAAACAAAATTTACAAATGCCAT 58.513 26.923 12.67 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.878968 TGGTGTAGATGTGGGAATCTAGA 58.121 43.478 0.00 0.00 39.31 2.43
32 33 2.125512 GGAGGCAACGTGCTCGAT 60.126 61.111 16.04 0.00 44.28 3.59
33 34 2.942796 ATGGAGGCAACGTGCTCGA 61.943 57.895 16.04 0.00 44.28 4.04
34 35 2.434884 ATGGAGGCAACGTGCTCG 60.435 61.111 6.63 6.63 44.28 5.03
36 37 2.360350 CCATGGAGGCAACGTGCT 60.360 61.111 5.56 0.00 44.28 4.40
37 38 3.443045 CCCATGGAGGCAACGTGC 61.443 66.667 15.22 0.00 44.08 5.34
38 39 1.077501 ATCCCATGGAGGCAACGTG 60.078 57.895 15.22 0.00 46.39 4.49
39 40 1.077501 CATCCCATGGAGGCAACGT 60.078 57.895 15.22 0.00 46.39 3.99
40 41 0.394216 TTCATCCCATGGAGGCAACG 60.394 55.000 15.22 0.00 46.39 4.10
43 44 0.928505 ATGTTCATCCCATGGAGGCA 59.071 50.000 15.22 3.64 34.05 4.75
59 60 1.884579 CCTCAAGAAGCACAAGCATGT 59.115 47.619 0.00 0.00 45.49 3.21
172 173 6.482308 TGATTTCCTAAATTCGCTTACTAGCC 59.518 38.462 0.00 0.00 44.86 3.93
185 186 7.902920 ATAGTGCCACAATGATTTCCTAAAT 57.097 32.000 0.00 0.00 0.00 1.40
254 255 4.882427 TCATCAAACCTTCGTTTTGGTACA 59.118 37.500 0.00 0.00 40.28 2.90
284 285 0.602060 TGAGCCAATCAAATTGCGCA 59.398 45.000 5.66 5.66 38.25 6.09
435 503 4.389992 CGTATGATCCTATGTGGCAATCAC 59.610 45.833 0.00 0.00 46.23 3.06
462 530 1.729484 CGTGACGCGTGATCTGTGT 60.729 57.895 20.70 4.70 35.54 3.72
464 532 1.442184 GTCGTGACGCGTGATCTGT 60.442 57.895 20.70 0.00 42.13 3.41
465 533 0.798389 ATGTCGTGACGCGTGATCTG 60.798 55.000 20.70 2.26 42.13 2.90
466 534 0.523546 GATGTCGTGACGCGTGATCT 60.524 55.000 20.70 0.00 42.13 2.75
579 649 1.488393 ACAGGAAAGGGATGAGCTAGC 59.512 52.381 6.62 6.62 0.00 3.42
602 674 0.033208 AGAGAGGGAGGAGAGCACAG 60.033 60.000 0.00 0.00 0.00 3.66
603 675 0.033601 GAGAGAGGGAGGAGAGCACA 60.034 60.000 0.00 0.00 0.00 4.57
604 676 0.258774 AGAGAGAGGGAGGAGAGCAC 59.741 60.000 0.00 0.00 0.00 4.40
605 677 0.550914 GAGAGAGAGGGAGGAGAGCA 59.449 60.000 0.00 0.00 0.00 4.26
606 678 0.846693 AGAGAGAGAGGGAGGAGAGC 59.153 60.000 0.00 0.00 0.00 4.09
607 679 2.039084 GCTAGAGAGAGAGGGAGGAGAG 59.961 59.091 0.00 0.00 0.00 3.20
608 680 2.054799 GCTAGAGAGAGAGGGAGGAGA 58.945 57.143 0.00 0.00 0.00 3.71
610 682 2.206322 AGCTAGAGAGAGAGGGAGGA 57.794 55.000 0.00 0.00 0.00 3.71
611 683 2.039879 GGTAGCTAGAGAGAGAGGGAGG 59.960 59.091 0.00 0.00 0.00 4.30
612 684 2.979678 AGGTAGCTAGAGAGAGAGGGAG 59.020 54.545 0.00 0.00 0.00 4.30
613 685 2.976882 GAGGTAGCTAGAGAGAGAGGGA 59.023 54.545 0.00 0.00 0.00 4.20
614 686 2.979678 AGAGGTAGCTAGAGAGAGAGGG 59.020 54.545 0.00 0.00 0.00 4.30
615 687 3.904339 AGAGAGGTAGCTAGAGAGAGAGG 59.096 52.174 0.00 0.00 0.00 3.69
616 688 4.345257 ACAGAGAGGTAGCTAGAGAGAGAG 59.655 50.000 0.00 0.00 0.00 3.20
617 689 4.100963 CACAGAGAGGTAGCTAGAGAGAGA 59.899 50.000 0.00 0.00 0.00 3.10
908 980 2.146061 GGAGGGGATGGAGGAGCTG 61.146 68.421 0.00 0.00 0.00 4.24
915 987 1.240129 GAGATGGGGAGGGGATGGA 59.760 63.158 0.00 0.00 0.00 3.41
916 988 0.477202 ATGAGATGGGGAGGGGATGG 60.477 60.000 0.00 0.00 0.00 3.51
917 989 0.990374 GATGAGATGGGGAGGGGATG 59.010 60.000 0.00 0.00 0.00 3.51
918 990 0.178849 GGATGAGATGGGGAGGGGAT 60.179 60.000 0.00 0.00 0.00 3.85
943 1015 2.709475 GCAGCGCAGATAAACGGG 59.291 61.111 11.47 0.00 0.00 5.28
946 1018 0.583917 GCTAGGCAGCGCAGATAAAC 59.416 55.000 11.47 0.00 38.22 2.01
947 1019 2.992089 GCTAGGCAGCGCAGATAAA 58.008 52.632 11.47 0.00 38.22 1.40
965 1037 2.936498 GGAGATCTCGCTAGCTAGCTAG 59.064 54.545 37.09 37.09 46.85 3.42
966 1038 2.569853 AGGAGATCTCGCTAGCTAGCTA 59.430 50.000 36.02 27.49 46.85 3.32
967 1039 1.351017 AGGAGATCTCGCTAGCTAGCT 59.649 52.381 36.02 23.12 46.85 3.32
968 1040 1.737793 GAGGAGATCTCGCTAGCTAGC 59.262 57.143 31.88 31.88 45.62 3.42
1120 1192 2.886523 TGCTGATCACAAAAGGGAACAG 59.113 45.455 0.00 1.20 37.10 3.16
1168 1240 1.101635 TGGTCTGATCCGTAGCCGAG 61.102 60.000 0.00 0.00 35.63 4.63
1169 1241 1.077285 TGGTCTGATCCGTAGCCGA 60.077 57.895 0.00 0.00 35.63 5.54
1170 1242 1.360551 CTGGTCTGATCCGTAGCCG 59.639 63.158 0.00 0.00 0.00 5.52
1171 1243 1.068250 GCTGGTCTGATCCGTAGCC 59.932 63.158 0.00 0.00 0.00 3.93
1236 1311 4.550076 AGGACAGAAGAAATCACTCCAG 57.450 45.455 0.00 0.00 31.30 3.86
1251 1326 8.598075 GCAAGCAAATTAATTCAAATAGGACAG 58.402 33.333 0.10 0.00 0.00 3.51
1252 1327 8.313292 AGCAAGCAAATTAATTCAAATAGGACA 58.687 29.630 0.10 0.00 0.00 4.02
1253 1328 8.707938 AGCAAGCAAATTAATTCAAATAGGAC 57.292 30.769 0.10 0.00 0.00 3.85
1254 1329 8.530311 TGAGCAAGCAAATTAATTCAAATAGGA 58.470 29.630 0.10 0.00 0.00 2.94
1255 1330 8.598075 GTGAGCAAGCAAATTAATTCAAATAGG 58.402 33.333 0.10 0.00 0.00 2.57
1256 1331 9.362539 AGTGAGCAAGCAAATTAATTCAAATAG 57.637 29.630 0.10 0.00 0.00 1.73
1258 1333 8.611654 AAGTGAGCAAGCAAATTAATTCAAAT 57.388 26.923 0.10 0.00 0.00 2.32
1259 1334 8.436046 AAAGTGAGCAAGCAAATTAATTCAAA 57.564 26.923 0.10 0.00 0.00 2.69
1261 1336 7.436118 AGAAAGTGAGCAAGCAAATTAATTCA 58.564 30.769 0.10 0.00 0.00 2.57
1262 1337 7.880059 AGAAAGTGAGCAAGCAAATTAATTC 57.120 32.000 0.10 0.00 0.00 2.17
1264 1339 7.031975 GCTAGAAAGTGAGCAAGCAAATTAAT 58.968 34.615 0.00 0.00 38.62 1.40
1265 1340 6.207417 AGCTAGAAAGTGAGCAAGCAAATTAA 59.793 34.615 0.00 0.00 41.36 1.40
1268 1343 4.077822 AGCTAGAAAGTGAGCAAGCAAAT 58.922 39.130 0.00 0.00 41.36 2.32
1277 1362 8.770438 AATTGAGAAACTAGCTAGAAAGTGAG 57.230 34.615 27.45 0.44 0.00 3.51
1287 1372 7.337689 TCATGCATGTTAATTGAGAAACTAGCT 59.662 33.333 25.43 0.00 31.74 3.32
1293 1378 7.649533 AGGATCATGCATGTTAATTGAGAAA 57.350 32.000 25.43 2.66 0.00 2.52
1295 1380 7.339976 TCAAAGGATCATGCATGTTAATTGAGA 59.660 33.333 25.43 13.14 0.00 3.27
1307 1392 5.593968 GCATAACAATCAAAGGATCATGCA 58.406 37.500 0.00 0.00 36.97 3.96
1308 1393 4.678287 CGCATAACAATCAAAGGATCATGC 59.322 41.667 0.00 0.00 34.39 4.06
1309 1394 4.678287 GCGCATAACAATCAAAGGATCATG 59.322 41.667 0.30 0.00 31.88 3.07
1310 1395 4.338964 TGCGCATAACAATCAAAGGATCAT 59.661 37.500 5.66 0.00 31.88 2.45
1311 1396 3.693578 TGCGCATAACAATCAAAGGATCA 59.306 39.130 5.66 0.00 31.88 2.92
1330 1416 1.957668 TCCACCAATCATCTGATGCG 58.042 50.000 12.78 4.03 34.49 4.73
1343 1429 1.141665 CACGCTCGATGATCCACCA 59.858 57.895 0.00 0.00 0.00 4.17
1358 1444 1.435966 GAACGGCGTCGAAAACACG 60.436 57.895 20.03 0.00 40.11 4.49
1466 1552 2.018866 GCCGATCTTGAGCGATCCG 61.019 63.158 9.93 0.00 37.16 4.18
1467 1553 0.530650 TTGCCGATCTTGAGCGATCC 60.531 55.000 9.93 0.00 37.16 3.36
1468 1554 0.857935 CTTGCCGATCTTGAGCGATC 59.142 55.000 9.93 0.00 37.13 3.69
1544 1630 1.738099 CCTCGGCTTCTTGACACCG 60.738 63.158 0.00 0.00 46.97 4.94
1698 1784 8.372459 AGTGACCACATACTAATTAACAAGACA 58.628 33.333 2.78 0.00 0.00 3.41
1699 1785 8.773404 AGTGACCACATACTAATTAACAAGAC 57.227 34.615 2.78 0.00 0.00 3.01
1700 1786 9.214957 CAAGTGACCACATACTAATTAACAAGA 57.785 33.333 2.78 0.00 0.00 3.02
1711 1807 4.838986 ACTTCTACCAAGTGACCACATACT 59.161 41.667 2.78 0.00 0.00 2.12
1712 1808 5.148651 ACTTCTACCAAGTGACCACATAC 57.851 43.478 2.78 0.00 0.00 2.39
1713 1809 6.014647 AGTACTTCTACCAAGTGACCACATA 58.985 40.000 2.78 0.00 0.00 2.29
1714 1810 4.838986 AGTACTTCTACCAAGTGACCACAT 59.161 41.667 2.78 0.00 0.00 3.21
1715 1811 4.220724 AGTACTTCTACCAAGTGACCACA 58.779 43.478 2.78 0.00 0.00 4.17
1731 1827 6.653740 GCCATTAACTAACTTGTGGAGTACTT 59.346 38.462 0.00 0.00 37.72 2.24
1735 1831 5.242795 AGCCATTAACTAACTTGTGGAGT 57.757 39.130 0.00 0.00 41.47 3.85
1736 1832 7.527457 GTTAAGCCATTAACTAACTTGTGGAG 58.473 38.462 4.11 0.00 44.88 3.86
1737 1833 6.148150 CGTTAAGCCATTAACTAACTTGTGGA 59.852 38.462 8.70 0.00 45.72 4.02
1738 1834 6.311723 CGTTAAGCCATTAACTAACTTGTGG 58.688 40.000 8.70 0.00 45.72 4.17
1739 1835 6.072893 ACCGTTAAGCCATTAACTAACTTGTG 60.073 38.462 8.70 0.00 45.72 3.33
1757 1853 4.630940 CCGGAGCAAATTAGTTACCGTTAA 59.369 41.667 0.00 0.00 37.67 2.01
2020 2120 3.414700 GGTGGAAGCAGCGTCGTG 61.415 66.667 1.97 0.00 0.00 4.35
2074 2174 3.644606 AGCAGGAGCAGTGGTGGG 61.645 66.667 0.00 0.00 45.49 4.61
2102 2214 0.099082 GGTGTCGACGAGATCACTCC 59.901 60.000 11.62 3.67 39.76 3.85
2392 2513 5.741388 ACACTAGCAACAAGAACAAGAAG 57.259 39.130 0.00 0.00 0.00 2.85
2429 2550 5.583061 ACACACAAACGAATCACAAGACTTA 59.417 36.000 0.00 0.00 0.00 2.24
2459 2583 3.010696 TCTCTCTCTTCCTCACTGCCTTA 59.989 47.826 0.00 0.00 0.00 2.69
2461 2585 1.357420 TCTCTCTCTTCCTCACTGCCT 59.643 52.381 0.00 0.00 0.00 4.75
2462 2586 1.846007 TCTCTCTCTTCCTCACTGCC 58.154 55.000 0.00 0.00 0.00 4.85
2463 2587 3.290710 AGATCTCTCTCTTCCTCACTGC 58.709 50.000 0.00 0.00 0.00 4.40
2464 2588 5.928976 TCTAGATCTCTCTCTTCCTCACTG 58.071 45.833 0.00 0.00 32.66 3.66
2465 2589 5.072329 CCTCTAGATCTCTCTCTTCCTCACT 59.928 48.000 0.00 0.00 32.66 3.41
2466 2590 5.071788 TCCTCTAGATCTCTCTCTTCCTCAC 59.928 48.000 0.00 0.00 32.66 3.51
2467 2591 5.223655 TCCTCTAGATCTCTCTCTTCCTCA 58.776 45.833 0.00 0.00 32.66 3.86
2468 2592 5.825593 TCCTCTAGATCTCTCTCTTCCTC 57.174 47.826 0.00 0.00 32.66 3.71
2469 2593 5.911178 TCTTCCTCTAGATCTCTCTCTTCCT 59.089 44.000 0.00 0.00 32.66 3.36
2470 2594 6.043243 TCTCTTCCTCTAGATCTCTCTCTTCC 59.957 46.154 0.00 0.00 32.66 3.46
2471 2595 7.067496 TCTCTTCCTCTAGATCTCTCTCTTC 57.933 44.000 0.00 0.00 32.66 2.87
2489 2613 5.712917 TCTCTCCTTGTTTCTACCTCTCTTC 59.287 44.000 0.00 0.00 0.00 2.87
2562 2691 3.578282 TCTCACAGTGTTTGCAGATCCTA 59.422 43.478 0.00 0.00 0.00 2.94
2563 2692 2.369860 TCTCACAGTGTTTGCAGATCCT 59.630 45.455 0.00 0.00 0.00 3.24
2587 2716 2.213499 CTCCAAACTGAACTCACGCTT 58.787 47.619 0.00 0.00 0.00 4.68
2590 2719 2.731976 GCTACTCCAAACTGAACTCACG 59.268 50.000 0.00 0.00 0.00 4.35
2591 2720 3.996480 AGCTACTCCAAACTGAACTCAC 58.004 45.455 0.00 0.00 0.00 3.51
2604 2733 3.119814 GGCAACAAAAAGCTAGCTACTCC 60.120 47.826 19.70 7.22 0.00 3.85
2641 2770 5.072741 ACATGCTATATGGTAGCCTTTTGG 58.927 41.667 8.83 0.00 39.69 3.28
2642 2771 7.391554 ACATACATGCTATATGGTAGCCTTTTG 59.608 37.037 8.83 5.29 39.69 2.44
2643 2772 7.461749 ACATACATGCTATATGGTAGCCTTTT 58.538 34.615 8.83 0.00 39.69 2.27
2646 2776 6.627087 AACATACATGCTATATGGTAGCCT 57.373 37.500 8.83 0.00 39.69 4.58
2678 2809 5.009610 ACAGTACAAATGGTTCGAGCAAAAT 59.990 36.000 0.53 0.00 0.00 1.82
2705 2836 5.287035 CCGGTATTTCGGTATTATTACGAGC 59.713 44.000 0.00 0.00 44.60 5.03
2706 2837 6.859715 CCGGTATTTCGGTATTATTACGAG 57.140 41.667 0.00 0.00 44.60 4.18
2724 2858 2.088423 GCAACATTTCATGGTCCGGTA 58.912 47.619 0.00 0.00 33.60 4.02
2786 2924 7.776933 TTAAAGCAGATCATCACTGACATAC 57.223 36.000 0.00 0.00 37.54 2.39
2810 2948 1.405105 ACTGTGCGCACTGACAAAAAT 59.595 42.857 41.96 22.43 34.80 1.82
2843 2981 2.742774 CCTCAAAAACAGCGGGAAAAG 58.257 47.619 0.00 0.00 0.00 2.27
2855 2993 8.420222 TGATAAAGAGAATGTTTGCCTCAAAAA 58.580 29.630 0.00 0.00 35.03 1.94
2857 2995 7.523293 TGATAAAGAGAATGTTTGCCTCAAA 57.477 32.000 0.00 0.00 32.11 2.69
2887 3025 5.764192 GGAGAGAGTATAAGCTTCTCGGTTA 59.236 44.000 0.00 0.00 39.65 2.85
2889 3027 4.139038 GGAGAGAGTATAAGCTTCTCGGT 58.861 47.826 0.00 0.00 33.96 4.69
2899 3037 8.290463 ACACTTAGGGATAGGAGAGAGTATAA 57.710 38.462 0.00 0.00 0.00 0.98
2900 3038 7.740365 AGACACTTAGGGATAGGAGAGAGTATA 59.260 40.741 0.00 0.00 0.00 1.47
2901 3039 6.564927 AGACACTTAGGGATAGGAGAGAGTAT 59.435 42.308 0.00 0.00 0.00 2.12
2902 3040 5.912354 AGACACTTAGGGATAGGAGAGAGTA 59.088 44.000 0.00 0.00 0.00 2.59
2903 3041 4.729881 AGACACTTAGGGATAGGAGAGAGT 59.270 45.833 0.00 0.00 0.00 3.24
2904 3042 5.319043 AGACACTTAGGGATAGGAGAGAG 57.681 47.826 0.00 0.00 0.00 3.20
2905 3043 5.735733 AAGACACTTAGGGATAGGAGAGA 57.264 43.478 0.00 0.00 0.00 3.10
2906 3044 7.899648 TTTAAGACACTTAGGGATAGGAGAG 57.100 40.000 0.00 0.00 0.00 3.20
2907 3045 8.855804 AATTTAAGACACTTAGGGATAGGAGA 57.144 34.615 0.00 0.00 0.00 3.71
2928 3066 8.934023 TGGATGACCAAAGTTCTACTAAATTT 57.066 30.769 0.00 0.00 43.91 1.82
2929 3067 8.383175 TCTGGATGACCAAAGTTCTACTAAATT 58.617 33.333 0.00 0.00 46.32 1.82
2930 3068 7.918076 TCTGGATGACCAAAGTTCTACTAAAT 58.082 34.615 0.00 0.00 46.32 1.40
2931 3069 7.311092 TCTGGATGACCAAAGTTCTACTAAA 57.689 36.000 0.00 0.00 46.32 1.85
2932 3070 6.928348 TCTGGATGACCAAAGTTCTACTAA 57.072 37.500 0.00 0.00 46.32 2.24
2933 3071 6.928348 TTCTGGATGACCAAAGTTCTACTA 57.072 37.500 0.00 0.00 46.32 1.82
2934 3072 5.825593 TTCTGGATGACCAAAGTTCTACT 57.174 39.130 0.00 0.00 46.32 2.57
2935 3073 8.561738 TTATTTCTGGATGACCAAAGTTCTAC 57.438 34.615 0.00 0.00 46.32 2.59
2936 3074 8.383175 ACTTATTTCTGGATGACCAAAGTTCTA 58.617 33.333 0.00 0.00 46.32 2.10
2937 3075 7.175641 CACTTATTTCTGGATGACCAAAGTTCT 59.824 37.037 0.00 0.00 46.32 3.01
2938 3076 7.040409 ACACTTATTTCTGGATGACCAAAGTTC 60.040 37.037 0.00 0.00 46.32 3.01
2939 3077 6.777580 ACACTTATTTCTGGATGACCAAAGTT 59.222 34.615 0.00 0.00 46.32 2.66
2940 3078 6.306987 ACACTTATTTCTGGATGACCAAAGT 58.693 36.000 0.00 0.00 46.32 2.66
2941 3079 6.656693 AGACACTTATTTCTGGATGACCAAAG 59.343 38.462 0.00 0.00 46.32 2.77
2942 3080 6.542821 AGACACTTATTTCTGGATGACCAAA 58.457 36.000 0.00 0.00 46.32 3.28
2943 3081 6.126863 AGACACTTATTTCTGGATGACCAA 57.873 37.500 0.00 0.00 46.32 3.67
2944 3082 5.248248 TGAGACACTTATTTCTGGATGACCA 59.752 40.000 0.00 0.00 44.76 4.02
2945 3083 5.734720 TGAGACACTTATTTCTGGATGACC 58.265 41.667 0.00 0.00 0.00 4.02
2946 3084 6.876257 AGTTGAGACACTTATTTCTGGATGAC 59.124 38.462 0.00 0.00 0.00 3.06
2947 3085 7.009179 AGTTGAGACACTTATTTCTGGATGA 57.991 36.000 0.00 0.00 0.00 2.92
2948 3086 7.388776 TGAAGTTGAGACACTTATTTCTGGATG 59.611 37.037 0.00 0.00 37.11 3.51
2949 3087 7.453393 TGAAGTTGAGACACTTATTTCTGGAT 58.547 34.615 0.00 0.00 37.11 3.41
2950 3088 6.826668 TGAAGTTGAGACACTTATTTCTGGA 58.173 36.000 0.00 0.00 37.11 3.86
2951 3089 6.708054 ACTGAAGTTGAGACACTTATTTCTGG 59.292 38.462 0.00 0.00 37.11 3.86
2952 3090 7.721286 ACTGAAGTTGAGACACTTATTTCTG 57.279 36.000 0.00 0.00 37.11 3.02
2953 3091 9.832445 TTTACTGAAGTTGAGACACTTATTTCT 57.168 29.630 0.00 0.00 37.11 2.52
2956 3094 9.614792 AGTTTTACTGAAGTTGAGACACTTATT 57.385 29.630 0.00 0.00 37.11 1.40
2957 3095 9.614792 AAGTTTTACTGAAGTTGAGACACTTAT 57.385 29.630 0.00 0.00 37.11 1.73
2958 3096 9.444600 AAAGTTTTACTGAAGTTGAGACACTTA 57.555 29.630 0.00 0.00 37.11 2.24
2959 3097 7.923414 AAGTTTTACTGAAGTTGAGACACTT 57.077 32.000 0.00 0.00 39.84 3.16
2960 3098 7.923414 AAAGTTTTACTGAAGTTGAGACACT 57.077 32.000 0.00 0.00 0.00 3.55
2961 3099 8.880750 ACTAAAGTTTTACTGAAGTTGAGACAC 58.119 33.333 0.00 0.00 28.89 3.67
2966 3104 9.880157 AGTGTACTAAAGTTTTACTGAAGTTGA 57.120 29.630 0.00 0.00 29.95 3.18
2980 3118 9.428097 CCGTCCTAAAAATAAGTGTACTAAAGT 57.572 33.333 0.00 0.00 0.00 2.66
2981 3119 9.643693 TCCGTCCTAAAAATAAGTGTACTAAAG 57.356 33.333 0.00 0.00 0.00 1.85
2982 3120 9.643693 CTCCGTCCTAAAAATAAGTGTACTAAA 57.356 33.333 0.00 0.00 0.00 1.85
2983 3121 8.253113 CCTCCGTCCTAAAAATAAGTGTACTAA 58.747 37.037 0.00 0.00 0.00 2.24
2984 3122 7.615365 TCCTCCGTCCTAAAAATAAGTGTACTA 59.385 37.037 0.00 0.00 0.00 1.82
2985 3123 6.438425 TCCTCCGTCCTAAAAATAAGTGTACT 59.562 38.462 0.00 0.00 0.00 2.73
2986 3124 6.633856 TCCTCCGTCCTAAAAATAAGTGTAC 58.366 40.000 0.00 0.00 0.00 2.90
2987 3125 6.855763 TCCTCCGTCCTAAAAATAAGTGTA 57.144 37.500 0.00 0.00 0.00 2.90
2988 3126 5.750352 TCCTCCGTCCTAAAAATAAGTGT 57.250 39.130 0.00 0.00 0.00 3.55
2989 3127 6.171213 ACTTCCTCCGTCCTAAAAATAAGTG 58.829 40.000 0.00 0.00 0.00 3.16
2990 3128 6.370186 ACTTCCTCCGTCCTAAAAATAAGT 57.630 37.500 0.00 0.00 0.00 2.24
2991 3129 8.959705 AATACTTCCTCCGTCCTAAAAATAAG 57.040 34.615 0.00 0.00 0.00 1.73
2994 3132 9.916360 AATTAATACTTCCTCCGTCCTAAAAAT 57.084 29.630 0.00 0.00 0.00 1.82
3000 3138 9.338622 CAAATTAATTAATACTTCCTCCGTCCT 57.661 33.333 11.07 0.00 0.00 3.85
3001 3139 9.333724 TCAAATTAATTAATACTTCCTCCGTCC 57.666 33.333 11.07 0.00 0.00 4.79
3004 3142 9.612620 GCATCAAATTAATTAATACTTCCTCCG 57.387 33.333 11.07 0.00 0.00 4.63
3014 3152 9.602568 TTCAGCATGTGCATCAAATTAATTAAT 57.397 25.926 4.81 4.81 45.16 1.40
3069 3232 4.526970 GATGGAAAGTCATGCCTCCTTTA 58.473 43.478 0.00 0.00 0.00 1.85
3100 3266 9.810545 GATATACTAATCCAAGTTATGCCTCTC 57.189 37.037 0.00 0.00 0.00 3.20
3101 3267 9.554053 AGATATACTAATCCAAGTTATGCCTCT 57.446 33.333 0.00 0.00 0.00 3.69
3130 3296 9.586435 CCATCTAAGGTTTGAAATATTCCAAAC 57.414 33.333 18.91 18.91 46.71 2.93
3164 3346 8.033626 ACACTTGGCTTACTACTGACTTATTAC 58.966 37.037 0.00 0.00 0.00 1.89
3165 3347 8.130671 ACACTTGGCTTACTACTGACTTATTA 57.869 34.615 0.00 0.00 0.00 0.98
3168 3350 6.415206 AACACTTGGCTTACTACTGACTTA 57.585 37.500 0.00 0.00 0.00 2.24
3169 3351 4.957684 ACACTTGGCTTACTACTGACTT 57.042 40.909 0.00 0.00 0.00 3.01
3170 3352 4.957684 AACACTTGGCTTACTACTGACT 57.042 40.909 0.00 0.00 0.00 3.41
3171 3353 5.404667 GTGTAACACTTGGCTTACTACTGAC 59.595 44.000 0.00 0.00 36.32 3.51
3172 3354 5.069383 TGTGTAACACTTGGCTTACTACTGA 59.931 40.000 0.00 0.00 45.67 3.41
3173 3355 5.294356 TGTGTAACACTTGGCTTACTACTG 58.706 41.667 0.00 0.00 45.67 2.74
3218 3404 7.167924 ACACACATATCATGGCATTTGTAAA 57.832 32.000 0.00 0.00 33.60 2.01
3224 3410 6.534475 AAGAAACACACATATCATGGCATT 57.466 33.333 0.00 0.00 33.60 3.56
3231 3417 7.566760 ACAAGTGAAAGAAACACACATATCA 57.433 32.000 0.00 0.00 40.25 2.15


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

AutoCloner maintained by Alex Coulton.