Multiple sequence alignment - TraesCS6B01G296200

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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 TraesCS6B01G296200 chr6B 100.000 3982 0 0 1 3982 532042759 532046740 0.000000e+00 7354.0
1 TraesCS6B01G296200 chr6B 79.076 693 123 19 2229 2912 103663977 103664656 1.300000e-124 457.0
2 TraesCS6B01G296200 chr6B 81.584 505 52 25 119 595 445039265 445039756 2.900000e-101 379.0
3 TraesCS6B01G296200 chr6B 90.909 165 11 2 1982 2146 532044665 532044825 6.700000e-53 219.0
4 TraesCS6B01G296200 chr6B 90.909 165 11 2 1907 2067 532044740 532044904 6.700000e-53 219.0
5 TraesCS6B01G296200 chr6B 82.381 210 31 2 1253 1462 103663651 103663854 1.140000e-40 178.0
6 TraesCS6B01G296200 chr6D 92.964 1407 59 24 665 2054 348085917 348084534 0.000000e+00 2013.0
7 TraesCS6B01G296200 chr6D 96.789 1090 29 5 2134 3217 348084346 348083257 0.000000e+00 1814.0
8 TraesCS6B01G296200 chr6D 82.415 381 23 16 3641 3982 348082773 348082398 3.890000e-75 292.0
9 TraesCS6B01G296200 chr6D 75.318 628 115 30 1253 1861 43070404 43069798 8.490000e-67 265.0
10 TraesCS6B01G296200 chr6D 92.617 149 7 2 1985 2133 348084678 348084534 1.120000e-50 211.0
11 TraesCS6B01G296200 chr6A 91.284 1503 80 30 665 2152 495450426 495451892 0.000000e+00 2002.0
12 TraesCS6B01G296200 chr6A 95.041 968 27 14 2134 3084 495452157 495453120 0.000000e+00 1502.0
13 TraesCS6B01G296200 chr6A 92.157 153 11 1 1982 2133 495451656 495451808 8.670000e-52 215.0
14 TraesCS6B01G296200 chr6A 84.579 214 15 14 3725 3931 495453547 495453749 3.140000e-46 196.0
15 TraesCS6B01G296200 chr6A 79.752 242 19 14 1907 2133 495451735 495451961 8.920000e-32 148.0
16 TraesCS6B01G296200 chr6A 88.073 109 4 2 1955 2054 495451853 495451961 1.940000e-23 121.0
17 TraesCS6B01G296200 chr6A 92.683 82 6 0 2065 2146 495451660 495451741 6.990000e-23 119.0
18 TraesCS6B01G296200 chr6A 85.321 109 7 5 3165 3264 495453119 495453227 1.960000e-18 104.0
19 TraesCS6B01G296200 chr5B 89.685 1173 79 25 2065 3212 458386957 458388112 0.000000e+00 1458.0
20 TraesCS6B01G296200 chr5B 86.413 1104 80 42 909 1988 458385978 458387035 0.000000e+00 1144.0
21 TraesCS6B01G296200 chr5D 89.191 1175 81 27 2066 3212 381980093 381981249 0.000000e+00 1424.0
22 TraesCS6B01G296200 chr5D 85.896 1099 87 38 909 1988 381979121 381980170 0.000000e+00 1109.0
23 TraesCS6B01G296200 chr5A 89.308 1113 79 21 2085 3169 482316559 482317659 0.000000e+00 1360.0
24 TraesCS6B01G296200 chr5A 86.582 1021 76 30 909 1918 482315569 482316539 0.000000e+00 1070.0
25 TraesCS6B01G296200 chr2D 82.239 777 109 23 2146 2901 548081418 548080650 0.000000e+00 643.0
26 TraesCS6B01G296200 chr2D 97.473 277 6 1 1256 1531 68467435 68467159 4.660000e-129 472.0
27 TraesCS6B01G296200 chr2D 76.676 686 126 21 1245 1912 548082168 548081499 2.280000e-92 350.0
28 TraesCS6B01G296200 chr2D 100.000 75 0 0 1633 1707 68467161 68467087 5.370000e-29 139.0
29 TraesCS6B01G296200 chr2B 81.534 769 122 17 2146 2901 655010963 655010202 2.030000e-172 616.0
30 TraesCS6B01G296200 chr2B 76.710 687 127 24 1245 1912 655011718 655011046 6.330000e-93 351.0
31 TraesCS6B01G296200 chr2B 81.974 233 19 13 923 1142 681840480 681840258 4.090000e-40 176.0
32 TraesCS6B01G296200 chr2A 81.404 769 122 19 2146 2901 690928936 690929696 3.400000e-170 608.0
33 TraesCS6B01G296200 chr2A 77.551 686 121 21 1245 1912 690928182 690928852 2.250000e-102 383.0
34 TraesCS6B01G296200 chr1B 85.197 608 43 20 3 586 673185453 673186037 7.420000e-162 580.0
35 TraesCS6B01G296200 chr1D 80.775 619 68 24 3 595 144465670 144465077 1.700000e-118 436.0
36 TraesCS6B01G296200 chr1D 91.304 46 4 0 550 595 144464664 144464619 3.320000e-06 63.9
37 TraesCS6B01G296200 chr1A 82.617 512 53 15 111 595 144586598 144587100 1.710000e-113 420.0


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 TraesCS6B01G296200 chr6B 532042759 532046740 3981 False 2597.333333 7354 93.939333 1 3982 3 chr6B.!!$F3 3981
1 TraesCS6B01G296200 chr6B 103663651 103664656 1005 False 317.500000 457 80.728500 1253 2912 2 chr6B.!!$F2 1659
2 TraesCS6B01G296200 chr6D 348082398 348085917 3519 True 1082.500000 2013 91.196250 665 3982 4 chr6D.!!$R2 3317
3 TraesCS6B01G296200 chr6D 43069798 43070404 606 True 265.000000 265 75.318000 1253 1861 1 chr6D.!!$R1 608
4 TraesCS6B01G296200 chr6A 495450426 495453749 3323 False 550.875000 2002 88.611250 665 3931 8 chr6A.!!$F1 3266
5 TraesCS6B01G296200 chr5B 458385978 458388112 2134 False 1301.000000 1458 88.049000 909 3212 2 chr5B.!!$F1 2303
6 TraesCS6B01G296200 chr5D 381979121 381981249 2128 False 1266.500000 1424 87.543500 909 3212 2 chr5D.!!$F1 2303
7 TraesCS6B01G296200 chr5A 482315569 482317659 2090 False 1215.000000 1360 87.945000 909 3169 2 chr5A.!!$F1 2260
8 TraesCS6B01G296200 chr2D 548080650 548082168 1518 True 496.500000 643 79.457500 1245 2901 2 chr2D.!!$R2 1656
9 TraesCS6B01G296200 chr2B 655010202 655011718 1516 True 483.500000 616 79.122000 1245 2901 2 chr2B.!!$R2 1656
10 TraesCS6B01G296200 chr2A 690928182 690929696 1514 False 495.500000 608 79.477500 1245 2901 2 chr2A.!!$F1 1656
11 TraesCS6B01G296200 chr1B 673185453 673186037 584 False 580.000000 580 85.197000 3 586 1 chr1B.!!$F1 583
12 TraesCS6B01G296200 chr1D 144464619 144465670 1051 True 249.950000 436 86.039500 3 595 2 chr1D.!!$R1 592
13 TraesCS6B01G296200 chr1A 144586598 144587100 502 False 420.000000 420 82.617000 111 595 1 chr1A.!!$F1 484

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
648 1135 0.038343 CTGTGGGTTCGCATTTTGGG 60.038 55.000 0.0 0.0 32.43 4.12 F
884 1375 0.383949 GCCTTTCTCGCTCTCGATCT 59.616 55.000 0.0 0.0 44.56 2.75 F
1802 2359 1.068194 GTGACAGTCGAGGAGGACAAG 60.068 57.143 0.0 0.0 39.42 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 2514 0.674895 GCAGATCAAGCAGTTCGGGT 60.675 55.0 5.41 0.00 0.00 5.28 R
2028 2601 2.773993 TCAGCATCTGATCAAGCACA 57.226 45.0 14.53 0.95 35.39 4.57 R
3221 4199 0.112412 AAGAACATGAAACCGCCCCT 59.888 50.0 0.00 0.00 0.00 4.79 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
194 196 8.862074 TGAATAATGTTCTCATTTGCAATTTCG 58.138 29.630 0.00 0.00 43.12 3.46
197 199 7.481275 AATGTTCTCATTTGCAATTTCGTTT 57.519 28.000 0.00 0.00 40.88 3.60
199 201 6.272318 TGTTCTCATTTGCAATTTCGTTTCT 58.728 32.000 0.00 0.00 0.00 2.52
232 234 8.678199 CCTAGAAAATGTCTAAGAATCCCAAAC 58.322 37.037 0.00 0.00 38.41 2.93
374 398 1.542547 GGTTCATATACACCGGGCTGG 60.543 57.143 11.83 11.83 46.41 4.85
400 424 9.586435 GAATTTTATACACAAATTCCCAGGAAG 57.414 33.333 5.21 0.00 41.70 3.46
464 489 9.371540 ATCGTTTTGATCCCTCAGTGGAACTTA 62.372 40.741 0.00 0.00 36.62 2.24
522 551 9.607988 TTCATCACTGTAGTTTGTTTCTTCTAA 57.392 29.630 0.00 0.00 0.00 2.10
534 563 2.099141 TCTTCTAATGTTGCGCTGCT 57.901 45.000 9.73 0.00 0.00 4.24
545 574 3.057666 TGTTGCGCTGCTCATTTTATCAA 60.058 39.130 9.73 0.00 0.00 2.57
546 575 3.409851 TGCGCTGCTCATTTTATCAAG 57.590 42.857 9.73 0.00 0.00 3.02
625 1112 2.418368 TTTTGAGATCCATCACCGGG 57.582 50.000 6.32 0.00 0.00 5.73
626 1113 1.578897 TTTGAGATCCATCACCGGGA 58.421 50.000 6.32 0.00 39.14 5.14
627 1114 1.578897 TTGAGATCCATCACCGGGAA 58.421 50.000 6.32 0.00 38.09 3.97
628 1115 1.123077 TGAGATCCATCACCGGGAAG 58.877 55.000 6.32 0.00 38.09 3.46
629 1116 0.250081 GAGATCCATCACCGGGAAGC 60.250 60.000 6.32 0.00 38.09 3.86
630 1117 0.692419 AGATCCATCACCGGGAAGCT 60.692 55.000 6.32 0.00 38.09 3.74
631 1118 0.533755 GATCCATCACCGGGAAGCTG 60.534 60.000 6.32 0.00 38.09 4.24
632 1119 1.274703 ATCCATCACCGGGAAGCTGT 61.275 55.000 6.32 0.00 38.09 4.40
633 1120 1.746615 CCATCACCGGGAAGCTGTG 60.747 63.158 6.32 0.00 0.00 3.66
634 1121 1.746615 CATCACCGGGAAGCTGTGG 60.747 63.158 6.32 0.00 0.00 4.17
635 1122 2.971598 ATCACCGGGAAGCTGTGGG 61.972 63.158 6.32 0.00 0.00 4.61
636 1123 3.953775 CACCGGGAAGCTGTGGGT 61.954 66.667 6.32 0.00 0.00 4.51
637 1124 3.175710 ACCGGGAAGCTGTGGGTT 61.176 61.111 6.32 0.00 35.72 4.11
638 1125 2.359975 CCGGGAAGCTGTGGGTTC 60.360 66.667 0.00 0.00 45.85 3.62
642 1129 3.987404 GAAGCTGTGGGTTCGCAT 58.013 55.556 0.00 0.00 39.61 4.73
643 1130 2.257353 GAAGCTGTGGGTTCGCATT 58.743 52.632 0.00 0.00 39.61 3.56
644 1131 0.598065 GAAGCTGTGGGTTCGCATTT 59.402 50.000 0.00 0.00 39.61 2.32
645 1132 1.000274 GAAGCTGTGGGTTCGCATTTT 60.000 47.619 0.00 0.00 39.61 1.82
646 1133 0.314935 AGCTGTGGGTTCGCATTTTG 59.685 50.000 0.00 0.00 32.43 2.44
647 1134 0.667184 GCTGTGGGTTCGCATTTTGG 60.667 55.000 0.00 0.00 32.43 3.28
648 1135 0.038343 CTGTGGGTTCGCATTTTGGG 60.038 55.000 0.00 0.00 32.43 4.12
649 1136 1.374125 GTGGGTTCGCATTTTGGGC 60.374 57.895 0.00 0.00 0.00 5.36
650 1137 2.264480 GGGTTCGCATTTTGGGCC 59.736 61.111 0.00 0.00 0.00 5.80
651 1138 2.126110 GGTTCGCATTTTGGGCCG 60.126 61.111 0.00 0.00 0.00 6.13
652 1139 2.126110 GTTCGCATTTTGGGCCGG 60.126 61.111 0.00 0.00 0.00 6.13
653 1140 2.598985 TTCGCATTTTGGGCCGGT 60.599 55.556 1.90 0.00 0.00 5.28
654 1141 2.631580 TTCGCATTTTGGGCCGGTC 61.632 57.895 1.90 0.00 0.00 4.79
655 1142 3.061848 CGCATTTTGGGCCGGTCT 61.062 61.111 5.77 0.00 0.00 3.85
656 1143 2.885113 GCATTTTGGGCCGGTCTC 59.115 61.111 5.77 0.00 0.00 3.36
657 1144 1.678970 GCATTTTGGGCCGGTCTCT 60.679 57.895 5.77 0.00 0.00 3.10
658 1145 1.250840 GCATTTTGGGCCGGTCTCTT 61.251 55.000 5.77 0.00 0.00 2.85
659 1146 1.953311 GCATTTTGGGCCGGTCTCTTA 60.953 52.381 5.77 0.00 0.00 2.10
660 1147 2.654863 CATTTTGGGCCGGTCTCTTAT 58.345 47.619 5.77 0.00 0.00 1.73
661 1148 3.815809 CATTTTGGGCCGGTCTCTTATA 58.184 45.455 5.77 0.00 0.00 0.98
662 1149 4.204012 CATTTTGGGCCGGTCTCTTATAA 58.796 43.478 5.77 0.00 0.00 0.98
663 1150 4.513406 TTTTGGGCCGGTCTCTTATAAT 57.487 40.909 5.77 0.00 0.00 1.28
688 1175 2.109799 CCATAGAGCCCAGCACCG 59.890 66.667 0.00 0.00 0.00 4.94
836 1327 1.627297 ATCCGTGGCTTTCTCCTCCC 61.627 60.000 0.00 0.00 0.00 4.30
837 1328 2.294078 CCGTGGCTTTCTCCTCCCT 61.294 63.158 0.00 0.00 0.00 4.20
881 1372 2.485582 CGCCTTTCTCGCTCTCGA 59.514 61.111 0.00 0.00 43.28 4.04
884 1375 0.383949 GCCTTTCTCGCTCTCGATCT 59.616 55.000 0.00 0.00 44.56 2.75
900 1391 2.474359 CGATCTCGATCTGTTGATTGCC 59.526 50.000 5.47 0.00 43.02 4.52
978 1483 7.009540 CGATTTCTGCTGTTTGTTTCTTTCTTT 59.990 33.333 0.00 0.00 0.00 2.52
979 1484 7.581011 TTTCTGCTGTTTGTTTCTTTCTTTC 57.419 32.000 0.00 0.00 0.00 2.62
983 1488 7.542130 TCTGCTGTTTGTTTCTTTCTTTCTTTC 59.458 33.333 0.00 0.00 0.00 2.62
984 1489 7.378181 TGCTGTTTGTTTCTTTCTTTCTTTCT 58.622 30.769 0.00 0.00 0.00 2.52
1170 1678 3.227276 CCCCGACTCCCAGATCCG 61.227 72.222 0.00 0.00 0.00 4.18
1188 1696 3.487202 GCGGATTCGTTCTGCGCA 61.487 61.111 10.98 10.98 46.38 6.09
1414 1925 1.597742 GGAGAAGCTGCTCAACAACA 58.402 50.000 23.57 0.00 36.62 3.33
1581 2113 8.378565 ACTAATGCATTGAAGCTATAGGTGTAT 58.621 33.333 22.27 0.00 34.99 2.29
1607 2144 8.042515 TGTAGTAATATTTGGTGGTGGTTACTC 58.957 37.037 0.00 0.00 34.09 2.59
1610 2147 8.774183 AGTAATATTTGGTGGTGGTTACTCATA 58.226 33.333 0.00 0.00 0.00 2.15
1611 2148 9.569122 GTAATATTTGGTGGTGGTTACTCATAT 57.431 33.333 0.00 0.00 0.00 1.78
1618 2159 4.273480 GTGGTGGTTACTCATATGTGATGC 59.727 45.833 11.60 1.38 32.98 3.91
1802 2359 1.068194 GTGACAGTCGAGGAGGACAAG 60.068 57.143 0.00 0.00 39.42 3.16
1955 2523 9.498307 GAAAATGTTATTTATGTACCCGAACTG 57.502 33.333 0.00 0.00 0.00 3.16
2032 2605 7.760131 ATGTTATTTATGTGCTTGAATGTGC 57.240 32.000 0.00 0.00 0.00 4.57
2033 2606 6.923012 TGTTATTTATGTGCTTGAATGTGCT 58.077 32.000 0.00 0.00 0.00 4.40
2034 2607 7.377398 TGTTATTTATGTGCTTGAATGTGCTT 58.623 30.769 0.00 0.00 0.00 3.91
2035 2608 7.328982 TGTTATTTATGTGCTTGAATGTGCTTG 59.671 33.333 0.00 0.00 0.00 4.01
2036 2609 5.450592 TTTATGTGCTTGAATGTGCTTGA 57.549 34.783 0.00 0.00 0.00 3.02
2037 2610 5.648178 TTATGTGCTTGAATGTGCTTGAT 57.352 34.783 0.00 0.00 0.00 2.57
2038 2611 3.564235 TGTGCTTGAATGTGCTTGATC 57.436 42.857 0.00 0.00 0.00 2.92
2039 2612 2.885894 TGTGCTTGAATGTGCTTGATCA 59.114 40.909 0.00 0.00 0.00 2.92
2040 2613 3.057806 TGTGCTTGAATGTGCTTGATCAG 60.058 43.478 0.00 0.00 0.00 2.90
2041 2614 3.189910 GTGCTTGAATGTGCTTGATCAGA 59.810 43.478 0.00 0.00 0.00 3.27
2042 2615 4.014406 TGCTTGAATGTGCTTGATCAGAT 58.986 39.130 0.00 0.00 0.00 2.90
2043 2616 4.142469 TGCTTGAATGTGCTTGATCAGATG 60.142 41.667 0.00 0.00 0.00 2.90
2044 2617 4.352039 CTTGAATGTGCTTGATCAGATGC 58.648 43.478 0.00 3.06 0.00 3.91
2045 2618 3.617284 TGAATGTGCTTGATCAGATGCT 58.383 40.909 15.13 0.00 0.00 3.79
2046 2619 3.377172 TGAATGTGCTTGATCAGATGCTG 59.623 43.478 15.13 0.00 0.00 4.41
2047 2620 2.773993 TGTGCTTGATCAGATGCTGA 57.226 45.000 15.13 0.00 44.99 4.26
2048 2621 3.062122 TGTGCTTGATCAGATGCTGAA 57.938 42.857 15.13 2.82 44.04 3.02
2049 2622 3.617284 TGTGCTTGATCAGATGCTGAAT 58.383 40.909 15.13 0.00 44.04 2.57
2050 2623 4.014406 TGTGCTTGATCAGATGCTGAATT 58.986 39.130 15.13 0.00 44.04 2.17
2051 2624 5.187687 TGTGCTTGATCAGATGCTGAATTA 58.812 37.500 15.13 0.00 44.04 1.40
2052 2625 5.065602 TGTGCTTGATCAGATGCTGAATTAC 59.934 40.000 15.13 7.32 44.04 1.89
2053 2626 5.065602 GTGCTTGATCAGATGCTGAATTACA 59.934 40.000 15.13 0.00 44.04 2.41
2054 2627 5.826208 TGCTTGATCAGATGCTGAATTACAT 59.174 36.000 15.13 0.00 44.04 2.29
2055 2628 6.320418 TGCTTGATCAGATGCTGAATTACATT 59.680 34.615 15.13 0.00 44.04 2.71
2056 2629 6.856938 GCTTGATCAGATGCTGAATTACATTC 59.143 38.462 0.78 0.00 44.04 2.67
2057 2630 7.255173 GCTTGATCAGATGCTGAATTACATTCT 60.255 37.037 0.78 0.00 44.04 2.40
2058 2631 8.515695 TTGATCAGATGCTGAATTACATTCTT 57.484 30.769 0.78 0.00 44.04 2.52
2059 2632 8.151141 TGATCAGATGCTGAATTACATTCTTC 57.849 34.615 0.78 0.00 44.04 2.87
2060 2633 7.991460 TGATCAGATGCTGAATTACATTCTTCT 59.009 33.333 0.78 0.00 44.04 2.85
2061 2634 8.749026 ATCAGATGCTGAATTACATTCTTCTT 57.251 30.769 0.78 0.00 44.04 2.52
2062 2635 8.571461 TCAGATGCTGAATTACATTCTTCTTT 57.429 30.769 0.00 0.00 37.57 2.52
2063 2636 9.017509 TCAGATGCTGAATTACATTCTTCTTTT 57.982 29.630 0.00 0.00 37.57 2.27
2064 2637 9.635520 CAGATGCTGAATTACATTCTTCTTTTT 57.364 29.630 0.00 0.00 39.96 1.94
2076 2649 8.918202 ACATTCTTCTTTTTATACACTGTCCA 57.082 30.769 0.00 0.00 0.00 4.02
2077 2650 9.003658 ACATTCTTCTTTTTATACACTGTCCAG 57.996 33.333 0.00 0.00 0.00 3.86
2078 2651 7.435068 TTCTTCTTTTTATACACTGTCCAGC 57.565 36.000 0.00 0.00 0.00 4.85
2079 2652 6.530120 TCTTCTTTTTATACACTGTCCAGCA 58.470 36.000 0.00 0.00 0.00 4.41
2080 2653 7.168219 TCTTCTTTTTATACACTGTCCAGCAT 58.832 34.615 0.00 0.00 0.00 3.79
2081 2654 6.985188 TCTTTTTATACACTGTCCAGCATC 57.015 37.500 0.00 0.00 0.00 3.91
2082 2655 6.472016 TCTTTTTATACACTGTCCAGCATCA 58.528 36.000 0.00 0.00 0.00 3.07
2083 2656 6.939730 TCTTTTTATACACTGTCCAGCATCAA 59.060 34.615 0.00 0.00 0.00 2.57
2084 2657 7.446931 TCTTTTTATACACTGTCCAGCATCAAA 59.553 33.333 0.00 0.00 0.00 2.69
2085 2658 7.517614 TTTTATACACTGTCCAGCATCAAAA 57.482 32.000 0.00 0.00 0.00 2.44
2086 2659 7.517614 TTTATACACTGTCCAGCATCAAAAA 57.482 32.000 0.00 0.00 0.00 1.94
2771 3726 3.186909 TCTCGCCATTTCTTGTACGATG 58.813 45.455 0.00 0.00 33.29 3.84
2801 3756 6.695278 CGACATGTTAACCTGTTTGTTCATTT 59.305 34.615 16.29 0.00 0.00 2.32
2803 3758 8.195617 ACATGTTAACCTGTTTGTTCATTTTG 57.804 30.769 10.36 0.00 0.00 2.44
2804 3759 6.654793 TGTTAACCTGTTTGTTCATTTTGC 57.345 33.333 2.48 0.00 0.00 3.68
2981 3940 1.478510 AGCTTCGCCCATATCCGATAG 59.521 52.381 0.00 0.00 33.04 2.08
2996 3955 1.781429 CGATAGGACGAACAATGCGAG 59.219 52.381 0.00 0.00 35.09 5.03
3019 3979 3.608316 ATCTCTTGAACTGGACAGCTC 57.392 47.619 0.00 0.00 0.00 4.09
3217 4195 4.622740 GCTTTACTTTGTGTGCATTCATCC 59.377 41.667 0.00 0.00 0.00 3.51
3218 4196 5.565439 GCTTTACTTTGTGTGCATTCATCCT 60.565 40.000 0.00 0.00 0.00 3.24
3219 4197 6.403866 TTTACTTTGTGTGCATTCATCCTT 57.596 33.333 0.00 0.00 0.00 3.36
3221 4199 7.517614 TTACTTTGTGTGCATTCATCCTTTA 57.482 32.000 0.00 0.00 0.00 1.85
3222 4200 6.017400 ACTTTGTGTGCATTCATCCTTTAG 57.983 37.500 0.00 0.00 0.00 1.85
3230 4244 0.996583 TTCATCCTTTAGGGGCGGTT 59.003 50.000 0.00 0.00 35.41 4.44
3231 4245 0.996583 TCATCCTTTAGGGGCGGTTT 59.003 50.000 0.00 0.00 35.41 3.27
3264 4278 1.589716 AATCGCCCTTTGCTGAGCAC 61.590 55.000 6.64 0.00 38.71 4.40
3265 4279 3.741476 CGCCCTTTGCTGAGCACC 61.741 66.667 6.64 0.00 38.71 5.01
3267 4281 3.741476 CCCTTTGCTGAGCACCGC 61.741 66.667 6.64 0.00 38.71 5.68
3269 4283 2.253452 CTTTGCTGAGCACCGCAC 59.747 61.111 6.64 0.00 38.71 5.34
3270 4284 3.259425 CTTTGCTGAGCACCGCACC 62.259 63.158 6.64 0.00 38.71 5.01
3288 4302 4.506255 CCCGGGGCAGCCCTTTAG 62.506 72.222 30.52 17.88 44.66 1.85
3289 4303 4.506255 CCGGGGCAGCCCTTTAGG 62.506 72.222 30.52 22.45 44.66 2.69
3333 4354 9.646427 CTCCTAATATATGCTTCTTTCCTGTAC 57.354 37.037 0.00 0.00 0.00 2.90
3335 4356 9.646427 CCTAATATATGCTTCTTTCCTGTACTC 57.354 37.037 0.00 0.00 0.00 2.59
3343 4364 2.231478 TCTTTCCTGTACTCAAGCTCCG 59.769 50.000 0.00 0.00 0.00 4.63
3365 4390 3.438434 GCCAGAAACTGAACCTGAATCTC 59.562 47.826 0.00 0.00 32.44 2.75
3370 4395 7.303998 CAGAAACTGAACCTGAATCTCATTTC 58.696 38.462 0.00 0.00 32.44 2.17
3373 4398 5.251764 ACTGAACCTGAATCTCATTTCCTG 58.748 41.667 0.00 0.00 0.00 3.86
3374 4399 5.013495 ACTGAACCTGAATCTCATTTCCTGA 59.987 40.000 0.00 0.00 0.00 3.86
3375 4400 5.879763 TGAACCTGAATCTCATTTCCTGAA 58.120 37.500 0.00 0.00 32.14 3.02
3376 4401 6.306199 TGAACCTGAATCTCATTTCCTGAAA 58.694 36.000 0.00 0.00 32.14 2.69
3377 4402 6.950041 TGAACCTGAATCTCATTTCCTGAAAT 59.050 34.615 0.00 0.00 41.33 2.17
3378 4403 7.452501 TGAACCTGAATCTCATTTCCTGAAATT 59.547 33.333 2.42 0.00 38.84 1.82
3395 4420 5.957798 TGAAATTCATTCAGAAGTGCATCC 58.042 37.500 0.00 0.00 43.08 3.51
3398 4423 2.349590 TCATTCAGAAGTGCATCCGTG 58.650 47.619 0.00 0.00 0.00 4.94
3401 4426 3.610040 TTCAGAAGTGCATCCGTGTAT 57.390 42.857 0.00 0.00 0.00 2.29
3403 4428 2.233676 TCAGAAGTGCATCCGTGTATGT 59.766 45.455 0.00 0.00 0.00 2.29
3404 4429 3.445805 TCAGAAGTGCATCCGTGTATGTA 59.554 43.478 0.00 0.00 0.00 2.29
3406 4431 2.596904 AGTGCATCCGTGTATGTACC 57.403 50.000 0.00 0.00 41.70 3.34
3407 4432 1.138266 AGTGCATCCGTGTATGTACCC 59.862 52.381 0.00 0.00 41.70 3.69
3452 4533 5.831702 ATGGAGAGCAATCATTTTGACTC 57.168 39.130 0.00 0.00 0.00 3.36
3453 4534 3.686241 TGGAGAGCAATCATTTTGACTCG 59.314 43.478 0.00 0.00 32.12 4.18
3454 4535 3.935203 GGAGAGCAATCATTTTGACTCGA 59.065 43.478 0.00 0.00 32.12 4.04
3455 4536 4.393062 GGAGAGCAATCATTTTGACTCGAA 59.607 41.667 0.00 0.00 32.12 3.71
3456 4537 5.106555 GGAGAGCAATCATTTTGACTCGAAA 60.107 40.000 0.00 0.00 32.12 3.46
3457 4538 5.936054 AGAGCAATCATTTTGACTCGAAAG 58.064 37.500 0.00 0.00 32.12 2.62
3460 4541 6.320171 AGCAATCATTTTGACTCGAAAGATG 58.680 36.000 0.00 0.00 40.84 2.90
3461 4542 6.149973 AGCAATCATTTTGACTCGAAAGATGA 59.850 34.615 4.57 4.57 40.84 2.92
3465 4546 7.496529 TCATTTTGACTCGAAAGATGAGTTT 57.503 32.000 0.00 0.00 46.29 2.66
3466 4547 7.355017 TCATTTTGACTCGAAAGATGAGTTTG 58.645 34.615 0.00 0.00 46.29 2.93
3467 4548 6.918892 TTTTGACTCGAAAGATGAGTTTGA 57.081 33.333 0.00 0.00 46.29 2.69
3468 4549 7.496529 TTTTGACTCGAAAGATGAGTTTGAT 57.503 32.000 0.00 0.00 46.29 2.57
3471 4552 8.601845 TTGACTCGAAAGATGAGTTTGATTTA 57.398 30.769 0.00 0.00 46.29 1.40
3473 4554 8.495949 TGACTCGAAAGATGAGTTTGATTTAAC 58.504 33.333 0.00 0.00 46.29 2.01
3474 4555 7.807680 ACTCGAAAGATGAGTTTGATTTAACC 58.192 34.615 0.00 0.00 44.00 2.85
3475 4556 6.827641 TCGAAAGATGAGTTTGATTTAACCG 58.172 36.000 0.00 0.00 33.31 4.44
3476 4557 5.508224 CGAAAGATGAGTTTGATTTAACCGC 59.492 40.000 0.00 0.00 0.00 5.68
3478 4559 5.957842 AGATGAGTTTGATTTAACCGCAA 57.042 34.783 0.00 0.00 0.00 4.85
3479 4560 5.699839 AGATGAGTTTGATTTAACCGCAAC 58.300 37.500 0.00 0.00 0.00 4.17
3480 4561 4.902443 TGAGTTTGATTTAACCGCAACA 57.098 36.364 0.00 0.00 0.00 3.33
3481 4562 4.854399 TGAGTTTGATTTAACCGCAACAG 58.146 39.130 0.00 0.00 0.00 3.16
3484 4565 5.278604 AGTTTGATTTAACCGCAACAGAAC 58.721 37.500 0.00 0.00 0.00 3.01
3485 4566 5.067283 AGTTTGATTTAACCGCAACAGAACT 59.933 36.000 0.00 0.00 0.00 3.01
3486 4567 6.261381 AGTTTGATTTAACCGCAACAGAACTA 59.739 34.615 0.00 0.00 0.00 2.24
3487 4568 5.600908 TGATTTAACCGCAACAGAACTAC 57.399 39.130 0.00 0.00 0.00 2.73
3488 4569 5.057819 TGATTTAACCGCAACAGAACTACA 58.942 37.500 0.00 0.00 0.00 2.74
3489 4570 5.178623 TGATTTAACCGCAACAGAACTACAG 59.821 40.000 0.00 0.00 0.00 2.74
3492 4573 2.755650 ACCGCAACAGAACTACAGAAG 58.244 47.619 0.00 0.00 0.00 2.85
3493 4574 2.102588 ACCGCAACAGAACTACAGAAGT 59.897 45.455 0.00 0.00 41.49 3.01
3494 4575 3.319972 ACCGCAACAGAACTACAGAAGTA 59.680 43.478 0.00 0.00 37.50 2.24
3495 4576 4.021368 ACCGCAACAGAACTACAGAAGTAT 60.021 41.667 0.00 0.00 37.50 2.12
3496 4577 4.327357 CCGCAACAGAACTACAGAAGTATG 59.673 45.833 0.00 0.00 37.50 2.39
3497 4578 4.923871 CGCAACAGAACTACAGAAGTATGT 59.076 41.667 0.00 0.00 38.99 2.29
3517 4603 2.743928 CCAGTTCCACCGCAGCTC 60.744 66.667 0.00 0.00 0.00 4.09
3518 4604 2.345244 CAGTTCCACCGCAGCTCT 59.655 61.111 0.00 0.00 0.00 4.09
3519 4605 2.031516 CAGTTCCACCGCAGCTCTG 61.032 63.158 0.00 0.00 0.00 3.35
3520 4606 2.210013 AGTTCCACCGCAGCTCTGA 61.210 57.895 0.29 0.00 0.00 3.27
3521 4607 1.301716 GTTCCACCGCAGCTCTGAA 60.302 57.895 0.29 0.00 0.00 3.02
3532 4619 2.419324 GCAGCTCTGAATCTGAACTTGG 59.581 50.000 9.84 0.00 32.26 3.61
3568 4655 8.363390 ACGAGAAGCAGAATATAATTGAGATGA 58.637 33.333 0.00 0.00 0.00 2.92
3569 4656 8.862074 CGAGAAGCAGAATATAATTGAGATGAG 58.138 37.037 0.00 0.00 0.00 2.90
3570 4657 9.926158 GAGAAGCAGAATATAATTGAGATGAGA 57.074 33.333 0.00 0.00 0.00 3.27
3571 4658 9.932207 AGAAGCAGAATATAATTGAGATGAGAG 57.068 33.333 0.00 0.00 0.00 3.20
3573 4660 7.677892 AGCAGAATATAATTGAGATGAGAGCA 58.322 34.615 0.00 0.00 0.00 4.26
3574 4661 8.322828 AGCAGAATATAATTGAGATGAGAGCAT 58.677 33.333 0.00 0.00 37.47 3.79
3585 4672 4.717233 GATGAGAGCATCGGTCAGATAT 57.283 45.455 0.00 0.00 41.31 1.63
3586 4673 5.826601 GATGAGAGCATCGGTCAGATATA 57.173 43.478 0.00 0.00 41.31 0.86
3587 4674 6.201226 GATGAGAGCATCGGTCAGATATAA 57.799 41.667 0.00 0.00 41.31 0.98
3588 4675 6.596309 ATGAGAGCATCGGTCAGATATAAA 57.404 37.500 0.00 0.00 42.67 1.40
3589 4676 6.405278 TGAGAGCATCGGTCAGATATAAAA 57.595 37.500 0.00 0.00 42.67 1.52
3590 4677 6.216569 TGAGAGCATCGGTCAGATATAAAAC 58.783 40.000 0.00 0.00 42.67 2.43
3591 4678 5.542779 AGAGCATCGGTCAGATATAAAACC 58.457 41.667 0.00 0.00 42.67 3.27
3592 4679 4.642429 AGCATCGGTCAGATATAAAACCC 58.358 43.478 0.00 0.00 37.52 4.11
3593 4680 4.102524 AGCATCGGTCAGATATAAAACCCA 59.897 41.667 0.00 0.00 37.52 4.51
3594 4681 4.452455 GCATCGGTCAGATATAAAACCCAG 59.548 45.833 0.00 0.00 37.52 4.45
3595 4682 5.741964 GCATCGGTCAGATATAAAACCCAGA 60.742 44.000 0.00 0.00 37.52 3.86
3596 4683 6.467677 CATCGGTCAGATATAAAACCCAGAT 58.532 40.000 0.00 0.00 37.52 2.90
3597 4684 6.494666 TCGGTCAGATATAAAACCCAGATT 57.505 37.500 0.00 0.00 0.00 2.40
3598 4685 6.895782 TCGGTCAGATATAAAACCCAGATTT 58.104 36.000 0.00 0.00 0.00 2.17
3599 4686 6.990349 TCGGTCAGATATAAAACCCAGATTTC 59.010 38.462 0.00 0.00 0.00 2.17
3600 4687 6.073765 CGGTCAGATATAAAACCCAGATTTCG 60.074 42.308 0.00 0.00 0.00 3.46
3601 4688 6.766467 GGTCAGATATAAAACCCAGATTTCGT 59.234 38.462 0.00 0.00 0.00 3.85
3602 4689 7.282450 GGTCAGATATAAAACCCAGATTTCGTT 59.718 37.037 0.00 0.00 0.00 3.85
3603 4690 8.122952 GTCAGATATAAAACCCAGATTTCGTTG 58.877 37.037 0.00 0.00 0.00 4.10
3604 4691 6.912591 CAGATATAAAACCCAGATTTCGTTGC 59.087 38.462 0.00 0.00 0.00 4.17
3605 4692 2.415697 AAAACCCAGATTTCGTTGCG 57.584 45.000 0.00 0.00 0.00 4.85
3606 4693 1.600023 AAACCCAGATTTCGTTGCGA 58.400 45.000 0.00 0.00 0.00 5.10
3607 4694 1.600023 AACCCAGATTTCGTTGCGAA 58.400 45.000 0.00 0.00 44.28 4.70
3656 4756 4.560035 GCAATGTGGATCTGAATGTTTTCG 59.440 41.667 0.00 0.00 34.39 3.46
3701 4801 1.484240 AGCAGGCCACTCTATCTTGAC 59.516 52.381 5.01 0.00 0.00 3.18
3713 4834 5.664908 ACTCTATCTTGACCCAACTCATGAT 59.335 40.000 0.00 0.00 38.19 2.45
3714 4835 5.922053 TCTATCTTGACCCAACTCATGATG 58.078 41.667 0.00 0.00 36.33 3.07
3715 4836 2.715046 TCTTGACCCAACTCATGATGC 58.285 47.619 0.00 0.00 0.00 3.91
3716 4837 2.040145 TCTTGACCCAACTCATGATGCA 59.960 45.455 0.00 0.00 0.00 3.96
3717 4838 2.812836 TGACCCAACTCATGATGCAT 57.187 45.000 0.00 0.00 0.00 3.96
3718 4839 3.090210 TGACCCAACTCATGATGCATT 57.910 42.857 0.00 0.00 0.00 3.56
3719 4840 2.756207 TGACCCAACTCATGATGCATTG 59.244 45.455 0.00 0.00 0.00 2.82
3720 4841 2.100252 GACCCAACTCATGATGCATTGG 59.900 50.000 16.23 16.23 39.67 3.16
3721 4842 1.202486 CCCAACTCATGATGCATTGGC 60.202 52.381 17.23 0.00 38.81 4.52
3756 4879 5.213045 GCATACAGCAGTGACCTTCTTAGG 61.213 50.000 0.00 0.00 44.93 2.69
3773 4896 7.279536 CCTTCTTAGGGAGAACGGTAATTTAAC 59.720 40.741 0.00 0.00 39.44 2.01
3788 4911 3.309600 TTTAACCCAACCGAAAAGGGA 57.690 42.857 3.32 0.00 45.80 4.20
3793 4932 1.073284 CCCAACCGAAAAGGGAAGAGA 59.927 52.381 0.00 0.00 45.80 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 210 9.581289 TTGTTTGGGATTCTTAGACATTTTCTA 57.419 29.630 0.00 0.00 35.55 2.10
329 331 8.610896 CCATAAGCTTTTGAAATTTGTGAACAA 58.389 29.630 17.31 0.00 0.00 2.83
330 332 7.768120 ACCATAAGCTTTTGAAATTTGTGAACA 59.232 29.630 17.31 0.00 0.00 3.18
331 333 8.141835 ACCATAAGCTTTTGAAATTTGTGAAC 57.858 30.769 17.31 0.00 0.00 3.18
333 335 7.984050 TGAACCATAAGCTTTTGAAATTTGTGA 59.016 29.630 17.31 0.00 0.00 3.58
334 336 8.140677 TGAACCATAAGCTTTTGAAATTTGTG 57.859 30.769 17.31 2.00 0.00 3.33
335 337 8.907222 ATGAACCATAAGCTTTTGAAATTTGT 57.093 26.923 17.31 3.87 0.00 2.83
354 378 1.542547 CCAGCCCGGTGTATATGAACC 60.543 57.143 0.00 0.00 0.00 3.62
374 398 9.586435 CTTCCTGGGAATTTGTGTATAAAATTC 57.414 33.333 11.40 11.40 46.34 2.17
400 424 2.288273 CCAGGTCGCTAGCCACTATAAC 60.288 54.545 12.38 0.00 0.00 1.89
498 523 9.817365 CATTAGAAGAAACAAACTACAGTGATG 57.183 33.333 0.00 0.00 0.00 3.07
502 527 8.129211 GCAACATTAGAAGAAACAAACTACAGT 58.871 33.333 0.00 0.00 0.00 3.55
507 532 4.976116 GCGCAACATTAGAAGAAACAAACT 59.024 37.500 0.30 0.00 0.00 2.66
522 551 3.129113 TGATAAAATGAGCAGCGCAACAT 59.871 39.130 11.47 6.49 31.88 2.71
545 574 0.321122 CAAAGGCCGACAAGCTCTCT 60.321 55.000 0.00 0.00 0.00 3.10
546 575 0.603975 ACAAAGGCCGACAAGCTCTC 60.604 55.000 0.00 0.00 0.00 3.20
605 1092 2.307392 TCCCGGTGATGGATCTCAAAAA 59.693 45.455 0.00 0.00 0.00 1.94
606 1093 1.912731 TCCCGGTGATGGATCTCAAAA 59.087 47.619 0.00 0.00 0.00 2.44
607 1094 1.578897 TCCCGGTGATGGATCTCAAA 58.421 50.000 0.00 0.00 0.00 2.69
608 1095 1.486310 CTTCCCGGTGATGGATCTCAA 59.514 52.381 0.00 0.00 0.00 3.02
609 1096 1.123077 CTTCCCGGTGATGGATCTCA 58.877 55.000 0.00 0.00 0.00 3.27
610 1097 0.250081 GCTTCCCGGTGATGGATCTC 60.250 60.000 0.00 0.00 0.00 2.75
611 1098 0.692419 AGCTTCCCGGTGATGGATCT 60.692 55.000 0.00 0.00 0.00 2.75
612 1099 0.533755 CAGCTTCCCGGTGATGGATC 60.534 60.000 0.00 0.00 43.75 3.36
613 1100 1.274703 ACAGCTTCCCGGTGATGGAT 61.275 55.000 0.00 0.00 43.75 3.41
614 1101 1.918293 ACAGCTTCCCGGTGATGGA 60.918 57.895 0.00 0.00 43.75 3.41
615 1102 1.746615 CACAGCTTCCCGGTGATGG 60.747 63.158 0.00 0.00 43.75 3.51
616 1103 1.746615 CCACAGCTTCCCGGTGATG 60.747 63.158 0.00 1.53 43.75 3.07
617 1104 2.671070 CCACAGCTTCCCGGTGAT 59.329 61.111 0.00 0.00 43.75 3.06
618 1105 3.636231 CCCACAGCTTCCCGGTGA 61.636 66.667 0.00 0.00 43.75 4.02
619 1106 3.491598 AACCCACAGCTTCCCGGTG 62.492 63.158 0.00 0.00 46.37 4.94
620 1107 3.175710 AACCCACAGCTTCCCGGT 61.176 61.111 0.00 0.00 0.00 5.28
621 1108 2.359975 GAACCCACAGCTTCCCGG 60.360 66.667 0.00 0.00 0.00 5.73
622 1109 2.742372 CGAACCCACAGCTTCCCG 60.742 66.667 0.00 0.00 0.00 5.14
623 1110 3.056328 GCGAACCCACAGCTTCCC 61.056 66.667 0.00 0.00 0.00 3.97
624 1111 1.244019 AATGCGAACCCACAGCTTCC 61.244 55.000 0.00 0.00 0.00 3.46
625 1112 0.598065 AAATGCGAACCCACAGCTTC 59.402 50.000 0.00 0.00 0.00 3.86
626 1113 1.039856 AAAATGCGAACCCACAGCTT 58.960 45.000 0.00 0.00 0.00 3.74
627 1114 0.314935 CAAAATGCGAACCCACAGCT 59.685 50.000 0.00 0.00 0.00 4.24
628 1115 0.667184 CCAAAATGCGAACCCACAGC 60.667 55.000 0.00 0.00 0.00 4.40
629 1116 0.038343 CCCAAAATGCGAACCCACAG 60.038 55.000 0.00 0.00 0.00 3.66
630 1117 2.045280 CCCAAAATGCGAACCCACA 58.955 52.632 0.00 0.00 0.00 4.17
631 1118 1.374125 GCCCAAAATGCGAACCCAC 60.374 57.895 0.00 0.00 0.00 4.61
632 1119 2.578714 GGCCCAAAATGCGAACCCA 61.579 57.895 0.00 0.00 0.00 4.51
633 1120 2.264480 GGCCCAAAATGCGAACCC 59.736 61.111 0.00 0.00 0.00 4.11
634 1121 2.126110 CGGCCCAAAATGCGAACC 60.126 61.111 0.00 0.00 0.00 3.62
635 1122 2.126110 CCGGCCCAAAATGCGAAC 60.126 61.111 0.00 0.00 0.00 3.95
636 1123 2.598985 ACCGGCCCAAAATGCGAA 60.599 55.556 0.00 0.00 0.00 4.70
637 1124 3.059386 GACCGGCCCAAAATGCGA 61.059 61.111 0.00 0.00 0.00 5.10
638 1125 3.051392 GAGACCGGCCCAAAATGCG 62.051 63.158 0.00 0.00 0.00 4.73
639 1126 1.250840 AAGAGACCGGCCCAAAATGC 61.251 55.000 0.00 0.00 0.00 3.56
640 1127 2.122783 TAAGAGACCGGCCCAAAATG 57.877 50.000 0.00 0.00 0.00 2.32
641 1128 4.513406 TTATAAGAGACCGGCCCAAAAT 57.487 40.909 0.00 0.00 0.00 1.82
642 1129 4.204012 CATTATAAGAGACCGGCCCAAAA 58.796 43.478 0.00 0.00 0.00 2.44
643 1130 3.434453 CCATTATAAGAGACCGGCCCAAA 60.434 47.826 0.00 0.00 0.00 3.28
644 1131 2.105821 CCATTATAAGAGACCGGCCCAA 59.894 50.000 0.00 0.00 0.00 4.12
645 1132 1.697432 CCATTATAAGAGACCGGCCCA 59.303 52.381 0.00 0.00 0.00 5.36
646 1133 1.975680 TCCATTATAAGAGACCGGCCC 59.024 52.381 0.00 0.00 0.00 5.80
647 1134 3.557264 CCTTCCATTATAAGAGACCGGCC 60.557 52.174 0.00 0.00 0.00 6.13
648 1135 3.665190 CCTTCCATTATAAGAGACCGGC 58.335 50.000 0.00 0.00 0.00 6.13
649 1136 3.557264 GGCCTTCCATTATAAGAGACCGG 60.557 52.174 0.00 0.00 0.00 5.28
650 1137 3.557264 GGGCCTTCCATTATAAGAGACCG 60.557 52.174 0.84 0.00 35.00 4.79
651 1138 3.394606 TGGGCCTTCCATTATAAGAGACC 59.605 47.826 4.53 0.00 41.46 3.85
652 1139 4.706842 TGGGCCTTCCATTATAAGAGAC 57.293 45.455 4.53 0.00 41.46 3.36
688 1175 0.537828 TGCCCACGGTTTTAGGGTTC 60.538 55.000 3.50 0.00 44.69 3.62
725 1212 3.600898 AACGGCTAGCCACGGAACC 62.601 63.158 32.47 3.87 35.37 3.62
881 1372 3.118482 ACAGGCAATCAACAGATCGAGAT 60.118 43.478 0.00 0.00 0.00 2.75
884 1375 2.768253 ACAGGCAATCAACAGATCGA 57.232 45.000 0.00 0.00 0.00 3.59
900 1391 2.057316 GCAGATCGATCGGATGAACAG 58.943 52.381 26.72 8.18 34.82 3.16
978 1483 8.217799 TCCATGGTTAGAAGAAAGAAAGAAAGA 58.782 33.333 12.58 0.00 0.00 2.52
979 1484 8.293157 GTCCATGGTTAGAAGAAAGAAAGAAAG 58.707 37.037 12.58 0.00 0.00 2.62
983 1488 5.390991 GCGTCCATGGTTAGAAGAAAGAAAG 60.391 44.000 12.58 0.00 0.00 2.62
984 1489 4.454504 GCGTCCATGGTTAGAAGAAAGAAA 59.545 41.667 12.58 0.00 0.00 2.52
1188 1696 1.945394 GCATTCCATCGAACAGCTCAT 59.055 47.619 0.00 0.00 32.40 2.90
1235 1743 1.006922 TGCGCACACACAGAGAGAG 60.007 57.895 5.66 0.00 0.00 3.20
1392 1903 1.669115 GTTGAGCAGCTTCTCCGCA 60.669 57.895 11.01 0.00 32.22 5.69
1581 2113 7.920227 AGTAACCACCACCAAATATTACTACA 58.080 34.615 0.00 0.00 31.39 2.74
1590 2127 5.652014 CACATATGAGTAACCACCACCAAAT 59.348 40.000 10.38 0.00 0.00 2.32
1591 2128 5.007034 CACATATGAGTAACCACCACCAAA 58.993 41.667 10.38 0.00 0.00 3.28
1592 2129 4.287326 TCACATATGAGTAACCACCACCAA 59.713 41.667 10.38 0.00 0.00 3.67
1607 2144 4.816786 TTGTCAATCGGCATCACATATG 57.183 40.909 0.00 0.00 0.00 1.78
1610 2147 3.735820 GCAATTGTCAATCGGCATCACAT 60.736 43.478 7.40 0.00 0.00 3.21
1611 2148 2.415759 GCAATTGTCAATCGGCATCACA 60.416 45.455 7.40 0.00 0.00 3.58
1618 2159 2.730090 GCAGACTGCAATTGTCAATCGG 60.730 50.000 22.62 7.11 44.26 4.18
1946 2514 0.674895 GCAGATCAAGCAGTTCGGGT 60.675 55.000 5.41 0.00 0.00 5.28
2014 2587 5.450592 TCAAGCACATTCAAGCACATAAA 57.549 34.783 0.00 0.00 0.00 1.40
2015 2588 5.183522 TGATCAAGCACATTCAAGCACATAA 59.816 36.000 0.00 0.00 0.00 1.90
2016 2589 4.701171 TGATCAAGCACATTCAAGCACATA 59.299 37.500 0.00 0.00 0.00 2.29
2017 2590 3.508402 TGATCAAGCACATTCAAGCACAT 59.492 39.130 0.00 0.00 0.00 3.21
2018 2591 2.885894 TGATCAAGCACATTCAAGCACA 59.114 40.909 0.00 0.00 0.00 4.57
2019 2592 3.189910 TCTGATCAAGCACATTCAAGCAC 59.810 43.478 0.00 0.00 0.00 4.40
2020 2593 3.414269 TCTGATCAAGCACATTCAAGCA 58.586 40.909 0.00 0.00 0.00 3.91
2021 2594 4.352039 CATCTGATCAAGCACATTCAAGC 58.648 43.478 0.00 0.00 0.00 4.01
2022 2595 4.096532 AGCATCTGATCAAGCACATTCAAG 59.903 41.667 14.53 0.00 0.00 3.02
2023 2596 4.014406 AGCATCTGATCAAGCACATTCAA 58.986 39.130 14.53 0.00 0.00 2.69
2024 2597 3.377172 CAGCATCTGATCAAGCACATTCA 59.623 43.478 14.53 0.00 32.44 2.57
2025 2598 3.626217 TCAGCATCTGATCAAGCACATTC 59.374 43.478 14.53 0.00 35.39 2.67
2026 2599 3.617284 TCAGCATCTGATCAAGCACATT 58.383 40.909 14.53 0.00 35.39 2.71
2027 2600 3.277142 TCAGCATCTGATCAAGCACAT 57.723 42.857 14.53 0.00 35.39 3.21
2028 2601 2.773993 TCAGCATCTGATCAAGCACA 57.226 45.000 14.53 0.95 35.39 4.57
2029 2602 4.634184 AATTCAGCATCTGATCAAGCAC 57.366 40.909 14.53 0.00 40.39 4.40
2030 2603 5.187687 TGTAATTCAGCATCTGATCAAGCA 58.812 37.500 14.53 0.00 40.39 3.91
2031 2604 5.746307 TGTAATTCAGCATCTGATCAAGC 57.254 39.130 0.00 1.40 40.39 4.01
2051 2624 8.918202 TGGACAGTGTATAAAAAGAAGAATGT 57.082 30.769 0.00 0.00 0.00 2.71
2052 2625 7.965107 GCTGGACAGTGTATAAAAAGAAGAATG 59.035 37.037 0.00 0.00 0.00 2.67
2053 2626 7.665559 TGCTGGACAGTGTATAAAAAGAAGAAT 59.334 33.333 0.00 0.00 0.00 2.40
2054 2627 6.995686 TGCTGGACAGTGTATAAAAAGAAGAA 59.004 34.615 0.00 0.00 0.00 2.52
2055 2628 6.530120 TGCTGGACAGTGTATAAAAAGAAGA 58.470 36.000 0.00 0.00 0.00 2.87
2056 2629 6.801539 TGCTGGACAGTGTATAAAAAGAAG 57.198 37.500 0.00 0.00 0.00 2.85
2057 2630 6.939730 TGATGCTGGACAGTGTATAAAAAGAA 59.060 34.615 0.00 0.00 0.00 2.52
2058 2631 6.472016 TGATGCTGGACAGTGTATAAAAAGA 58.528 36.000 0.00 0.00 0.00 2.52
2059 2632 6.741992 TGATGCTGGACAGTGTATAAAAAG 57.258 37.500 0.00 0.00 0.00 2.27
2060 2633 7.517614 TTTGATGCTGGACAGTGTATAAAAA 57.482 32.000 0.00 0.00 0.00 1.94
2061 2634 7.517614 TTTTGATGCTGGACAGTGTATAAAA 57.482 32.000 0.00 0.00 0.00 1.52
2062 2635 7.517614 TTTTTGATGCTGGACAGTGTATAAA 57.482 32.000 0.00 0.00 0.00 1.40
2083 2656 9.723601 ACATTCAGGCACATAAATAACATTTTT 57.276 25.926 0.00 0.00 0.00 1.94
2084 2657 9.153721 CACATTCAGGCACATAAATAACATTTT 57.846 29.630 0.00 0.00 0.00 1.82
2085 2658 7.278424 GCACATTCAGGCACATAAATAACATTT 59.722 33.333 0.00 0.00 0.00 2.32
2086 2659 6.757947 GCACATTCAGGCACATAAATAACATT 59.242 34.615 0.00 0.00 0.00 2.71
2087 2660 6.097270 AGCACATTCAGGCACATAAATAACAT 59.903 34.615 0.00 0.00 0.00 2.71
2088 2661 5.418524 AGCACATTCAGGCACATAAATAACA 59.581 36.000 0.00 0.00 0.00 2.41
2089 2662 5.894807 AGCACATTCAGGCACATAAATAAC 58.105 37.500 0.00 0.00 0.00 1.89
2090 2663 6.152492 TCAAGCACATTCAGGCACATAAATAA 59.848 34.615 0.00 0.00 0.00 1.40
2091 2664 5.651576 TCAAGCACATTCAGGCACATAAATA 59.348 36.000 0.00 0.00 0.00 1.40
2092 2665 4.463539 TCAAGCACATTCAGGCACATAAAT 59.536 37.500 0.00 0.00 0.00 1.40
2771 3726 5.121768 ACAAACAGGTTAACATGTCGATAGC 59.878 40.000 24.59 0.00 40.26 2.97
2804 3759 3.312697 CACAGCATGACAAGATGATCAGG 59.687 47.826 2.51 0.00 39.69 3.86
2981 3940 0.447801 ATTGCTCGCATTGTTCGTCC 59.552 50.000 0.00 0.00 0.00 4.79
2996 3955 2.161211 GCTGTCCAGTTCAAGAGATTGC 59.839 50.000 0.00 0.00 0.00 3.56
3019 3979 6.560253 AGCCTATTTTCTGTACACAAACAG 57.440 37.500 0.00 0.00 46.78 3.16
3217 4195 1.834188 ACATGAAACCGCCCCTAAAG 58.166 50.000 0.00 0.00 0.00 1.85
3218 4196 2.164338 GAACATGAAACCGCCCCTAAA 58.836 47.619 0.00 0.00 0.00 1.85
3219 4197 1.353022 AGAACATGAAACCGCCCCTAA 59.647 47.619 0.00 0.00 0.00 2.69
3221 4199 0.112412 AAGAACATGAAACCGCCCCT 59.888 50.000 0.00 0.00 0.00 4.79
3222 4200 0.526211 GAAGAACATGAAACCGCCCC 59.474 55.000 0.00 0.00 0.00 5.80
3281 4295 0.179006 GCTCCATCAGGCCTAAAGGG 60.179 60.000 3.98 8.50 35.18 3.95
3282 4296 0.548031 TGCTCCATCAGGCCTAAAGG 59.452 55.000 3.98 7.67 38.53 3.11
3283 4297 2.502295 GATGCTCCATCAGGCCTAAAG 58.498 52.381 3.98 0.00 40.28 1.85
3284 4298 1.143684 GGATGCTCCATCAGGCCTAAA 59.856 52.381 3.98 0.00 42.13 1.85
3285 4299 0.767375 GGATGCTCCATCAGGCCTAA 59.233 55.000 3.98 0.00 42.13 2.69
3286 4300 0.400381 TGGATGCTCCATCAGGCCTA 60.400 55.000 3.98 0.00 42.67 3.93
3287 4301 1.695239 TGGATGCTCCATCAGGCCT 60.695 57.895 0.00 0.00 42.67 5.19
3288 4302 2.921435 TGGATGCTCCATCAGGCC 59.079 61.111 0.00 0.00 42.67 5.19
3304 4318 8.997323 CAGGAAAGAAGCATATATTAGGAGTTG 58.003 37.037 0.00 0.00 0.00 3.16
3343 4364 3.416156 AGATTCAGGTTCAGTTTCTGGC 58.584 45.455 0.00 0.00 31.51 4.85
3373 4398 5.032863 CGGATGCACTTCTGAATGAATTTC 58.967 41.667 0.00 0.00 33.71 2.17
3374 4399 4.460382 ACGGATGCACTTCTGAATGAATTT 59.540 37.500 3.12 0.00 33.71 1.82
3375 4400 4.012374 ACGGATGCACTTCTGAATGAATT 58.988 39.130 3.12 0.00 33.71 2.17
3376 4401 3.376234 CACGGATGCACTTCTGAATGAAT 59.624 43.478 3.12 0.00 33.71 2.57
3377 4402 2.743664 CACGGATGCACTTCTGAATGAA 59.256 45.455 3.12 0.00 0.00 2.57
3378 4403 2.289631 ACACGGATGCACTTCTGAATGA 60.290 45.455 3.12 0.00 0.00 2.57
3390 4415 1.138266 ACTGGGTACATACACGGATGC 59.862 52.381 7.13 0.00 38.24 3.91
3395 4420 4.250464 ACATCAAACTGGGTACATACACG 58.750 43.478 0.00 0.00 30.45 4.49
3401 4426 9.303116 ACATATTTTTACATCAAACTGGGTACA 57.697 29.630 0.00 0.00 0.00 2.90
3432 4513 3.935203 TCGAGTCAAAATGATTGCTCTCC 59.065 43.478 0.00 0.00 0.00 3.71
3437 4518 6.317088 TCATCTTTCGAGTCAAAATGATTGC 58.683 36.000 0.00 0.00 0.00 3.56
3440 4521 7.678947 AACTCATCTTTCGAGTCAAAATGAT 57.321 32.000 0.00 0.00 42.90 2.45
3452 4533 5.508224 GCGGTTAAATCAAACTCATCTTTCG 59.492 40.000 0.00 0.00 0.00 3.46
3453 4534 6.378582 TGCGGTTAAATCAAACTCATCTTTC 58.621 36.000 0.00 0.00 0.00 2.62
3454 4535 6.325919 TGCGGTTAAATCAAACTCATCTTT 57.674 33.333 0.00 0.00 0.00 2.52
3455 4536 5.957842 TGCGGTTAAATCAAACTCATCTT 57.042 34.783 0.00 0.00 0.00 2.40
3456 4537 5.240623 TGTTGCGGTTAAATCAAACTCATCT 59.759 36.000 0.00 0.00 0.00 2.90
3457 4538 5.457140 TGTTGCGGTTAAATCAAACTCATC 58.543 37.500 0.00 0.00 0.00 2.92
3460 4541 5.103290 TCTGTTGCGGTTAAATCAAACTC 57.897 39.130 0.00 0.00 0.00 3.01
3461 4542 5.067283 AGTTCTGTTGCGGTTAAATCAAACT 59.933 36.000 0.00 0.00 0.00 2.66
3465 4546 5.057819 TGTAGTTCTGTTGCGGTTAAATCA 58.942 37.500 0.00 0.00 0.00 2.57
3466 4547 5.407387 TCTGTAGTTCTGTTGCGGTTAAATC 59.593 40.000 0.00 0.00 0.00 2.17
3467 4548 5.302360 TCTGTAGTTCTGTTGCGGTTAAAT 58.698 37.500 0.00 0.00 0.00 1.40
3468 4549 4.695396 TCTGTAGTTCTGTTGCGGTTAAA 58.305 39.130 0.00 0.00 0.00 1.52
3471 4552 2.902705 TCTGTAGTTCTGTTGCGGTT 57.097 45.000 0.00 0.00 0.00 4.44
3473 4554 2.755650 ACTTCTGTAGTTCTGTTGCGG 58.244 47.619 0.00 0.00 31.29 5.69
3474 4555 4.923871 ACATACTTCTGTAGTTCTGTTGCG 59.076 41.667 0.00 0.00 38.33 4.85
3475 4556 6.310711 GGTACATACTTCTGTAGTTCTGTTGC 59.689 42.308 0.00 0.00 38.33 4.17
3476 4557 6.812160 GGGTACATACTTCTGTAGTTCTGTTG 59.188 42.308 0.00 0.00 38.33 3.33
3478 4559 6.014647 TGGGTACATACTTCTGTAGTTCTGT 58.985 40.000 0.00 0.84 38.33 3.41
3479 4560 6.153000 ACTGGGTACATACTTCTGTAGTTCTG 59.847 42.308 0.00 0.00 38.33 3.02
3480 4561 6.254522 ACTGGGTACATACTTCTGTAGTTCT 58.745 40.000 0.00 0.00 38.33 3.01
3481 4562 6.527057 ACTGGGTACATACTTCTGTAGTTC 57.473 41.667 0.00 0.00 38.33 3.01
3484 4565 5.421056 TGGAACTGGGTACATACTTCTGTAG 59.579 44.000 0.00 0.00 32.45 2.74
3485 4566 5.186409 GTGGAACTGGGTACATACTTCTGTA 59.814 44.000 0.00 0.00 0.00 2.74
3486 4567 4.020485 GTGGAACTGGGTACATACTTCTGT 60.020 45.833 0.00 0.00 0.00 3.41
3487 4568 4.504858 GTGGAACTGGGTACATACTTCTG 58.495 47.826 0.00 0.00 0.00 3.02
3488 4569 3.518303 GGTGGAACTGGGTACATACTTCT 59.482 47.826 0.00 0.00 36.74 2.85
3489 4570 3.677976 CGGTGGAACTGGGTACATACTTC 60.678 52.174 0.00 0.00 40.35 3.01
3492 4573 1.741394 GCGGTGGAACTGGGTACATAC 60.741 57.143 0.00 0.00 45.56 2.39
3493 4574 0.538118 GCGGTGGAACTGGGTACATA 59.462 55.000 0.00 0.00 45.56 2.29
3494 4575 1.298667 GCGGTGGAACTGGGTACAT 59.701 57.895 0.00 0.00 45.56 2.29
3495 4576 2.107041 CTGCGGTGGAACTGGGTACA 62.107 60.000 0.00 0.00 45.56 2.90
3496 4577 1.375523 CTGCGGTGGAACTGGGTAC 60.376 63.158 0.00 0.00 45.56 3.34
3497 4578 3.065306 CTGCGGTGGAACTGGGTA 58.935 61.111 0.00 0.00 45.56 3.69
3532 4619 2.029828 TCTGCTTCTCGTCTTCAGAACC 60.030 50.000 0.00 0.00 31.62 3.62
3568 4655 5.511545 GGGTTTTATATCTGACCGATGCTCT 60.512 44.000 0.00 0.00 33.48 4.09
3569 4656 4.691216 GGGTTTTATATCTGACCGATGCTC 59.309 45.833 0.00 0.00 33.48 4.26
3570 4657 4.102524 TGGGTTTTATATCTGACCGATGCT 59.897 41.667 0.00 0.00 33.48 3.79
3571 4658 4.385825 TGGGTTTTATATCTGACCGATGC 58.614 43.478 0.00 0.00 33.48 3.91
3573 4660 6.688073 ATCTGGGTTTTATATCTGACCGAT 57.312 37.500 0.00 0.00 36.11 4.18
3574 4661 6.494666 AATCTGGGTTTTATATCTGACCGA 57.505 37.500 0.00 0.00 32.91 4.69
3575 4662 6.073765 CGAAATCTGGGTTTTATATCTGACCG 60.074 42.308 0.00 0.00 32.91 4.79
3576 4663 6.766467 ACGAAATCTGGGTTTTATATCTGACC 59.234 38.462 0.00 0.00 0.00 4.02
3577 4664 7.787725 ACGAAATCTGGGTTTTATATCTGAC 57.212 36.000 0.00 0.00 0.00 3.51
3578 4665 7.201696 GCAACGAAATCTGGGTTTTATATCTGA 60.202 37.037 0.00 0.00 0.00 3.27
3579 4666 6.912591 GCAACGAAATCTGGGTTTTATATCTG 59.087 38.462 0.00 0.00 0.00 2.90
3580 4667 6.238374 CGCAACGAAATCTGGGTTTTATATCT 60.238 38.462 0.00 0.00 0.00 1.98
3581 4668 5.907391 CGCAACGAAATCTGGGTTTTATATC 59.093 40.000 0.00 0.00 0.00 1.63
3582 4669 5.587043 TCGCAACGAAATCTGGGTTTTATAT 59.413 36.000 0.00 0.00 31.06 0.86
3583 4670 4.936411 TCGCAACGAAATCTGGGTTTTATA 59.064 37.500 0.00 0.00 31.06 0.98
3584 4671 3.754323 TCGCAACGAAATCTGGGTTTTAT 59.246 39.130 0.00 0.00 31.06 1.40
3585 4672 3.139850 TCGCAACGAAATCTGGGTTTTA 58.860 40.909 0.00 0.00 31.06 1.52
3586 4673 1.950909 TCGCAACGAAATCTGGGTTTT 59.049 42.857 0.00 0.00 31.06 2.43
3587 4674 1.600023 TCGCAACGAAATCTGGGTTT 58.400 45.000 0.00 0.00 31.06 3.27
3588 4675 1.600023 TTCGCAACGAAATCTGGGTT 58.400 45.000 0.00 0.00 43.00 4.11
3589 4676 3.315765 TTCGCAACGAAATCTGGGT 57.684 47.368 0.00 0.00 43.00 4.51
3597 4684 2.159824 TCACAAACTGTTTCGCAACGAA 59.840 40.909 2.13 0.00 44.28 3.85
3598 4685 1.732809 TCACAAACTGTTTCGCAACGA 59.267 42.857 2.13 0.00 35.40 3.85
3599 4686 2.166741 TCACAAACTGTTTCGCAACG 57.833 45.000 2.13 0.00 35.40 4.10
3600 4687 3.177643 CGATTCACAAACTGTTTCGCAAC 59.822 43.478 2.13 0.00 0.00 4.17
3601 4688 3.064134 TCGATTCACAAACTGTTTCGCAA 59.936 39.130 2.13 0.00 29.90 4.85
3602 4689 2.609916 TCGATTCACAAACTGTTTCGCA 59.390 40.909 2.13 0.00 29.90 5.10
3603 4690 3.247563 TCGATTCACAAACTGTTTCGC 57.752 42.857 2.13 0.00 29.90 4.70
3604 4691 4.846137 GGATTCGATTCACAAACTGTTTCG 59.154 41.667 2.13 3.36 0.00 3.46
3605 4692 6.002062 AGGATTCGATTCACAAACTGTTTC 57.998 37.500 2.13 0.00 0.00 2.78
3606 4693 5.048713 GGAGGATTCGATTCACAAACTGTTT 60.049 40.000 9.36 0.00 0.00 2.83
3607 4694 4.455877 GGAGGATTCGATTCACAAACTGTT 59.544 41.667 9.36 0.00 0.00 3.16
3608 4695 4.003648 GGAGGATTCGATTCACAAACTGT 58.996 43.478 9.36 0.00 0.00 3.55
3609 4696 3.375299 GGGAGGATTCGATTCACAAACTG 59.625 47.826 9.36 0.00 0.00 3.16
3610 4697 3.610911 GGGAGGATTCGATTCACAAACT 58.389 45.455 9.36 0.00 0.00 2.66
3611 4698 2.683362 GGGGAGGATTCGATTCACAAAC 59.317 50.000 9.36 0.00 0.00 2.93
3612 4699 2.679639 CGGGGAGGATTCGATTCACAAA 60.680 50.000 9.36 0.00 0.00 2.83
3613 4700 1.134521 CGGGGAGGATTCGATTCACAA 60.135 52.381 9.36 0.00 0.00 3.33
3678 4778 0.979709 AGATAGAGTGGCCTGCTGCA 60.980 55.000 3.32 0.88 43.89 4.41
3679 4779 0.179936 AAGATAGAGTGGCCTGCTGC 59.820 55.000 3.32 0.00 40.16 5.25
3680 4780 1.483827 TCAAGATAGAGTGGCCTGCTG 59.516 52.381 3.32 0.00 0.00 4.41
3681 4781 1.484240 GTCAAGATAGAGTGGCCTGCT 59.516 52.381 3.32 1.36 0.00 4.24
3682 4782 1.474143 GGTCAAGATAGAGTGGCCTGC 60.474 57.143 3.32 0.00 36.54 4.85
3701 4801 1.202486 GCCAATGCATCATGAGTTGGG 60.202 52.381 22.71 12.52 39.68 4.12
3719 4840 0.248621 GTATGCTGTTCGGCAATGCC 60.249 55.000 15.52 15.52 45.68 4.40
3720 4841 0.451383 TGTATGCTGTTCGGCAATGC 59.549 50.000 10.37 0.00 45.68 3.56
3721 4842 1.532505 GCTGTATGCTGTTCGGCAATG 60.533 52.381 10.37 3.10 45.68 2.82
3722 4843 0.734889 GCTGTATGCTGTTCGGCAAT 59.265 50.000 10.37 2.84 45.68 3.56
3723 4844 0.605050 TGCTGTATGCTGTTCGGCAA 60.605 50.000 10.37 0.00 45.68 4.52
3756 4879 4.156556 GGTTGGGTTAAATTACCGTTCTCC 59.843 45.833 0.00 0.00 39.18 3.71
3773 4896 1.073284 TCTCTTCCCTTTTCGGTTGGG 59.927 52.381 0.00 0.00 42.20 4.12
3787 4910 1.187087 TCTCTTCCCGGCTTCTCTTC 58.813 55.000 0.00 0.00 0.00 2.87
3788 4911 1.552792 CTTCTCTTCCCGGCTTCTCTT 59.447 52.381 0.00 0.00 0.00 2.85
3793 4932 0.252284 TCCTCTTCTCTTCCCGGCTT 60.252 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.