Multiple sequence alignment - TraesCS4A01G373000

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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 TraesCS4A01G373000 chr4A 100.000 2130 0 0 1 2130 648259908 648262037 0.000000e+00 3934.0
1 TraesCS4A01G373000 chr4A 86.982 1375 106 44 694 2049 648133105 648134425 0.000000e+00 1480.0
2 TraesCS4A01G373000 chr4A 88.889 639 49 8 1498 2127 648654542 648655167 0.000000e+00 767.0
3 TraesCS4A01G373000 chr4A 100.000 331 0 0 2445 2775 648262352 648262682 1.830000e-171 612.0
4 TraesCS4A01G373000 chr4A 89.226 297 32 0 1118 1414 648654189 648654485 3.380000e-99 372.0
5 TraesCS4A01G373000 chr4A 95.455 176 8 0 1596 1771 648134564 648134739 5.850000e-72 281.0
6 TraesCS4A01G373000 chr4A 88.263 213 13 6 1732 1942 648136728 648136930 7.680000e-61 244.0
7 TraesCS4A01G373000 chr4A 82.353 102 15 1 675 773 648335574 648335675 4.920000e-13 86.1
8 TraesCS4A01G373000 chr7A 84.705 1288 110 42 618 1892 40694950 40696163 0.000000e+00 1206.0
9 TraesCS4A01G373000 chr7A 88.318 214 14 4 1890 2103 40696212 40696414 2.130000e-61 246.0
10 TraesCS4A01G373000 chr6B 94.842 601 26 4 3 600 691953331 691952733 0.000000e+00 933.0
11 TraesCS4A01G373000 chr6B 94.611 501 24 2 3 500 109133307 109132807 0.000000e+00 773.0
12 TraesCS4A01G373000 chr6B 92.430 251 17 2 2526 2775 40135393 40135642 9.450000e-95 357.0
13 TraesCS4A01G373000 chr6B 90.361 249 23 1 2524 2771 130505677 130505925 2.670000e-85 326.0
14 TraesCS4A01G373000 chr7D 84.908 762 60 25 665 1414 41366262 41365544 0.000000e+00 719.0
15 TraesCS4A01G373000 chr7D 84.646 762 62 25 665 1414 41259173 41259891 0.000000e+00 708.0
16 TraesCS4A01G373000 chr7D 91.196 443 35 2 972 1414 41325295 41325733 1.420000e-167 599.0
17 TraesCS4A01G373000 chr7D 80.879 774 86 27 618 1377 41274903 41275628 1.120000e-153 553.0
18 TraesCS4A01G373000 chr7D 87.441 422 40 8 1503 1917 41259954 41260369 8.990000e-130 473.0
19 TraesCS4A01G373000 chr7D 82.022 267 20 11 675 938 41306887 41307128 4.690000e-48 202.0
20 TraesCS4A01G373000 chr7D 74.515 412 60 36 1226 1600 41409109 41409512 1.340000e-28 137.0
21 TraesCS4A01G373000 chr7D 89.552 67 7 0 870 936 41343861 41343795 4.920000e-13 86.1
22 TraesCS4A01G373000 chr7D 95.349 43 2 0 2483 2525 41260450 41260492 4.960000e-08 69.4
23 TraesCS4A01G373000 chr3D 91.133 406 17 2 3 407 445862518 445862905 1.460000e-147 532.0
24 TraesCS4A01G373000 chr3D 96.244 213 5 3 399 609 445862961 445863172 2.050000e-91 346.0
25 TraesCS4A01G373000 chr3B 95.732 328 14 0 3 330 27496869 27497196 1.890000e-146 529.0
26 TraesCS4A01G373000 chr3B 94.071 253 14 1 2524 2775 133004185 133003933 1.560000e-102 383.0
27 TraesCS4A01G373000 chr3B 90.909 253 20 2 2524 2775 122582517 122582267 1.230000e-88 337.0
28 TraesCS4A01G373000 chr1D 96.266 241 9 0 3 243 379878938 379878698 2.000000e-106 396.0
29 TraesCS4A01G373000 chr7B 84.778 427 24 6 5 407 568672938 568672529 9.320000e-105 390.0
30 TraesCS4A01G373000 chr7B 95.436 241 11 0 3 243 502651609 502651849 4.340000e-103 385.0
31 TraesCS4A01G373000 chr7B 95.215 209 7 3 406 612 568672468 568672261 7.410000e-86 327.0
32 TraesCS4A01G373000 chr4D 95.851 241 10 0 3 243 454817048 454817288 9.320000e-105 390.0
33 TraesCS4A01G373000 chr6A 86.992 369 16 6 34 399 575468231 575467892 1.210000e-103 387.0
34 TraesCS4A01G373000 chr5D 95.436 241 11 0 3 243 285476918 285477158 4.340000e-103 385.0
35 TraesCS4A01G373000 chr1B 93.676 253 15 1 2524 2775 178093237 178093489 7.250000e-101 377.0
36 TraesCS4A01G373000 chr1B 90.441 272 23 3 138 407 543090553 543090823 3.400000e-94 355.0
37 TraesCS4A01G373000 chr1B 90.119 253 24 1 2524 2775 645961652 645961904 7.410000e-86 327.0
38 TraesCS4A01G373000 chr1B 93.897 213 10 3 399 609 543090879 543091090 4.460000e-83 318.0
39 TraesCS4A01G373000 chr5B 92.885 253 17 1 2524 2775 363683365 363683617 1.570000e-97 366.0
40 TraesCS4A01G373000 chr5B 88.235 85 6 2 202 283 258999226 258999309 6.330000e-17 99.0
41 TraesCS4A01G373000 chrUn 82.477 428 63 11 990 1416 48826196 48826612 5.650000e-97 364.0
42 TraesCS4A01G373000 chr2B 91.304 253 21 1 2524 2775 432720394 432720142 7.360000e-91 344.0
43 TraesCS4A01G373000 chr2B 91.129 248 21 1 2525 2771 110766072 110766319 4.430000e-88 335.0
44 TraesCS4A01G373000 chr6D 88.095 84 6 3 206 285 5406370 5406453 2.270000e-16 97.1


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 TraesCS4A01G373000 chr4A 648259908 648262682 2774 False 2273.000000 3934 100.000000 1 2775 2 chr4A.!!$F3 2774
1 TraesCS4A01G373000 chr4A 648133105 648136930 3825 False 668.333333 1480 90.233333 694 2049 3 chr4A.!!$F2 1355
2 TraesCS4A01G373000 chr4A 648654189 648655167 978 False 569.500000 767 89.057500 1118 2127 2 chr4A.!!$F4 1009
3 TraesCS4A01G373000 chr7A 40694950 40696414 1464 False 726.000000 1206 86.511500 618 2103 2 chr7A.!!$F1 1485
4 TraesCS4A01G373000 chr6B 691952733 691953331 598 True 933.000000 933 94.842000 3 600 1 chr6B.!!$R2 597
5 TraesCS4A01G373000 chr6B 109132807 109133307 500 True 773.000000 773 94.611000 3 500 1 chr6B.!!$R1 497
6 TraesCS4A01G373000 chr7D 41365544 41366262 718 True 719.000000 719 84.908000 665 1414 1 chr7D.!!$R2 749
7 TraesCS4A01G373000 chr7D 41274903 41275628 725 False 553.000000 553 80.879000 618 1377 1 chr7D.!!$F1 759
8 TraesCS4A01G373000 chr7D 41259173 41260492 1319 False 416.800000 708 89.145333 665 2525 3 chr7D.!!$F5 1860
9 TraesCS4A01G373000 chr3D 445862518 445863172 654 False 439.000000 532 93.688500 3 609 2 chr3D.!!$F1 606
10 TraesCS4A01G373000 chr7B 568672261 568672938 677 True 358.500000 390 89.996500 5 612 2 chr7B.!!$R1 607
11 TraesCS4A01G373000 chr1B 543090553 543091090 537 False 336.500000 355 92.169000 138 609 2 chr1B.!!$F3 471

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
831 931 0.1023 CACGACCTATCATGCCGTCA 59.898 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2708 4538 0.033366 GCCATGCTTTCCAACGGTTT 59.967 50.0 0.0 0.0 0.0 3.27 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
122 123 8.194433 AGACATGATGCGCTTAAGATATTATG 57.806 34.615 9.73 10.86 0.00 1.90
172 195 6.849151 AGGTAGGAATGTTGTCTTTAGGTTT 58.151 36.000 0.00 0.00 0.00 3.27
173 196 6.715264 AGGTAGGAATGTTGTCTTTAGGTTTG 59.285 38.462 0.00 0.00 0.00 2.93
312 337 0.986019 TAGGGTTCACGGGCATCCAT 60.986 55.000 0.00 0.00 0.00 3.41
367 393 2.493278 CGGCATTTTCCTTCTCCATTGT 59.507 45.455 0.00 0.00 0.00 2.71
539 631 6.706295 TCATAATCAATACATGCCCGTGATA 58.294 36.000 0.00 0.00 0.00 2.15
585 678 8.802267 TCAAAATGACCCTAGAACAAATAAAGG 58.198 33.333 0.00 0.00 0.00 3.11
609 702 8.235230 AGGGACCTTTCTATACATAGAGAATGA 58.765 37.037 9.54 0.00 40.23 2.57
610 703 9.041354 GGGACCTTTCTATACATAGAGAATGAT 57.959 37.037 9.54 0.00 40.23 2.45
633 726 1.138036 CTCGTACATTCGTCGCCCA 59.862 57.895 0.00 0.00 0.00 5.36
634 727 1.138047 CTCGTACATTCGTCGCCCAC 61.138 60.000 0.00 0.00 0.00 4.61
747 847 4.332543 TCCCCCGGCTGAACTCCT 62.333 66.667 0.00 0.00 0.00 3.69
757 857 3.179939 GAACTCCTTCGACGCCGC 61.180 66.667 0.00 0.00 35.37 6.53
804 904 2.228914 GCCTCGCATCGTTCGTACC 61.229 63.158 0.00 0.00 0.00 3.34
805 905 1.138036 CCTCGCATCGTTCGTACCA 59.862 57.895 0.00 0.00 0.00 3.25
808 908 1.803922 CGCATCGTTCGTACCAGCA 60.804 57.895 0.00 0.00 0.00 4.41
810 910 1.847818 GCATCGTTCGTACCAGCATA 58.152 50.000 0.00 0.00 0.00 3.14
811 911 2.404215 GCATCGTTCGTACCAGCATAT 58.596 47.619 0.00 0.00 0.00 1.78
812 912 2.408704 GCATCGTTCGTACCAGCATATC 59.591 50.000 0.00 0.00 0.00 1.63
813 913 3.638484 CATCGTTCGTACCAGCATATCA 58.362 45.455 0.00 0.00 0.00 2.15
814 914 3.074504 TCGTTCGTACCAGCATATCAC 57.925 47.619 0.00 0.00 0.00 3.06
815 915 1.779157 CGTTCGTACCAGCATATCACG 59.221 52.381 0.00 0.00 0.00 4.35
816 916 2.540157 CGTTCGTACCAGCATATCACGA 60.540 50.000 0.00 0.00 39.63 4.35
817 917 2.768833 TCGTACCAGCATATCACGAC 57.231 50.000 0.00 0.00 36.77 4.34
818 918 1.335810 TCGTACCAGCATATCACGACC 59.664 52.381 0.00 0.00 36.77 4.79
819 919 1.337071 CGTACCAGCATATCACGACCT 59.663 52.381 0.00 0.00 34.66 3.85
820 920 2.551032 CGTACCAGCATATCACGACCTA 59.449 50.000 0.00 0.00 34.66 3.08
821 921 3.190744 CGTACCAGCATATCACGACCTAT 59.809 47.826 0.00 0.00 34.66 2.57
822 922 3.944055 ACCAGCATATCACGACCTATC 57.056 47.619 0.00 0.00 0.00 2.08
823 923 3.230976 ACCAGCATATCACGACCTATCA 58.769 45.455 0.00 0.00 0.00 2.15
824 924 3.834813 ACCAGCATATCACGACCTATCAT 59.165 43.478 0.00 0.00 0.00 2.45
825 925 4.179298 CCAGCATATCACGACCTATCATG 58.821 47.826 0.00 0.00 0.00 3.07
826 926 3.615937 CAGCATATCACGACCTATCATGC 59.384 47.826 0.00 0.00 38.02 4.06
827 927 2.932614 GCATATCACGACCTATCATGCC 59.067 50.000 0.00 0.00 33.00 4.40
828 928 3.182182 CATATCACGACCTATCATGCCG 58.818 50.000 0.00 0.00 0.00 5.69
829 929 1.040646 ATCACGACCTATCATGCCGT 58.959 50.000 0.00 0.00 0.00 5.68
830 930 0.384309 TCACGACCTATCATGCCGTC 59.616 55.000 0.00 0.00 0.00 4.79
831 931 0.102300 CACGACCTATCATGCCGTCA 59.898 55.000 0.00 0.00 0.00 4.35
832 932 1.040646 ACGACCTATCATGCCGTCAT 58.959 50.000 0.00 0.00 0.00 3.06
833 933 1.000163 ACGACCTATCATGCCGTCATC 60.000 52.381 0.00 0.00 0.00 2.92
834 934 1.670087 CGACCTATCATGCCGTCATCC 60.670 57.143 0.00 0.00 0.00 3.51
872 972 1.216977 CACGACCCAGCACCGATTA 59.783 57.895 0.00 0.00 0.00 1.75
874 974 0.322322 ACGACCCAGCACCGATTAAA 59.678 50.000 0.00 0.00 0.00 1.52
894 994 2.047179 GTCGTCTTCCACCCTGCC 60.047 66.667 0.00 0.00 0.00 4.85
929 1029 5.523916 ACACCATATCGAATTTGCTCACTAC 59.476 40.000 0.00 0.00 0.00 2.73
939 1039 1.557099 TGCTCACTACCACTACCCAG 58.443 55.000 0.00 0.00 0.00 4.45
943 1043 1.203137 TCACTACCACTACCCAGCACT 60.203 52.381 0.00 0.00 0.00 4.40
944 1044 1.204941 CACTACCACTACCCAGCACTC 59.795 57.143 0.00 0.00 0.00 3.51
957 1066 1.954528 GCACTCAGCAAGCACACAT 59.045 52.632 0.00 0.00 44.79 3.21
960 1069 2.420642 CACTCAGCAAGCACACATAGT 58.579 47.619 0.00 0.00 0.00 2.12
963 1072 2.928757 CTCAGCAAGCACACATAGTCTC 59.071 50.000 0.00 0.00 0.00 3.36
965 1074 2.671888 CAGCAAGCACACATAGTCTCTG 59.328 50.000 0.00 0.00 0.00 3.35
966 1075 2.301296 AGCAAGCACACATAGTCTCTGT 59.699 45.455 0.00 0.00 0.00 3.41
968 1077 3.862267 GCAAGCACACATAGTCTCTGTAG 59.138 47.826 0.00 0.00 0.00 2.74
984 1107 9.635404 AGTCTCTGTAGATATATATAGGTTGCC 57.365 37.037 0.00 0.00 33.30 4.52
985 1108 9.409918 GTCTCTGTAGATATATATAGGTTGCCA 57.590 37.037 0.00 0.00 33.30 4.92
986 1109 9.634021 TCTCTGTAGATATATATAGGTTGCCAG 57.366 37.037 0.00 0.99 0.00 4.85
987 1110 9.634021 CTCTGTAGATATATATAGGTTGCCAGA 57.366 37.037 0.00 4.66 0.00 3.86
988 1111 9.409918 TCTGTAGATATATATAGGTTGCCAGAC 57.590 37.037 0.00 0.00 0.00 3.51
995 1118 0.321671 TAGGTTGCCAGACTCAGTGC 59.678 55.000 0.00 0.00 0.00 4.40
1017 1140 2.225019 CAGTGCAAACATCAGTCAGTCC 59.775 50.000 0.00 0.00 0.00 3.85
1050 1173 0.108329 TCCCTCGCGCCTTTAGAAAG 60.108 55.000 0.00 0.00 35.79 2.62
1052 1175 1.706287 CCTCGCGCCTTTAGAAAGCC 61.706 60.000 0.00 0.00 34.69 4.35
1053 1176 1.004320 TCGCGCCTTTAGAAAGCCA 60.004 52.632 0.00 0.00 34.69 4.75
1054 1177 1.134694 CGCGCCTTTAGAAAGCCAC 59.865 57.895 0.00 0.00 34.69 5.01
1055 1178 1.134694 GCGCCTTTAGAAAGCCACG 59.865 57.895 0.00 2.14 34.69 4.94
1056 1179 1.574702 GCGCCTTTAGAAAGCCACGT 61.575 55.000 0.00 0.00 34.69 4.49
1057 1180 1.717194 CGCCTTTAGAAAGCCACGTA 58.283 50.000 0.00 0.00 34.69 3.57
1058 1181 1.392510 CGCCTTTAGAAAGCCACGTAC 59.607 52.381 0.00 0.00 34.69 3.67
1059 1182 1.392510 GCCTTTAGAAAGCCACGTACG 59.607 52.381 15.01 15.01 34.69 3.67
1060 1183 2.680577 CCTTTAGAAAGCCACGTACGT 58.319 47.619 16.72 16.72 34.69 3.57
1061 1184 3.836949 CCTTTAGAAAGCCACGTACGTA 58.163 45.455 22.34 0.00 34.69 3.57
1075 1199 2.346821 TACGTACGCACCGTCGATCG 62.347 60.000 16.72 9.36 41.54 3.69
1077 1201 1.931612 GTACGCACCGTCGATCGAC 60.932 63.158 33.22 33.22 41.54 4.20
1089 1220 4.287720 CGTCGATCGACCTTGATTGATTA 58.712 43.478 35.48 0.86 40.12 1.75
1093 1224 4.681942 CGATCGACCTTGATTGATTACTCC 59.318 45.833 10.26 0.00 32.39 3.85
1097 1228 4.372656 GACCTTGATTGATTACTCCCTCG 58.627 47.826 0.00 0.00 0.00 4.63
1099 1230 2.910688 TGATTGATTACTCCCTCGGC 57.089 50.000 0.00 0.00 0.00 5.54
1378 1509 4.250305 ACAAGGCCGCACGGTTCT 62.250 61.111 11.27 6.13 37.65 3.01
1379 1510 2.978010 CAAGGCCGCACGGTTCTT 60.978 61.111 11.27 11.66 37.65 2.52
1381 1512 3.767630 AAGGCCGCACGGTTCTTGT 62.768 57.895 11.27 0.00 37.65 3.16
1618 1756 1.521840 CATCTGCTTCTTCGCTCATCG 59.478 52.381 0.00 0.00 40.15 3.84
1698 1848 4.514781 TCGGCATGTGTCCAGTATATAC 57.485 45.455 4.60 4.60 0.00 1.47
1729 1879 3.873910 TCGATCCTTCTTTGGTTGATCC 58.126 45.455 0.00 0.00 0.00 3.36
1806 1959 0.937304 CGGCCAAGGAACGATACATG 59.063 55.000 2.24 0.00 0.00 3.21
1849 2004 6.659361 TTATACGAGCTCGAGATATGTACC 57.341 41.667 40.58 0.00 43.02 3.34
1851 2006 3.478509 ACGAGCTCGAGATATGTACCTT 58.521 45.455 40.58 12.21 43.02 3.50
1867 2022 1.200483 CCTTGCGACGCTGTATGTAG 58.800 55.000 22.08 6.63 0.00 2.74
1868 2023 1.469251 CCTTGCGACGCTGTATGTAGT 60.469 52.381 22.08 0.00 0.00 2.73
1869 2024 2.223409 CCTTGCGACGCTGTATGTAGTA 60.223 50.000 22.08 0.00 0.00 1.82
1872 2027 5.366829 TTGCGACGCTGTATGTAGTATAT 57.633 39.130 22.08 0.00 0.00 0.86
1954 2158 2.101750 TGAGGCACACGAAACTGAAGTA 59.898 45.455 0.00 0.00 0.00 2.24
1992 2196 9.520204 CTGTTGATTATGTTTTGTGTTTCTTCT 57.480 29.630 0.00 0.00 0.00 2.85
2002 2206 7.754924 TGTTTTGTGTTTCTTCTGAATTCTGAC 59.245 33.333 13.97 4.69 31.56 3.51
2042 2246 1.352352 AGGACTTGTGACAGATTGGGG 59.648 52.381 0.00 0.00 0.00 4.96
2052 2256 4.080863 GTGACAGATTGGGGTGTAATCTCT 60.081 45.833 0.00 0.00 41.60 3.10
2054 2258 3.846588 ACAGATTGGGGTGTAATCTCTGT 59.153 43.478 0.00 0.00 41.60 3.41
2055 2259 4.194640 CAGATTGGGGTGTAATCTCTGTG 58.805 47.826 0.00 0.00 41.60 3.66
2056 2260 3.200825 AGATTGGGGTGTAATCTCTGTGG 59.799 47.826 0.00 0.00 39.96 4.17
2058 2262 1.906574 TGGGGTGTAATCTCTGTGGTC 59.093 52.381 0.00 0.00 0.00 4.02
2099 2303 1.141657 TGACAGGGGCTATCTTCATGC 59.858 52.381 0.00 0.00 0.00 4.06
2106 2310 3.556004 GGGGCTATCTTCATGCTGAGTAC 60.556 52.174 0.00 0.00 0.00 2.73
2118 2322 0.610174 CTGAGTACTTGCTGGGCAGA 59.390 55.000 0.00 0.00 40.61 4.26
2469 2673 3.649073 GGTTGTTTACCAAATGTCAGCC 58.351 45.455 0.00 0.00 46.92 4.85
2470 2674 3.068873 GGTTGTTTACCAAATGTCAGCCA 59.931 43.478 0.00 0.00 46.92 4.75
2471 2675 4.048504 GTTGTTTACCAAATGTCAGCCAC 58.951 43.478 0.00 0.00 34.07 5.01
2472 2676 2.625790 TGTTTACCAAATGTCAGCCACC 59.374 45.455 0.00 0.00 0.00 4.61
2473 2677 2.625790 GTTTACCAAATGTCAGCCACCA 59.374 45.455 0.00 0.00 0.00 4.17
2474 2678 2.198827 TACCAAATGTCAGCCACCAG 57.801 50.000 0.00 0.00 0.00 4.00
2475 2679 0.185901 ACCAAATGTCAGCCACCAGT 59.814 50.000 0.00 0.00 0.00 4.00
2476 2680 0.883833 CCAAATGTCAGCCACCAGTC 59.116 55.000 0.00 0.00 0.00 3.51
2477 2681 0.518636 CAAATGTCAGCCACCAGTCG 59.481 55.000 0.00 0.00 0.00 4.18
2478 2682 0.606401 AAATGTCAGCCACCAGTCGG 60.606 55.000 0.00 0.00 38.77 4.79
2484 2688 3.574780 GCCACCAGTCGGCTAAAC 58.425 61.111 0.00 0.00 46.56 2.01
2488 2692 1.270625 CCACCAGTCGGCTAAACAAGA 60.271 52.381 0.00 0.00 34.57 3.02
2525 2729 4.695560 GGGTCGACCAAGAACCAG 57.304 61.111 34.40 0.00 46.99 4.00
2527 2731 1.477685 GGGTCGACCAAGAACCAGGA 61.478 60.000 34.40 0.00 46.99 3.86
2530 2734 1.124780 TCGACCAAGAACCAGGACAA 58.875 50.000 0.00 0.00 0.00 3.18
2533 2737 2.884639 CGACCAAGAACCAGGACAAAAT 59.115 45.455 0.00 0.00 0.00 1.82
2535 2739 4.700213 CGACCAAGAACCAGGACAAAATAT 59.300 41.667 0.00 0.00 0.00 1.28
2536 2740 5.391950 CGACCAAGAACCAGGACAAAATATG 60.392 44.000 0.00 0.00 0.00 1.78
2539 2743 5.336690 CCAAGAACCAGGACAAAATATGTGG 60.337 44.000 0.00 0.00 44.12 4.17
2540 2744 4.998051 AGAACCAGGACAAAATATGTGGT 58.002 39.130 0.00 0.00 44.12 4.16
2543 2747 3.831911 ACCAGGACAAAATATGTGGTTGG 59.168 43.478 0.00 0.00 44.12 3.77
2548 2752 6.591062 CAGGACAAAATATGTGGTTGGAAATG 59.409 38.462 0.00 0.00 44.12 2.32
2549 2753 5.874261 GGACAAAATATGTGGTTGGAAATGG 59.126 40.000 0.00 0.00 44.12 3.16
2550 2754 6.432403 ACAAAATATGTGGTTGGAAATGGT 57.568 33.333 0.00 0.00 41.93 3.55
2551 2755 7.310113 GGACAAAATATGTGGTTGGAAATGGTA 60.310 37.037 0.00 0.00 44.12 3.25
2553 2757 7.234577 ACAAAATATGTGGTTGGAAATGGTACT 59.765 33.333 0.00 0.00 41.93 2.73
2554 2758 7.790782 AAATATGTGGTTGGAAATGGTACTT 57.209 32.000 0.00 0.00 0.00 2.24
2555 2759 7.404671 AATATGTGGTTGGAAATGGTACTTC 57.595 36.000 0.00 0.00 0.00 3.01
2558 2762 5.310451 TGTGGTTGGAAATGGTACTTCTAC 58.690 41.667 0.00 0.00 0.00 2.59
2560 2764 5.411669 GTGGTTGGAAATGGTACTTCTACAG 59.588 44.000 0.00 0.00 0.00 2.74
2561 2765 5.308497 TGGTTGGAAATGGTACTTCTACAGA 59.692 40.000 0.00 0.00 0.00 3.41
2562 2766 6.012858 TGGTTGGAAATGGTACTTCTACAGAT 60.013 38.462 0.00 0.00 0.00 2.90
2563 2767 6.884836 GGTTGGAAATGGTACTTCTACAGATT 59.115 38.462 0.00 0.00 0.00 2.40
2565 2769 8.793592 GTTGGAAATGGTACTTCTACAGATTTT 58.206 33.333 0.00 0.00 0.00 1.82
2566 2770 8.335532 TGGAAATGGTACTTCTACAGATTTTG 57.664 34.615 0.00 0.00 0.00 2.44
2567 2771 7.393234 TGGAAATGGTACTTCTACAGATTTTGG 59.607 37.037 0.00 0.00 0.00 3.28
2568 2772 7.148069 GGAAATGGTACTTCTACAGATTTTGGG 60.148 40.741 0.00 0.00 0.00 4.12
2569 2773 6.636454 ATGGTACTTCTACAGATTTTGGGA 57.364 37.500 0.00 0.00 0.00 4.37
2571 2775 5.045869 TGGTACTTCTACAGATTTTGGGAGG 60.046 44.000 0.00 0.00 0.00 4.30
2572 2776 5.189145 GGTACTTCTACAGATTTTGGGAGGA 59.811 44.000 0.00 0.00 0.00 3.71
2573 2777 6.126739 GGTACTTCTACAGATTTTGGGAGGAT 60.127 42.308 0.00 0.00 0.00 3.24
2574 2778 7.070821 GGTACTTCTACAGATTTTGGGAGGATA 59.929 40.741 0.00 0.00 0.00 2.59
2575 2779 6.890293 ACTTCTACAGATTTTGGGAGGATAC 58.110 40.000 0.00 0.00 0.00 2.24
2576 2780 6.443849 ACTTCTACAGATTTTGGGAGGATACA 59.556 38.462 0.00 0.00 41.41 2.29
2577 2781 7.127955 ACTTCTACAGATTTTGGGAGGATACAT 59.872 37.037 0.00 0.00 41.41 2.29
2578 2782 6.830912 TCTACAGATTTTGGGAGGATACATG 58.169 40.000 0.00 0.00 41.41 3.21
2579 2783 4.796606 ACAGATTTTGGGAGGATACATGG 58.203 43.478 0.00 0.00 41.41 3.66
2590 4420 1.903183 GGATACATGGCTAGGGGAGAC 59.097 57.143 0.00 0.00 0.00 3.36
2592 4422 1.113517 TACATGGCTAGGGGAGACGC 61.114 60.000 0.00 0.00 45.13 5.19
2593 4423 2.844839 ATGGCTAGGGGAGACGCC 60.845 66.667 0.00 0.00 46.15 5.68
2608 4438 3.948719 GCCCCCGGCGATCCAATA 61.949 66.667 9.30 0.00 39.62 1.90
2609 4439 3.077907 CCCCCGGCGATCCAATAT 58.922 61.111 9.30 0.00 0.00 1.28
2611 4441 1.078426 CCCCGGCGATCCAATATCC 60.078 63.158 9.30 0.00 0.00 2.59
2612 4442 1.078426 CCCGGCGATCCAATATCCC 60.078 63.158 9.30 0.00 0.00 3.85
2613 4443 1.553690 CCCGGCGATCCAATATCCCT 61.554 60.000 9.30 0.00 0.00 4.20
2614 4444 0.324943 CCGGCGATCCAATATCCCTT 59.675 55.000 9.30 0.00 0.00 3.95
2615 4445 1.271379 CCGGCGATCCAATATCCCTTT 60.271 52.381 9.30 0.00 0.00 3.11
2616 4446 2.076863 CGGCGATCCAATATCCCTTTC 58.923 52.381 0.00 0.00 0.00 2.62
2620 4450 4.223032 GGCGATCCAATATCCCTTTCTCTA 59.777 45.833 0.00 0.00 0.00 2.43
2621 4451 5.104735 GGCGATCCAATATCCCTTTCTCTAT 60.105 44.000 0.00 0.00 0.00 1.98
2622 4452 6.098409 GGCGATCCAATATCCCTTTCTCTATA 59.902 42.308 0.00 0.00 0.00 1.31
2623 4453 7.364762 GGCGATCCAATATCCCTTTCTCTATAA 60.365 40.741 0.00 0.00 0.00 0.98
2624 4454 8.207545 GCGATCCAATATCCCTTTCTCTATAAT 58.792 37.037 0.00 0.00 0.00 1.28
2634 4464 9.732130 ATCCCTTTCTCTATAATATTGTTCAGC 57.268 33.333 0.00 0.00 0.00 4.26
2636 4466 7.872993 CCCTTTCTCTATAATATTGTTCAGCGA 59.127 37.037 0.00 0.00 0.00 4.93
2661 4491 2.207041 CGCTTACGTTGCAACAGTAC 57.793 50.000 28.01 16.94 33.53 2.73
2663 4493 2.981805 CGCTTACGTTGCAACAGTACTA 59.018 45.455 28.01 15.03 33.53 1.82
2664 4494 3.181546 CGCTTACGTTGCAACAGTACTAC 60.182 47.826 28.01 18.17 33.53 2.73
2666 4496 4.209703 GCTTACGTTGCAACAGTACTACAA 59.790 41.667 28.01 15.24 0.00 2.41
2667 4497 5.107220 GCTTACGTTGCAACAGTACTACAAT 60.107 40.000 28.01 6.33 0.00 2.71
2668 4498 6.089820 GCTTACGTTGCAACAGTACTACAATA 59.910 38.462 28.01 12.75 0.00 1.90
2670 4500 5.291178 ACGTTGCAACAGTACTACAATACA 58.709 37.500 28.01 0.00 0.00 2.29
2671 4501 5.754406 ACGTTGCAACAGTACTACAATACAA 59.246 36.000 28.01 0.00 0.00 2.41
2672 4502 6.068931 CGTTGCAACAGTACTACAATACAAC 58.931 40.000 28.01 5.47 0.00 3.32
2673 4503 6.368213 GTTGCAACAGTACTACAATACAACC 58.632 40.000 24.52 0.00 0.00 3.77
2675 4505 5.221762 TGCAACAGTACTACAATACAACCCT 60.222 40.000 0.00 0.00 0.00 4.34
2676 4506 5.350640 GCAACAGTACTACAATACAACCCTC 59.649 44.000 0.00 0.00 0.00 4.30
2678 4508 6.282199 ACAGTACTACAATACAACCCTCTG 57.718 41.667 0.00 0.00 0.00 3.35
2679 4509 6.014647 ACAGTACTACAATACAACCCTCTGA 58.985 40.000 0.00 0.00 0.00 3.27
2680 4510 6.495872 ACAGTACTACAATACAACCCTCTGAA 59.504 38.462 0.00 0.00 0.00 3.02
2681 4511 7.180408 ACAGTACTACAATACAACCCTCTGAAT 59.820 37.037 0.00 0.00 0.00 2.57
2682 4512 7.492669 CAGTACTACAATACAACCCTCTGAATG 59.507 40.741 0.00 0.00 0.00 2.67
2683 4513 6.374417 ACTACAATACAACCCTCTGAATGT 57.626 37.500 0.00 0.00 0.00 2.71
2684 4514 6.779860 ACTACAATACAACCCTCTGAATGTT 58.220 36.000 0.00 0.00 0.00 2.71
2685 4515 6.879458 ACTACAATACAACCCTCTGAATGTTC 59.121 38.462 0.00 0.00 0.00 3.18
2686 4516 5.630121 ACAATACAACCCTCTGAATGTTCA 58.370 37.500 0.00 0.00 35.57 3.18
2687 4517 6.068010 ACAATACAACCCTCTGAATGTTCAA 58.932 36.000 0.00 0.00 36.64 2.69
2690 4520 5.712152 ACAACCCTCTGAATGTTCAATTC 57.288 39.130 0.00 0.00 36.64 2.17
2691 4521 5.139727 ACAACCCTCTGAATGTTCAATTCA 58.860 37.500 1.20 1.20 36.64 2.57
2698 4528 5.557891 CTGAATGTTCAATTCAGGAGGAC 57.442 43.478 16.75 0.00 46.75 3.85
2699 4529 4.002982 TGAATGTTCAATTCAGGAGGACG 58.997 43.478 0.00 0.00 33.55 4.79
2700 4530 1.808411 TGTTCAATTCAGGAGGACGC 58.192 50.000 0.00 0.00 0.00 5.19
2702 4532 2.565391 TGTTCAATTCAGGAGGACGCTA 59.435 45.455 0.00 0.00 0.00 4.26
2703 4533 3.190874 GTTCAATTCAGGAGGACGCTAG 58.809 50.000 0.00 0.00 0.00 3.42
2704 4534 1.137086 TCAATTCAGGAGGACGCTAGC 59.863 52.381 4.06 4.06 0.00 3.42
2705 4535 0.103208 AATTCAGGAGGACGCTAGCG 59.897 55.000 34.27 34.27 46.03 4.26
2706 4536 1.739338 ATTCAGGAGGACGCTAGCGG 61.739 60.000 37.66 21.35 44.69 5.52
2707 4537 3.905678 CAGGAGGACGCTAGCGGG 61.906 72.222 37.66 14.91 44.69 6.13
2708 4538 4.124943 AGGAGGACGCTAGCGGGA 62.125 66.667 37.66 0.00 44.69 5.14
2723 4553 2.421220 GGGAAACCGTTGGAAAGCA 58.579 52.632 0.00 0.00 43.64 3.91
2725 4555 1.336795 GGGAAACCGTTGGAAAGCATG 60.337 52.381 0.00 0.00 43.64 4.06
2726 4556 1.336795 GGAAACCGTTGGAAAGCATGG 60.337 52.381 0.00 0.00 0.00 3.66
2727 4557 0.033366 AAACCGTTGGAAAGCATGGC 59.967 50.000 0.00 0.00 0.00 4.40
2728 4558 0.827507 AACCGTTGGAAAGCATGGCT 60.828 50.000 0.00 0.00 42.56 4.75
2729 4559 1.244019 ACCGTTGGAAAGCATGGCTC 61.244 55.000 0.00 0.00 38.25 4.70
2731 4561 1.243342 CGTTGGAAAGCATGGCTCCA 61.243 55.000 0.00 0.00 38.25 3.86
2732 4562 1.188863 GTTGGAAAGCATGGCTCCAT 58.811 50.000 0.00 0.00 38.25 3.41
2733 4563 1.135721 GTTGGAAAGCATGGCTCCATC 59.864 52.381 0.00 0.00 38.25 3.51
2734 4564 0.627451 TGGAAAGCATGGCTCCATCT 59.373 50.000 0.00 0.00 38.25 2.90
2735 4565 1.030457 GGAAAGCATGGCTCCATCTG 58.970 55.000 0.00 0.00 38.25 2.90
2736 4566 1.030457 GAAAGCATGGCTCCATCTGG 58.970 55.000 0.00 0.00 38.25 3.86
2738 4568 0.395311 AAGCATGGCTCCATCTGGTG 60.395 55.000 0.00 0.00 38.25 4.17
2739 4569 1.225426 GCATGGCTCCATCTGGTGA 59.775 57.895 0.00 0.00 33.90 4.02
2740 4570 0.818445 GCATGGCTCCATCTGGTGAG 60.818 60.000 0.00 0.00 33.90 3.51
2741 4571 0.835276 CATGGCTCCATCTGGTGAGA 59.165 55.000 0.00 0.00 33.90 3.27
2742 4572 1.211212 CATGGCTCCATCTGGTGAGAA 59.789 52.381 0.00 0.00 33.90 2.87
2743 4573 0.907486 TGGCTCCATCTGGTGAGAAG 59.093 55.000 2.54 0.00 36.34 2.85
2747 4577 3.204526 GCTCCATCTGGTGAGAAGATTG 58.795 50.000 2.54 0.00 31.92 2.67
2749 4579 4.444591 GCTCCATCTGGTGAGAAGATTGAT 60.445 45.833 2.54 0.00 31.92 2.57
2750 4580 5.032327 TCCATCTGGTGAGAAGATTGATG 57.968 43.478 0.00 0.00 31.92 3.07
2753 4583 5.622180 CATCTGGTGAGAAGATTGATGGAT 58.378 41.667 0.00 0.00 31.92 3.41
2754 4584 5.032327 TCTGGTGAGAAGATTGATGGATG 57.968 43.478 0.00 0.00 0.00 3.51
2755 4585 4.472470 TCTGGTGAGAAGATTGATGGATGT 59.528 41.667 0.00 0.00 0.00 3.06
2756 4586 4.774124 TGGTGAGAAGATTGATGGATGTC 58.226 43.478 0.00 0.00 0.00 3.06
2766 4596 5.248020 AGATTGATGGATGTCCACCTATCTC 59.752 44.000 12.77 3.53 45.13 2.75
2767 4597 7.153847 AGATTGATGGATGTCCACCTATCTCA 61.154 42.308 12.77 5.80 45.13 3.27
2768 4598 8.575628 AGATTGATGGATGTCCACCTATCTCAA 61.576 40.741 12.77 12.92 45.13 3.02
2772 4602 4.192317 GGATGTCCACCTATCTCAACAAC 58.808 47.826 0.00 0.00 35.64 3.32
2773 4603 3.695830 TGTCCACCTATCTCAACAACC 57.304 47.619 0.00 0.00 0.00 3.77
2774 4604 2.304761 TGTCCACCTATCTCAACAACCC 59.695 50.000 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 195 0.595567 GTCGAAGTACCGTGCACACA 60.596 55.000 18.64 0.00 0.00 3.72
173 196 0.595567 TGTCGAAGTACCGTGCACAC 60.596 55.000 18.64 7.72 0.00 3.82
212 235 8.026607 TGGCTTGTTTGCTTGTCTTAATTATAC 58.973 33.333 0.00 0.00 0.00 1.47
226 249 2.629137 TGAATGTGATGGCTTGTTTGCT 59.371 40.909 0.00 0.00 0.00 3.91
285 310 3.139077 GCCCGTGAACCCTATATGAAAG 58.861 50.000 0.00 0.00 0.00 2.62
312 337 5.369404 TGATGGGAAAATACATAGGAGCTCA 59.631 40.000 17.19 0.00 0.00 4.26
367 393 2.815211 GCTGATCGTGCAGGCGAA 60.815 61.111 3.35 0.00 44.38 4.70
609 702 3.979495 GGCGACGAATGTACGAGAAATAT 59.021 43.478 0.00 0.00 37.03 1.28
610 703 3.365832 GGCGACGAATGTACGAGAAATA 58.634 45.455 0.00 0.00 37.03 1.40
611 704 2.190981 GGCGACGAATGTACGAGAAAT 58.809 47.619 0.00 0.00 37.03 2.17
612 705 1.621107 GGCGACGAATGTACGAGAAA 58.379 50.000 0.00 0.00 37.03 2.52
613 706 0.179156 GGGCGACGAATGTACGAGAA 60.179 55.000 0.00 0.00 37.03 2.87
614 707 1.307355 TGGGCGACGAATGTACGAGA 61.307 55.000 0.00 0.00 37.03 4.04
615 708 1.138036 TGGGCGACGAATGTACGAG 59.862 57.895 0.00 0.00 37.03 4.18
616 709 1.153978 GTGGGCGACGAATGTACGA 60.154 57.895 0.00 0.00 37.03 3.43
678 771 1.126846 AGTCGTAACGTTCTACGGTCG 59.873 52.381 20.10 8.94 36.37 4.79
687 780 1.973138 CGGTGATCAGTCGTAACGTT 58.027 50.000 5.88 5.88 0.00 3.99
738 834 1.801913 CGGCGTCGAAGGAGTTCAG 60.802 63.158 1.44 0.00 39.00 3.02
757 857 3.576356 GGATGACGGCATGCACGG 61.576 66.667 19.03 15.03 41.89 4.94
792 892 3.425525 GTGATATGCTGGTACGAACGATG 59.574 47.826 0.14 0.00 0.00 3.84
804 904 3.615937 GCATGATAGGTCGTGATATGCTG 59.384 47.826 0.00 0.00 42.78 4.41
805 905 3.368843 GGCATGATAGGTCGTGATATGCT 60.369 47.826 0.00 0.00 42.78 3.79
808 908 2.826128 ACGGCATGATAGGTCGTGATAT 59.174 45.455 0.00 0.00 45.93 1.63
810 910 1.040646 ACGGCATGATAGGTCGTGAT 58.959 50.000 0.00 0.00 45.93 3.06
811 911 2.500352 ACGGCATGATAGGTCGTGA 58.500 52.632 0.00 0.00 45.93 4.35
814 914 1.670087 GGATGACGGCATGATAGGTCG 60.670 57.143 9.52 0.00 39.68 4.79
815 915 1.338200 GGGATGACGGCATGATAGGTC 60.338 57.143 9.52 0.00 34.11 3.85
816 916 0.687354 GGGATGACGGCATGATAGGT 59.313 55.000 9.52 0.00 34.11 3.08
817 917 0.979665 AGGGATGACGGCATGATAGG 59.020 55.000 9.52 0.00 34.11 2.57
818 918 2.693069 GAAGGGATGACGGCATGATAG 58.307 52.381 9.52 0.00 34.11 2.08
819 919 1.000843 CGAAGGGATGACGGCATGATA 59.999 52.381 9.52 0.00 34.11 2.15
820 920 0.250038 CGAAGGGATGACGGCATGAT 60.250 55.000 9.52 0.00 34.11 2.45
821 921 1.143838 CGAAGGGATGACGGCATGA 59.856 57.895 9.52 0.00 34.11 3.07
822 922 2.537560 GCGAAGGGATGACGGCATG 61.538 63.158 9.52 0.00 34.11 4.06
823 923 2.203070 GCGAAGGGATGACGGCAT 60.203 61.111 1.48 1.48 37.47 4.40
824 924 3.371097 GAGCGAAGGGATGACGGCA 62.371 63.158 0.00 0.00 0.00 5.69
825 925 2.586357 GAGCGAAGGGATGACGGC 60.586 66.667 0.00 0.00 0.00 5.68
826 926 2.107141 GGAGCGAAGGGATGACGG 59.893 66.667 0.00 0.00 0.00 4.79
827 927 2.107141 GGGAGCGAAGGGATGACG 59.893 66.667 0.00 0.00 0.00 4.35
828 928 1.443828 GAGGGAGCGAAGGGATGAC 59.556 63.158 0.00 0.00 0.00 3.06
829 929 1.762460 GGAGGGAGCGAAGGGATGA 60.762 63.158 0.00 0.00 0.00 2.92
830 930 2.066393 TGGAGGGAGCGAAGGGATG 61.066 63.158 0.00 0.00 0.00 3.51
831 931 2.066999 GTGGAGGGAGCGAAGGGAT 61.067 63.158 0.00 0.00 0.00 3.85
832 932 2.683933 GTGGAGGGAGCGAAGGGA 60.684 66.667 0.00 0.00 0.00 4.20
833 933 2.873557 TAGGTGGAGGGAGCGAAGGG 62.874 65.000 0.00 0.00 0.00 3.95
834 934 0.760945 ATAGGTGGAGGGAGCGAAGG 60.761 60.000 0.00 0.00 0.00 3.46
872 972 0.974383 AGGGTGGAAGACGACGATTT 59.026 50.000 0.00 0.00 0.00 2.17
874 974 1.890894 CAGGGTGGAAGACGACGAT 59.109 57.895 0.00 0.00 0.00 3.73
894 994 0.742990 ATATGGTGTTGGTCGCGGTG 60.743 55.000 6.13 0.00 0.00 4.94
906 1006 5.050091 GGTAGTGAGCAAATTCGATATGGTG 60.050 44.000 2.59 0.00 0.00 4.17
929 1029 1.078848 GCTGAGTGCTGGGTAGTGG 60.079 63.158 0.00 0.00 38.95 4.00
939 1039 1.129998 CTATGTGTGCTTGCTGAGTGC 59.870 52.381 0.00 0.00 43.25 4.40
943 1043 2.564504 AGAGACTATGTGTGCTTGCTGA 59.435 45.455 0.00 0.00 0.00 4.26
944 1044 2.671888 CAGAGACTATGTGTGCTTGCTG 59.328 50.000 0.00 0.00 0.00 4.41
960 1069 9.634021 CTGGCAACCTATATATATCTACAGAGA 57.366 37.037 0.00 0.00 35.71 3.10
963 1072 9.415008 AGTCTGGCAACCTATATATATCTACAG 57.585 37.037 0.00 0.97 0.00 2.74
965 1074 9.409918 TGAGTCTGGCAACCTATATATATCTAC 57.590 37.037 0.00 0.00 0.00 2.59
966 1075 9.634021 CTGAGTCTGGCAACCTATATATATCTA 57.366 37.037 0.00 0.00 0.00 1.98
968 1077 8.194104 CACTGAGTCTGGCAACCTATATATATC 58.806 40.741 0.00 0.00 0.00 1.63
978 1101 1.968540 GGCACTGAGTCTGGCAACC 60.969 63.158 1.82 0.00 34.38 3.77
983 1106 1.670406 GCACTGGCACTGAGTCTGG 60.670 63.158 1.82 0.00 40.72 3.86
984 1107 3.963222 GCACTGGCACTGAGTCTG 58.037 61.111 0.00 0.00 40.72 3.51
995 1118 2.224606 ACTGACTGATGTTTGCACTGG 58.775 47.619 0.00 0.00 0.00 4.00
1017 1140 2.048503 GGGAGTGGTCCGTTGTCG 60.049 66.667 0.00 0.00 45.05 4.35
1033 1156 1.716172 GCTTTCTAAAGGCGCGAGG 59.284 57.895 12.10 0.00 36.53 4.63
1055 1178 0.921214 GATCGACGGTGCGTACGTAC 60.921 60.000 25.76 25.76 45.68 3.67
1056 1179 1.348250 GATCGACGGTGCGTACGTA 59.652 57.895 17.90 10.06 45.68 3.57
1058 1181 3.009599 CGATCGACGGTGCGTACG 61.010 66.667 10.26 11.84 41.37 3.67
1059 1182 1.931612 GTCGATCGACGGTGCGTAC 60.932 63.158 30.46 7.26 41.37 3.67
1060 1183 2.400798 GTCGATCGACGGTGCGTA 59.599 61.111 30.46 0.00 41.37 4.42
1061 1184 4.471726 GGTCGATCGACGGTGCGT 62.472 66.667 34.69 0.00 45.41 5.24
1075 1199 4.372656 CGAGGGAGTAATCAATCAAGGTC 58.627 47.826 0.00 0.00 0.00 3.85
1077 1201 3.733337 CCGAGGGAGTAATCAATCAAGG 58.267 50.000 0.00 0.00 0.00 3.61
1297 1428 4.203076 GGCATAGGCGTCGACCGT 62.203 66.667 10.58 7.18 42.47 4.83
1347 1478 3.083600 CTTGTCGATTGCGCCGTCC 62.084 63.158 4.18 0.00 37.46 4.79
1378 1509 2.811431 CGTATTTGGAGAGGTGCAACAA 59.189 45.455 3.64 0.00 39.98 2.83
1379 1510 2.422597 CGTATTTGGAGAGGTGCAACA 58.577 47.619 3.64 0.00 39.98 3.33
1381 1512 1.448985 GCGTATTTGGAGAGGTGCAA 58.551 50.000 0.00 0.00 31.08 4.08
1490 1621 3.547613 GCTGCATCAACGGAATCTTGATC 60.548 47.826 0.00 0.00 36.42 2.92
1698 1848 5.334414 CCAAAGAAGGATCGAACTTCAGTTG 60.334 44.000 25.59 24.79 45.18 3.16
1823 1978 8.824781 GGTACATATCTCGAGCTCGTATAATAA 58.175 37.037 33.33 13.31 40.80 1.40
1828 1983 4.834534 AGGTACATATCTCGAGCTCGTAT 58.165 43.478 33.33 27.50 40.80 3.06
1849 2004 1.909376 ACTACATACAGCGTCGCAAG 58.091 50.000 21.09 13.88 0.00 4.01
1851 2006 5.446875 GCTATATACTACATACAGCGTCGCA 60.447 44.000 21.09 0.00 0.00 5.10
1895 2099 5.105310 CCCTCATGGCACTAGGTACATATAC 60.105 48.000 14.13 0.00 0.00 1.47
1897 2101 3.840666 CCCTCATGGCACTAGGTACATAT 59.159 47.826 14.13 0.00 0.00 1.78
1954 2158 7.870509 ACATAATCAACAGCACAGATTACAT 57.129 32.000 0.00 0.00 37.14 2.29
1992 2196 4.330894 GCTGAATGATGTCGTCAGAATTCA 59.669 41.667 8.44 16.25 40.92 2.57
2002 2206 4.571984 TCCTTGTTATGCTGAATGATGTCG 59.428 41.667 0.00 0.00 0.00 4.35
2038 2242 1.906574 GACCACAGAGATTACACCCCA 59.093 52.381 0.00 0.00 0.00 4.96
2042 2246 4.745649 GGTACAGACCACAGAGATTACAC 58.254 47.826 0.00 0.00 46.12 2.90
2099 2303 0.610174 TCTGCCCAGCAAGTACTCAG 59.390 55.000 0.00 0.00 38.41 3.35
2106 2310 1.734137 GCATCATCTGCCCAGCAAG 59.266 57.895 0.00 0.00 45.66 4.01
2449 2653 4.048504 GTGGCTGACATTTGGTAAACAAC 58.951 43.478 0.00 0.00 39.19 3.32
2450 2654 3.068873 GGTGGCTGACATTTGGTAAACAA 59.931 43.478 0.00 0.00 37.28 2.83
2451 2655 2.625790 GGTGGCTGACATTTGGTAAACA 59.374 45.455 0.00 0.00 0.00 2.83
2452 2656 2.625790 TGGTGGCTGACATTTGGTAAAC 59.374 45.455 0.00 0.00 0.00 2.01
2453 2657 2.890311 CTGGTGGCTGACATTTGGTAAA 59.110 45.455 0.00 0.00 0.00 2.01
2454 2658 2.158534 ACTGGTGGCTGACATTTGGTAA 60.159 45.455 0.00 0.00 0.00 2.85
2455 2659 1.423541 ACTGGTGGCTGACATTTGGTA 59.576 47.619 0.00 0.00 0.00 3.25
2456 2660 0.185901 ACTGGTGGCTGACATTTGGT 59.814 50.000 0.00 0.00 0.00 3.67
2457 2661 0.883833 GACTGGTGGCTGACATTTGG 59.116 55.000 0.00 0.00 0.00 3.28
2458 2662 0.518636 CGACTGGTGGCTGACATTTG 59.481 55.000 0.00 0.00 0.00 2.32
2459 2663 0.606401 CCGACTGGTGGCTGACATTT 60.606 55.000 0.00 0.00 0.00 2.32
2460 2664 1.003355 CCGACTGGTGGCTGACATT 60.003 57.895 0.00 0.00 0.00 2.71
2461 2665 2.665000 CCGACTGGTGGCTGACAT 59.335 61.111 0.00 0.00 0.00 3.06
2468 2672 1.156736 CTTGTTTAGCCGACTGGTGG 58.843 55.000 0.00 0.00 37.67 4.61
2469 2673 2.069273 CTCTTGTTTAGCCGACTGGTG 58.931 52.381 0.00 0.00 37.67 4.17
2470 2674 1.608283 GCTCTTGTTTAGCCGACTGGT 60.608 52.381 0.00 0.00 37.67 4.00
2471 2675 1.079503 GCTCTTGTTTAGCCGACTGG 58.920 55.000 0.00 0.00 33.73 4.00
2472 2676 1.728971 CTGCTCTTGTTTAGCCGACTG 59.271 52.381 0.00 0.00 39.30 3.51
2473 2677 1.941668 GCTGCTCTTGTTTAGCCGACT 60.942 52.381 0.00 0.00 39.30 4.18
2474 2678 0.444260 GCTGCTCTTGTTTAGCCGAC 59.556 55.000 0.00 0.00 39.30 4.79
2475 2679 1.014044 CGCTGCTCTTGTTTAGCCGA 61.014 55.000 0.00 0.00 39.30 5.54
2476 2680 1.291877 ACGCTGCTCTTGTTTAGCCG 61.292 55.000 0.00 0.00 39.30 5.52
2477 2681 0.444260 GACGCTGCTCTTGTTTAGCC 59.556 55.000 0.00 0.00 39.30 3.93
2478 2682 1.136224 GTGACGCTGCTCTTGTTTAGC 60.136 52.381 0.00 0.00 40.50 3.09
2479 2683 2.096713 GTGTGACGCTGCTCTTGTTTAG 60.097 50.000 0.00 0.00 0.00 1.85
2480 2684 1.864711 GTGTGACGCTGCTCTTGTTTA 59.135 47.619 0.00 0.00 0.00 2.01
2481 2685 0.657840 GTGTGACGCTGCTCTTGTTT 59.342 50.000 0.00 0.00 0.00 2.83
2482 2686 1.490693 CGTGTGACGCTGCTCTTGTT 61.491 55.000 0.00 0.00 33.65 2.83
2483 2687 1.951130 CGTGTGACGCTGCTCTTGT 60.951 57.895 0.00 0.00 33.65 3.16
2484 2688 2.849007 CGTGTGACGCTGCTCTTG 59.151 61.111 0.00 0.00 33.65 3.02
2525 2729 5.874261 CCATTTCCAACCACATATTTTGTCC 59.126 40.000 0.00 0.00 36.00 4.02
2527 2731 6.432403 ACCATTTCCAACCACATATTTTGT 57.568 33.333 0.00 0.00 39.91 2.83
2530 2734 7.673926 AGAAGTACCATTTCCAACCACATATTT 59.326 33.333 0.00 0.00 0.00 1.40
2533 2737 6.134535 AGAAGTACCATTTCCAACCACATA 57.865 37.500 0.00 0.00 0.00 2.29
2535 2739 4.447138 AGAAGTACCATTTCCAACCACA 57.553 40.909 0.00 0.00 0.00 4.17
2536 2740 5.310451 TGTAGAAGTACCATTTCCAACCAC 58.690 41.667 0.00 0.00 0.00 4.16
2537 2741 5.308497 TCTGTAGAAGTACCATTTCCAACCA 59.692 40.000 0.00 0.00 0.00 3.67
2539 2743 7.923414 AATCTGTAGAAGTACCATTTCCAAC 57.077 36.000 0.00 0.00 0.00 3.77
2540 2744 8.792633 CAAAATCTGTAGAAGTACCATTTCCAA 58.207 33.333 0.00 0.00 0.00 3.53
2543 2747 7.610305 TCCCAAAATCTGTAGAAGTACCATTTC 59.390 37.037 0.00 0.00 0.00 2.17
2548 2752 5.189145 TCCTCCCAAAATCTGTAGAAGTACC 59.811 44.000 0.00 0.00 0.00 3.34
2549 2753 6.295719 TCCTCCCAAAATCTGTAGAAGTAC 57.704 41.667 0.00 0.00 0.00 2.73
2550 2754 7.622081 TGTATCCTCCCAAAATCTGTAGAAGTA 59.378 37.037 0.00 0.00 0.00 2.24
2551 2755 6.443849 TGTATCCTCCCAAAATCTGTAGAAGT 59.556 38.462 0.00 0.00 0.00 3.01
2553 2757 6.884472 TGTATCCTCCCAAAATCTGTAGAA 57.116 37.500 0.00 0.00 0.00 2.10
2554 2758 6.183361 CCATGTATCCTCCCAAAATCTGTAGA 60.183 42.308 0.00 0.00 0.00 2.59
2555 2759 6.000219 CCATGTATCCTCCCAAAATCTGTAG 59.000 44.000 0.00 0.00 0.00 2.74
2558 2762 3.571401 GCCATGTATCCTCCCAAAATCTG 59.429 47.826 0.00 0.00 0.00 2.90
2560 2764 3.837355 AGCCATGTATCCTCCCAAAATC 58.163 45.455 0.00 0.00 0.00 2.17
2561 2765 3.979501 AGCCATGTATCCTCCCAAAAT 57.020 42.857 0.00 0.00 0.00 1.82
2562 2766 3.138283 CCTAGCCATGTATCCTCCCAAAA 59.862 47.826 0.00 0.00 0.00 2.44
2563 2767 2.711009 CCTAGCCATGTATCCTCCCAAA 59.289 50.000 0.00 0.00 0.00 3.28
2565 2769 1.485019 CCCTAGCCATGTATCCTCCCA 60.485 57.143 0.00 0.00 0.00 4.37
2566 2770 1.280457 CCCTAGCCATGTATCCTCCC 58.720 60.000 0.00 0.00 0.00 4.30
2567 2771 1.203313 TCCCCTAGCCATGTATCCTCC 60.203 57.143 0.00 0.00 0.00 4.30
2568 2772 2.183679 CTCCCCTAGCCATGTATCCTC 58.816 57.143 0.00 0.00 0.00 3.71
2569 2773 1.795786 TCTCCCCTAGCCATGTATCCT 59.204 52.381 0.00 0.00 0.00 3.24
2571 2775 1.546476 CGTCTCCCCTAGCCATGTATC 59.454 57.143 0.00 0.00 0.00 2.24
2572 2776 1.633774 CGTCTCCCCTAGCCATGTAT 58.366 55.000 0.00 0.00 0.00 2.29
2573 2777 1.113517 GCGTCTCCCCTAGCCATGTA 61.114 60.000 0.00 0.00 0.00 2.29
2574 2778 2.435693 GCGTCTCCCCTAGCCATGT 61.436 63.158 0.00 0.00 0.00 3.21
2575 2779 2.423446 GCGTCTCCCCTAGCCATG 59.577 66.667 0.00 0.00 0.00 3.66
2592 4422 1.078426 GATATTGGATCGCCGGGGG 60.078 63.158 19.63 4.42 36.79 5.40
2593 4423 1.078426 GGATATTGGATCGCCGGGG 60.078 63.158 13.31 13.31 36.79 5.73
2594 4424 1.078426 GGGATATTGGATCGCCGGG 60.078 63.158 2.18 0.00 36.79 5.73
2595 4425 0.324943 AAGGGATATTGGATCGCCGG 59.675 55.000 0.00 0.00 36.79 6.13
2596 4426 2.076863 GAAAGGGATATTGGATCGCCG 58.923 52.381 0.00 0.00 36.79 6.46
2597 4427 3.008485 AGAGAAAGGGATATTGGATCGCC 59.992 47.826 0.00 0.00 0.00 5.54
2598 4428 4.278975 AGAGAAAGGGATATTGGATCGC 57.721 45.455 0.00 0.00 0.00 4.58
2608 4438 9.732130 GCTGAACAATATTATAGAGAAAGGGAT 57.268 33.333 0.00 0.00 0.00 3.85
2609 4439 7.872993 CGCTGAACAATATTATAGAGAAAGGGA 59.127 37.037 0.00 0.00 0.00 4.20
2611 4441 8.818141 TCGCTGAACAATATTATAGAGAAAGG 57.182 34.615 0.00 0.00 0.00 3.11
2642 4472 1.790623 AGTACTGTTGCAACGTAAGCG 59.209 47.619 25.16 13.40 45.62 4.68
2645 4475 6.922407 TGTATTGTAGTACTGTTGCAACGTAA 59.078 34.615 25.16 16.65 0.00 3.18
2646 4476 6.445475 TGTATTGTAGTACTGTTGCAACGTA 58.555 36.000 23.79 22.69 0.00 3.57
2648 4478 5.832568 TGTATTGTAGTACTGTTGCAACG 57.167 39.130 23.79 19.64 0.00 4.10
2649 4479 6.368213 GGTTGTATTGTAGTACTGTTGCAAC 58.632 40.000 22.83 22.83 33.83 4.17
2650 4480 5.470777 GGGTTGTATTGTAGTACTGTTGCAA 59.529 40.000 5.39 0.00 0.00 4.08
2651 4481 4.998672 GGGTTGTATTGTAGTACTGTTGCA 59.001 41.667 5.39 0.00 0.00 4.08
2654 4484 6.495872 TCAGAGGGTTGTATTGTAGTACTGTT 59.504 38.462 5.39 0.00 0.00 3.16
2655 4485 6.014647 TCAGAGGGTTGTATTGTAGTACTGT 58.985 40.000 5.39 0.00 0.00 3.55
2656 4486 6.525578 TCAGAGGGTTGTATTGTAGTACTG 57.474 41.667 5.39 0.00 0.00 2.74
2657 4487 7.180408 ACATTCAGAGGGTTGTATTGTAGTACT 59.820 37.037 0.00 0.00 0.00 2.73
2658 4488 7.328737 ACATTCAGAGGGTTGTATTGTAGTAC 58.671 38.462 0.00 0.00 0.00 2.73
2659 4489 7.490657 ACATTCAGAGGGTTGTATTGTAGTA 57.509 36.000 0.00 0.00 0.00 1.82
2660 4490 6.374417 ACATTCAGAGGGTTGTATTGTAGT 57.626 37.500 0.00 0.00 0.00 2.73
2661 4491 6.878923 TGAACATTCAGAGGGTTGTATTGTAG 59.121 38.462 0.00 0.00 32.50 2.74
2663 4493 5.630121 TGAACATTCAGAGGGTTGTATTGT 58.370 37.500 0.00 0.00 32.50 2.71
2664 4494 6.573664 TTGAACATTCAGAGGGTTGTATTG 57.426 37.500 0.00 0.00 38.61 1.90
2666 4496 6.947733 TGAATTGAACATTCAGAGGGTTGTAT 59.052 34.615 0.00 0.00 38.61 2.29
2667 4497 6.303054 TGAATTGAACATTCAGAGGGTTGTA 58.697 36.000 0.00 0.00 38.61 2.41
2668 4498 5.139727 TGAATTGAACATTCAGAGGGTTGT 58.860 37.500 0.00 0.00 38.61 3.32
2678 4508 3.181506 GCGTCCTCCTGAATTGAACATTC 60.182 47.826 0.00 0.00 0.00 2.67
2679 4509 2.749621 GCGTCCTCCTGAATTGAACATT 59.250 45.455 0.00 0.00 0.00 2.71
2680 4510 2.026822 AGCGTCCTCCTGAATTGAACAT 60.027 45.455 0.00 0.00 0.00 2.71
2681 4511 1.347707 AGCGTCCTCCTGAATTGAACA 59.652 47.619 0.00 0.00 0.00 3.18
2682 4512 2.100605 AGCGTCCTCCTGAATTGAAC 57.899 50.000 0.00 0.00 0.00 3.18
2683 4513 2.418746 GCTAGCGTCCTCCTGAATTGAA 60.419 50.000 0.00 0.00 0.00 2.69
2684 4514 1.137086 GCTAGCGTCCTCCTGAATTGA 59.863 52.381 0.00 0.00 0.00 2.57
2685 4515 1.576356 GCTAGCGTCCTCCTGAATTG 58.424 55.000 0.00 0.00 0.00 2.32
2686 4516 0.103208 CGCTAGCGTCCTCCTGAATT 59.897 55.000 28.66 0.00 34.35 2.17
2687 4517 1.736586 CGCTAGCGTCCTCCTGAAT 59.263 57.895 28.66 0.00 34.35 2.57
2690 4520 3.905678 CCCGCTAGCGTCCTCCTG 61.906 72.222 33.18 17.10 37.81 3.86
2691 4521 3.657038 TTCCCGCTAGCGTCCTCCT 62.657 63.158 33.18 0.00 37.81 3.69
2692 4522 2.718073 TTTCCCGCTAGCGTCCTCC 61.718 63.158 33.18 0.00 37.81 4.30
2693 4523 1.518792 GTTTCCCGCTAGCGTCCTC 60.519 63.158 33.18 16.53 37.81 3.71
2694 4524 2.577593 GTTTCCCGCTAGCGTCCT 59.422 61.111 33.18 0.00 37.81 3.85
2705 4535 0.966179 ATGCTTTCCAACGGTTTCCC 59.034 50.000 0.00 0.00 0.00 3.97
2706 4536 1.336795 CCATGCTTTCCAACGGTTTCC 60.337 52.381 0.00 0.00 0.00 3.13
2707 4537 1.934849 GCCATGCTTTCCAACGGTTTC 60.935 52.381 0.00 0.00 0.00 2.78
2708 4538 0.033366 GCCATGCTTTCCAACGGTTT 59.967 50.000 0.00 0.00 0.00 3.27
2712 4542 1.243342 TGGAGCCATGCTTTCCAACG 61.243 55.000 8.17 0.00 39.88 4.10
2714 4544 1.006281 AGATGGAGCCATGCTTTCCAA 59.994 47.619 6.76 1.15 39.88 3.53
2715 4545 0.627451 AGATGGAGCCATGCTTTCCA 59.373 50.000 6.76 11.83 39.88 3.53
2716 4546 1.030457 CAGATGGAGCCATGCTTTCC 58.970 55.000 6.76 0.00 39.88 3.13
2717 4547 1.030457 CCAGATGGAGCCATGCTTTC 58.970 55.000 6.76 0.00 39.88 2.62
2719 4549 0.395311 CACCAGATGGAGCCATGCTT 60.395 55.000 6.76 0.00 39.88 3.91
2720 4550 1.226542 CACCAGATGGAGCCATGCT 59.773 57.895 6.76 1.60 43.88 3.79
2721 4551 0.818445 CTCACCAGATGGAGCCATGC 60.818 60.000 6.76 0.00 36.70 4.06
2722 4552 0.835276 TCTCACCAGATGGAGCCATG 59.165 55.000 6.76 0.00 36.70 3.66
2723 4553 1.489649 CTTCTCACCAGATGGAGCCAT 59.510 52.381 5.72 0.71 39.69 4.40
2725 4555 1.198713 TCTTCTCACCAGATGGAGCC 58.801 55.000 5.72 0.00 38.94 4.70
2726 4556 3.118482 TCAATCTTCTCACCAGATGGAGC 60.118 47.826 5.72 0.00 38.94 4.70
2727 4557 4.750021 TCAATCTTCTCACCAGATGGAG 57.250 45.455 5.72 0.00 38.94 3.86
2728 4558 5.032327 CATCAATCTTCTCACCAGATGGA 57.968 43.478 5.72 0.00 35.55 3.41
2729 4559 4.135306 CCATCAATCTTCTCACCAGATGG 58.865 47.826 0.00 0.00 43.29 3.51
2731 4561 5.132312 ACATCCATCAATCTTCTCACCAGAT 59.868 40.000 0.00 0.00 31.94 2.90
2732 4562 4.472470 ACATCCATCAATCTTCTCACCAGA 59.528 41.667 0.00 0.00 0.00 3.86
2733 4563 4.778579 ACATCCATCAATCTTCTCACCAG 58.221 43.478 0.00 0.00 0.00 4.00
2734 4564 4.384537 GGACATCCATCAATCTTCTCACCA 60.385 45.833 0.00 0.00 35.64 4.17
2735 4565 4.133078 GGACATCCATCAATCTTCTCACC 58.867 47.826 0.00 0.00 35.64 4.02
2736 4566 4.774124 TGGACATCCATCAATCTTCTCAC 58.226 43.478 0.00 0.00 42.01 3.51
2749 4579 3.449918 TGTTGAGATAGGTGGACATCCA 58.550 45.455 0.00 0.00 45.30 3.41
2750 4580 4.192317 GTTGTTGAGATAGGTGGACATCC 58.808 47.826 0.00 0.00 0.00 3.51
2753 4583 2.304761 GGGTTGTTGAGATAGGTGGACA 59.695 50.000 0.00 0.00 0.00 4.02
2754 4584 2.987232 GGGTTGTTGAGATAGGTGGAC 58.013 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.