Multiple sequence alignment - TraesCS6B01G224400

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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 TraesCS6B01G224400 chr6B 100.000 4763 0 0 1 4763 341762161 341766923 0.000000e+00 8796
1 TraesCS6B01G224400 chr6B 83.855 607 66 12 4181 4763 352248270 352247672 2.510000e-152 549
2 TraesCS6B01G224400 chr6D 94.390 1640 75 8 832 2467 261011891 261010265 0.000000e+00 2503
3 TraesCS6B01G224400 chr6D 95.472 1546 51 8 2505 4035 261010260 261008719 0.000000e+00 2449
4 TraesCS6B01G224400 chr6A 90.183 1640 114 18 832 2467 369548239 369549835 0.000000e+00 2093
5 TraesCS6B01G224400 chr6A 89.511 1411 105 19 832 2238 369546808 369548179 0.000000e+00 1746
6 TraesCS6B01G224400 chr6A 95.938 837 28 2 3202 4035 369574637 369575470 0.000000e+00 1352
7 TraesCS6B01G224400 chr6A 88.779 811 89 2 10 819 96434318 96435127 0.000000e+00 992
8 TraesCS6B01G224400 chr6A 91.549 568 30 9 2652 3203 369573989 369574554 0.000000e+00 767
9 TraesCS6B01G224400 chr6A 94.366 142 8 0 2504 2645 369549839 369549980 8.030000e-53 219
10 TraesCS6B01G224400 chr3B 91.352 821 62 4 2 819 97752712 97753526 0.000000e+00 1114
11 TraesCS6B01G224400 chr2D 90.667 825 74 2 1 822 629233529 629232705 0.000000e+00 1094
12 TraesCS6B01G224400 chr2D 75.499 902 173 37 1652 2542 183615977 183616841 9.600000e-107 398
13 TraesCS6B01G224400 chr2D 81.847 314 46 8 1802 2110 383339013 383339320 2.200000e-63 254
14 TraesCS6B01G224400 chr2A 89.831 826 75 6 1 822 706884917 706884097 0.000000e+00 1051
15 TraesCS6B01G224400 chr2A 90.236 635 56 3 1 629 68890177 68890811 0.000000e+00 824
16 TraesCS6B01G224400 chr2A 83.652 471 29 17 1 465 758080871 758080443 2.670000e-107 399
17 TraesCS6B01G224400 chr7D 89.614 828 71 5 1 822 621162488 621161670 0.000000e+00 1038
18 TraesCS6B01G224400 chr7D 77.899 914 160 27 1645 2538 623567882 623568773 9.080000e-147 531
19 TraesCS6B01G224400 chr3D 89.066 814 86 3 10 822 55369328 55368517 0.000000e+00 1007
20 TraesCS6B01G224400 chr1D 88.257 826 77 9 1 819 421086588 421087400 0.000000e+00 970
21 TraesCS6B01G224400 chr1D 83.594 896 124 18 1650 2538 158110485 158111364 0.000000e+00 819
22 TraesCS6B01G224400 chr2B 85.867 842 64 23 1 819 749884331 749885140 0.000000e+00 845
23 TraesCS6B01G224400 chr2B 85.865 665 54 12 177 822 412260783 412260140 0.000000e+00 671
24 TraesCS6B01G224400 chr2B 92.473 186 11 2 1 183 412262512 412262327 3.660000e-66 263
25 TraesCS6B01G224400 chr5A 91.013 612 46 1 56 667 651644808 651645410 0.000000e+00 817
26 TraesCS6B01G224400 chr5A 84.124 485 70 6 2057 2538 348716580 348717060 3.360000e-126 462
27 TraesCS6B01G224400 chr5A 81.026 585 84 18 1968 2548 350526536 350525975 1.570000e-119 440
28 TraesCS6B01G224400 chr5B 81.567 906 139 19 1645 2538 295379003 295379892 0.000000e+00 723
29 TraesCS6B01G224400 chr1A 81.453 895 136 17 1650 2538 224807384 224806514 0.000000e+00 706
30 TraesCS6B01G224400 chr5D 83.958 667 92 9 1645 2304 262837277 262837935 4.050000e-175 625
31 TraesCS6B01G224400 chr1B 81.718 454 60 14 1645 2092 222299117 222298681 1.630000e-94 357
32 TraesCS6B01G224400 chr4A 78.947 456 79 9 1650 2097 601183832 601184278 1.300000e-75 294


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 TraesCS6B01G224400 chr6B 341762161 341766923 4762 False 8796.000000 8796 100.000000 1 4763 1 chr6B.!!$F1 4762
1 TraesCS6B01G224400 chr6B 352247672 352248270 598 True 549.000000 549 83.855000 4181 4763 1 chr6B.!!$R1 582
2 TraesCS6B01G224400 chr6D 261008719 261011891 3172 True 2476.000000 2503 94.931000 832 4035 2 chr6D.!!$R1 3203
3 TraesCS6B01G224400 chr6A 369546808 369549980 3172 False 1352.666667 2093 91.353333 832 2645 3 chr6A.!!$F2 1813
4 TraesCS6B01G224400 chr6A 369573989 369575470 1481 False 1059.500000 1352 93.743500 2652 4035 2 chr6A.!!$F3 1383
5 TraesCS6B01G224400 chr6A 96434318 96435127 809 False 992.000000 992 88.779000 10 819 1 chr6A.!!$F1 809
6 TraesCS6B01G224400 chr3B 97752712 97753526 814 False 1114.000000 1114 91.352000 2 819 1 chr3B.!!$F1 817
7 TraesCS6B01G224400 chr2D 629232705 629233529 824 True 1094.000000 1094 90.667000 1 822 1 chr2D.!!$R1 821
8 TraesCS6B01G224400 chr2D 183615977 183616841 864 False 398.000000 398 75.499000 1652 2542 1 chr2D.!!$F1 890
9 TraesCS6B01G224400 chr2A 706884097 706884917 820 True 1051.000000 1051 89.831000 1 822 1 chr2A.!!$R1 821
10 TraesCS6B01G224400 chr2A 68890177 68890811 634 False 824.000000 824 90.236000 1 629 1 chr2A.!!$F1 628
11 TraesCS6B01G224400 chr7D 621161670 621162488 818 True 1038.000000 1038 89.614000 1 822 1 chr7D.!!$R1 821
12 TraesCS6B01G224400 chr7D 623567882 623568773 891 False 531.000000 531 77.899000 1645 2538 1 chr7D.!!$F1 893
13 TraesCS6B01G224400 chr3D 55368517 55369328 811 True 1007.000000 1007 89.066000 10 822 1 chr3D.!!$R1 812
14 TraesCS6B01G224400 chr1D 421086588 421087400 812 False 970.000000 970 88.257000 1 819 1 chr1D.!!$F2 818
15 TraesCS6B01G224400 chr1D 158110485 158111364 879 False 819.000000 819 83.594000 1650 2538 1 chr1D.!!$F1 888
16 TraesCS6B01G224400 chr2B 749884331 749885140 809 False 845.000000 845 85.867000 1 819 1 chr2B.!!$F1 818
17 TraesCS6B01G224400 chr2B 412260140 412262512 2372 True 467.000000 671 89.169000 1 822 2 chr2B.!!$R1 821
18 TraesCS6B01G224400 chr5A 651644808 651645410 602 False 817.000000 817 91.013000 56 667 1 chr5A.!!$F2 611
19 TraesCS6B01G224400 chr5A 350525975 350526536 561 True 440.000000 440 81.026000 1968 2548 1 chr5A.!!$R1 580
20 TraesCS6B01G224400 chr5B 295379003 295379892 889 False 723.000000 723 81.567000 1645 2538 1 chr5B.!!$F1 893
21 TraesCS6B01G224400 chr1A 224806514 224807384 870 True 706.000000 706 81.453000 1650 2538 1 chr1A.!!$R1 888
22 TraesCS6B01G224400 chr5D 262837277 262837935 658 False 625.000000 625 83.958000 1645 2304 1 chr5D.!!$F1 659

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
826 2428 0.244994 GCAACCAAACACACCACACA 59.755 50.0 0.00 0.0 0.0 3.72 F
1111 2713 0.037303 ACCTCGTACTTCTCACCCGA 59.963 55.0 0.00 0.0 0.0 5.14 F
2007 3630 0.095935 CTTTCTCCGCAGCGACAATG 59.904 55.0 18.75 0.0 0.0 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 3674 0.534412 CTTCCACGAGCTCCATGACT 59.466 55.0 8.47 0.00 0.00 3.41 R
2467 5525 0.960364 GCCGTTTTGCAGGATCTCCA 60.960 55.0 0.00 0.00 38.89 3.86 R
3963 7126 0.322816 TCAATCAAGGCTGGCAGTCC 60.323 55.0 16.87 16.94 0.00 3.85 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
144 151 3.118956 ACGGCGAAGAAGAAGAAGATGAT 60.119 43.478 16.62 0.00 0.00 2.45
266 1823 1.369091 CCCGAAATCCACCTTCTGCG 61.369 60.000 0.00 0.00 0.00 5.18
269 1826 1.535462 CGAAATCCACCTTCTGCGTTT 59.465 47.619 0.00 0.00 0.00 3.60
288 1845 5.741425 CGTTTCGATCTTGCATGTATGAAT 58.259 37.500 3.56 0.00 0.00 2.57
309 1866 6.257849 TGAATTCGTATGAACTGCTATGAACC 59.742 38.462 0.00 0.00 36.81 3.62
578 2176 1.831736 ACGGTGAGGCTAATAACTGCT 59.168 47.619 0.00 0.00 0.00 4.24
582 2180 3.134081 GGTGAGGCTAATAACTGCTGGTA 59.866 47.826 0.00 0.00 0.00 3.25
703 2302 1.598130 GCGTTTCCAGTGAGCCAGT 60.598 57.895 0.00 0.00 0.00 4.00
710 2309 1.483595 CCAGTGAGCCAGTCCCAGAA 61.484 60.000 0.00 0.00 0.00 3.02
724 2323 5.474876 CAGTCCCAGAAATGCTTTAAGAAGT 59.525 40.000 0.00 0.00 35.25 3.01
736 2335 2.741759 TAAGAAGTGTGCGATGCAGA 57.258 45.000 0.00 0.00 40.08 4.26
754 2353 6.538945 TGCAGACCTAATAATATATGCGGA 57.461 37.500 0.00 0.00 35.23 5.54
780 2379 3.323691 TCAAACAGACCGAATCCTTCTCA 59.676 43.478 0.00 0.00 0.00 3.27
823 2425 4.825377 GGCAACCAAACACACCAC 57.175 55.556 0.00 0.00 0.00 4.16
824 2426 1.893786 GGCAACCAAACACACCACA 59.106 52.632 0.00 0.00 0.00 4.17
825 2427 0.459411 GGCAACCAAACACACCACAC 60.459 55.000 0.00 0.00 0.00 3.82
826 2428 0.244994 GCAACCAAACACACCACACA 59.755 50.000 0.00 0.00 0.00 3.72
827 2429 1.989430 CAACCAAACACACCACACAC 58.011 50.000 0.00 0.00 0.00 3.82
828 2430 0.892063 AACCAAACACACCACACACC 59.108 50.000 0.00 0.00 0.00 4.16
829 2431 0.968393 ACCAAACACACCACACACCC 60.968 55.000 0.00 0.00 0.00 4.61
830 2432 0.682855 CCAAACACACCACACACCCT 60.683 55.000 0.00 0.00 0.00 4.34
913 2515 1.891919 TGCTCCGTGCTTTGACCAC 60.892 57.895 0.00 0.00 43.37 4.16
916 2518 1.238439 CTCCGTGCTTTGACCACAAT 58.762 50.000 0.00 0.00 35.85 2.71
921 2523 0.950836 TGCTTTGACCACAATCACCG 59.049 50.000 0.00 0.00 35.85 4.94
988 2590 1.072538 TGAGTTTTCCCCTCCCCCA 60.073 57.895 0.00 0.00 0.00 4.96
1050 2652 1.892819 GCAGCCACTACCTCAGCTCA 61.893 60.000 0.00 0.00 31.93 4.26
1111 2713 0.037303 ACCTCGTACTTCTCACCCGA 59.963 55.000 0.00 0.00 0.00 5.14
1185 2787 4.139420 CTCAAGCTCAACGCCGCG 62.139 66.667 12.14 12.14 40.39 6.46
1253 2855 3.087906 GGAGCCGGGCCCTAAGAA 61.088 66.667 22.43 0.00 0.00 2.52
1266 2868 2.302157 CCCTAAGAACCAGAACCTCGTT 59.698 50.000 0.00 0.00 0.00 3.85
1277 2879 3.267974 CCTCGTTGAGGCCAAAGC 58.732 61.111 5.01 0.00 43.29 3.51
1278 2880 1.600636 CCTCGTTGAGGCCAAAGCA 60.601 57.895 5.01 0.00 43.29 3.91
1279 2881 0.962356 CCTCGTTGAGGCCAAAGCAT 60.962 55.000 5.01 0.00 43.29 3.79
1570 3175 4.047822 GCACATTGTTGAAATCGTTTGGA 58.952 39.130 0.00 0.00 0.00 3.53
1582 3187 1.202604 TCGTTTGGAGTTGTGGACCTC 60.203 52.381 0.00 0.00 0.00 3.85
1628 3233 7.061054 TGCAGTGGTAGTAGAAGTAGATATGT 58.939 38.462 0.00 0.00 0.00 2.29
1675 3280 1.412710 AGCAGATCCGCTAAAATCCGA 59.587 47.619 0.29 0.00 41.55 4.55
1697 3309 5.064198 CGATACTGCAAAATCGTTTTAGGGA 59.936 40.000 17.80 0.00 40.01 4.20
1748 3360 3.781307 CCCCGGCGGAACTGATCA 61.781 66.667 30.79 0.00 0.00 2.92
1811 3423 7.244192 GCTAGAAAATAGTTCATCACAACCAC 58.756 38.462 0.00 0.00 0.00 4.16
1871 3492 1.931172 ACAAAAAGTCGACGGTCACTG 59.069 47.619 10.46 6.86 0.00 3.66
1942 3563 4.379243 CGTGCTCCTCCTTGGCGT 62.379 66.667 0.00 0.00 35.26 5.68
1944 3565 2.922503 TGCTCCTCCTTGGCGTCA 60.923 61.111 0.00 0.00 35.26 4.35
1960 3583 0.803117 GTCAGAGACGGTCGATGACA 59.197 55.000 28.40 7.87 36.99 3.58
1961 3584 0.803117 TCAGAGACGGTCGATGACAC 59.197 55.000 12.39 0.00 33.68 3.67
1962 3585 0.179161 CAGAGACGGTCGATGACACC 60.179 60.000 9.22 0.00 33.68 4.16
1982 3605 1.000521 TACCTTCTTCTCCGGCCGA 60.001 57.895 30.73 12.25 0.00 5.54
1998 3621 1.227999 CCGACAAAGCTTTCTCCGCA 61.228 55.000 9.23 0.00 0.00 5.69
2007 3630 0.095935 CTTTCTCCGCAGCGACAATG 59.904 55.000 18.75 0.00 0.00 2.82
2051 3674 2.083774 CTGCAAATGCGGGAAGAGTTA 58.916 47.619 6.32 0.00 45.83 2.24
2120 3743 4.221422 GAGCCGGCCATAGTCGCA 62.221 66.667 26.15 0.00 40.68 5.10
2409 5467 1.074775 GGAATGGATATGCGGGCCA 59.925 57.895 4.39 0.00 35.91 5.36
2467 5525 3.636764 GGATCTGTTCGGGCCAATAAAAT 59.363 43.478 4.39 0.00 0.00 1.82
2620 5680 3.723097 TTTTGGAGGTGGCGTGGCA 62.723 57.895 0.00 0.00 0.00 4.92
2682 5742 4.525100 GGCACTTTTATGGGAAGGTTTACA 59.475 41.667 0.00 0.00 0.00 2.41
2707 5768 1.202940 GGGTCATTTCCCCCTAGATGC 60.203 57.143 0.00 0.00 41.54 3.91
2719 5780 1.770658 CCTAGATGCAGGGGATGTTGA 59.229 52.381 0.00 0.00 31.47 3.18
3031 6093 0.447801 GGTATGCAGCACAAGGAACG 59.552 55.000 0.00 0.00 0.00 3.95
3079 6141 2.224769 CCCATTGTTGTGTAGTCCTGGT 60.225 50.000 0.00 0.00 0.00 4.00
3085 6147 3.199071 TGTTGTGTAGTCCTGGTCTTGTT 59.801 43.478 0.00 0.00 0.00 2.83
3086 6148 3.746045 TGTGTAGTCCTGGTCTTGTTC 57.254 47.619 0.00 0.00 0.00 3.18
3087 6149 2.367567 TGTGTAGTCCTGGTCTTGTTCC 59.632 50.000 0.00 0.00 0.00 3.62
3141 6217 4.263435 CTCCGTTCTAGTAGAAGAGGTGT 58.737 47.826 23.40 0.00 34.42 4.16
3247 6407 1.437625 GCTGAAGGAAGTGAGACTGC 58.562 55.000 0.00 0.00 0.00 4.40
3248 6408 1.943507 GCTGAAGGAAGTGAGACTGCC 60.944 57.143 0.00 0.00 44.82 4.85
3264 6424 2.503356 ACTGCCATTTGTTCCCAAAACA 59.497 40.909 0.00 0.00 43.43 2.83
3327 6490 6.174720 TCCATAGTTGTTTCTGTGAAGAGT 57.825 37.500 0.00 0.00 0.00 3.24
3346 6509 9.936759 TGAAGAGTTTTAAAATGTTCAAACCTT 57.063 25.926 13.71 5.68 33.22 3.50
3466 6629 7.995463 TTTTCCCTTGTTTATTTTGTTCTCG 57.005 32.000 0.00 0.00 0.00 4.04
3566 6729 1.336755 CCGTTTTGTGCAGCCTTAAGT 59.663 47.619 0.97 0.00 0.00 2.24
3610 6773 1.973138 CTTGCTGCAGGAATTTGACG 58.027 50.000 21.68 4.65 0.00 4.35
3798 6961 8.277197 TCAGTTTATTAGGTAGTCTAGGTGCTA 58.723 37.037 0.00 0.00 0.00 3.49
3904 7067 8.671384 TGTTATAACTTCCATGTATTAGCACC 57.329 34.615 16.33 0.00 0.00 5.01
3922 7085 2.033801 CACCTGTTGACTTTCAAGGCTG 59.966 50.000 0.00 0.00 37.00 4.85
3936 7099 0.691413 AGGCTGGCCTTAGGAGGTAC 60.691 60.000 8.50 0.00 45.70 3.34
3937 7100 0.691413 GGCTGGCCTTAGGAGGTACT 60.691 60.000 3.32 0.00 45.44 2.73
3938 7101 1.412649 GGCTGGCCTTAGGAGGTACTA 60.413 57.143 3.32 0.00 45.44 1.82
3944 7107 4.897670 TGGCCTTAGGAGGTACTAACATAC 59.102 45.833 3.32 0.00 45.44 2.39
3951 7114 5.386924 AGGAGGTACTAACATACTGCCTAG 58.613 45.833 0.00 0.00 41.55 3.02
3963 7126 1.279271 ACTGCCTAGGCTTGTAACCTG 59.721 52.381 33.07 13.97 42.51 4.00
4019 7182 1.059006 CCTAGCTCCAGGGCTTCCAT 61.059 60.000 0.00 0.00 42.97 3.41
4035 7198 5.450965 GGCTTCCATCATTGTAATTCCACTG 60.451 44.000 0.00 0.00 0.00 3.66
4036 7199 5.450965 GCTTCCATCATTGTAATTCCACTGG 60.451 44.000 0.00 0.00 0.00 4.00
4037 7200 5.449297 TCCATCATTGTAATTCCACTGGA 57.551 39.130 0.00 0.00 0.00 3.86
4038 7201 5.439721 TCCATCATTGTAATTCCACTGGAG 58.560 41.667 0.00 0.00 31.21 3.86
4039 7202 4.581824 CCATCATTGTAATTCCACTGGAGG 59.418 45.833 0.00 0.00 31.21 4.30
4040 7203 4.927267 TCATTGTAATTCCACTGGAGGT 57.073 40.909 0.00 0.00 31.21 3.85
4041 7204 4.588899 TCATTGTAATTCCACTGGAGGTG 58.411 43.478 0.00 0.00 44.96 4.00
4042 7205 4.042809 TCATTGTAATTCCACTGGAGGTGT 59.957 41.667 0.00 0.00 43.94 4.16
4043 7206 4.447138 TTGTAATTCCACTGGAGGTGTT 57.553 40.909 0.00 0.00 43.94 3.32
4044 7207 4.447138 TGTAATTCCACTGGAGGTGTTT 57.553 40.909 0.00 0.00 43.94 2.83
4045 7208 4.141287 TGTAATTCCACTGGAGGTGTTTG 58.859 43.478 0.00 0.00 43.94 2.93
4046 7209 3.312736 AATTCCACTGGAGGTGTTTGT 57.687 42.857 0.00 0.00 43.94 2.83
4047 7210 2.818751 TTCCACTGGAGGTGTTTGTT 57.181 45.000 0.00 0.00 43.94 2.83
4048 7211 2.818751 TCCACTGGAGGTGTTTGTTT 57.181 45.000 0.00 0.00 43.94 2.83
4049 7212 3.094484 TCCACTGGAGGTGTTTGTTTT 57.906 42.857 0.00 0.00 43.94 2.43
4050 7213 2.757868 TCCACTGGAGGTGTTTGTTTTG 59.242 45.455 0.00 0.00 43.94 2.44
4051 7214 2.159114 CCACTGGAGGTGTTTGTTTTGG 60.159 50.000 0.00 0.00 43.94 3.28
4052 7215 2.107366 ACTGGAGGTGTTTGTTTTGGG 58.893 47.619 0.00 0.00 0.00 4.12
4053 7216 0.827368 TGGAGGTGTTTGTTTTGGGC 59.173 50.000 0.00 0.00 0.00 5.36
4054 7217 0.827368 GGAGGTGTTTGTTTTGGGCA 59.173 50.000 0.00 0.00 0.00 5.36
4055 7218 1.208293 GGAGGTGTTTGTTTTGGGCAA 59.792 47.619 0.00 0.00 0.00 4.52
4056 7219 2.355209 GGAGGTGTTTGTTTTGGGCAAA 60.355 45.455 0.00 0.00 33.96 3.68
4057 7220 3.339141 GAGGTGTTTGTTTTGGGCAAAA 58.661 40.909 0.00 0.00 37.54 2.44
4058 7221 3.944650 GAGGTGTTTGTTTTGGGCAAAAT 59.055 39.130 0.00 0.00 41.64 1.82
4059 7222 3.693578 AGGTGTTTGTTTTGGGCAAAATG 59.306 39.130 0.00 0.00 41.64 2.32
4060 7223 3.433709 GTGTTTGTTTTGGGCAAAATGC 58.566 40.909 0.00 0.00 41.64 3.56
4071 7234 1.708822 GCAAAATGCCCCGTTAACTG 58.291 50.000 3.71 0.00 37.42 3.16
4072 7235 1.000394 GCAAAATGCCCCGTTAACTGT 60.000 47.619 3.71 0.00 37.42 3.55
4073 7236 2.547007 GCAAAATGCCCCGTTAACTGTT 60.547 45.455 3.71 0.00 37.42 3.16
4074 7237 3.723260 CAAAATGCCCCGTTAACTGTTT 58.277 40.909 3.71 0.00 0.00 2.83
4075 7238 4.796618 GCAAAATGCCCCGTTAACTGTTTA 60.797 41.667 3.71 0.00 37.42 2.01
4076 7239 4.508461 AAATGCCCCGTTAACTGTTTAC 57.492 40.909 3.71 0.00 0.00 2.01
4077 7240 1.510776 TGCCCCGTTAACTGTTTACG 58.489 50.000 21.14 21.14 0.00 3.18
4078 7241 0.798159 GCCCCGTTAACTGTTTACGG 59.202 55.000 32.55 32.55 42.91 4.02
4079 7242 1.877680 GCCCCGTTAACTGTTTACGGT 60.878 52.381 34.70 1.89 41.84 4.83
4080 7243 1.799994 CCCCGTTAACTGTTTACGGTG 59.200 52.381 34.70 26.54 41.84 4.94
4081 7244 1.799994 CCCGTTAACTGTTTACGGTGG 59.200 52.381 34.70 23.41 41.84 4.61
4082 7245 2.547642 CCCGTTAACTGTTTACGGTGGA 60.548 50.000 34.70 1.34 41.84 4.02
4083 7246 3.129871 CCGTTAACTGTTTACGGTGGAA 58.870 45.455 31.65 3.87 38.94 3.53
4084 7247 3.559242 CCGTTAACTGTTTACGGTGGAAA 59.441 43.478 31.65 3.22 38.94 3.13
4085 7248 4.517287 CGTTAACTGTTTACGGTGGAAAC 58.483 43.478 20.55 5.76 37.32 2.78
4086 7249 4.552572 CGTTAACTGTTTACGGTGGAAACC 60.553 45.833 20.55 0.00 36.20 3.27
4087 7250 2.713863 ACTGTTTACGGTGGAAACCA 57.286 45.000 2.40 0.00 36.20 3.67
4088 7251 3.002038 ACTGTTTACGGTGGAAACCAA 57.998 42.857 2.40 0.00 36.20 3.67
4089 7252 3.354467 ACTGTTTACGGTGGAAACCAAA 58.646 40.909 2.40 0.00 36.20 3.28
4090 7253 3.762823 ACTGTTTACGGTGGAAACCAAAA 59.237 39.130 2.40 0.00 36.20 2.44
4091 7254 4.220163 ACTGTTTACGGTGGAAACCAAAAA 59.780 37.500 2.40 0.00 36.20 1.94
4092 7255 4.492611 TGTTTACGGTGGAAACCAAAAAC 58.507 39.130 12.04 12.04 36.20 2.43
4093 7256 3.417690 TTACGGTGGAAACCAAAAACG 57.582 42.857 0.00 0.00 34.18 3.60
4094 7257 1.175654 ACGGTGGAAACCAAAAACGT 58.824 45.000 0.00 0.00 34.18 3.99
4095 7258 1.545136 ACGGTGGAAACCAAAAACGTT 59.455 42.857 0.00 0.00 34.18 3.99
4096 7259 2.751806 ACGGTGGAAACCAAAAACGTTA 59.248 40.909 0.00 0.00 34.18 3.18
4097 7260 3.107407 CGGTGGAAACCAAAAACGTTAC 58.893 45.455 0.00 0.00 34.18 2.50
4098 7261 3.107407 GGTGGAAACCAAAAACGTTACG 58.893 45.455 0.00 2.19 34.18 3.18
4099 7262 2.531103 GTGGAAACCAAAAACGTTACGC 59.469 45.455 4.09 0.00 34.18 4.42
4100 7263 2.163010 TGGAAACCAAAAACGTTACGCA 59.837 40.909 4.09 0.00 0.00 5.24
4101 7264 2.531103 GGAAACCAAAAACGTTACGCAC 59.469 45.455 4.09 0.00 0.00 5.34
4111 7274 2.201188 CGTTACGCACGTTTGGTAAG 57.799 50.000 0.00 0.00 44.49 2.34
4112 7275 1.522258 CGTTACGCACGTTTGGTAAGT 59.478 47.619 0.00 0.00 44.49 2.24
4113 7276 2.657162 CGTTACGCACGTTTGGTAAGTG 60.657 50.000 0.00 0.00 44.49 3.16
4114 7277 2.222007 TACGCACGTTTGGTAAGTGT 57.778 45.000 0.00 0.00 38.10 3.55
4115 7278 2.222007 ACGCACGTTTGGTAAGTGTA 57.778 45.000 0.00 0.00 38.10 2.90
4116 7279 1.860326 ACGCACGTTTGGTAAGTGTAC 59.140 47.619 0.00 0.00 38.10 2.90
4117 7280 1.136830 CGCACGTTTGGTAAGTGTACG 60.137 52.381 0.00 0.00 38.10 3.67
4118 7281 1.860326 GCACGTTTGGTAAGTGTACGT 59.140 47.619 0.00 0.00 45.21 3.57
4120 7283 3.163630 ACGTTTGGTAAGTGTACGTGT 57.836 42.857 0.00 0.00 43.02 4.49
4121 7284 4.300189 ACGTTTGGTAAGTGTACGTGTA 57.700 40.909 0.00 0.00 43.02 2.90
4122 7285 4.677584 ACGTTTGGTAAGTGTACGTGTAA 58.322 39.130 0.00 0.00 43.02 2.41
4123 7286 5.288804 ACGTTTGGTAAGTGTACGTGTAAT 58.711 37.500 0.00 0.00 43.02 1.89
4124 7287 5.402270 ACGTTTGGTAAGTGTACGTGTAATC 59.598 40.000 0.00 0.00 43.02 1.75
4125 7288 5.164061 CGTTTGGTAAGTGTACGTGTAATCC 60.164 44.000 0.00 0.00 0.00 3.01
4126 7289 4.095410 TGGTAAGTGTACGTGTAATCCG 57.905 45.455 0.00 0.00 0.00 4.18
4127 7290 3.755905 TGGTAAGTGTACGTGTAATCCGA 59.244 43.478 0.00 0.00 0.00 4.55
4128 7291 4.398988 TGGTAAGTGTACGTGTAATCCGAT 59.601 41.667 0.00 0.00 0.00 4.18
4129 7292 4.736793 GGTAAGTGTACGTGTAATCCGATG 59.263 45.833 0.00 0.00 0.00 3.84
4130 7293 2.805845 AGTGTACGTGTAATCCGATGC 58.194 47.619 0.00 0.00 0.00 3.91
4131 7294 1.856597 GTGTACGTGTAATCCGATGCC 59.143 52.381 0.00 0.00 0.00 4.40
4132 7295 1.752498 TGTACGTGTAATCCGATGCCT 59.248 47.619 0.00 0.00 0.00 4.75
4133 7296 2.223641 TGTACGTGTAATCCGATGCCTC 60.224 50.000 0.00 0.00 0.00 4.70
4134 7297 0.104304 ACGTGTAATCCGATGCCTCC 59.896 55.000 0.00 0.00 0.00 4.30
4135 7298 0.939577 CGTGTAATCCGATGCCTCCG 60.940 60.000 0.00 0.00 0.00 4.63
4136 7299 1.069090 TGTAATCCGATGCCTCCGC 59.931 57.895 0.00 0.00 0.00 5.54
4151 7314 2.978010 CGCAAACGGTTCCAGGCT 60.978 61.111 0.00 0.00 34.97 4.58
4152 7315 2.551912 CGCAAACGGTTCCAGGCTT 61.552 57.895 0.00 0.00 34.97 4.35
4153 7316 1.007387 GCAAACGGTTCCAGGCTTG 60.007 57.895 0.00 0.00 0.00 4.01
4154 7317 1.007387 CAAACGGTTCCAGGCTTGC 60.007 57.895 0.00 0.00 0.00 4.01
4155 7318 1.152756 AAACGGTTCCAGGCTTGCT 60.153 52.632 0.00 0.00 0.00 3.91
4156 7319 1.455383 AAACGGTTCCAGGCTTGCTG 61.455 55.000 0.00 0.00 0.00 4.41
4157 7320 2.281761 CGGTTCCAGGCTTGCTGT 60.282 61.111 0.00 0.00 0.00 4.40
4158 7321 2.620112 CGGTTCCAGGCTTGCTGTG 61.620 63.158 0.00 0.00 0.00 3.66
4159 7322 2.270986 GGTTCCAGGCTTGCTGTGG 61.271 63.158 7.81 7.81 0.00 4.17
4160 7323 1.228245 GTTCCAGGCTTGCTGTGGA 60.228 57.895 11.38 11.38 38.65 4.02
4161 7324 0.610232 GTTCCAGGCTTGCTGTGGAT 60.610 55.000 14.65 0.00 40.11 3.41
4162 7325 0.322816 TTCCAGGCTTGCTGTGGATC 60.323 55.000 14.65 0.00 40.11 3.36
4163 7326 2.110967 CCAGGCTTGCTGTGGATCG 61.111 63.158 8.26 0.00 32.60 3.69
4164 7327 1.078918 CAGGCTTGCTGTGGATCGA 60.079 57.895 0.00 0.00 0.00 3.59
4165 7328 0.463295 CAGGCTTGCTGTGGATCGAT 60.463 55.000 0.00 0.00 0.00 3.59
4166 7329 1.123077 AGGCTTGCTGTGGATCGATA 58.877 50.000 0.00 0.00 0.00 2.92
4167 7330 1.202580 AGGCTTGCTGTGGATCGATAC 60.203 52.381 0.00 0.00 0.00 2.24
4168 7331 1.221414 GCTTGCTGTGGATCGATACC 58.779 55.000 4.85 6.08 0.00 2.73
4169 7332 1.473257 GCTTGCTGTGGATCGATACCA 60.473 52.381 4.85 8.72 34.84 3.25
4175 7338 2.120765 TGGATCGATACCACCCACG 58.879 57.895 4.85 0.00 32.03 4.94
4176 7339 0.396001 TGGATCGATACCACCCACGA 60.396 55.000 4.85 0.00 39.01 4.35
4177 7340 0.031721 GGATCGATACCACCCACGAC 59.968 60.000 0.00 0.00 37.58 4.34
4178 7341 0.031721 GATCGATACCACCCACGACC 59.968 60.000 0.00 0.00 37.58 4.79
4179 7342 1.397390 ATCGATACCACCCACGACCC 61.397 60.000 0.00 0.00 37.58 4.46
4232 7395 2.493278 GCATTGGCACACTTTATCCACT 59.507 45.455 0.00 0.00 39.29 4.00
4237 7400 1.732259 GCACACTTTATCCACTCCGTG 59.268 52.381 0.00 0.00 0.00 4.94
4243 7406 1.262417 TTATCCACTCCGTGTGCTGA 58.738 50.000 0.89 0.00 44.92 4.26
4244 7407 0.530744 TATCCACTCCGTGTGCTGAC 59.469 55.000 0.89 0.00 44.92 3.51
4248 7411 2.341543 CTCCGTGTGCTGACTGCT 59.658 61.111 5.87 0.00 43.37 4.24
4251 7414 2.661566 CCGTGTGCTGACTGCTTCG 61.662 63.158 5.87 7.42 43.37 3.79
4267 7430 1.402968 CTTCGTGATTGGGCCAATGAG 59.597 52.381 35.23 23.65 33.90 2.90
4287 7450 1.875576 GCGACAGCCTGGAATATGGAG 60.876 57.143 0.00 0.00 37.42 3.86
4308 7471 5.462398 GGAGCAATACGTGGAACTTATACTG 59.538 44.000 0.00 0.00 29.02 2.74
4317 7480 2.545113 GGAACTTATACTGCGCGGATGA 60.545 50.000 25.98 8.04 0.00 2.92
4318 7481 2.882927 ACTTATACTGCGCGGATGAA 57.117 45.000 25.98 11.88 0.00 2.57
4327 7490 2.034879 CGCGGATGAAGGTGCTGTT 61.035 57.895 0.00 0.00 0.00 3.16
4345 7508 1.252904 TTGGGAGAGGTTACGGTCCG 61.253 60.000 10.48 10.48 0.00 4.79
4350 7513 0.605083 AGAGGTTACGGTCCGGTTTC 59.395 55.000 17.28 5.88 0.00 2.78
4351 7514 0.390340 GAGGTTACGGTCCGGTTTCC 60.390 60.000 17.28 11.95 0.00 3.13
4358 7521 2.258726 GGTCCGGTTTCCAGTGTGC 61.259 63.158 0.00 0.00 0.00 4.57
4362 7525 0.250124 CCGGTTTCCAGTGTGCTACA 60.250 55.000 0.00 0.00 0.00 2.74
4377 7540 2.029623 GCTACACCACCGAATCCTCTA 58.970 52.381 0.00 0.00 0.00 2.43
4382 7545 0.105039 CCACCGAATCCTCTAGCACC 59.895 60.000 0.00 0.00 0.00 5.01
4393 7556 2.503356 CCTCTAGCACCTGTTCCAGATT 59.497 50.000 0.00 0.00 32.44 2.40
4398 7561 4.640771 AGCACCTGTTCCAGATTTCTTA 57.359 40.909 0.00 0.00 32.44 2.10
4399 7562 4.327680 AGCACCTGTTCCAGATTTCTTAC 58.672 43.478 0.00 0.00 32.44 2.34
4404 7567 6.037610 CACCTGTTCCAGATTTCTTACATAGC 59.962 42.308 0.00 0.00 32.44 2.97
4407 7570 5.586243 TGTTCCAGATTTCTTACATAGCTGC 59.414 40.000 0.00 0.00 0.00 5.25
4408 7571 4.708177 TCCAGATTTCTTACATAGCTGCC 58.292 43.478 0.00 0.00 0.00 4.85
4412 7575 5.119898 CAGATTTCTTACATAGCTGCCGATC 59.880 44.000 0.00 0.00 0.00 3.69
4414 7577 3.924918 TCTTACATAGCTGCCGATCTC 57.075 47.619 0.00 0.00 0.00 2.75
4425 7588 0.179097 GCCGATCTCAGAACAGGTCC 60.179 60.000 0.00 0.00 0.00 4.46
4430 7593 3.447586 CGATCTCAGAACAGGTCCCTTTA 59.552 47.826 0.00 0.00 0.00 1.85
4431 7594 4.678309 CGATCTCAGAACAGGTCCCTTTAC 60.678 50.000 0.00 0.00 0.00 2.01
4452 7629 0.031857 TGGCACAAATTGTTCTGGCG 59.968 50.000 0.00 0.00 31.92 5.69
4477 7662 0.341961 AGTGGGGTAGGACCAGCATA 59.658 55.000 0.00 0.00 41.02 3.14
4499 7684 3.099267 ACATAGTCGACATTAGCCAGC 57.901 47.619 19.50 0.00 0.00 4.85
4512 7697 2.109799 CCAGCCAGGCCGTCATAG 59.890 66.667 8.22 0.00 0.00 2.23
4515 7700 2.203070 GCCAGGCCGTCATAGTGG 60.203 66.667 0.00 0.00 0.00 4.00
4521 7706 1.327690 GGCCGTCATAGTGGACCTCA 61.328 60.000 0.00 0.00 34.24 3.86
4522 7707 0.103208 GCCGTCATAGTGGACCTCAG 59.897 60.000 0.00 0.00 34.24 3.35
4523 7708 1.763968 CCGTCATAGTGGACCTCAGA 58.236 55.000 0.00 0.00 34.24 3.27
4525 7710 2.159226 CCGTCATAGTGGACCTCAGAAC 60.159 54.545 0.00 0.00 34.24 3.01
4530 7715 4.838423 TCATAGTGGACCTCAGAACAGAAA 59.162 41.667 0.00 0.00 0.00 2.52
4562 7747 3.065510 TCGTCTCTCATCGTTTCAGATCC 59.934 47.826 0.00 0.00 0.00 3.36
4566 7751 4.646492 TCTCTCATCGTTTCAGATCCATCA 59.354 41.667 0.00 0.00 0.00 3.07
4567 7752 5.303845 TCTCTCATCGTTTCAGATCCATCAT 59.696 40.000 0.00 0.00 0.00 2.45
4570 7755 6.825213 TCTCATCGTTTCAGATCCATCATTTT 59.175 34.615 0.00 0.00 0.00 1.82
4581 7766 3.911868 TCCATCATTTTGAAACCTTGCG 58.088 40.909 0.00 0.00 0.00 4.85
4582 7767 2.995258 CCATCATTTTGAAACCTTGCGG 59.005 45.455 0.00 0.00 0.00 5.69
4624 7809 4.142966 GGACGGAAATCTAAGGTTCGTTTG 60.143 45.833 0.00 0.00 0.00 2.93
4628 7813 5.623673 CGGAAATCTAAGGTTCGTTTGTTTG 59.376 40.000 0.00 0.00 0.00 2.93
4633 7818 5.882553 TCTAAGGTTCGTTTGTTTGAAACC 58.117 37.500 5.50 0.00 32.13 3.27
4645 7830 5.146010 TGTTTGAAACCTTCTGCAAGTTT 57.854 34.783 5.50 4.13 33.76 2.66
4650 7835 6.463995 TGAAACCTTCTGCAAGTTTTGTAT 57.536 33.333 5.59 0.00 33.76 2.29
4652 7837 4.749245 ACCTTCTGCAAGTTTTGTATCG 57.251 40.909 0.00 0.00 33.76 2.92
4653 7838 3.058224 ACCTTCTGCAAGTTTTGTATCGC 60.058 43.478 0.00 0.00 33.76 4.58
4660 7845 4.276183 TGCAAGTTTTGTATCGCCAACTTA 59.724 37.500 0.00 0.00 37.36 2.24
4670 7855 6.742109 TGTATCGCCAACTTAGTACTAATCC 58.258 40.000 15.57 2.79 0.00 3.01
4701 7886 9.959749 TGTTTCCACTATTTTTAGATCAACAAC 57.040 29.630 0.00 0.00 0.00 3.32
4717 7902 4.338118 TCAACAACTGGTTTGATTCCTGTC 59.662 41.667 0.00 0.00 37.72 3.51
4746 7931 3.599704 GGCGGCAAGGGATCATGC 61.600 66.667 3.07 8.41 41.82 4.06
4751 7936 1.188863 GGCAAGGGATCATGCTGTTT 58.811 50.000 14.51 0.00 42.20 2.83
4756 7941 1.637553 AGGGATCATGCTGTTTGTCCT 59.362 47.619 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 21 1.745115 GCATGTGCACCGCCTCTTA 60.745 57.895 15.69 0.00 41.59 2.10
206 1763 1.587066 GGGATAGGGGGTACACAACA 58.413 55.000 0.00 0.00 0.00 3.33
266 1823 6.355405 CGAATTCATACATGCAAGATCGAAAC 59.645 38.462 6.22 0.00 0.00 2.78
269 1826 5.049828 ACGAATTCATACATGCAAGATCGA 58.950 37.500 6.22 0.00 0.00 3.59
288 1845 5.079689 TGGTTCATAGCAGTTCATACGAA 57.920 39.130 0.00 0.00 0.00 3.85
309 1866 8.543774 AGATAAGCATAGGGGTAATTCATACTG 58.456 37.037 0.00 0.00 34.74 2.74
362 1919 2.560504 TGCACGCTTTATTCGATCCAT 58.439 42.857 0.00 0.00 0.00 3.41
373 1949 0.792640 CTCTTCGACATGCACGCTTT 59.207 50.000 7.82 0.00 0.00 3.51
462 2057 1.605058 AAGACCACCGGACTCCATCG 61.605 60.000 9.46 0.00 0.00 3.84
510 2108 0.916358 CCCACTCCCCCAACTCTCAT 60.916 60.000 0.00 0.00 0.00 2.90
522 2120 2.301738 CCCCACTCTTCCCCACTCC 61.302 68.421 0.00 0.00 0.00 3.85
578 2176 0.320073 CGTTGCTTCCCGAAGTACCA 60.320 55.000 6.34 0.00 40.45 3.25
582 2180 3.041940 CGCGTTGCTTCCCGAAGT 61.042 61.111 0.00 0.00 40.45 3.01
600 2198 4.421479 CGGCCACGCTCGAGAAGT 62.421 66.667 18.75 12.50 0.00 3.01
703 2302 5.241506 CACACTTCTTAAAGCATTTCTGGGA 59.758 40.000 0.00 0.00 40.09 4.37
710 2309 4.726416 CATCGCACACTTCTTAAAGCATT 58.274 39.130 0.00 0.00 35.81 3.56
724 2323 3.535280 TTATTAGGTCTGCATCGCACA 57.465 42.857 0.00 0.00 33.79 4.57
754 2353 5.420409 GAAGGATTCGGTCTGTTTGATAGT 58.580 41.667 0.00 0.00 34.17 2.12
819 2421 2.224209 CGAAAGACTAAGGGTGTGTGGT 60.224 50.000 0.00 0.00 0.00 4.16
822 2424 2.036862 GGACGAAAGACTAAGGGTGTGT 59.963 50.000 0.00 0.00 0.00 3.72
823 2425 2.612221 GGGACGAAAGACTAAGGGTGTG 60.612 54.545 0.00 0.00 0.00 3.82
824 2426 1.622312 GGGACGAAAGACTAAGGGTGT 59.378 52.381 0.00 0.00 0.00 4.16
825 2427 1.621814 TGGGACGAAAGACTAAGGGTG 59.378 52.381 0.00 0.00 0.00 4.61
826 2428 2.019807 TGGGACGAAAGACTAAGGGT 57.980 50.000 0.00 0.00 0.00 4.34
827 2429 2.158943 GGATGGGACGAAAGACTAAGGG 60.159 54.545 0.00 0.00 0.00 3.95
828 2430 2.158943 GGGATGGGACGAAAGACTAAGG 60.159 54.545 0.00 0.00 0.00 2.69
829 2431 2.158943 GGGGATGGGACGAAAGACTAAG 60.159 54.545 0.00 0.00 0.00 2.18
830 2432 1.835531 GGGGATGGGACGAAAGACTAA 59.164 52.381 0.00 0.00 0.00 2.24
988 2590 1.227556 GATCCATAACGGCAGCGGT 60.228 57.895 0.00 0.00 33.14 5.68
1050 2652 3.958147 CTTGGTGCGGCGGATGAGT 62.958 63.158 9.78 0.00 0.00 3.41
1097 2699 0.458025 CGGCTTCGGGTGAGAAGTAC 60.458 60.000 8.29 0.00 46.82 2.73
1111 2713 2.262915 CAGCTTCGTCTCCGGCTT 59.737 61.111 0.00 0.00 30.62 4.35
1275 2877 0.622665 CTTCCCTCTCCACCAATGCT 59.377 55.000 0.00 0.00 0.00 3.79
1277 2879 1.630369 TCACTTCCCTCTCCACCAATG 59.370 52.381 0.00 0.00 0.00 2.82
1278 2880 2.044793 TCACTTCCCTCTCCACCAAT 57.955 50.000 0.00 0.00 0.00 3.16
1279 2881 1.814429 TTCACTTCCCTCTCCACCAA 58.186 50.000 0.00 0.00 0.00 3.67
1451 3056 2.355108 GGATGCTGTACCTTCTTGAGCA 60.355 50.000 4.50 4.50 43.46 4.26
1570 3175 1.069765 CTGCACGAGGTCCACAACT 59.930 57.895 0.00 0.00 0.00 3.16
1582 3187 1.532437 TGACTGCATTTTCTCTGCACG 59.468 47.619 0.00 0.00 44.30 5.34
1675 3280 6.680378 GCATCCCTAAAACGATTTTGCAGTAT 60.680 38.462 6.83 0.00 34.19 2.12
1811 3423 8.213518 AGTTTGTATTTCCTATGTATGCACTG 57.786 34.615 0.00 0.00 0.00 3.66
1871 3492 1.655329 CTCTACCTCGGCATCGACC 59.345 63.158 0.00 0.00 40.88 4.79
1877 3498 1.609501 ACCAAGCTCTACCTCGGCA 60.610 57.895 0.00 0.00 0.00 5.69
1942 3563 0.803117 GTGTCATCGACCGTCTCTGA 59.197 55.000 0.00 0.00 0.00 3.27
1944 3565 2.181584 GGTGTCATCGACCGTCTCT 58.818 57.895 0.00 0.00 0.00 3.10
1960 3583 1.602327 GCCGGAGAAGAAGGTACGGT 61.602 60.000 5.05 0.00 42.98 4.83
1961 3584 1.141234 GCCGGAGAAGAAGGTACGG 59.859 63.158 5.05 0.00 43.81 4.02
1962 3585 1.141234 GGCCGGAGAAGAAGGTACG 59.859 63.158 5.05 0.00 0.00 3.67
1963 3586 1.141234 CGGCCGGAGAAGAAGGTAC 59.859 63.158 20.10 0.00 0.00 3.34
1964 3587 1.000521 TCGGCCGGAGAAGAAGGTA 60.001 57.895 27.83 0.00 0.00 3.08
1982 3605 1.845809 CGCTGCGGAGAAAGCTTTGT 61.846 55.000 18.30 13.50 36.74 2.83
2051 3674 0.534412 CTTCCACGAGCTCCATGACT 59.466 55.000 8.47 0.00 0.00 3.41
2164 3788 3.005539 ATGACACGGAGGCTGGCT 61.006 61.111 2.24 2.24 0.00 4.75
2371 5429 2.479730 CCTCCGATGCTATATGTACGGC 60.480 54.545 0.00 0.00 40.12 5.68
2467 5525 0.960364 GCCGTTTTGCAGGATCTCCA 60.960 55.000 0.00 0.00 38.89 3.86
2514 5574 2.036992 AGCATCTCTAGCAAATCCGGAG 59.963 50.000 11.34 0.00 0.00 4.63
2515 5575 2.036475 GAGCATCTCTAGCAAATCCGGA 59.964 50.000 6.61 6.61 0.00 5.14
2650 5710 2.478370 CCATAAAAGTGCCACATCAGCG 60.478 50.000 0.00 0.00 0.00 5.18
2656 5716 2.158385 ACCTTCCCATAAAAGTGCCACA 60.158 45.455 0.00 0.00 0.00 4.17
2659 5719 4.525100 TGTAAACCTTCCCATAAAAGTGCC 59.475 41.667 0.00 0.00 0.00 5.01
2660 5720 5.336451 CCTGTAAACCTTCCCATAAAAGTGC 60.336 44.000 0.00 0.00 0.00 4.40
2707 5768 2.431954 AATCTGCTCAACATCCCCTG 57.568 50.000 0.00 0.00 0.00 4.45
2719 5780 2.290323 GGCGGAACCCATATAATCTGCT 60.290 50.000 5.53 0.00 42.47 4.24
2993 6055 1.614051 CCAGATAGCCACTTTGGTGCA 60.614 52.381 0.00 0.00 40.46 4.57
3031 6093 1.160137 CTGACTACCTTTGCACTGGC 58.840 55.000 4.23 0.00 41.68 4.85
3085 6147 1.637338 ACATGCTCTCTGTCTGTGGA 58.363 50.000 0.00 0.00 0.00 4.02
3086 6148 2.159128 CCTACATGCTCTCTGTCTGTGG 60.159 54.545 0.00 0.00 0.00 4.17
3087 6149 2.757314 TCCTACATGCTCTCTGTCTGTG 59.243 50.000 0.00 0.00 0.00 3.66
3141 6217 4.263068 CCCTTTGCCTCTTCTCTTACAGAA 60.263 45.833 0.00 0.00 38.95 3.02
3159 6235 3.330701 TGACTAGCTTCCAATCACCCTTT 59.669 43.478 0.00 0.00 0.00 3.11
3162 6238 2.911484 CTGACTAGCTTCCAATCACCC 58.089 52.381 0.00 0.00 0.00 4.61
3264 6424 4.176753 AGGGCTAAAAGGTAGTTCTTCCT 58.823 43.478 0.00 0.00 35.34 3.36
3442 6605 6.477360 GCGAGAACAAAATAAACAAGGGAAAA 59.523 34.615 0.00 0.00 0.00 2.29
3466 6629 4.067192 ACAAATGAAAGAAATGGCCAAGC 58.933 39.130 10.96 1.33 0.00 4.01
3610 6773 4.530857 AGCAGGGCCGTATGACGC 62.531 66.667 0.00 0.00 40.91 5.19
3798 6961 4.223953 AGATGTTCCCATACGGACTACAT 58.776 43.478 0.00 0.00 42.46 2.29
3904 7067 1.000938 GCCAGCCTTGAAAGTCAACAG 60.001 52.381 0.00 0.00 32.21 3.16
3922 7085 8.409292 GCAGTATGTTAGTACCTCCTAAGGCC 62.409 50.000 0.00 0.00 42.58 5.19
3936 7099 4.408182 ACAAGCCTAGGCAGTATGTTAG 57.592 45.455 34.70 15.23 44.88 2.34
3937 7100 5.395990 GGTTACAAGCCTAGGCAGTATGTTA 60.396 44.000 34.70 22.16 44.88 2.41
3938 7101 4.514401 GTTACAAGCCTAGGCAGTATGTT 58.486 43.478 34.70 16.77 44.88 2.71
3944 7107 1.407437 CCAGGTTACAAGCCTAGGCAG 60.407 57.143 34.70 27.18 44.88 4.85
3951 7114 0.960861 GGCAGTCCAGGTTACAAGCC 60.961 60.000 0.00 0.00 34.57 4.35
3963 7126 0.322816 TCAATCAAGGCTGGCAGTCC 60.323 55.000 16.87 16.94 0.00 3.85
4019 7182 4.588899 CACCTCCAGTGGAATTACAATGA 58.411 43.478 19.51 5.07 43.26 2.57
4035 7198 0.827368 TGCCCAAAACAAACACCTCC 59.173 50.000 0.00 0.00 0.00 4.30
4036 7199 2.682155 TTGCCCAAAACAAACACCTC 57.318 45.000 0.00 0.00 0.00 3.85
4037 7200 3.425162 TTTTGCCCAAAACAAACACCT 57.575 38.095 2.26 0.00 36.77 4.00
4038 7201 3.733380 GCATTTTGCCCAAAACAAACACC 60.733 43.478 8.21 0.00 42.32 4.16
4039 7202 3.433709 GCATTTTGCCCAAAACAAACAC 58.566 40.909 8.21 0.00 42.32 3.32
4040 7203 3.772060 GCATTTTGCCCAAAACAAACA 57.228 38.095 8.21 0.00 42.32 2.83
4052 7215 1.000394 ACAGTTAACGGGGCATTTTGC 60.000 47.619 10.55 0.00 44.08 3.68
4053 7216 3.378911 AACAGTTAACGGGGCATTTTG 57.621 42.857 10.55 0.00 0.00 2.44
4054 7217 4.557097 CGTAAACAGTTAACGGGGCATTTT 60.557 41.667 10.55 4.07 0.00 1.82
4055 7218 3.058085 CGTAAACAGTTAACGGGGCATTT 60.058 43.478 10.55 4.40 0.00 2.32
4056 7219 2.485038 CGTAAACAGTTAACGGGGCATT 59.515 45.455 10.55 2.94 0.00 3.56
4057 7220 2.078392 CGTAAACAGTTAACGGGGCAT 58.922 47.619 10.55 0.00 0.00 4.40
4058 7221 1.510776 CGTAAACAGTTAACGGGGCA 58.489 50.000 10.55 0.00 0.00 5.36
4059 7222 0.798159 CCGTAAACAGTTAACGGGGC 59.202 55.000 10.55 0.00 39.96 5.80
4060 7223 1.799994 CACCGTAAACAGTTAACGGGG 59.200 52.381 16.51 9.43 46.95 5.73
4061 7224 1.799994 CCACCGTAAACAGTTAACGGG 59.200 52.381 16.51 4.87 46.95 5.28
4063 7226 4.517287 GTTTCCACCGTAAACAGTTAACG 58.483 43.478 0.00 0.00 36.92 3.18
4064 7227 4.847633 GGTTTCCACCGTAAACAGTTAAC 58.152 43.478 0.00 0.00 38.34 2.01
4077 7240 3.107407 CGTAACGTTTTTGGTTTCCACC 58.893 45.455 5.91 0.00 44.56 4.61
4078 7241 2.531103 GCGTAACGTTTTTGGTTTCCAC 59.469 45.455 5.91 0.00 30.78 4.02
4079 7242 2.163010 TGCGTAACGTTTTTGGTTTCCA 59.837 40.909 5.91 0.00 0.00 3.53
4080 7243 2.531103 GTGCGTAACGTTTTTGGTTTCC 59.469 45.455 5.91 0.00 0.00 3.13
4081 7244 3.804262 GTGCGTAACGTTTTTGGTTTC 57.196 42.857 5.91 0.00 0.00 2.78
4093 7256 2.284952 ACACTTACCAAACGTGCGTAAC 59.715 45.455 0.00 0.00 32.07 2.50
4094 7257 2.548875 ACACTTACCAAACGTGCGTAA 58.451 42.857 0.00 0.00 32.07 3.18
4095 7258 2.222007 ACACTTACCAAACGTGCGTA 57.778 45.000 0.00 0.00 32.07 4.42
4096 7259 1.860326 GTACACTTACCAAACGTGCGT 59.140 47.619 0.00 0.00 32.07 5.24
4097 7260 1.136830 CGTACACTTACCAAACGTGCG 60.137 52.381 0.00 0.00 32.07 5.34
4098 7261 1.860326 ACGTACACTTACCAAACGTGC 59.140 47.619 0.00 0.00 44.34 5.34
4100 7263 3.163630 ACACGTACACTTACCAAACGT 57.836 42.857 0.00 0.00 46.72 3.99
4101 7264 5.164061 GGATTACACGTACACTTACCAAACG 60.164 44.000 0.00 0.00 39.37 3.60
4102 7265 5.164061 CGGATTACACGTACACTTACCAAAC 60.164 44.000 0.00 0.00 0.00 2.93
4103 7266 4.922692 CGGATTACACGTACACTTACCAAA 59.077 41.667 0.00 0.00 0.00 3.28
4104 7267 4.217334 TCGGATTACACGTACACTTACCAA 59.783 41.667 0.00 0.00 0.00 3.67
4105 7268 3.755905 TCGGATTACACGTACACTTACCA 59.244 43.478 0.00 0.00 0.00 3.25
4106 7269 4.355543 TCGGATTACACGTACACTTACC 57.644 45.455 0.00 0.00 0.00 2.85
4107 7270 4.205792 GCATCGGATTACACGTACACTTAC 59.794 45.833 0.00 0.00 0.00 2.34
4108 7271 4.353737 GCATCGGATTACACGTACACTTA 58.646 43.478 0.00 0.00 0.00 2.24
4109 7272 3.184541 GCATCGGATTACACGTACACTT 58.815 45.455 0.00 0.00 0.00 3.16
4110 7273 2.480759 GGCATCGGATTACACGTACACT 60.481 50.000 0.00 0.00 0.00 3.55
4111 7274 1.856597 GGCATCGGATTACACGTACAC 59.143 52.381 0.00 0.00 0.00 2.90
4112 7275 1.752498 AGGCATCGGATTACACGTACA 59.248 47.619 0.00 0.00 0.00 2.90
4113 7276 2.391879 GAGGCATCGGATTACACGTAC 58.608 52.381 0.00 0.00 0.00 3.67
4114 7277 1.338973 GGAGGCATCGGATTACACGTA 59.661 52.381 0.00 0.00 0.00 3.57
4115 7278 0.104304 GGAGGCATCGGATTACACGT 59.896 55.000 0.00 0.00 0.00 4.49
4116 7279 0.939577 CGGAGGCATCGGATTACACG 60.940 60.000 0.00 0.00 0.00 4.49
4117 7280 1.222115 GCGGAGGCATCGGATTACAC 61.222 60.000 10.34 0.00 39.62 2.90
4118 7281 1.069090 GCGGAGGCATCGGATTACA 59.931 57.895 10.34 0.00 39.62 2.41
4119 7282 1.069090 TGCGGAGGCATCGGATTAC 59.931 57.895 10.34 0.00 46.21 1.89
4120 7283 3.544772 TGCGGAGGCATCGGATTA 58.455 55.556 10.34 0.00 46.21 1.75
4134 7297 2.551912 AAGCCTGGAACCGTTTGCG 61.552 57.895 0.00 0.00 37.95 4.85
4135 7298 1.007387 CAAGCCTGGAACCGTTTGC 60.007 57.895 0.00 0.00 0.00 3.68
4136 7299 1.007387 GCAAGCCTGGAACCGTTTG 60.007 57.895 0.00 0.00 0.00 2.93
4137 7300 1.152756 AGCAAGCCTGGAACCGTTT 60.153 52.632 0.00 0.00 0.00 3.60
4138 7301 1.898574 CAGCAAGCCTGGAACCGTT 60.899 57.895 0.00 0.00 37.93 4.44
4139 7302 2.281761 CAGCAAGCCTGGAACCGT 60.282 61.111 0.00 0.00 37.93 4.83
4140 7303 2.281761 ACAGCAAGCCTGGAACCG 60.282 61.111 0.00 0.00 46.14 4.44
4141 7304 2.270986 CCACAGCAAGCCTGGAACC 61.271 63.158 0.00 0.00 46.14 3.62
4142 7305 0.610232 ATCCACAGCAAGCCTGGAAC 60.610 55.000 11.76 0.00 46.14 3.62
4143 7306 0.322816 GATCCACAGCAAGCCTGGAA 60.323 55.000 11.76 0.00 46.14 3.53
4144 7307 1.300963 GATCCACAGCAAGCCTGGA 59.699 57.895 10.51 10.51 46.14 3.86
4145 7308 2.110967 CGATCCACAGCAAGCCTGG 61.111 63.158 0.00 0.00 46.14 4.45
4147 7310 1.123077 TATCGATCCACAGCAAGCCT 58.877 50.000 0.00 0.00 0.00 4.58
4148 7311 1.221414 GTATCGATCCACAGCAAGCC 58.779 55.000 0.00 0.00 0.00 4.35
4149 7312 1.221414 GGTATCGATCCACAGCAAGC 58.779 55.000 0.00 0.00 0.00 4.01
4150 7313 2.602257 TGGTATCGATCCACAGCAAG 57.398 50.000 0.00 0.00 0.00 4.01
4157 7320 0.396001 TCGTGGGTGGTATCGATCCA 60.396 55.000 0.00 6.84 0.00 3.41
4158 7321 0.031721 GTCGTGGGTGGTATCGATCC 59.968 60.000 0.00 3.95 34.93 3.36
4159 7322 0.031721 GGTCGTGGGTGGTATCGATC 59.968 60.000 0.00 0.00 34.93 3.69
4160 7323 1.397390 GGGTCGTGGGTGGTATCGAT 61.397 60.000 2.16 2.16 34.93 3.59
4161 7324 2.053865 GGGTCGTGGGTGGTATCGA 61.054 63.158 0.00 0.00 0.00 3.59
4162 7325 2.497770 GGGTCGTGGGTGGTATCG 59.502 66.667 0.00 0.00 0.00 2.92
4163 7326 2.738938 GGGGGTCGTGGGTGGTATC 61.739 68.421 0.00 0.00 0.00 2.24
4164 7327 2.689771 GGGGGTCGTGGGTGGTAT 60.690 66.667 0.00 0.00 0.00 2.73
4209 7372 1.202290 GGATAAAGTGTGCCAATGCCG 60.202 52.381 0.00 0.00 36.33 5.69
4210 7373 1.824230 TGGATAAAGTGTGCCAATGCC 59.176 47.619 0.00 0.00 36.33 4.40
4211 7374 2.493278 AGTGGATAAAGTGTGCCAATGC 59.507 45.455 0.00 0.00 38.26 3.56
4212 7375 3.129287 GGAGTGGATAAAGTGTGCCAATG 59.871 47.826 0.00 0.00 31.18 2.82
4213 7376 3.356290 GGAGTGGATAAAGTGTGCCAAT 58.644 45.455 0.00 0.00 31.18 3.16
4243 7406 1.675641 GGCCCAATCACGAAGCAGT 60.676 57.895 0.00 0.00 0.00 4.40
4244 7407 1.243342 TTGGCCCAATCACGAAGCAG 61.243 55.000 0.00 0.00 0.00 4.24
4248 7411 1.462616 CTCATTGGCCCAATCACGAA 58.537 50.000 5.84 0.00 31.05 3.85
4251 7414 1.031571 TCGCTCATTGGCCCAATCAC 61.032 55.000 5.84 0.00 31.05 3.06
4267 7430 0.106708 TCCATATTCCAGGCTGTCGC 59.893 55.000 14.43 0.00 0.00 5.19
4287 7450 4.317839 CGCAGTATAAGTTCCACGTATTGC 60.318 45.833 0.00 0.00 29.26 3.56
4308 7471 3.869272 CAGCACCTTCATCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
4317 7480 1.062488 ACCTCTCCCAACAGCACCTT 61.062 55.000 0.00 0.00 0.00 3.50
4318 7481 1.062488 AACCTCTCCCAACAGCACCT 61.062 55.000 0.00 0.00 0.00 4.00
4327 7490 1.679977 CGGACCGTAACCTCTCCCA 60.680 63.158 5.48 0.00 0.00 4.37
4358 7521 2.034812 GCTAGAGGATTCGGTGGTGTAG 59.965 54.545 0.00 0.00 0.00 2.74
4362 7525 0.824759 GTGCTAGAGGATTCGGTGGT 59.175 55.000 0.00 0.00 0.00 4.16
4363 7526 0.105039 GGTGCTAGAGGATTCGGTGG 59.895 60.000 0.00 0.00 0.00 4.61
4365 7528 1.115467 CAGGTGCTAGAGGATTCGGT 58.885 55.000 0.00 0.00 0.00 4.69
4393 7556 3.636764 TGAGATCGGCAGCTATGTAAGAA 59.363 43.478 0.00 0.00 0.00 2.52
4398 7561 1.697284 TCTGAGATCGGCAGCTATGT 58.303 50.000 12.18 0.00 33.45 2.29
4399 7562 2.223900 TGTTCTGAGATCGGCAGCTATG 60.224 50.000 12.18 0.00 33.45 2.23
4404 7567 0.534412 ACCTGTTCTGAGATCGGCAG 59.466 55.000 11.12 11.12 34.71 4.85
4407 7570 0.461961 GGGACCTGTTCTGAGATCGG 59.538 60.000 0.00 0.00 0.00 4.18
4408 7571 1.479709 AGGGACCTGTTCTGAGATCG 58.520 55.000 0.00 0.00 0.00 3.69
4412 7575 4.256920 CATGTAAAGGGACCTGTTCTGAG 58.743 47.826 0.00 0.00 0.00 3.35
4414 7577 3.347216 CCATGTAAAGGGACCTGTTCTG 58.653 50.000 0.00 0.00 0.00 3.02
4425 7588 5.406175 CAGAACAATTTGTGCCATGTAAAGG 59.594 40.000 2.13 0.00 0.00 3.11
4430 7593 2.548493 GCCAGAACAATTTGTGCCATGT 60.548 45.455 2.13 0.00 0.00 3.21
4431 7594 2.070783 GCCAGAACAATTTGTGCCATG 58.929 47.619 2.13 0.00 0.00 3.66
4441 7618 0.250901 ACTTGCTCCGCCAGAACAAT 60.251 50.000 0.00 0.00 30.37 2.71
4442 7619 1.148273 ACTTGCTCCGCCAGAACAA 59.852 52.632 0.00 0.00 0.00 2.83
4446 7623 4.020617 CCCACTTGCTCCGCCAGA 62.021 66.667 0.00 0.00 0.00 3.86
4452 7629 1.602771 GTCCTACCCCACTTGCTCC 59.397 63.158 0.00 0.00 0.00 4.70
4461 7638 1.562475 TGTTTATGCTGGTCCTACCCC 59.438 52.381 0.00 0.00 37.50 4.95
4477 7662 3.871594 GCTGGCTAATGTCGACTATGTTT 59.128 43.478 17.92 5.46 0.00 2.83
4499 7684 1.144057 GTCCACTATGACGGCCTGG 59.856 63.158 0.00 0.00 0.00 4.45
4512 7697 2.147150 GCTTTCTGTTCTGAGGTCCAC 58.853 52.381 0.00 0.00 0.00 4.02
4515 7700 3.006967 TGGTAGCTTTCTGTTCTGAGGTC 59.993 47.826 0.00 0.00 0.00 3.85
4521 7706 2.028930 CGACCTGGTAGCTTTCTGTTCT 60.029 50.000 0.00 0.00 0.00 3.01
4522 7707 2.288886 ACGACCTGGTAGCTTTCTGTTC 60.289 50.000 6.88 0.00 0.00 3.18
4523 7708 1.692519 ACGACCTGGTAGCTTTCTGTT 59.307 47.619 6.88 0.00 0.00 3.16
4525 7710 1.546476 AGACGACCTGGTAGCTTTCTG 59.454 52.381 6.88 0.00 0.00 3.02
4530 7715 0.328592 TGAGAGACGACCTGGTAGCT 59.671 55.000 6.88 5.35 0.00 3.32
4581 7766 2.460918 CATGTCGACGAACTCCATACC 58.539 52.381 11.62 0.00 0.00 2.73
4582 7767 2.098607 TCCATGTCGACGAACTCCATAC 59.901 50.000 11.62 0.00 0.00 2.39
4607 7792 7.490079 GGTTTCAAACAAACGAACCTTAGATTT 59.510 33.333 1.93 0.00 37.39 2.17
4624 7809 5.408299 ACAAAACTTGCAGAAGGTTTCAAAC 59.592 36.000 0.00 0.00 44.34 2.93
4628 7813 5.625311 CGATACAAAACTTGCAGAAGGTTTC 59.375 40.000 0.00 0.00 44.34 2.78
4633 7818 3.058293 TGGCGATACAAAACTTGCAGAAG 60.058 43.478 0.00 0.00 35.07 2.85
4645 7830 7.069085 AGGATTAGTACTAAGTTGGCGATACAA 59.931 37.037 19.58 0.00 0.00 2.41
4650 7835 7.592885 AATAGGATTAGTACTAAGTTGGCGA 57.407 36.000 19.58 3.35 0.00 5.54
4652 7837 8.959705 ACAAATAGGATTAGTACTAAGTTGGC 57.040 34.615 19.58 7.37 29.96 4.52
4686 7871 9.528018 GAATCAAACCAGTTGTTGATCTAAAAA 57.472 29.630 0.00 0.00 37.23 1.94
4688 7873 7.505585 AGGAATCAAACCAGTTGTTGATCTAAA 59.494 33.333 0.00 0.00 37.23 1.85
4697 7882 3.885297 CAGACAGGAATCAAACCAGTTGT 59.115 43.478 0.00 0.00 38.47 3.32
4700 7885 3.864789 ACAGACAGGAATCAAACCAGT 57.135 42.857 0.00 0.00 0.00 4.00
4701 7886 3.503748 GGAACAGACAGGAATCAAACCAG 59.496 47.826 0.00 0.00 0.00 4.00
4703 7888 3.756117 AGGAACAGACAGGAATCAAACC 58.244 45.455 0.00 0.00 0.00 3.27
4717 7902 3.423154 GCCGCCGTCAAGGAACAG 61.423 66.667 0.00 0.00 45.00 3.16


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

AutoCloner maintained by Alex Coulton.