Multiple sequence alignment - TraesCS3D01G111500

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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 TraesCS3D01G111500 chr3D 100.000 3706 0 0 571 4276 64855651 64859356 0.000000e+00 6844.0
1 TraesCS3D01G111500 chr3D 100.000 298 0 0 1 298 64855081 64855378 6.250000e-153 551.0
2 TraesCS3D01G111500 chr3D 96.644 298 10 0 1 298 524198844 524198547 2.970000e-136 496.0
3 TraesCS3D01G111500 chr3B 94.024 3196 123 23 897 4041 108238815 108241993 0.000000e+00 4782.0
4 TraesCS3D01G111500 chr3B 97.727 176 2 1 4038 4211 520146247 520146422 6.950000e-78 302.0
5 TraesCS3D01G111500 chr3B 97.207 179 2 2 4036 4211 810951132 810950954 2.500000e-77 300.0
6 TraesCS3D01G111500 chr3A 96.664 2398 61 3 1000 3378 75590168 75592565 0.000000e+00 3967.0
7 TraesCS3D01G111500 chr3A 92.998 457 24 4 3587 4041 75592564 75593014 0.000000e+00 660.0
8 TraesCS3D01G111500 chr3A 95.082 61 2 1 4206 4266 75592997 75593056 1.270000e-15 95.3
9 TraesCS3D01G111500 chr7D 97.452 314 7 1 571 883 402671699 402672012 6.290000e-148 534.0
10 TraesCS3D01G111500 chr7D 97.134 314 8 1 571 883 460639816 460640129 2.930000e-146 529.0
11 TraesCS3D01G111500 chr7D 96.644 298 10 0 1 298 548271270 548271567 2.970000e-136 496.0
12 TraesCS3D01G111500 chr7D 100.000 28 0 0 913 940 47822223 47822250 8.000000e-03 52.8
13 TraesCS3D01G111500 chr7D 96.774 31 1 0 913 943 574916536 574916566 8.000000e-03 52.8
14 TraesCS3D01G111500 chr5D 97.134 314 8 1 571 883 7010574 7010887 2.930000e-146 529.0
15 TraesCS3D01G111500 chr5D 97.419 310 7 1 574 882 432505677 432505368 1.050000e-145 527.0
16 TraesCS3D01G111500 chr5D 96.309 298 11 0 1 298 111596805 111597102 1.380000e-134 490.0
17 TraesCS3D01G111500 chr5D 96.321 299 10 1 1 298 432506056 432505758 1.380000e-134 490.0
18 TraesCS3D01G111500 chr4D 97.134 314 8 1 571 883 488740510 488740823 2.930000e-146 529.0
19 TraesCS3D01G111500 chr4D 96.825 315 7 3 571 883 92080285 92080598 1.360000e-144 523.0
20 TraesCS3D01G111500 chr4D 100.000 28 0 0 913 940 28782371 28782398 8.000000e-03 52.8
21 TraesCS3D01G111500 chr4A 96.835 316 9 1 571 885 705057529 705057844 1.050000e-145 527.0
22 TraesCS3D01G111500 chr4A 100.000 28 0 0 913 940 646602501 646602528 8.000000e-03 52.8
23 TraesCS3D01G111500 chr2D 97.125 313 7 1 571 883 349010901 349011211 1.050000e-145 527.0
24 TraesCS3D01G111500 chr2D 96.980 298 9 0 1 298 142523038 142523335 6.380000e-138 501.0
25 TraesCS3D01G111500 chr2D 100.000 28 0 0 916 943 160677536 160677509 8.000000e-03 52.8
26 TraesCS3D01G111500 chr1B 96.835 316 8 2 571 885 582584790 582585104 1.050000e-145 527.0
27 TraesCS3D01G111500 chr1B 97.674 172 1 2 4042 4211 456742364 456742194 4.180000e-75 292.0
28 TraesCS3D01G111500 chr1B 100.000 28 0 0 913 940 370953907 370953934 8.000000e-03 52.8
29 TraesCS3D01G111500 chr6D 97.315 298 8 0 1 298 413389459 413389162 1.370000e-139 507.0
30 TraesCS3D01G111500 chr6D 96.980 298 8 1 1 298 427236688 427236984 2.300000e-137 499.0
31 TraesCS3D01G111500 chr6D 98.225 169 1 1 4041 4207 136706546 136706378 1.160000e-75 294.0
32 TraesCS3D01G111500 chr1D 96.644 298 10 0 1 298 395974879 395974582 2.970000e-136 496.0
33 TraesCS3D01G111500 chr1D 96.309 298 11 0 1 298 471281241 471280944 1.380000e-134 490.0
34 TraesCS3D01G111500 chr1D 95.506 178 4 3 4033 4208 326471538 326471363 9.050000e-72 281.0
35 TraesCS3D01G111500 chr6B 98.256 172 1 1 4038 4207 52572616 52572445 2.500000e-77 300.0
36 TraesCS3D01G111500 chr6B 98.235 170 1 1 4040 4207 415732214 415732045 3.230000e-76 296.0
37 TraesCS3D01G111500 chr6B 97.143 175 3 1 4042 4214 358303198 358303024 1.160000e-75 294.0
38 TraesCS3D01G111500 chr1A 97.191 178 2 2 4033 4208 413787300 413787124 8.990000e-77 298.0
39 TraesCS3D01G111500 chr1A 96.610 177 4 1 4035 4209 208903964 208903788 4.180000e-75 292.0
40 TraesCS3D01G111500 chr1A 97.647 170 2 1 4040 4207 515590019 515590188 1.500000e-74 291.0
41 TraesCS3D01G111500 chrUn 98.235 170 1 1 4040 4207 48495525 48495356 3.230000e-76 296.0
42 TraesCS3D01G111500 chrUn 98.235 170 1 1 4040 4207 235110848 235110679 3.230000e-76 296.0
43 TraesCS3D01G111500 chrUn 98.235 170 1 1 4040 4207 386426511 386426342 3.230000e-76 296.0
44 TraesCS3D01G111500 chrUn 98.204 167 1 1 4042 4206 75470690 75470856 1.500000e-74 291.0
45 TraesCS3D01G111500 chrUn 98.204 167 1 1 4042 4206 112608420 112608254 1.500000e-74 291.0
46 TraesCS3D01G111500 chrUn 97.647 170 2 1 4040 4207 237212709 237212878 1.500000e-74 291.0
47 TraesCS3D01G111500 chrUn 97.605 167 2 1 4042 4206 279937718 279937552 7.000000e-73 285.0
48 TraesCS3D01G111500 chrUn 97.605 167 2 1 4042 4206 292395667 292395501 7.000000e-73 285.0
49 TraesCS3D01G111500 chrUn 97.590 166 2 1 4044 4207 267455468 267455303 2.520000e-72 283.0
50 TraesCS3D01G111500 chrUn 96.491 171 3 2 4042 4210 10129707 10129538 3.260000e-71 279.0
51 TraesCS3D01G111500 chr5B 97.688 173 2 1 4037 4207 428847344 428847172 3.230000e-76 296.0
52 TraesCS3D01G111500 chr5B 96.774 31 1 0 913 943 31270032 31270002 8.000000e-03 52.8
53 TraesCS3D01G111500 chr5B 100.000 28 0 0 913 940 689862181 689862208 8.000000e-03 52.8
54 TraesCS3D01G111500 chr2A 97.688 173 2 1 4040 4210 65400498 65400326 3.230000e-76 296.0
55 TraesCS3D01G111500 chr7A 97.143 175 3 1 4036 4208 143050437 143050263 1.160000e-75 294.0
56 TraesCS3D01G111500 chr6A 98.225 169 1 1 4040 4206 582491246 582491078 1.160000e-75 294.0
57 TraesCS3D01G111500 chr5A 97.688 173 1 2 4041 4211 219579068 219578897 1.160000e-75 294.0
58 TraesCS3D01G111500 chr4B 97.674 172 2 1 4042 4211 78609149 78609320 1.160000e-75 294.0
59 TraesCS3D01G111500 chr4B 98.214 168 1 1 4042 4207 106047639 106047806 4.180000e-75 292.0
60 TraesCS3D01G111500 chr4B 98.214 168 1 1 4042 4207 171146753 171146586 4.180000e-75 292.0
61 TraesCS3D01G111500 chr4B 98.214 168 1 1 4041 4206 553510686 553510519 4.180000e-75 292.0
62 TraesCS3D01G111500 chr7B 96.774 31 1 0 913 943 719163909 719163879 8.000000e-03 52.8


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 TraesCS3D01G111500 chr3D 64855081 64859356 4275 False 3697.5 6844 100.000000 1 4276 2 chr3D.!!$F1 4275
1 TraesCS3D01G111500 chr3B 108238815 108241993 3178 False 4782.0 4782 94.024000 897 4041 1 chr3B.!!$F1 3144
2 TraesCS3D01G111500 chr3A 75590168 75593056 2888 False 1574.1 3967 94.914667 1000 4266 3 chr3A.!!$F1 3266
3 TraesCS3D01G111500 chr5D 432505368 432506056 688 True 508.5 527 96.870000 1 882 2 chr5D.!!$R1 881

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
208 210 0.980231 GAGGAGGAGTGAGGCCATGT 60.980 60.000 5.01 0.0 0.0 3.21 F
944 947 1.303806 GCCTCCAAAACGCCCCTAA 60.304 57.895 0.00 0.0 0.0 2.69 F
2537 2587 0.815213 TGCAAGAGTGTGGTGTCTGC 60.815 55.000 0.00 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1445 1461 0.308993 GAAACTAGGGCATGCGCATC 59.691 55.0 33.01 19.2 41.24 3.91 R
2779 2829 1.117150 AGATTTGCCATCACCATGCC 58.883 50.0 0.00 0.0 0.00 4.40 R
4166 4234 0.036875 GGTGAAGTCCTCCCCACTTG 59.963 60.0 0.00 0.0 34.10 3.16 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
177 178 2.234908 CGAGGAGGAGAAGTGGATTTGT 59.765 50.000 0.00 0.00 0.00 2.83
208 210 0.980231 GAGGAGGAGTGAGGCCATGT 60.980 60.000 5.01 0.00 0.00 3.21
212 214 2.606587 GGAGTGAGGCCATGTGGGT 61.607 63.158 5.01 0.00 39.65 4.51
226 228 1.618447 TGGGTAGGGAAGGAAGGGC 60.618 63.158 0.00 0.00 0.00 5.19
783 786 2.032681 GGGAGAGGGTGTGTGTGC 59.967 66.667 0.00 0.00 0.00 4.57
827 830 7.413475 AGATCGTCAATGTCACTTAATATGC 57.587 36.000 0.00 0.00 0.00 3.14
943 946 2.353573 GCCTCCAAAACGCCCCTA 59.646 61.111 0.00 0.00 0.00 3.53
944 947 1.303806 GCCTCCAAAACGCCCCTAA 60.304 57.895 0.00 0.00 0.00 2.69
960 963 2.432510 CCCTAATCGTGGAGAAGCTCTT 59.567 50.000 0.00 0.00 0.00 2.85
961 964 3.637229 CCCTAATCGTGGAGAAGCTCTTA 59.363 47.826 0.00 0.00 0.00 2.10
962 965 4.282195 CCCTAATCGTGGAGAAGCTCTTAT 59.718 45.833 0.00 0.00 0.00 1.73
963 966 5.221541 CCCTAATCGTGGAGAAGCTCTTATT 60.222 44.000 0.00 0.00 0.00 1.40
964 967 6.015350 CCCTAATCGTGGAGAAGCTCTTATTA 60.015 42.308 0.00 0.00 0.00 0.98
965 968 7.434492 CCTAATCGTGGAGAAGCTCTTATTAA 58.566 38.462 0.00 0.00 0.00 1.40
966 969 8.091449 CCTAATCGTGGAGAAGCTCTTATTAAT 58.909 37.037 0.00 0.00 0.00 1.40
967 970 9.482627 CTAATCGTGGAGAAGCTCTTATTAATT 57.517 33.333 0.00 0.00 0.00 1.40
969 972 9.832445 AATCGTGGAGAAGCTCTTATTAATTAA 57.168 29.630 0.00 0.00 0.00 1.40
970 973 8.644318 TCGTGGAGAAGCTCTTATTAATTAAC 57.356 34.615 0.00 0.00 0.00 2.01
971 974 7.709613 TCGTGGAGAAGCTCTTATTAATTAACC 59.290 37.037 0.00 0.00 0.00 2.85
972 975 7.041984 CGTGGAGAAGCTCTTATTAATTAACCC 60.042 40.741 0.00 0.00 0.00 4.11
973 976 7.993758 GTGGAGAAGCTCTTATTAATTAACCCT 59.006 37.037 0.00 0.00 0.00 4.34
974 977 8.211629 TGGAGAAGCTCTTATTAATTAACCCTC 58.788 37.037 0.00 0.00 0.00 4.30
981 984 2.047002 TTAATTAACCCTCGGGCTGC 57.953 50.000 0.82 0.00 39.32 5.25
994 997 3.818787 GCTGCTTGACCCCGCATG 61.819 66.667 0.00 0.00 35.32 4.06
997 1000 3.499737 GCTTGACCCCGCATGACG 61.500 66.667 0.00 0.00 43.15 4.35
1488 1504 7.276658 TCTGTGCTTATTATTTGGTCGGAATA 58.723 34.615 0.00 0.00 0.00 1.75
1575 1599 6.128391 GCATTGTACCTCGTGTCATTTTTCTA 60.128 38.462 0.00 0.00 0.00 2.10
1611 1635 4.813750 AATCTTTGCTGAGGAAAATGGG 57.186 40.909 0.00 0.00 0.00 4.00
1613 1637 3.424703 TCTTTGCTGAGGAAAATGGGAG 58.575 45.455 0.00 0.00 0.00 4.30
1657 1699 3.363182 GCACGTTATTAACAACACGCAGA 60.363 43.478 7.31 0.00 36.05 4.26
1803 1845 5.888161 AGGAATGCAATTAGGTGACCTTTAG 59.112 40.000 10.53 0.00 36.07 1.85
1837 1879 9.820229 GAACATTTTCTGTCGATTGTTTGTATA 57.180 29.630 0.00 0.00 36.98 1.47
2372 2422 2.703416 TCATCAACTGTCATGGTCTGC 58.297 47.619 0.00 0.00 0.00 4.26
2396 2446 7.147976 GCGGATATGCTAAGAATGGAAAAATT 58.852 34.615 0.00 0.00 0.00 1.82
2537 2587 0.815213 TGCAAGAGTGTGGTGTCTGC 60.815 55.000 0.00 0.00 0.00 4.26
2657 2707 6.177610 TGGGTTTTGTAAGATACTGTCCATC 58.822 40.000 0.00 0.00 0.00 3.51
2956 3006 4.273318 GAATACAGGATTGAACCCAAGCT 58.727 43.478 0.00 0.00 38.63 3.74
3185 3235 5.041951 ACGTGTTTTTATCGAACATGCAT 57.958 34.783 6.36 0.00 44.12 3.96
3309 3360 1.071542 TGTCCACGATTTTGGAGCTGA 59.928 47.619 0.00 0.00 46.75 4.26
3325 3376 4.067896 GAGCTGAAGGTGAGAAACATCAA 58.932 43.478 0.00 0.00 30.93 2.57
3344 3395 6.604795 ACATCAAGAAAATCATAGGACCCTTG 59.395 38.462 0.00 0.00 33.20 3.61
3354 3405 6.630203 TCATAGGACCCTTGTAAAGCTTAA 57.370 37.500 0.00 0.00 44.44 1.85
3401 3452 3.981071 TGGCTGTGCTAGTCTTTATGT 57.019 42.857 0.00 0.00 0.00 2.29
3404 3455 5.800296 TGGCTGTGCTAGTCTTTATGTTAA 58.200 37.500 0.00 0.00 0.00 2.01
3408 3459 6.183360 GCTGTGCTAGTCTTTATGTTAACCTG 60.183 42.308 2.48 0.00 0.00 4.00
3428 3479 4.462834 CCTGGTAAATTTCTGAAAGGGGAC 59.537 45.833 8.95 4.33 0.00 4.46
3429 3480 5.068215 TGGTAAATTTCTGAAAGGGGACA 57.932 39.130 8.95 2.87 0.00 4.02
3473 3529 5.104193 AGACTTGCAGGTAATCATGAGGAAT 60.104 40.000 0.00 0.00 0.00 3.01
3475 3531 6.058183 ACTTGCAGGTAATCATGAGGAATAC 58.942 40.000 0.00 2.23 32.17 1.89
3769 3829 7.951347 ATGGATTGAGCTATCATATTTTCCC 57.049 36.000 0.00 0.00 34.73 3.97
3770 3830 6.851318 TGGATTGAGCTATCATATTTTCCCA 58.149 36.000 0.00 0.00 34.73 4.37
3771 3831 6.944290 TGGATTGAGCTATCATATTTTCCCAG 59.056 38.462 0.00 0.00 34.73 4.45
3772 3832 6.944862 GGATTGAGCTATCATATTTTCCCAGT 59.055 38.462 0.00 0.00 34.73 4.00
3773 3833 8.103305 GGATTGAGCTATCATATTTTCCCAGTA 58.897 37.037 0.00 0.00 34.73 2.74
3774 3834 9.678260 GATTGAGCTATCATATTTTCCCAGTAT 57.322 33.333 0.00 0.00 34.73 2.12
3776 3836 9.866655 TTGAGCTATCATATTTTCCCAGTATTT 57.133 29.630 0.00 0.00 34.73 1.40
3777 3837 9.866655 TGAGCTATCATATTTTCCCAGTATTTT 57.133 29.630 0.00 0.00 0.00 1.82
3783 3843 7.066781 TCATATTTTCCCAGTATTTTCCTCCC 58.933 38.462 0.00 0.00 0.00 4.30
3818 3883 6.319048 AGATGAGATAATTGGTGTGGTTCT 57.681 37.500 0.00 0.00 0.00 3.01
3914 3980 1.636988 GTCGTCGGTAATGGGTCTTG 58.363 55.000 0.00 0.00 0.00 3.02
3935 4001 0.399454 AGTTGTGTGAGCTGCCAGAT 59.601 50.000 0.00 0.00 0.00 2.90
3977 4043 2.238646 TCCAGAAGCACGGGTATTTCAT 59.761 45.455 0.00 0.00 35.40 2.57
4041 4109 6.056090 TGTAACATATTCTGGCAACACCTA 57.944 37.500 0.00 0.00 46.17 3.08
4043 4111 6.943146 TGTAACATATTCTGGCAACACCTAAA 59.057 34.615 0.00 0.00 46.17 1.85
4044 4112 6.515272 AACATATTCTGGCAACACCTAAAG 57.485 37.500 0.00 0.00 46.17 1.85
4045 4113 4.949856 ACATATTCTGGCAACACCTAAAGG 59.050 41.667 0.00 0.00 46.17 3.11
4046 4114 3.806949 ATTCTGGCAACACCTAAAGGA 57.193 42.857 2.23 0.00 46.17 3.36
4047 4115 2.561478 TCTGGCAACACCTAAAGGAC 57.439 50.000 2.23 0.00 46.17 3.85
4048 4116 1.771854 TCTGGCAACACCTAAAGGACA 59.228 47.619 2.23 0.00 46.17 4.02
4049 4117 2.154462 CTGGCAACACCTAAAGGACAG 58.846 52.381 2.23 0.00 46.17 3.51
4050 4118 1.771854 TGGCAACACCTAAAGGACAGA 59.228 47.619 2.23 0.00 46.17 3.41
4051 4119 2.152016 GGCAACACCTAAAGGACAGAC 58.848 52.381 2.23 0.00 38.94 3.51
4052 4120 2.152016 GCAACACCTAAAGGACAGACC 58.848 52.381 2.23 0.00 38.94 3.85
4053 4121 2.779506 CAACACCTAAAGGACAGACCC 58.220 52.381 2.23 0.00 40.05 4.46
4054 4122 2.105821 CAACACCTAAAGGACAGACCCA 59.894 50.000 2.23 0.00 40.05 4.51
4055 4123 1.978580 ACACCTAAAGGACAGACCCAG 59.021 52.381 2.23 0.00 40.05 4.45
4056 4124 1.978580 CACCTAAAGGACAGACCCAGT 59.021 52.381 2.23 0.00 40.05 4.00
4057 4125 1.978580 ACCTAAAGGACAGACCCAGTG 59.021 52.381 2.23 0.00 40.05 3.66
4058 4126 1.339151 CCTAAAGGACAGACCCAGTGC 60.339 57.143 0.00 0.00 40.05 4.40
4059 4127 1.347707 CTAAAGGACAGACCCAGTGCA 59.652 52.381 0.00 0.00 40.05 4.57
4060 4128 0.773644 AAAGGACAGACCCAGTGCAT 59.226 50.000 0.00 0.00 40.05 3.96
4061 4129 1.656587 AAGGACAGACCCAGTGCATA 58.343 50.000 0.00 0.00 40.05 3.14
4062 4130 1.198713 AGGACAGACCCAGTGCATAG 58.801 55.000 0.00 0.00 40.05 2.23
4063 4131 1.195115 GGACAGACCCAGTGCATAGA 58.805 55.000 0.00 0.00 0.00 1.98
4064 4132 1.555075 GGACAGACCCAGTGCATAGAA 59.445 52.381 0.00 0.00 0.00 2.10
4065 4133 2.419297 GGACAGACCCAGTGCATAGAAG 60.419 54.545 0.00 0.00 0.00 2.85
4066 4134 1.065854 ACAGACCCAGTGCATAGAAGC 60.066 52.381 0.00 0.00 0.00 3.86
4067 4135 1.209019 CAGACCCAGTGCATAGAAGCT 59.791 52.381 0.00 0.00 34.99 3.74
4068 4136 1.484240 AGACCCAGTGCATAGAAGCTC 59.516 52.381 0.00 0.00 34.99 4.09
4069 4137 0.543749 ACCCAGTGCATAGAAGCTCC 59.456 55.000 0.00 0.00 34.99 4.70
4070 4138 0.179034 CCCAGTGCATAGAAGCTCCC 60.179 60.000 0.00 0.00 34.99 4.30
4071 4139 0.543277 CCAGTGCATAGAAGCTCCCA 59.457 55.000 0.00 0.00 34.99 4.37
4072 4140 1.661341 CAGTGCATAGAAGCTCCCAC 58.339 55.000 0.00 0.00 34.99 4.61
4073 4141 1.065926 CAGTGCATAGAAGCTCCCACA 60.066 52.381 0.00 0.00 34.99 4.17
4074 4142 1.842562 AGTGCATAGAAGCTCCCACAT 59.157 47.619 0.00 0.00 34.99 3.21
4075 4143 1.945394 GTGCATAGAAGCTCCCACATG 59.055 52.381 0.00 0.00 34.99 3.21
4076 4144 1.134007 TGCATAGAAGCTCCCACATGG 60.134 52.381 0.00 0.00 34.99 3.66
4077 4145 1.133976 GCATAGAAGCTCCCACATGGT 60.134 52.381 0.00 0.00 34.77 3.55
4078 4146 2.569059 CATAGAAGCTCCCACATGGTG 58.431 52.381 0.00 0.00 34.77 4.17
4087 4155 2.356278 CACATGGTGGGGTCTGGG 59.644 66.667 0.00 0.00 0.00 4.45
4088 4156 2.941025 ACATGGTGGGGTCTGGGG 60.941 66.667 0.00 0.00 0.00 4.96
4089 4157 2.613696 CATGGTGGGGTCTGGGGA 60.614 66.667 0.00 0.00 0.00 4.81
4090 4158 2.286425 ATGGTGGGGTCTGGGGAG 60.286 66.667 0.00 0.00 0.00 4.30
4091 4159 3.970363 ATGGTGGGGTCTGGGGAGG 62.970 68.421 0.00 0.00 0.00 4.30
4093 4161 4.348495 GTGGGGTCTGGGGAGGGA 62.348 72.222 0.00 0.00 0.00 4.20
4094 4162 3.300962 TGGGGTCTGGGGAGGGAT 61.301 66.667 0.00 0.00 0.00 3.85
4095 4163 2.044620 GGGGTCTGGGGAGGGATT 59.955 66.667 0.00 0.00 0.00 3.01
4096 4164 1.320512 GGGGTCTGGGGAGGGATTA 59.679 63.158 0.00 0.00 0.00 1.75
4097 4165 0.103876 GGGGTCTGGGGAGGGATTAT 60.104 60.000 0.00 0.00 0.00 1.28
4098 4166 1.153565 GGGGTCTGGGGAGGGATTATA 59.846 57.143 0.00 0.00 0.00 0.98
4099 4167 2.552367 GGGTCTGGGGAGGGATTATAG 58.448 57.143 0.00 0.00 0.00 1.31
4100 4168 2.552367 GGTCTGGGGAGGGATTATAGG 58.448 57.143 0.00 0.00 0.00 2.57
4101 4169 2.113777 GGTCTGGGGAGGGATTATAGGA 59.886 54.545 0.00 0.00 0.00 2.94
4102 4170 3.441054 GGTCTGGGGAGGGATTATAGGAA 60.441 52.174 0.00 0.00 0.00 3.36
4103 4171 3.583526 GTCTGGGGAGGGATTATAGGAAC 59.416 52.174 0.00 0.00 0.00 3.62
4104 4172 2.913617 CTGGGGAGGGATTATAGGAACC 59.086 54.545 0.00 0.00 0.00 3.62
4105 4173 2.531463 TGGGGAGGGATTATAGGAACCT 59.469 50.000 0.00 0.00 0.00 3.50
4106 4174 3.741438 TGGGGAGGGATTATAGGAACCTA 59.259 47.826 2.93 2.93 0.00 3.08
4107 4175 4.202901 TGGGGAGGGATTATAGGAACCTAG 60.203 50.000 6.72 0.00 31.45 3.02
4108 4176 4.202912 GGGGAGGGATTATAGGAACCTAGT 60.203 50.000 6.72 0.00 31.45 2.57
4109 4177 5.024785 GGGAGGGATTATAGGAACCTAGTC 58.975 50.000 6.72 4.93 31.45 2.59
4110 4178 5.222589 GGGAGGGATTATAGGAACCTAGTCT 60.223 48.000 6.72 0.00 31.45 3.24
4111 4179 6.324544 GGAGGGATTATAGGAACCTAGTCTT 58.675 44.000 6.72 0.00 31.45 3.01
4112 4180 7.477008 GGAGGGATTATAGGAACCTAGTCTTA 58.523 42.308 6.72 0.00 31.45 2.10
4113 4181 7.396907 GGAGGGATTATAGGAACCTAGTCTTAC 59.603 44.444 6.72 0.00 31.45 2.34
4114 4182 7.247500 AGGGATTATAGGAACCTAGTCTTACC 58.753 42.308 6.72 4.95 31.45 2.85
4115 4183 6.440010 GGGATTATAGGAACCTAGTCTTACCC 59.560 46.154 6.72 9.62 31.45 3.69
4116 4184 6.440010 GGATTATAGGAACCTAGTCTTACCCC 59.560 46.154 6.72 0.00 31.45 4.95
4117 4185 6.618836 TTATAGGAACCTAGTCTTACCCCT 57.381 41.667 6.72 0.00 31.45 4.79
4118 4186 3.117552 AGGAACCTAGTCTTACCCCTG 57.882 52.381 0.00 0.00 0.00 4.45
4119 4187 1.485480 GGAACCTAGTCTTACCCCTGC 59.515 57.143 0.00 0.00 0.00 4.85
4120 4188 2.185387 GAACCTAGTCTTACCCCTGCA 58.815 52.381 0.00 0.00 0.00 4.41
4121 4189 2.337359 ACCTAGTCTTACCCCTGCAA 57.663 50.000 0.00 0.00 0.00 4.08
4122 4190 2.627933 ACCTAGTCTTACCCCTGCAAA 58.372 47.619 0.00 0.00 0.00 3.68
4123 4191 2.572104 ACCTAGTCTTACCCCTGCAAAG 59.428 50.000 0.00 0.00 0.00 2.77
4124 4192 2.572104 CCTAGTCTTACCCCTGCAAAGT 59.428 50.000 0.00 0.00 0.00 2.66
4125 4193 2.568623 AGTCTTACCCCTGCAAAGTG 57.431 50.000 0.00 0.00 0.00 3.16
4126 4194 0.881796 GTCTTACCCCTGCAAAGTGC 59.118 55.000 0.00 0.00 45.29 4.40
4137 4205 1.978542 GCAAAGTGCAATGCAGAGAG 58.021 50.000 8.73 0.33 44.26 3.20
4138 4206 1.402456 GCAAAGTGCAATGCAGAGAGG 60.402 52.381 8.73 0.00 44.26 3.69
4139 4207 0.886563 AAAGTGCAATGCAGAGAGGC 59.113 50.000 8.73 0.00 40.08 4.70
4140 4208 0.037877 AAGTGCAATGCAGAGAGGCT 59.962 50.000 8.73 0.00 40.08 4.58
4142 4210 1.378119 TGCAATGCAGAGAGGCTGG 60.378 57.895 2.72 0.00 45.03 4.85
4143 4211 1.378250 GCAATGCAGAGAGGCTGGT 60.378 57.895 0.00 0.00 45.03 4.00
4144 4212 0.964358 GCAATGCAGAGAGGCTGGTT 60.964 55.000 0.00 0.00 45.03 3.67
4145 4213 1.093159 CAATGCAGAGAGGCTGGTTC 58.907 55.000 0.00 0.00 45.03 3.62
4146 4214 0.392193 AATGCAGAGAGGCTGGTTCG 60.392 55.000 0.00 0.00 45.03 3.95
4147 4215 1.260538 ATGCAGAGAGGCTGGTTCGA 61.261 55.000 0.00 0.00 45.03 3.71
4148 4216 1.293498 GCAGAGAGGCTGGTTCGAA 59.707 57.895 0.00 0.00 45.03 3.71
4149 4217 1.016653 GCAGAGAGGCTGGTTCGAAC 61.017 60.000 20.14 20.14 45.03 3.95
4158 4226 3.479979 GGTTCGAACCCAGGACCT 58.520 61.111 33.02 0.00 43.43 3.85
4159 4227 1.295746 GGTTCGAACCCAGGACCTC 59.704 63.158 33.02 7.79 43.43 3.85
4160 4228 1.192803 GGTTCGAACCCAGGACCTCT 61.193 60.000 33.02 0.00 43.43 3.69
4161 4229 0.685660 GTTCGAACCCAGGACCTCTT 59.314 55.000 17.68 0.00 0.00 2.85
4162 4230 0.685097 TTCGAACCCAGGACCTCTTG 59.315 55.000 0.00 0.00 0.00 3.02
4163 4231 1.192146 TCGAACCCAGGACCTCTTGG 61.192 60.000 0.00 0.00 42.20 3.61
4164 4232 1.002011 GAACCCAGGACCTCTTGGC 60.002 63.158 0.00 0.00 41.31 4.52
4165 4233 1.774217 AACCCAGGACCTCTTGGCA 60.774 57.895 0.00 0.00 41.31 4.92
4166 4234 2.069165 AACCCAGGACCTCTTGGCAC 62.069 60.000 0.00 0.00 41.31 5.01
4167 4235 2.528818 CCCAGGACCTCTTGGCACA 61.529 63.158 0.00 0.00 41.31 4.57
4178 4246 2.449518 TGGCACAAGTGGGGAGGA 60.450 61.111 2.00 0.00 31.92 3.71
4179 4247 2.034221 GGCACAAGTGGGGAGGAC 59.966 66.667 2.00 0.00 0.00 3.85
4180 4248 2.529744 GGCACAAGTGGGGAGGACT 61.530 63.158 2.00 0.00 0.00 3.85
4181 4249 1.456287 GCACAAGTGGGGAGGACTT 59.544 57.895 2.00 0.00 33.82 3.01
4182 4250 0.606673 GCACAAGTGGGGAGGACTTC 60.607 60.000 2.00 0.00 31.05 3.01
4183 4251 0.764890 CACAAGTGGGGAGGACTTCA 59.235 55.000 0.00 0.00 31.05 3.02
4184 4252 0.765510 ACAAGTGGGGAGGACTTCAC 59.234 55.000 0.00 0.00 31.05 3.18
4190 4258 1.003233 GGGAGGACTTCACCACTGC 60.003 63.158 0.00 0.00 0.00 4.40
4191 4259 1.374758 GGAGGACTTCACCACTGCG 60.375 63.158 0.00 0.00 0.00 5.18
4192 4260 2.029844 GAGGACTTCACCACTGCGC 61.030 63.158 0.00 0.00 0.00 6.09
4193 4261 3.050275 GGACTTCACCACTGCGCC 61.050 66.667 4.18 0.00 0.00 6.53
4194 4262 2.280797 GACTTCACCACTGCGCCA 60.281 61.111 4.18 0.00 0.00 5.69
4195 4263 2.281070 ACTTCACCACTGCGCCAG 60.281 61.111 4.18 4.99 37.52 4.85
4196 4264 3.052082 CTTCACCACTGCGCCAGG 61.052 66.667 4.18 6.64 35.51 4.45
4208 4276 3.492353 GCCAGGCCTGCCCTCATA 61.492 66.667 28.39 0.00 44.09 2.15
4209 4277 2.838467 GCCAGGCCTGCCCTCATAT 61.838 63.158 28.39 0.00 44.09 1.78
4210 4278 1.849116 CCAGGCCTGCCCTCATATT 59.151 57.895 28.39 0.00 44.09 1.28
4211 4279 0.251077 CCAGGCCTGCCCTCATATTC 60.251 60.000 28.39 0.00 44.09 1.75
4212 4280 0.769873 CAGGCCTGCCCTCATATTCT 59.230 55.000 22.33 0.00 44.09 2.40
4213 4281 0.769873 AGGCCTGCCCTCATATTCTG 59.230 55.000 3.11 0.00 41.21 3.02
4214 4282 0.251077 GGCCTGCCCTCATATTCTGG 60.251 60.000 0.00 0.00 0.00 3.86
4215 4283 0.892814 GCCTGCCCTCATATTCTGGC 60.893 60.000 0.00 0.00 44.27 4.85
4220 4288 1.678101 GCCCTCATATTCTGGCAACAC 59.322 52.381 0.00 0.00 46.17 3.32
4221 4289 2.301346 CCCTCATATTCTGGCAACACC 58.699 52.381 0.00 0.00 46.17 4.16
4222 4290 2.092212 CCCTCATATTCTGGCAACACCT 60.092 50.000 0.00 0.00 46.17 4.00
4223 4291 3.209410 CCTCATATTCTGGCAACACCTC 58.791 50.000 0.00 0.00 46.17 3.85
4224 4292 3.370846 CCTCATATTCTGGCAACACCTCA 60.371 47.826 0.00 0.00 46.17 3.86
4225 4293 3.609853 TCATATTCTGGCAACACCTCAC 58.390 45.455 0.00 0.00 46.17 3.51
4226 4294 3.264193 TCATATTCTGGCAACACCTCACT 59.736 43.478 0.00 0.00 46.17 3.41
4227 4295 2.664402 ATTCTGGCAACACCTCACTT 57.336 45.000 0.00 0.00 46.17 3.16
4228 4296 1.967319 TTCTGGCAACACCTCACTTC 58.033 50.000 0.00 0.00 46.17 3.01
4229 4297 1.131638 TCTGGCAACACCTCACTTCT 58.868 50.000 0.00 0.00 46.17 2.85
4230 4298 2.325484 TCTGGCAACACCTCACTTCTA 58.675 47.619 0.00 0.00 46.17 2.10
4245 4313 6.271488 TCACTTCTAAAAATCATGGGCTTG 57.729 37.500 0.00 0.00 0.00 4.01
4260 4328 3.768757 TGGGCTTGTTCAGGATTATTTGG 59.231 43.478 0.00 0.00 0.00 3.28
4266 4334 3.689161 TGTTCAGGATTATTTGGTGAGCG 59.311 43.478 0.00 0.00 0.00 5.03
4267 4335 2.288666 TCAGGATTATTTGGTGAGCGC 58.711 47.619 0.00 0.00 0.00 5.92
4268 4336 2.016318 CAGGATTATTTGGTGAGCGCA 58.984 47.619 11.47 0.00 0.00 6.09
4269 4337 2.423185 CAGGATTATTTGGTGAGCGCAA 59.577 45.455 11.47 0.00 0.00 4.85
4270 4338 3.088532 AGGATTATTTGGTGAGCGCAAA 58.911 40.909 11.47 0.18 0.00 3.68
4271 4339 3.119495 AGGATTATTTGGTGAGCGCAAAC 60.119 43.478 11.47 7.11 0.00 2.93
4272 4340 3.366883 GGATTATTTGGTGAGCGCAAACA 60.367 43.478 11.47 2.72 0.00 2.83
4273 4341 2.987413 TATTTGGTGAGCGCAAACAG 57.013 45.000 11.47 0.00 0.00 3.16
4274 4342 1.317613 ATTTGGTGAGCGCAAACAGA 58.682 45.000 11.47 1.27 0.00 3.41
4275 4343 1.317613 TTTGGTGAGCGCAAACAGAT 58.682 45.000 11.47 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.245266 TGCGCCAACGAGATCAAGTA 59.755 50.000 4.18 0.00 43.93 2.24
46 47 1.343069 AGGAGCTTGTCGAGGAGTTT 58.657 50.000 0.00 0.00 0.00 2.66
48 49 1.757682 CTAGGAGCTTGTCGAGGAGT 58.242 55.000 0.00 0.00 0.00 3.85
81 82 2.282110 CCGTCCACATGGCCACAA 60.282 61.111 8.16 0.00 34.44 3.33
82 83 4.343323 CCCGTCCACATGGCCACA 62.343 66.667 8.16 0.00 34.44 4.17
208 210 1.618447 GCCCTTCCTTCCCTACCCA 60.618 63.158 0.00 0.00 0.00 4.51
212 214 1.079621 TGACGCCCTTCCTTCCCTA 59.920 57.895 0.00 0.00 0.00 3.53
226 228 1.202770 GGGGAATGGATAAGGGTGACG 60.203 57.143 0.00 0.00 0.00 4.35
278 280 4.175489 GCGTCGCTACAGAGCCGA 62.175 66.667 10.68 0.00 46.86 5.54
570 572 4.152284 AGGACGATGTAAAAGGGGAATC 57.848 45.455 0.00 0.00 0.00 2.52
571 573 4.586306 AAGGACGATGTAAAAGGGGAAT 57.414 40.909 0.00 0.00 0.00 3.01
572 574 4.376225 AAAGGACGATGTAAAAGGGGAA 57.624 40.909 0.00 0.00 0.00 3.97
716 718 2.603473 CACTCGGGAGGTGGGACA 60.603 66.667 0.00 0.00 0.00 4.02
805 808 7.442062 TCATGCATATTAAGTGACATTGACGAT 59.558 33.333 0.00 0.00 0.00 3.73
901 904 7.308830 GCCGAGCTCCATGAAGAATTTAATTAT 60.309 37.037 8.47 0.00 0.00 1.28
911 914 1.680522 GAGGCCGAGCTCCATGAAGA 61.681 60.000 8.47 0.00 0.00 2.87
921 924 4.103103 GCGTTTTGGAGGCCGAGC 62.103 66.667 0.00 0.00 33.08 5.03
943 946 9.832445 TTAATTAATAAGAGCTTCTCCACGATT 57.168 29.630 0.00 0.00 0.00 3.34
944 947 9.262358 GTTAATTAATAAGAGCTTCTCCACGAT 57.738 33.333 0.31 0.00 0.00 3.73
960 963 3.393278 AGCAGCCCGAGGGTTAATTAATA 59.607 43.478 10.26 0.00 37.65 0.98
961 964 2.174854 AGCAGCCCGAGGGTTAATTAAT 59.825 45.455 10.26 0.00 37.65 1.40
962 965 1.562475 AGCAGCCCGAGGGTTAATTAA 59.438 47.619 10.26 0.00 37.65 1.40
963 966 1.209621 AGCAGCCCGAGGGTTAATTA 58.790 50.000 10.26 0.00 37.65 1.40
964 967 0.331616 AAGCAGCCCGAGGGTTAATT 59.668 50.000 10.26 0.00 37.65 1.40
965 968 0.394352 CAAGCAGCCCGAGGGTTAAT 60.394 55.000 10.26 0.00 37.65 1.40
966 969 1.002624 CAAGCAGCCCGAGGGTTAA 60.003 57.895 10.26 0.00 37.65 2.01
967 970 1.916273 TCAAGCAGCCCGAGGGTTA 60.916 57.895 10.26 0.00 37.65 2.85
968 971 3.249189 TCAAGCAGCCCGAGGGTT 61.249 61.111 10.26 0.00 37.65 4.11
969 972 4.021925 GTCAAGCAGCCCGAGGGT 62.022 66.667 10.26 0.00 37.65 4.34
970 973 4.785453 GGTCAAGCAGCCCGAGGG 62.785 72.222 3.22 3.22 38.57 4.30
971 974 4.785453 GGGTCAAGCAGCCCGAGG 62.785 72.222 0.00 0.00 36.54 4.63
981 984 1.811266 CTCGTCATGCGGGGTCAAG 60.811 63.158 9.16 0.00 41.72 3.02
994 997 1.010574 CTCGCGTCTCCATCTCGTC 60.011 63.158 5.77 0.00 0.00 4.20
997 1000 2.352915 CGCTCGCGTCTCCATCTC 60.353 66.667 5.77 0.00 34.35 2.75
1445 1461 0.308993 GAAACTAGGGCATGCGCATC 59.691 55.000 33.01 19.20 41.24 3.91
1611 1635 6.144724 GCATATATTGACCAACTCGACTTCTC 59.855 42.308 0.00 0.00 0.00 2.87
1613 1637 5.753438 TGCATATATTGACCAACTCGACTTC 59.247 40.000 0.00 0.00 0.00 3.01
1657 1699 2.867624 TGCTCCAACAAAGAAGCAGAT 58.132 42.857 0.00 0.00 0.00 2.90
1803 1845 6.780706 TCGACAGAAAATGTTCTACCTTTC 57.219 37.500 0.00 0.00 44.17 2.62
1818 1860 9.653287 AGAAGATTATACAAACAATCGACAGAA 57.347 29.630 0.00 0.00 36.48 3.02
1837 1879 9.485206 CATCAATTTCCAACTTTCAAGAAGATT 57.515 29.630 0.00 0.00 0.00 2.40
1971 2021 3.831323 TGGAGACCAGAAGCAAATGAAA 58.169 40.909 0.00 0.00 0.00 2.69
2372 2422 8.352201 TCAATTTTTCCATTCTTAGCATATCCG 58.648 33.333 0.00 0.00 0.00 4.18
2396 2446 5.151297 TGAATATGGAGCGAGCAATATCA 57.849 39.130 0.00 0.00 0.00 2.15
2537 2587 5.474876 GCTCAATAGGGTAATTTCATCAGGG 59.525 44.000 0.00 0.00 0.00 4.45
2649 2699 2.039818 AGAGCATTGCAGATGGACAG 57.960 50.000 11.91 0.00 0.00 3.51
2657 2707 9.823098 GAGAACATATTAATAAGAGCATTGCAG 57.177 33.333 11.91 0.00 0.00 4.41
2777 2827 1.483415 GATTTGCCATCACCATGCCTT 59.517 47.619 0.00 0.00 0.00 4.35
2779 2829 1.117150 AGATTTGCCATCACCATGCC 58.883 50.000 0.00 0.00 0.00 4.40
2956 3006 3.884693 CACCATACAGCCATAATGCTCAA 59.115 43.478 0.00 0.00 40.32 3.02
3020 3070 7.412853 GTCTTACATGCATTGACTTTATGAGG 58.587 38.462 0.00 0.00 0.00 3.86
3185 3235 4.211125 TGTTCCAGTTACCAGATTTTGCA 58.789 39.130 0.00 0.00 0.00 4.08
3309 3360 7.587037 TGATTTTCTTGATGTTTCTCACCTT 57.413 32.000 0.00 0.00 0.00 3.50
3325 3376 6.603599 GCTTTACAAGGGTCCTATGATTTTCT 59.396 38.462 2.04 0.00 0.00 2.52
3386 3437 6.171213 ACCAGGTTAACATAAAGACTAGCAC 58.829 40.000 8.10 0.00 0.00 4.40
3401 3452 6.495526 CCCCTTTCAGAAATTTACCAGGTTAA 59.504 38.462 0.00 0.00 0.00 2.01
3404 3455 4.107311 TCCCCTTTCAGAAATTTACCAGGT 59.893 41.667 0.00 0.00 0.00 4.00
3408 3459 6.605471 AATGTCCCCTTTCAGAAATTTACC 57.395 37.500 0.00 0.00 0.00 2.85
3496 3552 9.868277 ACTTCAATTGTGAGTTCAAAATACAAA 57.132 25.926 5.13 0.00 32.86 2.83
3506 3563 8.514594 TCATTATGGAACTTCAATTGTGAGTTC 58.485 33.333 29.10 29.10 39.10 3.01
3553 3613 5.541953 TGACCACCTATGAGATGATTCTG 57.458 43.478 0.00 0.00 30.30 3.02
3554 3614 6.465464 CCATTGACCACCTATGAGATGATTCT 60.465 42.308 0.00 0.00 31.03 2.40
3567 3627 0.105760 TTGTTGCCCATTGACCACCT 60.106 50.000 0.00 0.00 0.00 4.00
3703 3763 2.039084 CTGCCTGTGTCTTCCCTTAACT 59.961 50.000 0.00 0.00 0.00 2.24
3767 3827 1.557832 TGACGGGAGGAAAATACTGGG 59.442 52.381 0.00 0.00 0.00 4.45
3768 3828 3.560636 ATGACGGGAGGAAAATACTGG 57.439 47.619 0.00 0.00 0.00 4.00
3769 3829 9.938280 TTAATATATGACGGGAGGAAAATACTG 57.062 33.333 0.00 0.00 0.00 2.74
3773 3833 9.672673 CATCTTAATATATGACGGGAGGAAAAT 57.327 33.333 0.00 0.00 0.00 1.82
3774 3834 8.876181 TCATCTTAATATATGACGGGAGGAAAA 58.124 33.333 0.00 0.00 0.00 2.29
3775 3835 8.430573 TCATCTTAATATATGACGGGAGGAAA 57.569 34.615 0.00 0.00 0.00 3.13
3776 3836 7.893833 TCTCATCTTAATATATGACGGGAGGAA 59.106 37.037 0.00 0.00 0.00 3.36
3777 3837 7.410991 TCTCATCTTAATATATGACGGGAGGA 58.589 38.462 0.00 0.00 0.00 3.71
3935 4001 8.217799 TCTGGATTCAAAGTTCTTAAGAAAGGA 58.782 33.333 19.30 11.33 35.58 3.36
3977 4043 1.229177 TCTGACTACTGCTGCCCCA 60.229 57.895 0.00 0.00 0.00 4.96
4041 4109 0.773644 ATGCACTGGGTCTGTCCTTT 59.226 50.000 0.00 0.00 36.25 3.11
4043 4111 1.198713 CTATGCACTGGGTCTGTCCT 58.801 55.000 0.00 0.00 36.25 3.85
4044 4112 1.195115 TCTATGCACTGGGTCTGTCC 58.805 55.000 0.00 0.00 0.00 4.02
4045 4113 2.898705 CTTCTATGCACTGGGTCTGTC 58.101 52.381 0.00 0.00 0.00 3.51
4046 4114 1.065854 GCTTCTATGCACTGGGTCTGT 60.066 52.381 0.00 0.00 0.00 3.41
4047 4115 1.209019 AGCTTCTATGCACTGGGTCTG 59.791 52.381 0.00 0.00 34.99 3.51
4048 4116 1.484240 GAGCTTCTATGCACTGGGTCT 59.516 52.381 0.00 0.00 34.99 3.85
4049 4117 1.474143 GGAGCTTCTATGCACTGGGTC 60.474 57.143 0.00 0.00 34.99 4.46
4050 4118 0.543749 GGAGCTTCTATGCACTGGGT 59.456 55.000 0.00 0.00 34.99 4.51
4051 4119 0.179034 GGGAGCTTCTATGCACTGGG 60.179 60.000 0.00 0.00 34.99 4.45
4052 4120 0.543277 TGGGAGCTTCTATGCACTGG 59.457 55.000 0.00 0.00 34.99 4.00
4053 4121 1.065926 TGTGGGAGCTTCTATGCACTG 60.066 52.381 0.00 0.00 34.99 3.66
4054 4122 1.279496 TGTGGGAGCTTCTATGCACT 58.721 50.000 0.00 0.00 34.99 4.40
4055 4123 1.945394 CATGTGGGAGCTTCTATGCAC 59.055 52.381 0.00 0.00 34.99 4.57
4056 4124 1.134007 CCATGTGGGAGCTTCTATGCA 60.134 52.381 0.00 0.00 40.01 3.96
4057 4125 1.133976 ACCATGTGGGAGCTTCTATGC 60.134 52.381 3.77 0.00 41.15 3.14
4058 4126 2.569059 CACCATGTGGGAGCTTCTATG 58.431 52.381 3.77 0.00 41.15 2.23
4070 4138 2.356278 CCCAGACCCCACCATGTG 59.644 66.667 0.00 0.00 0.00 3.21
4071 4139 2.941025 CCCCAGACCCCACCATGT 60.941 66.667 0.00 0.00 0.00 3.21
4072 4140 2.613696 TCCCCAGACCCCACCATG 60.614 66.667 0.00 0.00 0.00 3.66
4073 4141 2.286425 CTCCCCAGACCCCACCAT 60.286 66.667 0.00 0.00 0.00 3.55
4074 4142 4.675303 CCTCCCCAGACCCCACCA 62.675 72.222 0.00 0.00 0.00 4.17
4076 4144 3.660092 ATCCCTCCCCAGACCCCAC 62.660 68.421 0.00 0.00 0.00 4.61
4077 4145 1.542093 TAATCCCTCCCCAGACCCCA 61.542 60.000 0.00 0.00 0.00 4.96
4078 4146 0.103876 ATAATCCCTCCCCAGACCCC 60.104 60.000 0.00 0.00 0.00 4.95
4079 4147 2.552367 CTATAATCCCTCCCCAGACCC 58.448 57.143 0.00 0.00 0.00 4.46
4080 4148 2.113777 TCCTATAATCCCTCCCCAGACC 59.886 54.545 0.00 0.00 0.00 3.85
4081 4149 3.562108 TCCTATAATCCCTCCCCAGAC 57.438 52.381 0.00 0.00 0.00 3.51
4082 4150 3.441054 GGTTCCTATAATCCCTCCCCAGA 60.441 52.174 0.00 0.00 0.00 3.86
4083 4151 2.913617 GGTTCCTATAATCCCTCCCCAG 59.086 54.545 0.00 0.00 0.00 4.45
4084 4152 2.531463 AGGTTCCTATAATCCCTCCCCA 59.469 50.000 0.00 0.00 0.00 4.96
4085 4153 3.293215 AGGTTCCTATAATCCCTCCCC 57.707 52.381 0.00 0.00 0.00 4.81
4086 4154 5.024785 GACTAGGTTCCTATAATCCCTCCC 58.975 50.000 0.00 0.00 0.00 4.30
4087 4155 5.906254 AGACTAGGTTCCTATAATCCCTCC 58.094 45.833 0.00 0.00 0.00 4.30
4088 4156 7.396907 GGTAAGACTAGGTTCCTATAATCCCTC 59.603 44.444 0.00 0.00 0.00 4.30
4089 4157 7.247500 GGTAAGACTAGGTTCCTATAATCCCT 58.753 42.308 0.00 0.00 0.00 4.20
4090 4158 6.440010 GGGTAAGACTAGGTTCCTATAATCCC 59.560 46.154 0.00 4.36 0.00 3.85
4091 4159 6.440010 GGGGTAAGACTAGGTTCCTATAATCC 59.560 46.154 0.00 0.00 0.00 3.01
4092 4160 7.178805 CAGGGGTAAGACTAGGTTCCTATAATC 59.821 44.444 0.00 0.00 0.00 1.75
4093 4161 7.017531 CAGGGGTAAGACTAGGTTCCTATAAT 58.982 42.308 0.00 0.00 0.00 1.28
4094 4162 6.379579 CAGGGGTAAGACTAGGTTCCTATAA 58.620 44.000 0.00 0.00 0.00 0.98
4095 4163 5.694949 GCAGGGGTAAGACTAGGTTCCTATA 60.695 48.000 0.00 0.00 0.00 1.31
4096 4164 4.817286 CAGGGGTAAGACTAGGTTCCTAT 58.183 47.826 0.00 0.00 0.00 2.57
4097 4165 3.629282 GCAGGGGTAAGACTAGGTTCCTA 60.629 52.174 0.00 0.00 0.00 2.94
4098 4166 2.893153 GCAGGGGTAAGACTAGGTTCCT 60.893 54.545 0.00 0.00 0.00 3.36
4099 4167 1.485480 GCAGGGGTAAGACTAGGTTCC 59.515 57.143 0.00 0.00 0.00 3.62
4100 4168 2.185387 TGCAGGGGTAAGACTAGGTTC 58.815 52.381 0.00 0.00 0.00 3.62
4101 4169 2.337359 TGCAGGGGTAAGACTAGGTT 57.663 50.000 0.00 0.00 0.00 3.50
4102 4170 2.337359 TTGCAGGGGTAAGACTAGGT 57.663 50.000 0.00 0.00 0.00 3.08
4103 4171 2.572104 ACTTTGCAGGGGTAAGACTAGG 59.428 50.000 2.16 0.00 0.00 3.02
4104 4172 3.600388 CACTTTGCAGGGGTAAGACTAG 58.400 50.000 2.16 0.00 0.00 2.57
4105 4173 2.290071 GCACTTTGCAGGGGTAAGACTA 60.290 50.000 2.16 0.00 44.26 2.59
4106 4174 1.545651 GCACTTTGCAGGGGTAAGACT 60.546 52.381 2.16 0.00 44.26 3.24
4107 4175 0.881796 GCACTTTGCAGGGGTAAGAC 59.118 55.000 2.16 0.00 44.26 3.01
4108 4176 3.339547 GCACTTTGCAGGGGTAAGA 57.660 52.632 2.16 0.00 44.26 2.10
4118 4186 1.402456 CCTCTCTGCATTGCACTTTGC 60.402 52.381 7.38 8.20 45.29 3.68
4119 4187 1.402456 GCCTCTCTGCATTGCACTTTG 60.402 52.381 7.38 0.00 33.79 2.77
4120 4188 0.886563 GCCTCTCTGCATTGCACTTT 59.113 50.000 7.38 0.00 33.79 2.66
4121 4189 0.037877 AGCCTCTCTGCATTGCACTT 59.962 50.000 7.38 0.00 33.79 3.16
4122 4190 0.677098 CAGCCTCTCTGCATTGCACT 60.677 55.000 7.38 0.00 35.78 4.40
4123 4191 1.654954 CCAGCCTCTCTGCATTGCAC 61.655 60.000 7.38 0.00 41.50 4.57
4124 4192 1.378119 CCAGCCTCTCTGCATTGCA 60.378 57.895 11.50 11.50 41.50 4.08
4125 4193 0.964358 AACCAGCCTCTCTGCATTGC 60.964 55.000 0.46 0.46 41.50 3.56
4126 4194 1.093159 GAACCAGCCTCTCTGCATTG 58.907 55.000 0.00 0.00 41.50 2.82
4127 4195 0.392193 CGAACCAGCCTCTCTGCATT 60.392 55.000 0.00 0.00 41.50 3.56
4128 4196 1.220206 CGAACCAGCCTCTCTGCAT 59.780 57.895 0.00 0.00 41.50 3.96
4129 4197 1.471829 TTCGAACCAGCCTCTCTGCA 61.472 55.000 0.00 0.00 41.50 4.41
4130 4198 1.016653 GTTCGAACCAGCCTCTCTGC 61.017 60.000 17.68 0.00 41.50 4.26
4131 4199 3.129792 GTTCGAACCAGCCTCTCTG 57.870 57.895 17.68 0.00 42.49 3.35
4142 4210 0.685660 AAGAGGTCCTGGGTTCGAAC 59.314 55.000 20.14 20.14 0.00 3.95
4143 4211 0.685097 CAAGAGGTCCTGGGTTCGAA 59.315 55.000 0.00 0.00 0.00 3.71
4144 4212 1.192146 CCAAGAGGTCCTGGGTTCGA 61.192 60.000 0.00 0.00 30.82 3.71
4145 4213 1.296715 CCAAGAGGTCCTGGGTTCG 59.703 63.158 0.00 0.00 30.82 3.95
4146 4214 1.002011 GCCAAGAGGTCCTGGGTTC 60.002 63.158 0.00 0.00 38.32 3.62
4147 4215 1.774217 TGCCAAGAGGTCCTGGGTT 60.774 57.895 0.00 0.00 38.32 4.11
4148 4216 2.121963 TGCCAAGAGGTCCTGGGT 60.122 61.111 0.00 0.00 38.32 4.51
4149 4217 2.067932 TTGTGCCAAGAGGTCCTGGG 62.068 60.000 0.00 0.00 39.14 4.45
4150 4218 0.607489 CTTGTGCCAAGAGGTCCTGG 60.607 60.000 0.00 0.00 37.19 4.45
4151 4219 0.109342 ACTTGTGCCAAGAGGTCCTG 59.891 55.000 18.22 0.00 37.19 3.86
4152 4220 0.109342 CACTTGTGCCAAGAGGTCCT 59.891 55.000 18.22 0.00 37.19 3.85
4153 4221 0.890996 CCACTTGTGCCAAGAGGTCC 60.891 60.000 18.22 0.00 37.19 4.46
4154 4222 0.890996 CCCACTTGTGCCAAGAGGTC 60.891 60.000 21.11 0.00 37.19 3.85
4155 4223 1.151450 CCCACTTGTGCCAAGAGGT 59.849 57.895 21.11 2.99 37.19 3.85
4156 4224 1.604593 CCCCACTTGTGCCAAGAGG 60.605 63.158 18.22 18.17 38.23 3.69
4157 4225 0.607489 CTCCCCACTTGTGCCAAGAG 60.607 60.000 18.22 11.85 0.00 2.85
4158 4226 1.455849 CTCCCCACTTGTGCCAAGA 59.544 57.895 18.22 0.00 0.00 3.02
4159 4227 1.604593 CCTCCCCACTTGTGCCAAG 60.605 63.158 11.87 11.87 0.00 3.61
4160 4228 2.081787 TCCTCCCCACTTGTGCCAA 61.082 57.895 0.00 0.00 0.00 4.52
4161 4229 2.449518 TCCTCCCCACTTGTGCCA 60.450 61.111 0.00 0.00 0.00 4.92
4162 4230 2.034221 GTCCTCCCCACTTGTGCC 59.966 66.667 0.00 0.00 0.00 5.01
4163 4231 0.606673 GAAGTCCTCCCCACTTGTGC 60.607 60.000 0.00 0.00 34.10 4.57
4164 4232 0.764890 TGAAGTCCTCCCCACTTGTG 59.235 55.000 0.00 0.00 34.10 3.33
4165 4233 0.765510 GTGAAGTCCTCCCCACTTGT 59.234 55.000 0.00 0.00 34.10 3.16
4166 4234 0.036875 GGTGAAGTCCTCCCCACTTG 59.963 60.000 0.00 0.00 34.10 3.16
4167 4235 0.401395 TGGTGAAGTCCTCCCCACTT 60.401 55.000 0.00 0.00 36.77 3.16
4168 4236 1.128188 GTGGTGAAGTCCTCCCCACT 61.128 60.000 0.00 0.00 41.83 4.00
4169 4237 1.128188 AGTGGTGAAGTCCTCCCCAC 61.128 60.000 0.00 0.00 44.69 4.61
4170 4238 1.127567 CAGTGGTGAAGTCCTCCCCA 61.128 60.000 0.00 0.00 0.00 4.96
4171 4239 1.679898 CAGTGGTGAAGTCCTCCCC 59.320 63.158 0.00 0.00 0.00 4.81
4172 4240 1.003233 GCAGTGGTGAAGTCCTCCC 60.003 63.158 0.00 0.00 0.00 4.30
4173 4241 1.374758 CGCAGTGGTGAAGTCCTCC 60.375 63.158 0.00 0.00 0.00 4.30
4174 4242 2.029844 GCGCAGTGGTGAAGTCCTC 61.030 63.158 0.30 0.00 0.00 3.71
4175 4243 2.031163 GCGCAGTGGTGAAGTCCT 59.969 61.111 0.30 0.00 0.00 3.85
4176 4244 3.050275 GGCGCAGTGGTGAAGTCC 61.050 66.667 10.83 0.00 0.00 3.85
4177 4245 2.280797 TGGCGCAGTGGTGAAGTC 60.281 61.111 10.83 0.00 0.00 3.01
4178 4246 2.281070 CTGGCGCAGTGGTGAAGT 60.281 61.111 10.83 0.00 0.00 3.01
4179 4247 3.052082 CCTGGCGCAGTGGTGAAG 61.052 66.667 10.83 0.00 0.00 3.02
4192 4260 0.251077 GAATATGAGGGCAGGCCTGG 60.251 60.000 33.46 15.81 36.10 4.45
4193 4261 0.769873 AGAATATGAGGGCAGGCCTG 59.230 55.000 29.34 29.34 36.10 4.85
4194 4262 0.769873 CAGAATATGAGGGCAGGCCT 59.230 55.000 17.36 17.36 36.10 5.19
4195 4263 0.251077 CCAGAATATGAGGGCAGGCC 60.251 60.000 4.33 4.33 0.00 5.19
4196 4264 0.892814 GCCAGAATATGAGGGCAGGC 60.893 60.000 6.85 0.00 45.70 4.85
4197 4265 3.336122 GCCAGAATATGAGGGCAGG 57.664 57.895 6.85 0.00 45.70 4.85
4200 4268 1.678101 GTGTTGCCAGAATATGAGGGC 59.322 52.381 0.00 0.00 46.58 5.19
4201 4269 2.092212 AGGTGTTGCCAGAATATGAGGG 60.092 50.000 0.00 0.00 40.61 4.30
4202 4270 3.209410 GAGGTGTTGCCAGAATATGAGG 58.791 50.000 0.00 0.00 40.61 3.86
4203 4271 3.624861 GTGAGGTGTTGCCAGAATATGAG 59.375 47.826 0.00 0.00 40.61 2.90
4204 4272 3.264193 AGTGAGGTGTTGCCAGAATATGA 59.736 43.478 0.00 0.00 40.61 2.15
4205 4273 3.614092 AGTGAGGTGTTGCCAGAATATG 58.386 45.455 0.00 0.00 40.61 1.78
4206 4274 4.018960 AGAAGTGAGGTGTTGCCAGAATAT 60.019 41.667 0.00 0.00 40.61 1.28
4207 4275 3.327757 AGAAGTGAGGTGTTGCCAGAATA 59.672 43.478 0.00 0.00 40.61 1.75
4208 4276 2.107204 AGAAGTGAGGTGTTGCCAGAAT 59.893 45.455 0.00 0.00 40.61 2.40
4209 4277 1.490490 AGAAGTGAGGTGTTGCCAGAA 59.510 47.619 0.00 0.00 40.61 3.02
4210 4278 1.131638 AGAAGTGAGGTGTTGCCAGA 58.868 50.000 0.00 0.00 40.61 3.86
4211 4279 2.839486 TAGAAGTGAGGTGTTGCCAG 57.161 50.000 0.00 0.00 40.61 4.85
4212 4280 3.569194 TTTAGAAGTGAGGTGTTGCCA 57.431 42.857 0.00 0.00 40.61 4.92
4213 4281 4.911514 TTTTTAGAAGTGAGGTGTTGCC 57.088 40.909 0.00 0.00 37.58 4.52
4214 4282 6.072112 TGATTTTTAGAAGTGAGGTGTTGC 57.928 37.500 0.00 0.00 0.00 4.17
4215 4283 7.086376 CCATGATTTTTAGAAGTGAGGTGTTG 58.914 38.462 0.00 0.00 0.00 3.33
4216 4284 6.209391 CCCATGATTTTTAGAAGTGAGGTGTT 59.791 38.462 0.00 0.00 0.00 3.32
4217 4285 5.711976 CCCATGATTTTTAGAAGTGAGGTGT 59.288 40.000 0.00 0.00 0.00 4.16
4218 4286 5.393461 GCCCATGATTTTTAGAAGTGAGGTG 60.393 44.000 0.00 0.00 0.00 4.00
4219 4287 4.706962 GCCCATGATTTTTAGAAGTGAGGT 59.293 41.667 0.00 0.00 0.00 3.85
4220 4288 4.952335 AGCCCATGATTTTTAGAAGTGAGG 59.048 41.667 0.00 0.00 0.00 3.86
4221 4289 6.071728 ACAAGCCCATGATTTTTAGAAGTGAG 60.072 38.462 0.00 0.00 0.00 3.51
4222 4290 5.774690 ACAAGCCCATGATTTTTAGAAGTGA 59.225 36.000 0.00 0.00 0.00 3.41
4223 4291 6.029346 ACAAGCCCATGATTTTTAGAAGTG 57.971 37.500 0.00 0.00 0.00 3.16
4224 4292 6.267471 TGAACAAGCCCATGATTTTTAGAAGT 59.733 34.615 0.00 0.00 0.00 3.01
4225 4293 6.690530 TGAACAAGCCCATGATTTTTAGAAG 58.309 36.000 0.00 0.00 0.00 2.85
4226 4294 6.295236 CCTGAACAAGCCCATGATTTTTAGAA 60.295 38.462 0.00 0.00 0.00 2.10
4227 4295 5.185635 CCTGAACAAGCCCATGATTTTTAGA 59.814 40.000 0.00 0.00 0.00 2.10
4228 4296 5.185635 TCCTGAACAAGCCCATGATTTTTAG 59.814 40.000 0.00 0.00 0.00 1.85
4229 4297 5.083122 TCCTGAACAAGCCCATGATTTTTA 58.917 37.500 0.00 0.00 0.00 1.52
4230 4298 3.903090 TCCTGAACAAGCCCATGATTTTT 59.097 39.130 0.00 0.00 0.00 1.94
4245 4313 3.487544 GCGCTCACCAAATAATCCTGAAC 60.488 47.826 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.