Multiple sequence alignment - TraesCS7D01G121100

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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 TraesCS7D01G121100 chr7D 100.000 5516 0 0 1 5516 75265630 75271145 0.000000e+00 10187.0
1 TraesCS7D01G121100 chr7A 90.979 3536 207 41 1 3491 79538157 79541625 0.000000e+00 4660.0
2 TraesCS7D01G121100 chr7A 87.065 1724 161 23 3490 5180 79541672 79543366 0.000000e+00 1892.0
3 TraesCS7D01G121100 chr7B 87.639 1982 140 35 1545 3491 20835254 20837165 0.000000e+00 2206.0
4 TraesCS7D01G121100 chr7B 85.146 1710 162 38 3490 5181 20837212 20838847 0.000000e+00 1666.0
5 TraesCS7D01G121100 chr7B 87.562 1005 77 26 526 1497 20834263 20835252 0.000000e+00 1120.0
6 TraesCS7D01G121100 chr7B 88.889 270 25 3 4292 4557 20846509 20846777 1.480000e-85 327.0
7 TraesCS7D01G121100 chr7B 89.450 218 20 2 5302 5516 20838903 20839120 7.040000e-69 272.0
8 TraesCS7D01G121100 chr4D 81.657 1352 157 48 1750 3035 133728378 133729704 0.000000e+00 1038.0
9 TraesCS7D01G121100 chr4D 88.038 418 41 8 3080 3491 133729705 133730119 2.310000e-133 486.0
10 TraesCS7D01G121100 chr4D 80.784 536 64 18 4283 4809 133730356 133730861 3.120000e-102 383.0
11 TraesCS7D01G121100 chr4D 93.233 133 9 0 1341 1473 133727728 133727860 4.360000e-46 196.0
12 TraesCS7D01G121100 chr4A 86.228 639 69 13 2415 3035 427459137 427458500 0.000000e+00 675.0
13 TraesCS7D01G121100 chr4A 79.705 542 64 25 4292 4820 427457562 427457054 3.160000e-92 350.0
14 TraesCS7D01G121100 chr1D 82.766 499 71 13 2994 3487 160539804 160539316 1.100000e-116 431.0
15 TraesCS7D01G121100 chr1D 82.353 272 43 5 4292 4561 160539071 160538803 1.190000e-56 231.0
16 TraesCS7D01G121100 chr1D 92.079 101 8 0 5173 5273 135048028 135048128 5.760000e-30 143.0
17 TraesCS7D01G121100 chr2B 83.180 327 46 8 4324 4644 116324526 116324203 1.940000e-74 291.0
18 TraesCS7D01G121100 chr2B 97.436 39 1 0 5293 5331 788582712 788582674 3.570000e-07 67.6
19 TraesCS7D01G121100 chr1B 82.822 326 49 6 4324 4644 478568507 478568184 9.040000e-73 285.0
20 TraesCS7D01G121100 chr1B 94.624 93 5 0 5172 5264 352885047 352884955 1.600000e-30 145.0
21 TraesCS7D01G121100 chr6B 96.809 94 3 0 5174 5267 153532434 153532341 2.060000e-34 158.0
22 TraesCS7D01G121100 chr6B 94.595 37 2 0 5295 5331 205092300 205092336 2.150000e-04 58.4
23 TraesCS7D01G121100 chr2D 93.750 96 6 0 5176 5271 649821915 649821820 1.600000e-30 145.0
24 TraesCS7D01G121100 chr2D 92.079 101 8 0 5173 5273 513253216 513253116 5.760000e-30 143.0
25 TraesCS7D01G121100 chr2D 80.734 109 12 3 5233 5332 188810549 188810441 5.930000e-10 76.8
26 TraesCS7D01G121100 chr2D 97.436 39 1 0 5293 5331 150380685 150380723 3.570000e-07 67.6
27 TraesCS7D01G121100 chrUn 92.079 101 8 0 5173 5273 67634466 67634366 5.760000e-30 143.0
28 TraesCS7D01G121100 chrUn 75.694 144 35 0 459 602 28299708 28299851 7.660000e-09 73.1
29 TraesCS7D01G121100 chr6D 92.157 102 7 1 5171 5271 452939109 452939008 5.760000e-30 143.0
30 TraesCS7D01G121100 chr5D 92.079 101 8 0 5173 5273 347656209 347656109 5.760000e-30 143.0
31 TraesCS7D01G121100 chr3D 79.703 202 35 5 429 627 313180345 313180543 2.070000e-29 141.0
32 TraesCS7D01G121100 chr3D 100.000 32 0 0 5300 5331 541072235 541072266 5.970000e-05 60.2
33 TraesCS7D01G121100 chr1A 90.566 106 7 3 5161 5265 245535576 245535679 2.680000e-28 137.0
34 TraesCS7D01G121100 chr1A 94.444 36 2 0 5293 5328 77278334 77278369 7.720000e-04 56.5
35 TraesCS7D01G121100 chr3B 79.661 177 34 2 447 623 406651255 406651081 5.800000e-25 126.0
36 TraesCS7D01G121100 chr3A 78.218 202 38 5 429 627 419334167 419333969 2.090000e-24 124.0
37 TraesCS7D01G121100 chr5B 97.436 39 1 0 5293 5331 236259382 236259344 3.570000e-07 67.6
38 TraesCS7D01G121100 chr4B 94.737 38 2 0 5293 5330 41866848 41866885 5.970000e-05 60.2


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 TraesCS7D01G121100 chr7D 75265630 75271145 5515 False 10187.00 10187 100.00000 1 5516 1 chr7D.!!$F1 5515
1 TraesCS7D01G121100 chr7A 79538157 79543366 5209 False 3276.00 4660 89.02200 1 5180 2 chr7A.!!$F1 5179
2 TraesCS7D01G121100 chr7B 20834263 20839120 4857 False 1316.00 2206 87.44925 526 5516 4 chr7B.!!$F2 4990
3 TraesCS7D01G121100 chr4D 133727728 133730861 3133 False 525.75 1038 85.92800 1341 4809 4 chr4D.!!$F1 3468
4 TraesCS7D01G121100 chr4A 427457054 427459137 2083 True 512.50 675 82.96650 2415 4820 2 chr4A.!!$R1 2405
5 TraesCS7D01G121100 chr1D 160538803 160539804 1001 True 331.00 431 82.55950 2994 4561 2 chr1D.!!$R1 1567

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
856 884 0.699577 TCCAACCAAACCCTCTCCCA 60.700 55.000 0.00 0.00 0.00 4.37 F
1647 1738 1.007387 CGGTTCCTGTTTTGCTGGC 60.007 57.895 0.00 0.00 36.29 4.85 F
2222 2568 0.031857 CTCCAGCTAGCATGGTCTCG 59.968 60.000 23.87 12.73 39.01 4.04 F
3143 3527 0.108520 CCAACATCACATTGGCAGCC 60.109 55.000 3.66 3.66 40.25 4.85 F
3144 3528 0.604073 CAACATCACATTGGCAGCCA 59.396 50.000 11.22 11.22 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1881 1.002087 GGGTTCTGGAAAGAGCGAAGA 59.998 52.381 0.00 0.0 0.00 2.87 R
3128 3511 0.821517 ATGTGGCTGCCAATGTGATG 59.178 50.000 25.23 0.0 34.18 3.07 R
3890 4624 0.602638 CCAGTCACCAAAGTGCGCTA 60.603 55.000 9.73 0.0 44.16 4.26 R
4127 4861 0.675633 GTGAACAGGGTTTGCAGCAT 59.324 50.000 0.00 0.0 0.00 3.79 R
4593 5331 1.139853 GACCGAATGGAGAGCAAGGAT 59.860 52.381 0.00 0.0 39.21 3.24 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
239 240 1.805428 AAGTTGTTCATGCCCCGCAC 61.805 55.000 0.00 0.00 43.04 5.34
282 283 6.587990 CGAGCTTCAAGAAATCTTTAGAGACA 59.412 38.462 0.00 0.00 33.99 3.41
308 309 6.893958 ATTCATCTCTATGTGAACGAACAC 57.106 37.500 9.07 9.07 37.19 3.32
325 326 9.545611 GAACGAACACACGGTATATAAATTTTT 57.454 29.630 0.00 0.00 37.61 1.94
359 360 7.716612 TCATTCTCATAGCGAAAGTCTCATTA 58.283 34.615 0.00 0.00 0.00 1.90
366 367 5.041191 AGCGAAAGTCTCATTATTGGGAT 57.959 39.130 0.00 0.00 34.06 3.85
382 383 2.825861 GGATGCCCCATGCTTTATTG 57.174 50.000 0.00 0.00 42.00 1.90
385 386 3.134442 GGATGCCCCATGCTTTATTGAAA 59.866 43.478 0.00 0.00 42.00 2.69
386 387 4.383989 GGATGCCCCATGCTTTATTGAAAA 60.384 41.667 0.00 0.00 42.00 2.29
388 389 5.176741 TGCCCCATGCTTTATTGAAAATT 57.823 34.783 0.00 0.00 42.00 1.82
390 391 5.184711 GCCCCATGCTTTATTGAAAATTGA 58.815 37.500 0.00 0.00 36.87 2.57
411 412 5.376625 TGAGAGTATGTCAAAGCAGGTTTT 58.623 37.500 0.00 0.00 34.38 2.43
496 497 6.339587 TCCAACAAATCTCACCCATTTAAC 57.660 37.500 0.00 0.00 0.00 2.01
517 518 2.291153 CCACATCCATCCAAAGGTCTGT 60.291 50.000 0.00 0.00 0.00 3.41
521 522 2.054021 TCCATCCAAAGGTCTGTGTCA 58.946 47.619 0.00 0.00 0.00 3.58
529 530 5.063204 CCAAAGGTCTGTGTCACTTCAATA 58.937 41.667 4.27 0.00 0.00 1.90
557 558 4.533222 CGTTAAACACATTCAACACCCTC 58.467 43.478 0.00 0.00 0.00 4.30
811 839 0.759346 ACCAGCGTCAAACCTCTCTT 59.241 50.000 0.00 0.00 0.00 2.85
814 842 2.483876 CAGCGTCAAACCTCTCTTCAA 58.516 47.619 0.00 0.00 0.00 2.69
856 884 0.699577 TCCAACCAAACCCTCTCCCA 60.700 55.000 0.00 0.00 0.00 4.37
917 949 1.548719 GAACCCCAAATTTCTTCCCCG 59.451 52.381 0.00 0.00 0.00 5.73
922 954 1.474077 CCAAATTTCTTCCCCGCAGAG 59.526 52.381 0.00 0.00 0.00 3.35
962 1001 6.716628 TGAAACAGTGCTCCTGAGATTTTATT 59.283 34.615 10.39 0.00 44.49 1.40
1063 1102 1.075698 TCCTCTCCCTCGACAAGTTCT 59.924 52.381 0.00 0.00 0.00 3.01
1268 1310 3.805928 CCCCCTTCCCTTTTTGCC 58.194 61.111 0.00 0.00 0.00 4.52
1473 1516 5.163834 GCATCTTCGTCGTTTGGGTAATTTA 60.164 40.000 0.00 0.00 0.00 1.40
1485 1528 6.806388 TTGGGTAATTTACGTTCCTCTTTC 57.194 37.500 0.00 0.00 0.00 2.62
1502 1545 4.569943 TCTTTCCTAGTGCTACTTTGCTG 58.430 43.478 0.00 0.00 0.00 4.41
1507 1550 1.528129 AGTGCTACTTTGCTGCTTCC 58.472 50.000 0.00 0.00 0.00 3.46
1593 1681 5.296151 AGGAGCAATCCATTCTAATTCGA 57.704 39.130 0.00 0.00 0.00 3.71
1647 1738 1.007387 CGGTTCCTGTTTTGCTGGC 60.007 57.895 0.00 0.00 36.29 4.85
1682 1774 3.676873 GCCTTGCAATTTCCCATGTACTG 60.677 47.826 0.00 0.00 0.00 2.74
1684 1776 4.704540 CCTTGCAATTTCCCATGTACTGTA 59.295 41.667 0.00 0.00 0.00 2.74
1685 1777 5.360714 CCTTGCAATTTCCCATGTACTGTAT 59.639 40.000 0.00 0.00 0.00 2.29
1686 1778 5.833406 TGCAATTTCCCATGTACTGTATG 57.167 39.130 0.00 0.00 0.00 2.39
1687 1779 5.260424 TGCAATTTCCCATGTACTGTATGT 58.740 37.500 0.00 0.00 0.00 2.29
1688 1780 5.356751 TGCAATTTCCCATGTACTGTATGTC 59.643 40.000 0.00 0.00 0.00 3.06
1689 1781 5.221048 GCAATTTCCCATGTACTGTATGTCC 60.221 44.000 0.00 0.00 0.00 4.02
1690 1782 5.975988 ATTTCCCATGTACTGTATGTCCT 57.024 39.130 0.00 0.00 0.00 3.85
1692 1784 6.479972 TTTCCCATGTACTGTATGTCCTAG 57.520 41.667 0.00 0.00 0.00 3.02
1693 1785 5.138758 TCCCATGTACTGTATGTCCTAGT 57.861 43.478 0.00 0.00 0.00 2.57
1695 1787 6.304624 TCCCATGTACTGTATGTCCTAGTAG 58.695 44.000 0.00 0.00 0.00 2.57
1696 1788 5.477291 CCCATGTACTGTATGTCCTAGTAGG 59.523 48.000 10.24 10.24 36.46 3.18
1764 1928 3.855858 AGATCTTCGCTCTTTCCAGAAC 58.144 45.455 0.00 0.00 0.00 3.01
1806 2093 5.086104 TCTTGACTATCCTGCTTTACACC 57.914 43.478 0.00 0.00 0.00 4.16
1898 2206 0.321919 TTGCTGACAGATGGTGAGGC 60.322 55.000 6.65 0.00 30.56 4.70
1913 2221 1.876497 GAGGCATTTCGCTTTGGCCA 61.876 55.000 0.00 0.00 46.96 5.36
1951 2275 4.830826 ACAAGTTCGAACAAATCCCTTC 57.169 40.909 28.78 0.00 0.00 3.46
1952 2276 4.204012 ACAAGTTCGAACAAATCCCTTCA 58.796 39.130 28.78 0.00 0.00 3.02
2012 2336 3.225104 AGCATTCCACATTTCGCCATAT 58.775 40.909 0.00 0.00 0.00 1.78
2035 2359 1.623081 AACGACGTGGCGCAATAGTG 61.623 55.000 10.83 0.00 33.86 2.74
2067 2394 7.834068 TCTCTCTAATCAAAGTTTCCAATCG 57.166 36.000 0.00 0.00 0.00 3.34
2130 2457 9.559958 CTAGTTGGTATGCTTTATTTGTTTCTG 57.440 33.333 0.00 0.00 0.00 3.02
2165 2501 8.556194 GTTGAGTGTTGTCAGATGTTTGTAATA 58.444 33.333 0.00 0.00 0.00 0.98
2181 2517 9.737427 TGTTTGTAATAGTGTGGTGTTATTTTG 57.263 29.630 0.00 0.00 0.00 2.44
2222 2568 0.031857 CTCCAGCTAGCATGGTCTCG 59.968 60.000 23.87 12.73 39.01 4.04
2232 2578 2.968574 AGCATGGTCTCGATTCTGGTAT 59.031 45.455 0.00 0.00 0.00 2.73
2271 2618 9.671279 ACTTCAATTTTGGAATGACTTCTTTTT 57.329 25.926 0.00 0.00 0.00 1.94
2463 2823 4.351874 AGTGTGCTTTAGAAAGTAGGCA 57.648 40.909 4.05 0.00 38.28 4.75
2500 2862 5.069781 GTCTAGGCACTCTCACCATTCTTAT 59.930 44.000 0.00 0.00 41.75 1.73
2673 3035 4.403734 ACGGGCTTTTTATCAAAGAAGGA 58.596 39.130 0.00 0.00 0.00 3.36
2795 3157 2.630098 AGCACTGATACACACTGACTGT 59.370 45.455 0.00 0.00 0.00 3.55
2805 3167 9.457436 TGATACACACTGACTGTTATAGAAGTA 57.543 33.333 0.00 0.00 0.00 2.24
2806 3168 9.719279 GATACACACTGACTGTTATAGAAGTAC 57.281 37.037 0.00 0.00 0.00 2.73
2807 3169 7.520451 ACACACTGACTGTTATAGAAGTACA 57.480 36.000 0.00 0.00 0.00 2.90
2846 3222 3.126343 GGTAATTGGTTGCTGTAAGGTCG 59.874 47.826 0.00 0.00 0.00 4.79
2849 3225 0.470766 TGGTTGCTGTAAGGTCGGTT 59.529 50.000 0.00 0.00 0.00 4.44
2902 3281 7.387948 TCTTCTGACTCCTTTTGCAGTTTATAC 59.612 37.037 0.00 0.00 0.00 1.47
2910 3289 7.639378 TCCTTTTGCAGTTTATACCCTATCTT 58.361 34.615 0.00 0.00 0.00 2.40
2938 3317 2.094803 TCAAAATGCATACGGTGGCAAG 60.095 45.455 12.25 0.00 44.20 4.01
2941 3320 1.832883 ATGCATACGGTGGCAAGAAA 58.167 45.000 12.25 0.00 44.20 2.52
2944 3323 1.065551 GCATACGGTGGCAAGAAATCC 59.934 52.381 0.00 0.00 0.00 3.01
2956 3335 3.512680 CAAGAAATCCGCTCTTACGAGT 58.487 45.455 0.00 0.00 39.53 4.18
2965 3345 2.541556 GCTCTTACGAGTGTGAATCCC 58.458 52.381 0.00 0.00 39.53 3.85
2966 3346 2.094182 GCTCTTACGAGTGTGAATCCCA 60.094 50.000 0.00 0.00 39.53 4.37
2967 3347 3.430929 GCTCTTACGAGTGTGAATCCCAT 60.431 47.826 0.00 0.00 39.53 4.00
2968 3348 4.202121 GCTCTTACGAGTGTGAATCCCATA 60.202 45.833 0.00 0.00 39.53 2.74
2996 3376 6.405731 GGGAAATCTTGTACAATGCAGCAATA 60.406 38.462 9.13 0.00 0.00 1.90
3041 3421 7.669427 ACAAAGATTGCTTCCATTGTTTATGA 58.331 30.769 0.00 0.00 33.44 2.15
3042 3422 8.316214 ACAAAGATTGCTTCCATTGTTTATGAT 58.684 29.630 0.00 0.00 33.44 2.45
3043 3423 9.158233 CAAAGATTGCTTCCATTGTTTATGATT 57.842 29.630 0.00 0.00 32.60 2.57
3044 3424 9.729281 AAAGATTGCTTCCATTGTTTATGATTT 57.271 25.926 0.00 0.00 32.60 2.17
3113 3493 9.673454 AGAACAAATATCGTTTCCTTTGTTTAC 57.327 29.630 12.01 3.22 46.28 2.01
3128 3511 6.143278 CCTTTGTTTACGCTTAATTGTCCAAC 59.857 38.462 0.00 0.00 0.00 3.77
3143 3527 0.108520 CCAACATCACATTGGCAGCC 60.109 55.000 3.66 3.66 40.25 4.85
3144 3528 0.604073 CAACATCACATTGGCAGCCA 59.396 50.000 11.22 11.22 0.00 4.75
3151 3535 2.230992 TCACATTGGCAGCCACATTTAC 59.769 45.455 15.89 0.00 30.78 2.01
3156 3540 1.612950 TGGCAGCCACATTTACTGTTG 59.387 47.619 11.22 0.00 35.29 3.33
3190 3574 6.096705 TGTGATGATTTTCAGGTGTTCAAACT 59.903 34.615 0.00 0.00 0.00 2.66
3314 3971 6.403636 CCATTTGGGTGAGTATTCTTCTTTCG 60.404 42.308 0.00 0.00 0.00 3.46
3417 4077 9.773328 AAACTAATGTTGACATGATATTTGACG 57.227 29.630 0.00 0.00 36.56 4.35
3440 4100 7.372714 ACGTTAAACAGGAAAAACTTGAAAGT 58.627 30.769 0.00 0.00 42.04 2.66
3472 4138 9.245481 TCCGTGTTAATAAAATCCACCTTTTAT 57.755 29.630 0.00 0.00 41.02 1.40
3491 4157 6.985188 TTTATGATCCTTTGTTTCCTCTCG 57.015 37.500 0.00 0.00 0.00 4.04
3495 4161 4.527038 TGATCCTTTGTTTCCTCTCGTAGT 59.473 41.667 0.00 0.00 0.00 2.73
3500 4216 5.277345 CCTTTGTTTCCTCTCGTAGTTTGTG 60.277 44.000 0.00 0.00 0.00 3.33
3511 4228 7.700656 CCTCTCGTAGTTTGTGAAATTGTTTTT 59.299 33.333 0.00 0.00 0.00 1.94
3545 4262 8.686334 CATAGGTATTCTTTGTTTAAGTGGCAT 58.314 33.333 0.00 0.00 35.28 4.40
3549 4266 8.520351 GGTATTCTTTGTTTAAGTGGCATAGTT 58.480 33.333 0.00 0.00 35.28 2.24
3550 4267 9.908152 GTATTCTTTGTTTAAGTGGCATAGTTT 57.092 29.630 0.00 0.00 35.28 2.66
3594 4324 4.829808 CACTCAAAGTGTCGATATGCATG 58.170 43.478 10.16 0.00 41.19 4.06
3639 4370 9.788960 AGAAAATCTTGAGTTGTTTCTACAAAC 57.211 29.630 0.00 0.00 45.33 2.93
3642 4373 6.102006 TCTTGAGTTGTTTCTACAAACGTG 57.898 37.500 0.00 0.00 45.33 4.49
3662 4393 4.788100 CGTGAGCTGAATATTTTGTTTCCG 59.212 41.667 0.00 0.00 0.00 4.30
3707 4438 7.671495 AAAAATGTGGAATTTTACTCATGCC 57.329 32.000 0.00 0.00 31.67 4.40
3725 4456 1.406539 GCCGCATCCAAATTCATGACT 59.593 47.619 0.00 0.00 0.00 3.41
3732 4463 5.125097 GCATCCAAATTCATGACTCTTGTCT 59.875 40.000 0.00 0.00 43.29 3.41
3753 4484 5.691754 GTCTTGATGACACGATGCATGTATA 59.308 40.000 2.46 0.00 44.73 1.47
3781 4512 1.219646 GGCACACATGGTTTGCAAAG 58.780 50.000 13.26 3.15 40.49 2.77
3829 4560 3.056607 GGGGACATTTTGATCACCAACAG 60.057 47.826 0.00 0.00 38.39 3.16
3831 4562 4.280677 GGGACATTTTGATCACCAACAGAA 59.719 41.667 0.00 0.00 33.85 3.02
3833 4564 5.458041 ACATTTTGATCACCAACAGAAGG 57.542 39.130 0.00 0.00 33.85 3.46
3853 4584 9.643693 CAGAAGGTATGCTTTGTTCAAAATAAT 57.356 29.630 0.00 0.00 0.00 1.28
3860 4594 6.153067 TGCTTTGTTCAAAATAATACACGGG 58.847 36.000 0.00 0.00 0.00 5.28
3877 4611 3.922240 CACGGGAGCAAAATTCTTTCATG 59.078 43.478 0.00 0.00 0.00 3.07
3913 4647 1.268539 CGCACTTTGGTGACTGGAAAC 60.269 52.381 0.00 0.00 45.61 2.78
3942 4676 8.154649 TCCTCTTTCACAGTTCATAAAGTTTC 57.845 34.615 0.00 0.00 32.15 2.78
3944 4678 9.273016 CCTCTTTCACAGTTCATAAAGTTTCTA 57.727 33.333 0.00 0.00 32.15 2.10
3965 4699 2.291209 TTGCTGCCTTTGATTCCTGA 57.709 45.000 0.00 0.00 0.00 3.86
3997 4731 8.950210 ACTGTTAAGTGAATGATTGGTTCATAG 58.050 33.333 0.00 0.00 38.57 2.23
4004 4738 7.387122 AGTGAATGATTGGTTCATAGATCATCG 59.613 37.037 0.00 0.00 44.51 3.84
4013 4747 4.855715 TCATAGATCATCGAACCCTGTC 57.144 45.455 0.00 0.00 0.00 3.51
4016 4750 5.363868 TCATAGATCATCGAACCCTGTCTTT 59.636 40.000 0.00 0.00 0.00 2.52
4021 4755 4.065088 TCATCGAACCCTGTCTTTCTTTG 58.935 43.478 0.00 0.00 0.00 2.77
4071 4805 4.256110 TGTATCAGTTGAAGGACATGCAG 58.744 43.478 0.00 0.00 0.00 4.41
4075 4809 3.144506 CAGTTGAAGGACATGCAGAAGT 58.855 45.455 0.00 0.00 0.00 3.01
4135 4869 4.241590 AGAAATCGAACAAATGCTGCAA 57.758 36.364 6.36 0.00 0.00 4.08
4141 4875 2.137523 GAACAAATGCTGCAAACCCTG 58.862 47.619 6.36 2.47 0.00 4.45
4146 4880 0.675633 ATGCTGCAAACCCTGTTCAC 59.324 50.000 6.36 0.00 0.00 3.18
4165 4899 3.944650 TCACGGTCACCATGGATTTATTG 59.055 43.478 21.47 4.91 0.00 1.90
4172 4906 2.322658 CCATGGATTTATTGCCTGGCT 58.677 47.619 21.03 2.51 0.00 4.75
4173 4907 2.701951 CCATGGATTTATTGCCTGGCTT 59.298 45.455 21.03 9.99 0.00 4.35
4174 4908 3.135167 CCATGGATTTATTGCCTGGCTTT 59.865 43.478 21.03 9.62 0.00 3.51
4175 4909 4.344679 CCATGGATTTATTGCCTGGCTTTA 59.655 41.667 21.03 8.57 0.00 1.85
4238 4972 3.057596 ACGGTTTGGAAATGCATGTAGTG 60.058 43.478 0.00 0.00 0.00 2.74
4265 4999 4.961730 TGCTTATAATGGGGCAGTTTGATT 59.038 37.500 0.00 0.00 0.00 2.57
4275 5009 3.658757 GCAGTTTGATTGCCCAGTTAA 57.341 42.857 0.00 0.00 35.54 2.01
4317 5051 9.767228 TTTGTAAAGAACACAACTATAGCTACA 57.233 29.630 0.00 0.00 38.00 2.74
4360 5095 4.713553 TGTTGCCATCTTCTGTAGTTGAA 58.286 39.130 0.00 0.00 0.00 2.69
4447 5184 6.869913 ACTTAACGCAGCTACTTTATGTTACA 59.130 34.615 0.00 0.00 0.00 2.41
4547 5285 3.146066 GGTGTACTTCATTCTTGGCACA 58.854 45.455 0.00 0.00 0.00 4.57
4589 5327 4.637534 CAGTAGAGGCAACAAATGTGCTAT 59.362 41.667 0.00 0.00 41.41 2.97
4590 5328 5.124457 CAGTAGAGGCAACAAATGTGCTATT 59.876 40.000 0.00 0.00 41.41 1.73
4593 5331 5.009631 AGAGGCAACAAATGTGCTATTACA 58.990 37.500 0.00 0.00 41.41 2.41
4689 5427 9.584008 TCTAATCCGTCCTACATAGAGTTAATT 57.416 33.333 0.00 0.00 0.00 1.40
4714 5452 2.863809 AGTGTCATGTGGTTTCCCTTC 58.136 47.619 0.00 0.00 0.00 3.46
4825 5571 9.764363 GTAGAAATTTTTGGTCTTTTGGAGAAT 57.236 29.630 0.00 0.00 35.79 2.40
4861 5607 3.752747 TGCCAGTTAGATGTGAATGTGTG 59.247 43.478 0.00 0.00 0.00 3.82
4904 5650 2.029649 ACATCAGTTGCAATGGTTGAGC 60.030 45.455 0.59 0.00 0.00 4.26
4941 5692 1.575576 GCATCAGATCTCCGCCATGC 61.576 60.000 0.00 0.00 0.00 4.06
4945 5696 2.108976 GATCTCCGCCATGCCGAA 59.891 61.111 0.00 0.00 0.00 4.30
4973 5724 6.610830 TCAGTTTAAGAGGTTCCTGGAAAAT 58.389 36.000 11.40 2.26 0.00 1.82
4977 5728 7.785028 AGTTTAAGAGGTTCCTGGAAAATTCTT 59.215 33.333 23.33 23.33 0.00 2.52
5118 5885 1.869767 AGAACTTGCAGAGCGTCTTTG 59.130 47.619 0.00 0.00 0.00 2.77
5123 5890 2.812358 TGCAGAGCGTCTTTGTTCTA 57.188 45.000 0.00 0.00 0.00 2.10
5129 5896 3.493503 AGAGCGTCTTTGTTCTAAAACGG 59.506 43.478 0.00 0.00 38.28 4.44
5171 5940 2.791560 CTGTTGTCTCGTGAGTTGTGAG 59.208 50.000 0.00 0.00 0.00 3.51
5180 5949 5.009310 TCTCGTGAGTTGTGAGTAAAAGCTA 59.991 40.000 0.00 0.00 0.00 3.32
5181 5950 4.980434 TCGTGAGTTGTGAGTAAAAGCTAC 59.020 41.667 0.00 0.00 0.00 3.58
5182 5951 4.982916 CGTGAGTTGTGAGTAAAAGCTACT 59.017 41.667 0.00 0.00 0.00 2.57
5183 5952 5.117287 CGTGAGTTGTGAGTAAAAGCTACTC 59.883 44.000 8.00 8.00 43.06 2.59
5184 5953 5.405873 GTGAGTTGTGAGTAAAAGCTACTCC 59.594 44.000 11.69 5.12 42.32 3.85
5185 5954 4.895961 AGTTGTGAGTAAAAGCTACTCCC 58.104 43.478 11.69 2.21 42.32 4.30
5186 5955 4.593634 AGTTGTGAGTAAAAGCTACTCCCT 59.406 41.667 11.69 1.75 42.32 4.20
5187 5956 4.803098 TGTGAGTAAAAGCTACTCCCTC 57.197 45.455 11.69 3.65 42.32 4.30
5188 5957 3.514309 TGTGAGTAAAAGCTACTCCCTCC 59.486 47.826 11.69 0.33 42.32 4.30
5189 5958 2.758979 TGAGTAAAAGCTACTCCCTCCG 59.241 50.000 11.69 0.00 42.32 4.63
5190 5959 2.759535 GAGTAAAAGCTACTCCCTCCGT 59.240 50.000 4.05 0.00 38.33 4.69
5191 5960 2.759535 AGTAAAAGCTACTCCCTCCGTC 59.240 50.000 0.00 0.00 0.00 4.79
5192 5961 1.939980 AAAAGCTACTCCCTCCGTCT 58.060 50.000 0.00 0.00 0.00 4.18
5193 5962 1.476477 AAAGCTACTCCCTCCGTCTC 58.524 55.000 0.00 0.00 0.00 3.36
5194 5963 0.331954 AAGCTACTCCCTCCGTCTCA 59.668 55.000 0.00 0.00 0.00 3.27
5195 5964 0.553819 AGCTACTCCCTCCGTCTCAT 59.446 55.000 0.00 0.00 0.00 2.90
5196 5965 1.775459 AGCTACTCCCTCCGTCTCATA 59.225 52.381 0.00 0.00 0.00 2.15
5197 5966 2.175069 AGCTACTCCCTCCGTCTCATAA 59.825 50.000 0.00 0.00 0.00 1.90
5198 5967 3.158676 GCTACTCCCTCCGTCTCATAAT 58.841 50.000 0.00 0.00 0.00 1.28
5199 5968 4.043059 AGCTACTCCCTCCGTCTCATAATA 59.957 45.833 0.00 0.00 0.00 0.98
5200 5969 4.951094 GCTACTCCCTCCGTCTCATAATAT 59.049 45.833 0.00 0.00 0.00 1.28
5201 5970 6.069556 AGCTACTCCCTCCGTCTCATAATATA 60.070 42.308 0.00 0.00 0.00 0.86
5202 5971 6.602406 GCTACTCCCTCCGTCTCATAATATAA 59.398 42.308 0.00 0.00 0.00 0.98
5203 5972 7.201750 GCTACTCCCTCCGTCTCATAATATAAG 60.202 44.444 0.00 0.00 0.00 1.73
5204 5973 6.791371 ACTCCCTCCGTCTCATAATATAAGA 58.209 40.000 0.00 0.00 0.00 2.10
5205 5974 7.239438 ACTCCCTCCGTCTCATAATATAAGAA 58.761 38.462 0.00 0.00 0.00 2.52
5206 5975 7.177041 ACTCCCTCCGTCTCATAATATAAGAAC 59.823 40.741 0.00 0.00 0.00 3.01
5207 5976 6.150641 TCCCTCCGTCTCATAATATAAGAACG 59.849 42.308 0.00 0.00 0.00 3.95
5208 5977 6.072064 CCCTCCGTCTCATAATATAAGAACGT 60.072 42.308 0.00 0.00 0.00 3.99
5209 5978 7.368833 CCTCCGTCTCATAATATAAGAACGTT 58.631 38.462 0.00 0.00 0.00 3.99
5210 5979 7.866393 CCTCCGTCTCATAATATAAGAACGTTT 59.134 37.037 0.46 0.00 0.00 3.60
5211 5980 9.245962 CTCCGTCTCATAATATAAGAACGTTTT 57.754 33.333 0.46 0.00 0.00 2.43
5212 5981 9.590451 TCCGTCTCATAATATAAGAACGTTTTT 57.410 29.630 9.22 9.22 0.00 1.94
5213 5982 9.632969 CCGTCTCATAATATAAGAACGTTTTTG 57.367 33.333 13.87 0.00 0.00 2.44
5218 5987 9.961266 TCATAATATAAGAACGTTTTTGACACG 57.039 29.630 13.87 0.00 43.52 4.49
5219 5988 9.961266 CATAATATAAGAACGTTTTTGACACGA 57.039 29.630 13.87 0.00 40.20 4.35
5221 5990 5.978934 ATAAGAACGTTTTTGACACGAGT 57.021 34.783 13.87 0.00 40.20 4.18
5222 5991 8.746922 ATATAAGAACGTTTTTGACACGAGTA 57.253 30.769 13.87 0.00 40.20 2.59
5223 5992 5.978934 AAGAACGTTTTTGACACGAGTAT 57.021 34.783 0.46 0.00 40.20 2.12
5224 5993 8.746922 ATAAGAACGTTTTTGACACGAGTATA 57.253 30.769 13.87 0.00 40.20 1.47
5225 5994 7.467557 AAGAACGTTTTTGACACGAGTATAA 57.532 32.000 0.46 0.00 40.20 0.98
5226 5995 7.647907 AGAACGTTTTTGACACGAGTATAAT 57.352 32.000 0.46 0.00 40.20 1.28
5227 5996 7.507304 AGAACGTTTTTGACACGAGTATAATG 58.493 34.615 0.46 0.00 40.20 1.90
5228 5997 6.774354 ACGTTTTTGACACGAGTATAATGT 57.226 33.333 0.00 0.00 40.20 2.71
5229 5998 7.181143 ACGTTTTTGACACGAGTATAATGTT 57.819 32.000 0.00 0.00 40.20 2.71
5230 5999 8.296799 ACGTTTTTGACACGAGTATAATGTTA 57.703 30.769 0.00 0.00 40.20 2.41
5231 6000 8.763356 ACGTTTTTGACACGAGTATAATGTTAA 58.237 29.630 0.00 0.00 40.20 2.01
5232 6001 9.583530 CGTTTTTGACACGAGTATAATGTTAAA 57.416 29.630 0.00 0.00 40.20 1.52
5236 6005 9.583530 TTTGACACGAGTATAATGTTAAAAACG 57.416 29.630 0.00 0.00 31.31 3.60
5237 6006 8.296799 TGACACGAGTATAATGTTAAAAACGT 57.703 30.769 0.00 0.00 0.00 3.99
5238 6007 8.763356 TGACACGAGTATAATGTTAAAAACGTT 58.237 29.630 0.00 0.00 42.83 3.99
5239 6008 9.243011 GACACGAGTATAATGTTAAAAACGTTC 57.757 33.333 0.00 0.00 40.80 3.95
5240 6009 8.981647 ACACGAGTATAATGTTAAAAACGTTCT 58.018 29.630 0.00 0.00 40.80 3.01
5241 6010 9.801714 CACGAGTATAATGTTAAAAACGTTCTT 57.198 29.630 0.00 0.00 40.80 2.52
5256 6025 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
5257 6026 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
5258 6027 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
5259 6028 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
5260 6029 6.631766 CGTTCTTATATTTTGGGACAGAGGGA 60.632 42.308 0.00 0.00 42.39 4.20
5261 6030 6.500589 TCTTATATTTTGGGACAGAGGGAG 57.499 41.667 0.00 0.00 42.39 4.30
5369 6156 2.028567 GCAGCAACAGAGGTAGAAGAGT 60.029 50.000 0.00 0.00 0.00 3.24
5376 6163 6.037830 GCAACAGAGGTAGAAGAGTACTAGAG 59.962 46.154 0.00 0.00 0.00 2.43
5381 6169 4.103627 AGGTAGAAGAGTACTAGAGGCTCC 59.896 50.000 11.71 0.00 0.00 4.70
5415 6205 1.677576 TCAGGCAAACAGCTGAAACTG 59.322 47.619 23.35 18.92 44.79 3.16
5422 6212 2.829741 ACAGCTGAAACTGGAGAGAC 57.170 50.000 23.35 0.00 42.21 3.36
5429 6219 3.914312 TGAAACTGGAGAGACACGATTC 58.086 45.455 0.00 0.00 0.00 2.52
5430 6220 3.320826 TGAAACTGGAGAGACACGATTCA 59.679 43.478 0.00 0.00 0.00 2.57
5435 6225 6.227298 ACTGGAGAGACACGATTCAAATAT 57.773 37.500 0.00 0.00 0.00 1.28
5439 6229 7.102993 TGGAGAGACACGATTCAAATATCAAA 58.897 34.615 0.00 0.00 0.00 2.69
5440 6230 7.606073 TGGAGAGACACGATTCAAATATCAAAA 59.394 33.333 0.00 0.00 0.00 2.44
5442 6232 8.553459 AGAGACACGATTCAAATATCAAAACT 57.447 30.769 0.00 0.00 0.00 2.66
5448 6238 7.162546 CACGATTCAAATATCAAAACTACGCAG 59.837 37.037 0.00 0.00 0.00 5.18
5453 6243 6.746822 TCAAATATCAAAACTACGCAGCATTG 59.253 34.615 0.00 0.00 0.00 2.82
5466 6256 0.110486 AGCATTGGGTTGAGGTCGTT 59.890 50.000 0.00 0.00 0.00 3.85
5468 6258 1.335872 GCATTGGGTTGAGGTCGTTTG 60.336 52.381 0.00 0.00 0.00 2.93
5474 6264 1.076332 GTTGAGGTCGTTTGGATCGG 58.924 55.000 0.00 0.00 0.00 4.18
5495 6285 4.381411 GGTACATGAAAGCCACCTAGATC 58.619 47.826 0.00 0.00 0.00 2.75
5507 6297 3.243569 CCACCTAGATCATCGGACAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
5510 6300 2.969628 AGATCATCGGACAAGACCAC 57.030 50.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 7.995289 TGATTTGGACCATATGTCATGTTTAC 58.005 34.615 1.71 0.00 46.38 2.01
165 166 7.557719 CACTCCATGGGTTATAAACTTCTTCAT 59.442 37.037 13.02 0.00 0.00 2.57
282 283 9.035607 GTGTTCGTTCACATAGAGATGAATAAT 57.964 33.333 7.58 0.00 37.19 1.28
325 326 4.344968 TCGCTATGAGAATGATGGGAAGAA 59.655 41.667 0.00 0.00 0.00 2.52
382 383 7.025963 CCTGCTTTGACATACTCTCAATTTTC 58.974 38.462 0.00 0.00 0.00 2.29
385 386 5.564550 ACCTGCTTTGACATACTCTCAATT 58.435 37.500 0.00 0.00 0.00 2.32
386 387 5.171339 ACCTGCTTTGACATACTCTCAAT 57.829 39.130 0.00 0.00 0.00 2.57
388 389 4.623932 AACCTGCTTTGACATACTCTCA 57.376 40.909 0.00 0.00 0.00 3.27
390 391 5.594317 ACAAAAACCTGCTTTGACATACTCT 59.406 36.000 2.70 0.00 37.25 3.24
457 458 0.323302 TGGATGTCCGCAACTTGCTA 59.677 50.000 11.93 0.00 42.25 3.49
459 460 0.387239 GTTGGATGTCCGCAACTTGC 60.387 55.000 3.44 3.44 40.69 4.01
461 462 1.686355 TTGTTGGATGTCCGCAACTT 58.314 45.000 0.00 0.00 39.43 2.66
471 472 5.410355 AAATGGGTGAGATTTGTTGGATG 57.590 39.130 0.00 0.00 0.00 3.51
496 497 2.291153 ACAGACCTTTGGATGGATGTGG 60.291 50.000 0.00 0.00 30.98 4.17
517 518 8.775527 TGTTTAACGCTAAATATTGAAGTGACA 58.224 29.630 15.09 8.33 29.86 3.58
529 530 6.639279 GGTGTTGAATGTGTTTAACGCTAAAT 59.361 34.615 10.08 0.00 41.42 1.40
548 549 8.786898 CATGATATTAATTAGTGGAGGGTGTTG 58.213 37.037 0.00 0.00 0.00 3.33
693 716 7.541743 CGTGCAATAAACGTGAAATTTAGAA 57.458 32.000 0.00 0.00 36.31 2.10
747 774 1.247419 ATATCTCCGGCAGCCTCTCG 61.247 60.000 10.54 0.00 0.00 4.04
856 884 0.391263 GGAGAGGAATTTGGACGCGT 60.391 55.000 13.85 13.85 0.00 6.01
917 949 1.089920 ATGATTTCGTGGTGCTCTGC 58.910 50.000 0.00 0.00 0.00 4.26
922 954 3.637432 TGTTTCAATGATTTCGTGGTGC 58.363 40.909 0.00 0.00 0.00 5.01
929 961 5.159209 CAGGAGCACTGTTTCAATGATTTC 58.841 41.667 0.65 0.00 42.42 2.17
972 1011 3.264450 ACATCCACGAATCTTCCTCCTTT 59.736 43.478 0.00 0.00 0.00 3.11
973 1012 2.840651 ACATCCACGAATCTTCCTCCTT 59.159 45.455 0.00 0.00 0.00 3.36
974 1013 2.169352 CACATCCACGAATCTTCCTCCT 59.831 50.000 0.00 0.00 0.00 3.69
1063 1102 0.895530 CGCTTGAGGTAGTGGAGGAA 59.104 55.000 0.00 0.00 0.00 3.36
1142 1184 4.082523 CCATGGGTCGGTGCGAGT 62.083 66.667 2.85 0.00 36.23 4.18
1255 1297 2.360801 TCTTTCACGGCAAAAAGGGAAG 59.639 45.455 0.00 0.00 34.08 3.46
1267 1309 4.739716 CACAAAAACTGGATTCTTTCACGG 59.260 41.667 0.00 0.00 0.00 4.94
1268 1310 4.739716 CCACAAAAACTGGATTCTTTCACG 59.260 41.667 0.00 0.00 0.00 4.35
1473 1516 2.249139 AGCACTAGGAAAGAGGAACGT 58.751 47.619 0.00 0.00 0.00 3.99
1485 1528 2.393271 AGCAGCAAAGTAGCACTAGG 57.607 50.000 0.00 0.00 36.85 3.02
1502 1545 1.607148 GTATGGCCGTATTTGGGAAGC 59.393 52.381 8.21 0.00 0.00 3.86
1507 1550 0.107081 TCCCGTATGGCCGTATTTGG 59.893 55.000 8.21 10.50 0.00 3.28
1609 1697 0.249120 TGGTACCACGCCAAGAGATG 59.751 55.000 11.60 0.00 32.29 2.90
1647 1738 1.384222 GCAAGGCTAATGGAACGGGG 61.384 60.000 0.00 0.00 0.00 5.73
1684 1776 9.939424 AAGAAAATAGTACTCCTACTAGGACAT 57.061 33.333 0.00 0.00 40.06 3.06
1685 1777 9.765295 AAAGAAAATAGTACTCCTACTAGGACA 57.235 33.333 0.00 0.00 40.06 4.02
1687 1779 9.765295 ACAAAGAAAATAGTACTCCTACTAGGA 57.235 33.333 0.00 4.65 43.43 2.94
1692 1784 9.708092 ACTTGACAAAGAAAATAGTACTCCTAC 57.292 33.333 0.00 0.00 36.84 3.18
1695 1787 9.052759 TGAACTTGACAAAGAAAATAGTACTCC 57.947 33.333 0.00 0.00 36.84 3.85
1746 1881 1.002087 GGGTTCTGGAAAGAGCGAAGA 59.998 52.381 0.00 0.00 0.00 2.87
1764 1928 6.486657 TCAAGAATAAAGAACAAGTGAGTGGG 59.513 38.462 0.00 0.00 0.00 4.61
1898 2206 1.135402 GGTAGTGGCCAAAGCGAAATG 60.135 52.381 7.24 0.00 41.24 2.32
1913 2221 3.460712 ACTTGTAACCAAACCAGGGTAGT 59.539 43.478 0.00 0.00 37.77 2.73
1951 2275 6.092748 GCCCTACATGAAACAGTAAAACATG 58.907 40.000 0.00 0.00 42.37 3.21
1952 2276 5.772672 TGCCCTACATGAAACAGTAAAACAT 59.227 36.000 0.00 0.00 0.00 2.71
2012 2336 1.642728 ATTGCGCCACGTCGTTATAA 58.357 45.000 4.18 0.00 0.00 0.98
2035 2359 9.943163 GAAACTTTGATTAGAGAGAATAATGCC 57.057 33.333 0.00 0.00 0.00 4.40
2067 2394 2.440247 CCGACCCTCAAATGCCCC 60.440 66.667 0.00 0.00 0.00 5.80
2130 2457 7.147143 TCTGACAACACTCAACTATCTAGAC 57.853 40.000 0.00 0.00 0.00 2.59
2165 2501 7.106439 TCACAATTCAAAATAACACCACACT 57.894 32.000 0.00 0.00 0.00 3.55
2181 2517 6.251376 GGAGTATTCGTTTTGCATCACAATTC 59.749 38.462 0.00 0.00 38.31 2.17
2184 2527 4.517075 TGGAGTATTCGTTTTGCATCACAA 59.483 37.500 0.00 0.00 36.13 3.33
2186 2529 4.651994 CTGGAGTATTCGTTTTGCATCAC 58.348 43.478 0.00 0.00 0.00 3.06
2222 2568 2.807967 TGCGCTGCATAATACCAGAATC 59.192 45.455 9.73 0.00 31.71 2.52
2232 2578 1.233919 TTGAAGTGTGCGCTGCATAA 58.766 45.000 9.73 0.53 41.91 1.90
2271 2618 6.355747 TGCATCACATACACCATAATGAAGA 58.644 36.000 0.00 0.00 0.00 2.87
2428 2788 5.993106 AAGCACACTAGTTTGAGAAGAAC 57.007 39.130 13.23 0.00 0.00 3.01
2463 2823 6.067217 AGTGCCTAGACATCCAAATTACTT 57.933 37.500 0.00 0.00 0.00 2.24
2500 2862 2.120312 TGTCAATCAATACCCCGGCTA 58.880 47.619 0.00 0.00 0.00 3.93
2673 3035 5.128827 TCTTGTCTTCACCAACTTGTAGTCT 59.871 40.000 0.00 0.00 0.00 3.24
2873 3249 5.136105 ACTGCAAAAGGAGTCAGAAGAAAT 58.864 37.500 0.00 0.00 0.00 2.17
2910 3289 6.096036 CCACCGTATGCATTTTGAAAACATA 58.904 36.000 3.54 0.00 0.00 2.29
2929 3308 1.982073 GAGCGGATTTCTTGCCACCG 61.982 60.000 0.00 0.00 45.26 4.94
2965 3345 7.546358 TGCATTGTACAAGATTTCCCTTTATG 58.454 34.615 14.65 3.76 0.00 1.90
2966 3346 7.631377 GCTGCATTGTACAAGATTTCCCTTTAT 60.631 37.037 14.65 0.00 0.00 1.40
2967 3347 6.350110 GCTGCATTGTACAAGATTTCCCTTTA 60.350 38.462 14.65 0.00 0.00 1.85
2968 3348 5.567423 GCTGCATTGTACAAGATTTCCCTTT 60.567 40.000 14.65 0.00 0.00 3.11
2977 3357 9.920133 TTAAAAATATTGCTGCATTGTACAAGA 57.080 25.926 14.65 0.00 0.00 3.02
3010 3390 3.831323 TGGAAGCAATCTTTGTTCCTCA 58.169 40.909 15.81 2.83 39.47 3.86
3011 3391 5.166398 CAATGGAAGCAATCTTTGTTCCTC 58.834 41.667 15.81 0.00 39.47 3.71
3041 3421 8.758829 TGTGGTACTGAACTCTACATCATAAAT 58.241 33.333 0.00 0.00 0.00 1.40
3042 3422 8.129496 TGTGGTACTGAACTCTACATCATAAA 57.871 34.615 0.00 0.00 0.00 1.40
3043 3423 7.712204 TGTGGTACTGAACTCTACATCATAA 57.288 36.000 0.00 0.00 0.00 1.90
3044 3424 7.342026 ACATGTGGTACTGAACTCTACATCATA 59.658 37.037 0.00 0.00 30.33 2.15
3045 3425 6.155221 ACATGTGGTACTGAACTCTACATCAT 59.845 38.462 0.00 0.00 30.33 2.45
3046 3426 5.480422 ACATGTGGTACTGAACTCTACATCA 59.520 40.000 0.00 0.00 30.33 3.07
3047 3427 5.967088 ACATGTGGTACTGAACTCTACATC 58.033 41.667 0.00 0.00 30.33 3.06
3048 3428 6.096987 CCTACATGTGGTACTGAACTCTACAT 59.903 42.308 9.11 0.00 31.77 2.29
3113 3493 4.418013 TGTGATGTTGGACAATTAAGCG 57.582 40.909 0.00 0.00 0.00 4.68
3128 3511 0.821517 ATGTGGCTGCCAATGTGATG 59.178 50.000 25.23 0.00 34.18 3.07
3190 3574 3.189080 CAGTCTGTCGAATGCAATTTGGA 59.811 43.478 0.00 0.00 38.29 3.53
3314 3971 3.729966 AGTAAAATAGAAGGGCTAGCGC 58.270 45.455 23.33 23.33 31.33 5.92
3350 4007 3.711190 TCACCAAGAGCCAGCTTCATATA 59.289 43.478 0.00 0.00 0.00 0.86
3356 4013 1.615384 GGAATCACCAAGAGCCAGCTT 60.615 52.381 0.00 0.00 38.79 3.74
3440 4100 9.857957 GGTGGATTTTATTAACACGGAAATTAA 57.142 29.630 0.00 0.00 33.07 1.40
3472 4138 4.527038 ACTACGAGAGGAAACAAAGGATCA 59.473 41.667 0.00 0.00 0.00 2.92
3495 4161 8.498054 TGCAATAGGAAAAACAATTTCACAAA 57.502 26.923 3.63 0.00 0.00 2.83
3549 4266 8.090214 AGTGCGTTCTGGTAATAAAGTACTTAA 58.910 33.333 8.92 0.00 28.96 1.85
3550 4267 7.605449 AGTGCGTTCTGGTAATAAAGTACTTA 58.395 34.615 8.92 0.00 28.96 2.24
3620 4351 6.102006 TCACGTTTGTAGAAACAACTCAAG 57.898 37.500 15.04 0.47 45.18 3.02
3639 4370 4.788100 CGGAAACAAAATATTCAGCTCACG 59.212 41.667 0.00 0.00 0.00 4.35
3642 4373 4.732784 TGCGGAAACAAAATATTCAGCTC 58.267 39.130 10.89 0.00 43.92 4.09
3689 4420 2.163412 TGCGGCATGAGTAAAATTCCAC 59.837 45.455 0.00 0.00 0.00 4.02
3690 4421 2.441410 TGCGGCATGAGTAAAATTCCA 58.559 42.857 0.00 0.00 0.00 3.53
3707 4438 4.142534 ACAAGAGTCATGAATTTGGATGCG 60.143 41.667 16.63 0.00 0.00 4.73
3732 4463 5.355596 TGTATACATGCATCGTGTCATCAA 58.644 37.500 0.08 0.00 35.12 2.57
3742 4473 4.456566 TGCCACATGATGTATACATGCATC 59.543 41.667 22.93 9.93 45.95 3.91
3747 4478 4.779696 TGTGTGCCACATGATGTATACAT 58.220 39.130 18.31 18.31 39.62 2.29
3776 4507 8.344831 TGTTCATACTTATATCATGCACTTTGC 58.655 33.333 0.00 0.00 45.29 3.68
3792 4523 4.927267 TGTCCCCTCAATGTTCATACTT 57.073 40.909 0.00 0.00 0.00 2.24
3796 4527 5.085920 TCAAAATGTCCCCTCAATGTTCAT 58.914 37.500 0.00 0.00 0.00 2.57
3804 4535 2.378208 TGGTGATCAAAATGTCCCCTCA 59.622 45.455 0.00 0.00 0.00 3.86
3805 4536 3.085952 TGGTGATCAAAATGTCCCCTC 57.914 47.619 0.00 0.00 0.00 4.30
3807 4538 2.896685 TGTTGGTGATCAAAATGTCCCC 59.103 45.455 0.00 0.00 37.08 4.81
3831 4562 9.855021 GTGTATTATTTTGAACAAAGCATACCT 57.145 29.630 15.07 3.35 0.00 3.08
3833 4564 8.794406 CCGTGTATTATTTTGAACAAAGCATAC 58.206 33.333 12.97 12.97 0.00 2.39
3853 4584 4.138290 TGAAAGAATTTTGCTCCCGTGTA 58.862 39.130 0.00 0.00 39.27 2.90
3854 4585 2.955660 TGAAAGAATTTTGCTCCCGTGT 59.044 40.909 0.00 0.00 39.27 4.49
3855 4586 3.641437 TGAAAGAATTTTGCTCCCGTG 57.359 42.857 0.00 0.00 39.27 4.94
3877 4611 6.632834 CCAAAGTGCGCTATACACAATAATTC 59.367 38.462 9.73 0.00 40.59 2.17
3885 4619 2.093783 GTCACCAAAGTGCGCTATACAC 59.906 50.000 9.73 0.00 44.16 2.90
3887 4621 2.348666 CAGTCACCAAAGTGCGCTATAC 59.651 50.000 9.73 0.00 44.16 1.47
3890 4624 0.602638 CCAGTCACCAAAGTGCGCTA 60.603 55.000 9.73 0.00 44.16 4.26
3894 4628 1.067060 GGTTTCCAGTCACCAAAGTGC 59.933 52.381 0.00 0.00 44.16 4.40
3913 4647 7.229506 ACTTTATGAACTGTGAAAGAGGAAAGG 59.770 37.037 10.07 0.00 33.90 3.11
3930 4664 7.466746 AGGCAGCAAATAGAAACTTTATGAA 57.533 32.000 0.00 0.00 0.00 2.57
3942 4676 4.400251 TCAGGAATCAAAGGCAGCAAATAG 59.600 41.667 0.00 0.00 0.00 1.73
3944 4678 3.167485 TCAGGAATCAAAGGCAGCAAAT 58.833 40.909 0.00 0.00 0.00 2.32
3965 4699 9.520515 ACCAATCATTCACTTAACAGTAAATCT 57.479 29.630 0.00 0.00 0.00 2.40
3979 4713 7.386025 TCGATGATCTATGAACCAATCATTCAC 59.614 37.037 0.00 0.00 46.85 3.18
3997 4731 4.130286 AGAAAGACAGGGTTCGATGATC 57.870 45.455 0.00 0.00 0.00 2.92
4004 4738 5.348986 GGAAAACAAAGAAAGACAGGGTTC 58.651 41.667 0.00 0.00 0.00 3.62
4009 4743 4.037690 CAGCGGAAAACAAAGAAAGACAG 58.962 43.478 0.00 0.00 0.00 3.51
4013 4747 5.336744 TGTAACAGCGGAAAACAAAGAAAG 58.663 37.500 0.00 0.00 0.00 2.62
4016 4750 4.261405 CCATGTAACAGCGGAAAACAAAGA 60.261 41.667 0.00 0.00 0.00 2.52
4021 4755 2.550606 TGACCATGTAACAGCGGAAAAC 59.449 45.455 0.00 0.00 0.00 2.43
4056 4790 2.351157 GCACTTCTGCATGTCCTTCAAC 60.351 50.000 0.00 0.00 43.62 3.18
4071 4805 7.986085 ATATGTTGTATAGGGAATGCACTTC 57.014 36.000 0.00 0.00 28.95 3.01
4125 4859 1.761784 TGAACAGGGTTTGCAGCATTT 59.238 42.857 0.00 0.00 0.00 2.32
4126 4860 1.069049 GTGAACAGGGTTTGCAGCATT 59.931 47.619 0.00 0.00 0.00 3.56
4127 4861 0.675633 GTGAACAGGGTTTGCAGCAT 59.324 50.000 0.00 0.00 0.00 3.79
4141 4875 1.821216 AATCCATGGTGACCGTGAAC 58.179 50.000 24.81 0.00 42.73 3.18
4146 4880 2.034558 GGCAATAAATCCATGGTGACCG 59.965 50.000 12.58 0.00 0.00 4.79
4165 4899 5.845391 TGGTGTAATAAATAAAGCCAGGC 57.155 39.130 1.84 1.84 0.00 4.85
4238 4972 3.500343 ACTGCCCCATTATAAGCATTCC 58.500 45.455 0.00 0.00 34.16 3.01
4265 4999 6.532988 AACTTGTAACTTTTTAACTGGGCA 57.467 33.333 0.00 0.00 0.00 5.36
4317 5051 1.659794 GCATTCAGCAACACGGGTT 59.340 52.632 0.00 0.00 44.79 4.11
4418 5154 3.662247 AAGTAGCTGCGTTAAGTCACT 57.338 42.857 0.00 0.00 0.00 3.41
4447 5184 7.877097 GGTCTTCATATCTCTGATATTTGCTGT 59.123 37.037 0.00 0.00 0.00 4.40
4589 5327 3.432186 CCGAATGGAGAGCAAGGATGTAA 60.432 47.826 0.00 0.00 37.49 2.41
4590 5328 2.103094 CCGAATGGAGAGCAAGGATGTA 59.897 50.000 0.00 0.00 37.49 2.29
4593 5331 1.139853 GACCGAATGGAGAGCAAGGAT 59.860 52.381 0.00 0.00 39.21 3.24
4658 5396 7.560626 ACTCTATGTAGGACGGATTAGAAGTTT 59.439 37.037 0.00 0.00 0.00 2.66
4714 5452 5.545723 AGATCCCTAAAGTCCTCCACATATG 59.454 44.000 0.00 0.00 0.00 1.78
4825 5571 1.355381 ACTGGCATCTCAAACCATCCA 59.645 47.619 0.00 0.00 31.79 3.41
4941 5692 6.206829 AGGAACCTCTTAAACTGAAAATTCGG 59.793 38.462 0.44 0.44 39.48 4.30
4945 5696 6.610830 TCCAGGAACCTCTTAAACTGAAAAT 58.389 36.000 0.00 0.00 0.00 1.82
4981 5732 7.759489 AGTACATAGACAAGCAATGGAAAAA 57.241 32.000 0.00 0.00 0.00 1.94
5089 5856 3.181487 GCTCTGCAAGTTCTGTCCAAAAA 60.181 43.478 0.00 0.00 33.76 1.94
5171 5940 2.759535 AGACGGAGGGAGTAGCTTTTAC 59.240 50.000 0.00 0.00 0.00 2.01
5180 5949 6.791371 TCTTATATTATGAGACGGAGGGAGT 58.209 40.000 0.00 0.00 0.00 3.85
5181 5950 7.540299 GTTCTTATATTATGAGACGGAGGGAG 58.460 42.308 0.00 0.00 0.00 4.30
5182 5951 6.150641 CGTTCTTATATTATGAGACGGAGGGA 59.849 42.308 0.00 0.00 0.00 4.20
5183 5952 6.072064 ACGTTCTTATATTATGAGACGGAGGG 60.072 42.308 16.71 2.79 0.00 4.30
5184 5953 6.910995 ACGTTCTTATATTATGAGACGGAGG 58.089 40.000 16.71 6.29 0.00 4.30
5185 5954 8.798748 AAACGTTCTTATATTATGAGACGGAG 57.201 34.615 0.00 6.40 0.00 4.63
5186 5955 9.590451 AAAAACGTTCTTATATTATGAGACGGA 57.410 29.630 0.00 0.00 0.00 4.69
5187 5956 9.632969 CAAAAACGTTCTTATATTATGAGACGG 57.367 33.333 0.00 8.31 0.00 4.79
5192 5961 9.961266 CGTGTCAAAAACGTTCTTATATTATGA 57.039 29.630 0.00 0.00 36.31 2.15
5193 5962 9.961266 TCGTGTCAAAAACGTTCTTATATTATG 57.039 29.630 0.00 0.00 41.70 1.90
5195 5964 9.195411 ACTCGTGTCAAAAACGTTCTTATATTA 57.805 29.630 0.00 0.00 41.70 0.98
5196 5965 8.080083 ACTCGTGTCAAAAACGTTCTTATATT 57.920 30.769 0.00 0.00 41.70 1.28
5197 5966 7.647907 ACTCGTGTCAAAAACGTTCTTATAT 57.352 32.000 0.00 0.00 41.70 0.86
5198 5967 8.746922 ATACTCGTGTCAAAAACGTTCTTATA 57.253 30.769 0.00 0.00 41.70 0.98
5199 5968 5.978934 ACTCGTGTCAAAAACGTTCTTAT 57.021 34.783 0.00 0.00 41.70 1.73
5200 5969 8.572828 TTATACTCGTGTCAAAAACGTTCTTA 57.427 30.769 0.00 0.00 41.70 2.10
5201 5970 5.978934 ATACTCGTGTCAAAAACGTTCTT 57.021 34.783 0.00 0.00 41.70 2.52
5202 5971 7.170320 ACATTATACTCGTGTCAAAAACGTTCT 59.830 33.333 0.00 0.00 41.70 3.01
5203 5972 7.285788 ACATTATACTCGTGTCAAAAACGTTC 58.714 34.615 0.00 0.00 41.70 3.95
5204 5973 7.181143 ACATTATACTCGTGTCAAAAACGTT 57.819 32.000 0.00 0.00 41.70 3.99
5205 5974 6.774354 ACATTATACTCGTGTCAAAAACGT 57.226 33.333 0.00 0.00 41.70 3.99
5206 5975 9.583530 TTTAACATTATACTCGTGTCAAAAACG 57.416 29.630 0.00 0.00 42.36 3.60
5210 5979 9.583530 CGTTTTTAACATTATACTCGTGTCAAA 57.416 29.630 0.00 0.00 0.00 2.69
5211 5980 8.763356 ACGTTTTTAACATTATACTCGTGTCAA 58.237 29.630 0.00 0.00 0.00 3.18
5212 5981 8.296799 ACGTTTTTAACATTATACTCGTGTCA 57.703 30.769 0.00 0.00 0.00 3.58
5213 5982 9.243011 GAACGTTTTTAACATTATACTCGTGTC 57.757 33.333 0.46 0.00 0.00 3.67
5214 5983 8.981647 AGAACGTTTTTAACATTATACTCGTGT 58.018 29.630 0.46 0.00 0.00 4.49
5215 5984 9.801714 AAGAACGTTTTTAACATTATACTCGTG 57.198 29.630 0.46 0.00 0.00 4.35
5230 5999 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
5231 6000 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
5232 6001 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
5233 6002 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
5234 6003 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
5235 6004 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
5236 6005 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
5237 6006 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
5238 6007 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
5239 6008 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
5240 6009 6.183361 GCTACTCCCTCTGTCCCAAAATATAA 60.183 42.308 0.00 0.00 0.00 0.98
5241 6010 5.307196 GCTACTCCCTCTGTCCCAAAATATA 59.693 44.000 0.00 0.00 0.00 0.86
5242 6011 4.103311 GCTACTCCCTCTGTCCCAAAATAT 59.897 45.833 0.00 0.00 0.00 1.28
5243 6012 3.454812 GCTACTCCCTCTGTCCCAAAATA 59.545 47.826 0.00 0.00 0.00 1.40
5244 6013 2.239907 GCTACTCCCTCTGTCCCAAAAT 59.760 50.000 0.00 0.00 0.00 1.82
5245 6014 1.628846 GCTACTCCCTCTGTCCCAAAA 59.371 52.381 0.00 0.00 0.00 2.44
5246 6015 1.203313 AGCTACTCCCTCTGTCCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
5247 6016 0.413832 AGCTACTCCCTCTGTCCCAA 59.586 55.000 0.00 0.00 0.00 4.12
5248 6017 1.215673 CTAGCTACTCCCTCTGTCCCA 59.784 57.143 0.00 0.00 0.00 4.37
5249 6018 1.215924 ACTAGCTACTCCCTCTGTCCC 59.784 57.143 0.00 0.00 0.00 4.46
5250 6019 2.740506 ACTAGCTACTCCCTCTGTCC 57.259 55.000 0.00 0.00 0.00 4.02
5251 6020 4.383173 GAGTACTAGCTACTCCCTCTGTC 58.617 52.174 15.86 0.00 44.14 3.51
5252 6021 4.426736 GAGTACTAGCTACTCCCTCTGT 57.573 50.000 15.86 0.00 44.14 3.41
5260 6029 2.791749 AGGGAGGGAGTACTAGCTACT 58.208 52.381 0.00 5.12 38.52 2.57
5261 6030 4.720775 TTAGGGAGGGAGTACTAGCTAC 57.279 50.000 0.00 0.00 0.00 3.58
5295 6064 8.467598 AGAGCGTTTAGATCAGTAAAGTAATGA 58.532 33.333 0.00 0.00 37.82 2.57
5347 6134 1.067565 TCTTCTACCTCTGTTGCTGCG 60.068 52.381 0.00 0.00 0.00 5.18
5369 6156 7.618019 ATTGTATTGATTGGAGCCTCTAGTA 57.382 36.000 0.00 0.00 0.00 1.82
5376 6163 5.594926 CCTGAAATTGTATTGATTGGAGCC 58.405 41.667 0.00 0.00 0.00 4.70
5381 6169 7.622672 GCTGTTTGCCTGAAATTGTATTGATTG 60.623 37.037 0.00 0.00 35.15 2.67
5415 6205 7.539712 TTTGATATTTGAATCGTGTCTCTCC 57.460 36.000 0.00 0.00 0.00 3.71
5422 6212 6.958752 TGCGTAGTTTTGATATTTGAATCGTG 59.041 34.615 0.00 0.00 0.00 4.35
5429 6219 6.020440 CCAATGCTGCGTAGTTTTGATATTTG 60.020 38.462 15.37 2.99 0.00 2.32
5430 6220 6.035843 CCAATGCTGCGTAGTTTTGATATTT 58.964 36.000 15.37 0.00 0.00 1.40
5435 6225 1.539388 CCCAATGCTGCGTAGTTTTGA 59.461 47.619 15.37 0.00 0.00 2.69
5439 6229 0.881118 CAACCCAATGCTGCGTAGTT 59.119 50.000 1.53 0.00 0.00 2.24
5440 6230 0.036164 TCAACCCAATGCTGCGTAGT 59.964 50.000 1.53 0.00 0.00 2.73
5442 6232 0.676466 CCTCAACCCAATGCTGCGTA 60.676 55.000 0.00 0.00 0.00 4.42
5448 6238 0.958822 AAACGACCTCAACCCAATGC 59.041 50.000 0.00 0.00 0.00 3.56
5453 6243 1.450025 GATCCAAACGACCTCAACCC 58.550 55.000 0.00 0.00 0.00 4.11
5466 6256 2.026729 TGGCTTTCATGTACCGATCCAA 60.027 45.455 0.00 0.00 0.00 3.53
5468 6258 1.940613 GTGGCTTTCATGTACCGATCC 59.059 52.381 0.00 0.00 0.00 3.36
5474 6264 5.023533 TGATCTAGGTGGCTTTCATGTAC 57.976 43.478 0.00 0.00 0.00 2.90
5495 6285 2.169832 ACTTGTGGTCTTGTCCGATG 57.830 50.000 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.