Multiple sequence alignment - TraesCS1A01G333900

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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 TraesCS1A01G333900 chr1A 100.000 4353 0 0 2343 6695 521640986 521645338 0.000000e+00 8039.0
1 TraesCS1A01G333900 chr1A 100.000 1959 0 0 1 1959 521638644 521640602 0.000000e+00 3618.0
2 TraesCS1A01G333900 chr1A 83.146 534 66 17 3893 4413 521672352 521672874 3.660000e-127 466.0
3 TraesCS1A01G333900 chr1A 93.182 88 5 1 3754 3840 506544446 506544533 1.960000e-25 128.0
4 TraesCS1A01G333900 chr1B 94.638 2387 94 14 3836 6202 576217421 576219793 0.000000e+00 3668.0
5 TraesCS1A01G333900 chr1B 87.808 1665 102 34 363 1957 576214062 576215695 0.000000e+00 1857.0
6 TraesCS1A01G333900 chr1B 91.905 803 45 12 2371 3171 576215702 576216486 0.000000e+00 1105.0
7 TraesCS1A01G333900 chr1B 89.820 501 28 11 6202 6695 576219829 576220313 7.370000e-174 621.0
8 TraesCS1A01G333900 chr1B 88.235 408 40 4 3893 4298 576221362 576221763 1.310000e-131 481.0
9 TraesCS1A01G333900 chr1B 90.654 321 28 2 3222 3542 576216719 576217037 6.210000e-115 425.0
10 TraesCS1A01G333900 chr1B 86.589 343 33 11 10 347 576213672 576214006 3.810000e-97 366.0
11 TraesCS1A01G333900 chr1B 91.810 232 12 1 3529 3753 576217188 576217419 3.900000e-82 316.0
12 TraesCS1A01G333900 chr1B 77.419 310 19 18 5792 6066 576222809 576223102 3.260000e-28 137.0
13 TraesCS1A01G333900 chr1B 94.318 88 4 1 3754 3840 553143960 553144047 4.210000e-27 134.0
14 TraesCS1A01G333900 chr1B 86.486 111 7 1 4303 4413 576221813 576221915 1.530000e-21 115.0
15 TraesCS1A01G333900 chr1D 94.510 2386 88 23 3836 6200 426597513 426599876 0.000000e+00 3640.0
16 TraesCS1A01G333900 chr1D 89.856 1252 79 15 723 1955 426594659 426595881 0.000000e+00 1565.0
17 TraesCS1A01G333900 chr1D 90.291 824 41 18 2366 3155 426595882 426596700 0.000000e+00 1042.0
18 TraesCS1A01G333900 chr1D 93.928 527 31 1 3223 3749 426596984 426597509 0.000000e+00 795.0
19 TraesCS1A01G333900 chr1D 82.480 371 14 22 26 347 426593744 426594112 1.840000e-70 278.0
20 TraesCS1A01G333900 chr1D 93.182 88 5 1 3754 3840 410499374 410499461 1.960000e-25 128.0
21 TraesCS1A01G333900 chr1D 96.667 60 2 0 405 464 426594220 426594279 4.270000e-17 100.0
22 TraesCS1A01G333900 chr5B 86.257 764 74 20 995 1739 85623389 85622638 0.000000e+00 800.0
23 TraesCS1A01G333900 chr3B 88.424 311 30 3 1424 1734 275005962 275005658 2.950000e-98 370.0
24 TraesCS1A01G333900 chr3B 80.345 290 28 16 6422 6695 460248324 460248600 6.850000e-45 193.0
25 TraesCS1A01G333900 chr7B 87.629 291 30 3 995 1282 112652885 112653172 3.870000e-87 333.0
26 TraesCS1A01G333900 chr7B 77.070 157 25 9 4060 4212 594034998 594035147 5.570000e-11 80.5
27 TraesCS1A01G333900 chr3D 83.776 339 33 13 1401 1739 218736447 218736763 1.090000e-77 302.0
28 TraesCS1A01G333900 chr3D 86.364 286 26 5 995 1276 218735546 218735822 3.920000e-77 300.0
29 TraesCS1A01G333900 chr3D 87.619 210 19 5 1014 1219 41135196 41135402 3.120000e-58 237.0
30 TraesCS1A01G333900 chr5A 85.263 285 32 5 3946 4227 649472186 649471909 1.100000e-72 285.0
31 TraesCS1A01G333900 chr5A 81.522 184 21 5 4182 4357 649471919 649471741 9.050000e-29 139.0
32 TraesCS1A01G333900 chr4B 84.362 243 29 6 1014 1250 654802925 654802686 5.220000e-56 230.0
33 TraesCS1A01G333900 chr4A 86.190 210 22 4 1014 1219 636216939 636216733 3.140000e-53 220.0
34 TraesCS1A01G333900 chr7A 82.949 217 29 7 1014 1225 595408610 595408397 8.860000e-44 189.0
35 TraesCS1A01G333900 chr7A 75.796 157 31 7 4058 4212 635074502 635074653 9.310000e-09 73.1
36 TraesCS1A01G333900 chr6B 83.684 190 15 9 1014 1201 653201384 653201209 1.490000e-36 165.0
37 TraesCS1A01G333900 chr6B 92.391 92 6 1 3747 3837 48981425 48981516 5.450000e-26 130.0
38 TraesCS1A01G333900 chr6B 93.182 88 5 1 3751 3837 48874036 48874123 1.960000e-25 128.0
39 TraesCS1A01G333900 chr2D 92.135 89 6 1 3752 3839 150380739 150380651 2.540000e-24 124.0
40 TraesCS1A01G333900 chr6D 92.045 88 6 1 3751 3837 26814894 26814981 9.120000e-24 122.0
41 TraesCS1A01G333900 chr6D 92.045 88 6 1 3751 3837 26894982 26895069 9.120000e-24 122.0
42 TraesCS1A01G333900 chr3A 92.045 88 6 1 3752 3838 394481542 394481629 9.120000e-24 122.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G333900 chr1A 521638644 521645338 6694 False 5828.500000 8039 100.000000 1 6695 2 chr1A.!!$F3 6694
1 TraesCS1A01G333900 chr1A 521672352 521672874 522 False 466.000000 466 83.146000 3893 4413 1 chr1A.!!$F2 520
2 TraesCS1A01G333900 chr1B 576213672 576223102 9430 False 909.100000 3668 88.536400 10 6695 10 chr1B.!!$F2 6685
3 TraesCS1A01G333900 chr1D 426593744 426599876 6132 False 1236.666667 3640 91.288667 26 6200 6 chr1D.!!$F2 6174
4 TraesCS1A01G333900 chr5B 85622638 85623389 751 True 800.000000 800 86.257000 995 1739 1 chr5B.!!$R1 744
5 TraesCS1A01G333900 chr3D 218735546 218736763 1217 False 301.000000 302 85.070000 995 1739 2 chr3D.!!$F2 744

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
183 205 1.002134 CCGATGGCCAAGTCCACTT 60.002 57.895 10.96 0.0 39.25 3.16 F
908 1149 1.003718 GATCCCCTTTATCCGCCCG 60.004 63.158 0.00 0.0 0.00 6.13 F
1548 2337 0.035056 CCATTTCAGGCGGTCTCCTT 60.035 55.000 0.00 0.0 33.25 3.36 F
1673 2466 0.317160 ACGAGTCCAGATGCGTTGAA 59.683 50.000 0.00 0.0 32.42 2.69 F
3193 4027 0.346574 TGAGGGGGATGGGATCTTGA 59.653 55.000 0.00 0.0 0.00 3.02 F
3195 4029 0.348370 AGGGGGATGGGATCTTGACT 59.652 55.000 0.00 0.0 0.00 3.41 F
3197 4031 1.133668 GGGGGATGGGATCTTGACTTG 60.134 57.143 0.00 0.0 0.00 3.16 F
3553 4768 1.422781 TGATGGATGCCTCTGGGATTC 59.577 52.381 0.00 0.0 32.75 2.52 F
5157 6412 0.109723 CGGACTTCCTGGGGACAAAA 59.890 55.000 0.00 0.0 42.06 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1581 0.179124 GTACCTGCTTGAGCGAGGAG 60.179 60.000 20.71 5.73 45.83 3.69 R
2794 3626 0.457851 GTCATACGCAGCAGGAGAGT 59.542 55.000 0.00 0.00 0.00 3.24 R
3348 4399 0.107214 ATACCCAGTTGTCCATGCCG 60.107 55.000 0.00 0.00 0.00 5.69 R
3490 4541 0.602562 GTGCCATAAGCTGCAACCAA 59.397 50.000 1.02 0.00 44.23 3.67 R
4657 5911 1.340114 GGTGGAAGAGGTGCTAAAGGG 60.340 57.143 0.00 0.00 0.00 3.95 R
4734 5988 1.620822 AAGGGTAGCTGGTGCAAAAG 58.379 50.000 0.00 0.00 42.74 2.27 R
4962 6217 3.181469 TGAGGTCCGCCAATAATAGTCAC 60.181 47.826 0.00 0.00 37.19 3.67 R
5232 6487 1.340889 TGTGGGCTGATTTGTTTGCTC 59.659 47.619 0.00 0.00 0.00 4.26 R
6017 7285 0.541863 ACGGCATTGGAGGAAGGTAG 59.458 55.000 0.00 0.00 0.00 3.18 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
118 129 2.077413 GCTATCGGAGCCTGAAGATG 57.923 55.000 0.00 0.00 46.41 2.90
183 205 1.002134 CCGATGGCCAAGTCCACTT 60.002 57.895 10.96 0.00 39.25 3.16
253 300 2.202743 CACCGCACCGATCGATGT 60.203 61.111 18.66 3.57 0.00 3.06
606 717 2.671963 GGTCGCACCCCACCTTTC 60.672 66.667 0.00 0.00 30.04 2.62
607 718 2.671963 GTCGCACCCCACCTTTCC 60.672 66.667 0.00 0.00 0.00 3.13
608 719 3.172106 TCGCACCCCACCTTTCCA 61.172 61.111 0.00 0.00 0.00 3.53
682 898 4.596585 CACCACCCACCCACCCAC 62.597 72.222 0.00 0.00 0.00 4.61
697 913 2.097466 CACCCACACACACAGAAAACTC 59.903 50.000 0.00 0.00 0.00 3.01
718 934 3.386402 TCCACATACGGACAGCATCAATA 59.614 43.478 0.00 0.00 0.00 1.90
759 995 2.180017 ACGTAGCGTGCGGTTAGG 59.820 61.111 0.68 0.00 39.18 2.69
760 996 2.581409 CGTAGCGTGCGGTTAGGG 60.581 66.667 0.68 0.00 0.00 3.53
761 997 2.575461 GTAGCGTGCGGTTAGGGT 59.425 61.111 0.68 0.00 0.00 4.34
766 1002 4.419921 GTGCGGTTAGGGTGGGGG 62.420 72.222 0.00 0.00 0.00 5.40
887 1128 4.124943 TCGTCTCCCTCCCTCCCG 62.125 72.222 0.00 0.00 0.00 5.14
908 1149 1.003718 GATCCCCTTTATCCGCCCG 60.004 63.158 0.00 0.00 0.00 6.13
915 1156 2.966182 CTTTATCCGCCCGTCGTCCC 62.966 65.000 0.00 0.00 36.19 4.46
984 1225 3.866582 GGGAGATCACAGCCCCGG 61.867 72.222 0.00 0.00 35.76 5.73
1129 1376 3.864686 CCGCCGAGCAAATCCACG 61.865 66.667 0.00 0.00 0.00 4.94
1130 1377 2.813474 CGCCGAGCAAATCCACGA 60.813 61.111 0.00 0.00 0.00 4.35
1329 1581 2.597903 GGCAGGATCACCTTCCCC 59.402 66.667 0.00 0.00 45.36 4.81
1347 1599 1.323271 CCTCCTCGCTCAAGCAGGTA 61.323 60.000 15.48 6.49 42.21 3.08
1395 1684 2.586357 GCCGCTCCGATCTGGTTC 60.586 66.667 3.97 0.00 39.52 3.62
1419 2208 3.855589 CGGCCGATTTGCGCGTTA 61.856 61.111 24.07 0.00 39.11 3.18
1446 2235 2.359975 CGGTCTGAGGGTTTGGCC 60.360 66.667 0.00 0.00 0.00 5.36
1472 2261 0.828022 TGGTCCTTGTGTTGAGTCGT 59.172 50.000 0.00 0.00 0.00 4.34
1548 2337 0.035056 CCATTTCAGGCGGTCTCCTT 60.035 55.000 0.00 0.00 33.25 3.36
1551 2340 2.050836 TTTCAGGCGGTCTCCTTGCA 62.051 55.000 0.00 0.00 33.25 4.08
1572 2364 9.781834 CTTGCAAGTACTAGCATCTATAGATAC 57.218 37.037 18.65 9.79 40.94 2.24
1591 2383 1.656441 GCTAGATGCAATTGCGGGG 59.344 57.895 24.58 13.56 45.83 5.73
1616 2408 2.358003 GCAGCAGGTTCAGAGCGT 60.358 61.111 0.00 0.00 0.00 5.07
1617 2409 1.963338 GCAGCAGGTTCAGAGCGTT 60.963 57.895 0.00 0.00 0.00 4.84
1618 2410 1.510480 GCAGCAGGTTCAGAGCGTTT 61.510 55.000 0.00 0.00 0.00 3.60
1619 2411 0.947244 CAGCAGGTTCAGAGCGTTTT 59.053 50.000 0.00 0.00 0.00 2.43
1620 2412 2.143122 CAGCAGGTTCAGAGCGTTTTA 58.857 47.619 0.00 0.00 0.00 1.52
1622 2414 2.744202 AGCAGGTTCAGAGCGTTTTATG 59.256 45.455 0.00 0.00 0.00 1.90
1673 2466 0.317160 ACGAGTCCAGATGCGTTGAA 59.683 50.000 0.00 0.00 32.42 2.69
1745 2538 5.883685 AGTGATATCTTCAGATGCAAGGA 57.116 39.130 3.98 0.00 34.17 3.36
1769 2562 3.512033 ACTAGAAGCGAGGAACATGTC 57.488 47.619 0.00 0.00 0.00 3.06
1784 2577 2.959707 ACATGTCGACCTTATCCTCTCC 59.040 50.000 14.12 0.00 0.00 3.71
1809 2602 7.549842 CCATTTTCTTCATTTGGTTGCATCATA 59.450 33.333 0.00 0.00 0.00 2.15
1865 2668 2.419297 GGCAGTGAGATTGTAGGACCAG 60.419 54.545 0.00 0.00 0.00 4.00
1880 2683 4.918588 AGGACCAGGTTAGTAAAACCATG 58.081 43.478 9.44 4.98 42.69 3.66
1888 2691 6.150474 CAGGTTAGTAAAACCATGTTAGGGTG 59.850 42.308 9.44 0.00 42.69 4.61
1926 2729 6.699575 ATATGGAAGTTGCTTATTGTGACC 57.300 37.500 0.00 0.00 0.00 4.02
1932 2735 4.072131 AGTTGCTTATTGTGACCGATTGT 58.928 39.130 0.00 0.00 0.00 2.71
1957 2760 2.222819 CGATTCTTGCCTGTTTCTACGC 60.223 50.000 0.00 0.00 0.00 4.42
2587 3390 7.232534 TGGCTCCTTTGTGTTTATAACTCAATT 59.767 33.333 7.58 0.00 42.36 2.32
2589 3392 7.062255 GCTCCTTTGTGTTTATAACTCAATTGC 59.938 37.037 0.00 6.70 42.36 3.56
2640 3443 5.450965 GCTTCAATAGGGTTTCCACATCATG 60.451 44.000 0.00 0.00 34.83 3.07
2684 3487 6.821665 CCAAACTGCCTAGTAATAAGCAACTA 59.178 38.462 0.00 0.00 35.69 2.24
2712 3515 8.515414 AAGGACAAGTATATGTCTTTTTCAAGC 58.485 33.333 7.31 0.00 44.32 4.01
2794 3626 2.246469 TGTAGGTAACACCGTTGCCTA 58.754 47.619 16.70 16.70 44.90 3.93
2893 3727 8.366671 ACTTCTTTTACTCAGTCACAACATAC 57.633 34.615 0.00 0.00 0.00 2.39
2894 3728 7.169308 ACTTCTTTTACTCAGTCACAACATACG 59.831 37.037 0.00 0.00 0.00 3.06
2926 3760 3.181436 CGAGGACCCTTATACCTACTCCA 60.181 52.174 0.00 0.00 33.89 3.86
2958 3792 9.846248 CCACTTCCATTATTTAAAGAAGACTTG 57.154 33.333 16.67 4.62 36.39 3.16
3155 3989 4.446719 CCGCCTAATATGTCGTACCTTTTC 59.553 45.833 0.00 0.00 0.00 2.29
3171 4005 3.925913 CCTTTTCTTGTTTGTGTGTGGTG 59.074 43.478 0.00 0.00 0.00 4.17
3172 4006 3.584406 TTTCTTGTTTGTGTGTGGTGG 57.416 42.857 0.00 0.00 0.00 4.61
3173 4007 2.208132 TCTTGTTTGTGTGTGGTGGT 57.792 45.000 0.00 0.00 0.00 4.16
3174 4008 2.520069 TCTTGTTTGTGTGTGGTGGTT 58.480 42.857 0.00 0.00 0.00 3.67
3175 4009 2.230025 TCTTGTTTGTGTGTGGTGGTTG 59.770 45.455 0.00 0.00 0.00 3.77
3176 4010 1.911057 TGTTTGTGTGTGGTGGTTGA 58.089 45.000 0.00 0.00 0.00 3.18
3177 4011 1.815613 TGTTTGTGTGTGGTGGTTGAG 59.184 47.619 0.00 0.00 0.00 3.02
3178 4012 1.134175 GTTTGTGTGTGGTGGTTGAGG 59.866 52.381 0.00 0.00 0.00 3.86
3179 4013 0.395036 TTGTGTGTGGTGGTTGAGGG 60.395 55.000 0.00 0.00 0.00 4.30
3180 4014 1.528309 GTGTGTGGTGGTTGAGGGG 60.528 63.158 0.00 0.00 0.00 4.79
3181 4015 2.115266 GTGTGGTGGTTGAGGGGG 59.885 66.667 0.00 0.00 0.00 5.40
3182 4016 2.039298 TGTGGTGGTTGAGGGGGA 60.039 61.111 0.00 0.00 0.00 4.81
3183 4017 1.465188 TGTGGTGGTTGAGGGGGAT 60.465 57.895 0.00 0.00 0.00 3.85
3184 4018 1.000896 GTGGTGGTTGAGGGGGATG 60.001 63.158 0.00 0.00 0.00 3.51
3185 4019 2.237965 TGGTGGTTGAGGGGGATGG 61.238 63.158 0.00 0.00 0.00 3.51
3186 4020 2.683475 GTGGTTGAGGGGGATGGG 59.317 66.667 0.00 0.00 0.00 4.00
3187 4021 1.928567 GTGGTTGAGGGGGATGGGA 60.929 63.158 0.00 0.00 0.00 4.37
3188 4022 1.086565 TGGTTGAGGGGGATGGGAT 59.913 57.895 0.00 0.00 0.00 3.85
3189 4023 0.993509 TGGTTGAGGGGGATGGGATC 60.994 60.000 0.00 0.00 0.00 3.36
3190 4024 0.699231 GGTTGAGGGGGATGGGATCT 60.699 60.000 0.00 0.00 0.00 2.75
3191 4025 1.226311 GTTGAGGGGGATGGGATCTT 58.774 55.000 0.00 0.00 0.00 2.40
3192 4026 1.133668 GTTGAGGGGGATGGGATCTTG 60.134 57.143 0.00 0.00 0.00 3.02
3193 4027 0.346574 TGAGGGGGATGGGATCTTGA 59.653 55.000 0.00 0.00 0.00 3.02
3194 4028 0.767998 GAGGGGGATGGGATCTTGAC 59.232 60.000 0.00 0.00 0.00 3.18
3195 4029 0.348370 AGGGGGATGGGATCTTGACT 59.652 55.000 0.00 0.00 0.00 3.41
3196 4030 1.226311 GGGGGATGGGATCTTGACTT 58.774 55.000 0.00 0.00 0.00 3.01
3197 4031 1.133668 GGGGGATGGGATCTTGACTTG 60.134 57.143 0.00 0.00 0.00 3.16
3198 4032 1.566231 GGGGATGGGATCTTGACTTGT 59.434 52.381 0.00 0.00 0.00 3.16
3199 4033 2.024941 GGGGATGGGATCTTGACTTGTT 60.025 50.000 0.00 0.00 0.00 2.83
3200 4034 3.282885 GGGATGGGATCTTGACTTGTTC 58.717 50.000 0.00 0.00 0.00 3.18
3201 4035 2.939103 GGATGGGATCTTGACTTGTTCG 59.061 50.000 0.00 0.00 0.00 3.95
3202 4036 3.369471 GGATGGGATCTTGACTTGTTCGA 60.369 47.826 0.00 0.00 0.00 3.71
3203 4037 3.762407 TGGGATCTTGACTTGTTCGAA 57.238 42.857 0.00 0.00 0.00 3.71
3204 4038 3.664107 TGGGATCTTGACTTGTTCGAAG 58.336 45.455 0.00 0.00 0.00 3.79
3205 4039 3.071023 TGGGATCTTGACTTGTTCGAAGT 59.929 43.478 0.00 0.00 0.00 3.01
3206 4040 4.065789 GGGATCTTGACTTGTTCGAAGTT 58.934 43.478 0.00 0.00 0.00 2.66
3207 4041 5.221561 TGGGATCTTGACTTGTTCGAAGTTA 60.222 40.000 0.00 0.00 0.00 2.24
3208 4042 5.348997 GGGATCTTGACTTGTTCGAAGTTAG 59.651 44.000 0.00 0.00 0.00 2.34
3209 4043 6.157211 GGATCTTGACTTGTTCGAAGTTAGA 58.843 40.000 0.00 1.37 0.00 2.10
3210 4044 6.814146 GGATCTTGACTTGTTCGAAGTTAGAT 59.186 38.462 0.00 6.12 36.02 1.98
3211 4045 7.201478 GGATCTTGACTTGTTCGAAGTTAGATG 60.201 40.741 14.18 0.37 34.76 2.90
3212 4046 5.926542 TCTTGACTTGTTCGAAGTTAGATGG 59.073 40.000 0.00 0.00 0.00 3.51
3213 4047 4.566004 TGACTTGTTCGAAGTTAGATGGG 58.434 43.478 0.00 0.00 0.00 4.00
3214 4048 3.933332 GACTTGTTCGAAGTTAGATGGGG 59.067 47.826 0.00 0.00 0.00 4.96
3215 4049 3.326880 ACTTGTTCGAAGTTAGATGGGGT 59.673 43.478 0.00 0.00 0.00 4.95
3216 4050 3.604875 TGTTCGAAGTTAGATGGGGTC 57.395 47.619 0.00 0.00 0.00 4.46
3217 4051 2.901192 TGTTCGAAGTTAGATGGGGTCA 59.099 45.455 0.00 0.00 0.00 4.02
3218 4052 3.517901 TGTTCGAAGTTAGATGGGGTCAT 59.482 43.478 0.00 0.00 36.09 3.06
3240 4290 1.752498 TGCGTATCCGTGGTACATCTT 59.248 47.619 0.00 0.00 44.52 2.40
3337 4387 6.370718 GTGTCATTCTTTCGTTTGGGTAGTAT 59.629 38.462 0.00 0.00 0.00 2.12
3348 4399 6.148150 TCGTTTGGGTAGTATTTTCACATGAC 59.852 38.462 0.00 0.00 0.00 3.06
3378 4429 6.213802 TGGACAACTGGGTATAGACATTACAA 59.786 38.462 0.00 0.00 0.00 2.41
3381 4432 7.103641 ACAACTGGGTATAGACATTACAACTG 58.896 38.462 0.00 0.00 0.00 3.16
3405 4456 8.201554 TGAGGAGATTAATCAAAATTGAGACG 57.798 34.615 17.56 0.00 41.08 4.18
3441 4492 2.364002 CACCGGTTCATTGGACCTTTTT 59.636 45.455 2.97 0.00 34.95 1.94
3490 4541 6.069963 AGGCACAGAAGATGATTAGTAACCTT 60.070 38.462 0.00 0.00 0.00 3.50
3496 4547 8.454106 CAGAAGATGATTAGTAACCTTTGGTTG 58.546 37.037 11.78 0.00 46.35 3.77
3553 4768 1.422781 TGATGGATGCCTCTGGGATTC 59.577 52.381 0.00 0.00 32.75 2.52
3645 4860 7.707624 TCCTCATCTGTATTTTGATTTGCTT 57.292 32.000 0.00 0.00 0.00 3.91
3676 4898 7.097192 TCAACCTCATGACACACTTTATAGAC 58.903 38.462 0.00 0.00 0.00 2.59
3692 4914 8.947115 ACTTTATAGACTGCAGTAATGAAAACC 58.053 33.333 21.73 3.59 0.00 3.27
3749 4971 7.655328 CAGACTTATCTTTCCAGTATGCTTAGG 59.345 40.741 0.00 0.00 30.42 2.69
3753 4975 8.548880 TTATCTTTCCAGTATGCTTAGGTAGT 57.451 34.615 0.00 0.00 31.97 2.73
3754 4976 9.650714 TTATCTTTCCAGTATGCTTAGGTAGTA 57.349 33.333 0.00 0.00 31.97 1.82
3755 4977 7.344095 TCTTTCCAGTATGCTTAGGTAGTAC 57.656 40.000 0.00 0.00 31.97 2.73
3756 4978 7.124052 TCTTTCCAGTATGCTTAGGTAGTACT 58.876 38.462 0.00 0.00 31.97 2.73
3757 4979 6.956202 TTCCAGTATGCTTAGGTAGTACTC 57.044 41.667 0.00 0.00 31.97 2.59
3758 4980 5.383476 TCCAGTATGCTTAGGTAGTACTCC 58.617 45.833 0.00 0.48 31.97 3.85
3759 4981 4.523558 CCAGTATGCTTAGGTAGTACTCCC 59.476 50.000 0.00 0.00 31.97 4.30
3760 4982 5.386924 CAGTATGCTTAGGTAGTACTCCCT 58.613 45.833 12.22 12.22 34.74 4.20
3761 4983 5.474189 CAGTATGCTTAGGTAGTACTCCCTC 59.526 48.000 10.79 0.00 32.08 4.30
3762 4984 3.309600 TGCTTAGGTAGTACTCCCTCC 57.690 52.381 10.79 4.42 32.08 4.30
3763 4985 2.228925 GCTTAGGTAGTACTCCCTCCG 58.771 57.143 10.79 4.57 32.08 4.63
3764 4986 2.422661 GCTTAGGTAGTACTCCCTCCGT 60.423 54.545 10.79 0.00 32.08 4.69
3765 4987 3.181450 GCTTAGGTAGTACTCCCTCCGTA 60.181 52.174 10.79 0.00 32.08 4.02
3766 4988 4.687219 GCTTAGGTAGTACTCCCTCCGTAA 60.687 50.000 10.79 0.00 32.08 3.18
3767 4989 5.440610 CTTAGGTAGTACTCCCTCCGTAAA 58.559 45.833 10.79 0.00 32.08 2.01
3768 4990 3.895998 AGGTAGTACTCCCTCCGTAAAG 58.104 50.000 0.11 0.00 0.00 1.85
3769 4991 3.525199 AGGTAGTACTCCCTCCGTAAAGA 59.475 47.826 0.11 0.00 0.00 2.52
3770 4992 4.167697 AGGTAGTACTCCCTCCGTAAAGAT 59.832 45.833 0.11 0.00 0.00 2.40
3771 4993 4.892345 GGTAGTACTCCCTCCGTAAAGATT 59.108 45.833 0.00 0.00 0.00 2.40
3772 4994 6.064717 GGTAGTACTCCCTCCGTAAAGATTA 58.935 44.000 0.00 0.00 0.00 1.75
3773 4995 6.718912 GGTAGTACTCCCTCCGTAAAGATTAT 59.281 42.308 0.00 0.00 0.00 1.28
3774 4996 7.885399 GGTAGTACTCCCTCCGTAAAGATTATA 59.115 40.741 0.00 0.00 0.00 0.98
3775 4997 9.289782 GTAGTACTCCCTCCGTAAAGATTATAA 57.710 37.037 0.00 0.00 0.00 0.98
3776 4998 8.406730 AGTACTCCCTCCGTAAAGATTATAAG 57.593 38.462 0.00 0.00 0.00 1.73
3777 4999 8.223330 AGTACTCCCTCCGTAAAGATTATAAGA 58.777 37.037 0.00 0.00 0.00 2.10
3778 5000 7.527568 ACTCCCTCCGTAAAGATTATAAGAG 57.472 40.000 0.00 0.00 0.00 2.85
3779 5001 6.015265 ACTCCCTCCGTAAAGATTATAAGAGC 60.015 42.308 0.00 0.00 0.00 4.09
3780 5002 5.048224 TCCCTCCGTAAAGATTATAAGAGCG 60.048 44.000 0.00 0.00 0.00 5.03
3781 5003 5.278858 CCCTCCGTAAAGATTATAAGAGCGT 60.279 44.000 0.00 0.00 0.00 5.07
3782 5004 6.214399 CCTCCGTAAAGATTATAAGAGCGTT 58.786 40.000 0.00 0.00 0.00 4.84
3783 5005 6.700520 CCTCCGTAAAGATTATAAGAGCGTTT 59.299 38.462 0.00 0.00 0.00 3.60
3784 5006 7.864379 CCTCCGTAAAGATTATAAGAGCGTTTA 59.136 37.037 0.00 0.00 0.00 2.01
3785 5007 8.792831 TCCGTAAAGATTATAAGAGCGTTTAG 57.207 34.615 0.00 0.00 0.00 1.85
3786 5008 8.623903 TCCGTAAAGATTATAAGAGCGTTTAGA 58.376 33.333 0.00 0.00 0.00 2.10
3787 5009 9.408069 CCGTAAAGATTATAAGAGCGTTTAGAT 57.592 33.333 0.00 0.00 0.00 1.98
3800 5022 8.635877 AGAGCGTTTAGATCACTAAAGTAATG 57.364 34.615 0.00 0.00 45.42 1.90
3801 5023 8.251721 AGAGCGTTTAGATCACTAAAGTAATGT 58.748 33.333 0.00 0.00 45.42 2.71
3802 5024 8.773404 AGCGTTTAGATCACTAAAGTAATGTT 57.227 30.769 0.00 0.00 45.42 2.71
3803 5025 9.216117 AGCGTTTAGATCACTAAAGTAATGTTT 57.784 29.630 0.00 0.00 45.42 2.83
3804 5026 9.821662 GCGTTTAGATCACTAAAGTAATGTTTT 57.178 29.630 0.00 0.00 45.42 2.43
3810 5032 9.821662 AGATCACTAAAGTAATGTTTTAAACGC 57.178 29.630 3.28 0.00 0.00 4.84
3811 5033 9.821662 GATCACTAAAGTAATGTTTTAAACGCT 57.178 29.630 3.28 0.00 0.00 5.07
3812 5034 9.821662 ATCACTAAAGTAATGTTTTAAACGCTC 57.178 29.630 3.28 0.00 0.00 5.03
3813 5035 9.048446 TCACTAAAGTAATGTTTTAAACGCTCT 57.952 29.630 3.28 0.00 0.00 4.09
3814 5036 9.659830 CACTAAAGTAATGTTTTAAACGCTCTT 57.340 29.630 3.28 3.24 0.00 2.85
3831 5053 8.608844 AACGCTCTTATATTTCTTTATGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
3832 5054 7.162082 ACGCTCTTATATTTCTTTATGGAGGG 58.838 38.462 0.00 0.00 35.06 4.30
3833 5055 7.016268 ACGCTCTTATATTTCTTTATGGAGGGA 59.984 37.037 0.00 0.00 34.22 4.20
3834 5056 7.547370 CGCTCTTATATTTCTTTATGGAGGGAG 59.453 40.741 0.00 0.00 33.23 4.30
4089 5311 4.831155 AGCTGATTGGTGGATTATTCATGG 59.169 41.667 0.00 0.00 0.00 3.66
4091 5313 3.896888 TGATTGGTGGATTATTCATGGCC 59.103 43.478 0.00 0.00 0.00 5.36
4097 5319 2.244510 TGGATTATTCATGGCCACTGGT 59.755 45.455 8.16 0.00 0.00 4.00
4101 5323 5.010012 GGATTATTCATGGCCACTGGTTTAG 59.990 44.000 8.16 0.00 0.00 1.85
4218 5444 2.571212 ACCTCGTTTTCATTGCTGACA 58.429 42.857 0.00 0.00 0.00 3.58
4301 5527 2.479566 TCCCATCTGTCAGTTTCTGC 57.520 50.000 0.00 0.00 0.00 4.26
4339 5588 8.141909 TCAGTATGTACTATTCTGTGCATAACC 58.858 37.037 6.93 0.00 43.40 2.85
4417 5666 6.039047 GGAGATCTGCTTTATGATTTTCTGCA 59.961 38.462 7.03 0.00 0.00 4.41
4456 5705 4.646040 AGCTGATAGTTGCCAAAATATGCA 59.354 37.500 0.00 0.00 35.27 3.96
4538 5787 3.618594 TCTTCACAGCGATACTTTGCATC 59.381 43.478 0.00 0.00 34.39 3.91
4622 5875 4.580580 GTCTTGGCCAAGTTGAATATAGGG 59.419 45.833 37.97 14.77 39.38 3.53
4636 5890 6.199376 TGAATATAGGGGTATGGATAAGCGA 58.801 40.000 0.00 0.00 0.00 4.93
4657 5911 3.567478 AGTAATGCCCATCCTGAACTC 57.433 47.619 0.00 0.00 0.00 3.01
4879 6134 4.394920 TGATCGGTAATGCTTTTCAAGGAC 59.605 41.667 0.00 0.00 0.00 3.85
4962 6217 0.321653 AACCAAAGCTACTCCTGGCG 60.322 55.000 0.00 0.00 31.74 5.69
5097 6352 7.807977 TCAAGTCTATTTCCTGGATATTTGC 57.192 36.000 4.94 0.00 0.00 3.68
5157 6412 0.109723 CGGACTTCCTGGGGACAAAA 59.890 55.000 0.00 0.00 42.06 2.44
5517 6772 1.416401 TCCGTGAAGAACTTCCAGCTT 59.584 47.619 11.30 0.00 38.77 3.74
5777 7032 0.549469 TTAATCCGGGAGAAAGGGGC 59.451 55.000 0.00 0.00 0.00 5.80
5859 7114 3.209410 GGATTTGACTCTATGGCTGTGG 58.791 50.000 0.00 0.00 0.00 4.17
5954 7210 2.340337 CCGTTTTACCCTTCACGTAGG 58.660 52.381 0.00 0.00 34.92 3.18
5988 7256 2.236766 GGGCTGCTAATCTGCATTGAT 58.763 47.619 0.00 0.00 42.48 2.57
6072 7343 4.927267 ATCCCTTTTGTGGTCTACATGA 57.073 40.909 0.00 0.00 39.48 3.07
6138 7410 5.872617 TGTTTAGTGTAGCTGCAAACGATAT 59.127 36.000 5.91 0.00 32.95 1.63
6177 7449 0.401738 CAACTCACCACCATGGGACT 59.598 55.000 18.09 0.00 43.37 3.85
6224 7533 2.480555 CGGCGGCAATGAACACTC 59.519 61.111 10.53 0.00 0.00 3.51
6225 7534 2.034879 CGGCGGCAATGAACACTCT 61.035 57.895 10.53 0.00 0.00 3.24
6230 7539 2.935238 GCGGCAATGAACACTCTTCCTA 60.935 50.000 0.00 0.00 0.00 2.94
6241 7550 6.500751 TGAACACTCTTCCTATTTCCCTAACT 59.499 38.462 0.00 0.00 0.00 2.24
6273 7582 2.008752 TATGAGCACACCACATGACG 57.991 50.000 0.00 0.00 0.00 4.35
6307 7616 0.249741 CGACCGACAAAGGGTGAACT 60.250 55.000 0.00 0.00 38.07 3.01
6357 7666 6.989437 CAATTGAGTTGTTCATGCATGATTC 58.011 36.000 29.13 23.24 36.56 2.52
6396 7711 9.039870 CATAAACTCTCATCAGATGACTAAACC 57.960 37.037 9.21 0.00 35.06 3.27
6463 7779 3.367703 CCAAATTGATCAACACCAGAGGC 60.368 47.826 11.07 0.00 0.00 4.70
6488 7804 4.835284 ACTTCCAGAAAGATTCTCTCCC 57.165 45.455 0.00 0.00 38.11 4.30
6510 7826 4.084171 CCATAGCGCTAACATCATCAACAG 60.084 45.833 22.98 0.00 0.00 3.16
6553 7875 9.736023 AAAAAGCAACACAAAACAAATACAAAA 57.264 22.222 0.00 0.00 0.00 2.44
6554 7876 9.736023 AAAAGCAACACAAAACAAATACAAAAA 57.264 22.222 0.00 0.00 0.00 1.94
6555 7877 8.947304 AAGCAACACAAAACAAATACAAAAAG 57.053 26.923 0.00 0.00 0.00 2.27
6556 7878 8.093659 AGCAACACAAAACAAATACAAAAAGT 57.906 26.923 0.00 0.00 0.00 2.66
6557 7879 8.227119 AGCAACACAAAACAAATACAAAAAGTC 58.773 29.630 0.00 0.00 0.00 3.01
6558 7880 8.012241 GCAACACAAAACAAATACAAAAAGTCA 58.988 29.630 0.00 0.00 0.00 3.41
6559 7881 9.869844 CAACACAAAACAAATACAAAAAGTCAA 57.130 25.926 0.00 0.00 0.00 3.18
6561 7883 9.871299 ACACAAAACAAATACAAAAAGTCAAAC 57.129 25.926 0.00 0.00 0.00 2.93
6562 7884 9.869844 CACAAAACAAATACAAAAAGTCAAACA 57.130 25.926 0.00 0.00 0.00 2.83
6634 7956 5.964958 ATGTGTAATGAAACTCACCCTTG 57.035 39.130 0.00 0.00 0.00 3.61
6645 7967 8.877864 TGAAACTCACCCTTGACAATATTATT 57.122 30.769 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.470567 GCCACGTCGAGCGAACTG 61.471 66.667 13.06 3.00 44.77 3.16
1 2 4.719369 GGCCACGTCGAGCGAACT 62.719 66.667 13.06 0.00 44.77 3.01
24 25 4.479993 GCCTGCTCCTGACGGCAT 62.480 66.667 0.00 0.00 42.06 4.40
103 114 0.820226 CAGACATCTTCAGGCTCCGA 59.180 55.000 0.00 0.00 0.00 4.55
105 116 1.134551 GTCCAGACATCTTCAGGCTCC 60.135 57.143 0.00 0.00 30.67 4.70
113 124 2.093973 GTGTCATCCGTCCAGACATCTT 60.094 50.000 0.00 0.00 43.35 2.40
118 129 0.108615 CCAGTGTCATCCGTCCAGAC 60.109 60.000 0.00 0.00 0.00 3.51
183 205 2.360852 GGACCCGTCGAGACCAGA 60.361 66.667 0.00 0.00 0.00 3.86
227 256 3.770424 GGTGCGGTGCGTACGTTC 61.770 66.667 17.90 9.96 42.91 3.95
231 260 3.252484 GATCGGTGCGGTGCGTAC 61.252 66.667 0.00 0.00 41.39 3.67
232 261 4.840288 CGATCGGTGCGGTGCGTA 62.840 66.667 7.38 0.00 0.00 4.42
553 663 3.524606 CGGGTGGGCTCGACGTAT 61.525 66.667 0.00 0.00 42.12 3.06
647 761 0.037590 TGCGAAATGGTAAGTGGGCT 59.962 50.000 0.00 0.00 0.00 5.19
648 762 0.170339 GTGCGAAATGGTAAGTGGGC 59.830 55.000 0.00 0.00 0.00 5.36
679 895 2.097466 GTGGAGTTTTCTGTGTGTGTGG 59.903 50.000 0.00 0.00 0.00 4.17
680 896 2.746904 TGTGGAGTTTTCTGTGTGTGTG 59.253 45.455 0.00 0.00 0.00 3.82
681 897 3.066291 TGTGGAGTTTTCTGTGTGTGT 57.934 42.857 0.00 0.00 0.00 3.72
682 898 4.318760 CGTATGTGGAGTTTTCTGTGTGTG 60.319 45.833 0.00 0.00 0.00 3.82
697 913 2.022764 TTGATGCTGTCCGTATGTGG 57.977 50.000 0.00 0.00 0.00 4.17
745 980 2.574929 CACCCTAACCGCACGCTA 59.425 61.111 0.00 0.00 0.00 4.26
759 995 2.124278 GCGGATCTTTCCCCCACC 60.124 66.667 0.00 0.00 39.01 4.61
760 996 2.513897 CGCGGATCTTTCCCCCAC 60.514 66.667 0.00 0.00 39.01 4.61
761 997 2.685743 TCGCGGATCTTTCCCCCA 60.686 61.111 6.13 0.00 39.01 4.96
766 1002 2.585247 CGGGGTCGCGGATCTTTC 60.585 66.667 6.13 0.00 0.00 2.62
786 1022 1.308998 GGGGTGCTCACGGATAAATG 58.691 55.000 0.00 0.00 0.00 2.32
836 1072 2.046507 GCAGTGAGACCAGCCAGG 60.047 66.667 0.00 0.00 45.67 4.45
838 1074 4.687215 GCGCAGTGAGACCAGCCA 62.687 66.667 0.30 0.00 0.00 4.75
887 1128 1.671379 GCGGATAAAGGGGATCGGC 60.671 63.158 0.00 0.00 40.84 5.54
930 1171 1.939769 AAGCTTCCGAGGCGAGAGAC 61.940 60.000 0.00 0.00 42.06 3.36
960 1201 2.041922 TGTGATCTCCCTCCCCGG 60.042 66.667 0.00 0.00 0.00 5.73
968 1209 3.866582 CCCGGGGCTGTGATCTCC 61.867 72.222 14.71 0.00 0.00 3.71
984 1225 4.148825 ATGCTGGAGACGGTCGCC 62.149 66.667 22.16 22.16 39.64 5.54
1122 1369 2.363795 TCGGCCTCCTCGTGGATT 60.364 61.111 6.68 0.00 42.29 3.01
1123 1370 2.835431 CTCGGCCTCCTCGTGGAT 60.835 66.667 6.68 0.00 42.29 3.41
1129 1376 3.213402 CTCGTCCTCGGCCTCCTC 61.213 72.222 0.00 0.00 37.69 3.71
1130 1377 4.824515 CCTCGTCCTCGGCCTCCT 62.825 72.222 0.00 0.00 37.69 3.69
1329 1581 0.179124 GTACCTGCTTGAGCGAGGAG 60.179 60.000 20.71 5.73 45.83 3.69
1429 2218 2.359975 GGCCAAACCCTCAGACCG 60.360 66.667 0.00 0.00 0.00 4.79
1439 2228 3.834447 GACCAAACGCCGGCCAAAC 62.834 63.158 23.46 2.19 0.00 2.93
1446 2235 1.720694 AACACAAGGACCAAACGCCG 61.721 55.000 0.00 0.00 0.00 6.46
1489 2278 2.299867 ACCATTTCCACAATCAACAGCC 59.700 45.455 0.00 0.00 0.00 4.85
1548 2337 7.414208 GCGTATCTATAGATGCTAGTACTTGCA 60.414 40.741 29.48 29.48 44.51 4.08
1551 2340 9.537192 CTAGCGTATCTATAGATGCTAGTACTT 57.463 37.037 31.36 14.64 42.78 2.24
1591 2383 2.751259 TCTGAACCTGCTGCAATTCATC 59.249 45.455 22.13 10.18 31.00 2.92
1649 2442 3.247006 ACGCATCTGGACTCGTAATTT 57.753 42.857 0.00 0.00 33.02 1.82
1650 2443 2.930040 CAACGCATCTGGACTCGTAATT 59.070 45.455 0.00 0.00 34.50 1.40
1652 2445 1.542472 TCAACGCATCTGGACTCGTAA 59.458 47.619 0.00 0.00 34.50 3.18
1745 2538 5.978814 ACATGTTCCTCGCTTCTAGTAAAT 58.021 37.500 0.00 0.00 0.00 1.40
1769 2562 5.283457 AGAAAATGGAGAGGATAAGGTCG 57.717 43.478 0.00 0.00 0.00 4.79
1784 2577 6.788684 TGATGCAACCAAATGAAGAAAATG 57.211 33.333 0.00 0.00 0.00 2.32
1809 2602 5.181622 TCACCAAAAAGTAACGTGTGAACTT 59.818 36.000 0.00 0.00 35.01 2.66
1865 2668 6.005823 ACACCCTAACATGGTTTTACTAACC 58.994 40.000 0.00 0.00 40.67 2.85
1880 2683 7.875327 ATATGAACATACCAAACACCCTAAC 57.125 36.000 0.00 0.00 0.00 2.34
1888 2691 9.950680 CAACTTCCATATATGAACATACCAAAC 57.049 33.333 14.54 0.00 0.00 2.93
1932 2735 5.518847 CGTAGAAACAGGCAAGAATCGATTA 59.481 40.000 11.38 0.00 0.00 1.75
2356 3159 1.712000 ATTATACGCCCACCCACCCC 61.712 60.000 0.00 0.00 0.00 4.95
2357 3160 0.536460 CATTATACGCCCACCCACCC 60.536 60.000 0.00 0.00 0.00 4.61
2358 3161 0.470766 TCATTATACGCCCACCCACC 59.529 55.000 0.00 0.00 0.00 4.61
2359 3162 2.561478 ATCATTATACGCCCACCCAC 57.439 50.000 0.00 0.00 0.00 4.61
2360 3163 2.973406 TGTATCATTATACGCCCACCCA 59.027 45.455 0.00 0.00 40.84 4.51
2361 3164 3.688694 TGTATCATTATACGCCCACCC 57.311 47.619 0.00 0.00 40.84 4.61
2362 3165 7.625606 GCTTTTATGTATCATTATACGCCCACC 60.626 40.741 0.00 0.00 40.84 4.61
2363 3166 7.119262 AGCTTTTATGTATCATTATACGCCCAC 59.881 37.037 0.00 0.00 40.84 4.61
2364 3167 7.165485 AGCTTTTATGTATCATTATACGCCCA 58.835 34.615 0.00 0.00 40.84 5.36
2365 3168 7.611213 AGCTTTTATGTATCATTATACGCCC 57.389 36.000 0.00 0.00 40.84 6.13
2366 3169 8.717821 TGAAGCTTTTATGTATCATTATACGCC 58.282 33.333 0.00 0.00 40.84 5.68
2367 3170 9.530129 GTGAAGCTTTTATGTATCATTATACGC 57.470 33.333 0.00 0.00 40.84 4.42
2431 3234 2.353208 GGCTGTGCGGAGAATATAGAGG 60.353 54.545 0.00 0.00 0.00 3.69
2441 3244 4.767255 GGTCCAGGCTGTGCGGAG 62.767 72.222 14.43 0.00 0.00 4.63
2556 3359 8.428852 AGTTATAAACACAAAGGAGCCAAAAAT 58.571 29.630 0.00 0.00 0.00 1.82
2587 3390 2.794282 GCGGCGTCAATTTCATAATGCA 60.794 45.455 9.37 0.00 0.00 3.96
2589 3392 3.338818 AGCGGCGTCAATTTCATAATG 57.661 42.857 9.37 0.00 0.00 1.90
2640 3443 9.006215 CAGTTTGGCGCTACTTATTAAAAATAC 57.994 33.333 7.64 0.00 0.00 1.89
2698 3501 8.114331 TCATGTATGAAGCTTGAAAAAGACAT 57.886 30.769 2.10 0.51 33.08 3.06
2699 3502 7.509141 TCATGTATGAAGCTTGAAAAAGACA 57.491 32.000 2.10 0.00 33.08 3.41
2761 3564 8.553696 CGGTGTTACCTACATTATTTTCCATAC 58.446 37.037 0.00 0.00 39.39 2.39
2785 3617 1.153549 GCAGGAGAGTAGGCAACGG 60.154 63.158 0.00 0.00 46.39 4.44
2794 3626 0.457851 GTCATACGCAGCAGGAGAGT 59.542 55.000 0.00 0.00 0.00 3.24
2893 3727 2.158959 GGTCCTCGTCGTGAATGCG 61.159 63.158 0.00 0.00 0.00 4.73
2894 3728 1.810030 GGGTCCTCGTCGTGAATGC 60.810 63.158 0.00 0.00 0.00 3.56
2958 3792 7.437748 TGCTAGGATTCTATTTAGACTTCAGC 58.562 38.462 0.00 0.00 30.81 4.26
3155 3989 2.230025 TCAACCACCACACACAAACAAG 59.770 45.455 0.00 0.00 0.00 3.16
3171 4005 0.699231 AGATCCCATCCCCCTCAACC 60.699 60.000 0.00 0.00 0.00 3.77
3172 4006 1.133668 CAAGATCCCATCCCCCTCAAC 60.134 57.143 0.00 0.00 0.00 3.18
3173 4007 1.225373 CAAGATCCCATCCCCCTCAA 58.775 55.000 0.00 0.00 0.00 3.02
3174 4008 0.346574 TCAAGATCCCATCCCCCTCA 59.653 55.000 0.00 0.00 0.00 3.86
3175 4009 0.767998 GTCAAGATCCCATCCCCCTC 59.232 60.000 0.00 0.00 0.00 4.30
3176 4010 0.348370 AGTCAAGATCCCATCCCCCT 59.652 55.000 0.00 0.00 0.00 4.79
3177 4011 1.133668 CAAGTCAAGATCCCATCCCCC 60.134 57.143 0.00 0.00 0.00 5.40
3178 4012 1.566231 ACAAGTCAAGATCCCATCCCC 59.434 52.381 0.00 0.00 0.00 4.81
3179 4013 3.282885 GAACAAGTCAAGATCCCATCCC 58.717 50.000 0.00 0.00 0.00 3.85
3180 4014 2.939103 CGAACAAGTCAAGATCCCATCC 59.061 50.000 0.00 0.00 0.00 3.51
3181 4015 3.861840 TCGAACAAGTCAAGATCCCATC 58.138 45.455 0.00 0.00 0.00 3.51
3182 4016 3.981071 TCGAACAAGTCAAGATCCCAT 57.019 42.857 0.00 0.00 0.00 4.00
3183 4017 3.071023 ACTTCGAACAAGTCAAGATCCCA 59.929 43.478 0.00 0.00 0.00 4.37
3184 4018 3.665190 ACTTCGAACAAGTCAAGATCCC 58.335 45.455 0.00 0.00 0.00 3.85
3185 4019 6.157211 TCTAACTTCGAACAAGTCAAGATCC 58.843 40.000 0.00 0.00 0.00 3.36
3186 4020 7.201478 CCATCTAACTTCGAACAAGTCAAGATC 60.201 40.741 0.00 0.00 33.91 2.75
3187 4021 6.591834 CCATCTAACTTCGAACAAGTCAAGAT 59.408 38.462 0.00 1.22 35.26 2.40
3188 4022 5.926542 CCATCTAACTTCGAACAAGTCAAGA 59.073 40.000 0.00 0.00 31.27 3.02
3189 4023 5.120830 CCCATCTAACTTCGAACAAGTCAAG 59.879 44.000 0.00 0.00 0.00 3.02
3190 4024 4.994852 CCCATCTAACTTCGAACAAGTCAA 59.005 41.667 0.00 0.00 0.00 3.18
3191 4025 4.562757 CCCCATCTAACTTCGAACAAGTCA 60.563 45.833 0.00 0.00 0.00 3.41
3192 4026 3.933332 CCCCATCTAACTTCGAACAAGTC 59.067 47.826 0.00 0.00 0.00 3.01
3193 4027 3.326880 ACCCCATCTAACTTCGAACAAGT 59.673 43.478 0.00 0.00 0.00 3.16
3194 4028 3.933332 GACCCCATCTAACTTCGAACAAG 59.067 47.826 0.00 0.00 0.00 3.16
3195 4029 3.325425 TGACCCCATCTAACTTCGAACAA 59.675 43.478 0.00 0.00 0.00 2.83
3196 4030 2.901192 TGACCCCATCTAACTTCGAACA 59.099 45.455 0.00 0.00 0.00 3.18
3197 4031 3.604875 TGACCCCATCTAACTTCGAAC 57.395 47.619 0.00 0.00 0.00 3.95
3198 4032 4.402056 GATGACCCCATCTAACTTCGAA 57.598 45.455 0.00 0.00 44.42 3.71
3209 4043 0.687354 GGATACGCAGATGACCCCAT 59.313 55.000 0.00 0.00 35.29 4.00
3210 4044 2.133195 GGATACGCAGATGACCCCA 58.867 57.895 0.00 0.00 0.00 4.96
3337 4387 1.539388 GTCCATGCCGTCATGTGAAAA 59.461 47.619 5.62 0.00 46.64 2.29
3348 4399 0.107214 ATACCCAGTTGTCCATGCCG 60.107 55.000 0.00 0.00 0.00 5.69
3378 4429 9.171877 GTCTCAATTTTGATTAATCTCCTCAGT 57.828 33.333 16.24 0.00 36.46 3.41
3381 4432 8.425577 TCGTCTCAATTTTGATTAATCTCCTC 57.574 34.615 16.24 0.00 36.46 3.71
3399 4450 2.737359 GCGGTGGTTAATCATCGTCTCA 60.737 50.000 21.69 0.00 42.63 3.27
3405 4456 0.655733 CGGTGCGGTGGTTAATCATC 59.344 55.000 0.00 0.00 0.00 2.92
3432 4483 3.017442 GAGCTACCATGGAAAAAGGTCC 58.983 50.000 21.47 6.44 36.87 4.46
3441 4492 8.762645 CCTAATATTTATGAGAGCTACCATGGA 58.237 37.037 21.47 0.67 0.00 3.41
3485 4536 5.429915 GCCATAAGCTGCAACCAAAGGTT 62.430 47.826 1.02 0.00 42.26 3.50
3490 4541 0.602562 GTGCCATAAGCTGCAACCAA 59.397 50.000 1.02 0.00 44.23 3.67
3496 4547 3.848272 TTTAACAGTGCCATAAGCTGC 57.152 42.857 0.00 0.00 44.23 5.25
3586 4801 2.971330 TGCTGGGTTCATCCACATTTTT 59.029 40.909 0.00 0.00 38.11 1.94
3591 4806 1.327303 GTTTGCTGGGTTCATCCACA 58.673 50.000 0.00 0.00 38.11 4.17
3692 4914 7.305474 AGGAAACAACTTTAGATTACATTGCG 58.695 34.615 0.00 0.00 0.00 4.85
3749 4971 7.757941 ATAATCTTTACGGAGGGAGTACTAC 57.242 40.000 0.00 0.00 0.00 2.73
3753 4975 7.176340 GCTCTTATAATCTTTACGGAGGGAGTA 59.824 40.741 0.00 0.00 0.00 2.59
3754 4976 6.015265 GCTCTTATAATCTTTACGGAGGGAGT 60.015 42.308 0.00 0.00 0.00 3.85
3755 4977 6.391537 GCTCTTATAATCTTTACGGAGGGAG 58.608 44.000 0.00 0.00 0.00 4.30
3756 4978 5.048224 CGCTCTTATAATCTTTACGGAGGGA 60.048 44.000 0.00 0.00 35.51 4.20
3757 4979 5.162075 CGCTCTTATAATCTTTACGGAGGG 58.838 45.833 0.00 0.00 0.00 4.30
3758 4980 5.770417 ACGCTCTTATAATCTTTACGGAGG 58.230 41.667 0.00 0.00 0.00 4.30
3759 4981 7.695869 AAACGCTCTTATAATCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
3760 4982 8.623903 TCTAAACGCTCTTATAATCTTTACGGA 58.376 33.333 0.00 0.00 0.00 4.69
3761 4983 8.792831 TCTAAACGCTCTTATAATCTTTACGG 57.207 34.615 0.00 0.00 0.00 4.02
3774 4996 9.088512 CATTACTTTAGTGATCTAAACGCTCTT 57.911 33.333 0.00 0.00 40.05 2.85
3775 4997 8.251721 ACATTACTTTAGTGATCTAAACGCTCT 58.748 33.333 0.00 0.00 40.05 4.09
3776 4998 8.408743 ACATTACTTTAGTGATCTAAACGCTC 57.591 34.615 0.00 0.00 40.05 5.03
3777 4999 8.773404 AACATTACTTTAGTGATCTAAACGCT 57.227 30.769 0.00 0.00 40.05 5.07
3778 5000 9.821662 AAAACATTACTTTAGTGATCTAAACGC 57.178 29.630 0.00 0.00 40.05 4.84
3784 5006 9.821662 GCGTTTAAAACATTACTTTAGTGATCT 57.178 29.630 0.00 0.00 0.00 2.75
3785 5007 9.821662 AGCGTTTAAAACATTACTTTAGTGATC 57.178 29.630 0.00 0.00 0.00 2.92
3786 5008 9.821662 GAGCGTTTAAAACATTACTTTAGTGAT 57.178 29.630 0.00 0.00 0.00 3.06
3787 5009 9.048446 AGAGCGTTTAAAACATTACTTTAGTGA 57.952 29.630 0.00 0.00 0.00 3.41
3788 5010 9.659830 AAGAGCGTTTAAAACATTACTTTAGTG 57.340 29.630 0.00 0.00 0.00 2.74
3805 5027 9.057089 CCTCCATAAAGAAATATAAGAGCGTTT 57.943 33.333 0.00 0.00 0.00 3.60
3806 5028 7.661847 CCCTCCATAAAGAAATATAAGAGCGTT 59.338 37.037 0.00 0.00 0.00 4.84
3807 5029 7.016268 TCCCTCCATAAAGAAATATAAGAGCGT 59.984 37.037 0.00 0.00 0.00 5.07
3808 5030 7.386851 TCCCTCCATAAAGAAATATAAGAGCG 58.613 38.462 0.00 0.00 0.00 5.03
3809 5031 8.379331 ACTCCCTCCATAAAGAAATATAAGAGC 58.621 37.037 0.00 0.00 0.00 4.09
3817 5039 9.170890 TGTGATATACTCCCTCCATAAAGAAAT 57.829 33.333 0.00 0.00 0.00 2.17
3818 5040 8.561536 TGTGATATACTCCCTCCATAAAGAAA 57.438 34.615 0.00 0.00 0.00 2.52
3819 5041 8.742125 ATGTGATATACTCCCTCCATAAAGAA 57.258 34.615 0.00 0.00 0.00 2.52
3822 5044 9.782900 TGATATGTGATATACTCCCTCCATAAA 57.217 33.333 0.00 0.00 0.00 1.40
3823 5045 9.426534 CTGATATGTGATATACTCCCTCCATAA 57.573 37.037 0.00 0.00 0.00 1.90
3824 5046 8.791749 TCTGATATGTGATATACTCCCTCCATA 58.208 37.037 0.00 0.00 0.00 2.74
3825 5047 7.656354 TCTGATATGTGATATACTCCCTCCAT 58.344 38.462 0.00 0.00 0.00 3.41
3826 5048 7.044496 TCTGATATGTGATATACTCCCTCCA 57.956 40.000 0.00 0.00 0.00 3.86
3827 5049 7.962995 TTCTGATATGTGATATACTCCCTCC 57.037 40.000 0.00 0.00 0.00 4.30
3828 5050 7.925483 GCATTCTGATATGTGATATACTCCCTC 59.075 40.741 0.00 0.00 0.00 4.30
3829 5051 7.401204 TGCATTCTGATATGTGATATACTCCCT 59.599 37.037 0.00 0.00 0.00 4.20
3830 5052 7.559486 TGCATTCTGATATGTGATATACTCCC 58.441 38.462 0.00 0.00 0.00 4.30
3831 5053 7.224362 GCTGCATTCTGATATGTGATATACTCC 59.776 40.741 0.00 0.00 0.00 3.85
3832 5054 7.980662 AGCTGCATTCTGATATGTGATATACTC 59.019 37.037 1.02 0.00 0.00 2.59
3833 5055 7.849160 AGCTGCATTCTGATATGTGATATACT 58.151 34.615 1.02 0.00 0.00 2.12
3834 5056 8.489990 AAGCTGCATTCTGATATGTGATATAC 57.510 34.615 1.02 0.00 0.00 1.47
3888 5110 5.072162 TCCGTTAGGGCTGTCAAAACAGA 62.072 47.826 9.65 0.00 45.94 3.41
4089 5311 5.735766 AGATCTACTTTCTAAACCAGTGGC 58.264 41.667 9.78 0.00 0.00 5.01
4339 5588 3.593096 AGGACATGACTATGCATATGCG 58.407 45.455 22.21 11.02 45.83 4.73
4383 5632 3.817709 AAGCAGATCTCCTAGCACTTC 57.182 47.619 5.65 0.00 0.00 3.01
4417 5666 7.687388 ACTATCAGCTGAATCCAACATGATAT 58.313 34.615 22.50 0.81 30.28 1.63
4456 5705 5.263599 TGAGCCATCATCAGGTGTAAATTT 58.736 37.500 0.00 0.00 0.00 1.82
4464 5713 3.416253 GCATGAGCCATCATCAGGT 57.584 52.632 0.00 0.00 44.58 4.00
4538 5787 6.421801 GTGGTCCTTTTGATTCAAATGTTCTG 59.578 38.462 12.39 3.47 33.19 3.02
4622 5875 4.392138 GGCATTACTTCGCTTATCCATACC 59.608 45.833 0.00 0.00 0.00 2.73
4636 5890 3.372025 GGAGTTCAGGATGGGCATTACTT 60.372 47.826 0.00 0.00 36.16 2.24
4657 5911 1.340114 GGTGGAAGAGGTGCTAAAGGG 60.340 57.143 0.00 0.00 0.00 3.95
4728 5982 3.989817 GGTAGCTGGTGCAAAAGAAAATG 59.010 43.478 0.00 0.00 42.74 2.32
4729 5983 3.006859 GGGTAGCTGGTGCAAAAGAAAAT 59.993 43.478 0.00 0.00 42.74 1.82
4730 5984 2.364002 GGGTAGCTGGTGCAAAAGAAAA 59.636 45.455 0.00 0.00 42.74 2.29
4731 5985 1.960689 GGGTAGCTGGTGCAAAAGAAA 59.039 47.619 0.00 0.00 42.74 2.52
4734 5988 1.620822 AAGGGTAGCTGGTGCAAAAG 58.379 50.000 0.00 0.00 42.74 2.27
4848 6102 9.698309 TGAAAAGCATTACCGATCAAAAATTTA 57.302 25.926 0.00 0.00 0.00 1.40
4849 6103 8.600449 TGAAAAGCATTACCGATCAAAAATTT 57.400 26.923 0.00 0.00 0.00 1.82
4857 6112 4.394920 TGTCCTTGAAAAGCATTACCGATC 59.605 41.667 0.00 0.00 44.44 3.69
4879 6134 6.992063 ACTCAAGTAGCCAACATCTAAATG 57.008 37.500 0.00 0.00 38.93 2.32
4962 6217 3.181469 TGAGGTCCGCCAATAATAGTCAC 60.181 47.826 0.00 0.00 37.19 3.67
5097 6352 3.457610 AACAATGTTCAGGCCAACAAG 57.542 42.857 12.25 10.41 39.69 3.16
5232 6487 1.340889 TGTGGGCTGATTTGTTTGCTC 59.659 47.619 0.00 0.00 0.00 4.26
5490 6745 1.737008 GTTCTTCACGGAGGCGACC 60.737 63.158 0.00 0.00 0.00 4.79
5777 7032 2.791503 CGAGTACAGTATCACAGTGCCG 60.792 54.545 0.00 0.00 0.00 5.69
5859 7114 4.506288 GGAGTGCCATTTACAAACAACAAC 59.494 41.667 0.00 0.00 0.00 3.32
5954 7210 1.463674 CAGCCCCAAACCATGTCTAC 58.536 55.000 0.00 0.00 0.00 2.59
5988 7256 7.982761 AACGACATGTACAAGGGTTAATTTA 57.017 32.000 0.00 0.00 0.00 1.40
6017 7285 0.541863 ACGGCATTGGAGGAAGGTAG 59.458 55.000 0.00 0.00 0.00 3.18
6085 7356 8.373256 CAGACAACGATACAAATGTTACTACTG 58.627 37.037 0.00 0.00 0.00 2.74
6104 7376 6.593978 CAGCTACACTAAACAATCAGACAAC 58.406 40.000 0.00 0.00 0.00 3.32
6138 7410 3.229293 TGCTGGTGGTTTTCATTCATGA 58.771 40.909 0.00 0.00 34.44 3.07
6177 7449 5.303259 TGGTATGTAGCTGCATCCATTTA 57.697 39.130 21.26 0.00 0.00 1.40
6224 7533 9.945904 GACCATTATAGTTAGGGAAATAGGAAG 57.054 37.037 0.00 0.00 0.00 3.46
6225 7534 9.455144 TGACCATTATAGTTAGGGAAATAGGAA 57.545 33.333 0.00 0.00 0.00 3.36
6241 7550 6.183361 TGGTGTGCTCATATGTGACCATTATA 60.183 38.462 8.94 0.00 32.29 0.98
6333 7642 6.811665 AGAATCATGCATGAACAACTCAATTG 59.188 34.615 31.79 0.00 40.69 2.32
6353 7662 9.377312 AGAGTTTATGACAAGCTTTAGAGAATC 57.623 33.333 0.00 0.00 0.00 2.52
6357 7666 8.715191 ATGAGAGTTTATGACAAGCTTTAGAG 57.285 34.615 0.00 0.00 0.00 2.43
6488 7804 4.610007 GCTGTTGATGATGTTAGCGCTATG 60.610 45.833 19.60 0.00 0.00 2.23
6530 7852 8.563732 ACTTTTTGTATTTGTTTTGTGTTGCTT 58.436 25.926 0.00 0.00 0.00 3.91
6573 7895 7.366226 AGGATCTCTGGTCTCTTTTAGGATTA 58.634 38.462 0.00 0.00 0.00 1.75
6607 7929 5.414454 GGGTGAGTTTCATTACACATAAGCA 59.586 40.000 0.00 0.00 35.33 3.91
6608 7930 5.648092 AGGGTGAGTTTCATTACACATAAGC 59.352 40.000 0.00 0.00 35.33 3.09
6609 7931 7.390440 TCAAGGGTGAGTTTCATTACACATAAG 59.610 37.037 0.00 0.00 35.33 1.73
6611 7933 6.653320 GTCAAGGGTGAGTTTCATTACACATA 59.347 38.462 0.00 0.00 33.27 2.29
6612 7934 5.473504 GTCAAGGGTGAGTTTCATTACACAT 59.526 40.000 0.00 0.00 33.27 3.21
6613 7935 4.819630 GTCAAGGGTGAGTTTCATTACACA 59.180 41.667 0.00 0.00 33.27 3.72
6614 7936 4.819630 TGTCAAGGGTGAGTTTCATTACAC 59.180 41.667 0.00 0.00 33.27 2.90
6654 7976 9.319143 CCAAAGAATAATAGATTCAGAAGACGT 57.681 33.333 0.00 0.00 0.00 4.34
6655 7977 9.534565 TCCAAAGAATAATAGATTCAGAAGACG 57.465 33.333 0.53 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.