Multiple sequence alignment - TraesCS1B01G336600

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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 TraesCS1B01G336600 chr1B 100.000 4802 0 0 1 4802 563542787 563537986 0.000000e+00 8868.0
1 TraesCS1B01G336600 chr1B 99.018 509 3 1 733 1241 563539100 563538594 0.000000e+00 911.0
2 TraesCS1B01G336600 chr1B 99.018 509 3 1 3688 4194 563542055 563541547 0.000000e+00 911.0
3 TraesCS1B01G336600 chr1B 99.000 500 5 0 3689 4188 16672946 16672447 0.000000e+00 896.0
4 TraesCS1B01G336600 chr1B 98.611 504 5 1 734 1237 16672946 16672445 0.000000e+00 891.0
5 TraesCS1B01G336600 chr1B 93.401 394 22 3 4193 4582 563546810 563546417 8.960000e-162 580.0
6 TraesCS1B01G336600 chr1B 91.901 284 23 0 450 733 563547089 563546806 9.680000e-107 398.0
7 TraesCS1B01G336600 chr1B 85.366 287 38 2 454 739 563307968 563307685 1.310000e-75 294.0
8 TraesCS1B01G336600 chr1B 85.199 277 38 1 457 733 563384010 563383737 1.020000e-71 281.0
9 TraesCS1B01G336600 chr1B 86.641 262 18 9 3955 4204 21357818 21358074 1.700000e-69 274.0
10 TraesCS1B01G336600 chr1B 84.615 273 38 4 454 725 563316706 563316437 7.920000e-68 268.0
11 TraesCS1B01G336600 chr1B 82.123 179 15 11 269 445 563316825 563316662 2.330000e-28 137.0
12 TraesCS1B01G336600 chr1B 98.246 57 1 0 389 445 563542347 563542291 3.060000e-17 100.0
13 TraesCS1B01G336600 chr1B 86.301 73 9 1 4193 4265 563444409 563444338 1.430000e-10 78.7
14 TraesCS1B01G336600 chr3B 96.824 3463 90 3 734 4193 763557841 763561286 0.000000e+00 5768.0
15 TraesCS1B01G336600 chr3B 92.899 2380 136 13 1340 3703 281517251 281519613 0.000000e+00 3428.0
16 TraesCS1B01G336600 chr3B 94.821 1622 81 1 1340 2958 449153046 449154667 0.000000e+00 2527.0
17 TraesCS1B01G336600 chr3B 96.506 1202 35 2 2994 4188 793127093 793128294 0.000000e+00 1980.0
18 TraesCS1B01G336600 chr3B 98.814 506 6 0 3689 4194 763557841 763558346 0.000000e+00 902.0
19 TraesCS1B01G336600 chr3B 85.997 707 97 2 2569 3274 448759196 448759901 0.000000e+00 756.0
20 TraesCS1B01G336600 chr3B 84.017 707 111 2 2569 3274 497432231 497431526 0.000000e+00 678.0
21 TraesCS1B01G336600 chr2B 93.185 2377 144 8 1343 3703 724653243 724650869 0.000000e+00 3476.0
22 TraesCS1B01G336600 chr2B 88.932 2051 224 3 1225 3274 797173919 797175967 0.000000e+00 2527.0
23 TraesCS1B01G336600 chr2B 97.116 971 25 2 3224 4192 106116796 106115827 0.000000e+00 1635.0
24 TraesCS1B01G336600 chr7B 94.300 2228 78 5 734 2958 372580212 372578031 0.000000e+00 3365.0
25 TraesCS1B01G336600 chr7B 96.336 1201 41 2 2994 4192 372578130 372576931 0.000000e+00 1971.0
26 TraesCS1B01G336600 chr7B 99.211 507 4 0 733 1239 372577437 372576931 0.000000e+00 915.0
27 TraesCS1B01G336600 chr7B 99.012 506 5 0 3689 4194 372580212 372579707 0.000000e+00 907.0
28 TraesCS1B01G336600 chr7B 87.179 234 17 6 4582 4802 727394982 727394749 2.220000e-63 254.0
29 TraesCS1B01G336600 chr7B 87.444 223 22 5 4582 4802 231199890 231199672 7.980000e-63 252.0
30 TraesCS1B01G336600 chr7B 83.410 217 30 4 4580 4796 57269841 57269631 3.790000e-46 196.0
31 TraesCS1B01G336600 chr2A 94.922 1930 92 2 1035 2958 712856195 712858124 0.000000e+00 3016.0
32 TraesCS1B01G336600 chr2A 93.427 1780 116 1 1179 2958 52076439 52074661 0.000000e+00 2638.0
33 TraesCS1B01G336600 chr2A 94.857 175 9 0 742 916 4145954 4145780 1.700000e-69 274.0
34 TraesCS1B01G336600 chr2A 85.520 221 29 3 4582 4802 612827811 612828028 1.340000e-55 228.0
35 TraesCS1B01G336600 chr2A 91.339 127 9 2 932 1058 4145509 4145385 6.390000e-39 172.0
36 TraesCS1B01G336600 chr6B 94.047 1915 93 3 734 2648 133450734 133448841 0.000000e+00 2885.0
37 TraesCS1B01G336600 chr6B 96.087 1201 42 2 2994 4193 133448573 133447377 0.000000e+00 1953.0
38 TraesCS1B01G336600 chr6B 97.638 508 7 2 733 1240 133447879 133447377 0.000000e+00 867.0
39 TraesCS1B01G336600 chr6B 83.929 224 24 9 4582 4802 542172015 542171801 2.270000e-48 204.0
40 TraesCS1B01G336600 chr7A 92.946 1772 123 2 1187 2958 65073581 65075350 0.000000e+00 2579.0
41 TraesCS1B01G336600 chrUn 91.372 1866 160 1 1230 3095 16475463 16473599 0.000000e+00 2553.0
42 TraesCS1B01G336600 chrUn 83.951 243 15 9 4582 4802 208668398 208668158 1.350000e-50 211.0
43 TraesCS1B01G336600 chrUn 83.951 243 15 9 4582 4802 256168059 256167819 1.350000e-50 211.0
44 TraesCS1B01G336600 chr4A 93.641 1667 99 6 985 2648 593189944 593191606 0.000000e+00 2484.0
45 TraesCS1B01G336600 chr5A 93.723 1163 67 1 2569 3725 702867623 702866461 0.000000e+00 1738.0
46 TraesCS1B01G336600 chr5A 93.161 541 29 2 3224 3756 461878491 461877951 0.000000e+00 787.0
47 TraesCS1B01G336600 chr5A 85.646 209 22 3 4592 4800 668758565 668758765 3.760000e-51 213.0
48 TraesCS1B01G336600 chr4B 91.747 727 52 5 2994 3713 75566258 75566983 0.000000e+00 1003.0
49 TraesCS1B01G336600 chr4B 85.484 248 13 10 4578 4802 462206157 462206404 2.230000e-58 237.0
50 TraesCS1B01G336600 chr4B 83.128 243 19 3 4582 4802 190182592 190182350 8.150000e-48 202.0
51 TraesCS1B01G336600 chr3A 92.791 541 31 2 3224 3756 36383438 36382898 0.000000e+00 776.0
52 TraesCS1B01G336600 chr1D 93.130 393 23 2 4193 4582 416689411 416689020 1.500000e-159 573.0
53 TraesCS1B01G336600 chr1D 92.386 394 25 3 4193 4582 416703696 416703304 1.510000e-154 556.0
54 TraesCS1B01G336600 chr1D 94.118 323 16 3 123 445 416689962 416689643 5.590000e-134 488.0
55 TraesCS1B01G336600 chr1D 94.464 289 15 1 445 733 416689694 416689407 1.230000e-120 444.0
56 TraesCS1B01G336600 chr1D 88.927 289 30 2 446 733 416703979 416703692 5.910000e-94 355.0
57 TraesCS1B01G336600 chr1D 76.731 361 46 13 4193 4549 416625328 416625002 2.970000e-37 167.0
58 TraesCS1B01G336600 chr1D 88.000 100 9 3 4267 4365 416664972 416664875 1.090000e-21 115.0
59 TraesCS1B01G336600 chr1D 77.451 204 23 9 4193 4384 416662657 416662465 3.060000e-17 100.0
60 TraesCS1B01G336600 chr1D 93.617 47 2 1 4193 4239 416665593 416665548 8.620000e-08 69.4
61 TraesCS1B01G336600 chr1A 92.132 394 25 4 4193 4582 514050905 514050514 7.020000e-153 551.0
62 TraesCS1B01G336600 chr1A 94.753 324 16 1 123 445 514038590 514038267 1.990000e-138 503.0
63 TraesCS1B01G336600 chr1A 95.341 279 13 0 445 723 514038319 514038041 1.230000e-120 444.0
64 TraesCS1B01G336600 chr1A 89.619 289 30 0 445 733 514051189 514050901 7.590000e-98 368.0
65 TraesCS1B01G336600 chr1A 85.614 285 34 6 457 739 513896315 513896036 4.700000e-75 292.0
66 TraesCS1B01G336600 chr1A 78.873 355 47 15 4193 4531 513896046 513895704 1.050000e-51 215.0
67 TraesCS1B01G336600 chr1A 80.447 179 18 9 269 445 513896438 513896275 2.350000e-23 121.0
68 TraesCS1B01G336600 chr1A 86.207 116 10 6 274 388 513934047 513933937 2.350000e-23 121.0
69 TraesCS1B01G336600 chr4D 84.774 243 15 1 4582 4802 332376558 332376316 1.740000e-54 224.0
70 TraesCS1B01G336600 chr4D 88.360 189 17 4 4592 4779 426208246 426208430 6.260000e-54 222.0
71 TraesCS1B01G336600 chr5D 89.080 174 17 2 4579 4752 10067017 10067188 1.050000e-51 215.0


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 TraesCS1B01G336600 chr1B 563537986 563542787 4801 True 8868.000000 8868 100.000000 1 4802 1 chr1B.!!$R4 4801
1 TraesCS1B01G336600 chr1B 16672445 16672946 501 True 893.500000 896 98.805500 734 4188 2 chr1B.!!$R5 3454
2 TraesCS1B01G336600 chr1B 563538594 563542347 3753 True 640.666667 911 98.760667 389 4194 3 chr1B.!!$R7 3805
3 TraesCS1B01G336600 chr1B 563546417 563547089 672 True 489.000000 580 92.651000 450 4582 2 chr1B.!!$R8 4132
4 TraesCS1B01G336600 chr3B 281517251 281519613 2362 False 3428.000000 3428 92.899000 1340 3703 1 chr3B.!!$F1 2363
5 TraesCS1B01G336600 chr3B 763557841 763561286 3445 False 3335.000000 5768 97.819000 734 4194 2 chr3B.!!$F5 3460
6 TraesCS1B01G336600 chr3B 449153046 449154667 1621 False 2527.000000 2527 94.821000 1340 2958 1 chr3B.!!$F3 1618
7 TraesCS1B01G336600 chr3B 793127093 793128294 1201 False 1980.000000 1980 96.506000 2994 4188 1 chr3B.!!$F4 1194
8 TraesCS1B01G336600 chr3B 448759196 448759901 705 False 756.000000 756 85.997000 2569 3274 1 chr3B.!!$F2 705
9 TraesCS1B01G336600 chr3B 497431526 497432231 705 True 678.000000 678 84.017000 2569 3274 1 chr3B.!!$R1 705
10 TraesCS1B01G336600 chr2B 724650869 724653243 2374 True 3476.000000 3476 93.185000 1343 3703 1 chr2B.!!$R2 2360
11 TraesCS1B01G336600 chr2B 797173919 797175967 2048 False 2527.000000 2527 88.932000 1225 3274 1 chr2B.!!$F1 2049
12 TraesCS1B01G336600 chr2B 106115827 106116796 969 True 1635.000000 1635 97.116000 3224 4192 1 chr2B.!!$R1 968
13 TraesCS1B01G336600 chr7B 372576931 372580212 3281 True 1789.500000 3365 97.214750 733 4194 4 chr7B.!!$R4 3461
14 TraesCS1B01G336600 chr2A 712856195 712858124 1929 False 3016.000000 3016 94.922000 1035 2958 1 chr2A.!!$F2 1923
15 TraesCS1B01G336600 chr2A 52074661 52076439 1778 True 2638.000000 2638 93.427000 1179 2958 1 chr2A.!!$R1 1779
16 TraesCS1B01G336600 chr2A 4145385 4145954 569 True 223.000000 274 93.098000 742 1058 2 chr2A.!!$R2 316
17 TraesCS1B01G336600 chr6B 133447377 133450734 3357 True 1901.666667 2885 95.924000 733 4193 3 chr6B.!!$R2 3460
18 TraesCS1B01G336600 chr7A 65073581 65075350 1769 False 2579.000000 2579 92.946000 1187 2958 1 chr7A.!!$F1 1771
19 TraesCS1B01G336600 chrUn 16473599 16475463 1864 True 2553.000000 2553 91.372000 1230 3095 1 chrUn.!!$R1 1865
20 TraesCS1B01G336600 chr4A 593189944 593191606 1662 False 2484.000000 2484 93.641000 985 2648 1 chr4A.!!$F1 1663
21 TraesCS1B01G336600 chr5A 702866461 702867623 1162 True 1738.000000 1738 93.723000 2569 3725 1 chr5A.!!$R2 1156
22 TraesCS1B01G336600 chr5A 461877951 461878491 540 True 787.000000 787 93.161000 3224 3756 1 chr5A.!!$R1 532
23 TraesCS1B01G336600 chr4B 75566258 75566983 725 False 1003.000000 1003 91.747000 2994 3713 1 chr4B.!!$F1 719
24 TraesCS1B01G336600 chr3A 36382898 36383438 540 True 776.000000 776 92.791000 3224 3756 1 chr3A.!!$R1 532
25 TraesCS1B01G336600 chr1D 416689020 416689962 942 True 501.666667 573 93.904000 123 4582 3 chr1D.!!$R3 4459
26 TraesCS1B01G336600 chr1D 416703304 416703979 675 True 455.500000 556 90.656500 446 4582 2 chr1D.!!$R4 4136
27 TraesCS1B01G336600 chr1A 514038041 514038590 549 True 473.500000 503 95.047000 123 723 2 chr1A.!!$R3 600
28 TraesCS1B01G336600 chr1A 514050514 514051189 675 True 459.500000 551 90.875500 445 4582 2 chr1A.!!$R4 4137
29 TraesCS1B01G336600 chr1A 513895704 513896438 734 True 209.333333 292 81.644667 269 4531 3 chr1A.!!$R2 4262

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
116 117 0.108945 GCTGTTGGCATGGAAGCTTC 60.109 55.0 18.54 18.54 41.35 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4300 4783 1.388547 GTCACAGCCACAAACCTTCA 58.611 50.0 0.0 0.0 0.0 3.02 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
36 37 7.552458 AAAAACTGAAATTTGGAATCCACAC 57.448 32.000 0.00 0.00 30.78 3.82
37 38 4.871933 ACTGAAATTTGGAATCCACACC 57.128 40.909 0.00 0.00 30.78 4.16
38 39 3.578282 ACTGAAATTTGGAATCCACACCC 59.422 43.478 0.00 0.00 30.78 4.61
39 40 2.560542 TGAAATTTGGAATCCACACCCG 59.439 45.455 0.00 0.00 30.78 5.28
40 41 2.595750 AATTTGGAATCCACACCCGA 57.404 45.000 0.00 0.00 30.78 5.14
41 42 2.595750 ATTTGGAATCCACACCCGAA 57.404 45.000 0.00 0.00 30.78 4.30
42 43 1.611519 TTTGGAATCCACACCCGAAC 58.388 50.000 0.00 0.00 30.78 3.95
43 44 0.768622 TTGGAATCCACACCCGAACT 59.231 50.000 0.00 0.00 30.78 3.01
44 45 0.323629 TGGAATCCACACCCGAACTC 59.676 55.000 0.00 0.00 0.00 3.01
45 46 0.323629 GGAATCCACACCCGAACTCA 59.676 55.000 0.00 0.00 0.00 3.41
46 47 1.271163 GGAATCCACACCCGAACTCAA 60.271 52.381 0.00 0.00 0.00 3.02
47 48 1.804748 GAATCCACACCCGAACTCAAC 59.195 52.381 0.00 0.00 0.00 3.18
48 49 0.762418 ATCCACACCCGAACTCAACA 59.238 50.000 0.00 0.00 0.00 3.33
49 50 0.762418 TCCACACCCGAACTCAACAT 59.238 50.000 0.00 0.00 0.00 2.71
50 51 1.972075 TCCACACCCGAACTCAACATA 59.028 47.619 0.00 0.00 0.00 2.29
51 52 2.073816 CCACACCCGAACTCAACATAC 58.926 52.381 0.00 0.00 0.00 2.39
52 53 2.289444 CCACACCCGAACTCAACATACT 60.289 50.000 0.00 0.00 0.00 2.12
53 54 3.056393 CCACACCCGAACTCAACATACTA 60.056 47.826 0.00 0.00 0.00 1.82
54 55 3.924686 CACACCCGAACTCAACATACTAC 59.075 47.826 0.00 0.00 0.00 2.73
55 56 3.575256 ACACCCGAACTCAACATACTACA 59.425 43.478 0.00 0.00 0.00 2.74
56 57 4.222145 ACACCCGAACTCAACATACTACAT 59.778 41.667 0.00 0.00 0.00 2.29
57 58 4.804139 CACCCGAACTCAACATACTACATC 59.196 45.833 0.00 0.00 0.00 3.06
58 59 4.464951 ACCCGAACTCAACATACTACATCA 59.535 41.667 0.00 0.00 0.00 3.07
59 60 5.043903 CCCGAACTCAACATACTACATCAG 58.956 45.833 0.00 0.00 0.00 2.90
60 61 5.394224 CCCGAACTCAACATACTACATCAGT 60.394 44.000 0.00 0.00 41.62 3.41
61 62 5.744345 CCGAACTCAACATACTACATCAGTC 59.256 44.000 0.00 0.00 38.80 3.51
62 63 6.404844 CCGAACTCAACATACTACATCAGTCT 60.405 42.308 0.00 0.00 38.80 3.24
63 64 7.030165 CGAACTCAACATACTACATCAGTCTT 58.970 38.462 0.00 0.00 38.80 3.01
64 65 7.008719 CGAACTCAACATACTACATCAGTCTTG 59.991 40.741 0.00 0.00 38.80 3.02
65 66 7.233389 ACTCAACATACTACATCAGTCTTGT 57.767 36.000 0.00 0.00 38.80 3.16
66 67 8.349568 ACTCAACATACTACATCAGTCTTGTA 57.650 34.615 0.00 0.00 38.80 2.41
67 68 8.972127 ACTCAACATACTACATCAGTCTTGTAT 58.028 33.333 0.00 0.00 38.80 2.29
68 69 9.809096 CTCAACATACTACATCAGTCTTGTATT 57.191 33.333 0.00 0.00 38.80 1.89
71 72 8.425577 ACATACTACATCAGTCTTGTATTTGC 57.574 34.615 0.00 0.00 38.80 3.68
72 73 8.040727 ACATACTACATCAGTCTTGTATTTGCA 58.959 33.333 0.00 0.00 38.80 4.08
73 74 9.049523 CATACTACATCAGTCTTGTATTTGCAT 57.950 33.333 0.00 0.00 38.80 3.96
74 75 7.545362 ACTACATCAGTCTTGTATTTGCATC 57.455 36.000 0.00 0.00 28.33 3.91
75 76 7.334090 ACTACATCAGTCTTGTATTTGCATCT 58.666 34.615 0.00 0.00 28.33 2.90
76 77 8.478066 ACTACATCAGTCTTGTATTTGCATCTA 58.522 33.333 0.00 0.00 28.33 1.98
77 78 7.545362 ACATCAGTCTTGTATTTGCATCTAC 57.455 36.000 0.00 0.00 0.00 2.59
78 79 7.334090 ACATCAGTCTTGTATTTGCATCTACT 58.666 34.615 7.47 0.00 0.00 2.57
79 80 8.478066 ACATCAGTCTTGTATTTGCATCTACTA 58.522 33.333 7.47 0.72 0.00 1.82
80 81 9.317936 CATCAGTCTTGTATTTGCATCTACTAA 57.682 33.333 7.47 0.00 0.00 2.24
81 82 8.703604 TCAGTCTTGTATTTGCATCTACTAAC 57.296 34.615 7.47 4.14 0.00 2.34
82 83 8.311109 TCAGTCTTGTATTTGCATCTACTAACA 58.689 33.333 7.47 0.00 0.00 2.41
83 84 8.598924 CAGTCTTGTATTTGCATCTACTAACAG 58.401 37.037 7.47 1.03 0.00 3.16
84 85 7.766278 AGTCTTGTATTTGCATCTACTAACAGG 59.234 37.037 7.47 0.00 0.00 4.00
85 86 6.538742 TCTTGTATTTGCATCTACTAACAGGC 59.461 38.462 7.47 0.00 0.00 4.85
86 87 5.739959 TGTATTTGCATCTACTAACAGGCA 58.260 37.500 7.47 0.00 0.00 4.75
87 88 5.817296 TGTATTTGCATCTACTAACAGGCAG 59.183 40.000 7.47 0.00 32.31 4.85
88 89 3.981071 TTGCATCTACTAACAGGCAGT 57.019 42.857 0.00 0.00 32.31 4.40
89 90 3.526931 TGCATCTACTAACAGGCAGTC 57.473 47.619 0.00 0.00 0.00 3.51
90 91 2.168521 TGCATCTACTAACAGGCAGTCC 59.831 50.000 0.00 0.00 0.00 3.85
91 92 2.432510 GCATCTACTAACAGGCAGTCCT 59.567 50.000 0.00 0.00 45.66 3.85
101 102 1.577736 AGGCAGTCCTGATTAGCTGT 58.422 50.000 0.00 0.00 42.34 4.40
102 103 1.912043 AGGCAGTCCTGATTAGCTGTT 59.088 47.619 0.00 0.00 42.34 3.16
103 104 2.012673 GGCAGTCCTGATTAGCTGTTG 58.987 52.381 0.00 0.00 0.00 3.33
104 105 2.012673 GCAGTCCTGATTAGCTGTTGG 58.987 52.381 0.00 0.00 0.00 3.77
105 106 2.012673 CAGTCCTGATTAGCTGTTGGC 58.987 52.381 0.00 0.00 42.19 4.52
106 107 1.630369 AGTCCTGATTAGCTGTTGGCA 59.370 47.619 0.00 0.00 44.79 4.92
107 108 2.240667 AGTCCTGATTAGCTGTTGGCAT 59.759 45.455 0.00 0.00 44.79 4.40
108 109 2.357009 GTCCTGATTAGCTGTTGGCATG 59.643 50.000 0.00 0.00 44.79 4.06
109 110 1.679680 CCTGATTAGCTGTTGGCATGG 59.320 52.381 0.00 0.00 44.79 3.66
110 111 2.646930 CTGATTAGCTGTTGGCATGGA 58.353 47.619 0.00 0.00 44.79 3.41
111 112 3.018856 CTGATTAGCTGTTGGCATGGAA 58.981 45.455 0.00 0.00 44.79 3.53
112 113 3.018856 TGATTAGCTGTTGGCATGGAAG 58.981 45.455 0.00 0.00 44.79 3.46
113 114 1.176527 TTAGCTGTTGGCATGGAAGC 58.823 50.000 0.00 0.00 44.79 3.86
114 115 0.329261 TAGCTGTTGGCATGGAAGCT 59.671 50.000 15.14 15.14 45.72 3.74
115 116 0.541296 AGCTGTTGGCATGGAAGCTT 60.541 50.000 0.00 0.00 41.31 3.74
116 117 0.108945 GCTGTTGGCATGGAAGCTTC 60.109 55.000 18.54 18.54 41.35 3.86
117 118 0.169672 CTGTTGGCATGGAAGCTTCG 59.830 55.000 19.91 7.86 34.17 3.79
118 119 1.243342 TGTTGGCATGGAAGCTTCGG 61.243 55.000 19.91 12.81 34.17 4.30
119 120 2.342650 TTGGCATGGAAGCTTCGGC 61.343 57.895 19.91 20.74 42.17 5.54
136 137 4.398549 TCGGCGTAGAACTTCATTTTTG 57.601 40.909 6.85 0.00 0.00 2.44
200 201 2.024176 TTCCCTAAGCAGAGGACACA 57.976 50.000 5.51 0.00 39.15 3.72
205 206 2.826128 CCTAAGCAGAGGACACACACTA 59.174 50.000 0.00 0.00 39.15 2.74
230 231 1.214367 TTGTTCGAGCCGACAAAGTC 58.786 50.000 0.00 0.00 34.89 3.01
243 244 6.071952 AGCCGACAAAGTCAAATCAACATAAT 60.072 34.615 0.00 0.00 32.09 1.28
263 264 9.245962 ACATAATCGATAAGTTACAGCTACAAC 57.754 33.333 0.00 0.00 0.00 3.32
409 411 1.423845 CGCACTTCGTGTAATGGCC 59.576 57.895 0.00 0.00 35.75 5.36
410 412 1.019278 CGCACTTCGTGTAATGGCCT 61.019 55.000 3.32 0.00 35.75 5.19
411 413 0.727398 GCACTTCGTGTAATGGCCTC 59.273 55.000 3.32 0.00 35.75 4.70
412 414 1.943968 GCACTTCGTGTAATGGCCTCA 60.944 52.381 3.32 0.00 35.75 3.86
413 415 2.002586 CACTTCGTGTAATGGCCTCAG 58.997 52.381 3.32 0.00 0.00 3.35
414 416 1.899814 ACTTCGTGTAATGGCCTCAGA 59.100 47.619 3.32 0.00 0.00 3.27
415 417 2.301870 ACTTCGTGTAATGGCCTCAGAA 59.698 45.455 3.32 0.00 0.00 3.02
416 418 2.672961 TCGTGTAATGGCCTCAGAAG 57.327 50.000 3.32 0.00 0.00 2.85
417 419 2.176045 TCGTGTAATGGCCTCAGAAGA 58.824 47.619 3.32 0.00 0.00 2.87
418 420 2.565391 TCGTGTAATGGCCTCAGAAGAA 59.435 45.455 3.32 0.00 0.00 2.52
419 421 2.932614 CGTGTAATGGCCTCAGAAGAAG 59.067 50.000 3.32 0.00 0.00 2.85
420 422 3.617531 CGTGTAATGGCCTCAGAAGAAGT 60.618 47.826 3.32 0.00 0.00 3.01
421 423 4.381612 CGTGTAATGGCCTCAGAAGAAGTA 60.382 45.833 3.32 0.00 0.00 2.24
422 424 5.112686 GTGTAATGGCCTCAGAAGAAGTAG 58.887 45.833 3.32 0.00 0.00 2.57
423 425 2.998316 ATGGCCTCAGAAGAAGTAGC 57.002 50.000 3.32 0.00 0.00 3.58
424 426 0.905357 TGGCCTCAGAAGAAGTAGCC 59.095 55.000 3.32 0.00 39.41 3.93
425 427 0.905357 GGCCTCAGAAGAAGTAGCCA 59.095 55.000 0.00 0.00 38.79 4.75
426 428 1.279271 GGCCTCAGAAGAAGTAGCCAA 59.721 52.381 0.00 0.00 38.79 4.52
427 429 2.290323 GGCCTCAGAAGAAGTAGCCAAA 60.290 50.000 0.00 0.00 38.79 3.28
428 430 3.006247 GCCTCAGAAGAAGTAGCCAAAG 58.994 50.000 0.00 0.00 0.00 2.77
429 431 3.307059 GCCTCAGAAGAAGTAGCCAAAGA 60.307 47.826 0.00 0.00 0.00 2.52
430 432 4.502962 CCTCAGAAGAAGTAGCCAAAGAG 58.497 47.826 0.00 0.00 0.00 2.85
431 433 4.502962 CTCAGAAGAAGTAGCCAAAGAGG 58.497 47.826 0.00 0.00 41.84 3.69
432 434 4.160329 TCAGAAGAAGTAGCCAAAGAGGA 58.840 43.478 0.00 0.00 41.22 3.71
433 435 4.221703 TCAGAAGAAGTAGCCAAAGAGGAG 59.778 45.833 0.00 0.00 41.22 3.69
434 436 4.020662 CAGAAGAAGTAGCCAAAGAGGAGT 60.021 45.833 0.00 0.00 41.22 3.85
435 437 3.971245 AGAAGTAGCCAAAGAGGAGTG 57.029 47.619 0.00 0.00 41.22 3.51
436 438 2.027653 AGAAGTAGCCAAAGAGGAGTGC 60.028 50.000 0.00 0.00 41.22 4.40
437 439 0.615850 AGTAGCCAAAGAGGAGTGCC 59.384 55.000 0.00 0.00 41.22 5.01
438 440 0.741221 GTAGCCAAAGAGGAGTGCCG 60.741 60.000 0.00 0.00 41.22 5.69
439 441 1.192146 TAGCCAAAGAGGAGTGCCGT 61.192 55.000 0.00 0.00 41.22 5.68
440 442 2.035442 GCCAAAGAGGAGTGCCGTC 61.035 63.158 0.00 0.00 41.22 4.79
441 443 1.371183 CCAAAGAGGAGTGCCGTCA 59.629 57.895 0.00 0.00 41.22 4.35
442 444 0.250295 CCAAAGAGGAGTGCCGTCAA 60.250 55.000 0.00 0.00 41.22 3.18
443 445 1.151668 CAAAGAGGAGTGCCGTCAAG 58.848 55.000 0.00 0.00 39.96 3.02
1132 1142 9.175312 TGTGTACTAGTACTACTACTACTACGT 57.825 37.037 28.56 0.00 37.00 3.57
1133 1143 9.440784 GTGTACTAGTACTACTACTACTACGTG 57.559 40.741 28.56 0.00 37.00 4.49
4300 4783 2.555757 GTCTCTGACTTGGCTTGCAAAT 59.444 45.455 0.00 0.00 0.00 2.32
4459 4946 5.473931 CAGTTGATAGCTGTAGTGTTCTGT 58.526 41.667 0.00 0.00 0.00 3.41
4465 4952 2.560542 AGCTGTAGTGTTCTGTCCTCTG 59.439 50.000 0.00 0.00 0.00 3.35
4466 4953 2.928731 GCTGTAGTGTTCTGTCCTCTGC 60.929 54.545 0.00 0.00 0.00 4.26
4512 4999 2.093764 CCATGTGTTTGGTTGTGTGGTT 60.094 45.455 0.00 0.00 31.74 3.67
4522 5009 2.034179 GGTTGTGTGGTTAGCTGGTTTC 59.966 50.000 0.00 0.00 0.00 2.78
4534 5021 2.164219 AGCTGGTTTCCGCATTATTGTG 59.836 45.455 0.00 0.00 0.00 3.33
4539 5026 1.172175 TTCCGCATTATTGTGCAGCA 58.828 45.000 0.00 0.00 45.30 4.41
4582 5069 7.697691 CCTACTGCTGTTGGTTTTTATATGAG 58.302 38.462 14.54 0.00 34.99 2.90
4583 5070 6.515272 ACTGCTGTTGGTTTTTATATGAGG 57.485 37.500 0.00 0.00 0.00 3.86
4584 5071 5.105756 ACTGCTGTTGGTTTTTATATGAGGC 60.106 40.000 0.00 0.00 0.00 4.70
4585 5072 5.016173 TGCTGTTGGTTTTTATATGAGGCT 58.984 37.500 0.00 0.00 0.00 4.58
4586 5073 6.184068 TGCTGTTGGTTTTTATATGAGGCTA 58.816 36.000 0.00 0.00 0.00 3.93
4587 5074 6.318648 TGCTGTTGGTTTTTATATGAGGCTAG 59.681 38.462 0.00 0.00 0.00 3.42
4588 5075 6.318900 GCTGTTGGTTTTTATATGAGGCTAGT 59.681 38.462 0.00 0.00 0.00 2.57
4589 5076 7.148069 GCTGTTGGTTTTTATATGAGGCTAGTT 60.148 37.037 0.00 0.00 0.00 2.24
4590 5077 8.050778 TGTTGGTTTTTATATGAGGCTAGTTG 57.949 34.615 0.00 0.00 0.00 3.16
4591 5078 7.668052 TGTTGGTTTTTATATGAGGCTAGTTGT 59.332 33.333 0.00 0.00 0.00 3.32
4592 5079 9.169592 GTTGGTTTTTATATGAGGCTAGTTGTA 57.830 33.333 0.00 0.00 0.00 2.41
4593 5080 9.742144 TTGGTTTTTATATGAGGCTAGTTGTAA 57.258 29.630 0.00 0.00 0.00 2.41
4594 5081 9.914834 TGGTTTTTATATGAGGCTAGTTGTAAT 57.085 29.630 0.00 0.00 0.00 1.89
4599 5086 9.778741 TTTATATGAGGCTAGTTGTAATGGAAG 57.221 33.333 0.00 0.00 0.00 3.46
4600 5087 5.700402 ATGAGGCTAGTTGTAATGGAAGT 57.300 39.130 0.00 0.00 0.00 3.01
4601 5088 6.808321 ATGAGGCTAGTTGTAATGGAAGTA 57.192 37.500 0.00 0.00 0.00 2.24
4602 5089 6.808321 TGAGGCTAGTTGTAATGGAAGTAT 57.192 37.500 0.00 0.00 0.00 2.12
4603 5090 7.195374 TGAGGCTAGTTGTAATGGAAGTATT 57.805 36.000 0.00 0.00 0.00 1.89
4604 5091 8.313944 TGAGGCTAGTTGTAATGGAAGTATTA 57.686 34.615 0.00 0.00 0.00 0.98
4605 5092 8.934697 TGAGGCTAGTTGTAATGGAAGTATTAT 58.065 33.333 0.00 0.00 0.00 1.28
4624 5111 9.770097 AGTATTATATGTAGTATCATGCATGCC 57.230 33.333 22.25 11.72 0.00 4.40
4625 5112 9.546428 GTATTATATGTAGTATCATGCATGCCA 57.454 33.333 22.25 8.84 0.00 4.92
4627 5114 9.636789 ATTATATGTAGTATCATGCATGCCAAT 57.363 29.630 22.25 12.74 0.00 3.16
4628 5115 7.949690 ATATGTAGTATCATGCATGCCAATT 57.050 32.000 22.25 8.61 0.00 2.32
4630 5117 7.764141 ATGTAGTATCATGCATGCCAATTAA 57.236 32.000 22.25 2.92 0.00 1.40
4631 5118 7.205737 TGTAGTATCATGCATGCCAATTAAG 57.794 36.000 22.25 0.00 0.00 1.85
4632 5119 5.130292 AGTATCATGCATGCCAATTAAGC 57.870 39.130 22.25 4.42 0.00 3.09
4633 5120 4.585581 AGTATCATGCATGCCAATTAAGCA 59.414 37.500 22.25 4.92 45.94 3.91
4634 5121 3.889520 TCATGCATGCCAATTAAGCAA 57.110 38.095 22.25 0.00 44.83 3.91
4635 5122 4.409718 TCATGCATGCCAATTAAGCAAT 57.590 36.364 22.25 0.00 44.83 3.56
4636 5123 4.771903 TCATGCATGCCAATTAAGCAATT 58.228 34.783 22.25 0.00 44.83 2.32
4637 5124 5.186942 TCATGCATGCCAATTAAGCAATTT 58.813 33.333 22.25 0.00 44.83 1.82
4638 5125 5.648526 TCATGCATGCCAATTAAGCAATTTT 59.351 32.000 22.25 0.00 44.83 1.82
4639 5126 5.298197 TGCATGCCAATTAAGCAATTTTG 57.702 34.783 16.68 2.45 44.83 2.44
4640 5127 5.001874 TGCATGCCAATTAAGCAATTTTGA 58.998 33.333 16.68 0.00 44.83 2.69
4641 5128 5.648526 TGCATGCCAATTAAGCAATTTTGAT 59.351 32.000 16.68 0.00 44.83 2.57
4642 5129 5.968848 GCATGCCAATTAAGCAATTTTGATG 59.031 36.000 6.36 0.93 44.83 3.07
4643 5130 6.183360 GCATGCCAATTAAGCAATTTTGATGA 60.183 34.615 6.36 0.00 44.83 2.92
4644 5131 6.971527 TGCCAATTAAGCAATTTTGATGAG 57.028 33.333 0.02 0.00 37.28 2.90
4645 5132 6.699366 TGCCAATTAAGCAATTTTGATGAGA 58.301 32.000 0.02 0.00 37.28 3.27
4646 5133 7.332557 TGCCAATTAAGCAATTTTGATGAGAT 58.667 30.769 0.02 0.00 37.28 2.75
4647 5134 7.279090 TGCCAATTAAGCAATTTTGATGAGATG 59.721 33.333 0.02 0.00 37.28 2.90
4648 5135 7.279313 GCCAATTAAGCAATTTTGATGAGATGT 59.721 33.333 0.00 0.00 31.82 3.06
4649 5136 8.814235 CCAATTAAGCAATTTTGATGAGATGTC 58.186 33.333 0.00 0.00 31.82 3.06
4650 5137 9.361315 CAATTAAGCAATTTTGATGAGATGTCA 57.639 29.630 0.00 0.00 32.62 3.58
4654 5141 8.515695 AAGCAATTTTGATGAGATGTCATAGA 57.484 30.769 5.15 0.00 43.92 1.98
4655 5142 8.515695 AGCAATTTTGATGAGATGTCATAGAA 57.484 30.769 5.15 1.15 43.92 2.10
4656 5143 9.132923 AGCAATTTTGATGAGATGTCATAGAAT 57.867 29.630 5.15 4.07 43.92 2.40
4657 5144 9.745880 GCAATTTTGATGAGATGTCATAGAATT 57.254 29.630 5.15 9.32 43.92 2.17
4677 5164 8.876303 AGAATTAAATGAAGAAAGAGAGCCTT 57.124 30.769 0.00 0.00 36.47 4.35
4678 5165 8.738106 AGAATTAAATGAAGAAAGAGAGCCTTG 58.262 33.333 0.00 0.00 34.79 3.61
4679 5166 8.641498 AATTAAATGAAGAAAGAGAGCCTTGA 57.359 30.769 0.00 0.00 34.79 3.02
4680 5167 7.678947 TTAAATGAAGAAAGAGAGCCTTGAG 57.321 36.000 0.00 0.00 34.79 3.02
4681 5168 4.906747 ATGAAGAAAGAGAGCCTTGAGT 57.093 40.909 0.00 0.00 34.79 3.41
4682 5169 6.365970 AATGAAGAAAGAGAGCCTTGAGTA 57.634 37.500 0.00 0.00 34.79 2.59
4683 5170 6.558488 ATGAAGAAAGAGAGCCTTGAGTAT 57.442 37.500 0.00 0.00 34.79 2.12
4684 5171 5.971763 TGAAGAAAGAGAGCCTTGAGTATC 58.028 41.667 0.00 0.00 34.79 2.24
4741 5228 9.658799 ATGCTACTTTATGTCATGTATGATACC 57.341 33.333 0.00 0.00 39.30 2.73
4742 5229 8.646900 TGCTACTTTATGTCATGTATGATACCA 58.353 33.333 0.00 0.00 39.30 3.25
4743 5230 9.489084 GCTACTTTATGTCATGTATGATACCAA 57.511 33.333 0.00 0.00 39.30 3.67
4746 5233 9.851686 ACTTTATGTCATGTATGATACCAACAT 57.148 29.630 14.66 14.66 39.30 2.71
4765 5252 9.661563 ACCAACATATAATACCATGTATTACGG 57.338 33.333 8.44 5.02 34.32 4.02
4766 5253 9.878667 CCAACATATAATACCATGTATTACGGA 57.121 33.333 8.44 0.30 34.32 4.69
4776 5263 7.770366 ACCATGTATTACGGATGTAGTATCA 57.230 36.000 0.00 0.00 0.00 2.15
4777 5264 8.362464 ACCATGTATTACGGATGTAGTATCAT 57.638 34.615 0.00 0.00 0.00 2.45
4778 5265 9.470399 ACCATGTATTACGGATGTAGTATCATA 57.530 33.333 0.00 0.00 0.00 2.15
4779 5266 9.731819 CCATGTATTACGGATGTAGTATCATAC 57.268 37.037 0.00 0.00 0.00 2.39
4782 5269 9.511272 TGTATTACGGATGTAGTATCATACACT 57.489 33.333 0.00 0.00 38.43 3.55
4785 5272 9.736414 ATTACGGATGTAGTATCATACACTAGT 57.264 33.333 0.00 0.00 38.43 2.57
4788 5275 9.381033 ACGGATGTAGTATCATACACTAGTATC 57.619 37.037 0.00 0.00 38.88 2.24
4789 5276 9.379791 CGGATGTAGTATCATACACTAGTATCA 57.620 37.037 0.00 0.00 38.88 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.542005 GGTGTGGATTCCAAATTTCAGTTTTT 59.458 34.615 7.05 0.00 34.18 1.94
13 14 6.054941 GGTGTGGATTCCAAATTTCAGTTTT 58.945 36.000 7.05 0.00 34.18 2.43
14 15 5.454613 GGGTGTGGATTCCAAATTTCAGTTT 60.455 40.000 7.05 0.00 34.18 2.66
15 16 4.040339 GGGTGTGGATTCCAAATTTCAGTT 59.960 41.667 7.05 0.00 34.18 3.16
16 17 3.578282 GGGTGTGGATTCCAAATTTCAGT 59.422 43.478 7.05 0.00 34.18 3.41
17 18 3.367292 CGGGTGTGGATTCCAAATTTCAG 60.367 47.826 7.05 0.00 34.18 3.02
18 19 2.560542 CGGGTGTGGATTCCAAATTTCA 59.439 45.455 7.05 0.00 34.18 2.69
19 20 2.823154 TCGGGTGTGGATTCCAAATTTC 59.177 45.455 7.05 0.00 34.18 2.17
20 21 2.883026 TCGGGTGTGGATTCCAAATTT 58.117 42.857 7.05 0.00 34.18 1.82
21 22 2.560981 GTTCGGGTGTGGATTCCAAATT 59.439 45.455 7.05 0.00 34.18 1.82
22 23 2.167662 GTTCGGGTGTGGATTCCAAAT 58.832 47.619 7.05 0.00 34.18 2.32
23 24 1.144093 AGTTCGGGTGTGGATTCCAAA 59.856 47.619 7.05 0.00 34.18 3.28
24 25 0.768622 AGTTCGGGTGTGGATTCCAA 59.231 50.000 7.05 0.00 34.18 3.53
25 26 0.323629 GAGTTCGGGTGTGGATTCCA 59.676 55.000 0.00 0.00 0.00 3.53
26 27 0.323629 TGAGTTCGGGTGTGGATTCC 59.676 55.000 0.00 0.00 0.00 3.01
27 28 1.804748 GTTGAGTTCGGGTGTGGATTC 59.195 52.381 0.00 0.00 0.00 2.52
28 29 1.142060 TGTTGAGTTCGGGTGTGGATT 59.858 47.619 0.00 0.00 0.00 3.01
29 30 0.762418 TGTTGAGTTCGGGTGTGGAT 59.238 50.000 0.00 0.00 0.00 3.41
30 31 0.762418 ATGTTGAGTTCGGGTGTGGA 59.238 50.000 0.00 0.00 0.00 4.02
31 32 2.073816 GTATGTTGAGTTCGGGTGTGG 58.926 52.381 0.00 0.00 0.00 4.17
32 33 3.040147 AGTATGTTGAGTTCGGGTGTG 57.960 47.619 0.00 0.00 0.00 3.82
33 34 3.575256 TGTAGTATGTTGAGTTCGGGTGT 59.425 43.478 0.00 0.00 0.00 4.16
34 35 4.182693 TGTAGTATGTTGAGTTCGGGTG 57.817 45.455 0.00 0.00 0.00 4.61
35 36 4.464951 TGATGTAGTATGTTGAGTTCGGGT 59.535 41.667 0.00 0.00 0.00 5.28
36 37 5.006153 TGATGTAGTATGTTGAGTTCGGG 57.994 43.478 0.00 0.00 0.00 5.14
37 38 5.651530 ACTGATGTAGTATGTTGAGTTCGG 58.348 41.667 0.00 0.00 38.04 4.30
38 39 6.556212 AGACTGATGTAGTATGTTGAGTTCG 58.444 40.000 0.00 0.00 40.53 3.95
39 40 7.815068 ACAAGACTGATGTAGTATGTTGAGTTC 59.185 37.037 0.00 0.00 40.53 3.01
40 41 7.671302 ACAAGACTGATGTAGTATGTTGAGTT 58.329 34.615 0.00 0.00 40.53 3.01
41 42 7.233389 ACAAGACTGATGTAGTATGTTGAGT 57.767 36.000 0.00 0.00 40.53 3.41
42 43 9.809096 AATACAAGACTGATGTAGTATGTTGAG 57.191 33.333 0.00 0.00 40.53 3.02
45 46 8.883731 GCAAATACAAGACTGATGTAGTATGTT 58.116 33.333 0.00 0.00 40.53 2.71
46 47 8.040727 TGCAAATACAAGACTGATGTAGTATGT 58.959 33.333 0.00 0.00 40.53 2.29
47 48 8.424274 TGCAAATACAAGACTGATGTAGTATG 57.576 34.615 0.00 0.00 40.53 2.39
48 49 9.265901 GATGCAAATACAAGACTGATGTAGTAT 57.734 33.333 0.00 0.00 40.53 2.12
49 50 8.478066 AGATGCAAATACAAGACTGATGTAGTA 58.522 33.333 0.00 0.00 40.53 1.82
50 51 7.334090 AGATGCAAATACAAGACTGATGTAGT 58.666 34.615 0.00 0.00 44.02 2.73
51 52 7.783090 AGATGCAAATACAAGACTGATGTAG 57.217 36.000 0.00 0.00 36.75 2.74
52 53 8.478066 AGTAGATGCAAATACAAGACTGATGTA 58.522 33.333 12.61 0.00 37.64 2.29
53 54 7.334090 AGTAGATGCAAATACAAGACTGATGT 58.666 34.615 12.61 0.00 34.81 3.06
54 55 7.783090 AGTAGATGCAAATACAAGACTGATG 57.217 36.000 12.61 0.00 0.00 3.07
55 56 9.319143 GTTAGTAGATGCAAATACAAGACTGAT 57.681 33.333 12.61 0.00 0.00 2.90
56 57 8.311109 TGTTAGTAGATGCAAATACAAGACTGA 58.689 33.333 12.61 0.00 0.00 3.41
57 58 8.479313 TGTTAGTAGATGCAAATACAAGACTG 57.521 34.615 12.61 0.00 0.00 3.51
58 59 7.766278 CCTGTTAGTAGATGCAAATACAAGACT 59.234 37.037 12.61 1.87 0.00 3.24
59 60 7.466050 GCCTGTTAGTAGATGCAAATACAAGAC 60.466 40.741 12.61 8.74 0.00 3.01
60 61 6.538742 GCCTGTTAGTAGATGCAAATACAAGA 59.461 38.462 12.61 4.86 0.00 3.02
61 62 6.316140 TGCCTGTTAGTAGATGCAAATACAAG 59.684 38.462 12.61 5.92 0.00 3.16
62 63 6.176896 TGCCTGTTAGTAGATGCAAATACAA 58.823 36.000 12.61 4.38 0.00 2.41
63 64 5.739959 TGCCTGTTAGTAGATGCAAATACA 58.260 37.500 12.61 1.20 0.00 2.29
64 65 5.817816 ACTGCCTGTTAGTAGATGCAAATAC 59.182 40.000 0.00 0.00 0.00 1.89
65 66 5.989477 ACTGCCTGTTAGTAGATGCAAATA 58.011 37.500 0.00 0.00 0.00 1.40
66 67 4.848357 ACTGCCTGTTAGTAGATGCAAAT 58.152 39.130 0.00 0.00 0.00 2.32
67 68 4.253685 GACTGCCTGTTAGTAGATGCAAA 58.746 43.478 0.00 0.00 0.00 3.68
68 69 3.369471 GGACTGCCTGTTAGTAGATGCAA 60.369 47.826 0.00 0.00 0.00 4.08
69 70 2.168521 GGACTGCCTGTTAGTAGATGCA 59.831 50.000 0.00 0.00 0.00 3.96
70 71 2.432510 AGGACTGCCTGTTAGTAGATGC 59.567 50.000 0.00 0.00 44.90 3.91
83 84 2.012673 CAACAGCTAATCAGGACTGCC 58.987 52.381 0.00 0.00 33.35 4.85
84 85 2.012673 CCAACAGCTAATCAGGACTGC 58.987 52.381 0.00 0.00 33.35 4.40
85 86 2.012673 GCCAACAGCTAATCAGGACTG 58.987 52.381 0.00 0.00 38.99 3.51
86 87 1.630369 TGCCAACAGCTAATCAGGACT 59.370 47.619 0.00 0.00 44.23 3.85
87 88 2.113860 TGCCAACAGCTAATCAGGAC 57.886 50.000 0.00 0.00 44.23 3.85
88 89 2.646930 CATGCCAACAGCTAATCAGGA 58.353 47.619 0.00 0.00 44.23 3.86
89 90 1.679680 CCATGCCAACAGCTAATCAGG 59.320 52.381 0.00 0.00 44.23 3.86
90 91 2.646930 TCCATGCCAACAGCTAATCAG 58.353 47.619 0.00 0.00 44.23 2.90
91 92 2.804986 TCCATGCCAACAGCTAATCA 57.195 45.000 0.00 0.00 44.23 2.57
92 93 2.223665 GCTTCCATGCCAACAGCTAATC 60.224 50.000 0.00 0.00 44.23 1.75
93 94 1.753073 GCTTCCATGCCAACAGCTAAT 59.247 47.619 0.00 0.00 44.23 1.73
94 95 1.176527 GCTTCCATGCCAACAGCTAA 58.823 50.000 0.00 0.00 44.23 3.09
95 96 0.329261 AGCTTCCATGCCAACAGCTA 59.671 50.000 0.00 0.00 44.23 3.32
96 97 0.541296 AAGCTTCCATGCCAACAGCT 60.541 50.000 0.00 0.00 42.76 4.24
97 98 0.108945 GAAGCTTCCATGCCAACAGC 60.109 55.000 15.97 0.00 44.14 4.40
98 99 0.169672 CGAAGCTTCCATGCCAACAG 59.830 55.000 20.62 0.00 0.00 3.16
99 100 1.243342 CCGAAGCTTCCATGCCAACA 61.243 55.000 20.62 0.00 0.00 3.33
100 101 1.508088 CCGAAGCTTCCATGCCAAC 59.492 57.895 20.62 0.00 0.00 3.77
101 102 2.342650 GCCGAAGCTTCCATGCCAA 61.343 57.895 20.62 0.00 35.50 4.52
102 103 2.751436 GCCGAAGCTTCCATGCCA 60.751 61.111 20.62 0.00 35.50 4.92
103 104 3.880846 CGCCGAAGCTTCCATGCC 61.881 66.667 20.62 3.98 36.60 4.40
104 105 1.766143 CTACGCCGAAGCTTCCATGC 61.766 60.000 20.62 18.13 36.60 4.06
105 106 0.179111 TCTACGCCGAAGCTTCCATG 60.179 55.000 20.62 12.17 36.60 3.66
106 107 0.535335 TTCTACGCCGAAGCTTCCAT 59.465 50.000 20.62 6.29 36.60 3.41
107 108 0.389426 GTTCTACGCCGAAGCTTCCA 60.389 55.000 20.62 0.56 36.60 3.53
108 109 0.108756 AGTTCTACGCCGAAGCTTCC 60.109 55.000 20.62 6.76 36.60 3.46
109 110 1.654602 GAAGTTCTACGCCGAAGCTTC 59.345 52.381 16.84 16.84 36.60 3.86
110 111 1.000506 TGAAGTTCTACGCCGAAGCTT 59.999 47.619 0.00 0.00 36.60 3.74
111 112 0.601558 TGAAGTTCTACGCCGAAGCT 59.398 50.000 4.17 0.00 36.60 3.74
112 113 1.641577 ATGAAGTTCTACGCCGAAGC 58.358 50.000 4.17 0.00 0.00 3.86
113 114 4.663636 AAAATGAAGTTCTACGCCGAAG 57.336 40.909 4.17 0.00 0.00 3.79
114 115 4.273969 ACAAAAATGAAGTTCTACGCCGAA 59.726 37.500 4.17 0.00 0.00 4.30
115 116 3.810941 ACAAAAATGAAGTTCTACGCCGA 59.189 39.130 4.17 0.00 0.00 5.54
116 117 4.141855 ACAAAAATGAAGTTCTACGCCG 57.858 40.909 4.17 0.00 0.00 6.46
117 118 7.593644 ACAAATACAAAAATGAAGTTCTACGCC 59.406 33.333 4.17 0.00 0.00 5.68
118 119 8.502161 ACAAATACAAAAATGAAGTTCTACGC 57.498 30.769 4.17 0.00 0.00 4.42
119 120 9.878599 AGACAAATACAAAAATGAAGTTCTACG 57.121 29.630 4.17 0.00 0.00 3.51
129 130 8.519492 ACGATTTCCAGACAAATACAAAAATG 57.481 30.769 0.00 0.00 0.00 2.32
136 137 8.742554 ATTTTGAACGATTTCCAGACAAATAC 57.257 30.769 0.00 0.00 0.00 1.89
243 244 5.100259 GCAGTTGTAGCTGTAACTTATCGA 58.900 41.667 12.96 0.00 38.65 3.59
263 264 3.959535 AAATTGTTGGGGTACATGCAG 57.040 42.857 0.00 0.00 0.00 4.41
340 342 5.410924 TCTTTGGTCGTCTCATGTTCATAG 58.589 41.667 0.00 0.00 0.00 2.23
395 397 2.672961 TCTGAGGCCATTACACGAAG 57.327 50.000 5.01 0.00 0.00 3.79
396 398 2.565391 TCTTCTGAGGCCATTACACGAA 59.435 45.455 5.01 5.11 0.00 3.85
397 399 2.176045 TCTTCTGAGGCCATTACACGA 58.824 47.619 5.01 0.00 0.00 4.35
398 400 2.672961 TCTTCTGAGGCCATTACACG 57.327 50.000 5.01 0.00 0.00 4.49
399 401 3.944087 ACTTCTTCTGAGGCCATTACAC 58.056 45.455 5.01 0.00 0.00 2.90
400 402 4.383118 GCTACTTCTTCTGAGGCCATTACA 60.383 45.833 5.01 0.00 0.00 2.41
401 403 4.123506 GCTACTTCTTCTGAGGCCATTAC 58.876 47.826 5.01 0.00 0.00 1.89
402 404 3.134804 GGCTACTTCTTCTGAGGCCATTA 59.865 47.826 5.01 0.00 38.16 1.90
403 405 2.092699 GGCTACTTCTTCTGAGGCCATT 60.093 50.000 5.01 0.00 38.16 3.16
404 406 1.488393 GGCTACTTCTTCTGAGGCCAT 59.512 52.381 5.01 0.00 38.16 4.40
405 407 0.905357 GGCTACTTCTTCTGAGGCCA 59.095 55.000 5.01 0.00 38.16 5.36
406 408 0.905357 TGGCTACTTCTTCTGAGGCC 59.095 55.000 0.00 0.00 38.67 5.19
407 409 2.770164 TTGGCTACTTCTTCTGAGGC 57.230 50.000 0.00 0.00 35.18 4.70
408 410 4.502962 CTCTTTGGCTACTTCTTCTGAGG 58.497 47.826 0.00 0.00 0.00 3.86
409 411 4.221703 TCCTCTTTGGCTACTTCTTCTGAG 59.778 45.833 0.00 0.00 35.26 3.35
410 412 4.160329 TCCTCTTTGGCTACTTCTTCTGA 58.840 43.478 0.00 0.00 35.26 3.27
411 413 4.020662 ACTCCTCTTTGGCTACTTCTTCTG 60.021 45.833 0.00 0.00 35.26 3.02
412 414 4.020662 CACTCCTCTTTGGCTACTTCTTCT 60.021 45.833 0.00 0.00 35.26 2.85
413 415 4.249661 CACTCCTCTTTGGCTACTTCTTC 58.750 47.826 0.00 0.00 35.26 2.87
414 416 3.558109 GCACTCCTCTTTGGCTACTTCTT 60.558 47.826 0.00 0.00 35.26 2.52
415 417 2.027653 GCACTCCTCTTTGGCTACTTCT 60.028 50.000 0.00 0.00 35.26 2.85
416 418 2.351455 GCACTCCTCTTTGGCTACTTC 58.649 52.381 0.00 0.00 35.26 3.01
417 419 1.003696 GGCACTCCTCTTTGGCTACTT 59.996 52.381 0.00 0.00 35.47 2.24
418 420 0.615850 GGCACTCCTCTTTGGCTACT 59.384 55.000 0.00 0.00 35.47 2.57
419 421 0.741221 CGGCACTCCTCTTTGGCTAC 60.741 60.000 0.00 0.00 36.17 3.58
420 422 1.192146 ACGGCACTCCTCTTTGGCTA 61.192 55.000 0.00 0.00 36.17 3.93
421 423 2.348998 CGGCACTCCTCTTTGGCT 59.651 61.111 0.00 0.00 36.17 4.75
422 424 2.032681 ACGGCACTCCTCTTTGGC 59.967 61.111 0.00 0.00 35.26 4.52
423 425 0.250295 TTGACGGCACTCCTCTTTGG 60.250 55.000 0.00 0.00 37.10 3.28
424 426 1.151668 CTTGACGGCACTCCTCTTTG 58.848 55.000 0.00 0.00 0.00 2.77
425 427 0.035458 CCTTGACGGCACTCCTCTTT 59.965 55.000 0.00 0.00 0.00 2.52
426 428 1.674057 CCTTGACGGCACTCCTCTT 59.326 57.895 0.00 0.00 0.00 2.85
427 429 3.382111 CCTTGACGGCACTCCTCT 58.618 61.111 0.00 0.00 0.00 3.69
4300 4783 1.388547 GTCACAGCCACAAACCTTCA 58.611 50.000 0.00 0.00 0.00 3.02
4459 4946 0.976641 ACAAACGAGGATGCAGAGGA 59.023 50.000 0.00 0.00 0.00 3.71
4465 4952 1.089920 ATCAGCACAAACGAGGATGC 58.910 50.000 0.00 0.00 38.39 3.91
4466 4953 3.189080 TGAAATCAGCACAAACGAGGATG 59.811 43.478 0.00 0.00 0.00 3.51
4512 4999 3.376859 CACAATAATGCGGAAACCAGCTA 59.623 43.478 0.00 0.00 0.00 3.32
4534 5021 2.297880 TCATAATGCATCCCATTGCTGC 59.702 45.455 0.00 0.00 43.77 5.25
4539 5026 5.771666 CAGTAGGTTCATAATGCATCCCATT 59.228 40.000 0.00 0.00 45.75 3.16
4551 5038 4.634012 AACCAACAGCAGTAGGTTCATA 57.366 40.909 0.00 0.00 40.12 2.15
4579 5066 6.808321 ATACTTCCATTACAACTAGCCTCA 57.192 37.500 0.00 0.00 0.00 3.86
4598 5085 9.770097 GGCATGCATGATACTACATATAATACT 57.230 33.333 30.64 0.00 0.00 2.12
4599 5086 9.546428 TGGCATGCATGATACTACATATAATAC 57.454 33.333 30.64 5.71 0.00 1.89
4601 5088 9.636789 ATTGGCATGCATGATACTACATATAAT 57.363 29.630 30.64 9.67 0.00 1.28
4602 5089 9.465199 AATTGGCATGCATGATACTACATATAA 57.535 29.630 30.64 7.95 0.00 0.98
4604 5091 7.949690 AATTGGCATGCATGATACTACATAT 57.050 32.000 30.64 6.53 0.00 1.78
4605 5092 8.860780 TTAATTGGCATGCATGATACTACATA 57.139 30.769 30.64 8.92 0.00 2.29
4606 5093 7.576287 GCTTAATTGGCATGCATGATACTACAT 60.576 37.037 30.64 9.86 0.00 2.29
4607 5094 6.294120 GCTTAATTGGCATGCATGATACTACA 60.294 38.462 30.64 14.28 0.00 2.74
4608 5095 6.088824 GCTTAATTGGCATGCATGATACTAC 58.911 40.000 30.64 10.90 0.00 2.73
4609 5096 5.769162 TGCTTAATTGGCATGCATGATACTA 59.231 36.000 30.64 15.48 34.56 1.82
4610 5097 4.585581 TGCTTAATTGGCATGCATGATACT 59.414 37.500 30.64 11.76 34.56 2.12
4611 5098 4.873817 TGCTTAATTGGCATGCATGATAC 58.126 39.130 30.64 18.45 34.56 2.24
4612 5099 5.532664 TTGCTTAATTGGCATGCATGATA 57.467 34.783 30.64 14.66 39.54 2.15
4613 5100 4.409718 TTGCTTAATTGGCATGCATGAT 57.590 36.364 30.64 12.15 39.54 2.45
4614 5101 3.889520 TTGCTTAATTGGCATGCATGA 57.110 38.095 30.64 10.12 39.54 3.07
4615 5102 5.493133 AAATTGCTTAATTGGCATGCATG 57.507 34.783 22.70 22.70 39.54 4.06
4616 5103 5.648526 TCAAAATTGCTTAATTGGCATGCAT 59.351 32.000 21.36 1.70 39.54 3.96
4617 5104 5.001874 TCAAAATTGCTTAATTGGCATGCA 58.998 33.333 21.36 0.00 39.54 3.96
4618 5105 5.548706 TCAAAATTGCTTAATTGGCATGC 57.451 34.783 9.90 9.90 39.54 4.06
4619 5106 7.279090 TCTCATCAAAATTGCTTAATTGGCATG 59.721 33.333 8.38 0.00 39.54 4.06
4620 5107 7.332557 TCTCATCAAAATTGCTTAATTGGCAT 58.667 30.769 8.38 0.00 39.54 4.40
4621 5108 6.699366 TCTCATCAAAATTGCTTAATTGGCA 58.301 32.000 4.21 4.21 37.97 4.92
4622 5109 7.279313 ACATCTCATCAAAATTGCTTAATTGGC 59.721 33.333 0.00 0.00 0.00 4.52
4623 5110 8.712285 ACATCTCATCAAAATTGCTTAATTGG 57.288 30.769 0.00 0.00 0.00 3.16
4624 5111 9.361315 TGACATCTCATCAAAATTGCTTAATTG 57.639 29.630 0.00 0.00 0.00 2.32
4628 5115 9.617523 TCTATGACATCTCATCAAAATTGCTTA 57.382 29.630 0.00 0.00 38.21 3.09
4629 5116 8.515695 TCTATGACATCTCATCAAAATTGCTT 57.484 30.769 0.00 0.00 38.21 3.91
4630 5117 8.515695 TTCTATGACATCTCATCAAAATTGCT 57.484 30.769 0.00 0.00 38.21 3.91
4631 5118 9.745880 AATTCTATGACATCTCATCAAAATTGC 57.254 29.630 0.00 0.00 38.21 3.56
4651 5138 9.965902 AAGGCTCTCTTTCTTCATTTAATTCTA 57.034 29.630 0.00 0.00 29.99 2.10
4652 5139 8.738106 CAAGGCTCTCTTTCTTCATTTAATTCT 58.262 33.333 0.00 0.00 32.41 2.40
4653 5140 8.734386 TCAAGGCTCTCTTTCTTCATTTAATTC 58.266 33.333 0.00 0.00 32.41 2.17
4654 5141 8.641498 TCAAGGCTCTCTTTCTTCATTTAATT 57.359 30.769 0.00 0.00 32.41 1.40
4655 5142 7.887495 ACTCAAGGCTCTCTTTCTTCATTTAAT 59.113 33.333 0.00 0.00 32.41 1.40
4656 5143 7.227156 ACTCAAGGCTCTCTTTCTTCATTTAA 58.773 34.615 0.00 0.00 32.41 1.52
4657 5144 6.773638 ACTCAAGGCTCTCTTTCTTCATTTA 58.226 36.000 0.00 0.00 32.41 1.40
4658 5145 5.629125 ACTCAAGGCTCTCTTTCTTCATTT 58.371 37.500 0.00 0.00 32.41 2.32
4659 5146 5.240013 ACTCAAGGCTCTCTTTCTTCATT 57.760 39.130 0.00 0.00 32.41 2.57
4660 5147 4.906747 ACTCAAGGCTCTCTTTCTTCAT 57.093 40.909 0.00 0.00 32.41 2.57
4661 5148 5.481824 TGATACTCAAGGCTCTCTTTCTTCA 59.518 40.000 0.00 0.00 32.41 3.02
4662 5149 5.971763 TGATACTCAAGGCTCTCTTTCTTC 58.028 41.667 0.00 0.00 32.41 2.87
4663 5150 6.558488 ATGATACTCAAGGCTCTCTTTCTT 57.442 37.500 0.00 0.00 32.41 2.52
4664 5151 7.508636 TGATATGATACTCAAGGCTCTCTTTCT 59.491 37.037 0.00 0.00 32.41 2.52
4665 5152 7.665690 TGATATGATACTCAAGGCTCTCTTTC 58.334 38.462 0.00 0.00 32.41 2.62
4666 5153 7.609097 TGATATGATACTCAAGGCTCTCTTT 57.391 36.000 0.00 0.00 32.41 2.52
4667 5154 7.454066 TCATGATATGATACTCAAGGCTCTCTT 59.546 37.037 0.00 0.00 33.59 2.85
4668 5155 6.952938 TCATGATATGATACTCAAGGCTCTCT 59.047 38.462 0.00 0.00 33.59 3.10
4669 5156 7.167924 TCATGATATGATACTCAAGGCTCTC 57.832 40.000 0.00 0.00 33.59 3.20
4715 5202 9.658799 GGTATCATACATGACATAAAGTAGCAT 57.341 33.333 0.00 0.00 40.03 3.79
4716 5203 8.646900 TGGTATCATACATGACATAAAGTAGCA 58.353 33.333 0.00 0.00 40.03 3.49
4717 5204 9.489084 TTGGTATCATACATGACATAAAGTAGC 57.511 33.333 0.00 0.00 40.03 3.58
4720 5207 9.851686 ATGTTGGTATCATACATGACATAAAGT 57.148 29.630 0.00 0.00 40.03 2.66
4739 5226 9.661563 CCGTAATACATGGTATTATATGTTGGT 57.338 33.333 10.90 0.00 38.41 3.67
4740 5227 9.878667 TCCGTAATACATGGTATTATATGTTGG 57.121 33.333 10.90 7.58 38.41 3.77
4750 5237 9.470399 TGATACTACATCCGTAATACATGGTAT 57.530 33.333 0.00 0.00 34.56 2.73
4751 5238 8.866970 TGATACTACATCCGTAATACATGGTA 57.133 34.615 0.00 0.00 34.56 3.25
4752 5239 7.770366 TGATACTACATCCGTAATACATGGT 57.230 36.000 0.00 0.00 34.56 3.55
4753 5240 9.731819 GTATGATACTACATCCGTAATACATGG 57.268 37.037 0.00 0.00 34.18 3.66
4756 5243 9.511272 AGTGTATGATACTACATCCGTAATACA 57.489 33.333 4.03 0.00 34.33 2.29
4759 5246 9.736414 ACTAGTGTATGATACTACATCCGTAAT 57.264 33.333 4.03 0.00 34.33 1.89
4762 5249 9.381033 GATACTAGTGTATGATACTACATCCGT 57.619 37.037 5.39 0.00 39.29 4.69
4763 5250 9.379791 TGATACTAGTGTATGATACTACATCCG 57.620 37.037 5.39 0.00 39.29 4.18


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

AutoCloner maintained by Alex Coulton.