Multiple sequence alignment - TraesCS4B01G184100

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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 TraesCS4B01G184100 chr4B 100.000 6809 0 0 1 6809 403276106 403269298 0.000000e+00 12574.0
1 TraesCS4B01G184100 chr4B 92.105 152 7 5 4389 4539 14529774 14529627 6.920000e-50 209.0
2 TraesCS4B01G184100 chr4B 95.276 127 5 1 2362 2488 403273669 403273544 4.160000e-47 200.0
3 TraesCS4B01G184100 chr4B 95.276 127 5 1 2438 2563 403273745 403273619 4.160000e-47 200.0
4 TraesCS4B01G184100 chr4B 77.043 257 38 8 684 927 277228771 277229019 1.990000e-25 128.0
5 TraesCS4B01G184100 chr4B 90.698 86 8 0 597 682 277228624 277228709 1.550000e-21 115.0
6 TraesCS4B01G184100 chr4B 89.535 86 9 0 597 682 561738854 561738939 7.220000e-20 110.0
7 TraesCS4B01G184100 chr4D 95.519 2544 48 12 1 2488 323119870 323117337 0.000000e+00 4006.0
8 TraesCS4B01G184100 chr4D 95.486 1994 34 12 2438 4390 323117463 323115485 0.000000e+00 3133.0
9 TraesCS4B01G184100 chr4D 97.970 788 14 1 4519 5306 323115476 323114691 0.000000e+00 1365.0
10 TraesCS4B01G184100 chr4D 95.409 501 7 5 5415 5914 323114660 323114175 0.000000e+00 784.0
11 TraesCS4B01G184100 chr4D 91.104 326 18 6 6029 6354 323113698 323113384 1.360000e-116 431.0
12 TraesCS4B01G184100 chr4D 90.683 322 24 6 6493 6809 323112894 323112574 2.270000e-114 424.0
13 TraesCS4B01G184100 chr4D 92.994 157 11 0 6360 6516 323113343 323113187 5.310000e-56 230.0
14 TraesCS4B01G184100 chr4D 92.208 154 9 3 4369 4522 106682396 106682246 1.490000e-51 215.0
15 TraesCS4B01G184100 chr4D 95.960 99 4 0 5324 5422 335315830 335315732 1.970000e-35 161.0
16 TraesCS4B01G184100 chr4A 94.543 2547 54 15 1 2488 149026754 149029274 0.000000e+00 3855.0
17 TraesCS4B01G184100 chr4A 95.522 1809 35 12 2438 4216 149029148 149030940 0.000000e+00 2850.0
18 TraesCS4B01G184100 chr4A 93.272 758 14 7 4519 5273 149031403 149032126 0.000000e+00 1083.0
19 TraesCS4B01G184100 chr4A 98.600 500 7 0 5415 5914 149032171 149032670 0.000000e+00 885.0
20 TraesCS4B01G184100 chr4A 92.715 453 27 5 6360 6807 149033385 149033836 0.000000e+00 649.0
21 TraesCS4B01G184100 chr4A 96.795 156 2 1 4235 4390 149031084 149031236 2.440000e-64 257.0
22 TraesCS4B01G184100 chr4A 88.325 197 11 7 1 194 149026636 149026823 6.870000e-55 226.0
23 TraesCS4B01G184100 chr4A 96.875 96 3 0 5321 5416 674937187 674937282 1.970000e-35 161.0
24 TraesCS4B01G184100 chr4A 89.474 114 6 2 6262 6373 149033244 149033353 9.210000e-29 139.0
25 TraesCS4B01G184100 chr4A 90.698 86 8 0 597 682 507759908 507759993 1.550000e-21 115.0
26 TraesCS4B01G184100 chr7D 76.000 1400 230 59 2972 4321 614678743 614677400 1.610000e-175 627.0
27 TraesCS4B01G184100 chr7D 77.331 697 82 35 1523 2209 195772226 195772856 6.540000e-90 342.0
28 TraesCS4B01G184100 chr7D 73.349 424 91 13 1030 1447 614680251 614679844 3.310000e-28 137.0
29 TraesCS4B01G184100 chr7D 92.647 68 2 1 1382 1446 614928557 614928624 2.020000e-15 95.3
30 TraesCS4B01G184100 chr7A 75.286 1400 236 60 2972 4321 710834426 710833087 9.910000e-158 568.0
31 TraesCS4B01G184100 chr7A 75.910 714 105 27 3648 4321 707122466 707123152 3.090000e-78 303.0
32 TraesCS4B01G184100 chr7A 96.154 52 2 0 5415 5466 57478738 57478789 1.220000e-12 86.1
33 TraesCS4B01G184100 chr7B 77.067 750 93 36 1523 2262 159613545 159614225 6.490000e-95 359.0
34 TraesCS4B01G184100 chr7B 76.636 749 100 35 1523 2262 159615600 159616282 1.820000e-90 344.0
35 TraesCS4B01G184100 chr7B 83.204 387 49 8 986 1362 159616461 159616841 2.350000e-89 340.0
36 TraesCS4B01G184100 chr7B 90.698 86 8 0 597 682 724623094 724623009 1.550000e-21 115.0
37 TraesCS4B01G184100 chr2D 87.273 220 19 5 713 932 453553019 453553229 6.820000e-60 243.0
38 TraesCS4B01G184100 chr2D 96.970 132 4 0 4387 4518 536091025 536091156 8.890000e-54 222.0
39 TraesCS4B01G184100 chr2D 95.283 106 4 1 5314 5418 650861494 650861389 4.220000e-37 167.0
40 TraesCS4B01G184100 chr2D 81.503 173 16 5 38 210 453552220 453552376 1.990000e-25 128.0
41 TraesCS4B01G184100 chr2D 85.965 114 8 4 818 928 453553584 453553692 1.550000e-21 115.0
42 TraesCS4B01G184100 chr2D 81.818 110 19 1 92 200 453552614 453552723 2.620000e-14 91.6
43 TraesCS4B01G184100 chr2D 85.507 69 10 0 1349 1417 455514840 455514908 9.470000e-09 73.1
44 TraesCS4B01G184100 chr1B 96.350 137 5 0 4381 4517 683747952 683748088 6.870000e-55 226.0
45 TraesCS4B01G184100 chr1B 77.734 256 38 7 684 927 187961882 187961634 9.210000e-29 139.0
46 TraesCS4B01G184100 chr1B 89.535 86 9 0 597 682 105149558 105149473 7.220000e-20 110.0
47 TraesCS4B01G184100 chr1B 89.535 86 9 0 597 682 187962029 187961944 7.220000e-20 110.0
48 TraesCS4B01G184100 chr3A 94.366 142 6 2 4389 4530 642715942 642715803 4.140000e-52 217.0
49 TraesCS4B01G184100 chr3A 100.000 91 0 0 5325 5415 685700891 685700801 1.170000e-37 169.0
50 TraesCS4B01G184100 chr3A 97.826 92 1 1 5324 5414 24718931 24718840 2.540000e-34 158.0
51 TraesCS4B01G184100 chr1D 94.326 141 7 1 4380 4519 469018548 469018688 1.490000e-51 215.0
52 TraesCS4B01G184100 chr2B 93.662 142 9 0 4376 4517 42149293 42149152 5.350000e-51 213.0
53 TraesCS4B01G184100 chr2B 91.228 114 7 2 5326 5437 470530825 470530713 1.180000e-32 152.0
54 TraesCS4B01G184100 chr2B 90.698 86 8 0 597 682 441277142 441277227 1.550000e-21 115.0
55 TraesCS4B01G184100 chr2B 94.915 59 3 0 87 145 532545840 532545898 7.270000e-15 93.5
56 TraesCS4B01G184100 chr1A 93.151 146 8 2 4380 4524 485564021 485564165 5.350000e-51 213.0
57 TraesCS4B01G184100 chr2A 92.053 151 9 3 4378 4525 41235512 41235662 6.920000e-50 209.0
58 TraesCS4B01G184100 chr2A 96.000 100 3 1 5329 5428 342544212 342544310 1.970000e-35 161.0
59 TraesCS4B01G184100 chr5D 94.393 107 2 4 5311 5415 229934112 229934216 1.970000e-35 161.0
60 TraesCS4B01G184100 chr6D 92.661 109 7 1 5309 5416 31474835 31474943 9.140000e-34 156.0
61 TraesCS4B01G184100 chr6D 86.275 102 13 1 1349 1449 17365543 17365644 7.220000e-20 110.0
62 TraesCS4B01G184100 chrUn 77.734 256 38 7 684 927 318270342 318270094 9.210000e-29 139.0
63 TraesCS4B01G184100 chrUn 77.432 257 37 8 684 927 442301366 442301614 4.280000e-27 134.0
64 TraesCS4B01G184100 chrUn 88.889 99 5 1 829 927 430504357 430504449 4.310000e-22 117.0
65 TraesCS4B01G184100 chrUn 89.535 86 9 0 597 682 318270489 318270404 7.220000e-20 110.0
66 TraesCS4B01G184100 chrUn 100.000 45 0 0 5415 5459 328631001 328631045 4.380000e-12 84.2
67 TraesCS4B01G184100 chr5A 77.432 257 37 8 684 927 132142704 132142952 4.280000e-27 134.0
68 TraesCS4B01G184100 chr6B 90.698 86 8 0 597 682 105663533 105663448 1.550000e-21 115.0
69 TraesCS4B01G184100 chr6B 80.132 151 21 9 1329 1476 30354922 30355066 3.360000e-18 104.0
70 TraesCS4B01G184100 chr6B 84.906 106 13 3 1329 1432 30465014 30465118 3.360000e-18 104.0
71 TraesCS4B01G184100 chr6B 86.022 93 12 1 1349 1440 30490880 30490972 1.560000e-16 99.0
72 TraesCS4B01G184100 chr6B 100.000 47 0 0 5415 5461 466653442 466653488 3.380000e-13 87.9
73 TraesCS4B01G184100 chr6B 100.000 30 0 0 1930 1959 30355377 30355406 1.000000e-03 56.5
74 TraesCS4B01G184100 chr5B 90.698 86 8 0 597 682 476398503 476398418 1.550000e-21 115.0
75 TraesCS4B01G184100 chr5B 90.698 86 8 0 597 682 555482995 555483080 1.550000e-21 115.0
76 TraesCS4B01G184100 chr5B 100.000 45 0 0 5415 5459 121733970 121733926 4.380000e-12 84.2
77 TraesCS4B01G184100 chr5B 100.000 45 0 0 5415 5459 509429105 509429149 4.380000e-12 84.2
78 TraesCS4B01G184100 chr6A 85.263 95 9 5 1329 1421 18080867 18080958 7.270000e-15 93.5
79 TraesCS4B01G184100 chr6A 100.000 45 0 0 5415 5459 303374182 303374226 4.380000e-12 84.2
80 TraesCS4B01G184100 chr6A 100.000 30 0 0 1930 1959 18081318 18081347 1.000000e-03 56.5


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 TraesCS4B01G184100 chr4B 403269298 403276106 6808 True 4324.666667 12574 96.850667 1 6809 3 chr4B.!!$R2 6808
1 TraesCS4B01G184100 chr4D 323112574 323119870 7296 True 1481.857143 4006 94.166429 1 6809 7 chr4D.!!$R3 6808
2 TraesCS4B01G184100 chr4A 149026636 149033836 7200 False 1243.000000 3855 93.655750 1 6807 8 chr4A.!!$F3 6806
3 TraesCS4B01G184100 chr7D 614677400 614680251 2851 True 382.000000 627 74.674500 1030 4321 2 chr7D.!!$R1 3291
4 TraesCS4B01G184100 chr7D 195772226 195772856 630 False 342.000000 342 77.331000 1523 2209 1 chr7D.!!$F1 686
5 TraesCS4B01G184100 chr7A 710833087 710834426 1339 True 568.000000 568 75.286000 2972 4321 1 chr7A.!!$R1 1349
6 TraesCS4B01G184100 chr7A 707122466 707123152 686 False 303.000000 303 75.910000 3648 4321 1 chr7A.!!$F2 673
7 TraesCS4B01G184100 chr7B 159613545 159616841 3296 False 347.666667 359 78.969000 986 2262 3 chr7B.!!$F1 1276

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
149 271 1.133699 TCGCCTCTCCGGTCCTATTTA 60.134 52.381 0.0 0.0 34.25 1.40 F
274 397 1.417517 TGGTTGCTTCTGCTCTTCTCA 59.582 47.619 0.0 0.0 40.48 3.27 F
833 978 2.601905 GGCCCTTAATCCAAGCATGAT 58.398 47.619 0.0 0.0 32.41 2.45 F
2671 3460 0.034670 AGGGCTGCTCTTTGTGATCC 60.035 55.000 0.0 0.0 0.00 3.36 F
2672 3461 0.034670 GGGCTGCTCTTTGTGATCCT 60.035 55.000 0.0 0.0 0.00 3.24 F
3393 4209 1.152546 ACCACCAACAGGAAAGGGC 60.153 57.895 0.0 0.0 0.00 5.19 F
4606 5615 0.318762 AGTCAAGTCAAGAGGCGGTC 59.681 55.000 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 2365 1.613437 CCCGATTGCAAAACTTGGTCT 59.387 47.619 1.71 0.0 0.00 3.85 R
1689 2409 2.223479 CGAATAAATGTTTGGCCCCTCG 60.223 50.000 0.00 0.0 0.00 4.63 R
2800 3609 1.620822 ACCAACTCCAAAGCACATCC 58.379 50.000 0.00 0.0 0.00 3.51 R
4493 5502 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.0 0.00 2.17 R
4494 5503 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.0 0.00 1.82 R
4868 5877 1.200716 CTCACAAATGGCACGCAGATT 59.799 47.619 0.00 0.0 0.00 2.40 R
5915 6936 0.100503 ACTGCACCAAAAACAGCGTC 59.899 50.000 0.00 0.0 34.72 5.19 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
149 271 1.133699 TCGCCTCTCCGGTCCTATTTA 60.134 52.381 0.00 0.00 34.25 1.40
274 397 1.417517 TGGTTGCTTCTGCTCTTCTCA 59.582 47.619 0.00 0.00 40.48 3.27
300 423 3.006133 TGGCGGCTGATGGTGGTA 61.006 61.111 11.43 0.00 0.00 3.25
416 539 3.134081 TCCCATCGTTCTTATCCCTGTTC 59.866 47.826 0.00 0.00 0.00 3.18
833 978 2.601905 GGCCCTTAATCCAAGCATGAT 58.398 47.619 0.00 0.00 32.41 2.45
849 994 3.118665 GCATGATTTACCAACCTGCCAAT 60.119 43.478 0.00 0.00 0.00 3.16
998 1143 4.819630 TCGTTCCTTTATCAAGTTTGCTGT 59.180 37.500 0.00 0.00 0.00 4.40
999 1144 5.049680 TCGTTCCTTTATCAAGTTTGCTGTC 60.050 40.000 0.00 0.00 0.00 3.51
1180 1599 8.649591 AGAGAATGACAGAATCAAGTATGCTAT 58.350 33.333 0.00 0.00 41.93 2.97
1504 2188 2.989166 GCATGCACTGTTTAAAGGAAGC 59.011 45.455 14.21 0.00 0.00 3.86
1647 2365 5.705902 CAATGATGCTTCAGTTCAACATGA 58.294 37.500 8.40 0.00 34.73 3.07
2447 3218 7.844493 ATACATAATTGTTTCATGCCTCCAT 57.156 32.000 0.00 0.00 37.28 3.41
2448 3219 8.938801 ATACATAATTGTTTCATGCCTCCATA 57.061 30.769 0.00 0.00 37.28 2.74
2449 3220 7.281040 ACATAATTGTTTCATGCCTCCATAG 57.719 36.000 0.00 0.00 29.55 2.23
2450 3221 6.835488 ACATAATTGTTTCATGCCTCCATAGT 59.165 34.615 0.00 0.00 29.55 2.12
2451 3222 7.342799 ACATAATTGTTTCATGCCTCCATAGTT 59.657 33.333 0.00 0.00 29.55 2.24
2452 3223 8.849168 CATAATTGTTTCATGCCTCCATAGTTA 58.151 33.333 0.00 0.00 0.00 2.24
2453 3224 6.699575 ATTGTTTCATGCCTCCATAGTTAC 57.300 37.500 0.00 0.00 0.00 2.50
2454 3225 5.172687 TGTTTCATGCCTCCATAGTTACA 57.827 39.130 0.00 0.00 0.00 2.41
2455 3226 5.565509 TGTTTCATGCCTCCATAGTTACAA 58.434 37.500 0.00 0.00 0.00 2.41
2456 3227 6.186957 TGTTTCATGCCTCCATAGTTACAAT 58.813 36.000 0.00 0.00 0.00 2.71
2457 3228 6.663093 TGTTTCATGCCTCCATAGTTACAATT 59.337 34.615 0.00 0.00 0.00 2.32
2458 3229 6.698008 TTCATGCCTCCATAGTTACAATTG 57.302 37.500 3.24 3.24 0.00 2.32
2459 3230 4.580167 TCATGCCTCCATAGTTACAATTGC 59.420 41.667 5.05 0.00 0.00 3.56
2460 3231 4.235079 TGCCTCCATAGTTACAATTGCT 57.765 40.909 5.05 0.00 0.00 3.91
2461 3232 5.366482 TGCCTCCATAGTTACAATTGCTA 57.634 39.130 5.05 0.00 0.00 3.49
2462 3233 5.123227 TGCCTCCATAGTTACAATTGCTAC 58.877 41.667 5.05 3.87 0.00 3.58
2463 3234 5.123227 GCCTCCATAGTTACAATTGCTACA 58.877 41.667 5.05 0.00 0.00 2.74
2464 3235 5.765182 GCCTCCATAGTTACAATTGCTACAT 59.235 40.000 5.05 0.00 0.00 2.29
2465 3236 6.934645 GCCTCCATAGTTACAATTGCTACATA 59.065 38.462 5.05 0.02 0.00 2.29
2466 3237 7.444183 GCCTCCATAGTTACAATTGCTACATAA 59.556 37.037 5.05 0.00 0.00 1.90
2467 3238 8.993121 CCTCCATAGTTACAATTGCTACATAAG 58.007 37.037 5.05 0.02 0.00 1.73
2468 3239 9.547753 CTCCATAGTTACAATTGCTACATAAGT 57.452 33.333 5.05 2.19 0.00 2.24
2469 3240 9.899661 TCCATAGTTACAATTGCTACATAAGTT 57.100 29.630 5.05 0.00 0.00 2.66
2473 3244 8.848474 AGTTACAATTGCTACATAAGTTCACT 57.152 30.769 5.05 0.00 0.00 3.41
2474 3245 9.284968 AGTTACAATTGCTACATAAGTTCACTT 57.715 29.630 5.05 0.00 39.85 3.16
2481 3252 7.520119 TGCTACATAAGTTCACTTATTGTCG 57.480 36.000 9.15 8.52 44.33 4.35
2482 3253 6.035650 TGCTACATAAGTTCACTTATTGTCGC 59.964 38.462 18.86 18.86 44.33 5.19
2483 3254 6.035650 GCTACATAAGTTCACTTATTGTCGCA 59.964 38.462 19.72 7.60 44.33 5.10
2484 3255 6.985188 ACATAAGTTCACTTATTGTCGCAT 57.015 33.333 9.15 0.00 44.33 4.73
2485 3256 6.775088 ACATAAGTTCACTTATTGTCGCATG 58.225 36.000 9.15 2.35 44.33 4.06
2486 3257 6.371548 ACATAAGTTCACTTATTGTCGCATGT 59.628 34.615 9.15 2.89 44.33 3.21
2487 3258 5.689383 AAGTTCACTTATTGTCGCATGTT 57.311 34.783 0.00 0.00 33.79 2.71
2488 3259 5.689383 AGTTCACTTATTGTCGCATGTTT 57.311 34.783 0.00 0.00 0.00 2.83
2489 3260 5.451908 AGTTCACTTATTGTCGCATGTTTG 58.548 37.500 0.00 0.00 0.00 2.93
2490 3261 4.418013 TCACTTATTGTCGCATGTTTGG 57.582 40.909 0.00 0.00 0.00 3.28
2491 3262 4.068599 TCACTTATTGTCGCATGTTTGGA 58.931 39.130 0.00 0.00 0.00 3.53
2492 3263 4.699735 TCACTTATTGTCGCATGTTTGGAT 59.300 37.500 0.00 0.00 0.00 3.41
2493 3264 5.877564 TCACTTATTGTCGCATGTTTGGATA 59.122 36.000 0.00 0.00 0.00 2.59
2494 3265 6.542005 TCACTTATTGTCGCATGTTTGGATAT 59.458 34.615 0.00 0.00 0.00 1.63
2495 3266 6.634035 CACTTATTGTCGCATGTTTGGATATG 59.366 38.462 0.00 0.00 0.00 1.78
2496 3267 4.572985 ATTGTCGCATGTTTGGATATGG 57.427 40.909 0.00 0.00 0.00 2.74
2497 3268 3.274095 TGTCGCATGTTTGGATATGGA 57.726 42.857 0.00 0.00 0.00 3.41
2498 3269 3.615155 TGTCGCATGTTTGGATATGGAA 58.385 40.909 0.00 0.00 0.00 3.53
2499 3270 4.206375 TGTCGCATGTTTGGATATGGAAT 58.794 39.130 0.00 0.00 0.00 3.01
2500 3271 5.372373 TGTCGCATGTTTGGATATGGAATA 58.628 37.500 0.00 0.00 0.00 1.75
2501 3272 5.238432 TGTCGCATGTTTGGATATGGAATAC 59.762 40.000 0.00 0.00 0.00 1.89
2502 3273 5.238432 GTCGCATGTTTGGATATGGAATACA 59.762 40.000 0.00 0.00 0.00 2.29
2503 3274 6.003326 TCGCATGTTTGGATATGGAATACAT 58.997 36.000 0.00 0.00 43.68 2.29
2504 3275 7.119116 GTCGCATGTTTGGATATGGAATACATA 59.881 37.037 0.00 0.00 45.60 2.29
2505 3276 7.663493 TCGCATGTTTGGATATGGAATACATAA 59.337 33.333 0.00 0.00 44.75 1.90
2506 3277 8.461222 CGCATGTTTGGATATGGAATACATAAT 58.539 33.333 0.00 0.00 44.75 1.28
2514 3285 9.567776 TGGATATGGAATACATAATTGTTTCGT 57.432 29.630 0.00 0.00 44.75 3.85
2515 3286 9.825972 GGATATGGAATACATAATTGTTTCGTG 57.174 33.333 0.00 0.00 44.75 4.35
2516 3287 9.329913 GATATGGAATACATAATTGTTTCGTGC 57.670 33.333 0.00 0.00 44.75 5.34
2517 3288 5.885881 TGGAATACATAATTGTTTCGTGCC 58.114 37.500 0.00 0.00 37.28 5.01
2518 3289 5.650266 TGGAATACATAATTGTTTCGTGCCT 59.350 36.000 0.00 0.00 37.28 4.75
2519 3290 6.183360 TGGAATACATAATTGTTTCGTGCCTC 60.183 38.462 0.00 0.00 37.28 4.70
2520 3291 5.751243 ATACATAATTGTTTCGTGCCTCC 57.249 39.130 0.00 0.00 37.28 4.30
2521 3292 3.417101 ACATAATTGTTTCGTGCCTCCA 58.583 40.909 0.00 0.00 29.55 3.86
2638 3409 6.481644 GCTCATCCTCCTGTTAATAGAACTTG 59.518 42.308 0.00 0.00 0.00 3.16
2669 3458 0.694771 TCAGGGCTGCTCTTTGTGAT 59.305 50.000 0.00 0.00 0.00 3.06
2670 3459 1.093159 CAGGGCTGCTCTTTGTGATC 58.907 55.000 0.00 0.00 0.00 2.92
2671 3460 0.034670 AGGGCTGCTCTTTGTGATCC 60.035 55.000 0.00 0.00 0.00 3.36
2672 3461 0.034670 GGGCTGCTCTTTGTGATCCT 60.035 55.000 0.00 0.00 0.00 3.24
2673 3462 1.210478 GGGCTGCTCTTTGTGATCCTA 59.790 52.381 0.00 0.00 0.00 2.94
2674 3463 2.356125 GGGCTGCTCTTTGTGATCCTAA 60.356 50.000 0.00 0.00 0.00 2.69
2800 3609 5.593502 AGGAGGATCTACTGTACTTTTACCG 59.406 44.000 0.00 0.00 33.73 4.02
3393 4209 1.152546 ACCACCAACAGGAAAGGGC 60.153 57.895 0.00 0.00 0.00 5.19
3415 4231 1.713078 AGAATTGAAAGGGCAGGAGGT 59.287 47.619 0.00 0.00 0.00 3.85
3619 4436 6.209192 ACTTGCATGTCAGGTGATTTTCAATA 59.791 34.615 0.00 0.00 33.37 1.90
3760 4578 5.990386 TGTTTTTGATGGAAATGACACCATG 59.010 36.000 0.00 0.00 45.41 3.66
3766 4584 7.479352 TGATGGAAATGACACCATGTATTTT 57.521 32.000 0.00 0.00 45.41 1.82
3767 4585 8.586879 TGATGGAAATGACACCATGTATTTTA 57.413 30.769 0.00 0.00 45.41 1.52
3768 4586 9.199645 TGATGGAAATGACACCATGTATTTTAT 57.800 29.630 0.00 0.00 45.41 1.40
3795 4613 5.854010 TCTAGGTGGACATAACTGATGAC 57.146 43.478 0.00 0.00 39.06 3.06
4100 4930 5.889853 ACCGGGGGATATTAAGTTCTTTTTC 59.110 40.000 6.32 0.00 0.00 2.29
4319 5285 6.183360 CCACGTGGATGAATGCTAAAACTAAT 60.183 38.462 31.31 0.00 37.39 1.73
4320 5286 7.011950 CCACGTGGATGAATGCTAAAACTAATA 59.988 37.037 31.31 0.00 37.39 0.98
4321 5287 8.064222 CACGTGGATGAATGCTAAAACTAATAG 58.936 37.037 7.95 0.00 0.00 1.73
4339 5305 9.750783 AACTAATAGTAAGAGAGTAGTCACCAA 57.249 33.333 0.00 0.00 0.00 3.67
4398 5369 4.341235 TCATGTTTCATAGTACTCCCTCCG 59.659 45.833 0.00 0.00 0.00 4.63
4403 5374 2.242965 TCATAGTACTCCCTCCGTTCCA 59.757 50.000 0.00 0.00 0.00 3.53
4408 5379 2.971901 ACTCCCTCCGTTCCAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
4409 5380 2.791655 ACTCCCTCCGTTCCAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
4410 5381 2.375509 ACTCCCTCCGTTCCAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
4411 5382 3.181433 ACTCCCTCCGTTCCAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
4417 5388 5.472137 CCTCCGTTCCAAAATTCTTGTCTTA 59.528 40.000 0.00 0.00 0.00 2.10
4418 5389 6.348540 CCTCCGTTCCAAAATTCTTGTCTTAG 60.349 42.308 0.00 0.00 0.00 2.18
4419 5390 6.292923 TCCGTTCCAAAATTCTTGTCTTAGA 58.707 36.000 0.00 0.00 0.00 2.10
4420 5391 6.940298 TCCGTTCCAAAATTCTTGTCTTAGAT 59.060 34.615 0.00 0.00 0.00 1.98
4421 5392 7.447238 TCCGTTCCAAAATTCTTGTCTTAGATT 59.553 33.333 0.00 0.00 0.00 2.40
4422 5393 8.082242 CCGTTCCAAAATTCTTGTCTTAGATTT 58.918 33.333 0.00 0.00 0.00 2.17
4424 5395 9.750125 GTTCCAAAATTCTTGTCTTAGATTTGT 57.250 29.630 0.00 0.00 28.79 2.83
4425 5396 9.965824 TTCCAAAATTCTTGTCTTAGATTTGTC 57.034 29.630 0.00 0.00 28.79 3.18
4435 5406 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
4437 5408 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
4438 5409 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
4445 5416 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
4446 5417 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
4447 5418 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
4448 5419 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
4450 5421 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
4451 5422 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
4452 5423 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
4453 5424 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
4455 5426 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
4456 5427 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
4460 5431 9.778993 GATGTATCAAGTCACGTTTTAGTAGTA 57.221 33.333 0.00 0.00 0.00 1.82
4461 5432 9.784680 ATGTATCAAGTCACGTTTTAGTAGTAG 57.215 33.333 0.00 0.00 0.00 2.57
4513 5522 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
4514 5523 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4515 5524 1.732117 TTTTGGGACGGAGGGAGTAA 58.268 50.000 0.00 0.00 0.00 2.24
4516 5525 1.961133 TTTGGGACGGAGGGAGTAAT 58.039 50.000 0.00 0.00 0.00 1.89
4517 5526 2.852714 TTGGGACGGAGGGAGTAATA 57.147 50.000 0.00 0.00 0.00 0.98
4606 5615 0.318762 AGTCAAGTCAAGAGGCGGTC 59.681 55.000 0.00 0.00 0.00 4.79
4787 5796 2.192664 ACATTCGGTGGTTGTATGCA 57.807 45.000 0.00 0.00 0.00 3.96
4788 5797 2.722094 ACATTCGGTGGTTGTATGCAT 58.278 42.857 3.79 3.79 0.00 3.96
4868 5877 1.488705 ATGAACGCAGGGGGAGACAA 61.489 55.000 0.00 0.00 0.00 3.18
4949 5961 4.811024 ACAATATGAGCGTGATAGTGGTTG 59.189 41.667 0.00 0.00 0.00 3.77
5083 6095 0.323725 AGCCCAGCAACGGAAATGAT 60.324 50.000 0.00 0.00 0.00 2.45
5306 6318 1.077993 ACCACTCTTAGGGTCTGAGCT 59.922 52.381 6.83 0.00 29.34 4.09
5308 6320 1.480137 CACTCTTAGGGTCTGAGCTGG 59.520 57.143 6.83 0.00 0.00 4.85
5309 6321 1.118838 CTCTTAGGGTCTGAGCTGGG 58.881 60.000 6.83 0.00 0.00 4.45
5310 6322 0.710588 TCTTAGGGTCTGAGCTGGGA 59.289 55.000 6.83 0.00 0.00 4.37
5311 6323 1.292242 TCTTAGGGTCTGAGCTGGGAT 59.708 52.381 6.83 0.00 0.00 3.85
5312 6324 1.415659 CTTAGGGTCTGAGCTGGGATG 59.584 57.143 6.83 0.00 0.00 3.51
5329 6349 3.440872 GGGATGGTTTACGTTGCATTGTA 59.559 43.478 0.00 0.00 0.00 2.41
5330 6350 4.408694 GGATGGTTTACGTTGCATTGTAC 58.591 43.478 0.00 0.00 0.00 2.90
5331 6351 4.155280 GGATGGTTTACGTTGCATTGTACT 59.845 41.667 0.00 0.00 0.00 2.73
5332 6352 4.735662 TGGTTTACGTTGCATTGTACTC 57.264 40.909 0.00 0.00 0.00 2.59
5333 6353 3.499157 TGGTTTACGTTGCATTGTACTCC 59.501 43.478 0.00 0.00 0.00 3.85
5334 6354 3.120095 GGTTTACGTTGCATTGTACTCCC 60.120 47.826 0.00 0.00 0.00 4.30
5335 6355 3.688694 TTACGTTGCATTGTACTCCCT 57.311 42.857 0.00 0.00 0.00 4.20
5336 6356 2.094762 ACGTTGCATTGTACTCCCTC 57.905 50.000 0.00 0.00 0.00 4.30
5337 6357 1.623811 ACGTTGCATTGTACTCCCTCT 59.376 47.619 0.00 0.00 0.00 3.69
5338 6358 2.002586 CGTTGCATTGTACTCCCTCTG 58.997 52.381 0.00 0.00 0.00 3.35
5339 6359 2.612972 CGTTGCATTGTACTCCCTCTGT 60.613 50.000 0.00 0.00 0.00 3.41
5340 6360 3.368013 CGTTGCATTGTACTCCCTCTGTA 60.368 47.826 0.00 0.00 0.00 2.74
5341 6361 4.575885 GTTGCATTGTACTCCCTCTGTAA 58.424 43.478 0.00 0.00 0.00 2.41
5342 6362 4.901197 TGCATTGTACTCCCTCTGTAAA 57.099 40.909 0.00 0.00 0.00 2.01
5343 6363 4.575885 TGCATTGTACTCCCTCTGTAAAC 58.424 43.478 0.00 0.00 0.00 2.01
5344 6364 4.286032 TGCATTGTACTCCCTCTGTAAACT 59.714 41.667 0.00 0.00 0.00 2.66
5345 6365 5.482526 TGCATTGTACTCCCTCTGTAAACTA 59.517 40.000 0.00 0.00 0.00 2.24
5346 6366 6.014070 TGCATTGTACTCCCTCTGTAAACTAA 60.014 38.462 0.00 0.00 0.00 2.24
5347 6367 7.048512 GCATTGTACTCCCTCTGTAAACTAAT 58.951 38.462 0.00 0.00 0.00 1.73
5348 6368 8.202137 GCATTGTACTCCCTCTGTAAACTAATA 58.798 37.037 0.00 0.00 0.00 0.98
5355 6375 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
5356 6376 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
5357 6377 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
5358 6378 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
5359 6379 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
5404 6424 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
5405 6425 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
5406 6426 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
5407 6427 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
5408 6428 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
5409 6429 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
5410 6430 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
5411 6431 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
5412 6432 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
5413 6433 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
5414 6434 9.294614 CTTATATTAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
5764 6785 0.927537 TCAACGACAAGCACGAGTTG 59.072 50.000 0.00 0.72 42.29 3.16
5814 6835 9.482627 CATACACTCCTTCTCTTCATAATAACC 57.517 37.037 0.00 0.00 0.00 2.85
5869 6890 6.659668 TCATCCTAACAGAATCTCTATACCCG 59.340 42.308 0.00 0.00 0.00 5.28
5876 6897 5.764192 ACAGAATCTCTATACCCGTGTCTAC 59.236 44.000 0.00 0.00 0.00 2.59
5914 6935 5.105997 GGAGTTCATTCAGAAACTGGATTGG 60.106 44.000 0.00 0.00 38.13 3.16
5915 6936 4.768968 AGTTCATTCAGAAACTGGATTGGG 59.231 41.667 0.00 0.00 38.13 4.12
5916 6937 4.656100 TCATTCAGAAACTGGATTGGGA 57.344 40.909 0.00 0.00 24.89 4.37
5917 6938 4.335416 TCATTCAGAAACTGGATTGGGAC 58.665 43.478 0.00 0.00 24.89 4.46
5918 6939 2.472695 TCAGAAACTGGATTGGGACG 57.527 50.000 0.00 0.00 31.51 4.79
5919 6940 0.804989 CAGAAACTGGATTGGGACGC 59.195 55.000 0.00 0.00 0.00 5.19
5920 6941 0.693049 AGAAACTGGATTGGGACGCT 59.307 50.000 0.00 0.00 0.00 5.07
5921 6942 0.804989 GAAACTGGATTGGGACGCTG 59.195 55.000 0.00 0.00 0.00 5.18
5926 6970 1.613437 CTGGATTGGGACGCTGTTTTT 59.387 47.619 0.00 0.00 0.00 1.94
6027 7410 4.778143 GTCGTGCTTCCCGCCCAT 62.778 66.667 0.00 0.00 38.05 4.00
6089 7472 1.635663 CGGCCATTTTTCTCGTCGCT 61.636 55.000 2.24 0.00 0.00 4.93
6093 7476 1.241744 CATTTTTCTCGTCGCTTGCG 58.758 50.000 8.87 8.87 0.00 4.85
6141 7525 0.104304 CAAGGCCTATCTAACCGCGT 59.896 55.000 5.16 0.00 0.00 6.01
6165 7549 1.330829 GCTAGCGGCTATGAAACAACC 59.669 52.381 10.62 0.00 38.06 3.77
6166 7550 2.627945 CTAGCGGCTATGAAACAACCA 58.372 47.619 10.62 0.00 0.00 3.67
6191 7575 3.774766 ACCAAGGCATGTATAGACACTCA 59.225 43.478 0.00 0.00 38.76 3.41
6196 7580 6.491714 AGGCATGTATAGACACTCATTTCT 57.508 37.500 0.00 0.00 38.76 2.52
6209 7593 3.201045 ACTCATTTCTTTCTAGGCCTCCC 59.799 47.826 9.68 0.00 0.00 4.30
6210 7594 2.509964 TCATTTCTTTCTAGGCCTCCCC 59.490 50.000 9.68 0.00 0.00 4.81
6219 7603 0.115349 TAGGCCTCCCCTAGATCTGC 59.885 60.000 9.68 0.00 44.08 4.26
6260 7644 0.618680 CCATCTCACCACCCTCCTCA 60.619 60.000 0.00 0.00 0.00 3.86
6275 7842 1.051812 CCTCAGGCATAGGGAATCGT 58.948 55.000 0.00 0.00 0.00 3.73
6296 7863 1.064017 GTGGTTCCATTGGGCTCCATA 60.064 52.381 14.12 0.00 38.32 2.74
6297 7864 1.858910 TGGTTCCATTGGGCTCCATAT 59.141 47.619 2.09 0.00 33.76 1.78
6298 7865 3.059853 TGGTTCCATTGGGCTCCATATA 58.940 45.455 2.09 0.00 33.76 0.86
6299 7866 3.662148 TGGTTCCATTGGGCTCCATATAT 59.338 43.478 2.09 0.00 33.76 0.86
6329 7896 0.885879 ACTGTGCCAACGAGATACGA 59.114 50.000 0.00 0.00 45.77 3.43
6448 8062 3.689872 TGGACTCATAGCTAGGGAAGT 57.310 47.619 5.42 2.39 0.00 3.01
6449 8063 3.995636 TGGACTCATAGCTAGGGAAGTT 58.004 45.455 5.42 0.00 0.00 2.66
6450 8064 5.138758 TGGACTCATAGCTAGGGAAGTTA 57.861 43.478 5.42 0.00 0.00 2.24
6480 8094 0.469917 CCACACCATCTATCCCGCTT 59.530 55.000 0.00 0.00 0.00 4.68
6486 8100 2.771943 ACCATCTATCCCGCTTTCTTCA 59.228 45.455 0.00 0.00 0.00 3.02
6508 8122 3.885724 TGAGTGGCTTCACGAATATGA 57.114 42.857 0.00 0.00 45.55 2.15
6521 8451 7.586714 TCACGAATATGAATGTGCTGATATC 57.413 36.000 0.00 0.00 32.48 1.63
6584 8514 2.210116 CATGTATGTTCACGGGGCTAC 58.790 52.381 0.00 0.00 0.00 3.58
6759 8773 3.286751 GGTGCGCTGTGGCTCAAA 61.287 61.111 9.73 0.00 34.83 2.69
6760 8774 2.253452 GTGCGCTGTGGCTCAAAG 59.747 61.111 9.73 0.00 34.83 2.77
6762 8776 3.360340 GCGCTGTGGCTCAAAGCT 61.360 61.111 13.40 0.00 42.12 3.74
6763 8777 2.866028 CGCTGTGGCTCAAAGCTC 59.134 61.111 13.40 0.00 42.12 4.09
6764 8778 2.866028 GCTGTGGCTCAAAGCTCG 59.134 61.111 9.40 0.00 41.18 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 271 2.602217 GCATCGACAGCAAAAACGAACT 60.602 45.455 6.80 0.00 38.22 3.01
300 423 5.032846 TGAGACTCCTCCTCCAACAATAAT 58.967 41.667 0.00 0.00 38.66 1.28
337 460 5.453198 GGAGAAGAGAACAGGAATGGAGATC 60.453 48.000 0.00 0.00 0.00 2.75
343 466 4.450053 GGATGGAGAAGAGAACAGGAATG 58.550 47.826 0.00 0.00 0.00 2.67
416 539 5.177142 CAGAATCATCAGAGTTGCCGATAAG 59.823 44.000 0.00 0.00 0.00 1.73
833 978 1.892474 GCAGATTGGCAGGTTGGTAAA 59.108 47.619 0.00 0.00 0.00 2.01
1180 1599 6.639563 TCACGAAATCCTTTCATAGATGACA 58.360 36.000 0.00 0.00 39.63 3.58
1504 2188 8.880750 CACAGATGCTATGATGTTATGATAAGG 58.119 37.037 0.00 0.00 0.00 2.69
1647 2365 1.613437 CCCGATTGCAAAACTTGGTCT 59.387 47.619 1.71 0.00 0.00 3.85
1689 2409 2.223479 CGAATAAATGTTTGGCCCCTCG 60.223 50.000 0.00 0.00 0.00 4.63
1861 2597 6.266131 AGGCTGAATCAACCATATTCCTAA 57.734 37.500 5.40 0.00 33.28 2.69
1862 2598 5.912149 AGGCTGAATCAACCATATTCCTA 57.088 39.130 5.40 0.00 33.28 2.94
1863 2599 4.803329 AGGCTGAATCAACCATATTCCT 57.197 40.909 5.40 0.00 33.28 3.36
1864 2600 4.023707 CGAAGGCTGAATCAACCATATTCC 60.024 45.833 5.40 0.00 33.28 3.01
1865 2601 4.576463 ACGAAGGCTGAATCAACCATATTC 59.424 41.667 5.40 0.00 34.55 1.75
1866 2602 4.526970 ACGAAGGCTGAATCAACCATATT 58.473 39.130 5.40 0.00 0.00 1.28
1867 2603 4.156455 ACGAAGGCTGAATCAACCATAT 57.844 40.909 5.40 0.00 0.00 1.78
2447 3218 9.938280 AGTGAACTTATGTAGCAATTGTAACTA 57.062 29.630 7.40 0.00 0.00 2.24
2448 3219 8.848474 AGTGAACTTATGTAGCAATTGTAACT 57.152 30.769 7.40 0.00 0.00 2.24
2455 3226 8.604035 CGACAATAAGTGAACTTATGTAGCAAT 58.396 33.333 14.79 0.00 45.55 3.56
2456 3227 7.412563 GCGACAATAAGTGAACTTATGTAGCAA 60.413 37.037 24.66 4.39 45.55 3.91
2457 3228 6.035650 GCGACAATAAGTGAACTTATGTAGCA 59.964 38.462 24.66 4.90 45.55 3.49
2458 3229 6.035650 TGCGACAATAAGTGAACTTATGTAGC 59.964 38.462 23.89 23.89 45.55 3.58
2459 3230 7.520119 TGCGACAATAAGTGAACTTATGTAG 57.480 36.000 14.79 14.47 45.55 2.74
2460 3231 7.547722 ACATGCGACAATAAGTGAACTTATGTA 59.452 33.333 14.79 4.59 45.55 2.29
2461 3232 6.371548 ACATGCGACAATAAGTGAACTTATGT 59.628 34.615 14.79 13.99 45.55 2.29
2462 3233 6.775088 ACATGCGACAATAAGTGAACTTATG 58.225 36.000 14.79 11.60 45.55 1.90
2464 3235 6.795098 AACATGCGACAATAAGTGAACTTA 57.205 33.333 5.43 5.43 42.04 2.24
2465 3236 5.689383 AACATGCGACAATAAGTGAACTT 57.311 34.783 0.71 0.71 39.85 2.66
2466 3237 5.451908 CAAACATGCGACAATAAGTGAACT 58.548 37.500 0.00 0.00 0.00 3.01
2467 3238 4.616802 CCAAACATGCGACAATAAGTGAAC 59.383 41.667 0.00 0.00 0.00 3.18
2468 3239 4.517075 TCCAAACATGCGACAATAAGTGAA 59.483 37.500 0.00 0.00 0.00 3.18
2469 3240 4.068599 TCCAAACATGCGACAATAAGTGA 58.931 39.130 0.00 0.00 0.00 3.41
2470 3241 4.418013 TCCAAACATGCGACAATAAGTG 57.582 40.909 0.00 0.00 0.00 3.16
2471 3242 6.238731 CCATATCCAAACATGCGACAATAAGT 60.239 38.462 0.00 0.00 0.00 2.24
2472 3243 6.017192 TCCATATCCAAACATGCGACAATAAG 60.017 38.462 0.00 0.00 0.00 1.73
2473 3244 5.825151 TCCATATCCAAACATGCGACAATAA 59.175 36.000 0.00 0.00 0.00 1.40
2474 3245 5.372373 TCCATATCCAAACATGCGACAATA 58.628 37.500 0.00 0.00 0.00 1.90
2475 3246 4.206375 TCCATATCCAAACATGCGACAAT 58.794 39.130 0.00 0.00 0.00 2.71
2476 3247 3.615155 TCCATATCCAAACATGCGACAA 58.385 40.909 0.00 0.00 0.00 3.18
2477 3248 3.274095 TCCATATCCAAACATGCGACA 57.726 42.857 0.00 0.00 0.00 4.35
2478 3249 4.836125 ATTCCATATCCAAACATGCGAC 57.164 40.909 0.00 0.00 0.00 5.19
2479 3250 5.372373 TGTATTCCATATCCAAACATGCGA 58.628 37.500 0.00 0.00 0.00 5.10
2480 3251 5.687770 TGTATTCCATATCCAAACATGCG 57.312 39.130 0.00 0.00 0.00 4.73
2488 3259 9.567776 ACGAAACAATTATGTATTCCATATCCA 57.432 29.630 0.00 0.00 39.40 3.41
2489 3260 9.825972 CACGAAACAATTATGTATTCCATATCC 57.174 33.333 0.00 0.00 39.40 2.59
2490 3261 9.329913 GCACGAAACAATTATGTATTCCATATC 57.670 33.333 0.00 0.00 39.40 1.63
2491 3262 8.296713 GGCACGAAACAATTATGTATTCCATAT 58.703 33.333 0.00 0.00 39.40 1.78
2492 3263 7.500892 AGGCACGAAACAATTATGTATTCCATA 59.499 33.333 0.00 0.00 39.40 2.74
2493 3264 6.321181 AGGCACGAAACAATTATGTATTCCAT 59.679 34.615 0.00 0.00 39.40 3.41
2494 3265 5.650266 AGGCACGAAACAATTATGTATTCCA 59.350 36.000 0.00 0.00 39.40 3.53
2495 3266 6.131544 AGGCACGAAACAATTATGTATTCC 57.868 37.500 0.00 0.00 39.40 3.01
2496 3267 6.183360 TGGAGGCACGAAACAATTATGTATTC 60.183 38.462 0.00 0.00 39.40 1.75
2497 3268 5.650266 TGGAGGCACGAAACAATTATGTATT 59.350 36.000 0.00 0.00 39.40 1.89
2498 3269 5.189928 TGGAGGCACGAAACAATTATGTAT 58.810 37.500 0.00 0.00 39.40 2.29
2499 3270 4.580868 TGGAGGCACGAAACAATTATGTA 58.419 39.130 0.00 0.00 39.40 2.29
2500 3271 3.417101 TGGAGGCACGAAACAATTATGT 58.583 40.909 0.00 0.00 43.14 2.29
2501 3272 4.637483 ATGGAGGCACGAAACAATTATG 57.363 40.909 0.00 0.00 0.00 1.90
2502 3273 5.437060 ACTATGGAGGCACGAAACAATTAT 58.563 37.500 0.00 0.00 0.00 1.28
2503 3274 4.839121 ACTATGGAGGCACGAAACAATTA 58.161 39.130 0.00 0.00 0.00 1.40
2504 3275 3.686016 ACTATGGAGGCACGAAACAATT 58.314 40.909 0.00 0.00 0.00 2.32
2505 3276 3.350219 ACTATGGAGGCACGAAACAAT 57.650 42.857 0.00 0.00 0.00 2.71
2506 3277 2.851263 ACTATGGAGGCACGAAACAA 57.149 45.000 0.00 0.00 0.00 2.83
2507 3278 2.851263 AACTATGGAGGCACGAAACA 57.149 45.000 0.00 0.00 0.00 2.83
2508 3279 3.592059 TGTAACTATGGAGGCACGAAAC 58.408 45.455 0.00 0.00 0.00 2.78
2509 3280 3.965379 TGTAACTATGGAGGCACGAAA 57.035 42.857 0.00 0.00 0.00 3.46
2510 3281 3.965379 TTGTAACTATGGAGGCACGAA 57.035 42.857 0.00 0.00 0.00 3.85
2511 3282 4.188462 CAATTGTAACTATGGAGGCACGA 58.812 43.478 0.00 0.00 0.00 4.35
2512 3283 3.242739 GCAATTGTAACTATGGAGGCACG 60.243 47.826 7.40 0.00 0.00 5.34
2513 3284 3.947834 AGCAATTGTAACTATGGAGGCAC 59.052 43.478 7.40 0.00 0.00 5.01
2514 3285 4.235079 AGCAATTGTAACTATGGAGGCA 57.765 40.909 7.40 0.00 0.00 4.75
2515 3286 5.123227 TGTAGCAATTGTAACTATGGAGGC 58.877 41.667 7.40 0.00 0.00 4.70
2516 3287 8.902540 TTATGTAGCAATTGTAACTATGGAGG 57.097 34.615 7.40 0.00 0.00 4.30
2517 3288 9.547753 ACTTATGTAGCAATTGTAACTATGGAG 57.452 33.333 7.40 7.41 0.00 3.86
2518 3289 9.899661 AACTTATGTAGCAATTGTAACTATGGA 57.100 29.630 7.40 0.00 0.00 3.41
2638 3409 3.894257 GCCCTGAGCAAGTTTTTCC 57.106 52.632 0.00 0.00 42.97 3.13
2763 3572 7.401493 CAGTAGATCCTCCTTATCATACCCATT 59.599 40.741 0.00 0.00 0.00 3.16
2800 3609 1.620822 ACCAACTCCAAAGCACATCC 58.379 50.000 0.00 0.00 0.00 3.51
3088 3899 9.787435 ACAAATTCCAAACTGAGTAATACTACA 57.213 29.630 0.00 0.00 0.00 2.74
3393 4209 2.012673 CTCCTGCCCTTTCAATTCTCG 58.987 52.381 0.00 0.00 0.00 4.04
3415 4231 3.263425 GGTTCTCATCCCTGGTTACTTGA 59.737 47.826 0.00 0.00 0.00 3.02
3439 4255 4.130857 GTCGTCCTGTGATATCTCTCTGA 58.869 47.826 3.98 0.00 0.00 3.27
3769 4587 7.606456 GTCATCAGTTATGTCCACCTAGAAAAA 59.394 37.037 0.00 0.00 36.89 1.94
3770 4588 7.103641 GTCATCAGTTATGTCCACCTAGAAAA 58.896 38.462 0.00 0.00 36.89 2.29
3771 4589 6.212589 TGTCATCAGTTATGTCCACCTAGAAA 59.787 38.462 0.00 0.00 36.89 2.52
4100 4930 2.575532 TGTTGCCCTTTCAGAACTCAG 58.424 47.619 0.00 0.00 0.00 3.35
4319 5285 8.740906 CAGATTTTGGTGACTACTCTCTTACTA 58.259 37.037 0.00 0.00 0.00 1.82
4320 5286 7.607250 CAGATTTTGGTGACTACTCTCTTACT 58.393 38.462 0.00 0.00 0.00 2.24
4321 5287 6.311690 GCAGATTTTGGTGACTACTCTCTTAC 59.688 42.308 0.00 0.00 0.00 2.34
4339 5305 6.136857 TGTCTCTATGGGTACTAGCAGATTT 58.863 40.000 0.00 0.00 0.00 2.17
4398 5369 9.750125 ACAAATCTAAGACAAGAATTTTGGAAC 57.250 29.630 0.00 0.00 33.04 3.62
4408 5379 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
4409 5380 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
4411 5382 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
4419 5390 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
4420 5391 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
4421 5392 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
4422 5393 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
4424 5395 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
4425 5396 6.916387 ACGTGACTTGATACATCCGTATTTAG 59.084 38.462 0.00 0.00 38.48 1.85
4427 5398 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
4428 5399 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
4430 5401 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
4431 5402 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
4432 5403 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
4433 5404 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
4435 5406 9.784680 CTACTACTAAAACGTGACTTGATACAT 57.215 33.333 0.00 0.00 0.00 2.29
4436 5407 9.002600 TCTACTACTAAAACGTGACTTGATACA 57.997 33.333 0.00 0.00 0.00 2.29
4440 5411 9.002600 TGTATCTACTACTAAAACGTGACTTGA 57.997 33.333 0.00 0.00 0.00 3.02
4443 5414 8.619546 GGATGTATCTACTACTAAAACGTGACT 58.380 37.037 0.00 0.00 0.00 3.41
4444 5415 8.400947 TGGATGTATCTACTACTAAAACGTGAC 58.599 37.037 0.00 0.00 0.00 3.67
4445 5416 8.510243 TGGATGTATCTACTACTAAAACGTGA 57.490 34.615 0.00 0.00 0.00 4.35
4479 5474 8.726988 CGTCCCAAAATTCTTGTCTTAGATTTA 58.273 33.333 0.00 0.00 0.00 1.40
4480 5475 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
4481 5476 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
4482 5477 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
4483 5478 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
4484 5479 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
4491 5500 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
4492 5501 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
4493 5502 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
4494 5503 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
4499 5508 4.474303 TTATATTACTCCCTCCGTCCCA 57.526 45.455 0.00 0.00 0.00 4.37
4502 5511 6.685657 ACGAAATTATATTACTCCCTCCGTC 58.314 40.000 0.00 0.00 0.00 4.79
4536 5545 8.028938 ACAAGAGATGTGTAATTTTGTTATGGC 58.971 33.333 0.00 0.00 41.93 4.40
4606 5615 2.611974 AACGCTGCCTTACAAAATCG 57.388 45.000 0.00 0.00 0.00 3.34
4787 5796 2.435437 GCAAATGGAAACCAGCCCATAT 59.565 45.455 0.00 0.00 41.98 1.78
4788 5797 1.830477 GCAAATGGAAACCAGCCCATA 59.170 47.619 0.00 0.00 41.98 2.74
4868 5877 1.200716 CTCACAAATGGCACGCAGATT 59.799 47.619 0.00 0.00 0.00 2.40
5083 6095 2.962827 GACAGAGCCGTCGTCGTCA 61.963 63.158 0.71 0.00 35.01 4.35
5306 6318 2.208132 ATGCAACGTAAACCATCCCA 57.792 45.000 0.00 0.00 0.00 4.37
5308 6320 3.569250 ACAATGCAACGTAAACCATCC 57.431 42.857 0.00 0.00 0.00 3.51
5309 6321 5.291293 AGTACAATGCAACGTAAACCATC 57.709 39.130 0.00 0.00 0.00 3.51
5310 6322 4.155280 GGAGTACAATGCAACGTAAACCAT 59.845 41.667 0.00 0.00 0.00 3.55
5311 6323 3.499157 GGAGTACAATGCAACGTAAACCA 59.501 43.478 0.00 0.00 0.00 3.67
5312 6324 3.120095 GGGAGTACAATGCAACGTAAACC 60.120 47.826 0.00 2.63 0.00 3.27
5329 6349 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
5330 6350 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
5331 6351 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
5332 6352 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
5333 6353 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
5378 6398 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
5379 6399 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
5380 6400 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
5381 6401 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
5382 6402 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
5383 6403 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
5384 6404 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
5385 6405 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
5386 6406 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
5387 6407 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
5388 6408 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
5390 6410 9.950496 CTAGTACTCCCTCCGTAAACTAATATA 57.050 37.037 0.00 0.00 0.00 0.86
5391 6411 8.443979 ACTAGTACTCCCTCCGTAAACTAATAT 58.556 37.037 0.00 0.00 0.00 1.28
5392 6412 7.806180 ACTAGTACTCCCTCCGTAAACTAATA 58.194 38.462 0.00 0.00 0.00 0.98
5393 6413 6.667661 ACTAGTACTCCCTCCGTAAACTAAT 58.332 40.000 0.00 0.00 0.00 1.73
5394 6414 6.067217 ACTAGTACTCCCTCCGTAAACTAA 57.933 41.667 0.00 0.00 0.00 2.24
5395 6415 5.700402 ACTAGTACTCCCTCCGTAAACTA 57.300 43.478 0.00 0.00 0.00 2.24
5396 6416 4.582973 ACTAGTACTCCCTCCGTAAACT 57.417 45.455 0.00 0.00 0.00 2.66
5397 6417 5.645624 GAAACTAGTACTCCCTCCGTAAAC 58.354 45.833 0.00 0.00 0.00 2.01
5398 6418 4.396166 CGAAACTAGTACTCCCTCCGTAAA 59.604 45.833 0.00 0.00 0.00 2.01
5399 6419 3.941483 CGAAACTAGTACTCCCTCCGTAA 59.059 47.826 0.00 0.00 0.00 3.18
5400 6420 3.535561 CGAAACTAGTACTCCCTCCGTA 58.464 50.000 0.00 0.00 0.00 4.02
5401 6421 2.363683 CGAAACTAGTACTCCCTCCGT 58.636 52.381 0.00 0.00 0.00 4.69
5402 6422 1.065251 GCGAAACTAGTACTCCCTCCG 59.935 57.143 0.00 0.43 0.00 4.63
5403 6423 2.099427 CAGCGAAACTAGTACTCCCTCC 59.901 54.545 0.00 0.00 0.00 4.30
5404 6424 2.099427 CCAGCGAAACTAGTACTCCCTC 59.901 54.545 0.00 0.00 0.00 4.30
5405 6425 2.100989 CCAGCGAAACTAGTACTCCCT 58.899 52.381 0.00 0.00 0.00 4.20
5406 6426 2.097825 TCCAGCGAAACTAGTACTCCC 58.902 52.381 0.00 0.00 0.00 4.30
5407 6427 3.015327 TCTCCAGCGAAACTAGTACTCC 58.985 50.000 0.00 0.00 0.00 3.85
5408 6428 4.904253 ATCTCCAGCGAAACTAGTACTC 57.096 45.455 0.00 0.00 0.00 2.59
5409 6429 5.662674 AAATCTCCAGCGAAACTAGTACT 57.337 39.130 0.00 0.00 0.00 2.73
5410 6430 5.446073 GCAAAATCTCCAGCGAAACTAGTAC 60.446 44.000 0.00 0.00 0.00 2.73
5411 6431 4.630069 GCAAAATCTCCAGCGAAACTAGTA 59.370 41.667 0.00 0.00 0.00 1.82
5412 6432 3.437049 GCAAAATCTCCAGCGAAACTAGT 59.563 43.478 0.00 0.00 0.00 2.57
5413 6433 3.686726 AGCAAAATCTCCAGCGAAACTAG 59.313 43.478 0.00 0.00 0.00 2.57
5414 6434 3.674997 AGCAAAATCTCCAGCGAAACTA 58.325 40.909 0.00 0.00 0.00 2.24
5591 6612 2.886523 TGATCCAAAAAGCACACCAGAG 59.113 45.455 0.00 0.00 0.00 3.35
5764 6785 3.333804 GAATATGGCAGAGCTCTAAGGC 58.666 50.000 17.75 17.76 0.00 4.35
5814 6835 2.695666 ACCTCTATCCTCCACAATGACG 59.304 50.000 0.00 0.00 0.00 4.35
5869 6890 9.668497 AACTCCATAATTTTTAGAGGTAGACAC 57.332 33.333 0.00 0.00 0.00 3.67
5914 6935 0.594796 CTGCACCAAAAACAGCGTCC 60.595 55.000 0.00 0.00 0.00 4.79
5915 6936 0.100503 ACTGCACCAAAAACAGCGTC 59.899 50.000 0.00 0.00 34.72 5.19
5916 6937 0.100503 GACTGCACCAAAAACAGCGT 59.899 50.000 0.00 0.00 34.72 5.07
5917 6938 0.594796 GGACTGCACCAAAAACAGCG 60.595 55.000 0.00 0.00 34.72 5.18
5918 6939 0.459489 TGGACTGCACCAAAAACAGC 59.541 50.000 0.00 0.00 36.96 4.40
5919 6940 2.957491 TTGGACTGCACCAAAAACAG 57.043 45.000 6.32 0.00 45.36 3.16
5926 6970 2.079170 TTGGATTTTGGACTGCACCA 57.921 45.000 0.00 0.00 38.24 4.17
6027 7410 1.078072 ACACGATGGGCGCCATTAA 60.078 52.632 30.85 11.08 45.26 1.40
6089 7472 1.827315 CTCGACAGAAAACGGCGCAA 61.827 55.000 10.83 0.00 0.00 4.85
6093 7476 1.390463 GACATCTCGACAGAAAACGGC 59.610 52.381 0.00 0.00 30.24 5.68
6165 7549 3.206150 GTCTATACATGCCTTGGTGGTG 58.794 50.000 0.00 0.00 38.35 4.17
6166 7550 2.843730 TGTCTATACATGCCTTGGTGGT 59.156 45.455 0.00 0.00 38.35 4.16
6191 7575 2.865199 AGGGGAGGCCTAGAAAGAAAT 58.135 47.619 4.42 0.00 0.00 2.17
6196 7580 2.798368 AGATCTAGGGGAGGCCTAGAAA 59.202 50.000 4.42 0.00 45.96 2.52
6219 7603 1.025041 GCATAGAAAAAGGCCGAGGG 58.975 55.000 0.00 0.00 0.00 4.30
6260 7644 0.469917 CCACACGATTCCCTATGCCT 59.530 55.000 0.00 0.00 0.00 4.75
6275 7842 1.076549 GGAGCCCAATGGAACCACA 59.923 57.895 0.00 0.00 0.00 4.17
6296 7863 3.455910 TGGCACAGTAGCTCCTCAAATAT 59.544 43.478 0.00 0.00 34.17 1.28
6297 7864 2.837591 TGGCACAGTAGCTCCTCAAATA 59.162 45.455 0.00 0.00 34.17 1.40
6298 7865 1.630369 TGGCACAGTAGCTCCTCAAAT 59.370 47.619 0.00 0.00 34.17 2.32
6299 7866 1.055849 TGGCACAGTAGCTCCTCAAA 58.944 50.000 0.00 0.00 34.17 2.69
6469 8083 4.162320 ACTCATTGAAGAAAGCGGGATAGA 59.838 41.667 0.00 0.00 0.00 1.98
6480 8094 2.807967 CGTGAAGCCACTCATTGAAGAA 59.192 45.455 0.00 0.00 41.06 2.52
6486 8100 4.769688 TCATATTCGTGAAGCCACTCATT 58.230 39.130 0.00 0.00 41.06 2.57
6508 8122 5.047847 GCAAAATGCAGATATCAGCACATT 58.952 37.500 23.22 17.85 44.26 2.71
6584 8514 7.388460 ACCTTGCAAGAAGATAAAGATGAAG 57.612 36.000 28.05 7.29 0.00 3.02
6685 8699 2.050350 CAAGCCACCTGAGCCCATG 61.050 63.158 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.