Multiple sequence alignment - TraesCS5A01G188700

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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 TraesCS5A01G188700 chr5A 100.000 6220 0 0 1 6220 390371467 390365248 0.000000e+00 11487.0
1 TraesCS5A01G188700 chr5A 83.516 1280 169 32 3998 5258 397783664 397784920 0.000000e+00 1157.0
2 TraesCS5A01G188700 chr5A 82.639 1296 169 39 3998 5255 415629026 415627749 0.000000e+00 1096.0
3 TraesCS5A01G188700 chr5A 86.179 492 52 8 2370 2849 626027076 626026589 9.240000e-143 518.0
4 TraesCS5A01G188700 chr5A 86.158 419 40 7 4342 4757 396419384 396418981 2.660000e-118 436.0
5 TraesCS5A01G188700 chr5A 92.093 215 13 3 2140 2352 177613993 177613781 3.640000e-77 300.0
6 TraesCS5A01G188700 chr5A 85.475 179 23 2 992 1167 397782586 397782764 3.830000e-42 183.0
7 TraesCS5A01G188700 chr5A 81.622 185 21 8 5640 5820 390240306 390240131 2.340000e-29 141.0
8 TraesCS5A01G188700 chr5A 80.982 163 23 6 1 156 540279554 540279393 8.470000e-24 122.0
9 TraesCS5A01G188700 chr5A 92.982 57 4 0 3285 3341 404627970 404628026 4.000000e-12 84.2
10 TraesCS5A01G188700 chr5D 93.637 3379 137 34 2514 5847 307087813 307091158 0.000000e+00 4977.0
11 TraesCS5A01G188700 chr5D 89.021 1849 121 39 1 1827 307085246 307087034 0.000000e+00 2215.0
12 TraesCS5A01G188700 chr5D 82.734 1280 179 32 3998 5258 300144089 300145345 0.000000e+00 1101.0
13 TraesCS5A01G188700 chr5D 96.091 307 12 0 2169 2475 307087511 307087817 9.310000e-138 501.0
14 TraesCS5A01G188700 chr5D 92.748 262 15 3 1853 2113 307087255 307087513 5.890000e-100 375.0
15 TraesCS5A01G188700 chr5D 91.163 215 15 3 2140 2352 169954986 169955198 7.890000e-74 289.0
16 TraesCS5A01G188700 chr5D 84.490 245 33 4 5978 6218 298141119 298141362 2.900000e-58 237.0
17 TraesCS5A01G188700 chr5D 82.273 220 32 6 6004 6219 298465855 298465639 3.830000e-42 183.0
18 TraesCS5A01G188700 chr5D 84.884 172 23 2 998 1166 300143000 300143171 2.980000e-38 171.0
19 TraesCS5A01G188700 chr5D 80.892 157 25 4 2 156 237459800 237459953 1.100000e-22 119.0
20 TraesCS5A01G188700 chr5D 95.833 72 3 0 6149 6220 307091342 307091413 3.940000e-22 117.0
21 TraesCS5A01G188700 chr5D 76.923 195 26 11 1835 2017 125783351 125783164 6.640000e-15 93.5
22 TraesCS5A01G188700 chr5B 93.813 2893 124 17 3341 6217 352309138 352311991 0.000000e+00 4300.0
23 TraesCS5A01G188700 chr5B 90.338 1863 111 20 1 1830 352305569 352307395 0.000000e+00 2379.0
24 TraesCS5A01G188700 chr5B 82.995 1282 172 34 3998 5258 343949211 343950467 0.000000e+00 1118.0
25 TraesCS5A01G188700 chr5B 90.471 850 53 12 2514 3341 352308258 352309101 0.000000e+00 1096.0
26 TraesCS5A01G188700 chr5B 94.542 568 26 3 1910 2475 352307698 352308262 0.000000e+00 872.0
27 TraesCS5A01G188700 chr5B 82.919 925 127 24 4354 5257 339980726 339979812 0.000000e+00 804.0
28 TraesCS5A01G188700 chr5B 82.360 822 115 23 4457 5258 340137498 340136687 0.000000e+00 688.0
29 TraesCS5A01G188700 chr5B 82.339 821 117 22 4457 5258 340327571 340326760 0.000000e+00 688.0
30 TraesCS5A01G188700 chr5B 86.992 492 50 7 2370 2849 622970581 622971070 5.480000e-150 542.0
31 TraesCS5A01G188700 chr5B 85.972 499 49 9 2370 2849 633310584 633310088 1.200000e-141 514.0
32 TraesCS5A01G188700 chr5B 92.271 207 12 3 2148 2352 166829610 166829406 2.190000e-74 291.0
33 TraesCS5A01G188700 chr5B 83.761 234 34 4 5990 6220 339098340 339098108 1.050000e-52 219.0
34 TraesCS5A01G188700 chr5B 84.302 172 24 2 998 1166 343948122 343948293 1.390000e-36 165.0
35 TraesCS5A01G188700 chr5B 80.556 216 25 9 5978 6191 352312664 352312864 3.880000e-32 150.0
36 TraesCS5A01G188700 chr5B 78.146 151 18 8 1877 2017 545015724 545015579 1.440000e-11 82.4
37 TraesCS5A01G188700 chr3D 81.401 1285 187 29 4012 5264 482007265 482006001 0.000000e+00 1002.0
38 TraesCS5A01G188700 chr3D 78.882 161 25 6 3 156 11591463 11591621 3.970000e-17 100.0
39 TraesCS5A01G188700 chr2A 90.605 479 38 3 2370 2848 393114202 393114673 4.090000e-176 628.0
40 TraesCS5A01G188700 chr2A 97.368 38 1 0 3245 3282 13034781 13034818 1.450000e-06 65.8
41 TraesCS5A01G188700 chr3A 87.273 495 48 7 2367 2848 38273573 38273081 9.110000e-153 551.0
42 TraesCS5A01G188700 chr3A 81.250 336 48 9 2850 3180 150062234 150062559 2.220000e-64 257.0
43 TraesCS5A01G188700 chr3A 80.745 161 22 5 3 155 1933016 1933175 3.940000e-22 117.0
44 TraesCS5A01G188700 chr3A 77.564 156 23 6 5 149 85282065 85281911 4.000000e-12 84.2
45 TraesCS5A01G188700 chr7A 85.774 478 51 9 2386 2849 648145225 648144751 2.010000e-134 490.0
46 TraesCS5A01G188700 chr7B 85.249 461 52 9 2402 2848 709246803 709247261 1.580000e-125 460.0
47 TraesCS5A01G188700 chr7B 76.074 163 31 6 3 157 93259198 93259360 1.860000e-10 78.7
48 TraesCS5A01G188700 chr6B 84.969 326 35 12 2854 3177 63994245 63993932 1.010000e-82 318.0
49 TraesCS5A01G188700 chr6B 89.937 159 16 0 2370 2528 447885648 447885806 8.170000e-49 206.0
50 TraesCS5A01G188700 chr6B 93.333 60 4 0 3285 3344 63994110 63994051 8.590000e-14 89.8
51 TraesCS5A01G188700 chrUn 84.049 326 38 8 2854 3177 75414493 75414806 1.010000e-77 302.0
52 TraesCS5A01G188700 chrUn 96.154 52 2 0 3285 3336 254789984 254790035 1.110000e-12 86.1
53 TraesCS5A01G188700 chrUn 94.545 55 3 0 3285 3339 335944787 335944733 1.110000e-12 86.1
54 TraesCS5A01G188700 chr4D 83.232 328 43 3 2852 3177 12500747 12501064 2.190000e-74 291.0
55 TraesCS5A01G188700 chr4D 89.286 112 5 4 3181 3285 83279777 83279888 3.910000e-27 134.0
56 TraesCS5A01G188700 chr3B 81.873 331 47 7 2849 3177 621524919 621524600 3.700000e-67 267.0
57 TraesCS5A01G188700 chr3B 80.435 138 18 7 26 156 11177625 11177490 5.130000e-16 97.1
58 TraesCS5A01G188700 chr3B 91.667 60 5 0 3285 3344 377709070 377709011 4.000000e-12 84.2
59 TraesCS5A01G188700 chr4A 81.682 333 45 9 2849 3177 670826472 670826152 4.780000e-66 263.0
60 TraesCS5A01G188700 chr6D 85.202 223 20 8 2370 2580 287018207 287018428 3.780000e-52 217.0
61 TraesCS5A01G188700 chr6D 84.071 113 15 3 3068 3177 799112 799224 8.530000e-19 106.0
62 TraesCS5A01G188700 chr6A 84.545 220 21 7 2373 2580 438588227 438588009 8.170000e-49 206.0
63 TraesCS5A01G188700 chr6A 94.545 55 3 0 3285 3339 601946804 601946858 1.110000e-12 86.1
64 TraesCS5A01G188700 chr1B 85.326 184 27 0 2867 3050 686830569 686830386 2.290000e-44 191.0
65 TraesCS5A01G188700 chr7D 80.000 150 15 8 1877 2017 183725381 183725524 5.130000e-16 97.1
66 TraesCS5A01G188700 chr7D 77.108 166 25 10 3 156 540615678 540615842 4.000000e-12 84.2
67 TraesCS5A01G188700 chr4B 91.667 60 5 0 3285 3344 660946087 660946028 4.000000e-12 84.2
68 TraesCS5A01G188700 chr4B 95.238 42 2 0 1877 1918 630382868 630382827 4.020000e-07 67.6
69 TraesCS5A01G188700 chr4B 95.238 42 2 0 1877 1918 630385903 630385862 4.020000e-07 67.6
70 TraesCS5A01G188700 chr2B 95.122 41 2 0 3245 3285 18927128 18927088 1.450000e-06 65.8
71 TraesCS5A01G188700 chr2B 95.122 41 2 0 3245 3285 18930646 18930606 1.450000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G188700 chr5A 390365248 390371467 6219 True 11487.0 11487 100.0000 1 6220 1 chr5A.!!$R3 6219
1 TraesCS5A01G188700 chr5A 415627749 415629026 1277 True 1096.0 1096 82.6390 3998 5255 1 chr5A.!!$R5 1257
2 TraesCS5A01G188700 chr5A 397782586 397784920 2334 False 670.0 1157 84.4955 992 5258 2 chr5A.!!$F2 4266
3 TraesCS5A01G188700 chr5D 307085246 307091413 6167 False 1637.0 4977 93.4660 1 6220 5 chr5D.!!$F5 6219
4 TraesCS5A01G188700 chr5D 300143000 300145345 2345 False 636.0 1101 83.8090 998 5258 2 chr5D.!!$F4 4260
5 TraesCS5A01G188700 chr5B 352305569 352312864 7295 False 1759.4 4300 89.9440 1 6217 5 chr5B.!!$F3 6216
6 TraesCS5A01G188700 chr5B 339979812 339980726 914 True 804.0 804 82.9190 4354 5257 1 chr5B.!!$R3 903
7 TraesCS5A01G188700 chr5B 340136687 340137498 811 True 688.0 688 82.3600 4457 5258 1 chr5B.!!$R4 801
8 TraesCS5A01G188700 chr5B 340326760 340327571 811 True 688.0 688 82.3390 4457 5258 1 chr5B.!!$R5 801
9 TraesCS5A01G188700 chr5B 343948122 343950467 2345 False 641.5 1118 83.6485 998 5258 2 chr5B.!!$F2 4260
10 TraesCS5A01G188700 chr3D 482006001 482007265 1264 True 1002.0 1002 81.4010 4012 5264 1 chr3D.!!$R1 1252

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
966 992 0.040204 ATCCAAGAAACCAGCTGGGG 59.960 55.0 35.42 24.81 42.91 4.96 F
1882 2169 0.105760 TCATTGCCCCACAACAAGGT 60.106 50.0 0.00 0.00 42.27 3.50 F
2522 2838 0.254178 ATCAGCTGTCAGGCCGAATT 59.746 50.0 14.67 0.00 0.00 2.17 F
3063 3387 0.320374 CTAGCAGACCAAACCCGACA 59.680 55.0 0.00 0.00 0.00 4.35 F
3750 4321 0.843309 ATGATTACGCCCATCCACCA 59.157 50.0 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2516 2832 0.031178 GCAGCAGGCCAATAATTCGG 59.969 55.000 5.01 0.00 36.11 4.30 R
3737 4308 0.107214 CTACAATGGTGGATGGGCGT 60.107 55.000 0.00 0.00 0.00 5.68 R
3819 4390 2.180276 TCCCCTCTCTTTGCAGTAGAC 58.820 52.381 0.00 0.00 0.00 2.59 R
4070 4641 3.920231 TCAGCAAGCTTGTCATATCCT 57.080 42.857 26.55 11.09 0.00 3.24 R
5325 5940 0.754587 TGGCTGCCATGTTTGACACA 60.755 50.000 19.30 0.00 40.71 3.72 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
60 67 5.186198 TCTCAAGATGATATATCGGCTCGA 58.814 41.667 8.19 2.43 41.13 4.04
67 74 4.770795 TGATATATCGGCTCGATCTCTCA 58.229 43.478 12.43 9.16 43.45 3.27
71 78 0.466124 TCGGCTCGATCTCTCAGAGA 59.534 55.000 6.90 6.90 43.20 3.10
88 95 1.001860 GAGATGCTCATGAGGTAGGGC 59.998 57.143 23.89 9.99 0.00 5.19
91 98 0.396556 TGCTCATGAGGTAGGGCGTA 60.397 55.000 23.89 0.00 0.00 4.42
101 110 2.897969 AGGTAGGGCGTATGTTCATAGG 59.102 50.000 7.79 7.79 0.00 2.57
128 137 5.969435 TGAGTGTATGCGCGTATATATAAGC 59.031 40.000 19.79 17.64 34.97 3.09
129 138 6.132791 AGTGTATGCGCGTATATATAAGCT 57.867 37.500 19.79 7.90 35.94 3.74
132 141 5.975344 TGTATGCGCGTATATATAAGCTTCC 59.025 40.000 19.79 13.92 35.94 3.46
142 151 4.785511 ATATAAGCTTCCGCGTCTGTAT 57.214 40.909 0.00 0.00 42.32 2.29
177 187 3.709653 ACCAGGAGAGCATACCGAAAATA 59.290 43.478 0.00 0.00 0.00 1.40
266 278 1.332904 CGGTGAGTTGACAAAAGCGTC 60.333 52.381 9.13 0.00 36.40 5.19
278 290 6.276847 TGACAAAAGCGTCCATTTTACAATT 58.723 32.000 0.00 0.00 34.88 2.32
281 293 8.067780 ACAAAAGCGTCCATTTTACAATTAAC 57.932 30.769 0.00 0.00 0.00 2.01
282 294 7.707035 ACAAAAGCGTCCATTTTACAATTAACA 59.293 29.630 0.00 0.00 0.00 2.41
283 295 8.707839 CAAAAGCGTCCATTTTACAATTAACAT 58.292 29.630 0.00 0.00 0.00 2.71
348 362 2.418368 AGTGACAGACTTGGTTGCAA 57.582 45.000 0.00 0.00 0.00 4.08
371 385 6.476243 AAAAATACGACGTGCTTACAGAAT 57.524 33.333 11.56 0.00 0.00 2.40
374 388 1.278238 CGACGTGCTTACAGAATCCC 58.722 55.000 0.00 0.00 0.00 3.85
381 395 4.448210 GTGCTTACAGAATCCCGGATTTA 58.552 43.478 14.06 0.31 31.89 1.40
386 400 7.139392 GCTTACAGAATCCCGGATTTAAATTC 58.861 38.462 14.06 0.00 31.89 2.17
389 403 5.523369 CAGAATCCCGGATTTAAATTCTGC 58.477 41.667 14.06 0.00 43.50 4.26
406 420 2.734723 CGACACGGGCACACAGAG 60.735 66.667 0.00 0.00 0.00 3.35
432 447 0.804364 CATGTGCCAGCGCTCTAAAA 59.196 50.000 7.13 0.00 35.36 1.52
435 450 1.885887 TGTGCCAGCGCTCTAAAATTT 59.114 42.857 7.13 0.00 35.36 1.82
438 453 4.098416 GTGCCAGCGCTCTAAAATTTAAG 58.902 43.478 7.13 0.00 35.36 1.85
471 486 7.914537 AAAGCTCTAAATTTTGACGAGTTTG 57.085 32.000 0.00 0.00 0.00 2.93
591 606 5.401531 GGGGATTTGTACCCTTTCTTTTC 57.598 43.478 0.00 0.00 46.03 2.29
597 612 2.071540 GTACCCTTTCTTTTCCCGTCG 58.928 52.381 0.00 0.00 0.00 5.12
628 643 3.435186 GCCGCCTGGTTGCTTCTC 61.435 66.667 0.00 0.00 37.67 2.87
629 644 2.747855 CCGCCTGGTTGCTTCTCC 60.748 66.667 0.00 0.00 0.00 3.71
691 706 1.055040 GATCTCATCTCCCCACCCAG 58.945 60.000 0.00 0.00 0.00 4.45
705 720 4.232061 CCAGCCCAACCCAACCCA 62.232 66.667 0.00 0.00 0.00 4.51
706 721 2.123077 CAGCCCAACCCAACCCAA 60.123 61.111 0.00 0.00 0.00 4.12
707 722 2.123033 AGCCCAACCCAACCCAAC 60.123 61.111 0.00 0.00 0.00 3.77
850 876 1.569072 ACCCATACCAAATCTCCACCC 59.431 52.381 0.00 0.00 0.00 4.61
966 992 0.040204 ATCCAAGAAACCAGCTGGGG 59.960 55.000 35.42 24.81 42.91 4.96
968 994 2.118294 AAGAAACCAGCTGGGGGC 59.882 61.111 35.42 22.72 42.91 5.80
1035 1061 2.808244 GAGCTCTTCACGAGATCCTTG 58.192 52.381 6.43 0.00 46.84 3.61
1290 1334 6.604735 TTCTTGCTTCAGTACAGTCTTTTC 57.395 37.500 0.00 0.00 0.00 2.29
1332 1396 3.837213 AACTGATGTAACTGTGCATGC 57.163 42.857 11.82 11.82 29.11 4.06
1333 1397 2.086869 ACTGATGTAACTGTGCATGCC 58.913 47.619 16.68 7.25 29.11 4.40
1334 1398 1.402968 CTGATGTAACTGTGCATGCCC 59.597 52.381 16.68 3.59 29.11 5.36
1335 1399 1.004628 TGATGTAACTGTGCATGCCCT 59.995 47.619 16.68 0.00 29.11 5.19
1336 1400 1.402968 GATGTAACTGTGCATGCCCTG 59.597 52.381 16.68 10.61 29.11 4.45
1337 1401 0.399833 TGTAACTGTGCATGCCCTGA 59.600 50.000 16.68 0.00 0.00 3.86
1338 1402 0.804989 GTAACTGTGCATGCCCTGAC 59.195 55.000 16.68 7.12 0.00 3.51
1339 1403 0.399833 TAACTGTGCATGCCCTGACA 59.600 50.000 16.68 11.79 0.00 3.58
1340 1404 0.251474 AACTGTGCATGCCCTGACAT 60.251 50.000 16.68 0.00 0.00 3.06
1348 1412 3.880047 CATGCCCTGACATGTCAATTT 57.120 42.857 27.63 9.76 42.05 1.82
1349 1413 3.517602 CATGCCCTGACATGTCAATTTG 58.482 45.455 27.63 16.42 42.05 2.32
1350 1414 2.596346 TGCCCTGACATGTCAATTTGT 58.404 42.857 27.63 0.00 39.39 2.83
1351 1415 2.296752 TGCCCTGACATGTCAATTTGTG 59.703 45.455 27.63 15.39 39.39 3.33
1352 1416 2.297033 GCCCTGACATGTCAATTTGTGT 59.703 45.455 27.63 0.00 39.39 3.72
1353 1417 3.505680 GCCCTGACATGTCAATTTGTGTA 59.494 43.478 27.63 3.40 39.39 2.90
1382 1466 3.570125 TGAGCCTCTGTAACTATGGATCG 59.430 47.826 0.00 0.00 36.15 3.69
1394 1478 7.984617 TGTAACTATGGATCGAATTGTCAATCA 59.015 33.333 0.00 0.00 0.00 2.57
1395 1479 7.864108 AACTATGGATCGAATTGTCAATCAA 57.136 32.000 0.00 0.00 40.53 2.57
1396 1480 7.251704 ACTATGGATCGAATTGTCAATCAAC 57.748 36.000 0.00 0.00 38.97 3.18
1397 1481 6.823182 ACTATGGATCGAATTGTCAATCAACA 59.177 34.615 0.00 0.00 38.97 3.33
1398 1482 5.550232 TGGATCGAATTGTCAATCAACAG 57.450 39.130 0.00 0.00 38.97 3.16
1399 1483 5.244755 TGGATCGAATTGTCAATCAACAGA 58.755 37.500 0.00 0.00 38.97 3.41
1400 1484 5.882000 TGGATCGAATTGTCAATCAACAGAT 59.118 36.000 0.00 0.66 38.97 2.90
1523 1614 4.636648 TCGTGACTGCTTTTTGGAAAGTTA 59.363 37.500 1.43 0.00 43.36 2.24
1529 1620 4.927422 TGCTTTTTGGAAAGTTACCTTCG 58.073 39.130 1.43 0.00 43.36 3.79
1549 1640 8.974408 ACCTTCGCTTTAACAAAATAATCAAAC 58.026 29.630 0.00 0.00 0.00 2.93
1593 1684 5.588240 CCACTTGTTTTCCCTCTTGTTTAC 58.412 41.667 0.00 0.00 0.00 2.01
1610 1701 4.140963 GTTTACGGCGGTACTTTTAAACG 58.859 43.478 13.24 0.00 0.00 3.60
1650 1741 6.042781 AGTGTGTGATTCTTTGGGTTCTACTA 59.957 38.462 0.00 0.00 0.00 1.82
1709 1800 6.200854 TGTTGTGCTATATTGCTAGTGAATCG 59.799 38.462 10.48 0.00 0.00 3.34
1710 1801 6.084326 TGTGCTATATTGCTAGTGAATCGA 57.916 37.500 10.48 0.00 0.00 3.59
1719 1810 3.447229 TGCTAGTGAATCGAATGTGAGGA 59.553 43.478 0.00 0.00 0.00 3.71
1739 1830 3.391296 GGAGGGACATGCTACTATCCAAA 59.609 47.826 0.00 0.00 32.45 3.28
1776 1867 7.603180 ATCATAGAACATGTACTGGAAGCTA 57.397 36.000 0.00 0.00 37.60 3.32
1778 1869 8.023021 TCATAGAACATGTACTGGAAGCTAAT 57.977 34.615 0.00 0.00 37.60 1.73
1779 1870 9.143155 TCATAGAACATGTACTGGAAGCTAATA 57.857 33.333 0.00 0.00 37.60 0.98
1780 1871 9.416794 CATAGAACATGTACTGGAAGCTAATAG 57.583 37.037 0.00 0.00 37.60 1.73
1781 1872 6.821388 AGAACATGTACTGGAAGCTAATAGG 58.179 40.000 0.00 0.00 37.60 2.57
1782 1873 5.552870 ACATGTACTGGAAGCTAATAGGG 57.447 43.478 0.00 0.00 37.60 3.53
1783 1874 5.216622 ACATGTACTGGAAGCTAATAGGGA 58.783 41.667 0.00 0.00 37.60 4.20
1784 1875 5.846714 ACATGTACTGGAAGCTAATAGGGAT 59.153 40.000 0.00 0.00 37.60 3.85
1785 1876 6.330250 ACATGTACTGGAAGCTAATAGGGATT 59.670 38.462 0.00 0.00 37.60 3.01
1786 1877 7.512746 ACATGTACTGGAAGCTAATAGGGATTA 59.487 37.037 0.00 0.00 37.60 1.75
1787 1878 7.924358 TGTACTGGAAGCTAATAGGGATTAA 57.076 36.000 0.00 0.00 37.60 1.40
1788 1879 7.732996 TGTACTGGAAGCTAATAGGGATTAAC 58.267 38.462 0.00 0.00 37.60 2.01
1789 1880 6.824958 ACTGGAAGCTAATAGGGATTAACA 57.175 37.500 0.00 0.00 37.60 2.41
1793 1884 7.004086 TGGAAGCTAATAGGGATTAACATTGG 58.996 38.462 0.00 0.00 0.00 3.16
1794 1885 6.434340 GGAAGCTAATAGGGATTAACATTGGG 59.566 42.308 0.00 0.00 0.00 4.12
1830 1921 9.249457 CCTCTCTTACTTTTTGGAATTTTCAAC 57.751 33.333 0.00 0.00 0.00 3.18
1832 1923 8.754080 TCTCTTACTTTTTGGAATTTTCAACCA 58.246 29.630 0.00 0.00 0.00 3.67
1834 1925 7.984617 TCTTACTTTTTGGAATTTTCAACCAGG 59.015 33.333 0.00 0.00 35.08 4.45
1835 1926 5.436175 ACTTTTTGGAATTTTCAACCAGGG 58.564 37.500 0.00 0.00 35.08 4.45
1836 1927 4.429854 TTTTGGAATTTTCAACCAGGGG 57.570 40.909 0.00 0.00 35.08 4.79
1837 1928 2.022718 TGGAATTTTCAACCAGGGGG 57.977 50.000 0.00 0.00 41.29 5.40
1872 2159 1.762370 CCCACCTTAATTCATTGCCCC 59.238 52.381 0.00 0.00 0.00 5.80
1882 2169 0.105760 TCATTGCCCCACAACAAGGT 60.106 50.000 0.00 0.00 42.27 3.50
1923 2237 1.603739 GGTCCAAGTGAACAGGGGC 60.604 63.158 0.00 0.00 0.00 5.80
1931 2245 3.256960 GAACAGGGGCCACAGGGA 61.257 66.667 8.31 0.00 35.59 4.20
1999 2315 3.797559 AGGGAGAACAAAGAGGGAAAG 57.202 47.619 0.00 0.00 0.00 2.62
2049 2365 2.598565 CTAGGGATCGACAGGGAATCA 58.401 52.381 0.00 0.00 0.00 2.57
2055 2371 3.600388 GATCGACAGGGAATCAAAGTGT 58.400 45.455 0.00 0.00 0.00 3.55
2058 2374 5.160607 TCGACAGGGAATCAAAGTGTATT 57.839 39.130 0.00 0.00 0.00 1.89
2177 2493 4.122046 TGGCTGAATACAGTTGATCGATG 58.878 43.478 0.54 0.00 45.04 3.84
2295 2611 4.771577 ACAGAGATAGGCATAGATCAGGTG 59.228 45.833 0.00 0.00 0.00 4.00
2352 2668 4.883021 TCTTCTCCCACTAGTACCTGAT 57.117 45.455 0.00 0.00 0.00 2.90
2357 2673 4.477581 TCTCCCACTAGTACCTGATACACT 59.522 45.833 0.00 0.00 36.09 3.55
2360 2676 3.068307 CCACTAGTACCTGATACACTGCC 59.932 52.174 0.00 0.00 36.09 4.85
2449 2765 2.361119 CCTTCCCGATATGAGAACGTGA 59.639 50.000 0.00 0.00 0.00 4.35
2486 2802 3.818295 TGGTAGGCCCAGTTAATTTGT 57.182 42.857 0.00 0.00 38.72 2.83
2487 2803 3.692690 TGGTAGGCCCAGTTAATTTGTC 58.307 45.455 0.00 0.00 38.72 3.18
2488 2804 3.332485 TGGTAGGCCCAGTTAATTTGTCT 59.668 43.478 0.00 0.00 38.72 3.41
2489 2805 3.694566 GGTAGGCCCAGTTAATTTGTCTG 59.305 47.826 0.00 0.00 0.00 3.51
2490 2806 3.806949 AGGCCCAGTTAATTTGTCTGA 57.193 42.857 0.00 0.00 0.00 3.27
2491 2807 3.421844 AGGCCCAGTTAATTTGTCTGAC 58.578 45.455 0.00 0.00 0.00 3.51
2492 2808 3.153919 GGCCCAGTTAATTTGTCTGACA 58.846 45.455 6.36 6.36 0.00 3.58
2493 2809 3.572255 GGCCCAGTTAATTTGTCTGACAA 59.428 43.478 18.69 18.69 36.11 3.18
2494 2810 4.321230 GGCCCAGTTAATTTGTCTGACAAG 60.321 45.833 21.13 9.45 39.53 3.16
2495 2811 4.798574 CCCAGTTAATTTGTCTGACAAGC 58.201 43.478 21.13 11.47 39.53 4.01
2496 2812 4.520492 CCCAGTTAATTTGTCTGACAAGCT 59.480 41.667 21.13 15.09 39.53 3.74
2497 2813 5.455392 CCAGTTAATTTGTCTGACAAGCTG 58.545 41.667 21.13 20.87 39.53 4.24
2498 2814 5.455392 CAGTTAATTTGTCTGACAAGCTGG 58.545 41.667 21.13 7.12 39.53 4.85
2499 2815 5.009010 CAGTTAATTTGTCTGACAAGCTGGT 59.991 40.000 21.13 0.00 39.53 4.00
2500 2816 5.594317 AGTTAATTTGTCTGACAAGCTGGTT 59.406 36.000 21.13 14.48 39.53 3.67
2501 2817 6.096846 AGTTAATTTGTCTGACAAGCTGGTTT 59.903 34.615 21.13 12.31 39.53 3.27
2502 2818 5.343307 AATTTGTCTGACAAGCTGGTTTT 57.657 34.783 21.13 7.13 39.53 2.43
2503 2819 6.463995 AATTTGTCTGACAAGCTGGTTTTA 57.536 33.333 21.13 5.87 39.53 1.52
2504 2820 6.655078 ATTTGTCTGACAAGCTGGTTTTAT 57.345 33.333 21.13 7.81 39.53 1.40
2505 2821 5.689383 TTGTCTGACAAGCTGGTTTTATC 57.311 39.130 18.69 0.00 32.34 1.75
2506 2822 4.713553 TGTCTGACAAGCTGGTTTTATCA 58.286 39.130 8.27 0.00 0.00 2.15
2507 2823 4.756642 TGTCTGACAAGCTGGTTTTATCAG 59.243 41.667 8.27 14.52 34.68 2.90
2516 2832 2.421424 CTGGTTTTATCAGCTGTCAGGC 59.579 50.000 14.67 1.25 0.00 4.85
2517 2833 1.745653 GGTTTTATCAGCTGTCAGGCC 59.254 52.381 14.67 0.00 0.00 5.19
2518 2834 1.398390 GTTTTATCAGCTGTCAGGCCG 59.602 52.381 14.67 0.00 0.00 6.13
2522 2838 0.254178 ATCAGCTGTCAGGCCGAATT 59.746 50.000 14.67 0.00 0.00 2.17
2579 2895 2.642807 CCTGTTCCCTCCCTACTTTTCA 59.357 50.000 0.00 0.00 0.00 2.69
2614 2930 1.664321 GCCTTCCAGATTGGCTGCAG 61.664 60.000 10.11 10.11 43.50 4.41
2642 2958 3.565482 TCAGAACATCAAGGCAACACTTC 59.435 43.478 0.00 0.00 41.41 3.01
2679 2995 6.711277 TGTAGCCTAGGATTGCATATTTAGG 58.289 40.000 14.75 9.37 0.00 2.69
2713 3029 4.422073 TGCATGTTGCTATTAGCCTAGT 57.578 40.909 13.01 0.00 45.31 2.57
2715 3031 5.541845 TGCATGTTGCTATTAGCCTAGTAG 58.458 41.667 13.01 0.00 45.31 2.57
2779 3095 5.816919 ACCGATAAATTCAGTTAAATGGCG 58.183 37.500 2.65 0.00 0.00 5.69
2786 3102 2.980568 TCAGTTAAATGGCGGATTCGT 58.019 42.857 2.65 0.00 38.89 3.85
2793 3109 1.779569 ATGGCGGATTCGTCGATTAC 58.220 50.000 0.00 0.00 45.11 1.89
2797 3113 1.671469 CGGATTCGTCGATTACTCCG 58.329 55.000 16.43 16.43 39.58 4.63
2804 3120 3.461061 TCGTCGATTACTCCGTACTCAT 58.539 45.455 0.00 0.00 0.00 2.90
2845 3161 6.235231 ACCAGTTACCGATATCTTGAACAT 57.765 37.500 0.34 0.00 0.00 2.71
2903 3219 1.284715 CACTACACTGCACCGTCGA 59.715 57.895 0.00 0.00 0.00 4.20
2905 3221 1.284715 CTACACTGCACCGTCGACA 59.715 57.895 17.16 0.00 0.00 4.35
2908 3224 1.880796 CACTGCACCGTCGACACAA 60.881 57.895 17.16 0.00 0.00 3.33
2944 3267 0.745845 ATCCGAGACTGCACAATGCC 60.746 55.000 0.00 0.00 44.23 4.40
2993 3317 1.002134 AAAGGGTCATGTGAGGCCG 60.002 57.895 0.00 0.00 0.00 6.13
2994 3318 2.484287 AAAGGGTCATGTGAGGCCGG 62.484 60.000 0.00 0.00 0.00 6.13
3060 3384 1.745489 GCCTAGCAGACCAAACCCG 60.745 63.158 0.00 0.00 0.00 5.28
3062 3386 0.391263 CCTAGCAGACCAAACCCGAC 60.391 60.000 0.00 0.00 0.00 4.79
3063 3387 0.320374 CTAGCAGACCAAACCCGACA 59.680 55.000 0.00 0.00 0.00 4.35
3065 3389 1.227853 GCAGACCAAACCCGACACT 60.228 57.895 0.00 0.00 0.00 3.55
3072 3396 0.888736 CAAACCCGACACTGCCATGA 60.889 55.000 0.00 0.00 0.00 3.07
3105 3429 3.430862 GCAATCGAAGGCACCGCA 61.431 61.111 6.78 0.00 0.00 5.69
3182 3615 4.521062 GCGAGGCCGAGATGCAGT 62.521 66.667 0.00 0.00 38.22 4.40
3240 3674 1.598130 GAGTCGCAACTGCAGGGTT 60.598 57.895 19.93 1.43 42.21 4.11
3248 3689 2.810400 GCAACTGCAGGGTTGAAGAGTA 60.810 50.000 19.93 0.00 46.55 2.59
3360 3838 4.608774 ACCGTCGACCCCAGACCA 62.609 66.667 10.58 0.00 35.33 4.02
3367 3845 2.532715 ACCCCAGACCAGCCACAT 60.533 61.111 0.00 0.00 0.00 3.21
3381 3859 4.344865 ACATCACCACCACCCGCC 62.345 66.667 0.00 0.00 0.00 6.13
3435 3913 6.018343 CCTCTCTTATTTAACTTAGCTGCAGC 60.018 42.308 31.53 31.53 42.49 5.25
3585 4065 1.133025 CCAGTTTATGGCTTCCTTGCG 59.867 52.381 0.00 0.00 43.83 4.85
3721 4292 7.996066 ACATGGTTGCAGTATGTATTATTACCA 59.004 33.333 9.84 5.79 39.31 3.25
3722 4293 8.845227 CATGGTTGCAGTATGTATTATTACCAA 58.155 33.333 2.46 0.00 39.31 3.67
3723 4294 8.988546 TGGTTGCAGTATGTATTATTACCAAT 57.011 30.769 0.00 0.00 39.31 3.16
3749 4320 2.851263 TATGATTACGCCCATCCACC 57.149 50.000 0.00 0.00 0.00 4.61
3750 4321 0.843309 ATGATTACGCCCATCCACCA 59.157 50.000 0.00 0.00 0.00 4.17
3763 4334 3.565482 CCATCCACCATTGTAGTACATGC 59.435 47.826 3.28 0.00 0.00 4.06
3764 4335 3.990959 TCCACCATTGTAGTACATGCA 57.009 42.857 3.28 0.00 0.00 3.96
3862 4433 4.327680 ACTGAAATAAGCCAGAACAGACC 58.672 43.478 0.00 0.00 34.65 3.85
3869 4440 3.018423 AGCCAGAACAGACCAGTTTTT 57.982 42.857 0.00 0.00 0.00 1.94
3913 4484 7.174772 TGCTGTCATGTCACATTAAAACTGTAT 59.825 33.333 0.00 0.00 0.00 2.29
4274 4845 5.124457 GCCTGATCAAAAGATGAAGTAAGCA 59.876 40.000 0.00 0.00 42.54 3.91
4483 5062 1.423721 CGATGTCTCACCATGTGGCG 61.424 60.000 0.00 0.00 39.32 5.69
4838 5429 2.032681 GGTGTCTGGTGCCACTCC 59.967 66.667 0.00 0.00 0.00 3.85
5038 5643 2.538222 TGGTGGGTACTGATTTACCGA 58.462 47.619 0.00 0.00 42.39 4.69
5099 5704 1.209275 CGATGTTCGATCCGGTCAGC 61.209 60.000 0.00 0.00 43.74 4.26
5144 5751 7.849026 TCTCGTTGTTAAATCTGTTTTCTTTCG 59.151 33.333 0.00 0.00 0.00 3.46
5147 5754 7.096640 CGTTGTTAAATCTGTTTTCTTTCGCAT 60.097 33.333 0.00 0.00 0.00 4.73
5198 5813 6.313519 TGCTATTAAACAGATTCTGAGGGT 57.686 37.500 20.33 4.85 35.18 4.34
5238 5853 5.435686 TTAATCTGTAGGTTGCTGGATGT 57.564 39.130 0.00 0.00 0.00 3.06
5281 5896 4.358214 TGTGTTCCCTACAGGATGATACA 58.642 43.478 0.00 0.00 46.94 2.29
5295 5910 4.383552 GGATGATACATCCATCACCCTAGC 60.384 50.000 21.28 0.00 41.52 3.42
5325 5940 5.677319 TTCACTAGACCGGATCAATCTTT 57.323 39.130 9.46 0.00 0.00 2.52
5507 6122 2.595095 TGACGTCGTTGTGTAATATGCG 59.405 45.455 11.62 0.00 0.00 4.73
5766 6387 7.913423 ACACAGACATCTTCATTTTATCATCG 58.087 34.615 0.00 0.00 0.00 3.84
5771 6392 9.265901 AGACATCTTCATTTTATCATCGTAAGG 57.734 33.333 0.00 0.00 38.47 2.69
5826 6447 9.717942 TCCAAACCCACAATTTATGAAATTTAG 57.282 29.630 0.00 0.00 38.97 1.85
5845 6467 9.484806 AAATTTAGATTTGAATCTCCATGACCT 57.515 29.630 9.38 0.00 44.30 3.85
5847 6469 8.884124 TTTAGATTTGAATCTCCATGACCTTT 57.116 30.769 9.38 0.00 44.30 3.11
5861 6483 7.410174 TCCATGACCTTTGAAATTGTACCTAT 58.590 34.615 0.00 0.00 0.00 2.57
5894 6516 9.589461 TTAGTTCTAAAATTACCCATCCAAACA 57.411 29.630 0.00 0.00 0.00 2.83
5914 6536 7.489113 CCAAACATCTTATTTACATCTTGGCAC 59.511 37.037 0.00 0.00 0.00 5.01
5915 6537 6.363577 ACATCTTATTTACATCTTGGCACG 57.636 37.500 0.00 0.00 0.00 5.34
5955 6577 1.872952 TGTTTTGCATGACTGGTCTCG 59.127 47.619 0.00 0.00 0.00 4.04
6010 6632 0.315251 GGACTGAAAACTGCCTTGCC 59.685 55.000 0.00 0.00 0.00 4.52
6038 6660 3.193263 CATATGCTATGGCCGACAGATC 58.807 50.000 0.00 0.00 37.74 2.75
6065 6707 0.174845 TGGTTTCATCCCTCGTAGCG 59.825 55.000 0.00 0.00 0.00 4.26
6066 6708 0.529992 GGTTTCATCCCTCGTAGCGG 60.530 60.000 0.00 0.00 0.00 5.52
6086 6728 3.119849 CGGAAAGCTGGAATGTTAACTGG 60.120 47.826 7.22 0.00 0.00 4.00
6117 6759 3.057315 GCTCTTGCATGTGGTGTGTTTAT 60.057 43.478 0.00 0.00 39.41 1.40
6124 6766 4.437390 GCATGTGGTGTGTTTATCTAGTGC 60.437 45.833 0.00 0.00 0.00 4.40
6129 6771 4.994852 TGGTGTGTTTATCTAGTGCAAGTC 59.005 41.667 0.00 0.00 0.00 3.01
6130 6772 4.994852 GGTGTGTTTATCTAGTGCAAGTCA 59.005 41.667 0.00 0.00 0.00 3.41
6132 6774 6.363473 GTGTGTTTATCTAGTGCAAGTCAAC 58.637 40.000 0.00 0.00 0.00 3.18
6135 6777 1.726853 ATCTAGTGCAAGTCAACGGC 58.273 50.000 0.00 0.00 0.00 5.68
6136 6778 0.679505 TCTAGTGCAAGTCAACGGCT 59.320 50.000 0.00 0.00 0.00 5.52
6137 6779 1.071605 CTAGTGCAAGTCAACGGCTC 58.928 55.000 0.00 0.00 0.00 4.70
6138 6780 0.391228 TAGTGCAAGTCAACGGCTCA 59.609 50.000 0.00 0.00 0.00 4.26
6139 6781 1.160329 AGTGCAAGTCAACGGCTCAC 61.160 55.000 0.00 0.00 0.00 3.51
6171 6816 8.306313 AGTTGAGGTTTTAGGAAAAGACAAAT 57.694 30.769 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.064060 AGATTGATGAAGTCACCAAAGACAA 58.936 36.000 0.00 0.00 40.98 3.18
18 19 5.868454 TGAGATTGATGAAGTCACCAAAGA 58.132 37.500 0.00 0.00 32.26 2.52
67 74 2.607499 CCCTACCTCATGAGCATCTCT 58.393 52.381 17.76 0.00 34.92 3.10
71 78 1.050988 ACGCCCTACCTCATGAGCAT 61.051 55.000 17.76 9.87 0.00 3.79
88 95 7.148738 GCATACACTCATTCCTATGAACATACG 60.149 40.741 0.00 0.00 40.17 3.06
91 98 5.698089 CGCATACACTCATTCCTATGAACAT 59.302 40.000 0.00 0.00 40.17 2.71
101 110 8.556517 TTATATATACGCGCATACACTCATTC 57.443 34.615 5.73 0.00 0.00 2.67
128 137 1.710013 ACACAATACAGACGCGGAAG 58.290 50.000 12.47 0.99 0.00 3.46
129 138 2.157834 AACACAATACAGACGCGGAA 57.842 45.000 12.47 0.00 0.00 4.30
159 169 6.679327 AAAGTTATTTTCGGTATGCTCTCC 57.321 37.500 0.00 0.00 0.00 3.71
194 204 4.074970 CTCACTCCATGCCTTGTTAGTTT 58.925 43.478 0.00 0.00 0.00 2.66
197 207 2.012673 GCTCACTCCATGCCTTGTTAG 58.987 52.381 0.00 0.00 0.00 2.34
198 208 1.630369 AGCTCACTCCATGCCTTGTTA 59.370 47.619 0.00 0.00 0.00 2.41
289 303 5.757320 GTGGATTGATGAAGATTGATCTCGT 59.243 40.000 0.00 0.00 35.76 4.18
320 334 0.318784 AGTCTGTCACTTTCGTCCGC 60.319 55.000 0.00 0.00 26.56 5.54
348 362 5.910637 TTCTGTAAGCACGTCGTATTTTT 57.089 34.783 0.00 0.00 0.00 1.94
371 385 2.940410 GTCGCAGAATTTAAATCCGGGA 59.060 45.455 0.00 0.00 39.69 5.14
374 388 3.342269 CGTGTCGCAGAATTTAAATCCG 58.658 45.455 0.10 3.16 39.69 4.18
381 395 1.599518 TGCCCGTGTCGCAGAATTT 60.600 52.632 0.00 0.00 39.69 1.82
389 403 2.693250 TTCTCTGTGTGCCCGTGTCG 62.693 60.000 0.00 0.00 0.00 4.35
432 447 8.706322 TTTAGAGCTTTTCTTGGGACTTAAAT 57.294 30.769 0.00 0.00 37.36 1.40
435 450 8.706322 AAATTTAGAGCTTTTCTTGGGACTTA 57.294 30.769 0.00 0.00 37.36 2.24
438 453 7.382488 GTCAAAATTTAGAGCTTTTCTTGGGAC 59.618 37.037 0.00 0.00 37.36 4.46
471 486 1.794222 CTGGATTTCGTTGTCGCCC 59.206 57.895 0.00 0.00 36.96 6.13
548 563 1.521450 TTGTCTCCGGTCGACTGGTC 61.521 60.000 36.33 27.28 43.01 4.02
627 642 1.083242 GCGGCGTTATTGGTTACGGA 61.083 55.000 9.37 0.00 38.17 4.69
628 643 1.085501 AGCGGCGTTATTGGTTACGG 61.086 55.000 9.37 0.00 38.17 4.02
629 644 1.256117 GTAGCGGCGTTATTGGTTACG 59.744 52.381 9.37 0.00 40.55 3.18
691 706 3.238497 GGTTGGGTTGGGTTGGGC 61.238 66.667 0.00 0.00 0.00 5.36
705 720 4.938756 TCCACTGGGGCTGGGGTT 62.939 66.667 0.00 0.00 36.21 4.11
706 721 4.701437 ATCCACTGGGGCTGGGGT 62.701 66.667 0.00 0.00 36.21 4.95
707 722 3.350163 AATCCACTGGGGCTGGGG 61.350 66.667 0.00 0.00 36.21 4.96
902 928 2.107141 GATCCGAGAAGCCCACGG 59.893 66.667 0.00 0.00 46.71 4.94
966 992 3.366052 TCCAAATCCAAGAACCTAGCC 57.634 47.619 0.00 0.00 0.00 3.93
968 994 5.372373 GGAGATCCAAATCCAAGAACCTAG 58.628 45.833 0.00 0.00 35.54 3.02
1098 1127 2.833582 GCGACGAGGATGGGGAGA 60.834 66.667 0.00 0.00 0.00 3.71
1191 1235 3.308866 CGGATCCGATGAACCACTAAAAC 59.691 47.826 30.62 0.00 42.83 2.43
1226 1270 1.068748 CCAGCAACTAACTGCAGCTTG 60.069 52.381 15.27 11.21 45.18 4.01
1290 1334 8.059798 AGTTTTATGAGAAAACTGATCCATGG 57.940 34.615 16.17 4.97 45.58 3.66
1332 1396 4.761739 AGTACACAAATTGACATGTCAGGG 59.238 41.667 26.48 18.99 41.13 4.45
1333 1397 5.469760 TCAGTACACAAATTGACATGTCAGG 59.530 40.000 26.48 19.21 41.13 3.86
1334 1398 6.544038 TCAGTACACAAATTGACATGTCAG 57.456 37.500 26.48 18.02 41.13 3.51
1335 1399 6.486320 ACATCAGTACACAAATTGACATGTCA 59.514 34.615 24.56 24.56 37.91 3.58
1336 1400 6.798476 CACATCAGTACACAAATTGACATGTC 59.202 38.462 19.27 19.27 0.00 3.06
1337 1401 6.486320 TCACATCAGTACACAAATTGACATGT 59.514 34.615 0.00 0.00 0.00 3.21
1338 1402 6.901265 TCACATCAGTACACAAATTGACATG 58.099 36.000 0.00 0.00 0.00 3.21
1339 1403 6.348786 GCTCACATCAGTACACAAATTGACAT 60.349 38.462 0.00 0.00 0.00 3.06
1340 1404 5.049474 GCTCACATCAGTACACAAATTGACA 60.049 40.000 0.00 0.00 0.00 3.58
1341 1405 5.385617 GCTCACATCAGTACACAAATTGAC 58.614 41.667 0.00 0.00 0.00 3.18
1342 1406 4.455533 GGCTCACATCAGTACACAAATTGA 59.544 41.667 0.00 0.00 0.00 2.57
1343 1407 4.456911 AGGCTCACATCAGTACACAAATTG 59.543 41.667 0.00 0.00 0.00 2.32
1344 1408 4.655963 AGGCTCACATCAGTACACAAATT 58.344 39.130 0.00 0.00 0.00 1.82
1345 1409 4.019860 AGAGGCTCACATCAGTACACAAAT 60.020 41.667 18.26 0.00 0.00 2.32
1346 1410 3.324846 AGAGGCTCACATCAGTACACAAA 59.675 43.478 18.26 0.00 0.00 2.83
1347 1411 2.899900 AGAGGCTCACATCAGTACACAA 59.100 45.455 18.26 0.00 0.00 3.33
1348 1412 2.232208 CAGAGGCTCACATCAGTACACA 59.768 50.000 18.26 0.00 0.00 3.72
1349 1413 2.232452 ACAGAGGCTCACATCAGTACAC 59.768 50.000 18.26 0.00 0.00 2.90
1350 1414 2.529632 ACAGAGGCTCACATCAGTACA 58.470 47.619 18.26 0.00 0.00 2.90
1351 1415 4.158764 AGTTACAGAGGCTCACATCAGTAC 59.841 45.833 18.26 3.73 0.00 2.73
1352 1416 4.344978 AGTTACAGAGGCTCACATCAGTA 58.655 43.478 18.26 6.57 0.00 2.74
1353 1417 3.169099 AGTTACAGAGGCTCACATCAGT 58.831 45.455 18.26 7.51 0.00 3.41
1382 1466 9.766277 GTCTTTCTATCTGTTGATTGACAATTC 57.234 33.333 1.39 0.00 40.76 2.17
1417 1508 4.816385 TGCTATGGTGCTGTATTTTCTAGC 59.184 41.667 0.00 0.00 37.93 3.42
1523 1614 8.974408 GTTTGATTATTTTGTTAAAGCGAAGGT 58.026 29.630 0.00 0.00 44.60 3.50
1529 1620 9.213799 TCCATGGTTTGATTATTTTGTTAAAGC 57.786 29.630 12.58 0.00 0.00 3.51
1549 1640 3.427503 GGCATCTAAAAACGTGTCCATGG 60.428 47.826 4.97 4.97 0.00 3.66
1593 1684 2.061028 AGACGTTTAAAAGTACCGCCG 58.939 47.619 6.77 0.00 0.00 6.46
1650 1741 9.985730 CTCACATGCCATTTAACCAATAATATT 57.014 29.630 0.00 0.00 0.00 1.28
1709 1800 1.211457 AGCATGTCCCTCCTCACATTC 59.789 52.381 0.00 0.00 30.48 2.67
1710 1801 1.293062 AGCATGTCCCTCCTCACATT 58.707 50.000 0.00 0.00 30.48 2.71
1719 1810 5.653255 AATTTGGATAGTAGCATGTCCCT 57.347 39.130 0.00 0.00 29.74 4.20
1754 1845 9.416794 CTATTAGCTTCCAGTACATGTTCTATG 57.583 37.037 2.30 0.00 0.00 2.23
1778 1869 9.753674 GATGATATTTCCCAATGTTAATCCCTA 57.246 33.333 0.00 0.00 0.00 3.53
1779 1870 7.675619 GGATGATATTTCCCAATGTTAATCCCT 59.324 37.037 0.00 0.00 29.52 4.20
1780 1871 7.675619 AGGATGATATTTCCCAATGTTAATCCC 59.324 37.037 0.00 0.00 32.69 3.85
1781 1872 8.655935 AGGATGATATTTCCCAATGTTAATCC 57.344 34.615 2.80 0.00 32.58 3.01
1782 1873 9.525826 AGAGGATGATATTTCCCAATGTTAATC 57.474 33.333 2.80 0.00 33.45 1.75
1783 1874 9.525826 GAGAGGATGATATTTCCCAATGTTAAT 57.474 33.333 2.80 0.00 33.45 1.40
1784 1875 8.727149 AGAGAGGATGATATTTCCCAATGTTAA 58.273 33.333 2.80 0.00 33.45 2.01
1785 1876 8.280258 AGAGAGGATGATATTTCCCAATGTTA 57.720 34.615 2.80 0.00 33.45 2.41
1786 1877 7.159201 AGAGAGGATGATATTTCCCAATGTT 57.841 36.000 2.80 0.00 33.45 2.71
1787 1878 6.776887 AGAGAGGATGATATTTCCCAATGT 57.223 37.500 2.80 0.00 33.45 2.71
1788 1879 8.381636 AGTAAGAGAGGATGATATTTCCCAATG 58.618 37.037 2.80 0.00 33.45 2.82
1789 1880 8.517323 AGTAAGAGAGGATGATATTTCCCAAT 57.483 34.615 2.80 0.00 33.45 3.16
1843 1934 4.528920 TGAATTAAGGTGGGGAAATACCG 58.471 43.478 0.00 0.00 41.85 4.02
1844 1935 6.685368 GCAATGAATTAAGGTGGGGAAATACC 60.685 42.308 0.00 0.00 37.23 2.73
1845 1936 6.280643 GCAATGAATTAAGGTGGGGAAATAC 58.719 40.000 0.00 0.00 0.00 1.89
1846 1937 5.365314 GGCAATGAATTAAGGTGGGGAAATA 59.635 40.000 0.00 0.00 0.00 1.40
1847 1938 4.164030 GGCAATGAATTAAGGTGGGGAAAT 59.836 41.667 0.00 0.00 0.00 2.17
1848 1939 3.517500 GGCAATGAATTAAGGTGGGGAAA 59.482 43.478 0.00 0.00 0.00 3.13
1849 1940 3.103742 GGCAATGAATTAAGGTGGGGAA 58.896 45.455 0.00 0.00 0.00 3.97
1850 1941 2.625617 GGGCAATGAATTAAGGTGGGGA 60.626 50.000 0.00 0.00 0.00 4.81
1851 1942 1.762370 GGGCAATGAATTAAGGTGGGG 59.238 52.381 0.00 0.00 0.00 4.96
1872 2159 1.289276 GGCTGCAAAACCTTGTTGTG 58.711 50.000 0.50 0.00 34.79 3.33
1923 2237 3.871485 CTCAATCTCTTCTTCCCTGTGG 58.129 50.000 0.00 0.00 0.00 4.17
1958 2274 1.278238 GCTATGTGTGCTGTCGGTAC 58.722 55.000 0.00 0.00 0.00 3.34
1959 2275 0.892063 TGCTATGTGTGCTGTCGGTA 59.108 50.000 0.00 0.00 0.00 4.02
1999 2315 0.661187 CACGGTGCTCATTGTTGTGC 60.661 55.000 0.00 0.00 41.60 4.57
2049 2365 8.143835 CCTTGATTTCTTGGTTCAATACACTTT 58.856 33.333 0.00 0.00 0.00 2.66
2081 2397 8.463607 GTGCTCTAGTTCTTCAGTTCTTATACT 58.536 37.037 0.00 0.00 0.00 2.12
2082 2398 8.463607 AGTGCTCTAGTTCTTCAGTTCTTATAC 58.536 37.037 0.00 0.00 0.00 1.47
2083 2399 8.582657 AGTGCTCTAGTTCTTCAGTTCTTATA 57.417 34.615 0.00 0.00 0.00 0.98
2084 2400 7.475137 AGTGCTCTAGTTCTTCAGTTCTTAT 57.525 36.000 0.00 0.00 0.00 1.73
2159 2475 3.466836 GGGCATCGATCAACTGTATTCA 58.533 45.455 0.00 0.00 0.00 2.57
2160 2476 2.808543 GGGGCATCGATCAACTGTATTC 59.191 50.000 0.00 0.00 0.00 1.75
2161 2477 2.439507 AGGGGCATCGATCAACTGTATT 59.560 45.455 0.00 0.00 0.00 1.89
2165 2481 0.467384 AGAGGGGCATCGATCAACTG 59.533 55.000 0.00 0.00 0.00 3.16
2295 2611 1.967779 GAGGGCTAGGATGAGAGGAAC 59.032 57.143 0.00 0.00 0.00 3.62
2357 2673 1.609580 GGAACAGTGATTACACCGGCA 60.610 52.381 0.00 0.00 46.99 5.69
2360 2676 6.509517 CGATATTTGGAACAGTGATTACACCG 60.510 42.308 0.00 0.00 46.99 4.94
2475 2791 5.009010 ACCAGCTTGTCAGACAAATTAACTG 59.991 40.000 16.85 16.33 37.69 3.16
2476 2792 5.133221 ACCAGCTTGTCAGACAAATTAACT 58.867 37.500 16.85 6.96 37.69 2.24
2477 2793 5.438761 ACCAGCTTGTCAGACAAATTAAC 57.561 39.130 16.85 4.95 37.69 2.01
2478 2794 6.463995 AAACCAGCTTGTCAGACAAATTAA 57.536 33.333 16.85 0.00 37.69 1.40
2479 2795 6.463995 AAAACCAGCTTGTCAGACAAATTA 57.536 33.333 16.85 0.00 37.69 1.40
2480 2796 5.343307 AAAACCAGCTTGTCAGACAAATT 57.657 34.783 16.85 5.52 37.69 1.82
2481 2797 6.265196 TGATAAAACCAGCTTGTCAGACAAAT 59.735 34.615 16.85 6.19 37.69 2.32
2482 2798 5.592282 TGATAAAACCAGCTTGTCAGACAAA 59.408 36.000 16.85 0.00 37.69 2.83
2483 2799 5.129634 TGATAAAACCAGCTTGTCAGACAA 58.870 37.500 15.39 15.39 36.54 3.18
2484 2800 4.713553 TGATAAAACCAGCTTGTCAGACA 58.286 39.130 0.00 0.00 0.00 3.41
2485 2801 5.288543 CTGATAAAACCAGCTTGTCAGAC 57.711 43.478 3.69 0.00 41.82 3.51
2495 2811 2.421424 GCCTGACAGCTGATAAAACCAG 59.579 50.000 23.35 13.72 34.88 4.00
2496 2812 2.436417 GCCTGACAGCTGATAAAACCA 58.564 47.619 23.35 5.36 0.00 3.67
2497 2813 1.745653 GGCCTGACAGCTGATAAAACC 59.254 52.381 23.35 10.53 0.00 3.27
2498 2814 1.398390 CGGCCTGACAGCTGATAAAAC 59.602 52.381 23.35 5.44 42.00 2.43
2499 2815 1.277842 TCGGCCTGACAGCTGATAAAA 59.722 47.619 23.35 0.00 43.22 1.52
2500 2816 0.901827 TCGGCCTGACAGCTGATAAA 59.098 50.000 23.35 1.32 43.22 1.40
2501 2817 2.590704 TCGGCCTGACAGCTGATAA 58.409 52.632 23.35 4.05 43.22 1.75
2502 2818 4.355151 TCGGCCTGACAGCTGATA 57.645 55.556 23.35 7.64 43.22 2.15
2504 2820 0.901827 TAATTCGGCCTGACAGCTGA 59.098 50.000 23.35 0.00 46.37 4.26
2505 2821 1.959042 ATAATTCGGCCTGACAGCTG 58.041 50.000 13.48 13.48 40.71 4.24
2506 2822 2.292267 CAATAATTCGGCCTGACAGCT 58.708 47.619 0.00 0.00 0.00 4.24
2507 2823 1.334869 CCAATAATTCGGCCTGACAGC 59.665 52.381 0.00 0.00 0.00 4.40
2508 2824 1.334869 GCCAATAATTCGGCCTGACAG 59.665 52.381 0.00 0.00 42.82 3.51
2509 2825 1.388547 GCCAATAATTCGGCCTGACA 58.611 50.000 0.00 0.00 42.82 3.58
2516 2832 0.031178 GCAGCAGGCCAATAATTCGG 59.969 55.000 5.01 0.00 36.11 4.30
2517 2833 0.317269 CGCAGCAGGCCAATAATTCG 60.317 55.000 5.01 0.00 40.31 3.34
2518 2834 3.557207 CGCAGCAGGCCAATAATTC 57.443 52.632 5.01 0.00 40.31 2.17
2546 2862 0.759060 GGAACAGGCCAGTTTTGGGT 60.759 55.000 15.43 0.00 45.16 4.51
2550 2866 0.178961 GGAGGGAACAGGCCAGTTTT 60.179 55.000 15.43 4.28 0.00 2.43
2579 2895 0.911525 AGGCCATAGACCTGCACACT 60.912 55.000 5.01 0.00 35.72 3.55
2614 2930 2.686405 TGCCTTGATGTTCTGATGATGC 59.314 45.455 0.00 0.00 0.00 3.91
2779 3095 2.770699 ACGGAGTAATCGACGAATCC 57.229 50.000 0.00 6.67 41.94 3.01
2793 3109 1.471676 GGCAAGGTGATGAGTACGGAG 60.472 57.143 0.00 0.00 0.00 4.63
2797 3113 2.604046 ATCGGCAAGGTGATGAGTAC 57.396 50.000 0.00 0.00 0.00 2.73
2804 3120 1.414919 GGTACCATATCGGCAAGGTGA 59.585 52.381 7.15 0.00 39.03 4.02
2845 3161 5.364778 CCGATGTCATTAGATTACACCCAA 58.635 41.667 0.00 0.00 0.00 4.12
2888 3204 1.008194 GTGTCGACGGTGCAGTGTA 60.008 57.895 11.62 0.00 0.00 2.90
3060 3384 0.886043 TGCAGTGTCATGGCAGTGTC 60.886 55.000 30.38 23.38 40.79 3.67
3062 3386 1.577922 GTGCAGTGTCATGGCAGTG 59.422 57.895 27.30 27.30 41.42 3.66
3063 3387 1.601759 GGTGCAGTGTCATGGCAGT 60.602 57.895 0.00 0.00 38.38 4.40
3065 3389 2.669229 CGGTGCAGTGTCATGGCA 60.669 61.111 0.00 0.00 34.70 4.92
3072 3396 3.269347 GCGTCAACGGTGCAGTGT 61.269 61.111 0.00 0.00 40.23 3.55
3105 3429 1.151777 CGTTGTGCAGTCTCGGTTGT 61.152 55.000 0.00 0.00 0.00 3.32
3182 3615 0.463654 AGTTGACCTTGCAGTTGCGA 60.464 50.000 0.00 0.00 45.83 5.10
3240 3674 3.468071 TTCTGGGGTAGCTACTCTTCA 57.532 47.619 22.84 12.47 0.00 3.02
3248 3689 2.254152 TGAGTCATTCTGGGGTAGCT 57.746 50.000 0.00 0.00 0.00 3.32
3342 3820 4.065281 GGTCTGGGGTCGACGGTG 62.065 72.222 9.92 0.00 32.24 4.94
3360 3838 2.436109 GGTGGTGGTGATGTGGCT 59.564 61.111 0.00 0.00 0.00 4.75
3381 3859 3.423253 TTGGTGGTTGTGGGTCGGG 62.423 63.158 0.00 0.00 0.00 5.14
3435 3913 7.789273 AGTCAAGATAGATTCAAGAGCAATG 57.211 36.000 0.00 0.00 0.00 2.82
3580 4060 8.723260 CATTGTTTTCAAAATTTTGTACGCAAG 58.277 29.630 25.98 16.43 43.39 4.01
3585 4065 7.855409 GGCTCCATTGTTTTCAAAATTTTGTAC 59.145 33.333 25.98 21.44 43.39 2.90
3722 4293 9.944376 GTGGATGGGCGTAATCATATATTATAT 57.056 33.333 0.00 0.00 0.00 0.86
3723 4294 8.372459 GGTGGATGGGCGTAATCATATATTATA 58.628 37.037 0.00 0.00 0.00 0.98
3724 4295 7.147391 TGGTGGATGGGCGTAATCATATATTAT 60.147 37.037 0.00 0.00 0.00 1.28
3737 4308 0.107214 CTACAATGGTGGATGGGCGT 60.107 55.000 0.00 0.00 0.00 5.68
3742 4313 4.198530 TGCATGTACTACAATGGTGGATG 58.801 43.478 0.00 0.00 0.00 3.51
3749 4320 7.624661 CATGAGTTACTGCATGTACTACAATG 58.375 38.462 13.03 0.00 37.65 2.82
3750 4321 7.776933 CATGAGTTACTGCATGTACTACAAT 57.223 36.000 13.03 0.00 37.65 2.71
3803 4374 8.445275 TGCAGTAGACAATTTAGAGTCAAAAA 57.555 30.769 0.00 0.00 37.23 1.94
3804 4375 8.445275 TTGCAGTAGACAATTTAGAGTCAAAA 57.555 30.769 0.00 0.00 37.23 2.44
3805 4376 8.445275 TTTGCAGTAGACAATTTAGAGTCAAA 57.555 30.769 0.00 0.00 37.23 2.69
3806 4377 7.931407 TCTTTGCAGTAGACAATTTAGAGTCAA 59.069 33.333 0.00 0.00 37.23 3.18
3807 4378 7.441836 TCTTTGCAGTAGACAATTTAGAGTCA 58.558 34.615 0.00 0.00 37.23 3.41
3808 4379 7.815068 TCTCTTTGCAGTAGACAATTTAGAGTC 59.185 37.037 0.00 0.00 33.88 3.36
3809 4380 7.671302 TCTCTTTGCAGTAGACAATTTAGAGT 58.329 34.615 0.00 0.00 33.88 3.24
3819 4390 2.180276 TCCCCTCTCTTTGCAGTAGAC 58.820 52.381 0.00 0.00 0.00 2.59
3822 4393 2.303022 CAGTTCCCCTCTCTTTGCAGTA 59.697 50.000 0.00 0.00 0.00 2.74
3869 4440 6.095432 ACAGCAAATATAACAAACTGGCAA 57.905 33.333 0.00 0.00 0.00 4.52
3887 4458 5.299028 ACAGTTTTAATGTGACATGACAGCA 59.701 36.000 0.00 1.27 0.00 4.41
4070 4641 3.920231 TCAGCAAGCTTGTCATATCCT 57.080 42.857 26.55 11.09 0.00 3.24
4274 4845 9.348476 AGAATAAAAGAGCTTCTTGTTTCTCTT 57.652 29.630 0.00 0.00 44.91 2.85
4334 4909 9.477484 GGGAGAAAGAAAAGAAAAATTAAGGTC 57.523 33.333 0.00 0.00 0.00 3.85
4483 5062 6.428159 AGGACATAACAATCAGAACAACAGTC 59.572 38.462 0.00 0.00 0.00 3.51
5038 5643 6.211184 TGGATTGGATTTGTTTGACTAGCATT 59.789 34.615 0.00 0.00 0.00 3.56
5099 5704 5.106157 ACGAGAAAATGGGCAAGACAAATAG 60.106 40.000 0.00 0.00 0.00 1.73
5144 5751 9.286946 GCTTATAAGAAATCAATATGCTGATGC 57.713 33.333 16.85 0.00 36.16 3.91
5147 5754 8.786898 GTGGCTTATAAGAAATCAATATGCTGA 58.213 33.333 16.85 0.00 0.00 4.26
5198 5813 6.813649 CAGATTAATCTTCGTGGTCTTCTTCA 59.186 38.462 15.49 0.00 34.22 3.02
5281 5896 1.135094 CAGTGGCTAGGGTGATGGAT 58.865 55.000 0.00 0.00 0.00 3.41
5295 5910 2.496070 TCCGGTCTAGTGAAATCAGTGG 59.504 50.000 0.00 0.00 0.00 4.00
5325 5940 0.754587 TGGCTGCCATGTTTGACACA 60.755 50.000 19.30 0.00 40.71 3.72
5507 6122 3.349488 GTTGCAAACTGAGTTACCACC 57.651 47.619 0.00 0.00 45.32 4.61
5611 6227 1.849039 AGCTGGAGATGCTTATTGGGT 59.151 47.619 0.00 0.00 37.52 4.51
5656 6272 4.053295 AGTTGCAAAAGCAGCACATAAAG 58.947 39.130 0.00 0.00 42.54 1.85
5657 6273 4.057406 AGTTGCAAAAGCAGCACATAAA 57.943 36.364 0.00 0.00 42.54 1.40
5658 6274 3.731652 AGTTGCAAAAGCAGCACATAA 57.268 38.095 0.00 0.00 42.54 1.90
5801 6422 9.717942 TCTAAATTTCATAAATTGTGGGTTTGG 57.282 29.630 0.00 0.00 40.05 3.28
5826 6447 6.764308 TCAAAGGTCATGGAGATTCAAATC 57.236 37.500 0.00 0.00 35.64 2.17
5868 6490 9.589461 TGTTTGGATGGGTAATTTTAGAACTAA 57.411 29.630 0.00 0.00 0.00 2.24
5869 6491 9.762381 ATGTTTGGATGGGTAATTTTAGAACTA 57.238 29.630 0.00 0.00 0.00 2.24
5870 6492 8.664669 ATGTTTGGATGGGTAATTTTAGAACT 57.335 30.769 0.00 0.00 0.00 3.01
5889 6511 7.218773 CGTGCCAAGATGTAAATAAGATGTTTG 59.781 37.037 0.00 0.00 0.00 2.93
5894 6516 6.112734 TCACGTGCCAAGATGTAAATAAGAT 58.887 36.000 11.67 0.00 0.00 2.40
5914 6536 2.699954 AGGCTCCAAGTAAACATCACG 58.300 47.619 0.00 0.00 0.00 4.35
5915 6537 3.821033 ACAAGGCTCCAAGTAAACATCAC 59.179 43.478 0.00 0.00 0.00 3.06
5955 6577 4.501400 CCTTGGTGAAGTTTGGGATGAAAC 60.501 45.833 0.00 0.00 36.28 2.78
6027 6649 2.202987 CTGCCTGATCTGTCGGCC 60.203 66.667 11.49 0.00 40.77 6.13
6030 6652 0.036952 ACCAACTGCCTGATCTGTCG 60.037 55.000 0.00 0.00 0.00 4.35
6038 6660 0.890683 GGGATGAAACCAACTGCCTG 59.109 55.000 0.00 0.00 0.00 4.85
6065 6707 4.079253 TCCAGTTAACATTCCAGCTTTCC 58.921 43.478 8.61 0.00 0.00 3.13
6066 6708 5.703876 CTTCCAGTTAACATTCCAGCTTTC 58.296 41.667 8.61 0.00 0.00 2.62
6073 6715 3.191371 CACAGGCTTCCAGTTAACATTCC 59.809 47.826 8.61 0.34 0.00 3.01
6117 6759 0.679505 AGCCGTTGACTTGCACTAGA 59.320 50.000 0.00 0.00 0.00 2.43
6124 6766 0.588252 CCTTGTGAGCCGTTGACTTG 59.412 55.000 0.00 0.00 0.00 3.16
6129 6771 1.283793 CTTGCCTTGTGAGCCGTTG 59.716 57.895 0.00 0.00 0.00 4.10
6130 6772 0.751643 AACTTGCCTTGTGAGCCGTT 60.752 50.000 0.00 0.00 0.00 4.44
6132 6774 1.165907 TCAACTTGCCTTGTGAGCCG 61.166 55.000 0.00 0.00 0.00 5.52
6135 6777 1.972872 ACCTCAACTTGCCTTGTGAG 58.027 50.000 0.00 0.00 0.00 3.51
6136 6778 2.435372 AACCTCAACTTGCCTTGTGA 57.565 45.000 0.00 0.00 0.00 3.58
6137 6779 3.525268 AAAACCTCAACTTGCCTTGTG 57.475 42.857 0.00 0.00 0.00 3.33
6138 6780 3.636764 CCTAAAACCTCAACTTGCCTTGT 59.363 43.478 0.00 0.00 0.00 3.16
6139 6781 3.888930 TCCTAAAACCTCAACTTGCCTTG 59.111 43.478 0.00 0.00 0.00 3.61
6171 6816 1.689813 TGAAACGGCCTCAACTCTACA 59.310 47.619 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.