Multiple sequence alignment - TraesCS5D01G019000

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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 TraesCS5D01G019000 chr5D 100.000 3125 0 0 1 3125 11363861 11366985 0.000000e+00 5771.0
1 TraesCS5D01G019000 chr5D 86.069 1730 157 38 834 2543 11614383 11612718 0.000000e+00 1783.0
2 TraesCS5D01G019000 chr5D 75.491 1273 247 38 1017 2270 459750357 459751583 2.100000e-156 562.0
3 TraesCS5D01G019000 chr5D 74.941 1277 246 44 1017 2270 459762945 459764170 4.620000e-143 518.0
4 TraesCS5D01G019000 chr5D 75.020 1257 241 43 1017 2250 459758484 459759690 5.980000e-142 514.0
5 TraesCS5D01G019000 chr5D 79.301 773 97 35 1705 2471 11576101 11575386 1.690000e-132 483.0
6 TraesCS5D01G019000 chr5D 95.189 291 14 0 546 836 527893365 527893655 7.900000e-126 460.0
7 TraesCS5D01G019000 chr5D 80.381 367 61 7 2765 3124 2613790 2614152 5.140000e-68 268.0
8 TraesCS5D01G019000 chr5D 87.500 168 8 8 834 989 11617472 11617306 6.880000e-42 182.0
9 TraesCS5D01G019000 chr5D 83.696 184 10 9 2066 2249 11574477 11574314 4.170000e-34 156.0
10 TraesCS5D01G019000 chr5D 85.443 158 8 6 2361 2513 11574264 11574117 1.940000e-32 150.0
11 TraesCS5D01G019000 chr5D 83.648 159 19 5 2443 2595 11611808 11611651 3.250000e-30 143.0
12 TraesCS5D01G019000 chrUn 95.889 1581 46 5 834 2405 312563019 312564589 0.000000e+00 2542.0
13 TraesCS5D01G019000 chrUn 89.781 685 35 13 2447 3125 312564584 312565239 0.000000e+00 845.0
14 TraesCS5D01G019000 chrUn 93.122 378 25 1 2 378 374947659 374948036 1.270000e-153 553.0
15 TraesCS5D01G019000 chrUn 93.464 306 19 1 74 378 461627431 461627736 1.320000e-123 453.0
16 TraesCS5D01G019000 chrUn 80.654 367 60 7 2765 3124 103116585 103116223 1.100000e-69 274.0
17 TraesCS5D01G019000 chrUn 87.952 166 8 5 382 535 374948457 374948622 5.320000e-43 185.0
18 TraesCS5D01G019000 chrUn 87.952 166 8 5 382 535 461628157 461628322 5.320000e-43 185.0
19 TraesCS5D01G019000 chrUn 87.500 72 6 1 2580 2648 422505846 422505775 2.580000e-11 80.5
20 TraesCS5D01G019000 chr5B 86.028 1732 163 33 834 2543 11477271 11478945 0.000000e+00 1784.0
21 TraesCS5D01G019000 chr5B 81.377 1278 189 34 888 2126 11605569 11604302 0.000000e+00 996.0
22 TraesCS5D01G019000 chr5B 75.191 1177 201 66 1003 2130 12580730 12581864 3.650000e-129 472.0
23 TraesCS5D01G019000 chr5B 86.626 329 22 9 131 441 11476556 11476880 8.300000e-91 344.0
24 TraesCS5D01G019000 chr5B 83.721 215 32 2 2435 2648 11603694 11603482 1.900000e-47 200.0
25 TraesCS5D01G019000 chr5B 84.932 146 17 3 2443 2583 11480703 11480848 3.250000e-30 143.0
26 TraesCS5D01G019000 chr5B 100.000 32 0 0 2648 2679 11506082 11506113 3.370000e-05 60.2
27 TraesCS5D01G019000 chr1A 86.776 1520 142 27 834 2340 99749981 99748508 0.000000e+00 1639.0
28 TraesCS5D01G019000 chr1A 81.146 1326 203 37 836 2126 99640977 99642290 0.000000e+00 1020.0
29 TraesCS5D01G019000 chr1A 79.639 776 97 34 1705 2471 99726181 99725458 4.650000e-138 501.0
30 TraesCS5D01G019000 chr1A 86.697 218 26 3 2432 2648 99650880 99651095 4.030000e-59 239.0
31 TraesCS5D01G019000 chr1A 84.507 71 8 3 2527 2595 99746152 99746083 2.010000e-07 67.6
32 TraesCS5D01G019000 chr1A 100.000 34 0 0 2648 2681 99720875 99720842 2.600000e-06 63.9
33 TraesCS5D01G019000 chr5A 76.118 1185 225 25 978 2123 9470422 9469257 4.520000e-158 568.0
34 TraesCS5D01G019000 chr5A 74.441 1162 211 60 1014 2130 9510328 9509208 3.730000e-114 422.0
35 TraesCS5D01G019000 chr6D 92.225 373 23 4 2758 3125 76110896 76110525 9.930000e-145 523.0
36 TraesCS5D01G019000 chr1D 95.502 289 13 0 546 834 110458236 110458524 2.200000e-126 462.0
37 TraesCS5D01G019000 chr1D 83.673 343 47 8 2786 3124 223347823 223348160 6.510000e-82 315.0
38 TraesCS5D01G019000 chr3D 95.189 291 14 0 546 836 47603394 47603684 7.900000e-126 460.0
39 TraesCS5D01G019000 chr4D 95.172 290 13 1 547 836 367717527 367717239 1.020000e-124 457.0
40 TraesCS5D01G019000 chr2D 95.156 289 14 0 546 834 608377903 608378191 1.020000e-124 457.0
41 TraesCS5D01G019000 chr2D 93.793 290 17 1 547 836 139511801 139511513 4.790000e-118 435.0
42 TraesCS5D01G019000 chr2D 80.381 367 61 7 2765 3124 633490616 633490254 5.140000e-68 268.0
43 TraesCS5D01G019000 chr7D 93.559 295 16 2 549 843 70708762 70708471 1.330000e-118 436.0
44 TraesCS5D01G019000 chr7D 93.793 290 17 1 547 836 561578917 561578629 4.790000e-118 435.0
45 TraesCS5D01G019000 chr7D 93.448 290 17 2 547 835 471961775 471962063 2.230000e-116 429.0
46 TraesCS5D01G019000 chr7D 80.811 370 56 10 2764 3124 15073883 15073520 3.070000e-70 276.0
47 TraesCS5D01G019000 chr4A 80.371 377 60 10 2756 3124 78791096 78790726 1.100000e-69 274.0
48 TraesCS5D01G019000 chr2A 83.265 245 32 8 2765 3004 14983328 14983088 1.890000e-52 217.0


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 TraesCS5D01G019000 chr5D 11363861 11366985 3124 False 5771.000000 5771 100.000000 1 3125 1 chr5D.!!$F2 3124
1 TraesCS5D01G019000 chr5D 11611651 11617472 5821 True 702.666667 1783 85.739000 834 2595 3 chr5D.!!$R2 1761
2 TraesCS5D01G019000 chr5D 459750357 459751583 1226 False 562.000000 562 75.491000 1017 2270 1 chr5D.!!$F3 1253
3 TraesCS5D01G019000 chr5D 459758484 459764170 5686 False 516.000000 518 74.980500 1017 2270 2 chr5D.!!$F5 1253
4 TraesCS5D01G019000 chr5D 11574117 11576101 1984 True 263.000000 483 82.813333 1705 2513 3 chr5D.!!$R1 808
5 TraesCS5D01G019000 chrUn 312563019 312565239 2220 False 1693.500000 2542 92.835000 834 3125 2 chrUn.!!$F1 2291
6 TraesCS5D01G019000 chrUn 374947659 374948622 963 False 369.000000 553 90.537000 2 535 2 chrUn.!!$F2 533
7 TraesCS5D01G019000 chrUn 461627431 461628322 891 False 319.000000 453 90.708000 74 535 2 chrUn.!!$F3 461
8 TraesCS5D01G019000 chr5B 11476556 11480848 4292 False 757.000000 1784 85.862000 131 2583 3 chr5B.!!$F3 2452
9 TraesCS5D01G019000 chr5B 11603482 11605569 2087 True 598.000000 996 82.549000 888 2648 2 chr5B.!!$R1 1760
10 TraesCS5D01G019000 chr5B 12580730 12581864 1134 False 472.000000 472 75.191000 1003 2130 1 chr5B.!!$F2 1127
11 TraesCS5D01G019000 chr1A 99640977 99642290 1313 False 1020.000000 1020 81.146000 836 2126 1 chr1A.!!$F1 1290
12 TraesCS5D01G019000 chr1A 99746083 99749981 3898 True 853.300000 1639 85.641500 834 2595 2 chr1A.!!$R3 1761
13 TraesCS5D01G019000 chr1A 99725458 99726181 723 True 501.000000 501 79.639000 1705 2471 1 chr1A.!!$R2 766
14 TraesCS5D01G019000 chr5A 9469257 9470422 1165 True 568.000000 568 76.118000 978 2123 1 chr5A.!!$R1 1145
15 TraesCS5D01G019000 chr5A 9509208 9510328 1120 True 422.000000 422 74.441000 1014 2130 1 chr5A.!!$R2 1116

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
256 258 1.136141 GTTGAGCGTCTGCAACATCAG 60.136 52.381 0.0 0.0 46.23 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 9150 0.391395 ACCACAACGACGACAACCAA 60.391 50.0 0.0 0.0 0.0 3.67 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
72 73 1.303309 GATGTAGCACCACCTGATGC 58.697 55.000 0.00 0.00 42.39 3.91
92 93 1.864176 GGTTGTAACTCGTTGGCCG 59.136 57.895 0.00 0.00 38.13 6.13
104 105 4.728102 TGGCCGTCGGTTGTAGCG 62.728 66.667 13.94 0.00 40.97 4.26
198 200 3.561213 CTGCAGCTCGTCATGGCG 61.561 66.667 14.91 14.91 0.00 5.69
202 204 3.749064 AGCTCGTCATGGCGTCGT 61.749 61.111 20.64 1.91 0.00 4.34
256 258 1.136141 GTTGAGCGTCTGCAACATCAG 60.136 52.381 0.00 0.00 46.23 2.90
267 269 1.464997 GCAACATCAGTTCGGTCCTTC 59.535 52.381 0.00 0.00 35.28 3.46
355 357 2.068821 AGAGAGGCGCATGGATGGT 61.069 57.895 10.83 0.00 0.00 3.55
444 869 2.702270 AGAAAAGAAACATGGGCCCT 57.298 45.000 25.70 5.48 0.00 5.19
512 1244 4.861102 AGCTTCACATTCTTCTTTTGGG 57.139 40.909 0.00 0.00 0.00 4.12
515 1247 4.279420 GCTTCACATTCTTCTTTTGGGAGT 59.721 41.667 0.00 0.00 0.00 3.85
539 1271 4.379339 AATAGGCACAACAAAAACGTGT 57.621 36.364 0.00 0.00 33.13 4.49
546 1278 3.122613 CACAACAAAAACGTGTGTGCAAT 59.877 39.130 0.00 0.00 0.00 3.56
548 1280 4.923871 ACAACAAAAACGTGTGTGCAATAA 59.076 33.333 0.00 0.00 0.00 1.40
549 1281 5.061560 ACAACAAAAACGTGTGTGCAATAAG 59.938 36.000 0.00 0.00 0.00 1.73
550 1282 4.987832 ACAAAAACGTGTGTGCAATAAGA 58.012 34.783 0.00 0.00 0.00 2.10
551 1283 4.796312 ACAAAAACGTGTGTGCAATAAGAC 59.204 37.500 0.00 0.00 0.00 3.01
552 1284 4.893424 AAAACGTGTGTGCAATAAGACT 57.107 36.364 0.00 0.00 0.00 3.24
554 1286 5.591643 AAACGTGTGTGCAATAAGACTAG 57.408 39.130 0.00 0.00 0.00 2.57
555 1287 2.993899 ACGTGTGTGCAATAAGACTAGC 59.006 45.455 0.00 0.00 0.00 3.42
556 1288 2.348666 CGTGTGTGCAATAAGACTAGCC 59.651 50.000 0.00 0.00 0.00 3.93
557 1289 3.334691 GTGTGTGCAATAAGACTAGCCA 58.665 45.455 0.00 0.00 0.00 4.75
558 1290 3.125316 GTGTGTGCAATAAGACTAGCCAC 59.875 47.826 0.00 0.00 0.00 5.01
559 1291 3.244387 TGTGTGCAATAAGACTAGCCACA 60.244 43.478 0.00 0.00 36.52 4.17
560 1292 3.751175 GTGTGCAATAAGACTAGCCACAA 59.249 43.478 0.00 0.00 32.33 3.33
561 1293 4.396166 GTGTGCAATAAGACTAGCCACAAT 59.604 41.667 0.00 0.00 32.33 2.71
562 1294 4.395854 TGTGCAATAAGACTAGCCACAATG 59.604 41.667 0.00 0.00 0.00 2.82
563 1295 3.947196 TGCAATAAGACTAGCCACAATGG 59.053 43.478 0.00 0.00 41.55 3.16
577 1309 4.814771 GCCACAATGGGTAGTAACATAGAC 59.185 45.833 0.00 0.00 38.19 2.59
578 1310 5.396436 GCCACAATGGGTAGTAACATAGACT 60.396 44.000 0.00 0.00 38.19 3.24
579 1311 6.183360 GCCACAATGGGTAGTAACATAGACTA 60.183 42.308 0.00 0.00 38.19 2.59
581 1313 7.069578 CCACAATGGGTAGTAACATAGACTAGT 59.930 40.741 0.00 0.00 32.67 2.57
582 1314 9.128404 CACAATGGGTAGTAACATAGACTAGTA 57.872 37.037 0.00 0.00 30.08 1.82
583 1315 9.705103 ACAATGGGTAGTAACATAGACTAGTAA 57.295 33.333 0.00 0.00 30.08 2.24
584 1316 9.962783 CAATGGGTAGTAACATAGACTAGTAAC 57.037 37.037 0.00 0.00 30.08 2.50
585 1317 9.705103 AATGGGTAGTAACATAGACTAGTAACA 57.295 33.333 0.00 0.00 30.08 2.41
586 1318 9.878737 ATGGGTAGTAACATAGACTAGTAACAT 57.121 33.333 0.00 0.00 30.08 2.71
587 1319 9.128404 TGGGTAGTAACATAGACTAGTAACATG 57.872 37.037 0.00 2.36 30.08 3.21
588 1320 8.574737 GGGTAGTAACATAGACTAGTAACATGG 58.425 40.741 0.00 0.00 30.08 3.66
589 1321 9.129532 GGTAGTAACATAGACTAGTAACATGGT 57.870 37.037 0.00 0.93 30.08 3.55
591 1323 7.490000 AGTAACATAGACTAGTAACATGGTGC 58.510 38.462 10.25 9.18 0.00 5.01
592 1324 5.932619 ACATAGACTAGTAACATGGTGCA 57.067 39.130 0.45 0.00 0.00 4.57
593 1325 6.485830 ACATAGACTAGTAACATGGTGCAT 57.514 37.500 0.45 0.00 0.00 3.96
594 1326 6.283694 ACATAGACTAGTAACATGGTGCATG 58.716 40.000 0.45 0.00 46.18 4.06
607 1339 6.775939 CATGGTGCATGTTACTAGTCTATG 57.224 41.667 0.00 4.16 37.12 2.23
609 1341 6.294361 TGGTGCATGTTACTAGTCTATGTT 57.706 37.500 0.00 0.00 0.00 2.71
610 1342 7.412853 TGGTGCATGTTACTAGTCTATGTTA 57.587 36.000 0.00 0.00 0.00 2.41
613 1345 8.627403 GGTGCATGTTACTAGTCTATGTTACTA 58.373 37.037 0.00 0.00 0.00 1.82
614 1346 9.448294 GTGCATGTTACTAGTCTATGTTACTAC 57.552 37.037 0.00 0.00 0.00 2.73
615 1347 8.627403 TGCATGTTACTAGTCTATGTTACTACC 58.373 37.037 0.00 0.00 0.00 3.18
626 1358 8.947305 AGTCTATGTTACTACCTCTATAGTGGT 58.053 37.037 25.52 25.52 43.53 4.16
627 1359 9.001542 GTCTATGTTACTACCTCTATAGTGGTG 57.998 40.741 28.80 21.61 41.50 4.17
628 1360 8.942033 TCTATGTTACTACCTCTATAGTGGTGA 58.058 37.037 28.80 15.38 41.50 4.02
630 1362 6.966751 TGTTACTACCTCTATAGTGGTGAGT 58.033 40.000 28.80 25.91 41.50 3.41
631 1363 8.094284 TGTTACTACCTCTATAGTGGTGAGTA 57.906 38.462 28.80 25.19 41.50 2.59
632 1364 8.551440 TGTTACTACCTCTATAGTGGTGAGTAA 58.449 37.037 28.80 27.75 41.50 2.24
633 1365 8.835439 GTTACTACCTCTATAGTGGTGAGTAAC 58.165 40.741 32.61 32.61 42.06 2.50
634 1366 6.966751 ACTACCTCTATAGTGGTGAGTAACA 58.033 40.000 28.80 11.85 41.50 2.41
636 1368 8.721479 ACTACCTCTATAGTGGTGAGTAACATA 58.279 37.037 28.80 10.67 41.50 2.29
638 1370 8.410673 ACCTCTATAGTGGTGAGTAACATATG 57.589 38.462 22.66 0.00 40.10 1.78
639 1371 8.005388 ACCTCTATAGTGGTGAGTAACATATGT 58.995 37.037 22.66 1.41 40.10 2.29
641 1373 8.762481 TCTATAGTGGTGAGTAACATATGTGT 57.238 34.615 9.63 2.63 41.28 3.72
642 1374 8.847196 TCTATAGTGGTGAGTAACATATGTGTC 58.153 37.037 9.63 7.57 37.67 3.67
643 1375 4.744570 AGTGGTGAGTAACATATGTGTCG 58.255 43.478 9.63 0.00 37.67 4.35
644 1376 4.219944 AGTGGTGAGTAACATATGTGTCGT 59.780 41.667 9.63 0.00 37.67 4.34
645 1377 5.416639 AGTGGTGAGTAACATATGTGTCGTA 59.583 40.000 9.63 0.00 37.67 3.43
646 1378 6.071784 AGTGGTGAGTAACATATGTGTCGTAA 60.072 38.462 9.63 0.00 37.67 3.18
648 1380 6.094719 GGTGAGTAACATATGTGTCGTAACA 58.905 40.000 9.63 1.71 37.67 2.41
649 1381 6.755141 GGTGAGTAACATATGTGTCGTAACAT 59.245 38.462 9.63 9.93 43.21 2.71
650 1382 7.253983 GGTGAGTAACATATGTGTCGTAACATG 60.254 40.741 9.63 0.00 40.93 3.21
651 1383 6.254804 TGAGTAACATATGTGTCGTAACATGC 59.745 38.462 9.63 0.00 40.93 4.06
652 1384 6.103330 AGTAACATATGTGTCGTAACATGCA 58.897 36.000 9.63 0.00 40.93 3.96
653 1385 5.871465 AACATATGTGTCGTAACATGCAA 57.129 34.783 9.63 0.00 40.93 4.08
654 1386 5.216566 ACATATGTGTCGTAACATGCAAC 57.783 39.130 7.78 0.00 40.93 4.17
655 1387 4.693095 ACATATGTGTCGTAACATGCAACA 59.307 37.500 7.78 0.00 40.93 3.33
656 1388 3.536158 ATGTGTCGTAACATGCAACAC 57.464 42.857 8.32 8.32 39.32 3.32
657 1389 2.556257 TGTGTCGTAACATGCAACACT 58.444 42.857 14.68 0.00 40.60 3.55
658 1390 2.939756 TGTGTCGTAACATGCAACACTT 59.060 40.909 14.68 0.00 40.60 3.16
660 1392 4.571176 TGTGTCGTAACATGCAACACTTTA 59.429 37.500 14.68 0.00 40.60 1.85
663 1395 6.635239 GTGTCGTAACATGCAACACTTTATTT 59.365 34.615 8.05 0.00 37.81 1.40
664 1396 7.799447 GTGTCGTAACATGCAACACTTTATTTA 59.201 33.333 8.05 0.00 37.81 1.40
665 1397 8.508062 TGTCGTAACATGCAACACTTTATTTAT 58.492 29.630 0.00 0.00 0.00 1.40
666 1398 9.337091 GTCGTAACATGCAACACTTTATTTATT 57.663 29.630 0.00 0.00 0.00 1.40
671 1403 8.066612 ACATGCAACACTTTATTTATTAGGCT 57.933 30.769 0.00 0.00 0.00 4.58
672 1404 9.184523 ACATGCAACACTTTATTTATTAGGCTA 57.815 29.630 0.00 0.00 0.00 3.93
687 1419 9.998106 TTTATTAGGCTATAGACACATCTTTCC 57.002 33.333 8.68 0.00 36.29 3.13
688 1420 7.863901 ATTAGGCTATAGACACATCTTTCCT 57.136 36.000 8.68 1.12 36.29 3.36
689 1421 7.676683 TTAGGCTATAGACACATCTTTCCTT 57.323 36.000 8.68 0.00 36.29 3.36
690 1422 5.923204 AGGCTATAGACACATCTTTCCTTG 58.077 41.667 8.68 0.00 36.29 3.61
691 1423 5.663106 AGGCTATAGACACATCTTTCCTTGA 59.337 40.000 8.68 0.00 36.29 3.02
693 1425 7.510685 AGGCTATAGACACATCTTTCCTTGATA 59.489 37.037 8.68 0.00 36.29 2.15
694 1426 8.317679 GGCTATAGACACATCTTTCCTTGATAT 58.682 37.037 3.21 0.00 36.29 1.63
695 1427 9.149225 GCTATAGACACATCTTTCCTTGATATG 57.851 37.037 3.21 0.00 36.29 1.78
700 1432 6.990341 CACATCTTTCCTTGATATGTGTGA 57.010 37.500 0.00 0.00 41.46 3.58
701 1433 7.563888 CACATCTTTCCTTGATATGTGTGAT 57.436 36.000 0.00 0.00 41.46 3.06
703 1435 7.066645 CACATCTTTCCTTGATATGTGTGATGT 59.933 37.037 0.00 0.00 41.46 3.06
704 1436 7.613022 ACATCTTTCCTTGATATGTGTGATGTT 59.387 33.333 0.00 0.00 37.94 2.71
706 1438 8.492673 TCTTTCCTTGATATGTGTGATGTTAC 57.507 34.615 0.00 0.00 0.00 2.50
707 1439 8.321353 TCTTTCCTTGATATGTGTGATGTTACT 58.679 33.333 0.00 0.00 0.00 2.24
710 1442 7.795047 TCCTTGATATGTGTGATGTTACTCAT 58.205 34.615 0.00 0.00 38.11 2.90
711 1443 8.923270 TCCTTGATATGTGTGATGTTACTCATA 58.077 33.333 0.00 0.00 39.73 2.15
713 1445 9.755804 CTTGATATGTGTGATGTTACTCATACT 57.244 33.333 10.75 3.32 38.84 2.12
719 1451 8.803397 TGTGTGATGTTACTCATACTACTAGT 57.197 34.615 0.00 0.00 37.92 2.57
720 1452 9.895138 TGTGTGATGTTACTCATACTACTAGTA 57.105 33.333 1.89 1.89 37.92 1.82
742 1474 7.213216 GTAACTAGCTATGTTACTACTCCCC 57.787 44.000 24.17 8.39 43.56 4.81
743 1475 5.666474 ACTAGCTATGTTACTACTCCCCT 57.334 43.478 0.00 0.00 0.00 4.79
744 1476 5.633117 ACTAGCTATGTTACTACTCCCCTC 58.367 45.833 0.00 0.00 0.00 4.30
745 1477 4.817874 AGCTATGTTACTACTCCCCTCT 57.182 45.455 0.00 0.00 0.00 3.69
746 1478 5.145513 AGCTATGTTACTACTCCCCTCTT 57.854 43.478 0.00 0.00 0.00 2.85
747 1479 5.530243 AGCTATGTTACTACTCCCCTCTTT 58.470 41.667 0.00 0.00 0.00 2.52
748 1480 5.965091 AGCTATGTTACTACTCCCCTCTTTT 59.035 40.000 0.00 0.00 0.00 2.27
750 1482 6.762187 GCTATGTTACTACTCCCCTCTTTTTC 59.238 42.308 0.00 0.00 0.00 2.29
751 1483 6.954352 ATGTTACTACTCCCCTCTTTTTCT 57.046 37.500 0.00 0.00 0.00 2.52
752 1484 6.758806 TGTTACTACTCCCCTCTTTTTCTT 57.241 37.500 0.00 0.00 0.00 2.52
753 1485 6.766429 TGTTACTACTCCCCTCTTTTTCTTC 58.234 40.000 0.00 0.00 0.00 2.87
755 1487 7.017254 TGTTACTACTCCCCTCTTTTTCTTCAT 59.983 37.037 0.00 0.00 0.00 2.57
756 1488 6.455690 ACTACTCCCCTCTTTTTCTTCATT 57.544 37.500 0.00 0.00 0.00 2.57
758 1490 7.985589 ACTACTCCCCTCTTTTTCTTCATTTA 58.014 34.615 0.00 0.00 0.00 1.40
759 1491 8.615705 ACTACTCCCCTCTTTTTCTTCATTTAT 58.384 33.333 0.00 0.00 0.00 1.40
760 1492 9.467796 CTACTCCCCTCTTTTTCTTCATTTATT 57.532 33.333 0.00 0.00 0.00 1.40
762 1494 8.807118 ACTCCCCTCTTTTTCTTCATTTATTTC 58.193 33.333 0.00 0.00 0.00 2.17
763 1495 8.956446 TCCCCTCTTTTTCTTCATTTATTTCT 57.044 30.769 0.00 0.00 0.00 2.52
764 1496 9.379770 TCCCCTCTTTTTCTTCATTTATTTCTT 57.620 29.630 0.00 0.00 0.00 2.52
766 1498 8.929746 CCCTCTTTTTCTTCATTTATTTCTTGC 58.070 33.333 0.00 0.00 0.00 4.01
767 1499 8.929746 CCTCTTTTTCTTCATTTATTTCTTGCC 58.070 33.333 0.00 0.00 0.00 4.52
768 1500 9.480053 CTCTTTTTCTTCATTTATTTCTTGCCA 57.520 29.630 0.00 0.00 0.00 4.92
770 1502 8.954950 TTTTTCTTCATTTATTTCTTGCCACA 57.045 26.923 0.00 0.00 0.00 4.17
772 1504 8.761575 TTTCTTCATTTATTTCTTGCCACATC 57.238 30.769 0.00 0.00 0.00 3.06
773 1505 7.465353 TCTTCATTTATTTCTTGCCACATCA 57.535 32.000 0.00 0.00 0.00 3.07
774 1506 8.070034 TCTTCATTTATTTCTTGCCACATCAT 57.930 30.769 0.00 0.00 0.00 2.45
775 1507 8.192774 TCTTCATTTATTTCTTGCCACATCATC 58.807 33.333 0.00 0.00 0.00 2.92
776 1508 7.649533 TCATTTATTTCTTGCCACATCATCT 57.350 32.000 0.00 0.00 0.00 2.90
777 1509 8.750515 TCATTTATTTCTTGCCACATCATCTA 57.249 30.769 0.00 0.00 0.00 1.98
778 1510 8.623903 TCATTTATTTCTTGCCACATCATCTAC 58.376 33.333 0.00 0.00 0.00 2.59
780 1512 8.579850 TTTATTTCTTGCCACATCATCTACTT 57.420 30.769 0.00 0.00 0.00 2.24
782 1514 9.679661 TTATTTCTTGCCACATCATCTACTTTA 57.320 29.630 0.00 0.00 0.00 1.85
784 1516 7.792374 TTCTTGCCACATCATCTACTTTATC 57.208 36.000 0.00 0.00 0.00 1.75
785 1517 7.129457 TCTTGCCACATCATCTACTTTATCT 57.871 36.000 0.00 0.00 0.00 1.98
786 1518 8.250143 TCTTGCCACATCATCTACTTTATCTA 57.750 34.615 0.00 0.00 0.00 1.98
787 1519 8.704668 TCTTGCCACATCATCTACTTTATCTAA 58.295 33.333 0.00 0.00 0.00 2.10
788 1520 9.330063 CTTGCCACATCATCTACTTTATCTAAA 57.670 33.333 0.00 0.00 0.00 1.85
828 1560 9.830186 ACTATCTATGTTATTCCTACTGTGGAT 57.170 33.333 0.00 0.00 35.83 3.41
831 1563 9.830186 ATCTATGTTATTCCTACTGTGGATAGT 57.170 33.333 0.00 0.00 35.83 2.12
1074 3353 3.676605 TCGTGCATCGTGGACCGT 61.677 61.111 8.22 0.00 35.09 4.83
1323 3602 1.258445 CCCTACTTCACCTCCGCACT 61.258 60.000 0.00 0.00 0.00 4.40
1978 4353 0.369589 CCTCGACGACGTCTACACTC 59.630 60.000 24.36 0.00 40.69 3.51
1989 4364 1.219124 CTACACTCGCAGGCCACAT 59.781 57.895 5.01 0.00 0.00 3.21
2014 4389 2.166664 GTCGTCCAGCAGAAGGAGTATT 59.833 50.000 0.00 0.00 35.42 1.89
2168 9054 1.637338 TGAGGCGGCTCATCATAGAT 58.363 50.000 35.14 0.00 29.45 1.98
2253 9150 4.854839 GCGTTTCTTTGTTGTTGTACTTGT 59.145 37.500 0.00 0.00 0.00 3.16
2257 9154 5.968528 TCTTTGTTGTTGTACTTGTTGGT 57.031 34.783 0.00 0.00 0.00 3.67
2260 9157 5.455056 TTGTTGTTGTACTTGTTGGTTGT 57.545 34.783 0.00 0.00 0.00 3.32
2261 9158 5.049398 TGTTGTTGTACTTGTTGGTTGTC 57.951 39.130 0.00 0.00 0.00 3.18
2262 9159 4.092816 GTTGTTGTACTTGTTGGTTGTCG 58.907 43.478 0.00 0.00 0.00 4.35
2263 9160 3.336468 TGTTGTACTTGTTGGTTGTCGT 58.664 40.909 0.00 0.00 0.00 4.34
2264 9161 3.371591 TGTTGTACTTGTTGGTTGTCGTC 59.628 43.478 0.00 0.00 0.00 4.20
2265 9162 2.195096 TGTACTTGTTGGTTGTCGTCG 58.805 47.619 0.00 0.00 0.00 5.12
2266 9163 2.195922 GTACTTGTTGGTTGTCGTCGT 58.804 47.619 0.00 0.00 0.00 4.34
2341 9268 2.045586 TGTATGTCGTCGTTGTTGTCG 58.954 47.619 0.00 0.00 0.00 4.35
2342 9269 2.046313 GTATGTCGTCGTTGTTGTCGT 58.954 47.619 0.00 0.00 0.00 4.34
2343 9270 1.126079 ATGTCGTCGTTGTTGTCGTC 58.874 50.000 0.00 0.00 0.00 4.20
2344 9271 0.179169 TGTCGTCGTTGTTGTCGTCA 60.179 50.000 0.00 0.00 0.00 4.35
2345 9272 0.497265 GTCGTCGTTGTTGTCGTCAG 59.503 55.000 0.00 0.00 0.00 3.51
2346 9273 0.099259 TCGTCGTTGTTGTCGTCAGT 59.901 50.000 0.00 0.00 0.00 3.41
2347 9274 0.918619 CGTCGTTGTTGTCGTCAGTT 59.081 50.000 0.00 0.00 0.00 3.16
2348 9275 2.110990 CGTCGTTGTTGTCGTCAGTTA 58.889 47.619 0.00 0.00 0.00 2.24
2418 9349 6.599356 TGTCAACTATTTAGACTGCTACCA 57.401 37.500 0.00 0.00 33.56 3.25
2419 9350 7.182817 TGTCAACTATTTAGACTGCTACCAT 57.817 36.000 0.00 0.00 33.56 3.55
2420 9351 8.301252 TGTCAACTATTTAGACTGCTACCATA 57.699 34.615 0.00 0.00 33.56 2.74
2421 9352 8.924303 TGTCAACTATTTAGACTGCTACCATAT 58.076 33.333 0.00 0.00 33.56 1.78
2422 9353 9.197694 GTCAACTATTTAGACTGCTACCATATG 57.802 37.037 0.00 0.00 0.00 1.78
2425 9358 7.911651 ACTATTTAGACTGCTACCATATGCAT 58.088 34.615 3.79 3.79 38.59 3.96
2433 9366 5.186021 ACTGCTACCATATGCATCTACCTAC 59.814 44.000 0.19 0.00 38.59 3.18
2519 10690 1.006391 CGCCGTATTTTCAGTACTGCG 60.006 52.381 18.45 13.76 44.71 5.18
2652 13447 8.512956 AGCTGCAACTGAATATTTGATGATATC 58.487 33.333 1.02 0.00 0.00 1.63
2795 13777 4.083484 CGAAACGGAGGTAAAAGATTTGCT 60.083 41.667 0.00 0.00 0.00 3.91
2800 13782 5.123979 ACGGAGGTAAAAGATTTGCTTCATC 59.876 40.000 5.67 0.00 35.24 2.92
2839 13824 9.699703 AGTTAAGAGTTGCTTTTACAAACAAAA 57.300 25.926 0.00 0.00 38.05 2.44
2871 13856 7.203910 AGATTATTACAAAGCCACTACTCTCG 58.796 38.462 0.00 0.00 0.00 4.04
2881 13866 0.031314 ACTACTCTCGCGGCATGATG 59.969 55.000 6.13 0.00 0.00 3.07
2882 13867 0.031314 CTACTCTCGCGGCATGATGT 59.969 55.000 6.13 0.00 0.00 3.06
2883 13868 0.459899 TACTCTCGCGGCATGATGTT 59.540 50.000 6.13 0.00 0.00 2.71
2884 13869 0.391661 ACTCTCGCGGCATGATGTTT 60.392 50.000 6.13 0.00 0.00 2.83
2885 13870 0.302890 CTCTCGCGGCATGATGTTTC 59.697 55.000 6.13 0.00 0.00 2.78
2886 13871 1.089481 TCTCGCGGCATGATGTTTCC 61.089 55.000 6.13 0.00 0.00 3.13
2887 13872 2.051804 CTCGCGGCATGATGTTTCCC 62.052 60.000 6.13 0.00 0.00 3.97
2888 13873 2.405805 CGCGGCATGATGTTTCCCA 61.406 57.895 0.00 0.00 0.00 4.37
2889 13874 1.889454 GCGGCATGATGTTTCCCAA 59.111 52.632 0.00 0.00 0.00 4.12
2890 13875 0.179129 GCGGCATGATGTTTCCCAAG 60.179 55.000 0.00 0.00 0.00 3.61
2891 13876 1.176527 CGGCATGATGTTTCCCAAGT 58.823 50.000 0.00 0.00 0.00 3.16
2892 13877 1.135315 CGGCATGATGTTTCCCAAGTG 60.135 52.381 0.00 0.00 0.00 3.16
2893 13878 1.404583 GGCATGATGTTTCCCAAGTGC 60.405 52.381 0.00 0.00 0.00 4.40
2894 13879 1.404583 GCATGATGTTTCCCAAGTGCC 60.405 52.381 0.00 0.00 0.00 5.01
2895 13880 2.173519 CATGATGTTTCCCAAGTGCCT 58.826 47.619 0.00 0.00 0.00 4.75
2896 13881 1.909700 TGATGTTTCCCAAGTGCCTC 58.090 50.000 0.00 0.00 0.00 4.70
2897 13882 0.804989 GATGTTTCCCAAGTGCCTCG 59.195 55.000 0.00 0.00 0.00 4.63
2898 13883 1.244019 ATGTTTCCCAAGTGCCTCGC 61.244 55.000 0.00 0.00 0.00 5.03
2899 13884 2.668212 TTTCCCAAGTGCCTCGCG 60.668 61.111 0.00 0.00 0.00 5.87
2925 13910 1.610886 GGTGACCCAAAGTGTAGCCTC 60.611 57.143 0.00 0.00 0.00 4.70
2926 13911 1.071699 GTGACCCAAAGTGTAGCCTCA 59.928 52.381 0.00 0.00 0.00 3.86
2955 13940 3.104512 TGTTGGAGAGGATAATGGACGT 58.895 45.455 0.00 0.00 0.00 4.34
2958 13943 3.371034 TGGAGAGGATAATGGACGTGAA 58.629 45.455 0.00 0.00 0.00 3.18
2960 13945 3.372954 GAGAGGATAATGGACGTGAACG 58.627 50.000 0.00 0.40 46.33 3.95
2992 13977 3.242772 GCCTAAAAACTCTAGCATTCCGC 60.243 47.826 0.00 0.00 42.91 5.54
3016 14001 2.858260 GCACCAAATCGTCCAACAAGTG 60.858 50.000 0.00 0.00 0.00 3.16
3025 14010 1.267806 GTCCAACAAGTGAGCATGGTG 59.732 52.381 0.00 0.00 34.00 4.17
3051 14036 3.508840 CATCGCCTTCCGGTTGCC 61.509 66.667 0.00 0.00 37.59 4.52
3082 14067 4.948847 TCTCGGACATATTGATTCACCAG 58.051 43.478 0.00 0.00 0.00 4.00
3089 14074 6.065976 ACATATTGATTCACCAGTCCTTGA 57.934 37.500 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 0.465705 ATCAGGTGGTGCTACATCCG 59.534 55.000 0.00 0.00 0.00 4.18
72 73 1.571215 GGCCAACGAGTTACAACCGG 61.571 60.000 0.00 0.00 0.00 5.28
92 93 2.461110 CCATGGCGCTACAACCGAC 61.461 63.158 7.64 0.00 0.00 4.79
198 200 1.141019 TGGAGAGCGCCATTACGAC 59.859 57.895 2.29 0.00 31.66 4.34
202 204 1.153369 GCTGTGGAGAGCGCCATTA 60.153 57.895 2.29 0.00 40.68 1.90
256 258 2.654912 CGCACACGAAGGACCGAAC 61.655 63.158 0.00 0.00 43.93 3.95
283 285 1.001393 ACGGGCCATCGTTGGATTT 60.001 52.632 16.83 0.00 46.92 2.17
355 357 1.913262 ATCCTCCACAGCCACACGA 60.913 57.895 0.00 0.00 0.00 4.35
463 890 2.978010 CACTTTCGGCCGGTTGCT 60.978 61.111 27.83 0.80 40.92 3.91
512 1244 6.693978 ACGTTTTTGTTGTGCCTATTTTACTC 59.306 34.615 0.00 0.00 0.00 2.59
515 1247 6.253727 CACACGTTTTTGTTGTGCCTATTTTA 59.746 34.615 0.00 0.00 37.11 1.52
539 1271 3.694043 TGTGGCTAGTCTTATTGCACA 57.306 42.857 0.00 0.00 0.00 4.57
546 1278 4.359105 ACTACCCATTGTGGCTAGTCTTA 58.641 43.478 0.00 0.00 35.79 2.10
548 1280 2.834113 ACTACCCATTGTGGCTAGTCT 58.166 47.619 0.00 0.00 35.79 3.24
549 1281 4.081309 TGTTACTACCCATTGTGGCTAGTC 60.081 45.833 7.13 0.00 35.79 2.59
550 1282 3.841845 TGTTACTACCCATTGTGGCTAGT 59.158 43.478 8.55 8.55 35.79 2.57
551 1283 4.481368 TGTTACTACCCATTGTGGCTAG 57.519 45.455 0.00 0.00 35.79 3.42
552 1284 5.900699 TCTATGTTACTACCCATTGTGGCTA 59.099 40.000 0.00 0.00 35.79 3.93
554 1286 4.814771 GTCTATGTTACTACCCATTGTGGC 59.185 45.833 0.00 0.00 35.79 5.01
555 1287 6.235231 AGTCTATGTTACTACCCATTGTGG 57.765 41.667 0.00 0.00 37.25 4.17
556 1288 8.008513 ACTAGTCTATGTTACTACCCATTGTG 57.991 38.462 0.00 0.00 0.00 3.33
557 1289 9.705103 TTACTAGTCTATGTTACTACCCATTGT 57.295 33.333 0.00 0.00 0.00 2.71
558 1290 9.962783 GTTACTAGTCTATGTTACTACCCATTG 57.037 37.037 0.00 0.00 0.00 2.82
559 1291 9.705103 TGTTACTAGTCTATGTTACTACCCATT 57.295 33.333 0.00 0.00 0.00 3.16
560 1292 9.878737 ATGTTACTAGTCTATGTTACTACCCAT 57.121 33.333 0.00 0.00 0.00 4.00
561 1293 9.128404 CATGTTACTAGTCTATGTTACTACCCA 57.872 37.037 0.00 0.00 0.00 4.51
562 1294 8.574737 CCATGTTACTAGTCTATGTTACTACCC 58.425 40.741 0.00 0.00 0.00 3.69
563 1295 9.129532 ACCATGTTACTAGTCTATGTTACTACC 57.870 37.037 0.00 0.00 0.00 3.18
566 1298 7.123697 TGCACCATGTTACTAGTCTATGTTACT 59.876 37.037 0.00 0.00 0.00 2.24
567 1299 7.262772 TGCACCATGTTACTAGTCTATGTTAC 58.737 38.462 0.00 0.00 0.00 2.50
569 1301 6.294361 TGCACCATGTTACTAGTCTATGTT 57.706 37.500 0.00 0.00 0.00 2.71
570 1302 5.932619 TGCACCATGTTACTAGTCTATGT 57.067 39.130 0.00 0.00 0.00 2.29
571 1303 6.775939 CATGCACCATGTTACTAGTCTATG 57.224 41.667 0.00 2.86 37.12 2.23
584 1316 6.283694 ACATAGACTAGTAACATGCACCATG 58.716 40.000 0.00 3.80 46.18 3.66
585 1317 6.485830 ACATAGACTAGTAACATGCACCAT 57.514 37.500 0.00 0.00 0.00 3.55
586 1318 5.932619 ACATAGACTAGTAACATGCACCA 57.067 39.130 0.00 0.00 0.00 4.17
587 1319 7.490000 AGTAACATAGACTAGTAACATGCACC 58.510 38.462 0.00 0.00 0.00 5.01
588 1320 9.448294 GTAGTAACATAGACTAGTAACATGCAC 57.552 37.037 0.00 2.46 30.08 4.57
589 1321 8.627403 GGTAGTAACATAGACTAGTAACATGCA 58.373 37.037 0.00 0.00 30.08 3.96
600 1332 8.947305 ACCACTATAGAGGTAGTAACATAGACT 58.053 37.037 19.09 0.00 37.24 3.24
601 1333 9.001542 CACCACTATAGAGGTAGTAACATAGAC 57.998 40.741 19.92 0.00 36.88 2.59
602 1334 8.942033 TCACCACTATAGAGGTAGTAACATAGA 58.058 37.037 19.92 8.43 36.88 1.98
603 1335 9.221933 CTCACCACTATAGAGGTAGTAACATAG 57.778 40.741 19.92 6.41 36.88 2.23
604 1336 8.721479 ACTCACCACTATAGAGGTAGTAACATA 58.279 37.037 19.92 0.84 36.88 2.29
607 1339 8.835439 GTTACTCACCACTATAGAGGTAGTAAC 58.165 40.741 31.61 31.61 41.27 2.50
609 1341 8.094284 TGTTACTCACCACTATAGAGGTAGTA 57.906 38.462 19.92 20.66 36.88 1.82
610 1342 6.966751 TGTTACTCACCACTATAGAGGTAGT 58.033 40.000 19.92 21.43 36.88 2.73
613 1345 8.005388 ACATATGTTACTCACCACTATAGAGGT 58.995 37.037 15.41 15.41 39.64 3.85
614 1346 8.300286 CACATATGTTACTCACCACTATAGAGG 58.700 40.741 14.07 14.07 33.76 3.69
615 1347 8.851145 ACACATATGTTACTCACCACTATAGAG 58.149 37.037 5.37 0.00 34.46 2.43
617 1349 7.803659 CGACACATATGTTACTCACCACTATAG 59.196 40.741 5.37 0.00 39.95 1.31
618 1350 7.283807 ACGACACATATGTTACTCACCACTATA 59.716 37.037 5.37 0.00 39.95 1.31
620 1352 5.416639 ACGACACATATGTTACTCACCACTA 59.583 40.000 5.37 0.00 39.95 2.74
621 1353 4.219944 ACGACACATATGTTACTCACCACT 59.780 41.667 5.37 0.00 39.95 4.00
622 1354 4.491676 ACGACACATATGTTACTCACCAC 58.508 43.478 5.37 0.00 39.95 4.16
623 1355 4.794278 ACGACACATATGTTACTCACCA 57.206 40.909 5.37 0.00 39.95 4.17
624 1356 6.094719 TGTTACGACACATATGTTACTCACC 58.905 40.000 5.37 0.00 39.95 4.02
625 1357 7.609632 CATGTTACGACACATATGTTACTCAC 58.390 38.462 5.37 0.14 39.95 3.51
626 1358 6.254804 GCATGTTACGACACATATGTTACTCA 59.745 38.462 5.37 0.54 39.95 3.41
627 1359 6.254804 TGCATGTTACGACACATATGTTACTC 59.745 38.462 5.37 0.45 39.95 2.59
628 1360 6.103330 TGCATGTTACGACACATATGTTACT 58.897 36.000 5.37 0.00 39.95 2.24
630 1362 6.369065 TGTTGCATGTTACGACACATATGTTA 59.631 34.615 5.37 0.00 39.95 2.41
631 1363 5.180304 TGTTGCATGTTACGACACATATGTT 59.820 36.000 5.37 0.00 39.95 2.71
632 1364 4.693095 TGTTGCATGTTACGACACATATGT 59.307 37.500 1.41 1.41 43.71 2.29
633 1365 5.215239 TGTTGCATGTTACGACACATATG 57.785 39.130 0.00 0.00 38.91 1.78
639 1371 5.933187 ATAAAGTGTTGCATGTTACGACA 57.067 34.783 0.00 0.00 40.71 4.35
644 1376 9.796120 GCCTAATAAATAAAGTGTTGCATGTTA 57.204 29.630 0.00 0.00 0.00 2.41
645 1377 8.531146 AGCCTAATAAATAAAGTGTTGCATGTT 58.469 29.630 0.00 0.00 0.00 2.71
646 1378 8.066612 AGCCTAATAAATAAAGTGTTGCATGT 57.933 30.769 0.00 0.00 0.00 3.21
663 1395 8.958060 AGGAAAGATGTGTCTATAGCCTAATA 57.042 34.615 0.00 0.00 33.30 0.98
664 1396 7.863901 AGGAAAGATGTGTCTATAGCCTAAT 57.136 36.000 0.00 0.00 33.30 1.73
665 1397 7.344612 TCAAGGAAAGATGTGTCTATAGCCTAA 59.655 37.037 0.00 0.00 33.30 2.69
666 1398 6.839134 TCAAGGAAAGATGTGTCTATAGCCTA 59.161 38.462 0.00 0.00 33.30 3.93
667 1399 5.663106 TCAAGGAAAGATGTGTCTATAGCCT 59.337 40.000 0.00 0.00 33.30 4.58
668 1400 5.918608 TCAAGGAAAGATGTGTCTATAGCC 58.081 41.667 0.00 0.00 33.30 3.93
669 1401 9.149225 CATATCAAGGAAAGATGTGTCTATAGC 57.851 37.037 0.00 0.00 33.30 2.97
671 1403 9.987272 CACATATCAAGGAAAGATGTGTCTATA 57.013 33.333 3.12 0.00 43.18 1.31
672 1404 8.899427 CACATATCAAGGAAAGATGTGTCTAT 57.101 34.615 3.12 0.00 43.18 1.98
679 1411 7.563888 ACATCACACATATCAAGGAAAGATG 57.436 36.000 0.00 0.00 36.24 2.90
680 1412 9.113838 GTAACATCACACATATCAAGGAAAGAT 57.886 33.333 0.00 0.00 0.00 2.40
681 1413 8.321353 AGTAACATCACACATATCAAGGAAAGA 58.679 33.333 0.00 0.00 0.00 2.52
685 1417 7.181569 TGAGTAACATCACACATATCAAGGA 57.818 36.000 0.00 0.00 0.00 3.36
686 1418 8.982685 GTATGAGTAACATCACACATATCAAGG 58.017 37.037 0.00 0.00 40.07 3.61
687 1419 9.755804 AGTATGAGTAACATCACACATATCAAG 57.244 33.333 0.00 0.00 40.07 3.02
693 1425 9.409918 ACTAGTAGTATGAGTAACATCACACAT 57.590 33.333 0.00 0.00 40.07 3.21
694 1426 8.803397 ACTAGTAGTATGAGTAACATCACACA 57.197 34.615 0.00 0.00 40.07 3.72
719 1451 7.073470 AGAGGGGAGTAGTAACATAGCTAGTTA 59.927 40.741 0.00 5.74 0.00 2.24
720 1452 6.028258 AGGGGAGTAGTAACATAGCTAGTT 57.972 41.667 0.00 6.69 0.00 2.24
721 1453 5.373257 AGAGGGGAGTAGTAACATAGCTAGT 59.627 44.000 0.00 0.00 0.00 2.57
724 1456 4.817874 AGAGGGGAGTAGTAACATAGCT 57.182 45.455 0.00 0.00 0.00 3.32
725 1457 5.873146 AAAGAGGGGAGTAGTAACATAGC 57.127 43.478 0.00 0.00 0.00 2.97
726 1458 8.080363 AGAAAAAGAGGGGAGTAGTAACATAG 57.920 38.462 0.00 0.00 0.00 2.23
727 1459 8.445361 AAGAAAAAGAGGGGAGTAGTAACATA 57.555 34.615 0.00 0.00 0.00 2.29
728 1460 6.954352 AGAAAAAGAGGGGAGTAGTAACAT 57.046 37.500 0.00 0.00 0.00 2.71
730 1462 6.766429 TGAAGAAAAAGAGGGGAGTAGTAAC 58.234 40.000 0.00 0.00 0.00 2.50
732 1464 7.569599 AATGAAGAAAAAGAGGGGAGTAGTA 57.430 36.000 0.00 0.00 0.00 1.82
733 1465 6.455690 AATGAAGAAAAAGAGGGGAGTAGT 57.544 37.500 0.00 0.00 0.00 2.73
734 1466 9.467796 AATAAATGAAGAAAAAGAGGGGAGTAG 57.532 33.333 0.00 0.00 0.00 2.57
735 1467 9.822727 AAATAAATGAAGAAAAAGAGGGGAGTA 57.177 29.630 0.00 0.00 0.00 2.59
737 1469 9.029368 AGAAATAAATGAAGAAAAAGAGGGGAG 57.971 33.333 0.00 0.00 0.00 4.30
738 1470 8.956446 AGAAATAAATGAAGAAAAAGAGGGGA 57.044 30.769 0.00 0.00 0.00 4.81
739 1471 9.428097 CAAGAAATAAATGAAGAAAAAGAGGGG 57.572 33.333 0.00 0.00 0.00 4.79
741 1473 8.929746 GGCAAGAAATAAATGAAGAAAAAGAGG 58.070 33.333 0.00 0.00 0.00 3.69
742 1474 9.480053 TGGCAAGAAATAAATGAAGAAAAAGAG 57.520 29.630 0.00 0.00 0.00 2.85
743 1475 9.260002 GTGGCAAGAAATAAATGAAGAAAAAGA 57.740 29.630 0.00 0.00 0.00 2.52
744 1476 9.044150 TGTGGCAAGAAATAAATGAAGAAAAAG 57.956 29.630 0.00 0.00 0.00 2.27
745 1477 8.954950 TGTGGCAAGAAATAAATGAAGAAAAA 57.045 26.923 0.00 0.00 0.00 1.94
746 1478 9.206870 GATGTGGCAAGAAATAAATGAAGAAAA 57.793 29.630 0.00 0.00 0.00 2.29
747 1479 8.366401 TGATGTGGCAAGAAATAAATGAAGAAA 58.634 29.630 0.00 0.00 0.00 2.52
748 1480 7.894708 TGATGTGGCAAGAAATAAATGAAGAA 58.105 30.769 0.00 0.00 0.00 2.52
750 1482 8.195436 AGATGATGTGGCAAGAAATAAATGAAG 58.805 33.333 0.00 0.00 0.00 3.02
751 1483 8.070034 AGATGATGTGGCAAGAAATAAATGAA 57.930 30.769 0.00 0.00 0.00 2.57
752 1484 7.649533 AGATGATGTGGCAAGAAATAAATGA 57.350 32.000 0.00 0.00 0.00 2.57
753 1485 8.627403 AGTAGATGATGTGGCAAGAAATAAATG 58.373 33.333 0.00 0.00 0.00 2.32
755 1487 8.579850 AAGTAGATGATGTGGCAAGAAATAAA 57.420 30.769 0.00 0.00 0.00 1.40
756 1488 8.579850 AAAGTAGATGATGTGGCAAGAAATAA 57.420 30.769 0.00 0.00 0.00 1.40
758 1490 8.757982 ATAAAGTAGATGATGTGGCAAGAAAT 57.242 30.769 0.00 0.00 0.00 2.17
759 1491 8.049117 AGATAAAGTAGATGATGTGGCAAGAAA 58.951 33.333 0.00 0.00 0.00 2.52
760 1492 7.568349 AGATAAAGTAGATGATGTGGCAAGAA 58.432 34.615 0.00 0.00 0.00 2.52
762 1494 8.893219 TTAGATAAAGTAGATGATGTGGCAAG 57.107 34.615 0.00 0.00 0.00 4.01
763 1495 9.851686 ATTTAGATAAAGTAGATGATGTGGCAA 57.148 29.630 0.00 0.00 0.00 4.52
805 1537 9.830186 ACTATCCACAGTAGGAATAACATAGAT 57.170 33.333 0.00 0.00 41.92 1.98
806 1538 9.298250 GACTATCCACAGTAGGAATAACATAGA 57.702 37.037 0.00 0.00 41.92 1.98
807 1539 9.303116 AGACTATCCACAGTAGGAATAACATAG 57.697 37.037 0.00 0.00 41.92 2.23
809 1541 9.656323 TTAGACTATCCACAGTAGGAATAACAT 57.344 33.333 0.00 0.00 41.92 2.71
813 1545 9.144298 CCTTTTAGACTATCCACAGTAGGAATA 57.856 37.037 0.00 0.00 41.92 1.75
814 1546 7.071321 CCCTTTTAGACTATCCACAGTAGGAAT 59.929 40.741 0.00 0.00 41.92 3.01
815 1547 6.383147 CCCTTTTAGACTATCCACAGTAGGAA 59.617 42.308 0.00 0.00 41.92 3.36
816 1548 5.897824 CCCTTTTAGACTATCCACAGTAGGA 59.102 44.000 0.00 0.00 43.01 2.94
817 1549 5.897824 TCCCTTTTAGACTATCCACAGTAGG 59.102 44.000 0.00 0.00 0.00 3.18
818 1550 7.604657 ATCCCTTTTAGACTATCCACAGTAG 57.395 40.000 0.00 0.00 0.00 2.57
819 1551 7.635089 GCAATCCCTTTTAGACTATCCACAGTA 60.635 40.741 0.00 0.00 0.00 2.74
820 1552 6.653989 CAATCCCTTTTAGACTATCCACAGT 58.346 40.000 0.00 0.00 0.00 3.55
821 1553 5.529060 GCAATCCCTTTTAGACTATCCACAG 59.471 44.000 0.00 0.00 0.00 3.66
822 1554 5.437060 GCAATCCCTTTTAGACTATCCACA 58.563 41.667 0.00 0.00 0.00 4.17
823 1555 4.822350 GGCAATCCCTTTTAGACTATCCAC 59.178 45.833 0.00 0.00 0.00 4.02
824 1556 4.476846 TGGCAATCCCTTTTAGACTATCCA 59.523 41.667 0.00 0.00 0.00 3.41
825 1557 5.048846 TGGCAATCCCTTTTAGACTATCC 57.951 43.478 0.00 0.00 0.00 2.59
826 1558 5.066593 CCTGGCAATCCCTTTTAGACTATC 58.933 45.833 0.00 0.00 0.00 2.08
827 1559 4.141158 CCCTGGCAATCCCTTTTAGACTAT 60.141 45.833 0.00 0.00 0.00 2.12
828 1560 3.202151 CCCTGGCAATCCCTTTTAGACTA 59.798 47.826 0.00 0.00 0.00 2.59
829 1561 2.024941 CCCTGGCAATCCCTTTTAGACT 60.025 50.000 0.00 0.00 0.00 3.24
830 1562 2.025321 TCCCTGGCAATCCCTTTTAGAC 60.025 50.000 0.00 0.00 0.00 2.59
831 1563 2.025321 GTCCCTGGCAATCCCTTTTAGA 60.025 50.000 0.00 0.00 0.00 2.10
1978 4353 2.167219 CGACACTATGTGGCCTGCG 61.167 63.158 3.32 0.00 38.55 5.18
1989 4364 0.888619 CCTTCTGCTGGACGACACTA 59.111 55.000 0.00 0.00 0.00 2.74
2045 4420 2.827190 CGATCTCGTCGGGGACCA 60.827 66.667 0.00 0.00 46.47 4.02
2142 9020 1.301716 TGAGCCGCCTCAAACTGAC 60.302 57.895 0.00 0.00 44.79 3.51
2143 9021 3.147132 TGAGCCGCCTCAAACTGA 58.853 55.556 0.00 0.00 44.79 3.41
2253 9150 0.391395 ACCACAACGACGACAACCAA 60.391 50.000 0.00 0.00 0.00 3.67
2257 9154 1.135527 AGAGAACCACAACGACGACAA 59.864 47.619 0.00 0.00 0.00 3.18
2260 9157 0.596600 GCAGAGAACCACAACGACGA 60.597 55.000 0.00 0.00 0.00 4.20
2261 9158 0.874175 TGCAGAGAACCACAACGACG 60.874 55.000 0.00 0.00 0.00 5.12
2262 9159 1.512926 ATGCAGAGAACCACAACGAC 58.487 50.000 0.00 0.00 0.00 4.34
2263 9160 3.521560 GATATGCAGAGAACCACAACGA 58.478 45.455 0.00 0.00 0.00 3.85
2264 9161 2.609459 GGATATGCAGAGAACCACAACG 59.391 50.000 0.00 0.00 0.00 4.10
2265 9162 3.609853 TGGATATGCAGAGAACCACAAC 58.390 45.455 0.00 0.00 0.00 3.32
2266 9163 3.264193 ACTGGATATGCAGAGAACCACAA 59.736 43.478 28.65 0.00 0.00 3.33
2341 9268 5.858581 CAGCCTGCAAATTAAGTTAACTGAC 59.141 40.000 9.34 0.00 0.00 3.51
2342 9269 5.534654 ACAGCCTGCAAATTAAGTTAACTGA 59.465 36.000 9.34 0.00 0.00 3.41
2343 9270 5.772521 ACAGCCTGCAAATTAAGTTAACTG 58.227 37.500 9.34 0.00 0.00 3.16
2344 9271 6.405278 AACAGCCTGCAAATTAAGTTAACT 57.595 33.333 1.12 1.12 0.00 2.24
2345 9272 7.223777 TGAAAACAGCCTGCAAATTAAGTTAAC 59.776 33.333 0.00 0.00 0.00 2.01
2346 9273 7.268586 TGAAAACAGCCTGCAAATTAAGTTAA 58.731 30.769 0.00 0.00 0.00 2.01
2347 9274 6.810911 TGAAAACAGCCTGCAAATTAAGTTA 58.189 32.000 0.00 0.00 0.00 2.24
2348 9275 5.669477 TGAAAACAGCCTGCAAATTAAGTT 58.331 33.333 0.00 0.00 0.00 2.66
2420 9351 9.845740 TTAAACAACATATGTAGGTAGATGCAT 57.154 29.630 9.21 0.00 42.99 3.96
2421 9352 9.674068 TTTAAACAACATATGTAGGTAGATGCA 57.326 29.630 9.21 0.00 42.99 3.96
2519 10690 5.509272 CACACGATACAATCAGAAAATGTGC 59.491 40.000 0.00 0.00 0.00 4.57
2652 13447 9.639601 TCTTCAACATACAATCAGTACTAGTTG 57.360 33.333 0.00 14.54 40.71 3.16
2767 13749 6.812879 ATCTTTTACCTCCGTTTCGAAAAT 57.187 33.333 13.10 0.00 0.00 1.82
2768 13750 6.622833 AATCTTTTACCTCCGTTTCGAAAA 57.377 33.333 13.10 0.00 0.00 2.29
2769 13751 6.432107 CAAATCTTTTACCTCCGTTTCGAAA 58.568 36.000 6.47 6.47 0.00 3.46
2770 13752 5.561339 GCAAATCTTTTACCTCCGTTTCGAA 60.561 40.000 0.00 0.00 0.00 3.71
2778 13760 5.418840 TGGATGAAGCAAATCTTTTACCTCC 59.581 40.000 0.00 0.00 34.56 4.30
2839 13824 8.525290 AGTGGCTTTGTAATAATCTTATTGCT 57.475 30.769 10.68 0.00 36.89 3.91
2855 13840 1.078759 CCGCGAGAGTAGTGGCTTTG 61.079 60.000 8.23 0.00 32.08 2.77
2871 13856 0.179129 CTTGGGAAACATCATGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
2881 13866 2.954611 GCGAGGCACTTGGGAAAC 59.045 61.111 0.00 0.00 41.55 2.78
2900 13885 4.636435 ACTTTGGGTCACCGCCGG 62.636 66.667 0.00 0.00 40.75 6.13
2901 13886 2.718747 TACACTTTGGGTCACCGCCG 62.719 60.000 0.00 0.00 40.75 6.46
2902 13887 0.953960 CTACACTTTGGGTCACCGCC 60.954 60.000 0.00 0.00 40.75 6.13
2903 13888 1.574702 GCTACACTTTGGGTCACCGC 61.575 60.000 0.00 0.00 40.75 5.68
2904 13889 0.953960 GGCTACACTTTGGGTCACCG 60.954 60.000 0.00 0.00 40.75 4.94
2905 13890 0.400594 AGGCTACACTTTGGGTCACC 59.599 55.000 0.00 0.00 37.24 4.02
2925 13910 3.969287 TCCTCTCCAACATCAAGAGTG 57.031 47.619 0.00 0.00 35.76 3.51
2926 13911 6.409005 CCATTATCCTCTCCAACATCAAGAGT 60.409 42.308 0.00 0.00 35.76 3.24
2955 13940 0.753867 TAGGCACAAGTCCACGTTCA 59.246 50.000 0.00 0.00 0.00 3.18
2958 13943 2.335316 TTTTAGGCACAAGTCCACGT 57.665 45.000 0.00 0.00 0.00 4.49
2960 13945 3.883489 AGAGTTTTTAGGCACAAGTCCAC 59.117 43.478 0.00 0.00 0.00 4.02
2992 13977 0.165944 GTTGGACGATTTGGTGCGAG 59.834 55.000 0.00 0.00 0.00 5.03
2995 13980 1.336755 ACTTGTTGGACGATTTGGTGC 59.663 47.619 0.00 0.00 0.00 5.01
3016 14001 2.512515 GCGTCCCTCACCATGCTC 60.513 66.667 0.00 0.00 0.00 4.26
3025 14010 4.162690 AAGGCGATGGCGTCCCTC 62.163 66.667 14.61 0.12 44.82 4.30
3044 14029 1.927174 CGAGAAGAATACAGGCAACCG 59.073 52.381 0.00 0.00 37.17 4.44
3051 14036 8.824159 AATCAATATGTCCGAGAAGAATACAG 57.176 34.615 0.00 0.00 0.00 2.74
3082 14067 3.520290 TGATGACGTACCATCAAGGAC 57.480 47.619 15.39 0.00 46.88 3.85
3089 14074 2.166459 CACTGGACTGATGACGTACCAT 59.834 50.000 0.00 0.00 0.00 3.55
3095 14080 2.230025 ACTTCTCACTGGACTGATGACG 59.770 50.000 0.00 0.00 0.00 4.35
3103 14089 3.733337 ACATTGACACTTCTCACTGGAC 58.267 45.455 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.