Multiple sequence alignment - TraesCS2A01G589000

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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 TraesCS2A01G589000 chr2A 100.000 2655 0 0 1 2655 777840181 777837527 0.000000e+00 4903.0
1 TraesCS2A01G589000 chr2A 84.114 598 61 20 864 1435 777812796 777812207 5.000000e-152 547.0
2 TraesCS2A01G589000 chr2A 83.183 553 61 23 990 1521 777627293 777626752 6.650000e-131 477.0
3 TraesCS2A01G589000 chr2A 99.500 200 1 0 108 307 777819473 777819274 5.400000e-97 364.0
4 TraesCS2A01G589000 chr2A 89.781 274 15 3 360 623 777819267 777818997 3.270000e-89 339.0
5 TraesCS2A01G589000 chr2A 82.913 357 45 11 1731 2082 777810636 777810291 9.230000e-80 307.0
6 TraesCS2A01G589000 chr2A 92.432 185 11 1 991 1175 777615950 777615769 7.290000e-66 261.0
7 TraesCS2A01G589000 chr2A 89.865 148 15 0 679 826 777813748 777813601 9.700000e-45 191.0
8 TraesCS2A01G589000 chr2A 88.125 160 17 2 424 582 777813955 777813797 3.490000e-44 189.0
9 TraesCS2A01G589000 chr2A 86.905 168 10 7 1298 1461 777810924 777810765 7.550000e-41 178.0
10 TraesCS2A01G589000 chr2A 86.538 156 5 1 3 142 777816211 777816056 9.840000e-35 158.0
11 TraesCS2A01G589000 chr2A 91.228 114 10 0 192 305 777814403 777814290 3.540000e-34 156.0
12 TraesCS2A01G589000 chr2A 86.765 136 11 5 355 489 777816804 777816675 7.660000e-31 145.0
13 TraesCS2A01G589000 chr2A 78.636 220 27 12 1081 1294 778798099 778798304 7.710000e-26 128.0
14 TraesCS2A01G589000 chr2A 92.771 83 3 2 355 437 777814063 777813984 1.670000e-22 117.0
15 TraesCS2A01G589000 chr2A 91.566 83 7 0 92 174 777816976 777816894 6.010000e-22 115.0
16 TraesCS2A01G589000 chr2A 77.540 187 29 9 2282 2457 777810148 777809964 1.680000e-17 100.0
17 TraesCS2A01G589000 chr2A 95.745 47 2 0 1131 1177 723061132 723061178 2.830000e-10 76.8
18 TraesCS2A01G589000 chr2D 83.542 559 57 23 985 1521 635161290 635161835 8.540000e-135 490.0
19 TraesCS2A01G589000 chr2D 93.548 93 4 1 1 93 635155007 635155097 1.280000e-28 137.0
20 TraesCS2A01G589000 chr2B 82.745 510 61 18 985 1480 779251335 779251831 1.890000e-116 429.0
21 TraesCS2A01G589000 chr2B 94.764 191 9 1 94 283 779178521 779178711 2.000000e-76 296.0
22 TraesCS2A01G589000 chr2B 76.058 685 79 42 880 1525 779179125 779179763 7.240000e-71 278.0
23 TraesCS2A01G589000 chr2B 79.908 433 39 28 352 759 779178718 779179127 9.360000e-70 274.0
24 TraesCS2A01G589000 chr2B 89.333 225 8 3 3 227 779175255 779175463 4.360000e-68 268.0
25 TraesCS2A01G589000 chr2B 84.528 265 21 5 420 664 779250687 779250951 7.340000e-61 244.0
26 TraesCS2A01G589000 chr2B 78.947 285 45 8 1798 2082 779252201 779252470 2.100000e-41 180.0
27 TraesCS2A01G589000 chr2B 76.623 385 45 19 2282 2625 779252612 779252992 1.260000e-38 171.0
28 TraesCS2A01G589000 chr2B 82.162 185 18 7 991 1175 779259487 779259656 7.660000e-31 145.0
29 TraesCS2A01G589000 chr2B 82.031 128 18 4 2501 2627 779180538 779180661 1.300000e-18 104.0
30 TraesCS2A01G589000 chr2B 100.000 29 0 0 65 93 779178476 779178504 1.000000e-03 54.7


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 TraesCS2A01G589000 chr2A 777837527 777840181 2654 True 4903.000000 4903 100.000000 1 2655 1 chr2A.!!$R3 2654
1 TraesCS2A01G589000 chr2A 777626752 777627293 541 True 477.000000 477 83.183000 990 1521 1 chr2A.!!$R2 531
2 TraesCS2A01G589000 chr2A 777809964 777819473 9509 True 223.538462 547 88.277769 3 2457 13 chr2A.!!$R4 2454
3 TraesCS2A01G589000 chr2D 635161290 635161835 545 False 490.000000 490 83.542000 985 1521 1 chr2D.!!$F2 536
4 TraesCS2A01G589000 chr2B 779250687 779252992 2305 False 256.000000 429 80.710750 420 2625 4 chr2B.!!$F3 2205
5 TraesCS2A01G589000 chr2B 779175255 779180661 5406 False 212.450000 296 87.015667 3 2627 6 chr2B.!!$F2 2624

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
644 3916 0.460284 ATGGACTAAACTCCGCTGCG 60.460 55.0 16.34 16.34 32.22 5.18 F
1411 12145 0.390866 CTCGATCAAGCAGTGTGCCT 60.391 55.0 0.00 0.00 46.52 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 12420 0.394938 ACGTCCAATACAGGCACACA 59.605 50.0 0.0 0.0 0.0 3.72 R
2374 13293 0.716108 GTCCTTTGCGATGAGACACG 59.284 55.0 0.0 0.0 0.0 4.49 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
70 71 3.616821 TGCTTTCACGTACTCATGCATAC 59.383 43.478 0.00 0.00 0.00 2.39
83 84 2.655364 CATACGTGCTCGCTCGGG 60.655 66.667 16.22 3.66 41.18 5.14
84 85 4.570663 ATACGTGCTCGCTCGGGC 62.571 66.667 16.22 7.26 43.05 6.13
118 119 2.669569 GCAAACTCCAGCCGCTGA 60.670 61.111 22.35 7.11 32.44 4.26
308 3501 3.758521 CGTACAAGACGTGTTAACACC 57.241 47.619 28.43 17.61 46.86 4.16
309 3502 3.374745 CGTACAAGACGTGTTAACACCT 58.625 45.455 28.43 19.44 46.86 4.00
310 3503 4.536065 CGTACAAGACGTGTTAACACCTA 58.464 43.478 28.43 7.34 46.86 3.08
311 3504 4.379793 CGTACAAGACGTGTTAACACCTAC 59.620 45.833 28.43 20.00 46.86 3.18
312 3505 4.660789 ACAAGACGTGTTAACACCTACT 57.339 40.909 28.43 21.55 43.66 2.57
313 3506 4.614946 ACAAGACGTGTTAACACCTACTC 58.385 43.478 28.43 18.38 43.66 2.59
314 3507 3.930634 AGACGTGTTAACACCTACTCC 57.069 47.619 28.43 13.50 43.66 3.85
315 3508 2.560105 AGACGTGTTAACACCTACTCCC 59.440 50.000 28.43 12.34 43.66 4.30
316 3509 2.560105 GACGTGTTAACACCTACTCCCT 59.440 50.000 28.43 5.18 43.66 4.20
317 3510 2.967887 ACGTGTTAACACCTACTCCCTT 59.032 45.455 28.43 3.61 43.66 3.95
318 3511 3.389002 ACGTGTTAACACCTACTCCCTTT 59.611 43.478 28.43 2.26 43.66 3.11
319 3512 3.744426 CGTGTTAACACCTACTCCCTTTG 59.256 47.826 28.43 9.70 43.66 2.77
320 3513 4.711399 GTGTTAACACCTACTCCCTTTGT 58.289 43.478 25.31 0.00 40.85 2.83
321 3514 5.128205 GTGTTAACACCTACTCCCTTTGTT 58.872 41.667 25.31 0.00 40.85 2.83
322 3515 5.008316 GTGTTAACACCTACTCCCTTTGTTG 59.992 44.000 25.31 0.00 40.85 3.33
323 3516 5.104444 TGTTAACACCTACTCCCTTTGTTGA 60.104 40.000 3.59 0.00 32.73 3.18
324 3517 3.771577 ACACCTACTCCCTTTGTTGAG 57.228 47.619 0.00 0.00 34.73 3.02
325 3518 2.372172 ACACCTACTCCCTTTGTTGAGG 59.628 50.000 0.00 0.00 36.52 3.86
335 3528 4.736126 CCTTTGTTGAGGGACAAGTTTT 57.264 40.909 0.00 0.00 40.33 2.43
336 3529 5.084818 CCTTTGTTGAGGGACAAGTTTTT 57.915 39.130 0.00 0.00 40.33 1.94
337 3530 5.109210 CCTTTGTTGAGGGACAAGTTTTTC 58.891 41.667 0.00 0.00 40.33 2.29
338 3531 4.729227 TTGTTGAGGGACAAGTTTTTCC 57.271 40.909 0.00 0.00 39.30 3.13
339 3532 2.685897 TGTTGAGGGACAAGTTTTTCCG 59.314 45.455 0.00 0.00 39.30 4.30
340 3533 1.975660 TGAGGGACAAGTTTTTCCGG 58.024 50.000 0.00 0.00 32.00 5.14
341 3534 1.491332 TGAGGGACAAGTTTTTCCGGA 59.509 47.619 0.00 0.00 32.00 5.14
342 3535 1.878088 GAGGGACAAGTTTTTCCGGAC 59.122 52.381 1.83 0.00 32.00 4.79
343 3536 1.213430 AGGGACAAGTTTTTCCGGACA 59.787 47.619 1.83 0.00 32.00 4.02
344 3537 1.607148 GGGACAAGTTTTTCCGGACAG 59.393 52.381 1.83 0.00 32.00 3.51
345 3538 2.567985 GGACAAGTTTTTCCGGACAGA 58.432 47.619 1.83 0.00 0.00 3.41
346 3539 2.548480 GGACAAGTTTTTCCGGACAGAG 59.452 50.000 1.83 0.00 0.00 3.35
347 3540 3.463944 GACAAGTTTTTCCGGACAGAGA 58.536 45.455 1.83 0.00 0.00 3.10
348 3541 3.467803 ACAAGTTTTTCCGGACAGAGAG 58.532 45.455 1.83 0.00 0.00 3.20
349 3542 3.134081 ACAAGTTTTTCCGGACAGAGAGA 59.866 43.478 1.83 0.00 0.00 3.10
350 3543 3.669251 AGTTTTTCCGGACAGAGAGAG 57.331 47.619 1.83 0.00 0.00 3.20
438 3631 1.182667 GTAGTTTGGCCCATGGTTCC 58.817 55.000 11.73 11.98 0.00 3.62
456 3707 3.140325 TCCAGTGGGTTCAGTTCAATC 57.860 47.619 9.92 0.00 34.93 2.67
641 3913 0.905357 AGCATGGACTAAACTCCGCT 59.095 50.000 0.00 0.00 32.22 5.52
644 3916 0.460284 ATGGACTAAACTCCGCTGCG 60.460 55.000 16.34 16.34 32.22 5.18
669 9137 1.450848 ATGCGACGGGAGAGACGTA 60.451 57.895 0.00 0.00 45.68 3.57
671 9139 2.699809 CGACGGGAGAGACGTACG 59.300 66.667 15.01 15.01 45.68 3.67
672 9140 1.807165 CGACGGGAGAGACGTACGA 60.807 63.158 24.41 0.00 45.68 3.43
673 9141 1.150567 CGACGGGAGAGACGTACGAT 61.151 60.000 24.41 10.07 45.68 3.73
674 9142 0.581053 GACGGGAGAGACGTACGATC 59.419 60.000 24.41 18.50 45.68 3.69
700 9168 2.663196 GACTACCGCACCTGCCTT 59.337 61.111 0.00 0.00 37.91 4.35
708 9180 1.543802 CCGCACCTGCCTTTCATAAAA 59.456 47.619 0.00 0.00 37.91 1.52
710 9182 3.368323 CCGCACCTGCCTTTCATAAAAAT 60.368 43.478 0.00 0.00 37.91 1.82
712 9184 5.451798 CCGCACCTGCCTTTCATAAAAATAT 60.452 40.000 0.00 0.00 37.91 1.28
732 9204 0.776810 TTCTTCCCCAGAATGTGCCA 59.223 50.000 0.00 0.00 36.51 4.92
735 9207 2.580322 TCTTCCCCAGAATGTGCCAATA 59.420 45.455 0.00 0.00 0.00 1.90
768 9240 1.069049 CAGCCAAACTTTGTTCCTGGG 59.931 52.381 0.00 0.00 0.00 4.45
770 9242 1.413118 CCAAACTTTGTTCCTGGGCT 58.587 50.000 0.00 0.00 0.00 5.19
862 10069 4.262635 CCTGATGGACGGCTCATATTTAGT 60.263 45.833 0.00 0.00 34.57 2.24
896 10140 3.813166 GCTGGCTTACTATAAATTCCGCA 59.187 43.478 0.00 0.00 0.00 5.69
901 10145 5.333111 GGCTTACTATAAATTCCGCAACTCG 60.333 44.000 0.00 0.00 38.08 4.18
942 10186 1.816863 GCAACCACCAGACTCCGAGA 61.817 60.000 1.33 0.00 0.00 4.04
959 10203 1.679153 GAGAGGTAGAGGCAGTAGCAC 59.321 57.143 0.00 0.00 44.61 4.40
968 10212 2.105466 GCAGTAGCACAGCAGAGGC 61.105 63.158 0.00 0.00 41.58 4.70
973 10217 1.611474 TAGCACAGCAGAGGCAGAGG 61.611 60.000 0.00 0.00 44.61 3.69
974 10218 2.436292 CACAGCAGAGGCAGAGGC 60.436 66.667 0.00 0.00 44.61 4.70
975 10219 2.926779 ACAGCAGAGGCAGAGGCA 60.927 61.111 0.00 0.00 44.61 4.75
976 10220 2.125065 CAGCAGAGGCAGAGGCAG 60.125 66.667 0.00 0.00 44.61 4.85
977 10221 2.284478 AGCAGAGGCAGAGGCAGA 60.284 61.111 0.00 0.00 44.61 4.26
978 10222 2.187424 GCAGAGGCAGAGGCAGAG 59.813 66.667 0.00 0.00 43.71 3.35
979 10223 2.187424 CAGAGGCAGAGGCAGAGC 59.813 66.667 0.00 0.00 43.71 4.09
1023 10267 4.951963 GCCGGATTCCCTCTCGCG 62.952 72.222 5.05 0.00 0.00 5.87
1049 10293 1.045911 ATCCTCGCCTTCCACCTCTC 61.046 60.000 0.00 0.00 0.00 3.20
1225 10492 4.593597 TCACGAACGAATGAATTAAGCC 57.406 40.909 0.14 0.00 0.00 4.35
1227 10494 4.634004 TCACGAACGAATGAATTAAGCCAT 59.366 37.500 0.14 0.00 0.00 4.40
1245 10514 5.876612 GCCATTAGCTAATCTGATCCTTG 57.123 43.478 16.21 3.67 38.99 3.61
1255 10524 3.144657 TCTGATCCTTGTTGCATGTGT 57.855 42.857 0.00 0.00 0.00 3.72
1256 10525 4.284829 TCTGATCCTTGTTGCATGTGTA 57.715 40.909 0.00 0.00 0.00 2.90
1283 10555 3.568007 TGTCCGACTAATTTGCTGCTTTT 59.432 39.130 0.00 0.00 0.00 2.27
1285 10557 3.057596 TCCGACTAATTTGCTGCTTTTGG 60.058 43.478 0.00 0.00 0.00 3.28
1286 10558 3.244976 CGACTAATTTGCTGCTTTTGGG 58.755 45.455 0.00 0.00 0.00 4.12
1287 10559 3.057596 CGACTAATTTGCTGCTTTTGGGA 60.058 43.478 0.00 0.00 0.00 4.37
1288 10560 4.380867 CGACTAATTTGCTGCTTTTGGGAT 60.381 41.667 0.00 0.00 0.00 3.85
1329 10611 1.199615 TGCATGGTGACTTCCGGATA 58.800 50.000 4.15 0.00 0.00 2.59
1330 10612 1.134521 TGCATGGTGACTTCCGGATAC 60.135 52.381 4.15 2.33 0.00 2.24
1370 12104 4.505301 CGTACACGACGTCTTCTGTATA 57.495 45.455 14.70 0.00 46.86 1.47
1377 12111 5.288712 CACGACGTCTTCTGTATAATTGCTT 59.711 40.000 14.70 0.00 0.00 3.91
1378 12112 5.867716 ACGACGTCTTCTGTATAATTGCTTT 59.132 36.000 14.70 0.00 0.00 3.51
1379 12113 6.178507 CGACGTCTTCTGTATAATTGCTTTG 58.821 40.000 14.70 0.00 0.00 2.77
1380 12114 5.869350 ACGTCTTCTGTATAATTGCTTTGC 58.131 37.500 0.00 0.00 0.00 3.68
1387 12121 7.389803 TCTGTATAATTGCTTTGCTTGCTTA 57.610 32.000 0.00 0.00 0.00 3.09
1399 12133 2.002586 GCTTGCTTACTTGCTCGATCA 58.997 47.619 0.00 0.00 0.00 2.92
1410 12144 1.975363 GCTCGATCAAGCAGTGTGCC 61.975 60.000 0.00 0.00 46.52 5.01
1411 12145 0.390866 CTCGATCAAGCAGTGTGCCT 60.391 55.000 0.00 0.00 46.52 4.75
1412 12146 0.671472 TCGATCAAGCAGTGTGCCTG 60.671 55.000 0.00 0.00 46.52 4.85
1469 12220 2.691526 GACATCACATACTGGACCCGTA 59.308 50.000 0.00 0.00 0.00 4.02
1492 12243 4.341487 TGATTAGACTCGACTTTCCTCCA 58.659 43.478 0.00 0.00 0.00 3.86
1493 12244 4.158025 TGATTAGACTCGACTTTCCTCCAC 59.842 45.833 0.00 0.00 0.00 4.02
1528 12281 1.829222 GATTCCTGTCTTGGACCCGTA 59.171 52.381 0.00 0.00 35.58 4.02
1530 12283 1.946984 TCCTGTCTTGGACCCGTATT 58.053 50.000 0.00 0.00 0.00 1.89
1540 12299 6.822170 GTCTTGGACCCGTATTTTCTTTAGAT 59.178 38.462 0.00 0.00 0.00 1.98
1556 12361 6.773638 TCTTTAGATCATCCTAAATCAGCCC 58.226 40.000 0.00 0.00 37.80 5.19
1585 12390 1.678101 GATTGCGATAGGGCTGCTTTT 59.322 47.619 0.00 0.00 0.00 2.27
1592 12397 2.584835 TAGGGCTGCTTTTGTGTCAT 57.415 45.000 0.00 0.00 0.00 3.06
1606 12411 2.146342 GTGTCATGTGTTCCTGTCCTG 58.854 52.381 0.00 0.00 0.00 3.86
1613 12418 1.968540 GTTCCTGTCCTGCCACTGC 60.969 63.158 0.00 0.00 38.26 4.40
1615 12420 4.320456 CCTGTCCTGCCACTGCGT 62.320 66.667 0.00 0.00 41.78 5.24
1624 12429 3.653009 CCACTGCGTGTGTGCCTG 61.653 66.667 8.50 0.00 44.81 4.85
1637 12446 1.076332 GTGCCTGTATTGGACGTCAC 58.924 55.000 18.91 7.37 0.00 3.67
1641 12450 2.159627 GCCTGTATTGGACGTCACTTTG 59.840 50.000 18.91 0.84 0.00 2.77
1644 12453 3.799366 TGTATTGGACGTCACTTTGTGT 58.201 40.909 18.91 0.00 34.79 3.72
1650 12459 1.333619 GACGTCACTTTGTGTTGCCAT 59.666 47.619 11.55 0.00 34.79 4.40
1653 12462 2.289274 CGTCACTTTGTGTTGCCATGTA 59.711 45.455 0.00 0.00 34.79 2.29
1668 12477 2.093973 CCATGTAAGAGCGAGTCCAACT 60.094 50.000 0.00 0.00 0.00 3.16
1691 12500 6.070824 ACTGAAGAAACAAATTTTGACACCCT 60.071 34.615 15.81 3.13 0.00 4.34
1693 12502 7.841956 TGAAGAAACAAATTTTGACACCCTAA 58.158 30.769 15.81 0.00 0.00 2.69
1694 12503 8.314751 TGAAGAAACAAATTTTGACACCCTAAA 58.685 29.630 15.81 0.00 0.00 1.85
1695 12504 9.325198 GAAGAAACAAATTTTGACACCCTAAAT 57.675 29.630 15.81 0.00 32.88 1.40
1696 12505 8.887036 AGAAACAAATTTTGACACCCTAAATC 57.113 30.769 15.81 0.23 30.84 2.17
1697 12506 7.931407 AGAAACAAATTTTGACACCCTAAATCC 59.069 33.333 15.81 0.00 30.84 3.01
1698 12507 6.994421 ACAAATTTTGACACCCTAAATCCT 57.006 33.333 15.81 0.00 30.84 3.24
1699 12508 6.993079 ACAAATTTTGACACCCTAAATCCTC 58.007 36.000 15.81 0.00 30.84 3.71
1700 12509 6.553100 ACAAATTTTGACACCCTAAATCCTCA 59.447 34.615 15.81 0.00 30.84 3.86
1701 12510 7.235399 ACAAATTTTGACACCCTAAATCCTCAT 59.765 33.333 15.81 0.00 30.84 2.90
1702 12511 7.797121 AATTTTGACACCCTAAATCCTCATT 57.203 32.000 0.00 0.00 30.84 2.57
1703 12512 7.797121 ATTTTGACACCCTAAATCCTCATTT 57.203 32.000 0.00 0.00 36.18 2.32
1704 12513 6.588719 TTTGACACCCTAAATCCTCATTTG 57.411 37.500 0.00 0.00 33.95 2.32
1705 12514 4.016444 TGACACCCTAAATCCTCATTTGC 58.984 43.478 0.00 0.00 33.95 3.68
1706 12515 4.016444 GACACCCTAAATCCTCATTTGCA 58.984 43.478 0.00 0.00 33.95 4.08
1707 12516 4.613437 ACACCCTAAATCCTCATTTGCAT 58.387 39.130 0.00 0.00 33.95 3.96
1708 12517 5.025453 ACACCCTAAATCCTCATTTGCATT 58.975 37.500 0.00 0.00 33.95 3.56
1709 12518 5.484998 ACACCCTAAATCCTCATTTGCATTT 59.515 36.000 0.00 0.00 33.95 2.32
1710 12519 6.044682 CACCCTAAATCCTCATTTGCATTTC 58.955 40.000 0.00 0.00 33.95 2.17
1711 12520 5.163519 ACCCTAAATCCTCATTTGCATTTCG 60.164 40.000 0.00 0.00 33.95 3.46
1712 12521 4.741676 CCTAAATCCTCATTTGCATTTCGC 59.258 41.667 0.00 0.00 42.89 4.70
1753 12567 0.743701 CTCATTTGCAGAGCCTCGCT 60.744 55.000 9.33 0.00 43.88 4.93
1807 12680 3.499563 CCAACCTCCCCAAAACATGTCTA 60.500 47.826 0.00 0.00 0.00 2.59
1860 12733 8.637099 TCAAAACAACCATATGACAAAGATTCA 58.363 29.630 3.65 0.00 0.00 2.57
1959 12836 9.760660 GTATTGTCATTACTGTTGACTCAAATC 57.239 33.333 12.39 0.00 43.12 2.17
1960 12837 7.800155 TTGTCATTACTGTTGACTCAAATCA 57.200 32.000 12.39 0.00 43.12 2.57
1981 12858 0.531753 TACACACACAGCACGCACAT 60.532 50.000 0.00 0.00 0.00 3.21
2006 12883 1.100463 AACACAAGACACGCATGCCA 61.100 50.000 13.15 0.00 0.00 4.92
2008 12885 0.241749 CACAAGACACGCATGCCAAT 59.758 50.000 13.15 0.00 0.00 3.16
2012 12889 2.042686 AGACACGCATGCCAATACAT 57.957 45.000 13.15 0.00 0.00 2.29
2019 12896 4.023792 CACGCATGCCAATACATATTCACT 60.024 41.667 13.15 0.00 0.00 3.41
2020 12897 4.580167 ACGCATGCCAATACATATTCACTT 59.420 37.500 13.15 0.00 0.00 3.16
2023 12900 6.073058 CGCATGCCAATACATATTCACTTACT 60.073 38.462 13.15 0.00 0.00 2.24
2028 12905 8.046708 TGCCAATACATATTCACTTACTCAGTT 58.953 33.333 0.00 0.00 30.92 3.16
2089 12985 8.946085 GTAAATATCAGTGATCACTTTGGACAA 58.054 33.333 25.84 12.10 40.20 3.18
2101 12997 7.687941 TCACTTTGGACAAGGAGATTTTATC 57.312 36.000 0.95 0.00 0.00 1.75
2102 12998 6.659242 TCACTTTGGACAAGGAGATTTTATCC 59.341 38.462 0.95 0.00 37.07 2.59
2111 13007 6.381133 ACAAGGAGATTTTATCCACCCATTTC 59.619 38.462 0.00 0.00 39.47 2.17
2116 13012 0.553819 TTATCCACCCATTTCCCCCG 59.446 55.000 0.00 0.00 0.00 5.73
2170 13088 6.433093 CCACCTAAAACTACATTTGGTTAGCT 59.567 38.462 0.00 0.00 0.00 3.32
2171 13089 7.361799 CCACCTAAAACTACATTTGGTTAGCTC 60.362 40.741 0.00 0.00 0.00 4.09
2178 13097 4.946784 ACATTTGGTTAGCTCGACAATC 57.053 40.909 0.00 0.00 0.00 2.67
2193 13112 6.481644 GCTCGACAATCTCAGGATTAGAAAAT 59.518 38.462 0.00 0.00 39.87 1.82
2194 13113 7.653713 GCTCGACAATCTCAGGATTAGAAAATA 59.346 37.037 0.00 0.00 39.87 1.40
2214 13133 9.981114 GAAAATAATGGTTTTTCCTTCTTCTCA 57.019 29.630 0.00 0.00 37.19 3.27
2220 13139 9.685276 AATGGTTTTTCCTTCTTCTCAATTTTT 57.315 25.926 0.00 0.00 37.07 1.94
2242 13161 8.871686 TTTTTCTTTTGATAAACAGAGCTTCC 57.128 30.769 0.00 0.00 0.00 3.46
2243 13162 7.823745 TTTCTTTTGATAAACAGAGCTTCCT 57.176 32.000 0.00 0.00 0.00 3.36
2244 13163 7.440523 TTCTTTTGATAAACAGAGCTTCCTC 57.559 36.000 0.00 0.00 38.42 3.71
2246 13165 6.876257 TCTTTTGATAAACAGAGCTTCCTCTC 59.124 38.462 0.00 0.00 45.21 3.20
2247 13166 4.744795 TGATAAACAGAGCTTCCTCTCC 57.255 45.455 0.00 0.00 45.21 3.71
2248 13167 3.131223 TGATAAACAGAGCTTCCTCTCCG 59.869 47.826 0.00 0.00 45.21 4.63
2249 13168 1.633774 AAACAGAGCTTCCTCTCCGA 58.366 50.000 0.00 0.00 45.21 4.55
2250 13169 1.859302 AACAGAGCTTCCTCTCCGAT 58.141 50.000 0.00 0.00 45.21 4.18
2251 13170 1.859302 ACAGAGCTTCCTCTCCGATT 58.141 50.000 0.00 0.00 45.21 3.34
2252 13171 2.183679 ACAGAGCTTCCTCTCCGATTT 58.816 47.619 0.00 0.00 45.21 2.17
2253 13172 2.167487 ACAGAGCTTCCTCTCCGATTTC 59.833 50.000 0.00 0.00 45.21 2.17
2254 13173 2.430332 CAGAGCTTCCTCTCCGATTTCT 59.570 50.000 0.00 0.00 45.21 2.52
2255 13174 2.430332 AGAGCTTCCTCTCCGATTTCTG 59.570 50.000 0.00 0.00 45.21 3.02
2256 13175 2.167487 GAGCTTCCTCTCCGATTTCTGT 59.833 50.000 0.00 0.00 35.16 3.41
2257 13176 2.569404 AGCTTCCTCTCCGATTTCTGTT 59.431 45.455 0.00 0.00 0.00 3.16
2258 13177 3.769844 AGCTTCCTCTCCGATTTCTGTTA 59.230 43.478 0.00 0.00 0.00 2.41
2259 13178 4.407296 AGCTTCCTCTCCGATTTCTGTTAT 59.593 41.667 0.00 0.00 0.00 1.89
2260 13179 5.104735 AGCTTCCTCTCCGATTTCTGTTATT 60.105 40.000 0.00 0.00 0.00 1.40
2261 13180 6.098409 AGCTTCCTCTCCGATTTCTGTTATTA 59.902 38.462 0.00 0.00 0.00 0.98
2262 13181 6.422400 GCTTCCTCTCCGATTTCTGTTATTAG 59.578 42.308 0.00 0.00 0.00 1.73
2263 13182 7.655521 TTCCTCTCCGATTTCTGTTATTAGA 57.344 36.000 0.00 0.00 0.00 2.10
2264 13183 7.841282 TCCTCTCCGATTTCTGTTATTAGAT 57.159 36.000 0.00 0.00 0.00 1.98
2265 13184 8.935614 TCCTCTCCGATTTCTGTTATTAGATA 57.064 34.615 0.00 0.00 0.00 1.98
2266 13185 9.535170 TCCTCTCCGATTTCTGTTATTAGATAT 57.465 33.333 0.00 0.00 0.00 1.63
2267 13186 9.796120 CCTCTCCGATTTCTGTTATTAGATATC 57.204 37.037 0.00 0.00 34.08 1.63
2315 13234 7.619964 TTCCTAAAACCGGATTAATGAGTTC 57.380 36.000 9.46 0.00 0.00 3.01
2321 13240 5.532664 ACCGGATTAATGAGTTCTAGGAC 57.467 43.478 9.46 0.00 0.00 3.85
2328 13247 9.050601 GGATTAATGAGTTCTAGGACAAATGAG 57.949 37.037 3.42 0.00 0.00 2.90
2368 13287 5.824904 CAAATCAGTTTGGTCTATCCTGG 57.175 43.478 0.00 0.00 40.78 4.45
2374 13293 7.540474 TCAGTTTGGTCTATCCTGGATATAC 57.460 40.000 16.45 17.86 37.07 1.47
2382 13301 5.938710 GTCTATCCTGGATATACGTGTCTCA 59.061 44.000 16.45 0.00 0.00 3.27
2383 13302 6.600032 GTCTATCCTGGATATACGTGTCTCAT 59.400 42.308 16.45 0.00 0.00 2.90
2384 13303 5.906113 ATCCTGGATATACGTGTCTCATC 57.094 43.478 7.59 0.00 0.00 2.92
2385 13304 3.751698 TCCTGGATATACGTGTCTCATCG 59.248 47.826 0.00 0.00 0.00 3.84
2386 13305 3.493272 CTGGATATACGTGTCTCATCGC 58.507 50.000 0.00 0.00 0.00 4.58
2390 13309 4.383052 GGATATACGTGTCTCATCGCAAAG 59.617 45.833 0.00 0.00 0.00 2.77
2392 13311 0.317160 ACGTGTCTCATCGCAAAGGA 59.683 50.000 0.00 0.00 0.00 3.36
2393 13312 0.716108 CGTGTCTCATCGCAAAGGAC 59.284 55.000 0.00 0.00 0.00 3.85
2397 13316 3.189287 GTGTCTCATCGCAAAGGACAAAT 59.811 43.478 0.00 0.00 38.40 2.32
2399 13318 3.436704 GTCTCATCGCAAAGGACAAATGA 59.563 43.478 0.00 0.00 0.00 2.57
2400 13319 3.436704 TCTCATCGCAAAGGACAAATGAC 59.563 43.478 0.00 0.00 0.00 3.06
2403 13322 5.185454 TCATCGCAAAGGACAAATGACTAT 58.815 37.500 0.00 0.00 0.00 2.12
2404 13323 5.647658 TCATCGCAAAGGACAAATGACTATT 59.352 36.000 0.00 0.00 0.00 1.73
2407 13326 6.837992 TCGCAAAGGACAAATGACTATTAAC 58.162 36.000 0.00 0.00 0.00 2.01
2408 13327 6.027749 CGCAAAGGACAAATGACTATTAACC 58.972 40.000 0.00 0.00 0.00 2.85
2409 13328 6.348950 CGCAAAGGACAAATGACTATTAACCA 60.349 38.462 0.00 0.00 0.00 3.67
2420 13348 5.754782 TGACTATTAACCATGTGCTCCAAT 58.245 37.500 0.00 0.00 0.00 3.16
2433 13361 2.231964 TGCTCCAATTTCCAGCAATCAC 59.768 45.455 1.09 0.00 40.22 3.06
2558 13517 7.728847 TGTATTCACAACAGCCATATATGAC 57.271 36.000 14.54 2.16 0.00 3.06
2561 13520 6.682423 TTCACAACAGCCATATATGACAAG 57.318 37.500 14.54 2.42 0.00 3.16
2565 13524 7.557358 TCACAACAGCCATATATGACAAGAATT 59.443 33.333 14.54 0.00 0.00 2.17
2566 13525 8.192774 CACAACAGCCATATATGACAAGAATTT 58.807 33.333 14.54 0.00 0.00 1.82
2568 13527 9.590451 CAACAGCCATATATGACAAGAATTTTT 57.410 29.630 14.54 0.00 0.00 1.94
2569 13528 9.807649 AACAGCCATATATGACAAGAATTTTTC 57.192 29.630 14.54 0.00 0.00 2.29
2650 13610 8.693120 TTTTATTTGTCAACATACTACCCACA 57.307 30.769 0.00 0.00 0.00 4.17
2651 13611 7.675962 TTATTTGTCAACATACTACCCACAC 57.324 36.000 0.00 0.00 0.00 3.82
2652 13612 4.691326 TTGTCAACATACTACCCACACA 57.309 40.909 0.00 0.00 0.00 3.72
2653 13613 4.691326 TGTCAACATACTACCCACACAA 57.309 40.909 0.00 0.00 0.00 3.33
2654 13614 4.637276 TGTCAACATACTACCCACACAAG 58.363 43.478 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.392461 AAGCCATGCAACGTCCGTAT 60.392 50.000 0.00 0.00 0.00 3.06
1 2 0.604243 AAAGCCATGCAACGTCCGTA 60.604 50.000 0.00 0.00 0.00 4.02
7 8 1.219646 AAAGCAAAAGCCATGCAACG 58.780 45.000 8.45 0.00 46.22 4.10
78 79 2.972505 AACGTGCAAGTGCCCGAG 60.973 61.111 14.99 0.00 44.47 4.63
79 80 3.276091 CAACGTGCAAGTGCCCGA 61.276 61.111 14.99 0.00 44.47 5.14
80 81 3.521308 GACAACGTGCAAGTGCCCG 62.521 63.158 5.91 6.61 46.94 6.13
81 82 1.999071 TTGACAACGTGCAAGTGCCC 61.999 55.000 5.91 0.00 41.18 5.36
82 83 0.592247 CTTGACAACGTGCAAGTGCC 60.592 55.000 5.91 0.00 41.18 5.01
83 84 1.202348 GCTTGACAACGTGCAAGTGC 61.202 55.000 20.29 0.00 42.57 4.40
84 85 0.098552 TGCTTGACAACGTGCAAGTG 59.901 50.000 20.29 3.47 42.57 3.16
85 86 0.808125 TTGCTTGACAACGTGCAAGT 59.192 45.000 20.29 0.00 42.57 3.16
86 87 1.583404 GTTTGCTTGACAACGTGCAAG 59.417 47.619 17.03 17.03 44.52 4.01
87 88 1.201181 AGTTTGCTTGACAACGTGCAA 59.799 42.857 8.74 8.74 42.60 4.08
88 89 0.808125 AGTTTGCTTGACAACGTGCA 59.192 45.000 0.00 0.00 38.23 4.57
89 90 1.466855 GAGTTTGCTTGACAACGTGC 58.533 50.000 0.00 0.00 38.23 5.34
90 91 1.400142 TGGAGTTTGCTTGACAACGTG 59.600 47.619 0.00 0.00 38.23 4.49
314 3507 4.736126 AAAACTTGTCCCTCAACAAAGG 57.264 40.909 0.00 0.00 38.60 3.11
315 3508 5.109210 GGAAAAACTTGTCCCTCAACAAAG 58.891 41.667 0.00 0.00 38.60 2.77
316 3509 4.381079 CGGAAAAACTTGTCCCTCAACAAA 60.381 41.667 0.00 0.00 38.60 2.83
317 3510 3.129638 CGGAAAAACTTGTCCCTCAACAA 59.870 43.478 0.00 0.00 37.56 2.83
318 3511 2.685897 CGGAAAAACTTGTCCCTCAACA 59.314 45.455 0.00 0.00 32.18 3.33
319 3512 2.034179 CCGGAAAAACTTGTCCCTCAAC 59.966 50.000 0.00 0.00 32.18 3.18
320 3513 2.092321 TCCGGAAAAACTTGTCCCTCAA 60.092 45.455 0.00 0.00 34.61 3.02
321 3514 1.491332 TCCGGAAAAACTTGTCCCTCA 59.509 47.619 0.00 0.00 0.00 3.86
322 3515 1.878088 GTCCGGAAAAACTTGTCCCTC 59.122 52.381 5.23 0.00 0.00 4.30
323 3516 1.213430 TGTCCGGAAAAACTTGTCCCT 59.787 47.619 5.23 0.00 0.00 4.20
324 3517 1.607148 CTGTCCGGAAAAACTTGTCCC 59.393 52.381 5.23 0.00 0.00 4.46
325 3518 2.548480 CTCTGTCCGGAAAAACTTGTCC 59.452 50.000 5.23 0.00 0.00 4.02
326 3519 3.463944 TCTCTGTCCGGAAAAACTTGTC 58.536 45.455 5.23 0.00 0.00 3.18
327 3520 3.134081 TCTCTCTGTCCGGAAAAACTTGT 59.866 43.478 5.23 0.00 0.00 3.16
328 3521 3.728845 TCTCTCTGTCCGGAAAAACTTG 58.271 45.455 5.23 0.00 0.00 3.16
329 3522 3.388350 ACTCTCTCTGTCCGGAAAAACTT 59.612 43.478 5.23 0.00 0.00 2.66
330 3523 2.966516 ACTCTCTCTGTCCGGAAAAACT 59.033 45.455 5.23 0.00 0.00 2.66
331 3524 3.388345 ACTCTCTCTGTCCGGAAAAAC 57.612 47.619 5.23 0.00 0.00 2.43
332 3525 3.057736 CGTACTCTCTCTGTCCGGAAAAA 60.058 47.826 5.23 0.00 0.00 1.94
333 3526 2.486982 CGTACTCTCTCTGTCCGGAAAA 59.513 50.000 5.23 0.00 0.00 2.29
334 3527 2.082231 CGTACTCTCTCTGTCCGGAAA 58.918 52.381 5.23 0.00 0.00 3.13
335 3528 1.002888 ACGTACTCTCTCTGTCCGGAA 59.997 52.381 5.23 0.00 0.00 4.30
336 3529 0.612229 ACGTACTCTCTCTGTCCGGA 59.388 55.000 0.00 0.00 0.00 5.14
337 3530 0.727970 CACGTACTCTCTCTGTCCGG 59.272 60.000 0.00 0.00 0.00 5.14
338 3531 0.097325 GCACGTACTCTCTCTGTCCG 59.903 60.000 0.00 0.00 0.00 4.79
339 3532 0.452585 GGCACGTACTCTCTCTGTCC 59.547 60.000 0.00 0.00 0.00 4.02
340 3533 1.131504 CAGGCACGTACTCTCTCTGTC 59.868 57.143 0.00 0.00 0.00 3.51
341 3534 1.169577 CAGGCACGTACTCTCTCTGT 58.830 55.000 0.00 0.00 0.00 3.41
342 3535 1.400142 CTCAGGCACGTACTCTCTCTG 59.600 57.143 0.00 0.00 0.00 3.35
343 3536 1.279558 TCTCAGGCACGTACTCTCTCT 59.720 52.381 0.00 0.00 0.00 3.10
344 3537 1.740297 TCTCAGGCACGTACTCTCTC 58.260 55.000 0.00 0.00 0.00 3.20
345 3538 2.201921 TTCTCAGGCACGTACTCTCT 57.798 50.000 0.00 0.00 0.00 3.10
346 3539 3.512033 ATTTCTCAGGCACGTACTCTC 57.488 47.619 0.00 0.00 0.00 3.20
347 3540 4.219944 TGTTATTTCTCAGGCACGTACTCT 59.780 41.667 0.00 0.00 0.00 3.24
348 3541 4.491676 TGTTATTTCTCAGGCACGTACTC 58.508 43.478 0.00 0.00 0.00 2.59
349 3542 4.530710 TGTTATTTCTCAGGCACGTACT 57.469 40.909 0.00 0.00 0.00 2.73
350 3543 5.600908 TTTGTTATTTCTCAGGCACGTAC 57.399 39.130 0.00 0.00 0.00 3.67
438 3631 3.146104 AGGATTGAACTGAACCCACTG 57.854 47.619 0.00 0.00 0.00 3.66
569 3832 2.550423 CCTGACATCATCATCCTCAGCC 60.550 54.545 0.00 0.00 36.48 4.85
668 9136 3.144506 GGTAGTCCTGAATCCGATCGTA 58.855 50.000 15.09 0.00 0.00 3.43
669 9137 1.955080 GGTAGTCCTGAATCCGATCGT 59.045 52.381 15.09 0.00 0.00 3.73
671 9139 1.336056 GCGGTAGTCCTGAATCCGATC 60.336 57.143 6.09 0.00 43.22 3.69
672 9140 0.674534 GCGGTAGTCCTGAATCCGAT 59.325 55.000 6.09 0.00 43.22 4.18
673 9141 0.681887 TGCGGTAGTCCTGAATCCGA 60.682 55.000 6.09 0.00 43.22 4.55
674 9142 0.527817 GTGCGGTAGTCCTGAATCCG 60.528 60.000 0.00 0.00 43.37 4.18
732 9204 0.108138 GCTGAGGTGGCACGAGTATT 60.108 55.000 12.17 0.00 0.00 1.89
735 9207 4.008933 GGCTGAGGTGGCACGAGT 62.009 66.667 12.17 0.00 0.00 4.18
896 10140 1.229209 TGCTCTTCCCCTCCGAGTT 60.229 57.895 0.00 0.00 0.00 3.01
901 10145 0.616111 TGTCTCTGCTCTTCCCCTCC 60.616 60.000 0.00 0.00 0.00 4.30
942 10186 1.479709 CTGTGCTACTGCCTCTACCT 58.520 55.000 0.00 0.00 38.71 3.08
955 10199 2.663796 CTCTGCCTCTGCTGTGCT 59.336 61.111 8.67 0.00 38.71 4.40
959 10203 2.125065 CTGCCTCTGCCTCTGCTG 60.125 66.667 0.00 0.00 38.71 4.41
968 10212 4.527583 GGAGCGGCTCTGCCTCTG 62.528 72.222 27.47 0.00 44.36 3.35
973 10217 3.207669 CAATGGGAGCGGCTCTGC 61.208 66.667 27.47 13.18 0.00 4.26
974 10218 2.110967 CACAATGGGAGCGGCTCTG 61.111 63.158 27.47 20.03 0.00 3.35
975 10219 2.270205 CACAATGGGAGCGGCTCT 59.730 61.111 27.47 7.18 0.00 4.09
976 10220 2.825836 CCACAATGGGAGCGGCTC 60.826 66.667 21.57 21.57 32.67 4.70
1033 10277 2.726351 GGGAGAGGTGGAAGGCGAG 61.726 68.421 0.00 0.00 0.00 5.03
1049 10293 2.756283 ACGGCGAGAGGAGAAGGG 60.756 66.667 16.62 0.00 0.00 3.95
1225 10492 6.261603 TGCAACAAGGATCAGATTAGCTAATG 59.738 38.462 23.51 11.91 0.00 1.90
1227 10494 5.744171 TGCAACAAGGATCAGATTAGCTAA 58.256 37.500 8.99 8.99 0.00 3.09
1255 10524 4.629634 CAGCAAATTAGTCGGACATGTGTA 59.370 41.667 1.15 0.00 0.00 2.90
1256 10525 3.436704 CAGCAAATTAGTCGGACATGTGT 59.563 43.478 1.15 0.00 0.00 3.72
1269 10541 5.421277 CATCATCCCAAAAGCAGCAAATTA 58.579 37.500 0.00 0.00 0.00 1.40
1283 10555 3.658705 TGAATGATCCATCCATCATCCCA 59.341 43.478 0.00 0.00 41.78 4.37
1285 10557 4.098044 GCATGAATGATCCATCCATCATCC 59.902 45.833 0.00 0.00 41.78 3.51
1286 10558 4.705023 TGCATGAATGATCCATCCATCATC 59.295 41.667 0.00 0.00 41.78 2.92
1287 10559 4.672899 TGCATGAATGATCCATCCATCAT 58.327 39.130 0.00 0.00 44.05 2.45
1288 10560 4.107127 TGCATGAATGATCCATCCATCA 57.893 40.909 0.00 0.00 37.20 3.07
1329 10611 0.821517 TACCATTCGGATCTGCACGT 59.178 50.000 0.00 0.00 35.59 4.49
1330 10612 1.209128 GTACCATTCGGATCTGCACG 58.791 55.000 0.00 0.00 35.59 5.34
1331 10613 1.209128 CGTACCATTCGGATCTGCAC 58.791 55.000 0.00 0.00 35.59 4.57
1332 10614 0.821517 ACGTACCATTCGGATCTGCA 59.178 50.000 0.00 0.00 35.59 4.41
1364 12087 7.253422 AGTAAGCAAGCAAAGCAATTATACAG 58.747 34.615 0.00 0.00 0.00 2.74
1370 12104 3.495753 GCAAGTAAGCAAGCAAAGCAATT 59.504 39.130 0.00 0.00 0.00 2.32
1377 12111 1.877637 TCGAGCAAGTAAGCAAGCAA 58.122 45.000 0.00 0.00 36.85 3.91
1378 12112 2.002586 GATCGAGCAAGTAAGCAAGCA 58.997 47.619 0.00 0.00 36.85 3.91
1379 12113 2.002586 TGATCGAGCAAGTAAGCAAGC 58.997 47.619 0.00 0.00 36.85 4.01
1380 12114 3.484886 GCTTGATCGAGCAAGTAAGCAAG 60.485 47.826 35.74 16.17 45.41 4.01
1410 12144 1.268899 AGCTAACAAGCAAGCAAGCAG 59.731 47.619 3.19 0.00 41.32 4.24
1411 12145 1.321474 AGCTAACAAGCAAGCAAGCA 58.679 45.000 3.19 0.00 41.32 3.91
1412 12146 2.744202 TCTAGCTAACAAGCAAGCAAGC 59.256 45.455 0.00 0.00 41.32 4.01
1413 12147 3.999663 ACTCTAGCTAACAAGCAAGCAAG 59.000 43.478 0.00 0.00 41.32 4.01
1469 12220 4.956700 TGGAGGAAAGTCGAGTCTAATCAT 59.043 41.667 0.00 0.00 0.00 2.45
1514 12266 4.360951 AAGAAAATACGGGTCCAAGACA 57.639 40.909 0.00 0.00 33.68 3.41
1530 12283 7.721399 GGGCTGATTTAGGATGATCTAAAGAAA 59.279 37.037 0.00 0.00 40.97 2.52
1540 12299 2.489619 GGCATGGGCTGATTTAGGATGA 60.490 50.000 0.00 0.00 40.87 2.92
1556 12361 1.471287 CCTATCGCAATCATGGGCATG 59.529 52.381 0.00 0.00 39.24 4.06
1585 12390 1.768275 AGGACAGGAACACATGACACA 59.232 47.619 0.00 0.00 0.00 3.72
1592 12397 1.148273 GTGGCAGGACAGGAACACA 59.852 57.895 0.00 0.00 0.00 3.72
1613 12418 0.796312 GTCCAATACAGGCACACACG 59.204 55.000 0.00 0.00 0.00 4.49
1615 12420 0.394938 ACGTCCAATACAGGCACACA 59.605 50.000 0.00 0.00 0.00 3.72
1624 12429 4.523813 CAACACAAAGTGACGTCCAATAC 58.476 43.478 14.12 4.21 36.96 1.89
1644 12453 1.405526 GGACTCGCTCTTACATGGCAA 60.406 52.381 0.00 0.00 0.00 4.52
1650 12459 2.235891 TCAGTTGGACTCGCTCTTACA 58.764 47.619 0.00 0.00 0.00 2.41
1653 12462 1.964223 TCTTCAGTTGGACTCGCTCTT 59.036 47.619 0.00 0.00 0.00 2.85
1668 12477 6.293004 AGGGTGTCAAAATTTGTTTCTTCA 57.707 33.333 5.56 0.00 0.00 3.02
1721 12530 9.538508 GCTCTGCAAATGAGGATTATTTTATTT 57.461 29.630 3.87 0.00 32.57 1.40
1722 12531 8.146412 GGCTCTGCAAATGAGGATTATTTTATT 58.854 33.333 3.87 0.00 32.57 1.40
1723 12532 7.508296 AGGCTCTGCAAATGAGGATTATTTTAT 59.492 33.333 3.87 0.00 32.57 1.40
1724 12533 6.835488 AGGCTCTGCAAATGAGGATTATTTTA 59.165 34.615 3.87 0.00 32.57 1.52
1725 12534 5.659971 AGGCTCTGCAAATGAGGATTATTTT 59.340 36.000 3.87 0.00 32.57 1.82
1726 12535 5.206587 AGGCTCTGCAAATGAGGATTATTT 58.793 37.500 3.87 0.00 32.57 1.40
1727 12536 4.801164 AGGCTCTGCAAATGAGGATTATT 58.199 39.130 3.87 0.00 32.57 1.40
1728 12537 4.396522 GAGGCTCTGCAAATGAGGATTAT 58.603 43.478 7.40 0.00 32.57 1.28
1729 12538 3.742327 CGAGGCTCTGCAAATGAGGATTA 60.742 47.826 13.50 0.00 32.57 1.75
1753 12567 9.989296 TCATAAAAATGGAGAAGGGATCTTTTA 57.011 29.630 0.00 0.00 38.96 1.52
1938 12815 7.426929 AGTGATTTGAGTCAACAGTAATGAC 57.573 36.000 4.68 0.61 45.94 3.06
1939 12816 8.147704 TGTAGTGATTTGAGTCAACAGTAATGA 58.852 33.333 4.68 0.00 0.00 2.57
1945 12822 5.523552 TGTGTGTAGTGATTTGAGTCAACAG 59.476 40.000 4.68 0.00 0.00 3.16
1951 12828 3.809832 GCTGTGTGTGTAGTGATTTGAGT 59.190 43.478 0.00 0.00 0.00 3.41
1959 12836 1.151172 TGCGTGCTGTGTGTGTAGTG 61.151 55.000 0.00 0.00 0.00 2.74
1960 12837 1.142965 TGCGTGCTGTGTGTGTAGT 59.857 52.632 0.00 0.00 0.00 2.73
1981 12858 2.347731 TGCGTGTCTTGTGTTGTGTTA 58.652 42.857 0.00 0.00 0.00 2.41
2012 12889 9.244292 AGAGATGTGTAACTGAGTAAGTGAATA 57.756 33.333 0.00 0.00 39.81 1.75
2019 12896 5.185249 GTGGGAGAGATGTGTAACTGAGTAA 59.815 44.000 0.00 0.00 38.04 2.24
2020 12897 4.705507 GTGGGAGAGATGTGTAACTGAGTA 59.294 45.833 0.00 0.00 38.04 2.59
2023 12900 3.506398 TGTGGGAGAGATGTGTAACTGA 58.494 45.455 0.00 0.00 38.04 3.41
2028 12905 1.937191 TGCTGTGGGAGAGATGTGTA 58.063 50.000 0.00 0.00 0.00 2.90
2089 12985 5.458595 GGAAATGGGTGGATAAAATCTCCT 58.541 41.667 0.00 0.00 33.69 3.69
2101 12997 1.455587 CATCGGGGGAAATGGGTGG 60.456 63.158 0.00 0.00 0.00 4.61
2102 12998 0.751643 GTCATCGGGGGAAATGGGTG 60.752 60.000 0.00 0.00 0.00 4.61
2131 13028 0.540365 AGGTGGTTGGACATTGGCAG 60.540 55.000 0.00 0.00 0.00 4.85
2194 13113 9.685276 AAAAATTGAGAAGAAGGAAAAACCATT 57.315 25.926 0.00 0.00 42.04 3.16
2217 13136 8.695456 AGGAAGCTCTGTTTATCAAAAGAAAAA 58.305 29.630 0.00 0.00 0.00 1.94
2218 13137 8.237811 AGGAAGCTCTGTTTATCAAAAGAAAA 57.762 30.769 0.00 0.00 0.00 2.29
2219 13138 7.721399 AGAGGAAGCTCTGTTTATCAAAAGAAA 59.279 33.333 0.00 0.00 31.60 2.52
2220 13139 7.227156 AGAGGAAGCTCTGTTTATCAAAAGAA 58.773 34.615 0.00 0.00 31.60 2.52
2221 13140 6.773638 AGAGGAAGCTCTGTTTATCAAAAGA 58.226 36.000 0.00 0.00 31.60 2.52
2222 13141 6.093357 GGAGAGGAAGCTCTGTTTATCAAAAG 59.907 42.308 0.00 0.00 35.26 2.27
2223 13142 5.940470 GGAGAGGAAGCTCTGTTTATCAAAA 59.060 40.000 0.00 0.00 35.26 2.44
2224 13143 5.491982 GGAGAGGAAGCTCTGTTTATCAAA 58.508 41.667 0.00 0.00 35.26 2.69
2225 13144 4.382040 CGGAGAGGAAGCTCTGTTTATCAA 60.382 45.833 0.00 0.00 36.69 2.57
2226 13145 3.131223 CGGAGAGGAAGCTCTGTTTATCA 59.869 47.826 0.00 0.00 36.69 2.15
2227 13146 3.381908 TCGGAGAGGAAGCTCTGTTTATC 59.618 47.826 0.00 0.00 41.15 1.75
2228 13147 3.366396 TCGGAGAGGAAGCTCTGTTTAT 58.634 45.455 0.00 0.00 41.15 1.40
2229 13148 2.803956 TCGGAGAGGAAGCTCTGTTTA 58.196 47.619 0.00 0.00 41.15 2.01
2230 13149 1.633774 TCGGAGAGGAAGCTCTGTTT 58.366 50.000 0.00 0.00 41.15 2.83
2231 13150 1.859302 ATCGGAGAGGAAGCTCTGTT 58.141 50.000 0.00 0.00 43.63 3.16
2232 13151 1.859302 AATCGGAGAGGAAGCTCTGT 58.141 50.000 0.00 0.00 43.63 3.41
2233 13152 2.430332 AGAAATCGGAGAGGAAGCTCTG 59.570 50.000 0.00 0.00 43.63 3.35
2234 13153 2.430332 CAGAAATCGGAGAGGAAGCTCT 59.570 50.000 0.00 0.00 43.63 4.09
2235 13154 2.167487 ACAGAAATCGGAGAGGAAGCTC 59.833 50.000 0.00 0.00 43.63 4.09
2236 13155 2.183679 ACAGAAATCGGAGAGGAAGCT 58.816 47.619 0.00 0.00 43.63 3.74
2237 13156 2.682155 ACAGAAATCGGAGAGGAAGC 57.318 50.000 0.00 0.00 43.63 3.86
2238 13157 7.717568 TCTAATAACAGAAATCGGAGAGGAAG 58.282 38.462 0.00 0.00 43.63 3.46
2239 13158 7.655521 TCTAATAACAGAAATCGGAGAGGAA 57.344 36.000 0.00 0.00 43.63 3.36
2240 13159 7.841282 ATCTAATAACAGAAATCGGAGAGGA 57.159 36.000 0.00 0.00 43.63 3.71
2241 13160 9.796120 GATATCTAATAACAGAAATCGGAGAGG 57.204 37.037 0.00 0.00 43.63 3.69
2257 13176 9.967346 GCTGTAACAGACAAGTGATATCTAATA 57.033 33.333 3.98 0.00 37.70 0.98
2258 13177 8.478066 TGCTGTAACAGACAAGTGATATCTAAT 58.522 33.333 3.98 0.00 37.70 1.73
2259 13178 7.836842 TGCTGTAACAGACAAGTGATATCTAA 58.163 34.615 3.98 0.00 37.70 2.10
2260 13179 7.404671 TGCTGTAACAGACAAGTGATATCTA 57.595 36.000 3.98 0.00 37.70 1.98
2261 13180 6.286240 TGCTGTAACAGACAAGTGATATCT 57.714 37.500 3.98 0.00 37.70 1.98
2262 13181 6.018425 CCATGCTGTAACAGACAAGTGATATC 60.018 42.308 0.00 0.00 37.70 1.63
2263 13182 5.819379 CCATGCTGTAACAGACAAGTGATAT 59.181 40.000 0.00 0.00 37.70 1.63
2264 13183 5.178061 CCATGCTGTAACAGACAAGTGATA 58.822 41.667 0.00 0.00 37.70 2.15
2265 13184 4.005650 CCATGCTGTAACAGACAAGTGAT 58.994 43.478 0.00 0.00 37.70 3.06
2266 13185 3.181455 ACCATGCTGTAACAGACAAGTGA 60.181 43.478 0.00 0.00 37.70 3.41
2267 13186 3.141398 ACCATGCTGTAACAGACAAGTG 58.859 45.455 0.00 0.00 37.70 3.16
2268 13187 3.492102 ACCATGCTGTAACAGACAAGT 57.508 42.857 0.00 0.00 37.70 3.16
2269 13188 4.836125 AAACCATGCTGTAACAGACAAG 57.164 40.909 0.00 0.00 37.70 3.16
2270 13189 5.451242 GGAAAAACCATGCTGTAACAGACAA 60.451 40.000 0.00 0.00 36.69 3.18
2271 13190 4.037446 GGAAAAACCATGCTGTAACAGACA 59.963 41.667 0.00 0.00 38.79 3.41
2272 13191 4.278419 AGGAAAAACCATGCTGTAACAGAC 59.722 41.667 0.00 0.00 42.04 3.51
2273 13192 4.469657 AGGAAAAACCATGCTGTAACAGA 58.530 39.130 0.00 0.00 42.04 3.41
2274 13193 4.853924 AGGAAAAACCATGCTGTAACAG 57.146 40.909 0.00 0.00 42.04 3.16
2275 13194 6.716934 TTTAGGAAAAACCATGCTGTAACA 57.283 33.333 0.00 0.00 42.04 2.41
2276 13195 7.402811 GTTTTAGGAAAAACCATGCTGTAAC 57.597 36.000 2.97 0.00 45.77 2.50
2315 13234 8.888579 AACCGATTAATACTCATTTGTCCTAG 57.111 34.615 0.00 0.00 0.00 3.02
2346 13265 5.500234 TCCAGGATAGACCAAACTGATTTG 58.500 41.667 0.00 0.00 44.19 2.32
2360 13279 6.238239 CGATGAGACACGTATATCCAGGATAG 60.238 46.154 14.78 4.21 0.00 2.08
2368 13287 4.383052 CCTTTGCGATGAGACACGTATATC 59.617 45.833 0.00 0.00 0.00 1.63
2374 13293 0.716108 GTCCTTTGCGATGAGACACG 59.284 55.000 0.00 0.00 0.00 4.49
2382 13301 7.415206 GGTTAATAGTCATTTGTCCTTTGCGAT 60.415 37.037 0.00 0.00 0.00 4.58
2383 13302 6.128117 GGTTAATAGTCATTTGTCCTTTGCGA 60.128 38.462 0.00 0.00 0.00 5.10
2384 13303 6.027749 GGTTAATAGTCATTTGTCCTTTGCG 58.972 40.000 0.00 0.00 0.00 4.85
2385 13304 6.919721 TGGTTAATAGTCATTTGTCCTTTGC 58.080 36.000 0.00 0.00 0.00 3.68
2386 13305 8.522830 ACATGGTTAATAGTCATTTGTCCTTTG 58.477 33.333 0.00 0.00 0.00 2.77
2390 13309 6.095440 AGCACATGGTTAATAGTCATTTGTCC 59.905 38.462 0.00 0.00 0.00 4.02
2392 13311 6.095440 GGAGCACATGGTTAATAGTCATTTGT 59.905 38.462 0.00 0.00 0.00 2.83
2393 13312 6.095300 TGGAGCACATGGTTAATAGTCATTTG 59.905 38.462 0.00 0.00 0.00 2.32
2397 13316 4.835284 TGGAGCACATGGTTAATAGTCA 57.165 40.909 0.00 0.00 0.00 3.41
2399 13318 6.096846 GGAAATTGGAGCACATGGTTAATAGT 59.903 38.462 0.00 0.00 0.00 2.12
2400 13319 6.096705 TGGAAATTGGAGCACATGGTTAATAG 59.903 38.462 0.00 0.00 0.00 1.73
2403 13322 4.155709 TGGAAATTGGAGCACATGGTTAA 58.844 39.130 0.00 0.00 0.00 2.01
2404 13323 3.763360 CTGGAAATTGGAGCACATGGTTA 59.237 43.478 0.00 0.00 0.00 2.85
2407 13326 1.134907 GCTGGAAATTGGAGCACATGG 60.135 52.381 0.00 0.00 32.70 3.66
2408 13327 1.546923 TGCTGGAAATTGGAGCACATG 59.453 47.619 0.00 0.00 37.81 3.21
2409 13328 1.927487 TGCTGGAAATTGGAGCACAT 58.073 45.000 0.00 0.00 37.81 3.21
2507 13466 7.092444 ACAGTTAGAGATTATGATTGTTCCCCA 60.092 37.037 0.00 0.00 0.00 4.96
2627 13587 7.225011 TGTGTGGGTAGTATGTTGACAAATAA 58.775 34.615 0.00 0.00 0.00 1.40
2628 13588 6.770542 TGTGTGGGTAGTATGTTGACAAATA 58.229 36.000 0.00 0.00 0.00 1.40
2629 13589 5.626142 TGTGTGGGTAGTATGTTGACAAAT 58.374 37.500 0.00 0.00 0.00 2.32
2630 13590 5.037383 TGTGTGGGTAGTATGTTGACAAA 57.963 39.130 0.00 0.00 0.00 2.83
2631 13591 4.691326 TGTGTGGGTAGTATGTTGACAA 57.309 40.909 0.00 0.00 0.00 3.18
2632 13592 4.637276 CTTGTGTGGGTAGTATGTTGACA 58.363 43.478 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.