Multiple sequence alignment - TraesCS3A01G302100

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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 TraesCS3A01G302100 chr3A 100.000 4898 0 0 1 4898 535322796 535327693 0.000000e+00 9046.0
1 TraesCS3A01G302100 chr3A 94.513 893 19 4 1483 2349 18827298 18826410 0.000000e+00 1351.0
2 TraesCS3A01G302100 chr3A 84.310 478 66 7 3419 3894 535719209 535719679 4.470000e-125 459.0
3 TraesCS3A01G302100 chr3D 93.180 2214 117 17 2702 4898 414767859 414765663 0.000000e+00 3221.0
4 TraesCS3A01G302100 chr3D 92.426 779 31 12 718 1492 414769406 414768652 0.000000e+00 1086.0
5 TraesCS3A01G302100 chr3D 88.787 544 42 8 1484 2018 496697193 496696660 0.000000e+00 649.0
6 TraesCS3A01G302100 chr3D 93.498 323 19 2 45 367 414770067 414769747 3.430000e-131 479.0
7 TraesCS3A01G302100 chr3D 84.551 479 64 9 3419 3894 414640312 414639841 2.670000e-127 466.0
8 TraesCS3A01G302100 chr3D 90.323 341 29 1 2020 2360 584350463 584350799 1.250000e-120 444.0
9 TraesCS3A01G302100 chr3D 89.961 259 15 7 394 648 414769747 414769496 1.700000e-84 324.0
10 TraesCS3A01G302100 chr3D 91.083 157 14 0 1001 1157 414641866 414641710 3.840000e-51 213.0
11 TraesCS3A01G302100 chr3D 90.446 157 14 1 2414 2570 414768042 414767887 6.430000e-49 206.0
12 TraesCS3A01G302100 chr3D 93.651 63 3 1 2353 2414 414768667 414768605 5.220000e-15 93.5
13 TraesCS3A01G302100 chr3D 81.905 105 16 3 1050 1153 471044533 471044431 8.740000e-13 86.1
14 TraesCS3A01G302100 chr3B 91.903 1692 83 19 2485 4164 540659396 540657747 0.000000e+00 2316.0
15 TraesCS3A01G302100 chr3B 91.343 797 32 19 718 1501 540660876 540660104 0.000000e+00 1055.0
16 TraesCS3A01G302100 chr3B 84.130 460 69 3 3436 3894 540482550 540482094 4.500000e-120 442.0
17 TraesCS3A01G302100 chr3B 92.273 220 14 2 4292 4511 540657391 540657175 4.760000e-80 309.0
18 TraesCS3A01G302100 chr3B 82.250 400 29 16 267 651 540661266 540660894 1.710000e-79 307.0
19 TraesCS3A01G302100 chr3B 90.506 158 15 0 1000 1157 540484021 540483864 4.970000e-50 209.0
20 TraesCS3A01G302100 chr3B 96.364 55 1 1 2361 2414 540660116 540660062 6.750000e-14 89.8
21 TraesCS3A01G302100 chr2A 88.073 545 46 9 1483 2018 758368996 758368462 3.220000e-176 628.0
22 TraesCS3A01G302100 chr2A 90.606 330 27 4 2021 2348 678376059 678375732 7.530000e-118 435.0
23 TraesCS3A01G302100 chr2A 89.602 327 24 7 2025 2350 50434462 50434145 1.640000e-109 407.0
24 TraesCS3A01G302100 chr2A 83.861 316 37 9 1484 1787 50434146 50434459 6.200000e-74 289.0
25 TraesCS3A01G302100 chr5A 86.823 554 51 7 1483 2018 387226237 387225688 2.520000e-167 599.0
26 TraesCS3A01G302100 chr6D 86.837 547 57 6 1480 2018 414120432 414120971 9.070000e-167 597.0
27 TraesCS3A01G302100 chr1A 86.556 543 49 11 1490 2018 535037593 535038125 1.180000e-160 577.0
28 TraesCS3A01G302100 chr4B 85.278 557 58 11 1483 2018 603142568 603143121 1.990000e-153 553.0
29 TraesCS3A01G302100 chr5B 85.125 558 55 13 1484 2018 544532829 544532277 3.330000e-151 545.0
30 TraesCS3A01G302100 chr7A 86.720 497 38 16 1545 2017 717467581 717468073 1.210000e-145 527.0
31 TraesCS3A01G302100 chr1B 90.578 329 30 1 2021 2349 655254601 655254274 7.530000e-118 435.0
32 TraesCS3A01G302100 chr1B 97.368 38 1 0 1064 1101 133075744 133075781 1.140000e-06 65.8
33 TraesCS3A01G302100 chr2B 89.970 329 30 3 2021 2349 45554328 45554653 5.860000e-114 422.0
34 TraesCS3A01G302100 chr4A 88.957 326 32 4 2021 2346 64577933 64578254 2.750000e-107 399.0
35 TraesCS3A01G302100 chr4A 88.182 330 38 1 2020 2349 478095556 478095884 4.600000e-105 392.0
36 TraesCS3A01G302100 chr6B 88.685 327 27 7 2025 2350 96681592 96681275 1.650000e-104 390.0
37 TraesCS3A01G302100 chr6B 82.595 316 41 9 1484 1787 96681276 96681589 2.910000e-67 267.0
38 TraesCS3A01G302100 chr1D 77.283 427 60 19 1480 1874 462904476 462904897 2.970000e-52 217.0
39 TraesCS3A01G302100 chr1D 100.000 38 0 0 1064 1101 80537156 80537193 2.450000e-08 71.3
40 TraesCS3A01G302100 chr5D 82.530 166 27 2 4726 4890 503436567 503436403 1.420000e-30 145.0
41 TraesCS3A01G302100 chr5D 81.905 105 16 3 1050 1153 493833690 493833792 8.740000e-13 86.1


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 TraesCS3A01G302100 chr3A 535322796 535327693 4897 False 9046.000000 9046 100.000000 1 4898 1 chr3A.!!$F1 4897
1 TraesCS3A01G302100 chr3A 18826410 18827298 888 True 1351.000000 1351 94.513000 1483 2349 1 chr3A.!!$R1 866
2 TraesCS3A01G302100 chr3D 414765663 414770067 4404 True 901.583333 3221 92.193667 45 4898 6 chr3D.!!$R4 4853
3 TraesCS3A01G302100 chr3D 496696660 496697193 533 True 649.000000 649 88.787000 1484 2018 1 chr3D.!!$R2 534
4 TraesCS3A01G302100 chr3D 414639841 414641866 2025 True 339.500000 466 87.817000 1001 3894 2 chr3D.!!$R3 2893
5 TraesCS3A01G302100 chr3B 540657175 540661266 4091 True 815.360000 2316 90.826600 267 4511 5 chr3B.!!$R2 4244
6 TraesCS3A01G302100 chr3B 540482094 540484021 1927 True 325.500000 442 87.318000 1000 3894 2 chr3B.!!$R1 2894
7 TraesCS3A01G302100 chr2A 758368462 758368996 534 True 628.000000 628 88.073000 1483 2018 1 chr2A.!!$R3 535
8 TraesCS3A01G302100 chr5A 387225688 387226237 549 True 599.000000 599 86.823000 1483 2018 1 chr5A.!!$R1 535
9 TraesCS3A01G302100 chr6D 414120432 414120971 539 False 597.000000 597 86.837000 1480 2018 1 chr6D.!!$F1 538
10 TraesCS3A01G302100 chr1A 535037593 535038125 532 False 577.000000 577 86.556000 1490 2018 1 chr1A.!!$F1 528
11 TraesCS3A01G302100 chr4B 603142568 603143121 553 False 553.000000 553 85.278000 1483 2018 1 chr4B.!!$F1 535
12 TraesCS3A01G302100 chr5B 544532277 544532829 552 True 545.000000 545 85.125000 1484 2018 1 chr5B.!!$R1 534

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
739 799 0.108585 TGGCTGAAGAAACGGAAGCT 59.891 50.000 0.00 0.00 34.29 3.74 F
988 1054 0.455295 GAGTGCGTTCGAGAGTGAGG 60.455 60.000 0.00 0.00 0.00 3.86 F
989 1055 0.889638 AGTGCGTTCGAGAGTGAGGA 60.890 55.000 0.00 0.00 0.00 3.71 F
990 1056 0.455295 GTGCGTTCGAGAGTGAGGAG 60.455 60.000 0.00 0.00 0.00 3.69 F
1158 1231 0.955428 TCGCCAGGAACGTACGTACT 60.955 55.000 23.12 19.46 0.00 2.73 F
2600 3640 1.032114 GCCTGCATTCAGTACCACCC 61.032 60.000 0.00 0.00 38.66 4.61 F
3207 4623 3.257393 CTCGTATGCTTGAAGCTTGAGT 58.743 45.455 18.94 2.25 42.97 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 3665 0.322456 TGCTGTAGTGGCCATGGAAC 60.322 55.000 18.40 13.06 0.00 3.62 R
2630 3670 0.465097 GATGCTGCTGTAGTGGCCAT 60.465 55.000 9.72 0.00 0.00 4.40 R
2632 3672 0.813210 GAGATGCTGCTGTAGTGGCC 60.813 60.000 0.00 0.00 0.00 5.36 R
2774 3832 3.120269 GCTGCAGAGAACAACATGAAGAG 60.120 47.826 20.43 0.00 0.00 2.85 R
2965 4025 7.177832 TGCTAGCTTTGTTATACTACAAGGA 57.822 36.000 17.23 0.00 39.06 3.36 R
3537 4957 0.177836 CGAGCCACACATCCACCATA 59.822 55.000 0.00 0.00 0.00 2.74 R
4521 6167 0.389391 TAGCGCCTCATCTAAGCACC 59.611 55.000 2.29 0.00 0.00 5.01 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
21 22 4.202245 GGTAAATATAGCGGAGATGCCA 57.798 45.455 0.00 0.00 35.94 4.92
22 23 4.770795 GGTAAATATAGCGGAGATGCCAT 58.229 43.478 0.00 0.00 35.94 4.40
23 24 4.572389 GGTAAATATAGCGGAGATGCCATG 59.428 45.833 0.00 0.00 35.94 3.66
24 25 2.996249 ATATAGCGGAGATGCCATGG 57.004 50.000 7.63 7.63 35.94 3.66
25 26 1.644509 TATAGCGGAGATGCCATGGT 58.355 50.000 14.67 0.00 35.94 3.55
26 27 0.767375 ATAGCGGAGATGCCATGGTT 59.233 50.000 14.67 0.59 35.94 3.67
27 28 0.546122 TAGCGGAGATGCCATGGTTT 59.454 50.000 14.67 0.16 35.94 3.27
28 29 0.323725 AGCGGAGATGCCATGGTTTT 60.324 50.000 14.67 0.00 35.94 2.43
29 30 1.064758 AGCGGAGATGCCATGGTTTTA 60.065 47.619 14.67 0.00 35.94 1.52
30 31 1.065551 GCGGAGATGCCATGGTTTTAC 59.934 52.381 14.67 2.84 35.94 2.01
31 32 1.330521 CGGAGATGCCATGGTTTTACG 59.669 52.381 14.67 5.63 35.94 3.18
32 33 2.639065 GGAGATGCCATGGTTTTACGA 58.361 47.619 14.67 0.00 36.34 3.43
33 34 2.614057 GGAGATGCCATGGTTTTACGAG 59.386 50.000 14.67 0.00 36.34 4.18
34 35 2.017049 AGATGCCATGGTTTTACGAGC 58.983 47.619 14.67 0.00 0.00 5.03
35 36 1.065551 GATGCCATGGTTTTACGAGCC 59.934 52.381 14.67 0.00 0.00 4.70
36 37 1.302383 TGCCATGGTTTTACGAGCCG 61.302 55.000 14.67 0.00 0.00 5.52
37 38 1.022451 GCCATGGTTTTACGAGCCGA 61.022 55.000 14.67 0.00 0.00 5.54
38 39 1.006832 CCATGGTTTTACGAGCCGAG 58.993 55.000 2.57 0.00 0.00 4.63
39 40 0.373716 CATGGTTTTACGAGCCGAGC 59.626 55.000 1.50 0.00 0.00 5.03
40 41 0.743345 ATGGTTTTACGAGCCGAGCC 60.743 55.000 1.50 0.00 0.00 4.70
41 42 1.079336 GGTTTTACGAGCCGAGCCT 60.079 57.895 1.50 0.00 0.00 4.58
42 43 0.672711 GGTTTTACGAGCCGAGCCTT 60.673 55.000 1.50 0.00 0.00 4.35
43 44 1.154197 GTTTTACGAGCCGAGCCTTT 58.846 50.000 1.50 0.00 0.00 3.11
73 74 2.313317 AGGGCCGACGAGTTTATATGA 58.687 47.619 0.00 0.00 0.00 2.15
85 86 6.128227 ACGAGTTTATATGAGATCCGCTAGAC 60.128 42.308 0.00 0.00 0.00 2.59
121 122 4.202524 ACCACATTGTTCAAGCCTTAGGTA 60.203 41.667 0.00 0.00 0.00 3.08
146 147 1.631405 TGGGCATTAGTTTTGCAGCT 58.369 45.000 0.00 0.00 41.95 4.24
155 156 6.498304 CATTAGTTTTGCAGCTAATCCGAAT 58.502 36.000 13.70 0.00 36.20 3.34
158 159 4.098416 GTTTTGCAGCTAATCCGAATGAC 58.902 43.478 0.00 0.00 0.00 3.06
195 196 6.053005 AGGAAGACGTTTTTGTCACTATGAA 58.947 36.000 0.00 0.00 41.41 2.57
221 222 5.637810 TGTTTGTGATAACTTCGTCCATCTC 59.362 40.000 0.00 0.00 0.00 2.75
224 225 5.789521 TGTGATAACTTCGTCCATCTCAAA 58.210 37.500 0.00 0.00 0.00 2.69
229 230 7.606073 TGATAACTTCGTCCATCTCAAAATTGA 59.394 33.333 0.00 0.00 35.57 2.57
230 231 6.824305 AACTTCGTCCATCTCAAAATTGAT 57.176 33.333 0.00 0.00 36.46 2.57
263 264 3.872459 ATCTCATTGAAGCTTAGGGGG 57.128 47.619 0.00 0.00 0.00 5.40
410 411 2.567615 AGAAACAAGCGTCCCATAGAGT 59.432 45.455 0.00 0.00 0.00 3.24
476 485 4.840005 GGCCCCTCAGCAGCGTAC 62.840 72.222 0.00 0.00 0.00 3.67
566 578 2.515376 GAGATGCGCGGATCTCAAG 58.485 57.895 45.56 5.44 45.38 3.02
636 652 6.861055 TCGCTGAAAAGTGAAAACCAATTATC 59.139 34.615 0.00 0.00 32.14 1.75
637 653 6.089417 CGCTGAAAAGTGAAAACCAATTATCC 59.911 38.462 0.00 0.00 32.14 2.59
638 654 6.089417 GCTGAAAAGTGAAAACCAATTATCCG 59.911 38.462 0.00 0.00 32.14 4.18
640 656 7.717568 TGAAAAGTGAAAACCAATTATCCGAA 58.282 30.769 0.00 0.00 32.14 4.30
643 659 8.587952 AAAGTGAAAACCAATTATCCGAAAAG 57.412 30.769 0.00 0.00 32.14 2.27
644 660 7.519032 AGTGAAAACCAATTATCCGAAAAGA 57.481 32.000 0.00 0.00 0.00 2.52
645 661 7.947282 AGTGAAAACCAATTATCCGAAAAGAA 58.053 30.769 0.00 0.00 0.00 2.52
646 662 8.585018 AGTGAAAACCAATTATCCGAAAAGAAT 58.415 29.630 0.00 0.00 0.00 2.40
647 663 9.849166 GTGAAAACCAATTATCCGAAAAGAATA 57.151 29.630 0.00 0.00 0.00 1.75
662 678 9.410556 CCGAAAAGAATATCAATCACAAAAACT 57.589 29.630 0.00 0.00 0.00 2.66
674 690 3.751175 TCACAAAAACTGAATAGAGCGGG 59.249 43.478 0.00 0.00 0.00 6.13
676 692 2.420058 AAAACTGAATAGAGCGGGGG 57.580 50.000 0.00 0.00 0.00 5.40
711 727 6.822073 AAAAACTCGTGCAAAAATAAGGAC 57.178 33.333 0.00 0.00 0.00 3.85
723 783 6.034577 GCAAAAATAAGGACGACTAAAATGGC 59.965 38.462 0.00 0.00 0.00 4.40
739 799 0.108585 TGGCTGAAGAAACGGAAGCT 59.891 50.000 0.00 0.00 34.29 3.74
747 807 3.088789 AGAAACGGAAGCTCCTAGAGA 57.911 47.619 0.00 0.00 33.30 3.10
824 890 3.775654 CTCTCCCACTCCACGGCC 61.776 72.222 0.00 0.00 0.00 6.13
890 956 3.949885 TTAGCCGAGACCCCGAGCA 62.950 63.158 0.00 0.00 0.00 4.26
901 967 1.144936 CCCGAGCATGGTCTTCTCC 59.855 63.158 21.73 0.00 0.00 3.71
902 968 1.617018 CCCGAGCATGGTCTTCTCCA 61.617 60.000 21.73 0.00 42.01 3.86
904 970 1.539929 CCGAGCATGGTCTTCTCCATC 60.540 57.143 21.73 0.00 45.23 3.51
905 971 1.539929 CGAGCATGGTCTTCTCCATCC 60.540 57.143 21.73 0.00 45.23 3.51
979 1045 0.580104 AAAAGGTTCGAGTGCGTTCG 59.420 50.000 3.52 3.52 41.79 3.95
984 1050 3.651645 TCGAGTGCGTTCGAGAGT 58.348 55.556 8.11 0.00 44.00 3.24
985 1051 1.206831 TCGAGTGCGTTCGAGAGTG 59.793 57.895 8.11 0.00 44.00 3.51
986 1052 1.206831 CGAGTGCGTTCGAGAGTGA 59.793 57.895 3.83 0.00 43.03 3.41
987 1053 0.791238 CGAGTGCGTTCGAGAGTGAG 60.791 60.000 3.83 0.00 43.03 3.51
988 1054 0.455295 GAGTGCGTTCGAGAGTGAGG 60.455 60.000 0.00 0.00 0.00 3.86
989 1055 0.889638 AGTGCGTTCGAGAGTGAGGA 60.890 55.000 0.00 0.00 0.00 3.71
990 1056 0.455295 GTGCGTTCGAGAGTGAGGAG 60.455 60.000 0.00 0.00 0.00 3.69
1158 1231 0.955428 TCGCCAGGAACGTACGTACT 60.955 55.000 23.12 19.46 0.00 2.73
1255 1338 3.134458 GCCTCTAATTTCACGAGGATGG 58.866 50.000 8.63 0.00 45.67 3.51
1337 1420 2.586792 GGTCGCTTCCATGCCTCT 59.413 61.111 0.00 0.00 0.00 3.69
1398 1485 4.152759 GCTGTCGCTCTCGTATAATCTAGT 59.847 45.833 0.00 0.00 36.96 2.57
1399 1486 5.348179 GCTGTCGCTCTCGTATAATCTAGTA 59.652 44.000 0.00 0.00 36.96 1.82
1465 1552 5.277857 AGACTGGGGTTCGATATTTACAG 57.722 43.478 0.00 0.00 0.00 2.74
1473 1560 7.162082 GGGGTTCGATATTTACAGATCATTCT 58.838 38.462 0.00 0.00 0.00 2.40
1474 1561 8.311836 GGGGTTCGATATTTACAGATCATTCTA 58.688 37.037 0.00 0.00 0.00 2.10
1475 1562 9.360093 GGGTTCGATATTTACAGATCATTCTAG 57.640 37.037 0.00 0.00 0.00 2.43
1476 1563 9.915629 GGTTCGATATTTACAGATCATTCTAGT 57.084 33.333 0.00 0.00 0.00 2.57
1950 2314 5.817296 GGGAAGAAACTTTGAAAAAGTGCAT 59.183 36.000 6.16 0.00 0.00 3.96
2349 2742 7.014518 TCGAGGACGAAAAATATACTTATCCCA 59.985 37.037 0.00 0.00 45.74 4.37
2350 2743 7.328737 CGAGGACGAAAAATATACTTATCCCAG 59.671 40.741 0.00 0.00 42.66 4.45
2351 2744 8.030913 AGGACGAAAAATATACTTATCCCAGT 57.969 34.615 0.00 0.00 0.00 4.00
2449 3489 5.279910 GCATATTCTCTTCCAGTATGAGGCT 60.280 44.000 0.00 0.00 39.69 4.58
2531 3571 1.763770 CAGGAGTCCCAAGCAACCT 59.236 57.895 5.25 0.00 33.88 3.50
2546 3586 2.669364 CAACCTGCAAATGCTCAGAAC 58.331 47.619 6.97 0.00 42.66 3.01
2549 3589 1.135859 CCTGCAAATGCTCAGAACGTC 60.136 52.381 6.97 0.00 42.66 4.34
2550 3590 1.802960 CTGCAAATGCTCAGAACGTCT 59.197 47.619 6.97 0.00 42.66 4.18
2561 3601 2.792674 TCAGAACGTCTACAGCAAAACG 59.207 45.455 0.00 0.00 40.77 3.60
2571 3611 3.609103 ACAGCAAAACGTAAAGCAGAG 57.391 42.857 8.44 1.71 0.00 3.35
2575 3615 3.112580 GCAAAACGTAAAGCAGAGCAAA 58.887 40.909 0.00 0.00 0.00 3.68
2600 3640 1.032114 GCCTGCATTCAGTACCACCC 61.032 60.000 0.00 0.00 38.66 4.61
2605 3645 3.616219 TGCATTCAGTACCACCCATTAC 58.384 45.455 0.00 0.00 0.00 1.89
2607 3647 3.869065 CATTCAGTACCACCCATTACGT 58.131 45.455 0.00 0.00 0.00 3.57
2735 3775 3.631686 TGATAGTAATTGTGGCATGTGGC 59.368 43.478 0.00 0.00 43.74 5.01
2758 3810 6.858478 GGCTTCTGTTTTTAGAGATTTGACAC 59.142 38.462 0.00 0.00 0.00 3.67
2760 3812 7.589221 GCTTCTGTTTTTAGAGATTTGACACAG 59.411 37.037 0.00 0.00 0.00 3.66
2765 3823 9.219603 TGTTTTTAGAGATTTGACACAGGATAG 57.780 33.333 0.00 0.00 0.00 2.08
2774 3832 7.768120 AGATTTGACACAGGATAGAACTCATTC 59.232 37.037 0.00 0.00 34.78 2.67
2965 4025 7.865707 TGTTTGTTTTGCTGTTAATGTTGTTT 58.134 26.923 0.00 0.00 0.00 2.83
3163 4307 7.926555 CCTGGCATTATATTAGGAGTTATACCG 59.073 40.741 0.00 0.00 0.00 4.02
3179 4595 8.272545 AGTTATACCGTTTGGAGTTTTAATCC 57.727 34.615 0.00 0.00 39.21 3.01
3207 4623 3.257393 CTCGTATGCTTGAAGCTTGAGT 58.743 45.455 18.94 2.25 42.97 3.41
3210 4626 4.515191 TCGTATGCTTGAAGCTTGAGTTTT 59.485 37.500 18.94 0.00 42.97 2.43
3249 4669 9.691362 AATAATTAGTTAACAACCACAAGCTTG 57.309 29.630 24.84 24.84 0.00 4.01
3290 4710 5.954757 TGAGTTATGGTAAGGTTTCCCAAA 58.045 37.500 0.00 0.00 0.00 3.28
3439 4859 8.970859 ATCCTCATAACTCTGGTTCTATTTTG 57.029 34.615 0.00 0.00 36.92 2.44
3454 4874 9.378597 GGTTCTATTTTGTTTTTCTCTTCGTAC 57.621 33.333 0.00 0.00 0.00 3.67
3537 4957 0.108424 GCGACATCAAGGAGTCAGCT 60.108 55.000 0.00 0.00 34.48 4.24
3585 5005 3.254654 CATCAGTACACCGCCGCG 61.255 66.667 5.59 5.59 0.00 6.46
3647 5067 2.665603 GGGAGCCACTGACCAGAC 59.334 66.667 3.76 0.00 0.00 3.51
3659 5079 1.141881 ACCAGACGGTCATCGATGC 59.858 57.895 20.81 14.84 44.71 3.91
3944 5364 2.073816 CGAAATAAGCCGAGGTGTGTT 58.926 47.619 0.00 0.00 0.00 3.32
3945 5365 2.482721 CGAAATAAGCCGAGGTGTGTTT 59.517 45.455 0.00 0.00 0.00 2.83
3964 5384 2.436646 CCCCGATGTGTGCCTGTC 60.437 66.667 0.00 0.00 0.00 3.51
4031 5451 1.134995 TGTGCTTGCGATCCTGTCTAG 60.135 52.381 0.00 0.00 0.00 2.43
4089 5509 8.474025 TGGTTTAATAATAAATTGTGCCCAGAG 58.526 33.333 0.00 0.00 33.76 3.35
4158 5579 4.821805 GTCCATTAGCAATTTAGCTGCCTA 59.178 41.667 0.00 0.00 46.11 3.93
4204 5625 0.663568 AGTCTGTTTCGGAAGACGCG 60.664 55.000 3.53 3.53 46.05 6.01
4206 5627 1.663702 CTGTTTCGGAAGACGCGGT 60.664 57.895 12.47 0.00 43.86 5.68
4246 5667 7.060421 GATCCATAAGATTGGGAACCTGTTTA 58.940 38.462 0.00 0.00 43.04 2.01
4263 5684 3.960102 TGTTTATGCCATTTGATCCTCCC 59.040 43.478 0.00 0.00 0.00 4.30
4278 5699 7.265599 TGATCCTCCCAAGTTGAATAGTTTA 57.734 36.000 3.87 0.00 0.00 2.01
4280 5701 8.167392 TGATCCTCCCAAGTTGAATAGTTTAAA 58.833 33.333 3.87 0.00 0.00 1.52
4287 5708 6.210078 CAAGTTGAATAGTTTAAACGGCCAA 58.790 36.000 12.54 11.94 0.00 4.52
4288 5709 6.394025 AGTTGAATAGTTTAAACGGCCAAA 57.606 33.333 12.54 4.12 0.00 3.28
4289 5710 6.443792 AGTTGAATAGTTTAAACGGCCAAAG 58.556 36.000 12.54 0.00 0.00 2.77
4290 5711 6.263617 AGTTGAATAGTTTAAACGGCCAAAGA 59.736 34.615 12.54 0.00 0.00 2.52
4291 5712 6.636562 TGAATAGTTTAAACGGCCAAAGAA 57.363 33.333 12.54 0.00 0.00 2.52
4292 5713 6.440436 TGAATAGTTTAAACGGCCAAAGAAC 58.560 36.000 12.54 0.45 0.00 3.01
4293 5714 3.720949 AGTTTAAACGGCCAAAGAACC 57.279 42.857 12.54 0.00 0.00 3.62
4294 5715 3.025262 AGTTTAAACGGCCAAAGAACCA 58.975 40.909 12.54 0.00 0.00 3.67
4295 5716 3.639561 AGTTTAAACGGCCAAAGAACCAT 59.360 39.130 12.54 0.00 0.00 3.55
4296 5717 4.828387 AGTTTAAACGGCCAAAGAACCATA 59.172 37.500 12.54 0.00 0.00 2.74
4297 5718 5.479027 AGTTTAAACGGCCAAAGAACCATAT 59.521 36.000 12.54 0.00 0.00 1.78
4298 5719 3.866883 AAACGGCCAAAGAACCATATG 57.133 42.857 2.24 0.00 0.00 1.78
4299 5720 2.799126 ACGGCCAAAGAACCATATGA 57.201 45.000 2.24 0.00 0.00 2.15
4300 5721 3.297134 ACGGCCAAAGAACCATATGAT 57.703 42.857 2.24 0.00 0.00 2.45
4301 5722 3.631250 ACGGCCAAAGAACCATATGATT 58.369 40.909 2.24 0.00 0.00 2.57
4302 5723 3.632145 ACGGCCAAAGAACCATATGATTC 59.368 43.478 2.24 2.27 0.00 2.52
4307 5953 6.772716 GGCCAAAGAACCATATGATTCTTCTA 59.227 38.462 22.72 0.00 42.89 2.10
4381 6027 4.525912 ATTTGTCCAATGCTTCTTCACC 57.474 40.909 0.00 0.00 0.00 4.02
4389 6035 1.608055 TGCTTCTTCACCATGGTGTG 58.392 50.000 37.49 30.26 45.55 3.82
4437 6083 1.829533 CCACAAGCCTGGCAACACT 60.830 57.895 22.65 0.00 46.17 3.55
4493 6139 2.521465 CCCTGGTGCAGTTTGCCA 60.521 61.111 0.00 0.00 44.23 4.92
4536 6182 1.661341 CACAGGTGCTTAGATGAGGC 58.339 55.000 0.00 0.00 0.00 4.70
4542 6188 2.550978 GTGCTTAGATGAGGCGCTAAA 58.449 47.619 7.64 0.00 34.21 1.85
4577 6223 2.898612 GACTAGGGGTCCTAACCTATGC 59.101 54.545 0.00 0.00 45.66 3.14
4605 6251 5.020795 TGTTATCTATGGGCCGAGCTAATA 58.979 41.667 0.00 0.00 0.00 0.98
4615 6261 1.067495 CCGAGCTAATAGCCCACTAGC 60.067 57.143 8.88 0.00 43.77 3.42
4616 6262 1.067495 CGAGCTAATAGCCCACTAGCC 60.067 57.143 8.88 0.00 43.77 3.93
4621 6267 1.041447 AATAGCCCACTAGCCGTCGT 61.041 55.000 0.00 0.00 0.00 4.34
4670 6316 3.074412 CGTAAGCAAGATGGAAACCACT 58.926 45.455 0.00 0.00 35.80 4.00
4672 6318 1.915141 AGCAAGATGGAAACCACTGG 58.085 50.000 0.00 0.00 35.80 4.00
4688 6334 4.158025 ACCACTGGAGACTTCGTATACTTG 59.842 45.833 0.71 0.00 0.00 3.16
4699 6345 7.760340 AGACTTCGTATACTTGAAGGACAATTC 59.240 37.037 18.82 9.98 44.59 2.17
4735 6381 3.706600 TTATTCCTAGTTGCCAACCGT 57.293 42.857 3.45 0.00 0.00 4.83
4742 6388 1.750193 AGTTGCCAACCGTCCATATG 58.250 50.000 3.45 0.00 0.00 1.78
4776 6422 2.027192 CACCCCGGTGCATATATAAGCT 60.027 50.000 10.99 0.00 39.39 3.74
4781 6427 3.055819 CCGGTGCATATATAAGCTGAGGT 60.056 47.826 10.99 0.00 0.00 3.85
4789 6435 8.210946 TGCATATATAAGCTGAGGTGTTTAGTT 58.789 33.333 10.99 0.00 0.00 2.24
4791 6437 9.764363 CATATATAAGCTGAGGTGTTTAGTTCA 57.236 33.333 0.00 0.00 0.00 3.18
4806 6452 9.672086 GTGTTTAGTTCATAAAGCACAATTACA 57.328 29.630 0.00 0.00 36.48 2.41
4830 6476 3.323691 GCCTTAGGGTTTGGAACACAATT 59.676 43.478 0.00 0.00 39.21 2.32
4838 6484 8.608185 AGGGTTTGGAACACAATTATATGATT 57.392 30.769 0.00 0.00 39.29 2.57
4840 6486 9.665719 GGGTTTGGAACACAATTATATGATTTT 57.334 29.630 0.00 0.00 39.29 1.82
4860 6506 8.816894 TGATTTTGAGGTAGATTCTCTTGTACT 58.183 33.333 0.00 0.00 32.78 2.73
4877 6523 4.874199 TGTACTCTGTACCCCATCACATA 58.126 43.478 5.55 0.00 0.00 2.29
4890 6536 8.372877 ACCCCATCACATAAATACAATCAAAA 57.627 30.769 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.202245 TGGCATCTCCGCTATATTTACC 57.798 45.455 0.00 0.00 37.80 2.85
1 2 4.572389 CCATGGCATCTCCGCTATATTTAC 59.428 45.833 0.00 0.00 37.80 2.01
2 3 4.225042 ACCATGGCATCTCCGCTATATTTA 59.775 41.667 13.04 0.00 37.80 1.40
3 4 3.009473 ACCATGGCATCTCCGCTATATTT 59.991 43.478 13.04 0.00 37.80 1.40
5 6 2.191400 ACCATGGCATCTCCGCTATAT 58.809 47.619 13.04 0.00 37.80 0.86
6 7 1.644509 ACCATGGCATCTCCGCTATA 58.355 50.000 13.04 0.00 37.80 1.31
7 8 0.767375 AACCATGGCATCTCCGCTAT 59.233 50.000 13.04 0.00 37.80 2.97
8 9 0.546122 AAACCATGGCATCTCCGCTA 59.454 50.000 13.04 0.00 37.80 4.26
9 10 0.323725 AAAACCATGGCATCTCCGCT 60.324 50.000 13.04 0.00 37.80 5.52
10 11 1.065551 GTAAAACCATGGCATCTCCGC 59.934 52.381 13.04 0.00 37.80 5.54
11 12 1.330521 CGTAAAACCATGGCATCTCCG 59.669 52.381 13.04 3.69 37.80 4.63
12 13 2.614057 CTCGTAAAACCATGGCATCTCC 59.386 50.000 13.04 0.00 0.00 3.71
13 14 2.032178 GCTCGTAAAACCATGGCATCTC 59.968 50.000 13.04 0.00 0.00 2.75
14 15 2.017049 GCTCGTAAAACCATGGCATCT 58.983 47.619 13.04 0.00 0.00 2.90
15 16 1.065551 GGCTCGTAAAACCATGGCATC 59.934 52.381 13.04 0.00 0.00 3.91
16 17 1.102978 GGCTCGTAAAACCATGGCAT 58.897 50.000 13.04 0.00 0.00 4.40
17 18 1.302383 CGGCTCGTAAAACCATGGCA 61.302 55.000 13.04 0.00 0.00 4.92
18 19 1.022451 TCGGCTCGTAAAACCATGGC 61.022 55.000 13.04 0.00 0.00 4.40
19 20 1.006832 CTCGGCTCGTAAAACCATGG 58.993 55.000 11.19 11.19 0.00 3.66
20 21 0.373716 GCTCGGCTCGTAAAACCATG 59.626 55.000 0.00 0.00 0.00 3.66
21 22 0.743345 GGCTCGGCTCGTAAAACCAT 60.743 55.000 0.00 0.00 0.00 3.55
22 23 1.375013 GGCTCGGCTCGTAAAACCA 60.375 57.895 0.00 0.00 0.00 3.67
23 24 0.672711 AAGGCTCGGCTCGTAAAACC 60.673 55.000 0.00 0.00 0.00 3.27
24 25 1.154197 AAAGGCTCGGCTCGTAAAAC 58.846 50.000 0.00 0.00 0.00 2.43
25 26 1.802365 GAAAAGGCTCGGCTCGTAAAA 59.198 47.619 0.00 0.00 0.00 1.52
26 27 1.270412 TGAAAAGGCTCGGCTCGTAAA 60.270 47.619 0.00 0.00 0.00 2.01
27 28 0.319083 TGAAAAGGCTCGGCTCGTAA 59.681 50.000 0.00 0.00 0.00 3.18
28 29 0.535335 ATGAAAAGGCTCGGCTCGTA 59.465 50.000 0.00 0.00 0.00 3.43
29 30 1.021390 CATGAAAAGGCTCGGCTCGT 61.021 55.000 0.00 0.00 0.00 4.18
30 31 1.021390 ACATGAAAAGGCTCGGCTCG 61.021 55.000 0.00 0.00 0.00 5.03
31 32 2.024176 TACATGAAAAGGCTCGGCTC 57.976 50.000 0.00 0.00 0.00 4.70
32 33 2.489938 TTACATGAAAAGGCTCGGCT 57.510 45.000 0.00 0.00 0.00 5.52
33 34 3.569250 TTTTACATGAAAAGGCTCGGC 57.431 42.857 0.00 0.00 31.90 5.54
41 42 2.226912 CGTCGGCCCTTTTACATGAAAA 59.773 45.455 0.00 1.41 35.67 2.29
42 43 1.807742 CGTCGGCCCTTTTACATGAAA 59.192 47.619 0.00 0.00 0.00 2.69
43 44 1.002201 TCGTCGGCCCTTTTACATGAA 59.998 47.619 0.00 0.00 0.00 2.57
56 57 4.167268 GGATCTCATATAAACTCGTCGGC 58.833 47.826 0.00 0.00 0.00 5.54
73 74 1.993956 AGAGCATGTCTAGCGGATCT 58.006 50.000 0.00 0.00 37.01 2.75
85 86 3.507233 ACAATGTGGTGGTTTAGAGCATG 59.493 43.478 0.00 0.00 35.44 4.06
121 122 2.289631 GCAAAACTAATGCCCAAGCCTT 60.290 45.455 0.00 0.00 37.85 4.35
155 156 3.383505 TCTTCCTTCACTGAACGAAGTCA 59.616 43.478 20.77 8.21 45.00 3.41
158 159 2.726760 CGTCTTCCTTCACTGAACGAAG 59.273 50.000 17.80 17.80 39.69 3.79
170 171 6.053005 TCATAGTGACAAAAACGTCTTCCTT 58.947 36.000 0.00 0.00 36.82 3.36
172 173 5.917541 TCATAGTGACAAAAACGTCTTCC 57.082 39.130 0.00 0.00 36.82 3.46
203 204 7.606073 TCAATTTTGAGATGGACGAAGTTATCA 59.394 33.333 0.00 0.00 37.03 2.15
221 222 7.530010 AGATACTGAACCGACAATCAATTTTG 58.470 34.615 0.00 0.00 0.00 2.44
224 225 6.406370 TGAGATACTGAACCGACAATCAATT 58.594 36.000 0.00 0.00 0.00 2.32
229 230 5.977635 TCAATGAGATACTGAACCGACAAT 58.022 37.500 0.00 0.00 0.00 2.71
230 231 5.400066 TCAATGAGATACTGAACCGACAA 57.600 39.130 0.00 0.00 0.00 3.18
263 264 1.132643 CACTCTAGACGCACACCCTAC 59.867 57.143 0.00 0.00 0.00 3.18
385 386 4.825085 TCTATGGGACGCTTGTTTCTTTTT 59.175 37.500 0.00 0.00 0.00 1.94
386 387 4.394729 TCTATGGGACGCTTGTTTCTTTT 58.605 39.130 0.00 0.00 0.00 2.27
387 388 4.003648 CTCTATGGGACGCTTGTTTCTTT 58.996 43.478 0.00 0.00 0.00 2.52
388 389 3.008049 ACTCTATGGGACGCTTGTTTCTT 59.992 43.478 0.00 0.00 0.00 2.52
389 390 2.567615 ACTCTATGGGACGCTTGTTTCT 59.432 45.455 0.00 0.00 0.00 2.52
390 391 2.973945 ACTCTATGGGACGCTTGTTTC 58.026 47.619 0.00 0.00 0.00 2.78
410 411 4.716794 TCCGCTTGGTTTACTTCCTTTTA 58.283 39.130 0.00 0.00 0.00 1.52
440 441 3.991773 GGCCGGAAATTAAGTTTGTTTCC 59.008 43.478 5.05 16.18 44.64 3.13
636 652 9.410556 AGTTTTTGTGATTGATATTCTTTTCGG 57.589 29.630 0.00 0.00 0.00 4.30
646 662 8.390354 CGCTCTATTCAGTTTTTGTGATTGATA 58.610 33.333 0.00 0.00 0.00 2.15
647 663 7.246311 CGCTCTATTCAGTTTTTGTGATTGAT 58.754 34.615 0.00 0.00 0.00 2.57
648 664 6.348458 CCGCTCTATTCAGTTTTTGTGATTGA 60.348 38.462 0.00 0.00 0.00 2.57
649 665 5.796935 CCGCTCTATTCAGTTTTTGTGATTG 59.203 40.000 0.00 0.00 0.00 2.67
650 666 5.106157 CCCGCTCTATTCAGTTTTTGTGATT 60.106 40.000 0.00 0.00 0.00 2.57
657 673 2.420058 CCCCCGCTCTATTCAGTTTT 57.580 50.000 0.00 0.00 0.00 2.43
692 708 3.185797 GTCGTCCTTATTTTTGCACGAGT 59.814 43.478 0.00 0.00 36.97 4.18
708 724 3.596214 TCTTCAGCCATTTTAGTCGTCC 58.404 45.455 0.00 0.00 0.00 4.79
709 725 5.383130 GTTTCTTCAGCCATTTTAGTCGTC 58.617 41.667 0.00 0.00 0.00 4.20
710 726 4.084013 CGTTTCTTCAGCCATTTTAGTCGT 60.084 41.667 0.00 0.00 0.00 4.34
711 727 4.394795 CGTTTCTTCAGCCATTTTAGTCG 58.605 43.478 0.00 0.00 0.00 4.18
712 728 4.454504 TCCGTTTCTTCAGCCATTTTAGTC 59.545 41.667 0.00 0.00 0.00 2.59
714 730 5.371115 TTCCGTTTCTTCAGCCATTTTAG 57.629 39.130 0.00 0.00 0.00 1.85
716 732 3.552890 GCTTCCGTTTCTTCAGCCATTTT 60.553 43.478 0.00 0.00 0.00 1.82
723 783 2.464157 AGGAGCTTCCGTTTCTTCAG 57.536 50.000 0.00 0.00 42.75 3.02
764 824 3.959991 GAGGTGGAAGGTGCGGCTC 62.960 68.421 0.00 0.00 0.00 4.70
901 967 0.781920 ATGGGATGGGATGTGGGATG 59.218 55.000 0.00 0.00 0.00 3.51
902 968 1.078955 GATGGGATGGGATGTGGGAT 58.921 55.000 0.00 0.00 0.00 3.85
903 969 1.067762 GGATGGGATGGGATGTGGGA 61.068 60.000 0.00 0.00 0.00 4.37
904 970 1.462035 GGATGGGATGGGATGTGGG 59.538 63.158 0.00 0.00 0.00 4.61
905 971 1.073722 CGGATGGGATGGGATGTGG 59.926 63.158 0.00 0.00 0.00 4.17
935 1001 5.432680 TCTCTCTTCTTCTCGGTAGGTAA 57.567 43.478 0.00 0.00 0.00 2.85
936 1002 5.432680 TTCTCTCTTCTTCTCGGTAGGTA 57.567 43.478 0.00 0.00 0.00 3.08
937 1003 4.304048 TTCTCTCTTCTTCTCGGTAGGT 57.696 45.455 0.00 0.00 0.00 3.08
963 1029 1.081376 CTCGAACGCACTCGAACCT 60.081 57.895 8.32 0.00 46.53 3.50
979 1045 3.950397 TCTCTTCTCACTCCTCACTCTC 58.050 50.000 0.00 0.00 0.00 3.20
984 1050 2.106566 GCCATCTCTTCTCACTCCTCA 58.893 52.381 0.00 0.00 0.00 3.86
985 1051 2.362077 GAGCCATCTCTTCTCACTCCTC 59.638 54.545 0.00 0.00 36.42 3.71
986 1052 2.387757 GAGCCATCTCTTCTCACTCCT 58.612 52.381 0.00 0.00 36.42 3.69
987 1053 1.412343 GGAGCCATCTCTTCTCACTCC 59.588 57.143 0.00 0.00 39.31 3.85
988 1054 1.066908 CGGAGCCATCTCTTCTCACTC 59.933 57.143 0.00 0.00 39.31 3.51
989 1055 1.110442 CGGAGCCATCTCTTCTCACT 58.890 55.000 0.00 0.00 39.31 3.41
990 1056 0.103937 CCGGAGCCATCTCTTCTCAC 59.896 60.000 0.00 0.00 39.31 3.51
1158 1231 4.849310 GCGGCGGTTAGGGCATGA 62.849 66.667 9.78 0.00 0.00 3.07
1184 1262 2.017049 CAGTCACGGATGGGAAATTCC 58.983 52.381 2.79 2.79 35.23 3.01
1228 1306 3.407698 TCGTGAAATTAGAGGCAAGCAA 58.592 40.909 0.00 0.00 0.00 3.91
1398 1485 9.744468 TTCTTCTGAAATTCGAATCGTGATATA 57.256 29.630 11.83 0.00 0.00 0.86
1399 1486 8.648557 TTCTTCTGAAATTCGAATCGTGATAT 57.351 30.769 11.83 0.00 0.00 1.63
1465 1552 9.523168 ACTTATCCCTGTACTACTAGAATGATC 57.477 37.037 0.00 0.00 0.00 2.92
1673 1826 2.550978 CGCACCCGAGTATCTTTGATT 58.449 47.619 0.00 0.00 36.29 2.57
1968 2336 5.379732 AATAACATAGGACGAGCTCTAGC 57.620 43.478 12.85 0.31 42.49 3.42
1978 2346 3.120792 TCGCGCTCAAATAACATAGGAC 58.879 45.455 5.56 0.00 0.00 3.85
2073 2466 2.622942 GTTTGGACATTTCAGGTGCTCA 59.377 45.455 0.00 0.00 0.00 4.26
2349 2742 7.871463 GCGGAAAAACTCATACCATATACTACT 59.129 37.037 0.00 0.00 0.00 2.57
2350 2743 7.654520 TGCGGAAAAACTCATACCATATACTAC 59.345 37.037 0.00 0.00 0.00 2.73
2351 2744 7.728148 TGCGGAAAAACTCATACCATATACTA 58.272 34.615 0.00 0.00 0.00 1.82
2358 2751 1.810151 GCTGCGGAAAAACTCATACCA 59.190 47.619 0.00 0.00 0.00 3.25
2411 2807 5.817816 AGAGAATATGCTTCTTACAAACCGG 59.182 40.000 0.00 0.00 0.00 5.28
2419 3459 9.147732 TCATACTGGAAGAGAATATGCTTCTTA 57.852 33.333 0.00 0.00 40.20 2.10
2449 3489 1.144708 TCCATGAGCAACACAGGGAAA 59.855 47.619 0.00 0.00 43.56 3.13
2531 3571 1.882912 AGACGTTCTGAGCATTTGCA 58.117 45.000 5.20 0.00 45.16 4.08
2546 3586 3.060138 TGCTTTACGTTTTGCTGTAGACG 60.060 43.478 0.00 0.00 41.00 4.18
2549 3589 4.702392 CTCTGCTTTACGTTTTGCTGTAG 58.298 43.478 0.00 0.00 0.00 2.74
2550 3590 3.059188 GCTCTGCTTTACGTTTTGCTGTA 60.059 43.478 0.00 0.00 0.00 2.74
2561 3601 4.156739 AGGCTACATTTTGCTCTGCTTTAC 59.843 41.667 0.00 0.00 0.00 2.01
2571 3611 3.184541 CTGAATGCAGGCTACATTTTGC 58.815 45.455 13.95 3.00 37.85 3.68
2575 3615 3.054434 TGGTACTGAATGCAGGCTACATT 60.054 43.478 12.71 12.71 46.60 2.71
2600 3640 3.740044 AAAATGCGACAGGACGTAATG 57.260 42.857 0.00 0.00 35.59 1.90
2625 3665 0.322456 TGCTGTAGTGGCCATGGAAC 60.322 55.000 18.40 13.06 0.00 3.62
2627 3667 1.603842 CTGCTGTAGTGGCCATGGA 59.396 57.895 18.40 0.00 0.00 3.41
2629 3669 0.750546 ATGCTGCTGTAGTGGCCATG 60.751 55.000 9.72 0.00 0.00 3.66
2630 3670 0.465097 GATGCTGCTGTAGTGGCCAT 60.465 55.000 9.72 0.00 0.00 4.40
2631 3671 1.078214 GATGCTGCTGTAGTGGCCA 60.078 57.895 0.00 0.00 0.00 5.36
2632 3672 0.813210 GAGATGCTGCTGTAGTGGCC 60.813 60.000 0.00 0.00 0.00 5.36
2670 3710 9.926158 TCAAACAAAATATGACTTATGCATGTT 57.074 25.926 10.16 0.00 0.00 2.71
2671 3711 9.357652 GTCAAACAAAATATGACTTATGCATGT 57.642 29.630 10.16 0.00 40.18 3.21
2735 3775 8.072567 CCTGTGTCAAATCTCTAAAAACAGAAG 58.927 37.037 0.00 0.00 35.63 2.85
2758 3810 7.499292 ACATGAAGAGAATGAGTTCTATCCTG 58.501 38.462 0.00 0.00 44.57 3.86
2760 3812 7.768120 ACAACATGAAGAGAATGAGTTCTATCC 59.232 37.037 0.00 0.00 44.57 2.59
2765 3823 7.387397 AGAGAACAACATGAAGAGAATGAGTTC 59.613 37.037 0.00 13.42 40.14 3.01
2774 3832 3.120269 GCTGCAGAGAACAACATGAAGAG 60.120 47.826 20.43 0.00 0.00 2.85
2965 4025 7.177832 TGCTAGCTTTGTTATACTACAAGGA 57.822 36.000 17.23 0.00 39.06 3.36
3163 4307 7.201617 CGAGGATAGTGGATTAAAACTCCAAAC 60.202 40.741 0.00 0.00 44.19 2.93
3179 4595 3.738282 GCTTCAAGCATACGAGGATAGTG 59.262 47.826 3.89 0.00 41.89 2.74
3249 4669 3.564225 ACTCATGTTTTTGTCTTCCGACC 59.436 43.478 0.00 0.00 39.47 4.79
3439 4859 7.325579 ACGTGATTCTAGTACGAAGAGAAAAAC 59.674 37.037 14.76 7.12 40.01 2.43
3537 4957 0.177836 CGAGCCACACATCCACCATA 59.822 55.000 0.00 0.00 0.00 2.74
3585 5005 0.813210 CGAAGAGAATGGGGCTCAGC 60.813 60.000 0.00 0.00 34.85 4.26
3647 5067 1.860950 CAAGGTTAGCATCGATGACCG 59.139 52.381 29.20 11.52 35.56 4.79
3657 5077 6.147164 CGTTCTTGATCTTAACAAGGTTAGCA 59.853 38.462 0.00 0.00 43.11 3.49
3659 5079 7.510630 CACGTTCTTGATCTTAACAAGGTTAG 58.489 38.462 0.00 0.00 43.11 2.34
3944 5364 2.933287 AGGCACACATCGGGGGAA 60.933 61.111 0.00 0.00 0.00 3.97
3945 5365 3.716195 CAGGCACACATCGGGGGA 61.716 66.667 0.00 0.00 0.00 4.81
3964 5384 1.934589 TCACAAGAACACACACTCGG 58.065 50.000 0.00 0.00 0.00 4.63
4031 5451 6.541641 AGGAATGCTCATTTCAGTACAAGATC 59.458 38.462 3.93 0.00 0.00 2.75
4180 5601 2.824341 GTCTTCCGAAACAGACTCCCTA 59.176 50.000 0.00 0.00 37.12 3.53
4224 5645 6.461509 GCATAAACAGGTTCCCAATCTTATGG 60.462 42.308 0.00 0.00 40.35 2.74
4246 5667 2.023695 ACTTGGGAGGATCAAATGGCAT 60.024 45.455 0.00 0.00 36.25 4.40
4263 5684 5.764131 TGGCCGTTTAAACTATTCAACTTG 58.236 37.500 16.01 0.00 0.00 3.16
4278 5699 3.426615 TCATATGGTTCTTTGGCCGTTT 58.573 40.909 2.13 0.00 0.00 3.60
4280 5701 2.799126 TCATATGGTTCTTTGGCCGT 57.201 45.000 2.13 0.00 0.00 5.68
4307 5953 5.995897 GGCCGTTGAAACTATCCAATATAGT 59.004 40.000 0.00 0.00 36.48 2.12
4381 6027 3.678289 TCCTCTGAACAATCACACCATG 58.322 45.455 0.00 0.00 0.00 3.66
4389 6035 4.217118 AGTGCAAACATCCTCTGAACAATC 59.783 41.667 0.00 0.00 0.00 2.67
4437 6083 5.414765 TCTTTACAGACGTGATTCAGCTCTA 59.585 40.000 0.00 0.00 0.00 2.43
4521 6167 0.389391 TAGCGCCTCATCTAAGCACC 59.611 55.000 2.29 0.00 0.00 5.01
4536 6182 0.810031 CGGGACACCCTCATTTAGCG 60.810 60.000 5.27 0.00 42.67 4.26
4542 6188 0.397254 CTAGTCCGGGACACCCTCAT 60.397 60.000 27.87 8.86 42.67 2.90
4577 6223 1.453155 GGCCCATAGATAACATGCCG 58.547 55.000 0.00 0.00 0.00 5.69
4605 6251 2.580601 AAACGACGGCTAGTGGGCT 61.581 57.895 0.00 0.00 38.46 5.19
4615 6261 0.529992 GGCTATCCTCCAAACGACGG 60.530 60.000 0.00 0.00 0.00 4.79
4616 6262 0.870307 CGGCTATCCTCCAAACGACG 60.870 60.000 0.00 0.00 0.00 5.12
4621 6267 3.780624 GCTTCGGCTATCCTCCAAA 57.219 52.632 0.00 0.00 38.08 3.28
4670 6316 5.125097 GTCCTTCAAGTATACGAAGTCTCCA 59.875 44.000 15.26 0.00 43.93 3.86
4672 6318 6.192234 TGTCCTTCAAGTATACGAAGTCTC 57.808 41.667 15.26 8.55 43.93 3.36
4688 6334 7.067494 ACATGCCAACTATTAGAATTGTCCTTC 59.933 37.037 0.00 0.00 0.00 3.46
4699 6345 9.561069 ACTAGGAATAAACATGCCAACTATTAG 57.439 33.333 0.00 0.00 0.00 1.73
4707 6353 4.981806 GCAACTAGGAATAAACATGCCA 57.018 40.909 0.00 0.00 0.00 4.92
4735 6381 3.895656 GTGCCTAGGTCTACACATATGGA 59.104 47.826 11.31 0.00 33.23 3.41
4742 6388 1.673808 CGGGGTGCCTAGGTCTACAC 61.674 65.000 11.31 9.58 0.00 2.90
4776 6422 6.058833 TGTGCTTTATGAACTAAACACCTCA 58.941 36.000 0.00 0.00 34.24 3.86
4789 6435 6.588719 AAGGCTTGTAATTGTGCTTTATGA 57.411 33.333 0.00 0.00 0.00 2.15
4791 6437 6.096846 CCCTAAGGCTTGTAATTGTGCTTTAT 59.903 38.462 10.69 0.00 0.00 1.40
4793 6439 4.220602 CCCTAAGGCTTGTAATTGTGCTTT 59.779 41.667 10.69 0.00 0.00 3.51
4794 6440 3.763897 CCCTAAGGCTTGTAATTGTGCTT 59.236 43.478 10.69 0.00 0.00 3.91
4806 6452 2.091555 TGTGTTCCAAACCCTAAGGCTT 60.092 45.455 4.58 4.58 36.11 4.35
4860 6506 6.816616 TGTATTTATGTGATGGGGTACAGA 57.183 37.500 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.