Multiple sequence alignment - TraesCS2A01G532600

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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 TraesCS2A01G532600 chr2A 100.000 6405 0 0 1 6405 748911525 748905121 0.000000e+00 11828.0
1 TraesCS2A01G532600 chr2A 85.973 1269 139 26 1069 2313 749385206 749386459 0.000000e+00 1321.0
2 TraesCS2A01G532600 chr2A 84.501 1342 165 24 1010 2317 721729595 721728263 0.000000e+00 1286.0
3 TraesCS2A01G532600 chr2A 88.679 371 38 4 2796 3164 748870864 748870496 3.520000e-122 449.0
4 TraesCS2A01G532600 chr2A 83.921 454 61 5 3258 3701 748870449 748869998 2.130000e-114 424.0
5 TraesCS2A01G532600 chr2A 84.281 299 46 1 3273 3571 749388099 749388396 2.260000e-74 291.0
6 TraesCS2A01G532600 chr2A 80.214 374 62 9 2800 3164 749387610 749387980 2.940000e-68 270.0
7 TraesCS2A01G532600 chr2A 100.000 33 0 0 5540 5572 499767923 499767891 1.930000e-05 62.1
8 TraesCS2A01G532600 chr2B 90.283 6473 421 91 5 6405 754655600 754649264 0.000000e+00 8277.0
9 TraesCS2A01G532600 chr2B 86.404 1243 137 19 1090 2313 755150716 755149487 0.000000e+00 1330.0
10 TraesCS2A01G532600 chr2B 85.557 1274 146 22 1074 2317 708716246 708714981 0.000000e+00 1299.0
11 TraesCS2A01G532600 chr2B 93.648 551 29 4 4698 5247 754622624 754622079 0.000000e+00 819.0
12 TraesCS2A01G532600 chr2B 77.488 1266 221 43 1089 2317 756173765 756175003 0.000000e+00 701.0
13 TraesCS2A01G532600 chr2B 88.993 427 31 8 3489 3911 754628672 754628258 1.230000e-141 514.0
14 TraesCS2A01G532600 chr2B 75.973 745 147 24 2815 3550 755148934 755148213 7.900000e-94 355.0
15 TraesCS2A01G532600 chr2B 83.415 205 29 4 2963 3164 755010429 755010631 1.100000e-42 185.0
16 TraesCS2A01G532600 chr2D 91.074 3137 192 42 85 3167 618144104 618141002 0.000000e+00 4161.0
17 TraesCS2A01G532600 chr2D 94.080 2517 113 22 3908 6405 618140254 618137755 0.000000e+00 3790.0
18 TraesCS2A01G532600 chr2D 84.826 1351 162 22 1001 2317 586961710 586960369 0.000000e+00 1319.0
19 TraesCS2A01G532600 chr2D 85.118 1317 144 25 1034 2313 618333434 618334735 0.000000e+00 1299.0
20 TraesCS2A01G532600 chr2D 81.811 1270 177 35 1089 2317 586846897 586845641 0.000000e+00 1016.0
21 TraesCS2A01G532600 chr2D 91.643 694 45 6 3221 3906 618140996 618140308 0.000000e+00 948.0
22 TraesCS2A01G532600 chr2D 78.877 1264 219 34 1089 2317 618876015 618877265 0.000000e+00 811.0
23 TraesCS2A01G532600 chr2D 83.648 318 51 1 3254 3571 618336478 618336794 1.350000e-76 298.0
24 TraesCS2A01G532600 chr2D 81.132 371 62 8 2800 3164 618336088 618336456 2.260000e-74 291.0
25 TraesCS2A01G532600 chr2D 79.487 156 27 5 252 404 398096428 398096275 8.780000e-19 106.0
26 TraesCS2A01G532600 chr4A 83.575 207 26 7 3945 4150 137887510 137887709 3.050000e-43 187.0
27 TraesCS2A01G532600 chr5D 83.099 71 12 0 4018 4088 393979946 393979876 1.490000e-06 65.8
28 TraesCS2A01G532600 chr5A 100.000 34 0 0 5537 5570 657242230 657242197 5.360000e-06 63.9
29 TraesCS2A01G532600 chr5A 100.000 31 0 0 5540 5570 32139792 32139762 2.490000e-04 58.4
30 TraesCS2A01G532600 chr5A 100.000 31 0 0 5540 5570 685063504 685063474 2.490000e-04 58.4
31 TraesCS2A01G532600 chr5A 97.059 34 1 0 5537 5570 706591927 706591960 2.490000e-04 58.4
32 TraesCS2A01G532600 chr6A 97.059 34 1 0 5537 5570 579386617 579386650 2.490000e-04 58.4
33 TraesCS2A01G532600 chr1A 97.059 34 1 0 5537 5570 394602551 394602584 2.490000e-04 58.4


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 TraesCS2A01G532600 chr2A 748905121 748911525 6404 True 11828.000000 11828 100.000000 1 6405 1 chr2A.!!$R3 6404
1 TraesCS2A01G532600 chr2A 721728263 721729595 1332 True 1286.000000 1286 84.501000 1010 2317 1 chr2A.!!$R2 1307
2 TraesCS2A01G532600 chr2A 749385206 749388396 3190 False 627.333333 1321 83.489333 1069 3571 3 chr2A.!!$F1 2502
3 TraesCS2A01G532600 chr2A 748869998 748870864 866 True 436.500000 449 86.300000 2796 3701 2 chr2A.!!$R4 905
4 TraesCS2A01G532600 chr2B 754649264 754655600 6336 True 8277.000000 8277 90.283000 5 6405 1 chr2B.!!$R4 6400
5 TraesCS2A01G532600 chr2B 708714981 708716246 1265 True 1299.000000 1299 85.557000 1074 2317 1 chr2B.!!$R1 1243
6 TraesCS2A01G532600 chr2B 755148213 755150716 2503 True 842.500000 1330 81.188500 1090 3550 2 chr2B.!!$R5 2460
7 TraesCS2A01G532600 chr2B 754622079 754622624 545 True 819.000000 819 93.648000 4698 5247 1 chr2B.!!$R2 549
8 TraesCS2A01G532600 chr2B 756173765 756175003 1238 False 701.000000 701 77.488000 1089 2317 1 chr2B.!!$F2 1228
9 TraesCS2A01G532600 chr2D 618137755 618144104 6349 True 2966.333333 4161 92.265667 85 6405 3 chr2D.!!$R4 6320
10 TraesCS2A01G532600 chr2D 586960369 586961710 1341 True 1319.000000 1319 84.826000 1001 2317 1 chr2D.!!$R3 1316
11 TraesCS2A01G532600 chr2D 586845641 586846897 1256 True 1016.000000 1016 81.811000 1089 2317 1 chr2D.!!$R2 1228
12 TraesCS2A01G532600 chr2D 618876015 618877265 1250 False 811.000000 811 78.877000 1089 2317 1 chr2D.!!$F1 1228
13 TraesCS2A01G532600 chr2D 618333434 618336794 3360 False 629.333333 1299 83.299333 1034 3571 3 chr2D.!!$F2 2537

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
971 998 0.181114 TGAGCTGTGCTGTGGAAACT 59.819 50.000 0.00 0.00 39.88 2.66 F
1206 1269 0.105039 CCAAGAGGTACCTCGGCATC 59.895 60.000 31.53 11.96 46.90 3.91 F
1299 1368 1.554042 CGCTGGTGCTTAACGACGTT 61.554 55.000 18.47 18.47 36.97 3.99 F
2595 4583 2.083774 GGAACCAATCGCTCACATTCA 58.916 47.619 0.00 0.00 0.00 2.57 F
3219 5253 2.370189 CTCTCTCTCTCTCTCTCTCCCC 59.630 59.091 0.00 0.00 0.00 4.81 F
3664 5760 0.242825 CTAGGTCCTCGCGTTTCACA 59.757 55.000 5.77 0.00 0.00 3.58 F
4556 6733 0.463204 CAGGCGAGAGTGTGATCCAT 59.537 55.000 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 2367 1.132588 GAGGCGTAGATCAACGATGC 58.867 55.0 0.00 0.00 45.68 3.91 R
3205 5239 0.034960 CACACGGGGAGAGAGAGAGA 60.035 60.0 0.00 0.00 0.00 3.10 R
3206 5240 0.322997 ACACACGGGGAGAGAGAGAG 60.323 60.0 0.00 0.00 0.00 3.20 R
3642 5738 0.179108 GAAACGCGAGGACCTAGCAT 60.179 55.0 24.15 8.45 31.74 3.79 R
4749 6926 0.394352 ATCCCCTTCATGGAACGCAC 60.394 55.0 0.00 0.00 38.35 5.34 R
5122 7299 0.952280 TTAGCTCGGGCAGTATCTCG 59.048 55.0 11.40 0.00 41.70 4.04 R
6139 8316 0.108520 ACGTTATCACATCCGCCGTT 60.109 50.0 0.00 0.00 0.00 4.44 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
29 30 8.378565 GGAATCACCATAATCTATCAAGGAAGA 58.621 37.037 0.00 0.00 38.79 2.87
49 50 8.997734 AGGAAGACCTTATTCTTGAATCACTAT 58.002 33.333 0.00 0.00 45.36 2.12
75 76 7.060421 AGAGGAGAATACTCAACCAACAAAAA 58.940 34.615 0.00 0.00 44.22 1.94
77 78 8.250143 AGGAGAATACTCAACCAACAAAAATT 57.750 30.769 0.00 0.00 44.22 1.82
108 110 4.595762 TGTGTGTAGACTAACAAGGACC 57.404 45.455 0.00 0.00 0.00 4.46
147 149 0.457035 TAGGACACCGCGGTTACATC 59.543 55.000 32.11 22.48 0.00 3.06
152 154 0.672401 CACCGCGGTTACATCACCTT 60.672 55.000 32.11 0.00 34.22 3.50
166 168 8.968242 GTTACATCACCTTTTCAAAGATTTGAC 58.032 33.333 7.49 0.00 45.99 3.18
167 169 6.208644 ACATCACCTTTTCAAAGATTTGACG 58.791 36.000 7.49 0.68 45.99 4.35
169 171 4.037446 TCACCTTTTCAAAGATTTGACGGG 59.963 41.667 7.49 11.49 45.99 5.28
170 172 3.958147 ACCTTTTCAAAGATTTGACGGGT 59.042 39.130 7.49 12.02 45.99 5.28
186 188 1.796459 CGGGTGGTCGTTTAAGACTTG 59.204 52.381 0.00 0.00 40.76 3.16
215 217 9.503399 GTTACTCCCTCCATTCGAAAATATAAT 57.497 33.333 0.00 0.00 0.00 1.28
219 221 6.947733 TCCCTCCATTCGAAAATATAATGCAT 59.052 34.615 0.00 0.00 30.81 3.96
475 480 0.887933 TAGCGATCGATGCCATGCTA 59.112 50.000 21.57 4.90 34.08 3.49
498 505 7.169982 GCTATGCATTTACTACTTACTGGACTG 59.830 40.741 3.54 0.00 0.00 3.51
506 513 3.340814 ACTTACTGGACTGGAGCAATG 57.659 47.619 0.00 0.00 0.00 2.82
509 516 0.842030 ACTGGACTGGAGCAATGGGA 60.842 55.000 0.00 0.00 0.00 4.37
516 523 4.508047 GGACTGGAGCAATGGGAATATCAT 60.508 45.833 0.00 0.00 0.00 2.45
519 526 7.365921 GGACTGGAGCAATGGGAATATCATATA 60.366 40.741 0.00 0.00 0.00 0.86
543 550 1.135689 GCTACGGTTGGCACTTTGATG 60.136 52.381 0.00 0.00 0.00 3.07
544 551 2.422597 CTACGGTTGGCACTTTGATGA 58.577 47.619 0.00 0.00 0.00 2.92
558 565 8.677300 GGCACTTTGATGAAGTCTAATGAATTA 58.323 33.333 0.00 0.00 45.40 1.40
590 597 6.323996 AGCCACACTATAGCTTGTACTATTCA 59.676 38.462 0.00 0.00 34.66 2.57
618 625 5.671742 GCAAGAGCTAATTTCTCATCTCC 57.328 43.478 9.25 0.00 37.91 3.71
621 628 2.728839 GAGCTAATTTCTCATCTCCGCG 59.271 50.000 0.00 0.00 0.00 6.46
643 650 4.032217 CGATGACTGTGATTGCTCTGTTAC 59.968 45.833 0.00 0.00 0.00 2.50
674 681 1.795525 CGCGTCACATCTACCACTGAG 60.796 57.143 0.00 0.00 0.00 3.35
705 715 2.353889 CTGATGATCGCAACTTCCTTGG 59.646 50.000 0.00 0.00 0.00 3.61
723 733 1.203038 TGGAAAATTGGCTGCTCCTGA 60.203 47.619 0.00 0.00 35.26 3.86
750 760 4.143410 GGCGAAACCGAAATGTTTGAATTC 60.143 41.667 0.00 0.00 38.51 2.17
757 767 6.158598 ACCGAAATGTTTGAATTCCAATCTG 58.841 36.000 2.27 0.00 34.23 2.90
805 815 5.764192 AGTCCCATCTCTATCAAGTACGTAC 59.236 44.000 18.10 18.10 0.00 3.67
806 816 4.753610 TCCCATCTCTATCAAGTACGTACG 59.246 45.833 19.49 15.01 0.00 3.67
807 817 4.514441 CCCATCTCTATCAAGTACGTACGT 59.486 45.833 25.98 25.98 0.00 3.57
808 818 5.698089 CCCATCTCTATCAAGTACGTACGTA 59.302 44.000 23.60 23.60 0.00 3.57
840 853 7.647907 ACAGACCAAATTAACAAGTACGTAG 57.352 36.000 0.00 0.00 0.00 3.51
842 855 7.927629 ACAGACCAAATTAACAAGTACGTAGAA 59.072 33.333 0.00 0.00 0.00 2.10
843 856 8.767085 CAGACCAAATTAACAAGTACGTAGAAA 58.233 33.333 0.00 0.00 0.00 2.52
872 894 3.383698 TCTCGGTCCAAGAGAGGTAAT 57.616 47.619 0.00 0.00 39.57 1.89
892 914 7.983484 AGGTAATAACTTAATTACACGACCAGG 59.017 37.037 8.52 0.00 41.92 4.45
894 921 3.688694 ACTTAATTACACGACCAGGCA 57.311 42.857 0.00 0.00 0.00 4.75
966 993 1.313091 ATGCATGAGCTGTGCTGTGG 61.313 55.000 18.40 0.00 39.88 4.17
967 994 1.673337 GCATGAGCTGTGCTGTGGA 60.673 57.895 12.26 0.00 39.88 4.02
968 995 1.239296 GCATGAGCTGTGCTGTGGAA 61.239 55.000 12.26 0.00 39.88 3.53
969 996 1.241165 CATGAGCTGTGCTGTGGAAA 58.759 50.000 0.00 0.00 39.88 3.13
970 997 1.068748 CATGAGCTGTGCTGTGGAAAC 60.069 52.381 0.00 0.00 39.88 2.78
971 998 0.181114 TGAGCTGTGCTGTGGAAACT 59.819 50.000 0.00 0.00 39.88 2.66
972 999 0.590195 GAGCTGTGCTGTGGAAACTG 59.410 55.000 0.00 0.00 39.88 3.16
987 1014 2.978156 AACTGGAAAGAGGCATCCAA 57.022 45.000 0.00 0.00 44.77 3.53
1117 1156 3.080121 AGAGGGGCCAGAAGCTCG 61.080 66.667 4.39 0.00 46.23 5.03
1143 1194 2.733593 GACACGCTCGTTTCGGCT 60.734 61.111 0.00 0.00 0.00 5.52
1176 1233 0.324830 CCCTCGGGTTCTTCTCTCCT 60.325 60.000 0.00 0.00 0.00 3.69
1206 1269 0.105039 CCAAGAGGTACCTCGGCATC 59.895 60.000 31.53 11.96 46.90 3.91
1299 1368 1.554042 CGCTGGTGCTTAACGACGTT 61.554 55.000 18.47 18.47 36.97 3.99
1371 1443 4.394712 AACTTCCTGCCCGCCTCG 62.395 66.667 0.00 0.00 0.00 4.63
1471 1543 3.718210 GATCAGCCGTCGGACACCC 62.718 68.421 17.49 0.00 0.00 4.61
1589 1662 3.952675 CGCACGCTGCAAACCAGT 61.953 61.111 0.00 0.00 45.36 4.00
2139 2273 2.267006 CGCTGGATGAGTGCAGGT 59.733 61.111 0.00 0.00 43.34 4.00
2421 4331 6.496338 ACAAGCTACACTACTTTTTATGGC 57.504 37.500 0.00 0.00 0.00 4.40
2471 4381 7.340743 TCAGTGGAAAAGGTGAATTTGTTAAGA 59.659 33.333 0.00 0.00 0.00 2.10
2526 4510 8.922058 AATATGAAGTGTCAATTCAAGCAATC 57.078 30.769 18.66 0.00 39.92 2.67
2536 4520 6.088616 GTCAATTCAAGCAATCTAAAGCACAC 59.911 38.462 0.00 0.00 0.00 3.82
2539 4523 5.512753 TCAAGCAATCTAAAGCACACAAA 57.487 34.783 0.00 0.00 0.00 2.83
2582 4566 9.810545 CTTAGTTCTACAAAATTTTGGAACCAA 57.189 29.630 29.62 25.20 42.34 3.67
2595 4583 2.083774 GGAACCAATCGCTCACATTCA 58.916 47.619 0.00 0.00 0.00 2.57
2722 4714 3.160679 AGTTTCTGGATGGGGAACAAG 57.839 47.619 0.00 0.00 0.00 3.16
2924 4950 3.951680 TGGTGGAGAAGGAAAAACAGAAC 59.048 43.478 0.00 0.00 0.00 3.01
2944 4970 9.331282 ACAGAACAATAGGTAAATTATGCTCTC 57.669 33.333 0.00 0.00 0.00 3.20
3015 5048 6.672836 GCATGGTAAATGCAATGTTGTAAAGC 60.673 38.462 5.46 0.00 44.00 3.51
3164 5198 6.811665 GGATTTAGCATTGTTTACAAGGTTCC 59.188 38.462 8.77 5.01 39.56 3.62
3167 5201 4.729868 AGCATTGTTTACAAGGTTCCTCT 58.270 39.130 8.77 0.00 39.56 3.69
3168 5202 4.762251 AGCATTGTTTACAAGGTTCCTCTC 59.238 41.667 8.77 0.00 39.56 3.20
3170 5204 5.106515 GCATTGTTTACAAGGTTCCTCTCTC 60.107 44.000 8.77 0.00 39.56 3.20
3174 5208 5.602978 TGTTTACAAGGTTCCTCTCTCTCTT 59.397 40.000 0.00 0.00 0.00 2.85
3177 5211 4.488770 ACAAGGTTCCTCTCTCTCTTTCT 58.511 43.478 0.00 0.00 0.00 2.52
3178 5212 4.526650 ACAAGGTTCCTCTCTCTCTTTCTC 59.473 45.833 0.00 0.00 0.00 2.87
3179 5213 4.675063 AGGTTCCTCTCTCTCTTTCTCT 57.325 45.455 0.00 0.00 0.00 3.10
3180 5214 4.600062 AGGTTCCTCTCTCTCTTTCTCTC 58.400 47.826 0.00 0.00 0.00 3.20
3181 5215 4.292306 AGGTTCCTCTCTCTCTTTCTCTCT 59.708 45.833 0.00 0.00 0.00 3.10
3182 5216 4.640647 GGTTCCTCTCTCTCTTTCTCTCTC 59.359 50.000 0.00 0.00 0.00 3.20
3183 5217 5.501156 GTTCCTCTCTCTCTTTCTCTCTCT 58.499 45.833 0.00 0.00 0.00 3.10
3184 5218 5.359194 TCCTCTCTCTCTTTCTCTCTCTC 57.641 47.826 0.00 0.00 0.00 3.20
3185 5219 5.032846 TCCTCTCTCTCTTTCTCTCTCTCT 58.967 45.833 0.00 0.00 0.00 3.10
3186 5220 5.129485 TCCTCTCTCTCTTTCTCTCTCTCTC 59.871 48.000 0.00 0.00 0.00 3.20
3187 5221 5.130145 CCTCTCTCTCTTTCTCTCTCTCTCT 59.870 48.000 0.00 0.00 0.00 3.10
3188 5222 6.227298 TCTCTCTCTTTCTCTCTCTCTCTC 57.773 45.833 0.00 0.00 0.00 3.20
3190 5224 6.097554 TCTCTCTCTTTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
3191 5225 5.960811 TCTCTCTTTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3192 5226 6.097554 TCTCTCTTTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
3194 5228 6.097554 TCTCTTTCTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
3195 5229 5.960811 TCTTTCTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3196 5230 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
3197 5231 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3198 5232 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3199 5233 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3200 5234 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3202 5236 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3203 5237 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3204 5238 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3205 5239 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3206 5240 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3207 5241 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3208 5242 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3209 5243 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3212 5246 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3214 5248 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3215 5249 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3216 5250 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3217 5251 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
3218 5252 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
3219 5253 2.370189 CTCTCTCTCTCTCTCTCTCCCC 59.630 59.091 0.00 0.00 0.00 4.81
3242 5311 3.372514 GTGTGTGTGTGTGTGTGTTATCA 59.627 43.478 0.00 0.00 0.00 2.15
3266 5350 4.093743 GGGGAAACATCATTGGTTAAGGT 58.906 43.478 0.00 0.00 31.24 3.50
3560 5647 6.075984 ACATCTACATATTCGGTACTCCCTT 58.924 40.000 0.00 0.00 0.00 3.95
3561 5648 6.208994 ACATCTACATATTCGGTACTCCCTTC 59.791 42.308 0.00 0.00 0.00 3.46
3586 5680 7.886970 TCTTCATGGAATTTCTCAAGTTCTCAT 59.113 33.333 0.00 0.00 0.00 2.90
3656 5752 0.533755 ATTGCATGCTAGGTCCTCGC 60.534 55.000 20.33 8.46 0.00 5.03
3662 5758 1.214589 GCTAGGTCCTCGCGTTTCA 59.785 57.895 5.77 0.00 0.00 2.69
3664 5760 0.242825 CTAGGTCCTCGCGTTTCACA 59.757 55.000 5.77 0.00 0.00 3.58
3763 5859 4.686091 GCTTGGCAACCTTAACATTTTCTC 59.314 41.667 0.00 0.00 0.00 2.87
3782 5878 2.549754 CTCTGCAGGACAAAATCGTGTT 59.450 45.455 15.13 0.00 43.76 3.32
3785 5881 4.024387 TCTGCAGGACAAAATCGTGTTTAC 60.024 41.667 15.13 0.00 43.76 2.01
3802 5898 7.486551 TCGTGTTTACAAGGTTTTTCAAATCTG 59.513 33.333 0.00 0.00 0.00 2.90
3805 5901 9.883142 TGTTTACAAGGTTTTTCAAATCTGAAT 57.117 25.926 0.00 0.00 41.22 2.57
3835 5931 9.759259 CATACATATAGATTTGCGTGGTTTATG 57.241 33.333 0.00 0.00 0.00 1.90
3839 5935 4.419522 AGATTTGCGTGGTTTATGTGTC 57.580 40.909 0.00 0.00 0.00 3.67
3953 6105 7.414222 AGAAAACGTTGTATATACTCCCTCA 57.586 36.000 13.89 0.00 0.00 3.86
3967 6119 7.989947 ATACTCCCTCATGTCCTTTTTAGTA 57.010 36.000 0.00 0.00 0.00 1.82
3974 6126 7.667219 CCCTCATGTCCTTTTTAGTATGCATAT 59.333 37.037 10.16 2.05 0.00 1.78
3993 6145 5.867174 GCATATAAGTTTTTGCCCGAAGTTT 59.133 36.000 0.00 0.00 0.00 2.66
4014 6166 6.651225 AGTTTAAGCATCTCTACTTTGACCAC 59.349 38.462 0.00 0.00 0.00 4.16
4179 6335 5.483811 TCGACTTGCCACAAATCTAATACA 58.516 37.500 0.00 0.00 0.00 2.29
4345 6511 1.346062 AGCAGCTTTCAGAGAGTCCA 58.654 50.000 0.00 0.00 0.00 4.02
4380 6546 9.892130 TTGGATGTTAAATTTAGGTGTTTTGTT 57.108 25.926 0.00 0.00 0.00 2.83
4381 6547 9.892130 TGGATGTTAAATTTAGGTGTTTTGTTT 57.108 25.926 0.00 0.00 0.00 2.83
4467 6644 3.935203 CACACCTAATCTTCGTGCTTCAT 59.065 43.478 0.00 0.00 0.00 2.57
4501 6678 4.357996 AGAAGGTTAGAATTACTACGCGC 58.642 43.478 5.73 0.00 0.00 6.86
4529 6706 2.658285 CATGGTGTTGCATACCTCCAT 58.342 47.619 18.25 15.78 39.44 3.41
4556 6733 0.463204 CAGGCGAGAGTGTGATCCAT 59.537 55.000 0.00 0.00 0.00 3.41
4586 6763 2.491675 AACCCGGGAACATTCTTCTC 57.508 50.000 32.02 0.00 0.00 2.87
4639 6816 1.140804 GCACCGCCAAACTGTTTGT 59.859 52.632 26.35 9.79 38.98 2.83
4749 6926 3.243771 GGATCCGACATACCTAACACTGG 60.244 52.174 0.00 0.00 0.00 4.00
4809 6986 1.152525 GGGAGGGGAGATGACGCTA 60.153 63.158 0.00 0.00 0.00 4.26
4903 7080 4.455070 AGGCTTCTTTCCCAAGTAAGTT 57.545 40.909 0.00 0.00 0.00 2.66
4962 7139 4.354071 TGCACGGTTCATATTGACATTG 57.646 40.909 0.00 0.00 0.00 2.82
5063 7240 2.224159 GCCTGGGAACTGTGGGAGA 61.224 63.158 0.00 0.00 0.00 3.71
5092 7269 4.021104 AGGATCATTGAACTTCTCGACACA 60.021 41.667 0.00 0.00 0.00 3.72
5122 7299 3.787001 CTCCCCAAGTCCGAGCCC 61.787 72.222 0.00 0.00 0.00 5.19
5206 7383 1.072806 GATGATAGGCCAGCCATGTCA 59.927 52.381 12.03 11.66 38.92 3.58
5250 7427 6.987992 ACAAGCACAACATCTCAAATTGATTT 59.012 30.769 0.00 0.00 0.00 2.17
5353 7530 4.080919 CCCACTACAATTGAGGTGAGATCA 60.081 45.833 25.16 0.00 32.12 2.92
5387 7564 4.826274 TCCAGCTATTGTTGTCTAGCTT 57.174 40.909 0.00 0.00 46.51 3.74
5409 7586 7.039784 AGCTTGCAACCAATCTAATTAAGTTCA 60.040 33.333 0.00 0.00 0.00 3.18
5436 7613 7.633789 ACATAGGAATCATTTACACAGAACCT 58.366 34.615 0.00 0.00 0.00 3.50
5612 7789 4.994744 GTGCTCACCAAAATGCCC 57.005 55.556 0.00 0.00 0.00 5.36
5613 7790 1.080569 GTGCTCACCAAAATGCCCG 60.081 57.895 0.00 0.00 0.00 6.13
5614 7791 2.125952 GCTCACCAAAATGCCCGC 60.126 61.111 0.00 0.00 0.00 6.13
5615 7792 2.639327 GCTCACCAAAATGCCCGCT 61.639 57.895 0.00 0.00 0.00 5.52
5616 7793 1.312371 GCTCACCAAAATGCCCGCTA 61.312 55.000 0.00 0.00 0.00 4.26
5617 7794 1.173043 CTCACCAAAATGCCCGCTAA 58.827 50.000 0.00 0.00 0.00 3.09
5618 7795 1.133025 CTCACCAAAATGCCCGCTAAG 59.867 52.381 0.00 0.00 0.00 2.18
5619 7796 1.173043 CACCAAAATGCCCGCTAAGA 58.827 50.000 0.00 0.00 0.00 2.10
5620 7797 1.133025 CACCAAAATGCCCGCTAAGAG 59.867 52.381 0.00 0.00 0.00 2.85
5621 7798 1.271926 ACCAAAATGCCCGCTAAGAGT 60.272 47.619 0.00 0.00 0.00 3.24
5626 7803 2.200373 ATGCCCGCTAAGAGTTTGTT 57.800 45.000 0.00 0.00 0.00 2.83
5831 8008 1.963172 TGGCAGCTCAGAGCAATATG 58.037 50.000 24.64 14.38 45.56 1.78
5875 8052 1.679032 CCTCCTCCTTTTTGTAGGCCG 60.679 57.143 0.00 0.00 35.15 6.13
5880 8057 1.500396 CTTTTTGTAGGCCGACCGC 59.500 57.895 13.95 0.00 42.76 5.68
5913 8090 6.544564 TCTTTGGGTATTTATCCGGAATCAAC 59.455 38.462 9.01 3.34 0.00 3.18
5962 8139 6.316890 TGGAACCAAAGTACAAGTAGTCAAAC 59.683 38.462 0.00 0.00 0.00 2.93
5963 8140 6.238566 GGAACCAAAGTACAAGTAGTCAAACC 60.239 42.308 0.00 0.00 0.00 3.27
5973 8150 2.039879 AGTAGTCAAACCGGGCATTCTT 59.960 45.455 6.32 0.00 0.00 2.52
6004 8181 3.436243 AGAGAGAACGGGAGATTGAGTT 58.564 45.455 0.00 0.00 0.00 3.01
6006 8183 4.081917 AGAGAGAACGGGAGATTGAGTTTC 60.082 45.833 0.00 0.00 0.00 2.78
6093 8270 5.048013 GGGAGGTTGTGTGGAAAGATTTAAG 60.048 44.000 0.00 0.00 0.00 1.85
6190 8367 9.527157 TCTTATTTCACCATTTGGAAGTCATTA 57.473 29.630 3.01 0.00 38.94 1.90
6272 8449 5.405935 TTGACATAGTTAGCAAGCTGAGA 57.594 39.130 4.53 0.00 0.00 3.27
6276 8453 1.650528 AGTTAGCAAGCTGAGAGGGT 58.349 50.000 4.53 0.00 0.00 4.34
6296 8473 4.381612 GGGTTTCCTGCAAAGCTATTTACC 60.382 45.833 0.00 0.00 41.50 2.85
6331 8508 1.157585 GCCCAAGAACGGAAAGAGAC 58.842 55.000 0.00 0.00 0.00 3.36
6342 8519 4.957296 ACGGAAAGAGACTTGAGCTTTTA 58.043 39.130 0.00 0.00 32.45 1.52
6352 8529 9.160496 AGAGACTTGAGCTTTTATGTTCTATTG 57.840 33.333 0.00 0.00 0.00 1.90
6369 8546 8.877195 TGTTCTATTGAGAGTTTTAGGGTAAGT 58.123 33.333 0.00 0.00 31.77 2.24
6370 8547 9.152595 GTTCTATTGAGAGTTTTAGGGTAAGTG 57.847 37.037 0.00 0.00 31.77 3.16
6381 8558 2.541466 AGGGTAAGTGGAAGAGTGAGG 58.459 52.381 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.240405 TCCTTGATAGATTATGGTGATTCCCAT 59.760 37.037 10.36 10.36 46.86 4.00
2 3 7.020827 TCCTTGATAGATTATGGTGATTCCC 57.979 40.000 0.00 0.00 34.77 3.97
4 5 9.213799 GTCTTCCTTGATAGATTATGGTGATTC 57.786 37.037 0.00 0.00 0.00 2.52
6 7 7.515514 AGGTCTTCCTTGATAGATTATGGTGAT 59.484 37.037 0.00 0.00 42.12 3.06
7 8 6.846505 AGGTCTTCCTTGATAGATTATGGTGA 59.153 38.462 0.00 0.00 42.12 4.02
8 9 7.072263 AGGTCTTCCTTGATAGATTATGGTG 57.928 40.000 0.00 0.00 42.12 4.17
29 30 9.661954 TCCTCTATAGTGATTCAAGAATAAGGT 57.338 33.333 3.34 0.00 0.00 3.50
49 50 6.928348 TTGTTGGTTGAGTATTCTCCTCTA 57.072 37.500 0.00 0.00 39.75 2.43
108 110 4.702131 CCTAGACCAGTTCATTTTGGAAGG 59.298 45.833 0.00 0.00 37.89 3.46
166 168 1.796459 CAAGTCTTAAACGACCACCCG 59.204 52.381 0.00 0.00 34.46 5.28
167 169 2.148768 CCAAGTCTTAAACGACCACCC 58.851 52.381 0.00 0.00 34.46 4.61
169 171 3.725490 ACTCCAAGTCTTAAACGACCAC 58.275 45.455 0.00 0.00 34.46 4.16
170 172 4.411256 AACTCCAAGTCTTAAACGACCA 57.589 40.909 0.00 0.00 34.46 4.02
413 417 8.417884 CCTTTCCAAATACAAGGTGAACTAAAA 58.582 33.333 0.00 0.00 33.57 1.52
416 420 6.713450 GTCCTTTCCAAATACAAGGTGAACTA 59.287 38.462 0.00 0.00 38.62 2.24
420 424 4.069304 CGTCCTTTCCAAATACAAGGTGA 58.931 43.478 0.00 0.00 38.62 4.02
475 480 6.156256 TCCAGTCCAGTAAGTAGTAAATGCAT 59.844 38.462 0.00 0.00 0.00 3.96
486 493 2.026822 CCATTGCTCCAGTCCAGTAAGT 60.027 50.000 0.00 0.00 0.00 2.24
490 497 0.842030 TCCCATTGCTCCAGTCCAGT 60.842 55.000 0.00 0.00 0.00 4.00
491 498 0.329261 TTCCCATTGCTCCAGTCCAG 59.671 55.000 0.00 0.00 0.00 3.86
492 499 1.002069 ATTCCCATTGCTCCAGTCCA 58.998 50.000 0.00 0.00 0.00 4.02
493 500 3.181440 TGATATTCCCATTGCTCCAGTCC 60.181 47.826 0.00 0.00 0.00 3.85
494 501 4.090761 TGATATTCCCATTGCTCCAGTC 57.909 45.455 0.00 0.00 0.00 3.51
498 505 5.468072 CGCTATATGATATTCCCATTGCTCC 59.532 44.000 0.00 0.00 0.00 4.70
506 513 4.547532 CGTAGCCGCTATATGATATTCCC 58.452 47.826 2.79 0.00 0.00 3.97
509 516 5.348986 CAACCGTAGCCGCTATATGATATT 58.651 41.667 2.79 0.00 0.00 1.28
516 523 1.364901 GCCAACCGTAGCCGCTATA 59.635 57.895 2.79 0.00 0.00 1.31
543 550 9.988815 TGGCTCTAGATTAATTCATTAGACTTC 57.011 33.333 0.00 0.00 0.00 3.01
544 551 9.771534 GTGGCTCTAGATTAATTCATTAGACTT 57.228 33.333 0.00 0.00 0.00 3.01
558 565 5.600484 ACAAGCTATAGTGTGGCTCTAGATT 59.400 40.000 0.00 0.00 44.79 2.40
566 573 6.513180 TGAATAGTACAAGCTATAGTGTGGC 58.487 40.000 0.84 0.00 31.94 5.01
618 625 0.299895 GAGCAATCACAGTCATCGCG 59.700 55.000 0.00 0.00 0.00 5.87
621 628 4.331168 GGTAACAGAGCAATCACAGTCATC 59.669 45.833 0.00 0.00 0.00 2.92
692 702 3.059166 CCAATTTTCCAAGGAAGTTGCG 58.941 45.455 16.95 10.51 35.38 4.85
705 715 3.320626 GTTTCAGGAGCAGCCAATTTTC 58.679 45.455 0.00 0.00 40.02 2.29
750 760 5.181690 TCTGTTTTCGTTTTCCAGATTGG 57.818 39.130 0.00 0.00 39.43 3.16
757 767 8.865978 ACTAAAAATGTTCTGTTTTCGTTTTCC 58.134 29.630 0.00 0.00 31.78 3.13
806 816 6.425721 TGTTAATTTGGTCTGTAGTGTGCTAC 59.574 38.462 0.00 0.00 45.85 3.58
807 817 6.526526 TGTTAATTTGGTCTGTAGTGTGCTA 58.473 36.000 0.00 0.00 0.00 3.49
808 818 5.373222 TGTTAATTTGGTCTGTAGTGTGCT 58.627 37.500 0.00 0.00 0.00 4.40
818 831 8.891671 TTTCTACGTACTTGTTAATTTGGTCT 57.108 30.769 0.00 0.00 0.00 3.85
840 853 7.495934 TCTCTTGGACCGAGATCATAAAATTTC 59.504 37.037 12.12 0.00 32.86 2.17
842 855 6.889198 TCTCTTGGACCGAGATCATAAAATT 58.111 36.000 12.12 0.00 32.86 1.82
843 856 6.463614 CCTCTCTTGGACCGAGATCATAAAAT 60.464 42.308 12.12 0.00 36.95 1.82
872 894 5.149973 TGCCTGGTCGTGTAATTAAGTTA 57.850 39.130 0.00 0.00 0.00 2.24
885 907 0.667993 TTTCAAAGCTTGCCTGGTCG 59.332 50.000 0.00 0.00 0.00 4.79
892 914 1.131771 GCGACCTTTTCAAAGCTTGC 58.868 50.000 0.00 0.00 34.69 4.01
894 921 2.297701 TCTGCGACCTTTTCAAAGCTT 58.702 42.857 0.00 0.00 34.69 3.74
966 993 2.795329 TGGATGCCTCTTTCCAGTTTC 58.205 47.619 0.00 0.00 37.10 2.78
967 994 2.893489 GTTGGATGCCTCTTTCCAGTTT 59.107 45.455 0.00 0.00 42.73 2.66
968 995 2.158475 TGTTGGATGCCTCTTTCCAGTT 60.158 45.455 0.00 0.00 42.73 3.16
969 996 1.425066 TGTTGGATGCCTCTTTCCAGT 59.575 47.619 0.00 0.00 42.73 4.00
970 997 2.205022 TGTTGGATGCCTCTTTCCAG 57.795 50.000 0.00 0.00 42.73 3.86
971 998 2.621407 GGATGTTGGATGCCTCTTTCCA 60.621 50.000 0.00 0.00 40.24 3.53
972 999 2.027385 GGATGTTGGATGCCTCTTTCC 58.973 52.381 0.00 0.00 0.00 3.13
987 1014 0.395686 CTCTCATGGCGGATGGATGT 59.604 55.000 0.00 0.00 32.26 3.06
1176 1233 3.636231 CTCTTGGTGGACGCCCCA 61.636 66.667 0.00 0.00 44.25 4.96
1206 1269 0.944311 CGTTGGACACGGAGAACCAG 60.944 60.000 0.00 0.00 45.89 4.00
1290 1359 1.373748 GAGGCTGCCAACGTCGTTA 60.374 57.895 22.65 0.00 0.00 3.18
1299 1368 4.020617 CCCAAGACGAGGCTGCCA 62.021 66.667 22.65 0.00 0.00 4.92
1588 1661 1.070289 GGATGATCTCCGGTAACCCAC 59.930 57.143 0.00 0.00 33.29 4.61
1589 1662 1.420430 GGATGATCTCCGGTAACCCA 58.580 55.000 0.00 0.00 33.29 4.51
1656 1730 0.735287 GGGACGCCGTTGAAGTAGAC 60.735 60.000 0.00 0.00 0.00 2.59
2129 2263 3.051210 CACCTCGACCTGCACTCA 58.949 61.111 0.00 0.00 0.00 3.41
2233 2367 1.132588 GAGGCGTAGATCAACGATGC 58.867 55.000 0.00 0.00 45.68 3.91
2399 4309 5.447279 CGGCCATAAAAAGTAGTGTAGCTTG 60.447 44.000 2.24 0.00 0.00 4.01
2403 4313 3.311596 GCCGGCCATAAAAAGTAGTGTAG 59.688 47.826 18.11 0.00 0.00 2.74
2411 4321 3.383185 TCCATAAAGCCGGCCATAAAAAG 59.617 43.478 26.15 5.66 0.00 2.27
2421 4331 2.721425 TTTACCCTCCATAAAGCCGG 57.279 50.000 0.00 0.00 0.00 6.13
2511 4495 6.088616 GTGTGCTTTAGATTGCTTGAATTGAC 59.911 38.462 0.00 0.00 0.00 3.18
2582 4566 6.988580 TGATTTAATCTCTGAATGTGAGCGAT 59.011 34.615 6.50 0.00 0.00 4.58
2639 4630 8.738645 ATGTTGGAAAACTATATGAACTCTCC 57.261 34.615 0.00 0.00 0.00 3.71
2658 4649 6.485313 TGTCCAGTCTACTTACAAAATGTTGG 59.515 38.462 0.00 0.00 39.22 3.77
2669 4660 3.786553 ACCCACATGTCCAGTCTACTTA 58.213 45.455 0.00 0.00 0.00 2.24
2694 4685 3.084786 CCCATCCAGAAACTTGAAGTCC 58.915 50.000 0.00 0.00 0.00 3.85
2944 4970 7.756272 TGCAAATAACAACAAGATTGAGCTATG 59.244 33.333 0.00 0.00 0.00 2.23
3015 5048 3.514546 GCAAAACGAGCTTGCGTG 58.485 55.556 0.00 0.00 44.86 5.34
3039 5072 4.808042 CCATGGTAGGATTTGGAGGAATT 58.192 43.478 2.57 0.00 0.00 2.17
3129 5163 1.306296 GCTAAATCCACCCTGCCCA 59.694 57.895 0.00 0.00 0.00 5.36
3164 5198 6.098124 AGAGAGAGAGAGAGAAAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
3167 5201 5.960811 AGAGAGAGAGAGAGAGAAAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
3168 5202 6.098124 AGAGAGAGAGAGAGAGAGAAAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
3170 5204 6.098124 AGAGAGAGAGAGAGAGAGAGAAAGAG 59.902 46.154 0.00 0.00 0.00 2.85
3174 5208 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
3177 5211 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3178 5212 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3179 5213 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3180 5214 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3181 5215 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3182 5216 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3183 5217 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3184 5218 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3185 5219 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3186 5220 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3187 5221 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3188 5222 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3190 5224 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3191 5225 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3192 5226 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3194 5228 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
3195 5229 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
3196 5230 3.323403 GGGAGAGAGAGAGAGAGAGAGAG 59.677 56.522 0.00 0.00 0.00 3.20
3197 5231 3.309296 GGGAGAGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
3198 5232 2.370189 GGGGAGAGAGAGAGAGAGAGAG 59.630 59.091 0.00 0.00 0.00 3.20
3199 5233 2.408565 GGGGAGAGAGAGAGAGAGAGA 58.591 57.143 0.00 0.00 0.00 3.10
3200 5234 1.070758 CGGGGAGAGAGAGAGAGAGAG 59.929 61.905 0.00 0.00 0.00 3.20
3202 5236 0.837272 ACGGGGAGAGAGAGAGAGAG 59.163 60.000 0.00 0.00 0.00 3.20
3203 5237 0.544223 CACGGGGAGAGAGAGAGAGA 59.456 60.000 0.00 0.00 0.00 3.10
3204 5238 0.254747 ACACGGGGAGAGAGAGAGAG 59.745 60.000 0.00 0.00 0.00 3.20
3205 5239 0.034960 CACACGGGGAGAGAGAGAGA 60.035 60.000 0.00 0.00 0.00 3.10
3206 5240 0.322997 ACACACGGGGAGAGAGAGAG 60.323 60.000 0.00 0.00 0.00 3.20
3207 5241 0.609406 CACACACGGGGAGAGAGAGA 60.609 60.000 0.00 0.00 0.00 3.10
3208 5242 0.896019 ACACACACGGGGAGAGAGAG 60.896 60.000 0.00 0.00 0.00 3.20
3209 5243 1.153061 ACACACACGGGGAGAGAGA 59.847 57.895 0.00 0.00 0.00 3.10
3212 5246 1.300931 CACACACACACGGGGAGAG 60.301 63.158 0.00 0.00 0.00 3.20
3214 5248 1.887242 CACACACACACACGGGGAG 60.887 63.158 0.00 0.00 0.00 4.30
3215 5249 2.188207 CACACACACACACGGGGA 59.812 61.111 0.00 0.00 0.00 4.81
3216 5250 2.124901 ACACACACACACACGGGG 60.125 61.111 0.00 0.00 0.00 5.73
3217 5251 1.743623 ACACACACACACACACGGG 60.744 57.895 0.00 0.00 0.00 5.28
3218 5252 1.295357 ACACACACACACACACACGG 61.295 55.000 0.00 0.00 0.00 4.94
3219 5253 0.515127 AACACACACACACACACACG 59.485 50.000 0.00 0.00 0.00 4.49
3242 5311 4.716287 CCTTAACCAATGATGTTTCCCCAT 59.284 41.667 0.00 0.00 0.00 4.00
3266 5350 8.570488 CAATGGCTGCTTTTCTATATGTCAATA 58.430 33.333 0.00 0.00 0.00 1.90
3560 5647 7.226441 TGAGAACTTGAGAAATTCCATGAAGA 58.774 34.615 0.00 0.00 0.00 2.87
3561 5648 7.444629 TGAGAACTTGAGAAATTCCATGAAG 57.555 36.000 0.00 0.00 0.00 3.02
3642 5738 0.179108 GAAACGCGAGGACCTAGCAT 60.179 55.000 24.15 8.45 31.74 3.79
3656 5752 3.177643 GTGCGTGAGAAATTTGTGAAACG 59.822 43.478 0.00 3.09 42.39 3.60
3662 5758 2.034432 TGCATGTGCGTGAGAAATTTGT 59.966 40.909 0.00 0.00 45.83 2.83
3664 5760 3.581024 ATGCATGTGCGTGAGAAATTT 57.419 38.095 0.00 0.00 45.83 1.82
3715 5811 8.470002 GCTAATGATTAGGGTGAAAAACTGAAT 58.530 33.333 13.60 0.00 33.80 2.57
3716 5812 7.669722 AGCTAATGATTAGGGTGAAAAACTGAA 59.330 33.333 13.60 0.00 33.80 3.02
3717 5813 7.175104 AGCTAATGATTAGGGTGAAAAACTGA 58.825 34.615 13.60 0.00 33.80 3.41
3718 5814 7.396540 AGCTAATGATTAGGGTGAAAAACTG 57.603 36.000 13.60 0.00 33.80 3.16
3719 5815 7.093771 CCAAGCTAATGATTAGGGTGAAAAACT 60.094 37.037 13.60 0.00 33.80 2.66
3720 5816 7.035612 CCAAGCTAATGATTAGGGTGAAAAAC 58.964 38.462 13.60 0.00 33.80 2.43
3721 5817 6.350949 GCCAAGCTAATGATTAGGGTGAAAAA 60.351 38.462 13.60 0.00 33.80 1.94
3727 5823 3.951563 TGCCAAGCTAATGATTAGGGT 57.048 42.857 13.60 0.00 33.80 4.34
3763 5859 3.354089 AAACACGATTTTGTCCTGCAG 57.646 42.857 6.78 6.78 0.00 4.41
3805 5901 8.445275 ACCACGCAAATCTATATGTATGAAAA 57.555 30.769 0.00 0.00 0.00 2.29
3806 5902 8.445275 AACCACGCAAATCTATATGTATGAAA 57.555 30.769 0.00 0.00 0.00 2.69
3807 5903 8.445275 AAACCACGCAAATCTATATGTATGAA 57.555 30.769 0.00 0.00 0.00 2.57
3926 6073 9.807649 GAGGGAGTATATACAACGTTTTCTTAA 57.192 33.333 15.18 0.00 0.00 1.85
3937 6084 7.931015 AAAGGACATGAGGGAGTATATACAA 57.069 36.000 15.18 0.00 0.00 2.41
3967 6119 5.127031 ACTTCGGGCAAAAACTTATATGCAT 59.873 36.000 3.79 3.79 40.51 3.96
3974 6126 5.163540 TGCTTAAACTTCGGGCAAAAACTTA 60.164 36.000 0.00 0.00 0.00 2.24
3982 6134 2.027192 AGAGATGCTTAAACTTCGGGCA 60.027 45.455 0.00 0.00 37.32 5.36
3983 6135 2.633488 AGAGATGCTTAAACTTCGGGC 58.367 47.619 0.00 0.00 0.00 6.13
3984 6136 5.012328 AGTAGAGATGCTTAAACTTCGGG 57.988 43.478 0.00 0.00 0.00 5.14
3993 6145 5.246203 AGTGTGGTCAAAGTAGAGATGCTTA 59.754 40.000 0.00 0.00 0.00 3.09
4157 6313 5.560148 GTGTATTAGATTTGTGGCAAGTCG 58.440 41.667 0.00 0.00 0.00 4.18
4164 6320 9.755064 CTTTTACTTCGTGTATTAGATTTGTGG 57.245 33.333 0.00 0.00 0.00 4.17
4179 6335 2.302157 CCCTCTGGTCCTTTTACTTCGT 59.698 50.000 0.00 0.00 0.00 3.85
4369 6535 6.783708 TTATGGACTGAAAACAAAACACCT 57.216 33.333 0.00 0.00 0.00 4.00
4371 6537 9.313118 AGAAATTATGGACTGAAAACAAAACAC 57.687 29.630 0.00 0.00 0.00 3.32
4467 6644 0.555769 AACCTTCTTGCCCAGTCCAA 59.444 50.000 0.00 0.00 0.00 3.53
4501 6678 2.021793 CAACACCATGCGCGATCG 59.978 61.111 12.10 11.69 39.07 3.69
4529 6706 1.683707 ACTCTCGCCTGATCCTGCA 60.684 57.895 4.67 0.00 0.00 4.41
4556 6733 0.831288 TCCCGGGTTTAAGGTCACGA 60.831 55.000 22.86 0.00 31.69 4.35
4586 6763 2.028420 TTGGCTTCCACTCATCATCG 57.972 50.000 0.00 0.00 30.78 3.84
4639 6816 0.469331 AGGCCCAGTCCGATTATCGA 60.469 55.000 16.78 0.00 43.74 3.59
4749 6926 0.394352 ATCCCCTTCATGGAACGCAC 60.394 55.000 0.00 0.00 38.35 5.34
4809 6986 5.092781 CCAAAGCTATAAACGTCGCATTTT 58.907 37.500 0.00 0.00 0.00 1.82
4932 7109 1.171549 TGAACCGTGCATGCACATGT 61.172 50.000 40.95 34.22 46.47 3.21
4962 7139 1.604604 TGTAGAGCTTTGCAACACCC 58.395 50.000 0.00 0.00 0.00 4.61
5063 7240 7.708752 GTCGAGAAGTTCAATGATCCTATTCTT 59.291 37.037 5.50 0.00 0.00 2.52
5092 7269 2.275380 GGGGAGCGGCACAATTGTT 61.275 57.895 8.77 0.00 0.00 2.83
5122 7299 0.952280 TTAGCTCGGGCAGTATCTCG 59.048 55.000 11.40 0.00 41.70 4.04
5206 7383 3.561143 TGTAAACATGGCCACAACTTCT 58.439 40.909 8.16 0.00 0.00 2.85
5250 7427 2.092049 TCTAGTACCGATCTTCTGGGCA 60.092 50.000 0.00 0.00 0.00 5.36
5353 7530 2.373335 AGCTGGATCTACTCGATGGT 57.627 50.000 0.00 0.00 30.84 3.55
5363 7540 4.954875 GCTAGACAACAATAGCTGGATCT 58.045 43.478 0.00 0.00 40.99 2.75
5387 7564 9.237187 TGTATGAACTTAATTAGATTGGTTGCA 57.763 29.630 0.00 0.00 0.00 4.08
5409 7586 9.561069 GGTTCTGTGTAAATGATTCCTATGTAT 57.439 33.333 0.00 0.00 0.00 2.29
5436 7613 7.648039 AAGGTACTAACATCACAACCAAAAA 57.352 32.000 0.00 0.00 38.49 1.94
5496 7673 2.595124 TCGCTATTCCGCATCTTTCA 57.405 45.000 0.00 0.00 0.00 2.69
5612 7789 8.283291 ACTTCAAAGAATAACAAACTCTTAGCG 58.717 33.333 0.00 0.00 0.00 4.26
5613 7790 9.387123 CACTTCAAAGAATAACAAACTCTTAGC 57.613 33.333 0.00 0.00 0.00 3.09
5614 7791 9.884465 CCACTTCAAAGAATAACAAACTCTTAG 57.116 33.333 0.00 0.00 0.00 2.18
5615 7792 8.349983 GCCACTTCAAAGAATAACAAACTCTTA 58.650 33.333 0.00 0.00 0.00 2.10
5616 7793 7.203218 GCCACTTCAAAGAATAACAAACTCTT 58.797 34.615 0.00 0.00 0.00 2.85
5617 7794 6.513393 CGCCACTTCAAAGAATAACAAACTCT 60.513 38.462 0.00 0.00 0.00 3.24
5618 7795 5.625311 CGCCACTTCAAAGAATAACAAACTC 59.375 40.000 0.00 0.00 0.00 3.01
5619 7796 5.507315 CCGCCACTTCAAAGAATAACAAACT 60.507 40.000 0.00 0.00 0.00 2.66
5620 7797 4.679654 CCGCCACTTCAAAGAATAACAAAC 59.320 41.667 0.00 0.00 0.00 2.93
5621 7798 4.339814 ACCGCCACTTCAAAGAATAACAAA 59.660 37.500 0.00 0.00 0.00 2.83
5626 7803 2.039216 TCCACCGCCACTTCAAAGAATA 59.961 45.455 0.00 0.00 0.00 1.75
5698 7875 5.154932 CGTTTGAATCACGAACTAGAGTCT 58.845 41.667 0.00 0.00 40.20 3.24
5804 7981 1.209019 CTCTGAGCTGCCAAGTACCAT 59.791 52.381 0.00 0.00 0.00 3.55
5875 8052 0.960861 CCAAAGAAAGGGGAGCGGTC 60.961 60.000 5.93 5.93 0.00 4.79
5931 8108 6.688637 ACTTGTACTTTGGTTCCAAACTAC 57.311 37.500 18.38 18.38 33.15 2.73
5939 8116 6.510638 CGGTTTGACTACTTGTACTTTGGTTC 60.511 42.308 0.00 0.00 0.00 3.62
5944 8121 4.383173 CCCGGTTTGACTACTTGTACTTT 58.617 43.478 0.00 0.00 0.00 2.66
5973 8150 1.593196 CGTTCTCTCTTGGGTTGCAA 58.407 50.000 0.00 0.00 0.00 4.08
6028 8205 5.258841 AGCCATTTGATCAAGAGACAATGA 58.741 37.500 14.38 0.00 0.00 2.57
6093 8270 4.573201 TGCCGCAGTGGTATTTATTTCTAC 59.427 41.667 0.89 0.00 41.21 2.59
6112 8289 5.560966 AGACTATTAATTGTGGTTTGCCG 57.439 39.130 7.29 0.00 37.67 5.69
6139 8316 0.108520 ACGTTATCACATCCGCCGTT 60.109 50.000 0.00 0.00 0.00 4.44
6179 8356 1.064017 GGGTGCCCATAATGACTTCCA 60.064 52.381 1.66 0.00 35.81 3.53
6190 8367 2.043652 GCATGTCAGGGTGCCCAT 60.044 61.111 10.26 0.00 38.92 4.00
6272 8449 2.907458 ATAGCTTTGCAGGAAACCCT 57.093 45.000 0.00 0.00 0.00 4.34
6276 8453 5.885912 CCTAGGTAAATAGCTTTGCAGGAAA 59.114 40.000 0.00 0.00 35.39 3.13
6296 8473 0.179006 GGGCTTGGGAAGATGCCTAG 60.179 60.000 0.00 0.00 44.36 3.02
6314 8491 3.728845 TCAAGTCTCTTTCCGTTCTTGG 58.271 45.455 0.00 0.00 34.82 3.61
6331 8508 9.160496 ACTCTCAATAGAACATAAAAGCTCAAG 57.840 33.333 0.00 0.00 0.00 3.02
6342 8519 9.892130 CTTACCCTAAAACTCTCAATAGAACAT 57.108 33.333 0.00 0.00 0.00 2.71
6352 8529 6.014413 ACTCTTCCACTTACCCTAAAACTCTC 60.014 42.308 0.00 0.00 0.00 3.20
6369 8546 6.753913 ATATCAAATAGCCTCACTCTTCCA 57.246 37.500 0.00 0.00 0.00 3.53
6370 8547 7.671302 TGTATATCAAATAGCCTCACTCTTCC 58.329 38.462 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.