Multiple sequence alignment - TraesCS4D01G251200

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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 TraesCS4D01G251200 chr4D 100.000 5387 0 0 1 5387 419423760 419418374 0.000000e+00 9949
1 TraesCS4D01G251200 chr4D 88.085 235 27 1 2159 2392 338871683 338871449 1.480000e-70 278
2 TraesCS4D01G251200 chr4D 87.448 239 28 2 2156 2392 132377679 132377917 1.910000e-69 274
3 TraesCS4D01G251200 chr4B 91.210 3652 194 51 926 4535 517495026 517491460 0.000000e+00 4848
4 TraesCS4D01G251200 chr4B 94.422 251 10 2 4578 4826 517491464 517491216 3.040000e-102 383
5 TraesCS4D01G251200 chr4A 95.472 1524 53 8 2862 4375 45133872 45135389 0.000000e+00 2418
6 TraesCS4D01G251200 chr4A 91.395 1534 106 15 952 2472 45131933 45133453 0.000000e+00 2078
7 TraesCS4D01G251200 chr4A 92.814 334 18 5 2534 2865 45133441 45133770 3.770000e-131 479
8 TraesCS4D01G251200 chr4A 85.915 355 47 3 4377 4730 45135437 45135789 5.090000e-100 375
9 TraesCS4D01G251200 chr4A 90.722 194 13 1 37 230 45131726 45131914 2.490000e-63 254
10 TraesCS4D01G251200 chr3D 98.080 677 9 3 236 911 345757197 345757870 0.000000e+00 1175
11 TraesCS4D01G251200 chr3D 88.559 236 24 3 2159 2392 189623672 189623906 3.180000e-72 283
12 TraesCS4D01G251200 chr3D 87.449 247 28 3 2159 2403 250129645 250129890 1.140000e-71 281
13 TraesCS4D01G251200 chr3D 88.136 236 25 3 2159 2392 120011681 120011447 1.480000e-70 278
14 TraesCS4D01G251200 chr7D 97.661 684 10 5 236 918 621221517 621220839 0.000000e+00 1170
15 TraesCS4D01G251200 chr7D 97.063 681 12 4 236 911 181642237 181642914 0.000000e+00 1140
16 TraesCS4D01G251200 chr7D 97.054 679 12 4 236 913 134721609 134722280 0.000000e+00 1136
17 TraesCS4D01G251200 chr7D 92.268 582 37 5 4812 5387 14925220 14924641 0.000000e+00 819
18 TraesCS4D01G251200 chr7A 93.851 683 32 6 236 915 127659866 127659191 0.000000e+00 1020
19 TraesCS4D01G251200 chr6A 92.362 707 39 11 236 939 36402304 36402998 0.000000e+00 992
20 TraesCS4D01G251200 chr1D 92.868 687 35 9 236 917 478814812 478814135 0.000000e+00 985
21 TraesCS4D01G251200 chr3B 92.952 681 38 6 236 914 80094111 80093439 0.000000e+00 983
22 TraesCS4D01G251200 chr3A 92.847 685 37 7 236 917 696045236 696045911 0.000000e+00 983
23 TraesCS4D01G251200 chr2D 93.276 580 33 2 4814 5387 56634536 56633957 0.000000e+00 850
24 TraesCS4D01G251200 chr2D 93.333 570 34 2 4819 5384 346438369 346437800 0.000000e+00 839
25 TraesCS4D01G251200 chr2D 92.427 581 35 5 4814 5387 500589637 500590215 0.000000e+00 821
26 TraesCS4D01G251200 chr2D 92.970 569 27 4 4819 5384 644013197 644013755 0.000000e+00 817
27 TraesCS4D01G251200 chr2B 92.794 569 35 3 4819 5384 412293170 412292605 0.000000e+00 819
28 TraesCS4D01G251200 chr2B 92.443 569 37 3 4819 5387 742784996 742784434 0.000000e+00 808
29 TraesCS4D01G251200 chr6B 92.281 583 32 8 4817 5387 636476500 636475919 0.000000e+00 815
30 TraesCS4D01G251200 chr2A 92.308 572 37 3 4819 5384 549957588 549958158 0.000000e+00 806
31 TraesCS4D01G251200 chr5D 87.866 239 27 2 2156 2392 241192091 241192329 4.110000e-71 279
32 TraesCS4D01G251200 chr1A 87.712 236 27 2 2159 2392 99005030 99004795 1.910000e-69 274


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 TraesCS4D01G251200 chr4D 419418374 419423760 5386 True 9949.0 9949 100.0000 1 5387 1 chr4D.!!$R2 5386
1 TraesCS4D01G251200 chr4B 517491216 517495026 3810 True 2615.5 4848 92.8160 926 4826 2 chr4B.!!$R1 3900
2 TraesCS4D01G251200 chr4A 45131726 45135789 4063 False 1120.8 2418 91.2636 37 4730 5 chr4A.!!$F1 4693
3 TraesCS4D01G251200 chr3D 345757197 345757870 673 False 1175.0 1175 98.0800 236 911 1 chr3D.!!$F3 675
4 TraesCS4D01G251200 chr7D 621220839 621221517 678 True 1170.0 1170 97.6610 236 918 1 chr7D.!!$R2 682
5 TraesCS4D01G251200 chr7D 181642237 181642914 677 False 1140.0 1140 97.0630 236 911 1 chr7D.!!$F2 675
6 TraesCS4D01G251200 chr7D 134721609 134722280 671 False 1136.0 1136 97.0540 236 913 1 chr7D.!!$F1 677
7 TraesCS4D01G251200 chr7D 14924641 14925220 579 True 819.0 819 92.2680 4812 5387 1 chr7D.!!$R1 575
8 TraesCS4D01G251200 chr7A 127659191 127659866 675 True 1020.0 1020 93.8510 236 915 1 chr7A.!!$R1 679
9 TraesCS4D01G251200 chr6A 36402304 36402998 694 False 992.0 992 92.3620 236 939 1 chr6A.!!$F1 703
10 TraesCS4D01G251200 chr1D 478814135 478814812 677 True 985.0 985 92.8680 236 917 1 chr1D.!!$R1 681
11 TraesCS4D01G251200 chr3B 80093439 80094111 672 True 983.0 983 92.9520 236 914 1 chr3B.!!$R1 678
12 TraesCS4D01G251200 chr3A 696045236 696045911 675 False 983.0 983 92.8470 236 917 1 chr3A.!!$F1 681
13 TraesCS4D01G251200 chr2D 56633957 56634536 579 True 850.0 850 93.2760 4814 5387 1 chr2D.!!$R1 573
14 TraesCS4D01G251200 chr2D 346437800 346438369 569 True 839.0 839 93.3330 4819 5384 1 chr2D.!!$R2 565
15 TraesCS4D01G251200 chr2D 500589637 500590215 578 False 821.0 821 92.4270 4814 5387 1 chr2D.!!$F1 573
16 TraesCS4D01G251200 chr2D 644013197 644013755 558 False 817.0 817 92.9700 4819 5384 1 chr2D.!!$F2 565
17 TraesCS4D01G251200 chr2B 412292605 412293170 565 True 819.0 819 92.7940 4819 5384 1 chr2B.!!$R1 565
18 TraesCS4D01G251200 chr2B 742784434 742784996 562 True 808.0 808 92.4430 4819 5387 1 chr2B.!!$R2 568
19 TraesCS4D01G251200 chr6B 636475919 636476500 581 True 815.0 815 92.2810 4817 5387 1 chr6B.!!$R1 570
20 TraesCS4D01G251200 chr2A 549957588 549958158 570 False 806.0 806 92.3080 4819 5384 1 chr2A.!!$F1 565

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
159 160 0.670162 GCACCGCCAATGATTATGCT 59.330 50.0 0.00 0.00 0.0 3.79 F
568 575 0.814010 AGCTGCAAACGTCGACCTTT 60.814 50.0 10.58 8.37 0.0 3.11 F
2241 2277 0.028770 TCTGTGCGAAAAGTTTGCCG 59.971 50.0 6.36 6.36 0.0 5.69 F
3776 3947 0.530650 AGCGCCAATCAGTATGTCCG 60.531 55.0 2.29 0.00 37.4 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1253 1276 0.246635 GGACTCAGCAGCTTACCGAA 59.753 55.000 0.00 0.0 0.00 4.30 R
2286 2322 0.695803 AGCTAGCTTGGGTGGGCTAT 60.696 55.000 12.68 0.0 39.79 2.97 R
4076 4247 1.071471 CACGAGCCAGTCCAAGGTT 59.929 57.895 0.00 0.0 0.00 3.50 R
4871 5097 0.036010 ATCCACTCAAACCGGCTCAG 60.036 55.000 0.00 0.0 0.00 3.35 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
24 25 6.723298 TTCATACACCAACTTCCAATTTGT 57.277 33.333 0.00 0.00 0.00 2.83
25 26 6.723298 TCATACACCAACTTCCAATTTGTT 57.277 33.333 0.00 0.00 0.00 2.83
26 27 6.511416 TCATACACCAACTTCCAATTTGTTG 58.489 36.000 0.00 0.00 40.26 3.33
35 36 3.154827 TCCAATTTGTTGGAGGAGGTC 57.845 47.619 5.82 0.00 45.55 3.85
36 37 2.716424 TCCAATTTGTTGGAGGAGGTCT 59.284 45.455 5.82 0.00 45.55 3.85
37 38 3.140144 TCCAATTTGTTGGAGGAGGTCTT 59.860 43.478 5.82 0.00 45.55 3.01
38 39 3.256631 CCAATTTGTTGGAGGAGGTCTTG 59.743 47.826 0.92 0.00 44.82 3.02
61 62 4.872124 GCATGATTTGGATTGGGACTTTTC 59.128 41.667 0.00 0.00 0.00 2.29
86 87 3.018973 GCAAAAGGCGTGACACGA 58.981 55.556 31.08 0.00 46.05 4.35
96 97 1.852895 GCGTGACACGACATATCTTCC 59.147 52.381 31.08 5.69 46.05 3.46
117 118 7.502561 TCTTCCTTTTTCCTTCTCGAAGAAAAT 59.497 33.333 8.19 0.00 40.79 1.82
122 123 6.787085 TTTCCTTCTCGAAGAAAATGAGAC 57.213 37.500 8.19 0.00 40.79 3.36
154 155 2.350458 GGGTGCACCGCCAATGATT 61.350 57.895 29.08 0.00 35.42 2.57
159 160 0.670162 GCACCGCCAATGATTATGCT 59.330 50.000 0.00 0.00 0.00 3.79
168 169 5.177326 GCCAATGATTATGCTTTTGGACAA 58.823 37.500 4.26 0.00 39.33 3.18
188 189 6.929606 GGACAACTCGCCATACTTATCTTTAT 59.070 38.462 0.00 0.00 0.00 1.40
224 225 6.962182 TCATCTGATCACTAAGTTTTCCCAT 58.038 36.000 0.00 0.00 0.00 4.00
230 231 6.599244 TGATCACTAAGTTTTCCCATAGCAAG 59.401 38.462 0.00 0.00 0.00 4.01
232 233 4.702131 CACTAAGTTTTCCCATAGCAAGCT 59.298 41.667 0.00 0.00 0.00 3.74
233 234 4.702131 ACTAAGTTTTCCCATAGCAAGCTG 59.298 41.667 4.53 0.00 0.00 4.24
234 235 3.439857 AGTTTTCCCATAGCAAGCTGA 57.560 42.857 4.53 0.00 0.00 4.26
324 329 5.957842 ATTCAATACTTTGAGCCGTTTGA 57.042 34.783 0.00 0.00 42.60 2.69
568 575 0.814010 AGCTGCAAACGTCGACCTTT 60.814 50.000 10.58 8.37 0.00 3.11
935 949 6.931840 GGCCTAAGATAGATAAACAACAGAGG 59.068 42.308 0.00 0.00 0.00 3.69
986 1000 1.134401 GTCATCCGAGCCATCCAAAGA 60.134 52.381 0.00 0.00 0.00 2.52
994 1008 3.119849 CGAGCCATCCAAAGAAAAACGAT 60.120 43.478 0.00 0.00 0.00 3.73
1006 1020 1.949465 AAAACGATCGGGCCAGATAC 58.051 50.000 19.01 11.09 0.00 2.24
1087 1101 1.687297 GGACGGTCATCTTCCTCCCC 61.687 65.000 10.76 0.00 0.00 4.81
1088 1102 1.687297 GACGGTCATCTTCCTCCCCC 61.687 65.000 2.62 0.00 0.00 5.40
1089 1103 1.689233 CGGTCATCTTCCTCCCCCA 60.689 63.158 0.00 0.00 0.00 4.96
1090 1104 1.915983 GGTCATCTTCCTCCCCCAC 59.084 63.158 0.00 0.00 0.00 4.61
1091 1105 1.636769 GGTCATCTTCCTCCCCCACC 61.637 65.000 0.00 0.00 0.00 4.61
1092 1106 1.307866 TCATCTTCCTCCCCCACCC 60.308 63.158 0.00 0.00 0.00 4.61
1093 1107 2.044620 ATCTTCCTCCCCCACCCC 59.955 66.667 0.00 0.00 0.00 4.95
1094 1108 2.591821 ATCTTCCTCCCCCACCCCT 61.592 63.158 0.00 0.00 0.00 4.79
1132 1154 3.322466 CCGCCACTCCCCACTCTT 61.322 66.667 0.00 0.00 0.00 2.85
1133 1155 2.046892 CGCCACTCCCCACTCTTG 60.047 66.667 0.00 0.00 0.00 3.02
1134 1156 2.883828 CGCCACTCCCCACTCTTGT 61.884 63.158 0.00 0.00 0.00 3.16
1189 1211 2.509336 CCGCCTTCTAGCACACCG 60.509 66.667 0.00 0.00 0.00 4.94
1190 1212 2.509336 CGCCTTCTAGCACACCGG 60.509 66.667 0.00 0.00 0.00 5.28
1248 1271 4.593864 GCCGACAGAGATCCGGGC 62.594 72.222 0.00 0.00 43.17 6.13
1250 1273 3.147595 CGACAGAGATCCGGGCCA 61.148 66.667 4.39 0.00 0.00 5.36
1253 1276 1.074926 ACAGAGATCCGGGCCATCT 60.075 57.895 4.39 4.03 33.01 2.90
1255 1278 0.034616 CAGAGATCCGGGCCATCTTC 59.965 60.000 4.39 0.00 30.30 2.87
1266 1289 0.462759 GCCATCTTCGGTAAGCTGCT 60.463 55.000 0.00 0.00 32.36 4.24
1269 1292 2.200067 CATCTTCGGTAAGCTGCTGAG 58.800 52.381 1.35 0.00 32.36 3.35
1280 1303 4.664267 TGCTGAGTCCCCCTGCCT 62.664 66.667 0.00 0.00 0.00 4.75
1319 1342 1.079612 GTCCCGATTCGTTTCCGGT 60.080 57.895 0.00 0.00 41.53 5.28
1327 1350 2.032071 CGTTTCCGGTTCCTGCCT 59.968 61.111 0.00 0.00 0.00 4.75
1537 1560 4.309933 TCTATGCCTTGCACGATGATAAG 58.690 43.478 0.00 0.00 43.04 1.73
1570 1593 0.257905 TAGCCTGAAGCCGAGGAGTA 59.742 55.000 0.00 0.00 45.47 2.59
1581 1608 0.381089 CGAGGAGTAACCAGTAGGCG 59.619 60.000 0.00 0.00 42.04 5.52
1621 1648 4.949238 CCATGGGAATTGTGTGACTGATAA 59.051 41.667 2.85 0.00 0.00 1.75
1635 1662 9.871238 GTGTGACTGATAACTTCTTAGGATTTA 57.129 33.333 0.00 0.00 0.00 1.40
1657 1684 8.506168 TTTATGGGTCTGATGACATTTTCTAC 57.494 34.615 0.00 0.00 44.61 2.59
1658 1685 5.762179 TGGGTCTGATGACATTTTCTACT 57.238 39.130 0.00 0.00 44.61 2.57
1659 1686 5.734720 TGGGTCTGATGACATTTTCTACTC 58.265 41.667 0.00 0.00 44.61 2.59
1660 1687 4.806247 GGGTCTGATGACATTTTCTACTCG 59.194 45.833 0.00 0.00 44.61 4.18
1661 1688 5.411781 GGTCTGATGACATTTTCTACTCGT 58.588 41.667 0.00 0.00 44.61 4.18
1662 1689 6.405508 GGGTCTGATGACATTTTCTACTCGTA 60.406 42.308 0.00 0.00 44.61 3.43
1704 1731 3.006323 ACTCGATTATCTAAGCAGGGCTG 59.994 47.826 0.00 0.00 39.62 4.85
1727 1754 5.648526 TGAGTCGAGTCTGCTAGAAACTATT 59.351 40.000 20.51 0.00 0.00 1.73
1758 1785 3.521727 ACCTGTTTGAGGAGTCATAGGT 58.478 45.455 0.00 0.00 46.33 3.08
1761 1788 4.938226 CCTGTTTGAGGAGTCATAGGTTTC 59.062 45.833 0.00 0.00 46.33 2.78
1777 1804 7.459125 TCATAGGTTTCATTAGGCTCTGGATAT 59.541 37.037 0.00 0.00 0.00 1.63
1778 1805 6.521527 AGGTTTCATTAGGCTCTGGATATT 57.478 37.500 0.00 0.00 0.00 1.28
1804 1831 4.654915 TGATTGTGAACCTGTCATGATGT 58.345 39.130 0.00 0.00 38.90 3.06
1871 1899 6.432162 TCACATCTCTTTGCTTAAGAATTGCT 59.568 34.615 6.67 0.00 42.19 3.91
1879 1907 4.858935 TGCTTAAGAATTGCTGTGTTCAC 58.141 39.130 6.67 0.00 0.00 3.18
1908 1937 8.905702 CGATACAATTAAATAGCTCAATTTGGC 58.094 33.333 4.95 0.00 31.63 4.52
1933 1962 4.623932 TTAGCATCAACTCAGAACCTGT 57.376 40.909 0.00 0.00 32.61 4.00
1946 1975 6.150140 ACTCAGAACCTGTTATTGCTTTCATC 59.850 38.462 0.00 0.00 32.61 2.92
1947 1976 6.003326 TCAGAACCTGTTATTGCTTTCATCA 58.997 36.000 0.00 0.00 32.61 3.07
1949 1978 7.177216 TCAGAACCTGTTATTGCTTTCATCAAT 59.823 33.333 0.00 0.00 34.50 2.57
1950 1979 7.816031 CAGAACCTGTTATTGCTTTCATCAATT 59.184 33.333 0.00 0.00 35.87 2.32
2005 2041 8.948853 TTTGTAATTTATGTTCAGAAGAAGCG 57.051 30.769 0.00 0.00 33.63 4.68
2090 2126 6.821665 GCCATGTGTAGACTTTGTAGGATTTA 59.178 38.462 0.00 0.00 0.00 1.40
2122 2158 6.502158 CCTCCCATAGTTCTATTTAGGGATGT 59.498 42.308 13.34 0.00 42.53 3.06
2124 2160 9.101325 CTCCCATAGTTCTATTTAGGGATGTTA 57.899 37.037 13.34 0.00 42.53 2.41
2172 2208 3.487376 GCTTTTGCTTTGGTTCTTTTGCC 60.487 43.478 0.00 0.00 43.35 4.52
2225 2261 2.021457 AGTGGGTCGTTGGTTTTTCTG 58.979 47.619 0.00 0.00 0.00 3.02
2241 2277 0.028770 TCTGTGCGAAAAGTTTGCCG 59.971 50.000 6.36 6.36 0.00 5.69
2242 2278 1.539776 CTGTGCGAAAAGTTTGCCGC 61.540 55.000 21.52 21.52 46.82 6.53
2262 2298 1.745489 GGAAGCGAGCCGATTTGGT 60.745 57.895 0.00 0.00 35.04 3.67
2286 2322 6.620877 TCTCCTGATCTAGCAAGGTTTTTA 57.379 37.500 0.00 0.00 0.00 1.52
2392 2428 5.934781 ACTATTCTTGCCTAGGATCCAAAG 58.065 41.667 14.75 10.78 0.00 2.77
2451 2487 3.119990 ACCGAGCGGATTAAAACAATGTG 60.120 43.478 16.83 0.00 38.96 3.21
2489 2525 3.861840 TCCATTAGTGTGCAGTAAGCTC 58.138 45.455 5.80 0.00 45.94 4.09
2497 2533 3.937706 GTGTGCAGTAAGCTCAGATGATT 59.062 43.478 0.00 0.00 46.32 2.57
2502 2538 6.536582 GTGCAGTAAGCTCAGATGATTTCTTA 59.463 38.462 0.00 0.00 45.94 2.10
2509 2545 8.443953 AAGCTCAGATGATTTCTTACATAACC 57.556 34.615 0.00 0.00 29.93 2.85
2510 2546 6.995091 AGCTCAGATGATTTCTTACATAACCC 59.005 38.462 0.00 0.00 29.93 4.11
2511 2547 6.767902 GCTCAGATGATTTCTTACATAACCCA 59.232 38.462 0.00 0.00 29.93 4.51
2512 2548 7.446625 GCTCAGATGATTTCTTACATAACCCAT 59.553 37.037 0.00 0.00 29.93 4.00
2515 2551 9.224267 CAGATGATTTCTTACATAACCCATAGG 57.776 37.037 0.00 0.00 33.19 2.57
2523 2559 7.250454 TCTTACATAACCCATAGGCCATAGTA 58.750 38.462 5.01 0.00 36.11 1.82
2531 2567 4.326530 CCCATAGGCCATAGTAGATCTCCT 60.327 50.000 5.01 0.00 0.00 3.69
2611 2650 9.999883 GTTACGTTAGTGATAACTAACTGTTTG 57.000 33.333 24.60 14.41 45.85 2.93
2618 2657 8.220755 AGTGATAACTAACTGTTTGAAAAGCA 57.779 30.769 8.91 0.68 39.89 3.91
2639 2678 4.635765 GCAACTGCAGGTCTAATGTGATAA 59.364 41.667 19.93 0.00 41.59 1.75
2642 2681 5.994250 ACTGCAGGTCTAATGTGATAACAT 58.006 37.500 19.93 0.00 0.00 2.71
2707 2746 4.433615 TGATGCTCCTTCACGATAAGTTC 58.566 43.478 0.00 0.00 0.00 3.01
2729 2768 5.245531 TCCCAGCAGTAAGAATGTTTACAG 58.754 41.667 0.00 0.00 36.27 2.74
2922 3067 2.981859 ACCTAATCAACTAGGCCACG 57.018 50.000 5.01 0.00 42.09 4.94
2934 3079 2.645838 AGGCCACGCATCATTAATCT 57.354 45.000 5.01 0.00 0.00 2.40
2941 3088 4.262377 CCACGCATCATTAATCTCTCCTCT 60.262 45.833 0.00 0.00 0.00 3.69
2942 3089 4.922692 CACGCATCATTAATCTCTCCTCTC 59.077 45.833 0.00 0.00 0.00 3.20
2954 3101 5.026038 TCTCTCCTCTCGACTAAAGTAGG 57.974 47.826 0.00 0.00 0.00 3.18
3160 3309 5.010922 ACTGCTGGCTTTATTTCATTTGTGA 59.989 36.000 0.00 0.00 0.00 3.58
3161 3310 6.040209 TGCTGGCTTTATTTCATTTGTGAT 57.960 33.333 0.00 0.00 0.00 3.06
3162 3311 5.870433 TGCTGGCTTTATTTCATTTGTGATG 59.130 36.000 0.00 0.00 0.00 3.07
3197 3356 8.227791 TCACTTTTCGCTCAACATAAATAGTTC 58.772 33.333 0.00 0.00 0.00 3.01
3243 3414 6.945636 TGGTATTCCCTAGGTATGGTATTG 57.054 41.667 8.29 0.00 0.00 1.90
3246 3417 7.351454 TGGTATTCCCTAGGTATGGTATTGTTT 59.649 37.037 8.29 0.00 0.00 2.83
3680 3851 1.949257 CAACCTCAAGTTCCCACGC 59.051 57.895 0.00 0.00 36.18 5.34
3776 3947 0.530650 AGCGCCAATCAGTATGTCCG 60.531 55.000 2.29 0.00 37.40 4.79
3821 3992 2.033602 CACCACCGAAGAACCCCC 59.966 66.667 0.00 0.00 0.00 5.40
3845 4016 3.106552 CGAGCAGAGACCTCCTCG 58.893 66.667 9.91 9.91 46.49 4.63
3968 4139 3.004419 CGCTCGTGATAATGTTCCTCCTA 59.996 47.826 0.00 0.00 0.00 2.94
4076 4247 5.899547 TCTGATCCTCTACTTTGCTTATCCA 59.100 40.000 0.00 0.00 0.00 3.41
4158 4329 7.653767 AGTACAGTTTATGTAGCTTTGTGAC 57.346 36.000 0.00 0.00 45.06 3.67
4334 4510 4.898829 TGTTGTTCTTGTTCATGAGTGG 57.101 40.909 0.00 0.00 0.00 4.00
4407 4629 1.432270 CCGCTCTTTCGGGAATGCTC 61.432 60.000 0.00 0.00 45.38 4.26
4448 4671 8.569641 TCATACAGTTGTTTACATTTTGGTACC 58.430 33.333 4.43 4.43 0.00 3.34
4488 4712 1.361668 GCATCCGCATGTCGAAGTGT 61.362 55.000 10.48 0.00 41.67 3.55
4494 4718 1.506309 GCATGTCGAAGTGTGGTGCA 61.506 55.000 0.00 0.00 0.00 4.57
4535 4759 0.603439 CTTGCCCAACCAAACATGGC 60.603 55.000 0.00 0.00 42.49 4.40
4538 4762 1.745264 CCCAACCAAACATGGCGTT 59.255 52.632 0.00 0.00 40.50 4.84
4548 4772 0.964860 ACATGGCGTTGGCATTGCTA 60.965 50.000 8.82 0.00 46.61 3.49
4560 4784 5.664294 TGGCATTGCTATTCATCAAGTTT 57.336 34.783 8.82 0.00 0.00 2.66
4626 4850 0.463833 CCTTGGCCCTGACGAATACC 60.464 60.000 0.00 0.00 0.00 2.73
4666 4890 4.478195 CGGAGAACGCCTACACTG 57.522 61.111 0.00 0.00 34.82 3.66
4682 4906 4.460948 ACACTGAATTGCAAATCCATCC 57.539 40.909 11.91 0.00 0.00 3.51
4730 4954 3.060607 GCCGCTACACATGTTTTTGTTTG 60.061 43.478 0.00 0.00 0.00 2.93
4798 5024 7.478520 ACCAATAACACGCTGATAAGATTAC 57.521 36.000 0.00 0.00 0.00 1.89
4886 5112 1.546476 CTCTACTGAGCCGGTTTGAGT 59.454 52.381 1.90 6.23 33.12 3.41
4905 5131 1.340889 GTGGATGCAGGCAAAAAGACA 59.659 47.619 0.00 0.00 0.00 3.41
4906 5132 2.028748 GTGGATGCAGGCAAAAAGACAT 60.029 45.455 0.00 0.00 0.00 3.06
4927 5153 4.209307 TCGGATGCACATAGTTTGGTTA 57.791 40.909 0.00 0.00 0.00 2.85
5097 5323 6.092533 CACACATAATCTGAACATGTAGTGCA 59.907 38.462 0.00 0.00 33.65 4.57
5140 5366 9.303537 GACAGTTCATCCTAACTACTATCAAAC 57.696 37.037 0.00 0.00 37.61 2.93
5203 5429 3.599343 AGTTCATCGATGTTGCTGCTAA 58.401 40.909 24.09 6.55 0.00 3.09
5210 5437 5.200368 TCGATGTTGCTGCTAATAGATCA 57.800 39.130 0.00 0.00 0.00 2.92
5331 5595 1.484653 GCCCACTCCAACCTTTTGTTT 59.515 47.619 0.00 0.00 34.00 2.83
5337 5601 4.869861 CACTCCAACCTTTTGTTTTTCCAG 59.130 41.667 0.00 0.00 34.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.748132 ACAAATTGGAAGTTGGTGTATGAAG 58.252 36.000 4.74 0.00 38.22 3.02
3 4 6.768029 CAACAAATTGGAAGTTGGTGTATG 57.232 37.500 8.99 0.00 44.16 2.39
17 18 3.305608 GCAAGACCTCCTCCAACAAATTG 60.306 47.826 0.00 0.00 35.40 2.32
18 19 2.893489 GCAAGACCTCCTCCAACAAATT 59.107 45.455 0.00 0.00 0.00 1.82
19 20 2.158475 TGCAAGACCTCCTCCAACAAAT 60.158 45.455 0.00 0.00 0.00 2.32
20 21 1.214175 TGCAAGACCTCCTCCAACAAA 59.786 47.619 0.00 0.00 0.00 2.83
21 22 0.843309 TGCAAGACCTCCTCCAACAA 59.157 50.000 0.00 0.00 0.00 2.83
22 23 1.067295 ATGCAAGACCTCCTCCAACA 58.933 50.000 0.00 0.00 0.00 3.33
23 24 1.003580 TCATGCAAGACCTCCTCCAAC 59.996 52.381 0.00 0.00 0.00 3.77
24 25 1.361204 TCATGCAAGACCTCCTCCAA 58.639 50.000 0.00 0.00 0.00 3.53
25 26 1.588239 ATCATGCAAGACCTCCTCCA 58.412 50.000 0.00 0.00 0.00 3.86
26 27 2.686915 CAAATCATGCAAGACCTCCTCC 59.313 50.000 0.00 0.00 0.00 4.30
27 28 2.686915 CCAAATCATGCAAGACCTCCTC 59.313 50.000 0.00 0.00 0.00 3.71
28 29 2.309755 TCCAAATCATGCAAGACCTCCT 59.690 45.455 0.00 0.00 0.00 3.69
29 30 2.726821 TCCAAATCATGCAAGACCTCC 58.273 47.619 0.00 0.00 0.00 4.30
30 31 4.441079 CCAATCCAAATCATGCAAGACCTC 60.441 45.833 0.00 0.00 0.00 3.85
31 32 3.449737 CCAATCCAAATCATGCAAGACCT 59.550 43.478 0.00 0.00 0.00 3.85
32 33 3.431207 CCCAATCCAAATCATGCAAGACC 60.431 47.826 0.00 0.00 0.00 3.85
33 34 3.448301 TCCCAATCCAAATCATGCAAGAC 59.552 43.478 0.00 0.00 0.00 3.01
34 35 3.448301 GTCCCAATCCAAATCATGCAAGA 59.552 43.478 0.00 0.00 0.00 3.02
35 36 3.449737 AGTCCCAATCCAAATCATGCAAG 59.550 43.478 0.00 0.00 0.00 4.01
36 37 3.443052 AGTCCCAATCCAAATCATGCAA 58.557 40.909 0.00 0.00 0.00 4.08
37 38 3.104519 AGTCCCAATCCAAATCATGCA 57.895 42.857 0.00 0.00 0.00 3.96
38 39 4.476628 AAAGTCCCAATCCAAATCATGC 57.523 40.909 0.00 0.00 0.00 4.06
61 62 0.384725 CACGCCTTTTGCTCTTGACG 60.385 55.000 0.00 0.00 38.05 4.35
78 79 6.402226 GGAAAAAGGAAGATATGTCGTGTCAC 60.402 42.308 0.00 0.00 0.00 3.67
83 84 6.712276 AGAAGGAAAAAGGAAGATATGTCGT 58.288 36.000 0.00 0.00 0.00 4.34
86 87 6.947464 TCGAGAAGGAAAAAGGAAGATATGT 58.053 36.000 0.00 0.00 0.00 2.29
96 97 7.800847 GTCTCATTTTCTTCGAGAAGGAAAAAG 59.199 37.037 19.55 18.36 45.85 2.27
117 118 2.623416 CCCATGCTGTAGATACGTCTCA 59.377 50.000 3.60 0.00 35.87 3.27
154 155 1.810151 GGCGAGTTGTCCAAAAGCATA 59.190 47.619 0.00 0.00 0.00 3.14
159 160 3.134574 AGTATGGCGAGTTGTCCAAAA 57.865 42.857 0.00 0.00 35.75 2.44
195 196 9.118300 GGAAAACTTAGTGATCAGATGATGAAT 57.882 33.333 0.00 0.00 42.53 2.57
196 197 7.554118 GGGAAAACTTAGTGATCAGATGATGAA 59.446 37.037 0.00 0.00 42.53 2.57
197 198 7.050377 GGGAAAACTTAGTGATCAGATGATGA 58.950 38.462 0.00 0.00 43.70 2.92
198 199 6.825213 TGGGAAAACTTAGTGATCAGATGATG 59.175 38.462 0.00 0.00 34.37 3.07
199 200 6.962182 TGGGAAAACTTAGTGATCAGATGAT 58.038 36.000 0.00 0.00 37.51 2.45
224 225 0.867746 CAAACGCACTCAGCTTGCTA 59.132 50.000 7.25 0.00 42.61 3.49
230 231 1.081840 GCTTCCAAACGCACTCAGC 60.082 57.895 0.00 0.00 40.87 4.26
232 233 0.749818 TTGGCTTCCAAACGCACTCA 60.750 50.000 0.00 0.00 40.92 3.41
233 234 0.383949 TTTGGCTTCCAAACGCACTC 59.616 50.000 6.91 0.00 46.92 3.51
234 235 0.385390 CTTTGGCTTCCAAACGCACT 59.615 50.000 6.91 0.00 46.92 4.40
568 575 4.381185 CCGAGGTAGTTAACACATGCACTA 60.381 45.833 8.61 0.00 0.00 2.74
935 949 5.968528 TGTCTCTAGAGAGGAACTTGTTC 57.031 43.478 22.95 7.62 41.55 3.18
947 961 1.068472 ACGCCACGTTTGTCTCTAGAG 60.068 52.381 13.98 13.98 36.35 2.43
948 962 0.956633 ACGCCACGTTTGTCTCTAGA 59.043 50.000 0.00 0.00 36.35 2.43
949 963 1.335597 TGACGCCACGTTTGTCTCTAG 60.336 52.381 11.50 0.00 41.37 2.43
955 969 2.314647 CGGATGACGCCACGTTTGT 61.315 57.895 0.00 0.00 41.37 2.83
986 1000 2.285977 GTATCTGGCCCGATCGTTTTT 58.714 47.619 13.56 0.00 0.00 1.94
994 1008 2.900273 GCAGTGTATCTGGCCCGA 59.100 61.111 0.00 0.00 43.78 5.14
1087 1101 2.365635 ACGATGGGAGAGGGGTGG 60.366 66.667 0.00 0.00 0.00 4.61
1088 1102 1.381872 AGACGATGGGAGAGGGGTG 60.382 63.158 0.00 0.00 0.00 4.61
1089 1103 1.075896 GAGACGATGGGAGAGGGGT 60.076 63.158 0.00 0.00 0.00 4.95
1090 1104 1.834822 GGAGACGATGGGAGAGGGG 60.835 68.421 0.00 0.00 0.00 4.79
1091 1105 1.075970 TGGAGACGATGGGAGAGGG 60.076 63.158 0.00 0.00 0.00 4.30
1092 1106 1.395826 GGTGGAGACGATGGGAGAGG 61.396 65.000 0.00 0.00 0.00 3.69
1093 1107 1.395826 GGGTGGAGACGATGGGAGAG 61.396 65.000 0.00 0.00 0.00 3.20
1094 1108 1.381327 GGGTGGAGACGATGGGAGA 60.381 63.158 0.00 0.00 0.00 3.71
1166 1188 0.461961 GTGCTAGAAGGCGGTCATCT 59.538 55.000 0.00 0.00 34.52 2.90
1227 1250 3.889044 GGATCTCTGTCGGCGCGA 61.889 66.667 12.10 0.00 0.00 5.87
1248 1271 1.134699 TCAGCAGCTTACCGAAGATGG 60.135 52.381 0.00 0.00 36.31 3.51
1250 1273 1.827969 ACTCAGCAGCTTACCGAAGAT 59.172 47.619 0.00 0.00 34.25 2.40
1253 1276 0.246635 GGACTCAGCAGCTTACCGAA 59.753 55.000 0.00 0.00 0.00 4.30
1255 1278 1.153549 GGGACTCAGCAGCTTACCG 60.154 63.158 0.00 0.00 0.00 4.02
1269 1292 1.419720 GGGATTAGAGGCAGGGGGAC 61.420 65.000 0.00 0.00 0.00 4.46
1292 1315 0.591659 CGAATCGGGACAGATCGCTA 59.408 55.000 0.00 0.00 35.65 4.26
1327 1350 1.776580 GTAACATCACGAACGCGCA 59.223 52.632 5.73 0.00 42.48 6.09
1537 1560 2.027192 TCAGGCTACAAACCATCTGTCC 60.027 50.000 0.00 0.00 0.00 4.02
1570 1593 2.124411 ACATTATCCCGCCTACTGGTT 58.876 47.619 0.00 0.00 35.27 3.67
1581 1608 6.074648 TCCCATGGAATTACAACATTATCCC 58.925 40.000 15.22 0.00 0.00 3.85
1621 1648 7.348274 TCATCAGACCCATAAATCCTAAGAAGT 59.652 37.037 0.00 0.00 0.00 3.01
1635 1662 6.319048 AGTAGAAAATGTCATCAGACCCAT 57.681 37.500 0.00 0.00 44.33 4.00
1657 1684 9.328845 GTCTATATATTCCCTACCTTCTACGAG 57.671 40.741 0.00 0.00 0.00 4.18
1658 1685 9.055689 AGTCTATATATTCCCTACCTTCTACGA 57.944 37.037 0.00 0.00 0.00 3.43
1659 1686 9.328845 GAGTCTATATATTCCCTACCTTCTACG 57.671 40.741 0.00 0.00 0.00 3.51
1660 1687 9.328845 CGAGTCTATATATTCCCTACCTTCTAC 57.671 40.741 0.00 0.00 0.00 2.59
1661 1688 9.276791 TCGAGTCTATATATTCCCTACCTTCTA 57.723 37.037 0.00 0.00 0.00 2.10
1662 1689 8.160434 TCGAGTCTATATATTCCCTACCTTCT 57.840 38.462 0.00 0.00 0.00 2.85
1704 1731 5.744666 ATAGTTTCTAGCAGACTCGACTC 57.255 43.478 0.00 0.00 0.00 3.36
1727 1754 5.130477 ACTCCTCAAACAGGTTCAGTTAGAA 59.870 40.000 0.00 0.00 43.95 2.10
1758 1785 8.659527 TCATACAATATCCAGAGCCTAATGAAA 58.340 33.333 0.00 0.00 0.00 2.69
1761 1788 8.890718 CAATCATACAATATCCAGAGCCTAATG 58.109 37.037 0.00 0.00 0.00 1.90
1777 1804 6.237154 TCATGACAGGTTCACAATCATACAA 58.763 36.000 0.00 0.00 36.92 2.41
1778 1805 5.803552 TCATGACAGGTTCACAATCATACA 58.196 37.500 0.00 0.00 36.92 2.29
1830 1858 7.999679 AGAGATGTGATTTCTTGTTTTCAACA 58.000 30.769 0.00 0.00 40.21 3.33
1849 1877 6.527023 CACAGCAATTCTTAAGCAAAGAGATG 59.473 38.462 0.00 6.60 44.95 2.90
1853 1881 5.772825 ACACAGCAATTCTTAAGCAAAGA 57.227 34.783 0.00 0.00 42.62 2.52
1854 1882 5.978919 TGAACACAGCAATTCTTAAGCAAAG 59.021 36.000 0.00 0.00 36.45 2.77
1871 1899 6.546972 TTTAATTGTATCGCAGTGAACACA 57.453 33.333 7.68 0.00 0.00 3.72
1879 1907 9.669353 AAATTGAGCTATTTAATTGTATCGCAG 57.331 29.630 0.00 0.00 0.00 5.18
1908 1937 5.233050 CAGGTTCTGAGTTGATGCTAATACG 59.767 44.000 0.00 0.00 32.44 3.06
1946 1975 3.441572 CCAAGTCTAGTTCAGCCCAATTG 59.558 47.826 0.00 0.00 0.00 2.32
1947 1976 3.074538 ACCAAGTCTAGTTCAGCCCAATT 59.925 43.478 0.00 0.00 0.00 2.32
1949 1978 2.054799 ACCAAGTCTAGTTCAGCCCAA 58.945 47.619 0.00 0.00 0.00 4.12
1950 1979 1.729586 ACCAAGTCTAGTTCAGCCCA 58.270 50.000 0.00 0.00 0.00 5.36
2005 2041 8.296713 TGCTTATAGTGGTCAAAAGAAAACATC 58.703 33.333 0.00 0.00 0.00 3.06
2122 2158 3.016736 GCTGAGCTATTGCCCAACTTAA 58.983 45.455 0.00 0.00 40.80 1.85
2124 2160 1.005215 AGCTGAGCTATTGCCCAACTT 59.995 47.619 4.49 0.00 36.99 2.66
2158 2194 2.364002 GCTGGTAGGCAAAAGAACCAAA 59.636 45.455 0.00 0.00 41.30 3.28
2172 2208 1.377725 CACAGGGCAAGGCTGGTAG 60.378 63.158 0.00 0.00 0.00 3.18
2225 2261 3.221008 GCGGCAAACTTTTCGCAC 58.779 55.556 11.83 0.00 46.33 5.34
2242 2278 2.511600 AAATCGGCTCGCTTCCGG 60.512 61.111 0.00 0.00 46.43 5.14
2262 2298 5.505181 AAAACCTTGCTAGATCAGGAGAA 57.495 39.130 8.82 0.00 0.00 2.87
2286 2322 0.695803 AGCTAGCTTGGGTGGGCTAT 60.696 55.000 12.68 0.00 39.79 2.97
2392 2428 2.409948 AGCTGCACATTAAGGACTCC 57.590 50.000 1.02 0.00 0.00 3.85
2475 2511 2.964740 TCATCTGAGCTTACTGCACAC 58.035 47.619 0.00 0.00 45.94 3.82
2485 2521 6.995091 GGGTTATGTAAGAAATCATCTGAGCT 59.005 38.462 0.00 0.00 38.79 4.09
2489 2525 9.224267 CCTATGGGTTATGTAAGAAATCATCTG 57.776 37.037 0.00 0.00 38.79 2.90
2497 2533 5.922960 ATGGCCTATGGGTTATGTAAGAA 57.077 39.130 3.32 0.00 34.45 2.52
2502 2538 5.661565 TCTACTATGGCCTATGGGTTATGT 58.338 41.667 3.32 0.00 34.45 2.29
2508 2544 3.964031 GGAGATCTACTATGGCCTATGGG 59.036 52.174 3.32 0.00 0.00 4.00
2509 2545 4.877773 AGGAGATCTACTATGGCCTATGG 58.122 47.826 5.36 0.26 0.00 2.74
2510 2546 5.514169 TGAGGAGATCTACTATGGCCTATG 58.486 45.833 7.68 0.00 0.00 2.23
2511 2547 5.255207 ACTGAGGAGATCTACTATGGCCTAT 59.745 44.000 7.68 0.00 0.00 2.57
2512 2548 4.604050 ACTGAGGAGATCTACTATGGCCTA 59.396 45.833 7.68 0.00 0.00 3.93
2513 2549 3.401002 ACTGAGGAGATCTACTATGGCCT 59.599 47.826 7.68 1.47 0.00 5.19
2514 2550 3.773560 ACTGAGGAGATCTACTATGGCC 58.226 50.000 7.68 0.00 0.00 5.36
2515 2551 6.902771 TTAACTGAGGAGATCTACTATGGC 57.097 41.667 7.68 0.00 0.00 4.40
2523 2559 8.324191 TCATGGTAAATTAACTGAGGAGATCT 57.676 34.615 0.00 0.00 0.00 2.75
2601 2640 5.101628 TGCAGTTGCTTTTCAAACAGTTAG 58.898 37.500 5.62 0.00 42.66 2.34
2611 2650 4.022849 ACATTAGACCTGCAGTTGCTTTTC 60.023 41.667 13.81 0.00 42.66 2.29
2616 2655 2.426522 TCACATTAGACCTGCAGTTGC 58.573 47.619 13.81 1.05 42.50 4.17
2617 2656 5.643348 TGTTATCACATTAGACCTGCAGTTG 59.357 40.000 13.81 0.00 0.00 3.16
2618 2657 5.804639 TGTTATCACATTAGACCTGCAGTT 58.195 37.500 13.81 0.00 0.00 3.16
2639 2678 9.555727 AACTGTTTAGACAAACTACATGTATGT 57.444 29.630 5.91 8.16 43.73 2.29
2642 2681 9.826574 AAGAACTGTTTAGACAAACTACATGTA 57.173 29.630 5.25 5.25 43.73 2.29
2707 2746 5.003804 ACTGTAAACATTCTTACTGCTGGG 58.996 41.667 0.00 0.00 35.34 4.45
2869 3014 3.087031 AGTCGGCTTTGTAGCTACACTA 58.913 45.455 26.02 15.58 46.90 2.74
2872 3017 1.890489 TCAGTCGGCTTTGTAGCTACA 59.110 47.619 22.67 22.67 46.90 2.74
2922 3067 5.048083 AGTCGAGAGGAGAGATTAATGATGC 60.048 44.000 0.00 0.00 0.00 3.91
2934 3079 4.840716 ACCTACTTTAGTCGAGAGGAGA 57.159 45.455 3.95 0.00 0.00 3.71
2941 3088 6.544931 ACTGCATATGTACCTACTTTAGTCGA 59.455 38.462 4.29 0.00 0.00 4.20
2942 3089 6.736123 ACTGCATATGTACCTACTTTAGTCG 58.264 40.000 4.29 0.00 0.00 4.18
2954 3101 5.107837 GCGATGTTACTGACTGCATATGTAC 60.108 44.000 4.29 0.00 0.00 2.90
3079 3228 7.776969 ACAAGACAGGCAATGAGTCATATTAAT 59.223 33.333 5.94 0.00 34.80 1.40
3160 3309 3.755378 AGCGAAAAGTGAAATGCTCTCAT 59.245 39.130 0.00 0.00 33.53 2.90
3161 3310 3.141398 AGCGAAAAGTGAAATGCTCTCA 58.859 40.909 0.00 0.00 0.00 3.27
3162 3311 3.187227 TGAGCGAAAAGTGAAATGCTCTC 59.813 43.478 12.54 0.00 46.69 3.20
3243 3414 2.294233 TCAGAATGCCTCACAAGCAAAC 59.706 45.455 0.00 0.00 44.83 2.93
3246 3417 2.502142 ATCAGAATGCCTCACAAGCA 57.498 45.000 0.00 0.00 45.94 3.91
3680 3851 4.380531 TCCACAGCAGAAAGTAGTTCTTG 58.619 43.478 0.00 0.00 44.64 3.02
3776 3947 2.281761 CTGGTGCCACCACTGGAC 60.282 66.667 13.83 0.00 44.79 4.02
3821 3992 2.807045 GTCTCTGCTCGTGCCGTG 60.807 66.667 7.05 1.85 38.71 4.94
3845 4016 3.137533 GGCATTTCTATCTCTGGCAGAC 58.862 50.000 14.43 0.00 32.26 3.51
3879 4050 3.663176 CACGCTGGCAGTGTTGGG 61.663 66.667 29.77 15.94 36.71 4.12
3968 4139 1.680207 GGGACGGCGTAGAGAACTATT 59.320 52.381 14.74 0.00 0.00 1.73
3998 4169 1.292223 GTACAGGAGCAGAACCGCA 59.708 57.895 0.00 0.00 0.00 5.69
4076 4247 1.071471 CACGAGCCAGTCCAAGGTT 59.929 57.895 0.00 0.00 0.00 3.50
4158 4329 4.396166 AGATATCCAAGCTTTGTTTCACCG 59.604 41.667 0.00 0.00 0.00 4.94
4334 4510 4.617253 AGGAAAATTACAAAGGTTGGGC 57.383 40.909 0.00 0.00 34.12 5.36
4488 4712 2.959372 CGGACGTCTACTGCACCA 59.041 61.111 16.46 0.00 0.00 4.17
4494 4718 1.367599 CGAGAAGGCGGACGTCTACT 61.368 60.000 16.46 8.36 38.07 2.57
4535 4759 3.696281 TGATGAATAGCAATGCCAACG 57.304 42.857 0.00 0.00 0.00 4.10
4538 4762 5.664294 AAACTTGATGAATAGCAATGCCA 57.336 34.783 0.00 0.00 30.87 4.92
4666 4890 1.538849 GGGCGGATGGATTTGCAATTC 60.539 52.381 11.98 11.98 0.00 2.17
4730 4954 2.775890 AGCATGTGTAGCTGCATATCC 58.224 47.619 11.03 2.61 41.61 2.59
4871 5097 0.036010 ATCCACTCAAACCGGCTCAG 60.036 55.000 0.00 0.00 0.00 3.35
4886 5112 1.702182 TGTCTTTTTGCCTGCATCCA 58.298 45.000 0.00 0.00 0.00 3.41
4905 5131 3.281727 ACCAAACTATGTGCATCCGAT 57.718 42.857 0.00 0.00 0.00 4.18
4906 5132 2.779755 ACCAAACTATGTGCATCCGA 57.220 45.000 0.00 0.00 0.00 4.55
4927 5153 2.039746 TGCAACTAAGGTACATGCAGGT 59.960 45.455 9.77 9.77 41.67 4.00
5097 5323 8.220755 TGAACTGTCATTTGTTTAACTAGCTT 57.779 30.769 0.00 0.00 0.00 3.74
5140 5366 7.072177 TGGCTCTTAATAATTTGAACTGTCG 57.928 36.000 0.00 0.00 0.00 4.35
5203 5429 7.481297 AGAGGAAGATGAAGAGGATGATCTAT 58.519 38.462 0.00 0.00 0.00 1.98
5210 5437 6.098695 CAGAAGAAGAGGAAGATGAAGAGGAT 59.901 42.308 0.00 0.00 0.00 3.24
5331 5595 1.974265 TTGACAATGACGCCTGGAAA 58.026 45.000 0.00 0.00 0.00 3.13
5337 5601 3.034569 GGCATTTGACAATGACGCC 57.965 52.632 0.00 0.00 42.35 5.68


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

AutoCloner maintained by Alex Coulton.