Multiple sequence alignment - TraesCS3D01G089300

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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 TraesCS3D01G089300 chr3D 100.000 3542 0 0 1 3542 45244019 45247560 0.000000e+00 6541.0
1 TraesCS3D01G089300 chr3D 86.200 529 63 8 3018 3540 427151762 427151238 6.640000e-157 564.0
2 TraesCS3D01G089300 chr3D 85.472 530 66 8 3018 3542 451894691 451894168 3.110000e-150 542.0
3 TraesCS3D01G089300 chr3B 86.688 1600 133 29 9 1561 70873559 70875125 0.000000e+00 1701.0
4 TraesCS3D01G089300 chr3B 92.881 590 28 6 1724 2300 70875164 70875752 0.000000e+00 845.0
5 TraesCS3D01G089300 chr3B 89.780 499 36 8 2472 2959 70875927 70876421 3.000000e-175 625.0
6 TraesCS3D01G089300 chr3B 83.748 523 77 7 3018 3535 109920801 109921320 4.110000e-134 488.0
7 TraesCS3D01G089300 chr3B 89.655 174 10 3 2285 2457 70875776 70875942 7.700000e-52 215.0
8 TraesCS3D01G089300 chr6D 78.549 1585 224 61 871 2413 422601035 422602545 0.000000e+00 937.0
9 TraesCS3D01G089300 chr6D 80.715 1203 158 42 1241 2414 421661910 421663067 0.000000e+00 869.0
10 TraesCS3D01G089300 chr6D 80.699 1202 159 43 1241 2414 421679884 421681040 0.000000e+00 867.0
11 TraesCS3D01G089300 chr6D 80.167 1195 161 41 1249 2414 421467876 421466729 0.000000e+00 824.0
12 TraesCS3D01G089300 chr6D 79.716 1198 166 45 1239 2413 422215479 422216622 0.000000e+00 795.0
13 TraesCS3D01G089300 chr6D 81.076 1004 126 35 1241 2217 421689239 421690205 0.000000e+00 743.0
14 TraesCS3D01G089300 chr6D 81.361 676 96 17 1758 2414 420969739 420969075 1.130000e-144 523.0
15 TraesCS3D01G089300 chr6D 76.282 312 43 26 871 1172 422215150 422215440 1.710000e-28 137.0
16 TraesCS3D01G089300 chr6A 80.237 1179 163 35 1265 2414 564278739 564277602 0.000000e+00 822.0
17 TraesCS3D01G089300 chr6A 79.933 1191 154 48 1246 2413 565340482 565341610 0.000000e+00 797.0
18 TraesCS3D01G089300 chr6A 76.506 332 39 20 871 1187 565340142 565340449 1.020000e-30 145.0
19 TraesCS3D01G089300 chr6B 79.866 1192 168 42 1253 2413 634503860 634502710 0.000000e+00 806.0
20 TraesCS3D01G089300 chr6B 85.171 526 69 8 3021 3542 659618833 659618313 6.730000e-147 531.0
21 TraesCS3D01G089300 chr6B 94.000 50 3 0 876 925 636744463 636744512 3.790000e-10 76.8
22 TraesCS3D01G089300 chr3A 85.679 810 58 25 1 774 57098224 57099011 0.000000e+00 800.0
23 TraesCS3D01G089300 chr2D 85.822 529 70 4 3018 3542 568947602 568947075 1.110000e-154 556.0
24 TraesCS3D01G089300 chr4B 83.932 529 75 8 3018 3540 562615200 562615724 6.830000e-137 497.0
25 TraesCS3D01G089300 chr4B 83.712 528 78 6 3018 3541 481491229 481491752 3.180000e-135 492.0
26 TraesCS3D01G089300 chr5D 83.302 533 81 7 3015 3542 454725863 454726392 5.320000e-133 484.0
27 TraesCS3D01G089300 chr1D 83.551 535 66 13 3017 3540 224573787 224573264 6.880000e-132 481.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G089300 chr3D 45244019 45247560 3541 False 6541.0 6541 100.0000 1 3542 1 chr3D.!!$F1 3541
1 TraesCS3D01G089300 chr3D 427151238 427151762 524 True 564.0 564 86.2000 3018 3540 1 chr3D.!!$R1 522
2 TraesCS3D01G089300 chr3D 451894168 451894691 523 True 542.0 542 85.4720 3018 3542 1 chr3D.!!$R2 524
3 TraesCS3D01G089300 chr3B 70873559 70876421 2862 False 846.5 1701 89.7510 9 2959 4 chr3B.!!$F2 2950
4 TraesCS3D01G089300 chr3B 109920801 109921320 519 False 488.0 488 83.7480 3018 3535 1 chr3B.!!$F1 517
5 TraesCS3D01G089300 chr6D 422601035 422602545 1510 False 937.0 937 78.5490 871 2413 1 chr6D.!!$F4 1542
6 TraesCS3D01G089300 chr6D 421661910 421663067 1157 False 869.0 869 80.7150 1241 2414 1 chr6D.!!$F1 1173
7 TraesCS3D01G089300 chr6D 421679884 421681040 1156 False 867.0 867 80.6990 1241 2414 1 chr6D.!!$F2 1173
8 TraesCS3D01G089300 chr6D 421466729 421467876 1147 True 824.0 824 80.1670 1249 2414 1 chr6D.!!$R2 1165
9 TraesCS3D01G089300 chr6D 421689239 421690205 966 False 743.0 743 81.0760 1241 2217 1 chr6D.!!$F3 976
10 TraesCS3D01G089300 chr6D 420969075 420969739 664 True 523.0 523 81.3610 1758 2414 1 chr6D.!!$R1 656
11 TraesCS3D01G089300 chr6D 422215150 422216622 1472 False 466.0 795 77.9990 871 2413 2 chr6D.!!$F5 1542
12 TraesCS3D01G089300 chr6A 564277602 564278739 1137 True 822.0 822 80.2370 1265 2414 1 chr6A.!!$R1 1149
13 TraesCS3D01G089300 chr6A 565340142 565341610 1468 False 471.0 797 78.2195 871 2413 2 chr6A.!!$F1 1542
14 TraesCS3D01G089300 chr6B 634502710 634503860 1150 True 806.0 806 79.8660 1253 2413 1 chr6B.!!$R1 1160
15 TraesCS3D01G089300 chr6B 659618313 659618833 520 True 531.0 531 85.1710 3021 3542 1 chr6B.!!$R2 521
16 TraesCS3D01G089300 chr3A 57098224 57099011 787 False 800.0 800 85.6790 1 774 1 chr3A.!!$F1 773
17 TraesCS3D01G089300 chr2D 568947075 568947602 527 True 556.0 556 85.8220 3018 3542 1 chr2D.!!$R1 524
18 TraesCS3D01G089300 chr4B 562615200 562615724 524 False 497.0 497 83.9320 3018 3540 1 chr4B.!!$F2 522
19 TraesCS3D01G089300 chr4B 481491229 481491752 523 False 492.0 492 83.7120 3018 3541 1 chr4B.!!$F1 523
20 TraesCS3D01G089300 chr5D 454725863 454726392 529 False 484.0 484 83.3020 3015 3542 1 chr5D.!!$F1 527
21 TraesCS3D01G089300 chr1D 224573264 224573787 523 True 481.0 481 83.5510 3017 3540 1 chr1D.!!$R1 523

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
857 920 0.468226 TCGTGCTTGGGAAACAGTCT 59.532 50.0 0.00 0.0 0.0 3.24 F
1475 1602 0.035820 TGCGCCCTTTAATTCCGACT 60.036 50.0 4.18 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2463 2677 0.327924 ACATGTTTCATCTCCCCGCA 59.672 50.0 0.00 0.00 0.00 5.69 R
3103 3326 0.316196 GCAAAGGCGCGTTATGCTAG 60.316 55.0 27.17 13.19 43.27 3.42 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
27 28 5.695851 ACACTGCTATTTCTGAAACAAGG 57.304 39.130 4.73 0.00 0.00 3.61
88 89 4.096382 AGTGACGCAATCTTGTTCTTTTGT 59.904 37.500 0.00 0.00 0.00 2.83
90 91 4.797868 TGACGCAATCTTGTTCTTTTGTTG 59.202 37.500 0.00 0.00 0.00 3.33
98 99 7.972832 ATCTTGTTCTTTTGTTGTATCCGTA 57.027 32.000 0.00 0.00 0.00 4.02
99 100 7.416154 TCTTGTTCTTTTGTTGTATCCGTAG 57.584 36.000 0.00 0.00 0.00 3.51
105 106 7.534085 TCTTTTGTTGTATCCGTAGCATTAG 57.466 36.000 0.00 0.00 0.00 1.73
106 107 7.324935 TCTTTTGTTGTATCCGTAGCATTAGA 58.675 34.615 0.00 0.00 0.00 2.10
232 237 1.335324 GGCTGTCACTCACACATTTGC 60.335 52.381 0.00 0.00 0.00 3.68
235 240 1.334556 TGTCACTCACACATTTGCTGC 59.665 47.619 0.00 0.00 0.00 5.25
282 298 7.958053 TGCTTTTAGTTACCAGAACTAGAAC 57.042 36.000 0.00 0.00 34.58 3.01
313 329 9.985730 ATATCAAACAGAAATGTCACATTTGTT 57.014 25.926 20.68 16.23 0.00 2.83
314 330 7.522901 TCAAACAGAAATGTCACATTTGTTG 57.477 32.000 20.68 18.51 0.00 3.33
315 331 7.095910 TCAAACAGAAATGTCACATTTGTTGT 58.904 30.769 20.68 19.09 39.91 3.32
317 333 6.206395 ACAGAAATGTCACATTTGTTGTCA 57.794 33.333 20.68 0.00 36.00 3.58
547 563 9.669353 GTGCATTATTTAGGAACAGATACATTG 57.331 33.333 0.00 0.00 0.00 2.82
558 578 4.780815 ACAGATACATTGTACACATGGGG 58.219 43.478 16.95 0.00 0.00 4.96
610 631 6.317789 TGCACTGTAGAGGAGAAAATTTTG 57.682 37.500 8.47 0.00 0.00 2.44
611 632 6.061441 TGCACTGTAGAGGAGAAAATTTTGA 58.939 36.000 8.47 0.00 0.00 2.69
612 633 6.017109 TGCACTGTAGAGGAGAAAATTTTGAC 60.017 38.462 8.47 1.99 0.00 3.18
652 689 1.674441 CAAATCTGCCAGCATCGATGT 59.326 47.619 25.47 10.56 0.00 3.06
653 690 1.306148 AATCTGCCAGCATCGATGTG 58.694 50.000 25.47 20.25 0.00 3.21
693 734 0.756442 AGTTGTGGCTGCCAACATGT 60.756 50.000 25.23 10.69 43.61 3.21
741 802 1.964373 AGGCGGCTTTGTAACACGG 60.964 57.895 5.25 0.00 0.00 4.94
780 843 3.997021 GTGTACCAGGTTGAATCTCTGTG 59.003 47.826 0.00 0.00 0.00 3.66
803 866 2.623878 TTGTTCGTTGCAGGGAGTTA 57.376 45.000 0.00 0.00 0.00 2.24
839 902 1.135972 TCGAGCGCTTTTTCTTGCATC 60.136 47.619 13.26 0.00 0.00 3.91
857 920 0.468226 TCGTGCTTGGGAAACAGTCT 59.532 50.000 0.00 0.00 0.00 3.24
861 924 0.884704 GCTTGGGAAACAGTCTCGCA 60.885 55.000 0.00 0.00 34.29 5.10
963 1038 4.502282 CGATTCGTGTCTAGTAGTACGTCT 59.498 45.833 20.68 13.43 37.74 4.18
964 1039 5.683302 CGATTCGTGTCTAGTAGTACGTCTA 59.317 44.000 20.68 12.64 37.74 2.59
967 1042 9.186323 GATTCGTGTCTAGTAGTACGTCTATAA 57.814 37.037 20.68 12.56 37.74 0.98
1018 1093 7.012138 CCTCCTATCTATATATACACGCACGTT 59.988 40.741 0.00 0.00 0.00 3.99
1069 1167 1.201647 TCGCTGGAAAACTAGACTCGG 59.798 52.381 0.00 0.00 0.00 4.63
1072 1170 2.864968 CTGGAAAACTAGACTCGGTCG 58.135 52.381 0.00 0.00 37.67 4.79
1079 1177 3.839051 ACTAGACTCGGTCGTAAAACC 57.161 47.619 0.00 0.00 37.67 3.27
1081 1179 2.428888 AGACTCGGTCGTAAAACCAC 57.571 50.000 0.00 0.00 39.43 4.16
1090 1189 4.033817 CGGTCGTAAAACCACTTGTGTTTA 59.966 41.667 0.00 0.00 39.43 2.01
1091 1190 5.447010 CGGTCGTAAAACCACTTGTGTTTAA 60.447 40.000 0.00 0.00 39.43 1.52
1105 1204 1.271488 TGTTTAACCCCCATCGTCCAC 60.271 52.381 0.00 0.00 0.00 4.02
1112 1211 1.320344 CCCCATCGTCCACTCGAGAA 61.320 60.000 21.68 0.64 43.00 2.87
1172 1272 5.243283 GTCACCTTCCTCGGTACATATACAT 59.757 44.000 0.00 0.00 34.94 2.29
1176 1276 2.751259 TCCTCGGTACATATACATCGGC 59.249 50.000 0.00 0.00 32.40 5.54
1180 1280 3.129813 TCGGTACATATACATCGGCATCC 59.870 47.826 0.00 0.00 32.40 3.51
1183 1283 5.488341 GGTACATATACATCGGCATCCTTT 58.512 41.667 0.00 0.00 32.40 3.11
1227 1328 4.083590 GGCATCTCTCTTCACTGTGTTTTC 60.084 45.833 7.79 0.00 0.00 2.29
1237 1338 2.113131 CTGTGTTTTCCCACGCCGAC 62.113 60.000 0.00 0.00 38.20 4.79
1255 1377 1.126846 GACGCGTCCATCTGTTCTTTG 59.873 52.381 28.61 0.00 0.00 2.77
1324 1446 2.563798 ATTGTTGGTGCTGGTGCCG 61.564 57.895 0.00 0.00 38.71 5.69
1401 1523 4.276926 GGAAAGTATGGAGCCTGCAATTAG 59.723 45.833 0.00 0.00 0.00 1.73
1475 1602 0.035820 TGCGCCCTTTAATTCCGACT 60.036 50.000 4.18 0.00 0.00 4.18
1485 1616 5.299279 CCTTTAATTCCGACTGGCATATTGT 59.701 40.000 0.00 0.00 34.14 2.71
1487 1618 7.012894 CCTTTAATTCCGACTGGCATATTGTTA 59.987 37.037 0.00 0.00 34.14 2.41
1634 1765 4.000325 CCATCGTGTGATCAAGGTAACAA 59.000 43.478 0.00 0.00 32.33 2.83
1638 1769 4.876679 TCGTGTGATCAAGGTAACAACAAA 59.123 37.500 0.00 0.00 41.41 2.83
1650 1787 8.316214 CAAGGTAACAACAAACCCTCTAGTATA 58.684 37.037 0.00 0.00 36.34 1.47
1652 1789 8.483758 AGGTAACAACAAACCCTCTAGTATATG 58.516 37.037 0.00 0.00 36.34 1.78
1654 1791 9.310716 GTAACAACAAACCCTCTAGTATATGTC 57.689 37.037 0.00 0.00 0.00 3.06
1673 1810 3.055747 TGTCGCTACACACCCATCAAATA 60.056 43.478 0.00 0.00 0.00 1.40
1674 1811 3.936453 GTCGCTACACACCCATCAAATAA 59.064 43.478 0.00 0.00 0.00 1.40
1675 1812 3.936453 TCGCTACACACCCATCAAATAAC 59.064 43.478 0.00 0.00 0.00 1.89
1676 1813 3.064820 CGCTACACACCCATCAAATAACC 59.935 47.826 0.00 0.00 0.00 2.85
1677 1814 3.380320 GCTACACACCCATCAAATAACCC 59.620 47.826 0.00 0.00 0.00 4.11
1678 1815 2.815158 ACACACCCATCAAATAACCCC 58.185 47.619 0.00 0.00 0.00 4.95
1679 1816 2.381961 ACACACCCATCAAATAACCCCT 59.618 45.455 0.00 0.00 0.00 4.79
1680 1817 3.023832 CACACCCATCAAATAACCCCTC 58.976 50.000 0.00 0.00 0.00 4.30
1681 1818 2.024369 ACACCCATCAAATAACCCCTCC 60.024 50.000 0.00 0.00 0.00 4.30
1682 1819 1.573857 ACCCATCAAATAACCCCTCCC 59.426 52.381 0.00 0.00 0.00 4.30
1683 1820 1.133167 CCCATCAAATAACCCCTCCCC 60.133 57.143 0.00 0.00 0.00 4.81
1684 1821 1.859574 CCATCAAATAACCCCTCCCCT 59.140 52.381 0.00 0.00 0.00 4.79
1685 1822 3.060611 CCATCAAATAACCCCTCCCCTA 58.939 50.000 0.00 0.00 0.00 3.53
1686 1823 3.181433 CCATCAAATAACCCCTCCCCTAC 60.181 52.174 0.00 0.00 0.00 3.18
1687 1824 3.519370 TCAAATAACCCCTCCCCTACT 57.481 47.619 0.00 0.00 0.00 2.57
1688 1825 3.822880 TCAAATAACCCCTCCCCTACTT 58.177 45.455 0.00 0.00 0.00 2.24
1693 1830 1.894699 ACCCCTCCCCTACTTCATTC 58.105 55.000 0.00 0.00 0.00 2.67
1694 1831 0.759346 CCCCTCCCCTACTTCATTCG 59.241 60.000 0.00 0.00 0.00 3.34
1696 1833 2.330216 CCCTCCCCTACTTCATTCGAT 58.670 52.381 0.00 0.00 0.00 3.59
1702 1839 5.914033 TCCCCTACTTCATTCGATGTTTAG 58.086 41.667 0.00 0.00 32.23 1.85
1704 1841 5.753921 CCCCTACTTCATTCGATGTTTAGAC 59.246 44.000 0.00 0.00 32.23 2.59
1710 1847 6.590292 ACTTCATTCGATGTTTAGACGTCATT 59.410 34.615 19.50 0.00 41.03 2.57
1844 1985 4.339530 TGGACGATCAGTTTCTCTATCCAG 59.660 45.833 0.00 0.00 0.00 3.86
1854 1995 0.179034 CTCTATCCAGTTGGGCAGCC 60.179 60.000 1.26 1.26 36.21 4.85
1892 2033 2.983907 TATTATTGGACGGGTTGCGA 57.016 45.000 0.00 0.00 0.00 5.10
1914 2058 3.950395 AGGTACGTGGGTTACTATCTCAC 59.050 47.826 0.00 0.00 0.00 3.51
1917 2061 4.240881 ACGTGGGTTACTATCTCACCTA 57.759 45.455 0.00 0.00 0.00 3.08
1930 2074 8.343168 ACTATCTCACCTAATGCATCTAGTAC 57.657 38.462 0.00 0.00 0.00 2.73
2041 2203 4.040829 TGCTAACAGCTATCTGCCATATGT 59.959 41.667 1.24 0.00 44.10 2.29
2057 2219 4.464008 CATATGTTGGATGGCCTAGTGTT 58.536 43.478 3.32 0.00 34.31 3.32
2066 2228 2.436417 TGGCCTAGTGTTTTCATCAGC 58.564 47.619 3.32 0.00 0.00 4.26
2249 2411 2.052782 ATGTAACCGGGGCAGATTTC 57.947 50.000 6.32 0.00 0.00 2.17
2278 2440 2.288666 GCTGTCAAAGTGTCCTGTTCA 58.711 47.619 0.00 0.00 0.00 3.18
2300 2462 2.097825 AGTCAAGGAATGCATCAAGCC 58.902 47.619 0.00 0.00 44.83 4.35
2355 2567 6.869695 TCATAGTTTCCGCACAGAGTTAATA 58.130 36.000 0.00 0.00 0.00 0.98
2356 2568 6.755141 TCATAGTTTCCGCACAGAGTTAATAC 59.245 38.462 0.00 0.00 0.00 1.89
2357 2569 4.890088 AGTTTCCGCACAGAGTTAATACA 58.110 39.130 0.00 0.00 0.00 2.29
2358 2570 4.929808 AGTTTCCGCACAGAGTTAATACAG 59.070 41.667 0.00 0.00 0.00 2.74
2359 2571 2.888594 TCCGCACAGAGTTAATACAGC 58.111 47.619 0.00 0.00 0.00 4.40
2360 2572 2.496070 TCCGCACAGAGTTAATACAGCT 59.504 45.455 0.00 0.00 0.00 4.24
2361 2573 2.860735 CCGCACAGAGTTAATACAGCTC 59.139 50.000 0.00 0.00 34.84 4.09
2393 2606 5.352846 TGTCTGTTTTGTCGAAGTCAATTCA 59.647 36.000 0.00 0.00 37.83 2.57
2445 2659 8.340618 CTTCTTTGGAAGGTAGATTTTGATGA 57.659 34.615 0.00 0.00 43.68 2.92
2446 2660 8.704849 TTCTTTGGAAGGTAGATTTTGATGAA 57.295 30.769 0.00 0.00 0.00 2.57
2447 2661 8.704849 TCTTTGGAAGGTAGATTTTGATGAAA 57.295 30.769 0.00 0.00 0.00 2.69
2448 2662 8.576442 TCTTTGGAAGGTAGATTTTGATGAAAC 58.424 33.333 0.00 0.00 0.00 2.78
2449 2663 7.831691 TTGGAAGGTAGATTTTGATGAAACA 57.168 32.000 0.00 0.00 0.00 2.83
2450 2664 8.421249 TTGGAAGGTAGATTTTGATGAAACAT 57.579 30.769 0.00 0.00 0.00 2.71
2451 2665 7.829725 TGGAAGGTAGATTTTGATGAAACATG 58.170 34.615 0.00 0.00 0.00 3.21
2452 2666 7.451255 TGGAAGGTAGATTTTGATGAAACATGT 59.549 33.333 0.00 0.00 0.00 3.21
2453 2667 8.956426 GGAAGGTAGATTTTGATGAAACATGTA 58.044 33.333 0.00 0.00 0.00 2.29
2454 2668 9.994432 GAAGGTAGATTTTGATGAAACATGTAG 57.006 33.333 0.00 0.00 0.00 2.74
2455 2669 9.520515 AAGGTAGATTTTGATGAAACATGTAGT 57.479 29.630 0.00 0.00 0.00 2.73
2456 2670 9.520515 AGGTAGATTTTGATGAAACATGTAGTT 57.479 29.630 0.00 0.00 43.89 2.24
2487 2701 4.682320 GCGGGGAGATGAAACATGTAGTTA 60.682 45.833 0.00 0.00 40.26 2.24
2570 2785 0.768622 AACACTTTCCCGATGGACCA 59.231 50.000 0.00 0.00 41.57 4.02
2572 2787 1.354368 ACACTTTCCCGATGGACCAAT 59.646 47.619 0.00 0.00 41.57 3.16
2583 2798 4.695455 CCGATGGACCAATTGTATGGATAC 59.305 45.833 0.00 0.00 43.54 2.24
2589 2804 5.453621 GGACCAATTGTATGGATACGGTGTA 60.454 44.000 4.43 0.00 43.54 2.90
2604 2819 1.108776 GTGTAGTCCGCCACCTATGA 58.891 55.000 0.00 0.00 0.00 2.15
2606 2821 1.064240 TGTAGTCCGCCACCTATGAGA 60.064 52.381 0.00 0.00 0.00 3.27
2647 2863 9.601971 TTGTACAATTTCGCTATTTTCTTGTAC 57.398 29.630 3.59 13.09 43.63 2.90
2767 2983 4.151798 GCAATTCTTTTGCACTCGAGTAC 58.848 43.478 19.57 13.98 44.34 2.73
2778 2994 4.758674 TGCACTCGAGTACTACTACAACTT 59.241 41.667 19.57 0.00 0.00 2.66
2781 2997 6.403418 GCACTCGAGTACTACTACAACTTGAT 60.403 42.308 19.57 0.00 34.07 2.57
2807 3023 7.811236 TGAACATTTTGTAACGGAGTAGTCTAG 59.189 37.037 0.00 0.00 45.00 2.43
2813 3029 2.211250 ACGGAGTAGTCTAGTTGGCA 57.789 50.000 0.00 0.00 41.94 4.92
2814 3030 2.522185 ACGGAGTAGTCTAGTTGGCAA 58.478 47.619 0.00 0.00 41.94 4.52
2822 3038 3.660865 AGTCTAGTTGGCAAACCTTACG 58.339 45.455 0.00 0.00 36.94 3.18
2880 3096 5.897377 AATACGAAGGGGAAAACAATGAG 57.103 39.130 0.00 0.00 0.00 2.90
2881 3097 3.502123 ACGAAGGGGAAAACAATGAGA 57.498 42.857 0.00 0.00 0.00 3.27
2892 3108 1.523758 ACAATGAGAACCGAAGCCAC 58.476 50.000 0.00 0.00 0.00 5.01
2893 3109 1.072331 ACAATGAGAACCGAAGCCACT 59.928 47.619 0.00 0.00 0.00 4.00
2899 3115 0.321653 GAACCGAAGCCACTGACCAT 60.322 55.000 0.00 0.00 0.00 3.55
2900 3116 0.321653 AACCGAAGCCACTGACCATC 60.322 55.000 0.00 0.00 0.00 3.51
2941 3164 2.492012 GGAACTCGTATCGGCTCTCTA 58.508 52.381 0.00 0.00 0.00 2.43
2942 3165 2.223845 GGAACTCGTATCGGCTCTCTAC 59.776 54.545 0.00 0.00 0.00 2.59
2943 3166 1.500108 ACTCGTATCGGCTCTCTACG 58.500 55.000 0.00 0.00 39.56 3.51
2944 3167 0.791422 CTCGTATCGGCTCTCTACGG 59.209 60.000 0.00 0.00 38.90 4.02
2945 3168 1.207085 CGTATCGGCTCTCTACGGC 59.793 63.158 0.00 0.00 35.72 5.68
2961 3184 2.822255 GCGCGTTGGCCCAGATAA 60.822 61.111 8.43 0.00 35.02 1.75
2962 3185 2.823829 GCGCGTTGGCCCAGATAAG 61.824 63.158 8.43 0.00 35.02 1.73
2963 3186 1.153449 CGCGTTGGCCCAGATAAGA 60.153 57.895 0.00 0.00 35.02 2.10
2964 3187 0.742990 CGCGTTGGCCCAGATAAGAA 60.743 55.000 0.00 0.00 35.02 2.52
2965 3188 0.733150 GCGTTGGCCCAGATAAGAAC 59.267 55.000 0.00 0.00 0.00 3.01
2966 3189 1.948611 GCGTTGGCCCAGATAAGAACA 60.949 52.381 0.00 0.00 0.00 3.18
2967 3190 2.432444 CGTTGGCCCAGATAAGAACAA 58.568 47.619 0.00 0.00 0.00 2.83
2968 3191 2.161609 CGTTGGCCCAGATAAGAACAAC 59.838 50.000 0.00 0.00 34.88 3.32
2969 3192 3.421844 GTTGGCCCAGATAAGAACAACT 58.578 45.455 0.00 0.00 35.24 3.16
2970 3193 3.806949 TGGCCCAGATAAGAACAACTT 57.193 42.857 0.00 0.00 42.04 2.66
2971 3194 4.112634 TGGCCCAGATAAGAACAACTTT 57.887 40.909 0.00 0.00 39.72 2.66
2972 3195 4.479158 TGGCCCAGATAAGAACAACTTTT 58.521 39.130 0.00 0.00 39.72 2.27
2973 3196 4.898861 TGGCCCAGATAAGAACAACTTTTT 59.101 37.500 0.00 0.00 39.72 1.94
3002 3225 9.621629 TTTTTAGAACCAGATCAGAACAACTAA 57.378 29.630 0.00 0.00 0.00 2.24
3003 3226 8.833231 TTTAGAACCAGATCAGAACAACTAAG 57.167 34.615 0.00 0.00 0.00 2.18
3004 3227 5.799213 AGAACCAGATCAGAACAACTAAGG 58.201 41.667 0.00 0.00 0.00 2.69
3005 3228 3.944087 ACCAGATCAGAACAACTAAGGC 58.056 45.455 0.00 0.00 0.00 4.35
3006 3229 3.327757 ACCAGATCAGAACAACTAAGGCA 59.672 43.478 0.00 0.00 0.00 4.75
3007 3230 4.018960 ACCAGATCAGAACAACTAAGGCAT 60.019 41.667 0.00 0.00 0.00 4.40
3008 3231 4.334759 CCAGATCAGAACAACTAAGGCATG 59.665 45.833 0.00 0.00 0.00 4.06
3009 3232 5.181009 CAGATCAGAACAACTAAGGCATGA 58.819 41.667 0.00 0.00 0.00 3.07
3010 3233 5.064452 CAGATCAGAACAACTAAGGCATGAC 59.936 44.000 0.00 0.00 0.00 3.06
3011 3234 4.623932 TCAGAACAACTAAGGCATGACT 57.376 40.909 0.00 0.00 0.00 3.41
3012 3235 4.569943 TCAGAACAACTAAGGCATGACTC 58.430 43.478 0.00 0.00 0.00 3.36
3013 3236 4.040339 TCAGAACAACTAAGGCATGACTCA 59.960 41.667 0.00 0.00 0.00 3.41
3014 3237 4.391216 CAGAACAACTAAGGCATGACTCAG 59.609 45.833 0.00 0.00 0.00 3.35
3015 3238 2.704572 ACAACTAAGGCATGACTCAGC 58.295 47.619 0.00 0.00 0.00 4.26
3016 3239 2.038952 ACAACTAAGGCATGACTCAGCA 59.961 45.455 0.00 0.00 0.00 4.41
3088 3311 4.819630 ACAAATCACGTACACACCAATCTT 59.180 37.500 0.00 0.00 0.00 2.40
3095 3318 6.315642 TCACGTACACACCAATCTTGTAAAAA 59.684 34.615 0.00 0.00 0.00 1.94
3103 3326 8.327429 CACACCAATCTTGTAAAAATGAACAAC 58.673 33.333 0.00 0.00 32.43 3.32
3169 3394 7.645402 AGTAAAATTACAAACAAGACCGAAGG 58.355 34.615 6.13 0.00 45.10 3.46
3262 3488 4.553330 AATGACGGATTACCTTCACACT 57.447 40.909 0.00 0.00 44.99 3.55
3355 3584 4.640201 ACCATTACCGTTGAATGAATCAGG 59.360 41.667 3.48 0.00 39.77 3.86
3401 3631 1.857217 CGAACTTCAGATCTGGCATCG 59.143 52.381 22.42 20.39 0.00 3.84
3496 3727 3.708403 TCTTTCAGATGCCACAGATGT 57.292 42.857 0.00 0.00 0.00 3.06
3516 3747 3.200605 TGTAGACCACAATCTGCATCCAT 59.799 43.478 0.00 0.00 36.53 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.373224 AGATTGCTTTAGAAGGCTGCC 58.627 47.619 11.65 11.65 0.00 4.85
63 64 6.183360 ACAAAAGAACAAGATTGCGTCACTTA 60.183 34.615 0.00 0.00 0.00 2.24
69 70 4.743493 ACAACAAAAGAACAAGATTGCGT 58.257 34.783 0.00 0.00 0.00 5.24
88 89 7.985184 AGAAATTGTCTAATGCTACGGATACAA 59.015 33.333 0.00 0.00 33.56 2.41
90 91 7.948278 AGAAATTGTCTAATGCTACGGATAC 57.052 36.000 0.00 0.00 33.56 2.24
105 106 9.950680 TCAAACACTTAGAATCAAGAAATTGTC 57.049 29.630 0.00 0.00 0.00 3.18
169 172 7.809546 TCTGTGTGATATCCTAGTTCTAGTG 57.190 40.000 0.00 0.00 0.00 2.74
255 271 9.569122 TTCTAGTTCTGGTAACTAAAAGCATTT 57.431 29.630 0.00 0.00 37.44 2.32
256 272 9.000486 GTTCTAGTTCTGGTAACTAAAAGCATT 58.000 33.333 0.00 0.00 32.89 3.56
257 273 8.376270 AGTTCTAGTTCTGGTAACTAAAAGCAT 58.624 33.333 0.00 0.00 32.89 3.79
306 322 4.925054 CCTGCATTAAGGTGACAACAAATG 59.075 41.667 12.07 12.07 32.17 2.32
313 329 1.340017 GCCTCCTGCATTAAGGTGACA 60.340 52.381 10.00 0.00 40.77 3.58
314 330 1.383523 GCCTCCTGCATTAAGGTGAC 58.616 55.000 10.00 0.00 40.77 3.67
315 331 3.882131 GCCTCCTGCATTAAGGTGA 57.118 52.632 10.00 0.00 40.77 4.02
505 521 0.323360 GCACCCCTTAGCCATGAACA 60.323 55.000 0.00 0.00 0.00 3.18
514 530 6.126409 TGTTCCTAAATAATGCACCCCTTAG 58.874 40.000 0.00 0.00 0.00 2.18
547 563 1.812571 CAGTTTGAGCCCCATGTGTAC 59.187 52.381 0.00 0.00 0.00 2.90
558 578 0.819259 TGTGCAGGGACAGTTTGAGC 60.819 55.000 0.00 0.00 0.00 4.26
612 633 2.062890 GCGACATCTAAACGCCGACG 62.063 60.000 0.00 0.00 45.35 5.12
622 659 1.953559 GGCAGATTTGGCGACATCTA 58.046 50.000 0.00 0.00 42.32 1.98
652 689 2.796557 TGAACAAAATACCCCGCATCA 58.203 42.857 0.00 0.00 0.00 3.07
653 690 3.859411 TTGAACAAAATACCCCGCATC 57.141 42.857 0.00 0.00 0.00 3.91
660 697 5.234116 CAGCCACAACTTTGAACAAAATACC 59.766 40.000 0.00 0.00 0.00 2.73
661 698 5.276820 GCAGCCACAACTTTGAACAAAATAC 60.277 40.000 0.00 0.00 0.00 1.89
741 802 5.048364 TGGTACACACAAATACTTCCAATGC 60.048 40.000 0.00 0.00 0.00 3.56
780 843 1.007387 CCCTGCAACGAACAAAGCC 60.007 57.895 0.00 0.00 0.00 4.35
803 866 2.678190 GCTCGACCAGCTACAGGAATTT 60.678 50.000 0.00 0.00 45.83 1.82
839 902 0.868406 GAGACTGTTTCCCAAGCACG 59.132 55.000 0.00 0.00 0.00 5.34
857 920 1.807755 GCAATGGACTGCTATCTGCGA 60.808 52.381 0.00 0.00 46.63 5.10
963 1038 9.075678 GGATACAAGAAGCTGTAGGTAGTTATA 57.924 37.037 0.00 0.00 35.32 0.98
964 1039 7.785506 AGGATACAAGAAGCTGTAGGTAGTTAT 59.214 37.037 0.00 0.00 35.32 1.89
967 1042 5.520751 AGGATACAAGAAGCTGTAGGTAGT 58.479 41.667 0.00 0.00 35.32 2.73
975 1050 2.103941 GGAGGGAGGATACAAGAAGCTG 59.896 54.545 0.00 0.00 41.41 4.24
1069 1167 5.738693 GGTTAAACACAAGTGGTTTTACGAC 59.261 40.000 8.97 1.76 41.38 4.34
1072 1170 5.350633 GGGGTTAAACACAAGTGGTTTTAC 58.649 41.667 8.97 7.86 41.38 2.01
1079 1177 2.227865 CGATGGGGGTTAAACACAAGTG 59.772 50.000 0.00 0.00 0.00 3.16
1081 1179 2.486592 GACGATGGGGGTTAAACACAAG 59.513 50.000 0.00 0.00 0.00 3.16
1090 1189 2.656069 CGAGTGGACGATGGGGGTT 61.656 63.158 0.00 0.00 35.09 4.11
1091 1190 3.075005 CGAGTGGACGATGGGGGT 61.075 66.667 0.00 0.00 35.09 4.95
1105 1204 4.378356 CGGATCTTCATAGCTCTTCTCGAG 60.378 50.000 5.93 5.93 42.88 4.04
1112 1211 1.342819 GTGCCGGATCTTCATAGCTCT 59.657 52.381 5.05 0.00 0.00 4.09
1186 1286 1.067821 GCCGATTCCACACACCAAAAA 59.932 47.619 0.00 0.00 0.00 1.94
1187 1287 0.671251 GCCGATTCCACACACCAAAA 59.329 50.000 0.00 0.00 0.00 2.44
1188 1288 0.466372 TGCCGATTCCACACACCAAA 60.466 50.000 0.00 0.00 0.00 3.28
1189 1289 0.251121 ATGCCGATTCCACACACCAA 60.251 50.000 0.00 0.00 0.00 3.67
1190 1290 0.676466 GATGCCGATTCCACACACCA 60.676 55.000 0.00 0.00 0.00 4.17
1191 1291 0.392998 AGATGCCGATTCCACACACC 60.393 55.000 0.00 0.00 0.00 4.16
1192 1292 1.009829 GAGATGCCGATTCCACACAC 58.990 55.000 0.00 0.00 0.00 3.82
1193 1293 0.904649 AGAGATGCCGATTCCACACA 59.095 50.000 0.00 0.00 0.00 3.72
1194 1294 1.137872 AGAGAGATGCCGATTCCACAC 59.862 52.381 0.00 0.00 0.00 3.82
1195 1295 1.489481 AGAGAGATGCCGATTCCACA 58.511 50.000 0.00 0.00 0.00 4.17
1196 1296 2.159043 TGAAGAGAGATGCCGATTCCAC 60.159 50.000 0.00 0.00 0.00 4.02
1197 1297 2.110578 TGAAGAGAGATGCCGATTCCA 58.889 47.619 0.00 0.00 0.00 3.53
1198 1298 2.102252 AGTGAAGAGAGATGCCGATTCC 59.898 50.000 0.00 0.00 0.00 3.01
1199 1299 3.122297 CAGTGAAGAGAGATGCCGATTC 58.878 50.000 0.00 0.00 0.00 2.52
1200 1300 2.499289 ACAGTGAAGAGAGATGCCGATT 59.501 45.455 0.00 0.00 0.00 3.34
1201 1301 2.106566 ACAGTGAAGAGAGATGCCGAT 58.893 47.619 0.00 0.00 0.00 4.18
1202 1302 1.203287 CACAGTGAAGAGAGATGCCGA 59.797 52.381 0.00 0.00 0.00 5.54
1203 1303 1.067283 ACACAGTGAAGAGAGATGCCG 60.067 52.381 7.81 0.00 0.00 5.69
1204 1304 2.758736 ACACAGTGAAGAGAGATGCC 57.241 50.000 7.81 0.00 0.00 4.40
1205 1305 4.083590 GGAAAACACAGTGAAGAGAGATGC 60.084 45.833 7.81 0.00 0.00 3.91
1237 1338 1.148310 ACAAAGAACAGATGGACGCG 58.852 50.000 3.53 3.53 0.00 6.01
1240 1346 4.821805 TCCAGAAACAAAGAACAGATGGAC 59.178 41.667 0.00 0.00 29.63 4.02
1324 1446 1.112113 TCACTAGCATCGTTCCCTCC 58.888 55.000 0.00 0.00 0.00 4.30
1332 1454 0.525668 GACACCCGTCACTAGCATCG 60.526 60.000 0.00 0.00 42.13 3.84
1401 1523 3.323751 AATGTGTACCACGTACCCTTC 57.676 47.619 0.00 0.00 38.14 3.46
1431 1556 5.007921 AGGCAAATTGAAGTGCACATTTTTC 59.992 36.000 21.04 14.17 42.74 2.29
1475 1602 4.727677 TCCATGCATCTAACAATATGCCA 58.272 39.130 0.00 0.00 46.34 4.92
1485 1616 3.623703 AGCACATGTTCCATGCATCTAA 58.376 40.909 0.00 0.00 41.97 2.10
1487 1618 2.139323 AGCACATGTTCCATGCATCT 57.861 45.000 0.00 0.00 41.97 2.90
1634 1765 4.894114 AGCGACATATACTAGAGGGTTTGT 59.106 41.667 0.00 0.00 0.00 2.83
1638 1769 5.002516 GTGTAGCGACATATACTAGAGGGT 58.997 45.833 2.07 0.00 38.04 4.34
1650 1787 0.901827 TGATGGGTGTGTAGCGACAT 59.098 50.000 2.07 0.00 38.04 3.06
1652 1789 1.803334 TTTGATGGGTGTGTAGCGAC 58.197 50.000 0.00 0.00 0.00 5.19
1654 1791 3.064820 GGTTATTTGATGGGTGTGTAGCG 59.935 47.826 0.00 0.00 0.00 4.26
1673 1810 2.206223 GAATGAAGTAGGGGAGGGGTT 58.794 52.381 0.00 0.00 0.00 4.11
1674 1811 1.894699 GAATGAAGTAGGGGAGGGGT 58.105 55.000 0.00 0.00 0.00 4.95
1675 1812 0.759346 CGAATGAAGTAGGGGAGGGG 59.241 60.000 0.00 0.00 0.00 4.79
1676 1813 1.789523 TCGAATGAAGTAGGGGAGGG 58.210 55.000 0.00 0.00 0.00 4.30
1677 1814 2.700897 ACATCGAATGAAGTAGGGGAGG 59.299 50.000 0.00 0.00 0.00 4.30
1678 1815 4.408182 AACATCGAATGAAGTAGGGGAG 57.592 45.455 0.00 0.00 0.00 4.30
1679 1816 4.837093 AAACATCGAATGAAGTAGGGGA 57.163 40.909 0.00 0.00 0.00 4.81
1680 1817 5.753921 GTCTAAACATCGAATGAAGTAGGGG 59.246 44.000 0.00 0.00 0.00 4.79
1681 1818 5.459107 CGTCTAAACATCGAATGAAGTAGGG 59.541 44.000 0.00 0.00 0.00 3.53
1682 1819 6.034591 ACGTCTAAACATCGAATGAAGTAGG 58.965 40.000 0.00 0.00 0.00 3.18
1683 1820 6.745907 TGACGTCTAAACATCGAATGAAGTAG 59.254 38.462 17.92 0.00 0.00 2.57
1684 1821 6.614160 TGACGTCTAAACATCGAATGAAGTA 58.386 36.000 17.92 0.00 0.00 2.24
1685 1822 5.466819 TGACGTCTAAACATCGAATGAAGT 58.533 37.500 17.92 0.00 0.00 3.01
1686 1823 6.575083 ATGACGTCTAAACATCGAATGAAG 57.425 37.500 17.92 0.00 0.00 3.02
1687 1824 6.961359 AATGACGTCTAAACATCGAATGAA 57.039 33.333 17.92 0.00 0.00 2.57
1688 1825 6.961359 AAATGACGTCTAAACATCGAATGA 57.039 33.333 17.92 0.00 0.00 2.57
1710 1847 9.823647 TTCAGGTAAATTCATAGCAAACAAAAA 57.176 25.926 0.00 0.00 0.00 1.94
1747 1884 8.832521 CGGTGCTTGTGAACCTATAATAATTTA 58.167 33.333 0.00 0.00 39.85 1.40
1892 2033 3.950395 GTGAGATAGTAACCCACGTACCT 59.050 47.826 0.00 0.00 0.00 3.08
1914 2058 8.807118 TCCTAATTCAGTACTAGATGCATTAGG 58.193 37.037 23.24 23.24 45.97 2.69
1917 2061 7.148641 CGTCCTAATTCAGTACTAGATGCATT 58.851 38.462 0.00 0.00 0.00 3.56
1930 2074 8.020819 TCAAATTAAACTTGCGTCCTAATTCAG 58.979 33.333 0.00 0.00 0.00 3.02
2010 2172 5.931146 GCAGATAGCTGTTAGCATTAGACAT 59.069 40.000 10.15 0.00 45.56 3.06
2041 2203 3.517296 TGAAAACACTAGGCCATCCAA 57.483 42.857 5.01 0.00 33.74 3.53
2057 2219 5.428253 ACCTTATAAGCTTCGCTGATGAAA 58.572 37.500 0.00 0.00 39.62 2.69
2066 2228 3.244579 GGTTGCGTACCTTATAAGCTTCG 59.755 47.826 0.00 10.90 44.10 3.79
2186 2348 1.717032 TGTAGTGCTTCCACCACTCT 58.283 50.000 0.00 0.00 42.22 3.24
2249 2411 1.066002 CACTTTGACAGCAACCCACAG 59.934 52.381 0.00 0.00 32.79 3.66
2278 2440 3.887716 GGCTTGATGCATTCCTTGACTAT 59.112 43.478 0.00 0.00 45.15 2.12
2300 2462 5.867174 TGTGTGTTTTACATACTCCTCGATG 59.133 40.000 7.94 0.00 40.33 3.84
2358 2570 2.453983 AAACAGACAGAGCTGAGAGC 57.546 50.000 4.21 0.00 42.84 4.09
2359 2571 3.726607 ACAAAACAGACAGAGCTGAGAG 58.273 45.455 4.21 0.00 39.20 3.20
2360 2572 3.722147 GACAAAACAGACAGAGCTGAGA 58.278 45.455 4.21 0.00 39.20 3.27
2361 2573 2.474359 CGACAAAACAGACAGAGCTGAG 59.526 50.000 4.21 0.00 39.20 3.35
2393 2606 2.753452 AGAATCATGTCGACCGTGTACT 59.247 45.455 14.12 9.84 0.00 2.73
2459 2673 2.311463 TGTTTCATCTCCCCGCAAAAA 58.689 42.857 0.00 0.00 0.00 1.94
2460 2674 1.988293 TGTTTCATCTCCCCGCAAAA 58.012 45.000 0.00 0.00 0.00 2.44
2461 2675 1.818060 CATGTTTCATCTCCCCGCAAA 59.182 47.619 0.00 0.00 0.00 3.68
2462 2676 1.271871 ACATGTTTCATCTCCCCGCAA 60.272 47.619 0.00 0.00 0.00 4.85
2463 2677 0.327924 ACATGTTTCATCTCCCCGCA 59.672 50.000 0.00 0.00 0.00 5.69
2464 2678 2.213499 CTACATGTTTCATCTCCCCGC 58.787 52.381 2.30 0.00 0.00 6.13
2465 2679 3.543680 ACTACATGTTTCATCTCCCCG 57.456 47.619 2.30 0.00 0.00 5.73
2466 2680 5.741011 TGTAACTACATGTTTCATCTCCCC 58.259 41.667 2.30 0.00 39.89 4.81
2487 2701 8.896744 CAATCCATTCTCAACAAGTATACATGT 58.103 33.333 7.91 7.91 0.00 3.21
2511 2725 9.941325 AAATGGATAAACTTAATTGCATGTCAA 57.059 25.926 5.27 5.27 39.32 3.18
2564 2779 3.456644 ACCGTATCCATACAATTGGTCCA 59.543 43.478 10.83 0.00 38.01 4.02
2570 2785 5.508489 CGGACTACACCGTATCCATACAATT 60.508 44.000 0.00 0.00 46.70 2.32
2572 2787 3.316029 CGGACTACACCGTATCCATACAA 59.684 47.826 0.00 0.00 46.70 2.41
2589 2804 1.043816 CATCTCATAGGTGGCGGACT 58.956 55.000 0.00 0.00 0.00 3.85
2753 2969 5.240183 AGTTGTAGTAGTACTCGAGTGCAAA 59.760 40.000 31.11 18.23 29.98 3.68
2759 2975 7.304919 TCATCAAGTTGTAGTAGTACTCGAG 57.695 40.000 11.84 11.84 0.00 4.04
2761 2977 7.303261 TGTTCATCAAGTTGTAGTAGTACTCG 58.697 38.462 5.96 0.00 0.00 4.18
2762 2978 9.640963 AATGTTCATCAAGTTGTAGTAGTACTC 57.359 33.333 5.96 0.00 0.00 2.59
2778 2994 6.932400 ACTACTCCGTTACAAAATGTTCATCA 59.068 34.615 0.00 0.00 0.00 3.07
2781 2997 6.518493 AGACTACTCCGTTACAAAATGTTCA 58.482 36.000 0.00 0.00 0.00 3.18
2822 3038 5.751028 CCAGTCTCCGACAATCTCTAAAATC 59.249 44.000 0.00 0.00 34.60 2.17
2844 3060 6.322712 CCCCTTCGTATTTCATTTAAATCCCA 59.677 38.462 0.00 0.00 38.71 4.37
2850 3066 8.179509 TGTTTTCCCCTTCGTATTTCATTTAA 57.820 30.769 0.00 0.00 0.00 1.52
2880 3096 0.321653 ATGGTCAGTGGCTTCGGTTC 60.322 55.000 0.00 0.00 0.00 3.62
2881 3097 0.321653 GATGGTCAGTGGCTTCGGTT 60.322 55.000 0.00 0.00 0.00 4.44
2892 3108 3.094062 ATGGTCCGGCGATGGTCAG 62.094 63.158 9.30 0.00 0.00 3.51
2893 3109 3.080765 ATGGTCCGGCGATGGTCA 61.081 61.111 9.30 0.00 0.00 4.02
2934 3157 3.248171 CAACGCGCCGTAGAGAGC 61.248 66.667 5.73 0.00 39.99 4.09
2945 3168 0.742990 TTCTTATCTGGGCCAACGCG 60.743 55.000 8.04 3.53 35.02 6.01
2976 3199 9.621629 TTAGTTGTTCTGATCTGGTTCTAAAAA 57.378 29.630 0.00 0.00 0.00 1.94
2977 3200 9.273016 CTTAGTTGTTCTGATCTGGTTCTAAAA 57.727 33.333 0.00 0.00 0.00 1.52
2978 3201 7.878127 CCTTAGTTGTTCTGATCTGGTTCTAAA 59.122 37.037 0.00 0.00 0.00 1.85
2979 3202 7.386851 CCTTAGTTGTTCTGATCTGGTTCTAA 58.613 38.462 0.00 2.96 0.00 2.10
2980 3203 6.574465 GCCTTAGTTGTTCTGATCTGGTTCTA 60.574 42.308 0.00 0.00 0.00 2.10
2981 3204 5.799213 CCTTAGTTGTTCTGATCTGGTTCT 58.201 41.667 0.00 0.00 0.00 3.01
2982 3205 4.393371 GCCTTAGTTGTTCTGATCTGGTTC 59.607 45.833 0.00 0.00 0.00 3.62
2983 3206 4.202461 TGCCTTAGTTGTTCTGATCTGGTT 60.202 41.667 0.00 0.00 0.00 3.67
2984 3207 3.327757 TGCCTTAGTTGTTCTGATCTGGT 59.672 43.478 0.00 0.00 0.00 4.00
2985 3208 3.942829 TGCCTTAGTTGTTCTGATCTGG 58.057 45.455 0.00 0.00 0.00 3.86
2986 3209 5.064452 GTCATGCCTTAGTTGTTCTGATCTG 59.936 44.000 0.00 0.00 0.00 2.90
2987 3210 5.046014 AGTCATGCCTTAGTTGTTCTGATCT 60.046 40.000 0.00 0.00 0.00 2.75
2988 3211 5.181748 AGTCATGCCTTAGTTGTTCTGATC 58.818 41.667 0.00 0.00 0.00 2.92
2989 3212 5.171339 AGTCATGCCTTAGTTGTTCTGAT 57.829 39.130 0.00 0.00 0.00 2.90
2990 3213 4.040339 TGAGTCATGCCTTAGTTGTTCTGA 59.960 41.667 0.00 0.00 0.00 3.27
2991 3214 4.318332 TGAGTCATGCCTTAGTTGTTCTG 58.682 43.478 0.00 0.00 0.00 3.02
2992 3215 4.573900 CTGAGTCATGCCTTAGTTGTTCT 58.426 43.478 0.00 0.00 0.00 3.01
2993 3216 3.126000 GCTGAGTCATGCCTTAGTTGTTC 59.874 47.826 0.00 0.00 0.00 3.18
2994 3217 3.077359 GCTGAGTCATGCCTTAGTTGTT 58.923 45.455 0.00 0.00 0.00 2.83
2995 3218 2.038952 TGCTGAGTCATGCCTTAGTTGT 59.961 45.455 10.72 0.00 0.00 3.32
2996 3219 2.703416 TGCTGAGTCATGCCTTAGTTG 58.297 47.619 10.72 0.00 0.00 3.16
2997 3220 3.641434 ATGCTGAGTCATGCCTTAGTT 57.359 42.857 10.72 0.00 0.00 2.24
2998 3221 3.641434 AATGCTGAGTCATGCCTTAGT 57.359 42.857 10.72 0.00 0.00 2.24
2999 3222 4.978083 AAAATGCTGAGTCATGCCTTAG 57.022 40.909 10.72 0.00 0.00 2.18
3069 3292 4.002906 ACAAGATTGGTGTGTACGTGAT 57.997 40.909 0.00 0.00 0.00 3.06
3088 3311 7.535940 GCGTTATGCTAGTTGTTCATTTTTACA 59.464 33.333 0.00 0.00 41.73 2.41
3095 3318 2.030457 GCGCGTTATGCTAGTTGTTCAT 59.970 45.455 8.43 0.00 43.27 2.57
3103 3326 0.316196 GCAAAGGCGCGTTATGCTAG 60.316 55.000 27.17 13.19 43.27 3.42
3169 3394 4.421058 GTTGGTGTCAAACTCAAAGGTTC 58.579 43.478 0.00 0.00 34.28 3.62
3175 3400 0.736053 GGCGTTGGTGTCAAACTCAA 59.264 50.000 0.00 0.00 34.28 3.02
3180 3405 2.124653 ACGGGCGTTGGTGTCAAA 60.125 55.556 0.00 0.00 34.28 2.69
3214 3439 0.537143 CTTTGGTGGCTGTGGTGCTA 60.537 55.000 0.00 0.00 0.00 3.49
3216 3441 0.821711 TACTTTGGTGGCTGTGGTGC 60.822 55.000 0.00 0.00 0.00 5.01
3420 3650 5.544176 GGATGACAGATATGGTTTCCTCCTA 59.456 44.000 0.00 0.00 0.00 2.94
3491 3722 4.444022 GGATGCAGATTGTGGTCTACATCT 60.444 45.833 13.74 0.00 43.70 2.90
3496 3727 4.454678 GAATGGATGCAGATTGTGGTCTA 58.545 43.478 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.