Multiple sequence alignment - TraesCS5A01G423400

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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 TraesCS5A01G423400 chr5A 100.000 2663 0 0 1 2663 609210663 609213325 0.000000e+00 4918.0
1 TraesCS5A01G423400 chr5A 79.707 818 83 38 693 1428 609240571 609241387 5.080000e-142 514.0
2 TraesCS5A01G423400 chr5A 86.452 155 21 0 1510 1664 609241577 609241731 1.270000e-38 171.0
3 TraesCS5A01G423400 chr5A 82.692 104 14 3 1793 1894 46151225 46151326 3.650000e-14 89.8
4 TraesCS5A01G423400 chr5B 85.408 932 81 20 692 1583 601344236 601345152 0.000000e+00 917.0
5 TraesCS5A01G423400 chr5B 88.312 616 48 14 2051 2663 601345600 601346194 0.000000e+00 717.0
6 TraesCS5A01G423400 chr5B 91.667 432 32 1 1463 1894 601345175 601345602 1.760000e-166 595.0
7 TraesCS5A01G423400 chr5B 78.713 808 82 31 695 1428 601337405 601338196 8.690000e-125 457.0
8 TraesCS5A01G423400 chr5B 89.789 284 24 3 1546 1829 601338224 601338502 2.520000e-95 359.0
9 TraesCS5A01G423400 chr5B 87.582 306 20 2 1 288 601336767 601337072 3.280000e-89 339.0
10 TraesCS5A01G423400 chr5B 89.308 159 17 0 1892 2050 488180220 488180062 1.620000e-47 200.0
11 TraesCS5A01G423400 chr5D 88.595 719 53 11 795 1502 488355479 488356179 0.000000e+00 846.0
12 TraesCS5A01G423400 chr5D 94.628 242 12 1 1684 1924 488356332 488356573 9.000000e-100 374.0
13 TraesCS5A01G423400 chr5D 95.858 169 6 1 267 434 488354869 488355037 3.380000e-69 272.0
14 TraesCS5A01G423400 chr5D 89.071 183 14 6 1529 1707 488356134 488356314 3.450000e-54 222.0
15 TraesCS5A01G423400 chr5D 87.019 208 7 2 1 188 488354642 488354849 1.610000e-52 217.0
16 TraesCS5A01G423400 chr5D 86.486 185 13 5 496 672 488355166 488355346 2.710000e-45 193.0
17 TraesCS5A01G423400 chr5D 88.525 122 3 4 683 793 488355329 488355450 1.290000e-28 137.0
18 TraesCS5A01G423400 chr5D 91.026 78 5 2 423 500 488355053 488355128 1.300000e-18 104.0
19 TraesCS5A01G423400 chr2D 90.683 161 15 0 1890 2050 624365936 624365776 5.770000e-52 215.0
20 TraesCS5A01G423400 chrUn 89.506 162 17 0 1889 2050 96474148 96473987 3.470000e-49 206.0
21 TraesCS5A01G423400 chrUn 100.000 61 0 0 250 310 86516598 86516658 2.170000e-21 113.0
22 TraesCS5A01G423400 chrUn 100.000 61 0 0 250 310 206784116 206784176 2.170000e-21 113.0
23 TraesCS5A01G423400 chrUn 100.000 61 0 0 250 310 345389182 345389122 2.170000e-21 113.0
24 TraesCS5A01G423400 chr1D 89.937 159 16 0 1892 2050 332997336 332997178 3.470000e-49 206.0
25 TraesCS5A01G423400 chr7A 90.385 156 13 1 1892 2047 544895905 544896058 1.250000e-48 204.0
26 TraesCS5A01G423400 chr7A 88.623 167 18 1 1888 2053 356367282 356367448 4.490000e-48 202.0
27 TraesCS5A01G423400 chr4D 88.690 168 18 1 1889 2055 386984665 386984832 1.250000e-48 204.0
28 TraesCS5A01G423400 chr4D 100.000 61 0 0 250 310 123320943 123321003 2.170000e-21 113.0
29 TraesCS5A01G423400 chr2B 89.571 163 14 3 1892 2053 722081534 722081374 1.250000e-48 204.0
30 TraesCS5A01G423400 chr7B 89.375 160 17 0 1888 2047 295079839 295079998 4.490000e-48 202.0
31 TraesCS5A01G423400 chr7D 100.000 61 0 0 250 310 203485458 203485518 2.170000e-21 113.0
32 TraesCS5A01G423400 chr3D 100.000 61 0 0 250 310 213395602 213395662 2.170000e-21 113.0
33 TraesCS5A01G423400 chr3D 100.000 61 0 0 250 310 523768808 523768868 2.170000e-21 113.0
34 TraesCS5A01G423400 chr1B 93.478 46 3 0 2613 2658 674797996 674798041 4.760000e-08 69.4


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 TraesCS5A01G423400 chr5A 609210663 609213325 2662 False 4918.000 4918 100.000000 1 2663 1 chr5A.!!$F2 2662
1 TraesCS5A01G423400 chr5A 609240571 609241731 1160 False 342.500 514 83.079500 693 1664 2 chr5A.!!$F3 971
2 TraesCS5A01G423400 chr5B 601344236 601346194 1958 False 743.000 917 88.462333 692 2663 3 chr5B.!!$F2 1971
3 TraesCS5A01G423400 chr5B 601336767 601338502 1735 False 385.000 457 85.361333 1 1829 3 chr5B.!!$F1 1828
4 TraesCS5A01G423400 chr5D 488354642 488356573 1931 False 295.625 846 90.151000 1 1924 8 chr5D.!!$F1 1923

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
794 938 0.038526 TTTGAGAGGACGCGGTTCTC 60.039 55.0 22.08 22.08 38.39 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2602 0.107703 TGTCAAGGATGATGGCCGTC 60.108 55.0 18.69 18.69 38.01 4.79 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
43 44 6.183360 TGCTTTCTTCTCCTTTTCTTGTCTTG 60.183 38.462 0.00 0.00 0.00 3.02
69 70 5.335504 CCTCTTTGCTGATGAGGTTCTTTTC 60.336 44.000 11.81 0.00 42.17 2.29
119 138 9.546909 CAGTGCTAATTTAGAGTTGTTTACATG 57.453 33.333 7.63 0.00 0.00 3.21
156 175 2.514803 CCTGGAATTCCACCGACTTTT 58.485 47.619 23.63 0.00 42.01 2.27
175 197 4.488126 TTTTGCTCATCACACTTGCTAC 57.512 40.909 0.00 0.00 0.00 3.58
199 221 5.775686 TGAATGAAAAGGCACATCTTCAAG 58.224 37.500 0.00 0.00 31.94 3.02
201 223 6.040729 TGAATGAAAAGGCACATCTTCAAGAA 59.959 34.615 0.00 0.00 31.94 2.52
203 225 6.219417 TGAAAAGGCACATCTTCAAGAAAA 57.781 33.333 0.00 0.00 0.00 2.29
204 226 6.638610 TGAAAAGGCACATCTTCAAGAAAAA 58.361 32.000 0.00 0.00 0.00 1.94
223 245 3.923273 AAATTTCCCTTCCCTCCAACT 57.077 42.857 0.00 0.00 0.00 3.16
262 284 2.031682 CGATCCTCCGGAAATGCAATTC 60.032 50.000 5.23 5.92 33.67 2.17
314 336 1.617755 CTTCGCTCGCTCGCTTTCAA 61.618 55.000 0.00 0.00 0.00 2.69
374 396 2.828520 CAGTCAGTAGCTTCCTTCTCCA 59.171 50.000 0.00 0.00 0.00 3.86
381 403 3.133141 AGCTTCCTTCTCCACAAGTTC 57.867 47.619 0.00 0.00 0.00 3.01
401 423 7.181569 AGTTCCCTTTTCACAAGAATTTGAA 57.818 32.000 0.00 0.00 37.73 2.69
421 443 6.419980 TGAAAAACTTCCATTGCACTTTTG 57.580 33.333 0.00 0.00 0.00 2.44
426 474 5.799681 ACTTCCATTGCACTTTTGTTTTG 57.200 34.783 0.00 0.00 0.00 2.44
427 475 5.486526 ACTTCCATTGCACTTTTGTTTTGA 58.513 33.333 0.00 0.00 0.00 2.69
430 478 5.728471 TCCATTGCACTTTTGTTTTGAGAA 58.272 33.333 0.00 0.00 0.00 2.87
432 480 6.822676 TCCATTGCACTTTTGTTTTGAGAAAT 59.177 30.769 0.00 0.00 0.00 2.17
474 522 1.664965 AAACACGAGCCTCGCACTC 60.665 57.895 15.20 0.00 45.12 3.51
500 548 1.465200 GCTAGCTACTAGGCGGGCTT 61.465 60.000 10.13 0.00 34.88 4.35
502 550 0.185416 TAGCTACTAGGCGGGCTTCT 59.815 55.000 10.13 2.69 36.40 2.85
503 551 1.068250 GCTACTAGGCGGGCTTCTG 59.932 63.158 10.13 3.44 0.00 3.02
547 637 1.887707 GCGTGGCATACCTACCTGC 60.888 63.158 0.00 0.00 36.63 4.85
599 697 7.506328 AAAAACCTGTATAACAAGTCACCTC 57.494 36.000 0.00 0.00 0.00 3.85
600 698 5.818678 AACCTGTATAACAAGTCACCTCA 57.181 39.130 0.00 0.00 0.00 3.86
601 699 5.818678 ACCTGTATAACAAGTCACCTCAA 57.181 39.130 0.00 0.00 0.00 3.02
602 700 6.182507 ACCTGTATAACAAGTCACCTCAAA 57.817 37.500 0.00 0.00 0.00 2.69
603 701 6.597562 ACCTGTATAACAAGTCACCTCAAAA 58.402 36.000 0.00 0.00 0.00 2.44
604 702 7.057894 ACCTGTATAACAAGTCACCTCAAAAA 58.942 34.615 0.00 0.00 0.00 1.94
671 803 0.250727 CGAGAGCAAACAAAGGGGGA 60.251 55.000 0.00 0.00 0.00 4.81
672 804 1.614317 CGAGAGCAAACAAAGGGGGAT 60.614 52.381 0.00 0.00 0.00 3.85
673 805 2.095461 GAGAGCAAACAAAGGGGGATC 58.905 52.381 0.00 0.00 0.00 3.36
674 806 1.186200 GAGCAAACAAAGGGGGATCC 58.814 55.000 1.92 1.92 0.00 3.36
787 931 2.563471 AGATACGTTTGAGAGGACGC 57.437 50.000 0.00 0.00 42.67 5.19
793 937 0.319641 GTTTGAGAGGACGCGGTTCT 60.320 55.000 12.47 10.20 0.00 3.01
794 938 0.038526 TTTGAGAGGACGCGGTTCTC 60.039 55.000 22.08 22.08 38.39 2.87
795 939 1.874345 TTGAGAGGACGCGGTTCTCC 61.874 60.000 24.33 16.91 38.87 3.71
866 1044 1.522580 GTCTCTGGCCGATTCCTGC 60.523 63.158 0.00 0.00 0.00 4.85
871 1053 4.838152 GGCCGATTCCTGCGCAGA 62.838 66.667 38.06 20.46 0.00 4.26
872 1054 2.590007 GCCGATTCCTGCGCAGAT 60.590 61.111 38.06 24.44 0.00 2.90
873 1055 1.300931 GCCGATTCCTGCGCAGATA 60.301 57.895 38.06 24.46 0.00 1.98
879 1061 0.315251 TTCCTGCGCAGATAGATCCG 59.685 55.000 38.06 18.60 0.00 4.18
902 1084 4.778415 CGACTCGGAGCGTGGGTG 62.778 72.222 4.58 0.00 0.00 4.61
903 1085 3.371063 GACTCGGAGCGTGGGTGA 61.371 66.667 4.58 0.00 0.00 4.02
904 1086 2.680352 ACTCGGAGCGTGGGTGAT 60.680 61.111 4.58 0.00 0.00 3.06
905 1087 2.202797 CTCGGAGCGTGGGTGATG 60.203 66.667 0.00 0.00 0.00 3.07
906 1088 2.994995 TCGGAGCGTGGGTGATGT 60.995 61.111 0.00 0.00 0.00 3.06
941 1148 5.241506 AGCATACACACACATAAATATGGGC 59.758 40.000 2.59 0.00 40.75 5.36
969 1176 0.802607 CGCCTGAGCTTCTACCGAAC 60.803 60.000 0.00 0.00 36.60 3.95
1025 1235 0.108424 AGCCTGATGAACAGCTCGAC 60.108 55.000 0.00 0.00 44.52 4.20
1037 1247 2.178521 CTCGACGAAGGTCACCGG 59.821 66.667 0.00 0.00 43.61 5.28
1040 1250 2.737376 GACGAAGGTCACCGGTGC 60.737 66.667 30.25 23.00 42.91 5.01
1087 1324 2.133281 TCACATCAATCCCTTGCCAG 57.867 50.000 0.00 0.00 32.11 4.85
1102 1348 1.521010 CCAGTGCAGAGCTCGATGG 60.521 63.158 8.37 9.41 0.00 3.51
1111 1357 3.785859 GCTCGATGGAGGCCACCA 61.786 66.667 25.10 25.10 44.41 4.17
1221 1476 3.753797 AGACCAAGAAGAAGATTTTCCGC 59.246 43.478 0.00 0.00 33.64 5.54
1302 1563 4.592426 GCTAAACGCCGTCCTTCT 57.408 55.556 0.00 0.00 0.00 2.85
1342 1603 3.930634 AGATGAAGGACAGCTTTTTGC 57.069 42.857 0.00 0.00 43.03 3.68
1459 1792 4.776322 TGGCGATTCCAGCGGTGG 62.776 66.667 27.73 27.73 46.63 4.61
1488 1821 1.301244 CGGGGAGAAGGATGATGCG 60.301 63.158 0.00 0.00 0.00 4.73
1489 1822 1.072159 GGGGAGAAGGATGATGCGG 59.928 63.158 0.00 0.00 0.00 5.69
1491 1824 1.958205 GGAGAAGGATGATGCGGCG 60.958 63.158 0.51 0.51 0.00 6.46
1506 1875 1.425428 GGCGGCGACATCTTTTCAG 59.575 57.895 12.98 0.00 0.00 3.02
1527 1896 2.356535 GGTGGAGAAGGATGATGCAACT 60.357 50.000 0.00 0.00 0.00 3.16
1557 2043 3.652057 TTTCATGGGGAGAAGGATGAC 57.348 47.619 0.00 0.00 0.00 3.06
1559 2045 0.833287 CATGGGGAGAAGGATGACGT 59.167 55.000 0.00 0.00 0.00 4.34
1636 2122 2.027625 CCGGGAGTCGTCAAGCAAC 61.028 63.158 0.00 0.00 37.11 4.17
1682 2215 9.833917 AACTTAGGCCTAGTAGTTATCATTTTC 57.166 33.333 22.91 0.00 0.00 2.29
1802 2336 8.349568 AGTGATGTGTACACTGATCTTAACTA 57.650 34.615 25.60 2.22 45.19 2.24
1841 2375 1.421268 AGGGTGATTGTTGCTGTGAGA 59.579 47.619 0.00 0.00 0.00 3.27
1895 2429 5.516044 TGTACCAGCTCTTCCATTCTACTA 58.484 41.667 0.00 0.00 0.00 1.82
1897 2431 4.615513 ACCAGCTCTTCCATTCTACTACT 58.384 43.478 0.00 0.00 0.00 2.57
1909 2443 6.664816 TCCATTCTACTACTTCCGTTCCTAAA 59.335 38.462 0.00 0.00 0.00 1.85
1940 2474 9.846248 AGTCTTTTTATACATTTCAATGCAGAC 57.154 29.630 0.00 0.00 40.04 3.51
1941 2475 9.846248 GTCTTTTTATACATTTCAATGCAGACT 57.154 29.630 0.00 0.00 40.04 3.24
1948 2482 6.349973 ACATTTCAATGCAGACTACATACG 57.650 37.500 0.00 0.00 40.04 3.06
1949 2483 5.294306 ACATTTCAATGCAGACTACATACGG 59.706 40.000 0.00 0.00 40.04 4.02
1950 2484 4.729227 TTCAATGCAGACTACATACGGA 57.271 40.909 0.00 0.00 0.00 4.69
1951 2485 4.307443 TCAATGCAGACTACATACGGAG 57.693 45.455 0.00 0.00 0.00 4.63
1952 2486 2.797156 CAATGCAGACTACATACGGAGC 59.203 50.000 0.00 0.00 0.00 4.70
1953 2487 1.470051 TGCAGACTACATACGGAGCA 58.530 50.000 0.00 0.00 0.00 4.26
1954 2488 1.822371 TGCAGACTACATACGGAGCAA 59.178 47.619 0.00 0.00 0.00 3.91
1955 2489 2.232696 TGCAGACTACATACGGAGCAAA 59.767 45.455 0.00 0.00 0.00 3.68
1956 2490 3.118775 TGCAGACTACATACGGAGCAAAT 60.119 43.478 0.00 0.00 0.00 2.32
1957 2491 3.871594 GCAGACTACATACGGAGCAAATT 59.128 43.478 0.00 0.00 0.00 1.82
1958 2492 4.260375 GCAGACTACATACGGAGCAAATTG 60.260 45.833 0.00 0.00 0.00 2.32
1959 2493 5.109210 CAGACTACATACGGAGCAAATTGA 58.891 41.667 0.00 0.00 0.00 2.57
1960 2494 5.755375 CAGACTACATACGGAGCAAATTGAT 59.245 40.000 0.00 0.00 0.00 2.57
1961 2495 6.258727 CAGACTACATACGGAGCAAATTGATT 59.741 38.462 0.00 0.00 0.00 2.57
1962 2496 6.258727 AGACTACATACGGAGCAAATTGATTG 59.741 38.462 0.00 0.00 42.21 2.67
1963 2497 6.112734 ACTACATACGGAGCAAATTGATTGA 58.887 36.000 0.00 0.00 41.85 2.57
1964 2498 5.895636 ACATACGGAGCAAATTGATTGAA 57.104 34.783 0.00 0.00 41.85 2.69
1965 2499 6.455360 ACATACGGAGCAAATTGATTGAAT 57.545 33.333 0.00 0.00 41.85 2.57
1966 2500 6.498304 ACATACGGAGCAAATTGATTGAATC 58.502 36.000 0.00 0.00 41.85 2.52
1967 2501 6.319658 ACATACGGAGCAAATTGATTGAATCT 59.680 34.615 6.73 0.00 41.85 2.40
1968 2502 7.498900 ACATACGGAGCAAATTGATTGAATCTA 59.501 33.333 6.73 0.00 41.85 1.98
1969 2503 6.124088 ACGGAGCAAATTGATTGAATCTAC 57.876 37.500 6.73 0.00 41.85 2.59
1970 2504 5.647658 ACGGAGCAAATTGATTGAATCTACA 59.352 36.000 6.73 0.00 41.85 2.74
1971 2505 6.319658 ACGGAGCAAATTGATTGAATCTACAT 59.680 34.615 6.73 0.00 41.85 2.29
1972 2506 7.148018 ACGGAGCAAATTGATTGAATCTACATT 60.148 33.333 6.73 0.20 41.85 2.71
1973 2507 7.377928 CGGAGCAAATTGATTGAATCTACATTC 59.622 37.037 6.73 0.00 41.85 2.67
1974 2508 8.411683 GGAGCAAATTGATTGAATCTACATTCT 58.588 33.333 6.73 0.00 41.85 2.40
2015 2549 8.692110 ACATTCGTATGTAGTTCGTATTCAAA 57.308 30.769 5.81 0.00 43.12 2.69
2016 2550 9.309516 ACATTCGTATGTAGTTCGTATTCAAAT 57.690 29.630 5.81 0.00 43.12 2.32
2017 2551 9.779237 CATTCGTATGTAGTTCGTATTCAAATC 57.221 33.333 0.00 0.00 0.00 2.17
2018 2552 9.745880 ATTCGTATGTAGTTCGTATTCAAATCT 57.254 29.630 0.00 0.00 0.00 2.40
2019 2553 8.778141 TCGTATGTAGTTCGTATTCAAATCTC 57.222 34.615 0.00 0.00 0.00 2.75
2020 2554 8.618677 TCGTATGTAGTTCGTATTCAAATCTCT 58.381 33.333 0.00 0.00 0.00 3.10
2021 2555 8.893884 CGTATGTAGTTCGTATTCAAATCTCTC 58.106 37.037 0.00 0.00 0.00 3.20
2022 2556 9.731819 GTATGTAGTTCGTATTCAAATCTCTCA 57.268 33.333 0.00 0.00 0.00 3.27
2024 2558 9.653287 ATGTAGTTCGTATTCAAATCTCTCAAA 57.347 29.630 0.00 0.00 0.00 2.69
2025 2559 9.483916 TGTAGTTCGTATTCAAATCTCTCAAAA 57.516 29.630 0.00 0.00 0.00 2.44
2026 2560 9.959775 GTAGTTCGTATTCAAATCTCTCAAAAG 57.040 33.333 0.00 0.00 0.00 2.27
2027 2561 8.833231 AGTTCGTATTCAAATCTCTCAAAAGA 57.167 30.769 0.00 0.00 0.00 2.52
2028 2562 8.713271 AGTTCGTATTCAAATCTCTCAAAAGAC 58.287 33.333 0.00 0.00 0.00 3.01
2029 2563 8.713271 GTTCGTATTCAAATCTCTCAAAAGACT 58.287 33.333 0.00 0.00 0.00 3.24
2030 2564 8.833231 TCGTATTCAAATCTCTCAAAAGACTT 57.167 30.769 0.00 0.00 0.00 3.01
2031 2565 9.923143 TCGTATTCAAATCTCTCAAAAGACTTA 57.077 29.630 0.00 0.00 0.00 2.24
2044 2578 9.595823 TCTCAAAAGACTTATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2045 2579 9.595823 CTCAAAAGACTTATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2046 2580 9.595823 TCAAAAGACTTATATTTAGGAACGGAG 57.404 33.333 0.00 0.00 0.00 4.63
2048 2582 8.943909 AAAGACTTATATTTAGGAACGGAGTG 57.056 34.615 0.00 0.00 45.00 3.51
2049 2583 7.893124 AGACTTATATTTAGGAACGGAGTGA 57.107 36.000 0.00 0.00 45.00 3.41
2100 2634 3.423749 TCCTTGACATGCACATTGTGAT 58.576 40.909 20.77 8.21 35.23 3.06
2105 2639 2.492881 GACATGCACATTGTGATCCCAA 59.507 45.455 20.77 0.00 35.23 4.12
2107 2641 3.255725 CATGCACATTGTGATCCCAAAC 58.744 45.455 20.77 0.72 35.23 2.93
2108 2642 2.314246 TGCACATTGTGATCCCAAACA 58.686 42.857 20.77 3.39 35.23 2.83
2109 2643 2.898612 TGCACATTGTGATCCCAAACAT 59.101 40.909 20.77 0.00 35.23 2.71
2110 2644 3.324268 TGCACATTGTGATCCCAAACATT 59.676 39.130 20.77 0.00 35.23 2.71
2111 2645 4.525874 TGCACATTGTGATCCCAAACATTA 59.474 37.500 20.77 0.00 35.23 1.90
2112 2646 5.187381 TGCACATTGTGATCCCAAACATTAT 59.813 36.000 20.77 0.00 35.23 1.28
2113 2647 6.379417 TGCACATTGTGATCCCAAACATTATA 59.621 34.615 20.77 0.00 35.23 0.98
2114 2648 6.919662 GCACATTGTGATCCCAAACATTATAG 59.080 38.462 20.77 0.00 35.23 1.31
2115 2649 7.416664 GCACATTGTGATCCCAAACATTATAGT 60.417 37.037 20.77 0.00 35.23 2.12
2116 2650 8.469200 CACATTGTGATCCCAAACATTATAGTT 58.531 33.333 11.45 0.00 35.23 2.24
2117 2651 8.686334 ACATTGTGATCCCAAACATTATAGTTC 58.314 33.333 0.00 0.00 0.00 3.01
2118 2652 8.685427 CATTGTGATCCCAAACATTATAGTTCA 58.315 33.333 0.00 0.00 0.00 3.18
2119 2653 8.642935 TTGTGATCCCAAACATTATAGTTCAA 57.357 30.769 0.00 0.00 0.00 2.69
2120 2654 8.821686 TGTGATCCCAAACATTATAGTTCAAT 57.178 30.769 0.00 0.00 0.00 2.57
2121 2655 9.253832 TGTGATCCCAAACATTATAGTTCAATT 57.746 29.630 0.00 0.00 0.00 2.32
2148 2682 2.703536 TGTAGGTCAGTGGTGTGTTCAT 59.296 45.455 0.00 0.00 0.00 2.57
2155 2689 5.338056 GGTCAGTGGTGTGTTCATCCTAATA 60.338 44.000 0.00 0.00 0.00 0.98
2168 2702 8.843262 TGTTCATCCTAATATTCTTCATTGCAG 58.157 33.333 0.00 0.00 0.00 4.41
2174 2708 6.485984 CCTAATATTCTTCATTGCAGCACTCT 59.514 38.462 0.00 0.00 0.00 3.24
2186 2720 0.882042 AGCACTCTGCCGACAAGTTG 60.882 55.000 0.00 0.00 46.52 3.16
2205 2739 4.815308 AGTTGCTCATAGACAATCATGCTC 59.185 41.667 0.00 0.00 0.00 4.26
2207 2741 2.735663 GCTCATAGACAATCATGCTCCG 59.264 50.000 0.00 0.00 0.00 4.63
2208 2742 3.553715 GCTCATAGACAATCATGCTCCGA 60.554 47.826 0.00 0.00 0.00 4.55
2215 2749 2.485426 ACAATCATGCTCCGAACAACTG 59.515 45.455 0.00 0.00 0.00 3.16
2232 2766 0.036732 CTGCTACAAGGGCAAGGTCA 59.963 55.000 0.00 0.00 39.30 4.02
2236 2770 0.323360 TACAAGGGCAAGGTCATGGC 60.323 55.000 0.00 0.00 44.56 4.40
2294 2828 6.052840 CAATGAATGTTGGATCTACTTCCG 57.947 41.667 0.00 0.00 38.74 4.30
2299 2833 4.920640 TGTTGGATCTACTTCCGATCTC 57.079 45.455 0.00 0.00 38.74 2.75
2312 2846 0.319383 CGATCTCCTGATGCCTTCCG 60.319 60.000 0.00 0.00 32.19 4.30
2313 2847 0.602372 GATCTCCTGATGCCTTCCGC 60.602 60.000 0.00 0.00 32.19 5.54
2327 2861 2.438975 CCGCCAGCACATGACCAT 60.439 61.111 0.00 0.00 0.00 3.55
2371 2905 3.184581 CAGGACGAACAACACTTTCTAGC 59.815 47.826 0.00 0.00 0.00 3.42
2372 2906 3.128349 GGACGAACAACACTTTCTAGCA 58.872 45.455 0.00 0.00 0.00 3.49
2392 2926 0.465460 TTGAGGTGGTGGTGAAGTGC 60.465 55.000 0.00 0.00 0.00 4.40
2445 2979 7.905604 TTGAGGATGTGTAATGTTTACTCTG 57.094 36.000 0.00 0.00 0.00 3.35
2449 2983 5.291128 GGATGTGTAATGTTTACTCTGTCGG 59.709 44.000 0.00 0.00 0.00 4.79
2457 2991 5.654603 TGTTTACTCTGTCGGTCATGTAT 57.345 39.130 0.00 0.00 0.00 2.29
2458 2992 6.032956 TGTTTACTCTGTCGGTCATGTATT 57.967 37.500 0.00 0.00 0.00 1.89
2473 3007 7.097834 GGTCATGTATTACTCTGCCTATAACC 58.902 42.308 0.00 0.00 0.00 2.85
2480 3014 9.136952 GTATTACTCTGCCTATAACCGTATTTG 57.863 37.037 0.00 0.00 0.00 2.32
2503 3037 7.356089 TGTCACTATTATGTCGGTCCTAAAT 57.644 36.000 0.00 0.00 0.00 1.40
2508 3042 9.706691 CACTATTATGTCGGTCCTAAATTATGT 57.293 33.333 0.00 0.00 0.00 2.29
2520 3054 9.965824 GGTCCTAAATTATGTTCATTAATGTGG 57.034 33.333 14.97 0.00 0.00 4.17
2526 3060 9.462174 AAATTATGTTCATTAATGTGGTATGCG 57.538 29.630 14.97 0.00 0.00 4.73
2531 3065 4.257731 TCATTAATGTGGTATGCGTGTGT 58.742 39.130 14.97 0.00 0.00 3.72
2539 3073 4.082136 TGTGGTATGCGTGTGTTATGACTA 60.082 41.667 0.00 0.00 0.00 2.59
2586 3121 6.951971 AGTGCTTTAATCTATGTTCCTCACT 58.048 36.000 0.00 0.00 0.00 3.41
2589 3124 7.119846 GTGCTTTAATCTATGTTCCTCACTGTT 59.880 37.037 0.00 0.00 0.00 3.16
2599 3134 3.558931 TCCTCACTGTTGATGTGTTGT 57.441 42.857 0.00 0.00 36.83 3.32
2617 3152 4.202000 TGTTGTTTGTTGTGCCTATGACTG 60.202 41.667 0.00 0.00 0.00 3.51
2624 3159 1.416030 TGTGCCTATGACTGTGTGTGT 59.584 47.619 0.00 0.00 0.00 3.72
2625 3160 1.800586 GTGCCTATGACTGTGTGTGTG 59.199 52.381 0.00 0.00 0.00 3.82
2626 3161 1.691434 TGCCTATGACTGTGTGTGTGA 59.309 47.619 0.00 0.00 0.00 3.58
2627 3162 2.302733 TGCCTATGACTGTGTGTGTGAT 59.697 45.455 0.00 0.00 0.00 3.06
2628 3163 2.674852 GCCTATGACTGTGTGTGTGATG 59.325 50.000 0.00 0.00 0.00 3.07
2647 3184 3.981071 TGATAACCTCACCACTCCAAG 57.019 47.619 0.00 0.00 0.00 3.61
2659 3196 2.637872 CCACTCCAAGAAGAGGTTACCA 59.362 50.000 3.51 0.00 38.26 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 3.475566 TGCAAGAAATCTCTATCCGGG 57.524 47.619 0.00 0.00 0.00 5.73
119 138 2.034221 GGCTGGACCAAGGGTGAC 59.966 66.667 0.00 0.00 35.25 3.67
156 175 3.069289 CAGTAGCAAGTGTGATGAGCAA 58.931 45.455 0.00 0.00 0.00 3.91
175 197 5.381174 TGAAGATGTGCCTTTTCATTCAG 57.619 39.130 0.00 0.00 0.00 3.02
201 223 4.347876 CAGTTGGAGGGAAGGGAAATTTTT 59.652 41.667 0.00 0.00 0.00 1.94
203 225 3.142028 TCAGTTGGAGGGAAGGGAAATTT 59.858 43.478 0.00 0.00 0.00 1.82
204 226 2.721906 TCAGTTGGAGGGAAGGGAAATT 59.278 45.455 0.00 0.00 0.00 1.82
205 227 2.358258 TCAGTTGGAGGGAAGGGAAAT 58.642 47.619 0.00 0.00 0.00 2.17
223 245 8.757495 GGAGGATCGATGGAACAAATTCTTTCA 61.757 40.741 0.54 0.00 37.99 2.69
262 284 3.083997 CCCCTTCCCTCACCCGAG 61.084 72.222 0.00 0.00 39.16 4.63
374 396 7.310361 TCAAATTCTTGTGAAAAGGGAACTTGT 60.310 33.333 0.00 0.00 40.81 3.16
401 423 6.816134 AAACAAAAGTGCAATGGAAGTTTT 57.184 29.167 0.00 0.00 35.90 2.43
421 443 9.076596 GTGCAATGGAAGTATATTTCTCAAAAC 57.923 33.333 7.79 0.00 0.00 2.43
430 478 9.420118 TGGAATAAAGTGCAATGGAAGTATATT 57.580 29.630 0.00 0.00 0.00 1.28
432 480 8.815565 TTGGAATAAAGTGCAATGGAAGTATA 57.184 30.769 0.00 0.00 0.00 1.47
474 522 1.528292 CCTAGTAGCTAGCGGGCCAG 61.528 65.000 9.55 0.00 33.12 4.85
500 548 2.877097 TACAGAAATTGGGCTGCAGA 57.123 45.000 20.43 0.00 35.57 4.26
502 550 2.101783 CCATACAGAAATTGGGCTGCA 58.898 47.619 0.50 0.00 35.57 4.41
503 551 1.202452 GCCATACAGAAATTGGGCTGC 60.202 52.381 0.00 0.00 38.37 5.25
575 673 7.057894 TGAGGTGACTTGTTATACAGGTTTTT 58.942 34.615 0.00 0.00 44.43 1.94
576 674 6.597562 TGAGGTGACTTGTTATACAGGTTTT 58.402 36.000 0.00 0.00 44.43 2.43
577 675 6.182507 TGAGGTGACTTGTTATACAGGTTT 57.817 37.500 0.00 0.00 44.43 3.27
578 676 5.818678 TGAGGTGACTTGTTATACAGGTT 57.181 39.130 0.00 0.00 44.43 3.50
579 677 5.818678 TTGAGGTGACTTGTTATACAGGT 57.181 39.130 0.00 0.00 44.43 4.00
580 678 7.504924 TTTTTGAGGTGACTTGTTATACAGG 57.495 36.000 0.00 0.00 44.43 4.00
685 817 3.111484 TGCTTTCTCCCCCTTTGTTTTT 58.889 40.909 0.00 0.00 0.00 1.94
686 818 2.700371 CTGCTTTCTCCCCCTTTGTTTT 59.300 45.455 0.00 0.00 0.00 2.43
687 819 2.091333 TCTGCTTTCTCCCCCTTTGTTT 60.091 45.455 0.00 0.00 0.00 2.83
688 820 1.499007 TCTGCTTTCTCCCCCTTTGTT 59.501 47.619 0.00 0.00 0.00 2.83
689 821 1.149101 TCTGCTTTCTCCCCCTTTGT 58.851 50.000 0.00 0.00 0.00 2.83
690 822 2.373224 GATCTGCTTTCTCCCCCTTTG 58.627 52.381 0.00 0.00 0.00 2.77
691 823 1.065126 CGATCTGCTTTCTCCCCCTTT 60.065 52.381 0.00 0.00 0.00 3.11
870 1052 1.080434 GTCGGCCTGCGGATCTATC 60.080 63.158 0.00 0.00 0.00 2.08
871 1053 1.528292 GAGTCGGCCTGCGGATCTAT 61.528 60.000 0.00 0.00 0.00 1.98
872 1054 2.123854 AGTCGGCCTGCGGATCTA 60.124 61.111 0.00 0.00 0.00 1.98
873 1055 3.532155 GAGTCGGCCTGCGGATCT 61.532 66.667 0.00 2.84 0.00 2.75
895 1077 2.100631 GCGGAAGACATCACCCACG 61.101 63.158 0.00 0.00 0.00 4.94
896 1078 1.745489 GGCGGAAGACATCACCCAC 60.745 63.158 0.00 0.00 40.66 4.61
897 1079 2.668632 GGCGGAAGACATCACCCA 59.331 61.111 0.00 0.00 40.66 4.51
898 1080 2.511600 CGGCGGAAGACATCACCC 60.512 66.667 0.00 0.00 41.50 4.61
899 1081 2.511600 CCGGCGGAAGACATCACC 60.512 66.667 24.41 0.00 41.50 4.02
900 1082 1.519455 CTCCGGCGGAAGACATCAC 60.519 63.158 30.59 0.00 41.50 3.06
901 1083 2.892640 CTCCGGCGGAAGACATCA 59.107 61.111 30.59 4.61 41.50 3.07
902 1084 2.586357 GCTCCGGCGGAAGACATC 60.586 66.667 30.59 10.70 41.50 3.06
903 1085 1.399744 TATGCTCCGGCGGAAGACAT 61.400 55.000 30.59 30.03 41.50 3.06
904 1086 2.055633 TATGCTCCGGCGGAAGACA 61.056 57.895 30.59 26.17 41.50 3.41
905 1087 1.591863 GTATGCTCCGGCGGAAGAC 60.592 63.158 30.59 19.35 42.25 3.01
906 1088 2.055633 TGTATGCTCCGGCGGAAGA 61.056 57.895 30.59 19.15 42.25 2.87
941 1148 1.684386 AAGCTCAGGCGATCTCCAGG 61.684 60.000 4.19 0.00 44.37 4.45
1025 1235 3.818121 TTGGCACCGGTGACCTTCG 62.818 63.158 37.07 9.95 37.98 3.79
1037 1247 1.270550 CCTCTGTTTCCATGTTGGCAC 59.729 52.381 0.00 0.00 37.47 5.01
1040 1250 0.523072 CGCCTCTGTTTCCATGTTGG 59.477 55.000 0.00 0.00 39.43 3.77
1087 1324 1.227205 CCTCCATCGAGCTCTGCAC 60.227 63.158 12.85 0.00 34.49 4.57
1092 1329 2.107953 GTGGCCTCCATCGAGCTC 59.892 66.667 3.32 2.73 35.28 4.09
1102 1348 2.146342 CATATCGACATTGGTGGCCTC 58.854 52.381 3.32 0.00 0.00 4.70
1111 1357 5.171476 CGCCTCTATTTCCATATCGACATT 58.829 41.667 0.00 0.00 0.00 2.71
1229 1484 1.346068 GTATGTCATCCAGCTCCTCCC 59.654 57.143 0.00 0.00 0.00 4.30
1294 1555 2.100603 GCCGACGAGAGAAGGACG 59.899 66.667 0.00 0.00 34.20 4.79
1459 1792 1.807142 CTTCTCCCCGTGAAAAGAAGC 59.193 52.381 0.00 0.00 38.58 3.86
1461 1794 2.051692 TCCTTCTCCCCGTGAAAAGAA 58.948 47.619 0.00 0.00 0.00 2.52
1488 1821 1.425428 CTGAAAAGATGTCGCCGCC 59.575 57.895 0.00 0.00 0.00 6.13
1489 1822 1.298859 ACCTGAAAAGATGTCGCCGC 61.299 55.000 0.00 0.00 0.00 6.53
1491 1824 0.804989 CCACCTGAAAAGATGTCGCC 59.195 55.000 0.00 0.00 0.00 5.54
1506 1875 2.019984 GTTGCATCATCCTTCTCCACC 58.980 52.381 0.00 0.00 0.00 4.61
1527 1896 1.004161 TCCCCATGAAAAGATGTCGCA 59.996 47.619 0.00 0.00 0.00 5.10
1557 2043 2.621055 AGGAGAAGATGTAGCTGCTACG 59.379 50.000 28.76 0.00 39.58 3.51
1559 2045 3.386078 CCAAGGAGAAGATGTAGCTGCTA 59.614 47.826 5.02 5.02 29.82 3.49
1636 2122 2.629639 ATTTTCTTAACGCCGCTTGG 57.370 45.000 0.00 0.00 0.00 3.61
1679 2212 9.984190 ACTAAAACTAAAACACACCAAAAGAAA 57.016 25.926 0.00 0.00 0.00 2.52
1680 2213 9.984190 AACTAAAACTAAAACACACCAAAAGAA 57.016 25.926 0.00 0.00 0.00 2.52
1681 2214 9.413048 CAACTAAAACTAAAACACACCAAAAGA 57.587 29.630 0.00 0.00 0.00 2.52
1682 2215 9.198837 ACAACTAAAACTAAAACACACCAAAAG 57.801 29.630 0.00 0.00 0.00 2.27
1743 2277 7.670605 AGGCCTAAGTTATACTACATGACAA 57.329 36.000 1.29 0.00 0.00 3.18
1802 2336 5.302568 CACCCTAATACATGGATTGCACATT 59.697 40.000 13.77 0.00 0.00 2.71
1841 2375 8.041323 CCAGAAGTATAATGTGTAGAACCAACT 58.959 37.037 0.00 0.00 0.00 3.16
1924 2458 6.478673 CCGTATGTAGTCTGCATTGAAATGTA 59.521 38.462 8.84 0.00 38.65 2.29
1925 2459 5.294306 CCGTATGTAGTCTGCATTGAAATGT 59.706 40.000 8.84 0.00 38.65 2.71
1926 2460 5.523552 TCCGTATGTAGTCTGCATTGAAATG 59.476 40.000 8.84 0.00 39.40 2.32
1927 2461 5.670485 TCCGTATGTAGTCTGCATTGAAAT 58.330 37.500 8.84 0.00 0.00 2.17
1928 2462 5.079689 TCCGTATGTAGTCTGCATTGAAA 57.920 39.130 8.84 0.00 0.00 2.69
1929 2463 4.682787 CTCCGTATGTAGTCTGCATTGAA 58.317 43.478 8.84 0.00 0.00 2.69
1930 2464 3.490933 GCTCCGTATGTAGTCTGCATTGA 60.491 47.826 8.84 3.63 0.00 2.57
1931 2465 2.797156 GCTCCGTATGTAGTCTGCATTG 59.203 50.000 8.84 2.79 0.00 2.82
1932 2466 2.430694 TGCTCCGTATGTAGTCTGCATT 59.569 45.455 8.84 0.00 0.00 3.56
1933 2467 2.031870 TGCTCCGTATGTAGTCTGCAT 58.968 47.619 8.57 8.57 0.00 3.96
1934 2468 1.470051 TGCTCCGTATGTAGTCTGCA 58.530 50.000 0.00 0.00 0.00 4.41
1935 2469 2.579207 TTGCTCCGTATGTAGTCTGC 57.421 50.000 0.00 0.00 0.00 4.26
1936 2470 5.109210 TCAATTTGCTCCGTATGTAGTCTG 58.891 41.667 0.00 0.00 0.00 3.51
1937 2471 5.339008 TCAATTTGCTCCGTATGTAGTCT 57.661 39.130 0.00 0.00 0.00 3.24
1938 2472 6.257849 TCAATCAATTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 35.16 2.59
1939 2473 6.112734 TCAATCAATTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 35.16 2.73
1940 2474 6.603237 TCAATCAATTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 35.16 2.74
1941 2475 6.993786 TTCAATCAATTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 35.16 2.29
1942 2476 5.895636 TTCAATCAATTTGCTCCGTATGT 57.104 34.783 0.00 0.00 35.16 2.29
1943 2477 6.732154 AGATTCAATCAATTTGCTCCGTATG 58.268 36.000 0.00 0.00 35.16 2.39
1944 2478 6.949352 AGATTCAATCAATTTGCTCCGTAT 57.051 33.333 0.00 0.00 35.16 3.06
1945 2479 6.821160 TGTAGATTCAATCAATTTGCTCCGTA 59.179 34.615 0.00 0.00 35.16 4.02
1946 2480 5.647658 TGTAGATTCAATCAATTTGCTCCGT 59.352 36.000 0.00 0.00 35.16 4.69
1947 2481 6.122850 TGTAGATTCAATCAATTTGCTCCG 57.877 37.500 0.00 0.00 35.16 4.63
1948 2482 8.411683 AGAATGTAGATTCAATCAATTTGCTCC 58.588 33.333 14.46 0.00 40.59 4.70
1988 2522 9.955208 TTGAATACGAACTACATACGAATGTAT 57.045 29.630 0.00 0.00 45.33 2.29
1989 2523 9.786105 TTTGAATACGAACTACATACGAATGTA 57.214 29.630 0.00 0.00 44.66 2.29
1991 2525 9.779237 GATTTGAATACGAACTACATACGAATG 57.221 33.333 0.00 0.00 39.17 2.67
1992 2526 9.745880 AGATTTGAATACGAACTACATACGAAT 57.254 29.630 0.00 0.00 0.00 3.34
1993 2527 9.229784 GAGATTTGAATACGAACTACATACGAA 57.770 33.333 0.00 0.00 0.00 3.85
1994 2528 8.618677 AGAGATTTGAATACGAACTACATACGA 58.381 33.333 0.00 0.00 0.00 3.43
1995 2529 8.783999 AGAGATTTGAATACGAACTACATACG 57.216 34.615 0.00 0.00 0.00 3.06
1996 2530 9.731819 TGAGAGATTTGAATACGAACTACATAC 57.268 33.333 0.00 0.00 0.00 2.39
1998 2532 9.653287 TTTGAGAGATTTGAATACGAACTACAT 57.347 29.630 0.00 0.00 0.00 2.29
1999 2533 9.483916 TTTTGAGAGATTTGAATACGAACTACA 57.516 29.630 0.00 0.00 0.00 2.74
2000 2534 9.959775 CTTTTGAGAGATTTGAATACGAACTAC 57.040 33.333 0.00 0.00 0.00 2.73
2001 2535 9.923143 TCTTTTGAGAGATTTGAATACGAACTA 57.077 29.630 0.00 0.00 0.00 2.24
2002 2536 8.713271 GTCTTTTGAGAGATTTGAATACGAACT 58.287 33.333 0.00 0.00 0.00 3.01
2003 2537 8.713271 AGTCTTTTGAGAGATTTGAATACGAAC 58.287 33.333 0.00 0.00 0.00 3.95
2004 2538 8.833231 AGTCTTTTGAGAGATTTGAATACGAA 57.167 30.769 0.00 0.00 0.00 3.85
2005 2539 8.833231 AAGTCTTTTGAGAGATTTGAATACGA 57.167 30.769 0.00 0.00 0.00 3.43
2018 2552 9.595823 CCGTTCCTAAATATAAGTCTTTTGAGA 57.404 33.333 0.00 0.00 0.00 3.27
2019 2553 9.595823 TCCGTTCCTAAATATAAGTCTTTTGAG 57.404 33.333 0.00 0.00 0.00 3.02
2020 2554 9.595823 CTCCGTTCCTAAATATAAGTCTTTTGA 57.404 33.333 0.00 0.00 0.00 2.69
2021 2555 9.379791 ACTCCGTTCCTAAATATAAGTCTTTTG 57.620 33.333 0.00 0.00 0.00 2.44
2022 2556 9.379791 CACTCCGTTCCTAAATATAAGTCTTTT 57.620 33.333 0.00 0.00 0.00 2.27
2023 2557 8.755977 TCACTCCGTTCCTAAATATAAGTCTTT 58.244 33.333 0.00 0.00 0.00 2.52
2024 2558 8.302515 TCACTCCGTTCCTAAATATAAGTCTT 57.697 34.615 0.00 0.00 0.00 3.01
2025 2559 7.893124 TCACTCCGTTCCTAAATATAAGTCT 57.107 36.000 0.00 0.00 0.00 3.24
2026 2560 9.623350 GTATCACTCCGTTCCTAAATATAAGTC 57.377 37.037 0.00 0.00 0.00 3.01
2027 2561 9.139734 TGTATCACTCCGTTCCTAAATATAAGT 57.860 33.333 0.00 0.00 0.00 2.24
2029 2563 9.923143 CATGTATCACTCCGTTCCTAAATATAA 57.077 33.333 0.00 0.00 0.00 0.98
2030 2564 9.304335 TCATGTATCACTCCGTTCCTAAATATA 57.696 33.333 0.00 0.00 0.00 0.86
2031 2565 8.088981 GTCATGTATCACTCCGTTCCTAAATAT 58.911 37.037 0.00 0.00 0.00 1.28
2032 2566 7.068962 TGTCATGTATCACTCCGTTCCTAAATA 59.931 37.037 0.00 0.00 0.00 1.40
2033 2567 6.127168 TGTCATGTATCACTCCGTTCCTAAAT 60.127 38.462 0.00 0.00 0.00 1.40
2034 2568 5.186215 TGTCATGTATCACTCCGTTCCTAAA 59.814 40.000 0.00 0.00 0.00 1.85
2035 2569 4.707934 TGTCATGTATCACTCCGTTCCTAA 59.292 41.667 0.00 0.00 0.00 2.69
2036 2570 4.274978 TGTCATGTATCACTCCGTTCCTA 58.725 43.478 0.00 0.00 0.00 2.94
2037 2571 3.096852 TGTCATGTATCACTCCGTTCCT 58.903 45.455 0.00 0.00 0.00 3.36
2038 2572 3.520290 TGTCATGTATCACTCCGTTCC 57.480 47.619 0.00 0.00 0.00 3.62
2039 2573 4.682787 TGATGTCATGTATCACTCCGTTC 58.317 43.478 10.10 0.00 30.03 3.95
2040 2574 4.736126 TGATGTCATGTATCACTCCGTT 57.264 40.909 10.10 0.00 30.03 4.44
2041 2575 4.625028 CATGATGTCATGTATCACTCCGT 58.375 43.478 13.53 0.79 46.40 4.69
2067 2601 1.143838 TCAAGGATGATGGCCGTCG 59.856 57.895 20.05 4.76 0.00 5.12
2068 2602 0.107703 TGTCAAGGATGATGGCCGTC 60.108 55.000 18.69 18.69 38.01 4.79
2111 2645 9.959721 ACTGACCTACAATGTAAATTGAACTAT 57.040 29.630 12.75 0.00 35.60 2.12
2112 2646 9.214957 CACTGACCTACAATGTAAATTGAACTA 57.785 33.333 12.75 0.00 35.60 2.24
2113 2647 7.174946 CCACTGACCTACAATGTAAATTGAACT 59.825 37.037 12.75 0.00 35.60 3.01
2114 2648 7.040686 ACCACTGACCTACAATGTAAATTGAAC 60.041 37.037 12.75 0.35 35.60 3.18
2115 2649 7.001674 ACCACTGACCTACAATGTAAATTGAA 58.998 34.615 12.75 0.00 35.60 2.69
2116 2650 6.429692 CACCACTGACCTACAATGTAAATTGA 59.570 38.462 12.75 0.00 35.60 2.57
2117 2651 6.206634 ACACCACTGACCTACAATGTAAATTG 59.793 38.462 3.94 3.94 37.54 2.32
2118 2652 6.206634 CACACCACTGACCTACAATGTAAATT 59.793 38.462 0.00 0.00 0.00 1.82
2119 2653 5.705441 CACACCACTGACCTACAATGTAAAT 59.295 40.000 0.00 0.00 0.00 1.40
2120 2654 5.060506 CACACCACTGACCTACAATGTAAA 58.939 41.667 0.00 0.00 0.00 2.01
2121 2655 4.101898 ACACACCACTGACCTACAATGTAA 59.898 41.667 0.00 0.00 0.00 2.41
2122 2656 3.644265 ACACACCACTGACCTACAATGTA 59.356 43.478 0.00 0.00 0.00 2.29
2123 2657 2.438021 ACACACCACTGACCTACAATGT 59.562 45.455 0.00 0.00 0.00 2.71
2124 2658 3.126001 ACACACCACTGACCTACAATG 57.874 47.619 0.00 0.00 0.00 2.82
2135 2669 7.200434 AGAATATTAGGATGAACACACCACT 57.800 36.000 0.00 0.00 0.00 4.00
2148 2682 6.359804 AGTGCTGCAATGAAGAATATTAGGA 58.640 36.000 2.77 0.00 0.00 2.94
2168 2702 1.571460 CAACTTGTCGGCAGAGTGC 59.429 57.895 5.77 0.00 44.08 4.40
2174 2708 1.275010 TCTATGAGCAACTTGTCGGCA 59.725 47.619 0.00 0.00 0.00 5.69
2186 2720 2.735663 CGGAGCATGATTGTCTATGAGC 59.264 50.000 0.00 0.00 0.00 4.26
2205 2739 1.156736 CCCTTGTAGCAGTTGTTCGG 58.843 55.000 0.00 0.00 0.00 4.30
2207 2741 1.604604 TGCCCTTGTAGCAGTTGTTC 58.395 50.000 0.00 0.00 34.69 3.18
2208 2742 1.956477 CTTGCCCTTGTAGCAGTTGTT 59.044 47.619 0.00 0.00 42.17 2.83
2215 2749 1.098050 CATGACCTTGCCCTTGTAGC 58.902 55.000 0.00 0.00 0.00 3.58
2232 2766 2.274760 GGCTCTGCCTTCTGCCAT 59.725 61.111 0.73 0.00 46.69 4.40
2254 2788 1.803453 TTGGCCTCCCTGATGCCTTT 61.803 55.000 3.32 0.00 42.47 3.11
2263 2797 1.620524 CCAACATTCATTGGCCTCCCT 60.621 52.381 3.32 0.00 42.69 4.20
2274 2808 5.363868 AGATCGGAAGTAGATCCAACATTCA 59.636 40.000 2.94 0.00 44.02 2.57
2294 2828 0.602372 GCGGAAGGCATCAGGAGATC 60.602 60.000 0.00 0.00 42.87 2.75
2312 2846 0.666913 GATCATGGTCATGTGCTGGC 59.333 55.000 0.00 0.00 39.72 4.85
2313 2847 1.315690 GGATCATGGTCATGTGCTGG 58.684 55.000 8.54 0.00 39.72 4.85
2327 2861 2.125147 CGGCTTCGCTTGGGATCA 60.125 61.111 0.00 0.00 0.00 2.92
2351 2885 3.128349 TGCTAGAAAGTGTTGTTCGTCC 58.872 45.455 0.00 0.00 0.00 4.79
2371 2905 1.881973 CACTTCACCACCACCTCAATG 59.118 52.381 0.00 0.00 0.00 2.82
2372 2906 1.819305 GCACTTCACCACCACCTCAAT 60.819 52.381 0.00 0.00 0.00 2.57
2406 2940 3.559069 TCCTCAATCATTGCAAGGGATC 58.441 45.455 11.73 0.00 0.00 3.36
2408 2942 3.293337 CATCCTCAATCATTGCAAGGGA 58.707 45.455 11.73 8.64 0.00 4.20
2409 2943 3.028850 ACATCCTCAATCATTGCAAGGG 58.971 45.455 11.73 2.73 0.00 3.95
2445 2979 3.068307 AGGCAGAGTAATACATGACCGAC 59.932 47.826 0.00 0.00 0.00 4.79
2449 2983 6.807230 CGGTTATAGGCAGAGTAATACATGAC 59.193 42.308 0.00 0.00 0.00 3.06
2457 2991 7.116075 ACAAATACGGTTATAGGCAGAGTAA 57.884 36.000 0.00 0.00 0.00 2.24
2458 2992 6.321945 TGACAAATACGGTTATAGGCAGAGTA 59.678 38.462 0.00 0.00 0.00 2.59
2473 3007 6.143438 GGACCGACATAATAGTGACAAATACG 59.857 42.308 0.00 0.00 0.00 3.06
2480 3014 9.924650 ATAATTTAGGACCGACATAATAGTGAC 57.075 33.333 0.00 0.00 0.00 3.67
2503 3037 7.066404 ACACGCATACCACATTAATGAACATAA 59.934 33.333 22.16 2.93 0.00 1.90
2508 3042 4.697828 ACACACGCATACCACATTAATGAA 59.302 37.500 22.16 4.94 0.00 2.57
2510 3044 4.614555 ACACACGCATACCACATTAATG 57.385 40.909 14.01 14.01 0.00 1.90
2520 3054 5.047847 ACCATAGTCATAACACACGCATAC 58.952 41.667 0.00 0.00 0.00 2.39
2586 3121 3.677121 GCACAACAAACAACACATCAACA 59.323 39.130 0.00 0.00 0.00 3.33
2589 3124 2.495270 AGGCACAACAAACAACACATCA 59.505 40.909 0.00 0.00 0.00 3.07
2599 3134 3.314913 CACACAGTCATAGGCACAACAAA 59.685 43.478 0.00 0.00 0.00 2.83
2625 3160 4.162320 TCTTGGAGTGGTGAGGTTATCATC 59.838 45.833 0.00 0.00 40.92 2.92
2626 3161 4.104086 TCTTGGAGTGGTGAGGTTATCAT 58.896 43.478 0.00 0.00 40.92 2.45
2627 3162 3.516586 TCTTGGAGTGGTGAGGTTATCA 58.483 45.455 0.00 0.00 34.79 2.15
2628 3163 4.223032 TCTTCTTGGAGTGGTGAGGTTATC 59.777 45.833 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.