Multiple sequence alignment - TraesCS4B01G184000

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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 TraesCS4B01G184000 chr4B 100.000 4208 0 0 1 4208 403265988 403261781 0.000000e+00 7771
1 TraesCS4B01G184000 chr4A 88.849 3049 196 58 167 3127 149035110 149038102 0.000000e+00 3615
2 TraesCS4B01G184000 chr4A 83.556 450 49 14 3355 3797 149038424 149038855 8.480000e-107 398
3 TraesCS4B01G184000 chr4A 94.068 236 4 3 3973 4208 149039055 149039280 2.410000e-92 350
4 TraesCS4B01G184000 chr4A 88.380 284 12 6 3089 3356 149038115 149038393 5.250000e-84 322
5 TraesCS4B01G184000 chr4D 94.511 1257 49 5 2117 3356 323109466 323108213 0.000000e+00 1921
6 TraesCS4B01G184000 chr4D 87.088 1394 103 47 705 2054 323110833 323109473 0.000000e+00 1506
7 TraesCS4B01G184000 chr4D 88.676 574 25 15 3662 4208 323107861 323107301 0.000000e+00 664
8 TraesCS4B01G184000 chr4D 80.363 662 80 22 78 707 323111502 323110859 1.380000e-124 457
9 TraesCS4B01G184000 chr4D 96.111 180 6 1 3378 3556 323108144 323107965 4.120000e-75 292
10 TraesCS4B01G184000 chr4D 83.934 305 44 4 2 305 40117415 40117715 1.910000e-73 287
11 TraesCS4B01G184000 chr5D 87.662 308 33 5 1 306 322192261 322191957 1.860000e-93 353
12 TraesCS4B01G184000 chr1B 87.097 310 37 3 1 309 1183337 1183030 8.660000e-92 348
13 TraesCS4B01G184000 chr1B 85.668 307 40 4 1 305 10223189 10223493 1.890000e-83 320
14 TraesCS4B01G184000 chr2D 86.971 307 33 4 1 306 37760419 37760119 5.210000e-89 339
15 TraesCS4B01G184000 chr2D 85.294 306 42 3 1 305 106269852 106270155 3.160000e-81 313
16 TraesCS4B01G184000 chr5B 87.000 300 34 5 3 300 391808941 391808645 2.420000e-87 333
17 TraesCS4B01G184000 chr5A 85.294 306 38 6 1 303 698541 698842 4.090000e-80 309
18 TraesCS4B01G184000 chr5A 89.714 175 18 0 309 483 705956301 705956127 1.520000e-54 224
19 TraesCS4B01G184000 chr7A 83.987 306 45 4 1 305 116601867 116602169 1.480000e-74 291


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 TraesCS4B01G184000 chr4B 403261781 403265988 4207 True 7771.00 7771 100.00000 1 4208 1 chr4B.!!$R1 4207
1 TraesCS4B01G184000 chr4A 149035110 149039280 4170 False 1171.25 3615 88.71325 167 4208 4 chr4A.!!$F1 4041
2 TraesCS4B01G184000 chr4D 323107301 323111502 4201 True 968.00 1921 89.34980 78 4208 5 chr4D.!!$R1 4130

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
933 1014 0.252742 TCTTCCCCACTTCCTCCTCC 60.253 60.0 0.00 0.0 0.0 4.30 F
1290 1378 0.036010 CTGGTTTCGAGTGGGATGCT 60.036 55.0 0.00 0.0 0.0 3.79 F
1985 2132 0.103937 GGTGAAGGAGCTCAGGATCG 59.896 60.0 17.19 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 2420 0.737219 CATAGCAACAGGGCAAGAGC 59.263 55.0 0.00 0.0 41.1 4.09 R
2580 2728 1.708993 GGCTGCCTGACCCCATATCA 61.709 60.0 12.43 0.0 0.0 2.15 R
3807 4108 0.179081 GGAATCTGCCCCGAGTGTAC 60.179 60.0 0.00 0.0 0.0 2.90 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
25 26 7.765307 TGAATACCTCAATCAAATGAAAGAGC 58.235 34.615 8.94 0.00 31.68 4.09
26 27 7.613022 TGAATACCTCAATCAAATGAAAGAGCT 59.387 33.333 8.94 0.00 31.68 4.09
27 28 7.951347 ATACCTCAATCAAATGAAAGAGCTT 57.049 32.000 8.94 0.00 31.68 3.74
28 29 6.661304 ACCTCAATCAAATGAAAGAGCTTT 57.339 33.333 8.94 0.00 35.14 3.51
29 30 7.765695 ACCTCAATCAAATGAAAGAGCTTTA 57.234 32.000 8.94 0.00 32.11 1.85
30 31 8.181904 ACCTCAATCAAATGAAAGAGCTTTAA 57.818 30.769 8.94 0.00 32.11 1.52
31 32 8.641541 ACCTCAATCAAATGAAAGAGCTTTAAA 58.358 29.630 8.94 0.00 32.11 1.52
32 33 9.480053 CCTCAATCAAATGAAAGAGCTTTAAAA 57.520 29.630 8.94 0.00 32.11 1.52
38 39 9.927668 TCAAATGAAAGAGCTTTAAAATAAGGG 57.072 29.630 0.00 0.00 32.11 3.95
39 40 9.927668 CAAATGAAAGAGCTTTAAAATAAGGGA 57.072 29.630 0.00 0.00 32.11 4.20
41 42 9.929180 AATGAAAGAGCTTTAAAATAAGGGAAC 57.071 29.630 0.00 0.00 32.11 3.62
42 43 8.472007 TGAAAGAGCTTTAAAATAAGGGAACA 57.528 30.769 0.00 0.00 32.11 3.18
43 44 9.088987 TGAAAGAGCTTTAAAATAAGGGAACAT 57.911 29.630 0.00 0.00 32.11 2.71
87 88 2.728007 GGAGACCCCCTTGAGAAATTG 58.272 52.381 0.00 0.00 0.00 2.32
93 94 2.562738 CCCCCTTGAGAAATTGTTGACC 59.437 50.000 0.00 0.00 0.00 4.02
94 95 3.500343 CCCCTTGAGAAATTGTTGACCT 58.500 45.455 0.00 0.00 0.00 3.85
95 96 4.508405 CCCCCTTGAGAAATTGTTGACCTA 60.508 45.833 0.00 0.00 0.00 3.08
119 120 6.566197 GTCAAAATCAGGTGACTCAATTCT 57.434 37.500 0.00 0.00 40.82 2.40
122 123 8.567948 GTCAAAATCAGGTGACTCAATTCTAAA 58.432 33.333 0.00 0.00 40.82 1.85
124 125 9.918630 CAAAATCAGGTGACTCAATTCTAAATT 57.081 29.630 0.00 0.00 40.21 1.82
125 126 9.918630 AAAATCAGGTGACTCAATTCTAAATTG 57.081 29.630 6.14 6.14 40.21 2.32
126 127 8.641498 AATCAGGTGACTCAATTCTAAATTGT 57.359 30.769 11.10 0.00 40.21 2.71
127 128 9.739276 AATCAGGTGACTCAATTCTAAATTGTA 57.261 29.630 11.10 0.45 40.21 2.41
128 129 8.777865 TCAGGTGACTCAATTCTAAATTGTAG 57.222 34.615 11.10 9.78 40.21 2.74
130 131 8.660373 CAGGTGACTCAATTCTAAATTGTAGTC 58.340 37.037 21.90 21.90 40.21 2.59
132 133 9.220767 GGTGACTCAATTCTAAATTGTAGTCTT 57.779 33.333 24.91 8.36 37.25 3.01
164 166 9.914131 ACTGTGAAGATTAAAAATTAGAAAGCC 57.086 29.630 0.00 0.00 0.00 4.35
165 167 9.358872 CTGTGAAGATTAAAAATTAGAAAGCCC 57.641 33.333 0.00 0.00 0.00 5.19
177 187 7.625828 AATTAGAAAGCCCAGTGTATTGTAC 57.374 36.000 0.00 0.00 0.00 2.90
182 192 6.322712 AGAAAGCCCAGTGTATTGTACAAAAA 59.677 34.615 13.23 0.84 40.93 1.94
216 227 7.032377 AGAGAGTTTTGAGAAATTGTTGACC 57.968 36.000 0.00 0.00 0.00 4.02
217 228 6.603201 AGAGAGTTTTGAGAAATTGTTGACCA 59.397 34.615 0.00 0.00 0.00 4.02
218 229 7.122650 AGAGAGTTTTGAGAAATTGTTGACCAA 59.877 33.333 0.00 0.00 37.49 3.67
234 245 2.168326 CCAAGTCAAAATTGGGTGGC 57.832 50.000 0.00 0.00 42.95 5.01
236 247 1.415659 CAAGTCAAAATTGGGTGGCCA 59.584 47.619 0.00 0.00 0.00 5.36
242 253 4.023279 GTCAAAATTGGGTGGCCAAATTTC 60.023 41.667 21.34 9.95 32.56 2.17
266 277 9.695526 TTCAATTGGAGACTTCAATTAATTGTG 57.304 29.630 23.95 19.73 41.28 3.33
267 278 9.076781 TCAATTGGAGACTTCAATTAATTGTGA 57.923 29.630 23.95 10.82 41.28 3.58
271 282 5.163612 GGAGACTTCAATTAATTGTGAGGCC 60.164 44.000 23.95 19.39 38.84 5.19
273 284 5.649831 AGACTTCAATTAATTGTGAGGCCTC 59.350 40.000 26.78 26.78 38.84 4.70
274 285 4.706962 ACTTCAATTAATTGTGAGGCCTCC 59.293 41.667 29.95 20.55 38.84 4.30
277 288 5.271598 TCAATTAATTGTGAGGCCTCCAAT 58.728 37.500 29.32 29.32 38.84 3.16
278 289 5.721000 TCAATTAATTGTGAGGCCTCCAATT 59.279 36.000 37.12 37.12 40.33 2.32
294 305 2.168521 CCAATTCTAGGGAGCTTCGTGA 59.831 50.000 0.00 0.00 0.00 4.35
295 306 3.181461 CCAATTCTAGGGAGCTTCGTGAT 60.181 47.826 0.00 0.00 0.00 3.06
296 307 4.039245 CCAATTCTAGGGAGCTTCGTGATA 59.961 45.833 0.00 0.00 0.00 2.15
297 308 5.279708 CCAATTCTAGGGAGCTTCGTGATAT 60.280 44.000 0.00 0.00 0.00 1.63
298 309 6.071334 CCAATTCTAGGGAGCTTCGTGATATA 60.071 42.308 0.00 0.00 0.00 0.86
299 310 6.767524 ATTCTAGGGAGCTTCGTGATATAG 57.232 41.667 0.00 0.00 0.00 1.31
306 317 8.680039 AGGGAGCTTCGTGATATAGTATATAC 57.320 38.462 4.60 4.60 0.00 1.47
324 340 9.104965 AGTATATACGATGCATCTCTACTCTTC 57.895 37.037 23.73 7.39 0.00 2.87
333 349 5.877012 TGCATCTCTACTCTTCATTTCAACC 59.123 40.000 0.00 0.00 0.00 3.77
352 368 7.346751 TCAACCTTTTCAGCTTTTTACATCT 57.653 32.000 0.00 0.00 0.00 2.90
423 439 5.437946 CTTCCCTATCCAAACCTACTTTCC 58.562 45.833 0.00 0.00 0.00 3.13
424 440 4.706616 TCCCTATCCAAACCTACTTTCCT 58.293 43.478 0.00 0.00 0.00 3.36
430 446 4.714632 TCCAAACCTACTTTCCTTGACAG 58.285 43.478 0.00 0.00 0.00 3.51
496 512 2.777114 TGGCCATGCTCTAATACTTGGA 59.223 45.455 0.00 0.00 33.96 3.53
801 872 4.452733 GCCGTGTCCCCTCCTTCG 62.453 72.222 0.00 0.00 0.00 3.79
892 967 0.972471 CCCAAGGAACCTGCCATTCC 60.972 60.000 3.15 3.15 45.23 3.01
933 1014 0.252742 TCTTCCCCACTTCCTCCTCC 60.253 60.000 0.00 0.00 0.00 4.30
934 1015 0.252927 CTTCCCCACTTCCTCCTCCT 60.253 60.000 0.00 0.00 0.00 3.69
935 1016 0.252742 TTCCCCACTTCCTCCTCCTC 60.253 60.000 0.00 0.00 0.00 3.71
1202 1286 1.326548 CGTGTAGTTTATGGCGCCTTC 59.673 52.381 29.70 9.76 0.00 3.46
1290 1378 0.036010 CTGGTTTCGAGTGGGATGCT 60.036 55.000 0.00 0.00 0.00 3.79
1354 1442 2.348666 CGAATGACTCGGTCAATTGGAC 59.651 50.000 5.42 2.73 45.96 4.02
1377 1479 4.260948 CGTATACTTCGTAGGTCTGGGTTC 60.261 50.000 0.56 0.00 0.00 3.62
1383 1485 1.275291 CGTAGGTCTGGGTTCATGTGT 59.725 52.381 0.00 0.00 0.00 3.72
1397 1499 1.000385 CATGTGTGCGGTGGAATTTGT 60.000 47.619 0.00 0.00 0.00 2.83
1403 1505 1.072489 TGCGGTGGAATTTGTAGTGGA 59.928 47.619 0.00 0.00 0.00 4.02
1404 1506 1.467342 GCGGTGGAATTTGTAGTGGAC 59.533 52.381 0.00 0.00 0.00 4.02
1405 1507 2.773487 CGGTGGAATTTGTAGTGGACA 58.227 47.619 0.00 0.00 35.78 4.02
1406 1508 2.482721 CGGTGGAATTTGTAGTGGACAC 59.517 50.000 0.00 0.00 37.96 3.67
1407 1509 3.482436 GGTGGAATTTGTAGTGGACACA 58.518 45.455 5.14 0.00 37.96 3.72
1408 1510 3.886505 GGTGGAATTTGTAGTGGACACAA 59.113 43.478 5.14 0.00 37.96 3.33
1409 1511 4.023193 GGTGGAATTTGTAGTGGACACAAG 60.023 45.833 5.14 0.00 37.96 3.16
1410 1512 4.023193 GTGGAATTTGTAGTGGACACAAGG 60.023 45.833 5.14 0.00 37.96 3.61
1411 1513 4.141367 TGGAATTTGTAGTGGACACAAGGA 60.141 41.667 5.14 0.00 37.96 3.36
1412 1514 4.825085 GGAATTTGTAGTGGACACAAGGAA 59.175 41.667 5.14 0.00 37.96 3.36
1413 1515 5.048713 GGAATTTGTAGTGGACACAAGGAAG 60.049 44.000 5.14 0.00 37.96 3.46
1414 1516 3.485463 TTGTAGTGGACACAAGGAAGG 57.515 47.619 5.14 0.00 37.96 3.46
1415 1517 2.684943 TGTAGTGGACACAAGGAAGGA 58.315 47.619 5.14 0.00 31.20 3.36
1416 1518 3.042682 TGTAGTGGACACAAGGAAGGAA 58.957 45.455 5.14 0.00 31.20 3.36
1441 1543 3.507622 AGTGCCTTAATTCAGAAAGCCAC 59.492 43.478 0.00 0.00 32.69 5.01
1458 1560 1.136252 CCACAGATTTCGCGTGAAGTG 60.136 52.381 11.73 15.07 35.06 3.16
1460 1562 2.220824 CACAGATTTCGCGTGAAGTGAA 59.779 45.455 18.71 3.48 46.51 3.18
1464 1566 3.652292 TTCGCGTGAAGTGAAGTCA 57.348 47.368 7.45 0.00 43.68 3.41
1518 1624 6.816140 GCTTATAAGATGGTGATTAGCCTCTC 59.184 42.308 16.85 0.00 0.00 3.20
1523 1629 2.392662 TGGTGATTAGCCTCTCCTCAG 58.607 52.381 0.00 0.00 31.49 3.35
1532 1638 3.521727 AGCCTCTCCTCAGAAGGTTAAA 58.478 45.455 0.00 0.00 43.82 1.52
1533 1639 3.262151 AGCCTCTCCTCAGAAGGTTAAAC 59.738 47.826 0.00 0.00 43.82 2.01
1572 1679 4.202253 ACAACTGAACACTGTCTAGCATGA 60.202 41.667 0.00 0.00 0.00 3.07
1575 1686 6.286240 ACTGAACACTGTCTAGCATGATAA 57.714 37.500 0.00 0.00 0.00 1.75
1592 1703 9.217278 AGCATGATAATTCATACTGATTGACTC 57.783 33.333 0.00 0.00 40.70 3.36
1593 1704 8.996271 GCATGATAATTCATACTGATTGACTCA 58.004 33.333 0.00 0.00 40.70 3.41
1624 1735 9.467796 TGAAAACACATTATATGTATGAACCCA 57.532 29.630 6.64 0.00 42.70 4.51
1625 1736 9.950680 GAAAACACATTATATGTATGAACCCAG 57.049 33.333 6.64 0.00 42.70 4.45
1626 1737 7.510549 AACACATTATATGTATGAACCCAGC 57.489 36.000 6.64 0.00 42.70 4.85
1627 1738 6.600388 ACACATTATATGTATGAACCCAGCA 58.400 36.000 6.64 0.00 42.70 4.41
1628 1739 7.059788 ACACATTATATGTATGAACCCAGCAA 58.940 34.615 6.64 0.00 42.70 3.91
1629 1740 7.013274 ACACATTATATGTATGAACCCAGCAAC 59.987 37.037 6.64 0.00 42.70 4.17
1630 1741 7.013178 CACATTATATGTATGAACCCAGCAACA 59.987 37.037 6.64 0.00 42.70 3.33
1631 1742 6.935741 TTATATGTATGAACCCAGCAACAC 57.064 37.500 0.00 0.00 0.00 3.32
1653 1764 1.214062 CAGTCTGTCTGTCTCGGGC 59.786 63.158 0.00 0.00 39.17 6.13
1654 1765 1.075836 AGTCTGTCTGTCTCGGGCT 59.924 57.895 0.00 0.00 0.00 5.19
1656 1767 0.389166 GTCTGTCTGTCTCGGGCTTG 60.389 60.000 0.00 0.00 0.00 4.01
1657 1768 0.539669 TCTGTCTGTCTCGGGCTTGA 60.540 55.000 0.00 0.00 0.00 3.02
1659 1770 0.976641 TGTCTGTCTCGGGCTTGAAT 59.023 50.000 0.00 0.00 0.00 2.57
1661 1772 0.391661 TCTGTCTCGGGCTTGAATGC 60.392 55.000 0.00 0.00 0.00 3.56
1662 1773 1.699656 CTGTCTCGGGCTTGAATGCG 61.700 60.000 0.00 0.00 0.00 4.73
1771 1913 5.028549 TGCACAATTTACCCACATGTTTT 57.971 34.783 0.00 0.00 0.00 2.43
1772 1914 5.431765 TGCACAATTTACCCACATGTTTTT 58.568 33.333 0.00 0.00 0.00 1.94
1773 1915 5.525378 TGCACAATTTACCCACATGTTTTTC 59.475 36.000 0.00 0.00 0.00 2.29
1777 1919 7.281999 CACAATTTACCCACATGTTTTTCCTTT 59.718 33.333 0.00 0.00 0.00 3.11
1781 1923 4.285863 ACCCACATGTTTTTCCTTTCTCA 58.714 39.130 0.00 0.00 0.00 3.27
1783 1925 5.163416 ACCCACATGTTTTTCCTTTCTCAAG 60.163 40.000 0.00 0.00 0.00 3.02
1784 1926 5.163416 CCCACATGTTTTTCCTTTCTCAAGT 60.163 40.000 0.00 0.00 0.00 3.16
1785 1927 6.340522 CCACATGTTTTTCCTTTCTCAAGTT 58.659 36.000 0.00 0.00 0.00 2.66
1788 1930 8.720562 CACATGTTTTTCCTTTCTCAAGTTTTT 58.279 29.630 0.00 0.00 0.00 1.94
1790 1932 9.154847 CATGTTTTTCCTTTCTCAAGTTTTTCT 57.845 29.630 0.00 0.00 0.00 2.52
1872 2015 6.701937 CATGCAATTCATCATGTAAGTTTGC 58.298 36.000 14.22 14.22 38.85 3.68
1900 2047 2.091555 GGATAGAGTCACCCTGGAGACT 60.092 54.545 14.95 14.95 45.91 3.24
1943 2090 1.878088 CTGTGACTTGCAATGCTCTGT 59.122 47.619 6.82 2.32 0.00 3.41
1945 2092 3.475575 TGTGACTTGCAATGCTCTGTAA 58.524 40.909 6.82 0.00 0.00 2.41
1983 2130 1.202330 CTGGTGAAGGAGCTCAGGAT 58.798 55.000 17.19 0.00 0.00 3.24
1984 2131 1.138661 CTGGTGAAGGAGCTCAGGATC 59.861 57.143 17.19 8.08 0.00 3.36
1985 2132 0.103937 GGTGAAGGAGCTCAGGATCG 59.896 60.000 17.19 0.00 0.00 3.69
1986 2133 0.820871 GTGAAGGAGCTCAGGATCGT 59.179 55.000 17.19 0.00 0.00 3.73
1987 2134 2.025155 GTGAAGGAGCTCAGGATCGTA 58.975 52.381 17.19 0.00 0.00 3.43
1988 2135 2.034053 GTGAAGGAGCTCAGGATCGTAG 59.966 54.545 17.19 0.00 0.00 3.51
1989 2136 1.000717 GAAGGAGCTCAGGATCGTAGC 60.001 57.143 17.19 4.82 36.48 3.58
1990 2137 0.106469 AGGAGCTCAGGATCGTAGCA 60.106 55.000 17.19 0.00 38.75 3.49
1991 2138 0.313672 GGAGCTCAGGATCGTAGCAG 59.686 60.000 17.19 0.99 38.75 4.24
2032 2179 4.454161 TCGGTAACTGTGATGTTGATTTGG 59.546 41.667 0.00 0.00 0.00 3.28
2043 2190 5.484644 TGATGTTGATTTGGTTTCATCCCAT 59.515 36.000 0.00 0.00 33.20 4.00
2044 2191 5.149973 TGTTGATTTGGTTTCATCCCATG 57.850 39.130 0.00 0.00 0.00 3.66
2093 2240 3.455910 TGCAGCTAAGGATTGTATCAGGT 59.544 43.478 0.00 0.00 0.00 4.00
2101 2248 7.389053 GCTAAGGATTGTATCAGGTATTTGGAG 59.611 40.741 0.00 0.00 0.00 3.86
2104 2251 6.564152 AGGATTGTATCAGGTATTTGGAGGAT 59.436 38.462 0.00 0.00 0.00 3.24
2111 2258 6.425210 TCAGGTATTTGGAGGATCATGTAG 57.575 41.667 0.00 0.00 36.25 2.74
2122 2269 4.293494 AGGATCATGTAGTGTGGACATCT 58.707 43.478 0.00 0.00 35.31 2.90
2151 2298 4.655649 TCCTGCTGATATATCTTGTGTGGT 59.344 41.667 13.79 0.00 0.00 4.16
2172 2319 5.470777 TGGTTACTAGCGTTTTTGCTATGTT 59.529 36.000 0.00 0.00 45.79 2.71
2291 2438 0.622665 AGCTCTTGCCCTGTTGCTAT 59.377 50.000 0.00 0.00 40.80 2.97
2305 2452 5.357878 CCTGTTGCTATGTTGACATATTGGT 59.642 40.000 4.44 0.00 38.09 3.67
2331 2478 5.156355 GCCATGATATTGTAGAAAATGGCG 58.844 41.667 7.91 0.00 46.35 5.69
2557 2705 1.318158 GGCTGCATCAAAGAGTGGGG 61.318 60.000 0.50 0.00 0.00 4.96
2566 2714 2.158813 TCAAAGAGTGGGGAGTTCACAC 60.159 50.000 0.00 0.00 37.58 3.82
2808 2956 3.038280 TCAAGCGAAGAGGATATTGGGA 58.962 45.455 0.00 0.00 0.00 4.37
3009 3157 2.092914 GGGAAGAATCGGACTGATGGTT 60.093 50.000 0.00 0.00 37.39 3.67
3134 3330 4.463186 AGATAACTACAGAAGTGGCGAAGT 59.537 41.667 0.00 0.00 38.88 3.01
3135 3331 3.470645 AACTACAGAAGTGGCGAAGTT 57.529 42.857 0.00 0.00 38.88 2.66
3204 3406 4.619233 GGGGGTTTCAGCCTGTTT 57.381 55.556 0.00 0.00 35.71 2.83
3287 3489 5.228945 AGCACCACTTATACTGAACTTGT 57.771 39.130 0.00 0.00 0.00 3.16
3327 3542 2.614057 GGGAAGTGATTCTTGTATGGCG 59.386 50.000 0.00 0.00 36.40 5.69
3391 3653 5.350504 AGAACACATCTGGGAGTATCTTG 57.649 43.478 0.00 0.00 36.88 3.02
3392 3654 4.780021 AGAACACATCTGGGAGTATCTTGT 59.220 41.667 0.00 0.00 36.88 3.16
3393 3655 5.958380 AGAACACATCTGGGAGTATCTTGTA 59.042 40.000 0.00 0.00 36.88 2.41
3394 3656 5.599999 ACACATCTGGGAGTATCTTGTAC 57.400 43.478 0.00 0.00 33.73 2.90
3537 3801 5.952347 TCAGAATGAGCTCCTTTCTACTGTA 59.048 40.000 21.87 8.56 42.56 2.74
3539 3808 6.700960 CAGAATGAGCTCCTTTCTACTGTATG 59.299 42.308 21.87 10.23 39.69 2.39
3555 3824 5.507077 ACTGTATGTTTTACTTGTTGCACG 58.493 37.500 0.00 0.00 0.00 5.34
3558 3827 6.367421 TGTATGTTTTACTTGTTGCACGATC 58.633 36.000 0.00 0.00 0.00 3.69
3559 3828 3.867665 TGTTTTACTTGTTGCACGATCG 58.132 40.909 14.88 14.88 0.00 3.69
3564 3833 3.896648 ACTTGTTGCACGATCGATTTT 57.103 38.095 24.34 0.00 0.00 1.82
3579 3848 5.242069 TCGATTTTCAGTTTGCTTCACAA 57.758 34.783 0.00 0.00 36.13 3.33
3583 3852 5.643379 TTTTCAGTTTGCTTCACAACTCT 57.357 34.783 0.00 0.00 38.23 3.24
3590 3859 5.417580 AGTTTGCTTCACAACTCTTTAACCA 59.582 36.000 0.00 0.00 38.23 3.67
3605 3874 7.342541 ACTCTTTAACCAATCTCTACTACTCCC 59.657 40.741 0.00 0.00 0.00 4.30
3617 3887 5.642165 TCTACTACTCCCTCCATTCCATAC 58.358 45.833 0.00 0.00 0.00 2.39
3631 3901 8.378172 TCCATTCCATACTTCGTATTGAAATC 57.622 34.615 5.11 0.00 35.08 2.17
3637 3907 9.350951 TCCATACTTCGTATTGAAATCTCTAGA 57.649 33.333 0.00 0.00 35.79 2.43
3677 3975 2.680965 GGGAATCCCGGAGCCAAA 59.319 61.111 0.90 0.00 32.13 3.28
3678 3976 1.000145 GGGAATCCCGGAGCCAAAA 60.000 57.895 0.90 0.00 32.13 2.44
3679 3977 0.397114 GGGAATCCCGGAGCCAAAAT 60.397 55.000 0.90 0.00 32.13 1.82
3733 4034 2.176546 CGCAAGCAACCCGACATG 59.823 61.111 0.00 0.00 0.00 3.21
3739 4040 3.430862 CAACCCGACATGGCCACG 61.431 66.667 8.16 7.59 35.87 4.94
3798 4099 5.049818 GCATGACTCCATTCCGATTAAAGAG 60.050 44.000 0.00 0.00 0.00 2.85
3807 4108 7.229306 TCCATTCCGATTAAAGAGGATGATTTG 59.771 37.037 0.00 0.00 33.57 2.32
3811 4112 7.561251 TCCGATTAAAGAGGATGATTTGTACA 58.439 34.615 0.00 0.00 0.00 2.90
3817 4118 3.133003 AGAGGATGATTTGTACACTCGGG 59.867 47.826 0.00 0.00 0.00 5.14
3847 4148 3.470645 AGTTAGCGACTGGAGTTTTGT 57.529 42.857 0.00 0.00 37.17 2.83
3849 4150 2.870411 GTTAGCGACTGGAGTTTTGTGT 59.130 45.455 0.00 0.00 0.00 3.72
3855 4230 4.813296 GACTGGAGTTTTGTGTCGAAAT 57.187 40.909 0.00 0.00 0.00 2.17
3856 4231 4.773510 GACTGGAGTTTTGTGTCGAAATC 58.226 43.478 0.00 0.00 0.00 2.17
3874 4249 6.373216 TCGAAATCCAACCCAAATTGTACTAG 59.627 38.462 0.00 0.00 0.00 2.57
3905 4280 8.795786 TCTCAAATTATCAAACCGACAAAAAG 57.204 30.769 0.00 0.00 0.00 2.27
4022 4409 9.546428 AAATATCTTTTTGTCCACCAAAGAAAG 57.454 29.630 5.65 0.00 43.63 2.62
4023 4410 6.790232 ATCTTTTTGTCCACCAAAGAAAGA 57.210 33.333 0.00 0.00 43.63 2.52
4024 4411 6.597832 TCTTTTTGTCCACCAAAGAAAGAA 57.402 33.333 0.00 0.00 43.63 2.52
4025 4412 6.998802 TCTTTTTGTCCACCAAAGAAAGAAA 58.001 32.000 0.00 0.00 43.63 2.52
4078 4465 7.886405 TCTATGCTATCTACTACGTGTACTG 57.114 40.000 0.00 0.00 0.00 2.74
4079 4466 7.440198 TCTATGCTATCTACTACGTGTACTGT 58.560 38.462 0.00 0.00 0.00 3.55
4080 4467 8.579863 TCTATGCTATCTACTACGTGTACTGTA 58.420 37.037 0.00 0.00 0.00 2.74
4081 4468 9.368674 CTATGCTATCTACTACGTGTACTGTAT 57.631 37.037 0.00 0.00 0.00 2.29
4082 4469 7.649370 TGCTATCTACTACGTGTACTGTATC 57.351 40.000 0.00 0.00 0.00 2.24
4101 4488 4.615588 ATCTGTATAGAAGAAGCAGGGC 57.384 45.455 0.00 0.00 36.32 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.613022 AGCTCTTTCATTTGATTGAGGTATTCA 59.387 33.333 10.96 0.00 34.88 2.57
1 2 7.994194 AGCTCTTTCATTTGATTGAGGTATTC 58.006 34.615 10.96 0.00 34.88 1.75
2 3 7.951347 AGCTCTTTCATTTGATTGAGGTATT 57.049 32.000 10.96 0.00 34.88 1.89
3 4 7.951347 AAGCTCTTTCATTTGATTGAGGTAT 57.049 32.000 12.24 4.73 35.26 2.73
4 5 7.765695 AAAGCTCTTTCATTTGATTGAGGTA 57.234 32.000 12.24 0.00 35.26 3.08
5 6 6.661304 AAAGCTCTTTCATTTGATTGAGGT 57.339 33.333 0.00 8.32 36.66 3.85
6 7 9.480053 TTTTAAAGCTCTTTCATTTGATTGAGG 57.520 29.630 0.00 0.00 34.23 3.86
12 13 9.927668 CCCTTATTTTAAAGCTCTTTCATTTGA 57.072 29.630 0.00 0.00 34.23 2.69
13 14 9.927668 TCCCTTATTTTAAAGCTCTTTCATTTG 57.072 29.630 0.00 0.00 34.23 2.32
15 16 9.929180 GTTCCCTTATTTTAAAGCTCTTTCATT 57.071 29.630 0.00 0.00 34.23 2.57
16 17 9.088987 TGTTCCCTTATTTTAAAGCTCTTTCAT 57.911 29.630 0.00 0.00 34.23 2.57
17 18 8.472007 TGTTCCCTTATTTTAAAGCTCTTTCA 57.528 30.769 0.00 0.00 34.23 2.69
67 68 2.041755 ACAATTTCTCAAGGGGGTCTCC 59.958 50.000 0.00 0.00 0.00 3.71
68 69 3.441500 ACAATTTCTCAAGGGGGTCTC 57.558 47.619 0.00 0.00 0.00 3.36
69 70 3.140144 TCAACAATTTCTCAAGGGGGTCT 59.860 43.478 0.00 0.00 0.00 3.85
70 71 3.255888 GTCAACAATTTCTCAAGGGGGTC 59.744 47.826 0.00 0.00 0.00 4.46
71 72 3.230976 GTCAACAATTTCTCAAGGGGGT 58.769 45.455 0.00 0.00 0.00 4.95
72 73 2.562738 GGTCAACAATTTCTCAAGGGGG 59.437 50.000 0.00 0.00 0.00 5.40
73 74 3.500343 AGGTCAACAATTTCTCAAGGGG 58.500 45.455 0.00 0.00 0.00 4.79
74 75 5.316987 ACTAGGTCAACAATTTCTCAAGGG 58.683 41.667 0.00 0.00 0.00 3.95
75 76 5.997746 TGACTAGGTCAACAATTTCTCAAGG 59.002 40.000 0.00 0.00 39.78 3.61
76 77 7.496529 TTGACTAGGTCAACAATTTCTCAAG 57.503 36.000 8.75 0.00 45.88 3.02
105 106 8.598041 AGACTACAATTTAGAATTGAGTCACCT 58.402 33.333 25.88 15.33 37.91 4.00
106 107 8.779354 AGACTACAATTTAGAATTGAGTCACC 57.221 34.615 25.88 14.12 37.91 4.02
139 140 9.358872 GGGCTTTCTAATTTTTAATCTTCACAG 57.641 33.333 0.00 0.00 0.00 3.66
143 144 9.358872 CACTGGGCTTTCTAATTTTTAATCTTC 57.641 33.333 0.00 0.00 0.00 2.87
144 145 8.870116 ACACTGGGCTTTCTAATTTTTAATCTT 58.130 29.630 0.00 0.00 0.00 2.40
145 146 8.422577 ACACTGGGCTTTCTAATTTTTAATCT 57.577 30.769 0.00 0.00 0.00 2.40
150 152 7.962441 ACAATACACTGGGCTTTCTAATTTTT 58.038 30.769 0.00 0.00 0.00 1.94
155 157 6.116711 TGTACAATACACTGGGCTTTCTAA 57.883 37.500 0.00 0.00 32.89 2.10
159 161 6.472686 TTTTTGTACAATACACTGGGCTTT 57.527 33.333 9.56 0.00 38.63 3.51
187 197 9.525409 CAACAATTTCTCAAAACTCTCTCATTT 57.475 29.630 0.00 0.00 0.00 2.32
190 200 7.201732 GGTCAACAATTTCTCAAAACTCTCTCA 60.202 37.037 0.00 0.00 0.00 3.27
191 201 7.135467 GGTCAACAATTTCTCAAAACTCTCTC 58.865 38.462 0.00 0.00 0.00 3.20
192 202 6.603201 TGGTCAACAATTTCTCAAAACTCTCT 59.397 34.615 0.00 0.00 0.00 3.10
199 209 6.522625 TGACTTGGTCAACAATTTCTCAAA 57.477 33.333 0.00 0.00 39.78 2.69
216 227 1.415659 TGGCCACCCAATTTTGACTTG 59.584 47.619 0.00 0.00 38.46 3.16
217 228 1.799933 TGGCCACCCAATTTTGACTT 58.200 45.000 0.00 0.00 38.46 3.01
218 229 1.799933 TTGGCCACCCAATTTTGACT 58.200 45.000 3.88 0.00 46.01 3.41
233 244 5.540911 TGAAGTCTCCAATTGAAATTTGGC 58.459 37.500 7.12 0.00 0.00 4.52
234 245 8.611654 AATTGAAGTCTCCAATTGAAATTTGG 57.388 30.769 7.12 0.00 41.20 3.28
242 253 9.350357 CTCACAATTAATTGAAGTCTCCAATTG 57.650 33.333 30.18 15.30 42.28 2.32
253 264 4.671831 TGGAGGCCTCACAATTAATTGAA 58.328 39.130 33.29 17.87 40.14 2.69
260 271 3.463048 AGAATTGGAGGCCTCACAATT 57.537 42.857 36.70 36.70 40.13 2.32
262 273 2.239654 CCTAGAATTGGAGGCCTCACAA 59.760 50.000 33.29 30.22 0.00 3.33
266 277 1.696884 CTCCCTAGAATTGGAGGCCTC 59.303 57.143 25.59 25.59 43.69 4.70
267 278 1.813102 CTCCCTAGAATTGGAGGCCT 58.187 55.000 3.86 3.86 43.69 5.19
273 284 2.168521 TCACGAAGCTCCCTAGAATTGG 59.831 50.000 0.00 0.00 0.00 3.16
274 285 3.526931 TCACGAAGCTCCCTAGAATTG 57.473 47.619 0.00 0.00 0.00 2.32
277 288 5.632118 ACTATATCACGAAGCTCCCTAGAA 58.368 41.667 0.00 0.00 0.00 2.10
278 289 5.244189 ACTATATCACGAAGCTCCCTAGA 57.756 43.478 0.00 0.00 0.00 2.43
290 301 9.748100 GAGATGCATCGTATATACTATATCACG 57.252 37.037 20.67 0.00 0.00 4.35
298 309 9.104965 GAAGAGTAGAGATGCATCGTATATACT 57.895 37.037 20.67 21.17 0.00 2.12
299 310 8.884726 TGAAGAGTAGAGATGCATCGTATATAC 58.115 37.037 20.67 17.62 0.00 1.47
306 317 5.981915 TGAAATGAAGAGTAGAGATGCATCG 59.018 40.000 20.67 0.00 0.00 3.84
324 340 8.195617 TGTAAAAAGCTGAAAAGGTTGAAATG 57.804 30.769 0.00 0.00 0.00 2.32
333 349 8.077991 TGTGATCAGATGTAAAAAGCTGAAAAG 58.922 33.333 0.00 0.00 40.38 2.27
367 383 4.748144 GAGGCAGGTGCTTGGGGG 62.748 72.222 1.26 0.00 41.70 5.40
398 414 2.434702 AGTAGGTTTGGATAGGGAAGCG 59.565 50.000 0.00 0.00 0.00 4.68
423 439 2.101415 TCATGTAGGATCGGCTGTCAAG 59.899 50.000 0.00 0.00 0.00 3.02
424 440 2.107366 TCATGTAGGATCGGCTGTCAA 58.893 47.619 0.00 0.00 0.00 3.18
430 446 0.102481 ACGTGTCATGTAGGATCGGC 59.898 55.000 0.00 0.00 0.00 5.54
496 512 9.933240 AGTGGGTGTAGTATAGATTAAACTAGT 57.067 33.333 0.00 0.00 0.00 2.57
516 532 2.559922 TTTGTCACCGGCAAGTGGGT 62.560 55.000 0.00 0.00 38.34 4.51
518 534 1.358759 GTTTGTCACCGGCAAGTGG 59.641 57.895 0.00 0.00 38.34 4.00
662 702 4.764823 TGAATTGACCGGAGTAGCAAAAAT 59.235 37.500 9.46 0.00 0.00 1.82
703 743 7.339721 TCACAAAACTCTAGGTAGGTCATCTAG 59.660 40.741 0.00 0.00 33.65 2.43
892 967 9.888637 GAAGAAACGAATAATAACGAGAGAAAG 57.111 33.333 0.00 0.00 0.00 2.62
1105 1186 6.397831 TCGACGAACTGGTTAACATAATTG 57.602 37.500 8.10 0.00 0.00 2.32
1106 1187 5.063060 GCTCGACGAACTGGTTAACATAATT 59.937 40.000 8.10 0.00 0.00 1.40
1107 1188 4.565564 GCTCGACGAACTGGTTAACATAAT 59.434 41.667 8.10 0.00 0.00 1.28
1108 1189 3.922240 GCTCGACGAACTGGTTAACATAA 59.078 43.478 8.10 0.00 0.00 1.90
1109 1190 3.504863 GCTCGACGAACTGGTTAACATA 58.495 45.455 8.10 0.00 0.00 2.29
1110 1191 2.334838 GCTCGACGAACTGGTTAACAT 58.665 47.619 8.10 0.00 0.00 2.71
1181 1265 0.248289 AGGCGCCATAAACTACACGT 59.752 50.000 31.54 0.00 0.00 4.49
1290 1378 4.770531 TCGTCTAGAAACCCAAGATCAGAA 59.229 41.667 0.00 0.00 0.00 3.02
1354 1442 3.209410 ACCCAGACCTACGAAGTATACG 58.791 50.000 0.00 0.00 44.56 3.06
1377 1479 1.000385 ACAAATTCCACCGCACACATG 60.000 47.619 0.00 0.00 0.00 3.21
1383 1485 1.072489 TCCACTACAAATTCCACCGCA 59.928 47.619 0.00 0.00 0.00 5.69
1397 1499 3.907474 TCATTCCTTCCTTGTGTCCACTA 59.093 43.478 0.00 0.00 0.00 2.74
1403 1505 2.508526 GCACTCATTCCTTCCTTGTGT 58.491 47.619 0.00 0.00 0.00 3.72
1404 1506 1.815003 GGCACTCATTCCTTCCTTGTG 59.185 52.381 0.00 0.00 0.00 3.33
1405 1507 1.707427 AGGCACTCATTCCTTCCTTGT 59.293 47.619 0.00 0.00 0.00 3.16
1406 1508 2.503895 AGGCACTCATTCCTTCCTTG 57.496 50.000 0.00 0.00 0.00 3.61
1407 1509 4.657814 TTAAGGCACTCATTCCTTCCTT 57.342 40.909 0.00 0.00 41.47 3.36
1408 1510 4.870021 ATTAAGGCACTCATTCCTTCCT 57.130 40.909 0.00 0.00 41.47 3.36
1409 1511 4.949856 TGAATTAAGGCACTCATTCCTTCC 59.050 41.667 0.00 0.00 41.47 3.46
1410 1512 5.882557 TCTGAATTAAGGCACTCATTCCTTC 59.117 40.000 0.00 0.00 41.47 3.46
1411 1513 5.819991 TCTGAATTAAGGCACTCATTCCTT 58.180 37.500 0.00 0.00 44.32 3.36
1412 1514 5.441718 TCTGAATTAAGGCACTCATTCCT 57.558 39.130 0.00 0.00 38.49 3.36
1413 1515 6.515272 TTTCTGAATTAAGGCACTCATTCC 57.485 37.500 0.00 0.00 38.49 3.01
1414 1516 6.032717 GCTTTCTGAATTAAGGCACTCATTC 58.967 40.000 0.00 0.00 38.49 2.67
1415 1517 5.105595 GGCTTTCTGAATTAAGGCACTCATT 60.106 40.000 8.70 0.00 43.94 2.57
1416 1518 4.400567 GGCTTTCTGAATTAAGGCACTCAT 59.599 41.667 8.70 0.00 43.94 2.90
1441 1543 2.476619 ACTTCACTTCACGCGAAATCTG 59.523 45.455 15.93 0.00 0.00 2.90
1450 1552 4.224715 TCAGTACTGACTTCACTTCACG 57.775 45.455 21.74 0.00 34.14 4.35
1491 1597 6.841601 AGGCTAATCACCATCTTATAAGCAA 58.158 36.000 7.67 0.00 0.00 3.91
1532 1638 7.639113 TCAGTTGTCCTTATTTTTGTTCAGT 57.361 32.000 0.00 0.00 0.00 3.41
1533 1639 7.973388 TGTTCAGTTGTCCTTATTTTTGTTCAG 59.027 33.333 0.00 0.00 0.00 3.02
1548 1655 3.717707 TGCTAGACAGTGTTCAGTTGTC 58.282 45.455 0.00 8.42 41.10 3.18
1575 1686 9.623000 TTCATGAATGAGTCAATCAGTATGAAT 57.377 29.630 15.77 0.00 43.98 2.57
1622 1733 1.745087 ACAGACTGTTTGTGTTGCTGG 59.255 47.619 1.07 0.00 0.00 4.85
1623 1734 2.679837 AGACAGACTGTTTGTGTTGCTG 59.320 45.455 10.01 0.00 0.00 4.41
1624 1735 2.679837 CAGACAGACTGTTTGTGTTGCT 59.320 45.455 16.13 1.23 41.30 3.91
1625 1736 3.056952 CAGACAGACTGTTTGTGTTGC 57.943 47.619 16.13 0.00 41.30 4.17
1650 1761 0.171231 GTTCTTCCGCATTCAAGCCC 59.829 55.000 0.00 0.00 0.00 5.19
1653 1764 2.813754 TCCAAGTTCTTCCGCATTCAAG 59.186 45.455 0.00 0.00 0.00 3.02
1654 1765 2.813754 CTCCAAGTTCTTCCGCATTCAA 59.186 45.455 0.00 0.00 0.00 2.69
1656 1767 2.427506 ACTCCAAGTTCTTCCGCATTC 58.572 47.619 0.00 0.00 0.00 2.67
1657 1768 2.568623 ACTCCAAGTTCTTCCGCATT 57.431 45.000 0.00 0.00 0.00 3.56
1659 1770 1.337823 GCTACTCCAAGTTCTTCCGCA 60.338 52.381 0.00 0.00 0.00 5.69
1661 1772 2.743636 TGCTACTCCAAGTTCTTCCG 57.256 50.000 0.00 0.00 0.00 4.30
1662 1773 5.966742 AAATTGCTACTCCAAGTTCTTCC 57.033 39.130 0.00 0.00 27.96 3.46
1731 1871 1.262417 GCATGTGCACTCATGGTATCG 59.738 52.381 19.41 0.00 43.54 2.92
1771 1913 5.913137 TGCAGAAAAACTTGAGAAAGGAA 57.087 34.783 0.00 0.00 0.00 3.36
1772 1914 6.772716 AGTATGCAGAAAAACTTGAGAAAGGA 59.227 34.615 0.00 0.00 0.00 3.36
1773 1915 6.860023 CAGTATGCAGAAAAACTTGAGAAAGG 59.140 38.462 0.00 0.00 0.00 3.11
1777 1919 6.942532 AACAGTATGCAGAAAAACTTGAGA 57.057 33.333 0.00 0.00 42.53 3.27
1781 1923 7.433680 CCCTTAAACAGTATGCAGAAAAACTT 58.566 34.615 0.00 0.00 42.53 2.66
1783 1925 6.156519 CCCCTTAAACAGTATGCAGAAAAAC 58.843 40.000 0.00 0.00 42.53 2.43
1784 1926 5.245075 CCCCCTTAAACAGTATGCAGAAAAA 59.755 40.000 0.00 0.00 42.53 1.94
1785 1927 4.770010 CCCCCTTAAACAGTATGCAGAAAA 59.230 41.667 0.00 0.00 42.53 2.29
1788 1930 2.356741 GCCCCCTTAAACAGTATGCAGA 60.357 50.000 0.00 0.00 42.53 4.26
1790 1932 1.638589 AGCCCCCTTAAACAGTATGCA 59.361 47.619 0.00 0.00 42.53 3.96
1872 2015 1.974236 GGGTGACTCTATCCATCCCAG 59.026 57.143 0.00 0.00 34.07 4.45
1931 2078 2.068519 CGACAGTTACAGAGCATTGCA 58.931 47.619 11.91 0.00 0.00 4.08
1943 2090 2.333926 CGCACAATTCTCCGACAGTTA 58.666 47.619 0.00 0.00 0.00 2.24
1945 2092 1.291877 GCGCACAATTCTCCGACAGT 61.292 55.000 0.30 0.00 0.00 3.55
2032 2179 7.336931 ACTTGTTACACTATCATGGGATGAAAC 59.663 37.037 0.00 0.00 43.50 2.78
2043 2190 9.146984 GTAAATGCACTACTTGTTACACTATCA 57.853 33.333 0.00 0.00 0.00 2.15
2044 2191 9.367444 AGTAAATGCACTACTTGTTACACTATC 57.633 33.333 4.77 0.00 0.00 2.08
2093 2240 5.665360 TCCACACTACATGATCCTCCAAATA 59.335 40.000 0.00 0.00 0.00 1.40
2101 2248 4.679373 AGATGTCCACACTACATGATCC 57.321 45.455 0.00 0.00 37.69 3.36
2104 2251 6.605471 AAACTAGATGTCCACACTACATGA 57.395 37.500 0.00 0.00 37.69 3.07
2111 2258 3.437049 GCAGGAAAACTAGATGTCCACAC 59.563 47.826 11.58 0.00 32.19 3.82
2122 2269 8.486210 ACACAAGATATATCAGCAGGAAAACTA 58.514 33.333 15.08 0.00 0.00 2.24
2227 2374 6.041865 AGACTCATAGATCCAGTGATTGAAGG 59.958 42.308 0.00 0.00 0.00 3.46
2268 2415 1.679944 GCAACAGGGCAAGAGCTATCA 60.680 52.381 0.00 0.00 41.70 2.15
2273 2420 0.737219 CATAGCAACAGGGCAAGAGC 59.263 55.000 0.00 0.00 41.10 4.09
2371 2518 9.081204 AGCAATATCAATTCAATAGCATACCAA 57.919 29.630 0.00 0.00 0.00 3.67
2566 2714 5.653769 ACCCCATATCAAAACAGTTCATGAG 59.346 40.000 0.00 0.00 0.00 2.90
2580 2728 1.708993 GGCTGCCTGACCCCATATCA 61.709 60.000 12.43 0.00 0.00 2.15
2808 2956 2.158755 CCAGCCAGAGGAAATTATCGGT 60.159 50.000 0.00 0.00 0.00 4.69
3009 3157 2.997303 CAACCCGTTGATGACATCGTAA 59.003 45.455 10.79 0.00 42.93 3.18
3134 3330 5.874810 GTCTCACTGTATGTTGGCTCATAAA 59.125 40.000 4.99 0.55 33.01 1.40
3135 3331 5.419542 GTCTCACTGTATGTTGGCTCATAA 58.580 41.667 4.99 0.00 33.01 1.90
3199 3401 5.410067 TCCAAGCTTCAAGTTTCAAAACAG 58.590 37.500 0.00 1.03 41.30 3.16
3204 3406 6.349611 GCTGATATCCAAGCTTCAAGTTTCAA 60.350 38.462 0.00 0.00 0.00 2.69
3327 3542 9.716507 ATGCAAACGTTTCTATTATACACAATC 57.283 29.630 11.37 0.00 0.00 2.67
3391 3653 5.093849 TGTTTCCCCAAGTATGCTAGTAC 57.906 43.478 0.00 0.00 0.00 2.73
3392 3654 4.163458 CCTGTTTCCCCAAGTATGCTAGTA 59.837 45.833 0.00 0.00 0.00 1.82
3393 3655 3.054361 CCTGTTTCCCCAAGTATGCTAGT 60.054 47.826 0.00 0.00 0.00 2.57
3394 3656 3.054361 ACCTGTTTCCCCAAGTATGCTAG 60.054 47.826 0.00 0.00 0.00 3.42
3537 3801 4.212425 TCGATCGTGCAACAAGTAAAACAT 59.788 37.500 15.94 0.00 35.74 2.71
3539 3808 4.123276 TCGATCGTGCAACAAGTAAAAC 57.877 40.909 15.94 0.00 35.74 2.43
3555 3824 5.451908 TGTGAAGCAAACTGAAAATCGATC 58.548 37.500 0.00 0.00 0.00 3.69
3558 3827 5.036737 AGTTGTGAAGCAAACTGAAAATCG 58.963 37.500 0.00 0.00 39.03 3.34
3559 3828 6.268566 AGAGTTGTGAAGCAAACTGAAAATC 58.731 36.000 0.00 0.00 39.03 2.17
3564 3833 6.404293 GGTTAAAGAGTTGTGAAGCAAACTGA 60.404 38.462 0.00 0.00 39.03 3.41
3579 3848 7.342541 GGGAGTAGTAGAGATTGGTTAAAGAGT 59.657 40.741 0.00 0.00 0.00 3.24
3583 3852 6.610425 GGAGGGAGTAGTAGAGATTGGTTAAA 59.390 42.308 0.00 0.00 0.00 1.52
3590 3859 5.103043 TGGAATGGAGGGAGTAGTAGAGATT 60.103 44.000 0.00 0.00 0.00 2.40
3617 3887 9.243637 CCTTCTTCTAGAGATTTCAATACGAAG 57.756 37.037 0.00 0.00 34.32 3.79
3637 3907 6.771267 CCCGTTTCTAAATATAAGCCCTTCTT 59.229 38.462 0.00 0.00 38.79 2.52
3639 3909 6.293698 TCCCGTTTCTAAATATAAGCCCTTC 58.706 40.000 0.00 0.00 0.00 3.46
3677 3975 2.228822 GGCGACAGTGGACAAATGAATT 59.771 45.455 0.00 0.00 0.00 2.17
3678 3976 1.812571 GGCGACAGTGGACAAATGAAT 59.187 47.619 0.00 0.00 0.00 2.57
3679 3977 1.234821 GGCGACAGTGGACAAATGAA 58.765 50.000 0.00 0.00 0.00 2.57
3733 4034 1.310904 TTGTGGAAGTTTACGTGGCC 58.689 50.000 0.00 0.00 0.00 5.36
3798 4099 2.561569 CCCCGAGTGTACAAATCATCC 58.438 52.381 0.00 0.00 0.00 3.51
3807 4108 0.179081 GGAATCTGCCCCGAGTGTAC 60.179 60.000 0.00 0.00 0.00 2.90
3811 4112 1.201429 AACTGGAATCTGCCCCGAGT 61.201 55.000 0.00 0.00 0.00 4.18
3817 4118 1.134670 AGTCGCTAACTGGAATCTGCC 60.135 52.381 0.00 0.00 36.65 4.85
3846 4147 3.934457 ATTTGGGTTGGATTTCGACAC 57.066 42.857 0.00 0.00 33.69 3.67
3847 4148 3.639094 ACAATTTGGGTTGGATTTCGACA 59.361 39.130 0.78 0.00 33.40 4.35
3849 4150 5.074115 AGTACAATTTGGGTTGGATTTCGA 58.926 37.500 0.78 0.00 33.40 3.71
3855 4230 4.042311 TCTGCTAGTACAATTTGGGTTGGA 59.958 41.667 0.78 0.00 33.40 3.53
3856 4231 4.331968 TCTGCTAGTACAATTTGGGTTGG 58.668 43.478 0.78 0.00 33.40 3.77
3874 4249 6.688813 GTCGGTTTGATAATTTGAGAATCTGC 59.311 38.462 0.00 0.00 34.92 4.26
3905 4280 4.104383 TGATAATTTGAGGATCCTGGCC 57.896 45.455 22.02 5.35 0.00 5.36
3978 4365 7.293828 AGATATTTTGGCCCCTTTTTGAAAAA 58.706 30.769 0.00 2.83 0.00 1.94
3983 4370 7.369607 CAAAAAGATATTTTGGCCCCTTTTTG 58.630 34.615 20.96 20.96 46.01 2.44
3984 4371 7.066142 ACAAAAAGATATTTTGGCCCCTTTTT 58.934 30.769 15.61 7.98 42.09 1.94
4078 4465 5.474825 GCCCTGCTTCTTCTATACAGATAC 58.525 45.833 0.00 0.00 0.00 2.24
4079 4466 4.218635 CGCCCTGCTTCTTCTATACAGATA 59.781 45.833 0.00 0.00 0.00 1.98
4080 4467 3.006323 CGCCCTGCTTCTTCTATACAGAT 59.994 47.826 0.00 0.00 0.00 2.90
4081 4468 2.362397 CGCCCTGCTTCTTCTATACAGA 59.638 50.000 0.00 0.00 0.00 3.41
4082 4469 2.546795 CCGCCCTGCTTCTTCTATACAG 60.547 54.545 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.