Multiple sequence alignment - TraesCS2D01G338800

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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 TraesCS2D01G338800 chr2D 100.000 4085 0 0 1 4085 432039189 432035105 0.000000e+00 7544.0
1 TraesCS2D01G338800 chr2A 91.627 1469 80 30 1952 3384 554428288 554429749 0.000000e+00 1991.0
2 TraesCS2D01G338800 chr2A 86.559 744 49 15 3377 4085 554450892 554451619 0.000000e+00 773.0
3 TraesCS2D01G338800 chr2A 71.785 1244 293 52 598 1811 707756856 707755641 2.390000e-77 300.0
4 TraesCS2D01G338800 chr2B 86.458 1403 101 41 1887 3253 510799895 510798546 0.000000e+00 1456.0
5 TraesCS2D01G338800 chr2B 87.950 722 52 13 3274 3972 510798424 510797715 0.000000e+00 819.0
6 TraesCS2D01G338800 chr2B 81.647 1008 155 17 598 1602 448696774 448697754 0.000000e+00 809.0
7 TraesCS2D01G338800 chr2B 83.333 78 6 6 1736 1811 222623757 222623829 9.480000e-07 65.8
8 TraesCS2D01G338800 chr2B 94.737 38 2 0 4047 4084 510797622 510797585 4.410000e-05 60.2
9 TraesCS2D01G338800 chr3A 77.104 1236 254 23 598 1817 393916050 393917272 0.000000e+00 688.0
10 TraesCS2D01G338800 chr6D 86.723 595 50 11 1 566 221837268 221836674 5.760000e-178 634.0
11 TraesCS2D01G338800 chr6D 83.926 591 58 15 1 557 221835231 221834644 7.770000e-147 531.0
12 TraesCS2D01G338800 chr3B 88.705 363 34 6 206 566 475989379 475989022 1.740000e-118 436.0
13 TraesCS2D01G338800 chr3B 88.401 319 35 2 247 564 27106977 27107294 2.300000e-102 383.0
14 TraesCS2D01G338800 chr3B 97.143 35 1 0 4050 4084 572076572 572076606 4.410000e-05 60.2
15 TraesCS2D01G338800 chr7D 90.154 325 29 3 243 566 241963300 241962978 1.760000e-113 420.0
16 TraesCS2D01G338800 chr7D 87.616 323 38 2 243 564 241945874 241945553 1.390000e-99 374.0
17 TraesCS2D01G338800 chr7D 85.227 352 46 4 208 557 449445462 449445809 1.400000e-94 357.0
18 TraesCS2D01G338800 chr7D 87.273 55 4 2 1757 1811 214775146 214775095 4.410000e-05 60.2
19 TraesCS2D01G338800 chr1A 89.308 318 32 2 248 564 540733111 540732795 8.230000e-107 398.0
20 TraesCS2D01G338800 chr1A 69.969 646 179 15 599 1237 356478609 356477972 2.010000e-18 104.0
21 TraesCS2D01G338800 chr4B 77.640 644 136 7 987 1625 649095792 649095152 6.410000e-103 385.0
22 TraesCS2D01G338800 chr4A 86.441 354 42 5 206 557 98591029 98591378 2.300000e-102 383.0
23 TraesCS2D01G338800 chr4A 72.508 1244 283 52 598 1811 533573783 533574997 8.400000e-92 348.0
24 TraesCS2D01G338800 chr5A 80.321 498 86 11 1322 1811 681239149 681238656 2.320000e-97 366.0
25 TraesCS2D01G338800 chr5A 91.525 59 3 2 1754 1811 582851650 582851593 3.380000e-11 80.5
26 TraesCS2D01G338800 chr4D 90.476 189 17 1 1 188 37371670 37371482 8.770000e-62 248.0
27 TraesCS2D01G338800 chr4D 93.590 78 4 1 1734 1811 493792246 493792322 9.280000e-22 115.0
28 TraesCS2D01G338800 chr7A 82.692 156 14 10 1669 1819 251256685 251256538 4.290000e-25 126.0
29 TraesCS2D01G338800 chr1D 74.667 300 68 8 599 894 285060024 285059729 4.290000e-25 126.0
30 TraesCS2D01G338800 chr1B 89.831 59 4 2 1753 1811 564444687 564444631 1.570000e-09 75.0
31 TraesCS2D01G338800 chr6B 88.136 59 5 2 1755 1811 156403561 156403619 7.330000e-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 TraesCS2D01G338800 chr2D 432035105 432039189 4084 True 7544.0 7544 100.0000 1 4085 1 chr2D.!!$R1 4084
1 TraesCS2D01G338800 chr2A 554428288 554429749 1461 False 1991.0 1991 91.6270 1952 3384 1 chr2A.!!$F1 1432
2 TraesCS2D01G338800 chr2A 554450892 554451619 727 False 773.0 773 86.5590 3377 4085 1 chr2A.!!$F2 708
3 TraesCS2D01G338800 chr2A 707755641 707756856 1215 True 300.0 300 71.7850 598 1811 1 chr2A.!!$R1 1213
4 TraesCS2D01G338800 chr2B 448696774 448697754 980 False 809.0 809 81.6470 598 1602 1 chr2B.!!$F2 1004
5 TraesCS2D01G338800 chr2B 510797585 510799895 2310 True 778.4 1456 89.7150 1887 4084 3 chr2B.!!$R1 2197
6 TraesCS2D01G338800 chr3A 393916050 393917272 1222 False 688.0 688 77.1040 598 1817 1 chr3A.!!$F1 1219
7 TraesCS2D01G338800 chr6D 221834644 221837268 2624 True 582.5 634 85.3245 1 566 2 chr6D.!!$R1 565
8 TraesCS2D01G338800 chr4B 649095152 649095792 640 True 385.0 385 77.6400 987 1625 1 chr4B.!!$R1 638
9 TraesCS2D01G338800 chr4A 533573783 533574997 1214 False 348.0 348 72.5080 598 1811 1 chr4A.!!$F2 1213

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
520 550 0.174845 CGCTGTGGAAGATCGGGTAA 59.825 55.0 0.0 0.0 0.00 2.85 F
1602 1863 0.039074 ACAGAAACTGGCGTCTCTCG 60.039 55.0 0.0 0.0 37.49 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 2151 0.101759 CATGGGCCATTTCTTGAGCG 59.898 55.0 18.46 0.0 0.0 5.03 R
3407 4022 0.245539 CCGCCGTTCTTTCTAGTCCA 59.754 55.0 0.00 0.0 0.0 4.02 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
36 37 1.071471 AACACCAGCTTCCGTGGAG 59.929 57.895 9.50 0.00 38.57 3.86
51 52 0.609151 TGGAGCCGAATTTCCGTACA 59.391 50.000 0.00 0.00 36.22 2.90
58 59 1.997606 CGAATTTCCGTACACCTCCAC 59.002 52.381 0.00 0.00 0.00 4.02
70 71 2.158871 ACACCTCCACGTTATGTTGTGT 60.159 45.455 0.00 0.00 34.28 3.72
102 106 9.827411 GAATTCAAGTACAAGTTTGTTAGGATC 57.173 33.333 2.46 0.00 42.35 3.36
125 129 9.103861 GATCCTTATTTTTGTTTTTGTCAACCA 57.896 29.630 0.00 0.00 0.00 3.67
126 130 8.848474 TCCTTATTTTTGTTTTTGTCAACCAA 57.152 26.923 0.00 0.00 0.00 3.67
134 138 6.371809 TGTTTTTGTCAACCAACTAGCTAG 57.628 37.500 19.44 19.44 31.20 3.42
154 158 5.468072 GCTAGCTAGTATGGTACGTGAGTTA 59.532 44.000 21.62 0.00 46.40 2.24
165 169 5.702209 TGGTACGTGAGTTATTTTCCTTTCC 59.298 40.000 0.00 0.00 46.40 3.13
172 177 7.441836 GTGAGTTATTTTCCTTTCCAATTGGT 58.558 34.615 23.76 4.08 36.34 3.67
176 181 9.693739 AGTTATTTTCCTTTCCAATTGGTTTTT 57.306 25.926 23.76 3.99 36.34 1.94
240 270 4.342772 GCTAATGCTTTGTCAATGTACGG 58.657 43.478 0.00 0.00 36.03 4.02
241 271 4.094294 GCTAATGCTTTGTCAATGTACGGA 59.906 41.667 0.00 0.00 36.03 4.69
244 274 2.811431 TGCTTTGTCAATGTACGGAAGG 59.189 45.455 0.92 0.00 0.00 3.46
245 275 2.161609 GCTTTGTCAATGTACGGAAGGG 59.838 50.000 0.92 0.00 0.00 3.95
296 326 5.420421 TGAACAAGGTTCAGAAAATGTCCAA 59.580 36.000 7.66 0.00 0.00 3.53
298 328 6.089249 ACAAGGTTCAGAAAATGTCCAATC 57.911 37.500 0.00 0.00 0.00 2.67
301 331 7.505585 ACAAGGTTCAGAAAATGTCCAATCTTA 59.494 33.333 0.00 0.00 0.00 2.10
313 343 2.711009 TCCAATCTTAGGGCGATCCAAT 59.289 45.455 0.00 0.00 38.24 3.16
321 351 1.134280 AGGGCGATCCAATCTTGAGTG 60.134 52.381 0.00 0.00 38.24 3.51
326 356 4.394920 GGCGATCCAATCTTGAGTGTTTTA 59.605 41.667 0.00 0.00 0.00 1.52
340 370 9.185192 CTTGAGTGTTTTATGTGATTTTCCTTC 57.815 33.333 0.00 0.00 0.00 3.46
345 375 6.712998 TGTTTTATGTGATTTTCCTTCGAGGA 59.287 34.615 0.00 0.00 44.10 3.71
360 390 5.507482 CCTTCGAGGAAATCTATTAGCGACA 60.507 44.000 0.00 0.00 37.67 4.35
376 406 2.159517 GCGACAAAGGGTTGATCATCAC 60.160 50.000 0.00 0.00 38.20 3.06
432 462 1.782569 TCTTTGTTCGCGTACTGTTCG 59.217 47.619 16.93 2.26 0.00 3.95
463 493 3.549794 AGAGATTGCTATTGGAGGTTGC 58.450 45.455 0.00 0.00 0.00 4.17
473 503 1.219393 GGAGGTTGCGAGGAGGAAG 59.781 63.158 0.00 0.00 0.00 3.46
479 509 3.839432 GCGAGGAGGAAGACGGGG 61.839 72.222 0.00 0.00 0.00 5.73
490 520 0.250770 AAGACGGGGAAAGAACTGCC 60.251 55.000 0.00 0.00 0.00 4.85
504 534 1.886313 CTGCCGATCTTGCATCGCT 60.886 57.895 7.17 0.00 39.95 4.93
508 538 1.640069 CGATCTTGCATCGCTGTGG 59.360 57.895 0.00 0.00 34.66 4.17
512 542 2.845019 CTTGCATCGCTGTGGAAGA 58.155 52.632 12.10 0.00 46.62 2.87
515 545 0.807275 TGCATCGCTGTGGAAGATCG 60.807 55.000 0.00 0.00 0.00 3.69
518 548 1.330655 ATCGCTGTGGAAGATCGGGT 61.331 55.000 0.00 0.00 0.00 5.28
519 549 0.681887 TCGCTGTGGAAGATCGGGTA 60.682 55.000 0.00 0.00 0.00 3.69
520 550 0.174845 CGCTGTGGAAGATCGGGTAA 59.825 55.000 0.00 0.00 0.00 2.85
526 556 3.317149 TGTGGAAGATCGGGTAATCTACG 59.683 47.826 0.00 0.00 34.90 3.51
539 569 2.486951 ATCTACGCGCACGAATTAGT 57.513 45.000 5.73 0.00 43.93 2.24
552 582 3.065095 ACGAATTAGTGTCTCGCTAGTCC 59.935 47.826 0.00 0.00 36.03 3.85
557 587 1.674651 TGTCTCGCTAGTCCGTGCT 60.675 57.895 0.00 0.00 0.00 4.40
566 596 2.099263 GCTAGTCCGTGCTACATCAAGA 59.901 50.000 0.00 0.00 0.00 3.02
567 597 3.243569 GCTAGTCCGTGCTACATCAAGAT 60.244 47.826 0.00 0.00 0.00 2.40
582 612 6.438259 CATCAAGATGTTGCTTTGATCTCT 57.562 37.500 0.00 0.00 34.23 3.10
583 613 6.853720 CATCAAGATGTTGCTTTGATCTCTT 58.146 36.000 0.00 0.00 34.23 2.85
585 615 7.984422 TCAAGATGTTGCTTTGATCTCTTTA 57.016 32.000 0.00 0.00 33.23 1.85
587 617 8.292448 TCAAGATGTTGCTTTGATCTCTTTAAC 58.708 33.333 0.00 0.00 33.23 2.01
588 618 7.750229 AGATGTTGCTTTGATCTCTTTAACA 57.250 32.000 0.00 1.41 0.00 2.41
589 619 8.169977 AGATGTTGCTTTGATCTCTTTAACAA 57.830 30.769 8.63 0.00 31.57 2.83
590 620 8.800332 AGATGTTGCTTTGATCTCTTTAACAAT 58.200 29.630 8.63 1.39 31.57 2.71
592 622 9.846248 ATGTTGCTTTGATCTCTTTAACAATAC 57.154 29.630 8.63 0.00 31.57 1.89
593 623 8.296713 TGTTGCTTTGATCTCTTTAACAATACC 58.703 33.333 0.00 0.00 0.00 2.73
594 624 7.994425 TGCTTTGATCTCTTTAACAATACCA 57.006 32.000 0.00 0.00 0.00 3.25
596 626 7.665559 TGCTTTGATCTCTTTAACAATACCAGT 59.334 33.333 0.00 0.00 0.00 4.00
672 857 0.179004 TTGTGGCGTGGGACAAGATT 60.179 50.000 0.00 0.00 44.16 2.40
692 877 0.319083 TGCCGACCGAAGAAGCTTAA 59.681 50.000 0.00 0.00 0.00 1.85
699 884 1.740025 CCGAAGAAGCTTAAAGGGCTG 59.260 52.381 0.00 0.00 40.19 4.85
720 905 3.075882 TGGGGATCAGAAACATGAAAGGT 59.924 43.478 0.00 0.00 31.76 3.50
722 907 3.696548 GGGATCAGAAACATGAAAGGTCC 59.303 47.826 0.00 0.00 31.76 4.46
724 909 3.762407 TCAGAAACATGAAAGGTCCGA 57.238 42.857 0.00 0.00 0.00 4.55
776 961 0.687354 AAGAGAACTGACCCACGCAT 59.313 50.000 0.00 0.00 0.00 4.73
780 965 3.196207 AACTGACCCACGCATGCCT 62.196 57.895 13.15 0.00 0.00 4.75
807 992 1.374190 GCTGCCCATGATCGAGGAT 59.626 57.895 4.90 0.00 0.00 3.24
868 1053 0.535102 CGTGGGAAGTGGTGAAAGCT 60.535 55.000 0.00 0.00 33.76 3.74
871 1056 1.494721 TGGGAAGTGGTGAAAGCTTCT 59.505 47.619 0.00 0.00 38.77 2.85
924 1109 1.522806 GGTGTCGGATATTGCGCCA 60.523 57.895 4.18 0.00 0.00 5.69
1004 1189 6.574073 GCTCTTACTGAAGATAGATGGATGGG 60.574 46.154 0.00 0.00 40.95 4.00
1034 1219 4.730187 ACGCTACCGCCTCATTCATGAG 62.730 54.545 9.53 9.53 44.46 2.90
1074 1259 2.234661 TCTTTGTCATGCGATCTCCACT 59.765 45.455 0.00 0.00 0.00 4.00
1079 1264 1.520120 ATGCGATCTCCACTGTGCG 60.520 57.895 1.29 1.26 0.00 5.34
1092 1277 2.102553 GTGCGTCGAGACCTAGCC 59.897 66.667 0.00 0.00 0.00 3.93
1160 1345 6.849502 ACACAGCAAAGTTGATCTATGATTG 58.150 36.000 0.00 0.00 0.00 2.67
1189 1374 3.878667 GCCTTCCCAGATCCCCGG 61.879 72.222 0.00 0.00 0.00 5.73
1211 1396 1.519408 GCGGCTTGTACTTGGAGAAA 58.481 50.000 0.00 0.00 0.00 2.52
1244 1429 8.540388 ACCTCTTAAGTGCAAGTTATTCATCTA 58.460 33.333 1.63 0.00 30.60 1.98
1262 1447 0.249120 TAGTTGGCGCTGCAGTACAT 59.751 50.000 16.64 1.20 0.00 2.29
1276 1461 2.027745 CAGTACATGCTGTGGAACTCCT 60.028 50.000 0.00 0.00 38.04 3.69
1295 1480 0.898326 TACAGGAGAGCAAGGCACGA 60.898 55.000 0.00 0.00 0.00 4.35
1305 1490 2.076863 GCAAGGCACGAACTACAAGAT 58.923 47.619 0.00 0.00 0.00 2.40
1349 1534 0.518636 TTGCAGAGCGAAGACAATGC 59.481 50.000 0.00 0.00 0.00 3.56
1368 1553 3.405831 TGCTGATCATATACTTGCCAGC 58.594 45.455 0.00 0.00 40.35 4.85
1378 1563 0.105964 ACTTGCCAGCTGTACGTTCA 59.894 50.000 13.81 0.00 0.00 3.18
1431 1691 3.327757 TCCTCAGACTAAATGTGCAAGGT 59.672 43.478 0.00 0.00 0.00 3.50
1455 1715 0.321564 CCCATGCGGACACTTTCTCA 60.322 55.000 0.00 0.00 0.00 3.27
1501 1761 2.826488 AGTTCACTGGAGCAGATAGGT 58.174 47.619 0.00 0.00 35.18 3.08
1559 1820 3.194755 ACCTTTGGAAGCAAAGAAACGTT 59.805 39.130 0.00 0.00 42.94 3.99
1591 1852 4.618920 ATAGGACGGAACAACAGAAACT 57.381 40.909 0.00 0.00 0.00 2.66
1598 1859 1.940613 GAACAACAGAAACTGGCGTCT 59.059 47.619 0.00 0.00 35.51 4.18
1602 1863 0.039074 ACAGAAACTGGCGTCTCTCG 60.039 55.000 0.00 0.00 37.49 4.04
1604 1865 1.199327 CAGAAACTGGCGTCTCTCGTA 59.801 52.381 0.00 0.00 42.13 3.43
1605 1866 2.093106 AGAAACTGGCGTCTCTCGTAT 58.907 47.619 0.00 0.00 42.13 3.06
1620 1883 3.134623 TCTCGTATCCATTGGTGCTTGAT 59.865 43.478 1.86 0.00 0.00 2.57
1625 1888 3.940209 TCCATTGGTGCTTGATGAAAC 57.060 42.857 1.86 0.00 0.00 2.78
1695 1960 1.831736 TGAGGAGTTAGCTTAGGGTGC 59.168 52.381 0.00 0.00 0.00 5.01
1696 1961 1.831736 GAGGAGTTAGCTTAGGGTGCA 59.168 52.381 0.00 0.00 0.00 4.57
1698 1963 2.436173 AGGAGTTAGCTTAGGGTGCATC 59.564 50.000 0.00 0.00 0.00 3.91
1705 1970 1.138266 GCTTAGGGTGCATCCGAGTTA 59.862 52.381 19.50 1.87 37.00 2.24
1708 1973 0.617820 AGGGTGCATCCGAGTTAGGT 60.618 55.000 11.20 0.00 37.00 3.08
1721 1986 3.005050 CGAGTTAGGTGTTGGAGTGTGTA 59.995 47.826 0.00 0.00 0.00 2.90
1722 1987 4.304939 GAGTTAGGTGTTGGAGTGTGTAC 58.695 47.826 0.00 0.00 0.00 2.90
1730 1995 0.896940 TGGAGTGTGTACCCCGTCTC 60.897 60.000 0.00 0.00 0.00 3.36
1731 1996 1.505353 GAGTGTGTACCCCGTCTCG 59.495 63.158 0.00 0.00 0.00 4.04
1745 2010 0.572590 GTCTCGGATTGTTCGCATCG 59.427 55.000 0.00 0.00 0.00 3.84
1776 2042 8.376942 CGAGCTTCTTGTAATTAACTCTCTTTC 58.623 37.037 0.00 0.00 0.00 2.62
1836 2102 6.625532 AAAAACCCTCCAATGCTCATTAAT 57.374 33.333 0.00 0.00 0.00 1.40
1837 2103 6.625532 AAAACCCTCCAATGCTCATTAATT 57.374 33.333 0.00 0.00 0.00 1.40
1838 2104 7.732222 AAAACCCTCCAATGCTCATTAATTA 57.268 32.000 0.00 0.00 0.00 1.40
1839 2105 6.966534 AACCCTCCAATGCTCATTAATTAG 57.033 37.500 0.00 0.00 0.00 1.73
1840 2106 6.018433 ACCCTCCAATGCTCATTAATTAGT 57.982 37.500 0.00 0.00 0.00 2.24
1841 2107 5.829924 ACCCTCCAATGCTCATTAATTAGTG 59.170 40.000 1.66 1.66 0.00 2.74
1842 2108 6.064060 CCCTCCAATGCTCATTAATTAGTGA 58.936 40.000 9.97 9.97 0.00 3.41
1843 2109 6.718454 CCCTCCAATGCTCATTAATTAGTGAT 59.282 38.462 10.71 0.00 0.00 3.06
1844 2110 7.232127 CCCTCCAATGCTCATTAATTAGTGATT 59.768 37.037 10.71 1.17 0.00 2.57
1845 2111 8.636213 CCTCCAATGCTCATTAATTAGTGATTT 58.364 33.333 10.71 3.90 0.00 2.17
1846 2112 9.674824 CTCCAATGCTCATTAATTAGTGATTTC 57.325 33.333 10.71 5.07 0.00 2.17
1847 2113 8.344831 TCCAATGCTCATTAATTAGTGATTTCG 58.655 33.333 10.71 1.74 0.00 3.46
1848 2114 8.131100 CCAATGCTCATTAATTAGTGATTTCGT 58.869 33.333 10.71 3.48 0.00 3.85
1851 2117 9.764363 ATGCTCATTAATTAGTGATTTCGTAGA 57.236 29.630 10.71 0.00 0.00 2.59
1852 2118 9.594478 TGCTCATTAATTAGTGATTTCGTAGAA 57.406 29.630 10.71 0.00 45.90 2.10
1878 2144 7.899178 AAAACAACTTTTAACTCAACCCAAG 57.101 32.000 0.00 0.00 0.00 3.61
1879 2145 5.006153 ACAACTTTTAACTCAACCCAAGC 57.994 39.130 0.00 0.00 0.00 4.01
1880 2146 4.142026 ACAACTTTTAACTCAACCCAAGCC 60.142 41.667 0.00 0.00 0.00 4.35
1881 2147 3.910989 ACTTTTAACTCAACCCAAGCCT 58.089 40.909 0.00 0.00 0.00 4.58
1882 2148 4.286707 ACTTTTAACTCAACCCAAGCCTT 58.713 39.130 0.00 0.00 0.00 4.35
1883 2149 5.451354 ACTTTTAACTCAACCCAAGCCTTA 58.549 37.500 0.00 0.00 0.00 2.69
1884 2150 5.535030 ACTTTTAACTCAACCCAAGCCTTAG 59.465 40.000 0.00 0.00 0.00 2.18
1885 2151 1.911057 AACTCAACCCAAGCCTTAGC 58.089 50.000 0.00 0.00 40.32 3.09
1889 2155 1.377333 AACCCAAGCCTTAGCGCTC 60.377 57.895 16.34 0.00 46.67 5.03
1896 2162 2.409948 AGCCTTAGCGCTCAAGAAAT 57.590 45.000 16.34 3.24 46.67 2.17
1906 2172 2.378038 GCTCAAGAAATGGCCCATGTA 58.622 47.619 0.00 0.00 0.00 2.29
1924 2190 0.254747 TAGGCCCAGAAATGAACCCG 59.745 55.000 0.00 0.00 0.00 5.28
1948 2214 4.090588 CGCCTTCGCCCTAACCCA 62.091 66.667 0.00 0.00 0.00 4.51
1951 2217 1.101635 GCCTTCGCCCTAACCCATTC 61.102 60.000 0.00 0.00 0.00 2.67
1985 2251 4.172512 CCTCCTGCATCTGCCGCT 62.173 66.667 0.00 0.00 41.18 5.52
2007 2280 3.342627 CGAAACCGCAAGTCGCCA 61.343 61.111 0.00 0.00 37.30 5.69
2069 2342 0.807667 CCTTCAATCCGGTGAGCTCG 60.808 60.000 9.64 0.00 0.00 5.03
2081 2354 0.900182 TGAGCTCGCCCTCTCTTCAA 60.900 55.000 9.64 0.00 33.02 2.69
2084 2357 2.101582 GAGCTCGCCCTCTCTTCAATTA 59.898 50.000 0.00 0.00 0.00 1.40
2131 2404 3.086282 GGCCTTTTTGTTCTTCCGGATA 58.914 45.455 4.15 0.00 0.00 2.59
2147 2420 5.313712 TCCGGATATTGGATTTTAAGAGCC 58.686 41.667 0.00 0.00 0.00 4.70
2252 2525 0.454600 GCCGTAGACATCGAGGTGAA 59.545 55.000 7.79 0.00 0.00 3.18
2260 2533 1.144057 ATCGAGGTGAATCCGTGGC 59.856 57.895 0.00 0.00 41.99 5.01
2283 2556 6.179040 GCCCAATCTAATCTCAGATGCTTAT 58.821 40.000 0.00 0.00 35.42 1.73
2287 2560 8.937884 CCAATCTAATCTCAGATGCTTATCTTG 58.062 37.037 0.00 0.00 35.42 3.02
2288 2561 8.444715 CAATCTAATCTCAGATGCTTATCTTGC 58.555 37.037 0.00 0.00 35.42 4.01
2297 2571 1.210478 TGCTTATCTTGCCTGTCCCTC 59.790 52.381 0.00 0.00 0.00 4.30
2298 2572 1.488393 GCTTATCTTGCCTGTCCCTCT 59.512 52.381 0.00 0.00 0.00 3.69
2301 2579 4.698575 CTTATCTTGCCTGTCCCTCTTAC 58.301 47.826 0.00 0.00 0.00 2.34
2306 2584 1.205460 GCCTGTCCCTCTTACCCCAA 61.205 60.000 0.00 0.00 0.00 4.12
2322 2600 0.750249 CCAACCCACCCAAAACTGTC 59.250 55.000 0.00 0.00 0.00 3.51
2330 2608 2.757868 CACCCAAAACTGTCCTGTTTCA 59.242 45.455 3.27 0.00 38.98 2.69
2331 2609 3.194542 CACCCAAAACTGTCCTGTTTCAA 59.805 43.478 3.27 0.00 38.98 2.69
2332 2610 3.447229 ACCCAAAACTGTCCTGTTTCAAG 59.553 43.478 3.27 0.00 38.98 3.02
2333 2611 3.447742 CCAAAACTGTCCTGTTTCAAGC 58.552 45.455 3.27 0.00 38.98 4.01
2334 2612 3.119173 CCAAAACTGTCCTGTTTCAAGCA 60.119 43.478 3.27 0.00 38.98 3.91
2336 2614 5.111293 CAAAACTGTCCTGTTTCAAGCATT 58.889 37.500 3.27 0.00 38.98 3.56
2337 2615 4.574599 AACTGTCCTGTTTCAAGCATTC 57.425 40.909 0.00 0.00 0.00 2.67
2423 2722 6.579865 CGGAGTACCTCTGGTAAATAAATGT 58.420 40.000 0.00 0.00 40.12 2.71
2469 2779 4.142403 TGCTTTGTTCTTGGAAGTTCAGTG 60.142 41.667 5.01 0.00 0.00 3.66
2477 2787 0.947244 GGAAGTTCAGTGGCACTGTG 59.053 55.000 38.27 21.65 46.03 3.66
2557 2867 2.698797 AGTCCGGTTTCTCTGTCTTTCA 59.301 45.455 0.00 0.00 0.00 2.69
2559 2869 3.495001 GTCCGGTTTCTCTGTCTTTCAAG 59.505 47.826 0.00 0.00 0.00 3.02
2560 2870 2.224314 CCGGTTTCTCTGTCTTTCAAGC 59.776 50.000 0.00 0.00 0.00 4.01
2561 2871 3.134458 CGGTTTCTCTGTCTTTCAAGCT 58.866 45.455 0.00 0.00 0.00 3.74
2562 2872 4.307432 CGGTTTCTCTGTCTTTCAAGCTA 58.693 43.478 0.00 0.00 0.00 3.32
2563 2873 4.387256 CGGTTTCTCTGTCTTTCAAGCTAG 59.613 45.833 0.00 0.00 0.00 3.42
2564 2874 5.301555 GGTTTCTCTGTCTTTCAAGCTAGT 58.698 41.667 0.00 0.00 0.00 2.57
2565 2875 6.456501 GGTTTCTCTGTCTTTCAAGCTAGTA 58.543 40.000 0.00 0.00 0.00 1.82
2566 2876 6.588373 GGTTTCTCTGTCTTTCAAGCTAGTAG 59.412 42.308 0.00 0.00 0.00 2.57
2587 2900 0.808125 AGTTGCGTGCACAGTTTTCA 59.192 45.000 18.64 1.41 0.00 2.69
2810 3213 3.419943 TGCACCTTGTTCATGATGCTTA 58.580 40.909 15.60 0.00 34.18 3.09
3124 3616 3.215151 GTCTCGGACACAGATGGATAGA 58.785 50.000 0.00 0.00 32.09 1.98
3253 3747 3.032459 TGTAAACTGGGGTTTTGTTCCC 58.968 45.455 0.00 0.00 42.28 3.97
3286 3894 3.610677 GCCAATTTCGTACAATTTTCCCG 59.389 43.478 0.00 0.00 0.00 5.14
3299 3907 5.167845 CAATTTTCCCGTGGATTTTACTGG 58.832 41.667 0.00 0.00 0.00 4.00
3304 3912 2.167662 CCGTGGATTTTACTGGCCTTT 58.832 47.619 3.32 0.00 0.00 3.11
3366 3981 0.181587 TGACTGGCCCGTGAAAGAAA 59.818 50.000 3.79 0.00 0.00 2.52
3389 4004 0.837691 AGTGGTGGTCTCTGGATGCA 60.838 55.000 0.00 0.00 0.00 3.96
3454 4069 1.747367 CTGTCGAGACGAGGCTCCT 60.747 63.158 9.32 0.22 36.23 3.69
3495 4110 2.347490 CTCCCCACACCTGTTCGG 59.653 66.667 0.00 0.00 39.35 4.30
3523 4145 1.140252 GCTTCTTATAGCGGGGTTCCA 59.860 52.381 0.00 0.00 0.00 3.53
3524 4146 2.835027 CTTCTTATAGCGGGGTTCCAC 58.165 52.381 0.00 0.00 0.00 4.02
3525 4147 2.170012 TCTTATAGCGGGGTTCCACT 57.830 50.000 0.00 0.00 0.00 4.00
3585 4207 2.657237 CTCGTCCCGCTTCCTGTT 59.343 61.111 0.00 0.00 0.00 3.16
3754 4389 4.328712 CCTTTTTGTTTGTTGTACTGCCAC 59.671 41.667 0.00 0.00 0.00 5.01
3759 4394 2.809696 GTTTGTTGTACTGCCACCGTAT 59.190 45.455 0.00 0.00 0.00 3.06
3806 4443 7.306749 GCGGCAAATTGGATGATTAATTAACTG 60.307 37.037 0.00 0.00 0.00 3.16
3838 4475 3.769844 AGTTTAAGCCGATTCAGGAGAGA 59.230 43.478 0.00 0.00 0.00 3.10
3839 4476 4.116238 GTTTAAGCCGATTCAGGAGAGAG 58.884 47.826 0.00 0.00 0.00 3.20
3840 4477 0.463620 AAGCCGATTCAGGAGAGAGC 59.536 55.000 0.00 0.00 0.00 4.09
3841 4478 0.396974 AGCCGATTCAGGAGAGAGCT 60.397 55.000 0.00 0.00 0.00 4.09
3842 4479 0.249405 GCCGATTCAGGAGAGAGCTG 60.249 60.000 0.00 0.00 0.00 4.24
3920 4568 5.479375 TCGGTGGATTTTAGTCTTGTAGAGT 59.521 40.000 0.00 0.00 0.00 3.24
3972 4791 1.141657 TGGAGAGCACAGGAATATGGC 59.858 52.381 0.00 0.00 0.00 4.40
4041 5035 2.034558 AGTGGTTGGTGCTGAAAATTCG 59.965 45.455 0.00 0.00 0.00 3.34
4042 5036 2.028130 TGGTTGGTGCTGAAAATTCGT 58.972 42.857 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.012745 AGCTGGTGTTGATTCCTTCTTAATT 58.987 36.000 0.00 0.00 0.00 1.40
16 17 1.227823 CCACGGAAGCTGGTGTTGA 60.228 57.895 10.72 0.00 32.30 3.18
19 20 2.743718 CTCCACGGAAGCTGGTGT 59.256 61.111 10.72 0.00 34.98 4.16
21 22 4.021925 GGCTCCACGGAAGCTGGT 62.022 66.667 6.02 0.00 34.98 4.00
36 37 1.004595 GAGGTGTACGGAAATTCGGC 58.995 55.000 0.23 0.00 0.00 5.54
51 52 2.922740 ACACAACATAACGTGGAGGT 57.077 45.000 0.00 0.00 37.45 3.85
58 59 5.121611 TGAATTCTGCCTACACAACATAACG 59.878 40.000 7.05 0.00 0.00 3.18
70 71 6.770785 ACAAACTTGTACTTGAATTCTGCCTA 59.229 34.615 7.05 0.00 40.16 3.93
102 106 8.726068 AGTTGGTTGACAAAAACAAAAATAAGG 58.274 29.630 14.28 0.00 41.58 2.69
134 138 7.168804 GGAAAATAACTCACGTACCATACTAGC 59.831 40.741 0.00 0.00 0.00 3.42
176 181 9.096823 TCTAACCTAGACTCCTGACAAATAAAA 57.903 33.333 0.00 0.00 0.00 1.52
219 249 5.794687 TCCGTACATTGACAAAGCATTAG 57.205 39.130 0.00 0.00 0.00 1.73
223 253 2.811431 CCTTCCGTACATTGACAAAGCA 59.189 45.455 0.00 0.00 0.00 3.91
228 258 0.687920 TGCCCTTCCGTACATTGACA 59.312 50.000 0.00 0.00 0.00 3.58
232 262 2.556622 CAAAACTGCCCTTCCGTACATT 59.443 45.455 0.00 0.00 0.00 2.71
240 270 5.629435 CGAATAAAACTCAAAACTGCCCTTC 59.371 40.000 0.00 0.00 0.00 3.46
241 271 5.068591 ACGAATAAAACTCAAAACTGCCCTT 59.931 36.000 0.00 0.00 0.00 3.95
244 274 5.516090 TCACGAATAAAACTCAAAACTGCC 58.484 37.500 0.00 0.00 0.00 4.85
245 275 6.199393 ACTCACGAATAAAACTCAAAACTGC 58.801 36.000 0.00 0.00 0.00 4.40
296 326 3.648067 TCAAGATTGGATCGCCCTAAGAT 59.352 43.478 0.00 0.00 35.38 2.40
298 328 3.181461 ACTCAAGATTGGATCGCCCTAAG 60.181 47.826 0.00 0.00 35.38 2.18
301 331 1.134280 CACTCAAGATTGGATCGCCCT 60.134 52.381 0.00 0.00 35.38 5.19
313 343 8.463930 AGGAAAATCACATAAAACACTCAAGA 57.536 30.769 0.00 0.00 0.00 3.02
321 351 7.141100 TCCTCGAAGGAAAATCACATAAAAC 57.859 36.000 1.64 0.00 42.51 2.43
340 370 5.175856 CCTTTGTCGCTAATAGATTTCCTCG 59.824 44.000 0.00 0.00 0.00 4.63
345 375 6.177610 TCAACCCTTTGTCGCTAATAGATTT 58.822 36.000 0.00 0.00 34.02 2.17
360 390 3.941483 GTCGATGTGATGATCAACCCTTT 59.059 43.478 0.00 0.00 0.00 3.11
409 439 4.088923 CGAACAGTACGCGAACAAAGATAA 59.911 41.667 15.93 0.00 0.00 1.75
432 462 0.108138 AGCAATCTCTACCCGTGCAC 60.108 55.000 6.82 6.82 37.68 4.57
463 493 1.255667 TTTCCCCGTCTTCCTCCTCG 61.256 60.000 0.00 0.00 0.00 4.63
473 503 2.033194 CGGCAGTTCTTTCCCCGTC 61.033 63.158 0.00 0.00 34.56 4.79
479 509 1.806542 TGCAAGATCGGCAGTTCTTTC 59.193 47.619 10.51 4.30 35.01 2.62
490 520 0.807275 TCCACAGCGATGCAAGATCG 60.807 55.000 0.00 3.84 43.72 3.69
504 534 3.317149 CGTAGATTACCCGATCTTCCACA 59.683 47.826 0.00 0.00 37.54 4.17
508 538 2.582687 CGCGTAGATTACCCGATCTTC 58.417 52.381 0.00 0.00 37.54 2.87
512 542 0.318445 GTGCGCGTAGATTACCCGAT 60.318 55.000 8.43 0.00 32.05 4.18
515 545 0.526096 TTCGTGCGCGTAGATTACCC 60.526 55.000 20.50 0.00 39.49 3.69
518 548 3.727227 CACTAATTCGTGCGCGTAGATTA 59.273 43.478 20.50 18.69 39.49 1.75
519 549 2.534349 CACTAATTCGTGCGCGTAGATT 59.466 45.455 20.50 18.58 39.49 2.40
520 550 2.117137 CACTAATTCGTGCGCGTAGAT 58.883 47.619 20.50 9.59 39.49 1.98
526 556 0.294887 CGAGACACTAATTCGTGCGC 59.705 55.000 9.85 0.00 38.45 6.09
539 569 0.392060 TAGCACGGACTAGCGAGACA 60.392 55.000 0.00 0.00 35.48 3.41
552 582 2.674852 AGCAACATCTTGATGTAGCACG 59.325 45.455 15.50 5.15 33.81 5.34
557 587 7.108194 AGAGATCAAAGCAACATCTTGATGTA 58.892 34.615 15.50 0.46 33.81 2.29
566 596 9.846248 GTATTGTTAAAGAGATCAAAGCAACAT 57.154 29.630 0.00 0.00 0.00 2.71
567 597 8.296713 GGTATTGTTAAAGAGATCAAAGCAACA 58.703 33.333 0.00 0.00 0.00 3.33
570 600 7.665559 ACTGGTATTGTTAAAGAGATCAAAGCA 59.334 33.333 0.00 0.00 0.00 3.91
571 601 8.045176 ACTGGTATTGTTAAAGAGATCAAAGC 57.955 34.615 0.00 0.00 0.00 3.51
574 604 9.613428 CCATACTGGTATTGTTAAAGAGATCAA 57.387 33.333 0.00 0.00 31.35 2.57
575 605 8.988060 TCCATACTGGTATTGTTAAAGAGATCA 58.012 33.333 0.00 0.00 39.03 2.92
577 607 9.784531 CATCCATACTGGTATTGTTAAAGAGAT 57.215 33.333 0.00 0.00 39.03 2.75
578 608 8.768397 ACATCCATACTGGTATTGTTAAAGAGA 58.232 33.333 0.00 0.00 39.03 3.10
579 609 8.830580 CACATCCATACTGGTATTGTTAAAGAG 58.169 37.037 0.00 0.00 39.03 2.85
580 610 8.544622 TCACATCCATACTGGTATTGTTAAAGA 58.455 33.333 0.00 0.00 39.03 2.52
581 611 8.731275 TCACATCCATACTGGTATTGTTAAAG 57.269 34.615 0.00 0.00 39.03 1.85
582 612 9.337396 GATCACATCCATACTGGTATTGTTAAA 57.663 33.333 0.00 0.00 39.03 1.52
583 613 7.655732 CGATCACATCCATACTGGTATTGTTAA 59.344 37.037 0.00 0.00 39.03 2.01
585 615 5.991606 CGATCACATCCATACTGGTATTGTT 59.008 40.000 0.00 0.00 39.03 2.83
587 617 5.541845 ACGATCACATCCATACTGGTATTG 58.458 41.667 0.00 0.00 39.03 1.90
588 618 5.808366 ACGATCACATCCATACTGGTATT 57.192 39.130 0.00 0.00 39.03 1.89
589 619 5.540337 AGAACGATCACATCCATACTGGTAT 59.460 40.000 0.00 0.00 39.03 2.73
590 620 4.893524 AGAACGATCACATCCATACTGGTA 59.106 41.667 0.00 0.00 39.03 3.25
591 621 3.706594 AGAACGATCACATCCATACTGGT 59.293 43.478 0.00 0.00 39.03 4.00
592 622 4.327982 AGAACGATCACATCCATACTGG 57.672 45.455 0.00 0.00 39.43 4.00
593 623 6.457392 CCAAAAGAACGATCACATCCATACTG 60.457 42.308 0.00 0.00 0.00 2.74
594 624 5.586243 CCAAAAGAACGATCACATCCATACT 59.414 40.000 0.00 0.00 0.00 2.12
596 626 4.881273 CCCAAAAGAACGATCACATCCATA 59.119 41.667 0.00 0.00 0.00 2.74
672 857 0.319083 TAAGCTTCTTCGGTCGGCAA 59.681 50.000 0.00 0.00 0.00 4.52
692 877 0.332972 GTTTCTGATCCCCAGCCCTT 59.667 55.000 0.00 0.00 42.62 3.95
699 884 3.696548 GACCTTTCATGTTTCTGATCCCC 59.303 47.826 0.00 0.00 0.00 4.81
720 905 2.225791 CTCGGAGTGCCAATGTCGGA 62.226 60.000 0.00 0.00 0.00 4.55
722 907 1.079819 ACTCGGAGTGCCAATGTCG 60.080 57.895 10.41 0.00 0.00 4.35
724 909 0.036952 CTCACTCGGAGTGCCAATGT 60.037 55.000 28.92 0.00 45.54 2.71
790 975 0.036577 GGATCCTCGATCATGGGCAG 60.037 60.000 3.84 0.00 40.50 4.85
807 992 4.444838 ATAGCACGCGCGTTGGGA 62.445 61.111 35.90 19.22 45.49 4.37
842 1027 1.061546 ACCACTTCCCACGGTAATGT 58.938 50.000 0.00 0.00 0.00 2.71
868 1053 4.443457 CCACTTGTCTCTCCAGAACAAGAA 60.443 45.833 23.75 2.65 38.62 2.52
871 1056 3.038280 TCCACTTGTCTCTCCAGAACAA 58.962 45.455 0.00 0.00 0.00 2.83
924 1109 1.600636 CACCGATGCCACCAACAGT 60.601 57.895 0.00 0.00 0.00 3.55
936 1121 1.070758 ACAACTCTTGTCTGCACCGAT 59.929 47.619 0.00 0.00 40.56 4.18
937 1122 0.464036 ACAACTCTTGTCTGCACCGA 59.536 50.000 0.00 0.00 40.56 4.69
1004 1189 4.849329 CGGTAGCGTCGCAGTCCC 62.849 72.222 21.09 11.70 0.00 4.46
1026 1211 2.621998 GCATTGTAGCTGGCTCATGAAT 59.378 45.455 0.00 0.00 0.00 2.57
1034 1219 0.387929 ATGCATGCATTGTAGCTGGC 59.612 50.000 27.46 0.00 35.71 4.85
1041 1226 3.945981 TGACAAAGATGCATGCATTGT 57.054 38.095 32.60 30.62 36.70 2.71
1074 1259 2.697761 GGCTAGGTCTCGACGCACA 61.698 63.158 0.00 0.00 0.00 4.57
1079 1264 0.606604 TGGTTTGGCTAGGTCTCGAC 59.393 55.000 0.00 0.00 0.00 4.20
1146 1331 5.063186 CGAGCATAGGCAATCATAGATCAAC 59.937 44.000 0.67 0.00 44.61 3.18
1160 1345 1.301322 GGAAGGCTCGAGCATAGGC 60.301 63.158 36.27 22.18 44.36 3.93
1189 1374 1.298859 CTCCAAGTACAAGCCGCCAC 61.299 60.000 0.00 0.00 0.00 5.01
1244 1429 1.003355 ATGTACTGCAGCGCCAACT 60.003 52.632 15.27 0.00 0.00 3.16
1262 1447 0.976641 CCTGTAGGAGTTCCACAGCA 59.023 55.000 17.81 5.19 40.54 4.41
1276 1461 0.898326 TCGTGCCTTGCTCTCCTGTA 60.898 55.000 0.00 0.00 0.00 2.74
1295 1480 3.070446 TGGTGACGGTTGATCTTGTAGTT 59.930 43.478 0.00 0.00 0.00 2.24
1305 1490 2.158943 TGTGTAACATGGTGACGGTTGA 60.159 45.455 0.00 0.00 45.67 3.18
1336 1521 2.391616 TGATCAGCATTGTCTTCGCT 57.608 45.000 0.00 0.00 36.10 4.93
1349 1534 4.639334 ACAGCTGGCAAGTATATGATCAG 58.361 43.478 19.93 0.00 0.00 2.90
1368 1553 1.060713 CTTCCTGCGTGAACGTACAG 58.939 55.000 4.59 4.36 42.22 2.74
1378 1563 0.391661 CTATGCCACACTTCCTGCGT 60.392 55.000 0.00 0.00 0.00 5.24
1431 1691 1.537814 AAGTGTCCGCATGGGTCGTA 61.538 55.000 9.14 0.00 37.00 3.43
1501 1761 0.467290 GACCAAGGTGTCAAAGCCCA 60.467 55.000 0.00 0.00 35.29 5.36
1559 1820 4.712829 TGTTCCGTCCTATTGAACATCCTA 59.287 41.667 0.00 0.00 42.36 2.94
1591 1852 1.067060 CAATGGATACGAGAGACGCCA 59.933 52.381 0.00 0.00 46.94 5.69
1598 1859 2.499693 TCAAGCACCAATGGATACGAGA 59.500 45.455 6.16 0.00 42.51 4.04
1602 1863 5.343249 GTTTCATCAAGCACCAATGGATAC 58.657 41.667 6.16 0.00 0.00 2.24
1604 1865 3.196254 GGTTTCATCAAGCACCAATGGAT 59.804 43.478 6.16 0.00 32.66 3.41
1605 1866 2.562298 GGTTTCATCAAGCACCAATGGA 59.438 45.455 6.16 0.00 32.66 3.41
1639 1902 2.895372 CTACACCAATCCCGCGGC 60.895 66.667 22.85 0.00 0.00 6.53
1641 1904 1.227263 CTCCTACACCAATCCCGCG 60.227 63.158 0.00 0.00 0.00 6.46
1668 1933 5.104735 CCCTAAGCTAACTCCTCACAAATCT 60.105 44.000 0.00 0.00 0.00 2.40
1670 1935 4.536489 ACCCTAAGCTAACTCCTCACAAAT 59.464 41.667 0.00 0.00 0.00 2.32
1695 1960 2.233922 ACTCCAACACCTAACTCGGATG 59.766 50.000 0.00 0.00 0.00 3.51
1696 1961 2.233922 CACTCCAACACCTAACTCGGAT 59.766 50.000 0.00 0.00 0.00 4.18
1698 1963 1.343465 ACACTCCAACACCTAACTCGG 59.657 52.381 0.00 0.00 0.00 4.63
1705 1970 0.763035 GGGTACACACTCCAACACCT 59.237 55.000 0.00 0.00 0.00 4.00
1708 1973 1.049855 ACGGGGTACACACTCCAACA 61.050 55.000 0.00 0.00 46.96 3.33
1730 1995 0.527600 TCTCCGATGCGAACAATCCG 60.528 55.000 0.00 0.00 0.00 4.18
1731 1996 0.931005 GTCTCCGATGCGAACAATCC 59.069 55.000 0.00 0.00 0.00 3.01
1745 2010 6.100668 AGTTAATTACAAGAAGCTCGTCTCC 58.899 40.000 0.00 0.00 0.00 3.71
1752 2017 8.379331 AGGAAAGAGAGTTAATTACAAGAAGCT 58.621 33.333 0.00 0.00 0.00 3.74
1780 2046 8.283992 CGCCAATGACGTACCATATTTTTATAA 58.716 33.333 0.00 0.00 0.00 0.98
1818 2084 6.064060 TCACTAATTAATGAGCATTGGAGGG 58.936 40.000 5.99 0.20 32.50 4.30
1819 2085 7.756395 ATCACTAATTAATGAGCATTGGAGG 57.244 36.000 2.76 0.00 32.50 4.30
1820 2086 9.674824 GAAATCACTAATTAATGAGCATTGGAG 57.325 33.333 2.76 1.34 32.50 3.86
1821 2087 8.344831 CGAAATCACTAATTAATGAGCATTGGA 58.655 33.333 2.76 0.00 32.50 3.53
1822 2088 8.131100 ACGAAATCACTAATTAATGAGCATTGG 58.869 33.333 2.76 2.66 32.50 3.16
1825 2091 9.764363 TCTACGAAATCACTAATTAATGAGCAT 57.236 29.630 2.76 0.00 0.00 3.79
1826 2092 9.594478 TTCTACGAAATCACTAATTAATGAGCA 57.406 29.630 2.76 0.00 0.00 4.26
1853 2119 7.094975 GCTTGGGTTGAGTTAAAAGTTGTTTTT 60.095 33.333 0.00 0.00 41.68 1.94
1854 2120 6.370442 GCTTGGGTTGAGTTAAAAGTTGTTTT 59.630 34.615 0.00 0.00 39.31 2.43
1855 2121 5.872617 GCTTGGGTTGAGTTAAAAGTTGTTT 59.127 36.000 0.00 0.00 0.00 2.83
1856 2122 5.416083 GCTTGGGTTGAGTTAAAAGTTGTT 58.584 37.500 0.00 0.00 0.00 2.83
1857 2123 4.142026 GGCTTGGGTTGAGTTAAAAGTTGT 60.142 41.667 0.00 0.00 0.00 3.32
1858 2124 4.099419 AGGCTTGGGTTGAGTTAAAAGTTG 59.901 41.667 0.00 0.00 0.00 3.16
1859 2125 4.286707 AGGCTTGGGTTGAGTTAAAAGTT 58.713 39.130 0.00 0.00 0.00 2.66
1860 2126 3.910989 AGGCTTGGGTTGAGTTAAAAGT 58.089 40.909 0.00 0.00 0.00 2.66
1861 2127 4.937201 AAGGCTTGGGTTGAGTTAAAAG 57.063 40.909 0.00 0.00 0.00 2.27
1862 2128 4.279922 GCTAAGGCTTGGGTTGAGTTAAAA 59.720 41.667 10.69 0.00 35.22 1.52
1863 2129 3.824443 GCTAAGGCTTGGGTTGAGTTAAA 59.176 43.478 10.69 0.00 35.22 1.52
1864 2130 3.418047 GCTAAGGCTTGGGTTGAGTTAA 58.582 45.455 10.69 0.00 35.22 2.01
1865 2131 2.614481 CGCTAAGGCTTGGGTTGAGTTA 60.614 50.000 10.69 0.00 36.09 2.24
1866 2132 1.882352 CGCTAAGGCTTGGGTTGAGTT 60.882 52.381 10.69 0.00 36.09 3.01
1867 2133 0.321653 CGCTAAGGCTTGGGTTGAGT 60.322 55.000 10.69 0.00 36.09 3.41
1868 2134 1.648467 GCGCTAAGGCTTGGGTTGAG 61.648 60.000 10.69 0.00 36.09 3.02
1869 2135 1.674322 GCGCTAAGGCTTGGGTTGA 60.674 57.895 10.69 0.00 36.09 3.18
1870 2136 1.648467 GAGCGCTAAGGCTTGGGTTG 61.648 60.000 11.50 1.77 44.93 3.77
1871 2137 1.377333 GAGCGCTAAGGCTTGGGTT 60.377 57.895 11.50 6.42 44.93 4.11
1872 2138 2.124507 TTGAGCGCTAAGGCTTGGGT 62.125 55.000 11.50 4.58 44.93 4.51
1873 2139 1.372087 CTTGAGCGCTAAGGCTTGGG 61.372 60.000 11.50 9.39 44.93 4.12
1874 2140 0.391661 TCTTGAGCGCTAAGGCTTGG 60.392 55.000 11.50 8.36 44.93 3.61
1875 2141 1.442769 TTCTTGAGCGCTAAGGCTTG 58.557 50.000 11.50 1.02 44.93 4.01
1876 2142 2.185004 TTTCTTGAGCGCTAAGGCTT 57.815 45.000 11.50 4.58 44.93 4.35
1878 2144 1.064654 CCATTTCTTGAGCGCTAAGGC 59.935 52.381 11.50 0.00 0.00 4.35
1879 2145 1.064654 GCCATTTCTTGAGCGCTAAGG 59.935 52.381 11.50 2.66 0.00 2.69
1880 2146 1.064654 GGCCATTTCTTGAGCGCTAAG 59.935 52.381 11.50 14.58 0.00 2.18
1881 2147 1.094785 GGCCATTTCTTGAGCGCTAA 58.905 50.000 11.50 0.00 0.00 3.09
1882 2148 0.748005 GGGCCATTTCTTGAGCGCTA 60.748 55.000 11.50 0.00 34.14 4.26
1883 2149 2.048603 GGGCCATTTCTTGAGCGCT 61.049 57.895 11.27 11.27 34.14 5.92
1884 2150 1.669999 ATGGGCCATTTCTTGAGCGC 61.670 55.000 14.78 0.00 36.03 5.92
1885 2151 0.101759 CATGGGCCATTTCTTGAGCG 59.898 55.000 18.46 0.00 0.00 5.03
1889 2155 1.410153 GCCTACATGGGCCATTTCTTG 59.590 52.381 18.46 9.68 45.92 3.02
1906 2172 1.000896 CGGGTTCATTTCTGGGCCT 60.001 57.895 4.53 0.00 0.00 5.19
1946 2212 2.113986 GCGGGATGAGGGGAATGG 59.886 66.667 0.00 0.00 0.00 3.16
1948 2214 3.178611 GGGCGGGATGAGGGGAAT 61.179 66.667 0.00 0.00 0.00 3.01
2069 2342 3.914426 TGGAGTAATTGAAGAGAGGGC 57.086 47.619 0.00 0.00 0.00 5.19
2081 2354 1.072331 GGGCACATCCGATGGAGTAAT 59.928 52.381 13.00 0.00 34.05 1.89
2084 2357 1.274703 AAGGGCACATCCGATGGAGT 61.275 55.000 13.00 0.00 34.05 3.85
2131 2404 2.943033 CCGACGGCTCTTAAAATCCAAT 59.057 45.455 0.00 0.00 0.00 3.16
2252 2525 2.039084 GAGATTAGATTGGGCCACGGAT 59.961 50.000 5.23 0.00 0.00 4.18
2260 2533 7.622713 AGATAAGCATCTGAGATTAGATTGGG 58.377 38.462 0.00 0.00 40.15 4.12
2283 2556 1.276622 GGTAAGAGGGACAGGCAAGA 58.723 55.000 0.00 0.00 0.00 3.02
2287 2560 1.205460 TTGGGGTAAGAGGGACAGGC 61.205 60.000 0.00 0.00 0.00 4.85
2288 2561 0.618981 GTTGGGGTAAGAGGGACAGG 59.381 60.000 0.00 0.00 0.00 4.00
2297 2571 0.188834 TTTGGGTGGGTTGGGGTAAG 59.811 55.000 0.00 0.00 0.00 2.34
2298 2572 0.640495 TTTTGGGTGGGTTGGGGTAA 59.360 50.000 0.00 0.00 0.00 2.85
2301 2579 1.074850 AGTTTTGGGTGGGTTGGGG 60.075 57.895 0.00 0.00 0.00 4.96
2306 2584 0.106217 CAGGACAGTTTTGGGTGGGT 60.106 55.000 0.00 0.00 0.00 4.51
2322 2600 3.760151 TCTGATGGAATGCTTGAAACAGG 59.240 43.478 0.00 0.00 0.00 4.00
2330 2608 5.446860 ACATTCTCATCTGATGGAATGCTT 58.553 37.500 33.16 23.63 43.69 3.91
2331 2609 5.050126 ACATTCTCATCTGATGGAATGCT 57.950 39.130 33.16 25.33 43.69 3.79
2332 2610 5.769484 AACATTCTCATCTGATGGAATGC 57.231 39.130 33.16 0.00 43.69 3.56
2333 2611 7.067129 ACTGAAACATTCTCATCTGATGGAATG 59.933 37.037 32.47 32.47 44.45 2.67
2334 2612 7.117397 ACTGAAACATTCTCATCTGATGGAAT 58.883 34.615 17.06 18.67 33.44 3.01
2336 2614 6.058553 ACTGAAACATTCTCATCTGATGGA 57.941 37.500 17.06 10.53 0.00 3.41
2337 2615 6.754702 AACTGAAACATTCTCATCTGATGG 57.245 37.500 17.06 8.49 0.00 3.51
2469 2779 0.320771 AATCGACAGTCCACAGTGCC 60.321 55.000 0.00 0.00 0.00 5.01
2477 2787 2.158959 CACGCGGAATCGACAGTCC 61.159 63.158 12.47 0.00 39.00 3.85
2557 2867 2.230508 TGCACGCAACTACTACTAGCTT 59.769 45.455 0.00 0.00 0.00 3.74
2559 2869 1.918609 GTGCACGCAACTACTACTAGC 59.081 52.381 0.00 0.00 0.00 3.42
2560 2870 3.172050 CTGTGCACGCAACTACTACTAG 58.828 50.000 13.13 0.00 0.00 2.57
2561 2871 2.555325 ACTGTGCACGCAACTACTACTA 59.445 45.455 13.13 0.00 0.00 1.82
2562 2872 1.340248 ACTGTGCACGCAACTACTACT 59.660 47.619 13.13 0.00 0.00 2.57
2563 2873 1.779569 ACTGTGCACGCAACTACTAC 58.220 50.000 13.13 0.00 0.00 2.73
2564 2874 2.519377 AACTGTGCACGCAACTACTA 57.481 45.000 13.13 0.00 0.00 1.82
2565 2875 1.663695 AAACTGTGCACGCAACTACT 58.336 45.000 13.13 0.00 0.00 2.57
2566 2876 2.223157 TGAAAACTGTGCACGCAACTAC 60.223 45.455 13.13 1.77 0.00 2.73
2778 3181 2.944129 ACAAGGTGCAGGAAAGCTTTA 58.056 42.857 12.68 0.00 33.24 1.85
2779 3182 1.780503 ACAAGGTGCAGGAAAGCTTT 58.219 45.000 12.53 12.53 33.24 3.51
2784 3187 2.942804 TCATGAACAAGGTGCAGGAAA 58.057 42.857 0.00 0.00 28.30 3.13
2810 3213 3.716601 AGCTGCGCAAATTAAACAAACT 58.283 36.364 13.05 0.00 0.00 2.66
2972 3456 0.252479 CTGGACAGCCTCTGCAAGAT 59.748 55.000 0.00 0.00 45.62 2.40
3124 3616 1.589716 GATTGCTTCAGGCGCCTTGT 61.590 55.000 30.60 2.44 45.43 3.16
3161 3653 3.548014 GGGTGACACAAACAACATTCTCG 60.548 47.826 8.08 0.00 0.00 4.04
3253 3747 1.401931 CGAAATTGGCTGCAGACTTGG 60.402 52.381 22.80 4.24 0.00 3.61
3286 3894 8.251750 GATTTTAAAAGGCCAGTAAAATCCAC 57.748 34.615 27.90 16.08 42.78 4.02
3299 3907 1.797713 GCGCGGAGGATTTTAAAAGGC 60.798 52.381 8.83 1.33 0.00 4.35
3304 3912 0.746563 CCCAGCGCGGAGGATTTTAA 60.747 55.000 17.96 0.00 36.56 1.52
3341 3950 4.295119 ACGGGCCAGTCACACGTC 62.295 66.667 4.39 0.00 31.39 4.34
3356 3971 3.377172 ACCACCACTCTTTTTCTTTCACG 59.623 43.478 0.00 0.00 0.00 4.35
3366 3981 2.103153 TCCAGAGACCACCACTCTTT 57.897 50.000 0.00 0.00 41.94 2.52
3407 4022 0.245539 CCGCCGTTCTTTCTAGTCCA 59.754 55.000 0.00 0.00 0.00 4.02
3430 4045 1.210413 CTCGTCTCGACAGGTGGTG 59.790 63.158 0.00 0.00 0.00 4.17
3495 4110 0.320858 GCTATAAGAAGCGGGAGGGC 60.321 60.000 0.00 0.00 31.76 5.19
3503 4125 1.140252 TGGAACCCCGCTATAAGAAGC 59.860 52.381 0.00 0.00 39.21 3.86
3505 4127 2.994186 GTGGAACCCCGCTATAAGAA 57.006 50.000 0.00 0.00 39.82 2.52
3517 4139 2.813908 CTGGCGCGTAGTGGAACC 60.814 66.667 8.43 0.00 37.80 3.62
3518 4140 3.488090 GCTGGCGCGTAGTGGAAC 61.488 66.667 8.43 0.00 39.19 3.62
3573 4195 4.351054 AGGGCAACAGGAAGCGGG 62.351 66.667 0.00 0.00 39.74 6.13
3732 4367 4.328712 GGTGGCAGTACAACAAACAAAAAG 59.671 41.667 0.00 0.00 0.00 2.27
3754 4389 5.556382 GCAATCGTCAAACAGTCATATACGG 60.556 44.000 0.00 0.00 0.00 4.02
3759 4394 3.125146 GCAGCAATCGTCAAACAGTCATA 59.875 43.478 0.00 0.00 0.00 2.15
3806 4443 1.025113 GGCTTAAACTCGAGGGTGCC 61.025 60.000 18.41 17.44 0.00 5.01
3838 4475 0.463654 TCCAAACGTGCAACTCAGCT 60.464 50.000 0.00 0.00 34.99 4.24
3839 4476 0.317020 GTCCAAACGTGCAACTCAGC 60.317 55.000 0.00 0.00 31.75 4.26
3840 4477 1.261619 GAGTCCAAACGTGCAACTCAG 59.738 52.381 12.92 0.00 36.64 3.35
3841 4478 1.295792 GAGTCCAAACGTGCAACTCA 58.704 50.000 12.92 0.00 36.64 3.41
3842 4479 0.232303 CGAGTCCAAACGTGCAACTC 59.768 55.000 9.41 9.41 34.81 3.01
3920 4568 4.937201 TCATAATCGCTCTCCTTTAGCA 57.063 40.909 0.00 0.00 40.08 3.49
3972 4791 0.320374 TAGCTGGACCAAGTTCACCG 59.680 55.000 0.00 0.00 0.00 4.94
4022 5016 2.028130 ACGAATTTTCAGCACCAACCA 58.972 42.857 0.00 0.00 0.00 3.67
4041 5035 6.237969 GCTTGCAGAAGATAGCTAACACTAAC 60.238 42.308 0.00 0.00 0.00 2.34
4042 5036 5.812642 GCTTGCAGAAGATAGCTAACACTAA 59.187 40.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.