Multiple sequence alignment - TraesCS5D01G179100

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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 TraesCS5D01G179100 chr5D 100.000 3741 0 0 1 3741 278309561 278313301 0.000000e+00 6909.0
1 TraesCS5D01G179100 chr5B 93.890 1702 94 4 2041 3741 316379344 316381036 0.000000e+00 2558.0
2 TraesCS5D01G179100 chr5B 89.199 787 27 20 536 1274 316377874 316378650 0.000000e+00 929.0
3 TraesCS5D01G179100 chr5B 85.593 236 20 8 1816 2038 316379066 316379300 6.250000e-58 235.0
4 TraesCS5D01G179100 chr5B 95.205 146 4 3 341 485 316377275 316377418 1.050000e-55 228.0
5 TraesCS5D01G179100 chr5B 95.902 122 5 0 208 329 316377169 316377290 8.200000e-47 198.0
6 TraesCS5D01G179100 chr5B 87.963 108 12 1 1549 1656 316378968 316379074 3.920000e-25 126.0
7 TraesCS5D01G179100 chr5A 92.173 1712 113 8 2044 3741 370191299 370189595 0.000000e+00 2399.0
8 TraesCS5D01G179100 chr5A 87.840 1176 59 36 542 1654 370192703 370191549 0.000000e+00 1303.0
9 TraesCS5D01G179100 chr5A 91.124 338 18 5 1 329 370193159 370192825 7.370000e-122 448.0
10 TraesCS5D01G179100 chr5A 87.037 216 25 3 1828 2041 370191540 370191326 1.340000e-59 241.0
11 TraesCS5D01G179100 chr1B 85.577 208 29 1 1030 1237 242248735 242248529 2.260000e-52 217.0
12 TraesCS5D01G179100 chr1A 85.577 208 29 1 1030 1237 175178822 175178616 2.260000e-52 217.0
13 TraesCS5D01G179100 chr1A 82.639 144 20 5 1671 1813 23858044 23858183 5.070000e-24 122.0
14 TraesCS5D01G179100 chr1D 85.366 205 29 1 1030 1234 184470882 184471085 1.050000e-50 211.0
15 TraesCS5D01G179100 chr1D 83.942 137 19 2 1670 1806 488706648 488706515 1.090000e-25 128.0
16 TraesCS5D01G179100 chr1D 80.137 146 27 2 1670 1815 111093642 111093499 1.420000e-19 108.0
17 TraesCS5D01G179100 chr2B 88.435 147 13 3 1670 1816 575932974 575933116 1.380000e-39 174.0
18 TraesCS5D01G179100 chr2A 88.276 145 13 4 1671 1814 30572270 30572129 1.790000e-38 171.0
19 TraesCS5D01G179100 chr2D 86.395 147 12 4 1670 1816 491496548 491496686 1.800000e-33 154.0
20 TraesCS5D01G179100 chr3A 84.247 146 16 6 1670 1812 737659795 737659654 6.520000e-28 135.0
21 TraesCS5D01G179100 chr6B 84.677 124 17 2 1694 1817 239309836 239309715 5.070000e-24 122.0
22 TraesCS5D01G179100 chr3D 82.517 143 21 4 1670 1811 341677540 341677679 5.070000e-24 122.0
23 TraesCS5D01G179100 chr4D 93.478 46 2 1 1052 1097 476865642 476865686 2.410000e-07 67.6
24 TraesCS5D01G179100 chr4B 93.478 46 2 1 1052 1097 600917296 600917340 2.410000e-07 67.6
25 TraesCS5D01G179100 chr4A 93.478 46 2 1 1052 1097 683606227 683606271 2.410000e-07 67.6


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 TraesCS5D01G179100 chr5D 278309561 278313301 3740 False 6909.000000 6909 100.0000 1 3741 1 chr5D.!!$F1 3740
1 TraesCS5D01G179100 chr5B 316377169 316381036 3867 False 712.333333 2558 91.2920 208 3741 6 chr5B.!!$F1 3533
2 TraesCS5D01G179100 chr5A 370189595 370193159 3564 True 1097.750000 2399 89.5435 1 3741 4 chr5A.!!$R1 3740

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
510 521 0.036022 AGAGAGAAGGCAACAGCACC 59.964 55.0 0.00 0.0 41.41 5.01 F
519 530 0.596082 GCAACAGCACCGGTACATTT 59.404 50.0 6.87 0.0 0.00 2.32 F
1525 2038 0.606401 CGGTCCTTGGTCAGTGCAAT 60.606 55.0 0.00 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2840 0.250038 GCTGATGCCGAGGCTTATCA 60.250 55.000 15.75 14.74 42.51 2.15 R
2098 2876 1.342174 AGGTGCTGCCAAAAGACATTG 59.658 47.619 0.00 0.00 40.61 2.82 R
3130 3919 0.258774 AAACAAGCTCACACCCAGGT 59.741 50.000 0.00 0.00 0.00 4.00 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
89 90 2.816958 CAGCACTAGCAGGCACCG 60.817 66.667 4.70 0.00 45.49 4.94
103 104 3.570212 ACCGAAAGCCACCCTGCT 61.570 61.111 0.00 0.00 45.43 4.24
104 105 3.058160 CCGAAAGCCACCCTGCTG 61.058 66.667 0.00 0.00 41.80 4.41
105 106 2.281761 CGAAAGCCACCCTGCTGT 60.282 61.111 0.00 0.00 41.80 4.40
156 165 0.742990 GCATTCCCCGTGAACGATGA 60.743 55.000 4.03 0.00 43.02 2.92
163 172 1.469940 CCCGTGAACGATGAGAGGAAG 60.470 57.143 4.03 0.00 43.02 3.46
164 173 1.469940 CCGTGAACGATGAGAGGAAGG 60.470 57.143 4.03 0.00 43.02 3.46
188 197 0.105246 AGGAGGTAGGAGATGGCAGG 60.105 60.000 0.00 0.00 0.00 4.85
249 259 1.740296 ACGTGGGATTTCGCCGAAG 60.740 57.895 0.00 0.00 0.00 3.79
337 347 6.518208 AAAGTATTTTAATGCTACCCGCAA 57.482 33.333 0.00 0.00 44.97 4.85
338 348 6.926313 AAAGTATTTTAATGCTACCCGCAAA 58.074 32.000 0.00 0.00 44.97 3.68
339 349 7.379750 AAAGTATTTTAATGCTACCCGCAAAA 58.620 30.769 0.00 0.00 44.97 2.44
340 350 7.873505 AAAGTATTTTAATGCTACCCGCAAAAA 59.126 29.630 0.00 0.00 44.97 1.94
427 438 6.118170 CCATACTGTCATGGTCAATTTCTCT 58.882 40.000 0.00 0.00 40.62 3.10
485 496 2.428544 AGGCACTGTTTGTGGTACAA 57.571 45.000 0.00 0.00 46.27 2.41
486 497 2.297701 AGGCACTGTTTGTGGTACAAG 58.702 47.619 0.00 0.00 46.27 3.16
487 498 2.021457 GGCACTGTTTGTGGTACAAGT 58.979 47.619 0.00 0.00 46.27 3.16
506 517 4.264460 AGTACAAGAGAGAAGGCAACAG 57.736 45.455 0.00 0.00 41.41 3.16
509 520 1.534595 CAAGAGAGAAGGCAACAGCAC 59.465 52.381 0.00 0.00 41.41 4.40
510 521 0.036022 AGAGAGAAGGCAACAGCACC 59.964 55.000 0.00 0.00 41.41 5.01
511 522 1.294659 GAGAGAAGGCAACAGCACCG 61.295 60.000 0.00 0.00 41.41 4.94
512 523 2.281761 AGAAGGCAACAGCACCGG 60.282 61.111 0.00 0.00 41.41 5.28
513 524 2.594592 GAAGGCAACAGCACCGGT 60.595 61.111 0.00 0.00 41.41 5.28
514 525 1.302192 GAAGGCAACAGCACCGGTA 60.302 57.895 6.87 0.00 41.41 4.02
515 526 1.574702 GAAGGCAACAGCACCGGTAC 61.575 60.000 6.87 0.00 41.41 3.34
516 527 2.281208 GGCAACAGCACCGGTACA 60.281 61.111 6.87 0.00 0.00 2.90
517 528 1.674322 GGCAACAGCACCGGTACAT 60.674 57.895 6.87 0.00 0.00 2.29
518 529 1.241315 GGCAACAGCACCGGTACATT 61.241 55.000 6.87 0.00 0.00 2.71
519 530 0.596082 GCAACAGCACCGGTACATTT 59.404 50.000 6.87 0.00 0.00 2.32
520 531 1.000717 GCAACAGCACCGGTACATTTT 60.001 47.619 6.87 0.00 0.00 1.82
521 532 2.544903 GCAACAGCACCGGTACATTTTT 60.545 45.455 6.87 0.00 0.00 1.94
555 977 4.759516 AAACAGCACCGGTACATTTTAG 57.240 40.909 6.87 0.00 0.00 1.85
732 1164 0.952010 CATCATCATCATCGCCGCCA 60.952 55.000 0.00 0.00 0.00 5.69
839 1282 3.334583 TCTCCTAAATCGCAAGCACTT 57.665 42.857 0.00 0.00 37.18 3.16
881 1324 1.300931 GCAACAGACAGTCCTGCGA 60.301 57.895 0.00 0.00 37.68 5.10
909 1357 2.002625 CCAGGAAGGAGAAAGGGGG 58.997 63.158 0.00 0.00 41.22 5.40
941 1416 4.329638 TTTCTGTCCTGAGAGGAGATCT 57.670 45.455 0.00 0.00 46.90 2.75
988 1463 1.342819 CAGGGAGATTAAGAGCCGAGG 59.657 57.143 0.00 0.00 0.00 4.63
1300 1798 1.069204 GCTGTATCTTGGCCTCGATCA 59.931 52.381 3.32 5.74 0.00 2.92
1308 1806 5.756195 TCTTGGCCTCGATCATTTTATTG 57.244 39.130 3.32 0.00 0.00 1.90
1310 1808 6.353323 TCTTGGCCTCGATCATTTTATTGTA 58.647 36.000 3.32 0.00 0.00 2.41
1314 1812 6.545666 TGGCCTCGATCATTTTATTGTATTGT 59.454 34.615 3.32 0.00 0.00 2.71
1315 1813 7.717436 TGGCCTCGATCATTTTATTGTATTGTA 59.283 33.333 3.32 0.00 0.00 2.41
1316 1814 8.730680 GGCCTCGATCATTTTATTGTATTGTAT 58.269 33.333 0.00 0.00 0.00 2.29
1381 1890 4.579340 TGATGTACTACAGCACTACTAGCC 59.421 45.833 2.94 0.00 39.86 3.93
1450 1963 9.474920 GAATGAATGAAGTTTGTTGTATGGAAA 57.525 29.630 0.00 0.00 0.00 3.13
1452 1965 8.815141 TGAATGAAGTTTGTTGTATGGAAATG 57.185 30.769 0.00 0.00 0.00 2.32
1453 1966 8.420222 TGAATGAAGTTTGTTGTATGGAAATGT 58.580 29.630 0.00 0.00 0.00 2.71
1454 1967 8.592105 AATGAAGTTTGTTGTATGGAAATGTG 57.408 30.769 0.00 0.00 0.00 3.21
1455 1968 6.511416 TGAAGTTTGTTGTATGGAAATGTGG 58.489 36.000 0.00 0.00 0.00 4.17
1456 1969 6.322456 TGAAGTTTGTTGTATGGAAATGTGGA 59.678 34.615 0.00 0.00 0.00 4.02
1457 1970 6.723298 AGTTTGTTGTATGGAAATGTGGAA 57.277 33.333 0.00 0.00 0.00 3.53
1463 1976 2.973694 ATGGAAATGTGGAATGCAGC 57.026 45.000 0.00 0.00 0.00 5.25
1471 1984 1.020437 GTGGAATGCAGCTAGGCTTC 58.980 55.000 0.00 0.00 36.40 3.86
1475 1988 2.103941 GGAATGCAGCTAGGCTTCTAGT 59.896 50.000 0.00 0.00 41.83 2.57
1476 1989 3.432890 GGAATGCAGCTAGGCTTCTAGTT 60.433 47.826 0.00 0.00 41.83 2.24
1478 1991 3.252974 TGCAGCTAGGCTTCTAGTTTC 57.747 47.619 0.00 0.00 41.83 2.78
1479 1992 2.093447 TGCAGCTAGGCTTCTAGTTTCC 60.093 50.000 0.00 0.00 41.83 3.13
1480 1993 2.169561 GCAGCTAGGCTTCTAGTTTCCT 59.830 50.000 0.00 0.00 41.83 3.36
1483 1996 4.890581 CAGCTAGGCTTCTAGTTTCCTCTA 59.109 45.833 0.00 0.00 41.83 2.43
1485 1998 6.717540 CAGCTAGGCTTCTAGTTTCCTCTATA 59.282 42.308 0.00 0.00 41.83 1.31
1507 2020 4.160635 GGTTTCGCGCATGGTCCG 62.161 66.667 8.75 0.00 0.00 4.79
1525 2038 0.606401 CGGTCCTTGGTCAGTGCAAT 60.606 55.000 0.00 0.00 0.00 3.56
1536 2049 4.408596 TGGTCAGTGCAATAGTGATGGATA 59.591 41.667 0.00 0.00 40.69 2.59
1558 2104 7.013655 GGATATGTTTGGTCTCTGCAATTATGT 59.986 37.037 0.00 0.00 0.00 2.29
1648 2368 2.940410 TCCTCGCCCGAAAATTATGTTC 59.060 45.455 0.00 0.00 0.00 3.18
1656 2376 5.519927 GCCCGAAAATTATGTTCAGAATTGG 59.480 40.000 6.24 4.97 0.00 3.16
1657 2377 6.042143 CCCGAAAATTATGTTCAGAATTGGG 58.958 40.000 6.24 8.55 0.00 4.12
1658 2378 6.042143 CCGAAAATTATGTTCAGAATTGGGG 58.958 40.000 6.24 5.07 0.00 4.96
1661 2381 6.933514 AAATTATGTTCAGAATTGGGGTGT 57.066 33.333 6.24 0.00 0.00 4.16
1662 2382 6.933514 AATTATGTTCAGAATTGGGGTGTT 57.066 33.333 4.89 0.00 0.00 3.32
1663 2383 6.933514 ATTATGTTCAGAATTGGGGTGTTT 57.066 33.333 0.00 0.00 0.00 2.83
1664 2384 4.871933 ATGTTCAGAATTGGGGTGTTTC 57.128 40.909 0.00 0.00 0.00 2.78
1665 2385 3.909732 TGTTCAGAATTGGGGTGTTTCT 58.090 40.909 0.00 0.00 0.00 2.52
1666 2386 5.055265 TGTTCAGAATTGGGGTGTTTCTA 57.945 39.130 0.00 0.00 0.00 2.10
1667 2387 5.070001 TGTTCAGAATTGGGGTGTTTCTAG 58.930 41.667 0.00 0.00 0.00 2.43
1668 2388 4.993705 TCAGAATTGGGGTGTTTCTAGT 57.006 40.909 0.00 0.00 0.00 2.57
1669 2389 5.319043 TCAGAATTGGGGTGTTTCTAGTT 57.681 39.130 0.00 0.00 0.00 2.24
1670 2390 5.313712 TCAGAATTGGGGTGTTTCTAGTTC 58.686 41.667 0.00 0.00 0.00 3.01
1671 2391 5.073144 TCAGAATTGGGGTGTTTCTAGTTCT 59.927 40.000 0.00 0.00 0.00 3.01
1672 2392 5.412904 CAGAATTGGGGTGTTTCTAGTTCTC 59.587 44.000 0.00 0.00 0.00 2.87
1673 2393 4.993705 ATTGGGGTGTTTCTAGTTCTCA 57.006 40.909 0.00 0.00 0.00 3.27
1674 2394 4.993705 TTGGGGTGTTTCTAGTTCTCAT 57.006 40.909 0.00 0.00 0.00 2.90
1675 2395 4.553330 TGGGGTGTTTCTAGTTCTCATC 57.447 45.455 0.00 0.00 0.00 2.92
1676 2396 4.168101 TGGGGTGTTTCTAGTTCTCATCT 58.832 43.478 0.00 0.00 0.00 2.90
1677 2397 5.338632 TGGGGTGTTTCTAGTTCTCATCTA 58.661 41.667 0.00 0.00 0.00 1.98
1678 2398 5.783360 TGGGGTGTTTCTAGTTCTCATCTAA 59.217 40.000 0.00 0.00 0.00 2.10
1679 2399 6.107343 GGGGTGTTTCTAGTTCTCATCTAAC 58.893 44.000 0.00 0.00 0.00 2.34
1680 2400 6.070710 GGGGTGTTTCTAGTTCTCATCTAACT 60.071 42.308 0.00 0.00 40.25 2.24
1681 2401 7.036829 GGGTGTTTCTAGTTCTCATCTAACTC 58.963 42.308 0.00 0.00 38.18 3.01
1682 2402 7.036829 GGTGTTTCTAGTTCTCATCTAACTCC 58.963 42.308 0.00 0.00 38.18 3.85
1683 2403 7.093684 GGTGTTTCTAGTTCTCATCTAACTCCT 60.094 40.741 0.00 0.00 38.18 3.69
1684 2404 8.958506 GTGTTTCTAGTTCTCATCTAACTCCTA 58.041 37.037 0.00 0.00 38.18 2.94
1685 2405 8.958506 TGTTTCTAGTTCTCATCTAACTCCTAC 58.041 37.037 0.00 0.00 38.18 3.18
1686 2406 8.958506 GTTTCTAGTTCTCATCTAACTCCTACA 58.041 37.037 0.00 0.00 38.18 2.74
1687 2407 8.508883 TTCTAGTTCTCATCTAACTCCTACAC 57.491 38.462 0.00 0.00 38.18 2.90
1688 2408 7.055378 TCTAGTTCTCATCTAACTCCTACACC 58.945 42.308 0.00 0.00 38.18 4.16
1689 2409 4.641094 AGTTCTCATCTAACTCCTACACCG 59.359 45.833 0.00 0.00 31.56 4.94
1690 2410 4.232188 TCTCATCTAACTCCTACACCGT 57.768 45.455 0.00 0.00 0.00 4.83
1691 2411 4.597004 TCTCATCTAACTCCTACACCGTT 58.403 43.478 0.00 0.00 0.00 4.44
1692 2412 4.398358 TCTCATCTAACTCCTACACCGTTG 59.602 45.833 0.00 0.00 0.00 4.10
1693 2413 3.446161 TCATCTAACTCCTACACCGTTGG 59.554 47.826 0.00 0.00 0.00 3.77
1694 2414 3.159213 TCTAACTCCTACACCGTTGGA 57.841 47.619 0.00 0.00 35.32 3.53
1695 2415 3.705051 TCTAACTCCTACACCGTTGGAT 58.295 45.455 0.00 0.00 36.91 3.41
1696 2416 3.698040 TCTAACTCCTACACCGTTGGATC 59.302 47.826 0.00 0.00 36.91 3.36
1697 2417 2.233305 ACTCCTACACCGTTGGATCT 57.767 50.000 0.00 0.00 36.91 2.75
1698 2418 2.537143 ACTCCTACACCGTTGGATCTT 58.463 47.619 0.00 0.00 36.91 2.40
1699 2419 3.705051 ACTCCTACACCGTTGGATCTTA 58.295 45.455 0.00 0.00 36.91 2.10
1700 2420 3.446516 ACTCCTACACCGTTGGATCTTAC 59.553 47.826 0.00 0.00 36.91 2.34
1701 2421 3.433343 TCCTACACCGTTGGATCTTACA 58.567 45.455 0.00 0.00 33.01 2.41
1702 2422 4.028131 TCCTACACCGTTGGATCTTACAT 58.972 43.478 0.00 0.00 33.01 2.29
1703 2423 4.119862 CCTACACCGTTGGATCTTACATG 58.880 47.826 0.00 0.00 30.33 3.21
1704 2424 3.973206 ACACCGTTGGATCTTACATGA 57.027 42.857 0.00 0.00 0.00 3.07
1705 2425 4.280436 ACACCGTTGGATCTTACATGAA 57.720 40.909 0.00 0.00 0.00 2.57
1706 2426 4.253685 ACACCGTTGGATCTTACATGAAG 58.746 43.478 0.00 0.00 36.38 3.02
1716 2436 4.137116 TCTTACATGAAGATTCGTGGGG 57.863 45.455 16.87 8.07 46.03 4.96
1717 2437 3.772572 TCTTACATGAAGATTCGTGGGGA 59.227 43.478 16.87 9.79 46.03 4.81
1718 2438 4.408921 TCTTACATGAAGATTCGTGGGGAT 59.591 41.667 16.87 1.49 46.03 3.85
1719 2439 3.652057 ACATGAAGATTCGTGGGGATT 57.348 42.857 16.87 0.00 46.03 3.01
1720 2440 3.545703 ACATGAAGATTCGTGGGGATTC 58.454 45.455 16.87 0.00 46.03 2.52
1721 2441 3.200825 ACATGAAGATTCGTGGGGATTCT 59.799 43.478 16.87 0.00 46.03 2.40
1722 2442 4.202441 CATGAAGATTCGTGGGGATTCTT 58.798 43.478 6.85 1.72 44.13 2.52
1723 2443 4.301072 TGAAGATTCGTGGGGATTCTTT 57.699 40.909 3.32 0.00 42.47 2.52
1724 2444 4.261801 TGAAGATTCGTGGGGATTCTTTC 58.738 43.478 3.32 0.00 42.47 2.62
1725 2445 4.019321 TGAAGATTCGTGGGGATTCTTTCT 60.019 41.667 3.32 0.00 42.47 2.52
1726 2446 4.576330 AGATTCGTGGGGATTCTTTCTT 57.424 40.909 0.00 0.00 32.79 2.52
1727 2447 4.923415 AGATTCGTGGGGATTCTTTCTTT 58.077 39.130 0.00 0.00 32.79 2.52
1728 2448 5.325239 AGATTCGTGGGGATTCTTTCTTTT 58.675 37.500 0.00 0.00 32.79 2.27
1729 2449 6.481643 AGATTCGTGGGGATTCTTTCTTTTA 58.518 36.000 0.00 0.00 32.79 1.52
1730 2450 7.119387 AGATTCGTGGGGATTCTTTCTTTTAT 58.881 34.615 0.00 0.00 32.79 1.40
1731 2451 7.615757 AGATTCGTGGGGATTCTTTCTTTTATT 59.384 33.333 0.00 0.00 32.79 1.40
1732 2452 7.533289 TTCGTGGGGATTCTTTCTTTTATTT 57.467 32.000 0.00 0.00 0.00 1.40
1733 2453 8.638629 TTCGTGGGGATTCTTTCTTTTATTTA 57.361 30.769 0.00 0.00 0.00 1.40
1734 2454 8.817092 TCGTGGGGATTCTTTCTTTTATTTAT 57.183 30.769 0.00 0.00 0.00 1.40
1735 2455 9.250246 TCGTGGGGATTCTTTCTTTTATTTATT 57.750 29.630 0.00 0.00 0.00 1.40
1736 2456 9.869757 CGTGGGGATTCTTTCTTTTATTTATTT 57.130 29.630 0.00 0.00 0.00 1.40
1764 2484 9.575868 TTGTTTGGTTAATCAAATAGTGTAGGA 57.424 29.630 16.58 0.00 38.64 2.94
1765 2485 9.226606 TGTTTGGTTAATCAAATAGTGTAGGAG 57.773 33.333 16.58 0.00 38.64 3.69
1766 2486 9.227777 GTTTGGTTAATCAAATAGTGTAGGAGT 57.772 33.333 16.58 0.00 38.64 3.85
1767 2487 9.802039 TTTGGTTAATCAAATAGTGTAGGAGTT 57.198 29.630 9.86 0.00 32.39 3.01
1775 2495 9.647918 ATCAAATAGTGTAGGAGTTAGATGAGA 57.352 33.333 0.00 0.00 0.00 3.27
1776 2496 8.904834 TCAAATAGTGTAGGAGTTAGATGAGAC 58.095 37.037 0.00 0.00 0.00 3.36
1777 2497 8.908903 CAAATAGTGTAGGAGTTAGATGAGACT 58.091 37.037 0.00 0.00 0.00 3.24
1778 2498 9.482175 AAATAGTGTAGGAGTTAGATGAGACTT 57.518 33.333 0.00 0.00 0.00 3.01
1779 2499 9.482175 AATAGTGTAGGAGTTAGATGAGACTTT 57.518 33.333 0.00 0.00 0.00 2.66
1780 2500 7.164230 AGTGTAGGAGTTAGATGAGACTTTG 57.836 40.000 0.00 0.00 0.00 2.77
1781 2501 6.722129 AGTGTAGGAGTTAGATGAGACTTTGT 59.278 38.462 0.00 0.00 0.00 2.83
1782 2502 7.233757 AGTGTAGGAGTTAGATGAGACTTTGTT 59.766 37.037 0.00 0.00 0.00 2.83
1783 2503 8.521176 GTGTAGGAGTTAGATGAGACTTTGTTA 58.479 37.037 0.00 0.00 0.00 2.41
1784 2504 9.085645 TGTAGGAGTTAGATGAGACTTTGTTAA 57.914 33.333 0.00 0.00 0.00 2.01
1787 2507 9.660180 AGGAGTTAGATGAGACTTTGTTAATTC 57.340 33.333 0.00 0.00 0.00 2.17
1788 2508 9.660180 GGAGTTAGATGAGACTTTGTTAATTCT 57.340 33.333 0.00 0.00 0.00 2.40
1814 2534 7.816513 TCATCTAGATGAGAATTAGCAAATCCG 59.183 37.037 27.93 0.03 42.42 4.18
1815 2535 7.055667 TCTAGATGAGAATTAGCAAATCCGT 57.944 36.000 0.00 0.00 0.00 4.69
1816 2536 7.500992 TCTAGATGAGAATTAGCAAATCCGTT 58.499 34.615 0.00 0.00 0.00 4.44
1817 2537 8.638873 TCTAGATGAGAATTAGCAAATCCGTTA 58.361 33.333 0.00 0.00 0.00 3.18
1818 2538 7.721286 AGATGAGAATTAGCAAATCCGTTAG 57.279 36.000 0.00 0.00 0.00 2.34
1819 2539 7.500992 AGATGAGAATTAGCAAATCCGTTAGA 58.499 34.615 0.00 0.00 0.00 2.10
1820 2540 7.987458 AGATGAGAATTAGCAAATCCGTTAGAA 59.013 33.333 0.00 0.00 0.00 2.10
1821 2541 8.682936 ATGAGAATTAGCAAATCCGTTAGAAT 57.317 30.769 0.00 0.00 0.00 2.40
1822 2542 8.506168 TGAGAATTAGCAAATCCGTTAGAATT 57.494 30.769 0.00 0.00 0.00 2.17
1823 2543 8.397906 TGAGAATTAGCAAATCCGTTAGAATTG 58.602 33.333 0.00 0.00 38.26 2.32
1824 2544 8.506168 AGAATTAGCAAATCCGTTAGAATTGA 57.494 30.769 0.00 0.00 37.54 2.57
1825 2545 8.398665 AGAATTAGCAAATCCGTTAGAATTGAC 58.601 33.333 0.00 0.00 37.54 3.18
1826 2546 7.624360 ATTAGCAAATCCGTTAGAATTGACA 57.376 32.000 0.00 0.00 37.54 3.58
1838 2558 8.540492 CCGTTAGAATTGACATACAGATGTTAC 58.460 37.037 0.00 0.00 46.64 2.50
1841 2561 5.523916 AGAATTGACATACAGATGTTACGCC 59.476 40.000 0.00 0.00 46.64 5.68
1847 2567 2.831685 ACAGATGTTACGCCTGTTCA 57.168 45.000 4.13 0.00 37.86 3.18
1856 2576 2.961522 ACGCCTGTTCATTTACAACG 57.038 45.000 0.00 0.00 35.19 4.10
1861 2581 3.002862 GCCTGTTCATTTACAACGACACA 59.997 43.478 0.00 0.00 0.00 3.72
1866 2586 7.322699 CCTGTTCATTTACAACGACACAAATAC 59.677 37.037 0.00 0.00 0.00 1.89
1901 2621 6.511416 ACAAATTTGATGTTTGTTCGATCCA 58.489 32.000 24.64 0.00 44.84 3.41
1907 2627 5.459768 TGATGTTTGTTCGATCCAAATGTG 58.540 37.500 12.25 0.00 34.59 3.21
1957 2678 5.815581 TGCCTTACATTTTGACACCTATCT 58.184 37.500 0.00 0.00 0.00 1.98
2015 2744 8.157476 TGCAATTAGGGGTAAGATTAGAATCTC 58.843 37.037 5.26 0.00 44.67 2.75
2038 2767 7.121611 TCTCCCGAAAAACTTTAAACAACTTCT 59.878 33.333 0.00 0.00 0.00 2.85
2042 2817 8.531530 CCGAAAAACTTTAAACAACTTCTCATG 58.468 33.333 0.00 0.00 0.00 3.07
2062 2840 3.889815 TGGCACATTAAGCAGCTTAGAT 58.110 40.909 14.58 8.95 0.00 1.98
2063 2841 3.628942 TGGCACATTAAGCAGCTTAGATG 59.371 43.478 22.68 22.68 0.00 2.90
2113 2891 5.126061 ACCTAATAGCAATGTCTTTTGGCAG 59.874 40.000 0.00 0.00 37.52 4.85
2114 2892 3.515330 ATAGCAATGTCTTTTGGCAGC 57.485 42.857 0.00 0.00 37.52 5.25
2115 2893 1.042229 AGCAATGTCTTTTGGCAGCA 58.958 45.000 0.00 0.00 37.52 4.41
2121 2899 2.875296 TGTCTTTTGGCAGCACCTAAT 58.125 42.857 0.00 0.00 40.22 1.73
2126 2904 5.064834 GTCTTTTGGCAGCACCTAATAGTAC 59.935 44.000 0.00 0.00 40.22 2.73
2127 2905 3.553828 TTGGCAGCACCTAATAGTACC 57.446 47.619 0.00 0.00 40.22 3.34
2135 2913 5.775701 CAGCACCTAATAGTACCAGGTCTAT 59.224 44.000 0.00 0.40 40.77 1.98
2142 2920 8.925338 CCTAATAGTACCAGGTCTATCAGTTTT 58.075 37.037 0.00 0.00 0.00 2.43
2187 2966 6.389830 TTGCAAATGAACAGTACTGATTGT 57.610 33.333 29.30 10.93 0.00 2.71
2193 2972 6.942532 ATGAACAGTACTGATTGTTGTTGT 57.057 33.333 29.30 0.21 35.79 3.32
2196 2975 7.915508 TGAACAGTACTGATTGTTGTTGTAAG 58.084 34.615 29.30 0.00 35.79 2.34
2203 2982 4.593157 TGATTGTTGTTGTAAGTGAACGC 58.407 39.130 0.00 0.00 0.00 4.84
2213 2992 6.019640 TGTTGTAAGTGAACGCTAACAGTAAC 60.020 38.462 0.00 0.00 0.00 2.50
2236 3024 1.304464 GCCTACCCCAGCTTGCTTT 60.304 57.895 0.00 0.00 0.00 3.51
2242 3030 2.728007 ACCCCAGCTTGCTTTCTTATC 58.272 47.619 0.00 0.00 0.00 1.75
2302 3090 4.800355 GGTAACAGGTACCGAGCG 57.200 61.111 6.18 0.00 43.08 5.03
2377 3165 2.048127 AAGCGCCAGTCCTTCGAC 60.048 61.111 2.29 0.00 39.50 4.20
2431 3219 2.094894 CCATGCTGACAAGAACATCGTC 59.905 50.000 0.00 0.00 0.00 4.20
2503 3291 1.707427 ACAGAGGATGCCAAGGAGTTT 59.293 47.619 0.00 0.00 0.00 2.66
2560 3348 0.036010 CTCTCGAGGCCACCAATGTT 60.036 55.000 13.56 0.00 0.00 2.71
2656 3444 2.294132 CTAACTCCGGCGGGAACTCC 62.294 65.000 27.98 0.00 43.27 3.85
2905 3694 5.538849 TTGTATCTGATTATACGGTGGCA 57.461 39.130 0.00 0.00 35.48 4.92
2956 3745 4.036380 GGATGTAATTAGCCCAACCTTTCG 59.964 45.833 0.00 0.00 0.00 3.46
2975 3764 1.597937 CGTGCTGGTTTTGCTGTTCTC 60.598 52.381 0.00 0.00 0.00 2.87
3067 3856 4.152402 ACAGAACGACATGAGAAAAATCGG 59.848 41.667 0.00 0.00 37.11 4.18
3130 3919 7.015195 TGCATGCATCCTACTAGTTGTATAGAA 59.985 37.037 18.46 0.00 0.00 2.10
3170 3959 9.562583 TTGTTTTGTTTTATATCCGCTTGATAC 57.437 29.630 0.00 0.00 38.75 2.24
3446 4235 4.058817 CCTTTGGTTGAGATATAGACGGC 58.941 47.826 0.00 0.00 0.00 5.68
3512 4301 5.618236 ACCCCGTTAATTCTAAATCCTAGC 58.382 41.667 0.00 0.00 0.00 3.42
3563 4352 4.919754 GCTAAACATCAAGCACCTGAAAAG 59.080 41.667 0.00 0.00 38.63 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 2.786539 TTCGGTGCCTGCTAGTGCTG 62.787 60.000 0.00 0.00 40.48 4.41
78 79 2.046314 GGCTTTCGGTGCCTGCTA 60.046 61.111 6.93 0.00 46.38 3.49
89 90 1.474077 CAATACAGCAGGGTGGCTTTC 59.526 52.381 3.33 0.00 42.71 2.62
98 99 3.346315 TCATTGTGGACAATACAGCAGG 58.654 45.455 4.71 0.00 44.10 4.85
126 127 1.310216 GGGGAATGCACGGTTACCAC 61.310 60.000 1.13 0.00 30.68 4.16
127 128 1.001887 GGGGAATGCACGGTTACCA 60.002 57.895 1.13 0.00 30.68 3.25
135 136 1.024579 ATCGTTCACGGGGAATGCAC 61.025 55.000 7.34 0.00 41.42 4.57
140 149 0.530744 CTCTCATCGTTCACGGGGAA 59.469 55.000 0.00 0.00 40.29 3.97
156 165 0.118144 ACCTCCTGCTTCCTTCCTCT 59.882 55.000 0.00 0.00 0.00 3.69
163 172 1.691434 CATCTCCTACCTCCTGCTTCC 59.309 57.143 0.00 0.00 0.00 3.46
164 173 1.691434 CCATCTCCTACCTCCTGCTTC 59.309 57.143 0.00 0.00 0.00 3.86
204 213 4.385825 ACCTTGTTGCTTCATTCGACTTA 58.614 39.130 0.00 0.00 0.00 2.24
249 259 1.285950 GCAGCGGTTCTGGTTTTCC 59.714 57.895 0.00 0.00 43.06 3.13
341 351 9.646336 CGAGCTTATAACGCATTAAAATACTTT 57.354 29.630 8.84 0.00 0.00 2.66
342 352 8.823818 ACGAGCTTATAACGCATTAAAATACTT 58.176 29.630 0.00 0.00 0.00 2.24
343 353 8.361592 ACGAGCTTATAACGCATTAAAATACT 57.638 30.769 0.00 0.00 0.00 2.12
344 354 8.982925 AACGAGCTTATAACGCATTAAAATAC 57.017 30.769 0.00 0.00 0.00 1.89
345 355 7.999878 CGAACGAGCTTATAACGCATTAAAATA 59.000 33.333 0.00 0.00 0.00 1.40
346 356 6.844279 CGAACGAGCTTATAACGCATTAAAAT 59.156 34.615 0.00 0.00 0.00 1.82
347 357 6.179880 CGAACGAGCTTATAACGCATTAAAA 58.820 36.000 0.00 0.00 0.00 1.52
348 358 5.720239 CGAACGAGCTTATAACGCATTAAA 58.280 37.500 0.00 0.00 0.00 1.52
349 359 4.317558 GCGAACGAGCTTATAACGCATTAA 60.318 41.667 16.61 0.00 43.18 1.40
350 360 3.180980 GCGAACGAGCTTATAACGCATTA 59.819 43.478 16.61 0.00 43.18 1.90
351 361 2.034001 GCGAACGAGCTTATAACGCATT 60.034 45.455 16.61 2.03 43.18 3.56
352 362 1.521423 GCGAACGAGCTTATAACGCAT 59.479 47.619 16.61 0.00 43.18 4.73
353 363 0.918619 GCGAACGAGCTTATAACGCA 59.081 50.000 16.61 0.00 43.18 5.24
354 364 0.918619 TGCGAACGAGCTTATAACGC 59.081 50.000 15.34 15.34 43.79 4.84
355 365 2.940137 GTTGCGAACGAGCTTATAACG 58.060 47.619 0.00 0.00 38.13 3.18
427 438 1.658994 AAAACGGTGCTTGTTCTCGA 58.341 45.000 0.00 0.00 0.00 4.04
449 460 6.848696 ACAGTGCCTGTTCTTTTTGGTAAAAG 60.849 38.462 2.38 4.42 42.59 2.27
481 492 5.069914 TGTTGCCTTCTCTCTTGTACTTGTA 59.930 40.000 0.00 0.00 0.00 2.41
482 493 4.141711 TGTTGCCTTCTCTCTTGTACTTGT 60.142 41.667 0.00 0.00 0.00 3.16
483 494 4.380531 TGTTGCCTTCTCTCTTGTACTTG 58.619 43.478 0.00 0.00 0.00 3.16
484 495 4.636249 CTGTTGCCTTCTCTCTTGTACTT 58.364 43.478 0.00 0.00 0.00 2.24
485 496 3.556004 GCTGTTGCCTTCTCTCTTGTACT 60.556 47.826 0.00 0.00 0.00 2.73
486 497 2.739379 GCTGTTGCCTTCTCTCTTGTAC 59.261 50.000 0.00 0.00 0.00 2.90
487 498 2.368548 TGCTGTTGCCTTCTCTCTTGTA 59.631 45.455 0.00 0.00 38.71 2.41
532 543 4.394439 AAAATGTACCGGTGCTGTTTTT 57.606 36.364 23.67 20.41 0.00 1.94
533 544 4.581409 ACTAAAATGTACCGGTGCTGTTTT 59.419 37.500 27.65 27.65 0.00 2.43
534 545 4.139038 ACTAAAATGTACCGGTGCTGTTT 58.861 39.130 23.67 22.12 0.00 2.83
555 977 2.093658 CCACCCACACCAGATGTACTAC 60.094 54.545 0.00 0.00 40.64 2.73
732 1164 1.002069 ATGATGATGGTGGTGGTGGT 58.998 50.000 0.00 0.00 0.00 4.16
881 1324 3.454858 TCTCCTTCCTGGCTACTGAAAT 58.545 45.455 0.00 0.00 35.26 2.17
909 1357 3.595108 GACAGAAAACGGCGCCTGC 62.595 63.158 26.68 4.02 41.71 4.85
941 1416 2.438021 ACAACCAAGACTAGACCAGCAA 59.562 45.455 0.00 0.00 0.00 3.91
988 1463 0.825840 CGAGACATCTCCCTCCCTCC 60.826 65.000 3.30 0.00 39.79 4.30
1310 1808 9.407380 TGCTTCTCCAATACAATACAATACAAT 57.593 29.630 0.00 0.00 0.00 2.71
1330 1828 9.838339 GGCCTATATGTACAATAATATGCTTCT 57.162 33.333 0.00 0.00 0.00 2.85
1331 1829 9.613428 TGGCCTATATGTACAATAATATGCTTC 57.387 33.333 3.32 0.00 0.00 3.86
1346 1844 6.351371 GCTGTAGTACATCATGGCCTATATGT 60.351 42.308 17.57 17.57 36.56 2.29
1363 1872 2.569059 CGGGCTAGTAGTGCTGTAGTA 58.431 52.381 0.00 0.00 0.00 1.82
1367 1876 2.893398 GCGGGCTAGTAGTGCTGT 59.107 61.111 0.00 0.00 0.00 4.40
1381 1890 5.287226 ACAAGAAGATAATTACTACCGCGG 58.713 41.667 26.86 26.86 0.00 6.46
1436 1949 5.931146 GCATTCCACATTTCCATACAACAAA 59.069 36.000 0.00 0.00 0.00 2.83
1444 1957 2.463752 AGCTGCATTCCACATTTCCAT 58.536 42.857 1.02 0.00 0.00 3.41
1450 1963 0.549950 AGCCTAGCTGCATTCCACAT 59.450 50.000 1.02 0.00 37.57 3.21
1451 1964 0.329261 AAGCCTAGCTGCATTCCACA 59.671 50.000 1.02 0.00 39.62 4.17
1452 1965 1.020437 GAAGCCTAGCTGCATTCCAC 58.980 55.000 1.02 0.00 39.62 4.02
1453 1966 0.914644 AGAAGCCTAGCTGCATTCCA 59.085 50.000 1.02 0.00 39.62 3.53
1454 1967 2.103941 ACTAGAAGCCTAGCTGCATTCC 59.896 50.000 1.02 0.00 44.87 3.01
1455 1968 3.467374 ACTAGAAGCCTAGCTGCATTC 57.533 47.619 1.02 0.00 44.87 2.67
1456 1969 3.922171 AACTAGAAGCCTAGCTGCATT 57.078 42.857 1.02 0.00 44.87 3.56
1457 1970 3.432890 GGAAACTAGAAGCCTAGCTGCAT 60.433 47.826 1.02 0.00 44.87 3.96
1471 1984 9.141400 GCGAAACCAATATATAGAGGAAACTAG 57.859 37.037 9.56 0.00 44.43 2.57
1475 1988 5.407387 GCGCGAAACCAATATATAGAGGAAA 59.593 40.000 12.10 0.00 0.00 3.13
1476 1989 4.927425 GCGCGAAACCAATATATAGAGGAA 59.073 41.667 12.10 0.00 0.00 3.36
1478 1991 4.242475 TGCGCGAAACCAATATATAGAGG 58.758 43.478 12.10 2.51 0.00 3.69
1479 1992 5.220472 CCATGCGCGAAACCAATATATAGAG 60.220 44.000 12.10 0.00 0.00 2.43
1480 1993 4.629634 CCATGCGCGAAACCAATATATAGA 59.370 41.667 12.10 0.00 0.00 1.98
1483 1996 3.146066 ACCATGCGCGAAACCAATATAT 58.854 40.909 12.10 0.00 0.00 0.86
1485 1998 1.333619 GACCATGCGCGAAACCAATAT 59.666 47.619 12.10 0.00 0.00 1.28
1507 2020 2.290323 ACTATTGCACTGACCAAGGACC 60.290 50.000 0.00 0.00 0.00 4.46
1525 2038 6.686378 GCAGAGACCAAACATATCCATCACTA 60.686 42.308 0.00 0.00 0.00 2.74
1536 2049 6.392354 CAACATAATTGCAGAGACCAAACAT 58.608 36.000 0.00 0.00 0.00 2.71
1558 2104 7.759489 AAAGCAGACAGTGTATTAATTCCAA 57.241 32.000 0.00 0.00 0.00 3.53
1632 2352 5.519927 CCAATTCTGAACATAATTTTCGGGC 59.480 40.000 0.00 0.00 31.26 6.13
1633 2353 6.042143 CCCAATTCTGAACATAATTTTCGGG 58.958 40.000 0.00 0.00 31.26 5.14
1648 2368 5.316987 AGAACTAGAAACACCCCAATTCTG 58.683 41.667 0.00 0.00 35.22 3.02
1656 2376 6.937392 AGTTAGATGAGAACTAGAAACACCC 58.063 40.000 0.00 0.00 35.36 4.61
1657 2377 7.036829 GGAGTTAGATGAGAACTAGAAACACC 58.963 42.308 0.00 0.00 37.27 4.16
1658 2378 7.832769 AGGAGTTAGATGAGAACTAGAAACAC 58.167 38.462 0.00 0.00 37.27 3.32
1661 2381 8.958506 GTGTAGGAGTTAGATGAGAACTAGAAA 58.041 37.037 0.00 0.00 37.27 2.52
1662 2382 7.556996 GGTGTAGGAGTTAGATGAGAACTAGAA 59.443 40.741 0.00 0.00 37.27 2.10
1663 2383 7.055378 GGTGTAGGAGTTAGATGAGAACTAGA 58.945 42.308 0.00 0.00 37.27 2.43
1664 2384 6.017770 CGGTGTAGGAGTTAGATGAGAACTAG 60.018 46.154 0.00 0.00 37.27 2.57
1665 2385 5.821470 CGGTGTAGGAGTTAGATGAGAACTA 59.179 44.000 0.00 0.00 37.27 2.24
1666 2386 4.641094 CGGTGTAGGAGTTAGATGAGAACT 59.359 45.833 0.00 0.00 39.85 3.01
1667 2387 4.398673 ACGGTGTAGGAGTTAGATGAGAAC 59.601 45.833 0.00 0.00 0.00 3.01
1668 2388 4.597004 ACGGTGTAGGAGTTAGATGAGAA 58.403 43.478 0.00 0.00 0.00 2.87
1669 2389 4.232188 ACGGTGTAGGAGTTAGATGAGA 57.768 45.455 0.00 0.00 0.00 3.27
1670 2390 4.440250 CCAACGGTGTAGGAGTTAGATGAG 60.440 50.000 0.00 0.00 0.00 2.90
1671 2391 3.446161 CCAACGGTGTAGGAGTTAGATGA 59.554 47.826 0.00 0.00 0.00 2.92
1672 2392 3.446161 TCCAACGGTGTAGGAGTTAGATG 59.554 47.826 0.00 0.00 0.00 2.90
1673 2393 3.705051 TCCAACGGTGTAGGAGTTAGAT 58.295 45.455 0.00 0.00 0.00 1.98
1674 2394 3.159213 TCCAACGGTGTAGGAGTTAGA 57.841 47.619 0.00 0.00 0.00 2.10
1675 2395 3.700038 AGATCCAACGGTGTAGGAGTTAG 59.300 47.826 0.00 0.00 34.40 2.34
1676 2396 3.705051 AGATCCAACGGTGTAGGAGTTA 58.295 45.455 0.00 0.00 34.40 2.24
1677 2397 2.537143 AGATCCAACGGTGTAGGAGTT 58.463 47.619 0.00 0.00 34.40 3.01
1678 2398 2.233305 AGATCCAACGGTGTAGGAGT 57.767 50.000 0.00 0.00 34.40 3.85
1679 2399 3.446161 TGTAAGATCCAACGGTGTAGGAG 59.554 47.826 0.00 0.00 34.40 3.69
1680 2400 3.433343 TGTAAGATCCAACGGTGTAGGA 58.567 45.455 0.00 0.00 35.59 2.94
1681 2401 3.880047 TGTAAGATCCAACGGTGTAGG 57.120 47.619 0.00 0.00 0.00 3.18
1682 2402 5.006153 TCATGTAAGATCCAACGGTGTAG 57.994 43.478 0.00 0.00 0.00 2.74
1683 2403 5.186215 TCTTCATGTAAGATCCAACGGTGTA 59.814 40.000 0.00 0.00 39.36 2.90
1684 2404 3.973206 TCATGTAAGATCCAACGGTGT 57.027 42.857 0.00 0.00 0.00 4.16
1685 2405 4.503910 TCTTCATGTAAGATCCAACGGTG 58.496 43.478 0.00 0.00 39.36 4.94
1686 2406 4.819105 TCTTCATGTAAGATCCAACGGT 57.181 40.909 0.00 0.00 39.36 4.83
1696 2416 4.137116 TCCCCACGAATCTTCATGTAAG 57.863 45.455 0.00 0.00 36.45 2.34
1697 2417 4.771114 ATCCCCACGAATCTTCATGTAA 57.229 40.909 0.00 0.00 0.00 2.41
1698 2418 4.408921 AGAATCCCCACGAATCTTCATGTA 59.591 41.667 0.00 0.00 24.78 2.29
1699 2419 3.200825 AGAATCCCCACGAATCTTCATGT 59.799 43.478 0.00 0.00 24.78 3.21
1700 2420 3.813443 AGAATCCCCACGAATCTTCATG 58.187 45.455 0.00 0.00 24.78 3.07
1701 2421 4.510167 AAGAATCCCCACGAATCTTCAT 57.490 40.909 0.00 0.00 36.17 2.57
1702 2422 4.019321 AGAAAGAATCCCCACGAATCTTCA 60.019 41.667 0.00 0.00 39.39 3.02
1703 2423 4.518249 AGAAAGAATCCCCACGAATCTTC 58.482 43.478 0.00 0.00 39.39 2.87
1704 2424 4.576330 AGAAAGAATCCCCACGAATCTT 57.424 40.909 0.00 0.00 41.62 2.40
1705 2425 4.576330 AAGAAAGAATCCCCACGAATCT 57.424 40.909 0.00 0.00 31.65 2.40
1706 2426 5.644977 AAAAGAAAGAATCCCCACGAATC 57.355 39.130 0.00 0.00 0.00 2.52
1707 2427 7.718334 AATAAAAGAAAGAATCCCCACGAAT 57.282 32.000 0.00 0.00 0.00 3.34
1708 2428 7.533289 AAATAAAAGAAAGAATCCCCACGAA 57.467 32.000 0.00 0.00 0.00 3.85
1709 2429 8.817092 ATAAATAAAAGAAAGAATCCCCACGA 57.183 30.769 0.00 0.00 0.00 4.35
1710 2430 9.869757 AAATAAATAAAAGAAAGAATCCCCACG 57.130 29.630 0.00 0.00 0.00 4.94
1738 2458 9.575868 TCCTACACTATTTGATTAACCAAACAA 57.424 29.630 0.00 0.00 38.65 2.83
1739 2459 9.226606 CTCCTACACTATTTGATTAACCAAACA 57.773 33.333 0.00 0.00 38.65 2.83
1740 2460 9.227777 ACTCCTACACTATTTGATTAACCAAAC 57.772 33.333 0.00 0.00 38.65 2.93
1741 2461 9.802039 AACTCCTACACTATTTGATTAACCAAA 57.198 29.630 0.00 0.00 39.93 3.28
1749 2469 9.647918 TCTCATCTAACTCCTACACTATTTGAT 57.352 33.333 0.00 0.00 0.00 2.57
1750 2470 8.904834 GTCTCATCTAACTCCTACACTATTTGA 58.095 37.037 0.00 0.00 0.00 2.69
1751 2471 8.908903 AGTCTCATCTAACTCCTACACTATTTG 58.091 37.037 0.00 0.00 0.00 2.32
1752 2472 9.482175 AAGTCTCATCTAACTCCTACACTATTT 57.518 33.333 0.00 0.00 0.00 1.40
1753 2473 9.482175 AAAGTCTCATCTAACTCCTACACTATT 57.518 33.333 0.00 0.00 0.00 1.73
1754 2474 8.908903 CAAAGTCTCATCTAACTCCTACACTAT 58.091 37.037 0.00 0.00 0.00 2.12
1755 2475 7.889073 ACAAAGTCTCATCTAACTCCTACACTA 59.111 37.037 0.00 0.00 0.00 2.74
1756 2476 6.722129 ACAAAGTCTCATCTAACTCCTACACT 59.278 38.462 0.00 0.00 0.00 3.55
1757 2477 6.926313 ACAAAGTCTCATCTAACTCCTACAC 58.074 40.000 0.00 0.00 0.00 2.90
1758 2478 7.540474 AACAAAGTCTCATCTAACTCCTACA 57.460 36.000 0.00 0.00 0.00 2.74
1761 2481 9.660180 GAATTAACAAAGTCTCATCTAACTCCT 57.340 33.333 0.00 0.00 0.00 3.69
1762 2482 9.660180 AGAATTAACAAAGTCTCATCTAACTCC 57.340 33.333 0.00 0.00 0.00 3.85
1788 2508 7.816513 CGGATTTGCTAATTCTCATCTAGATGA 59.183 37.037 29.17 29.17 44.83 2.92
1789 2509 7.601886 ACGGATTTGCTAATTCTCATCTAGATG 59.398 37.037 24.32 24.32 40.09 2.90
1790 2510 7.675062 ACGGATTTGCTAATTCTCATCTAGAT 58.325 34.615 0.00 0.00 33.05 1.98
1791 2511 7.055667 ACGGATTTGCTAATTCTCATCTAGA 57.944 36.000 0.00 0.00 0.00 2.43
1792 2512 7.721286 AACGGATTTGCTAATTCTCATCTAG 57.279 36.000 0.00 0.00 0.00 2.43
1793 2513 8.638873 TCTAACGGATTTGCTAATTCTCATCTA 58.361 33.333 0.00 0.00 0.00 1.98
1794 2514 7.500992 TCTAACGGATTTGCTAATTCTCATCT 58.499 34.615 0.00 0.00 0.00 2.90
1795 2515 7.715265 TCTAACGGATTTGCTAATTCTCATC 57.285 36.000 0.00 0.00 0.00 2.92
1796 2516 8.682936 ATTCTAACGGATTTGCTAATTCTCAT 57.317 30.769 0.00 0.00 0.00 2.90
1797 2517 8.397906 CAATTCTAACGGATTTGCTAATTCTCA 58.602 33.333 0.00 0.00 31.48 3.27
1798 2518 8.612619 TCAATTCTAACGGATTTGCTAATTCTC 58.387 33.333 0.00 0.00 36.08 2.87
1799 2519 8.398665 GTCAATTCTAACGGATTTGCTAATTCT 58.601 33.333 0.00 0.00 36.08 2.40
1800 2520 8.181573 TGTCAATTCTAACGGATTTGCTAATTC 58.818 33.333 0.00 0.00 36.08 2.17
1801 2521 8.050778 TGTCAATTCTAACGGATTTGCTAATT 57.949 30.769 0.00 0.00 36.08 1.40
1802 2522 7.624360 TGTCAATTCTAACGGATTTGCTAAT 57.376 32.000 0.00 0.00 36.08 1.73
1803 2523 7.624360 ATGTCAATTCTAACGGATTTGCTAA 57.376 32.000 0.00 0.00 36.08 3.09
1804 2524 7.766738 TGTATGTCAATTCTAACGGATTTGCTA 59.233 33.333 0.00 0.00 36.08 3.49
1805 2525 6.597672 TGTATGTCAATTCTAACGGATTTGCT 59.402 34.615 0.00 0.00 36.08 3.91
1806 2526 6.781138 TGTATGTCAATTCTAACGGATTTGC 58.219 36.000 0.00 0.00 36.08 3.68
1807 2527 8.196802 TCTGTATGTCAATTCTAACGGATTTG 57.803 34.615 0.00 0.00 36.92 2.32
1808 2528 8.830580 CATCTGTATGTCAATTCTAACGGATTT 58.169 33.333 0.00 0.00 32.12 2.17
1809 2529 7.987458 ACATCTGTATGTCAATTCTAACGGATT 59.013 33.333 0.00 0.00 42.92 3.01
1810 2530 7.500992 ACATCTGTATGTCAATTCTAACGGAT 58.499 34.615 0.00 0.00 42.92 4.18
1811 2531 6.873997 ACATCTGTATGTCAATTCTAACGGA 58.126 36.000 0.00 0.00 42.92 4.69
1812 2532 7.539712 AACATCTGTATGTCAATTCTAACGG 57.460 36.000 0.00 0.00 45.79 4.44
1813 2533 8.259872 CGTAACATCTGTATGTCAATTCTAACG 58.740 37.037 0.00 0.00 45.79 3.18
1814 2534 8.056571 GCGTAACATCTGTATGTCAATTCTAAC 58.943 37.037 0.00 0.00 45.79 2.34
1815 2535 7.223971 GGCGTAACATCTGTATGTCAATTCTAA 59.776 37.037 0.00 0.00 45.79 2.10
1816 2536 6.700081 GGCGTAACATCTGTATGTCAATTCTA 59.300 38.462 0.00 0.00 45.79 2.10
1817 2537 5.523916 GGCGTAACATCTGTATGTCAATTCT 59.476 40.000 0.00 0.00 45.79 2.40
1818 2538 5.523916 AGGCGTAACATCTGTATGTCAATTC 59.476 40.000 0.00 0.00 45.79 2.17
1819 2539 5.294306 CAGGCGTAACATCTGTATGTCAATT 59.706 40.000 0.00 0.00 45.79 2.32
1820 2540 4.811024 CAGGCGTAACATCTGTATGTCAAT 59.189 41.667 0.00 0.00 45.79 2.57
1821 2541 4.180817 CAGGCGTAACATCTGTATGTCAA 58.819 43.478 0.00 0.00 45.79 3.18
1822 2542 3.194755 ACAGGCGTAACATCTGTATGTCA 59.805 43.478 0.00 0.00 45.79 3.58
1823 2543 3.782046 ACAGGCGTAACATCTGTATGTC 58.218 45.455 0.00 0.00 45.79 3.06
1825 2545 4.180817 TGAACAGGCGTAACATCTGTATG 58.819 43.478 0.00 0.00 40.41 2.39
1826 2546 4.465632 TGAACAGGCGTAACATCTGTAT 57.534 40.909 0.00 0.00 40.41 2.29
1838 2558 2.222213 TGTCGTTGTAAATGAACAGGCG 59.778 45.455 0.00 0.00 44.67 5.52
1841 2561 8.067784 AGTATTTGTGTCGTTGTAAATGAACAG 58.932 33.333 0.00 0.00 44.67 3.16
1847 2567 7.499321 TGGAAGTATTTGTGTCGTTGTAAAT 57.501 32.000 0.00 0.00 0.00 1.40
1856 2576 6.811253 TGTTACCATGGAAGTATTTGTGTC 57.189 37.500 21.47 0.00 0.00 3.67
1866 2586 8.497554 CAAACATCAAATTTGTTACCATGGAAG 58.502 33.333 21.47 4.75 36.32 3.46
1900 2620 5.823209 TGCAACTATCTGATCCACATTTG 57.177 39.130 0.00 0.00 0.00 2.32
1901 2621 6.124340 TGATGCAACTATCTGATCCACATTT 58.876 36.000 0.00 0.00 0.00 2.32
1907 2627 6.313411 GCTATTCTGATGCAACTATCTGATCC 59.687 42.308 0.00 0.00 35.73 3.36
1908 2628 6.872547 TGCTATTCTGATGCAACTATCTGATC 59.127 38.462 0.00 0.00 35.73 2.92
1909 2629 6.766429 TGCTATTCTGATGCAACTATCTGAT 58.234 36.000 0.00 0.00 35.73 2.90
1910 2630 6.165700 TGCTATTCTGATGCAACTATCTGA 57.834 37.500 0.00 0.00 34.51 3.27
1911 2631 6.620949 GCATGCTATTCTGATGCAACTATCTG 60.621 42.308 11.37 0.00 41.78 2.90
1912 2632 5.411977 GCATGCTATTCTGATGCAACTATCT 59.588 40.000 11.37 0.00 41.78 1.98
1914 2634 4.458295 GGCATGCTATTCTGATGCAACTAT 59.542 41.667 18.92 0.00 43.58 2.12
1915 2635 3.817084 GGCATGCTATTCTGATGCAACTA 59.183 43.478 18.92 0.00 43.58 2.24
1916 2636 2.621998 GGCATGCTATTCTGATGCAACT 59.378 45.455 18.92 0.00 43.58 3.16
1920 2641 3.817084 TGTAAGGCATGCTATTCTGATGC 59.183 43.478 18.92 0.00 41.51 3.91
2015 2744 7.030768 TGAGAAGTTGTTTAAAGTTTTTCGGG 58.969 34.615 0.00 0.00 0.00 5.14
2030 2759 4.082571 GCTTAATGTGCCATGAGAAGTTGT 60.083 41.667 0.00 0.00 0.00 3.32
2038 2767 2.133281 AGCTGCTTAATGTGCCATGA 57.867 45.000 0.00 0.00 0.00 3.07
2042 2817 3.879295 TCATCTAAGCTGCTTAATGTGCC 59.121 43.478 25.80 0.00 0.00 5.01
2062 2840 0.250038 GCTGATGCCGAGGCTTATCA 60.250 55.000 15.75 14.74 42.51 2.15
2063 2841 2.537863 GCTGATGCCGAGGCTTATC 58.462 57.895 15.75 11.02 42.51 1.75
2082 2860 5.555017 AGACATTGCTATTAGGTGCCATAG 58.445 41.667 0.00 0.00 0.00 2.23
2098 2876 1.342174 AGGTGCTGCCAAAAGACATTG 59.658 47.619 0.00 0.00 40.61 2.82
2113 2891 5.773680 TGATAGACCTGGTACTATTAGGTGC 59.226 44.000 15.36 7.76 44.51 5.01
2114 2892 7.005296 ACTGATAGACCTGGTACTATTAGGTG 58.995 42.308 24.61 12.95 44.51 4.00
2157 2935 9.462174 TCAGTACTGTTCATTTGCAAAATTAAG 57.538 29.630 21.99 12.35 0.00 1.85
2162 2940 7.264221 ACAATCAGTACTGTTCATTTGCAAAA 58.736 30.769 21.99 0.00 0.00 2.44
2170 2949 6.942532 ACAACAACAATCAGTACTGTTCAT 57.057 33.333 21.99 6.25 33.51 2.57
2176 2955 7.254319 CGTTCACTTACAACAACAATCAGTACT 60.254 37.037 0.00 0.00 0.00 2.73
2187 2966 4.871557 ACTGTTAGCGTTCACTTACAACAA 59.128 37.500 0.00 0.00 29.60 2.83
2193 2972 7.062605 GCTATTGTTACTGTTAGCGTTCACTTA 59.937 37.037 0.00 0.00 0.00 2.24
2196 2975 5.445540 GGCTATTGTTACTGTTAGCGTTCAC 60.446 44.000 3.21 0.00 38.32 3.18
2203 2982 5.129815 TGGGGTAGGCTATTGTTACTGTTAG 59.870 44.000 0.00 0.00 0.00 2.34
2213 2992 1.972872 CAAGCTGGGGTAGGCTATTG 58.027 55.000 0.00 0.00 37.87 1.90
2236 3024 8.675705 TGTTGAAAGTGAACAATCAGATAAGA 57.324 30.769 0.00 0.00 35.88 2.10
2242 3030 9.173939 GTTTAGATGTTGAAAGTGAACAATCAG 57.826 33.333 0.00 0.00 36.90 2.90
2302 3090 3.094572 TCTGTAGTAGGCACTGGTTACC 58.905 50.000 0.00 0.00 41.52 2.85
2377 3165 4.935495 AGCCACCGCGCCATATGG 62.935 66.667 18.07 18.07 41.18 2.74
2431 3219 1.957668 TGTTCCCGATGAGCATGATG 58.042 50.000 0.00 0.00 0.00 3.07
2560 3348 1.280133 CCTGTCATGAAGGCCTTCTCA 59.720 52.381 38.38 28.81 40.14 3.27
2656 3444 1.229428 TCGTTCCTTTCAGCAAGCTG 58.771 50.000 15.67 15.67 44.86 4.24
2881 3670 6.530120 TGCCACCGTATAATCAGATACAAAT 58.470 36.000 0.00 0.00 32.70 2.32
2956 3745 1.269257 GGAGAACAGCAAAACCAGCAC 60.269 52.381 0.00 0.00 0.00 4.40
3067 3856 0.393808 TTTGTATCAGCCGGCCCTTC 60.394 55.000 26.15 11.04 0.00 3.46
3130 3919 0.258774 AAACAAGCTCACACCCAGGT 59.741 50.000 0.00 0.00 0.00 4.00
3170 3959 6.073222 GGGTACTTTATCAACTCATAATGCCG 60.073 42.308 0.00 0.00 0.00 5.69
3226 4015 5.036117 ACCAACATTGACAGTACTCTTGT 57.964 39.130 0.00 0.00 0.00 3.16
3446 4235 6.970484 ACACTACAAAATTACAGCCAAGAAG 58.030 36.000 0.00 0.00 0.00 2.85
3491 4280 5.469084 GGTGCTAGGATTTAGAATTAACGGG 59.531 44.000 0.00 0.00 0.00 5.28
3512 4301 4.156008 GCGGAAATATAATGGCTTAGGGTG 59.844 45.833 0.00 0.00 0.00 4.61
3611 4401 1.201429 ATGGAGTCCACGGCCTTTCT 61.201 55.000 15.86 0.00 35.80 2.52
3613 4403 1.002134 CATGGAGTCCACGGCCTTT 60.002 57.895 15.86 0.00 35.80 3.11
3614 4404 2.671070 CATGGAGTCCACGGCCTT 59.329 61.111 15.86 0.00 35.80 4.35
3644 4434 3.110178 GGTTCCCGCTCGTTCACG 61.110 66.667 0.00 0.00 41.45 4.35
3691 4481 3.935993 CCAGTCAGGTTTCGGACAT 57.064 52.632 0.00 0.00 39.92 3.06
3702 4492 2.343758 CCGACCCACACCAGTCAG 59.656 66.667 0.00 0.00 33.08 3.51


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

AutoCloner maintained by Alex Coulton.