Multiple sequence alignment - TraesCS5B01G107700

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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 TraesCS5B01G107700 chr5B 100.000 3429 0 0 1 3429 146808755 146805327 0.000000e+00 6333
1 TraesCS5B01G107700 chr5B 90.435 115 10 1 1730 1843 586876169 586876055 2.130000e-32 150
2 TraesCS5B01G107700 chr5A 88.422 1477 64 49 55 1480 170098325 170099745 0.000000e+00 1681
3 TraesCS5B01G107700 chr5A 85.420 727 51 23 1466 2184 170099765 170100444 0.000000e+00 704
4 TraesCS5B01G107700 chr5A 83.187 571 56 19 2196 2761 170100487 170101022 1.430000e-133 486
5 TraesCS5B01G107700 chr5A 90.435 115 10 1 1730 1843 597850030 597849916 2.130000e-32 150
6 TraesCS5B01G107700 chr5A 87.500 104 9 3 1740 1843 415195433 415195334 2.160000e-22 117
7 TraesCS5B01G107700 chr5D 93.454 1054 41 7 234 1282 135062639 135061609 0.000000e+00 1539
8 TraesCS5B01G107700 chr5D 84.274 1399 99 52 1466 2821 135061436 135060116 0.000000e+00 1253
9 TraesCS5B01G107700 chr5D 88.889 378 22 11 3068 3429 135059056 135058683 6.750000e-122 448
10 TraesCS5B01G107700 chr5D 89.516 248 18 1 1 240 135062920 135062673 1.200000e-79 307
11 TraesCS5B01G107700 chr2A 90.164 122 10 2 1722 1843 459446606 459446725 1.270000e-34 158
12 TraesCS5B01G107700 chr2A 89.344 122 10 3 1722 1843 459507727 459507845 2.130000e-32 150
13 TraesCS5B01G107700 chr2A 88.525 122 12 2 1722 1843 459545524 459545643 2.760000e-31 147
14 TraesCS5B01G107700 chr6D 98.851 87 1 0 2965 3051 166796209 166796295 4.580000e-34 156
15 TraesCS5B01G107700 chr3D 97.778 90 2 0 2962 3051 127344085 127344174 4.580000e-34 156
16 TraesCS5B01G107700 chr3D 86.538 104 10 3 1740 1843 126612539 126612440 1.010000e-20 111
17 TraesCS5B01G107700 chr4A 94.949 99 4 1 2958 3056 166305196 166305293 1.650000e-33 154
18 TraesCS5B01G107700 chr7A 95.699 93 4 0 2965 3057 111835322 111835230 2.130000e-32 150
19 TraesCS5B01G107700 chr6A 94.000 100 5 1 2966 3064 7122666 7122765 2.130000e-32 150
20 TraesCS5B01G107700 chr3B 89.831 118 6 6 2945 3058 22211100 22211215 2.760000e-31 147
21 TraesCS5B01G107700 chr3B 92.308 104 6 2 2961 3063 264012977 264013079 2.760000e-31 147
22 TraesCS5B01G107700 chr3B 87.903 124 14 1 2966 3089 283360477 283360355 9.920000e-31 145
23 TraesCS5B01G107700 chr3B 87.903 124 14 1 2966 3089 283376091 283375969 9.920000e-31 145


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 TraesCS5B01G107700 chr5B 146805327 146808755 3428 True 6333.00 6333 100.000000 1 3429 1 chr5B.!!$R1 3428
1 TraesCS5B01G107700 chr5A 170098325 170101022 2697 False 957.00 1681 85.676333 55 2761 3 chr5A.!!$F1 2706
2 TraesCS5B01G107700 chr5D 135058683 135062920 4237 True 886.75 1539 89.033250 1 3429 4 chr5D.!!$R1 3428

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
203 212 0.035458 GTATGGGAGCTGGGGATTCG 59.965 60.0 0.0 0.0 0.0 3.34 F
1382 1455 0.179070 TGTTGCGGTTGTCTGTGCTA 60.179 50.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1462 0.028505 CATGTAGCCAACTGCATCGC 59.971 55.0 0.00 0.0 44.92 4.58 R
2870 3417 0.393537 CAGCCATGGGTTCAGTCCTC 60.394 60.0 15.37 0.0 0.00 3.71 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
18 19 2.162716 GGTGGCAACTCACGTCATC 58.837 57.895 0.00 0.00 38.46 2.92
20 21 1.071605 GTGGCAACTCACGTCATCTC 58.928 55.000 0.00 0.00 37.61 2.75
22 23 1.078759 GGCAACTCACGTCATCTCCG 61.079 60.000 0.00 0.00 0.00 4.63
57 58 3.684305 CGAAAGCTGTGATGTCAACCATA 59.316 43.478 0.00 0.00 32.56 2.74
105 114 4.761235 TCGAGTCACAACTTAGTACCAG 57.239 45.455 0.00 0.00 35.28 4.00
186 195 7.573710 AGCCATATTTCACCATAACTGAAGTA 58.426 34.615 0.00 0.00 0.00 2.24
192 201 5.614324 TCACCATAACTGAAGTATGGGAG 57.386 43.478 13.55 7.00 43.70 4.30
195 204 4.141620 ACCATAACTGAAGTATGGGAGCTG 60.142 45.833 13.55 0.00 43.70 4.24
203 212 0.035458 GTATGGGAGCTGGGGATTCG 59.965 60.000 0.00 0.00 0.00 3.34
351 407 2.292521 ACCTAGAGCACTGGGAATCAGA 60.293 50.000 20.13 0.00 45.87 3.27
406 462 2.036256 GGCATTGCAGGGAGGTGT 59.964 61.111 11.39 0.00 0.00 4.16
519 575 0.967887 TCGGCACCTTCCTCTCTCTG 60.968 60.000 0.00 0.00 0.00 3.35
538 594 3.685214 CTTCCCCTGCGACGACGAG 62.685 68.421 12.29 5.69 42.66 4.18
578 636 4.876107 CAGTGGAGTAAGAAACAACACAGT 59.124 41.667 0.00 0.00 38.63 3.55
633 694 0.526524 CGGGATGAAGACGAGTGCTC 60.527 60.000 0.00 0.00 0.00 4.26
634 695 0.820871 GGGATGAAGACGAGTGCTCT 59.179 55.000 0.00 0.00 0.00 4.09
635 696 1.202359 GGGATGAAGACGAGTGCTCTC 60.202 57.143 5.69 5.69 37.35 3.20
636 697 1.202359 GGATGAAGACGAGTGCTCTCC 60.202 57.143 10.08 0.00 37.40 3.71
637 698 0.453793 ATGAAGACGAGTGCTCTCCG 59.546 55.000 10.08 7.89 37.40 4.63
638 699 1.137825 GAAGACGAGTGCTCTCCGG 59.862 63.158 10.08 0.00 37.40 5.14
692 753 2.650116 GCGGAGTGGAGCAGGAGAA 61.650 63.158 0.00 0.00 0.00 2.87
743 804 3.749064 ACGGCGAGTCGTGCAGAT 61.749 61.111 16.62 0.00 42.21 2.90
744 805 3.250323 CGGCGAGTCGTGCAGATG 61.250 66.667 15.08 0.00 0.00 2.90
745 806 2.181777 GGCGAGTCGTGCAGATGA 59.818 61.111 15.08 0.00 0.00 2.92
891 954 1.035139 TTTACCGGCGTCTCCCTATC 58.965 55.000 6.01 0.00 0.00 2.08
892 955 0.184451 TTACCGGCGTCTCCCTATCT 59.816 55.000 6.01 0.00 0.00 1.98
893 956 1.059098 TACCGGCGTCTCCCTATCTA 58.941 55.000 6.01 0.00 0.00 1.98
894 957 0.404812 ACCGGCGTCTCCCTATCTAT 59.595 55.000 6.01 0.00 0.00 1.98
935 998 2.967946 GCCGCCACCTACCCTTTCT 61.968 63.158 0.00 0.00 0.00 2.52
996 1059 3.353836 GCGAACAAGAAGGCGGCA 61.354 61.111 13.08 0.00 0.00 5.69
1139 1209 1.408405 CCCGCGGCTAGATATCTCCTA 60.408 57.143 22.85 0.00 0.00 2.94
1151 1221 5.576128 AGATATCTCCTAGCTAGACCAACC 58.424 45.833 22.70 5.69 0.00 3.77
1176 1248 1.689273 GGCCGGATCTGTGTCTTAGAT 59.311 52.381 5.05 0.00 37.59 1.98
1213 1285 1.996292 ATATCATTCGATCGTGGCGG 58.004 50.000 15.94 2.07 32.73 6.13
1218 1290 2.023414 ATTCGATCGTGGCGGGCTTA 62.023 55.000 15.94 0.00 0.00 3.09
1245 1317 3.428534 GGCGATTAAAACCTTGTTTGCTG 59.571 43.478 0.00 0.00 0.00 4.41
1250 1322 6.088085 CGATTAAAACCTTGTTTGCTGACATC 59.912 38.462 0.00 0.00 0.00 3.06
1257 1329 5.356190 ACCTTGTTTGCTGACATCTCATATG 59.644 40.000 0.00 0.00 0.00 1.78
1261 1333 7.543947 TGTTTGCTGACATCTCATATGTAAG 57.456 36.000 1.90 0.00 34.35 2.34
1310 1382 8.183536 TGATTAATCGGTCAAATTCTCACATTG 58.816 33.333 10.80 0.00 0.00 2.82
1311 1383 7.680442 TTAATCGGTCAAATTCTCACATTGA 57.320 32.000 0.00 0.00 0.00 2.57
1312 1384 6.764308 AATCGGTCAAATTCTCACATTGAT 57.236 33.333 0.00 0.00 35.70 2.57
1330 1403 7.169140 CACATTGATTGATTGTATGCCTTGATG 59.831 37.037 0.00 0.00 0.00 3.07
1334 1407 6.604396 TGATTGATTGTATGCCTTGATGAAGT 59.396 34.615 0.00 0.00 0.00 3.01
1336 1409 5.499313 TGATTGTATGCCTTGATGAAGTCA 58.501 37.500 0.00 0.00 34.25 3.41
1339 1412 7.774625 TGATTGTATGCCTTGATGAAGTCATTA 59.225 33.333 0.00 0.00 36.54 1.90
1340 1413 8.701908 ATTGTATGCCTTGATGAAGTCATTAT 57.298 30.769 0.00 0.00 36.54 1.28
1368 1441 9.740239 ATCTTCATATGATGTGTATTTTGTTGC 57.260 29.630 15.93 0.00 0.00 4.17
1369 1442 7.909641 TCTTCATATGATGTGTATTTTGTTGCG 59.090 33.333 15.93 0.00 0.00 4.85
1372 1445 4.576216 TGATGTGTATTTTGTTGCGGTT 57.424 36.364 0.00 0.00 0.00 4.44
1373 1446 4.294232 TGATGTGTATTTTGTTGCGGTTG 58.706 39.130 0.00 0.00 0.00 3.77
1374 1447 3.784701 TGTGTATTTTGTTGCGGTTGT 57.215 38.095 0.00 0.00 0.00 3.32
1375 1448 3.696898 TGTGTATTTTGTTGCGGTTGTC 58.303 40.909 0.00 0.00 0.00 3.18
1376 1449 3.378742 TGTGTATTTTGTTGCGGTTGTCT 59.621 39.130 0.00 0.00 0.00 3.41
1377 1450 3.728718 GTGTATTTTGTTGCGGTTGTCTG 59.271 43.478 0.00 0.00 0.00 3.51
1378 1451 3.378742 TGTATTTTGTTGCGGTTGTCTGT 59.621 39.130 0.00 0.00 0.00 3.41
1379 1452 2.270275 TTTTGTTGCGGTTGTCTGTG 57.730 45.000 0.00 0.00 0.00 3.66
1380 1453 0.179150 TTTGTTGCGGTTGTCTGTGC 60.179 50.000 0.00 0.00 0.00 4.57
1381 1454 1.029408 TTGTTGCGGTTGTCTGTGCT 61.029 50.000 0.00 0.00 0.00 4.40
1382 1455 0.179070 TGTTGCGGTTGTCTGTGCTA 60.179 50.000 0.00 0.00 0.00 3.49
1383 1456 1.156736 GTTGCGGTTGTCTGTGCTAT 58.843 50.000 0.00 0.00 0.00 2.97
1384 1457 1.535462 GTTGCGGTTGTCTGTGCTATT 59.465 47.619 0.00 0.00 0.00 1.73
1385 1458 1.438651 TGCGGTTGTCTGTGCTATTC 58.561 50.000 0.00 0.00 0.00 1.75
1386 1459 1.001974 TGCGGTTGTCTGTGCTATTCT 59.998 47.619 0.00 0.00 0.00 2.40
1387 1460 1.661112 GCGGTTGTCTGTGCTATTCTC 59.339 52.381 0.00 0.00 0.00 2.87
1388 1461 1.920574 CGGTTGTCTGTGCTATTCTCG 59.079 52.381 0.00 0.00 0.00 4.04
1389 1462 2.271800 GGTTGTCTGTGCTATTCTCGG 58.728 52.381 0.00 0.00 0.00 4.63
1390 1463 1.661112 GTTGTCTGTGCTATTCTCGGC 59.339 52.381 0.00 0.00 0.00 5.54
1391 1464 0.179137 TGTCTGTGCTATTCTCGGCG 60.179 55.000 0.00 0.00 0.00 6.46
1392 1465 0.100682 GTCTGTGCTATTCTCGGCGA 59.899 55.000 10.14 10.14 0.00 5.54
1393 1466 1.032794 TCTGTGCTATTCTCGGCGAT 58.967 50.000 11.27 0.00 0.00 4.58
1394 1467 1.135046 CTGTGCTATTCTCGGCGATG 58.865 55.000 11.27 4.92 0.00 3.84
1395 1468 0.875908 TGTGCTATTCTCGGCGATGC 60.876 55.000 11.27 10.70 0.00 3.91
1403 1476 4.393155 TCGGCGATGCAGTTGGCT 62.393 61.111 4.99 0.00 45.15 4.75
1406 1479 1.745115 GGCGATGCAGTTGGCTACA 60.745 57.895 1.24 0.00 45.15 2.74
1416 1489 3.499918 GCAGTTGGCTACATGTATCATCC 59.500 47.826 5.91 6.37 40.25 3.51
1428 1501 2.288213 TGTATCATCCGATTCTGGCGTC 60.288 50.000 0.00 0.00 32.73 5.19
1452 1525 8.352942 GTCCTTCATATGGCGATTAAAATCTTT 58.647 33.333 2.13 0.00 33.24 2.52
1487 1614 7.936847 ACTCTGTTAGATGTGTTCAAACCATTA 59.063 33.333 0.00 0.00 0.00 1.90
1521 1648 3.882288 TGATGTGCAAGTAGCTTCACAAA 59.118 39.130 0.00 6.93 45.94 2.83
1522 1649 3.691049 TGTGCAAGTAGCTTCACAAAC 57.309 42.857 0.00 0.00 45.94 2.93
1523 1650 3.013219 TGTGCAAGTAGCTTCACAAACA 58.987 40.909 0.00 0.00 45.94 2.83
1524 1651 3.441922 TGTGCAAGTAGCTTCACAAACAA 59.558 39.130 0.00 0.00 45.94 2.83
1525 1652 4.037690 GTGCAAGTAGCTTCACAAACAAG 58.962 43.478 0.00 0.00 45.94 3.16
1526 1653 3.694072 TGCAAGTAGCTTCACAAACAAGT 59.306 39.130 0.00 0.00 45.94 3.16
1527 1654 4.878971 TGCAAGTAGCTTCACAAACAAGTA 59.121 37.500 0.00 0.00 45.94 2.24
1528 1655 5.355630 TGCAAGTAGCTTCACAAACAAGTAA 59.644 36.000 0.00 0.00 45.94 2.24
1529 1656 6.039270 TGCAAGTAGCTTCACAAACAAGTAAT 59.961 34.615 0.00 0.00 45.94 1.89
1530 1657 6.360681 GCAAGTAGCTTCACAAACAAGTAATG 59.639 38.462 0.00 0.00 41.15 1.90
1535 1662 3.889196 TCACAAACAAGTAATGCGACC 57.111 42.857 0.00 0.00 0.00 4.79
1548 1675 2.743636 TGCGACCAGAACTAGGAAAG 57.256 50.000 0.00 0.00 0.00 2.62
1566 1693 6.900194 AGGAAAGTATTGCTAGAATTGCCTA 58.100 36.000 0.41 0.00 35.19 3.93
1567 1694 6.995091 AGGAAAGTATTGCTAGAATTGCCTAG 59.005 38.462 0.41 0.00 35.19 3.02
1568 1695 6.768381 GGAAAGTATTGCTAGAATTGCCTAGT 59.232 38.462 0.00 0.00 38.64 2.57
1569 1696 7.283354 GGAAAGTATTGCTAGAATTGCCTAGTT 59.717 37.037 0.00 0.00 38.64 2.24
1571 1698 9.681062 AAAGTATTGCTAGAATTGCCTAGTTAA 57.319 29.630 0.00 0.00 38.64 2.01
1579 1706 9.508567 GCTAGAATTGCCTAGTTAATTTCTTTG 57.491 33.333 0.00 0.00 38.64 2.77
1599 1729 7.995289 TCTTTGACTTAACAAGCATTTCTTCA 58.005 30.769 0.00 0.00 31.27 3.02
1600 1730 8.465999 TCTTTGACTTAACAAGCATTTCTTCAA 58.534 29.630 0.00 0.00 31.27 2.69
1601 1731 8.994429 TTTGACTTAACAAGCATTTCTTCAAA 57.006 26.923 0.00 0.00 31.27 2.69
1602 1732 7.985634 TGACTTAACAAGCATTTCTTCAAAC 57.014 32.000 0.00 0.00 31.27 2.93
1628 1758 4.817464 TGTGCGGTAACAAACTGAAATAGT 59.183 37.500 0.00 0.00 42.89 2.12
1641 1771 3.814625 TGAAATAGTGTGTGGTTGCTGA 58.185 40.909 0.00 0.00 0.00 4.26
1676 1806 7.081976 CGTACCATTCGATCACTGATGTTATA 58.918 38.462 0.00 0.00 0.00 0.98
1677 1807 7.755373 CGTACCATTCGATCACTGATGTTATAT 59.245 37.037 0.00 0.00 0.00 0.86
1688 1818 8.437360 TCACTGATGTTATATTGTGATGAACC 57.563 34.615 0.00 0.00 30.78 3.62
1850 1980 5.414454 TGGCTTCATCAAGGTATACAACAAC 59.586 40.000 5.01 0.00 0.00 3.32
1935 2065 8.135382 TCCCTTCCTATTTATATGTAGTCTGC 57.865 38.462 0.00 0.00 0.00 4.26
1949 2079 3.396260 AGTCTGCAAGTAAACGGCTTA 57.604 42.857 0.00 0.00 33.76 3.09
1957 2087 5.009210 TGCAAGTAAACGGCTTAAAATGTCT 59.991 36.000 0.00 0.00 0.00 3.41
1969 2099 8.612619 CGGCTTAAAATGTCTGTTATGACTTAT 58.387 33.333 0.00 0.00 37.79 1.73
2004 2134 8.473219 TGGTATTGCATTAGCTCTAGATAGATG 58.527 37.037 16.27 0.00 42.74 2.90
2010 2140 7.014615 TGCATTAGCTCTAGATAGATGTGTGAA 59.985 37.037 0.00 0.00 42.74 3.18
2017 2147 8.580720 GCTCTAGATAGATGTGTGAATCCTTAA 58.419 37.037 0.00 0.00 0.00 1.85
2026 2156 4.943705 TGTGTGAATCCTTAATGCCTTCTC 59.056 41.667 0.00 0.00 0.00 2.87
2027 2157 5.189180 GTGTGAATCCTTAATGCCTTCTCT 58.811 41.667 0.00 0.00 0.00 3.10
2039 2169 4.890158 TGCCTTCTCTAGTGTTTGATGA 57.110 40.909 0.00 0.00 0.00 2.92
2040 2170 5.426689 TGCCTTCTCTAGTGTTTGATGAT 57.573 39.130 0.00 0.00 0.00 2.45
2041 2171 5.423015 TGCCTTCTCTAGTGTTTGATGATC 58.577 41.667 0.00 0.00 0.00 2.92
2042 2172 5.046376 TGCCTTCTCTAGTGTTTGATGATCA 60.046 40.000 0.00 0.00 0.00 2.92
2104 2234 7.230510 TGACTGGTTAACAAATTAATGTGCTCT 59.769 33.333 8.10 0.00 32.91 4.09
2105 2235 7.370383 ACTGGTTAACAAATTAATGTGCTCTG 58.630 34.615 8.10 0.00 32.91 3.35
2106 2236 7.014230 ACTGGTTAACAAATTAATGTGCTCTGT 59.986 33.333 8.10 0.00 32.91 3.41
2136 2266 6.349300 TCTCTATGGTTGGCTCATTTACTTC 58.651 40.000 0.00 0.00 0.00 3.01
2138 2268 3.134574 TGGTTGGCTCATTTACTTCGT 57.865 42.857 0.00 0.00 0.00 3.85
2184 2314 7.830940 TTTGCTGGCATTTTATTACATTGAG 57.169 32.000 0.00 0.00 0.00 3.02
2187 2317 6.154192 TGCTGGCATTTTATTACATTGAGGAA 59.846 34.615 0.00 0.00 0.00 3.36
2188 2318 6.476706 GCTGGCATTTTATTACATTGAGGAAC 59.523 38.462 0.00 0.00 0.00 3.62
2189 2319 7.473735 TGGCATTTTATTACATTGAGGAACA 57.526 32.000 0.00 0.00 0.00 3.18
2208 2369 2.108250 ACAAGTTCTATTGTGGCCTGGT 59.892 45.455 3.32 0.00 41.76 4.00
2209 2370 2.489329 CAAGTTCTATTGTGGCCTGGTG 59.511 50.000 3.32 0.00 0.00 4.17
2222 2383 2.827921 GGCCTGGTGATTTCTGAAATGT 59.172 45.455 19.59 0.00 0.00 2.71
2223 2384 3.259123 GGCCTGGTGATTTCTGAAATGTT 59.741 43.478 19.59 0.00 0.00 2.71
2228 2393 7.037438 CCTGGTGATTTCTGAAATGTTTATGG 58.963 38.462 19.59 10.57 0.00 2.74
2285 2450 4.325972 TGTCTTGATGTTCTTATGCAGCA 58.674 39.130 0.00 0.00 0.00 4.41
2288 2453 4.577693 TCTTGATGTTCTTATGCAGCATCC 59.422 41.667 12.38 0.00 36.17 3.51
2296 2461 4.847198 TCTTATGCAGCATCCTTTCTTCA 58.153 39.130 12.38 0.00 0.00 3.02
2366 2532 9.975218 AATTTGTAGTTAGACATACCATTTCCT 57.025 29.630 0.00 0.00 0.00 3.36
2378 2544 2.428890 ACCATTTCCTTCGTTTGTGCAA 59.571 40.909 0.00 0.00 0.00 4.08
2384 2550 4.545823 TCCTTCGTTTGTGCAAAACTAG 57.454 40.909 16.84 14.06 31.33 2.57
2385 2551 3.042887 CCTTCGTTTGTGCAAAACTAGC 58.957 45.455 16.84 0.00 31.33 3.42
2389 2555 2.213131 CGTTTGTGCAAAACTAGCGTTG 59.787 45.455 16.84 2.33 32.65 4.10
2461 2627 2.497675 CTGCTACCCTGAAGTGAAGCTA 59.502 50.000 0.00 0.00 0.00 3.32
2475 2641 4.472833 AGTGAAGCTAATCAGGGATGAAGT 59.527 41.667 0.00 0.00 0.00 3.01
2482 2648 6.101734 AGCTAATCAGGGATGAAGTAATGGAA 59.898 38.462 0.00 0.00 0.00 3.53
2484 2650 5.983333 ATCAGGGATGAAGTAATGGAACT 57.017 39.130 0.00 0.00 0.00 3.01
2491 2657 7.995488 AGGGATGAAGTAATGGAACTCTTAATG 59.005 37.037 0.00 0.00 0.00 1.90
2519 2685 8.593945 AGGCTTAATTTCAATTCCAGTAATGA 57.406 30.769 0.00 0.00 0.00 2.57
2526 2692 7.465353 TTTCAATTCCAGTAATGATTGCTCA 57.535 32.000 0.00 0.00 35.41 4.26
2548 2714 6.424032 TCAGTACTCTGAGAGTGGCTTTATA 58.576 40.000 24.52 0.00 44.58 0.98
2602 2768 5.890985 TGAACATGAGTTAATTACCCATGGG 59.109 40.000 30.23 30.23 44.67 4.00
2604 2770 5.282032 AACATGAGTTAATTACCCATGGGGT 60.282 40.000 34.27 21.34 44.67 4.95
2625 2792 5.450550 GGGTAGCCTTTTATCATTCTGTTGC 60.451 44.000 2.95 0.00 0.00 4.17
2637 2804 2.418368 TCTGTTGCCTGTGTTTGTCT 57.582 45.000 0.00 0.00 0.00 3.41
2660 2827 6.013379 TCTCCTCTCATTGTCATTGGTAGTTT 60.013 38.462 0.00 0.00 0.00 2.66
2668 2835 9.787435 TCATTGTCATTGGTAGTTTTAAGTACT 57.213 29.630 7.26 0.00 35.60 2.73
2705 2874 6.313905 AGAACGTATTGGCTCAATTTCTGTAG 59.686 38.462 5.85 0.00 35.54 2.74
2706 2875 5.730550 ACGTATTGGCTCAATTTCTGTAGA 58.269 37.500 5.85 0.00 35.54 2.59
2723 2892 2.281761 AAGACCAGCAACCCAGCG 60.282 61.111 0.00 0.00 40.15 5.18
2734 2903 2.287009 GCAACCCAGCGAATATGCTTAC 60.287 50.000 0.00 0.00 44.46 2.34
2737 2906 3.886123 ACCCAGCGAATATGCTTACTTT 58.114 40.909 0.00 0.00 44.46 2.66
2770 2939 4.339247 AGTTGTTGCATATATGTGGCCTTC 59.661 41.667 14.14 0.00 0.00 3.46
2793 2962 0.530744 ACGCTTATGGAAGACGCTCA 59.469 50.000 0.00 0.00 36.37 4.26
2818 2989 6.973229 AAAATTATTGAAGCACATGAAGGC 57.027 33.333 0.00 0.00 0.00 4.35
2819 2990 5.927281 AATTATTGAAGCACATGAAGGCT 57.073 34.783 0.00 2.23 43.46 4.58
2820 2991 4.707030 TTATTGAAGCACATGAAGGCTG 57.293 40.909 0.00 0.00 40.93 4.85
2821 2992 1.985473 TTGAAGCACATGAAGGCTGT 58.015 45.000 0.00 0.00 40.93 4.40
2822 2993 1.985473 TGAAGCACATGAAGGCTGTT 58.015 45.000 0.00 0.00 40.93 3.16
2823 2994 1.881973 TGAAGCACATGAAGGCTGTTC 59.118 47.619 0.00 2.02 40.93 3.18
2824 2995 1.881973 GAAGCACATGAAGGCTGTTCA 59.118 47.619 0.00 4.78 40.93 3.18
2825 2996 1.985473 AGCACATGAAGGCTGTTCAA 58.015 45.000 0.00 0.00 39.30 2.69
2826 2997 2.309613 AGCACATGAAGGCTGTTCAAA 58.690 42.857 0.00 0.00 39.30 2.69
2827 2998 2.895404 AGCACATGAAGGCTGTTCAAAT 59.105 40.909 0.00 0.00 39.30 2.32
2828 2999 4.081406 AGCACATGAAGGCTGTTCAAATA 58.919 39.130 0.00 0.00 39.30 1.40
2829 3000 4.082571 AGCACATGAAGGCTGTTCAAATAC 60.083 41.667 0.00 0.00 39.30 1.89
2832 3003 4.460382 ACATGAAGGCTGTTCAAATACCAG 59.540 41.667 0.00 0.00 31.55 4.00
2833 3004 4.365514 TGAAGGCTGTTCAAATACCAGA 57.634 40.909 0.00 0.00 0.00 3.86
2835 3006 4.041567 TGAAGGCTGTTCAAATACCAGAGA 59.958 41.667 0.00 0.00 0.00 3.10
2841 3388 6.317857 GCTGTTCAAATACCAGAGAATGAAC 58.682 40.000 8.96 8.96 44.15 3.18
2847 3394 4.679373 ATACCAGAGAATGAACGAGCAT 57.321 40.909 0.00 0.00 0.00 3.79
2849 3396 3.679389 ACCAGAGAATGAACGAGCATTT 58.321 40.909 8.44 1.28 38.53 2.32
2867 3414 4.082245 GCATTTGTGTAATGGTGTAAGCCT 60.082 41.667 0.00 0.00 43.20 4.58
2868 3415 5.124776 GCATTTGTGTAATGGTGTAAGCCTA 59.875 40.000 0.00 0.00 43.20 3.93
2870 3417 4.481368 TGTGTAATGGTGTAAGCCTAGG 57.519 45.455 3.67 3.67 0.00 3.02
2871 3418 4.098155 TGTGTAATGGTGTAAGCCTAGGA 58.902 43.478 14.75 0.00 0.00 2.94
2872 3419 4.161565 TGTGTAATGGTGTAAGCCTAGGAG 59.838 45.833 14.75 0.00 0.00 3.69
2875 3422 1.861982 TGGTGTAAGCCTAGGAGGAC 58.138 55.000 14.75 6.69 37.67 3.85
2876 3423 1.361543 TGGTGTAAGCCTAGGAGGACT 59.638 52.381 14.75 0.00 37.67 3.85
2884 3433 1.972207 GCCTAGGAGGACTGAACCCAT 60.972 57.143 14.75 0.00 37.67 4.00
2887 3436 1.077429 GGAGGACTGAACCCATGGC 60.077 63.158 6.09 0.00 0.00 4.40
2924 3473 8.851541 AAAAATTTACGTGTACTCCATCCTAA 57.148 30.769 0.00 0.00 0.00 2.69
2925 3474 8.851541 AAAATTTACGTGTACTCCATCCTAAA 57.148 30.769 0.00 0.00 0.00 1.85
2926 3475 8.851541 AAATTTACGTGTACTCCATCCTAAAA 57.148 30.769 0.00 0.00 0.00 1.52
2927 3476 8.851541 AATTTACGTGTACTCCATCCTAAAAA 57.148 30.769 0.00 0.00 0.00 1.94
2948 3497 4.715527 AAGAGCGTTTAGGTAGTAGTGG 57.284 45.455 0.00 0.00 0.00 4.00
2949 3498 3.960571 AGAGCGTTTAGGTAGTAGTGGA 58.039 45.455 0.00 0.00 0.00 4.02
2950 3499 4.338879 AGAGCGTTTAGGTAGTAGTGGAA 58.661 43.478 0.00 0.00 0.00 3.53
2951 3500 4.157472 AGAGCGTTTAGGTAGTAGTGGAAC 59.843 45.833 0.00 0.00 0.00 3.62
2952 3501 3.828451 AGCGTTTAGGTAGTAGTGGAACA 59.172 43.478 0.00 0.00 41.43 3.18
2958 3507 8.246180 CGTTTAGGTAGTAGTGGAACATAAGAA 58.754 37.037 0.00 0.00 44.52 2.52
2959 3508 9.933723 GTTTAGGTAGTAGTGGAACATAAGAAA 57.066 33.333 0.00 0.00 44.52 2.52
2961 3510 9.537852 TTAGGTAGTAGTGGAACATAAGAAAGA 57.462 33.333 0.00 0.00 44.52 2.52
2963 3512 8.312564 AGGTAGTAGTGGAACATAAGAAAGAAC 58.687 37.037 0.00 0.00 44.52 3.01
2964 3513 8.092687 GGTAGTAGTGGAACATAAGAAAGAACA 58.907 37.037 0.00 0.00 44.52 3.18
2968 3517 9.654663 GTAGTGGAACATAAGAAAGAACATACT 57.345 33.333 0.00 0.00 44.52 2.12
2970 3519 7.824779 AGTGGAACATAAGAAAGAACATACTCC 59.175 37.037 0.00 0.00 44.52 3.85
2980 3529 7.387643 AGAAAGAACATACTCCCTCTGTAAAC 58.612 38.462 0.00 0.00 0.00 2.01
2981 3530 6.936968 AAGAACATACTCCCTCTGTAAACT 57.063 37.500 0.00 0.00 0.00 2.66
2992 3541 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2994 3543 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
3051 3684 6.907853 ATATTAGTTTACGGAGGGAGTACC 57.092 41.667 0.00 0.00 40.67 3.34
3053 3686 3.111741 AGTTTACGGAGGGAGTACCAT 57.888 47.619 0.00 0.00 43.89 3.55
3054 3687 3.029570 AGTTTACGGAGGGAGTACCATC 58.970 50.000 0.00 0.00 45.04 3.51
3056 3689 3.393426 TTACGGAGGGAGTACCATCTT 57.607 47.619 0.00 0.00 45.10 2.40
3058 3691 2.946785 ACGGAGGGAGTACCATCTTAG 58.053 52.381 0.00 0.00 45.10 2.18
3059 3692 2.244252 ACGGAGGGAGTACCATCTTAGT 59.756 50.000 0.00 0.00 45.10 2.24
3061 3694 3.819902 CGGAGGGAGTACCATCTTAGTAC 59.180 52.174 0.00 0.00 45.10 2.73
3090 4123 9.874205 ATTAACTCATGGTTGGTTAATGAAATG 57.126 29.630 17.41 0.00 41.54 2.32
3096 4129 8.465999 TCATGGTTGGTTAATGAAATGTGATAC 58.534 33.333 0.00 0.00 0.00 2.24
3097 4130 7.164230 TGGTTGGTTAATGAAATGTGATACC 57.836 36.000 0.00 0.00 0.00 2.73
3099 4132 6.153680 GGTTGGTTAATGAAATGTGATACCCA 59.846 38.462 0.00 0.00 0.00 4.51
3115 4150 3.719173 ACCCAAAACATGTGGTAAACG 57.281 42.857 0.00 0.00 32.72 3.60
3122 4157 5.508200 AAACATGTGGTAAACGTTGATGT 57.492 34.783 0.00 1.34 0.00 3.06
3125 4160 5.543714 ACATGTGGTAAACGTTGATGTCTA 58.456 37.500 0.00 0.00 0.00 2.59
3143 4191 9.952188 TGATGTCTATTCTAAGTGATCTAAACG 57.048 33.333 0.00 0.00 0.00 3.60
3150 4198 7.827819 TTCTAAGTGATCTAAACGTTGATGG 57.172 36.000 0.00 0.00 0.00 3.51
3159 4207 5.592054 TCTAAACGTTGATGGCTGATCTAG 58.408 41.667 0.00 0.00 31.55 2.43
3163 4211 2.735663 CGTTGATGGCTGATCTAGATGC 59.264 50.000 10.74 8.26 31.55 3.91
3179 4227 2.808543 AGATGCGGAACTTGACTCAAAC 59.191 45.455 0.00 0.00 0.00 2.93
3195 4243 2.447429 TCAAACCCCCATCAAAGGTGTA 59.553 45.455 0.00 0.00 33.05 2.90
3197 4245 0.331616 ACCCCCATCAAAGGTGTAGC 59.668 55.000 0.00 0.00 30.97 3.58
3260 4308 3.383620 TTTGTTGCATTGGTGATGGAC 57.616 42.857 0.00 0.00 35.66 4.02
3264 4312 2.127271 TGCATTGGTGATGGACGATT 57.873 45.000 0.00 0.00 36.21 3.34
3276 4324 5.796935 GTGATGGACGATTGACAGATTTTTG 59.203 40.000 0.00 0.00 0.00 2.44
3338 4387 2.149973 ATGCCTTTGATCCAGAACCC 57.850 50.000 0.00 0.00 0.00 4.11
3358 4407 1.456296 GCCACAGATGTTGCATGAGA 58.544 50.000 0.00 0.00 36.77 3.27
3405 4454 1.021968 ACTCCAAACTTGTTCGCCAC 58.978 50.000 0.00 0.00 0.00 5.01
3414 4463 0.375454 TTGTTCGCCACGTGTTTCTG 59.625 50.000 15.65 0.00 0.00 3.02
3416 4465 2.876879 TTCGCCACGTGTTTCTGCG 61.877 57.895 24.10 24.10 46.09 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.123674 ACGAAAGTGCGGAGATGAC 57.876 52.632 0.00 0.00 46.97 3.06
105 114 4.346734 ACTTGATGACAATGCGATTGAC 57.653 40.909 13.53 9.14 42.83 3.18
186 195 2.455565 CCGAATCCCCAGCTCCCAT 61.456 63.158 0.00 0.00 0.00 4.00
192 201 0.467290 TATTTGGCCGAATCCCCAGC 60.467 55.000 22.04 0.00 31.73 4.85
195 204 1.318576 CACTATTTGGCCGAATCCCC 58.681 55.000 22.04 0.00 0.00 4.81
220 229 1.549170 TCCCCTTGAGTTCTAGTTCGC 59.451 52.381 0.00 0.00 0.00 4.70
292 348 1.606350 CGAGTTTGGTGTCTCGCGAC 61.606 60.000 3.71 0.00 44.82 5.19
538 594 1.068472 ACTGACGTGTCCTCGAATGTC 60.068 52.381 0.00 1.05 34.70 3.06
578 636 2.440796 CGCCCCTACCTACCGTCA 60.441 66.667 0.00 0.00 0.00 4.35
674 735 2.570582 CTTCTCCTGCTCCACTCCGC 62.571 65.000 0.00 0.00 0.00 5.54
743 804 5.105187 GGCCTCAGATATATGTGCTGTATCA 60.105 44.000 4.99 0.00 32.02 2.15
744 805 5.355596 GGCCTCAGATATATGTGCTGTATC 58.644 45.833 4.99 0.00 0.00 2.24
745 806 4.163078 GGGCCTCAGATATATGTGCTGTAT 59.837 45.833 0.84 0.00 0.00 2.29
792 853 3.427573 GGCTTAAAGGGCCTCTTTGTTA 58.572 45.455 22.34 0.00 44.68 2.41
891 954 2.356382 CGAGCGGGAGAGGCTTATATAG 59.644 54.545 0.00 0.00 41.72 1.31
892 955 2.366533 CGAGCGGGAGAGGCTTATATA 58.633 52.381 0.00 0.00 41.72 0.86
893 956 1.178276 CGAGCGGGAGAGGCTTATAT 58.822 55.000 0.00 0.00 41.72 0.86
894 957 1.524863 GCGAGCGGGAGAGGCTTATA 61.525 60.000 0.00 0.00 41.72 0.98
935 998 4.467084 GGATGCGCGTGGGAGGAA 62.467 66.667 6.97 0.00 0.00 3.36
996 1059 1.303317 GTTGGAGTGCCCCATCGTT 60.303 57.895 0.00 0.00 35.87 3.85
1139 1209 1.590147 CCGAACGGTTGGTCTAGCT 59.410 57.895 0.00 0.00 0.00 3.32
1151 1221 2.885644 CACAGATCCGGCCGAACG 60.886 66.667 30.73 10.73 0.00 3.95
1176 1248 6.339587 TGATATATGTCGCCAACTACATCA 57.660 37.500 0.00 0.00 37.50 3.07
1213 1285 6.327279 AGGTTTTAATCGCCATATTAAGCC 57.673 37.500 0.00 0.00 33.90 4.35
1218 1290 6.312672 GCAAACAAGGTTTTAATCGCCATATT 59.687 34.615 0.00 0.00 0.00 1.28
1245 1317 8.198109 ACCTAACACACTTACATATGAGATGTC 58.802 37.037 10.38 0.00 33.76 3.06
1250 1322 6.535150 CCACACCTAACACACTTACATATGAG 59.465 42.308 10.38 0.00 0.00 2.90
1257 1329 4.056050 CTGACCACACCTAACACACTTAC 58.944 47.826 0.00 0.00 0.00 2.34
1261 1333 1.140252 ACCTGACCACACCTAACACAC 59.860 52.381 0.00 0.00 0.00 3.82
1285 1357 8.397906 TCAATGTGAGAATTTGACCGATTAATC 58.602 33.333 5.30 5.30 0.00 1.75
1291 1363 5.704978 TCAATCAATGTGAGAATTTGACCGA 59.295 36.000 0.00 0.00 32.61 4.69
1310 1382 7.035840 ACTTCATCAAGGCATACAATCAATC 57.964 36.000 0.00 0.00 33.37 2.67
1311 1383 6.604396 TGACTTCATCAAGGCATACAATCAAT 59.396 34.615 0.00 0.00 43.33 2.57
1312 1384 5.945191 TGACTTCATCAAGGCATACAATCAA 59.055 36.000 0.00 0.00 43.33 2.57
1368 1441 1.920574 CGAGAATAGCACAGACAACCG 59.079 52.381 0.00 0.00 0.00 4.44
1369 1442 2.271800 CCGAGAATAGCACAGACAACC 58.728 52.381 0.00 0.00 0.00 3.77
1372 1445 0.179137 CGCCGAGAATAGCACAGACA 60.179 55.000 0.00 0.00 0.00 3.41
1373 1446 0.100682 TCGCCGAGAATAGCACAGAC 59.899 55.000 0.00 0.00 0.00 3.51
1374 1447 1.032794 ATCGCCGAGAATAGCACAGA 58.967 50.000 0.00 0.00 0.00 3.41
1375 1448 1.135046 CATCGCCGAGAATAGCACAG 58.865 55.000 0.00 0.00 0.00 3.66
1376 1449 0.875908 GCATCGCCGAGAATAGCACA 60.876 55.000 0.00 0.00 0.00 4.57
1377 1450 0.875908 TGCATCGCCGAGAATAGCAC 60.876 55.000 0.00 0.00 32.76 4.40
1378 1451 0.598419 CTGCATCGCCGAGAATAGCA 60.598 55.000 0.00 0.00 35.17 3.49
1379 1452 0.598680 ACTGCATCGCCGAGAATAGC 60.599 55.000 0.00 0.00 0.00 2.97
1380 1453 1.524355 CAACTGCATCGCCGAGAATAG 59.476 52.381 0.00 0.00 0.00 1.73
1381 1454 1.570813 CAACTGCATCGCCGAGAATA 58.429 50.000 0.00 0.00 0.00 1.75
1382 1455 1.091771 CCAACTGCATCGCCGAGAAT 61.092 55.000 0.00 0.00 0.00 2.40
1383 1456 1.741401 CCAACTGCATCGCCGAGAA 60.741 57.895 0.00 0.00 0.00 2.87
1384 1457 2.125552 CCAACTGCATCGCCGAGA 60.126 61.111 0.00 0.00 0.00 4.04
1385 1458 2.906182 TAGCCAACTGCATCGCCGAG 62.906 60.000 0.00 0.00 44.83 4.63
1386 1459 3.012859 TAGCCAACTGCATCGCCGA 62.013 57.895 0.00 0.00 44.83 5.54
1387 1460 2.511373 TAGCCAACTGCATCGCCG 60.511 61.111 0.00 0.00 44.83 6.46
1388 1461 1.097547 ATGTAGCCAACTGCATCGCC 61.098 55.000 0.00 0.00 44.92 5.54
1389 1462 0.028505 CATGTAGCCAACTGCATCGC 59.971 55.000 0.00 0.00 44.92 4.58
1390 1463 1.372582 ACATGTAGCCAACTGCATCG 58.627 50.000 0.00 0.00 44.92 3.84
1391 1464 4.129380 TGATACATGTAGCCAACTGCATC 58.871 43.478 17.99 4.99 44.92 3.91
1393 1466 3.625649 TGATACATGTAGCCAACTGCA 57.374 42.857 17.99 0.00 44.83 4.41
1394 1467 3.499918 GGATGATACATGTAGCCAACTGC 59.500 47.826 17.99 2.84 41.71 4.40
1395 1468 3.742882 CGGATGATACATGTAGCCAACTG 59.257 47.826 17.99 13.56 0.00 3.16
1403 1476 4.618227 CGCCAGAATCGGATGATACATGTA 60.618 45.833 8.27 8.27 33.40 2.29
1406 1479 2.300152 ACGCCAGAATCGGATGATACAT 59.700 45.455 0.00 0.00 33.40 2.29
1416 1489 2.509052 TATGAAGGACGCCAGAATCG 57.491 50.000 0.00 0.00 0.00 3.34
1428 1501 9.533253 AAAAAGATTTTAATCGCCATATGAAGG 57.467 29.630 3.65 0.00 40.35 3.46
1457 1530 8.784043 GGTTTGAACACATCTAACAGAGTTAAT 58.216 33.333 5.43 0.00 43.04 1.40
1476 1549 4.584325 ACAGCAAGCTCTTAATGGTTTGAA 59.416 37.500 0.00 0.00 0.00 2.69
1487 1614 0.879765 GCACATCACAGCAAGCTCTT 59.120 50.000 0.00 0.00 0.00 2.85
1511 1638 3.563808 TCGCATTACTTGTTTGTGAAGCT 59.436 39.130 0.00 0.00 0.00 3.74
1521 1648 3.402628 AGTTCTGGTCGCATTACTTGT 57.597 42.857 0.00 0.00 0.00 3.16
1522 1649 3.865745 CCTAGTTCTGGTCGCATTACTTG 59.134 47.826 0.00 0.00 0.00 3.16
1523 1650 3.767673 TCCTAGTTCTGGTCGCATTACTT 59.232 43.478 0.00 0.00 0.00 2.24
1524 1651 3.362706 TCCTAGTTCTGGTCGCATTACT 58.637 45.455 0.00 0.00 0.00 2.24
1525 1652 3.795623 TCCTAGTTCTGGTCGCATTAC 57.204 47.619 0.00 0.00 0.00 1.89
1526 1653 4.222145 ACTTTCCTAGTTCTGGTCGCATTA 59.778 41.667 0.00 0.00 31.29 1.90
1527 1654 3.008049 ACTTTCCTAGTTCTGGTCGCATT 59.992 43.478 0.00 0.00 31.29 3.56
1528 1655 2.567615 ACTTTCCTAGTTCTGGTCGCAT 59.432 45.455 0.00 0.00 31.29 4.73
1529 1656 1.968493 ACTTTCCTAGTTCTGGTCGCA 59.032 47.619 0.00 0.00 31.29 5.10
1530 1657 2.745515 ACTTTCCTAGTTCTGGTCGC 57.254 50.000 0.00 0.00 31.29 5.19
1535 1662 9.606631 AATTCTAGCAATACTTTCCTAGTTCTG 57.393 33.333 0.00 0.00 38.33 3.02
1571 1698 9.822185 AAGAAATGCTTGTTAAGTCAAAGAAAT 57.178 25.926 0.00 0.00 34.93 2.17
1575 1702 8.633075 TTGAAGAAATGCTTGTTAAGTCAAAG 57.367 30.769 0.00 0.00 36.83 2.77
1579 1706 6.345015 GCGTTTGAAGAAATGCTTGTTAAGTC 60.345 38.462 0.00 0.00 46.50 3.01
1628 1758 1.065491 AGACAAGTCAGCAACCACACA 60.065 47.619 2.72 0.00 0.00 3.72
1676 1806 7.056006 TCATAAGCATACTGGTTCATCACAAT 58.944 34.615 0.00 0.00 39.08 2.71
1677 1807 6.413892 TCATAAGCATACTGGTTCATCACAA 58.586 36.000 0.00 0.00 39.08 3.33
1688 1818 7.922811 TCAGTACAATCACTCATAAGCATACTG 59.077 37.037 0.00 0.00 0.00 2.74
1699 1829 2.615391 TGGGGTCAGTACAATCACTCA 58.385 47.619 0.00 0.00 0.00 3.41
1933 2063 5.009210 AGACATTTTAAGCCGTTTACTTGCA 59.991 36.000 0.00 0.00 0.00 4.08
1934 2064 5.342259 CAGACATTTTAAGCCGTTTACTTGC 59.658 40.000 0.00 0.00 0.00 4.01
1935 2065 6.435428 ACAGACATTTTAAGCCGTTTACTTG 58.565 36.000 0.00 0.00 0.00 3.16
1975 2105 9.494271 CTATCTAGAGCTAATGCAATACCAAAA 57.506 33.333 0.00 0.00 42.74 2.44
1976 2106 8.870116 TCTATCTAGAGCTAATGCAATACCAAA 58.130 33.333 0.00 0.00 42.74 3.28
1977 2107 8.422577 TCTATCTAGAGCTAATGCAATACCAA 57.577 34.615 0.00 0.00 42.74 3.67
1978 2108 8.473219 CATCTATCTAGAGCTAATGCAATACCA 58.527 37.037 0.00 0.00 42.74 3.25
1979 2109 8.474025 ACATCTATCTAGAGCTAATGCAATACC 58.526 37.037 0.00 0.00 42.74 2.73
1980 2110 9.299963 CACATCTATCTAGAGCTAATGCAATAC 57.700 37.037 0.00 0.00 42.74 1.89
1981 2111 9.029368 ACACATCTATCTAGAGCTAATGCAATA 57.971 33.333 0.00 0.00 42.74 1.90
1982 2112 7.818446 CACACATCTATCTAGAGCTAATGCAAT 59.182 37.037 0.00 0.00 42.74 3.56
1983 2113 7.014615 TCACACATCTATCTAGAGCTAATGCAA 59.985 37.037 0.00 0.00 42.74 4.08
1984 2114 6.491403 TCACACATCTATCTAGAGCTAATGCA 59.509 38.462 0.00 0.00 42.74 3.96
1985 2115 6.918626 TCACACATCTATCTAGAGCTAATGC 58.081 40.000 0.00 0.00 35.50 3.56
1986 2116 9.571810 GATTCACACATCTATCTAGAGCTAATG 57.428 37.037 0.00 2.49 35.50 1.90
1987 2117 8.748412 GGATTCACACATCTATCTAGAGCTAAT 58.252 37.037 0.00 0.00 35.50 1.73
1988 2118 7.947332 AGGATTCACACATCTATCTAGAGCTAA 59.053 37.037 0.00 0.00 35.50 3.09
1989 2119 7.465960 AGGATTCACACATCTATCTAGAGCTA 58.534 38.462 0.00 0.00 35.50 3.32
1990 2120 6.314120 AGGATTCACACATCTATCTAGAGCT 58.686 40.000 0.00 0.00 35.50 4.09
1991 2121 6.588719 AGGATTCACACATCTATCTAGAGC 57.411 41.667 0.00 0.00 35.50 4.09
1994 2124 9.149225 GCATTAAGGATTCACACATCTATCTAG 57.851 37.037 0.00 0.00 0.00 2.43
1995 2125 8.097038 GGCATTAAGGATTCACACATCTATCTA 58.903 37.037 0.00 0.00 0.00 1.98
1996 2126 6.939163 GGCATTAAGGATTCACACATCTATCT 59.061 38.462 0.00 0.00 0.00 1.98
1997 2127 6.939163 AGGCATTAAGGATTCACACATCTATC 59.061 38.462 0.00 0.00 0.00 2.08
1998 2128 6.845908 AGGCATTAAGGATTCACACATCTAT 58.154 36.000 0.00 0.00 0.00 1.98
2004 2134 5.189180 AGAGAAGGCATTAAGGATTCACAC 58.811 41.667 7.83 1.37 0.00 3.82
2010 2140 6.567602 AACACTAGAGAAGGCATTAAGGAT 57.432 37.500 0.00 0.00 0.00 3.24
2017 2147 5.426689 TCATCAAACACTAGAGAAGGCAT 57.573 39.130 0.00 0.00 0.00 4.40
2027 2157 9.778741 GGAATAGGTATTGATCATCAAACACTA 57.221 33.333 3.63 7.35 40.12 2.74
2064 2194 7.936847 TGTTAACCAGTCAGTTATCTCATTTGT 59.063 33.333 2.48 0.00 32.45 2.83
2077 2207 7.370383 AGCACATTAATTTGTTAACCAGTCAG 58.630 34.615 2.48 0.00 0.00 3.51
2081 2211 7.370383 ACAGAGCACATTAATTTGTTAACCAG 58.630 34.615 2.48 0.00 0.00 4.00
2095 2225 7.288852 ACCATAGAGAACTATACAGAGCACATT 59.711 37.037 0.00 0.00 37.24 2.71
2104 2234 5.897250 TGAGCCAACCATAGAGAACTATACA 59.103 40.000 0.00 0.00 37.24 2.29
2105 2235 6.406692 TGAGCCAACCATAGAGAACTATAC 57.593 41.667 0.00 0.00 37.24 1.47
2106 2236 7.618019 AATGAGCCAACCATAGAGAACTATA 57.382 36.000 0.00 0.00 37.24 1.31
2109 2239 4.851639 AATGAGCCAACCATAGAGAACT 57.148 40.909 0.00 0.00 0.00 3.01
2151 2281 2.736144 ATGCCAGCAAAACACATCTG 57.264 45.000 0.00 0.00 0.00 2.90
2184 2314 3.191371 CAGGCCACAATAGAACTTGTTCC 59.809 47.826 5.01 0.00 37.25 3.62
2187 2317 2.108250 ACCAGGCCACAATAGAACTTGT 59.892 45.455 5.01 0.00 39.91 3.16
2188 2318 2.489329 CACCAGGCCACAATAGAACTTG 59.511 50.000 5.01 0.00 0.00 3.16
2189 2319 2.375174 TCACCAGGCCACAATAGAACTT 59.625 45.455 5.01 0.00 0.00 2.66
2208 2369 9.076781 TCTGAACCATAAACATTTCAGAAATCA 57.923 29.630 5.32 0.00 46.89 2.57
2228 2393 7.736447 AGCTTGGCTATTATGTTATCTGAAC 57.264 36.000 0.00 0.00 36.99 3.18
2259 2424 6.092670 GCTGCATAAGAACATCAAGACAACTA 59.907 38.462 0.00 0.00 0.00 2.24
2285 2450 3.715834 AGGCTAGATGCTGAAGAAAGGAT 59.284 43.478 0.00 0.00 42.39 3.24
2288 2453 4.768583 AGAAGGCTAGATGCTGAAGAAAG 58.231 43.478 0.00 0.00 42.39 2.62
2358 2524 2.791383 TGCACAAACGAAGGAAATGG 57.209 45.000 0.00 0.00 0.00 3.16
2359 2525 4.566360 AGTTTTGCACAAACGAAGGAAATG 59.434 37.500 14.56 0.00 35.42 2.32
2360 2526 4.754322 AGTTTTGCACAAACGAAGGAAAT 58.246 34.783 14.56 0.00 35.42 2.17
2361 2527 4.181309 AGTTTTGCACAAACGAAGGAAA 57.819 36.364 14.56 0.00 35.42 3.13
2362 2528 3.859411 AGTTTTGCACAAACGAAGGAA 57.141 38.095 14.56 0.00 35.42 3.36
2363 2529 3.242936 GCTAGTTTTGCACAAACGAAGGA 60.243 43.478 19.01 7.86 35.42 3.36
2364 2530 3.042887 GCTAGTTTTGCACAAACGAAGG 58.957 45.455 19.01 12.53 35.42 3.46
2365 2531 2.713976 CGCTAGTTTTGCACAAACGAAG 59.286 45.455 14.56 15.53 35.42 3.79
2366 2532 2.096174 ACGCTAGTTTTGCACAAACGAA 59.904 40.909 14.56 9.09 35.42 3.85
2384 2550 9.730420 AAGAACATAATCCAATAATTACAACGC 57.270 29.630 0.00 0.00 0.00 4.84
2405 2571 3.685836 ACGGTACTGCAACAAAAGAAC 57.314 42.857 0.23 0.00 0.00 3.01
2461 2627 6.159398 AGAGTTCCATTACTTCATCCCTGATT 59.841 38.462 0.00 0.00 0.00 2.57
2475 2641 6.327386 AGCCTTCCATTAAGAGTTCCATTA 57.673 37.500 0.00 0.00 37.38 1.90
2482 2648 8.650143 TTGAAATTAAGCCTTCCATTAAGAGT 57.350 30.769 0.00 0.00 37.38 3.24
2491 2657 6.286240 ACTGGAATTGAAATTAAGCCTTCC 57.714 37.500 0.00 0.00 33.02 3.46
2526 2692 7.906199 AATATAAAGCCACTCTCAGAGTACT 57.094 36.000 7.11 5.31 41.37 2.73
2533 2699 7.345691 TCCATCAAAATATAAAGCCACTCTCA 58.654 34.615 0.00 0.00 0.00 3.27
2602 2768 5.450550 GGCAACAGAATGATAAAAGGCTACC 60.451 44.000 0.00 0.00 39.69 3.18
2604 2770 5.357878 CAGGCAACAGAATGATAAAAGGCTA 59.642 40.000 0.00 0.00 39.69 3.93
2607 2773 5.047802 ACACAGGCAACAGAATGATAAAAGG 60.048 40.000 0.00 0.00 39.69 3.11
2609 2775 6.403866 AACACAGGCAACAGAATGATAAAA 57.596 33.333 0.00 0.00 39.69 1.52
2625 2792 3.692257 ATGAGAGGAGACAAACACAGG 57.308 47.619 0.00 0.00 0.00 4.00
2637 2804 5.762179 AACTACCAATGACAATGAGAGGA 57.238 39.130 0.00 0.00 0.00 3.71
2692 2861 5.240891 TGCTGGTCTTCTACAGAAATTGAG 58.759 41.667 0.00 0.00 36.86 3.02
2698 2867 2.038557 GGGTTGCTGGTCTTCTACAGAA 59.961 50.000 0.00 0.00 36.86 3.02
2699 2868 1.623811 GGGTTGCTGGTCTTCTACAGA 59.376 52.381 0.00 0.00 36.86 3.41
2705 2874 2.328099 CGCTGGGTTGCTGGTCTTC 61.328 63.158 0.00 0.00 0.00 2.87
2706 2875 2.281761 CGCTGGGTTGCTGGTCTT 60.282 61.111 0.00 0.00 0.00 3.01
2747 2916 3.902218 AGGCCACATATATGCAACAACT 58.098 40.909 12.79 1.63 0.00 3.16
2761 2930 1.681538 TAAGCGTTTTGAAGGCCACA 58.318 45.000 5.01 1.11 42.95 4.17
2770 2939 2.159627 AGCGTCTTCCATAAGCGTTTTG 59.840 45.455 0.00 0.00 35.81 2.44
2803 2974 1.881973 GAACAGCCTTCATGTGCTTCA 59.118 47.619 4.75 0.00 35.12 3.02
2818 2989 6.368791 TCGTTCATTCTCTGGTATTTGAACAG 59.631 38.462 12.43 6.71 41.73 3.16
2819 2990 6.227522 TCGTTCATTCTCTGGTATTTGAACA 58.772 36.000 12.43 0.23 41.73 3.18
2820 2991 6.673316 GCTCGTTCATTCTCTGGTATTTGAAC 60.673 42.308 0.00 0.00 39.51 3.18
2821 2992 5.351465 GCTCGTTCATTCTCTGGTATTTGAA 59.649 40.000 0.00 0.00 0.00 2.69
2822 2993 4.870426 GCTCGTTCATTCTCTGGTATTTGA 59.130 41.667 0.00 0.00 0.00 2.69
2823 2994 4.631377 TGCTCGTTCATTCTCTGGTATTTG 59.369 41.667 0.00 0.00 0.00 2.32
2824 2995 4.832248 TGCTCGTTCATTCTCTGGTATTT 58.168 39.130 0.00 0.00 0.00 1.40
2825 2996 4.471904 TGCTCGTTCATTCTCTGGTATT 57.528 40.909 0.00 0.00 0.00 1.89
2826 2997 4.679373 ATGCTCGTTCATTCTCTGGTAT 57.321 40.909 0.00 0.00 0.00 2.73
2827 2998 4.471904 AATGCTCGTTCATTCTCTGGTA 57.528 40.909 0.36 0.00 31.49 3.25
2828 2999 3.340814 AATGCTCGTTCATTCTCTGGT 57.659 42.857 0.36 0.00 31.49 4.00
2829 3000 3.438087 ACAAATGCTCGTTCATTCTCTGG 59.562 43.478 5.62 0.00 35.77 3.86
2832 3003 4.410492 ACACAAATGCTCGTTCATTCTC 57.590 40.909 5.62 0.00 35.77 2.87
2833 3004 5.940192 TTACACAAATGCTCGTTCATTCT 57.060 34.783 5.62 0.00 35.77 2.40
2835 3006 5.048083 ACCATTACACAAATGCTCGTTCATT 60.048 36.000 0.36 0.36 43.18 2.57
2841 3388 3.829886 ACACCATTACACAAATGCTCG 57.170 42.857 0.00 0.00 43.18 5.03
2847 3394 5.013287 TCCTAGGCTTACACCATTACACAAA 59.987 40.000 2.96 0.00 0.00 2.83
2849 3396 4.098155 TCCTAGGCTTACACCATTACACA 58.902 43.478 2.96 0.00 0.00 3.72
2867 3414 1.879575 CCATGGGTTCAGTCCTCCTA 58.120 55.000 2.85 0.00 0.00 2.94
2868 3415 1.566298 GCCATGGGTTCAGTCCTCCT 61.566 60.000 15.13 0.00 0.00 3.69
2870 3417 0.393537 CAGCCATGGGTTCAGTCCTC 60.394 60.000 15.37 0.00 0.00 3.71
2871 3418 0.842030 TCAGCCATGGGTTCAGTCCT 60.842 55.000 15.37 0.00 0.00 3.85
2872 3419 0.678048 GTCAGCCATGGGTTCAGTCC 60.678 60.000 15.37 0.00 0.00 3.85
2875 3422 1.100510 CATGTCAGCCATGGGTTCAG 58.899 55.000 15.37 3.21 46.03 3.02
2876 3423 3.269578 CATGTCAGCCATGGGTTCA 57.730 52.632 15.37 16.56 46.03 3.18
2899 3448 8.851541 TTAGGATGGAGTACACGTAAATTTTT 57.148 30.769 0.00 0.00 0.00 1.94
2900 3449 8.851541 TTTAGGATGGAGTACACGTAAATTTT 57.148 30.769 0.00 0.00 0.00 1.82
2902 3451 8.851541 TTTTTAGGATGGAGTACACGTAAATT 57.148 30.769 0.00 0.00 0.00 1.82
2924 3473 5.930569 CCACTACTACCTAAACGCTCTTTTT 59.069 40.000 0.00 0.00 0.00 1.94
2925 3474 5.244626 TCCACTACTACCTAAACGCTCTTTT 59.755 40.000 0.00 0.00 0.00 2.27
2926 3475 4.768968 TCCACTACTACCTAAACGCTCTTT 59.231 41.667 0.00 0.00 0.00 2.52
2927 3476 4.338879 TCCACTACTACCTAAACGCTCTT 58.661 43.478 0.00 0.00 0.00 2.85
2928 3477 3.960571 TCCACTACTACCTAAACGCTCT 58.039 45.455 0.00 0.00 0.00 4.09
2929 3478 4.082571 TGTTCCACTACTACCTAAACGCTC 60.083 45.833 0.00 0.00 0.00 5.03
2930 3479 3.828451 TGTTCCACTACTACCTAAACGCT 59.172 43.478 0.00 0.00 0.00 5.07
2931 3480 4.178545 TGTTCCACTACTACCTAAACGC 57.821 45.455 0.00 0.00 0.00 4.84
2932 3481 7.765307 TCTTATGTTCCACTACTACCTAAACG 58.235 38.462 0.00 0.00 0.00 3.60
2933 3482 9.933723 TTTCTTATGTTCCACTACTACCTAAAC 57.066 33.333 0.00 0.00 0.00 2.01
2935 3484 9.537852 TCTTTCTTATGTTCCACTACTACCTAA 57.462 33.333 0.00 0.00 0.00 2.69
2936 3485 9.537852 TTCTTTCTTATGTTCCACTACTACCTA 57.462 33.333 0.00 0.00 0.00 3.08
2937 3486 8.312564 GTTCTTTCTTATGTTCCACTACTACCT 58.687 37.037 0.00 0.00 0.00 3.08
2938 3487 8.092687 TGTTCTTTCTTATGTTCCACTACTACC 58.907 37.037 0.00 0.00 0.00 3.18
2939 3488 9.654663 ATGTTCTTTCTTATGTTCCACTACTAC 57.345 33.333 0.00 0.00 0.00 2.73
2941 3490 9.654663 GTATGTTCTTTCTTATGTTCCACTACT 57.345 33.333 0.00 0.00 0.00 2.57
2942 3491 9.654663 AGTATGTTCTTTCTTATGTTCCACTAC 57.345 33.333 0.00 0.00 0.00 2.73
2943 3492 9.871238 GAGTATGTTCTTTCTTATGTTCCACTA 57.129 33.333 0.00 0.00 0.00 2.74
2944 3493 7.824779 GGAGTATGTTCTTTCTTATGTTCCACT 59.175 37.037 0.00 0.00 0.00 4.00
2945 3494 7.065923 GGGAGTATGTTCTTTCTTATGTTCCAC 59.934 40.741 0.00 0.00 0.00 4.02
2946 3495 7.037586 AGGGAGTATGTTCTTTCTTATGTTCCA 60.038 37.037 0.00 0.00 0.00 3.53
2947 3496 7.339482 AGGGAGTATGTTCTTTCTTATGTTCC 58.661 38.462 0.00 0.00 0.00 3.62
2948 3497 8.261522 AGAGGGAGTATGTTCTTTCTTATGTTC 58.738 37.037 0.00 0.00 0.00 3.18
2949 3498 8.043710 CAGAGGGAGTATGTTCTTTCTTATGTT 58.956 37.037 0.00 0.00 0.00 2.71
2950 3499 7.181125 ACAGAGGGAGTATGTTCTTTCTTATGT 59.819 37.037 0.00 0.00 0.00 2.29
2951 3500 7.560368 ACAGAGGGAGTATGTTCTTTCTTATG 58.440 38.462 0.00 0.00 0.00 1.90
2952 3501 7.741554 ACAGAGGGAGTATGTTCTTTCTTAT 57.258 36.000 0.00 0.00 0.00 1.73
2958 3507 6.936968 AGTTTACAGAGGGAGTATGTTCTT 57.063 37.500 0.00 0.00 31.40 2.52
2959 3508 8.611051 ATTAGTTTACAGAGGGAGTATGTTCT 57.389 34.615 0.00 0.00 31.40 3.01
2968 3517 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
3019 3652 9.387257 CCCTCCGTAAACTAATATAAAAGTGTT 57.613 33.333 0.00 0.00 0.00 3.32
3022 3655 8.985922 ACTCCCTCCGTAAACTAATATAAAAGT 58.014 33.333 0.00 0.00 0.00 2.66
3029 3662 5.765510 TGGTACTCCCTCCGTAAACTAATA 58.234 41.667 0.00 0.00 0.00 0.98
3033 3666 2.610438 TGGTACTCCCTCCGTAAACT 57.390 50.000 0.00 0.00 0.00 2.66
3034 3667 3.029570 AGATGGTACTCCCTCCGTAAAC 58.970 50.000 0.00 0.00 0.00 2.01
3054 3687 9.886132 ACCAACCATGAGTTAATAAGTACTAAG 57.114 33.333 0.00 0.00 36.18 2.18
3065 3698 8.865090 ACATTTCATTAACCAACCATGAGTTAA 58.135 29.630 0.00 3.75 36.18 2.01
3066 3699 8.303156 CACATTTCATTAACCAACCATGAGTTA 58.697 33.333 0.00 0.00 36.18 2.24
3075 4108 7.164230 TGGGTATCACATTTCATTAACCAAC 57.836 36.000 0.00 0.00 26.90 3.77
3090 4123 5.968528 TTACCACATGTTTTGGGTATCAC 57.031 39.130 12.24 0.00 38.59 3.06
3096 4129 3.719173 ACGTTTACCACATGTTTTGGG 57.281 42.857 0.00 0.00 38.59 4.12
3097 4130 4.673441 TCAACGTTTACCACATGTTTTGG 58.327 39.130 0.00 0.00 40.32 3.28
3099 4132 5.897050 ACATCAACGTTTACCACATGTTTT 58.103 33.333 0.00 0.00 0.00 2.43
3125 4160 7.011482 GCCATCAACGTTTAGATCACTTAGAAT 59.989 37.037 0.00 0.00 0.00 2.40
3143 4191 2.735663 CGCATCTAGATCAGCCATCAAC 59.264 50.000 1.03 0.00 33.29 3.18
3150 4198 2.799412 CAAGTTCCGCATCTAGATCAGC 59.201 50.000 1.03 3.53 0.00 4.26
3159 4207 2.095718 GGTTTGAGTCAAGTTCCGCATC 60.096 50.000 5.56 0.00 0.00 3.91
3163 4211 1.235724 GGGGTTTGAGTCAAGTTCCG 58.764 55.000 5.56 0.00 0.00 4.30
3179 4227 0.748005 CGCTACACCTTTGATGGGGG 60.748 60.000 0.00 0.00 34.06 5.40
3195 4243 1.660560 GCCATCCTCAATTGCACGCT 61.661 55.000 0.00 0.00 0.00 5.07
3197 4245 0.742505 ATGCCATCCTCAATTGCACG 59.257 50.000 0.00 0.00 38.71 5.34
3260 4308 5.409520 TGGAGTCTCAAAAATCTGTCAATCG 59.590 40.000 1.47 0.00 0.00 3.34
3264 4312 5.296151 ACTGGAGTCTCAAAAATCTGTCA 57.704 39.130 1.47 0.00 0.00 3.58
3358 4407 1.001633 AGCTTCCGTGTGGTTTATCGT 59.998 47.619 0.00 0.00 36.30 3.73
3393 4442 0.375803 GAAACACGTGGCGAACAAGT 59.624 50.000 21.57 0.00 42.69 3.16
3395 4444 0.375454 CAGAAACACGTGGCGAACAA 59.625 50.000 21.57 0.00 0.00 2.83
3396 4445 2.010670 CAGAAACACGTGGCGAACA 58.989 52.632 21.57 0.00 0.00 3.18
3397 4446 1.368850 GCAGAAACACGTGGCGAAC 60.369 57.895 21.57 6.45 0.00 3.95
3405 4454 2.355363 TCCGTCCGCAGAAACACG 60.355 61.111 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.