Multiple sequence alignment - TraesCS6D01G302900

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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 TraesCS6D01G302900 chr6D 100.000 3359 0 0 1 3359 411770231 411766873 0.000000e+00 6204
1 TraesCS6D01G302900 chr6D 86.116 569 37 18 2751 3309 411726348 411725812 2.910000e-160 575
2 TraesCS6D01G302900 chr6A 85.360 1974 193 55 1423 3356 556678492 556676575 0.000000e+00 1956
3 TraesCS6D01G302900 chr6A 85.212 1224 83 24 193 1381 556679660 556678500 0.000000e+00 1168
4 TraesCS6D01G302900 chr6A 87.368 570 30 17 2752 3309 556669947 556669408 1.710000e-172 616
5 TraesCS6D01G302900 chr6A 78.451 891 117 31 1758 2624 99973631 99974470 2.310000e-141 512
6 TraesCS6D01G302900 chr6A 81.618 272 40 8 346 614 109177701 109177965 2.030000e-52 217
7 TraesCS6D01G302900 chr6B 84.217 1755 155 56 734 2444 619494352 619492676 0.000000e+00 1594
8 TraesCS6D01G302900 chr6B 86.402 956 68 24 2446 3359 619484624 619483689 0.000000e+00 989
9 TraesCS6D01G302900 chr6B 85.191 628 40 23 2709 3309 619405094 619404493 2.230000e-166 595
10 TraesCS6D01G302900 chr6B 83.188 458 54 13 222 677 619494791 619494355 6.750000e-107 398
11 TraesCS6D01G302900 chr6B 85.062 241 19 10 356 594 597291706 597291481 2.610000e-56 230
12 TraesCS6D01G302900 chr5D 87.412 707 65 12 1748 2444 358668848 358668156 0.000000e+00 791
13 TraesCS6D01G302900 chr3A 83.824 340 43 9 2731 3066 541226283 541225952 2.520000e-81 313
14 TraesCS6D01G302900 chr3B 81.765 340 49 9 2731 3066 536429047 536429377 4.270000e-69 272
15 TraesCS6D01G302900 chr3B 82.609 253 35 6 349 599 284380242 284380487 7.300000e-52 215
16 TraesCS6D01G302900 chr3B 81.250 272 38 10 345 614 519860917 519860657 1.220000e-49 207
17 TraesCS6D01G302900 chr3B 80.827 266 42 6 349 614 97756143 97755887 2.040000e-47 200
18 TraesCS6D01G302900 chr7D 86.512 215 17 4 1807 2021 32581403 32581201 3.370000e-55 226
19 TraesCS6D01G302900 chr5A 81.818 253 37 5 349 599 571792405 571792160 1.580000e-48 204
20 TraesCS6D01G302900 chr1B 81.783 258 34 11 366 619 644579587 644579835 1.580000e-48 204
21 TraesCS6D01G302900 chr1D 82.609 230 31 7 390 619 467118966 467119186 9.510000e-46 195
22 TraesCS6D01G302900 chr2D 81.081 259 25 11 2101 2359 178526983 178526749 5.720000e-43 185
23 TraesCS6D01G302900 chr2D 80.216 278 28 14 2085 2359 178694767 178694514 2.060000e-42 183
24 TraesCS6D01G302900 chr3D 87.162 148 17 2 2919 3065 410518476 410518622 2.070000e-37 167
25 TraesCS6D01G302900 chr2B 80.247 243 23 9 2101 2343 235902553 235902336 3.470000e-35 159
26 TraesCS6D01G302900 chr2B 88.636 132 11 2 2101 2232 235899885 235899758 1.250000e-34 158
27 TraesCS6D01G302900 chr2A 78.277 267 26 13 2087 2350 193578516 193578279 3.490000e-30 143


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 TraesCS6D01G302900 chr6D 411766873 411770231 3358 True 6204 6204 100.0000 1 3359 1 chr6D.!!$R2 3358
1 TraesCS6D01G302900 chr6D 411725812 411726348 536 True 575 575 86.1160 2751 3309 1 chr6D.!!$R1 558
2 TraesCS6D01G302900 chr6A 556676575 556679660 3085 True 1562 1956 85.2860 193 3356 2 chr6A.!!$R2 3163
3 TraesCS6D01G302900 chr6A 556669408 556669947 539 True 616 616 87.3680 2752 3309 1 chr6A.!!$R1 557
4 TraesCS6D01G302900 chr6A 99973631 99974470 839 False 512 512 78.4510 1758 2624 1 chr6A.!!$F1 866
5 TraesCS6D01G302900 chr6B 619492676 619494791 2115 True 996 1594 83.7025 222 2444 2 chr6B.!!$R4 2222
6 TraesCS6D01G302900 chr6B 619483689 619484624 935 True 989 989 86.4020 2446 3359 1 chr6B.!!$R3 913
7 TraesCS6D01G302900 chr6B 619404493 619405094 601 True 595 595 85.1910 2709 3309 1 chr6B.!!$R2 600
8 TraesCS6D01G302900 chr5D 358668156 358668848 692 True 791 791 87.4120 1748 2444 1 chr5D.!!$R1 696

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
720 733 0.537143 ACGTCCTTGAGGCAAATGCA 60.537 50.0 7.8 0.0 44.36 3.96 F
1552 1597 0.106335 CGGATCAGATGCTGAGGCTT 59.894 55.0 0.0 0.0 44.08 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1804 0.250858 TGACCCTGCACATTCCACAG 60.251 55.0 0.0 0.0 0.0 3.66 R
2728 2830 0.320421 GCGGCTGGTTAGTTCTGACA 60.320 55.0 0.0 0.0 0.0 3.58 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
29 30 9.522804 AAACATTTTCACGTACACATTACATTT 57.477 25.926 0.00 0.00 0.00 2.32
30 31 9.522804 AACATTTTCACGTACACATTACATTTT 57.477 25.926 0.00 0.00 0.00 1.82
31 32 9.522804 ACATTTTCACGTACACATTACATTTTT 57.477 25.926 0.00 0.00 0.00 1.94
157 158 8.883789 AACGTAACATACATTTATTTGAACGG 57.116 30.769 0.00 0.00 0.00 4.44
158 159 8.031848 ACGTAACATACATTTATTTGAACGGT 57.968 30.769 0.00 0.00 0.00 4.83
159 160 8.170553 ACGTAACATACATTTATTTGAACGGTC 58.829 33.333 0.00 0.00 0.00 4.79
160 161 8.385111 CGTAACATACATTTATTTGAACGGTCT 58.615 33.333 0.33 0.00 0.00 3.85
212 213 5.119279 TGGTTGAAACACGTGAACATTTTTG 59.881 36.000 25.01 0.00 0.00 2.44
214 215 6.035542 GGTTGAAACACGTGAACATTTTTGAT 59.964 34.615 25.01 0.00 0.00 2.57
224 225 7.918033 ACGTGAACATTTTTGATATGTCACAAA 59.082 29.630 6.28 6.28 38.12 2.83
225 226 8.750416 CGTGAACATTTTTGATATGTCACAAAA 58.250 29.630 7.70 10.07 41.88 2.44
284 285 1.059942 GCTAATTTTGTGCACCGTGC 58.940 50.000 16.93 16.93 45.29 5.34
294 295 2.287308 TGTGCACCGTGCTAACATTTTC 60.287 45.455 23.52 4.72 45.31 2.29
304 305 5.164196 CGTGCTAACATTTTCCAAATTCGTG 60.164 40.000 0.00 0.00 0.00 4.35
379 382 5.294356 TCCGTTCCATAATGTAGTGCATAC 58.706 41.667 0.00 0.00 36.67 2.39
459 472 8.574251 TTTGTATCTACAATTGCAGTACCAAT 57.426 30.769 5.05 0.00 44.72 3.16
614 627 7.484975 CACTACATTACTTAAGAGAGGGAGTG 58.515 42.308 18.26 18.26 0.00 3.51
633 646 9.720769 AGGGAGTGTGTATTTATAATATTTCGG 57.279 33.333 0.00 0.00 0.00 4.30
690 703 5.104982 GGAAATATGGAAGTTGATTTGGGCA 60.105 40.000 0.00 0.00 0.00 5.36
704 717 4.012138 GGCAGGCCCATTTTACGT 57.988 55.556 0.00 0.00 0.00 3.57
705 718 1.807226 GGCAGGCCCATTTTACGTC 59.193 57.895 0.00 0.00 0.00 4.34
706 719 1.663379 GGCAGGCCCATTTTACGTCC 61.663 60.000 0.00 0.00 0.00 4.79
707 720 0.679960 GCAGGCCCATTTTACGTCCT 60.680 55.000 0.00 0.00 0.00 3.85
708 721 1.834188 CAGGCCCATTTTACGTCCTT 58.166 50.000 0.00 0.00 0.00 3.36
709 722 1.472480 CAGGCCCATTTTACGTCCTTG 59.528 52.381 0.00 0.00 0.00 3.61
710 723 1.353022 AGGCCCATTTTACGTCCTTGA 59.647 47.619 0.00 0.00 0.00 3.02
711 724 1.743394 GGCCCATTTTACGTCCTTGAG 59.257 52.381 0.00 0.00 0.00 3.02
712 725 1.743394 GCCCATTTTACGTCCTTGAGG 59.257 52.381 0.00 0.00 0.00 3.86
713 726 1.743394 CCCATTTTACGTCCTTGAGGC 59.257 52.381 0.00 0.00 34.44 4.70
714 727 2.432444 CCATTTTACGTCCTTGAGGCA 58.568 47.619 0.00 0.00 34.44 4.75
715 728 2.817258 CCATTTTACGTCCTTGAGGCAA 59.183 45.455 0.00 0.00 34.44 4.52
716 729 3.254657 CCATTTTACGTCCTTGAGGCAAA 59.745 43.478 0.00 0.00 34.44 3.68
717 730 4.082245 CCATTTTACGTCCTTGAGGCAAAT 60.082 41.667 0.00 0.00 34.44 2.32
718 731 4.497473 TTTTACGTCCTTGAGGCAAATG 57.503 40.909 0.00 0.00 34.44 2.32
719 732 1.448985 TACGTCCTTGAGGCAAATGC 58.551 50.000 0.00 0.00 41.14 3.56
720 733 0.537143 ACGTCCTTGAGGCAAATGCA 60.537 50.000 7.80 0.00 44.36 3.96
721 734 0.813184 CGTCCTTGAGGCAAATGCAT 59.187 50.000 7.80 0.00 44.36 3.96
743 756 2.203788 AGGGAGCCGTGACTTGGA 60.204 61.111 0.00 0.00 0.00 3.53
755 768 1.271543 TGACTTGGAGCCCATGTTCAG 60.272 52.381 12.07 2.55 41.09 3.02
805 823 1.490910 GCCCTTACAGCTAGGTCCAAT 59.509 52.381 0.37 0.00 0.00 3.16
815 833 0.739462 TAGGTCCAATTCGCACGCAG 60.739 55.000 0.00 0.00 0.00 5.18
883 901 3.041940 AGCCGACGCTTTTGTCCG 61.042 61.111 0.00 0.00 45.55 4.79
921 939 3.804193 CGGCTTGGCTTCCGCTTC 61.804 66.667 0.38 0.00 39.14 3.86
986 1004 1.447838 GCCTCGCGTTCTTGGATCA 60.448 57.895 5.77 0.00 0.00 2.92
1112 1143 2.043248 TCTGCCGGGACCTCTACC 60.043 66.667 2.18 0.00 0.00 3.18
1225 1262 3.986006 GTCGGTGGTGGTGCGAGA 61.986 66.667 0.00 0.00 0.00 4.04
1232 1269 1.070786 GGTGGTGCGAGAACAGGAA 59.929 57.895 0.00 0.00 0.00 3.36
1235 1272 0.318441 TGGTGCGAGAACAGGAAGAG 59.682 55.000 0.00 0.00 0.00 2.85
1377 1414 2.608016 CCATCATCATCGACTGGTACGG 60.608 54.545 0.00 0.00 42.99 4.02
1389 1426 2.047560 GTACGGCACCAGGACCAC 60.048 66.667 0.00 0.00 0.00 4.16
1398 1435 2.930019 CAGGACCACCCCTGCTCA 60.930 66.667 0.00 0.00 46.16 4.26
1399 1436 2.121963 AGGACCACCCCTGCTCAA 60.122 61.111 0.00 0.00 34.68 3.02
1400 1437 1.542375 AGGACCACCCCTGCTCAAT 60.542 57.895 0.00 0.00 34.68 2.57
1401 1438 0.253160 AGGACCACCCCTGCTCAATA 60.253 55.000 0.00 0.00 34.68 1.90
1402 1439 0.846693 GGACCACCCCTGCTCAATAT 59.153 55.000 0.00 0.00 0.00 1.28
1403 1440 1.477558 GGACCACCCCTGCTCAATATG 60.478 57.143 0.00 0.00 0.00 1.78
1404 1441 0.106519 ACCACCCCTGCTCAATATGC 60.107 55.000 0.00 0.00 0.00 3.14
1405 1442 0.106569 CCACCCCTGCTCAATATGCA 60.107 55.000 0.00 0.00 38.81 3.96
1406 1443 1.027357 CACCCCTGCTCAATATGCAC 58.973 55.000 0.00 0.00 36.37 4.57
1407 1444 0.106519 ACCCCTGCTCAATATGCACC 60.107 55.000 0.00 0.00 36.37 5.01
1408 1445 0.825010 CCCCTGCTCAATATGCACCC 60.825 60.000 0.00 0.00 36.37 4.61
1409 1446 0.184451 CCCTGCTCAATATGCACCCT 59.816 55.000 0.00 0.00 36.37 4.34
1410 1447 1.315690 CCTGCTCAATATGCACCCTG 58.684 55.000 0.00 0.00 36.37 4.45
1411 1448 1.315690 CTGCTCAATATGCACCCTGG 58.684 55.000 0.00 0.00 36.37 4.45
1412 1449 0.752743 TGCTCAATATGCACCCTGGC 60.753 55.000 0.00 0.00 35.31 4.85
1413 1450 1.458639 GCTCAATATGCACCCTGGCC 61.459 60.000 0.00 0.00 0.00 5.36
1414 1451 1.152984 TCAATATGCACCCTGGCCG 60.153 57.895 0.00 0.00 0.00 6.13
1415 1452 2.195567 CAATATGCACCCTGGCCGG 61.196 63.158 3.88 3.88 0.00 6.13
1416 1453 4.586235 ATATGCACCCTGGCCGGC 62.586 66.667 21.18 21.18 0.00 6.13
1453 1491 0.599558 TGCAGTGCAGCTTGATTTCC 59.400 50.000 15.37 0.00 33.32 3.13
1454 1492 0.599558 GCAGTGCAGCTTGATTTCCA 59.400 50.000 11.09 0.00 0.00 3.53
1456 1494 2.424601 GCAGTGCAGCTTGATTTCCATA 59.575 45.455 11.09 0.00 0.00 2.74
1457 1495 3.119388 GCAGTGCAGCTTGATTTCCATAA 60.119 43.478 11.09 0.00 0.00 1.90
1462 1500 3.688272 CAGCTTGATTTCCATAACTGCG 58.312 45.455 0.00 0.00 0.00 5.18
1475 1513 1.097547 AACTGCGTTGCTGCTCTGTT 61.098 50.000 0.00 1.91 35.36 3.16
1479 1517 1.673400 TGCGTTGCTGCTCTGTTTTTA 59.327 42.857 0.00 0.00 35.36 1.52
1480 1518 2.044135 GCGTTGCTGCTCTGTTTTTAC 58.956 47.619 0.00 0.00 0.00 2.01
1481 1519 2.287009 GCGTTGCTGCTCTGTTTTTACT 60.287 45.455 0.00 0.00 0.00 2.24
1482 1520 3.059188 GCGTTGCTGCTCTGTTTTTACTA 60.059 43.478 0.00 0.00 0.00 1.82
1483 1521 4.702392 CGTTGCTGCTCTGTTTTTACTAG 58.298 43.478 0.00 0.00 0.00 2.57
1484 1522 4.211374 CGTTGCTGCTCTGTTTTTACTAGT 59.789 41.667 0.00 0.00 0.00 2.57
1485 1523 5.404366 CGTTGCTGCTCTGTTTTTACTAGTA 59.596 40.000 0.00 0.00 0.00 1.82
1502 1540 6.834959 ACTAGTAAATCAGCATTCATGTCG 57.165 37.500 0.00 0.00 0.00 4.35
1503 1541 4.542662 AGTAAATCAGCATTCATGTCGC 57.457 40.909 0.00 0.00 0.00 5.19
1504 1542 4.194640 AGTAAATCAGCATTCATGTCGCT 58.805 39.130 0.00 0.00 36.10 4.93
1509 1547 2.274437 CAGCATTCATGTCGCTGTAGT 58.726 47.619 19.09 0.00 46.36 2.73
1523 1568 5.581085 GTCGCTGTAGTCTTCAACCATTTAT 59.419 40.000 0.00 0.00 0.00 1.40
1542 1587 3.524095 ATCTCAGTCCTCGGATCAGAT 57.476 47.619 0.00 0.00 0.00 2.90
1552 1597 0.106335 CGGATCAGATGCTGAGGCTT 59.894 55.000 0.00 0.00 44.08 4.35
1553 1598 1.474677 CGGATCAGATGCTGAGGCTTT 60.475 52.381 0.00 0.00 44.08 3.51
1554 1599 2.224137 CGGATCAGATGCTGAGGCTTTA 60.224 50.000 0.00 0.00 44.08 1.85
1555 1600 3.401182 GGATCAGATGCTGAGGCTTTAG 58.599 50.000 3.36 0.00 44.08 1.85
1569 1614 5.069914 TGAGGCTTTAGTCAGTGTGTTCTTA 59.930 40.000 0.00 0.00 0.00 2.10
1607 1652 1.476085 TGCCGGAAATGCATTTACCTG 59.524 47.619 25.36 21.42 32.85 4.00
1634 1679 1.422531 AGCTGGAGAAGATAGCAGGG 58.577 55.000 0.00 0.00 39.84 4.45
1688 1738 9.785982 TGAAATGATTTCATACCGTATCCATAA 57.214 29.630 16.04 0.00 44.21 1.90
1731 1781 7.860649 ATTGGGATTATTGATAGCATTTGGT 57.139 32.000 0.00 0.00 0.00 3.67
1732 1782 8.954834 ATTGGGATTATTGATAGCATTTGGTA 57.045 30.769 0.00 0.00 0.00 3.25
1733 1783 8.954834 TTGGGATTATTGATAGCATTTGGTAT 57.045 30.769 2.08 2.08 40.97 2.73
1746 1796 9.979897 ATAGCATTTGGTATATATCCACAACAT 57.020 29.630 0.58 0.00 37.01 2.71
1754 1804 9.283768 TGGTATATATCCACAACATTCAATCAC 57.716 33.333 0.00 0.00 0.00 3.06
1770 1820 0.250858 TCACTGTGGAATGTGCAGGG 60.251 55.000 8.11 0.00 35.15 4.45
1771 1821 0.538057 CACTGTGGAATGTGCAGGGT 60.538 55.000 0.00 0.00 34.79 4.34
1804 1854 7.658179 TGATTCTGACTAAACAACACATCTC 57.342 36.000 0.00 0.00 0.00 2.75
1805 1855 6.650807 TGATTCTGACTAAACAACACATCTCC 59.349 38.462 0.00 0.00 0.00 3.71
1811 1862 6.706270 TGACTAAACAACACATCTCCTTCTTC 59.294 38.462 0.00 0.00 0.00 2.87
1812 1863 5.998363 ACTAAACAACACATCTCCTTCTTCC 59.002 40.000 0.00 0.00 0.00 3.46
1822 1873 1.480137 CTCCTTCTTCCGCAGAGTCAT 59.520 52.381 0.00 0.00 31.12 3.06
1841 1892 6.738114 AGTCATGTTTTACTTTGTGGATGTG 58.262 36.000 0.00 0.00 0.00 3.21
1877 1928 1.235724 CCGTGGTGAAAAGAGGGAAC 58.764 55.000 0.00 0.00 0.00 3.62
1900 1951 9.463443 GAACATAAGTGTAAGTCAGCAAATTTT 57.537 29.630 0.00 0.00 37.67 1.82
1907 1958 6.918022 GTGTAAGTCAGCAAATTTTAGCTTGT 59.082 34.615 0.00 0.00 39.50 3.16
1908 1959 6.917477 TGTAAGTCAGCAAATTTTAGCTTGTG 59.083 34.615 0.00 0.00 39.50 3.33
1913 1964 6.363357 GTCAGCAAATTTTAGCTTGTGTTAGG 59.637 38.462 0.00 0.00 39.50 2.69
1949 2004 6.648879 TTGAAGGGGAAATTTGAGTACTTG 57.351 37.500 0.00 0.00 0.00 3.16
1954 2009 4.556233 GGGAAATTTGAGTACTTGTTGGC 58.444 43.478 0.00 0.00 0.00 4.52
2024 2083 1.065564 GCTCCCATCTGTCTCTGCTTT 60.066 52.381 0.00 0.00 0.00 3.51
2070 2133 9.702726 CTATTCAGGTAACGTCATATTTGTTTG 57.297 33.333 0.00 0.00 46.39 2.93
2073 2136 6.021596 CAGGTAACGTCATATTTGTTTGCTC 58.978 40.000 0.00 0.00 46.39 4.26
2077 2140 4.475944 ACGTCATATTTGTTTGCTCAAGC 58.524 39.130 0.00 0.00 42.50 4.01
2098 2161 3.181483 GCTCTGCATTTGTCCCTTTATGG 60.181 47.826 0.00 0.00 0.00 2.74
2134 2200 2.847441 TCTCATGATGATGCTTGCTCC 58.153 47.619 0.00 0.00 0.00 4.70
2234 2300 5.994668 GGATGAGGTTAGAGAAATGATCCAC 59.005 44.000 0.00 0.00 0.00 4.02
2248 2314 4.002906 TGATCCACAAGTACAAGTGACC 57.997 45.455 16.47 7.66 37.97 4.02
2305 2373 0.749649 ATGATCTCCTCGGACACTGC 59.250 55.000 0.00 0.00 0.00 4.40
2351 2423 3.386078 CCAGCTCCTTAATACAGCAGAGA 59.614 47.826 0.00 0.00 35.46 3.10
2360 2432 4.989875 AATACAGCAGAGATGGCCTATT 57.010 40.909 3.32 0.00 0.00 1.73
2363 2435 2.104451 ACAGCAGAGATGGCCTATTCTG 59.896 50.000 19.98 19.98 39.94 3.02
2380 2452 3.502191 TCTGTTGGTCTGTTGCAAAAC 57.498 42.857 0.00 1.10 0.00 2.43
2381 2453 2.165437 TCTGTTGGTCTGTTGCAAAACC 59.835 45.455 16.29 16.29 0.00 3.27
2382 2454 1.205893 TGTTGGTCTGTTGCAAAACCC 59.794 47.619 18.99 10.37 0.00 4.11
2407 2481 8.836413 CCTCACTTGAATACTTCAGTTTTGTAA 58.164 33.333 0.00 0.00 41.38 2.41
2511 2607 5.541845 TCTGTAGAACTGAACAATCCACAG 58.458 41.667 0.00 0.00 37.62 3.66
2518 2614 4.269183 ACTGAACAATCCACAGTCACAAA 58.731 39.130 0.00 0.00 40.19 2.83
2520 2616 5.185668 TGAACAATCCACAGTCACAAATG 57.814 39.130 0.00 0.00 0.00 2.32
2539 2635 7.588854 CACAAATGATACAGAAGACAAACTGTG 59.411 37.037 0.00 0.00 45.20 3.66
2585 2681 7.650890 TCCCGATTCAAATCAATGAACATATG 58.349 34.615 0.00 0.00 41.78 1.78
2600 2696 0.850784 ATATGTACAAGGCCCCACCC 59.149 55.000 0.00 0.00 40.58 4.61
2616 2712 2.166254 CCACCCAACCTGATTTACATGC 59.834 50.000 0.00 0.00 0.00 4.06
2617 2713 3.091545 CACCCAACCTGATTTACATGCT 58.908 45.455 0.00 0.00 0.00 3.79
2618 2714 3.091545 ACCCAACCTGATTTACATGCTG 58.908 45.455 0.00 0.00 0.00 4.41
2619 2715 3.245229 ACCCAACCTGATTTACATGCTGA 60.245 43.478 0.00 0.00 0.00 4.26
2620 2716 3.379372 CCCAACCTGATTTACATGCTGAG 59.621 47.826 0.00 0.00 0.00 3.35
2621 2717 4.012374 CCAACCTGATTTACATGCTGAGT 58.988 43.478 0.00 0.00 0.00 3.41
2622 2718 4.460382 CCAACCTGATTTACATGCTGAGTT 59.540 41.667 0.00 0.00 0.00 3.01
2623 2719 5.047802 CCAACCTGATTTACATGCTGAGTTT 60.048 40.000 0.00 0.00 0.00 2.66
2624 2720 6.449698 CAACCTGATTTACATGCTGAGTTTT 58.550 36.000 0.00 0.00 0.00 2.43
2692 2788 2.618709 CAAACCCAGGACAGTTCAGAAC 59.381 50.000 5.00 5.00 0.00 3.01
2693 2789 1.507140 ACCCAGGACAGTTCAGAACA 58.493 50.000 15.85 0.00 0.00 3.18
2694 2790 1.417890 ACCCAGGACAGTTCAGAACAG 59.582 52.381 15.85 10.03 0.00 3.16
2695 2791 1.694150 CCCAGGACAGTTCAGAACAGA 59.306 52.381 15.85 0.00 0.00 3.41
2696 2792 2.104792 CCCAGGACAGTTCAGAACAGAA 59.895 50.000 15.85 0.00 0.00 3.02
2700 2796 6.176183 CCAGGACAGTTCAGAACAGAATTAT 58.824 40.000 15.85 0.00 0.00 1.28
2715 2817 6.987386 ACAGAATTATCAAGCTCGCTAGTAT 58.013 36.000 0.00 0.00 0.00 2.12
2724 2826 3.768878 AGCTCGCTAGTATCTACCCATT 58.231 45.455 0.00 0.00 0.00 3.16
2740 2842 4.766404 CCCATTTGGTGTCAGAACTAAC 57.234 45.455 0.00 0.00 0.00 2.34
2743 2845 4.216257 CCATTTGGTGTCAGAACTAACCAG 59.784 45.833 0.00 0.00 43.31 4.00
2809 2914 2.717809 GCGACGACCACGAAGAAGC 61.718 63.158 0.00 0.00 42.66 3.86
2816 2933 1.372499 CCACGAAGAAGCCGACGAA 60.372 57.895 0.00 0.00 0.00 3.85
3091 3211 2.679837 CGGTGGATCAGTCAATCAAAGG 59.320 50.000 0.00 0.00 0.00 3.11
3099 3219 0.740737 GTCAATCAAAGGGGATGGCG 59.259 55.000 0.00 0.00 0.00 5.69
3140 3294 0.456221 AGGTCGCTCTTGTGTATCGG 59.544 55.000 0.00 0.00 0.00 4.18
3147 3301 2.205074 CTCTTGTGTATCGGTGGATGC 58.795 52.381 0.00 0.00 36.00 3.91
3292 3455 1.587613 GCAAACGCAAGCGGTGAAA 60.588 52.632 19.30 0.00 40.27 2.69
3309 3480 0.452585 AAACGTTGTGGGTTTCGTGG 59.547 50.000 0.00 0.00 36.65 4.94
3310 3481 1.378124 AACGTTGTGGGTTTCGTGGG 61.378 55.000 0.00 0.00 36.65 4.61
3311 3482 2.725641 GTTGTGGGTTTCGTGGGC 59.274 61.111 0.00 0.00 0.00 5.36
3312 3483 2.902846 TTGTGGGTTTCGTGGGCG 60.903 61.111 0.00 0.00 39.92 6.13
3318 3489 2.746277 GTTTCGTGGGCGCCTGAT 60.746 61.111 28.56 0.00 38.14 2.90
3319 3490 2.033448 TTTCGTGGGCGCCTGATT 59.967 55.556 28.56 0.00 38.14 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.522804 AAATGTAATGTGTACGTGAAAATGTTT 57.477 25.926 0.00 0.00 0.00 2.83
5 6 9.522804 AAAAATGTAATGTGTACGTGAAAATGT 57.477 25.926 0.00 0.00 0.00 2.71
131 132 9.332301 CCGTTCAAATAAATGTATGTTACGTTT 57.668 29.630 0.00 9.19 46.41 3.60
132 133 8.505625 ACCGTTCAAATAAATGTATGTTACGTT 58.494 29.630 0.00 0.00 39.46 3.99
133 134 8.031848 ACCGTTCAAATAAATGTATGTTACGT 57.968 30.769 0.00 0.00 0.00 3.57
134 135 8.385111 AGACCGTTCAAATAAATGTATGTTACG 58.615 33.333 0.00 0.00 0.00 3.18
173 174 9.615295 GTGTTTCAACCATGTATACGTTATTTT 57.385 29.630 0.00 0.00 0.00 1.82
174 175 7.958567 CGTGTTTCAACCATGTATACGTTATTT 59.041 33.333 0.00 0.00 0.00 1.40
175 176 7.118101 ACGTGTTTCAACCATGTATACGTTATT 59.882 33.333 0.00 0.00 37.02 1.40
176 177 6.591062 ACGTGTTTCAACCATGTATACGTTAT 59.409 34.615 0.00 0.00 37.02 1.89
177 178 5.925397 ACGTGTTTCAACCATGTATACGTTA 59.075 36.000 0.00 0.00 37.02 3.18
178 179 4.751098 ACGTGTTTCAACCATGTATACGTT 59.249 37.500 0.00 0.00 37.02 3.99
179 180 4.150980 CACGTGTTTCAACCATGTATACGT 59.849 41.667 7.58 0.00 38.94 3.57
180 181 4.386350 TCACGTGTTTCAACCATGTATACG 59.614 41.667 16.51 0.00 35.12 3.06
181 182 5.849357 TCACGTGTTTCAACCATGTATAC 57.151 39.130 16.51 0.00 0.00 1.47
182 183 5.758784 TGTTCACGTGTTTCAACCATGTATA 59.241 36.000 16.51 0.00 0.00 1.47
183 184 4.576873 TGTTCACGTGTTTCAACCATGTAT 59.423 37.500 16.51 0.00 0.00 2.29
184 185 3.939592 TGTTCACGTGTTTCAACCATGTA 59.060 39.130 16.51 0.00 0.00 2.29
185 186 2.750166 TGTTCACGTGTTTCAACCATGT 59.250 40.909 16.51 0.00 0.00 3.21
186 187 3.412981 TGTTCACGTGTTTCAACCATG 57.587 42.857 16.51 0.00 0.00 3.66
187 188 4.647424 AATGTTCACGTGTTTCAACCAT 57.353 36.364 16.51 6.27 0.00 3.55
188 189 4.442375 AAATGTTCACGTGTTTCAACCA 57.558 36.364 16.51 4.31 0.00 3.67
189 190 5.346281 TCAAAAATGTTCACGTGTTTCAACC 59.654 36.000 16.51 0.00 0.00 3.77
190 191 6.382821 TCAAAAATGTTCACGTGTTTCAAC 57.617 33.333 16.51 12.80 0.00 3.18
191 192 8.750416 CATATCAAAAATGTTCACGTGTTTCAA 58.250 29.630 16.51 0.00 0.00 2.69
276 277 1.268352 TGGAAAATGTTAGCACGGTGC 59.732 47.619 25.00 25.00 45.46 5.01
284 285 8.741101 TTCATCACGAATTTGGAAAATGTTAG 57.259 30.769 0.00 0.00 0.00 2.34
335 336 7.173032 ACGGAGGAAGTATATTCCAAAAACTT 58.827 34.615 9.20 0.00 41.00 2.66
337 338 6.997239 ACGGAGGAAGTATATTCCAAAAAC 57.003 37.500 9.20 0.00 41.00 2.43
353 356 3.181469 GCACTACATTATGGAACGGAGGA 60.181 47.826 0.00 0.00 0.00 3.71
437 442 7.786178 TGATTGGTACTGCAATTGTAGATAC 57.214 36.000 27.53 22.21 0.00 2.24
543 556 8.772705 GTCAAGCATCATAAATTTTGACCAAAA 58.227 29.630 9.94 9.94 43.48 2.44
654 667 8.670521 ACTTCCATATTTCCTTTTTCCATCTT 57.329 30.769 0.00 0.00 0.00 2.40
655 668 8.534496 CAACTTCCATATTTCCTTTTTCCATCT 58.466 33.333 0.00 0.00 0.00 2.90
656 669 8.531146 TCAACTTCCATATTTCCTTTTTCCATC 58.469 33.333 0.00 0.00 0.00 3.51
657 670 8.434589 TCAACTTCCATATTTCCTTTTTCCAT 57.565 30.769 0.00 0.00 0.00 3.41
658 671 7.847711 TCAACTTCCATATTTCCTTTTTCCA 57.152 32.000 0.00 0.00 0.00 3.53
665 678 5.129320 GCCCAAATCAACTTCCATATTTCCT 59.871 40.000 0.00 0.00 0.00 3.36
677 690 4.118584 GGCCTGCCCAAATCAACT 57.881 55.556 0.00 0.00 0.00 3.16
690 703 1.353022 TCAAGGACGTAAAATGGGCCT 59.647 47.619 4.53 0.00 0.00 5.19
698 711 2.227865 GCATTTGCCTCAAGGACGTAAA 59.772 45.455 0.00 0.00 37.39 2.01
699 712 1.810151 GCATTTGCCTCAAGGACGTAA 59.190 47.619 0.00 0.00 37.39 3.18
700 713 1.271108 TGCATTTGCCTCAAGGACGTA 60.271 47.619 0.00 0.00 41.18 3.57
701 714 0.537143 TGCATTTGCCTCAAGGACGT 60.537 50.000 0.00 0.00 41.18 4.34
702 715 0.813184 ATGCATTTGCCTCAAGGACG 59.187 50.000 0.00 0.00 41.18 4.79
703 716 2.097825 AGATGCATTTGCCTCAAGGAC 58.902 47.619 0.00 0.00 41.18 3.85
704 717 2.097036 CAGATGCATTTGCCTCAAGGA 58.903 47.619 4.04 0.00 41.18 3.36
705 718 1.136305 CCAGATGCATTTGCCTCAAGG 59.864 52.381 11.66 7.49 41.18 3.61
706 719 2.097036 TCCAGATGCATTTGCCTCAAG 58.903 47.619 11.66 0.00 41.18 3.02
707 720 2.097036 CTCCAGATGCATTTGCCTCAA 58.903 47.619 11.66 0.00 41.18 3.02
708 721 1.683938 CCTCCAGATGCATTTGCCTCA 60.684 52.381 11.66 0.00 41.18 3.86
709 722 1.030457 CCTCCAGATGCATTTGCCTC 58.970 55.000 11.66 0.00 41.18 4.70
710 723 0.396695 CCCTCCAGATGCATTTGCCT 60.397 55.000 11.66 0.00 41.18 4.75
711 724 0.396139 TCCCTCCAGATGCATTTGCC 60.396 55.000 11.66 0.00 41.18 4.52
712 725 1.030457 CTCCCTCCAGATGCATTTGC 58.970 55.000 11.66 0.00 42.50 3.68
713 726 1.030457 GCTCCCTCCAGATGCATTTG 58.970 55.000 10.22 10.22 0.00 2.32
714 727 0.106318 GGCTCCCTCCAGATGCATTT 60.106 55.000 0.00 0.00 0.00 2.32
715 728 1.535685 GGCTCCCTCCAGATGCATT 59.464 57.895 0.00 0.00 0.00 3.56
716 729 2.815945 CGGCTCCCTCCAGATGCAT 61.816 63.158 0.00 0.00 0.00 3.96
717 730 3.473647 CGGCTCCCTCCAGATGCA 61.474 66.667 0.00 0.00 0.00 3.96
718 731 3.474570 ACGGCTCCCTCCAGATGC 61.475 66.667 0.00 0.00 0.00 3.91
719 732 2.060383 TCACGGCTCCCTCCAGATG 61.060 63.158 0.00 0.00 0.00 2.90
720 733 2.060980 GTCACGGCTCCCTCCAGAT 61.061 63.158 0.00 0.00 0.00 2.90
721 734 2.680352 GTCACGGCTCCCTCCAGA 60.680 66.667 0.00 0.00 0.00 3.86
743 756 2.045926 GACCGCTGAACATGGGCT 60.046 61.111 0.00 0.00 0.00 5.19
805 823 2.024022 GTTTGTGCTGCGTGCGAA 59.976 55.556 0.00 0.00 46.63 4.70
883 901 2.231721 GGAGAGGCTTATCCGTATGACC 59.768 54.545 0.00 0.00 40.77 4.02
986 1004 2.031919 TGGTCTGCGCGTGGAATT 59.968 55.556 8.43 0.00 0.00 2.17
1058 1089 3.446570 GAGCAGCGGCATTGGCTT 61.447 61.111 12.44 0.00 44.61 4.35
1210 1247 3.041940 GTTCTCGCACCACCACCG 61.042 66.667 0.00 0.00 0.00 4.94
1211 1248 1.961277 CTGTTCTCGCACCACCACC 60.961 63.158 0.00 0.00 0.00 4.61
1216 1253 0.318441 CTCTTCCTGTTCTCGCACCA 59.682 55.000 0.00 0.00 0.00 4.17
1217 1254 0.390472 CCTCTTCCTGTTCTCGCACC 60.390 60.000 0.00 0.00 0.00 5.01
1218 1255 0.603569 TCCTCTTCCTGTTCTCGCAC 59.396 55.000 0.00 0.00 0.00 5.34
1219 1256 0.891373 CTCCTCTTCCTGTTCTCGCA 59.109 55.000 0.00 0.00 0.00 5.10
1225 1262 0.193574 TCACCCCTCCTCTTCCTGTT 59.806 55.000 0.00 0.00 0.00 3.16
1232 1269 4.787280 CGCCCTCACCCCTCCTCT 62.787 72.222 0.00 0.00 0.00 3.69
1383 1420 0.846693 ATATTGAGCAGGGGTGGTCC 59.153 55.000 2.36 0.00 35.63 4.46
1384 1421 1.972872 CATATTGAGCAGGGGTGGTC 58.027 55.000 0.00 0.00 36.89 4.02
1385 1422 0.106519 GCATATTGAGCAGGGGTGGT 60.107 55.000 0.00 0.00 0.00 4.16
1386 1423 0.106569 TGCATATTGAGCAGGGGTGG 60.107 55.000 0.00 0.00 37.02 4.61
1387 1424 1.027357 GTGCATATTGAGCAGGGGTG 58.973 55.000 0.00 0.00 43.63 4.61
1388 1425 0.106519 GGTGCATATTGAGCAGGGGT 60.107 55.000 0.00 0.00 43.63 4.95
1389 1426 0.825010 GGGTGCATATTGAGCAGGGG 60.825 60.000 0.00 0.00 43.63 4.79
1394 1431 1.458639 GGCCAGGGTGCATATTGAGC 61.459 60.000 0.00 0.00 0.00 4.26
1395 1432 1.168407 CGGCCAGGGTGCATATTGAG 61.168 60.000 2.24 0.00 0.00 3.02
1396 1433 1.152984 CGGCCAGGGTGCATATTGA 60.153 57.895 2.24 0.00 0.00 2.57
1398 1435 2.195683 CCGGCCAGGGTGCATATT 59.804 61.111 2.24 0.00 35.97 1.28
1399 1436 4.586235 GCCGGCCAGGGTGCATAT 62.586 66.667 18.11 0.00 41.48 1.78
1418 1455 2.779033 GCAGCTGCAATGGTAGGCC 61.779 63.158 33.36 0.00 41.59 5.19
1419 1456 2.803479 GCAGCTGCAATGGTAGGC 59.197 61.111 33.36 1.04 41.59 3.93
1462 1500 5.674933 ACTAGTAAAAACAGAGCAGCAAC 57.325 39.130 0.00 0.00 0.00 4.17
1479 1517 5.235186 GCGACATGAATGCTGATTTACTAGT 59.765 40.000 0.00 0.00 0.00 2.57
1480 1518 5.464722 AGCGACATGAATGCTGATTTACTAG 59.535 40.000 0.00 0.00 37.62 2.57
1481 1519 5.359756 AGCGACATGAATGCTGATTTACTA 58.640 37.500 0.00 0.00 37.62 1.82
1482 1520 4.194640 AGCGACATGAATGCTGATTTACT 58.805 39.130 0.00 0.00 37.62 2.24
1483 1521 4.542662 AGCGACATGAATGCTGATTTAC 57.457 40.909 0.00 0.00 37.62 2.01
1495 1533 3.575630 GTTGAAGACTACAGCGACATGA 58.424 45.455 0.00 0.00 0.00 3.07
1496 1534 2.668457 GGTTGAAGACTACAGCGACATG 59.332 50.000 0.00 0.00 0.00 3.21
1498 1536 1.684450 TGGTTGAAGACTACAGCGACA 59.316 47.619 0.00 0.00 0.00 4.35
1499 1537 2.433868 TGGTTGAAGACTACAGCGAC 57.566 50.000 0.00 0.00 0.00 5.19
1500 1538 3.678056 AATGGTTGAAGACTACAGCGA 57.322 42.857 0.00 0.00 0.00 4.93
1501 1539 5.812642 AGATAAATGGTTGAAGACTACAGCG 59.187 40.000 0.00 0.00 0.00 5.18
1502 1540 6.818644 TGAGATAAATGGTTGAAGACTACAGC 59.181 38.462 0.00 0.00 0.00 4.40
1503 1541 8.037758 ACTGAGATAAATGGTTGAAGACTACAG 58.962 37.037 0.00 0.00 0.00 2.74
1504 1542 7.907389 ACTGAGATAAATGGTTGAAGACTACA 58.093 34.615 0.00 0.00 0.00 2.74
1505 1543 7.492994 GGACTGAGATAAATGGTTGAAGACTAC 59.507 40.741 0.00 0.00 0.00 2.73
1506 1544 7.400339 AGGACTGAGATAAATGGTTGAAGACTA 59.600 37.037 0.00 0.00 0.00 2.59
1507 1545 6.214412 AGGACTGAGATAAATGGTTGAAGACT 59.786 38.462 0.00 0.00 0.00 3.24
1508 1546 6.410540 AGGACTGAGATAAATGGTTGAAGAC 58.589 40.000 0.00 0.00 0.00 3.01
1509 1547 6.627087 AGGACTGAGATAAATGGTTGAAGA 57.373 37.500 0.00 0.00 0.00 2.87
1523 1568 2.580962 CATCTGATCCGAGGACTGAGA 58.419 52.381 0.00 0.00 0.00 3.27
1542 1587 1.694150 ACACTGACTAAAGCCTCAGCA 59.306 47.619 0.00 0.00 43.56 4.41
1552 1597 4.897076 TCCTGGTAAGAACACACTGACTAA 59.103 41.667 0.00 0.00 0.00 2.24
1553 1598 4.476297 TCCTGGTAAGAACACACTGACTA 58.524 43.478 0.00 0.00 0.00 2.59
1554 1599 3.305720 TCCTGGTAAGAACACACTGACT 58.694 45.455 0.00 0.00 0.00 3.41
1555 1600 3.746045 TCCTGGTAAGAACACACTGAC 57.254 47.619 0.00 0.00 0.00 3.51
1569 1614 3.736224 CCAGCTGGCCATCCTGGT 61.736 66.667 30.74 14.79 40.92 4.00
1634 1679 2.171003 CAGACCAACCCTGGAAATTCC 58.829 52.381 4.79 4.79 46.92 3.01
1705 1755 9.551339 ACCAAATGCTATCAATAATCCCAATAT 57.449 29.630 0.00 0.00 0.00 1.28
1706 1756 8.954834 ACCAAATGCTATCAATAATCCCAATA 57.045 30.769 0.00 0.00 0.00 1.90
1708 1758 8.954834 ATACCAAATGCTATCAATAATCCCAA 57.045 30.769 0.00 0.00 0.00 4.12
1718 1768 9.448438 GTTGTGGATATATACCAAATGCTATCA 57.552 33.333 5.72 0.00 39.22 2.15
1719 1769 9.448438 TGTTGTGGATATATACCAAATGCTATC 57.552 33.333 5.72 0.00 39.22 2.08
1720 1770 9.979897 ATGTTGTGGATATATACCAAATGCTAT 57.020 29.630 5.72 0.00 39.22 2.97
1721 1771 9.806448 AATGTTGTGGATATATACCAAATGCTA 57.194 29.630 5.72 0.00 39.22 3.49
1722 1772 8.710749 AATGTTGTGGATATATACCAAATGCT 57.289 30.769 5.72 0.00 39.22 3.79
1723 1773 8.575589 TGAATGTTGTGGATATATACCAAATGC 58.424 33.333 5.72 0.00 39.22 3.56
1727 1777 9.859152 TGATTGAATGTTGTGGATATATACCAA 57.141 29.630 5.72 1.42 39.22 3.67
1728 1778 9.283768 GTGATTGAATGTTGTGGATATATACCA 57.716 33.333 0.00 0.00 34.84 3.25
1729 1779 9.507329 AGTGATTGAATGTTGTGGATATATACC 57.493 33.333 0.00 0.00 0.00 2.73
1732 1782 8.843262 CACAGTGATTGAATGTTGTGGATATAT 58.157 33.333 0.00 0.00 33.98 0.86
1733 1783 8.212317 CACAGTGATTGAATGTTGTGGATATA 57.788 34.615 0.00 0.00 33.98 0.86
1746 1796 3.220940 TGCACATTCCACAGTGATTGAA 58.779 40.909 0.62 0.00 37.97 2.69
1754 1804 0.250858 TGACCCTGCACATTCCACAG 60.251 55.000 0.00 0.00 0.00 3.66
1786 1836 6.174720 AGAAGGAGATGTGTTGTTTAGTCA 57.825 37.500 0.00 0.00 0.00 3.41
1802 1852 0.891373 TGACTCTGCGGAAGAAGGAG 59.109 55.000 0.00 0.00 37.37 3.69
1804 1854 1.066573 ACATGACTCTGCGGAAGAAGG 60.067 52.381 0.00 0.00 37.37 3.46
1805 1855 2.376808 ACATGACTCTGCGGAAGAAG 57.623 50.000 0.00 0.00 38.49 2.85
1811 1862 4.024048 ACAAAGTAAAACATGACTCTGCGG 60.024 41.667 0.00 0.00 0.00 5.69
1812 1863 4.905866 CACAAAGTAAAACATGACTCTGCG 59.094 41.667 0.00 0.00 0.00 5.18
1822 1873 9.743057 CTTTATTCACATCCACAAAGTAAAACA 57.257 29.630 0.00 0.00 0.00 2.83
1841 1892 2.161609 CACGGCCTGTGGAACTTTATTC 59.838 50.000 16.84 0.00 45.21 1.75
1877 1928 9.065871 GCTAAAATTTGCTGACTTACACTTATG 57.934 33.333 0.00 0.00 0.00 1.90
1907 1958 6.647334 TTCAAATTGATGAAGTGCCTAACA 57.353 33.333 0.00 0.00 34.50 2.41
1918 1969 7.016465 ACTCAAATTTCCCCTTCAAATTGATGA 59.984 33.333 10.03 0.43 34.39 2.92
1919 1970 7.163441 ACTCAAATTTCCCCTTCAAATTGATG 58.837 34.615 0.00 0.00 34.39 3.07
1920 1971 7.320384 ACTCAAATTTCCCCTTCAAATTGAT 57.680 32.000 0.00 0.00 34.39 2.57
1954 2009 5.914074 CAGATGATATCAGAGTCGTTGTGAG 59.086 44.000 11.78 0.00 31.90 3.51
1993 2052 1.211457 AGATGGGAGCCATGACAGAAC 59.789 52.381 0.00 0.00 45.26 3.01
2024 2083 7.833682 TGAATAGTGGGCATTTTCTGAAGATTA 59.166 33.333 0.00 0.00 0.00 1.75
2070 2133 1.135460 GGACAAATGCAGAGCTTGAGC 60.135 52.381 0.00 0.00 42.49 4.26
2073 2136 1.542492 AGGGACAAATGCAGAGCTTG 58.458 50.000 0.00 0.00 0.00 4.01
2077 2140 4.019174 ACCATAAAGGGACAAATGCAGAG 58.981 43.478 0.00 0.00 43.89 3.35
2117 2183 4.760204 TGAATAGGAGCAAGCATCATCATG 59.240 41.667 0.00 0.00 0.00 3.07
2234 2300 7.033791 AGTATGTAATCGGTCACTTGTACTTG 58.966 38.462 0.00 0.00 0.00 3.16
2305 2373 9.062524 TGGAATATAGTTTTATTGATCGGGTTG 57.937 33.333 0.00 0.00 0.00 3.77
2351 2423 2.578021 ACAGACCAACAGAATAGGCCAT 59.422 45.455 5.01 0.00 0.00 4.40
2360 2432 2.165437 GGTTTTGCAACAGACCAACAGA 59.835 45.455 16.83 0.00 34.15 3.41
2363 2435 1.480545 AGGGTTTTGCAACAGACCAAC 59.519 47.619 21.02 12.61 34.15 3.77
2492 2588 5.163353 TGTGACTGTGGATTGTTCAGTTCTA 60.163 40.000 0.00 0.00 41.58 2.10
2511 2607 7.800380 CAGTTTGTCTTCTGTATCATTTGTGAC 59.200 37.037 0.00 0.00 0.00 3.67
2518 2614 7.445121 TCTTCACAGTTTGTCTTCTGTATCAT 58.555 34.615 0.00 0.00 42.05 2.45
2520 2616 7.715265 TTCTTCACAGTTTGTCTTCTGTATC 57.285 36.000 0.00 0.00 42.05 2.24
2539 2635 8.786898 TCGGGATGATGAATTATTTGATTCTTC 58.213 33.333 6.57 6.57 39.12 2.87
2585 2681 1.605451 GTTGGGTGGGGCCTTGTAC 60.605 63.158 0.84 0.00 37.43 2.90
2600 2696 5.633830 AACTCAGCATGTAAATCAGGTTG 57.366 39.130 0.00 0.00 39.65 3.77
2643 2739 4.024725 CGTGGTTTGACCGTTTGAGATTTA 60.025 41.667 0.00 0.00 42.58 1.40
2692 2788 7.312154 AGATACTAGCGAGCTTGATAATTCTG 58.688 38.462 12.99 0.00 0.00 3.02
2693 2789 7.461182 AGATACTAGCGAGCTTGATAATTCT 57.539 36.000 12.99 2.56 0.00 2.40
2694 2790 7.698970 GGTAGATACTAGCGAGCTTGATAATTC 59.301 40.741 12.99 0.19 0.00 2.17
2695 2791 7.363094 GGGTAGATACTAGCGAGCTTGATAATT 60.363 40.741 12.99 0.00 0.00 1.40
2696 2792 6.095720 GGGTAGATACTAGCGAGCTTGATAAT 59.904 42.308 12.99 0.00 0.00 1.28
2700 2796 3.147629 GGGTAGATACTAGCGAGCTTGA 58.852 50.000 12.99 0.00 0.00 3.02
2724 2826 2.486548 GGCTGGTTAGTTCTGACACCAA 60.487 50.000 0.00 0.00 0.00 3.67
2728 2830 0.320421 GCGGCTGGTTAGTTCTGACA 60.320 55.000 0.00 0.00 0.00 3.58
2740 2842 2.435586 CTTGGAGTCAGCGGCTGG 60.436 66.667 28.18 11.17 31.51 4.85
2743 2845 3.123620 CAGCTTGGAGTCAGCGGC 61.124 66.667 0.00 0.00 0.00 6.53
2809 2914 0.737715 CTCTCCTTTGCCTTCGTCGG 60.738 60.000 0.00 0.00 0.00 4.79
2816 2933 1.179814 ACGACGACTCTCCTTTGCCT 61.180 55.000 0.00 0.00 0.00 4.75
2820 2937 0.888285 ACCGACGACGACTCTCCTTT 60.888 55.000 9.28 0.00 42.66 3.11
2822 2939 2.033755 CACCGACGACGACTCTCCT 61.034 63.158 9.28 0.00 42.66 3.69
2825 2942 3.735029 GGCACCGACGACGACTCT 61.735 66.667 9.28 0.00 42.66 3.24
3091 3211 0.734889 CACAAGTGATTCGCCATCCC 59.265 55.000 0.00 0.00 0.00 3.85
3099 3219 3.943381 TCATCATCTGCCACAAGTGATTC 59.057 43.478 0.94 0.00 0.00 2.52
3140 3294 3.499737 CACCGCCGAAGCATCCAC 61.500 66.667 0.00 0.00 39.83 4.02
3246 3408 4.561606 ACGACCGAGAGAAAAATAATCACG 59.438 41.667 0.00 0.00 0.00 4.35
3292 3455 1.820481 CCCACGAAACCCACAACGT 60.820 57.895 0.00 0.00 39.53 3.99
3313 3484 4.481112 GCAACGCGGCCAATCAGG 62.481 66.667 12.47 0.00 41.84 3.86
3314 3485 2.476534 AAAGCAACGCGGCCAATCAG 62.477 55.000 12.47 0.00 0.00 2.90
3315 3486 2.560119 AAAGCAACGCGGCCAATCA 61.560 52.632 12.47 0.00 0.00 2.57
3316 3487 2.088178 CAAAGCAACGCGGCCAATC 61.088 57.895 12.47 0.00 0.00 2.67
3317 3488 2.049248 CAAAGCAACGCGGCCAAT 60.049 55.556 12.47 0.00 0.00 3.16
3318 3489 4.940593 GCAAAGCAACGCGGCCAA 62.941 61.111 12.47 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.