Multiple sequence alignment - TraesCS7A01G249100

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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 TraesCS7A01G249100 chr7A 100.000 9258 0 0 1 9258 231540567 231549824 0.000000e+00 17097.0
1 TraesCS7A01G249100 chr7A 92.713 1043 70 5 2057 3097 571321527 571320489 0.000000e+00 1500.0
2 TraesCS7A01G249100 chr7A 92.447 1046 71 6 2054 3098 694567344 694568382 0.000000e+00 1487.0
3 TraesCS7A01G249100 chr7A 89.327 431 29 7 1662 2078 694566978 694567405 8.240000e-145 525.0
4 TraesCS7A01G249100 chr7D 96.502 6203 120 40 3100 9258 219290738 219296887 0.000000e+00 10163.0
5 TraesCS7A01G249100 chr7D 88.067 1190 118 11 1 1172 219289132 219290315 0.000000e+00 1389.0
6 TraesCS7A01G249100 chr7D 88.170 448 31 13 1234 1671 219290307 219290742 1.780000e-141 514.0
7 TraesCS7A01G249100 chr7B 95.970 5509 170 28 3499 8978 181039170 181033685 0.000000e+00 8896.0
8 TraesCS7A01G249100 chr7B 87.614 1098 99 18 1 1083 181041733 181040658 0.000000e+00 1240.0
9 TraesCS7A01G249100 chr7B 85.546 595 54 16 1081 1665 181040384 181039812 2.230000e-165 593.0
10 TraesCS7A01G249100 chr7B 92.058 277 10 4 8982 9258 181033583 181033319 6.780000e-101 379.0
11 TraesCS7A01G249100 chr7B 84.518 394 19 12 3102 3465 181039804 181039423 1.480000e-92 351.0
12 TraesCS7A01G249100 chr6A 92.922 1441 88 4 1670 3097 78005400 78006839 0.000000e+00 2084.0
13 TraesCS7A01G249100 chr6A 92.490 1438 92 4 1670 3097 78157914 78159345 0.000000e+00 2043.0
14 TraesCS7A01G249100 chr6A 92.202 1449 88 6 1672 3097 99770004 99768558 0.000000e+00 2026.0
15 TraesCS7A01G249100 chr6A 91.597 1440 97 10 1670 3097 584929113 584927686 0.000000e+00 1967.0
16 TraesCS7A01G249100 chr2A 91.354 1411 104 6 1703 3097 731253823 731252415 0.000000e+00 1914.0
17 TraesCS7A01G249100 chr2A 91.711 1122 88 3 1978 3098 543349995 543351112 0.000000e+00 1552.0
18 TraesCS7A01G249100 chr2A 88.785 428 31 7 1664 2078 767620688 767621111 8.290000e-140 508.0
19 TraesCS7A01G249100 chr2A 88.152 422 34 6 1670 2078 14408918 14409336 1.080000e-133 488.0
20 TraesCS7A01G249100 chr2A 85.000 60 5 3 4150 4206 637984511 637984569 3.610000e-04 58.4
21 TraesCS7A01G249100 chr5A 92.470 1089 75 6 2015 3098 525121344 525122430 0.000000e+00 1550.0
22 TraesCS7A01G249100 chr5A 90.704 398 28 1 1670 2058 120001157 120000760 1.070000e-143 521.0
23 TraesCS7A01G249100 chr4A 92.344 1045 77 3 2054 3097 36151349 36152391 0.000000e+00 1483.0
24 TraesCS7A01G249100 chr4A 90.521 422 24 6 1670 2078 36150992 36151410 2.270000e-150 544.0
25 TraesCS7A01G249100 chr4A 88.929 280 26 4 1791 2068 629455505 629455229 3.200000e-89 340.0
26 TraesCS7A01G249100 chr6B 85.165 1456 164 33 1670 3097 565046632 565045201 0.000000e+00 1445.0
27 TraesCS7A01G249100 chr3A 89.731 409 31 3 1660 2058 746579924 746579517 6.410000e-141 512.0
28 TraesCS7A01G249100 chr2B 81.934 393 57 11 1670 2058 65682289 65682671 4.170000e-83 320.0


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 TraesCS7A01G249100 chr7A 231540567 231549824 9257 False 17097.0 17097 100.0000 1 9258 1 chr7A.!!$F1 9257
1 TraesCS7A01G249100 chr7A 571320489 571321527 1038 True 1500.0 1500 92.7130 2057 3097 1 chr7A.!!$R1 1040
2 TraesCS7A01G249100 chr7A 694566978 694568382 1404 False 1006.0 1487 90.8870 1662 3098 2 chr7A.!!$F2 1436
3 TraesCS7A01G249100 chr7D 219289132 219296887 7755 False 4022.0 10163 90.9130 1 9258 3 chr7D.!!$F1 9257
4 TraesCS7A01G249100 chr7B 181033319 181041733 8414 True 2291.8 8896 89.1412 1 9258 5 chr7B.!!$R1 9257
5 TraesCS7A01G249100 chr6A 78005400 78006839 1439 False 2084.0 2084 92.9220 1670 3097 1 chr6A.!!$F1 1427
6 TraesCS7A01G249100 chr6A 78157914 78159345 1431 False 2043.0 2043 92.4900 1670 3097 1 chr6A.!!$F2 1427
7 TraesCS7A01G249100 chr6A 99768558 99770004 1446 True 2026.0 2026 92.2020 1672 3097 1 chr6A.!!$R1 1425
8 TraesCS7A01G249100 chr6A 584927686 584929113 1427 True 1967.0 1967 91.5970 1670 3097 1 chr6A.!!$R2 1427
9 TraesCS7A01G249100 chr2A 731252415 731253823 1408 True 1914.0 1914 91.3540 1703 3097 1 chr2A.!!$R1 1394
10 TraesCS7A01G249100 chr2A 543349995 543351112 1117 False 1552.0 1552 91.7110 1978 3098 1 chr2A.!!$F2 1120
11 TraesCS7A01G249100 chr5A 525121344 525122430 1086 False 1550.0 1550 92.4700 2015 3098 1 chr5A.!!$F1 1083
12 TraesCS7A01G249100 chr4A 36150992 36152391 1399 False 1013.5 1483 91.4325 1670 3097 2 chr4A.!!$F1 1427
13 TraesCS7A01G249100 chr6B 565045201 565046632 1431 True 1445.0 1445 85.1650 1670 3097 1 chr6B.!!$R1 1427


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
832 849 0.600557 TAGCGCCCAAACACCATTTG 59.399 50.000 2.29 0.00 0.00 2.32 F
1299 1604 0.031178 AACTCGTGTTTCGGTAGCGT 59.969 50.000 14.79 0.00 40.32 5.07 F
3017 3487 0.249911 AAAGTCCGTTTGCTCTCGCT 60.250 50.000 0.00 0.00 36.97 4.93 F
3075 3547 0.033796 ACGGGGTCGGACAGAATAGA 60.034 55.000 10.76 0.00 41.39 1.98 F
4705 5468 0.035534 TATGATGCCACACGGTTGCT 60.036 50.000 0.00 0.00 33.28 3.91 F
4708 5471 0.378257 GATGCCACACGGTTGCTATG 59.622 55.000 0.00 0.00 33.28 2.23 F
5526 6290 1.077501 TAGCAGCACCCATGGAAGC 60.078 57.895 15.22 16.66 0.00 3.86 F
6861 7625 1.003580 TCCTGCTTGACCATTGACTCC 59.996 52.381 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 2312 0.322975 ACAAGTGCATCGAGAAGGCT 59.677 50.000 0.0 0.0 0.00 4.58 R
3054 3526 0.033796 TATTCTGTCCGACCCCGTCT 60.034 55.000 0.0 0.0 0.00 4.18 R
4708 5471 0.037590 TCTGGCCCAATACACACACC 59.962 55.000 0.0 0.0 0.00 4.16 R
4753 5516 1.883275 CTCGGCCTACATAGAGACCAG 59.117 57.143 0.0 0.0 32.84 4.00 R
5862 6626 0.263172 ATGTGGGGTTTGGTGGTGAA 59.737 50.000 0.0 0.0 0.00 3.18 R
6431 7195 2.819608 TCGCTGGAGGAAATTTTCTTGG 59.180 45.455 0.0 0.0 0.00 3.61 R
7417 8181 1.220749 GCACCAGTCCCGCTCATTA 59.779 57.895 0.0 0.0 0.00 1.90 R
8315 9079 0.250770 GTTCCACACCCTCTGGTTCC 60.251 60.000 0.0 0.0 44.75 3.62 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
30 31 4.630069 GCTCTTGGCGTTCAACTTTATCTA 59.370 41.667 0.00 0.00 0.00 1.98
31 32 5.121768 GCTCTTGGCGTTCAACTTTATCTAA 59.878 40.000 0.00 0.00 0.00 2.10
32 33 6.183360 GCTCTTGGCGTTCAACTTTATCTAAT 60.183 38.462 0.00 0.00 0.00 1.73
48 49 9.413734 CTTTATCTAATCTTTTTGGGTGATCCT 57.586 33.333 0.00 0.00 36.20 3.24
64 65 2.249309 TCCTAGAGGAACCAAGGGTC 57.751 55.000 0.00 0.00 42.18 4.46
101 103 8.918202 TGAAGGTACAATAAGATGACAAAAGT 57.082 30.769 0.00 0.00 0.00 2.66
110 112 2.108952 AGATGACAAAAGTGAAGGGCCT 59.891 45.455 0.00 0.00 0.00 5.19
116 118 1.332195 AAAGTGAAGGGCCTTGAAGC 58.668 50.000 26.47 9.85 0.00 3.86
122 124 2.991540 GGGCCTTGAAGCACCCAC 60.992 66.667 14.53 0.00 42.33 4.61
127 129 1.402787 CCTTGAAGCACCCACACTTT 58.597 50.000 0.00 0.00 0.00 2.66
133 135 2.363306 AGCACCCACACTTTCATTGA 57.637 45.000 0.00 0.00 0.00 2.57
141 143 5.163513 CCCACACTTTCATTGAATAAGCAC 58.836 41.667 0.00 0.00 0.00 4.40
145 147 5.238432 ACACTTTCATTGAATAAGCACGACA 59.762 36.000 0.00 0.00 0.00 4.35
214 216 7.119846 GCTAGTCCTTGCATTTTACATATAGGG 59.880 40.741 0.00 0.00 0.00 3.53
216 218 7.354312 AGTCCTTGCATTTTACATATAGGGTT 58.646 34.615 0.00 0.00 0.00 4.11
317 319 1.536676 CACTTGGGGTGGTGACCTT 59.463 57.895 2.11 0.00 42.66 3.50
343 345 2.624029 CCCCATATCCACCAGTTTTGCT 60.624 50.000 0.00 0.00 0.00 3.91
365 367 0.804989 CGGCGAAGGAAGAAGCAAAT 59.195 50.000 0.00 0.00 0.00 2.32
414 420 2.353406 CCTTTTAGCTTCTCGTCGGGAA 60.353 50.000 7.45 7.45 0.00 3.97
520 530 2.150719 ACCACATCCACAACCGGGA 61.151 57.895 6.32 0.00 39.14 5.14
527 537 3.253838 CACAACCGGGAAGGGGGA 61.254 66.667 6.32 0.00 46.96 4.81
528 539 2.450897 ACAACCGGGAAGGGGGAA 60.451 61.111 6.32 0.00 46.96 3.97
552 563 1.073025 ACCGATGAGCACCAAAGCA 59.927 52.632 0.00 0.00 36.85 3.91
557 568 0.957395 ATGAGCACCAAAGCACCTCG 60.957 55.000 0.00 0.00 36.85 4.63
571 582 2.651361 CTCGGTGGACGCTCTTGT 59.349 61.111 0.00 0.00 43.86 3.16
636 647 1.950828 CCTCATCTGCATCTTCGCTT 58.049 50.000 0.00 0.00 0.00 4.68
637 648 2.286872 CCTCATCTGCATCTTCGCTTT 58.713 47.619 0.00 0.00 0.00 3.51
643 654 2.093288 TCTGCATCTTCGCTTTCTCCAT 60.093 45.455 0.00 0.00 0.00 3.41
651 662 2.464459 GCTTTCTCCATCACGGCGG 61.464 63.158 13.24 0.00 33.14 6.13
683 700 4.314522 TGGGGCAAACTCATTATCTTCA 57.685 40.909 0.00 0.00 0.00 3.02
717 734 0.988832 ACGGGGACAATGAAGCCTTA 59.011 50.000 0.00 0.00 0.00 2.69
793 810 2.815308 CGACCCATAAGCTCCGCT 59.185 61.111 0.00 0.00 42.56 5.52
832 849 0.600557 TAGCGCCCAAACACCATTTG 59.399 50.000 2.29 0.00 0.00 2.32
843 860 1.963515 ACACCATTTGAAGGCAAGTCC 59.036 47.619 0.00 0.00 35.04 3.85
904 921 2.270434 TTCCCTAACCATCTCCAGCT 57.730 50.000 0.00 0.00 0.00 4.24
925 942 2.034687 AGCGCCATCAAGCAAGGT 59.965 55.556 2.29 0.00 35.48 3.50
938 955 1.498865 GCAAGGTATGTGATCGGCCG 61.499 60.000 22.12 22.12 0.00 6.13
952 969 4.360405 GCCGGGGAGCCAAAGGAA 62.360 66.667 2.18 0.00 0.00 3.36
968 985 1.694696 AGGAAACTCTCAACGGAGCTT 59.305 47.619 0.00 0.00 41.13 3.74
970 987 2.289133 GGAAACTCTCAACGGAGCTTCT 60.289 50.000 0.00 0.00 41.13 2.85
983 1000 3.222603 GGAGCTTCTAGAAGGAGAGAGG 58.777 54.545 29.22 7.11 38.80 3.69
988 1005 4.630184 GCTTCTAGAAGGAGAGAGGGAAGA 60.630 50.000 29.22 0.00 38.80 2.87
1003 1020 6.657875 AGAGGGAAGAAAGTGATAAGAATGG 58.342 40.000 0.00 0.00 0.00 3.16
1004 1021 5.760131 AGGGAAGAAAGTGATAAGAATGGG 58.240 41.667 0.00 0.00 0.00 4.00
1007 1024 3.903467 AGAAAGTGATAAGAATGGGCCC 58.097 45.455 17.59 17.59 0.00 5.80
1025 1042 3.704566 GGCCCCTTATCCAGGTTAAAAAG 59.295 47.826 0.00 0.00 42.02 2.27
1032 1049 8.536175 CCCTTATCCAGGTTAAAAAGCAATTAA 58.464 33.333 0.00 0.00 42.02 1.40
1125 1428 7.543359 AACAAAAGATTCATGGAGGAAATCA 57.457 32.000 6.79 0.00 0.00 2.57
1159 1462 8.015087 GGTTAAACCTTGCAAAGCATTATTTTC 58.985 33.333 0.00 0.00 44.44 2.29
1160 1463 5.844301 AACCTTGCAAAGCATTATTTTCG 57.156 34.783 0.00 0.00 44.44 3.46
1200 1503 2.806745 CGAGTTCTTGCAAGTTCCCTCA 60.807 50.000 25.19 1.79 0.00 3.86
1205 1508 1.000171 CTTGCAAGTTCCCTCAAAGCC 60.000 52.381 18.65 0.00 0.00 4.35
1208 1511 1.000171 GCAAGTTCCCTCAAAGCCTTG 60.000 52.381 0.00 0.00 34.03 3.61
1223 1526 2.494870 AGCCTTGAAGCAACCATCAATC 59.505 45.455 0.00 0.00 35.20 2.67
1226 1529 3.367703 CCTTGAAGCAACCATCAATCCAC 60.368 47.826 0.00 0.00 35.20 4.02
1228 1531 2.557924 TGAAGCAACCATCAATCCACAC 59.442 45.455 0.00 0.00 0.00 3.82
1232 1535 2.231964 GCAACCATCAATCCACACACAT 59.768 45.455 0.00 0.00 0.00 3.21
1235 1538 5.584442 CAACCATCAATCCACACACATATG 58.416 41.667 0.00 0.00 0.00 1.78
1236 1539 4.858850 ACCATCAATCCACACACATATGT 58.141 39.130 1.41 1.41 40.80 2.29
1274 1577 9.061435 AGTAAGATTTAGCAAGCATTTCTATCC 57.939 33.333 0.00 0.00 0.00 2.59
1279 1582 4.382345 AGCAAGCATTTCTATCCTTTGC 57.618 40.909 0.00 0.00 0.00 3.68
1280 1583 3.765511 AGCAAGCATTTCTATCCTTTGCA 59.234 39.130 8.71 0.00 35.79 4.08
1288 1593 3.678056 TCTATCCTTTGCAACTCGTGT 57.322 42.857 0.00 0.00 0.00 4.49
1295 1600 1.937278 TTGCAACTCGTGTTTCGGTA 58.063 45.000 0.00 0.00 40.32 4.02
1296 1601 1.493772 TGCAACTCGTGTTTCGGTAG 58.506 50.000 0.00 0.00 40.32 3.18
1299 1604 0.031178 AACTCGTGTTTCGGTAGCGT 59.969 50.000 14.79 0.00 40.32 5.07
1321 1626 3.646162 TCCTACCAATCATAGCCGTCAAT 59.354 43.478 0.00 0.00 0.00 2.57
1323 1628 3.845781 ACCAATCATAGCCGTCAATCT 57.154 42.857 0.00 0.00 0.00 2.40
1351 1656 8.734218 ATGATGATAATTCTCATGGATGCTAC 57.266 34.615 10.77 0.00 36.01 3.58
1355 1660 8.193953 TGATAATTCTCATGGATGCTACAGTA 57.806 34.615 0.00 0.00 0.00 2.74
1356 1661 8.309656 TGATAATTCTCATGGATGCTACAGTAG 58.690 37.037 2.85 2.85 0.00 2.57
1357 1662 6.737720 AATTCTCATGGATGCTACAGTAGA 57.262 37.500 12.15 0.00 0.00 2.59
1358 1663 5.781210 TTCTCATGGATGCTACAGTAGAG 57.219 43.478 12.15 0.00 0.00 2.43
1359 1664 4.797743 TCTCATGGATGCTACAGTAGAGT 58.202 43.478 12.15 0.00 0.00 3.24
1360 1665 5.204292 TCTCATGGATGCTACAGTAGAGTT 58.796 41.667 12.15 0.00 0.00 3.01
1361 1666 5.658634 TCTCATGGATGCTACAGTAGAGTTT 59.341 40.000 12.15 0.00 0.00 2.66
1363 1668 6.711277 TCATGGATGCTACAGTAGAGTTTTT 58.289 36.000 12.15 0.00 0.00 1.94
1364 1669 6.595326 TCATGGATGCTACAGTAGAGTTTTTG 59.405 38.462 12.15 2.34 0.00 2.44
1365 1670 6.109156 TGGATGCTACAGTAGAGTTTTTGA 57.891 37.500 12.15 0.00 0.00 2.69
1366 1671 5.932303 TGGATGCTACAGTAGAGTTTTTGAC 59.068 40.000 12.15 0.00 0.00 3.18
1377 1682 4.860072 AGAGTTTTTGACTTTTCATCCGC 58.140 39.130 0.00 0.00 39.19 5.54
1418 1724 1.080025 GCTACCTCGCCAAGAACGT 60.080 57.895 0.00 0.00 0.00 3.99
1435 1741 2.159382 ACGTCGGGCTTGAATTCAAAT 58.841 42.857 20.82 0.00 35.15 2.32
1436 1742 2.095263 ACGTCGGGCTTGAATTCAAATG 60.095 45.455 20.82 13.38 35.15 2.32
1449 1755 6.545508 TGAATTCAAATGTTCATCTGTAGCG 58.454 36.000 5.45 0.00 29.93 4.26
1453 1759 2.967599 ATGTTCATCTGTAGCGAGCA 57.032 45.000 0.00 0.00 0.00 4.26
1477 1783 4.503741 AACACCATTTTTCTCACCGATG 57.496 40.909 0.00 0.00 0.00 3.84
1525 1840 3.627577 AGGCCAAGTACAATAATGAAGCG 59.372 43.478 5.01 0.00 0.00 4.68
1585 1903 2.588034 GATACGAGGCCGGGCAAC 60.588 66.667 31.59 21.52 40.78 4.17
1626 1944 2.987547 AAAGCGACCCGAGACCGA 60.988 61.111 0.00 0.00 38.22 4.69
1627 1945 2.991076 AAAGCGACCCGAGACCGAG 61.991 63.158 0.00 0.00 38.22 4.63
1703 2021 1.366111 CGCGATCCCAAACGGACATT 61.366 55.000 0.00 0.00 46.09 2.71
1755 2073 2.175035 GATTTGGGGTCGTGTCCGGA 62.175 60.000 0.00 0.00 33.95 5.14
1909 2240 8.522542 TTTTGACTAGTAAAGTAAGGCCAAAA 57.477 30.769 5.01 1.69 39.07 2.44
1981 2312 2.708861 TGCTTCCTTGAGTTGGGTTAGA 59.291 45.455 0.00 0.00 0.00 2.10
2019 2389 2.038952 TGTTGTTGATCTGTGGAGGAGG 59.961 50.000 0.00 0.00 0.00 4.30
2020 2390 1.279496 TGTTGATCTGTGGAGGAGGG 58.721 55.000 0.00 0.00 0.00 4.30
2021 2391 1.280457 GTTGATCTGTGGAGGAGGGT 58.720 55.000 0.00 0.00 0.00 4.34
2022 2392 1.208293 GTTGATCTGTGGAGGAGGGTC 59.792 57.143 0.00 0.00 0.00 4.46
2023 2393 0.684479 TGATCTGTGGAGGAGGGTCG 60.684 60.000 0.00 0.00 0.00 4.79
2024 2394 0.395862 GATCTGTGGAGGAGGGTCGA 60.396 60.000 0.00 0.00 0.00 4.20
2025 2395 0.263172 ATCTGTGGAGGAGGGTCGAT 59.737 55.000 0.00 0.00 0.00 3.59
2026 2396 0.395862 TCTGTGGAGGAGGGTCGATC 60.396 60.000 0.00 0.00 0.00 3.69
2027 2397 0.396417 CTGTGGAGGAGGGTCGATCT 60.396 60.000 0.00 0.00 0.00 2.75
2028 2398 0.684479 TGTGGAGGAGGGTCGATCTG 60.684 60.000 0.00 0.00 0.00 2.90
2029 2399 1.075970 TGGAGGAGGGTCGATCTGG 60.076 63.158 0.00 0.00 0.00 3.86
2030 2400 2.503382 GGAGGAGGGTCGATCTGGC 61.503 68.421 0.00 0.00 0.00 4.85
2031 2401 1.758514 GAGGAGGGTCGATCTGGCA 60.759 63.158 0.00 0.00 0.00 4.92
2032 2402 1.074926 AGGAGGGTCGATCTGGCAT 60.075 57.895 0.00 0.00 0.00 4.40
2033 2403 1.118356 AGGAGGGTCGATCTGGCATC 61.118 60.000 0.00 0.00 0.00 3.91
2034 2404 1.369321 GAGGGTCGATCTGGCATCC 59.631 63.158 0.00 0.00 0.00 3.51
2035 2405 1.074926 AGGGTCGATCTGGCATCCT 60.075 57.895 0.00 0.00 0.00 3.24
2036 2406 1.118356 AGGGTCGATCTGGCATCCTC 61.118 60.000 0.00 0.00 0.00 3.71
2037 2407 1.369321 GGTCGATCTGGCATCCTCC 59.631 63.158 0.00 0.00 0.00 4.30
2038 2408 1.118356 GGTCGATCTGGCATCCTCCT 61.118 60.000 0.00 0.00 0.00 3.69
2039 2409 0.755686 GTCGATCTGGCATCCTCCTT 59.244 55.000 0.00 0.00 0.00 3.36
2040 2410 1.139853 GTCGATCTGGCATCCTCCTTT 59.860 52.381 0.00 0.00 0.00 3.11
2041 2411 1.414181 TCGATCTGGCATCCTCCTTTC 59.586 52.381 0.00 0.00 0.00 2.62
2042 2412 1.415659 CGATCTGGCATCCTCCTTTCT 59.584 52.381 0.00 0.00 0.00 2.52
2043 2413 2.158842 CGATCTGGCATCCTCCTTTCTT 60.159 50.000 0.00 0.00 0.00 2.52
2044 2414 3.475575 GATCTGGCATCCTCCTTTCTTC 58.524 50.000 0.00 0.00 0.00 2.87
2045 2415 2.555664 TCTGGCATCCTCCTTTCTTCT 58.444 47.619 0.00 0.00 0.00 2.85
2046 2416 2.915604 TCTGGCATCCTCCTTTCTTCTT 59.084 45.455 0.00 0.00 0.00 2.52
2047 2417 3.054802 TCTGGCATCCTCCTTTCTTCTTC 60.055 47.826 0.00 0.00 0.00 2.87
2048 2418 2.644299 TGGCATCCTCCTTTCTTCTTCA 59.356 45.455 0.00 0.00 0.00 3.02
2049 2419 3.074390 TGGCATCCTCCTTTCTTCTTCAA 59.926 43.478 0.00 0.00 0.00 2.69
2050 2420 3.693578 GGCATCCTCCTTTCTTCTTCAAG 59.306 47.826 0.00 0.00 0.00 3.02
2051 2421 3.128415 GCATCCTCCTTTCTTCTTCAAGC 59.872 47.826 0.00 0.00 0.00 4.01
2052 2422 4.587891 CATCCTCCTTTCTTCTTCAAGCT 58.412 43.478 0.00 0.00 0.00 3.74
2053 2423 5.738909 CATCCTCCTTTCTTCTTCAAGCTA 58.261 41.667 0.00 0.00 0.00 3.32
2054 2424 5.413309 TCCTCCTTTCTTCTTCAAGCTAG 57.587 43.478 0.00 0.00 0.00 3.42
2055 2425 5.087323 TCCTCCTTTCTTCTTCAAGCTAGA 58.913 41.667 0.00 0.00 0.00 2.43
2065 2435 3.449018 TCTTCAAGCTAGAAGGCTCGATT 59.551 43.478 0.00 0.00 44.01 3.34
2068 2438 3.195610 TCAAGCTAGAAGGCTCGATTTGA 59.804 43.478 0.00 0.00 42.24 2.69
2073 2443 3.616956 AGAAGGCTCGATTTGACATCA 57.383 42.857 0.00 0.00 0.00 3.07
2130 2566 2.093075 CCTCCTCACACCTAGTCTCGTA 60.093 54.545 0.00 0.00 0.00 3.43
2132 2568 3.542648 TCCTCACACCTAGTCTCGTATG 58.457 50.000 0.00 0.00 0.00 2.39
2562 3002 3.831651 GCTAGAGGAGGAGCCACTA 57.168 57.895 0.00 0.00 38.61 2.74
2690 3130 4.726304 CCCTAAAACCGGCCGGCA 62.726 66.667 43.58 24.51 39.32 5.69
2751 3191 2.609610 CGAGGGGAAGGGGTTGGA 60.610 66.667 0.00 0.00 0.00 3.53
2872 3341 2.943036 AGAAAAAGGCCCGTCTTGTA 57.057 45.000 0.00 0.00 0.00 2.41
2904 3374 2.429930 CAAGGGGAGGACACGCAA 59.570 61.111 0.00 0.00 0.00 4.85
2964 3434 3.053896 GCGGCGTAAACTTGGGCT 61.054 61.111 9.37 0.00 0.00 5.19
3013 3483 1.947456 GGACAAAAGTCCGTTTGCTCT 59.053 47.619 5.75 0.00 41.33 4.09
3017 3487 0.249911 AAAGTCCGTTTGCTCTCGCT 60.250 50.000 0.00 0.00 36.97 4.93
3070 3542 2.675423 CAGACGGGGTCGGACAGA 60.675 66.667 10.76 0.00 41.39 3.41
3075 3547 0.033796 ACGGGGTCGGACAGAATAGA 60.034 55.000 10.76 0.00 41.39 1.98
3098 3570 2.985847 GTGGTGGAGTTGGCCTGC 60.986 66.667 3.32 0.00 0.00 4.85
3099 3571 4.641645 TGGTGGAGTTGGCCTGCG 62.642 66.667 3.32 0.00 33.44 5.18
3212 3699 2.165301 GCATCAGTCGTACCCGCAC 61.165 63.158 0.00 0.00 0.00 5.34
3213 3700 1.518572 CATCAGTCGTACCCGCACC 60.519 63.158 0.00 0.00 0.00 5.01
3214 3701 1.980232 ATCAGTCGTACCCGCACCA 60.980 57.895 0.00 0.00 0.00 4.17
3215 3702 1.945354 ATCAGTCGTACCCGCACCAG 61.945 60.000 0.00 0.00 0.00 4.00
3216 3703 4.065281 AGTCGTACCCGCACCAGC 62.065 66.667 0.00 0.00 37.42 4.85
3234 3721 2.707849 CGCCAGTACCAGTACCGCT 61.708 63.158 12.94 0.00 36.75 5.52
3469 3990 3.696782 CGCTACACGCTAGTTGAGT 57.303 52.632 0.96 0.00 36.13 3.41
3470 3991 1.978542 CGCTACACGCTAGTTGAGTT 58.021 50.000 0.96 0.00 36.13 3.01
3471 3992 1.649171 CGCTACACGCTAGTTGAGTTG 59.351 52.381 0.96 0.00 36.13 3.16
3472 3993 2.667448 CGCTACACGCTAGTTGAGTTGA 60.667 50.000 0.96 0.00 36.13 3.18
3473 3994 2.917971 GCTACACGCTAGTTGAGTTGAG 59.082 50.000 0.96 0.00 35.14 3.02
3486 4007 2.093288 TGAGTTGAGCAGCTAATCCCAG 60.093 50.000 0.00 0.00 0.00 4.45
3527 4267 4.806339 CTCGCCCTCCCCTTCCCT 62.806 72.222 0.00 0.00 0.00 4.20
3531 4271 4.038804 CCCTCCCCTTCCCTCCCA 62.039 72.222 0.00 0.00 0.00 4.37
3532 4272 2.692741 CCTCCCCTTCCCTCCCAC 60.693 72.222 0.00 0.00 0.00 4.61
3533 4273 2.692741 CTCCCCTTCCCTCCCACC 60.693 72.222 0.00 0.00 0.00 4.61
3534 4274 4.364686 TCCCCTTCCCTCCCACCC 62.365 72.222 0.00 0.00 0.00 4.61
3656 4404 1.519408 CGTTTCCACCATTTCTCCGT 58.481 50.000 0.00 0.00 0.00 4.69
3832 4589 0.951558 GGTTTTGATCCGTGCTGTGT 59.048 50.000 0.00 0.00 0.00 3.72
3836 4593 3.188786 GATCCGTGCTGTGTCGCC 61.189 66.667 0.00 0.00 0.00 5.54
3855 4612 2.819595 GGCTTGCGCAGATCCGAA 60.820 61.111 11.31 0.00 38.10 4.30
3870 4627 1.375523 CGAAGGAGAACCAACCGGG 60.376 63.158 6.32 0.00 44.81 5.73
4159 4922 2.440599 GGGCTGAACCACCACCAT 59.559 61.111 0.00 0.00 42.05 3.55
4165 4928 0.110295 TGAACCACCACCATCACCAG 59.890 55.000 0.00 0.00 0.00 4.00
4300 5063 1.592669 GATGGATGTGAGCCCGACG 60.593 63.158 0.00 0.00 0.00 5.12
4356 5119 2.745492 GTCACAGGAGCAGGCTGC 60.745 66.667 31.56 31.56 45.46 5.25
4514 5277 0.676466 CAGCGCCAAGGATTACCACA 60.676 55.000 2.29 0.00 38.94 4.17
4625 5388 1.089920 ATGATCGTGCCTGCAAACTC 58.910 50.000 0.00 0.00 0.00 3.01
4697 5460 5.073554 AGGGATTTATGTCTATGATGCCACA 59.926 40.000 0.00 0.00 0.00 4.17
4698 5461 5.182001 GGGATTTATGTCTATGATGCCACAC 59.818 44.000 0.00 0.00 0.00 3.82
4700 5463 2.245159 ATGTCTATGATGCCACACGG 57.755 50.000 0.00 0.00 0.00 4.94
4702 5465 1.277842 TGTCTATGATGCCACACGGTT 59.722 47.619 0.00 0.00 33.28 4.44
4703 5466 1.665679 GTCTATGATGCCACACGGTTG 59.334 52.381 0.00 0.00 33.28 3.77
4704 5467 0.378257 CTATGATGCCACACGGTTGC 59.622 55.000 0.00 0.00 33.28 4.17
4705 5468 0.035534 TATGATGCCACACGGTTGCT 60.036 50.000 0.00 0.00 33.28 3.91
4706 5469 0.035534 ATGATGCCACACGGTTGCTA 60.036 50.000 0.00 0.00 33.28 3.49
4707 5470 0.035534 TGATGCCACACGGTTGCTAT 60.036 50.000 0.00 0.00 33.28 2.97
4708 5471 0.378257 GATGCCACACGGTTGCTATG 59.622 55.000 0.00 0.00 33.28 2.23
4753 5516 8.743714 AGAAATGGTTTCTCTATCCAATGTTTC 58.256 33.333 0.00 0.00 46.62 2.78
4770 5533 3.451178 TGTTTCTGGTCTCTATGTAGGCC 59.549 47.826 0.00 0.00 41.94 5.19
4931 5694 4.924305 ACAGATGTTGCTTCACAATTGT 57.076 36.364 4.92 4.92 41.27 2.71
5039 5802 4.760530 TGATCCCCTACTGAACTTGATG 57.239 45.455 0.00 0.00 0.00 3.07
5526 6290 1.077501 TAGCAGCACCCATGGAAGC 60.078 57.895 15.22 16.66 0.00 3.86
5832 6596 1.363807 GCCACCGCTTGAGCTTTTT 59.636 52.632 1.07 0.00 39.32 1.94
5862 6626 3.361174 CGGCCAACGGAAAATGGT 58.639 55.556 2.24 0.00 39.00 3.55
5883 6647 1.713647 TCACCACCAAACCCCACATAT 59.286 47.619 0.00 0.00 0.00 1.78
5913 6677 4.458989 TGTTATGCTTCAACATCTGGTTCC 59.541 41.667 0.00 0.00 37.72 3.62
5972 6736 5.705905 AGGTAATTTATATCGAAGCTTGCCC 59.294 40.000 2.10 0.00 0.00 5.36
6003 6767 1.533625 TATGTCACAAGCCAAGGTGC 58.466 50.000 0.00 0.00 35.04 5.01
6005 6769 2.594303 TCACAAGCCAAGGTGCCG 60.594 61.111 0.00 0.00 35.04 5.69
6044 6808 3.056304 GCTTTCAACCTAATTTGCGCAA 58.944 40.909 21.02 21.02 0.00 4.85
6405 7169 8.749499 GCAATAGAATTGTTGCACATTTATCTC 58.251 33.333 12.43 0.00 46.84 2.75
6431 7195 7.112565 CACATCGTATGATTTTTAATGCAGCTC 59.887 37.037 0.00 0.00 30.49 4.09
6432 7196 6.060028 TCGTATGATTTTTAATGCAGCTCC 57.940 37.500 0.00 0.00 0.00 4.70
6603 7367 4.604156 TCTCTATTCCTGCTCACTCTTCA 58.396 43.478 0.00 0.00 0.00 3.02
6624 7388 8.869109 TCTTCAATGGGTTTTGACTATGAATTT 58.131 29.630 0.00 0.00 35.42 1.82
6861 7625 1.003580 TCCTGCTTGACCATTGACTCC 59.996 52.381 0.00 0.00 0.00 3.85
7105 7869 6.668323 AGGTGATTACAACTTTGAATGTTCG 58.332 36.000 0.00 0.00 41.81 3.95
7891 8655 2.447443 TCTCCTGAAGTGTATGCGACT 58.553 47.619 0.00 0.00 0.00 4.18
7993 8757 7.274250 GTGCTCAACAAAGGTGAAATTCATATC 59.726 37.037 0.00 0.00 0.00 1.63
8430 9194 2.224917 TGGATAAAACCTTGCCGGAAGT 60.225 45.455 5.05 0.00 36.31 3.01
8480 9248 1.138661 CCAGCTTCTAAGGGCAGAGAG 59.861 57.143 0.00 0.00 0.00 3.20
8887 9665 7.392113 TGGTTTATTCGATTACCATCACAACTT 59.608 33.333 4.84 0.00 35.82 2.66
8888 9666 8.241367 GGTTTATTCGATTACCATCACAACTTT 58.759 33.333 0.00 0.00 0.00 2.66
8889 9667 9.061610 GTTTATTCGATTACCATCACAACTTTG 57.938 33.333 0.00 0.00 0.00 2.77
8890 9668 5.621197 TTCGATTACCATCACAACTTTGG 57.379 39.130 0.00 0.00 36.56 3.28
8891 9669 4.900684 TCGATTACCATCACAACTTTGGA 58.099 39.130 0.00 0.00 34.52 3.53
8892 9670 4.935205 TCGATTACCATCACAACTTTGGAG 59.065 41.667 0.00 0.00 34.52 3.86
8901 9679 2.618709 CACAACTTTGGAGTGGAGTTCC 59.381 50.000 0.00 0.00 35.91 3.62
8903 9681 0.396811 ACTTTGGAGTGGAGTTCCCG 59.603 55.000 0.00 0.00 37.93 5.14
8905 9683 1.621814 CTTTGGAGTGGAGTTCCCGTA 59.378 52.381 0.00 0.00 37.93 4.02
9180 10061 2.347490 GCAGAAGCCGGAACCAGA 59.653 61.111 5.05 0.00 33.58 3.86
9181 10062 1.302511 GCAGAAGCCGGAACCAGAA 60.303 57.895 5.05 0.00 33.58 3.02
9182 10063 1.301677 GCAGAAGCCGGAACCAGAAG 61.302 60.000 5.05 0.00 33.58 2.85
9183 10064 0.674895 CAGAAGCCGGAACCAGAAGG 60.675 60.000 5.05 0.00 42.21 3.46
9186 10067 4.344865 GCCGGAACCAGAAGGCCA 62.345 66.667 5.05 0.00 43.54 5.36
9187 10068 2.045926 CCGGAACCAGAAGGCCAG 60.046 66.667 5.01 0.00 39.06 4.85
9188 10069 2.592993 CCGGAACCAGAAGGCCAGA 61.593 63.158 5.01 0.00 39.06 3.86
9189 10070 1.374947 CGGAACCAGAAGGCCAGAA 59.625 57.895 5.01 0.00 39.06 3.02
9190 10071 0.250727 CGGAACCAGAAGGCCAGAAA 60.251 55.000 5.01 0.00 39.06 2.52
9191 10072 1.248486 GGAACCAGAAGGCCAGAAAC 58.752 55.000 5.01 0.00 39.06 2.78
9214 10095 2.507769 TGATCTGCACAGCTCGCG 60.508 61.111 0.00 0.00 0.00 5.87
9228 10109 3.539107 CGCGCGGTAGGAAACGAC 61.539 66.667 24.84 0.00 34.90 4.34
9237 10118 4.373771 GGAAACGACGCCTTTCCT 57.626 55.556 18.05 0.00 42.41 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.492524 TCCTCTAGGATCACCCAAAAAGATT 59.507 40.000 0.00 0.00 39.78 2.40
31 32 5.039645 TCCTCTAGGATCACCCAAAAAGAT 58.960 41.667 0.00 0.00 39.78 2.40
32 33 4.435137 TCCTCTAGGATCACCCAAAAAGA 58.565 43.478 0.00 0.00 39.78 2.52
48 49 1.203087 TGACGACCCTTGGTTCCTCTA 60.203 52.381 0.00 0.00 35.25 2.43
50 51 0.613777 ATGACGACCCTTGGTTCCTC 59.386 55.000 0.00 0.00 35.25 3.71
54 55 2.358322 ACAAATGACGACCCTTGGTT 57.642 45.000 0.00 0.00 35.25 3.67
64 65 9.702726 CTTATTGTACCTTCATAACAAATGACG 57.297 33.333 0.00 0.00 36.75 4.35
101 103 1.228552 GGTGCTTCAAGGCCCTTCA 60.229 57.895 0.00 0.00 0.00 3.02
110 112 2.136298 TGAAAGTGTGGGTGCTTCAA 57.864 45.000 0.00 0.00 0.00 2.69
116 118 5.163513 GCTTATTCAATGAAAGTGTGGGTG 58.836 41.667 0.00 0.00 31.21 4.61
122 124 5.688823 TGTCGTGCTTATTCAATGAAAGTG 58.311 37.500 0.00 0.00 0.00 3.16
127 129 6.976636 TGTATTGTCGTGCTTATTCAATGA 57.023 33.333 0.00 0.00 32.27 2.57
141 143 8.980610 TGGTTACCGATATAATTTGTATTGTCG 58.019 33.333 0.00 0.00 0.00 4.35
169 171 7.119846 GGACTAGCTTGCATTTTCTCTTTTCTA 59.880 37.037 0.00 0.00 0.00 2.10
171 173 6.072230 AGGACTAGCTTGCATTTTCTCTTTTC 60.072 38.462 0.00 0.00 0.00 2.29
214 216 4.084693 CGGTTTTACTTTCTGACCTCGAAC 60.085 45.833 0.00 0.00 0.00 3.95
216 218 3.645884 CGGTTTTACTTTCTGACCTCGA 58.354 45.455 0.00 0.00 0.00 4.04
283 285 3.010314 TGGTTTATCCCCGGCGGT 61.010 61.111 26.32 9.22 34.77 5.68
286 288 1.035385 CCAAGTGGTTTATCCCCGGC 61.035 60.000 0.00 0.00 34.77 6.13
317 319 1.998444 CTGGTGGATATGGGGCAGCA 61.998 60.000 0.00 0.00 0.00 4.41
343 345 2.047274 CTTCTTCCTTCGCCGCCA 60.047 61.111 0.00 0.00 0.00 5.69
365 367 2.890945 TGTATCTAGCATTAGCCGAGCA 59.109 45.455 0.00 0.00 43.56 4.26
414 420 1.202348 CGTCATCAGCTCCGTCATTCT 60.202 52.381 0.00 0.00 0.00 2.40
460 467 5.189145 TCATAGTTGTTCCCCTACTTCTTCC 59.811 44.000 0.00 0.00 31.40 3.46
527 537 3.329889 TGCTCATCGGTGCCCCTT 61.330 61.111 0.00 0.00 32.64 3.95
528 539 4.101448 GTGCTCATCGGTGCCCCT 62.101 66.667 0.00 0.00 32.64 4.79
541 552 2.281761 CCGAGGTGCTTTGGTGCT 60.282 61.111 0.00 0.00 0.00 4.40
552 563 2.600769 AAGAGCGTCCACCGAGGT 60.601 61.111 0.00 0.00 39.56 3.85
557 568 0.798776 CATCAACAAGAGCGTCCACC 59.201 55.000 0.00 0.00 0.00 4.61
571 582 1.748493 GCAATTCCTTACCCGCATCAA 59.252 47.619 0.00 0.00 0.00 2.57
578 589 2.014594 CGAGCGCAATTCCTTACCC 58.985 57.895 11.47 0.00 0.00 3.69
636 647 4.467084 GGCCGCCGTGATGGAGAA 62.467 66.667 0.00 0.00 40.56 2.87
662 673 4.314522 TGAAGATAATGAGTTTGCCCCA 57.685 40.909 0.00 0.00 0.00 4.96
717 734 2.496817 GCTGGAGCCGAAGACGAT 59.503 61.111 0.00 0.00 42.66 3.73
738 755 1.645034 CTCTTACATGTGGTGCTCCG 58.355 55.000 9.11 0.00 36.30 4.63
793 810 2.335681 TACCAGAGGGGATTGTGTCA 57.664 50.000 0.00 0.00 41.15 3.58
885 902 1.839994 CAGCTGGAGATGGTTAGGGAA 59.160 52.381 5.57 0.00 0.00 3.97
918 935 0.179045 GGCCGATCACATACCTTGCT 60.179 55.000 0.00 0.00 0.00 3.91
919 936 1.498865 CGGCCGATCACATACCTTGC 61.499 60.000 24.07 0.00 0.00 4.01
925 942 2.123208 TCCCCGGCCGATCACATA 60.123 61.111 30.73 0.92 0.00 2.29
938 955 0.405973 AGAGTTTCCTTTGGCTCCCC 59.594 55.000 0.00 0.00 0.00 4.81
947 964 1.694696 AGCTCCGTTGAGAGTTTCCTT 59.305 47.619 0.00 0.00 41.42 3.36
952 969 3.422796 TCTAGAAGCTCCGTTGAGAGTT 58.577 45.455 0.00 0.00 41.42 3.01
968 985 5.015817 ACTTTCTTCCCTCTCTCCTTCTAGA 59.984 44.000 0.00 0.00 0.00 2.43
970 987 5.020132 CACTTTCTTCCCTCTCTCCTTCTA 58.980 45.833 0.00 0.00 0.00 2.10
983 1000 4.339530 GGCCCATTCTTATCACTTTCTTCC 59.660 45.833 0.00 0.00 0.00 3.46
988 1005 2.587307 AGGGGCCCATTCTTATCACTTT 59.413 45.455 27.72 0.00 0.00 2.66
1032 1049 9.634021 TTTATGGGGAAAAGCAAATTTAAAACT 57.366 25.926 0.00 0.00 0.00 2.66
1045 1062 7.346471 TCTCATAGGAGTTTTATGGGGAAAAG 58.654 38.462 4.02 0.00 42.05 2.27
1050 1074 7.560796 AGTATCTCATAGGAGTTTTATGGGG 57.439 40.000 4.02 0.00 42.05 4.96
1087 1111 9.979578 TGAATCTTTTGTTATTGTTGTGCTATT 57.020 25.926 0.00 0.00 0.00 1.73
1106 1409 8.827832 TGTTATTGATTTCCTCCATGAATCTT 57.172 30.769 0.00 0.00 32.41 2.40
1112 1415 6.780457 ACCTTGTTATTGATTTCCTCCATG 57.220 37.500 0.00 0.00 0.00 3.66
1159 1462 6.255215 ACTCGAAAACATAAAATACATGCCG 58.745 36.000 0.00 0.00 0.00 5.69
1160 1463 7.968405 AGAACTCGAAAACATAAAATACATGCC 59.032 33.333 0.00 0.00 0.00 4.40
1179 1482 1.801178 GAGGGAACTTGCAAGAACTCG 59.199 52.381 32.50 6.51 44.43 4.18
1200 1503 2.318908 TGATGGTTGCTTCAAGGCTTT 58.681 42.857 0.00 0.00 0.00 3.51
1205 1508 3.256383 TGTGGATTGATGGTTGCTTCAAG 59.744 43.478 0.00 0.00 35.47 3.02
1208 1511 2.557924 TGTGTGGATTGATGGTTGCTTC 59.442 45.455 0.00 0.00 0.00 3.86
1244 1547 8.669243 AGAAATGCTTGCTAAATCTTACTACAC 58.331 33.333 0.00 0.00 0.00 2.90
1248 1551 9.061435 GGATAGAAATGCTTGCTAAATCTTACT 57.939 33.333 0.00 0.00 0.00 2.24
1274 1577 1.063469 ACCGAAACACGAGTTGCAAAG 59.937 47.619 0.00 0.00 45.77 2.77
1279 1582 0.433492 CGCTACCGAAACACGAGTTG 59.567 55.000 0.00 0.00 45.77 3.16
1280 1583 0.031178 ACGCTACCGAAACACGAGTT 59.969 50.000 0.00 0.00 45.77 3.01
1295 1600 1.344763 GGCTATGATTGGTAGGACGCT 59.655 52.381 0.00 0.00 0.00 5.07
1296 1601 1.797025 GGCTATGATTGGTAGGACGC 58.203 55.000 0.00 0.00 0.00 5.19
1299 1604 2.673258 TGACGGCTATGATTGGTAGGA 58.327 47.619 0.00 0.00 0.00 2.94
1306 1611 5.614308 TCATTCAGATTGACGGCTATGATT 58.386 37.500 0.00 0.00 0.00 2.57
1321 1626 9.449719 CATCCATGAGAATTATCATCATTCAGA 57.550 33.333 12.58 4.30 37.84 3.27
1323 1628 7.888546 AGCATCCATGAGAATTATCATCATTCA 59.111 33.333 12.58 0.00 37.84 2.57
1344 1649 7.659652 AAGTCAAAAACTCTACTGTAGCATC 57.340 36.000 9.98 0.00 37.17 3.91
1351 1656 7.072030 CGGATGAAAAGTCAAAAACTCTACTG 58.928 38.462 0.00 0.00 37.17 2.74
1355 1660 4.554723 CGCGGATGAAAAGTCAAAAACTCT 60.555 41.667 0.00 0.00 37.17 3.24
1356 1661 3.664025 CGCGGATGAAAAGTCAAAAACTC 59.336 43.478 0.00 0.00 37.17 3.01
1357 1662 3.550030 CCGCGGATGAAAAGTCAAAAACT 60.550 43.478 24.07 0.00 41.10 2.66
1358 1663 2.724174 CCGCGGATGAAAAGTCAAAAAC 59.276 45.455 24.07 0.00 37.30 2.43
1359 1664 2.359531 ACCGCGGATGAAAAGTCAAAAA 59.640 40.909 35.90 0.00 37.30 1.94
1360 1665 1.950909 ACCGCGGATGAAAAGTCAAAA 59.049 42.857 35.90 0.00 37.30 2.44
1361 1666 1.265635 CACCGCGGATGAAAAGTCAAA 59.734 47.619 35.90 0.00 37.30 2.69
1363 1668 0.953471 CCACCGCGGATGAAAAGTCA 60.953 55.000 35.90 0.00 38.41 3.41
1364 1669 0.953960 ACCACCGCGGATGAAAAGTC 60.954 55.000 35.90 0.00 38.63 3.01
1365 1670 0.536460 AACCACCGCGGATGAAAAGT 60.536 50.000 35.90 15.51 38.63 2.66
1366 1671 0.596082 AAACCACCGCGGATGAAAAG 59.404 50.000 35.90 14.89 38.63 2.27
1418 1724 3.571828 TGAACATTTGAATTCAAGCCCGA 59.428 39.130 19.64 6.48 37.15 5.14
1435 1741 2.967599 ATGCTCGCTACAGATGAACA 57.032 45.000 0.00 0.00 0.00 3.18
1436 1742 4.566759 TGTTTATGCTCGCTACAGATGAAC 59.433 41.667 0.00 0.00 0.00 3.18
1449 1755 5.863935 GGTGAGAAAAATGGTGTTTATGCTC 59.136 40.000 0.00 0.00 0.00 4.26
1453 1759 6.208599 ACATCGGTGAGAAAAATGGTGTTTAT 59.791 34.615 0.65 0.00 0.00 1.40
1525 1840 1.644786 GAACGGTGGTACTGCATGGC 61.645 60.000 0.00 0.00 0.00 4.40
1560 1878 2.491022 GGCCTCGTATCCTCTGCGT 61.491 63.158 0.00 0.00 34.27 5.24
1703 2021 2.409975 GACAGAATCCGGACAAAACGA 58.590 47.619 6.12 0.00 0.00 3.85
1755 2073 4.082523 CCGCATCCCAGGACACGT 62.083 66.667 8.79 0.00 0.00 4.49
1941 2272 8.282256 AGGAAGCAGTTATGGAAATTAGGTATT 58.718 33.333 0.00 0.00 0.00 1.89
1947 2278 7.175104 ACTCAAGGAAGCAGTTATGGAAATTA 58.825 34.615 0.00 0.00 0.00 1.40
1964 2295 1.628846 GGCTCTAACCCAACTCAAGGA 59.371 52.381 0.00 0.00 0.00 3.36
1981 2312 0.322975 ACAAGTGCATCGAGAAGGCT 59.677 50.000 0.00 0.00 0.00 4.58
2019 2389 1.118356 AGGAGGATGCCAGATCGACC 61.118 60.000 0.00 0.00 0.00 4.79
2020 2390 0.755686 AAGGAGGATGCCAGATCGAC 59.244 55.000 0.00 0.00 0.00 4.20
2021 2391 1.414181 GAAAGGAGGATGCCAGATCGA 59.586 52.381 0.00 0.00 0.00 3.59
2022 2392 1.415659 AGAAAGGAGGATGCCAGATCG 59.584 52.381 0.00 0.00 0.00 3.69
2023 2393 3.136260 AGAAGAAAGGAGGATGCCAGATC 59.864 47.826 0.00 0.00 0.00 2.75
2024 2394 3.121688 AGAAGAAAGGAGGATGCCAGAT 58.878 45.455 0.00 0.00 0.00 2.90
2025 2395 2.555664 AGAAGAAAGGAGGATGCCAGA 58.444 47.619 0.00 0.00 0.00 3.86
2026 2396 3.277715 GAAGAAGAAAGGAGGATGCCAG 58.722 50.000 0.00 0.00 0.00 4.85
2027 2397 2.644299 TGAAGAAGAAAGGAGGATGCCA 59.356 45.455 0.00 0.00 0.00 4.92
2028 2398 3.356529 TGAAGAAGAAAGGAGGATGCC 57.643 47.619 0.00 0.00 0.00 4.40
2029 2399 3.128415 GCTTGAAGAAGAAAGGAGGATGC 59.872 47.826 0.00 0.00 0.00 3.91
2030 2400 4.587891 AGCTTGAAGAAGAAAGGAGGATG 58.412 43.478 0.00 0.00 0.00 3.51
2031 2401 4.925390 AGCTTGAAGAAGAAAGGAGGAT 57.075 40.909 0.00 0.00 0.00 3.24
2032 2402 5.087323 TCTAGCTTGAAGAAGAAAGGAGGA 58.913 41.667 0.00 0.00 0.00 3.71
2033 2403 5.413309 TCTAGCTTGAAGAAGAAAGGAGG 57.587 43.478 0.00 0.00 0.00 4.30
2041 2411 3.186119 CGAGCCTTCTAGCTTGAAGAAG 58.814 50.000 31.32 23.33 45.70 2.85
2042 2412 3.238108 CGAGCCTTCTAGCTTGAAGAA 57.762 47.619 31.32 16.43 45.70 2.52
2043 2413 2.949451 CGAGCCTTCTAGCTTGAAGA 57.051 50.000 31.32 9.89 45.70 2.87
2047 2417 3.308323 GTCAAATCGAGCCTTCTAGCTTG 59.692 47.826 0.00 0.00 45.15 4.01
2048 2418 3.055819 TGTCAAATCGAGCCTTCTAGCTT 60.056 43.478 0.00 0.00 45.15 3.74
2050 2420 2.893637 TGTCAAATCGAGCCTTCTAGC 58.106 47.619 0.00 0.00 0.00 3.42
2051 2421 4.686972 TGATGTCAAATCGAGCCTTCTAG 58.313 43.478 0.00 0.00 0.00 2.43
2052 2422 4.736126 TGATGTCAAATCGAGCCTTCTA 57.264 40.909 0.00 0.00 0.00 2.10
2053 2423 3.616956 TGATGTCAAATCGAGCCTTCT 57.383 42.857 0.00 0.00 0.00 2.85
2054 2424 3.249559 GGATGATGTCAAATCGAGCCTTC 59.750 47.826 0.00 0.00 0.00 3.46
2055 2425 3.118112 AGGATGATGTCAAATCGAGCCTT 60.118 43.478 0.00 0.00 0.00 4.35
2065 2435 6.072286 GCTTGAAGAAGAAAGGATGATGTCAA 60.072 38.462 0.00 0.00 0.00 3.18
2068 2438 4.704057 GGCTTGAAGAAGAAAGGATGATGT 59.296 41.667 0.00 0.00 0.00 3.06
2073 2443 2.305927 TCCGGCTTGAAGAAGAAAGGAT 59.694 45.455 0.00 0.00 0.00 3.24
2130 2566 7.766278 CACTTGTTGTTAGATTAGAGGCTACAT 59.234 37.037 0.00 0.00 0.00 2.29
2132 2568 6.036191 GCACTTGTTGTTAGATTAGAGGCTAC 59.964 42.308 0.00 0.00 0.00 3.58
2447 2886 4.710695 TCGTCGGCGCATCGTTGT 62.711 61.111 10.83 0.00 38.14 3.32
2467 2906 2.639327 GCTCGGTGCTTGCCCAAAT 61.639 57.895 0.00 0.00 38.95 2.32
2562 3002 2.993264 GCAAGGCCACATGCAGGT 60.993 61.111 19.61 0.00 43.89 4.00
2588 3028 2.764128 CCTCGCTGGAAGGCCCTA 60.764 66.667 0.00 0.00 38.35 3.53
2690 3130 2.906897 CACCTGGTTTGCGCACCT 60.907 61.111 11.12 0.00 37.75 4.00
2751 3191 2.126812 GTTCAGACGCGAGCTCGT 60.127 61.111 34.46 19.03 46.38 4.18
2799 3248 0.832135 TCCACTCTTTCCCTCGCTGT 60.832 55.000 0.00 0.00 0.00 4.40
2809 3278 2.895424 CGCACCCCCTCCACTCTTT 61.895 63.158 0.00 0.00 0.00 2.52
2888 3358 1.073199 CTTTGCGTGTCCTCCCCTT 59.927 57.895 0.00 0.00 0.00 3.95
2964 3434 2.435938 GCTTTCGACCCATCCGCA 60.436 61.111 0.00 0.00 0.00 5.69
3013 3483 3.825160 AAAACAGCCCAGCGAGCGA 62.825 57.895 0.00 0.00 34.64 4.93
3046 3518 0.604578 CCGACCCCGTCTGTTTAAGA 59.395 55.000 0.00 0.00 0.00 2.10
3048 3520 0.318120 GTCCGACCCCGTCTGTTTAA 59.682 55.000 0.00 0.00 0.00 1.52
3054 3526 0.033796 TATTCTGTCCGACCCCGTCT 60.034 55.000 0.00 0.00 0.00 4.18
3070 3542 0.456221 CTCCACCACGCGACTCTATT 59.544 55.000 15.93 0.00 0.00 1.73
3075 3547 2.029073 CAACTCCACCACGCGACT 59.971 61.111 15.93 0.00 0.00 4.18
3164 3636 2.612251 CTCTCCCCCTCTCCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
3190 3662 1.521681 GGGTACGACTGATGCTGCC 60.522 63.158 0.00 0.00 0.00 4.85
3212 3699 1.153628 GTACTGGTACTGGCGCTGG 60.154 63.158 7.64 2.58 33.45 4.85
3213 3700 1.153628 GGTACTGGTACTGGCGCTG 60.154 63.158 7.64 2.99 36.36 5.18
3214 3701 2.707849 CGGTACTGGTACTGGCGCT 61.708 63.158 7.64 0.00 38.46 5.92
3215 3702 2.202703 CGGTACTGGTACTGGCGC 60.203 66.667 0.00 0.00 38.46 6.53
3216 3703 1.378882 TAGCGGTACTGGTACTGGCG 61.379 60.000 17.89 11.07 41.52 5.69
3217 3704 0.101939 GTAGCGGTACTGGTACTGGC 59.898 60.000 28.69 16.09 41.52 4.85
3356 3857 2.509561 GAGAGGGAAGGAACGCGC 60.510 66.667 5.73 0.00 0.00 6.86
3358 3859 2.509561 GCGAGAGGGAAGGAACGC 60.510 66.667 0.00 0.00 39.33 4.84
3359 3860 2.184579 GGCGAGAGGGAAGGAACG 59.815 66.667 0.00 0.00 0.00 3.95
3360 3861 2.585153 GGGCGAGAGGGAAGGAAC 59.415 66.667 0.00 0.00 0.00 3.62
3361 3862 2.687566 GGGGCGAGAGGGAAGGAA 60.688 66.667 0.00 0.00 0.00 3.36
3362 3863 3.684628 AGGGGCGAGAGGGAAGGA 61.685 66.667 0.00 0.00 0.00 3.36
3469 3990 0.107017 GGCTGGGATTAGCTGCTCAA 60.107 55.000 4.91 0.00 43.22 3.02
3470 3991 1.528824 GGCTGGGATTAGCTGCTCA 59.471 57.895 4.91 0.00 43.22 4.26
3471 3992 1.228094 GGGCTGGGATTAGCTGCTC 60.228 63.158 4.91 0.00 43.22 4.26
3472 3993 2.922234 GGGCTGGGATTAGCTGCT 59.078 61.111 7.57 7.57 43.22 4.24
3473 3994 2.592861 CGGGCTGGGATTAGCTGC 60.593 66.667 0.00 0.00 43.22 5.25
3523 4263 4.332543 AAGAGCGGGTGGGAGGGA 62.333 66.667 0.00 0.00 0.00 4.20
3526 4266 3.358076 GACGAAGAGCGGGTGGGAG 62.358 68.421 0.00 0.00 46.49 4.30
3527 4267 3.379445 GACGAAGAGCGGGTGGGA 61.379 66.667 0.00 0.00 46.49 4.37
3530 4270 2.202492 CGAGACGAAGAGCGGGTG 60.202 66.667 0.00 0.00 46.49 4.61
3531 4271 3.441290 CCGAGACGAAGAGCGGGT 61.441 66.667 0.00 0.00 46.49 5.28
3532 4272 4.856607 GCCGAGACGAAGAGCGGG 62.857 72.222 0.00 0.00 46.49 6.13
3533 4273 3.743091 GAGCCGAGACGAAGAGCGG 62.743 68.421 0.00 0.00 46.49 5.52
3535 4275 2.054140 ATCGAGCCGAGACGAAGAGC 62.054 60.000 0.00 0.00 39.91 4.09
3676 4424 2.746277 CCCGCGGAGAAAACAGGG 60.746 66.667 30.73 0.44 0.00 4.45
3842 4599 1.604147 TTCTCCTTCGGATCTGCGCA 61.604 55.000 10.98 10.98 0.00 6.09
3844 4601 0.528684 GGTTCTCCTTCGGATCTGCG 60.529 60.000 0.00 0.00 0.00 5.18
3934 4691 0.179062 GCTGGATCTGGTGCAGGTAG 60.179 60.000 11.54 0.00 45.55 3.18
4159 4922 4.259131 TGCTGCTGCTGCTGGTGA 62.259 61.111 27.67 8.50 40.48 4.02
4228 4991 3.314331 CTCAGGTCACCGGCACCT 61.314 66.667 18.27 18.27 45.89 4.00
4300 5063 2.231721 AGGCGAAGAAGACAAGGTAGTC 59.768 50.000 0.00 0.00 38.81 2.59
4356 5119 1.414550 GAACCCTCTTGCTAGGCCTAG 59.585 57.143 32.12 32.12 35.09 3.02
4631 5394 8.074972 GCAAAGAATCATGCCACAAAAATTTTA 58.925 29.630 3.34 0.00 36.56 1.52
4635 5398 5.310451 AGCAAAGAATCATGCCACAAAAAT 58.690 33.333 7.30 0.00 43.57 1.82
4697 5460 0.107831 ACACACACCATAGCAACCGT 59.892 50.000 0.00 0.00 0.00 4.83
4698 5461 2.087501 TACACACACCATAGCAACCG 57.912 50.000 0.00 0.00 0.00 4.44
4700 5463 3.128589 CCCAATACACACACCATAGCAAC 59.871 47.826 0.00 0.00 0.00 4.17
4702 5465 2.943646 GCCCAATACACACACCATAGCA 60.944 50.000 0.00 0.00 0.00 3.49
4703 5466 1.676006 GCCCAATACACACACCATAGC 59.324 52.381 0.00 0.00 0.00 2.97
4704 5467 2.297701 GGCCCAATACACACACCATAG 58.702 52.381 0.00 0.00 0.00 2.23
4705 5468 1.636003 TGGCCCAATACACACACCATA 59.364 47.619 0.00 0.00 0.00 2.74
4706 5469 0.407528 TGGCCCAATACACACACCAT 59.592 50.000 0.00 0.00 0.00 3.55
4707 5470 0.251121 CTGGCCCAATACACACACCA 60.251 55.000 0.00 0.00 0.00 4.17
4708 5471 0.037590 TCTGGCCCAATACACACACC 59.962 55.000 0.00 0.00 0.00 4.16
4753 5516 1.883275 CTCGGCCTACATAGAGACCAG 59.117 57.143 0.00 0.00 32.84 4.00
4770 5533 9.530129 CAACTTTTAGTAACTAAAATGCTCTCG 57.470 33.333 0.00 0.00 42.53 4.04
4931 5694 5.413309 TTTTCTTGGTTTTCAGGAAGCAA 57.587 34.783 2.80 2.80 41.48 3.91
5039 5802 2.977405 ATCAACAAGTGAAAGAGCGC 57.023 45.000 0.00 0.00 40.50 5.92
5082 5846 1.073964 CACCTGTCAATGCAGAGACG 58.926 55.000 14.35 10.00 38.70 4.18
5526 6290 4.319177 GCTGCTTATATACTTCAGGTGGG 58.681 47.826 0.00 0.00 0.00 4.61
5832 6596 2.706890 GTTGGCCGTTCTGAATCCTTA 58.293 47.619 0.00 0.00 0.00 2.69
5862 6626 0.263172 ATGTGGGGTTTGGTGGTGAA 59.737 50.000 0.00 0.00 0.00 3.18
5883 6647 6.093082 CAGATGTTGAAGCATAACATGACTGA 59.907 38.462 15.10 0.00 45.82 3.41
5913 6677 3.534554 TGATGTTGATGGAGAATGGTCG 58.465 45.455 0.00 0.00 0.00 4.79
5972 6736 6.088824 GGCTTGTGACATAATCAACTGAAAG 58.911 40.000 0.00 0.00 39.72 2.62
6003 6767 7.642194 TGAAAGCGCATCTAAAATAATAAACGG 59.358 33.333 11.47 0.00 0.00 4.44
6044 6808 9.020731 AGTACGATCCTACAAAATGGAAAATTT 57.979 29.630 4.93 0.00 35.81 1.82
6370 7134 6.895607 CAACAATTCTATTGCATGCATTCA 57.104 33.333 23.37 7.20 0.00 2.57
6405 7169 6.914215 AGCTGCATTAAAAATCATACGATGTG 59.086 34.615 1.02 0.00 30.13 3.21
6431 7195 2.819608 TCGCTGGAGGAAATTTTCTTGG 59.180 45.455 0.00 0.00 0.00 3.61
6432 7196 3.503748 ACTCGCTGGAGGAAATTTTCTTG 59.496 43.478 0.00 0.00 44.93 3.02
6603 7367 9.625747 AAAACAAATTCATAGTCAAAACCCATT 57.374 25.926 0.00 0.00 0.00 3.16
6861 7625 3.324117 CAGTGGATCCTGCATAGATTCG 58.676 50.000 14.23 0.00 0.00 3.34
7105 7869 1.792949 CTGTTCTCAACCTGCACGTAC 59.207 52.381 0.00 0.00 0.00 3.67
7417 8181 1.220749 GCACCAGTCCCGCTCATTA 59.779 57.895 0.00 0.00 0.00 1.90
7891 8655 2.270352 ATGAGCCGTTGTTCCTGAAA 57.730 45.000 0.00 0.00 0.00 2.69
7993 8757 1.745087 CCAACATTCCCTGGTTGATCG 59.255 52.381 6.12 0.00 45.50 3.69
8315 9079 0.250770 GTTCCACACCCTCTGGTTCC 60.251 60.000 0.00 0.00 44.75 3.62
8368 9132 3.837578 CATGTCCATGGGCAGAGC 58.162 61.111 25.65 3.10 35.24 4.09
8430 9194 8.040002 TGATTATCCCCACATATCAACACTTA 57.960 34.615 0.00 0.00 0.00 2.24
8480 9248 3.092301 CTCCAATCCCCCTTTTCTTGAC 58.908 50.000 0.00 0.00 0.00 3.18
8770 9543 2.607187 CCTGCTACCGTCTAAACACAG 58.393 52.381 0.00 0.00 0.00 3.66
8887 9665 0.971386 GTACGGGAACTCCACTCCAA 59.029 55.000 0.00 0.00 37.91 3.53
8888 9666 0.113776 AGTACGGGAACTCCACTCCA 59.886 55.000 0.00 0.00 37.91 3.86
8889 9667 0.531200 CAGTACGGGAACTCCACTCC 59.469 60.000 0.00 0.00 37.91 3.85
8890 9668 1.254954 ACAGTACGGGAACTCCACTC 58.745 55.000 0.00 0.00 37.91 3.51
8891 9669 1.713297 AACAGTACGGGAACTCCACT 58.287 50.000 0.00 0.00 37.91 4.00
8892 9670 2.538512 AAACAGTACGGGAACTCCAC 57.461 50.000 0.00 0.00 37.91 4.02
8901 9679 4.935808 AGGCTTTCTATCAAAACAGTACGG 59.064 41.667 0.00 0.00 0.00 4.02
8903 9681 5.123979 CCCAGGCTTTCTATCAAAACAGTAC 59.876 44.000 0.00 0.00 0.00 2.73
8905 9683 4.082125 CCCAGGCTTTCTATCAAAACAGT 58.918 43.478 0.00 0.00 0.00 3.55
8938 9717 4.059511 CAAGGAAATGCATGCACAGAAAA 58.940 39.130 25.37 0.00 0.00 2.29
9175 10056 0.535102 CGTGTTTCTGGCCTTCTGGT 60.535 55.000 3.32 0.00 35.27 4.00
9180 10061 2.203153 ACGCGTGTTTCTGGCCTT 60.203 55.556 12.93 0.00 0.00 4.35
9181 10062 2.731691 ATCACGCGTGTTTCTGGCCT 62.732 55.000 35.74 9.99 0.00 5.19
9182 10063 2.240612 GATCACGCGTGTTTCTGGCC 62.241 60.000 35.74 13.12 0.00 5.36
9183 10064 1.132640 GATCACGCGTGTTTCTGGC 59.867 57.895 35.74 13.82 0.00 4.85
9184 10065 0.439985 CAGATCACGCGTGTTTCTGG 59.560 55.000 38.11 28.37 37.79 3.86
9185 10066 0.179240 GCAGATCACGCGTGTTTCTG 60.179 55.000 39.54 39.54 40.92 3.02
9186 10067 0.599991 TGCAGATCACGCGTGTTTCT 60.600 50.000 35.74 31.78 0.00 2.52
9187 10068 0.451135 GTGCAGATCACGCGTGTTTC 60.451 55.000 35.74 30.35 35.76 2.78
9188 10069 1.569493 GTGCAGATCACGCGTGTTT 59.431 52.632 35.74 25.17 35.76 2.83
9189 10070 3.244105 GTGCAGATCACGCGTGTT 58.756 55.556 35.74 29.11 35.76 3.32
9214 10095 3.184003 GGCGTCGTTTCCTACCGC 61.184 66.667 0.00 0.00 43.35 5.68



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

AutoCloner maintained by Alex Coulton.