Multiple sequence alignment - TraesCS1D01G200700

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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 TraesCS1D01G200700 chr1D 100.000 5690 0 0 1 5690 283573698 283568009 0.000000e+00 10508.0
1 TraesCS1D01G200700 chr1B 95.290 3333 114 16 1428 4751 385173518 385170220 0.000000e+00 5245.0
2 TraesCS1D01G200700 chr1B 84.800 1250 98 49 209 1394 385174738 385173517 0.000000e+00 1171.0
3 TraesCS1D01G200700 chr1B 91.214 626 30 11 5074 5690 385166940 385166331 0.000000e+00 828.0
4 TraesCS1D01G200700 chr1B 92.829 251 12 4 4803 5050 385170221 385169974 5.420000e-95 359.0
5 TraesCS1D01G200700 chr1A 95.023 3275 109 19 1524 4751 355333366 355330099 0.000000e+00 5096.0
6 TraesCS1D01G200700 chr1A 91.554 1409 85 21 1 1399 355334999 355333615 0.000000e+00 1912.0
7 TraesCS1D01G200700 chr1A 93.376 619 27 9 5074 5690 355329068 355328462 0.000000e+00 904.0
8 TraesCS1D01G200700 chr1A 88.889 270 21 4 4803 5072 355330100 355329840 1.980000e-84 324.0
9 TraesCS1D01G200700 chr7D 96.078 51 2 0 1 51 520873026 520872976 3.650000e-12 84.2
10 TraesCS1D01G200700 chr7D 100.000 28 0 0 4781 4808 613869063 613869090 1.000000e-02 52.8
11 TraesCS1D01G200700 chr4A 100.000 29 0 0 4779 4807 646776712 646776740 3.000000e-03 54.7
12 TraesCS1D01G200700 chr7B 100.000 28 0 0 4781 4808 62852570 62852597 1.000000e-02 52.8
13 TraesCS1D01G200700 chr6B 96.774 31 1 0 4781 4811 191598128 191598098 1.000000e-02 52.8
14 TraesCS1D01G200700 chr5B 100.000 28 0 0 4781 4808 126604629 126604602 1.000000e-02 52.8
15 TraesCS1D01G200700 chr5B 96.774 31 1 0 4781 4811 679686612 679686582 1.000000e-02 52.8
16 TraesCS1D01G200700 chr5A 96.774 31 1 0 4781 4811 328445166 328445136 1.000000e-02 52.8
17 TraesCS1D01G200700 chr3B 100.000 28 0 0 4779 4806 499194121 499194094 1.000000e-02 52.8
18 TraesCS1D01G200700 chr2D 100.000 28 0 0 4781 4808 12630877 12630904 1.000000e-02 52.8


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 TraesCS1D01G200700 chr1D 283568009 283573698 5689 True 10508.00 10508 100.00000 1 5690 1 chr1D.!!$R1 5689
1 TraesCS1D01G200700 chr1B 385166331 385174738 8407 True 1900.75 5245 91.03325 209 5690 4 chr1B.!!$R1 5481
2 TraesCS1D01G200700 chr1A 355328462 355334999 6537 True 2059.00 5096 92.21050 1 5690 4 chr1A.!!$R1 5689

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
274 275 0.108424 CAAGGTGGAGAGAAGGAGCG 60.108 60.0 0.00 0.00 0.00 5.03 F
430 434 0.403304 TACATGGATGGGCCCCTCAT 60.403 55.0 26.35 19.76 34.97 2.90 F
1410 1489 0.168568 GCTGCTTCTGCTTCTGCTTC 59.831 55.0 0.00 0.00 40.48 3.86 F
1423 1502 0.107017 CTGCTTCATTCATCCGGGGT 60.107 55.0 0.00 0.00 0.00 4.95 F
1424 1503 0.107214 TGCTTCATTCATCCGGGGTC 60.107 55.0 0.00 0.00 0.00 4.46 F
1425 1504 0.181350 GCTTCATTCATCCGGGGTCT 59.819 55.0 0.00 0.00 0.00 3.85 F
1664 1910 0.317479 ATATCGCTCAAGGTACCGCC 59.683 55.0 6.18 0.00 37.58 6.13 F
2136 2390 0.673022 CTCTTCTCACAGCAGTGGCC 60.673 60.0 9.58 0.00 45.91 5.36 F
3196 3475 0.823356 TCCTTGCCTTCAAGCACCAC 60.823 55.0 0.00 0.00 46.38 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1409 1488 0.031111 AGGAGACCCCGGATGAATGA 60.031 55.000 0.73 0.0 40.87 2.57 R
1412 1491 0.618458 CAAAGGAGACCCCGGATGAA 59.382 55.000 0.73 0.0 40.87 2.57 R
3141 3419 0.033109 GCCCTGCAAGATTTACCCCT 60.033 55.000 0.00 0.0 34.07 4.79 R
3147 3425 2.041620 TCCAACTAGCCCTGCAAGATTT 59.958 45.455 0.00 0.0 34.07 2.17 R
3196 3475 4.812626 ACAGCAAGAAAAGCAAAGAATTGG 59.187 37.500 0.00 0.0 37.02 3.16 R
3380 3659 5.409826 GTGTGAAACCTCTGAACCATCTTAG 59.590 44.000 0.00 0.0 34.36 2.18 R
3602 3884 2.926200 CAGCTACAGAGATGAAACCACG 59.074 50.000 0.00 0.0 41.90 4.94 R
3893 4183 1.001406 CCCCTGATAGCCTTCGACATC 59.999 57.143 0.00 0.0 0.00 3.06 R
4749 5046 0.192566 ATTATGGGGCGGAGGGAGTA 59.807 55.000 0.00 0.0 0.00 2.59 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
84 85 3.425162 GTGGAATCACCTGGTTCTTCT 57.575 47.619 14.49 0.00 37.92 2.85
99 100 7.400599 TGGTTCTTCTCTTTAGCGACTATAA 57.599 36.000 0.00 0.00 0.00 0.98
149 150 1.348064 CACTACCACAACAGGAGGGA 58.652 55.000 0.00 0.00 0.00 4.20
174 175 2.504681 GGCCAAAATCACGCGCTG 60.505 61.111 5.73 3.89 0.00 5.18
202 203 1.768870 AGCCATCGTAGCCACCTTATT 59.231 47.619 0.00 0.00 0.00 1.40
274 275 0.108424 CAAGGTGGAGAGAAGGAGCG 60.108 60.000 0.00 0.00 0.00 5.03
297 300 2.038557 ACAACTAGGCAAGAACCGACAT 59.961 45.455 0.00 0.00 33.69 3.06
316 319 2.224495 TATGCCAAAAGGCCGCAAGC 62.224 55.000 6.34 3.75 42.60 4.01
342 346 3.573967 AGGTTGAAATGAAAAGATGGCGT 59.426 39.130 0.00 0.00 0.00 5.68
362 366 3.057876 CGTTGGTCCTAGCTAGCTATCTG 60.058 52.174 24.36 15.54 0.00 2.90
415 419 8.224720 ACCTTTGGCCTACATACAAATATACAT 58.775 33.333 3.32 0.00 34.06 2.29
430 434 0.403304 TACATGGATGGGCCCCTCAT 60.403 55.000 26.35 19.76 34.97 2.90
490 494 1.197812 GGGCCAGCAATGGAGAAATT 58.802 50.000 4.39 0.00 0.00 1.82
505 511 3.416156 AGAAATTGGAAGAGGAGTGTGC 58.584 45.455 0.00 0.00 0.00 4.57
509 515 2.283529 GGAAGAGGAGTGTGCGGGA 61.284 63.158 0.00 0.00 0.00 5.14
523 537 2.325082 CGGGACCGGAGCAAACAAG 61.325 63.158 9.46 0.00 35.56 3.16
594 608 5.790593 AGATGCTCTTTTTGATTGCAATGT 58.209 33.333 18.59 0.00 37.20 2.71
683 698 4.246458 GTTAGTGAAGGCGATGACTTCTT 58.754 43.478 13.18 4.94 46.92 2.52
684 699 2.966050 AGTGAAGGCGATGACTTCTTC 58.034 47.619 13.18 6.93 46.92 2.87
685 700 2.300152 AGTGAAGGCGATGACTTCTTCA 59.700 45.455 13.18 3.54 46.92 3.02
686 701 2.413453 GTGAAGGCGATGACTTCTTCAC 59.587 50.000 13.18 15.94 46.92 3.18
687 702 2.037121 TGAAGGCGATGACTTCTTCACA 59.963 45.455 13.18 0.00 46.92 3.58
688 703 2.839486 AGGCGATGACTTCTTCACAA 57.161 45.000 0.00 0.00 36.92 3.33
689 704 3.126001 AGGCGATGACTTCTTCACAAA 57.874 42.857 0.00 0.00 36.92 2.83
723 740 7.484035 ACAAACTGAGATATAAAATCGAGCC 57.516 36.000 0.00 0.00 0.00 4.70
726 743 8.397906 CAAACTGAGATATAAAATCGAGCCAAA 58.602 33.333 0.00 0.00 0.00 3.28
728 745 7.920738 ACTGAGATATAAAATCGAGCCAAAAC 58.079 34.615 0.00 0.00 0.00 2.43
769 786 9.521841 TTAATAAAACTGAGACAGAGAGAGAGA 57.478 33.333 5.76 0.00 35.18 3.10
770 787 5.964958 AAAACTGAGACAGAGAGAGAGAG 57.035 43.478 5.76 0.00 35.18 3.20
771 788 4.908601 AACTGAGACAGAGAGAGAGAGA 57.091 45.455 5.76 0.00 35.18 3.10
772 789 4.478206 ACTGAGACAGAGAGAGAGAGAG 57.522 50.000 5.76 0.00 35.18 3.20
773 790 4.096681 ACTGAGACAGAGAGAGAGAGAGA 58.903 47.826 5.76 0.00 35.18 3.10
774 791 4.161189 ACTGAGACAGAGAGAGAGAGAGAG 59.839 50.000 5.76 0.00 35.18 3.20
775 792 4.352893 TGAGACAGAGAGAGAGAGAGAGA 58.647 47.826 0.00 0.00 0.00 3.10
776 793 4.403752 TGAGACAGAGAGAGAGAGAGAGAG 59.596 50.000 0.00 0.00 0.00 3.20
780 797 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
797 814 3.051803 AGAGAGAGAGAGAGAGGGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
956 1011 0.460284 CGCGGGTCTTACTTCAGCAT 60.460 55.000 0.00 0.00 0.00 3.79
991 1056 1.734477 CACGGAGCAGAACAGGACG 60.734 63.158 0.00 0.00 0.00 4.79
993 1069 2.435059 GGAGCAGAACAGGACGGC 60.435 66.667 0.00 0.00 0.00 5.68
1097 1174 1.445582 CCTGGTACGTCGTTGGCTC 60.446 63.158 1.78 0.00 0.00 4.70
1106 1183 2.743928 CGTTGGCTCTCCACCAGC 60.744 66.667 0.00 0.00 43.33 4.85
1118 1195 0.670546 CCACCAGCATCTTTCGTCGT 60.671 55.000 0.00 0.00 0.00 4.34
1400 1479 3.800863 CTGCTGCCGCTGCTTCTG 61.801 66.667 21.13 7.12 38.71 3.02
1403 1482 3.054503 CTGCCGCTGCTTCTGCTT 61.055 61.111 0.70 0.00 40.48 3.91
1404 1483 3.036783 CTGCCGCTGCTTCTGCTTC 62.037 63.158 0.70 0.00 40.48 3.86
1405 1484 2.745492 GCCGCTGCTTCTGCTTCT 60.745 61.111 0.00 0.00 40.48 2.85
1406 1485 3.036783 GCCGCTGCTTCTGCTTCTG 62.037 63.158 0.00 0.00 40.48 3.02
1407 1486 2.479650 CGCTGCTTCTGCTTCTGC 59.520 61.111 0.00 0.00 40.48 4.26
1408 1487 2.033755 CGCTGCTTCTGCTTCTGCT 61.034 57.895 0.00 0.00 40.48 4.24
1409 1488 1.575576 CGCTGCTTCTGCTTCTGCTT 61.576 55.000 0.00 0.00 40.48 3.91
1410 1489 0.168568 GCTGCTTCTGCTTCTGCTTC 59.831 55.000 0.00 0.00 40.48 3.86
1411 1490 1.520494 CTGCTTCTGCTTCTGCTTCA 58.480 50.000 0.00 0.00 40.48 3.02
1412 1491 2.085320 CTGCTTCTGCTTCTGCTTCAT 58.915 47.619 0.00 0.00 40.48 2.57
1413 1492 2.488545 CTGCTTCTGCTTCTGCTTCATT 59.511 45.455 0.00 0.00 40.48 2.57
1414 1493 2.486982 TGCTTCTGCTTCTGCTTCATTC 59.513 45.455 0.00 0.00 40.48 2.67
1415 1494 2.486982 GCTTCTGCTTCTGCTTCATTCA 59.513 45.455 0.00 0.00 40.48 2.57
1416 1495 3.128938 GCTTCTGCTTCTGCTTCATTCAT 59.871 43.478 0.00 0.00 40.48 2.57
1417 1496 4.731193 GCTTCTGCTTCTGCTTCATTCATC 60.731 45.833 0.00 0.00 40.48 2.92
1418 1497 3.276857 TCTGCTTCTGCTTCATTCATCC 58.723 45.455 0.00 0.00 40.48 3.51
1419 1498 2.011947 TGCTTCTGCTTCATTCATCCG 58.988 47.619 0.00 0.00 40.48 4.18
1420 1499 1.332997 GCTTCTGCTTCATTCATCCGG 59.667 52.381 0.00 0.00 36.03 5.14
1421 1500 1.945394 CTTCTGCTTCATTCATCCGGG 59.055 52.381 0.00 0.00 0.00 5.73
1422 1501 0.181114 TCTGCTTCATTCATCCGGGG 59.819 55.000 0.00 0.00 0.00 5.73
1423 1502 0.107017 CTGCTTCATTCATCCGGGGT 60.107 55.000 0.00 0.00 0.00 4.95
1424 1503 0.107214 TGCTTCATTCATCCGGGGTC 60.107 55.000 0.00 0.00 0.00 4.46
1425 1504 0.181350 GCTTCATTCATCCGGGGTCT 59.819 55.000 0.00 0.00 0.00 3.85
1426 1505 1.811941 GCTTCATTCATCCGGGGTCTC 60.812 57.143 0.00 0.00 0.00 3.36
1430 1509 1.212935 CATTCATCCGGGGTCTCCTTT 59.787 52.381 0.00 0.00 0.00 3.11
1547 1793 5.742453 AGTACAGAGTACAAAACATATCGCG 59.258 40.000 0.00 0.00 0.00 5.87
1662 1908 1.340248 ACCATATCGCTCAAGGTACCG 59.660 52.381 6.18 0.00 0.00 4.02
1664 1910 0.317479 ATATCGCTCAAGGTACCGCC 59.683 55.000 6.18 0.00 37.58 6.13
1674 1920 0.834687 AGGTACCGCCTCTTCACCAA 60.835 55.000 6.18 0.00 46.96 3.67
1693 1946 3.480470 CAATCTCTCCAACACCACAACT 58.520 45.455 0.00 0.00 0.00 3.16
1696 1949 1.942657 CTCTCCAACACCACAACTGTG 59.057 52.381 2.72 2.72 45.23 3.66
1725 1978 7.910162 CAGTTGGTCATAATTATTTTCTGTCCG 59.090 37.037 0.00 0.00 0.00 4.79
1729 1982 6.292703 GGTCATAATTATTTTCTGTCCGTCGG 60.293 42.308 4.39 4.39 0.00 4.79
1822 2076 3.578282 TGCTCCACTCTTAACATCAGACA 59.422 43.478 0.00 0.00 0.00 3.41
1831 2085 8.655092 CACTCTTAACATCAGACAAATCTTCTC 58.345 37.037 0.00 0.00 30.42 2.87
1845 2099 8.092521 ACAAATCTTCTCTAATTATGCCATCG 57.907 34.615 0.00 0.00 0.00 3.84
1848 2102 4.284490 TCTTCTCTAATTATGCCATCGCCT 59.716 41.667 0.00 0.00 0.00 5.52
1852 2106 1.512926 AATTATGCCATCGCCTCGTC 58.487 50.000 0.00 0.00 0.00 4.20
1941 2195 3.643320 TCTATGGTGCTTTGATCGGATCT 59.357 43.478 18.16 0.00 0.00 2.75
2004 2258 1.139947 GCTGTCCTCGTGCTCTACC 59.860 63.158 0.00 0.00 0.00 3.18
2136 2390 0.673022 CTCTTCTCACAGCAGTGGCC 60.673 60.000 9.58 0.00 45.91 5.36
2394 2648 4.072131 TCTTGGGATGCTTGTAAGTTCAC 58.928 43.478 0.00 0.00 0.00 3.18
2815 3069 4.595762 AGCAATGATAATTGGATGTGGC 57.404 40.909 4.90 0.00 32.43 5.01
3136 3414 6.376018 TGTTAAGGTTGCCATTTCCAGTATAC 59.624 38.462 0.00 0.00 0.00 1.47
3141 3419 3.039743 TGCCATTTCCAGTATACGGGTA 58.960 45.455 19.80 9.40 32.79 3.69
3146 3424 1.234806 TCCAGTATACGGGTAGGGGT 58.765 55.000 19.80 0.00 32.79 4.95
3147 3425 2.427872 TCCAGTATACGGGTAGGGGTA 58.572 52.381 19.80 0.00 32.79 3.69
3196 3475 0.823356 TCCTTGCCTTCAAGCACCAC 60.823 55.000 0.00 0.00 46.38 4.16
3222 3501 4.032703 TCTTTGCTTTTCTTGCTGTGTC 57.967 40.909 0.00 0.00 0.00 3.67
3736 4018 9.860898 GGCTTCAACATGTAGATTTCTTATTTT 57.139 29.630 0.00 0.00 0.00 1.82
3893 4183 9.940166 GTATTGTTAACTTTCAAATATACCCCG 57.060 33.333 7.22 0.00 0.00 5.73
3989 4280 5.885912 ACACTTATTCACACTTTCCTGTTGT 59.114 36.000 0.00 0.00 0.00 3.32
4023 4314 2.744494 GCAGGCTGTCTCCCTATTCTTG 60.744 54.545 17.16 0.00 0.00 3.02
4111 4402 0.613260 TGGCTGCTACCAGGTACTTG 59.387 55.000 0.00 0.00 39.54 3.16
4161 4453 9.799106 CCATAAAATAGTACAAGAGGATTCCAT 57.201 33.333 5.29 0.00 0.00 3.41
4166 4458 4.366267 AGTACAAGAGGATTCCATGGAGT 58.634 43.478 15.53 12.79 0.00 3.85
4170 4462 5.934781 ACAAGAGGATTCCATGGAGTAATC 58.065 41.667 15.53 14.80 0.00 1.75
4175 4467 7.770662 AGAGGATTCCATGGAGTAATCTAGTA 58.229 38.462 19.67 1.95 31.66 1.82
4202 4494 6.403746 GCCTTGCCTTTCTGAAATACTAGTTC 60.404 42.308 0.00 0.00 0.00 3.01
4213 4505 6.542852 TGAAATACTAGTTCGCTTGCATTTC 58.457 36.000 0.00 8.44 40.19 2.17
4284 4576 5.423290 TCTTTGGCTATCTGATGAGAAGTGA 59.577 40.000 0.00 0.00 0.00 3.41
4458 4750 2.178856 GCCTGCTGCTCTTTCCTTC 58.821 57.895 0.00 0.00 36.87 3.46
4548 4842 8.840321 CAAGTAGTCATCTTTTCCTTTTTCTGA 58.160 33.333 0.00 0.00 0.00 3.27
4702 4996 6.611642 AGCCAAACTGTAGATCCAACTATCTA 59.388 38.462 0.00 0.00 37.41 1.98
4749 5046 7.411486 TCTTTACTGCTCTTATTACTCAGCT 57.589 36.000 0.00 0.00 32.76 4.24
4750 5047 8.521170 TCTTTACTGCTCTTATTACTCAGCTA 57.479 34.615 0.00 0.00 32.76 3.32
4751 5048 8.407064 TCTTTACTGCTCTTATTACTCAGCTAC 58.593 37.037 0.00 0.00 32.76 3.58
4752 5049 7.883391 TTACTGCTCTTATTACTCAGCTACT 57.117 36.000 0.00 0.00 32.76 2.57
4753 5050 6.385649 ACTGCTCTTATTACTCAGCTACTC 57.614 41.667 0.00 0.00 32.76 2.59
4754 5051 5.300792 ACTGCTCTTATTACTCAGCTACTCC 59.699 44.000 0.00 0.00 32.76 3.85
4755 5052 4.585162 TGCTCTTATTACTCAGCTACTCCC 59.415 45.833 0.00 0.00 32.76 4.30
4756 5053 4.830600 GCTCTTATTACTCAGCTACTCCCT 59.169 45.833 0.00 0.00 0.00 4.20
4757 5054 5.048294 GCTCTTATTACTCAGCTACTCCCTC 60.048 48.000 0.00 0.00 0.00 4.30
4758 5055 5.386924 TCTTATTACTCAGCTACTCCCTCC 58.613 45.833 0.00 0.00 0.00 4.30
4759 5056 2.054232 TTACTCAGCTACTCCCTCCG 57.946 55.000 0.00 0.00 0.00 4.63
4760 5057 0.465824 TACTCAGCTACTCCCTCCGC 60.466 60.000 0.00 0.00 0.00 5.54
4761 5058 2.442272 TCAGCTACTCCCTCCGCC 60.442 66.667 0.00 0.00 0.00 6.13
4762 5059 3.541713 CAGCTACTCCCTCCGCCC 61.542 72.222 0.00 0.00 0.00 6.13
4763 5060 4.862823 AGCTACTCCCTCCGCCCC 62.863 72.222 0.00 0.00 0.00 5.80
4765 5062 2.122813 CTACTCCCTCCGCCCCAT 60.123 66.667 0.00 0.00 0.00 4.00
4766 5063 1.155390 CTACTCCCTCCGCCCCATA 59.845 63.158 0.00 0.00 0.00 2.74
4767 5064 0.471211 CTACTCCCTCCGCCCCATAA 60.471 60.000 0.00 0.00 0.00 1.90
4768 5065 0.192566 TACTCCCTCCGCCCCATAAT 59.807 55.000 0.00 0.00 0.00 1.28
4769 5066 0.697854 ACTCCCTCCGCCCCATAATT 60.698 55.000 0.00 0.00 0.00 1.40
4770 5067 0.478507 CTCCCTCCGCCCCATAATTT 59.521 55.000 0.00 0.00 0.00 1.82
4771 5068 1.702957 CTCCCTCCGCCCCATAATTTA 59.297 52.381 0.00 0.00 0.00 1.40
4772 5069 2.107552 CTCCCTCCGCCCCATAATTTAA 59.892 50.000 0.00 0.00 0.00 1.52
4773 5070 2.107552 TCCCTCCGCCCCATAATTTAAG 59.892 50.000 0.00 0.00 0.00 1.85
4774 5071 2.514803 CCTCCGCCCCATAATTTAAGG 58.485 52.381 0.00 0.00 0.00 2.69
4775 5072 1.886542 CTCCGCCCCATAATTTAAGGC 59.113 52.381 5.74 5.74 40.33 4.35
4779 5076 3.812156 GCCCCATAATTTAAGGCGTTT 57.188 42.857 0.00 0.00 33.18 3.60
4780 5077 4.131649 GCCCCATAATTTAAGGCGTTTT 57.868 40.909 0.00 0.00 33.18 2.43
4781 5078 4.509616 GCCCCATAATTTAAGGCGTTTTT 58.490 39.130 0.00 0.00 33.18 1.94
4782 5079 5.662456 GCCCCATAATTTAAGGCGTTTTTA 58.338 37.500 0.00 0.00 33.18 1.52
4783 5080 5.521010 GCCCCATAATTTAAGGCGTTTTTAC 59.479 40.000 0.00 0.00 33.18 2.01
4784 5081 6.631962 CCCCATAATTTAAGGCGTTTTTACA 58.368 36.000 0.00 0.00 0.00 2.41
4785 5082 7.269316 CCCCATAATTTAAGGCGTTTTTACAT 58.731 34.615 0.00 0.00 0.00 2.29
4786 5083 7.766738 CCCCATAATTTAAGGCGTTTTTACATT 59.233 33.333 0.00 0.00 0.00 2.71
4787 5084 9.804758 CCCATAATTTAAGGCGTTTTTACATTA 57.195 29.630 0.00 0.00 0.00 1.90
4791 5088 8.710835 AATTTAAGGCGTTTTTACATTATGGG 57.289 30.769 0.00 0.00 0.00 4.00
4792 5089 7.463961 TTTAAGGCGTTTTTACATTATGGGA 57.536 32.000 0.00 0.00 0.00 4.37
4793 5090 4.976224 AGGCGTTTTTACATTATGGGAC 57.024 40.909 0.00 0.00 0.00 4.46
4918 5217 2.073816 GAGCGAAAAACCATCGAAGGA 58.926 47.619 14.76 0.00 42.76 3.36
4941 5240 8.040132 AGGACAGAATCTGTGAAATCTAGAAAG 58.960 37.037 21.81 0.00 45.44 2.62
4945 5244 8.655092 CAGAATCTGTGAAATCTAGAAAGTGAC 58.345 37.037 1.31 0.00 0.00 3.67
4956 5255 3.045601 AGAAAGTGACGTCTCAATGGG 57.954 47.619 17.92 0.00 0.00 4.00
4999 5298 4.362279 GTGCAAACACACACAGAATTGAT 58.638 39.130 0.00 0.00 46.61 2.57
5000 5299 4.207635 GTGCAAACACACACAGAATTGATG 59.792 41.667 0.00 0.00 46.61 3.07
5099 8501 0.183731 GGGAGGGAAACTATGCTGGG 59.816 60.000 0.00 0.00 0.00 4.45
5101 8503 2.124411 GGAGGGAAACTATGCTGGGTA 58.876 52.381 0.00 0.00 0.00 3.69
5187 8594 6.705302 TCTGAATTAGCTGAGACTTTGATGT 58.295 36.000 0.00 0.00 0.00 3.06
5211 8618 8.690884 TGTTCTGTTGGTTTTAATTCATCTCAA 58.309 29.630 0.00 0.00 0.00 3.02
5217 8624 8.567948 GTTGGTTTTAATTCATCTCAACTCTGA 58.432 33.333 0.00 0.00 32.93 3.27
5258 8665 0.883833 CCCTGCTTGCACCAAGTTAG 59.116 55.000 6.80 5.86 42.77 2.34
5260 8667 0.110056 CTGCTTGCACCAAGTTAGCG 60.110 55.000 6.80 0.00 42.77 4.26
5310 8719 0.595095 CAAAGACCAGCAGCACTTCC 59.405 55.000 0.00 0.00 0.00 3.46
5548 8958 1.202336 CGAATTGGGCAGCCATTCTTC 60.202 52.381 15.19 9.22 0.00 2.87
5554 8964 0.969409 GGCAGCCATTCTTCAGCCTT 60.969 55.000 6.55 0.00 39.02 4.35
5575 8985 2.230992 TGGAAACATTGCCCATTTCTCG 59.769 45.455 0.00 0.00 33.68 4.04
5646 9057 8.874816 CATTTTAGTTTTACTCTCCAGCTCTAC 58.125 37.037 0.00 0.00 0.00 2.59
5647 9059 7.778185 TTTAGTTTTACTCTCCAGCTCTACT 57.222 36.000 0.00 0.00 0.00 2.57
5655 9067 1.728971 CTCCAGCTCTACTTGTTTGCG 59.271 52.381 0.00 0.00 0.00 4.85
5656 9068 0.166814 CCAGCTCTACTTGTTTGCGC 59.833 55.000 0.00 0.00 0.00 6.09
5658 9070 0.035458 AGCTCTACTTGTTTGCGCCT 59.965 50.000 4.18 0.00 0.00 5.52
5659 9071 0.875059 GCTCTACTTGTTTGCGCCTT 59.125 50.000 4.18 0.00 0.00 4.35
5660 9072 1.400242 GCTCTACTTGTTTGCGCCTTG 60.400 52.381 4.18 0.00 0.00 3.61
5661 9073 0.591170 TCTACTTGTTTGCGCCTTGC 59.409 50.000 4.18 0.00 46.70 4.01
5681 9093 7.171337 GCCTTGCATCAAAATAAAGAAACTTGA 59.829 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.409358 TCTGATGATCGATTTAACCTCTGATA 57.591 34.615 0.00 0.00 0.00 2.15
75 76 5.916661 ATAGTCGCTAAAGAGAAGAACCA 57.083 39.130 0.00 0.00 0.00 3.67
84 85 8.734218 TTCTCTCTCTTTATAGTCGCTAAAGA 57.266 34.615 5.34 5.34 40.90 2.52
161 162 0.179181 CATCAGCAGCGCGTGATTTT 60.179 50.000 17.08 0.00 30.72 1.82
189 190 4.081642 TCACAGAGTCAATAAGGTGGCTAC 60.082 45.833 0.00 0.00 32.29 3.58
191 192 2.906389 TCACAGAGTCAATAAGGTGGCT 59.094 45.455 0.00 0.00 35.74 4.75
202 203 1.661509 CAAGCGCGTCACAGAGTCA 60.662 57.895 8.43 0.00 0.00 3.41
274 275 0.517316 CGGTTCTTGCCTAGTTGTGC 59.483 55.000 0.00 0.00 0.00 4.57
316 319 6.095377 GCCATCTTTTCATTTCAACCTACTG 58.905 40.000 0.00 0.00 0.00 2.74
342 346 4.402829 CTCAGATAGCTAGCTAGGACCAA 58.597 47.826 27.42 7.09 31.45 3.67
362 366 1.227380 CATGCCCGACTACTGCCTC 60.227 63.158 0.00 0.00 0.00 4.70
458 462 4.439901 GGCCCCTCCCCTCTCCTT 62.440 72.222 0.00 0.00 0.00 3.36
477 481 4.019174 TCCTCTTCCAATTTCTCCATTGC 58.981 43.478 0.00 0.00 33.42 3.56
490 494 2.583441 CCCGCACACTCCTCTTCCA 61.583 63.158 0.00 0.00 0.00 3.53
505 511 2.281208 TTGTTTGCTCCGGTCCCG 60.281 61.111 0.00 0.00 39.44 5.14
509 515 0.600255 CGAGACTTGTTTGCTCCGGT 60.600 55.000 0.00 0.00 0.00 5.28
523 537 1.597461 CAAACCCTCCCTCCGAGAC 59.403 63.158 0.00 0.00 41.63 3.36
627 642 0.949105 CCGGCTACACGTTGCTTCTT 60.949 55.000 3.74 0.00 0.00 2.52
629 644 1.623973 GACCGGCTACACGTTGCTTC 61.624 60.000 0.00 0.00 0.00 3.86
630 645 1.666872 GACCGGCTACACGTTGCTT 60.667 57.895 0.00 0.00 0.00 3.91
632 647 3.475774 CGACCGGCTACACGTTGC 61.476 66.667 0.00 0.00 0.00 4.17
633 648 3.475774 GCGACCGGCTACACGTTG 61.476 66.667 0.00 0.00 39.11 4.10
640 655 2.358193 ATAATGCACGCGACCGGCTA 62.358 55.000 15.93 0.85 40.44 3.93
683 698 6.918626 TCAGTTTGTTTCTTGTGATTTGTGA 58.081 32.000 0.00 0.00 0.00 3.58
684 699 7.028962 TCTCAGTTTGTTTCTTGTGATTTGTG 58.971 34.615 0.00 0.00 0.00 3.33
685 700 7.156876 TCTCAGTTTGTTTCTTGTGATTTGT 57.843 32.000 0.00 0.00 0.00 2.83
686 701 9.903682 ATATCTCAGTTTGTTTCTTGTGATTTG 57.096 29.630 0.00 0.00 0.00 2.32
754 771 4.646945 TCTCTCTCTCTCTCTCTCTGTCTC 59.353 50.000 0.00 0.00 0.00 3.36
756 773 4.646945 TCTCTCTCTCTCTCTCTCTCTGTC 59.353 50.000 0.00 0.00 0.00 3.51
758 775 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
760 777 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
762 779 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
763 780 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
764 781 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
765 782 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
766 783 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
767 784 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
768 785 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
769 786 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
770 787 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
771 788 3.051803 TCCCTCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
772 789 3.309296 TCCCTCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
773 790 3.051803 TCTCCCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
774 791 3.309296 TCTCCCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
775 792 3.051803 TCTCTCCCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
776 793 3.309296 TCTCTCCCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
780 797 3.309296 TCTCTCTCTCCCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
797 814 0.606944 ACGCTTCCACGACTCTCTCT 60.607 55.000 0.00 0.00 36.70 3.10
956 1011 1.022735 GTGCTAGGAGTAGTGCGCTA 58.977 55.000 9.73 1.99 33.71 4.26
991 1056 0.814457 TTGGACGCCATTAATGTGCC 59.186 50.000 14.25 9.68 31.53 5.01
993 1069 2.091541 ACCTTGGACGCCATTAATGTG 58.908 47.619 14.25 8.74 31.53 3.21
1084 1161 4.084265 TGGAGAGCCAACGACGTA 57.916 55.556 0.00 0.00 42.49 3.57
1097 1174 1.363744 GACGAAAGATGCTGGTGGAG 58.636 55.000 0.00 0.00 0.00 3.86
1106 1183 3.052940 TCGATCAGACGACGAAAGATG 57.947 47.619 0.00 0.00 37.37 2.90
1353 1430 2.480419 GTGGCAGTACAGCAGTAAGTTG 59.520 50.000 12.66 0.00 35.83 3.16
1390 1469 1.575576 AAGCAGAAGCAGAAGCAGCG 61.576 55.000 0.00 0.00 45.49 5.18
1392 1471 1.520494 TGAAGCAGAAGCAGAAGCAG 58.480 50.000 0.00 0.00 45.49 4.24
1393 1472 2.195741 ATGAAGCAGAAGCAGAAGCA 57.804 45.000 0.00 0.00 45.49 3.91
1394 1473 2.486982 TGAATGAAGCAGAAGCAGAAGC 59.513 45.455 0.00 0.00 45.49 3.86
1395 1474 4.201930 GGATGAATGAAGCAGAAGCAGAAG 60.202 45.833 0.00 0.00 45.49 2.85
1396 1475 3.693085 GGATGAATGAAGCAGAAGCAGAA 59.307 43.478 0.00 0.00 45.49 3.02
1397 1476 3.276857 GGATGAATGAAGCAGAAGCAGA 58.723 45.455 0.00 0.00 45.49 4.26
1398 1477 2.031807 CGGATGAATGAAGCAGAAGCAG 59.968 50.000 0.00 0.00 45.49 4.24
1399 1478 2.011947 CGGATGAATGAAGCAGAAGCA 58.988 47.619 0.00 0.00 45.49 3.91
1400 1479 1.332997 CCGGATGAATGAAGCAGAAGC 59.667 52.381 0.00 0.00 42.56 3.86
1401 1480 1.945394 CCCGGATGAATGAAGCAGAAG 59.055 52.381 0.73 0.00 0.00 2.85
1402 1481 1.408683 CCCCGGATGAATGAAGCAGAA 60.409 52.381 0.73 0.00 0.00 3.02
1403 1482 0.181114 CCCCGGATGAATGAAGCAGA 59.819 55.000 0.73 0.00 0.00 4.26
1404 1483 0.107017 ACCCCGGATGAATGAAGCAG 60.107 55.000 0.73 0.00 0.00 4.24
1405 1484 0.107214 GACCCCGGATGAATGAAGCA 60.107 55.000 0.73 0.00 0.00 3.91
1406 1485 0.181350 AGACCCCGGATGAATGAAGC 59.819 55.000 0.73 0.00 0.00 3.86
1407 1486 1.202698 GGAGACCCCGGATGAATGAAG 60.203 57.143 0.73 0.00 0.00 3.02
1408 1487 0.837272 GGAGACCCCGGATGAATGAA 59.163 55.000 0.73 0.00 0.00 2.57
1409 1488 0.031111 AGGAGACCCCGGATGAATGA 60.031 55.000 0.73 0.00 40.87 2.57
1410 1489 0.839946 AAGGAGACCCCGGATGAATG 59.160 55.000 0.73 0.00 40.87 2.67
1411 1490 1.212935 CAAAGGAGACCCCGGATGAAT 59.787 52.381 0.73 0.00 40.87 2.57
1412 1491 0.618458 CAAAGGAGACCCCGGATGAA 59.382 55.000 0.73 0.00 40.87 2.57
1413 1492 1.271840 CCAAAGGAGACCCCGGATGA 61.272 60.000 0.73 0.00 40.87 2.92
1414 1493 1.224592 CCAAAGGAGACCCCGGATG 59.775 63.158 0.73 0.00 40.87 3.51
1415 1494 1.082206 TCCAAAGGAGACCCCGGAT 59.918 57.895 0.73 0.00 40.87 4.18
1416 1495 2.534493 TCCAAAGGAGACCCCGGA 59.466 61.111 0.73 0.00 40.87 5.14
1430 1509 1.971167 GCGTGATTTGGGTGCTCCA 60.971 57.895 7.20 0.85 45.43 3.86
1662 1908 1.556911 TGGAGAGATTGGTGAAGAGGC 59.443 52.381 0.00 0.00 0.00 4.70
1664 1910 3.999663 GTGTTGGAGAGATTGGTGAAGAG 59.000 47.826 0.00 0.00 0.00 2.85
1667 1913 2.441375 TGGTGTTGGAGAGATTGGTGAA 59.559 45.455 0.00 0.00 0.00 3.18
1674 1920 2.439507 ACAGTTGTGGTGTTGGAGAGAT 59.560 45.455 0.00 0.00 0.00 2.75
1716 1969 0.878523 CTGCAACCGACGGACAGAAA 60.879 55.000 23.38 0.00 0.00 2.52
1725 1978 3.948719 TGGGGGACTGCAACCGAC 61.949 66.667 3.94 0.90 0.00 4.79
1729 1982 1.678970 GGATGTGGGGGACTGCAAC 60.679 63.158 0.00 0.00 0.00 4.17
1822 2076 6.150140 GGCGATGGCATAATTAGAGAAGATTT 59.850 38.462 0.00 0.00 42.47 2.17
1831 2085 2.668457 GACGAGGCGATGGCATAATTAG 59.332 50.000 0.00 0.00 42.47 1.73
1848 2102 4.191544 CAGATTAAAATGAGGCCAGACGA 58.808 43.478 5.01 0.00 0.00 4.20
1852 2106 2.033801 CGGCAGATTAAAATGAGGCCAG 59.966 50.000 5.01 0.00 39.87 4.85
2004 2258 1.000607 GATTGCACAGCATAGCATGGG 60.001 52.381 0.00 0.00 40.94 4.00
2046 2300 3.491342 TGTGGTAAGCAATTAGGCACAA 58.509 40.909 0.00 0.00 35.83 3.33
2136 2390 4.166144 ACCACCATGATAAGGAAGTTAGGG 59.834 45.833 0.00 0.00 0.00 3.53
2394 2648 7.189079 AGAAGGGGAAAAGAAGTATCTACTG 57.811 40.000 0.00 0.00 36.50 2.74
2815 3069 2.301346 ACCTGCTGAAAGAACACCAAG 58.699 47.619 0.00 0.00 34.07 3.61
2855 3109 4.654262 ACAGAACTCTAGGACAGGTCAAAA 59.346 41.667 1.41 0.00 0.00 2.44
2856 3110 4.223953 ACAGAACTCTAGGACAGGTCAAA 58.776 43.478 1.41 0.00 0.00 2.69
2957 3211 6.575162 AAACACCACATAAAGATCAACCTC 57.425 37.500 0.00 0.00 0.00 3.85
3136 3414 1.210967 TGCAAGATTTACCCCTACCCG 59.789 52.381 0.00 0.00 0.00 5.28
3141 3419 0.033109 GCCCTGCAAGATTTACCCCT 60.033 55.000 0.00 0.00 34.07 4.79
3146 3424 3.265737 TCCAACTAGCCCTGCAAGATTTA 59.734 43.478 0.00 0.00 34.07 1.40
3147 3425 2.041620 TCCAACTAGCCCTGCAAGATTT 59.958 45.455 0.00 0.00 34.07 2.17
3196 3475 4.812626 ACAGCAAGAAAAGCAAAGAATTGG 59.187 37.500 0.00 0.00 37.02 3.16
3222 3501 9.338291 GTGTGCAAATAATGATAGCTATCAATG 57.662 33.333 33.98 26.08 44.96 2.82
3380 3659 5.409826 GTGTGAAACCTCTGAACCATCTTAG 59.590 44.000 0.00 0.00 34.36 2.18
3581 3863 8.154856 ACCACGGCATTAGTAATACTTTCATAT 58.845 33.333 0.00 0.00 0.00 1.78
3582 3864 7.502696 ACCACGGCATTAGTAATACTTTCATA 58.497 34.615 0.00 0.00 0.00 2.15
3584 3866 5.736813 ACCACGGCATTAGTAATACTTTCA 58.263 37.500 0.00 0.00 0.00 2.69
3602 3884 2.926200 CAGCTACAGAGATGAAACCACG 59.074 50.000 0.00 0.00 41.90 4.94
3747 4029 7.384932 ACTTCAACTTGGTTATATTTTTGCAGC 59.615 33.333 0.00 0.00 0.00 5.25
3893 4183 1.001406 CCCCTGATAGCCTTCGACATC 59.999 57.143 0.00 0.00 0.00 3.06
3941 4231 5.665360 TGGATACATCTCCATCAAAGTACCA 59.335 40.000 0.00 0.00 46.17 3.25
3942 4232 6.174720 TGGATACATCTCCATCAAAGTACC 57.825 41.667 0.00 0.00 46.17 3.34
3989 4280 1.612950 CAGCCTGCACATAACAACCAA 59.387 47.619 0.00 0.00 0.00 3.67
4080 4371 3.118738 GGTAGCAGCCAACATACAGTAGT 60.119 47.826 0.00 0.00 0.00 2.73
4111 4402 2.781681 TAAGGGTAAGCCAACTCTGC 57.218 50.000 0.00 0.00 36.17 4.26
4161 4453 3.641906 GCAAGGCCTACTAGATTACTCCA 59.358 47.826 5.16 0.00 0.00 3.86
4202 4494 1.139163 GTTTGGTGGAAATGCAAGCG 58.861 50.000 0.00 0.00 0.00 4.68
4213 4505 4.647424 TTAACTGCTCAAAGTTTGGTGG 57.353 40.909 15.47 7.57 40.77 4.61
4284 4576 7.547227 GGACCAAATGATAACTGCAAAGTAAT 58.453 34.615 0.00 0.00 0.00 1.89
4458 4750 3.319122 CCAAGGACCAAGGAAAAACTCAG 59.681 47.826 0.00 0.00 0.00 3.35
4530 4824 7.440255 AGCACAATTCAGAAAAAGGAAAAGATG 59.560 33.333 0.00 0.00 0.00 2.90
4539 4833 6.016777 AGTCCTACAGCACAATTCAGAAAAAG 60.017 38.462 0.00 0.00 0.00 2.27
4548 4842 4.460382 CCAATCAAGTCCTACAGCACAATT 59.540 41.667 0.00 0.00 0.00 2.32
4749 5046 0.192566 ATTATGGGGCGGAGGGAGTA 59.807 55.000 0.00 0.00 0.00 2.59
4750 5047 0.697854 AATTATGGGGCGGAGGGAGT 60.698 55.000 0.00 0.00 0.00 3.85
4751 5048 0.478507 AAATTATGGGGCGGAGGGAG 59.521 55.000 0.00 0.00 0.00 4.30
4752 5049 1.822425 TAAATTATGGGGCGGAGGGA 58.178 50.000 0.00 0.00 0.00 4.20
4753 5050 2.514803 CTTAAATTATGGGGCGGAGGG 58.485 52.381 0.00 0.00 0.00 4.30
4754 5051 2.514803 CCTTAAATTATGGGGCGGAGG 58.485 52.381 0.00 0.00 0.00 4.30
4755 5052 1.886542 GCCTTAAATTATGGGGCGGAG 59.113 52.381 7.00 0.00 33.30 4.63
4756 5053 1.989706 GCCTTAAATTATGGGGCGGA 58.010 50.000 7.00 0.00 33.30 5.54
4759 5056 3.812156 AAACGCCTTAAATTATGGGGC 57.188 42.857 17.81 10.55 38.85 5.80
4760 5057 6.631962 TGTAAAAACGCCTTAAATTATGGGG 58.368 36.000 16.75 16.75 40.41 4.96
4761 5058 8.710835 AATGTAAAAACGCCTTAAATTATGGG 57.289 30.769 7.00 0.00 0.00 4.00
4765 5062 9.804758 CCCATAATGTAAAAACGCCTTAAATTA 57.195 29.630 0.00 0.00 0.00 1.40
4766 5063 8.532819 TCCCATAATGTAAAAACGCCTTAAATT 58.467 29.630 0.00 0.00 0.00 1.82
4767 5064 7.977293 GTCCCATAATGTAAAAACGCCTTAAAT 59.023 33.333 0.00 0.00 0.00 1.40
4768 5065 7.039923 TGTCCCATAATGTAAAAACGCCTTAAA 60.040 33.333 0.00 0.00 0.00 1.52
4769 5066 6.433404 TGTCCCATAATGTAAAAACGCCTTAA 59.567 34.615 0.00 0.00 0.00 1.85
4770 5067 5.944599 TGTCCCATAATGTAAAAACGCCTTA 59.055 36.000 0.00 0.00 0.00 2.69
4771 5068 4.767928 TGTCCCATAATGTAAAAACGCCTT 59.232 37.500 0.00 0.00 0.00 4.35
4772 5069 4.337145 TGTCCCATAATGTAAAAACGCCT 58.663 39.130 0.00 0.00 0.00 5.52
4773 5070 4.396790 TCTGTCCCATAATGTAAAAACGCC 59.603 41.667 0.00 0.00 0.00 5.68
4774 5071 5.448632 CCTCTGTCCCATAATGTAAAAACGC 60.449 44.000 0.00 0.00 0.00 4.84
4775 5072 5.065988 CCCTCTGTCCCATAATGTAAAAACG 59.934 44.000 0.00 0.00 0.00 3.60
4776 5073 6.184789 TCCCTCTGTCCCATAATGTAAAAAC 58.815 40.000 0.00 0.00 0.00 2.43
4777 5074 6.011981 ACTCCCTCTGTCCCATAATGTAAAAA 60.012 38.462 0.00 0.00 0.00 1.94
4778 5075 5.491078 ACTCCCTCTGTCCCATAATGTAAAA 59.509 40.000 0.00 0.00 0.00 1.52
4779 5076 5.036916 ACTCCCTCTGTCCCATAATGTAAA 58.963 41.667 0.00 0.00 0.00 2.01
4780 5077 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
4781 5078 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
4782 5079 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
4783 5080 5.832539 AATACTCCCTCTGTCCCATAATG 57.167 43.478 0.00 0.00 0.00 1.90
4784 5081 6.160459 ACAAAATACTCCCTCTGTCCCATAAT 59.840 38.462 0.00 0.00 0.00 1.28
4785 5082 5.491078 ACAAAATACTCCCTCTGTCCCATAA 59.509 40.000 0.00 0.00 0.00 1.90
4786 5083 5.036916 ACAAAATACTCCCTCTGTCCCATA 58.963 41.667 0.00 0.00 0.00 2.74
4787 5084 3.852578 ACAAAATACTCCCTCTGTCCCAT 59.147 43.478 0.00 0.00 0.00 4.00
4788 5085 3.256704 ACAAAATACTCCCTCTGTCCCA 58.743 45.455 0.00 0.00 0.00 4.37
4789 5086 5.045797 ACTTACAAAATACTCCCTCTGTCCC 60.046 44.000 0.00 0.00 0.00 4.46
4790 5087 5.875359 CACTTACAAAATACTCCCTCTGTCC 59.125 44.000 0.00 0.00 0.00 4.02
4791 5088 6.465084 ACACTTACAAAATACTCCCTCTGTC 58.535 40.000 0.00 0.00 0.00 3.51
4792 5089 6.435292 ACACTTACAAAATACTCCCTCTGT 57.565 37.500 0.00 0.00 0.00 3.41
4793 5090 7.612677 ACTACACTTACAAAATACTCCCTCTG 58.387 38.462 0.00 0.00 0.00 3.35
4794 5091 7.793948 ACTACACTTACAAAATACTCCCTCT 57.206 36.000 0.00 0.00 0.00 3.69
4889 5188 3.476552 TGGTTTTTCGCTCATGAAGACT 58.523 40.909 0.00 0.00 0.00 3.24
4918 5217 8.370940 TCACTTTCTAGATTTCACAGATTCTGT 58.629 33.333 13.61 13.61 46.51 3.41
4941 5240 3.564225 AGTTTTTCCCATTGAGACGTCAC 59.436 43.478 19.50 12.69 30.10 3.67
4945 5244 4.829064 TTCAGTTTTTCCCATTGAGACG 57.171 40.909 0.00 0.00 0.00 4.18
4956 5255 5.951494 GCACACGTTTTGATTTCAGTTTTTC 59.049 36.000 0.00 0.00 0.00 2.29
4999 5298 8.750515 TGCTGGATGTCATTATCTAAATTTCA 57.249 30.769 0.00 0.00 0.00 2.69
5072 5371 5.857845 AGCATAGTTTCCCTCCCCTATTTAT 59.142 40.000 0.00 0.00 0.00 1.40
5099 8501 6.635030 AAACTGACCAAAACTGGAATCTAC 57.365 37.500 0.00 0.00 0.00 2.59
5101 8503 5.656416 TGAAAACTGACCAAAACTGGAATCT 59.344 36.000 0.00 0.00 0.00 2.40
5110 8512 9.311916 CATACAAGAAATGAAAACTGACCAAAA 57.688 29.630 0.00 0.00 0.00 2.44
5187 8594 8.912988 AGTTGAGATGAATTAAAACCAACAGAA 58.087 29.630 0.00 0.00 36.18 3.02
5217 8624 5.368145 GGCAAACCCTCAGAAATTTCTTTT 58.632 37.500 18.16 12.52 34.74 2.27
5258 8665 2.305252 CATGTATGCATGCAGTACGC 57.695 50.000 26.69 13.53 44.87 4.42
5390 8800 7.205297 ACTCCAACAGATGAAACAAATTCTTG 58.795 34.615 0.00 0.00 38.92 3.02
5528 8938 0.819582 AAGAATGGCTGCCCAATTCG 59.180 50.000 17.53 0.00 46.14 3.34
5548 8958 0.037046 GGGCAATGTTTCCAAGGCTG 60.037 55.000 0.00 0.00 0.00 4.85
5554 8964 2.230992 CGAGAAATGGGCAATGTTTCCA 59.769 45.455 0.00 0.00 33.46 3.53
5575 8985 1.927895 CAGACCACGATACAAGCCTC 58.072 55.000 0.00 0.00 0.00 4.70
5620 9030 7.913674 AGAGCTGGAGAGTAAAACTAAAATG 57.086 36.000 0.00 0.00 0.00 2.32
5633 9044 2.999355 GCAAACAAGTAGAGCTGGAGAG 59.001 50.000 0.00 0.00 0.00 3.20
5655 9067 7.171337 TCAAGTTTCTTTATTTTGATGCAAGGC 59.829 33.333 0.00 0.00 0.00 4.35
5656 9068 8.490355 GTCAAGTTTCTTTATTTTGATGCAAGG 58.510 33.333 0.00 0.00 31.28 3.61
5658 9070 9.598517 AAGTCAAGTTTCTTTATTTTGATGCAA 57.401 25.926 0.00 0.00 31.28 4.08
5659 9071 9.598517 AAAGTCAAGTTTCTTTATTTTGATGCA 57.401 25.926 0.00 0.00 33.00 3.96


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

AutoCloner maintained by Alex Coulton.