Multiple sequence alignment - TraesCS4A01G307100

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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 TraesCS4A01G307100 chr4A 100.000 3125 0 0 1 3125 601198426 601195302 0.000000e+00 5771.0
1 TraesCS4A01G307100 chr4A 81.301 246 28 8 1580 1823 444119030 444118801 1.910000e-42 183.0
2 TraesCS4A01G307100 chr4A 80.377 265 30 13 1556 1816 239817892 239818138 6.880000e-42 182.0
3 TraesCS4A01G307100 chr4A 90.000 140 13 1 1367 1505 239817745 239817884 2.480000e-41 180.0
4 TraesCS4A01G307100 chr4B 89.978 1337 87 23 1 1299 5538135 5536808 0.000000e+00 1683.0
5 TraesCS4A01G307100 chr4B 82.646 1164 103 40 1617 2734 5536457 5535347 0.000000e+00 939.0
6 TraesCS4A01G307100 chr4B 81.242 757 83 33 1556 2273 286455383 286454647 9.790000e-155 556.0
7 TraesCS4A01G307100 chr4B 92.674 273 10 7 1059 1322 188424911 188424640 4.890000e-103 385.0
8 TraesCS4A01G307100 chr4B 90.845 142 12 1 1367 1507 232727683 232727824 4.110000e-44 189.0
9 TraesCS4A01G307100 chr4B 78.113 265 37 10 1556 1816 232727830 232728077 6.980000e-32 148.0
10 TraesCS4A01G307100 chr4B 83.140 172 15 7 2932 3090 5535153 5534983 9.030000e-31 145.0
11 TraesCS4A01G307100 chrUn 83.704 1528 117 55 1556 3031 60958694 60957247 0.000000e+00 1321.0
12 TraesCS4A01G307100 chrUn 91.324 680 22 12 644 1289 60959671 60958995 0.000000e+00 894.0
13 TraesCS4A01G307100 chrUn 90.135 446 36 6 121 561 60960693 60960251 9.720000e-160 573.0
14 TraesCS4A01G307100 chrUn 93.684 95 5 1 1 95 60960785 60960692 1.170000e-29 141.0
15 TraesCS4A01G307100 chr7D 88.828 546 38 17 764 1288 597684299 597683756 0.000000e+00 649.0
16 TraesCS4A01G307100 chr7D 80.000 265 31 14 1556 1816 183565328 183565574 3.200000e-40 176.0
17 TraesCS4A01G307100 chr7D 88.276 145 16 1 1367 1510 563087157 563087013 4.140000e-39 172.0
18 TraesCS4A01G307100 chr7A 86.408 618 48 24 764 1357 690362337 690362942 0.000000e+00 643.0
19 TraesCS4A01G307100 chr7A 80.499 682 79 24 1631 2272 143840856 143841523 1.010000e-129 473.0
20 TraesCS4A01G307100 chr7A 79.771 262 31 13 1559 1816 655256439 655256196 1.490000e-38 171.0
21 TraesCS4A01G307100 chr7A 97.143 35 1 0 2831 2865 660488805 660488839 3.370000e-05 60.2
22 TraesCS4A01G307100 chr2D 83.091 757 74 19 1556 2272 10248099 10247357 9.450000e-180 640.0
23 TraesCS4A01G307100 chr2D 97.357 227 5 1 1065 1290 131968031 131967805 4.890000e-103 385.0
24 TraesCS4A01G307100 chr2D 82.189 466 40 16 1835 2272 274432571 274432121 8.240000e-96 361.0
25 TraesCS4A01G307100 chr2D 81.250 256 23 10 1556 1803 131967559 131967321 1.910000e-42 183.0
26 TraesCS4A01G307100 chr2D 79.545 264 32 8 1557 1816 581871861 581871616 5.360000e-38 169.0
27 TraesCS4A01G307100 chr2D 90.826 109 9 1 2922 3029 122864260 122864152 9.030000e-31 145.0
28 TraesCS4A01G307100 chr3D 82.275 756 80 32 1557 2272 443995938 443996679 3.450000e-169 604.0
29 TraesCS4A01G307100 chr3D 89.720 107 10 1 2923 3029 516202475 516202370 5.440000e-28 135.0
30 TraesCS4A01G307100 chr7B 91.379 290 12 10 1045 1322 412244870 412245158 4.890000e-103 385.0
31 TraesCS4A01G307100 chr7B 100.000 31 0 0 2831 2861 18504052 18504022 1.210000e-04 58.4
32 TraesCS4A01G307100 chr7B 94.118 34 2 0 2826 2859 528866012 528865979 6.000000e-03 52.8
33 TraesCS4A01G307100 chr3B 90.847 295 11 10 1045 1324 646451398 646451691 6.320000e-102 381.0
34 TraesCS4A01G307100 chr3B 83.905 379 42 10 1900 2272 778177901 778177536 8.300000e-91 344.0
35 TraesCS4A01G307100 chr3B 83.641 379 43 9 1900 2272 778204829 778204464 3.860000e-89 339.0
36 TraesCS4A01G307100 chr3B 90.845 142 12 1 1367 1507 721309604 721309745 4.110000e-44 189.0
37 TraesCS4A01G307100 chr5D 96.916 227 6 1 1065 1290 444011887 444011661 2.270000e-101 379.0
38 TraesCS4A01G307100 chr5D 81.641 256 23 9 1556 1803 444011415 444011176 1.140000e-44 191.0
39 TraesCS4A01G307100 chr5D 91.781 73 6 0 1438 1510 444011490 444011418 5.510000e-18 102.0
40 TraesCS4A01G307100 chr5D 100.000 36 0 0 2606 2641 42549104 42549069 2.010000e-07 67.6
41 TraesCS4A01G307100 chr6D 91.034 145 12 1 1367 1510 64660877 64661021 8.840000e-46 195.0
42 TraesCS4A01G307100 chr6D 80.377 265 30 11 1556 1816 64661024 64661270 6.880000e-42 182.0
43 TraesCS4A01G307100 chr2A 91.549 142 11 1 1367 1507 695181896 695182037 8.840000e-46 195.0
44 TraesCS4A01G307100 chr1D 89.655 145 14 1 1367 1510 285763623 285763479 1.910000e-42 183.0
45 TraesCS4A01G307100 chr1D 80.894 246 29 8 1580 1823 5744225 5743996 8.910000e-41 178.0
46 TraesCS4A01G307100 chr1D 90.654 107 9 1 2923 3029 7349850 7349745 1.170000e-29 141.0
47 TraesCS4A01G307100 chr1D 84.127 126 19 1 2916 3041 325485969 325485845 1.520000e-23 121.0
48 TraesCS4A01G307100 chr1D 91.781 73 6 0 1438 1510 5744331 5744259 5.510000e-18 102.0
49 TraesCS4A01G307100 chr1D 96.875 32 1 0 2834 2865 476750965 476750934 2.000000e-03 54.7
50 TraesCS4A01G307100 chr5A 80.534 262 29 13 1559 1816 98737748 98737505 6.880000e-42 182.0
51 TraesCS4A01G307100 chr5B 80.000 265 31 13 1556 1816 121407309 121407555 3.200000e-40 176.0
52 TraesCS4A01G307100 chr5B 87.069 116 13 2 2914 3029 208523297 208523410 2.530000e-26 130.0
53 TraesCS4A01G307100 chr5B 100.000 36 0 0 2606 2641 37067943 37067978 2.010000e-07 67.6
54 TraesCS4A01G307100 chr1A 79.389 262 32 13 1559 1816 552052306 552052063 6.930000e-37 165.0
55 TraesCS4A01G307100 chr1A 87.826 115 14 0 2916 3030 419032265 419032379 5.440000e-28 135.0
56 TraesCS4A01G307100 chr1A 92.683 41 2 1 2826 2865 544368508 544368548 1.210000e-04 58.4
57 TraesCS4A01G307100 chr2B 90.476 105 9 1 2922 3025 175630308 175630204 1.510000e-28 137.0
58 TraesCS4A01G307100 chr4D 85.714 126 17 1 2904 3029 428978931 428978807 7.030000e-27 132.0
59 TraesCS4A01G307100 chr3A 97.727 44 1 0 2822 2865 702538860 702538903 3.340000e-10 76.8
60 TraesCS4A01G307100 chr6B 97.143 35 1 0 2831 2865 525115542 525115576 3.370000e-05 60.2


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 TraesCS4A01G307100 chr4A 601195302 601198426 3124 True 5771.000000 5771 100.000000 1 3125 1 chr4A.!!$R2 3124
1 TraesCS4A01G307100 chr4B 5534983 5538135 3152 True 922.333333 1683 85.254667 1 3090 3 chr4B.!!$R3 3089
2 TraesCS4A01G307100 chr4B 286454647 286455383 736 True 556.000000 556 81.242000 1556 2273 1 chr4B.!!$R2 717
3 TraesCS4A01G307100 chrUn 60957247 60960785 3538 True 732.250000 1321 89.711750 1 3031 4 chrUn.!!$R1 3030
4 TraesCS4A01G307100 chr7D 597683756 597684299 543 True 649.000000 649 88.828000 764 1288 1 chr7D.!!$R2 524
5 TraesCS4A01G307100 chr7A 690362337 690362942 605 False 643.000000 643 86.408000 764 1357 1 chr7A.!!$F3 593
6 TraesCS4A01G307100 chr7A 143840856 143841523 667 False 473.000000 473 80.499000 1631 2272 1 chr7A.!!$F1 641
7 TraesCS4A01G307100 chr2D 10247357 10248099 742 True 640.000000 640 83.091000 1556 2272 1 chr2D.!!$R1 716
8 TraesCS4A01G307100 chr2D 131967321 131968031 710 True 284.000000 385 89.303500 1065 1803 2 chr2D.!!$R5 738
9 TraesCS4A01G307100 chr3D 443995938 443996679 741 False 604.000000 604 82.275000 1557 2272 1 chr3D.!!$F1 715
10 TraesCS4A01G307100 chr5D 444011176 444011887 711 True 224.000000 379 90.112667 1065 1803 3 chr5D.!!$R2 738

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
361 364 0.033504 GTGCGGTGGACTTCTCTTCA 59.966 55.0 0.00 0.0 0.00 3.02 F
461 464 0.179062 GATGACTCCAAGCGATGCCT 60.179 55.0 0.00 0.0 0.00 4.75 F
1500 2156 0.316204 GGCTGCTGCATCTTTGTTGT 59.684 50.0 17.89 0.0 41.91 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1935 0.038526 CACGTATCCTACCATCCCGC 60.039 60.0 0.00 0.0 0.0 6.13 R
2000 2712 0.108138 GCCGTTGATCTGCAGGTAGT 60.108 55.0 15.13 0.0 0.0 2.73 R
2564 3297 0.031585 GGGTCAAAAGAAACGGGCAC 59.968 55.0 0.00 0.0 0.0 5.01 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
107 108 2.285368 ATTGCTCGTGGAGGGGGA 60.285 61.111 0.00 0.00 0.00 4.81
256 257 3.792736 GTACATGAGGGCCGGCCA 61.793 66.667 44.46 27.31 37.98 5.36
266 267 1.379309 GGCCGGCCATGTCCTTTTA 60.379 57.895 40.73 0.00 35.81 1.52
320 323 1.317613 ACATCGTTGCAAAGGAAGCA 58.682 45.000 12.54 0.00 44.59 3.91
321 324 1.888512 ACATCGTTGCAAAGGAAGCAT 59.111 42.857 12.54 0.00 44.59 3.79
331 334 3.366273 GCAAAGGAAGCATGAATTGACGA 60.366 43.478 0.00 0.00 0.00 4.20
361 364 0.033504 GTGCGGTGGACTTCTCTTCA 59.966 55.000 0.00 0.00 0.00 3.02
386 389 3.384532 GGTTCCGTAGCCCCGACA 61.385 66.667 0.00 0.00 0.00 4.35
403 406 2.612972 CGACAAGGGTGCAGTGAGTTAT 60.613 50.000 0.00 0.00 0.00 1.89
461 464 0.179062 GATGACTCCAAGCGATGCCT 60.179 55.000 0.00 0.00 0.00 4.75
469 472 0.656259 CAAGCGATGCCTCATCAGTG 59.344 55.000 7.47 0.00 40.54 3.66
483 486 5.278414 CCTCATCAGTGTGCATTGTTGTTTA 60.278 40.000 0.00 0.00 0.00 2.01
530 536 2.160813 ACCGTTGTATCATGCCGTTTTC 59.839 45.455 0.00 0.00 0.00 2.29
532 538 3.485216 CCGTTGTATCATGCCGTTTTCTC 60.485 47.826 0.00 0.00 0.00 2.87
582 606 9.702253 TTGTGTAAGGGCCTCATTAATTTAATA 57.298 29.630 6.46 0.00 0.00 0.98
638 662 8.402798 TCTAAAAATGTCATGGTCAAAGCTTA 57.597 30.769 0.00 0.00 0.00 3.09
641 665 6.839124 AAATGTCATGGTCAAAGCTTATCA 57.161 33.333 0.00 0.00 0.00 2.15
683 1191 0.323178 TACGACGGAGCCTCCTTTCT 60.323 55.000 9.52 0.00 33.30 2.52
688 1196 1.002544 ACGGAGCCTCCTTTCTCTTTG 59.997 52.381 9.52 0.00 33.30 2.77
693 1201 1.546548 GCCTCCTTTCTCTTTGCACCT 60.547 52.381 0.00 0.00 0.00 4.00
772 1280 7.276878 ACGGTTTTTAAATGTCCAAGAAACTTG 59.723 33.333 4.73 4.73 0.00 3.16
780 1288 6.923199 ATGTCCAAGAAACTTGAAATGGAT 57.077 33.333 12.25 0.00 39.02 3.41
812 1324 6.139679 TCTTTTGAGGGTTAATGGACTCAT 57.860 37.500 0.00 0.00 39.46 2.90
866 1378 2.283821 GCCCAACAGCCCATTCCA 60.284 61.111 0.00 0.00 0.00 3.53
923 1435 3.083997 CCCCTCCTCCTCCCAACG 61.084 72.222 0.00 0.00 0.00 4.10
970 1498 2.018086 CTCCCCCTCCTCCTCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
973 1501 1.456705 CCCCTCCTCCTCCTCTTCG 60.457 68.421 0.00 0.00 0.00 3.79
1319 1913 2.351111 CGGATCTCTTCTTGCTTGCTTC 59.649 50.000 0.00 0.00 0.00 3.86
1327 1921 0.606401 CTTGCTTGCTTCCTTCCCGA 60.606 55.000 0.00 0.00 0.00 5.14
1333 1927 0.608640 TGCTTCCTTCCCGAGAGAAC 59.391 55.000 0.00 0.00 0.00 3.01
1341 1935 1.669604 TCCCGAGAGAACTGAGATCG 58.330 55.000 0.00 0.00 0.00 3.69
1357 1951 1.134560 GATCGCGGGATGGTAGGATAC 59.865 57.143 20.80 0.00 35.06 2.24
1363 1957 2.313317 GGGATGGTAGGATACGTGTGA 58.687 52.381 0.00 0.00 44.28 3.58
1364 1958 2.696707 GGGATGGTAGGATACGTGTGAA 59.303 50.000 0.00 0.00 44.28 3.18
1365 1959 3.243771 GGGATGGTAGGATACGTGTGAAG 60.244 52.174 0.00 0.00 44.28 3.02
1371 2017 4.992951 GGTAGGATACGTGTGAAGTGTTTT 59.007 41.667 0.00 0.00 44.28 2.43
1405 2055 7.718314 TCAGTAGTACTCTGTACAAGAACAAGA 59.282 37.037 16.77 0.00 33.37 3.02
1406 2056 8.350722 CAGTAGTACTCTGTACAAGAACAAGAA 58.649 37.037 0.00 0.00 33.37 2.52
1412 2062 4.565166 TCTGTACAAGAACAAGAACACACG 59.435 41.667 0.00 0.00 29.54 4.49
1414 2064 2.080693 ACAAGAACAAGAACACACGCA 58.919 42.857 0.00 0.00 0.00 5.24
1429 2079 2.664518 GCATGCGCTCTAGGCCTC 60.665 66.667 9.68 0.00 37.74 4.70
1431 2081 1.300775 CATGCGCTCTAGGCCTCTG 60.301 63.158 9.68 3.39 37.74 3.35
1455 2105 4.759782 AGATAGGGCGTATATGATTGTGC 58.240 43.478 0.00 0.00 0.00 4.57
1457 2107 3.045601 AGGGCGTATATGATTGTGCTC 57.954 47.619 0.00 0.00 0.00 4.26
1469 2119 4.740268 TGATTGTGCTCTGAATTGATTGC 58.260 39.130 0.00 0.00 0.00 3.56
1470 2120 4.461431 TGATTGTGCTCTGAATTGATTGCT 59.539 37.500 0.00 0.00 0.00 3.91
1500 2156 0.316204 GGCTGCTGCATCTTTGTTGT 59.684 50.000 17.89 0.00 41.91 3.32
1510 2166 6.255453 GCTGCATCTTTGTTGTTAGTTTTTGA 59.745 34.615 0.00 0.00 0.00 2.69
1511 2167 7.518731 TGCATCTTTGTTGTTAGTTTTTGAC 57.481 32.000 0.00 0.00 0.00 3.18
1512 2168 7.319646 TGCATCTTTGTTGTTAGTTTTTGACT 58.680 30.769 0.00 0.00 42.55 3.41
1513 2169 7.816995 TGCATCTTTGTTGTTAGTTTTTGACTT 59.183 29.630 0.00 0.00 39.86 3.01
1514 2170 8.655970 GCATCTTTGTTGTTAGTTTTTGACTTT 58.344 29.630 0.00 0.00 39.86 2.66
1519 2175 9.922305 TTTGTTGTTAGTTTTTGACTTTTTGTG 57.078 25.926 0.00 0.00 39.86 3.33
1520 2176 7.568433 TGTTGTTAGTTTTTGACTTTTTGTGC 58.432 30.769 0.00 0.00 39.86 4.57
1521 2177 7.224753 TGTTGTTAGTTTTTGACTTTTTGTGCA 59.775 29.630 0.00 0.00 39.86 4.57
1522 2178 7.344910 TGTTAGTTTTTGACTTTTTGTGCAG 57.655 32.000 0.00 0.00 39.86 4.41
1523 2179 6.926272 TGTTAGTTTTTGACTTTTTGTGCAGT 59.074 30.769 0.00 0.00 39.86 4.40
1524 2180 8.082852 TGTTAGTTTTTGACTTTTTGTGCAGTA 58.917 29.630 0.00 0.00 39.86 2.74
1525 2181 9.083080 GTTAGTTTTTGACTTTTTGTGCAGTAT 57.917 29.630 0.00 0.00 39.86 2.12
1526 2182 7.524294 AGTTTTTGACTTTTTGTGCAGTATG 57.476 32.000 0.00 0.00 33.92 2.39
1527 2183 7.319646 AGTTTTTGACTTTTTGTGCAGTATGA 58.680 30.769 0.00 0.00 33.65 2.15
1528 2184 7.275560 AGTTTTTGACTTTTTGTGCAGTATGAC 59.724 33.333 0.00 0.00 33.65 3.06
1529 2185 5.826601 TTGACTTTTTGTGCAGTATGACA 57.173 34.783 0.00 0.00 39.69 3.58
1530 2186 5.422666 TGACTTTTTGTGCAGTATGACAG 57.577 39.130 0.00 0.00 39.69 3.51
1531 2187 4.881273 TGACTTTTTGTGCAGTATGACAGT 59.119 37.500 0.00 0.00 39.69 3.55
1532 2188 5.356751 TGACTTTTTGTGCAGTATGACAGTT 59.643 36.000 0.00 0.00 39.69 3.16
1533 2189 5.821204 ACTTTTTGTGCAGTATGACAGTTC 58.179 37.500 0.00 0.00 39.69 3.01
1534 2190 5.356751 ACTTTTTGTGCAGTATGACAGTTCA 59.643 36.000 0.00 0.00 39.69 3.18
1535 2191 4.811555 TTTGTGCAGTATGACAGTTCAC 57.188 40.909 0.00 0.00 39.69 3.18
1536 2192 3.751479 TGTGCAGTATGACAGTTCACT 57.249 42.857 0.00 0.00 39.69 3.41
1537 2193 3.653344 TGTGCAGTATGACAGTTCACTC 58.347 45.455 0.00 0.00 39.69 3.51
1538 2194 3.321968 TGTGCAGTATGACAGTTCACTCT 59.678 43.478 0.00 0.00 39.69 3.24
1539 2195 3.677121 GTGCAGTATGACAGTTCACTCTG 59.323 47.826 0.00 0.00 39.69 3.35
1540 2196 3.257393 GCAGTATGACAGTTCACTCTGG 58.743 50.000 0.00 0.00 39.69 3.86
1541 2197 3.306364 GCAGTATGACAGTTCACTCTGGT 60.306 47.826 0.00 0.00 39.69 4.00
1542 2198 4.489810 CAGTATGACAGTTCACTCTGGTC 58.510 47.826 0.00 0.00 39.69 4.02
1543 2199 4.021981 CAGTATGACAGTTCACTCTGGTCA 60.022 45.833 0.00 0.00 39.69 4.02
1544 2200 4.774726 AGTATGACAGTTCACTCTGGTCAT 59.225 41.667 13.18 13.18 39.48 3.06
1545 2201 4.630644 ATGACAGTTCACTCTGGTCATT 57.369 40.909 0.00 0.00 39.48 2.57
1546 2202 3.732212 TGACAGTTCACTCTGGTCATTG 58.268 45.455 0.00 0.00 39.48 2.82
1547 2203 3.070018 GACAGTTCACTCTGGTCATTGG 58.930 50.000 0.00 0.00 39.48 3.16
1548 2204 2.705658 ACAGTTCACTCTGGTCATTGGA 59.294 45.455 0.00 0.00 39.48 3.53
1549 2205 3.328931 ACAGTTCACTCTGGTCATTGGAT 59.671 43.478 0.00 0.00 39.48 3.41
1550 2206 4.532126 ACAGTTCACTCTGGTCATTGGATA 59.468 41.667 0.00 0.00 39.48 2.59
1551 2207 4.872691 CAGTTCACTCTGGTCATTGGATAC 59.127 45.833 0.00 0.00 0.00 2.24
1552 2208 4.080863 AGTTCACTCTGGTCATTGGATACC 60.081 45.833 0.00 0.00 36.24 2.73
1553 2209 2.771943 TCACTCTGGTCATTGGATACCC 59.228 50.000 0.00 0.00 34.69 3.69
1554 2210 2.774234 CACTCTGGTCATTGGATACCCT 59.226 50.000 0.00 0.00 34.69 4.34
1564 2220 5.300286 GTCATTGGATACCCTCAGATTTTGG 59.700 44.000 0.00 0.00 0.00 3.28
1569 2225 1.632589 ACCCTCAGATTTTGGTTGGC 58.367 50.000 0.00 0.00 0.00 4.52
1578 2241 2.374830 TTTTGGTTGGCGTGCCATGG 62.375 55.000 15.40 7.63 46.64 3.66
1607 2270 5.353678 GCTAGGATGCAGTGGATTTGATATC 59.646 44.000 0.00 0.00 0.00 1.63
1613 2276 5.202765 TGCAGTGGATTTGATATCACCATT 58.797 37.500 14.67 9.24 33.19 3.16
1632 2295 7.830697 TCACCATTCAGTGATCATTTATGTCTT 59.169 33.333 0.00 0.00 41.78 3.01
1642 2305 6.936335 TGATCATTTATGTCTTGTGTCACAGT 59.064 34.615 5.67 0.00 0.00 3.55
1643 2306 8.093927 TGATCATTTATGTCTTGTGTCACAGTA 58.906 33.333 5.67 0.00 0.00 2.74
1644 2307 9.102757 GATCATTTATGTCTTGTGTCACAGTAT 57.897 33.333 5.67 2.81 0.00 2.12
1647 2310 9.546909 CATTTATGTCTTGTGTCACAGTATTTC 57.453 33.333 5.67 0.00 0.00 2.17
1658 2321 7.549134 TGTGTCACAGTATTTCCATAATCTGAC 59.451 37.037 0.18 0.00 0.00 3.51
1667 2330 9.125026 GTATTTCCATAATCTGACTTGGACATT 57.875 33.333 8.43 0.82 37.97 2.71
1669 2332 6.065976 TCCATAATCTGACTTGGACATTGT 57.934 37.500 0.00 0.00 33.40 2.71
1689 2358 5.431420 TGTACAGTGCTAATGGTGTTTTG 57.569 39.130 0.00 0.00 0.00 2.44
1691 2360 2.035832 ACAGTGCTAATGGTGTTTTGCC 59.964 45.455 0.00 0.00 0.00 4.52
1694 2363 1.617850 TGCTAATGGTGTTTTGCCTGG 59.382 47.619 0.00 0.00 0.00 4.45
1695 2364 1.066929 GCTAATGGTGTTTTGCCTGGG 60.067 52.381 0.00 0.00 0.00 4.45
1727 2396 4.083324 ACCATTGACTTGTAGCGTTTCATG 60.083 41.667 0.00 0.00 0.00 3.07
1735 2407 5.938125 ACTTGTAGCGTTTCATGGAGTTAAT 59.062 36.000 0.00 0.00 0.00 1.40
1739 2413 7.269316 TGTAGCGTTTCATGGAGTTAATATGA 58.731 34.615 0.00 0.00 0.00 2.15
1804 2479 2.888834 ACTGTCAACAATTTGTGCCC 57.111 45.000 2.13 0.00 34.02 5.36
1824 2502 0.517316 GGCTTGCCTTGAACTGTACG 59.483 55.000 4.11 0.00 0.00 3.67
1825 2503 0.517316 GCTTGCCTTGAACTGTACGG 59.483 55.000 0.00 0.00 0.00 4.02
1826 2504 1.876416 GCTTGCCTTGAACTGTACGGA 60.876 52.381 9.17 0.00 0.00 4.69
1827 2505 2.069273 CTTGCCTTGAACTGTACGGAG 58.931 52.381 9.17 0.00 0.00 4.63
1866 2554 6.090783 GCAAGTTGTGTTTAGCTATTTACCC 58.909 40.000 4.48 0.00 0.00 3.69
1916 2626 1.743958 CTGCTCTTCTGCCATTTCCAG 59.256 52.381 0.00 0.00 0.00 3.86
1917 2627 1.074405 TGCTCTTCTGCCATTTCCAGT 59.926 47.619 0.00 0.00 0.00 4.00
1990 2702 3.776969 TGCTGATGATCTTACTCACCCTT 59.223 43.478 0.00 0.00 0.00 3.95
1998 2710 5.187186 TGATCTTACTCACCCTTTGTCTACC 59.813 44.000 0.00 0.00 0.00 3.18
1999 2711 4.748701 TCTTACTCACCCTTTGTCTACCT 58.251 43.478 0.00 0.00 0.00 3.08
2000 2712 5.895807 TCTTACTCACCCTTTGTCTACCTA 58.104 41.667 0.00 0.00 0.00 3.08
2019 2731 0.108138 ACTACCTGCAGATCAACGGC 60.108 55.000 17.39 0.00 39.97 5.68
2025 2737 2.520904 GCAGATCAACGGCTCGCTC 61.521 63.158 0.00 0.00 36.79 5.03
2140 2856 4.761739 ACACCTGATTTACCTCATGTGTTG 59.238 41.667 8.65 0.00 46.27 3.33
2219 2948 2.956799 TTCAGCGAGGCACTTTGGCA 62.957 55.000 2.29 0.00 46.46 4.92
2331 3062 2.957491 TTTGTTGCTGTCCCTGTTTG 57.043 45.000 0.00 0.00 0.00 2.93
2363 3094 7.971201 TCTTCAGCTATATGAATGTTCCATCT 58.029 34.615 0.00 0.00 38.47 2.90
2383 3114 7.070198 TCCATCTGGTCGTATAATTGAACCTTA 59.930 37.037 0.00 0.00 36.34 2.69
2384 3115 7.878127 CCATCTGGTCGTATAATTGAACCTTAT 59.122 37.037 0.00 0.00 0.00 1.73
2387 3118 9.104965 TCTGGTCGTATAATTGAACCTTATTTG 57.895 33.333 0.00 0.00 0.00 2.32
2424 3157 0.968405 TAGTTGCGAGGGTAACGGTT 59.032 50.000 0.00 0.00 42.71 4.44
2433 3166 5.052481 GCGAGGGTAACGGTTTATAAGATT 58.948 41.667 0.00 0.00 37.60 2.40
2434 3167 5.525012 GCGAGGGTAACGGTTTATAAGATTT 59.475 40.000 0.00 0.00 37.60 2.17
2482 3215 3.122948 CGGGAGGATTAAATTATCGTGCG 59.877 47.826 0.00 0.00 33.32 5.34
2499 3232 1.994074 TGCGCATGATTTTGATGCAAC 59.006 42.857 5.66 0.00 45.50 4.17
2512 3245 2.618241 TGATGCAACTCTGTGTGGTTTC 59.382 45.455 0.00 0.00 0.00 2.78
2513 3246 2.121291 TGCAACTCTGTGTGGTTTCA 57.879 45.000 0.00 0.00 0.00 2.69
2564 3297 0.542702 ACCTGGCTTCCCCATTGTTG 60.543 55.000 0.00 0.00 44.33 3.33
2572 3305 2.206536 CCCCATTGTTGTGCCCGTT 61.207 57.895 0.00 0.00 0.00 4.44
2591 3324 4.142249 CCGTTTCTTTTGACCCAACTCTTT 60.142 41.667 0.00 0.00 0.00 2.52
2598 3331 8.990163 TCTTTTGACCCAACTCTTTAATAACT 57.010 30.769 0.00 0.00 0.00 2.24
2600 3333 7.429636 TTTGACCCAACTCTTTAATAACTCG 57.570 36.000 0.00 0.00 0.00 4.18
2604 3337 6.171213 ACCCAACTCTTTAATAACTCGAAGG 58.829 40.000 0.00 0.00 0.00 3.46
2709 3450 5.520288 TGTTCTGTTTTCTCTTCTCAACTCG 59.480 40.000 0.00 0.00 0.00 4.18
2735 3476 8.494016 AAATACAGAAAGCTACACTATGAACC 57.506 34.615 0.00 0.00 0.00 3.62
2776 3517 2.092323 CTGCTAAAGCTTGTTACCCCC 58.908 52.381 0.00 0.00 42.66 5.40
2777 3518 1.708551 TGCTAAAGCTTGTTACCCCCT 59.291 47.619 0.00 0.00 42.66 4.79
2778 3519 2.109304 TGCTAAAGCTTGTTACCCCCTT 59.891 45.455 0.00 0.00 42.66 3.95
2779 3520 3.162666 GCTAAAGCTTGTTACCCCCTTT 58.837 45.455 0.00 0.00 38.21 3.11
2780 3521 3.056821 GCTAAAGCTTGTTACCCCCTTTG 60.057 47.826 0.00 0.00 38.21 2.77
2781 3522 3.322191 AAAGCTTGTTACCCCCTTTGA 57.678 42.857 0.00 0.00 0.00 2.69
2785 3526 5.987019 AGCTTGTTACCCCCTTTGATATA 57.013 39.130 0.00 0.00 0.00 0.86
2786 3527 6.335781 AGCTTGTTACCCCCTTTGATATAA 57.664 37.500 0.00 0.00 0.00 0.98
2787 3528 6.922540 AGCTTGTTACCCCCTTTGATATAAT 58.077 36.000 0.00 0.00 0.00 1.28
2790 3531 7.255486 GCTTGTTACCCCCTTTGATATAATGAC 60.255 40.741 0.00 0.00 0.00 3.06
2791 3532 6.292923 TGTTACCCCCTTTGATATAATGACG 58.707 40.000 0.00 0.00 0.00 4.35
2809 3550 5.085636 TGACGTTTTGGTAGATTTGAACG 57.914 39.130 5.07 5.07 43.68 3.95
2817 3558 2.158943 GGTAGATTTGAACGGAGGGAGG 60.159 54.545 0.00 0.00 0.00 4.30
2858 3703 9.445786 GTACCAAATCAACGACAATTAATATGG 57.554 33.333 0.00 0.00 0.00 2.74
2861 3706 9.748708 CCAAATCAACGACAATTAATATGGATT 57.251 29.630 0.00 0.00 0.00 3.01
2869 3714 9.436957 ACGACAATTAATATGGATTGGACTATC 57.563 33.333 13.06 3.96 37.53 2.08
2983 3828 6.863275 TGATTCGGATGTATATAGACGCATT 58.137 36.000 0.00 0.00 0.00 3.56
2985 3830 7.817478 TGATTCGGATGTATATAGACGCATTTT 59.183 33.333 0.00 0.00 0.00 1.82
3000 3847 7.816640 AGACGCATTTTAGTGTGTTTATTCAT 58.183 30.769 0.00 0.00 42.45 2.57
3025 3872 5.934043 TCATTTCAGTCTGTATGTTGTCCAG 59.066 40.000 13.61 0.00 0.00 3.86
3042 3900 9.685276 TGTTGTCCAGATTAACATCTCATAATT 57.315 29.630 0.00 0.00 37.71 1.40
3051 3909 5.818136 AACATCTCATAATTGTGAACGGG 57.182 39.130 6.35 0.00 0.00 5.28
3052 3910 3.627577 ACATCTCATAATTGTGAACGGGC 59.372 43.478 6.35 0.00 0.00 6.13
3060 3918 1.466025 TTGTGAACGGGCGGAGTACT 61.466 55.000 0.00 0.00 0.00 2.73
3090 3948 2.355010 AATGCCAGAGCCTTATGTCC 57.645 50.000 0.00 0.00 38.69 4.02
3091 3949 0.475906 ATGCCAGAGCCTTATGTCCC 59.524 55.000 0.00 0.00 38.69 4.46
3092 3950 0.913934 TGCCAGAGCCTTATGTCCCA 60.914 55.000 0.00 0.00 38.69 4.37
3093 3951 0.179034 GCCAGAGCCTTATGTCCCAG 60.179 60.000 0.00 0.00 0.00 4.45
3094 3952 0.179034 CCAGAGCCTTATGTCCCAGC 60.179 60.000 0.00 0.00 0.00 4.85
3095 3953 0.835941 CAGAGCCTTATGTCCCAGCT 59.164 55.000 0.00 0.00 36.25 4.24
3096 3954 3.696306 GAGCCTTATGTCCCAGCTC 57.304 57.895 0.00 0.00 42.74 4.09
3097 3955 3.012153 AGCCTTATGTCCCAGCTCA 57.988 52.632 0.00 0.00 0.00 4.26
3098 3956 1.289160 AGCCTTATGTCCCAGCTCAA 58.711 50.000 0.00 0.00 0.00 3.02
3099 3957 1.635487 AGCCTTATGTCCCAGCTCAAA 59.365 47.619 0.00 0.00 0.00 2.69
3100 3958 2.243221 AGCCTTATGTCCCAGCTCAAAT 59.757 45.455 0.00 0.00 0.00 2.32
3101 3959 2.360165 GCCTTATGTCCCAGCTCAAATG 59.640 50.000 0.00 0.00 0.00 2.32
3102 3960 3.889815 CCTTATGTCCCAGCTCAAATGA 58.110 45.455 0.00 0.00 0.00 2.57
3103 3961 3.629398 CCTTATGTCCCAGCTCAAATGAC 59.371 47.826 0.00 0.00 0.00 3.06
3104 3962 4.521146 CTTATGTCCCAGCTCAAATGACT 58.479 43.478 0.00 0.00 0.00 3.41
3105 3963 2.189594 TGTCCCAGCTCAAATGACTG 57.810 50.000 0.00 6.21 0.00 3.51
3110 3968 2.189594 CAGCTCAAATGACTGGACCA 57.810 50.000 0.00 0.00 0.00 4.02
3111 3969 1.808945 CAGCTCAAATGACTGGACCAC 59.191 52.381 0.00 0.00 0.00 4.16
3112 3970 1.168714 GCTCAAATGACTGGACCACC 58.831 55.000 0.00 0.00 0.00 4.61
3113 3971 1.826385 CTCAAATGACTGGACCACCC 58.174 55.000 0.00 0.00 34.81 4.61
3114 3972 1.352352 CTCAAATGACTGGACCACCCT 59.648 52.381 0.00 0.00 35.38 4.34
3115 3973 1.073763 TCAAATGACTGGACCACCCTG 59.926 52.381 0.00 0.00 39.53 4.45
3117 3975 0.401738 AATGACTGGACCACCCTGTG 59.598 55.000 0.00 0.00 45.67 3.66
3118 3976 0.473694 ATGACTGGACCACCCTGTGA 60.474 55.000 0.00 0.00 45.67 3.58
3119 3977 0.692756 TGACTGGACCACCCTGTGAA 60.693 55.000 0.00 0.00 45.67 3.18
3120 3978 0.693049 GACTGGACCACCCTGTGAAT 59.307 55.000 0.00 0.00 45.67 2.57
3121 3979 1.073923 GACTGGACCACCCTGTGAATT 59.926 52.381 0.00 0.00 45.67 2.17
3122 3980 1.202927 ACTGGACCACCCTGTGAATTG 60.203 52.381 0.00 0.00 44.25 2.32
3123 3981 0.850100 TGGACCACCCTGTGAATTGT 59.150 50.000 0.00 0.00 35.23 2.71
3124 3982 2.039746 CTGGACCACCCTGTGAATTGTA 59.960 50.000 0.00 0.00 35.23 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.964031 GGGGTGCATGTATCCCATAAAAA 59.036 43.478 25.99 0.00 40.97 1.94
90 91 2.285368 TCCCCCTCCACGAGCAAT 60.285 61.111 0.00 0.00 0.00 3.56
198 199 3.230134 CCAGATTCCAACAAAAGGGTGA 58.770 45.455 0.00 0.00 0.00 4.02
256 257 3.440173 CCAGCACAACGATAAAAGGACAT 59.560 43.478 0.00 0.00 0.00 3.06
320 323 4.456911 ACTTCAAGCACATCGTCAATTCAT 59.543 37.500 0.00 0.00 0.00 2.57
321 324 3.814842 ACTTCAAGCACATCGTCAATTCA 59.185 39.130 0.00 0.00 0.00 2.57
331 334 1.518056 CCACCGCACTTCAAGCACAT 61.518 55.000 0.00 0.00 0.00 3.21
361 364 0.252197 GGCTACGGAACCCTCAACAT 59.748 55.000 0.00 0.00 0.00 2.71
386 389 3.521126 AGATCATAACTCACTGCACCCTT 59.479 43.478 0.00 0.00 0.00 3.95
403 406 0.687757 AGGCAACCGGAGCTAGATCA 60.688 55.000 9.46 0.00 37.17 2.92
461 464 4.652421 AAACAACAATGCACACTGATGA 57.348 36.364 8.84 0.00 0.00 2.92
469 472 3.368323 CCCCCAGATAAACAACAATGCAC 60.368 47.826 0.00 0.00 0.00 4.57
483 486 0.112412 GAACAACCACACCCCCAGAT 59.888 55.000 0.00 0.00 0.00 2.90
530 536 4.437239 ACACACACAACAAAGAGAGAGAG 58.563 43.478 0.00 0.00 0.00 3.20
532 538 5.106555 ACAAACACACACAACAAAGAGAGAG 60.107 40.000 0.00 0.00 0.00 3.20
638 662 1.212935 CCCCCTCTCGGAATTTGTGAT 59.787 52.381 0.00 0.00 0.00 3.06
641 665 1.073098 AACCCCCTCTCGGAATTTGT 58.927 50.000 0.00 0.00 0.00 2.83
693 1201 6.981762 ATCTGAAAAATGTGTGTTTGCAAA 57.018 29.167 8.05 8.05 0.00 3.68
790 1298 7.013655 CCATATGAGTCCATTAACCCTCAAAAG 59.986 40.741 3.65 0.00 37.48 2.27
794 1302 5.223655 TCCATATGAGTCCATTAACCCTCA 58.776 41.667 3.65 0.00 38.24 3.86
862 1374 0.110486 GGTTTCTCTGTGGGCTGGAA 59.890 55.000 0.00 0.00 0.00 3.53
866 1378 1.280457 CTAGGGTTTCTCTGTGGGCT 58.720 55.000 0.00 0.00 0.00 5.19
923 1435 2.034048 GCGGGGAGAAGAGATGGGTC 62.034 65.000 0.00 0.00 0.00 4.46
1319 1913 1.840737 TCTCAGTTCTCTCGGGAAGG 58.159 55.000 0.00 0.00 0.00 3.46
1327 1921 0.394488 TCCCGCGATCTCAGTTCTCT 60.394 55.000 8.23 0.00 0.00 3.10
1333 1927 0.242286 CTACCATCCCGCGATCTCAG 59.758 60.000 8.23 0.00 0.00 3.35
1341 1935 0.038526 CACGTATCCTACCATCCCGC 60.039 60.000 0.00 0.00 0.00 6.13
1357 1951 1.740585 TGACCCAAAACACTTCACACG 59.259 47.619 0.00 0.00 0.00 4.49
1363 1957 3.366052 ACTGACTGACCCAAAACACTT 57.634 42.857 0.00 0.00 0.00 3.16
1364 1958 3.454812 ACTACTGACTGACCCAAAACACT 59.545 43.478 0.00 0.00 0.00 3.55
1365 1959 3.805207 ACTACTGACTGACCCAAAACAC 58.195 45.455 0.00 0.00 0.00 3.32
1371 2017 3.074094 ACAGAGTACTACTGACTGACCCA 59.926 47.826 21.64 0.00 38.55 4.51
1412 2062 2.664518 GAGGCCTAGAGCGCATGC 60.665 66.667 4.42 7.91 45.17 4.06
1414 2064 0.468214 TACAGAGGCCTAGAGCGCAT 60.468 55.000 4.42 0.00 45.17 4.73
1429 2079 6.975197 CACAATCATATACGCCCTATCTACAG 59.025 42.308 0.00 0.00 0.00 2.74
1431 2081 5.749109 GCACAATCATATACGCCCTATCTAC 59.251 44.000 0.00 0.00 0.00 2.59
1455 2105 3.442625 TCCAGCAAGCAATCAATTCAGAG 59.557 43.478 0.00 0.00 0.00 3.35
1457 2107 3.861276 TCCAGCAAGCAATCAATTCAG 57.139 42.857 0.00 0.00 0.00 3.02
1469 2119 1.748122 AGCAGCCGAATCCAGCAAG 60.748 57.895 0.00 0.00 0.00 4.01
1470 2120 2.042259 CAGCAGCCGAATCCAGCAA 61.042 57.895 0.00 0.00 0.00 3.91
1500 2156 9.081997 CATACTGCACAAAAAGTCAAAAACTAA 57.918 29.630 0.00 0.00 37.17 2.24
1510 2166 5.356751 TGAACTGTCATACTGCACAAAAAGT 59.643 36.000 0.00 0.00 0.00 2.66
1511 2167 5.682862 GTGAACTGTCATACTGCACAAAAAG 59.317 40.000 0.00 0.00 35.80 2.27
1512 2168 5.356751 AGTGAACTGTCATACTGCACAAAAA 59.643 36.000 0.00 0.00 35.80 1.94
1513 2169 4.881273 AGTGAACTGTCATACTGCACAAAA 59.119 37.500 0.00 0.00 35.80 2.44
1514 2170 4.450976 AGTGAACTGTCATACTGCACAAA 58.549 39.130 0.00 0.00 35.80 2.83
1515 2171 4.058124 GAGTGAACTGTCATACTGCACAA 58.942 43.478 0.00 0.00 35.80 3.33
1516 2172 3.321968 AGAGTGAACTGTCATACTGCACA 59.678 43.478 0.00 0.00 35.80 4.57
1517 2173 3.677121 CAGAGTGAACTGTCATACTGCAC 59.323 47.826 0.00 0.00 35.80 4.57
1518 2174 3.306294 CCAGAGTGAACTGTCATACTGCA 60.306 47.826 0.00 0.00 37.90 4.41
1519 2175 3.257393 CCAGAGTGAACTGTCATACTGC 58.743 50.000 0.00 0.00 37.90 4.40
1520 2176 4.021981 TGACCAGAGTGAACTGTCATACTG 60.022 45.833 0.00 0.00 38.42 2.74
1521 2177 4.152647 TGACCAGAGTGAACTGTCATACT 58.847 43.478 0.00 0.00 35.80 2.12
1522 2178 4.521130 TGACCAGAGTGAACTGTCATAC 57.479 45.455 0.00 0.00 35.80 2.39
1523 2179 5.482006 CAATGACCAGAGTGAACTGTCATA 58.518 41.667 12.63 0.00 37.50 2.15
1524 2180 4.321718 CAATGACCAGAGTGAACTGTCAT 58.678 43.478 8.38 8.38 38.69 3.06
1525 2181 3.494924 CCAATGACCAGAGTGAACTGTCA 60.495 47.826 5.02 5.02 36.30 3.58
1526 2182 3.070018 CCAATGACCAGAGTGAACTGTC 58.930 50.000 0.00 0.00 36.30 3.51
1527 2183 2.705658 TCCAATGACCAGAGTGAACTGT 59.294 45.455 0.00 0.00 36.30 3.55
1528 2184 3.407424 TCCAATGACCAGAGTGAACTG 57.593 47.619 0.00 0.00 37.61 3.16
1529 2185 4.080863 GGTATCCAATGACCAGAGTGAACT 60.081 45.833 0.00 0.00 35.65 3.01
1530 2186 4.192317 GGTATCCAATGACCAGAGTGAAC 58.808 47.826 0.00 0.00 35.65 3.18
1531 2187 3.199946 GGGTATCCAATGACCAGAGTGAA 59.800 47.826 0.00 0.00 37.47 3.18
1532 2188 2.771943 GGGTATCCAATGACCAGAGTGA 59.228 50.000 0.00 0.00 37.47 3.41
1533 2189 2.774234 AGGGTATCCAATGACCAGAGTG 59.226 50.000 0.00 0.00 37.47 3.51
1534 2190 3.041946 GAGGGTATCCAATGACCAGAGT 58.958 50.000 0.00 0.00 37.47 3.24
1535 2191 3.041211 TGAGGGTATCCAATGACCAGAG 58.959 50.000 0.00 0.00 37.47 3.35
1536 2192 3.041211 CTGAGGGTATCCAATGACCAGA 58.959 50.000 0.00 0.00 37.47 3.86
1537 2193 3.041211 TCTGAGGGTATCCAATGACCAG 58.959 50.000 0.00 0.00 37.47 4.00
1538 2194 3.129262 TCTGAGGGTATCCAATGACCA 57.871 47.619 0.00 0.00 37.47 4.02
1539 2195 4.713792 AATCTGAGGGTATCCAATGACC 57.286 45.455 0.00 0.00 34.83 4.02
1540 2196 5.300286 CCAAAATCTGAGGGTATCCAATGAC 59.700 44.000 0.00 0.00 34.83 3.06
1541 2197 5.044179 ACCAAAATCTGAGGGTATCCAATGA 60.044 40.000 0.00 0.00 34.83 2.57
1542 2198 5.203528 ACCAAAATCTGAGGGTATCCAATG 58.796 41.667 0.00 0.00 34.83 2.82
1543 2199 5.472301 ACCAAAATCTGAGGGTATCCAAT 57.528 39.130 0.00 0.00 34.83 3.16
1544 2200 4.946160 ACCAAAATCTGAGGGTATCCAA 57.054 40.909 0.00 0.00 34.83 3.53
1545 2201 4.569653 CCAACCAAAATCTGAGGGTATCCA 60.570 45.833 0.00 0.00 34.83 3.41
1546 2202 3.954258 CCAACCAAAATCTGAGGGTATCC 59.046 47.826 0.00 0.00 32.21 2.59
1547 2203 3.381590 GCCAACCAAAATCTGAGGGTATC 59.618 47.826 0.00 0.00 32.21 2.24
1548 2204 3.365472 GCCAACCAAAATCTGAGGGTAT 58.635 45.455 0.00 0.00 32.21 2.73
1549 2205 2.802719 GCCAACCAAAATCTGAGGGTA 58.197 47.619 0.00 0.00 32.21 3.69
1550 2206 1.632589 GCCAACCAAAATCTGAGGGT 58.367 50.000 0.00 0.00 34.43 4.34
1551 2207 0.527565 CGCCAACCAAAATCTGAGGG 59.472 55.000 0.00 0.00 0.00 4.30
1552 2208 1.068333 CACGCCAACCAAAATCTGAGG 60.068 52.381 0.00 0.00 0.00 3.86
1553 2209 1.666888 GCACGCCAACCAAAATCTGAG 60.667 52.381 0.00 0.00 0.00 3.35
1554 2210 0.313672 GCACGCCAACCAAAATCTGA 59.686 50.000 0.00 0.00 0.00 3.27
1569 2225 1.893137 TCCTAGCTATACCATGGCACG 59.107 52.381 13.04 0.00 39.48 5.34
1578 2241 5.413309 AATCCACTGCATCCTAGCTATAC 57.587 43.478 0.00 0.00 34.99 1.47
1607 2270 7.563888 AGACATAAATGATCACTGAATGGTG 57.436 36.000 0.00 0.00 38.44 4.17
1613 2276 7.118245 GTGACACAAGACATAAATGATCACTGA 59.882 37.037 0.00 0.00 34.21 3.41
1632 2295 7.549134 GTCAGATTATGGAAATACTGTGACACA 59.451 37.037 8.26 8.26 33.32 3.72
1642 2305 9.123902 CAATGTCCAAGTCAGATTATGGAAATA 57.876 33.333 5.58 0.00 43.21 1.40
1643 2306 7.616935 ACAATGTCCAAGTCAGATTATGGAAAT 59.383 33.333 3.96 2.33 43.21 2.17
1644 2307 6.947733 ACAATGTCCAAGTCAGATTATGGAAA 59.052 34.615 3.96 0.27 43.21 3.13
1647 2310 6.823182 TGTACAATGTCCAAGTCAGATTATGG 59.177 38.462 0.00 0.00 0.00 2.74
1658 2321 5.163723 CCATTAGCACTGTACAATGTCCAAG 60.164 44.000 6.15 0.00 0.00 3.61
1667 2330 4.261405 GCAAAACACCATTAGCACTGTACA 60.261 41.667 0.00 0.00 0.00 2.90
1669 2332 3.254657 GGCAAAACACCATTAGCACTGTA 59.745 43.478 0.00 0.00 0.00 2.74
1689 2358 0.323725 ATGGTGATGTTGACCCAGGC 60.324 55.000 0.00 0.00 31.84 4.85
1691 2360 2.489329 GTCAATGGTGATGTTGACCCAG 59.511 50.000 6.92 0.00 45.20 4.45
1712 2381 5.856126 TTAACTCCATGAAACGCTACAAG 57.144 39.130 0.00 0.00 0.00 3.16
1727 2396 7.412853 CAGCAACATCAAGTCATATTAACTCC 58.587 38.462 0.00 0.00 0.00 3.85
1735 2407 3.941573 TCAGCAGCAACATCAAGTCATA 58.058 40.909 0.00 0.00 0.00 2.15
1739 2413 2.033801 GTGTTCAGCAGCAACATCAAGT 59.966 45.455 1.88 0.00 36.19 3.16
1804 2479 0.517316 GTACAGTTCAAGGCAAGCCG 59.483 55.000 5.28 0.00 41.95 5.52
1824 2502 3.526931 TGCAGTGCTCTAATGTACTCC 57.473 47.619 17.60 0.00 30.70 3.85
1825 2503 4.499183 ACTTGCAGTGCTCTAATGTACTC 58.501 43.478 17.60 0.00 30.70 2.59
1826 2504 4.543590 ACTTGCAGTGCTCTAATGTACT 57.456 40.909 17.60 0.00 33.28 2.73
1827 2505 4.452455 ACAACTTGCAGTGCTCTAATGTAC 59.548 41.667 17.60 0.00 0.00 2.90
1828 2506 4.452114 CACAACTTGCAGTGCTCTAATGTA 59.548 41.667 17.60 0.00 0.00 2.29
1830 2508 3.251729 ACACAACTTGCAGTGCTCTAATG 59.748 43.478 17.60 11.16 39.30 1.90
1831 2509 3.480470 ACACAACTTGCAGTGCTCTAAT 58.520 40.909 17.60 0.00 39.30 1.73
1833 2511 2.620251 ACACAACTTGCAGTGCTCTA 57.380 45.000 17.60 0.76 39.30 2.43
1866 2554 2.153645 TGAAGCACAGGTACATGCAAG 58.846 47.619 7.57 0.00 43.82 4.01
1966 2678 3.133721 GGGTGAGTAAGATCATCAGCACT 59.866 47.826 16.18 0.00 41.93 4.40
1990 2702 4.311520 TCTGCAGGTAGTAGGTAGACAA 57.688 45.455 15.13 0.00 0.00 3.18
1998 2710 2.799917 GCCGTTGATCTGCAGGTAGTAG 60.800 54.545 15.13 0.00 0.00 2.57
1999 2711 1.136305 GCCGTTGATCTGCAGGTAGTA 59.864 52.381 15.13 0.00 0.00 1.82
2000 2712 0.108138 GCCGTTGATCTGCAGGTAGT 60.108 55.000 15.13 0.00 0.00 2.73
2140 2856 1.271379 TGGACTAGAAAACAGGCAGCC 60.271 52.381 1.84 1.84 0.00 4.85
2219 2948 2.143122 CAACATACTTGTGGCACGAGT 58.857 47.619 35.67 35.67 44.61 4.18
2303 3034 4.048504 GGGACAGCAACAAATACAAACAC 58.951 43.478 0.00 0.00 0.00 3.32
2331 3062 7.646314 ACATTCATATAGCTGAAGAAACATGC 58.354 34.615 0.00 0.00 38.47 4.06
2363 3094 8.795842 ACAAATAAGGTTCAATTATACGACCA 57.204 30.769 0.00 0.00 32.81 4.02
2420 3153 9.595823 TTCAGAGGAACTAAATCTTATAAACCG 57.404 33.333 0.00 0.00 41.55 4.44
2455 3188 7.118680 GCACGATAATTTAATCCTCCCGAAATA 59.881 37.037 0.00 0.00 0.00 1.40
2482 3215 4.326278 CACAGAGTTGCATCAAAATCATGC 59.674 41.667 0.00 0.00 45.92 4.06
2499 3232 3.068590 AGGCAAATTGAAACCACACAGAG 59.931 43.478 0.00 0.00 0.00 3.35
2512 3245 5.088680 ACCACCATTATTCAGGCAAATTG 57.911 39.130 0.00 0.00 0.00 2.32
2513 3246 5.012975 ACAACCACCATTATTCAGGCAAATT 59.987 36.000 0.00 0.00 0.00 1.82
2564 3297 0.031585 GGGTCAAAAGAAACGGGCAC 59.968 55.000 0.00 0.00 0.00 5.01
2572 3305 9.416284 AGTTATTAAAGAGTTGGGTCAAAAGAA 57.584 29.630 0.00 0.00 0.00 2.52
2591 3324 5.605488 AGGAATTAGGGCCTTCGAGTTATTA 59.395 40.000 13.45 0.00 0.00 0.98
2598 3331 1.874129 TCAGGAATTAGGGCCTTCGA 58.126 50.000 13.45 0.00 30.41 3.71
2600 3333 4.170468 TGATTCAGGAATTAGGGCCTTC 57.830 45.455 13.45 2.50 30.41 3.46
2604 3337 4.526970 TCTGTTGATTCAGGAATTAGGGC 58.473 43.478 0.00 0.00 36.25 5.19
2709 3450 8.604890 GGTTCATAGTGTAGCTTTCTGTATTTC 58.395 37.037 0.00 0.00 0.00 2.17
2735 3476 3.755378 AGCTGAAACTTGCTATTGGACTG 59.245 43.478 0.00 0.00 37.81 3.51
2771 3512 5.382664 AACGTCATTATATCAAAGGGGGT 57.617 39.130 0.00 0.00 0.00 4.95
2772 3513 6.460953 CCAAAACGTCATTATATCAAAGGGGG 60.461 42.308 0.00 0.00 0.00 5.40
2773 3514 6.096282 ACCAAAACGTCATTATATCAAAGGGG 59.904 38.462 0.00 0.00 0.00 4.79
2774 3515 7.095695 ACCAAAACGTCATTATATCAAAGGG 57.904 36.000 0.00 0.00 0.00 3.95
2775 3516 9.104965 TCTACCAAAACGTCATTATATCAAAGG 57.895 33.333 0.00 0.00 0.00 3.11
2785 3526 6.140110 CGTTCAAATCTACCAAAACGTCATT 58.860 36.000 0.00 0.00 35.89 2.57
2786 3527 5.334569 CCGTTCAAATCTACCAAAACGTCAT 60.335 40.000 0.00 0.00 38.17 3.06
2787 3528 4.024725 CCGTTCAAATCTACCAAAACGTCA 60.025 41.667 0.00 0.00 38.17 4.35
2790 3531 4.378046 CCTCCGTTCAAATCTACCAAAACG 60.378 45.833 0.00 0.00 39.20 3.60
2791 3532 4.082949 CCCTCCGTTCAAATCTACCAAAAC 60.083 45.833 0.00 0.00 0.00 2.43
2809 3550 4.838904 ACTTTGTATTGTACCTCCCTCC 57.161 45.455 0.00 0.00 0.00 4.30
2858 3703 9.364989 GCTCAGATTTATGTAGATAGTCCAATC 57.635 37.037 0.00 0.00 0.00 2.67
2861 3706 7.839680 TGCTCAGATTTATGTAGATAGTCCA 57.160 36.000 0.00 0.00 0.00 4.02
2877 3722 9.282569 GGTGAAAAATAGATAGATTGCTCAGAT 57.717 33.333 0.00 0.00 0.00 2.90
2896 3741 6.413892 AGAAATTCCAAAAGCAAGGTGAAAA 58.586 32.000 0.00 0.00 0.00 2.29
2900 3745 4.751600 GGAAGAAATTCCAAAAGCAAGGTG 59.248 41.667 2.14 0.00 40.79 4.00
2959 3804 5.890424 TGCGTCTATATACATCCGAATCA 57.110 39.130 0.00 0.00 0.00 2.57
3000 3847 6.295249 TGGACAACATACAGACTGAAATGAA 58.705 36.000 21.47 0.00 0.00 2.57
3025 3872 8.070171 CCCGTTCACAATTATGAGATGTTAATC 58.930 37.037 0.00 0.00 0.00 1.75
3042 3900 0.608856 TAGTACTCCGCCCGTTCACA 60.609 55.000 0.00 0.00 0.00 3.58
3051 3909 7.011669 TGGCATTACTTTTAATTAGTACTCCGC 59.988 37.037 0.00 0.00 0.00 5.54
3052 3910 8.428186 TGGCATTACTTTTAATTAGTACTCCG 57.572 34.615 0.00 0.00 0.00 4.63
3060 3918 7.954666 AAGGCTCTGGCATTACTTTTAATTA 57.045 32.000 0.00 0.00 40.82 1.40
3091 3949 1.808945 GTGGTCCAGTCATTTGAGCTG 59.191 52.381 0.00 0.00 0.00 4.24
3092 3950 1.271597 GGTGGTCCAGTCATTTGAGCT 60.272 52.381 0.00 0.00 0.00 4.09
3093 3951 1.168714 GGTGGTCCAGTCATTTGAGC 58.831 55.000 0.00 0.00 0.00 4.26
3094 3952 1.352352 AGGGTGGTCCAGTCATTTGAG 59.648 52.381 0.00 0.00 38.24 3.02
3095 3953 1.073763 CAGGGTGGTCCAGTCATTTGA 59.926 52.381 0.00 0.00 38.24 2.69
3096 3954 1.202927 ACAGGGTGGTCCAGTCATTTG 60.203 52.381 0.00 0.00 38.24 2.32
3097 3955 1.149101 ACAGGGTGGTCCAGTCATTT 58.851 50.000 0.00 0.00 38.24 2.32
3098 3956 0.401738 CACAGGGTGGTCCAGTCATT 59.598 55.000 0.00 0.00 38.24 2.57
3099 3957 0.473694 TCACAGGGTGGTCCAGTCAT 60.474 55.000 0.00 0.00 38.24 3.06
3100 3958 0.692756 TTCACAGGGTGGTCCAGTCA 60.693 55.000 0.00 0.00 38.24 3.41
3101 3959 0.693049 ATTCACAGGGTGGTCCAGTC 59.307 55.000 0.00 0.00 38.24 3.51
3102 3960 1.149101 AATTCACAGGGTGGTCCAGT 58.851 50.000 0.00 0.00 38.24 4.00
3103 3961 1.202927 ACAATTCACAGGGTGGTCCAG 60.203 52.381 0.00 0.00 38.24 3.86
3104 3962 0.850100 ACAATTCACAGGGTGGTCCA 59.150 50.000 0.00 0.00 38.24 4.02
3105 3963 2.871096 TACAATTCACAGGGTGGTCC 57.129 50.000 0.00 0.00 33.87 4.46


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

AutoCloner maintained by Alex Coulton.