Multiple sequence alignment - TraesCS3D01G003700

Loading Multiple Alignment...

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 TraesCS3D01G003700 chr3D 100.000 4129 0 0 1 4129 1637188 1633060 0.000000e+00 7625
1 TraesCS3D01G003700 chr3D 100.000 57 0 0 711 767 1636421 1636365 5.650000e-19 106
2 TraesCS3D01G003700 chr3D 100.000 57 0 0 768 824 1636478 1636422 5.650000e-19 106
3 TraesCS3D01G003700 chr3B 91.686 3380 227 26 299 3650 3664244 3660891 0.000000e+00 4636
4 TraesCS3D01G003700 chr3B 91.959 3333 214 26 346 3650 5172109 5175415 0.000000e+00 4621
5 TraesCS3D01G003700 chr3B 92.216 334 23 2 3699 4031 3660772 3660441 1.740000e-128 470
6 TraesCS3D01G003700 chr3B 92.508 307 20 2 3699 4004 5175527 5175831 1.760000e-118 436
7 TraesCS3D01G003700 chr3A 91.845 3225 227 11 839 4052 7472268 7469069 0.000000e+00 4466
8 TraesCS3D01G003700 chr3A 89.791 764 76 2 3 765 7473145 7472383 0.000000e+00 977
9 TraesCS3D01G003700 chr3A 73.451 1081 245 30 2057 3112 36480560 36479497 6.520000e-98 368
10 TraesCS3D01G003700 chr4B 72.643 2270 524 77 890 3112 82311419 82309200 0.000000e+00 662
11 TraesCS3D01G003700 chrUn 96.373 386 14 0 2259 2644 480652057 480652442 1.620000e-178 636
12 TraesCS3D01G003700 chrUn 70.917 1788 456 54 916 2666 245874293 245872533 3.030000e-96 363
13 TraesCS3D01G003700 chrUn 70.917 1788 456 54 916 2666 260284626 260286386 3.030000e-96 363
14 TraesCS3D01G003700 chr4D 72.133 2250 519 88 913 3112 55286200 55284009 2.140000e-162 582
15 TraesCS3D01G003700 chr4D 76.874 1094 191 37 2054 3116 84795836 84794774 2.790000e-156 562
16 TraesCS3D01G003700 chr4A 74.645 1128 233 34 2005 3112 541876895 541877989 2.260000e-122 449
17 TraesCS3D01G003700 chr4A 71.795 1677 391 60 1324 2964 541800980 541802610 6.430000e-108 401
18 TraesCS3D01G003700 chr5A 70.137 1681 435 54 920 2562 650280454 650282105 1.140000e-65 261
19 TraesCS3D01G003700 chr2D 74.872 585 127 14 2005 2577 644170159 644169583 8.860000e-62 248
20 TraesCS3D01G003700 chr2B 73.391 575 126 19 2005 2562 755632186 755631622 5.450000e-44 189
21 TraesCS3D01G003700 chr6D 75.618 283 48 12 2204 2484 2351146 2350883 2.020000e-23 121


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 TraesCS3D01G003700 chr3D 1633060 1637188 4128 True 2612.333333 7625 100.0000 1 4129 3 chr3D.!!$R1 4128
1 TraesCS3D01G003700 chr3B 3660441 3664244 3803 True 2553.000000 4636 91.9510 299 4031 2 chr3B.!!$R1 3732
2 TraesCS3D01G003700 chr3B 5172109 5175831 3722 False 2528.500000 4621 92.2335 346 4004 2 chr3B.!!$F1 3658
3 TraesCS3D01G003700 chr3A 7469069 7473145 4076 True 2721.500000 4466 90.8180 3 4052 2 chr3A.!!$R2 4049
4 TraesCS3D01G003700 chr3A 36479497 36480560 1063 True 368.000000 368 73.4510 2057 3112 1 chr3A.!!$R1 1055
5 TraesCS3D01G003700 chr4B 82309200 82311419 2219 True 662.000000 662 72.6430 890 3112 1 chr4B.!!$R1 2222
6 TraesCS3D01G003700 chrUn 245872533 245874293 1760 True 363.000000 363 70.9170 916 2666 1 chrUn.!!$R1 1750
7 TraesCS3D01G003700 chrUn 260284626 260286386 1760 False 363.000000 363 70.9170 916 2666 1 chrUn.!!$F1 1750
8 TraesCS3D01G003700 chr4D 55284009 55286200 2191 True 582.000000 582 72.1330 913 3112 1 chr4D.!!$R1 2199
9 TraesCS3D01G003700 chr4D 84794774 84795836 1062 True 562.000000 562 76.8740 2054 3116 1 chr4D.!!$R2 1062
10 TraesCS3D01G003700 chr4A 541876895 541877989 1094 False 449.000000 449 74.6450 2005 3112 1 chr4A.!!$F2 1107
11 TraesCS3D01G003700 chr4A 541800980 541802610 1630 False 401.000000 401 71.7950 1324 2964 1 chr4A.!!$F1 1640
12 TraesCS3D01G003700 chr5A 650280454 650282105 1651 False 261.000000 261 70.1370 920 2562 1 chr5A.!!$F1 1642
13 TraesCS3D01G003700 chr2D 644169583 644170159 576 True 248.000000 248 74.8720 2005 2577 1 chr2D.!!$R1 572

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
745 747 0.038166 ACGTTCCCACATGCCATCTT 59.962 50.0 0.0 0.0 0.00 2.40 F
796 798 0.321298 ACAGGTACGTTCCCACATGC 60.321 55.0 7.7 0.0 29.81 4.06 F
1916 2022 0.818040 ACAACTTCAAGCCCGTCCAC 60.818 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1982 0.107017 ACATGGCATGCAGGTAGGTC 60.107 55.0 26.7 0.0 0.0 3.85 R
2114 2223 0.321298 TCTTCCACTGCCGGTTAAGC 60.321 55.0 1.9 0.0 0.0 3.09 R
3230 3371 0.758685 TGGGGCAAACAAAGGACCAG 60.759 55.0 0.0 0.0 0.0 4.00 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
54 55 1.938577 GCATGATGGTCACTACAGCAG 59.061 52.381 0.00 0.00 37.69 4.24
73 74 0.598065 GGACAGTTTGTGATGGTGCC 59.402 55.000 0.00 0.00 0.00 5.01
91 92 1.315257 CCCATGGTGGCTTACAGTGC 61.315 60.000 11.73 0.00 35.79 4.40
104 105 1.022982 ACAGTGCGCAGACCATGATG 61.023 55.000 12.22 2.25 0.00 3.07
117 118 5.122869 CAGACCATGATGTGTAGTTCTTTGG 59.877 44.000 0.00 0.00 0.00 3.28
161 162 8.518920 GGCTGTCGCTACTTGAATTCAAGAAG 62.519 46.154 41.13 29.35 44.70 2.85
170 171 4.336889 TGAATTCAAGAAGACGGTCAGT 57.663 40.909 5.45 0.00 0.00 3.41
171 172 5.462530 TGAATTCAAGAAGACGGTCAGTA 57.537 39.130 5.45 0.00 0.00 2.74
239 240 1.768684 GCCACTGGGAAGGTGTCTCA 61.769 60.000 0.00 0.00 34.68 3.27
250 251 0.389948 GGTGTCTCATGTGGGACGAC 60.390 60.000 8.38 7.53 35.45 4.34
251 252 0.732880 GTGTCTCATGTGGGACGACG 60.733 60.000 8.38 0.00 35.45 5.12
275 276 0.391927 CCCCGCCTCGTGTTATTTCA 60.392 55.000 0.00 0.00 0.00 2.69
289 290 9.047371 TCGTGTTATTTCACTCAATCTTACAAA 57.953 29.630 0.00 0.00 36.33 2.83
290 291 9.103048 CGTGTTATTTCACTCAATCTTACAAAC 57.897 33.333 0.00 0.00 36.33 2.93
305 306 1.418637 ACAAACCGAGGTTTAGCAGGA 59.581 47.619 18.62 0.00 45.32 3.86
317 318 4.822350 GGTTTAGCAGGACAAATATCTCCC 59.178 45.833 0.00 0.00 0.00 4.30
329 330 7.218314 ACAAATATCTCCCTCTCTTGGAAAT 57.782 36.000 0.00 0.00 0.00 2.17
344 345 8.602424 TCTCTTGGAAATCTTACATTCCTACAA 58.398 33.333 6.16 0.00 44.43 2.41
350 351 9.050601 GGAAATCTTACATTCCTACAATCTCTG 57.949 37.037 0.00 0.00 41.54 3.35
371 372 9.753674 TCTCTGTTCCTACCAAATAATTCATTT 57.246 29.630 0.00 0.00 37.32 2.32
374 375 9.289303 CTGTTCCTACCAAATAATTCATTTTCG 57.711 33.333 0.00 0.00 34.49 3.46
416 417 4.085357 TGGTCATATGCATAACCTCCAC 57.915 45.455 22.39 9.25 32.82 4.02
424 426 2.292267 GCATAACCTCCACACCATCTG 58.708 52.381 0.00 0.00 0.00 2.90
430 432 1.678123 CCTCCACACCATCTGCTTGAG 60.678 57.143 0.00 0.00 0.00 3.02
495 497 1.549203 CAGCCTAATGGTGCTTTGGT 58.451 50.000 0.00 0.00 35.12 3.67
498 500 1.892474 GCCTAATGGTGCTTTGGTTGA 59.108 47.619 0.00 0.00 35.27 3.18
499 501 2.352715 GCCTAATGGTGCTTTGGTTGAC 60.353 50.000 0.00 0.00 35.27 3.18
528 530 7.040823 GGAATAATCTAGCTGGTCAATTTCCTG 60.041 40.741 0.00 0.06 0.00 3.86
599 601 1.047801 GAGCCATCCCTTCCTCTCTC 58.952 60.000 0.00 0.00 0.00 3.20
601 603 1.753368 GCCATCCCTTCCTCTCTCGG 61.753 65.000 0.00 0.00 0.00 4.63
622 624 4.154015 CGGCAATATCACAACACTGAGAAA 59.846 41.667 0.00 0.00 0.00 2.52
653 655 8.624367 TTTTCTCGTTTAATAACATTGAGGGA 57.376 30.769 0.00 0.00 33.75 4.20
699 701 1.860484 GCACAAGCTGCAGTTCCTCC 61.860 60.000 16.64 0.00 46.29 4.30
701 703 0.403271 ACAAGCTGCAGTTCCTCCAT 59.597 50.000 16.64 0.00 0.00 3.41
706 708 2.276740 GCAGTTCCTCCATGGGGG 59.723 66.667 26.49 26.49 36.20 5.40
742 744 0.393808 GGTACGTTCCCACATGCCAT 60.394 55.000 0.00 0.00 0.00 4.40
743 745 1.014352 GTACGTTCCCACATGCCATC 58.986 55.000 0.00 0.00 0.00 3.51
744 746 0.908910 TACGTTCCCACATGCCATCT 59.091 50.000 0.00 0.00 0.00 2.90
745 747 0.038166 ACGTTCCCACATGCCATCTT 59.962 50.000 0.00 0.00 0.00 2.40
746 748 1.280710 ACGTTCCCACATGCCATCTTA 59.719 47.619 0.00 0.00 0.00 2.10
747 749 2.290641 ACGTTCCCACATGCCATCTTAA 60.291 45.455 0.00 0.00 0.00 1.85
748 750 2.752354 CGTTCCCACATGCCATCTTAAA 59.248 45.455 0.00 0.00 0.00 1.52
749 751 3.381272 CGTTCCCACATGCCATCTTAAAT 59.619 43.478 0.00 0.00 0.00 1.40
750 752 4.578516 CGTTCCCACATGCCATCTTAAATA 59.421 41.667 0.00 0.00 0.00 1.40
751 753 5.241506 CGTTCCCACATGCCATCTTAAATAT 59.758 40.000 0.00 0.00 0.00 1.28
752 754 6.239008 CGTTCCCACATGCCATCTTAAATATT 60.239 38.462 0.00 0.00 0.00 1.28
753 755 6.899393 TCCCACATGCCATCTTAAATATTC 57.101 37.500 0.00 0.00 0.00 1.75
754 756 5.774690 TCCCACATGCCATCTTAAATATTCC 59.225 40.000 0.00 0.00 0.00 3.01
755 757 5.776716 CCCACATGCCATCTTAAATATTCCT 59.223 40.000 0.00 0.00 0.00 3.36
756 758 6.294899 CCCACATGCCATCTTAAATATTCCTG 60.295 42.308 0.00 0.00 0.00 3.86
757 759 6.154445 CACATGCCATCTTAAATATTCCTGC 58.846 40.000 0.00 0.00 0.00 4.85
758 760 6.015688 CACATGCCATCTTAAATATTCCTGCT 60.016 38.462 0.00 0.00 0.00 4.24
759 761 6.208204 ACATGCCATCTTAAATATTCCTGCTC 59.792 38.462 0.00 0.00 0.00 4.26
760 762 5.945310 TGCCATCTTAAATATTCCTGCTCT 58.055 37.500 0.00 0.00 0.00 4.09
761 763 6.000219 TGCCATCTTAAATATTCCTGCTCTC 59.000 40.000 0.00 0.00 0.00 3.20
762 764 6.000219 GCCATCTTAAATATTCCTGCTCTCA 59.000 40.000 0.00 0.00 0.00 3.27
763 765 6.488006 GCCATCTTAAATATTCCTGCTCTCAA 59.512 38.462 0.00 0.00 0.00 3.02
764 766 7.176340 GCCATCTTAAATATTCCTGCTCTCAAT 59.824 37.037 0.00 0.00 0.00 2.57
765 767 8.512956 CCATCTTAAATATTCCTGCTCTCAATG 58.487 37.037 0.00 0.00 0.00 2.82
766 768 8.512956 CATCTTAAATATTCCTGCTCTCAATGG 58.487 37.037 0.00 0.00 0.00 3.16
767 769 6.488006 TCTTAAATATTCCTGCTCTCAATGGC 59.512 38.462 0.00 0.00 0.00 4.40
768 770 3.870538 ATATTCCTGCTCTCAATGGCA 57.129 42.857 0.00 0.00 36.94 4.92
769 771 2.519771 ATTCCTGCTCTCAATGGCAA 57.480 45.000 0.00 0.00 38.02 4.52
770 772 2.519771 TTCCTGCTCTCAATGGCAAT 57.480 45.000 0.00 0.00 38.02 3.56
771 773 3.650281 TTCCTGCTCTCAATGGCAATA 57.350 42.857 0.00 0.00 38.02 1.90
772 774 3.650281 TCCTGCTCTCAATGGCAATAA 57.350 42.857 0.00 0.00 38.02 1.40
773 775 3.548770 TCCTGCTCTCAATGGCAATAAG 58.451 45.455 0.00 0.00 38.02 1.73
774 776 3.054139 TCCTGCTCTCAATGGCAATAAGT 60.054 43.478 0.00 0.00 38.02 2.24
775 777 3.698040 CCTGCTCTCAATGGCAATAAGTT 59.302 43.478 0.00 0.00 38.02 2.66
776 778 4.439700 CCTGCTCTCAATGGCAATAAGTTG 60.440 45.833 0.00 0.00 38.02 3.16
777 779 4.334552 TGCTCTCAATGGCAATAAGTTGA 58.665 39.130 0.00 0.00 37.53 3.18
778 780 4.156556 TGCTCTCAATGGCAATAAGTTGAC 59.843 41.667 0.00 0.00 44.00 3.18
786 788 3.332034 GGCAATAAGTTGACAGGTACGT 58.668 45.455 0.00 0.00 43.18 3.57
787 789 3.749609 GGCAATAAGTTGACAGGTACGTT 59.250 43.478 0.00 0.00 43.18 3.99
788 790 4.142966 GGCAATAAGTTGACAGGTACGTTC 60.143 45.833 0.00 0.00 43.18 3.95
789 791 4.142966 GCAATAAGTTGACAGGTACGTTCC 60.143 45.833 2.44 2.44 37.53 3.62
790 792 2.538512 AAGTTGACAGGTACGTTCCC 57.461 50.000 7.70 1.45 0.00 3.97
791 793 1.416243 AGTTGACAGGTACGTTCCCA 58.584 50.000 7.70 0.00 0.00 4.37
792 794 1.069668 AGTTGACAGGTACGTTCCCAC 59.930 52.381 7.70 0.68 0.00 4.61
793 795 1.121378 TTGACAGGTACGTTCCCACA 58.879 50.000 7.70 3.31 0.00 4.17
794 796 1.344065 TGACAGGTACGTTCCCACAT 58.656 50.000 7.70 0.00 0.00 3.21
795 797 1.001520 TGACAGGTACGTTCCCACATG 59.998 52.381 7.70 3.37 32.91 3.21
796 798 0.321298 ACAGGTACGTTCCCACATGC 60.321 55.000 7.70 0.00 29.81 4.06
797 799 1.024579 CAGGTACGTTCCCACATGCC 61.025 60.000 7.70 0.00 0.00 4.40
798 800 1.003112 GGTACGTTCCCACATGCCA 60.003 57.895 0.00 0.00 0.00 4.92
810 812 6.899393 TCCCACATGCCATCTTAAATATTC 57.101 37.500 0.00 0.00 0.00 1.75
827 829 6.753913 AATATTCCTGCTCTCAATGGTCTA 57.246 37.500 0.00 0.00 0.00 2.59
836 838 2.573462 TCTCAATGGTCTAAGCCTTGCT 59.427 45.455 0.00 0.00 42.56 3.91
837 839 2.681848 CTCAATGGTCTAAGCCTTGCTG 59.318 50.000 0.00 0.00 39.62 4.41
850 950 1.684983 CCTTGCTGCCCTATTCATTGG 59.315 52.381 0.00 0.00 0.00 3.16
880 980 4.257267 TCCAAGCTATACACCATCGATG 57.743 45.455 18.76 18.76 0.00 3.84
888 988 6.434340 AGCTATACACCATCGATGTATCAAGA 59.566 38.462 23.27 3.22 41.34 3.02
952 1052 6.828785 ACTCACCAAACTGTCTTACTTGAATT 59.171 34.615 0.00 0.00 0.00 2.17
990 1090 1.419374 ACGCTCGTAACAAGCAAGAG 58.581 50.000 0.00 0.00 39.81 2.85
1038 1138 6.018343 CCAATTGCACCGAGTTACAAATTTTT 60.018 34.615 0.00 0.00 0.00 1.94
1113 1213 1.980765 TCTGACCAGCTCCAACATCTT 59.019 47.619 0.00 0.00 0.00 2.40
1117 1217 3.569701 TGACCAGCTCCAACATCTTTTTC 59.430 43.478 0.00 0.00 0.00 2.29
1129 1229 6.203338 CCAACATCTTTTTCTGGGAACAAATG 59.797 38.462 0.00 0.00 42.06 2.32
1134 1234 9.059260 CATCTTTTTCTGGGAACAAATGAATTT 57.941 29.630 0.00 0.00 42.06 1.82
1146 1246 7.171508 GGAACAAATGAATTTTCAGGAGGTTTC 59.828 37.037 0.00 0.00 41.08 2.78
1206 1306 9.067986 AGTTTAGGGTTAGAAGAAAATCAGTTG 57.932 33.333 0.00 0.00 0.00 3.16
1483 1583 9.976511 CTACAATAAGTCGAATTGGGTTATCTA 57.023 33.333 8.63 0.00 38.41 1.98
1487 1587 8.888579 ATAAGTCGAATTGGGTTATCTAACAG 57.111 34.615 8.63 0.00 37.92 3.16
1635 1735 5.884792 AGTCATTGAGTTGGATCAGAATTCC 59.115 40.000 0.65 0.00 0.00 3.01
1738 1843 1.202290 CCATACCAAAGTCCATTGCGC 60.202 52.381 0.00 0.00 0.00 6.09
1876 1982 1.600023 CGGTGGAGTCCTAGAGCTAG 58.400 60.000 11.33 0.00 0.00 3.42
1892 1998 1.123077 CTAGACCTACCTGCATGCCA 58.877 55.000 16.68 2.21 0.00 4.92
1916 2022 0.818040 ACAACTTCAAGCCCGTCCAC 60.818 55.000 0.00 0.00 0.00 4.02
1937 2043 2.226437 CACACACTTGGCCACTATGTTC 59.774 50.000 3.88 0.00 0.00 3.18
1995 2104 1.635663 CCGGTTTCGTGTCCATGCTC 61.636 60.000 0.00 0.00 33.95 4.26
2120 2229 3.502595 GGTTTCTCCTTGTCCAGCTTAAC 59.497 47.826 0.00 0.00 0.00 2.01
2184 2293 2.667969 TCGAGATGAAAATGTGACTGCG 59.332 45.455 0.00 0.00 0.00 5.18
2262 2371 0.884704 ATGCTTTGAGGAACGTGCGT 60.885 50.000 0.00 0.00 0.00 5.24
2281 2390 2.205074 GTCACCGCAATCTAGTCCATG 58.795 52.381 0.00 0.00 0.00 3.66
2299 2408 2.391616 TGTCCTTACTGCATGCTCTG 57.608 50.000 20.33 11.45 0.00 3.35
2566 2684 0.838554 TCATGTTGGGGACTTCGGGA 60.839 55.000 0.00 0.00 0.00 5.14
2936 3076 2.107204 AGTGTTGCAGATTCTTGACCCT 59.893 45.455 0.00 0.00 0.00 4.34
3022 3163 2.036475 TGCAGAGTCTCCTTTCTGTGAC 59.964 50.000 0.00 0.00 42.17 3.67
3037 3178 3.447586 TCTGTGACTAGTATTGGGCTGTC 59.552 47.826 0.00 0.00 0.00 3.51
3112 3253 1.071857 GCTGCATGGGATCAGAGATGA 59.928 52.381 0.00 0.00 32.26 2.92
3153 3294 5.420409 ACTGAGACGAAAGCTAAATAAGGG 58.580 41.667 0.00 0.00 0.00 3.95
3154 3295 4.766375 TGAGACGAAAGCTAAATAAGGGG 58.234 43.478 0.00 0.00 0.00 4.79
3157 3298 6.070653 TGAGACGAAAGCTAAATAAGGGGTTA 60.071 38.462 0.00 0.00 0.00 2.85
3158 3299 6.346896 AGACGAAAGCTAAATAAGGGGTTAG 58.653 40.000 0.00 0.00 0.00 2.34
3159 3300 6.058553 ACGAAAGCTAAATAAGGGGTTAGT 57.941 37.500 0.00 0.00 31.24 2.24
3160 3301 7.124750 AGACGAAAGCTAAATAAGGGGTTAGTA 59.875 37.037 0.00 0.00 31.24 1.82
3161 3302 7.044181 ACGAAAGCTAAATAAGGGGTTAGTAC 58.956 38.462 0.00 0.00 31.24 2.73
3162 3303 7.093156 ACGAAAGCTAAATAAGGGGTTAGTACT 60.093 37.037 0.00 0.00 31.24 2.73
3163 3304 8.416329 CGAAAGCTAAATAAGGGGTTAGTACTA 58.584 37.037 0.00 0.00 31.24 1.82
3175 3316 9.901172 AAGGGGTTAGTACTATTATCAGTTTTG 57.099 33.333 2.79 0.00 0.00 2.44
3176 3317 9.054580 AGGGGTTAGTACTATTATCAGTTTTGT 57.945 33.333 2.79 0.00 0.00 2.83
3177 3318 9.322773 GGGGTTAGTACTATTATCAGTTTTGTC 57.677 37.037 2.79 0.00 0.00 3.18
3220 3361 2.365582 ACAACGAGTGTTTGCCTTCTT 58.634 42.857 0.00 0.00 37.01 2.52
3221 3362 2.097466 ACAACGAGTGTTTGCCTTCTTG 59.903 45.455 0.00 0.00 37.01 3.02
3230 3371 7.043325 CGAGTGTTTGCCTTCTTGTACTATATC 60.043 40.741 0.00 0.00 0.00 1.63
3248 3389 0.469144 TCTGGTCCTTTGTTTGCCCC 60.469 55.000 0.00 0.00 0.00 5.80
3263 3404 5.129485 TGTTTGCCCCAAATGAGAAACTAAA 59.871 36.000 0.00 0.00 35.74 1.85
3279 3420 6.938030 AGAAACTAAACATGTAACCGATTGGA 59.062 34.615 5.81 0.00 39.21 3.53
3283 3424 7.942990 ACTAAACATGTAACCGATTGGAAAAA 58.057 30.769 5.81 0.00 39.21 1.94
3355 3496 7.270047 TCCAAACAGACCCTTATAGTTATTCG 58.730 38.462 0.00 0.00 0.00 3.34
3401 3542 4.697514 ACTGATTCACCATGATAGAACCG 58.302 43.478 0.00 0.00 0.00 4.44
3417 3558 4.028825 AGAACCGCCTTGTATAGGTACTT 58.971 43.478 0.00 0.00 46.61 2.24
3423 3564 4.745125 CGCCTTGTATAGGTACTTGACATG 59.255 45.833 0.00 0.00 46.61 3.21
3511 3662 4.464008 TGGGCATAAGATTGAATCACCTC 58.536 43.478 8.03 0.00 0.00 3.85
3530 3681 1.129624 TCTGTTGTTGTGTTCACGTGC 59.870 47.619 11.67 0.00 0.00 5.34
3539 3690 2.034076 GTGTTCACGTGCGAATTTCAC 58.966 47.619 11.67 7.99 0.00 3.18
3639 3790 6.183360 CCTGCAAAACATTATTGTGCATAACC 60.183 38.462 5.02 0.00 33.42 2.85
3690 3841 4.083581 ACAATTTTGCTACGATGTCTGC 57.916 40.909 0.00 0.00 0.00 4.26
3708 3942 7.646548 TGTCTGCTAATAACTAGATCACACT 57.353 36.000 0.00 0.00 0.00 3.55
3782 4016 1.439679 GGACATGGTCGTTGGTCTTC 58.560 55.000 0.00 0.00 32.65 2.87
4016 4251 1.893137 TGATACTGAACCTGCGTCACT 59.107 47.619 0.00 0.00 0.00 3.41
4032 4267 4.613031 GCGTCACTTAAAATCAGAGCAAAC 59.387 41.667 0.00 0.00 0.00 2.93
4038 4273 3.626028 AAAATCAGAGCAAACGGTCAC 57.374 42.857 0.00 0.00 33.19 3.67
4048 4283 0.458260 AAACGGTCACCAAAAGTGCC 59.542 50.000 0.00 0.00 46.81 5.01
4052 4287 1.515521 GGTCACCAAAAGTGCCGAGG 61.516 60.000 0.00 0.00 46.81 4.63
4053 4288 0.534203 GTCACCAAAAGTGCCGAGGA 60.534 55.000 0.00 0.00 46.81 3.71
4054 4289 0.250295 TCACCAAAAGTGCCGAGGAG 60.250 55.000 0.00 0.00 46.81 3.69
4055 4290 1.073199 ACCAAAAGTGCCGAGGAGG 59.927 57.895 0.00 0.00 44.97 4.30
4056 4291 1.675641 CCAAAAGTGCCGAGGAGGG 60.676 63.158 0.00 0.00 41.48 4.30
4057 4292 1.374947 CAAAAGTGCCGAGGAGGGA 59.625 57.895 0.00 0.00 41.48 4.20
4058 4293 0.674895 CAAAAGTGCCGAGGAGGGAG 60.675 60.000 0.00 0.00 42.71 4.30
4059 4294 1.842381 AAAAGTGCCGAGGAGGGAGG 61.842 60.000 0.00 0.00 42.71 4.30
4060 4295 4.787280 AGTGCCGAGGAGGGAGGG 62.787 72.222 0.00 0.00 42.71 4.30
4064 4299 4.862823 CCGAGGAGGGAGGGGGAC 62.863 77.778 0.00 0.00 35.97 4.46
4066 4301 4.862823 GAGGAGGGAGGGGGACGG 62.863 77.778 0.00 0.00 0.00 4.79
4077 4312 4.162690 GGGACGGCGAGGCTTCAT 62.163 66.667 16.62 0.00 0.00 2.57
4078 4313 2.125106 GGACGGCGAGGCTTCATT 60.125 61.111 16.62 0.00 0.00 2.57
4079 4314 2.464459 GGACGGCGAGGCTTCATTG 61.464 63.158 16.62 0.00 0.00 2.82
4080 4315 2.436646 ACGGCGAGGCTTCATTGG 60.437 61.111 16.62 0.00 0.00 3.16
4081 4316 3.204827 CGGCGAGGCTTCATTGGG 61.205 66.667 0.00 0.00 0.00 4.12
4082 4317 2.272146 GGCGAGGCTTCATTGGGA 59.728 61.111 0.00 0.00 0.00 4.37
4083 4318 1.821332 GGCGAGGCTTCATTGGGAG 60.821 63.158 0.00 0.00 0.00 4.30
4084 4319 2.476320 GCGAGGCTTCATTGGGAGC 61.476 63.158 0.00 4.88 0.00 4.70
4087 4322 2.360191 GGCTTCATTGGGAGCCCA 59.640 61.111 16.53 3.58 45.63 5.36
4088 4323 1.075748 GGCTTCATTGGGAGCCCAT 60.076 57.895 9.46 0.00 46.64 4.00
4089 4324 1.111715 GGCTTCATTGGGAGCCCATC 61.112 60.000 9.46 0.00 46.64 3.51
4090 4325 0.396139 GCTTCATTGGGAGCCCATCA 60.396 55.000 9.46 0.00 46.64 3.07
4091 4326 1.688772 CTTCATTGGGAGCCCATCAG 58.311 55.000 9.46 2.76 46.64 2.90
4092 4327 0.396139 TTCATTGGGAGCCCATCAGC 60.396 55.000 9.46 0.00 46.64 4.26
4093 4328 1.229359 CATTGGGAGCCCATCAGCT 59.771 57.895 9.46 0.00 46.64 4.24
4094 4329 0.475475 CATTGGGAGCCCATCAGCTA 59.525 55.000 9.46 0.00 46.64 3.32
4095 4330 1.075050 CATTGGGAGCCCATCAGCTAT 59.925 52.381 9.46 0.00 46.64 2.97
4096 4331 2.116869 TTGGGAGCCCATCAGCTATA 57.883 50.000 9.46 0.00 46.64 1.31
4097 4332 1.649321 TGGGAGCCCATCAGCTATAG 58.351 55.000 3.58 0.00 45.15 1.31
4098 4333 1.149923 TGGGAGCCCATCAGCTATAGA 59.850 52.381 3.58 0.00 45.15 1.98
4099 4334 2.225727 TGGGAGCCCATCAGCTATAGAT 60.226 50.000 3.58 0.00 45.15 1.98
4100 4335 2.170187 GGGAGCCCATCAGCTATAGATG 59.830 54.545 11.87 11.87 45.15 2.90
4107 4342 3.842820 CATCAGCTATAGATGGTCACCG 58.157 50.000 17.55 0.00 39.30 4.94
4108 4343 2.945456 TCAGCTATAGATGGTCACCGT 58.055 47.619 17.55 0.00 31.33 4.83
4109 4344 2.885266 TCAGCTATAGATGGTCACCGTC 59.115 50.000 17.55 8.15 39.68 4.79
4110 4345 2.623416 CAGCTATAGATGGTCACCGTCA 59.377 50.000 18.77 4.82 41.68 4.35
4111 4346 2.623889 AGCTATAGATGGTCACCGTCAC 59.376 50.000 18.77 2.26 41.68 3.67
4112 4347 2.623889 GCTATAGATGGTCACCGTCACT 59.376 50.000 18.77 7.18 41.68 3.41
4113 4348 3.551046 GCTATAGATGGTCACCGTCACTG 60.551 52.174 18.77 6.43 41.68 3.66
4114 4349 1.182667 TAGATGGTCACCGTCACTGG 58.817 55.000 18.77 0.00 41.68 4.00
4115 4350 0.541998 AGATGGTCACCGTCACTGGA 60.542 55.000 18.77 0.00 41.68 3.86
4116 4351 0.320374 GATGGTCACCGTCACTGGAA 59.680 55.000 11.57 0.00 39.22 3.53
4117 4352 0.762418 ATGGTCACCGTCACTGGAAA 59.238 50.000 0.00 0.00 0.00 3.13
4118 4353 0.762418 TGGTCACCGTCACTGGAAAT 59.238 50.000 0.00 0.00 0.00 2.17
4119 4354 1.156736 GGTCACCGTCACTGGAAATG 58.843 55.000 0.00 0.00 0.00 2.32
4120 4355 1.542547 GGTCACCGTCACTGGAAATGT 60.543 52.381 0.00 0.00 0.00 2.71
4121 4356 2.218603 GTCACCGTCACTGGAAATGTT 58.781 47.619 0.00 0.00 0.00 2.71
4122 4357 2.616842 GTCACCGTCACTGGAAATGTTT 59.383 45.455 0.00 0.00 0.00 2.83
4123 4358 3.066203 GTCACCGTCACTGGAAATGTTTT 59.934 43.478 0.00 0.00 0.00 2.43
4124 4359 3.697045 TCACCGTCACTGGAAATGTTTTT 59.303 39.130 0.00 0.00 0.00 1.94
4125 4360 4.882427 TCACCGTCACTGGAAATGTTTTTA 59.118 37.500 0.00 0.00 0.00 1.52
4126 4361 5.008217 TCACCGTCACTGGAAATGTTTTTAG 59.992 40.000 0.00 0.00 0.00 1.85
4127 4362 4.277423 ACCGTCACTGGAAATGTTTTTAGG 59.723 41.667 0.00 0.00 0.00 2.69
4128 4363 4.320935 CCGTCACTGGAAATGTTTTTAGGG 60.321 45.833 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.027192 GGTATCTTTGCTCCACTCACCA 60.027 50.000 0.00 0.00 0.00 4.17
2 3 2.237392 AGGTATCTTTGCTCCACTCACC 59.763 50.000 0.00 0.00 0.00 4.02
3 4 3.265791 CAGGTATCTTTGCTCCACTCAC 58.734 50.000 0.00 0.00 0.00 3.51
5 6 2.911484 CCAGGTATCTTTGCTCCACTC 58.089 52.381 0.00 0.00 0.00 3.51
9 10 0.255890 TGGCCAGGTATCTTTGCTCC 59.744 55.000 0.00 0.00 0.00 4.70
54 55 0.598065 GGCACCATCACAAACTGTCC 59.402 55.000 0.00 0.00 0.00 4.02
73 74 1.647545 CGCACTGTAAGCCACCATGG 61.648 60.000 11.19 11.19 41.55 3.66
91 92 2.299993 ACTACACATCATGGTCTGCG 57.700 50.000 0.00 0.00 0.00 5.18
104 105 6.262273 TCTTGTTTCCATCCAAAGAACTACAC 59.738 38.462 0.00 0.00 0.00 2.90
117 118 2.352960 GCCGATCTGTCTTGTTTCCATC 59.647 50.000 0.00 0.00 0.00 3.51
169 170 3.004752 AGGCTTGATGTGGGTCAATAC 57.995 47.619 0.00 0.00 37.47 1.89
170 171 3.010027 TCAAGGCTTGATGTGGGTCAATA 59.990 43.478 25.38 0.00 37.47 1.90
171 172 2.173519 CAAGGCTTGATGTGGGTCAAT 58.826 47.619 22.64 0.00 37.47 2.57
182 183 0.684535 TCCACGACATCAAGGCTTGA 59.315 50.000 30.29 30.29 45.01 3.02
260 261 4.631813 AGATTGAGTGAAATAACACGAGGC 59.368 41.667 0.00 0.00 44.35 4.70
275 276 4.618920 ACCTCGGTTTGTAAGATTGAGT 57.381 40.909 0.00 0.00 0.00 3.41
289 290 1.053424 TTGTCCTGCTAAACCTCGGT 58.947 50.000 0.00 0.00 0.00 4.69
290 291 2.178912 TTTGTCCTGCTAAACCTCGG 57.821 50.000 0.00 0.00 0.00 4.63
305 306 6.642733 TTTCCAAGAGAGGGAGATATTTGT 57.357 37.500 0.00 0.00 35.46 2.83
317 318 8.260818 TGTAGGAATGTAAGATTTCCAAGAGAG 58.739 37.037 4.66 0.00 43.21 3.20
329 330 7.400339 AGGAACAGAGATTGTAGGAATGTAAGA 59.600 37.037 0.00 0.00 39.73 2.10
344 345 9.927081 AATGAATTATTTGGTAGGAACAGAGAT 57.073 29.630 0.00 0.00 0.00 2.75
350 351 7.704899 CCCGAAAATGAATTATTTGGTAGGAAC 59.295 37.037 0.00 0.00 38.93 3.62
416 417 4.820897 TGTTACTACTCAAGCAGATGGTG 58.179 43.478 0.00 0.00 0.00 4.17
424 426 5.163814 CCTTGCAATCTGTTACTACTCAAGC 60.164 44.000 0.00 0.00 0.00 4.01
430 432 5.488341 TCCTTCCTTGCAATCTGTTACTAC 58.512 41.667 0.00 0.00 0.00 2.73
492 494 6.042093 CCAGCTAGATTATTCCTAGTCAACCA 59.958 42.308 0.00 0.00 36.77 3.67
495 497 6.839134 TGACCAGCTAGATTATTCCTAGTCAA 59.161 38.462 0.00 0.00 36.77 3.18
498 500 7.863901 ATTGACCAGCTAGATTATTCCTAGT 57.136 36.000 0.00 0.00 36.77 2.57
499 501 9.213799 GAAATTGACCAGCTAGATTATTCCTAG 57.786 37.037 0.00 0.00 37.31 3.02
528 530 5.465056 GCTCTTGCAGATGACTAGGTAAATC 59.535 44.000 0.00 0.00 39.41 2.17
582 584 1.745264 CGAGAGAGGAAGGGATGGC 59.255 63.158 0.00 0.00 0.00 4.40
599 601 3.261580 TCTCAGTGTTGTGATATTGCCG 58.738 45.455 0.00 0.00 0.00 5.69
601 603 5.091431 GCTTTCTCAGTGTTGTGATATTGC 58.909 41.667 0.00 0.00 0.00 3.56
622 624 9.559958 CAATGTTATTAAACGAGAAAATGAGCT 57.440 29.630 0.00 0.00 38.53 4.09
633 635 8.801882 AGATTTCCCTCAATGTTATTAAACGA 57.198 30.769 0.00 0.00 38.53 3.85
699 701 1.481772 CAACTTATTGGCACCCCCATG 59.518 52.381 0.00 0.00 44.89 3.66
701 703 0.780637 TCAACTTATTGGCACCCCCA 59.219 50.000 0.00 0.00 43.51 4.96
706 708 3.124636 CGTACCTGTCAACTTATTGGCAC 59.875 47.826 0.00 0.00 45.49 5.01
742 744 6.488006 GCCATTGAGAGCAGGAATATTTAAGA 59.512 38.462 0.00 0.00 0.00 2.10
743 745 6.263842 TGCCATTGAGAGCAGGAATATTTAAG 59.736 38.462 0.00 0.00 33.08 1.85
744 746 6.128486 TGCCATTGAGAGCAGGAATATTTAA 58.872 36.000 0.00 0.00 33.08 1.52
745 747 5.693961 TGCCATTGAGAGCAGGAATATTTA 58.306 37.500 0.00 0.00 33.08 1.40
746 748 4.539726 TGCCATTGAGAGCAGGAATATTT 58.460 39.130 0.00 0.00 33.08 1.40
747 749 4.174704 TGCCATTGAGAGCAGGAATATT 57.825 40.909 0.00 0.00 33.08 1.28
748 750 3.870538 TGCCATTGAGAGCAGGAATAT 57.129 42.857 0.00 0.00 33.08 1.28
749 751 3.650281 TTGCCATTGAGAGCAGGAATA 57.350 42.857 0.00 0.00 40.73 1.75
750 752 2.519771 TTGCCATTGAGAGCAGGAAT 57.480 45.000 0.00 0.00 40.73 3.01
751 753 2.519771 ATTGCCATTGAGAGCAGGAA 57.480 45.000 0.00 0.00 40.73 3.36
752 754 3.054139 ACTTATTGCCATTGAGAGCAGGA 60.054 43.478 0.00 0.00 40.73 3.86
753 755 3.285484 ACTTATTGCCATTGAGAGCAGG 58.715 45.455 0.00 0.00 40.73 4.85
754 756 4.397103 TCAACTTATTGCCATTGAGAGCAG 59.603 41.667 0.00 0.00 40.73 4.24
755 757 4.156556 GTCAACTTATTGCCATTGAGAGCA 59.843 41.667 0.00 0.00 35.63 4.26
756 758 4.156556 TGTCAACTTATTGCCATTGAGAGC 59.843 41.667 0.00 0.00 35.63 4.09
757 759 5.163683 CCTGTCAACTTATTGCCATTGAGAG 60.164 44.000 3.66 3.66 40.39 3.20
758 760 4.701651 CCTGTCAACTTATTGCCATTGAGA 59.298 41.667 0.00 0.00 35.63 3.27
759 761 4.460382 ACCTGTCAACTTATTGCCATTGAG 59.540 41.667 0.00 0.00 35.63 3.02
760 762 4.406456 ACCTGTCAACTTATTGCCATTGA 58.594 39.130 0.00 0.00 35.63 2.57
761 763 4.789012 ACCTGTCAACTTATTGCCATTG 57.211 40.909 0.00 0.00 35.63 2.82
762 764 4.394920 CGTACCTGTCAACTTATTGCCATT 59.605 41.667 0.00 0.00 35.63 3.16
763 765 3.938963 CGTACCTGTCAACTTATTGCCAT 59.061 43.478 0.00 0.00 35.63 4.40
764 766 3.244284 ACGTACCTGTCAACTTATTGCCA 60.244 43.478 0.00 0.00 35.63 4.92
765 767 3.332034 ACGTACCTGTCAACTTATTGCC 58.668 45.455 0.00 0.00 35.63 4.52
766 768 4.142966 GGAACGTACCTGTCAACTTATTGC 60.143 45.833 0.00 0.00 35.63 3.56
767 769 4.390909 GGGAACGTACCTGTCAACTTATTG 59.609 45.833 2.15 0.00 37.14 1.90
768 770 4.040706 TGGGAACGTACCTGTCAACTTATT 59.959 41.667 10.19 0.00 0.00 1.40
769 771 3.579586 TGGGAACGTACCTGTCAACTTAT 59.420 43.478 10.19 0.00 0.00 1.73
770 772 2.964464 TGGGAACGTACCTGTCAACTTA 59.036 45.455 10.19 0.00 0.00 2.24
771 773 1.764134 TGGGAACGTACCTGTCAACTT 59.236 47.619 10.19 0.00 0.00 2.66
772 774 1.069668 GTGGGAACGTACCTGTCAACT 59.930 52.381 10.19 0.00 0.00 3.16
773 775 1.202557 TGTGGGAACGTACCTGTCAAC 60.203 52.381 10.19 1.34 0.00 3.18
774 776 1.121378 TGTGGGAACGTACCTGTCAA 58.879 50.000 10.19 0.00 0.00 3.18
775 777 1.001520 CATGTGGGAACGTACCTGTCA 59.998 52.381 10.19 7.46 0.00 3.58
776 778 1.722011 CATGTGGGAACGTACCTGTC 58.278 55.000 10.19 0.00 0.00 3.51
777 779 0.321298 GCATGTGGGAACGTACCTGT 60.321 55.000 10.19 0.00 0.00 4.00
778 780 1.024579 GGCATGTGGGAACGTACCTG 61.025 60.000 10.19 0.00 0.00 4.00
779 781 1.298667 GGCATGTGGGAACGTACCT 59.701 57.895 10.19 0.00 0.00 3.08
780 782 0.393808 ATGGCATGTGGGAACGTACC 60.394 55.000 0.00 2.40 0.00 3.34
781 783 1.014352 GATGGCATGTGGGAACGTAC 58.986 55.000 3.81 0.00 0.00 3.67
782 784 0.908910 AGATGGCATGTGGGAACGTA 59.091 50.000 3.81 0.00 0.00 3.57
783 785 0.038166 AAGATGGCATGTGGGAACGT 59.962 50.000 3.81 0.00 0.00 3.99
784 786 2.036958 TAAGATGGCATGTGGGAACG 57.963 50.000 3.81 0.00 0.00 3.95
785 787 6.655078 ATATTTAAGATGGCATGTGGGAAC 57.345 37.500 3.81 0.00 0.00 3.62
786 788 6.267471 GGAATATTTAAGATGGCATGTGGGAA 59.733 38.462 3.81 0.00 0.00 3.97
787 789 5.774690 GGAATATTTAAGATGGCATGTGGGA 59.225 40.000 3.81 0.00 0.00 4.37
788 790 5.776716 AGGAATATTTAAGATGGCATGTGGG 59.223 40.000 3.81 0.00 0.00 4.61
789 791 6.684686 CAGGAATATTTAAGATGGCATGTGG 58.315 40.000 3.81 0.00 0.00 4.17
790 792 6.015688 AGCAGGAATATTTAAGATGGCATGTG 60.016 38.462 3.81 0.00 0.00 3.21
791 793 6.073314 AGCAGGAATATTTAAGATGGCATGT 58.927 36.000 3.81 0.00 0.00 3.21
792 794 6.433404 AGAGCAGGAATATTTAAGATGGCATG 59.567 38.462 3.81 0.00 0.00 4.06
793 795 6.550163 AGAGCAGGAATATTTAAGATGGCAT 58.450 36.000 0.00 0.00 0.00 4.40
794 796 5.945310 AGAGCAGGAATATTTAAGATGGCA 58.055 37.500 0.00 0.00 0.00 4.92
795 797 6.000219 TGAGAGCAGGAATATTTAAGATGGC 59.000 40.000 0.00 0.00 0.00 4.40
796 798 8.512956 CATTGAGAGCAGGAATATTTAAGATGG 58.487 37.037 0.00 0.00 0.00 3.51
797 799 8.512956 CCATTGAGAGCAGGAATATTTAAGATG 58.487 37.037 0.00 0.00 0.00 2.90
798 800 8.223330 ACCATTGAGAGCAGGAATATTTAAGAT 58.777 33.333 0.00 0.00 0.00 2.40
810 812 2.559440 GCTTAGACCATTGAGAGCAGG 58.441 52.381 0.00 0.00 0.00 4.85
827 829 0.332632 TGAATAGGGCAGCAAGGCTT 59.667 50.000 0.00 0.00 43.56 4.35
836 838 4.545678 AGCATTTACCAATGAATAGGGCA 58.454 39.130 0.00 0.00 42.35 5.36
837 839 5.509670 GGAAGCATTTACCAATGAATAGGGC 60.510 44.000 0.00 0.00 42.35 5.19
904 1004 4.019792 TGCCAATGGTGCTATATACTGG 57.980 45.455 0.00 0.00 0.00 4.00
905 1005 5.532406 AGTTTGCCAATGGTGCTATATACTG 59.468 40.000 0.00 0.00 0.00 2.74
910 1010 3.694072 GTGAGTTTGCCAATGGTGCTATA 59.306 43.478 0.00 0.00 0.00 1.31
970 1070 2.030540 ACTCTTGCTTGTTACGAGCGTA 60.031 45.455 18.46 9.11 43.02 4.42
990 1090 2.409948 AGCTGCTCATAAACTCCCAC 57.590 50.000 0.00 0.00 0.00 4.61
1038 1138 7.093814 CCTTGTAGGTGATTCCATTTCATTGAA 60.094 37.037 0.00 0.00 39.02 2.69
1098 1198 3.057033 CCAGAAAAAGATGTTGGAGCTGG 60.057 47.826 0.00 0.00 35.04 4.85
1113 1213 7.498570 CCTGAAAATTCATTTGTTCCCAGAAAA 59.501 33.333 0.00 0.00 36.46 2.29
1117 1217 6.100404 TCCTGAAAATTCATTTGTTCCCAG 57.900 37.500 0.00 0.00 36.46 4.45
1146 1246 4.274459 CGAAGATTTTCTATGCCAGAAGGG 59.726 45.833 0.00 0.00 44.10 3.95
1206 1306 3.552890 GCCATTCTGGAAAAACACCTGTC 60.553 47.826 0.00 0.00 40.96 3.51
1483 1583 3.587506 AGTGGCCCATCTAGTTTACTGTT 59.412 43.478 0.00 0.00 0.00 3.16
1484 1584 3.182152 AGTGGCCCATCTAGTTTACTGT 58.818 45.455 0.00 0.00 0.00 3.55
1487 1587 3.200165 AGGAAGTGGCCCATCTAGTTTAC 59.800 47.826 0.00 0.00 0.00 2.01
1522 1622 3.441572 AGATACAACAGTTGCTTGGCATC 59.558 43.478 13.56 6.80 38.76 3.91
1667 1767 3.754965 AGCACTTCCAAGTTGCTTATGA 58.245 40.909 0.00 0.00 38.98 2.15
1738 1843 6.936900 TCTAGTTGTTGAAGGAATTTCAGAGG 59.063 38.462 0.00 0.00 46.01 3.69
1876 1982 0.107017 ACATGGCATGCAGGTAGGTC 60.107 55.000 26.70 0.00 0.00 3.85
1892 1998 2.812011 GACGGGCTTGAAGTTGTAACAT 59.188 45.455 0.00 0.00 0.00 2.71
1916 2022 1.896220 ACATAGTGGCCAAGTGTGTG 58.104 50.000 7.24 3.82 32.74 3.82
1937 2043 4.521146 AGCTAGTGGAATCATCACTTTGG 58.479 43.478 1.99 0.00 42.17 3.28
2100 2209 3.751518 GGTTAAGCTGGACAAGGAGAAA 58.248 45.455 0.00 0.00 0.00 2.52
2114 2223 0.321298 TCTTCCACTGCCGGTTAAGC 60.321 55.000 1.90 0.00 0.00 3.09
2120 2229 0.537188 ACTGTATCTTCCACTGCCGG 59.463 55.000 0.00 0.00 0.00 6.13
2179 2288 2.872858 GAGAAAAGACTTTCACCGCAGT 59.127 45.455 0.00 0.00 42.99 4.40
2184 2293 4.682401 GTCTCGAGAGAAAAGACTTTCACC 59.318 45.833 17.22 0.00 42.99 4.02
2262 2371 1.831106 ACATGGACTAGATTGCGGTGA 59.169 47.619 0.00 0.00 0.00 4.02
2281 2390 1.661341 CCAGAGCATGCAGTAAGGAC 58.339 55.000 21.98 0.67 0.00 3.85
2424 2533 3.588336 CTCAGCCTTTGAGCCAGC 58.412 61.111 0.00 0.00 46.30 4.85
3022 3163 2.939103 GTGCAAGACAGCCCAATACTAG 59.061 50.000 0.00 0.00 0.00 2.57
3037 3178 2.358737 GGGACGACCTGGTGCAAG 60.359 66.667 2.82 0.00 35.85 4.01
3112 3253 8.832521 CGTCTCAGTCTTATGTAAAGAGATACT 58.167 37.037 0.00 0.00 33.76 2.12
3126 3267 7.974501 CCTTATTTAGCTTTCGTCTCAGTCTTA 59.025 37.037 0.00 0.00 0.00 2.10
3131 3272 4.811557 CCCCTTATTTAGCTTTCGTCTCAG 59.188 45.833 0.00 0.00 0.00 3.35
3220 3361 6.821665 GCAAACAAAGGACCAGATATAGTACA 59.178 38.462 0.00 0.00 0.00 2.90
3221 3362 6.260271 GGCAAACAAAGGACCAGATATAGTAC 59.740 42.308 0.00 0.00 0.00 2.73
3230 3371 0.758685 TGGGGCAAACAAAGGACCAG 60.759 55.000 0.00 0.00 0.00 4.00
3248 3389 8.286800 TCGGTTACATGTTTAGTTTCTCATTTG 58.713 33.333 2.30 0.00 0.00 2.32
3347 3488 7.925993 TGATGAAAGTCAAAACACGAATAACT 58.074 30.769 0.00 0.00 0.00 2.24
3355 3496 8.345565 AGTTACTGATGATGAAAGTCAAAACAC 58.654 33.333 0.00 0.00 0.00 3.32
3423 3564 1.666189 GAGACTCGCCTAAACAATGGC 59.334 52.381 0.00 0.00 45.25 4.40
3511 3662 1.534028 GCACGTGAACACAACAACAG 58.466 50.000 22.23 0.00 0.00 3.16
3604 3755 1.969208 TGTTTTGCAGGCAATGGATCA 59.031 42.857 7.62 0.00 35.70 2.92
3639 3790 3.790212 CTCGATTAGCTGATGCACATG 57.210 47.619 0.00 0.00 42.74 3.21
3662 3813 4.153958 TCGTAGCAAAATTGTTGCGATT 57.846 36.364 16.32 0.00 46.96 3.34
3667 3818 4.321745 GCAGACATCGTAGCAAAATTGTTG 59.678 41.667 0.00 0.00 0.00 3.33
3758 3992 1.447838 CAACGACCATGTCCCCGAG 60.448 63.158 0.00 0.00 0.00 4.63
3782 4016 2.651361 CCCATAGCGACCTAGGCG 59.349 66.667 9.30 14.65 35.00 5.52
3941 4175 5.311649 AGTGGCATAGAATATCTTGGATGGT 59.688 40.000 0.00 0.00 0.00 3.55
3954 4188 4.574892 TGACGATTTTCAGTGGCATAGAA 58.425 39.130 0.00 0.00 0.00 2.10
3958 4192 2.352651 CGATGACGATTTTCAGTGGCAT 59.647 45.455 0.00 0.00 42.66 4.40
4016 4251 4.023536 GGTGACCGTTTGCTCTGATTTTAA 60.024 41.667 0.00 0.00 0.00 1.52
4038 4273 1.675641 CCCTCCTCGGCACTTTTGG 60.676 63.158 0.00 0.00 0.00 3.28
4060 4295 3.682292 AATGAAGCCTCGCCGTCCC 62.682 63.158 0.00 0.00 0.00 4.46
4061 4296 2.125106 AATGAAGCCTCGCCGTCC 60.125 61.111 0.00 0.00 0.00 4.79
4062 4297 2.464459 CCAATGAAGCCTCGCCGTC 61.464 63.158 0.00 0.00 0.00 4.79
4063 4298 2.436646 CCAATGAAGCCTCGCCGT 60.437 61.111 0.00 0.00 0.00 5.68
4064 4299 3.204827 CCCAATGAAGCCTCGCCG 61.205 66.667 0.00 0.00 0.00 6.46
4065 4300 1.821332 CTCCCAATGAAGCCTCGCC 60.821 63.158 0.00 0.00 0.00 5.54
4066 4301 2.476320 GCTCCCAATGAAGCCTCGC 61.476 63.158 0.00 0.00 0.00 5.03
4067 4302 1.821332 GGCTCCCAATGAAGCCTCG 60.821 63.158 16.15 0.00 43.58 4.63
4068 4303 1.454663 GGGCTCCCAATGAAGCCTC 60.455 63.158 20.57 10.96 45.97 4.70
4069 4304 2.240918 TGGGCTCCCAATGAAGCCT 61.241 57.895 20.57 0.00 45.97 4.58
4070 4305 2.360191 TGGGCTCCCAATGAAGCC 59.640 61.111 15.41 15.41 44.12 4.35
4079 4314 1.944177 TCTATAGCTGATGGGCTCCC 58.056 55.000 0.00 0.00 42.97 4.30
4080 4315 3.540314 CATCTATAGCTGATGGGCTCC 57.460 52.381 0.00 0.00 42.97 4.70
4086 4321 3.256879 ACGGTGACCATCTATAGCTGATG 59.743 47.826 1.11 0.34 40.51 3.07
4087 4322 3.501349 ACGGTGACCATCTATAGCTGAT 58.499 45.455 1.11 0.00 0.00 2.90
4088 4323 2.885266 GACGGTGACCATCTATAGCTGA 59.115 50.000 1.11 0.00 0.00 4.26
4089 4324 2.623416 TGACGGTGACCATCTATAGCTG 59.377 50.000 1.11 0.00 0.00 4.24
4090 4325 2.623889 GTGACGGTGACCATCTATAGCT 59.376 50.000 1.11 0.00 0.00 3.32
4091 4326 2.623889 AGTGACGGTGACCATCTATAGC 59.376 50.000 1.11 0.00 0.00 2.97
4092 4327 3.004839 CCAGTGACGGTGACCATCTATAG 59.995 52.174 1.11 0.00 0.00 1.31
4093 4328 2.956333 CCAGTGACGGTGACCATCTATA 59.044 50.000 1.11 0.00 0.00 1.31
4094 4329 1.757118 CCAGTGACGGTGACCATCTAT 59.243 52.381 1.11 0.00 0.00 1.98
4095 4330 1.182667 CCAGTGACGGTGACCATCTA 58.817 55.000 1.11 0.00 0.00 1.98
4096 4331 0.541998 TCCAGTGACGGTGACCATCT 60.542 55.000 1.11 0.00 0.00 2.90
4097 4332 0.320374 TTCCAGTGACGGTGACCATC 59.680 55.000 1.11 0.00 0.00 3.51
4098 4333 0.762418 TTTCCAGTGACGGTGACCAT 59.238 50.000 1.11 0.00 0.00 3.55
4099 4334 0.762418 ATTTCCAGTGACGGTGACCA 59.238 50.000 1.11 0.00 0.00 4.02
4100 4335 1.156736 CATTTCCAGTGACGGTGACC 58.843 55.000 0.00 0.00 0.00 4.02
4101 4336 1.878953 ACATTTCCAGTGACGGTGAC 58.121 50.000 0.00 0.00 0.00 3.67
4102 4337 2.631160 AACATTTCCAGTGACGGTGA 57.369 45.000 0.00 0.00 0.00 4.02
4103 4338 3.708563 AAAACATTTCCAGTGACGGTG 57.291 42.857 0.00 0.00 0.00 4.94
4104 4339 4.277423 CCTAAAAACATTTCCAGTGACGGT 59.723 41.667 0.00 0.00 0.00 4.83
4105 4340 4.320935 CCCTAAAAACATTTCCAGTGACGG 60.321 45.833 0.00 0.00 0.00 4.79
4106 4341 4.794169 CCCTAAAAACATTTCCAGTGACG 58.206 43.478 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.