Multiple sequence alignment - TraesCS4A01G196700

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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 TraesCS4A01G196700 chr4A 100.000 3642 0 0 1 3642 478753731 478750090 0.000000e+00 6726.0
1 TraesCS4A01G196700 chr4A 86.154 130 12 2 1401 1530 478866727 478866604 6.340000e-28 135.0
2 TraesCS4A01G196700 chr4D 91.200 1125 55 19 1882 2975 97383524 97384635 0.000000e+00 1489.0
3 TraesCS4A01G196700 chr4D 94.875 878 23 7 893 1757 97382663 97383531 0.000000e+00 1352.0
4 TraesCS4A01G196700 chr4D 79.380 742 121 15 997 1722 97377869 97378594 9.080000e-136 494.0
5 TraesCS4A01G196700 chr4D 74.697 577 116 20 2334 2904 97379107 97379659 2.830000e-56 230.0
6 TraesCS4A01G196700 chr4D 91.304 115 10 0 1956 2070 97381399 97381513 1.350000e-34 158.0
7 TraesCS4A01G196700 chr4D 88.372 129 5 6 735 853 97382550 97382678 2.930000e-31 147.0
8 TraesCS4A01G196700 chr4D 97.826 46 1 0 633 678 97381511 97381556 3.010000e-11 80.5
9 TraesCS4A01G196700 chr4D 100.000 33 0 0 670 702 97382505 97382537 1.090000e-05 62.1
10 TraesCS4A01G196700 chr4B 94.145 854 42 4 1951 2803 139106588 139107434 0.000000e+00 1293.0
11 TraesCS4A01G196700 chr4B 93.537 882 34 10 894 1757 139105625 139106501 0.000000e+00 1291.0
12 TraesCS4A01G196700 chr4B 89.353 695 70 4 1 694 139063488 139064179 0.000000e+00 870.0
13 TraesCS4A01G196700 chr4B 79.039 749 115 20 997 1726 139024066 139024791 3.290000e-130 475.0
14 TraesCS4A01G196700 chr4B 88.083 193 13 6 2788 2975 139107451 139107638 1.700000e-53 220.0
15 TraesCS4A01G196700 chr4B 89.167 120 6 2 741 853 139105520 139105639 3.790000e-30 143.0
16 TraesCS4A01G196700 chr5B 86.736 671 68 11 2976 3639 644868284 644868940 0.000000e+00 726.0
17 TraesCS4A01G196700 chr5B 88.021 576 47 11 3067 3639 232262952 232263508 0.000000e+00 662.0
18 TraesCS4A01G196700 chr7B 89.410 576 45 9 3067 3639 468940897 468941459 0.000000e+00 712.0
19 TraesCS4A01G196700 chr7B 87.153 576 52 12 3067 3639 137523088 137523644 5.130000e-178 634.0
20 TraesCS4A01G196700 chr7B 86.165 571 41 13 3067 3634 579448611 579449146 1.880000e-162 582.0
21 TraesCS4A01G196700 chr7D 89.223 566 50 4 3083 3639 159911499 159912062 0.000000e+00 697.0
22 TraesCS4A01G196700 chr7D 79.857 561 94 16 8 560 30383945 30384494 3.410000e-105 392.0
23 TraesCS4A01G196700 chr1D 88.215 577 35 11 3067 3639 113901261 113901808 0.000000e+00 658.0
24 TraesCS4A01G196700 chr1D 80.893 560 103 3 1 557 102771050 102771608 4.320000e-119 438.0
25 TraesCS4A01G196700 chr1D 79.613 569 96 17 8 566 457075645 457075087 1.230000e-104 390.0
26 TraesCS4A01G196700 chr1D 95.082 122 6 0 1761 1882 270900883 270901004 3.710000e-45 193.0
27 TraesCS4A01G196700 chr5A 86.261 575 50 9 3067 3639 401616699 401617246 6.730000e-167 597.0
28 TraesCS4A01G196700 chr5A 80.645 558 94 12 8 560 645418415 645417867 1.560000e-113 420.0
29 TraesCS4A01G196700 chr5A 83.081 396 60 5 3245 3636 401618049 401617657 1.610000e-93 353.0
30 TraesCS4A01G196700 chr5A 90.845 142 10 3 1750 1891 577784062 577784200 1.730000e-43 187.0
31 TraesCS4A01G196700 chr6A 86.239 545 36 11 3067 3608 454633852 454634360 4.110000e-154 555.0
32 TraesCS4A01G196700 chr6A 79.286 560 98 16 8 560 97584631 97585179 3.430000e-100 375.0
33 TraesCS4A01G196700 chrUn 84.456 579 38 16 3067 3642 26876537 26877066 1.160000e-144 523.0
34 TraesCS4A01G196700 chrUn 81.625 566 92 8 4 565 468000527 467999970 3.310000e-125 459.0
35 TraesCS4A01G196700 chrUn 93.600 125 8 0 1758 1882 28638428 28638552 1.730000e-43 187.0
36 TraesCS4A01G196700 chr6D 83.601 561 82 7 1 557 468144836 468145390 5.390000e-143 518.0
37 TraesCS4A01G196700 chr6D 95.082 122 6 0 1761 1882 345490423 345490302 3.710000e-45 193.0
38 TraesCS4A01G196700 chr2D 89.024 410 29 5 3234 3639 7809352 7809749 9.080000e-136 494.0
39 TraesCS4A01G196700 chr2D 85.348 273 25 6 2977 3235 7809136 7809407 5.990000e-68 268.0
40 TraesCS4A01G196700 chr2D 94.400 125 7 0 1758 1882 299720497 299720621 3.710000e-45 193.0
41 TraesCS4A01G196700 chr7A 79.893 562 94 13 8 560 646090573 646090022 9.480000e-106 394.0
42 TraesCS4A01G196700 chr7A 95.082 122 6 0 1761 1882 466311264 466311143 3.710000e-45 193.0
43 TraesCS4A01G196700 chr7A 95.041 121 6 0 1761 1881 486228315 486228195 1.330000e-44 191.0
44 TraesCS4A01G196700 chr2B 95.902 122 5 0 1761 1882 154497638 154497759 7.980000e-47 198.0
45 TraesCS4A01G196700 chr3D 94.400 125 7 0 1758 1882 359257717 359257841 3.710000e-45 193.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G196700 chr4A 478750090 478753731 3641 True 6726.000 6726 100.00000 1 3642 1 chr4A.!!$R1 3641
1 TraesCS4A01G196700 chr4D 97377869 97384635 6766 False 501.575 1489 89.70675 633 2975 8 chr4D.!!$F1 2342
2 TraesCS4A01G196700 chr4B 139063488 139064179 691 False 870.000 870 89.35300 1 694 1 chr4B.!!$F2 693
3 TraesCS4A01G196700 chr4B 139105520 139107638 2118 False 736.750 1293 91.23300 741 2975 4 chr4B.!!$F3 2234
4 TraesCS4A01G196700 chr4B 139024066 139024791 725 False 475.000 475 79.03900 997 1726 1 chr4B.!!$F1 729
5 TraesCS4A01G196700 chr5B 644868284 644868940 656 False 726.000 726 86.73600 2976 3639 1 chr5B.!!$F2 663
6 TraesCS4A01G196700 chr5B 232262952 232263508 556 False 662.000 662 88.02100 3067 3639 1 chr5B.!!$F1 572
7 TraesCS4A01G196700 chr7B 468940897 468941459 562 False 712.000 712 89.41000 3067 3639 1 chr7B.!!$F2 572
8 TraesCS4A01G196700 chr7B 137523088 137523644 556 False 634.000 634 87.15300 3067 3639 1 chr7B.!!$F1 572
9 TraesCS4A01G196700 chr7B 579448611 579449146 535 False 582.000 582 86.16500 3067 3634 1 chr7B.!!$F3 567
10 TraesCS4A01G196700 chr7D 159911499 159912062 563 False 697.000 697 89.22300 3083 3639 1 chr7D.!!$F2 556
11 TraesCS4A01G196700 chr7D 30383945 30384494 549 False 392.000 392 79.85700 8 560 1 chr7D.!!$F1 552
12 TraesCS4A01G196700 chr1D 113901261 113901808 547 False 658.000 658 88.21500 3067 3639 1 chr1D.!!$F2 572
13 TraesCS4A01G196700 chr1D 102771050 102771608 558 False 438.000 438 80.89300 1 557 1 chr1D.!!$F1 556
14 TraesCS4A01G196700 chr1D 457075087 457075645 558 True 390.000 390 79.61300 8 566 1 chr1D.!!$R1 558
15 TraesCS4A01G196700 chr5A 401616699 401617246 547 False 597.000 597 86.26100 3067 3639 1 chr5A.!!$F1 572
16 TraesCS4A01G196700 chr5A 645417867 645418415 548 True 420.000 420 80.64500 8 560 1 chr5A.!!$R2 552
17 TraesCS4A01G196700 chr6A 454633852 454634360 508 False 555.000 555 86.23900 3067 3608 1 chr6A.!!$F2 541
18 TraesCS4A01G196700 chr6A 97584631 97585179 548 False 375.000 375 79.28600 8 560 1 chr6A.!!$F1 552
19 TraesCS4A01G196700 chrUn 26876537 26877066 529 False 523.000 523 84.45600 3067 3642 1 chrUn.!!$F1 575
20 TraesCS4A01G196700 chrUn 467999970 468000527 557 True 459.000 459 81.62500 4 565 1 chrUn.!!$R1 561
21 TraesCS4A01G196700 chr6D 468144836 468145390 554 False 518.000 518 83.60100 1 557 1 chr6D.!!$F1 556
22 TraesCS4A01G196700 chr2D 7809136 7809749 613 False 381.000 494 87.18600 2977 3639 2 chr2D.!!$F2 662
23 TraesCS4A01G196700 chr7A 646090022 646090573 551 True 394.000 394 79.89300 8 560 1 chr7A.!!$R3 552

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
110 111 0.173708 CTAGGTCTGACCCGAGTTGC 59.826 60.0 22.81 0.0 39.75 4.17 F
356 359 0.322456 TAGTTTGCTGATTGCGGGCT 60.322 50.0 0.00 0.0 46.63 5.19 F
1876 5877 0.169009 CTTTAAGGCACCGAAGCTGC 59.831 55.0 0.00 0.0 34.17 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 5820 0.395586 TTGACATATGGGCCAGCCAC 60.396 55.000 13.78 2.96 37.98 5.01 R
2267 6295 0.043183 TCTGCTTCTCCCCATCTCCA 59.957 55.000 0.00 0.00 0.00 3.86 R
3122 7213 1.650363 CCACGTTCCGTTTTGGGTC 59.350 57.895 0.00 0.00 38.32 4.46 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
110 111 0.173708 CTAGGTCTGACCCGAGTTGC 59.826 60.000 22.81 0.00 39.75 4.17
127 128 5.410746 CGAGTTGCTTATATCTGGCAATGAT 59.589 40.000 11.28 0.00 45.55 2.45
158 159 2.036862 GTGTCGTTCCCTTGTAGAAGGT 59.963 50.000 16.93 0.00 46.84 3.50
211 214 6.023603 TCAGGGTGAAAACCTAGATTCTACT 58.976 40.000 0.00 0.00 36.32 2.57
237 240 1.003839 GTTGGATCAGGTGACGCCA 60.004 57.895 7.99 0.42 40.61 5.69
239 242 1.480212 TTGGATCAGGTGACGCCAGT 61.480 55.000 7.99 0.00 40.61 4.00
280 283 6.395426 TTCTTCAAGACATTGCTGTTGAAT 57.605 33.333 8.35 0.00 33.71 2.57
315 318 5.989168 TCGGTATGGTGTCATGATATGTTTC 59.011 40.000 0.00 0.00 34.96 2.78
325 328 6.200854 TGTCATGATATGTTTCGTGCAGATAC 59.799 38.462 0.00 0.00 33.50 2.24
354 357 3.376859 TGTTATAGTTTGCTGATTGCGGG 59.623 43.478 0.00 0.00 46.63 6.13
356 359 0.322456 TAGTTTGCTGATTGCGGGCT 60.322 50.000 0.00 0.00 46.63 5.19
389 396 7.094334 CCTTAGGTTATTTTCTTTTTCCTCGCT 60.094 37.037 0.00 0.00 0.00 4.93
394 403 5.712152 ATTTTCTTTTTCCTCGCTGATGT 57.288 34.783 0.00 0.00 0.00 3.06
432 443 6.751514 ATATGACTTTGTTATTTGCCGTCA 57.248 33.333 0.00 0.00 34.84 4.35
456 468 1.854227 TTGTGTATGCGTGTCGTTGA 58.146 45.000 0.00 0.00 0.00 3.18
469 481 3.063452 GTGTCGTTGATGTTGACTGTGTT 59.937 43.478 0.00 0.00 33.81 3.32
521 533 8.391106 GTGTGTTCATTATGTTTGTATCCTCTC 58.609 37.037 0.00 0.00 0.00 3.20
524 536 9.817809 TGTTCATTATGTTTGTATCCTCTCTAC 57.182 33.333 0.00 0.00 0.00 2.59
606 619 1.258445 ACCCTAACAGACGGAGCAGG 61.258 60.000 0.00 0.00 0.00 4.85
702 4670 6.199531 GTCGCACGTATCAGGTATCAATAAAA 59.800 38.462 0.00 0.00 0.00 1.52
703 4671 6.199531 TCGCACGTATCAGGTATCAATAAAAC 59.800 38.462 0.00 0.00 0.00 2.43
706 4674 7.464977 GCACGTATCAGGTATCAATAAAACGTT 60.465 37.037 0.00 0.00 37.71 3.99
707 4675 8.385111 CACGTATCAGGTATCAATAAAACGTTT 58.615 33.333 7.96 7.96 37.71 3.60
709 4677 8.060090 CGTATCAGGTATCAATAAAACGTTTCC 58.940 37.037 15.01 8.44 0.00 3.13
710 4678 6.746745 TCAGGTATCAATAAAACGTTTCCC 57.253 37.500 15.01 4.73 0.00 3.97
714 4682 5.648960 GGTATCAATAAAACGTTTCCCCTCA 59.351 40.000 15.01 0.00 0.00 3.86
715 4683 6.151480 GGTATCAATAAAACGTTTCCCCTCAA 59.849 38.462 15.01 0.00 0.00 3.02
716 4684 6.658188 ATCAATAAAACGTTTCCCCTCAAA 57.342 33.333 15.01 0.00 0.00 2.69
717 4685 6.466885 TCAATAAAACGTTTCCCCTCAAAA 57.533 33.333 15.01 0.00 0.00 2.44
718 4686 6.875076 TCAATAAAACGTTTCCCCTCAAAAA 58.125 32.000 15.01 0.00 0.00 1.94
843 4820 5.078256 TCTTCTTTTCTCGACTAGAACCCT 58.922 41.667 0.00 0.00 44.02 4.34
853 4830 3.190118 CGACTAGAACCCTACACGAGTTT 59.810 47.826 0.00 0.00 0.00 2.66
854 4831 4.320788 CGACTAGAACCCTACACGAGTTTT 60.321 45.833 0.00 0.00 0.00 2.43
855 4832 5.536260 GACTAGAACCCTACACGAGTTTTT 58.464 41.667 0.00 0.00 0.00 1.94
879 4856 2.951229 TTTTGGAGAGGAACCTGACC 57.049 50.000 0.00 2.35 0.00 4.02
880 4857 1.814429 TTTGGAGAGGAACCTGACCA 58.186 50.000 0.00 4.94 0.00 4.02
881 4858 1.352083 TTGGAGAGGAACCTGACCAG 58.648 55.000 0.00 0.00 32.51 4.00
882 4859 0.487325 TGGAGAGGAACCTGACCAGA 59.513 55.000 0.00 0.00 0.00 3.86
883 4860 1.132849 TGGAGAGGAACCTGACCAGAA 60.133 52.381 0.00 0.00 0.00 3.02
884 4861 2.192263 GGAGAGGAACCTGACCAGAAT 58.808 52.381 0.00 0.00 0.00 2.40
885 4862 2.169561 GGAGAGGAACCTGACCAGAATC 59.830 54.545 0.00 0.00 0.00 2.52
886 4863 1.827969 AGAGGAACCTGACCAGAATCG 59.172 52.381 0.00 0.00 0.00 3.34
887 4864 0.905357 AGGAACCTGACCAGAATCGG 59.095 55.000 0.00 0.00 0.00 4.18
888 4865 0.902531 GGAACCTGACCAGAATCGGA 59.097 55.000 0.00 0.00 0.00 4.55
889 4866 1.405661 GGAACCTGACCAGAATCGGAC 60.406 57.143 0.00 0.00 0.00 4.79
890 4867 1.275291 GAACCTGACCAGAATCGGACA 59.725 52.381 0.00 0.00 0.00 4.02
891 4868 0.608640 ACCTGACCAGAATCGGACAC 59.391 55.000 0.00 0.00 0.00 3.67
915 4892 1.000955 CCCTACACGAGTTGCTCAAGT 59.999 52.381 0.00 0.00 0.00 3.16
986 4964 1.362406 GCTAGCCTGCGTGAAAGGTC 61.362 60.000 2.29 0.00 37.13 3.85
987 4965 1.078759 CTAGCCTGCGTGAAAGGTCG 61.079 60.000 0.00 0.00 37.13 4.79
1175 5176 5.051173 GCATCTTCATCAACTACATCGACTG 60.051 44.000 0.00 0.00 0.00 3.51
1290 5291 3.610040 TCAATCGTAGACCACTGCAAT 57.390 42.857 0.00 0.00 42.51 3.56
1419 5420 1.087771 CATACCTTGCGTTCGACCCC 61.088 60.000 0.00 0.00 0.00 4.95
1461 5462 0.950836 TGCTTTTGATCCCGTGTGTG 59.049 50.000 0.00 0.00 0.00 3.82
1638 5639 4.274459 CCACTAGAGCCAAAATCTATGTGC 59.726 45.833 0.00 0.00 32.72 4.57
1639 5640 4.025396 CACTAGAGCCAAAATCTATGTGCG 60.025 45.833 0.00 0.00 29.80 5.34
1726 5727 2.346545 GCGTTTGTCGTCAGGTATTACC 59.653 50.000 4.57 4.57 42.13 2.85
1756 5757 2.094957 GCAGAGTCGCACTTCTACTTCT 60.095 50.000 2.68 0.00 0.00 2.85
1757 5758 3.753842 CAGAGTCGCACTTCTACTTCTC 58.246 50.000 0.00 0.00 0.00 2.87
1758 5759 2.417239 AGAGTCGCACTTCTACTTCTCG 59.583 50.000 0.00 0.00 0.00 4.04
1759 5760 2.415857 GAGTCGCACTTCTACTTCTCGA 59.584 50.000 0.00 0.00 0.00 4.04
1760 5761 2.812591 AGTCGCACTTCTACTTCTCGAA 59.187 45.455 0.00 0.00 0.00 3.71
1761 5762 2.909863 GTCGCACTTCTACTTCTCGAAC 59.090 50.000 0.00 0.00 0.00 3.95
1762 5763 1.905687 CGCACTTCTACTTCTCGAACG 59.094 52.381 0.00 0.00 0.00 3.95
1763 5764 2.412455 CGCACTTCTACTTCTCGAACGA 60.412 50.000 0.00 0.00 0.00 3.85
1764 5765 3.728268 CGCACTTCTACTTCTCGAACGAT 60.728 47.826 0.00 0.00 0.00 3.73
1765 5766 3.544285 GCACTTCTACTTCTCGAACGATG 59.456 47.826 0.00 0.00 0.00 3.84
1766 5767 3.544285 CACTTCTACTTCTCGAACGATGC 59.456 47.826 0.00 0.00 0.00 3.91
1767 5768 3.440872 ACTTCTACTTCTCGAACGATGCT 59.559 43.478 0.00 0.00 0.00 3.79
1768 5769 4.082679 ACTTCTACTTCTCGAACGATGCTT 60.083 41.667 0.00 0.00 0.00 3.91
1769 5770 4.017380 TCTACTTCTCGAACGATGCTTC 57.983 45.455 0.00 0.00 0.00 3.86
1776 5777 4.379174 AACGATGCTTCGGTGCTT 57.621 50.000 23.79 8.13 45.42 3.91
1777 5778 2.629002 AACGATGCTTCGGTGCTTT 58.371 47.368 23.79 7.79 45.42 3.51
1778 5779 1.803334 AACGATGCTTCGGTGCTTTA 58.197 45.000 23.79 0.00 45.42 1.85
1779 5780 2.147958 AACGATGCTTCGGTGCTTTAA 58.852 42.857 23.79 0.00 45.42 1.52
1780 5781 2.159627 AACGATGCTTCGGTGCTTTAAG 59.840 45.455 23.79 0.00 45.42 1.85
1781 5782 1.062587 CGATGCTTCGGTGCTTTAAGG 59.937 52.381 13.82 0.00 41.74 2.69
1782 5783 0.811281 ATGCTTCGGTGCTTTAAGGC 59.189 50.000 1.97 1.97 0.00 4.35
1783 5784 0.536233 TGCTTCGGTGCTTTAAGGCA 60.536 50.000 8.37 8.37 40.15 4.75
1801 5802 5.552870 AGGCACCTACCTTTGTATCTATG 57.447 43.478 0.00 0.00 36.28 2.23
1802 5803 5.216622 AGGCACCTACCTTTGTATCTATGA 58.783 41.667 0.00 0.00 36.28 2.15
1803 5804 5.070580 AGGCACCTACCTTTGTATCTATGAC 59.929 44.000 0.00 0.00 36.28 3.06
1804 5805 5.163343 GGCACCTACCTTTGTATCTATGACA 60.163 44.000 0.00 0.00 0.00 3.58
1805 5806 6.464465 GGCACCTACCTTTGTATCTATGACAT 60.464 42.308 0.00 0.00 0.00 3.06
1806 5807 7.256190 GGCACCTACCTTTGTATCTATGACATA 60.256 40.741 0.00 0.00 0.00 2.29
1807 5808 8.314751 GCACCTACCTTTGTATCTATGACATAT 58.685 37.037 0.00 0.00 0.00 1.78
1808 5809 9.645059 CACCTACCTTTGTATCTATGACATATG 57.355 37.037 0.00 0.00 0.00 1.78
1809 5810 9.601810 ACCTACCTTTGTATCTATGACATATGA 57.398 33.333 10.38 0.00 0.00 2.15
1811 5812 9.579768 CTACCTTTGTATCTATGACATATGAGC 57.420 37.037 10.38 1.49 0.00 4.26
1812 5813 7.390027 ACCTTTGTATCTATGACATATGAGCC 58.610 38.462 10.38 0.00 0.00 4.70
1813 5814 6.820656 CCTTTGTATCTATGACATATGAGCCC 59.179 42.308 10.38 0.00 0.00 5.19
1814 5815 6.933514 TTGTATCTATGACATATGAGCCCA 57.066 37.500 10.38 2.28 0.00 5.36
1815 5816 6.933514 TGTATCTATGACATATGAGCCCAA 57.066 37.500 10.38 0.00 0.00 4.12
1816 5817 6.701340 TGTATCTATGACATATGAGCCCAAC 58.299 40.000 10.38 0.00 0.00 3.77
1817 5818 5.830799 ATCTATGACATATGAGCCCAACA 57.169 39.130 10.38 0.00 0.00 3.33
1818 5819 5.219343 TCTATGACATATGAGCCCAACAG 57.781 43.478 10.38 4.43 0.00 3.16
1819 5820 2.715749 TGACATATGAGCCCAACAGG 57.284 50.000 10.38 0.00 39.47 4.00
1820 5821 1.915489 TGACATATGAGCCCAACAGGT 59.085 47.619 10.38 0.00 38.26 4.00
1821 5822 2.292267 GACATATGAGCCCAACAGGTG 58.708 52.381 10.38 0.00 38.26 4.00
1830 5831 4.601794 CAACAGGTGGCTGGCCCA 62.602 66.667 9.28 0.00 42.79 5.36
1837 5838 3.752622 TGGCTGGCCCATATGTCA 58.247 55.556 9.28 0.00 39.18 3.58
1838 5839 2.005921 TGGCTGGCCCATATGTCAA 58.994 52.632 9.28 0.00 39.18 3.18
1839 5840 0.557238 TGGCTGGCCCATATGTCAAT 59.443 50.000 9.28 0.00 39.18 2.57
1840 5841 0.963962 GGCTGGCCCATATGTCAATG 59.036 55.000 0.00 0.00 0.00 2.82
1841 5842 1.479205 GGCTGGCCCATATGTCAATGA 60.479 52.381 0.00 0.00 0.00 2.57
1842 5843 1.610522 GCTGGCCCATATGTCAATGAC 59.389 52.381 6.41 6.41 0.00 3.06
1843 5844 2.233271 CTGGCCCATATGTCAATGACC 58.767 52.381 11.24 0.00 0.00 4.02
1844 5845 1.133513 TGGCCCATATGTCAATGACCC 60.134 52.381 11.24 3.42 0.00 4.46
1845 5846 1.133513 GGCCCATATGTCAATGACCCA 60.134 52.381 11.24 0.00 0.00 4.51
1846 5847 2.665165 GCCCATATGTCAATGACCCAA 58.335 47.619 11.24 0.00 0.00 4.12
1847 5848 3.030291 GCCCATATGTCAATGACCCAAA 58.970 45.455 11.24 0.00 0.00 3.28
1848 5849 3.068590 GCCCATATGTCAATGACCCAAAG 59.931 47.826 11.24 0.00 0.00 2.77
1849 5850 3.638160 CCCATATGTCAATGACCCAAAGG 59.362 47.826 11.24 6.48 40.04 3.11
1850 5851 3.068590 CCATATGTCAATGACCCAAAGGC 59.931 47.826 11.24 0.00 36.11 4.35
1851 5852 2.307496 ATGTCAATGACCCAAAGGCA 57.693 45.000 11.24 0.00 36.11 4.75
1852 5853 1.619654 TGTCAATGACCCAAAGGCAG 58.380 50.000 11.24 0.00 36.11 4.85
1853 5854 0.890683 GTCAATGACCCAAAGGCAGG 59.109 55.000 1.10 0.00 36.11 4.85
1854 5855 0.482446 TCAATGACCCAAAGGCAGGT 59.518 50.000 0.00 0.00 39.75 4.00
1855 5856 0.604578 CAATGACCCAAAGGCAGGTG 59.395 55.000 0.00 0.00 36.17 4.00
1856 5857 1.187567 AATGACCCAAAGGCAGGTGC 61.188 55.000 0.00 0.00 36.17 5.01
1874 5875 3.249687 CCTTTAAGGCACCGAAGCT 57.750 52.632 0.00 0.00 34.17 3.74
1875 5876 0.804989 CCTTTAAGGCACCGAAGCTG 59.195 55.000 0.00 0.00 34.17 4.24
1876 5877 0.169009 CTTTAAGGCACCGAAGCTGC 59.831 55.000 0.00 0.00 34.17 5.25
1877 5878 1.573829 TTTAAGGCACCGAAGCTGCG 61.574 55.000 7.28 7.28 35.31 5.18
1878 5879 2.725203 TTAAGGCACCGAAGCTGCGT 62.725 55.000 14.34 0.00 35.31 5.24
1882 5883 4.379243 CACCGAAGCTGCGTCCCT 62.379 66.667 14.34 0.00 0.00 4.20
1883 5884 2.678934 ACCGAAGCTGCGTCCCTA 60.679 61.111 14.34 0.00 0.00 3.53
1884 5885 2.202756 CCGAAGCTGCGTCCCTAC 60.203 66.667 14.34 0.00 0.00 3.18
1885 5886 2.711922 CCGAAGCTGCGTCCCTACT 61.712 63.158 14.34 0.00 0.00 2.57
1886 5887 1.215647 CGAAGCTGCGTCCCTACTT 59.784 57.895 5.73 0.00 0.00 2.24
1887 5888 0.802607 CGAAGCTGCGTCCCTACTTC 60.803 60.000 5.73 0.00 34.71 3.01
1888 5889 0.533032 GAAGCTGCGTCCCTACTTCT 59.467 55.000 4.11 0.00 35.09 2.85
1889 5890 0.977395 AAGCTGCGTCCCTACTTCTT 59.023 50.000 0.00 0.00 0.00 2.52
1964 5992 8.654997 ACTTCACCACTATAGCTATGAATTGAT 58.345 33.333 16.77 0.00 0.00 2.57
1990 6018 5.545658 TTTGCAGATTATCTTTGTCGGAC 57.454 39.130 0.00 0.00 0.00 4.79
1991 6019 4.200838 TGCAGATTATCTTTGTCGGACA 57.799 40.909 6.76 6.76 0.00 4.02
2214 6242 2.100197 AGATTTCCGGATCGACACAGA 58.900 47.619 4.15 0.00 0.00 3.41
2267 6295 1.033574 GGATGGAGGACGACGAGAAT 58.966 55.000 0.00 0.00 0.00 2.40
2269 6297 0.747255 ATGGAGGACGACGAGAATGG 59.253 55.000 0.00 0.00 0.00 3.16
2270 6298 0.323087 TGGAGGACGACGAGAATGGA 60.323 55.000 0.00 0.00 0.00 3.41
2294 6322 2.238144 TGGGGAGAAGCAGATGAAGAAG 59.762 50.000 0.00 0.00 0.00 2.85
2317 6345 1.610886 GGAGAAGGAGAAAACGGTGGG 60.611 57.143 0.00 0.00 0.00 4.61
2402 6430 5.585445 GCTGATTATGGATGCTTCTATGGAG 59.415 44.000 8.49 1.50 0.00 3.86
2431 6459 0.853530 ACTTCCTTGGCTTTCACCCT 59.146 50.000 0.00 0.00 0.00 4.34
2594 6622 0.324552 CACCCCTTGCATGATTGGGA 60.325 55.000 16.24 0.00 42.11 4.37
2595 6623 0.032813 ACCCCTTGCATGATTGGGAG 60.033 55.000 16.24 10.02 42.11 4.30
2601 6629 0.332293 TGCATGATTGGGAGGCTTCA 59.668 50.000 0.00 0.00 0.00 3.02
2602 6630 1.030457 GCATGATTGGGAGGCTTCAG 58.970 55.000 0.00 0.00 0.00 3.02
2604 6632 2.573369 CATGATTGGGAGGCTTCAGAG 58.427 52.381 0.00 0.00 0.00 3.35
2626 6654 0.737715 ATGCTTCAAGGAGTCGTCGC 60.738 55.000 0.00 0.00 0.00 5.19
2627 6655 2.095252 GCTTCAAGGAGTCGTCGCC 61.095 63.158 0.00 0.00 0.00 5.54
2628 6656 1.801913 CTTCAAGGAGTCGTCGCCG 60.802 63.158 0.00 0.00 38.56 6.46
2629 6657 2.473664 CTTCAAGGAGTCGTCGCCGT 62.474 60.000 0.00 0.00 38.56 5.68
2630 6658 2.467946 TTCAAGGAGTCGTCGCCGTC 62.468 60.000 0.00 0.00 38.56 4.79
2631 6659 4.099170 AAGGAGTCGTCGCCGTCG 62.099 66.667 0.00 0.00 38.56 5.12
2640 6668 1.443194 GTCGCCGTCGCAGAAGTTA 60.443 57.895 0.00 0.00 39.69 2.24
2649 6677 3.241804 CGTCGCAGAAGTTAGAGCATTTC 60.242 47.826 0.00 0.00 39.69 2.17
2650 6678 2.923655 TCGCAGAAGTTAGAGCATTTCG 59.076 45.455 0.00 0.00 0.00 3.46
2659 6687 1.896220 AGAGCATTTCGGCTGTTTGA 58.104 45.000 0.00 0.00 45.99 2.69
2672 6700 5.580691 TCGGCTGTTTGACTGAACAATATAG 59.419 40.000 0.00 0.00 38.90 1.31
2700 6728 1.749258 GCCGATGTTTGGGTCCTCC 60.749 63.158 0.00 0.00 0.00 4.30
2716 6744 4.320870 GTCCTCCGTTTTACCTTTGATGA 58.679 43.478 0.00 0.00 0.00 2.92
2724 6752 6.015504 CGTTTTACCTTTGATGATGTTCTCG 58.984 40.000 0.00 0.00 0.00 4.04
2754 6782 2.807895 CGGCAGGTCGGTTACGTG 60.808 66.667 0.00 0.00 44.94 4.49
2813 6873 4.930405 GGTCTAGTTAAGTGCCAAGAAGTC 59.070 45.833 0.00 0.00 0.00 3.01
2816 6876 7.376615 GTCTAGTTAAGTGCCAAGAAGTCTTA 58.623 38.462 0.00 0.00 34.28 2.10
2817 6877 7.542824 GTCTAGTTAAGTGCCAAGAAGTCTTAG 59.457 40.741 0.00 0.00 34.28 2.18
2818 6878 4.998033 AGTTAAGTGCCAAGAAGTCTTAGC 59.002 41.667 4.73 4.73 40.27 3.09
2819 6879 2.481289 AGTGCCAAGAAGTCTTAGCC 57.519 50.000 8.66 1.73 39.34 3.93
2853 6918 6.169094 TCTCTGGTTTCTTCAGCTATTTGAG 58.831 40.000 0.00 0.00 32.63 3.02
2854 6919 5.869579 TCTGGTTTCTTCAGCTATTTGAGT 58.130 37.500 0.00 0.00 32.63 3.41
2855 6920 7.004555 TCTGGTTTCTTCAGCTATTTGAGTA 57.995 36.000 0.00 0.00 32.63 2.59
2856 6921 7.624549 TCTGGTTTCTTCAGCTATTTGAGTAT 58.375 34.615 0.00 0.00 32.63 2.12
2857 6922 7.766278 TCTGGTTTCTTCAGCTATTTGAGTATC 59.234 37.037 0.00 0.00 32.63 2.24
2896 6964 6.238211 GCATGAATGAGTAGACATGTACAACC 60.238 42.308 0.00 0.00 41.14 3.77
2923 6991 0.878416 TGCACCGATAGTTTGCAACC 59.122 50.000 0.00 0.00 46.41 3.77
2945 7013 3.560882 CCTGAGCTTTGGGTTCTTCTGAT 60.561 47.826 0.00 0.00 0.00 2.90
3051 7120 7.315247 TCTTCAAACGAAATTGACAGAAGAA 57.685 32.000 0.00 0.00 38.95 2.52
3056 7125 6.391227 AACGAAATTGACAGAAGAAACCAT 57.609 33.333 0.00 0.00 0.00 3.55
3059 7128 5.619981 CGAAATTGACAGAAGAAACCATCCC 60.620 44.000 0.00 0.00 0.00 3.85
3063 7132 1.707427 ACAGAAGAAACCATCCCAGCT 59.293 47.619 0.00 0.00 0.00 4.24
3122 7213 1.430632 CGCATAACAGCCAGCCAAG 59.569 57.895 0.00 0.00 0.00 3.61
3123 7214 1.026182 CGCATAACAGCCAGCCAAGA 61.026 55.000 0.00 0.00 0.00 3.02
3175 7267 4.065281 GCCGTCTAGTGGCGTGGT 62.065 66.667 11.95 0.00 43.70 4.16
3210 7303 2.388121 CCTACGTTTCGTTTCGTCTGT 58.612 47.619 0.00 0.00 41.54 3.41
3220 7313 7.317177 GTTTCGTTTCGTCTGTATTTTGTTTG 58.683 34.615 0.00 0.00 0.00 2.93
3403 7497 3.822192 CCGTCGCGGGTCTCATCA 61.822 66.667 6.13 0.00 44.15 3.07
3414 7508 0.755686 GTCTCATCATCGGCCTCCTT 59.244 55.000 0.00 0.00 0.00 3.36
3415 7509 1.964223 GTCTCATCATCGGCCTCCTTA 59.036 52.381 0.00 0.00 0.00 2.69
3425 7519 2.967946 GCCTCCTTACACCGGCCTT 61.968 63.158 0.00 0.00 36.56 4.35
3504 7610 2.135581 ACCCGACGGACTTTCACCA 61.136 57.895 17.49 0.00 0.00 4.17
3524 7630 1.437772 CCGTAGTCTCATCGTCGGCT 61.438 60.000 0.00 0.00 0.00 5.52
3579 7685 4.421479 CGTCGGCCTCTTCGCACT 62.421 66.667 0.00 0.00 0.00 4.40
3588 7694 0.392193 CTCTTCGCACTGGCCTCATT 60.392 55.000 3.32 0.00 36.38 2.57
3626 7732 2.411701 CGCAGGCCTTATCGTCGA 59.588 61.111 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 4.345859 AGGGAACGACACAAAACTATCA 57.654 40.909 0.00 0.00 0.00 2.15
137 138 2.685100 CCTTCTACAAGGGAACGACAC 58.315 52.381 0.00 0.00 45.27 3.67
158 159 6.466812 TCAGTCTGAACATATCTGAGCAAAA 58.533 36.000 0.00 0.00 36.77 2.44
211 214 0.986019 ACCTGATCCAACCGCCCATA 60.986 55.000 0.00 0.00 0.00 2.74
280 283 3.887110 ACACCATACCGACGATGAGATTA 59.113 43.478 0.00 0.00 0.00 1.75
315 318 1.640428 ACAATGACCGTATCTGCACG 58.360 50.000 0.00 0.00 41.59 5.34
325 328 5.794687 TCAGCAAACTATAACAATGACCG 57.205 39.130 0.00 0.00 0.00 4.79
354 357 0.468648 ATAACCTAAGGCGACCCAGC 59.531 55.000 0.00 0.00 0.00 4.85
356 359 3.264964 AGAAAATAACCTAAGGCGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
443 455 1.194547 GTCAACATCAACGACACGCAT 59.805 47.619 0.00 0.00 0.00 4.73
450 462 3.526534 TGAACACAGTCAACATCAACGA 58.473 40.909 0.00 0.00 0.00 3.85
456 468 5.555017 AGCTAGAATGAACACAGTCAACAT 58.445 37.500 0.00 0.00 32.13 2.71
469 481 3.254411 CGGTCTCTGCATAGCTAGAATGA 59.746 47.826 0.00 0.00 0.00 2.57
521 533 4.854399 TGTTGGCTCAAAATGAAACGTAG 58.146 39.130 0.00 0.00 0.00 3.51
524 536 5.462034 TTTTGTTGGCTCAAAATGAAACG 57.538 34.783 13.78 0.00 40.73 3.60
568 580 3.400255 GGTATTTCTAACCGATCCCAGC 58.600 50.000 0.00 0.00 0.00 4.85
606 619 1.473677 TGCAGCTGTGGTTTATGCATC 59.526 47.619 16.64 0.00 41.65 3.91
717 4685 8.013378 CACGTCTCGTTTTATTGATACCTTTTT 58.987 33.333 0.00 0.00 38.32 1.94
718 4686 7.360607 CCACGTCTCGTTTTATTGATACCTTTT 60.361 37.037 0.00 0.00 38.32 2.27
719 4687 6.091713 CCACGTCTCGTTTTATTGATACCTTT 59.908 38.462 0.00 0.00 38.32 3.11
720 4688 5.579511 CCACGTCTCGTTTTATTGATACCTT 59.420 40.000 0.00 0.00 38.32 3.50
721 4689 5.107133 CCACGTCTCGTTTTATTGATACCT 58.893 41.667 0.00 0.00 38.32 3.08
722 4690 4.866486 ACCACGTCTCGTTTTATTGATACC 59.134 41.667 0.00 0.00 38.32 2.73
723 4691 5.346822 ACACCACGTCTCGTTTTATTGATAC 59.653 40.000 0.00 0.00 38.32 2.24
724 4692 5.472148 ACACCACGTCTCGTTTTATTGATA 58.528 37.500 0.00 0.00 38.32 2.15
725 4693 4.312443 ACACCACGTCTCGTTTTATTGAT 58.688 39.130 0.00 0.00 38.32 2.57
726 4694 3.719924 ACACCACGTCTCGTTTTATTGA 58.280 40.909 0.00 0.00 38.32 2.57
727 4695 4.461992 AACACCACGTCTCGTTTTATTG 57.538 40.909 0.00 0.00 38.32 1.90
728 4696 4.812626 AGAAACACCACGTCTCGTTTTATT 59.187 37.500 7.06 0.00 38.32 1.40
729 4697 4.374399 AGAAACACCACGTCTCGTTTTAT 58.626 39.130 7.06 0.00 38.32 1.40
730 4698 3.784338 AGAAACACCACGTCTCGTTTTA 58.216 40.909 7.06 0.00 38.32 1.52
731 4699 2.624636 AGAAACACCACGTCTCGTTTT 58.375 42.857 7.06 0.00 38.32 2.43
732 4700 2.304751 AGAAACACCACGTCTCGTTT 57.695 45.000 5.65 5.65 38.32 3.60
733 4701 2.360165 AGTAGAAACACCACGTCTCGTT 59.640 45.455 0.00 0.00 38.32 3.85
795 4768 2.680913 GCGGCGCTGCTTATATGGG 61.681 63.158 33.43 0.00 0.00 4.00
859 4836 2.512056 TGGTCAGGTTCCTCTCCAAAAA 59.488 45.455 8.38 0.00 0.00 1.94
861 4838 1.699634 CTGGTCAGGTTCCTCTCCAAA 59.300 52.381 10.88 0.00 0.00 3.28
862 4839 1.132849 TCTGGTCAGGTTCCTCTCCAA 60.133 52.381 10.88 3.26 0.00 3.53
863 4840 0.487325 TCTGGTCAGGTTCCTCTCCA 59.513 55.000 9.81 9.81 0.00 3.86
866 4843 1.827969 CGATTCTGGTCAGGTTCCTCT 59.172 52.381 0.00 0.00 0.00 3.69
867 4844 1.134670 CCGATTCTGGTCAGGTTCCTC 60.135 57.143 0.00 0.00 0.00 3.71
868 4845 0.905357 CCGATTCTGGTCAGGTTCCT 59.095 55.000 0.00 0.00 0.00 3.36
869 4846 0.902531 TCCGATTCTGGTCAGGTTCC 59.097 55.000 0.00 0.00 0.00 3.62
870 4847 1.275291 TGTCCGATTCTGGTCAGGTTC 59.725 52.381 0.00 0.00 0.00 3.62
871 4848 1.002087 GTGTCCGATTCTGGTCAGGTT 59.998 52.381 0.00 0.00 0.00 3.50
872 4849 0.608640 GTGTCCGATTCTGGTCAGGT 59.391 55.000 0.00 0.00 0.00 4.00
873 4850 0.458543 CGTGTCCGATTCTGGTCAGG 60.459 60.000 0.00 0.00 35.63 3.86
874 4851 0.526211 TCGTGTCCGATTCTGGTCAG 59.474 55.000 0.00 0.00 38.40 3.51
875 4852 0.963225 TTCGTGTCCGATTCTGGTCA 59.037 50.000 0.00 0.00 43.80 4.02
876 4853 1.347320 GTTCGTGTCCGATTCTGGTC 58.653 55.000 0.00 0.00 43.80 4.02
877 4854 0.037605 GGTTCGTGTCCGATTCTGGT 60.038 55.000 0.00 0.00 43.80 4.00
878 4855 0.739813 GGGTTCGTGTCCGATTCTGG 60.740 60.000 0.00 0.00 43.80 3.86
879 4856 0.246635 AGGGTTCGTGTCCGATTCTG 59.753 55.000 0.00 0.00 43.80 3.02
880 4857 1.475682 GTAGGGTTCGTGTCCGATTCT 59.524 52.381 0.00 0.00 43.80 2.40
881 4858 1.203052 TGTAGGGTTCGTGTCCGATTC 59.797 52.381 0.00 0.00 43.80 2.52
882 4859 1.067354 GTGTAGGGTTCGTGTCCGATT 60.067 52.381 0.00 0.00 43.80 3.34
883 4860 0.529378 GTGTAGGGTTCGTGTCCGAT 59.471 55.000 0.00 0.00 43.80 4.18
884 4861 1.855213 CGTGTAGGGTTCGTGTCCGA 61.855 60.000 0.00 0.00 42.41 4.55
885 4862 1.443194 CGTGTAGGGTTCGTGTCCG 60.443 63.158 0.00 0.00 0.00 4.79
886 4863 0.109412 CTCGTGTAGGGTTCGTGTCC 60.109 60.000 0.00 0.00 0.00 4.02
887 4864 0.595095 ACTCGTGTAGGGTTCGTGTC 59.405 55.000 0.00 0.00 0.00 3.67
888 4865 1.035139 AACTCGTGTAGGGTTCGTGT 58.965 50.000 0.00 0.00 40.01 4.49
889 4866 1.415374 CAACTCGTGTAGGGTTCGTG 58.585 55.000 0.00 0.00 42.80 4.35
890 4867 0.319297 GCAACTCGTGTAGGGTTCGT 60.319 55.000 0.00 0.00 42.80 3.85
891 4868 0.038526 AGCAACTCGTGTAGGGTTCG 60.039 55.000 0.00 0.00 42.80 3.95
895 4872 1.000955 ACTTGAGCAACTCGTGTAGGG 59.999 52.381 0.00 0.00 32.35 3.53
986 4964 3.197790 CCATGTCTGGCTTCCGCG 61.198 66.667 0.00 0.00 35.23 6.46
987 4965 2.109126 GTCCATGTCTGGCTTCCGC 61.109 63.158 0.00 0.00 42.80 5.54
988 4966 1.450312 GGTCCATGTCTGGCTTCCG 60.450 63.158 0.00 0.00 42.80 4.30
989 4967 0.393537 CTGGTCCATGTCTGGCTTCC 60.394 60.000 0.00 0.00 42.80 3.46
990 4968 0.615331 TCTGGTCCATGTCTGGCTTC 59.385 55.000 0.00 0.00 42.80 3.86
991 4969 0.326264 GTCTGGTCCATGTCTGGCTT 59.674 55.000 0.00 0.00 42.80 4.35
992 4970 1.557269 GGTCTGGTCCATGTCTGGCT 61.557 60.000 0.00 0.00 42.80 4.75
993 4971 1.078143 GGTCTGGTCCATGTCTGGC 60.078 63.158 0.00 0.00 42.80 4.85
994 4972 1.219124 CGGTCTGGTCCATGTCTGG 59.781 63.158 0.00 0.00 44.64 3.86
1281 5282 1.888018 CAAGAGGCCATTGCAGTGG 59.112 57.895 23.20 23.20 42.35 4.00
1290 5291 2.681976 GCTCTCATAAAGCAAGAGGCCA 60.682 50.000 5.01 0.00 46.50 5.36
1419 5420 2.423898 ATAGTGGGGTGAGACGGCG 61.424 63.158 4.80 4.80 0.00 6.46
1461 5462 0.890996 CAGGGTCCACTTTGTCAGGC 60.891 60.000 0.00 0.00 0.00 4.85
1740 5741 2.896243 TCGAGAAGTAGAAGTGCGAC 57.104 50.000 0.00 0.00 0.00 5.19
1762 5763 1.202188 GCCTTAAAGCACCGAAGCATC 60.202 52.381 2.02 0.00 36.85 3.91
1763 5764 0.811281 GCCTTAAAGCACCGAAGCAT 59.189 50.000 2.02 0.00 36.85 3.79
1764 5765 0.536233 TGCCTTAAAGCACCGAAGCA 60.536 50.000 0.00 0.00 38.00 3.91
1765 5766 2.253513 TGCCTTAAAGCACCGAAGC 58.746 52.632 0.00 0.00 38.00 3.86
1779 5780 5.070580 GTCATAGATACAAAGGTAGGTGCCT 59.929 44.000 0.00 0.00 41.41 4.75
1780 5781 5.163343 TGTCATAGATACAAAGGTAGGTGCC 60.163 44.000 0.00 0.00 31.88 5.01
1781 5782 5.914033 TGTCATAGATACAAAGGTAGGTGC 58.086 41.667 0.00 0.00 31.88 5.01
1782 5783 9.645059 CATATGTCATAGATACAAAGGTAGGTG 57.355 37.037 0.00 0.00 31.88 4.00
1783 5784 9.601810 TCATATGTCATAGATACAAAGGTAGGT 57.398 33.333 1.90 0.00 31.88 3.08
1785 5786 9.579768 GCTCATATGTCATAGATACAAAGGTAG 57.420 37.037 1.90 0.00 31.88 3.18
1786 5787 8.531982 GGCTCATATGTCATAGATACAAAGGTA 58.468 37.037 1.90 0.00 0.00 3.08
1787 5788 7.390027 GGCTCATATGTCATAGATACAAAGGT 58.610 38.462 1.90 0.00 0.00 3.50
1788 5789 6.820656 GGGCTCATATGTCATAGATACAAAGG 59.179 42.308 1.90 0.00 0.00 3.11
1789 5790 7.389232 TGGGCTCATATGTCATAGATACAAAG 58.611 38.462 1.90 0.00 0.00 2.77
1790 5791 7.315066 TGGGCTCATATGTCATAGATACAAA 57.685 36.000 1.90 0.00 0.00 2.83
1791 5792 6.933514 TGGGCTCATATGTCATAGATACAA 57.066 37.500 1.90 0.00 0.00 2.41
1792 5793 6.269769 TGTTGGGCTCATATGTCATAGATACA 59.730 38.462 1.90 0.00 0.00 2.29
1793 5794 6.701340 TGTTGGGCTCATATGTCATAGATAC 58.299 40.000 1.90 0.00 0.00 2.24
1794 5795 6.070596 CCTGTTGGGCTCATATGTCATAGATA 60.071 42.308 1.90 0.00 0.00 1.98
1795 5796 5.280368 CCTGTTGGGCTCATATGTCATAGAT 60.280 44.000 1.90 0.00 0.00 1.98
1796 5797 4.040829 CCTGTTGGGCTCATATGTCATAGA 59.959 45.833 1.90 0.00 0.00 1.98
1797 5798 4.202398 ACCTGTTGGGCTCATATGTCATAG 60.202 45.833 1.90 0.00 39.10 2.23
1798 5799 3.716353 ACCTGTTGGGCTCATATGTCATA 59.284 43.478 1.90 0.00 39.10 2.15
1799 5800 2.511218 ACCTGTTGGGCTCATATGTCAT 59.489 45.455 1.90 0.00 39.10 3.06
1800 5801 1.915489 ACCTGTTGGGCTCATATGTCA 59.085 47.619 1.90 0.00 39.10 3.58
1801 5802 2.292267 CACCTGTTGGGCTCATATGTC 58.708 52.381 1.90 0.00 39.10 3.06
1802 5803 1.064463 CCACCTGTTGGGCTCATATGT 60.064 52.381 1.90 0.00 42.54 2.29
1803 5804 1.683943 CCACCTGTTGGGCTCATATG 58.316 55.000 0.00 0.00 42.54 1.78
1813 5814 2.497792 TATGGGCCAGCCACCTGTTG 62.498 60.000 13.78 0.00 37.38 3.33
1814 5815 1.583784 ATATGGGCCAGCCACCTGTT 61.584 55.000 13.78 0.00 37.38 3.16
1815 5816 2.008723 ATATGGGCCAGCCACCTGT 61.009 57.895 13.78 0.00 37.38 4.00
1816 5817 1.529948 CATATGGGCCAGCCACCTG 60.530 63.158 13.78 0.00 38.85 4.00
1817 5818 1.999634 GACATATGGGCCAGCCACCT 62.000 60.000 13.78 0.00 37.98 4.00
1818 5819 1.529244 GACATATGGGCCAGCCACC 60.529 63.158 13.78 0.00 37.98 4.61
1819 5820 0.395586 TTGACATATGGGCCAGCCAC 60.396 55.000 13.78 2.96 37.98 5.01
1820 5821 0.557238 ATTGACATATGGGCCAGCCA 59.443 50.000 13.78 0.00 37.98 4.75
1821 5822 0.963962 CATTGACATATGGGCCAGCC 59.036 55.000 13.78 0.00 0.00 4.85
1822 5823 1.610522 GTCATTGACATATGGGCCAGC 59.389 52.381 13.78 0.00 32.09 4.85
1823 5824 2.233271 GGTCATTGACATATGGGCCAG 58.767 52.381 13.78 0.00 33.68 4.85
1824 5825 1.133513 GGGTCATTGACATATGGGCCA 60.134 52.381 18.09 9.61 33.68 5.36
1825 5826 1.133513 TGGGTCATTGACATATGGGCC 60.134 52.381 18.09 8.73 33.68 5.80
1826 5827 2.363306 TGGGTCATTGACATATGGGC 57.637 50.000 18.09 0.00 33.68 5.36
1827 5828 3.638160 CCTTTGGGTCATTGACATATGGG 59.362 47.826 18.09 10.15 33.68 4.00
1828 5829 3.068590 GCCTTTGGGTCATTGACATATGG 59.931 47.826 18.09 12.97 33.68 2.74
1829 5830 3.700539 TGCCTTTGGGTCATTGACATATG 59.299 43.478 18.09 0.00 33.68 1.78
1830 5831 3.956199 CTGCCTTTGGGTCATTGACATAT 59.044 43.478 18.09 0.00 33.68 1.78
1831 5832 3.355378 CTGCCTTTGGGTCATTGACATA 58.645 45.455 18.09 3.86 33.68 2.29
1832 5833 2.173519 CTGCCTTTGGGTCATTGACAT 58.826 47.619 18.09 0.00 33.68 3.06
1833 5834 1.619654 CTGCCTTTGGGTCATTGACA 58.380 50.000 18.09 0.00 33.68 3.58
1834 5835 0.890683 CCTGCCTTTGGGTCATTGAC 59.109 55.000 8.34 8.34 34.45 3.18
1835 5836 0.482446 ACCTGCCTTTGGGTCATTGA 59.518 50.000 0.00 0.00 34.45 2.57
1836 5837 0.604578 CACCTGCCTTTGGGTCATTG 59.395 55.000 0.00 0.00 32.95 2.82
1837 5838 1.187567 GCACCTGCCTTTGGGTCATT 61.188 55.000 0.00 0.00 32.95 2.57
1838 5839 1.607467 GCACCTGCCTTTGGGTCAT 60.607 57.895 0.00 0.00 32.95 3.06
1839 5840 2.203480 GCACCTGCCTTTGGGTCA 60.203 61.111 0.00 0.00 32.95 4.02
1856 5857 0.804989 CAGCTTCGGTGCCTTAAAGG 59.195 55.000 0.00 0.00 38.80 3.11
1865 5866 3.001902 TAGGGACGCAGCTTCGGTG 62.002 63.158 11.19 0.00 0.00 4.94
1866 5867 2.678934 TAGGGACGCAGCTTCGGT 60.679 61.111 11.19 0.00 0.00 4.69
1867 5868 2.202756 GTAGGGACGCAGCTTCGG 60.203 66.667 11.19 0.00 0.00 4.30
1868 5869 0.802607 GAAGTAGGGACGCAGCTTCG 60.803 60.000 3.63 3.63 0.00 3.79
1869 5870 0.533032 AGAAGTAGGGACGCAGCTTC 59.467 55.000 14.09 14.09 36.69 3.86
1870 5871 0.977395 AAGAAGTAGGGACGCAGCTT 59.023 50.000 0.00 0.00 0.00 3.74
1871 5872 0.977395 AAAGAAGTAGGGACGCAGCT 59.023 50.000 0.00 0.00 0.00 4.24
1872 5873 1.464997 CAAAAGAAGTAGGGACGCAGC 59.535 52.381 0.00 0.00 0.00 5.25
1873 5874 2.737252 GACAAAAGAAGTAGGGACGCAG 59.263 50.000 0.00 0.00 0.00 5.18
1874 5875 2.367567 AGACAAAAGAAGTAGGGACGCA 59.632 45.455 0.00 0.00 0.00 5.24
1875 5876 3.041508 AGACAAAAGAAGTAGGGACGC 57.958 47.619 0.00 0.00 0.00 5.19
1876 5877 5.780984 ACTAAGACAAAAGAAGTAGGGACG 58.219 41.667 0.00 0.00 0.00 4.79
1877 5878 6.812656 GCTACTAAGACAAAAGAAGTAGGGAC 59.187 42.308 9.22 0.00 39.87 4.46
1878 5879 6.932947 GCTACTAAGACAAAAGAAGTAGGGA 58.067 40.000 9.22 0.00 39.87 4.20
1879 5880 5.805994 CGCTACTAAGACAAAAGAAGTAGGG 59.194 44.000 9.51 9.51 43.04 3.53
1880 5881 6.388278 ACGCTACTAAGACAAAAGAAGTAGG 58.612 40.000 9.22 3.53 39.87 3.18
1881 5882 7.870588 AACGCTACTAAGACAAAAGAAGTAG 57.129 36.000 0.00 0.00 41.56 2.57
1882 5883 8.652810 AAAACGCTACTAAGACAAAAGAAGTA 57.347 30.769 0.00 0.00 0.00 2.24
1883 5884 7.494952 AGAAAACGCTACTAAGACAAAAGAAGT 59.505 33.333 0.00 0.00 0.00 3.01
1884 5885 7.852516 AGAAAACGCTACTAAGACAAAAGAAG 58.147 34.615 0.00 0.00 0.00 2.85
1885 5886 7.709613 AGAGAAAACGCTACTAAGACAAAAGAA 59.290 33.333 0.00 0.00 0.00 2.52
1886 5887 7.208080 AGAGAAAACGCTACTAAGACAAAAGA 58.792 34.615 0.00 0.00 0.00 2.52
1887 5888 7.409465 AGAGAAAACGCTACTAAGACAAAAG 57.591 36.000 0.00 0.00 0.00 2.27
1888 5889 7.781548 AAGAGAAAACGCTACTAAGACAAAA 57.218 32.000 0.00 0.00 0.00 2.44
1964 5992 8.181573 GTCCGACAAAGATAATCTGCAAAATTA 58.818 33.333 4.23 4.23 0.00 1.40
1990 6018 7.189512 GCATCTTAATTACTTGGTACTTGCTG 58.810 38.462 0.00 0.00 0.00 4.41
1991 6019 6.318900 GGCATCTTAATTACTTGGTACTTGCT 59.681 38.462 0.00 0.00 0.00 3.91
2214 6242 3.634397 TTTCAAATCCCTCGAGCTCAT 57.366 42.857 15.40 0.00 0.00 2.90
2248 6276 1.033574 ATTCTCGTCGTCCTCCATCC 58.966 55.000 0.00 0.00 0.00 3.51
2267 6295 0.043183 TCTGCTTCTCCCCATCTCCA 59.957 55.000 0.00 0.00 0.00 3.86
2269 6297 2.045524 TCATCTGCTTCTCCCCATCTC 58.954 52.381 0.00 0.00 0.00 2.75
2270 6298 2.187239 TCATCTGCTTCTCCCCATCT 57.813 50.000 0.00 0.00 0.00 2.90
2294 6322 3.067833 CACCGTTTTCTCCTTCTCCTTC 58.932 50.000 0.00 0.00 0.00 3.46
2317 6345 9.585099 CATTCTAGATTCTCTGGTATTAGCATC 57.415 37.037 0.00 0.00 0.00 3.91
2402 6430 1.675116 GCCAAGGAAGTAGACGTTCCC 60.675 57.143 0.00 0.00 44.12 3.97
2431 6459 4.647399 CCCAAGAAAACAACCTCCTTGTAA 59.353 41.667 0.00 0.00 42.70 2.41
2563 6591 2.785562 CAAGGGGTGTACGGAAATGAA 58.214 47.619 0.00 0.00 0.00 2.57
2594 6622 1.627329 TGAAGCATGACTCTGAAGCCT 59.373 47.619 0.00 0.00 0.00 4.58
2595 6623 2.105006 TGAAGCATGACTCTGAAGCC 57.895 50.000 0.00 0.00 0.00 4.35
2601 6629 2.094286 CGACTCCTTGAAGCATGACTCT 60.094 50.000 0.00 0.00 0.00 3.24
2602 6630 2.266554 CGACTCCTTGAAGCATGACTC 58.733 52.381 0.00 0.00 0.00 3.36
2604 6632 1.996191 GACGACTCCTTGAAGCATGAC 59.004 52.381 0.00 0.00 0.00 3.06
2626 6654 0.109272 TGCTCTAACTTCTGCGACGG 60.109 55.000 0.00 0.00 0.00 4.79
2627 6655 1.914634 ATGCTCTAACTTCTGCGACG 58.085 50.000 0.00 0.00 0.00 5.12
2628 6656 3.241804 CGAAATGCTCTAACTTCTGCGAC 60.242 47.826 0.00 0.00 0.00 5.19
2629 6657 2.923655 CGAAATGCTCTAACTTCTGCGA 59.076 45.455 0.00 0.00 0.00 5.10
2630 6658 2.029728 CCGAAATGCTCTAACTTCTGCG 59.970 50.000 0.00 0.00 0.00 5.18
2631 6659 2.223135 GCCGAAATGCTCTAACTTCTGC 60.223 50.000 0.00 0.00 0.00 4.26
2636 6664 2.770164 ACAGCCGAAATGCTCTAACT 57.230 45.000 0.00 0.00 40.32 2.24
2640 6668 1.537202 GTCAAACAGCCGAAATGCTCT 59.463 47.619 0.00 0.00 40.32 4.09
2649 6677 4.685169 ATATTGTTCAGTCAAACAGCCG 57.315 40.909 0.00 0.00 40.08 5.52
2650 6678 5.880332 TCCTATATTGTTCAGTCAAACAGCC 59.120 40.000 0.00 0.00 40.08 4.85
2659 6687 5.300286 GCTGCCATTTCCTATATTGTTCAGT 59.700 40.000 0.00 0.00 0.00 3.41
2672 6700 0.532115 AAACATCGGCTGCCATTTCC 59.468 50.000 20.29 0.00 0.00 3.13
2700 6728 6.015504 CGAGAACATCATCAAAGGTAAAACG 58.984 40.000 0.00 0.00 0.00 3.60
2716 6744 2.808543 GGAGCAGTTTCAACGAGAACAT 59.191 45.455 0.00 0.00 35.56 2.71
2724 6752 3.744559 TGCCGGAGCAGTTTCAAC 58.255 55.556 5.05 0.00 46.52 3.18
2754 6782 5.796350 AATGATACAGAACGCAGGTTAAC 57.204 39.130 0.00 0.00 36.24 2.01
2791 6851 5.785243 AGACTTCTTGGCACTTAACTAGAC 58.215 41.667 0.00 0.00 0.00 2.59
2813 6873 4.219288 ACCAGAGAAATGCAAAAGGCTAAG 59.781 41.667 0.00 0.00 45.15 2.18
2816 6876 2.601905 ACCAGAGAAATGCAAAAGGCT 58.398 42.857 0.00 0.00 45.15 4.58
2817 6877 3.391506 AACCAGAGAAATGCAAAAGGC 57.608 42.857 0.00 0.00 45.13 4.35
2818 6878 5.205759 AGAAACCAGAGAAATGCAAAAGG 57.794 39.130 0.00 0.00 0.00 3.11
2819 6879 6.275335 TGAAGAAACCAGAGAAATGCAAAAG 58.725 36.000 0.00 0.00 0.00 2.27
2872 6937 6.019559 CGGTTGTACATGTCTACTCATTCATG 60.020 42.308 0.00 0.00 42.00 3.07
2878 6943 5.654603 ATTCGGTTGTACATGTCTACTCA 57.345 39.130 0.00 0.00 0.00 3.41
2884 6949 3.723835 GCACGAATTCGGTTGTACATGTC 60.724 47.826 29.79 10.11 44.95 3.06
2923 6991 2.157738 CAGAAGAACCCAAAGCTCAGG 58.842 52.381 0.00 0.00 0.00 3.86
2945 7013 4.445453 CATCCAAGTGAATCATCGAGGAA 58.555 43.478 2.91 0.00 0.00 3.36
2993 7061 2.971330 TCAATTTCATTGGCAGGTGGTT 59.029 40.909 2.71 0.00 40.61 3.67
3027 7096 6.918892 TCTTCTGTCAATTTCGTTTGAAGA 57.081 33.333 0.00 0.00 37.36 2.87
3051 7120 2.036256 GCCACAGCTGGGATGGTT 59.964 61.111 20.22 0.00 38.13 3.67
3122 7213 1.650363 CCACGTTCCGTTTTGGGTC 59.350 57.895 0.00 0.00 38.32 4.46
3123 7214 1.824760 CCCACGTTCCGTTTTGGGT 60.825 57.895 0.00 0.00 38.32 4.51
3210 7303 8.240682 CCATTATTCGTCAGACCAAACAAAATA 58.759 33.333 0.00 0.00 0.00 1.40
3220 7313 1.935933 ACGCCATTATTCGTCAGACC 58.064 50.000 0.00 0.00 33.09 3.85
3277 7370 6.466308 CGAATCTATGGCATTATTCGTCAA 57.534 37.500 29.99 5.40 43.39 3.18
3403 7497 2.432300 CCGGTGTAAGGAGGCCGAT 61.432 63.158 0.00 0.00 46.33 4.18
3414 7508 2.265424 GGCGTTAAGGCCGGTGTA 59.735 61.111 22.38 0.00 44.40 2.90
3504 7610 1.712977 GCCGACGATGAGACTACGGT 61.713 60.000 0.00 0.00 41.92 4.83
3588 7694 4.704833 GCGAAGGTCTGCCAGGCA 62.705 66.667 15.23 15.23 37.19 4.75


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

AutoCloner maintained by Alex Coulton.