Multiple sequence alignment - TraesCS7A01G444200

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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 TraesCS7A01G444200 chr7A 100.000 5701 0 0 1 5701 638691849 638697549 0.000000e+00 10528.0
1 TraesCS7A01G444200 chr7A 93.276 699 42 4 1 694 668818405 668817707 0.000000e+00 1026.0
2 TraesCS7A01G444200 chr7A 92.396 697 46 5 3 692 28124776 28124080 0.000000e+00 987.0
3 TraesCS7A01G444200 chr7A 83.190 696 99 15 1 686 240006784 240007471 6.270000e-174 621.0
4 TraesCS7A01G444200 chr7A 93.600 125 5 3 5177 5300 645026051 645026173 3.510000e-42 183.0
5 TraesCS7A01G444200 chr7B 93.661 1893 95 11 1813 3692 644517829 644519709 0.000000e+00 2808.0
6 TraesCS7A01G444200 chr7B 91.815 1686 76 23 962 2611 597693916 597695575 0.000000e+00 2292.0
7 TraesCS7A01G444200 chr7B 91.053 1330 84 19 3702 5005 597696657 597697977 0.000000e+00 1764.0
8 TraesCS7A01G444200 chr7B 90.744 1048 66 12 2647 3690 597695575 597696595 0.000000e+00 1369.0
9 TraesCS7A01G444200 chr7B 89.548 775 49 14 3789 4542 644525163 644525926 0.000000e+00 953.0
10 TraesCS7A01G444200 chr7B 86.230 748 44 28 1105 1802 644508315 644509053 0.000000e+00 756.0
11 TraesCS7A01G444200 chr7B 79.606 711 108 22 3 695 147159368 147160059 5.170000e-130 475.0
12 TraesCS7A01G444200 chr7B 97.015 67 2 0 779 845 597693837 597693903 4.670000e-21 113.0
13 TraesCS7A01G444200 chr7B 96.429 56 2 0 3739 3794 644519787 644519842 6.080000e-15 93.5
14 TraesCS7A01G444200 chr7B 97.059 34 0 1 5296 5329 598446295 598446327 7.980000e-04 56.5
15 TraesCS7A01G444200 chr7D 91.161 1946 78 40 728 2611 552946695 552948608 0.000000e+00 2555.0
16 TraesCS7A01G444200 chr7D 90.722 1509 89 29 3702 5187 552949728 552951208 0.000000e+00 1964.0
17 TraesCS7A01G444200 chr7D 93.673 1059 54 3 2647 3692 552948608 552949666 0.000000e+00 1572.0
18 TraesCS7A01G444200 chr7D 93.974 697 38 2 1 693 21790363 21789667 0.000000e+00 1051.0
19 TraesCS7A01G444200 chr7D 86.667 705 75 11 1 693 87370175 87369478 0.000000e+00 763.0
20 TraesCS7A01G444200 chr7D 90.452 199 13 3 5295 5489 552951204 552951400 2.040000e-64 257.0
21 TraesCS7A01G444200 chr7D 96.522 115 2 2 5178 5292 227507233 227507121 7.540000e-44 189.0
22 TraesCS7A01G444200 chr7D 93.846 65 4 0 1327 1391 242337135 242337071 1.310000e-16 99.0
23 TraesCS7A01G444200 chr7D 84.848 99 10 2 4827 4920 552955165 552955263 1.690000e-15 95.3
24 TraesCS7A01G444200 chr3A 83.381 1047 124 28 1589 2610 707348900 707347879 0.000000e+00 924.0
25 TraesCS7A01G444200 chr3A 85.792 549 64 7 3138 3685 707347506 707346971 2.300000e-158 569.0
26 TraesCS7A01G444200 chr3A 81.459 658 88 19 4095 4739 707346509 707345873 5.100000e-140 508.0
27 TraesCS7A01G444200 chr3A 95.906 171 7 0 1327 1497 707349200 707349030 1.560000e-70 278.0
28 TraesCS7A01G444200 chr5D 82.870 864 111 21 2855 3686 374261450 374262308 0.000000e+00 741.0
29 TraesCS7A01G444200 chr5D 92.208 77 4 2 1984 2060 374261162 374261236 2.170000e-19 108.0
30 TraesCS7A01G444200 chr5D 95.385 65 3 0 1327 1391 441286944 441286880 2.810000e-18 104.0
31 TraesCS7A01G444200 chr2B 85.265 699 83 11 1 686 748574149 748573458 0.000000e+00 702.0
32 TraesCS7A01G444200 chr5A 90.698 387 22 3 1 386 410532336 410532709 2.370000e-138 503.0
33 TraesCS7A01G444200 chr5A 88.852 305 21 9 382 686 410550166 410550457 4.200000e-96 363.0
34 TraesCS7A01G444200 chr5A 96.491 114 4 0 5180 5293 657200315 657200428 7.540000e-44 189.0
35 TraesCS7A01G444200 chr4B 80.916 655 94 17 55 693 617206260 617206899 6.640000e-134 488.0
36 TraesCS7A01G444200 chr5B 80.190 631 94 14 75 686 309468140 309468758 1.460000e-120 444.0
37 TraesCS7A01G444200 chr5B 85.348 273 23 4 3417 3689 446032576 446032321 3.390000e-67 267.0
38 TraesCS7A01G444200 chr5B 92.500 80 6 0 1984 2063 446039832 446039753 1.300000e-21 115.0
39 TraesCS7A01G444200 chr5B 89.655 58 6 0 1444 1501 181360843 181360900 2.200000e-09 75.0
40 TraesCS7A01G444200 chr1B 95.833 120 5 0 5173 5292 386204473 386204592 1.620000e-45 195.0
41 TraesCS7A01G444200 chr1D 98.182 110 2 0 5186 5295 48024729 48024620 5.830000e-45 193.0
42 TraesCS7A01G444200 chr3B 96.491 114 4 0 5179 5292 52786605 52786718 7.540000e-44 189.0
43 TraesCS7A01G444200 chr3D 97.273 110 3 0 5185 5294 381640808 381640917 2.710000e-43 187.0
44 TraesCS7A01G444200 chr3D 84.034 119 13 3 1273 1391 580252122 580252234 6.040000e-20 110.0
45 TraesCS7A01G444200 chr3D 87.097 62 8 0 1440 1501 33040859 33040920 2.850000e-08 71.3
46 TraesCS7A01G444200 chr2D 94.262 122 6 1 5186 5307 155516976 155517096 9.750000e-43 185.0
47 TraesCS7A01G444200 chr2D 95.455 44 1 1 1327 1369 583746626 583746583 1.020000e-07 69.4
48 TraesCS7A01G444200 chr6D 96.396 111 4 0 5182 5292 67156538 67156428 3.510000e-42 183.0
49 TraesCS7A01G444200 chr6D 91.549 71 5 1 1327 1397 76998187 76998118 4.700000e-16 97.1
50 TraesCS7A01G444200 chr6D 86.207 58 8 0 1444 1501 76998120 76998063 4.770000e-06 63.9


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 TraesCS7A01G444200 chr7A 638691849 638697549 5700 False 10528.00 10528 100.00000 1 5701 1 chr7A.!!$F2 5700
1 TraesCS7A01G444200 chr7A 668817707 668818405 698 True 1026.00 1026 93.27600 1 694 1 chr7A.!!$R2 693
2 TraesCS7A01G444200 chr7A 28124080 28124776 696 True 987.00 987 92.39600 3 692 1 chr7A.!!$R1 689
3 TraesCS7A01G444200 chr7A 240006784 240007471 687 False 621.00 621 83.19000 1 686 1 chr7A.!!$F1 685
4 TraesCS7A01G444200 chr7B 644517829 644519842 2013 False 1450.75 2808 95.04500 1813 3794 2 chr7B.!!$F6 1981
5 TraesCS7A01G444200 chr7B 597693837 597697977 4140 False 1384.50 2292 92.65675 779 5005 4 chr7B.!!$F5 4226
6 TraesCS7A01G444200 chr7B 644525163 644525926 763 False 953.00 953 89.54800 3789 4542 1 chr7B.!!$F4 753
7 TraesCS7A01G444200 chr7B 644508315 644509053 738 False 756.00 756 86.23000 1105 1802 1 chr7B.!!$F3 697
8 TraesCS7A01G444200 chr7B 147159368 147160059 691 False 475.00 475 79.60600 3 695 1 chr7B.!!$F1 692
9 TraesCS7A01G444200 chr7D 552946695 552955263 8568 False 1288.66 2555 90.17120 728 5489 5 chr7D.!!$F1 4761
10 TraesCS7A01G444200 chr7D 21789667 21790363 696 True 1051.00 1051 93.97400 1 693 1 chr7D.!!$R1 692
11 TraesCS7A01G444200 chr7D 87369478 87370175 697 True 763.00 763 86.66700 1 693 1 chr7D.!!$R2 692
12 TraesCS7A01G444200 chr3A 707345873 707349200 3327 True 569.75 924 86.63450 1327 4739 4 chr3A.!!$R1 3412
13 TraesCS7A01G444200 chr5D 374261162 374262308 1146 False 424.50 741 87.53900 1984 3686 2 chr5D.!!$F1 1702
14 TraesCS7A01G444200 chr2B 748573458 748574149 691 True 702.00 702 85.26500 1 686 1 chr2B.!!$R1 685
15 TraesCS7A01G444200 chr4B 617206260 617206899 639 False 488.00 488 80.91600 55 693 1 chr4B.!!$F1 638
16 TraesCS7A01G444200 chr5B 309468140 309468758 618 False 444.00 444 80.19000 75 686 1 chr5B.!!$F2 611

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
530 559 0.108804 CGGCGTTCCAGAGTATGTGT 60.109 55.000 0.0 0.0 0.00 3.72 F
771 801 0.404426 TCGGTCTCCTTCTGTCCTGA 59.596 55.000 0.0 0.0 0.00 3.86 F
1591 1738 0.178967 TGTGATGTGGGTGGCAATGT 60.179 50.000 0.0 0.0 0.00 2.71 F
2601 2769 1.001378 CTTCACCCTGGCAAAAGTTCG 60.001 52.381 0.0 0.0 0.00 3.95 F
3876 4161 0.031857 CATTTTGGTGCTTCACGGCA 59.968 50.000 0.0 0.0 40.15 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1653 0.036388 TGATCGACCAACAGAAGGGC 60.036 55.0 0.00 0.0 0.00 5.19 R
2726 2894 0.244721 GCAGATCAAACAGGGTTGGC 59.755 55.0 0.00 0.0 0.00 4.52 R
2750 2918 0.251916 TTGATCCTGTTAGTGGGCGG 59.748 55.0 0.00 0.0 0.00 6.13 R
4319 4679 0.248661 CCAGTCGTATGGAGCAGTCG 60.249 60.0 2.94 0.0 43.57 4.18 R
5182 5568 0.037303 TCTGAACGGAGGGAGTACGT 59.963 55.0 0.00 0.0 43.43 3.57 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
43 44 1.667236 CCAAGGCTTGCATCGTATGA 58.333 50.000 21.77 0.00 0.00 2.15
199 209 6.824196 TGATGTGTTTTGTTTGTACCAGAGTA 59.176 34.615 0.00 0.00 0.00 2.59
295 308 3.676291 AATTAATTGCCAACCGTTGCT 57.324 38.095 5.68 0.00 0.00 3.91
376 391 8.840833 TTCTCTTTATTATATATTGCGCACCA 57.159 30.769 11.12 0.00 0.00 4.17
501 518 0.325296 ATAAGTCGGTGCAGGGAGGA 60.325 55.000 0.00 0.00 0.00 3.71
530 559 0.108804 CGGCGTTCCAGAGTATGTGT 60.109 55.000 0.00 0.00 0.00 3.72
592 621 5.416639 GTGGATAGCATGATTATCATTGGCA 59.583 40.000 16.34 6.32 34.28 4.92
615 644 1.478510 GATGGTGAAGAGGAGAAGCGA 59.521 52.381 0.00 0.00 0.00 4.93
626 655 5.498393 AGAGGAGAAGCGATAATACGGATA 58.502 41.667 0.00 0.00 0.00 2.59
634 663 3.192001 GCGATAATACGGATAGGTCACCA 59.808 47.826 0.00 0.00 0.00 4.17
635 664 4.142227 GCGATAATACGGATAGGTCACCAT 60.142 45.833 0.00 0.00 0.00 3.55
686 716 3.037431 TGCAACGCAAAGGCATATTTT 57.963 38.095 0.00 0.00 41.24 1.82
687 717 3.397482 TGCAACGCAAAGGCATATTTTT 58.603 36.364 0.00 0.00 41.24 1.94
707 737 5.710513 TTTTAGTAAGAGACCTACGTGCA 57.289 39.130 0.00 0.00 0.00 4.57
708 738 5.710513 TTTAGTAAGAGACCTACGTGCAA 57.289 39.130 0.00 0.00 0.00 4.08
709 739 3.572604 AGTAAGAGACCTACGTGCAAC 57.427 47.619 0.00 0.00 0.00 4.17
721 751 3.399879 GTGCAACGTGGCAAATAGG 57.600 52.632 21.54 0.00 46.93 2.57
722 752 0.878416 GTGCAACGTGGCAAATAGGA 59.122 50.000 21.54 0.00 46.93 2.94
723 753 1.135689 GTGCAACGTGGCAAATAGGAG 60.136 52.381 21.54 0.00 46.93 3.69
724 754 1.165270 GCAACGTGGCAAATAGGAGT 58.835 50.000 10.88 0.00 0.00 3.85
725 755 1.135689 GCAACGTGGCAAATAGGAGTG 60.136 52.381 10.88 0.00 0.00 3.51
726 756 1.468520 CAACGTGGCAAATAGGAGTGG 59.531 52.381 0.00 0.00 0.00 4.00
732 762 2.180204 CAAATAGGAGTGGCCCGCG 61.180 63.158 0.00 0.00 37.37 6.46
750 780 3.450115 GCTAGACCGCGGTCCACT 61.450 66.667 45.66 33.15 45.59 4.00
754 784 4.477975 GACCGCGGTCCACTCTCG 62.478 72.222 41.88 8.64 39.08 4.04
760 790 2.408241 CGGTCCACTCTCGGTCTCC 61.408 68.421 0.00 0.00 0.00 3.71
763 793 0.812549 GTCCACTCTCGGTCTCCTTC 59.187 60.000 0.00 0.00 0.00 3.46
766 796 1.540267 CACTCTCGGTCTCCTTCTGT 58.460 55.000 0.00 0.00 0.00 3.41
771 801 0.404426 TCGGTCTCCTTCTGTCCTGA 59.596 55.000 0.00 0.00 0.00 3.86
896 949 1.718361 CGCCGCGTAATCAATCAATCG 60.718 52.381 4.92 0.00 0.00 3.34
1500 1590 1.043116 CCGATGGCTACCTGGTGAGA 61.043 60.000 10.23 0.00 0.00 3.27
1501 1591 1.043816 CGATGGCTACCTGGTGAGAT 58.956 55.000 10.23 0.00 0.00 2.75
1502 1592 1.269988 CGATGGCTACCTGGTGAGATG 60.270 57.143 10.23 0.00 0.00 2.90
1507 1597 2.622436 GCTACCTGGTGAGATGAACAC 58.378 52.381 10.23 0.00 37.51 3.32
1508 1598 2.881074 CTACCTGGTGAGATGAACACG 58.119 52.381 10.23 0.00 38.90 4.49
1518 1608 1.819288 AGATGAACACGGACGATGAGT 59.181 47.619 0.00 0.00 0.00 3.41
1527 1617 2.682893 GACGATGAGTCCACCATGC 58.317 57.895 0.00 0.00 43.95 4.06
1541 1648 2.488937 CACCATGCTGTAGATTGTTGCA 59.511 45.455 0.00 0.00 38.05 4.08
1546 1653 5.062934 CCATGCTGTAGATTGTTGCATTTTG 59.937 40.000 0.00 0.00 41.65 2.44
1549 1684 3.924144 TGTAGATTGTTGCATTTTGCCC 58.076 40.909 0.00 0.00 44.23 5.36
1551 1686 3.775261 AGATTGTTGCATTTTGCCCTT 57.225 38.095 0.00 0.00 44.23 3.95
1552 1687 3.667360 AGATTGTTGCATTTTGCCCTTC 58.333 40.909 0.00 0.00 44.23 3.46
1555 1690 1.761784 TGTTGCATTTTGCCCTTCTGT 59.238 42.857 0.00 0.00 44.23 3.41
1557 1692 2.529780 TGCATTTTGCCCTTCTGTTG 57.470 45.000 0.00 0.00 44.23 3.33
1558 1693 1.070445 TGCATTTTGCCCTTCTGTTGG 59.930 47.619 0.00 0.00 44.23 3.77
1562 1697 0.181587 TTTGCCCTTCTGTTGGTCGA 59.818 50.000 0.00 0.00 0.00 4.20
1569 1704 2.625737 CTTCTGTTGGTCGATCATGCT 58.374 47.619 0.00 0.00 0.00 3.79
1587 1734 0.322726 CTGATGTGATGTGGGTGGCA 60.323 55.000 0.00 0.00 0.00 4.92
1591 1738 0.178967 TGTGATGTGGGTGGCAATGT 60.179 50.000 0.00 0.00 0.00 2.71
1787 1934 3.479269 CTCGCGCAGGTTCGGAAC 61.479 66.667 12.41 12.41 0.00 3.62
1848 2014 5.708230 TGGTTACATTTGGAAGCTAACGAAT 59.292 36.000 6.31 0.00 0.00 3.34
1982 2148 1.442148 GGCTTACCTCCTACCGCTG 59.558 63.158 0.00 0.00 0.00 5.18
2144 2310 1.002366 ATTGCTCACGCTGTCGAATC 58.998 50.000 0.00 0.00 39.41 2.52
2222 2388 4.820173 CCTGGAGGGTATTTCGTTTATTCC 59.180 45.833 0.00 0.00 0.00 3.01
2254 2420 3.127203 GCTTATGCTCATCATGATCCAGC 59.873 47.826 21.96 21.96 36.63 4.85
2407 2573 1.589716 GCACTTCCTCCCATGTGTGC 61.590 60.000 0.00 0.00 42.69 4.57
2500 2666 1.888512 GCTCACTTTCCTGATTTGCCA 59.111 47.619 0.00 0.00 0.00 4.92
2509 2675 5.643379 TTCCTGATTTGCCACAAGATTAC 57.357 39.130 0.00 0.00 0.00 1.89
2558 2725 9.678260 ATCTATTGTATTGTCTCTTGCTTTCTT 57.322 29.630 0.00 0.00 0.00 2.52
2559 2726 9.155975 TCTATTGTATTGTCTCTTGCTTTCTTC 57.844 33.333 0.00 0.00 0.00 2.87
2560 2727 7.992754 ATTGTATTGTCTCTTGCTTTCTTCT 57.007 32.000 0.00 0.00 0.00 2.85
2562 2729 8.539770 TTGTATTGTCTCTTGCTTTCTTCTAG 57.460 34.615 0.00 0.00 0.00 2.43
2563 2730 7.671302 TGTATTGTCTCTTGCTTTCTTCTAGT 58.329 34.615 0.00 0.00 0.00 2.57
2564 2731 7.600375 TGTATTGTCTCTTGCTTTCTTCTAGTG 59.400 37.037 0.00 0.00 0.00 2.74
2601 2769 1.001378 CTTCACCCTGGCAAAAGTTCG 60.001 52.381 0.00 0.00 0.00 3.95
2664 2832 3.954258 AGCCATAACCCTTTATTGAGCAC 59.046 43.478 0.00 0.00 0.00 4.40
2750 2918 3.073274 ACCCTGTTTGATCTGCCTTAC 57.927 47.619 0.00 0.00 0.00 2.34
2775 2943 3.081804 CCACTAACAGGATCAAACCACC 58.918 50.000 0.00 0.00 0.00 4.61
2783 2951 1.620822 GATCAAACCACCTGTTGCCT 58.379 50.000 0.00 0.00 37.23 4.75
2797 2965 2.012673 GTTGCCTGCTCTATCACTTGG 58.987 52.381 0.00 0.00 0.00 3.61
2805 2973 5.102953 TGCTCTATCACTTGGCATTAAGT 57.897 39.130 0.00 0.00 41.37 2.24
2872 3051 2.232941 CTCTTTGCTGGCCATGACAATT 59.767 45.455 5.51 0.00 0.00 2.32
2895 3074 1.228800 TGCATGCCACCACCATTGA 60.229 52.632 16.68 0.00 0.00 2.57
3215 3424 1.812571 CTTGTGCCCTGATGGTGTAAC 59.187 52.381 0.00 0.00 36.04 2.50
3254 3463 4.938226 CAGGAGTTAACAAGGCTAAAGGAG 59.062 45.833 8.61 0.00 0.00 3.69
3302 3511 3.953775 CAGCACCACCCCCTCGTT 61.954 66.667 0.00 0.00 0.00 3.85
3353 3562 8.133627 AGAATTTTTCTGAAGACAATGTGAGTG 58.866 33.333 0.00 0.00 38.91 3.51
3354 3570 6.757897 TTTTTCTGAAGACAATGTGAGTGT 57.242 33.333 0.00 0.00 0.00 3.55
3363 3579 6.889301 AGACAATGTGAGTGTTTTGATGAT 57.111 33.333 0.00 0.00 0.00 2.45
3408 3624 4.349048 CACCCTTCCCAGATGATGATCTTA 59.651 45.833 0.00 0.00 36.75 2.10
3589 3805 4.757149 GGATGTCTGGGTAATGAATGTAGC 59.243 45.833 0.00 0.00 0.00 3.58
3654 3870 4.339247 GTGGTTTGATAGGGACAATCCATG 59.661 45.833 0.00 0.00 43.88 3.66
3686 3902 8.918202 AAGATGTTTGTGAAATACCTTCTGTA 57.082 30.769 0.00 0.00 34.86 2.74
3821 4098 3.378911 TTGACAAGTGCTCATACGTGA 57.621 42.857 0.00 0.00 34.72 4.35
3874 4159 1.602668 CCACATTTTGGTGCTTCACGG 60.603 52.381 0.00 0.00 41.10 4.94
3875 4160 0.031994 ACATTTTGGTGCTTCACGGC 59.968 50.000 0.00 0.00 34.83 5.68
3876 4161 0.031857 CATTTTGGTGCTTCACGGCA 59.968 50.000 0.00 0.00 40.15 5.69
3878 4163 1.034838 TTTTGGTGCTTCACGGCAGT 61.035 50.000 0.00 0.00 43.25 4.40
3879 4164 1.034838 TTTGGTGCTTCACGGCAGTT 61.035 50.000 0.00 0.00 43.25 3.16
3881 4166 0.179043 TGGTGCTTCACGGCAGTTTA 60.179 50.000 0.00 0.00 43.25 2.01
3883 4168 1.135689 GGTGCTTCACGGCAGTTTATG 60.136 52.381 0.00 0.00 43.25 1.90
3885 4170 2.031157 GTGCTTCACGGCAGTTTATGTT 60.031 45.455 0.00 0.00 43.25 2.71
3886 4171 2.621055 TGCTTCACGGCAGTTTATGTTT 59.379 40.909 0.00 0.00 37.29 2.83
3888 4173 3.821841 CTTCACGGCAGTTTATGTTTCC 58.178 45.455 0.00 0.00 0.00 3.13
3889 4174 2.156098 TCACGGCAGTTTATGTTTCCC 58.844 47.619 0.00 0.00 0.00 3.97
3956 4302 6.667007 TGTCATTATACTGAATGCACACTG 57.333 37.500 0.00 0.00 36.85 3.66
4049 4401 3.895232 TTTCCTTCCTAGCTGCTACAG 57.105 47.619 5.02 0.00 34.12 2.74
4071 4423 1.274447 AGTACCCTGCCGTTAACTGAC 59.726 52.381 3.71 0.00 0.00 3.51
4319 4679 5.346181 ACTTGATGCTTCCTAGTTCCTAC 57.654 43.478 0.00 0.00 0.00 3.18
4335 4695 1.002684 CCTACGACTGCTCCATACGAC 60.003 57.143 0.00 0.00 0.00 4.34
4430 4791 1.226323 CTACGACCTCCTTCACGCG 60.226 63.158 3.53 3.53 0.00 6.01
4658 5022 6.534436 CAGATGATGAAAGAGTCTTGATCGTT 59.466 38.462 6.06 3.70 31.76 3.85
4719 5083 1.561250 CAAGCAAGCGCAAAACTGC 59.439 52.632 11.47 10.22 42.27 4.40
4741 5116 8.317679 ACTGCTCTTGTTCTGATCTTATTAACT 58.682 33.333 0.00 0.00 0.00 2.24
4754 5129 6.790285 TCTTATTAACTGTCGTTTCCCAAC 57.210 37.500 0.00 0.00 34.59 3.77
4757 5132 1.578583 AACTGTCGTTTCCCAACTCG 58.421 50.000 0.00 0.00 0.00 4.18
4767 5142 4.251268 GTTTCCCAACTCGTAGCTGTATT 58.749 43.478 0.00 0.00 0.00 1.89
4771 5146 7.534723 TTCCCAACTCGTAGCTGTATTATAT 57.465 36.000 0.00 0.00 0.00 0.86
4772 5147 6.920817 TCCCAACTCGTAGCTGTATTATATG 58.079 40.000 0.00 0.00 0.00 1.78
4787 5162 8.123639 TGTATTATATGGTAGTTCTCTGCCTC 57.876 38.462 4.27 0.00 44.89 4.70
4788 5163 7.950684 TGTATTATATGGTAGTTCTCTGCCTCT 59.049 37.037 4.27 0.00 44.89 3.69
4797 5172 4.357325 AGTTCTCTGCCTCTTCCATTAGA 58.643 43.478 0.00 0.00 0.00 2.10
4802 5177 4.836825 TCTGCCTCTTCCATTAGAACTTG 58.163 43.478 0.00 0.00 0.00 3.16
4803 5178 3.347216 TGCCTCTTCCATTAGAACTTGC 58.653 45.455 0.00 0.00 0.00 4.01
4878 5253 6.461577 AGAGATAGGAGGAGTATGACATGA 57.538 41.667 0.00 0.00 0.00 3.07
4910 5285 6.376978 CAGACTTCAATGGTTCAGAATTCAC 58.623 40.000 8.44 0.00 0.00 3.18
4917 5292 4.163441 TGGTTCAGAATTCACAGGACAA 57.837 40.909 8.44 0.00 0.00 3.18
4979 5360 5.964758 TGATGCCATTTTAGAATTGACACC 58.035 37.500 0.00 0.00 0.00 4.16
5010 5391 3.261580 GCCATTGGCCATTACTTTTCAC 58.738 45.455 17.28 0.00 44.06 3.18
5015 5396 2.811431 TGGCCATTACTTTTCACGTCAG 59.189 45.455 0.00 0.00 0.00 3.51
5032 5413 4.871557 ACGTCAGTGTGTTAGTAAAAAGCA 59.128 37.500 0.00 0.00 0.00 3.91
5107 5488 7.814264 AAGTTCATGTCTCTTTTTGTCTGAT 57.186 32.000 0.00 0.00 0.00 2.90
5111 5492 8.725148 GTTCATGTCTCTTTTTGTCTGATATGT 58.275 33.333 0.00 0.00 31.37 2.29
5112 5493 8.853077 TCATGTCTCTTTTTGTCTGATATGTT 57.147 30.769 0.00 0.00 31.37 2.71
5164 5550 9.997482 GATGAAATTTCCGCTTAATTAAGTACA 57.003 29.630 22.94 7.37 35.75 2.90
5169 5555 6.913873 TTCCGCTTAATTAAGTACATGGTC 57.086 37.500 22.94 6.21 35.75 4.02
5170 5556 6.229936 TCCGCTTAATTAAGTACATGGTCT 57.770 37.500 22.94 0.00 35.75 3.85
5173 5559 7.286087 TCCGCTTAATTAAGTACATGGTCTCTA 59.714 37.037 22.94 3.28 35.75 2.43
5184 5570 3.509388 GGTCTCTAACCCACACACG 57.491 57.895 0.00 0.00 42.85 4.49
5185 5571 0.677842 GGTCTCTAACCCACACACGT 59.322 55.000 0.00 0.00 42.85 4.49
5186 5572 1.888512 GGTCTCTAACCCACACACGTA 59.111 52.381 0.00 0.00 42.85 3.57
5187 5573 2.352127 GGTCTCTAACCCACACACGTAC 60.352 54.545 0.00 0.00 42.85 3.67
5188 5574 2.555757 GTCTCTAACCCACACACGTACT 59.444 50.000 0.00 0.00 0.00 2.73
5189 5575 2.816087 TCTCTAACCCACACACGTACTC 59.184 50.000 0.00 0.00 0.00 2.59
5190 5576 1.888512 TCTAACCCACACACGTACTCC 59.111 52.381 0.00 0.00 0.00 3.85
5191 5577 0.968405 TAACCCACACACGTACTCCC 59.032 55.000 0.00 0.00 0.00 4.30
5192 5578 0.761702 AACCCACACACGTACTCCCT 60.762 55.000 0.00 0.00 0.00 4.20
5193 5579 1.183676 ACCCACACACGTACTCCCTC 61.184 60.000 0.00 0.00 0.00 4.30
5194 5580 1.590147 CCACACACGTACTCCCTCC 59.410 63.158 0.00 0.00 0.00 4.30
5195 5581 1.211969 CACACACGTACTCCCTCCG 59.788 63.158 0.00 0.00 0.00 4.63
5196 5582 1.228367 ACACACGTACTCCCTCCGT 60.228 57.895 0.00 0.00 34.71 4.69
5197 5583 0.825010 ACACACGTACTCCCTCCGTT 60.825 55.000 0.00 0.00 31.46 4.44
5198 5584 0.109412 CACACGTACTCCCTCCGTTC 60.109 60.000 0.00 0.00 31.46 3.95
5199 5585 0.538057 ACACGTACTCCCTCCGTTCA 60.538 55.000 0.00 0.00 31.46 3.18
5200 5586 0.170561 CACGTACTCCCTCCGTTCAG 59.829 60.000 0.00 0.00 31.46 3.02
5201 5587 0.037303 ACGTACTCCCTCCGTTCAGA 59.963 55.000 0.00 0.00 0.00 3.27
5202 5588 1.171308 CGTACTCCCTCCGTTCAGAA 58.829 55.000 0.00 0.00 0.00 3.02
5203 5589 1.749634 CGTACTCCCTCCGTTCAGAAT 59.250 52.381 0.00 0.00 0.00 2.40
5204 5590 2.165845 CGTACTCCCTCCGTTCAGAATT 59.834 50.000 0.00 0.00 0.00 2.17
5205 5591 3.379372 CGTACTCCCTCCGTTCAGAATTA 59.621 47.826 0.00 0.00 0.00 1.40
5206 5592 3.889520 ACTCCCTCCGTTCAGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
5207 5593 3.442076 ACTCCCTCCGTTCAGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
5208 5594 3.838903 ACTCCCTCCGTTCAGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
5209 5595 4.184629 CTCCCTCCGTTCAGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
5210 5596 3.581332 TCCCTCCGTTCAGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
5211 5597 3.933332 CCCTCCGTTCAGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
5212 5598 3.612860 CCTCCGTTCAGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
5213 5599 2.991190 TCCGTTCAGAATTACTTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
5214 5600 2.734606 CCGTTCAGAATTACTTGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
5215 5601 3.181530 CCGTTCAGAATTACTTGTCGCAG 60.182 47.826 0.00 0.00 0.00 5.18
5216 5602 3.673338 CGTTCAGAATTACTTGTCGCAGA 59.327 43.478 0.00 0.00 0.00 4.26
5217 5603 4.149922 CGTTCAGAATTACTTGTCGCAGAA 59.850 41.667 0.00 0.00 39.69 3.02
5218 5604 5.333035 CGTTCAGAATTACTTGTCGCAGAAA 60.333 40.000 0.00 0.00 39.69 2.52
5219 5605 6.603095 GTTCAGAATTACTTGTCGCAGAAAT 58.397 36.000 0.00 0.00 39.69 2.17
5220 5606 7.411480 CGTTCAGAATTACTTGTCGCAGAAATA 60.411 37.037 0.00 0.00 39.69 1.40
5221 5607 7.525688 TCAGAATTACTTGTCGCAGAAATAG 57.474 36.000 0.00 0.00 39.69 1.73
5222 5608 7.320399 TCAGAATTACTTGTCGCAGAAATAGA 58.680 34.615 0.00 0.00 39.69 1.98
5223 5609 7.981789 TCAGAATTACTTGTCGCAGAAATAGAT 59.018 33.333 0.00 0.00 39.69 1.98
5224 5610 8.060679 CAGAATTACTTGTCGCAGAAATAGATG 58.939 37.037 0.00 0.00 39.69 2.90
5225 5611 7.766278 AGAATTACTTGTCGCAGAAATAGATGT 59.234 33.333 0.00 0.00 39.69 3.06
5226 5612 8.942338 AATTACTTGTCGCAGAAATAGATGTA 57.058 30.769 0.00 0.00 39.69 2.29
5227 5613 9.547753 AATTACTTGTCGCAGAAATAGATGTAT 57.452 29.630 0.00 0.00 39.69 2.29
5228 5614 8.575565 TTACTTGTCGCAGAAATAGATGTATC 57.424 34.615 0.00 0.00 39.69 2.24
5229 5615 6.810911 ACTTGTCGCAGAAATAGATGTATCT 58.189 36.000 0.00 0.00 39.69 1.98
5230 5616 7.941919 ACTTGTCGCAGAAATAGATGTATCTA 58.058 34.615 4.22 4.22 40.45 1.98
5231 5617 8.079203 ACTTGTCGCAGAAATAGATGTATCTAG 58.921 37.037 7.57 0.00 39.84 2.43
5232 5618 7.745620 TGTCGCAGAAATAGATGTATCTAGA 57.254 36.000 7.57 0.00 39.84 2.43
5233 5619 7.585867 TGTCGCAGAAATAGATGTATCTAGAC 58.414 38.462 0.00 7.60 39.84 2.59
5234 5620 6.739100 GTCGCAGAAATAGATGTATCTAGACG 59.261 42.308 0.00 5.27 39.84 4.18
5235 5621 6.427242 TCGCAGAAATAGATGTATCTAGACGT 59.573 38.462 0.00 0.00 42.20 4.34
5236 5622 7.601508 TCGCAGAAATAGATGTATCTAGACGTA 59.398 37.037 0.00 0.00 42.20 3.57
5237 5623 8.391859 CGCAGAAATAGATGTATCTAGACGTAT 58.608 37.037 0.00 0.00 42.20 3.06
5263 5649 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
5264 5650 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
5265 5651 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
5266 5652 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
5267 5653 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
5268 5654 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
5269 5655 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
5270 5656 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
5271 5657 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
5272 5658 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
5273 5659 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
5274 5660 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
5275 5661 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
5276 5662 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
5277 5663 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
5278 5664 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
5279 5665 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
5280 5666 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
5281 5667 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
5282 5668 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
5283 5669 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
5284 5670 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
5285 5671 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
5286 5672 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
5287 5673 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
5288 5674 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
5289 5675 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
5290 5676 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
5291 5677 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
5292 5678 1.856629 ATTCCGAACGGAGGGAGTAA 58.143 50.000 15.34 0.34 46.06 2.24
5293 5679 1.180029 TTCCGAACGGAGGGAGTAAG 58.820 55.000 15.34 0.00 46.06 2.34
5325 5711 1.069090 GGTCTGGTCTCGTGCAACA 59.931 57.895 0.00 0.00 35.74 3.33
5364 5754 4.953868 TCCCGCAACCGTGACACG 62.954 66.667 21.02 21.02 42.11 4.49
5381 5771 2.343758 GCTCTCCTTGCACCGACA 59.656 61.111 0.00 0.00 0.00 4.35
5402 5792 2.437180 CCATGGCTGAGCTGCGAA 60.437 61.111 3.72 0.00 0.00 4.70
5420 5810 3.712187 CGAAGGAGAAACTAGGAGATGC 58.288 50.000 0.00 0.00 0.00 3.91
5422 5812 2.035632 AGGAGAAACTAGGAGATGCCG 58.964 52.381 0.00 0.00 43.43 5.69
5436 5826 2.281484 GCCGAGGTGAACCAGCAA 60.281 61.111 1.62 0.00 38.89 3.91
5439 5829 0.535102 CCGAGGTGAACCAGCAAAGT 60.535 55.000 1.62 0.00 38.89 2.66
5441 5831 1.798813 CGAGGTGAACCAGCAAAGTAC 59.201 52.381 1.62 0.00 38.89 2.73
5446 5836 3.568007 GGTGAACCAGCAAAGTACATGAA 59.432 43.478 0.00 0.00 35.64 2.57
5499 6285 8.776061 AGAGCTAGGTCTGAAGTAGATATTTT 57.224 34.615 23.27 0.00 37.83 1.82
5531 6317 7.568199 ACTCCAAAATAACAAGAATATCCGG 57.432 36.000 0.00 0.00 0.00 5.14
5535 6321 8.441572 TCCAAAATAACAAGAATATCCGGGATA 58.558 33.333 18.62 18.62 0.00 2.59
5645 6472 6.459670 AAGGAAACCGTAACATTTTTCAGT 57.540 33.333 0.00 0.00 30.88 3.41
5656 6483 7.326063 CGTAACATTTTTCAGTGGATTTCCTTC 59.674 37.037 0.00 0.00 36.82 3.46
5658 6485 6.515832 ACATTTTTCAGTGGATTTCCTTCAC 58.484 36.000 0.00 0.00 36.82 3.18
5663 6490 4.541705 TCAGTGGATTTCCTTCACCAAAA 58.458 39.130 0.00 0.00 36.82 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.225491 CCTTGGCGACGATTTCTTCAAA 59.775 45.455 0.00 0.00 0.00 2.69
12 13 0.321653 AGCCTTGGCGACGATTTCTT 60.322 50.000 5.95 0.00 0.00 2.52
143 153 6.128254 GGTTAAAAATCAGGCTACAGAGACAC 60.128 42.308 0.00 0.00 30.20 3.67
150 160 4.830046 TGCAAGGTTAAAAATCAGGCTACA 59.170 37.500 0.00 0.00 0.00 2.74
199 209 0.819582 AAATATCCACGTCCGACCGT 59.180 50.000 0.00 0.00 42.87 4.83
234 244 6.539103 GGTTTCATACACCTTCTTCATCCTAC 59.461 42.308 0.00 0.00 0.00 3.18
376 391 9.153721 CATTGTATGCAATTGTTCTTTTACCAT 57.846 29.630 6.26 1.37 42.91 3.55
592 621 2.354203 GCTTCTCCTCTTCACCATCGTT 60.354 50.000 0.00 0.00 0.00 3.85
598 627 3.802948 TTATCGCTTCTCCTCTTCACC 57.197 47.619 0.00 0.00 0.00 4.02
615 644 6.127140 GCCTAATGGTGACCTATCCGTATTAT 60.127 42.308 2.11 0.00 35.27 1.28
626 655 1.915489 TCATGTGCCTAATGGTGACCT 59.085 47.619 2.11 0.00 35.27 3.85
634 663 8.370182 AGAAACAAATCTTTTCATGTGCCTAAT 58.630 29.630 0.00 0.00 35.72 1.73
635 664 7.725251 AGAAACAAATCTTTTCATGTGCCTAA 58.275 30.769 0.00 0.00 35.72 2.69
686 716 5.464168 GTTGCACGTAGGTCTCTTACTAAA 58.536 41.667 0.00 0.00 0.00 1.85
687 717 4.378770 CGTTGCACGTAGGTCTCTTACTAA 60.379 45.833 0.00 0.00 36.74 2.24
703 733 0.878416 TCCTATTTGCCACGTTGCAC 59.122 50.000 14.66 0.00 41.88 4.57
704 734 1.164411 CTCCTATTTGCCACGTTGCA 58.836 50.000 10.70 10.70 40.07 4.08
705 735 1.135689 CACTCCTATTTGCCACGTTGC 60.136 52.381 4.35 4.35 0.00 4.17
706 736 1.468520 CCACTCCTATTTGCCACGTTG 59.531 52.381 0.00 0.00 0.00 4.10
707 737 1.821216 CCACTCCTATTTGCCACGTT 58.179 50.000 0.00 0.00 0.00 3.99
708 738 0.676782 GCCACTCCTATTTGCCACGT 60.677 55.000 0.00 0.00 0.00 4.49
709 739 1.376609 GGCCACTCCTATTTGCCACG 61.377 60.000 0.00 0.00 41.76 4.94
710 740 1.037579 GGGCCACTCCTATTTGCCAC 61.038 60.000 4.39 0.00 43.96 5.01
711 741 1.306296 GGGCCACTCCTATTTGCCA 59.694 57.895 4.39 0.00 43.96 4.92
712 742 1.823899 CGGGCCACTCCTATTTGCC 60.824 63.158 4.39 0.00 41.42 4.52
713 743 2.481471 GCGGGCCACTCCTATTTGC 61.481 63.158 4.39 0.00 34.39 3.68
714 744 2.180204 CGCGGGCCACTCCTATTTG 61.180 63.158 4.39 0.00 34.39 2.32
715 745 2.189521 CGCGGGCCACTCCTATTT 59.810 61.111 4.39 0.00 34.39 1.40
716 746 3.861797 CCGCGGGCCACTCCTATT 61.862 66.667 20.10 0.00 34.39 1.73
732 762 4.509737 GTGGACCGCGGTCTAGCC 62.510 72.222 46.25 35.13 44.04 3.93
734 764 1.716826 GAGAGTGGACCGCGGTCTAG 61.717 65.000 46.25 17.66 44.04 2.43
750 780 0.699399 AGGACAGAAGGAGACCGAGA 59.301 55.000 0.00 0.00 0.00 4.04
754 784 0.534873 GCTCAGGACAGAAGGAGACC 59.465 60.000 0.00 0.00 0.00 3.85
760 790 1.298014 GGGTGGCTCAGGACAGAAG 59.702 63.158 0.00 0.00 0.00 2.85
763 793 3.721706 GGGGGTGGCTCAGGACAG 61.722 72.222 0.00 0.00 0.00 3.51
896 949 2.385315 TGCTCGTTGATTCGATCGATC 58.615 47.619 20.18 15.68 39.12 3.69
904 961 2.401195 GCGGCTGCTCGTTGATTC 59.599 61.111 11.21 0.00 38.39 2.52
1111 1168 4.135153 GAGGCAGAGGAGCGCGAA 62.135 66.667 12.10 0.00 34.64 4.70
1500 1590 2.279582 GACTCATCGTCCGTGTTCAT 57.720 50.000 0.00 0.00 36.62 2.57
1501 1591 3.786809 GACTCATCGTCCGTGTTCA 57.213 52.632 0.00 0.00 36.62 3.18
1518 1608 3.346315 CAACAATCTACAGCATGGTGGA 58.654 45.455 27.32 19.56 43.62 4.02
1525 1615 3.989167 GCAAAATGCAACAATCTACAGCA 59.011 39.130 0.00 0.00 44.26 4.41
1541 1648 1.613437 CGACCAACAGAAGGGCAAAAT 59.387 47.619 0.00 0.00 31.91 1.82
1546 1653 0.036388 TGATCGACCAACAGAAGGGC 60.036 55.000 0.00 0.00 0.00 5.19
1549 1684 2.350804 CAGCATGATCGACCAACAGAAG 59.649 50.000 0.00 0.00 39.69 2.85
1551 1686 1.550072 TCAGCATGATCGACCAACAGA 59.450 47.619 0.00 0.00 42.56 3.41
1552 1687 2.014335 TCAGCATGATCGACCAACAG 57.986 50.000 0.00 0.00 42.56 3.16
1569 1704 0.112025 TTGCCACCCACATCACATCA 59.888 50.000 0.00 0.00 0.00 3.07
1587 1734 2.026262 ACCTGATCGGCACCTAAACATT 60.026 45.455 0.00 0.00 35.61 2.71
1591 1738 0.251916 CCACCTGATCGGCACCTAAA 59.748 55.000 0.00 0.00 35.61 1.85
1620 1767 2.989824 CGTCCACACCTCGTCCCT 60.990 66.667 0.00 0.00 0.00 4.20
1816 1971 5.452636 GCTTCCAAATGTAACCAAAAGGTGA 60.453 40.000 0.00 0.00 0.00 4.02
2144 2310 0.742281 CATCCCTCTGCAACCAGTCG 60.742 60.000 0.00 0.00 40.09 4.18
2222 2388 1.483827 TGAGCATAAGCCTCTGGTGAG 59.516 52.381 0.00 0.00 43.56 3.51
2254 2420 4.039245 TCTGCTTCCATATCTTCCGGTTAG 59.961 45.833 0.00 0.00 0.00 2.34
2407 2573 2.791655 CATCTGGGTCATCATCATGGG 58.208 52.381 0.00 0.00 0.00 4.00
2532 2698 9.678260 AAGAAAGCAAGAGACAATACAATAGAT 57.322 29.630 0.00 0.00 0.00 1.98
2542 2708 5.918608 ACACTAGAAGAAAGCAAGAGACAA 58.081 37.500 0.00 0.00 0.00 3.18
2557 2724 9.944376 AAGTATATTTCAAGCAGAACACTAGAA 57.056 29.630 0.00 0.00 35.56 2.10
2558 2725 9.587772 GAAGTATATTTCAAGCAGAACACTAGA 57.412 33.333 0.00 0.00 35.56 2.43
2559 2726 9.371136 TGAAGTATATTTCAAGCAGAACACTAG 57.629 33.333 8.12 0.00 35.56 2.57
2560 2727 9.151471 GTGAAGTATATTTCAAGCAGAACACTA 57.849 33.333 11.80 0.00 38.69 2.74
2561 2728 7.119846 GGTGAAGTATATTTCAAGCAGAACACT 59.880 37.037 11.80 0.00 38.69 3.55
2562 2729 7.244192 GGTGAAGTATATTTCAAGCAGAACAC 58.756 38.462 11.80 0.00 38.69 3.32
2563 2730 6.374333 GGGTGAAGTATATTTCAAGCAGAACA 59.626 38.462 11.80 0.00 38.69 3.18
2564 2731 6.599638 AGGGTGAAGTATATTTCAAGCAGAAC 59.400 38.462 11.80 0.00 38.69 3.01
2601 2769 3.120060 CCTTTGTCTGCTCTAACATGTGC 60.120 47.826 0.00 0.00 0.00 4.57
2664 2832 7.726033 ACCCTTCTATATTATGACTAGCCAG 57.274 40.000 0.00 0.00 0.00 4.85
2726 2894 0.244721 GCAGATCAAACAGGGTTGGC 59.755 55.000 0.00 0.00 0.00 4.52
2750 2918 0.251916 TTGATCCTGTTAGTGGGCGG 59.748 55.000 0.00 0.00 0.00 6.13
2775 2943 2.676839 CAAGTGATAGAGCAGGCAACAG 59.323 50.000 0.00 0.00 41.41 3.16
2783 2951 5.102953 ACTTAATGCCAAGTGATAGAGCA 57.897 39.130 0.00 0.00 37.37 4.26
2797 2965 2.035066 GGGGCACATGATGACTTAATGC 59.965 50.000 0.00 0.00 36.10 3.56
2805 2973 2.785269 AGAATAAGGGGGCACATGATGA 59.215 45.455 0.00 0.00 0.00 2.92
2999 3190 8.989980 ACTACTACAGTTTCAAACTAGAAATGC 58.010 33.333 1.43 0.00 40.46 3.56
3072 3265 6.653320 TCTTTATTAACAGTTACAGCACCAGG 59.347 38.462 0.00 0.00 0.00 4.45
3128 3321 5.998363 GGAAGAACTACAAGTGAAGTTGGAT 59.002 40.000 3.10 0.00 36.10 3.41
3177 3371 5.163663 GCACAAGTATGCTAGCCAACATTTA 60.164 40.000 13.29 0.00 42.62 1.40
3180 3374 2.684881 GCACAAGTATGCTAGCCAACAT 59.315 45.455 13.29 0.92 42.62 2.71
3196 3390 1.880221 CGTTACACCATCAGGGCACAA 60.880 52.381 0.00 0.00 42.05 3.33
3246 3455 2.003301 GAAGCAGTTCGGCTCCTTTAG 58.997 52.381 0.00 0.00 45.07 1.85
3254 3463 2.747855 CCAGGGAAGCAGTTCGGC 60.748 66.667 0.00 0.00 32.92 5.54
3255 3464 2.747855 GCCAGGGAAGCAGTTCGG 60.748 66.667 0.00 0.00 32.92 4.30
3302 3511 5.879763 TGAACTGATTCCAATCTCTTCCAA 58.120 37.500 1.13 0.00 36.39 3.53
3363 3579 4.337836 TGCGGCTTCATATAGCAAAATCAA 59.662 37.500 0.00 0.00 43.02 2.57
3408 3624 6.270231 AGACAGTATTCCAAGGTTAGACACTT 59.730 38.462 0.00 0.00 0.00 3.16
3589 3805 3.386932 TTCCAGATTCCATGAAAGGGG 57.613 47.619 0.00 0.00 39.14 4.79
3654 3870 7.390718 AGGTATTTCACAAACATCTTACCAGTC 59.609 37.037 0.00 0.00 32.18 3.51
3874 4159 7.425606 CCAACATATAGGGAAACATAAACTGC 58.574 38.462 0.00 0.00 0.00 4.40
3888 4173 6.769512 ACTATTGCTACACCCAACATATAGG 58.230 40.000 0.00 0.00 0.00 2.57
3889 4174 9.944376 AATACTATTGCTACACCCAACATATAG 57.056 33.333 0.00 0.00 0.00 1.31
4049 4401 2.028748 TCAGTTAACGGCAGGGTACTTC 60.029 50.000 0.31 0.00 0.00 3.01
4071 4423 1.600023 TACAGTTTTTCCAGTGCCCG 58.400 50.000 0.00 0.00 0.00 6.13
4151 4507 7.814264 ATCAAGAATGGAAACTATTAGGCAG 57.186 36.000 0.00 0.00 0.00 4.85
4319 4679 0.248661 CCAGTCGTATGGAGCAGTCG 60.249 60.000 2.94 0.00 43.57 4.18
4335 4695 7.976135 ATAAATAGAATCAAGCAGTAGCCAG 57.024 36.000 0.00 0.00 43.56 4.85
4430 4791 1.261480 TCTCAGAGAACAGGAGCCAC 58.739 55.000 0.00 0.00 0.00 5.01
4636 4997 6.983307 CCTAACGATCAAGACTCTTTCATCAT 59.017 38.462 0.00 1.22 0.00 2.45
4637 5001 6.152831 TCCTAACGATCAAGACTCTTTCATCA 59.847 38.462 0.00 0.00 0.00 3.07
4658 5022 4.163427 CCTGATCCCATAGCTTCTTCCTA 58.837 47.826 0.00 0.00 0.00 2.94
4719 5083 8.802856 CGACAGTTAATAAGATCAGAACAAGAG 58.197 37.037 0.00 0.00 0.00 2.85
4741 5116 1.603678 GCTACGAGTTGGGAAACGACA 60.604 52.381 0.00 0.00 35.81 4.35
4754 5129 8.948145 AGAACTACCATATAATACAGCTACGAG 58.052 37.037 0.00 0.00 0.00 4.18
4767 5142 5.775701 GGAAGAGGCAGAGAACTACCATATA 59.224 44.000 0.00 0.00 32.22 0.86
4771 5146 2.180276 GGAAGAGGCAGAGAACTACCA 58.820 52.381 0.00 0.00 32.22 3.25
4772 5147 2.180276 TGGAAGAGGCAGAGAACTACC 58.820 52.381 0.00 0.00 0.00 3.18
4783 5158 3.127721 GTGCAAGTTCTAATGGAAGAGGC 59.872 47.826 0.00 0.00 34.23 4.70
4787 5162 4.516698 AGTGTGTGCAAGTTCTAATGGAAG 59.483 41.667 0.00 0.00 34.23 3.46
4788 5163 4.460263 AGTGTGTGCAAGTTCTAATGGAA 58.540 39.130 0.00 0.00 0.00 3.53
4797 5172 4.718961 AGAAAGGATAGTGTGTGCAAGTT 58.281 39.130 0.00 0.00 0.00 2.66
4802 5177 2.271800 CGGAGAAAGGATAGTGTGTGC 58.728 52.381 0.00 0.00 0.00 4.57
4803 5178 2.271800 GCGGAGAAAGGATAGTGTGTG 58.728 52.381 0.00 0.00 0.00 3.82
4878 5253 3.825328 ACCATTGAAGTCTGCAACTCTT 58.175 40.909 0.00 0.64 37.17 2.85
4910 5285 2.863401 TCGACGACCATATTGTCCTG 57.137 50.000 0.00 0.00 38.38 3.86
4917 5292 6.706270 AGATTAGCATTTTTCGACGACCATAT 59.294 34.615 0.00 0.00 0.00 1.78
5010 5391 5.398176 TGCTTTTTACTAACACACTGACG 57.602 39.130 0.00 0.00 0.00 4.35
5072 5453 5.406780 AGAGACATGAACTTAAGCTTTGACG 59.593 40.000 3.20 0.00 0.00 4.35
5074 5455 7.807977 AAAGAGACATGAACTTAAGCTTTGA 57.192 32.000 3.20 0.00 0.00 2.69
5169 5555 2.094854 GGAGTACGTGTGTGGGTTAGAG 60.095 54.545 0.00 0.00 0.00 2.43
5170 5556 1.888512 GGAGTACGTGTGTGGGTTAGA 59.111 52.381 0.00 0.00 0.00 2.10
5173 5559 0.761702 AGGGAGTACGTGTGTGGGTT 60.762 55.000 0.00 0.00 0.00 4.11
5182 5568 0.037303 TCTGAACGGAGGGAGTACGT 59.963 55.000 0.00 0.00 43.43 3.57
5183 5569 1.171308 TTCTGAACGGAGGGAGTACG 58.829 55.000 0.00 0.00 0.00 3.67
5184 5570 3.889520 AATTCTGAACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
5185 5571 4.607239 AGTAATTCTGAACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
5186 5572 3.442076 AGTAATTCTGAACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
5187 5573 4.184629 CAAGTAATTCTGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
5188 5574 3.581332 ACAAGTAATTCTGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
5189 5575 3.933332 GACAAGTAATTCTGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
5190 5576 3.612860 CGACAAGTAATTCTGAACGGAGG 59.387 47.826 0.00 0.00 0.00 4.30
5191 5577 3.060895 GCGACAAGTAATTCTGAACGGAG 59.939 47.826 0.00 0.00 0.00 4.63
5192 5578 2.991190 GCGACAAGTAATTCTGAACGGA 59.009 45.455 0.00 0.00 0.00 4.69
5193 5579 2.734606 TGCGACAAGTAATTCTGAACGG 59.265 45.455 0.00 0.00 0.00 4.44
5194 5580 3.673338 TCTGCGACAAGTAATTCTGAACG 59.327 43.478 0.00 0.00 0.00 3.95
5195 5581 5.591643 TTCTGCGACAAGTAATTCTGAAC 57.408 39.130 0.00 0.00 0.00 3.18
5196 5582 6.801539 ATTTCTGCGACAAGTAATTCTGAA 57.198 33.333 0.00 0.00 0.00 3.02
5197 5583 7.320399 TCTATTTCTGCGACAAGTAATTCTGA 58.680 34.615 0.00 0.00 0.00 3.27
5198 5584 7.525688 TCTATTTCTGCGACAAGTAATTCTG 57.474 36.000 0.00 0.00 0.00 3.02
5199 5585 7.766278 ACATCTATTTCTGCGACAAGTAATTCT 59.234 33.333 0.00 0.00 0.00 2.40
5200 5586 7.910304 ACATCTATTTCTGCGACAAGTAATTC 58.090 34.615 0.00 0.00 0.00 2.17
5201 5587 7.849804 ACATCTATTTCTGCGACAAGTAATT 57.150 32.000 0.00 0.00 0.00 1.40
5202 5588 9.197694 GATACATCTATTTCTGCGACAAGTAAT 57.802 33.333 0.00 0.00 0.00 1.89
5203 5589 8.414003 AGATACATCTATTTCTGCGACAAGTAA 58.586 33.333 0.00 0.00 34.85 2.24
5204 5590 7.941919 AGATACATCTATTTCTGCGACAAGTA 58.058 34.615 0.00 0.00 34.85 2.24
5205 5591 6.810911 AGATACATCTATTTCTGCGACAAGT 58.189 36.000 0.00 0.00 34.85 3.16
5206 5592 8.293157 TCTAGATACATCTATTTCTGCGACAAG 58.707 37.037 0.00 0.00 38.60 3.16
5207 5593 8.076781 GTCTAGATACATCTATTTCTGCGACAA 58.923 37.037 0.00 0.00 38.60 3.18
5208 5594 7.571428 CGTCTAGATACATCTATTTCTGCGACA 60.571 40.741 0.00 0.00 38.60 4.35
5209 5595 6.739100 CGTCTAGATACATCTATTTCTGCGAC 59.261 42.308 0.00 2.21 38.60 5.19
5210 5596 6.427242 ACGTCTAGATACATCTATTTCTGCGA 59.573 38.462 0.00 0.00 38.60 5.10
5211 5597 6.604012 ACGTCTAGATACATCTATTTCTGCG 58.396 40.000 0.00 0.00 38.60 5.18
5237 5623 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
5238 5624 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
5239 5625 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
5240 5626 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
5241 5627 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
5242 5628 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
5243 5629 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
5244 5630 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
5245 5631 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
5246 5632 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
5247 5633 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
5248 5634 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
5249 5635 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
5250 5636 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
5251 5637 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
5252 5638 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
5253 5639 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
5254 5640 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
5255 5641 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
5256 5642 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
5257 5643 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
5258 5644 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
5259 5645 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
5260 5646 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
5261 5647 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
5262 5648 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
5263 5649 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
5264 5650 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
5265 5651 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
5266 5652 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
5267 5653 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
5268 5654 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
5269 5655 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
5270 5656 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
5271 5657 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
5272 5658 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
5273 5659 1.755380 CTTACTCCCTCCGTTCGGAAT 59.245 52.381 14.79 2.09 33.41 3.01
5274 5660 1.180029 CTTACTCCCTCCGTTCGGAA 58.820 55.000 14.79 0.04 33.41 4.30
5275 5661 0.329261 TCTTACTCCCTCCGTTCGGA 59.671 55.000 13.34 13.34 0.00 4.55
5276 5662 0.455005 GTCTTACTCCCTCCGTTCGG 59.545 60.000 4.74 4.74 0.00 4.30
5277 5663 0.098376 CGTCTTACTCCCTCCGTTCG 59.902 60.000 0.00 0.00 0.00 3.95
5278 5664 1.172175 ACGTCTTACTCCCTCCGTTC 58.828 55.000 0.00 0.00 0.00 3.95
5279 5665 2.489722 GTTACGTCTTACTCCCTCCGTT 59.510 50.000 0.00 0.00 0.00 4.44
5280 5666 2.087646 GTTACGTCTTACTCCCTCCGT 58.912 52.381 0.00 0.00 0.00 4.69
5281 5667 1.403323 GGTTACGTCTTACTCCCTCCG 59.597 57.143 0.00 0.00 0.00 4.63
5282 5668 2.450476 TGGTTACGTCTTACTCCCTCC 58.550 52.381 0.00 0.00 0.00 4.30
5283 5669 4.401837 AGATTGGTTACGTCTTACTCCCTC 59.598 45.833 0.00 0.00 0.00 4.30
5284 5670 4.159879 CAGATTGGTTACGTCTTACTCCCT 59.840 45.833 0.00 0.00 0.00 4.20
5285 5671 4.430908 CAGATTGGTTACGTCTTACTCCC 58.569 47.826 0.00 0.00 0.00 4.30
5286 5672 4.430908 CCAGATTGGTTACGTCTTACTCC 58.569 47.826 0.00 0.00 31.35 3.85
5325 5711 1.830587 TTCCGAGTGACAGCATGCCT 61.831 55.000 15.66 3.13 42.53 4.75
5364 5754 2.029844 GTGTCGGTGCAAGGAGAGC 61.030 63.158 0.00 0.00 0.00 4.09
5365 5755 1.374758 GGTGTCGGTGCAAGGAGAG 60.375 63.158 0.00 0.00 0.00 3.20
5402 5792 2.035632 CGGCATCTCCTAGTTTCTCCT 58.964 52.381 0.00 0.00 0.00 3.69
5411 5801 1.112113 GTTCACCTCGGCATCTCCTA 58.888 55.000 0.00 0.00 0.00 2.94
5413 5803 1.153349 GGTTCACCTCGGCATCTCC 60.153 63.158 0.00 0.00 0.00 3.71
5420 5810 0.535102 ACTTTGCTGGTTCACCTCGG 60.535 55.000 0.00 0.00 36.82 4.63
5422 5812 2.846193 TGTACTTTGCTGGTTCACCTC 58.154 47.619 0.00 0.00 36.82 3.85
5518 6304 5.640158 TTTGGTATCCCGGATATTCTTGT 57.360 39.130 10.43 0.00 0.00 3.16
5528 6314 3.150767 TCAACAACTTTTGGTATCCCGG 58.849 45.455 0.00 0.00 34.12 5.73
5529 6315 4.839668 TTCAACAACTTTTGGTATCCCG 57.160 40.909 0.00 0.00 34.12 5.14
5531 6317 9.535878 TTGTAATTTCAACAACTTTTGGTATCC 57.464 29.630 0.00 0.00 32.07 2.59
5615 6404 7.875327 AAATGTTACGGTTTCCTTAGCATAT 57.125 32.000 3.14 0.00 30.54 1.78
5616 6405 7.690952 AAAATGTTACGGTTTCCTTAGCATA 57.309 32.000 3.14 0.00 30.54 3.14
5617 6406 6.584185 AAAATGTTACGGTTTCCTTAGCAT 57.416 33.333 0.00 0.00 32.43 3.79
5618 6407 6.039493 TGAAAAATGTTACGGTTTCCTTAGCA 59.961 34.615 0.00 0.00 0.00 3.49
5620 6409 7.589954 CACTGAAAAATGTTACGGTTTCCTTAG 59.410 37.037 0.00 0.00 0.00 2.18
5621 6410 7.419204 CACTGAAAAATGTTACGGTTTCCTTA 58.581 34.615 0.00 0.00 0.00 2.69
5622 6411 6.270064 CACTGAAAAATGTTACGGTTTCCTT 58.730 36.000 0.00 0.00 0.00 3.36
5624 6413 4.979815 CCACTGAAAAATGTTACGGTTTCC 59.020 41.667 0.00 0.00 0.00 3.13
5626 6415 5.838531 TCCACTGAAAAATGTTACGGTTT 57.161 34.783 0.00 0.00 0.00 3.27
5663 6490 5.824097 ACCATCGGCCGTTACTTATTTATTT 59.176 36.000 27.15 0.00 0.00 1.40
5666 6493 4.405116 ACCATCGGCCGTTACTTATTTA 57.595 40.909 27.15 0.67 0.00 1.40
5673 6500 0.654160 GCTAAACCATCGGCCGTTAC 59.346 55.000 27.15 7.09 0.00 2.50
5674 6501 0.806884 CGCTAAACCATCGGCCGTTA 60.807 55.000 27.15 14.76 0.00 3.18
5676 6503 2.510064 TTCGCTAAACCATCGGCCGT 62.510 55.000 27.15 10.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.