Multiple sequence alignment - TraesCS7D01G149600

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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 TraesCS7D01G149600 chr7D 100.000 3368 0 0 1 3368 98619007 98622374 0.000000e+00 6220.0
1 TraesCS7D01G149600 chr7D 92.174 115 6 3 2854 2966 52233504 52233617 3.480000e-35 159.0
2 TraesCS7D01G149600 chr7A 92.458 1737 86 19 787 2494 100719308 100721028 0.000000e+00 2440.0
3 TraesCS7D01G149600 chr7A 83.929 224 27 6 2483 2701 100721082 100721301 4.400000e-49 206.0
4 TraesCS7D01G149600 chr7B 88.459 1447 93 27 1463 2868 53629387 53630800 0.000000e+00 1679.0
5 TraesCS7D01G149600 chr7B 91.429 700 44 8 950 1640 331540312 331539620 0.000000e+00 946.0
6 TraesCS7D01G149600 chr7B 95.066 527 17 1 826 1343 53628534 53629060 0.000000e+00 821.0
7 TraesCS7D01G149600 chr7B 85.283 530 69 9 3 526 53621136 53621662 3.820000e-149 538.0
8 TraesCS7D01G149600 chr7B 85.432 405 26 18 2965 3368 53632274 53632646 1.130000e-104 390.0
9 TraesCS7D01G149600 chr7B 89.597 298 28 1 2211 2505 331539370 331539073 3.170000e-100 375.0
10 TraesCS7D01G149600 chr7B 76.647 501 99 14 231 720 650563403 650562910 9.270000e-66 261.0
11 TraesCS7D01G149600 chr7B 76.600 500 101 12 231 720 650575225 650574732 9.270000e-66 261.0
12 TraesCS7D01G149600 chr7B 90.769 195 6 5 1833 2025 331539561 331539377 2.010000e-62 250.0
13 TraesCS7D01G149600 chr2B 91.903 704 44 6 947 1640 254787856 254787156 0.000000e+00 972.0
14 TraesCS7D01G149600 chr2B 91.582 297 22 1 2212 2505 254786906 254786610 1.130000e-109 407.0
15 TraesCS7D01G149600 chr2B 89.231 195 8 5 1833 2025 254787097 254786914 7.270000e-57 231.0
16 TraesCS7D01G149600 chr2B 97.849 93 2 0 2879 2971 653585346 653585438 9.670000e-36 161.0
17 TraesCS7D01G149600 chr2B 95.050 101 5 0 2869 2969 653585445 653585345 3.480000e-35 159.0
18 TraesCS7D01G149600 chrUn 90.682 440 28 10 947 1375 265946220 265946657 1.050000e-159 573.0
19 TraesCS7D01G149600 chrUn 90.500 400 25 11 947 1335 433014780 433014383 1.790000e-142 516.0
20 TraesCS7D01G149600 chrUn 92.256 297 20 1 2212 2505 265947293 265947589 5.200000e-113 418.0
21 TraesCS7D01G149600 chrUn 92.256 297 20 1 2212 2505 324063314 324063018 5.200000e-113 418.0
22 TraesCS7D01G149600 chrUn 92.727 220 16 0 1421 1640 265946823 265947042 5.420000e-83 318.0
23 TraesCS7D01G149600 chrUn 92.727 220 16 0 1421 1640 324063784 324063565 5.420000e-83 318.0
24 TraesCS7D01G149600 chrUn 90.769 195 6 4 1833 2025 265947101 265947285 2.010000e-62 250.0
25 TraesCS7D01G149600 chrUn 90.769 195 6 4 1833 2025 324063506 324063322 2.010000e-62 250.0
26 TraesCS7D01G149600 chr6D 81.802 577 47 31 871 1434 9346447 9346978 6.680000e-117 431.0
27 TraesCS7D01G149600 chr6D 79.180 610 108 11 132 723 337846664 337847272 4.050000e-109 405.0
28 TraesCS7D01G149600 chr6A 84.653 404 29 19 871 1261 11252378 11251995 4.100000e-99 372.0
29 TraesCS7D01G149600 chr6A 93.421 76 3 2 1357 1430 11251932 11251857 9.880000e-21 111.0
30 TraesCS7D01G149600 chr2D 78.089 607 109 18 124 713 616500621 616500022 2.470000e-96 363.0
31 TraesCS7D01G149600 chr6B 82.030 473 37 26 961 1412 17377202 17377647 3.200000e-95 359.0
32 TraesCS7D01G149600 chr4A 77.320 582 114 13 132 697 153257688 153258267 9.010000e-86 327.0
33 TraesCS7D01G149600 chr4A 95.745 47 2 0 1366 1412 724134385 724134339 3.600000e-10 76.8
34 TraesCS7D01G149600 chr4D 76.809 608 116 18 132 723 30143125 30143723 5.420000e-83 318.0
35 TraesCS7D01G149600 chr4D 98.876 89 1 0 2879 2967 5081574 5081662 3.480000e-35 159.0
36 TraesCS7D01G149600 chr3A 78.526 475 88 11 252 717 20292267 20292736 1.960000e-77 300.0
37 TraesCS7D01G149600 chr3A 96.842 95 3 0 2879 2973 86793037 86792943 3.480000e-35 159.0
38 TraesCS7D01G149600 chr3A 92.105 114 6 3 2858 2969 100888827 100888715 1.250000e-34 158.0
39 TraesCS7D01G149600 chr4B 76.732 563 111 14 177 724 32810790 32811347 2.540000e-76 296.0
40 TraesCS7D01G149600 chr3D 96.907 97 0 2 2870 2966 527767465 527767372 3.480000e-35 159.0
41 TraesCS7D01G149600 chr5D 95.918 98 3 1 2879 2976 411741667 411741571 1.250000e-34 158.0
42 TraesCS7D01G149600 chr5A 93.333 105 5 2 2881 2985 663975461 663975359 1.620000e-33 154.0


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 TraesCS7D01G149600 chr7D 98619007 98622374 3367 False 6220.000000 6220 100.000000 1 3368 1 chr7D.!!$F2 3367
1 TraesCS7D01G149600 chr7A 100719308 100721301 1993 False 1323.000000 2440 88.193500 787 2701 2 chr7A.!!$F1 1914
2 TraesCS7D01G149600 chr7B 53628534 53632646 4112 False 963.333333 1679 89.652333 826 3368 3 chr7B.!!$F2 2542
3 TraesCS7D01G149600 chr7B 53621136 53621662 526 False 538.000000 538 85.283000 3 526 1 chr7B.!!$F1 523
4 TraesCS7D01G149600 chr7B 331539073 331540312 1239 True 523.666667 946 90.598333 950 2505 3 chr7B.!!$R3 1555
5 TraesCS7D01G149600 chr2B 254786610 254787856 1246 True 536.666667 972 90.905333 947 2505 3 chr2B.!!$R2 1558
6 TraesCS7D01G149600 chrUn 265946220 265947589 1369 False 389.750000 573 91.608500 947 2505 4 chrUn.!!$F1 1558
7 TraesCS7D01G149600 chrUn 324063018 324063784 766 True 328.666667 418 91.917333 1421 2505 3 chrUn.!!$R2 1084
8 TraesCS7D01G149600 chr6D 9346447 9346978 531 False 431.000000 431 81.802000 871 1434 1 chr6D.!!$F1 563
9 TraesCS7D01G149600 chr6D 337846664 337847272 608 False 405.000000 405 79.180000 132 723 1 chr6D.!!$F2 591
10 TraesCS7D01G149600 chr6A 11251857 11252378 521 True 241.500000 372 89.037000 871 1430 2 chr6A.!!$R1 559
11 TraesCS7D01G149600 chr2D 616500022 616500621 599 True 363.000000 363 78.089000 124 713 1 chr2D.!!$R1 589
12 TraesCS7D01G149600 chr4A 153257688 153258267 579 False 327.000000 327 77.320000 132 697 1 chr4A.!!$F1 565
13 TraesCS7D01G149600 chr4D 30143125 30143723 598 False 318.000000 318 76.809000 132 723 1 chr4D.!!$F2 591
14 TraesCS7D01G149600 chr4B 32810790 32811347 557 False 296.000000 296 76.732000 177 724 1 chr4B.!!$F1 547

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
130 131 0.977395 ACAGAAACCCCCTTCTCTCG 59.023 55.000 0.0 0.0 33.25 4.04 F
512 530 1.063027 CAACGACGATGACTACGGCTA 59.937 52.381 0.0 0.0 36.56 3.93 F
1262 1312 1.137086 CCTCTACAAGGTCACCATCGG 59.863 57.143 0.0 0.0 40.67 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1840 1.135689 GCAACAATCTGCGACCGAAAT 60.136 47.619 0.00 0.0 31.5 2.17 R
2185 2475 2.051334 TCCGGCAAACATAATCCTGG 57.949 50.000 0.00 0.0 0.0 4.45 R
2798 3172 0.034863 GGGATCCACGCCACCTAAAA 60.035 55.000 15.23 0.0 0.0 1.52 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
31 32 5.881923 TGATACATACAACTAGGGGGTTC 57.118 43.478 0.00 0.00 0.00 3.62
32 33 5.282129 TGATACATACAACTAGGGGGTTCA 58.718 41.667 0.00 0.00 0.00 3.18
33 34 5.908831 TGATACATACAACTAGGGGGTTCAT 59.091 40.000 0.00 0.00 0.00 2.57
35 36 4.855340 ACATACAACTAGGGGGTTCATTG 58.145 43.478 0.00 0.00 0.00 2.82
36 37 4.291249 ACATACAACTAGGGGGTTCATTGT 59.709 41.667 0.00 0.00 34.77 2.71
37 38 3.154827 ACAACTAGGGGGTTCATTGTG 57.845 47.619 0.00 0.00 0.00 3.33
48 49 4.244862 GGGTTCATTGTGGCTTATGTTTG 58.755 43.478 0.00 0.00 0.00 2.93
68 69 8.279970 TGTTTGAATACTATGGACCAAGAATG 57.720 34.615 0.00 0.00 0.00 2.67
130 131 0.977395 ACAGAAACCCCCTTCTCTCG 59.023 55.000 0.00 0.00 33.25 4.04
206 211 2.281070 CCATGGATTCGCCTCCCG 60.281 66.667 5.56 0.00 37.63 5.14
276 291 5.906073 TCCGGTTAGTAGTTTAGGTTATGC 58.094 41.667 0.00 0.00 0.00 3.14
309 324 2.034879 CATGTGTGGTGCTCGGACC 61.035 63.158 0.10 0.10 36.43 4.46
318 333 4.286320 GCTCGGACCGATGGCGAT 62.286 66.667 18.71 0.00 40.82 4.58
374 392 2.426024 CCTCCTCGAGTTCGTCCATTTA 59.574 50.000 12.31 0.00 40.80 1.40
417 435 4.131088 GGTCGCCTGACGTCTCCC 62.131 72.222 17.92 3.59 46.49 4.30
429 447 1.309950 CGTCTCCCTAGAGCGATGAA 58.690 55.000 0.00 0.00 40.08 2.57
437 455 2.288518 CCTAGAGCGATGAACTTAGGCC 60.289 54.545 0.00 0.00 0.00 5.19
452 470 4.222145 ACTTAGGCCTTCTCGTTATGTGAA 59.778 41.667 12.58 0.00 0.00 3.18
458 476 5.221263 GGCCTTCTCGTTATGTGAAGAGATA 60.221 44.000 15.30 0.00 46.36 1.98
512 530 1.063027 CAACGACGATGACTACGGCTA 59.937 52.381 0.00 0.00 36.56 3.93
539 561 1.690985 TGGTCGGGGCATGTCCATA 60.691 57.895 20.13 1.55 36.21 2.74
550 573 2.420129 GCATGTCCATAAAGACTCCCGT 60.420 50.000 0.00 0.00 37.66 5.28
654 678 2.546789 GTCGTTCGGTGGTCTCAAAATT 59.453 45.455 0.00 0.00 0.00 1.82
662 686 4.681025 CGGTGGTCTCAAAATTTCAATGTG 59.319 41.667 0.00 0.00 0.00 3.21
699 723 8.196771 TGTTTGAGATGCTTTGTACTTTTGATT 58.803 29.630 0.00 0.00 0.00 2.57
752 776 7.770801 AAAGAAAAGAAAACTTATGCACACC 57.229 32.000 0.00 0.00 0.00 4.16
753 777 6.715347 AGAAAAGAAAACTTATGCACACCT 57.285 33.333 0.00 0.00 0.00 4.00
754 778 6.739112 AGAAAAGAAAACTTATGCACACCTC 58.261 36.000 0.00 0.00 0.00 3.85
755 779 6.547510 AGAAAAGAAAACTTATGCACACCTCT 59.452 34.615 0.00 0.00 0.00 3.69
756 780 5.948992 AAGAAAACTTATGCACACCTCTC 57.051 39.130 0.00 0.00 0.00 3.20
757 781 4.973168 AGAAAACTTATGCACACCTCTCA 58.027 39.130 0.00 0.00 0.00 3.27
758 782 5.376625 AGAAAACTTATGCACACCTCTCAA 58.623 37.500 0.00 0.00 0.00 3.02
759 783 6.006449 AGAAAACTTATGCACACCTCTCAAT 58.994 36.000 0.00 0.00 0.00 2.57
760 784 6.491403 AGAAAACTTATGCACACCTCTCAATT 59.509 34.615 0.00 0.00 0.00 2.32
761 785 5.886960 AACTTATGCACACCTCTCAATTC 57.113 39.130 0.00 0.00 0.00 2.17
762 786 4.265073 ACTTATGCACACCTCTCAATTCC 58.735 43.478 0.00 0.00 0.00 3.01
763 787 2.885135 ATGCACACCTCTCAATTCCA 57.115 45.000 0.00 0.00 0.00 3.53
764 788 2.655090 TGCACACCTCTCAATTCCAA 57.345 45.000 0.00 0.00 0.00 3.53
765 789 2.942804 TGCACACCTCTCAATTCCAAA 58.057 42.857 0.00 0.00 0.00 3.28
766 790 3.295093 TGCACACCTCTCAATTCCAAAA 58.705 40.909 0.00 0.00 0.00 2.44
767 791 3.703556 TGCACACCTCTCAATTCCAAAAA 59.296 39.130 0.00 0.00 0.00 1.94
794 818 8.744568 AATTATCCAAAGTCAATCTCTTCTCC 57.255 34.615 0.00 0.00 0.00 3.71
1262 1312 1.137086 CCTCTACAAGGTCACCATCGG 59.863 57.143 0.00 0.00 40.67 4.18
1316 1374 9.300681 AGGAAATTGATCTCTTGTGTTCATTTA 57.699 29.630 0.00 0.00 0.00 1.40
1483 1748 6.804295 GTGTAAGAGAACTGATAGAGTGTGTG 59.196 42.308 0.00 0.00 34.02 3.82
1554 1840 1.301716 GCACCAGGCTCTGTTTCGA 60.302 57.895 0.00 0.00 40.25 3.71
1562 1848 1.393883 GGCTCTGTTTCGATTTCGGTC 59.606 52.381 0.00 0.00 40.29 4.79
1628 1914 5.291858 TGTCTGATTTCGATAGCATTGTCAC 59.708 40.000 0.00 0.00 0.00 3.67
1634 1920 3.872696 TCGATAGCATTGTCACAATGGT 58.127 40.909 31.94 31.94 40.85 3.55
1635 1921 4.260985 TCGATAGCATTGTCACAATGGTT 58.739 39.130 33.79 22.87 38.96 3.67
1636 1922 4.699735 TCGATAGCATTGTCACAATGGTTT 59.300 37.500 33.79 27.37 38.96 3.27
1637 1923 5.877564 TCGATAGCATTGTCACAATGGTTTA 59.122 36.000 33.79 20.89 38.96 2.01
1638 1924 6.542005 TCGATAGCATTGTCACAATGGTTTAT 59.458 34.615 33.79 24.09 38.96 1.40
1639 1925 7.713073 TCGATAGCATTGTCACAATGGTTTATA 59.287 33.333 33.79 19.92 38.96 0.98
1640 1926 8.341903 CGATAGCATTGTCACAATGGTTTATAA 58.658 33.333 33.79 19.59 38.96 0.98
1664 1950 6.693315 TTTATAGTGTCCTGGCTAATTTGC 57.307 37.500 3.03 3.03 0.00 3.68
1726 2012 5.504665 GCAATCAATATGTTTCCTCGGTCAG 60.505 44.000 0.00 0.00 0.00 3.51
1944 2233 1.697297 CTGCCCCAGTTACCCCAAT 59.303 57.895 0.00 0.00 0.00 3.16
2185 2475 2.159085 ACCTGAAGTAGCTAACCGATGC 60.159 50.000 0.00 0.00 0.00 3.91
2206 2496 2.554032 CCAGGATTATGTTTGCCGGATC 59.446 50.000 5.05 0.00 0.00 3.36
2215 2512 1.068541 GTTTGCCGGATCTTGGTTGAC 60.069 52.381 5.05 0.00 0.00 3.18
2330 2627 1.076332 AAGGCGTCGTTGCAAGATAC 58.924 50.000 0.00 0.00 36.28 2.24
2374 2671 2.072298 GCACCTCTGCTTAGTCAGTTG 58.928 52.381 4.23 2.82 40.63 3.16
2526 2896 1.824329 TGAAAGGGTTTTGGCGCGA 60.824 52.632 12.10 0.00 0.00 5.87
2544 2914 2.594592 GCGTGAGGCCAGGTTGTT 60.595 61.111 5.01 0.00 34.80 2.83
2548 2918 0.465460 GTGAGGCCAGGTTGTTGTGA 60.465 55.000 5.01 0.00 0.00 3.58
2586 2956 4.202357 TGTTGAAGCTGAAGATGGTGTAGT 60.202 41.667 0.00 0.00 0.00 2.73
2590 2960 2.094494 AGCTGAAGATGGTGTAGTGTCG 60.094 50.000 0.00 0.00 0.00 4.35
2644 3014 5.126707 GCAATTCCTCATTTCCATCAGAAGT 59.873 40.000 0.00 0.00 35.40 3.01
2656 3026 3.307691 CCATCAGAAGTAAGTGCTTCCCA 60.308 47.826 5.63 0.00 44.27 4.37
2658 3028 4.008074 TCAGAAGTAAGTGCTTCCCAAG 57.992 45.455 5.63 0.00 44.27 3.61
2736 3110 1.970114 AATGCTGCAGCTCGCTTGT 60.970 52.632 36.61 12.92 43.06 3.16
2768 3142 6.478344 GTGACAAGTAGGCTGATTAGATTCAG 59.522 42.308 0.00 0.00 44.87 3.02
2797 3171 6.343703 TGATCATCATTGTCTCGACATTTCT 58.656 36.000 0.00 0.00 41.52 2.52
2798 3172 6.820152 TGATCATCATTGTCTCGACATTTCTT 59.180 34.615 0.00 0.00 41.52 2.52
2799 3173 7.335171 TGATCATCATTGTCTCGACATTTCTTT 59.665 33.333 0.00 0.00 41.52 2.52
2825 3199 1.053424 GGCGTGGATCCCCTGTAATA 58.947 55.000 9.90 0.00 0.00 0.98
2832 3206 5.650703 CGTGGATCCCCTGTAATAAAAGTTT 59.349 40.000 9.90 0.00 0.00 2.66
2834 3208 6.096423 GTGGATCCCCTGTAATAAAAGTTTCC 59.904 42.308 9.90 0.00 0.00 3.13
2835 3209 6.011096 TGGATCCCCTGTAATAAAAGTTTCCT 60.011 38.462 9.90 0.00 0.00 3.36
2849 3224 6.959639 AAAGTTTCCTATTGCTTTGTCAGA 57.040 33.333 0.00 0.00 30.97 3.27
2854 3229 4.825422 TCCTATTGCTTTGTCAGACTCTG 58.175 43.478 1.31 0.00 0.00 3.35
2855 3230 3.937706 CCTATTGCTTTGTCAGACTCTGG 59.062 47.826 6.20 0.00 31.51 3.86
2860 3236 3.181451 TGCTTTGTCAGACTCTGGAACAT 60.181 43.478 6.20 0.00 38.20 2.71
2868 3244 5.185249 GTCAGACTCTGGAACATGGTAGTAA 59.815 44.000 6.20 0.00 38.20 2.24
2871 3247 7.618117 TCAGACTCTGGAACATGGTAGTAATTA 59.382 37.037 6.20 0.00 38.20 1.40
2874 3250 8.834004 ACTCTGGAACATGGTAGTAATTACTA 57.166 34.615 19.30 19.30 38.20 1.82
2875 3251 9.263446 ACTCTGGAACATGGTAGTAATTACTAA 57.737 33.333 23.66 12.16 37.97 2.24
2876 3252 9.530633 CTCTGGAACATGGTAGTAATTACTAAC 57.469 37.037 27.06 27.06 44.71 2.34
2877 3253 8.192774 TCTGGAACATGGTAGTAATTACTAACG 58.807 37.037 27.52 19.58 46.83 3.18
2878 3254 7.839907 TGGAACATGGTAGTAATTACTAACGT 58.160 34.615 27.52 25.79 46.83 3.99
2889 3341 6.770303 AGTAATTACTAACGTCTACTCCCTCC 59.230 42.308 16.60 0.00 34.13 4.30
2892 3344 2.290577 ACTAACGTCTACTCCCTCCGTT 60.291 50.000 0.00 0.00 43.35 4.44
2896 3348 1.553706 GTCTACTCCCTCCGTTCCAA 58.446 55.000 0.00 0.00 0.00 3.53
2898 3350 2.500504 GTCTACTCCCTCCGTTCCAAAT 59.499 50.000 0.00 0.00 0.00 2.32
2900 3352 4.161001 GTCTACTCCCTCCGTTCCAAATTA 59.839 45.833 0.00 0.00 0.00 1.40
2901 3353 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2902 3354 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2903 3355 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2905 3357 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2907 3359 3.581755 CTCCGTTCCAAATTACTCGTCA 58.418 45.455 0.00 0.00 0.00 4.35
2908 3360 4.181578 CTCCGTTCCAAATTACTCGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2909 3361 3.930229 TCCGTTCCAAATTACTCGTCATG 59.070 43.478 0.00 0.00 0.00 3.07
2910 3362 3.063452 CCGTTCCAAATTACTCGTCATGG 59.937 47.826 0.00 0.00 0.00 3.66
2913 3365 5.334569 CGTTCCAAATTACTCGTCATGGTTT 60.335 40.000 0.00 0.00 0.00 3.27
2914 3366 6.443792 GTTCCAAATTACTCGTCATGGTTTT 58.556 36.000 0.00 0.00 0.00 2.43
2916 3368 7.372451 TCCAAATTACTCGTCATGGTTTTAG 57.628 36.000 0.00 0.00 0.00 1.85
2917 3369 6.938030 TCCAAATTACTCGTCATGGTTTTAGT 59.062 34.615 0.00 0.00 0.00 2.24
2918 3370 7.446013 TCCAAATTACTCGTCATGGTTTTAGTT 59.554 33.333 0.00 0.00 0.00 2.24
2919 3371 7.749126 CCAAATTACTCGTCATGGTTTTAGTTC 59.251 37.037 0.00 0.00 0.00 3.01
2921 3373 7.972832 ATTACTCGTCATGGTTTTAGTTCAA 57.027 32.000 0.00 0.00 0.00 2.69
2922 3374 7.789273 TTACTCGTCATGGTTTTAGTTCAAA 57.211 32.000 0.00 0.00 0.00 2.69
2923 3375 6.877611 ACTCGTCATGGTTTTAGTTCAAAT 57.122 33.333 0.00 0.00 0.00 2.32
2925 3377 7.712797 ACTCGTCATGGTTTTAGTTCAAATTT 58.287 30.769 0.00 0.00 0.00 1.82
2927 3379 7.708051 TCGTCATGGTTTTAGTTCAAATTTGA 58.292 30.769 16.91 16.91 34.92 2.69
2928 3380 8.191446 TCGTCATGGTTTTAGTTCAAATTTGAA 58.809 29.630 26.01 26.01 44.31 2.69
2941 3393 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
2944 4690 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2946 4692 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2949 4695 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
2952 4698 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2953 4699 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
2966 4712 4.720273 AGTAATTTGGAACGGAGGGAGTAT 59.280 41.667 0.00 0.00 0.00 2.12
2967 4713 5.901276 AGTAATTTGGAACGGAGGGAGTATA 59.099 40.000 0.00 0.00 0.00 1.47
2968 4714 5.906772 AATTTGGAACGGAGGGAGTATAT 57.093 39.130 0.00 0.00 0.00 0.86
2969 4715 4.682778 TTTGGAACGGAGGGAGTATATG 57.317 45.455 0.00 0.00 0.00 1.78
3004 4757 6.814954 ACTGTAGAGTGATGATTACCCAAT 57.185 37.500 0.00 0.00 0.00 3.16
3107 4860 2.295349 AGCTCATGTGAGTTTTGGCAAG 59.705 45.455 11.35 0.00 43.85 4.01
3112 4870 4.344679 TCATGTGAGTTTTGGCAAGGAAAT 59.655 37.500 0.00 0.00 0.00 2.17
3124 4882 3.064545 GGCAAGGAAATCGTCATTCTGAG 59.935 47.826 0.00 0.00 0.00 3.35
3126 4884 4.154918 GCAAGGAAATCGTCATTCTGAGTT 59.845 41.667 0.00 0.00 0.00 3.01
3127 4885 5.672321 GCAAGGAAATCGTCATTCTGAGTTC 60.672 44.000 0.00 0.00 38.19 3.01
3128 4886 5.413309 AGGAAATCGTCATTCTGAGTTCT 57.587 39.130 3.01 0.00 38.75 3.01
3129 4887 5.174395 AGGAAATCGTCATTCTGAGTTCTG 58.826 41.667 3.01 0.00 38.75 3.02
3130 4888 5.047021 AGGAAATCGTCATTCTGAGTTCTGA 60.047 40.000 3.01 0.00 38.75 3.27
3131 4889 5.062809 GGAAATCGTCATTCTGAGTTCTGAC 59.937 44.000 3.01 0.00 38.75 3.51
3132 4890 5.398603 AATCGTCATTCTGAGTTCTGACT 57.601 39.130 9.02 0.00 36.67 3.41
3151 4909 0.662619 TCTGAAAAACGCTGCCACAG 59.337 50.000 0.00 0.00 34.12 3.66
3253 5011 1.933853 GTTAGCTACCGCCAGAACATG 59.066 52.381 0.00 0.00 36.60 3.21
3254 5012 0.179084 TAGCTACCGCCAGAACATGC 60.179 55.000 0.00 0.00 36.60 4.06
3255 5013 2.472909 GCTACCGCCAGAACATGCC 61.473 63.158 0.00 0.00 0.00 4.40
3257 5015 0.464373 CTACCGCCAGAACATGCCAT 60.464 55.000 0.00 0.00 0.00 4.40
3258 5016 0.833949 TACCGCCAGAACATGCCATA 59.166 50.000 0.00 0.00 0.00 2.74
3259 5017 0.464373 ACCGCCAGAACATGCCATAG 60.464 55.000 0.00 0.00 0.00 2.23
3260 5018 0.179048 CCGCCAGAACATGCCATAGA 60.179 55.000 0.00 0.00 0.00 1.98
3261 5019 0.940126 CGCCAGAACATGCCATAGAC 59.060 55.000 0.00 0.00 0.00 2.59
3262 5020 0.940126 GCCAGAACATGCCATAGACG 59.060 55.000 0.00 0.00 0.00 4.18
3263 5021 1.743772 GCCAGAACATGCCATAGACGT 60.744 52.381 0.00 0.00 0.00 4.34
3264 5022 2.205074 CCAGAACATGCCATAGACGTC 58.795 52.381 7.70 7.70 0.00 4.34
3265 5023 2.205074 CAGAACATGCCATAGACGTCC 58.795 52.381 13.01 0.00 0.00 4.79
3266 5024 1.831106 AGAACATGCCATAGACGTCCA 59.169 47.619 13.01 0.00 0.00 4.02
3267 5025 2.159043 AGAACATGCCATAGACGTCCAG 60.159 50.000 13.01 1.97 0.00 3.86
3268 5026 0.179073 ACATGCCATAGACGTCCAGC 60.179 55.000 13.01 10.67 0.00 4.85
3269 5027 0.882042 CATGCCATAGACGTCCAGCC 60.882 60.000 13.01 0.00 0.00 4.85
3270 5028 1.337384 ATGCCATAGACGTCCAGCCA 61.337 55.000 13.01 3.97 0.00 4.75
3271 5029 1.220749 GCCATAGACGTCCAGCCAA 59.779 57.895 13.01 0.00 0.00 4.52
3272 5030 0.392461 GCCATAGACGTCCAGCCAAA 60.392 55.000 13.01 0.00 0.00 3.28
3273 5031 1.656652 CCATAGACGTCCAGCCAAAG 58.343 55.000 13.01 0.00 0.00 2.77
3274 5032 1.207089 CCATAGACGTCCAGCCAAAGA 59.793 52.381 13.01 0.00 0.00 2.52
3275 5033 2.354704 CCATAGACGTCCAGCCAAAGAA 60.355 50.000 13.01 0.00 0.00 2.52
3276 5034 2.450609 TAGACGTCCAGCCAAAGAAC 57.549 50.000 13.01 0.00 0.00 3.01
3277 5035 0.600255 AGACGTCCAGCCAAAGAACG 60.600 55.000 13.01 0.00 0.00 3.95
3278 5036 2.171489 GACGTCCAGCCAAAGAACGC 62.171 60.000 3.51 0.00 0.00 4.84
3279 5037 2.250939 CGTCCAGCCAAAGAACGCA 61.251 57.895 0.00 0.00 0.00 5.24
3280 5038 1.282875 GTCCAGCCAAAGAACGCAC 59.717 57.895 0.00 0.00 0.00 5.34
3281 5039 1.153066 TCCAGCCAAAGAACGCACA 60.153 52.632 0.00 0.00 0.00 4.57
3282 5040 1.165907 TCCAGCCAAAGAACGCACAG 61.166 55.000 0.00 0.00 0.00 3.66
3283 5041 1.165907 CCAGCCAAAGAACGCACAGA 61.166 55.000 0.00 0.00 0.00 3.41
3284 5042 0.040958 CAGCCAAAGAACGCACAGAC 60.041 55.000 0.00 0.00 0.00 3.51
3285 5043 1.082756 GCCAAAGAACGCACAGACG 60.083 57.895 0.00 0.00 39.50 4.18
3312 5077 1.454295 TGCGCTGCCATGGATGATT 60.454 52.632 18.40 0.00 0.00 2.57
3345 5110 2.158475 TGAGACAACAAGAGGCCCATTT 60.158 45.455 0.00 0.00 0.00 2.32
3346 5111 2.229784 GAGACAACAAGAGGCCCATTTG 59.770 50.000 0.00 4.36 0.00 2.32
3347 5112 1.273327 GACAACAAGAGGCCCATTTGG 59.727 52.381 13.95 0.00 37.09 3.28
3363 5128 2.791383 TTGGGAGCACGTGAAATTTG 57.209 45.000 22.23 0.00 0.00 2.32
3364 5129 0.313672 TGGGAGCACGTGAAATTTGC 59.686 50.000 22.23 0.85 36.45 3.68
3366 5131 0.598065 GGAGCACGTGAAATTTGCCT 59.402 50.000 22.23 3.40 36.91 4.75
3367 5132 1.666888 GGAGCACGTGAAATTTGCCTG 60.667 52.381 22.23 0.00 36.91 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.282129 TGAACCCCCTAGTTGTATGTATCA 58.718 41.667 0.00 0.00 0.00 2.15
24 25 1.756538 CATAAGCCACAATGAACCCCC 59.243 52.381 0.00 0.00 0.00 5.40
25 26 2.456577 ACATAAGCCACAATGAACCCC 58.543 47.619 0.00 0.00 0.00 4.95
26 27 4.021544 TCAAACATAAGCCACAATGAACCC 60.022 41.667 0.00 0.00 0.00 4.11
31 32 9.454585 CATAGTATTCAAACATAAGCCACAATG 57.545 33.333 0.00 0.00 0.00 2.82
32 33 8.632679 CCATAGTATTCAAACATAAGCCACAAT 58.367 33.333 0.00 0.00 0.00 2.71
33 34 7.831690 TCCATAGTATTCAAACATAAGCCACAA 59.168 33.333 0.00 0.00 0.00 3.33
35 36 7.255139 GGTCCATAGTATTCAAACATAAGCCAC 60.255 40.741 0.00 0.00 0.00 5.01
36 37 6.770785 GGTCCATAGTATTCAAACATAAGCCA 59.229 38.462 0.00 0.00 0.00 4.75
37 38 6.770785 TGGTCCATAGTATTCAAACATAAGCC 59.229 38.462 0.00 0.00 0.00 4.35
48 49 4.762251 GCCCATTCTTGGTCCATAGTATTC 59.238 45.833 0.00 0.00 41.91 1.75
68 69 1.888512 TCATTGTGCTTGAAAGAGCCC 59.111 47.619 0.00 0.00 42.01 5.19
109 110 2.766828 CGAGAGAAGGGGGTTTCTGTAT 59.233 50.000 0.00 0.00 37.53 2.29
113 114 1.624312 GAACGAGAGAAGGGGGTTTCT 59.376 52.381 0.00 0.00 40.02 2.52
206 211 2.336809 CCGGAGCGGCAGATAGAC 59.663 66.667 0.00 0.00 41.17 2.59
243 257 0.900647 ACTAACCGGAGCAGAGCACT 60.901 55.000 9.46 0.00 0.00 4.40
250 265 3.434309 ACCTAAACTACTAACCGGAGCA 58.566 45.455 9.46 0.00 0.00 4.26
309 324 1.260033 GAAGAAGAAGCATCGCCATCG 59.740 52.381 0.00 0.00 0.00 3.84
318 333 5.817816 AGAAGAAAAACTCGAAGAAGAAGCA 59.182 36.000 0.00 0.00 34.09 3.91
374 392 1.671845 GAAGCTCCGTCGACTATGTCT 59.328 52.381 14.70 1.38 0.00 3.41
400 418 4.131088 GGGAGACGTCAGGCGACC 62.131 72.222 19.50 10.27 44.77 4.79
402 420 1.451567 CTAGGGAGACGTCAGGCGA 60.452 63.158 19.50 0.00 44.77 5.54
417 435 2.625790 AGGCCTAAGTTCATCGCTCTAG 59.374 50.000 1.29 0.00 0.00 2.43
429 447 3.767673 TCACATAACGAGAAGGCCTAAGT 59.232 43.478 5.16 0.28 0.00 2.24
437 455 7.380870 CACCATATCTCTTCACATAACGAGAAG 59.619 40.741 0.00 0.00 42.00 2.85
452 470 9.911788 ATTTGAAACATCTAACACCATATCTCT 57.088 29.630 0.00 0.00 0.00 3.10
487 505 2.666344 CGTAGTCATCGTCGTTGAACCA 60.666 50.000 7.55 0.00 0.00 3.67
550 573 2.610479 GCTTGACCTTGTCGATGACAGA 60.610 50.000 0.00 0.00 43.69 3.41
627 651 0.314935 GACCACCGAACGACCACTAA 59.685 55.000 0.00 0.00 0.00 2.24
726 750 8.664798 GGTGTGCATAAGTTTTCTTTTCTTTTT 58.335 29.630 0.00 0.00 40.91 1.94
727 751 8.040727 AGGTGTGCATAAGTTTTCTTTTCTTTT 58.959 29.630 0.00 0.00 40.91 2.27
728 752 7.555965 AGGTGTGCATAAGTTTTCTTTTCTTT 58.444 30.769 0.00 0.00 40.91 2.52
729 753 7.068716 AGAGGTGTGCATAAGTTTTCTTTTCTT 59.931 33.333 0.00 0.00 40.91 2.52
730 754 6.547510 AGAGGTGTGCATAAGTTTTCTTTTCT 59.452 34.615 0.00 0.00 40.91 2.52
731 755 6.739112 AGAGGTGTGCATAAGTTTTCTTTTC 58.261 36.000 0.00 0.00 40.91 2.29
732 756 6.321181 TGAGAGGTGTGCATAAGTTTTCTTTT 59.679 34.615 0.00 0.00 40.91 2.27
733 757 5.827797 TGAGAGGTGTGCATAAGTTTTCTTT 59.172 36.000 0.00 0.00 40.91 2.52
734 758 5.376625 TGAGAGGTGTGCATAAGTTTTCTT 58.623 37.500 0.00 0.00 43.24 2.52
735 759 4.973168 TGAGAGGTGTGCATAAGTTTTCT 58.027 39.130 0.00 0.00 0.00 2.52
736 760 5.689383 TTGAGAGGTGTGCATAAGTTTTC 57.311 39.130 0.00 0.00 0.00 2.29
737 761 6.294731 GGAATTGAGAGGTGTGCATAAGTTTT 60.295 38.462 0.00 0.00 0.00 2.43
738 762 5.183904 GGAATTGAGAGGTGTGCATAAGTTT 59.816 40.000 0.00 0.00 0.00 2.66
739 763 4.702131 GGAATTGAGAGGTGTGCATAAGTT 59.298 41.667 0.00 0.00 0.00 2.66
740 764 4.263462 TGGAATTGAGAGGTGTGCATAAGT 60.263 41.667 0.00 0.00 0.00 2.24
741 765 4.264253 TGGAATTGAGAGGTGTGCATAAG 58.736 43.478 0.00 0.00 0.00 1.73
742 766 4.299586 TGGAATTGAGAGGTGTGCATAA 57.700 40.909 0.00 0.00 0.00 1.90
743 767 3.998913 TGGAATTGAGAGGTGTGCATA 57.001 42.857 0.00 0.00 0.00 3.14
744 768 2.885135 TGGAATTGAGAGGTGTGCAT 57.115 45.000 0.00 0.00 0.00 3.96
745 769 2.655090 TTGGAATTGAGAGGTGTGCA 57.345 45.000 0.00 0.00 0.00 4.57
746 770 4.320608 TTTTTGGAATTGAGAGGTGTGC 57.679 40.909 0.00 0.00 0.00 4.57
768 792 9.183368 GGAGAAGAGATTGACTTTGGATAATTT 57.817 33.333 0.00 0.00 0.00 1.82
769 793 8.331740 TGGAGAAGAGATTGACTTTGGATAATT 58.668 33.333 0.00 0.00 0.00 1.40
770 794 7.865820 TGGAGAAGAGATTGACTTTGGATAAT 58.134 34.615 0.00 0.00 0.00 1.28
771 795 7.257790 TGGAGAAGAGATTGACTTTGGATAA 57.742 36.000 0.00 0.00 0.00 1.75
772 796 6.874278 TGGAGAAGAGATTGACTTTGGATA 57.126 37.500 0.00 0.00 0.00 2.59
773 797 5.768980 TGGAGAAGAGATTGACTTTGGAT 57.231 39.130 0.00 0.00 0.00 3.41
774 798 5.567037 TTGGAGAAGAGATTGACTTTGGA 57.433 39.130 0.00 0.00 0.00 3.53
775 799 6.830873 ATTTGGAGAAGAGATTGACTTTGG 57.169 37.500 0.00 0.00 0.00 3.28
776 800 8.516811 CAAATTTGGAGAAGAGATTGACTTTG 57.483 34.615 10.49 0.00 0.00 2.77
812 836 3.219281 AGTGGTTTGCAAAGAACGGTAT 58.781 40.909 13.26 0.00 0.00 2.73
1114 1164 1.415672 TTGTTCCTCCTCGCCTTGGT 61.416 55.000 0.00 0.00 0.00 3.67
1262 1312 3.152341 CAGAGATTGTTATGGATGGGGC 58.848 50.000 0.00 0.00 0.00 5.80
1483 1748 4.762251 GGGGCATTCATGTTCTACTATTCC 59.238 45.833 0.00 0.00 0.00 3.01
1554 1840 1.135689 GCAACAATCTGCGACCGAAAT 60.136 47.619 0.00 0.00 31.50 2.17
1638 1924 8.846211 GCAAATTAGCCAGGACACTATAAATTA 58.154 33.333 0.00 0.00 0.00 1.40
1639 1925 7.468631 CGCAAATTAGCCAGGACACTATAAATT 60.469 37.037 0.00 0.00 0.00 1.82
1640 1926 6.017109 CGCAAATTAGCCAGGACACTATAAAT 60.017 38.462 0.00 0.00 0.00 1.40
1664 1950 7.411804 GCTTTCCACCATGAAAAATATCAAACG 60.412 37.037 0.00 0.00 34.06 3.60
1726 2012 5.994054 ACACTGCATATCCACATGAAGTATC 59.006 40.000 0.00 0.00 42.00 2.24
1822 2109 8.078596 GCTCTGCTTCTTTTATCTTTTCTTTCA 58.921 33.333 0.00 0.00 0.00 2.69
2047 2337 6.624352 TCTACATTAAGCGTACGTCCTAAT 57.376 37.500 17.90 13.50 0.00 1.73
2185 2475 2.051334 TCCGGCAAACATAATCCTGG 57.949 50.000 0.00 0.00 0.00 4.45
2215 2512 8.012957 AGAGAAACATACAGATACAGGTTAGG 57.987 38.462 0.00 0.00 0.00 2.69
2259 2556 2.688446 ACTGATTCTTATCGGAGCGTCA 59.312 45.455 0.00 0.00 39.15 4.35
2359 2656 3.935993 GGGCAACTGACTAAGCAGA 57.064 52.632 0.00 0.00 39.20 4.26
2374 2671 2.622436 CTGCTAAATATCTAGCCGGGC 58.378 52.381 12.11 12.11 43.13 6.13
2398 2700 4.593634 AGCTTCTACAGGGACTAGTTTTGT 59.406 41.667 0.00 5.05 36.02 2.83
2406 2708 2.498078 GCACTAAGCTTCTACAGGGACT 59.502 50.000 0.00 0.00 41.15 3.85
2526 2896 3.120086 AACAACCTGGCCTCACGCT 62.120 57.895 3.32 0.00 37.74 5.07
2544 2914 0.107410 AACAAAGCGTGGAGGTCACA 60.107 50.000 0.00 0.00 46.36 3.58
2548 2918 0.738389 CAACAACAAAGCGTGGAGGT 59.262 50.000 0.00 0.00 0.00 3.85
2609 2979 9.002600 GGAAATGAGGAATTGCAAAAATAAAGT 57.997 29.630 1.71 0.00 0.00 2.66
2610 2980 9.001542 TGGAAATGAGGAATTGCAAAAATAAAG 57.998 29.630 1.71 0.00 0.00 1.85
2612 2982 9.165035 GATGGAAATGAGGAATTGCAAAAATAA 57.835 29.630 1.71 0.00 30.56 1.40
2613 2983 8.319881 TGATGGAAATGAGGAATTGCAAAAATA 58.680 29.630 1.71 0.00 30.56 1.40
2614 2984 7.169591 TGATGGAAATGAGGAATTGCAAAAAT 58.830 30.769 1.71 0.00 30.56 1.82
2625 2995 6.409704 CACTTACTTCTGATGGAAATGAGGA 58.590 40.000 0.00 0.00 33.07 3.71
2656 3026 3.133542 TCTCCTCATGATTGACATCGCTT 59.866 43.478 0.00 0.00 37.07 4.68
2658 3028 2.799412 GTCTCCTCATGATTGACATCGC 59.201 50.000 14.17 0.00 37.07 4.58
2689 3063 1.433879 CATGTCCTCCTCGACGTCC 59.566 63.158 10.58 0.00 35.40 4.79
2736 3110 2.747989 CAGCCTACTTGTCACTCGACTA 59.252 50.000 0.00 0.00 43.06 2.59
2768 3142 7.880059 TGTCGAGACAATGATGATCATAATC 57.120 36.000 8.54 9.21 35.76 1.75
2788 3162 3.058501 ACGCCACCTAAAAAGAAATGTCG 60.059 43.478 0.00 0.00 0.00 4.35
2797 3171 1.614850 GGGATCCACGCCACCTAAAAA 60.615 52.381 15.23 0.00 0.00 1.94
2798 3172 0.034863 GGGATCCACGCCACCTAAAA 60.035 55.000 15.23 0.00 0.00 1.52
2799 3173 1.605453 GGGATCCACGCCACCTAAA 59.395 57.895 15.23 0.00 0.00 1.85
2825 3199 7.068716 AGTCTGACAAAGCAATAGGAAACTTTT 59.931 33.333 10.88 0.00 43.67 2.27
2832 3206 4.323028 CCAGAGTCTGACAAAGCAATAGGA 60.323 45.833 22.09 0.00 32.44 2.94
2834 3208 4.825422 TCCAGAGTCTGACAAAGCAATAG 58.175 43.478 22.09 0.10 32.44 1.73
2835 3209 4.890158 TCCAGAGTCTGACAAAGCAATA 57.110 40.909 22.09 0.00 32.44 1.90
2846 3221 5.661056 TTACTACCATGTTCCAGAGTCTG 57.339 43.478 13.56 13.56 0.00 3.51
2849 3224 7.735326 AGTAATTACTACCATGTTCCAGAGT 57.265 36.000 16.60 0.00 34.13 3.24
2854 3229 8.193438 AGACGTTAGTAATTACTACCATGTTCC 58.807 37.037 22.22 10.81 38.43 3.62
2860 3236 7.499232 GGGAGTAGACGTTAGTAATTACTACCA 59.501 40.741 22.22 8.60 39.82 3.25
2868 3244 4.133078 CGGAGGGAGTAGACGTTAGTAAT 58.867 47.826 0.00 0.00 0.00 1.89
2871 3247 1.280421 ACGGAGGGAGTAGACGTTAGT 59.720 52.381 0.00 0.00 33.54 2.24
2874 3250 3.353342 AACGGAGGGAGTAGACGTT 57.647 52.632 0.00 0.00 42.17 3.99
2875 3251 0.679321 GGAACGGAGGGAGTAGACGT 60.679 60.000 0.00 0.00 39.74 4.34
2876 3252 0.679002 TGGAACGGAGGGAGTAGACG 60.679 60.000 0.00 0.00 0.00 4.18
2877 3253 1.553706 TTGGAACGGAGGGAGTAGAC 58.446 55.000 0.00 0.00 0.00 2.59
2878 3254 2.314071 TTTGGAACGGAGGGAGTAGA 57.686 50.000 0.00 0.00 0.00 2.59
2889 3341 3.682858 ACCATGACGAGTAATTTGGAACG 59.317 43.478 0.00 0.00 0.00 3.95
2892 3344 6.938030 ACTAAAACCATGACGAGTAATTTGGA 59.062 34.615 0.00 0.00 0.00 3.53
2896 3348 7.972832 TGAACTAAAACCATGACGAGTAATT 57.027 32.000 0.00 0.00 0.00 1.40
2898 3350 7.789273 TTTGAACTAAAACCATGACGAGTAA 57.211 32.000 0.00 0.00 0.00 2.24
2900 3352 6.877611 ATTTGAACTAAAACCATGACGAGT 57.122 33.333 0.00 0.00 0.00 4.18
2901 3353 7.860373 TCAAATTTGAACTAAAACCATGACGAG 59.140 33.333 18.45 0.00 33.55 4.18
2902 3354 7.708051 TCAAATTTGAACTAAAACCATGACGA 58.292 30.769 18.45 0.00 33.55 4.20
2903 3355 7.922505 TCAAATTTGAACTAAAACCATGACG 57.077 32.000 18.45 0.00 33.55 4.35
2917 3369 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
2918 3370 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
2919 3371 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
2921 3373 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
2922 3374 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2923 3375 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
2925 3377 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2927 3379 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
2928 3380 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
2929 3381 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
2930 3382 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
2931 3383 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
2935 3387 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
2936 3388 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
2937 3389 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
2938 3390 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2939 3391 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2940 3392 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2941 3393 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2944 4690 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2946 4692 5.132144 ACATATACTCCCTCCGTTCCAAATT 59.868 40.000 0.00 0.00 0.00 1.82
2949 4695 3.649843 ACATATACTCCCTCCGTTCCAA 58.350 45.455 0.00 0.00 0.00 3.53
2952 4698 5.532664 AGAAACATATACTCCCTCCGTTC 57.467 43.478 0.00 0.00 0.00 3.95
2953 4699 5.424252 TGAAGAAACATATACTCCCTCCGTT 59.576 40.000 0.00 0.00 0.00 4.44
2966 4712 6.591448 CACTCTACAGTGCATGAAGAAACATA 59.409 38.462 0.00 0.00 43.77 2.29
2967 4713 5.410746 CACTCTACAGTGCATGAAGAAACAT 59.589 40.000 0.00 0.00 43.77 2.71
2968 4714 4.751600 CACTCTACAGTGCATGAAGAAACA 59.248 41.667 0.00 0.00 43.77 2.83
2969 4715 5.274881 CACTCTACAGTGCATGAAGAAAC 57.725 43.478 0.00 0.00 43.77 2.78
2998 4751 0.604578 GCTTGTGCATCACATTGGGT 59.395 50.000 0.11 0.00 44.16 4.51
2999 4752 0.457166 CGCTTGTGCATCACATTGGG 60.457 55.000 0.11 2.70 44.16 4.12
3000 4753 0.522626 TCGCTTGTGCATCACATTGG 59.477 50.000 0.11 0.00 44.16 3.16
3001 4754 2.159490 TCATCGCTTGTGCATCACATTG 60.159 45.455 0.11 0.00 44.16 2.82
3002 4755 2.086094 TCATCGCTTGTGCATCACATT 58.914 42.857 0.11 0.00 44.16 2.71
3003 4756 1.741528 TCATCGCTTGTGCATCACAT 58.258 45.000 0.11 0.00 44.16 3.21
3004 4757 1.741528 ATCATCGCTTGTGCATCACA 58.258 45.000 0.00 0.00 43.02 3.58
3017 4770 3.631145 CCAGGCAAATGGTAATCATCG 57.369 47.619 0.00 0.00 34.44 3.84
3068 4821 7.391554 ACATGAGCTGTGTAAACTGTCAATATT 59.608 33.333 0.00 0.00 36.48 1.28
3096 4849 2.955660 TGACGATTTCCTTGCCAAAACT 59.044 40.909 0.00 0.00 0.00 2.66
3107 4860 5.062809 GTCAGAACTCAGAATGACGATTTCC 59.937 44.000 0.00 0.00 42.56 3.13
3124 4882 3.846383 GCAGCGTTTTTCAGAGTCAGAAC 60.846 47.826 0.00 0.00 0.00 3.01
3126 4884 1.867233 GCAGCGTTTTTCAGAGTCAGA 59.133 47.619 0.00 0.00 0.00 3.27
3127 4885 1.069636 GGCAGCGTTTTTCAGAGTCAG 60.070 52.381 0.00 0.00 0.00 3.51
3128 4886 0.944386 GGCAGCGTTTTTCAGAGTCA 59.056 50.000 0.00 0.00 0.00 3.41
3129 4887 0.944386 TGGCAGCGTTTTTCAGAGTC 59.056 50.000 0.00 0.00 0.00 3.36
3130 4888 0.663153 GTGGCAGCGTTTTTCAGAGT 59.337 50.000 0.00 0.00 0.00 3.24
3131 4889 0.662619 TGTGGCAGCGTTTTTCAGAG 59.337 50.000 0.00 0.00 0.00 3.35
3132 4890 0.662619 CTGTGGCAGCGTTTTTCAGA 59.337 50.000 0.00 0.00 0.00 3.27
3133 4891 3.168628 CTGTGGCAGCGTTTTTCAG 57.831 52.632 0.00 0.00 0.00 3.02
3151 4909 1.092345 GGCCTCTGACTGAATTCGGC 61.092 60.000 14.40 11.44 33.16 5.54
3177 4935 4.645136 TGAGCGAGGTTCAGAGTTATATGT 59.355 41.667 0.00 0.00 0.00 2.29
3253 5011 0.392461 TTTGGCTGGACGTCTATGGC 60.392 55.000 16.46 16.97 0.00 4.40
3254 5012 1.207089 TCTTTGGCTGGACGTCTATGG 59.793 52.381 16.46 0.00 0.00 2.74
3255 5013 2.672961 TCTTTGGCTGGACGTCTATG 57.327 50.000 16.46 7.04 0.00 2.23
3257 5015 1.336517 CGTTCTTTGGCTGGACGTCTA 60.337 52.381 16.46 8.77 0.00 2.59
3258 5016 0.600255 CGTTCTTTGGCTGGACGTCT 60.600 55.000 16.46 0.00 0.00 4.18
3259 5017 1.860078 CGTTCTTTGGCTGGACGTC 59.140 57.895 7.13 7.13 0.00 4.34
3260 5018 2.251642 GCGTTCTTTGGCTGGACGT 61.252 57.895 0.00 0.00 0.00 4.34
3261 5019 2.250939 TGCGTTCTTTGGCTGGACG 61.251 57.895 3.02 3.02 0.00 4.79
3262 5020 1.282875 GTGCGTTCTTTGGCTGGAC 59.717 57.895 0.00 0.00 0.00 4.02
3263 5021 1.153066 TGTGCGTTCTTTGGCTGGA 60.153 52.632 0.00 0.00 0.00 3.86
3264 5022 1.165907 TCTGTGCGTTCTTTGGCTGG 61.166 55.000 0.00 0.00 0.00 4.85
3265 5023 0.040958 GTCTGTGCGTTCTTTGGCTG 60.041 55.000 0.00 0.00 0.00 4.85
3266 5024 1.498865 CGTCTGTGCGTTCTTTGGCT 61.499 55.000 0.00 0.00 0.00 4.75
3267 5025 1.082756 CGTCTGTGCGTTCTTTGGC 60.083 57.895 0.00 0.00 0.00 4.52
3268 5026 2.307363 ACGTCTGTGCGTTCTTTGG 58.693 52.632 0.00 0.00 43.04 3.28
3276 5034 1.007271 ACTCCAGAACGTCTGTGCG 60.007 57.895 12.10 0.00 42.80 5.34
3277 5035 1.560860 GCACTCCAGAACGTCTGTGC 61.561 60.000 12.10 11.38 42.80 4.57
3278 5036 1.278172 CGCACTCCAGAACGTCTGTG 61.278 60.000 12.10 6.88 42.80 3.66
3279 5037 1.007271 CGCACTCCAGAACGTCTGT 60.007 57.895 12.10 0.00 42.80 3.41
3280 5038 2.375766 GCGCACTCCAGAACGTCTG 61.376 63.158 0.30 7.72 43.91 3.51
3281 5039 2.049063 GCGCACTCCAGAACGTCT 60.049 61.111 0.30 0.00 0.00 4.18
3282 5040 2.049063 AGCGCACTCCAGAACGTC 60.049 61.111 11.47 0.00 0.00 4.34
3283 5041 2.356313 CAGCGCACTCCAGAACGT 60.356 61.111 11.47 0.00 0.00 3.99
3284 5042 3.782244 GCAGCGCACTCCAGAACG 61.782 66.667 11.47 0.00 0.00 3.95
3285 5043 3.426568 GGCAGCGCACTCCAGAAC 61.427 66.667 11.47 0.00 0.00 3.01
3294 5052 0.179023 TAATCATCCATGGCAGCGCA 60.179 50.000 11.47 0.00 0.00 6.09
3295 5053 0.239347 GTAATCATCCATGGCAGCGC 59.761 55.000 6.96 0.00 0.00 5.92
3312 5077 3.028130 TGTTGTCTCAGTGTCAGTGGTA 58.972 45.455 7.82 0.00 0.00 3.25
3345 5110 0.313672 GCAAATTTCACGTGCTCCCA 59.686 50.000 11.67 0.00 35.36 4.37
3346 5111 0.388520 GGCAAATTTCACGTGCTCCC 60.389 55.000 11.67 0.20 38.36 4.30
3347 5112 0.598065 AGGCAAATTTCACGTGCTCC 59.402 50.000 11.67 3.77 38.36 4.70


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

AutoCloner maintained by Alex Coulton.