Multiple sequence alignment - TraesCS6A01G342200

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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 TraesCS6A01G342200 chr6A 100.000 5069 0 0 1 5069 574910635 574915703 0.000000e+00 9361.0
1 TraesCS6A01G342200 chr6A 83.558 1411 210 14 2686 4080 575140853 575139449 0.000000e+00 1301.0
2 TraesCS6A01G342200 chr6A 84.647 482 66 5 2562 3039 575198138 575197661 1.650000e-129 473.0
3 TraesCS6A01G342200 chr6A 87.393 349 44 0 2744 3092 575101320 575100972 7.910000e-108 401.0
4 TraesCS6A01G342200 chr6A 89.355 310 28 2 1021 1325 575200227 575199918 7.960000e-103 385.0
5 TraesCS6A01G342200 chr6A 85.255 373 29 8 961 1325 575143363 575143009 1.340000e-95 361.0
6 TraesCS6A01G342200 chr6B 93.847 2584 115 19 1742 4291 647691769 647694342 0.000000e+00 3851.0
7 TraesCS6A01G342200 chr6B 83.259 2025 274 35 2090 4082 647589913 647591904 0.000000e+00 1801.0
8 TraesCS6A01G342200 chr6B 82.771 1718 273 21 2399 4099 647950703 647948992 0.000000e+00 1511.0
9 TraesCS6A01G342200 chr6B 84.207 1431 218 4 2654 4082 647930993 647929569 0.000000e+00 1384.0
10 TraesCS6A01G342200 chr6B 89.362 705 57 10 650 1342 647690682 647691380 0.000000e+00 870.0
11 TraesCS6A01G342200 chr6B 89.431 615 33 11 4288 4900 647694557 647695141 0.000000e+00 747.0
12 TraesCS6A01G342200 chr6B 90.417 480 33 11 776 1245 647588659 647589135 2.000000e-173 619.0
13 TraesCS6A01G342200 chr6B 88.525 488 45 6 1 483 647641369 647641850 9.460000e-162 580.0
14 TraesCS6A01G342200 chr6B 83.290 389 49 10 862 1245 647933006 647932629 1.350000e-90 344.0
15 TraesCS6A01G342200 chr6B 83.242 364 39 5 966 1324 647952491 647952145 1.060000e-81 315.0
16 TraesCS6A01G342200 chr6B 87.500 272 32 2 961 1232 647837385 647837116 3.810000e-81 313.0
17 TraesCS6A01G342200 chr6B 94.000 200 6 1 1590 1789 647691575 647691768 1.070000e-76 298.0
18 TraesCS6A01G342200 chr6B 89.412 170 13 3 492 661 647642160 647642324 5.140000e-50 209.0
19 TraesCS6A01G342200 chr6B 97.059 34 1 0 1557 1590 647691381 647691414 1.970000e-04 58.4
20 TraesCS6A01G342200 chr6D 90.220 818 59 8 595 1407 429666116 429666917 0.000000e+00 1048.0
21 TraesCS6A01G342200 chr6D 87.529 850 106 0 2949 3798 429674312 429675161 0.000000e+00 983.0
22 TraesCS6A01G342200 chr6D 91.078 538 39 6 72 608 429663924 429664453 0.000000e+00 719.0
23 TraesCS6A01G342200 chr6D 76.387 631 103 27 3817 4411 429708205 429708825 1.070000e-76 298.0
24 TraesCS6A01G342200 chr2D 77.448 1450 290 22 2662 4079 601109021 601110465 0.000000e+00 832.0
25 TraesCS6A01G342200 chr2A 77.714 1400 269 25 2662 4027 734586420 734587810 0.000000e+00 817.0
26 TraesCS6A01G342200 chr4A 76.597 1299 292 10 2789 4081 110638731 110637439 0.000000e+00 704.0
27 TraesCS6A01G342200 chr4A 88.235 255 23 5 984 1236 109843130 109843379 1.070000e-76 298.0
28 TraesCS6A01G342200 chr4D 75.766 1403 321 16 2686 4078 354136405 354137798 0.000000e+00 689.0
29 TraesCS6A01G342200 chr4D 87.597 258 25 5 987 1242 354890714 354890462 4.960000e-75 292.0
30 TraesCS6A01G342200 chr4B 95.597 159 6 1 4912 5069 35550445 35550287 2.340000e-63 254.0
31 TraesCS6A01G342200 chr4B 94.969 159 7 1 4912 5069 448648046 448648204 1.090000e-61 248.0
32 TraesCS6A01G342200 chr5B 94.969 159 7 1 4912 5069 31544629 31544787 1.090000e-61 248.0
33 TraesCS6A01G342200 chr5B 94.969 159 7 1 4912 5069 354608509 354608667 1.090000e-61 248.0
34 TraesCS6A01G342200 chr5B 94.969 159 7 1 4912 5069 464476039 464475881 1.090000e-61 248.0
35 TraesCS6A01G342200 chr5B 94.969 159 7 1 4912 5069 568349108 568348950 1.090000e-61 248.0
36 TraesCS6A01G342200 chr5B 94.969 159 7 1 4912 5069 568664560 568664402 1.090000e-61 248.0
37 TraesCS6A01G342200 chr1B 94.969 159 7 1 4912 5069 96939169 96939327 1.090000e-61 248.0
38 TraesCS6A01G342200 chr2B 93.413 167 8 3 4904 5069 86591739 86591903 1.410000e-60 244.0


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 TraesCS6A01G342200 chr6A 574910635 574915703 5068 False 9361.00 9361 100.0000 1 5069 1 chr6A.!!$F1 5068
1 TraesCS6A01G342200 chr6A 575139449 575143363 3914 True 831.00 1301 84.4065 961 4080 2 chr6A.!!$R2 3119
2 TraesCS6A01G342200 chr6A 575197661 575200227 2566 True 429.00 473 87.0010 1021 3039 2 chr6A.!!$R3 2018
3 TraesCS6A01G342200 chr6B 647588659 647591904 3245 False 1210.00 1801 86.8380 776 4082 2 chr6B.!!$F1 3306
4 TraesCS6A01G342200 chr6B 647690682 647695141 4459 False 1164.88 3851 92.7398 650 4900 5 chr6B.!!$F3 4250
5 TraesCS6A01G342200 chr6B 647948992 647952491 3499 True 913.00 1511 83.0065 966 4099 2 chr6B.!!$R3 3133
6 TraesCS6A01G342200 chr6B 647929569 647933006 3437 True 864.00 1384 83.7485 862 4082 2 chr6B.!!$R2 3220
7 TraesCS6A01G342200 chr6B 647641369 647642324 955 False 394.50 580 88.9685 1 661 2 chr6B.!!$F2 660
8 TraesCS6A01G342200 chr6D 429674312 429675161 849 False 983.00 983 87.5290 2949 3798 1 chr6D.!!$F1 849
9 TraesCS6A01G342200 chr6D 429663924 429666917 2993 False 883.50 1048 90.6490 72 1407 2 chr6D.!!$F3 1335
10 TraesCS6A01G342200 chr6D 429708205 429708825 620 False 298.00 298 76.3870 3817 4411 1 chr6D.!!$F2 594
11 TraesCS6A01G342200 chr2D 601109021 601110465 1444 False 832.00 832 77.4480 2662 4079 1 chr2D.!!$F1 1417
12 TraesCS6A01G342200 chr2A 734586420 734587810 1390 False 817.00 817 77.7140 2662 4027 1 chr2A.!!$F1 1365
13 TraesCS6A01G342200 chr4A 110637439 110638731 1292 True 704.00 704 76.5970 2789 4081 1 chr4A.!!$R1 1292
14 TraesCS6A01G342200 chr4D 354136405 354137798 1393 False 689.00 689 75.7660 2686 4078 1 chr4D.!!$F1 1392

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
346 351 1.044611 TGTGACGATGGACAAGGACA 58.955 50.000 0.0 0.0 0.00 4.02 F
985 2989 1.667830 CGTTTTCCTCTGCTCGGCA 60.668 57.895 0.0 0.0 36.92 5.69 F
2881 7086 0.753479 GATGAGGGAGACAGCGGAGA 60.753 60.000 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1232 3251 0.605589 GGTGGTGGTCAGTTGGTAGC 60.606 60.000 0.00 0.00 0.00 3.58 R
2889 7094 2.525124 ATCCTTCACCGTGGTGCCA 61.525 57.895 14.25 2.64 45.04 4.92 R
4808 9315 0.033366 GCCAAATTGCAAAGGGACGT 59.967 50.000 16.02 0.00 0.00 4.34 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
56 61 3.002862 GTGTTTGCAATAGAACCGACACA 59.997 43.478 17.53 5.72 36.91 3.72
163 168 1.741770 GGCTCACTGGCGTCGAATT 60.742 57.895 0.00 0.00 0.00 2.17
172 177 2.799540 GCGTCGAATTCGGCTCACC 61.800 63.158 27.91 11.33 42.59 4.02
234 239 2.304221 TCGGTATACCATCTCCCTGG 57.696 55.000 21.76 2.23 42.35 4.45
235 240 1.203137 TCGGTATACCATCTCCCTGGG 60.203 57.143 21.76 6.33 40.85 4.45
238 243 1.132495 GTATACCATCTCCCTGGGGGT 60.132 57.143 13.53 14.23 44.74 4.95
275 280 1.416401 ACCTTGGTTTCTCGAAGCTCA 59.584 47.619 0.00 0.00 36.70 4.26
297 302 4.524802 ACCATTGTCATGTCCATATGGT 57.475 40.909 21.28 17.88 40.54 3.55
346 351 1.044611 TGTGACGATGGACAAGGACA 58.955 50.000 0.00 0.00 0.00 4.02
382 387 1.756375 CGCAACTATGTGAGAGCGGC 61.756 60.000 0.00 0.00 44.05 6.53
487 493 7.627340 CATTGCCATCATTTGCTTTAAATCTC 58.373 34.615 0.00 0.00 36.87 2.75
752 2737 5.060446 CGATTTAAAATTCGCCAACAACCTC 59.940 40.000 0.00 0.00 0.00 3.85
985 2989 1.667830 CGTTTTCCTCTGCTCGGCA 60.668 57.895 0.00 0.00 36.92 5.69
999 3003 2.778679 GGCATCTGTCGCGTGAAC 59.221 61.111 5.77 0.00 0.00 3.18
1008 3012 3.425713 CGCGTGAACATGGCAGCT 61.426 61.111 0.00 0.00 0.00 4.24
1027 3031 4.452733 GCACTAAGGGCGACGGCT 62.453 66.667 21.48 4.79 39.81 5.52
1065 3069 4.759893 GGGACGACCTACTCCTGT 57.240 61.111 3.44 0.00 35.85 4.00
1246 3270 1.618837 GTGAGAGCTACCAACTGACCA 59.381 52.381 0.00 0.00 0.00 4.02
1315 3370 9.932207 TCGTTTATTAAGTTTCTCAGGTTCATA 57.068 29.630 0.00 0.00 0.00 2.15
1327 3680 3.568007 TCAGGTTCATAGGTTTGTGTTGC 59.432 43.478 0.00 0.00 0.00 4.17
1334 3687 8.413229 GGTTCATAGGTTTGTGTTGCATATATT 58.587 33.333 0.00 0.00 0.00 1.28
1367 3728 1.068055 GTTGCCAAATGCTCACTCAGG 60.068 52.381 0.00 0.00 42.00 3.86
1378 3742 6.737720 ATGCTCACTCAGGTATTCAGATTA 57.262 37.500 0.00 0.00 0.00 1.75
1392 3756 7.598493 GGTATTCAGATTACTGCATCTTCTCTC 59.402 40.741 0.00 0.00 43.17 3.20
1400 3764 3.204526 CTGCATCTTCTCTCCCATGTTC 58.795 50.000 0.00 0.00 0.00 3.18
1405 3769 5.184671 GCATCTTCTCTCCCATGTTCTTTTT 59.815 40.000 0.00 0.00 0.00 1.94
1406 3770 6.618811 CATCTTCTCTCCCATGTTCTTTTTG 58.381 40.000 0.00 0.00 0.00 2.44
1408 3772 6.129179 TCTTCTCTCCCATGTTCTTTTTGTT 58.871 36.000 0.00 0.00 0.00 2.83
1410 3774 6.147864 TCTCTCCCATGTTCTTTTTGTTTG 57.852 37.500 0.00 0.00 0.00 2.93
1411 3775 4.692228 TCTCCCATGTTCTTTTTGTTTGC 58.308 39.130 0.00 0.00 0.00 3.68
1412 3776 4.405358 TCTCCCATGTTCTTTTTGTTTGCT 59.595 37.500 0.00 0.00 0.00 3.91
1413 3777 4.440880 TCCCATGTTCTTTTTGTTTGCTG 58.559 39.130 0.00 0.00 0.00 4.41
1414 3778 4.161189 TCCCATGTTCTTTTTGTTTGCTGA 59.839 37.500 0.00 0.00 0.00 4.26
1415 3779 4.508861 CCCATGTTCTTTTTGTTTGCTGAG 59.491 41.667 0.00 0.00 0.00 3.35
1416 3780 5.350633 CCATGTTCTTTTTGTTTGCTGAGA 58.649 37.500 0.00 0.00 0.00 3.27
1417 3781 5.987347 CCATGTTCTTTTTGTTTGCTGAGAT 59.013 36.000 0.00 0.00 0.00 2.75
1418 3782 6.145048 CCATGTTCTTTTTGTTTGCTGAGATC 59.855 38.462 0.00 0.00 0.00 2.75
1419 3783 5.273170 TGTTCTTTTTGTTTGCTGAGATCG 58.727 37.500 0.00 0.00 0.00 3.69
1420 3784 4.488126 TCTTTTTGTTTGCTGAGATCGG 57.512 40.909 0.00 0.00 0.00 4.18
1421 3785 3.882888 TCTTTTTGTTTGCTGAGATCGGT 59.117 39.130 0.00 0.00 0.00 4.69
1422 3786 4.338118 TCTTTTTGTTTGCTGAGATCGGTT 59.662 37.500 0.00 0.00 0.00 4.44
1423 3787 4.647424 TTTTGTTTGCTGAGATCGGTTT 57.353 36.364 0.00 0.00 0.00 3.27
1424 3788 4.647424 TTTGTTTGCTGAGATCGGTTTT 57.353 36.364 0.00 0.00 0.00 2.43
1425 3789 4.647424 TTGTTTGCTGAGATCGGTTTTT 57.353 36.364 0.00 0.00 0.00 1.94
1456 3820 7.259882 TCAATATTGATCTGTGCCATGTTTTC 58.740 34.615 14.23 0.00 31.01 2.29
1459 3823 5.534207 TTGATCTGTGCCATGTTTTCTTT 57.466 34.783 0.00 0.00 0.00 2.52
1460 3824 5.534207 TGATCTGTGCCATGTTTTCTTTT 57.466 34.783 0.00 0.00 0.00 2.27
1461 3825 5.916318 TGATCTGTGCCATGTTTTCTTTTT 58.084 33.333 0.00 0.00 0.00 1.94
1490 3854 5.895636 TGGTTCTGCCATGTAGTTATTTG 57.104 39.130 0.00 0.00 43.61 2.32
1491 3855 5.321102 TGGTTCTGCCATGTAGTTATTTGT 58.679 37.500 0.00 0.00 43.61 2.83
1492 3856 5.772672 TGGTTCTGCCATGTAGTTATTTGTT 59.227 36.000 0.00 0.00 43.61 2.83
1494 3858 6.586082 GGTTCTGCCATGTAGTTATTTGTTTG 59.414 38.462 0.00 0.00 37.17 2.93
1495 3859 6.892658 TCTGCCATGTAGTTATTTGTTTGT 57.107 33.333 0.00 0.00 0.00 2.83
1497 3861 7.812648 TCTGCCATGTAGTTATTTGTTTGTAC 58.187 34.615 0.00 0.00 0.00 2.90
1504 3983 9.893305 ATGTAGTTATTTGTTTGTACAAGCTTC 57.107 29.630 21.06 8.94 44.56 3.86
1523 4002 1.351017 TCCAAGCACTAAGAACCCCTG 59.649 52.381 0.00 0.00 0.00 4.45
1526 4005 3.335579 CAAGCACTAAGAACCCCTGTAC 58.664 50.000 0.00 0.00 0.00 2.90
1527 4006 2.903926 AGCACTAAGAACCCCTGTACT 58.096 47.619 0.00 0.00 0.00 2.73
1531 4010 4.024670 CACTAAGAACCCCTGTACTAGCT 58.975 47.826 0.00 0.00 0.00 3.32
1536 4036 2.570386 ACCCCTGTACTAGCTGGATT 57.430 50.000 3.17 0.00 0.00 3.01
1538 4038 2.292918 ACCCCTGTACTAGCTGGATTCA 60.293 50.000 3.17 0.00 0.00 2.57
1541 4041 4.324254 CCCCTGTACTAGCTGGATTCAAAA 60.324 45.833 3.17 0.00 0.00 2.44
1542 4042 5.253330 CCCTGTACTAGCTGGATTCAAAAA 58.747 41.667 3.17 0.00 0.00 1.94
1656 4317 9.649167 GTTAGTACTACAACATAGGAAACACAT 57.351 33.333 0.91 0.00 0.00 3.21
1659 4320 7.972277 AGTACTACAACATAGGAAACACATACG 59.028 37.037 0.00 0.00 0.00 3.06
1706 4368 5.519927 GTGGAAACTTTCTTGTGAAATGTGG 59.480 40.000 1.57 0.00 40.85 4.17
1853 4576 8.556213 TCAAGAAACTGCGTTAAAAGGTATAT 57.444 30.769 0.00 0.00 0.00 0.86
1854 4577 9.005777 TCAAGAAACTGCGTTAAAAGGTATATT 57.994 29.630 0.00 0.00 0.00 1.28
1858 4581 7.933215 AACTGCGTTAAAAGGTATATTTCCT 57.067 32.000 0.00 0.00 36.81 3.36
1952 5088 3.448934 ACAATACATTGCAATTCCCCCA 58.551 40.909 9.83 0.00 41.38 4.96
2315 6474 8.248904 TGGCAATATTGAGTGGCTTATTAATT 57.751 30.769 19.73 0.00 45.69 1.40
2387 6558 7.305474 CACAACAAACTACATAATCAAGACCC 58.695 38.462 0.00 0.00 0.00 4.46
2404 6576 6.765989 TCAAGACCCAATTCCAGATAATTACG 59.234 38.462 0.00 0.00 0.00 3.18
2469 6642 1.714541 TTGCATTTGTGATGTGGGGT 58.285 45.000 0.00 0.00 0.00 4.95
2787 6992 3.896133 GGCCGTAGCGATCGACCA 61.896 66.667 21.57 0.00 41.24 4.02
2881 7086 0.753479 GATGAGGGAGACAGCGGAGA 60.753 60.000 0.00 0.00 0.00 3.71
2889 7094 0.039911 AGACAGCGGAGACCTACCTT 59.960 55.000 0.00 0.00 0.00 3.50
3123 7334 6.351711 CACCTTGGATATCTCTGTCATCAAA 58.648 40.000 2.05 0.00 0.00 2.69
3285 7502 2.898738 CTGATGCGGCTCAGGACT 59.101 61.111 16.67 0.00 39.20 3.85
3288 7505 3.382803 GATGCGGCTCAGGACTGCT 62.383 63.158 0.00 0.00 0.00 4.24
3306 7523 1.892819 CTTGCGAGAGGGCCAAGAGA 61.893 60.000 6.18 0.00 0.00 3.10
3330 7547 2.604686 TCTTCCACGGCAGAGGCT 60.605 61.111 0.00 0.00 40.87 4.58
3637 7854 2.978010 CCGCCATCCATAACGGCC 60.978 66.667 0.00 0.00 43.17 6.13
3675 7892 1.546961 ACGACTTGGTCCTTCTCGAT 58.453 50.000 8.94 0.00 0.00 3.59
3703 7920 1.448922 GCTGTCGCTCGGGATAGAGT 61.449 60.000 11.01 0.00 40.26 3.24
3806 8049 4.814294 CTACCAGACCGCCGTGCC 62.814 72.222 0.00 0.00 0.00 5.01
3838 8081 3.268032 AGGGGGAAGCAGGGTTGG 61.268 66.667 0.00 0.00 0.00 3.77
3870 8113 2.048444 ATCTGCTCGGCATGTTCAAT 57.952 45.000 0.00 0.00 38.13 2.57
3931 8174 3.120683 GCTCAATGTGACGTTCGAAATCA 60.121 43.478 0.00 4.16 0.00 2.57
3970 8213 2.104859 GTAACGGCGGAGGAAAGGC 61.105 63.158 13.24 0.00 0.00 4.35
4047 8291 5.643421 AGCAAGAGATTGATAGGATGGTT 57.357 39.130 0.00 0.00 0.00 3.67
4118 8372 3.334604 TCATGGCCATGAGGGTCC 58.665 61.111 38.91 0.00 42.20 4.46
4119 8373 1.308128 TCATGGCCATGAGGGTCCT 60.308 57.895 38.91 3.77 42.20 3.85
4120 8374 1.152819 CATGGCCATGAGGGTCCTG 60.153 63.158 37.84 11.54 42.20 3.86
4185 8466 5.458041 TGGATGCTTATTAGTACCGGTAC 57.542 43.478 33.16 33.16 36.35 3.34
4220 8501 1.807981 GCATTGCGCATGTGCATGT 60.808 52.632 32.67 21.72 45.78 3.21
4260 8541 9.471742 GCTTGTGTTTACTGTTATTTTGTTTTG 57.528 29.630 0.00 0.00 0.00 2.44
4309 8808 2.348411 AATTGCCTAAGGTGATCCGG 57.652 50.000 0.00 0.00 39.05 5.14
4447 8954 8.593057 TTTTGTAAATTGAACATTTGTTTGCG 57.407 26.923 0.00 0.00 38.56 4.85
4450 8957 3.857923 ATTGAACATTTGTTTGCGCAC 57.142 38.095 11.12 0.00 38.56 5.34
4451 8958 2.284263 TGAACATTTGTTTGCGCACA 57.716 40.000 11.12 0.00 38.56 4.57
4453 8960 1.071305 GAACATTTGTTTGCGCACAGC 60.071 47.619 11.12 3.46 41.85 4.40
4454 8961 4.511851 GAACATTTGTTTGCGCACAGCG 62.512 50.000 11.12 7.08 46.23 5.18
4465 8972 3.023949 GCACAGCGACCCCTCTGAT 62.024 63.158 0.00 0.00 34.57 2.90
4541 9048 9.471084 CGGTTTCTTTTAATGTCACCTTTATTT 57.529 29.630 0.00 0.00 0.00 1.40
4663 9170 3.057315 ACGAGCACATTTCTCCAAAATGG 60.057 43.478 13.36 0.00 40.84 3.16
4675 9182 6.874278 TCTCCAAAATGGTCTGAAGATCTA 57.126 37.500 0.00 0.00 39.03 1.98
4745 9252 3.636300 CACTGGAAAGTGGAACATGGAAA 59.364 43.478 0.00 0.00 44.52 3.13
4746 9253 4.099266 CACTGGAAAGTGGAACATGGAAAA 59.901 41.667 0.00 0.00 44.52 2.29
4747 9254 4.714308 ACTGGAAAGTGGAACATGGAAAAA 59.286 37.500 0.00 0.00 44.52 1.94
4769 9276 2.218239 GCTCGCTCGCTACTTGTCG 61.218 63.158 0.00 0.00 0.00 4.35
4780 9287 1.764571 TACTTGTCGGGGTTGCTGCT 61.765 55.000 0.00 0.00 0.00 4.24
4824 9331 4.119136 CAGAAAACGTCCCTTTGCAATTT 58.881 39.130 0.00 0.00 0.00 1.82
4840 9347 6.387972 TGCAATTTGGCTGCATTTTGATGC 62.388 41.667 0.50 4.50 44.67 3.91
4855 9362 7.095940 GCATTTTGATGCATAATGTGTCATACC 60.096 37.037 17.72 0.87 46.25 2.73
4871 9378 3.386078 TCATACCAGAGCTCCTGTGATTC 59.614 47.826 10.93 0.00 41.33 2.52
4884 9391 4.698304 TCCTGTGATTCCCGATGTAAAAAC 59.302 41.667 0.00 0.00 0.00 2.43
4889 9396 7.265673 TGTGATTCCCGATGTAAAAACAAAAA 58.734 30.769 0.00 0.00 0.00 1.94
4890 9397 7.436673 TGTGATTCCCGATGTAAAAACAAAAAG 59.563 33.333 0.00 0.00 0.00 2.27
4891 9398 7.650104 GTGATTCCCGATGTAAAAACAAAAAGA 59.350 33.333 0.00 0.00 0.00 2.52
4892 9399 7.865385 TGATTCCCGATGTAAAAACAAAAAGAG 59.135 33.333 0.00 0.00 0.00 2.85
4893 9400 5.525199 TCCCGATGTAAAAACAAAAAGAGC 58.475 37.500 0.00 0.00 0.00 4.09
4894 9401 5.300792 TCCCGATGTAAAAACAAAAAGAGCT 59.699 36.000 0.00 0.00 0.00 4.09
4895 9402 5.629435 CCCGATGTAAAAACAAAAAGAGCTC 59.371 40.000 5.27 5.27 0.00 4.09
4896 9403 5.629435 CCGATGTAAAAACAAAAAGAGCTCC 59.371 40.000 10.93 0.00 0.00 4.70
4897 9404 6.438763 CGATGTAAAAACAAAAAGAGCTCCT 58.561 36.000 10.93 0.00 0.00 3.69
4898 9405 6.360681 CGATGTAAAAACAAAAAGAGCTCCTG 59.639 38.462 10.93 5.65 0.00 3.86
4899 9406 6.524101 TGTAAAAACAAAAAGAGCTCCTGT 57.476 33.333 10.93 6.32 0.00 4.00
4900 9407 6.560711 TGTAAAAACAAAAAGAGCTCCTGTC 58.439 36.000 10.93 0.00 0.00 3.51
4901 9408 5.659440 AAAAACAAAAAGAGCTCCTGTCA 57.341 34.783 10.93 0.00 0.00 3.58
4902 9409 5.859205 AAAACAAAAAGAGCTCCTGTCAT 57.141 34.783 10.93 0.03 0.00 3.06
4903 9410 6.959639 AAAACAAAAAGAGCTCCTGTCATA 57.040 33.333 10.93 0.00 0.00 2.15
4904 9411 5.948992 AACAAAAAGAGCTCCTGTCATAC 57.051 39.130 10.93 0.00 0.00 2.39
4905 9412 4.327680 ACAAAAAGAGCTCCTGTCATACC 58.672 43.478 10.93 0.00 0.00 2.73
4906 9413 4.202461 ACAAAAAGAGCTCCTGTCATACCA 60.202 41.667 10.93 0.00 0.00 3.25
4907 9414 3.902881 AAAGAGCTCCTGTCATACCAG 57.097 47.619 10.93 0.00 0.00 4.00
4908 9415 2.836636 AGAGCTCCTGTCATACCAGA 57.163 50.000 10.93 0.00 34.23 3.86
4909 9416 2.665165 AGAGCTCCTGTCATACCAGAG 58.335 52.381 10.93 0.00 34.23 3.35
4910 9417 1.068434 GAGCTCCTGTCATACCAGAGC 59.932 57.143 0.87 2.15 36.61 4.09
4911 9418 0.249238 GCTCCTGTCATACCAGAGCG 60.249 60.000 0.00 0.00 34.23 5.03
4912 9419 0.387202 CTCCTGTCATACCAGAGCGG 59.613 60.000 0.00 0.00 42.50 5.52
4913 9420 1.043116 TCCTGTCATACCAGAGCGGG 61.043 60.000 0.00 0.00 40.22 6.13
4914 9421 1.227380 CTGTCATACCAGAGCGGGC 60.227 63.158 0.00 0.00 40.22 6.13
4915 9422 1.680522 CTGTCATACCAGAGCGGGCT 61.681 60.000 0.00 0.00 40.22 5.19
4916 9423 1.227380 GTCATACCAGAGCGGGCTG 60.227 63.158 0.00 0.00 40.22 4.85
4917 9424 1.685765 TCATACCAGAGCGGGCTGT 60.686 57.895 0.00 0.00 40.22 4.40
4918 9425 1.221840 CATACCAGAGCGGGCTGTT 59.778 57.895 0.00 0.00 40.22 3.16
4919 9426 0.392998 CATACCAGAGCGGGCTGTTT 60.393 55.000 0.00 0.00 40.22 2.83
4920 9427 0.392998 ATACCAGAGCGGGCTGTTTG 60.393 55.000 0.00 0.00 40.22 2.93
4921 9428 2.463589 TACCAGAGCGGGCTGTTTGG 62.464 60.000 0.00 5.95 40.22 3.28
4922 9429 2.032528 CAGAGCGGGCTGTTTGGA 59.967 61.111 0.00 0.00 0.00 3.53
4923 9430 1.377725 CAGAGCGGGCTGTTTGGAT 60.378 57.895 0.00 0.00 0.00 3.41
4924 9431 0.962356 CAGAGCGGGCTGTTTGGATT 60.962 55.000 0.00 0.00 0.00 3.01
4925 9432 0.962356 AGAGCGGGCTGTTTGGATTG 60.962 55.000 0.00 0.00 0.00 2.67
4926 9433 1.228552 AGCGGGCTGTTTGGATTGT 60.229 52.632 0.00 0.00 0.00 2.71
4927 9434 1.080569 GCGGGCTGTTTGGATTGTG 60.081 57.895 0.00 0.00 0.00 3.33
4928 9435 1.523154 GCGGGCTGTTTGGATTGTGA 61.523 55.000 0.00 0.00 0.00 3.58
4929 9436 0.240945 CGGGCTGTTTGGATTGTGAC 59.759 55.000 0.00 0.00 0.00 3.67
4930 9437 1.620822 GGGCTGTTTGGATTGTGACT 58.379 50.000 0.00 0.00 0.00 3.41
4931 9438 2.790433 GGGCTGTTTGGATTGTGACTA 58.210 47.619 0.00 0.00 0.00 2.59
4932 9439 3.356290 GGGCTGTTTGGATTGTGACTAT 58.644 45.455 0.00 0.00 0.00 2.12
4933 9440 4.523083 GGGCTGTTTGGATTGTGACTATA 58.477 43.478 0.00 0.00 0.00 1.31
4934 9441 5.133221 GGGCTGTTTGGATTGTGACTATAT 58.867 41.667 0.00 0.00 0.00 0.86
4935 9442 5.594317 GGGCTGTTTGGATTGTGACTATATT 59.406 40.000 0.00 0.00 0.00 1.28
4936 9443 6.096846 GGGCTGTTTGGATTGTGACTATATTT 59.903 38.462 0.00 0.00 0.00 1.40
4937 9444 7.284489 GGGCTGTTTGGATTGTGACTATATTTA 59.716 37.037 0.00 0.00 0.00 1.40
4938 9445 8.850156 GGCTGTTTGGATTGTGACTATATTTAT 58.150 33.333 0.00 0.00 0.00 1.40
4939 9446 9.884465 GCTGTTTGGATTGTGACTATATTTATC 57.116 33.333 0.00 0.00 0.00 1.75
4962 9469 7.949903 TCATATATTGCCACATGATTTTTGC 57.050 32.000 0.00 0.00 0.00 3.68
4963 9470 6.930164 TCATATATTGCCACATGATTTTTGCC 59.070 34.615 0.00 0.00 0.00 4.52
4964 9471 2.924757 TTGCCACATGATTTTTGCCA 57.075 40.000 0.00 0.00 0.00 4.92
4965 9472 2.166821 TGCCACATGATTTTTGCCAC 57.833 45.000 0.00 0.00 0.00 5.01
4966 9473 1.415289 TGCCACATGATTTTTGCCACA 59.585 42.857 0.00 0.00 0.00 4.17
4967 9474 1.799994 GCCACATGATTTTTGCCACAC 59.200 47.619 0.00 0.00 0.00 3.82
4968 9475 2.548493 GCCACATGATTTTTGCCACACT 60.548 45.455 0.00 0.00 0.00 3.55
4969 9476 3.731089 CCACATGATTTTTGCCACACTT 58.269 40.909 0.00 0.00 0.00 3.16
4970 9477 3.742369 CCACATGATTTTTGCCACACTTC 59.258 43.478 0.00 0.00 0.00 3.01
4971 9478 3.742369 CACATGATTTTTGCCACACTTCC 59.258 43.478 0.00 0.00 0.00 3.46
4972 9479 3.642848 ACATGATTTTTGCCACACTTCCT 59.357 39.130 0.00 0.00 0.00 3.36
4973 9480 4.101430 ACATGATTTTTGCCACACTTCCTT 59.899 37.500 0.00 0.00 0.00 3.36
4974 9481 5.304101 ACATGATTTTTGCCACACTTCCTTA 59.696 36.000 0.00 0.00 0.00 2.69
4975 9482 5.195001 TGATTTTTGCCACACTTCCTTAC 57.805 39.130 0.00 0.00 0.00 2.34
4976 9483 4.892934 TGATTTTTGCCACACTTCCTTACT 59.107 37.500 0.00 0.00 0.00 2.24
4977 9484 5.362430 TGATTTTTGCCACACTTCCTTACTT 59.638 36.000 0.00 0.00 0.00 2.24
4978 9485 4.647424 TTTTGCCACACTTCCTTACTTG 57.353 40.909 0.00 0.00 0.00 3.16
4979 9486 3.569194 TTGCCACACTTCCTTACTTGA 57.431 42.857 0.00 0.00 0.00 3.02
4980 9487 3.126001 TGCCACACTTCCTTACTTGAG 57.874 47.619 0.00 0.00 0.00 3.02
4981 9488 2.438021 TGCCACACTTCCTTACTTGAGT 59.562 45.455 0.00 0.00 0.00 3.41
4982 9489 3.118038 TGCCACACTTCCTTACTTGAGTT 60.118 43.478 0.00 0.00 0.00 3.01
4983 9490 3.251004 GCCACACTTCCTTACTTGAGTTG 59.749 47.826 0.00 0.00 0.00 3.16
4984 9491 3.251004 CCACACTTCCTTACTTGAGTTGC 59.749 47.826 0.00 0.00 0.00 4.17
4985 9492 4.130118 CACACTTCCTTACTTGAGTTGCT 58.870 43.478 0.00 0.00 0.00 3.91
4986 9493 4.212214 CACACTTCCTTACTTGAGTTGCTC 59.788 45.833 0.00 0.00 0.00 4.26
4987 9494 4.141711 ACACTTCCTTACTTGAGTTGCTCA 60.142 41.667 0.00 0.00 38.87 4.26
4988 9495 4.816385 CACTTCCTTACTTGAGTTGCTCAA 59.184 41.667 10.61 10.61 46.50 3.02
4998 9505 4.503741 TGAGTTGCTCAAATTGTTAGCC 57.496 40.909 4.54 0.00 37.57 3.93
4999 9506 3.888323 TGAGTTGCTCAAATTGTTAGCCA 59.112 39.130 4.54 0.00 37.57 4.75
5000 9507 4.229876 GAGTTGCTCAAATTGTTAGCCAC 58.770 43.478 4.54 4.08 35.33 5.01
5001 9508 3.636300 AGTTGCTCAAATTGTTAGCCACA 59.364 39.130 11.51 0.00 35.09 4.17
5002 9509 4.281688 AGTTGCTCAAATTGTTAGCCACAT 59.718 37.500 11.51 0.00 35.09 3.21
5003 9510 4.870123 TGCTCAAATTGTTAGCCACATT 57.130 36.364 4.54 0.00 34.43 2.71
5004 9511 5.212532 TGCTCAAATTGTTAGCCACATTT 57.787 34.783 4.54 0.00 34.43 2.32
5005 9512 5.609423 TGCTCAAATTGTTAGCCACATTTT 58.391 33.333 4.54 2.24 38.80 1.82
5017 9524 2.963432 CCACATTTTGGCTTGCCTAAG 58.037 47.619 13.18 3.76 39.07 2.18
5018 9525 2.354003 CCACATTTTGGCTTGCCTAAGG 60.354 50.000 13.18 10.73 39.07 2.69
5019 9526 1.901833 ACATTTTGGCTTGCCTAAGGG 59.098 47.619 13.18 9.49 34.40 3.95
5020 9527 2.178580 CATTTTGGCTTGCCTAAGGGA 58.821 47.619 13.18 0.00 34.40 4.20
5021 9528 2.390225 TTTTGGCTTGCCTAAGGGAA 57.610 45.000 13.18 0.00 34.40 3.97
5022 9529 2.621556 TTTGGCTTGCCTAAGGGAAT 57.378 45.000 13.18 0.00 31.43 3.01
5023 9530 2.143876 TTGGCTTGCCTAAGGGAATC 57.856 50.000 13.18 0.00 31.43 2.52
5024 9531 1.298953 TGGCTTGCCTAAGGGAATCT 58.701 50.000 13.18 0.00 31.43 2.40
5025 9532 1.640670 TGGCTTGCCTAAGGGAATCTT 59.359 47.619 13.18 0.00 39.40 2.40
5026 9533 2.027385 GGCTTGCCTAAGGGAATCTTG 58.973 52.381 4.11 0.00 36.93 3.02
5027 9534 1.406898 GCTTGCCTAAGGGAATCTTGC 59.593 52.381 0.00 0.00 36.93 4.01
5028 9535 2.027385 CTTGCCTAAGGGAATCTTGCC 58.973 52.381 0.00 0.00 39.23 4.52
5029 9536 0.998928 TGCCTAAGGGAATCTTGCCA 59.001 50.000 3.19 0.00 41.75 4.92
5030 9537 1.340991 TGCCTAAGGGAATCTTGCCAC 60.341 52.381 3.19 0.00 41.75 5.01
5031 9538 1.340991 GCCTAAGGGAATCTTGCCACA 60.341 52.381 3.19 0.00 41.75 4.17
5032 9539 2.369394 CCTAAGGGAATCTTGCCACAC 58.631 52.381 3.19 0.00 41.75 3.82
5033 9540 2.025887 CCTAAGGGAATCTTGCCACACT 60.026 50.000 3.19 0.00 41.75 3.55
5034 9541 2.683211 AAGGGAATCTTGCCACACTT 57.317 45.000 3.19 0.00 41.75 3.16
5035 9542 2.683211 AGGGAATCTTGCCACACTTT 57.317 45.000 3.19 0.00 41.75 2.66
5036 9543 2.519013 AGGGAATCTTGCCACACTTTC 58.481 47.619 3.19 0.00 41.75 2.62
5037 9544 2.108952 AGGGAATCTTGCCACACTTTCT 59.891 45.455 3.19 0.00 41.75 2.52
5038 9545 3.330701 AGGGAATCTTGCCACACTTTCTA 59.669 43.478 3.19 0.00 41.75 2.10
5039 9546 4.018050 AGGGAATCTTGCCACACTTTCTAT 60.018 41.667 3.19 0.00 41.75 1.98
5040 9547 4.096984 GGGAATCTTGCCACACTTTCTATG 59.903 45.833 0.00 0.00 38.72 2.23
5041 9548 4.702131 GGAATCTTGCCACACTTTCTATGT 59.298 41.667 0.00 0.00 0.00 2.29
5042 9549 5.163713 GGAATCTTGCCACACTTTCTATGTC 60.164 44.000 0.00 0.00 0.00 3.06
5043 9550 4.623932 TCTTGCCACACTTTCTATGTCT 57.376 40.909 0.00 0.00 0.00 3.41
5044 9551 5.738619 TCTTGCCACACTTTCTATGTCTA 57.261 39.130 0.00 0.00 0.00 2.59
5045 9552 6.299805 TCTTGCCACACTTTCTATGTCTAT 57.700 37.500 0.00 0.00 0.00 1.98
5046 9553 6.108687 TCTTGCCACACTTTCTATGTCTATG 58.891 40.000 0.00 0.00 0.00 2.23
5047 9554 5.675684 TGCCACACTTTCTATGTCTATGA 57.324 39.130 0.00 0.00 0.00 2.15
5048 9555 5.419542 TGCCACACTTTCTATGTCTATGAC 58.580 41.667 0.00 0.00 0.00 3.06
5049 9556 5.046663 TGCCACACTTTCTATGTCTATGACA 60.047 40.000 2.77 2.77 46.90 3.58
5058 9565 1.583556 TGTCTATGACATGTGGGGCT 58.416 50.000 1.15 0.00 37.67 5.19
5059 9566 1.486310 TGTCTATGACATGTGGGGCTC 59.514 52.381 1.15 0.00 37.67 4.70
5060 9567 1.486310 GTCTATGACATGTGGGGCTCA 59.514 52.381 1.15 0.00 32.09 4.26
5061 9568 1.486310 TCTATGACATGTGGGGCTCAC 59.514 52.381 11.49 11.49 46.23 3.51
5062 9569 1.487976 CTATGACATGTGGGGCTCACT 59.512 52.381 19.90 0.00 46.20 3.41
5063 9570 0.034767 ATGACATGTGGGGCTCACTG 60.035 55.000 19.90 15.99 46.20 3.66
5064 9571 2.034687 ACATGTGGGGCTCACTGC 59.965 61.111 19.90 0.00 46.20 4.40
5065 9572 2.353958 CATGTGGGGCTCACTGCT 59.646 61.111 19.90 0.16 46.20 4.24
5066 9573 1.748122 CATGTGGGGCTCACTGCTC 60.748 63.158 19.90 0.00 46.20 4.26
5067 9574 2.226315 ATGTGGGGCTCACTGCTCA 61.226 57.895 19.90 0.00 46.01 4.26
5068 9575 1.569030 ATGTGGGGCTCACTGCTCAT 61.569 55.000 19.90 0.00 46.01 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.672363 ACATGCCAACGTGATATGCTG 59.328 47.619 0.00 0.00 36.58 4.41
56 61 1.338105 TGCTCGACATGCTACAAGCTT 60.338 47.619 0.00 0.00 42.97 3.74
70 75 8.710835 TTTTCATACTACATATGTTTGCTCGA 57.289 30.769 14.77 1.85 41.44 4.04
101 106 4.508405 CCCAACTGAAGGTTAGGGATTTCA 60.508 45.833 0.00 0.00 43.03 2.69
102 107 4.017126 CCCAACTGAAGGTTAGGGATTTC 58.983 47.826 0.00 0.00 43.03 2.17
234 239 2.113139 CCACCATGCCGATACCCC 59.887 66.667 0.00 0.00 0.00 4.95
235 240 1.071471 CTCCACCATGCCGATACCC 59.929 63.158 0.00 0.00 0.00 3.69
238 243 0.468226 GGTTCTCCACCATGCCGATA 59.532 55.000 0.00 0.00 46.42 2.92
262 267 3.476552 ACAATGGTTGAGCTTCGAGAAA 58.523 40.909 0.00 0.00 0.00 2.52
264 269 2.037121 TGACAATGGTTGAGCTTCGAGA 59.963 45.455 0.00 0.00 0.00 4.04
265 270 2.416747 TGACAATGGTTGAGCTTCGAG 58.583 47.619 0.00 0.00 0.00 4.04
275 280 4.646040 CACCATATGGACATGACAATGGTT 59.354 41.667 28.77 0.00 43.43 3.67
297 302 1.153765 CACAGAATCTCGCTCGCCA 60.154 57.895 0.00 0.00 0.00 5.69
346 351 0.666577 GCGTTGTTGCTCCTCGTACT 60.667 55.000 0.00 0.00 0.00 2.73
393 398 2.168521 CTCGTCTATCCCATGTGGTTGT 59.831 50.000 0.00 0.00 34.77 3.32
487 493 9.726438 TTATACCAAAAGAAGAGAGAAGAAAGG 57.274 33.333 0.00 0.00 0.00 3.11
537 844 8.127150 AGCATAAAAAGAAAGTCTAAGGCAAT 57.873 30.769 0.00 0.00 0.00 3.56
538 845 7.524717 AGCATAAAAAGAAAGTCTAAGGCAA 57.475 32.000 0.00 0.00 0.00 4.52
539 846 7.524717 AAGCATAAAAAGAAAGTCTAAGGCA 57.475 32.000 0.00 0.00 0.00 4.75
724 2709 6.197364 TGTTGGCGAATTTTAAATCGGTAT 57.803 33.333 11.91 0.00 39.38 2.73
879 2879 0.747255 GTGCATAGGAAGGCGAGAGA 59.253 55.000 0.00 0.00 34.35 3.10
947 2951 2.342179 GAAGAGTGCAGAAGTACAGGC 58.658 52.381 0.00 0.00 32.20 4.85
985 2989 1.361668 GCCATGTTCACGCGACAGAT 61.362 55.000 15.93 0.00 0.00 2.90
999 3003 1.381928 CCTTAGTGCCAGCTGCCATG 61.382 60.000 8.66 0.00 40.16 3.66
1008 3012 4.077184 CCGTCGCCCTTAGTGCCA 62.077 66.667 0.00 0.00 0.00 4.92
1232 3251 0.605589 GGTGGTGGTCAGTTGGTAGC 60.606 60.000 0.00 0.00 0.00 3.58
1246 3270 3.243724 AGAAGAAGAACTAGCAGGTGGT 58.756 45.455 0.00 0.00 0.00 4.16
1334 3687 6.101332 GCATTTGGCAACTGAAGAATATGAA 58.899 36.000 20.24 0.00 43.97 2.57
1367 3728 7.598493 GGAGAGAAGATGCAGTAATCTGAATAC 59.402 40.741 0.00 0.00 39.84 1.89
1378 3742 2.194859 ACATGGGAGAGAAGATGCAGT 58.805 47.619 0.00 0.00 0.00 4.40
1392 3756 4.440880 TCAGCAAACAAAAAGAACATGGG 58.559 39.130 0.00 0.00 0.00 4.00
1400 3764 4.228912 ACCGATCTCAGCAAACAAAAAG 57.771 40.909 0.00 0.00 0.00 2.27
1424 3788 7.894708 TGGCACAGATCAATATTGAAGAAAAA 58.105 30.769 21.50 0.00 41.13 1.94
1425 3789 7.465353 TGGCACAGATCAATATTGAAGAAAA 57.535 32.000 21.50 0.00 41.13 2.29
1459 3823 1.323271 TGGCAGAACCACCGCAAAAA 61.323 50.000 0.00 0.00 46.36 1.94
1460 3824 1.754621 TGGCAGAACCACCGCAAAA 60.755 52.632 0.00 0.00 46.36 2.44
1461 3825 2.124109 TGGCAGAACCACCGCAAA 60.124 55.556 0.00 0.00 46.36 3.68
1469 3833 5.897377 ACAAATAACTACATGGCAGAACC 57.103 39.130 0.00 0.00 39.84 3.62
1470 3834 7.145323 ACAAACAAATAACTACATGGCAGAAC 58.855 34.615 0.00 0.00 0.00 3.01
1471 3835 7.283625 ACAAACAAATAACTACATGGCAGAA 57.716 32.000 0.00 0.00 0.00 3.02
1472 3836 6.892658 ACAAACAAATAACTACATGGCAGA 57.107 33.333 0.00 0.00 0.00 4.26
1473 3837 7.589395 TGTACAAACAAATAACTACATGGCAG 58.411 34.615 0.00 0.00 30.91 4.85
1475 3839 7.061789 GCTTGTACAAACAAATAACTACATGGC 59.938 37.037 10.03 0.00 44.79 4.40
1476 3840 8.296713 AGCTTGTACAAACAAATAACTACATGG 58.703 33.333 10.03 0.00 44.79 3.66
1477 3841 9.677567 AAGCTTGTACAAACAAATAACTACATG 57.322 29.630 10.03 0.00 44.79 3.21
1478 3842 9.893305 GAAGCTTGTACAAACAAATAACTACAT 57.107 29.630 2.10 0.00 44.79 2.29
1479 3843 8.347035 GGAAGCTTGTACAAACAAATAACTACA 58.653 33.333 2.10 0.00 44.79 2.74
1480 3844 8.347035 TGGAAGCTTGTACAAACAAATAACTAC 58.653 33.333 2.10 0.00 44.79 2.73
1481 3845 8.453238 TGGAAGCTTGTACAAACAAATAACTA 57.547 30.769 2.10 0.00 44.79 2.24
1482 3846 7.341445 TGGAAGCTTGTACAAACAAATAACT 57.659 32.000 2.10 0.00 44.79 2.24
1483 3847 7.995463 TTGGAAGCTTGTACAAACAAATAAC 57.005 32.000 2.10 0.00 44.79 1.89
1504 3983 1.073923 ACAGGGGTTCTTAGTGCTTGG 59.926 52.381 0.00 0.00 0.00 3.61
1552 4052 9.308000 GGACATGGGAATTGGATGTATATTTTA 57.692 33.333 0.00 0.00 30.39 1.52
1561 4061 3.022557 AGTGGACATGGGAATTGGATG 57.977 47.619 0.00 0.00 0.00 3.51
1634 4295 7.970061 TCGTATGTGTTTCCTATGTTGTAGTAC 59.030 37.037 0.00 0.00 0.00 2.73
1635 4296 8.054152 TCGTATGTGTTTCCTATGTTGTAGTA 57.946 34.615 0.00 0.00 0.00 1.82
1636 4297 6.927416 TCGTATGTGTTTCCTATGTTGTAGT 58.073 36.000 0.00 0.00 0.00 2.73
1637 4298 7.821595 TTCGTATGTGTTTCCTATGTTGTAG 57.178 36.000 0.00 0.00 0.00 2.74
1706 4368 7.496920 GTGTACAGAGGGGGTATTATTTTACAC 59.503 40.741 0.00 0.00 0.00 2.90
1837 4557 9.452287 AACTTAGGAAATATACCTTTTAACGCA 57.548 29.630 6.68 0.00 38.76 5.24
2014 5206 4.394729 TCCCACAACAGAAATACTTGTCC 58.605 43.478 0.00 0.00 0.00 4.02
2469 6642 7.360776 GGTTCAGAAAGCATTTTCACAAAACAA 60.361 33.333 1.77 0.00 44.14 2.83
2787 6992 3.369471 CCCTGTACTTCACCACGATCATT 60.369 47.826 0.00 0.00 0.00 2.57
2881 7086 2.747686 CGTGGTGCCAAGGTAGGT 59.252 61.111 0.00 0.00 0.00 3.08
2889 7094 2.525124 ATCCTTCACCGTGGTGCCA 61.525 57.895 14.25 2.64 45.04 4.92
3123 7334 8.415950 TGACATTAAAGGTACCATTGTCAATT 57.584 30.769 22.30 3.68 39.06 2.32
3285 7502 3.907260 CTTGGCCCTCTCGCAAGCA 62.907 63.158 0.00 0.00 37.18 3.91
3288 7505 1.480212 TTCTCTTGGCCCTCTCGCAA 61.480 55.000 0.00 0.00 0.00 4.85
3306 7523 1.202758 TCTGCCGTGGAAGACAACATT 60.203 47.619 0.00 0.00 0.00 2.71
3549 7766 2.494059 CAGAGCTTCTTCCCGTGAAAA 58.506 47.619 0.00 0.00 0.00 2.29
3637 7854 2.800544 CGTTCACCTTCTGGTTGTACTG 59.199 50.000 0.00 0.00 46.05 2.74
3657 7874 1.202582 ACATCGAGAAGGACCAAGTCG 59.797 52.381 0.00 0.00 32.65 4.18
3703 7920 1.003118 GCTCATGACACCACCTACCAA 59.997 52.381 0.00 0.00 0.00 3.67
3825 8068 0.895559 CCTTGACCAACCCTGCTTCC 60.896 60.000 0.00 0.00 0.00 3.46
3838 8081 3.557595 CCGAGCAGATTGTTATCCTTGAC 59.442 47.826 0.00 0.00 0.00 3.18
3951 8194 1.595357 CCTTTCCTCCGCCGTTACT 59.405 57.895 0.00 0.00 0.00 2.24
3970 8213 0.865769 CTGTTCTTGTTTCCGGTCGG 59.134 55.000 0.00 2.52 0.00 4.79
4047 8291 2.831685 AGTACTTGTTGGCATCACGA 57.168 45.000 8.81 0.00 0.00 4.35
4100 8354 0.700269 AGGACCCTCATGGCCATGAT 60.700 55.000 41.23 30.05 45.74 2.45
4102 8356 1.152819 CAGGACCCTCATGGCCATG 60.153 63.158 35.76 35.76 40.09 3.66
4118 8372 9.346725 GTGATTTTAGGATTAAACAAGCTTCAG 57.653 33.333 0.00 0.00 0.00 3.02
4119 8373 9.077885 AGTGATTTTAGGATTAAACAAGCTTCA 57.922 29.630 0.00 0.00 0.00 3.02
4120 8374 9.561270 GAGTGATTTTAGGATTAAACAAGCTTC 57.439 33.333 0.00 0.00 0.00 3.86
4185 8466 4.669318 CAATGCCAGAAGTTGCAGAATAG 58.331 43.478 0.00 0.00 41.46 1.73
4220 8501 1.192146 ACAAGCCAGGCTAGGACGAA 61.192 55.000 16.56 0.00 38.25 3.85
4284 8565 4.816925 GGATCACCTTAGGCAATTACTCAC 59.183 45.833 0.00 0.00 0.00 3.51
4294 8793 1.523938 GCACCGGATCACCTTAGGC 60.524 63.158 9.46 0.00 0.00 3.93
4309 8808 6.543736 GTTGACTTAAGCAAATACTAGGCAC 58.456 40.000 12.05 0.00 0.00 5.01
4340 8839 3.133691 TGAGCACTTGAGACACACATTC 58.866 45.455 0.00 0.00 0.00 2.67
4447 8954 3.023949 ATCAGAGGGGTCGCTGTGC 62.024 63.158 7.20 0.00 40.86 4.57
4450 8957 2.025767 CTCCATCAGAGGGGTCGCTG 62.026 65.000 0.07 0.00 41.30 5.18
4451 8958 1.760086 CTCCATCAGAGGGGTCGCT 60.760 63.158 0.07 0.00 39.13 4.93
4460 8967 3.435275 ACAGAGCAAGTACTCCATCAGA 58.565 45.455 0.00 0.00 37.39 3.27
4465 8972 2.300152 CCTGAACAGAGCAAGTACTCCA 59.700 50.000 0.00 0.00 37.39 3.86
4514 9021 4.499037 AGGTGACATTAAAAGAAACCGC 57.501 40.909 0.00 0.00 0.00 5.68
4644 9151 4.021719 CAGACCATTTTGGAGAAATGTGCT 60.022 41.667 0.00 4.83 40.96 4.40
4645 9152 4.022068 TCAGACCATTTTGGAGAAATGTGC 60.022 41.667 0.00 3.07 40.96 4.57
4653 9160 7.928307 TTTAGATCTTCAGACCATTTTGGAG 57.072 36.000 0.00 0.00 40.96 3.86
4710 9217 7.520119 CACTTTCCAGTGGTTTTAAGAAAAC 57.480 36.000 9.54 6.31 46.10 2.43
4745 9252 2.092882 GTAGCGAGCGAGCGGTTTT 61.093 57.895 7.32 0.00 42.51 2.43
4746 9253 2.488087 AAGTAGCGAGCGAGCGGTTT 62.488 55.000 7.32 0.00 42.51 3.27
4747 9254 2.991076 AAGTAGCGAGCGAGCGGTT 61.991 57.895 7.32 0.00 42.51 4.44
4748 9255 3.441290 AAGTAGCGAGCGAGCGGT 61.441 61.111 7.19 7.19 44.84 5.68
4758 9265 2.388232 GCAACCCCGACAAGTAGCG 61.388 63.158 0.00 0.00 0.00 4.26
4769 9276 2.043227 ACTCTAGATAGCAGCAACCCC 58.957 52.381 0.00 0.00 0.00 4.95
4780 9287 3.173965 GCCTGGCCCATTACTCTAGATA 58.826 50.000 7.66 0.00 0.00 1.98
4808 9315 0.033366 GCCAAATTGCAAAGGGACGT 59.967 50.000 16.02 0.00 0.00 4.34
4840 9347 4.993584 GGAGCTCTGGTATGACACATTATG 59.006 45.833 14.64 0.00 0.00 1.90
4841 9348 4.904251 AGGAGCTCTGGTATGACACATTAT 59.096 41.667 14.64 0.00 0.00 1.28
4871 9378 5.528870 AGCTCTTTTTGTTTTTACATCGGG 58.471 37.500 0.00 0.00 0.00 5.14
4884 9391 4.326826 TGGTATGACAGGAGCTCTTTTTG 58.673 43.478 14.64 9.71 0.00 2.44
4889 9396 2.665165 CTCTGGTATGACAGGAGCTCT 58.335 52.381 14.64 0.00 38.98 4.09
4890 9397 1.068434 GCTCTGGTATGACAGGAGCTC 59.932 57.143 4.71 4.71 37.99 4.09
4891 9398 1.118838 GCTCTGGTATGACAGGAGCT 58.881 55.000 12.59 0.00 37.99 4.09
4892 9399 0.249238 CGCTCTGGTATGACAGGAGC 60.249 60.000 0.00 0.00 38.98 4.70
4893 9400 0.387202 CCGCTCTGGTATGACAGGAG 59.613 60.000 0.00 0.00 38.98 3.69
4894 9401 1.043116 CCCGCTCTGGTATGACAGGA 61.043 60.000 0.00 0.00 38.98 3.86
4895 9402 1.443407 CCCGCTCTGGTATGACAGG 59.557 63.158 0.00 0.00 38.98 4.00
4896 9403 1.227380 GCCCGCTCTGGTATGACAG 60.227 63.158 0.00 0.00 39.84 3.51
4897 9404 1.685765 AGCCCGCTCTGGTATGACA 60.686 57.895 0.00 0.00 35.15 3.58
4898 9405 1.227380 CAGCCCGCTCTGGTATGAC 60.227 63.158 0.00 0.00 35.15 3.06
4899 9406 1.264749 AACAGCCCGCTCTGGTATGA 61.265 55.000 7.01 0.00 38.36 2.15
4900 9407 0.392998 AAACAGCCCGCTCTGGTATG 60.393 55.000 7.01 0.00 38.36 2.39
4901 9408 0.392998 CAAACAGCCCGCTCTGGTAT 60.393 55.000 7.01 0.00 38.36 2.73
4902 9409 1.003839 CAAACAGCCCGCTCTGGTA 60.004 57.895 7.01 0.00 38.36 3.25
4903 9410 2.281761 CAAACAGCCCGCTCTGGT 60.282 61.111 7.01 0.00 38.36 4.00
4904 9411 2.826777 ATCCAAACAGCCCGCTCTGG 62.827 60.000 7.01 3.56 38.36 3.86
4905 9412 0.962356 AATCCAAACAGCCCGCTCTG 60.962 55.000 1.29 1.29 39.86 3.35
4906 9413 0.962356 CAATCCAAACAGCCCGCTCT 60.962 55.000 0.00 0.00 0.00 4.09
4907 9414 1.244019 ACAATCCAAACAGCCCGCTC 61.244 55.000 0.00 0.00 0.00 5.03
4908 9415 1.228552 ACAATCCAAACAGCCCGCT 60.229 52.632 0.00 0.00 0.00 5.52
4909 9416 1.080569 CACAATCCAAACAGCCCGC 60.081 57.895 0.00 0.00 0.00 6.13
4910 9417 0.240945 GTCACAATCCAAACAGCCCG 59.759 55.000 0.00 0.00 0.00 6.13
4911 9418 1.620822 AGTCACAATCCAAACAGCCC 58.379 50.000 0.00 0.00 0.00 5.19
4912 9419 6.699575 AATATAGTCACAATCCAAACAGCC 57.300 37.500 0.00 0.00 0.00 4.85
4913 9420 9.884465 GATAAATATAGTCACAATCCAAACAGC 57.116 33.333 0.00 0.00 0.00 4.40
4936 9443 9.642327 GCAAAAATCATGTGGCAATATATGATA 57.358 29.630 14.24 0.00 37.75 2.15
4937 9444 7.604927 GGCAAAAATCATGTGGCAATATATGAT 59.395 33.333 10.26 10.26 39.59 2.45
4938 9445 6.930164 GGCAAAAATCATGTGGCAATATATGA 59.070 34.615 0.00 0.00 37.73 2.15
4939 9446 6.706716 TGGCAAAAATCATGTGGCAATATATG 59.293 34.615 6.99 0.00 43.91 1.78
4940 9447 6.828788 TGGCAAAAATCATGTGGCAATATAT 58.171 32.000 6.99 0.00 43.91 0.86
4941 9448 6.231258 TGGCAAAAATCATGTGGCAATATA 57.769 33.333 6.99 0.00 43.91 0.86
4942 9449 5.100344 TGGCAAAAATCATGTGGCAATAT 57.900 34.783 6.99 0.00 43.91 1.28
4943 9450 4.548451 TGGCAAAAATCATGTGGCAATA 57.452 36.364 6.99 0.00 43.91 1.90
4944 9451 3.420300 TGGCAAAAATCATGTGGCAAT 57.580 38.095 6.99 0.00 43.91 3.56
4945 9452 2.924757 TGGCAAAAATCATGTGGCAA 57.075 40.000 6.99 0.00 43.91 4.52
4946 9453 1.415289 TGTGGCAAAAATCATGTGGCA 59.585 42.857 5.53 5.53 44.57 4.92
4947 9454 1.799994 GTGTGGCAAAAATCATGTGGC 59.200 47.619 0.00 0.00 38.26 5.01
4948 9455 3.389925 AGTGTGGCAAAAATCATGTGG 57.610 42.857 0.00 0.00 0.00 4.17
4949 9456 3.742369 GGAAGTGTGGCAAAAATCATGTG 59.258 43.478 0.00 0.00 0.00 3.21
4950 9457 3.642848 AGGAAGTGTGGCAAAAATCATGT 59.357 39.130 0.00 0.00 0.00 3.21
4951 9458 4.261578 AGGAAGTGTGGCAAAAATCATG 57.738 40.909 0.00 0.00 0.00 3.07
4952 9459 4.961438 AAGGAAGTGTGGCAAAAATCAT 57.039 36.364 0.00 0.00 0.00 2.45
4953 9460 4.892934 AGTAAGGAAGTGTGGCAAAAATCA 59.107 37.500 0.00 0.00 0.00 2.57
4954 9461 5.453567 AGTAAGGAAGTGTGGCAAAAATC 57.546 39.130 0.00 0.00 0.00 2.17
4955 9462 5.362430 TCAAGTAAGGAAGTGTGGCAAAAAT 59.638 36.000 0.00 0.00 0.00 1.82
4956 9463 4.707448 TCAAGTAAGGAAGTGTGGCAAAAA 59.293 37.500 0.00 0.00 0.00 1.94
4957 9464 4.274147 TCAAGTAAGGAAGTGTGGCAAAA 58.726 39.130 0.00 0.00 0.00 2.44
4958 9465 3.882888 CTCAAGTAAGGAAGTGTGGCAAA 59.117 43.478 0.00 0.00 0.00 3.68
4959 9466 3.118038 ACTCAAGTAAGGAAGTGTGGCAA 60.118 43.478 0.00 0.00 0.00 4.52
4960 9467 2.438021 ACTCAAGTAAGGAAGTGTGGCA 59.562 45.455 0.00 0.00 0.00 4.92
4961 9468 3.127425 ACTCAAGTAAGGAAGTGTGGC 57.873 47.619 0.00 0.00 0.00 5.01
4962 9469 3.251004 GCAACTCAAGTAAGGAAGTGTGG 59.749 47.826 0.00 0.00 0.00 4.17
4963 9470 4.130118 AGCAACTCAAGTAAGGAAGTGTG 58.870 43.478 0.00 0.00 0.00 3.82
4964 9471 4.141711 TGAGCAACTCAAGTAAGGAAGTGT 60.142 41.667 0.00 0.00 37.57 3.55
4965 9472 4.380531 TGAGCAACTCAAGTAAGGAAGTG 58.619 43.478 0.00 0.00 37.57 3.16
4966 9473 4.689612 TGAGCAACTCAAGTAAGGAAGT 57.310 40.909 0.00 0.00 37.57 3.01
4975 9482 9.751134 TGTGGCTAACAATTTGAGCAACTCAAG 62.751 40.741 15.05 2.58 42.48 3.02
4976 9483 4.340666 TGGCTAACAATTTGAGCAACTCAA 59.659 37.500 5.94 5.94 46.93 3.02
4977 9484 3.888323 TGGCTAACAATTTGAGCAACTCA 59.112 39.130 2.79 0.00 38.87 3.41
4978 9485 4.229876 GTGGCTAACAATTTGAGCAACTC 58.770 43.478 2.79 0.00 37.21 3.01
4979 9486 3.636300 TGTGGCTAACAATTTGAGCAACT 59.364 39.130 15.05 0.00 40.27 3.16
4980 9487 3.976169 TGTGGCTAACAATTTGAGCAAC 58.024 40.909 9.59 9.59 40.06 4.17
4981 9488 4.870123 ATGTGGCTAACAATTTGAGCAA 57.130 36.364 2.79 0.00 43.61 3.91
4982 9489 4.870123 AATGTGGCTAACAATTTGAGCA 57.130 36.364 2.79 0.00 43.61 4.26
4998 9505 2.354003 CCCTTAGGCAAGCCAAAATGTG 60.354 50.000 14.40 0.09 38.92 3.21
4999 9506 1.901833 CCCTTAGGCAAGCCAAAATGT 59.098 47.619 14.40 0.00 38.92 2.71
5000 9507 2.178580 TCCCTTAGGCAAGCCAAAATG 58.821 47.619 14.40 4.48 38.92 2.32
5001 9508 2.621556 TCCCTTAGGCAAGCCAAAAT 57.378 45.000 14.40 0.00 38.92 1.82
5002 9509 2.390225 TTCCCTTAGGCAAGCCAAAA 57.610 45.000 14.40 6.31 38.92 2.44
5003 9510 2.042979 AGATTCCCTTAGGCAAGCCAAA 59.957 45.455 14.40 0.00 38.92 3.28
5004 9511 1.640670 AGATTCCCTTAGGCAAGCCAA 59.359 47.619 14.40 4.98 38.92 4.52
5005 9512 1.298953 AGATTCCCTTAGGCAAGCCA 58.701 50.000 14.40 0.00 38.92 4.75
5006 9513 2.027385 CAAGATTCCCTTAGGCAAGCC 58.973 52.381 2.02 2.02 32.86 4.35
5007 9514 1.406898 GCAAGATTCCCTTAGGCAAGC 59.593 52.381 0.00 0.00 32.86 4.01
5008 9515 2.027385 GGCAAGATTCCCTTAGGCAAG 58.973 52.381 0.00 0.00 32.86 4.01
5009 9516 1.357420 TGGCAAGATTCCCTTAGGCAA 59.643 47.619 0.00 0.00 36.41 4.52
5010 9517 0.998928 TGGCAAGATTCCCTTAGGCA 59.001 50.000 0.00 0.00 36.71 4.75
5011 9518 1.340991 TGTGGCAAGATTCCCTTAGGC 60.341 52.381 0.00 0.00 32.86 3.93
5012 9519 2.025887 AGTGTGGCAAGATTCCCTTAGG 60.026 50.000 0.00 0.00 32.86 2.69
5013 9520 3.356529 AGTGTGGCAAGATTCCCTTAG 57.643 47.619 0.00 0.00 32.86 2.18
5014 9521 3.806949 AAGTGTGGCAAGATTCCCTTA 57.193 42.857 0.00 0.00 32.86 2.69
5015 9522 2.683211 AAGTGTGGCAAGATTCCCTT 57.317 45.000 0.00 0.00 34.91 3.95
5016 9523 2.108952 AGAAAGTGTGGCAAGATTCCCT 59.891 45.455 0.00 0.00 0.00 4.20
5017 9524 2.519013 AGAAAGTGTGGCAAGATTCCC 58.481 47.619 0.00 0.00 0.00 3.97
5018 9525 4.702131 ACATAGAAAGTGTGGCAAGATTCC 59.298 41.667 0.00 0.00 0.00 3.01
5019 9526 5.645497 AGACATAGAAAGTGTGGCAAGATTC 59.355 40.000 0.00 0.00 0.00 2.52
5020 9527 5.564550 AGACATAGAAAGTGTGGCAAGATT 58.435 37.500 0.00 0.00 0.00 2.40
5021 9528 5.171339 AGACATAGAAAGTGTGGCAAGAT 57.829 39.130 0.00 0.00 0.00 2.40
5022 9529 4.623932 AGACATAGAAAGTGTGGCAAGA 57.376 40.909 0.00 0.00 0.00 3.02
5023 9530 6.036517 GTCATAGACATAGAAAGTGTGGCAAG 59.963 42.308 0.00 0.00 32.09 4.01
5024 9531 5.874810 GTCATAGACATAGAAAGTGTGGCAA 59.125 40.000 0.00 0.00 32.09 4.52
5025 9532 5.046663 TGTCATAGACATAGAAAGTGTGGCA 60.047 40.000 0.00 0.00 37.67 4.92
5026 9533 5.419542 TGTCATAGACATAGAAAGTGTGGC 58.580 41.667 0.00 0.00 37.67 5.01
5039 9546 1.486310 GAGCCCCACATGTCATAGACA 59.514 52.381 0.00 1.95 46.90 3.41
5040 9547 1.486310 TGAGCCCCACATGTCATAGAC 59.514 52.381 0.00 0.00 0.00 2.59
5041 9548 1.486310 GTGAGCCCCACATGTCATAGA 59.514 52.381 0.00 0.00 45.03 1.98
5042 9549 1.959042 GTGAGCCCCACATGTCATAG 58.041 55.000 0.00 0.00 45.03 2.23


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

AutoCloner maintained by Alex Coulton.