Multiple sequence alignment - TraesCS3B01G071000

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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 TraesCS3B01G071000 chr3B 100.000 3599 0 0 1 3599 42870068 42866470 0.000000e+00 6647
1 TraesCS3B01G071000 chr3B 90.238 881 54 14 1540 2394 809057269 809058143 0.000000e+00 1122
2 TraesCS3B01G071000 chr3B 90.625 384 33 3 91 473 791863320 791863701 1.150000e-139 507
3 TraesCS3B01G071000 chr3B 84.649 456 57 9 720 1169 42944354 42943906 3.300000e-120 442
4 TraesCS3B01G071000 chr3B 75.802 343 65 8 827 1163 585720607 585720937 1.340000e-34 158
5 TraesCS3B01G071000 chr3B 79.817 218 29 8 2471 2681 42942818 42942609 1.040000e-30 145
6 TraesCS3B01G071000 chr3B 87.500 104 8 4 2794 2896 42942481 42942382 8.170000e-22 115
7 TraesCS3B01G071000 chr3D 94.280 1381 51 13 1 1375 25786350 25784992 0.000000e+00 2087
8 TraesCS3B01G071000 chr3D 96.687 815 22 2 2396 3205 25784569 25783755 0.000000e+00 1351
9 TraesCS3B01G071000 chr3D 84.599 461 58 9 719 1173 25960321 25959868 2.550000e-121 446
10 TraesCS3B01G071000 chr3D 96.703 182 5 1 1362 1542 25784740 25784559 5.840000e-78 302
11 TraesCS3B01G071000 chr3D 79.656 349 42 17 2471 2802 25958778 25958442 1.300000e-54 224
12 TraesCS3B01G071000 chr3D 81.290 155 15 6 3059 3205 25957926 25957778 2.940000e-21 113
13 TraesCS3B01G071000 chr3D 88.298 94 8 2 1449 1542 25959374 25959284 3.800000e-20 110
14 TraesCS3B01G071000 chr1A 93.232 857 46 9 1539 2394 535771063 535771908 0.000000e+00 1251
15 TraesCS3B01G071000 chr1A 82.680 306 39 8 3298 3598 35333240 35333536 3.560000e-65 259
16 TraesCS3B01G071000 chr4B 92.907 860 53 6 1539 2394 450042506 450043361 0.000000e+00 1243
17 TraesCS3B01G071000 chr4B 96.104 77 2 1 3206 3281 19045832 19045756 1.360000e-24 124
18 TraesCS3B01G071000 chr5D 94.612 798 39 3 1539 2335 110602419 110603213 0.000000e+00 1232
19 TraesCS3B01G071000 chr5D 89.365 677 41 14 1539 2203 525316317 525315660 0.000000e+00 822
20 TraesCS3B01G071000 chr5D 84.211 266 32 6 481 741 321884325 321884585 2.150000e-62 250
21 TraesCS3B01G071000 chr5D 76.608 342 64 6 827 1163 321895176 321895506 1.330000e-39 174
22 TraesCS3B01G071000 chr5D 90.909 88 6 2 3207 3293 45478635 45478549 2.270000e-22 117
23 TraesCS3B01G071000 chr6A 91.512 860 46 12 1539 2394 215101859 215102695 0.000000e+00 1158
24 TraesCS3B01G071000 chr6A 84.281 299 34 8 3306 3599 190576506 190576216 2.740000e-71 279
25 TraesCS3B01G071000 chr6A 87.200 125 9 4 2700 2820 35272241 35272120 6.270000e-28 135
26 TraesCS3B01G071000 chr6A 92.405 79 4 2 3205 3282 483746402 483746479 1.060000e-20 111
27 TraesCS3B01G071000 chr7D 88.430 847 72 18 1538 2371 540881501 540882334 0.000000e+00 998
28 TraesCS3B01G071000 chr7D 85.047 321 34 10 3285 3599 256325311 256324999 7.500000e-82 315
29 TraesCS3B01G071000 chr3A 90.751 746 32 11 1655 2394 21320971 21321685 0.000000e+00 961
30 TraesCS3B01G071000 chr3A 85.580 319 31 9 3285 3597 652575813 652575504 1.610000e-83 320
31 TraesCS3B01G071000 chr3A 84.375 320 38 7 3285 3599 652710346 652710034 1.620000e-78 303
32 TraesCS3B01G071000 chr3A 82.778 360 40 11 825 1169 34922459 34922107 5.840000e-78 302
33 TraesCS3B01G071000 chr7B 87.337 845 79 19 1540 2371 584325094 584325923 0.000000e+00 942
34 TraesCS3B01G071000 chr7B 92.500 80 5 1 3204 3282 588498247 588498326 2.940000e-21 113
35 TraesCS3B01G071000 chr7A 86.471 850 85 20 1538 2371 623635807 623636642 0.000000e+00 905
36 TraesCS3B01G071000 chr7A 89.637 386 37 2 91 473 398920454 398920839 4.180000e-134 488
37 TraesCS3B01G071000 chr2D 93.688 602 25 3 1539 2140 639226874 639227462 0.000000e+00 889
38 TraesCS3B01G071000 chr2D 86.364 264 26 6 3285 3548 579217315 579217062 2.740000e-71 279
39 TraesCS3B01G071000 chr2D 75.872 344 67 6 825 1163 43836705 43836373 1.030000e-35 161
40 TraesCS3B01G071000 chr2D 91.358 81 6 1 3207 3286 644035576 644035496 3.800000e-20 110
41 TraesCS3B01G071000 chr6B 91.076 381 30 4 94 473 487207453 487207076 2.480000e-141 512
42 TraesCS3B01G071000 chr6B 90.289 381 34 3 94 473 487204204 487203826 2.500000e-136 496
43 TraesCS3B01G071000 chr6B 94.805 77 2 2 3206 3281 9967963 9967888 6.310000e-23 119
44 TraesCS3B01G071000 chr5B 90.814 381 33 2 94 473 697520209 697520588 3.210000e-140 508
45 TraesCS3B01G071000 chr5B 76.901 342 63 6 827 1163 373038392 373038722 2.850000e-41 180
46 TraesCS3B01G071000 chr1B 90.698 387 29 7 91 474 433177731 433178113 3.210000e-140 508
47 TraesCS3B01G071000 chr1D 91.200 375 28 5 94 467 184470416 184470046 4.150000e-139 505
48 TraesCS3B01G071000 chr1D 93.421 76 4 1 3207 3281 61575626 61575551 1.060000e-20 111
49 TraesCS3B01G071000 chr4D 89.394 396 35 6 86 474 131105071 131105466 3.230000e-135 492
50 TraesCS3B01G071000 chr6D 82.443 524 71 17 1546 2065 405589498 405588992 4.270000e-119 438
51 TraesCS3B01G071000 chr6D 85.759 316 30 11 3282 3597 143658331 143658631 1.610000e-83 320
52 TraesCS3B01G071000 chr2B 95.203 271 10 3 1539 1808 346673333 346673601 3.320000e-115 425
53 TraesCS3B01G071000 chr2B 84.127 315 37 11 3289 3599 441798723 441798418 3.510000e-75 292
54 TraesCS3B01G071000 chr4A 90.645 310 23 6 1527 1835 642669049 642668745 1.200000e-109 407
55 TraesCS3B01G071000 chr2A 82.919 322 42 10 3285 3599 314724895 314725210 9.840000e-71 278
56 TraesCS3B01G071000 chr5A 74.203 345 71 9 825 1163 417025399 417025731 1.050000e-25 128
57 TraesCS3B01G071000 chrUn 94.805 77 2 2 3206 3281 75943911 75943986 6.310000e-23 119
58 TraesCS3B01G071000 chrUn 93.506 77 4 1 3204 3279 178230061 178229985 2.940000e-21 113


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 TraesCS3B01G071000 chr3B 42866470 42870068 3598 True 6647.000000 6647 100.000000 1 3599 1 chr3B.!!$R1 3598
1 TraesCS3B01G071000 chr3B 809057269 809058143 874 False 1122.000000 1122 90.238000 1540 2394 1 chr3B.!!$F3 854
2 TraesCS3B01G071000 chr3B 42942382 42944354 1972 True 234.000000 442 83.988667 720 2896 3 chr3B.!!$R2 2176
3 TraesCS3B01G071000 chr3D 25783755 25786350 2595 True 1246.666667 2087 95.890000 1 3205 3 chr3D.!!$R1 3204
4 TraesCS3B01G071000 chr3D 25957778 25960321 2543 True 223.250000 446 83.460750 719 3205 4 chr3D.!!$R2 2486
5 TraesCS3B01G071000 chr1A 535771063 535771908 845 False 1251.000000 1251 93.232000 1539 2394 1 chr1A.!!$F2 855
6 TraesCS3B01G071000 chr4B 450042506 450043361 855 False 1243.000000 1243 92.907000 1539 2394 1 chr4B.!!$F1 855
7 TraesCS3B01G071000 chr5D 110602419 110603213 794 False 1232.000000 1232 94.612000 1539 2335 1 chr5D.!!$F1 796
8 TraesCS3B01G071000 chr5D 525315660 525316317 657 True 822.000000 822 89.365000 1539 2203 1 chr5D.!!$R2 664
9 TraesCS3B01G071000 chr6A 215101859 215102695 836 False 1158.000000 1158 91.512000 1539 2394 1 chr6A.!!$F1 855
10 TraesCS3B01G071000 chr7D 540881501 540882334 833 False 998.000000 998 88.430000 1538 2371 1 chr7D.!!$F1 833
11 TraesCS3B01G071000 chr3A 21320971 21321685 714 False 961.000000 961 90.751000 1655 2394 1 chr3A.!!$F1 739
12 TraesCS3B01G071000 chr7B 584325094 584325923 829 False 942.000000 942 87.337000 1540 2371 1 chr7B.!!$F1 831
13 TraesCS3B01G071000 chr7A 623635807 623636642 835 False 905.000000 905 86.471000 1538 2371 1 chr7A.!!$F2 833
14 TraesCS3B01G071000 chr2D 639226874 639227462 588 False 889.000000 889 93.688000 1539 2140 1 chr2D.!!$F1 601
15 TraesCS3B01G071000 chr6B 487203826 487207453 3627 True 504.000000 512 90.682500 94 473 2 chr6B.!!$R2 379
16 TraesCS3B01G071000 chr6D 405588992 405589498 506 True 438.000000 438 82.443000 1546 2065 1 chr6D.!!$R1 519

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
657 659 1.073722 CACCTCTGGGCAAGCTTCA 59.926 57.895 0.00 0.0 35.63 3.02 F
1337 1595 0.176680 CGTCCAGGACAAGGGATCTG 59.823 60.000 20.13 0.0 35.25 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 5072 0.761802 TTTTGGGCCCTTTTTCGCAT 59.238 45.0 25.7 0.0 0.00 4.73 R
3288 6600 0.758734 TGGACCGCCTAATGGAGATG 59.241 55.0 0.0 0.0 34.95 2.90 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
30 31 1.301677 TTTGCACGTGCGCCATATGA 61.302 50.000 33.22 12.43 45.83 2.15
38 39 3.926527 ACGTGCGCCATATGAATATACAG 59.073 43.478 4.18 0.00 0.00 2.74
71 72 3.673052 CGGCTCAAATACCATGGTTGTTG 60.673 47.826 25.38 24.74 0.00 3.33
72 73 3.258123 GGCTCAAATACCATGGTTGTTGT 59.742 43.478 25.38 0.39 0.00 3.32
76 77 3.296322 AATACCATGGTTGTTGTTGCG 57.704 42.857 25.38 0.00 0.00 4.85
80 81 1.832167 ATGGTTGTTGTTGCGCCCT 60.832 52.632 4.18 0.00 0.00 5.19
332 333 5.231702 TCGATGTGTATTTCGAGTTTGGAA 58.768 37.500 0.00 0.00 39.29 3.53
462 463 2.429930 CAAGGTTGGGAGCACCGA 59.570 61.111 0.00 0.00 44.64 4.69
517 519 1.477558 CCCCTCCCAATCACATAGCAC 60.478 57.143 0.00 0.00 0.00 4.40
530 532 4.826733 TCACATAGCACACTCACCATTTTT 59.173 37.500 0.00 0.00 0.00 1.94
584 586 9.473007 TTGAACATGATTACCCAATAGAATCAA 57.527 29.630 0.00 0.00 41.55 2.57
603 605 1.392589 AGACCAAACTGCCACACTTG 58.607 50.000 0.00 0.00 0.00 3.16
657 659 1.073722 CACCTCTGGGCAAGCTTCA 59.926 57.895 0.00 0.00 35.63 3.02
683 685 4.991056 CGAAGTGGAAATTCTCAGAACTGA 59.009 41.667 4.45 4.45 39.08 3.41
713 715 3.514777 TGCGAAACTACCTGCAGAG 57.485 52.632 17.39 8.22 32.73 3.35
806 811 4.681978 GCAGGTGAAGCCGACGGT 62.682 66.667 16.73 0.00 43.70 4.83
807 812 2.738521 CAGGTGAAGCCGACGGTG 60.739 66.667 16.73 0.00 43.70 4.94
841 849 2.270205 CCAAGATGGCAGCGAGGT 59.730 61.111 8.11 0.00 0.00 3.85
1116 1124 1.067295 TCACCCAACTCAGCTGGAAT 58.933 50.000 15.13 0.00 35.85 3.01
1163 1171 4.682859 GCTCAACTTGCTCATCTCAGGTAT 60.683 45.833 0.00 0.00 0.00 2.73
1169 1177 4.944619 TGCTCATCTCAGGTATTCGATT 57.055 40.909 0.00 0.00 0.00 3.34
1170 1178 4.876125 TGCTCATCTCAGGTATTCGATTC 58.124 43.478 0.00 0.00 0.00 2.52
1171 1179 4.342092 TGCTCATCTCAGGTATTCGATTCA 59.658 41.667 0.00 0.00 0.00 2.57
1172 1180 5.163416 TGCTCATCTCAGGTATTCGATTCAA 60.163 40.000 0.00 0.00 0.00 2.69
1173 1181 5.931146 GCTCATCTCAGGTATTCGATTCAAT 59.069 40.000 0.00 0.00 0.00 2.57
1182 1190 7.602644 TCAGGTATTCGATTCAATAAGCCATAC 59.397 37.037 0.00 0.00 0.00 2.39
1198 1206 4.081642 AGCCATACAGATCTTGTGTACGTT 60.082 41.667 0.00 0.00 41.10 3.99
1270 1295 4.264460 AGATCAGGCCGCTAGAATTAAG 57.736 45.455 0.00 0.00 0.00 1.85
1309 1520 1.602165 CCACTATCCCGTACGTCATGC 60.602 57.143 15.21 0.00 0.00 4.06
1321 1532 1.263217 ACGTCATGCTTTTGTTCCGTC 59.737 47.619 0.00 0.00 0.00 4.79
1337 1595 0.176680 CGTCCAGGACAAGGGATCTG 59.823 60.000 20.13 0.00 35.25 2.90
1490 2070 9.541143 TTATGCCTTTCTTTCCTTTTACTTTTG 57.459 29.630 0.00 0.00 0.00 2.44
1491 2071 5.815222 TGCCTTTCTTTCCTTTTACTTTTGC 59.185 36.000 0.00 0.00 0.00 3.68
1549 2129 1.122019 AGTCTTGTCAGGGCCGTCTT 61.122 55.000 0.00 0.00 0.00 3.01
1601 2181 9.504708 AATGCAAATTGTGATCCTAAAATTTCA 57.495 25.926 0.00 0.47 31.57 2.69
1855 4579 3.664107 TCAACAGCACACAAGATAGTCC 58.336 45.455 0.00 0.00 0.00 3.85
1905 4631 4.039245 ACCTGTTAGACATATCGGTGATGG 59.961 45.833 0.00 0.00 0.00 3.51
2040 4787 2.168521 GGGCTATGAACTGAGCTGTGTA 59.831 50.000 0.00 0.00 38.79 2.90
2278 5072 4.124943 AGGGAGCCCGCGACTAGA 62.125 66.667 8.23 0.00 41.95 2.43
2475 5433 4.133373 AGCGGCCAGGCATCCAAT 62.133 61.111 15.19 0.00 34.64 3.16
2476 5434 3.908081 GCGGCCAGGCATCCAATG 61.908 66.667 15.19 0.00 0.00 2.82
2580 5559 2.417719 GAACAGCAAGTGATCGACCTT 58.582 47.619 0.00 0.00 0.00 3.50
2638 5617 7.283127 GGATATGAAGTCTGGCATTTACTTTCA 59.717 37.037 10.25 9.90 33.72 2.69
2641 5620 6.913170 TGAAGTCTGGCATTTACTTTCAATC 58.087 36.000 10.25 1.04 33.72 2.67
2642 5621 5.551760 AGTCTGGCATTTACTTTCAATCG 57.448 39.130 0.00 0.00 0.00 3.34
2789 5774 8.362464 TCCTAGTCTATTTTACTCAGCTTTGA 57.638 34.615 0.00 0.00 0.00 2.69
2926 6225 6.477253 GTCCCCTTATTTTAGGATGAGGATC 58.523 44.000 0.00 0.00 35.40 3.36
3007 6307 0.460459 TTGGACAGAAACGTGCGACA 60.460 50.000 0.00 0.00 0.00 4.35
3112 6424 7.817962 ACATGTGTGTGAACCTATTAGTACTTC 59.182 37.037 0.00 0.00 37.14 3.01
3124 6436 9.697990 ACCTATTAGTACTTCTGTATATAGGGC 57.302 37.037 0.00 0.00 39.14 5.19
3149 6461 7.309177 CGAGTCAGATTATTTGATCCGTATCT 58.691 38.462 0.00 0.00 32.93 1.98
3172 6484 4.758165 TGATATGATTGTATGCTGCCACAG 59.242 41.667 0.00 0.00 34.12 3.66
3205 6517 2.252346 CGGCCTGCTCATCTGCATC 61.252 63.158 0.00 0.00 42.48 3.91
3206 6518 1.148723 GGCCTGCTCATCTGCATCT 59.851 57.895 0.00 0.00 42.48 2.90
3207 6519 0.465824 GGCCTGCTCATCTGCATCTT 60.466 55.000 0.00 0.00 42.48 2.40
3208 6520 1.390565 GCCTGCTCATCTGCATCTTT 58.609 50.000 0.00 0.00 42.48 2.52
3209 6521 2.569059 GCCTGCTCATCTGCATCTTTA 58.431 47.619 0.00 0.00 42.48 1.85
3210 6522 3.147629 GCCTGCTCATCTGCATCTTTAT 58.852 45.455 0.00 0.00 42.48 1.40
3211 6523 3.568853 GCCTGCTCATCTGCATCTTTATT 59.431 43.478 0.00 0.00 42.48 1.40
3212 6524 4.037684 GCCTGCTCATCTGCATCTTTATTT 59.962 41.667 0.00 0.00 42.48 1.40
3213 6525 5.451520 GCCTGCTCATCTGCATCTTTATTTT 60.452 40.000 0.00 0.00 42.48 1.82
3214 6526 5.977725 CCTGCTCATCTGCATCTTTATTTTG 59.022 40.000 0.00 0.00 42.48 2.44
3215 6527 6.183360 CCTGCTCATCTGCATCTTTATTTTGA 60.183 38.462 0.00 0.00 42.48 2.69
3216 6528 7.342769 TGCTCATCTGCATCTTTATTTTGAT 57.657 32.000 0.00 0.00 38.12 2.57
3217 6529 8.454570 TGCTCATCTGCATCTTTATTTTGATA 57.545 30.769 0.00 0.00 38.12 2.15
3218 6530 8.905850 TGCTCATCTGCATCTTTATTTTGATAA 58.094 29.630 0.00 0.00 38.12 1.75
3219 6531 9.909644 GCTCATCTGCATCTTTATTTTGATAAT 57.090 29.630 0.00 0.00 0.00 1.28
3233 6545 9.632807 TTATTTTGATAATAATTGGCCGTATGC 57.367 29.630 0.00 0.00 40.16 3.14
3234 6546 6.641169 TTTGATAATAATTGGCCGTATGCA 57.359 33.333 0.00 0.00 43.89 3.96
3235 6547 6.832520 TTGATAATAATTGGCCGTATGCAT 57.167 33.333 3.79 3.79 43.89 3.96
3236 6548 6.435430 TGATAATAATTGGCCGTATGCATC 57.565 37.500 0.19 4.06 43.89 3.91
3237 6549 5.942826 TGATAATAATTGGCCGTATGCATCA 59.057 36.000 0.19 6.36 43.89 3.07
3238 6550 6.602803 TGATAATAATTGGCCGTATGCATCAT 59.397 34.615 0.19 0.00 43.89 2.45
3239 6551 5.726980 AATAATTGGCCGTATGCATCATT 57.273 34.783 0.19 0.00 43.89 2.57
3240 6552 3.648339 AATTGGCCGTATGCATCATTC 57.352 42.857 0.19 0.00 43.89 2.67
3241 6553 2.346766 TTGGCCGTATGCATCATTCT 57.653 45.000 0.19 0.00 43.89 2.40
3242 6554 1.596603 TGGCCGTATGCATCATTCTG 58.403 50.000 0.19 0.00 43.89 3.02
3243 6555 1.140652 TGGCCGTATGCATCATTCTGA 59.859 47.619 0.19 0.00 43.89 3.27
3244 6556 2.224597 TGGCCGTATGCATCATTCTGAT 60.225 45.455 0.19 0.00 43.89 2.90
3253 6565 1.880675 CATCATTCTGATGCAGAGGCC 59.119 52.381 0.00 0.00 46.37 5.19
3254 6566 0.179065 TCATTCTGATGCAGAGGCCG 60.179 55.000 0.00 0.00 41.75 6.13
3255 6567 1.147824 ATTCTGATGCAGAGGCCGG 59.852 57.895 0.00 0.00 41.75 6.13
3256 6568 2.335092 ATTCTGATGCAGAGGCCGGG 62.335 60.000 2.18 0.00 41.75 5.73
3257 6569 4.559063 CTGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
3259 6571 3.564218 GATGCAGAGGCCGGGGAT 61.564 66.667 2.18 0.00 40.13 3.85
3260 6572 3.099170 ATGCAGAGGCCGGGGATT 61.099 61.111 2.18 0.00 40.13 3.01
3261 6573 2.631012 GATGCAGAGGCCGGGGATTT 62.631 60.000 2.18 0.00 40.13 2.17
3262 6574 2.517166 GCAGAGGCCGGGGATTTC 60.517 66.667 2.18 0.00 0.00 2.17
3263 6575 2.193248 CAGAGGCCGGGGATTTCC 59.807 66.667 2.18 0.00 0.00 3.13
3277 6589 4.610605 GGATTTCCCCCTTTTCGAAAAA 57.389 40.909 22.67 7.95 0.00 1.94
3302 6614 6.867662 AATTTAGAACATCTCCATTAGGCG 57.132 37.500 0.00 0.00 33.74 5.52
3303 6615 2.918712 AGAACATCTCCATTAGGCGG 57.081 50.000 0.00 0.00 33.74 6.13
3304 6616 2.119495 AGAACATCTCCATTAGGCGGT 58.881 47.619 0.00 0.00 33.74 5.68
3305 6617 2.103263 AGAACATCTCCATTAGGCGGTC 59.897 50.000 0.00 0.00 33.74 4.79
3306 6618 0.759346 ACATCTCCATTAGGCGGTCC 59.241 55.000 0.00 0.00 33.74 4.46
3307 6619 0.758734 CATCTCCATTAGGCGGTCCA 59.241 55.000 0.00 0.00 33.74 4.02
3308 6620 1.349026 CATCTCCATTAGGCGGTCCAT 59.651 52.381 0.00 0.00 33.74 3.41
3309 6621 2.391926 TCTCCATTAGGCGGTCCATA 57.608 50.000 0.00 0.00 33.74 2.74
3310 6622 2.902608 TCTCCATTAGGCGGTCCATAT 58.097 47.619 0.00 0.00 33.74 1.78
3311 6623 2.567169 TCTCCATTAGGCGGTCCATATG 59.433 50.000 0.00 0.00 33.74 1.78
3312 6624 2.303022 CTCCATTAGGCGGTCCATATGT 59.697 50.000 1.24 0.00 33.74 2.29
3313 6625 3.512496 TCCATTAGGCGGTCCATATGTA 58.488 45.455 1.24 0.00 33.74 2.29
3314 6626 3.904965 TCCATTAGGCGGTCCATATGTAA 59.095 43.478 1.24 0.00 33.74 2.41
3315 6627 4.348461 TCCATTAGGCGGTCCATATGTAAA 59.652 41.667 1.24 0.00 33.74 2.01
3316 6628 5.067273 CCATTAGGCGGTCCATATGTAAAA 58.933 41.667 1.24 0.00 33.74 1.52
3317 6629 5.533154 CCATTAGGCGGTCCATATGTAAAAA 59.467 40.000 1.24 0.00 33.74 1.94
3318 6630 6.208599 CCATTAGGCGGTCCATATGTAAAAAT 59.791 38.462 1.24 0.00 33.74 1.82
3319 6631 7.392113 CCATTAGGCGGTCCATATGTAAAAATA 59.608 37.037 1.24 0.00 33.74 1.40
3320 6632 8.788806 CATTAGGCGGTCCATATGTAAAAATAA 58.211 33.333 1.24 0.00 33.74 1.40
3321 6633 6.628919 AGGCGGTCCATATGTAAAAATAAC 57.371 37.500 1.24 0.00 33.74 1.89
3322 6634 6.362248 AGGCGGTCCATATGTAAAAATAACT 58.638 36.000 1.24 0.00 33.74 2.24
3323 6635 7.511268 AGGCGGTCCATATGTAAAAATAACTA 58.489 34.615 1.24 0.00 33.74 2.24
3324 6636 7.994334 AGGCGGTCCATATGTAAAAATAACTAA 59.006 33.333 1.24 0.00 33.74 2.24
3325 6637 8.071967 GGCGGTCCATATGTAAAAATAACTAAC 58.928 37.037 1.24 0.00 0.00 2.34
3326 6638 8.833493 GCGGTCCATATGTAAAAATAACTAACT 58.167 33.333 1.24 0.00 0.00 2.24
3343 6655 7.541122 AACTAACTATTGGATCTTCGAAAGC 57.459 36.000 0.00 0.00 0.00 3.51
3344 6656 6.640518 ACTAACTATTGGATCTTCGAAAGCA 58.359 36.000 0.00 0.00 0.00 3.91
3345 6657 7.103641 ACTAACTATTGGATCTTCGAAAGCAA 58.896 34.615 0.00 0.00 0.00 3.91
3346 6658 6.817765 AACTATTGGATCTTCGAAAGCAAA 57.182 33.333 0.00 0.00 0.00 3.68
3347 6659 6.817765 ACTATTGGATCTTCGAAAGCAAAA 57.182 33.333 0.00 0.00 0.00 2.44
3348 6660 7.214467 ACTATTGGATCTTCGAAAGCAAAAA 57.786 32.000 0.00 0.00 0.00 1.94
3380 6692 6.653526 CCAATAGATGGTCCATATGCAAAA 57.346 37.500 9.35 0.00 44.85 2.44
3381 6693 7.053316 CCAATAGATGGTCCATATGCAAAAA 57.947 36.000 9.35 0.00 44.85 1.94
3402 6714 2.052782 AAATTACATCTCCGCCACCC 57.947 50.000 0.00 0.00 0.00 4.61
3403 6715 0.179056 AATTACATCTCCGCCACCCG 60.179 55.000 0.00 0.00 0.00 5.28
3412 6724 2.897207 CGCCACCCGGAGATGTAA 59.103 61.111 0.73 0.00 32.98 2.41
3413 6725 1.219664 CGCCACCCGGAGATGTAAA 59.780 57.895 0.73 0.00 32.98 2.01
3414 6726 0.391927 CGCCACCCGGAGATGTAAAA 60.392 55.000 0.73 0.00 32.98 1.52
3415 6727 1.745827 CGCCACCCGGAGATGTAAAAT 60.746 52.381 0.73 0.00 32.98 1.82
3416 6728 2.484065 CGCCACCCGGAGATGTAAAATA 60.484 50.000 0.73 0.00 32.98 1.40
3417 6729 2.876550 GCCACCCGGAGATGTAAAATAC 59.123 50.000 0.73 0.00 0.00 1.89
3418 6730 3.683281 GCCACCCGGAGATGTAAAATACA 60.683 47.826 0.73 0.00 43.80 2.29
3419 6731 4.519213 CCACCCGGAGATGTAAAATACAA 58.481 43.478 0.73 0.00 42.76 2.41
3420 6732 4.334481 CCACCCGGAGATGTAAAATACAAC 59.666 45.833 0.73 0.00 42.76 3.32
3421 6733 4.938832 CACCCGGAGATGTAAAATACAACA 59.061 41.667 0.73 0.00 42.76 3.33
3422 6734 4.939439 ACCCGGAGATGTAAAATACAACAC 59.061 41.667 0.73 0.00 42.76 3.32
3423 6735 4.334481 CCCGGAGATGTAAAATACAACACC 59.666 45.833 0.73 4.82 42.76 4.16
3424 6736 5.183228 CCGGAGATGTAAAATACAACACCT 58.817 41.667 0.00 0.00 42.76 4.00
3425 6737 5.293569 CCGGAGATGTAAAATACAACACCTC 59.706 44.000 0.00 0.00 42.76 3.85
3426 6738 5.005394 CGGAGATGTAAAATACAACACCTCG 59.995 44.000 10.70 2.03 42.76 4.63
3427 6739 5.220605 GGAGATGTAAAATACAACACCTCGC 60.221 44.000 6.89 0.00 42.76 5.03
3428 6740 4.328983 AGATGTAAAATACAACACCTCGCG 59.671 41.667 0.00 0.00 42.76 5.87
3429 6741 2.737783 TGTAAAATACAACACCTCGCGG 59.262 45.455 6.13 0.00 35.38 6.46
3430 6742 3.803021 TGTAAAATACAACACCTCGCGGT 60.803 43.478 6.13 0.00 38.98 5.68
3438 6750 3.758172 ACCTCGCGGTGCAAATTT 58.242 50.000 6.13 0.00 43.51 1.82
3439 6751 2.935505 ACCTCGCGGTGCAAATTTA 58.064 47.368 6.13 0.00 43.51 1.40
3440 6752 0.519961 ACCTCGCGGTGCAAATTTAC 59.480 50.000 6.13 0.00 43.51 2.01
3441 6753 0.519519 CCTCGCGGTGCAAATTTACA 59.480 50.000 6.13 0.00 0.00 2.41
3442 6754 1.132262 CCTCGCGGTGCAAATTTACAT 59.868 47.619 6.13 0.00 0.00 2.29
3443 6755 2.440501 CTCGCGGTGCAAATTTACATC 58.559 47.619 6.13 0.00 0.00 3.06
3444 6756 2.080693 TCGCGGTGCAAATTTACATCT 58.919 42.857 6.13 0.00 0.00 2.90
3445 6757 2.159585 TCGCGGTGCAAATTTACATCTG 60.160 45.455 6.13 0.00 0.00 2.90
3446 6758 1.919918 GCGGTGCAAATTTACATCTGC 59.080 47.619 0.34 5.01 35.32 4.26
3447 6759 2.176369 CGGTGCAAATTTACATCTGCG 58.824 47.619 0.34 0.00 37.62 5.18
3448 6760 2.529151 GGTGCAAATTTACATCTGCGG 58.471 47.619 0.00 0.00 37.62 5.69
3449 6761 2.163412 GGTGCAAATTTACATCTGCGGA 59.837 45.455 0.00 0.00 37.62 5.54
3450 6762 3.429085 GTGCAAATTTACATCTGCGGAG 58.571 45.455 0.00 0.00 37.62 4.63
3451 6763 2.423185 TGCAAATTTACATCTGCGGAGG 59.577 45.455 5.47 5.47 37.62 4.30
3452 6764 2.796032 GCAAATTTACATCTGCGGAGGC 60.796 50.000 7.20 0.00 40.52 4.70
3461 6773 2.685017 TGCGGAGGCAGGAGATGT 60.685 61.111 0.00 0.00 46.21 3.06
3462 6774 1.381191 TGCGGAGGCAGGAGATGTA 60.381 57.895 0.00 0.00 46.21 2.29
3463 6775 0.975556 TGCGGAGGCAGGAGATGTAA 60.976 55.000 0.00 0.00 46.21 2.41
3464 6776 0.178068 GCGGAGGCAGGAGATGTAAA 59.822 55.000 0.00 0.00 39.62 2.01
3465 6777 1.406887 GCGGAGGCAGGAGATGTAAAA 60.407 52.381 0.00 0.00 39.62 1.52
3466 6778 2.939640 GCGGAGGCAGGAGATGTAAAAA 60.940 50.000 0.00 0.00 39.62 1.94
3467 6779 2.678336 CGGAGGCAGGAGATGTAAAAAC 59.322 50.000 0.00 0.00 0.00 2.43
3468 6780 3.017442 GGAGGCAGGAGATGTAAAAACC 58.983 50.000 0.00 0.00 0.00 3.27
3469 6781 2.678336 GAGGCAGGAGATGTAAAAACCG 59.322 50.000 0.00 0.00 0.00 4.44
3470 6782 1.132453 GGCAGGAGATGTAAAAACCGC 59.868 52.381 0.00 0.00 0.00 5.68
3471 6783 1.202031 GCAGGAGATGTAAAAACCGCG 60.202 52.381 0.00 0.00 0.00 6.46
3472 6784 1.396996 CAGGAGATGTAAAAACCGCGG 59.603 52.381 26.86 26.86 0.00 6.46
3473 6785 0.098200 GGAGATGTAAAAACCGCGGC 59.902 55.000 28.58 8.37 0.00 6.53
3474 6786 0.098200 GAGATGTAAAAACCGCGGCC 59.902 55.000 28.58 6.82 0.00 6.13
3475 6787 1.226184 GATGTAAAAACCGCGGCCG 60.226 57.895 28.58 24.05 0.00 6.13
3476 6788 3.331089 ATGTAAAAACCGCGGCCGC 62.331 57.895 39.82 39.82 37.85 6.53
3496 6808 3.418913 CCGCGTGCAATCGTCCAA 61.419 61.111 4.92 0.00 0.00 3.53
3497 6809 2.202171 CGCGTGCAATCGTCCAAC 60.202 61.111 0.00 0.00 0.00 3.77
3498 6810 2.175811 GCGTGCAATCGTCCAACC 59.824 61.111 0.00 0.00 0.00 3.77
3499 6811 2.474266 CGTGCAATCGTCCAACCG 59.526 61.111 0.00 0.00 0.00 4.44
3500 6812 2.867472 GTGCAATCGTCCAACCGG 59.133 61.111 0.00 0.00 0.00 5.28
3501 6813 3.053291 TGCAATCGTCCAACCGGC 61.053 61.111 0.00 0.00 0.00 6.13
3502 6814 3.810896 GCAATCGTCCAACCGGCC 61.811 66.667 0.00 0.00 0.00 6.13
3503 6815 2.046314 CAATCGTCCAACCGGCCT 60.046 61.111 0.00 0.00 0.00 5.19
3504 6816 1.674322 CAATCGTCCAACCGGCCTT 60.674 57.895 0.00 0.00 0.00 4.35
3505 6817 1.376812 AATCGTCCAACCGGCCTTC 60.377 57.895 0.00 0.00 0.00 3.46
3506 6818 2.119484 AATCGTCCAACCGGCCTTCA 62.119 55.000 0.00 0.00 0.00 3.02
3507 6819 2.521958 ATCGTCCAACCGGCCTTCAG 62.522 60.000 0.00 0.00 0.00 3.02
3508 6820 2.430367 GTCCAACCGGCCTTCAGT 59.570 61.111 0.00 0.00 0.00 3.41
3509 6821 1.228154 GTCCAACCGGCCTTCAGTT 60.228 57.895 0.00 0.00 0.00 3.16
3510 6822 1.072505 TCCAACCGGCCTTCAGTTC 59.927 57.895 0.00 0.00 0.00 3.01
3511 6823 1.228124 CCAACCGGCCTTCAGTTCA 60.228 57.895 0.00 0.00 0.00 3.18
3512 6824 0.609131 CCAACCGGCCTTCAGTTCAT 60.609 55.000 0.00 0.00 0.00 2.57
3513 6825 1.247567 CAACCGGCCTTCAGTTCATT 58.752 50.000 0.00 0.00 0.00 2.57
3514 6826 1.613437 CAACCGGCCTTCAGTTCATTT 59.387 47.619 0.00 0.00 0.00 2.32
3515 6827 1.534729 ACCGGCCTTCAGTTCATTTC 58.465 50.000 0.00 0.00 0.00 2.17
3516 6828 0.811281 CCGGCCTTCAGTTCATTTCC 59.189 55.000 0.00 0.00 0.00 3.13
3517 6829 0.811281 CGGCCTTCAGTTCATTTCCC 59.189 55.000 0.00 0.00 0.00 3.97
3518 6830 1.186200 GGCCTTCAGTTCATTTCCCC 58.814 55.000 0.00 0.00 0.00 4.81
3519 6831 1.186200 GCCTTCAGTTCATTTCCCCC 58.814 55.000 0.00 0.00 0.00 5.40
3520 6832 1.272704 GCCTTCAGTTCATTTCCCCCT 60.273 52.381 0.00 0.00 0.00 4.79
3521 6833 2.823152 GCCTTCAGTTCATTTCCCCCTT 60.823 50.000 0.00 0.00 0.00 3.95
3522 6834 3.092301 CCTTCAGTTCATTTCCCCCTTC 58.908 50.000 0.00 0.00 0.00 3.46
3523 6835 3.245407 CCTTCAGTTCATTTCCCCCTTCT 60.245 47.826 0.00 0.00 0.00 2.85
3524 6836 3.721087 TCAGTTCATTTCCCCCTTCTC 57.279 47.619 0.00 0.00 0.00 2.87
3525 6837 2.308866 TCAGTTCATTTCCCCCTTCTCC 59.691 50.000 0.00 0.00 0.00 3.71
3526 6838 1.641192 AGTTCATTTCCCCCTTCTCCC 59.359 52.381 0.00 0.00 0.00 4.30
3527 6839 1.641192 GTTCATTTCCCCCTTCTCCCT 59.359 52.381 0.00 0.00 0.00 4.20
3528 6840 1.596496 TCATTTCCCCCTTCTCCCTC 58.404 55.000 0.00 0.00 0.00 4.30
3529 6841 0.553333 CATTTCCCCCTTCTCCCTCC 59.447 60.000 0.00 0.00 0.00 4.30
3530 6842 0.627768 ATTTCCCCCTTCTCCCTCCC 60.628 60.000 0.00 0.00 0.00 4.30
3531 6843 3.635869 TTCCCCCTTCTCCCTCCCG 62.636 68.421 0.00 0.00 0.00 5.14
3580 6892 4.530857 CCACCCCGTCGCAGATCC 62.531 72.222 0.00 0.00 40.67 3.36
3581 6893 3.770040 CACCCCGTCGCAGATCCA 61.770 66.667 0.00 0.00 40.67 3.41
3582 6894 3.461773 ACCCCGTCGCAGATCCAG 61.462 66.667 0.00 0.00 40.67 3.86
3583 6895 4.899239 CCCCGTCGCAGATCCAGC 62.899 72.222 0.00 0.00 40.67 4.85
3584 6896 4.899239 CCCGTCGCAGATCCAGCC 62.899 72.222 2.49 0.00 40.67 4.85
3585 6897 3.842923 CCGTCGCAGATCCAGCCT 61.843 66.667 2.49 0.00 40.67 4.58
3586 6898 2.279120 CGTCGCAGATCCAGCCTC 60.279 66.667 2.49 0.00 40.67 4.70
3587 6899 2.279120 GTCGCAGATCCAGCCTCG 60.279 66.667 2.49 0.00 40.67 4.63
3588 6900 2.755876 TCGCAGATCCAGCCTCGT 60.756 61.111 2.49 0.00 0.00 4.18
3589 6901 2.279120 CGCAGATCCAGCCTCGTC 60.279 66.667 2.49 0.00 0.00 4.20
3590 6902 2.107953 GCAGATCCAGCCTCGTCC 59.892 66.667 0.00 0.00 0.00 4.79
3591 6903 2.818132 CAGATCCAGCCTCGTCCC 59.182 66.667 0.00 0.00 0.00 4.46
3592 6904 1.760086 CAGATCCAGCCTCGTCCCT 60.760 63.158 0.00 0.00 0.00 4.20
3593 6905 0.468214 CAGATCCAGCCTCGTCCCTA 60.468 60.000 0.00 0.00 0.00 3.53
3594 6906 0.468400 AGATCCAGCCTCGTCCCTAC 60.468 60.000 0.00 0.00 0.00 3.18
3595 6907 1.457831 ATCCAGCCTCGTCCCTACC 60.458 63.158 0.00 0.00 0.00 3.18
3596 6908 2.948801 ATCCAGCCTCGTCCCTACCC 62.949 65.000 0.00 0.00 0.00 3.69
3597 6909 3.155167 CAGCCTCGTCCCTACCCC 61.155 72.222 0.00 0.00 0.00 4.95
3598 6910 4.477119 AGCCTCGTCCCTACCCCC 62.477 72.222 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.409982 GCGCACGTGCAAACAGTTTT 61.410 50.000 37.03 0.00 42.21 2.43
17 18 3.242091 GCTGTATATTCATATGGCGCACG 60.242 47.826 10.83 0.00 0.00 5.34
30 31 1.003580 CGGGGGCTGATGCTGTATATT 59.996 52.381 0.00 0.00 39.59 1.28
71 72 0.733150 GATACTTTCCAGGGCGCAAC 59.267 55.000 10.83 0.24 0.00 4.17
72 73 0.393808 GGATACTTTCCAGGGCGCAA 60.394 55.000 10.83 0.00 44.74 4.85
76 77 0.463833 CACCGGATACTTTCCAGGGC 60.464 60.000 9.46 0.00 45.78 5.19
80 81 0.539986 GGAGCACCGGATACTTTCCA 59.460 55.000 9.46 0.00 45.78 3.53
227 228 9.551734 TTGACACTATTCAGATATGGATTTCTG 57.448 33.333 0.00 1.76 40.58 3.02
318 319 8.716646 AAAAATTTCAGTTCCAAACTCGAAAT 57.283 26.923 16.08 16.08 43.20 2.17
332 333 7.597288 AACTACAAGCCCTAAAAATTTCAGT 57.403 32.000 0.00 0.00 0.00 3.41
462 463 1.273041 GGGGGCAACAGGGAAAGTATT 60.273 52.381 0.00 0.00 39.74 1.89
517 519 5.185635 ACATCCATGGTAAAAATGGTGAGTG 59.814 40.000 12.58 1.88 44.27 3.51
530 532 2.645802 GGCCGTTTTACATCCATGGTA 58.354 47.619 12.58 0.00 0.00 3.25
564 566 7.815383 TGGTCTTGATTCTATTGGGTAATCAT 58.185 34.615 0.00 0.00 38.89 2.45
584 586 1.340991 ACAAGTGTGGCAGTTTGGTCT 60.341 47.619 9.47 0.00 0.00 3.85
609 611 1.139455 AGTTTGGTCCTCCGTCGAAAA 59.861 47.619 0.00 0.00 36.30 2.29
610 612 0.754472 AGTTTGGTCCTCCGTCGAAA 59.246 50.000 0.00 0.00 36.30 3.46
611 613 0.032952 CAGTTTGGTCCTCCGTCGAA 59.967 55.000 0.00 0.00 36.30 3.71
614 616 0.606604 TAGCAGTTTGGTCCTCCGTC 59.393 55.000 0.00 0.00 36.30 4.79
615 617 0.320697 GTAGCAGTTTGGTCCTCCGT 59.679 55.000 0.00 0.00 36.30 4.69
657 659 4.873746 TCTGAGAATTTCCACTTCGAGT 57.126 40.909 0.00 0.00 0.00 4.18
683 685 1.014352 GTTTCGCAGTGTGTGTCCTT 58.986 50.000 3.13 0.00 0.00 3.36
712 714 1.850998 GGGTGGGTTTTATAGGAGGCT 59.149 52.381 0.00 0.00 0.00 4.58
713 715 1.567175 TGGGTGGGTTTTATAGGAGGC 59.433 52.381 0.00 0.00 0.00 4.70
770 775 1.656652 CCGGTGGAAGATAGCAACAG 58.343 55.000 0.00 0.00 0.00 3.16
799 804 1.145803 GAAAGGAAAGACACCGTCGG 58.854 55.000 10.48 10.48 37.67 4.79
801 806 2.742589 GGATGAAAGGAAAGACACCGTC 59.257 50.000 0.00 0.00 0.00 4.79
802 807 2.552373 GGGATGAAAGGAAAGACACCGT 60.552 50.000 0.00 0.00 0.00 4.83
803 808 2.084546 GGGATGAAAGGAAAGACACCG 58.915 52.381 0.00 0.00 0.00 4.94
804 809 2.447443 GGGGATGAAAGGAAAGACACC 58.553 52.381 0.00 0.00 0.00 4.16
806 811 2.069775 TGGGGGATGAAAGGAAAGACA 58.930 47.619 0.00 0.00 0.00 3.41
807 812 2.899303 TGGGGGATGAAAGGAAAGAC 57.101 50.000 0.00 0.00 0.00 3.01
841 849 1.080354 CCTCCCACCTGACCCACTA 59.920 63.158 0.00 0.00 0.00 2.74
938 946 0.820226 CAGATCCCTCTCGCTCACAA 59.180 55.000 0.00 0.00 0.00 3.33
1116 1124 1.195115 CGATGACCTCCTTCCTGGAA 58.805 55.000 9.14 9.14 45.63 3.53
1163 1171 7.445121 AGATCTGTATGGCTTATTGAATCGAA 58.555 34.615 0.00 0.00 0.00 3.71
1169 1177 6.653020 ACACAAGATCTGTATGGCTTATTGA 58.347 36.000 0.00 0.00 36.10 2.57
1170 1178 6.932356 ACACAAGATCTGTATGGCTTATTG 57.068 37.500 0.00 0.00 36.10 1.90
1171 1179 6.701841 CGTACACAAGATCTGTATGGCTTATT 59.298 38.462 0.00 0.00 36.10 1.40
1172 1180 6.183360 ACGTACACAAGATCTGTATGGCTTAT 60.183 38.462 14.11 0.00 36.10 1.73
1173 1181 5.126545 ACGTACACAAGATCTGTATGGCTTA 59.873 40.000 14.11 0.00 36.10 3.09
1182 1190 4.442375 AGGAGAACGTACACAAGATCTG 57.558 45.455 0.00 0.00 0.00 2.90
1198 1206 4.766891 GGACATGAATGGACAAAAAGGAGA 59.233 41.667 0.00 0.00 0.00 3.71
1270 1295 1.599542 GGCGGAGATGCATAGTGAAAC 59.400 52.381 0.00 0.00 36.28 2.78
1309 1520 1.961793 TGTCCTGGACGGAACAAAAG 58.038 50.000 21.15 0.00 45.32 2.27
1321 1532 0.254178 CCACAGATCCCTTGTCCTGG 59.746 60.000 0.00 0.00 0.00 4.45
1490 2070 4.851010 ACACATAAGTTAACCAAACACGC 58.149 39.130 0.88 0.00 40.83 5.34
1491 2071 6.415573 GGAAACACATAAGTTAACCAAACACG 59.584 38.462 0.88 0.00 40.83 4.49
1530 2110 1.122019 AAGACGGCCCTGACAAGACT 61.122 55.000 0.00 0.00 0.00 3.24
1549 2129 1.428912 ACAGGGGCCTCAAATTTCTGA 59.571 47.619 4.79 0.00 0.00 3.27
1588 2168 9.462606 AACCGAGTATTCTTGAAATTTTAGGAT 57.537 29.630 0.00 0.00 0.00 3.24
1785 3906 4.089493 GCGCATATGCATCAATTCATCAAC 59.911 41.667 26.52 0.00 42.21 3.18
1828 3949 7.978982 ACTATCTTGTGTGCTGTTGAATAATC 58.021 34.615 0.00 0.00 0.00 1.75
1905 4631 1.527433 GCCAAGACCAAAGGTGAGGC 61.527 60.000 0.00 0.43 35.25 4.70
1986 4723 5.822519 TCAAGAACTAATTCCATGATTCCGG 59.177 40.000 0.00 0.00 35.18 5.14
2278 5072 0.761802 TTTTGGGCCCTTTTTCGCAT 59.238 45.000 25.70 0.00 0.00 4.73
2394 5285 3.614092 CACATATTGGCCTCACAAGACT 58.386 45.455 3.32 0.00 33.23 3.24
2475 5433 4.096003 GGGTTAGCAGCGCCTCCA 62.096 66.667 2.29 0.00 0.00 3.86
2638 5617 8.378172 TCTTTGAGAAATAACAGTTCACGATT 57.622 30.769 0.00 0.00 0.00 3.34
2641 5620 9.107367 GAAATCTTTGAGAAATAACAGTTCACG 57.893 33.333 0.00 0.00 0.00 4.35
2642 5621 9.107367 CGAAATCTTTGAGAAATAACAGTTCAC 57.893 33.333 0.00 0.00 0.00 3.18
2789 5774 8.682936 AGAATTTCTGACAAGTAAACAGACAT 57.317 30.769 0.00 0.00 39.80 3.06
2926 6225 9.878599 GGTATTTCAATGTATATTGTTTCCTCG 57.121 33.333 11.44 0.00 43.33 4.63
3112 6424 5.906113 AATCTGACTCGCCCTATATACAG 57.094 43.478 0.00 0.00 0.00 2.74
3124 6436 7.272299 CAGATACGGATCAAATAATCTGACTCG 59.728 40.741 10.99 0.00 41.73 4.18
3149 6461 4.716794 TGTGGCAGCATACAATCATATCA 58.283 39.130 0.00 0.00 0.00 2.15
3172 6484 2.093973 CAGGCCGATCTGTATGGGTATC 60.094 54.545 0.00 0.00 33.66 2.24
3207 6519 9.632807 GCATACGGCCAATTATTATCAAAATAA 57.367 29.630 2.24 0.00 36.11 1.40
3208 6520 8.797438 TGCATACGGCCAATTATTATCAAAATA 58.203 29.630 2.24 0.00 43.89 1.40
3209 6521 7.665690 TGCATACGGCCAATTATTATCAAAAT 58.334 30.769 2.24 0.00 43.89 1.82
3210 6522 7.043961 TGCATACGGCCAATTATTATCAAAA 57.956 32.000 2.24 0.00 43.89 2.44
3211 6523 6.641169 TGCATACGGCCAATTATTATCAAA 57.359 33.333 2.24 0.00 43.89 2.69
3212 6524 6.432472 TGATGCATACGGCCAATTATTATCAA 59.568 34.615 2.24 0.00 43.89 2.57
3213 6525 5.942826 TGATGCATACGGCCAATTATTATCA 59.057 36.000 2.24 6.18 43.89 2.15
3214 6526 6.435430 TGATGCATACGGCCAATTATTATC 57.565 37.500 2.24 3.86 43.89 1.75
3215 6527 7.340232 AGAATGATGCATACGGCCAATTATTAT 59.660 33.333 2.24 0.00 43.89 1.28
3216 6528 6.658816 AGAATGATGCATACGGCCAATTATTA 59.341 34.615 2.24 0.00 43.89 0.98
3217 6529 5.477984 AGAATGATGCATACGGCCAATTATT 59.522 36.000 2.24 0.00 43.89 1.40
3218 6530 5.012239 AGAATGATGCATACGGCCAATTAT 58.988 37.500 2.24 0.00 43.89 1.28
3219 6531 4.216042 CAGAATGATGCATACGGCCAATTA 59.784 41.667 2.24 0.00 39.87 1.40
3220 6532 3.005050 CAGAATGATGCATACGGCCAATT 59.995 43.478 2.24 0.00 39.87 2.32
3221 6533 2.555325 CAGAATGATGCATACGGCCAAT 59.445 45.455 2.24 0.00 39.87 3.16
3222 6534 1.948834 CAGAATGATGCATACGGCCAA 59.051 47.619 2.24 0.00 39.87 4.52
3223 6535 1.140652 TCAGAATGATGCATACGGCCA 59.859 47.619 2.24 0.00 42.56 5.36
3224 6536 1.882912 TCAGAATGATGCATACGGCC 58.117 50.000 0.00 0.00 42.56 6.13
3236 6548 1.164662 CCGGCCTCTGCATCAGAATG 61.165 60.000 0.00 0.00 40.18 2.67
3237 6549 1.147824 CCGGCCTCTGCATCAGAAT 59.852 57.895 0.00 0.00 40.18 2.40
3238 6550 2.586245 CCGGCCTCTGCATCAGAA 59.414 61.111 0.00 0.00 40.18 3.02
3239 6551 3.473647 CCCGGCCTCTGCATCAGA 61.474 66.667 0.00 0.00 38.25 3.27
3240 6552 4.559063 CCCCGGCCTCTGCATCAG 62.559 72.222 0.00 0.00 40.13 2.90
3242 6554 2.631012 AAATCCCCGGCCTCTGCATC 62.631 60.000 0.00 0.00 40.13 3.91
3243 6555 2.631012 GAAATCCCCGGCCTCTGCAT 62.631 60.000 0.00 0.00 40.13 3.96
3244 6556 3.338250 AAATCCCCGGCCTCTGCA 61.338 61.111 0.00 0.00 40.13 4.41
3245 6557 2.517166 GAAATCCCCGGCCTCTGC 60.517 66.667 0.00 0.00 0.00 4.26
3246 6558 2.193248 GGAAATCCCCGGCCTCTG 59.807 66.667 0.00 0.00 0.00 3.35
3256 6568 4.610605 TTTTTCGAAAAGGGGGAAATCC 57.389 40.909 21.53 0.00 30.55 3.01
3276 6588 8.190784 CGCCTAATGGAGATGTTCTAAATTTTT 58.809 33.333 0.00 0.00 34.95 1.94
3277 6589 7.201821 CCGCCTAATGGAGATGTTCTAAATTTT 60.202 37.037 0.00 0.00 34.95 1.82
3278 6590 6.263168 CCGCCTAATGGAGATGTTCTAAATTT 59.737 38.462 0.00 0.00 34.95 1.82
3279 6591 5.765182 CCGCCTAATGGAGATGTTCTAAATT 59.235 40.000 0.00 0.00 34.95 1.82
3280 6592 5.163195 ACCGCCTAATGGAGATGTTCTAAAT 60.163 40.000 0.00 0.00 34.95 1.40
3281 6593 4.163458 ACCGCCTAATGGAGATGTTCTAAA 59.837 41.667 0.00 0.00 34.95 1.85
3282 6594 3.709653 ACCGCCTAATGGAGATGTTCTAA 59.290 43.478 0.00 0.00 34.95 2.10
3283 6595 3.305720 ACCGCCTAATGGAGATGTTCTA 58.694 45.455 0.00 0.00 34.95 2.10
3284 6596 2.103263 GACCGCCTAATGGAGATGTTCT 59.897 50.000 0.00 0.00 34.95 3.01
3285 6597 2.484889 GACCGCCTAATGGAGATGTTC 58.515 52.381 0.00 0.00 34.95 3.18
3286 6598 1.141053 GGACCGCCTAATGGAGATGTT 59.859 52.381 0.00 0.00 34.95 2.71
3287 6599 0.759346 GGACCGCCTAATGGAGATGT 59.241 55.000 0.00 0.00 34.95 3.06
3288 6600 0.758734 TGGACCGCCTAATGGAGATG 59.241 55.000 0.00 0.00 34.95 2.90
3289 6601 1.734655 ATGGACCGCCTAATGGAGAT 58.265 50.000 0.00 0.00 34.95 2.75
3290 6602 2.391926 TATGGACCGCCTAATGGAGA 57.608 50.000 0.00 0.00 34.95 3.71
3291 6603 2.303022 ACATATGGACCGCCTAATGGAG 59.697 50.000 7.80 0.00 33.76 3.86
3292 6604 2.334977 ACATATGGACCGCCTAATGGA 58.665 47.619 7.80 0.00 33.76 3.41
3293 6605 2.859165 ACATATGGACCGCCTAATGG 57.141 50.000 7.80 0.00 33.76 3.16
3294 6606 6.627395 TTTTTACATATGGACCGCCTAATG 57.373 37.500 7.80 0.00 34.87 1.90
3295 6607 8.789762 GTTATTTTTACATATGGACCGCCTAAT 58.210 33.333 7.80 0.00 34.31 1.73
3296 6608 7.994334 AGTTATTTTTACATATGGACCGCCTAA 59.006 33.333 7.80 0.00 34.31 2.69
3297 6609 7.511268 AGTTATTTTTACATATGGACCGCCTA 58.489 34.615 7.80 0.00 34.31 3.93
3298 6610 6.362248 AGTTATTTTTACATATGGACCGCCT 58.638 36.000 7.80 0.00 34.31 5.52
3299 6611 6.628919 AGTTATTTTTACATATGGACCGCC 57.371 37.500 7.80 0.00 0.00 6.13
3300 6612 8.833493 AGTTAGTTATTTTTACATATGGACCGC 58.167 33.333 7.80 0.00 0.00 5.68
3317 6629 9.262358 GCTTTCGAAGATCCAATAGTTAGTTAT 57.738 33.333 0.00 0.00 35.04 1.89
3318 6630 8.255206 TGCTTTCGAAGATCCAATAGTTAGTTA 58.745 33.333 0.00 0.00 35.04 2.24
3319 6631 7.103641 TGCTTTCGAAGATCCAATAGTTAGTT 58.896 34.615 0.00 0.00 35.04 2.24
3320 6632 6.640518 TGCTTTCGAAGATCCAATAGTTAGT 58.359 36.000 0.00 0.00 35.04 2.24
3321 6633 7.539712 TTGCTTTCGAAGATCCAATAGTTAG 57.460 36.000 0.00 0.00 35.04 2.34
3322 6634 7.915293 TTTGCTTTCGAAGATCCAATAGTTA 57.085 32.000 0.00 0.00 35.04 2.24
3323 6635 6.817765 TTTGCTTTCGAAGATCCAATAGTT 57.182 33.333 0.00 0.00 35.04 2.24
3324 6636 6.817765 TTTTGCTTTCGAAGATCCAATAGT 57.182 33.333 0.00 0.00 35.04 2.12
3381 6693 2.758423 GGGTGGCGGAGATGTAATTTTT 59.242 45.455 0.00 0.00 0.00 1.94
3382 6694 2.375146 GGGTGGCGGAGATGTAATTTT 58.625 47.619 0.00 0.00 0.00 1.82
3383 6695 1.745827 CGGGTGGCGGAGATGTAATTT 60.746 52.381 0.00 0.00 0.00 1.82
3384 6696 0.179056 CGGGTGGCGGAGATGTAATT 60.179 55.000 0.00 0.00 0.00 1.40
3385 6697 1.445942 CGGGTGGCGGAGATGTAAT 59.554 57.895 0.00 0.00 0.00 1.89
3386 6698 2.727392 CCGGGTGGCGGAGATGTAA 61.727 63.158 0.00 0.00 0.00 2.41
3387 6699 3.151710 CCGGGTGGCGGAGATGTA 61.152 66.667 0.00 0.00 0.00 2.29
3393 6705 3.665515 TACATCTCCGGGTGGCGGA 62.666 63.158 0.00 0.00 34.14 5.54
3394 6706 2.246761 TTTACATCTCCGGGTGGCGG 62.247 60.000 0.00 0.00 34.14 6.13
3395 6707 0.391927 TTTTACATCTCCGGGTGGCG 60.392 55.000 0.00 0.00 34.14 5.69
3396 6708 2.052782 ATTTTACATCTCCGGGTGGC 57.947 50.000 0.00 0.00 34.14 5.01
3397 6709 4.145365 TGTATTTTACATCTCCGGGTGG 57.855 45.455 0.00 0.00 32.89 4.61
3398 6710 4.938832 TGTTGTATTTTACATCTCCGGGTG 59.061 41.667 0.00 0.66 38.68 4.61
3399 6711 4.939439 GTGTTGTATTTTACATCTCCGGGT 59.061 41.667 0.00 0.00 38.68 5.28
3400 6712 4.334481 GGTGTTGTATTTTACATCTCCGGG 59.666 45.833 0.00 0.00 38.68 5.73
3401 6713 5.183228 AGGTGTTGTATTTTACATCTCCGG 58.817 41.667 0.00 0.00 42.50 5.14
3402 6714 5.005394 CGAGGTGTTGTATTTTACATCTCCG 59.995 44.000 9.25 2.76 45.45 4.63
3403 6715 5.220605 GCGAGGTGTTGTATTTTACATCTCC 60.221 44.000 9.25 8.01 45.45 3.71
3404 6716 5.500290 CGCGAGGTGTTGTATTTTACATCTC 60.500 44.000 0.00 0.00 45.01 2.75
3405 6717 4.328983 CGCGAGGTGTTGTATTTTACATCT 59.671 41.667 0.00 0.00 38.39 2.90
3406 6718 4.574759 CGCGAGGTGTTGTATTTTACATC 58.425 43.478 0.00 0.00 38.68 3.06
3407 6719 4.593597 CGCGAGGTGTTGTATTTTACAT 57.406 40.909 0.00 0.00 38.68 2.29
3423 6735 2.095853 AGATGTAAATTTGCACCGCGAG 59.904 45.455 8.23 0.00 0.00 5.03
3424 6736 2.080693 AGATGTAAATTTGCACCGCGA 58.919 42.857 8.23 0.00 0.00 5.87
3425 6737 2.176369 CAGATGTAAATTTGCACCGCG 58.824 47.619 11.35 0.00 0.00 6.46
3426 6738 1.919918 GCAGATGTAAATTTGCACCGC 59.080 47.619 11.35 10.25 36.59 5.68
3427 6739 2.176369 CGCAGATGTAAATTTGCACCG 58.824 47.619 11.35 8.24 36.37 4.94
3428 6740 2.163412 TCCGCAGATGTAAATTTGCACC 59.837 45.455 11.35 1.20 36.37 5.01
3429 6741 3.429085 CTCCGCAGATGTAAATTTGCAC 58.571 45.455 11.35 6.02 36.37 4.57
3430 6742 2.423185 CCTCCGCAGATGTAAATTTGCA 59.577 45.455 11.51 11.51 36.37 4.08
3431 6743 2.796032 GCCTCCGCAGATGTAAATTTGC 60.796 50.000 0.00 0.00 34.03 3.68
3432 6744 2.423185 TGCCTCCGCAGATGTAAATTTG 59.577 45.455 0.00 0.00 41.12 2.32
3433 6745 2.722094 TGCCTCCGCAGATGTAAATTT 58.278 42.857 0.00 0.00 41.12 1.82
3434 6746 2.418368 TGCCTCCGCAGATGTAAATT 57.582 45.000 0.00 0.00 41.12 1.82
3444 6756 0.975556 TTACATCTCCTGCCTCCGCA 60.976 55.000 0.00 0.00 44.78 5.69
3445 6757 0.178068 TTTACATCTCCTGCCTCCGC 59.822 55.000 0.00 0.00 0.00 5.54
3446 6758 2.678336 GTTTTTACATCTCCTGCCTCCG 59.322 50.000 0.00 0.00 0.00 4.63
3447 6759 3.017442 GGTTTTTACATCTCCTGCCTCC 58.983 50.000 0.00 0.00 0.00 4.30
3448 6760 2.678336 CGGTTTTTACATCTCCTGCCTC 59.322 50.000 0.00 0.00 0.00 4.70
3449 6761 2.711542 CGGTTTTTACATCTCCTGCCT 58.288 47.619 0.00 0.00 0.00 4.75
3450 6762 1.132453 GCGGTTTTTACATCTCCTGCC 59.868 52.381 0.00 0.00 0.00 4.85
3451 6763 1.202031 CGCGGTTTTTACATCTCCTGC 60.202 52.381 0.00 0.00 0.00 4.85
3452 6764 1.396996 CCGCGGTTTTTACATCTCCTG 59.603 52.381 19.50 0.00 0.00 3.86
3453 6765 1.734163 CCGCGGTTTTTACATCTCCT 58.266 50.000 19.50 0.00 0.00 3.69
3454 6766 0.098200 GCCGCGGTTTTTACATCTCC 59.902 55.000 28.70 0.08 0.00 3.71
3455 6767 0.098200 GGCCGCGGTTTTTACATCTC 59.902 55.000 28.70 4.56 0.00 2.75
3456 6768 1.641123 CGGCCGCGGTTTTTACATCT 61.641 55.000 28.70 0.00 0.00 2.90
3457 6769 1.226184 CGGCCGCGGTTTTTACATC 60.226 57.895 28.70 5.99 0.00 3.06
3458 6770 2.871828 CGGCCGCGGTTTTTACAT 59.128 55.556 28.70 0.00 0.00 2.29
3459 6771 4.027923 GCGGCCGCGGTTTTTACA 62.028 61.111 37.24 0.00 0.00 2.41
3479 6791 3.418913 TTGGACGATTGCACGCGG 61.419 61.111 12.47 0.00 36.70 6.46
3480 6792 2.202171 GTTGGACGATTGCACGCG 60.202 61.111 3.53 3.53 36.70 6.01
3481 6793 2.175811 GGTTGGACGATTGCACGC 59.824 61.111 0.00 0.00 36.70 5.34
3482 6794 2.474266 CGGTTGGACGATTGCACG 59.526 61.111 0.00 0.00 39.31 5.34
3483 6795 2.867472 CCGGTTGGACGATTGCAC 59.133 61.111 0.00 0.00 37.49 4.57
3484 6796 3.053291 GCCGGTTGGACGATTGCA 61.053 61.111 1.90 0.00 37.49 4.08
3485 6797 3.810896 GGCCGGTTGGACGATTGC 61.811 66.667 1.90 0.00 37.49 3.56
3492 6804 1.072505 GAACTGAAGGCCGGTTGGA 59.927 57.895 1.90 0.00 44.04 3.53
3493 6805 0.609131 ATGAACTGAAGGCCGGTTGG 60.609 55.000 1.90 0.00 44.04 3.77
3494 6806 1.247567 AATGAACTGAAGGCCGGTTG 58.752 50.000 1.90 0.14 44.04 3.77
3495 6807 1.886542 GAAATGAACTGAAGGCCGGTT 59.113 47.619 1.90 1.26 46.53 4.44
3496 6808 1.534729 GAAATGAACTGAAGGCCGGT 58.465 50.000 1.90 0.00 35.44 5.28
3497 6809 0.811281 GGAAATGAACTGAAGGCCGG 59.189 55.000 0.00 0.00 0.00 6.13
3498 6810 0.811281 GGGAAATGAACTGAAGGCCG 59.189 55.000 0.00 0.00 0.00 6.13
3499 6811 1.186200 GGGGAAATGAACTGAAGGCC 58.814 55.000 0.00 0.00 0.00 5.19
3500 6812 1.186200 GGGGGAAATGAACTGAAGGC 58.814 55.000 0.00 0.00 0.00 4.35
3501 6813 2.907458 AGGGGGAAATGAACTGAAGG 57.093 50.000 0.00 0.00 0.00 3.46
3502 6814 4.013050 GAGAAGGGGGAAATGAACTGAAG 58.987 47.826 0.00 0.00 0.00 3.02
3503 6815 3.245264 GGAGAAGGGGGAAATGAACTGAA 60.245 47.826 0.00 0.00 0.00 3.02
3504 6816 2.308866 GGAGAAGGGGGAAATGAACTGA 59.691 50.000 0.00 0.00 0.00 3.41
3505 6817 2.621668 GGGAGAAGGGGGAAATGAACTG 60.622 54.545 0.00 0.00 0.00 3.16
3506 6818 1.641192 GGGAGAAGGGGGAAATGAACT 59.359 52.381 0.00 0.00 0.00 3.01
3507 6819 1.641192 AGGGAGAAGGGGGAAATGAAC 59.359 52.381 0.00 0.00 0.00 3.18
3508 6820 1.923148 GAGGGAGAAGGGGGAAATGAA 59.077 52.381 0.00 0.00 0.00 2.57
3509 6821 1.596496 GAGGGAGAAGGGGGAAATGA 58.404 55.000 0.00 0.00 0.00 2.57
3510 6822 0.553333 GGAGGGAGAAGGGGGAAATG 59.447 60.000 0.00 0.00 0.00 2.32
3511 6823 0.627768 GGGAGGGAGAAGGGGGAAAT 60.628 60.000 0.00 0.00 0.00 2.17
3512 6824 1.230182 GGGAGGGAGAAGGGGGAAA 60.230 63.158 0.00 0.00 0.00 3.13
3513 6825 2.459710 GGGAGGGAGAAGGGGGAA 59.540 66.667 0.00 0.00 0.00 3.97
3514 6826 4.089757 CGGGAGGGAGAAGGGGGA 62.090 72.222 0.00 0.00 0.00 4.81
3563 6875 4.530857 GGATCTGCGACGGGGTGG 62.531 72.222 0.00 0.00 0.00 4.61
3564 6876 3.723235 CTGGATCTGCGACGGGGTG 62.723 68.421 0.00 0.00 0.00 4.61
3565 6877 3.461773 CTGGATCTGCGACGGGGT 61.462 66.667 0.00 0.00 0.00 4.95
3566 6878 4.899239 GCTGGATCTGCGACGGGG 62.899 72.222 0.00 0.00 0.00 5.73
3567 6879 4.899239 GGCTGGATCTGCGACGGG 62.899 72.222 0.00 0.00 0.00 5.28
3568 6880 3.781770 GAGGCTGGATCTGCGACGG 62.782 68.421 0.00 0.00 0.00 4.79
3569 6881 2.279120 GAGGCTGGATCTGCGACG 60.279 66.667 0.00 0.00 0.00 5.12
3570 6882 2.279120 CGAGGCTGGATCTGCGAC 60.279 66.667 0.00 0.00 0.00 5.19
3571 6883 2.755876 ACGAGGCTGGATCTGCGA 60.756 61.111 2.65 0.00 0.00 5.10
3572 6884 2.279120 GACGAGGCTGGATCTGCG 60.279 66.667 2.65 0.00 0.00 5.18
3573 6885 2.107953 GGACGAGGCTGGATCTGC 59.892 66.667 2.65 0.00 0.00 4.26
3574 6886 0.468214 TAGGGACGAGGCTGGATCTG 60.468 60.000 2.65 0.00 0.00 2.90
3575 6887 0.468400 GTAGGGACGAGGCTGGATCT 60.468 60.000 2.65 0.29 0.00 2.75
3576 6888 1.465200 GGTAGGGACGAGGCTGGATC 61.465 65.000 2.65 0.00 0.00 3.36
3577 6889 1.457831 GGTAGGGACGAGGCTGGAT 60.458 63.158 2.65 0.00 0.00 3.41
3578 6890 2.043248 GGTAGGGACGAGGCTGGA 60.043 66.667 2.65 0.00 0.00 3.86
3579 6891 3.155167 GGGTAGGGACGAGGCTGG 61.155 72.222 0.00 0.00 0.00 4.85
3580 6892 3.155167 GGGGTAGGGACGAGGCTG 61.155 72.222 0.00 0.00 0.00 4.85
3581 6893 4.477119 GGGGGTAGGGACGAGGCT 62.477 72.222 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.