Multiple sequence alignment - TraesCS2D01G452900

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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 TraesCS2D01G452900 chr2D 100.000 3536 0 0 1 3536 562169191 562165656 0.000000e+00 6530.0
1 TraesCS2D01G452900 chr2D 91.189 1589 123 6 910 2498 411733652 411732081 0.000000e+00 2143.0
2 TraesCS2D01G452900 chr2D 83.444 604 77 21 2789 3379 400302711 400302118 1.120000e-149 540.0
3 TraesCS2D01G452900 chr2D 87.736 212 19 6 3171 3377 126970583 126970792 1.270000e-59 241.0
4 TraesCS2D01G452900 chr2D 90.449 178 17 0 3202 3379 615151582 615151405 5.900000e-58 235.0
5 TraesCS2D01G452900 chr2B 92.559 3064 146 32 482 3536 671753094 671750104 0.000000e+00 4320.0
6 TraesCS2D01G452900 chr2B 90.875 1589 125 6 910 2498 485444843 485443275 0.000000e+00 2113.0
7 TraesCS2D01G452900 chr2B 89.100 422 39 5 7 425 671753534 671753117 5.230000e-143 518.0
8 TraesCS2D01G452900 chr2B 77.920 625 102 25 2770 3376 596995154 596994548 1.210000e-94 357.0
9 TraesCS2D01G452900 chr2A 89.549 2239 151 36 486 2712 702853396 702851229 0.000000e+00 2761.0
10 TraesCS2D01G452900 chr2A 89.912 228 17 4 200 424 702853643 702853419 4.470000e-74 289.0
11 TraesCS2D01G452900 chr2A 84.689 209 31 1 3171 3379 739692712 739692919 1.290000e-49 207.0
12 TraesCS2D01G452900 chr3A 80.000 620 82 26 2783 3379 7313415 7314015 1.520000e-113 420.0
13 TraesCS2D01G452900 chr3A 78.003 591 70 28 2823 3369 7928048 7927474 2.050000e-82 316.0
14 TraesCS2D01G452900 chr4A 75.743 606 103 31 2788 3379 673745955 673746530 7.530000e-67 265.0
15 TraesCS2D01G452900 chr4A 92.500 40 3 0 3121 3160 671600474 671600513 1.370000e-04 58.4
16 TraesCS2D01G452900 chr7A 77.096 489 77 22 2914 3377 646127154 646126676 2.110000e-62 250.0
17 TraesCS2D01G452900 chr7A 86.792 53 5 2 3103 3153 674736891 674736839 1.370000e-04 58.4
18 TraesCS2D01G452900 chr7A 86.792 53 5 2 3103 3153 674751626 674751574 1.370000e-04 58.4
19 TraesCS2D01G452900 chr5D 75.156 640 93 38 2790 3379 389004491 389003868 1.270000e-59 241.0
20 TraesCS2D01G452900 chr5D 90.341 176 17 0 3202 3377 491269557 491269732 7.630000e-57 231.0
21 TraesCS2D01G452900 chr5D 84.579 214 27 6 2777 2989 455601427 455601635 1.290000e-49 207.0
22 TraesCS2D01G452900 chr5D 86.010 193 24 3 2777 2969 454831769 454831958 1.660000e-48 204.0
23 TraesCS2D01G452900 chr5D 82.439 205 36 0 1893 2097 425839799 425840003 2.800000e-41 180.0
24 TraesCS2D01G452900 chr7D 89.503 181 14 4 3202 3379 567338143 567338321 1.280000e-54 224.0
25 TraesCS2D01G452900 chr4D 76.375 491 70 30 2914 3379 78827345 78827814 4.590000e-54 222.0
26 TraesCS2D01G452900 chr4B 76.112 427 78 17 2790 3208 665418006 665417596 5.990000e-48 202.0
27 TraesCS2D01G452900 chr5A 75.979 383 89 2 1893 2272 540052857 540053239 1.000000e-45 195.0
28 TraesCS2D01G452900 chr3B 81.702 235 35 6 2788 3019 813317989 813317760 4.660000e-44 189.0
29 TraesCS2D01G452900 chr1B 79.060 234 41 8 2792 3024 678769390 678769164 1.700000e-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 TraesCS2D01G452900 chr2D 562165656 562169191 3535 True 6530 6530 100.0000 1 3536 1 chr2D.!!$R3 3535
1 TraesCS2D01G452900 chr2D 411732081 411733652 1571 True 2143 2143 91.1890 910 2498 1 chr2D.!!$R2 1588
2 TraesCS2D01G452900 chr2D 400302118 400302711 593 True 540 540 83.4440 2789 3379 1 chr2D.!!$R1 590
3 TraesCS2D01G452900 chr2B 671750104 671753534 3430 True 2419 4320 90.8295 7 3536 2 chr2B.!!$R3 3529
4 TraesCS2D01G452900 chr2B 485443275 485444843 1568 True 2113 2113 90.8750 910 2498 1 chr2B.!!$R1 1588
5 TraesCS2D01G452900 chr2B 596994548 596995154 606 True 357 357 77.9200 2770 3376 1 chr2B.!!$R2 606
6 TraesCS2D01G452900 chr2A 702851229 702853643 2414 True 1525 2761 89.7305 200 2712 2 chr2A.!!$R1 2512
7 TraesCS2D01G452900 chr3A 7313415 7314015 600 False 420 420 80.0000 2783 3379 1 chr3A.!!$F1 596
8 TraesCS2D01G452900 chr3A 7927474 7928048 574 True 316 316 78.0030 2823 3369 1 chr3A.!!$R1 546
9 TraesCS2D01G452900 chr4A 673745955 673746530 575 False 265 265 75.7430 2788 3379 1 chr4A.!!$F2 591
10 TraesCS2D01G452900 chr5D 389003868 389004491 623 True 241 241 75.1560 2790 3379 1 chr5D.!!$R1 589

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
655 663 0.107165 GTTGGAGAAATAGGCCGCCT 60.107 55.0 18.05 18.05 37.71 5.52 F
1066 1094 0.107654 GCTAGCCATCGTGTCCCTTT 60.108 55.0 2.29 0.00 0.00 3.11 F
2002 2030 0.179089 CCACTTCTGCGAGATCCAGG 60.179 60.0 0.00 0.00 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1834 0.794981 CGTCGCTGTCCTTCTCGAAG 60.795 60.000 0.0 0.0 38.14 3.79 R
2153 2181 2.108157 GCGCGACCCACATATCCA 59.892 61.111 12.1 0.0 0.00 3.41 R
3392 3555 1.298602 GAGCATCACACACACACACA 58.701 50.000 0.0 0.0 33.17 3.72 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
101 103 9.983804 CGAAAGACCCAAATTATAAAAGTCTAC 57.016 33.333 0.00 0.00 33.01 2.59
123 125 4.956075 ACATGTTTTCCAGTCCTCTGTTTT 59.044 37.500 0.00 0.00 39.82 2.43
124 126 4.981806 TGTTTTCCAGTCCTCTGTTTTG 57.018 40.909 0.00 0.00 39.82 2.44
125 127 4.594970 TGTTTTCCAGTCCTCTGTTTTGA 58.405 39.130 0.00 0.00 39.82 2.69
126 128 4.398044 TGTTTTCCAGTCCTCTGTTTTGAC 59.602 41.667 0.00 0.00 39.82 3.18
127 129 2.526304 TCCAGTCCTCTGTTTTGACG 57.474 50.000 0.00 0.00 39.82 4.35
130 132 0.759346 AGTCCTCTGTTTTGACGCCT 59.241 50.000 0.00 0.00 34.24 5.52
131 133 1.141053 AGTCCTCTGTTTTGACGCCTT 59.859 47.619 0.00 0.00 34.24 4.35
138 140 3.442273 TCTGTTTTGACGCCTTTGTTCTT 59.558 39.130 0.00 0.00 0.00 2.52
142 144 6.334202 TGTTTTGACGCCTTTGTTCTTAATT 58.666 32.000 0.00 0.00 0.00 1.40
152 154 6.646240 GCCTTTGTTCTTAATTGATTCTTGCA 59.354 34.615 0.00 0.00 0.00 4.08
168 170 6.817765 TTCTTGCATTTGTACCCTTCTTAG 57.182 37.500 0.00 0.00 0.00 2.18
182 184 4.498241 CCTTCTTAGCTTTTCCAAATGGC 58.502 43.478 0.00 0.00 34.44 4.40
190 192 3.865446 CTTTTCCAAATGGCCAGAATCC 58.135 45.455 13.05 0.00 34.44 3.01
227 230 4.680237 TGGCTCCGGTTGACGCAG 62.680 66.667 0.00 0.00 42.52 5.18
236 239 1.659794 GTTGACGCAGCCACCATTT 59.340 52.632 0.00 0.00 0.00 2.32
245 248 3.137533 GCAGCCACCATTTTTAGCAAAA 58.862 40.909 0.00 0.00 36.30 2.44
269 272 8.528917 AAAAGCATTTATTTACCGGAAAAGAC 57.471 30.769 9.46 0.00 37.28 3.01
283 286 5.120208 CCGGAAAAGACGATGCGATAATTAT 59.880 40.000 0.00 0.00 31.57 1.28
414 418 2.589014 GTTTGAAGCGCTGGAAATGAG 58.411 47.619 12.58 0.00 0.00 2.90
425 429 5.506317 GCGCTGGAAATGAGCTGTAAATAAT 60.506 40.000 0.00 0.00 34.03 1.28
427 431 6.634436 CGCTGGAAATGAGCTGTAAATAATTC 59.366 38.462 0.00 0.00 34.03 2.17
428 432 7.467811 CGCTGGAAATGAGCTGTAAATAATTCT 60.468 37.037 0.00 0.00 34.03 2.40
429 433 7.859875 GCTGGAAATGAGCTGTAAATAATTCTC 59.140 37.037 0.00 0.00 33.37 2.87
431 435 8.896744 TGGAAATGAGCTGTAAATAATTCTCTG 58.103 33.333 0.00 0.00 0.00 3.35
432 436 8.897752 GGAAATGAGCTGTAAATAATTCTCTGT 58.102 33.333 0.00 0.00 0.00 3.41
433 437 9.713740 GAAATGAGCTGTAAATAATTCTCTGTG 57.286 33.333 0.00 0.00 0.00 3.66
434 438 6.668541 TGAGCTGTAAATAATTCTCTGTGC 57.331 37.500 0.00 0.00 0.00 4.57
435 439 6.409704 TGAGCTGTAAATAATTCTCTGTGCT 58.590 36.000 0.00 0.00 0.00 4.40
436 440 7.555965 TGAGCTGTAAATAATTCTCTGTGCTA 58.444 34.615 0.00 0.00 0.00 3.49
437 441 7.492669 TGAGCTGTAAATAATTCTCTGTGCTAC 59.507 37.037 0.00 0.00 0.00 3.58
438 442 7.560368 AGCTGTAAATAATTCTCTGTGCTACT 58.440 34.615 0.00 0.00 0.00 2.57
439 443 8.696374 AGCTGTAAATAATTCTCTGTGCTACTA 58.304 33.333 0.00 0.00 0.00 1.82
440 444 8.756864 GCTGTAAATAATTCTCTGTGCTACTAC 58.243 37.037 0.00 0.00 0.00 2.73
448 452 8.810990 AATTCTCTGTGCTACTACTAGTAACT 57.189 34.615 3.76 0.00 29.00 2.24
449 453 7.846644 TTCTCTGTGCTACTACTAGTAACTC 57.153 40.000 3.76 0.00 29.00 3.01
450 454 6.347696 TCTCTGTGCTACTACTAGTAACTCC 58.652 44.000 3.76 0.00 29.00 3.85
461 465 5.579564 ACTAGTAACTCCAACCGAATCTC 57.420 43.478 0.00 0.00 0.00 2.75
466 470 2.444421 ACTCCAACCGAATCTCGTAGT 58.556 47.619 0.00 0.00 38.40 2.73
467 471 2.163815 ACTCCAACCGAATCTCGTAGTG 59.836 50.000 0.00 0.00 38.40 2.74
468 472 1.475280 TCCAACCGAATCTCGTAGTGG 59.525 52.381 0.00 0.42 38.40 4.00
470 474 1.203994 CAACCGAATCTCGTAGTGGGT 59.796 52.381 0.00 0.00 38.40 4.51
471 475 1.553706 ACCGAATCTCGTAGTGGGTT 58.446 50.000 0.00 0.00 38.40 4.11
472 476 2.726821 ACCGAATCTCGTAGTGGGTTA 58.273 47.619 0.00 0.00 38.40 2.85
473 477 3.294214 ACCGAATCTCGTAGTGGGTTAT 58.706 45.455 0.00 0.00 38.40 1.89
474 478 3.317430 ACCGAATCTCGTAGTGGGTTATC 59.683 47.826 0.00 0.00 38.40 1.75
475 479 3.317149 CCGAATCTCGTAGTGGGTTATCA 59.683 47.826 0.00 0.00 38.40 2.15
476 480 4.202080 CCGAATCTCGTAGTGGGTTATCAA 60.202 45.833 0.00 0.00 38.40 2.57
477 481 4.976731 CGAATCTCGTAGTGGGTTATCAAG 59.023 45.833 0.00 0.00 34.72 3.02
478 482 5.220989 CGAATCTCGTAGTGGGTTATCAAGA 60.221 44.000 0.00 0.00 34.72 3.02
479 483 5.776173 ATCTCGTAGTGGGTTATCAAGAG 57.224 43.478 0.00 0.00 0.00 2.85
480 484 4.851843 TCTCGTAGTGGGTTATCAAGAGA 58.148 43.478 0.00 0.00 0.00 3.10
484 488 7.228906 TCTCGTAGTGGGTTATCAAGAGATAAG 59.771 40.741 0.00 0.00 44.95 1.73
503 507 4.961511 TGACACGGTGACTGCGGC 62.962 66.667 16.29 0.00 0.00 6.53
537 541 2.411547 GCTGTTGTTTTCGTCGAGGATG 60.412 50.000 8.88 0.00 0.00 3.51
538 542 2.800544 CTGTTGTTTTCGTCGAGGATGT 59.199 45.455 8.88 0.00 0.00 3.06
623 631 4.166011 GCTGGTTGCGATCGGTGC 62.166 66.667 18.30 0.00 0.00 5.01
624 632 2.741985 CTGGTTGCGATCGGTGCA 60.742 61.111 18.30 3.13 41.38 4.57
625 633 2.046411 TGGTTGCGATCGGTGCAT 60.046 55.556 18.30 0.00 42.84 3.96
626 634 2.313717 CTGGTTGCGATCGGTGCATG 62.314 60.000 18.30 0.00 42.84 4.06
655 663 0.107165 GTTGGAGAAATAGGCCGCCT 60.107 55.000 18.05 18.05 37.71 5.52
689 697 1.281656 CCAAGGCCGAACACGTTTC 59.718 57.895 0.00 0.00 0.00 2.78
691 699 1.153127 AAGGCCGAACACGTTTCCA 60.153 52.632 0.00 0.00 0.00 3.53
692 700 1.164041 AAGGCCGAACACGTTTCCAG 61.164 55.000 0.00 0.00 0.00 3.86
693 701 1.595929 GGCCGAACACGTTTCCAGA 60.596 57.895 0.00 0.00 0.00 3.86
696 704 0.595567 CCGAACACGTTTCCAGACGA 60.596 55.000 4.29 0.00 45.47 4.20
699 707 2.400399 GAACACGTTTCCAGACGATCA 58.600 47.619 4.29 0.00 45.47 2.92
700 708 2.519377 ACACGTTTCCAGACGATCAA 57.481 45.000 4.29 0.00 45.47 2.57
701 709 3.040147 ACACGTTTCCAGACGATCAAT 57.960 42.857 4.29 0.00 45.47 2.57
714 722 3.034406 CGATCAATCGGGTCGTTTTTC 57.966 47.619 4.48 0.00 45.93 2.29
754 768 3.004106 AGCAGAGCATTTTCAGTGTGTTC 59.996 43.478 0.00 0.00 0.00 3.18
799 816 2.677836 CCATTATCACACCGTGTTCAGG 59.322 50.000 0.00 0.00 34.79 3.86
821 839 4.462133 GAGGGCAGTAGACACTAGACATA 58.538 47.826 0.00 0.00 32.21 2.29
877 895 0.916086 AAATATCGCCTCCCACCACA 59.084 50.000 0.00 0.00 0.00 4.17
900 919 1.227764 CGCTCTGCACAGCCCATAT 60.228 57.895 8.49 0.00 35.84 1.78
981 1000 1.359848 CCGCCACTACACTAGCTTTG 58.640 55.000 0.00 0.00 0.00 2.77
1035 1063 2.049156 TGCTCGACTGTGCTTCCG 60.049 61.111 0.00 0.00 35.65 4.30
1064 1092 1.680522 CTGCTAGCCATCGTGTCCCT 61.681 60.000 13.29 0.00 0.00 4.20
1065 1093 1.264749 TGCTAGCCATCGTGTCCCTT 61.265 55.000 13.29 0.00 0.00 3.95
1066 1094 0.107654 GCTAGCCATCGTGTCCCTTT 60.108 55.000 2.29 0.00 0.00 3.11
1067 1095 1.941325 CTAGCCATCGTGTCCCTTTC 58.059 55.000 0.00 0.00 0.00 2.62
1068 1096 0.539986 TAGCCATCGTGTCCCTTTCC 59.460 55.000 0.00 0.00 0.00 3.13
1069 1097 1.749258 GCCATCGTGTCCCTTTCCC 60.749 63.158 0.00 0.00 0.00 3.97
1108 1136 2.258726 GGCAACAACTCCACCGACC 61.259 63.158 0.00 0.00 0.00 4.79
1188 1216 4.736896 GCGTGGGACGGTGACTCC 62.737 72.222 0.00 0.00 42.82 3.85
1251 1279 1.138036 TGCGTCGTATCAAGACCCG 59.862 57.895 0.00 0.00 35.33 5.28
1264 1292 2.678934 ACCCGTCGCTGCCTTCTA 60.679 61.111 0.00 0.00 0.00 2.10
1767 1795 3.642778 CTACCGCACCTGGGACACG 62.643 68.421 0.00 0.00 0.00 4.49
1938 1966 2.800544 CAACCTGAACTACAACCTCACG 59.199 50.000 0.00 0.00 0.00 4.35
2002 2030 0.179089 CCACTTCTGCGAGATCCAGG 60.179 60.000 0.00 0.00 0.00 4.45
2295 2323 2.267642 CCGCCGATCCCACAGAAA 59.732 61.111 0.00 0.00 0.00 2.52
2299 2327 0.321653 GCCGATCCCACAGAAACAGT 60.322 55.000 0.00 0.00 0.00 3.55
2325 2353 3.631965 CCAAGGGGAGTCCAAGAGGAAA 61.632 54.545 12.30 0.00 40.83 3.13
2334 2362 1.695242 TCCAAGAGGAAAAGTGCCGTA 59.305 47.619 0.00 0.00 42.23 4.02
2430 2458 4.394712 AGACGGGGCAGAAAGGCG 62.395 66.667 0.00 0.00 45.36 5.52
2433 2461 4.697756 CGGGGCAGAAAGGCGACA 62.698 66.667 0.00 0.00 45.36 4.35
2469 2497 0.924823 AGCCAGAAGCCATTCCTGAT 59.075 50.000 0.00 0.00 45.47 2.90
2544 2575 1.322442 GCCAGACATAAATGGGCCTC 58.678 55.000 4.53 0.00 38.70 4.70
2582 2614 5.289675 CGAACAGACCATAGTGTGAGAAATC 59.710 44.000 0.00 0.00 39.62 2.17
2611 2643 5.699097 AGTTTCTTTATTTAACCTGCGCA 57.301 34.783 10.98 10.98 0.00 6.09
2664 2696 9.745018 AAGGCTCATTGCATATATATAAAGTGT 57.255 29.630 0.00 0.00 45.15 3.55
2665 2697 9.170734 AGGCTCATTGCATATATATAAAGTGTG 57.829 33.333 0.00 0.00 45.15 3.82
2666 2698 7.912250 GGCTCATTGCATATATATAAAGTGTGC 59.088 37.037 7.90 7.90 45.15 4.57
3379 3542 4.729227 GAACTTGAGGGTCCAAAAACAA 57.271 40.909 0.00 0.00 0.00 2.83
3380 3543 5.079689 GAACTTGAGGGTCCAAAAACAAA 57.920 39.130 0.00 0.00 0.00 2.83
3381 3544 5.483811 GAACTTGAGGGTCCAAAAACAAAA 58.516 37.500 0.00 0.00 0.00 2.44
3382 3545 5.491323 ACTTGAGGGTCCAAAAACAAAAA 57.509 34.783 0.00 0.00 0.00 1.94
3414 3577 2.096069 GTGTGTGTGTGTGATGCTCATC 60.096 50.000 3.03 3.03 38.29 2.92
3484 3647 0.175073 GCCGAACCGTGGAATCTACT 59.825 55.000 0.00 0.00 0.00 2.57
3493 3656 2.028930 CGTGGAATCTACTAGGCCCATC 60.029 54.545 0.00 0.00 0.00 3.51
3495 3658 1.066787 GGAATCTACTAGGCCCATCGC 60.067 57.143 0.00 0.00 0.00 4.58
3526 3689 3.669536 TGTGCATTTGGTCGTCTATTCA 58.330 40.909 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.681593 ACCAAGCTGTATTAAAGCGGAA 58.318 40.909 6.75 0.00 45.59 4.30
1 2 3.343941 ACCAAGCTGTATTAAAGCGGA 57.656 42.857 6.75 0.00 45.59 5.54
2 3 3.689649 AGAACCAAGCTGTATTAAAGCGG 59.310 43.478 0.14 0.00 45.59 5.52
3 4 4.946784 AGAACCAAGCTGTATTAAAGCG 57.053 40.909 0.14 0.00 45.59 4.68
30 31 8.561738 ACATGAAAATCCTAACGAACATAGTT 57.438 30.769 0.00 0.00 35.75 2.24
61 63 3.243907 GGTCTTTCGATCACAGGGATAGG 60.244 52.174 0.00 0.00 36.00 2.57
63 65 2.698797 GGGTCTTTCGATCACAGGGATA 59.301 50.000 0.00 0.00 36.00 2.59
123 125 5.957842 ATCAATTAAGAACAAAGGCGTCA 57.042 34.783 0.00 0.00 0.00 4.35
124 126 6.612306 AGAATCAATTAAGAACAAAGGCGTC 58.388 36.000 0.00 0.00 0.00 5.19
125 127 6.575162 AGAATCAATTAAGAACAAAGGCGT 57.425 33.333 0.00 0.00 0.00 5.68
126 128 6.183360 GCAAGAATCAATTAAGAACAAAGGCG 60.183 38.462 0.00 0.00 0.00 5.52
127 129 6.646240 TGCAAGAATCAATTAAGAACAAAGGC 59.354 34.615 0.00 0.00 0.00 4.35
131 133 9.545105 ACAAATGCAAGAATCAATTAAGAACAA 57.455 25.926 0.00 0.00 0.00 2.83
138 140 7.716799 AGGGTACAAATGCAAGAATCAATTA 57.283 32.000 0.00 0.00 0.00 1.40
142 144 5.324409 AGAAGGGTACAAATGCAAGAATCA 58.676 37.500 0.00 0.00 0.00 2.57
152 154 6.311735 TGGAAAAGCTAAGAAGGGTACAAAT 58.688 36.000 0.00 0.00 0.00 2.32
168 170 2.837532 TTCTGGCCATTTGGAAAAGC 57.162 45.000 5.51 0.00 37.39 3.51
182 184 2.449137 AGGGCATCTTTGGATTCTGG 57.551 50.000 0.00 0.00 0.00 3.86
190 192 3.067742 CCAGCTCATTTAGGGCATCTTTG 59.932 47.826 0.00 0.00 0.00 2.77
245 248 6.804783 CGTCTTTTCCGGTAAATAAATGCTTT 59.195 34.615 6.71 0.00 0.00 3.51
248 251 5.871539 TCGTCTTTTCCGGTAAATAAATGC 58.128 37.500 6.71 0.00 0.00 3.56
249 252 6.413818 GCATCGTCTTTTCCGGTAAATAAATG 59.586 38.462 6.71 9.44 0.00 2.32
250 253 6.492254 GCATCGTCTTTTCCGGTAAATAAAT 58.508 36.000 6.71 0.00 0.00 1.40
251 254 5.446206 CGCATCGTCTTTTCCGGTAAATAAA 60.446 40.000 6.71 0.00 0.00 1.40
253 256 3.552699 CGCATCGTCTTTTCCGGTAAATA 59.447 43.478 6.71 0.00 0.00 1.40
254 257 2.350498 CGCATCGTCTTTTCCGGTAAAT 59.650 45.455 6.71 0.00 0.00 1.40
269 272 5.348451 TCACCATCACATAATTATCGCATCG 59.652 40.000 0.00 0.00 0.00 3.84
283 286 1.135112 CCGACTTCGATCACCATCACA 60.135 52.381 0.00 0.00 43.02 3.58
344 348 0.102844 GCTCTGCTCTAGTGCTCCTG 59.897 60.000 17.08 6.77 41.51 3.86
414 418 7.778470 AGTAGCACAGAGAATTATTTACAGC 57.222 36.000 0.00 0.00 0.00 4.40
425 429 6.822676 GGAGTTACTAGTAGTAGCACAGAGAA 59.177 42.308 21.80 0.52 34.81 2.87
427 431 6.114089 TGGAGTTACTAGTAGTAGCACAGAG 58.886 44.000 21.80 0.00 34.81 3.35
428 432 6.058553 TGGAGTTACTAGTAGTAGCACAGA 57.941 41.667 21.80 7.42 34.81 3.41
429 433 6.404513 GGTTGGAGTTACTAGTAGTAGCACAG 60.405 46.154 21.80 0.00 34.81 3.66
431 435 5.448360 CGGTTGGAGTTACTAGTAGTAGCAC 60.448 48.000 21.80 16.65 34.81 4.40
432 436 4.637534 CGGTTGGAGTTACTAGTAGTAGCA 59.362 45.833 21.80 2.78 34.81 3.49
433 437 4.878397 TCGGTTGGAGTTACTAGTAGTAGC 59.122 45.833 14.50 14.50 31.47 3.58
434 438 6.992063 TTCGGTTGGAGTTACTAGTAGTAG 57.008 41.667 9.90 2.87 31.47 2.57
435 439 7.341805 AGATTCGGTTGGAGTTACTAGTAGTA 58.658 38.462 5.90 5.90 0.00 1.82
436 440 6.186234 AGATTCGGTTGGAGTTACTAGTAGT 58.814 40.000 8.14 8.14 0.00 2.73
437 441 6.511444 CGAGATTCGGTTGGAGTTACTAGTAG 60.511 46.154 2.23 0.00 36.00 2.57
438 442 5.295292 CGAGATTCGGTTGGAGTTACTAGTA 59.705 44.000 0.00 0.00 36.00 1.82
439 443 4.096081 CGAGATTCGGTTGGAGTTACTAGT 59.904 45.833 0.00 0.00 36.00 2.57
440 444 4.096081 ACGAGATTCGGTTGGAGTTACTAG 59.904 45.833 3.37 0.00 45.59 2.57
441 445 4.012374 ACGAGATTCGGTTGGAGTTACTA 58.988 43.478 3.37 0.00 45.59 1.82
442 446 2.824341 ACGAGATTCGGTTGGAGTTACT 59.176 45.455 3.37 0.00 45.59 2.24
443 447 3.227810 ACGAGATTCGGTTGGAGTTAC 57.772 47.619 3.37 0.00 45.59 2.50
444 448 4.012374 ACTACGAGATTCGGTTGGAGTTA 58.988 43.478 3.37 0.00 45.59 2.24
445 449 2.824341 ACTACGAGATTCGGTTGGAGTT 59.176 45.455 3.37 0.00 45.59 3.01
446 450 2.163815 CACTACGAGATTCGGTTGGAGT 59.836 50.000 3.37 0.00 45.59 3.85
447 451 2.479730 CCACTACGAGATTCGGTTGGAG 60.480 54.545 3.37 0.00 45.59 3.86
448 452 1.475280 CCACTACGAGATTCGGTTGGA 59.525 52.381 3.37 0.00 45.59 3.53
449 453 1.470979 CCCACTACGAGATTCGGTTGG 60.471 57.143 3.37 5.99 45.59 3.77
450 454 1.203994 ACCCACTACGAGATTCGGTTG 59.796 52.381 3.37 0.00 45.59 3.77
461 465 7.040473 ACTTATCTCTTGATAACCCACTACG 57.960 40.000 0.00 0.00 39.46 3.51
466 470 7.103641 GTGTCAACTTATCTCTTGATAACCCA 58.896 38.462 0.00 0.00 39.46 4.51
467 471 6.255887 CGTGTCAACTTATCTCTTGATAACCC 59.744 42.308 0.00 0.00 39.46 4.11
468 472 6.255887 CCGTGTCAACTTATCTCTTGATAACC 59.744 42.308 0.00 0.00 39.46 2.85
470 474 6.811665 CACCGTGTCAACTTATCTCTTGATAA 59.188 38.462 0.00 0.00 41.36 1.75
471 475 6.152154 TCACCGTGTCAACTTATCTCTTGATA 59.848 38.462 0.00 0.00 34.32 2.15
472 476 5.047306 TCACCGTGTCAACTTATCTCTTGAT 60.047 40.000 0.00 0.00 36.74 2.57
473 477 4.279922 TCACCGTGTCAACTTATCTCTTGA 59.720 41.667 0.00 0.00 0.00 3.02
474 478 4.386049 GTCACCGTGTCAACTTATCTCTTG 59.614 45.833 0.00 0.00 0.00 3.02
475 479 4.281182 AGTCACCGTGTCAACTTATCTCTT 59.719 41.667 0.00 0.00 0.00 2.85
476 480 3.827302 AGTCACCGTGTCAACTTATCTCT 59.173 43.478 0.00 0.00 0.00 3.10
477 481 3.921021 CAGTCACCGTGTCAACTTATCTC 59.079 47.826 0.00 0.00 0.00 2.75
478 482 3.861131 GCAGTCACCGTGTCAACTTATCT 60.861 47.826 0.00 0.00 0.00 1.98
479 483 2.412089 GCAGTCACCGTGTCAACTTATC 59.588 50.000 0.00 0.00 0.00 1.75
480 484 2.413837 GCAGTCACCGTGTCAACTTAT 58.586 47.619 0.00 0.00 0.00 1.73
484 488 2.594962 CCGCAGTCACCGTGTCAAC 61.595 63.158 0.00 0.00 0.00 3.18
509 513 0.165944 CGAAAACAACAGCTAGCCCG 59.834 55.000 12.13 5.56 0.00 6.13
512 516 1.790623 TCGACGAAAACAACAGCTAGC 59.209 47.619 6.62 6.62 0.00 3.42
515 519 1.202486 TCCTCGACGAAAACAACAGCT 60.202 47.619 0.00 0.00 0.00 4.24
537 541 2.405172 GAAGGGTCAAAGTCGTCTCAC 58.595 52.381 0.00 0.00 0.00 3.51
538 542 1.000607 CGAAGGGTCAAAGTCGTCTCA 60.001 52.381 0.00 0.00 0.00 3.27
602 606 3.257561 CGATCGCAACCAGCTCCG 61.258 66.667 0.26 0.00 42.61 4.63
615 623 1.871772 GCTATGGCATGCACCGATC 59.128 57.895 21.36 0.64 38.54 3.69
618 626 4.318021 GCGCTATGGCATGCACCG 62.318 66.667 21.36 14.16 38.60 4.94
620 628 3.112126 AACGCGCTATGGCATGCAC 62.112 57.895 21.36 9.64 38.60 4.57
621 629 2.823593 AACGCGCTATGGCATGCA 60.824 55.556 21.36 6.13 38.60 3.96
622 630 2.352686 CAACGCGCTATGGCATGC 60.353 61.111 9.90 9.90 38.60 4.06
623 631 2.109538 CTCCAACGCGCTATGGCATG 62.110 60.000 20.04 10.81 38.60 4.06
624 632 1.889105 CTCCAACGCGCTATGGCAT 60.889 57.895 20.04 4.88 38.60 4.40
625 633 2.511373 CTCCAACGCGCTATGGCA 60.511 61.111 20.04 10.44 38.60 4.92
626 634 1.366111 TTTCTCCAACGCGCTATGGC 61.366 55.000 20.04 0.00 36.62 4.40
655 663 2.356278 GGTGGATCCAAGCTGGCA 59.644 61.111 18.20 0.00 37.47 4.92
689 697 3.214119 ACGACCCGATTGATCGTCTGG 62.214 57.143 11.90 8.65 45.50 3.86
691 699 2.490165 ACGACCCGATTGATCGTCT 58.510 52.632 11.90 0.00 45.50 4.18
695 703 3.007635 AGGAAAAACGACCCGATTGATC 58.992 45.455 0.00 0.00 0.00 2.92
696 704 3.007635 GAGGAAAAACGACCCGATTGAT 58.992 45.455 0.00 0.00 0.00 2.57
699 707 1.072648 TGGAGGAAAAACGACCCGATT 59.927 47.619 0.00 0.00 0.00 3.34
700 708 0.688487 TGGAGGAAAAACGACCCGAT 59.312 50.000 0.00 0.00 0.00 4.18
701 709 0.249996 GTGGAGGAAAAACGACCCGA 60.250 55.000 0.00 0.00 0.00 5.14
703 711 1.607148 CAAGTGGAGGAAAAACGACCC 59.393 52.381 0.00 0.00 0.00 4.46
705 713 2.940410 TCACAAGTGGAGGAAAAACGAC 59.060 45.455 0.00 0.00 0.00 4.34
706 714 3.118555 TCTCACAAGTGGAGGAAAAACGA 60.119 43.478 0.00 0.00 33.18 3.85
707 715 3.202906 TCTCACAAGTGGAGGAAAAACG 58.797 45.455 0.00 0.00 33.18 3.60
708 716 3.565902 CCTCTCACAAGTGGAGGAAAAAC 59.434 47.826 22.59 0.00 44.09 2.43
709 717 3.458118 TCCTCTCACAAGTGGAGGAAAAA 59.542 43.478 25.13 12.05 45.43 1.94
710 718 3.045634 TCCTCTCACAAGTGGAGGAAAA 58.954 45.455 25.13 12.29 45.43 2.29
711 719 2.689658 TCCTCTCACAAGTGGAGGAAA 58.310 47.619 25.13 12.77 45.43 3.13
712 720 2.398754 TCCTCTCACAAGTGGAGGAA 57.601 50.000 25.13 15.37 45.43 3.36
713 721 2.251818 CTTCCTCTCACAAGTGGAGGA 58.748 52.381 24.26 24.26 46.05 3.71
714 722 1.338579 GCTTCCTCTCACAAGTGGAGG 60.339 57.143 21.72 21.72 44.00 4.30
733 747 3.004106 AGAACACACTGAAAATGCTCTGC 59.996 43.478 0.00 0.00 0.00 4.26
754 768 2.159448 TCATGCATTTTTACCCGCGAAG 60.159 45.455 8.23 0.00 0.00 3.79
799 816 2.724454 TGTCTAGTGTCTACTGCCCTC 58.276 52.381 0.00 0.00 37.78 4.30
821 839 5.278169 GCACAAATGATTTCTGTCACTGTCT 60.278 40.000 0.00 0.00 29.67 3.41
877 895 2.974698 GCTGTGCAGAGCGTGGTT 60.975 61.111 21.06 0.00 0.00 3.67
900 919 3.935828 TCGAATCACGATTGTTTGGCATA 59.064 39.130 0.00 0.00 46.45 3.14
981 1000 1.693627 TGGGACTACTAGCTGCTAGC 58.306 55.000 31.08 17.40 42.84 3.42
986 1005 0.394565 GGCCATGGGACTACTAGCTG 59.605 60.000 15.13 0.00 0.00 4.24
1014 1033 3.890936 AAGCACAGTCGAGCAGGCC 62.891 63.158 0.00 0.00 0.00 5.19
1015 1034 2.358003 AAGCACAGTCGAGCAGGC 60.358 61.111 0.00 0.00 0.00 4.85
1017 1036 2.091112 CGGAAGCACAGTCGAGCAG 61.091 63.158 0.00 0.00 0.00 4.24
1018 1037 2.049156 CGGAAGCACAGTCGAGCA 60.049 61.111 0.00 0.00 0.00 4.26
1019 1038 2.049063 ACGGAAGCACAGTCGAGC 60.049 61.111 0.00 0.00 0.00 5.03
1020 1039 2.375766 GCACGGAAGCACAGTCGAG 61.376 63.158 0.00 0.00 0.00 4.04
1021 1040 2.355837 GCACGGAAGCACAGTCGA 60.356 61.111 0.00 0.00 0.00 4.20
1022 1041 3.414700 GGCACGGAAGCACAGTCG 61.415 66.667 0.00 0.00 35.83 4.18
1188 1216 2.480555 GGCAAGAACATGGACGCG 59.519 61.111 3.53 3.53 0.00 6.01
1196 1224 1.066093 TTCGTCGACGGCAAGAACA 59.934 52.632 35.05 12.79 40.29 3.18
1251 1279 1.805945 CACGGTAGAAGGCAGCGAC 60.806 63.158 1.06 0.00 40.00 5.19
1264 1292 1.079405 CCGTCATGTAAGGCACGGT 60.079 57.895 12.03 0.00 45.53 4.83
1308 1336 1.139095 GCGGACGAGGAAGGTGTAG 59.861 63.158 0.00 0.00 0.00 2.74
1527 1555 2.125391 GACGGGGCGAAGGTAACC 60.125 66.667 0.00 0.00 37.17 2.85
1767 1795 3.335579 GCCGAATATGTAAGGGATGTCC 58.664 50.000 0.00 0.00 0.00 4.02
1796 1824 2.754658 TCTCGAAGGAGACCCCGC 60.755 66.667 0.00 0.00 44.28 6.13
1806 1834 0.794981 CGTCGCTGTCCTTCTCGAAG 60.795 60.000 0.00 0.00 38.14 3.79
1938 1966 3.399181 TCCACGGGCAGGATCCAC 61.399 66.667 15.82 5.28 0.00 4.02
2153 2181 2.108157 GCGCGACCCACATATCCA 59.892 61.111 12.10 0.00 0.00 3.41
2157 2185 4.075854 TGCAGCGCGACCCACATA 62.076 61.111 12.10 0.00 0.00 2.29
2295 2323 2.258109 GACTCCCCTTGGTAGAACTGT 58.742 52.381 0.00 0.00 0.00 3.55
2299 2327 2.158066 TCTTGGACTCCCCTTGGTAGAA 60.158 50.000 0.00 0.00 35.38 2.10
2430 2458 2.380410 GCACACGACCACCGATGTC 61.380 63.158 0.00 0.00 41.76 3.06
2433 2461 3.626680 CTCGCACACGACCACCGAT 62.627 63.158 0.00 0.00 45.12 4.18
2469 2497 3.681909 GGGACCATGGGCTTGTTTA 57.318 52.632 19.55 0.00 0.00 2.01
2544 2575 3.497262 GTCTGTTCGTAACTTCTTTGGGG 59.503 47.826 0.00 0.00 0.00 4.96
2611 2643 6.204688 TCTGAGATGCACGAACTTTTGTATTT 59.795 34.615 0.00 0.00 0.00 1.40
2993 3049 3.009723 CGAAGCATCTTGGTAACCACAT 58.990 45.455 0.00 0.00 30.78 3.21
3381 3544 9.979578 ATCACACACACACACATATAAATTTTT 57.020 25.926 0.00 0.00 0.00 1.94
3382 3545 9.409312 CATCACACACACACACATATAAATTTT 57.591 29.630 0.00 0.00 0.00 1.82
3383 3546 7.541783 GCATCACACACACACACATATAAATTT 59.458 33.333 0.00 0.00 0.00 1.82
3384 3547 7.028962 GCATCACACACACACACATATAAATT 58.971 34.615 0.00 0.00 0.00 1.82
3385 3548 6.375174 AGCATCACACACACACACATATAAAT 59.625 34.615 0.00 0.00 0.00 1.40
3386 3549 5.704978 AGCATCACACACACACACATATAAA 59.295 36.000 0.00 0.00 0.00 1.40
3387 3550 5.244755 AGCATCACACACACACACATATAA 58.755 37.500 0.00 0.00 0.00 0.98
3388 3551 4.831107 AGCATCACACACACACACATATA 58.169 39.130 0.00 0.00 0.00 0.86
3389 3552 3.678289 AGCATCACACACACACACATAT 58.322 40.909 0.00 0.00 0.00 1.78
3390 3553 3.066380 GAGCATCACACACACACACATA 58.934 45.455 0.00 0.00 33.17 2.29
3391 3554 1.875514 GAGCATCACACACACACACAT 59.124 47.619 0.00 0.00 33.17 3.21
3392 3555 1.298602 GAGCATCACACACACACACA 58.701 50.000 0.00 0.00 33.17 3.72
3393 3556 1.298602 TGAGCATCACACACACACAC 58.701 50.000 0.00 0.00 42.56 3.82
3394 3557 3.776616 TGAGCATCACACACACACA 57.223 47.368 0.00 0.00 42.56 3.72
3446 3609 7.979537 GGTTCGGCCAAATTTCTATATCTTTTT 59.020 33.333 2.24 0.00 37.17 1.94
3447 3610 7.489160 GGTTCGGCCAAATTTCTATATCTTTT 58.511 34.615 2.24 0.00 37.17 2.27
3448 3611 6.238648 CGGTTCGGCCAAATTTCTATATCTTT 60.239 38.462 2.24 0.00 36.97 2.52
3449 3612 5.238650 CGGTTCGGCCAAATTTCTATATCTT 59.761 40.000 2.24 0.00 36.97 2.40
3455 3618 1.807742 CACGGTTCGGCCAAATTTCTA 59.192 47.619 2.24 0.00 36.97 2.10
3499 3662 1.865788 CGACCAAATGCACAGTGGGG 61.866 60.000 14.76 2.80 36.69 4.96


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

AutoCloner maintained by Alex Coulton.