Multiple sequence alignment - TraesCS2B01G406400

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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 TraesCS2B01G406400 chr2B 100.000 3589 0 0 1 3589 575834176 575837764 0.000000e+00 6628
1 TraesCS2B01G406400 chr2B 94.398 482 24 3 352 832 513061297 513061776 0.000000e+00 737
2 TraesCS2B01G406400 chr2B 94.191 482 27 1 353 833 692909861 692909380 0.000000e+00 734
3 TraesCS2B01G406400 chr2B 92.323 508 36 3 345 850 726709102 726709608 0.000000e+00 719
4 TraesCS2B01G406400 chr2B 92.126 508 37 3 345 850 726750502 726751008 0.000000e+00 713
5 TraesCS2B01G406400 chr2D 92.432 2841 110 40 814 3589 491192717 491195517 0.000000e+00 3958
6 TraesCS2B01G406400 chr2D 93.023 258 8 4 1 248 491192429 491192686 5.660000e-98 368
7 TraesCS2B01G406400 chr2A 91.279 2557 100 41 831 3323 635510576 635513073 0.000000e+00 3373
8 TraesCS2B01G406400 chr2A 86.631 374 15 16 1 352 635510224 635510584 7.270000e-102 381
9 TraesCS2B01G406400 chr2A 87.189 281 10 10 3335 3589 635517022 635517302 2.710000e-76 296
10 TraesCS2B01G406400 chr5B 94.617 483 25 1 353 834 277805932 277805450 0.000000e+00 747
11 TraesCS2B01G406400 chr7A 94.410 483 26 1 352 833 696779744 696779262 0.000000e+00 741
12 TraesCS2B01G406400 chr5A 93.699 492 30 1 343 833 481919878 481920369 0.000000e+00 736
13 TraesCS2B01G406400 chr1A 94.179 481 27 1 353 832 32475387 32475867 0.000000e+00 732
14 TraesCS2B01G406400 chr1A 80.282 213 30 8 2332 2538 390709561 390709767 2.230000e-32 150
15 TraesCS2B01G406400 chrUn 93.996 483 28 1 353 834 16987890 16988372 0.000000e+00 730
16 TraesCS2B01G406400 chr6D 77.591 656 89 36 1960 2594 312558754 312559372 9.540000e-91 344
17 TraesCS2B01G406400 chr6B 77.356 658 87 42 1960 2594 514478652 514478034 2.070000e-87 333
18 TraesCS2B01G406400 chr6A 81.994 361 53 9 2244 2594 449181943 449182301 2.710000e-76 296
19 TraesCS2B01G406400 chr3A 82.051 195 23 11 2332 2520 504024846 504025034 4.800000e-34 156
20 TraesCS2B01G406400 chr1B 79.621 211 35 8 2332 2538 420685667 420685873 1.040000e-30 145


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 TraesCS2B01G406400 chr2B 575834176 575837764 3588 False 6628 6628 100.000000 1 3589 1 chr2B.!!$F2 3588
1 TraesCS2B01G406400 chr2B 726709102 726709608 506 False 719 719 92.323000 345 850 1 chr2B.!!$F3 505
2 TraesCS2B01G406400 chr2B 726750502 726751008 506 False 713 713 92.126000 345 850 1 chr2B.!!$F4 505
3 TraesCS2B01G406400 chr2D 491192429 491195517 3088 False 2163 3958 92.727500 1 3589 2 chr2D.!!$F1 3588
4 TraesCS2B01G406400 chr2A 635510224 635517302 7078 False 1350 3373 88.366333 1 3589 3 chr2A.!!$F1 3588
5 TraesCS2B01G406400 chr6D 312558754 312559372 618 False 344 344 77.591000 1960 2594 1 chr6D.!!$F1 634
6 TraesCS2B01G406400 chr6B 514478034 514478652 618 True 333 333 77.356000 1960 2594 1 chr6B.!!$R1 634

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
438 462 0.036765 CGGGAACAAGGTCGGATTCA 60.037 55.0 0.00 0.0 0.00 2.57 F
493 517 0.173481 TGCTCCTCGATTCAGGTTCG 59.827 55.0 0.00 0.0 37.94 3.95 F
630 654 0.323816 TGCTGATCGTCAGGGAGTCT 60.324 55.0 14.19 0.0 44.43 3.24 F
1757 1822 0.108396 TCTTGCTGCCTTGCTGTGTA 59.892 50.0 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 1312 1.009389 AGAGCGCTCGTTTTCTTCCG 61.009 55.000 30.39 0.0 34.09 4.30 R
1742 1807 1.135286 GGAAATACACAGCAAGGCAGC 60.135 52.381 0.00 0.0 0.00 5.25 R
2234 2323 1.270550 GCCTTTTGCTTGCTGCTCTTA 59.729 47.619 0.00 0.0 43.37 2.10 R
3121 3262 0.179124 CCGTCTGCTCTGCTCCTAAC 60.179 60.000 0.00 0.0 0.00 2.34 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
188 198 1.574702 GCGTCACCCTTCTTTTCCGG 61.575 60.000 0.00 0.00 0.00 5.14
248 267 1.179152 TCGAAGGCCAGTGTCGATAA 58.821 50.000 5.01 0.00 38.78 1.75
249 268 1.754803 TCGAAGGCCAGTGTCGATAAT 59.245 47.619 5.01 0.00 38.78 1.28
250 269 2.953648 TCGAAGGCCAGTGTCGATAATA 59.046 45.455 5.01 0.00 38.78 0.98
251 270 3.050619 CGAAGGCCAGTGTCGATAATAC 58.949 50.000 5.01 0.00 36.92 1.89
252 271 3.490249 CGAAGGCCAGTGTCGATAATACA 60.490 47.826 5.01 0.00 36.92 2.29
253 272 4.632153 GAAGGCCAGTGTCGATAATACAT 58.368 43.478 5.01 0.00 0.00 2.29
254 273 5.564063 CGAAGGCCAGTGTCGATAATACATA 60.564 44.000 5.01 0.00 36.92 2.29
255 274 5.135508 AGGCCAGTGTCGATAATACATAC 57.864 43.478 5.01 0.00 0.00 2.39
257 276 5.069914 AGGCCAGTGTCGATAATACATACAA 59.930 40.000 5.01 0.00 0.00 2.41
258 277 5.756347 GGCCAGTGTCGATAATACATACAAA 59.244 40.000 0.00 0.00 0.00 2.83
259 278 6.426937 GGCCAGTGTCGATAATACATACAAAT 59.573 38.462 0.00 0.00 0.00 2.32
260 279 7.601130 GGCCAGTGTCGATAATACATACAAATA 59.399 37.037 0.00 0.00 0.00 1.40
261 280 8.433126 GCCAGTGTCGATAATACATACAAATAC 58.567 37.037 0.00 0.00 0.00 1.89
262 281 9.471084 CCAGTGTCGATAATACATACAAATACA 57.529 33.333 0.00 0.00 0.00 2.29
302 321 2.475466 GGCGAGTCGACCGATACCA 61.475 63.158 24.32 0.00 0.00 3.25
315 337 3.004524 ACCGATACCAAGAAGATAGCGAC 59.995 47.826 0.00 0.00 29.49 5.19
343 366 8.332464 TGGCGACATAAAATAAAGATAGAAACG 58.668 33.333 0.00 0.00 33.40 3.60
344 367 7.797123 GGCGACATAAAATAAAGATAGAAACGG 59.203 37.037 0.00 0.00 0.00 4.44
345 368 8.333186 GCGACATAAAATAAAGATAGAAACGGT 58.667 33.333 0.00 0.00 0.00 4.83
349 372 9.646336 CATAAAATAAAGATAGAAACGGTTCGG 57.354 33.333 7.71 0.00 38.90 4.30
350 373 6.673154 AAATAAAGATAGAAACGGTTCGGG 57.327 37.500 7.71 0.00 38.90 5.14
392 416 2.132352 GGTAGGCCGTCCCTCGATT 61.132 63.158 0.00 0.00 44.96 3.34
426 450 2.309528 CAGAATCGGATTCGGGAACA 57.690 50.000 21.48 0.00 43.92 3.18
438 462 0.036765 CGGGAACAAGGTCGGATTCA 60.037 55.000 0.00 0.00 0.00 2.57
458 482 6.812481 TTCAGTACGATTCGATGAAGATTG 57.188 37.500 13.95 0.39 0.00 2.67
459 483 5.281727 TCAGTACGATTCGATGAAGATTGG 58.718 41.667 13.95 0.00 0.00 3.16
485 509 2.188994 GCAGCCTGCTCCTCGATT 59.811 61.111 10.04 0.00 40.96 3.34
493 517 0.173481 TGCTCCTCGATTCAGGTTCG 59.827 55.000 0.00 0.00 37.94 3.95
513 537 1.200020 GAGGATCCAACAGCCAAAACG 59.800 52.381 15.82 0.00 30.00 3.60
572 596 0.818938 GGACTCCTCGTTCTTCCTCC 59.181 60.000 0.00 0.00 0.00 4.30
579 603 1.827969 CTCGTTCTTCCTCCAGTCCAT 59.172 52.381 0.00 0.00 0.00 3.41
590 614 4.018506 TCCTCCAGTCCATTAATTGCAAGA 60.019 41.667 4.94 0.00 0.00 3.02
607 631 4.397103 TGCAAGAGATCCATTAACAGCAAG 59.603 41.667 0.00 0.00 0.00 4.01
630 654 0.323816 TGCTGATCGTCAGGGAGTCT 60.324 55.000 14.19 0.00 44.43 3.24
633 657 2.095461 CTGATCGTCAGGGAGTCTTCA 58.905 52.381 7.01 0.00 40.71 3.02
636 660 3.515502 TGATCGTCAGGGAGTCTTCATTT 59.484 43.478 0.00 0.00 0.00 2.32
688 712 0.817013 GTACCGGGTTCATCGTACCA 59.183 55.000 4.31 0.00 37.40 3.25
743 767 6.636562 AAATCGTTCGAGAGATGTATACCT 57.363 37.500 0.00 0.00 41.60 3.08
797 821 2.999063 TCCCTCGTTCCCGTTCCC 60.999 66.667 0.00 0.00 35.01 3.97
798 822 3.001406 CCCTCGTTCCCGTTCCCT 61.001 66.667 0.00 0.00 35.01 4.20
813 837 2.218454 CCCTGTTCCCACCGTACCA 61.218 63.158 0.00 0.00 0.00 3.25
814 838 1.559065 CCCTGTTCCCACCGTACCAT 61.559 60.000 0.00 0.00 0.00 3.55
858 882 1.667722 GAGCACCAAAGGCCAAAGG 59.332 57.895 5.01 5.55 0.00 3.11
963 992 2.356313 CGTGAGGCGACACTGCTT 60.356 61.111 13.74 0.00 44.77 3.91
1028 1057 1.470098 CCAAACGCTCATCCCTTCTTG 59.530 52.381 0.00 0.00 0.00 3.02
1191 1232 2.437396 GGGAGATTACCGGGGCGAA 61.437 63.158 6.32 0.00 0.00 4.70
1205 1254 2.959707 GGGGCGAAAGAGATAGAGAGAA 59.040 50.000 0.00 0.00 0.00 2.87
1270 1328 1.130009 GACGGAAGAAAACGAGCGC 59.870 57.895 0.00 0.00 0.00 5.92
1287 1345 1.917303 GCGCTCTTTCTCTTTCTCTCG 59.083 52.381 0.00 0.00 0.00 4.04
1351 1409 0.533978 TGTGTGTATGTGTGCGCCTT 60.534 50.000 4.18 0.00 0.00 4.35
1368 1426 1.604604 CTTCTTTTGGGCCGTGAAGA 58.395 50.000 17.05 14.11 37.03 2.87
1388 1446 1.528542 CGAGAGGATGGACGCCCTA 60.529 63.158 0.00 0.00 31.84 3.53
1593 1657 3.837570 AAGTTGAACGACGGGCCCC 62.838 63.158 18.66 1.00 0.00 5.80
1595 1659 4.323477 TTGAACGACGGGCCCCAG 62.323 66.667 18.66 10.48 0.00 4.45
1674 1738 0.821711 CCTGCCGGTGAGGTTTCAAA 60.822 55.000 12.35 0.00 43.70 2.69
1742 1807 9.205916 CGTACGTGGTGAATTAATTATTTCTTG 57.794 33.333 7.22 8.01 0.00 3.02
1757 1822 0.108396 TCTTGCTGCCTTGCTGTGTA 59.892 50.000 0.00 0.00 0.00 2.90
1994 2077 2.932083 GACCATATGCGCGCTGTCG 61.932 63.158 33.29 17.61 39.07 4.35
2006 2089 4.421479 CTGTCGACGGAGGCGCTT 62.421 66.667 20.01 0.00 0.00 4.68
2012 2095 4.699522 ACGGAGGCGCTTGTTCCC 62.700 66.667 7.64 0.00 0.00 3.97
2013 2096 4.697756 CGGAGGCGCTTGTTCCCA 62.698 66.667 7.64 0.00 0.00 4.37
2063 2152 4.361971 TCGGGGTGGTCGCTCTCT 62.362 66.667 0.00 0.00 0.00 3.10
2066 2155 3.775654 GGGTGGTCGCTCTCTGGG 61.776 72.222 0.00 0.00 0.00 4.45
2160 2249 2.656002 CCTACTTCCTGATGGACTCGA 58.344 52.381 0.00 0.00 43.06 4.04
2234 2323 0.535102 CCAAGAAGTCCAAGCACGGT 60.535 55.000 0.00 0.00 0.00 4.83
2264 2353 1.109323 AGCAAAAGGCCAAGAAGCGT 61.109 50.000 5.01 0.00 46.50 5.07
2288 2377 1.770324 CAAGCCCAAGAACCTCCCT 59.230 57.895 0.00 0.00 0.00 4.20
2456 2551 3.217743 CTCCTCCCCGAGTACCGC 61.218 72.222 0.00 0.00 36.84 5.68
2603 2705 2.516225 TAGCTCGCTCGCTGGCTA 60.516 61.111 6.84 8.02 41.12 3.93
2663 2765 4.608951 GCCCGTATCAGTCTTTGTACTAG 58.391 47.826 0.00 0.00 0.00 2.57
2676 2778 2.977914 TGTACTAGCGTACTCGAACCT 58.022 47.619 0.00 0.00 44.97 3.50
2807 2918 3.264450 CCTCCAACTCCACCTTCATTAGT 59.736 47.826 0.00 0.00 0.00 2.24
2808 2919 4.508662 CTCCAACTCCACCTTCATTAGTC 58.491 47.826 0.00 0.00 0.00 2.59
2817 2928 4.192317 CACCTTCATTAGTCTGTTAGGGC 58.808 47.826 0.00 0.00 0.00 5.19
2882 2993 4.766404 ACTTTATTTCCAGCTTTGTCCG 57.234 40.909 0.00 0.00 0.00 4.79
2954 3065 2.853705 TGGCGGTGCTTAGTTTTTACT 58.146 42.857 0.00 0.00 0.00 2.24
2962 3073 7.254795 GCGGTGCTTAGTTTTTACTATCATCAT 60.255 37.037 0.00 0.00 0.00 2.45
3020 3136 2.563179 TGAAGGAAAAGAGGAGAGACGG 59.437 50.000 0.00 0.00 0.00 4.79
3022 3138 1.203199 AGGAAAAGAGGAGAGACGGGT 60.203 52.381 0.00 0.00 0.00 5.28
3034 3150 0.608582 AGACGGGTAGAGAGCAACGT 60.609 55.000 0.00 0.00 37.26 3.99
3035 3151 0.456312 GACGGGTAGAGAGCAACGTG 60.456 60.000 0.00 0.00 34.43 4.49
3108 3249 3.253188 GGTGTTGTCACATGTAACAGCAT 59.747 43.478 26.02 0.00 46.38 3.79
3109 3250 4.848370 GGTGTTGTCACATGTAACAGCATG 60.848 45.833 26.02 4.71 46.38 4.06
3110 3251 4.024133 GTGTTGTCACATGTAACAGCATGA 60.024 41.667 20.04 0.00 46.65 3.07
3111 3252 4.761227 TGTTGTCACATGTAACAGCATGAT 59.239 37.500 14.11 0.00 46.65 2.45
3112 3253 4.950434 TGTCACATGTAACAGCATGATG 57.050 40.909 9.94 9.94 46.65 3.07
3113 3254 3.127376 TGTCACATGTAACAGCATGATGC 59.873 43.478 11.67 9.89 46.65 3.91
3128 3269 5.608676 CATGATGCATGCTTAGTTAGGAG 57.391 43.478 20.33 0.00 35.02 3.69
3129 3270 3.470709 TGATGCATGCTTAGTTAGGAGC 58.529 45.455 20.33 0.00 39.33 4.70
3139 3280 0.814457 AGTTAGGAGCAGAGCAGACG 59.186 55.000 0.00 0.00 0.00 4.18
3151 3292 3.059982 CAGACGGTTGAGGGCTCA 58.940 61.111 0.00 0.00 37.91 4.26
3178 3319 2.554893 GCGAGAGGTAGAAGTAGATGGG 59.445 54.545 0.00 0.00 0.00 4.00
3232 3373 2.284190 GTGTAAGAGCAGGAATGGAGC 58.716 52.381 0.00 0.00 0.00 4.70
3233 3374 2.093235 GTGTAAGAGCAGGAATGGAGCT 60.093 50.000 0.00 0.00 42.17 4.09
3262 3408 0.409092 TTGTTCATGGATGGCCCTGT 59.591 50.000 0.00 0.00 35.38 4.00
3325 3475 2.819422 TCGCAGTGTGTAGTCGTATC 57.181 50.000 3.13 0.00 0.00 2.24
3327 3477 2.095372 TCGCAGTGTGTAGTCGTATCTG 59.905 50.000 3.13 0.00 0.00 2.90
3439 7524 3.114616 CCGTGCCTGCTCTGTTCG 61.115 66.667 0.00 0.00 0.00 3.95
3479 7589 1.681166 GGACCTTGCATGCACTGAGAT 60.681 52.381 22.58 0.98 0.00 2.75
3480 7590 1.400846 GACCTTGCATGCACTGAGATG 59.599 52.381 22.58 4.91 0.00 2.90
3481 7591 0.100682 CCTTGCATGCACTGAGATGC 59.899 55.000 22.58 0.73 46.32 3.91
3482 7592 1.095600 CTTGCATGCACTGAGATGCT 58.904 50.000 22.58 0.00 46.28 3.79
3483 7593 1.472878 CTTGCATGCACTGAGATGCTT 59.527 47.619 22.58 0.00 46.28 3.91
3484 7594 1.092348 TGCATGCACTGAGATGCTTC 58.908 50.000 18.46 0.00 46.28 3.86
3515 7628 1.692749 AGTACCGCCATGTCCCCAT 60.693 57.895 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
214 230 4.276183 GGCCTTCGAACTCTTCTTCTTTTT 59.724 41.667 0.00 0.00 0.00 1.94
224 243 0.318762 GACACTGGCCTTCGAACTCT 59.681 55.000 3.32 0.00 0.00 3.24
269 288 4.389077 CGACTCGCCTACTCATTTCTTTTT 59.611 41.667 0.00 0.00 0.00 1.94
270 289 3.927142 CGACTCGCCTACTCATTTCTTTT 59.073 43.478 0.00 0.00 0.00 2.27
274 293 2.452105 GTCGACTCGCCTACTCATTTC 58.548 52.381 8.70 0.00 0.00 2.17
302 321 0.525668 CGCCACGTCGCTATCTTCTT 60.526 55.000 3.09 0.00 0.00 2.52
315 337 7.402811 TCTATCTTTATTTTATGTCGCCACG 57.597 36.000 0.00 0.00 0.00 4.94
343 366 1.070957 GGCTACTATGCCCCGAACC 59.929 63.158 0.00 0.00 46.82 3.62
344 367 4.773209 GGCTACTATGCCCCGAAC 57.227 61.111 0.00 0.00 46.82 3.95
408 432 2.420129 CCTTGTTCCCGAATCCGATTCT 60.420 50.000 17.14 0.00 37.13 2.40
411 435 0.909623 ACCTTGTTCCCGAATCCGAT 59.090 50.000 0.00 0.00 38.22 4.18
426 450 3.488721 CGAATCGTACTGAATCCGACCTT 60.489 47.826 0.00 0.00 32.86 3.50
438 462 4.621991 CCCAATCTTCATCGAATCGTACT 58.378 43.478 1.52 0.00 0.00 2.73
485 509 1.550524 CTGTTGGATCCTCGAACCTGA 59.449 52.381 14.23 0.00 34.73 3.86
493 517 1.200020 CGTTTTGGCTGTTGGATCCTC 59.800 52.381 14.23 6.93 0.00 3.71
496 520 0.729140 CGCGTTTTGGCTGTTGGATC 60.729 55.000 0.00 0.00 0.00 3.36
513 537 2.348591 GCGTGAGTAAATTATGCCTCGC 60.349 50.000 0.00 0.00 0.00 5.03
572 596 5.591472 TGGATCTCTTGCAATTAATGGACTG 59.409 40.000 0.00 0.00 0.00 3.51
579 603 7.122501 TGCTGTTAATGGATCTCTTGCAATTAA 59.877 33.333 0.00 0.00 0.00 1.40
607 631 0.465705 TCCCTGACGATCAGCATTCC 59.534 55.000 8.85 0.00 42.98 3.01
617 641 4.202315 TGAAAAATGAAGACTCCCTGACGA 60.202 41.667 0.00 0.00 0.00 4.20
647 671 1.952102 TACCATGGGTCGAGGAACGC 61.952 60.000 18.09 0.00 42.26 4.84
722 746 5.107026 CGAAGGTATACATCTCTCGAACGAT 60.107 44.000 5.01 0.00 0.00 3.73
767 791 2.283966 AGGGACGAGGGTCAGTGG 60.284 66.667 0.00 0.00 45.28 4.00
771 795 1.975407 GAACGAGGGACGAGGGTCA 60.975 63.158 0.00 0.00 45.28 4.02
797 821 3.004862 GTTTATGGTACGGTGGGAACAG 58.995 50.000 0.00 0.00 44.46 3.16
798 822 2.371179 TGTTTATGGTACGGTGGGAACA 59.629 45.455 0.00 0.00 38.70 3.18
813 837 4.338118 CCGAACCATAGTTGCCATGTTTAT 59.662 41.667 0.00 0.00 35.94 1.40
814 838 3.692101 CCGAACCATAGTTGCCATGTTTA 59.308 43.478 0.00 0.00 35.94 2.01
858 882 4.148174 CCAAATTTTTCGTCCGCTCTTTTC 59.852 41.667 0.00 0.00 0.00 2.29
963 992 1.067084 CGTGGGCACAACAAATGCA 59.933 52.632 0.00 0.00 45.27 3.96
1028 1057 4.416738 AGGCGGAGAAGGCAAGGC 62.417 66.667 0.00 0.00 39.37 4.35
1191 1232 9.927081 AAGATTCTCTCTTTCTCTCTATCTCTT 57.073 33.333 0.00 0.00 41.60 2.85
1230 1281 7.064253 CCGTCTTGTCCGAAGAAAACTTATAAT 59.936 37.037 0.00 0.00 0.00 1.28
1242 1300 2.433868 TTCTTCCGTCTTGTCCGAAG 57.566 50.000 0.00 0.00 0.00 3.79
1249 1307 1.136611 CGCTCGTTTTCTTCCGTCTTG 60.137 52.381 0.00 0.00 0.00 3.02
1251 1309 1.282930 GCGCTCGTTTTCTTCCGTCT 61.283 55.000 0.00 0.00 0.00 4.18
1254 1312 1.009389 AGAGCGCTCGTTTTCTTCCG 61.009 55.000 30.39 0.00 34.09 4.30
1270 1328 5.629020 CACAAGTCGAGAGAAAGAGAAAGAG 59.371 44.000 0.00 0.00 45.01 2.85
1287 1345 2.618709 CAGGAACCAAGAACCACAAGTC 59.381 50.000 0.00 0.00 0.00 3.01
1351 1409 1.314730 GTTCTTCACGGCCCAAAAGA 58.685 50.000 0.00 0.13 0.00 2.52
1368 1426 2.722201 GGGCGTCCATCCTCTCGTT 61.722 63.158 0.00 0.00 0.00 3.85
1595 1659 3.695022 ATACGACACGACGGGCTGC 62.695 63.158 0.00 0.00 37.61 5.25
1674 1738 1.230324 GAGAAGCGGTCAAAGTTGCT 58.770 50.000 0.00 0.00 39.89 3.91
1742 1807 1.135286 GGAAATACACAGCAAGGCAGC 60.135 52.381 0.00 0.00 0.00 5.25
1994 2077 3.119096 GGAACAAGCGCCTCCGTC 61.119 66.667 2.29 0.00 36.67 4.79
2070 2159 4.052229 CGAAGTGGAGTCCGGCGT 62.052 66.667 6.01 0.00 0.00 5.68
2084 2173 2.620112 GGTGGTCGACGAGGACGAA 61.620 63.158 9.92 0.00 41.31 3.85
2234 2323 1.270550 GCCTTTTGCTTGCTGCTCTTA 59.729 47.619 0.00 0.00 43.37 2.10
2249 2338 3.763671 CCACGCTTCTTGGCCTTT 58.236 55.556 3.32 0.00 0.00 3.11
2546 2641 2.734591 GTGGCGGTGACTGTGAGA 59.265 61.111 0.00 0.00 0.00 3.27
2807 2918 3.194968 GCAGTACTTAGTGCCCTAACAGA 59.805 47.826 4.92 0.00 44.74 3.41
2808 2919 3.522553 GCAGTACTTAGTGCCCTAACAG 58.477 50.000 4.92 0.00 44.74 3.16
2882 2993 6.109359 TGCTAGCTCATAGAAAAACTCCTTC 58.891 40.000 17.23 0.00 32.76 3.46
2976 3087 3.518992 CCAAAGGGAAGGTTGGTTCTA 57.481 47.619 0.00 0.00 39.61 2.10
3020 3136 4.187056 GGCACGTTGCTCTCTACC 57.813 61.111 9.31 0.00 44.28 3.18
3108 3249 3.118298 TGCTCCTAACTAAGCATGCATCA 60.118 43.478 21.98 2.90 43.30 3.07
3109 3250 3.470709 TGCTCCTAACTAAGCATGCATC 58.529 45.455 21.98 0.00 43.30 3.91
3110 3251 3.135348 TCTGCTCCTAACTAAGCATGCAT 59.865 43.478 21.98 11.22 46.69 3.96
3111 3252 2.501316 TCTGCTCCTAACTAAGCATGCA 59.499 45.455 21.98 0.00 46.69 3.96
3112 3253 3.129871 CTCTGCTCCTAACTAAGCATGC 58.870 50.000 10.51 10.51 46.69 4.06
3113 3254 3.129871 GCTCTGCTCCTAACTAAGCATG 58.870 50.000 0.00 0.00 46.69 4.06
3114 3255 2.768527 TGCTCTGCTCCTAACTAAGCAT 59.231 45.455 0.00 0.00 46.69 3.79
3115 3256 2.167281 CTGCTCTGCTCCTAACTAAGCA 59.833 50.000 0.00 0.00 45.83 3.91
3116 3257 2.428890 TCTGCTCTGCTCCTAACTAAGC 59.571 50.000 0.00 0.00 39.02 3.09
3117 3258 3.488384 CGTCTGCTCTGCTCCTAACTAAG 60.488 52.174 0.00 0.00 0.00 2.18
3118 3259 2.423892 CGTCTGCTCTGCTCCTAACTAA 59.576 50.000 0.00 0.00 0.00 2.24
3119 3260 2.017782 CGTCTGCTCTGCTCCTAACTA 58.982 52.381 0.00 0.00 0.00 2.24
3120 3261 0.814457 CGTCTGCTCTGCTCCTAACT 59.186 55.000 0.00 0.00 0.00 2.24
3121 3262 0.179124 CCGTCTGCTCTGCTCCTAAC 60.179 60.000 0.00 0.00 0.00 2.34
3122 3263 0.612174 ACCGTCTGCTCTGCTCCTAA 60.612 55.000 0.00 0.00 0.00 2.69
3123 3264 0.612174 AACCGTCTGCTCTGCTCCTA 60.612 55.000 0.00 0.00 0.00 2.94
3124 3265 1.910772 AACCGTCTGCTCTGCTCCT 60.911 57.895 0.00 0.00 0.00 3.69
3125 3266 1.739562 CAACCGTCTGCTCTGCTCC 60.740 63.158 0.00 0.00 0.00 4.70
3126 3267 0.735632 CTCAACCGTCTGCTCTGCTC 60.736 60.000 0.00 0.00 0.00 4.26
3127 3268 1.291588 CTCAACCGTCTGCTCTGCT 59.708 57.895 0.00 0.00 0.00 4.24
3128 3269 1.739562 CCTCAACCGTCTGCTCTGC 60.740 63.158 0.00 0.00 0.00 4.26
3129 3270 1.079543 CCCTCAACCGTCTGCTCTG 60.080 63.158 0.00 0.00 0.00 3.35
3130 3271 2.948720 GCCCTCAACCGTCTGCTCT 61.949 63.158 0.00 0.00 0.00 4.09
3139 3280 1.298014 CTGTCCTGAGCCCTCAACC 59.702 63.158 0.00 0.00 39.39 3.77
3151 3292 1.004979 ACTTCTACCTCTCGCTGTCCT 59.995 52.381 0.00 0.00 0.00 3.85
3232 3373 5.123502 CCATCCATGAACAAGAACTTCTCAG 59.876 44.000 0.00 0.00 0.00 3.35
3233 3374 5.005740 CCATCCATGAACAAGAACTTCTCA 58.994 41.667 0.00 0.00 0.00 3.27
3327 3477 1.132500 AGTTATGGCTCAGGGTAGGC 58.868 55.000 0.00 0.00 42.19 3.93
3428 7513 1.542030 AGGAGTACACGAACAGAGCAG 59.458 52.381 0.00 0.00 0.00 4.24
3429 7514 1.617322 AGGAGTACACGAACAGAGCA 58.383 50.000 0.00 0.00 0.00 4.26
3439 7524 5.349809 GTCCAAAGCTATGTAGGAGTACAC 58.650 45.833 0.00 0.00 42.06 2.90
3479 7589 1.895798 ACTGAATCACGAGGAGAAGCA 59.104 47.619 0.00 0.00 0.00 3.91
3480 7590 2.663826 ACTGAATCACGAGGAGAAGC 57.336 50.000 0.00 0.00 0.00 3.86
3481 7591 3.487711 CGGTACTGAATCACGAGGAGAAG 60.488 52.174 0.00 0.00 0.00 2.85
3482 7592 2.422479 CGGTACTGAATCACGAGGAGAA 59.578 50.000 0.00 0.00 0.00 2.87
3483 7593 2.014857 CGGTACTGAATCACGAGGAGA 58.985 52.381 0.00 0.00 0.00 3.71
3484 7594 1.534175 GCGGTACTGAATCACGAGGAG 60.534 57.143 5.68 0.00 0.00 3.69
3515 7628 3.648009 GTGGAAATTTCAAACCATCGCA 58.352 40.909 19.49 2.58 34.87 5.10


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

AutoCloner maintained by Alex Coulton.