Multiple sequence alignment - TraesCS7B01G288200

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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 TraesCS7B01G288200 chr7B 100.000 2287 0 0 1 2287 524060659 524058373 0.000000e+00 4224
1 TraesCS7B01G288200 chr7A 83.800 1679 156 35 1 1596 561601250 561599605 0.000000e+00 1487
2 TraesCS7B01G288200 chr7A 93.525 695 32 4 1597 2287 561599507 561598822 0.000000e+00 1022
3 TraesCS7B01G288200 chr7A 84.541 207 24 6 2085 2287 475949775 475949573 4.980000e-47 198
4 TraesCS7B01G288200 chr7D 84.928 1181 114 33 462 1596 495833329 495832167 0.000000e+00 1136
5 TraesCS7B01G288200 chr7D 93.013 687 20 7 1603 2287 495831743 495831083 0.000000e+00 977
6 TraesCS7B01G288200 chr3D 85.990 207 21 5 2085 2287 478984223 478984021 4.950000e-52 215
7 TraesCS7B01G288200 chr3B 85.024 207 23 5 2085 2287 741399267 741399065 1.070000e-48 204
8 TraesCS7B01G288200 chr4D 82.927 205 22 7 2085 2287 18721144 18720951 3.020000e-39 172


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 TraesCS7B01G288200 chr7B 524058373 524060659 2286 True 4224.0 4224 100.0000 1 2287 1 chr7B.!!$R1 2286
1 TraesCS7B01G288200 chr7A 561598822 561601250 2428 True 1254.5 1487 88.6625 1 2287 2 chr7A.!!$R2 2286
2 TraesCS7B01G288200 chr7D 495831083 495833329 2246 True 1056.5 1136 88.9705 462 2287 2 chr7D.!!$R1 1825

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
644 688 0.10412 GGTTGGGTGTCCTGTTTTGC 59.896 55.0 0.0 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1660 0.674581 CGATGAACAGAAGCCAGCCA 60.675 55.0 0.0 0.0 0.0 4.75 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
27 28 7.617041 TTTGTTATTTTTGTTCCCCAAGTTG 57.383 32.000 0.00 0.00 33.75 3.16
40 41 4.714308 TCCCCAAGTTGTGAGTTGAATTTT 59.286 37.500 1.45 0.00 38.26 1.82
42 43 5.294060 CCCCAAGTTGTGAGTTGAATTTTTG 59.706 40.000 1.45 0.00 38.26 2.44
44 45 6.593382 CCCAAGTTGTGAGTTGAATTTTTGAA 59.407 34.615 1.45 0.00 38.26 2.69
45 46 7.280652 CCCAAGTTGTGAGTTGAATTTTTGAAT 59.719 33.333 1.45 0.00 38.26 2.57
52 57 9.823098 TGTGAGTTGAATTTTTGAATTTTTGTG 57.177 25.926 0.00 0.00 0.00 3.33
63 68 9.442047 TTTTTGAATTTTTGTGACATGTTAGGT 57.558 25.926 0.00 0.00 0.00 3.08
161 166 0.887933 GCATAACAACACCCCCACAG 59.112 55.000 0.00 0.00 0.00 3.66
162 167 1.544724 CATAACAACACCCCCACAGG 58.455 55.000 0.00 0.00 0.00 4.00
163 168 0.251608 ATAACAACACCCCCACAGGC 60.252 55.000 0.00 0.00 0.00 4.85
164 169 1.357272 TAACAACACCCCCACAGGCT 61.357 55.000 0.00 0.00 0.00 4.58
166 171 3.580319 AACACCCCCACAGGCTCC 61.580 66.667 0.00 0.00 0.00 4.70
167 172 4.918360 ACACCCCCACAGGCTCCA 62.918 66.667 0.00 0.00 0.00 3.86
169 174 2.000701 CACCCCCACAGGCTCCATA 61.001 63.158 0.00 0.00 0.00 2.74
170 175 2.001269 ACCCCCACAGGCTCCATAC 61.001 63.158 0.00 0.00 0.00 2.39
171 176 2.757124 CCCCCACAGGCTCCATACC 61.757 68.421 0.00 0.00 0.00 2.73
172 177 2.505982 CCCACAGGCTCCATACCG 59.494 66.667 0.00 0.00 0.00 4.02
173 178 2.367202 CCCACAGGCTCCATACCGT 61.367 63.158 0.00 0.00 0.00 4.83
174 179 1.602237 CCACAGGCTCCATACCGTT 59.398 57.895 0.00 0.00 0.00 4.44
175 180 0.744414 CCACAGGCTCCATACCGTTG 60.744 60.000 0.00 0.00 0.00 4.10
176 181 0.744414 CACAGGCTCCATACCGTTGG 60.744 60.000 0.00 0.00 38.18 3.77
178 183 2.516225 GGCTCCATACCGTTGGGC 60.516 66.667 0.00 0.00 37.37 5.36
179 184 2.590092 GCTCCATACCGTTGGGCT 59.410 61.111 0.00 0.00 37.37 5.19
180 185 1.819632 GCTCCATACCGTTGGGCTG 60.820 63.158 0.00 0.00 37.37 4.85
181 186 1.153168 CTCCATACCGTTGGGCTGG 60.153 63.158 0.82 0.82 39.62 4.85
183 188 2.272146 CATACCGTTGGGCTGGCT 59.728 61.111 0.00 0.00 36.48 4.75
185 190 0.107410 CATACCGTTGGGCTGGCTTA 60.107 55.000 0.00 0.00 36.48 3.09
186 191 0.843984 ATACCGTTGGGCTGGCTTAT 59.156 50.000 0.00 0.00 36.48 1.73
188 193 2.774799 CCGTTGGGCTGGCTTATGC 61.775 63.158 0.00 0.00 38.76 3.14
190 195 1.811860 GTTGGGCTGGCTTATGCTG 59.188 57.895 0.00 0.00 39.59 4.41
191 196 0.967380 GTTGGGCTGGCTTATGCTGT 60.967 55.000 0.00 0.00 39.59 4.40
192 197 0.966875 TTGGGCTGGCTTATGCTGTG 60.967 55.000 0.00 0.00 39.59 3.66
198 204 1.542915 CTGGCTTATGCTGTGCTTGTT 59.457 47.619 0.13 0.00 39.59 2.83
199 205 1.962807 TGGCTTATGCTGTGCTTGTTT 59.037 42.857 0.13 0.00 39.59 2.83
220 226 6.127563 TGTTTGGTCTTTAGGAACCAACTTTC 60.128 38.462 6.47 0.46 41.35 2.62
229 235 5.183014 AGGAACCAACTTTCGATGAAAAC 57.817 39.130 0.00 0.00 30.84 2.43
279 285 3.678289 TGGATCTGTTGTCAATCCACAG 58.322 45.455 2.10 0.00 43.06 3.66
296 302 2.280457 GCCCAGAGCGGCTACATC 60.280 66.667 0.60 0.00 46.10 3.06
299 305 1.040646 CCCAGAGCGGCTACATCTAA 58.959 55.000 0.60 0.00 0.00 2.10
300 306 1.412710 CCCAGAGCGGCTACATCTAAA 59.587 52.381 0.60 0.00 0.00 1.85
304 310 4.291783 CAGAGCGGCTACATCTAAACTAC 58.708 47.826 0.60 0.00 0.00 2.73
305 311 3.318557 AGAGCGGCTACATCTAAACTACC 59.681 47.826 0.60 0.00 0.00 3.18
311 323 5.527033 GGCTACATCTAAACTACCCTTACG 58.473 45.833 0.00 0.00 0.00 3.18
320 332 8.071177 TCTAAACTACCCTTACGCTTCTTATT 57.929 34.615 0.00 0.00 0.00 1.40
321 333 9.189156 TCTAAACTACCCTTACGCTTCTTATTA 57.811 33.333 0.00 0.00 0.00 0.98
322 334 9.978044 CTAAACTACCCTTACGCTTCTTATTAT 57.022 33.333 0.00 0.00 0.00 1.28
354 366 8.281212 ACATGAAAAATTCCATCACTACTACC 57.719 34.615 0.00 0.00 0.00 3.18
368 381 4.081586 CACTACTACCTCTTGTTTCCCCTC 60.082 50.000 0.00 0.00 0.00 4.30
371 384 1.128188 ACCTCTTGTTTCCCCTCGCT 61.128 55.000 0.00 0.00 0.00 4.93
376 389 0.467290 TTGTTTCCCCTCGCTGCTTT 60.467 50.000 0.00 0.00 0.00 3.51
378 391 1.671054 TTTCCCCTCGCTGCTTTCG 60.671 57.895 0.00 0.00 0.00 3.46
419 432 3.248171 GCCGTCGACGTGCATCTC 61.248 66.667 32.27 14.11 37.74 2.75
420 433 2.579787 CCGTCGACGTGCATCTCC 60.580 66.667 33.49 0.00 37.74 3.71
432 445 3.257873 CGTGCATCTCCCATCTTCTCTAT 59.742 47.826 0.00 0.00 0.00 1.98
437 450 6.958778 TGCATCTCCCATCTTCTCTATAGAAT 59.041 38.462 3.57 0.00 40.92 2.40
438 451 7.093421 TGCATCTCCCATCTTCTCTATAGAATG 60.093 40.741 3.57 4.70 40.92 2.67
439 452 7.123997 GCATCTCCCATCTTCTCTATAGAATGA 59.876 40.741 11.98 7.35 40.92 2.57
441 454 8.648698 TCTCCCATCTTCTCTATAGAATGAAG 57.351 38.462 18.98 18.98 40.92 3.02
442 455 8.231007 TCTCCCATCTTCTCTATAGAATGAAGT 58.769 37.037 21.96 12.49 40.92 3.01
443 456 8.187913 TCCCATCTTCTCTATAGAATGAAGTG 57.812 38.462 21.96 19.09 40.92 3.16
444 457 7.786943 TCCCATCTTCTCTATAGAATGAAGTGT 59.213 37.037 21.96 14.05 40.92 3.55
445 458 7.871973 CCCATCTTCTCTATAGAATGAAGTGTG 59.128 40.741 21.96 20.40 40.92 3.82
446 459 8.637099 CCATCTTCTCTATAGAATGAAGTGTGA 58.363 37.037 21.96 10.56 40.92 3.58
447 460 9.681692 CATCTTCTCTATAGAATGAAGTGTGAG 57.318 37.037 21.96 11.11 40.92 3.51
448 461 9.639563 ATCTTCTCTATAGAATGAAGTGTGAGA 57.360 33.333 21.96 9.79 40.92 3.27
449 462 9.119418 TCTTCTCTATAGAATGAAGTGTGAGAG 57.881 37.037 21.96 3.28 40.92 3.20
450 463 7.270757 TCTCTATAGAATGAAGTGTGAGAGC 57.729 40.000 3.57 0.00 0.00 4.09
451 464 6.830838 TCTCTATAGAATGAAGTGTGAGAGCA 59.169 38.462 3.57 0.00 0.00 4.26
452 465 7.340487 TCTCTATAGAATGAAGTGTGAGAGCAA 59.660 37.037 3.57 0.00 0.00 3.91
453 466 7.261325 TCTATAGAATGAAGTGTGAGAGCAAC 58.739 38.462 0.00 0.00 0.00 4.17
454 467 4.077300 AGAATGAAGTGTGAGAGCAACA 57.923 40.909 0.00 0.00 0.00 3.33
455 468 4.649692 AGAATGAAGTGTGAGAGCAACAT 58.350 39.130 0.00 0.00 0.00 2.71
456 469 5.798132 AGAATGAAGTGTGAGAGCAACATA 58.202 37.500 0.00 0.00 0.00 2.29
457 470 6.233434 AGAATGAAGTGTGAGAGCAACATAA 58.767 36.000 0.00 0.00 0.00 1.90
458 471 6.883217 AGAATGAAGTGTGAGAGCAACATAAT 59.117 34.615 0.00 0.00 0.00 1.28
459 472 8.043113 AGAATGAAGTGTGAGAGCAACATAATA 58.957 33.333 0.00 0.00 0.00 0.98
460 473 6.968131 TGAAGTGTGAGAGCAACATAATAC 57.032 37.500 0.00 0.00 0.00 1.89
474 487 7.440255 AGCAACATAATACGAGGGTAACATAAC 59.560 37.037 0.00 0.00 39.74 1.89
484 497 3.068560 GGGTAACATAACACTCGTGCAA 58.931 45.455 0.00 0.00 39.74 4.08
507 520 3.066760 GTGAAAGTGGAAGAGTTGGTTGG 59.933 47.826 0.00 0.00 0.00 3.77
512 525 1.210967 TGGAAGAGTTGGTTGGTCGTT 59.789 47.619 0.00 0.00 0.00 3.85
531 544 0.387929 TTGCGGTGAAGTCGAAGTCT 59.612 50.000 0.00 0.00 0.00 3.24
536 549 2.031069 CGGTGAAGTCGAAGTCTCTTGA 60.031 50.000 0.00 0.00 0.00 3.02
549 568 0.826715 CTCTTGATCGGGGAGAAGCA 59.173 55.000 4.12 0.00 0.00 3.91
556 575 0.250234 TCGGGGAGAAGCAATGACAG 59.750 55.000 0.00 0.00 0.00 3.51
561 580 3.265791 GGGAGAAGCAATGACAGTGTAG 58.734 50.000 4.63 0.00 0.00 2.74
564 583 4.560128 GAGAAGCAATGACAGTGTAGTGA 58.440 43.478 4.63 0.00 0.00 3.41
579 598 3.382227 TGTAGTGACAACCTCAACGAAGA 59.618 43.478 0.00 0.00 30.68 2.87
582 601 3.322254 AGTGACAACCTCAACGAAGATCT 59.678 43.478 0.00 0.00 0.00 2.75
603 630 6.456795 TCTTCTCTTCGATGATGTGTGTAT 57.543 37.500 0.95 0.00 0.00 2.29
644 688 0.104120 GGTTGGGTGTCCTGTTTTGC 59.896 55.000 0.00 0.00 0.00 3.68
657 701 3.001127 CCTGTTTTGCGGACATGTTTTTG 59.999 43.478 0.00 0.00 0.00 2.44
696 740 9.931210 GTTAATTAACCGGTCAATTCTCTATTG 57.069 33.333 19.20 0.00 44.14 1.90
702 746 5.875359 ACCGGTCAATTCTCTATTGTCTTTC 59.125 40.000 0.00 0.00 43.41 2.62
703 747 5.874810 CCGGTCAATTCTCTATTGTCTTTCA 59.125 40.000 0.00 0.00 43.41 2.69
706 750 6.317391 GGTCAATTCTCTATTGTCTTTCAGGG 59.683 42.308 0.00 0.00 43.41 4.45
716 762 2.143925 GTCTTTCAGGGTCTGGTTTCG 58.856 52.381 0.00 0.00 31.51 3.46
754 807 2.548464 AGAGCCTGATCTGGACTTCT 57.452 50.000 21.91 16.13 0.00 2.85
847 915 2.827755 GGTTCTCCTTTCCTCTCCTCT 58.172 52.381 0.00 0.00 0.00 3.69
852 926 3.093057 CTCCTTTCCTCTCCTCTTTCGA 58.907 50.000 0.00 0.00 0.00 3.71
858 932 1.341581 CCTCTCCTCTTTCGACTCCCT 60.342 57.143 0.00 0.00 0.00 4.20
921 995 3.081409 GCCAGGGTTAGCCGAGGA 61.081 66.667 16.77 0.00 32.92 3.71
978 1052 0.318762 GCTGACGAAGAACTCCCACT 59.681 55.000 0.00 0.00 0.00 4.00
1076 1150 0.108281 GCCGTCTCCTTCTGGTAACC 60.108 60.000 0.00 0.00 34.23 2.85
1081 1155 2.038557 GTCTCCTTCTGGTAACCTGCAA 59.961 50.000 0.00 0.00 34.23 4.08
1084 1158 2.026262 TCCTTCTGGTAACCTGCAATCC 60.026 50.000 0.00 0.00 34.23 3.01
1086 1160 0.251916 TCTGGTAACCTGCAATCCGG 59.748 55.000 0.00 0.00 0.00 5.14
1088 1162 0.322098 TGGTAACCTGCAATCCGGTG 60.322 55.000 0.00 0.00 32.86 4.94
1095 1169 3.987404 GCAATCCGGTGCAGTTCT 58.013 55.556 11.92 0.00 44.29 3.01
1096 1170 3.153024 GCAATCCGGTGCAGTTCTA 57.847 52.632 11.92 0.00 44.29 2.10
1098 1172 1.009829 CAATCCGGTGCAGTTCTAGC 58.990 55.000 0.00 0.00 0.00 3.42
1106 1180 0.621571 TGCAGTTCTAGCATCCCCCT 60.622 55.000 0.00 0.00 37.02 4.79
1112 1186 0.493639 TCTAGCATCCCCCTAGCCAT 59.506 55.000 0.00 0.00 33.83 4.40
1120 1194 0.113190 CCCCCTAGCCATCCAAATCC 59.887 60.000 0.00 0.00 0.00 3.01
1121 1195 0.852842 CCCCTAGCCATCCAAATCCA 59.147 55.000 0.00 0.00 0.00 3.41
1133 1207 4.249638 TCCAAATCCATGTTCCTAAGGG 57.750 45.455 0.00 0.00 0.00 3.95
1289 1363 1.271926 GCTCACCCCAAACCATAGTGT 60.272 52.381 0.00 0.00 0.00 3.55
1324 1398 5.592587 TCCCTTCCTTCTTTTTCCACATA 57.407 39.130 0.00 0.00 0.00 2.29
1342 1416 4.151335 CACATATGCTTAGAATGCTCGACC 59.849 45.833 1.58 0.00 0.00 4.79
1346 1423 1.855360 GCTTAGAATGCTCGACCGAAG 59.145 52.381 0.00 0.00 0.00 3.79
1386 1463 5.356751 CAGCCAATGTGCTTAAACCATAGTA 59.643 40.000 0.00 0.00 40.32 1.82
1387 1464 5.590259 AGCCAATGTGCTTAAACCATAGTAG 59.410 40.000 0.00 0.00 38.85 2.57
1388 1465 5.357032 GCCAATGTGCTTAAACCATAGTAGT 59.643 40.000 0.00 0.00 0.00 2.73
1468 1570 4.769215 CATGTCTGTTGATGTATGCGATG 58.231 43.478 0.00 0.00 0.00 3.84
1472 1574 3.132824 TCTGTTGATGTATGCGATGGACT 59.867 43.478 0.00 0.00 0.00 3.85
1482 1584 0.958822 GCGATGGACTGGTTTTGGTT 59.041 50.000 0.00 0.00 0.00 3.67
1483 1585 1.068541 GCGATGGACTGGTTTTGGTTC 60.069 52.381 0.00 0.00 0.00 3.62
1545 1648 3.066621 GCAATGGTGCCTCATCGAATAAA 59.933 43.478 0.00 0.00 45.68 1.40
1546 1649 4.601019 CAATGGTGCCTCATCGAATAAAC 58.399 43.478 0.00 0.00 0.00 2.01
1547 1650 3.342377 TGGTGCCTCATCGAATAAACA 57.658 42.857 0.00 0.00 0.00 2.83
1548 1651 3.006940 TGGTGCCTCATCGAATAAACAC 58.993 45.455 0.00 0.00 0.00 3.32
1549 1652 3.270877 GGTGCCTCATCGAATAAACACT 58.729 45.455 9.97 0.00 0.00 3.55
1550 1653 4.081365 TGGTGCCTCATCGAATAAACACTA 60.081 41.667 9.97 3.15 0.00 2.74
1552 1655 5.220605 GGTGCCTCATCGAATAAACACTAAC 60.221 44.000 9.97 0.00 0.00 2.34
1554 1657 4.873827 GCCTCATCGAATAAACACTAACCA 59.126 41.667 0.00 0.00 0.00 3.67
1556 1659 6.038271 GCCTCATCGAATAAACACTAACCAAT 59.962 38.462 0.00 0.00 0.00 3.16
1557 1660 7.415206 GCCTCATCGAATAAACACTAACCAATT 60.415 37.037 0.00 0.00 0.00 2.32
1558 1661 7.910162 CCTCATCGAATAAACACTAACCAATTG 59.090 37.037 0.00 0.00 0.00 2.32
1577 1682 0.674895 GGCTGGCTTCTGTTCATCGT 60.675 55.000 0.00 0.00 0.00 3.73
1586 1691 5.324697 GCTTCTGTTCATCGTGTAATTTCC 58.675 41.667 0.00 0.00 0.00 3.13
1679 2201 6.889177 TGAACAAAGCCAATGGTCATTATCTA 59.111 34.615 0.00 0.00 39.49 1.98
1922 2445 3.068165 GCCAAGCAGTTCTGGTAAAAAGT 59.932 43.478 4.95 0.00 0.00 2.66
2094 2618 1.545651 GCACCTAAGCTGGAAAGTGGT 60.546 52.381 0.00 0.00 0.00 4.16
2159 2683 6.222038 TGCCTATCCGTATCTGAAATATCC 57.778 41.667 0.00 0.00 0.00 2.59
2256 2783 9.466497 AGTATGAGATTTTGACACAAATATGGT 57.534 29.630 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.650322 TCAACTCACAACTTGGGGAAC 58.350 47.619 0.00 0.00 0.00 3.62
40 41 6.478344 GCACCTAACATGTCACAAAAATTCAA 59.522 34.615 0.00 0.00 0.00 2.69
42 43 5.982516 TGCACCTAACATGTCACAAAAATTC 59.017 36.000 0.00 0.00 0.00 2.17
44 45 5.528043 TGCACCTAACATGTCACAAAAAT 57.472 34.783 0.00 0.00 0.00 1.82
45 46 4.991153 TGCACCTAACATGTCACAAAAA 57.009 36.364 0.00 0.00 0.00 1.94
52 57 4.818534 CATACCATGCACCTAACATGTC 57.181 45.455 0.00 0.00 42.74 3.06
124 129 4.685169 ATGCAACCTGTTTATGTCGAAG 57.315 40.909 0.00 0.00 0.00 3.79
153 158 2.757124 GGTATGGAGCCTGTGGGGG 61.757 68.421 0.00 0.00 35.12 5.40
154 159 2.919043 GGTATGGAGCCTGTGGGG 59.081 66.667 0.00 0.00 38.36 4.96
161 166 2.516225 GCCCAACGGTATGGAGCC 60.516 66.667 5.80 0.00 43.54 4.70
162 167 1.819632 CAGCCCAACGGTATGGAGC 60.820 63.158 5.80 7.38 43.54 4.70
163 168 1.153168 CCAGCCCAACGGTATGGAG 60.153 63.158 5.80 0.00 43.54 3.86
164 169 2.994699 CCAGCCCAACGGTATGGA 59.005 61.111 5.80 0.00 43.54 3.41
166 171 0.107410 TAAGCCAGCCCAACGGTATG 60.107 55.000 0.00 0.00 0.00 2.39
167 172 0.843984 ATAAGCCAGCCCAACGGTAT 59.156 50.000 0.00 0.00 0.00 2.73
169 174 1.378514 CATAAGCCAGCCCAACGGT 60.379 57.895 0.00 0.00 0.00 4.83
170 175 2.774799 GCATAAGCCAGCCCAACGG 61.775 63.158 0.00 0.00 33.58 4.44
171 176 1.750399 AGCATAAGCCAGCCCAACG 60.750 57.895 0.00 0.00 43.56 4.10
172 177 0.967380 ACAGCATAAGCCAGCCCAAC 60.967 55.000 0.00 0.00 43.56 3.77
173 178 0.966875 CACAGCATAAGCCAGCCCAA 60.967 55.000 0.00 0.00 43.56 4.12
174 179 1.378911 CACAGCATAAGCCAGCCCA 60.379 57.895 0.00 0.00 43.56 5.36
175 180 2.779033 GCACAGCATAAGCCAGCCC 61.779 63.158 0.00 0.00 43.56 5.19
176 181 1.318158 AAGCACAGCATAAGCCAGCC 61.318 55.000 0.00 0.00 43.56 4.85
178 183 1.171308 ACAAGCACAGCATAAGCCAG 58.829 50.000 0.00 0.00 43.56 4.85
179 184 1.619654 AACAAGCACAGCATAAGCCA 58.380 45.000 0.00 0.00 43.56 4.75
180 185 2.331194 CAAACAAGCACAGCATAAGCC 58.669 47.619 0.00 0.00 43.56 4.35
181 186 2.288395 ACCAAACAAGCACAGCATAAGC 60.288 45.455 0.00 0.00 42.56 3.09
183 188 3.221771 AGACCAAACAAGCACAGCATAA 58.778 40.909 0.00 0.00 0.00 1.90
185 190 1.696063 AGACCAAACAAGCACAGCAT 58.304 45.000 0.00 0.00 0.00 3.79
186 191 1.473258 AAGACCAAACAAGCACAGCA 58.527 45.000 0.00 0.00 0.00 4.41
188 193 3.882888 TCCTAAAGACCAAACAAGCACAG 59.117 43.478 0.00 0.00 0.00 3.66
190 195 4.499188 GGTTCCTAAAGACCAAACAAGCAC 60.499 45.833 0.00 0.00 35.95 4.40
191 196 3.634910 GGTTCCTAAAGACCAAACAAGCA 59.365 43.478 0.00 0.00 35.95 3.91
192 197 3.634910 TGGTTCCTAAAGACCAAACAAGC 59.365 43.478 0.00 0.00 42.68 4.01
199 205 4.131596 CGAAAGTTGGTTCCTAAAGACCA 58.868 43.478 0.00 0.00 43.87 4.02
241 247 8.409358 ACAGATCCAGTTTAGCTATTTGTTTT 57.591 30.769 0.00 0.00 0.00 2.43
242 248 8.299570 CAACAGATCCAGTTTAGCTATTTGTTT 58.700 33.333 0.00 0.00 0.00 2.83
259 265 2.421424 GCTGTGGATTGACAACAGATCC 59.579 50.000 8.82 4.23 39.81 3.36
262 268 1.545428 GGGCTGTGGATTGACAACAGA 60.545 52.381 8.82 0.00 0.00 3.41
264 270 0.184692 TGGGCTGTGGATTGACAACA 59.815 50.000 0.00 0.00 0.00 3.33
265 271 0.883833 CTGGGCTGTGGATTGACAAC 59.116 55.000 0.00 0.00 0.00 3.32
295 301 5.990120 AAGAAGCGTAAGGGTAGTTTAGA 57.010 39.130 0.00 0.00 38.28 2.10
296 302 9.978044 ATAATAAGAAGCGTAAGGGTAGTTTAG 57.022 33.333 0.00 0.00 38.28 1.85
342 354 5.420409 GGGAAACAAGAGGTAGTAGTGATG 58.580 45.833 0.00 0.00 0.00 3.07
348 360 3.094572 CGAGGGGAAACAAGAGGTAGTA 58.905 50.000 0.00 0.00 0.00 1.82
354 366 1.301677 GCAGCGAGGGGAAACAAGAG 61.302 60.000 0.00 0.00 0.00 2.85
410 423 1.411977 AGAGAAGATGGGAGATGCACG 59.588 52.381 0.00 0.00 0.00 5.34
412 425 5.896963 TCTATAGAGAAGATGGGAGATGCA 58.103 41.667 0.00 0.00 0.00 3.96
413 426 6.849085 TTCTATAGAGAAGATGGGAGATGC 57.151 41.667 2.02 0.00 36.75 3.91
416 429 8.231007 ACTTCATTCTATAGAGAAGATGGGAGA 58.769 37.037 26.63 2.67 44.90 3.71
419 432 7.871973 CACACTTCATTCTATAGAGAAGATGGG 59.128 40.741 26.63 20.11 44.90 4.00
420 433 8.637099 TCACACTTCATTCTATAGAGAAGATGG 58.363 37.037 26.63 19.72 44.90 3.51
432 445 5.213891 TGTTGCTCTCACACTTCATTCTA 57.786 39.130 0.00 0.00 0.00 2.10
437 450 5.576774 CGTATTATGTTGCTCTCACACTTCA 59.423 40.000 0.00 0.00 0.00 3.02
438 451 5.805486 TCGTATTATGTTGCTCTCACACTTC 59.195 40.000 0.00 0.00 0.00 3.01
439 452 5.720202 TCGTATTATGTTGCTCTCACACTT 58.280 37.500 0.00 0.00 0.00 3.16
441 454 4.504461 CCTCGTATTATGTTGCTCTCACAC 59.496 45.833 0.00 0.00 0.00 3.82
442 455 4.441495 CCCTCGTATTATGTTGCTCTCACA 60.441 45.833 0.00 0.00 0.00 3.58
443 456 4.051922 CCCTCGTATTATGTTGCTCTCAC 58.948 47.826 0.00 0.00 0.00 3.51
444 457 3.704566 ACCCTCGTATTATGTTGCTCTCA 59.295 43.478 0.00 0.00 0.00 3.27
445 458 4.323553 ACCCTCGTATTATGTTGCTCTC 57.676 45.455 0.00 0.00 0.00 3.20
446 459 5.128171 TGTTACCCTCGTATTATGTTGCTCT 59.872 40.000 0.00 0.00 0.00 4.09
447 460 5.353938 TGTTACCCTCGTATTATGTTGCTC 58.646 41.667 0.00 0.00 0.00 4.26
448 461 5.347620 TGTTACCCTCGTATTATGTTGCT 57.652 39.130 0.00 0.00 0.00 3.91
449 462 7.225145 TGTTATGTTACCCTCGTATTATGTTGC 59.775 37.037 0.00 0.00 0.00 4.17
450 463 8.545420 GTGTTATGTTACCCTCGTATTATGTTG 58.455 37.037 0.00 0.00 0.00 3.33
451 464 8.480501 AGTGTTATGTTACCCTCGTATTATGTT 58.519 33.333 0.00 0.00 0.00 2.71
452 465 8.015185 AGTGTTATGTTACCCTCGTATTATGT 57.985 34.615 0.00 0.00 0.00 2.29
453 466 7.325338 CGAGTGTTATGTTACCCTCGTATTATG 59.675 40.741 0.00 0.00 39.92 1.90
454 467 7.365741 CGAGTGTTATGTTACCCTCGTATTAT 58.634 38.462 0.00 0.00 39.92 1.28
455 468 6.728200 CGAGTGTTATGTTACCCTCGTATTA 58.272 40.000 0.00 0.00 39.92 0.98
456 469 5.585390 CGAGTGTTATGTTACCCTCGTATT 58.415 41.667 0.00 0.00 39.92 1.89
457 470 5.179045 CGAGTGTTATGTTACCCTCGTAT 57.821 43.478 0.00 0.00 39.92 3.06
458 471 4.621068 CGAGTGTTATGTTACCCTCGTA 57.379 45.455 0.00 0.00 39.92 3.43
459 472 3.498927 CGAGTGTTATGTTACCCTCGT 57.501 47.619 0.00 0.00 39.92 4.18
460 473 3.176708 CACGAGTGTTATGTTACCCTCG 58.823 50.000 7.02 7.02 46.75 4.63
474 487 1.003545 CCACTTTCACTTGCACGAGTG 60.004 52.381 11.61 11.61 46.58 3.51
484 497 3.933861 ACCAACTCTTCCACTTTCACT 57.066 42.857 0.00 0.00 0.00 3.41
507 520 1.200839 CGACTTCACCGCAAACGAC 59.799 57.895 0.00 0.00 43.93 4.34
512 525 0.387929 AGACTTCGACTTCACCGCAA 59.612 50.000 0.00 0.00 0.00 4.85
531 544 1.275666 TTGCTTCTCCCCGATCAAGA 58.724 50.000 0.00 0.00 0.00 3.02
536 549 0.911769 TGTCATTGCTTCTCCCCGAT 59.088 50.000 0.00 0.00 0.00 4.18
549 568 4.100963 TGAGGTTGTCACTACACTGTCATT 59.899 41.667 0.00 0.00 34.61 2.57
556 575 3.088194 TCGTTGAGGTTGTCACTACAC 57.912 47.619 0.00 0.00 34.61 2.90
561 580 3.654414 AGATCTTCGTTGAGGTTGTCAC 58.346 45.455 0.00 0.00 33.71 3.67
564 583 4.282195 AGAGAAGATCTTCGTTGAGGTTGT 59.718 41.667 25.88 7.86 43.97 3.32
579 598 5.336150 ACACACATCATCGAAGAGAAGAT 57.664 39.130 0.00 0.00 43.63 2.40
582 601 4.805719 GCATACACACATCATCGAAGAGAA 59.194 41.667 0.00 0.00 43.63 2.87
589 608 3.374988 ACAAAGGCATACACACATCATCG 59.625 43.478 0.00 0.00 0.00 3.84
591 618 3.444742 CCACAAAGGCATACACACATCAT 59.555 43.478 0.00 0.00 0.00 2.45
603 630 1.074775 CTGGCTACCCACAAAGGCA 59.925 57.895 0.00 0.00 45.01 4.75
644 688 3.172229 ACCAAACCAAAAACATGTCCG 57.828 42.857 0.00 0.00 0.00 4.79
657 701 6.421501 CCGGTTAATTAACTGAAAACCAAACC 59.578 38.462 30.45 11.99 43.54 3.27
696 740 2.143925 CGAAACCAGACCCTGAAAGAC 58.856 52.381 0.00 0.00 34.07 3.01
725 771 4.077822 CAGATCAGGCTCTTCCACTTTTT 58.922 43.478 0.00 0.00 37.29 1.94
754 807 1.062365 CGTTACGTGCCGTCCGATA 59.938 57.895 0.00 0.00 41.54 2.92
847 915 3.755628 CGGCGGAGGGAGTCGAAA 61.756 66.667 0.00 0.00 39.29 3.46
898 972 2.669240 GCTAACCCTGGCTTCGGT 59.331 61.111 0.00 0.00 0.00 4.69
921 995 1.940613 GAAAACCGTTGCTCAGACAGT 59.059 47.619 0.00 0.00 0.00 3.55
978 1052 2.595095 CGCTGGGATTTGGGGCTA 59.405 61.111 0.00 0.00 0.00 3.93
1081 1155 0.833287 ATGCTAGAACTGCACCGGAT 59.167 50.000 9.46 0.00 43.59 4.18
1084 1158 0.811616 GGGATGCTAGAACTGCACCG 60.812 60.000 0.00 0.00 43.59 4.94
1086 1160 0.464554 GGGGGATGCTAGAACTGCAC 60.465 60.000 0.00 0.00 43.59 4.57
1088 1162 1.346068 CTAGGGGGATGCTAGAACTGC 59.654 57.143 0.00 0.00 0.00 4.40
1090 1164 1.723288 GCTAGGGGGATGCTAGAACT 58.277 55.000 0.00 0.00 0.00 3.01
1095 1169 0.547712 GGATGGCTAGGGGGATGCTA 60.548 60.000 0.00 0.00 0.00 3.49
1096 1170 1.849823 GGATGGCTAGGGGGATGCT 60.850 63.158 0.00 0.00 0.00 3.79
1098 1172 0.852842 TTTGGATGGCTAGGGGGATG 59.147 55.000 0.00 0.00 0.00 3.51
1106 1180 3.205056 AGGAACATGGATTTGGATGGCTA 59.795 43.478 0.00 0.00 0.00 3.93
1112 1186 3.596046 ACCCTTAGGAACATGGATTTGGA 59.404 43.478 0.00 0.00 36.73 3.53
1120 1194 3.089284 GGTCCAAACCCTTAGGAACATG 58.911 50.000 0.00 0.00 38.99 3.21
1121 1195 3.451402 GGTCCAAACCCTTAGGAACAT 57.549 47.619 0.00 0.00 38.99 2.71
1133 1207 2.230660 CAGAACAAGGGAGGTCCAAAC 58.769 52.381 0.00 0.00 38.24 2.93
1265 1339 2.203294 GGTTTGGGGTGAGCGTGT 60.203 61.111 0.00 0.00 0.00 4.49
1289 1363 5.193728 AGAAGGAAGGGAAATAGCATTACCA 59.806 40.000 1.57 0.00 35.57 3.25
1324 1398 1.409064 TCGGTCGAGCATTCTAAGCAT 59.591 47.619 15.89 0.00 0.00 3.79
1342 1416 4.785658 GCTGCATCATCATCTTGTTCTTCG 60.786 45.833 0.00 0.00 0.00 3.79
1346 1423 2.686405 TGGCTGCATCATCATCTTGTTC 59.314 45.455 0.50 0.00 0.00 3.18
1386 1463 8.368668 ACTTTACATCTAAGCAACTTACTGACT 58.631 33.333 0.00 0.00 0.00 3.41
1387 1464 8.535690 ACTTTACATCTAAGCAACTTACTGAC 57.464 34.615 0.00 0.00 0.00 3.51
1388 1465 8.988934 CAACTTTACATCTAAGCAACTTACTGA 58.011 33.333 0.00 0.00 0.00 3.41
1468 1570 1.617322 GGGAGAACCAAAACCAGTCC 58.383 55.000 0.00 0.00 39.85 3.85
1482 1584 2.612972 GCTCAAGACAAACGATGGGAGA 60.613 50.000 0.00 0.00 0.00 3.71
1483 1585 1.734465 GCTCAAGACAAACGATGGGAG 59.266 52.381 0.00 0.00 0.00 4.30
1545 1648 1.203050 AGCCAGCCAATTGGTTAGTGT 60.203 47.619 25.19 2.43 40.49 3.55
1546 1649 1.549203 AGCCAGCCAATTGGTTAGTG 58.451 50.000 25.19 16.40 40.49 2.74
1547 1650 2.171003 GAAGCCAGCCAATTGGTTAGT 58.829 47.619 25.19 6.77 40.49 2.24
1548 1651 2.165030 CAGAAGCCAGCCAATTGGTTAG 59.835 50.000 25.19 14.15 40.49 2.34
1549 1652 2.170166 CAGAAGCCAGCCAATTGGTTA 58.830 47.619 25.19 0.00 40.49 2.85
1550 1653 0.971386 CAGAAGCCAGCCAATTGGTT 59.029 50.000 25.19 17.51 40.49 3.67
1552 1655 0.971386 AACAGAAGCCAGCCAATTGG 59.029 50.000 20.81 20.81 41.35 3.16
1554 1657 1.999648 TGAACAGAAGCCAGCCAATT 58.000 45.000 0.00 0.00 0.00 2.32
1556 1659 1.538047 GATGAACAGAAGCCAGCCAA 58.462 50.000 0.00 0.00 0.00 4.52
1557 1660 0.674581 CGATGAACAGAAGCCAGCCA 60.675 55.000 0.00 0.00 0.00 4.75
1558 1661 0.674895 ACGATGAACAGAAGCCAGCC 60.675 55.000 0.00 0.00 0.00 4.85
1586 1691 9.383519 ACAACACTCTTATACCATATTGACAAG 57.616 33.333 0.00 0.00 0.00 3.16
1679 2201 4.019860 ACTCCATAGTGAGTGCAAGAACAT 60.020 41.667 0.00 0.00 43.80 2.71
1738 2260 6.818142 GGCTCCAGCAAACATAATTAAACAAT 59.182 34.615 0.03 0.00 44.36 2.71
1756 2278 3.452627 AGAACTATGGTGTAAGGCTCCAG 59.547 47.826 0.00 0.00 43.13 3.86
1922 2445 9.671279 TGCTTAGATCTTCATCTGAAAATGTTA 57.329 29.630 0.00 0.00 39.90 2.41
2122 2646 4.065088 GGATAGGCATTTTCTCGCATACA 58.935 43.478 0.00 0.00 0.00 2.29
2159 2683 1.444836 TCCATTTTAGTTCGGGTGCG 58.555 50.000 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.