Multiple sequence alignment - TraesCS6B01G302200

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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 TraesCS6B01G302200 chr6B 100.000 3695 0 0 1 3695 542008237 542011931 0.000000e+00 6824.0
1 TraesCS6B01G302200 chr6D 94.689 2316 87 17 1388 3695 360340045 360342332 0.000000e+00 3563.0
2 TraesCS6B01G302200 chr6D 86.214 1400 121 47 1 1370 360338606 360339963 0.000000e+00 1450.0
3 TraesCS6B01G302200 chr6A 95.592 2019 73 7 1681 3695 501498328 501500334 0.000000e+00 3221.0
4 TraesCS6B01G302200 chr6A 91.948 534 20 10 1112 1626 501497785 501498314 0.000000e+00 726.0
5 TraesCS6B01G302200 chr6A 82.048 791 86 36 1 774 501496271 501497022 1.130000e-174 623.0
6 TraesCS6B01G302200 chr6A 94.093 237 13 1 828 1064 501497464 501497699 3.510000e-95 359.0
7 TraesCS6B01G302200 chrUn 84.211 95 15 0 3601 3695 60348275 60348369 3.930000e-15 93.5
8 TraesCS6B01G302200 chr4B 84.211 95 15 0 3601 3695 622436082 622436176 3.930000e-15 93.5


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 TraesCS6B01G302200 chr6B 542008237 542011931 3694 False 6824.00 6824 100.00000 1 3695 1 chr6B.!!$F1 3694
1 TraesCS6B01G302200 chr6D 360338606 360342332 3726 False 2506.50 3563 90.45150 1 3695 2 chr6D.!!$F1 3694
2 TraesCS6B01G302200 chr6A 501496271 501500334 4063 False 1232.25 3221 90.92025 1 3695 4 chr6A.!!$F1 3694

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
649 702 0.179140 CATGCCTTGGCGCGTTAATT 60.179 50.0 8.43 0.0 0.0 1.40 F
867 1334 0.613777 CGACAGTCTAGGGGGCTTTT 59.386 55.0 0.00 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2588 0.263765 ACTCGGGCCTTATCCCAGTA 59.736 55.0 0.84 0.0 46.92 2.74 R
2728 3335 0.179004 AAACCAACATCAGTCGGCCA 60.179 50.0 2.24 0.0 0.00 5.36 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
24 25 2.952310 ACAAAAAGCCTGAGTTGAGACC 59.048 45.455 0.00 0.00 0.00 3.85
25 26 2.278332 AAAAGCCTGAGTTGAGACCC 57.722 50.000 0.00 0.00 0.00 4.46
26 27 1.439543 AAAGCCTGAGTTGAGACCCT 58.560 50.000 0.00 0.00 0.00 4.34
31 32 2.621929 GCCTGAGTTGAGACCCTCTAGA 60.622 54.545 0.00 0.00 0.00 2.43
50 51 6.708285 TCTAGAGTTTCCAAAAGTGGGATAC 58.292 40.000 0.00 0.00 46.01 2.24
81 82 1.919918 ACGGCAATGTTGTTTGTGTG 58.080 45.000 0.00 0.00 0.00 3.82
85 86 3.668191 CGGCAATGTTGTTTGTGTGATAC 59.332 43.478 0.00 0.00 0.00 2.24
86 87 4.556501 CGGCAATGTTGTTTGTGTGATACT 60.557 41.667 0.00 0.00 0.00 2.12
89 90 6.747280 GGCAATGTTGTTTGTGTGATACTATC 59.253 38.462 0.00 0.00 0.00 2.08
90 91 7.304735 GCAATGTTGTTTGTGTGATACTATCA 58.695 34.615 0.00 0.00 36.84 2.15
112 113 7.813852 TCACTTATCGAAAAGCTTAGAGAAC 57.186 36.000 0.00 0.00 0.00 3.01
114 115 5.805994 ACTTATCGAAAAGCTTAGAGAACGG 59.194 40.000 0.00 0.00 0.00 4.44
138 139 4.773149 ACGTTCTCCCCATAATCTCCTATC 59.227 45.833 0.00 0.00 0.00 2.08
154 155 0.800683 TATCGCGACTTCCTGCAACG 60.801 55.000 12.93 0.00 0.00 4.10
156 157 2.594962 CGCGACTTCCTGCAACGTT 61.595 57.895 0.00 0.00 0.00 3.99
170 171 2.614212 CAACGTTGCGCAATATAGACG 58.386 47.619 27.79 25.53 36.65 4.18
231 234 1.798813 CTTGTCCTTTACACGAGGTGC 59.201 52.381 0.00 0.00 38.00 5.01
232 235 0.753867 TGTCCTTTACACGAGGTGCA 59.246 50.000 0.00 0.00 36.98 4.57
271 276 9.630098 CATGAATTTTGCAAGTTAGTAAGACAT 57.370 29.630 0.00 0.00 0.00 3.06
301 306 4.644234 CCTTGCATCCACATACATGGTTTA 59.356 41.667 0.00 0.00 40.95 2.01
305 310 7.180322 TGCATCCACATACATGGTTTATTTT 57.820 32.000 0.00 0.00 40.95 1.82
306 311 8.298729 TGCATCCACATACATGGTTTATTTTA 57.701 30.769 0.00 0.00 40.95 1.52
337 345 2.611974 CCTTTTATGGCACGTGTGAC 57.388 50.000 18.38 8.67 39.62 3.67
354 362 4.384547 GTGTGACGGCATTATTTTTGTTCC 59.615 41.667 0.00 0.00 0.00 3.62
405 445 6.579666 CCTTTTACGTTACAAATGGTGCTAAC 59.420 38.462 0.00 0.00 0.00 2.34
441 486 7.178074 CACATACATTGTATGATGATCGATGC 58.822 38.462 33.07 0.00 36.57 3.91
452 497 0.385751 GATCGATGCCGTGGAAGAGA 59.614 55.000 0.54 0.00 37.05 3.10
453 498 1.000283 GATCGATGCCGTGGAAGAGAT 60.000 52.381 0.54 0.00 37.05 2.75
454 499 1.687563 TCGATGCCGTGGAAGAGATA 58.312 50.000 0.00 0.00 37.05 1.98
455 500 2.239400 TCGATGCCGTGGAAGAGATAT 58.761 47.619 0.00 0.00 37.05 1.63
456 501 3.418047 TCGATGCCGTGGAAGAGATATA 58.582 45.455 0.00 0.00 37.05 0.86
459 504 4.673061 CGATGCCGTGGAAGAGATATAGAC 60.673 50.000 0.00 0.00 0.00 2.59
461 506 3.958147 TGCCGTGGAAGAGATATAGACAA 59.042 43.478 0.00 0.00 0.00 3.18
463 508 5.105106 TGCCGTGGAAGAGATATAGACAAAA 60.105 40.000 0.00 0.00 0.00 2.44
465 510 6.238130 GCCGTGGAAGAGATATAGACAAAAAC 60.238 42.308 0.00 0.00 0.00 2.43
527 572 6.313905 TCTCTTCAGTTGAAAGACAAGACAAC 59.686 38.462 0.00 0.00 41.61 3.32
541 586 5.297547 ACAAGACAACTCACGTCATTGTAT 58.702 37.500 8.22 3.64 36.70 2.29
551 596 5.281727 TCACGTCATTGTATGAGATGCTAC 58.718 41.667 0.00 0.00 40.53 3.58
556 601 6.258727 CGTCATTGTATGAGATGCTACCTTTT 59.741 38.462 0.00 0.00 40.53 2.27
597 642 5.964168 GCGAGAATCTTTTCATCACATCTTG 59.036 40.000 0.00 0.00 34.08 3.02
605 650 8.908786 TCTTTTCATCACATCTTGTCTTAACT 57.091 30.769 0.00 0.00 0.00 2.24
606 651 9.996554 TCTTTTCATCACATCTTGTCTTAACTA 57.003 29.630 0.00 0.00 0.00 2.24
639 684 4.260985 TCACATACTTGTACATGCCTTGG 58.739 43.478 8.58 0.00 33.76 3.61
640 685 3.016736 ACATACTTGTACATGCCTTGGC 58.983 45.455 8.58 4.43 33.16 4.52
649 702 0.179140 CATGCCTTGGCGCGTTAATT 60.179 50.000 8.43 0.00 0.00 1.40
650 703 0.179140 ATGCCTTGGCGCGTTAATTG 60.179 50.000 8.43 0.00 0.00 2.32
661 714 4.033587 GGCGCGTTAATTGTTTCTAGATGA 59.966 41.667 8.43 0.00 0.00 2.92
704 757 2.158652 CCATCTTGTCATGCCCTGATCT 60.159 50.000 0.00 0.00 35.97 2.75
716 770 6.844917 TCATGCCCTGATCTGATATGAGATAT 59.155 38.462 4.52 0.00 32.57 1.63
737 791 7.770433 AGATATTTAGATGCTTGTGCTGTTGTA 59.230 33.333 0.00 0.00 40.48 2.41
774 828 8.361139 CACGTAGGGATTTGAGTCTCTTATATT 58.639 37.037 0.65 0.00 29.97 1.28
779 833 8.830741 AGGGATTTGAGTCTCTTATATTATGGG 58.169 37.037 0.65 0.00 0.00 4.00
780 834 8.826765 GGGATTTGAGTCTCTTATATTATGGGA 58.173 37.037 0.65 0.00 0.00 4.37
801 855 9.924010 ATGGGATATAGAGTGAGTATTAGGTAC 57.076 37.037 0.00 0.00 0.00 3.34
848 1315 5.189180 AGTTATTCCTCAGAATGGAGCAAC 58.811 41.667 0.00 0.00 42.78 4.17
858 1325 2.949451 ATGGAGCAACGACAGTCTAG 57.051 50.000 0.00 0.00 0.00 2.43
867 1334 0.613777 CGACAGTCTAGGGGGCTTTT 59.386 55.000 0.00 0.00 0.00 2.27
897 1364 4.262891 AGGTTCCATCTCTGATCTCTCA 57.737 45.455 0.00 0.00 0.00 3.27
900 1367 4.358851 GTTCCATCTCTGATCTCTCAACG 58.641 47.826 0.00 0.00 0.00 4.10
931 1398 6.295719 CCTATAAATAGGCGTTCCCATACT 57.704 41.667 3.12 0.00 43.08 2.12
933 1400 2.256117 AATAGGCGTTCCCATACTGC 57.744 50.000 0.00 0.00 35.39 4.40
980 1447 2.361757 AGAGATCTTGATCGACCTGCAG 59.638 50.000 6.78 6.78 0.00 4.41
997 1464 1.065564 GCAGGAAGAATCTGTGGAGCT 60.066 52.381 0.00 0.00 34.89 4.09
1011 1478 1.227205 GAGCTCGATGGACAGCAGG 60.227 63.158 0.00 0.00 38.18 4.85
1055 1522 5.411977 TGAGGTAACAAAACGTTGAGAAACA 59.588 36.000 0.00 0.00 38.63 2.83
1082 1549 5.821516 TTTTTCTTGGCTAACTTCGTTGA 57.178 34.783 0.00 0.00 0.00 3.18
1083 1550 6.385649 TTTTTCTTGGCTAACTTCGTTGAT 57.614 33.333 0.00 0.00 0.00 2.57
1085 1552 7.499321 TTTTCTTGGCTAACTTCGTTGATAA 57.501 32.000 0.00 0.00 0.00 1.75
1086 1553 6.476243 TTCTTGGCTAACTTCGTTGATAAC 57.524 37.500 0.00 0.00 0.00 1.89
1087 1554 4.933400 TCTTGGCTAACTTCGTTGATAACC 59.067 41.667 0.00 0.00 0.00 2.85
1088 1555 3.602483 TGGCTAACTTCGTTGATAACCC 58.398 45.455 0.00 0.00 0.00 4.11
1090 1557 3.602483 GCTAACTTCGTTGATAACCCCA 58.398 45.455 0.00 0.00 0.00 4.96
1092 1559 3.782656 AACTTCGTTGATAACCCCAGT 57.217 42.857 0.00 0.00 0.00 4.00
1093 1560 3.782656 ACTTCGTTGATAACCCCAGTT 57.217 42.857 0.00 0.00 40.15 3.16
1094 1561 4.094830 ACTTCGTTGATAACCCCAGTTT 57.905 40.909 0.00 0.00 37.42 2.66
1095 1562 5.231702 ACTTCGTTGATAACCCCAGTTTA 57.768 39.130 0.00 0.00 37.42 2.01
1098 1565 5.231702 TCGTTGATAACCCCAGTTTAAGT 57.768 39.130 0.00 0.00 37.42 2.24
1101 1568 5.318630 GTTGATAACCCCAGTTTAAGTCCA 58.681 41.667 0.00 0.00 37.42 4.02
1102 1569 4.913784 TGATAACCCCAGTTTAAGTCCAC 58.086 43.478 0.00 0.00 37.42 4.02
1103 1570 4.600111 TGATAACCCCAGTTTAAGTCCACT 59.400 41.667 0.00 0.00 37.42 4.00
1104 1571 3.965470 AACCCCAGTTTAAGTCCACTT 57.035 42.857 0.00 0.00 39.85 3.16
1105 1572 3.965470 ACCCCAGTTTAAGTCCACTTT 57.035 42.857 0.00 0.00 37.40 2.66
1106 1573 3.828921 ACCCCAGTTTAAGTCCACTTTC 58.171 45.455 0.00 0.00 37.40 2.62
1107 1574 2.812011 CCCCAGTTTAAGTCCACTTTCG 59.188 50.000 0.00 0.00 37.40 3.46
1108 1575 3.495453 CCCCAGTTTAAGTCCACTTTCGA 60.495 47.826 0.00 0.00 37.40 3.71
1109 1576 4.324267 CCCAGTTTAAGTCCACTTTCGAT 58.676 43.478 0.00 0.00 37.40 3.59
1218 1728 2.418746 GGAGCACATGAAGGTGTCGTAT 60.419 50.000 0.00 0.00 40.89 3.06
1340 1869 3.735240 CGATCTCTAGCTGCAAACATCTC 59.265 47.826 1.02 0.00 0.00 2.75
1399 1996 4.624843 GCTCCTTGTGATCTTGATCTTGGA 60.625 45.833 11.31 11.07 0.00 3.53
1480 2077 3.464907 CATCTGCCTCAACATCTTCGAT 58.535 45.455 0.00 0.00 0.00 3.59
1486 2083 2.366916 CCTCAACATCTTCGATAGCCCT 59.633 50.000 0.00 0.00 0.00 5.19
1544 2141 2.871427 CGCGCTGCTCCGGTAATTC 61.871 63.158 5.56 0.00 0.00 2.17
1555 2152 4.708177 CTCCGGTAATTCATGTTCTCCAT 58.292 43.478 0.00 0.00 0.00 3.41
1589 2186 3.522553 CCACCATCGACCTCTTCTTAAC 58.477 50.000 0.00 0.00 0.00 2.01
1590 2187 3.056107 CCACCATCGACCTCTTCTTAACA 60.056 47.826 0.00 0.00 0.00 2.41
1591 2188 4.383118 CCACCATCGACCTCTTCTTAACAT 60.383 45.833 0.00 0.00 0.00 2.71
1592 2189 4.568359 CACCATCGACCTCTTCTTAACATG 59.432 45.833 0.00 0.00 0.00 3.21
1627 2224 0.821711 TCCCGGCCAACTTTTCACAG 60.822 55.000 2.24 0.00 0.00 3.66
1637 2234 5.393902 CAACTTTTCACAGAAATGTTGGC 57.606 39.130 26.74 0.00 39.53 4.52
1639 2236 3.380004 ACTTTTCACAGAAATGTTGGCGA 59.620 39.130 5.51 0.00 0.00 5.54
1657 2254 3.456280 GCGAGAGAGCAGAAATCAGAAT 58.544 45.455 0.00 0.00 37.05 2.40
1679 2276 3.268072 TCTGATGTCTCTCTTCTCCCTCA 59.732 47.826 0.00 0.00 0.00 3.86
1815 2418 4.509600 GCCTTATTGGAGAAGATGAGAACG 59.490 45.833 0.00 0.00 38.35 3.95
1870 2473 2.029290 CGGTCACAAACTACAGGTAGCT 60.029 50.000 6.38 0.00 36.66 3.32
1893 2496 4.785914 TCACCTTGGAATCCATTACCAGTA 59.214 41.667 1.39 0.00 35.08 2.74
1952 2555 6.890663 TTGTTTTCTGAAGTGCAAAAGATG 57.109 33.333 0.00 0.00 0.00 2.90
1985 2588 2.551270 TGGCTCTTCAGGTATGAGGTT 58.449 47.619 0.00 0.00 36.61 3.50
2015 2618 1.457831 GCCCGAGTACCTGAGGGAT 60.458 63.158 14.46 0.00 46.64 3.85
2165 2768 1.519455 CGAGCGCCTAGGTTTGGAG 60.519 63.158 11.31 0.00 0.00 3.86
2223 2826 5.724328 TCAGTGAGCTATAGTTTGTTCCTG 58.276 41.667 0.84 0.19 0.00 3.86
2434 3040 3.365472 ACCCTTTGGTCATTGCCTAATC 58.635 45.455 0.00 0.00 43.06 1.75
2728 3335 0.480252 AAAGAGAACAAGGCAGGGCT 59.520 50.000 0.00 0.00 0.00 5.19
2770 3377 6.928348 TGGTCATATTCCATCCGTAGTAAT 57.072 37.500 0.00 0.00 0.00 1.89
2771 3378 8.425237 TTGGTCATATTCCATCCGTAGTAATA 57.575 34.615 0.00 0.00 34.75 0.98
2772 3379 7.833786 TGGTCATATTCCATCCGTAGTAATAC 58.166 38.462 0.00 0.00 0.00 1.89
2773 3380 7.093640 TGGTCATATTCCATCCGTAGTAATACC 60.094 40.741 0.00 0.00 0.00 2.73
2774 3381 6.971184 GTCATATTCCATCCGTAGTAATACCG 59.029 42.308 0.00 0.00 0.00 4.02
2775 3382 6.885918 TCATATTCCATCCGTAGTAATACCGA 59.114 38.462 0.00 0.00 0.00 4.69
2776 3383 4.836125 TTCCATCCGTAGTAATACCGAC 57.164 45.455 0.00 0.00 0.00 4.79
2974 3581 6.294176 GGCAGATAAACAGGCCTATAACAATG 60.294 42.308 3.98 1.17 43.09 2.82
3065 3672 2.159043 CCGCAGAAGATCATACCTGTGT 60.159 50.000 0.00 0.00 35.91 3.72
3110 3717 5.106197 TGTGCACAACTATAGAAATGCCTTG 60.106 40.000 19.28 1.20 32.02 3.61
3132 3739 7.704472 CCTTGCATTTGTGTCACTAAACTTTAA 59.296 33.333 4.27 0.00 0.00 1.52
3158 3765 1.130561 GTTTTAGCATCTGCCCGTGTC 59.869 52.381 0.00 0.00 43.38 3.67
3245 3852 2.094442 TCGAATGATTGTCAGCACGGTA 60.094 45.455 0.00 0.00 0.00 4.02
3554 4161 7.442364 ACTGATAACTTGGATTATCATCAACCG 59.558 37.037 8.28 0.60 45.84 4.44
3670 4277 5.814705 CACAAAGATAAAAGTTGGTTTGGCA 59.185 36.000 0.00 0.00 30.75 4.92
3675 4282 1.178276 AAAGTTGGTTTGGCACGTGA 58.822 45.000 22.23 0.00 0.00 4.35
3686 4293 1.293924 GGCACGTGAGGAAGATGATG 58.706 55.000 22.23 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 9.737427 TTCTCTAAGCTTTTCGATAAGTGATAG 57.263 33.333 15.62 14.15 0.00 2.08
86 87 9.517609 GTTCTCTAAGCTTTTCGATAAGTGATA 57.482 33.333 15.62 7.06 0.00 2.15
89 90 6.237595 CCGTTCTCTAAGCTTTTCGATAAGTG 60.238 42.308 15.62 0.00 0.00 3.16
90 91 5.805994 CCGTTCTCTAAGCTTTTCGATAAGT 59.194 40.000 15.62 1.53 0.00 2.24
91 92 6.020520 GTCCGTTCTCTAAGCTTTTCGATAAG 60.021 42.308 3.20 10.85 0.00 1.73
93 94 5.338365 GTCCGTTCTCTAAGCTTTTCGATA 58.662 41.667 3.20 0.00 0.00 2.92
94 95 4.174762 GTCCGTTCTCTAAGCTTTTCGAT 58.825 43.478 3.20 0.00 0.00 3.59
95 96 3.572584 GTCCGTTCTCTAAGCTTTTCGA 58.427 45.455 3.20 0.00 0.00 3.71
96 97 2.341760 CGTCCGTTCTCTAAGCTTTTCG 59.658 50.000 3.20 1.26 0.00 3.46
114 115 2.966516 AGGAGATTATGGGGAGAACGTC 59.033 50.000 0.00 0.00 0.00 4.34
123 124 2.755655 AGTCGCGATAGGAGATTATGGG 59.244 50.000 14.06 0.00 0.00 4.00
138 139 2.594962 AACGTTGCAGGAAGTCGCG 61.595 57.895 0.00 0.00 0.00 5.87
158 159 1.282248 CGTGGGGCGTCTATATTGCG 61.282 60.000 0.00 0.00 35.54 4.85
184 185 9.263538 AGATAAATAAATAATGAACGTACGCCA 57.736 29.630 16.72 14.17 0.00 5.69
214 215 1.732259 CATGCACCTCGTGTAAAGGAC 59.268 52.381 0.00 0.00 37.35 3.85
271 276 7.394077 CCATGTATGTGGATGCAAGGAATTATA 59.606 37.037 0.00 0.00 42.02 0.98
282 287 9.593134 TTTAAAATAAACCATGTATGTGGATGC 57.407 29.630 0.00 0.00 42.02 3.91
318 326 1.136085 CGTCACACGTGCCATAAAAGG 60.136 52.381 17.22 0.00 36.74 3.11
322 330 2.030401 GCCGTCACACGTGCCATAA 61.030 57.895 17.22 0.00 40.58 1.90
323 331 2.433491 GCCGTCACACGTGCCATA 60.433 61.111 17.22 0.00 40.58 2.74
372 412 8.870879 CCATTTGTAACGTAAAAGGAACAAAAA 58.129 29.630 2.94 0.00 39.45 1.94
373 413 8.033626 ACCATTTGTAACGTAAAAGGAACAAAA 58.966 29.630 9.81 0.00 39.45 2.44
374 414 7.488471 CACCATTTGTAACGTAAAAGGAACAAA 59.512 33.333 9.81 8.48 40.07 2.83
375 415 6.973474 CACCATTTGTAACGTAAAAGGAACAA 59.027 34.615 9.81 1.08 32.02 2.83
376 416 6.496571 CACCATTTGTAACGTAAAAGGAACA 58.503 36.000 9.81 0.00 32.02 3.18
377 417 5.400188 GCACCATTTGTAACGTAAAAGGAAC 59.600 40.000 9.81 0.00 32.02 3.62
378 418 5.299782 AGCACCATTTGTAACGTAAAAGGAA 59.700 36.000 9.81 0.00 32.02 3.36
379 419 4.822896 AGCACCATTTGTAACGTAAAAGGA 59.177 37.500 9.81 0.00 32.02 3.36
380 420 5.116069 AGCACCATTTGTAACGTAAAAGG 57.884 39.130 2.77 2.77 33.39 3.11
381 421 7.357303 AGTTAGCACCATTTGTAACGTAAAAG 58.643 34.615 0.00 0.00 31.90 2.27
382 422 7.261829 AGTTAGCACCATTTGTAACGTAAAA 57.738 32.000 0.00 0.00 31.90 1.52
383 423 6.864360 AGTTAGCACCATTTGTAACGTAAA 57.136 33.333 0.00 0.00 31.90 2.01
384 424 6.864360 AAGTTAGCACCATTTGTAACGTAA 57.136 33.333 0.00 0.00 31.90 3.18
385 425 7.585286 CTAAGTTAGCACCATTTGTAACGTA 57.415 36.000 0.00 0.00 31.90 3.57
386 426 6.476243 CTAAGTTAGCACCATTTGTAACGT 57.524 37.500 0.00 0.00 31.90 3.99
422 462 3.681417 ACGGCATCGATCATCATACAATG 59.319 43.478 0.00 0.00 40.11 2.82
430 470 1.143305 CTTCCACGGCATCGATCATC 58.857 55.000 0.00 0.00 40.11 2.92
431 471 0.752658 TCTTCCACGGCATCGATCAT 59.247 50.000 0.00 0.00 40.11 2.45
432 472 0.103026 CTCTTCCACGGCATCGATCA 59.897 55.000 0.00 0.00 40.11 2.92
433 473 0.385751 TCTCTTCCACGGCATCGATC 59.614 55.000 0.00 0.00 40.11 3.69
441 486 6.816640 TGTTTTTGTCTATATCTCTTCCACGG 59.183 38.462 0.00 0.00 0.00 4.94
497 542 7.601886 TCTTGTCTTTCAACTGAAGAGATCATC 59.398 37.037 0.00 0.00 35.21 2.92
498 543 7.387397 GTCTTGTCTTTCAACTGAAGAGATCAT 59.613 37.037 0.00 0.00 35.21 2.45
499 544 6.703607 GTCTTGTCTTTCAACTGAAGAGATCA 59.296 38.462 0.00 0.00 35.21 2.92
500 545 6.703607 TGTCTTGTCTTTCAACTGAAGAGATC 59.296 38.462 0.00 0.00 35.21 2.75
501 546 6.586344 TGTCTTGTCTTTCAACTGAAGAGAT 58.414 36.000 0.00 0.00 35.21 2.75
505 550 6.092670 TGAGTTGTCTTGTCTTTCAACTGAAG 59.907 38.462 12.89 0.00 46.51 3.02
506 551 5.937540 TGAGTTGTCTTGTCTTTCAACTGAA 59.062 36.000 12.89 0.00 46.51 3.02
507 552 5.351465 GTGAGTTGTCTTGTCTTTCAACTGA 59.649 40.000 12.89 3.50 46.51 3.41
508 553 5.563842 GTGAGTTGTCTTGTCTTTCAACTG 58.436 41.667 12.89 0.00 46.51 3.16
510 555 4.092968 ACGTGAGTTGTCTTGTCTTTCAAC 59.907 41.667 0.00 0.00 46.40 3.18
511 556 4.250464 ACGTGAGTTGTCTTGTCTTTCAA 58.750 39.130 0.00 0.00 46.40 2.69
527 572 4.366586 AGCATCTCATACAATGACGTGAG 58.633 43.478 0.00 7.55 39.47 3.51
541 586 7.568349 AGATGTAATGAAAAGGTAGCATCTCA 58.432 34.615 0.00 0.00 37.77 3.27
614 659 3.879295 AGGCATGTACAAGTATGTGATGC 59.121 43.478 0.00 14.50 46.13 3.91
616 661 4.883585 CCAAGGCATGTACAAGTATGTGAT 59.116 41.667 0.00 0.00 40.84 3.06
624 669 1.137404 GCGCCAAGGCATGTACAAG 59.863 57.895 12.19 0.00 42.06 3.16
629 674 1.312371 ATTAACGCGCCAAGGCATGT 61.312 50.000 5.73 5.65 42.06 3.21
630 675 0.179140 AATTAACGCGCCAAGGCATG 60.179 50.000 5.73 4.98 42.06 4.06
632 677 1.211449 CAATTAACGCGCCAAGGCA 59.789 52.632 5.73 0.00 42.06 4.75
639 684 4.956184 GTCATCTAGAAACAATTAACGCGC 59.044 41.667 5.73 0.00 0.00 6.86
640 685 5.952064 GTGTCATCTAGAAACAATTAACGCG 59.048 40.000 3.53 3.53 34.40 6.01
649 702 3.005050 ACGTTCCGTGTCATCTAGAAACA 59.995 43.478 0.00 1.55 39.18 2.83
650 703 3.572584 ACGTTCCGTGTCATCTAGAAAC 58.427 45.455 0.00 0.00 39.18 2.78
661 714 4.479619 GTGTTCTCTTATACGTTCCGTGT 58.520 43.478 0.00 0.00 41.39 4.49
685 738 2.775960 TCAGATCAGGGCATGACAAGAT 59.224 45.455 3.00 2.21 41.91 2.40
704 757 9.159364 GCACAAGCATCTAAATATCTCATATCA 57.841 33.333 0.00 0.00 41.58 2.15
716 770 4.819088 TGTACAACAGCACAAGCATCTAAA 59.181 37.500 0.00 0.00 45.49 1.85
737 791 0.898789 CCCTACGTGACTCCCAGTGT 60.899 60.000 0.00 0.00 0.00 3.55
783 837 9.102757 CGTTGTTAGTACCTAATACTCACTCTA 57.897 37.037 0.00 0.00 43.47 2.43
784 838 7.414984 GCGTTGTTAGTACCTAATACTCACTCT 60.415 40.741 0.00 0.00 43.47 3.24
785 839 6.690528 GCGTTGTTAGTACCTAATACTCACTC 59.309 42.308 0.00 0.00 43.47 3.51
786 840 6.405176 GGCGTTGTTAGTACCTAATACTCACT 60.405 42.308 0.00 0.00 43.47 3.41
787 841 5.745769 GGCGTTGTTAGTACCTAATACTCAC 59.254 44.000 0.00 0.00 43.47 3.51
788 842 5.653769 AGGCGTTGTTAGTACCTAATACTCA 59.346 40.000 0.00 0.00 43.47 3.41
789 843 5.975939 CAGGCGTTGTTAGTACCTAATACTC 59.024 44.000 0.00 0.00 43.47 2.59
790 844 5.680665 GCAGGCGTTGTTAGTACCTAATACT 60.681 44.000 0.00 0.00 46.39 2.12
791 845 4.505556 GCAGGCGTTGTTAGTACCTAATAC 59.494 45.833 0.00 0.00 0.00 1.89
792 846 4.160065 TGCAGGCGTTGTTAGTACCTAATA 59.840 41.667 0.00 0.00 0.00 0.98
793 847 3.055675 TGCAGGCGTTGTTAGTACCTAAT 60.056 43.478 0.00 0.00 0.00 1.73
794 848 2.299582 TGCAGGCGTTGTTAGTACCTAA 59.700 45.455 0.00 0.00 0.00 2.69
798 852 1.202031 GCATGCAGGCGTTGTTAGTAC 60.202 52.381 14.21 0.00 0.00 2.73
801 855 0.179181 CTGCATGCAGGCGTTGTTAG 60.179 55.000 35.39 10.64 40.17 2.34
823 877 6.560003 TGCTCCATTCTGAGGAATAACTAA 57.440 37.500 0.00 0.00 39.87 2.24
848 1315 0.613777 AAAAGCCCCCTAGACTGTCG 59.386 55.000 1.52 0.00 0.00 4.35
858 1325 0.881796 CTTCACGAGAAAAAGCCCCC 59.118 55.000 0.00 0.00 32.35 5.40
867 1334 3.056536 CAGAGATGGAACCTTCACGAGAA 60.057 47.826 8.94 0.00 0.00 2.87
897 1364 3.008049 CCTATTTATAGGCCAGCCTCGTT 59.992 47.826 16.01 4.23 44.43 3.85
928 1395 0.175760 GTTGGCGAGGATGAGCAGTA 59.824 55.000 0.00 0.00 34.54 2.74
931 1398 2.244117 GAGGTTGGCGAGGATGAGCA 62.244 60.000 0.00 0.00 34.54 4.26
933 1400 1.227089 CGAGGTTGGCGAGGATGAG 60.227 63.158 0.00 0.00 0.00 2.90
980 1447 1.478510 TCGAGCTCCACAGATTCTTCC 59.521 52.381 8.47 0.00 0.00 3.46
997 1464 2.060383 CCCTCCTGCTGTCCATCGA 61.060 63.158 0.00 0.00 0.00 3.59
1011 1478 3.519930 GTCTCCGCGGACTCCCTC 61.520 72.222 27.28 7.21 33.81 4.30
1069 1536 6.315912 AACTGGGGTTATCAACGAAGTTAGC 61.316 44.000 0.00 0.00 40.92 3.09
1073 1540 3.782656 AACTGGGGTTATCAACGAAGT 57.217 42.857 0.00 0.00 36.46 3.01
1074 1541 5.704053 ACTTAAACTGGGGTTATCAACGAAG 59.296 40.000 0.00 0.00 34.90 3.79
1075 1542 5.623169 ACTTAAACTGGGGTTATCAACGAA 58.377 37.500 0.00 0.00 34.90 3.85
1076 1543 5.231702 ACTTAAACTGGGGTTATCAACGA 57.768 39.130 0.00 0.00 34.90 3.85
1078 1545 5.182570 GTGGACTTAAACTGGGGTTATCAAC 59.817 44.000 0.00 0.00 34.90 3.18
1080 1547 4.600111 AGTGGACTTAAACTGGGGTTATCA 59.400 41.667 0.00 0.00 34.90 2.15
1081 1548 5.175388 AGTGGACTTAAACTGGGGTTATC 57.825 43.478 0.00 0.00 34.90 1.75
1082 1549 5.594199 AAGTGGACTTAAACTGGGGTTAT 57.406 39.130 0.00 0.00 34.90 1.89
1083 1550 5.379187 GAAAGTGGACTTAAACTGGGGTTA 58.621 41.667 0.00 0.00 34.61 2.85
1085 1552 3.746432 CGAAAGTGGACTTAAACTGGGGT 60.746 47.826 0.00 0.00 34.61 4.95
1086 1553 2.812011 CGAAAGTGGACTTAAACTGGGG 59.188 50.000 0.00 0.00 34.61 4.96
1087 1554 3.735591 TCGAAAGTGGACTTAAACTGGG 58.264 45.455 0.00 0.00 34.61 4.45
1088 1555 4.378459 GCATCGAAAGTGGACTTAAACTGG 60.378 45.833 0.00 0.00 34.61 4.00
1090 1557 4.642429 AGCATCGAAAGTGGACTTAAACT 58.358 39.130 0.00 0.00 34.61 2.66
1092 1559 4.320202 GCAAGCATCGAAAGTGGACTTAAA 60.320 41.667 0.00 0.00 34.61 1.52
1093 1560 3.188460 GCAAGCATCGAAAGTGGACTTAA 59.812 43.478 0.00 0.00 34.61 1.85
1094 1561 2.742053 GCAAGCATCGAAAGTGGACTTA 59.258 45.455 0.00 0.00 34.61 2.24
1095 1562 1.537202 GCAAGCATCGAAAGTGGACTT 59.463 47.619 0.00 0.00 37.91 3.01
1098 1565 0.036732 AGGCAAGCATCGAAAGTGGA 59.963 50.000 0.00 0.00 0.00 4.02
1101 1568 2.744202 CAGTTAGGCAAGCATCGAAAGT 59.256 45.455 0.00 0.00 0.00 2.66
1102 1569 3.002791 TCAGTTAGGCAAGCATCGAAAG 58.997 45.455 0.00 0.00 0.00 2.62
1103 1570 3.052455 TCAGTTAGGCAAGCATCGAAA 57.948 42.857 0.00 0.00 0.00 3.46
1104 1571 2.760634 TCAGTTAGGCAAGCATCGAA 57.239 45.000 0.00 0.00 0.00 3.71
1105 1572 2.621338 CTTCAGTTAGGCAAGCATCGA 58.379 47.619 0.00 0.00 0.00 3.59
1106 1573 1.063174 GCTTCAGTTAGGCAAGCATCG 59.937 52.381 0.63 0.00 41.87 3.84
1107 1574 2.086869 TGCTTCAGTTAGGCAAGCATC 58.913 47.619 3.82 0.00 45.91 3.91
1108 1575 2.205022 TGCTTCAGTTAGGCAAGCAT 57.795 45.000 3.82 0.00 45.91 3.79
1312 1825 5.221322 TGTTTGCAGCTAGAGATCGATATGT 60.221 40.000 0.00 0.00 0.00 2.29
1315 1828 4.918810 TGTTTGCAGCTAGAGATCGATA 57.081 40.909 0.00 0.00 0.00 2.92
1316 1829 3.808466 TGTTTGCAGCTAGAGATCGAT 57.192 42.857 0.00 0.00 0.00 3.59
1317 1830 3.382865 AGATGTTTGCAGCTAGAGATCGA 59.617 43.478 0.00 0.00 39.90 3.59
1318 1831 3.715495 AGATGTTTGCAGCTAGAGATCG 58.285 45.455 0.00 0.00 39.90 3.69
1319 1832 4.947645 AGAGATGTTTGCAGCTAGAGATC 58.052 43.478 0.00 0.00 42.00 2.75
1340 1869 2.806818 CTGCTGTTGATGCCATAGCTAG 59.193 50.000 0.00 0.00 40.80 3.42
1375 1908 3.176552 AGATCAAGATCACAAGGAGCG 57.823 47.619 12.21 0.00 40.22 5.03
1399 1996 1.678970 GGGCAGCGGACCTTCATTT 60.679 57.895 0.00 0.00 40.08 2.32
1486 2083 3.545574 TGATATCTGGCGGCGGCA 61.546 61.111 33.97 33.97 42.47 5.69
1544 2141 4.494690 CGATTGAACGGAATGGAGAACATG 60.495 45.833 0.00 0.00 40.44 3.21
1555 2152 0.322098 ATGGTGGCGATTGAACGGAA 60.322 50.000 0.00 0.00 0.00 4.30
1627 2224 1.396301 CTGCTCTCTCGCCAACATTTC 59.604 52.381 0.00 0.00 0.00 2.17
1636 2233 2.575694 TCTGATTTCTGCTCTCTCGC 57.424 50.000 0.00 0.00 0.00 5.03
1637 2234 4.741185 CAGATTCTGATTTCTGCTCTCTCG 59.259 45.833 8.00 0.00 33.56 4.04
1639 2236 5.936187 TCAGATTCTGATTTCTGCTCTCT 57.064 39.130 12.38 0.00 39.36 3.10
1657 2254 3.268072 TGAGGGAGAAGAGAGACATCAGA 59.732 47.826 0.00 0.00 0.00 3.27
1665 2262 5.482163 AAAAGAAGTGAGGGAGAAGAGAG 57.518 43.478 0.00 0.00 0.00 3.20
1769 2372 2.031012 CTTGCGCAGAGGTCCACA 59.969 61.111 11.31 0.00 0.00 4.17
1870 2473 3.591527 ACTGGTAATGGATTCCAAGGTGA 59.408 43.478 9.98 0.00 36.95 4.02
1906 2509 9.159254 ACAATCCATCTAGTTGATCCTTGTATA 57.841 33.333 2.20 0.00 31.71 1.47
1908 2511 7.437713 ACAATCCATCTAGTTGATCCTTGTA 57.562 36.000 2.20 0.00 31.71 2.41
1909 2512 6.319048 ACAATCCATCTAGTTGATCCTTGT 57.681 37.500 2.20 4.16 32.05 3.16
1913 2516 7.554118 TCAGAAAACAATCCATCTAGTTGATCC 59.446 37.037 2.20 0.00 32.05 3.36
1952 2555 1.831580 AGAGCCAAATGGTCAGCTTC 58.168 50.000 0.71 0.00 44.10 3.86
1985 2588 0.263765 ACTCGGGCCTTATCCCAGTA 59.736 55.000 0.84 0.00 46.92 2.74
2015 2618 1.755959 ACAAGTTTCAGTGGCATTGCA 59.244 42.857 11.39 0.00 0.00 4.08
2165 2768 3.144506 CCTGATCATGAATGCTGGGTAC 58.855 50.000 0.00 0.00 0.00 3.34
2223 2826 4.688413 CGAGGCAATTAAGGAAGAGATAGC 59.312 45.833 0.00 0.00 0.00 2.97
2269 2873 4.133820 CCTGCACGTCCATGGATAAATTA 58.866 43.478 19.62 2.67 0.00 1.40
2728 3335 0.179004 AAACCAACATCAGTCGGCCA 60.179 50.000 2.24 0.00 0.00 5.36
2770 3377 9.494271 AAGATAATTAGACATACGTAGTCGGTA 57.506 33.333 15.04 8.37 43.93 4.02
2771 3378 7.976135 AGATAATTAGACATACGTAGTCGGT 57.024 36.000 15.04 5.84 43.93 4.69
2772 3379 9.114965 CAAAGATAATTAGACATACGTAGTCGG 57.885 37.037 15.04 3.22 43.93 4.79
2773 3380 9.114965 CCAAAGATAATTAGACATACGTAGTCG 57.885 37.037 15.04 4.36 43.93 4.18
3065 3672 7.769970 TGCACATACAAGATCATCACTGATTTA 59.230 33.333 0.00 0.00 42.27 1.40
3110 3717 6.640907 CCCTTAAAGTTTAGTGACACAAATGC 59.359 38.462 8.59 0.00 0.00 3.56
3153 3760 2.031516 CCAAGCAGGCAGAGACACG 61.032 63.158 0.00 0.00 0.00 4.49
3158 3765 2.045536 GACCCCAAGCAGGCAGAG 60.046 66.667 0.00 0.00 35.39 3.35
3245 3852 6.550854 TCAAGAATGACTTTGGGACAGATTTT 59.449 34.615 0.00 0.00 42.39 1.82
3551 4158 3.764237 AGATGTGTTTGGAGTTACGGT 57.236 42.857 0.00 0.00 0.00 4.83
3554 4161 7.544915 GTCCTAGTTAGATGTGTTTGGAGTTAC 59.455 40.741 0.00 0.00 0.00 2.50
3670 4277 3.259374 ACACTTCATCATCTTCCTCACGT 59.741 43.478 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.