Multiple sequence alignment - TraesCS3A01G007000

Loading Multiple Alignment...

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 TraesCS3A01G007000 chr3A 100.000 2504 0 0 1 2504 7433761 7431258 0.000000e+00 4625.0
1 TraesCS3A01G007000 chr3A 89.693 553 49 5 1955 2504 7355177 7355724 0.000000e+00 699.0
2 TraesCS3A01G007000 chr3D 95.038 524 26 0 994 1517 1602972 1602449 0.000000e+00 824.0
3 TraesCS3A01G007000 chr3D 82.335 968 106 35 21 950 1603921 1602981 0.000000e+00 780.0
4 TraesCS3A01G007000 chr3B 84.320 676 69 18 995 1639 5207218 5207887 5.880000e-176 627.0
5 TraesCS3A01G007000 chr3B 88.180 533 52 6 995 1516 3629128 3628596 2.110000e-175 625.0
6 TraesCS3A01G007000 chr3B 89.922 387 26 2 2118 2502 4635328 4635703 1.040000e-133 486.0
7 TraesCS3A01G007000 chr3B 89.147 387 29 2 2118 2502 5145330 5144955 1.050000e-128 470.0
8 TraesCS3A01G007000 chr3B 89.031 392 19 8 2118 2504 3736569 3736941 4.880000e-127 464.0
9 TraesCS3A01G007000 chr3B 83.096 491 65 12 374 852 3629736 3629252 4.950000e-117 431.0
10 TraesCS3A01G007000 chr3B 91.209 273 24 0 2232 2504 4639926 4640198 3.040000e-99 372.0
11 TraesCS3A01G007000 chr3B 91.176 272 23 1 2232 2502 5167144 5166873 3.930000e-98 368.0
12 TraesCS3A01G007000 chr3B 90.602 266 25 0 2239 2504 4647369 4647634 1.100000e-93 353.0
13 TraesCS3A01G007000 chr3B 90.226 266 26 0 2239 2504 3746867 3747132 5.130000e-92 348.0
14 TraesCS3A01G007000 chr3B 81.905 420 58 11 445 852 5206693 5207106 3.090000e-89 339.0
15 TraesCS3A01G007000 chr3B 83.657 361 33 15 1279 1620 4638594 4638947 1.450000e-82 316.0
16 TraesCS3A01G007000 chr3B 82.591 247 11 18 729 943 3731924 3732170 3.290000e-44 189.0
17 TraesCS3A01G007000 chr3B 84.694 196 20 9 1970 2162 5151731 5151543 1.180000e-43 187.0
18 TraesCS3A01G007000 chr3B 97.619 42 1 0 1933 1974 3735372 3735413 3.450000e-09 73.1
19 TraesCS3A01G007000 chrUn 84.184 196 21 9 1970 2162 284572175 284571987 5.500000e-42 182.0
20 TraesCS3A01G007000 chr7D 78.723 235 40 8 2275 2504 20618661 20618432 5.580000e-32 148.0
21 TraesCS3A01G007000 chr7D 80.612 98 13 5 21 116 576099803 576099896 1.240000e-08 71.3
22 TraesCS3A01G007000 chr6D 77.165 127 22 5 153 273 454220348 454220473 1.610000e-07 67.6


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 TraesCS3A01G007000 chr3A 7431258 7433761 2503 True 4625.000000 4625 100.000000 1 2504 1 chr3A.!!$R1 2503
1 TraesCS3A01G007000 chr3A 7355177 7355724 547 False 699.000000 699 89.693000 1955 2504 1 chr3A.!!$F1 549
2 TraesCS3A01G007000 chr3D 1602449 1603921 1472 True 802.000000 824 88.686500 21 1517 2 chr3D.!!$R1 1496
3 TraesCS3A01G007000 chr3B 3628596 3629736 1140 True 528.000000 625 85.638000 374 1516 2 chr3B.!!$R4 1142
4 TraesCS3A01G007000 chr3B 5206693 5207887 1194 False 483.000000 627 83.112500 445 1639 2 chr3B.!!$F5 1194
5 TraesCS3A01G007000 chr3B 4635328 4640198 4870 False 391.333333 486 88.262667 1279 2504 3 chr3B.!!$F4 1225
6 TraesCS3A01G007000 chr3B 3731924 3736941 5017 False 242.033333 464 89.747000 729 2504 3 chr3B.!!$F3 1775

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
985 1068 0.033504 TCATAAATCGGCGAGCTCCC 59.966 55.0 17.22 9.59 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 7989 0.939577 TGCTTGAAGCGACGTGTCTC 60.94 55.0 13.05 0.0 46.26 3.36 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
30 31 6.676950 TGTTCTGTATAACAAAACTGCCATG 58.323 36.000 0.00 0.00 36.45 3.66
39 40 5.280654 ACAAAACTGCCATGTGAGAAATT 57.719 34.783 0.00 0.00 0.00 1.82
71 72 7.670009 TTTCCAAAATTGCCATGAATAAGTG 57.330 32.000 0.00 0.00 0.00 3.16
81 82 8.459521 TTGCCATGAATAAGTGAAAAATTACG 57.540 30.769 0.00 0.00 0.00 3.18
82 83 7.032580 TGCCATGAATAAGTGAAAAATTACGG 58.967 34.615 0.00 0.00 0.00 4.02
118 119 4.213270 GGCCATTGCAAAAAGACCTAAAAC 59.787 41.667 1.71 0.00 40.13 2.43
122 123 6.421405 CATTGCAAAAAGACCTAAAACTTGC 58.579 36.000 1.71 0.00 38.48 4.01
203 205 8.420222 CCACCTATAATTAAAAATGCATGTGGA 58.580 33.333 15.28 0.00 39.39 4.02
211 213 8.674263 ATTAAAAATGCATGTGGAAAGTTTCA 57.326 26.923 17.16 0.00 0.00 2.69
212 214 5.989551 AAAATGCATGTGGAAAGTTTCAC 57.010 34.783 17.16 12.91 34.71 3.18
217 219 4.629200 TGCATGTGGAAAGTTTCACAAAAC 59.371 37.500 17.16 12.05 45.39 2.43
344 348 5.897377 AAATACATACAGCAGTTTGGTCC 57.103 39.130 4.83 0.00 31.88 4.46
366 370 4.343814 CCCAAATGTTCACAAAACCCTACT 59.656 41.667 0.00 0.00 0.00 2.57
370 374 6.783708 AATGTTCACAAAACCCTACTTCAA 57.216 33.333 0.00 0.00 0.00 2.69
382 386 4.081807 ACCCTACTTCAATCGAGTGGTAAC 60.082 45.833 13.59 0.00 0.00 2.50
392 396 2.559668 TCGAGTGGTAACTGGTAAGTGG 59.440 50.000 0.00 0.00 36.52 4.00
397 401 1.339727 GGTAACTGGTAAGTGGCCCTG 60.340 57.143 0.00 0.00 36.51 4.45
448 452 3.883744 CTCCTCGCGCACCTTGGTT 62.884 63.158 8.75 0.00 0.00 3.67
483 487 5.468746 TGGAGAGAAAAACATAAGGAACGTG 59.531 40.000 0.00 0.00 0.00 4.49
524 528 2.747989 ACGAACGACTTCAGCTGATCTA 59.252 45.455 19.04 1.11 0.00 1.98
533 537 3.582714 TCAGCTGATCTATACATGGCG 57.417 47.619 13.74 0.00 0.00 5.69
561 565 2.034879 CGCCAAGATCCGTGCAACT 61.035 57.895 0.00 0.00 31.75 3.16
565 569 1.301716 AAGATCCGTGCAACTGCGT 60.302 52.632 0.00 0.00 45.83 5.24
566 570 0.884704 AAGATCCGTGCAACTGCGTT 60.885 50.000 0.00 0.00 45.83 4.84
576 581 1.717429 GCAACTGCGTTAAGTCGTTCG 60.717 52.381 0.00 0.00 0.00 3.95
579 584 4.999550 GCGTTAAGTCGTTCGCTG 57.000 55.556 0.00 0.00 44.28 5.18
603 608 4.699522 GCTCCCTGGCCGACGTTT 62.700 66.667 0.00 0.00 0.00 3.60
606 611 2.593436 CCCTGGCCGACGTTTGTT 60.593 61.111 0.00 0.00 0.00 2.83
636 643 3.068881 CGAAGGAGGAACAGGGCA 58.931 61.111 0.00 0.00 0.00 5.36
637 644 1.374947 CGAAGGAGGAACAGGGCAA 59.625 57.895 0.00 0.00 0.00 4.52
638 645 0.674895 CGAAGGAGGAACAGGGCAAG 60.675 60.000 0.00 0.00 0.00 4.01
639 646 0.962855 GAAGGAGGAACAGGGCAAGC 60.963 60.000 0.00 0.00 0.00 4.01
642 667 1.034292 GGAGGAACAGGGCAAGCATC 61.034 60.000 0.00 0.00 0.00 3.91
932 1007 1.750206 TGCTCTCAGTGATCTCTCTGC 59.250 52.381 0.00 0.00 37.38 4.26
959 1042 0.997932 CTTGCAAGCTCAGCGAGTAG 59.002 55.000 14.65 4.79 38.44 2.57
971 1054 2.486951 GCGAGTAGCCGTCTTCATAA 57.513 50.000 0.00 0.00 40.81 1.90
972 1055 2.805845 GCGAGTAGCCGTCTTCATAAA 58.194 47.619 0.00 0.00 40.81 1.40
974 1057 3.425858 GCGAGTAGCCGTCTTCATAAATC 59.574 47.826 0.00 0.00 40.81 2.17
975 1058 3.664486 CGAGTAGCCGTCTTCATAAATCG 59.336 47.826 0.00 0.00 0.00 3.34
976 1059 3.978687 AGTAGCCGTCTTCATAAATCGG 58.021 45.455 0.00 0.00 43.37 4.18
979 1062 1.847818 CCGTCTTCATAAATCGGCGA 58.152 50.000 13.87 13.87 35.01 5.54
980 1063 1.787155 CCGTCTTCATAAATCGGCGAG 59.213 52.381 17.22 0.43 35.01 5.03
981 1064 1.190323 CGTCTTCATAAATCGGCGAGC 59.810 52.381 17.22 0.00 0.00 5.03
982 1065 2.474816 GTCTTCATAAATCGGCGAGCT 58.525 47.619 17.22 7.28 0.00 4.09
985 1068 0.033504 TCATAAATCGGCGAGCTCCC 59.966 55.000 17.22 9.59 0.00 4.30
986 1069 1.006102 ATAAATCGGCGAGCTCCCG 60.006 57.895 27.82 27.82 46.88 5.14
987 1070 2.436087 ATAAATCGGCGAGCTCCCGG 62.436 60.000 30.73 18.44 45.60 5.73
1026 1295 3.080121 CTCCCCCTCTTCGCTGCT 61.080 66.667 0.00 0.00 0.00 4.24
1071 1340 1.289380 GGCGACTCTCGTCCTTGTT 59.711 57.895 0.00 0.00 42.81 2.83
1500 3498 1.566018 CCGACGTCCAAGCCAAGAAC 61.566 60.000 10.58 0.00 0.00 3.01
1509 3509 3.751175 TCCAAGCCAAGAACTAATCAACG 59.249 43.478 0.00 0.00 0.00 4.10
1533 3544 0.947244 GATCACCGGTGGATTGATGC 59.053 55.000 33.40 10.77 29.93 3.91
1539 3550 2.325857 GTGGATTGATGCTCGCGC 59.674 61.111 0.00 0.00 0.00 6.86
1540 3551 3.264159 TGGATTGATGCTCGCGCG 61.264 61.111 26.76 26.76 39.65 6.86
1541 3552 4.656558 GGATTGATGCTCGCGCGC 62.657 66.667 27.95 23.91 39.65 6.86
1542 3553 4.982838 GATTGATGCTCGCGCGCG 62.983 66.667 44.84 44.84 39.65 6.86
1570 3584 1.504359 TCGAATCAAGTCGCCGTTTT 58.496 45.000 0.00 0.00 40.88 2.43
1589 3605 2.704725 TTTCTGCTCGATTTTGGTGC 57.295 45.000 0.00 0.00 0.00 5.01
1592 3608 2.574212 GCTCGATTTTGGTGCGCG 60.574 61.111 0.00 0.00 0.00 6.86
1594 3610 1.509787 CTCGATTTTGGTGCGCGTG 60.510 57.895 8.43 0.00 0.00 5.34
1595 3611 2.170260 CTCGATTTTGGTGCGCGTGT 62.170 55.000 8.43 0.00 0.00 4.49
1596 3612 0.944788 TCGATTTTGGTGCGCGTGTA 60.945 50.000 8.43 0.00 0.00 2.90
1597 3613 0.787908 CGATTTTGGTGCGCGTGTAC 60.788 55.000 8.43 8.84 0.00 2.90
1622 3642 3.342627 CGCGACGGCAAAGGTTGA 61.343 61.111 0.00 0.00 39.92 3.18
1623 3643 2.251371 GCGACGGCAAAGGTTGAC 59.749 61.111 0.00 0.00 39.62 3.18
1640 3662 2.947621 CGACGCGTCCGGTGTATG 60.948 66.667 31.84 12.61 40.09 2.39
1641 3663 2.486504 GACGCGTCCGGTGTATGA 59.513 61.111 28.61 0.00 40.09 2.15
1642 3664 1.870901 GACGCGTCCGGTGTATGAC 60.871 63.158 28.61 0.00 40.09 3.06
1643 3665 2.581409 CGCGTCCGGTGTATGACC 60.581 66.667 0.00 0.00 42.07 4.02
1653 3675 3.795623 GGTGTATGACCGTACATCAGT 57.204 47.619 7.55 0.00 36.06 3.41
1654 3676 3.703420 GGTGTATGACCGTACATCAGTC 58.297 50.000 7.55 0.34 36.06 3.51
1657 3679 4.095932 GTGTATGACCGTACATCAGTCAGA 59.904 45.833 5.50 4.17 43.30 3.27
1658 3680 4.887655 TGTATGACCGTACATCAGTCAGAT 59.112 41.667 9.85 0.01 43.30 2.90
1666 3688 2.573941 CATCAGTCAGATGCGACAGA 57.426 50.000 0.00 0.00 46.90 3.41
1667 3689 2.461903 CATCAGTCAGATGCGACAGAG 58.538 52.381 0.00 0.00 46.90 3.35
1668 3690 0.172127 TCAGTCAGATGCGACAGAGC 59.828 55.000 0.00 0.00 38.43 4.09
1669 3691 1.138459 AGTCAGATGCGACAGAGCG 59.862 57.895 0.00 0.00 40.67 5.03
1670 3692 1.153939 GTCAGATGCGACAGAGCGT 60.154 57.895 0.00 0.00 40.67 5.07
1671 3693 0.098905 GTCAGATGCGACAGAGCGTA 59.901 55.000 0.00 0.00 40.67 4.42
1672 3694 0.378610 TCAGATGCGACAGAGCGTAG 59.621 55.000 0.00 0.00 40.67 3.51
1673 3695 0.099613 CAGATGCGACAGAGCGTAGT 59.900 55.000 0.00 0.00 40.67 2.73
1674 3696 1.330829 CAGATGCGACAGAGCGTAGTA 59.669 52.381 0.00 0.00 40.67 1.82
1675 3697 1.331138 AGATGCGACAGAGCGTAGTAC 59.669 52.381 0.00 0.00 40.67 2.73
1676 3698 1.063616 GATGCGACAGAGCGTAGTACA 59.936 52.381 0.38 0.00 40.67 2.90
1677 3699 0.167470 TGCGACAGAGCGTAGTACAC 59.833 55.000 0.38 0.00 40.67 2.90
1678 3700 0.167470 GCGACAGAGCGTAGTACACA 59.833 55.000 0.38 0.00 0.00 3.72
1679 3701 1.879646 CGACAGAGCGTAGTACACAC 58.120 55.000 0.38 0.00 0.00 3.82
1680 3702 1.196127 CGACAGAGCGTAGTACACACA 59.804 52.381 0.38 0.00 0.00 3.72
1681 3703 2.159558 CGACAGAGCGTAGTACACACAT 60.160 50.000 0.38 0.00 0.00 3.21
1682 3704 3.063045 CGACAGAGCGTAGTACACACATA 59.937 47.826 0.38 0.00 0.00 2.29
1683 3705 4.436451 CGACAGAGCGTAGTACACACATAA 60.436 45.833 0.38 0.00 0.00 1.90
1684 3706 4.982999 ACAGAGCGTAGTACACACATAAG 58.017 43.478 0.38 0.00 0.00 1.73
1685 3707 4.458295 ACAGAGCGTAGTACACACATAAGT 59.542 41.667 0.38 0.00 0.00 2.24
1707 3729 7.991084 AGTGTGTAATCAGTGTGTACTACTA 57.009 36.000 0.00 0.00 34.74 1.82
1708 3730 7.814642 AGTGTGTAATCAGTGTGTACTACTAC 58.185 38.462 0.00 0.00 34.74 2.73
1709 3731 7.664731 AGTGTGTAATCAGTGTGTACTACTACT 59.335 37.037 0.00 0.00 34.74 2.57
1710 3732 7.961827 GTGTGTAATCAGTGTGTACTACTACTC 59.038 40.741 0.00 0.00 34.74 2.59
1711 3733 7.662669 TGTGTAATCAGTGTGTACTACTACTCA 59.337 37.037 0.00 0.00 34.74 3.41
1712 3734 8.509690 GTGTAATCAGTGTGTACTACTACTCAA 58.490 37.037 0.00 0.00 34.74 3.02
1713 3735 8.509690 TGTAATCAGTGTGTACTACTACTCAAC 58.490 37.037 0.00 0.00 34.74 3.18
1714 3736 7.762588 AATCAGTGTGTACTACTACTCAACT 57.237 36.000 0.00 0.00 34.74 3.16
1715 3737 6.798315 TCAGTGTGTACTACTACTCAACTC 57.202 41.667 0.00 0.00 34.74 3.01
1717 3739 6.940867 TCAGTGTGTACTACTACTCAACTCAT 59.059 38.462 0.00 0.00 34.74 2.90
1741 4111 6.390721 TGTCGTGTCCATTTTTCTTGAAAAA 58.609 32.000 19.32 19.32 40.40 1.94
1748 4118 9.898152 TGTCCATTTTTCTTGAAAAACCTTAAT 57.102 25.926 19.39 4.47 40.40 1.40
1758 4128 9.965824 TCTTGAAAAACCTTAATGAGATTGTTC 57.034 29.630 0.00 0.00 0.00 3.18
1761 4131 8.792633 TGAAAAACCTTAATGAGATTGTTCGAT 58.207 29.630 0.00 0.00 0.00 3.59
1762 4132 8.970691 AAAAACCTTAATGAGATTGTTCGATG 57.029 30.769 0.00 0.00 0.00 3.84
1766 4136 9.613428 AACCTTAATGAGATTGTTCGATGATAA 57.387 29.630 0.00 0.00 0.00 1.75
1767 4137 9.613428 ACCTTAATGAGATTGTTCGATGATAAA 57.387 29.630 0.00 0.00 0.00 1.40
1768 4138 9.869844 CCTTAATGAGATTGTTCGATGATAAAC 57.130 33.333 0.00 0.00 0.00 2.01
1857 6472 7.170320 AGCTTGCTGTTAACAATGATTCTTTTG 59.830 33.333 10.03 0.00 0.00 2.44
1871 6487 7.435068 TGATTCTTTTGTGTAACTCTTAGCC 57.565 36.000 0.00 0.00 38.04 3.93
1889 6505 8.677148 TCTTAGCCATTGAATCTGGTAATTAC 57.323 34.615 7.09 7.09 36.10 1.89
1891 6507 4.821805 AGCCATTGAATCTGGTAATTACGG 59.178 41.667 9.46 5.38 36.10 4.02
1909 6525 2.620115 ACGGATGGACATGATTGATTGC 59.380 45.455 0.00 0.00 0.00 3.56
1944 6608 6.112734 AGCCGTGTTTTGTGATCTATTATGA 58.887 36.000 0.00 0.00 0.00 2.15
2079 6778 9.270640 GAGTGCTCAAGTTATGATTCTATGATT 57.729 33.333 0.00 0.00 37.44 2.57
2220 7902 6.641314 CACGACAATATATACAGGGTCTTGAC 59.359 42.308 0.00 0.00 29.27 3.18
2236 7918 5.107453 GGTCTTGACAAACTATTCAGACGTG 60.107 44.000 0.00 0.00 0.00 4.49
2307 7989 0.531532 CATCTTCCACTGCTAGCCCG 60.532 60.000 13.29 5.89 0.00 6.13
2348 8030 3.017323 CCGATGAGGTTGATGCGC 58.983 61.111 0.00 0.00 34.51 6.09
2363 8045 3.070302 TGATGCGCTGTTATACCCATGTA 59.930 43.478 9.73 0.00 0.00 2.29
2371 8053 6.517697 CGCTGTTATACCCATGTAATCCAGTA 60.518 42.308 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.410556 GCAGTTTTGTTATACAGAACATTGAAT 57.589 29.630 13.48 0.00 43.27 2.57
1 2 7.865385 GGCAGTTTTGTTATACAGAACATTGAA 59.135 33.333 13.48 0.00 43.27 2.69
2 3 7.013750 TGGCAGTTTTGTTATACAGAACATTGA 59.986 33.333 13.48 0.00 43.27 2.57
3 4 7.144661 TGGCAGTTTTGTTATACAGAACATTG 58.855 34.615 13.48 6.92 43.27 2.82
7 8 6.582295 CACATGGCAGTTTTGTTATACAGAAC 59.418 38.462 0.00 5.39 41.76 3.01
8 9 6.488344 TCACATGGCAGTTTTGTTATACAGAA 59.512 34.615 0.00 0.00 0.00 3.02
9 10 6.000840 TCACATGGCAGTTTTGTTATACAGA 58.999 36.000 0.00 0.00 0.00 3.41
11 12 6.000840 TCTCACATGGCAGTTTTGTTATACA 58.999 36.000 0.00 0.00 0.00 2.29
12 13 6.494893 TCTCACATGGCAGTTTTGTTATAC 57.505 37.500 0.00 0.00 0.00 1.47
13 14 7.517614 TTTCTCACATGGCAGTTTTGTTATA 57.482 32.000 0.00 0.00 0.00 0.98
15 16 5.843673 TTTCTCACATGGCAGTTTTGTTA 57.156 34.783 0.00 0.00 0.00 2.41
16 17 4.734398 TTTCTCACATGGCAGTTTTGTT 57.266 36.364 0.00 0.00 0.00 2.83
17 18 4.942761 ATTTCTCACATGGCAGTTTTGT 57.057 36.364 0.00 0.00 0.00 2.83
56 57 7.543868 CCGTAATTTTTCACTTATTCATGGCAA 59.456 33.333 0.00 0.00 0.00 4.52
57 58 7.032580 CCGTAATTTTTCACTTATTCATGGCA 58.967 34.615 0.00 0.00 0.00 4.92
59 60 9.289303 CTTCCGTAATTTTTCACTTATTCATGG 57.711 33.333 0.00 0.00 0.00 3.66
71 72 5.120053 CCATGGCAAACTTCCGTAATTTTTC 59.880 40.000 0.00 0.00 0.00 2.29
97 98 6.511605 GCAAGTTTTAGGTCTTTTTGCAATGG 60.512 38.462 0.00 0.00 39.25 3.16
118 119 0.109132 GCGTTCCAAATCCTGGCAAG 60.109 55.000 0.00 0.00 45.98 4.01
160 162 7.961326 ATAGGTGGAATAGCAATTTCTTTGT 57.039 32.000 0.00 0.00 37.65 2.83
176 178 8.420222 CCACATGCATTTTTAATTATAGGTGGA 58.580 33.333 15.28 0.00 41.43 4.02
203 205 3.719871 AGAGGGGGTTTTGTGAAACTTT 58.280 40.909 2.51 0.00 43.68 2.66
210 212 6.492087 TCACTATTTTTAGAGGGGGTTTTGTG 59.508 38.462 0.00 0.00 0.00 3.33
211 213 6.616577 TCACTATTTTTAGAGGGGGTTTTGT 58.383 36.000 0.00 0.00 0.00 2.83
212 214 7.718334 ATCACTATTTTTAGAGGGGGTTTTG 57.282 36.000 0.00 0.00 0.00 2.44
316 320 8.856103 ACCAAACTGCTGTATGTATTTTAAAGT 58.144 29.630 0.00 0.00 0.00 2.66
331 335 1.688197 ACATTTGGGACCAAACTGCTG 59.312 47.619 17.99 14.34 46.80 4.41
339 343 3.118592 GGTTTTGTGAACATTTGGGACCA 60.119 43.478 0.00 0.00 0.00 4.02
344 348 5.529581 AGTAGGGTTTTGTGAACATTTGG 57.470 39.130 0.00 0.00 0.00 3.28
366 370 5.011329 ACTTACCAGTTACCACTCGATTGAA 59.989 40.000 4.04 0.00 0.00 2.69
370 374 3.194968 CCACTTACCAGTTACCACTCGAT 59.805 47.826 0.00 0.00 0.00 3.59
402 406 3.362399 CTCACGTCCTCCTGCGCAT 62.362 63.158 12.24 0.00 0.00 4.73
465 469 2.655001 GCGCACGTTCCTTATGTTTTTC 59.345 45.455 0.30 0.00 0.00 2.29
471 475 1.202371 TCCTAGCGCACGTTCCTTATG 60.202 52.381 11.47 0.00 0.00 1.90
472 476 1.108776 TCCTAGCGCACGTTCCTTAT 58.891 50.000 11.47 0.00 0.00 1.73
473 477 0.889994 TTCCTAGCGCACGTTCCTTA 59.110 50.000 11.47 0.00 0.00 2.69
474 478 0.034337 TTTCCTAGCGCACGTTCCTT 59.966 50.000 11.47 0.00 0.00 3.36
476 480 1.785951 GTTTCCTAGCGCACGTTCC 59.214 57.895 11.47 0.00 0.00 3.62
496 500 1.709203 CTGAAGTCGTTCGTTGTCGAG 59.291 52.381 0.00 0.00 46.81 4.04
498 502 0.158928 GCTGAAGTCGTTCGTTGTCG 59.841 55.000 0.00 0.00 35.17 4.35
513 517 2.893489 ACGCCATGTATAGATCAGCTGA 59.107 45.455 20.79 20.79 0.00 4.26
565 569 1.404986 CCATCCCAGCGAACGACTTAA 60.405 52.381 0.00 0.00 0.00 1.85
566 570 0.174845 CCATCCCAGCGAACGACTTA 59.825 55.000 0.00 0.00 0.00 2.24
599 604 7.223971 TCCTTCGGAAATGATATCTAACAAACG 59.776 37.037 3.98 1.09 0.00 3.60
603 608 6.553476 TCCTCCTTCGGAAATGATATCTAACA 59.447 38.462 3.98 0.00 0.00 2.41
606 611 6.553476 TGTTCCTCCTTCGGAAATGATATCTA 59.447 38.462 3.98 0.00 44.19 1.98
627 632 1.648467 GGACGATGCTTGCCCTGTTC 61.648 60.000 0.00 0.00 0.00 3.18
630 637 1.817099 GAGGACGATGCTTGCCCTG 60.817 63.158 0.00 0.00 0.00 4.45
632 639 2.892425 CGAGGACGATGCTTGCCC 60.892 66.667 0.00 0.00 42.66 5.36
633 640 1.298859 AAACGAGGACGATGCTTGCC 61.299 55.000 0.00 0.00 42.66 4.52
634 641 0.179215 CAAACGAGGACGATGCTTGC 60.179 55.000 0.00 0.00 42.66 4.01
635 642 0.443869 CCAAACGAGGACGATGCTTG 59.556 55.000 0.00 0.00 42.66 4.01
636 643 0.034896 ACCAAACGAGGACGATGCTT 59.965 50.000 0.00 0.00 42.66 3.91
637 644 0.389948 GACCAAACGAGGACGATGCT 60.390 55.000 0.00 0.00 42.66 3.79
638 645 0.669318 TGACCAAACGAGGACGATGC 60.669 55.000 0.00 0.00 42.66 3.91
639 646 1.790755 TTGACCAAACGAGGACGATG 58.209 50.000 0.00 0.00 42.66 3.84
668 693 1.063174 CAGCTAATCACCTTTGAGCGC 59.937 52.381 0.00 0.00 34.35 5.92
886 955 2.123854 TAGGAGATGAGCCGCGGT 60.124 61.111 28.70 13.92 0.00 5.68
960 1043 1.787155 CTCGCCGATTTATGAAGACGG 59.213 52.381 12.10 12.10 45.26 4.79
961 1044 1.190323 GCTCGCCGATTTATGAAGACG 59.810 52.381 0.00 0.00 0.00 4.18
962 1045 2.473235 GAGCTCGCCGATTTATGAAGAC 59.527 50.000 0.00 0.00 0.00 3.01
963 1046 2.545952 GGAGCTCGCCGATTTATGAAGA 60.546 50.000 7.83 0.00 0.00 2.87
966 1049 0.033504 GGGAGCTCGCCGATTTATGA 59.966 55.000 19.61 0.00 0.00 2.15
967 1050 1.284982 CGGGAGCTCGCCGATTTATG 61.285 60.000 29.08 10.00 33.48 1.90
968 1051 1.006102 CGGGAGCTCGCCGATTTAT 60.006 57.895 29.08 0.00 33.48 1.40
1026 1295 4.382320 GCTCCGGCGGTGTGGTTA 62.382 66.667 27.32 2.99 0.00 2.85
1071 1340 0.750546 CCACCAGGACGACGAGGATA 60.751 60.000 0.00 0.00 36.89 2.59
1458 3453 2.564721 GGCTTTCTTGCTTGCCGGT 61.565 57.895 1.90 0.00 35.79 5.28
1491 3489 4.246458 GAGACGTTGATTAGTTCTTGGCT 58.754 43.478 0.00 0.00 0.00 4.75
1495 3493 5.800941 GTGATCGAGACGTTGATTAGTTCTT 59.199 40.000 0.00 0.00 0.00 2.52
1500 3498 3.036633 CGGTGATCGAGACGTTGATTAG 58.963 50.000 0.00 0.00 42.43 1.73
1509 3509 0.460311 AATCCACCGGTGATCGAGAC 59.540 55.000 36.07 0.00 42.43 3.36
1545 3556 2.468040 CGGCGACTTGATTCGATTAGTC 59.532 50.000 0.00 0.00 41.78 2.59
1547 3558 2.460918 ACGGCGACTTGATTCGATTAG 58.539 47.619 16.62 0.00 41.78 1.73
1570 3584 1.069296 CGCACCAAAATCGAGCAGAAA 60.069 47.619 0.00 0.00 0.00 2.52
1575 3589 2.574212 CGCGCACCAAAATCGAGC 60.574 61.111 8.75 0.00 0.00 5.03
1622 3642 3.434319 ATACACCGGACGCGTCGT 61.434 61.111 30.99 24.42 45.10 4.34
1623 3643 2.947621 CATACACCGGACGCGTCG 60.948 66.667 30.99 24.59 0.00 5.12
1624 3644 1.870901 GTCATACACCGGACGCGTC 60.871 63.158 30.67 30.67 0.00 5.19
1625 3645 2.180017 GTCATACACCGGACGCGT 59.820 61.111 13.85 13.85 0.00 6.01
1648 3670 1.202394 GCTCTGTCGCATCTGACTGAT 60.202 52.381 4.34 0.00 43.15 2.90
1649 3671 0.172127 GCTCTGTCGCATCTGACTGA 59.828 55.000 3.93 3.93 42.31 3.41
1651 3673 1.138459 CGCTCTGTCGCATCTGACT 59.862 57.895 0.00 0.00 39.64 3.41
1652 3674 0.098905 TACGCTCTGTCGCATCTGAC 59.901 55.000 0.00 0.00 39.37 3.51
1653 3675 0.378610 CTACGCTCTGTCGCATCTGA 59.621 55.000 0.00 0.00 0.00 3.27
1654 3676 0.099613 ACTACGCTCTGTCGCATCTG 59.900 55.000 0.00 0.00 0.00 2.90
1657 3679 1.092348 TGTACTACGCTCTGTCGCAT 58.908 50.000 0.00 0.00 0.00 4.73
1658 3680 0.167470 GTGTACTACGCTCTGTCGCA 59.833 55.000 0.00 0.00 0.00 5.10
1659 3681 0.167470 TGTGTACTACGCTCTGTCGC 59.833 55.000 0.00 0.00 0.00 5.19
1660 3682 1.196127 TGTGTGTACTACGCTCTGTCG 59.804 52.381 0.00 0.00 40.47 4.35
1661 3683 2.983402 TGTGTGTACTACGCTCTGTC 57.017 50.000 0.00 0.00 40.47 3.51
1662 3684 4.458295 ACTTATGTGTGTACTACGCTCTGT 59.542 41.667 0.00 0.00 40.47 3.41
1664 3686 4.982999 CACTTATGTGTGTACTACGCTCT 58.017 43.478 0.62 0.00 40.47 4.09
1677 3699 7.598869 AGTACACACTGATTACACACTTATGTG 59.401 37.037 7.18 7.18 46.92 3.21
1678 3700 7.667557 AGTACACACTGATTACACACTTATGT 58.332 34.615 0.00 0.00 34.34 2.29
1679 3701 9.073368 GTAGTACACACTGATTACACACTTATG 57.927 37.037 0.00 0.00 36.14 1.90
1680 3702 9.021807 AGTAGTACACACTGATTACACACTTAT 57.978 33.333 2.52 0.00 36.14 1.73
1681 3703 8.400184 AGTAGTACACACTGATTACACACTTA 57.600 34.615 2.52 0.00 36.14 2.24
1682 3704 7.286215 AGTAGTACACACTGATTACACACTT 57.714 36.000 2.52 0.00 36.14 3.16
1683 3705 6.896021 AGTAGTACACACTGATTACACACT 57.104 37.500 2.52 0.00 36.14 3.55
1684 3706 7.814642 AGTAGTAGTACACACTGATTACACAC 58.185 38.462 10.33 0.00 36.14 3.82
1685 3707 7.662669 TGAGTAGTAGTACACACTGATTACACA 59.337 37.037 10.33 1.66 36.14 3.72
1686 3708 8.037382 TGAGTAGTAGTACACACTGATTACAC 57.963 38.462 10.33 0.81 36.14 2.90
1687 3709 8.509690 GTTGAGTAGTAGTACACACTGATTACA 58.490 37.037 10.33 2.29 36.14 2.41
1688 3710 8.728833 AGTTGAGTAGTAGTACACACTGATTAC 58.271 37.037 10.33 4.39 36.14 1.89
1689 3711 8.859236 AGTTGAGTAGTAGTACACACTGATTA 57.141 34.615 10.33 0.00 36.14 1.75
1690 3712 7.447545 TGAGTTGAGTAGTAGTACACACTGATT 59.552 37.037 10.33 0.00 36.14 2.57
1696 3718 6.128363 CGACATGAGTTGAGTAGTAGTACACA 60.128 42.308 10.33 7.09 0.00 3.72
1707 3729 1.686587 TGGACACGACATGAGTTGAGT 59.313 47.619 0.00 0.00 35.92 3.41
1708 3730 2.438868 TGGACACGACATGAGTTGAG 57.561 50.000 0.00 0.00 33.15 3.02
1709 3731 3.401033 AATGGACACGACATGAGTTGA 57.599 42.857 0.00 0.00 33.15 3.18
1710 3732 4.488126 AAAATGGACACGACATGAGTTG 57.512 40.909 0.00 0.00 35.14 3.16
1711 3733 4.821805 AGAAAAATGGACACGACATGAGTT 59.178 37.500 0.00 0.00 0.00 3.01
1712 3734 4.389374 AGAAAAATGGACACGACATGAGT 58.611 39.130 0.00 0.00 0.00 3.41
1713 3735 5.049474 TCAAGAAAAATGGACACGACATGAG 60.049 40.000 0.00 0.00 0.00 2.90
1714 3736 4.819088 TCAAGAAAAATGGACACGACATGA 59.181 37.500 0.00 0.00 0.00 3.07
1715 3737 5.107109 TCAAGAAAAATGGACACGACATG 57.893 39.130 0.00 0.00 0.00 3.21
1717 3739 5.568685 TTTCAAGAAAAATGGACACGACA 57.431 34.783 0.00 0.00 0.00 4.35
1741 4111 9.613428 TTTATCATCGAACAATCTCATTAAGGT 57.387 29.630 0.00 0.00 0.00 3.50
1748 4118 9.825972 GAAAAAGTTTATCATCGAACAATCTCA 57.174 29.630 0.00 0.00 0.00 3.27
1767 4137 9.470399 TGTAAGGTCCTTTTAGAAAGAAAAAGT 57.530 29.630 10.04 0.00 40.67 2.66
1780 4150 9.588096 AGAGAAATGTATTTGTAAGGTCCTTTT 57.412 29.630 10.04 0.00 0.00 2.27
1781 4151 9.588096 AAGAGAAATGTATTTGTAAGGTCCTTT 57.412 29.630 10.04 0.00 0.00 3.11
1782 4152 9.014297 CAAGAGAAATGTATTTGTAAGGTCCTT 57.986 33.333 9.62 9.62 0.00 3.36
1800 4192 1.338107 TGTCTCGGGCTCAAGAGAAA 58.662 50.000 0.32 0.00 44.07 2.52
1803 4195 1.066573 ACATTGTCTCGGGCTCAAGAG 60.067 52.381 0.00 0.00 35.91 2.85
1857 6472 6.037610 CCAGATTCAATGGCTAAGAGTTACAC 59.962 42.308 0.00 0.00 0.00 2.90
1871 6487 6.710295 TCCATCCGTAATTACCAGATTCAATG 59.290 38.462 10.01 2.91 0.00 2.82
1889 6505 2.350102 CGCAATCAATCATGTCCATCCG 60.350 50.000 0.00 0.00 0.00 4.18
1891 6507 3.313249 TGACGCAATCAATCATGTCCATC 59.687 43.478 0.00 0.00 33.02 3.51
1909 6525 2.399396 AACACGGCTCATTTTTGACG 57.601 45.000 0.00 0.00 0.00 4.35
1917 6533 2.783135 AGATCACAAAACACGGCTCAT 58.217 42.857 0.00 0.00 0.00 2.90
1989 6653 7.011857 TGGGACAAAAGTTAATCATTTGTTTGC 59.988 33.333 13.80 5.60 44.41 3.68
2044 6708 8.969260 TCATAACTTGAGCACTCATTATGAAT 57.031 30.769 22.54 5.24 42.48 2.57
2108 6807 9.800433 CATTGTGGTTTATTATGCATTTGTAGA 57.200 29.630 3.54 0.00 0.00 2.59
2167 7849 3.581755 TGATTCACTAGTAACCGTGCAC 58.418 45.455 6.82 6.82 0.00 4.57
2173 7855 6.746364 CGTGTACTTCTGATTCACTAGTAACC 59.254 42.308 0.00 0.00 0.00 2.85
2220 7902 3.788434 AACGCACGTCTGAATAGTTTG 57.212 42.857 0.00 0.00 0.00 2.93
2236 7918 2.738135 ACAACCTAATTGCACAAACGC 58.262 42.857 0.00 0.00 42.62 4.84
2251 7933 3.582780 CCGGAGACTAGTTGTTACAACC 58.417 50.000 22.64 9.02 0.00 3.77
2293 7975 2.052690 GTCTCGGGCTAGCAGTGGA 61.053 63.158 18.24 6.34 0.00 4.02
2307 7989 0.939577 TGCTTGAAGCGACGTGTCTC 60.940 55.000 13.05 0.00 46.26 3.36
2348 8030 7.963532 ACTACTGGATTACATGGGTATAACAG 58.036 38.462 0.00 0.00 33.49 3.16
2363 8045 3.541632 CGGCCAACATTACTACTGGATT 58.458 45.455 2.24 0.00 0.00 3.01
2371 8053 2.044352 GCCCCGGCCAACATTACT 60.044 61.111 2.24 0.00 34.56 2.24


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

AutoCloner maintained by Alex Coulton.