Multiple sequence alignment - TraesCS7A01G014200

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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 TraesCS7A01G014200 chr7A 100.000 3746 0 0 1 3746 6338972 6335227 0.000000e+00 6918.0
1 TraesCS7A01G014200 chr7D 92.841 3073 113 53 688 3746 5093688 5090709 0.000000e+00 4357.0
2 TraesCS7A01G014200 chr7D 86.629 531 58 4 146 672 5094642 5094121 3.240000e-160 575.0
3 TraesCS7A01G014200 chr4A 89.761 2256 106 62 688 2910 737479240 737481403 0.000000e+00 2771.0
4 TraesCS7A01G014200 chr4A 89.064 823 42 24 2943 3746 737481692 737482485 0.000000e+00 977.0
5 TraesCS7A01G014200 chr4A 81.818 693 93 16 1 672 737477966 737478646 5.470000e-153 551.0
6 TraesCS7A01G014200 chr4A 85.171 263 13 9 1631 1892 624737984 624738221 2.890000e-61 246.0
7 TraesCS7A01G014200 chr4A 93.651 63 3 1 1170 1232 624737906 624737967 3.980000e-15 93.5
8 TraesCS7A01G014200 chr3D 84.718 373 18 12 1525 1895 14127877 14127542 1.670000e-88 337.0
9 TraesCS7A01G014200 chr3D 87.778 180 13 6 1497 1676 387312432 387312262 6.340000e-48 202.0
10 TraesCS7A01G014200 chr3D 93.651 63 3 1 1170 1232 387312521 387312460 3.980000e-15 93.5
11 TraesCS7A01G014200 chr6D 89.615 260 21 3 1633 1892 205119454 205119707 3.610000e-85 326.0
12 TraesCS7A01G014200 chr6D 88.889 63 6 1 1170 1232 205119374 205119435 4.010000e-10 76.8
13 TraesCS7A01G014200 chr2D 83.000 300 50 1 2147 2446 502833139 502832841 1.710000e-68 270.0
14 TraesCS7A01G014200 chr2D 85.311 177 15 10 1500 1676 8148326 8148161 4.970000e-39 172.0
15 TraesCS7A01G014200 chr2D 92.063 63 4 1 1170 1232 8148418 8148357 1.850000e-13 87.9
16 TraesCS7A01G014200 chr1A 85.053 281 17 8 1631 1910 569372604 569372348 2.870000e-66 263.0
17 TraesCS7A01G014200 chr1A 90.476 63 5 1 1170 1232 569372682 569372621 8.620000e-12 82.4
18 TraesCS7A01G014200 chr4D 87.333 150 18 1 133 282 319268093 319268241 1.790000e-38 171.0
19 TraesCS7A01G014200 chr4D 96.875 32 1 0 1278 1309 143564335 143564304 2.000000e-03 54.7
20 TraesCS7A01G014200 chr4B 87.333 150 18 1 133 282 396714457 396714605 1.790000e-38 171.0
21 TraesCS7A01G014200 chr6B 84.066 182 16 8 1497 1676 720008740 720008910 2.990000e-36 163.0
22 TraesCS7A01G014200 chrUn 84.762 105 16 0 133 237 65058569 65058465 5.120000e-19 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G014200 chr7A 6335227 6338972 3745 True 6918 6918 100.000 1 3746 1 chr7A.!!$R1 3745
1 TraesCS7A01G014200 chr7D 5090709 5094642 3933 True 2466 4357 89.735 146 3746 2 chr7D.!!$R1 3600
2 TraesCS7A01G014200 chr4A 737477966 737482485 4519 False 1433 2771 86.881 1 3746 3 chr4A.!!$F2 3745

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
965 1607 0.323633 CATGGTGATGGTGCCAAGGA 60.324 55.000 0.0 0.0 38.38 3.36 F
1028 1674 1.066908 CAAGAAAGAAAAGGCACCGCA 59.933 47.619 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2718 3389 3.118454 CATGCCGACACCGACACC 61.118 66.667 0.0 0.0 38.22 4.16 R
2901 3582 4.679654 ACAGTTTTTCGGCATTTCGAATTC 59.320 37.500 0.0 0.0 46.50 2.17 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
46 47 4.686839 CATGCATGCAGATTCATAGAGG 57.313 45.455 26.69 0.00 0.00 3.69
47 48 3.851458 TGCATGCAGATTCATAGAGGT 57.149 42.857 18.46 0.00 0.00 3.85
48 49 3.473625 TGCATGCAGATTCATAGAGGTG 58.526 45.455 18.46 0.00 0.00 4.00
50 51 4.101430 TGCATGCAGATTCATAGAGGTGTA 59.899 41.667 18.46 0.00 0.00 2.90
51 52 5.221783 TGCATGCAGATTCATAGAGGTGTAT 60.222 40.000 18.46 0.00 0.00 2.29
52 53 5.121925 GCATGCAGATTCATAGAGGTGTATG 59.878 44.000 14.21 0.00 32.94 2.39
53 54 5.876651 TGCAGATTCATAGAGGTGTATGT 57.123 39.130 0.00 0.00 32.93 2.29
54 55 5.604565 TGCAGATTCATAGAGGTGTATGTG 58.395 41.667 0.00 0.00 32.93 3.21
55 56 5.129320 TGCAGATTCATAGAGGTGTATGTGT 59.871 40.000 0.00 0.00 32.93 3.72
59 60 8.417106 CAGATTCATAGAGGTGTATGTGTTAGT 58.583 37.037 0.00 0.00 32.93 2.24
76 77 7.921787 TGTGTTAGTTATGTACTGTGTTTTGG 58.078 34.615 0.00 0.00 37.73 3.28
125 133 5.127491 AGTAAGCATCGTAGCTCTAGAACT 58.873 41.667 0.54 0.54 45.89 3.01
126 134 6.289834 AGTAAGCATCGTAGCTCTAGAACTA 58.710 40.000 0.00 0.00 45.89 2.24
128 136 3.500680 AGCATCGTAGCTCTAGAACTAGC 59.499 47.826 3.03 3.99 42.18 3.42
154 162 0.325577 TCTAGCATGGCAGTGGAGGA 60.326 55.000 0.00 0.00 0.00 3.71
189 199 9.528489 AAACATCAAGTTCCTAAGCCTAATTAA 57.472 29.630 0.00 0.00 40.26 1.40
279 295 0.837940 GGATTTTCGGAGGGTAGGCT 59.162 55.000 0.00 0.00 0.00 4.58
280 296 1.212195 GGATTTTCGGAGGGTAGGCTT 59.788 52.381 0.00 0.00 0.00 4.35
281 297 2.436911 GGATTTTCGGAGGGTAGGCTTA 59.563 50.000 0.00 0.00 0.00 3.09
282 298 3.072622 GGATTTTCGGAGGGTAGGCTTAT 59.927 47.826 0.00 0.00 0.00 1.73
283 299 4.285260 GGATTTTCGGAGGGTAGGCTTATA 59.715 45.833 0.00 0.00 0.00 0.98
289 305 5.021458 TCGGAGGGTAGGCTTATATTAAGG 58.979 45.833 0.00 0.00 0.00 2.69
323 343 4.767928 CCCTATAGTAGAATCGCCACTCTT 59.232 45.833 0.00 0.00 0.00 2.85
339 359 4.398319 CACTCTTTAGAACATGGGGTTGT 58.602 43.478 0.00 0.00 40.63 3.32
344 368 6.074648 TCTTTAGAACATGGGGTTGTTGAAT 58.925 36.000 0.00 0.00 40.63 2.57
354 378 4.351407 TGGGGTTGTTGAATTGGACTAGTA 59.649 41.667 0.00 0.00 0.00 1.82
378 402 2.125106 GCGTTCGATCCAGCCCTT 60.125 61.111 0.00 0.00 0.00 3.95
403 427 2.512910 TCCCCCACCATGATGACTAT 57.487 50.000 0.00 0.00 0.00 2.12
406 430 2.039480 CCCCCACCATGATGACTATGAG 59.961 54.545 0.00 0.00 0.00 2.90
440 464 2.501723 GAGGTGAACCAAGCTCCAGATA 59.498 50.000 1.62 0.00 38.49 1.98
441 465 3.118531 AGGTGAACCAAGCTCCAGATAT 58.881 45.455 1.62 0.00 38.89 1.63
452 476 2.235898 GCTCCAGATATAGGAAGCCCTG 59.764 54.545 0.00 0.00 44.15 4.45
473 497 1.004277 TGAGCTTACCGAGGCCAAAAT 59.996 47.619 5.01 0.00 0.00 1.82
482 507 3.278574 CCGAGGCCAAAATAGTCATTGA 58.721 45.455 5.01 0.00 0.00 2.57
484 509 3.689161 CGAGGCCAAAATAGTCATTGACA 59.311 43.478 18.57 5.61 34.60 3.58
501 526 3.812262 TGACATCTAGATCCGACCGTAA 58.188 45.455 1.03 0.00 0.00 3.18
528 553 1.685820 CACTGGAACCCTTCTCCCC 59.314 63.158 0.00 0.00 31.32 4.81
529 554 1.918800 ACTGGAACCCTTCTCCCCG 60.919 63.158 0.00 0.00 31.32 5.73
624 649 1.307866 TCCCCTCCCACTCCCATTC 60.308 63.158 0.00 0.00 0.00 2.67
625 650 2.386935 CCCCTCCCACTCCCATTCC 61.387 68.421 0.00 0.00 0.00 3.01
628 653 3.406595 CTCCCACTCCCATTCCGGC 62.407 68.421 0.00 0.00 0.00 6.13
632 657 3.782443 ACTCCCATTCCGGCCGAC 61.782 66.667 30.73 0.00 0.00 4.79
660 685 1.617947 CGGAGGAGGGGAGAACTTGG 61.618 65.000 0.00 0.00 0.00 3.61
664 689 0.542333 GGAGGGGAGAACTTGGCTAC 59.458 60.000 0.00 0.00 0.00 3.58
665 690 0.542333 GAGGGGAGAACTTGGCTACC 59.458 60.000 0.00 0.00 35.49 3.18
672 697 3.008049 GGAGAACTTGGCTACCTCTCAAA 59.992 47.826 8.68 0.00 35.30 2.69
673 698 4.249661 GAGAACTTGGCTACCTCTCAAAG 58.750 47.826 0.00 0.00 34.06 2.77
676 701 4.278975 ACTTGGCTACCTCTCAAAGAAG 57.721 45.455 0.00 0.00 0.00 2.85
677 702 3.904339 ACTTGGCTACCTCTCAAAGAAGA 59.096 43.478 0.00 0.00 0.00 2.87
678 703 4.348168 ACTTGGCTACCTCTCAAAGAAGAA 59.652 41.667 0.00 0.00 0.00 2.52
679 704 4.974645 TGGCTACCTCTCAAAGAAGAAA 57.025 40.909 0.00 0.00 0.00 2.52
681 706 4.593206 TGGCTACCTCTCAAAGAAGAAAGA 59.407 41.667 0.00 0.00 0.00 2.52
682 707 5.071788 TGGCTACCTCTCAAAGAAGAAAGAA 59.928 40.000 0.00 0.00 0.00 2.52
683 708 5.998363 GGCTACCTCTCAAAGAAGAAAGAAA 59.002 40.000 0.00 0.00 0.00 2.52
685 710 7.308288 GGCTACCTCTCAAAGAAGAAAGAAAAG 60.308 40.741 0.00 0.00 0.00 2.27
686 711 7.227711 GCTACCTCTCAAAGAAGAAAGAAAAGT 59.772 37.037 0.00 0.00 0.00 2.66
693 1318 8.841444 TCAAAGAAGAAAGAAAAGTGAATTCG 57.159 30.769 0.04 0.00 32.04 3.34
696 1321 4.147219 AGAAAGAAAAGTGAATTCGCCG 57.853 40.909 15.29 0.00 32.04 6.46
697 1322 2.989422 AAGAAAAGTGAATTCGCCGG 57.011 45.000 15.29 0.00 32.04 6.13
703 1328 1.154225 GTGAATTCGCCGGTGCAAG 60.154 57.895 11.05 0.00 37.32 4.01
704 1329 2.202479 GAATTCGCCGGTGCAAGC 60.202 61.111 11.05 0.00 37.32 4.01
718 1343 1.453155 GCAAGCTGCAAAGGCTACTA 58.547 50.000 1.02 0.00 44.26 1.82
719 1344 1.131315 GCAAGCTGCAAAGGCTACTAC 59.869 52.381 1.02 0.00 44.26 2.73
720 1345 1.740025 CAAGCTGCAAAGGCTACTACC 59.260 52.381 1.02 0.00 39.30 3.18
761 1386 1.538047 ACCATGCACAATCACCACTC 58.462 50.000 0.00 0.00 0.00 3.51
762 1387 1.074405 ACCATGCACAATCACCACTCT 59.926 47.619 0.00 0.00 0.00 3.24
764 1389 2.617276 CCATGCACAATCACCACTCTCT 60.617 50.000 0.00 0.00 0.00 3.10
765 1390 2.936919 TGCACAATCACCACTCTCTT 57.063 45.000 0.00 0.00 0.00 2.85
773 1402 2.689658 TCACCACTCTCTTGGAGGAAA 58.310 47.619 0.00 0.00 45.83 3.13
777 1406 3.716872 ACCACTCTCTTGGAGGAAAAAGA 59.283 43.478 0.00 0.00 45.83 2.52
778 1407 4.166144 ACCACTCTCTTGGAGGAAAAAGAA 59.834 41.667 0.00 0.00 45.83 2.52
780 1409 5.009110 CCACTCTCTTGGAGGAAAAAGAAAC 59.991 44.000 0.00 0.00 45.83 2.78
781 1410 5.009110 CACTCTCTTGGAGGAAAAAGAAACC 59.991 44.000 0.00 0.00 45.83 3.27
783 1412 5.515106 TCTCTTGGAGGAAAAAGAAACCAA 58.485 37.500 0.00 0.00 36.27 3.67
784 1413 5.955355 TCTCTTGGAGGAAAAAGAAACCAAA 59.045 36.000 0.00 0.00 37.04 3.28
828 1459 1.958288 TCTCTCCTTCCCCTTCCAAG 58.042 55.000 0.00 0.00 0.00 3.61
839 1470 2.449137 CCTTCCAAGAGGGCATTCAT 57.551 50.000 0.00 0.00 36.21 2.57
866 1497 5.680665 GCCCATTCATTTCAGATTTCACTCC 60.681 44.000 0.00 0.00 0.00 3.85
867 1498 5.655532 CCCATTCATTTCAGATTTCACTCCT 59.344 40.000 0.00 0.00 0.00 3.69
868 1499 6.183360 CCCATTCATTTCAGATTTCACTCCTC 60.183 42.308 0.00 0.00 0.00 3.71
886 1517 3.328050 TCCTCACTCTCACTCAGTCACTA 59.672 47.826 0.00 0.00 0.00 2.74
909 1540 2.367512 AGGTCCCCATCTCCAGCC 60.368 66.667 0.00 0.00 0.00 4.85
910 1541 3.866582 GGTCCCCATCTCCAGCCG 61.867 72.222 0.00 0.00 0.00 5.52
911 1542 2.764128 GTCCCCATCTCCAGCCGA 60.764 66.667 0.00 0.00 0.00 5.54
912 1543 2.764128 TCCCCATCTCCAGCCGAC 60.764 66.667 0.00 0.00 0.00 4.79
913 1544 3.866582 CCCCATCTCCAGCCGACC 61.867 72.222 0.00 0.00 0.00 4.79
914 1545 3.866582 CCCATCTCCAGCCGACCC 61.867 72.222 0.00 0.00 0.00 4.46
915 1546 4.227134 CCATCTCCAGCCGACCCG 62.227 72.222 0.00 0.00 0.00 5.28
916 1547 3.147595 CATCTCCAGCCGACCCGA 61.148 66.667 0.00 0.00 0.00 5.14
917 1548 3.148279 ATCTCCAGCCGACCCGAC 61.148 66.667 0.00 0.00 0.00 4.79
939 1581 2.191641 GCTGAGCTCCATCCACCC 59.808 66.667 12.15 0.00 0.00 4.61
940 1582 2.673200 GCTGAGCTCCATCCACCCA 61.673 63.158 12.15 0.00 0.00 4.51
941 1583 1.992519 GCTGAGCTCCATCCACCCAT 61.993 60.000 12.15 0.00 0.00 4.00
962 1604 4.438255 CCATGGTGATGGTGCCAA 57.562 55.556 2.57 0.00 43.98 4.52
963 1605 2.195389 CCATGGTGATGGTGCCAAG 58.805 57.895 2.57 0.00 43.98 3.61
965 1607 0.323633 CATGGTGATGGTGCCAAGGA 60.324 55.000 0.00 0.00 38.38 3.36
982 1627 4.195416 CAAGGAGGAGGACATAAAAGAGC 58.805 47.826 0.00 0.00 0.00 4.09
983 1628 3.454858 AGGAGGAGGACATAAAAGAGCA 58.545 45.455 0.00 0.00 0.00 4.26
984 1629 4.043596 AGGAGGAGGACATAAAAGAGCAT 58.956 43.478 0.00 0.00 0.00 3.79
985 1630 4.476479 AGGAGGAGGACATAAAAGAGCATT 59.524 41.667 0.00 0.00 0.00 3.56
986 1631 4.819088 GGAGGAGGACATAAAAGAGCATTC 59.181 45.833 0.00 0.00 0.00 2.67
1024 1670 1.412343 TGGCCAAGAAAGAAAAGGCAC 59.588 47.619 0.61 0.00 46.96 5.01
1026 1672 1.602920 GCCAAGAAAGAAAAGGCACCG 60.603 52.381 0.00 0.00 44.59 4.94
1028 1674 1.066908 CAAGAAAGAAAAGGCACCGCA 59.933 47.619 0.00 0.00 0.00 5.69
1080 1730 3.772560 CGCACGCACATACACGCA 61.773 61.111 0.00 0.00 0.00 5.24
1092 1742 4.742201 CACGCACACCTCCTCCCG 62.742 72.222 0.00 0.00 0.00 5.14
1377 2030 3.333189 CGCTGGATCATGGACGCG 61.333 66.667 3.53 3.53 34.50 6.01
1491 2147 4.735132 TTTGACGAGCGCCGGGAG 62.735 66.667 19.73 0.00 43.93 4.30
1588 2250 1.559065 GGTCCATTTCCCCGTCTCCA 61.559 60.000 0.00 0.00 0.00 3.86
1598 2260 3.414700 CGTCTCCACCGCAACAGC 61.415 66.667 0.00 0.00 0.00 4.40
2679 3350 2.730626 CTTCCACGTCGAGAAGCAG 58.269 57.895 13.91 0.00 33.64 4.24
2682 3353 2.091112 CCACGTCGAGAAGCAGCAG 61.091 63.158 0.00 0.00 0.00 4.24
2683 3354 2.091112 CACGTCGAGAAGCAGCAGG 61.091 63.158 0.00 0.00 0.00 4.85
2799 3475 4.322499 CCCGGTACAGTTGTAGTTCATCTT 60.322 45.833 0.00 0.00 0.00 2.40
2800 3476 4.625742 CCGGTACAGTTGTAGTTCATCTTG 59.374 45.833 0.00 0.00 0.00 3.02
2801 3477 5.227908 CGGTACAGTTGTAGTTCATCTTGT 58.772 41.667 0.00 0.00 0.00 3.16
2821 3497 6.534793 TCTTGTTGCCAAAACTTGAATCTTTC 59.465 34.615 0.00 0.00 0.00 2.62
2870 3551 9.342308 CCAATCTTGGTGTGTGATATATTACTT 57.658 33.333 8.88 0.00 43.43 2.24
2901 3582 4.439057 CAATTTGAGGCATGAAGAATGGG 58.561 43.478 0.00 0.00 36.71 4.00
3152 4094 7.926555 TCCTGTTATAATTTGTAGTAGCAGAGC 59.073 37.037 0.00 0.00 30.04 4.09
3154 4096 9.265901 CTGTTATAATTTGTAGTAGCAGAGCAT 57.734 33.333 0.00 0.00 30.04 3.79
3225 4167 9.670442 ACAGATCCCTAATTAAACCAGAGTATA 57.330 33.333 0.00 0.00 0.00 1.47
3227 4169 9.900112 AGATCCCTAATTAAACCAGAGTATAGT 57.100 33.333 0.00 0.00 0.00 2.12
3299 4241 7.148356 TGCTGATTGATGTGACAACTCTAATTC 60.148 37.037 0.00 0.00 32.50 2.17
3458 4402 5.173854 GCATACTGCACACTTGTTTTCTTTC 59.826 40.000 0.00 0.00 44.26 2.62
3460 4404 3.763897 ACTGCACACTTGTTTTCTTTCCT 59.236 39.130 0.00 0.00 0.00 3.36
3461 4405 4.142381 ACTGCACACTTGTTTTCTTTCCTC 60.142 41.667 0.00 0.00 0.00 3.71
3474 4418 7.673504 TGTTTTCTTTCCTCCCATGAATTATCA 59.326 33.333 0.00 0.00 40.57 2.15
3581 4528 1.250476 GAAAATGCAACTGTAGCGCG 58.750 50.000 0.00 0.00 33.85 6.86
3582 4529 0.729140 AAAATGCAACTGTAGCGCGC 60.729 50.000 26.66 26.66 33.85 6.86
3615 4566 7.995289 TGAAATTTAGGGTAACATGTATGCTG 58.005 34.615 0.00 0.00 39.74 4.41
3620 4571 5.228945 AGGGTAACATGTATGCTGTATCC 57.771 43.478 0.00 0.00 39.74 2.59
3629 4580 1.626686 ATGCTGTATCCTCCTCCTCG 58.373 55.000 0.00 0.00 0.00 4.63
3718 4675 1.753073 GTGCATTGCCCTAATCTTGCT 59.247 47.619 6.12 0.00 0.00 3.91
3719 4676 2.167075 GTGCATTGCCCTAATCTTGCTT 59.833 45.455 6.12 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.147328 CACATACACCTCTATGAATCTGCATG 59.853 42.308 0.00 0.00 0.00 4.06
30 31 6.183361 ACACATACACCTCTATGAATCTGCAT 60.183 38.462 0.00 0.00 0.00 3.96
31 32 5.129320 ACACATACACCTCTATGAATCTGCA 59.871 40.000 0.00 0.00 0.00 4.41
33 34 8.417106 ACTAACACATACACCTCTATGAATCTG 58.583 37.037 0.00 0.00 0.00 2.90
34 35 8.540507 ACTAACACATACACCTCTATGAATCT 57.459 34.615 0.00 0.00 0.00 2.40
38 39 9.197306 ACATAACTAACACATACACCTCTATGA 57.803 33.333 0.00 0.00 0.00 2.15
42 43 8.467598 CAGTACATAACTAACACATACACCTCT 58.532 37.037 0.00 0.00 35.76 3.69
43 44 8.248945 ACAGTACATAACTAACACATACACCTC 58.751 37.037 0.00 0.00 35.76 3.85
44 45 8.033038 CACAGTACATAACTAACACATACACCT 58.967 37.037 0.00 0.00 35.76 4.00
45 46 7.816031 ACACAGTACATAACTAACACATACACC 59.184 37.037 0.00 0.00 35.76 4.16
46 47 8.752766 ACACAGTACATAACTAACACATACAC 57.247 34.615 0.00 0.00 35.76 2.90
47 48 9.767228 AAACACAGTACATAACTAACACATACA 57.233 29.630 0.00 0.00 35.76 2.29
50 51 8.564574 CCAAAACACAGTACATAACTAACACAT 58.435 33.333 0.00 0.00 35.76 3.21
51 52 7.769507 TCCAAAACACAGTACATAACTAACACA 59.230 33.333 0.00 0.00 35.76 3.72
52 53 8.145316 TCCAAAACACAGTACATAACTAACAC 57.855 34.615 0.00 0.00 35.76 3.32
53 54 8.734218 TTCCAAAACACAGTACATAACTAACA 57.266 30.769 0.00 0.00 35.76 2.41
54 55 9.048446 TCTTCCAAAACACAGTACATAACTAAC 57.952 33.333 0.00 0.00 35.76 2.34
55 56 9.616156 TTCTTCCAAAACACAGTACATAACTAA 57.384 29.630 0.00 0.00 35.76 2.24
94 99 3.243101 GCTACGATGCTTACTAGAGTGCA 60.243 47.826 0.00 3.70 39.83 4.57
125 133 2.435437 TGCCATGCTAGATTCACAGCTA 59.565 45.455 10.49 0.00 38.63 3.32
126 134 1.211212 TGCCATGCTAGATTCACAGCT 59.789 47.619 10.49 0.00 38.63 4.24
128 136 2.612672 CACTGCCATGCTAGATTCACAG 59.387 50.000 0.00 0.00 0.00 3.66
131 139 1.839354 TCCACTGCCATGCTAGATTCA 59.161 47.619 0.00 0.00 0.00 2.57
134 142 0.763652 CCTCCACTGCCATGCTAGAT 59.236 55.000 0.00 0.00 0.00 1.98
154 162 9.178758 CTTAGGAACTTGATGTTTTAAGCCTAT 57.821 33.333 0.00 0.00 41.75 2.57
231 245 6.288294 TCAGCTAAATATACCACATGACCAC 58.712 40.000 0.00 0.00 0.00 4.16
267 283 4.382793 GCCTTAATATAAGCCTACCCTCCG 60.383 50.000 0.00 0.00 0.00 4.63
323 343 5.011533 CCAATTCAACAACCCCATGTTCTAA 59.988 40.000 0.00 0.00 41.44 2.10
361 385 1.706287 GAAAGGGCTGGATCGAACGC 61.706 60.000 0.00 0.00 0.00 4.84
364 388 0.914417 AGGGAAAGGGCTGGATCGAA 60.914 55.000 0.00 0.00 0.00 3.71
378 402 0.554865 ATCATGGTGGGGGAAGGGAA 60.555 55.000 0.00 0.00 0.00 3.97
403 427 3.724209 TCACCTCCTCCTCATATCTCTCA 59.276 47.826 0.00 0.00 0.00 3.27
406 430 3.576550 GGTTCACCTCCTCCTCATATCTC 59.423 52.174 0.00 0.00 0.00 2.75
440 464 1.589414 AAGCTCACAGGGCTTCCTAT 58.411 50.000 0.00 0.00 45.45 2.57
441 465 1.831736 GTAAGCTCACAGGGCTTCCTA 59.168 52.381 7.49 0.00 45.45 2.94
452 476 0.321298 TTTGGCCTCGGTAAGCTCAC 60.321 55.000 3.32 0.00 0.00 3.51
473 497 5.473846 GGTCGGATCTAGATGTCAATGACTA 59.526 44.000 10.74 1.62 33.15 2.59
482 507 3.814283 GAGTTACGGTCGGATCTAGATGT 59.186 47.826 10.74 3.14 0.00 3.06
484 509 3.065655 CGAGTTACGGTCGGATCTAGAT 58.934 50.000 4.47 4.47 38.46 1.98
501 526 1.598130 GGTTCCAGTGCAAGCGAGT 60.598 57.895 0.00 0.00 0.00 4.18
604 629 4.741239 TGGGAGTGGGAGGGGAGC 62.741 72.222 0.00 0.00 0.00 4.70
624 649 4.570663 GATGGTCTCGTCGGCCGG 62.571 72.222 27.83 10.69 37.11 6.13
625 650 4.907034 CGATGGTCTCGTCGGCCG 62.907 72.222 22.12 22.12 45.68 6.13
637 662 1.075226 TTCTCCCCTCCTCCGATGG 60.075 63.158 0.00 0.00 0.00 3.51
640 665 0.614979 CAAGTTCTCCCCTCCTCCGA 60.615 60.000 0.00 0.00 0.00 4.55
643 668 0.912006 AGCCAAGTTCTCCCCTCCTC 60.912 60.000 0.00 0.00 0.00 3.71
645 670 0.542333 GTAGCCAAGTTCTCCCCTCC 59.458 60.000 0.00 0.00 0.00 4.30
660 685 7.227711 ACTTTTCTTTCTTCTTTGAGAGGTAGC 59.772 37.037 0.00 0.00 0.00 3.58
664 689 7.559590 TCACTTTTCTTTCTTCTTTGAGAGG 57.440 36.000 0.00 0.00 0.00 3.69
672 697 5.560953 CGGCGAATTCACTTTTCTTTCTTCT 60.561 40.000 0.00 0.00 0.00 2.85
673 698 4.613031 CGGCGAATTCACTTTTCTTTCTTC 59.387 41.667 0.00 0.00 0.00 2.87
676 701 3.234386 CCGGCGAATTCACTTTTCTTTC 58.766 45.455 9.30 0.00 0.00 2.62
677 702 2.621526 ACCGGCGAATTCACTTTTCTTT 59.378 40.909 9.30 0.00 0.00 2.52
678 703 2.031157 CACCGGCGAATTCACTTTTCTT 60.031 45.455 9.30 0.00 0.00 2.52
679 704 1.535462 CACCGGCGAATTCACTTTTCT 59.465 47.619 9.30 0.00 0.00 2.52
681 706 0.039527 GCACCGGCGAATTCACTTTT 60.040 50.000 9.30 0.00 0.00 2.27
682 707 1.169661 TGCACCGGCGAATTCACTTT 61.170 50.000 9.30 0.00 45.35 2.66
683 708 1.169661 TTGCACCGGCGAATTCACTT 61.170 50.000 9.30 0.00 45.35 3.16
685 710 1.154225 CTTGCACCGGCGAATTCAC 60.154 57.895 9.30 0.00 45.35 3.18
686 711 2.976840 GCTTGCACCGGCGAATTCA 61.977 57.895 9.30 0.00 45.35 2.57
703 1328 1.066143 TCAGGTAGTAGCCTTTGCAGC 60.066 52.381 0.00 0.00 41.13 5.25
704 1329 2.234908 ACTCAGGTAGTAGCCTTTGCAG 59.765 50.000 0.00 0.00 41.13 4.41
715 1340 3.206150 CACAACTTGCAACTCAGGTAGT 58.794 45.455 0.00 0.00 41.49 2.73
718 1343 2.128771 ACACAACTTGCAACTCAGGT 57.871 45.000 0.00 0.00 36.47 4.00
719 1344 2.801063 CAACACAACTTGCAACTCAGG 58.199 47.619 0.00 0.00 0.00 3.86
720 1345 2.187707 GCAACACAACTTGCAACTCAG 58.812 47.619 0.00 0.00 45.07 3.35
761 1386 5.852282 TTGGTTTCTTTTTCCTCCAAGAG 57.148 39.130 0.00 0.00 30.68 2.85
762 1387 6.613153 TTTTGGTTTCTTTTTCCTCCAAGA 57.387 33.333 0.00 0.00 36.53 3.02
783 1412 9.507329 AAAAGGCTTTTCTTTCTTCTTCTTTTT 57.493 25.926 19.14 0.00 36.09 1.94
784 1413 9.155975 GAAAAGGCTTTTCTTTCTTCTTCTTTT 57.844 29.630 34.37 6.97 44.29 2.27
839 1470 2.734755 ATCTGAAATGAATGGGCCGA 57.265 45.000 0.00 0.00 0.00 5.54
866 1497 3.126858 GCTAGTGACTGAGTGAGAGTGAG 59.873 52.174 0.00 0.00 0.00 3.51
867 1498 3.078097 GCTAGTGACTGAGTGAGAGTGA 58.922 50.000 0.00 0.00 0.00 3.41
868 1499 2.163412 GGCTAGTGACTGAGTGAGAGTG 59.837 54.545 0.00 0.00 0.00 3.51
910 1541 3.827898 CTCAGCTCGGGTCGGGTC 61.828 72.222 0.00 0.00 0.00 4.46
913 1544 4.200283 GAGCTCAGCTCGGGTCGG 62.200 72.222 11.89 0.00 45.85 4.79
922 1553 1.992519 ATGGGTGGATGGAGCTCAGC 61.993 60.000 17.19 4.43 0.00 4.26
924 1555 0.621280 TGATGGGTGGATGGAGCTCA 60.621 55.000 17.19 1.87 0.00 4.26
959 1601 4.775236 CTCTTTTATGTCCTCCTCCTTGG 58.225 47.826 0.00 0.00 37.10 3.61
960 1602 4.195416 GCTCTTTTATGTCCTCCTCCTTG 58.805 47.826 0.00 0.00 0.00 3.61
962 1604 3.454858 TGCTCTTTTATGTCCTCCTCCT 58.545 45.455 0.00 0.00 0.00 3.69
963 1605 3.914426 TGCTCTTTTATGTCCTCCTCC 57.086 47.619 0.00 0.00 0.00 4.30
965 1607 4.162320 TCGAATGCTCTTTTATGTCCTCCT 59.838 41.667 0.00 0.00 0.00 3.69
982 1627 5.276773 CCACCATTTGTTTTTGTGTCGAATG 60.277 40.000 0.00 0.00 34.55 2.67
983 1628 4.808364 CCACCATTTGTTTTTGTGTCGAAT 59.192 37.500 0.00 0.00 0.00 3.34
984 1629 4.177026 CCACCATTTGTTTTTGTGTCGAA 58.823 39.130 0.00 0.00 0.00 3.71
985 1630 3.775202 CCACCATTTGTTTTTGTGTCGA 58.225 40.909 0.00 0.00 0.00 4.20
986 1631 2.283884 GCCACCATTTGTTTTTGTGTCG 59.716 45.455 0.00 0.00 0.00 4.35
1024 1670 1.201578 CGCGTGTATGCTTATGCGG 59.798 57.895 0.00 0.93 43.34 5.69
1026 1672 0.654472 GTGCGCGTGTATGCTTATGC 60.654 55.000 8.43 0.00 40.20 3.14
1028 1674 0.650512 GTGTGCGCGTGTATGCTTAT 59.349 50.000 8.43 0.00 0.00 1.73
1080 1730 2.037527 GGAGACGGGAGGAGGTGT 59.962 66.667 0.00 0.00 0.00 4.16
1092 1742 3.197766 TGGTGGTGATCATAAGTGGAGAC 59.802 47.826 0.00 0.00 0.00 3.36
1474 2130 4.735132 CTCCCGGCGCTCGTCAAA 62.735 66.667 7.64 0.00 37.11 2.69
1489 2145 3.844090 GTGCTCCTCCGCCTCCTC 61.844 72.222 0.00 0.00 0.00 3.71
1496 2152 3.708220 GAGAAGGCGTGCTCCTCCG 62.708 68.421 2.71 0.00 34.82 4.63
1497 2153 2.185608 GAGAAGGCGTGCTCCTCC 59.814 66.667 2.71 0.00 34.82 4.30
1607 2269 1.372245 ATCTCCATCTCCTCCCCCGA 61.372 60.000 0.00 0.00 0.00 5.14
1839 2501 3.453679 GGCGAGAGGACGGAGCTT 61.454 66.667 0.00 0.00 0.00 3.74
1996 2661 4.367023 CCCGAAGCCGACGTCCAA 62.367 66.667 10.58 0.00 38.22 3.53
2100 2765 4.101790 GGCGACACCAATGCCGTG 62.102 66.667 0.00 0.00 39.30 4.94
2718 3389 3.118454 CATGCCGACACCGACACC 61.118 66.667 0.00 0.00 38.22 4.16
2799 3475 7.793353 TTGAGAAAGATTCAAGTTTTGGCAACA 60.793 33.333 0.00 0.00 35.93 3.33
2800 3476 6.042143 TGAGAAAGATTCAAGTTTTGGCAAC 58.958 36.000 0.00 0.00 0.00 4.17
2801 3477 6.219417 TGAGAAAGATTCAAGTTTTGGCAA 57.781 33.333 0.00 0.00 0.00 4.52
2870 3551 6.233905 TCATGCCTCAAATTGCTAGTAGTA 57.766 37.500 0.00 0.00 0.00 1.82
2871 3552 5.102953 TCATGCCTCAAATTGCTAGTAGT 57.897 39.130 0.00 0.00 0.00 2.73
2872 3553 5.819379 TCTTCATGCCTCAAATTGCTAGTAG 59.181 40.000 0.00 0.00 0.00 2.57
2901 3582 4.679654 ACAGTTTTTCGGCATTTCGAATTC 59.320 37.500 0.00 0.00 46.50 2.17
3068 4008 6.100404 TGGAAAATCCTTGTTGATTTCCAG 57.900 37.500 12.80 0.00 42.58 3.86
3225 4167 9.948964 ATTGATGCATACACATACATACATACT 57.051 29.630 0.00 0.00 0.00 2.12
3227 4169 9.941325 TGATTGATGCATACACATACATACATA 57.059 29.630 0.00 0.00 0.00 2.29
3228 4170 8.851541 TGATTGATGCATACACATACATACAT 57.148 30.769 0.00 0.00 0.00 2.29
3229 4171 7.095102 GCTGATTGATGCATACACATACATACA 60.095 37.037 0.00 0.00 0.00 2.29
3230 4172 7.239271 GCTGATTGATGCATACACATACATAC 58.761 38.462 0.00 0.00 0.00 2.39
3231 4173 6.372381 GGCTGATTGATGCATACACATACATA 59.628 38.462 0.00 0.00 0.00 2.29
3232 4174 5.182570 GGCTGATTGATGCATACACATACAT 59.817 40.000 0.00 0.00 0.00 2.29
3233 4175 4.516321 GGCTGATTGATGCATACACATACA 59.484 41.667 0.00 0.00 0.00 2.29
3234 4176 4.758674 AGGCTGATTGATGCATACACATAC 59.241 41.667 0.00 0.00 0.00 2.39
3235 4177 4.758165 CAGGCTGATTGATGCATACACATA 59.242 41.667 9.42 0.00 0.00 2.29
3236 4178 3.568430 CAGGCTGATTGATGCATACACAT 59.432 43.478 9.42 0.00 0.00 3.21
3237 4179 2.946990 CAGGCTGATTGATGCATACACA 59.053 45.455 9.42 0.00 0.00 3.72
3238 4180 2.287427 GCAGGCTGATTGATGCATACAC 60.287 50.000 20.86 0.00 38.54 2.90
3299 4241 8.897752 CAGAGGGGACAAAGAAAAATCTTATAG 58.102 37.037 0.00 0.00 0.00 1.31
3447 4389 6.745794 AATTCATGGGAGGAAAGAAAACAA 57.254 33.333 0.00 0.00 0.00 2.83
3449 4391 8.066612 TGATAATTCATGGGAGGAAAGAAAAC 57.933 34.615 0.00 0.00 0.00 2.43
3474 4418 5.749462 AGCTGAGGAAAAGCATACTTACAT 58.251 37.500 0.00 0.00 43.37 2.29
3478 4422 3.760684 CCAAGCTGAGGAAAAGCATACTT 59.239 43.478 0.00 0.00 43.37 2.24
3479 4423 3.009473 TCCAAGCTGAGGAAAAGCATACT 59.991 43.478 5.72 0.00 43.37 2.12
3480 4424 3.347216 TCCAAGCTGAGGAAAAGCATAC 58.653 45.455 5.72 0.00 43.37 2.39
3482 4426 2.592102 TCCAAGCTGAGGAAAAGCAT 57.408 45.000 5.72 0.00 43.37 3.79
3483 4427 2.363306 TTCCAAGCTGAGGAAAAGCA 57.637 45.000 16.29 0.00 41.94 3.91
3581 4528 7.832769 TGTTACCCTAAATTTCAGTATTTGGC 58.167 34.615 0.00 0.00 0.00 4.52
3582 4529 9.801873 CATGTTACCCTAAATTTCAGTATTTGG 57.198 33.333 0.00 0.00 0.00 3.28
3615 4566 2.865079 TGATGACGAGGAGGAGGATAC 58.135 52.381 0.00 0.00 0.00 2.24
3620 4571 2.870175 AGGTATGATGACGAGGAGGAG 58.130 52.381 0.00 0.00 0.00 3.69
3629 4580 7.280205 CCCTTGTTTAACAGTAGGTATGATGAC 59.720 40.741 13.01 0.00 26.67 3.06
3718 4675 4.966965 TTGGTTAACGAAACAGAGCAAA 57.033 36.364 0.00 0.00 40.08 3.68
3719 4676 5.508200 AATTGGTTAACGAAACAGAGCAA 57.492 34.783 7.15 0.00 40.08 3.91


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

AutoCloner maintained by Alex Coulton.