Multiple sequence alignment - TraesCS2D01G422000

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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 TraesCS2D01G422000 chr2D 100.000 4073 0 0 1 4073 535564697 535568769 0.000000e+00 7522
1 TraesCS2D01G422000 chr2A 94.255 2646 105 24 786 3406 678666772 678669395 0.000000e+00 4000
2 TraesCS2D01G422000 chr2A 75.579 475 67 29 25 479 678666082 678666527 5.370000e-44 189
3 TraesCS2D01G422000 chr2B 93.967 2652 108 18 776 3405 636770939 636773560 0.000000e+00 3964
4 TraesCS2D01G422000 chr2B 91.777 681 34 8 3396 4073 774481043 774481704 0.000000e+00 928
5 TraesCS2D01G422000 chr2B 91.667 672 34 7 3405 4073 640596741 640597393 0.000000e+00 911
6 TraesCS2D01G422000 chr2B 92.089 493 21 7 1 490 636770161 636770638 0.000000e+00 678
7 TraesCS2D01G422000 chr2B 80.124 322 47 8 2503 2810 636774444 636774762 1.470000e-54 224
8 TraesCS2D01G422000 chr2B 91.473 129 11 0 632 760 636770828 636770956 1.160000e-40 178
9 TraesCS2D01G422000 chr3D 99.100 667 6 0 3407 4073 283970270 283969604 0.000000e+00 1199
10 TraesCS2D01G422000 chr3B 95.522 670 24 4 3407 4073 193609008 193608342 0.000000e+00 1066
11 TraesCS2D01G422000 chr5A 94.196 672 31 6 3406 4073 567083988 567083321 0.000000e+00 1018
12 TraesCS2D01G422000 chr5A 93.309 553 29 6 3391 3937 406421001 406421551 0.000000e+00 809
13 TraesCS2D01G422000 chr5A 93.662 142 8 1 3932 4073 406473560 406473700 1.150000e-50 211
14 TraesCS2D01G422000 chr7A 92.431 436 23 4 3406 3833 138518774 138518341 7.480000e-172 614
15 TraesCS2D01G422000 chr7A 94.737 247 10 2 3829 4073 138512933 138512688 8.260000e-102 381
16 TraesCS2D01G422000 chr7A 86.580 231 28 2 3405 3632 138511636 138511866 6.760000e-63 252
17 TraesCS2D01G422000 chr3A 92.081 442 24 5 3640 4073 371250582 371251020 2.690000e-171 612
18 TraesCS2D01G422000 chr6B 93.496 246 11 2 3407 3647 377906093 377905848 1.080000e-95 361


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 TraesCS2D01G422000 chr2D 535564697 535568769 4072 False 7522.0 7522 100.00000 1 4073 1 chr2D.!!$F1 4072
1 TraesCS2D01G422000 chr2A 678666082 678669395 3313 False 2094.5 4000 84.91700 25 3406 2 chr2A.!!$F1 3381
2 TraesCS2D01G422000 chr2B 636770161 636774762 4601 False 1261.0 3964 89.41325 1 3405 4 chr2B.!!$F3 3404
3 TraesCS2D01G422000 chr2B 774481043 774481704 661 False 928.0 928 91.77700 3396 4073 1 chr2B.!!$F2 677
4 TraesCS2D01G422000 chr2B 640596741 640597393 652 False 911.0 911 91.66700 3405 4073 1 chr2B.!!$F1 668
5 TraesCS2D01G422000 chr3D 283969604 283970270 666 True 1199.0 1199 99.10000 3407 4073 1 chr3D.!!$R1 666
6 TraesCS2D01G422000 chr3B 193608342 193609008 666 True 1066.0 1066 95.52200 3407 4073 1 chr3B.!!$R1 666
7 TraesCS2D01G422000 chr5A 567083321 567083988 667 True 1018.0 1018 94.19600 3406 4073 1 chr5A.!!$R1 667
8 TraesCS2D01G422000 chr5A 406421001 406421551 550 False 809.0 809 93.30900 3391 3937 1 chr5A.!!$F1 546

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
551 595 0.170339 GTACCCACGCTGGATTTTGC 59.830 55.0 5.71 0.0 40.96 3.68 F
763 859 0.180406 AGTATCACGCATCAACCCCC 59.820 55.0 0.00 0.0 0.00 5.40 F
950 1049 0.249826 GCTCTATCTCCCTGCAGCAC 60.250 60.0 8.66 0.0 0.00 4.40 F
1502 1602 0.526954 ATCGACATACCCGAACACGC 60.527 55.0 0.00 0.0 39.62 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2134 2252 0.179029 CACGGGACTGGTTGGTTCTT 60.179 55.000 0.00 0.0 0.00 2.52 R
2751 2882 1.896220 TAGCCTGCAGTGAAAAGTGG 58.104 50.000 13.81 0.0 0.00 4.00 R
2781 2912 1.325355 CCATGATGATGGTTGCCCTC 58.675 55.000 2.51 0.0 43.98 4.30 R
3353 3504 1.742268 TGTGAGAGACTCAGCTGATCG 59.258 52.381 18.63 9.3 41.46 3.69 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
131 133 3.436243 TGTGACCCAAGAAAAACCAACT 58.564 40.909 0.00 0.00 0.00 3.16
158 160 1.589716 AAAGAGCCCAGCGAACATGC 61.590 55.000 0.00 0.00 0.00 4.06
159 161 3.869272 GAGCCCAGCGAACATGCG 61.869 66.667 0.00 0.00 40.67 4.73
160 162 4.393155 AGCCCAGCGAACATGCGA 62.393 61.111 0.00 0.00 40.67 5.10
161 163 3.204827 GCCCAGCGAACATGCGAT 61.205 61.111 0.00 0.00 40.67 4.58
162 164 1.887242 GCCCAGCGAACATGCGATA 60.887 57.895 0.00 0.00 40.67 2.92
163 165 1.934463 CCCAGCGAACATGCGATAC 59.066 57.895 0.00 0.00 40.67 2.24
164 166 0.809636 CCCAGCGAACATGCGATACA 60.810 55.000 0.00 0.00 40.67 2.29
165 167 1.220529 CCAGCGAACATGCGATACAT 58.779 50.000 0.00 0.00 40.66 2.29
203 205 1.616865 CTTCGTACAGGGAACACTGGA 59.383 52.381 8.93 0.00 42.75 3.86
305 312 1.602311 GGCAGGAATATGTCAGCCAG 58.398 55.000 0.00 0.00 44.36 4.85
327 345 1.473258 TTGACAGCTTGCACACCTTT 58.527 45.000 0.00 0.00 0.00 3.11
335 353 2.604614 GCTTGCACACCTTTTTACCTCG 60.605 50.000 0.00 0.00 0.00 4.63
368 388 0.755686 AGGCCTCTCGATGGTCAATC 59.244 55.000 0.00 0.00 0.00 2.67
369 389 0.465705 GGCCTCTCGATGGTCAATCA 59.534 55.000 0.00 0.00 34.68 2.57
370 390 1.134401 GGCCTCTCGATGGTCAATCAA 60.134 52.381 0.00 0.00 34.68 2.57
371 391 2.486191 GGCCTCTCGATGGTCAATCAAT 60.486 50.000 0.00 0.00 34.68 2.57
400 420 1.081509 CCGCACCACCGAAAACATG 60.082 57.895 0.00 0.00 0.00 3.21
421 441 2.483491 GAGCAAGCAGACTCCTGAAAAG 59.517 50.000 0.00 0.00 43.02 2.27
422 442 1.068679 GCAAGCAGACTCCTGAAAAGC 60.069 52.381 0.00 0.00 43.02 3.51
424 444 1.063183 AGCAGACTCCTGAAAAGCCT 58.937 50.000 0.00 0.00 43.02 4.58
425 445 2.260822 AGCAGACTCCTGAAAAGCCTA 58.739 47.619 0.00 0.00 43.02 3.93
427 447 2.744741 GCAGACTCCTGAAAAGCCTAAC 59.255 50.000 0.00 0.00 43.02 2.34
429 449 4.646572 CAGACTCCTGAAAAGCCTAACTT 58.353 43.478 0.00 0.00 43.02 2.66
430 450 4.453819 CAGACTCCTGAAAAGCCTAACTTG 59.546 45.833 0.00 0.00 43.02 3.16
477 498 2.875933 TGCACTAAAACCGACCAGAAAG 59.124 45.455 0.00 0.00 0.00 2.62
478 499 2.350484 GCACTAAAACCGACCAGAAAGC 60.350 50.000 0.00 0.00 0.00 3.51
479 500 2.096417 CACTAAAACCGACCAGAAAGCG 60.096 50.000 0.00 0.00 0.00 4.68
480 501 0.869730 TAAAACCGACCAGAAAGCGC 59.130 50.000 0.00 0.00 0.00 5.92
481 502 1.098712 AAAACCGACCAGAAAGCGCA 61.099 50.000 11.47 0.00 0.00 6.09
482 503 0.889186 AAACCGACCAGAAAGCGCAT 60.889 50.000 11.47 0.00 0.00 4.73
483 504 1.298859 AACCGACCAGAAAGCGCATC 61.299 55.000 11.47 7.77 0.00 3.91
517 561 2.620112 CGCCAAGCACACCTTCCTG 61.620 63.158 0.00 0.00 0.00 3.86
522 566 2.360475 GCACACCTTCCTGCCCTC 60.360 66.667 0.00 0.00 0.00 4.30
524 568 2.936032 ACACCTTCCTGCCCTCCC 60.936 66.667 0.00 0.00 0.00 4.30
525 569 2.612115 CACCTTCCTGCCCTCCCT 60.612 66.667 0.00 0.00 0.00 4.20
527 571 0.695803 CACCTTCCTGCCCTCCCTAT 60.696 60.000 0.00 0.00 0.00 2.57
531 575 1.694696 CTTCCTGCCCTCCCTATACAC 59.305 57.143 0.00 0.00 0.00 2.90
534 578 1.479942 CCTGCCCTCCCTATACACGTA 60.480 57.143 0.00 0.00 0.00 3.57
535 579 1.612463 CTGCCCTCCCTATACACGTAC 59.388 57.143 0.00 0.00 0.00 3.67
537 581 1.625511 CCCTCCCTATACACGTACCC 58.374 60.000 0.00 0.00 0.00 3.69
538 582 1.133388 CCCTCCCTATACACGTACCCA 60.133 57.143 0.00 0.00 0.00 4.51
539 583 1.959282 CCTCCCTATACACGTACCCAC 59.041 57.143 0.00 0.00 0.00 4.61
548 592 4.609995 CGTACCCACGCTGGATTT 57.390 55.556 5.71 0.00 40.96 2.17
549 593 2.849081 CGTACCCACGCTGGATTTT 58.151 52.632 5.71 0.00 40.96 1.82
550 594 0.446222 CGTACCCACGCTGGATTTTG 59.554 55.000 5.71 0.00 40.96 2.44
551 595 0.170339 GTACCCACGCTGGATTTTGC 59.830 55.000 5.71 0.00 40.96 3.68
552 596 0.250945 TACCCACGCTGGATTTTGCA 60.251 50.000 5.71 0.00 40.96 4.08
553 597 1.213537 CCCACGCTGGATTTTGCAG 59.786 57.895 5.71 0.00 40.96 4.41
554 598 1.213537 CCACGCTGGATTTTGCAGG 59.786 57.895 0.00 0.00 40.96 4.85
556 600 2.182537 CGCTGGATTTTGCAGGGC 59.817 61.111 0.49 0.00 41.27 5.19
557 601 2.182537 GCTGGATTTTGCAGGGCG 59.817 61.111 0.00 0.00 36.25 6.13
558 602 2.342650 GCTGGATTTTGCAGGGCGA 61.343 57.895 0.00 0.00 36.25 5.54
569 613 1.745087 TGCAGGGCGAAATTCAGAATC 59.255 47.619 0.00 0.00 0.00 2.52
576 620 1.678101 CGAAATTCAGAATCAGGCCCC 59.322 52.381 0.00 0.00 0.00 5.80
577 621 2.034878 GAAATTCAGAATCAGGCCCCC 58.965 52.381 0.00 0.00 0.00 5.40
578 622 1.312884 AATTCAGAATCAGGCCCCCT 58.687 50.000 0.00 0.00 0.00 4.79
584 628 2.470938 GAATCAGGCCCCCTATCCGC 62.471 65.000 0.00 0.00 29.64 5.54
746 842 5.623956 TCCGGATACCATGTCATTAAAGT 57.376 39.130 0.00 0.00 0.00 2.66
751 847 7.117812 CCGGATACCATGTCATTAAAGTATCAC 59.882 40.741 0.00 9.69 38.41 3.06
752 848 7.148804 CGGATACCATGTCATTAAAGTATCACG 60.149 40.741 16.41 14.20 38.41 4.35
753 849 5.734855 ACCATGTCATTAAAGTATCACGC 57.265 39.130 0.00 0.00 0.00 5.34
754 850 5.182487 ACCATGTCATTAAAGTATCACGCA 58.818 37.500 0.00 0.00 0.00 5.24
755 851 5.822519 ACCATGTCATTAAAGTATCACGCAT 59.177 36.000 0.00 0.00 0.00 4.73
756 852 6.017934 ACCATGTCATTAAAGTATCACGCATC 60.018 38.462 0.00 0.00 0.00 3.91
757 853 6.018016 CCATGTCATTAAAGTATCACGCATCA 60.018 38.462 0.00 0.00 0.00 3.07
758 854 6.976636 TGTCATTAAAGTATCACGCATCAA 57.023 33.333 0.00 0.00 0.00 2.57
759 855 6.771076 TGTCATTAAAGTATCACGCATCAAC 58.229 36.000 0.00 0.00 0.00 3.18
760 856 6.183360 TGTCATTAAAGTATCACGCATCAACC 60.183 38.462 0.00 0.00 0.00 3.77
761 857 5.295787 TCATTAAAGTATCACGCATCAACCC 59.704 40.000 0.00 0.00 0.00 4.11
762 858 2.038387 AAGTATCACGCATCAACCCC 57.962 50.000 0.00 0.00 0.00 4.95
763 859 0.180406 AGTATCACGCATCAACCCCC 59.820 55.000 0.00 0.00 0.00 5.40
880 976 0.550914 ACCTGGACAAAGGACAGCAA 59.449 50.000 0.00 0.00 40.02 3.91
882 978 1.477558 CCTGGACAAAGGACAGCAACT 60.478 52.381 0.00 0.00 40.02 3.16
894 990 1.152030 AGCAACTCTCCTCACCCCA 60.152 57.895 0.00 0.00 0.00 4.96
895 991 1.197430 AGCAACTCTCCTCACCCCAG 61.197 60.000 0.00 0.00 0.00 4.45
918 1015 4.741342 CGCCTCCTATATTAAAGTACCCG 58.259 47.826 0.00 0.00 0.00 5.28
948 1047 0.467384 TTGCTCTATCTCCCTGCAGC 59.533 55.000 8.66 0.00 35.02 5.25
950 1049 0.249826 GCTCTATCTCCCTGCAGCAC 60.250 60.000 8.66 0.00 0.00 4.40
952 1051 1.693062 CTCTATCTCCCTGCAGCACAT 59.307 52.381 8.66 0.00 0.00 3.21
956 1055 1.499368 TCTCCCTGCAGCACATATCA 58.501 50.000 8.66 0.00 0.00 2.15
966 1065 2.032290 CAGCACATATCACATTCAGGCG 60.032 50.000 0.00 0.00 0.00 5.52
967 1066 1.942657 GCACATATCACATTCAGGCGT 59.057 47.619 0.00 0.00 0.00 5.68
969 1068 3.559655 GCACATATCACATTCAGGCGTAA 59.440 43.478 0.00 0.00 0.00 3.18
970 1069 4.552767 GCACATATCACATTCAGGCGTAAC 60.553 45.833 0.00 0.00 0.00 2.50
971 1070 4.024893 CACATATCACATTCAGGCGTAACC 60.025 45.833 0.00 0.00 39.61 2.85
994 1094 2.148768 CAGCAATTCAGCAGAGTCACA 58.851 47.619 0.00 0.00 36.85 3.58
995 1095 2.095869 CAGCAATTCAGCAGAGTCACAC 60.096 50.000 0.00 0.00 36.85 3.82
997 1097 1.462283 CAATTCAGCAGAGTCACACCG 59.538 52.381 0.00 0.00 0.00 4.94
998 1098 0.671781 ATTCAGCAGAGTCACACCGC 60.672 55.000 0.00 0.00 0.00 5.68
999 1099 3.108289 CAGCAGAGTCACACCGCG 61.108 66.667 0.00 0.00 0.00 6.46
1000 1100 3.295273 AGCAGAGTCACACCGCGA 61.295 61.111 8.23 0.00 0.00 5.87
1001 1101 2.125912 GCAGAGTCACACCGCGAT 60.126 61.111 8.23 0.00 0.00 4.58
1003 1103 1.080501 CAGAGTCACACCGCGATGT 60.081 57.895 8.23 2.49 0.00 3.06
1164 1264 2.969238 GCCATCGCGTCCATCCTG 60.969 66.667 5.77 0.00 0.00 3.86
1305 1405 1.679641 CATGGTGCACATCCTGCCA 60.680 57.895 20.43 5.71 46.51 4.92
1496 1596 1.819903 TGACAACATCGACATACCCGA 59.180 47.619 0.00 0.00 40.53 5.14
1497 1597 2.231721 TGACAACATCGACATACCCGAA 59.768 45.455 0.00 0.00 39.62 4.30
1498 1598 2.601763 GACAACATCGACATACCCGAAC 59.398 50.000 0.00 0.00 39.62 3.95
1499 1599 2.028839 ACAACATCGACATACCCGAACA 60.029 45.455 0.00 0.00 39.62 3.18
1500 1600 2.288961 ACATCGACATACCCGAACAC 57.711 50.000 0.00 0.00 39.62 3.32
1501 1601 1.197055 CATCGACATACCCGAACACG 58.803 55.000 0.00 0.00 39.62 4.49
1502 1602 0.526954 ATCGACATACCCGAACACGC 60.527 55.000 0.00 0.00 39.62 5.34
1503 1603 2.162754 CGACATACCCGAACACGCC 61.163 63.158 0.00 0.00 0.00 5.68
1504 1604 2.125832 ACATACCCGAACACGCCG 60.126 61.111 0.00 0.00 0.00 6.46
1525 1625 4.332543 ACGAGGAAGGGAGGGCCA 62.333 66.667 6.18 0.00 35.15 5.36
1644 1758 5.069251 CAGGGTGGTATCTCAGGTAAGTAAG 59.931 48.000 0.00 0.00 0.00 2.34
1645 1759 5.043582 AGGGTGGTATCTCAGGTAAGTAAGA 60.044 44.000 0.00 0.00 0.00 2.10
1646 1760 5.302313 GGGTGGTATCTCAGGTAAGTAAGAG 59.698 48.000 0.00 0.00 0.00 2.85
1647 1761 5.221283 GGTGGTATCTCAGGTAAGTAAGAGC 60.221 48.000 0.00 0.00 0.00 4.09
1648 1762 5.360144 GTGGTATCTCAGGTAAGTAAGAGCA 59.640 44.000 0.00 0.00 0.00 4.26
1649 1763 5.594725 TGGTATCTCAGGTAAGTAAGAGCAG 59.405 44.000 0.00 0.00 0.00 4.24
1650 1764 4.664150 ATCTCAGGTAAGTAAGAGCAGC 57.336 45.455 0.00 0.00 0.00 5.25
1651 1765 2.761208 TCTCAGGTAAGTAAGAGCAGCC 59.239 50.000 0.00 0.00 0.00 4.85
1652 1766 2.497675 CTCAGGTAAGTAAGAGCAGCCA 59.502 50.000 0.00 0.00 0.00 4.75
1653 1767 2.233922 TCAGGTAAGTAAGAGCAGCCAC 59.766 50.000 0.00 0.00 0.00 5.01
1654 1768 2.234908 CAGGTAAGTAAGAGCAGCCACT 59.765 50.000 0.00 0.00 0.00 4.00
1655 1769 2.498078 AGGTAAGTAAGAGCAGCCACTC 59.502 50.000 0.00 0.00 36.91 3.51
1656 1770 2.418884 GGTAAGTAAGAGCAGCCACTCC 60.419 54.545 0.12 0.00 37.39 3.85
1657 1771 1.352083 AAGTAAGAGCAGCCACTCCA 58.648 50.000 0.12 0.00 37.39 3.86
1767 1884 3.366781 GGGAGCATGAAAGAAGCAACTTC 60.367 47.826 0.00 0.00 40.45 3.01
2000 2117 7.602265 CCATAAAGAAACACAAATAAACAGGGG 59.398 37.037 0.00 0.00 0.00 4.79
2012 2129 1.686236 AACAGGGGATGGGAATGAGT 58.314 50.000 0.00 0.00 0.00 3.41
2134 2252 7.014711 TGTTTGCCAAGTTGGTAGATATTTTGA 59.985 33.333 22.85 0.00 40.46 2.69
2169 2287 7.414762 CCAGTCCCGTGTTAAATAACCATAAAG 60.415 40.741 1.13 0.00 35.37 1.85
2172 2290 8.298854 GTCCCGTGTTAAATAACCATAAAGTTT 58.701 33.333 1.13 0.00 35.37 2.66
2201 2320 2.403561 AGGTTCTAGAGCTGGGAATCC 58.596 52.381 6.54 0.00 34.08 3.01
2224 2343 3.130869 TGGTGCATTCAGTGATAATTGGC 59.869 43.478 0.00 0.00 0.00 4.52
2605 2733 7.182206 AGGGAGAAAATAGGAAGTTGCTAGTTA 59.818 37.037 15.97 0.00 28.86 2.24
2733 2861 4.072131 CCAGAGCAACAAAAGGCTAAGTA 58.928 43.478 0.00 0.00 41.22 2.24
2759 2890 8.084684 AGCTAACATCTTTGATTTCCACTTTTC 58.915 33.333 0.00 0.00 0.00 2.29
2760 2891 7.867403 GCTAACATCTTTGATTTCCACTTTTCA 59.133 33.333 0.00 0.00 0.00 2.69
2762 2893 7.352079 ACATCTTTGATTTCCACTTTTCACT 57.648 32.000 0.00 0.00 0.00 3.41
2781 2912 2.821969 ACTGCAGGCTAATTTCAAGGTG 59.178 45.455 19.93 0.00 0.00 4.00
3353 3504 8.228464 CAGTAGGTTTCGGACTTTCTAAATTTC 58.772 37.037 0.00 0.00 0.00 2.17
3381 3532 4.526262 AGCTGAGTCTCTCACACTAACAAT 59.474 41.667 0.65 0.00 35.39 2.71
3394 3545 4.033019 CACTAACAATGAATCTGCATGCG 58.967 43.478 14.09 8.20 0.00 4.73
3634 3786 3.634397 TCTAAGTTCATGGCCCTCTTG 57.366 47.619 0.00 0.00 0.00 3.02
4027 4897 1.437986 CCGACCATTCTCGAGACCC 59.562 63.158 16.36 1.82 35.58 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.488006 CCCAATCCAAAGTTGATAAGATCGAT 59.512 38.462 0.00 0.00 0.00 3.59
68 69 3.716006 CACTGACCTTGGCGCACG 61.716 66.667 10.83 0.00 0.00 5.34
102 103 6.458210 GTTTTTCTTGGGTCACAATCATCAT 58.542 36.000 0.00 0.00 38.65 2.45
131 133 1.968017 CTGGGCTCTTTTCGCTGCA 60.968 57.895 0.00 0.00 0.00 4.41
158 160 2.110990 CAAAATGCACGCCATGTATCG 58.889 47.619 0.00 0.00 31.50 2.92
159 161 2.462889 CCAAAATGCACGCCATGTATC 58.537 47.619 0.00 0.00 31.50 2.24
160 162 1.471327 GCCAAAATGCACGCCATGTAT 60.471 47.619 0.00 0.00 34.68 2.29
161 163 0.108898 GCCAAAATGCACGCCATGTA 60.109 50.000 0.00 0.00 33.49 2.29
162 164 1.374505 GCCAAAATGCACGCCATGT 60.375 52.632 0.00 0.00 33.49 3.21
163 165 2.101835 GGCCAAAATGCACGCCATG 61.102 57.895 0.00 0.00 41.25 3.66
164 166 2.265424 GGCCAAAATGCACGCCAT 59.735 55.556 0.00 0.00 41.25 4.40
165 167 4.001226 GGGCCAAAATGCACGCCA 62.001 61.111 4.39 0.00 43.50 5.69
166 168 4.758251 GGGGCCAAAATGCACGCC 62.758 66.667 4.39 0.00 40.85 5.68
203 205 1.447317 GGCGTTGGCGATGGAATGAT 61.447 55.000 0.00 0.00 41.24 2.45
238 240 0.592500 CCGAGATCACACGACATCCG 60.593 60.000 0.00 0.00 45.44 4.18
327 345 2.259204 CGACCGGTGCGAGGTAAA 59.741 61.111 14.63 0.00 43.01 2.01
350 368 0.465705 TGATTGACCATCGAGAGGCC 59.534 55.000 6.60 0.00 34.08 5.19
368 388 3.508840 GCGGGTTCGGCCAGATTG 61.509 66.667 2.24 0.00 39.65 2.67
369 389 4.028490 TGCGGGTTCGGCCAGATT 62.028 61.111 2.24 0.00 39.65 2.40
370 390 4.778143 GTGCGGGTTCGGCCAGAT 62.778 66.667 2.24 0.00 39.65 2.90
400 420 2.175878 TTTCAGGAGTCTGCTTGCTC 57.824 50.000 0.00 0.00 40.69 4.26
422 442 0.174845 TCGTCATCGGCCAAGTTAGG 59.825 55.000 2.24 0.00 37.69 2.69
424 444 0.604073 TGTCGTCATCGGCCAAGTTA 59.396 50.000 2.24 0.00 41.33 2.24
425 445 0.036388 ATGTCGTCATCGGCCAAGTT 60.036 50.000 2.24 0.00 41.33 2.66
427 447 0.374758 CAATGTCGTCATCGGCCAAG 59.625 55.000 2.24 0.00 41.33 3.61
429 449 1.018752 CACAATGTCGTCATCGGCCA 61.019 55.000 2.24 0.00 41.33 5.36
430 450 1.019278 ACACAATGTCGTCATCGGCC 61.019 55.000 0.00 0.00 41.33 6.13
477 498 3.344215 CGGCTGAGGATGATGCGC 61.344 66.667 0.00 0.00 0.00 6.09
478 499 3.344215 GCGGCTGAGGATGATGCG 61.344 66.667 0.00 0.00 0.00 4.73
479 500 2.976903 GGCGGCTGAGGATGATGC 60.977 66.667 0.00 0.00 0.00 3.91
480 501 0.954449 GATGGCGGCTGAGGATGATG 60.954 60.000 11.43 0.00 0.00 3.07
481 502 1.374190 GATGGCGGCTGAGGATGAT 59.626 57.895 11.43 0.00 0.00 2.45
482 503 2.824546 GATGGCGGCTGAGGATGA 59.175 61.111 11.43 0.00 0.00 2.92
483 504 2.664185 CGATGGCGGCTGAGGATG 60.664 66.667 11.43 0.00 0.00 3.51
517 561 0.964700 GGTACGTGTATAGGGAGGGC 59.035 60.000 0.00 0.00 0.00 5.19
534 578 1.526575 CTGCAAAATCCAGCGTGGGT 61.527 55.000 4.52 0.00 38.32 4.51
535 579 1.213537 CTGCAAAATCCAGCGTGGG 59.786 57.895 4.52 0.00 38.32 4.61
537 581 1.213537 CCCTGCAAAATCCAGCGTG 59.786 57.895 0.00 0.00 0.00 5.34
538 582 2.639327 GCCCTGCAAAATCCAGCGT 61.639 57.895 0.00 0.00 0.00 5.07
539 583 2.182537 GCCCTGCAAAATCCAGCG 59.817 61.111 0.00 0.00 0.00 5.18
540 584 1.876497 TTCGCCCTGCAAAATCCAGC 61.876 55.000 0.00 0.00 0.00 4.85
541 585 0.602562 TTTCGCCCTGCAAAATCCAG 59.397 50.000 0.00 0.00 0.00 3.86
542 586 1.265236 ATTTCGCCCTGCAAAATCCA 58.735 45.000 0.00 0.00 0.00 3.41
543 587 2.270923 GAATTTCGCCCTGCAAAATCC 58.729 47.619 0.00 0.00 0.00 3.01
544 588 2.925563 CTGAATTTCGCCCTGCAAAATC 59.074 45.455 0.00 0.00 0.00 2.17
545 589 2.562298 TCTGAATTTCGCCCTGCAAAAT 59.438 40.909 0.00 0.00 0.00 1.82
546 590 1.959985 TCTGAATTTCGCCCTGCAAAA 59.040 42.857 0.00 0.00 0.00 2.44
547 591 1.614996 TCTGAATTTCGCCCTGCAAA 58.385 45.000 0.00 0.00 0.00 3.68
548 592 1.614996 TTCTGAATTTCGCCCTGCAA 58.385 45.000 0.00 0.00 0.00 4.08
549 593 1.745087 GATTCTGAATTTCGCCCTGCA 59.255 47.619 4.11 0.00 0.00 4.41
550 594 1.745087 TGATTCTGAATTTCGCCCTGC 59.255 47.619 4.11 0.00 0.00 4.85
551 595 2.357009 CCTGATTCTGAATTTCGCCCTG 59.643 50.000 4.11 0.00 0.00 4.45
552 596 2.648059 CCTGATTCTGAATTTCGCCCT 58.352 47.619 4.11 0.00 0.00 5.19
553 597 1.066152 GCCTGATTCTGAATTTCGCCC 59.934 52.381 4.11 0.00 0.00 6.13
554 598 1.066152 GGCCTGATTCTGAATTTCGCC 59.934 52.381 15.29 15.29 0.00 5.54
555 599 1.066152 GGGCCTGATTCTGAATTTCGC 59.934 52.381 0.84 6.22 0.00 4.70
556 600 1.678101 GGGGCCTGATTCTGAATTTCG 59.322 52.381 0.84 0.00 0.00 3.46
557 601 2.034878 GGGGGCCTGATTCTGAATTTC 58.965 52.381 0.84 0.00 0.00 2.17
558 602 1.648037 AGGGGGCCTGATTCTGAATTT 59.352 47.619 0.84 0.00 29.57 1.82
563 607 0.695347 GGATAGGGGGCCTGATTCTG 59.305 60.000 0.84 0.00 34.61 3.02
576 620 0.038159 GATGGACGAAGGCGGATAGG 60.038 60.000 0.00 0.00 43.17 2.57
577 621 0.038159 GGATGGACGAAGGCGGATAG 60.038 60.000 0.00 0.00 43.17 2.08
578 622 0.757561 TGGATGGACGAAGGCGGATA 60.758 55.000 0.00 0.00 43.17 2.59
584 628 1.536922 CGATCACTGGATGGACGAAGG 60.537 57.143 0.00 0.00 32.67 3.46
636 732 1.820906 CATCCATGGTCACCAGCCG 60.821 63.158 12.58 0.00 36.75 5.52
669 765 2.267642 CAGGATCCACGGCCGAAA 59.732 61.111 35.90 17.03 0.00 3.46
672 768 3.550431 ATCCAGGATCCACGGCCG 61.550 66.667 26.86 26.86 0.00 6.13
674 770 2.111878 CCATCCAGGATCCACGGC 59.888 66.667 15.82 0.00 41.22 5.68
773 869 4.212425 TGTCGTTGATGCGTGATACTTTTT 59.788 37.500 0.00 0.00 0.00 1.94
774 870 3.743911 TGTCGTTGATGCGTGATACTTTT 59.256 39.130 0.00 0.00 0.00 2.27
775 871 3.122948 GTGTCGTTGATGCGTGATACTTT 59.877 43.478 0.00 0.00 0.00 2.66
776 872 2.666508 GTGTCGTTGATGCGTGATACTT 59.333 45.455 0.00 0.00 0.00 2.24
777 873 2.094700 AGTGTCGTTGATGCGTGATACT 60.095 45.455 0.00 0.00 0.00 2.12
778 874 2.259618 AGTGTCGTTGATGCGTGATAC 58.740 47.619 0.00 0.00 0.00 2.24
779 875 2.647529 AGTGTCGTTGATGCGTGATA 57.352 45.000 0.00 0.00 0.00 2.15
780 876 1.795768 AAGTGTCGTTGATGCGTGAT 58.204 45.000 0.00 0.00 0.00 3.06
781 877 1.260297 CAAAGTGTCGTTGATGCGTGA 59.740 47.619 0.00 0.00 0.00 4.35
782 878 1.662360 CAAAGTGTCGTTGATGCGTG 58.338 50.000 0.00 0.00 0.00 5.34
783 879 0.041312 GCAAAGTGTCGTTGATGCGT 60.041 50.000 0.24 0.00 0.00 5.24
784 880 0.041400 TGCAAAGTGTCGTTGATGCG 60.041 50.000 0.00 0.00 36.62 4.73
880 976 2.681778 CGCTGGGGTGAGGAGAGT 60.682 66.667 0.00 0.00 0.00 3.24
894 990 4.222366 GGGTACTTTAATATAGGAGGCGCT 59.778 45.833 7.64 0.00 0.00 5.92
895 991 4.502016 GGGTACTTTAATATAGGAGGCGC 58.498 47.826 0.00 0.00 0.00 6.53
918 1015 0.462759 ATAGAGCAAGAGCCAACGCC 60.463 55.000 0.00 0.00 43.56 5.68
948 1047 4.024893 GGTTACGCCTGAATGTGATATGTG 60.025 45.833 0.00 0.00 0.00 3.21
950 1049 4.126437 TGGTTACGCCTGAATGTGATATG 58.874 43.478 0.00 0.00 38.35 1.78
952 1051 3.897141 TGGTTACGCCTGAATGTGATA 57.103 42.857 0.00 0.00 38.35 2.15
956 1055 2.632377 CTGATGGTTACGCCTGAATGT 58.368 47.619 0.00 0.00 38.35 2.71
966 1065 3.691118 TCTGCTGAATTGCTGATGGTTAC 59.309 43.478 0.00 0.00 36.30 2.50
967 1066 3.943381 CTCTGCTGAATTGCTGATGGTTA 59.057 43.478 0.00 0.00 39.50 2.85
969 1068 2.290768 ACTCTGCTGAATTGCTGATGGT 60.291 45.455 0.00 0.00 39.50 3.55
970 1069 2.355132 GACTCTGCTGAATTGCTGATGG 59.645 50.000 0.00 0.00 39.50 3.51
971 1070 3.007635 TGACTCTGCTGAATTGCTGATG 58.992 45.455 0.00 0.00 39.50 3.07
994 1094 4.157120 GGTAGCCCACATCGCGGT 62.157 66.667 6.13 0.00 0.00 5.68
995 1095 3.673956 TTGGTAGCCCACATCGCGG 62.674 63.158 6.13 0.00 41.67 6.46
997 1097 2.472909 GCTTGGTAGCCCACATCGC 61.473 63.158 0.00 0.00 41.67 4.58
998 1098 3.813596 GCTTGGTAGCCCACATCG 58.186 61.111 0.00 0.00 41.67 3.84
1017 1117 1.208614 GAGAAGCGCTTGCAAGGTG 59.791 57.895 30.47 15.25 42.66 4.00
1263 1363 3.134127 GCAAGGATGACACCGGCC 61.134 66.667 0.00 0.00 34.73 6.13
1269 1369 2.350895 CCGGTGGCAAGGATGACA 59.649 61.111 4.39 0.00 44.25 3.58
1311 1411 2.654877 GAGGTGAGCCCGTCGAAA 59.345 61.111 0.00 0.00 38.74 3.46
1359 1459 1.362355 CGCAAAAGGGAAGCCGTTT 59.638 52.632 0.00 0.00 42.38 3.60
1496 1596 4.052229 CCTCGTCTCCGGCGTGTT 62.052 66.667 6.01 0.00 33.95 3.32
1498 1598 3.685214 CTTCCTCGTCTCCGGCGTG 62.685 68.421 6.01 0.00 33.95 5.34
1499 1599 3.441290 CTTCCTCGTCTCCGGCGT 61.441 66.667 6.01 0.00 33.95 5.68
1500 1600 4.194720 CCTTCCTCGTCTCCGGCG 62.195 72.222 0.00 0.00 33.95 6.46
1501 1601 3.839432 CCCTTCCTCGTCTCCGGC 61.839 72.222 0.00 0.00 33.95 6.13
1502 1602 2.044252 TCCCTTCCTCGTCTCCGG 60.044 66.667 0.00 0.00 33.95 5.14
1503 1603 2.122167 CCTCCCTTCCTCGTCTCCG 61.122 68.421 0.00 0.00 0.00 4.63
1504 1604 1.758906 CCCTCCCTTCCTCGTCTCC 60.759 68.421 0.00 0.00 0.00 3.71
1509 1609 2.330924 GATTGGCCCTCCCTTCCTCG 62.331 65.000 0.00 0.00 0.00 4.63
1525 1625 0.452987 GCGTGCACATGTGGATGATT 59.547 50.000 35.31 0.00 39.86 2.57
1599 1699 1.065491 TGCCGGATTGTGTCAGCTATT 60.065 47.619 5.05 0.00 0.00 1.73
1644 1758 1.601759 TGCTTTGGAGTGGCTGCTC 60.602 57.895 0.00 1.88 34.89 4.26
1645 1759 1.900498 GTGCTTTGGAGTGGCTGCT 60.900 57.895 0.00 0.00 0.00 4.24
1646 1760 1.530013 ATGTGCTTTGGAGTGGCTGC 61.530 55.000 0.00 0.00 0.00 5.25
1647 1761 1.741706 CTATGTGCTTTGGAGTGGCTG 59.258 52.381 0.00 0.00 0.00 4.85
1648 1762 1.340405 CCTATGTGCTTTGGAGTGGCT 60.340 52.381 0.00 0.00 0.00 4.75
1649 1763 1.098050 CCTATGTGCTTTGGAGTGGC 58.902 55.000 0.00 0.00 0.00 5.01
1650 1764 2.026822 AGTCCTATGTGCTTTGGAGTGG 60.027 50.000 0.00 0.00 31.68 4.00
1651 1765 3.340814 AGTCCTATGTGCTTTGGAGTG 57.659 47.619 0.00 0.00 31.68 3.51
1652 1766 3.307762 GGAAGTCCTATGTGCTTTGGAGT 60.308 47.826 0.00 0.00 34.05 3.85
1653 1767 3.054802 AGGAAGTCCTATGTGCTTTGGAG 60.055 47.826 0.00 0.00 46.48 3.86
1654 1768 2.912956 AGGAAGTCCTATGTGCTTTGGA 59.087 45.455 0.00 0.00 46.48 3.53
1655 1769 3.012518 CAGGAAGTCCTATGTGCTTTGG 58.987 50.000 0.00 0.00 46.65 3.28
1656 1770 3.012518 CCAGGAAGTCCTATGTGCTTTG 58.987 50.000 0.00 0.00 46.65 2.77
1657 1771 2.619074 GCCAGGAAGTCCTATGTGCTTT 60.619 50.000 0.00 0.00 46.65 3.51
1741 1855 2.291089 TGCTTCTTTCATGCTCCCATCA 60.291 45.455 0.00 0.00 0.00 3.07
1836 1953 8.408601 AGATATTTTGGAACATTATGTGCTGAC 58.591 33.333 3.05 0.00 39.30 3.51
2000 2117 7.251321 AGGTATTGATCTACTCATTCCCATC 57.749 40.000 0.00 0.00 32.72 3.51
2012 2129 8.577296 CAGACCTTTCGAATAGGTATTGATCTA 58.423 37.037 23.31 0.00 45.88 1.98
2134 2252 0.179029 CACGGGACTGGTTGGTTCTT 60.179 55.000 0.00 0.00 0.00 2.52
2169 2287 4.034975 GCTCTAGAACCTGCATGATGAAAC 59.965 45.833 0.00 0.00 0.00 2.78
2172 2290 3.036819 AGCTCTAGAACCTGCATGATGA 58.963 45.455 0.00 0.00 0.00 2.92
2201 2320 4.735578 GCCAATTATCACTGAATGCACCAG 60.736 45.833 14.38 14.38 37.64 4.00
2224 2343 2.862536 CACAGATGCTCCTAATGACACG 59.137 50.000 0.00 0.00 0.00 4.49
2501 2627 9.713740 GAAGAAAATCATCAGTATGTGTTCATC 57.286 33.333 0.00 0.00 37.40 2.92
2534 2660 8.201554 AGCTGTTGTATATAGTGTGTTGATTG 57.798 34.615 0.00 0.00 0.00 2.67
2597 2725 7.561722 ACTGGAATATCAGTTCTCTAACTAGCA 59.438 37.037 0.00 0.00 44.28 3.49
2598 2726 7.947282 ACTGGAATATCAGTTCTCTAACTAGC 58.053 38.462 0.00 0.00 44.28 3.42
2642 2770 6.262944 TGCTTTCTTCAGAATCTTTGCTTACA 59.737 34.615 0.00 0.00 33.54 2.41
2714 2842 4.084889 GCTACTTAGCCTTTTGTTGCTC 57.915 45.455 0.00 0.00 43.39 4.26
2733 2861 7.530426 AAAGTGGAAATCAAAGATGTTAGCT 57.470 32.000 0.00 0.00 0.00 3.32
2751 2882 1.896220 TAGCCTGCAGTGAAAAGTGG 58.104 50.000 13.81 0.00 0.00 4.00
2759 2890 2.821969 ACCTTGAAATTAGCCTGCAGTG 59.178 45.455 13.81 5.37 0.00 3.66
2760 2891 2.821969 CACCTTGAAATTAGCCTGCAGT 59.178 45.455 13.81 0.00 0.00 4.40
2762 2893 3.084039 CTCACCTTGAAATTAGCCTGCA 58.916 45.455 0.00 0.00 0.00 4.41
2781 2912 1.325355 CCATGATGATGGTTGCCCTC 58.675 55.000 2.51 0.00 43.98 4.30
3214 3352 7.012327 CCAAGAGTATGTTGTTTTGAGAGACAA 59.988 37.037 0.00 0.00 37.73 3.18
3216 3354 6.706270 TCCAAGAGTATGTTGTTTTGAGAGAC 59.294 38.462 0.00 0.00 37.73 3.36
3353 3504 1.742268 TGTGAGAGACTCAGCTGATCG 59.258 52.381 18.63 9.30 41.46 3.69
3381 3532 4.157472 TGGAAAAATACGCATGCAGATTCA 59.843 37.500 19.57 7.40 0.00 2.57
3634 3786 2.249557 CTGCAGTGCCGAGTTGCATC 62.250 60.000 13.72 0.00 45.72 3.91
4027 4897 2.035321 GAGCTCGAATAGGGAGGAACAG 59.965 54.545 0.00 0.00 32.10 3.16


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

AutoCloner maintained by Alex Coulton.