Multiple sequence alignment - TraesCS3D01G030300

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 TraesCS3D01G030300 chr3D 100.000 3559 0 0 1 3559 11209625 11206067 0.000000e+00 6573.0
1 TraesCS3D01G030300 chr3D 92.727 55 4 0 1519 1573 574707334 574707388 2.950000e-11 80.5
2 TraesCS3D01G030300 chr3D 100.000 41 0 0 1524 1564 27678892 27678932 3.810000e-10 76.8
3 TraesCS3D01G030300 chrUn 95.032 2496 116 4 1069 3558 336216991 336219484 0.000000e+00 3916.0
4 TraesCS3D01G030300 chrUn 94.375 1440 73 4 2125 3558 393352921 393354358 0.000000e+00 2204.0
5 TraesCS3D01G030300 chrUn 96.144 1141 38 3 765 1902 322442231 322443368 0.000000e+00 1858.0
6 TraesCS3D01G030300 chrUn 94.562 754 40 1 1 754 322441430 322442182 0.000000e+00 1164.0
7 TraesCS3D01G030300 chrUn 94.467 723 39 1 1 723 279693846 279694567 0.000000e+00 1112.0
8 TraesCS3D01G030300 chrUn 72.864 398 89 13 1963 2355 336218865 336219248 6.240000e-23 119.0
9 TraesCS3D01G030300 chrUn 72.864 398 89 13 1963 2355 393353739 393354122 6.240000e-23 119.0
10 TraesCS3D01G030300 chr3A 94.050 1479 79 5 2087 3558 18799536 18798060 0.000000e+00 2235.0
11 TraesCS3D01G030300 chr3A 96.305 1299 41 4 765 2060 18800823 18799529 0.000000e+00 2126.0
12 TraesCS3D01G030300 chr3A 94.828 754 37 2 1 754 18801623 18800872 0.000000e+00 1175.0
13 TraesCS3D01G030300 chr3A 94.562 754 37 3 1 754 17859330 17858581 0.000000e+00 1162.0
14 TraesCS3D01G030300 chr3A 96.187 577 15 4 765 1338 17858532 17857960 0.000000e+00 937.0
15 TraesCS3D01G030300 chr3A 72.959 392 87 13 1969 2355 18798673 18798296 6.240000e-23 119.0
16 TraesCS3D01G030300 chr5B 87.958 191 21 2 3369 3558 542689815 542690004 1.290000e-54 224.0
17 TraesCS3D01G030300 chr4B 87.766 188 22 1 3372 3558 659399824 659399637 5.980000e-53 219.0
18 TraesCS3D01G030300 chr2B 87.234 188 21 3 3373 3558 163430816 163431002 1.000000e-50 211.0
19 TraesCS3D01G030300 chr1A 87.166 187 23 1 3373 3558 22533814 22534000 1.000000e-50 211.0
20 TraesCS3D01G030300 chr7D 86.598 194 21 5 3368 3558 184387545 184387736 3.600000e-50 209.0
21 TraesCS3D01G030300 chr7D 93.478 46 3 0 1519 1564 476009945 476009990 6.380000e-08 69.4
22 TraesCS3D01G030300 chr7B 86.528 193 23 3 3368 3558 348123279 348123088 3.600000e-50 209.0
23 TraesCS3D01G030300 chr7B 93.750 48 1 2 1527 1573 736106193 736106239 1.770000e-08 71.3
24 TraesCS3D01G030300 chr6B 95.652 46 2 0 1519 1564 21125694 21125739 1.370000e-09 75.0
25 TraesCS3D01G030300 chr7A 89.091 55 5 1 1519 1573 654912012 654912065 2.290000e-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 TraesCS3D01G030300 chr3D 11206067 11209625 3558 True 6573.00 6573 100.0000 1 3559 1 chr3D.!!$R1 3558
1 TraesCS3D01G030300 chrUn 336216991 336219484 2493 False 2017.50 3916 83.9480 1069 3558 2 chrUn.!!$F3 2489
2 TraesCS3D01G030300 chrUn 322441430 322443368 1938 False 1511.00 1858 95.3530 1 1902 2 chrUn.!!$F2 1901
3 TraesCS3D01G030300 chrUn 393352921 393354358 1437 False 1161.50 2204 83.6195 1963 3558 2 chrUn.!!$F4 1595
4 TraesCS3D01G030300 chrUn 279693846 279694567 721 False 1112.00 1112 94.4670 1 723 1 chrUn.!!$F1 722
5 TraesCS3D01G030300 chr3A 18798060 18801623 3563 True 1413.75 2235 89.5355 1 3558 4 chr3A.!!$R2 3557
6 TraesCS3D01G030300 chr3A 17857960 17859330 1370 True 1049.50 1162 95.3745 1 1338 2 chr3A.!!$R1 1337

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
176 177 0.107165 AATTCCTTCCCTACCGCTGC 60.107 55.0 0.0 0.0 0.0 5.25 F
374 376 0.179137 TGGAGCGACGCAATCTACTG 60.179 55.0 23.7 0.0 0.0 2.74 F
1546 1589 0.323629 TTTTCTACACCCCAGCTCGG 59.676 55.0 0.0 0.0 0.0 4.63 F
1547 1590 0.834687 TTTCTACACCCCAGCTCGGT 60.835 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 1590 0.179043 TAGTTTCTTGCGTGGGTGCA 60.179 50.0 0.00 0.0 44.61 4.57 R
1909 1952 0.830444 ACGGTTGTAGCCTCCAGTGA 60.830 55.0 0.00 0.0 0.00 3.41 R
2525 2574 0.179234 TCCAACGCCAGTCACTCAAA 59.821 50.0 0.00 0.0 0.00 2.69 R
3346 3395 0.466922 GATTGGTGCTCCTGGGATGG 60.467 60.0 6.34 0.0 34.23 3.51 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
109 110 4.411927 TGTCTCATTATAGGAGGAGGAGC 58.588 47.826 4.29 0.00 33.18 4.70
135 136 0.246360 TGATGATGACGTTGTCGGCT 59.754 50.000 0.00 0.00 46.49 5.52
154 155 3.654143 TCGTCCTCGTCCTCCCCA 61.654 66.667 0.00 0.00 38.33 4.96
155 156 3.141488 CGTCCTCGTCCTCCCCAG 61.141 72.222 0.00 0.00 0.00 4.45
173 174 3.398694 GGAATTCCTTCCCTACCGC 57.601 57.895 17.73 0.00 44.56 5.68
176 177 0.107165 AATTCCTTCCCTACCGCTGC 60.107 55.000 0.00 0.00 0.00 5.25
185 186 3.438017 CTACCGCTGCTGCCTCCTC 62.438 68.421 10.24 0.00 35.36 3.71
248 250 1.674057 CAGTCGGAGGCTTCCAACT 59.326 57.895 16.07 9.44 45.33 3.16
337 339 5.543507 ATTCGAGGCATCTTTGATAGAGT 57.456 39.130 0.00 0.00 36.02 3.24
342 344 5.537188 GAGGCATCTTTGATAGAGTAGTGG 58.463 45.833 0.00 0.00 36.02 4.00
372 374 1.132588 GATGGAGCGACGCAATCTAC 58.867 55.000 23.70 1.80 0.00 2.59
374 376 0.179137 TGGAGCGACGCAATCTACTG 60.179 55.000 23.70 0.00 0.00 2.74
448 450 3.500680 GGTTATTTGTGAGTTCCGCTTCA 59.499 43.478 0.00 0.00 0.00 3.02
467 469 5.163571 GCTTCAGTGATCTCTCATAGTGACA 60.164 44.000 0.00 0.00 32.98 3.58
471 473 6.776603 TCAGTGATCTCTCATAGTGACATCAT 59.223 38.462 0.00 0.00 32.98 2.45
564 566 3.196901 TGGAAACACTAGGTATCATGCGT 59.803 43.478 0.00 0.00 33.40 5.24
582 584 6.259167 TCATGCGTTTGTACCTATTAATGGTC 59.741 38.462 11.39 6.34 38.88 4.02
619 621 4.301072 TTCCTTGTTATAAGCACTGCCT 57.699 40.909 0.00 0.00 0.00 4.75
644 646 9.345517 CTGAAGATTGCTCGAAAATCATTTTTA 57.654 29.630 17.99 5.07 36.65 1.52
658 660 6.687081 ATCATTTTTAGGCGAAAATCCGTA 57.313 33.333 6.35 0.00 37.17 4.02
659 661 6.114221 TCATTTTTAGGCGAAAATCCGTAG 57.886 37.500 6.35 0.00 37.17 3.51
755 757 3.650183 CGTTGCTCGCAAATAACGT 57.350 47.368 5.83 0.00 40.50 3.99
756 758 1.945207 CGTTGCTCGCAAATAACGTT 58.055 45.000 5.88 5.88 40.50 3.99
758 760 2.086849 CGTTGCTCGCAAATAACGTTTG 59.913 45.455 5.91 0.00 40.50 2.93
759 761 3.293262 GTTGCTCGCAAATAACGTTTGA 58.707 40.909 5.91 0.00 37.70 2.69
760 762 3.181826 TGCTCGCAAATAACGTTTGAG 57.818 42.857 5.91 0.30 0.00 3.02
761 763 1.905049 GCTCGCAAATAACGTTTGAGC 59.095 47.619 5.91 12.02 0.00 4.26
762 764 2.158143 CTCGCAAATAACGTTTGAGCG 58.842 47.619 22.38 22.38 44.45 5.03
763 765 1.136197 TCGCAAATAACGTTTGAGCGG 60.136 47.619 25.46 14.03 43.41 5.52
902 943 0.396811 ACCAGTTTAGACGCTGCCTT 59.603 50.000 0.00 0.00 0.00 4.35
906 947 3.555518 CAGTTTAGACGCTGCCTTTTTC 58.444 45.455 0.00 0.00 0.00 2.29
907 948 2.223377 AGTTTAGACGCTGCCTTTTTCG 59.777 45.455 0.00 0.00 0.00 3.46
908 949 0.515564 TTAGACGCTGCCTTTTTCGC 59.484 50.000 0.00 0.00 0.00 4.70
1027 1070 4.189188 ACGGAATCGAGGCGACGG 62.189 66.667 0.00 0.00 39.18 4.79
1065 1108 2.418197 GGAACCGATGATGGAGACGAAA 60.418 50.000 0.00 0.00 0.00 3.46
1066 1109 3.259064 GAACCGATGATGGAGACGAAAA 58.741 45.455 0.00 0.00 0.00 2.29
1067 1110 2.893637 ACCGATGATGGAGACGAAAAG 58.106 47.619 0.00 0.00 0.00 2.27
1084 1127 0.910088 AAGGAGGAGAACGGGGAAGG 60.910 60.000 0.00 0.00 0.00 3.46
1096 1139 3.459063 GGAAGGAGGGGTCCGTCG 61.459 72.222 3.96 0.00 38.82 5.12
1098 1141 4.698625 AAGGAGGGGTCCGTCGCT 62.699 66.667 3.96 0.68 34.28 4.93
1196 1239 1.630126 ATCCACGCCATCTGCCTTCT 61.630 55.000 0.00 0.00 36.24 2.85
1278 1321 2.420129 CCATGTTCTTCCTAGGGTTCCG 60.420 54.545 9.46 0.00 0.00 4.30
1279 1322 2.019807 TGTTCTTCCTAGGGTTCCGT 57.980 50.000 9.46 0.00 0.00 4.69
1316 1359 3.290948 AAAGGGCACTGTACAAGTTCA 57.709 42.857 0.00 0.00 36.83 3.18
1317 1360 2.550830 AGGGCACTGTACAAGTTCAG 57.449 50.000 0.00 5.45 36.83 3.02
1365 1408 7.433680 GCCCAGTTAAAATCGAATTATGGAAT 58.566 34.615 12.26 0.00 0.00 3.01
1396 1439 1.273724 TGGGGAATTGGATGGCATGTT 60.274 47.619 3.81 0.00 0.00 2.71
1429 1472 4.848562 ATTTCGACAAAGGGTTTTCTCC 57.151 40.909 0.00 0.00 0.00 3.71
1503 1546 2.187958 TGTTAGACATGGAGGTGAGGG 58.812 52.381 0.00 0.00 0.00 4.30
1516 1559 6.184789 TGGAGGTGAGGGTATAAAATCAAAC 58.815 40.000 0.00 0.00 0.00 2.93
1521 1564 6.657541 GGTGAGGGTATAAAATCAAACTGACA 59.342 38.462 0.00 0.00 0.00 3.58
1541 1584 4.398319 ACAGTGATTTTTCTACACCCCAG 58.602 43.478 0.00 0.00 35.47 4.45
1546 1589 0.323629 TTTTCTACACCCCAGCTCGG 59.676 55.000 0.00 0.00 0.00 4.63
1547 1590 0.834687 TTTCTACACCCCAGCTCGGT 60.835 55.000 0.00 0.00 0.00 4.69
1587 1630 2.672098 TGGCAACCCAAACACTGTAAT 58.328 42.857 0.00 0.00 38.46 1.89
1591 1634 3.824443 GCAACCCAAACACTGTAATACCT 59.176 43.478 0.00 0.00 0.00 3.08
1593 1636 5.768317 CAACCCAAACACTGTAATACCTTG 58.232 41.667 0.00 0.00 0.00 3.61
1662 1705 6.017026 TGTGTTATTGTTCCATTGACGCTTAA 60.017 34.615 0.00 0.00 0.00 1.85
1699 1742 5.502079 TGACCAACACCAGTTTTTCTTAGA 58.498 37.500 0.00 0.00 35.28 2.10
1791 1834 8.635765 AGGTTTCTCACAAGCAAAATCTAATA 57.364 30.769 0.00 0.00 0.00 0.98
1853 1896 1.029408 GTGCGGTTGGGCATGTGATA 61.029 55.000 0.00 0.00 45.99 2.15
1909 1952 3.673484 GTGCCACGCTTGTGCCAT 61.673 61.111 2.15 0.00 42.46 4.40
1913 1956 1.968017 CCACGCTTGTGCCATCACT 60.968 57.895 0.00 0.00 43.49 3.41
1959 2002 1.283905 TCGACCACATCCTGGAGTCTA 59.716 52.381 1.52 0.00 43.95 2.59
2051 2094 0.957395 AGAAGTCATGCCCACTTGCG 60.957 55.000 3.19 0.00 34.10 4.85
2108 2151 1.002868 CTTGACCACCCAGCTCCTG 60.003 63.158 0.00 0.00 0.00 3.86
2120 2163 1.451028 GCTCCTGCACCATCTCACC 60.451 63.158 0.00 0.00 39.41 4.02
2132 2175 2.188524 CATCTCACCGACGATCACAAG 58.811 52.381 0.00 0.00 0.00 3.16
2156 2199 6.670027 AGATACCAGTTACAGAGTTTCCATCT 59.330 38.462 0.00 0.00 0.00 2.90
2183 2226 2.644676 TGTCTCACCCTCGAGATACAG 58.355 52.381 15.71 4.57 43.69 2.74
2257 2306 0.875059 GCTAAGTTCACACCAGTGCC 59.125 55.000 0.00 0.00 45.49 5.01
2408 2457 3.728845 TGTAAGCACCAGTCTTTCAGAC 58.271 45.455 0.00 0.00 45.38 3.51
2455 2504 1.688197 CCCATTTCTTGTGCCAACAGT 59.312 47.619 0.00 0.00 37.67 3.55
2468 2517 3.807622 TGCCAACAGTTTCTTCTAACTCG 59.192 43.478 0.00 0.00 36.24 4.18
2489 2538 1.617018 CCACTACCAGCAGCAGCCTA 61.617 60.000 0.00 0.00 43.56 3.93
2515 2564 3.554934 TCCGCATTGCAAAGATAATCCT 58.445 40.909 1.71 0.00 0.00 3.24
2525 2574 4.530875 CAAAGATAATCCTTGACAGGCCT 58.469 43.478 0.00 0.00 40.58 5.19
2526 2575 4.870021 AAGATAATCCTTGACAGGCCTT 57.130 40.909 0.00 0.00 40.58 4.35
2528 2577 4.530875 AGATAATCCTTGACAGGCCTTTG 58.469 43.478 0.00 0.00 40.58 2.77
2573 2622 2.852449 TCGTAGCCTGATACTGGAGAG 58.148 52.381 0.00 0.00 0.00 3.20
2585 2634 2.843701 ACTGGAGAGTTGCTCACAAAG 58.156 47.619 0.00 0.00 45.81 2.77
2613 2662 8.221766 CGTGTTAGAAGTTTTGTCTTTATCCTC 58.778 37.037 0.00 0.00 0.00 3.71
2668 2717 4.251543 TCGTCTTGTACATCTTCAGCAA 57.748 40.909 0.00 0.00 0.00 3.91
2723 2772 4.448210 TCGTGCTTTCTTCTTTACTTGGT 58.552 39.130 0.00 0.00 0.00 3.67
2810 2859 4.837860 TCCATAGGGCATTTGTTGAACTTT 59.162 37.500 0.00 0.00 0.00 2.66
2819 2868 7.201548 GGGCATTTGTTGAACTTTAATGCTATG 60.202 37.037 26.14 7.26 46.25 2.23
2892 2941 0.321564 TGTCCATGAACGCTCCCTTG 60.322 55.000 0.00 0.00 0.00 3.61
2905 2954 0.032615 TCCCTTGTGGTTGTGCCTTT 60.033 50.000 0.00 0.00 38.35 3.11
2923 2972 5.262588 CCTTTGGCATTACTCATAAACCC 57.737 43.478 0.00 0.00 0.00 4.11
2933 2982 7.661437 GCATTACTCATAAACCCTGTCATCATA 59.339 37.037 0.00 0.00 0.00 2.15
2949 2998 5.698545 GTCATCATAATCAGGTACCTTGCTC 59.301 44.000 13.15 0.00 0.00 4.26
2966 3015 2.189521 CCCACTCCATGTACGGGC 59.810 66.667 0.00 0.00 0.00 6.13
3103 3152 3.179830 ACATCTCAACGACGAGCATAAC 58.820 45.455 0.00 0.00 32.75 1.89
3147 3196 2.537560 GGCATCGTTCCATCCTGCG 61.538 63.158 0.00 0.00 33.69 5.18
3179 3228 1.330234 AATGCATGTTCACCACAGCA 58.670 45.000 0.00 0.00 41.09 4.41
3180 3229 1.552578 ATGCATGTTCACCACAGCAT 58.447 45.000 0.00 0.00 41.53 3.79
3181 3230 0.883153 TGCATGTTCACCACAGCATC 59.117 50.000 0.00 0.00 39.40 3.91
3184 3233 1.395954 CATGTTCACCACAGCATCGAG 59.604 52.381 0.00 0.00 39.40 4.04
3191 3240 3.005539 ACAGCATCGAGGGTGGCT 61.006 61.111 29.78 10.19 40.47 4.75
3229 3278 2.594592 ACACCAGTGCCGCCTTTC 60.595 61.111 0.00 0.00 0.00 2.62
3265 3314 5.592054 TCGATCTTGTGTATTGATCCTCAC 58.408 41.667 0.00 0.00 34.70 3.51
3297 3346 1.598130 AGCGCAGGTTCAGTTGTCC 60.598 57.895 11.47 0.00 27.67 4.02
3325 3374 0.388659 TCAACTGCAACACCATTGGC 59.611 50.000 1.54 0.00 0.00 4.52
3340 3389 4.041567 ACCATTGGCTGATATCCGTATTCA 59.958 41.667 1.54 0.00 0.00 2.57
3346 3395 7.202016 TGGCTGATATCCGTATTCAATTTTC 57.798 36.000 0.00 0.00 0.00 2.29
3358 3407 2.738743 TCAATTTTCCATCCCAGGAGC 58.261 47.619 0.00 0.00 39.25 4.70
3362 3411 1.139498 TTTCCATCCCAGGAGCACCA 61.139 55.000 2.07 0.00 39.25 4.17
3371 3420 1.815003 CCAGGAGCACCAATCTGTTTC 59.185 52.381 2.07 0.00 38.94 2.78
3376 3425 4.651045 AGGAGCACCAATCTGTTTCTTTTT 59.349 37.500 2.07 0.00 38.94 1.94
3399 3448 2.708030 AAAGGAGGAAGACCCCCGGT 62.708 60.000 0.00 0.00 39.44 5.28
3415 3464 1.142748 GGTCTCTGCATCTGGACGG 59.857 63.158 0.00 0.00 0.00 4.79
3433 3482 1.202440 CGGTGCATGCAGCCATTTTAT 60.202 47.619 36.56 0.00 44.83 1.40
3513 3562 4.523083 TGGCAATATTTTTCGCTACTCCT 58.477 39.130 0.00 0.00 0.00 3.69
3517 3566 6.651225 GGCAATATTTTTCGCTACTCCTATCT 59.349 38.462 0.00 0.00 0.00 1.98
3532 3581 5.600484 ACTCCTATCTACTTGATGAAGGGTG 59.400 44.000 0.00 0.00 33.64 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.260002 AGTTAGGCTTTGTGTTGAATTATTTTG 57.740 29.630 0.00 0.00 0.00 2.44
28 29 8.453238 TGTTTATAGTTAGGCTTTGTGTTGAA 57.547 30.769 0.00 0.00 0.00 2.69
109 110 4.027050 CGACAACGTCATCATCATCTCTTG 60.027 45.833 0.00 0.00 32.09 3.02
135 136 2.360852 GGGAGGACGAGGACGACA 60.361 66.667 0.00 0.00 42.66 4.35
155 156 0.837940 AGCGGTAGGGAAGGAATTCC 59.162 55.000 17.31 17.31 40.38 3.01
248 250 7.915293 AATATCGACAACACACAATTAAGGA 57.085 32.000 0.00 0.00 0.00 3.36
303 305 6.601332 AGATGCCTCGAATTCCCTTTTAATA 58.399 36.000 0.00 0.00 0.00 0.98
337 339 1.403814 CATCTCCTTCGCCTCCACTA 58.596 55.000 0.00 0.00 0.00 2.74
342 344 1.068921 GCTCCATCTCCTTCGCCTC 59.931 63.158 0.00 0.00 0.00 4.70
372 374 3.129109 CACGAATCCATCACAGATCCAG 58.871 50.000 0.00 0.00 0.00 3.86
374 376 2.487934 CCACGAATCCATCACAGATCC 58.512 52.381 0.00 0.00 0.00 3.36
448 450 6.776603 TGATGATGTCACTATGAGAGATCACT 59.223 38.462 5.34 0.00 45.00 3.41
467 469 5.953548 TGTCATTCCAACTTCCAATGATGAT 59.046 36.000 0.00 0.00 38.48 2.45
471 473 4.280677 GGTTGTCATTCCAACTTCCAATGA 59.719 41.667 4.29 0.00 43.36 2.57
564 566 8.682710 GCAAAGATGACCATTAATAGGTACAAA 58.317 33.333 8.88 0.00 40.09 2.83
582 584 2.950433 AGGAAACAATGCGCAAAGATG 58.050 42.857 17.11 14.09 0.00 2.90
589 591 4.265320 GCTTATAACAAGGAAACAATGCGC 59.735 41.667 0.00 0.00 0.00 6.09
619 621 9.345517 CTAAAAATGATTTTCGAGCAATCTTCA 57.654 29.630 16.28 3.46 39.42 3.02
644 646 3.429960 GGTTAGACTACGGATTTTCGCCT 60.430 47.826 0.00 0.00 0.00 5.52
658 660 4.210158 ACCGCACAGGGTTAGACT 57.790 55.556 0.00 0.00 46.96 3.24
688 690 3.401033 AAAGATGTGTGGTCGTCATCA 57.599 42.857 0.00 0.00 39.96 3.07
713 715 3.017442 CTCAGATAACGACACCTCTGGA 58.983 50.000 0.00 0.00 36.59 3.86
856 896 8.286097 CAGTTGAGATCTTCTTCACCTAAAAAC 58.714 37.037 0.00 0.00 0.00 2.43
902 943 4.153475 GTGGCTTATAGTTGACTGCGAAAA 59.847 41.667 0.00 0.00 0.00 2.29
906 947 2.616960 TGTGGCTTATAGTTGACTGCG 58.383 47.619 0.00 0.00 0.00 5.18
907 948 3.751175 TGTTGTGGCTTATAGTTGACTGC 59.249 43.478 0.00 0.00 0.00 4.40
908 949 4.142816 GCTGTTGTGGCTTATAGTTGACTG 60.143 45.833 0.00 0.00 0.00 3.51
1027 1070 4.436998 CTCCGTGGACCTCGTGCC 62.437 72.222 14.41 0.00 0.00 5.01
1065 1108 0.910088 CCTTCCCCGTTCTCCTCCTT 60.910 60.000 0.00 0.00 0.00 3.36
1066 1109 1.306226 CCTTCCCCGTTCTCCTCCT 60.306 63.158 0.00 0.00 0.00 3.69
1067 1110 1.305887 TCCTTCCCCGTTCTCCTCC 60.306 63.158 0.00 0.00 0.00 4.30
1196 1239 8.585881 CGAGGTCAATTTAGAATAGATTAGGGA 58.414 37.037 0.00 0.00 0.00 4.20
1289 1332 4.015872 TGTACAGTGCCCTTTTTAGAGG 57.984 45.455 0.00 0.00 36.52 3.69
1305 1348 5.918576 CACGAGTTGTATCTGAACTTGTACA 59.081 40.000 0.00 0.00 43.37 2.90
1316 1359 5.334491 CGATCTATGCTCACGAGTTGTATCT 60.334 44.000 0.00 0.00 0.00 1.98
1317 1360 4.848841 CGATCTATGCTCACGAGTTGTATC 59.151 45.833 0.00 0.00 0.00 2.24
1365 1408 3.392947 TCCAATTCCCCAATGCTACGATA 59.607 43.478 0.00 0.00 0.00 2.92
1516 1559 4.455877 GGGGTGTAGAAAAATCACTGTCAG 59.544 45.833 0.00 0.00 33.30 3.51
1521 1564 3.074538 AGCTGGGGTGTAGAAAAATCACT 59.925 43.478 0.00 0.00 33.30 3.41
1530 1573 2.443781 ACCGAGCTGGGGTGTAGA 59.556 61.111 19.90 0.00 44.64 2.59
1546 1589 1.299089 GTTTCTTGCGTGGGTGCAC 60.299 57.895 8.80 8.80 46.25 4.57
1547 1590 0.179043 TAGTTTCTTGCGTGGGTGCA 60.179 50.000 0.00 0.00 44.61 4.57
1555 1598 1.135402 GGGTTGCCATAGTTTCTTGCG 60.135 52.381 0.00 0.00 0.00 4.85
1587 1630 5.372343 AATATCTCATGGTGTGCAAGGTA 57.628 39.130 0.00 0.00 0.00 3.08
1591 1634 7.643569 AAACATAATATCTCATGGTGTGCAA 57.356 32.000 0.00 0.00 0.00 4.08
1593 1636 7.483307 ACAAAACATAATATCTCATGGTGTGC 58.517 34.615 0.00 0.00 31.33 4.57
1699 1742 5.005299 GCAGCGTACATGTTTTCAAGTTTTT 59.995 36.000 2.30 0.00 33.65 1.94
1791 1834 3.658757 ATGCACCACGCTTTAATTGTT 57.341 38.095 0.00 0.00 43.06 2.83
1909 1952 0.830444 ACGGTTGTAGCCTCCAGTGA 60.830 55.000 0.00 0.00 0.00 3.41
1913 1956 1.302192 GCAACGGTTGTAGCCTCCA 60.302 57.895 20.92 0.00 0.00 3.86
1959 2002 3.424105 GGAGCAAGGGGCCTGGAT 61.424 66.667 0.84 0.00 46.50 3.41
2108 2151 0.872021 GATCGTCGGTGAGATGGTGC 60.872 60.000 0.00 0.00 36.53 5.01
2120 2163 3.422417 ACTGGTATCTTGTGATCGTCG 57.578 47.619 0.00 0.00 34.32 5.12
2132 2175 6.758886 CAGATGGAAACTCTGTAACTGGTATC 59.241 42.308 0.00 0.00 36.26 2.24
2195 2244 6.179906 TCTTCTTCTTTCATGTGGAGAACT 57.820 37.500 0.00 0.00 0.00 3.01
2257 2306 1.139163 GACAACATTGCCAAAAGGCG 58.861 50.000 1.66 0.00 37.77 5.52
2319 2368 5.998363 AGAAATCAACCTCACACCTAAACTC 59.002 40.000 0.00 0.00 0.00 3.01
2324 2373 5.568825 GCAGTAGAAATCAACCTCACACCTA 60.569 44.000 0.00 0.00 0.00 3.08
2455 2504 3.056322 GGTAGTGGGCGAGTTAGAAGAAA 60.056 47.826 0.00 0.00 0.00 2.52
2468 2517 2.437359 CTGCTGCTGGTAGTGGGC 60.437 66.667 0.00 0.00 0.00 5.36
2489 2538 1.255882 TCTTTGCAATGCGGATGGTT 58.744 45.000 0.00 0.00 0.00 3.67
2515 2564 1.490490 AGTCACTCAAAGGCCTGTCAA 59.510 47.619 5.69 0.00 0.00 3.18
2525 2574 0.179234 TCCAACGCCAGTCACTCAAA 59.821 50.000 0.00 0.00 0.00 2.69
2526 2575 0.179234 TTCCAACGCCAGTCACTCAA 59.821 50.000 0.00 0.00 0.00 3.02
2528 2577 1.464997 GATTTCCAACGCCAGTCACTC 59.535 52.381 0.00 0.00 0.00 3.51
2573 2622 2.825086 AACACGTCTTTGTGAGCAAC 57.175 45.000 0.24 0.00 42.55 4.17
2585 2634 8.008279 GGATAAAGACAAAACTTCTAACACGTC 58.992 37.037 0.00 0.00 0.00 4.34
2613 2662 3.126343 AGTTTAATTTAGTTGCGGCCTCG 59.874 43.478 0.00 0.00 39.81 4.63
2668 2717 9.892130 CATATTCCTAGTAAAACAGAACCTCTT 57.108 33.333 0.00 0.00 0.00 2.85
2810 2859 6.811253 AAACGAAAAGGTGTCATAGCATTA 57.189 33.333 0.00 0.00 0.00 1.90
2819 2868 9.378597 GAAAAACTAGATAAACGAAAAGGTGTC 57.621 33.333 0.00 0.00 0.00 3.67
2857 2906 7.459795 TCATGGACAAACACAAATATTAGCA 57.540 32.000 0.00 0.00 0.00 3.49
2905 2954 4.018870 TGACAGGGTTTATGAGTAATGCCA 60.019 41.667 0.00 0.00 0.00 4.92
2923 2972 5.468072 GCAAGGTACCTGATTATGATGACAG 59.532 44.000 17.14 0.00 0.00 3.51
2933 2982 1.282157 GTGGGAGCAAGGTACCTGATT 59.718 52.381 17.14 3.34 0.00 2.57
2949 2998 2.189521 GCCCGTACATGGAGTGGG 59.810 66.667 10.43 10.43 43.02 4.61
2966 3015 1.126113 GTAACGTGTCTTGATGGTGCG 59.874 52.381 0.00 0.00 0.00 5.34
3058 3107 4.431131 AGCATGGGAGTTGGGGCG 62.431 66.667 0.00 0.00 0.00 6.13
3074 3123 1.728971 GTCGTTGAGATGTTGCAGGAG 59.271 52.381 0.00 0.00 0.00 3.69
3103 3152 2.943690 CTCAAACTCAGATGATGGGCAG 59.056 50.000 0.00 0.00 29.47 4.85
3147 3196 1.605710 CATGCATTTCGTCCTGGATCC 59.394 52.381 4.20 4.20 0.00 3.36
3179 3228 3.790437 CAGGCAGCCACCCTCGAT 61.790 66.667 15.80 0.00 0.00 3.59
3181 3230 4.335647 AACAGGCAGCCACCCTCG 62.336 66.667 15.80 0.00 0.00 4.63
3184 3233 3.971702 AGGAACAGGCAGCCACCC 61.972 66.667 15.80 8.72 0.00 4.61
3191 3240 3.572255 GTGAATTTTACCAGGAACAGGCA 59.428 43.478 0.00 0.00 39.28 4.75
3235 3284 2.607668 TACACAAGATCGAGGCGGCG 62.608 60.000 0.51 0.51 0.00 6.46
3237 3286 1.860950 CAATACACAAGATCGAGGCGG 59.139 52.381 0.00 0.00 0.00 6.13
3265 3314 3.051392 GCGCTTCCAATCAACGGGG 62.051 63.158 0.00 0.00 0.00 5.73
3297 3346 1.135257 TGTTGCAGTTGAAACCAACCG 60.135 47.619 10.72 0.00 43.66 4.44
3325 3374 8.454106 GGATGGAAAATTGAATACGGATATCAG 58.546 37.037 4.83 2.80 0.00 2.90
3340 3389 2.460669 GTGCTCCTGGGATGGAAAATT 58.539 47.619 0.00 0.00 35.43 1.82
3346 3395 0.466922 GATTGGTGCTCCTGGGATGG 60.467 60.000 6.34 0.00 34.23 3.51
3376 3425 2.971901 GGGGTCTTCCTCCTTTTCAA 57.028 50.000 0.00 0.00 35.33 2.69
3392 3441 2.765807 AGATGCAGAGACCGGGGG 60.766 66.667 6.32 0.00 0.00 5.40
3399 3448 1.893062 CACCGTCCAGATGCAGAGA 59.107 57.895 0.00 0.00 0.00 3.10
3415 3464 6.607735 AATTAATAAAATGGCTGCATGCAC 57.392 33.333 18.46 13.69 45.15 4.57
3502 3551 6.296803 TCATCAAGTAGATAGGAGTAGCGAA 58.703 40.000 0.00 0.00 34.43 4.70
3513 3562 3.069586 CGGCACCCTTCATCAAGTAGATA 59.930 47.826 0.00 0.00 34.43 1.98
3517 3566 1.271856 TCGGCACCCTTCATCAAGTA 58.728 50.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.