Multiple sequence alignment - TraesCS3B01G443700

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 TraesCS3B01G443700 chr3B 100.000 4756 0 0 1 4756 684138101 684133346 0.000000e+00 8783.0
1 TraesCS3B01G443700 chr3B 93.409 531 30 4 1 528 370891036 370890508 0.000000e+00 782.0
2 TraesCS3B01G443700 chr3D 93.419 3723 195 25 526 4223 519596358 519600055 0.000000e+00 5472.0
3 TraesCS3B01G443700 chr3D 85.897 2964 347 38 1291 4218 519644323 519641395 0.000000e+00 3092.0
4 TraesCS3B01G443700 chr3D 87.573 1030 107 13 2617 3634 519620583 519621603 0.000000e+00 1173.0
5 TraesCS3B01G443700 chr3D 94.518 529 27 2 1 528 478695888 478695361 0.000000e+00 815.0
6 TraesCS3B01G443700 chr3D 93.774 530 29 4 1 528 306270168 306270695 0.000000e+00 793.0
7 TraesCS3B01G443700 chr3D 93.195 529 34 2 1 528 358927518 358928045 0.000000e+00 776.0
8 TraesCS3B01G443700 chr3D 92.523 535 34 6 4223 4756 519600093 519600622 0.000000e+00 761.0
9 TraesCS3B01G443700 chr3D 96.970 33 1 0 4091 4123 475580012 475580044 6.650000e-04 56.5
10 TraesCS3B01G443700 chr3A 92.555 3640 231 22 526 4142 654517640 654521262 0.000000e+00 5184.0
11 TraesCS3B01G443700 chr3A 92.439 2870 183 15 632 3493 654498904 654501747 0.000000e+00 4067.0
12 TraesCS3B01G443700 chr3A 85.436 2973 355 42 1290 4218 654584759 654581821 0.000000e+00 3020.0
13 TraesCS3B01G443700 chr3A 90.909 726 52 4 3515 4227 654501739 654502463 0.000000e+00 963.0
14 TraesCS3B01G443700 chr3A 91.418 536 43 3 4223 4756 654541459 654541993 0.000000e+00 732.0
15 TraesCS3B01G443700 chr3A 90.892 538 44 5 4223 4756 654502495 654503031 0.000000e+00 717.0
16 TraesCS3B01G443700 chr3A 89.027 483 48 5 2621 3101 654559975 654560454 1.140000e-165 593.0
17 TraesCS3B01G443700 chr3A 86.774 499 52 9 3097 3589 654562133 654562623 1.160000e-150 544.0
18 TraesCS3B01G443700 chr3A 81.157 536 72 15 4222 4756 654581779 654581272 2.060000e-108 403.0
19 TraesCS3B01G443700 chrUn 91.563 3378 254 17 870 4223 101062265 101065635 0.000000e+00 4630.0
20 TraesCS3B01G443700 chrUn 89.591 538 52 4 4222 4756 101065672 101066208 0.000000e+00 680.0
21 TraesCS3B01G443700 chr6A 91.577 3158 216 26 873 3988 35564038 35560889 0.000000e+00 4313.0
22 TraesCS3B01G443700 chr7D 95.066 527 23 3 1 526 480013615 480013091 0.000000e+00 826.0
23 TraesCS3B01G443700 chr7D 73.381 1946 428 67 1421 3318 612711783 612713686 4.010000e-180 641.0
24 TraesCS3B01G443700 chr2D 93.750 528 30 3 1 527 368125273 368125798 0.000000e+00 789.0
25 TraesCS3B01G443700 chr2D 93.573 529 32 2 1 528 368067914 368068441 0.000000e+00 787.0
26 TraesCS3B01G443700 chr5B 93.750 528 27 6 1 526 445851277 445850754 0.000000e+00 787.0
27 TraesCS3B01G443700 chr5B 87.032 347 37 8 526 868 522854112 522853770 7.470000e-103 385.0
28 TraesCS3B01G443700 chr5D 93.409 531 30 5 1 528 398835632 398835104 0.000000e+00 782.0
29 TraesCS3B01G443700 chr5D 86.705 346 40 6 526 868 400401371 400401713 3.470000e-101 379.0
30 TraesCS3B01G443700 chr7B 74.111 1603 341 52 1766 3329 702196546 702194979 1.140000e-165 593.0
31 TraesCS3B01G443700 chr4D 87.069 348 36 9 526 868 128921556 128921213 7.470000e-103 385.0
32 TraesCS3B01G443700 chr5A 86.994 346 37 8 526 867 680906392 680906051 2.690000e-102 383.0
33 TraesCS3B01G443700 chr4B 87.106 349 32 11 526 867 565311186 565311528 2.690000e-102 383.0
34 TraesCS3B01G443700 chr2B 86.819 349 35 10 526 868 637789911 637789568 3.470000e-101 379.0
35 TraesCS3B01G443700 chr4A 86.705 346 39 6 526 868 546616004 546615663 1.250000e-100 377.0


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 TraesCS3B01G443700 chr3B 684133346 684138101 4755 True 8783.000000 8783 100.000000 1 4756 1 chr3B.!!$R2 4755
1 TraesCS3B01G443700 chr3B 370890508 370891036 528 True 782.000000 782 93.409000 1 528 1 chr3B.!!$R1 527
2 TraesCS3B01G443700 chr3D 519596358 519600622 4264 False 3116.500000 5472 92.971000 526 4756 2 chr3D.!!$F5 4230
3 TraesCS3B01G443700 chr3D 519641395 519644323 2928 True 3092.000000 3092 85.897000 1291 4218 1 chr3D.!!$R2 2927
4 TraesCS3B01G443700 chr3D 519620583 519621603 1020 False 1173.000000 1173 87.573000 2617 3634 1 chr3D.!!$F4 1017
5 TraesCS3B01G443700 chr3D 478695361 478695888 527 True 815.000000 815 94.518000 1 528 1 chr3D.!!$R1 527
6 TraesCS3B01G443700 chr3D 306270168 306270695 527 False 793.000000 793 93.774000 1 528 1 chr3D.!!$F1 527
7 TraesCS3B01G443700 chr3D 358927518 358928045 527 False 776.000000 776 93.195000 1 528 1 chr3D.!!$F2 527
8 TraesCS3B01G443700 chr3A 654517640 654521262 3622 False 5184.000000 5184 92.555000 526 4142 1 chr3A.!!$F1 3616
9 TraesCS3B01G443700 chr3A 654498904 654503031 4127 False 1915.666667 4067 91.413333 632 4756 3 chr3A.!!$F3 4124
10 TraesCS3B01G443700 chr3A 654581272 654584759 3487 True 1711.500000 3020 83.296500 1290 4756 2 chr3A.!!$R1 3466
11 TraesCS3B01G443700 chr3A 654541459 654541993 534 False 732.000000 732 91.418000 4223 4756 1 chr3A.!!$F2 533
12 TraesCS3B01G443700 chr3A 654559975 654562623 2648 False 568.500000 593 87.900500 2621 3589 2 chr3A.!!$F4 968
13 TraesCS3B01G443700 chrUn 101062265 101066208 3943 False 2655.000000 4630 90.577000 870 4756 2 chrUn.!!$F1 3886
14 TraesCS3B01G443700 chr6A 35560889 35564038 3149 True 4313.000000 4313 91.577000 873 3988 1 chr6A.!!$R1 3115
15 TraesCS3B01G443700 chr7D 480013091 480013615 524 True 826.000000 826 95.066000 1 526 1 chr7D.!!$R1 525
16 TraesCS3B01G443700 chr7D 612711783 612713686 1903 False 641.000000 641 73.381000 1421 3318 1 chr7D.!!$F1 1897
17 TraesCS3B01G443700 chr2D 368125273 368125798 525 False 789.000000 789 93.750000 1 527 1 chr2D.!!$F2 526
18 TraesCS3B01G443700 chr2D 368067914 368068441 527 False 787.000000 787 93.573000 1 528 1 chr2D.!!$F1 527
19 TraesCS3B01G443700 chr5B 445850754 445851277 523 True 787.000000 787 93.750000 1 526 1 chr5B.!!$R1 525
20 TraesCS3B01G443700 chr5D 398835104 398835632 528 True 782.000000 782 93.409000 1 528 1 chr5D.!!$R1 527
21 TraesCS3B01G443700 chr7B 702194979 702196546 1567 True 593.000000 593 74.111000 1766 3329 1 chr7B.!!$R1 1563

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
851 863 1.273606 CGGTAGATCGATGATGGCCTT 59.726 52.381 0.54 0.0 0.00 4.35 F
1647 1721 0.457035 CCCTGTTGGAAATCCATGCG 59.543 55.000 2.38 0.0 46.97 4.73 F
1650 1724 0.897401 TGTTGGAAATCCATGCGCCA 60.897 50.000 4.18 0.0 46.97 5.69 F
3257 5047 0.534203 TGGTCAAGCCCTCGTGTTTC 60.534 55.000 0.00 0.0 36.04 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1773 0.468226 TTCGGCTCAAGTTCCACAGT 59.532 50.000 0.00 0.00 0.00 3.55 R
3113 4891 0.998928 ATATGAGGGTGTGGGCACAA 59.001 50.000 0.00 0.00 46.95 3.33 R
3331 5123 3.479489 ACATGAGTCAACAAGATGCACA 58.521 40.909 0.00 0.00 0.00 4.57 R
4275 6147 0.595567 GCAATGCATGGCCACATACG 60.596 55.000 15.73 4.46 34.99 3.06 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
37 38 5.103000 CAGAATCGTTTCGGTCTACTTGAT 58.897 41.667 0.72 0.00 36.93 2.57
53 54 3.118261 ACTTGATATGGACGTGATGCCTT 60.118 43.478 0.00 0.00 0.00 4.35
100 103 3.550561 TGTCATAACTTTGCGCTTTTCG 58.449 40.909 9.73 0.00 42.12 3.46
181 184 3.041946 CTCTAGTGAAACCTATGGCCCT 58.958 50.000 0.00 0.00 37.80 5.19
182 185 3.456277 CTCTAGTGAAACCTATGGCCCTT 59.544 47.826 0.00 0.00 37.80 3.95
394 403 6.257630 GTGTTTGATTGTTTGTGCAGGTATTT 59.742 34.615 0.00 0.00 0.00 1.40
404 413 5.289917 TGTGCAGGTATTTGTGATTTACG 57.710 39.130 0.00 0.00 0.00 3.18
423 432 3.354467 ACGGTGTTCTTCTCCTACTAGG 58.646 50.000 0.00 0.00 36.46 3.02
461 470 9.886132 GTTCTCAAACTGAGGGAAATACTTATA 57.114 33.333 3.92 0.00 44.39 0.98
528 537 2.873649 GCAAGCTCAAGAAGTAGCAGGT 60.874 50.000 0.00 0.00 41.32 4.00
529 538 3.406764 CAAGCTCAAGAAGTAGCAGGTT 58.593 45.455 0.00 0.00 41.32 3.50
530 539 4.569943 CAAGCTCAAGAAGTAGCAGGTTA 58.430 43.478 0.00 0.00 41.32 2.85
531 540 5.181748 CAAGCTCAAGAAGTAGCAGGTTAT 58.818 41.667 0.00 0.00 41.32 1.89
546 555 4.160626 GCAGGTTATAGTTGGACTCTGAGT 59.839 45.833 10.66 10.66 0.00 3.41
575 584 6.382087 TGGTGTGTAGATAGGATATGGAGTT 58.618 40.000 0.00 0.00 0.00 3.01
576 585 6.267699 TGGTGTGTAGATAGGATATGGAGTTG 59.732 42.308 0.00 0.00 0.00 3.16
630 642 7.994425 CTCTTATCTAATGAGAGGCTAGACA 57.006 40.000 0.00 0.00 38.83 3.41
643 655 3.774766 AGGCTAGACACATGATGTAACCA 59.225 43.478 0.00 0.00 43.56 3.67
664 676 4.500205 CCAATGCCAACATAATAGCACAGG 60.500 45.833 0.00 0.00 38.21 4.00
665 677 3.364460 TGCCAACATAATAGCACAGGT 57.636 42.857 0.00 0.00 0.00 4.00
668 680 4.196193 GCCAACATAATAGCACAGGTACA 58.804 43.478 0.00 0.00 0.00 2.90
670 682 5.182487 CCAACATAATAGCACAGGTACACA 58.818 41.667 0.00 0.00 0.00 3.72
681 693 2.356780 GGTACACAGGGGAGTCGGG 61.357 68.421 0.00 0.00 0.00 5.14
685 697 3.923645 ACAGGGGAGTCGGGGACA 61.924 66.667 0.00 0.00 34.60 4.02
697 709 4.101448 GGGACATGTGCCGGAGCT 62.101 66.667 21.48 0.00 40.80 4.09
760 772 3.178611 CCCCATAGTCAGGCCCCC 61.179 72.222 0.00 0.00 0.00 5.40
765 777 3.341469 ATAGTCAGGCCCCCGGGAA 62.341 63.158 26.32 0.00 37.50 3.97
851 863 1.273606 CGGTAGATCGATGATGGCCTT 59.726 52.381 0.54 0.00 0.00 4.35
1005 1017 1.302949 GCAGGGCTGGACCACATAA 59.697 57.895 0.00 0.00 42.05 1.90
1015 1027 1.548719 GGACCACATAAAACAAGGGGC 59.451 52.381 0.00 0.00 0.00 5.80
1022 1034 5.303971 CACATAAAACAAGGGGCAATTTCA 58.696 37.500 0.00 0.00 0.00 2.69
1032 1044 3.845398 AGGGGCAATTTCATCCATCAAAA 59.155 39.130 0.00 0.00 0.00 2.44
1237 1260 2.519063 CAAGCACCACCACTGCCA 60.519 61.111 0.00 0.00 35.01 4.92
1266 1308 3.368501 CTCCCTCCCCTCTCCCCA 61.369 72.222 0.00 0.00 0.00 4.96
1286 1347 2.359404 GTCCTCACCTCTCCCCGA 59.641 66.667 0.00 0.00 0.00 5.14
1287 1348 2.053277 GTCCTCACCTCTCCCCGAC 61.053 68.421 0.00 0.00 0.00 4.79
1288 1349 3.141488 CCTCACCTCTCCCCGACG 61.141 72.222 0.00 0.00 0.00 5.12
1289 1350 2.361357 CTCACCTCTCCCCGACGT 60.361 66.667 0.00 0.00 0.00 4.34
1294 1355 2.045242 CTCTCCCCGACGTCCTCA 60.045 66.667 10.58 0.00 0.00 3.86
1392 1463 2.622942 TGCAAAAGCTTCGATGGAGTTT 59.377 40.909 0.00 0.00 0.00 2.66
1401 1472 4.686972 CTTCGATGGAGTTTAGATCTGCA 58.313 43.478 5.18 0.00 37.63 4.41
1492 1563 2.013405 AGGCTCCCCTGCATCAAAT 58.987 52.632 0.00 0.00 40.94 2.32
1531 1602 1.363807 CTCTCACGGCGATGGCATA 59.636 57.895 16.62 0.00 42.47 3.14
1620 1691 1.198713 GCCAGATCTCTTGTCCTCCA 58.801 55.000 0.00 0.00 0.00 3.86
1647 1721 0.457035 CCCTGTTGGAAATCCATGCG 59.543 55.000 2.38 0.00 46.97 4.73
1650 1724 0.897401 TGTTGGAAATCCATGCGCCA 60.897 50.000 4.18 0.00 46.97 5.69
1699 1773 1.153329 AACTCGTTGTTGTCCGCCA 60.153 52.632 0.00 0.00 37.52 5.69
1703 1777 2.177580 CGTTGTTGTCCGCCACTGT 61.178 57.895 0.00 0.00 0.00 3.55
1826 1900 6.543465 ACCTACATCATGTTGGACAATGTATG 59.457 38.462 23.30 5.72 44.30 2.39
1995 2072 7.345653 TGTGATCTAAGGGTGAATTCACTATCT 59.654 37.037 31.81 23.83 45.73 1.98
2024 2101 4.276926 GGAGCTTGTTGTGAACTCATTCTT 59.723 41.667 0.00 0.00 35.69 2.52
2037 2114 6.543465 TGAACTCATTCTTGACAGAACATGTT 59.457 34.615 11.78 11.78 42.05 2.71
2176 2257 5.542635 ACAGAGGAGTCTATTGTGTTTGGTA 59.457 40.000 0.00 0.00 0.00 3.25
2191 2272 6.103997 GTGTTTGGTATTTGGTATCTCGAGA 58.896 40.000 19.19 19.19 0.00 4.04
2381 2464 1.131126 CTATGAGCCCAACTTTGCACG 59.869 52.381 0.00 0.00 0.00 5.34
2481 2564 4.451096 GCACTCGTGTTTTATCTCCTTCAA 59.549 41.667 0.00 0.00 0.00 2.69
2609 2694 7.156673 AGTAGCTTACATTTACTTTTCGGTCA 58.843 34.615 0.00 0.00 0.00 4.02
2652 2737 0.898320 AGATTGTCCCTGTGAGTCCG 59.102 55.000 0.00 0.00 0.00 4.79
2827 2912 6.010850 AGGTCTCATCAAGTAACACTAGACA 58.989 40.000 0.00 0.00 32.95 3.41
3027 3121 9.593134 TTTATATGTTTATGGTGGTTGAAATGC 57.407 29.630 0.00 0.00 0.00 3.56
3028 3122 4.264460 TGTTTATGGTGGTTGAAATGCC 57.736 40.909 0.00 0.00 0.00 4.40
3095 3190 8.848474 TCCATTAGTAGCTAATTCTAAATGCC 57.152 34.615 0.00 0.00 34.83 4.40
3113 4891 1.412343 GCCATATTCCCACGGCATTTT 59.588 47.619 0.00 0.00 44.25 1.82
3257 5047 0.534203 TGGTCAAGCCCTCGTGTTTC 60.534 55.000 0.00 0.00 36.04 2.78
3269 5059 4.272504 CCCTCGTGTTTCGCATATGTATTT 59.727 41.667 4.29 0.00 39.67 1.40
3277 5067 6.524933 TGTTTCGCATATGTATTTTGGTTTCG 59.475 34.615 4.29 0.00 0.00 3.46
3331 5123 9.589461 TGTCTAGCTAGAGTAGGCTATAATTTT 57.411 33.333 23.87 0.00 39.79 1.82
3356 5149 6.207221 TGTGCATCTTGTTGACTCATGTTAAT 59.793 34.615 0.00 0.00 0.00 1.40
3386 5180 3.196254 CCTCTATTGGGTGCATGCTTTTT 59.804 43.478 20.33 1.62 0.00 1.94
3483 5277 7.349859 TCATACCTAAATTGACTATCCTTGGGT 59.650 37.037 0.00 0.00 0.00 4.51
3680 5487 6.012113 AGAAGACATCCAAAATCAACCATCA 58.988 36.000 0.00 0.00 0.00 3.07
3720 5527 3.407698 TGCATATGTGGTTTCTCGTTGT 58.592 40.909 4.29 0.00 0.00 3.32
3728 5535 1.732259 GGTTTCTCGTTGTGCATCGAT 59.268 47.619 10.85 0.00 35.57 3.59
3865 5673 8.902540 AAGTTAATGTGTCAACTTATGTCAGA 57.097 30.769 0.00 0.00 41.86 3.27
3910 5718 4.096382 ACATGTTTCCACCGAATTATGCTC 59.904 41.667 0.00 0.00 30.54 4.26
4014 5823 7.859325 TTTCTAACTATTGCACCCTACAATC 57.141 36.000 0.00 0.00 38.62 2.67
4020 5829 5.951747 ACTATTGCACCCTACAATCAACAAT 59.048 36.000 0.00 0.00 38.62 2.71
4046 5863 7.206687 AGATGCATCTTCTGTTACTTAGCTAC 58.793 38.462 23.75 0.00 31.97 3.58
4047 5864 6.280855 TGCATCTTCTGTTACTTAGCTACA 57.719 37.500 0.00 0.00 0.00 2.74
4169 6003 0.462789 ACACCTTTGTCCGACGTCTT 59.537 50.000 14.70 0.00 0.00 3.01
4176 6010 3.235481 TCCGACGTCTTGGCCCAA 61.235 61.111 14.70 0.00 0.00 4.12
4218 6052 7.129425 AGGACTCAGAAGACTTGGAGTATATT 58.871 38.462 15.53 3.85 40.48 1.28
4275 6147 8.338259 CGCTTGCATCCTATATTATCCATAAAC 58.662 37.037 0.00 0.00 0.00 2.01
4347 6219 9.366216 GGACAAATCCTAAACAAATCCAATAAC 57.634 33.333 0.00 0.00 42.45 1.89
4348 6220 9.366216 GACAAATCCTAAACAAATCCAATAACC 57.634 33.333 0.00 0.00 0.00 2.85
4417 6296 9.277565 CTTTGACATAAGACATTTTAATGACCG 57.722 33.333 9.32 0.00 39.67 4.79
4422 6301 8.883731 ACATAAGACATTTTAATGACCGAAGAG 58.116 33.333 9.32 0.00 39.67 2.85
4511 6390 8.301002 TGCTCAAAATTTTATAGGTACAACCAC 58.699 33.333 2.44 0.00 41.95 4.16
4580 6459 7.475771 TCCATTTACAAACATGTTTCTTTGC 57.524 32.000 20.85 0.00 31.63 3.68
4590 6469 2.758130 TGTTTCTTTGCCCCCTCTTTT 58.242 42.857 0.00 0.00 0.00 2.27
4621 6500 9.590451 AAACCATTATTGCTTGAAGATAACATG 57.410 29.630 0.00 0.00 0.00 3.21
4632 6511 8.571336 GCTTGAAGATAACATGTTAGGCATAAT 58.429 33.333 22.03 6.00 35.74 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.563808 GCAATAAAGGCATCACGTCCATA 59.436 43.478 0.00 0.00 0.00 2.74
53 54 6.482898 ACCAAGGCAATGATTATGCAATAA 57.517 33.333 0.00 0.00 45.60 1.40
100 103 6.546395 ACAAATTACTGTCGAGCAATTGATC 58.454 36.000 13.73 13.73 0.00 2.92
394 403 4.039973 AGGAGAAGAACACCGTAAATCACA 59.960 41.667 0.00 0.00 34.46 3.58
404 413 4.771054 TCAACCTAGTAGGAGAAGAACACC 59.229 45.833 23.50 0.00 37.67 4.16
423 432 5.763204 TCAGTTTGAGAACCAAGGTATCAAC 59.237 40.000 15.46 11.96 35.28 3.18
461 470 2.240667 AGGGTGATGCAGCAAAGTAGAT 59.759 45.455 6.05 0.00 33.07 1.98
528 537 6.262496 CCATACGACTCAGAGTCCAACTATAA 59.738 42.308 22.65 2.49 42.12 0.98
529 538 5.763698 CCATACGACTCAGAGTCCAACTATA 59.236 44.000 22.65 7.99 42.12 1.31
530 539 4.580995 CCATACGACTCAGAGTCCAACTAT 59.419 45.833 22.65 10.68 42.12 2.12
531 540 3.945921 CCATACGACTCAGAGTCCAACTA 59.054 47.826 22.65 9.06 42.12 2.24
546 555 6.602009 CCATATCCTATCTACACACCATACGA 59.398 42.308 0.00 0.00 0.00 3.43
624 636 5.008019 GGCATTGGTTACATCATGTGTCTAG 59.992 44.000 0.00 0.00 42.29 2.43
630 642 3.831333 TGTTGGCATTGGTTACATCATGT 59.169 39.130 0.00 0.00 0.00 3.21
643 655 4.280819 ACCTGTGCTATTATGTTGGCATT 58.719 39.130 0.00 0.00 37.05 3.56
664 676 2.356780 CCCCGACTCCCCTGTGTAC 61.357 68.421 0.00 0.00 0.00 2.90
665 677 2.038329 CCCCGACTCCCCTGTGTA 59.962 66.667 0.00 0.00 0.00 2.90
668 680 3.254035 ATGTCCCCGACTCCCCTGT 62.254 63.158 0.00 0.00 33.15 4.00
670 682 2.365635 CATGTCCCCGACTCCCCT 60.366 66.667 0.00 0.00 33.15 4.79
681 693 2.512515 GAGCTCCGGCACATGTCC 60.513 66.667 0.87 0.00 41.70 4.02
707 719 1.143183 CGCTACAATACCGCACCCT 59.857 57.895 0.00 0.00 0.00 4.34
738 750 3.142393 CCTGACTATGGGGGCTCG 58.858 66.667 0.00 0.00 0.00 5.03
765 777 5.876612 GAGGTTACTCGATACGGATACAT 57.123 43.478 0.00 0.00 33.35 2.29
779 791 6.017400 TCGAGATTTGTTAACGAGGTTACT 57.983 37.500 0.26 0.00 0.00 2.24
784 796 4.862574 TGACATCGAGATTTGTTAACGAGG 59.137 41.667 0.26 0.00 39.86 4.63
795 807 3.373130 CACACAAGCATGACATCGAGATT 59.627 43.478 0.00 0.00 0.00 2.40
939 951 3.269381 TCTCCCAACTTTGCCTTATCCAT 59.731 43.478 0.00 0.00 0.00 3.41
1005 1017 2.978278 TGGATGAAATTGCCCCTTGTTT 59.022 40.909 0.00 0.00 0.00 2.83
1096 1119 8.881262 GGATTCCTTATTTGACCCTAGAGATTA 58.119 37.037 0.00 0.00 0.00 1.75
1167 1190 0.913205 TAGTGGTGTGTGGTGGTGTT 59.087 50.000 0.00 0.00 0.00 3.32
1237 1260 3.648660 AGGGAGGGGAATGGGGGT 61.649 66.667 0.00 0.00 0.00 4.95
1266 1308 2.363147 GGGAGAGGTGAGGACGCT 60.363 66.667 0.00 0.00 0.00 5.07
1286 1347 2.037527 GGGGAGAGGTGAGGACGT 59.962 66.667 0.00 0.00 0.00 4.34
1287 1348 3.141488 CGGGGAGAGGTGAGGACG 61.141 72.222 0.00 0.00 0.00 4.79
1288 1349 2.760385 CCGGGGAGAGGTGAGGAC 60.760 72.222 0.00 0.00 0.00 3.85
1289 1350 4.779733 GCCGGGGAGAGGTGAGGA 62.780 72.222 2.18 0.00 0.00 3.71
1392 1463 1.683385 CCCAGACGACATGCAGATCTA 59.317 52.381 0.00 0.00 0.00 1.98
1401 1472 2.816411 TCTAGGAAACCCAGACGACAT 58.184 47.619 0.00 0.00 0.00 3.06
1511 1582 4.899239 GCCATCGCCGTGAGAGGG 62.899 72.222 4.47 4.47 41.99 4.30
1599 1670 0.467804 GAGGACAAGAGATCTGGCCC 59.532 60.000 0.00 0.00 0.00 5.80
1647 1721 2.827642 GCCATGTCCTGCTCTGGC 60.828 66.667 0.00 0.00 46.54 4.85
1650 1724 2.996395 CTGGCCATGTCCTGCTCT 59.004 61.111 5.51 0.00 0.00 4.09
1699 1773 0.468226 TTCGGCTCAAGTTCCACAGT 59.532 50.000 0.00 0.00 0.00 3.55
1703 1777 1.416401 ACTCTTTCGGCTCAAGTTCCA 59.584 47.619 0.00 0.00 0.00 3.53
1851 1928 2.034685 CGTCTCGAGCATAGGGAATTCA 59.965 50.000 7.81 0.00 0.00 2.57
1995 2072 0.469494 TCACAACAAGCTCCTGCAGA 59.531 50.000 17.39 0.00 42.74 4.26
2024 2101 6.072728 GGCTACAATGTTAACATGTTCTGTCA 60.073 38.462 21.46 10.36 36.98 3.58
2037 2114 1.568597 AGCATGGGGGCTACAATGTTA 59.431 47.619 0.00 0.00 43.70 2.41
2176 2257 4.444876 CCCCAACATCTCGAGATACCAAAT 60.445 45.833 26.87 1.71 32.63 2.32
2191 2272 2.990967 CGCCTGCAACCCCAACAT 60.991 61.111 0.00 0.00 0.00 2.71
2381 2464 5.012561 ACAACCATATGCTTCTCTATCTCCC 59.987 44.000 0.00 0.00 0.00 4.30
2609 2694 8.502738 TCTATTGGGCATTCTTCTTTTACCTAT 58.497 33.333 0.00 0.00 0.00 2.57
2843 2928 3.089284 TGAAGCATAGGTCTCGAAGACA 58.911 45.455 14.26 0.00 46.79 3.41
2920 3012 5.211973 TCTACTTCATGTAGGAGGATGCTT 58.788 41.667 11.35 0.00 46.45 3.91
2950 3044 8.671028 TCAAAGAAACTTACAAGAAGTAACACC 58.329 33.333 0.00 0.00 37.77 4.16
3027 3121 2.053865 AATTGGGATGCCAGTGCGG 61.054 57.895 5.91 0.00 41.78 5.69
3028 3122 1.140161 CAATTGGGATGCCAGTGCG 59.860 57.895 5.91 0.00 41.78 5.34
3095 3190 3.864583 CACAAAAATGCCGTGGGAATATG 59.135 43.478 0.00 0.00 0.00 1.78
3113 4891 0.998928 ATATGAGGGTGTGGGCACAA 59.001 50.000 0.00 0.00 46.95 3.33
3219 5006 8.684386 TTGACCATTAGAGAACATTGTAAACA 57.316 30.769 0.00 0.00 0.00 2.83
3257 5047 5.204833 CCTCGAAACCAAAATACATATGCG 58.795 41.667 1.58 0.00 0.00 4.73
3269 5059 5.993441 CCTAGTTCTTTAACCTCGAAACCAA 59.007 40.000 0.00 0.00 36.15 3.67
3277 5067 6.174049 AGTTGATGCCTAGTTCTTTAACCTC 58.826 40.000 0.00 0.00 36.15 3.85
3331 5123 3.479489 ACATGAGTCAACAAGATGCACA 58.521 40.909 0.00 0.00 0.00 4.57
3386 5180 6.523840 CCCTTGATGGAACTTTTTGATGAAA 58.476 36.000 0.00 0.00 38.35 2.69
3459 5253 7.707467 ACCCAAGGATAGTCAATTTAGGTAT 57.293 36.000 0.00 0.00 0.00 2.73
3728 5535 5.414789 TTGACATGGAAAGGACGATCTTA 57.585 39.130 0.00 0.00 0.00 2.10
3810 5618 5.211174 TGAATTGCATCACAACCATTCAA 57.789 34.783 4.18 0.00 42.27 2.69
3972 5780 3.509184 AGAAAAGAGAGCAAATGGAAGGC 59.491 43.478 0.00 0.00 0.00 4.35
3983 5791 5.065346 GGGTGCAATAGTTAGAAAAGAGAGC 59.935 44.000 0.00 0.00 0.00 4.09
4014 5823 8.206325 AGTAACAGAAGATGCATCTATTGTTG 57.794 34.615 37.85 28.49 40.58 3.33
4020 5829 7.353414 AGCTAAGTAACAGAAGATGCATCTA 57.647 36.000 28.92 10.08 35.76 1.98
4086 5906 1.229272 ACCCCTAGGCCGTAACACA 60.229 57.895 2.05 0.00 36.11 3.72
4126 5960 0.766674 TGACCTAAGGTGCCACAGGT 60.767 55.000 5.11 5.11 44.11 4.00
4129 5963 1.136828 AACTGACCTAAGGTGCCACA 58.863 50.000 0.00 0.00 35.25 4.17
4218 6052 2.167693 CGCAGGATCCTAGTTGGTTGTA 59.832 50.000 15.67 0.00 37.07 2.41
4275 6147 0.595567 GCAATGCATGGCCACATACG 60.596 55.000 15.73 4.46 34.99 3.06
4365 6243 4.469657 TCACCAATTATGCTTCATACCCC 58.530 43.478 0.00 0.00 0.00 4.95
4485 6364 8.301002 GTGGTTGTACCTATAAAATTTTGAGCA 58.699 33.333 13.76 2.51 39.58 4.26
4535 6414 6.762333 TGGATCATAATGTTGTCTCGATCAT 58.238 36.000 0.00 0.00 31.52 2.45
4536 6415 6.160576 TGGATCATAATGTTGTCTCGATCA 57.839 37.500 0.00 0.00 31.52 2.92
4537 6416 7.664082 AATGGATCATAATGTTGTCTCGATC 57.336 36.000 0.00 0.00 0.00 3.69
4538 6417 8.993121 GTAAATGGATCATAATGTTGTCTCGAT 58.007 33.333 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.