Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005498.1 Hibiscus syriacus cultivar Beakdansim tig00012651_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70179
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3727 original size:29 final size:29
Alignment explanation
Indices: 3694--3782 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 29
3684 GATTAATTTG
3694 GGGATGAAATTGAAATATTCAAAAGTTTA
1 GGGATGAAATTGAAATATTCAAAAGTTTA
* * *
3723 GGGATAAAATTAGAAATGAGGTC-ATAGTTTA
1 GGGATGAAATT-GAAAT-A-TTCAAAAGTTTA
** *
3754 TAGATGAAATT-AGAATGTTCAAAAGTTTA
1 GGGATGAAATTGA-AATATTCAAAAGTTTA
3783 AGGACTAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
28 2 0.04
29 18 0.39
30 8 0.17
31 16 0.35
32 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.31
Consensus pattern (29 bp):
GGGATGAAATTGAAATATTCAAAAGTTTA
Found at i:3836 original size:59 final size:60
Alignment explanation
Indices: 3697--3857 Score: 188
Period size: 60 Copynumber: 2.7 Consensus size: 60
3687 TAATTTGGGG
* * * *
3697 ATGAAATTGAAATATTCAAAAGTTTAGGGATAAAATTAGAAATGAGGTCATAGTTTATAG
1 ATGAAATTAAAATATTCAAAAGTTTAAGGATAAATTTAGAAATGAGGTCATAGTTTATAA
* * *
3757 ATGAAATTAGAATGTTCAAAAGTTTAAGGACT-AATTTAG-AATGAGAGTCATAATTT-TAAA
1 ATGAAATTAAAATATTCAAAAGTTTAAGGA-TAAATTTAGAAATGAG-GTCATAGTTTAT-AA
*
3817 AT-AAATTAAAATATTCAAAAGTTTAAGGATCAATTTA-AAAT
1 ATGAAATTAAAATATTCAAAAGTTTAAGGATAAATTTAGAAAT
3858 TGATTATAGC
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
58 1 0.01
59 41 0.47
60 44 0.51
61 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (60 bp):
ATGAAATTAAAATATTCAAAAGTTTAAGGATAAATTTAGAAATGAGGTCATAGTTTATAA
Found at i:21548 original size:21 final size:21
Alignment explanation
Indices: 21528--21669 Score: 139
Period size: 20 Copynumber: 6.9 Consensus size: 21
21518 ATTCGCGTTG
*
21528 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* ** *
21549 AAAATCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
21569 CATTTCGCGTTGCGATAG-TC
1 CATTTCGCGTTGCGATAGTTC
* * *
21589 TATAGTCGCGTTGCGAT-TTTC
1 CAT-TTCGCGTTGCGATAGTTC
*
21610 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* * *
21631 AAATTCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
21651 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
21670 CTACAGTTGT
Statistics
Matches: 93, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
20 47 0.51
21 46 0.49
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (21 bp):
CATTTCGCGTTGCGATAGTTC
Found at i:21573 original size:41 final size:41
Alignment explanation
Indices: 21528--21669 Score: 241
Period size: 41 Copynumber: 3.5 Consensus size: 41
21518 ATTCGCGTTG
21528 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
21569 CATTTCGCGTTGCGATAGTCT-ATAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
*
21610 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
21651 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
21670 CTACAGTTGT
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
40 1 0.01
41 93 0.98
42 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:21623 original size:82 final size:83
Alignment explanation
Indices: 21528--21710 Score: 300
Period size: 82 Copynumber: 2.2 Consensus size: 83
21518 ATTCGCGTTG
*
21528 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTATA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
21593 GTCG-CGTTGCGATTTTC
66 GTCGTCGTTGCGATTTTC
*
21610 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
*
21675 GTTGTCGTTGCGATTTTC
66 GTCGTCGTTGCGATTTTC
*
21693 CAAATT--CGTTGCGATAGT
1 C-ATTTCGCGTTGCGATAGT
21711 CTACAGTTGT
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
82 78 0.82
83 14 0.15
84 3 0.03
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.38
Consensus pattern (83 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
GTCGTCGTTGCGATTTTC
Found at i:21686 original size:22 final size:22
Alignment explanation
Indices: 21658--21729 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
21648 TTCCATTTCG
21658 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
21680 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
21699 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
21721 CGTTGCGAT
1 CGTTGCGAT
21730 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:21703 original size:19 final size:19
Alignment explanation
Indices: 21679--21744 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
21669 TCTACAGTTG
21679 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
21698 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
21719 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
21739 TCGTTG
1 TCGTTG
21745 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:21744 original size:123 final size:121
Alignment explanation
Indices: 21528--21752 Score: 294
Period size: 123 Copynumber: 1.8 Consensus size: 121
21518 ATTCGCGTTG
* *
21528 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTATA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACA
*
21593 GTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
65 GTCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
* * *
21651 CATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCCGTTGCGATAGTCTA
* *
21714 CAGTTGTCGTTGCGATTTTCCAAATT-CGTTGTGATAGTT
63 CAGTCG-CGTTGCGATTTTCC-AATTCCGTTGCGATAGTT
21753 AAAAAAAGAT
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
123 54 0.61
124 29 0.33
125 6 0.07
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.39
Consensus pattern (121 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAG
TCGCGTTGCGATTTTCCAATTCCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
Found at i:21751 original size:41 final size:40
Alignment explanation
Indices: 21528--21735 Score: 235
Period size: 41 Copynumber: 5.0 Consensus size: 40
21518 ATTCGCGTTG
* * *
21528 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCT-ACAGTTGCGTTGCGATTTTC
* *
21569 CATTTCGCGTTGCGATAGTCTATAGTCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCTACAGTTGCGTTGCGATTTTC
*
21610 CATTTCGCGTTGCGATAGT-TGA-AATTCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCT-ACAGTT-GCGTTGCGATTTTC
21651 CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTC
*
21693 CAAATT-CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 C-ATTTCCGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTC
21734 CA
1 CA
21736 AATTCGTTGT
Statistics
Matches: 154, Mismatches: 6, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
40 4 0.03
41 128 0.83
42 19 0.12
43 3 0.02
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (40 bp):
CATTTCCGTTGCGATAGTCTACAGTTGCGTTGCGATTTTC
Found at i:21751 original size:82 final size:80
Alignment explanation
Indices: 21535--21735 Score: 264
Period size: 82 Copynumber: 2.5 Consensus size: 80
21525 TTGCATTTCG
* *
21535 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTATAGTCGCGT
1 CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTC-CGTTGCGATAGTCTACAGTCGCGT
*
21600 TGCGATTTTCCATTTC
65 TGCGATTTTCCAATTC
*
21616 GCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTC
1 -CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTC-CGTTGCGATAGTCTACAGTCG-C
21681 GTTGCGATTTTCCAAATT-
63 GTTGCGATTTTCC-AATTC
*
21699 CGTTGCGATAGTCT-ACAGTT-GTCGTTGCGATTTTCCA
1 CGTTGCGATAGT-TGA-AATTCG-CGTTGCGATTTTCCA
21736 AATTCGTTGT
Statistics
Matches: 109, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
82 73 0.67
83 33 0.30
84 3 0.03
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.38
Consensus pattern (80 bp):
CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCCGTTGCGATAGTCTACAGTCGCGTT
GCGATTTTCCAATTC
Found at i:22366 original size:6 final size:6
Alignment explanation
Indices: 22350--22430 Score: 155
Period size: 6 Copynumber: 13.7 Consensus size: 6
22340 TCTCGTCTCG
22350 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
22397 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
22431 ATTTTCGCAA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 70 0.93
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:24892 original size:2 final size:2
Alignment explanation
Indices: 24885--24974 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
24875 TATAAATTTA
24885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24969 AT AT AT
1 AT AT AT
24975 CCATATTAAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25124 original size:14 final size:15
Alignment explanation
Indices: 25105--25146 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
25095 AATAGTAACT
25105 AAAATAAAAATTG-G
1 AAAATAAAAATTGAG
25119 AAAATAACTAAATTGAG
1 AAAATAA--AAATTGAG
25136 ACAAATAAAAA
1 A-AAATAAAAA
25147 AAATTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 7 0.29
16 9 0.38
17 2 0.08
18 6 0.25
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (15 bp):
AAAATAAAAATTGAG
Found at i:26802 original size:53 final size:53
Alignment explanation
Indices: 26737--26859 Score: 165
Period size: 53 Copynumber: 2.3 Consensus size: 53
26727 GGGATTAAGG
**
26737 AACTCGAACAATCTTCTAAAAATGGGTTCGCTCCCTCTTGCTTCAGGGAGTAC
1 AACTCGAACAATCTTCTAAAAACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAC
* **** *
26790 AACTCGAACAATCGTCTGCCTACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
1 AACTCGAACAATCTTCTAAAAACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAC
*
26843 AACTCGAACAATTTTCT
1 AACTCGAACAATCTTCT
26860 GGTGTAATTC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (53 bp):
AACTCGAACAATCTTCTAAAAACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAC
Found at i:27387 original size:80 final size:80
Alignment explanation
Indices: 27295--27577 Score: 449
Period size: 80 Copynumber: 3.5 Consensus size: 80
27285 CTTATGGATG
* * *
27295 ACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGACGGATTTGCTTCACTGCTCTTCCGT
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCGT
27360 GAAGGCTTAAAAATT
66 GAAGGCTTAAAAATT
* * *
27375 ACCCGAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACTACTCTTCGGT
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCGT
27440 GAAGGCTTAAAAATT
66 GAAGGCTTAAAAATT
* * * *
27455 ACCCAAAGTATTTAATTATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACTACTCTTCCGT
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCGT
** *
27520 GAAGGCTTACCAGTT
66 GAAGGCTTAAAAATT
27535 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
27578 CCCGAAGGAC
Statistics
Matches: 185, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 185 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (80 bp):
ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCGT
GAAGGCTTAAAAATT
Found at i:27992 original size:38 final size:38
Alignment explanation
Indices: 27950--28066 Score: 161
Period size: 38 Copynumber: 3.2 Consensus size: 38
27940 TCTTGCTCTA
27950 AAGGCTTACAGATGGATTTGCTTCACTACTCTTCCGTG
1 AAGGCTTACAGATGGATTTGCTTCACTACTCTTCCGTG
* *
27988 AAGGCTTA-AGATGG---CGCTTCACTACTCTTCGGTG
1 AAGGCTTACAGATGGATTTGCTTCACTACTCTTCCGTG
** *
28022 AAGTTTTACAAATGGATTTGCTTCACTACTCTTCCGTG
1 AAGGCTTACAGATGGATTTGCTTCACTACTCTTCCGTG
28060 AAGGCTT
1 AAGGCTT
28067 GACTTTGCCC
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
34 24 0.36
35 5 0.08
37 6 0.09
38 31 0.47
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (38 bp):
AAGGCTTACAGATGGATTTGCTTCACTACTCTTCCGTG
Found at i:38321 original size:22 final size:23
Alignment explanation
Indices: 38293--38355 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
38283 AGTTTGTTTT
*
38293 TTGTGTTTGTGT-TGTTCATTTA
1 TTGTGTTCGTGTATGTTCATTTA
*
38315 TTGTGTTCGTTTATGTTCATTTA
1 TTGTGTTCGTGTATGTTCATTTA
** *
38338 TTACGTTCGTTTATGTTC
1 TTGTGTTCGTGTATGTTC
38356 GTTCGTTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 10 0.28
23 26 0.72
ACGTcount: A:0.11, C:0.10, G:0.19, T:0.60
Consensus pattern (23 bp):
TTGTGTTCGTGTATGTTCATTTA
Found at i:38335 original size:23 final size:23
Alignment explanation
Indices: 38305--38355 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
38295 GTGTTTGTGT
**
38305 TGTTCATTTATTGTGTTCGTTTA
1 TGTTCATTTATTACGTTCGTTTA
38328 TGTTCATTTATTACGTTCGTTTA
1 TGTTCATTTATTACGTTCGTTTA
38351 TGTTC
1 TGTTC
38356 GTTCGTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.59
Consensus pattern (23 bp):
TGTTCATTTATTACGTTCGTTTA
Found at i:38384 original size:34 final size:36
Alignment explanation
Indices: 38319--38392 Score: 107
Period size: 34 Copynumber: 2.1 Consensus size: 36
38309 CATTTATTGT
38319 GTTCGTTTATGTTCATTTATTACGTTCGTTTATGTTC
1 GTTCGTTTATGTTCA-TTATTACGTTCGTTTATGTTC
* *
38356 GTTCGTTTGTGTTCA-T-TTACGTTTGTTTATGTTC
1 GTTCGTTTATGTTCATTATTACGTTCGTTTATGTTC
38390 GTT
1 GTT
38393 TGTTATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 20 0.57
35 1 0.03
37 14 0.40
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58
Consensus pattern (36 bp):
GTTCGTTTATGTTCATTATTACGTTCGTTTATGTTC
Found at i:38679 original size:46 final size:47
Alignment explanation
Indices: 38595--38684 Score: 137
Period size: 46 Copynumber: 1.9 Consensus size: 47
38585 TGATAGAGCA
* ** *
38595 CTACCTAAAATGTTATTTTTTTCTATTGGAAATGTTAATATCAATTG
1 CTACCTAAAATGTTATTTTTTTCTACTAAAAATATTAATATCAATTG
38642 CTACCTAAAATGTTA-TTTTTTCTACTAAAAATATTAATATCAA
1 CTACCTAAAATGTTATTTTTTTCTACTAAAAATATTAATATCAA
38685 AAATATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 24 0.62
47 15 0.38
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (47 bp):
CTACCTAAAATGTTATTTTTTTCTACTAAAAATATTAATATCAATTG
Found at i:38913 original size:16 final size:16
Alignment explanation
Indices: 38892--38924 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38882 TAATAAATAA
38892 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
38908 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
38924 A
1 A
38925 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:39014 original size:16 final size:16
Alignment explanation
Indices: 38993--39037 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
38983 TAATAAATAA
*
38993 ACGAACATACACGAAC
1 ACGAACATAAACGAAC
39009 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
39025 ACGAACATAAACG
1 ACGAACATAAACG
39038 TTGGAGACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.53, C:0.27, G:0.13, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:49271 original size:2 final size:2
Alignment explanation
Indices: 49264--49293 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49254 AGTTTTGCTT
49264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49294 AGCTTCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55655 original size:20 final size:20
Alignment explanation
Indices: 55609--55657 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
55599 ATTTATTATT
*
55609 ATTTTATAAAATATAATAAGT
1 ATTTTATAAAATATAAT-AGA
55630 ATTTTATAATAATATAAT-GA
1 ATTTTATAA-AATATAATAGA
55650 ATTTTATA
1 ATTTTATA
55658 TTTTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
ATTTTATAAAATATAATAGA
Done.