Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006247.1 Hibiscus syriacus cultivar Beakdansim tig00014890_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: 48560
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11885 original size:33 final size:32
Alignment explanation
Indices: 11815--11886 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
11805 TTTTTTAGTA
* *
11815 TTCGGGTCGGATTTTTTAAAAAAAAAATTGGG
1 TTCGGGTAGGATTTTTTAAAAAAAAAATTGAG
* **
11847 ATCGGGTAGGATTTTTTTTAAAAAAAATTCGAG
1 TTCGGGTAGGATTTTTTAAAAAAAAAATT-GAG
11880 TTCGGGT
1 TTCGGGT
11887 CGGGTCGGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 25 0.76
33 8 0.24
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (32 bp):
TTCGGGTAGGATTTTTTAAAAAAAAAATTGAG
Found at i:11926 original size:28 final size:28
Alignment explanation
Indices: 11895--11948 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
11885 GTCGGGTCGG
*
11895 GTTTTTTTAAGTTTGATATTCAGGTCAA
1 GTTTTTTTAAGTGTGATATTCAGGTCAA
*
11923 GTTTTTTTAAGTGTGATATTCGGGTC
1 GTTTTTTTAAGTGTGATATTCAGGTC
11949 GGGTTCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.50
Consensus pattern (28 bp):
GTTTTTTTAAGTGTGATATTCAGGTCAA
Found at i:12534 original size:16 final size:16
Alignment explanation
Indices: 12513--12577 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
12503 AGGTTTCAGA
*
12513 TTCAGATTCTAATTCC
1 TTCAGATTCCAATTCC
*
12529 TTCAGATCCCAATTCC
1 TTCAGATTCCAATTCC
* * *
12545 TCCAGAATCCAATTTC
1 TTCAGATTCCAATTCC
12561 TTCACAGATTCCAATTC
1 TT--CAGATTCCAATTC
12578 TCTCGTAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
16 27 0.71
18 11 0.29
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.35
Consensus pattern (16 bp):
TTCAGATTCCAATTCC
Found at i:13857 original size:42 final size:42
Alignment explanation
Indices: 13798--13881 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
13788 AACAGGAAGA
*
13798 AAGCAAAACAGAGGAAGACGATAAGGGATCATCGCTCTGCCT
1 AAGCAAAACAGAGGAAGACGATAAGGGATCATCACTCTGCCT
13840 AAGCAAAACAGAGGAAGACGATAAGGGATCATCACTCTGCCT
1 AAGCAAAACAGAGGAAGACGATAAGGGATCATCACTCTGCCT
13882 CTAACAATGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (42 bp):
AAGCAAAACAGAGGAAGACGATAAGGGATCATCACTCTGCCT
Found at i:15397 original size:68 final size:68
Alignment explanation
Indices: 15288--15562 Score: 397
Period size: 68 Copynumber: 4.0 Consensus size: 68
15278 AAAAGATTAA
* *
15288 GAGGCCTAACTGAGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
15353 TTT
66 TTT
* ** * *
15356 GAGGCCTAACTATTTATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAACTAAATGTC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
15421 TTT
66 TTT
* * * *
15424 GAGGCTTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
15489 TTT
66 TTT
* * * * *
15492 GAGGCCTAACTGTGCATATGACAGAAAAGTGTCAATTATGTCAGTTAGATGAAAGATTAAGTATC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
*
15557 GTT
66 TTT
15560 GAG
1 GAG
15563 TAAATGAAAA
Statistics
Matches: 181, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 181 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (68 bp):
GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
TTT
Found at i:15632 original size:80 final size:78
Alignment explanation
Indices: 15494--15879 Score: 391
Period size: 80 Copynumber: 5.0 Consensus size: 78
15484 GTGCCTTTGA
* * * * *
15494 GGCCTAACTGTGC-ATATGACAGAAAAGTGTCAATTATGTCAGTTAGATGAAAGATTAAGTATCG
1 GGCCTAGCTGTGCAAT-TGGCAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGTA-CG
*
15558 TTGAGTAAATGAAAAT
63 TTGAGTAAAAGAAAAT
15574 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGCAAGTTAGATGAACGGTTAAGTACCGT
1 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGC-AGTTAGATGAACGGTTAAGTA-CGT
15639 TGAGTAAAAGAAAAT
64 TGAGTAAAAGAAAAT
* * *
15654 GGCCTAGCTGTGTAATTGGCAGAATGATGTCAATTATGCCAGTTAGATGAACGG-T---TA----
1 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGTACGTT
15711 -AGTAAAAGAAAAT
65 GAGTAAAAGAAAAT
* * * *
15724 GGCCTAGTTGTGCAGTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAGTACAGT
1 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGTAC-GT
15789 TGAGTAAAAGAATAAT
64 TGAGTAAAAGAA-AAT
*** * * * **
15805 TATCTAACTGTGC-ATTGGTAGAAAGGTGTCAATTATGTCAGTTAGACGAAC-GTTAAACACCGT
1 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGTA-CGT
*
15868 TGAGTAAGAGAA
64 TGAGTAAAAGAA
15880 TGGATAAATT
Statistics
Matches: 264, Mismatches: 27, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
70 62 0.23
71 1 0.00
74 2 0.01
76 2 0.01
79 21 0.08
80 162 0.61
81 14 0.05
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (78 bp):
GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGCAGTTAGATGAACGGTTAAGTACGTTG
AGTAAAAGAAAAT
Found at i:15754 original size:70 final size:70
Alignment explanation
Indices: 15641--15784 Score: 243
Period size: 70 Copynumber: 2.1 Consensus size: 70
15631 AGTACCGTTG
* *
15641 AGTAAAAGAAAATGGCCTAGCTGTGTAATTGGCAGAATGATGTCAATTATGCCAGTTAGATGAAC
1 AGTAAAAGAAAATGGCCTAGCTGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAAC
15706 GGTTA
66 GGTTA
* * *
15711 AGTAAAAGAAAATGGCCTAGTTGTGCAGTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAAC
1 AGTAAAAGAAAATGGCCTAGCTGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAAC
15776 GGTTA
66 GGTTA
15781 AGTA
1 AGTA
15785 CAGTTGAGTA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.27
Consensus pattern (70 bp):
AGTAAAAGAAAATGGCCTAGCTGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAAC
GGTTA
Found at i:15755 original size:150 final size:149
Alignment explanation
Indices: 15556--15860 Score: 423
Period size: 150 Copynumber: 2.0 Consensus size: 149
15546 GATTAAGTAT
* * *
15556 CGTTGAGTAAATGAAAATGGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGCAAGTTAGA
1 CGTTAAGTAAAAGAAAATGGCCTAGCTGTGCAATTGGCAGAAAGATGTCAATTATGCAAGTTAGA
* * * *
15621 TGAACGGTTAAGTACCGTTGAGTAAAAGAA-AATGGCCTAGCTGTGTAATTGGCAGAATGATGTC
66 TGAACGGTTAAGTACAGTTGAGTAAAAGAATAATGACCTAACTGTG-AATTGGCAGAAAGATGTC
*
15685 AATTATGCCAGTTAGATGAA
130 AATTATGCCAGTTAGACGAA
* * * *
15705 CGGTTAAGTAAAAGAAAATGGCCTAGTTGTGCAGTTGGTAGAAAGATGTCAATTATGCCAGTTAG
1 C-GTTAAGTAAAAGAAAATGGCCTAGCTGTGCAATTGGCAGAAAGATGTCAATTATGCAAGTTAG
* * * * *
15770 ATGAACGGTTAAGTACAGTTGAGTAAAAGAATAATTATCTAACTGTGCATTGGTAGAAAGGTGTC
65 ATGAACGGTTAAGTACAGTTGAGTAAAAGAATAATGACCTAACTGTGAATTGGCAGAAAGATGTC
*
15835 AATTATGTCAGTTAGACGAA
130 AATTATGCCAGTTAGACGAA
15855 CGTTAA
1 CGTTAA
15861 ACACCGTTGA
Statistics
Matches: 136, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
149 6 0.04
150 119 0.88
151 11 0.08
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (149 bp):
CGTTAAGTAAAAGAAAATGGCCTAGCTGTGCAATTGGCAGAAAGATGTCAATTATGCAAGTTAGA
TGAACGGTTAAGTACAGTTGAGTAAAAGAATAATGACCTAACTGTGAATTGGCAGAAAGATGTCA
ATTATGCCAGTTAGACGAA
Found at i:17494 original size:16 final size:16
Alignment explanation
Indices: 17473--17505 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17463 TAATAAATAA
17473 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
17489 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
17505 A
1 A
17506 AAATGTTTTT
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:17599 original size:16 final size:16
Alignment explanation
Indices: 17578--17646 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
17568 TAAATAAACG
17578 AACATAAACGAACACA
1 AACATAAACGAACACA
*
17594 AACATAAACGAACACG
1 AACATAAACGAACACA
*
17610 AACATAAATGAACACA
1 AACATAAACGAACACA
*
17626 AACATAAACGAACATA
1 AACATAAACGAACACA
17642 AACAT
1 AACAT
17647 TGGAGACCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.61, C:0.22, G:0.07, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:18307 original size:24 final size:24
Alignment explanation
Indices: 18272--18322 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
18262 GATTGGCTTA
*
18272 AACATAAATGAATGAACATAACCG
1 AACATAAATGAACGAACATAACCG
* *
18296 AACATAACTGAACGAACATAACTG
1 AACATAAATGAACGAACATAACCG
18320 AAC
1 AAC
18323 GTTCACGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.16
Consensus pattern (24 bp):
AACATAAATGAACGAACATAACCG
Found at i:18311 original size:14 final size:14
Alignment explanation
Indices: 18294--18323 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
18284 TGAACATAAC
18294 CGAACATAACTGAA
1 CGAACATAACTGAA
18308 CGAACATAACTGAA
1 CGAACATAACTGAA
18322 CG
1 CG
18324 TTCACGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (14 bp):
CGAACATAACTGAA
Found at i:18602 original size:64 final size:63
Alignment explanation
Indices: 18516--18674 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 63
18506 TGCACTAAGA
* *
18516 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCTATGCATG-GCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-AGCCAGAGTGCATCGATGCATGTG-T
* * **
18579 GGTGTATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGATGCATGTGT
1 -GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAGCCAGAGTGCATCGATGCATGTGT
*
18644 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
18675 CAATTTATTT
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 2 0.02
64 54 0.64
65 24 0.29
66 4 0.05
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAGCCAGAGTGCATCGATGCATGTGT
Found at i:19923 original size:65 final size:63
Alignment explanation
Indices: 19854--20013 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 63
19844 AATTAAATTG
*
19854 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTAATGCATCGATGCACA-ACCATGCACCGATGCACTGAGGATATTT-TG-
19918 A
63 A
* * * ** *
19919 AACATCGAATGTATTTAATGCATCGATGCACCAGCCATGCATCGATGCACTTTGGCTATTTTGA
1 AACATCGAATGCATTTAATGCATCGATGCA-CAACCATGCACCGATGCACTGAGGATATTTTGA
* *
19983 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTAATGCATCGATGCAC
20014 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 1 0.01
64 28 0.34
65 49 0.59
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTAATGCATCGATGCACAACCATGCACCGATGCACTGAGGATATTTTGA
Found at i:20013 original size:17 final size:19
Alignment explanation
Indices: 19985--20033 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
19975 TATTTTGAAA
19985 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
20003 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
20022 CACCGATGCACT
1 CATCGATGCACT
20034 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:28624 original size:65 final size:64
Alignment explanation
Indices: 28500--28700 Score: 189
Period size: 65 Copynumber: 3.1 Consensus size: 64
28490 TTTTTCAAAG
* * *
28500 TGATGCA-CTGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATG
1 TGATGCATC-GATGCAACAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATG
28561 CATT
61 CATT
* *
28565 TCATGCATCGATG-AACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCAACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
28628 TT
63 TT
* * * * * *
28630 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCAACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
28694 TGATGCA
1 TGATGCA
28701 CTCTTAGTGC
Statistics
Matches: 114, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 40 0.35
65 64 0.56
66 7 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCAACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:30414 original size:23 final size:23
Alignment explanation
Indices: 30388--30432 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
30378 CACCACAACT
*
30388 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
30411 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
30433 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:30670 original size:149 final size:149
Alignment explanation
Indices: 30411--30714 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
30401 CGAAGTGCCC
* *
30411 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAAGTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
30476 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
30541 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
30560 CGTAGAAGTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAAGTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
30625 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCGAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
30690 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
30709 CGTAGA
1 CGTAGA
30715 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CGTAGAAGTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:31638 original size:20 final size:18
Alignment explanation
Indices: 31599--31633 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31589 TCCCATCTAG
31599 CTTATATTATATGTTCAT
1 CTTATATTATATGTTCAT
31617 CTTATCATT-TATGTTCA
1 CTTAT-ATTATATGTTCA
31634 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATATTATATGTTCAT
Found at i:32242 original size:21 final size:21
Alignment explanation
Indices: 32218--32262 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32208 TCTTGTTCGT
* *
32218 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
32239 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
32260 TTG
1 TTG
32263 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:38424 original size:452 final size:452
Alignment explanation
Indices: 37580--38426 Score: 1408
Period size: 452 Copynumber: 1.9 Consensus size: 452
37570 CTATACCTTC
* *
37580 TGTTGGGTTATGGGGTCCAGCGATCACCCTAAGGGATTCTATCGTGTATGGGCGCGATATTGGTG
1 TGTTGGGTTATGGGGTCCAACGATCACCCTAAGGGATTCTATCGTGTATGGGCGCGATATCGGTG
* * * *
37645 CGTGACTGCCCAACCTGTCGAGGCCCACGTGTGCCTTGCGAAGCCCCCTAGGCCCGCCCGCAGTA
66 CGTGACTGCCCAACCTGCCGAGGCCCACATATGCCTTGCGAAGCCCCCTAGGCCCGCCCGCAGCA
* *
37710 TGCTATAGATGCGGGGCTCTGCAATGCCATGGTGAACTGTGGGGGGTGCCCCACAAGAATCCACC
131 CGCTATAGATGCGGGGCTCTGCAATGCCATGGTGAACTGTGGGAGGTGCCCCACAAGAATCCACC
* * * * ** *
37775 TTAGTTTGGGGAATCCAGTGATCACCCACTATAAAGATATGAGGTTAAAATGGTCTACCTACTTA
196 TTAGTTGGGGGAACCCAATGATCACCCACTACAAAGATATGAGGTTAAAATGACCCACCTACTTA
* *
37840 TCACCAATTGGTTTTAAGAAGGAATGTTGACCATTCGCTTTAGAACTCTATGGTTAAGCGTACTT
261 TCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTATGGTTAAGCGTACTT
*
37905 GGACTAGGGAAATCCAATGATGGGTGACCCACTGGGAAGTTGTTCAGAAATGAATGACTCAATCC
326 GGACTAGGGAAATCCAAGGATGGGTGACCCACTGGGAAGTTGTTCAGAAATGAATGACTCAATCC
37970 TAACAACTGGTATCAGAGCAGGTTGCAGGTTCGAATTCCCCAGATGTCGTTGGGAGGGTGAT
391 TAACAACTGGTATCAGAGCAGGTTGCAGGTTCGAATTCCCCAGATGTCGTTGGGAGGGTGAT
* * * *
38032 TGTTGGGTTATGGGGTCCAACGATCACCTTTAGGGATTTTATTGTGTATGGGCGCGATATCGGTG
1 TGTTGGGTTATGGGGTCCAACGATCACCCTAAGGGATTCTATCGTGTATGGGCGCGATATCGGTG
38097 CGTGACTGCCCAACCTGCCGAGGCCCACATATGCCTTGCGAAG-CCCCTAGGCCCGCCCGCAGCA
66 CGTGACTGCCCAACCTGCCGAGGCCCACATATGCCTTGCGAAGCCCCCTAGGCCCGCCCGCAGCA
* *
38161 CGCTATAGATGCGGGGCTCTGCAATGCCGTGGTGAACTGTGGGAGGTGCCCCACAAGAATTCACC
131 CGCTATAGATGCGGGGCTCTGCAATGCCATGGTGAACTGTGGGAGGTGCCCCACAAGAATCCACC
* *
38226 TTGGCTTGGGGGAACCCAATGATCACTCACTACAAAGATATGAGGTTAAAATGACCCACCTACTT
196 TTAG-TTGGGGGAACCCAATGATCACCCACTACAAAGATATGAGGTTAAAATGACCCACCTACTT
*
38291 ATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTATGGTTAAGCGTGCT
260 ATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTATGGTTAAGCGTACT
** *
38356 TGGACTAGGGAAATCCAAGGATGGGTGACCCGTTGGGAAGTTGTTCAGAAATGAATGACTCGATC
325 TGGACTAGGGAAATCCAAGGATGGGTGACCCACTGGGAAGTTGTTCAGAAATGAATGACTCAATC
38421 CTAACA
390 CTAACA
38427 CTTTCAATGT
Statistics
Matches: 364, Mismatches: 30, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
451 84 0.23
452 280 0.77
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (452 bp):
TGTTGGGTTATGGGGTCCAACGATCACCCTAAGGGATTCTATCGTGTATGGGCGCGATATCGGTG
CGTGACTGCCCAACCTGCCGAGGCCCACATATGCCTTGCGAAGCCCCCTAGGCCCGCCCGCAGCA
CGCTATAGATGCGGGGCTCTGCAATGCCATGGTGAACTGTGGGAGGTGCCCCACAAGAATCCACC
TTAGTTGGGGGAACCCAATGATCACCCACTACAAAGATATGAGGTTAAAATGACCCACCTACTTA
TCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTATGGTTAAGCGTACTT
GGACTAGGGAAATCCAAGGATGGGTGACCCACTGGGAAGTTGTTCAGAAATGAATGACTCAATCC
TAACAACTGGTATCAGAGCAGGTTGCAGGTTCGAATTCCCCAGATGTCGTTGGGAGGGTGAT
Done.