Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003174.1 Hibiscus syriacus cultivar Beakdansim tig00006677_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: 44699
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2188 original size:42 final size:42
Alignment explanation
Indices: 2040--2196 Score: 132
Period size: 41 Copynumber: 3.8 Consensus size: 42
2030 ACAAACACCA
* *
2040 CTATCGCGGCGTTTGTAT-AAAAACGCCGCT-AATTACCACT
1 CTATTGCGGCGTTTGTTTAAAAAACGCCGCTAAATTACCACT
* * * *
2080 CTATTGCGGCATTTGTTGAAAAAACGCCACTATAA--A-CATAT
1 CTATTGCGGCGTTTGTTTAAAAAACGCCGCTA-AATTACCA-CT
* *
2121 CTTTTGCGGCG--T-TTTAACTATAAACGCTGCTAAATTACCACT
1 CTATTGCGGCGTTTGTTTAA--A-AAACGCCGCTAAATTACCACT
*
2163 CTATTACGGCGTTTGTTTAAAAAACGCCGCTAAA
1 CTATTGCGGCGTTTGTTTAAAAAACGCCGCTAAA
2197 GTATCATTTT
Statistics
Matches: 89, Mismatches: 15, Indels: 24
0.70 0.12 0.19
Matches are distributed among these distances:
38 4 0.04
39 1 0.01
40 19 0.21
41 31 0.35
42 23 0.26
43 5 0.06
44 1 0.01
45 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (42 bp):
CTATTGCGGCGTTTGTTTAAAAAACGCCGCTAAATTACCACT
Found at i:2227 original size:82 final size:81
Alignment explanation
Indices: 2045--2230 Score: 214
Period size: 83 Copynumber: 2.3 Consensus size: 81
2035 CACCACTATC
* * *
2045 GCGGCGTTTGTATAAAAACGCCGCTAATTACCACTCTATTGCGGCATTTGTTGAAAAAACGCCAC
1 GCGGCGTTTGAATATAAACGCCGCTAATTACCACTCTATTACGGCATTTGTTGAAAAAACGCCAC
2110 TATAAACATATCTTTT
66 TATAAACATATCTTTT
* * * *
2126 GCGGCGTTTTAACTATAAACGCTGCTAAATTACCACTCTATTACGGCGTTTGTTTAAAAAACGCC
1 GCGGCGTTTGAA-TATAAACGCCGCT-AATTACCACTCTATTACGGCATTTGTTGAAAAAACGCC
* **
2191 GCTA-AAGTATCAT-TTTT
64 ACTATAAACAT-ATCTTTT
* *
2208 GTGGCGTTTGGATAGTAAACGCC
1 GCGGCGTTTGAATA-TAAACGCC
2231 ACGATATGCT
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
81 12 0.14
82 35 0.40
83 40 0.46
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (81 bp):
GCGGCGTTTGAATATAAACGCCGCTAATTACCACTCTATTACGGCATTTGTTGAAAAAACGCCAC
TATAAACATATCTTTT
Found at i:2822 original size:2 final size:2
Alignment explanation
Indices: 2815--2858 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2805 AATATTTTAA
2815 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
2857 AT
1 AT
2859 TTTTTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10892 original size:12 final size:12
Alignment explanation
Indices: 10855--10893 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10845 TTACCGTTCT
*
10855 CGTCCCTGTGTC
1 CGTCCCCGTGTC
*
10867 CCTCCCCGTGTC
1 CGTCCCCGTGTC
*
10879 CGTCCTCGTGTC
1 CGTCCCCGTGTC
10891 CGT
1 CGT
10894 ATCTGTATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.46, G:0.23, T:0.31
Consensus pattern (12 bp):
CGTCCCCGTGTC
Found at i:12084 original size:18 final size:19
Alignment explanation
Indices: 12056--12092 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
12046 ATGTTTGATT
*
12056 TTTTATCTTCTTTGAGTTG
1 TTTTATCTTCTTTAAGTTG
12075 TTTT-TCTTCTTTAAGTTG
1 TTTTATCTTCTTTAAGTTG
12093 AAACTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.11, C:0.11, G:0.14, T:0.65
Consensus pattern (19 bp):
TTTTATCTTCTTTAAGTTG
Found at i:12207 original size:21 final size:21
Alignment explanation
Indices: 12165--12208 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12155 AATTTAATTT
*
12165 ATATTTATATTTTTATTTCAA
1 ATATTTATATTTTTATTACAA
*
12186 ATATTTTTATTTATTA-TACAA
1 ATATTTATATTT-TTATTACAA
12207 AT
1 AT
12209 TCATAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTATATTTTTATTACAA
Found at i:12259 original size:2 final size:2
Alignment explanation
Indices: 12252--12282 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12242 CATAAATTTA
12252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12283 AAAAATGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14085 original size:14 final size:14
Alignment explanation
Indices: 14068--14096 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
14058 CGTTCATATG
14068 TATCTATATACATA
1 TATCTATATACATA
14082 TATCTATATACATA
1 TATCTATATACATA
14096 T
1 T
14097 GGACTAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (14 bp):
TATCTATATACATA
Found at i:16937 original size:13 final size:13
Alignment explanation
Indices: 16904--16937 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16894 GATCTTCTTT
16904 TTATTATTATTTA
1 TTATTATTATTTA
* *
16917 ATAATATTATTTA
1 TTATTATTATTTA
16930 TTATTATT
1 TTATTATT
16938 TTAATTACAT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:17792 original size:12 final size:14
Alignment explanation
Indices: 17761--17794 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
17751 TCCAGAGAGC
17761 TCTCTCCCACTCTT
1 TCTCTCCCACTCTT
17775 TCTCTCCCACTCTT
1 TCTCTCCCACTCTT
17789 TCTCTC
1 TCTCTC
17795 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.06, C:0.50, G:0.00, T:0.44
Consensus pattern (14 bp):
TCTCTCCCACTCTT
Found at i:18004 original size:33 final size:34
Alignment explanation
Indices: 17941--18015 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 34
17931 CTCATTTGTA
*
17941 ATATTTTATTTTAGCCATTAATGAAAATATA-TT
1 ATATTTTATTTTAGCCACTAATGAAAATATATTT
***
17974 ATATTTTATTTTGAG-CACTAATGTTTATATATTT
1 ATATTTTATTTT-AGCCACTAATGAAAATATATTT
*
18008 TTATTTTA
1 ATATTTTA
18016 GTCATGTTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 24 0.69
34 11 0.31
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (34 bp):
ATATTTTATTTTAGCCACTAATGAAAATATATTT
Found at i:18363 original size:30 final size:30
Alignment explanation
Indices: 18328--18570 Score: 223
Period size: 30 Copynumber: 8.2 Consensus size: 30
18318 ACTGTTCAGC
18328 CCTTTAACTTTATGTCTTT-GCTATTTTAGT
1 CCTTTAACTTTATGT-TTTAGCTATTTTAGT
* * * * * *
18358 TCTTTAAGTTTCTATTTTATCTATTTTGGT
1 CCTTTAACTTTATGTTTTAGCTATTTTAGT
* * *
18388 CCTTGAACTTTCTTTTTTAGCTATTTTAGT
1 CCTTTAACTTTATGTTTTAGCTATTTTAGT
18418 CCTTTAAGCTTCTAT-TTTT-GCTATTTTAGT
1 CCTTTAA-CTT-TATGTTTTAGCTATTTTAGT
* * *
18448 CCTGTAAGTTTCTGTTTTAGCTATTTTAGT
1 CCTTTAACTTTATGTTTTAGCTATTTTAGT
**
18478 CCTCCAAGC-TTATGTTTTTA-CTATTTTAGT
1 CCTTTAA-CTTTATG-TTTTAGCTATTTTAGT
* *
18508 CCTGTAAGTTCTAT-TTTT-GCTATTTTAGT
1 CCTTTAACTT-TATGTTTTAGCTATTTTAGT
*
18537 CCTTTAAATTTATGTTTTAGCTATTTTAG-
1 CCTTTAACTTTATGTTTTAGCTATTTTAGT
18566 CCTTT
1 CCTTT
18571 CAAGTTTGGT
Statistics
Matches: 175, Mismatches: 26, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
28 5 0.03
29 40 0.23
30 113 0.65
31 15 0.09
32 2 0.01
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (30 bp):
CCTTTAACTTTATGTTTTAGCTATTTTAGT
Found at i:18438 original size:90 final size:90
Alignment explanation
Indices: 18328--18565 Score: 306
Period size: 90 Copynumber: 2.7 Consensus size: 90
18318 ACTGTTCAGC
* * * *
18328 CCTTTAA-CTT-TATGTCTTTGCTATTTTAGTTCTTTAAGTTTCTATTTTATCTATTTTGGTCCT
1 CCTTTAAGCTTCTAT-T-TTTGCTATTTTAGTCCTTTAAGTTTCTGTTTTAGCTATTTTAGTCCT
** *
18391 TGAA-CTT-TCTTTTTTAGCTATTTTAGT
64 CCAAGCTTAT-GTTTTTA-CTATTTTAGT
*
18418 CCTTTAAGCTTCTATTTTTGCTATTTTAGTCCTGTAAGTTTCTGTTTTAGCTATTTTAGTCCTCC
1 CCTTTAAGCTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTCTGTTTTAGCTATTTTAGTCCTCC
18483 AAGCTTATGTTTTTACTATTTTAGT
66 AAGCTTATGTTTTTACTATTTTAGT
* * *
18508 CCTGTAAG-TTCTATTTTTGCTATTTTAGTCCTTTAAATTTATGTTTTAGCTATTTTAG
1 CCTTTAAGCTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTCTGTTTTAGCTATTTTAG
18566 CCTTTCAAGT
Statistics
Matches: 132, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
89 47 0.36
90 68 0.52
91 13 0.10
92 4 0.03
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (90 bp):
CCTTTAAGCTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTCTGTTTTAGCTATTTTAGTCCTCC
AAGCTTATGTTTTTACTATTTTAGT
Found at i:18718 original size:2 final size:2
Alignment explanation
Indices: 18711--18748 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
18701 ATTTGTAAAC
18711 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
18749 TCTATTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29799 original size:3 final size:3
Alignment explanation
Indices: 29785--29848 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
29775 ACAATAAAAG
*
29785 AAT AAT AGT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29832 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
29849 AATTAAAAGC
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:30783 original size:38 final size:38
Alignment explanation
Indices: 30736--30868 Score: 101
Period size: 38 Copynumber: 3.5 Consensus size: 38
30726 AAGACAAGGC
30736 TGAGGTTTCTAGGGAAACAATTTTTAGAAAAACCAAAT
1 TGAGGTTTCTAGGGAAACAATTTTTAGAAAAACCAAAT
* * * * * * ***
30774 TGAGTTTTCTA-TGATATAAGTCTTA-AGAAGGTCATAAT
1 TGAGGTTTCTAGGGAAACAATTTTTAGA-AAAACCA-AAT
* * *
30812 TGAGGTTTCTAGGGAAACAATCTTAAGAAATACCAAAT
1 TGAGGTTTCTAGGGAAACAATTTTTAGAAAAACCAAAT
* *
30850 TGAGTTTTCT-GGGATACAA
1 TGAGGTTTCTAGGGAAACAA
30869 GTCCTAAGAA
Statistics
Matches: 69, Mismatches: 22, Indels: 9
0.69 0.22 0.09
Matches are distributed among these distances:
36 1 0.01
37 21 0.30
38 35 0.51
39 11 0.16
40 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (38 bp):
TGAGGTTTCTAGGGAAACAATTTTTAGAAAAACCAAAT
Found at i:30891 original size:38 final size:39
Alignment explanation
Indices: 30771--30902 Score: 130
Period size: 38 Copynumber: 3.5 Consensus size: 39
30761 AGAAAAACCA
* * * *
30771 AATTGAGTTTTCTA-TGATATAAGTCTTAAGAAGGTCAT
1 AATTGAGGTTTCTAGGGATACAAGTCTTAAGAAGGTCAC
* *
30809 AATTGAGGTTTCTAGGGAAACAA-TCTTAAGAA-AT-ACC
1 AATTGAGGTTTCTAGGGATACAAGTCTTAAGAAGGTCA-C
* *
30846 AAATTGAGTTTTCT-GGGATACAAGTCCTAAGAAGGTCAC
1 -AATTGAGGTTTCTAGGGATACAAGTCTTAAGAAGGTCAC
*
30885 AGTTGAGGTTTCTAGGGA
1 AATTGAGGTTTCTAGGGA
30903 ATTAATCTTA
Statistics
Matches: 75, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
36 1 0.01
37 9 0.12
38 53 0.71
39 11 0.15
40 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (39 bp):
AATTGAGGTTTCTAGGGATACAAGTCTTAAGAAGGTCAC
Found at i:30915 original size:38 final size:38
Alignment explanation
Indices: 30794--30916 Score: 119
Period size: 38 Copynumber: 3.2 Consensus size: 38
30784 ATGATATAAG
* *
30794 TCTTAAGAAGGTCATAATTGAGGTTTCTAGGGAAACAA
1 TCTTAAGAAGGTCACAATTGAGGTTTCTAGGGAATCAA
* *
30832 TCTTAAGAA-AT-ACCAAATTGAGTTTTCT-GGG-ATACAA
1 TCTTAAGAAGGTCA-C-AATTGAGGTTTCTAGGGAAT-CAA
* * *
30869 GTCCTAAGAAGGTCACAGTTGAGGTTTCTAGGGAATTAA
1 -TCTTAAGAAGGTCACAATTGAGGTTTCTAGGGAATCAA
30908 TCTTAAGAA
1 TCTTAAGAA
30917 ATACAAAATG
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
36 2 0.03
37 7 0.10
38 48 0.72
39 7 0.10
40 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (38 bp):
TCTTAAGAAGGTCACAATTGAGGTTTCTAGGGAATCAA
Found at i:30918 original size:76 final size:76
Alignment explanation
Indices: 30736--30925 Score: 272
Period size: 76 Copynumber: 2.5 Consensus size: 76
30726 AAGACAAGGC
* * * * * *
30736 TGAGGTTTCTAGGGAAACAATTTTTAGAAAAACCAAATTGAGTTTTCTATGATATAAGTCTTAAG
1 TGAGGTTTCTAGGGAAACAATCTTAAGAAATACCAAATTGAGTTTTCTAGGATACAAGTCCTAAG
*
30801 AAGGTCATAAT
66 AAGGTCACAAT
*
30812 TGAGGTTTCTAGGGAAACAATCTTAAGAAATACCAAATTGAGTTTTCTGGGATACAAGTCCTAAG
1 TGAGGTTTCTAGGGAAACAATCTTAAGAAATACCAAATTGAGTTTTCTAGGATACAAGTCCTAAG
*
30877 AAGGTCACAGT
66 AAGGTCACAAT
** *
30888 TGAGGTTTCTAGGGAATTAATCTTAAGAAATACAAAAT
1 TGAGGTTTCTAGGGAAACAATCTTAAGAAATACCAAAT
30926 GATTTCTCAA
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 102 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (76 bp):
TGAGGTTTCTAGGGAAACAATCTTAAGAAATACCAAATTGAGTTTTCTAGGATACAAGTCCTAAG
AAGGTCACAAT
Found at i:31353 original size:51 final size:50
Alignment explanation
Indices: 31298--31399 Score: 118
Period size: 50 Copynumber: 2.0 Consensus size: 50
31288 AAAATGTTAG
31298 GTTGAAGAAGGATA-CTACAAAAAAGTTGACTC-CTCTCCACGAGAAAGTCAA
1 GTTGAA-AAGGATATC-ACAAAAAAGTTGACTCTCTCTCC-CGAGAAAGTCAA
* * * * *
31349 GTTGAAAATGATATCACTAAAAGGTTGACTCTTTTTCCCGAGAAAGTCAA
1 GTTGAAAAGGATATCACAAAAAAGTTGACTCTCTCTCCCGAGAAAGTCAA
31399 G
1 G
31400 AATGCCATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 33 0.75
51 11 0.25
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (50 bp):
GTTGAAAAGGATATCACAAAAAAGTTGACTCTCTCTCCCGAGAAAGTCAA
Found at i:31412 original size:45 final size:45
Alignment explanation
Indices: 31317--32139 Score: 643
Period size: 45 Copynumber: 18.6 Consensus size: 45
31307 GGATACTACA
* * *
31317 AAAAAGTTGACTCCTCTCCACGAGAAAGTCAAGTTGAAAATGATATCACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAA---G--AATGACATCACT
* * * *
31367 AAAAGGTTGACTCTTTTTCCCGAGAAAGTCAAGAATGCCATCACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * *
31412 AAAAGGTTGACTCCT-TT-ATGCGAGAAAGTTAATAATCATATCACT
1 AAAAGGTTGACTCCTCTTCA--CGAGAAAGTCAAGAATGACATCACT
* *
31457 AAAAGGTTGACTCTTCTTCGCGAG-AAGTCAAGAATGACATCACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* *
31501 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAAAGACAACACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * *
31546 AAAAGATTGACTCCTCTTCGCGAGAAAGTCAATAATGACAACACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * * * *
31591 GAAAGATTGACTCCTTTTCATGAGAAAGTCAAGAATAACATAACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * * *
31636 AAAAAGTTGAATCATCTTCTCGAGAAAGT-AAGAATTACATCACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * * *
31680 AAAATGCTT-ACTCTTTTTCACGAGAAAGTCAAGAAGGACAACACT
1 AAAA-GGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
** *
31725 AAAATATTGACTCCTCTTCACAAGAAAGTC---AA-G-----ACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * * * *
31761 AACAGATTGACTCCTCTTCATGAGAACGTCAAGAATGAAAACACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * * *
31806 GAAAGATTGACTCCTCTTCAAGAGAAAGTTAAGAATAACATCACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * *
31851 AAAAAGTTAACTTCTCTTCACGAGAAAGTCAAG-ATGGACAACACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAAT-GACATCACT
* * *
31896 AAAAGATTGACTCCTCTTCACGATAAAGT------T-A-A-GACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * * * * * * *
31932 GAAAGATTAACTCCTCTTCATGAGTACGTCAAGAGTGAAAACACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * *
31977 AAAAGATTGACT-CTCTTCATGAGAAAGTCAAGAATAACATCACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * * *
32021 AAAAAGTTGATTCATCTTCACGAGAAAGTCAAGAATAACATAACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * * * *
32066 AAAAGATTGACTCTTCTTTATGAGAAAGTCAAGAATGACAACATT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
* * * *
32111 GAAAGATTAACTCATCTTCACGAGAAAGT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGT
32140 TAAGTTGAAG
Statistics
Matches: 621, Mismatches: 124, Indels: 61
0.77 0.15 0.08
Matches are distributed among these distances:
36 54 0.09
37 1 0.00
38 1 0.00
39 2 0.00
40 2 0.00
41 1 0.00
42 3 0.00
43 1 0.00
44 113 0.18
45 413 0.67
46 2 0.00
47 1 0.00
50 27 0.04
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (45 bp):
AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATGACATCACT
Found at i:31762 original size:36 final size:36
Alignment explanation
Indices: 31722--31794 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
31712 GAAGGACAAC
*
31722 ACTAAAATATTGACTCCTCTTCACAAGAAAGTCAAG
1 ACTAAAAGATTGACTCCTCTTCACAAGAAAGTCAAG
* ** *
31758 ACTAACAGATTGACTCCTCTTCATGAGAACGTCAAG
1 ACTAAAAGATTGACTCCTCTTCACAAGAAAGTCAAG
31794 A
1 A
31795 ATGAAAACAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (36 bp):
ACTAAAAGATTGACTCCTCTTCACAAGAAAGTCAAG
Found at i:31804 original size:81 final size:82
Alignment explanation
Indices: 31696--32009 Score: 305
Period size: 81 Copynumber: 3.8 Consensus size: 82
31686 CTTACTCTTT
* * *
31696 TTCACGAGAAAGTCAAGAAGGACAACACTAAAATATTGACTCCTCTTCACAAGAAAGTCAAGACT
1 TTCACGAGAAAGTCAAGAATGAAAACACTAAAAGATTGACTCCTCTTCACAAGAAAGTCAAGACT
*
31761 -AACAGATTGACTCCTC
66 CAACAGATTAACTCCTC
* * * *
31777 TTCATGAGAACGTCAAGAATGAAAACACTGAAAGATTGACTCCTCTTCA-AGAGAAAGTTAAGAA
1 TTCACGAGAAAGTCAAGAATGAAAACACTAAAAGATTGACTCCTCTTCACA-AGAAAGTCAAG--
* * *
31841 TAACATCACTAAAAAGTTAACTTCTC
63 --AC-TCA--ACAGA-TTAACTCCTC
* * * *
31867 TTCACGAGAAAGTCAAG-ATGGACAACACTAAAAGATTGACTCCTCTTCACGATAAAGTTAAGAC
1 TTCACGAGAAAGTCAAGAAT-GAAAACACTAAAAGATTGACTCCTCTTCACAAGAAAGTCAAGAC
*
31931 TGAA-AGATTAACTCCTC
65 TCAACAGATTAACTCCTC
* * * * **
31948 TTCATGAGTACGTCAAGAGTGAAAACACTAAAAGATTGACT-CTCTTCATGAGAAAGTCAAGA
1 TTCACGAGAAAGTCAAGAATGAAAACACTAAAAGATTGACTCCTCTTCACAAGAAAGTCAAGA
32010 ATAACATCAC
Statistics
Matches: 192, Mismatches: 28, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
80 19 0.10
81 96 0.50
82 3 0.02
83 1 0.01
85 4 0.02
86 3 0.02
87 1 0.01
89 5 0.03
90 60 0.31
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (82 bp):
TTCACGAGAAAGTCAAGAATGAAAACACTAAAAGATTGACTCCTCTTCACAAGAAAGTCAAGACT
CAACAGATTAACTCCTC
Found at i:31995 original size:215 final size:213
Alignment explanation
Indices: 31498--32143 Score: 620
Period size: 215 Copynumber: 3.0 Consensus size: 213
31488 GAATGACATC
* * **
31498 ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAAAGACAACACTAAAAGATTGACTCCTCT
1 ACTAAAAGATTAACTCCTCTTCA-GAG--AGTCAAGAGTGACAACACTAAAAGATTGACTCCTCT
** * * * *
31563 TCGCGAGAAAGTCAATAATGACAACACTGAAAGATTGACTCCTTTTCATGAGAAAGTCAAGAATA
63 TCATGAGAAAGTCAAGAATGAAAACACTGAAAGATTGACTCCTCTTCAAGAGAAAGTCAAGAATA
* * * *
31628 ACATAACTAAAAAGTTGAA-TCATCTTCTCGAGAAAGT-AAGAATTACATCACTAAAATGCTTAC
128 ACATAACTAAAAAGTT-AACTCATCTTCACGAGAAAGTCAAGAATGACAACACTAAAA-GATTAC
* * *
31691 TCTTTTTCACGAGAAAGTCAAGAAGGACAA
191 TCATCTTCACGAGAAAGT---TAA-G---A
* * * * *
31721 CACTAAAATATTGACTCCTCTTCACA-AG--AA-AGT--CAAGACTAACAGATTGACTCCTCTTC
1 -ACTAAAAGATTAACTCCTCTTCAGAGAGTCAAGAGTGACAACACTAAAAGATTGACTCCTCTTC
* *
31780 ATGAGAACGTCAAGAATGAAAACACTGAAAGATTGACTCCTCTTCAAGAGAAAGTTAAGAATAAC
65 ATGAGAAAGTCAAGAATGAAAACACTGAAAGATTGACTCCTCTTCAAGAGAAAGTCAAGAATAAC
*
31845 ATCACTAAAAAGTTAACTTC-TCTTCACGAGAAAGTCAAG-ATGGACAACACTAAAAGATTGACT
130 ATAACTAAAAAGTTAAC-TCATCTTCACGAGAAAGTCAAGAAT-GACAACACTAAAAGATT-ACT
* *
31908 CCTCTTCACGATAAAGTTAAG-
192 CATCTTCACGAGAAAGTTAAGA
* *
31929 ACTGAAAGATTAACTCCTCTTCATGAGTACGTCAAGAGTGAAAACACTAAAAGATTGACT-CTCT
1 ACTAAAAGATTAACTCCTCTTCA-GAG-A-GTCAAGAGTGACAACACTAAAAGATTGACTCCTCT
* * * * *
31993 TCATGAGAAAGTCAAGAAT-AACATCACT-AAAAAGTTGATTCATCTTCACGAGAAAGTCAAGAA
63 TCATGAGAAAGTCAAGAATGAA-AACACTGAAAGA-TTGACTCCTCTTCAAGAGAAAGTCAAGAA
* * * * * *
32056 TAACATAACT-AAAAGATTGACTCTTCTTTATGAGAAAGTCAAGAATGACAACATTGAAAGATTA
126 TAACATAACTAAAAAG-TTAACTCATCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGATT-
32120 ACTCATCTTCACGAGAAAGTTAAG
189 ACTCATCTTCACGAGAAAGTTAAG
32144 TTGAAGTTTC
Statistics
Matches: 356, Mismatches: 47, Indels: 47
0.79 0.10 0.10
Matches are distributed among these distances:
207 20 0.06
208 1 0.00
210 1 0.00
211 1 0.00
212 1 0.00
213 4 0.01
214 18 0.05
215 232 0.65
216 51 0.14
217 1 0.00
218 2 0.01
220 2 0.01
223 1 0.00
224 21 0.06
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (213 bp):
ACTAAAAGATTAACTCCTCTTCAGAGAGTCAAGAGTGACAACACTAAAAGATTGACTCCTCTTCA
TGAGAAAGTCAAGAATGAAAACACTGAAAGATTGACTCCTCTTCAAGAGAAAGTCAAGAATAACA
TAACTAAAAAGTTAACTCATCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGATTACTCATC
TTCACGAGAAAGTTAAGA
Found at i:32039 original size:125 final size:126
Alignment explanation
Indices: 31803--32054 Score: 298
Period size: 125 Copynumber: 2.0 Consensus size: 126
31793 GAATGAAAAC
* * *
31803 ACTGAAAGATTGACTCCTCTTCAAGAGAAAGTTAAGAATAACATCACTAAAAAGTTAACTTCTCT
1 ACTGAAAGATTAACTCCTCTTCAAGAGAAAGTCAAGAATAACAACACTAAAAAGTTAACTTCTCT
* * * *
31868 TCACGAGAAAGTCAAGATGGACAACACTAAAAGATTGACTCCTCTTCACGATAAAGTTAAG
66 TCACGAGAAAGTCAAGATGAACAACACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAG
* * * * *
31929 ACTGAAAGATTAACTCCTCTTCATGAGTACGTCAAGAGTGAA-AACACT-AAAAGATTGAC-TCT
1 ACTGAAAGATTAACTCCTCTTCAAGAGAAAGTCAAGAAT-AACAACACTAAAAAG-TTAACTTCT
* * *
31991 CTTCATGAGAAAGTCAAGAAT-AACATCACTAAAA-AGTTGATTCATCTTCACGAGAAAGTCAAG
64 CTTCACGAGAAAGTCAAG-ATGAACAACACTAAAAGA-TTGACTCATCTTCACGAGAAAGTCAAG
32054 A
1 A
32055 ATAACATAAC
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
124 1 0.01
125 60 0.56
126 44 0.41
127 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (126 bp):
ACTGAAAGATTAACTCCTCTTCAAGAGAAAGTCAAGAATAACAACACTAAAAAGTTAACTTCTCT
TCACGAGAAAGTCAAGATGAACAACACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAG
Found at i:32054 original size:260 final size:262
Alignment explanation
Indices: 31453--32139 Score: 669
Period size: 260 Copynumber: 2.6 Consensus size: 262
31443 ATAATCATAT
* * *
31453 CACTAAAAGGTTGACTCTTCTTCGCGAG-AAGTCAAGAATGACATCACTAAAAGGTTGACTCCTC
1 CACTAAAAGATTGACTC-TCTTCACGAGAAAGTCAAGAAT-ACATCACTAAAAAGTTGACTCCTC
* * ** *
31517 TTCACGAGAAAGTCAAGAAAGACAACACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAATAAT
64 TTCACGAGAAAGTCAAGAATGAAAACACTAAAAGATTGACTCCTCTTCAAGAGAAAGTCAAGAAT
* * * *
31582 GACAACACTGAAAGATTGACTCCTTTTCATGAGAAAGTCAAGAATAACATAACTAAAAAGTTGAA
129 GACAACACTGAAAGATTAACTTCTCTTCACGAGAAAGTCAAGAATAACATAACTAAAAAGTTGAA
* * * *
31647 TCATCTTCTCGAGAAAGTAAGAATTACATCACTAAAATGCTTACTCTTTTTCACGAGAAAGTCAA
194 TCATCTTCACGAGAAAGTAAG-A--ACATCAC-AAAAT-CTAACTCCTCTTCACGAGAAAGTCAA
*
31712 GAAGGACAA
254 GAAGGAAAA
* * * *
31721 CACTAAAATATTGACTCCTCTTCACAAGAAAGTCAAG---AC-T-A--ACAGA-TTGACTCCTCT
1 CACTAAAAGATTGACT-CTCTTCACGAGAAAGTCAAGAATACATCACTAAAAAGTTGACTCCTCT
* * * * *
31778 TCATGAGAACGTCAAGAATGAAAACACTGAAAGATTGACTCCTCTTCAAGAGAAAGTTAAGAATA
65 TCACGAGAAAGTCAAGAATGAAAACACTAAAAGATTGACTCCTCTTCAAGAGAAAGTCAAGAATG
* * *
31843 ACATCACT-AAAAAGTTAACTTCTCTTCACGAGAAAGTCAAG-ATGGACA-ACACT-AAAAGATT
130 ACAACACTGAAAGA-TTAACTTCTCTTCACGAGAAAGTCAAGAAT-AACATA-ACTAAAAAG-TT
* * * * * * * *
31904 GACTCCTCTTCACGATAAAGTTAAG-AC-TGA-AAGAT-TAACTCCTCTTCATGAGTACGTCAAG
191 GAATCATCTTCACGAGAAAG-TAAGAACATCACAAAATCTAACTCCTCTTCACGAGAAAGTCAAG
31965 -AGTGAAAA
255 AAG-GAAAA
* * *
31973 CACTAAAAGATTGACTCTCTTCATGAGAAAGTCAAGAATAACATCACTAAAAAGTTGATTCATCT
1 CACTAAAAGATTGACTCTCTTCACGAGAAAGTCAAGAAT-ACATCACTAAAAAGTTGACTCCTCT
* * *
32038 TCACGAGAAAGTCAAGAAT-AACATA-ACTAAAAGATTGACTCTTCTTTATGAGAAAGTCAAGAA
65 TCACGAGAAAGTCAAGAATGAA-A-ACACTAAAAGATTGACTCCTCTTCAAGAGAAAGTCAAGAA
*
32101 TGACAACATTGAAAGATTAAC-TCATCTTCACGAGAAAGT
128 TGACAACACTGAAAGATTAACTTC-TCTTCACGAGAAAGT
32140 TAAGTTGAAG
Statistics
Matches: 343, Mismatches: 55, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
251 20 0.06
252 39 0.11
254 4 0.01
255 2 0.01
256 3 0.01
257 3 0.01
259 19 0.06
260 207 0.60
261 11 0.03
263 1 0.00
264 1 0.00
265 2 0.01
268 22 0.06
269 9 0.03
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.24
Consensus pattern (262 bp):
CACTAAAAGATTGACTCTCTTCACGAGAAAGTCAAGAATACATCACTAAAAAGTTGACTCCTCTT
CACGAGAAAGTCAAGAATGAAAACACTAAAAGATTGACTCCTCTTCAAGAGAAAGTCAAGAATGA
CAACACTGAAAGATTAACTTCTCTTCACGAGAAAGTCAAGAATAACATAACTAAAAAGTTGAATC
ATCTTCACGAGAAAGTAAGAACATCACAAAATCTAACTCCTCTTCACGAGAAAGTCAAGAAGGAA
AA
Found at i:33653 original size:14 final size:14
Alignment explanation
Indices: 33629--33655 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33619 TTTTTCCTCT
33629 CATTTTTTGCTTCA
1 CATTTTTTGCTTCA
33643 CATTTTTTGCTTC
1 CATTTTTTGCTTC
33656 TTTTTATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.22, G:0.07, T:0.59
Consensus pattern (14 bp):
CATTTTTTGCTTCA
Found at i:34148 original size:14 final size:14
Alignment explanation
Indices: 34129--34156 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34119 CATGATAAAA
34129 TTATTTCAATCATT
1 TTATTTCAATCATT
34143 TTATTTCAATCATT
1 TTATTTCAATCATT
34157 CCCTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTTCAATCATT
Found at i:38585 original size:3 final size:3
Alignment explanation
Indices: 38572--38624 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
38562 ATGGCCATGA
38572 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38619 AAT AAT
1 AAT AAT
38625 GATAGAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40065 original size:60 final size:60
Alignment explanation
Indices: 39897--40050 Score: 161
Period size: 60 Copynumber: 2.5 Consensus size: 60
39887 ACCCTCATTT
* * * * ** *
39897 TAAATTAGTCCC-CAAATTTTAAAATATTTCAGTTCCATCCTTAAACTATG--ATTACAATTT
1 TAAATTAGTCCCTAAAATTTT-AAACATTTCAATTTCATCCCCAAACTATGACATT--AATTC
*
39957 TAAATTAGTCCTTAAAATTTTAAACATTTCAATTTCATCCCCAAACTATGACATTAATTC
1 TAAATTAGTCCCTAAAATTTTAAACATTTCAATTTCATCCCCAAACTATGACATTAATTC
* *
40017 TAAATTAGTCCCTAAATTTTTTGAACATTTCAAT
1 TAAATTAGTCCCTAAA-ATTTTAAACATTTCAAT
40051 GTTGTCCTAA
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
60 54 0.68
61 22 0.28
62 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (60 bp):
TAAATTAGTCCCTAAAATTTTAAACATTTCAATTTCATCCCCAAACTATGACATTAATTC
Found at i:40609 original size:16 final size:15
Alignment explanation
Indices: 40578--40612 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40568 ACTTATATAA
*
40578 TTTTAAAAATTTATT
1 TTTTAAAAATTAATT
40593 TTTTAAAAATTCAATT
1 TTTTAAAAATT-AATT
40609 TTTT
1 TTTT
40613 TAATTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTAAAAATTAATT
Found at i:43393 original size:20 final size:20
Alignment explanation
Indices: 43357--43394 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43347 ATCCTATTCC
**
43357 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
43377 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
43395 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Done.