Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008823.1 Hibiscus syriacus cultivar Beakdansim tig00111993_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: 1111368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1085194 original size:20 final size:21
Alignment explanation
Indices: 1085169--1085261 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1085159 TTTTCCCAAT
*
1085169 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1085189 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1085210 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1085230 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1085251 TCGCAATGCGA
1 TCGCAATGCGA
1085262 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1085214 original size:41 final size:41
Alignment explanation
Indices: 1085169--1085261 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1085159 TTTTCCCAAT
1085169 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1085210 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1085251 TCGCAATGCGA
1 TCGCAATGCGA
1085262 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1085326 original size:20 final size:20
Alignment explanation
Indices: 1085296--1085364 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
1085286 AAAAAATCAT
* *
1085296 AACGAGATACTTACTTTCG-
1 AACGCGATACTGACTTTCGC
1085315 AACCGCGATACTGACTTTCGC
1 AA-CGCGATACTGACTTTCGC
*
1085336 AACGCGATTCTGACTTTCGC
1 AACGCGATACTGACTTTCGC
1085356 AACGCGATA
1 AACGCGATA
1085365 ATACATAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (20 bp):
AACGCGATACTGACTTTCGC
Found at i:1085580 original size:22 final size:22
Alignment explanation
Indices: 1085552--1085595 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1085542 CACTCTCTCA
1085552 CCCATCTCC-GACGAAATCCGTC
1 CCCATCTCCAG-CGAAATCCGTC
1085574 CCCATCTCCAGCGAAATCCGTC
1 CCCATCTCCAGCGAAATCCGTC
1085596 TATCTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAGCGAAATCCGTC
Found at i:1085602 original size:20 final size:21
Alignment explanation
Indices: 1085552--1085603 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1085542 CACTCTCTCA
1085552 CCCATCTCC-GACGAAATCCGT
1 CCCATCTCCAG-CGAAATCCGT
1085573 CCCCATCTCCAGCGAAATCCGT
1 -CCCATCTCCAGCGAAATCCGT
*
1085595 -CTATCTCCA
1 CCCATCTCCA
1085604 TCTCTCAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.29
22 19 0.68
23 1 0.04
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (21 bp):
CCCATCTCCAGCGAAATCCGT
Found at i:1085897 original size:20 final size:20
Alignment explanation
Indices: 1085874--1085915 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1085864 GATAGTCGAA
1085874 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
1085894 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
1085914 TT
1 TT
1085916 TAGAAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.17, G:0.19, T:0.55
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:1087257 original size:18 final size:18
Alignment explanation
Indices: 1087236--1087280 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1087226 TCCACTTCGG
*
1087236 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1087254 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1087272 GAGCCATCA
1 GAGCCATCA
1087281 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1087787 original size:20 final size:20
Alignment explanation
Indices: 1087762--1087807 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1087752 TAGTTTACTT
1087762 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
1087782 TCGCAACGTGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1087802 TCGCAA
1 TCGCAA
1087808 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1087816 original size:19 final size:19
Alignment explanation
Indices: 1087773--1087827 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1087763 CGCAACACGA
1087773 AAATGACTATCGCAACGTGG
1 AAATGACTATCGCAAC-TGG
*
1087793 AAATGGCTATCGCAA-TGCG
1 AAATGACTATCGCAACTG-G
**
1087812 AAATGAAAATCGCAAC
1 AAATGACTATCGCAAC
1087828 GACAAAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 14 0.48
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (19 bp):
AAATGACTATCGCAACTGG
Found at i:1087836 original size:14 final size:14
Alignment explanation
Indices: 1087817--1087874 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1087807 ATGCGAAATG
1087817 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1087831 AAAATCACAATGCGAA
1 AAAATCGCAA--CGAC
1087847 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1087863 AAAATCGTAACG
1 AAAATCGCAACG
1087875 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.54
16 8 0.23
18 8 0.23
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1087859 original size:32 final size:33
Alignment explanation
Indices: 1087805--1087891 Score: 140
Period size: 32 Copynumber: 2.7 Consensus size: 33
1087795 ATGGCTATCG
1087805 CAATGCGAAATGAAAATCGCAACGACAAAATCA
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
1087838 CAATGCGAAATG-AAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
* *
1087870 TAACGCGAAATGAAAATCGCAA
1 CAATGCGAAATGAAAATCGCAA
1087892 TGCGATTTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 29 0.58
33 21 0.42
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:1087927 original size:14 final size:14
Alignment explanation
Indices: 1087908--1087965 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1087898 TTGTGTTTCG
1087908 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1087922 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1087938 CGTGTTGCGATTTTGT
1 C--GTTGCGATTTTGT
1087954 CGTTGCGATTTT
1 CGTTGCGATTTT
1087966 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.58
16 6 0.16
18 10 0.26
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1087937 original size:19 final size:18
Alignment explanation
Indices: 1087923--1088039 Score: 71
Period size: 20 Copynumber: 6.4 Consensus size: 18
1087913 CGATTTTGTC
1087923 GTTGCGATTTCATTTCGT
1 GTTGCGATTTCATTTCGT
*
1087941 GTTGCGATTT--TGTC--
1 GTTGCGATTTCATTTCGT
*
1087955 GTTGCGATTTTCATTTCGC
1 GTTGCGA-TTTCATTTCGT
* ** *
1087974 ATTGCGATAGCCATTTCCGC
1 GTTGCGAT-TTCATTT-CGT
* *
1087994 GTTGCGATAGTCATTTCGC
1 GTTGCGAT-TTCATTTCGT
*
1088013 GTTGCGATTTTAAGTTTCGT
1 GTTGCGA-TTTCA-TTTCGT
1088033 GTTGCGA
1 GTTGCGA
1088040 AAGTAAACTA
Statistics
Matches: 80, Mismatches: 10, Indels: 16
0.75 0.09 0.15
Matches are distributed among these distances:
14 7 0.09
15 3 0.04
16 3 0.04
17 3 0.04
18 11 0.14
19 23 0.29
20 30 0.38
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.43
Consensus pattern (18 bp):
GTTGCGATTTCATTTCGT
Found at i:1087945 original size:32 final size:33
Alignment explanation
Indices: 1087903--1087981 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1087893 GCGATTTGTG
1087903 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1087935 TTTCGTGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1087968 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1087982 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 26 0.60
33 17 0.40
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1088000 original size:20 final size:19
Alignment explanation
Indices: 1087966--1088020 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1087956 TTGCGATTTT
*
1087966 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1087985 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1088005 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1088021 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1089920 original size:14 final size:14
Alignment explanation
Indices: 1089888--1089922 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1089878 GATTGTTTAA
1089888 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
1089902 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
1089916 TTGATTT
1 TTGATTT
1089923 ATTTAATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1090050 original size:14 final size:14
Alignment explanation
Indices: 1090031--1090084 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1090021 CGAAATGGCT
1090031 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1090045 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1090064 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1090078 ATCGCAA
1 ATCGCAA
1090085 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1090102 original size:33 final size:33
Alignment explanation
Indices: 1090012--1090089 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
1090002 AAAACAGACT
* ***
1090012 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1090045 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1090078 ATCGCAATGCGA
1 ATCGCAATGCGA
1090090 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:1090133 original size:20 final size:20
Alignment explanation
Indices: 1090108--1090165 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1090098 TCGCATTGCG
*
1090108 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1090128 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1090148 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1090166 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1091248 original size:24 final size:24
Alignment explanation
Indices: 1091221--1091274 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1091211 GTATTCAAAA
* *
1091221 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1091245 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1091269 TTTGAT
1 TTTGAT
1091275 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1091466 original size:12 final size:12
Alignment explanation
Indices: 1091449--1091473 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1091439 ATATAATCCT
1091449 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1091461 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1091473 G
1 G
1091474 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1093803 original size:33 final size:33
Alignment explanation
Indices: 1093761--1093887 Score: 166
Period size: 33 Copynumber: 3.8 Consensus size: 33
1093751 GGAAATTACT
* *
1093761 ATCGCAATGCGAAATGAAAATCACAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1093794 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1093826 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1093860 ACCGCAATGCGAAATGAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1093888 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1093817 original size:19 final size:19
Alignment explanation
Indices: 1093741--1093852 Score: 73
Period size: 19 Copynumber: 6.4 Consensus size: 19
1093731 CTTAATGTCT
* **
1093741 ATCGCAATGCGGAAATTACT
1 ATCGCAATGC-GAAATGAAA
1093761 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1093780 ATCACAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
1093794 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1093813 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1093827 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1093846 ATCGCAA
1 ATCGCAA
1093853 CGAGGGAACC
Statistics
Matches: 69, Mismatches: 13, Indels: 21
0.67 0.13 0.20
Matches are distributed among these distances:
14 18 0.26
15 2 0.03
16 3 0.04
17 3 0.04
18 2 0.03
19 31 0.45
20 10 0.14
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.19
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1093844 original size:66 final size:66
Alignment explanation
Indices: 1093762--1093894 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
1093752 GAAATTACTA
* * *
1093762 TCGCAATGCGAAATGAAAATCACAATGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAACCGCAATGCGAAATGAAAATCGCAACGCGAAT
1093827 T
66 T
* * *
1093828 TCGCAATGCGAAATGAAAATCGCAACGAGGGAACCGCAATGCGAAATGAAAATTGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAACCGCAATGCGAAATGAAAATCGCAACGCGAAT
1093893 T
66 T
1093894 T
1 T
1093895 AATTTTGCGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAACCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1094069 original size:14 final size:14
Alignment explanation
Indices: 1094050--1094086 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1094040 CATCAATTAA
1094050 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1094064 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1094078 ACAAATCAA
1 ACAAATCAA
1094087 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1095529 original size:42 final size:42
Alignment explanation
Indices: 1095483--1095566 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1095473 CGATGACAGT
* *
1095483 GGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTAAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * *
1095525 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTAAACGATAGGAGGGGACTCTCGAGGAATGATAGG
1095567 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTAAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1097650 original size:33 final size:33
Alignment explanation
Indices: 1097593--1097680 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
1097583 ACGAGATAAT
* *
1097593 GAGAATCACAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1097627 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
1097660 GACAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
1097681 AAATCGTAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 37 0.74
34 13 0.26
ACGTcount: A:0.40, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1097685 original size:19 final size:19
Alignment explanation
Indices: 1097568--1097733 Score: 111
Period size: 20 Copynumber: 9.1 Consensus size: 19
1097558 TCTTTTGGTT
*
1097568 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
1097587 GATAATGAGAATCACAACGC
1 GA-AATGAAAATCGCAACGC
**
1097607 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1097625 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1097641 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1097659 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1097674 GAAATGAAAATCGTAACCGC
1 GAAATGAAAATCGCAA-CGC
1097694 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1097713 GAAAT-AAAATTCGCAATGC
1 GAAATGAAAA-TCGCAACGC
1097732 GA
1 GA
1097734 TTTTTGTTTC
Statistics
Matches: 116, Mismatches: 17, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 8 0.07
19 38 0.33
20 43 0.37
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1097744 original size:19 final size:19
Alignment explanation
Indices: 1097722--1097764 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1097712 CGAAATAAAA
*
1097722 TTCGCAATGCGATTTTTGT
1 TTCGCAATGCGATTTTTAT
** *
1097741 TTCGCGTTGCGTTTTTTAT
1 TTCGCAATGCGATTTTTAT
1097760 TTCGC
1 TTCGC
1097765 GTTGCGATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (19 bp):
TTCGCAATGCGATTTTTAT
Found at i:1097765 original size:19 final size:19
Alignment explanation
Indices: 1097729--1097809 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
1097719 AAATTCGCAA
*
1097729 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1097748 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1097767 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
1097781 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1097801 TGCGATTTT
1 TGCGATTTT
1097810 CATTCTCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 22 0.45
20 11 0.22
ACGTcount: A:0.10, C:0.17, G:0.23, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1098391 original size:20 final size:20
Alignment explanation
Indices: 1098366--1098421 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1098356 GCGATTTTGT
1098366 ATTATCGCATTGCGATAGTA
1 ATTATCGCATTGCGATAGTA
*
1098386 ATTATCGCATTGCGATAGTC
1 ATTATCGCATTGCGATAGTA
*
1098406 AGTATCGCATTGCGAT
1 ATTATCGCATTGCGAT
1098422 TTTCCCAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
ATTATCGCATTGCGATAGTA
Found at i:1098440 original size:61 final size:60
Alignment explanation
Indices: 1098328--1098462 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 60
1098318 CGCTATGTAA
* * * ** *
1098328 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAATT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGAT-GTAATT
* * * *
1098389 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGATTTACTT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGATGTAATT
1098449 ATTCGCATTGCGAA
1 A-TCGCATTGCGAA
1098463 TTGGGAAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
60 5 0.08
61 54 0.89
62 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (60 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATGTAATT
Found at i:1099976 original size:25 final size:26
Alignment explanation
Indices: 1099929--1099994 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 26
1099919 TATGACGCTT
* *
1099929 ATATTTTATTTATGTGATATTTTGATAA
1 ATATATTA-TTAT-TGATATTTTAATAA
**
1099957 ATATATTATTATTGAT-TTTTAATCT
1 ATATATTATTATTGATATTTTAATAA
*
1099982 ATTTATTATTATT
1 ATATATTATTATT
1099995 ATTAGAACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 18 0.55
26 4 0.12
27 4 0.12
28 7 0.21
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.61
Consensus pattern (26 bp):
ATATATTATTATTGATATTTTAATAA
Found at i:1103065 original size:13 final size:13
Alignment explanation
Indices: 1103047--1103085 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1103037 GTCATAAATC
1103047 TATGACGCGCATT
1 TATGACGCGCATT
**
1103060 TATGACATGCATT
1 TATGACGCGCATT
1103073 TATGACGCGCATT
1 TATGACGCGCATT
1103086 GAGCGTCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:1106379 original size:22 final size:22
Alignment explanation
Indices: 1106353--1106424 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
1106343 ATGTGAAATT
1106353 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
1106375 TGTCCCGAAAGG-CCACTGTATA
1 TGTCCCG-AAGGACCACTGTATA
*
1106397 TGTCCCGAAAGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
1106419 TGTCCC
1 TGTCCC
1106425 TCGACTCTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 3 0.06
22 40 0.85
23 4 0.09
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGTATA
Found at i:1106610 original size:22 final size:22
Alignment explanation
Indices: 1106585--1106637 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1106575 CATATTCCAC
1106585 ATATTCATATA-CATAAATATGT
1 ATATT-ATATATCATAAATATGT
* *
1106607 ATATTATATATCATATATATAT
1 ATATTATATATCATAAATATGT
*
1106629 ATCTTATAT
1 ATATTATAT
1106638 CACTATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATTATATATCATAAATATGT
Found at i:1110302 original size:24 final size:24
Alignment explanation
Indices: 1110271--1110316 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1110261 ATAATCATTA
1110271 ATCATTTTATCCTAATTATTACAT
1 ATCATTTTATCCTAATTATTACAT
1110295 ATCATTTTATCCTAATTATTAC
1 ATCATTTTATCCTAATTATTAC
1110317 TCTTATCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (24 bp):
ATCATTTTATCCTAATTATTACAT
Found at i:1110637 original size:22 final size:22
Alignment explanation
Indices: 1110611--1110660 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1110601 ATGTGAAATT
1110611 TGTCCCGAAGAACCACTGTATA
1 TGTCCCGAAGAACCACTGTATA
* *
1110633 TGTCCCGAAGCACTACTGTATA
1 TGTCCCGAAGAACCACTGTATA
1110655 TGTCCC
1 TGTCCC
1110661 TCGACTCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (22 bp):
TGTCCCGAAGAACCACTGTATA
Done.