Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003064.1 Hibiscus syriacus cultivar Beakdansim tig00006388_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: 58069
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Found at i:925 original size:13 final size:13
Alignment explanation
Indices: 919--961 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
909 TAAAAAAATT
919 ATTTAAAATAAAA
1 ATTTAAAATAAAA
* *
932 ATTTAAAATTATA
1 ATTTAAAATAAAA
* *
945 TTTTAAAATCAAA
1 ATTTAAAATAAAA
958 ATTT
1 ATTT
962 TCTCAAATCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTTAAAATAAAA
Found at i:937 original size:26 final size:26
Alignment explanation
Indices: 907--961 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
897 CTTATATAAT
907 TTTAAAAAAAT-TATTTAAAATAAAAA
1 TTTAAAAAAATAT-TTTAAAATAAAAA
** *
933 TTTAAAATTATATTTTAAAATCAAAA
1 TTTAAAAAAATATTTTAAAATAAAAA
959 TTT
1 TTT
962 TCTCAAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
TTTAAAAAAATATTTTAAAATAAAAA
Found at i:1818 original size:27 final size:27
Alignment explanation
Indices: 1778--1840 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
1768 GAGCAGTTAG
* * * *
1778 AACTCGATTTGGTCGAAATTCGGTAAA
1 AACTCGACTCGGTCGAAACTCGATAAA
1805 AACTCGACTCGGTCGAAACTCGATAAA
1 AACTCGACTCGGTCGAAACTCGATAAA
*
1832 ATCTCGACT
1 AACTCGACT
1841 TGGATTGACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (27 bp):
AACTCGACTCGGTCGAAACTCGATAAA
Found at i:2238 original size:16 final size:16
Alignment explanation
Indices: 2209--2252 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2199 ATGAGCATCG
**
2209 CTTAACGAATAATGAA
1 CTTAACGAGCAATGAA
* *
2225 CTTAATGAGCAATGAG
1 CTTAACGAGCAATGAA
2241 CTTAACGAGCAA
1 CTTAACGAGCAA
2253 CGAGTCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (16 bp):
CTTAACGAGCAATGAA
Found at i:5085 original size:13 final size:13
Alignment explanation
Indices: 5069--5108 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
5059 CAAAGGATGA
5069 AAAGAAAGAAGAG
1 AAAGAAAGAAGAG
5082 AAAG--AG-AGA-
1 AAAGAAAGAAGAG
5091 AAAGAAAGAAGAG
1 AAAGAAAGAAGAG
5104 AAAGA
1 AAAGA
5109 GATACCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.17
10 3 0.13
11 4 0.17
12 3 0.13
13 9 0.39
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAG
Found at i:5092 original size:22 final size:22
Alignment explanation
Indices: 5067--5110 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5057 AACAAAGGAT
5067 GAAAAGAAAGAAGAGAAAGAGA
1 GAAAAGAAAGAAGAGAAAGAGA
5089 GAAAAGAAAGAAGAGAAAGAGA
1 GAAAAGAAAGAAGAGAAAGAGA
5111 TACCATTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (22 bp):
GAAAAGAAAGAAGAGAAAGAGA
Found at i:9944 original size:32 final size:32
Alignment explanation
Indices: 9903--9972 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
9893 ATTACTTTCA
*
9903 TGACATGGCACATGTTACATCATTATTTTGGG
1 TGACATGGCACATGTTACATCATCATTTTGGG
9935 TGACATGGCACATGTTACATCATCATTTTGGG
1 TGACATGGCACATGTTACATCATCATTTTGGG
9967 TGACAT
1 TGACAT
9973 TGCATGCCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (32 bp):
TGACATGGCACATGTTACATCATCATTTTGGG
Found at i:18009 original size:94 final size:94
Alignment explanation
Indices: 17892--18067 Score: 264
Period size: 94 Copynumber: 1.9 Consensus size: 94
17882 ATGTAGCATC
* *
17892 GATACCATGGTATGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATAC-CGAAGG
1 GATACCATGGTAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATACTCGAAGA
**
17956 GGGTATCGGTACCATAGCGTAGTAGTATA
66 GGGTATCAATACCATAGCGTAGTAGTATA
** * *
17985 GATACCATGGTGAGGGTATCGATACCAGGCTACATCGAAGCTAATTTTGGTATCGATACTGGAAG
1 GATACCATGGT-AGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATACTCGAAG
18050 AGGGTATCAATACCATAG
65 AGGGTATCAATACCATAG
18068 TAGGGTAGTA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 11 0.15
94 43 0.59
95 19 0.26
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (94 bp):
GATACCATGGTAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATACTCGAAGA
GGGTATCAATACCATAGCGTAGTAGTATA
Found at i:18097 original size:27 final size:25
Alignment explanation
Indices: 18059--18108 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 25
18049 GAGGGTATCA
18059 ATACCATAGTAGGGTAGTATCGATATG
1 ATACCATAGTAGGGT--TATCGATATG
18086 ATACCATAGTAGGGTTATCGATA
1 ATACCATAGTAGGGTTATCGATA
18109 CTAAAGAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 8 0.35
27 15 0.65
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (25 bp):
ATACCATAGTAGGGTTATCGATATG
Found at i:18866 original size:45 final size:45
Alignment explanation
Indices: 18527--18867 Score: 386
Period size: 45 Copynumber: 7.6 Consensus size: 45
18517 TATTGGCATG
* * *
18527 AAAGGATGCCATAGTTGAAATGTATATGGGTACATTATCAACAGA
1 AAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGA
* * *
18572 AAAGTATACTATGGTTGAAATGTATAT-GGTACATTATCAACAGA
1 AAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGA
* *
18616 AAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAG-
1 AAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGA
* * *
18660 AATGTATGC--TAGTTGAAATGCATATGGGTTGGTGCATTATCAATAGA
1 AAAGTATGCTATAGTTGAAATGCATAT--G--GGTACATTATCAACAGA
* * * *
18707 AAAGCATGCTAGAGTTGAAATGTATATGGGTATATTATCAACAGA
1 AAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGA
* * *
18752 AAAGTATACTATGGTTGAAATGTATATGGGTACATTATCAACAGA
1 AAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGA
* * *
18797 AAAGTATACAATAGTTGAAATGCATATGGGTGCATTATCAACAGA
1 AAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGA
* * *
18842 AAA-TATGTTATAATTTAAAGTGCATA
1 AAAGTATGCTATAGTTGAAA-TGCATA
18868 ATGGTGTATT
Statistics
Matches: 254, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
42 15 0.06
44 60 0.24
45 142 0.56
46 15 0.06
47 8 0.03
49 14 0.06
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (45 bp):
AAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGA
Found at i:22804 original size:13 final size:13
Alignment explanation
Indices: 22769--22811 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
22759 ATAAATCTAC
22769 GACGCGCATTTAT
1 GACGCGCATTTAT
* *
22782 GACACACATTTAT
1 GACGCGCATTTAT
*
22795 GACGCGCATTAAT
1 GACGCGCATTTAT
22808 GACG
1 GACG
22812 TTCATTGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (13 bp):
GACGCGCATTTAT
Found at i:22901 original size:83 final size:85
Alignment explanation
Indices: 22789--23009 Score: 272
Period size: 85 Copynumber: 2.6 Consensus size: 85
22779 TATGACACAC
* * *
22789 ATTTATGACGCGCAT-TAATGACGTT-CATTGAGTGTCATTGAAGCCCCCGTCATAAAT-TAAGA
1 ATTTATGACACGCATGT-ATGAC-TTACATTGCGTGTCATTGAAGCCCCCGTCATAAATCT-ACA
*
22851 TGA-A-ACATTTTTGCGTCATAA
63 TGACATACATTTGTGCGTCATAA
* * * * *
22872 ATTTATGACATGCATGTATGACTTACATTGCGCGTTATTGAAGCCCCCGTCATAAATCTTCTTGA
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATCTACATGA
*
22937 CATACATTTGTGTGTCATAA
66 CATACATTTGTGCGTCATAA
* *
22957 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGTCAT
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCAT
23010 TAAAAAAGAC
Statistics
Matches: 118, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
82 2 0.02
83 50 0.42
84 3 0.03
85 63 0.53
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATCTACATGA
CATACATTTGTGCGTCATAA
Found at i:23035 original size:85 final size:84
Alignment explanation
Indices: 22789--23037 Score: 247
Period size: 85 Copynumber: 3.0 Consensus size: 84
22779 TATGACACAC
* * * *
22789 ATTTATGACGCGCAT-TAATGACGTT-CATTGAGTGTCATTGAAGCCCCCGTCATAAATTAAGAT
1 ATTTATGACACGCATGT-ATGAC-TTACATTGCGTGTCATTGAAGCCCCCGTCATAAA-AAAGAC
* *
22852 G--AAACATTTTTGCGTCATAA
63 GACAAACATTTGTGTGTCATAA
* * * ****
22872 ATTTATGACATGCATGTATGACTTACATTGCGCGTTATTGAAGCCCCCGTCAT-AAATCTTCTTG
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAAAAAGAC--G
*
22936 ACATACATTTGTGTGTCATAA
64 ACAAACATTTGTGTGTCATAA
* *
22957 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAAAAAAGACGA
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCA-TAAAAAAGACGA
* *
23022 CAAACGTTCGTGTGTC
65 CAAACATTTGTGTGTC
23038 GTGATTGTAT
Statistics
Matches: 132, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
82 4 0.03
83 44 0.33
84 1 0.01
85 78 0.59
86 1 0.01
87 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (84 bp):
ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAAAAAGACGAC
AAACATTTGTGTGTCATAA
Found at i:25045 original size:51 final size:50
Alignment explanation
Indices: 24960--25077 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 50
24950 CTTTGCGGTG
*
24960 TTCCCTCCTCCTTTTCTTTCTTTTTTCCCCTCTTCGGCGTCCCTTCTCCT
1 TTCCCTCTTCCTTTTCTTTCTTTTTTCCCCTCTTCGGCGTCCCTTCTCCT
* * *
25010 TTACCCTCTTCCTTTTCTTTCTCTTTTT-TCGTCTTCGGTGTCCCTTCTCCT
1 TT-CCCTCTTCCTTTTCTTTCT-TTTTTCCCCTCTTCGGCGTCCCTTCTCCT
*
25061 TTCGCTTCTTCCTTTTC
1 TTC-CCTCTTCCTTTTC
25078 AACAAGTTCT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
50 3 0.05
51 52 0.87
52 5 0.08
ACGTcount: A:0.01, C:0.39, G:0.07, T:0.53
Consensus pattern (50 bp):
TTCCCTCTTCCTTTTCTTTCTTTTTTCCCCTCTTCGGCGTCCCTTCTCCT
Found at i:28943 original size:15 final size:15
Alignment explanation
Indices: 28913--28953 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
28903 GATGCTTTAT
*
28913 TTTTCATTCTTTGACG
1 TTTTC-TTCTTAGACG
28929 TTTTCTTCTTAGACG
1 TTTTCTTCTTAGACG
*
28944 TTGTCTTCTT
1 TTTTCTTCTT
28954 GCCCCATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.10, C:0.20, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTTCTTCTTAGACG
Found at i:33326 original size:13 final size:13
Alignment explanation
Indices: 33304--33356 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
33294 TCATAAATAT
33304 ATGACGCGCATTG
1 ATGACGCGCATTG
* *
33317 ATGACACGCATTT
1 ATGACGCGCATTG
* * *
33330 ATGACTCACATTT
1 ATGACGCGCATTG
33343 ATGACGCGCATTG
1 ATGACGCGCATTG
33356 A
1 A
33357 GCTTCATTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (13 bp):
ATGACGCGCATTG
Found at i:33341 original size:26 final size:26
Alignment explanation
Indices: 33303--33354 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
33293 GTCATAAATA
*
33303 TATGACGCGCATTGATGACACGCATT
1 TATGACGCACATTGATGACACGCATT
* * *
33329 TATGACTCACATTTATGACGCGCATT
1 TATGACGCACATTGATGACACGCATT
33355 GAGCTTCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (26 bp):
TATGACGCACATTGATGACACGCATT
Found at i:35004 original size:20 final size:20
Alignment explanation
Indices: 34955--35006 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
34945 TAGTTGAAAA
*
34955 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
34975 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
34995 TCGCGTTGCGAT
1 TCGCGTTGCGAT
35007 AGTCTACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:35066 original size:22 final size:22
Alignment explanation
Indices: 35037--35090 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
35027 TTTTCCAAAT
35037 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
* *
35059 TTGTTGCGAAAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
35081 TCGTTGCGAT
1 TCGTTGCGAT
35091 TTTCCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:35200 original size:6 final size:6
Alignment explanation
Indices: 35189--35215 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
35179 GACACGTATC
35189 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
35216 TGAGACGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:35712 original size:6 final size:6
Alignment explanation
Indices: 35703--35746 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
35693 GTCTCGTCTC
35703 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
35747 AATACGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:35865 original size:19 final size:19
Alignment explanation
Indices: 35841--35909 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
35831 CAACGAATTT
35841 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
35860 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
*
35882 TTGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
35901 TCGCAACGA
1 TCGCAACGA
35910 CAACTGTAGA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 21 0.57
20 2 0.05
21 2 0.05
22 12 0.32
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:35888 original size:22 final size:22
Alignment explanation
Indices: 35859--35930 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
35849 AATTTGGAAA
35859 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * * **
35881 ATTGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
35900 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
35922 ATCGCAACG
1 ATCGCAACG
35931 CGAACTGGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 2 0.05
22 21 0.57
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:35888 original size:41 final size:41
Alignment explanation
Indices: 35841--36107 Score: 270
Period size: 41 Copynumber: 6.6 Consensus size: 41
35831 CAACGAATTT
35841 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
*
35882 TTGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
* * * *
35923 TCGCAACGCGAA-CTGGAAAATCGCAACG-CGATTTTCA-ACTA
1 TCGCAA--CGAATTTGGAAAATCGCAACGACAACTGT-AGACTA
* * ** * *
35964 TCACAACGCGATTTTCAACTATCGCAACG-CGA-T-T----T-
1 TCGCAACG-AATTTGGAA-AATCGCAACGACAACTGTAGACTA
35999 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
*
36040 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAAACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
*
36081 TCGCAACGCGAA-ATGGAAAATCGCAAC
1 TCGCAA--CGAATTTGGAAAATCGCAAC
36108 ACGATTTTCA
Statistics
Matches: 190, Mismatches: 20, Indels: 31
0.79 0.08 0.13
Matches are distributed among these distances:
33 9 0.05
34 8 0.04
35 8 0.04
36 2 0.01
39 2 0.01
40 3 0.02
41 108 0.57
42 42 0.22
43 8 0.04
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:35936 original size:22 final size:22
Alignment explanation
Indices: 35855--35953 Score: 68
Period size: 22 Copynumber: 4.7 Consensus size: 22
35845 AACGAATTTG
35855 GAAAATCGCAACGAC-AACTGTA
1 GAAAATCGCAACG-CGAACTGTA
** * * *
35877 GACTATTGCAA--CGAA-TTTG
1 GAAAATCGCAACGCGAACTGTA
35896 GAAAATCGCAACGAC-AACTGTA
1 GAAAATCGCAACG-CGAACTGTA
**
35918 GACTATCGCAACGCGAACTG--
1 GAAAATCGCAACGCGAACTGTA
35938 GAAAATCGCAACGCGA
1 GAAAATCGCAACGCGA
35954 TTTTCAACTA
Statistics
Matches: 57, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
19 11 0.19
20 16 0.28
21 3 0.05
22 27 0.47
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.16
Consensus pattern (22 bp):
GAAAATCGCAACGCGAACTGTA
Found at i:35947 original size:20 final size:20
Alignment explanation
Indices: 35894--35953 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
35884 GCAACGAATT
35894 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
**
35914 TGTAGACTATCGCAACGCGAAC
1 TG--GAAAATCGCAACGCGAAC
35936 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
35954 TTTTCAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 16 0.48
21 1 0.03
22 16 0.48
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.13
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:35972 original size:21 final size:21
Alignment explanation
Indices: 35946--36000 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
35936 TGGAAAATCG
35946 CAACGCGATTTTCAACTATCA
1 CAACGCGATTTTCAACTATCA
*
35967 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCA
35988 CAACGCGATTTTC
1 CAACGCGATTTTC
36001 GCAACGAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (21 bp):
CAACGCGATTTTCAACTATCA
Found at i:36023 original size:19 final size:19
Alignment explanation
Indices: 35999--36067 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
35989 AACGCGATTT
35999 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
36018 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
36040 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
36059 TCGCAACGA
1 TCGCAACGA
36068 CAACTGTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 22 0.56
20 2 0.05
21 2 0.05
22 13 0.33
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:36045 original size:22 final size:22
Alignment explanation
Indices: 36017--36088 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
36007 AATTTGGAAA
36017 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
36039 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
36058 ATCGCAACGACAACTGTAAACT
1 ATCGCAACGACAACTGTAGACT
36080 ATCGCAACG
1 ATCGCAACG
36089 CGAAATGGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:36105 original size:20 final size:20
Alignment explanation
Indices: 36011--36107 Score: 72
Period size: 22 Copynumber: 4.7 Consensus size: 20
36001 GCAACGAATT
*
36011 TGGAAAATCGCAACGACAAC
1 TGGAAAATCGCAACGACAAA
** **
36031 TGTAGACTATCGCAACGA-ATT
1 TG--GAAAATCGCAACGACAAA
*
36052 TGGAAAATCGCAACGACAAC
1 TGGAAAATCGCAACGACAAA
*
36072 TGTAAACTATCGCAACG-CGAAA
1 TGGAAA--ATCGCAACGAC-AAA
36094 TGGAAAATCGCAAC
1 TGGAAAATCGCAAC
36108 ACGATTTTCA
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
19 12 0.20
20 16 0.27
21 4 0.07
22 28 0.47
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
TGGAAAATCGCAACGACAAA
Found at i:36133 original size:158 final size:158
Alignment explanation
Indices: 35818--36153 Score: 575
Period size: 158 Copynumber: 2.1 Consensus size: 158
35808 AAAATCTTTT
* * *
35818 TTTTTAACTATCACAACG-AATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TTTTCAACTATCGCAACGCGATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
* * *
35882 TTGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAAATCGC
66 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAAACTATCGCAACGCGAAATGGAAAATCGC
*
35947 AACGCGATTTTCAACTATCACAACGCGA
131 AACACGATTTTCAACTATCACAACGCGA
35975 TTTTCAACTATCGCAACGCGATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TTTTCAACTATCGCAACGCGATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
36040 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAAACTATCGCAACGCGAAATGGAAAATCGC
66 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAAACTATCGCAACGCGAAATGGAAAATCGC
* *
36105 AACACGATTTTCAACTATCGCAATGCGA
131 AACACGATTTTCAACTATCACAACGCGA
*
36133 TTTTCAATTATCGCAACGCGA
1 TTTTCAACTATCGCAACGCGA
36154 AATGCAACGC
Statistics
Matches: 168, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
157 16 0.10
158 152 0.90
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (158 bp):
TTTTCAACTATCGCAACGCGATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAAACTATCGCAACGCGAAATGGAAAATCGC
AACACGATTTTCAACTATCACAACGCGA
Found at i:36153 original size:21 final size:21
Alignment explanation
Indices: 36100--36153 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
36090 GAAATGGAAA
*
36100 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
36121 ATCGCAATGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
36142 ATCGCAACGCGA
1 ATCGCAACGCGA
36154 AATGCAACGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:41255 original size:95 final size:94
Alignment explanation
Indices: 41060--41261 Score: 239
Period size: 95 Copynumber: 2.1 Consensus size: 94
41050 TACCATGGTA
* * * *
41060 AGGGTATCGATACCAGGAAATATTGAACCTAATTTTGGTATCGATACCGAAGGGGGTATCAGTAC
1 AGGGTATCGATACCAGGAAACATCGAACCTAATTTTAGTATCGATACAGAAGGGGGTATCAGTAC
* *
41125 AATAGTATAGTAGTATTGATACCATAGTG
66 AATAGTATAGTAGTATGGATACCATAATG
** * *
41154 AGGGTATCGATACCAGGCTACATCGAAGCTAATTTTAGTATCGATACTAGAAGGGGGTAT-TGAT
1 AGGGTATCGATACCAGGAAACATCGAACCTAATTTTAGTATCGATAC-AGAAGGGGGTATCAG-T
* *
41218 ACCATAGTA-AGGTAGTATGGATACTATAAT-
64 ACAATAGTATA-GTAGTATGGATACCATAATG
41248 AGGGGTATCGATAC
1 A-GGGTATCGATAC
41262 TAAAAATCCA
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
94 44 0.48
95 48 0.52
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (94 bp):
AGGGTATCGATACCAGGAAACATCGAACCTAATTTTAGTATCGATACAGAAGGGGGTATCAGTAC
AATAGTATAGTAGTATGGATACCATAATG
Found at i:41714 original size:45 final size:45
Alignment explanation
Indices: 41678--41816 Score: 145
Period size: 45 Copynumber: 3.1 Consensus size: 45
41668 TATTGGCATG
*
41678 AAAGGATGCCATAGTTGAAATGTATATGGGTACATTATCAACAGA
1 AAAGGATACCATAGTTGAAATGTATATGGGTACATTATCAACAGA
* * * * *
41723 AAAGTATACTATGGTTGAAATGTATATAGGTACATTATCAACATA
1 AAAGGATACCATAGTTGAAATGTATATGGGTACATTATCAACAGA
* *** ** *
41768 AATA-TATGTTATAGTTGAAATGCGTATGGGTGCATTATCAACAGA
1 AA-AGGATACCATAGTTGAAATGTATATGGGTACATTATCAACAGA
41813 AAAG
1 AAAG
41817 ATGTTATAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.01
45 76 0.97
46 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.30
Consensus pattern (45 bp):
AAAGGATACCATAGTTGAAATGTATATGGGTACATTATCAACAGA
Found at i:41850 original size:45 final size:45
Alignment explanation
Indices: 41651--41855 Score: 139
Period size: 45 Copynumber: 4.6 Consensus size: 45
41641 TGAAAATACT
*** * ** *
41651 AATGCATATGGGTGCATTATTGGCATGAAA-GGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAATAGATGTTATAATTGA
* * ** **
41696 AATGTATATGGGTACATTATCAACAGAAA-AGTATACTATGGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAATAG-ATGTTATAATTGA
* * * * * *
41741 AATGTATATAGGTACATTATCAACATAAATATATGTTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAATAGATGTTATAATTGA
* *
41786 AATGCGTATGGGTGCATTATCAACAGAAA-AGATGTTATAATTTA
1 AATGCATATGGGTGCATTATCAACAGAAATAGATGTTATAATTGA
* *
41830 AAGTGCATAAT-GGTGTATTATAAACA
1 AA-TGCAT-ATGGGTGCATTATCAACA
41856 TAAGTGGAGG
Statistics
Matches: 130, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
44 19 0.15
45 108 0.83
46 3 0.02
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAATAGATGTTATAATTGA
Found at i:41850 original size:90 final size:90
Alignment explanation
Indices: 41688--41858 Score: 202
Period size: 90 Copynumber: 1.9 Consensus size: 90
41678 AAAGGATGCC
* ** *
41688 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATAGG
1 ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAATTGAAATGCATATAGG
*
41753 TACATTATCAACATAAATATATGTT
66 TACATTATAAACATAAATATATGTT
* * ** *
41778 ATAGTTGAAATGCGTATGGGTGCATTATCAACAGAAAAG-ATGTTATAATTTAAAGTGCATA-AT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAATTGAAA-TGCATATA-
**
41841 GGTGTATTATAAACATAA
64 GGTACATTATAAACATAA
41859 GTGGAGGTTA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
89 11 0.16
90 56 0.84
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (90 bp):
ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAATTGAAATGCATATAGG
TACATTATAAACATAAATATATGTT
Found at i:47484 original size:22 final size:22
Alignment explanation
Indices: 47454--47495 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
47444 CTAGAAGGGG
*
47454 GTATTGATACCATAGTAGGGTA
1 GTATGGATACCATAGTAGGGTA
*
47476 GTATGGATACTATAGTAGGG
1 GTATGGATACCATAGTAGGG
47496 GTATCGATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.31
Consensus pattern (22 bp):
GTATGGATACCATAGTAGGGTA
Found at i:47503 original size:95 final size:94
Alignment explanation
Indices: 47292--47505 Score: 286
Period size: 94 Copynumber: 2.3 Consensus size: 94
47282 ATGTACTATC
* * *
47292 GATACCATGGTAAGGGTATCGATACCAGGAAATATCGAACCTAATTTTGGTATCGATACCGAAGG
1 GATACCATAGTAAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATACAGAAGG
* *
47357 GGGTATCAGTACAATAGTATAGTAGTATT
66 GGGTATCAGTACAATAGTAGAGTAGTATG
** *
47386 GATACCATAGTAAGGGTATCGATACCAGGCTACATCGAAGCTAATTTTGGTATCGATACTAGAAG
1 GATACCATAGTAAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATAC-AGAAG
* * *
47451 GGGGTAT-TGATACCATAGTAGGGTAGTATG
65 GGGGTATCAG-TACAATAGTAGAGTAGTATG
* *
47481 GATACTATAGTAGGGGTATCGATAC
1 GATACCATAGTAAGGGTATCGATAC
47506 TAAAAATCCA
Statistics
Matches: 105, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
94 55 0.52
95 50 0.48
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (94 bp):
GATACCATAGTAAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATACAGAAGG
GGGTATCAGTACAATAGTAGAGTAGTATG
Found at i:47982 original size:45 final size:44
Alignment explanation
Indices: 47930--48060 Score: 174
Period size: 45 Copynumber: 2.9 Consensus size: 44
47920 AAAGGATGCC
*
47930 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGAGTACATTATCAACAGAAAA-TATACT
* *
47975 ATGGTTGAAATGTATAT-ATGTACATTATCAACAGAAATATATATT
1 ATAGTTGAAATGTATATGA-GTACATTATCAACAGAAA-ATATACT
** *
48020 ATAGTTGAAATGCGTATGAGTGCATTATCAACAGAAAATAT
1 ATAGTTGAAATGTATATGAGTACATTATCAACAGAAAATAT
48061 GTTATAATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
44 4 0.05
45 70 0.92
46 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (44 bp):
ATAGTTGAAATGTATATGAGTACATTATCAACAGAAAATATACT
Found at i:48092 original size:45 final size:45
Alignment explanation
Indices: 47934--48097 Score: 138
Period size: 45 Copynumber: 3.6 Consensus size: 45
47924 GATGCCATAG
* * * * **
47934 TTGAAATGTATATGGGTACATTATCAACAGAAA-AGTATACTATGG
1 TTGAAATGCATATGAGTGCATTATCAACAGAAATA-TATATTATAA
* * *
47979 TTGAAATGTATAT-ATGTACATTATCAACAGAAATATATATTATAG
1 TTGAAATGCATATGA-GTGCATTATCAACAGAAATATATATTATAA
* *
48024 TTGAAATGCGTATGAGTGCATTATCAACAGAAA-ATATGTTATAA
1 TTGAAATGCATATGAGTGCATTATCAACAGAAATATATATTATAA
* * *
48068 TTTAAAGTGCATAATG-GTGTATTATAAACA
1 TTGAAA-TGCAT-ATGAGTGCATTATCAACA
48098 TAAGTGGAGG
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
44 14 0.14
45 83 0.81
46 5 0.05
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.34
Consensus pattern (45 bp):
TTGAAATGCATATGAGTGCATTATCAACAGAAATATATATTATAA
Done.