Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 64
Found at i:993779 original size:7 final size:7
Alignment explanation
Indices: 993767--993803 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
993757 GTCAAAGGAA
993767 GTCAACG
1 GTCAACG
993774 GTCAACG
1 GTCAACG
993781 GTC-ACG
1 GTCAACG
993787 GTCAACG
1 GTCAACG
993794 GTCAACG
1 GTCAACG
993801 GTC
1 GTC
993804 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:993789 original size:13 final size:14
Alignment explanation
Indices: 993767--993803 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
993757 GTCAAAGGAA
993767 GTCAACGGTCAACG
1 GTCAACGGTCAACG
993781 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
993794 GTCAACGGTC
1 GTCAACGGTC
993804 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:993810 original size:5 final size:5
Alignment explanation
Indices: 993800--993846 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
993790 AACGGTCAAC
* * *
993800 GGTCG GGTCG GGTC- AGTCG GGTCG GGTCG GGTC- AGTCG GGTTG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
993847 AGACCGTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 6 0.18
5 28 0.82
ACGTcount: A:0.04, C:0.19, G:0.53, T:0.23
Consensus pattern (5 bp):
GGTCG
Found at i:993820 original size:9 final size:9
Alignment explanation
Indices: 993806--993840 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
993796 CAACGGTCGG
993806 GTCGGGTCA
1 GTCGGGTCA
*
993815 GTCGGGTCGG
1 GTCGGGTC-A
993825 GTCGGGTCA
1 GTCGGGTCA
993834 GTCGGGT
1 GTCGGGT
993841 TGGGTCAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.06, C:0.20, G:0.51, T:0.23
Consensus pattern (9 bp):
GTCGGGTCA
Found at i:993822 original size:19 final size:19
Alignment explanation
Indices: 993800--993846 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
993790 AACGGTCAAC
993800 GGTCGGGTCGGGTCAGTCG
1 GGTCGGGTCGGGTCAGTCG
993819 GGTCGGGTCGGGTCAGTCG
1 GGTCGGGTCGGGTCAGTCG
*
993838 GGTTGGGTC
1 GGTCGGGTC
993847 AGACCGTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.04, C:0.19, G:0.53, T:0.23
Consensus pattern (19 bp):
GGTCGGGTCGGGTCAGTCG
Found at i:993847 original size:14 final size:14
Alignment explanation
Indices: 993801--993827 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
993791 ACGGTCAACG
993801 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
993815 GTCGGGTCGGGTC
1 GTCGGGTCGGGTC
993828 GGGTCAGTCG
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:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:993869 original size:19 final size:19
Alignment explanation
Indices: 993845--993884 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
993835 TCGGGTTGGG
993845 TCAGACC-GTTCAAACCGGT
1 TCAGACCAG-TCAAACCGGT
993864 TCAGACCAGTCAAACCGGT
1 TCAGACCAGTCAAACCGGT
993883 TC
1 TC
993885 GAACCGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (19 bp):
TCAGACCAGTCAAACCGGT
Found at i:1001032 original size:13 final size:14
Alignment explanation
Indices: 1001014--1001043 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1001004 GTCAAAGGAA
1001014 GTCAACGGTC-ACG
1 GTCAACGGTCAACG
1001027 GTCAACGGTCAACG
1 GTCAACGGTCAACG
1001041 GTC
1 GTC
1001044 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:1001034 original size:7 final size:7
Alignment explanation
Indices: 1001014--1001043 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1001004 GTCAAAGGAA
1001014 GTCAACG
1 GTCAACG
1001021 GTC-ACG
1 GTCAACG
1001027 GTCAACG
1 GTCAACG
1001034 GTCAACG
1 GTCAACG
1001041 GTC
1 GTC
1001044 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:1001050 original size:5 final size:5
Alignment explanation
Indices: 1001040--1001086 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
1001030 AACGGTCAAC
* * *
1001040 GGTCG GGTCG GGTC- AGTCG GGTCG GGTCG GGTC- AGTCG GGTTG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1001087 AGACCGTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 6 0.18
5 28 0.82
ACGTcount: A:0.04, C:0.19, G:0.53, T:0.23
Consensus pattern (5 bp):
GGTCG
Found at i:1001060 original size:9 final size:9
Alignment explanation
Indices: 1001046--1001080 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1001036 CAACGGTCGG
1001046 GTCGGGTCA
1 GTCGGGTCA
*
1001055 GTCGGGTCGG
1 GTCGGGTC-A
1001065 GTCGGGTCA
1 GTCGGGTCA
1001074 GTCGGGT
1 GTCGGGT
1001081 TGGGTCAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.06, C:0.20, G:0.51, T:0.23
Consensus pattern (9 bp):
GTCGGGTCA
Found at i:1001062 original size:19 final size:19
Alignment explanation
Indices: 1001040--1001086 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1001030 AACGGTCAAC
1001040 GGTCGGGTCGGGTCAGTCG
1 GGTCGGGTCGGGTCAGTCG
1001059 GGTCGGGTCGGGTCAGTCG
1 GGTCGGGTCGGGTCAGTCG
*
1001078 GGTTGGGTC
1 GGTCGGGTC
1001087 AGACCGTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.04, C:0.19, G:0.53, T:0.23
Consensus pattern (19 bp):
GGTCGGGTCGGGTCAGTCG
Found at i:1001087 original size:14 final size:14
Alignment explanation
Indices: 1001041--1001067 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1001031 ACGGTCAACG
1001041 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
1001055 GTCGGGTCGGGTC
1 GTCGGGTCGGGTC
1001068 GGGTCAGTCG
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:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:1001109 original size:19 final size:19
Alignment explanation
Indices: 1001085--1001124 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1001075 TCGGGTTGGG
1001085 TCAGACC-GTTCAAACCGGT
1 TCAGACCAG-TCAAACCGGT
*
1001104 TCAGACCAGTCAAACTGGT
1 TCAGACCAGTCAAACCGGT
1001123 TC
1 TC
1001125 GAACCGGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (19 bp):
TCAGACCAGTCAAACCGGT
Found at i:1003009 original size:19 final size:19
Alignment explanation
Indices: 1002985--1003038 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1002975 GTCGGGTCAG
*
1002985 ACCGGTCAAACCAGTTCG-A
1 ACCGGTCAAACC-GGTCGAA
*
1003004 ACCGGTTCGAACCGGTCGAA
1 ACCGG-TCAAACCGGTCGAA
1003024 ACCGGTCAAACCGGT
1 ACCGGTCAAACCGGT
1003039 TTCCAGCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (19 bp):
ACCGGTCAAACCGGTCGAA
Found at i:1003034 original size:9 final size:9
Alignment explanation
Indices: 1002979--1003038 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
1002969 GGGTCAGTCG
*
1002979 GGTCAGACC
1 GGTCAAACC
1002988 GGTCAAACC
1 GGTCAAACC
* *
1002997 AGTTCGAACC
1 -GGTCAAACC
*
1003007 GGTTCGAACC
1 GG-TCAAACC
1003017 GGTCGAAACC
1 GGTC-AAACC
1003027 GGTCAAACC
1 GGTCAAACC
1003036 GGT
1 GGT
1003039 TTCCAGCCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 19 0.44
10 24 0.56
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1010245 original size:21 final size:21
Alignment explanation
Indices: 1010220--1010270 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1010210 AATATGCTCA
*
1010220 TTAATTTTTCAAATTGGTCA-T
1 TTAATTTTTCAAATT-GACATT
**
1010241 TTAATAATTCAAATTGACATT
1 TTAATTTTTCAAATTGACATT
1010262 TTAATTTTT
1 TTAATTTTT
1010271 TGAATTGAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (21 bp):
TTAATTTTTCAAATTGACATT
Found at i:1020099 original size:30 final size:30
Alignment explanation
Indices: 1020065--1020127 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1020055 ACATACATAA
1020065 TGTTTAACTTGGAGCAACCTCTCTAGATGT
1 TGTTTAACTTGGAGCAACCTCTCTAGATGT
* *
1020095 TGTTTTACTTGGAGCAATCTCTCTAGATGT
1 TGTTTAACTTGGAGCAACCTCTCTAGATGT
1020125 TGT
1 TGT
1020128 AATAATTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (30 bp):
TGTTTAACTTGGAGCAACCTCTCTAGATGT
Found at i:1028810 original size:36 final size:36
Alignment explanation
Indices: 1028766--1028836 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
1028756 TAAACGTAAG
* * *
1028766 AATAATTAAATTTATTGAATAATTTTAGAGGTTAAT
1 AATAATTAAAGTTATAGAATAATTTTAAAGGTTAAT
*
1028802 AATAATTAAAGTTATAGAATTATTTTAAAGGTTAA
1 AATAATTAAAGTTATAGAATAATTTTAAAGGTTAA
1028837 AAGAAGTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.42
Consensus pattern (36 bp):
AATAATTAAAGTTATAGAATAATTTTAAAGGTTAAT
Found at i:1030258 original size:21 final size:19
Alignment explanation
Indices: 1030227--1030273 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
1030217 TTAGTTCGCC
* *
1030227 CCCTGAAATTTTAGTTCATT
1 CCCTTAAATTTAAGTTCA-T
1030247 CCTCTTAAATTTAAGTTCAT
1 CC-CTTAAATTTAAGTTCAT
1030267 CCCTTAA
1 CCCTTAA
1030274 CATAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 5 0.21
21 14 0.58
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (19 bp):
CCCTTAAATTTAAGTTCAT
Found at i:1030452 original size:14 final size:14
Alignment explanation
Indices: 1030433--1030466 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1030423 AGTAATTTTA
1030433 AAGGGGACGTTTGC
1 AAGGGGACGTTTGC
1030447 AAGGGGACGTTTGC
1 AAGGGGACGTTTGC
*
1030461 ATGGGG
1 AAGGGG
1030467 GAATGTGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.47, T:0.21
Consensus pattern (14 bp):
AAGGGGACGTTTGC
Found at i:1031079 original size:20 final size:20
Alignment explanation
Indices: 1031054--1031127 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
1031044 TATTCCCTGA
1031054 TAATCTTACATTCCCACTGG
1 TAATCTTACATTCCCACTGG
1031074 TAATCTTACATTCCCACTGG
1 TAATCTTACATTCCCACTGG
*
1031094 TAATCTTACATTCCCACTGA
1 TAATCTTACATTCCCACTGG
1031114 TAATCTTACATTCC
1 TAATCTTACATTCC
1031128 GTGAACCAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.27, C:0.30, G:0.07, T:0.36
Consensus pattern (20 bp):
TAATCTTACATTCCCACTGG
Found at i:1031595 original size:18 final size:18
Alignment explanation
Indices: 1031568--1031602 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1031558 GAATTTATGC
*
1031568 TTATTTTTTTAAATATTA
1 TTATTGTTTTAAATATTA
*
1031586 TTATTGTTTTTAATATT
1 TTATTGTTTTAAATATT
1031603 TTTCAGCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTATTGTTTTAAATATTA
Found at i:1033812 original size:30 final size:30
Alignment explanation
Indices: 1033778--1033841 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
1033768 ACAAATCAGA
*
1033778 CACTAACATTATCGTTTGTTACAAAATGGT
1 CACTAACATTATCGTTTGTTACAAAATAGT
1033808 CACTAACATTATCGTTTGTTACAAAATAGT
1 CACTAACATTATCGTTTGTTACAAAATAGT
1033838 CACT
1 CACT
1033842 CGATGTTAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (30 bp):
CACTAACATTATCGTTTGTTACAAAATAGT
Found at i:1034500 original size:23 final size:23
Alignment explanation
Indices: 1034438--1034500 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1034428 ATGAAACATG
*
1034438 CAGTTACATACTTTCATAACACA
1 CAGTTACATATTTTCATAACACA
* * * *
1034461 CATTTACATATTCTCATATCATA
1 CAGTTACATATTTTCATAACACA
1034484 CAGTTACATATTTTCAT
1 CAGTTACATATTTTCAT
1034501 CTCTTACCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (23 bp):
CAGTTACATATTTTCATAACACA
Found at i:1037992 original size:16 final size:16
Alignment explanation
Indices: 1037971--1038008 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1037961 TGATGGAGTT
*
1037971 AGGAAGGATTAAATAA
1 AGGAAGGATTAAAGAA
1037987 AGGAAGGATTAAAGAA
1 AGGAAGGATTAAAGAA
1038003 AGGAAG
1 AGGAAG
1038009 TAGAAAAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.32, T:0.13
Consensus pattern (16 bp):
AGGAAGGATTAAAGAA
Found at i:1039181 original size:23 final size:23
Alignment explanation
Indices: 1039155--1039213 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1039145 ATCTTATATA
1039155 GCACTACGGTGCAATTCTACGCG
1 GCACTACGGTGCAATTCTACGCG
* *
1039178 GCACTTCGGTGCAATTCTACGTG
1 GCACTACGGTGCAATTCTACGCG
1039201 GCAC-ATCGGTGCA
1 GCACTA-CGGTGCA
1039214 TTTATACGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGCG
Found at i:1039221 original size:23 final size:23
Alignment explanation
Indices: 1039161--1039213 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1039151 TATAGCACTA
*
1039161 CGGTGCAATTCTACGCGGCACTT
1 CGGTGCAATTCTACGCGGCACAT
*
1039184 CGGTGCAATTCTACGTGGCACAT
1 CGGTGCAATTCTACGCGGCACAT
1039207 CGGTGCA
1 CGGTGCA
1039214 TTTATACGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACAT
Found at i:1045390 original size:63 final size:64
Alignment explanation
Indices: 1045251--1045412 Score: 170
Period size: 63 Copynumber: 2.5 Consensus size: 64
1045241 ATTGTTCAAG
* * ** *
1045251 GTGTATCGATGCACATGAAGTGCATCGATGCACTAATTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCACTTAAAATAAAAACATCGAATGCCATCA
* * * *
1045315 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAATAG-GATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCACTTAAAATAAAAACATCGAAT-GCCA-TC
1045378 A
64 A
* *
1045379 -TGTATCGATGCA-TAGATAGTGCATCGATTCACCC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCC
1045413 GTCAAGGGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.02
63 46 0.55
64 36 0.43
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCACTTAAAATAAAAACATCGAATGCCATCA
Found at i:1047377 original size:21 final size:21
Alignment explanation
Indices: 1047328--1047377 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1047318 ATTCGGCTGA
* *
1047328 TGAAACAAGAGTTTATGAACT
1 TGAAACAGGAGTTTATGAAAT
*
1047349 TAAAACAGGAGTTTATGAAAT
1 TGAAACAGGAGTTTATGAAAT
1047370 TGAAACAG
1 TGAAACAG
1047378 ATGAACCGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (21 bp):
TGAAACAGGAGTTTATGAAAT
Found at i:1051028 original size:23 final size:23
Alignment explanation
Indices: 1050996--1051077 Score: 101
Period size: 23 Copynumber: 3.6 Consensus size: 23
1050986 ATCTTATATA
*
1050996 GCACTACGGTGCAATTCTACACG
1 GCACTTCGGTGCAATTCTACACG
* **
1051019 GTACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACACG
***
1051042 GCACTTCGGTGCAATTCTATGTG
1 GCACTTCGGTGCAATTCTACACG
1051065 GCACTTCGGTGCA
1 GCACTTCGGTGCA
1051078 TTTATACGAG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACACG
Found at i:1058004 original size:23 final size:23
Alignment explanation
Indices: 1057984--1058031 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1057974 GGAACAATCT
* *
1057984 TATATGGCACTACGGTGCAATTC
1 TATACGGCACTACAGTGCAATTC
*
1058007 TATACGGCACTTCAGTGCAATTC
1 TATACGGCACTACAGTGCAATTC
1058030 TA
1 TA
1058032 CGTGGCACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (23 bp):
TATACGGCACTACAGTGCAATTC
Found at i:1058038 original size:23 final size:23
Alignment explanation
Indices: 1057987--1058041 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
1057977 ACAATCTTAT
* * *
1057987 ATGGCACTACGGTGCAATTCTAT
1 ATGGCACTTCAGTGCAATTCTAC
*
1058010 ACGGCACTTCAGTGCAATTCTAC
1 ATGGCACTTCAGTGCAATTCTAC
*
1058033 GTGGCACTT
1 ATGGCACTT
1058042 TGGATTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (23 bp):
ATGGCACTTCAGTGCAATTCTAC
Found at i:1062719 original size:37 final size:38
Alignment explanation
Indices: 1062678--1062751 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
1062668 TTTTGTTCGG
* *
1062678 GTCGGGTCGGG-TTTTTTAAGTGTGATATTTGGGTCGA
1 GTCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGA
1062715 GTCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCG
1 GTCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCG
1062752 GGTTCAGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 11 0.32
38 23 0.68
ACGTcount: A:0.14, C:0.09, G:0.36, T:0.41
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGA
Found at i:1062861 original size:243 final size:244
Alignment explanation
Indices: 1062460--1063045 Score: 835
Period size: 253 Copynumber: 2.4 Consensus size: 244
1062450 GGTGAAACTT
* * * *
1062460 TATTTTGGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTAGGGTTCGGGTTTAGGGT
1 TATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGT
1062525 GAAAAAAA-CGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTT
66 GAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTT
* * *
1062589 TTTTAAATAAAAATAATTTTTTATTA-TT-TCGGGTC-G-G-ATTTCTAATTCATATATTCGGGT
131 TATTAAATAAAAATAATTTTTTATTATTTGTCGGGTCGGCGAATTTATAACTCATATATTCGGGT
1062649 CGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGA
196 CGGGTCGGATGAAACTTTATTTTG-T----TCGGGTCGGGTTTTTTAAGTGTGA
* *
1062703 TATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGGGTTCAGGTTTAGGGT
1 TATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGT
* * *
1062768 GAAAAAAACCGGACGGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCATTGTTTT
66 GAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTT
1062833 TATTAAATAAAAAT-ATTTTTTATTATTTCGGGTCGGGTCGGGTCGAATTTATAACTCATATATT
131 TATTAAATAAAAATAATTTTTTATTATTT---GTCGGGTC-GG-CGAATTTATAACTCATATATT
1062897 CGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGA
191 CGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGA
* **
1062951 TATTCGGGTTAAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAAGTCGGGTTCGGGTTT
1 TATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTC-GG----GTCGGGTTCGGGTTT
* *
1063016 ATGGTTAAAAAAACCGGACCGACCCGAAAA
61 AGGGTGAAAAAAACCGGACCGACCCGAAAA
1063046 AAAAAATATA
Statistics
Matches: 307, Mismatches: 20, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
243 78 0.25
244 68 0.22
248 70 0.23
249 2 0.01
250 1 0.00
252 2 0.01
253 86 0.28
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.37
Consensus pattern (244 bp):
TATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGT
GAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTT
TATTAAATAAAAATAATTTTTTATTATTTGTCGGGTCGGCGAATTTATAACTCATATATTCGGGT
CGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGA
Found at i:1062988 original size:38 final size:38
Alignment explanation
Indices: 1062927--1063015 Score: 153
Period size: 38 Copynumber: 2.3 Consensus size: 38
1062917 TTTATTTTGT
*
1062927 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTTAAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAAG
1062964 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAAG
1063002 TCGGGTTCGGGTTT
1 TCGGG-TCGGGTTT
1063016 ATGGTTAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 10 0.20
38 31 0.63
39 8 0.16
ACGTcount: A:0.13, C:0.10, G:0.36, T:0.40
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAAG
Found at i:1063225 original size:12 final size:12
Alignment explanation
Indices: 1063208--1063232 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1063198 TTAAATAAAA
1063208 ATAGTTTTTGGT
1 ATAGTTTTTGGT
1063220 ATAGTTTTTGGT
1 ATAGTTTTTGGT
1063232 A
1 A
1063233 ACTAATTAAC
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:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (12 bp):
ATAGTTTTTGGT
Found at i:1063566 original size:16 final size:18
Alignment explanation
Indices: 1063545--1063589 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1063535 TATGGAATTG
1063545 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
1063561 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
1063579 GATTCCTATTC
1 GATTCCAATTC
1063590 TCTCATAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 13 0.50
ACGTcount: A:0.27, C:0.31, G:0.07, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1066856 original size:14 final size:14
Alignment explanation
Indices: 1066837--1066895 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 14
1066827 CAAATAATGT
1066837 AATTGGTTTTCTGG
1 AATTGGTTTTCTGG
*
1066851 AATTGGTTTTTCAGAAATGT
1 AATTGG-TTTTC-----TGG
1066871 AATTGGTTTTCTGG
1 AATTGGTTTTCTGG
1066885 AATTGGTTTTC
1 AATTGGTTTTC
1066896 AAGAAATCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
14 19 0.51
15 5 0.14
19 5 0.14
20 8 0.22
ACGTcount: A:0.20, C:0.07, G:0.24, T:0.49
Consensus pattern (14 bp):
AATTGGTTTTCTGG
Found at i:1066875 original size:34 final size:34
Alignment explanation
Indices: 1066832--1066902 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
1066822 ACATCCAAAT
1066832 AATGTAATTGGTTTTCTGGAATTGGTTTTTC-AGA
1 AATGTAATTGGTTTTCTGGAATTGG-TTTTCAAGA
1066866 AATGTAATTGGTTTTCTGGAATTGGTTTTCAAGA
1 AATGTAATTGGTTTTCTGGAATTGGTTTTCAAGA
1066900 AAT
1 AAT
1066903 CCAATTACAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 5 0.14
34 31 0.86
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.45
Consensus pattern (34 bp):
AATGTAATTGGTTTTCTGGAATTGGTTTTCAAGA
Found at i:1067909 original size:15 final size:15
Alignment explanation
Indices: 1067889--1067924 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1067879 AAAATTAAAT
1067889 TGATAAAGTGACAGA
1 TGATAAAGTGACAGA
*
1067904 TGATAAAGTGATAGA
1 TGATAAAGTGACAGA
1067919 TGATAA
1 TGATAA
1067925 TGGAACGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.25, T:0.25
Consensus pattern (15 bp):
TGATAAAGTGACAGA
Found at i:1068793 original size:60 final size:59
Alignment explanation
Indices: 1068694--1068821 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 59
1068684 TAAAGTATAT
* *
1068694 AAATGGTCCTCTGACTATAATGTATTACTTCATTAAGTCCCTCAACCATTAAGAGTTACA
1 AAATGGTCCTCCGACTAT-ATGTATTACTTCATTAAGTCCCTCAACCATTAAAAGTTACA
** * ** *
1068754 AAATGGTCCTCCGACTAT-TGGTAGTTACTTTGTTGAGTCCCTTGACTATTAAAAGTTACA
1 AAATGGTCCTCCGACTATAT-GTA-TTACTTCATTAAGTCCCTCAACCATTAAAAGTTACA
1068814 AAATGGTC
1 AAATGGTC
1068822 ACCCACTATT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 1 0.02
59 3 0.05
60 54 0.93
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (59 bp):
AAATGGTCCTCCGACTATATGTATTACTTCATTAAGTCCCTCAACCATTAAAAGTTACA
Found at i:1069571 original size:20 final size:20
Alignment explanation
Indices: 1069527--1069752 Score: 177
Period size: 20 Copynumber: 11.2 Consensus size: 20
1069517 AATGACCAAC
*
1069527 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
1069546 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
1069566 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
1069586 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
1069606 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
1069627 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
1069648 AAAATCGCAACGCGATTTCAAG
1 AAAATCGCAACGCGA-TT-AAG
1069670 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
1069688 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
1069710 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
1069730 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
1069748 AAAAT
1 AAAAT
1069753 GAGTAAATTC
Statistics
Matches: 174, Mismatches: 16, Indels: 33
0.78 0.07 0.15
Matches are distributed among these distances:
18 7 0.04
19 17 0.10
20 120 0.69
21 11 0.06
22 19 0.11
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:1069683 original size:40 final size:40
Alignment explanation
Indices: 1069527--1069744 Score: 214
Period size: 40 Copynumber: 5.4 Consensus size: 40
1069517 AATGACCAAC
** * *
1069527 AAAATCGCAACGCGAAAT-AAAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTCAAGAATCGCAACGCGATTCAG
* ****
1069566 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G--TCAAAAG
1 AAAATCGCAACG-CGATTTCAAGAATCGCAACGCGATTC---AG
*
1069606 AAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGAT-TT-CAAGAATCGCAACGCGATTCAG
*
1069648 AAAATCGCAACGCGATTTCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTCAAGAATCGCAACGCGATTCAG
*
1069688 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATTTCAAGAATCGCAACGCGATT-CAG
*
1069728 AGAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
1069745 AAGAAAATGA
Statistics
Matches: 153, Mismatches: 14, Indels: 23
0.81 0.07 0.12
Matches are distributed among these distances:
37 1 0.01
39 15 0.10
40 100 0.65
41 7 0.05
42 27 0.18
43 1 0.01
45 2 0.01
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATTTCAAGAATCGCAACGCGATTCAG
Found at i:1069721 original size:60 final size:60
Alignment explanation
Indices: 1069527--1069752 Score: 214
Period size: 60 Copynumber: 3.8 Consensus size: 60
1069517 AATGACCAAC
* * * * **
1069527 AAAATCGCAACGCGAAAT--AAAAATCGCAACGCGATTTAGAAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACGCG-ATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACG-CGATTCAG
* *** *
1069586 AAAATCGCAACG-G--TCAAAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTC-CAAG--AATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCAG
*
1069648 AAAATCGCAACGCGATTTCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CAG
*
1069708 AGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAAT
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAAT
1069753 GAGTAAATTC
Statistics
Matches: 140, Mismatches: 15, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
55 1 0.01
58 3 0.02
59 12 0.09
60 71 0.51
61 11 0.08
62 37 0.26
63 1 0.01
64 3 0.02
65 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (60 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAG
Found at i:1069859 original size:6 final size:6
Alignment explanation
Indices: 1069848--1070009 Score: 303
Period size: 6 Copynumber: 27.5 Consensus size: 6
1069838 GACACGTATT
1069848 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1069896 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1069944 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1069992 ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
1070010 CGAGACGAGA
Statistics
Matches: 156, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.10
6 141 0.90
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1070527 original size:6 final size:6
Alignment explanation
Indices: 1070506--1070650 Score: 276
Period size: 6 Copynumber: 24.5 Consensus size: 6
1070496 TCTCGTCTCG
1070506 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1070552 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1070600 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1070648 GGT
1 GGT
1070651 AATAGTAATA
Statistics
Matches: 139, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.07
6 129 0.93
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1070784 original size:20 final size:20
Alignment explanation
Indices: 1070759--1071025 Score: 287
Period size: 20 Copynumber: 12.8 Consensus size: 20
1070749 CTCATTTTCT
1070759 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1070779 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
1070800 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
1070819 GAATCGCGTTGCGATTTGCGATTTTCT
1 GAATCGCGTTGCGA-TT-C----TT-G
1070846 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1070866 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
1070887 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1070906 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1070926 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
*
1070947 -AATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1070966 GAAGATCGCGTTGCGATTCTCT-
1 G-A-ATCGCGTTGCGATTCT-TG
* *
1070988 TAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1071008 GAATATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
1071026 TTCTTTTGAC
Statistics
Matches: 214, Mismatches: 8, Indels: 48
0.79 0.03 0.18
Matches are distributed among these distances:
18 15 0.07
19 1 0.00
20 127 0.59
21 7 0.03
22 44 0.21
23 1 0.00
25 1 0.00
26 4 0.02
27 14 0.07
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:1070898 original size:87 final size:87
Alignment explanation
Indices: 1070752--1070921 Score: 340
Period size: 87 Copynumber: 2.0 Consensus size: 87
1070742 GAATTTACTC
1070752 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCT
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCT
1070817 TGGAATCGCGTTGCGATTTGCG
66 TGGAATCGCGTTGCGATTTGCG
1070839 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCT
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCT
1070904 TGGAATCGCGTTGCGATT
66 TGGAATCGCGTTGCGATT
1070922 CTTGGAATCG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.39
Consensus pattern (87 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCT
TGGAATCGCGTTGCGATTTGCG
Found at i:1071041 original size:20 final size:20
Alignment explanation
Indices: 1071016--1071069 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1071006 TGGAATATCG
* *
1071016 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
1071036 CGTTGCGATTTTCTTTTCAA
1 CGTTGCGATTTTCTTTTCAA
1071056 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
1071070 AAATCGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.20, G:0.19, T:0.50
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:1071081 original size:20 final size:19
Alignment explanation
Indices: 1071058--1071106 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1071048 CTTTTCAACG
1071058 TTGCGATTTTCTAAATCGCA
1 TTGCGATTTT-TAAATCGCA
** *
1071078 TTGCGATTTTTATTTCGCG
1 TTGCGATTTTTAAATCGCA
1071097 TTGCGATTTT
1 TTGCGATTTT
1071107 GTTGGTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTTAAATCGCA
Found at i:1073130 original size:24 final size:24
Alignment explanation
Indices: 1073086--1073140 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
1073076 TCGTGATCAA
*
1073086 TAATT-AATTATAAACAAAATATT
1 TAATTAAATTATAAACAAAATAAT
** *
1073109 TAATTAAATTATATTCATAATAAT
1 TAATTAAATTATAAACAAAATAAT
*
1073133 CAATTAAA
1 TAATTAAA
1073141 AAGTATAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (24 bp):
TAATTAAATTATAAACAAAATAAT
Found at i:1075981 original size:44 final size:44
Alignment explanation
Indices: 1075918--1076011 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 44
1075908 ATGGAGTAGA
1075918 CATTTTAATCTGTTTGAACTGATTAAAACTAATTGTACCTATAC
1 CATTTTAATCTGTTTGAACTGATTAAAACTAATTGTACCTATAC
*
1075962 CATTTTAATCTGTTTGAACTGATTAAAACTTATTGTACCTATAC
1 CATTTTAATCTGTTTGAACTGATTAAAACTAATTGTACCTATAC
1076006 CATTTT
1 CATTTT
1076012 TGGTGTAGGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.44
Consensus pattern (44 bp):
CATTTTAATCTGTTTGAACTGATTAAAACTAATTGTACCTATAC
Found at i:1077760 original size:15 final size:16
Alignment explanation
Indices: 1077740--1077769 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1077730 GACATGTTGA
1077740 TGAACT-TTATGACAC
1 TGAACTATTATGACAC
1077755 TGAACTATTATGACA
1 TGAACTATTATGACA
1077770 ATATGAAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (16 bp):
TGAACTATTATGACAC
Found at i:1080928 original size:16 final size:16
Alignment explanation
Indices: 1080909--1080940 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1080899 ATTGAGTCCA
1080909 TTGACTATTAAAAGTT
1 TTGACTATTAAAAGTT
1080925 TTGACTATTAAAAGTT
1 TTGACTATTAAAAGTT
1080941 AAAGATGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
TTGACTATTAAAAGTT
Found at i:1081690 original size:29 final size:28
Alignment explanation
Indices: 1081658--1081729 Score: 94
Period size: 26 Copynumber: 2.6 Consensus size: 28
1081648 ATAAATACCT
*
1081658 AATATCTAAATTATTTTTTTATCAGAATA
1 AATA-CTAAATTATTTTTTTATCAAAATA
1081687 AATACT--ATTATTTTTTTATCAAAATA
1 AATACTAAATTATTTTTTTATCAAAATA
*
1081713 AGTACTTAAATTATTTT
1 AATAC-TAAATTATTTT
1081730 ATGTCAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 23 0.61
27 1 0.03
28 2 0.05
29 12 0.32
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (28 bp):
AATACTAAATTATTTTTTTATCAAAATA
Found at i:1081729 original size:26 final size:26
Alignment explanation
Indices: 1081674--1081758 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
1081664 TAAATTATTT
* * * *
1081674 TTTTATCAGAATAAATAC-TATTATTT
1 TTTTATCAAAATAAGTACTTA-AATTA
1081700 TTTTATCAAAATAAGTACTTAAATTA
1 TTTTATCAAAATAAGTACTTAAATTA
* * *
1081726 TTTTATGTCAAAATATGTAATTAAACTA
1 TTTTA--TCAAAATAAGTACTTAAATTA
1081754 TTTTA
1 TTTTA
1081759 ACATCTAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
26 24 0.49
27 2 0.04
28 23 0.47
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (26 bp):
TTTTATCAAAATAAGTACTTAAATTA
Found at i:1081729 original size:28 final size:29
Alignment explanation
Indices: 1081664--1081757 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 29
1081654 ACCTAATATC
* *
1081664 TAAATTATTTTTTTATCAGAATAAATAC-
1 TAAATTATTTTTTTATCAAAATAAGTACT
1081692 T--ATTATTTTTTTATCAAAATAAGTACT
1 TAAATTATTTTTTTATCAAAATAAGTACT
* * * *
1081719 TAAATTA-TTTTATGTCAAAATATGTAAT
1 TAAATTATTTTTTTATCAAAATAAGTACT
*
1081747 TAAACTATTTT
1 TAAATTATTTT
1081758 AACATCTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
26 23 0.42
27 1 0.02
28 24 0.44
29 7 0.13
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (29 bp):
TAAATTATTTTTTTATCAAAATAAGTACT
Found at i:1084088 original size:28 final size:28
Alignment explanation
Indices: 1084044--1084104 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
1084034 AGGGTTGACG
*
1084044 CTGATGACAGTGACGGTGACAGTCACCA
1 CTGATGAAAGTGACGGTGACAGTCACCA
*
1084072 CTGATGAAAGTGGCGGTGACAGTCACCA
1 CTGATGAAAGTGACGGTGACAGTCACCA
*
1084100 TTGAT
1 CTGAT
1084105 CGACCGACGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (28 bp):
CTGATGAAAGTGACGGTGACAGTCACCA
Found at i:1086243 original size:19 final size:18
Alignment explanation
Indices: 1086215--1086250 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1086205 CGTTAGTTGA
1086215 CCTAGTGTATCGATACAT
1 CCTAGTGTATCGATACAT
*
1086233 CCTAGGTGTATCGGTACA
1 CCTA-GTGTATCGATACA
1086251 CTAATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (18 bp):
CCTAGTGTATCGATACAT
Found at i:1087940 original size:21 final size:20
Alignment explanation
Indices: 1087907--1087945 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1087897 TTCTACGTGG
1087907 TCCTTCGGACATATATGTAA
1 TCCTTCGGACATATATGTAA
*
1087927 TCCTTTGGAACATATATGT
1 TCCTTCGG-ACATATATGT
1087946 GGTACTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (20 bp):
TCCTTCGGACATATATGTAA
Found at i:1087953 original size:21 final size:21
Alignment explanation
Indices: 1087915--1087954 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1087905 GGTCCTTCGG
*
1087915 ACATATATGTAATCCTTTGGA
1 ACATATATGTAATACTTTGGA
**
1087936 ACATATATGTGGTACTTTG
1 ACATATATGTAATACTTTG
1087955 ATACACTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (21 bp):
ACATATATGTAATACTTTGGA
Found at i:1092009 original size:31 final size:31
Alignment explanation
Indices: 1091935--1092062 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
1091925 AAGAGTCGAG
1091935 AGTATACCTATGTTCTACGGAACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
* *
1091966 AGAATTACCTATG-TCTTTC-GAGACATATGGAC
1 AGTA-TACCTATGTTC-TACGGA-ACATATGGAC
* *
1091998 AGTATACCTATGTTCTAAGGAACATATGAAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
* * * *
1092029 AGTTTACCTAGGTTCTTCGGAACCTATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
1092060 AGT
1 AGT
1092063 TGCCAAGGAT
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 53 0.66
32 27 0.34
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (31 bp):
AGTATACCTATGTTCTACGGAACATATGGAC
Found at i:1092104 original size:30 final size:30
Alignment explanation
Indices: 1092050--1092121 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
1092040 GTTCTTCGGA
* * *
1092050 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
1092080 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
1092110 ACCTCTGGATAG
1 ACCTCTGGATAG
1092122 GTACTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:1095920 original size:21 final size:21
Alignment explanation
Indices: 1095887--1095926 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1095877 TTCTACGTGG
*
1095887 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
1095908 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
1095927 GGTACTTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:1096370 original size:6 final size:6
Alignment explanation
Indices: 1096359--1096385 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1096349 AACTCCATAA
1096359 GTATAT GTATAT GTATAT GTATAT GTA
1 GTATAT GTATAT GTATAT GTATAT GTA
1096386 ATAAAGTGGT
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:0.00, G:0.19, T:0.48
Consensus pattern (6 bp):
GTATAT
Found at i:1097819 original size:13 final size:13
Alignment explanation
Indices: 1097801--1097834 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1097791 TAAGATTTTC
*
1097801 TTTGAAAATCATT
1 TTTGAAAATCAAT
1097814 TTTG-AAATCAAT
1 TTTGAAAATCAAT
1097826 TTTGAAAAT
1 TTTGAAAAT
1097835 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:1109574 original size:49 final size:52
Alignment explanation
Indices: 1109468--1109586 Score: 163
Period size: 49 Copynumber: 2.3 Consensus size: 52
1109458 AAACGAAAAA
* * **
1109468 ATGTATTATTTATAATAATTCAGTAAAAACAAAACCTTCTTTTGAATATGAC
1 ATGTATTATTTATAATAATTCAATAAAAACAAAACCTTCTATCAAATATGAC
* *
1109520 GTGTATTATTTATAATAATTCAAT-AAAA-AAAA-TTTCTATCAAATATGAC
1 ATGTATTATTTATAATAATTCAATAAAAACAAAACCTTCTATCAAATATGAC
1109569 ATGTATTATTTATAATAA
1 ATGTATTATTTATAATAA
1109587 ATTCCGTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 30 0.50
50 4 0.07
51 4 0.07
52 22 0.37
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (52 bp):
ATGTATTATTTATAATAATTCAATAAAAACAAAACCTTCTATCAAATATGAC
Found at i:1130593 original size:2 final size:2
Alignment explanation
Indices: 1130586--1130613 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1130576 TTATTTAAAC
1130586 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
1130614 GACTGATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1131931 original size:14 final size:15
Alignment explanation
Indices: 1131912--1131945 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1131902 TTGTTATTAG
1131912 GTTTGGGCCAGTC-T
1 GTTTGGGCCAGTCTT
*
1131926 GTTTGGGTCAGTCTT
1 GTTTGGGCCAGTCTT
1131941 GTTTG
1 GTTTG
1131946 TAATCGGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.06, C:0.15, G:0.35, T:0.44
Consensus pattern (15 bp):
GTTTGGGCCAGTCTT
Found at i:1132037 original size:16 final size:15
Alignment explanation
Indices: 1131998--1132039 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1131988 ATTAATTATT
1131998 TAATAAAT-ATAATA
1 TAATAAATAATAATA
*
1132012 TAACATAATAATAATAA
1 TAATA-AATAATAAT-A
1132029 TAATAAATAAT
1 TAATAAATAAT
1132040 GTAAGCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 4 0.17
15 3 0.13
16 11 0.48
17 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAAATAATAATA
Found at i:1132326 original size:31 final size:31
Alignment explanation
Indices: 1132288--1132536 Score: 446
Period size: 31 Copynumber: 8.0 Consensus size: 31
1132278 AGGGTCGAGG
1132288 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1132319 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1132350 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1132381 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1132412 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1132443 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1132474 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1132505 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1132536 G
1 G
1132537 GTCCTTCGGG
Statistics
Matches: 212, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 211 1.00
32 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1133601 original size:12 final size:12
Alignment explanation
Indices: 1133586--1133613 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1133576 AAACGTAAAA
1133586 AAATGCAAATGT
1 AAATGCAAATGT
1133598 AAATGCAAATGT
1 AAATGCAAATGT
1133610 AAAT
1 AAAT
1133614 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:1133700 original size:7 final size:7
Alignment explanation
Indices: 1133666--1133707 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1133656 ATAAGAGTAT
1133666 AAATGCA
1 AAATGCA
* *
1133673 CAATGAA
1 AAATGCA
1133680 AAATGCA
1 AAATGCA
1133687 AAGATGCA
1 AA-ATGCA
1133695 AAATGC-
1 AAATGCA
1133701 AAATGCA
1 AAATGCA
1133708 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:1135230 original size:26 final size:26
Alignment explanation
Indices: 1135200--1135250 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1135190 CCTGAATAAA
*
1135200 AATA-AAAAAAAAT-ATTAATAAAAT
1 AATATAAAAAAAATAAGTAATAAAAT
*
1135224 AATATAAAAATAATAAGTAATAAAAT
1 AATATAAAAAAAATAAGTAATAAAAT
1135250 A
1 A
1135251 TTTGAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 8 0.35
26 11 0.48
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (26 bp):
AATATAAAAAAAATAAGTAATAAAAT
Found at i:1135235 original size:16 final size:16
Alignment explanation
Indices: 1135194--1135236 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1135184 TTTATACCTG
1135194 AATAAAAATAAAAAAA
1 AATAAAAATAAAAAAA
** *
1135210 AATATTAATAAAATAA
1 AATAAAAATAAAAAAA
*
1135226 TATAAAAATAA
1 AATAAAAATAA
1135237 TAAGTAATAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AATAAAAATAAAAAAA
Found at i:1136125 original size:2 final size:2
Alignment explanation
Indices: 1136118--1136151 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1136108 ATTTAAACAA
* *
1136118 AT AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1136152 GACTGATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:1140426 original size:19 final size:18
Alignment explanation
Indices: 1140365--1140478 Score: 97
Period size: 19 Copynumber: 6.1 Consensus size: 18
1140355 GAGGTTTATA
1140365 TTTTTTGAATGGTTT-GGG
1 TTTTTT-AATGGTTTAGGG
* *
1140383 TTTTTTTAGTGATTTAGGG
1 -TTTTTTAATGGTTTAGGG
**
1140402 GCTTTTAAGTGGTTTAGGG
1 TTTTTTAA-TGGTTTAGGG
1140421 TTTTTTAATGGTTTA-GG
1 TTTTTTAATGGTTTAGGG
* **
1140438 TTTTTAAAATTTTATTAGGG
1 TTTTT-TAATGGT-TTAGGG
1140458 TTTTTTAATGGTTTAGAGG
1 TTTTTTAATGGTTTAG-GG
1140477 TT
1 TT
1140479 ATATAAAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
17 7 0.09
18 26 0.35
19 35 0.47
20 7 0.09
ACGTcount: A:0.18, C:0.01, G:0.26, T:0.54
Consensus pattern (18 bp):
TTTTTTAATGGTTTAGGG
Found at i:1148968 original size:6 final size:6
Alignment explanation
Indices: 1148959--1148991 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
1148949 AAGCAGTGTG
1148959 AATGCA AATGCCA AATGCA AATGCA AATGCA AA
1 AATGCA AATG-CA AATGCA AATGCA AATGCA AA
1148992 AGGTGTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (6 bp):
AATGCA
Found at i:1150838 original size:13 final size:14
Alignment explanation
Indices: 1150813--1150844 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1150803 TTTTAGATAC
1150813 AATAAATATATTAA
1 AATAAATATATTAA
1150827 AATAAA-ATATTAA
1 AATAAATATATTAA
1150840 AATAA
1 AATAA
1150845 TAAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATAAATATATTAA
Found at i:1152311 original size:3 final size:3
Alignment explanation
Indices: 1152303--1152329 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1152293 TGTAATTATT
1152303 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1152330 ATTGGACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1154822 original size:2 final size:2
Alignment explanation
Indices: 1154810--1154840 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1154800 TTTTTCCACC
*
1154810 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1154841 TAATTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1161521 original size:17 final size:17
Alignment explanation
Indices: 1161497--1161539 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
1161487 TAATTAGTAT
1161497 AATAAAATATTATAA-AA
1 AATAAAATATTA-AATAA
*
1161514 AATTAAATATTAAATAA
1 AATAAAATATTAAATAA
1161531 AATAAAATA
1 AATAAAATA
1161540 ATAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAAAATATTAAATAA
Found at i:1162042 original size:2 final size:2
Alignment explanation
Indices: 1162035--1162060 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1162025 AAAGAATTAA
1162035 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
1162061 TTATTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1162764 original size:6 final size:6
Alignment explanation
Indices: 1162753--1162777 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1162743 ATAAAACATA
1162753 ATAATT ATAATT ATAATT ATAATT A
1 ATAATT ATAATT ATAATT ATAATT A
1162778 GTTATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:1166117 original size:18 final size:19
Alignment explanation
Indices: 1166077--1166119 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1166067 ATATATATAT
* * *
1166077 ATATATATATTATTCTTTC
1 ATATATATAATATTATTTA
1166096 ATAT-TATAATATTATTTA
1 ATATATATAATATTATTTA
1166114 ATATAT
1 ATATAT
1166120 CAATTGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATATATAATATTATTTA
Found at i:1168936 original size:13 final size:14
Alignment explanation
Indices: 1168918--1168950 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1168908 TATACCCTTT
*
1168918 CCCTAACTTA-AAA
1 CCCTAAATTATAAA
1168931 CCCTAAATTATAAA
1 CCCTAAATTATAAA
1168945 CCCTAA
1 CCCTAA
1168951 GTTGGTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAAATTATAAA
Found at i:1179172 original size:37 final size:37
Alignment explanation
Indices: 1179130--1179216 Score: 88
Period size: 42 Copynumber: 2.3 Consensus size: 37
1179120 AAAATTATAC
*
1179130 TTAAAATTTA-GTTTTT-TTTTGTTTTAGTATTCTATCAT
1 TTAAAATTTATGTTTTTGTTTTGTTTTAATATTC---CAT
* *
1179168 TAAAAACTTTAATTTTTTTGTTTTGTTTTAATATTCCAT
1 TTAAAA-TTT-ATGTTTTTGTTTTGTTTTAATATTCCAT
1179207 TTAAAATTTA
1 TTAAAATTTA
1179217 ACATTAAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
37 1 0.02
38 8 0.20
39 11 0.27
40 1 0.02
41 5 0.12
42 15 0.37
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (37 bp):
TTAAAATTTATGTTTTTGTTTTGTTTTAATATTCCAT
Found at i:1180537 original size:26 final size:27
Alignment explanation
Indices: 1180469--1180548 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 27
1180459 TACATTTATA
* *
1180469 TATATATATATATATACATATTTTGAAAC
1 TATATATATATATATA-GT-TTTTAAAAC
*
1180498 TACATATATAATATATAGTTTTTAAAAC
1 TATATATAT-ATATATAGTTTTTAAAAC
1180526 --TATATA-ATATATAGTTTTTAAAA
1 TATATATATATATATAGTTTTTAAAA
1180549 AAACATTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
24 17 0.37
26 5 0.11
28 8 0.17
29 9 0.20
30 7 0.15
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (27 bp):
TATATATATATATATAGTTTTTAAAAC
Found at i:1180550 original size:26 final size:24
Alignment explanation
Indices: 1180502--1180548 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1180492 TGAAACTACA
1180502 TATATAATATATAGTTTTTAAAAC
1 TATATAATATATAGTTTTTAAAAC
1180526 TATATAATATATAGTTTTTAAAA
1 TATATAATATATAGTTTTTAAAA
1180549 AAACATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
TATATAATATATAGTTTTTAAAAC
Found at i:1180631 original size:12 final size:12
Alignment explanation
Indices: 1180614--1180638 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1180604 ATATATATAG
1180614 TTTTTGAAAACA
1 TTTTTGAAAACA
1180626 TTTTTGAAAACA
1 TTTTTGAAAACA
1180638 T
1 T
1180639 ATATATTATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:1180703 original size:73 final size:73
Alignment explanation
Indices: 1180526--1180791 Score: 262
Period size: 71 Copynumber: 3.7 Consensus size: 73
1180516 TTTTTAAAAC
* * * *
1180526 TATATAATATATAGTTTTTAAAAAAACATTTTAGAAAACATATGTAATATATAATTTTTAAAATC
1 TATATATTATATAGTTTTT--AAAAACATTTTTGAAAACATATAT-AT-TATAATTTTGAAAA-C
1180591 ATTTTGAAAAC---
61 A-TTTGAAAACATT
* *
1180602 T-TATA-TATATAGTTTTTGAAAACATTTTTGAAAACATATATATTATAGTTTTGAAAACATTCT
1 TATATATTATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATAATTTTGAAAACATT-T
1180665 GAAAACATT
65 GAAAACATT
* * *
1180674 TATATATTATATAGTTTTT-AAAACGTTTTTGAAAAC-T-TATATAATATTTTTGAAAACATGTT
1 TATATATTATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATAATTTTGAAAACAT-TT
1180736 GAAAACATT
65 GAAAACATT
** ** **
1180745 CGTATATTATATAGTTTAAAAAAACA-TTTTGAAAATTTATATATTAT
1 TATATATTATATAGTTTTTAAAAACATTTTTGAAAACATATATATTAT
1180792 TTGTTTTTGA
Statistics
Matches: 165, Mismatches: 15, Indels: 23
0.81 0.07 0.11
Matches are distributed among these distances:
68 2 0.01
69 9 0.05
70 12 0.07
71 56 0.34
72 30 0.18
73 27 0.16
74 24 0.15
75 4 0.02
76 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (73 bp):
TATATATTATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATAATTTTGAAAACATTTG
AAAACATT
Found at i:1180708 original size:108 final size:110
Alignment explanation
Indices: 1180527--1180809 Score: 311
Period size: 108 Copynumber: 2.6 Consensus size: 110
1180517 TTTTAAAACT
* * * *
1180527 ATATAATATATAGTTTTTAAAAAAACATTTTAGAAAACA--TATGTAATATATAATTTTTAAAAT
1 ATATATTATATAG--TTTAAAAAAACATTTT-GAAAACATTTATATATTATATAGTTTTTAAAAT
*
1180590 CATTTTGAAAACTTATATATATAGTTTTTGAAAACATTTTTGAAAACA-T-
63 CATTTTGAAAACTTATATA-ATA-TTTTTGAAAACA-TGTTGAAAACATTC
** * *
1180639 ATATA-T-TATAGTTT-TGAAAACATTCTGAAAACATTTATATATTATATAGTTTTTAAAA-CGT
1 ATATATTATATAGTTTAAAAAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAATC-A
1180700 TTTTGAAAACTTATATAATATTTTTGAAAACATGTTGAAAACATTC
65 TTTTGAAAACTTATATAATATTTTTGAAAACATGTTGAAAACATTC
* *
1180746 GTATATTATATAGTTTAAAAAAACATTTTG-AAA-ATTTATATATTAT-TTGTTTTTGAAAAT-A
1 ATATATTATATAGTTTAAAAAAACATTTTGAAAACATTTATATATTATATAGTTTTT-AAAATCA
1180807 TTT
65 TTT
1180810 ATGTATACAT
Statistics
Matches: 147, Mismatches: 14, Indels: 25
0.79 0.08 0.13
Matches are distributed among these distances:
105 10 0.07
106 20 0.14
107 27 0.18
108 58 0.39
109 11 0.07
110 15 0.10
111 1 0.01
112 5 0.03
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.44
Consensus pattern (110 bp):
ATATATTATATAGTTTAAAAAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAATCAT
TTTGAAAACTTATATAATATTTTTGAAAACATGTTGAAAACATTC
Found at i:1180833 original size:3 final size:3
Alignment explanation
Indices: 1180821--1180858 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1180811 TGTATACATA
1180821 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1180859 TGGTCTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1182066 original size:7 final size:7
Alignment explanation
Indices: 1182054--1182111 Score: 73
Period size: 7 Copynumber: 8.0 Consensus size: 7
1182044 ACTTTTGAAA
1182054 TATTTTT
1 TATTTTT
1182061 TATTTTT
1 TATTTTT
1182068 TATTTTTT
1 TA-TTTTT
1182076 TATTTTT
1 TATTTTT
1182083 T-TATTTT
1 TAT-TTTT
1182090 TATTTTT
1 TATTTTT
*
1182097 TTTCTTTT
1 TAT-TTTT
1182105 TATTTTT
1 TATTTTT
1182112 CTTTTATTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
6 1 0.02
7 30 0.67
8 14 0.31
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.86
Consensus pattern (7 bp):
TATTTTT
Found at i:1182067 original size:1 final size:1
Alignment explanation
Indices: 1182056--1182116 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
1182046 TTTTGAAATA
* * * * * * * *
1182056 TTTTTTATTTTTTATTTTTTTATTTTTTTATTTTTATTTTTTTTCTTTTTATTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1182117 ATTTCTTTGA
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:1182074 original size:8 final size:8
Alignment explanation
Indices: 1182056--1182111 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
1182046 TTTTGAAATA
1182056 TTTTTTA-
1 TTTTTTAT
1182063 TTTTTTAT
1 TTTTTTAT
1182071 TTTTTTAT
1 TTTTTTAT
1182079 TTTTTTA-
1 TTTTTTAT
1182086 -TTTTTAT
1 TTTTTTAT
1182093 TTTTTT-T
1 TTTTTTAT
*
1182100 CTTTTTAT
1 TTTTTTAT
1182108 TTTT
1 TTTT
1182112 CTTTTATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
6 6 0.14
7 13 0.30
8 24 0.56
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1182076 original size:15 final size:14
Alignment explanation
Indices: 1182056--1182116 Score: 86
Period size: 15 Copynumber: 4.1 Consensus size: 14
1182046 TTTTGAAATA
1182056 TTTTTTATTTTTTAT
1 TTTTTTATTTTTT-T
1182071 TTTTTTATTTTTTT
1 TTTTTTATTTTTTT
*
1182085 ATTTTTATTTTTTT
1 TTTTTTATTTTTTT
1182099 TCTTTTTATTTTTCTT
1 T-TTTTTATTTTT-TT
1182115 TT
1 TT
1182117 ATTTCTTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.33
15 25 0.60
16 3 0.07
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTATTTTTTT
Found at i:1182082 original size:22 final size:22
Alignment explanation
Indices: 1182054--1182111 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 22
1182044 ACTTTTGAAA
1182054 TATTTTTTATTTTTTATTTTTT
1 TATTTTTTATTTTTTATTTTTT
1182076 TATTTTTT-TATTTTTATTTTTT
1 TATTTTTTAT-TTTTTATTTTTT
1182098 T-TCTTTTTATTTTT
1 TAT-TTTTTATTTTT
1182112 CTTTTATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.06
22 30 0.91
23 1 0.03
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.86
Consensus pattern (22 bp):
TATTTTTTATTTTTTATTTTTT
Found at i:1182116 original size:21 final size:21
Alignment explanation
Indices: 1182057--1182124 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
1182047 TTTGAAATAT
1182057 TTTTTATTTTTTATTTTTTTAT-
1 TTTTTA-TTTTTATTTTTTT-TC
1182079 TTTTT-TATTTTTATTTTTTTTC
1 TTTTTAT-TTT-TATTTTTTTTC
* *
1182101 TTTTTATTTTTCTTTTATTTC
1 TTTTTATTTTTATTTTTTTTC
1182122 TTT
1 TTT
1182125 GATTTACTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 1 0.03
21 16 0.40
22 22 0.55
23 1 0.03
ACGTcount: A:0.10, C:0.04, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTTATTTTTATTTTTTTTC
Found at i:1182136 original size:10 final size:10
Alignment explanation
Indices: 1182112--1182144 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1182102 TTTTATTTTT
*
1182112 CTTTTATTT-
1 CTTTGATTTA
1182121 CTTTGATTTA
1 CTTTGATTTA
1182131 CTTTGATTTA
1 CTTTGATTTA
1182141 CTTT
1 CTTT
1182145 TTTAATCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.67
Consensus pattern (10 bp):
CTTTGATTTA
Found at i:1182206 original size:2 final size:2
Alignment explanation
Indices: 1182199--1182243 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1182189 TTATTACTAT
1182199 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1182241 TA T
1 TA T
1182244 TCTATCTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1194069 original size:16 final size:15
Alignment explanation
Indices: 1194045--1194080 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1194035 ATTATATAAA
*
1194045 ATATAATGAATTATTT
1 ATATTATGAATTA-TT
1194061 ATATTATGAATTATT
1 ATATTATGAATTATT
1194076 ATATT
1 ATATT
1194081 TTGTATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
ATATTATGAATTATT
Found at i:1194312 original size:15 final size:16
Alignment explanation
Indices: 1194294--1194324 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1194284 CGGGTACTCG
1194294 AAAAT-CGGATACCCA
1 AAAATCCGGATACCCA
1194309 AAAATCCGGATACCCA
1 AAAATCCGGATACCCA
1194325 GATTTACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.29, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAATCCGGATACCCA
Found at i:1195024 original size:17 final size:17
Alignment explanation
Indices: 1195002--1195047 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
1194992 TCAAGTAAAA
*
1195002 ATAAATATTTAAATTTT
1 ATAAATATTTAAAATTT
*
1195019 ATAAATA-TAAAAATTT
1 ATAAATATTTAAAATTT
1195035 ATTAAATATTTAA
1 A-TAAATATTTAA
1195048 TCAAGTAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 8 0.33
17 13 0.54
18 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAAATATTTAAAATTT
Found at i:1195621 original size:31 final size:32
Alignment explanation
Indices: 1195554--1195627 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 32
1195544 GCTGAAGATT
* * * *
1195554 TATTTTGTAATAGTTTGATAAAATTTAATAAT
1 TATTTTATAATAGATTGATAAAATTAAATAAG
1195586 TATTTTATAATA-ATTGA-AAATATTAAATAAG
1 TATTTTATAATAGATTGATAAA-ATTAAATAAG
1195617 TATTTTATAAT
1 TATTTTATAAT
1195628 TTTTAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 3 0.08
31 23 0.62
32 11 0.30
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.49
Consensus pattern (32 bp):
TATTTTATAATAGATTGATAAAATTAAATAAG
Found at i:1204724 original size:8 final size:8
Alignment explanation
Indices: 1204711--1204751 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1204701 CTCATTTTCA
1204711 GAGAATTT
1 GAGAATTT
1204719 GAGAATTT
1 GAGAATTT
*
1204727 -AGAGTTT
1 GAGAATTT
*
1204734 GGGAATTT
1 GAGAATTT
1204742 GAGAATTT
1 GAGAATTT
1204750 GA
1 GA
1204752 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1205052 original size:128 final size:128
Alignment explanation
Indices: 1204822--1205449 Score: 1123
Period size: 128 Copynumber: 4.9 Consensus size: 128
1204812 TAATCAGAGT
*
1204822 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCA-AGAATATATTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
1204886 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATAGCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* **
1204949 ACTATTCACACGAAGGCGCGTTTTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
1205014 CATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* **
1205077 ACTATTCACATGAAGGTGCGTTCCTAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
1205142 CATTGCCCTATTATGTCACTCATGTCCCTCGGGAACACTAGATATATCAGTACTTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
1205205 ACTATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1205270 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
1205333 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
1205398 CATTGCCCTATTTTGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
1205450 AATCAGGTAA
Statistics
Matches: 476, Mismatches: 24, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
127 49 0.10
128 427 0.90
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:1206309 original size:34 final size:34
Alignment explanation
Indices: 1206271--1206371 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
1206261 AAAATTAATG
*
1206271 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
1206305 TTAAATTTCGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* *
1206339 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
1206372 AACATTTATC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:1206911 original size:21 final size:21
Alignment explanation
Indices: 1206881--1206974 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
1206871 TATGGTATAA
*
1206881 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
1206902 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1206923 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
* *
1206944 AACCCTGCGGGCTCGGAATAT
1 AACCCTGCGGGCTAGGAATGT
1206965 AACCCTGCGG
1 AACCCTGCGG
1206975 AGATGACATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 3 0.04
21 62 0.91
22 3 0.04
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1207005 original size:21 final size:21
Alignment explanation
Indices: 1206981--1207025 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1206971 GCGGAGATGA
* *
1206981 CATATAAACTGGTGGGCTTGG
1 CATATAAACTGGAGGGCTGGG
* *
1207002 CATATGAAGTGGAGGGCTGGG
1 CATATAAACTGGAGGGCTGGG
1207023 CAT
1 CAT
1207026 GTACCCCTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.13, G:0.38, T:0.24
Consensus pattern (21 bp):
CATATAAACTGGAGGGCTGGG
Found at i:1208790 original size:34 final size:31
Alignment explanation
Indices: 1208747--1208835 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
1208737 TTAATAATTC
*
1208747 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
1208781 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
1208812 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
1208836 AAAATACTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 6 0.13
32 16 0.35
33 2 0.04
34 22 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:1208812 original size:31 final size:33
Alignment explanation
Indices: 1208747--1208826 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
1208737 TTAATAATTC
* *
1208747 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
1208781 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
1208812 TATAAAATATAATAA
1 TA-AAAAAATAATAA
1208827 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:1209449 original size:3 final size:3
Alignment explanation
Indices: 1209441--1209509 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
1209431 ACGCCCCCAA
1209441 AAT AAT 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
*
1209489 AAT AAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
1209510 GTGTATTTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1210651 original size:17 final size:17
Alignment explanation
Indices: 1210631--1210675 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
1210621 TTGAACAAAG
1210631 TAGTTCATTGA-TTATAC
1 TAGTTCATTGATTTA-AC
*
1210648 TAGTTCATTTATTTAAC
1 TAGTTCATTGATTTAAC
1210665 TAGTTCATTGA
1 TAGTTCATTGA
1210676 ACAAGCTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TAGTTCATTGATTTAAC
Found at i:1212428 original size:21 final size:20
Alignment explanation
Indices: 1212402--1212445 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1212392 TATTTTTTTC
*
1212402 AAAAAAAAAAAAAAGGCAAA
1 AAAAAAAAAAAAAAAGCAAA
*
1212422 AAAAAAACAAAAAAAGCTAAA
1 AAAAAAAAAAAAAAAGC-AAA
1212443 AAA
1 AAA
1212446 GCCAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.84, C:0.07, G:0.07, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAGCAAA
Found at i:1212443 original size:20 final size:19
Alignment explanation
Indices: 1212402--1212445 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
1212392 TATTTTTTTC
*
1212402 AAAAAAAAAAAAAAGGCAA
1 AAAAAAAAAAAAAAAGCAA
1212421 AAAAAAAACAAAAAAAGCTAA
1 AAAAAAAA-AAAAAAAGC-AA
1212442 AAAA
1 AAAA
1212446 GCCAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 8 0.36
21 6 0.27
ACGTcount: A:0.84, C:0.07, G:0.07, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAGCAA
Found at i:1216160 original size:43 final size:46
Alignment explanation
Indices: 1216060--1216164 Score: 128
Period size: 49 Copynumber: 2.3 Consensus size: 46
1216050 AGGATCAGAT
* *
1216060 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATTTTTTAGTTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAACAATTGTTTAGTTA
1216109 TTATTATTTTATTAGGAATT-A-GAGTTAAAAC-A-TGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACAATTGTTTAG-TTA
1216152 TTATTATTTTATT
1 TTATTATTTTATT
1216165 CTTTAGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
42 6 0.11
43 17 0.32
44 9 0.17
48 1 0.02
49 20 0.38
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.52
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACAATTGTTTAGTTA
Found at i:1220400 original size:20 final size:20
Alignment explanation
Indices: 1220375--1220487 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
1220365 TTTTCCCAAT
1220375 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1220395 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1220416 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
1220436 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1220456 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1220477 TCGCAATGCGA
1 TCGCAATGCGA
1220488 TACTGACTAT
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
20 47 0.60
21 31 0.40
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1220702 original size:22 final size:23
Alignment explanation
Indices: 1220674--1220718 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1220664 CACTCTCTCA
1220674 CCCATCTCCGACG-AAATCCGTC
1 CCCATCTCCGACGAAAATCCGTC
*
1220696 CCCATCTCTGACGAAAATCCGTC
1 CCCATCTCCGACGAAAATCCGTC
1220719 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.20
Consensus pattern (23 bp):
CCCATCTCCGACGAAAATCCGTC
Done.