Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold45
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: 1930935
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 50924 characters in sequence are not A, C, G, or T
File 4 of 7
Found at i:860551 original size:8 final size:8
Alignment explanation
Indices: 860538--860577 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
860528 CCCCGATTGC
860538 ATGTTTGT
1 ATGTTTGT
860546 ATGTTTGT
1 ATGTTTGT
*
860554 ATGGTT-T
1 ATGTTTGT
860561 -TGTTTGT
1 ATGTTTGT
860568 ATGTTTGT
1 ATGTTTGT
860576 AT
1 AT
860578 TGCTCTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 4 0.14
7 2 0.07
8 22 0.79
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.62
Consensus pattern (8 bp):
ATGTTTGT
Found at i:862751 original size:92 final size:91
Alignment explanation
Indices: 862594--862802 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
862584 TTGATTTTAG
* * *
862594 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
862659 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
862686 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
862750 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
862778 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
862803 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:862765 original size:24 final size:25
Alignment explanation
Indices: 862730--862777 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
862720 TTATGAAATT
862730 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
862754 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
862778 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:862973 original size:16 final size:16
Alignment explanation
Indices: 862952--862993 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
862942 TTATTAAATT
*
862952 ATATATTTTAATTATA
1 ATATATTTTAATAATA
862968 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
862983 AT-TATGTTTAA
1 ATATAT-TTTAA
862994 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:862978 original size:15 final size:15
Alignment explanation
Indices: 862943--862984 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
862933 TTAAGAATTT
*
862943 TATTAAATTAT-ATA
1 TATTTAATTATAATA
862957 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
862971 TATTTAATAATAAT
1 TATTTAATTATAAT
862985 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:863144 original size:16 final size:16
Alignment explanation
Indices: 863123--863176 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
863113 CCATTATGCT
863123 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
863139 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
863155 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
863171 AATACA
1 ATTACA
863177 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.28, C:0.35, G:0.02, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:865696 original size:25 final size:24
Alignment explanation
Indices: 865637--865724 Score: 63
Period size: 25 Copynumber: 3.6 Consensus size: 24
865627 GTACATGCAT
* * *
865637 GCTCATACGAG-TGATAAACAGTAG
1 GCTCATACGAGCTGAGATA-AGTAA
* *
865661 GCTCCTTCGAGCTGA-ATAATGGTAA
1 GCTCATACGAGCTGAGATAA--GTAA
*
865686 GCTCATACGAGTTGAGTATAAGTAA
1 GCTCATACGAGCTGAG-ATAAGTAA
*
865711 GCTCATAAGAGCTG
1 GCTCATACGAGCTG
865725 GAATCGGTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
23 1 0.02
24 11 0.22
25 34 0.68
27 4 0.08
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (24 bp):
GCTCATACGAGCTGAGATAAGTAA
Found at i:873261 original size:24 final size:24
Alignment explanation
Indices: 873201--873262 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
873191 GAATCAATAT
* * *
873201 GCTCTCATATGCTAAAATCGGTAA
1 GCTCTCACAAGCTAAAACCGGTAA
*
873225 GCTCTCACGAGCTAAAACCGGTAA
1 GCTCTCACAAGCTAAAACCGGTAA
873249 GCTCAT-ACAAGCTA
1 GCTC-TCACAAGCTA
873263 TGGTGTGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (24 bp):
GCTCTCACAAGCTAAAACCGGTAA
Found at i:874204 original size:63 final size:63
Alignment explanation
Indices: 874084--874204 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
874074 GAACATAAGA
* * ***
874084 ATTCAAATTTCACTATTTCCAAACACTTATAATCCATTATCAACATTAATGGGCTAATAATTC
1 ATTCAAATTTCACTATTGCCAAACACTTATAATCCATTATCAAAATTAATAACCTAATAATTC
*
874147 ATTCAAATTTCACTCTTGCCAAACACTTATAATCCATTATCAAAATTAATAACCTAAT
1 ATTCAAATTTCACTATTGCCAAACACTTATAATCCATTATCAAAATTAATAACCTAAT
874205 TACCATATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (63 bp):
ATTCAAATTTCACTATTGCCAAACACTTATAATCCATTATCAAAATTAATAACCTAATAATTC
Found at i:882977 original size:40 final size:40
Alignment explanation
Indices: 882922--883007 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
882912 AATTATTGAA
* * * *
882922 TGTTTGCACATACGTGCCGCTGTTTGTACTTTGGTACTCC
1 TGTTTGCACACACGTGCCGCTATTTGTACTTCGGTACCCC
*
882962 TGTTTGCACACACGTGCCGCTATTTTTACTTCGGTACCCC
1 TGTTTGCACACACGTGCCGCTATTTGTACTTCGGTACCCC
883002 TGTTTG
1 TGTTTG
883008 TACTTCGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.13, C:0.27, G:0.21, T:0.40
Consensus pattern (40 bp):
TGTTTGCACACACGTGCCGCTATTTGTACTTCGGTACCCC
Found at i:885944 original size:15 final size:15
Alignment explanation
Indices: 885924--885953 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
885914 TTTCTCACTT
885924 TTCAATCATCCCTCA
1 TTCAATCATCCCTCA
*
885939 TTCAATCATCTCTCA
1 TTCAATCATCCCTCA
885954 CTTATTCATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (15 bp):
TTCAATCATCCCTCA
Found at i:887921 original size:3 final size:3
Alignment explanation
Indices: 887913--888008 Score: 122
Period size: 3 Copynumber: 32.3 Consensus size: 3
887903 ACCTTGCTTT
* *
887913 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
887961 ATA GTA ATA GTA ATA GTA ATA GTA ATA ATA ATA A-A ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
888008 A
1 A
888009 ATATATATTT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:890679 original size:14 final size:15
Alignment explanation
Indices: 890654--890693 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
890644 ATATTTTTTC
890654 AAGCTATA-TTTTAA
1 AAGCTATAGTTTTAA
*
890668 AAG-TATAGTTTTAT
1 AAGCTATAGTTTTAA
890682 AAGCTAT-GTTTT
1 AAGCTATAGTTTT
890694 TCCGAGCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 16 0.70
15 3 0.13
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (15 bp):
AAGCTATAGTTTTAA
Found at i:892186 original size:8 final size:8
Alignment explanation
Indices: 892173--892215 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
892163 TTCATCGTTC
892173 TTTTATTT
1 TTTTATTT
892181 TTTTATTT
1 TTTTATTT
* *
892189 ATATATATAT
1 -T-TTTATTT
892199 TTTTATTT
1 TTTTATTT
892207 TTTTATTT
1 TTTTATTT
892215 T
1 T
892216 GCTTTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 22 0.76
9 2 0.07
10 5 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTATTT
Found at i:892883 original size:54 final size:55
Alignment explanation
Indices: 892801--892922 Score: 219
Period size: 54 Copynumber: 2.2 Consensus size: 55
892791 TAATTTATTA
*
892801 TTATTATTATATTACTATTATTATTAGCGTAAGTACCC-TTTTTTATATGACAAT
1 TTATTTTTATATTACTATTATTATTAGCGTAAGTACCCTTTTTTTATATGACAAT
892855 TTATTTTTATATTACTATTATTATTAGCGTAAGTACCCTTTTTTTATATGACAAT
1 TTATTTTTATATTACTATTATTATTAGCGTAAGTACCCTTTTTTTATATGACAAT
892910 TTATTTTTTATAT
1 TTA-TTTTTATAT
892923 GCAATTTTAT
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
54 37 0.57
55 19 0.29
56 9 0.14
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.54
Consensus pattern (55 bp):
TTATTTTTATATTACTATTATTATTAGCGTAAGTACCCTTTTTTTATATGACAAT
Found at i:892933 original size:19 final size:19
Alignment explanation
Indices: 892894--892929 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
892884 TAAGTACCCT
892894 TTTTTTATATGACAATTTA
1 TTTTTTATATGACAATTTA
892913 TTTTTTATATG-CAATTT
1 TTTTTTATATGACAATTT
892930 TATTCTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTTTTATATGACAATTTA
Found at i:892981 original size:24 final size:22
Alignment explanation
Indices: 892940--893002 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 22
892930 TATTCTATAG
892940 GTTATTATTTTAGTATTTTTATCAATT
1 GTTATTA-TTTA--ATTTTTAT-AA-T
892967 GTTATTATTTAA-TTTTATAAT
1 GTTATTATTTAATTTTTATAAT
*
892988 G-TACTATTTAATTTT
1 GTTATTATTTAATTTT
893003 ATTTATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 9 0.26
21 5 0.15
22 2 0.06
23 6 0.18
24 1 0.03
26 4 0.12
27 7 0.21
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (22 bp):
GTTATTATTTAATTTTTATAAT
Found at i:904513 original size:42 final size:42
Alignment explanation
Indices: 904449--904529 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
904439 CCCAAAAAGA
904449 GCAGCTCAAATATTGATCAGAATAGGGCATG-AGATGGTCAGG
1 GCAGCTCAAATATTGATCAGAATAGGGCATGCAG-TGGTCAGG
* *
904491 GCAGTTCAAATATTGATCAGAATGGGGCATGCAGTGGTC
1 GCAGCTCAAATATTGATCAGAATAGGGCATGCAGTGGTC
904530 TTGCTATACT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (42 bp):
GCAGCTCAAATATTGATCAGAATAGGGCATGCAGTGGTCAGG
Found at i:905662 original size:45 final size:45
Alignment explanation
Indices: 905595--906117 Score: 629
Period size: 45 Copynumber: 11.5 Consensus size: 45
905585 GAACATATCG
* *
905595 AAGATAACAGATCTTGTCTTCCTGTCTTGGCAGCGAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
** * * *
905640 AAGATAGTAGATCTTGTTTTCCTATATTGGTAGCGAAGTAGATCG
1 AAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
* *
905685 AAGATAACGGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
* * * *
905730 ATGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
1 AAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
* *
905775 AAGATAACAGATCTTGTCTTCCCTTCCTATATTGGTAGCGAAGTAGATCG
1 AAGATAACAGATCTTG---T--CTTCCTGTATTGGTAGCGAAGTAGATCA
* * * * *
905825 AAGATAACAGATCTTGTCTTCCTATATTGGCAACGAAGTATATCG
1 AAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
* * *
905870 AAGATAACAGATCTTGTCTTCCTGTATTCGCAACGAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
* * * *
905915 AAGACAATAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
1 AAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
* *
905960 AAGATAACAGATCTTGTCTTCCTGTATGGGCAAG-GAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTGTATTGG-TAGCGAAGTAGATCA
* * *
906005 AAGATAGA-AAATCTTGTCTTCTTGTATTGGTAGTGAAGTAGATCA
1 AAGATA-ACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
*
906050 AAGATAACAGATCATGTCTTCCTGTATTGGTAGCGAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
* * * *
906095 AGGATAGCAG-TCTTATCTCCCTG
1 AAGATAACAGATCTTGTCTTCCTG
906118 AAGTTGCAAT
Statistics
Matches: 414, Mismatches: 55, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
44 13 0.03
45 352 0.85
46 3 0.01
47 1 0.00
48 1 0.00
50 44 0.11
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (45 bp):
AAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
Found at i:905744 original size:90 final size:90
Alignment explanation
Indices: 905591--906108 Score: 725
Period size: 90 Copynumber: 5.7 Consensus size: 90
905581 CAGAGAACAT
* *
905591 ATCGAAGATAACAGATCTTGTCTTCCTGTCTTGGCAGCGAAGTAGATCAAAGATAGTAGATCTTG
1 ATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTG
*
905656 TTTTCCTATATTGGTAGCGAAGTAG
66 TCTTCCTATATTGGTAGCGAAGTAG
* *
905681 ATCGAAGATAACGGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAATGATAGCAGATCTTG
1 ATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTG
905746 TCTTCCTATATTGGTAGCGAAGTAG
66 TCTTCCTATATTGGTAGCGAAGTAG
* * * *
905771 ATCGAAGATAACAGATCTTGTCTTCCCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGA
1 ATCGAAGATAACAGATCTTG---T--CTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGA
* * *
905836 TCTTGTCTTCCTATATTGGCAACGAAGTAT
61 TCTTGTCTTCCTATATTGGTAGCGAAGTAG
* * * **
905866 ATCGAAGATAACAGATCTTGTCTTCCTGTATTCGCAACGAAGTAGATCAAAGACAATAGATCTTG
1 ATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTG
905931 TCTTCCTATATTGGTAGCGAAGTAG
66 TCTTCCTATATTGGTAGCGAAGTAG
* * *
905956 ATCGAAGATAACAGATCTTGTCTTCCTGTATGGGCAAG-GAAGTAGATCAAAGATAGAAAATCTT
1 ATCGAAGATAACAGATCTTGTCTTCCTGTATTGGC-AGCGAAGTAGATCAAAGATAGCAGATCTT
* * *
906020 GTCTTCTTGTATTGGTAGTGAAGTAG
65 GTCTTCCTATATTGGTAGCGAAGTAG
* * * *
906046 ATCAAAGATAACAGATCATGTCTTCCTGTATTGGTAGCGAAGTAGATCAAGGATAGCAG-TCTT
1 ATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTT
906109 ATCTCCCTGA
Statistics
Matches: 380, Mismatches: 41, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
89 6 0.02
90 290 0.76
91 1 0.00
92 1 0.00
93 1 0.00
95 81 0.21
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (90 bp):
ATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTG
TCTTCCTATATTGGTAGCGAAGTAG
Found at i:905992 original size:135 final size:135
Alignment explanation
Indices: 905591--906093 Score: 704
Period size: 135 Copynumber: 3.7 Consensus size: 135
905581 CAGAGAACAT
* **
905591 ATCGAAGATAACAGATCTTGTCTTCCTGTCTTGGCAGCGAAGTAGATCAAAGATAGTAGATCTTG
1 ATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTG
* * *
905656 TTTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACGGATCTTGTCTTCCTGTATTGGCAGCGA
66 TCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAACGA
905721 AGTAG
131 AGTAG
* * * *
905726 ATC-AATGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTT
1 ATCGAA-GATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAACAGATCTT
*
905790 GTCTTCCCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTATATTGG
65 G---T--CTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTGG
*
905855 CAACGAAGTAT
125 CAACGAAGTAG
* * * *
905866 ATCGAAGATAACAGATCTTGTCTTCCTGTATTCGCAACGAAGTAGATCAAAGACAATAGATCTTG
1 ATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTG
* *
905931 TCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATGGGCAAGGA
66 TCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAACGA
905996 AGTAG
131 AGTAG
* * * * * *
906001 ATCAAAGATAGA-AAATCTTGTCTTCTTGTATTGGTAGTGAAGTAGATCAAAGATAACAGATCAT
1 ATCGAAGATA-ACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAACAGATCTT
*
906065 GTCTTCCTGTATTGGTAGCGAAGTAGATC
65 GTCTTCCTATATTGGTAGCGAAGTAGATC
906094 AAGGATAGCA
Statistics
Matches: 325, Mismatches: 35, Indels: 16
0.86 0.09 0.04
Matches are distributed among these distances:
134 2 0.01
135 200 0.62
136 1 0.00
137 1 0.00
138 1 0.00
140 118 0.36
141 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (135 bp):
ATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTG
TCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAACGA
AGTAG
Found at i:906181 original size:44 final size:44
Alignment explanation
Indices: 906105--906215 Score: 152
Period size: 44 Copynumber: 2.5 Consensus size: 44
906095 AGGATAGCAG
* *
906105 TCTTATCTCCCTGAAGTTGCAATGGAACAGACAAAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAACAGACAAAAGAAACCAA
* * *
906149 TGTTATCTCCCTGAAGTTGCAGTAGAGA-AGACAGAAGAAATCAA
1 TCTTATCTCCCTGAAGTTGCAGTAGA-ACAGACAAAAGAAACCAA
*
906193 TCTTATCTCCCTAAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGT
906216 GGAGCGGATC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 58 0.98
45 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAACAGACAAAAGAAACCAA
Found at i:906239 original size:44 final size:42
Alignment explanation
Indices: 906105--906265 Score: 133
Period size: 44 Copynumber: 3.7 Consensus size: 42
906095 AGGATAGCAG
* * *
906105 TCTTATCTCCCTGAAGTTGCAATGGAACAGACAAAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGATA--AA
* * * * *
906149 TGTTATCTCCCTGAAGTTGCAGTAGAGAAGACAGAAGAAATCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA-AA-AGATAAA
* *
906193 TCTTATCTCCCTAAAGTTGCAGTGGAGCGGATCAAAATGATAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAA-GATAAA
* * * * *
906237 TCTCATCTCTCTGAGGTTGTAGTAGAGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCA
906266 TATCGTATCA
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
43 1 0.01
44 84 0.92
45 4 0.04
46 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (42 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGATAAA
Found at i:911472 original size:45 final size:46
Alignment explanation
Indices: 911408--911551 Score: 170
Period size: 45 Copynumber: 3.2 Consensus size: 46
911398 NNNNNNATCG
* * *
911408 AAGATA-ACAGATCTTGTCTTCCTGTATGGGCAAG-GAAGTAGATCA
1 AAGATAGACAAATCTTGTCTTCCTGTATTGG-TAGCGAAGTAGATCA
* *
911453 AAGATAGA-AAATCTTGTCTTCTTGTATTGGTAGTGAAGTAGATCA
1 AAGATAGACAAATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
* *
911498 AAGATA-ACAGATCATGTCTTCCTGTATTGGTAGCGAAGTAGATTCA
1 AAGATAGACAAATCTTGTCTTCCTGTATTGGTAGCGAAGTAGA-TCA
*
911544 AGGATAGA
1 AAGATAGA
911552 GTCTTATCTC
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
44 3 0.04
45 72 0.85
46 9 0.11
47 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (46 bp):
AAGATAGACAAATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCA
Found at i:911629 original size:44 final size:44
Alignment explanation
Indices: 911553--911663 Score: 152
Period size: 44 Copynumber: 2.5 Consensus size: 44
911543 AAGGATAGAG
* *
911553 TCTTATCTCCCTGAAGTTGCAATGGAACAGACAAAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAACAGACAAAAGAAACCAA
* * *
911597 TGTTATCTCCCTGAAGTTGCAGTAGAGA-AGACAGAAGAAATCAA
1 TCTTATCTCCCTGAAGTTGCAGTAGA-ACAGACAAAAGAAACCAA
*
911641 TCTTATCTCCCTAAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGT
911664 GGAGCGGATC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 58 0.98
45 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAACAGACAAAAGAAACCAA
Found at i:911687 original size:44 final size:42
Alignment explanation
Indices: 911553--911713 Score: 133
Period size: 44 Copynumber: 3.7 Consensus size: 42
911543 AAGGATAGAG
* * *
911553 TCTTATCTCCCTGAAGTTGCAATGGAACAGACAAAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGATA--AA
* * * * *
911597 TGTTATCTCCCTGAAGTTGCAGTAGAGAAGACAGAAGAAATCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA-AA-AGATAAA
* *
911641 TCTTATCTCCCTAAAGTTGCAGTGGAGCGGATCAAAATGATAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAA-GATAAA
* * * * *
911685 TCTCATCTCTCTGAGGTTGTAGTAGAGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCA
911714 TATCGTATCA
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
43 1 0.01
44 84 0.92
45 4 0.04
46 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (42 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGATAAA
Found at i:913206 original size:3 final size:3
Alignment explanation
Indices: 913198--913238 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
913188 TTTAAAAATA
* *
913198 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
913239 GCGTAAGTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:913291 original size:19 final size:19
Alignment explanation
Indices: 913252--913287 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
913242 TAAGTACCCT
913252 TTTTTTATATGACAATTTA
1 TTTTTTATATGACAATTTA
913271 TTTTTTATATG-CAATTT
1 TTTTTTATATGACAATTT
913288 TATTCTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTTTTATATGACAATTTA
Found at i:913339 original size:24 final size:22
Alignment explanation
Indices: 913298--913360 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 22
913288 TATTCTATAG
913298 GTTATTATTTTAGTATTTTTATCAATT
1 GTTATTA-TTTA--ATTTTTAT-AA-T
913325 GTTATTATTTAA-TTTTATAAT
1 GTTATTATTTAATTTTTATAAT
*
913346 G-TACTATTTAATTTT
1 GTTATTATTTAATTTT
913361 ATTTATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 9 0.26
21 5 0.15
22 2 0.06
23 6 0.18
24 1 0.03
26 4 0.12
27 7 0.21
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (22 bp):
GTTATTATTTAATTTTTATAAT
Found at i:916193 original size:51 final size:50
Alignment explanation
Indices: 916090--916276 Score: 259
Period size: 51 Copynumber: 3.7 Consensus size: 50
916080 ATTTGGGTAA
*
916090 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
916140 AGAGGTCCCATGTAAGACCATGTCTTGTGACATGGCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTC-TGGGACATGGCATTGGCACCGAGATG
** *
916191 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCA-TGGACACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG-CACCGAGATG
** *
916241 AGAACATCCCATGTAAGACCATGTTTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
916277 TTTGACATGT
Statistics
Matches: 121, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
49 3 0.02
50 45 0.37
51 73 0.60
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:916273 original size:101 final size:101
Alignment explanation
Indices: 916090--916276 Score: 279
Period size: 101 Copynumber: 1.9 Consensus size: 101
916080 ATTTGGGTAA
* * **
916090 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAA
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATGAGACATCCCATGTAA
*
916155 GACCATGTCTTGTGACATGGCATTGGCACCAAGATG
66 GACCATGTCTTGGGACATGGCATTGGCACCAAGATG
* *
916191 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGC-ATGGACACCGATATGAGAACATCCCATGT
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGATGG-CACCGAGATGAG-ACATCCCATGT
916255 AAGACCATGT-TTGGGACATGGC
64 AAGACCATGTCTTGGGACATGGC
916277 TTTGACATGT
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
100 3 0.04
101 55 0.71
102 19 0.25
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (101 bp):
AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATGAGACATCCCATGTAA
GACCATGTCTTGGGACATGGCATTGGCACCAAGATG
Found at i:952354 original size:23 final size:23
Alignment explanation
Indices: 952322--952375 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
952312 CCCTTAGCAG
* ***
952322 AACTAAGAACTCGTAGTGCCCAT
1 AACTAGGAACTCGTACCACCCAT
952345 AACTAGGAACTCGTACCACCCAT
1 AACTAGGAACTCGTACCACCCAT
952368 AACTAGGA
1 AACTAGGA
952376 TATGTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.19
Consensus pattern (23 bp):
AACTAGGAACTCGTACCACCCAT
Found at i:959135 original size:27 final size:27
Alignment explanation
Indices: 959115--959203 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
959105 TATTTTGGTT
*
959115 ATTTTACCATTTGAGGCTATTTCGATA
1 ATTTTACCATTCGAGGCTATTTCGATA
* * * *
959142 ATTTTACCCTTCGAGGGTATTTCAATC
1 ATTTTACCATTCGAGGCTATTTCGATA
* * * *
959169 ATTTTACCCTTC-AGGAGTAATTCGATC
1 ATTTTACCATTCGAGG-CTATTTCGATA
959196 ATTTTACC
1 ATTTTACC
959204 CTTCACGGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.06
27 51 0.94
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (27 bp):
ATTTTACCATTCGAGGCTATTTCGATA
Found at i:959243 original size:54 final size:54
Alignment explanation
Indices: 959135--959253 Score: 161
Period size: 54 Copynumber: 2.2 Consensus size: 54
959125 TTGAGGCTAT
* * * *
959135 TTCGATAATTTTACCCTTCGAGGGTATTTCAATCATTTTACCCTTCAGGAGTAA
1 TTCGATCATTTTACCCTTCGAGGGTAATTCAATCATTTTACCCTCCAAGAGTAA
959189 TTCGATCATTTTACCCTTC-ACGGGTAATTCAATCATTTTACCCTCCAA-AGGTAA
1 TTCGATCATTTTACCCTTCGA-GGGTAATTCAATCATTTTACCCTCCAAGA-GTAA
*
959243 TTCGGTCATTT
1 TTCGATCATTT
959254 AAAAACCTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
53 2 0.03
54 56 0.97
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (54 bp):
TTCGATCATTTTACCCTTCGAGGGTAATTCAATCATTTTACCCTCCAAGAGTAA
Found at i:959251 original size:27 final size:27
Alignment explanation
Indices: 959135--959253 Score: 141
Period size: 27 Copynumber: 4.4 Consensus size: 27
959125 TTGAGGCTAT
* * *
959135 TTCGATAATTTTACCCTTCGAGGGTAT
1 TTCGATCATTTTACCCTTCAAGGGTAA
*
959162 TTCAATCATTTTACCCTTC-AGGAGTAA
1 TTCGATCATTTTACCCTTCAAGG-GTAA
*
959189 TTCGATCATTTTACCCTTCACGGGTAA
1 TTCGATCATTTTACCCTTCAAGGGTAA
* * *
959216 TTCAATCATTTTACCCTCCAAAGGTAA
1 TTCGATCATTTTACCCTTCAAGGGTAA
*
959243 TTCGGTCATTT
1 TTCGATCATTT
959254 AAAAACCTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 3 0.04
27 74 0.94
28 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (27 bp):
TTCGATCATTTTACCCTTCAAGGGTAA
Found at i:960746 original size:25 final size:25
Alignment explanation
Indices: 960709--960762 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
960699 TGAACCTCTG
960709 ACCTCCTTACCACACCTGTGACGCC
1 ACCTCCTTACCACACCTGTGACGCC
* **
960734 ACCTCCTTGCCACACCTGTGTTGCC
1 ACCTCCTTACCACACCTGTGACGCC
960759 ACCT
1 ACCT
960763 TTCCACTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.17, C:0.46, G:0.13, T:0.24
Consensus pattern (25 bp):
ACCTCCTTACCACACCTGTGACGCC
Found at i:960768 original size:22 final size:22
Alignment explanation
Indices: 960713--960768 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 22
960703 CCTCTGACCT
*
960713 CCTTACCACACCTGTGACGCCA
1 CCTTTCCACACCTGTGACGCCA
**
960735 CCTCCTTGCCACACCTGTGTTGCCA
1 CCT--TT-CCACACCTGTGACGCCA
960760 CCTTTCCAC
1 CCTTTCCAC
960769 TACACCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 7 0.25
23 2 0.07
24 1 0.04
25 18 0.64
ACGTcount: A:0.16, C:0.46, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTCCACACCTGTGACGCCA
Found at i:966346 original size:72 final size:72
Alignment explanation
Indices: 966221--966366 Score: 220
Period size: 72 Copynumber: 2.0 Consensus size: 72
966211 GCTCTAATAC
* * *
966221 CACTAAATCTAACACCTCTATCCTGTATCCGTCTCTAAATTACGACTATGGAGCATTACCAGAAG
1 CACTAAATCTAACACCTCTAGCCTGTACCCGTCTCTAAATTACGACTACGGAGCATTACCAGAAG
966286 TTAACAA
66 TTAACAA
* * * * *
966293 CACTAAATGTAACACCTCTAGCCTGTACCCGTCTCTAGATTATGGCTACGGAGCATTACCGGAAG
1 CACTAAATCTAACACCTCTAGCCTGTACCCGTCTCTAAATTACGACTACGGAGCATTACCAGAAG
966358 TTAACAA
66 TTAACAA
966365 CA
1 CA
966367 TACAACAACA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (72 bp):
CACTAAATCTAACACCTCTAGCCTGTACCCGTCTCTAAATTACGACTACGGAGCATTACCAGAAG
TTAACAA
Found at i:970340 original size:187 final size:188
Alignment explanation
Indices: 970014--970388 Score: 743
Period size: 187 Copynumber: 2.0 Consensus size: 188
970004 CAAACATCAC
970014 AAAAAATACATATACATTCATGGTAAAACCCTAAAATTTTAATAGTTTTGCAAATTAGTCCTCGA
1 AAAAAATACATATACATTCATGGTAAAACCCTAAAATTTTAATAGTTTTGCAAATTAGTCCTCGA
970079 GCTAGCTAGATTAAGCTACAACGACTCCAAAAACATAAAAATAATTAAAAACAGAACAAAAATGC
66 GCTAGCTAGATTAAGCTACAACGACTCCAAAAACATAAAAATAATTAAAAACAGAACAAAAATGC
970144 ACTTACATGCATGATGGACTACGGCTGAACCTTGAAAGGTCTTTAATGGCTTCCTTAG
131 ACTTACATGCATGATGGACTACGGCTGAACCTTGAAAGGTCTTTAATGGCTTCCTTAG
970202 AAAAAATACA-ATACATTCATGGTAAAACCCTAAAATTTTAATAGTTTTGCAAATTAGTCCTCGA
1 AAAAAATACATATACATTCATGGTAAAACCCTAAAATTTTAATAGTTTTGCAAATTAGTCCTCGA
970266 GCTAGCTAGATTAAGCTACAACGACTCCAAAAACATAAAAATAATTAAAAACAGAACAAAAATGC
66 GCTAGCTAGATTAAGCTACAACGACTCCAAAAACATAAAAATAATTAAAAACAGAACAAAAATGC
970331 ACTTACATGCATGATGGACTACGGCTGAACCTTGAAAGGTCTTTAATGGCTTCCTTAG
131 ACTTACATGCATGATGGACTACGGCTGAACCTTGAAAGGTCTTTAATGGCTTCCTTAG
970389 GTGAAAATTT
Statistics
Matches: 187, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
187 177 0.95
188 10 0.05
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (188 bp):
AAAAAATACATATACATTCATGGTAAAACCCTAAAATTTTAATAGTTTTGCAAATTAGTCCTCGA
GCTAGCTAGATTAAGCTACAACGACTCCAAAAACATAAAAATAATTAAAAACAGAACAAAAATGC
ACTTACATGCATGATGGACTACGGCTGAACCTTGAAAGGTCTTTAATGGCTTCCTTAG
Found at i:976847 original size:11 final size:11
Alignment explanation
Indices: 976826--976869 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
976816 TTCTCCCCCA
*
976826 TATTTTGTCTC
1 TATTTTCTCTC
*
976837 TTTTTTCTCTC
1 TATTTTCTCTC
*
976848 TATTTTCACT-
1 TATTTTCTCTC
976858 TATTTTCTCTC
1 TATTTTCTCTC
976869 T
1 T
976870 TGTCTAGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.66
Consensus pattern (11 bp):
TATTTTCTCTC
Found at i:979207 original size:17 final size:17
Alignment explanation
Indices: 979155--979207 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
979145 TATGGAAACA
*
979155 TAATCTTTGAGGATATG
1 TAATCTTTGAAGATATG
**
979172 CGATCTTTGATATGATATG
1 TAATCTTTGA-A-GATATG
979191 TAATCTTTGAAGATATG
1 TAATCTTTGAAGATATG
979208 ATTTTTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 14 0.48
18 1 0.03
19 14 0.48
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.42
Consensus pattern (17 bp):
TAATCTTTGAAGATATG
Found at i:985552 original size:29 final size:29
Alignment explanation
Indices: 985510--985567 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
985500 GTATTTTTCT
985510 CCCTTGACCGAATGTCATAGGGACCAAAA
1 CCCTTGACCGAATGTCATAGGGACCAAAA
985539 CCCTTGACCGAATGTCATAGGGACCAAAA
1 CCCTTGACCGAATGTCATAGGGACCAAAA
985568 GAATTATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (29 bp):
CCCTTGACCGAATGTCATAGGGACCAAAA
Found at i:986426 original size:50 final size:50
Alignment explanation
Indices: 986338--986459 Score: 118
Period size: 50 Copynumber: 2.4 Consensus size: 50
986328 ATCTATCGTA
* * * * * * *
986338 GCTTGTCCATAAAATGTTATCAGTGGCAGCATAACTGCATATCAGTGGAG
1 GCTTGTCCACAAAGTGTTATCAGCGACAGCATAACTGCAAATCAATAGAG
* ** * *
986388 GTTTGTCCACAAAGTGTTATCAGCGACAGTTTATCTGCAAATCAATAGTG
1 GCTTGTCCACAAAGTGTTATCAGCGACAGCATAACTGCAAATCAATAGAG
986438 GCTTGTCCACAAATGGTGTTAT
1 GCTTGTCCACAAA--GTGTTAT
986460 GGATGGATGA
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
50 50 0.88
52 7 0.12
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (50 bp):
GCTTGTCCACAAAGTGTTATCAGCGACAGCATAACTGCAAATCAATAGAG
Found at i:990075 original size:17 final size:16
Alignment explanation
Indices: 990029--990062 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
990019 ATTTTATTAA
*
990029 TTTCTCTTTATTTTTG
1 TTTCTCATTATTTTTG
990045 TTTCTCATTATTTTTG
1 TTTCTCATTATTTTTG
990061 TT
1 TT
990063 ATTTTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTCTCATTATTTTTG
Found at i:993408 original size:27 final size:27
Alignment explanation
Indices: 993378--993498 Score: 161
Period size: 27 Copynumber: 4.5 Consensus size: 27
993368 GTAAGGCTCT
993378 TGTAGGGTAAAATGACCGTAATGCCCC
1 TGTAGGGTAAAATGACCGTAATGCCCC
* * *
993405 TGTAGGATAAAATGACCGTAATGCTCG
1 TGTAGGGTAAAATGACCGTAATGCCCC
* * ** **
993432 TGTAGGATAAAATAACTATAATGCTTC
1 TGTAGGGTAAAATGACCGTAATGCCCC
993459 TGTAGGGTAAAATGACCGTAATGCCCC
1 TGTAGGGTAAAATGACCGTAATGCCCC
993486 TGTAGGGTAAAAT
1 TGTAGGGTAAAAT
993499 AACTATTTTA
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (27 bp):
TGTAGGGTAAAATGACCGTAATGCCCC
Found at i:993652 original size:24 final size:24
Alignment explanation
Indices: 993519--993640 Score: 163
Period size: 24 Copynumber: 5.1 Consensus size: 24
993509 CCCATCAGGG
993519 TTAAATGATTGATTTGTCTGTGAT
1 TTAAATGATTGATTTGTCTGTGAT
* * *
993543 GTAAATGATTGATTTGTCCGAGAT
1 TTAAATGATTGATTTGTCTGTGAT
* *
993567 GTAAATGATTGATTTGTCTATGAT
1 TTAAATGATTGATTTGTCTGTGAT
* * *
993591 TTAAATGACTGATTTGCCTGTAAT
1 TTAAATGATTGATTTGTCTGTGAT
*
993615 TTAAATGGTTGATTTGTCTGTGAT
1 TTAAATGATTGATTTGTCTGTGAT
993639 TT
1 TT
993641 GTATGACTGA
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 83 1.00
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.46
Consensus pattern (24 bp):
TTAAATGATTGATTTGTCTGTGAT
Found at i:993757 original size:27 final size:27
Alignment explanation
Indices: 993720--993780 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
993710 AGGAAGTAGT
993720 TTTCTGGTGGCTCT-GCCACA-ATCACTG
1 TTTCTGGTGGCT-TGGCCACATAT-ACTG
993747 TTTCTGGTGGCTTGGCCACATATACTG
1 TTTCTGGTGGCTTGGCCACATATACTG
*
993774 TTGCTGG
1 TTTCTGG
993781 CAGTTTTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 1 0.03
27 28 0.90
28 2 0.06
ACGTcount: A:0.13, C:0.25, G:0.26, T:0.36
Consensus pattern (27 bp):
TTTCTGGTGGCTTGGCCACATATACTG
Found at i:993850 original size:32 final size:32
Alignment explanation
Indices: 993814--993955 Score: 149
Period size: 32 Copynumber: 4.4 Consensus size: 32
993804 TGGCTTTTTA
* *
993814 CCGATCATATTACCATTACCGATGGCTGTGTG
1 CCGATCATATTACTATTACTGATGGCTGTGTG
* *
993846 CCGATCATATTACTACTACTGATGGCTTTGTG
1 CCGATCATATTACTATTACTGATGGCTGTGTG
* * * *
993878 CTGATCATACTACTATTACTGATCGATGTGTG
1 CCGATCATATTACTATTACTGATGGCTGTGTG
* * * * * *
993910 TCGATCATATTACTACTATTGGTGGCTTTCTG
1 CCGATCATATTACTATTACTGATGGCTGTGTG
*
993942 CCAATCATATTACT
1 CCGATCATATTACT
993956 GTACTTATGG
Statistics
Matches: 88, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 88 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (32 bp):
CCGATCATATTACTATTACTGATGGCTGTGTG
Found at i:993949 original size:64 final size:64
Alignment explanation
Indices: 993797--993955 Score: 201
Period size: 64 Copynumber: 2.5 Consensus size: 64
993787 TGCAGTGATG
* * * * *
993797 CTATTGATGGCTTTTTACCGATCATATTACCATTACCGATGGCTGTGTGCCGATCATATTACTA
1 CTATTGATGGCTTTCTGCCGATCATATTACTATTACCGATCGATGTGTGCCGATCATATTACTA
* * * * * *
993861 CTACTGATGGCTTTGTGCTGATCATACTACTATTACTGATCGATGTGTGTCGATCATATTACTA
1 CTATTGATGGCTTTCTGCCGATCATATTACTATTACCGATCGATGTGTGCCGATCATATTACTA
* *
993925 CTATTGGTGGCTTTCTGCCAATCATATTACT
1 CTATTGATGGCTTTCTGCCGATCATATTACT
993956 GTACTTATGG
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 79 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.39
Consensus pattern (64 bp):
CTATTGATGGCTTTCTGCCGATCATATTACTATTACCGATCGATGTGTGCCGATCATATTACTA
Found at i:995132 original size:40 final size:40
Alignment explanation
Indices: 995076--995452 Score: 420
Period size: 40 Copynumber: 9.4 Consensus size: 40
995066 ATTATTGCTA
* * *
995076 AATGCACAAACATGCCCATGTTTGTACTTCGATACCCCTG
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTG
* * *
995116 AATACACATACGTGCCCCTATTTGTACTTTGATACCCCTG
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTG
* *
995156 AATGCACATACGTGCCCTTGTTTGTACTT-TAGTACCCCTG
1 AATGCACATACGTGCCCCTGTTTGTACTTCGA-TACCCCTG
* * *
995196 AATGCACATATGTGCCCCTATTTGTACTTC-AGTACCTCTG
1 AATGCACATACGTGCCCCTGTTTGTACTTCGA-TACCCCTG
* * *
995236 AATGCACATACGTGCCCCTGTTTGTAATTCGGTAACCCTG
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTG
* * *
995276 AATACACATACGTACCCCTGTTTGTACTTC-AGTACCCTTG
1 AATGCACATACGTGCCCCTGTTTGTACTTCGA-TACCCCTG
* * * * * *
995316 AATGGACATACGTGACCTTATTTGTACTTCGGTACCACTG
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTG
* * * * * *
995356 AATGCACATATGTTCCCCTATTTGTAGTTTGGTACCCCTG
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTG
*
995396 AATGCACATACGTGCCCCTGTTTGTACTTCGACACCCCTG
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTG
995436 AACT-CACATACGTGCCC
1 AA-TGCACATACGTGCCC
995453 TATTTATACT
Statistics
Matches: 281, Mismatches: 50, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.00
40 279 0.99
41 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (40 bp):
AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTG
Found at i:995275 original size:120 final size:118
Alignment explanation
Indices: 995076--995463 Score: 465
Period size: 120 Copynumber: 3.2 Consensus size: 118
995066 ATTATTGCTA
* * * * *
995076 AATGCACAAACATGCCCATGTTTGTACTTCGATACCCCTGAATACACATACGTGCCCCTATTTGT
1 AATGCACATACGTGCCC-TATTTGTACTTCG-TACCACTGAATGCACATACGTGCCCCTATTTGT
* * *
995141 ACTTTGATACCCCTGAATGCACATACGTGCCCTTGTTTGTACTTTAGTACCCCTG
64 AATTTGGTACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTTAGTACCCCTG
* * *
995196 AATGCACATATGTGCCCCTATTTGTACTTCAGTACCTCTGAATGCACATACGTGCCCCTGTTTGT
1 AATGCACATACGTG-CCCTATTTGTACTTC-GTACCACTGAATGCACATACGTGCCCCTATTTGT
* * * * * *
995261 AATTCGGTAACCCTGAATACACATACGTACCCCTGTTTGTACTTCAGTACCCTTG
64 AATTTGGTACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTTAGTACCCCTG
* * * *
995316 AATGGACATACGTGACCTTATTTGTACTTCGGTACCACTGAATGCACATATGTTCCCCTATTTGT
1 AATGCACATACGTG-CCCTATTTGTACTTC-GTACCACTGAATGCACATACGTGCCCCTATTTGT
* * *
995381 AGTTTGGTACCCCTGAATGCACATACGTGCCCCTGTTTGTAC-TTCGACACCCCTG
64 AATTTGGTACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTTAG-TACCCCTG
*
995436 AACT-CACATACGTGCCCTATTTATACTT
1 AA-TGCACATACGTGCCCTATTTGTACTT
995464 TTGTAACCCT
Statistics
Matches: 227, Mismatches: 37, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
119 14 0.06
120 208 0.92
121 5 0.02
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.32
Consensus pattern (118 bp):
AATGCACATACGTGCCCTATTTGTACTTCGTACCACTGAATGCACATACGTGCCCCTATTTGTAA
TTTGGTACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTTAGTACCCCTG
Found at i:996544 original size:27 final size:27
Alignment explanation
Indices: 996514--996804 Score: 149
Period size: 27 Copynumber: 10.9 Consensus size: 27
996504 TCAACTCCTA
* *
996514 GGGGTATAACGGTCATTTTACCCTTCG
1 GGGGTATTACGGTAATTTTACCCTTCG
***
996541 GGGGTATTTTAGTAATTTTACCCTTCG
1 GGGGTATTACGGTAATTTTACCCTTCG
* * * *
996568 AGGGTATTTCGATAATTTTACCCTTTG
1 GGGGTATTACGGTAATTTTACCCTTCG
*
996595 GGGGTATTTA-TGTAATTTTACCCTTCG
1 GGGGTA-TTACGGTAATTTTACCCTTCG
* ** * * * **
996622 AGGGTATTTTGATAA-TTTAACTTTTA
1 GGGGTATTACGGTAATTTTACCCTTCG
* * * *
996648 GGGGTATTTCAGTAATTTTACACTTTG
1 GGGGTATTACGGTAATTTTACCCTTCG
* * * *
996675 AGGGTATTTCGATAATTTTACCCTTTG
1 GGGGTATTACGGTAATTTTACCCTTCG
* * ** *
996702 AGGTTAATT-CAATAATTTTACCTTTCG
1 GGGGT-ATTACGGTAATTTTACCCTTCG
* * **
996729 AGGGTATTTCAATAATTTTACCCTTCG
1 GGGGTATTACGGTAATTTTACCCTTCG
* ***
996756 AGGGTATT-TTATAATTTTACCCTTCG
1 GGGGTATTACGGTAATTTTACCCTTCG
* ** *
996782 AGGGTATTTTGATAATTTTACCC
1 GGGGTATTACGGTAATTTTACCC
996805 ACGATACGCA
Statistics
Matches: 214, Mismatches: 44, Indels: 12
0.79 0.16 0.04
Matches are distributed among these distances:
26 47 0.22
27 162 0.76
28 5 0.02
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (27 bp):
GGGGTATTACGGTAATTTTACCCTTCG
Found at i:996598 original size:54 final size:54
Alignment explanation
Indices: 996528--996804 Score: 362
Period size: 54 Copynumber: 5.2 Consensus size: 54
996518 TATAACGGTC
*
996528 ATTTTACCCTTCGGGGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTTGGGGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATA
*
996582 ATTTTACCCTTTGGGGGTA-TTTATGTAATTTTACCCTTCGAGGGTATTTTGATA
1 ATTTTACCCTTTGGGGGTATTTTA-GTAATTTTACCCTTCGAGGGTATTTCGATA
* * * * * *
996636 A-TTTAACTTTTAGGGGTATTTCAGTAATTTTACACTTTGAGGGTATTTCGATA
1 ATTTTACCCTTTGGGGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATA
* * * * * * *
996689 ATTTTACCCTTTGAGGTTAATTCAATAATTTTACCTTTCGAGGGTATTTCAATA
1 ATTTTACCCTTTGGGGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATA
* * *
996743 ATTTTACCCTTCGAGGGTATTTTA-TAATTTTACCCTTCGAGGGTATTTTGATA
1 ATTTTACCCTTTGGGGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATA
996796 ATTTTACCC
1 ATTTTACCC
996805 ACGATACGCA
Statistics
Matches: 193, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
53 81 0.42
54 112 0.58
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.45
Consensus pattern (54 bp):
ATTTTACCCTTTGGGGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATA
Found at i:996729 original size:107 final size:107
Alignment explanation
Indices: 996541--996804 Score: 361
Period size: 107 Copynumber: 2.5 Consensus size: 107
996531 TTACCCTTCG
* *
996541 GGGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTTGGGGGTATTTAT
1 GGGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTTGAGGGTATTCAT
* ** **
996606 GTAATTTTACCCTTCGAGGGTATTTTGATAATTTAACTTTTA
66 ATAATTTTACCCTTCGAGGGTATTTCAATAATTTAACCCTTA
* * * *
996648 GGGGTATTTCAGTAATTTTACACTTTGAGGGTATTTCGATAATTTTACCCTTTGAGGTTAATTCA
1 GGGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTTGAGGGT-ATTCA
* * *
996713 -ATAATTTTACCTTTCGAGGGTATTTCAATAATTTTACCCTTC
65 TATAATTTTACCCTTCGAGGGTATTTCAATAATTTAACCCTTA
*
996755 GAGGGTATTTTA-TAATTTTACCCTTCGAGGGTATTTTGATAATTTTACCC
1 G-GGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCC
996805 ACGATACGCA
Statistics
Matches: 137, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
107 124 0.91
108 13 0.09
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.45
Consensus pattern (107 bp):
GGGGTATTTTAGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTTGAGGGTATTCAT
ATAATTTTACCCTTCGAGGGTATTTCAATAATTTAACCCTTA
Found at i:997755 original size:17 final size:18
Alignment explanation
Indices: 997720--997761 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
997710 AATCAGCAAC
997720 AAGAGAAGAAAAAATAGAA
1 AAGA-AAGAAAAAATAGAA
*
997739 AAGAAAGAAGAAA-AGAA
1 AAGAAAGAAAAAATAGAA
997756 AAGAAA
1 AAGAAA
997762 AGATGAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 8 0.36
19 4 0.18
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
AAGAAAGAAAAAATAGAA
Found at i:999153 original size:41 final size:42
Alignment explanation
Indices: 999096--999184 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
999086 ACAGCCTAGC
* *
999096 ACACGGCCTAGCACAC-GACATGTG-GTGCTACTCAGTGAGTT
1 ACACGGCCTAGCACACGGACATATGAG-GCTACTCAGTAAGTT
*
999137 ACACGGCCT-GACACACGGGCATATGAGGCTACTCAGTAAGTT
1 ACACGGCCTAG-CACACGGACATATGAGGCTACTCAGTAAGTT
999179 ACACGG
1 ACACGG
999185 GTGAGGACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
40 1 0.02
41 14 0.33
42 26 0.62
43 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (42 bp):
ACACGGCCTAGCACACGGACATATGAGGCTACTCAGTAAGTT
Found at i:999837 original size:17 final size:17
Alignment explanation
Indices: 999816--999852 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
999806 CAGCACTTCT
*
999816 TTTTTATTCTTCTTTTTA
1 TTTTTATT-TTCTTTATA
999834 TTTTTATTTTCTTTATA
1 TTTTTATTTTCTTTATA
999851 TT
1 TT
999853 ATATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTCTTTATA
Found at i:1006844 original size:22 final size:22
Alignment explanation
Indices: 1006819--1006863 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1006809 AAATTATTAA
* *
1006819 TATATTAAATTTTCATTAATTT
1 TATAATAAATTTTCATAAATTT
*
1006841 TATAATAATTTTTCATAAATTT
1 TATAATAAATTTTCATAAATTT
1006863 T
1 T
1006864 GATTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TATAATAAATTTTCATAAATTT
Found at i:1009564 original size:48 final size:48
Alignment explanation
Indices: 1009488--1009622 Score: 173
Period size: 48 Copynumber: 2.8 Consensus size: 48
1009478 ATGTTCTATC
* * * *
1009488 ATGACACAAGAGTGGCAC-AGACTGTGTGCAGGCCACCGATATTCTGTT
1 ATGATACAAGGGTGGCACGA-ACTGTGTGCAGGCCACCGATATTATATT
* *
1009536 ATGATACAAGGGTGGCACGAACTGTGTGCAAGCCACTGATATTATATT
1 ATGATACAAGGGTGGCACGAACTGTGTGCAGGCCACCGATATTATATT
* * *
1009584 ATGATATAAGGGTGGCACGGACTATGTGCAGGCCACCGA
1 ATGATACAAGGGTGGCACGAACTGTGTGCAGGCCACCGA
1009623 AAATCTGCTA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
48 74 0.99
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (48 bp):
ATGATACAAGGGTGGCACGAACTGTGTGCAGGCCACCGATATTATATT
Found at i:1009646 original size:48 final size:48
Alignment explanation
Indices: 1009488--1009677 Score: 157
Period size: 48 Copynumber: 3.9 Consensus size: 48
1009478 ATGTTCTATC
* * *
1009488 ATGACAC-AAGAGTGGCACAGACTGTGTGCAGGCCACCGATATTCTGTT
1 ATGACACAAAG-GTGGCACGGACTGTGTGCAGGCCACCGAAAATCTGTT
* * * * * * * * *
1009536 ATGATACAAGGGTGGCACGAACTGTGTGCAAGCCACTGATATTATATT
1 ATGACACAAAGGTGGCACGGACTGTGTGCAGGCCACCGAAAATCTGTT
* * * * *
1009584 ATGATATAAGGGTGGCACGGACTATGTGCAGGCCACCGAAAATCTGCT
1 ATGACACAAAGGTGGCACGGACTGTGTGCAGGCCACCGAAAATCTGTT
* * * * *
1009632 ATTACACAAAGGTGGTATGGACTGTGTGCAGACCATCGAGAAATCT
1 ATGACACAAAGGTGGCACGGACTGTGTGCAGGCCACCGA-AAATCT
1009678 ATTTTTATTC
Statistics
Matches: 113, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
48 105 0.93
49 8 0.07
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (48 bp):
ATGACACAAAGGTGGCACGGACTGTGTGCAGGCCACCGAAAATCTGTT
Found at i:1010825 original size:43 final size:43
Alignment explanation
Indices: 1010752--1010954 Score: 262
Period size: 43 Copynumber: 4.7 Consensus size: 43
1010742 TAAAAGTGCT
* * * *
1010752 GCTATAGATCAGGACCTTTAGCAGCGCTTTTCCCACAAATGCC
1 GCTATAGATCATGACCTTTAGCGGCACTTTTCCCACAAACGCC
* * * *
1010795 GTTATAAATTATGACCTTTAGCGGCACTTTTACCACAAACGCC
1 GCTATAGATCATGACCTTTAGCGGCACTTTTCCCACAAACGCC
*
1010838 GCTATTGATCATGACCTTTAGCGGCACTTTTCCCACAAACGCC
1 GCTATAGATCATGACCTTTAGCGGCACTTTTCCCACAAACGCC
** **
1010881 GCTATAGATCATGACCTTTAGCGGTGCTTTTCCCACAAAATCC
1 GCTATAGATCATGACCTTTAGCGGCACTTTTCCCACAAACGCC
* * *
1010924 GCTATAGGTAATGACCTTTAGCGGCATTTTT
1 GCTATAGATCATGACCTTTAGCGGCACTTTT
1010955 AAAAAATGCC
Statistics
Matches: 137, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 137 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (43 bp):
GCTATAGATCATGACCTTTAGCGGCACTTTTCCCACAAACGCC
Found at i:1011375 original size:21 final size:21
Alignment explanation
Indices: 1011351--1011396 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1011341 TTGAACCTCA
*
1011351 GCTTCTCTCGCTGCTGCATCT
1 GCTTCCCTCGCTGCTGCATCT
*
1011372 GCTTCCCTCGTTGCTGCATCT
1 GCTTCCCTCGCTGCTGCATCT
1011393 GCTT
1 GCTT
1011397 TAAGTTGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.37, G:0.20, T:0.39
Consensus pattern (21 bp):
GCTTCCCTCGCTGCTGCATCT
Found at i:1019148 original size:16 final size:16
Alignment explanation
Indices: 1019125--1019180 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
1019115 CGTTTGGTTC
1019125 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* **
1019141 GTTGTAATTAAATAGA
1 GCTGTAATGGAATAGA
1019157 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
1019173 ACTGTAAT
1 GCTGTAAT
1019181 AGTAATTCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.30
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:1019213 original size:45 final size:43
Alignment explanation
Indices: 1019162--1019254 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 43
1019152 ATAGAGCTGT
1019162 AATGGAATAGAACTGTAATAGTAATTCAATTG-TTTCGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-ATTC--TTGCTTTCGTTGAATGG
*
1019207 AATGGAATAGAACTGTAATAGTATTCTTGTCTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCTTG-CTTTCGTTGAATGG
1019251 AATG
1 AATG
1019255 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
42 3 0.07
44 20 0.44
45 22 0.49
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (43 bp):
AATGGAATAGAACTGTAATAGTATTCTTGCTTTCGTTGAATGG
Found at i:1019460 original size:24 final size:21
Alignment explanation
Indices: 1019410--1019451 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
1019400 CATAATTATT
1019410 ATTAA-ATATAATTTAATAAA
1 ATTAATATATAATTTAATAAA
1019430 A-T-ATATATAATTTAATAAA
1 ATTAATATATAATTTAATAAA
1019449 ATT
1 ATT
1019452 CTTAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.05
19 17 0.85
20 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAATATATAATTTAATAAA
Found at i:1019462 original size:57 final size:56
Alignment explanation
Indices: 1019363--1019496 Score: 139
Period size: 56 Copynumber: 2.4 Consensus size: 56
1019353 TAATAAGATT
* * *
1019363 ATTT-ATACAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATAT-A
1 ATTTAATA-AAATAATATATAATTTAATAAAATTTTAACATAATTATTATT--ATATGA
* *
1019420 ATTTAATAAAAT-ATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGA
1 ATTTAATAAAATAATATATAATTTAATAAAATT-TTAACATAATTATTATTATATGA
* *
1019476 ATTTACTAAAATCATAATATA
1 ATTTAATAAAATAAT-ATATA
1019497 TAATAATATA
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
55 4 0.06
56 29 0.44
57 25 0.38
58 8 0.12
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (56 bp):
ATTTAATAAAATAATATATAATTTAATAAAATTTTAACATAATTATTATTATATGA
Found at i:1020872 original size:54 final size:54
Alignment explanation
Indices: 1020810--1020917 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
1020800 GAGGGGGCGA
*
1020810 CATCCATTCTTAAAGCCATGTAACGAAGCTTGCAAGGAAACAAATAGAAGATGG
1 CATCCATTCTTAAAGCCATGTAACAAAGCTTGCAAGGAAACAAATAGAAGATGG
*
1020864 CATCCATTCTTAAAGCCATGTAACAAATCTTGCAAGGAAACAAATAGAAGATGG
1 CATCCATTCTTAAAGCCATGTAACAAAGCTTGCAAGGAAACAAATAGAAGATGG
1020918 GAGCTTAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (54 bp):
CATCCATTCTTAAAGCCATGTAACAAAGCTTGCAAGGAAACAAATAGAAGATGG
Found at i:1027497 original size:64 final size:64
Alignment explanation
Indices: 1027418--1027557 Score: 253
Period size: 64 Copynumber: 2.2 Consensus size: 64
1027408 AAGTCGTACG
1027418 TTGACAAATTCACAGCAAAATTATAACACCATTGAGAAGGAGCTATTAGCTGTGGTATTTGCCT
1 TTGACAAATTCACAGCAAAATTATAACACCATTGAGAAGGAGCTATTAGCTGTGGTATTTGCCT
* * *
1027482 TTGACAAATTCACAGCTAAATTATACCACCATTGAGAAGGAGCTATTGGCTGTGGTATTTGCCT
1 TTGACAAATTCACAGCAAAATTATAACACCATTGAGAAGGAGCTATTAGCTGTGGTATTTGCCT
1027546 TTGACAAATTCA
1 TTGACAAATTCA
1027558 GAGTTTATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 73 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (64 bp):
TTGACAAATTCACAGCAAAATTATAACACCATTGAGAAGGAGCTATTAGCTGTGGTATTTGCCT
Found at i:1032203 original size:50 final size:50
Alignment explanation
Indices: 1032122--1032223 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 50
1032112 GAAATTCTAA
* *
1032122 ATGCATTAAAAGAACCCTACTACAAACTTACTTGCATTGCTATTGAAGTT
1 ATGCATTAAAAGAACCCTACTACAAACTTACTTGCATTGCTACTAAAGTT
* *
1032172 ATGCATTAAAAGAACCCTACTACAGATTTACTTGCATTGCTACTAAAGTT
1 ATGCATTAAAAGAACCCTACTACAAACTTACTTGCATTGCTACTAAAGTT
1032222 AT
1 AT
1032224 TCTACTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (50 bp):
ATGCATTAAAAGAACCCTACTACAAACTTACTTGCATTGCTACTAAAGTT
Found at i:1041254 original size:20 final size:20
Alignment explanation
Indices: 1041229--1041375 Score: 61
Period size: 20 Copynumber: 7.2 Consensus size: 20
1041219 CACATACGTG
1041229 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
* * *
1041249 CCCCTGATTGCACATATC--TG
1 CCCCTGTTTGTAC-T-TCGGTA
*
1041269 CCCCTGTTTGTATTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
** * * **
1041289 CCTTTGAATTGCACAGAC-GTA
1 CCCCTG-TTTGTAC-TTCGGTA
** *
1041310 CCTGTGTTTGTACTTCAGTA
1 CCCCTGTTTGTACTTCGGTA
* *
1041330 CCCCTGAATTT-TACAT-GCGTG
1 CCCCTG--TTTGTACTTCG-GTA
1041351 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
1041371 CCCCT
1 CCCCT
1041376 AGATATACTT
Statistics
Matches: 89, Mismatches: 26, Indels: 24
0.64 0.19 0.17
Matches are distributed among these distances:
18 2 0.02
19 5 0.06
20 50 0.56
21 26 0.29
22 6 0.07
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:1041338 original size:41 final size:41
Alignment explanation
Indices: 1041216--1041375 Score: 182
Period size: 41 Copynumber: 3.9 Consensus size: 41
1041206 TAATGATAAG
*
1041216 TTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTG-A
1 TTGCACAGACGTGCCCCTGTTTGTACTTCGGTACCCCTGAA
* * **
1041256 TTGCACATATC-TGCCCCTGTTTGTATTTCGGTACCTTTGAA
1 TTGCACAGA-CGTGCCCCTGTTTGTACTTCGGTACCCCTGAA
* ** *
1041297 TTGCACAGACGTACCTGTGTTTGTACTTCAGTACCCCTGAA
1 TTGCACAGACGTGCCCCTGTTTGTACTTCGGTACCCCTGAA
**
1041338 TTTTACATG-CGTGCCCCTGTTTGTACTTCGGTACCCCT
1 TTGCACA-GACGTGCCCCTGTTTGTACTTCGGTACCCCT
1041376 AGATATACTT
Statistics
Matches: 99, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
40 35 0.35
41 63 0.64
42 1 0.01
ACGTcount: A:0.16, C:0.29, G:0.19, T:0.36
Consensus pattern (41 bp):
TTGCACAGACGTGCCCCTGTTTGTACTTCGGTACCCCTGAA
Found at i:1048617 original size:41 final size:41
Alignment explanation
Indices: 1048558--1048803 Score: 219
Period size: 41 Copynumber: 6.0 Consensus size: 41
1048548 AGAATAATGA
* * * *
1048558 TGAATTGCACATACGTGCCCCTGTTTATATTTCGATACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * *
1048599 TGAATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * * *
1048640 TGAGTTGCACATACATGCCCTTCTTTGTACTTCGGT-CCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * * * * *
1048680 TAAATTTCATAGATGTGCCCCTATTTGTACTTTGGTACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * * * * *
1048721 TAAATTACACATACATGCCCATATTTGTACTTCGATACCCT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * *
1048762 TGAATTGCACAGACATGCCCC-AGTTTCTACTTAC-GTACCCC
1 TGAATTGCACATACGTGCCCCTA-TTTGTACTT-CGGTACCCC
1048803 T
1 T
1048804 AGATGTACTT
Statistics
Matches: 165, Mismatches: 37, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
40 30 0.18
41 134 0.81
42 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.35
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
Found at i:1052349 original size:33 final size:33
Alignment explanation
Indices: 1052307--1052372 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1052297 CTTGAATAAG
1052307 GGACGACATGCATGAATATGAATTGATTATGCT
1 GGACGACATGCATGAATATGAATTGATTATGCT
1052340 GGACGACATGCATGAATATGAATTGATTATGCT
1 GGACGACATGCATGAATATGAATTGATTATGCT
1052373 ATGTTTAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (33 bp):
GGACGACATGCATGAATATGAATTGATTATGCT
Found at i:1052515 original size:17 final size:15
Alignment explanation
Indices: 1052475--1052514 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1052465 GGGTGTTACA
*
1052475 GTGTGACTCAACTGT
1 GTGTGACACAACTGT
1052490 GTGTGACACAACTGT
1 GTGTGACACAACTGT
1052505 GTGTGACACA
1 GTGTGACACA
1052515 CGGCCAGGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (15 bp):
GTGTGACACAACTGT
Found at i:1055668 original size:12 final size:13
Alignment explanation
Indices: 1055651--1055679 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1055641 CTCATACATG
1055651 AATAAATAAA-GC
1 AATAAATAAATGC
1055663 AATAAATAAATGC
1 AATAAATAAATGC
1055676 AATA
1 AATA
1055680 GCTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:1060556 original size:99 final size:99
Alignment explanation
Indices: 1060443--1060641 Score: 335
Period size: 99 Copynumber: 2.0 Consensus size: 99
1060433 CATATATGTT
*
1060443 TTATCTTTAAACAAGAATCATTACTCCAAACAGAAAGTCATTTTGATGATGTTGCTATTATATCT
1 TTATCTTTAAACAAGAATCATTACTCCAAACAGAAAGTCATTTTGACGATGTTGCTATTATATCT
* * * *
1060508 TGTGGTTGGGGCTGCGTTAAAGAATGTTTTTGAC
66 TGTGGTTAGCGCTACATTAAAGAATGTTTTTGAC
* *
1060542 TTATCTTTAAACAAGAATCATTGCTCCATACAGAAAGTCATTTTGACGATGTTGCTATTATATCT
1 TTATCTTTAAACAAGAATCATTACTCCAAACAGAAAGTCATTTTGACGATGTTGCTATTATATCT
1060607 TGTGGTTAGCGCTACATTAAAGAATGTTTTTGAC
66 TGTGGTTAGCGCTACATTAAAGAATGTTTTTGAC
1060641 T
1 T
1060642 GGGCAGCACC
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 93 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (99 bp):
TTATCTTTAAACAAGAATCATTACTCCAAACAGAAAGTCATTTTGACGATGTTGCTATTATATCT
TGTGGTTAGCGCTACATTAAAGAATGTTTTTGAC
Found at i:1074939 original size:20 final size:19
Alignment explanation
Indices: 1074877--1074939 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
1074867 ATATTATTAA
1074877 ATTAATTTTAAAAT-AATT
1 ATTAATTTTAAAATAAATT
* *
1074895 ATTTATTAATTAAAA-AATTTT
1 ATTAATT--TTAAAATAA-ATT
1074916 ATTAATTTTAAAATAGAATT
1 ATTAATTTTAAAATA-AATT
1074936 ATTA
1 ATTA
1074940 GTTAAATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 6 0.17
19 6 0.17
20 14 0.40
21 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTAATTTTAAAATAAATT
Found at i:1082540 original size:17 final size:17
Alignment explanation
Indices: 1082520--1082552 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1082510 TAACATTCTT
1082520 TTTATGTTTAAGTTTAA
1 TTTATGTTTAAGTTTAA
*
1082537 TTTATTTTTAAGTTTA
1 TTTATGTTTAAGTTTA
1082553 TTATCAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (17 bp):
TTTATGTTTAAGTTTAA
Found at i:1083025 original size:14 final size:15
Alignment explanation
Indices: 1083005--1083040 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1082995 TTTACATGTA
1083005 ATTTTAAA-TGATTT
1 ATTTTAAATTGATTT
*
1083019 TTTTTAAATTGATTT
1 ATTTTAAATTGATTT
1083034 ATTTTAA
1 ATTTTAA
1083041 TTCGTTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTTTAAATTGATTT
Found at i:1087875 original size:23 final size:22
Alignment explanation
Indices: 1087851--1087893 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
1087841 ATGAGTATAT
1087851 ATATATATTATAAAAAA-ATGC
1 ATATATATTATAAAAAATATGC
1087872 ATATATATTATAAAAAATATGC
1 ATATATATTATAAAAAATATGC
1087894 GTGTGTATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (22 bp):
ATATATATTATAAAAAATATGC
Found at i:1087913 original size:3 final size:3
Alignment explanation
Indices: 1087905--1087975 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
1087895 TGTGTATAGA
*
1087905 AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAAT ATAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT AAT AAT
* * * *
1087952 GAT -GT AAT AAC AAT ATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1087976 TAAAAAAACA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 1 0.02
3 49 0.88
4 6 0.11
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1089776 original size:45 final size:45
Alignment explanation
Indices: 1089725--1090166 Score: 598
Period size: 45 Copynumber: 9.8 Consensus size: 45
1089715 TGCTATCCTC
* * *
1089725 GATCTACTTCGATACCAATATAGGAAGATAAGATCTGTTATATTT
1 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTT
* * * * * *
1089770 GATCTACTTCACTGCCAATACAGGAAAACAAGATATGTTATCTTC
1 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTT
* *
1089815 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGGTATTTTT
1 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTT
* * *
1089860 GATCTACTTCGCTACTAGTATAGGAAGACAAGATCTGTTATCTTC
1 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTT
*
1089905 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTT
1 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTT
* * * *
1089950 GATCTACTTCGCT-GCAGATACAGGAAGAAAAGATCTGTTATCTTC
1 GATCTACTTCGCTACCA-ATATAGGAAGACAAGATCTGTTATCTTT
* *
1089995 GATCTACTTTGCTACCAATATAGGAAGACAAGATCTGCTATCTTT
1 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTT
* * * * *
1090040 GATCTACTTCACTGCCAATATAGGAAGAAAAGAACTGTTATCTTC
1 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTT
*
1090085 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTT
1 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTT
* * *
1090130 GATCTACTTTGTTGCCAATATAGGAAGACAAGATCTG
1 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTG
1090167 CTGTTTTCAA
Statistics
Matches: 342, Mismatches: 53, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
44 2 0.01
45 338 0.99
46 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (45 bp):
GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTT
Found at i:1112433 original size:42 final size:44
Alignment explanation
Indices: 1112273--1112433 Score: 141
Period size: 44 Copynumber: 3.6 Consensus size: 44
1112263 TCCTATACCA
** *
1112273 CTGAAGTTGCAGTGGAATAGATTGAA-AAAGATGACAAATATTATCTTC
1 CTGAAGTTGCAGTGGAATAGATTGAAGCCA-AT----AATCTTATCTTC
*
1112321 CTGAAGTTGCAGTGGAATAGATTAAAGCCAATAATCTTATC-TC
1 CTGAAGTTGCAGTGGAATAGATTGAAGCCAATAATCTTATCTTC
*** * * *
1112364 CATGAAGTTGCAGTGGAGCGGATTGAAG-TAA-AGTTTTATCTTC
1 C-TGAAGTTGCAGTGGAATAGATTGAAGCCAATAATCTTATCTTC
*
1112407 CTGAAGTTGCAGTGGAATAGACTGAAG
1 CTGAAGTTGCAGTGGAATAGATTGAAG
1112434 ATAGCAAATG
Statistics
Matches: 95, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
42 29 0.31
43 8 0.08
44 30 0.32
48 27 0.28
49 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAATAGATTGAAGCCAATAATCTTATCTTC
Found at i:1112614 original size:44 final size:42
Alignment explanation
Indices: 1112492--1112645 Score: 134
Period size: 44 Copynumber: 3.6 Consensus size: 42
1112482 TAAATTGCAG
* * *
1112492 ATCTTATCTCTCTTAAGTTGCAGTAGAGCAGAT-CA-TAGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATGAAGTAGC-A
* * * *
1112533 ACCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAAGTTA-CA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGC-AGATGAAG-TAGCA
*
1112576 AGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGATAGCGA
1 A-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TGAAG-TAGC-A
* *
1112622 ATCTTATTTCTCTGAAGTTGCAGT
1 ATCTTATCTCCCTGAAGTTGCAGT
1112646 GGAACTGATT
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
41 24 0.27
42 3 0.03
43 5 0.06
44 32 0.36
45 23 0.26
46 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (42 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATGAAGTAGCA
Found at i:1112658 original size:89 final size:85
Alignment explanation
Indices: 1112493--1112740 Score: 210
Period size: 89 Copynumber: 2.8 Consensus size: 85
1112483 AAATTGCAGA
* * *
1112493 TCTTATCTCTCTTAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTGAAGTTGTAGTG
1 TCTTATCTCCCTAAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTG
*
1112558 GAGCAAGTTGAAGTTACAAG
66 GAACAAGTTGAAGTTACAAG
* * * * *
1112578 TCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATTTCTCTGAAGTTGC
1 TCTTATCTCCCTAAAGTTGCAGTAGAGCAGA-T---CATAGCAAACCTTATCTCCCTGAAGTTGC
* *
1112643 AGTGGAAC-TGATTGAAGCTATAAATTATAG
62 AGTGGAACAAG-TTGAAG-T-T--A-CA-AG
** * * * * * *
1112673 ATCTTATCTCTTTAAAGTTGTAGTAGAGTAGATCATATCAAACCTTATCTCCATAAAGTTGTAGT
1 -TCTTATCTCCCTAAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGT
1112738 GGA
65 GGA
1112741 GCAGATTGAA
Statistics
Matches: 127, Mismatches: 24, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
85 29 0.23
86 1 0.01
88 1 0.01
89 36 0.28
90 1 0.01
91 1 0.01
92 26 0.20
93 1 0.01
94 1 0.01
95 3 0.02
96 27 0.21
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (85 bp):
TCTTATCTCCCTAAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTG
GAACAAGTTGAAGTTACAAG
Found at i:1112664 original size:181 final size:181
Alignment explanation
Indices: 1112356--1112781 Score: 524
Period size: 181 Copynumber: 2.4 Consensus size: 181
1112346 AGCCAATAAT
* * * *
1112356 CTTATCTCCATGAAGTTGCAGTGGAGCGGATTGAAG-TA-AAGTTTTATCTTCCTGAAGTTGCAG
1 CTTATCTCCATGAAGTTGTAGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAG
* * * *
1112419 TGGAATAGACTGAAGATAGCAAATGTCATTCCCCTGAAGTGGCAGCGGAACAGGTTAGAGCTATA
66 TAGAACAGACTGAAGATAGCAAATCTCATTCCCCTGAAGTGGCAGCGGAACAGATTAGAGCTATA
*
1112484 AATTGCAGATCTTATCTCTCTT-AAGTTGCAGTAGAGCAGATCATAGCAAAC
131 AATTACAGATCTTATCTCT-TTAAAGTTGCAGTAGAGCAGATCATAGCAAAC
* *
1112535 CTTATCTCCCTGAAGTTGTAGTGGAGCA-AGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCA
1 CTTATCTCCATGAAGTTGTAGTGGAGCAGA-TTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
* * * * * * * *
1112599 GTAGAGCAGACTGAAGATAGCGAATCTTATTTCTCTGAAGTTGCAGTGGAACTGATT-GAAGCTA
65 GTAGAACAGACTGAAGATAGCAAATCTCATTCCCCTGAAGTGGCAGCGGAACAGATTAG-AGCTA
* * * *
1112663 TAAATTATAGATCTTATCTCTTTAAAGTTGTAGTAGAGTAGATCATATCAAAC
129 TAAATTACAGATCTTATCTCTTTAAAGTTGCAGTAGAGCAGATCATAGCAAAC
* * *
1112716 CTTATCTCCATAAAGTTGTAGTGGAGCAGATTGAA-TAAACCAA-TCCTATCTCCCTGAAGTTGC
1 CTTATCTCCATGAAGTTGTAGTGGAGCAGATTGAAGT-TA-CAAGTCTTATCTCCCTGAAGTTGC
1112779 AGT
64 AGT
1112782 GGAGTGAATT
Statistics
Matches: 211, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
178 1 0.00
179 31 0.15
180 6 0.03
181 169 0.80
182 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (181 bp):
CTTATCTCCATGAAGTTGTAGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAG
TAGAACAGACTGAAGATAGCAAATCTCATTCCCCTGAAGTGGCAGCGGAACAGATTAGAGCTATA
AATTACAGATCTTATCTCTTTAAAGTTGCAGTAGAGCAGATCATAGCAAAC
Found at i:1114460 original size:24 final size:24
Alignment explanation
Indices: 1114423--1114626 Score: 82
Period size: 24 Copynumber: 8.5 Consensus size: 24
1114413 TTATCAATAC
1114423 TATTTT-AATATTATAATATATTAT
1 TATTTTAAAT-TTATAATATATTAT
* * **
1114447 TATTCTAAATTTATCAT-TAACAT
1 TATTTTAAATTTATAATATATTAT
** * * *
1114470 TATTTTAGGTTTATCATGTATTTT
1 TATTTTAAATTTATAATATATTAT
*
1114494 TA-TTTAAAGTTA-ACATATATTAT
1 TATTTTAAATTTATA-ATATATTAT
* *
1114517 TATTTTGAATTTATCACGTATTATTAT
1 TATTTTAAATTTAT-A-ATA-TATTAT
*
1114544 TATTTT---TTTA-AATTATCATCAAT
1 TATTTTAAATTTATAA-TAT-AT-TAT
* * *
1114567 TTTTTTAAATTTATGATGTATTAT
1 TATTTTAAATTTATAATATATTAT
** * *
1114591 TATTCCAAATTTATTATATATTGTT
1 TATTTTAAATTTATAATATATT-AT
*
1114616 TATTGTAAATT
1 TATTTTAAATT
1114627 ACTCTATTCA
Statistics
Matches: 132, Mismatches: 33, Indels: 29
0.68 0.17 0.15
Matches are distributed among these distances:
21 1 0.01
22 5 0.04
23 41 0.31
24 47 0.36
25 15 0.11
26 10 0.08
27 13 0.10
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (24 bp):
TATTTTAAATTTATAATATATTAT
Found at i:1114885 original size:14 final size:15
Alignment explanation
Indices: 1114865--1114900 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1114855 TTTACATGTA
1114865 ATTTTAAA-TGATTT
1 ATTTTAAATTGATTT
*
1114879 TTTTTAAATTGATTT
1 ATTTTAAATTGATTT
1114894 ATTTTAA
1 ATTTTAA
1114901 TTCGTTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTTTAAATTGATTT
Found at i:1118527 original size:12 final size:12
Alignment explanation
Indices: 1118510--1118538 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1118500 TAGACAATAA
1118510 AAGAATAAGAAG
1 AAGAATAAGAAG
1118522 AAGAATAAGAAG
1 AAGAATAAGAAG
1118534 AAGAA
1 AAGAA
1118539 GACAATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (12 bp):
AAGAATAAGAAG
Found at i:1121027 original size:101 final size:101
Alignment explanation
Indices: 1120849--1121051 Score: 343
Period size: 101 Copynumber: 2.0 Consensus size: 101
1120839 ATCTTGATAA
*
1120849 ACAAAAAATCAAACATGGTGGTAAGGATCATAGAAGATTATGAACGACGCCAACAATATCTAATA
1 ACAAAAAATCAAACATGGTGGTAAGGATCATAGAAGATTATGAACGACGCCAAAAATATCTAATA
*
1120914 TATCACACAAGTAGAGACAATGAATAGATTTAAGTT
66 TATCACAAAAGTAGAGACAATGAATAGATTTAAGTT
** * **
1120950 ACAAAAAATTGAACATGGTGGTAAGGATCATCGAAGATTATGAGTGACGCCAAAAATATCTAATA
1 ACAAAAAATCAAACATGGTGGTAAGGATCATAGAAGATTATGAACGACGCCAAAAATATCTAATA
1121015 TATCACAAAAGTAGAGACAATGAATAGATTTAAGTT
66 TATCACAAAAGTAGAGACAATGAATAGATTTAAGTT
1121051 A
1 A
1121052 TAAATATAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (101 bp):
ACAAAAAATCAAACATGGTGGTAAGGATCATAGAAGATTATGAACGACGCCAAAAATATCTAATA
TATCACAAAAGTAGAGACAATGAATAGATTTAAGTT
Found at i:1129158 original size:16 final size:16
Alignment explanation
Indices: 1129137--1129170 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1129127 TGATTAGACC
*
1129137 ATACACCATTCACTCT
1 ATACACCATTCACGCT
1129153 ATACACCATTCACGCT
1 ATACACCATTCACGCT
1129169 AT
1 AT
1129171 GCCGCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.35, G:0.03, T:0.29
Consensus pattern (16 bp):
ATACACCATTCACGCT
Found at i:1139969 original size:17 final size:17
Alignment explanation
Indices: 1139930--1139986 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
1139920 TAATAGTATT
* *
1139930 ATAAATATTCAAAGTTA
1 ATAATTATTCAAATTTA
1139947 ATAATTATTCAAATTTA
1 ATAATTATTCAAATTTA
1139964 CA-AATT-TT-AAATTTA
1 -ATAATTATTCAAATTTA
*
1139979 ATGATTAT
1 ATAATTAT
1139987 ATAAAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 1 0.03
15 10 0.29
16 3 0.09
17 19 0.56
18 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (17 bp):
ATAATTATTCAAATTTA
Found at i:1140844 original size:16 final size:16
Alignment explanation
Indices: 1140823--1140854 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1140813 ATTGAATTAG
1140823 AATTTTAATTTTTTAA
1 AATTTTAATTTTTTAA
*
1140839 AATTTTTATTTTTTAA
1 AATTTTAATTTTTTAA
1140855 TTATTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATTTTAATTTTTTAA
Found at i:1141166 original size:17 final size:17
Alignment explanation
Indices: 1141144--1141178 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1141134 GATAGTAATT
1141144 ATAAAACAAATTTCGTC
1 ATAAAACAAATTTCGTC
1141161 ATAAAACAAATTTCGTC
1 ATAAAACAAATTTCGTC
1141178 A
1 A
1141179 ACTTTTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.29
Consensus pattern (17 bp):
ATAAAACAAATTTCGTC
Found at i:1145979 original size:51 final size:51
Alignment explanation
Indices: 1145922--1146089 Score: 275
Period size: 51 Copynumber: 3.3 Consensus size: 51
1145912 TGGATCACAT
* * *
1145922 TTATCACTTGTCACTTGTCCCTAATCAGGA-AAGGGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCA-GATAAGTGTAGCTAAAGCTACCAC
* *
1145973 TCATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTTCCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1146024 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1146075 TTATCACTTGTCACT
1 TTATCACTTGTCACT
1146090 GCTCAGAAGT
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 2 0.02
51 107 0.98
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:1149690 original size:47 final size:47
Alignment explanation
Indices: 1149572--1149761 Score: 181
Period size: 47 Copynumber: 4.0 Consensus size: 47
1149562 TCATTTTCTT
*
1149572 GATGCCATAAT-CCA-ACTATGGTCTTACA-TGTAATCACATATCACATACC
1 GATGCCAT-ATCCCAGA-TATGGTCTTACACAG-AATCACATATCAC--ACC
* * * * *
1149621 GATGCCATAGCCCAGCTATGGTCTT-CTACGGAATCACATATCACGCT
1 GATGCCATATCCCAGATATGGTCTTAC-ACAGAATCACATATCACACC
* * * *
1149668 GATGCCATATCCTAGATGTGGTCTTACACAGTAGCACATATCACACC
1 GATGCCATATCCCAGATATGGTCTTACACAGAATCACATATCACACC
*
1149715 GATGCCATATCCCAGATATGGTCTTACATAGAAATCACATAATCACA
1 GATGCCATATCCCAGATATGGTCTTACACAG-AATCACAT-ATCACA
1149762 TTTTCACATG
Statistics
Matches: 115, Mismatches: 19, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
47 65 0.57
48 9 0.08
49 40 0.35
50 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (47 bp):
GATGCCATATCCCAGATATGGTCTTACACAGAATCACATATCACACC
Found at i:1151104 original size:51 final size:51
Alignment explanation
Indices: 1151049--1151156 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 51
1151039 GATCACATTT
*
1151049 ATCACTTGCCACTTGTCCCTGATCAGGA-AAGGGTAGCTAAAACTACCACTC
1 ATCACTTGCCACTTGTCACTGATCA-GATAAGGGTAGCTAAAACTACCACTC
* * *
1151100 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
1 ATCACTTGCCACTTGTCACTGATCAGATAAGGGTAGCTAAAACTACCACTC
1151151 ATCACT
1 ATCACT
1151157 GATTAGATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 2 0.04
51 50 0.96
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (51 bp):
ATCACTTGCCACTTGTCACTGATCAGATAAGGGTAGCTAAAACTACCACTC
Found at i:1151165 original size:37 final size:37
Alignment explanation
Indices: 1151115--1151193 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
1151105 TTGTCACTTG
1151115 TCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
1 TCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
* * *
1151152 TCACTGATTAGATAAGTGTAGCTAAAGCTATCACTTA
1 TCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
1151189 TCACT
1 TCACT
1151194 TGTCACTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (37 bp):
TCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
Found at i:1151206 original size:88 final size:88
Alignment explanation
Indices: 1151081--1151244 Score: 283
Period size: 88 Copynumber: 1.9 Consensus size: 88
1151071 TCAGGAAAGG
*
1151081 GTAGCTAAAACTACCACTCATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 GTAGCTAAAACTACCACTCATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTAC
1151146 CACTCATCACTGATTAGATAAGT
66 CACTCATCACTGATTAGATAAGT
* * *
1151169 GTAGCTAAAGCTATCACTTATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTAC
1 GTAGCTAAAACTACCACTCATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTAC
*
1151234 CACTTATCACT
66 CACTCATCACT
1151245 TGTCACTGCT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 71 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (88 bp):
GTAGCTAAAACTACCACTCATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTAC
CACTCATCACTGATTAGATAAGT
Found at i:1151228 original size:51 final size:51
Alignment explanation
Indices: 1151152--1151251 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
1151142 CTACCACTCA
* * *
1151152 TCACTGATTAGATAAGTGTAGCTAAAGCTATCACTTATCACTTGTCACTTG
1 TCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTG
1151203 TCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACT
1 TCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACT
1151252 GCTCAGAAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (51 bp):
TCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTG
Found at i:1158115 original size:18 final size:17
Alignment explanation
Indices: 1158087--1158149 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 17
1158077 TTGATACATA
1158087 TTTTATTATTTGATTT-C
1 TTTTATTATTT-ATTTAC
1158104 TTTTATTTATTTATTTAC
1 TTTTA-TTATTTATTTAC
*
1158122 TTTT-CT-TTTATTT-C
1 TTTTATTATTTATTTAC
*
1158136 CTTTATTA-TTATTT
1 TTTTATTATTTATTT
1158150 TTAGTATAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 4 0.10
15 14 0.36
16 1 0.03
17 9 0.23
18 11 0.28
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTATTTAC
Found at i:1168153 original size:12 final size:12
Alignment explanation
Indices: 1168136--1168166 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1168126 ATTTAGCCTT
1168136 AAGTGAATATTG
1 AAGTGAATATTG
1168148 AAGTGAATATTG
1 AAGTGAATATTG
1168160 AAGTGAA
1 AAGTGAA
1168167 ATAAATTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (12 bp):
AAGTGAATATTG
Found at i:1169332 original size:21 final size:22
Alignment explanation
Indices: 1169306--1169361 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
1169296 AGTTTCCCCC
1169306 GTTTGCAGTGGCTATACAA-TT
1 GTTTGCAGTGGCTATACAATTT
*
1169327 GTTTGCAGTGGCTATATAATTT
1 GTTTGCAGTGGCTATACAATTT
* *
1169349 ATTTGCAGCGGCT
1 GTTTGCAGTGGCT
1169362 CCATCTGCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.39
Consensus pattern (22 bp):
GTTTGCAGTGGCTATACAATTT
Found at i:1175204 original size:18 final size:17
Alignment explanation
Indices: 1175176--1175210 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1175166 ATTTTTAAGA
*
1175176 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1175193 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1175211 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1175439 original size:43 final size:45
Alignment explanation
Indices: 1175375--1175464 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 45
1175365 ACCTCTATTC
* * *
1175375 CATTCAACCAAACACAAGATTA-C-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
1175418 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
1175463 CA
1 CA
1175465 CCTCTAATCC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 19 0.49
44 1 0.03
45 19 0.49
ACGTcount: A:0.38, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:1175479 original size:17 final size:16
Alignment explanation
Indices: 1175445--1175497 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
1175435 GATTAGCTAT
1175445 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1175461 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
1175478 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1175494 TACA
1 TACA
1175498 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1190974 original size:33 final size:33
Alignment explanation
Indices: 1190937--1191000 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1190927 TACTATCTTT
* *
1190937 ATGGACTATGTTTATTCTGTGTTTACTGTCCCA
1 ATGGACTATCTCTATTCTGTGTTTACTGTCCCA
* *
1190970 ATGGACTATCTCTGTTTTGTGTTTACTGTCC
1 ATGGACTATCTCTATTCTGTGTTTACTGTCC
1191001 TGGTGAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.47
Consensus pattern (33 bp):
ATGGACTATCTCTATTCTGTGTTTACTGTCCCA
Found at i:1191226 original size:35 final size:35
Alignment explanation
Indices: 1191180--1191251 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
1191170 GTCTTACTCA
1191180 TCATACCTTGTTGTCATAGAATCTTTCATCTATGG
1 TCATACCTTGTTGTCATAGAATCTTTCATCTATGG
*
1191215 TCATACCTTGTTGTCATAGCATCTTTCATCTATGG
1 TCATACCTTGTTGTCATAGAATCTTTCATCTATGG
1191250 TC
1 TC
1191252 TAACATCGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (35 bp):
TCATACCTTGTTGTCATAGAATCTTTCATCTATGG
Found at i:1193325 original size:19 final size:19
Alignment explanation
Indices: 1193301--1193337 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1193291 TAATTTAGCC
1193301 ATATTTATTT-TTTAATTTA
1 ATATTT-TTTATTTAATTTA
1193320 ATATTTTTTATTTAATTT
1 ATATTTTTTATTTAATTT
1193338 TTACATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
ATATTTTTTATTTAATTTA
Found at i:1193326 original size:14 final size:13
Alignment explanation
Indices: 1193303--1193354 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
1193293 ATTTAGCCAT
1193303 ATTT-ATTTTTTA
1 ATTTAATTTTTTA
*
1193315 ATTTAATATTTTTT
1 ATTTAAT-TTTTTA
1193329 ATTTAA-TTTTTA
1 ATTTAATTTTTTA
1193341 CATTCTAATTTTTT
1 -ATT-TAATTTTTT
1193355 TGTTTGTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 9 0.27
13 5 0.15
14 14 0.42
15 5 0.15
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTAATTTTTTA
Found at i:1193326 original size:15 final size:14
Alignment explanation
Indices: 1193306--1193339 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1193296 TAGCCATATT
1193306 TATTTTTTAATTTAA
1 TATTTTTT-ATTTAA
1193321 TATTTTTTATTTAA
1 TATTTTTTATTTAA
1193335 T-TTTT
1 TATTTT
1193340 ACATTCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 7 0.37
15 8 0.42
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTTATTTAA
Found at i:1193332 original size:26 final size:27
Alignment explanation
Indices: 1193302--1193355 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
1193292 AATTTAGCCA
*
1193302 TATTTATTTTTTA-ATT-TAATATTTTT
1 TATTTAATTTTTACATTCTAAT-TTTTT
1193328 TATTTAATTTTTACATTCTAATTTTTT
1 TATTTAATTTTTACATTCTAATTTTTT
1193355 T
1 T
1193356 GTTTGTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 12 0.48
27 9 0.36
28 4 0.16
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (27 bp):
TATTTAATTTTTACATTCTAATTTTTT
Found at i:1194804 original size:24 final size:24
Alignment explanation
Indices: 1194772--1194820 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1194762 AGTGTTATTT
1194772 TTTCAATTATAGGCTTTGGAGTGC
1 TTTCAATTATAGGCTTTGGAGTGC
1194796 TTTCAATTATAGGCTTTGGAGTGC
1 TTTCAATTATAGGCTTTGGAGTGC
1194820 T
1 T
1194821 CGAGGACTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.43
Consensus pattern (24 bp):
TTTCAATTATAGGCTTTGGAGTGC
Found at i:1211588 original size:28 final size:27
Alignment explanation
Indices: 1211507--1211677 Score: 231
Period size: 27 Copynumber: 6.3 Consensus size: 27
1211497 AGAGGTCAAT
*
1211507 AAATGACTGAAATGCCCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
*
1211534 AAATGATTGAAATACCCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
1211561 AAATGACTGAAATACCCCCCATAGGGTA
1 AAATGACTGAAATA-CCCCCATAGGGTA
*
1211589 AAATGA-TCGAAATGCCCCCTATAGGGTA
1 AAATGACT-GAAATACCCCC-ATAGGGTA
1211617 AAATGA-TCGAAATACCCCCATAGGGTA
1 AAATGACT-GAAATACCCCCATAGGGTA
** *
1211644 AAATGACCAAAATACCCCCATAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
1211671 AAA-GACT
1 AAATGACT
1211678 ATTATACCCC
Statistics
Matches: 131, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.02
27 78 0.60
28 50 0.38
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATGACTGAAATACCCCCATAGGGTA
Found at i:1211593 original size:55 final size:54
Alignment explanation
Indices: 1211507--1211677 Score: 247
Period size: 55 Copynumber: 3.1 Consensus size: 54
1211497 AGAGGTCAAT
* *
1211507 AAATGACTGAAATGCCCCCATAGGGTAAAATGATTGAAATACCCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTA
*
1211561 AAATGACTGAAATACCCCCCATAGGGTAAAATGATCGAAATGCCCCCTATAGGGTA
1 AAATGACTGAAATA-CCCCCATAGGGTAAAATGATCGAAATACCCCC-ATAGGGTA
* * *
1211617 AAATGA-TCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCCATAAGGTA
1 AAATGACT-GAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTA
1211671 AAA-GACT
1 AAATGACT
1211678 ATTATACCCC
Statistics
Matches: 106, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
53 2 0.02
54 24 0.23
55 60 0.57
56 20 0.19
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (54 bp):
AAATGACTGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTA
Found at i:1214561 original size:3 final size:3
Alignment explanation
Indices: 1214553--1214634 Score: 50
Period size: 3 Copynumber: 28.7 Consensus size: 3
1214543 TATTCATTTG
* *
1214553 TTA TTA TTA TT- TTA TTA TT- TTA ATA TTA TCT- TTT TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* * * *
1214595 TTTA TT- TTA TT- TTT TTA TTG TTA TTA TTA CTA ATA TTA TT
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1214635 GTTTTATAGT
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
2 11 0.18
3 47 0.76
4 4 0.06
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:1214570 original size:14 final size:13
Alignment explanation
Indices: 1214553--1214619 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 13
1214543 TATTCATTTG
1214553 TTATTATTATTTTA
1 TTATT-TTATTTTA
*
1214567 TTATTTTAATATTA
1 TTATTTT-ATTTTA
*
1214581 TCTTTTTTATTTTA
1 T-TATTTTATTTTA
*
1214595 TTTATTTTATTTTT
1 -TTATTTTATTTTA
1214609 TTATTGTTATT
1 TTATT-TTATT
1214620 ATTACTAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
13 7 0.16
14 31 0.70
15 6 0.14
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:1214592 original size:20 final size:19
Alignment explanation
Indices: 1214557--1214611 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
1214547 CATTTGTTAT
1214557 TATTATTTTATTATTTTAA
1 TATTATTTTATTATTTTAA
*
1214576 TATTATCTTTTTTATTTT-A
1 TATTAT-TTTATTATTTTAA
*
1214595 T-TTATTTTATTTTTTTA
1 TATTATTTTATTATTTTA
1214612 TTGTTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 9 0.29
18 4 0.13
19 8 0.26
20 10 0.32
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (19 bp):
TATTATTTTATTATTTTAA
Found at i:1223163 original size:49 final size:50
Alignment explanation
Indices: 1223104--1223200 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 50
1223094 TTCGTTTTCT
*
1223104 CGATGTCATAG-TCCAACTATGGTCTTACAC-GTAATCACA-AATCACATAC
1 CGATGCCATAGCT-CAACTATGGTCTTACACAG-AATCACATAATCACATAC
**
1223153 CGATGCCATAGCTCAGTTATGGTCTTACACAGAATCACATAATCACAT
1 CGATGCCATAGCTCAACTATGGTCTTACACAGAATCACATAATCACAT
1223201 GTTCACATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 32 0.76
50 10 0.24
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (50 bp):
CGATGCCATAGCTCAACTATGGTCTTACACAGAATCACATAATCACATAC
Found at i:1224164 original size:75 final size:75
Alignment explanation
Indices: 1224033--1224209 Score: 261
Period size: 75 Copynumber: 2.4 Consensus size: 75
1224023 TATCCGTTAT
* *
1224033 CGGTGGATTCAGCACTTAGCAACTACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTCAC
1224098 ATTTAAGA-TA
66 ATTTAA-ATTA
* *
1224108 --GTGTGAGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTC
1 CGGTG-GA-ATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTC
1224171 ACATTTAAATTA
64 ACATTTAAATTA
*
1224183 CGGTGGAATCAGCACGTAGCAACCACC
1 CGGTGGAATCAGCACTTAGCAACCACC
1224210 TTTATAGTCA
Statistics
Matches: 92, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
73 3 0.03
74 3 0.03
75 81 0.88
76 2 0.02
77 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTCAC
ATTTAAATTA
Done.