Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold403
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: 416698
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:120701 original size:79 final size:78
Alignment explanation
Indices: 120568--121037 Score: 480
Period size: 79 Copynumber: 6.0 Consensus size: 78
120558 TCATTCATGT
* * * * ***
120568 TTTTATTTCTAAAATACCGATTTTTCACCATCGGGGATACTCCAACCCTGTTATTTTCGAAAAGA
1 TTTTATTTCCAAAACACTGATTTTTCACAATCGGGGATACTCCAACCC-GTTATTTTCGAGGGGA
*
120633 TACTCTAACCCCAG
65 TACTCCAACCCCAG
* * * * *
120647 ATTTATTTCCAAAACATTGATTTTTCACCATCGGGGATATTCCAATCCCATTA-TTTCAGAGGGG
1 TTTTATTTCCAAAACACTGATTTTTCACAATCGGGGATACTCCAA-CCCGTTATTTTC-GAGGGG
*
120711 ATACTCCAACCCCGG
64 ATACTCCAACCCCAG
* * * * * ** *
120726 CTTTATTTCCAAAATATTGATTTTTCATAATTGGGGATACTCCAATCTTGTTATTTCCGAGGGGA
1 TTTTATTTCCAAAACACTGATTTTTCACAATCGGGGATACTCCAA-CCCGTTATTTTCGAGGGGA
*
120791 TACTCAAACCCCAG
65 TACTCCAACCCCAG
* * * * *
120805 TTTTATTTTCAAAATACTGATTTTTCACAATCGAGGATACTTCAACCCCATTATTTTCGAGGGGA
1 TTTTATTTCCAAAACACTGATTTTTCACAATCGGGGATACTCCAA-CCCGTTATTTTCGAGGGGA
* *
120870 TACTCTAACCCTAG
65 TACTCCAACCCCAG
* * * **
120884 TTTTATTTCCAAAACACTAATTTTTCACAATC-GGAATATTCCAACCTCGTTA-TTTCTGAATGG
1 TTTTATTTCCAAAACACTGATTTTTCACAATCGGGGATACTCCAACC-CGTTATTTTC-GAGGGG
* *
120947 ATACTCCAACCTCGG
64 ATACTCCAACCCCAG
* *
120962 TTTTATTTCCAAAACACTGATTTTTCATAATCGGAGATACTCCAACCCTGTTA-TTTCTGAGGGG
1 TTTTATTTCCAAAACACTGATTTTTCACAATCGGGGATACTCCAACCC-GTTATTTTC-GAGGGG
121026 ATACTCCAACCC
64 ATACTCCAACCC
121038 TGTTAGAAGG
Statistics
Matches: 324, Mismatches: 60, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
77 6 0.02
78 62 0.19
79 250 0.77
80 6 0.02
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.35
Consensus pattern (78 bp):
TTTTATTTCCAAAACACTGATTTTTCACAATCGGGGATACTCCAACCCGTTATTTTCGAGGGGAT
ACTCCAACCCCAG
Found at i:123050 original size:4 final size:4
Alignment explanation
Indices: 123041--123079 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
123031 TTTTGAGGTG
*
123041 TTTA TTTA TTTA TTTA TTCA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
123080 TGTTTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:129804 original size:24 final size:24
Alignment explanation
Indices: 129777--129823 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
129767 CATGTTAAAG
129777 ATGCATGAAACATAATAAAAAAAA
1 ATGCATGAAACATAATAAAAAAAA
129801 ATGCATGAAACATAATAAAAAAA
1 ATGCATGAAACATAATAAAAAAA
129824 TGCATGGTCA
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:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (24 bp):
ATGCATGAAACATAATAAAAAAAA
Found at i:129823 original size:22 final size:23
Alignment explanation
Indices: 129777--129829 Score: 90
Period size: 24 Copynumber: 2.3 Consensus size: 23
129767 CATGTTAAAG
129777 ATGCATGAAACATAATAAAAAAAA
1 ATGCATGAAACATAAT-AAAAAAA
129801 ATGCATGAAACATAAT-AAAAAA
1 ATGCATGAAACATAATAAAAAAA
129823 ATGCATG
1 ATGCATG
129830 GTCAAAGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 13 0.45
24 16 0.55
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.19
Consensus pattern (23 bp):
ATGCATGAAACATAATAAAAAAA
Found at i:130769 original size:20 final size:20
Alignment explanation
Indices: 130740--130814 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
130730 AAAAAGACAT
*
130740 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
130760 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
130780 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
130800 AATGTATCGATACAT
1 AATGTATCGATACAT
130815 CAGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:130808 original size:40 final size:39
Alignment explanation
Indices: 130737--130814 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
130727 GGTAAAAAGA
* *
130737 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
130776 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
130815 CAGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:131412 original size:32 final size:33
Alignment explanation
Indices: 131367--131437 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
131357 TTTTTTTTTA
*
131367 AAAAAAATGTGCCAAT-A-ACTTGTGTAGGCTTTG
1 AAAAAAATGTGCCAATGACACATGTG--GGCTTTG
*
131400 AAAAAAAT-TGCCACTGACACATGTGGGCTTTG
1 AAAAAAATGTGCCAATGACACATGTGGGCTTTG
131432 AAAAAA
1 AAAAAA
131438 GTGTTGCTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 19 0.56
33 9 0.26
34 6 0.18
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (33 bp):
AAAAAAATGTGCCAATGACACATGTGGGCTTTG
Found at i:131894 original size:115 final size:114
Alignment explanation
Indices: 131444--132924 Score: 2173
Period size: 115 Copynumber: 13.0 Consensus size: 114
131434 AAAAGTGTTG
* * * * *
131444 CTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACCTGCGTGGGCTTT-CAAAGAATGCCACTAA
1 CTGACTT--GTGGGCTTTGAAAGGGTGCCACTGA-CT-TGTGGGCTTTGAAAAGAGTGCCACTGA
* * *
131508 CTCGTGGGCTTTGAAAGGA-TGCTACTGACTTGTGGGCTTTGAAAGAGTGCCA
62 CTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* * * *
131560 CTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGGGCTTT-AAAAGGAGTGCCACTAAC
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAA-GAGTGCCACTGAC
* *
131624 TTGTGTGGGCTTTAAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA
63 -T-TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCA
* * * * *
131678 CTGAATTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCG-AAAGGGTGCCACTGACTTG
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
*
131742 TGGGCTCTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
66 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
** *
131790 CTGACTTGTGGGCTTTGAAAAGAATGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
* *
131855 GTGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCAA
65 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
*
131905 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTG
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
*
131970 TAGGCTTTGAAAGGAGTG-CACTGAC-T-T-GGC-TTGAAAGGGTGCCA
66 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* *
132014 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTAGAAAGGAGTGCCACTGACTTG
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
*
132079 TGGGCTTTGAAAGG-GTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCA
66 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCA
*
132128 CTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTT
1 CTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
*
132192 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGAGTGCCA
65 GTGGGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCA
* * * * *
132244 CTGAATTGTGGGCTTCGCAAGGGTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTG
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
* * *
132308 TGGGCTCTAAAAGG-GTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCA
66 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* * *
132356 CTGACTTGTGGGCTTTGAAATGAGTGCCACTGATTTATGGGCTTTGAAAAGAGTGCCACTGACTT
1 CTGACTTGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
*
132421 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
65 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* * * *
132471 CTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTAACTT
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
*
132536 GTAGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
65 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* *
132586 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTAGAAAAGAGTGCCACTGATTTG
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
132651 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCA
66 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCA
* * *
132701 CTGACTTGTGGTCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTG
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
132766 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCA
66 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAA-GGGTGCCA
*
132816 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTG
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
* *
132881 TGAGCTTTGAAAGGTGTGCCACTGACTTGTGGGCTTTGAAAGGG
66 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
132925 ATGAACATTC
Statistics
Matches: 1245, Mismatches: 93, Indels: 56
0.89 0.07 0.04
Matches are distributed among these distances:
108 3 0.00
109 94 0.08
110 4 0.00
111 2 0.00
112 67 0.05
113 98 0.08
114 312 0.25
115 526 0.42
116 49 0.04
117 50 0.04
118 40 0.03
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (114 bp):
CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
Found at i:132922 original size:29 final size:29
Alignment explanation
Indices: 131421--132923 Score: 2150
Period size: 29 Copynumber: 52.6 Consensus size: 29
131411 CACTGACACA
** ***
131421 TGTGGGCTTTGAAAAAAGTGTTGCTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
131450 TGCGTGGGCTTTAAAAGG-GTGCCACTGACCT
1 T--GTGGGCTTTGAAAGGAGTGCCACTGA-CT
* * * *
131481 GCGTGGGCTTTCAAA-GAATGCCACTAACT
1 -TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
131510 CGTGGGCTTTGAAAGGA-TGCTACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
131538 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* * *
131566 CGTGGGCTTTGAAAAG-GTACCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
131594 TGCGTGGGCTTTAAAAGGAGTGCCACTAACTT
1 T--GTGGGCTTTGAAAGGAGTGCCACTGAC-T
*
131626 GTGTGGGCTTTAAAAGG-GTGCCACTGACT
1 -TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
131655 TGTGGGCTTTGAAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
131684 TGTGGGCTTCGCAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
131712 TGTGGGCTTCGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
131740 TGTGGGCTCTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
131768 TGTGGGCTTTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* * *
131796 TGTGGGCTTTGAAAAGAATGCCACTGATT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
131825 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
131854 TGTGGGCTTTGAAAGGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
131883 TGTGGGCTTTGAAAGG-GTGCAACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
131911 TGTGGGCTTTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
131939 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
131968 TGTAGGCTTTGAAAGGAGTG-CACTGAC-
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
131995 T-T-GGC-TTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132020 TGTGGGCTTTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
132048 TGTGGGCTTAGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
132077 TGTGGGCTTTGAAAGG-GTGCCACTGATT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132105 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132134 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132163 TGTGGGCTTTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132191 TGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGGAGTGCCACTGAC-T
*
132221 GTGTGGGCTTTGAAA-GAGTGCCACTGAAT
1 -TGTGGGCTTTGAAAGGAGTGCCACTGACT
* * *
132250 TGTGGGCTTCGCAAGG-GTGCCACTAACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132278 TGTGGGCTTTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* * *
132306 TGTGGGCTCTAAAAGG-GTGCCACTAACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132334 TGTGGGCTTTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
132362 TGTGGGCTTTGAAATGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
132391 TATGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
132420 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132449 TGTGGGCTTTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
132477 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
132506 TGTGGGCTTTGAAAGGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
132535 TGTAGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132564 TGTGGGCTTTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132592 TGTGGGCTTTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* * *
132620 TGTGGGCTTAGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132649 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132678 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
132707 TGTGGTCTTTGAAAGG-GTGCCATTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132735 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132764 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
*
132793 TGTGGGCTTTGAAAGGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132822 TGTGGGCTTTGAAAGG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
132850 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
* *
132879 TGTGAGCTTTGAAAGGTGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACT
132908 TGTGGGCTTTGAAAGG
1 TGTGGGCTTTGAAAGG
132924 GATGAACATT
Statistics
Matches: 1342, Mismatches: 100, Indels: 64
0.89 0.07 0.04
Matches are distributed among these distances:
23 3 0.00
24 15 0.01
25 4 0.00
26 2 0.00
27 6 0.00
28 583 0.43
29 612 0.46
30 63 0.05
31 52 0.04
32 1 0.00
33 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.28
Consensus pattern (29 bp):
TGTGGGCTTTGAAAGGAGTGCCACTGACT
Found at i:134157 original size:1 final size:1
Alignment explanation
Indices: 134153--134227 Score: 78
Period size: 1 Copynumber: 75.0 Consensus size: 1
134143 TTTTTTGCTA
* * * * * * *
134153 TTTTTTCTTTTTTTTTGTTTTTTTTTGTTTTGTTTTTTTTTGTTTTTGTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
134218 GTTTTTTTTT
1 TTTTTTTTTT
134228 GGGTGTAAAG
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.01, G:0.09, T:0.89
Consensus pattern (1 bp):
T
Found at i:134173 original size:15 final size:14
Alignment explanation
Indices: 134155--134228 Score: 87
Period size: 15 Copynumber: 5.0 Consensus size: 14
134145 TTTTGCTATT
134155 TTTTCTTTTTTTTTG
1 TTTT-TTTTTTTTTG
134170 TTTTTTTTTGTTTTG
1 TTTTTTTTT-TTTTG
134185 TTTTTTTTTGTTTTTG
1 -TTTTTTTT-TTTTTG
134201 TTTTTGTTTTTTTT-
1 TTTTT-TTTTTTTTG
*
134215 TTTGTTTTTTTTTG
1 TTTTTTTTTTTTTG
134229 GGTGTAAAGG
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
13 8 0.15
14 9 0.17
15 19 0.36
16 16 0.30
17 1 0.02
ACGTcount: A:0.00, C:0.01, G:0.11, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTTTG
Found at i:134199 original size:34 final size:34
Alignment explanation
Indices: 134142--134228 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 34
134132 GACCCTTCTA
* * * *
134142 TTTTTTTGCTATTTTTTCTTTTT-TTTTGTTTTTT
1 TTTTTTTGTTTTTTTTTGTTTTTGTTTT-TGTTTT
134176 TTTGTTTTGTTTTTTTTTGTTTTTGTTTTTGTTTT
1 TTT-TTTTGTTTTTTTTTGTTTTTGTTTTTGTTTT
134211 TTTTTTTGTTTTTTTTTG
1 TTTTTTTGTTTTTTTTTG
134229 GGTGTAAAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
34 18 0.38
35 25 0.53
36 4 0.09
ACGTcount: A:0.01, C:0.02, G:0.10, T:0.86
Consensus pattern (34 bp):
TTTTTTTGTTTTTTTTTGTTTTTGTTTTTGTTTT
Found at i:134228 original size:10 final size:10
Alignment explanation
Indices: 134142--134228 Score: 99
Period size: 10 Copynumber: 8.8 Consensus size: 10
134132 GACCCTTCTA
*
134142 TTTTTTTGCT
1 TTTTTTTGTT
* *
134152 ATTTTTTCTT
1 TTTTTTTGTT
134162 TTTTTTTGTT
1 TTTTTTTGTT
134172 TTTTTTTGTT
1 TTTTTTTGTT
134182 TTGTTTTT-TT
1 TT-TTTTTGTT
134192 TTGTTTTTG-T
1 TT-TTTTTGTT
*
134202 TTTTGTT-TT
1 TTTTTTTGTT
134211 TTTTTTTGTT
1 TTTTTTTGTT
134221 TTTTTTTG
1 TTTTTTTG
134229 GGTGTAAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
9 11 0.17
10 50 0.76
11 5 0.08
ACGTcount: A:0.01, C:0.02, G:0.10, T:0.86
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:147315 original size:24 final size:24
Alignment explanation
Indices: 147288--147334 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
147278 CATTTTAAAG
147288 ATGCATGAAACATAATAAAAAAAA
1 ATGCATGAAACATAATAAAAAAAA
147312 ATGCATGAAACATAATAAAAAAA
1 ATGCATGAAACATAATAAAAAAA
147335 TGCATGGTCA
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:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (24 bp):
ATGCATGAAACATAATAAAAAAAA
Found at i:147334 original size:22 final size:23
Alignment explanation
Indices: 147288--147340 Score: 90
Period size: 24 Copynumber: 2.3 Consensus size: 23
147278 CATTTTAAAG
147288 ATGCATGAAACATAATAAAAAAAA
1 ATGCATGAAACATAAT-AAAAAAA
147312 ATGCATGAAACATAAT-AAAAAA
1 ATGCATGAAACATAATAAAAAAA
147334 ATGCATG
1 ATGCATG
147341 GTCAAAGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 13 0.45
24 16 0.55
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.19
Consensus pattern (23 bp):
ATGCATGAAACATAATAAAAAAA
Found at i:148279 original size:20 final size:20
Alignment explanation
Indices: 148250--148324 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
148240 AAAAAGACAT
*
148250 AATGTATCGATACATTACAG
1 AATGTATCGATACATTACAA
*
148270 AATATATCGATACATT-CATA
1 AATGTATCGATACATTACA-A
* *
148290 CATGTATCGATATATTGA-AA
1 AATGTATCGATACATT-ACAA
148310 AATGTATCGATACAT
1 AATGTATCGATACAT
148325 CAGGGTAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTACAA
Found at i:148318 original size:40 final size:39
Alignment explanation
Indices: 148247--148324 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
148237 GGTAAAAAGA
*
148247 CATAATGTATCGATACATTACAGAATATATCGATACATT
1 CATAATGTATCGATACATTACAAAATATATCGATACATT
* *
148286 CATACATGTATCGATATATTGA-AAAATGTATCGATACAT
1 CATA-ATGTATCGATACATT-ACAAAATATATCGATACAT
148325 CAGGGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 29 0.85
41 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTACAAAATATATCGATACATT
Found at i:149440 original size:304 final size:304
Alignment explanation
Indices: 149020--149634 Score: 1230
Period size: 304 Copynumber: 2.0 Consensus size: 304
149010 TTGATGAAGA
149020 AAGGTAGTATTGAGTTTTATGATAAAAAGAAAATCACAGCTGTCTAGCCTATGGACTCACTACCA
1 AAGGTAGTATTGAGTTTTATGATAAAAAGAAAATCACAGCTGTCTAGCCTATGGACTCACTACCA
149085 TCAATCAATGCCACAGAGGGTGGTGACGATACTCTTCCTTACAGTGTTGGAAGGCCACTTATTTT
66 TCAATCAATGCCACAGAGGGTGGTGACGATACTCTTCCTTACAGTGTTGGAAGGCCACTTATTTT
149150 GTTTGATAACCAACCACAAGCTTAAGTGGCTCCTATTCAGATTGTGCCGAGTTGATTATCCAATC
131 GTTTGATAACCAACCACAAGCTTAAGTGGCTCCTATTCAGATTGTGCCGAGTTGATTATCCAATC
149215 TTCAGCTCCATTCCCTTACAAGGACAACAAAACCGTTCCTTGGAACTATGAAAACAAAACCTAGA
196 TTCAGCTCCATTCCCTTACAAGGACAACAAAACCGTTCCTTGGAACTATGAAAACAAAACCTAGA
149280 TTATTAGAGAACCATATCAGCAAACCGATAATGTTGACCTTTCT
261 TTATTAGAGAACCATATCAGCAAACCGATAATGTTGACCTTTCT
149324 AAGGTAGTATTGAGTTTTATGATAAAAAGAAAATCACAGCTGTCTAGCCTATGGACTCACTACCA
1 AAGGTAGTATTGAGTTTTATGATAAAAAGAAAATCACAGCTGTCTAGCCTATGGACTCACTACCA
149389 TCAATCAATGCCACAGAGGGTGGTGACGATACTCTTCCTTACAGTGTTGGAAGGCCACTTATTTT
66 TCAATCAATGCCACAGAGGGTGGTGACGATACTCTTCCTTACAGTGTTGGAAGGCCACTTATTTT
149454 GTTTGATAACCAACCACAAGCTTAAGTGGCTCCTATTCAGATTGTGCCGAGTTGATTATCCAATC
131 GTTTGATAACCAACCACAAGCTTAAGTGGCTCCTATTCAGATTGTGCCGAGTTGATTATCCAATC
149519 TTCAGCTCCATTCCCTTACAAGGACAACAAAACCGTTCCTTGGAACTATGAAAACAAAACCTAGA
196 TTCAGCTCCATTCCCTTACAAGGACAACAAAACCGTTCCTTGGAACTATGAAAACAAAACCTAGA
149584 TTATTAGAGAACCATATCAGCAAACCGATAATGTTGACCTTTCT
261 TTATTAGAGAACCATATCAGCAAACCGATAATGTTGACCTTTCT
149628 AAGGTAG
1 AAGGTAG
149635 GTCACCTAAC
Statistics
Matches: 311, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
304 311 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (304 bp):
AAGGTAGTATTGAGTTTTATGATAAAAAGAAAATCACAGCTGTCTAGCCTATGGACTCACTACCA
TCAATCAATGCCACAGAGGGTGGTGACGATACTCTTCCTTACAGTGTTGGAAGGCCACTTATTTT
GTTTGATAACCAACCACAAGCTTAAGTGGCTCCTATTCAGATTGTGCCGAGTTGATTATCCAATC
TTCAGCTCCATTCCCTTACAAGGACAACAAAACCGTTCCTTGGAACTATGAAAACAAAACCTAGA
TTATTAGAGAACCATATCAGCAAACCGATAATGTTGACCTTTCT
Found at i:154755 original size:11 final size:11
Alignment explanation
Indices: 154724--154764 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
154714 TTTTTTCCAA
154724 AAAAAAAAACC
1 AAAAAAAAACC
**
154735 AAAACGAAACC
1 AAAAAAAAACC
154746 AAAAAAAAA-C
1 AAAAAAAAACC
154756 AAAAAAAAA
1 AAAAAAAAA
154765 GAAAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACC
Found at i:154763 original size:25 final size:24
Alignment explanation
Indices: 154720--154781 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
154710 CCTTTTTTTT
** *
154720 CCAAAAAAAAAAACCAAAACGAAA
1 CCAAAAAAAAAAAAAAAAAAGAAA
154744 CCAAAAAAAAACAAAAAAAAAGAAA
1 CCAAAAAAAAA-AAAAAAAAAGAAA
*
154769 --AAAATAAAAAAAA
1 CCAAAAAAAAAAAAA
154782 GGAGAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.12
23 8 0.24
24 11 0.33
25 10 0.30
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.02
Consensus pattern (24 bp):
CCAAAAAAAAAAAAAAAAAAGAAA
Found at i:154769 original size:20 final size:20
Alignment explanation
Indices: 154746--154791 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
154736 AAACGAAACC
154746 AAAAAAA-AACAAAAAAAAAG
1 AAAAAAATAA-AAAAAAAAAG
**
154766 AAAAAAATAAAAAAAAGGAG
1 AAAAAAATAAAAAAAAAAAG
154786 AAAAAA
1 AAAAAA
154792 GAGAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.87, C:0.02, G:0.09, T:0.02
Consensus pattern (20 bp):
AAAAAAATAAAAAAAAAAAG
Found at i:154803 original size:11 final size:11
Alignment explanation
Indices: 154776--154804 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
154766 AAAAAAATAA
154776 AAAAAAG-GAG
1 AAAAAAGAGAG
154786 AAAAAAGAGAG
1 AAAAAAGAGAG
154797 AAAAAAGA
1 AAAAAAGA
154805 AACCTGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:155874 original size:61 final size:61
Alignment explanation
Indices: 155799--156046 Score: 353
Period size: 61 Copynumber: 4.1 Consensus size: 61
155789 CGAAGAGCAG
* * *
155799 GCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAAAGTAAGAT
1 GCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAAGAC
* * *
155860 GCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGTACCTTTCAGTCCTCAAAGAGCAGGAC
1 GCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAAGAC
*
155921 GCCTTCTT-C-TTTAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAAGAC
1 GCCTT-TTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAAGAC
* *
155981 G-C-TTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC-TTCTAGTCCTCAAAGAGTAGGAC
1 GCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGTAAGAC
156040 GCGCTTT
1 GC-CTTT
156047 ATTTCCTTTT
Statistics
Matches: 167, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
57 2 0.01
58 5 0.03
59 46 0.28
60 48 0.29
61 62 0.37
62 4 0.02
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (61 bp):
GCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAAGAC
Found at i:156018 original size:119 final size:121
Alignment explanation
Indices: 155809--156041 Score: 373
Period size: 119 Copynumber: 1.9 Consensus size: 121
155799 GCCTTTTCCT
* * *
155809 TTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAAAGTAAGATGCCTTTTCCTTTTA
1 TTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGTAAGACGCCTTTTCCTTTCA
*
155874 AAGCCCACACAAGTTGGTGGTACCTT-TCAGTCCTCAAAGAGCAGGACGCCTTCTTC
66 AAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAGGACGCCTTCTTC
* *
155930 TTTAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAAGACG-C-TTTCCTTTCA
1 TTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGTAAGACGCCTTTTCCTTTCA
*
155993 AAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGACGC
66 AAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGC
156042 GCTTTATTTC
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
119 54 0.52
120 2 0.02
121 48 0.46
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (121 bp):
TTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGTAAGACGCCTTTTCCTTTCA
AAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTTC
Found at i:156081 original size:42 final size:41
Alignment explanation
Indices: 156022--156164 Score: 171
Period size: 43 Copynumber: 3.4 Consensus size: 41
156012 GCACCTTCTA
*
156022 GTCCTCAAAGAGTAGGACGCGCTTTATTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGTAGGACGCACTTTATTTCCTTTT-TCCTTT
* * *
156064 GTCCTCAAAGAGCAGGACACACTTAATTTCCTTCTTTTCCTTT
1 GTCCTCAAAGAGTAGGACGCACTTTATTTCC-T-TTTTCCTTT
* * * *
156107 GTCCTCAAAGAGGAAGACGCATTTTATCTT-CTTTTTCCTTA
1 GTCCTCAAAGAGTAGGACGCACTTTAT-TTCCTTTTTCCTTT
156148 GTCCTCAAAGAGTAGGA
1 GTCCTCAAAGAGTAGGA
156165 TGCCTTTTTC
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
41 23 0.27
42 28 0.33
43 30 0.35
44 5 0.06
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (41 bp):
GTCCTCAAAGAGTAGGACGCACTTTATTTCCTTTTTCCTTT
Found at i:156117 original size:43 final size:42
Alignment explanation
Indices: 156022--156164 Score: 159
Period size: 42 Copynumber: 3.4 Consensus size: 42
156012 GCACCTTCTA
* *
156022 GTCCTCAAAGAGTAGGACGCGCTTTATTTCCTT-TTCTCCTTT
1 GTCCTCAAAGAGTAGGACGCAC-TTATTTCCTTCTTTTCCTTT
* *
156064 GTCCTCAAAGAGCAGGACACACTTAATTTCCTTCTTTTCCTTT
1 GTCCTCAAAGAGTAGGACGCACTT-ATTTCCTTCTTTTCCTTT
* * *
156107 GTCCTCAAAGAGGAAGACGCA-TT-TTAT-CTTCTTTTTCCTTA
1 GTCCTCAAAGAGTAGGACGCACTTATT-TCCTTC-TTTTCCTTT
156148 GTCCTCAAAGAGTAGGA
1 GTCCTCAAAGAGTAGGA
156165 TGCCTTTTTC
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
40 6 0.07
41 26 0.30
42 29 0.33
43 26 0.30
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (42 bp):
GTCCTCAAAGAGTAGGACGCACTTATTTCCTTCTTTTCCTTT
Found at i:156342 original size:61 final size:61
Alignment explanation
Indices: 156147--156461 Score: 355
Period size: 61 Copynumber: 5.1 Consensus size: 61
156137 CTTTTTCCTT
* * *
156147 AGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTTAAAGCCCATACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
** * ** * * *
156209 AGTCCTTGAAGAGCAAGACATTTC-TTTTCTATTAAATCCCACACAAGTTGGTAGCA-CTTTC
1 AGTCCTCAAAGAGC-AG-GATGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * * *
156270 AGTCTTTAAAGAGCAGGATGCCTTTTTCTTTTAAAGCGCATAGAAATTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
156331 AATCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * ** * *
156392 AATCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTC
1 AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
156453 AGTCCTCAA
1 AGTCCTCAA
156462 GTTGGTCGCA
Statistics
Matches: 213, Mismatches: 36, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
59 3 0.01
60 27 0.13
61 139 0.65
62 34 0.16
63 7 0.03
64 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:156476 original size:25 final size:25
Alignment explanation
Indices: 156434--156485 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
156424 AAAGCCCACA
* *
156434 CAAGTTGGTGGCATCTTTCAGTCCT
1 CAAGTTGGTCGCACCTTTCAGTCCT
156459 CAAGTTGGTCGCACCTTTCAGTCCT
1 CAAGTTGGTCGCACCTTTCAGTCCT
156484 CA
1 CA
156486 GAGAGCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (25 bp):
CAAGTTGGTCGCACCTTTCAGTCCT
Found at i:156518 original size:86 final size:84
Alignment explanation
Indices: 156373--156530 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 84
156363 AAAGCCCACA
* * **
156373 CAAGTTGGTGGCACCTTTCAATCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAGCCCACACAAG
1 CAAGTTGGTCGCACCTTTCAATCCTCAAAGAGCAAAACACCTTTTCCTTTTAAAG-CC-CACAAG
156438 TTGGTGGCATCTTTCAGTCCT
64 TTGGTGGCATCTTTCAGTCCT
* * ** * *
156459 CAAGTTGGTCGCACCTTTCAGTCCTCAGAGAGCAAAACGTCTTTTCTTTTTGAAGCCCACAAGTT
1 CAAGTTGGTCGCACCTTTCAATCCTCAAAGAGCAAAACACCTTTTCCTTTTAAAGCCCACAAGTT
156524 GGTGGCA
66 GGTGGCA
156531 CCTTCTAGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 15 0.24
85 2 0.03
86 45 0.73
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (84 bp):
CAAGTTGGTCGCACCTTTCAATCCTCAAAGAGCAAAACACCTTTTCCTTTTAAAGCCCACAAGTT
GGTGGCATCTTTCAGTCCT
Found at i:156614 original size:41 final size:42
Alignment explanation
Indices: 156543--156655 Score: 140
Period size: 41 Copynumber: 2.7 Consensus size: 42
156533 TTCTAGTCCC
* ** *
156543 CAAAAAGCAGGATGCACTTTATTTCCTTTTCTT-TTTATCCT
1 CAAAGAGCAGGACACACTTTATTTCCTTTTCTTCTGTATCCT
* *
156584 CAAAGAGTAGGACACACTTTATTTCCTTTTCTTCTGTGTCCT
1 CAAAGAGCAGGACACACTTTATTTCCTTTTCTTCTGTATCCT
*
156626 TAAAGAGCAGGACACA-TTTAATTTCCTTTT
1 CAAAGAGCAGGACACACTTT-ATTTCCTTTT
156656 TTTCCTATGT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 32 0.52
42 30 0.48
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (42 bp):
CAAAGAGCAGGACACACTTTATTTCCTTTTCTTCTGTATCCT
Found at i:156650 original size:42 final size:41
Alignment explanation
Indices: 156560--156687 Score: 141
Period size: 42 Copynumber: 3.1 Consensus size: 41
156550 CAGGATGCAC
* * * *
156560 TTTATTTCCTTTTCTT-TTTATCCTCAAAGAGTAGGACACA
1 TTTATTTCCTTTTCTTCTATGTCCTTAAAGAGCAGGACACA
*
156600 CTTTATTTCCTTTTCTTCTGTGTCCTTAAAGAGCAGGACACA
1 -TTTATTTCCTTTTCTTCTATGTCCTTAAAGAGCAGGACACA
* * * *
156642 TTTAATTTCCTTTTTTTCCTATGTCCTTAAGGAGCAAGACCCA
1 TTT-ATTTCCTTTTCTT-CTATGTCCTTAAAGAGCAGGACACA
156685 TTT
1 TTT
156688 CATTCTCTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 19 0.25
42 32 0.43
43 24 0.32
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.44
Consensus pattern (41 bp):
TTTATTTCCTTTTCTTCTATGTCCTTAAAGAGCAGGACACA
Found at i:156840 original size:60 final size:61
Alignment explanation
Indices: 156738--156984 Score: 297
Period size: 53 Copynumber: 4.2 Consensus size: 61
156728 CTTTTCCTTT
* * *
156738 GTCCTCAAAGAGCGA-GACGCATTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACCTTTCA
1 GTCCTCAAAGAGC-ATGATGCCTTTTCTTTTTAAAGCCTACACAAGTTGGTGGCACCTTTCA
156799 GTCCTCAAAGAGCATGATGCCTTTT-TTTTTAAAG-CTCACACAAGTTGGTGGCACCTTTCA
1 GTCCTCAAAGAGCATGATGCCTTTTCTTTTTAAAGCCT-ACACAAGTTGGTGGCACCTTTCA
*
156859 GTCCTCAAAGAG--T-A-G----GTCTTTTTAAAGCCTACACAAGTTGGTGGCACCTTTCA
1 GTCCTCAAAGAGCATGATGCCTTTTCTTTTTAAAGCCTACACAAGTTGGTGGCACCTTTCA
* * *
156912 GTCCTCAAAGAGTAGGATGCCTTTTCTTTTCAAAGCCT--ACAAGTTGGTGGCACC-TTCTA
1 GTCCTCAAAGAGCATGATGCCTTTTCTTTTTAAAGCCTACACAAGTTGGTGGCACCTTTC-A
*
156971 GTCCTTAAAGAGCA
1 GTCCTCAAAGAGCA
156985 GGACACACTT
Statistics
Matches: 164, Mismatches: 9, Indels: 28
0.82 0.04 0.14
Matches are distributed among these distances:
52 1 0.01
53 44 0.27
54 2 0.01
56 2 0.01
57 2 0.01
58 4 0.02
59 31 0.19
60 44 0.27
61 34 0.21
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (61 bp):
GTCCTCAAAGAGCATGATGCCTTTTCTTTTTAAAGCCTACACAAGTTGGTGGCACCTTTCA
Found at i:156907 original size:113 final size:112
Alignment explanation
Indices: 156765--156982 Score: 350
Period size: 113 Copynumber: 1.9 Consensus size: 112
156755 CGCATTTTCC
* *
156765 TTTTAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCATGATGCCTTTT-TTTTT
1 TTTTAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTC
156829 AAAGCTCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGTAGGTCT
66 AAAGC-C-CACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGTAGGTCT
*
156878 TTTTAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGATGCCTTTTCTTTTC
1 TTTTAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTC
* *
156943 AAAGCCTACAAGTTGGTGGCACCTTCTAGTCCTTAAAGAG
66 AAAGCCCACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAG
156983 CAGGACACAC
Statistics
Matches: 98, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
112 30 0.31
113 59 0.60
114 9 0.09
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (112 bp):
TTTTAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTC
AAAGCCCACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGTCT
Found at i:157032 original size:42 final size:43
Alignment explanation
Indices: 156971--157063 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 43
156961 GCACCTTCTA
* *
156971 GTCCTTAAAGAGCAGGACACACTTT-ATTTCC-TTTTCTCCTAT
1 GTCCTCAAAGAGCAAGACACA-TTTAATTTCCTTTTTCTCCTAT
*
157013 GTCCTCAAAGAGCAAGACACATTTAATTTCCTTTTTTTCCTAT
1 GTCCTCAAAGAGCAAGACACATTTAATTTCCTTTTTCTCCTAT
157056 GTCCTCAA
1 GTCCTCAA
157064 GGAGTAAGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 3 0.07
42 25 0.54
43 18 0.39
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.38
Consensus pattern (43 bp):
GTCCTCAAAGAGCAAGACACATTTAATTTCCTTTTTCTCCTAT
Found at i:157695 original size:20 final size:20
Alignment explanation
Indices: 157670--157726 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
157660 TTTTCACAAT
*
157670 TTGTATCGGTACATTCTTCA
1 TTGTATCGATACATTCTTCA
*
157690 TTGTATCGATACATTTTTCA
1 TTGTATCGATACATTCTTCA
* *
157710 TTGCATTGATACATTCT
1 TTGTATCGATACATTCT
157727 GGGTTTTACC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (20 bp):
TTGTATCGATACATTCTTCA
Found at i:160137 original size:78 final size:79
Alignment explanation
Indices: 159867--160238 Score: 464
Period size: 79 Copynumber: 4.7 Consensus size: 79
159857 CTAAAATATC
* * * *
159867 GATTTTCCACCATCGGAGATACTCCAACCCCGTTATTTCCGAGGGGATACCCCAACCCCGACTTT
1 GATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTT
* *
159932 ATTTCCAAAACATT
66 ATTTTCAAAACACT
* * * * ** *
159946 GATTTTTCCCCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAA-TTCGGCTTT
1 GATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTT
160010 A-TTTCAAAACA-T
66 ATTTTCAAAACACT
* * * * *
160022 CGATTTTTCACAATTGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAATTT
1 -GATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTT
160087 TATTTTCAAAACACT
65 TATTTTCAAAACACT
* * * * * * *
160102 AATTTTTCACAATC-GAAATACTCTAACACCATTATTTTCGAGGGGATACTCCAACCTCGATTTT
1 GATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTT
160166 ATTTTCAAAACACT
66 ATTTTCAAAACACT
*
160180 GATTTTTCACAATCGGAGATTCTCCAACCCCGTTATTTTCGAGGGGGATACTCCAACCC
1 GATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTTCGA-GGGGATACTCCAACCC
160239 TGGGTTTTAT
Statistics
Matches: 250, Mismatches: 37, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
76 1 0.00
77 59 0.24
78 81 0.32
79 93 0.37
80 16 0.06
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (79 bp):
GATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTT
ATTTTCAAAACACT
Found at i:160167 original size:156 final size:156
Alignment explanation
Indices: 159849--160238 Score: 507
Period size: 156 Copynumber: 2.5 Consensus size: 156
159839 TCATTCATGT
* * *
159849 TTTTATTTCTAAAATATCGATTTTCCACCATCGGAGATACTCCAACCCCGTTATTTCCGAGGGGA
1 TTTTATTTC-AAAACATCGATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTCCGAGGGGA
* * * * * * ** *
159914 TACCCCAACCCCGACTTTATTTCCAAAACATTGATTTTTCCCCATCGGGGATACTCCAACCCTGT
65 TACTCCAACCCCAACTTTATTTCCAAAACACTAATTTTTCACAATCGGAAATACTCCAACCCTAT
* *
159979 TATTTTCGAGGGGATACTCCAATTCGG
130 TATTTTCGAGGGGATACTCCAACTCGA
* * *
160006 CTTTATTTCAAAACATCGATTTTTCACAATTGGGGATACTCCAACCCCGTTATTTCCGAGGGGAT
1 TTTTATTTCAAAACATCGATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTCCGAGGGGAT
* * *
160071 ACTCCAACCCCAATTTTATTTTCAAAACACTAATTTTTCACAATC-GAAATACTCTAACACC-AT
66 ACTCCAACCCCAACTTTATTTCCAAAACACTAATTTTTCACAATCGGAAATACTCCAAC-CCTAT
160134 TATTTTCGAGGGGATACTCCAACCTCGA
130 TATTTTCGAGGGGATACTCCAA-CTCGA
* *
160162 TTTTATTTTCAAAACA-CTGATTTTTCACAATCGGAGATTCTCCAACCCCGTTATTTTCGAGGGG
1 TTTTA-TTTCAAAACATC-GATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTCCGA-GGG
160226 GATACTCCAACCC
63 GATACTCCAACCC
160239 TGGGTTTTAT
Statistics
Matches: 203, Mismatches: 25, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
155 33 0.16
156 98 0.48
157 56 0.28
158 16 0.08
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (156 bp):
TTTTATTTCAAAACATCGATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTCCGAGGGGAT
ACTCCAACCCCAACTTTATTTCCAAAACACTAATTTTTCACAATCGGAAATACTCCAACCCTATT
ATTTTCGAGGGGATACTCCAACTCGA
Found at i:162209 original size:23 final size:23
Alignment explanation
Indices: 162140--162210 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
162130 TCCCTTTTTT
* *
162140 TTTTTTTGCTTTTGCTCCGTTTTTCA
1 TTTTTGTGCTTTTG--CC-TTTCTCA
* **
162166 TTTTTGTTTCTTTTGTGTTTCTCA
1 TTTTTG-TGCTTTTGCCTTTCTCA
162190 TTTTTGTGCTTTTGCCTTTCT
1 TTTTTGTGCTTTTGCCTTTCT
162211 TCTTCCTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
23 12 0.33
24 12 0.33
26 5 0.14
27 7 0.19
ACGTcount: A:0.03, C:0.17, G:0.13, T:0.68
Consensus pattern (23 bp):
TTTTTGTGCTTTTGCCTTTCTCA
Found at i:173903 original size:13 final size:13
Alignment explanation
Indices: 173885--173909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173875 ATAATGCACA
173885 GTATCGATACATT
1 GTATCGATACATT
173898 GTATCGATACAT
1 GTATCGATACAT
173910 GACCACTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:177082 original size:51 final size:52
Alignment explanation
Indices: 176976--177091 Score: 162
Period size: 51 Copynumber: 2.2 Consensus size: 52
176966 AACAACGCGA
* * *
176976 TTGGAGTATCCCCAATGGTGAAAAAATTGATATTTTGGAAATAAAAATGGTG
1 TTGGAGTATCCCCAATGGTGAAAAAATCGATATTTTGAAAATAAAAATGGGG
* * *
177028 TTGGAGTATCCCCGATGGTG-AAAAGTCGATATTTTGAAAATAAAATTGGGG
1 TTGGAGTATCCCCAATGGTGAAAAAATCGATATTTTGAAAATAAAAATGGGG
*
177079 TTGGAGTGTCCCC
1 TTGGAGTATCCCC
177092 TCGAAAACAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
51 38 0.67
52 19 0.33
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (52 bp):
TTGGAGTATCCCCAATGGTGAAAAAATCGATATTTTGAAAATAAAAATGGGG
Found at i:177160 original size:79 final size:79
Alignment explanation
Indices: 177021--177247 Score: 296
Period size: 79 Copynumber: 2.9 Consensus size: 79
177011 TGGAAATAAA
* * * *
177021 AATGGTGTTGGAGTATCCCCGATGGT-GAAAAGTCGATATTTT-GAAAATAAAATTGGGGTTGGA
1 AATGGGGTTGGAGTATCCCCGATGGTGGAAAA-TTGGTATTTTAG-AAATAAAATCGGGGTTGGA
* *
177084 GTGTCCCCTCGAAAAC
64 GTATCCCCTCAAAAAC
* * *
177100 AATGGGGTTGGAGTATCCCCGATGGTGGAAAATTGGTCTTTTAGAAATAAAACCGAGGTTGGAGT
1 AATGGGGTTGGAGTATCCCCGATGGTGGAAAATTGGTATTTTAGAAATAAAATCGGGGTTGGAGT
*
177165 ATCCCCTCAAAAAT
66 ATCCCCTCAAAAAC
* * * *
177179 AATAGGGTTGGAGTATCCCTGATGGTGGAAAATTGGTGTTTTAAAAATAAAATCGGGGTTGGAGT
1 AATGGGGTTGGAGTATCCCCGATGGTGGAAAATTGGTATTTTAGAAATAAAATCGGGGTTGGAGT
177244 ATCC
66 ATCC
177248 TCGAGATGAA
Statistics
Matches: 130, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
79 124 0.95
80 6 0.05
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (79 bp):
AATGGGGTTGGAGTATCCCCGATGGTGGAAAATTGGTATTTTAGAAATAAAATCGGGGTTGGAGT
ATCCCCTCAAAAAC
Found at i:177324 original size:51 final size:52
Alignment explanation
Indices: 177223--177349 Score: 141
Period size: 51 Copynumber: 2.5 Consensus size: 52
177213 GGTGTTTTAA
* * * ** *
177223 AAATAAAATCGGGGTTGGAGTATCCTCGAGATGAAAATTTTAATATTTTT-G
1 AAATAAAATCAGGGTTGGAGTATCCCCGAGATAAAAAAATCAATATTTTTGG
* *
177274 AAATAAAATCAAGGTTGGAGTATCCCCGAGATAAAAAAAATCGATA-TTTTGG
1 AAATAAAATCAGGGTTGGAGTATCCCCGAGAT-AAAAAAATCAATATTTTTGG
* *
177326 AAGTAAAAACAGGGTTGGAGTATC
1 AAATAAAATCAGGGTTGGAGTATC
177350 TCCTCGAAAG
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
51 33 0.52
52 30 0.48
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.28
Consensus pattern (52 bp):
AAATAAAATCAGGGTTGGAGTATCCCCGAGATAAAAAAATCAATATTTTTGG
Found at i:177343 original size:52 final size:51
Alignment explanation
Indices: 177223--177349 Score: 137
Period size: 52 Copynumber: 2.5 Consensus size: 51
177213 GGTGTTTTAA
* * * * ** * *
177223 AAATAAAATCGGGGTTGGAGTATCCTCGAGATGAAAATTTTAATATTTTTG
1 AAATAAAAACAGGGTTGGAGTATCCCCGAGATAAAAAAATCAATATTTTGG
* * *
177274 AAATAAAATCAAGGTTGGAGTATCCCCGAGATAAAAAAAATCGATATTTTGG
1 AAATAAAAACAGGGTTGGAGTATCCCCGAGAT-AAAAAAATCAATATTTTGG
*
177326 AAGTAAAAACAGGGTTGGAGTATC
1 AAATAAAAACAGGGTTGGAGTATC
177350 TCCTCGAAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
51 29 0.46
52 34 0.54
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.28
Consensus pattern (51 bp):
AAATAAAAACAGGGTTGGAGTATCCCCGAGATAAAAAAATCAATATTTTGG
Found at i:180825 original size:18 final size:18
Alignment explanation
Indices: 180802--180841 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
180792 ACACACACAC
*
180802 ACATATATATATATACAT
1 ACATATATATACATACAT
*
180820 ACATATATATACATATAT
1 ACATATATATACATACAT
180838 ACAT
1 ACAT
180842 CCATACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
ACATATATATACATACAT
Found at i:180831 original size:10 final size:10
Alignment explanation
Indices: 180804--180838 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
180794 ACACACACAC
*
180804 ATATATATAT
1 ATATATACAT
*
180814 ATACATACAT
1 ATATATACAT
180824 ATATATACAT
1 ATATATACAT
180834 ATATA
1 ATATA
180839 CATCCATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATACAT
Found at i:180835 original size:22 final size:22
Alignment explanation
Indices: 180802--180859 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
180792 ACACACACAC
180802 ACATATATATATATACATACAT
1 ACATATATATATATACATACAT
* * *
180824 ATATATACATATATACATCCAT
1 ACATATATATATATACATACAT
180846 ACATATATATATAT
1 ACATATATATATAT
180860 TAGTTTGACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (22 bp):
ACATATATATATATACATACAT
Found at i:180846 original size:26 final size:26
Alignment explanation
Indices: 180806--180856 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
180796 ACACACACAT
*
180806 ATATATATATACATACATATATATAC
1 ATATATACATACATACATATATATAC
*
180832 ATATATACATCCATACATATATATA
1 ATATATACATACATACATATATATA
180857 TATTAGTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATATACATACATACATATATATAC
Found at i:181047 original size:20 final size:20
Alignment explanation
Indices: 181022--181065 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
181012 GGATACTAAA
181022 GCATAGTTTTAGTGTAAAAT
1 GCATAGTTTTAGTGTAAAAT
181042 GCATAGTTTTAGTGTAAAAT
1 GCATAGTTTTAGTGTAAAAT
181062 GCAT
1 GCAT
181066 TGATTTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (20 bp):
GCATAGTTTTAGTGTAAAAT
Found at i:181132 original size:2 final size:2
Alignment explanation
Indices: 181125--181166 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
181115 TTAATTATCC
181125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
181167 GACCTTATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181323 original size:2 final size:2
Alignment explanation
Indices: 181316--181366 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
181306 TTAATTATCC
*
181316 AT AT AT AT AT AT AT AT AT AT AT AT AT GAG A- AT -T AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
*
181356 AT AT AT CT AT A
1 AT AT AT AT AT A
181367 CTTATAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
1 3 0.07
2 38 0.90
3 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:183089 original size:141 final size:140
Alignment explanation
Indices: 182912--183176 Score: 354
Period size: 141 Copynumber: 1.9 Consensus size: 140
182902 CCTACAGATG
* * *
182912 CCATAGGAATGTTAGAAATATTGAAAAGTTAAGATAATAATTTTTATTTGACTTTTAATTTCTGA
1 CCATAGGAATATTAGAAATATTGAAAAATTAAGATAATAATTTTCATTTGACTTTTAATTTCTG-
* **
182977 AAAAATT-ATTTTGTACCTTAATGGAAAA-CTGAAAAAATACAAAAAGTTTTAAAAATTTTCATA
65 AAAAATTCATTTCGTACCTTAATAAAAAATC-GAAAAAATACAAAAAGTTTT-AAAATTTTCATA
183040 CCCCTACGGATAC
128 CCCCTACGGATAC
* ** * * *
183053 CCATAGGAATATTAGAAATTTTGAAAAATTGGGATAATAATTTTCATTTGATTTTTATTTTTTGA
1 CCATAGGAATATTAGAAATATTGAAAAATTAAGATAATAATTTTCATTTGACTTTTAATTTCTGA
* **
183118 AAAATTCATTTCGTACCTTAATAAAAAATCGAAAAGATAGGAAAAGTTTTAAAATTTTC
66 AAAATTCATTTCGTACCTTAATAAAAAATCGAAAAAATACAAAAAGTTTTAAAATTTTC
183177 TAGACCTTTA
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
140 16 0.15
141 90 0.84
142 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (140 bp):
CCATAGGAATATTAGAAATATTGAAAAATTAAGATAATAATTTTCATTTGACTTTTAATTTCTGA
AAAATTCATTTCGTACCTTAATAAAAAATCGAAAAAATACAAAAAGTTTTAAAATTTTCATACCC
CTACGGATAC
Found at i:183204 original size:141 final size:141
Alignment explanation
Indices: 182912--183222 Score: 333
Period size: 141 Copynumber: 2.2 Consensus size: 141
182902 CCTACAGATG
* * * *
182912 CCATAGGAATGTTAGAAATATTGAAAAGTTAAGATAATAATTTTTATTTGACTTTTAATTTCTGA
1 CCATAAGAATATTAGAAATATTGAAAAATTAAGATAATAATTTTCATTTGACTTTTAATTTCTGA
* ** *
182977 AAAAATTATTTTGTACCTTAATGGAAAACTGAAAAAATACAAAAAGTTTTAAAAATTTTCATACC
66 AAAAATTATTTCGTACCTTAATAAAAAACTGAAAAAATACAAAAAGTTTTAAAAATTTTCAGACC
* *
183042 CCTACGGATAC
131 CCTACGGACAA
* * ** * * *
183053 CCATAGGAATATTAGAAATTTTGAAAAATTGGGATAATAATTTTCATTTGATTTTTATTTTTTG-
1 CCATAAGAATATTAGAAATATTGAAAAATTAAGATAATAATTTTCATTTGACTTTTAATTTCTGA
* **
183117 AAAAATTCATTTCGTACCTTAATAAAAAA-TCGAAAAGATAGGAAAAGTTTT-AAAATTTTCTAG
66 AAAAATT-ATTTCGTACCTTAATAAAAAACT-GAAAAAATACAAAAAGTTTTAAAAATTTTC-AG
**
183180 ACCTTTACGGACAA
128 ACCCCTACGGACAA
* * *
183194 CTATAAGAATAATAAAAATATAT-AAAAAT
1 CCATAAGAATATTAGAAATAT-TGAAAAAT
183223 GATTAAAATG
Statistics
Matches: 141, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
140 17 0.12
141 123 0.87
142 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (141 bp):
CCATAAGAATATTAGAAATATTGAAAAATTAAGATAATAATTTTCATTTGACTTTTAATTTCTGA
AAAAATTATTTCGTACCTTAATAAAAAACTGAAAAAATACAAAAAGTTTTAAAAATTTTCAGACC
CCTACGGACAA
Found at i:183798 original size:2 final size:2
Alignment explanation
Indices: 183774--183906 Score: 76
Period size: 2 Copynumber: 71.0 Consensus size: 2
183764 GTAATTTTTT
*
183774 TA TA T- TA TA TG T- TA TA T- TA TA TA TA TA TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
183811 -A TA TA AA TA TA TA TA AA CA -A CTA TA TA TA TA GTA -A TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA T-A
*
183853 TA CA TA -A TA TA -A TA TA TA TA GTA TA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
183892 TA CA TA -A TA TC TA TA
1 TA TA TA TA TA TA TA TA
183907 ACATATAATA
Statistics
Matches: 103, Mismatches: 11, Indels: 34
0.70 0.07 0.23
Matches are distributed among these distances:
1 13 0.13
2 83 0.81
3 7 0.07
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:183815 original size:21 final size:20
Alignment explanation
Indices: 183774--183917 Score: 78
Period size: 19 Copynumber: 7.5 Consensus size: 20
183764 GTAATTTTTT
* *
183774 TATAT-TATATGTTATATTA
1 TATATATATATATTATAATA
183793 TATATATATATATTATTAATA
1 TATATATATATATTA-TAATA
*
183814 TA-A-ATATATA-TA-AACA
1 TATATATATATATTATAATA
*
183830 -ACTATATATATA--GTAATA
1 TA-TATATATATATTATAATA
*
183848 TATGATACATA-A-TATAATA
1 TAT-ATATATATATTATAATA
183867 TATATAGTATATATAATATAATA
1 TATATA-TATATAT--TATAATA
* *
183890 TATACATA-ATATCTATAACA
1 TATATATATATAT-TATAATA
183910 TATA-ATAT
1 TATATATAT
183918 TTTATTTATT
Statistics
Matches: 99, Mismatches: 11, Indels: 29
0.71 0.08 0.21
Matches are distributed among these distances:
15 1 0.01
16 3 0.03
17 1 0.01
18 17 0.17
19 33 0.33
20 20 0.20
21 10 0.10
22 2 0.02
23 12 0.12
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (20 bp):
TATATATATATATTATAATA
Found at i:183849 original size:14 final size:13
Alignment explanation
Indices: 183786--183893 Score: 94
Period size: 14 Copynumber: 8.0 Consensus size: 13
183776 TATTATATGT
*
183786 TATATTATATATA
1 TATATAATATATA
*
183799 TATATATTAT-TA
1 TATATAATATATA
183811 -ATATAAATATATA
1 TATAT-AATATATA
* *
183824 TAAACAACTATATA
1 TATATAA-TATATA
183838 TATAGTAATATATGA
1 TATA-TAATATAT-A
*
183853 TACATAATATAATA
1 TATATAATAT-ATA
*
183867 TATATAGTATATA
1 TATATAATATATA
183880 TAATATAATATATA
1 T-ATATAATATATA
183894 CATAATATCT
Statistics
Matches: 76, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
11 4 0.05
12 6 0.08
13 16 0.21
14 42 0.55
15 8 0.11
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (13 bp):
TATATAATATATA
Found at i:183882 original size:23 final size:21
Alignment explanation
Indices: 183856--183901 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
183846 TATATGATAC
183856 ATAATATAATATATATAGTATAT
1 ATAATATAATATATATA-TA-AT
*
183879 ATAATATAATATATACATAAT
1 ATAATATAATATATATATAAT
183900 AT
1 AT
183902 CTATAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 2 0.09
23 16 0.73
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
ATAATATAATATATATATAAT
Found at i:183901 original size:9 final size:9
Alignment explanation
Indices: 183786--183913 Score: 83
Period size: 9 Copynumber: 14.4 Consensus size: 9
183776 TATTATATGT
*
183786 TATATTATA
1 TATATAATA
183795 TATAT-ATA
1 TATATAATA
*
183803 TAT-TATTA
1 TATATAATA
183811 -ATATAAATA
1 TATAT-AATA
183820 TATATAA-A
1 TATATAATA
*
183828 CA-ACTATATA
1 TATA-TA-ATA
183838 TATAGTAATA
1 TATA-TAATA
183848 TATGATACATA
1 TAT-ATA-ATA
183859 -ATATAATA
1 TATATAATA
*
183867 TATATAGTA
1 TATATAATA
183876 TATATAATA
1 TATATAATA
183885 TA-AT-ATA
1 TATATAATA
*
183892 TACATAATA
1 TATATAATA
* *
183901 TCTATAACA
1 TATATAATA
183910 TATA
1 TATA
183914 ATATTTTATT
Statistics
Matches: 95, Mismatches: 11, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
7 9 0.09
8 20 0.21
9 43 0.45
10 16 0.17
11 7 0.07
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (9 bp):
TATATAATA
Found at i:186494 original size:2 final size:2
Alignment explanation
Indices: 186489--186527 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
186479 AGATTTTTTA
186489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
186528 ACTTGTAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:191960 original size:3 final size:3
Alignment explanation
Indices: 191940--192016 Score: 97
Period size: 3 Copynumber: 26.3 Consensus size: 3
191930 CATAAATTTT
* **
191940 ATA ATA CATA AT- ATA ATA ATA A-A ATA TTA AGC AT- ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
191983 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
192017 GGATTGAATG
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
2 6 0.09
3 56 0.86
4 3 0.05
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:192183 original size:32 final size:32
Alignment explanation
Indices: 192147--192253 Score: 110
Period size: 32 Copynumber: 3.2 Consensus size: 32
192137 TCGTAGATAG
192147 AAATAAAAATTGTAGTTATCAATATATAATTA
1 AAATAAAAATTGTAGTTATCAATATATAATTA
* * **
192179 AAATAAAATTTATA-TATAT-ATATATATCTTATA
1 AAATAAAAATTGTAGT-TATCA-ATATATAAT-TA
*
192212 GAAATAAAAATGGTAGTTATCAATATATAATTTA
1 -AAATAAAAATTGTAGTTATCAATATATAA-TTA
192246 AAATAAAA
1 AAATAAAA
192254 TTATATAGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
31 2 0.03
32 22 0.37
33 10 0.17
34 22 0.37
35 3 0.05
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (32 bp):
AAATAAAAATTGTAGTTATCAATATATAATTA
Found at i:192263 original size:34 final size:34
Alignment explanation
Indices: 192159--192263 Score: 98
Period size: 34 Copynumber: 3.1 Consensus size: 34
192149 ATAAAAATTG
192159 TAGTTATCAATATATAA-TTAAAATAAAATT-TA
1 TAGTTATCAATATATAATTTAAAATAAAATTATA
* *
192191 TA--TAT-ATATATATATCTTATAGAAATAAAA--ATGG
1 TAGTTATCA-ATATATA-ATT-TA-AAATAAAATTAT-A
192225 TAGTTATCAATATATAATTTAAAATAAAATTATA
1 TAGTTATCAATATATAATTTAAAATAAAATTATA
192259 TAGTT
1 TAGTT
192264 TTAATAAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 22
0.69 0.05 0.27
Matches are distributed among these distances:
29 1 0.02
30 10 0.18
32 3 0.05
33 11 0.19
34 17 0.30
35 4 0.07
36 10 0.18
37 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (34 bp):
TAGTTATCAATATATAATTTAAAATAAAATTATA
Found at i:197186 original size:23 final size:24
Alignment explanation
Indices: 197152--197205 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
197142 GTAATAATGC
*
197152 ATATTTAAT-AAATTAAATTATATT
1 ATATTTAATAAAATAAAATTAT-TT
*
197176 AT-TTTATTAAAATAAAATTATTT
1 ATATTTAATAAAATAAAATTATTT
197199 ATATTTA
1 ATATTTA
197206 CTTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTTAATAAAATAAAATTATTT
Found at i:197760 original size:2 final size:2
Alignment explanation
Indices: 197753--197790 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
197743 TTTATCCCGC
197753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
197791 GAAATCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197954 original size:24 final size:24
Alignment explanation
Indices: 197920--197982 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
197910 GTTAAGAAAG
* *
197920 AAGAAAGAAAGGAAGGAAAAAAAA
1 AAGAAAGAAAGAAAAGAAAAAAAA
* *
197944 AAGAAATAAAGAAAAGAAAAGAAA
1 AAGAAAGAAAGAAAAGAAAAAAAA
* *
197968 AGGAAAGGAAGAAAA
1 AAGAAAGAAAGAAAA
197983 AAATTAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (24 bp):
AAGAAAGAAAGAAAAGAAAAAAAA
Found at i:199072 original size:20 final size:20
Alignment explanation
Indices: 199038--199097 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
199028 TTTCTACTAC
*
199038 TAAAACATTAATATTTTATAT
1 TAAAA-ATTATTATTTTATAT
* *
199059 TAAAAATTATTATTATATCT
1 TAAAAATTATTATTTTATAT
* *
199079 TAATAAAGTATAATTTTAT
1 TAA-AAATTATTATTTTAT
199098 TATTGAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAAAATTATTATTTTATAT
Found at i:207817 original size:29 final size:29
Alignment explanation
Indices: 207783--207839 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
207773 CTTTAGAAAT
207783 ATTTTATTCTATTTTATATAAAACAAGTG
1 ATTTTATTCTATTTTATATAAAACAAGTG
*
207812 ATTTTATTTTATTTTATATAAAACAAGT
1 ATTTTATTCTATTTTATATAAAACAAGT
207840 ATTCACATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (29 bp):
ATTTTATTCTATTTTATATAAAACAAGTG
Found at i:210562 original size:12 final size:12
Alignment explanation
Indices: 210503--210566 Score: 58
Period size: 12 Copynumber: 5.1 Consensus size: 12
210493 TTTTATTTTT
210503 ATTTAAAT-TTA
1 ATTTAAATATTA
210514 ATTATAAATATTA
1 ATT-TAAATATTA
* *
210527 ATATAAATTTTTTTA
1 ATTTAAA---TATTA
*
210542 ATTTTAATATTA
1 ATTTAAATATTA
210554 ATTTAAATATTA
1 ATTTAAATATTA
210566 A
1 A
210567 AATGAGTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
11 3 0.07
12 25 0.60
13 5 0.12
15 9 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTTAAATATTA
Found at i:210841 original size:19 final size:20
Alignment explanation
Indices: 210809--210846 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
210799 GTTAAATTTT
*
210809 TATATAATATTTTTTAAAAA
1 TATATAATACTTTTTAAAAA
210829 TATA-AATACTTTTTAAAA
1 TATATAATACTTTTTAAAA
210847 GACAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATAATACTTTTTAAAAA
Found at i:210859 original size:18 final size:17
Alignment explanation
Indices: 210838--210882 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
210828 ATATAAATAC
210838 TTTTTAAAAGACAACTTT
1 TTTTTAAAAG-CAACTTT
*
210856 TTTTTAACTAGCAACTTT
1 TTTTTAA-AAGCAACTTT
210874 TTTTTAAAA
1 TTTTTAAAA
210883 TATAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 21 0.88
19 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (17 bp):
TTTTTAAAAGCAACTTT
Found at i:210892 original size:18 final size:18
Alignment explanation
Indices: 210818--210893 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 18
210808 TTATATAATA
* *
210818 TTTTTTAAAAATATAAAT
1 TTTTTTTAAAATATAACT
** * *
210836 ACTTTTTAAAAGACAACT
1 TTTTTTTAAAATATAACT
* *
210854 TTTTTTT-AACTAGCAACT
1 TTTTTTTAAAATA-TAACT
210872 TTTTTTTAAAATATAA-T
1 TTTTTTTAAAATATAACT
210889 TTTTT
1 TTTTT
210894 ATTTTCACTC
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
17 9 0.20
18 31 0.70
19 4 0.09
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTTTTAAAATATAACT
Found at i:217618 original size:80 final size:79
Alignment explanation
Indices: 217505--217707 Score: 219
Period size: 80 Copynumber: 2.6 Consensus size: 79
217495 AATAACGGGG
* * * * * * *
217505 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG
*
217569 AAAAAAAAAATCAGGA
65 -AAAAAAAAACCAGGA
* * *
217585 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * * * *
217650 GAATAAAGCCGGGG
66 AAAAAAAACCAGGA
* *
217664 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
217708 GAGATAACAA
Statistics
Matches: 103, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
79 50 0.49
80 53 0.51
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAAACCAGGA
Found at i:217715 original size:28 final size:28
Alignment explanation
Indices: 217659--217735 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
217649 GGAATAAAGC
***
217659 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATGAAGTAA
217687 CGGGGTTGGAGTATCCCCGATG-AGATAA
1 CGGGGTTGGAGTATCCCCGATGAAG-TAA
** *
217715 CAAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
217736 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAGTAA
Found at i:217870 original size:52 final size:51
Alignment explanation
Indices: 217718--217889 Score: 202
Period size: 52 Copynumber: 3.3 Consensus size: 51
217708 GAGATAACAA
* * * * *
217718 GGTTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGA
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGT-GTTTT-AAAATAAAACCGG
* **
217770 AGTTGGAGTATCCCCGATTAAAGGAAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGGAAAAATTGGTGTTTT-AAAATAAAACCGG
* *
217823 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTACCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTA-AAATAAAACCGG
217875 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
217890 TCGGAAATAA
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
51 1 0.01
52 59 0.57
53 33 0.32
54 11 0.11
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTAAAATAAAACCGG
Found at i:217935 original size:27 final size:28
Alignment explanation
Indices: 217872--217947 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
217862 CCAATAAAAC
***
217872 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
217900 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
217927 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
217948 TGTGAAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:217949 original size:107 final size:106
Alignment explanation
Indices: 217605--217955 Score: 311
Period size: 107 Copynumber: 3.3 Consensus size: 106
217595 CCCTCGAAAA
* * * * * * *
217605 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTGGAAATAAAACCGGGGTTGGAG
* *
217670 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAGA
66 TATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGA-T
** * * * **
217712 TAACAAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGAAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTA-TTTTGGAAATAAAACCGGGGTTGGA
* * ** * ** **
217777 GTAT-CCC-C-G-ATTAAAGGAAAAATTGGTGT-T--TTGAAAAT
65 GTATCCCCTCGGAAATAACGG---GGTTGGAGTATCCCCGATGAT
* * ***
217815 AAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTACCAATAAAACCGGGGTTG
1 -TAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTTGGAAATAAAACCGGGGTTG
217880 GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
63 GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
217924 TAACGGGGTTGGAGTATCCCCGATTGTGAAAA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAA
217956 TTGAGAAACT
Statistics
Matches: 184, Mismatches: 46, Indels: 29
0.71 0.18 0.11
Matches are distributed among these distances:
104 11 0.06
105 45 0.24
106 26 0.14
107 65 0.35
108 27 0.15
109 10 0.05
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (106 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTGGAAATAAAACCGGGGTTGGAG
TATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:228112 original size:19 final size:19
Alignment explanation
Indices: 228088--228143 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
228078 TGTAACGATA
228088 CATTGTATCGATACATGCT
1 CATTGTATCGATACATGCT
*
228107 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
228126 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
228144 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:228197 original size:20 final size:20
Alignment explanation
Indices: 228172--228224 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
228162 CTAAGTGAAA
*
228172 TGTATCGATACATG-GGATAT
1 TGTATCGATACATGAAGA-AT
*
228192 TGTATCGATAAATGAAGAAT
1 TGTATCGATACATGAAGAAT
228212 TGTATCGATACAT
1 TGTATCGATACAT
228225 TATGCCCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:229054 original size:34 final size:35
Alignment explanation
Indices: 229000--229101 Score: 129
Period size: 34 Copynumber: 3.0 Consensus size: 35
228990 AACCTTACAA
*
229000 CCCT-ATCTTTTCACAA-GCTAAGATAGAACCTTTT
1 CCCTAATCTTTTCA-AAGGCTAAGATAGAACCTCTT
* *
229034 CCC-AATCTTTTCATAGGCTAAAATAGAACCTCTT
1 CCCTAATCTTTTCAAAGGCTAAGATAGAACCTCTT
* *
229068 CCCTATTTTTTTCAAAGGCTAAGATAGAACCTCT
1 CCCTAATCTTTTCAAAGGCTAAGATAGAACCTCT
229102 CAATCAGTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
33 1 0.02
34 31 0.53
35 26 0.45
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.34
Consensus pattern (35 bp):
CCCTAATCTTTTCAAAGGCTAAGATAGAACCTCTT
Found at i:229584 original size:21 final size:21
Alignment explanation
Indices: 229540--229596 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
229530 CATTGGGCCA
* *
229540 CATGTATCAATACAA-TTCAT
1 CATGTATCGATACAATTTAAT
229560 CATGTATCGATACAATTTAAT
1 CATGTATCGATACAATTTAAT
229581 CATGTATCGATACAAT
1 CATGTATCGATACAAT
229597 GTATCGATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (21 bp):
CATGTATCGATACAATTTAAT
Found at i:229600 original size:13 final size:13
Alignment explanation
Indices: 229582--229606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229572 CAATTTAATC
229582 ATGTATCGATACA
1 ATGTATCGATACA
229595 ATGTATCGATAC
1 ATGTATCGATAC
229607 TGTCAAAGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:229697 original size:33 final size:33
Alignment explanation
Indices: 229655--229719 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
229645 TAATTCATAG
229655 TGTATCGATACAAAGCAATTTGTATTAATACAA
1 TGTATCGATACAAAGCAATTTGTATTAATACAA
** *
229688 TGTATCGATACTTAGCAATTTGTATTGATACA
1 TGTATCGATACAAAGCAATTTGTATTAATACA
229720 TATGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAAAGCAATTTGTATTAATACAA
Found at i:229842 original size:21 final size:22
Alignment explanation
Indices: 229818--229859 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
229808 TACATCATGT
229818 ATTT-TTACTTGAAAAACATTG
1 ATTTATTACTTGAAAAACATTG
*
229839 ATTTATTGCTTGAAAAACATT
1 ATTTATTACTTGAAAAACATT
229860 TAGACTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (22 bp):
ATTTATTACTTGAAAAACATTG
Found at i:232736 original size:14 final size:13
Alignment explanation
Indices: 232714--232759 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
232704 AGCACAAGAC
232714 AAAAATATTAATA
1 AAAAATATTAATA
*
232727 AAAAATTATT-ATC
1 AAAAA-TATTAATA
*
232740 AACAAT-TTAATA
1 AAAAATATTAATA
232752 AAAAATAT
1 AAAAATAT
232760 GAACAAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
11 2 0.08
12 8 0.31
13 12 0.46
14 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAATATTAATA
Found at i:235087 original size:34 final size:34
Alignment explanation
Indices: 235044--235179 Score: 184
Period size: 34 Copynumber: 4.0 Consensus size: 34
235034 AACCTTACAA
*
235044 CCCTATCTTTTCACAGGCTAACATAGAACCT-TCT
1 CCCTATCTTTTCACAGGCTAAGATAGAACCTCT-T
* *
235078 CCCTATCTTTTCATAAGCTAAGATAGAACCTCTT
1 CCCTATCTTTTCACAGGCTAAGATAGAACCTCTT
**
235112 CCCTATCTTTTCACATACTAAGATAGAACCTCTT
1 CCCTATCTTTTCACAGGCTAAGATAGAACCTCTT
* *
235146 CCTTATCTTTTTCAAAGGCTAAGATAGAACCTCT
1 CCCTATC-TTTTCACAGGCTAAGATAGAACCTCT
235180 CAATCACTTC
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
34 66 0.73
35 24 0.27
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.35
Consensus pattern (34 bp):
CCCTATCTTTTCACAGGCTAAGATAGAACCTCTT
Found at i:235643 original size:20 final size:20
Alignment explanation
Indices: 235618--235671 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
235608 GTTGGGCCAT
*
235618 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTAATC
*
235638 ATGTATCGATACTATTTAATC
1 ATGTATCGATAC-AATTAATC
*
235659 ATATATCGATACA
1 ATGTATCGATACA
235672 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTAATC
Found at i:236333 original size:58 final size:57
Alignment explanation
Indices: 236242--236422 Score: 172
Period size: 58 Copynumber: 3.2 Consensus size: 57
236232 GAATACCCTC
* * * *
236242 AAAT-ATGGCAAATTACT-AAATAACCTTTAAATGCATTAAATTGTATAAATGGTCCT
1 AAATCATGGTAAATGACTAAAATAA-CTCTAAATGCATGAAATTGTATAAATGGTCCT
* * * *
236298 AAATCATGGTATATGACTAAAATGA-TGCATAAATGCATGAAATTATATAAATGGTCTT
1 AAATCATGGTAAATGACTAAAATAACT-C-TAAATGCATGAAATTGTATAAATGGTCCT
* * * * *
236356 AAATCATAGCAAATTACTAAAATAACTCTAAAATGCATGAAATTGCATAAATGG-CCC
1 AAATCATGGTAAATGACTAAAATAACTCT-AAATGCATGAAATTGTATAAATGGTCCT
*
236413 AAAACATGGT
1 AAATCATGGT
236423 TGTAGACACC
Statistics
Matches: 99, Mismatches: 20, Indels: 11
0.76 0.15 0.08
Matches are distributed among these distances:
56 5 0.05
57 19 0.19
58 74 0.75
59 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (57 bp):
AAATCATGGTAAATGACTAAAATAACTCTAAATGCATGAAATTGTATAAATGGTCCT
Found at i:236378 original size:29 final size:27
Alignment explanation
Indices: 236288--236378 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 27
236278 TAAATTGTAT
* * *
236288 AAATGGTCCTAAATCATGGTATATGACTA
1 AAATGGTCATAAATCAT-G-AAATTACTA
*
236317 AAATGATGCATAAATGCATGAAATTA-TA
1 AAATGGT-CATAAAT-CATGAAATTACTA
*
236345 TAAATGGTCTTAAATCATAGCAAATTACTA
1 -AAATGGTCATAAATCAT-G-AAATTACTA
236375 AAAT
1 AAAT
236379 AACTCTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
27 3 0.06
28 9 0.18
29 26 0.52
30 9 0.18
31 3 0.06
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (27 bp):
AAATGGTCATAAATCATGAAATTACTA
Found at i:236398 original size:29 final size:28
Alignment explanation
Indices: 236328--236399 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 28
236318 AATGATGCAT
** *
236328 AAATGCATGAAATTATATAAATGGTCTT
1 AAATGCATGAAATTATATAAATACTCTA
236356 AAAT-CATAGCAAATTACTA-AAATAACTCTA
1 AAATGCAT-G-AAATTA-TATAAAT-ACTCTA
236386 AAATGCATGAAATT
1 AAATGCATGAAATT
236400 GCATAAATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
27 3 0.08
28 5 0.14
29 15 0.42
30 10 0.28
31 3 0.08
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.31
Consensus pattern (28 bp):
AAATGCATGAAATTATATAAATACTCTA
Found at i:237186 original size:20 final size:20
Alignment explanation
Indices: 237161--237217 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
237151 TTTTACCCAG
* *
237161 ATGTATCAATATATTTTTCA
1 ATGTATCGATACATTTTTCA
*
237181 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
237201 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
237218 ATTTTTTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:237205 original size:70 final size:71
Alignment explanation
Indices: 237131--237262 Score: 230
Period size: 71 Copynumber: 1.9 Consensus size: 71
237121 TGAACAGTAC
*
237131 ATGTATCGATACATTCTA-TTTTTTACCCAGATGTATCAATATATTTTTCAATGTATCGATACAT
1 ATGTATCGATACATTCTATTTTTTTACCCAGATGTATCAATACATTTTTCAATGTATCGATACAT
237195 TTTTTA
66 TTTTTA
* *
237201 ATGTATCGATACATTTTATTTTTTTACCCATATGTATCAATACATTTTTCAATGTATCGATA
1 ATGTATCGATACATTCTATTTTTTTACCCAGATGTATCAATACATTTTTCAATGTATCGATA
237263 TATCTAGTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
70 17 0.29
71 41 0.71
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.47
Consensus pattern (71 bp):
ATGTATCGATACATTCTATTTTTTTACCCAGATGTATCAATACATTTTTCAATGTATCGATACAT
TTTTTA
Found at i:238201 original size:19 final size:19
Alignment explanation
Indices: 238166--238202 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
238156 TAGCCTTTGA
*
238166 TCATGCATTCTATTATGTT
1 TCATGCATTCTAATATGTT
*
238185 TCATGCATTTTAATATGT
1 TCATGCATTCTAATATGT
238203 ACGACATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (19 bp):
TCATGCATTCTAATATGTT
Found at i:240457 original size:29 final size:28
Alignment explanation
Indices: 240381--240457 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 28
240371 CGTTGCGACA
240381 ATGGTAAATTACTAAAATGGCCCTAAAATGC
1 ATGG-AAATTACT-AAATGGCCCTAAAA-GC
* *
240412 AT-GAAATTGCATAAATGGTCCTAAAA-C
1 ATGGAAATTAC-TAAATGGCCCTAAAAGC
240439 ATGGCAAATTACTACAATG
1 ATGG-AAATTACTA-AATG
240458 AATACGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
27 3 0.08
28 3 0.08
29 29 0.74
30 2 0.05
31 2 0.05
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (28 bp):
ATGGAAATTACTAAATGGCCCTAAAAGC
Found at i:241320 original size:10 final size:10
Alignment explanation
Indices: 241305--241339 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
241295 GAAACTATCA
241305 CTTTTTTTTT
1 CTTTTTTTTT
241315 CTTTTTTTTT
1 CTTTTTTTTT
*
241325 -TTTTTTTTA
1 CTTTTTTTTT
241334 CTTTTT
1 CTTTTT
241340 GGTTTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.89
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:241345 original size:19 final size:18
Alignment explanation
Indices: 241306--241346 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
241296 AAACTATCAC
**
241306 TTTTTTTTTCTTTTTTTT
1 TTTTTTTTTCTTTTTGGT
241324 TTTTTTTTTACTTTTTGGT
1 TTTTTTTTT-CTTTTTGGT
241343 TTTT
1 TTTT
241347 CTTAGCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.02, C:0.05, G:0.05, T:0.88
Consensus pattern (18 bp):
TTTTTTTTTCTTTTTGGT
Found at i:243129 original size:70 final size:72
Alignment explanation
Indices: 242990--243130 Score: 189
Period size: 71 Copynumber: 2.0 Consensus size: 72
242980 ATATTTTCTA
* * * * *
242990 GGCCTTTTTGAAATTGGCTGAACCTTATAGGGCTAATTTGTAATTTTTTCATAATGTTTACAAGC
1 GGCCTTTTTGAAATTAGCTCAACCCTATAGGGCTAATTTATAATTTTCTCATAATGTTTACAAGC
243055 ATTTAGT
66 ATTTAGT
* *
243062 GGCCTTTTTGAAGTTAGC-CAACCCT-TAGGGTCTAATTTATAATTTTCTCAT-ATTTTTACAAG
1 GGCCTTTTTGAAATTAGCTCAACCCTATAGGG-CTAATTTATAATTTTCTCATAATGTTTACAAG
243124 CATTTAG
65 CATTTAG
243131 GAGAGTTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
70 22 0.36
71 23 0.38
72 16 0.26
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (72 bp):
GGCCTTTTTGAAATTAGCTCAACCCTATAGGGCTAATTTATAATTTTCTCATAATGTTTACAAGC
ATTTAGT
Found at i:243163 original size:71 final size:71
Alignment explanation
Indices: 243010--243197 Score: 199
Period size: 70 Copynumber: 2.6 Consensus size: 71
243000 AAATTGGCTG
* * ** *
243010 AACCTTATAGGG-CTAATTTGTAATTTTTTCATAATGTTTACAAGCATTTAGTGGCCTTTTTGAA
1 AACCTTA-AGGGTCTAATTTATAA-TTTTTCATAATTTTTACAAGCATTTAGTGGCAGTTTTAAA
243074 GTTAGCCA
64 GTTAGCCA
*
243082 ACCCTT-AGGGTCTAATTTATAATTTTCTCAT-ATTTTTACAAGCATTTAG-GAG-AGTTTTAAA
1 AACCTTAAGGGTCTAATTTATAATTTT-TCATAATTTTTACAAGCATTTAGTG-GCAGTTTTAAA
*
243143 GTTGGCCA
64 GTTAGCCA
* *
243151 AACCTTAAAGGGT-TAATATAAAATTTTTCCATAATTTTTACAAGCAT
1 AACCTT-AAGGGTCTAATTTATAATTTTT-CATAATTTTTACAAGCAT
243198 ATATGTGCTT
Statistics
Matches: 99, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
69 20 0.20
70 41 0.41
71 33 0.33
72 5 0.05
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (71 bp):
AACCTTAAGGGTCTAATTTATAATTTTTCATAATTTTTACAAGCATTTAGTGGCAGTTTTAAAGT
TAGCCA
Found at i:243216 original size:71 final size:70
Alignment explanation
Indices: 243031--243217 Score: 186
Period size: 70 Copynumber: 2.7 Consensus size: 70
243021 GCTAATTTGT
* * * * *
243031 AATTTTTTCATAATGTTTACAAGCATTTAGTGGCCTTTTTGAAGTTAGCCAACCCTTAGGGTCTA
1 AATTTTTCCATAATTTTTACAAGCATTTAGT-GACTTTTAGAAGTTAGCCAAACCTTAGGGTCTA
* *
243096 ATTTAT
65 ATATAA
* * *
243102 AA-TTTTCTCAT-ATTTTTACAAGCATTTAGGAGAGTTTTA-AAGTTGGCCAAACCTTAAAGGGT
1 AATTTTTC-CATAATTTTTACAAGCATTTA-GTGACTTTTAGAAGTTAGCCAAACCTT--AGGGT
243164 -TAATATAA
62 CTAATATAA
*
243172 AATTTTTCCATAATTTTTACAAGCATATATGTG-CTTTTAGAAGTTA
1 AATTTTTCCATAATTTTTACAAGCATTTA-GTGACTTTTAGAAGTTA
243218 TTCTAACCTC
Statistics
Matches: 94, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
69 14 0.15
70 41 0.44
71 39 0.41
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (70 bp):
AATTTTTCCATAATTTTTACAAGCATTTAGTGACTTTTAGAAGTTAGCCAAACCTTAGGGTCTAA
TATAA
Found at i:255841 original size:20 final size:20
Alignment explanation
Indices: 255794--255868 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
255784 AAAAAGACAT
*
255794 AATGTATCGATACATTGA-A
1 AATGTATCGATACATTCATA
*
255813 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
255834 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
255854 AATGTATTGATACAT
1 AATGTATCGATACAT
255869 CTTGGTAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:255851 original size:40 final size:39
Alignment explanation
Indices: 255791--255868 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
255781 GGTAAAAAGA
*
255791 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
255830 CATACATGTATCGATATATTGAAAAATGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
255869 CTTGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:256497 original size:29 final size:29
Alignment explanation
Indices: 256445--257366 Score: 898
Period size: 29 Copynumber: 31.6 Consensus size: 29
256435 CACCAACTTG
* *
256445 TGTGGGTTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
256473 TGTGAGCTTCGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
256502 TGTGGGCTTTG-AAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
256530 TGTGGGTTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
256558 TGTGGGCTTTGAGAGGA-TGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
256586 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
256615 TATGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256643 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256672 TATGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256701 TGTGGGCTTTGAAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
256730 TGTGGGTTTTG-AAAGGGTGCCACTGAAT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256758 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
256786 TATAGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256815 TGTGGGCTTTGAAAAG-GTGCCATTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
256843 TGTAGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
256872 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256901 TGTGGGCTTTGAAAGGAGTGCCACTGA--
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256928 ------C-TTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256950 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256979 TGTGGGCTTTGAAAAGAGTG-CATTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
257007 TGTGGGCTTTGAAAAGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAAGAGTGCCACTGAC-T
* *
257037 GTGTGGGCTTTGAAATAG-GTTACCACCGACT
1 -TGTGGGCTTTGAAA-AGAG-TGCCACTGACT
* * **
257068 TGTGTGGTCTTTGAAATGGGTTGCCACCAACT
1 TGTG-GG-CTTTGAAAAGAG-TGCCACTGACT
* * *
257100 TGTGTAGGCATTGAAATGAGTTGCCACCGACTT
1 TGTG--GGCTTTGAAAAGAG-TGCCACTGAC-T
* * * **
257133 ATGTGGGCTTTCAAATGACTTGCCACCAACTT
1 -TGTGGGCTTTGAAAAGA-GTGCCACTGAC-T
* * **
257165 GTGTGGGCTTT-AAAATAGGTTACCACCAACTT
1 -TGTGGGCTTTGAAAAGA-G-TGCCACTGAC-T
**
257197 GTGTGGGCTTTGAAACA-AGTTGCCACCAACTT
1 -TGTGGGCTTTGAAA-AGAG-TGCCACTGAC-T
* * **
257229 GTGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T
* * *
257261 GTGTGGGCTTTGAAATGAGTTTCCACCGACTT
1 -TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T
*
257293 GTGTGGGCTTTGAAAAGAGTGCCACTGATT
1 -TGTGGGCTTTGAAAAGAGTGCCACTGACT
257323 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
257352 TATGGGCTTT-AAAAG
1 TGTGGGCTTTGAAAAG
257367 GGATGAACAT
Statistics
Matches: 780, Mismatches: 83, Indels: 62
0.84 0.09 0.07
Matches are distributed among these distances:
20 17 0.02
21 1 0.00
28 219 0.28
29 299 0.38
30 6 0.01
31 30 0.04
32 196 0.25
33 7 0.01
34 5 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACT
Found at i:256521 original size:57 final size:57
Alignment explanation
Indices: 256445--257366 Score: 859
Period size: 57 Copynumber: 15.8 Consensus size: 57
256435 CACCAACTTG
* * *
256445 TGTGGGTTTTGAAAGGGTGCCACTGACTTGTGAGCTTCGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
256502 TGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGTTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
256558 TGTGGGCTTTGAGAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
256615 TATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
256672 TATGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAAT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
256730 TGTGGGTTTTGAAAGGGTGCCACTGAATTGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * *
256786 TATAGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAG-GTGCCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
256843 TGTAGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256901 TGTGGGCTTTGAAAGGAGTGCCACTGA--------C-TTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
*
256950 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTG-CATTGACT
1 TGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
257007 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAATAG-GTTACCACCGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAA-AGAG-TGCCACTGACT
** * * *
257068 TGTGTGGTCTTTGAAATGGGTTGCCACCAACTTGTGTAGGCATTGAAATGAGTTGCCACCGACTT
1 TGTG-GG-CTTTGAAA-GGG-TGCCACTGACTTGTG--GGCTTTGAAAAGAG-TGCCACTGAC-T
* ** ** * * **
257133 ATGTGGGCTTTCAAATGACTTGCCACCAACTTGTGTGGGCTTT-AAAATAGGTTACCACCAACTT
1 -TGTGGGCTTTGAAA-G-GGTGCCACTGAC-T-TGTGGGCTTTGAAAAGA-G-TGCCACTGAC-T
* * ** * * **
257197 GTGTGGGCTTTGAAACAAGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTG-AA-AGGGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T
* * * *
257261 GTGTGGGCTTTGAAATGAGTTTCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCACTGATT
1 -TGTGGGCTTTGAAA-G-GGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
257323 TGTGGGCTTTGAAAAGAGTGCCACTGACTTATGGGCTTT-AAAAG
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAG
257367 GGATGAACAT
Statistics
Matches: 748, Mismatches: 77, Indels: 80
0.83 0.09 0.09
Matches are distributed among these distances:
49 47 0.06
50 1 0.00
56 73 0.10
57 258 0.34
58 114 0.15
59 16 0.02
60 11 0.01
61 22 0.03
62 14 0.02
63 22 0.03
64 152 0.20
65 9 0.01
66 9 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (57 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
Found at i:256934 original size:20 final size:20
Alignment explanation
Indices: 256909--256951 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
256899 CTTGTGGGCT
* *
256909 TTGAAAGGAGTGCCACTGAC
1 TTGAAAAGAGTGCCACTAAC
256929 TTGAAAAGAGTGCCACTAAC
1 TTGAAAAGAGTGCCACTAAC
256949 TTG
1 TTG
256952 TGGGCTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (20 bp):
TTGAAAAGAGTGCCACTAAC
Found at i:256952 original size:49 final size:49
Alignment explanation
Indices: 256880--256980 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
256870 TTTGTGGGCT
*
256880 TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGAC
1 TTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGAC
256929 TTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGAC
1 TTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGAC
256978 TTG
1 TTG
256981 TGGGCTTTGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (49 bp):
TTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGAC
Found at i:256969 original size:107 final size:105
Alignment explanation
Indices: 256823--257037 Score: 349
Period size: 107 Copynumber: 2.0 Consensus size: 105
256813 TTTGTGGGCT
* * *
256823 TTGAAAAGGTGCCATTGACTTGTAGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAG
1 TTGAAAAGGTGCCACTAACTTGTAGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG
*
256888 AGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGAC
66 AGTG-CACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
256929 TTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAA
1 TTGAAAAG-GTGCCACTAACTTGTAGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
*
256994 GAGTGCATTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
65 GAGTGCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
257035 TTG
1 TTG
257038 TGTGGGCTTT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
106 45 0.45
107 56 0.55
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (105 bp):
TTGAAAAGGTGCCACTAACTTGTAGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG
AGTGCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
Found at i:256980 original size:78 final size:77
Alignment explanation
Indices: 256851--257008 Score: 262
Period size: 78 Copynumber: 2.0 Consensus size: 77
256841 CTTGTAGGCT
* * *
256851 TTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
1 TTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
256916 GAGTGCCACTGAC
66 GAGTG-CACTGAC
*
256929 TTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAA
1 TTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
*
256994 GAGTGCATTGAC
66 GAGTGCACTGAC
257006 TTG
1 TTG
257009 TGGGCTTTGA
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
77 9 0.12
78 66 0.88
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (77 bp):
TTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
GAGTGCACTGAC
Found at i:257073 original size:32 final size:33
Alignment explanation
Indices: 256929--257346 Score: 390
Period size: 32 Copynumber: 13.5 Consensus size: 33
256919 TGCCACTGAC
*
256929 TTGAAA-AGAG-TGCCACTAAC-T-TGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
* **
256958 TTGAAA-GGAG-TGCCACTGAC-T-TGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
***
256987 TTGAAA-AGAG-TG-CATTGAC-T-TGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
**
257015 TTGAAA-AGAG-TGCCACTGACTTGTGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
* * *
257046 TTGAAATAG-GTTACCACCGACTTGTGTGGTCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
* * *
257078 TTGAAAT-GGGTTGCCACCAACTTGTGTAGGCA
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
* *
257110 TTGAAAT-GAGTTGCCACCGACTTATGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
* *
257142 TTCAAAT-GACTTGCCACCAACTTGTGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
* *
257174 TTAAAATAG-GTTACCACCAACTTGTGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
*
257206 TTGAAACA-AGTTGCCACCAACTTGTGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
*
257238 TTGAAAT-GGGTTGCCACCAACTTGTGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
* *
257270 TTGAAAT-GAGTTTCCACCGACTTGTGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
**
257302 TTGAAA-AGAG-TGCCACTGA-TT-TGTGGGCT
1 TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
257331 TTGAAA-AGAG-TGCCAC
1 TTGAAATAGAGTTGCCAC
257347 TGACTTATGG
Statistics
Matches: 344, Mismatches: 35, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
28 27 0.08
29 68 0.20
30 3 0.01
31 23 0.07
32 222 0.65
33 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (33 bp):
TTGAAATAGAGTTGCCACCAACTTGTGTGGGCT
Found at i:258613 original size:9 final size:9
Alignment explanation
Indices: 258600--258649 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
258590 TTCTTTGCTA
258600 TTTTTTCTTG
1 TTTTTT-TTG
258610 TTTTTTTTG
1 TTTTTTTTG
*
258619 --TTTTGT-
1 TTTTTTTTG
258625 TTTTTTTTG
1 TTTTTTTTG
258634 TTTTTTTTG
1 TTTTTTTTG
258643 TTTTTTT
1 TTTTTTT
258650 AAAGGATGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
7 5 0.14
8 5 0.14
9 19 0.54
10 6 0.17
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:258617 original size:14 final size:13
Alignment explanation
Indices: 258578--258649 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 13
258568 CATCTAGACC
*
258578 TTTTTCTTTTTTT
1 TTTTTGTTTTTTT
* * *
258591 TCTTTGCTATTTT
1 TTTTTGTTTTTTT
*
258604 TTCTTGTTTTTTT
1 TTTTTGTTTTTTT
258617 TGTTTTGTTTTTTT
1 T-TTTTGTTTTTTT
258631 TTGTTT-TTTTTGTT
1 TT-TTTGTTTTT-TT
258645 TTTTT
1 TTTTT
258650 AAAGGATGCC
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
13 28 0.60
14 19 0.40
ACGTcount: A:0.01, C:0.06, G:0.08, T:0.85
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:258627 original size:24 final size:24
Alignment explanation
Indices: 258600--258646 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
258590 TTCTTTGCTA
258600 TTTTTTCTTGTTTTTTTTGTTTTG
1 TTTTTTCTTGTTTTTTTTGTTTTG
*
258624 TTTTTTTTTGTTTTTTTTGTTTT
1 TTTTTTCTTGTTTTTTTTGTTTT
258647 TTTAAAGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (24 bp):
TTTTTTCTTGTTTTTTTTGTTTTG
Found at i:258632 original size:19 final size:19
Alignment explanation
Indices: 258610--258649 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
258600 TTTTTTCTTG
*
258610 TTTTT-TTTGTTTTGTTTT
1 TTTTTGTTTTTTTTGTTTT
258628 TTTTTGTTTTTTTTGTTTT
1 TTTTTGTTTTTTTTGTTTT
258647 TTT
1 TTT
258650 AAAGGATGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (19 bp):
TTTTTGTTTTTTTTGTTTT
Found at i:258649 original size:10 final size:10
Alignment explanation
Indices: 258613--258649 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
258603 TTTCTTGTTT
258613 TTTTTGTTTTG
1 TTTTT-TTTTG
258624 TTTTTTTTTG
1 TTTTTTTTTG
258634 -TTTTTTTTG
1 TTTTTTTTTG
258643 TTTTTTT
1 TTTTTTT
258650 AAAGGATGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.36
10 11 0.44
11 5 0.20
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:271708 original size:20 final size:19
Alignment explanation
Indices: 271679--271753 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
271669 AAAAAGACAT
271679 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
271698 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
271719 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
271739 AATGTATCGATACAT
1 AATGTATCGATACAT
271754 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:271736 original size:40 final size:39
Alignment explanation
Indices: 271676--271753 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
271666 GGTAAAAAGA
*
271676 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
271715 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
271754 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:272373 original size:27 final size:28
Alignment explanation
Indices: 272312--272412 Score: 141
Period size: 28 Copynumber: 3.6 Consensus size: 28
272302 TTAAAAAAAT
*
272312 GGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GGTGCCACTAAC-T-TGTGGGCTTTGAAAG
*
272342 GGTGCCACTAACTTGTGGG-ATTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
*
272369 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
*
272397 GGTGCCACTGACTTGT
1 GGTGCCACTAACTTGT
272413 AGGAAGTCAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
27 25 0.38
28 29 0.44
29 1 0.02
30 11 0.17
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.28
Consensus pattern (28 bp):
GGTGCCACTAACTTGTGGGCTTTGAAAG
Found at i:272402 original size:28 final size:28
Alignment explanation
Indices: 272327--272412 Score: 147
Period size: 28 Copynumber: 3.1 Consensus size: 28
272317 CACCAACTTG
*
272327 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
272355 TGTGGG-ATTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
272382 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
272410 TGT
1 TGT
272413 AGGAAGTCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 25 0.46
28 29 0.54
ACGTcount: A:0.20, C:0.16, G:0.35, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:284607 original size:20 final size:20
Alignment explanation
Indices: 284543--284617 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
284533 AAAAAGATAT
*
284543 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
* * * *
284563 AATATATCAATACATTCATA
1 AATGTATCGATACATTGAAA
* *
284583 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
*
284603 AATGTATTGATACAT
1 AATGTATCGATACAT
284618 CTGGGTAAAA
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:289731 original size:19 final size:18
Alignment explanation
Indices: 289705--289743 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
289695 TTTTTTACAT
289705 TTTAAACT-TTTAAATAAA
1 TTTAAACTATTT-AATAAA
289723 TTTAGAACTATTTAATAAA
1 TTTA-AACTATTTAATAAA
289742 TT
1 TT
289744 ATTCATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 12 0.63
20 3 0.16
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTAAACTATTTAATAAA
Found at i:289768 original size:23 final size:23
Alignment explanation
Indices: 289731--289782 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
289721 AATTTAGAAC
*
289731 TATTT-AATAAATTATTCAT-TAT
1 TATTTAAACAAATTATTCATGT-T
289753 TATTTAAACAAATTATTCATGTT
1 TATTTAAACAAATTATTCATGTT
289776 TATTTAA
1 TATTTAA
289783 TAATTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 21 0.78
24 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTTAAACAAATTATTCATGTT
Found at i:290536 original size:2 final size:2
Alignment explanation
Indices: 290529--290560 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
290519 TAACTTGTGC
290529 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
290561 GCTTTAGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:291882 original size:13 final size:13
Alignment explanation
Indices: 291864--291888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291854 TCTTAGTAAG
291864 TAAGAATTCTTAC
1 TAAGAATTCTTAC
291877 TAAGAATTCTTA
1 TAAGAATTCTTA
291889 ATGATCAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (13 bp):
TAAGAATTCTTAC
Done.